ReporterKey Affx ID Name Chromosome Position Sequence SNPType ProbeCount Tile Replicates DesignNumber Rank Strand SetBack taxonomy_key organism cust_id cust_chr cust_pos cust_ref cust_alt cust_cn_region tiling_order cust_type notes pconvert recommendation Error chip Category Gene reference Parentage/haplogroups/causal/… Comment Discovery breeds 468272553 Affx-1111832849 AX-519546269 1 18960 TGGAGCTGTGGCCACGCAGGCGGAATATGAAACGC[A/G]TTTTGGAGGCATAGGAGATCTGGGGCAAGGACCAA R 2 1 2 1 202000 f 74 goat 1_18960_AF-PAKI 1 18960 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38402380 Affx-122959030 AX-123272733 1 21647 TCTCCTCCCGCATCCAGTTAGGTACCACTTCCTAG[A/C]TCGATCAGCCCTGATAGAAATCTCAGGAGCAGATT M 2 1 2 1 202000 f 74 goat snp14078-scaffold1560-21647 1 41022348 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423358 Affx-122943149 AX-123293704 1 51801 TAATCTCCCTGGATTTTCCCTGCCCGACCTTGAAA[C/T]GATGCTAGAGAGCGCAGAGATCCAGCAGGATCCAG Y 2 1 2 1 101000 f 74 goat snp14079-scaffold1560-51801 1 41053350 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789107 Affx-122955870 AX-385276120 1 100946 CAAAATACCACTTGGTAGTTAGAAAGACTGAAAAG[C/T]AGCTTTTCTGTTGCCCTACATCAAGATTCGGCTTT Y 2 1 2 1 101000 r 74 goat snp14080-scaffold1560-100946 1 41102828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444637 Affx-122926927 AX-123314974 1 185575 TGCAGTAGTTACGAGGGTGGACTCCAGAGTCAAGT[C/T]GGTCTGCACTGTGAGACCTTGGTCAAGGACGTTAT Y 2 1 2 1 101000 f 74 goat snp14082-scaffold1560-185575 1 41188297 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777036 Affx-122958650 AX-385264158 1 228319 CTCTGTCAGTAACTGGGCTGAAGTTTTCCATTTCA[G/T]AGTTGATTTAAAATTAATCCGAACGGCTGGTTACC K 2 1 2 1 101000 f 74 goat snp14083-scaffold1560-228319 1 41231606 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772775 Affx-122969248 AX-385259920 1 297224 CACATCTGAAATTCTCACTCTCGTGACTCACCAAA[C/T]GTTACATGGCAATCAGGTAGATGGATTTTATTCTC Y 2 1 2 1 101000 f 74 goat snp14084-scaffold1560-297224 1 41300818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440829 Affx-122929273 AX-123311166 1 330454 ACAGACCCTCTGCCTGGAGGCTTGAACTGGCCTGC[A/G]TTCCCTCTTCTAAGACTTTTGCAGAAGATCTGGGA R 2 1 2 1 101000 r 74 goat snp14085-scaffold1560-330454 1 41333934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389185 Affx-122969082 AX-123259543 1 378997 CATGAAATGTTTTCCCAAATTATTTGTCCAAAACA[C/T]GCCTTAATTTTCATCCAAGGTGAGGAATGGGAAGA Y 2 1 2 1 101000 r 74 goat snp14086-scaffold1560-378997 1 41383727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391766 Affx-122967468 AX-123262123 1 412202 CCTGGGGGCAGTCCATTAGCCTCTCCAAGCGAAAG[C/T]GTTACCATTTTAAAAATCCAAAGAACAGCGCTGCA Y 2 1 2 1 201000 f 74 goat snp14087-scaffold1560-412202 1 41421847 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382849 Affx-122973534 AX-123253207 1 452762 ACACAAGTGTTCTTCACTGAGTTCTGAAGAGGAAG[C/T]GGGTGGCCGTGGTGAGGAGCAGGAGGAAGAGAAGC Y 2 1 2 1 101000 f 74 goat snp14088-scaffold1560-452762 1 41461484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419761 Affx-122945874 AX-123290109 1 488156 AAAGTAAATGACTTGGAAAGTAAGATGGTGGCAAG[C/T]GGAGCGTGAGGATAGGGTTTTGAGAAGAAATTTCT Y 2 1 2 1 101000 f 74 goat snp14089-scaffold1560-488156 1 41496881 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392992 Affx-122965661 AX-123263349 1 516844 ATGCAGGGTGTACTCGGTCACCAATTGAGCGTCAC[A/G]TGAGGGAGGAACAAACTTGCAGTGTGTCAAGTGAC R 2 1 2 1 201000 r 74 goat snp14090-scaffold1560-516844 1 41525458 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449111 Affx-122923581 AX-123319446 1 581464 GGCCATCGCCATGGCCAGGGTGTACCTTTTATGGC[A/G]TTTCTTGCAGCTGGGGGCAACATTTATGTCCAGAC R 2 1 2 1 202000 f 74 goat snp14091-scaffold1560-581464 1 41590174 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409983 Affx-122953281 AX-123280333 1 614162 AGTTTTAAAAATAAAACATAAAACGTAAGAACACT[A/G]AAGCCAAAATGGAAGATGAGGGAAGTCTTGCTTTT R 2 1 2 1 101000 r 74 goat snp14092-scaffold1560-614162 1 41622945 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404556 Affx-122957381 AX-123274908 1 666974 CGGCAAGCTGCAGCCAATGGGGTCCCAAAGAGTCA[G/T]AAACGACTTAGTGACTAAACACATAGGGAAGGGAA K 2 1 2 1 303000 f 74 goat snp14093-scaffold1560-666974 1 41772385 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381223 Affx-122974512 AX-123251581 1 721048 TCTCACAGTGAAATGAGAAGGTTTTGATTGTATGT[A/G]TTTACACCGTGACAGCCACGTGCACCTAGACTAAC R 2 1 2 1 101000 r 74 goat snp14094-scaffold1560-721048 1 41731107 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437153 Affx-122932140 AX-123307491 1 755958 GTTAGTAAATTTTCTGCTGTGTGCTCAGTCGCTTT[A/G]CTGTGTCTGACTCTTTGCAACCTCATAGACTGTAG R 2 1 2 1 103000 f 74 goat snp14095-scaffold1560-755958 1 41765765 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400762 Affx-122959882 AX-123271117 1 786871 ATGGCAGTGCCAAAGCACAGAAGGACCCAATTTCC[C/T]AGAGCCCTCACATAGCAAAGTTGCTTGGTCCAGTG Y 2 1 2 1 101000 f 74 goat snp14096-scaffold1560-786871 1 41797117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400763 Affx-122959882 AX-123271118 1 786871 ATGGCAGTGCCAAAGCACAGAAGGACCCAATTTCC[C/T]AGAGCCCTCACATAGCAAAGTTGCTTGGTCCAGTG Y 2 1 2 1 600000 r 74 goat snp14096-scaffold1560-786871 1 786871 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437763 Affx-122931711 AX-123308101 1 830197 ACTGAGATCCAGGATGGATCCAGCCCCCTGATATT[A/G]TACGAGACTCCCCTTGGCCCCAAGGGGTCCCAAAC R 2 1 2 1 202000 r 74 goat snp14097-scaffold1560-830197 1 41840238 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388556 Affx-122969180 AX-123258914 1 872326 ACCTCGAATCCAGGATGGACTCAGTCTAGCTTGGC[A/G]TCATCTTCAGGTTTACTTGCATTAACTGACACTCA R 2 1 2 1 101000 r 74 goat snp14098-scaffold1560-872326 1 41882235 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424904 Affx-122941307 AX-123295250 1 920888 TCATAACATGCCCTATCCATGTCCCTACCAAGATA[C/T]GAAGGCTTCCTGACACTGTTTTCACAGTCAACATG Y 2 1 2 1 101000 f 74 goat snp14099-scaffold1560-920888 1 47271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398577 Affx-122961502 AX-123268932 1 986550 TCTATGTACTGCTTAGGATGAGACAGACAGACATA[C/T]ATTCATTCACTCACTTAACTTCTCGGAACACCATG Y 2 1 2 1 201000 f 74 goat snp14100-scaffold1560-986550 1 113316 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380553 Affx-122975286 AX-123250911 1 1032913 GTGGAATCACCAGTTTATCACCAGGCCCAGCCTTA[C/T]GCCCCAAGCAGCTATGGGTCTGGTAAATGGCTACA Y 2 1 2 1 201000 f 74 goat snp14101-scaffold1560-1032913 1 159328 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400831 Affx-122959794 AX-123271186 1 1087568 TCTGCATACCATCCTAAAAGGTGATCAGTTTTGGA[C/T]ACCATGACTTTAATTTCAGCTTCTTTTTCTCAGCC Y 2 1 2 1 101000 f 74 goat snp2819-scaffold1082-727669 1 212193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778772 Affx-122975827 AX-385265882 1 1156554 TACAAAGGGATCTGATCAGGCCTGTTAAAGTTACC[A/G]TATAGATGACATGATTCCAAACTTCCTGTGCTTGA R 2 1 2 1 101000 f 74 goat snp2817-scaffold1082-658683 1 281100 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430886 Affx-122936876 AX-123301227 1 1200204 TGGGAGATTAAAGAAATAACATGTTTTTTCTTACT[A/G]TCAAAACGGTACATGTTTATTGAAGACAGCTCTGA R 2 1 2 1 101000 r 74 goat snp2816-scaffold1082-615033 1 324817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790867 Affx-122954109 AX-385277865 1 1257683 GTAGTGAGTGTCTGTTGAATATTTTATTTGAGGGC[A/G]TGGATTAAGATTCTTATAGAGGGAGTAGTTGTTTT R 2 1 2 1 101000 f 74 goat snp2815-scaffold1082-557554 1 382409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386182 Affx-122971373 AX-123256540 1 1290542 TCCATTGCCAATGACAAGTACTCGGGCTGCCATTG[C/T]GCTATCTGCAAAGCAGGAATTCAGCAGGAAGATGA Y 2 1 2 1 201000 f 74 goat snp2814-scaffold1082-524695 1 415331 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395962 Affx-122963563 AX-123266317 1 1332065 TCTCATCTGCCAAAGGTGCAAATGAGCACAAAATT[A/C]TGACATCTTGTAGTTGCTTATTAAAGGGTTCCTAA M 2 1 2 1 101000 f 74 goat snp2813-scaffold1082-483172 1 456935 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779591 Affx-122926656 AX-385266694 1 1376667 CTAACACTCGGCTTACATGCTCCTTAACATTTCAC[A/G]TTCTCTATGGACCATATAATTGAAACATGCAATGA R 2 1 2 1 101000 f 74 goat snp2812-scaffold1082-438570 1 496137 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395176 Affx-122964105 AX-123265531 1 1413162 TGGACATTGTTGCCTGGGCTGGGTGGTCAGGAGAC[A/G]GGGTCTTCTCCTTGGTTCTGGCAAGGACCTCGGGC R 2 1 2 1 201000 r 74 goat snp2811-scaffold1082-402075 1 533477 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795503 Affx-122933273 AX-385282458 1 1466572 TGCTGAGGAATTAACAGGTAAATCGATTCCTTTCT[A/G]TGGAAACTTGAGTAAGTCAACACTTCAGGGTTAGT R 2 1 2 1 101000 r 74 goat snp2810-scaffold1082-348665 1 586692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393594 Affx-122965377 AX-123263950 1 1502774 TGGACCGTTTTTCCAAAAGACTGGATTTAGGCCTT[A/G]AATGTATCATAAGATAGCAACGTGCCTTTTTGTGT R 2 1 2 1 201000 r 74 goat snp2809-scaffold1082-312463 1 623097 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421402 Affx-122943980 AX-123291749 1 1542077 AATTCACTCTCCACCCTGCTGCCAGAATGTTTCTA[C/T]GTGGAAAGTTGGAGCAAGTTATTTCTCCTTTTGAC Y 2 1 2 1 101000 r 74 goat snp2808-scaffold1082-273160 1 662449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409759 Affx-122953003 AX-123280110 1 1572127 CAAGTGACATTAACTGAATAAAAAAGCAGAAACCC[A/G]CATGAACAATAGTGGAAGAAGAGCAAAGAGAGCCA R 2 1 2 1 101000 r 74 goat snp2807-scaffold1082-243110 1 693185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796884 Affx-122964778 AX-385283826 1 1623890 TCTGGTCACATTCTTGACCTCAGCTTCTCAGGTCT[G/T]CAAAATGGGCATATAACCCATTTCATTAATAAAGT K 2 1 2 1 102000 f 74 goat snp2806-scaffold1082-191347 1 745961 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380077 Affx-122975551 AX-123250435 1 1679696 CATGTTCTAGATGAGCGAGTTGTCTCAAATTCCCC[A/G]CTTTCTTTTTTCTTTCCTTTCCAGCCTTGGTGGCT R 2 1 2 1 303000 f 74 goat snp2805-scaffold1082-135541 1 801872 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414741 Affx-122949723 AX-123285090 1 1718229 CTTGGGCCCCGCCAGGAAAAGGAACTTGGACCATC[A/G]TTCTGAGACCTACTTCTCTGATTCTCTGTTCCCCA R 2 1 2 1 101000 r 74 goat snp2804-scaffold1082-97008 1 840087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419533 Affx-122945431 AX-123289881 1 1764272 ACACTGCAGAGAGCTAGATGTTAAATCTTTATACC[G/T]CACACCACTGGCTGAAAGGAGCTTTTATCTTGGAG K 2 1 2 1 101000 f 74 goat snp2803-scaffold1082-50965 1 886848 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790091 Affx-122952440 AX-385277097 1 1804136 ACAATACTGTCATCACTCATAGATAATTCAGATGT[A/G]TCAATTATAATAAGTTCACAGCAGCAGCAAGCTCA R 2 1 2 1 101000 f 74 goat snp2802-scaffold1082-11101 1 926757 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436603 Affx-122932515 AX-123306941 1 1837193 ACCTGTGTATGTCCCACTGAAAGGCCGGACACCAG[A/G]CAGCCTCCCATTTCTCCTTTTGGACTTCCTCCTGG R 2 1 2 1 101000 f 74 goat snp59371-scaffold979-21857 1 959556 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438452 Affx-122931251 AX-123308790 1 1897292 TGAGAAGATGAAAGGGTTGCACTTAGCTTTTAAGT[A/G]TCTTCACTGATGAAACAAACAAACCAAATAACAAT R 2 1 2 1 101000 f 74 goat snp59372-scaffold979-81956 1 1019948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433954 Affx-122934275 AX-123304295 1 1941533 GGCAAACGTCAATCCCACTGCTCAGGAATAAGTTA[A/G]CCAGACGACAGGGGTGGGCAGATAAAAGTCCCCTG R 2 1 2 1 101000 f 74 goat snp59373-scaffold979-126197 1 1064316 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449556 Affx-122923244 AX-123319891 1 1975096 AGGACCAACCTCAGCACTGAGACAAAAAGCTGGAC[A/G]GCTGTGTTCCCAGCCTCACTCACCAAGCCCCGCAT R 2 1 2 1 101000 f 74 goat snp59374-scaffold979-159760 1 1098176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447218 Affx-122924979 AX-123317554 1 2013278 GTCTTAACTTTATCAAGCGATCGTCTCTGTATGTA[C/T]GTATCTATCAGCCATCTGTTTACCATCTGTCTACT Y 2 1 2 1 101000 f 74 goat snp59375-scaffold979-197942 1 1137176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430400 Affx-122937761 AX-123300741 1 2048005 GAGAGAGGAGGCAAAATTGTCCTGCCGTGGATCAG[C/T]GAGAGCAGAACACGGACACGAGGAGCTGGTCCATT Y 2 1 2 1 101000 f 74 goat snp59376-scaffold979-232669 1 1172623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432149 Affx-122936425 AX-123302490 1 2077428 TGCTCTACTCGTATCCAGCCACCCTTTCAGCCCCA[C/T]GTCAAGCACTTTTCCACAGACATTTCTCCAGTCTT Y 2 1 2 1 101000 r 74 goat snp59377-scaffold979-262092 1 1201782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446335 Affx-122925621 AX-123316671 1 2129907 TAAAGAAATTGTCATGGTGCACTCTTGTAATAAAT[C/T]ATAAATCAGTATTGTTAAGAAACATGAAAGAGAGG Y 2 1 2 1 101000 f 74 goat snp59378-scaffold979-314571 1 1253548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406328 Affx-122955451 AX-123276680 1 2185994 TTTCCCCTGGTTTGTGGTGGAAAACACATCTGTTT[C/T]ATACTCAGAACATCTCAGCTTGAGCCTATCTGCCA Y 2 1 2 1 101000 r 74 goat snp59379-scaffold979-370658 1 1310088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433687 Affx-122934547 AX-123304028 1 2237428 AAACCCAAAAGATCTCGTTGTAAGAGTCCCTGTCC[A/G]TGCTGACGTCTACAGCATGAAGCCCTGAAACAGTG R 2 1 2 1 101000 f 74 goat snp59380-scaffold979-422092 1 1361517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277454 Affx-1111835919 AX-519550958 1 2262262 TGAAGGTAAGGTCAGGTGTGTCTGTGCACTTAGAG[A/G]ATTGTATCATTTTTTGTACATGATATGTTTGGAAT R 2 1 2 1 101000 f 74 goat Random2.2K-2 1 2262262 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448886 Affx-122923262 AX-123319221 1 2281335 ATGGATACATTTTTAGGAAAATAAAATGTACCCAA[A/C]TAGAGATAGAATATGTATACAGACAACTTCGATAG M 2 1 2 1 103000 r 74 goat snp59381-scaffold979-465999 1 1405809 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416184 Affx-122948254 AX-123286533 1 2317613 GGAGGCTCAGATCTCAGCGGCTGCTACGTTTCATG[C/T]CTAGTCAAGAAATCCAGCCCCTGTGATCTGACAGG Y 2 1 2 1 201000 f 74 goat snp59382-scaffold979-502277 1 1440938 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450777 Affx-122921832 AX-123321111 1 2348977 CATTTATTAGCATATTTATGAAAAATTGTTAACAG[A/G]AGCATCATTTTAAAGAGTTGTATAGTTTCTCACTT R 2 1 2 1 101000 r 74 goat snp59383-scaffold979-533641 1 1472858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393892 Affx-122965116 AX-123264247 1 2406784 TGCAAGGAGCATTTGGGAAAATGAGTAATGTCTCT[A/G]TGTCTACATTTTCAAATGTGTACTGATAAAAAAGA R 2 1 2 1 101000 f 74 goat snp59384-scaffold979-591448 1 1529499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405299 Affx-122956845 AX-123275651 1 2448454 TGTCCCAGGTACAGACGTATATTGAGTTGTCTGTT[A/G]TTTTCTGCTTCCAAAGGGGTTCAGAATTTGAGGTG R 2 1 2 1 101000 f 74 goat snp59385-scaffold979-633118 1 1570176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447102 Affx-122924483 AX-123317438 1 2497256 GACAAGTTGACATGTCCTAAGTGTGAGAGATCGCT[A/G]CAGAGCCAACTGTCATAAACTGCTGAATTGGAGAG R 2 1 2 1 101000 f 74 goat snp59386-scaffold979-681920 1 1618998 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272477 Affx-1111832852 AX-519546199 1 2546794 CCTGTGTTAAAAACTGAGCTGTGAGCTCAGAGATA[A/C]AGAACAAAGGAAACCAAACAGAGGTAAAGACTACG M 2 1 2 1 201000 f 74 goat 1_2546794_AF-PAKI 1 2546794 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38411193 Affx-122952372 AX-123281543 1 2568316 TATTGAGTGCTTGGAAAATCTTAGAGGTGTTTCCA[C/T]CTACTGTGTGGTTGAATCTTCTTTGAAAACTAATG Y 2 1 2 1 101000 r 74 goat snp59388-scaffold979-752980 1 1690477 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420924 Affx-122944590 AX-123291271 1 2614938 GATTCTGGCCAGAACCGAATGTGTGACTGCTACAT[A/G]CTTTATTCTCTGCCCTAAGCTTGAAACAGTAAGGA R 2 1 2 1 101000 f 74 goat snp59389-scaffold979-799602 1 1737743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772138 Affx-122970016 AX-385259293 1 2659398 AGCCAGCAAGCCCAATCTGTGATGAGGGATAAGTC[A/G]CCATATTGAATTTTATGTATATTGACTTGGAAGCA R 2 1 2 1 101000 f 74 goat snp59390-scaffold979-844062 1 1781860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422942 Affx-122943026 AX-123293288 1 2695262 TAAACCCCAGTGGACCTTCTGCAGTTTAATTTAGA[C/T]GGGAGTTTCTAAGCTGCTTTCTGAAATGGCAAGGC Y 2 1 2 1 201000 f 74 goat snp59391-scaffold979-879926 1 1836750 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784245 Affx-122954932 AX-385271296 1 2750518 ACCCCCACCCTCAATTTCATAAGCCCTAAAGATTC[A/G]TCTTTGGGCAATGAATAAATCTTCAGAATCATTCC R 2 1 2 1 201000 r 74 goat snp59392-scaffold979-935182 1 1892194 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385339 Affx-122971656 AX-123255697 1 2788491 GTGCAGAACTTCCACGAGCAAAGAAAGGCTGAAAC[A/G]CAAGAATTTGCTGGGATGCTGTAGCAGGTTGAATT R 2 1 2 1 101000 f 74 goat snp59393-scaffold979-973155 1 1930088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439465 Affx-122930170 AX-123309802 1 2853843 GTTTTCTCAATCAACAAAAGCATGCATGAAAACGG[C/T]GCCCGGATCAAGAAACAGAACCCAGCCAACACCCA Y 2 1 2 1 101000 f 74 goat snp59394-scaffold979-1038507 1 1994962 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767409 Affx-122949119 AX-385254682 1 2889741 TTGACTAAGGAACACACAATAGCAATGTGATGATC[A/G]ACCTTCTTTTTTCTGAGTCAACATTATAATATGGT R 2 1 2 1 101000 f 74 goat snp59395-scaffold979-1074405 1 2030934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411017 Affx-122951979 AX-123281367 1 2921448 TCAAATGAGCCTCTCGGCAGAATTGGCATTCTTGA[G/T]GATGGATGGTAAGGTCGACGCTTTTTGTATGATAG K 2 1 2 1 101000 f 74 goat snp59396-scaffold979-1106112 1 2062608 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403149 Affx-122958098 AX-123273502 1 2957058 GCTTGCACAGAGCTCTGGCGAAAAGTAAGTCACGA[C/T]GAAGAGAGGAGCTTCCTGGAAGAAGAATGTCTGAG Y 2 1 2 1 201000 f 74 goat snp59397-scaffold979-1141722 1 2098231 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786164 Affx-122978286 AX-385273200 1 2985785 TGAGCAGATATGGATTTTACAGGTTATCTCCCTGA[C/T]ACAGTTGAAGTAGGTGGCCATCGCACTGGCTCACT Y 2 1 2 1 202000 r 74 goat snp59398-scaffold979-1170449 1 2127162 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603156 Affx-1002479372 AX-413837345 1 3004051 CCTGTTTACATTTTGCTTAGATTTCCTTGGGATTT[A/C]ATTTTGATGTGTGAGTTCTAGTGTGTGTTCCCTCT M 2 1 2 1 101000 r 74 goat 1_3004051_RH-map 1 3004051 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38433022 Affx-122935778 AX-123303363 1 3017024 TCTCAATCTTCAGTGAAGTTTCTTGGGCCCTCCTC[A/G]ACATCAAATAATCCTGCTCTCCAAGAAAGGAGGAC R 2 1 2 1 101000 r 74 goat snp59399-scaffold979-1201688 1 2158850 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436451 Affx-122932993 AX-123306789 1 3060222 AGACTGGGAGATCCGAAGGGCTTCCTTGAGCAGAC[A/G]CCATTTAAGTTGAGAATCGGGTGCATCAGGAGATG R 2 1 2 1 101000 r 74 goat snp59400-scaffold979-1244886 1 2202325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603586 Affx-1002479373 AX-413837738 1 3061337 GAAGATGCCCTGGAGGAGGGCATGGAAACCCATTC[G/T]AGTATTCTGCCCTGGAGAATCCTCATGGAAAGAGG K 2 1 2 1 303000 f 74 goat 1_3061337_RH-map 1 3061337 T G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320787478 Affx-122936280 AX-385274503 1 3100759 AGTCCCAGGGGAAATTGTTCTGTATAAACTGTTCT[A/G]TATTTTACCTCTTGATTACTGCTATGATTATCTTC R 2 1 2 1 101000 f 74 goat snp59401-scaffold979-1285423 1 2242567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274670 Affx-1111834432 AX-519548256 1 3119769 GGAAACATGTCAAGGGTAATGTAATCTTTGCAGAG[A/G]GGTGGAGGCCTG R 2 1 2 1 101000 f 74 goat GoatD01.035509 1 3119769 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38414452 Affx-122949574 AX-123284801 1 3161753 AGGTTGTGCTTGTGCGTGGCTAAGTATATATGCAC[A/G]TATCAAACTTGTGAACCCAACTGTTTGCACGTCAT R 2 1 2 1 101000 f 74 goat snp59402-scaffold979-1346417 1 2303447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603060 Affx-1002479374 AX-413837271 1 3191804 GGGAGCAGAAGTGAGCTGCTGCATATTAAAATACA[A/G]CTGGTATTATATAATAGCTCATGGTATCAAAGCTT R 2 1 2 1 101000 f 74 goat 1_3191804_RH-map 1 3191804 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38383771 Affx-122972427 AX-123254129 1 3200827 TTGAATTTTCCCAATTGTCCTTAAAAAACCACTTT[A/G]TTACAGTTGATTTGAGTTCATGTAGAACAATTCCA R 2 1 2 1 101000 f 74 goat snp59403-scaffold979-1385491 1 2342189 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403021 Affx-122958557 AX-123273374 1 3242012 AATACGCAAGACCATTCAGCACCTTAAAGCCACCC[A/G]TTGTCCCTCATTTACTTCCTCTTATCCTCCCACAA R 2 1 2 1 201000 r 74 goat snp23394-scaffold2342-28469 1 2386949 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603063 Affx-1002479375 AX-413837272 1 3277507 AAAATCTCTGTTAAAGACATTCAATAAAGTACTCG[A/C]TCACCACTTATTCCTTTGTTGTTGAAATTCAAGTA M 2 1 2 1 101000 f 74 goat 1_3277507_RH-map 1 3277507 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603162 Affx-1002479376 AX-413837351 1 3308297 TAATATATATCTTATATTAAAAATGTGAGAAGCAA[C/T]GTAGAAAAACTTTGCCCCTTTTCTCTCTCTTCTTT Y 2 1 2 1 101000 r 74 goat 1_3308297_RH-map 1 3308297 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38401312 Affx-122959847 AX-123271665 1 3331723 CCTTTTTACAGCTTTGAGTCTGTACCAGGCATATT[A/G]TACTTTATAAATATTGACTGATTTGATTTTCATAA R 2 1 2 1 101000 f 74 goat snp23396-scaffold2342-118180 1 2475759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603067 Affx-1002479377 AX-413837274 1 3341708 CTTCTTTCAATGTCATGTCTTTTTGCTCTTCTATA[C/G]TGTTTATGGGGTTCCCAAGGCAATAATACTGAAGT S 4 1 2 1 201000 f 74 goat 1_3341708_RH-map 1 3341708 C G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320802169 Affx-122971953 AX-385289073 1 3367820 CTTCTCTTTTTCTTAAGATCTTTAGCAAAGACTTC[C/T]ACCTTTTTTTCTTCTTGCTGTTGAATACTTGCTTT Y 2 1 2 1 101000 r 74 goat snp23397-scaffold2342-154277 1 2511898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603069 Affx-1002479378 AX-413837276 1 3368511 TCAGATTGATTATATTCTATGCAGCCAAAGATGGA[G/T]AAGGTCTATACAGTCAGTAAAAACAAGACCAGGAG K 2 1 2 1 303000 f 74 goat 1_3368511_RH-map 1 3368511 T G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38430211 Affx-122937337 AX-123300552 1 3396797 AGGGTGCAAGGTCATTGGGGTACCATCTAAAATAC[A/G]TTGGTCAGGACTTGTTTGATGAGAAGGGGCTTTTG R 2 1 2 1 101000 f 74 goat snp23398-scaffold2342-183254 1 2541134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430240 Affx-122937315 AX-123300581 1 3456156 ACTCGGTGTGATGTGAAACTATGGAGCTGATCACT[C/T]ACCCCATGTCACTGACAAAGAAAAACAGAAACAGA Y 2 1 2 1 101000 f 74 goat snp55868-scaffold868-1126684 1 2601371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603071 Affx-1002479379 AX-413837277 1 3485949 CACAAACATACACATACATAATGAAGAAAAATAAA[C/G]TCAAGCACAATACATTAATATATTCAAAGATATAG S 4 1 2 1 103000 f 74 goat 1_3485949_RH-map 1 3485949 C G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38382853 Affx-122973532 AX-123253211 1 3486635 AGGAACAGCACAGAGGGGCACAGAGCTTAAAGACC[A/G]GGACATCCCTTTTCTACTTCTAGGTCGGTCAGTTA R 2 1 2 1 101000 r 74 goat snp55867-scaffold868-1096205 1 2632391 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603646 Affx-1002479380 AX-413837785 1 3507304 GAATTTATTATATTAAAAAAGTAAATAAACATGTG[A/G]AAATAGTTTGAGTCTTATGGACCCTTGACAGGGTC R 2 1 2 1 101000 r 74 goat 1_3507304_RH-map 1 3507304 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38396966 Affx-122963168 AX-123267321 1 3546452 CTGACCCAGGCTTCCACAGAGCAAATGCTAAGCCT[A/G]CTGACTGTCAGTTCTTGTTGGGGCTTGTGCAGTGT R 2 1 2 1 202000 f 74 goat snp55866-scaffold868-1036388 1 2691960 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603073 Affx-1002479381 AX-413837278 1 3570452 CATCTTCTCAATCCTTGTCTCTAGGCTATTTATCT[G/T]TGATTCCATTTTGATTTCAAGATTTTGGATCATTT K 2 1 2 1 103000 f 74 goat 1_3570452_RH-map 1 3570452 G T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603171 Affx-1002479382 AX-413837359 1 3592225 ATCAAATGTTTGTTCTTTGTTATGCTACATAAAGT[A/G]CCCCTTTCTAAACATCGAAGATGTGAACAGTTGCT R 2 1 2 1 101000 r 74 goat 1_3592225_RH-map 1 3592225 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38409168 Affx-122953200 AX-123279519 1 3601450 ACATCAGAACGAACTTCTCAGCCAAGCCAATCACA[C/T]TGTCCTGCATGAGGCCCAAACAGGCGCTGTGCCCT Y 2 1 2 1 101000 f 74 goat snp55865-scaffold868-981390 1 2744278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603077 Affx-1002479383 AX-166869927 1 3624775 TCCTCGTGCTGCAATTCATGGGGTCACAAAGAGTC[A/G]GACACGACTGAGCGACTGAACTGAACTGAACTGAT R 2 1 2 1 303000 f 74 goat 1_3624775_RH-map 1 3624775 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320783778 Affx-122966365 AX-385270834 1 3634900 AAACCACATTATAGCCTTCATGTCCTATGTTTAGG[C/T]GAAAGAGGAATAAGAGTTGTATTTCCTCAATCATG Y 2 1 2 1 101000 f 74 goat snp55864-scaffold868-947940 1 2777812 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603175 Affx-1002479384 AX-413837362 1 3652751 GGTCACAAAAGAATCAGACATGACTCAGAAACTAA[A/G]TAACAATATGTTTGATTAGTTGAAGAATCATTACA R 2 1 2 1 201000 r 74 goat 1_3652751_RH-map 1 3652751 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603081 Affx-1002479385 AX-413837282 1 3668994 TTGTAGCTCACTGTCCCAAATCTTTTTGTTTCAGT[A/G]TCCTTCTTGTATAATTTATCAATAAATGCAGGAGC R 2 1 2 1 101000 f 74 goat 1_3668994_RH-map 1 3668994 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603179 Affx-1002479386 AX-413837366 1 3685336 GCTTCAATCATGAGAGGGGCTATGATCCTCTGCTT[C/T]ATGTTTGACTTCAGTTCTCTCTTCTTATCCTTCTA Y 2 1 2 1 201000 r 74 goat 1_3685336_RH-map 1 3685336 T C 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603086 Affx-1002479387 AX-413837285 1 3748182 TCAGACTGTGAAAGGGTTTTCACTGTTATGAAAGT[A/G]AATTTCTTCCCTTGGAAAGATCCATGCTACTTCTG R 2 1 2 1 101000 f 74 goat 1_3748182_RH-map 1 3748182 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320790314 Affx-122977412 AX-385277317 1 3750176 GGTAGAGTAGGGACATTTCCTAGAGGAAAGGCATT[A/G]CTGTTTACTTACTTATGAAAACAAGATCCAAGGCA R 2 1 2 1 101000 f 74 goat snp55862-scaffold868-832664 1 2893055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416763 Affx-122948181 AX-123287111 1 3824291 CAAAATGAGGATTGTAGCCTGTAAGGAGAAAATTC[A/G]TCATGAAGGACTCCAAGTCTGTGAAAGTTTTCTCA R 2 1 2 1 101000 f 74 goat snp55860-scaffold868-758549 1 2969339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798944 Affx-122936555 AX-385285874 1 3899785 GAGCCAGGAAAAGTTGACTGAGAGAGTATTTGTAA[C/T]GGAGGAAGAATATAGGAATAATGGTGATGATGATA Y 2 1 2 1 201000 r 74 goat snp55858-scaffold868-683055 1 3043796 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411813 Affx-122951250 AX-123282163 1 3935209 AGAGTGAGGGAATATTTCCACCTGTCCCAAAACTC[A/G]CTCAACCTGACCACAGCAATAAACAGACTAAATTT R 2 1 2 1 101000 f 74 goat snp55857-scaffold868-647631 1 3079285 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785264 Affx-122938764 AX-385272309 1 3974165 TTTTCATTTAAGCTAAGACCCAATTTAAATAATTC[A/G]TTAGAACAATGACTGTTCATCGCAAATCTGCTCTA R 2 1 2 1 101000 r 74 goat snp55856-scaffold868-608675 1 3118658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603088 Affx-1002479388 AX-413837286 1 3986406 TCACTGCGTCCATTGTTTTGCCATCTATTTGGCAT[A/G]AAGTGATGGGACCAGATGCCATGATCTTAGTTTTT R 2 1 2 1 103000 f 74 goat 1_3986406_RH-map 1 3986406 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320801626 Affx-122966463 AX-385288534 1 4013831 GGCAGAAGAAATCCCAAGATGGAGTTTCTGGGGAG[A/G]ATGAATTTCAAGAATCCCAGGGCAAAAGAAAAAGA R 2 1 2 1 101000 f 74 goat snp55855-scaffold868-569009 1 3157592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438924 Affx-122930424 AX-123309261 1 4063802 CCATCATATCAAAAGAGCCTGTCAGAGAGGTCAGT[A/G]CAGAGGAAAGAGGAGCCAAATGATGGAGAGACTTG R 2 1 2 1 101000 f 74 goat snp55854-scaffold868-519038 1 3207812 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438099 Affx-122931509 AX-123308437 1 4294906 TTGTTGACAGGGAAAAGAGTCCTATACTAGGTTCT[C/T]GGGATTGCTATAGCAAAGTACCATGAATTAGATGG Y 2 1 2 1 101000 f 74 goat snp55849-scaffold868-287934 1 3441506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476138 Affx-1251763640 AX-586011571 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 4 1 4 1 20000 f 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 539476394 Affx-1251763640 AX-423606319 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 4 1 4 1 20000 r 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 562165069 Affx-1251763640 AX-606940481 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 8 1 4 1 20100 f 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 562165280 Affx-1251763640 AX-606940691 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 8 1 4 1 20100 r 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 562165727 Affx-1251763640 AX-606941136 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 8 1 4 1 20100 f 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 562166518 Affx-1251763640 AX-606941926 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 8 1 4 1 20100 f 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 562166568 Affx-1251763640 AX-606941976 1 4377745 GGTCTCCTAGAGACAGAAACAGCAACCCACTATTC[-/CCAGTATTCTTTTTTTTTTTTTTTTAATTTTAAAATCTTTCCCTTATGCTGTACCCCATGCCTAATGAAAATCTATTCCC]AGTATTCTTGCCTGAGAAATCCCATGGACAGATTT - 8 1 4 1 20100 f 74 goat SV_134 1 4377745 - deletion junction SV-TF-chip 320801896 Affx-122970905 AX-385288803 1 4383048 TCCATGTACTGTGTGTCTTTTGGCAGAGTAGTAGC[A/G]TAGTGAGATTTATTTTCAACTCCAGTGTTTTTCCC R 2 1 2 1 101000 f 74 goat snp55847-scaffold868-199792 1 3530748 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789237 Affx-122977316 AX-385276248 1 4567031 CGCTGTCACAGAGTTACCCATGACTGGCAGAATTG[C/T]GATGCTTGCTCTTAAATACCTTAGAATTCATTCAT Y 2 1 2 1 101000 f 74 goat snp55842-scaffold868-15809 1 3714739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438373 Affx-122931314 AX-123308711 1 4587459 AATGTTGAAACCAATGACAATATTGCTCCACCAAG[C/T]GAAAGAACTCACTCAATCAACGAGTCAAGGCCTTA Y 2 1 2 1 103000 r 74 goat snp14436-scaffold1577-4520 1 3738974 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396301 Affx-122963089 AX-123266656 1 4619099 TGGTCAAGGTTACAAACTTCCAATTACAAATTAGA[C/T]GTCATGGGATACTGTATTGTACATCTGAAAGTTAT Y 2 1 2 1 101000 f 74 goat snp14437-scaffold1577-36160 1 3772200 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450366 Affx-122922097 AX-123320701 1 4668101 AAAAAAGCAAATGTACAGTTAGTATCAACAGCAGC[A/G]TGCGATGCTGGTGAAAAAAGGAATCAACAGCAATT R 2 1 2 1 101000 r 74 goat snp14438-scaffold1577-85162 1 3822282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778734 Affx-122957109 AX-385265845 1 4703639 TTTTCTCAATTTAAAAGGTAAAATTGTTCAGTGTC[A/G]TTTAGGTTTGGAAGAAATTATTTCATCCTTTCATG R 2 1 2 1 202000 f 74 goat snp14439-scaffold1577-120700 1 3858000 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771488 Affx-122975364 AX-385258646 1 4737308 CAAAAGATTTCCATCTCTGATAACCACTGTGTTCA[G/T]AATTAGAAGTTAGCATTTGGATTTTGGGGTCAAAT K 2 1 2 1 202000 r 74 goat snp14440-scaffold1577-154369 1 3892026 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448849 Affx-122923290 AX-123319185 1 4771512 GTGTCCACTTGGCTAGGATATGGTGTCCAGTTGTT[C/T]GCCAAACACCAACCCAGATGTTTCTGTATAATGTA Y 2 1 2 1 201000 r 74 goat snp14441-scaffold1577-188573 1 3926226 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387111 Affx-122970668 AX-123257469 1 4811546 TTTCACTGATTTTACTTATTTACCTTTCAGGTAGG[C/T]ATGGTTATTATTATCTCTTTTTTATAACCTCTGTG Y 2 1 2 1 101000 r 74 goat snp14442-scaffold1577-228607 1 3966599 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402334 Affx-122959068 AX-123272687 1 4875518 TGCCATGAGTGAATAAGATAAAACATAAAAGCCAA[C/T]GAGACAAGCTGGGCTAACTGCCTTTGCAAACTGCA Y 2 1 2 1 101000 r 74 goat snp14443-scaffold1577-292579 1 4030858 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772586 Affx-122922371 AX-385259735 1 4922650 CTAAAAAGTAAATTAAAGTGAATTCTCATTTTTCC[A/G]TAGTCATGAGGAAGCCCACACCTAGAGTTTCATTA R 2 1 2 1 101000 r 74 goat snp14444-scaffold1577-339711 1 4078341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378223 Affx-122976918 AX-123248582 1 5019966 CAAATTTCATACCACAAACCCCAATGTGGAAGAAA[C/T]GCATCTTCAGTTTCTAAAATCTGATTTAAATTCAA Y 2 1 2 1 201000 r 74 goat snp14446-scaffold1577-437027 1 4176907 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791888 Affx-122927329 AX-385278878 1 5049184 TGGAAATTGCTTCTCCCCTACTCTGCTTTATTTAC[C/T]ACCAAAGTATTTATCAAAGGCTAACATATCGGGCT Y 2 1 2 1 102000 f 74 goat snp14447-scaffold1577-466245 1 4206140 A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399834 Affx-122960257 AX-123270189 1 5059043 ATTTTAGCTCTTCTCCATCTCATCTTGAATTGCCT[A/G]TCCTTTCTTTACAAAGTGGTATTTTTTTCACCATG R 2 1 2 1 201000 r 74 goat snp19294-scaffold1944-916977 1 4215228 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780119 Affx-122958939 AX-385267216 1 5092811 CTTTCTGAAAGGATAATGTGTGGCACAGAGAAATA[G/T]ATTTAGTTATCACAATATTCCATGAAAGGGAGTAA K 2 1 2 1 101000 f 74 goat snp19293-scaffold1944-883209 1 4248285 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384509 Affx-122973051 AX-123254867 1 5123880 AAAACAAGTCATTAGATCAGCCTGAGGCAGGGGAG[A/C]TACATTCCACCTCTTAAAGGGAGGCATGGCAAAAG M 2 1 2 1 201000 r 74 goat snp19292-scaffold1944-852140 1 4280087 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408269 Affx-122953805 AX-123278620 1 5154584 AGAGAATTGGGCTATTTCAGATCTGTCACTGTCCA[C/T]GATGACAGATTAAGAATTGTCATCTTCCTTTGAGA Y 2 1 2 1 102000 f 74 goat snp19291-scaffold1944-821436 1 4311226 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271830 Affx-1111832861 AX-498625149 1 5207791 AAAGAAATACATTTAGAGCTTAAACTGTACTTGCA[A/G]CAGTCCAAGAGACAACGAAGCAGGCAAAGTTGGTG R 2 1 2 1 201000 f 74 goat 1_5207791_AF-PAKI 1 5207791 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38409573 Affx-122953583 AX-123279924 1 5211110 ACAATATTTATCCAATTCCTACTGAAAGTATCTTT[A/G]CGATTAATCAAATATTTTGTTTGTTTCGGACACCT R 2 1 2 1 103000 f 74 goat snp19290-scaffold1944-764910 1 4368265 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765028 Affx-122924958 AX-385252599 1 5240284 CATCTTCAGGAAGATGCACTGAAATGGAGGTAAGA[C/T]GAATCTACAGGCTTGTCATCATGCTCTAAGATCAA Y 2 1 2 1 101000 f 74 goat snp19289-scaffold1944-735736 1 4398046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437946 Affx-122931624 AX-123308284 1 5298941 CTGCTCAGTTTCCTCATGGTCCTTATCAATTCTTT[A/G]CATATCTGTTTACTTTATTAGAGACTCAGAGATGG R 2 1 2 1 101000 f 74 goat snp19288-scaffold1944-677079 1 4458236 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446876 Affx-122925237 AX-123317212 1 5345369 GTTTCCATTCATGGATTAAAGAGCAAGTTAAATTA[C/T]ACTGTCCTCTCCCAGATTTACTAAGGATGAGAAGG Y 2 1 2 1 101000 r 74 goat snp19287-scaffold1944-630651 1 4504251 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278315 Affx-1111836280 AX-519551801 1 5354789 TAAAATATATGAGGTCCAGTCAAATCTTAGTGTTA[A/T]TCAGCAACAAGTTTTAGTGGTGGTGTTGTTCAGTT W 4 1 2 1 101000 r 74 goat Random2.2K-5 1 5354789 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434338 Affx-122934730 AX-123304679 1 5389920 GCCAATGTTCCCACTCTTATTTCTCTCTTTTATTC[A/G]TTTACTCTGTTTTTTCAACATGTACATACTGAAGC R 2 1 2 1 201000 r 74 goat snp19286-scaffold1944-586100 1 4548618 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416718 Affx-122947553 AX-123287066 1 5433767 TTCATGGCAGCAGGCACACTTGTTTGAAGAATGCT[A/G]TACCAGAGGCTGATCCCCTTGAAAACAATAGCATG R 2 1 2 1 101000 r 74 goat snp19285-scaffold1944-542253 1 4593203 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385368 Affx-122971635 AX-123255726 1 5470121 ACTGTACTTTTGTTTAAGGAACTGAGAAAAATGCA[C/T]AGTATAAGTAAAAGCAGAATAATTATGATTAGCAT Y 2 1 2 1 101000 r 74 goat snp19284-scaffold1944-505899 1 4630009 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278276 Affx-1111836339 AX-519551763 1 5498712 TTTTAGAGGGAATCAGCTTATTACCAAATGCTCCA[A/G]CAGCAACTCACATAAGTATGAAGTTGATTAAGAGC R 2 1 2 1 101000 f 74 goat Random2.2K-6 1 5498712 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777180 Affx-122954436 AX-385264303 1 5564182 GGTGAGTGAAGGTAGATAAAAGTTAACAAAACTCA[C/T]ACCTGATATTTTCCACTTTCTCTTCAAATTAAGAG Y 2 1 2 1 201000 r 74 goat snp19282-scaffold1944-411838 1 4724100 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419625 Affx-122945976 AX-123289973 1 5619488 GGGGCCACTCTCAGACTGCAGAAATTCACAAAGAC[A/G]GTTTGTTCACACGAGAGCTCTGCTCCTCCGTAGCC R 2 1 2 1 101000 f 74 goat snp19281-scaffold1944-356532 1 4779498 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790393 Affx-122968758 AX-385277396 1 5684406 CTCCAGGAGACTTGCTGAATTTACTCTTTTCTTGA[C/T]AAACATACCACTTTCTTACCCACCGAGCAAGTAAA Y 2 1 2 1 101000 f 74 goat snp19280-scaffold1944-291614 1 4844324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399139 Affx-122960658 AX-123269494 1 5758725 TAAACTCTCAAGGTCTTGTGTGGATGTAAACCTAC[C/T]ATGTTCAATATGTTCTGGACCTAGAGTCCAGAAGT Y 2 1 2 1 201000 r 74 goat snp19278-scaffold1944-217295 1 4918536 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278558 Affx-1111836399 AX-185819423 1 5802008 TCTGCCTACTGGACACATGCCTTACCTCAGGGGAC[A/G]TGAATAGCATTTGCTCCATTACCTTCATCCTTACG R 2 1 2 1 101000 r 74 goat Random2.2K-7 1 5802008 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398228 Affx-122962210 AX-123268583 1 5834059 CTGGAGTCCCAACTAGTACATACAATTGTCTTAAC[A/G]TTTCCTTAGGAGGTTTCCAGGCAAACAAAAGTTAA R 2 1 2 1 101000 f 74 goat snp19277-scaffold1944-141961 1 4993671 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390704 Affx-122967939 AX-123261061 1 5884182 CTTTCTTCTTTTCTCTCAGTTGTAGGTTTACCATC[A/G]TGTTTTATTTTCTTGGGCTCCTAACTCACTGTGAA R 2 1 2 1 201000 f 74 goat snp19276-scaffold1944-91838 1 5044740 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772554 Affx-122978398 AX-385259704 1 5980393 AATCTGATGAAATAAGAGGCTGTGGACATGGGAAT[A/C]GTATTTGGGAGAGAAGAAACAATAGTTGTCCATGG M 2 1 2 1 101000 r 74 goat snp20593-scaffold2027-972600 1 5137732 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449181 Affx-122923527 AX-123319516 1 6026788 GCCAAATTAAAATCCCTGTTTTATAAGTATCACAA[A/G]GAGGTTTTCATCTTGCCACCCTGCTGCTTCTCTCG R 2 1 2 1 201000 f 74 goat snp20592-scaffold2027-926205 1 5184119 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791712 Affx-122974990 AX-385278703 1 6099517 ACACCCATGGTGTGTATGTGCTACAAATATTGTTC[A/G]TTACATTTAGTATTTGTGGTTCATTATTTCTGTGT R 2 1 2 1 101000 f 74 goat snp20591-scaffold2027-853476 1 5256876 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417049 Affx-122947523 AX-123287397 1 6158762 CTAGCAGAATGTGTGTAATGCTTGTAGAATGTTTA[C/T]GGTATACCAAAATAAAGAATTTTGGTAGAGGAACC Y 2 1 2 1 101000 f 74 goat snp20590-scaffold2027-794231 1 5316996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788795 Affx-122972268 AX-385275810 1 6233916 GATTCATGAGCGCCAGTGTTTTAAATGTCACCTGA[C/T]GTAAGCCTACTAGTAGCTCCATTTTAAAATTGGAA Y 2 1 2 1 101000 f 74 goat snp20588-scaffold2027-719077 1 5392991 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452033 Affx-122920899 AX-123322366 1 6273074 GACCAAAGAGCTTTGGGAATACCAAAGGTAGAATG[A/C]TTATGCAGAGGAGGTGACAGCAGAGATAGCCTTGA M 2 1 2 1 101000 f 74 goat snp20587-scaffold2027-679919 1 5432216 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438248 Affx-122931426 AX-123308586 1 6303282 TTCATTAAGACAATTAGAATAAATACACAGAGACC[C/T]GCAAAACAGTTAAAGTGATACCACTCAATGGTGTC Y 2 1 2 1 101000 r 74 goat snp20586-scaffold2027-649711 1 5460626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417304 Affx-122947230 AX-123287652 1 6347937 GTCTATGCCGTTGACCATCCTGAAGATAATGAATG[C/T]GAAGTTGAAATGTCACTTCAGGGAGAAGCAGATAT Y 2 1 2 1 101000 f 74 goat snp20585-scaffold2027-605056 1 5503616 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771562 Affx-122941172 AX-385258720 1 6392033 TAACTGACCAGTACACATATAAAAAGTTATTAACT[C/T]ACACTAAAAGTCAAATGAGGTGAAGAGCTAAGTCG Y 2 1 2 1 101000 r 74 goat snp20584-scaffold2027-560960 1 5547756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405465 Affx-122956033 AX-123275817 1 6426565 AGTTAGGAAAATAGGCGGATTGTCTAATTCTTCAT[A/G]CCACTGCAATGAATAGAGCAGTTCTGCAGCTAACA R 2 1 2 1 201000 f 74 goat "GoatD01.001540;snp20583-scaffold2027-526428" 1 5581623 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320774275 Affx-122954909 AX-385261411 1 6481255 TTCCTTTCTGCCATATTCCTACTACTAAGCTATGC[A/G]TGTAATTATACAGATAATTGAGTGTGGGCAATGTC R 2 1 2 1 101000 f 74 goat snp20582-scaffold2027-471738 1 5636419 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778762 Affx-122956008 AX-385265871 1 6513600 TACTTGACCCTTTTGCCCAATACTAGTTCTGCTCT[A/G]TCACTTCCCTGTAGGAAATCCTCTAGGTTTTACAT R 2 1 2 1 101000 f 74 goat snp20581-scaffold2027-439393 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433261 Affx-122935232 AX-123303602 1 6544523 GTCCATGGCTGTCAGTATGCAATGTCATTTTCACT[A/C]TCTGTGCACAAGTTAGTGGAAAACAAACCAAAAAA M 2 1 2 1 101000 f 74 goat snp20580-scaffold2027-408470 1 5700987 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764483 Affx-986698945 AX-385252163 1 6553494 AACCCGGACCCAGATTTGGCCTTGTACACCAATGG[C/T]ACCAGCCTGGTGAAACAAGGACAATGACTGTTGGA Y 2 1 2 1 600010 f 74 goat 1_6553494 1 6553494 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 38429139 Affx-122937997 AX-123299481 1 6588867 AAGTGAGATCTGAGCTCCCAAACCCACCGAGGGGC[A/G]TGGAAGGCACAGCAAGGAATTCCACAGTCACTGTG R 2 1 2 1 201000 r 74 goat snp20579-scaffold2027-364126 1 5744993 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437357 Affx-122931935 AX-123307695 1 6651364 ACAAGAGTCCCAGTGAACACAAAACTAAGACAAAA[C/T]GAAGTGTTTAGGAAGGAAAAAAGATTTTCTGTCCT Y 2 1 2 1 101000 f 74 goat snp20578-scaffold2027-301629 1 5807697 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376923 Affx-122977789 AX-123247282 1 6714298 CAAGAGACAATACAGAAAAATATACAAAACAAATG[C/T]ATAAGGTAAAAACACCTGTGCAGGCAGAATTCTAA Y 2 1 2 1 103000 r 74 goat snp20577-scaffold2027-238695 1 5871428 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429649 Affx-122937673 AX-123299990 1 6749957 CCTCTGGCAGGTTACTTATTCTCTCTGGGACTGAA[A/G]TTCTCATCTGTATGATCCGGATAAATATTATCTAG R 2 1 2 1 201000 r 74 goat snp20576-scaffold2027-203036 1 5907279 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778164 Affx-122962656 AX-385265279 1 6785383 AACTACGATTCCCACAAACCATAATCTGAGATAAA[C/T]GCCATATGACTCAGTAAATCTAAGGAAATGTCTCT Y 2 1 2 1 101000 r 74 goat snp20575-scaffold2027-167610 1 5942841 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797791 Affx-122932259 AX-385284730 1 6829201 TGTAAGTGTTTATGCCATCACCCCTCAATCTGCTG[C/T]ATATATACATTGATCCTATGGTAATTCACAAGTTT Y 2 1 2 1 102000 f 74 goat snp20574-scaffold2027-123792 1 5987184 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454214 Affx-122919281 AX-123324547 1 6864011 TTGCCTTCTACTGACCTTTTATAGATTTTTCTCCT[A/G]TTCTACTAAGAAGCCAGGGTTGGATATTGTCAAGA R 2 1 2 1 101000 r 74 goat snp20573-scaffold2027-88982 1 6022027 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770800 Affx-122940105 AX-385257964 1 6917248 TATCTACTACTTGCCAGGTGCTTTGGAAGCCTTAC[C/T]GATTCTTTCAACCATGCTCATTTACCAAGTGTTAT Y 2 1 2 1 101000 f 74 goat snp20572-scaffold2027-35745 1 6076169 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787321 Affx-122936999 AX-385274346 1 6947617 AGTTGTCCTTGCTCTGGCCCTTAGGGAACAGGTTA[C/T]GAATCACTCTGTACCCTGAGTGCTTATTTCTGTTG Y 2 1 2 1 201000 f 74 goat snp20571-scaffold2027-5376 1 6107244 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383166 Affx-122973229 AX-123253524 1 6953991 TGTCCTTGGGACATCTTTAGTTCATTCTTAGCATA[C/T]GCTTTTCTTTATTGTCTAAGTTTTTACGCTCATCC Y 2 1 2 1 101000 f 74 goat snp44228-scaffold601-899 1 6113419 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439043 Affx-122930334 AX-123309380 1 6984781 TGAGGGAGCCAGAGAAAGTGATGCAGAGTCAGTTA[C/T]AGGCTCTGTTCACATTCTATATCCAGCAAACAATG Y 2 1 2 1 101000 f 74 goat snp44229-scaffold601-31689 1 6144487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278789 Affx-1111836513 AX-519552262 1 7026543 AAAGATTTTAAATTATATGTGAAAACTATTTATGA[A/C]TTACATTTCTGTTTCATCAAAGATCAAAGGAAAAC M 2 1 2 1 101000 r 74 goat Random2.2K-9 1 7026543 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777823 Affx-122960093 AX-385264940 1 7044141 AAATAAGTTTATTTCAACTAAGGAATTATCTTACA[C/T]ATGCAAATATGTTCTCTGTTTTCTTTAAGCATTAT Y 2 1 2 1 101000 r 74 goat snp44230-scaffold601-91049 1 6203682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272492 Affx-1111835350 AX-519546214 1 7059443 GACTGGAAAATGTCAGCTTTCATTCCAATCCCAAA[A/G]AAAGGCAGTGCAAAGACGGTTAAATCATCATACAA R 2 1 2 1 101000 r 74 goat Random2.2K-10 1 7059443 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448735 Affx-122923833 AX-123319071 1 7077342 GTTAGCGACTGAGCAACAGCAAAGGTGCTTTGGAT[A/G]CACAAGAAGTTTATTCTGAGGCAGAAAGGAACTGA R 2 1 2 1 101000 r 74 goat snp44231-scaffold601-124250 1 6237063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426968 Affx-122940401 AX-123297313 1 7135412 ATCACTGAGCGTCATGGTAAACCAACCTCGGCTAG[C/T]ACTGGGAAGTGTGCACATTTCAAGAGGTGTTTATG Y 2 1 2 1 101000 r 74 goat snp44232-scaffold601-182320 1 6295772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396585 Affx-122962910 AX-123266940 1 7184932 AAAGAGATTACAAGCAGAGATGAAAGGAAACAGAC[C/T]AACGGACTTAGAAAACACACTTATGGTTACCAAAG Y 2 1 2 1 101000 r 74 goat snp44233-scaffold601-231840 1 6344651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423484 Affx-122942572 AX-123293830 1 7248445 TGGAAATAGTAACTATGCCAGGGTAAGCTCTGGCA[C/T]GTCTACTTTTCTTTTCACAGAAACTTACAAAATAA Y 2 1 2 1 101000 r 74 goat snp44234-scaffold601-295353 1 6407914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407378 Affx-122955264 AX-123277729 1 7302950 ACTGAGATTCTCTCACTGATATTCTTAATATTCAT[A/G]TAACTAACGACAGTTTTATCCATTGTATCTCCCAC R 2 1 2 1 101000 r 74 goat snp44235-scaffold601-349858 1 6462452 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385261 Affx-122972080 AX-123255619 1 7379068 AGTTAAAAAATGACCAAATATTTAAAATGACTCAA[A/G]CTGAATAAGATCTTGTTTAGCTCAGGTCTGTTAAA R 2 1 2 1 101000 r 74 goat snp44237-scaffold601-425976 1 6539441 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411078 Affx-122951934 AX-123281428 1 7423604 TTTCATTTGCTGACCCTTGTTCCAGACAGATAACA[C/T]GGGGGGAAACAGTACATAAATACAAAATAGGTCAG Y 2 1 2 1 101000 f 74 goat snp44238-scaffold601-470512 1 6584302 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423286 Affx-122942649 AX-123293632 1 7460334 CAAAAATGCCTTTAAACTGTTTTAAAATTCCAGTG[A/C]TGTACCTCCATGCAACACTCTTAATTGCCTTACAA M 2 1 2 1 101000 r 74 goat snp44239-scaffold601-507242 1 6621557 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784873 Affx-122963051 AX-385271920 1 7510327 AATTAAAAAAATAATATAAGCAGCAGTAGGGGAAC[A/G]TTCATTATGATCAAATGTCTCTATTCTACGAATTG R 2 1 2 1 101000 f 74 goat snp44240-scaffold601-557235 1 6671447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404633 Affx-122957320 AX-123274985 1 7580264 ACACTGGTATAACGCATGGGGCATAATACACAGTA[A/C]CTCTTGTGATCATTATATCCAATTTACAGATGAAA M 2 1 2 1 101000 f 74 goat snp44242-scaffold601-627172 1 6741956 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777366 Affx-122933698 AX-385264488 1 7634710 CTGTATCCCTGTCATAAGTAAGCTGTATCCCTGTC[A/G]TAGATTGGGCAATTGCATCAGCATCTCTTTCCATC R 2 1 2 1 101000 f 74 goat snp44243-scaffold601-681618 1 6793862 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385787 Affx-122971047 AX-123256145 1 7706584 CAACTTTGGTAGTAGTTTCACCATCTGCAGCAAAA[C/T]GTAAAATGTTTTCCTATTTTTATTAACAGCTACTG Y 2 1 2 1 103000 f 74 goat snp44244-scaffold601-753492 1 6864331 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446563 Affx-122924839 AX-123316899 1 7792228 CTCTCCCACACTTCTGAACACCAGAAAGTGCAAGC[A/G]TAGTACCACCCATAACCTTGGCCAGTGGGAAATGA R 2 1 2 1 201000 r 74 goat snp44245-scaffold601-839136 1 6946516 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379414 Affx-122976116 AX-123249772 1 7822598 AGTTGGGAAGGATTCTCTCCTGTGCAATCATCTTC[G/T]GATGCCTATTTGGGATGGTAACTGCTCTACTCAGT K 2 1 2 1 201000 r 74 goat snp44246-scaffold601-869506 1 6975496 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272561 Affx-1111832870 AX-519546277 1 7855338 GTGCTAAGTCACTTCAATCATGTCTCACTCTTTGC[A/G]ACCCCATGGACTGTAGCCCGCCAGGCTCCTCTGTC R 2 1 2 1 103000 f 74 goat 1_7855338_AF-PAKI 1 7855338 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435608 Affx-122933789 AX-123305948 1 7856190 AGGTGGCAGCTAAAAAGACTCTGAGGACAGCAAAG[C/T]AGTCATGTGACAATCAGGGACAGCATATTTCAGGA Y 2 1 2 1 101000 r 74 goat snp44247-scaffold601-903098 1 7011562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385067 Affx-122971818 AX-123255425 1 7911745 AACAAGACTATAAACCACAAAGATAATTATTAATG[C/T]ACATAAATATTAAAAATACCGGTCAGCATATGGAG Y 2 1 2 1 303000 f 74 goat snp44248-scaffold601-958653 1 7066484 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381793 Affx-122974288 AX-123252151 1 8008953 AATCATCTTACTATGACCACCCTATTCAAACCACC[A/G]TCATCCTCACCTGGAGACTTCCATTAGCTCTCTAA R 2 1 2 1 201000 r 74 goat snp44250-scaffold601-1055861 1 7160352 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392131 Affx-122966336 AX-123262488 1 8078447 CAAAGGGGCTTTGCTTCACAGCAAGTATCTAAGAA[C/T]GTTATTTTCAGTTTATGTCAGTGTTACATCAAGGG Y 2 1 2 1 101000 f 74 goat snp44251-scaffold601-1125355 1 7228763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276510 Affx-1111835453 AX-519550021 1 8129604 TCCCAGAATCATCAAGCCAAGTTTAACTTAGTTGG[A/G]TAGAGACATGAAAACTTGGCGCAGCTAAATTTTGC R 2 1 2 1 101000 f 74 goat Random2.2K-12 1 8129604 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797502 Affx-122926687 AX-385284441 1 8140152 TGAAAAAGTTTTGTCATCATTTCTGTTGTTACTGT[C/T]CATTTCAAATGCAGGTTATTATTAAAACAATTATC Y 2 1 2 1 102000 f 74 goat snp44252-scaffold601-1187060 1 7290562 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378232 Affx-122976912 AX-123248591 1 8188321 GTTTATGCTTTTCTTTCATTTTCCACCTCCTATAT[A/G]AGACTATTCCTTTAGCTTACCCTCTCCAGAAGTGT R 2 1 2 1 101000 r 74 goat snp44253-scaffold601-1235229 1 7345434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769739 Affx-122961897 AX-385256909 1 8270691 AGTTAAAAGAAAAAAGATCATACTAGATCCAGGAT[A/G]CATTCTACTACACAGACCTGTGTAACAGGTCTAAG R 2 1 2 1 201000 r 74 goat snp44254-scaffold601-1317599 1 7429034 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798810 Affx-122957286 AX-385285741 1 8295574 TAGGACACTGACTCATATTTTTCATCCGAGTGAAT[A/G]TGATTTATTCAGTGATCCTATATAAATGTATTATG R 2 1 2 1 101000 f 74 goat snp17081-scaffold1783-272495 1 7454440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780180 Affx-122972127 AX-385267276 1 8326207 TTTCACGATTCCATTACCTCTCACTCTTTTTTGCA[G/T]GTATGGATCTTGTGGATGATTCAAAGAACTATTGT K 2 1 2 1 101000 f 74 goat snp17080-scaffold1783-241862 1 7485263 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787022 Affx-122967395 AX-385274050 1 8361416 AACAATTAGTCAATCTAAGAAAGATTTATTGGAAA[C/T]AATTGAAGATTATTACCTGGGAAAAGCCACTTTGA Y 2 1 2 1 201000 f 74 goat snp17079-scaffold1783-206653 1 7520301 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797694 Affx-122939431 AX-385284633 1 8405670 CCACTCAGATTGTCATGCTGAACTACTGCATTGTC[A/G]GTTTTCTTTTACCATGATGATTTCTCTTGCACTTT R 2 1 2 1 101000 f 74 goat snp17078-scaffold1783-162399 1 7563723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783298 Affx-122929666 AX-385270363 1 8447700 TGCTTGTCTCCCAATATCTGAATTACAGATACAGA[A/G]GTAGATATAGATATATTTACTATGAAACATAAATT R 2 1 2 1 201000 r 74 goat snp17077-scaffold1783-120369 1 7605812 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412033 Affx-122951730 AX-123282383 1 8508813 GTAGGAAAAGGAATAAAAAAATAAAGTAATGAAAT[A/G]CATTTTTTAAGACATGCGTTTCCTCCCAAAGTATG R 2 1 2 1 101000 r 74 goat snp17076-scaffold1783-59256 1 7666912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795236 Affx-122935464 AX-385282194 1 8586569 CTCCTATTTAATGTTCTCTCTTATTATTTCCTCAT[A/G]CTACCCACAATGAAAATAATCTTGCAAAGCTCTAC R 2 1 2 1 101000 r 74 goat snp48423-scaffold688-18401 1 7745595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771822 Affx-122957453 AX-385258979 1 8620938 CTGATCTAAGATTGGGAAATGGCATGGTCATAAGA[C/T]AGAACTATGTTAGTAACTATTTAAGAAACCAACCA Y 2 1 2 1 101000 f 74 goat snp48424-scaffold688-52770 1 7779742 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379399 Affx-122976129 AX-123249757 1 8684730 AACTAACTAGCTGAGTAAATGCTATTGAAGTAAAT[A/G]ACTGTATAAATAGCATCAAAATGCAAAGCTTAGAA R 2 1 2 1 101000 f 74 goat snp48425-scaffold688-116562 1 7844147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399350 Affx-122961353 AX-123269705 1 8716725 CTGTAAAATTAAACATTGGTTTTGTGGTTTCAGTG[A/G]GCATAATAAATGTAAACTGTAAAATAGGTTAAAGT R 2 1 2 1 101000 f 74 goat snp48426-scaffold688-148557 1 7875834 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441635 Affx-122928635 AX-123311972 1 8754110 CAGAGGCAGTAGGAAATCTGTTCCAAAACCAGCTG[C/T]ACCACATCTGTTTTCCAGGGCATCAGTAGCAATGG Y 2 1 2 1 101000 r 74 goat snp48427-scaffold688-185942 1 7915964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403661 Affx-122957514 AX-123274013 1 8817404 ATTATATATATTAAATTCATATATCAGCACATTCA[A/G]TTTCAAAGTAGGACAACTTTGCTTCTGGATACATT R 2 1 2 1 101000 r 74 goat snp48429-scaffold688-249236 1 7980410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276813 Affx-1111835534 AX-519550322 1 8842614 GCAGACAAAACAGTCCTTTTATTATTTATTTATTT[A/T]TGGATGTGGACCTTTTATTAAGATCCCTATTAAAT W 4 1 2 1 202000 r 74 goat Random2.2K-13 1 8842614 T A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320782151 Affx-122930536 AX-385269229 1 8873761 AACTTTATGTTTTCTCCTGTAATAACAAGTACATC[A/C]TAAGTCATTTATTGTTCATTTGTTGTAGCAAAGCC M 2 1 2 1 201000 r 74 goat snp48430-scaffold688-305593 1 8037219 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798008 Affx-122945215 AX-385284944 1 8948806 TTATCATTTTAGCTAGTCCTAAGTCATTGCAAAGC[A/G]TCAACAGAGTTTACAAAGAGAACATTAAATTAATT R 2 1 2 1 101000 r 74 goat snp48432-scaffold688-380638 1 8112978 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790213 Affx-122970653 AX-385277217 1 8999891 TCTTAGAAATATAAGCAGAAATAGGCTTAAGGATC[A/G]GATAACTTTACACTCATCCAGGTAATCTGCTAACA R 2 1 2 1 101000 r 74 goat snp48433-scaffold688-431723 1 8164861 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795807 Affx-122952839 AX-385282760 1 9028982 GAGCAGGTCTGAACGAGGCATCTAGAATGGATTAA[C/T]GTTCTGCTTCAGGACCTGAATCATGTTTACTTTAG Y 2 1 2 1 101000 r 74 goat snp48434-scaffold688-460814 1 8194401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789859 Affx-122962433 AX-385276866 1 9068842 TTCAACTAATTTCATTTAAGCTTGACTGTGGATAC[A/G]TGGTCACTATAATATTCCTCATATTTTCTATAATG R 2 1 2 1 101000 f 74 goat snp48435-scaffold688-500674 1 8234362 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384436 Affx-122973106 AX-123254794 1 9106826 ATTGGACCAAGAGATGAAGTTTCTCAAAAACCAGG[A/G]ATTAAATGTTTGGATTTTAACTTAAAGGCAACAGG R 2 1 2 1 201000 r 74 goat snp48436-scaffold688-538658 1 8271780 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794700 Affx-122977703 AX-385281660 1 9142763 GGCAGGCTTTCTCAACTATGTTCATACATTTAAAA[A/G]AATTCATTAAGGTTTTTAAAAGAATGATCCTGGCT R 2 1 2 1 202000 r 74 goat snp48437-scaffold688-574595 1 8307924 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408711 Affx-122953429 AX-123279062 1 9179141 GTCATCTGATGTTTTAAGACCACAGTCCCCAACCT[A/G]TCTGGCATCAGGGACTGCTTTCATGGACTACAGTT R 2 1 2 1 201000 r 74 goat snp48438-scaffold688-610973 1 8344502 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799572 Affx-122921823 AX-385286502 1 9243355 GATTCTATTATGAGCAAGCTGACAAAGCTTTTGTT[A/G]CCTTCTCAGTTGGAGTAAGTTTTACATTGTAAGTT R 2 1 2 1 201000 r 74 goat snp48440-scaffold688-675187 1 8408276 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415169 Affx-122949011 AX-123285518 1 9301018 CAGGCTGAGCCAGCAGAATTACTGGCTTCTCCAAT[A/G]CAATTGTCAGAACAGGAATGACGGAATCAAGAGGT R 2 1 2 1 101000 f 74 goat snp48441-scaffold688-732850 1 8465295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447467 Affx-122924356 AX-123317803 1 9391925 CCTCCACTGCCAGGCTTTAGCCTGACACCTGGTCA[C/T]GTCTCAAGGTGTCTCCCTCTCAGATTTAATTAGCA Y 2 1 2 1 101000 r 74 goat snp48443-scaffold688-823757 1 8557176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786628 Affx-122936003 AX-385273660 1 9438142 AAGGTTGCAAAAAGTCTTACTCAACTAACAGGGTT[C/T]GGAATTTAACATGGCAAAACCTAGACCCTCAATAT Y 2 1 2 1 101000 f 74 goat snp48444-scaffold688-869974 1 8603434 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764706 Affx-122948825 AX-185846846 1 9472085 GTCAAGGAACGATGGAAGGAAAGTAGAATTCCTCA[A/G]TCTCTTTCTATTGAGCTGAATGATCTTCCAACTGA R 2 1 2 1 101000 f 74 goat snp48445-scaffold688-903917 1 8637284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393055 Affx-122965619 AX-123263412 1 9510059 GGTTTTGATGTCTTCATTTCTGCTGTCAGCCTCTG[C/T]AGGGTTCTGTCATTCCCAGCAGGGAGGGGGTCCTG Y 2 1 2 1 101000 f 74 goat snp48446-scaffold688-941891 1 8675129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434918 Affx-122934316 AX-123305258 1 9541542 CCAGATCTGGTCTACTGCCTGTTTTATGAAGAAAA[C/T]GTTCCTATGAAGCAGCCACACCCATGGTGTCTGCG Y 2 1 2 1 101000 f 74 goat snp48447-scaffold688-973374 1 8706726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418942 Affx-122946499 AX-123289290 1 9575706 CACTTTCCCAGGCCGGGTATAGTATCTGGTGTTAA[C/T]TTAGCACATCACAACACCTCTTCTTGACTACTCGT Y 2 1 2 1 101000 r 74 goat snp48448-scaffold688-1007538 1 8740743 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766746 Affx-122967861 AX-385254082 1 9652058 CAGTTACAAGGGAATTTTAATCAGCTTTATTGAAG[C/T]GTACCTATTAGACTTTTAAATTAACTGGAGGCCCT Y 2 1 2 1 303000 f 74 goat snp48449-scaffold688-1083890 NW_017195430.1 7321 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415124 Affx-122949430 AX-123285473 1 9706965 TGTCATATTTTGCTCTAGCAAAGGTTGCATGTGCT[A/G]TGCCATGCTAAGTCTCTTCAGTCGTGTCCGACTCT R 2 1 2 1 101000 f 74 goat snp48450-scaffold688-1138797 1 8869620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418015 Affx-122946654 AX-123288363 1 9740316 GGAAACTTACTTGAAATTCACATTCTCTGGTCCCA[C/T]CCCTGACCTCCTGATTCAGCATTGCTGGGCTGAGG Y 2 1 2 1 101000 f 74 goat snp48451-scaffold688-1172148 1 8903202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771542 Affx-122919842 AX-385258700 1 9805947 AACTTGAATCAACTTAGACTGAAAACACCCAAAGC[A/G]TGAAGTTAGGAATAAGCAATCGATGAAGAACGATG R 2 1 2 1 101000 f 74 goat snp48453-scaffold688-1237779 1 8968647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774671 Affx-122974221 AX-385261805 1 9835323 AAAGAGGGGGAGAGCACTGGGTTAGATCTAATTAC[A/G]TGGTATACCTTGGGATGATGCCCAAAAGGGCAACT R 2 1 2 1 201000 r 74 goat snp48454-scaffold688-1267155 1 8997440 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418841 Affx-122946142 AX-123289189 1 9875634 AAAGAACTTGGGTACTTTTAAAATAAGGAGATCTG[C/T]GCATGTTGTGTGCATGCATGTGAGTCTAAATATAT Y 2 1 2 1 101000 f 74 goat snp48455-scaffold688-1307466 1 9038325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388115 Affx-122969487 AX-123258473 1 9917052 AAGATATTCATGTAGGCCACGGGGCTGTTACTTTT[A/G]TAAACAAAACAATTCCAAAGCAGAGCTCCTCTGTA R 2 1 2 1 201000 r 74 goat snp48456-scaffold688-1348884 1 9080472 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393077 Affx-122965605 AX-123263434 1 9945578 TGAAATCTCCCTGTTTAGCTTAGCAAAAGTGACCC[C/T]TCACCTCTAGTAGCTTTTTGTTAAACTGTGCCTTT Y 2 1 2 1 101000 f 74 goat snp48457-scaffold688-1377410 1 9108778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402247 Affx-122959136 AX-123272600 1 9977903 TGTTCTCACTGGTGAATAAAAGGGTCTGGGGTACA[C/T]GGTGCCCTCTTTCTCTCACCTCATTGAGTCCCCAA Y 2 1 2 1 101000 f 74 goat snp48458-scaffold688-1409735 1 9141331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409037 Affx-122953861 AX-123279388 1 10011026 AGTGACATGTCTCACCCTCTTTCCACTAGCCTAAC[A/G]GACATTTTTAGTTGACTATTTTCTTCCCTCCTGAA R 2 1 2 1 201000 r 74 goat snp48459-scaffold688-1442858 1 9175161 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448961 Affx-122923132 AX-123319296 1 10043939 GGAGTCTCAAGCACTGGACAGCTGGGGAAGTCTCC[A/G]TTTTTCTCCGATTTTTAACCTTCCTCCTTCTCTCC R 2 1 2 1 101000 r 74 goat snp55833-scaffold867-19405 1 9207636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801904 Affx-122940749 AX-385288809 1 10149214 GAATATATGCTTTTAGGTCAGCATAGTACGTAAAA[G/T]CATAGACTCTGGGGACAGAATGCTAATTTCAAGCT K 2 1 2 1 102000 r 74 goat snp55836-scaffold867-124680 1 9313941 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399569 Affx-122961122 AX-123269924 1 10182767 GTGCTCTGCATTGAACCCCTGAGGTCTGTTTGTGA[C/T]GAAAGTCACAATGAGGCAAAAGTCCTTGTTCCTGG Y 2 1 2 1 102000 f 74 goat snp55837-scaffold867-158233 1 9347664 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439863 Affx-122930054 AX-123310200 1 10216707 CAGGTTCTTTGGTTAAATTAGCAGTCCCTTTTCAC[A/G]TCAGGCTTCTCTTCATTCGGCTACACAGATTTTTT R 2 1 2 1 101000 f 74 goat snp55838-scaffold867-192173 1 9382099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376128 Affx-122978868 AX-123246487 1 10247386 AAGGGACTGAAACTGATTGTGAACTGAAAAATTAC[G/T]ATGAGCTTTTGATTTAAGCAATGCCTACCAAAATA K 2 1 2 1 101000 f 74 goat snp55839-scaffold867-222852 1 9413786 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382236 Affx-122973962 AX-123252594 1 10330619 AGTTTCTCAACACTTTTAAAAAGGCATCAACAGAG[G/T]TTGTATCAATTACAATGCCTCCAGGAACTGTTACA K 2 1 2 1 101000 f 74 goat snp55841-scaffold867-306085 1 9498306 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400952 Affx-122959700 AX-123271305 1 10353936 GAGCAAAGAATATTTGGGGGAGAAAGAGTTCACAA[C/T]GCACAATGTGCCCCTAATGCTCTTCTGTTGCTTGA Y 2 1 2 1 201000 f 74 goat snp8479-scaffold1307-528093 1 9521685 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771436 Affx-122974379 AX-385258594 1 10388131 CTGAAGTAATTGATTGAATGTTCTACAGTACTGCA[C/T]AGAACAAAAGCCCAGATATCAAGTCAATATTCATG Y 2 1 2 1 101000 r 74 goat snp8478-scaffold1307-493898 1 9556496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272457 Affx-1111836714 AX-519546182 1 10408764 ACAAAAACTTGTTTGCACCAGGACTCAGGAGAAAG[A/G]AGCAGTGATCCCACAAGAGACTGACCCAGACTTGT R 2 1 2 1 103000 f 74 goat 1_10408764_AF-PAKI 1 10408764 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320798378 Affx-122973987 AX-385285312 1 10438434 TGTTTATTTCACAAGCACTTTCTCATTTTAAACTC[A/G]CAAGACTTATGACAAATTTCCACTTCACTCTTGAG R 2 1 2 1 101000 f 74 goat snp8477-scaffold1307-443595 1 9606365 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454319 Affx-122919244 AX-123324652 1 10493516 TTTTGTGATACTACTGAAAAGGCAAAATCTAGTTA[C/T]GTTTTTCCTTTGACCGAATAAAACTCCTGCAATTT Y 2 1 2 1 101000 f 74 goat snp8476-scaffold1307-388513 1 9662286 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439011 Affx-122930358 AX-123309348 1 10546669 CTAACACTAGACTTCTAACCATGGACTGCAATTTC[A/G]TTGGCTGGGCCAAGACACCTTGCCTATTTTTCATT R 2 1 2 1 101000 f 74 goat snp8475-scaffold1307-335360 1 9714340 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407580 Affx-122954664 AX-123277931 1 10579347 AGTTCTTCTCTTTTTCTCTATTAGTTAAAAGATAA[C/T]GAACCATTGTATATGCTTTTTCTGAGTTGCTTAAA Y 2 1 2 1 201000 f 74 goat snp8474-scaffold1307-302682 1 9747544 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765119 Affx-122966742 AX-385252679 1 10660683 CCAGTATAAGGCTTTGCCTCTTTGGTATGAAATAG[C/T]TTCATTAAATAACCACCCACTGCTCTCTCTAATCC Y 2 1 2 1 101000 f 74 goat snp8472-scaffold1307-221346 1 9830796 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792594 Affx-122968253 AX-385279574 1 10706551 ACATCACATATCAAATTTACTAATTTTAGTTAGTG[C/T]AAGACTCCATAGCATCCTATCCTGTCCAATGAAGC Y 2 1 2 1 101000 r 74 goat snp8471-scaffold1307-175478 1 9876800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405779 Affx-122955918 AX-123276131 1 10737123 TAAAGTAAGAACCTAGTTTTCCTCAAGTATAGATA[G/T]AGTGTAGCTTCTGAATTCATCCATGTGGCAACTTA K 2 1 2 1 201000 f 74 goat snp8470-scaffold1307-144906 1 9907995 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794450 Affx-122954449 AX-385281413 1 10766409 AAGAAGTGAACAAAAGTCTAAGAGTTACTAGTAAA[C/T]AATGATCATGAAAATAGAGTGAATATAATAAATGC Y 2 1 2 1 202000 r 74 goat snp8469-scaffold1307-115620 1 9938053 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780646 Affx-122949957 AX-385267736 1 10849927 ATTCTTGAACTTTGTTCAGCTTTACCAAATATGTC[C/T]GATTAACATTCCTGGAAGTTCACAAGTAGAGTGCA Y 2 1 2 1 101000 r 74 goat snp8467-scaffold1307-32102 1 10020932 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397852 Affx-122962458 AX-123268207 1 10896602 ATGGATTAACTAGCAGTCATATTTTCAGTGACCAC[A/G]TCTAACAGGAGGGAAACAAATTCTAAGTGAAGTCC R 2 1 2 1 101000 f 74 goat snp42339-scaffold559-14474 1 10121414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419872 Affx-122945361 AX-123290220 1 10928535 AGATAAATATTTTTTCTTTCTACTTTAGTTTTCAT[C/T]GATTTTAAGAAACGCATTCATCACTCTTAGAAGTT Y 2 1 2 1 101000 r 74 goat snp42340-scaffold559-46407 1 10152332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385122 Affx-122971776 AX-123255480 1 10976246 GGTATTATTTTCCAAAATATTCAGAATCCCTAGGA[C/T]GGGAAGAATACTACTTATCACAGACTTCCATCCCT Y 2 1 2 1 101000 r 74 goat snp42341-scaffold559-94118 1 10200055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409911 Affx-122952887 AX-123280262 1 11040773 GGAACATAGGTTTCTATGATATGTATCTAGGAGAT[A/G]CTAACAAAATAAAGTCTTATCTTTTTATGCTTCAA R 2 1 2 1 101000 f 74 goat snp42342-scaffold559-158645 1 10264446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792036 Affx-122956490 AX-385279024 1 11079155 AACTGATTCTAGTACCTGTGTGTTTCTGCTTAGAG[A/G]TGCTTAATGATTACACCCTTGATAGAACAAATCTT R 2 1 2 1 101000 f 74 goat snp42343-scaffold559-197027 1 10303410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772555 Affx-122973668 AX-385259705 1 11117868 ACACATTTTAATCATGTTTGTTTGAAAAGGCTGAC[A/G]TATAATATGTAATGACATCTGGTTGTCAGAAGTAC R 2 1 2 1 201000 f 74 goat snp42344-scaffold559-235740 1 10342341 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402864 Affx-122958238 AX-123273217 1 11150557 GTGTGAACACTCAATCATTCACTCAACAAATACTT[A/G]TCGGTAATATTTATTTGCCTGGTATTGTGTCAAAT R 2 1 2 1 201000 r 74 goat snp42345-scaffold559-268429 1 10374718 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799397 Affx-122927273 AX-385286327 1 11193184 TGAGCAATTTTACATATGCCTTAGATATATCAAAT[A/G]CAATGCTGGAGATCTCTGTATACTTAATGACTGCT R 2 1 2 1 101000 r 74 goat snp42346-scaffold559-311056 1 10418692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419032 Affx-122946032 AX-123289380 1 11222860 AAGTATATTGTACATTAGTGCAGTTCAGTTCAATC[A/G]CTCAGTTGTGTCTGACTGAATATTTAATGCAATGT R 2 1 2 1 303000 f 74 goat snp42347-scaffold559-340732 1 10448945 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798921 Affx-122964344 AX-385285851 1 11254849 TCTCCAGAAGATATGGGAAAAGTTTCAAGGCAAGG[C/T]AAAACTTTATTTGATCATCTTCAGAGACAGAGGGA Y 2 1 2 1 101000 f 74 goat snp42348-scaffold559-372721 1 10480653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398823 Affx-122961395 AX-123269178 1 11303237 GGGAGAGCAGGATAATTTTAGATTGTGTAAAAAGA[G/T]AAATATATATCTAGGAAAATGCAATGAAGCATACT K 2 1 2 1 101000 f 74 goat snp42349-scaffold559-421109 1 10529911 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388953 Affx-122968809 AX-123259311 1 11334926 TGGCTGTGCTGAGCCTCCAACAATTCATCAATTTC[A/G]CTTTCATCCCCCACCACAGTAGTTCCTGACCCAAC R 2 1 2 1 101000 f 74 goat snp42350-scaffold559-452798 1 10562733 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277139 Affx-1111835699 AX-519550645 1 11381248 ATAATAACAAATACTTATATGCTCTTCATTGGGTA[A/G]CTGTCTCAAAAATGCTTGGATTAAATAAGTCCCAA R 2 1 2 1 101000 r 74 goat Random2.2K-16 1 11381248 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430925 Affx-122936847 AX-123301266 1 11402862 CATAAAGCTATATCAGCCTGCTCTGAGCTATTTAA[C/T]AAAGAGATGTGAATTCTATCGCCTTCATTTAGCAA Y 2 1 2 1 101000 f 74 goat snp42351-scaffold559-520734 1 10632303 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780333 Affx-122958872 AX-385267428 1 11443598 GGTGCTTTCCAAGACCTGGAAGAAAGAGGAATATG[A/C]GGTGTTGTTGTTCAATACCTATAAAATTTCTGTAA M 2 1 2 1 101000 f 74 goat snp42352-scaffold559-561470 1 10673301 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442218 Affx-122928779 AX-123312555 1 11503151 TTCTACTTGGCTGGTCCATTGCCACGCAGGTATAA[C/T]ACAGTCAAAACTGAACTTGTTATTGTTGAATCAAC Y 2 1 2 1 101000 f 74 goat snp42354-scaffold559-621023 1 10733021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403249 Affx-122957881 AX-123273602 1 11543370 CAAGTTCCTCCTCCATGTTTCACCTCTTACTATTT[A/G]CAATGATCACCATATCGGTACTCCTCTCATAAAGC R 2 1 2 1 101000 r 74 goat snp42355-scaffold559-661242 1 10763058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430767 Affx-122937489 AX-123301108 1 11582672 ACTAGATTAACAGTGATCCAGGGAAGCCAGACTTG[C/T]GGTTTGCACTGGAATCTGGTAGCTGAGAATGAGAA Y 2 1 2 1 201000 r 74 goat snp42356-scaffold559-700544 1 10802319 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783501 Affx-122944746 AX-385270564 1 11621828 ATTAAAAAGATAATTTGTGCAAAGCACCTAGCACA[C/T]GGCATAGCAAATAATAAAGTTCAATAGATATAACT Y 2 1 2 1 101000 f 74 goat snp42357-scaffold559-739700 1 10841517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788183 Affx-122966352 AX-385275202 1 11676341 AACCAACTCCATAATGTAATATGCTCAGTGTATTT[A/G]TTTGTCTGACATAAAATTATGTACATGGATATGCC R 2 1 2 1 102000 r 74 goat snp42358-scaffold559-794213 1 10886462 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769061 Affx-122938869 AX-385256236 1 11724563 TAGCACTAGAATAAACGTTGAATCTGTTAGAAGAT[A/G]CTTACATAAGGTCTCAATGGAATCAGGCAGCTTCC R 2 1 2 1 101000 r 74 goat snp42359-scaffold559-842435 1 10935158 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768924 Affx-122938067 AX-385256100 1 11772216 TGTCATGGATAAGGCAAAACTGAAGTCTGCATAAA[G/T]AGTAAAGCTTTACCTTAAAGGGCACATTAAAGAAT K 2 1 2 1 101000 f 74 goat snp42360-scaffold559-890088 1 10982749 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390812 Affx-122967856 AX-123261169 1 11808128 GTACCACTTTTTCCTAGAAAGGACACATATTTGAT[C/T]GATTTAATCAGGACCACATCCTTGAAGGTCAGGCT Y 2 1 2 1 101000 f 74 goat snp42361-scaffold559-926000 1 11018785 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393233 Affx-122965481 AX-123263590 1 11850250 ATAAGTTTCACTGGGCCTAAGAGAAGCAATGCATG[C/T]ATTAGTAAGAATAAAGAAGAATCATTTATGTCTTA Y 2 1 2 1 101000 f 74 goat snp42362-scaffold559-968122 1 11061548 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783017 Affx-122977261 AX-385270085 1 11892475 AGAGAACTATGTGGCCTATTTTATCATTAATCGGT[A/G]GACTGATTAACTGCTCAATATTTATTGATAATTTT R 2 1 2 1 101000 f 74 goat snp42363-scaffold559-1010347 1 11103709 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802202 Affx-122937038 AX-385289106 1 12020360 TTTGATGGCTGGAAAGAAATTTAATTAAGCAATCA[C/T]AACCACAACTACACCAATGCCCAAAATATGATTTT Y 2 1 2 1 101000 f 74 goat snp15927-scaffold1670-150085 1 11230406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388600 Affx-122969150 AX-123258958 1 12070904 TCCTGTCATGTCTGTAAATTATTTTCCAACCCATG[C/T]ATGGACCATGACAAAAGATACAGATTCTAAAAGAA Y 2 1 2 1 201000 r 74 goat snp15926-scaffold1670-99541 1 11281018 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437490 Affx-122932360 AX-123307828 1 12116460 CTAAACTTACTGATGAACAGAACACAAAGGTTTCT[A/C]TGGTGGCTCAGTGGTAAAGAATCTGTCTGCAGTGC M 2 1 2 1 201000 f 74 goat snp15925-scaffold1670-53985 1 11325992 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795363 Affx-122943886 AX-385282319 1 12158309 TCAATGGAATGGAAGTAATGGATGTGAGAATAGAG[G/T]GTCTGTATTTTAAGATAAACTGATTATCAGTCTTA K 2 1 2 1 101000 f 74 goat snp15924-scaffold1670-12136 1 11367857 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399060 Affx-122960900 AX-123269415 1 12179283 TGCAAGTGGGAATCTCATAAGGCAATGAAGTAACC[G/T]CTACTAAGGCACTGTAAGATGAATAAAGCCCAGTA K 2 1 2 1 101000 f 74 goat snp16300-scaffold1716-229833 1 11631316 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434905 Affx-122934328 AX-123305245 1 12223615 GAGAGGATTGGTGAAGTTTATTGTATGATTATGTT[A/C]TTTGCTGTTCAACTTCAGCTTCTTCAGCATTACTG M 2 1 2 1 201000 f 74 goat snp16299-scaffold1716-185501 1 11676250 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412763 Affx-122950512 AX-123283112 1 12256522 TTTACTTGTTCACACTGGGTATCATTTTTCCTAAG[C/T]GACAGTTGGTATTTGGATATTACAATATCTGACCT Y 2 1 2 1 101000 f 74 goat snp16298-scaffold1716-152594 1 11709415 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775351 Affx-122936988 AX-385262482 1 12288852 AATTGAAGGAATTCGGAAAGGCAAGCAAGATTTCT[A/G]CCTCAATACAAATTCTTATCTAATAAGCGTTTATA R 2 1 2 1 101000 r 74 goat snp16297-scaffold1716-120264 1 11742753 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786193 Affx-122937316 AX-385273228 1 12320002 CAGTGAAATATTAGTCTATTTTGCTCCTGCATATT[G/T]ATAACTTTAATTTCACTTTAATACTATATTATTAA K 2 1 2 1 202000 r 74 goat snp16296-scaffold1716-89114 1 11774022 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793008 Affx-122973331 AX-385279986 1 12350681 TCAGGTTTATCATGGATATTCTATATAATGATATG[C/T]TGGCTGGTCATTTCATAAGACCTGGGTCATTGTTG Y 2 1 2 1 101000 r 74 goat snp16295-scaffold1716-58435 1 11804316 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770012 Affx-122941738 AX-385257179 1 12423536 CCTGCAGGCTAGGAGCAAAACAAAATTCTCTGTTG[C/T]ACAGCTGAATAATTAATTAAACATTGGTAAGTCTG Y 2 1 2 1 101000 f 74 goat snp2867-scaffold1084-438967 1 11996501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385923 Affx-122971567 AX-123256281 1 12458647 TTAGGAAACCATATTCTATTTTTGACATTTTAAAA[C/T]GAAATCAATTTGGCAATTCTGATATCAGTGTTAAG Y 2 1 2 1 103000 r 74 goat snp2866-scaffold1084-403856 1 12032537 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379234 Affx-122976270 AX-123249593 1 12492663 AATTTCTCACAAGGGAAGAATGAATTGTTACAGAC[A/C]TTTTCCTTCTCTTCTGCTAAACACTAAGGATCTCA M 2 1 2 1 101000 r 74 goat snp2865-scaffold1084-369840 1 12066863 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375704 Affx-122978646 AX-123246063 1 12527932 ATTATCAGCATCAGGCACTTCAGAAATATAATTGG[C/T]ACTCAAAAAATAATGTAAATAAGTGAATGAATGAA Y 2 1 2 1 101000 f 74 goat snp2864-scaffold1084-334571 1 12101917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428007 Affx-122939159 AX-123298350 1 12582082 ATTAATTTTCTTCTTATTTATGTTCTCATACAATT[A/C]GATTATTCAGCTTGAGAATTTCATATTGCAATCAG M 2 1 2 1 101000 r 74 goat snp2863-scaffold1084-280421 1 12165235 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794588 Affx-122950686 AX-385281550 1 12615744 TTTTATCAGAACATATTATTATTAATCTAGCAATT[A/C]TTTTAGGGAATAAATTATATTCTACTGGAGTAGGA M 2 1 2 1 202000 f 74 goat snp2862-scaffold1084-246759 1 12199316 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770643 Affx-122933602 AX-385257807 1 12648302 TGAAAGAGAAGGACTCAAAAATTTCTATTAACTTC[A/G]TCAAATCATAAAAATGACAGCACCAAAAAACTGAT R 2 1 2 1 201000 f 74 goat snp2861-scaffold1084-214201 1 12231940 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450532 Affx-122922488 AX-123320866 1 12727265 CACATTCACTTGGCTCATTTCAAAACTGTATTCTT[A/G]TTATAACAATCAGTGGCATTCCTGAGTAAAGTGAC R 2 1 2 1 201000 r 74 goat snp2859-scaffold1084-135238 1 12311515 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774243 Affx-122969079 AX-385261379 1 12771377 CAGTGATGTCCTTGAAGACACATTGTGACGGTTTT[A/G]CCTGTGGAGATCAGGATGCTTGACCATGACCATTC R 2 1 2 1 101000 r 74 goat snp2858-scaffold1084-91126 1 12354656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406312 Affx-122955463 AX-123276664 1 12810601 TTTCTCATTATTCTCTATGGTGCATATTCTTTCTT[A/G]CAGTGTTCTACTATACCCAACTTTGAATATAGGTT R 2 1 2 1 101000 r 74 goat snp2857-scaffold1084-51902 1 12394378 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793947 Affx-122955356 AX-385280916 1 12861853 TGCTCACACCCACACCTTCTTCCATAGAAGCGCCC[G/T]ACATCTAATTACTGTTTGACATGTGGTTATAAAGG K 2 1 2 1 102000 f 74 goat snp2856-scaffold1084-650 1 12446791 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788564 Affx-122939488 AX-385275581 1 12863672 AAGAAGTGGGAAGGCTATGGGCTCTGCATTCTTAT[A/C]TTCAAGATCTGATTCTTGCCATAGTACTAAGAATC M 2 1 2 1 101000 f 74 goat snp1254-scaffold10319-713 1 12464500 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426662 Affx-122939928 AX-123297008 1 12902821 GATTTTCTTAGTACAAATATTTTTATGGTTATTTT[A/G]CTCTATTTTAGCTATTGGTCTCTGATTTTAACAAA R 2 1 2 1 101000 r 74 goat snp31515-scaffold35-27797 1 12501694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271814 Affx-1111832836 AX-519545601 1 12912774 TCAGGGTCTTCCAATGAGTCAGCTCTTTGCATTAA[A/G]TGGCTAGAGTATTGGAGTTTCAGCTTCAACATCAT R 2 1 2 1 103000 f 74 goat 1_12912774_AF-PAKI 1 12912774 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320764492 Affx-986698949 AX-385252169 1 12919858 ATGGAGATGCTTTGAGATTTAAATGTTATAAAGTT[C/T]ATGTAAATAGATGCTAAATGTGTATATTTTAATTT Y 2 1 2 1 600010 f 74 goat 1_12919858 1 12919858 Ancestral_priority_1043 ancestry 0.702 recommended IMAGE 10K 10K ancestral 320799308 Affx-122944706 AX-385286238 1 12962407 TGTTTTCCCACTTGTTGATATAATTTAATAGTATA[G/T]CAGCAGACATCCATGGGAAAACAAATGAAAGAAGG K 2 1 2 1 101000 r 74 goat snp31516-scaffold35-87383 1 12561327 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417151 Affx-122947349 AX-123287499 1 12993640 TGTTCAAGCCCTAGATAACATGATTCTGTGCAAAA[C/T]AGGGAATCAGTTCAGTTCAGTCTCTCAGTTGTGTC Y 2 1 2 1 201000 f 74 goat snp31517-scaffold35-118616 1 12595927 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431227 Affx-122937146 AX-123301568 1 13028816 TGAAAAAGAATAATATTTTCTGTTACCACAGAAGG[C/T]AGAATTTTAGAAAAAGATTACTAAGCAATCCAAAG Y 2 1 2 1 103000 r 74 goat snp31518-scaffold35-153792 1 12631964 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448083 Affx-122924330 AX-123318419 1 13067345 AAGATAAAATTCTCATGAAAAAGAGGAACAATTTT[A/G]TTAACCACCTGCCAAAGCCATTAAAATGTAGACAC R 2 1 2 1 103000 r 74 goat snp31519-scaffold35-192321 1 12670183 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792015 Affx-122962376 AX-385279003 1 13093640 ATACTGTCACCTTTGTAAAAACAAGGGAATCATTA[A/C]ATTAGCAGTAATACTTTCTTGTTTTCTTGAACCTC M 2 1 2 1 201000 r 74 goat snp15439-scaffold1636-419017 1 12706212 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405553 Affx-122955964 AX-123275905 1 13125917 AAGCATCCACACAGTATCCTGTTTGATGTTTTGTT[G/T]TAGATAAAACATTGTCTGGCATGATTTTACCAAAC K 2 1 2 1 201000 r 74 goat snp15438-scaffold1636-386740 1 12738048 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277373 Affx-1111835816 AX-519550877 1 13142090 CATGTAAATTATAATATGAAAATGTGCACTATCCA[A/C]AAGGAAGAAACTTTATTACTGCCCTGCAACTATTA M 2 1 2 1 101000 r 74 goat Random2.2K-18 1 13142090 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320799095 Affx-122966915 AX-385286025 1 13159806 TGGTGTGTTTTCACCTGTCACACATTCGTATTCCA[C/T]GATCTATTGTTACAGGTACTCTTTATGAGAAAATA Y 2 1 2 1 101000 f 74 goat snp15437-scaffold1636-352851 1 12772721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405970 Affx-122955534 AX-123276322 1 13214828 TTACTCTTTTCTATTGAGAGGAGGACATGAGAGAA[C/T]GGGGCTTAATGTTTCATCCATTTGCATTCTAGTCA Y 2 1 2 1 101000 f 74 goat snp15436-scaffold1636-297829 1 12830355 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778558 Affx-122965520 AX-385265670 1 13245172 CATGTTTGTTATCCATGTCATTTTTGTGGCAACTT[A/G]TATCTTCAACTCTTTATCCCACTTTTTAAACTGAG R 2 1 2 1 101000 f 74 goat snp15435-scaffold1636-267485 1 12860739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778121 Affx-122977053 AX-385265235 1 13282213 GTATGTGGTGCGATTAGACAGAACTGATCTCATAT[A/G]TACTGACATTACACATGCAACATTTTGTTTGGTCG R 2 1 2 1 101000 r 74 goat snp15434-scaffold1636-230444 1 12898699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395763 Affx-122963678 AX-123266118 1 13311234 ACAAGCTATTTGAGGATAACTTCTTTACACAGAAA[C/T]GAAGAGTGAAGAACATATGTTACCTTAACATTTAT Y 2 1 2 1 101000 f 74 goat snp15433-scaffold1636-201423 1 12928354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417496 Affx-122947160 AX-123287844 1 13351528 TTCTTGTCTATAAAATGGAAATAAATTAAGACAGA[A/G]CATAAGATTGTCTAGGATTTATTTCCAGTTGGACT R 2 1 2 1 103000 r 74 goat snp15432-scaffold1636-161129 1 12969108 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796998 Affx-122931555 AX-385283939 1 13390072 TGTCAGTGAATAAATGATTATATGTAAAAAAGGCA[C/T]GTAGGGCTAATGTTTACCTCGAGTCTGCTCTTCAT Y 2 1 2 1 101000 r 74 goat snp15431-scaffold1636-122585 1 13008167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779671 Affx-122936358 AX-385266772 1 13427553 GTTTAAGAATGCTTTCTTTAAGAAAATGTGTTATC[A/G]CTTTTCTAGGAATCAAAAACATATGTCTTAGAATG R 2 1 2 1 101000 f 74 goat snp15430-scaffold1636-85104 1 13045365 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418133 Affx-122947114 AX-123288481 1 13459847 TTGAGAGTTTAAATATCAAATATAATAAAATGAAA[C/T]GCTAGAAGCCTTTTGCAGGTAGATATCATTATCTT Y 2 1 2 1 103000 r 74 goat snp15429-scaffold1636-52810 1 13077639 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453263 Affx-122920399 AX-123323596 1 13493406 AAAAGGGCTATTAAGACAAATACTTGGATTTTTGG[C/T]TTGAGGTAATGGGTTTGATGCAGGTATCAATTGCT Y 2 1 2 1 201000 r 74 goat snp15428-scaffold1636-19251 1 13110947 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800947 Affx-122959396 AX-385287862 1 13524719 CTTTATCCTGATAAAAATTCTAGACCTTAAAGTTA[C/T]TATGCTTAGATTCCTTACAAAAAGAAAAGAAACAT Y 2 1 2 1 101000 r 74 goat snp23407-scaffold235-11963 1 13147714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786271 Affx-122978627 AX-385273306 1 13553311 GACTGGTTTGGAGGATGGATTAAGACCTGAGTTTA[A/G]CAGTGCTAAATTTCAGGTGGTGTGAGATGCCCTTA R 2 1 2 1 101000 r 74 goat snp23408-scaffold235-40555 1 13177292 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430273 Affx-122937295 AX-123300614 1 13622642 TTGTGCAAAATGCAGCAATTTTTAACTAGAAAAAA[A/C]TGAATAAAAGTCACAAATATATTAGCTGGACCCAT M 2 1 2 1 201000 f 74 goat snp23410-scaffold235-109886 1 13248265 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778157 Affx-122936603 AX-385265271 1 13655885 AGAGAGTAGGACCATTCAGGAAAATTAAGCTAGTT[A/C]TATTTAAGCATGGAGACTTAAAGAGTATATAGTGG M 2 1 2 1 101000 f 74 goat snp23411-scaffold235-143129 1 13282538 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428658 Affx-122938654 AX-123299000 1 13687769 TCTCTTCTTTAAACACCAAGTTAATTATGACTTGT[C/T]GGGGCCTCTGATGGTATCTGATGACCTTTGAGACA Y 2 1 2 1 201000 f 74 goat snp23412-scaffold235-175013 1 13314796 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407352 Affx-122955280 AX-123277703 1 13719969 AGCTTATAAAGCCATTTAAAAGGCAATTACATTTG[C/T]GTCAAGACAAAAAAAGTCCCACGAATGTCACCTGT Y 2 1 2 1 201000 f 74 goat snp23413-scaffold235-207213 1 13347253 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786059 Affx-122934327 AX-385273095 1 13752505 TTCTTATCACTGTCAAACTGTGGGTTTAGTAATCT[A/G]TTCATGCAAGTTGAATTTGATCTTGAGCAAAAGTC R 2 1 2 1 101000 f 74 goat snp23414-scaffold235-239749 1 13380150 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777774 Affx-122924020 AX-385264892 1 13795356 GTAAGCATGAATGATTGTAAACCATTAACAAACAC[A/G]TGGAGTTTTCTCTACCAGGTAAATATGTCAAAATG R 2 1 2 1 101000 r 74 goat snp23415-scaffold235-282600 1 13423424 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378662 Affx-122977089 AX-123249021 1 13833009 GGGGCAGTGACACATGGACTGTTTTCTTCTTATGA[C/T]AGAGGGGAGAGGCTCAAGAGACAATGGCAAACCAT Y 2 1 2 1 101000 f 74 goat snp23416-scaffold235-320253 1 13461890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778543 Affx-122942885 AX-385265655 1 13861982 ATTCTCTGTTAACTGTTGCATTAACTCTTCTGTCT[A/G]CGTTCAAAATGTTTCCAATTATAATATACCCCTGA R 2 1 2 1 101000 f 74 goat snp23417-scaffold235-349226 1 13491289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793152 Affx-122956230 AX-385280130 1 13892976 CATGTAAAGACGAAATGCACTCGTATAGTTATGTC[A/G]TCTTTCTGTCTTTCTACCTATTTATCTAAAAGTTA R 2 1 2 1 201000 r 74 goat snp23418-scaffold235-380220 1 13523428 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273563 Affx-1111833673 AX-519547176 1 13946393 AGAGACTGAAAGTCCAAAGAAAAATAAAAGGAAGA[A/G]AAGAGCTCCCTGATGACAGTGTTCTGCAGAAAAGT R 2 1 2 1 202000 r 74 goat GoatD01.001135 1 13946393 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38441909 Affx-122928606 AX-123312246 1 13951768 TTAGGCAGAAGGGGAAGCTGAACTGAGATGTAGGT[A/G]CCACAGTAACCACCAGAAATTTTATAAGATATTTG R 2 1 2 1 201000 r 74 goat snp23419-scaffold235-439012 1 13583197 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476142 Affx-1251763644 AX-586011575 1 13975754 CTGATGAAGCTGAAAGGAAAGTAAAAAAGCTGGCT[-/TAAAACTCATGAAAATGGAGAGATCACAACAGACAACACAGCATGTAAGAATTAAAGATTTTAAAATTTAAAAAAAAAAA]AAAACTCAACATTCTAAAAAAACTAAGATCATCAC - 8 1 4 1 20000 f 74 goat SV_169 1 13975754 - deletion junction SV-TF-chip 560378493 Affx-1251763644 AX-605230908 1 13975754 CTGATGAAGCTGAAAGGAAAGTAAAAAAGCTGGCT[-/TAAAACTCATGAAAATGGAGAGATCACAACAGACAACACAGCATGTAAGAATTAAAGATTTTAAAATTTAAAAAAAAAAA]AAAACTCAACATTCTAAAAAAACTAAGATCATCAC - 8 1 4 1 20000 r 74 goat SV_169 1 13975754 - deletion junction SV-TF-chip 562165159 Affx-1251763644 AX-606940571 1 13975754 CTGATGAAGCTGAAAGGAAAGTAAAAAAGCTGGCT[-/TAAAACTCATGAAAATGGAGAGATCACAACAGACAACACAGCATGTAAGAATTAAAGATTTTAAAATTTAAAAAAAAAAA]AAAACTCAACATTCTAAAAAAACTAAGATCATCAC - 8 1 4 1 20100 r 74 goat SV_169 1 13975754 - deletion junction SV-TF-chip 562165220 Affx-1251763644 AX-606940632 1 13975754 CTGATGAAGCTGAAAGGAAAGTAAAAAAGCTGGCT[-/TAAAACTCATGAAAATGGAGAGATCACAACAGACAACACAGCATGTAAGAATTAAAGATTTTAAAATTTAAAAAAAAAAA]AAAACTCAACATTCTAAAAAAACTAAGATCATCAC - 8 1 4 1 20100 f 74 goat SV_169 1 13975754 - deletion junction SV-TF-chip 562166389 Affx-1251763644 AX-606941797 1 13975754 CTGATGAAGCTGAAAGGAAAGTAAAAAAGCTGGCT[-/TAAAACTCATGAAAATGGAGAGATCACAACAGACAACACAGCATGTAAGAATTAAAGATTTTAAAATTTAAAAAAAAAAA]AAAACTCAACATTCTAAAAAAACTAAGATCATCAC - 8 1 4 1 20100 r 74 goat SV_169 1 13975754 - deletion junction SV-TF-chip 38406347 Affx-122955437 AX-123276699 1 13994031 AAGACTGTTATTTCAGGGCTAAAAGTTGGGTATAC[A/G]TCAACTTAATGTTTCATTCCACATCTTCAAATGAG R 2 1 2 1 101000 r 74 goat snp23420-scaffold235-481275 1 13624612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394272 Affx-122964717 AX-123264627 1 14020087 GGATCAAACCCAGGTCTCCCACACTGCAGGCAGAT[A/G]CTTTACTAGCTGAGCCACAGAGGTCTATAACACTT R 2 1 2 1 103000 r 74 goat snp16371-scaffold1727-15166 1 13751034 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403289 Affx-122957850 AX-123273642 1 14077671 CTATGTTCCATTGTCAATTTATTCATCATTTAAAT[A/G]CAGTATCTGGACAGTTGCTGGAGGCATATGCAATA R 2 1 2 1 303000 f 74 goat snp16372-scaffold1727-72750 1 13807104 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451200 Affx-122921325 AX-123321534 1 14141421 TTTCCTGATATGTACTAAAAGAGATTAAAACTAAC[A/G]TAAGTCTTTAGGCTTAACATACATTGATTGAAGTT R 2 1 2 1 101000 f 74 goat snp16373-scaffold1727-136500 1 13871108 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389377 Affx-122968398 AX-123259735 1 14169936 TCCCCTAGGCATCAAAATCTCATTTATGCATTTGT[A/G]GAGTGCCTGATTTACAGAATTTAAACGCCTAGGGA R 2 1 2 1 101000 f 74 goat snp16374-scaffold1727-165015 1 13899660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770450 Affx-122975358 AX-385257616 1 14203008 TAGAGAGATGGTTTTTGCAGTCAGCTTCTCTTATG[A/C]CTTTCACCACTGAAATATAGCCATTTAGAAATGAT M 2 1 2 1 201000 r 74 goat snp16375-scaffold1727-198087 1 13933570 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776905 Affx-122939812 AX-385264029 1 14231667 TTCTCAAAAACTACACACCAAATTTACTGGATATT[A/G]TCAGTAAATTTAACCCAATGGTTCAGTTAAAATGA R 2 1 2 1 201000 r 74 goat snp16376-scaffold1727-226746 1 13963234 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421568 Affx-122943849 AX-123291915 1 14272734 ACTCCTTAGCCTGATATTGATGGACTTCCATATGG[C/T]ATTATCTTTCTGTTTAAGGACACCTTACAATTTGG Y 2 1 2 1 101000 r 74 goat snp16377-scaffold1727-267813 1 14010404 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419568 Affx-122945403 AX-123289916 1 14352381 ATTTAGCTAAAGCACAGGTTACCCAGACTGAATGA[C/T]TAGGGAAGGTAGCTAATGATCAGCTTCCTATAGGA Y 2 1 2 1 101000 r 74 goat snp16378-scaffold1727-347460 1 14089551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773611 Affx-122941871 AX-385260751 1 14384893 TAATAGTTCAGTGCTGATTCCAAATTTCCCAAACC[A/G]GCAATCTTACTTGTGTCAAATCCTATAGCATTTGC R 2 1 2 1 101000 f 74 goat snp16379-scaffold1727-379972 1 14122278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421235 Affx-122944120 AX-123291582 1 14421890 GATTATGAGCAACACTGTTGCATACCATTTTCTCC[C/T]TCAAACGCATTTTCTGCCTCTTAAAATATTTCTGC Y 2 1 2 1 101000 f 74 goat snp16380-scaffold1727-416969 1 14160137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439962 Affx-122929817 AX-123310299 1 14463980 GATTAAATTTCAGTCAATGTTTTGATTGAATTACT[A/G]TTCCCACCAGTTGACCCTTGCTGAACACTTTTGGA R 2 1 2 1 201000 f 74 goat snp16381-scaffold1727-459059 1 14202454 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802492 Affx-122925854 AX-385289396 1 14503982 CTCATTTATACAATAAAGGAGTTACACTAGATAAA[C/T]GCTAATATTTTATTGGGTCCAACACTGTATAATCT Y 2 1 2 1 101000 r 74 goat snp16382-scaffold1727-499061 1 14242917 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792970 Affx-122945814 AX-385279948 1 14544545 GGATAAACTCTCAAATTACACCTATAAAGAAGTCC[A/G]TGGCGAATAAACATGGCAGTGTAGTAAATGCACAC R 2 1 2 1 101000 r 74 goat snp16383-scaffold1727-539624 1 14283599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376968 Affx-122977756 AX-123247327 1 14589393 CAAGATTGCTTAACTGTAAAGCACAAGATATGCCC[G/T]AGGTCATTATGTGAAAGAAAAATGCTACCACTCTT K 2 1 2 1 101000 f 74 goat snp16384-scaffold1727-584472 1 14329021 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781886 Affx-122967570 AX-385268967 1 14633153 ACTCTCTACTCAACACACTGCCTCCTTTTACATGA[C/T]AAACTATCTCTGATAATAGAAAGAAATCAGCCTCA Y 2 1 2 1 101000 f 74 goat snp16385-scaffold1727-628232 1 14370655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413538 Affx-122950612 AX-123283887 1 14697913 AAGAATCCATTTAGTACCCAACCATTCAGCCAGAA[C/T]GCTTCAACAACCAATAACGTGATGTGAATTCTGAA Y 2 1 2 1 101000 r 74 goat snp16386-scaffold1727-692992 1 14435997 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437449 Affx-122932393 AX-123307787 1 14732095 TTCTTGCAACATTTTGGGTAATTTTCTGAAGTGTT[A/C]GTGAGCCAAATTACTGATCTTCATGAAGATGAGTA M 2 1 2 1 101000 r 74 goat snp16387-scaffold1727-727174 1 14470321 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401317 Affx-122959843 AX-123271670 1 14779903 AAGATAAAGTTTAAATTATTTCTTCATCTTCATAT[A/C]GAAGTCAACTGCCAATGAAGTTTCATCCTATTTAA M 2 1 2 1 101000 r 74 goat snp16388-scaffold1727-774982 1 14517944 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790403 Affx-122941182 AX-385277406 1 14814983 TCACAAGTTACAGATTGGTAAAAGGAAAATGCTAC[A/G]GAAAATAACAATTTTTGATGAAGCAATCAAAATCG R 2 1 2 1 101000 f 74 goat snp16389-scaffold1727-810062 1 14553692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795177 Affx-122963974 AX-385282135 1 14869528 TGGAATGTGAATTTCACTACAACTCTGATTAAAGC[C/T]TTCTCTTTTAAGTCCTTAATAGTTGTTTGTCTCAT Y 2 1 2 1 101000 f 74 goat snp22899-scaffold2280-49319 1 14608347 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409299 Affx-122953102 AX-123279650 1 14883481 CAGGGATACAAAAATAGCCTCTCTGTAGTAAAAGC[C/T]TCACAAAAAGTCTGGCATGGTTGCTCCATATTATT Y 2 1 2 1 101000 f 74 goat snp18406-scaffold1864-4910 1 14630040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777847 Affx-122926417 AX-385264964 1 14920942 CTTTCCAGATTTTGAGTAGTGAGAATAGAGTTCTC[A/G]AAAAACAGACATTGTTCAGAGGGTGAGAAATAGAA R 2 1 2 1 102000 f 74 goat snp18407-scaffold1864-42371 1 14668052 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802027 Affx-122930862 AX-385288931 1 14960526 TTCTTGTCTTCAAGCAATCATGAGTTTCAAGAATC[A/G]TGAACATGCCTTCTCTTGTCACAACTAAAATATGA R 2 1 2 1 101000 r 74 goat snp18408-scaffold1864-81955 1 14707743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426792 Affx-122940542 AX-123297138 1 15040338 GACTGAATGATGATTACTAAGATGCTTAAAGACCA[C/T]GCAACTTTATTTAAGGCAGGACTCACAAATATCTC Y 2 1 2 1 101000 f 74 goat snp18410-scaffold1864-161767 1 14788828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443674 Affx-122927182 AX-123314011 1 15093499 GTGTGGGACTCTTACGACCCCACACAGAGTAGCCT[A/G]CAGGGCTCCTCTGACCATAGGAATTGTCAGGCAAA R 2 1 2 1 303000 r 74 goat snp18411-scaffold1864-214928 1 14841795 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397641 Affx-122962616 AX-123267996 1 15125512 GTTCATTTGAATTTGGGGTTAATATTACCAGTAAC[A/G]GAATACAAGGTGAATATTAAATATGATATTATATT R 2 1 2 1 101000 f 74 goat snp18412-scaffold1864-246941 1 14874511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794023 Affx-122946782 AX-385280992 1 15180968 TCAAATAGTCAATTTATCATTTCATGGAAGTACTC[A/G]TTGCCATTGTTTCCACATTTCTAATCTAAAACATC R 2 1 2 1 303000 r 74 goat snp18413-scaffold1864-302397 1 14929867 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384190 Affx-122972406 AX-123254548 1 15248695 CAGAGTCCTGGAATCAGTCATTTCTCTAAGGAGCC[A/G]TGGTTCCCTCTATTGGAGAGTTATATTACAAACTA R 2 1 2 1 201000 r 74 goat snp18415-scaffold1864-370124 1 14998569 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410729 Affx-122952711 AX-123281079 1 15315349 CAAATCTTTTGTCCCACCTGATTACTGCAACCATG[A/G]GTTTACCCCATTTTTCCTGCCCAAATCATTAGGGA R 2 1 2 1 101000 r 74 goat snp18417-scaffold1864-436778 1 15067323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389367 Affx-122968456 AX-123259725 1 15380937 TAAACAAGTTTTTCTTTGTTGCATTTCAAAACACC[A/G]CTAAAATGACAAGAGTCATATAGGTCCCCAAGAAC R 2 1 2 1 101000 r 74 goat snp18418-scaffold1864-502366 1 15133883 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775400 Affx-122923272 AX-385262531 1 15417113 TCCATGGGGTCTTGAGTTGGACACAAACGTGCAAA[G/T]AATTAGTGATTAGTTAGTCATAATATTTGGTACAA K 2 1 2 1 101000 f 74 goat snp18419-scaffold1864-538542 1 15169302 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786197 Affx-122951076 AX-385273232 1 15458548 ATATGGATGCTATTCCAAATGCAGTGTTCTGAAAT[A/G]CAGGTAACACTGAAGAATGGGTATTTTCCATTTGG R 2 1 2 1 102000 r 74 goat snp18420-scaffold1864-579977 1 15211781 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419955 Affx-122945207 AX-123290303 1 15490697 CTAACACATAGCTTATATGTTATATATTTTTAGCT[A/G]CATAGTCTTAGATCCTTTTTTTATTTCATACAGAC R 2 1 2 1 101000 r 74 goat snp18421-scaffold1864-612126 1 15243638 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451209 Affx-122921972 AX-123321543 1 15528492 AGAGTATAAGATCTCATTTGCAGATAAATAGCTCA[C/T]AGGATTTTGAAGCATAGATTTGTGGTATCTTTGCT Y 2 1 2 1 101000 r 74 goat snp18422-scaffold1864-649921 1 15281751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409565 Affx-122953589 AX-123279916 1 15580030 TTCATACCATAAACATTTTAGCATCTTCTTCATAA[C/T]GACAGGCAGATAGCATTATATATACCTGTAACACG Y 2 1 2 1 201000 f 74 goat snp18423-scaffold1864-701459 1 15333412 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272600 Affx-1111832847 AX-519546313 1 15607879 AAACGCATGAGCCAGACAGCACTAGCCAAGAAAGC[A/C]TTCAGTTTCCTGACCCCACATAACATGACCCTAAA M 2 1 2 1 101000 r 74 goat 1_15607879_AF-PAKI 1 15607879 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320798617 Affx-122941262 AX-385285550 1 15625874 GAATCATTTCATGTAGTTTCCCTCATAGAACTATG[C/T]AGACATTTTCTAAATGTATCAGTCTAATTTTTTCT Y 2 1 2 1 101000 f 74 goat snp18424-scaffold1864-747303 1 15377225 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451838 Affx-122921462 AX-123322171 1 15675078 TGTCTGTGTATGCTTAGATACAATGACTATTCTCA[C/T]GTTTATGGTCATCCTTGTCATTCATGAAAATAGGG Y 2 1 2 1 101000 r 74 goat snp18425-scaffold1864-796507 1 15423607 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385137 Affx-122971766 AX-123255495 1 15713247 CACACTAGAACTACTTAACAGAATTAAGTTTCAAA[C/T]AGGTCTGAGGAAAAACAACAACAAAACAAACAAAC Y 2 1 2 1 201000 f 74 goat snp18426-scaffold1864-834676 1 15461775 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388076 Affx-122969516 AX-123258434 1 15750262 GATTTATTATTACTTTCCCAATCACCATTGCTTTG[C/T]ACTTCTACAAATACTAACAGACTCTTTGTTACTTT Y 2 1 2 1 101000 f 74 goat snp19490-scaffold197-29113 1 15499271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388467 Affx-122969244 AX-123258825 1 15809457 TAGATACTTAAAACAATGTCACTCTACTCAGTGGG[C/T]ATTTCTACACAAATACATAATAGGTTCGTTTTAAA Y 2 1 2 1 201000 r 74 goat snp19491-scaffold197-88308 1 15558791 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412411 Affx-122951437 AX-123282760 1 15865002 AGGTGAAGCAGTTTCTGCAGACCACAGGCTGCAGC[A/G]AAATTGTTCAAAAACGTCTGCTAAATGTTGCACAG R 2 1 2 1 101000 r 74 goat snp19492-scaffold197-143853 1 15607985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789768 Affx-122976768 AX-385276776 1 15898241 TAAAACTCCTTAATGAAGAGATGGTTTATAAAAGT[A/G]TATGCCGGAATGATGAAGAGCCACTAATAAAAATA R 2 1 2 1 101000 r 74 goat snp19493-scaffold197-177092 1 15641529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386367 Affx-122970852 AX-123256725 1 15930305 CATAAACATCAAGCTCAGATTTTTCATTTTAAGTT[A/G]CAGGACACTATGAATTTCCTTTCACTGGTTGACAA R 2 1 2 1 201000 f 74 goat snp19494-scaffold197-209156 1 15673363 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801207 Affx-122951951 AX-385288120 1 15961397 TTCTTACATATTAGAGGGAGCAAAACAGACCCTAC[A/G]TTAAATCACACTATTAGGACCCTATTATTTGGTGA R 2 1 2 1 101000 f 74 goat snp19495-scaffold197-240248 1 15704998 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423204 Affx-122942714 AX-123293550 1 15992368 CTTGAATTTTTTCTGAAATTTGTCAAATCCAAGTA[C/T]ATCACCAGGTGTTTTGGAACATCTGTCAGCTGCAA Y 2 1 2 1 101000 r 74 goat snp19496-scaffold197-271219 1 15735873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408205 Affx-122953854 AX-123278556 1 16050629 TGGTTCACAGGAAGACAAAATATGCAATTTTAAAA[C/T]GGTTGTGATTTTGAGGGGCTCTCTATTTGTTCTAG Y 2 1 2 1 303000 f 74 goat snp19497-scaffold197-329480 1 15795171 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418510 Affx-122946428 AX-123288858 1 16095004 TACAAATCCTGTTCAGATTCACTAGTTTTTCCATG[C/T]GCATTTTTTGGGTGTTAGTGTTATGTAATTTTATC Y 2 1 2 1 103000 f 74 goat snp19498-scaffold197-373855 1 15839481 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386024 Affx-122971491 AX-123256382 1 16141683 AAGATCCTAGAGGCTACCTTAAGCTCCTTAGCATG[C/T]AGTCCTTCTCCATCTTCTTTACTAGCAATGAAGTT Y 2 1 2 1 101000 f 74 goat snp19499-scaffold197-420534 1 15884859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453840 Affx-122919543 AX-123324173 1 16194476 TTTACTTCTTTCTTCTTTCCATATGGCAAAGTTTC[A/G]TGCTTAGTCAATGAGGTGTGTGAAAGTATGATGAA R 2 1 2 1 101000 f 74 goat snp19500-scaffold197-473327 1 15938301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797487 Affx-122959478 AX-385284426 1 16247710 AGTAGTTTTGAAAGGCAAGGACTTTTCAAATTATT[A/G]CTCTCTGTTGCTTTCTCAATTGGCTAGCGCCCAAA R 2 1 2 1 101000 r 74 goat snp19501-scaffold197-526561 1 15996266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768684 Affx-122921870 AX-385255862 1 16336958 ATTGATAAACTGCTTTAGGTTGAGAATAAAACTTC[A/G]TGATTATTGGGCCAGATTTTACAAATGCTTGTTAT R 2 1 2 1 101000 r 74 goat snp19503-scaffold197-615809 1 16086430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773072 Affx-122945495 AX-385260215 1 16385627 AGATAAAGGACAAGAAAGAGATGGCAGATTAACTG[C/T]TCAATCCTCCTTTACTGTCTTTCACAATCATTGAA Y 2 1 2 1 101000 f 74 goat snp19504-scaffold197-664478 1 16135116 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770863 Affx-122976015 AX-385258027 1 16417387 TCTACTGGTAAAATTTTAGATTCTTTAGAGAAGGT[A/G]CCCTAGATGCTATCTAAAATAATGTAGAATAAATA R 2 1 2 1 101000 f 74 goat snp19505-scaffold197-696238 1 16167120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439099 Affx-122931116 AX-123309436 1 16492927 CAAGAATTCAAATCCAAGACTCTCTCTCCAAGGCC[A/G]TTGTTTTACCAGGGTACCATAGAATTTGTAAGAAA R 2 1 2 1 201000 r 74 goat snp19507-scaffold197-771778 1 16243259 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397952 Affx-122961913 AX-123268307 1 16532941 CACACAATTAAGGAATTTAGCTCTTCAGAACTTCC[A/G]CATGGTAGTTTATGTAACCATTGATGTTCAACAAT R 2 1 2 1 201000 r 74 goat snp19508-scaffold197-811792 1 16283586 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413887 Affx-122949843 AX-123284236 1 16597410 CTTTACAAATTGTGTTCTTTCTTTCTTTGGAATAT[A/G]ACATTTAAGAGATGTTCTTTTGGCATCATTTGCTG R 2 1 2 1 103000 r 74 goat snp19509-scaffold197-876261 1 16347912 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432973 Affx-122935272 AX-123303314 1 16640472 CAAGAGAGATTTAGCCGGGATGAGTCTCCCAGCAC[G/T]CTCCCCAATGGAAAACACATAGAACTTCACAGTTA K 2 1 2 1 201000 r 74 goat snp19510-scaffold197-919323 1 16390838 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385300 Affx-122971684 AX-123255658 1 16713835 AATTATAGAAGCAAAAAATAAAACCCTGAAAAAAT[A/G]TGGCTCATTAATAGCAATTCTTGCTGACAAAATAG R 2 1 2 1 103000 r 74 goat snp19512-scaffold197-992686 1 16462542 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777485 Affx-122954100 AX-385264605 1 16805343 TGACTTCCCCAGTATCATACAGCTGACCTGAGCTA[C/T]AGCTGAACTGTAAGTTTCAGATCAAATCTCTTCTC Y 2 1 2 1 102000 f 74 goat snp19514-scaffold197-1084194 1 16555901 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415318 Affx-122948806 AX-123285667 1 16859866 AATCCACCCAAAAAAAACACATTATTTCAAAAATT[A/G]CATCAGGTTGGAAGTAGGTTCCTTCCCCATCAGAG R 2 1 2 1 101000 r 74 goat snp19515-scaffold197-1138717 1 16607936 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788330 Affx-122962306 AX-385275348 1 16916269 TTCTGTGGCAATTTCCAATTTGAGACAATCTAAAG[C/T]ATGTTAGGAATACAAGTCTGGAGGTATATTTCTTA Y 2 1 2 1 101000 f 74 goat snp19516-scaffold197-1195120 1 16665610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772068 Affx-122974700 AX-385259223 1 16949442 GTTTCTGTACCCTCTTGTCTCTTGTGAGTTGTCCA[G/T]AATTATATACAGGTTAAATATTACTTTATATTTAG K 2 1 2 1 202000 r 74 goat snp19517-scaffold197-1228293 1 16700132 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422974 Affx-122943004 AX-123293320 1 17045845 GATGTCAGGACATTAATCTCTCAGGGGCAAAAAGA[G/T]TCATCAACATACTGTTTGTCTCCTTAGGTCACAGA K 2 1 2 1 101000 f 74 goat snp19519-scaffold197-1324696 1 16797730 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430986 Affx-122936693 AX-123301327 1 17079512 GTGAGCCTGGGGAGATAGATCAGCCCTTTCTCTCT[A/G]CATATTCCTACCAACAAGCATGGACTTTCTTCCTA R 2 1 2 1 101000 r 74 goat snp19520-scaffold197-1358363 1 16830539 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769234 Affx-122969762 AX-385256407 1 17112156 GAATTTTAGTCTTTCCATGTATTCTTAATTATTCA[C/T]GGTAATCTGACTAAGGATTCATAAGCCACTTGCTA Y 2 1 2 1 101000 r 74 goat snp19521-scaffold197-1391007 1 16863396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422698 Affx-122943655 AX-123293044 1 17180168 AAATCCACTTGGCCATCTCCCAGTCTGTCTCATAC[A/G]CAGAATATTTTTGGTTCTTTCCCCTCCCATTTGTT R 2 1 2 1 201000 r 74 goat snp19522-scaffold197-1459019 1 16931963 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770833 Affx-122938466 AX-385257997 1 17290035 ATTAAACTTCAGGTAAAACTGTCCCTTAACTAAAG[C/T]GCAAGCAGGGTTAAGTGAAATCAAAGTAAAAGCTG Y 2 1 2 1 101000 r 74 goat snp19524-scaffold197-1568886 1 17037791 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794956 Affx-122963618 AX-385281916 1 17343621 CTTAGAAATAATTGATGAAGCAGATAAAAAATATG[C/T]AAAACTCTCAATGAAAACTTAAAGATTCCAGAAAG Y 2 1 2 1 101000 r 74 goat snp19525-scaffold197-1622472 1 17091020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777541 Affx-122932081 AX-385264660 1 17373796 AAGCACCACACAAGTGTAAAGCAATATTTATAGTT[A/G]TTACTTAACCACTTTTATACCTTTTAGCTTACCAC R 2 1 2 1 101000 f 74 goat snp19526-scaffold197-1652647 1 17121500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387263 Affx-122970553 AX-123257621 1 17404086 AGCTTGGCTACAGAAAGTGCTCACAGGTGAATATA[C/T]ACACTTCAGTCTCCAGAATCCTGCCAGCATTTTAT Y 2 1 2 1 201000 f 74 goat snp19527-scaffold197-1682937 1 17151965 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377056 Affx-122978295 AX-123247415 1 17462381 AATTCATTGTGCTTTAAAAGCTCCAAGTACAAATA[C/T]AATAATGAGTATACATAAAACAGATGAACTCATGG Y 2 1 2 1 101000 f 74 goat snp19528-scaffold197-1741232 1 17210716 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397671 Affx-122962592 AX-123268026 1 17546289 ATTTCAGCAAAGATTAGAGTAAAAAGTATTGGCCC[A/G]TGATAAATGGGTAACAGTGGTACTGAATGCATTGC R 2 1 2 1 101000 f 74 goat snp29443-scaffold3180-212691 1 17334849 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797283 Affx-122970022 AX-385284222 1 17580079 TTGAGATTCTCCTATGACAGTATCATATTTTAAAA[C/T]ATTTGTCTTCAAAGGGAAATTGCTAATTATCCTGC Y 2 1 2 1 202000 f 74 goat snp29442-scaffold3180-178901 1 17370077 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779419 Affx-122929951 AX-385266522 1 17625673 ATTGGGAAAAATCAAGTTAGAATTCTTATCGTTTA[G/T]AAAAGCACACTTTGAGGAATTAAAAAAGACTTTAA K 2 1 2 1 201000 r 74 goat snp29441-scaffold3180-133307 1 17415537 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799183 Affx-122956427 AX-385286113 1 17754620 CATATCCTTTCTTTGATTGGTACTTGAGGATGTGC[G/T]TAAGTAAAGTGAGGGAGTAAATTAAGAAATAATGC K 2 1 2 1 101000 f 74 goat snp29439-scaffold3180-4360 1 17545808 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403912 Affx-122957480 AX-123274264 1 17759900 TACCAATTGAGGAACAGCTTTTATGAGTAGACTTC[A/G]TGGAAAAGATTGATGCTTGTACCCATTAATAATAT R 2 1 2 1 101000 f 74 goat snp2705-scaffold1077-1700112 1 17569339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764610 Affx-122931537 AX-385252252 1 17808446 GGTTGGGATTTATGCTTCCCTAATGTCAGGGGCAT[A/G]CTAAATAATTATCCTTTGTGCAAACACATTGAAAA R 2 1 2 1 101000 f 74 goat snp2704-scaffold1077-1651566 1 17617912 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397101 Affx-122962701 AX-123267456 1 17843940 GCTTCTTAATAATAGGACTGGAATGAAAACTTCCT[A/G]GTACTGAATCTCCATCTCACTGCTTTTGGTGTGTG R 2 1 2 1 101000 r 74 goat snp2703-scaffold1077-1616072 1 17653273 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779271 Affx-122968770 AX-385266375 1 17908915 CCTCTCATTATTTCCTCAATCAAGATGTAGAATAA[C/T]TTTGCCAACTTTTTACTTACTATGACATTTCTCAT Y 2 1 2 1 202000 f 74 goat snp2702-scaffold1077-1551097 1 17719089 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420469 Affx-122944877 AX-123290816 1 17945287 TTTAATTTATGGAATATCCTCAGCTTCCCAGGTGG[C/T]GCCTGATTCTTGGCATCACTGATGGTTCTTGCTGG Y 2 1 2 1 201000 r 74 goat snp2701-scaffold1077-1514725 1 17755756 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476145 Affx-1251763647 AX-586011578 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 4 1 4 1 20000 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 539476400 Affx-1251763647 AX-586011804 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20000 r 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165135 Affx-1251763647 AX-606940547 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165389 Affx-1251763647 AX-606940800 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165414 Affx-1251763647 AX-606940825 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 r 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165459 Affx-1251763647 AX-606940870 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165550 Affx-1251763647 AX-606940961 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 562165997 Affx-1251763647 AX-606941407 1 17983033 AAAGTGAATTGGAAGTCAGAAAGATCAAATTAGTA[-/AGAATATAACCAATTTTCTTTTTTTTTTTTTTTGTACAATCTTTACCTGCTGTGTATTCCTCTGTCTCTTCATCTTGGTT]GAATATAACCAATTTTCAAAAATCATGTTTGTACA - 8 1 4 1 20100 f 74 goat SV_179 1 17983033 - deletion junction SV-TF-chip 38375649 Affx-122978689 AX-123246008 1 17997133 CAGTTCCCATCCCCTGTCACATGTTTAAGGACCAC[A/G]CATCAGCAGTTGGCTTCTCTCTTCTGTAAAATCAT R 2 1 2 1 101000 r 74 goat snp2700-scaffold1077-1462879 1 17808217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775878 Affx-122939225 AX-385263009 1 18053497 GTGTAACTATAATATACAGAGCCATTCAAATACAC[A/G]TTATAAAGAGAATGAAAAGGTACCTAAAATAGCAT R 2 1 2 1 201000 r 74 goat snp2699-scaffold1077-1406515 1 17864847 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450879 Affx-122922215 AX-123321213 1 18110254 CTCTGTATTTGGATGGCTAGAATTCTGTCCAGATT[A/C]TGCCTGTTTCATGAAGCGTTTCCTGAGTTCACTCC M 2 1 2 1 101000 f 74 goat snp2698-scaffold1077-1349758 1 17920803 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272602 Affx-1111832848 AX-519546315 1 18125748 AGACATGGTTTGATTTCTCTATATAGCTAATCTAG[A/G]GAGCACAGGATTGTTATTTTATCTAAAAGGGCTAT R 2 1 2 1 101000 r 74 goat 1_18125748_AF-PAKI 1 18125748 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445131 Affx-122926176 AX-123315468 1 18149506 AAATAATTATAGATTCACAGGAAATTGCAAAAATC[A/G]TACATGGAGGCTCCTTGTTCCATTCATCCAGCATG R 2 1 2 1 201000 f 74 goat snp2697-scaffold1077-1310506 1 17960341 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378282 Affx-122976870 AX-123248641 1 18198617 GAAATGGAGGTTTTCTAATTCCGGAATTTGGACTG[A/G]GATAAGAGTAAGGGGAAGGCATTCTGAGAGCTGGA R 2 1 2 1 201000 f 74 goat snp2696-scaffold1077-1261395 1 18014442 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408302 Affx-122953778 AX-123278653 1 18253882 AAAACACTACAGTGTTCTAGAAATCACCTAGTTCC[A/G]TGTAATTCATAAGCCTTGGTTATGAAATGATTTCT R 2 1 2 1 101000 f 74 goat snp2695-scaffold1077-1206130 1 18069593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442467 Affx-122927942 AX-123312804 1 18307237 TCAATGTGCATGGAGACATTTAGCCCCAACTGAGG[A/G]CAGAGTTTTGAATAAAGAAGGAGAATTAAACACAT R 2 1 2 1 201000 r 74 goat snp2694-scaffold1077-1152775 1 18122998 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392544 Affx-122966096 AX-123262901 1 18340697 CCAGAAGGAAAATAGCAGTAGTAGTGAGTCTCCAA[A/G]AAGACCTTTGACAATCCCCATCTCCTGGTCTTCAC R 2 1 2 1 101000 f 74 goat snp2693-scaffold1077-1119315 1 18156026 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393881 Affx-122965126 AX-123264236 1 18376008 AAATAGGTATTTTTAATCTGATAGGCCACCTCATG[C/T]GAAGAGTTGACTCATTGGAAAAGACTCTGATGCTG Y 2 1 2 1 303000 f 74 goat snp2692-scaffold1077-1084004 1 18190341 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419179 Affx-122945722 AX-123289527 1 18436490 CCCTGAGAAAGCTGACTATAGGCTTATGCTACATC[A/G]TGCAAGACAGGGAAGAAGTCTCCTGGGGAAACCGT R 2 1 2 1 101000 f 74 goat snp2691-scaffold1077-1023522 1 18252605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430529 Affx-122937205 AX-123300870 1 18467996 TTCCTGCTTCCCTGCACATGTACACCCACACATAC[A/C]AATATGACTATGGCCACAGAAAACTTCTATGTCTT M 2 1 2 1 201000 r 74 goat snp2690-scaffold1077-992016 1 18284228 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768719 Affx-122960103 AX-385255897 1 18516828 TTGAGACACATGGAGCTCCTTCCTAGGAAAGGAAG[C/T]TATCTTAAACCAATGTATGTAAGATCATGTTTTCA Y 2 1 2 1 102000 f 74 goat snp2689-scaffold1077-943184 1 18333202 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776918 Affx-122954159 AX-385264042 1 18560891 TATTAGGGAGAGCCACTTGGTAAAGCTGTATATGC[A/C]TGTTAGGGTGCTTGTCAATATATTTGCTCTGATAT M 2 1 2 1 101000 f 74 goat snp2688-scaffold1077-899121 1 18377589 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782722 Affx-122976367 AX-385269794 1 18602527 ACAAACCTAAAGATTAAAAGATTTAAGGTACATAG[C/T]AATGCATCTCCACAAGTACAACATGTAGATCTTGT Y 2 1 2 1 101000 r 74 goat snp2687-scaffold1077-857485 1 18419764 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382901 Affx-122973407 AX-123253259 1 18648980 AGTAGAGACAACCGTACTCCTGGTAGCTTCCAGGG[C/T]GATAGCTGTATTTTCTCTTTTACTACATTAGCTCA Y 2 1 2 1 101000 r 74 goat snp2686-scaffold1077-811032 1 18466695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386664 Affx-122970197 AX-123257022 1 18703429 ATCACAGAAACTTTGTAATTTGCCCAAGCTCACAC[A/G]TCTAGCAAATGGTGGAGCTGGAATTTAAGCACAGC R 2 1 2 1 202000 f 74 goat snp2685-scaffold1077-756583 1 18521280 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446519 Affx-122925027 AX-123316855 1 18734999 CTGAGCTACCAGGAGAGAAGAAATAAAGAATAAAT[A/G]TATCTTAATGTGCTACAGGAAACCAATGGATGAAT R 2 1 2 1 201000 r 74 goat snp2684-scaffold1077-725013 1 18553207 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432369 Affx-122935865 AX-123302710 1 18767669 ATCGACCCTTTAAAGTCATGAATTTTTCTGGGTCT[A/G]TCATTGTAGATTGGAGTCCAGATCATGGGCAATTC R 2 1 2 1 103000 f 74 goat snp2683-scaffold1077-692343 1 10051755 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446110 Affx-122925792 AX-123316447 1 18800966 TATGTGGGCTGAGCTCAGTCATGCCCAATTCTTTG[C/T]AACCCCATGGATTCTCTATGACTATTGAGGAGCTT Y 2 1 2 1 202000 r 74 goat snp2682-scaffold1077-659046 1 18619442 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802762 Affx-122933466 AX-385289661 1 18834475 ACTTGGGGAAAAGAAATACAGATATTCATAGATTG[C/T]GGTAGCTCAGTATCTACTGAGTTAAAATTGGGGCC Y 2 1 2 1 201000 f 74 goat snp2681-scaffold1077-625537 1 18653095 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430946 Affx-122936832 AX-123301287 1 18876050 TTTCATATAGCTGGAATGTCTGACAACTGCCAAAA[C/T]GAATAAGGCAGCACGGCAAGAGAGCCATAAAAGTT Y 2 1 2 1 102000 r 74 goat snp2680-scaffold1077-583962 1 18694091 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444059 Affx-122926856 AX-123314396 1 18905445 GTCACAAGCAAGTGCTGTGTTACAACTGTCCCACA[C/T]GAAGTATTTCTGTCTTTAGTAGACCACACTAATGT Y 2 1 2 1 201000 r 74 goat snp2679-scaffold1077-554567 1 18723440 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445972 Affx-122925890 AX-123316309 1 18946938 TGTGGTGCTATGAGCATTTATTTCTATTGTATTTA[G/T]AACTCTTTTATTTCTCTTAAGTGTATACCGAGGAC K 2 1 2 1 101000 f 74 goat snp2678-scaffold1077-513074 1 18765410 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778145 Affx-122954334 AX-385265261 1 18987098 CATAATATTGATTCTTGATGGAGGAACATCATTCT[A/G]TATAAGGAACTACACTTCCTCCTGCCTACTCCCAC R 2 1 2 1 101000 r 74 goat snp2677-scaffold1077-472914 1 18805752 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422853 Affx-122943095 AX-123293199 1 19019081 TCAGACTACTGAAGGGTGAAAGGTGGATTTAAGGT[A/G]AGGTATTTGCAGTTAGAAAGCCACTAGGTTGCTGC R 2 1 2 1 101000 f 74 goat snp2676-scaffold1077-440931 1 18837735 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393521 Affx-122965799 AX-123263877 1 19067346 TCAAATGGAAAACCTCTAACTTAAAAACACAATCA[A/G]TGCAAACCACAGCTCTTTCATACAATCTTCAAGAA R 2 1 2 1 101000 r 74 goat snp2675-scaffold1077-392666 1 18887414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800846 Affx-122969247 AX-385287761 1 19098932 AGCCAAGTATGGCTCTTGGGGAGTGAGAATGAAAG[C/T]GGTAGATGATGAGGATTATTGCCAAAGGGACAGAC Y 2 1 2 1 101000 f 74 goat snp2674-scaffold1077-361080 1 18918879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417996 Affx-122946669 AX-123288344 1 19136201 TTGGCCATTGCTTTATATAACACACAGGAGTCTAT[A/G]TTTGGAATTCGTTAGTCTTCTCTCACCTGTACATC R 2 1 2 1 101000 r 74 goat snp2673-scaffold1077-323811 1 18956296 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425636 Affx-122940894 AX-123295982 1 19199769 AGTCTATATAAAGGCTCACCCATGATAGTTTTAAA[C/T]GGCTTGCTTAGTAAAATCACTTTCCCTGTCATTTA Y 2 1 2 1 201000 f 74 goat snp2671-scaffold1077-260243 1 19019546 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384292 Affx-122972292 AX-123254650 1 19229782 AGAGTTTGGGATAAACTACTCCATCTGCCTGGAAG[C/T]GAATATCTGCCACATCTTCTGTGTTTGTTCTTCAG Y 2 1 2 1 101000 f 74 goat snp2670-scaffold1077-230230 1 19049735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379954 Affx-122975641 AX-123250312 1 19264942 ATGTCTAAGAAGGCCTTTTCACTAATTCTGTAGTC[A/G]GAATCCAGGCTCCAAATTAGACTGATAGCATATTT R 2 1 2 1 101000 f 74 goat snp2669-scaffold1077-195070 1 19085024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277694 Affx-1111835977 AX-519551193 1 19290545 TATTCTATTCTTTTATAAAGATGAAAATAAAATAT[A/G]AACTAAACATCATAGTATTTAAATCATTCTGCTTA R 2 1 2 1 101000 r 74 goat Random2.2K-21 1 19290545 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320790946 Affx-122975990 AX-385277943 1 19299651 CAAGTATGCCAATTTTGTCACATAATCATTAATGA[A/G]TAAACATGGGTTCAGTGGACTCTGGTTCGTTTTAC R 2 1 2 1 101000 r 74 goat snp2668-scaffold1077-160361 1 19119513 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429240 Affx-122937913 AX-123299582 1 19354423 AGCAGCATACAGAGTATTATGCTAAACCGTTATAG[C/T]GCCTCTGTTAAACACCTTTTAACTAATGTAGTAAA Y 2 1 2 1 101000 f 74 goat snp2667-scaffold1077-105589 1 19174073 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435943 Affx-122933540 AX-123306282 1 19397167 TGTGGAACAGTAGGAAACTTTTTAAAAAATGATAG[C/T]ACTATGCATGTTCTGACTTGAGAATTTTCCATAAT Y 2 1 2 1 103000 r 74 goat snp2666-scaffold1077-62845 1 19217337 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438312 Affx-122931358 AX-123308650 1 19457159 ATTTAGTTCATATACTTAAGTATGCAGGCAGCAAA[C/T]GGAGGAGCTAGGGGGCAAAGTCCAGCCCTGCTGTC Y 2 1 2 1 201000 f 74 goat snp2665-scaffold1077-2853 1 19277280 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435233 Affx-122934083 AX-123305573 1 19509817 AAGGAAAACAGAAAAATGCAAACTCCTATAGAATC[C/T]GGTCTACATCATGACTCCTTTGCATCTTATCGAGT Y 2 1 2 1 101000 r 74 goat snp56449-scaffold889-49706 1 19330053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443239 Affx-122927558 AX-123313576 1 19542010 CTCATAAGGAAAGAATTGGAATGAAAAGATGTAAA[C/T]AATAGTTCTAAGTTAAAAGAGAATGCAATCTCTGT Y 2 1 2 1 201000 r 74 goat snp56450-scaffold889-81899 1 19362028 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778988 Affx-122957579 AX-385266095 1 19577894 GTATGCCAAATATCATCACAATCAACTTTCATCAT[A/G]TATTCCTGAGTAGTTTTCAATCTCAGGTGTTTCTA R 2 1 2 1 101000 r 74 goat snp56451-scaffold889-117783 1 19397799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417692 Affx-122947461 AX-123288040 1 19609811 CTCATTGTCATTTACCTCTCAGGCTCCACCTCCCA[C/T]GGATTCGGGGATTATCTGCTTTGTTCACTTTTACA Y 2 1 2 1 101000 f 74 goat snp56452-scaffold889-149700 1 19429813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448736 Affx-122923832 AX-123319072 1 19651658 ATGCTCTTTCCTCAAAGGATCATTTCATAGCAGCT[A/C]TATGACAGGCTAAAAATCAGAACATGTTGTTCCTT M 2 1 2 1 201000 r 74 goat snp56453-scaffold889-191547 1 19471380 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777163 Affx-122922551 AX-385264286 1 19683465 GCTACTGTTGCTATATGATGGCACAGTTGAATAAA[C/T]GTGCCACAAAGCCCAAAACATTCATTGATCTTTTT Y 2 1 2 1 202000 r 74 goat snp56454-scaffold889-223354 1 19503096 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397862 Affx-122962451 AX-123268217 1 19712959 TATTAAACACTGGCAACTCCAGGATATGATCTATT[A/G]TAACTTTGATTTTCTCATTTGTATAATACCAACTA R 2 1 2 1 201000 r 74 goat snp56455-scaffold889-252848 1 19533214 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431072 Affx-122936632 AX-123301413 1 19757651 AAAGTAACATTTTTTTTCTTTAATTAAGATGTTCC[A/G]CATTTACTCAATCACTCTACATGCTGTTAAACATC R 2 1 2 1 101000 r 74 goat snp56456-scaffold889-297540 1 19577868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454302 Affx-122919259 AX-123324635 1 19795515 TTTTAGTAGGCAAATTAAAATATTTAGCCTCAATT[A/G]TATTTCAAATGTACAATTTAAAGTCAGTGACATAA R 2 1 2 1 303000 r 74 goat snp56457-scaffold889-335404 1 19616232 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796985 Affx-122966832 AX-385283926 1 19856019 GAACTATGTTTAGCTTCACAGTATATATACATTTG[C/T]ATTATGGAAATATGGAAAGGAAAACTAACTGGGTC Y 2 1 2 1 101000 r 74 goat snp56459-scaffold889-395908 1 19677244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390870 Affx-122967812 AX-123261227 1 19890667 TTTCTAGAAGAGTTGGATCGGGGGCAGATCCTCTC[A/C]TGTCATCTTCCTGTCCTCACATAGATTCACTCACT M 2 1 2 1 101000 r 74 goat snp56460-scaffold889-430556 1 19711896 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782738 Affx-122961124 AX-385269810 1 19944890 TTTTACTGTAATCCTATTTTATAGTGGAGGAACTT[A/G]GGCACAGAGGAGTTGAAGAGTTCACTCAAGACCAA R 2 1 2 1 101000 r 74 goat snp56461-scaffold889-484779 1 19766969 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384484 Affx-122973069 AX-123254842 1 20006375 TTCTTCCCTAAATGCTACTTCCCTAGTGTCAAAAG[C/T]ATCTTAGTTTTCACTTTTCTGACTGGAATCTTATA Y 2 1 2 1 101000 f 74 goat snp56462-scaffold889-546264 1 19828718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377290 Affx-122978117 AX-123247649 1 20061685 GGAGGCACTACAACCACCCCACATCTGTGAGTATG[C/T]GATATGGTAGATCCATGAACACGGGAAACAGTAAT Y 2 1 2 1 201000 r 74 goat snp56463-scaffold889-601574 1 19883705 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422036 Affx-122943619 AX-123292383 1 20093407 AATCTCTTAAACTAATAGAGCAAAATTAGCATGCT[C/T]TAAGTAGAACTTTCCAACTAGAATACCACATAACT Y 2 1 2 1 101000 r 74 goat snp56464-scaffold889-633296 1 19915406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418916 Affx-122946087 AX-123289264 1 20123791 ACTCTTTATGTCTCTCAGGTAACATGTATCACTAC[A/G]GTGATCCTTTGAGAAATTGAGGTGGAAACAAATTG R 2 1 2 1 101000 f 74 goat snp56465-scaffold889-663680 1 19946048 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384639 Affx-122972155 AX-123254997 1 20161733 AAGTCTGCTTCTTGTAGGACTAAGAGATGTAATCC[A/G]CTGTTTCACTGGAGCCCTGTTGGTGTGGTAGTAAG R 2 1 2 1 101000 f 74 goat snp56466-scaffold889-701622 1 19985203 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776762 Affx-122971179 AX-385263886 1 20198281 ATCATGTTATTGAGTCAGTTGCATGTAGTAACAGC[A/G]TTATCTATATCTTGAGATGTGTAATGTGTTTAACT R 2 1 2 1 101000 f 74 goat snp56467-scaffold889-738170 1 20022442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448211 Affx-122924229 AX-123318547 1 20226840 GTGGTATCAGTGCTAAGCTAGGATTGCATAGATTC[G/T]AAAAGTCACAATGGAGAGTAGGTATTTCTTGTACT K 2 1 2 1 101000 f 74 goat snp56468-scaffold889-766729 1 20051363 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454123 Affx-122919346 AX-123324456 1 20344598 TCAGTTTAGAGATAAATATCTTTGAACTCCTGATA[A/G]AGAAGAGCTATAGAAATAACATGTGCCATCTCAAG R 2 1 2 1 201000 f 74 goat snp56470-scaffold889-884487 1 20166884 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764892 Affx-122938902 AX-385252486 1 20385517 AGACATGAATGAAATTTGCTAGATTTTGTCACCTT[C/T]AGATGTTTTGTGAGGGTCTCTTTTCTGATTAATAA Y 2 1 2 1 101000 f 74 goat snp56471-scaffold889-925406 1 20208352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384496 Affx-122973059 AX-123254854 1 20415076 TCTAAATAATGCTTCTTACACCTTTATTCCAAATA[C/T]AGCTTTTAAGCATGTATCTTTGGCTTCAACCTGGC Y 2 1 2 1 101000 r 74 goat snp29894-scaffold325-4846 1 20238472 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390554 Affx-122967215 AX-123260911 1 20524193 AGAGGCTCCTGCTGTCTCAAACTGTCTCCTTCACG[A/C]GATGACCATGAACTGGGCTCAGAAATGATTTGAAC M 2 1 2 1 201000 r 74 goat snp29897-scaffold325-113963 1 20348412 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419079 Affx-122945796 AX-123289427 1 20556486 GCCGAGGATATTTACCAGACATTATAAAATGCGAA[C/T]AACATAAAGAAGTTCTATTTGAACATACATGTCCT Y 2 1 2 1 101000 f 74 goat snp29898-scaffold325-146256 1 20380745 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772526 Affx-122955048 AX-385259677 1 20609912 GAGACAGGTGAGCAGTTCATAAGAGCCATTCTTTC[A/G]TTTGAAAAATCAAGCACAGTCATCTGCCAGGGTTT R 2 1 2 1 101000 r 74 goat snp29899-scaffold325-199682 1 20435641 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402171 Affx-122959190 AX-123272524 1 20646880 AAATTGTCAGTCAGTACTTAGACAATCAACATCAC[G/T]ATGGACATGCTGATCTAAAAATGGCTTTAGAGGAG K 2 1 2 1 101000 r 74 goat snp29900-scaffold325-236650 1 20472127 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272555 Affx-1111832850 AX-519546271 1 20660990 GTGAAATAGCTTTGGCTGACAGTATCATTTATGGT[A/G]AGCACTATGGCATTTTTTTTTATTACTAGTTAATC R 2 1 2 1 101000 f 74 goat 1_20660990_AF-PAKI 1 20660990 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440371 Affx-122929642 AX-123310708 1 20703081 AGAAGGGTTGCGTTCTATTTCAGACGTGTTGAGTC[G/T]AAGGTGACTTCAGGACAATCCAGGGAAGATGTTCC K 2 1 2 1 101000 f 74 goat snp29901-scaffold325-292851 1 20528559 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423480 Affx-122942574 AX-123293826 1 20738138 GTAGCTATTCCTGTGACTCATAACATTCATGAAAC[A/G]TTAAAAGTACTGTCTTTTTTAGAGTAGGGCCTCTT R 2 1 2 1 101000 f 74 goat snp29902-scaffold325-327908 1 20563688 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800359 Affx-122930837 AX-385287281 1 20853430 CCTGAATAATAAGTCTACTTAGATGCTTGCTGGCT[A/G]CTTATTCAACATTCCAATATTTATACCCAAATTTG R 2 1 2 1 101000 f 74 goat snp29905-scaffold325-443200 1 20679854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382149 Affx-122974043 AX-123252507 1 20888598 AATGGAGTTATAAACCTCTCCACCTCTTTTTACTT[A/G]CCTCATTTAAAATTTATGGAATTTTGAACCCAAAA R 2 1 2 1 101000 f 74 goat snp29906-scaffold325-478368 1 20714937 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790791 Affx-122948194 AX-385277791 1 20939595 GAAATTAATTAAATTTCCAAGTGATTGTCTGGACA[A/G]CTTGCAAGATTATAAGCGTTTGTTAAACAACAAAT R 2 1 2 1 202000 r 74 goat snp29907-scaffold325-529365 1 20765979 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770400 Affx-122920168 AX-385257566 1 20979083 TGTCTGAGATTGTGCTTTTCCCTAGCTAACTGATA[C/T]GAAACGGTCATTTAGGATAAAACTGAGATGTTGGG Y 2 1 2 1 101000 f 74 goat snp29908-scaffold325-568853 1 20805849 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413771 Affx-122949929 AX-123284120 1 21033345 GTCATGCCAGTCATTACTCTCTTTGACTTACCTTG[C/T]GTTCTCAAGTCAATATGTTCCAGATTAATGAGGCA Y 2 1 2 1 201000 r 74 goat snp29909-scaffold325-623115 1 20860946 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403339 Affx-122957813 AX-123273692 1 21071169 GATGGGCTTGAATAATAGTATAAAAGCTAATGAAT[A/G]GCCATGTAATGTGACATTTTAAAAGAGTATTATGT R 2 1 2 1 101000 f 74 goat snp29910-scaffold325-660939 1 20898678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800104 Affx-122974126 AX-385287027 1 21104239 TAATAGGTTGGACAGAGGTTGAGTATGACTATTAC[A/G]CCTAAGTGACTGTTTCATGGAGCTTCTAGCTGGAC R 2 1 2 1 101000 r 74 goat snp29911-scaffold325-694009 1 20931282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422495 Affx-122943308 AX-123292841 1 21164412 TGCACAGTTTAGGACTCCTCACCTCTCTTTTGTGA[A/G]CAAAAGAAGAATTGGCTAAAACTGGGATCATTTCC R 2 1 2 1 101000 f 74 goat snp29912-scaffold325-754182 1 20990291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405677 Affx-122956559 AX-123276029 1 21228213 ATCATCAATCAGTTACACAAAGTCTGAGCCCCACA[A/G]TATATTAGACTATTTGAGCACTGTTGAGTATGTTA R 2 1 2 1 201000 r 74 goat snp29913-scaffold325-817983 1 21054055 A G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278021 Affx-1111836134 AX-519551513 1 21345248 CCTGGCGCTTTCAAGTGTAAAAACTGCCTCATATC[A/G]GTGACAGATTCCATCCATTGTATTCATACCGGATC R 2 1 2 1 101000 r 74 goat Random2.2K-25 1 21345248 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797917 Affx-122977143 AX-385284855 1 21393278 CACCTTGCCTGGGTTAAGACCATTAAGGTAATGTG[C/T]GAAAACAAAGCACCAAGACTTTGCTCTTTTGCAAT Y 2 1 2 1 201000 r 74 goat snp29917-scaffold325-983048 1 21220232 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415170 Affx-122949010 AX-123285519 1 21423543 ACATTTTACAAACCATGAACACCTTAAAATGTAGC[G/T]TAAGAAAAGCTTCCTATAAGCTTATTGACATCATC K 2 1 2 1 101000 f 74 goat snp29918-scaffold325-1013313 1 21250505 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380349 Affx-122975361 AX-123250707 1 21452884 CATTTAAAAGCAGGAGAAATGTAGACAAGATAAAG[C/T]GTGGATTACTTGAGTCAACTGAGGAAAATTACACC Y 2 1 2 1 101000 r 74 goat snp29919-scaffold325-1042654 1 21279864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446733 Affx-122924712 AX-123317069 1 21484685 AGAGCTTCAGAGGTTGATTGAGAAAAAATATTCAG[G/T]ATGAAAGCAGTAAAAAATGTGCTGCAGATAACATA K 2 1 2 1 101000 f 74 goat snp29920-scaffold325-1074455 1 21311623 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406363 Affx-122955421 AX-123276715 1 21515485 AAAATTTTAGAAGTTTAAGTGAGCTGCAACATCTG[C/T]AATTTCCAAAATTTTTAATGAAATCATAAATAACA Y 2 1 2 1 101000 f 74 goat snp29921-scaffold325-1105255 1 21342785 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404154 Affx-122957080 AX-123274506 1 21546410 AACATGAAAACCTATTTGAGAAAATTAAAAACTGT[A/G]CCACTGGACATAGAAGTCCTTATTAAAAACAGAAA R 2 1 2 1 101000 r 74 goat snp29922-scaffold325-1136180 1 21374409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429675 Affx-122937651 AX-123300016 1 21577560 ATTTATTCAGATATTTCATTACCAATTTACATTTT[A/G]TTTCTTTAATCTGCTATCATTCTCTGCTTCGATTT R 2 1 2 1 102000 r 74 goat snp29923-scaffold325-1167330 1 21405756 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770711 Affx-122924078 AX-385257875 1 21612084 AAACTCAATCCGTCTTTTCAGTGTCGCCTTGAATG[A/C]CAACTATGTCTTGGGAATTATCTGAATCTCTCAAT M 2 1 2 1 101000 f 74 goat snp29924-scaffold325-1201854 1 21440366 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782121 Affx-122947279 AX-385269199 1 21670755 TTGTCATTGTTACTGAACAATCTGAATTGATTGAC[C/T]CCGGAATGGATTTAAATCCCGTGGTAACCAGTCTC Y 2 1 2 1 101000 f 74 goat snp29925-scaffold325-1260525 1 21499298 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379879 Affx-122975782 AX-123250237 1 21705211 CTGAGCAGAGATAGCCACTCTCAATTAATGTTGAG[A/C]TGGTTGGATGGTATCACCAACTCAATGAATATGAA M 2 1 2 1 303000 f 74 goat snp29926-scaffold325-1294981 1 21533826 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769862 Affx-122936774 AX-186027589 1 21774903 AAGTGAAAGTATCAACTAATTCAAATTGATTCAGA[C/T]AAGAAGGGAAATGTATTAGCTCACAAAATAGGAAG Y 2 1 2 1 101000 r 74 goat snp14115-scaffold1564-24142 1 24066270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442183 Affx-122928802 AX-123312520 1 21834677 AGTATCAAGAAAACTCAAGGAAAAACCATAATTTG[C/T]AATATCTATTTAAAAACCCTTTTTTCTTTTTTTAT Y 2 1 2 1 103000 f 74 goat snp14116-scaffold1564-83916 1 24005696 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798520 Affx-122952317 AX-385285453 1 21889667 CAGAATTGAAGGTACTGTAAGCCTTTGTAGGCAGC[A/G]TAATTAAAGTAGAGTGATTACCTCAATGCCAATAA R 2 1 2 1 201000 r 74 goat snp14117-scaffold1564-138906 1 23951761 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400054 Affx-122960770 AX-123270409 1 21921333 AGTCACTCAGTCGTGTCCAACTCTTTGCAACCCGA[C/T]GGACTATACATATTATATATCTCTTCATTCCTCTA Y 2 1 2 1 201000 r 74 goat snp14118-scaffold1564-170572 1 23919379 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776740 Affx-122968845 AX-385263865 1 21963656 TGAATAGAATAAAACATAATGAAGAACACATGCTT[A/G]CTTGGTGCTAATGACATAACGTTTTGCAGTTTTAT R 2 1 2 1 101000 r 74 goat snp14119-scaffold1564-212895 1 23864512 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768406 Affx-122969435 AX-385255586 1 22005219 AGATCCCTCTTCTTGCCTGGTAAGAGCTCAGCTAA[C/T]GAGACTATCACAATTCAGCCAATAGAAAGCCTTTA Y 2 1 2 1 101000 f 74 goat snp14120-scaffold1564-254458 1 23823245 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424853 Affx-122941346 AX-123295199 1 22042592 TTCTTTGCCAGCACTGTCCCTAATTCATTGGAAAA[C/T]GGGTCTCTGTTCTTTGAGGAACAGCAGAGTCAGGT Y 2 1 2 1 102000 f 74 goat snp14121-scaffold1564-291831 1 23785929 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384414 Affx-122972195 AX-123254772 1 22075707 TTGCTTCACTGATACTAAGAGTGCTCACAATAGCA[C/T]ACCCTGCCCTCCTGGCTCCATCTTTAACAAAAATA Y 2 1 2 1 201000 f 74 goat snp14122-scaffold1564-324946 1 23752414 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786244 Affx-122955039 AX-385273279 1 22165524 TTAAGTGTAGCAGAGAAAGATAGAGTTTTGATTCT[A/G]TTTGCCAAAAGCATGGATATGCACTTTTTCCTTTC R 2 1 2 1 201000 f 74 goat snp14124-scaffold1564-414763 1 23662115 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774983 Affx-122977826 AX-385262115 1 22219198 TTTATGTTGCCCAAGGTGTATTACTGTTTCTTGTA[C/T]AGCTAGTACTTCTGAAACAATGTTGTCAGTTGAAC Y 2 1 2 1 101000 r 74 goat snp14125-scaffold1564-468437 1 23610448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443068 Affx-122928129 AX-123313405 1 22275513 CTACATTCAGCCCAAGCTGGCTTCAATCAAAGTCA[C/T]GCTACAGTTCTGTTATGCTAATGCCTGCTGCTGTG Y 2 1 2 1 101000 r 74 goat snp14126-scaffold1564-524752 1 23554202 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802744 Affx-122951007 AX-385289643 1 22320255 AGTGACAGGCAGTCCTTAAATGAAAATTCCCTCTG[C/T]GGATAGTGATATGCCTTTTCATTCTAGTATTGAAT Y 2 1 2 1 101000 f 74 goat snp14127-scaffold1564-569494 1 23509169 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768204 Affx-986698955 AX-385255391 1 22327472 GTATTTGTTCTGGACAAGAGACATGGATTTGTTAT[A/G]GGTTCTCTTGGGGCCACGACAGTTGTGTTCTTCAA R 2 1 2 1 600010 r 74 goat 1_22327472 1 22327472 Ancestral_priority_1043 ancestry 0.522 neutral IMAGE 10K 10K ancestral 38435002 Affx-122933818 AX-123305342 1 22355127 CCAAGAAAAGAAAATCTGTCTTCCTGTGATACCCT[A/G]GAGTCAGTCTTGGTCAGCCACAGAGTATATGCTCA R 2 1 2 1 201000 r 74 goat snp14128-scaffold1564-604366 1 23474379 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398940 Affx-122960991 AX-123269295 1 22393749 GGGTTGGCCTGATGGGACAAAAATGTCATGAAACA[C/T]AAGAGATGTATTAAATAATATGCCATTAAATTTTG Y 2 1 2 1 101000 f 74 goat snp14129-scaffold1564-642988 1 23435701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439928 Affx-122930008 AX-123310265 1 22449341 TTAAAGAAGAGCATGTTTGCTATTATTTTAATGCT[A/G]TAATTTAGAACGTCTTAATTTTAGTGGTGTTTTTT R 2 1 2 1 103000 r 74 goat snp14130-scaffold1564-698580 1 23380011 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396093 Affx-122963427 AX-123266448 1 22494076 AAAGAATAATTCATTAAGACATTTTTCTCAGAAAA[C/T]AGTCATATTACTAATTCTATTGCTAATAAATCACC Y 2 1 2 1 103000 r 74 goat snp14131-scaffold1564-743315 1 23335041 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433153 Affx-122935674 AX-123303494 1 22541129 TTTGCTCCTTCTGACCTTCATAATTATGTGTCTTC[A/G]TGCCAATGTGCTTTCTATTCCACGGTCTGCTTTTC R 2 1 2 1 101000 r 74 goat snp14132-scaffold1564-790368 1 23287987 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786607 Affx-122936972 AX-385273639 1 22594761 ATAGCATAAGCTAAGTGTCTACTTTTCCACTAAAT[A/G]CCTTCCTACACCTTAGATTTAAGGTGCTTTATCAT R 2 1 2 1 101000 r 74 goat snp14133-scaffold1564-844000 1 23233959 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405577 Affx-122955944 AX-123275929 1 22634173 TACCACAAGGACATGAAAGCCCAGAATGGAATCCT[A/G]CAAGAGATTATAAAATATTCTCCCCAAAGAGGCCA R 2 1 2 1 101000 r 74 goat snp14134-scaffold1564-883412 1 23194909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273960 Affx-1111833920 AX-519547565 1 22656188 CCTAGGAACCCCACACACTCTACCTGCAGATGCTA[A/C]TAAAAGCAAGTATACCAGGTCCTGTCACTCTGCAG M 2 1 2 1 101000 r 74 goat GoatD01.010459 1 22656188 T G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802093 Affx-122957822 AX-385288997 1 22683694 AAGGATGTCTAGCCTTATCACTTCCACTGAACACC[A/G]TACTGGAGGTTGTAGCCTGATCAATTAGGTAAGAA R 2 1 2 1 101000 f 74 goat snp14135-scaffold1564-932933 1 23146087 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395995 Affx-122963500 AX-123266350 1 22715731 GAACTGACACACAAGGATTCAAAAATCCCCTCTGA[C/T]GAGCTGTATAGCTTTGGGCAAAGATTTTGTCTAAT Y 2 1 2 1 101000 r 74 goat snp14136-scaffold1564-964970 1 23114054 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388320 Affx-122969369 AX-123258678 1 22773994 TATATGAATATAATTTTTAAATTGTGGATAATGCC[A/G]TAAAGAAGGATGTAGCAAAAAGAACTAGTTTGGAT R 2 1 2 1 101000 r 74 goat snp14137-scaffold1564-1023233 1 23055089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789754 Affx-122952153 AX-385276762 1 22804183 GCATAAAGCTTTACAGGACAGTAAAAGAAAACTGA[C/T]GTCAAGGTCCCAACTGGGTATGTCCCAAGTTAAAA Y 2 1 2 1 101000 r 74 goat snp14138-scaffold1564-1053422 1 23024932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438423 Affx-122931273 AX-123308761 1 22842438 TATACTTGAGCTTGGCCAACATGGGTAGTTGCAAG[C/T]GATTTTAAAGCAGAAAGAGGTGTACTTGGGAATTT Y 2 1 2 1 101000 f 74 goat snp38013-scaffold472-1246997 1 22986453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782994 Affx-122948945 AX-385270062 1 22873332 GCAAAGTCAGATTCATTACCTGCACTTAGCTTACA[A/G]TTCTTCAAGGATCCAACCACAGGAATATCTGTATT R 2 1 2 1 201000 r 74 goat snp38012-scaffold472-1216103 1 22955455 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783301 Affx-122937693 AX-385270366 1 22903275 TTACAATGAAGTGAGAGAGAAATCAGTGACTTGAC[A/G]TTTACAAGTCCCAACTGATTCGTTTATTTATTCAA R 2 1 2 1 102000 f 74 goat snp38011-scaffold472-1186160 1 22925465 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438408 Affx-122931285 AX-123308746 1 22965603 CAAGCAATTTTTTGAGCACCTGCTGAGTATGAGAC[A/G]TATTTCATGGTGAGTTTCTTAAACAAAACCCTCAC R 2 1 2 1 201000 r 74 goat snp38010-scaffold472-1123832 1 22863125 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781409 Affx-122958665 AX-385268494 1 23001312 ACCAACTTGATTCAGTTCAGAGAATTCCACCATTA[C/T]GATTCATGGAACACTATATACATTCCCTTATTTTG Y 2 1 2 1 101000 f 74 goat snp38009-scaffold472-1088123 1 22827028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769302 Affx-122945759 AX-385256473 1 23043409 ATACCGTAGTTAATATATCATTTTTCCAAAAACCT[A/G]CAGAAAAATCCTACTTGTGCTTTGTTGCAGTATGA R 2 1 2 1 201000 f 74 goat snp38008-scaffold472-1046026 1 22784752 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382323 Affx-122973898 AX-123252681 1 23137537 TATTTCAATATGCTTCCTCTCTGCTCCAAACGATG[C/T]GTAACTTTATGCAGTTTTGACTACTTTGAAATATT Y 2 1 2 1 201000 r 74 goat snp38006-scaffold472-951898 1 22690672 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770017 Affx-122968595 AX-385257183 1 23188544 TTGGGCACAGAGAAAGAGAAGGTCCTTTTCCATCT[A/G]CTAAATGATTAGAAACCCAGGTCCAGATTAGTAAA R 2 1 2 1 101000 f 74 goat snp38005-scaffold472-900891 1 22639513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404354 Affx-122956820 AX-123274706 1 23239362 GATCTGTTGATTAGAAGTTCACAAACGACATCTGA[C/T]AAAGCCATTTTTGTGTGCTTATGGGAGCCAAAGCA Y 2 1 2 1 101000 f 74 goat snp38004-scaffold472-850073 1 22588910 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773249 Affx-122953233 AX-385260392 1 23280550 CTGAATTCAGGAGGATGTTGGAAAGAGTGTTTTAA[C/T]GAAAGAAGGGAATCCGTCCTGTGCATAGATTTGGA Y 2 1 2 1 101000 r 74 goat snp38003-scaffold472-808885 1 22548057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443099 Affx-122928105 AX-123313436 1 23387334 TGTTTCTAGGTCTCTCCTCACCTCCAGCAGTTGGT[A/C]TGTGCCCAGGGTATGTAAAATCATTTCAATATTGG M 2 1 2 1 101000 r 74 goat snp38000-scaffold472-702101 1 22442246 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448747 Affx-122923323 AX-123319083 1 23421051 TTTTCCAGCACCATTTATTGAAGAAATTGTCTCTC[A/G]TCCATTGTACTGTCTTACCTCCTTTGGAGCTCTAG R 2 1 2 1 201000 r 74 goat snp37999-scaffold472-668384 1 22408502 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453064 Affx-122920061 AX-123323397 1 23461199 AACTTCTAGGATATATTCACAAAAATCCTTCCAAA[C/T]GGAAAGACAAACTTATTGTGGGTAAATGTAAAGAA Y 2 1 2 1 101000 r 74 goat snp37998-scaffold472-628236 1 22368850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278036 Affx-1111836141 AX-519551528 1 23478169 ATCAAATGATCTTTCTCAAGGTGGTAACAAAGGGA[A/G]ACATCAGATTATTTCAAGCTAAAATACTGTCTCCG R 2 1 2 1 101000 r 74 goat Random2.2K-26 1 23478169 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468271818 Affx-1111832851 AX-519545605 1 23480415 AAATGCACTGTCTTCTAAATCCTACCAACAAAAGT[A/G]TTCTTCAGAAATGACATTTTGAAATCAAATTAAGA R 2 1 2 1 101000 f 74 goat 1_23480415_AF-PAKI 1 23480415 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320800997 Affx-122937257 AX-385287911 1 23540244 TAGTTAAAAATCAAACCAGAAAGCCTACTGTCAAG[C/T]ACAATGTTATGTTATGTTTCTAGTCCAGAAATATT Y 2 1 2 1 101000 f 74 goat snp37997-scaffold472-549191 1 22295743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388429 Affx-122969273 AX-123258787 1 23574489 ACTGGAAAGAGCTGAGTTCAGTCCTACAGTAGCGC[A/C]CAGAGATCTGTGCTCAACATTATTGTGGCAGGCTG M 2 1 2 1 201000 r 74 goat snp37996-scaffold472-514946 1 22261615 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380501 Affx-122975701 AX-123250859 1 23620253 AGATTTATTTCCAGAAAGAGAATGTGTTTTATAGA[C/T]GGCTAGGAAGAAGAGGTTTTCTTCTTTTTTTCCTC Y 2 1 2 1 201000 f 74 goat snp37995-scaffold472-469182 1 22215833 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389776 Affx-122968229 AX-123260133 1 23650027 GGGTCCTTCCCAGGCAGGCTTGGCTTTCATGAGCC[A/G]TAGGGATGTAACTTTTTCCTGGGTGACCCTCTGAA R 2 1 2 1 101000 r 74 goat snp37994-scaffold472-439408 1 22186054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395942 Affx-122963578 AX-123266297 1 23746879 GCTCGTGACTGGCAGATACAGAATTTTCCTCTATA[C/T]GACTCACTTCCAAGCAATTTTAAAGCAAGGATGTT Y 2 1 2 1 101000 f 74 goat snp37992-scaffold472-342556 1 22086368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378501 Affx-122976653 AX-123248860 1 23780868 TTGTAATATTATTAAGCCAAACAATATAAGACAAT[A/G]TTAAAAAAACTTAGAGGCCTGCATAAGACATTGGG R 2 1 2 1 101000 r 74 goat snp37991-scaffold472-308567 1 22052438 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772213 Affx-122972170 AX-385259368 1 23831943 TGATGGCATGTTTCTTGGTTAAAGGAAATAGCTGT[A/G]CATAAAAACATTTGAGAGATCCCAAAGCATGGGTG R 2 1 2 1 101000 f 74 goat snp37990-scaffold472-257492 1 22001329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420042 Affx-122945139 AX-123290390 1 23868174 CATAGAGTCAACAGAAAAGAAATGAACAAAACCCA[A/G]ACTGCTTTCCTTCTGCAATCCTGCAAGTCTAGGCA R 2 1 2 1 101000 r 74 goat snp37989-scaffold472-221261 1 21965584 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768206 Affx-986698956 AX-385255393 1 23877003 TCACTCATCGCATACTCTTCCGTCAGTCATATAGC[A/G]CTTGTTATCGTCGCCATCCTCATCCAAACACCCTG R 2 1 2 1 600010 r 74 goat 1_23877003 1 23877003 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38375423 Affx-122979190 AX-123245782 1 23899049 AATACCAGTTCCTAGTAAAACGTTCAACATAATAC[A/G]CAAATCAAAAACTCAATTTACTCCTTTAAAAACAA R 2 1 2 1 101000 f 74 goat snp37988-scaffold472-190386 1 21934836 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394442 Affx-122965087 AX-123264797 1 23963947 TTCTAGAGTTTGGAGCTGTTTAGAAAAGATAAGAC[C/T]CTCTAGAGTCCCAAATTATTAGGTGGAACCTGTAA Y 2 1 2 1 101000 f 74 goat snp37987-scaffold472-125488 1 21870138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439207 Affx-122931034 AX-123309544 1 24023895 AAATGTAGTATGCGTACAGTCAGTGGTGCTTCTAG[C/T]GGAGACAAGTTAGCCTAGGTGAGCTTTGAGCTTCA Y 2 1 2 1 102000 r 74 goat snp37986-scaffold472-65540 1 21810725 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795202 Affx-122939135 AX-385282160 1 24058553 TTTCAGTTTCAGTACTATGGCACATCTATTAATCA[C/T]CATTAAGGCTGTCTGTGAAATATTTGGCAATATAG Y 2 1 2 1 101000 r 74 goat snp37985-scaffold472-30882 1 21776055 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390672 Affx-122967123 AX-123261029 1 24091022 ACTTTGGGCAGTGAAAATTTGTCTAAGTCACATTA[A/C]ATAAGGCCTTCCTTAATATTCACCATGTGGAATTT M 2 1 2 1 101000 f 74 goat snp8055-scaffold1292-1488 1 21737122 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780016 Affx-122928258 AX-385267115 1 24141291 ACTGTCTCCTAAGCTTGACCAAGCATTTCTGCTGA[C/T]GCTCAACACTGTTTTCCATTAAGCCCACATCCCAA Y 2 1 2 1 101000 r 74 goat snp8056-scaffold1292-51757 1 21685764 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273799 Affx-1111833850 AX-519547410 1 24161518 CACCTTCAGGCTTCCCTGCAAGGCAATTGATTAAA[A/G]TAAGGCTGCTGGCAGAAGGAGGCAGGGATACAGAA R 2 1 2 1 101000 f 74 goat GoatD01.007254 1 24161518 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402314 Affx-122959084 AX-123272667 1 24171311 AATCTTACCCTGACATATATTGACCACTACTCCAT[A/C]GCTCCAGCAGTAGCTGACACCAATGGCCAGTGTCC M 2 1 2 1 101000 f 74 goat snp8057-scaffold1292-81777 1 21655724 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431405 Affx-122936537 AX-123301746 1 24203790 AAATAATATTGAGAGGCACTCATTTGGTACACAAG[C/T]AATAGATTTTCCCTCTTGTTAAATTTTCACTAGTC Y 2 1 2 1 101000 f 74 goat snp8058-scaffold1292-114256 1 21622678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440339 Affx-122929668 AX-123310676 1 24245331 GGTATAAAAAATGACAAGGAGAGTTTATTCAAATG[C/T]GGTTTCTTGAGCCATGCCCAGAGATTCTGATTTGG Y 2 1 2 1 201000 f 74 goat snp8059-scaffold1292-155797 1 21580683 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439250 Affx-122931003 AX-123309587 1 24321451 AAAATCAGATGCATTTTAAAAGTTTCAGTTATTGT[A/G]ATCTTCAACTCTGATTGCTTCTTTTTTATACAGTC R 2 1 2 1 101000 r 74 goat snp46388-scaffold640-654371 1 24166036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784809 Affx-122939636 AX-385271856 1 24355230 CTCCCATACTCAGATTATTAGTAAAATTGGTGACT[C/T]GGGAAAATCACAAATGAATATGTCATAGATTCTAG Y 2 1 2 1 101000 r 74 goat snp46387-scaffold640-620592 1 24199807 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788872 Affx-122926170 AX-385275887 1 24384319 AACTATATACTGAAGAGATACATTCCTATCATAAG[C/T]GACTCTTAGAACTTTTCTCACAGTGTTTCTAGAGT Y 2 1 2 1 101000 r 74 goat snp46386-scaffold640-591503 1 24228795 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385358 Affx-122971643 AX-123255716 1 24414306 ATGTGAATGGATGAGAATAAAGTCTACAGATAAAC[A/G]CATAGCCCTATGTCTTAAGAAGCTCAACTGAGCAT R 2 1 2 1 101000 f 74 goat snp46385-scaffold640-561516 1 24258799 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411744 Affx-122951510 AX-123282094 1 24443294 TTCAACAAATTCAGTTTTGGACATATTGATGCCTG[A/G]ATACCAGAAATCTTTCCCATCATCTAACAGAAAGC R 2 1 2 1 101000 f 74 goat snp46384-scaffold640-532528 1 24288110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431837 Affx-122936091 AX-123302178 1 24487411 CAGCAGGAGCATTCTACTTCAGAGACTGTGGAAGC[A/G]TTTACCCAGGGTCTTTGGAATGCCCTACATCTTTC R 2 1 2 1 101000 r 74 goat snp46383-scaffold640-488411 1 24332905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426596 Affx-122939981 AX-123296942 1 24518167 GCAGGATTAGAAGTTAGAAGGAAGGAAGTCATAGA[C/T]GGAGAATCTTAGAGAACTGACAACAACCCCATGGC Y 2 1 2 1 101000 r 74 goat snp46382-scaffold640-457655 1 24363513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787585 Affx-122940352 AX-385274609 1 24551095 AAATTTGTAGTTTCAGGAAATTAGATGATTTTATG[C/T]AGCTTCAAATGACCTGTTCTTTCCTAACTTTTTGT Y 2 1 2 1 101000 r 74 goat snp46381-scaffold640-424727 1 24397173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774918 Affx-122954485 AX-385262051 1 24589984 GATGAATGCAGTAATGGGTCATGTGCAGAGAGCTA[C/T]GGACACGCAAATCTCAGCTGAATCCAACTGCCAAC Y 2 1 2 1 101000 r 74 goat snp46380-scaffold640-385838 1 24436611 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771598 Affx-122972464 AX-385258756 1 24653709 TTGACCATGTTCATGTGGTACCTGCACATCACTTG[C/T]ATGCTGAGTCTTTATTAATCCTAGTCAGGTGCAAG Y 2 1 2 1 101000 f 74 goat snp46379-scaffold640-322113 1 24501137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768005 Affx-122926136 AX-385255219 1 24682757 CATGCAAGAAATTAAGTTGTCTGTAACCTTTGGTG[C/T]GTGCATCATTTCCACATGAATAATCTCAATTCTAT Y 2 1 2 1 101000 f 74 goat snp46378-scaffold640-293065 1 24530658 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397759 Affx-122962525 AX-123268114 1 24716986 AAATGTTTCCCCAAAAAACACTTTGATAAGGAGTA[C/T]ATCATTGCCATCAGTGACACGGTGTGAAGATATCA Y 2 1 2 1 101000 r 74 goat snp46377-scaffold640-258836 1 24565049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420395 Affx-122944929 AX-123290742 1 24782455 TAAAAGAGCAAGATTTATGGGTACCTAGTTTATAG[A/C]GTGATACTGCAGTTATTAAAAGTATCTGACACTTA M 2 1 2 1 101000 f 74 goat snp46376-scaffold640-193367 1 24631520 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782871 Affx-122935125 AX-385269941 1 24811984 TCTAATATTGTAATCTTGAAGACAATAGTGCAGAA[G/T]AATTCATGGAACTAACTCAAGGAGTGGATGTGAGG K 2 1 2 1 101000 r 74 goat snp46375-scaffold640-163838 1 24660944 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452775 Affx-122920250 AX-123323108 1 24867569 TAGAGACATTGAAATGTTTTGTCACTAGCCTTAGA[C/T]TGCAAAATAAGTCCAAGTCAGAATTAGGTACACCC Y 2 1 2 1 101000 r 74 goat snp46374-scaffold640-108253 1 24717248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277904 Affx-1111836151 AX-519551400 1 24875022 TGATTTTGTAAAATACATCCTCAGCTGTAAATGGG[A/G]AGTTGTTAATGCTTTATCTGTTAACTTGTTTTTTA R 2 1 2 1 101000 f 74 goat Random2.2K-28 1 24875022 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793883 Affx-122968511 AX-385280852 1 24905413 GAGTATCTGTTGATTTAATTGTAACAAGTGACACA[C/T]GAGAAACATTGCATTTTGTGGCAGACACTGAGGCT Y 2 1 2 1 101000 r 74 goat snp46373-scaffold640-70409 1 24755419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800284 Affx-122953410 AX-385287207 1 24956218 ATAGGATATTTGTATAACAAATAGGTTGTTAGGGA[A/G]TAAGAACTATTGATCTAGATAATTATAATTCATAG R 2 1 2 1 201000 r 74 goat snp46372-scaffold640-19604 1 24806876 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416727 Affx-122947545 AX-123287075 1 24990211 CCTCCACTTACTTGTCTTGTCTTGGAATGGCTGTG[C/T]GTGTACTGAGGAGCTGACTGTACTCACAGCCTTTG Y 2 1 2 1 101000 f 74 goat snp23367-scaffold234-14290 1 24840552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778504 Affx-122935190 AX-385265618 1 25026568 TTACCTTGTGTTTTCACTGGGTCTGATATCTGGCT[A/G]GGATCACTAATTCCATATGCATTGGCAGCCCTCAC R 2 1 2 1 101000 f 74 goat snp23368-scaffold234-50647 1 24876581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386519 Affx-122970742 AX-123256877 1 25080657 GCCCAGTGAATTTTAGGACTTGGCTGAATTCCATA[C/T]TGAAGGTGCCAGGCATTCTAGAAACTAATATTTGG Y 2 1 2 1 101000 f 74 goat snp23369-scaffold234-104736 1 24929758 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800555 Affx-122939874 AX-385287474 1 25110294 TAAAGTCCTAACTCTGTGATTTCAATTGTATGAAC[A/G]CACACTTTACGTGTTGTTCCACTCTACCTAACAAG R 2 1 2 1 201000 f 74 goat snp23370-scaffold234-134373 1 24959442 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419205 Affx-122945701 AX-123289553 1 25143112 TTATATCAATGAAAGCAAACTAAAACCAGCATTAA[C/T]AGTCTCTAACATGCGTTAAGTTTATAACATTTGCT Y 2 1 2 1 101000 r 74 goat snp23371-scaffold234-167191 1 24991713 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773076 Affx-122967307 AX-385260219 1 25199226 CAAATAGGTACTAGGTAAACATGTCGCAGAGAAAG[C/T]ATCTTTCAGTAATAGCTAATTTCTCCAAAATTATT Y 2 1 2 1 101000 f 74 goat snp23372-scaffold234-223305 1 25048419 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401836 Affx-122959440 AX-123272189 1 25260500 TGCACACAAGCCATTGTTCCATTCCCGAAGAATTA[C/T]ATTAATCAATGCTCACAGGCTGCACCTCTGGAACA Y 2 1 2 1 101000 f 74 goat snp23374-scaffold234-284579 1 25110090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800915 Affx-122919514 AX-385287830 1 25323675 ATTTCTACATACTGTTTGCACAATTAAAGGTAAAT[A/G]CCCCTGATTCCTGTTATTTTCCACCAACATGCTTT R 2 1 2 1 101000 r 74 goat snp23376-scaffold234-347754 1 25172950 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390306 Affx-122967718 AX-123260663 1 25362618 CATGTTTCCCCGAAACCAAACTCAGGGTCACTCCG[C/T]CTTTCCTCTTCGTATCAGCATGTGCCCAATTTTAG Y 2 1 2 1 101000 r 74 goat snp23377-scaffold234-386697 1 25211936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400330 Affx-122960051 AX-123270685 1 25400408 TTGTGTTTTTACCAAGAACCAAGCCCCACGGAAGA[C/T]GGGTCTCCTGACTCTCTTCCACTAACACCTCTTGC Y 2 1 2 1 101000 r 74 goat snp23378-scaffold234-424487 1 25250180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395598 Affx-122963824 AX-123265953 1 25431902 TCTCAGACACCACCCCCACCTCATACTGAGGACGT[A/G]TCTTGTATCATAGAGTTCCCCTCGGTTTTCTATTG R 2 1 2 1 101000 r 74 goat snp23379-scaffold234-455981 1 25281125 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278066 Affx-1111836156 AX-519551556 1 25462691 ATAACTGCTCTCATTAATCAAATTCCTCCCAGGAG[A/G]TAGGTCAATATGAAATAAGATTAGAGCGGGGTTGT R 2 1 2 1 101000 r 74 goat Random2.2K-29 1 25462691 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776210 Affx-122962430 AX-385263338 1 25470047 GAAGAGGGTTTTGCTGCCACACTTTTCCCTCAAAC[A/G]TTACGCTAGAAAATTCCTATGATTTTCATCTTGAA R 2 1 2 1 101000 f 74 goat snp23380-scaffold234-494126 1 25319810 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437098 Affx-122932182 AX-123307436 1 25508908 CTTTTGTGTCTGGTCCTGTGTGTATGGATTCTCTT[C/T]AAGTGAAATTTGTTCTACTATAGATGGGTAATAAA Y 2 1 2 1 201000 r 74 goat snp23381-scaffold234-532987 1 25358890 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422130 Affx-122943550 AX-123292477 1 25556137 GATATATTAGTCACTGTGCTAAGCAATATAGTAAA[C/T]AAGACTTGAATAAAATAGGGTCCCAAATATTTAGG Y 2 1 2 1 201000 f 74 goat snp23382-scaffold234-580216 1 25405673 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799957 Affx-122968261 AX-385286883 1 25594447 GGAGCAGGGCTGAGTTAATGGGAAGGGGTTTTATG[C/T]AGAGCTGTTGTTTTCAGGAAAAGTTTCCTTCAGGT Y 2 1 2 1 101000 r 74 goat snp23383-scaffold234-618526 1 25443446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778851 Affx-122923003 AX-385265959 1 25623224 ATTTCTTGGCACCCTAATTTCCTAACTCTTGTAAC[A/G]GAAGTCTAGATGCACTAGACGATGTGGGAAATGAT R 2 1 2 1 201000 f 74 goat snp23384-scaffold234-647303 1 25473051 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382535 Affx-122973791 AX-123252893 1 25659580 TTTTCCTCCAAGCTCCCTGGCAATTTAATCATCCC[G/T]CACTAGATCCCTTAATGTGGGAATTACTCAAGGCT K 2 1 2 1 101000 r 74 goat snp23385-scaffold234-683659 1 25509749 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381470 Affx-122974973 AX-123251828 1 25722417 TCTATGTAAACTCTGTGCCATGTGGCAATAAGTTC[C/T]AGGATCATTCTAAACAATTTTAAATACCCAATTAA Y 2 1 2 1 101000 f 74 goat snp23386-scaffold234-746496 1 25572742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414914 Affx-122949110 AX-123285263 1 25747521 CATTTCTCTGGGCCTGAGAGCTAGTGTTGTAAATC[G/T]ACTTAGCATACCAAGCTATTCCAGGTAAGTATGTA K 2 1 2 1 101000 f 74 goat snp45807-scaffold629-1505 1 25597721 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802134 Affx-122924137 AX-385289038 1 25801803 TTCATTCGGGTAATATATCTGACACTGTAGTTCTG[C/T]AAGAAGGCTCTTGATTCAACACCCCCCAACTTTTT Y 2 1 2 1 101000 r 74 goat snp45808-scaffold629-55787 1 25652832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408243 Affx-122953823 AX-123278594 1 25856512 CCCATTCCATTTAGATTAACATCTCGAACCCTTAC[A/G]TTGGTTTACAATGATCCACATGATCTGTCCCCACT R 2 1 2 1 101000 f 74 goat snp45809-scaffold629-110496 1 25707994 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277925 Affx-1111836162 AX-519551420 1 25867206 TTATCCTAAAATGAAAGAGGTATTGAAGAATGTCT[C/G]CATAATATCTAATAATTTTTAAAACTTGCAAAACA S 4 1 2 1 101000 f 74 goat Random2.2K-30 1 25867206 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38389959 Affx-122968077 AX-123260316 1 25904425 GTTGTTAATTTAGACTGAATTGAGCAAAATAATTT[A/G]AGTGGAAGAATGCAGACAAGACAATGTATCAAGAA R 2 1 2 1 101000 r 74 goat snp45810-scaffold629-158409 1 25755690 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772485 Affx-122974463 AX-385259636 1 25949389 TTTGAAGACTTGAGCTTGGAAATCACTTGCCAAGG[C/T]TCTTTCTCGTATCCCACATCTAGTTGGTTATCTGA Y 2 1 2 1 101000 f 74 goat snp45811-scaffold629-203373 1 25800392 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770835 Affx-122932941 AX-385257999 1 26001420 AGGTGTGATTTTATCAAAATATTGCACATTCAACT[A/G]TTGAAATGGTTTGGTTATTACAACAAAGCAGCTAA R 2 1 2 1 101000 r 74 goat snp45812-scaffold629-255404 1 25852649 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796361 Affx-122919795 AX-385283311 1 26053184 CCTTTTTTGTTTTGTTCAGGTAGTTATGTAAAATC[A/G]TTTCTCATAAGCTTTGTTGTTACATGACTTGGCTT R 2 1 2 1 201000 r 74 goat snp45813-scaffold629-307168 1 25904072 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274363 Affx-1111834212 AX-519547958 1 26082022 GGCAGACGGGATGCTAAAACATGTCAGCCCAGCCC[A/G]GGGTTTGAGCTGCAGGCGCTAACCGTAGGGTGACC R 2 1 2 1 102000 f 74 goat GoatD01.025749 1 26082022 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320799273 Affx-122935174 AX-385286202 1 26085274 CCATGCTAGCATGACTTTTAGATTAGATATTTTAA[C/T]ATAGTTTGTTCCAAGAATTCATATATGTGTTTCAA Y 2 1 2 1 201000 r 74 goat snp45814-scaffold629-339258 1 25936370 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402765 Affx-122958316 AX-123273118 1 26120674 TGTATCAGAATTACTTACATGACCAGTTAACCCAT[G/T]GTAAAAATTTACCTTCTTGTCACATTATTTCAGAT K 2 1 2 1 101000 f 74 goat snp45815-scaffold629-374658 1 25970965 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792404 Affx-122934367 AX-385279385 1 26158811 ACTCAATTTATCATGTAATGCACTGATAGGGTAAT[A/G]TTAAAGTCATTGTTTGAATTTCAATTTGTGTTTCT R 2 1 2 1 201000 r 74 goat snp45816-scaffold629-412795 1 26009370 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437959 Affx-122931613 AX-123308297 1 26230231 CATTGTGCTTCAATTCTTCAGATTATACAACAAGA[C/T]GCATAAAGCAAAAGATACATGGAGAAAGGTTAAAG Y 2 1 2 1 101000 f 74 goat snp45817-scaffold629-484215 1 26080828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376846 Affx-122977906 AX-123247205 1 26258890 CTTGTTTGATGTATTAACATTCTTCTATTCATTGC[A/G]TCTTCACTGCCTAAGTTCTCTTTAACCTGGTTTAC R 2 1 2 1 101000 r 74 goat snp45818-scaffold629-512874 1 26109305 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793767 Affx-122935944 AX-385280739 1 26304035 CTGGAATAACTGGGTATTCCTCTTTATGCACCATC[A/G]TTTGTTTAGCCTAAGTGTAACATTTCATCCAGCAA R 2 1 2 1 101000 f 74 goat snp45819-scaffold629-558019 1 26155113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777406 Affx-122943459 AX-385264527 1 26359672 AGAGAGTATGCACTGATTGTCATAAATTTCTTAAC[G/T]GAATCCTGCGATGAAGTTAATCAGGAAATGGGGAC K 2 1 2 1 101000 r 74 goat snp45820-scaffold629-613656 1 26211106 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463632162 Affx-1110079937 AX-515113302 1 26383901 ACTGTCTATGGGGTTCTCTGGTGCTTCCCTGATGG[C/T]TCAGCTGTAAAGCATCCACCTTCAGTCAGGAGCCA Y 2 1 2 1 303000 r 74 goat 1_26383901_AF-PAKI 1 26383901 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320783836 Affx-122920702 AX-385270892 1 26388372 TGTTCTATCAGTGGATTTTACATTCCATTTAACAT[C/T]TCAGGAACTTGCAACAGGAACGTGAGGATCTTTGC Y 2 1 2 1 101000 r 74 goat snp45821-scaffold629-642356 1 26240146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769062 Affx-122952464 AX-385256237 1 26448728 TAAATCCCAAGAGTTTTCCTTGGAAATTATAAACC[C/T]TAAAATGTCTTTGTCTTTAGTTGTGACATATTTTA Y 2 1 2 1 202000 r 74 goat snp45822-scaffold629-702712 1 26300828 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387588 Affx-122970262 AX-123257946 1 26469618 TTCAGCCTGTCAATATTCAGAAAAAATATATTTAC[C/T]CAATATCCTGAAGAAAATCTATTTATCTGAGTAAA Y 2 1 2 1 303000 r 74 goat snp11780-scaffold1437-813 1 26324795 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449623 Affx-122923195 AX-123319958 1 26510216 TTGGCTGGAGCACAAGCTTCAGGATTTCTTGAAGA[C/T]ATCTTTTCAAGAAACTTAGAGATACCAAAGGAACA Y 2 1 2 1 103000 f 74 goat snp11781-scaffold1437-41411 1 26363652 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797051 Affx-122933538 AX-313468630 1 26583668 TTTTTAACTCCCAAACATTCTTAGAATCTGATTAA[C/T]GGAGGGCATCCAAGAAAGTGTTTATTGAAATGTTT Y 2 1 2 1 102000 r 74 goat snp11782-scaffold1437-114863 1 26438566 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442446 Affx-122927958 AX-123312783 1 26643752 GTTTCTTGCTCCATGTCATTCCTTGCTGTTCTGTC[A/G]CTCAGTCATGTCTGACTCTTTGCGACCCTATGGAC R 2 1 2 1 102000 f 74 goat snp11784-scaffold1437-174947 1 26495698 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793051 Affx-122971404 AX-385280029 1 26687203 TTGATGCCACATTGTTGAAATAAACCAACATTTAA[C/T]GTTCTGTGTACTCTATTTGTAAATTCCTGCTTTAC Y 2 1 2 1 201000 f 74 goat snp11785-scaffold1437-218398 1 26539816 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417088 Affx-122947492 AX-123287436 1 26717714 ATTATAATAGTCATAAGCAAATAATTTTTGCATTT[A/G]CTTGTACTACCCAAGACTTGCTTCCACATGCTTAC R 2 1 2 1 101000 r 74 goat snp11786-scaffold1437-248909 1 26573034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793959 Affx-122933853 AX-385280928 1 26777073 AAATTAAGGATAGAGAAAAACAGTGCTTTCCTTTG[A/G]TAAACATTTAGATGCTTTGGCACCAAAATAGAGTC R 2 1 2 1 101000 f 74 goat snp11787-scaffold1437-308268 1 26634080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409763 Affx-122952995 AX-123280114 1 26834535 ATGGATGCAACAAGAATTTGCTTGTTAAATAGTAG[C/T]AAAGTAGAAGTGATTGTTATGCCGTGTCCGAGCTT Y 2 1 2 1 101000 r 74 goat snp11788-scaffold1437-365730 1 26692538 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436015 Affx-122932743 AX-123306354 1 26882646 TGTCTTACATTATAGCTCTCCTCATAGGCAGCTTC[A/C]TTCTTCAAGACCAGCTAGAGGATCCCTTCCTCCAT M 2 1 2 1 101000 f 74 goat snp11789-scaffold1437-413841 1 26739201 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411925 Affx-122951162 AX-123282275 1 26920343 TTCCCATATTTTGATATTGTTATGCTATTAATCAA[G/T]ATTTTGATCCCAAACTTATCATCCTCATAAAGACC K 2 1 2 1 101000 r 74 goat snp11790-scaffold1437-451538 1 26776199 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800653 Affx-122956140 AX-385287572 1 26965515 GCCGCTGGTGAAAGGGAGCAAGTTAGACAATTTCC[A/G]CTTTATTAATACCACTGTGACTCTATTGTGCCATC R 2 1 2 1 101000 f 74 goat snp11791-scaffold1437-496710 1 26820994 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780289 Affx-122959358 AX-385267384 1 26996467 CACTTTCCATATTACTGGAACTACTAGGCCTCAAT[A/G]TGAAACTCTTATGAAAGTGAGTGCAAATTGGAAAA R 2 1 2 1 101000 f 74 goat snp11792-scaffold1437-527662 1 26852491 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767026 Affx-122938822 AX-385254318 1 27025932 GTTAGCCAAGGGAGTTTTAAGGTGACTAAGTTATT[A/G]CTGAAACATATATGGCTTTCTATTTTTTCACCTGG R 2 1 2 1 101000 f 74 goat snp11793-scaffold1437-557127 1 26882251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424368 Affx-122941844 AX-123294714 1 27066775 GTGATTTGTTTTCCTGCCTTTTAAATCATCATCTA[C/T]ACTGAAAACTTTATATTTATTTAAGGGAAATCTCT Y 2 1 2 1 101000 f 74 goat snp11794-scaffold1437-597970 1 26923861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440763 Affx-122929858 AX-123311100 1 27102919 TTTACAACTTTCTCTTTTGTCCTTCTCTCCCCATC[G/T]CTGTCTATGTCTCTGTCACTTTTTGCCTCTCTCTC K 2 1 2 1 101000 r 74 goat snp11795-scaffold1437-634114 1 26959531 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392644 Affx-122966450 AX-123263001 1 27118415 CTGTAAGCCTATAATATTTTTTTCTTAAGTAAGCA[C/T]ATTTAAAATCCACTGAAGCCTTTTCCTTTGTTGTT Y 2 1 2 1 103000 r 74 goat snp51940-scaffold763-313236 1 26989032 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786379 Affx-122966869 AX-385273413 1 27147074 ATATGTAAACACCTATTTGTTATCTATCTAGCTAT[C/T]TTGCTGTCATCTTTCTACCATCAATAATTTGTCTA Y 2 1 2 1 101000 r 74 goat snp51939-scaffold763-284577 1 27018059 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380985 Affx-122974680 AX-123251343 1 27194805 ATTGCTGAGGGATTGAACCTATTTCTTGGCTCATT[A/G]CTATGCATATGATAGACTGAAAGAATGACCTAGCA R 2 1 2 1 101000 r 74 goat snp51938-scaffold763-236846 1 27063464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796763 Affx-122953413 AX-385283707 1 27245777 ATAATTTAGTTATTATAATAATTAATCATTAGATT[A/G]CAGTAAAGTAATTTATTAGGAGAAACAGATATTTG R 2 1 2 1 202000 f 74 goat snp51937-scaffold763-185874 1 27114353 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769883 Affx-122936262 AX-385257052 1 27289997 TCACATAGCAATGGAAAAGAATTGATAAACAAAAG[C/T]AAAATTAGCAGTCTATGTCCAATCACATGAAACAA Y 2 1 2 1 101000 f 74 goat snp51936-scaffold763-141654 1 27158433 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792049 Affx-122955733 AX-385279037 1 27328970 GAAACTGAGATTGCTAAGTGAAATCATCTTTCTAT[A/G]TCTTACAATAAATGAGAGAAGCAGAATTTGAATGC R 2 1 2 1 101000 r 74 goat snp51935-scaffold763-102681 1 27197572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799614 Affx-122943842 AX-385286544 1 27380542 GTGGAGATGTAAGTTACTTCTATGGACTAGATAAA[G/T]AGGGGAGGAGCAATATAGGTGTAGGGAAATAAGAG K 2 1 2 1 103000 r 74 goat snp51934-scaffold763-51109 1 27249676 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778317 Affx-122960269 AX-385265432 1 27414767 GCAGAACTGAGTAGGACAATTAGCAAATTAGTGGC[G/T]TATTAGCACAATAGTAGTGTTTCTAATGACTTTTC K 2 1 2 1 101000 f 74 goat snp51933-scaffold763-16884 1 27284044 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411737 Affx-122951515 AX-123282087 1 27454715 ACAGTTCAATATTACCTTGAGTCTTTAAGATACAG[C/T]ATAGCCTTAGACTATATTAAGAACTATGTTGCATT Y 2 1 2 1 101000 f 74 goat snp15734-scaffold1652-1168377 1 27338324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773457 Affx-122936135 AX-385260599 1 27496126 CTGCTTTCTCCACCTTGTTTCAGGAGTAAGAAAAT[A/G]TGTGTGTAGTCTTCATGGGCAGGTCTATACTTAAA R 2 1 2 1 101000 f 74 goat snp15733-scaffold1652-1126966 1 27379911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439086 Affx-122931127 AX-123309423 1 27546768 TATTGATAAAGATAAGACCATGAAGAAATCAGCCA[C/T]GGGGTCTTGGTAAGCCATGTTAGGAATTTAGATCT Y 2 1 2 1 201000 f 74 goat snp15732-scaffold1652-1076324 1 27430949 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278096 Affx-1111836170 AX-519551586 1 27550186 CTTAGCAAGAAAAATTTGGTCTCTGTTACTCTCCT[A/G]TCTCCAATCTGTATTGAAAGCAACTAATCAAAATA R 2 1 2 1 201000 r 74 goat Random2.2K-31 1 27550186 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320765709 Affx-122971154 AX-385253171 1 27613258 TGTTCAGACTGAAACAGTCAGCTCTATAGTCAATT[C/T]GTAATTGATTATTGATCATAAGCATCCTGTTATAC Y 2 1 2 1 101000 f 74 goat snp15731-scaffold1652-1009834 1 27497574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417460 Affx-122947190 AX-123287808 1 27643134 TGTATGTGATGAGAATAGAAATGGCTGAGCACAAA[C/T]ATTTAAAGGCAAGGAAAAAAGGAGCAGAAGTCTTC Y 2 1 2 1 201000 f 74 goat snp15730-scaffold1652-979958 1 27527204 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786418 Affx-122945228 AX-385273452 1 27747045 TTGAAGGGACTTTAGAAGTTCACAGCTAATAGCAG[C/T]ACTCCTGTTCACTGTAAAGGAATGTTAATTTTGTC Y 2 1 2 1 101000 f 74 goat snp15728-scaffold1652-876047 1 27632005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786537 Affx-122939601 AX-385273570 1 27782288 CCATTACAAGCTATAAGTTATGCTTCATCTTGGCC[A/G]TTACTACAATCATTTTACACTTTATGAATTCTCAA R 2 1 2 1 101000 f 74 goat snp15727-scaffold1652-840804 1 27667084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768432 Affx-122930636 AX-385255612 1 27831294 TCAAAATTAGATGCAATGGGTAATTATTTTGGTAG[A/G]GAATATAAATTCAGGCTTTGATTCCTTTCATAGAT R 2 1 2 1 101000 r 74 goat snp15726-scaffold1652-791798 1 27716205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395876 Affx-122963998 AX-123266231 1 27862464 TATATACATTGCCATATACTTTCGGTAGGGCCCTT[G/T]CACTCGAACCCTTGAACTCCGCATTTGGCCAACGG K 2 1 2 1 101000 f 74 goat snp15725-scaffold1652-760628 1 27747113 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412681 Affx-122950767 AX-123283030 1 27908549 GCCTCCCTCCCCTTTCCACTCCAGGCAACACAGTC[A/G]CCCTGGGCCCCTTCAGTATTTCAGGTGTTACTCTA R 2 1 2 1 101000 r 74 goat snp15724-scaffold1652-714543 1 27793333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397714 Affx-122962557 AX-123268069 1 27937789 TGACATGTGTAATTTGCTTTAATTTCAAAGTAGAG[C/T]AATAGTTTGATTTCCTGACAGTGAAGCCAGCTGAT Y 2 1 2 1 201000 f 74 goat snp15723-scaffold1652-685303 1 27823343 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775291 Affx-122921768 AX-385262422 1 27981560 TTACATTAGTGATCATAATCGTAATTTAATGAGCA[G/T]AAAGAGCATGCTTTGATGGTTAGTGCCTGGTTACT K 2 1 2 1 101000 r 74 goat snp15722-scaffold1652-641532 1 27867105 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397998 Affx-122961796 AX-123268353 1 28016846 GTGTCAAGTATATAACAATATGAAAATTAAAATAC[A/G]TTTTAAGCTTCTAGCCCATTGTAGCACATTTGGGT R 2 1 2 1 102000 r 74 goat snp15721-scaffold1652-606246 1 27902505 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768837 Affx-122973230 AX-385256014 1 28074128 CACCTGATATACAGTGTCTCCTCCAATCTTTTGCC[A/G]TTTCCTATCTTCTGTCCCTGCCTCATTTTTCTCTG R 2 1 2 1 101000 f 74 goat snp15720-scaffold1652-548964 1 27959936 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391598 Affx-122966600 AX-123261955 1 28123734 TTATATCCAGTGTTGCTGATAAAATGCTGATAAAT[C/T]TGATTTTTATTCCTTTGTGTGTAATCAGCCTTTTC Y 2 1 2 1 101000 f 74 goat snp15719-scaffold1652-499358 1 28014323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423310 Affx-122942630 AX-123293656 1 28161414 GAAAGAAGAACACATTCTTCCTGGAAAGAATCAGG[C/T]AGGCTCGTCAGTTACAGGGGAGGTTAGAGAACAAT Y 2 1 2 1 201000 f 74 goat snp15718-scaffold1652-461678 1 28051500 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786431 Affx-122926381 AX-385273465 1 28202350 ACCAAATGTCACTTCAATTTATTCAGTATGAATTT[A/G]TCTTCCAAAAGAAGCTTAAAAATATACTGCTTGTT R 2 1 2 1 101000 r 74 goat snp15717-scaffold1652-420742 1 28092577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376043 Affx-122978937 AX-123246402 1 28239774 GCAGCTGGGATGTCTGCAAACTATTCTATAAGGGA[C/T]ACCAAAATATCACTAGAATAACTTGAATAGATCGT Y 2 1 2 1 201000 r 74 goat snp15716-scaffold1652-383318 1 28130282 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772197 Affx-122924570 AX-385259352 1 28292037 TATTCTGAAAGAAATCACTGTCTACCCTTCCATGA[A/G]AGATCCAAATTTCAGTACCTTAATTCAAATTTTAG R 2 1 2 1 101000 f 74 goat snp15715-scaffold1652-331055 1 28183186 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423273 Affx-122942660 AX-123293619 1 28324950 TTATCTAATGAACATATAGTTTCCACAGAAGCAGT[G/T]AAATATGCAAATATTTACACATATACACACAAACA K 2 1 2 1 101000 f 74 goat snp15714-scaffold1652-298142 1 28216763 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785539 Affx-122972230 AX-385272583 1 28363292 AATAGCAGGACAAACAAAATTCCTGAAGATTAATC[C/T]ATGACAGAGAACCTGGAAAGTTGGCACAGCCCTGA Y 2 1 2 1 101000 r 74 goat snp15713-scaffold1652-259800 1 28251788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793257 Affx-122950577 AX-385280235 1 28400001 AAGTATCCTATATAGCTTAGCAATAAATACAATTT[A/C]GCTAATCAAAATAATGTAAACATGATACAGTAATC M 2 1 2 1 101000 r 74 goat snp15712-scaffold1652-223091 1 28288909 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380997 Affx-122974670 AX-123251355 1 28446823 CTGCATGTCTTGTTGTACCAGTGACATCCCAGTTC[A/C]GTGCAAGCACATTAGCTGATTTTACAAGATACGTG M 2 1 2 1 101000 r 74 goat snp15711-scaffold1652-176269 1 28336136 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376949 Affx-122977769 AX-123247308 1 28515440 TACTAATGACTAACATTTATTATAGAGACAGTAAA[G/T]ATCACAGCCAGATCAGAAAGAGAAAATGACATCTG K 2 1 2 1 303000 f 74 goat snp15709-scaffold1652-107652 1 28404607 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422060 Affx-122943605 AX-123292407 1 28562872 TCAATTCAAACCCACAAAGTCAACCCACAGAGTCC[A/G]TGTTCTCAACTGCTACATGAGATAGCCTTCTGACT R 2 1 2 1 101000 r 74 goat snp15708-scaffold1652-60220 1 28451286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424187 Affx-122942517 AX-123294533 1 28601982 TTCATGAAAACTGACCCATCACTTGTTGTTAGCAA[C/T]ACATCTTTCTAAAAATTTAATTTTTAATAAATTCA Y 2 1 2 1 101000 f 74 goat snp15707-scaffold1652-21110 1 28490337 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403043 Affx-122958540 AX-123273396 1 28722307 CCCAGGATTGCTCACTAATTCTAGGATCTGAAACA[G/T]TGCCAAAGCTTTCAGGTAGGGTTGGAGGCCCTGAT K 2 1 2 1 101000 f 74 goat snp52909-scaffold794-813793 1 28610260 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387249 Affx-122970564 AX-123257607 1 28753361 GACAAATACTTGTAATACATGGCTTATTACATACT[A/G]CTCACAGTTGTTTTCTTTTTGTCTGGATAGAATGC R 2 1 2 1 101000 f 74 goat snp52908-scaffold794-782739 1 28641342 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769031 Affx-122945443 AX-385256206 1 28824214 TACTTTCAACTGTTGGATAAAACCTTTAGAGAGAG[A/G]CTACAGTTGAGGTAAAATATTTGGATTTGTAAGAA R 2 1 2 1 101000 r 74 goat snp52907-scaffold794-711886 1 28712948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788021 Affx-122969126 AX-385275042 1 28865894 ACTTATTCTACAACTGCATTTTTGTCTAATAGTTC[A/G]GCTGAACAATGTCCATTTTCCAGGGCTATTGATGA R 2 1 2 1 101000 r 74 goat snp52906-scaffold794-670206 1 28755163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411037 Affx-122951965 AX-123281387 1 28908572 TAGTCTATTGTTATTTGGATGAATATACTAGCACA[C/T]GAACATCCCTAGATAGACTGATAAAAATTAATATC Y 2 1 2 1 101000 f 74 goat snp52905-scaffold794-627528 1 28796310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389309 Affx-122968503 AX-123259667 1 28976732 TTAGTAGTACAATCATGAGCGGGGTTTTCAGCATT[A/G]TGATTTCATTATTTTGCTTTGCAACCTTTTAAAGC R 2 1 2 1 101000 f 74 goat snp52904-scaffold794-559368 1 28865198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787761 Affx-122921354 AX-385274784 1 29006364 TCATACGTTGTAAAATTGCGGTTGTTTCTAGCACT[A/G]CATTCTATTTGCTAAAGCTCTGCTAAAATTATTTA R 2 1 2 1 101000 f 74 goat snp52903-scaffold794-529736 1 28895337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447970 Affx-122923761 AX-123318306 1 29044980 AACTCTGCATACAAATTATCATGAGACAGATTAAA[C/T]GAGTAAAAACACTAGGAAAATTATTTACCACGCTT Y 2 1 2 1 201000 f 74 goat snp52902-scaffold794-491120 1 28933522 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408916 Affx-122953957 AX-123279267 1 29115476 TTTCTGGATGACATATTCTGGTTTCCTTCAGTAGG[A/G]AGGCAAGAACATGAATAAGAAGTGAATCAGTTAGA R 2 1 2 1 201000 r 74 goat snp52900-scaffold794-420624 1 29004543 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785972 Affx-122950890 AX-385273008 1 29190865 CTGAATGTATCTGGTTGCAAAGGAATAAAGGCATA[C/T]ATTCACATAGTTTCTATAACATAAAATCATCCATC Y 2 1 2 1 101000 f 74 goat snp52899-scaffold794-345235 1 29077702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777850 Affx-122970585 AX-385264967 1 29220763 TGTCCTGACCCTCTTATTTATCTCCTTTAAAAATG[C/T]AGTAAATCACAACTGCAGTTCCTTCCATCTCACCA Y 2 1 2 1 201000 f 74 goat snp52898-scaffold794-315337 1 29107970 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431528 Affx-122936223 AX-123301869 1 29264107 AGGGTGACAAATTCCATCACCTTTCAACCCATACC[A/G]CAACATATTCACAGGTCCCAGTGATAGTGGACATT R 2 1 2 1 101000 f 74 goat snp52897-scaffold794-271993 1 29151218 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794805 Affx-122960958 AX-385281765 1 29296737 ACATGTTGGAAAAGAGTTGAAAATCACTCTAGAAA[C/T]GGCCAAGATTGTTGTAAAGGGATTTTTAAAAGCAA Y 2 1 2 1 101000 r 74 goat snp52896-scaffold794-239363 1 29182861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778578 Affx-122944052 AX-385265690 1 29329957 GGGAGTGTGAAGGTAGTTTCATGGCCATAAAAGGG[C/T]ATCATTAATCATAATGATATGGTTACAGGATGAGT Y 2 1 2 1 202000 r 74 goat snp52895-scaffold794-206143 1 29215809 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444215 Affx-122927246 AX-123314552 1 29376251 CCAACACCTATTTATAATAAAAACTCTTAGTAAAC[G/T]AGAAATAGAGAGGAACTTTTGCAACTTGTTAAAGA K 2 1 2 1 103000 r 74 goat snp52894-scaffold794-159849 1 29262181 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776801 Affx-122924633 AX-385263925 1 29419176 ATGGATCACCTTCATTTATCCACTTAATTGTGGAT[A/G]TTCTTGGCCTTGAGCTTGACTGGGGCATTGCTATT R 2 1 2 1 102000 r 74 goat snp52893-scaffold794-116924 1 29306575 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405869 Affx-122955847 AX-123276221 1 29481587 CAATTTTATATCTTTCTTTTTACTCTCTACCTCTT[A/C]TTTATTTTGCATTAAGTGAAGGGTGCTGAAGTATT M 2 1 2 1 103000 r 74 goat snp52892-scaffold794-54513 1 29369334 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420793 Affx-122944691 AX-123291140 1 29513063 CCATATGACCCTCTCTACACCATGGGAATTAGATT[A/C]TTCAAGGAAAACAGCAGAACTCTGCTTCTGTTCCT M 2 1 2 1 101000 f 74 goat snp52891-scaffold794-23037 1 29400936 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272479 Affx-1111832853 AX-519546201 1 29530756 CACCTGGGACATTTGTCTTACAGCAGCAGAGAACT[A/G]TATTATGCCAACAACCTAAACAAGACTGAAAGTGA R 2 1 2 1 101000 f 74 goat 1_29530756_AF-PAKI 1 29530756 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445293 Affx-122925451 AX-123315630 1 29559298 GAGAAATGTTTGCTCCCAGAATTTCCCACAGTGGA[A/G]TGGCATAGGAGCAGGAGAATATGCATAGCTAAGAG R 2 1 2 1 101000 r 74 goat snp52334-scaffold778-553965 1 29447533 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432750 Affx-122935447 AX-123303091 1 29621257 GCCTTTTCCTAAATCAGCACCTGGGGTTAACGATT[A/G]CAATTCATGGGGGTTTAGTCACGAAGTCCCGTTCA R 2 1 2 1 201000 f 74 goat snp52333-scaffold778-492006 1 29510924 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447627 Affx-122923985 AX-123317963 1 29653611 AGCAGCAGGCAACCAGGGAAAGCACTTGTCATGGA[A/G]ATGGCAGAGGCAGAAGAGAAGGAGCAAAACATGAA R 2 1 2 1 201000 f 74 goat snp52332-scaffold778-459652 1 29543192 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443844 Affx-122927529 AX-123314181 1 29699022 AAGCAAATAGGCTTGTTTCACATAAAAATGAAAGG[C/T]GTATCAGTCTCCTATTTGTGAAATGACTTTGCATG Y 2 1 2 1 101000 r 74 goat snp52331-scaffold778-414241 1 29589044 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432894 Affx-122935332 AX-123303235 1 29751706 AATCAACGTAGAAACATTTTTCTTCCTCAGGCAAG[C/T]TGAATCTGACAGCAGTATAAAGCTTTTACAAAGGA Y 2 1 2 1 201000 r 74 goat snp52330-scaffold778-361557 1 29641780 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785610 Affx-122944572 AX-385272653 1 29810851 CACTTAATCCAAACCCTTATCTAAAATATAGTGGA[C/T]GATTATTTCACTAATAAAATCATTCAGTTATCTTG Y 2 1 2 1 201000 r 74 goat snp52329-scaffold778-302412 1 29701218 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800636 Affx-122941575 AX-385287555 1 29949507 TAATTTTGATATTCAAAGTTCCCCAACTGTTAATA[G/T]AATTATAATCGATGGGAAAAGATAATAAAAAGAAA K 2 1 2 1 102000 f 74 goat snp52326-scaffold778-163756 1 29842616 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417141 Affx-122947356 AX-123287489 1 29979019 GAAGACAGCTTGGTTTTCATCCAAGTGTTATTTTT[A/G]CAATGTTTGTTTACTTCTTAAAGCACAGCAGACTG R 2 1 2 1 101000 r 74 goat snp52325-scaffold778-134244 1 29872322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799987 Affx-122923417 AX-385286911 1 30032311 TCCTTTTAATCAAAGTATGCTCAAAGCATATATCC[A/G]TTAAAAGAGAACAGGAAAAACTCTCTGGTATAAAT R 2 1 2 1 103000 r 74 goat snp52324-scaffold778-80952 1 29917051 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788401 Affx-122951495 AX-385275419 1 30061645 TTAGAAATCTCTTATAATCAATTCTACATCTGTCT[A/G]TTAGAAGCAACAACCATCATCCTTTGAACTGTTTA R 2 1 2 1 101000 r 74 goat snp52323-scaffold778-51618 1 29946801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402651 Affx-122958381 AX-123273004 1 30106429 AATCTTCTGCATGCCTTTAGAAAGAGAATTAAAGG[C/T]TACCTAACTCACACCATTTTTACCAATGACATAAT Y 2 1 2 1 101000 r 74 goat snp52322-scaffold778-6834 1 29992398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783409 Affx-122924894 AX-385270472 1 30127029 TCCTCAAATGCTTTGATTTGTTAGAATGATAGCAG[A/C]TGTTCTGTTGAGAAAATCCCTGCAGTTTTGTTTCT M 2 1 2 1 101000 r 74 goat snp43727-scaffold586-1168057 1 30017075 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427363 Affx-122940100 AX-123297706 1 30172903 AAAAGTAGGAACCAGATGCCAAAGTCTGAATGTGC[A/G]TTCTATTCAAAGCATTGGGGCCCGTGGCTAACTCC R 2 1 2 1 201000 f 74 goat snp43726-scaffold586-1122183 1 30063468 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437564 Affx-122931887 AX-123307902 1 30206773 GTATCCTAATGATGCAAGCTTGTGCTCCCTAGAAA[C/T]GCAGAATGGAAGGTAAAATTTGATTATAAAATGAG Y 2 1 2 1 101000 f 74 goat snp43725-scaffold586-1088313 1 30097186 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770510 Affx-122965263 AX-385257675 1 30259548 AACCTCAAACTTCTTTCTCTCTTCTACACATAGTA[C/T]GACTATATATTTTTCTCCAAGCTAAAACATTTTAA Y 2 1 2 1 101000 f 74 goat snp43724-scaffold586-1035538 1 30150036 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768515 Affx-122964753 AX-385255695 1 30293371 TCAGCAGAGCTAAAGTCTTAAATGAGAATCCCAGT[C/T]ATTTTATTTGGTTCATAGAGACCTGATGATGACCT Y 2 1 2 1 101000 f 74 goat snp43723-scaffold586-1001715 1 30183991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419458 Affx-122945488 AX-123289806 1 30347541 TGCTATATCCCTTCATTCTTTAACATTTATGGATT[A/G]ACTTATCCTTCTCACTAGTTAGATTTTAGTAATAT R 2 1 2 1 201000 r 74 goat snp43722-scaffold586-947545 1 30238201 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794264 Affx-122943945 AX-385281229 1 30381955 CATGCCACTGAATGTTGTTCAAAAGTGGGTTCCTG[C/T]GGATCTTTCAATTGCTCAGTACAAAAGAACATGTT Y 2 1 2 1 101000 f 74 goat snp43721-scaffold586-913131 1 30272666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424444 Affx-122941789 AX-123294790 1 30433216 TTAAAGTAAAGCTAACAATGTTAAAAATGAGAATG[A/C]TCTTCCTAACCTGTACTGAAGAATAAATGAAATAT M 2 1 2 1 101000 r 74 goat snp43720-scaffold586-861870 1 30325096 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792026 Affx-122919704 AX-385279014 1 30471395 CCAGTGTGAATTTGTAGCACAAATGGAAACAAACT[A/G]TAATTGTTTTAAGCTCTATAGCTATGAAGCTATTT R 2 1 2 1 101000 f 74 goat snp43719-scaffold586-823691 1 30364149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394478 Affx-122964566 AX-123264833 1 30524748 ATACCGTTTCCTTGACTTCACATACATGCAGAAAA[G/T]ATAAATATATCAGAAAAAAACGAGAGAATAGAAGC K 2 1 2 1 303000 r 74 goat snp43718-scaffold586-770338 1 30418441 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424448 Affx-122941786 AX-123294794 1 30554005 GGTTGTAGTTTTTCCCTTCAGTACTTTTTAAACAT[A/G]TCCTGTCTTTCTCCTCTGGCCTGCAGAGTTTCTGC R 2 1 2 1 201000 f 74 goat snp43717-scaffold586-741081 1 30447867 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410018 Affx-122953257 AX-123280368 1 30584876 CAGGTGGACCTATATAAATCCAAAAAGGTTAATAG[C/T]ATAAATAAACACTATGTGTTTTATAGGCTGTTACA Y 2 1 2 1 101000 f 74 goat snp43716-scaffold586-710210 1 30478942 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802852 Affx-122925542 AX-385289750 1 30624582 TTACTCTGATGTAGACATCTTCTAAGAGCTTATGA[C/T]AATGAAGTCTCAGTTCTTATGAATTTTCCATTTTA Y 2 1 2 1 101000 f 74 goat snp43715-scaffold586-670504 1 30518648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786972 Affx-122922120 AX-385274001 1 30653276 GACTCTGAGAAACATTAGGAGGAGACATTTGGCAA[A/C]ATTTGCCATCAGGAAGACAAGGTAGAAAATAAATG M 2 1 2 1 101000 f 74 goat snp43714-scaffold586-641810 1 30547331 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790818 Affx-122921409 AX-385277818 1 30690969 GCTTGTGAAAACAAGTAATACTTTAAGAATCAAGG[A/C]GTGTTCTGTAAATATCTTTTTTCCTCCATCCACCA M 2 1 2 1 101000 r 74 goat snp43713-scaffold586-604117 1 30582775 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782941 Affx-122970302 AX-385270011 1 30762335 TGCTGGTCATATTTTTTGCAGATAAATGCAATAAT[A/C]TTTTCCAAGAATTGGGCAGTAAATAAAAGAGGTTC M 2 1 2 1 102000 f 74 goat snp43712-scaffold586-532751 1 30654781 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414502 Affx-122949535 AX-123284851 1 30796428 TGTGGATGCATTTGTGTGTGGAACATTCAAAGGGG[C/T]GCGAGGAAACTCTCTGATGTGATGGAGTTGTTTTA Y 2 1 2 1 101000 f 74 goat snp43711-scaffold586-498658 1 30689303 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431357 Affx-122937044 AX-123301698 1 30825755 TTCTACTTCCAGGCCATCTTCCCTGGTGCCTCAGA[C/T]GGTTAAAAATCTGCCTGCAATGAAAGAGACACAGG Y 2 1 2 1 103000 f 74 goat snp43710-scaffold586-469331 1 30719350 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427903 Affx-122939682 AX-123298246 1 30901588 TCACTAGCCAGCACGCTGAGCGCAGGTGGCTGCGA[A/G]CCAGCACGCTGAGCATGCCTGAGAGGAGATACCCC R 2 1 2 1 303000 r 74 goat snp43709-scaffold586-393498 1 30795267 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275399 Affx-1111834774 AX-519548972 1 30939116 GCCAACCTGCTTTTTAAAATTGACTGTTGGTATGA[A/G]TAATCTTTCACCTCATCAGATATTTTGGTCACTGC R 2 1 2 1 201000 r 74 goat GoatD01.052322 1 30939116 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38453543 Affx-122919787 AX-123323876 1 30958182 CAAACTCAATATTACCATTTTGTACTGACTTTCTC[G/T]CCATCTCTGTTTTCTTCCTTTTCACTGCATCTCTG K 2 1 2 1 201000 f 74 goat snp43708-scaffold586-336904 1 30852766 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419737 Affx-122945891 AX-123290085 1 31009965 TCACGTCTGAGGATCTTATCTAAACTGTTGAGAAG[A/G]TTCTTGTCTGCCGGTCCTAGGTATCAGTTCTCTTG R 2 1 2 1 101000 f 74 goat snp43707-scaffold586-285121 1 30904697 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436179 Affx-122932611 AX-123306518 1 31045734 TTCACTATCTCCCTGAGTTTGCTCACATTCATGTC[G/T]GTTGAATCTGTGATCCCGTTCAGTCTTCTCATCCT K 2 1 2 1 201000 r 74 goat snp43706-scaffold586-249352 1 30941455 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777559 Affx-122951796 AX-385264678 1 31076048 AATTTCTATTCTATATCCATATTTCAAAGGGGAGG[A/C]TAATCCAAACTATATAATGTTAATTCATCTTCTTT M 2 1 2 1 101000 f 74 goat snp43705-scaffold586-219038 1 30971355 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435144 Affx-122933675 AX-123305484 1 31142700 TGAGTTCAGACACATGAACAATCCAAGAGGTCTCA[A/G]AATTATCTTGCTTTCACAAAGCTATGGCCTTGGAA R 2 1 2 1 101000 r 74 goat snp43704-scaffold586-152386 1 31039453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383338 Affx-122972680 AX-123253696 1 31207931 TCATAGACATACTTTTCAAAGAAGTCAGCAACAGG[C/T]AAGGGAAGAAAACTGTAGAGGTTTAATATTTTGGG Y 2 1 2 1 202000 f 74 goat snp43703-scaffold586-87155 1 31104168 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393407 Affx-122965887 AX-123263763 1 31246803 AAGGTACTATAAACTTCAAGGTAAAAAGGAAGAAA[G/T]AGAGCTTATGCAAGAAGTAGGGGCACCAAAACTTC K 2 1 2 1 201000 f 74 goat snp43702-scaffold586-48283 NW_017216825.1 5106 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400479 Affx-122961296 AX-123270834 1 31290981 AAACTCTTGGTAATTTGGTAGAGGGCTCAGTTTGT[C/T]AATCATAATTCAATTAGAAATTTTTTAGAAGATAC Y 2 1 2 1 101000 f 74 goat snp43701-scaffold586-4105 1 31190808 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399771 Affx-122960306 AX-123270126 1 31300494 CTTGGAATGCTGTTGCTTCCCTTGGACTATCTATC[A/G]CAGGATATCGGCATGACTCATTTCTCCACCACCTT R 2 1 2 1 101000 r 74 goat snp39621-scaffold504-1771923 1 31200246 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452440 Affx-122920573 AX-123322773 1 31372611 ATTTACTCCAAAACATATCAAAATTACAAGTACAT[A/G]TAAAGCAACTCTTGCTGAGAATGACCTGAAGGCTA R 2 1 2 1 101000 r 74 goat snp39623-scaffold504-1844040 1 31273379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437575 Affx-122931878 AX-123307913 1 31406776 ATAAAATGAAGGGCCCCATGACTTGGCCTTGCTTG[C/T]AATGCCAAACTCAGAGCCTATGTCACATCTCTCTG Y 2 1 2 1 201000 r 74 goat snp39624-scaffold504-1878205 1 31308155 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392118 Affx-122966346 AX-123262475 1 31438929 ACATCATTGGGTGTAAAAGTAGTGGTAGATGACAT[A/G]GGTGTTTTTAAATGACTTTTTACTTTTTATATAAA R 2 1 2 1 101000 f 74 goat snp39625-scaffold504-1910358 1 31340588 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770969 Affx-122976126 AX-385258132 1 31468932 GTAGGATACAGTAAAAATGGCAGTTGAAGGCAACT[A/C]AGAATTGGCCAGAGATGATCATGTAGGCTCAGTGT M 2 1 2 1 101000 r 74 goat snp39626-scaffold504-1940361 1 31370413 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439638 Affx-122930615 AX-123309975 1 31505181 AGCAGCAAAAATATGGAATCTCACAGATCTCCATC[A/G]TCCCTTCTCCTATTGCATGAATATCTCCCCCTAAG R 2 1 2 1 101000 f 74 goat snp39627-scaffold504-1976610 1 31407403 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787354 Affx-122959444 AX-385274379 1 31572944 AAACCAGAATGCAATGGGCATTACAGGGAATTCAC[G/T]AAGAATTTGTAAATGCAGAAAGAAACCTCACTCCC K 2 1 2 1 201000 r 74 goat snp39628-scaffold504-2044373 1 31475731 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443046 Affx-122928146 AX-123313383 1 31650404 GAGAATTTCCTGCAAGTTGTAGGGACTTCTTACAA[C/T]GGTAATGGAGTTGGTGATAAGAATTGAGTATTTAA Y 2 1 2 1 101000 r 74 goat snp39629-scaffold504-2121833 1 31554758 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787942 Affx-122977847 AX-385274963 1 31686810 TTGCCTATCATGGACTCTGTGTACATGGAACAAGG[C/T]ATATTTTGTAGTAATAATTTTGTGTCTCTCTTTTC Y 2 1 2 1 101000 f 74 goat snp39630-scaffold504-2158239 1 31591091 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378367 Affx-122976820 AX-123248726 1 31735067 TTTTCCTTCACAGCAACCTTGATAGATTGACCTTA[G/T]GCCAAATTCTAGCCATTGCTCACCAGTATTATTTT K 2 1 2 1 101000 f 74 goat snp39631-scaffold504-2206496 1 31639443 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320791658 Affx-122942323 AX-385278649 1 31792497 TTAAATCTGCCTTATATTTCATCTTTTTGCATGCT[A/C]TTTAATCTCTAAATTTTTATCAGGGTGTAATTTTA M 2 1 2 1 102000 f 74 goat snp39632-scaffold504-2263926 1 31695876 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446053 Affx-122925834 AX-123316390 1 31844300 CAGTGGTTGCATGTTGACTAGTGTCTTAAAAAATG[C/T]ATATACATAGAAGAAAGGAGAGTTTTTCTATATTC Y 2 1 2 1 101000 f 74 goat snp39633-scaffold504-2315729 1 31747777 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782581 Affx-122960165 AX-385269655 1 31877341 ATCTCTAAGCCAAACTAGGATTTATCTTTTTGAGC[A/G]TGGTAAATTTGAAAGTCAATGAATAAGCTAAATAT R 2 1 2 1 101000 f 74 goat snp39634-scaffold504-2348770 1 31780687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422103 Affx-122943572 AX-123292450 1 31989669 TGGTAAGACTGTAACAAAAGGATAGCAATACTGGT[A/G]GTATTACTTAGATAAGACTTGCCATAAGGAACCTA R 2 1 2 1 101000 r 74 goat snp39636-scaffold504-2461098 1 31891409 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378873 Affx-122976510 AX-123249232 1 32029005 TGTTCAAACAAAATGAAAATAATTTTCTTCTGTTG[C/T]ACACTGAACAGTTGTCTTCTGAATTTTCTCTCATG Y 2 1 2 1 103000 r 74 goat snp39637-scaffold504-2500434 1 31930942 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272481 Affx-1111832854 AX-519546203 1 32052342 TGGTAATCTTATCCAAATCAGCCTTACAAAAATAC[A/C]AGAATAATATTTGACCAGATATTTGGGCATTACAT M 2 1 2 1 201000 f 74 goat 1_32052342_AF-PAKI 1 32052342 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378404 Affx-122976791 AX-123248763 1 32105813 AATCTTAGTTTTCTGAATGTTGAGCAGAAAGCTCA[G/T]CATTCAGATACTTGGTATTTTTCACATGACACAAA K 2 1 2 1 201000 r 74 goat snp39638-scaffold504-2577242 1 32007183 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793173 Affx-122977795 AX-385280151 1 32168715 TTTTCAACAAACGTACTTGAATAGAAGAGAACTAT[A/G]CTTCAGGCAAAATATCATAGCAATCAAAATCTTTG R 2 1 2 1 101000 f 74 goat snp39639-scaffold504-2640144 1 32070418 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414976 Affx-122949060 AX-123285325 1 32203281 TTCAGCCTTTTCTGAGTGACCTCTGTGATCCTGTT[A/G]GTTCCACTCACAGCACACAGAATTCTGCAAGTATC R 2 1 2 1 102000 f 74 goat snp39640-scaffold504-2674710 1 32104190 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453570 Affx-122919767 AX-123323903 1 32247874 CCCTAGCCTGACAATGTTTTCTCCTTGTTGATGAT[A/C]GGTAAATAACTTGGCTTCCCTGGTGACTCAGATGG M 2 1 2 1 101000 f 74 goat snp39641-scaffold504-2719303 1 32149008 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375375 Affx-122979225 AX-123245734 1 32284750 TTATCATAGTTGATTTAAGGATAATCTAATCCCCC[A/G]CCCTCATTTTCTTTCCTAGTTACATTTTTGGTGTC R 2 1 2 1 101000 r 74 goat snp39642-scaffold504-2756179 1 32185936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788909 Affx-122954246 AX-385275924 1 32317187 TCCCAGGTCAGGAGCTCTTCAGTCATCTTTAAACA[G/T]CATGGCAAAAGTATTCTGAGTATCCCATTTAAGAT K 2 1 2 1 101000 f 74 goat snp39643-scaffold504-2788616 1 32218548 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768585 Affx-122969662 AX-385255765 1 32371900 ATATCATAAATCAGTTTGGATTGGAAATATTTACA[C/T]GTCTCTATTTTCATGTCTGTCTTATAATATGTAAC Y 2 1 2 1 101000 r 74 goat snp39644-scaffold504-2843329 1 32273239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398866 Affx-122961047 AX-123269221 1 32400762 ATGCATTCATTGTTTAGCATAATTCTAAATCGTTG[C/T]AGAATTTTAATAATCACTAGTTTTCTTATTAATTT Y 2 1 2 1 101000 f 74 goat snp39645-scaffold504-2872191 1 32302098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781136 Affx-122935655 AX-385268221 1 32441442 TAATATGTTACTAGAAATGTAAAATAATAGAGATC[A/G]TAGAATACCACAAGTTATTCTGTGATTAGGGAGAT R 2 1 2 1 201000 f 74 goat snp39646-scaffold504-2912871 1 32341875 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448971 Affx-122923123 AX-123319306 1 32478836 ACTTTTAAGTAATAGCTAATTAATTAGAGTTGATC[A/G]TGTGAAGTTATGAAGGCAACGCCAAAGAAAGCTCA R 2 1 2 1 201000 f 74 goat snp39647-scaffold504-2950265 1 32380002 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427258 Affx-122939550 AX-123297601 1 32571782 TACTGCCCAGTTACACATGAAACCCAGTTACAAGA[A/G]GCCTTATTCCCTGGTGGCTCAGCAGTAAAATACCT R 2 1 2 1 101000 f 74 goat snp39649-scaffold504-3043211 1 32474058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787598 Affx-122964789 AX-385274622 1 32607163 TATATTAAGAAGCTCCACTTTGCAATCTGAATTGC[A/G]TAGATCAAATCCTGGTTTTTCAACTTACCTGATTT R 2 1 2 1 201000 f 74 goat snp39650-scaffold504-3078592 1 32510721 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419758 Affx-122945876 AX-123290106 1 32648201 GAAATTTTTCCCAGCTGTGTCCTTAAAAGATGCCT[A/G]CTTCTTCTCTTCCTTCTTTTTTAATTCATTTTATC R 2 1 2 1 103000 f 74 goat snp39651-scaffold504-3119630 1 32551520 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396927 Affx-122963197 AX-123267282 1 32701218 TATATAATGTGGTCACGAACTTCTGTGCTTGTGTC[A/G]TTTAGGTCTGGAAAGAAATTTTCCCCTTCAGGCTC R 2 1 2 1 101000 r 74 goat snp39652-scaffold504-3172647 1 32605549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441542 Affx-122928704 AX-123311879 1 32745517 ACCAGGGAACCCCCTGAAGGTGTTTTAAGTTCAGG[C/T]ATACCATCAAGAGCATTAAGGATGACTGAATCTAT Y 2 1 2 1 101000 r 74 goat snp39653-scaffold504-3216946 1 32649975 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377442 Affx-122977532 AX-123247801 1 32795978 ATTAAATTAGTTAGTGAATTAGTCAGCTTCTCCTA[A/G]TTTCTTACCATTTTATTTGTGTTTTAGATAAATAT R 2 1 2 1 101000 f 74 goat snp39654-scaffold504-3267407 1 32700396 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772166 Affx-122942405 AX-385259321 1 32854399 ACAAAAACCCAATTATTTTGAGGGATTATGTAAAT[A/G]TTCAGTGGAAAACTCCAACACCAAAGAATCCTCTC R 2 1 2 1 101000 r 74 goat snp39655-scaffold504-3325828 1 32759036 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798863 Affx-122961313 AX-385285793 1 32904812 CATGTTTGGCCATTAAATATAATCCTATTAAGTGT[A/G]TTCCCAAAATATTGCTGCTTGAAAGATCTCCCTTT R 2 1 2 1 101000 r 74 goat snp39656-scaffold504-3376241 1 32809892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802266 Affx-122972284 AX-385289170 1 32949446 CAACAAAATATGTAAAAACTTTCCGAAGTTTGTAC[A/G]CATGTTTCAGATTGTTCTTTGGATTTGTTGTTCGG R 2 1 2 1 101000 r 74 goat snp39657-scaffold504-3420875 1 32854543 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415223 Affx-122948968 AX-123285572 1 32992808 AACATACTGATAAACTTTAATTAATAATTGTATGG[C/T]AGTTTTCCGCTTTGAGAGGGATTTTCATAATGTGA Y 2 1 2 1 101000 r 74 goat snp39658-scaffold504-3464237 1 32898402 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771161 Affx-122972674 AX-385258321 1 33047065 TTTCTGGACACTGAGCATAACCTTCTTGCTTTCAA[A/G]CAAGAGTTTTCTCAGCAGCAAGTGCTCTGTGCTTA R 2 1 2 1 102000 r 74 goat snp39659-scaffold504-3518494 1 32953856 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405500 Affx-122956005 AX-123275852 1 33138232 CTTTGTAAACTCTACAATAAGAAGTCACTTCATCA[C/T]ATTACCTTTCAAATTTCTCTTCAAAGCAGGTGAAA Y 2 1 2 1 201000 f 74 goat snp39661-scaffold504-3609661 1 33046832 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777111 Affx-122968383 AX-385264234 1 33170352 TATTAATACAGTGTTGAACTCTTGCCAAGTTCTTC[A/G]TTCATTTTAAATATCACTAGAGTTGTTTTTAGTCA R 2 1 2 1 101000 f 74 goat snp39662-scaffold504-3641781 1 33078697 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449881 Affx-122922351 AX-123320216 1 33214499 TGATTTTTCTAAGTTAGATTTTTTTCCTCTCCTGA[G/T]CTCTTCTAGCCCTGCACATGTCTATATTTTAGCAC K 2 1 2 1 101000 r 74 goat snp33078-scaffold385-4043804 1 33122610 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796122 Affx-122973958 AX-385283073 1 33244710 GTAGTTCTGCAAATTCAAATTGTCAATACTTAGCG[A/C]GACTGCTGAGCATAGCATCTTTCACCCTATATATA M 2 1 2 1 101000 r 74 goat snp33077-scaffold385-4013593 1 33152870 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404933 Affx-122956435 AX-123275285 1 33277508 AGTGTGCAGCACTGAATAACAAACAATGACTGTTA[C/T]GGGAATTATAGTCTGAACCTTTATTAAGCATTCTT Y 2 1 2 1 101000 r 74 goat snp33076-scaffold385-3980795 1 33186052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785477 Affx-122975112 AX-385272522 1 33323047 ACACAGAATATAGAGTGGGATAAAATTAATGATTC[C/T]AAAGGAAAATGTTTTACTTTCCAGAATGTAAATGA Y 2 1 2 1 101000 r 74 goat snp33075-scaffold385-3935256 1 33232874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775475 Affx-122941155 AX-385262606 1 33367693 GTCTCCCACCTTTTACCCTTCCAACGATTTCTTCA[C/T]GGACTTCCCAAATTCTGCACTCTCTCTTTTCCTTC Y 2 1 2 1 101000 f 74 goat snp33074-scaffold385-3890610 1 33279852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408471 Affx-122954427 AX-123278822 1 33411509 TCCAATCTTTTTATTTAAATGCCTAGTTTATTCCT[A/G]TGTAGAAGTCAGAGGACTTCTTATTCCATAAATTG R 2 1 2 1 101000 r 74 goat snp33073-scaffold385-3846794 1 33323465 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445465 Affx-122925216 AX-123315802 1 33441438 CTTTCACTTAGCTCTTATATTTATCATATAAATTC[A/G]TAAATTATCATTCTGCTCTTTACCTGTCATCTCTG R 2 1 2 1 102000 r 74 goat snp33072-scaffold385-3816865 1 33353498 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444213 Affx-122927247 AX-123314550 1 33496096 CTCTCTTCCATTTATGAGCTTGAAACCTTAGTCAA[C/T]AGTTGTAGACAGACTTCCCAGTTAAATTGTTCCAC Y 2 1 2 1 101000 f 74 goat snp33071-scaffold385-3762207 1 33409174 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781335 Affx-122925732 AX-385268420 1 33556765 GGGAAGCCTCTTTGTGTAGTATGCAGTGCTTGAGG[C/T]CTATTTCCATTCTGTGGCATGATTTTGGCTAAGGT Y 2 1 2 1 201000 f 74 goat snp33070-scaffold385-3701538 1 33470260 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428955 Affx-122938881 AX-123299297 1 33652553 ATTAACAGCTCTGCCATGTCTGGCTCTGGCACTTG[A/C]TCTGCCTCTTCAAATTGTGTTTATTACTTTTTTCA M 2 1 2 1 101000 f 74 goat snp33068-scaffold385-3605750 1 33568531 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786446 Affx-122924677 AX-385273480 1 33683921 TTTTGTAAAAGTAATTCTCTCATAGAATACTTTGG[A/C]GTGCTAATGCTAGAGAGAAAACACAGCGACCAGCA M 2 1 2 1 201000 r 74 goat snp33067-scaffold385-3574382 1 33600278 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453877 Affx-122919516 AX-123324210 1 33743729 CATACCTTGGACTTCTGCGGCTCCTCCCCAGGGGT[A/G]CAAAGCAATGATGTGAGAAATTGAGTTGAGGGAGT R 2 1 2 1 101000 r 74 goat snp33066-scaffold385-3514574 1 33660195 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440511 Affx-122929351 AX-123310848 1 33779278 TCATAAGTAGCAAGTTAGAGTGCACCTCTTTGAAG[C/T]AGATATTTTATCAGTTCAGTTCAGTTCAGAAGCTC Y 2 1 2 1 101000 f 74 goat snp33065-scaffold385-3479025 1 33695905 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797438 Affx-122949131 AX-385284377 1 33822290 GTTAAGTAGAAAGAAAAATATAGGTGGATGTATTC[A/G]CTTTGAAACTTGATGTTTTTTATCTGACTTGCATG R 2 1 2 1 201000 f 74 goat snp33064-scaffold385-3436013 1 33739319 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768632 Affx-122946982 AX-385255811 1 33867309 GTTTGGGGTTCCTTTGCCCTATCTTAATTATGGCT[A/G]TTTTATATTTGTCCACATCCCTAAAATAGATGAAT R 2 1 2 1 101000 f 74 goat snp33063-scaffold385-3390994 1 33784322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392479 Affx-122966147 AX-123262836 1 33920665 GGCCCAATGTAGTCACAAGGGTCTTTATAAGAGGA[C/T]GATGGAGACATCAGAGTCAGAGAAAGTGATGATGG Y 2 1 2 1 202000 r 74 goat snp33062-scaffold385-3337638 1 33838037 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439175 Affx-122931057 AX-123309512 1 33972323 AATATTGCTGGTGAAATAAGCATCGTTGTCACATA[A/G]GATAAACAGTGGTGTATGTATGTACATCTGAAGTA R 2 1 2 1 102000 f 74 goat snp33061-scaffold385-3285980 1 33890095 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389891 Affx-122968128 AX-123260248 1 34010730 ACACTTGAATCTCATTCTCATAGGCCCTATTTCCA[G/T]CTGGCTTTAGAAAGAAATCTCAAAACTGATAAATC K 2 1 2 1 101000 f 74 goat snp33060-scaffold385-3247573 1 33928646 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770941 Affx-122944838 AX-385258104 1 34086621 ATCCCCAGAGATGTTTTTTACCCATCCTTTTAGCT[A/G]TTTCAGAGGATTAAAGGAGCTAAACTTTTATTCAG R 2 1 2 1 101000 f 74 goat snp33058-scaffold385-3171682 1 34004534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415393 Affx-122948748 AX-123285742 1 34120799 ACCTATTATATATACATGCATGTATGATTATAAAC[C/T]ACATGCTGTGTGGGAGTGGTGTGTACAGAAATAAC Y 2 1 2 1 303000 f 74 goat snp33057-scaffold385-3137504 1 34039039 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408321 Affx-122953764 AX-123278672 1 34165403 TTTTCCATCCCCTTCCAAGAACAGAGCCCAGGGGG[G/T]GCTTCAAAGATGTGCAGCTTTCCTCCCACTTTCAA K 2 1 2 1 101000 r 74 goat snp33056-scaffold385-3092900 1 34083982 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793704 Affx-122969553 AX-385280676 1 34223245 GCAGAGGTTGAGATCATGGTTATATAAACCATGTG[C/T]GAGACTATTCCATTGCATAGTAAAGCAAAATTTGC Y 2 1 2 1 201000 r 74 goat snp33055-scaffold385-3035058 1 34138097 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799808 Affx-122920212 AX-385286734 1 34277586 AATGTGTATGGCTGCACATCATTGGTTTTATAGTC[A/G]CAAAGTGTTCTTGTGTTATTTGGAATATGTAACAG R 2 1 2 1 101000 f 74 goat snp33054-scaffold385-2980717 1 34193175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435157 Affx-122933665 AX-123305497 1 34328839 ACATTTACATAGGAAAACAGTCTACTTTGGAGGCC[A/G]TCTCTTCATTCTTGTCTTTTTTCTCTTTCCTTTTT R 2 1 2 1 101000 f 74 goat snp33053-scaffold385-2929464 1 34244474 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384704 Affx-122972109 AX-123255062 1 34394851 TAACTCCTCTCTCTTTTTATATGAATTTTAATATC[A/G]TCCACACTTTATTGATTTTTGCAGCAATGGCTTTG R 2 1 2 1 101000 r 74 goat snp33052-scaffold385-2863452 1 34310491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789302 Affx-122920767 AX-385276313 1 34428777 GCCAAGGTGTACCAATGCAAACATAAAAGGGAAAG[C/T]AGCAATACAAGTTGAGAATGGGTGATTCTGGTAAG Y 2 1 2 1 101000 f 74 goat snp33051-scaffold385-2829526 1 34344499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778171 Affx-122959189 AX-385265286 1 34470009 CTTCTTTTTCACCAGTATCTGTTTATCTCCTGATG[C/T]GAACTTTTCCCTTAGAGTTCTATTTTATTGTTGTC Y 2 1 2 1 101000 f 74 goat snp33050-scaffold385-2788294 1 34383535 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377661 Affx-122977852 AX-123248020 1 34542502 AAATGATAGGATTGTTTCAAGAGTCTCAACAAAAA[C/T]TAACAGGAATTTGGTGAGTTAATAGCACACATTAT Y 2 1 2 1 201000 f 74 goat snp33049-scaffold385-2715801 1 34456345 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272483 Affx-1111832855 AX-519546205 1 34568359 CAATGCAGGAGACACAGGTTTGATCTCAGGGTCAG[A/G]AAGATCCCCTGGAGGAAATGATAATCCATTCCAGT R 2 1 2 1 303000 f 74 goat 1_34568359_AF-PAKI 1 34568359 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320776955 Affx-122929705 AX-385264079 1 34574697 AAGAAAAAAAATCGAGGCAAATTTGATGCAGTCAA[C/T]GAAATCAGACTATGGGCAATTTCAAAGGGCATATT Y 2 1 2 1 101000 r 74 goat snp33048-scaffold385-2683606 1 34488831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379405 Affx-122976124 AX-123249763 1 34604390 AGGCCAACCAAGAGTGCATATTATAAACATTGACA[C/T]ATAAATACTTGAAATCAATGAAAATGACTGTAGAG Y 2 1 2 1 101000 f 74 goat snp33047-scaffold385-2653913 1 34519393 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769578 Affx-122969229 AX-385256748 1 34661964 ATGACAATTTTAGATATCCTGCATTTGAGATAATG[A/G]GGAGTCAAATGGAAAAAGCAGAACAGAATATTTAG R 2 1 2 1 101000 r 74 goat snp33046-scaffold385-2596339 1 34577468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432904 Affx-122935323 AX-123303245 1 34700536 AAAGATGGGTGTGCATCGCTGAGATGGTCTGGGAA[A/G]CCAGTGGGTGGCCAGATAGATCCTGGAGAGCCCAG R 2 1 2 1 101000 f 74 goat snp33045-scaffold385-2557767 1 34616605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399325 Affx-122961372 AX-123269680 1 34733894 CCAGTCTTGCTGCTGGGTGCATGATGCCTCTATAA[C/T]ACGCTCTGCAAAACAAACGCTGAAATGTTTGCACA Y 2 1 2 1 201000 f 74 goat snp33044-scaffold385-2524409 1 34649810 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790135 Affx-122960685 AX-385277140 1 34765898 TTTGACACAATGAAGTATTGTCAAGGTTGCAAATC[A/G]TTTGATCAATATCTTGTCAACACATACAAGCTAAA R 2 1 2 1 201000 r 74 goat snp33043-scaffold385-2492405 1 34681855 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768233 Affx-122920824 AX-385255414 1 34854285 ACCTACTGGTGCTAATGTTCAATATTTTCAAGTTG[C/T]ATTTCTTTGCTTCTTACTCAAATACTATGAAGACG Y 2 1 2 1 101000 f 74 goat snp33041-scaffold385-2404018 1 34771056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423387 Affx-122943130 AX-123293733 1 34922766 GCCCTAATACAGACAATTTGAATGCAGTATAACTA[C/T]GATTGACTAAAATACATCAAATAAGATTAAATCCA Y 2 1 2 1 101000 f 74 goat snp33040-scaffold385-2335537 1 34839863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379121 Affx-122976745 AX-123249480 1 34968008 ACTGAAGAAATGCTGGAGAGCGGAAGACACTAATG[A/C]CTAAACACAATGCGAGATCAGAAACAATATCCTGA M 2 1 2 1 101000 f 74 goat snp33039-scaffold385-2290295 1 34885351 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442480 Affx-122927932 AX-123312817 1 35013622 TAGGGAATTACCAGAGATAGTTTTACCTAATCTTG[C/T]GTCAAATCACTCTTGGGCTGGGTTAATATAGCAAA Y 2 1 2 1 101000 r 74 goat snp33038-scaffold385-2244681 1 34931170 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427352 Affx-122940108 AX-123297695 1 35102649 CTCTGCTTGCCTGGCGTTTCTTTTAAGACTATTTT[A/C]AATAACACCAGCATCTTAAAACAATTTTAAAAATT M 2 1 2 1 102000 f 74 goat snp33037-scaffold385-2155654 1 35020771 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398464 Affx-122961589 AX-123268819 1 35142195 CTGTGTATAAGAAAATATATATAATCATTCATTTG[A/G]TTGGAAACACCATGAAAATGTTTCCCATGGGTACT R 2 1 2 1 103000 r 74 goat snp33036-scaffold385-2116108 1 35059688 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764520 Affx-986698961 AX-385252190 1 35175132 TCGAGGGGTTCTTCCTTAATCAGGGGTCTAACTGC[A/G]TCTACTACATTGCACGTGGGTTCTTTACTGACTGA R 2 1 2 1 600010 f 74 goat 1_35175132 1 35175132 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 38431369 Affx-122937034 AX-123301710 1 35179576 GAGCCATGGTGGGTGACTATCTTTAAGTCTTCTCT[A/G]CTATCTTCAGAAGAGTATCAAGCATCATTTCTGTC R 2 1 2 1 101000 r 74 goat snp33035-scaffold385-2078727 1 35097123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419350 Affx-122945641 AX-123289698 1 35236784 GAAGTGACTGTCCATTGTAAGGCTATTAAACAGTA[C/T]AAGCATATGCTTAACTCAACTATAGGGAAACAACA Y 2 1 2 1 101000 f 74 goat snp33034-scaffold385-2021519 1 35154404 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378090 Affx-122977161 AX-123248449 1 35280244 TAAACATAAAAGGTACCTGAAAACTGAAACAGAGA[A/C]TATAACTCAAAGAGCTAGATCCTGAAGCTAGTGAA M 2 1 2 1 101000 r 74 goat snp33033-scaffold385-1978059 1 35198354 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409749 Affx-122953011 AX-123280100 1 35310183 CTAGCTTTTCTAGGTCCAGCTCAGATAAAAATATT[A/G]CTTTGATGTCTCAATTATTCCAATTTAAGTGGATT R 2 1 2 1 101000 r 74 goat snp33032-scaffold385-1948120 1 35228638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791754 Affx-122964808 AX-385278745 1 35369088 ACTAATAATAATAACTGAGAGCATTTACATTATTC[A/G]TCTTTCCTTTTTACAGTAACTTTTTAATGCTCTCC R 2 1 2 1 101000 r 74 goat snp33031-scaffold385-1889215 1 35288988 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775430 Affx-122924492 AX-385262561 1 35427159 TCTCTTAGGATACTTCTCTATTCATTTCTTTATTC[A/G]TTTAGCTATTTATGTGTAAATGAAAATCTAGTATG R 2 1 2 1 202000 f 74 goat snp33030-scaffold385-1831144 1 35347269 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442535 Affx-122928536 AX-123312872 1 35484937 AAAACAGCTCAACTGAAATGAACAAGATCAGGACT[A/G]CTATAAGAGGATGGTACCCAGCTCCCTGGGCACAC R 2 1 2 1 101000 f 74 goat snp33029-scaffold385-1773366 1 35405378 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384146 Affx-122972805 AX-123254504 1 35528794 TATGGTGAGTGAAGAAGCAAAAACATTTAGAGAAG[G/T]GTCACCCCGGTTCATTTTCTAGTAGCTGGTTGATA K 2 1 2 1 101000 r 74 goat snp33028-scaffold385-1729509 1 35449368 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774895 Affx-122974207 AX-385262029 1 35560005 AATCCTTTCAACACTTACGGATTGAGAACCTACTA[C/T]GAGTCAGGTACTTCCCTAAGTGCTAGGGATGTGTA Y 2 1 2 1 101000 r 74 goat snp33027-scaffold385-1698298 1 35480656 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408476 Affx-122954423 AX-123278827 1 35620318 CATTTTTTCAGTAAATAGTTTGGAGCAACACACCA[G/T]GTGATCTTTCAGTTTAGAGGGATTATCTCAACCTG K 2 1 2 1 101000 r 74 goat snp33026-scaffold385-1637985 1 35542059 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796692 Affx-122933036 AX-385283637 1 35665220 TGAAGTCAAGGATTTTTTGGTCTATTTAGGTTCAC[A/G]ATTTGCACAGAGGGCTGTATCTTTTCCCACGTCAC R 2 1 2 1 101000 r 74 goat snp33025-scaffold385-1593083 1 35586673 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768221 Affx-986698964 AX-385255406 1 35668607 CTGACCTGCATATAGGTTTCTCAAGAGGCAGGCAG[A/G]TCTTTTATAATGAGCATCTAATGAGACAGTAGCCA R 2 1 2 1 600010 r 74 goat 1_35668607 1 35668607 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 38394014 Affx-122965015 AX-123264369 1 35725684 CTACATTGTACAGTGATTTCTAAATTAAAATAAGC[A/G]TAGATTGATGTCTGCCCCTTGCCATTTAGTGTTGA R 2 1 2 1 101000 r 74 goat snp33024-scaffold385-1532619 1 35647014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447640 Affx-122923976 AX-123317976 1 35758508 TATACATACAACTACGGAAGTTTCTGGAGCTGGTT[A/C]TAAAATATTGTGTTAGACTTTATAAAGTATGCAGT M 2 1 2 1 102000 f 74 goat snp33023-scaffold385-1499795 1 35679903 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429161 Affx-122937979 AX-123299503 1 35787611 AGAGACATAAGGAAATGTGTCACTTTGTTAAATGA[C/T]GAATGACTATTATTGTGGCATTTTATTAATATTTA Y 2 1 2 1 101000 f 74 goat snp33022-scaffold385-1470692 1 35708926 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798742 Affx-122930341 AX-385285673 1 35824319 AACATAGTGATTAGGAATAATATCCACCTTATTCT[A/G]CTCAGTTCAAATTCTAGGTGGACTCCATGCTGCTT R 2 1 2 1 101000 r 74 goat snp33021-scaffold385-1433984 1 35745570 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426966 Affx-122940402 AX-123297311 1 35872468 ATCCTGCAGAAAGCTAAGGCTTTTCAACATATTTG[C/T]GGCTTCATTGCAGGAAGCAGACTGTTATTTGTTGA Y 2 1 2 1 101000 f 74 goat snp33020-scaffold385-1385835 1 35793670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788074 Affx-122941272 AX-385275094 1 35908486 TGTGTCCAGGAAAATGACTCTAGAGAACTAGCACC[A/G]TGTCAGCCAAGTGTATGCTAAAGGTCTCTTTCATA R 2 1 2 1 101000 f 74 goat snp33019-scaffold385-1349817 1 35829812 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770808 Affx-122944956 AX-385257972 1 35938663 AGTAGAAAAGAATCAAGGATTGTTTGTTTCACTCA[G/T]ATTTTGCAAATAACAGTCAAATTGTTATTGATCAA K 2 1 2 1 101000 f 74 goat snp33018-scaffold385-1319640 1 35860363 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770686 Affx-122972459 AX-385257850 1 35974730 CCCTAAGGGAAAATGGATTTGGGTGCTGAAGAAGA[C/T]GGAGATGACTAAGACATTTGCAAGACTGTATTCCC Y 2 1 2 1 101000 f 74 goat snp33017-scaffold385-1283573 1 35892630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377725 Affx-122977390 AX-123248084 1 36010079 GAACATCACTAGCAAAAAACAAACAAAACTGATGG[C/T]AATCAGTGAGCTACGAAGTTTGCAGAAATACTTGA Y 2 1 2 1 103000 r 74 goat snp33016-scaffold385-1248224 1 35928096 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411471 Affx-122951801 AX-123281821 1 36058743 AAGATTGAATGACTAGGACAAGAATAAAGAGCTAG[C/T]GGATAAAAGATATCTCCAGGTCAAGTTCATTAACT Y 2 1 2 1 101000 r 74 goat snp33015-scaffold385-1199560 1 35975222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415406 Affx-122948737 AX-123285755 1 36100519 GTGTCTGGAAACATAGCCAAATTCTTCACTGTAAA[C/T]GGGCACTTTTTGAAGTACACTCTCACAGACACTAA Y 2 1 2 1 101000 f 74 goat snp33014-scaffold385-1157784 1 36016892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802467 Affx-122925705 AX-385289371 1 36159580 TTTCTAATTCTGCTTAGAAAATCTGATTTCTGTTC[A/G]TCCAGTTTGTTTCTAAACTTTGCAAACTTTTTTAT R 2 1 2 1 201000 f 74 goat snp33013-scaffold385-1098723 1 36075408 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454262 Affx-122919645 AX-123324595 1 36196279 TTCCTGAATACAATTATTGCCATTTATACCTGTAA[C/T]ATTTCTCCTGTCTTCTTTTTTATTATAATTATCAA Y 2 1 2 1 101000 f 74 goat snp33012-scaffold385-1062024 1 36112237 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434227 Affx-122934840 AX-123304568 1 36243448 AATCATTTTTTGTTAATATTATAAATGGCTATGTA[C/T]ATGATACGTAAAGAAAAGACAAGACAGTCATCTAA Y 2 1 2 1 101000 r 74 goat snp33011-scaffold385-1014855 1 36159321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416396 Affx-122947859 AX-123286745 1 36281052 TCTGATCTGTTGAAACTTGCTTTCCTGTTCTTTGA[C/T]GACATTGCTAAAATATCTCATAGCTTCTTGTTCAC Y 2 1 2 1 201000 r 74 goat snp33010-scaffold385-977251 1 36196783 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395788 Affx-122963661 AX-123266143 1 36339852 GTGTACATTTTTTTCCCTTTCTGCAAGAATTTGTG[C/T]AAGACTAGAATTACTCAGTTGTGAAACAAGTGTAC Y 2 1 2 1 303000 r 74 goat snp33009-scaffold385-918451 1 36255924 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415479 Affx-122948707 AX-123285828 1 36383616 GGACCAGCCCAGCTTTAGGACTCTTGTTTCAACAA[A/G]TAGTTGGACTGAGTCTTCTTCTGCAGTCCAATGCT R 2 1 2 1 101000 r 74 goat snp33008-scaffold385-874687 1 36299605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425381 Affx-122941564 AX-123295727 1 36419846 AAATTCCCCAGAGGCTTCTAGTGAATCACCAAACC[C/T]GAGGATGAGAATCACCAAACCTGTGTAAGGGAGCC Y 2 1 2 1 202000 r 74 goat snp33007-scaffold385-838457 1 36335724 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415966 Affx-122948421 AX-123286315 1 36451947 CTAGAAATCTCTAATTTTATGATAATTCAGATGTC[A/G]TTATGCATTTGTTCCAGACCCAAAAGGTACTTTAA R 2 1 2 1 101000 r 74 goat snp33006-scaffold385-806356 1 36367854 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393212 Affx-122965497 AX-123263569 1 36486943 AAGCTCTAAATGGTCTGGAGTAATATTAGCATAAA[C/T]AGATGGCAATTTCAAAAACACCTACTCTTAACAAT Y 2 1 2 1 101000 f 74 goat snp33005-scaffold385-771360 1 36402633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426252 Affx-122940335 AX-123296598 1 36517028 TTATAGTTCGCAATGTTTTATCATATATTTTGTTA[C/T]ACAGTCCTCATAAGAATGCTATGCTATAGGGACAG Y 2 1 2 1 101000 r 74 goat snp33004-scaffold385-741275 1 36434010 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776315 Affx-122967986 AX-385263443 1 36567970 ATTAGTTAATATCTTGTTAACAAGGTATTTCTTTG[A/C]GCTGAAGGGATAAAATGAGTTTTATTTCCTTCAAG M 2 1 2 1 101000 r 74 goat snp33003-scaffold385-690333 1 36485405 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405293 Affx-122956849 AX-123275645 1 36600695 GAAGTGTAAATGTGAGAAGGCTTCCTTAGTAGCAG[A/G]TAAAGAAGTCCTTTGTTTCTTGCATGAACTTAAAG R 2 1 2 1 101000 f 74 goat snp33002-scaffold385-657608 1 36518594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443233 Affx-122927562 AX-123313570 1 36648141 ATCGTAACTTAAGAAAATGAAAGGATTACCATTCT[A/G]TTCCCAGAAGAAAATATATTAAAATAAGTAAATGT R 2 1 2 1 101000 f 74 goat snp33001-scaffold385-610162 1 36565845 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787823 Affx-122939435 AX-385274846 1 36733745 AATATTATATTGCTTTCAAGTTTGACTGGACAACT[A/G]TTGCACAAACCTTCTCATATTTAGCATTCATTTGT R 2 1 2 1 101000 f 74 goat snp33000-scaffold385-524558 1 36651757 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791085 Affx-122927991 AX-385278080 1 36785168 CTTATTTAAAAAGCATACTGAAACAGGAAAAAATA[C/T]ACCATATGGCTTATATCAGTAAATTACTAAATCAC Y 2 1 2 1 201000 f 74 goat snp32999-scaffold385-473135 1 36703248 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436109 Affx-122932663 AX-123306448 1 36827094 CTACCTGAAACTATATTTATGATGATTTTGTGAGG[A/G]AGAATTTAAATTTATTTTCCTAAGGTTAATTTTCA R 2 1 2 1 101000 f 74 goat snp32998-scaffold385-431209 1 36745589 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435756 Affx-122932884 AX-123306095 1 36888070 TGACACTATCTGTTTCAGGTTGAGGGACTCCTTGA[C/T]TCAGAGCTATAGCCATGTTGACTTTTGGCCAGAAT Y 2 1 2 1 101000 f 74 goat snp32997-scaffold385-370233 1 36806837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422994 Affx-122942988 AX-123293340 1 36923275 CTGTTTGTATTCTTTTCTTAACTTCTCTCCTTCAT[G/T]TTATATTTAAGGATTGCCAGTCAGGGGAACAGCCC K 2 1 2 1 202000 f 74 goat snp32996-scaffold385-335028 1 36842054 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425272 Affx-122940974 AX-123295618 1 36967672 GAATAGTGAACAAGTCACTATGGGATGGAATAAAA[C/T]GGTTTAGCCTGATGTTTTCTGCCACTTGTAGTATG Y 2 1 2 1 201000 f 74 goat snp32995-scaffold385-290631 1 36886485 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441992 Affx-122928432 AX-123312329 1 37009256 GGGTGATTGTGTTTCCTCTCTGGATGAATTAGAGT[A/G]GTATATTTGAGATTATATTTCATTAGTTTTATTGC R 2 1 2 1 101000 f 74 goat snp32994-scaffold385-249047 1 36928989 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410120 Affx-122952819 AX-123280470 1 37047090 CAGCAGGCACTGGTGTTATGCTGGCCTTGGTTTCC[A/G]GTAACACAGTGCCCTTTGCCTTGTCCTTGGTGGAT R 2 1 2 1 202000 r 74 goat snp32993-scaffold385-211213 1 36966695 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381351 Affx-122974413 AX-123251709 1 37083740 GTACTCTTATTGTGTAGGAAGCAAATACACAAATA[C/T]ACATATACATAAATGTATCTTTTTATTATGGAAAT Y 2 1 2 1 101000 f 74 goat snp32992-scaffold385-174563 1 37003110 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412878 Affx-122950429 AX-123283227 1 37124395 TGTGATCTCTGGCTGAATGCTGAATGACTGAGCTT[C/T]ACCAGGAAATGGGAAGAAATGGAATAAACAGAATT Y 2 1 2 1 101000 f 74 goat snp32991-scaffold385-133908 1 37043827 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463637633 Affx-1110082673 AX-515118707 1 37207420 TCCTGGCCTCTAATATTCTGTTATAATTTTCTTTT[C/T]CTGTCCTGTTATATATTTCTTTGTCTCCTTTGGAC Y 2 1 2 1 201000 r 74 goat 1_37207420_AF-PAKI 1 37207420 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789618 Affx-122974987 AX-385276627 1 37218918 TGGTGTCTTTCTGAAGGCATTCTGTGAGGAGTTCT[A/G]CTAAGGTAACATTTCATTGATTGAGGATAGTAGGG R 2 1 2 1 101000 f 74 goat snp32990-scaffold385-39385 1 37138655 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781011 Affx-122945462 AX-385268098 1 37286107 CACCTAAGAGTGATGTTTGAATGACACCTTTAGTC[A/G]TTCAGCCCACAGAGTCCTGCAACCCACTTAGTACA R 2 1 2 1 101000 f 74 goat snp3220-scaffold1097-27705 1 37206100 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277967 Affx-1111836183 AX-519551461 1 37291883 CACAAGCTCATAAGTATTTCCCATAGATATCTTTT[A/T]AAAAGAATTGAAGAAGATAAATGGATAGGGGTATT W 4 1 2 1 103000 f 74 goat Random2.2K-34 1 37291883 A T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779215 Affx-122934523 AX-385266319 1 37340764 AAGAAAATCAATCATTTGATGGATTTTGTTGAGTG[C/T]AATGCTAACATCCTTCATCAGGATTTACAGTAAAA Y 2 1 2 1 101000 r 74 goat snp3221-scaffold1097-82362 1 37262202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278845 Affx-1111836633 AX-519552316 1 37373686 AATTACTTGCTCAACCATTTACAACTGTTTTCTCA[A/G]GAGGTGGCCTTTTTGTCTCTCAAGGAAATGACAAA R 2 1 2 1 201000 f 74 goat Random2.2K_MT-180 1 37373686 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382810 Affx-122973563 AX-123253168 1 37382051 GCCAAATTACTATGTGGAACAGAGCCCTTCCCTCC[A/G]TCCTATTTCTAATTGAACTTAACATAGGTGAGAAG R 2 1 2 1 201000 r 74 goat snp3222-scaffold1097-123649 1 37303405 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773686 Affx-122935480 AX-385260826 1 37421025 TTTTTTGAATAATGTAGATGATAGGCCTCTGTCCT[C/T]CTTGGAAGTACCTGGGACACATTGAAATGTGATTT Y 2 1 2 1 101000 f 74 goat snp3223-scaffold1097-162623 1 37341709 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397268 Affx-122962346 AX-123267623 1 37449902 AGGACACCTCTTAGGTAGGAATATTTGCAAGAGCA[A/G]AATCTCCTCAAGCCATGCCAACAGTGCTTCTATGG R 2 1 2 1 201000 f 74 goat snp3224-scaffold1097-191500 1 37369256 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789034 Affx-122919458 AX-385276047 1 37506683 TTCATCTATAAACCATCAGAATTATTTTTAGGAAT[A/G]CATTTTATTTATAAGCCATTGGAACCATTTAAAAC R 2 1 2 1 101000 f 74 goat snp3225-scaffold1097-248281 1 37410487 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800064 Affx-122957697 AX-385286987 1 37537584 AGGTGCCTGTGTCATGCATGGTCAGGTCCGATAAC[A/G]ATATATTTCCTTGGTACTTAAAGAAACCAAATTCC R 2 1 2 1 101000 f 74 goat snp3226-scaffold1097-279182 1 37441520 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379377 Affx-122976145 AX-123249736 1 37596237 ATTTCTGTAATATCACAAGTTACTTCCTCTCCATA[C/T]GCCAATTTCTTACCTCAATTCTAATCACAGTAGAT Y 2 1 2 1 101000 f 74 goat snp3227-scaffold1097-337835 1 37500953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400406 Affx-122959993 AX-123270761 1 37628188 ATGAAGTGATGCCCTTGGGTCTTATCCAAGTTGCT[A/G]TTTACTTCTGTGATGGAAGGAATGGTGACCTATAG R 2 1 2 1 201000 r 74 goat snp3228-scaffold1097-369786 1 37532726 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794407 Affx-122946840 AX-385281370 1 37664341 TCAGATTCTGACTTAGCAGCTCTATCAAGACTGTG[C/T]GTTTGTTTCTTTGCAGCTCTACCAACTCACAATAA Y 2 1 2 1 101000 f 74 goat snp3229-scaffold1097-405939 1 37569352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442142 Affx-122928326 AX-123312479 1 37706073 AATCTAGTTGAAGATTAAGCAATCATTATTCACAT[A/G]TTTAAGGGAAATGGGAGCTCACAACTTAGTGAAGT R 2 1 2 1 101000 r 74 goat snp3230-scaffold1097-447671 1 37611484 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800414 Affx-122940884 AX-385287335 1 37741603 TTACTCTGTGTCTCTCTGGGAGGAAATGTAAATAT[C/T]TGATGTGAAAACACTCAACTGATAGATAAAATATG Y 2 1 2 1 101000 f 74 goat snp3231-scaffold1097-483201 1 37647463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393037 Affx-122965633 AX-123263394 1 37803036 CTCTTCCAAGAAATGATAAATATTTATGTTACCTT[A/G]TTGACAATTTTTTAGAACTTTCTTTTTTTAATCTG R 2 1 2 1 201000 r 74 goat snp3232-scaffold1097-544634 1 37710199 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792929 Affx-122978819 AX-385279907 1 37818983 TATCCTTCCACTCAGTCTAATCTAGATTTCACATC[A/G]CTACTTCCCAATCTCCTTAAGAGGCCTCTCACTAA R 2 1 2 1 101000 r 74 goat snp50712-scaffold731-186 1 37725969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390220 Affx-122967782 AX-123260577 1 37849595 TTTCTACTTGTCTTTTTTTAAGAAAGATATCTTGA[A/G]ACTCTTACCATTATGGTTGACTTTAGAATAATTCC R 2 1 2 1 101000 r 74 goat snp50713-scaffold731-30798 1 37757044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782847 Affx-122933809 AX-385269918 1 37878921 GAAAAATGAGCCAAACTTATGTGAAATTCTCATGG[C/T]AACTCTTTCCCATAACCAACTCATATTCACATAAA Y 2 1 2 1 101000 f 74 goat snp50714-scaffold731-60124 1 37786349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449404 Affx-122922700 AX-123319739 1 37921830 CTCACTGGAATTTCACTGTTGGAGTGTGAAAGAAG[A/C]GATATCAGGAAGGAGTAATGCTTATTTCATTCTAA M 2 1 2 1 101000 f 74 goat snp50715-scaffold731-103033 1 37827402 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786498 Affx-122928750 AX-385273532 1 37975749 GACTATTTATTTCTGTTAAACTCACATAAAACATG[C/T]ATTGAAATTGAGTTAAATACTCCCATTCTATAAAC Y 2 1 2 1 101000 f 74 goat snp50716-scaffold731-156952 1 37881615 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387584 Affx-122970265 AX-123257942 1 38005141 AAAGTTATATTGTCAAGTGTATTTCCCATTATAAA[C/T]AAGCAAAATACAAAATGTTCTGATAACTTGCAAAT Y 2 1 2 1 101000 f 74 goat snp50717-scaffold731-186344 1 37911682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410758 Affx-122952690 AX-123281108 1 38078729 TTAAAGTTCCAAGAGTAAGCAACAGAACATAGTAC[A/G]TTAATAACCTCTAGGATCCTTTCCTCTCAAGGCTG R 2 1 2 1 101000 r 74 goat snp50718-scaffold731-259932 1 37974563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788581 Affx-122921182 AX-385275598 1 38117143 AGGAAGCTGCATCCTGGGATAAGAAGAATAAAAGT[A/G]CTAGGTGATATTATCAGAGGCCAGAATTTAATACC R 2 1 2 1 101000 f 74 goat snp50719-scaffold731-298346 1 38013596 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386779 Affx-122970109 AX-123257137 1 38157991 GATTCATTCTAGCATGCTTTATAGCAGTTGCTGCC[A/G]TTTGATAAGTAACTCCATATGGACTGATGCTGAAG R 2 1 2 1 101000 r 74 goat snp50720-scaffold731-339194 1 38056256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436090 Affx-122932683 AX-123306429 1 38200476 TACCTTTCTTTGAAAGACACTTTCTAATTTGTTAG[C/T]GGGTGTTGAAGGAAACTGCTATTGCCACTGAAGGA Y 2 1 2 1 201000 f 74 goat snp50721-scaffold731-381679 1 38098862 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768873 Affx-122957803 AX-385256050 1 38251382 GTAAATTTCACACCTGTATATTTTCTCAGTGAGTT[A/G]TTAATATGTAAGGGAATGCTGGGATTTAGAACTAT R 2 1 2 1 101000 f 74 goat snp50722-scaffold731-432585 1 38152280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779168 Affx-122931979 AX-385266272 1 38282037 AAAACATCATGAGCTAATTGACACTTTTGAGAGAT[A/G]TTTTTTGCTCTAAAGCCTTTTCCCAGATTAATCAA R 2 1 2 1 101000 r 74 goat snp50723-scaffold731-463240 1 38183892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404165 Affx-122957072 AX-123274517 1 38314030 TTTCCTCTGAAATGCTAGCATTCTTCAAAGGGAAC[A/G]TATCTCTAGCTTTTAAAAATATCTGTGGAATATTT R 2 1 2 1 101000 f 74 goat snp50724-scaffold731-495233 1 38216497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277997 Affx-1111836198 AX-519551489 1 38364804 CGATTAAGAGAATATGAGCAAGCAAGCAGGCATAC[A/G]TATATGGTTTTATGAAGTCCAATCGCAATTCTGGT R 2 1 2 1 101000 f 74 goat Random2.2K-36 1 38364804 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786405 Affx-122919406 AX-385273439 1 38380679 CAAATATGAGAAAAAGAGAATATGAGTTTATACTT[A/G]TCTATGTTTTGTTATAATAAAACATAGCCATTGTC R 2 1 2 1 201000 f 74 goat snp50725-scaffold731-561882 1 38282655 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773401 Affx-122975521 AX-385260543 1 38441496 TGTTTGCTCTAAGAAGATAGTCTCTTAATATTCTT[A/G]TTAAGTATATTTTATTAGGTTGATAAGCCAAAATG R 2 1 2 1 102000 f 74 goat snp50726-scaffold731-622699 1 38343797 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408117 Affx-122954251 AX-123278468 1 38497738 GTCTGTTCTAGGTCCTTCAATAAAGCCAGTATCTA[A/C]AGTATATCTCAATATGTATTTTTCTATAGAGGTAT M 2 1 2 1 101000 f 74 goat snp50727-scaffold731-678941 1 38400618 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788196 Affx-122941044 AX-385275215 1 38544627 ATCACTCTAAATGATGAGGTTTTATTGGTGCTAAT[A/G]ATTCAGAAGATTAAATGACAGGAAGCATCTTAAAG R 2 1 2 1 101000 r 74 goat snp50728-scaffold731-725830 1 38447218 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797967 Affx-122922044 AX-385284903 1 38570266 ACATAATTTCCATTTCTAGTTATCTTTATTCCTTT[A/G]TGAAGCTGAATATTTCCATCTGGTATTTGTTTTTC R 2 1 2 1 101000 r 74 goat snp54661-scaffold835-1131537 1 38472544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802159 Affx-122955166 AX-385289063 1 38600702 TTTTCCCTCTAATAACTCCTGCTTATTATACTACT[A/G]TATATTCAGTGATTCCCTTTTCAAAATACTAAAAT R 2 1 2 1 201000 r 74 goat snp54660-scaffold835-1101101 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797027 Affx-122926338 AX-385283968 1 38646884 CAAAAAATGACCTGTTACTAGCCTCATGGCCGTCA[G/T]ATTATGTTACAGGCTAGACTGAATTCCTGCAGCTC K 2 1 2 1 201000 r 74 goat snp54659-scaffold835-1054919 1 38552209 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802265 Affx-122932565 AX-385289169 1 38682659 GTCTATAACTGAATACTATAAATCAATGAAAAAAG[C/T]ATAATCAATCTATGGGGAAAGTTCTATGAATATAA Y 2 1 2 1 101000 f 74 goat snp54658-scaffold835-1019144 1 38588810 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776499 Affx-122953386 AX-385263626 1 38727175 AAAAGTTCGTATCTGTGTGATGTTATGTTACAAAG[C/T]ATGAGAATACGGAACAATTGCTTGTGATTGTTTAT Y 2 1 2 1 101000 r 74 goat snp54657-scaffold835-974628 1 38633539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386284 Affx-122970936 AX-123256642 1 38758902 CACTGAACTACCTATGCAATCTTCTTCCTGAGCAG[C/T]AGTTATTTTCCTAGGCCTTAAGGGATGTCTCAAAC Y 2 1 2 1 101000 r 74 goat snp54656-scaffold835-942901 1 38665588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432016 Affx-122935922 AX-123302357 1 38835121 TAGTCAGTATTACCTAAATTGTTTTTTAGGTCCAC[A/G]TTTAAATTGTATTCTGTGTTTTTGAGTCACAGTTA R 2 1 2 1 201000 r 74 goat snp54655-scaffold835-866682 1 38742639 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405229 Affx-122956891 AX-123275581 1 38891952 TCCATCTAGGAATCTGTCAAAGAAATAAAGCAGTC[A/G]TTAATTAAATCCAGTGATACTGAAGCAGATTTTAC R 2 1 2 1 202000 r 74 goat snp54654-scaffold835-809851 1 38797156 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785850 Affx-122938348 AX-385272887 1 38925927 GGAATCAACCTTCTTATGCTTAGTGATTTTCAATG[C/T]AAAATATTAACCTTTTGAACACATAATAGGAAGAT Y 2 1 2 1 101000 f 74 goat snp54653-scaffold835-775876 1 38831680 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799080 Affx-122939634 AX-385286010 1 38996315 TATTCTTTTTTGTTGTTTGGAGGCATATATTTGAA[C/T]ATAATGGTATATTTCAGTCTTAAATGTTCACTTCT Y 2 1 2 1 201000 r 74 goat snp54652-scaffold835-705488 1 38900381 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378495 Affx-122976657 AX-123248854 1 39101424 AGTAGTCTCTGACAGTCAGTAGCTGGTTTTACACT[A/G]TCATCAAGTCTTTGCTGTTCATAAGAACTTGTACA R 2 1 2 1 101000 r 74 goat snp54650-scaffold835-600379 1 39006247 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430929 Affx-122936845 AX-123301270 1 39131429 TTTACTTAATTCCATAGCTGTGTTTAGAATTTATG[C/T]AAGTTTGTCGGTTACTACTGGTTTTATTTTCTGAA Y 2 1 2 1 101000 f 74 goat snp54649-scaffold835-570374 1 39036266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440980 Affx-122928980 AX-123311317 1 39199482 TGCTGTATATTTTGTAATGACATGTCATTTGTTGT[A/G]TCATGGTTTTCCTCTTATTCTATATACTCCCTTAG R 2 1 2 1 201000 f 74 goat snp54648-scaffold835-502321 1 39106870 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771944 Affx-122956642 AX-385259100 1 39272991 CAATTCTTTGTTACAATAACATACAATGCCCTGCT[A/G]CATTTTTCTCTACCTATTTAAAGAACTTTGCCCCT R 2 1 2 1 201000 r 74 goat snp54647-scaffold835-428812 1 39180904 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768420 Affx-122952063 AX-385255600 1 39326464 CCTTCCATTCTGATCATATCAAGAGTTGTTCTCTC[A/G]TGCATAGACATATATTCTGAGTATGGGTTTGCCTT R 2 1 2 1 101000 r 74 goat snp54646-scaffold835-375339 NW_017212145.1 4338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414091 Affx-122949746 AX-123284440 1 39374544 AACTCTGACTTGCTTCTGTGTGAAAGAATGCAAAA[C/T]AACTCTCTTTACAGTAATTTATTTTATTTTTGTCT Y 2 1 2 1 103000 f 74 goat snp54645-scaffold835-327259 1 39285531 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779046 Affx-122932364 AX-385266152 1 39408423 GAAATAAAAACATATTAGTCTAGAATGCTTTGCAT[A/G]CATTAAAAATGTCAATTCTAGAGTCTCTTCAAAAT R 2 1 2 1 101000 r 74 goat snp54644-scaffold835-293380 1 39319428 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382523 Affx-122973799 AX-123252881 1 39467151 ATTAACATCACTGTGACGTGATGGTTAATTTTATG[C/T]GTCAACTTGACTAGGCTAGAGAGTACCCAGATTTG Y 2 1 2 1 202000 r 74 goat snp54642-scaffold835-234652 1 39376585 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776057 Affx-122964844 AX-385263187 1 39498397 ATAATAAATTCATAATTCATTCACTTAGGAAGCTA[G/T]AAAGAATGCACTAAGGAAAACTGCAACAATTATTG K 2 1 2 1 101000 r 74 goat snp54641-scaffold835-203406 1 39408080 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791439 Affx-122963688 AX-385278430 1 39564609 TTTTTAAGTTAAATGGAATAGAAACATTATGAAAA[C/T]GAGCTGATTCAGTTCCTATATTTAAAAGTCTGTTT Y 2 1 2 1 101000 r 74 goat snp54639-scaffold835-137194 1 39474944 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793628 Affx-122963992 AX-385280602 1 39598218 TTTTATAGCATATTTTAGCATTTGAGTTAAATGTA[C/T]GTTCCAAGATTTGTCTTATAATTTTCCTTTTTTGA Y 2 1 2 1 101000 r 74 goat snp54638-scaffold835-103585 1 39510206 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790482 Affx-122954458 AX-385277485 1 39630830 GCAAGTGACTGATTTTAACATAACTACATATTCAC[A/C]TTTAAGTAATTATGTATGAAATATACTTTTATAAC M 2 1 2 1 202000 r 74 goat snp54637-scaffold835-70973 1 39543168 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400620 Affx-122960378 AX-123270975 1 39679410 TTTATAAACATGGAATCGTGCCTATCTAAAAGGAC[A/G]CTGGAAAGATTAAATGAGATGTCTGCAAGTGTCCT R 2 1 2 1 101000 f 74 goat snp54636-scaffold835-22393 1 39591951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448559 Affx-122923422 AX-123318895 1 39725029 TCTTGTGTTTATGGCAAAGATGAAGAAAGAAAACT[A/G]TTCTGATGTATGCCCAGAGTGTCCTTCATAAGAAA R 2 1 2 1 102000 r 74 goat snp45624-scaffold627-23127 1 39649784 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447100 Affx-122924484 AX-123317436 1 39765979 TCATGGGGCCAATCCATTCTAAATCGCTCCTAAAC[A/G]CCAGCTTTACCATAATTTTTCTATATCTTTAGACT R 2 1 2 1 101000 f 74 goat snp45625-scaffold627-64077 1 39691067 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476146 Affx-1251763649 AX-586011579 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 4 1 4 1 20000 f 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 539476402 Affx-1251763649 AX-586011806 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 4 1 4 1 20000 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562165094 Affx-1251763649 AX-606940506 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 f 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166073 Affx-1251763649 AX-606941482 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166132 Affx-1251763649 AX-606941540 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166217 Affx-1251763649 AX-606941625 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166273 Affx-1251763649 AX-606941681 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166356 Affx-1251763649 AX-606941764 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 r 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 562166358 Affx-1251763649 AX-606941766 1 39773708 CATTCAACTATTTGACATACCAAAATATTTTTACT[-/GTAAAACTTAACTTTTTTTTTTATCTTTTTATTTTATTTTTTCTCCTCCCTGGCTGGGCAGGCAGCCTCAACCCCTTCTC]TAAAACTTAACTTTGTCATTTCCAGAAGCAGGGCA - 8 1 4 1 20100 f 74 goat SV_238 1 39773708 - deletion junction SV-TF-chip 320793759 Affx-122929684 AX-385280731 1 39818492 TTGACAATATTATGCCTCCAAATGTCAAAATAAGG[C/T]AGAGTTACACCTTTAAAGAGTTCTTTTTAAAACAA Y 2 1 2 1 101000 f 74 goat snp45626-scaffold627-116590 1 39744620 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789868 Affx-122924402 AX-385276875 1 39861782 TTCCACAACAGATTCTAAGCTGGATTCTACAACAG[C/T]GATTATCATACGGTCTCTATTCTTTAGAAAATCAA Y 2 1 2 1 101000 f 74 goat snp45627-scaffold627-159880 1 39794053 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396808 Affx-122963289 AX-123267163 1 39891664 CCTGCAAATTATACTCTACTCCCTAACCTGTAATT[A/G]TTTATTTAGCACTTATAACAGGATTAGAGTATTAT R 2 1 2 1 201000 r 74 goat snp45628-scaffold627-189762 1 39823947 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771970 Affx-122928209 AX-385259126 1 39937203 GAAAAATTGGTTGTAGGAAGTAACATATCAGTAAC[A/G]TATCAGCCCTTTCTTATACATTGAAGGAATCATAG R 2 1 2 1 101000 r 74 goat snp45629-scaffold627-235301 1 39870443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775363 Affx-122977884 AX-385262494 1 39974998 TATCAAAGGATGAAATATATTAACTGGAAAGAAAA[G/T]AAGAGGGAATCTTCTTGTTTCCTGGGACAATGGAG K 2 1 2 1 102000 r 74 goat snp45630-scaffold627-273096 1 39908671 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786216 Affx-122921120 AX-385273251 1 40008925 ACTTCATTTATGGAAATATAACATCCTCATATCTA[A/G]CCTCTGATGTTCTTTGTTTTATGTTCTTTATTTTA R 2 1 2 1 101000 r 74 goat snp45631-scaffold627-307023 1 39943149 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784532 Affx-122959662 AX-385271581 1 40064962 CTTAAACAGTTGCCTGGGTTCAGCGAAAAGCATCA[C/T]GGGCTGATGACTCAAGGTCTAAAAAAGCTTAGAAA Y 2 1 2 1 101000 f 74 goat snp45632-scaffold627-363060 1 40000300 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401681 Affx-122959559 AX-123272034 1 40098906 CTCGGATGTCCTCTTGGAATTGAAGAATTTAGGCA[C/T]GCTCACCTCTTGTGGCCTTCAATGTAATTTTCAGA Y 2 1 2 1 101000 f 74 goat snp45633-scaffold627-397004 1 40034873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772103 Affx-122963762 AX-385259258 1 40152526 ACTTATAAGAATGGATGGCCTTGCATGTAACACCT[A/G]TAAAGTAAAAATATTCATGAAAACTTACTCTTATC R 2 1 2 1 201000 r 74 goat snp45634-scaffold627-450624 1 40080187 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413167 Affx-122950345 AX-123283516 1 40242625 GTGAGGACACAAGACAATTCTGAAAAGAACAGTAT[A/G]CAATAGCCAAATCTATACTTACAGTAGATGCTATC R 2 1 2 1 101000 r 74 goat snp45635-scaffold627-540723 1 40170770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790996 Affx-122975835 AX-385277993 1 40351474 AGCAACATCTGGCATATTTATATTTAAGCATTCTT[A/G]CGTTGTTTTGACATCTTAAGAAATGACTTGAGTAA R 2 1 2 1 101000 f 74 goat snp45637-scaffold627-649572 NW_017213414.1 11436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271729 Affx-1111832856 AX-519545525 1 40382233 ATTTCTTATGAGTTTTGTATCACTTGAACTTGAAT[A/G]CTAAATAATTATGAGACAAAATATAAGACACTGGT R 2 1 2 1 101000 r 74 goat 1_40382233_AF-PAKI 1 40382233 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320793260 Affx-122978213 AX-385280238 1 40392392 TCATTTTATTGTTTTATGAGCATGATATTTTTATA[C/T]ACAGTGAGTACACCTTAAAGGACACATTAGATGAT Y 2 1 2 1 101000 r 74 goat snp45638-scaffold627-690490 1 40320736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407273 Affx-122955341 AX-123277624 1 40448394 TTCTGGTAAGTAACATAGAAAAAAGAGAACACTGA[C/T]ATTGTATATTAAATAAGAAAAATCTATAGGATCAG Y 2 1 2 1 101000 f 74 goat snp45639-scaffold627-746492 1 40376869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278041 Affx-1111836221 AX-519551532 1 40493433 CTACTACTCATATTTTAGGCAAATTTTGGGATATA[C/G]TGGACGACAGGGAGGCCTGATATGCTGTAGTTCGT S 4 1 2 1 201000 f 74 goat Random2.2K-40 1 40493433 G C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391266 Affx-122967364 AX-123261623 1 40536709 TACCACTGTATCCCCAGTATGTCTCAGTGCCTGCC[A/G]TATAATAGGTGCTCAGTAATATAGAGTCTACTAGC R 2 1 2 1 102000 r 74 goat snp45640-scaffold627-834807 1 40465437 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772135 Affx-122976298 AX-385259291 1 40646208 CCTACTGAATATAAATATAGGTAAGACCACTGGAC[A/G]TAACCCATATTTGGGGAAAATGTAATATTAATTTA R 2 1 2 1 202000 r 74 goat snp45642-scaffold627-944306 1 40576012 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443985 Affx-122926919 AX-123314322 1 40692485 CAGGTATATTATTGTACAGAAGCTCTCTAGAGTTT[A/C]TTCATCTTGCTTAAATAGCCCTTTATGCCCATTGA M 2 1 2 1 101000 r 74 goat snp45643-scaffold627-990583 1 40622392 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383012 Affx-122973321 AX-123253370 1 40737264 CTTGCTAATGCTTCATAACACACTCAGGCAAGAAT[A/G]GTTGCAATGTACTTCTTTTCAGCAGTTCATTTTTA R 2 1 2 1 101000 f 74 goat snp45644-scaffold627-1035362 1 40666859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794490 Affx-122968171 AX-385281453 1 40778205 CCTCAGCAAATAATCATTAAATTCCTATTATAATC[A/G]TAGCACCACACTAAATACTGTAAAGTAGATTACAA R 2 1 2 1 101000 f 74 goat snp45645-scaffold627-1076303 1 40707648 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415050 Affx-122949486 AX-123285399 1 40825652 AAACTAACATGAATAATTATTTTTTAGATAATTAT[A/G]CTCAACTCTGTGGGTCATATTGTTACTTTATTCTA R 2 1 2 1 101000 r 74 goat snp45646-scaffold627-1123750 1 40754893 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430535 Affx-122937200 AX-123300876 1 40877770 ATAGAAGAGGGTACTGACTGTTTCCTTTGTTTCTG[C/T]AATCTCCAAATCTAGTTTATAAGCATCCTTTCGTA Y 2 1 2 1 201000 r 74 goat snp45647-scaffold627-1175868 1 40807132 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797961 Affx-122974596 AX-385284897 1 40906966 TCTGTGTGTTCCTAACGTTTTCATCATTTGATTTG[A/G]AAAGCTCACCAATGTTTTTAACAAGAATCCCTTTG R 2 1 2 1 101000 r 74 goat snp45648-scaffold627-1205064 1 41912588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441850 Affx-122929042 AX-123312187 1 40985539 TTCTTTAAATATTGAGCCTCTGTTTCATTTTATAC[A/G]TGATTCTAGCTCAGAAAAAGCAACTTGAATATTTT R 2 1 2 1 101000 r 74 goat snp45650-scaffold627-1283637 1 41991755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438590 Affx-122930947 AX-123308927 1 41023263 CATGCATTCTGGGTTGGAACAAACCTCTGTTTCAT[G/T]TCCCATCATGTGTGTGTCTCTCCTATTCTGTAAGG K 2 1 2 1 101000 f 74 goat snp45651-scaffold627-1321361 1 42029469 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764475 Affx-986698941 AX-385252160 1 41040072 TACATTTGTGTGTCTCCACCTGCGTGGCCTCTGCA[A/G]GTGCTGCAGGTGACCTGGGTACTGCTGCTGGTGTT R 2 1 2 1 600010 f 74 goat 1_41040072 1 41040072 Ancestral_priority_1043 ancestry 0.504 neutral IMAGE 10K 10K ancestral 320768117 Affx-986698907 AX-385255319 1 41040084 TCTCCACCTGCGTGGCCTCTGCAAGTGCTGCAGGT[A/G]ACCTGGGTACTGCTGCTGGTGTTACTGGGATGTGC R 2 1 2 1 600010 r 74 goat 1_41040084 1 41040084 Ancestral_priority_1043 ancestry 0.452 neutral IMAGE 10K 10K ancestral 38416588 Affx-122947649 AX-123286936 1 41086564 AATGGGAGGCTTGTTTGGACTCAAGACTAGCCACA[C/T]GTGCTTTGCAGACAGCAGCTGCTCAATAAATGCTC Y 2 1 2 1 101000 f 74 goat snp45652-scaffold627-1384662 1 42092506 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394540 Affx-122964518 AX-123264895 1 41119103 GAAATATCTGGCAGGTCATATACCTCCTCACCACC[A/G]CTTAGTCATATCAGGGTGCCCTATGTGCCCCCCTC R 2 1 2 1 201000 r 74 goat snp45653-scaffold627-1417201 1 42124959 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796841 Affx-122925584 AX-385283784 1 41175942 CATTCAGTTTTAAGATATTTATGAATGACAAGTTA[C/T]GGACTAAGTTAACTGGTGTTTATAGCCTCCTCCAT Y 2 1 2 1 101000 r 74 goat snp45654-scaffold627-1474040 1 42183311 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408997 Affx-122953892 AX-123279348 1 41205379 TGGAAGTGAGTCAGATCCGCTTTAAGATATCAGGA[C/T]AGAAACCACTATATTCTTCTGAAAGAGAAAGATGG Y 2 1 2 1 101000 f 74 goat snp45655-scaffold627-1503477 1 42213350 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377639 Affx-122977870 AX-123247998 1 41240203 TAAAATAAAATTTAAAATTGAAGTCTCCTTTTCAT[A/G]CACAAAGTCTATAGGAAAATAAACTGAATAAATAA R 2 1 2 1 101000 r 74 goat snp45656-scaffold627-1538301 1 42248227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765422 Affx-122922880 AX-385252926 1 41291547 CATCTGCCCAGTCACTTAGTTAGTCTCTCTCCTTT[A/G]CTAATCACTCCTTCACATCTTACATGTCACCAAGT R 2 1 2 1 101000 f 74 goat snp45657-scaffold627-1589645 1 42300836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425314 Affx-122940943 AX-123295660 1 41321332 CACTGTTCAGTAGCCTTTTCTGGTCTTTTCTTTTC[A/G]CTCCTTGTGTGAGCCAATGTTCCTGGTTGCAACAT R 2 1 2 1 201000 r 74 goat snp45658-scaffold627-1619430 1 42330682 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802850 Affx-122978572 AX-385289748 1 41351022 CAGCTTTATGACTTAATAATTACCCACACACTGAG[A/C]TGAACATTTTGATTATTTAGTTTTAGGACTGCATA M 2 1 2 1 101000 f 74 goat snp45659-scaffold627-1649120 1 42360248 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423898 Affx-122942287 AX-123294244 1 41393212 CCACAAAGTAGCCCAAAAATCTGAATTCTCAAATT[A/C]AATTTGTGATGACCATCTATCCAACTGTCTCCTTT M 2 1 2 1 101000 r 74 goat snp45660-scaffold627-1691310 1 42402942 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775371 Affx-122928590 AX-385262502 1 41424091 ATTAAAATCATCACATGGTTGTAAAGATTAGATGT[A/G]TCTCTGTTTTGGTTACTATTCCAATCTTCTTGTGT R 2 1 2 1 101000 r 74 goat snp45661-scaffold627-1722189 1 42432156 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389014 Affx-122968640 AX-123259372 1 41467809 CTATTGCATAGCTCTGTGCTAGAGCAAAGGCTGCT[A/G]TGGCTGACAGGAAAACTCAGTTGTGAGAGATGGAG R 2 1 2 1 101000 f 74 goat snp45662-scaffold627-1765907 1 42476634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802003 Affx-122922758 AX-385288907 1 41515686 AAGAACTATCCTGTAAAGGAGGAGGTGTTCGTGGA[A/G]ATTCAAGCCAACAGGAGAGGTCTAGCTATCTAGCA R 2 1 2 1 101000 r 74 goat snp45663-scaffold627-1813784 1 42527294 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407689 Affx-122954582 AX-123278040 1 41575735 TACTACCAATTTTCCTCACAAATTTGTGCCAAGAC[C/T]CTACCCATTTTTTTCTGTCTGGACTCTGAACCTAG Y 2 1 2 1 101000 f 74 goat snp45664-scaffold627-1873833 1 42587747 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395912 Affx-122963603 AX-123266267 1 41619883 AACATGCCTGCCCTCTTCTGCTATTCCAAATACCT[C/T]CTCTCTATACATAATTATGCAGAATCTTACCTTAA Y 2 1 2 1 201000 r 74 goat snp45665-scaffold627-1917981 1 42631758 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440548 Affx-122929319 AX-123310885 1 41684337 CTTCCTCATGAAGCTTATAAACTAATAAGGGAAAC[A/G]TGCACAAAGAACAGAATATAGAGAATAATAGATGC R 2 1 2 1 101000 f 74 goat snp45667-scaffold627-1982435 1 42696022 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386993 Affx-122969949 AX-123257351 1 41720467 ATCCCTTGTGTTAGTATCTCCCTGGAAAATGAGCA[G/T]CAGGAGAGCTCCATAAGGAAAGAAAGGGACAATAA K 2 1 2 1 101000 f 74 goat snp45668-scaffold627-2018565 1 42733630 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427472 Affx-122940019 AX-123297815 1 41751899 CCAGACAAAGTCCTACTAATCCTCTGAGACCTAGT[C/T]CAAACTCTCTTTCAAAAACAAAAATTCTTTTAAGA Y 2 1 2 1 101000 f 74 goat snp45669-scaffold627-2049997 1 42765831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274919 Affx-1111834493 AX-519548501 1 41775891 TGCTCTCACCTCACCCCGGAAGCCTGGCCCCTCTA[A/C]GATCCCTGCAGATGCTGTCTGATCCATCTGCAACC M 2 1 2 1 202000 r 74 goat GoatD01.038250 1 41775891 T G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38444462 Affx-122926541 AX-123314799 1 41826427 GGCAGTAAATGAGTTAAAGAGAACTGAGGCCTTTC[C/T]ACCCATCACTACAGAGTCCTGTGTGTCTCCTTTAA Y 2 1 2 1 201000 f 74 goat snp45670-scaffold627-2124525 1 42840961 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414867 Affx-122949146 AX-123285216 1 41866739 ACACTTGTGTGATTTCTGTAGGAAAGACACCTGGA[A/G]GTGGATTTCCGAAGTCAAAAAAGCATAAATATTAA R 2 1 2 1 101000 r 74 goat snp45671-scaffold627-2164837 1 42881260 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773601 Affx-122969083 AX-385260741 1 41927914 GAAAATATTTAGCTTCTCTTTTAGAGATCTACCCA[C/T]AAATTCCTTCATCCCCCCAAAAGTTCATTTAAAAT Y 2 1 2 1 101000 f 74 goat snp45672-scaffold627-2226012 1 42943225 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411514 Affx-122951674 AX-123281864 1 41963997 AGCACCTACAAAATAATATCCCCAACAGAGAGCCA[C/T]GCAATGTGTATATAATTCAATTAAAATTCTCTACA Y 2 1 2 1 101000 f 74 goat snp45673-scaffold627-2262095 1 42979321 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439777 Affx-122930509 AX-123310114 1 42005589 TGTGGTTCCTTCAGAAGTAGCCAACTACAACTTCA[A/G]TGCTACCAAATCATTCCTTGTTTCCTCTTTAGCTA R 2 1 2 1 101000 f 74 goat snp45674-scaffold627-2303687 1 43021857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403296 Affx-122957845 AX-123273649 1 42056149 TTAACTAGGCTAGGAAAAGCTATATGGCTTCTGCT[C/T]ACTGCTTCTGAGATGCTGGCTCAGCTCTCTGGAAG Y 2 1 2 1 101000 f 74 goat snp45675-scaffold627-2354247 1 43072890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787531 Affx-122963317 AX-385274555 1 42169072 GAGTTATATAAAAATTAAGCTATTAAATCAATAGA[C/T]GAATGAATTTTCTTAGGTCTAGTTGGAAAGTCAAA Y 2 1 2 1 202000 f 74 goat snp45677-scaffold627-2467170 1 43186110 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768405 Affx-122952801 AX-385255585 1 42204788 CTTAAATTACAAGGTAATGAGTTTTTAATATCACT[A/G]TAAAGCAAAAAAACCAAGTTGTTGAAGTAGCTCTC R 2 1 2 1 101000 r 74 goat snp45678-scaffold627-2502886 1 43222479 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393764 Affx-122965206 AX-123264119 1 42246346 TATCCAAAAGCGTATTTCTTTTGGAGAAAACTGAT[A/G]CAAATGTGCTAAACTATGTTTGAGTTAGAAGCAGG R 2 1 2 1 101000 f 74 goat snp45679-scaffold627-2544444 1 43264436 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432821 Affx-122935391 AX-123303162 1 42283895 TCAGGGAAAGAGTTATTAAACCCAGTCTGGGATAA[A/C]ATGTTGAGATGGAATTGAATTTGGAGCCCTCTTCT M 2 1 2 1 101000 f 74 goat snp45680-scaffold627-2581993 1 43301912 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380698 Affx-122975165 AX-123251056 1 42315461 AAGAGAACCTCTTCGAAGTATAAGACATGAGTAGA[A/G]TATGGTACATGACTCATGGTTGAAAAATGTTTTAG R 2 1 2 1 101000 r 74 goat snp45681-scaffold627-2613559 1 43333599 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442021 Affx-122928410 AX-123312358 1 42476050 CAACCTGACATAACTCAGGAAAGAAACAATGATCA[C/T]GAAGAAGAGTCAATAAATATTACCCAAAGCAAAGC Y 2 1 2 1 101000 r 74 goat snp45684-scaffold627-2774148 1 43495461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790224 Affx-122923839 AX-385277228 1 42506261 AGCTACCAGTAAATGGTAACCAATAAAACGTTCAA[C/T]GTGGTAATTCACAAATTCATAAACTGAGAGCAAAC Y 2 1 2 1 101000 f 74 goat snp45685-scaffold627-2804359 1 43522281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388995 Affx-122968653 AX-123259353 1 42675968 AGATTTTTCCTAATTAAAGAAATAAAGAGGTGGAG[C/T]ACTTGGGAAAGGGAAGAATTCATAGTGGGAAAAGA Y 2 1 2 1 201000 f 74 goat snp45689-scaffold627-2974066 1 43695904 C T 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780973 Affx-122964132 AX-385268060 1 42719188 GTTTTAAGAGGAGTAAGTATTCAATTATCTAAATC[A/G]TCTCTCCCAAATCTGCTACAAAAGAAAAAAGCAGG R 2 1 2 1 101000 r 74 goat snp45690-scaffold627-3017286 1 43739121 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429441 Affx-122938502 AX-123299783 1 42764315 GGTAAACATGGAAGTGAACAAAACAGAAAACCTAT[A/G]CTCTCTGGAAAAAAAACAAAGTTATACTTTGGAAT R 2 1 2 1 201000 r 74 goat snp45691-scaffold627-3062413 1 43783780 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440573 Affx-122929301 AX-123310910 1 42842609 CTTCAGAACTAGGAGAGAAATGTGGTAAGAACCTG[C/T]GGTGTTAAAAAAGAAAATCATATGCAACTAGATGC Y 2 1 2 1 101000 f 74 goat snp45693-scaffold627-3140707 1 43862317 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271730 Affx-1111832857 AX-519545526 1 42912608 TAGAAAACCAGTGTCTCTGTCGCTTACTCTTTTTC[A/G]TTTTATTGACAACTTTTTAACCATGTAAAAACCAT R 2 1 2 1 201000 r 74 goat 1_42912608_AF-PAKI 1 42912608 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320801543 Affx-122975885 AX-385288452 1 42924341 TCAAAGTACAGGTGAACAGGTTTTTTAGTTGAAAC[G/T]CATTGTAGCAGTTCAGGATGTTACTAGAATAGTTG K 2 1 2 1 101000 f 74 goat snp45695-scaffold627-3222439 1 43943543 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405123 Affx-122956970 AX-123275475 1 42987386 ACAGAGACGTATGAAAATATAATGAGTCACTACAT[A/G]CTACCACACAGATTTGTAAAATCTCCATTTATTAT R 2 1 2 1 101000 f 74 goat snp45697-scaffold627-3285484 1 44006897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403820 Affx-122957957 AX-123274172 1 43019891 TGTAACAGTTTACAGTGTAGCCCCTGGAGTCACTC[C/T]GGAGTGTGCACAGCCCAAATGACGTAACCTTGGAA Y 2 1 2 1 101000 r 74 goat snp45698-scaffold627-3317989 1 44039576 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416709 Affx-122947560 AX-123287057 1 43085413 TACTCATTAATTTATCAAATATATAATTTTAAAAC[C/T]TCAGAATGCAAGGGCAGAGTTTAGTTACTAACTTT Y 2 1 2 1 102000 r 74 goat snp45699-scaffold627-3383511 1 44105754 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435947 Affx-122933537 AX-123306286 1 43126836 ACCCTAGCATATGTCACACACTCACCCCTGTGTGT[A/G]CACAGCAAAACACTATTCTAGACATTGTGTTTGAT R 2 1 2 1 101000 r 74 goat snp45700-scaffold627-3424934 1 44147063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396240 Affx-122963333 AX-123266595 1 43213913 TCTGTTTGTTTTATGTATAATGTTCAGGGGTTTTC[A/G]CTGTAACTTAATAGGAGGAATAGGGGAAAATATGA R 2 1 2 1 202000 f 74 goat snp45701-scaffold627-3512011 1 44234714 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409169 Affx-122953199 AX-123279520 1 43287950 AAGTCTCGGGTATTTATTTGAAGCCCTTGTGCCTG[A/C]AAACAGGTGAATGCCTGGGAGGGTAGCATCACCAG M 2 1 2 1 102000 f 74 goat snp45702-scaffold627-3586048 1 44307169 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411946 Affx-122951147 AX-123282296 1 43350764 GAAATAAATGGTGGTGAATCTAGGATAGCATCGTG[A/C]TTGTCTCTGTTTGGGAAAAAAAACAGTTGTCTCTG M 2 1 2 1 201000 f 74 goat snp45703-scaffold627-3648862 1 44370048 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429395 Affx-122938535 AX-123299737 1 43421226 TTCTATAGAACATAAGGCTGTCCAGGTTTTCATTG[G/T]AATTGTATTGAATCTATGGAAAGTTAACATCTTAC K 2 1 2 1 101000 f 74 goat snp45704-scaffold627-3719324 1 44440450 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404430 Affx-122956762 AX-123274782 1 43455370 AACCCCTATAATTTCAAAACAACTTCAAAAAGTGT[A/G]TTAGACATATTTGAGGGGCATTAGCTAAAACATTA R 2 1 2 1 201000 f 74 goat snp45705-scaffold627-3753468 1 44475064 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381717 Affx-122974701 AX-123252075 1 43523812 AAAACTTGGCTTTTGCCATACTATTTTTGAGAGTA[A/G]ACTCTCTTAATTTAGATTGCATCCTCCTCCACTTT R 2 1 2 1 101000 r 74 goat snp45706-scaffold627-3821910 1 44543678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451924 Affx-122921018 AX-123322257 1 43559892 TCATTACCACAGTGGTAAATAAACGCTCTGACTAC[A/G]TGCAAAGCTTCACCTCCTTCACATGTGCTGACAAC R 2 1 2 1 201000 f 74 goat snp45707-scaffold627-3857990 1 44580536 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440988 Affx-122928974 AX-123311325 1 43606522 TAATGTTTCTTGGCTAAAACTCATGTCTATTTGCT[A/G]TAAATTCTGGATTCGTCTTTCACCTGGAGCTGGGT R 2 1 2 1 101000 r 74 goat snp45708-scaffold627-3904620 1 44627650 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423251 Affx-122942676 AX-123293597 1 43641800 TGTTTAATGTAGTGGGAGTGGCCTTTGGAGTAAGA[C/T]GGTCTGGATTCAAATCTTAGCATTGTTTTTTAGTA Y 2 1 2 1 101000 f 74 goat snp45709-scaffold627-3939898 1 44663553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782627 Affx-122947481 AX-385269700 1 43679308 CCACATAATGATTTGAGGTGTGAAATTCTTGTTTT[A/G]TTCTTTCATCTACAAGCTCAGGCTTGGACTGATGC R 2 1 2 1 101000 r 74 goat snp45710-scaffold627-3977406 1 44700317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774788 Affx-122940393 AX-385261922 1 43722397 CTTTTATAAGTGGCTTAGAACTACAGTTTCTACAG[C/T]ATCTTCAACAAAGAGCAATAACTGTGGAAAGAAAT Y 2 1 2 1 101000 r 74 goat snp45711-scaffold627-4020495 1 44743752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410533 Affx-122952162 AX-123280883 1 43760353 ACCACAGTGCAGAGAGAATCAAGGAAAGAGGAGGA[C/T]ACACCTGGGAGGGATTTGATTTTGGAAACTCCAAA Y 2 1 2 1 201000 f 74 goat snp45712-scaffold627-4058451 1 44783106 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783054 Affx-122941389 AX-385270121 1 43810013 TATAGGGCTGTTATGAGGATTAGTTAATACATTTA[C/T]AAGTTAAAGATGATATCTAGTACACTGTAGGCACT Y 2 1 2 1 101000 f 74 goat snp45713-scaffold627-4108111 1 44833935 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787602 Affx-122961545 AX-385274625 1 43849860 CTATTCACCCAGTGACCACCATTATTACCTCTCCA[C/T]ATGTCTAAGAGTACATACTCATATGGAACATACTT Y 2 1 2 1 102000 f 74 goat snp45714-scaffold627-4147958 1 44874041 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274222 Affx-1111834075 AX-519547822 1 43860293 CCATGACACTCTATTTTGTTAAGTCCTTTAATAAG[A/G]TATGAGAACAAAGCTTTCTGTGTGGTTTTAGATCT R 2 1 2 1 101000 r 74 goat GoatD01.017256 1 43860293 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320782253 Affx-122971705 AX-385269331 1 43903364 AGGTTCTCATGAATACCTGACCTGTCAGCTTCCAA[C/T]GGTATGCCTAATACGGTGCTAGTAACTTTTGGGAT Y 2 1 2 1 101000 f 74 goat snp45715-scaffold627-4201462 1 44928327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411504 Affx-122951683 AX-123281854 1 43940061 CAGAGAAGATACAGTGGTAAGGAACCTTGCCTTTA[C/T]AATGTAAGACAGTATGAAAACAGTTTGTAACAAAA Y 2 1 2 1 201000 r 74 goat snp45716-scaffold627-4238159 1 44965062 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412800 Affx-122950488 AX-123283149 1 43971635 CCCTGAGGGGGATCCCAGTAGAGAAACATGAGAAC[A/G]TAGAACGTGTGCAACACGCTTTGACTGGGGACGTT R 2 1 2 1 201000 f 74 goat snp45717-scaffold627-4269733 1 44996660 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446767 Affx-122925319 AX-123317103 1 44019493 TTGTTATTGATGATACTTTGGGGAAAAAGCTGATA[C/T]ATAAAATGAAGGTAATAATTCAGATAGTCAAGATA Y 2 1 2 1 101000 f 74 goat snp45718-scaffold627-4317591 1 45044651 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423418 Affx-122942618 AX-123293764 1 44051428 GTGACTTAACCGTATCGTGTGAGGCATGCTCATAA[C/T]GGAGGGTACATTGGGCAGCTGATAGCTTTCATGGA Y 2 1 2 1 101000 f 74 goat snp45719-scaffold627-4349526 1 45076527 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410376 Affx-122952442 AX-123280726 1 44104991 ACTACTTTTTTTTTAAATACGCAGGACCCCAAACA[C/T]ACATTTCTGTTGATTAACTCTCCTGAGCCTTATCA Y 2 1 2 1 101000 r 74 goat snp45720-scaffold627-4403089 1 45127830 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385438 Affx-122971318 AX-123255796 1 44141261 ATTTGACCTAGGTTACCTTCTTCTCACAGATGGTG[A/C]CTGCAGCCATGAAATTAAAAGACGCTTACTCCTTG M 2 1 2 1 101000 f 74 goat snp45721-scaffold627-4439359 1 45164326 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424701 Affx-122941692 AX-123295047 1 44204071 TCAAGCCCTGTCTTCCCACCTCAATGCTTTGCATA[G/T]ACATGGAATACAGTTTGTTACTTGAACAAATAAAC K 2 1 2 1 201000 r 74 goat snp45722-scaffold627-4502169 1 45227493 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444945 Affx-122926689 AX-123315282 1 44246286 GAACATCATGGTTAGTAACAGTTGATCTTAGAACA[C/T]AGAAAATTTTAAAACTACATTAAAAGAAATCATTT Y 2 1 2 1 101000 f 74 goat snp45723-scaffold627-4544384 1 45270236 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278057 Affx-1111836229 AX-519551547 1 44276563 GGGTGGGGAGAAAAGAACAAATGAGGCCAGAAAAA[A/G]AAAGCAACCAAAGGAATAAAAAATCCTTTTAATAA R 2 1 2 1 103000 f 74 goat Random2.2K-41 1 44276563 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406149 Affx-122956180 AX-123276501 1 44282338 TAGTAAAGTTAAATCAATATGCTTTCAGCTGAGCT[A/C]CCTGCCACTTACAGTTATCCTCTGATCCTTAAATT M 2 1 2 1 101000 r 74 goat snp45724-scaffold627-4580436 1 45306556 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386592 Affx-122970689 AX-123256950 1 44322066 CTATATAAGTATGCTAAAACTGCACTTTCAATCAA[A/G]ATGTCCCTATAGTTTTCACTTGCCCAGAGTGGGAG R 2 1 2 1 101000 r 74 goat snp45725-scaffold627-4620164 1 45346020 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418349 Affx-122946592 AX-123288697 1 44354500 TTTCAGGCTTCAGCCCATAATATCACACTCCAGAG[C/T]GCCAGACTCTAATTTCCAACTGCCTGATGGCTATT Y 2 1 2 1 201000 r 74 goat snp45726-scaffold627-4652598 1 45379239 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778808 Affx-122962163 AX-385265916 1 44441627 ATTACCATATTAAGTGCAGGCCTTTGTTAGAAATT[A/C]TTCTGTAAGCAAAACCATCCACTCACCTTTGCAAG M 2 1 2 1 101000 f 74 goat snp45728-scaffold627-4739725 1 45469437 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452024 Affx-122920905 AX-123322357 1 44484946 CTTCATTTAACCACTGCAGAAGGCTTAAATTATCC[A/G]CTCATGGTTGGGTCCATGAGTTGACAAATATGAAT R 2 1 2 1 101000 f 74 goat snp45729-scaffold627-4783044 1 45512858 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787628 Affx-122973468 AX-385274651 1 44542856 GCAAGATACCAGTGAGACCTGTTGAAAAAGAAATA[C/T]AATCTTAACACAAAATCTAAGCAATACAGAAGAAT Y 2 1 2 1 101000 f 74 goat snp45730-scaffold627-4840954 1 45570681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436096 Affx-122932678 AX-123306435 1 44576529 AACATTATTTGGTCACAGTCAATTCATTTTTATCA[C/T]AGGACAAATTATTTCATATGACATCTAAATGCCTC Y 2 1 2 1 101000 r 74 goat snp45731-scaffold627-4874627 1 45604530 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433696 Affx-122934539 AX-123304037 1 44642395 AAAATGCAATCTACAAAAAAAACCTGGCATCTTTA[A/G]CTGGTGGAGAAACAAAAACCCACTAAATAATAGAA R 2 1 2 1 101000 f 74 goat snp45732-scaffold627-4940493 1 45672113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409532 Affx-122953615 AX-123279883 1 44713787 TTTAAAATGTAAGTCACATTGCTAAGATTTTTCAC[A/G]TTACTAATCTGTGACCATTCAAAATTTTGTTTTCC R 2 1 2 1 101000 r 74 goat snp45733-scaffold627-5011885 1 45743895 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404201 Affx-122957673 AX-123274553 1 44752854 ATCAGTAGCTAGAAATCTTGCCCAAAAGTCTACTA[C/T]AGGCCCAGTCAATTTGAGCCATCATTCTAACAAAT Y 2 1 2 1 101000 r 74 goat snp45734-scaffold627-5050952 1 45783017 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411566 Affx-122951634 AX-123281916 1 44798907 GTATCTAGTGCTGAGATTGGAATATAGATGCAGCA[G/T]AGCAGTAAATGTTGGATGAAGTGCATGCCTTATGG K 2 1 2 1 201000 f 74 goat snp45735-scaffold627-5097005 1 45829266 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431121 Affx-122936594 AX-123301462 1 44978248 CTGTATTAGTAAGAGGGTGGTATTCGGTGACTCTG[C/T]GGCTTCCAGGGCCCTGAAGGGGCCTGTGCACCAGG Y 2 1 2 1 101000 f 74 goat snp45738-scaffold627-5276346 1 46009213 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787755 Affx-122939991 AX-385274778 1 45017243 GTTTAACAAATGCTGGTTTTCTACCCACATTCCTT[A/C]GTTTCTCCATGGTAAAGTTGTGAGGTTATTTTCAA M 2 1 2 1 101000 f 74 goat snp45739-scaffold627-5315341 1 46047812 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396680 Affx-122962836 AX-123267035 1 45078234 TCACACTGCAGGCGGATTCTTTACCAGCTGAGCCA[C/T]GAGGGAAGCCCAAACTTATTTAGGTTGTACCCTAA Y 2 1 2 1 103000 r 74 goat snp45740-scaffold627-5376332 1 46108279 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476149 Affx-1251763652 AX-586011582 1 45086590 GATCCTTGATGCTCAGATGGTAAAGCCTGCAATGT[-/GGGAGACTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]GGAGACCCAGGTTCACATTCAATCCCTGGATCAGA - 4 1 4 1 20000 f 74 goat SV_256 1 45086590 - deletion junction SV-TF-chip 539476405 Affx-1251763652 AX-586011809 1 45086590 GATCCTTGATGCTCAGATGGTAAAGCCTGCAATGT[-/GGGAGACTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]GGAGACCCAGGTTCACATTCAATCCCTGGATCAGA - 8 1 4 1 20000 r 74 goat SV_256 1 45086590 - deletion junction SV-TF-chip 562165893 Affx-1251763652 AX-606941302 1 45086590 GATCCTTGATGCTCAGATGGTAAAGCCTGCAATGT[-/GGGAGACTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]GGAGACCCAGGTTCACATTCAATCCCTGGATCAGA - 8 1 4 1 20100 r 74 goat SV_256 1 45086590 - deletion junction SV-TF-chip 562166286 Affx-1251763652 AX-606941694 1 45086590 GATCCTTGATGCTCAGATGGTAAAGCCTGCAATGT[-/GGGAGACTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]GGAGACCCAGGTTCACATTCAATCCCTGGATCAGA - 8 1 4 1 20100 f 74 goat SV_256 1 45086590 - deletion junction SV-TF-chip 562166534 Affx-1251763652 AX-606941942 1 45086590 GATCCTTGATGCTCAGATGGTAAAGCCTGCAATGT[-/GGGAGACTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]GGAGACCCAGGTTCACATTCAATCCCTGGATCAGA - 8 1 4 1 20100 r 74 goat SV_256 1 45086590 - deletion junction SV-TF-chip 320781734 Affx-122958763 AX-385268816 1 45120445 ACCATGTTTTAAGATATGGCTTATTATGTTACCTT[A/G]CTGAGATCTCTTTAGAGCTAATTGTCAACAACCCT R 2 1 2 1 101000 r 74 goat snp45741-scaffold627-5418543 1 46151442 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787546 Affx-122933049 AX-385274570 1 45162409 AAGTTATAAAGTGATCACAATTGACTTCTATTTCA[C/T]CCTTTGACGTCAAGACCATTTATAGTTTGGTGTTT Y 2 1 2 1 101000 f 74 goat snp45742-scaffold627-5460507 1 46193883 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794721 Affx-122965569 AX-385281681 1 45191764 TGATTATCCATAGTGCTGATAAAGGCTCTGCTACT[A/G]TCTTTGGATTTGCAGCTGTTATTTTCACTCACCTT R 2 1 2 1 101000 f 74 goat snp45743-scaffold627-5489862 1 46223584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395272 Affx-122964085 AX-123265627 1 45240392 TTCCCATAATTGCCTCTGCCCCTGGGGTTAAGCAG[C/T]GGCTATATAAAGAGAAACAAGCAATGGGATTCCTT Y 2 1 2 1 101000 r 74 goat snp45744-scaffold627-5538490 1 46272440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431922 Affx-122935992 AX-123302263 1 45287136 ACATAAGAAGAGTACTTATATCCACTGTCAGAGAG[C/T]ACAGGCTAATTCTAATGAATAGCGTTTGGAAAAAG Y 2 1 2 1 101000 f 74 goat snp45745-scaffold627-5585234 1 46324507 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379111 Affx-122976752 AX-123249470 1 45318610 CAACTCCTGAACTTCTATTGGACCTTTTGGAACTC[A/C]TGAGACATCATAGTGAAAATTTAAAGGCATCAGCT M 2 1 2 1 101000 f 74 goat snp45746-scaffold627-5616708 1 46348481 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416049 Affx-122948352 AX-123286398 1 45352002 AAATTCCCTTTATCACCCTGTACTTCCACACAAAG[C/T]AGTGTTAGAAGCCAAATAAGATTCAGGGGCCAACT Y 2 1 2 1 101000 f 74 goat snp45747-scaffold627-5650100 1 46381671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776619 Affx-122967135 AX-385263746 1 45366965 AATTCAGAGAAGGAAAATTTAAAGGGGTTCTTGAG[C/T]GATCTCAGAAAAGCTGCCCAGGGAATGTTGAATAG Y 2 1 2 1 101000 r 74 goat snp12636-scaffold1480-1163799 1 46411147 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386655 Affx-122970204 AX-123257013 1 45417195 TAACCAAGAACTCAGTCAATTCTGCAAACTACTAA[C/T]GGAAGAAAAGCCAAGTAGATTTGGTAGGGGAAAAC Y 2 1 2 1 101000 f 74 goat snp12635-scaffold1480-1113569 1 46461277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423731 Affx-122942867 AX-123294077 1 45460504 CACTCTTAAAAATATATCAAACTATACTGTCTCCA[G/T]CACCCTCTATAGTTAACCACCTCTATAGCTACACA K 2 1 2 1 101000 r 74 goat snp12634-scaffold1480-1070260 1 46504863 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447842 Affx-122923901 AX-123318178 1 45512664 AAATAGGACGTGTAAAATTATTCATCTTTTTTTTC[C/T]CAAGATGCCTGGCAACTTTTGTACTTGTTGGAATA Y 2 1 2 1 103000 r 74 goat snp12633-scaffold1480-1018100 1 46557154 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428362 Affx-122938974 AX-123298705 1 45546537 ATTTTTGGGACCTAATTCATTTCCATCAGGTCATG[C/T]ATTTGCATTGCAAGGAAGGAAGAATAATTTTTCTA Y 2 1 2 1 101000 f 74 goat snp12632-scaffold1480-984227 1 46591721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398576 Affx-122961503 AX-123268931 1 45581766 TGGCTGAATGATTCTTTTGGAGGCTTAACTCTGTG[C/T]GTAACACTATCTGCCCAGATTTACCTCATATGCAG Y 2 1 2 1 101000 r 74 goat snp12631-scaffold1480-948998 1 46625453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271731 Affx-1111832858 AX-519545527 1 45587785 ATCTTGGTTGATAGTACTGACCAAAATAGGATTAT[A/G]TAATTTTCTTAGTTACACTGTGCTTAGTTTACTGC R 2 1 2 1 101000 r 74 goat 1_45587785_AF-PAKI 1 45587785 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320772990 Affx-122928551 AX-385260134 1 45614919 ATCACTCTTTACAGATACAGTTAGAGAAAAGATTG[A/G]TTTCAGACTTACCAGGAAATCTACTGTGGAGATTG R 2 1 2 1 101000 r 74 goat snp12630-scaffold1480-915845 1 46658757 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424906 Affx-122941306 AX-123295252 1 45646028 AAAAATGCATGCCATGGAATTCCTGTGCTAGATAA[C/T]GTGGTGAGGACTTAGAGAAGGGTGTCTTAGGGCTT Y 2 1 2 1 201000 f 74 goat snp12629-scaffold1480-884736 1 46689802 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417048 Affx-122947524 AX-123287396 1 45679436 GACCTAAGATTTGCCTGAATCCAAAGCTGTCAACC[A/G]CTTTAGCTTGTAGTACCTTCTACAATACCAGTCAG R 2 1 2 1 101000 r 74 goat snp12628-scaffold1480-851328 1 46723221 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381368 Affx-122974400 AX-123251726 1 45720761 GCGAGTCAGCGCTGAGGTGTCTTTTGAAAGAGTAT[A/G]CATTAGTGCAAGGTAACTCTACTACCATTTGCATC R 2 1 2 1 101000 r 74 goat snp12627-scaffold1480-810003 1 46765249 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416631 Affx-122947619 AX-123286979 1 45768638 GTTTAAAGCAGAATTAAAAGATAAAGTTCACAGCA[C/T]GCTACGTTGGAGATGGAAAGAAGAAACCAGCGTTG Y 2 1 2 1 101000 r 74 goat snp12626-scaffold1480-762126 1 46813492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411053 Affx-122951953 AX-123281403 1 45816172 TATAATGACTTTATGAATAGTAAAATAAAAGGAAA[C/T]GTATGTACTAAAATATTAGAGCAGAATAGGAAAAG Y 2 1 2 1 101000 r 74 goat snp12625-scaffold1480-714592 1 46861271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440852 Affx-122929257 AX-123311189 1 45846091 TGGTTTCAAGGGAACAGAATAAAAAATTCAATCAA[C/T]GTAGGAATTCAACAGAGAAAAATGAGGGTAGTAAC Y 2 1 2 1 101000 r 74 goat snp12624-scaffold1480-684673 1 46889973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380823 Affx-122975076 AX-123251181 1 45883122 AAAAGGCTGAAGGGAGTCTTAGTCCATAGTCAATT[A/G]TCCATTTAATCAACATCGTTTACTGAATCTCTAGC R 2 1 2 1 101000 r 74 goat snp12623-scaffold1480-647642 1 46929949 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797811 Affx-122946354 AX-385284750 1 46002412 CATATGAAATAACATGTACACATGGCATCATATGA[G/T]CAGGACCATCTGGAAAGAAGTGTCCAGAATCATCT K 2 1 2 1 101000 r 74 goat snp12621-scaffold1480-528352 1 47051236 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798792 Affx-122944785 AX-385285723 1 46035328 GCAATGATTCTGAGCCAGCAGGACTGGGTTCAGCC[A/G]CTGGATGTGCTAATTACTTGTTACTGAAACTTACA R 2 1 2 1 102000 f 74 goat snp12620-scaffold1480-495436 1 47084055 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417041 Affx-122947528 AX-123287389 1 46064190 CATGTTTCAACAGGAAGAAAATTAAAATCAAACAC[A/G]TTGTGGTTAAGAATGTAACAAACACATGGGAACTA R 2 1 2 1 101000 r 74 goat snp12619-scaffold1480-466574 1 47113193 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772831 Affx-122934344 AX-385259976 1 46094171 AAGAAAGAACAAAGAAAGCCAAAGAATGAAGGAGA[G/T]AAATGAAGACAAGTATTTAAGAAACTAGAAAATAA K 2 1 2 1 102000 f 74 goat snp12618-scaffold1480-436593 1 47143705 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388212 Affx-122969414 AX-123258570 1 46128996 TACCGATTCTTTAATTCTGAATGTAAGGGTAAACA[G/T]TTACAAACTGGAGAGGCCAGGTGCTCAGTGTAGCT K 2 1 2 1 201000 f 74 goat snp12617-scaffold1480-401768 1 47178831 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790770 Affx-122939064 AX-385277771 1 46188164 TACATAGGAAAAATGCATGTTACAGTGGAAAACTA[C/T]GAATTGTGGAGATCTTGGAGGACCCACTTCAGAAC Y 2 1 2 1 101000 r 74 goat snp12616-scaffold1480-342600 1 47238651 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779793 Affx-122961879 AX-385266893 1 46216784 CCTCATCACAGAATAAACTTTTTCCATATCCAGGA[C/T]GCCAGGACCCAAAATTCACCTATTTTCCATATTAA Y 2 1 2 1 101000 r 74 goat snp12615-scaffold1480-313980 1 47267647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440830 Affx-122929272 AX-123311167 1 46250999 AAGTGCTAAGGAGAAAATATAAACCAGTAGTAAAT[A/G]TTAAGCCCTAAGGAGGAATCTATTATTTTCAAGAG R 2 1 2 1 101000 r 74 goat snp12614-scaffold1480-279765 1 47302011 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782676 Affx-122955411 AX-385269749 1 46280585 AGGTTCAACTGAATTTATCTGTGCAATCCCAAATC[A/G]TAATCCCAGTGCTTGCTTCGGTAGCACATATACCA R 2 1 2 1 101000 r 74 goat snp12613-scaffold1480-250179 1 47332650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800608 Affx-122930274 AX-385287527 1 46311470 CTTTACCAAGTAAGTAATCAATAGCTTCCAGCTTC[A/C]GAAGGCTTTGCTTCATACAGTGTTTGGTTTGTCTC M 2 1 2 1 101000 r 74 goat snp12612-scaffold1480-219294 1 47363420 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392409 Affx-122966207 AX-123262766 1 46346553 TATTCTTTCTCTGCTCAGATTAATATTGTAAGACC[A/G]TGACTGCTATTACTAAAATTTTTACATACTTATTG R 2 1 2 1 101000 f 74 goat snp12611-scaffold1480-184211 1 47399390 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431805 Affx-122936115 AX-123302146 1 46383081 ATATTACTGAAAAAAAAATGTGGTATAGATGCTCA[C/T]GGTAGTTGTTTACAGATCTGTGAAACAAAAGCAGA Y 2 1 2 1 103000 r 74 goat snp12610-scaffold1480-147683 1 47436104 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476150 Affx-1251763653 AX-586011583 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 4 1 4 1 20000 f 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 539476406 Affx-1251763653 AX-586011810 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 4 1 4 1 20000 r 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562165051 Affx-1251763653 AX-606940463 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 r 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562165361 Affx-1251763653 AX-606940772 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 r 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562166094 Affx-1251763653 AX-606941503 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 f 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562166175 Affx-1251763653 AX-606941583 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 f 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562166295 Affx-1251763653 AX-606941703 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 f 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 562166411 Affx-1251763653 AX-606941819 1 46395478 TTTCTTTAGGAGTTTAAAATCTCTGAGGGTGAAGA[-/TCTGTTTTATTCATTTTTTTTTTTAATTTTTAAATTTTTTGTCTTCCCGTCCTATTTCTCCGCCATCTTTCCCTCTCCCC]CTGTTTTATTCATTTTTGTATCTCCTGTTCTTGGC - 8 1 4 1 20100 f 74 goat SV_261 1 46395478 - deletion junction SV-TF-chip 320788404 Affx-122933378 AX-385275422 1 46421838 CAAAAGAAAATTAAAAATCAACTTGGACAAAGGAG[C/T]GGTCAAGAGAATTATAACCATTTGCTACAATTCAA Y 2 1 2 1 101000 f 74 goat snp12609-scaffold1480-108926 1 47474944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398683 Affx-122961869 AX-123269038 1 46478263 TTTAACAATCAATTTAACTAATTCCTCCCTCCATC[A/G]CCTTTTAATACTCAAGCAATAAGCCTAATGGGCTT R 2 1 2 1 101000 r 74 goat snp12608-scaffold1480-52501 1 47531942 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421063 Affx-122944246 AX-123291410 1 46514933 GCAGAGTCACCACAGAATAGCCTGGTGGGGACATG[G/T]GAGGGTATTCTCTTGTCCTGGTTCAGTCTCAGGTT K 2 1 2 1 101000 r 74 goat snp12607-scaffold1480-15831 1 47569160 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421999 Affx-122943783 AX-123292346 1 46534808 CCATATATGTAATGTAAGGACTCTTGTTCATGTGC[A/G]TGAGAATATCTGTAGAATAATTATTTTAGCAGCAT R 2 1 2 1 101000 f 74 goat snp48341-scaffold686-887750 1 47619106 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376258 Affx-122978768 AX-123246617 1 46617720 CAAGAATACACAAAACCAGGTGTATAATGGCATTT[C/T]ATGGAGTTCTCTGTGGGGTTAGAACAGGATTAGTT Y 2 1 2 1 201000 f 74 goat snp48340-scaffold686-804838 1 47704739 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413662 Affx-122950115 AX-123284011 1 46671915 TGGCATCTCTTTTAGACTTAATTCCAGAAGAAAAA[C/T]CCAATCAGTTTTCAGGTCTGATTCCAAAGTTTTAC Y 2 1 2 1 202000 f 74 goat snp48339-scaffold686-750643 1 47759699 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785880 Affx-122934266 AX-385272916 1 46719634 CAAATATCAGTGCATATTACGTGAGCTGAAATAAA[A/G]TGTGATTTTATTGCACCAGGGATCCATTAAGCAGA R 2 1 2 1 101000 r 74 goat snp48338-scaffold686-702924 1 47807864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801578 Affx-122945423 AX-385288487 1 46774224 GAGTCTATATTTATTTATAATGTTCTTGATTTTAT[C/T]CATAAATCAGATTCACAGTGTAGCATATCTTAAAA Y 2 1 2 1 202000 f 74 goat snp48337-scaffold686-648334 1 47862256 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411410 Affx-122951843 AX-123281760 1 46820258 TTTGAGATTTATTTCTGTAACTCCCTAGATTTGTC[A/G]TCAACATTAGGACTAGTTTTGATCTACAGAATGTG R 2 1 2 1 101000 r 74 goat snp48336-scaffold686-602300 1 47909392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795559 Affx-122925467 AX-385282514 1 46866236 CAAATATTTCTGGTACCAAAGTCTGGAAATAGAAC[A/G]CCATGTTTTAGCTGCCAACTCAACATCAGTTTAAT R 2 1 2 1 101000 f 74 goat snp48335-scaffold686-556322 1 47955872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401733 Affx-122959519 AX-123272086 1 46960088 CATATATTGTCTTGAAATTAAAATTATGATGAAAA[C/T]AAATAGAGTAGAAAAACCTGAGATTTAAAGAAAGG Y 2 1 2 1 303000 f 74 goat snp48334-scaffold686-462470 1 48051444 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793657 Affx-122963263 AX-385280630 1 46994973 GACATATTCTGGTGAAACAAGAAGTTAAGTTATCT[A/G]AAATGGCTACAGTCTTTTTGAATGAATACTGTCTT R 2 1 2 1 101000 r 74 goat snp48333-scaffold686-427585 1 48085411 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768860 Affx-122929651 AX-385256037 1 47025267 TGAGGTTGTTTGTCATCACATTTGAAAAGGTTACT[G/T]CATGACCACTCAAATGAAGTGTGAAGCACTTAAAC K 2 1 2 1 101000 r 74 goat snp48332-scaffold686-397291 1 48115624 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278072 Affx-1111836237 AX-519551562 1 47051032 AGCAAATGCAAAGAGAAGCACTTGGAAAGACTGCT[A/G]GAGGATGGGAAGGCAAATGAAGATGCCACTGGAAT R 2 1 2 1 201000 f 74 goat Random2.2K-43 1 47051032 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444202 Affx-122927256 AX-123314539 1 47056527 TCTGAGGAACTGTAACTTTTTATTTTAACAGTAAA[C/T]GAGTAATCTTGAAATATAAGAAAATACATGAGTTT Y 2 1 2 1 103000 f 74 goat snp48331-scaffold686-366031 1 48147084 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776200 Affx-122945756 AX-385263328 1 47134189 TTTTAACTGAGATGTTAAAACCTATTTCAGGAATT[A/C]TTTTTGTCCATTTAATTATGCTTATACTTAATTAA M 2 1 2 1 102000 f 74 goat snp48329-scaffold686-288369 1 48225349 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406966 Affx-122955055 AX-123277317 1 47228711 GGCCACGACATCACTTATGCCTTCCCTCCTCTTTC[A/G]TGATACGCTTGGTGTACCCATTCATTGAGTTGTTG R 2 1 2 1 101000 r 74 goat snp48327-scaffold686-193847 1 48321647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434793 Affx-122933876 AX-123305134 1 47274139 GTGGTCTCTTTGGTAGGTTAGCTGTATGCAATGCC[A/G]TAAGGAGGGATTCTAGACAGCAGGTAACTGAGTAA R 2 1 2 1 101000 f 74 goat snp48326-scaffold686-148419 1 48368391 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767638 Affx-122920428 AX-385254882 1 47303473 AGTACACAGAAGCCAAAATGCCTTTTTATACATAT[A/C]TCAAACAACAATATCACTCTAAACACTATAACTTT M 2 1 2 1 101000 f 74 goat snp48325-scaffold686-119085 1 48397835 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793018 Affx-122945410 AX-385279996 1 47369912 ATTTATGAGGTAAATATATGTGTCAAGTACCATGG[C/T]AGGCTCTAAAAATGTGTTTGTGAGCATCACTTACT Y 2 1 2 1 101000 r 74 goat snp48324-scaffold686-52646 1 48464620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405845 Affx-122955865 AX-123276197 1 47451274 GAAACAAACATTGTGCGGTGGATCACTAGGGGTAA[G/T]AGTGAATAGAGACACTCCCATTTTCAAGCTTTTAT K 2 1 2 1 101000 f 74 goat snp7889-scaffold1284-28617 1 48564591 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403999 Affx-122957199 AX-123274351 1 47541704 GTGCCATATCTGAATCTAAGTGTTCAGAAGCCTCA[C/T]ATGGTTCTGTGTGTTCCTCTGTACTCTTACAAGTG Y 2 1 2 1 101000 f 74 goat snp7890-scaffold1284-119047 1 48656524 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436785 Affx-122932261 AX-123307123 1 47578594 CATCCTTTCCTCTGAAGTCAAATTTCATCATCATT[A/G]TTCCTTGTTGAGTTAATATTTTTCAGCACTTTAAA R 2 1 2 1 201000 r 74 goat snp7891-scaffold1284-155937 1 48693640 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796009 Affx-122950724 AX-385282961 1 47609798 CAGTTTCTACATTTCTTATGCTTTGATCTGGAAAT[G/T]TAAAATATGTGATGTAATGAAATCTGATAGTAGGT K 2 1 2 1 102000 r 74 goat snp7892-scaffold1284-187141 1 48725503 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446661 Affx-122924766 AX-123316997 1 47673747 TGTTCTGACATTTCATAGGAAGCCTTGCCCTGGAC[C/T]GTGATGGGGAAGGGCAGAATTGTTCTCATTCTACA Y 2 1 2 1 101000 f 74 goat snp7893-scaffold1284-251090 1 48790110 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768096 Affx-122970894 AX-385255298 1 47724253 TTAATCACAACTATTTCAAAACCCCTTCCTAATCG[G/T]TCTACCATCTGGGTCACTTCTGAATGTAATTTCTT K 2 1 2 1 202000 f 74 goat snp7894-scaffold1284-301596 1 48840674 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440399 Affx-122929618 AX-123310736 1 47793999 AATAATACTTAATAAATATATTTTTGTCATGTTTG[A/G]GCTGCATATCTTATTTAATTACTGAAACAGATAAT R 2 1 2 1 101000 r 74 goat snp55677-scaffold863-1765843 1 48911689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450936 Affx-122921769 AX-123321270 1 47867208 GCTAAAGGTAGAACGTACATCATGTACCTAGAAGG[C/T]GAATTAAATAAGGCTTAAGAGAGTCTCCTGGGAAA Y 2 1 2 1 101000 f 74 goat snp55676-scaffold863-1692634 1 48987492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441945 Affx-122928576 AX-123312282 1 47955633 GGTGATTTAGATAATCAAGAACTATACTTTAGAAC[A/G]TTTTGCAAAATATTGTCCTTATATTTAGACTTTAT R 2 1 2 1 101000 f 74 goat snp55675-scaffold863-1604209 1 49076511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408628 Affx-122953489 AX-123278979 1 48018399 TGTGTCTCTTTTGCTGTCTCGCATACCGGGTCATC[A/G]TTGCCTGATGCTTTAGTTTAATTGTGCATCCCACT R 2 1 2 1 101000 r 74 goat snp55674-scaffold863-1541443 1 49140292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797649 Affx-122932347 AX-385284589 1 48048986 TAACAGGACAATAAAAGATATCATCCAGATGTGCA[A/C]AGTTGACAGAAGATGGAACAATAAATTAGGATTAT M 2 1 2 1 101000 f 74 goat snp55673-scaffold863-1510856 1 49171800 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780350 Affx-122972303 AX-385267445 1 48089317 AGCGCAAAGTGGATAGTATATACAAAAGTGTCACA[A/G]GAGTTTAGGGAGAGATTGGTCTCTTAAGATTTCAG R 2 1 2 1 101000 r 74 goat snp55672-scaffold863-1470525 1 49212772 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771356 Affx-122961756 AX-385258514 1 48156301 AGAGTCACATAGTGGGATCAATTAAAGAAACAGTT[A/G]TAAAATATCATATTCCCTCTTTTTTATGCTTGTGT R 2 1 2 1 201000 r 74 goat snp55670-scaffold863-1403541 1 49280854 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785154 Affx-122925756 AX-385272200 1 48191227 CAGTTGATTAACATCAATATTGATAAATGTTAAAA[C/T]ATGTACACACAACTGCAGTTAAACATGAAACACCA Y 2 1 2 1 102000 r 74 goat snp55669-scaffold863-1368615 1 49316567 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403066 Affx-122958521 AX-123273419 1 48242578 TGGCCAAACAAACACCTCTGTGGTAATAGATGAGC[A/G]ATAGAGAGATCTGCTTGGTCTATGGAGAGGAAATA R 2 1 2 1 101000 f 74 goat snp55668-scaffold863-1317264 1 49367861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430134 Affx-122937397 AX-123300475 1 48277781 CTTTTGCCTTGATAGCATGCACAGAAGACTATGGG[A/G]AGCTCAATGTGGCCAGTGGTTATGTAACATTCCAT R 2 1 2 1 101000 f 74 goat snp55667-scaffold863-1282061 1 49402905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777837 Affx-122971797 AX-385264954 1 48351877 ACCTTCAACAATACCTCAAACTACAATCACTCCTG[A/C]GCTTGCTGACTTAATTACAAATACTAACAAATATC M 2 1 2 1 101000 f 74 goat snp55665-scaffold863-1207965 1 49476342 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399952 Affx-122960842 AX-123270307 1 48433286 TTTCTGTCTTAATTCCACTTCATCTGATATTAGCT[A/G]TGTTGCACTCAGTTTCTTTTGACTGGCATTGATCT R 2 1 2 1 101000 r 74 goat snp55663-scaffold863-1126556 1 49558720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271826 Affx-1111832859 AX-185407711 1 48439248 AGTTGGTGATGGACAGGGAGGCTTGGCGTGCTGCA[A/G]TTTATGGGGTCGCAAAGAGTCGGACATGAATGAGC R 2 1 2 1 303000 f 74 goat 1_48439248_AF-PAKI 1 48439248 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320769230 Affx-122949714 AX-186298626 1 48473913 GCTTAGAGTCAAAAGCATTGTATAGAATTTACTGA[C/T]GCTTGTGTCTGGAAGGAGTATTTTTCAGTCAAATC Y 2 1 2 1 101000 r 74 goat snp55662-scaffold863-1085929 1 49599249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414353 Affx-122950019 AX-123284702 1 48505482 AGTGGCCTTGTGGAGGAATGTTCTGTAGCACTAAC[G/T]AGTAACAGCTTTTTCTCTGAACTCCAAGCCCTCTC K 2 1 2 1 101000 f 74 goat snp55661-scaffold863-1054360 1 49630739 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792314 Affx-122949685 AX-385279296 1 48550525 TAAACTGAACAGTACACATGGGAGTTTCCTTACAG[C/T]ACTTTTTTGGATGAGACCACCTTTTGAAGAACTTT Y 2 1 2 1 101000 r 74 goat snp55660-scaffold863-1009317 1 49676483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407406 Affx-122955244 AX-123277757 1 48637775 CTTATTGGTATATCAGAGATCAATTTTTCTGGTTC[C/T]TAATTTTAAACACCAAGACCAGGAGAAACAAGAAG Y 2 1 2 1 101000 r 74 goat snp55659-scaffold863-922067 1 49764661 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278112 Affx-1111836258 AX-519551602 1 48656984 TAAGTAGGCCACATGAAGGAGTACATCAAGGCTGC[A/G]TATTGTCATGCTGTTTATTTAACTTCTATGTAGAG R 2 1 2 1 103000 f 74 goat Random2.2K-46 1 48656984 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401676 Affx-122959563 AX-123272029 1 48677242 TAAATGGTTCTCAATACAGGAGCACATTGATATAA[C/T]ATGAAGCATATAATTTCATTCATCCCGTCTCTGAA Y 2 1 2 1 101000 f 74 goat snp55658-scaffold863-882600 1 49804540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392617 Affx-122966042 AX-123262974 1 48766106 CATTTTGCATTTGAAGCAAATAGTAATTCTGCATT[A/G]TCCAGACCTTTAGGCTTCCCAGATGGCTCAATGGT R 2 1 2 1 201000 f 74 goat snp55656-scaffold863-793736 1 49895211 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791630 Affx-122970331 AX-385278621 1 48820405 ATAAGAAAGTATTTGCTGACCTTTTAATAGCACAA[C/T]AGTCAAGCTTTCACAGCCAAGATGTTCTTAGAAAA Y 2 1 2 1 101000 r 74 goat snp55655-scaffold863-739437 1 49949644 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414898 Affx-122949122 AX-123285247 1 48859203 AGTCTTAAGAGGTTTGGTGTTGCTTCAAGGACAGT[G/T]AAGTATAGAGAATGGTACCCACTGTAGCTTGTCTA K 2 1 2 1 101000 f 74 goat snp55654-scaffold863-700639 1 49988259 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426126 Affx-122940623 AX-123296472 1 48932670 TTCAACTATCCTGAGGATAATGATTTTCTTGAGGA[C/T]GGGGAGTCCTTTGAAATTCCATTCTTCTGAGAATA Y 2 1 2 1 202000 f 74 goat snp55652-scaffold863-627172 1 50064347 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796867 Affx-122961340 AX-385283810 1 48968913 TCCAGCTCTCTTGACTCTGGATTTCACCAACACTT[A/C]TCTTCTCAGGTCTTGCTATTAATATAGTCTTTCCC M 2 1 2 1 101000 f 74 goat snp55651-scaffold863-590929 1 50100577 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795207 Affx-122938688 AX-385282165 1 49036135 CATAAAAATCCCTCTGTAGTTTCATAAGTTTTCAT[A/G]CTTGAATATAACTCGGAAAATTTTACTAACTTTTT R 2 1 2 1 101000 f 74 goat snp55649-scaffold863-523707 1 50167374 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278299 Affx-1111836272 AX-519551784 1 49065262 TGACATTTACATGTAGCTCCTTTTCTTGACCAAGA[A/G]AATCTGTAGACCTAGGACCTTGTTTGGTTTAAAGT R 2 1 2 1 101000 r 74 goat Random2.2K-49 1 49065262 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425144 Affx-122941202 AX-123295490 1 49177314 CATCATCCAATGTAGCAGAACAAAAGGAGTTCTGA[A/G]GAGTTGTTCAGAAGGAAGGACTTCTACAGGCAGGC R 2 1 2 1 101000 f 74 goat snp55646-scaffold863-382528 1 50305997 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414639 Affx-122949328 AX-123284988 1 49210968 TCAATTTTATTGATATTCTCCATTATTCGTATTCC[A/G]TTCTCTGGTCTATTGAATGTCTTCAGGCTTCTTTC R 2 1 2 1 101000 r 74 goat snp55645-scaffold863-348874 1 50339728 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380012 Affx-122975601 AX-123250370 1 49271004 TAACTTATTCCCATATGGGGAGAGCTTGCTTACGA[G/T]TAGGACCAACACAGTGGGTGTTTGAGCACCTGGAA K 2 1 2 1 101000 f 74 goat snp55644-scaffold863-288838 1 50399829 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787470 Affx-122957175 AX-385274495 1 49309311 TTAGTGGATTTCCCTAGAGAACTATCTGTTTTAAG[C/T]CTCTTTACCTTTGTTGTTGACTATATTACTGGTCT Y 2 1 2 1 101000 r 74 goat snp55643-scaffold863-250531 1 50438031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398664 Affx-122961884 AX-123269019 1 49351443 TACAAGAGATAGTCATAAGAAGCTTCTGGCCAAGA[C/T]AGAGTCACAAGGGCTGGATTTACTGTTCCACCTGA Y 2 1 2 1 101000 r 74 goat snp55642-scaffold863-208399 1 50481152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428987 Affx-122938856 AX-123299329 1 49394331 CATCTAAGAACATTCATGTAAAATCTGTATGAGGA[C/T]ATATGTTTTATTTCTCTTTGCTAAATAGCAAAGAA Y 2 1 2 1 101000 f 74 goat snp55641-scaffold863-165511 1 50524009 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767776 Affx-122960106 AX-385255003 1 49449653 GCAATCAAAGGTACAAATCACTCCTACTCATTCTC[A/G]CATTTTAATGCAAGGGCTTTTAGGAATCATACTGA R 2 1 2 1 101000 f 74 goat snp55640-scaffold863-110189 1 50579371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379062 Affx-122976334 AX-123249421 1 49529228 ACAAAATGTCTATGAATCCCTGATTATAGTAAAGC[A/G]CCTCCAACTTTAATTCATTTCAATATTTCCGTTGG R 2 1 2 1 101000 f 74 goat snp55638-scaffold863-30614 1 50659866 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449699 Affx-122922544 AX-123320034 1 49590738 GGATTAAAGTAGATTAAAGGGATAATATAAGTAAA[C/T]GAAAAAGATGACAACAAACCAGAAAAATTTTTCTT Y 2 1 2 1 101000 f 74 goat snp27909-scaffold2996-56754 1 50722301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414449 Affx-122949946 AX-123284798 1 49620784 GGCAGAATTTCCCAGTTTCTCCAGCTTAGTTGTAG[C/T]AGTACTAGTAGTTGTAGTAGGAGTAGCATCAGCAG Y 2 1 2 1 201000 r 74 goat snp27908-scaffold2996-26708 1 50752322 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796747 Affx-122953903 AX-385283691 1 49652947 ATTTTGTCATGTAGTTTATTAATGCTTCTCTTAGC[A/G]TTAGTATTAAACTATTATTGGCCAATATTATTTTC R 2 1 2 1 101000 f 74 goat snp14230-scaffold1568-1787801 1 50789391 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441029 Affx-122928942 AX-123311366 1 49698034 CCTAACGTGCCTCTGCCCCTCAGTCAGGAAGCAGT[A/G]TACATGCCACAGTTAGGTGTTTGGGAAGAGCTACT R 2 1 2 1 101000 r 74 goat snp14229-scaffold1568-1742714 1 50834538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414872 Affx-122949142 AX-123285221 1 49747435 TCAAGAGAATCTATTTTTTTTCTAATAGGGATTGA[C/T]GAAGGGATAGTAAGAGAGAAGTGACTGAAAAGGAA Y 2 1 2 1 101000 r 74 goat snp14228-scaffold1568-1693313 1 50884075 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769925 Affx-122971899 AX-385257094 1 49799773 AAAAATATTGCTCCTTTTTATAGAGAACCAAATCA[C/T]AGCTATACCCAACCTTTGTGACATTAATGACAGAG Y 2 1 2 1 101000 r 74 goat snp14227-scaffold1568-1640975 1 50938524 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454076 Affx-122919380 AX-123324409 1 49861012 AATATTTTGTTTTTCTATATTGAAGAAATATCCTC[A/G]TTTGTTATTCTTGCAATACTTTCCACCACAGAAGT R 2 1 2 1 101000 r 74 goat snp14225-scaffold1568-1579736 1 50999753 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449571 Affx-122923233 AX-123319906 1 49890372 ACAGGAGTGCTGTGAGGTCAACAGGGAGGACACTG[C/T]AGTTAGAAACAGATGTTAGTGAACACGAAGCTTTG Y 2 1 2 1 101000 r 74 goat snp14224-scaffold1568-1550376 1 51029010 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769122 Affx-122976695 AX-385256297 1 49938352 CTGAGATGCTTTACTCCTTTTTGTATTCTATTCCA[C/T]TGGCAGAGTAAATCACATAGTGGTAGTTTTTGGCT Y 2 1 2 1 101000 f 74 goat snp14223-scaffold1568-1502396 1 51077800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419791 Affx-122945851 AX-123290139 1 49969607 TGACCCCTGCAGTCACAGTAGTGAGAGCTGCAAAG[A/G]CTTTTATTGGAAGAATATAAAGAAGCTGCAGTCTG R 2 1 2 1 201000 r 74 goat snp14222-scaffold1568-1471141 1 51109331 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800576 Affx-122951148 AX-385287495 1 50004337 GGGTAAAAGGAAGTCAAGCCACAGAAGAGGACCAA[C/T]ATTTCAGTTTGGAATATGTCAGCAAAACAGACAAG Y 2 1 2 1 101000 f 74 goat snp14221-scaffold1568-1436411 1 51144639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399339 Affx-122961361 AX-123269694 1 50038931 TCTACACAACAACCCTTGAGGCATTCCTAAAACAC[A/G]TGCACACATACAAACACCTACATACACAAGAAACA R 2 1 2 1 101000 f 74 goat snp14220-scaffold1568-1401817 1 51177975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440032 Affx-122929764 AX-123310369 1 50096433 ATTGATTAAATACATGGGGAGAAAGAGACCTTTAG[A/G]ATTTTGAAAGTGTAGATTTCTCCAAAGGGAATATA R 2 1 2 1 101000 r 74 goat snp14219-scaffold1568-1344315 1 51235629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432580 Affx-122935520 AX-123302921 1 50142331 TTGGCAAAAGGTAGGAGCATAGCCAGCATAATTTA[C/T]ACTGAAATTTTTAAGAAAACATAAATTTGAAAAGT Y 2 1 2 1 101000 f 74 goat snp14218-scaffold1568-1298417 1 51282663 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775019 Affx-122971224 AX-385262151 1 50177184 TATATTTACACACATAAACAAAGCAACATTTGGCA[A/G]TTTAGGATTTGTCAGGATAAAAGACATTTAATAAA R 2 1 2 1 101000 f 74 goat snp14217-scaffold1568-1263564 1 51317480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403238 Affx-122957890 AX-123273591 1 50214589 TTTATAGATTGATGGCAGTTTAAGTATCTTGGACC[A/G]TAGGTATTTCCATTTGGCATGATGCTGCTCTATAC R 2 1 2 1 101000 f 74 goat snp14216-scaffold1568-1226159 1 51353428 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803440 Affx-122945858 AX-385290270 1 50249719 TTGAAATTTCACACAAATGACACATCTCAAATATA[G/T]CCTGTCTCAAACTGGAATCATTTTTGTATCATCAA K 2 1 2 1 101000 r 74 goat snp14215-scaffold1568-1191029 1 51389058 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410243 Affx-122952543 AX-123280593 1 50294704 ACAAAGAGTTGGAAATGACTGAGGGACTGAACTGA[A/G]CTGAACTGATAGCATTAGCATTAGGGTCACCTGCT R 2 1 2 1 103000 r 74 goat snp14214-scaffold1568-1146044 1 51434143 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399242 Affx-122960579 AX-123269597 1 50342858 CCACAGAGGTCCTATATTAACTATATTAAAAATTC[C/T]AAATAATTGCTTTTGTTTGTGATTTTTGGGGAGGA Y 2 1 2 1 103000 r 74 goat snp14213-scaffold1568-1097890 1 51482441 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278360 Affx-1111836302 AX-519551846 1 50363538 ACTGCCAAAACTTGGAAGCAACCAAGATCGCCTTC[A/G]ATAGATGAGTGGGTTAAACAAATTGTACTACATCC R 2 1 2 1 201000 r 74 goat Random2.2K-54 1 50363538 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794891 Affx-122955514 AX-385281851 1 50415423 GCTTTACAGTATTGCGCTGGTTCCAGCTAAACATC[A/C]ACATTCCTGCCTCTTTTCTTAACTGCTCTCTCTGT M 2 1 2 1 101000 r 74 goat snp14211-scaffold1568-1025325 1 51555055 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409600 Affx-122953559 AX-123279951 1 50451247 ATTCATTCACTTATTATTTTAATGTTAAGTTTAGC[C/T]GTTTAGATGTCTTAGAATAGATAAAATCTTGGGTG Y 2 1 2 1 101000 r 74 goat snp14210-scaffold1568-989501 1 51590929 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769259 Affx-122953807 AX-385256432 1 50509093 AAAATGCCACCCATTTAAGACCAACTAAAAAAGGT[G/T]AACATTCATAAATAATAATGGCTAATATGTTGTGA K 2 1 2 1 201000 r 74 goat snp14209-scaffold1568-931655 1 51649274 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278219 Affx-1111836309 AX-519551707 1 50615387 GCCTAGGTTCAATTTTGATTTCAATTCAGTCACTC[A/C]GTCGTGTCTGACTCTTTGCAACCCCATGAACTGCA M 2 1 2 1 103000 f 74 goat Random2.2K-55 1 50615387 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413094 Affx-122950949 AX-123283443 1 50633096 GAAACATAGAGGCTTAACCACTGGATGTATAGGGA[C/T]GTCCCAAGAGGGTTCTCACCATTTACCTTTCTCTG Y 2 1 2 1 101000 r 74 goat snp14207-scaffold1568-807652 1 51773659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398251 Affx-122962190 AX-123268606 1 50665494 ATATTTTACTTGAAGGCTAGATACATCTTTTTGAA[C/T]TACTTGCTGATCCAATGCAGTGCTTTCCTAGTAGT Y 2 1 2 1 101000 r 74 goat snp14206-scaffold1568-775254 1 51806247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788918 Affx-122971913 AX-385275932 1 50701532 ATGATATTTACAAAAATTACATTACAATGGCAACC[A/G]CCTATTATGTCCAGGAATGAAGTCCACCCTGGATG R 2 1 2 1 101000 r 74 goat snp14205-scaffold1568-739216 1 51842984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776549 Affx-122951215 AX-385263676 1 50743524 TCATTTGTATTGACAGAGTATTTATACCCTTTTTA[A/G]TTTTCCTGTAGAAGGCTATCTGATGATTTAACTTT R 2 1 2 1 202000 f 74 goat snp14204-scaffold1568-697224 1 51885580 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388173 Affx-122969441 AX-123258531 1 50821403 TACTACTCATCTCAGTGTTACCTGACCAGGTATAA[C/T]AGAGGAAGGCAGTGGTTCCCAAAGTATATGATGCA Y 2 1 2 1 101000 f 74 goat snp14202-scaffold1568-619345 1 51964163 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446530 Affx-122925019 AX-123316866 1 50872296 CAAATATGCTTACTCTTATTGCTCACTCCCACCCC[G/T]ACCTATTTTTATATAGTTTTTACATTTTTGTAATG K 2 1 2 1 303000 r 74 goat snp14201-scaffold1568-568452 1 52015571 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789301 Affx-122939194 AX-385276312 1 50936371 ATCTATGTGCACATCCATAACAGACACACCTAAGA[C/T]AAAATGACACATGAAATGTTAAAAGTCAGGGATAT Y 2 1 2 1 101000 r 74 goat snp14199-scaffold1568-504377 1 52080052 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446901 Affx-122924706 AX-123317237 1 50996098 GGTGTGATCTGTTGTTGGGATCTGCTGATCCTGAA[A/G]TGCCCTCTCCTTACAGCACCCTACACCCTGCCTGT R 2 1 2 1 101000 f 74 goat snp14198-scaffold1568-444650 1 52140450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388400 Affx-122969295 AX-123258758 1 51033291 AGGGGGAATATTTCAAACATATATAAATACTTTCT[G/T]CCTTGACTACTCTGCAAAAACTGCTTCTCCAAATT K 2 1 2 1 101000 r 74 goat snp14197-scaffold1568-407457 1 52178031 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271827 Affx-1111832860 AX-519545613 1 51039466 CCCATCTATTCACCATGAAGTGATGGGACTGGATG[A/C]CATGATCTTAGTTTTCTGAATGTTGTTTTAAGACA M 2 1 2 1 103000 f 74 goat 1_51039466_AF-PAKI 1 51039466 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320765468 Affx-122938362 AX-385252965 1 51105459 GGGTTCATGTAACCCAGTCTGTTACTTTCAAGGCA[C/T]AATACCATGCACATAGAAACCTTAATGAAAATTAA Y 2 1 2 1 101000 f 74 goat snp14196-scaffold1568-335289 1 52250097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429672 Affx-122937654 AX-123300013 1 51134136 ACAACTGGAGAACAGGTTCCTAGAGGACAGGAGGT[A/G]TATACTGTAATTTCCTATAGTCCTCACAGTATCTC R 2 1 2 1 201000 r 74 goat snp14195-scaffold1568-306612 1 52278719 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434523 Affx-122934160 AX-123304864 1 51178523 TAGAAAATCTTTGGAAAGAGTAGTAATGTTCACAA[C/T]AACTAGGTTCTCTGCATAAAAATCAATTTAAGGGC Y 2 1 2 1 101000 f 74 goat snp14194-scaffold1568-262225 1 52323147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802610 Affx-122944743 AX-385289512 1 51234683 CAATTCCATTAAGTTAAAAGGATTAGCTTCCAAGG[C/T]ATTGTTGTCCTCTGATCCTATTTCATGTTAATTAC Y 2 1 2 1 101000 r 74 goat snp14193-scaffold1568-206065 1 52378620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378834 Affx-122976541 AX-123249193 1 51285370 TGTTGATCAAATAACTTTCAGAAATTTACAAGGGA[G/T]AAAACTTTCTGCTTAACCAGAAGCTGTCAGGCATT K 2 1 2 1 101000 r 74 goat snp14192-scaffold1568-155378 1 52429959 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278391 Affx-1111836317 AX-519551876 1 51314247 GAATTCTCCAGGCAAGAATACTGGAAAAAAATGAA[A/C]TCCTAGTAAATTGTTCATGGGAATGTGGGTTGAGG M 2 1 2 1 101000 r 74 goat Random2.2K-57 1 51314247 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386002 Affx-122971508 AX-123256360 1 51352595 CACTCTGCTTTATTCAGAAAGACAGTCTCTCCAAG[G/T]GTTCTCCTTGTGGTGAACACTCTTCCTACAATCTA K 2 1 2 1 201000 f 74 goat snp14191-scaffold1568-88153 1 52497288 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783013 Affx-122958246 AX-385270081 1 51408978 AGCAAAGCTAGCAGTGAAATTCAGGTCTAGGTGAG[C/T]GGCAGAAATAATTAGCATAGAGAGGAAAATAAATT Y 2 1 2 1 101000 f 74 goat snp14190-scaffold1568-31770 1 52553074 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441307 Affx-122929450 AX-123311644 1 51438357 TAGTCATTATCCCACCTGTGTTCTCACTGCTTCCC[A/G]TCTTCTCGACCAAGCAGCCTGGCTCCAAGAGGATA R 2 1 2 1 202000 r 74 goat snp14189-scaffold1568-2391 1 52582919 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410210 Affx-122952568 AX-123280560 1 51448183 CATGAACATATGCATATTGTAAGGCTGTAAGCTGG[C/T]CAGCTCCTCCCATCCTCTCCTGGTGTCACCCTCAC Y 2 1 2 1 101000 f 74 goat snp44268-scaffold602-533448 1 52592722 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791852 Affx-122949851 AX-385278842 1 51478600 AAAGTCTATGCCCTATAAGAAGGCAGGGATATGAC[C/T]GAGTCATAGTCACATAAGTTCCAACGCTGGATAGA Y 2 1 2 1 101000 f 74 goat snp44267-scaffold602-503031 1 52623696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412958 Affx-122951046 AX-123283307 1 51512389 TAAGTAACTTGCCTAAGCTTAAACACCTAGCAAGC[A/G]CTAAGTGTTGAGCCAAGTGTGTGCCCTTACCTGTA R 2 1 2 1 101000 f 74 goat snp44266-scaffold602-469242 1 52657481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407615 Affx-122954638 AX-123277966 1 51550081 TAGAAACTGAAAGCAACATGTTCAAGGCAACATTA[G/T]CTTTAACAGGAAAAAAATCTGTGAAAATGCTGAAC K 2 1 2 1 103000 f 74 goat snp44265-scaffold602-431550 1 52695498 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442639 Affx-122928453 AX-123312976 1 51603103 ACTCATTCCAGCAGAAGGAAAGACAGTCATGGGAG[C/T]GTGTTATGATATGAAGGGATCAGATGGTCCAGAGG Y 2 1 2 1 201000 r 74 goat snp44264-scaffold602-378528 1 52749255 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772279 Affx-122972722 AX-385259434 1 51631794 GAACCCAGTACCCAACCTGAAAGAGAACTGGATCA[C/T]TACAATACCCTGGAAGTTGTCCATGTGCTGCCCTG Y 2 1 2 1 201000 r 74 goat snp44263-scaffold602-349837 1 52778800 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449676 Affx-122922560 AX-123320011 1 51701247 GTAAATGGGCAATTATAACACAAGTGAAGTGTGTT[A/C]TGATGAACATAAATCCAGGAAGCTAGCAATGGCAA M 2 1 2 1 101000 r 74 goat snp44262-scaffold602-280384 1 52848242 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782962 Affx-122970360 AX-385270031 1 51738392 AAGCAAAGGAAGAGCAAGCCTCTACTACTCAAAAT[G/T]TAAAAGTAACCCTCTGAAGGGACATTTAGCAGGCT K 2 1 2 1 101000 f 74 goat snp44261-scaffold602-243239 1 52885658 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409132 Affx-122953300 AX-123279483 1 51785827 TCAATGTGACAAACACAGGAGCATTTACAATTCTC[A/G]TTTGTAACCTGGGTGGAAGATTCAAAGGTTTTTTT R 2 1 2 1 101000 f 74 goat snp44260-scaffold602-195804 1 52932798 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375767 Affx-122978595 AX-123246126 1 51814695 TTAACCATTCAGTTTCCAGGCACACGTTGCTCAGT[C/T]GGTGCTACCTGTTCACATCACTGCAGCCTTTTCAG Y 2 1 2 1 101000 f 74 goat snp44259-scaffold602-166936 1 52962642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381599 Affx-122974792 AX-123251957 1 51845923 GCTTTTTTCTTTTTATTTTCCTATGGGTTATTCTT[A/G]CAGTTTTCTTCTGTAAACAGGTTCATTATACAACA R 2 1 2 1 101000 r 74 goat snp44258-scaffold602-135708 1 52994341 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397515 Affx-122962053 AX-123267870 1 51885706 GTGACAGCGCAGAAGACAAAGCTACGGAGTGAGAA[C/T]GGTAAGGAAACTTTCAGTGTTGCTTCACTCACAAG Y 2 1 2 1 101000 f 74 goat snp44257-scaffold602-95925 1 53033952 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426563 Affx-122940170 AX-123296909 1 51942640 AATGCTCACTGTGGATGCTGTGCTGTGTGCTTTGT[A/G]TGCACGGTTCATTCAATCAAACAGCAAGTCTGCAA R 2 1 2 1 201000 r 74 goat snp44256-scaffold602-38991 1 53091421 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799455 Affx-122953780 AX-385286385 1 51972184 GCTCTTCCTAAGCAATGATGATGCCAGCTCATGTA[G/T]CTGTTGGCTTTAGTCATCCCCAGAAAAATAATAGG K 2 1 2 1 101000 f 74 goat snp44255-scaffold602-9447 1 53120951 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406408 Affx-122955219 AX-123276760 1 52025244 TTAAAAAAAAAGGCTGAAAACTACATGAAGTCTCT[A/G]CCTACACAGGTTTTTAAGAATAGGCAAATTGAGTG R 2 1 2 1 101000 r 74 goat snp29278-scaffold3155-43514 1 53173473 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397730 Affx-122962546 AX-123268085 1 52071174 TAAAAAATTGTCTTATCTTTAGGCAAAATGCATGC[A/G]TAAGTATTAGAGTAGAAATGCTGTGGCTATATATA R 2 1 2 1 101000 r 74 goat snp4116-scaffold113-5653 1 53217077 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386594 Affx-122970688 AX-123256952 1 52102759 TTTTTCTCCTATTAAAACATTTGCTAAGTCCTGTT[A/G]TACTTTCTTGGCTTTCTTTTCCATTTGACTATAGT R 2 1 2 1 101000 r 74 goat snp4117-scaffold113-37238 1 53248874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426682 Affx-122939912 AX-123297028 1 52199142 TATTTTGGATAAAGCAAAATGAGTCCCACTCCTAA[C/T]AGCAGTTATGTGAAGGTTCCTGTTTCCTTACACAA Y 2 1 2 1 101000 r 74 goat snp4119-scaffold113-133621 1 53347371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769294 Affx-122953995 AX-385256466 1 52230009 GAGGAATAGGAGAAAGAGAGTCATGAAAGATCAAG[A/C]TTATGTTCTGAACAGCTTGTTGAAGAGCGATACCT M 2 1 2 1 101000 f 74 goat snp4120-scaffold113-164488 1 53379210 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401174 Affx-122959354 AX-123271527 1 52294093 TTGGACAATCTTGTTCTATCTCCTGAGTATGTAAG[G/T]CTATGACTTGGGGAACATTGTAATGCAGGTCATTT K 2 1 2 1 101000 f 74 goat snp4121-scaffold113-228572 1 53434276 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384971 Affx-122971902 AX-123255329 1 52350335 CTGTTTTATACTACTCAGAATAATCTTAGAGATCA[C/T]AGAAAAGCCACATTTTAGGAAGAAAAATGCATATT Y 2 1 2 1 101000 f 74 goat snp4122-scaffold113-284814 1 53490004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397254 Affx-122962358 AX-123267609 1 52384163 TGCAGAATTTGTTTTAATGGGGAGAGGCCAAGAAA[C/T]GAAATAACCAAGGAGATAGTAGGTTAGAAGATAAA Y 2 1 2 1 101000 f 74 goat snp4123-scaffold113-318642 1 53524300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387531 Affx-122970307 AX-123257889 1 52412843 CTGGCTTCCCCCAGGGATATTCTCCCTCCAGGAGC[A/G]CCAATGAGATGAATCAGTACACACACTAGTTCTCT R 2 1 2 1 101000 r 74 goat snp4124-scaffold113-347322 1 53551600 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777728 Affx-122952374 AX-385264846 1 52442747 AACAAACATCCCTAAGTACACTGAATTCTGTTTAA[C/T]AGTCACTGACTACTTCCTAAATTCAAGGCACTGAA Y 2 1 2 1 101000 r 74 goat snp4125-scaffold113-377226 1 53581776 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415715 Affx-122948519 AX-123286064 1 52497803 CTCACCTTTCAGAGGTCCTCTATTCAGTAATTACC[A/G]TATCTTATAATGATTTATACAGTTTTTAAAAGACA R 2 1 2 1 101000 f 74 goat snp4126-scaffold113-432282 1 53636096 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404046 Affx-122957163 AX-123274398 1 52554930 GCTAATCTTATCTTTCTAGCACAATCTCAGACTCA[C/T]GGAAGGTTTTGATAAATGTTTAGTAAATAAATGAA Y 2 1 2 1 101000 f 74 goat snp4127-scaffold113-489409 1 53693006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400735 Affx-122959905 AX-123271090 1 52587178 AACTTCAAAACATACATACCTCTAAGAAAAAGGCA[C/T]GCTCCCAGGGAAAGGAAAAGACAGAAATGGCTCTC Y 2 1 2 1 201000 f 74 goat snp4128-scaffold113-521657 1 53720624 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393941 Affx-122965069 AX-123264296 1 52615821 CTTTAAAGCTACTCCTTTCCTAAAGAATCCATCTC[A/G]TTGTTTTTATACAGTAAACTGAAGCACATGCACGT R 2 1 2 1 101000 f 74 goat snp4129-scaffold113-550300 1 53749013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422438 Affx-122943354 AX-123292784 1 52651878 TTTACTTCGTCCTCCAGCCCCTGGTAACCATTTTT[A/C]TGCTCTCTGTTTTTATGTGTGATTTTTGTTTTAGA M 2 1 2 1 303000 r 74 goat snp4130-scaffold113-586357 1 53785296 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451165 Affx-122921351 AX-123321499 1 52687812 AATTGTCTGAATGTAAAACATGCAGGCTCAAAACC[A/G]TCTACCTCTGCACTGTGGGATGGCATCAGTATTCC R 2 1 2 1 101000 f 74 goat snp4131-scaffold113-622291 1 53821310 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442526 Affx-122928542 AX-123312863 1 52774571 CAAAAAGATCTTTGTTTAAAAGTCTAAGAAACAAT[C/T]TAACTGGGGAGATGGGATATTTGAGAGACAACAGA Y 2 1 2 1 101000 r 74 goat snp4132-scaffold113-709050 1 53907979 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418634 Affx-122946344 AX-123288982 1 52807778 GCTGGAGGCTCTTCCCCCCACCACCTGAGGCTTCA[A/G]TTTTCCAACTGCCCTAGACCTCTGGCATTCAGTCA R 2 1 2 1 101000 r 74 goat snp4133-scaffold113-742257 1 53933969 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422636 Affx-122943704 AX-123292982 1 52861695 AACCTACCAATCCAGAGTGGACTGCCTCTTTCTTC[A/G]TTCTTTCCTTGCCCGCCGTGTTTGGGGCCCAGTTT R 2 1 2 1 101000 f 74 goat snp4134-scaffold113-796174 1 53988594 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423427 Affx-122942611 AX-123293773 1 52904268 GAGTAAAAGGGCATGTAATAAAAGTCTTCCTTTCT[A/G]CCCTTTCTTAACATCCACCTGGTTCCCCTCCTAAG R 2 1 2 1 201000 f 74 goat snp4135-scaffold113-838747 1 54031246 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391025 Affx-122966876 AX-123261382 1 52937739 TCATCTCATAAAACATGATCTGGTTTTGTGATTGT[A/G]ATGGCAGATGCTACAGTTATCTGATTTCTTTCTAA R 2 1 2 1 101000 r 74 goat snp4136-scaffold113-872218 1 54065775 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278412 Affx-1111836327 AX-519551897 1 52944895 CAAACAGTAGAGGACAGGGAAGCCTGGCATGCTGC[A/G]ATCCACAGGGTCACAGGACTAAACAACAACATGCC R 2 1 2 1 102000 r 74 goat Random2.2K-58 1 52944895 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275245 Affx-1111834790 AX-123246127 1 52962642 CTGAAAAGGCTGCAGTGATGTGAACAGGTAGCACC[A/G]ACTGAGCAAC R 2 1 2 1 103000 f 74 goat GoatD01.052991 1 52962642 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38449754 Affx-122922453 AX-123320089 1 52971262 AGTCTATCCATTAGCATAAAGGTGTGCAGAGTTAA[C/T]GATGAGTAAACAATATGCATTTTATGTGTTTTACA Y 2 1 2 1 101000 f 74 goat snp4137-scaffold113-905741 1 54099509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399346 Affx-122961357 AX-123269701 1 53006233 GACCTGACCACTGGATGAAGCAGTCTTCATTCACA[A/G]GTTATTAACTATATGATTTGGACAGGCCTCAGCAC R 2 1 2 1 101000 r 74 goat snp4138-scaffold113-940712 1 54134166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794636 Affx-122922834 AX-385281597 1 53039735 TTGACAACATCCTCGTCAGTTCTGTCTAAATTTTG[C/T]GAGATATGCACTTGCTAATTTTATATATTATATAT Y 2 1 2 1 101000 f 74 goat snp4139-scaffold113-974214 1 54167880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419502 Affx-122945456 AX-123289850 1 53068437 GCTGAAGAAAAGGGAAATGTTATCTTGTAAGCAAC[C/T]GCTCTCCACCAGCAGCTGGGTAATAAAATTGCACA Y 2 1 2 1 201000 f 74 goat snp4140-scaffold113-1002916 1 54199056 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399412 Affx-122961238 AX-123269767 1 53106714 ATAAGCCTTTATTCTTTCTTTAAGAGCAACAATTG[C/T]GTCATCTATGTCCTACATATCACATGTTCAGTGTT Y 2 1 2 1 101000 r 74 goat snp4141-scaffold113-1041193 1 54238179 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789809 Affx-122965156 AX-385276816 1 53148518 TATTAAGCTGTGAAGTGACAGGCTAGACTAGAACT[A/G]TGTTCAAACTCTGCTCCTATCCATCTTGGAACTCT R 2 1 2 1 101000 f 74 goat snp4142-scaffold113-1082997 1 54279781 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407855 Affx-122954517 AX-123278206 1 53178256 TTTGGAAACACAGCTTCTCTAAGGCTGCTGTCCCT[C/T]GAGCCTGAGCAGTCAGTGGACCATGCTGCAAAGCT Y 2 1 2 1 101000 f 74 goat snp4143-scaffold113-1112735 1 54309548 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396135 Affx-122963398 AX-123266490 1 53213033 CAAATAAAAGAAAATTTGTTACCAACTGATTTATA[C/T]GGAAGCTGGAACTTCTGAAGAAAAATGGCCTGTGA Y 2 1 2 1 201000 f 74 goat snp4144-scaffold113-1147512 1 54344380 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380835 Affx-122975066 AX-123251193 1 53263948 ACAGCATCTAAGACTTACTTATTGTAGGTACTCAA[C/T]AGAGACCTCTTTGAAGAAAGAGGAAGAGGAGGGAG Y 2 1 2 1 201000 f 74 goat snp4145-scaffold113-1198427 1 54393770 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783652 Affx-122939691 AX-385270711 1 53325463 TGAAACTTCTTTAAAGTAGGAGGATAGTCTATTGT[A/G]TTCTGTTTGGACCCTGTCTCCATTATTTGTGCTTT R 2 1 2 1 101000 f 74 goat snp4147-scaffold113-1259942 1 54456423 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796632 Affx-122932063 AX-385283578 1 53371392 GTCTGGGTTAAACAATCACCAGTGGTATGAGAAGA[C/T]AGTTCACTTTTAGGCATCTCAGCATGTCTTAGTTA Y 2 1 2 1 101000 f 74 goat snp4148-scaffold113-1305871 1 54502712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783108 Affx-122956769 AX-385270175 1 53401600 CTGAATATTTCTACAGTTTGATAGTTGCTACTTAA[C/T]GTTCCTTAAATTCAATCATATATGTAAGAAGTTTA Y 2 1 2 1 101000 f 74 goat snp4149-scaffold113-1336079 1 54532857 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437721 Affx-122931741 AX-123308059 1 53453785 TCACTTATGTGTGTGTTCCATATGCACTGACATGC[A/G]TTAGCTTCAGATGAAAGGAGAAACTTTGTGCTCAT R 2 1 2 1 101000 f 74 goat snp4150-scaffold113-1388264 1 54585286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788657 Affx-122962995 AX-385275673 1 53491417 GTTGAAATCTACCAATAAGAGAAATGTACAAGACC[C/T]TCTTAGCTGTATTAGAAAGAGTCAGTGCTCATTCA Y 2 1 2 1 101000 r 74 goat snp4151-scaffold113-1425896 1 54623217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415780 Affx-122948916 AX-123286129 1 53524854 TGCTGCTACAGGCAAAGCAGATGTTGCTTCAGAAA[C/T]GTTTCTTCCCAAAGGGAAATCCATATGCAATTGAA Y 2 1 2 1 101000 f 74 goat snp4152-scaffold113-1459333 1 54655618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775029 Affx-122973436 AX-385262161 1 53569285 TAAAACATTATTTATTATGTAGGCATGATTTATTT[A/G]CTCTGTGAAAAGAAAGATTTTTTATTCACATACTT R 2 1 2 1 101000 r 74 goat snp4153-scaffold113-1503764 1 54703884 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772852 Affx-122954220 AX-385259997 1 53603860 AAGAATACTTAAAATCCAGTGATCTGCACTCAAGA[C/T]GCCATATTTCTGTCCCCCTTTCAGCTTAATTCTCT Y 2 1 2 1 101000 r 74 goat snp4154-scaffold113-1538339 1 54738946 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463646165 Affx-1110086955 AX-515127116 1 53633334 AGCTAGAGAGAAGCCCACATGCCACAAATAAGACA[C/T]GACCCAGTCAAATATATGGAGAAGGCGAGGGCACC Y 2 1 2 1 202000 r 74 goat 1_53633334_AF-PAKI 1 53633334 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435034 Affx-122933757 AX-123305374 1 53641334 AACAGAAAGAGAAAGTGTCTGAGACAGTCATGAGA[A/C]TGTACTGTTCACATCTTCTTTGATGAGAGAACTTT M 2 1 2 1 101000 f 74 goat snp4155-scaffold113-1575813 1 54776633 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420351 Affx-122944963 AX-123290698 1 53679140 GAAACACTGAGAGTGAAAGAAAGGGAGAAAGATGT[C/T]ATCTAATTTAATCTTTGCAACTCTGTGAGATACTA Y 2 1 2 1 102000 f 74 goat snp4156-scaffold113-1613619 1 54814006 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436928 Affx-122933192 AX-123307266 1 53708705 TGTTCTGTGAATGGAACATTTGAGTAAGTAGAGAA[C/T]GATGTGGCAAAACTTCTTTCTTTGATTTATTAATA Y 2 1 2 1 101000 f 74 goat snp4157-scaffold113-1643184 1 54843876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437422 Affx-122932413 AX-123307760 1 53764757 CTTGGCATTTCCTGGCTTCAAAACAGTCCCAGGTG[A/G]TTGAAACTTTAAGATAACTATATCAATATATATGA R 2 1 2 1 101000 f 74 goat snp4158-scaffold113-1699236 1 54901685 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380809 Affx-122975086 AX-123251167 1 53817917 CTCTGTATAAGAGGGAATTTGAAAAAAGACACAAC[A/G]TTTGTTTAAAAATAGTAATGTAATCTTAAGTAACT R 2 1 2 1 101000 f 74 goat snp4159-scaffold113-1752396 1 54955529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386101 Affx-122971434 AX-123256459 1 53848818 GGTAATGTTCTATTTACAGTGAAAATGTGAAATGC[A/G]TACATTTTTTATTCCCCCCACCCCCAACGAAGTCA R 2 1 2 1 201000 f 74 goat snp4160-scaffold113-1783297 1 54986636 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427557 Affx-122939490 AX-123297900 1 53881996 ACCACATAACAGCTTGCCCCCTAGATCTAATGTAA[A/G]TGGGAAATATTTCTGAGTAAGGACTGCATAAAGCA R 2 1 2 1 201000 r 74 goat snp4161-scaffold113-1816475 1 55020236 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446731 Affx-122924714 AX-123317067 1 53914625 CACAGATATGGAGGCTAGAAGTCTAAGATTAGAGC[A/G]CCAGCATGGTCCCATGAGAGCATTTTGAGGGGAGT R 2 1 2 1 101000 r 74 goat snp4162-scaffold113-1849104 1 55052910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803821 Affx-986696530 AX-385290561 1 53932591 ACTGGAAACAGCTTTGTCTCGGCCCAGTCATACTC[C/T]GCCCCCCTCTCCTGCAACAGCAGCCAGCCATACTC Y 2 1 2 1 600010 f 74 goat 1_53932591 1 53932591 Ancestral_priority_1043 ancestry 0.596 neutral IMAGE 10K 10K ancestral 320803826 Affx-986696533 AX-385290566 1 53932804 GCACTATAATGTATCATTTAATCCGGAACACTTAA[A/C]AAATTACACATAAAATACACATAAAATATAGACAT M 2 1 2 1 600010 f 74 goat 1_53932804 1 53932804 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320778684 Affx-122962718 AX-385265795 1 53953254 TGTAACAAATGTGAGAAAAGAATGGGGTATTCAAG[C/T]ATGGAGCTAGGCAGGGAGTATCAGTTAATTGGAGA Y 2 1 2 1 101000 r 74 goat snp4163-scaffold113-1887733 1 55091371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392017 Affx-122966482 AX-123262374 1 54016253 GAAATTTTAGCACTTCCACCTTCAAAGAACTAAGC[A/G]GCCCTTATTTAGACCAGGGGTGGGCAGAAAAATAA R 2 1 2 1 201000 f 74 goat snp4164-scaffold113-1950732 1 55154788 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435617 Affx-122933782 AX-123305957 1 54054344 TAAGAAATAAAAAACTGGAAATCTAAGAGTTACAT[A/G]CAAACTTAAGAGCTGTTACTCCCAACTCTGAAAAG R 2 1 2 1 201000 f 74 goat snp4165-scaffold113-1988823 1 55193988 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777081 Affx-122938685 AX-385264204 1 54096463 TTACTTAACATGTGAATGCTTAAATTTTAGAGTAA[C/T]GCATTGAGAGTAGAGGAAAAAATGGTCTCTCCTGT Y 2 1 2 1 101000 r 74 goat snp4166-scaffold113-2030942 1 55237486 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410480 Affx-122952203 AX-123280830 1 54135473 AAAAGGGAGAGTGTTTGAAGGCAGAAGCTCAGAAC[C/T]GGACTCTCCCCATAACACTTACGAGATGTGCTACC Y 2 1 2 1 101000 f 74 goat snp4167-scaffold113-2069952 1 55277076 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437589 Affx-122931868 AX-123307927 1 54165327 TGAAAGAGTATTCAAATAAGAGATCAGGAAGTGAA[C/T]AAATCTCTTACTAAGAAATGAATGGGATCTAATAT Y 2 1 2 1 101000 f 74 goat snp4168-scaffold113-2099806 1 55307142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383189 Affx-122973212 AX-123253547 1 54199048 AACAATCCAAGAAACAGAACTGCTAATTCACAGGA[C/T]ATGGATAGTTCTAAAGTTTTAATGTACATTCTAAT Y 2 1 2 1 201000 r 74 goat snp4169-scaffold113-2133527 1 55341198 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396692 Affx-122962829 AX-123267047 1 54243164 TCCAAGCTCTGTCCCAACCTGTCTCTTGGTAGTTC[A/G]CAGAGATTTGCAGCAGGCAAAGAAGTACTAATGGT R 2 1 2 1 101000 r 74 goat snp4170-scaffold113-2177643 1 55386065 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433510 Affx-122935019 AX-123303851 1 54271930 CAAGGAAGGCCTCTAAGCATTCCTTCAAGAACACA[C/T]GGTCCATCAACCATGAGACTTCCCTACCCAACAGC Y 2 1 2 1 201000 r 74 goat snp4171-scaffold113-2206409 1 55415843 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792525 Affx-122924853 AX-385279506 1 54329739 TTCATGCACTTAAGAGTTTCTAACTCACAACATTG[C/T]AATTGACCCTTCAATGATCCCCCTACTTGCAGCTC Y 2 1 2 1 201000 r 74 goat snp4172-scaffold113-2264218 1 55474455 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775137 Affx-122938506 AX-385262269 1 54367245 TTTCTGAATTTGAAAATTAAAGAATCTCTATTAAT[A/C]TTTTCCTTGCGCCTTCTCCTCCAGCAATAATACTT M 2 1 2 1 202000 f 74 goat snp4173-scaffold113-2301724 1 55511972 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437931 Affx-122931636 AX-123308269 1 54397760 TCAGCTAAACTCTAATCTGCCTTGAAGGAAAACTG[C/T]AGTCATTATTTATATTTCACCTGTGAGAGTTAAAT Y 2 1 2 1 101000 f 74 goat snp4174-scaffold113-2332239 1 55542668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442261 Affx-122928276 AX-123312598 1 54435814 AGCTTTCCTCCCACTGCTCTGCTACTAATTCATCC[C/T]TTTGCGCTGTGTGTGCTAAGTCGCTTCAGTCATGT Y 2 1 2 1 101000 f 74 goat snp4175-scaffold113-2370293 1 55581071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781202 Affx-122950269 AX-385268287 1 54483779 GTCATAGCTACAAGTTTTAAGATTTTTGGCCTTTA[C/T]AGAAACTTTCAGCGTTTCAATTTCAATCACAGCTT Y 2 1 2 1 101000 f 74 goat snp4176-scaffold113-2418258 1 55629430 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767886 Affx-122968403 AX-385255106 1 54532428 TGCATCTATTCATTAGCTAAGTGCTGGGTATGTAT[A/G]TAGTAGTCAGCCGAATAGACTAGATTATAATGAAG R 2 1 2 1 101000 f 74 goat snp4177-scaffold113-2466907 1 55678216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422501 Affx-122943304 AX-123292847 1 54566794 GATTTTCTAGCTGAACCTTGAAGAAAGAGTTTTCC[A/G]TTTCTGAGGGAAGTCAGTAAAAAAGCATTCTAGGC R 2 1 2 1 101000 r 74 goat snp4178-scaffold113-2501273 1 55712735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790624 Affx-122935144 AX-385277626 1 54615101 AGAGTCATTTAATATTCCTGCTCTTCCTGTCATCA[A/G]TTGAGCAGCCAGATTAACCCTTTTAAAGGACATGC R 2 1 2 1 101000 r 74 goat snp4179-scaffold113-2549580 1 55761118 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407262 Affx-122955349 AX-123277613 1 54649539 TATTAATTTTTTCCCACTTTATCACAGGCAGCAGT[A/G]CCTCTAAAGTTTATCCCACCGTGTAATAGGATCCC R 2 1 2 1 101000 r 74 goat snp4180-scaffold113-2584018 1 55795713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798563 Affx-122922813 AX-385285496 1 54717481 GCTAAGTGCAATTTAAGGAGTGAGGATGTGCAACC[G/T]GGAAAGTAAGCCATTAGCAATAAAGTTAGGCCATT K 2 1 2 1 101000 f 74 goat snp4182-scaffold113-2651960 1 55863809 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446800 Affx-122925297 AX-123317136 1 54766318 AAGAAGGCTGGAGGCAAATTCAATACGTGGTGAAA[C/T]GAATGTGTAGTGGAAGTGGAGCTATGTGTTTTCAG Y 2 1 2 1 101000 f 74 goat snp4183-scaffold113-2700797 1 55912815 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426696 Affx-122939901 AX-123297042 1 54821852 AGCACATCACTGGACTTGGCAGTGGTCTTGGCAAC[G/T]CATGATGTACCACCTTTCTGCCATCACTTAATAAC K 2 1 2 1 201000 r 74 goat snp4184-scaffold113-2756331 1 55967635 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417747 Affx-122947418 AX-123288095 1 54865591 ATAACAGAATTTGGGTTAGTGCAAAGGAAAGGTAC[A/G]TCTGGGCAGCTGGACACTCCCGTCTTAGGTGTTGC R 2 1 2 1 101000 f 74 goat snp4185-scaffold113-2800070 1 56011198 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453105 Affx-122920029 AX-123323438 1 54926113 ACTCATAGTCCTGGTAACCTAAGCTATGTGGATGT[A/G]TAAATGAGCTCCCTTGACCTCTGGTCCAGCCAATG R 2 1 2 1 101000 f 74 goat snp4186-scaffold113-2860592 1 56072310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772280 Affx-122963953 AX-385259436 1 54964549 TCATCATCTCCATTGTCACAAAGAACAACTGGATT[A/G]CTCTGTGTGGAATGCCTAGTCCAGAGCTGGCACGA R 2 1 2 1 202000 r 74 goat snp4187-scaffold113-2899028 1 56110177 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410358 Affx-122952997 AX-123280708 1 55007519 TTGAATGTTGAAGAGGATTTGCCATGTTGTGAGTG[C/T]AAACATAACCTTGAAACAGAAAAGACAAAAAGCAA Y 2 1 2 1 101000 f 74 goat snp4188-scaffold113-2941998 1 56153035 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445857 Affx-122925999 AX-123316194 1 55046263 ATCTGGGTAGTTTGGCTGATGCTTTAGATTGAACA[A/G]GTTTCTGGGTCAGTTTTAAAGTTTCTCTTTGGTGC R 2 1 2 1 101000 f 74 goat snp4189-scaffold113-2980742 1 56191399 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391922 Affx-122966939 AX-123262279 1 55091550 TCCCTGGGTATCAGGGAATAGCCATTATCCAAGCA[C/T]GGAGAAGAGCAAATCCCTGCTGGTATTCTCTGGCT Y 2 1 2 1 101000 f 74 goat snp24547-scaffold2495-471333 1 56236441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408017 Affx-122954305 AX-123278368 1 55123598 CACCATATAAGACTTATCTTAAGAAATGAATCCTT[A/G]AAAACATCAGCCCAGCAATGACAGAAAAGAATTCT R 2 1 2 1 201000 f 74 goat snp24546-scaffold2495-439285 1 56269055 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278292 Affx-1111836347 AX-519551779 1 55130041 TTCTAAATGGGCACCAACATGCATCCTAGTAAAAT[A/T]ACTGGACTTCAAAGATAAAGAAGAGGTAAAAAATA W 4 1 2 1 101000 f 74 goat Random2.2K-61 1 55130041 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38453495 Affx-122919825 AX-123323828 1 55153342 CAGACTAGTTCTCAGGGAGGAGGTAAGCCCTTTGA[C/T]GAAGAAAGCCACCTTGAATATTCTCTTGGGGGAAC Y 2 1 2 1 101000 f 74 goat snp24545-scaffold2495-409541 1 56299249 C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452575 Affx-122920511 AX-123322908 1 55194426 TGTGATTTCCTTTGCTTGCCATTTTAGTTACTTGC[A/G]GTCACCAGATATTCCAGAAGTAAACAATGTGTAAG R 2 1 2 1 201000 r 74 goat snp24544-scaffold2495-368457 1 56339817 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379668 Affx-122975928 AX-123250026 1 55226295 GAGAACCTGAGAGCATCAATGATAAGCTAACACAA[A/G]CAATAAAATGAATGTACTCTTTTTTTAAATGCTAA R 2 1 2 1 101000 f 74 goat snp24543-scaffold2495-336588 1 56372525 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415641 Affx-122948577 AX-123285990 1 55262534 TCCCGAAGGACAGGCTGGGGGGTTCCTGAGGCCTG[C/T]CTGAGGCTGTCCAAGTCTGCATCATCAAACTCGAC Y 2 1 2 1 101000 r 74 goat snp24542-scaffold2495-300349 1 56408820 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382989 Affx-122973340 AX-123253347 1 55294084 AGCTTAAACGTCTAAATATATGGTACCTCAGCTGA[C/T]AGATCTTGAAGCAGGTCAGAAAGCATACACCAGTT Y 2 1 2 1 201000 f 74 goat snp24541-scaffold2495-268799 1 56440284 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421219 Affx-122944133 AX-123291566 1 55331509 CTCCTCCCTCCTGAGCAATTCCAAAAAAACAAGTG[A/G]TCCCTGAAATTACAAATAAGGGTACAGACCTCCCC R 2 1 2 1 101000 r 74 goat snp24540-scaffold2495-231374 1 56477612 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447572 Affx-122924027 AX-123317908 1 55407095 TAGACACGTCAGAAGAGATGAATTATGTCATCCAA[C/T]ATTTAGTAGGTGCTCAGTAAGTATCTTTCAAGTGG Y 2 1 2 1 101000 f 74 goat snp24538-scaffold2495-155788 1 56552803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407882 Affx-122954497 AX-123278233 1 55477443 CTATGTTTCAGGCATTCTTCTGGGTGCTTGAGATG[C/T]GTCTGAAGAGATAGCTGAATAAAACAAACTCATTG Y 2 1 2 1 201000 r 74 goat snp24537-scaffold2495-85440 1 56625113 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397828 Affx-122962478 AX-123268183 1 55537727 GTTCAGTGGCTTGAAGAGTTATCTGTACTTTTCCC[A/G]TGGTTTCAGGAGAAGCTTTTGAAAAAGCCACTGCA R 2 1 2 1 201000 r 74 goat snp24536-scaffold2495-25156 1 56686399 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427888 Affx-122939694 AX-123298231 1 55579623 CCTTTATTATAGCATAATTACAATTATTACCTTTA[C/T]ACCTCTCCCCCCTTCTATAATTTTTTCCTCATTAA Y 2 1 2 1 201000 f 74 goat snp12450-scaffold1474-602914 1 56725680 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278463 Affx-1111836351 AX-519551946 1 55632931 AAAAAAAAAAAAGAGGATAAATCCAAAAATTAAGA[A/C]TAGAATCCAGGAGTTAAGAATAGTACTGATTTTGG M 2 1 2 1 101000 r 74 goat Random2.2K-62 1 55632931 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409418 Affx-122954127 AX-123279769 1 55699285 CATGGAGGTTCAAGTAATCATTAAACACGCAGAAA[C/T]AGCCAAGGTAGAGGGGATCGGAGCAGCAGAGTAAA Y 2 1 2 1 101000 f 74 goat snp12448-scaffold1474-483252 1 56841317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775081 Affx-122948651 AX-385262213 1 55747622 AGTTTATAAATTTTCACTGCCAAGAAAATTTTGTG[A/C]TTGAGTTATTCTAAGTGACTCAAATGTTTACAACT M 2 1 2 1 202000 r 74 goat snp12447-scaffold1474-434915 1 56888761 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447254 Affx-122924952 AX-123317590 1 55805334 TTTCAGTTAAAAAATTAAAAAGAAAAATTAAAGTC[A/G]AAAGACTCTTGCTCTTCTAAGAAAGTTAAATGAAT R 2 1 2 1 103000 r 74 goat snp12446-scaffold1474-377203 1 56946078 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380812 Affx-122975084 AX-123251170 1 55833968 TCAGGGAAGTTGAGTGGAGAGTACAGAAAGTTCCC[A/G]TATGTCCCCTGCCCTCAAACAGGCACAGCCTCTTA R 2 1 2 1 201000 f 74 goat snp12445-scaffold1474-348569 1 56975517 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398591 Affx-122961494 AX-123268946 1 55868059 TGTCAGTAGGCTGCCCCATCCTCAGTGAGTGACTC[C/T]AGCTGAGAGGCCCTGGACCACTTGATGCTCAACTT Y 2 1 2 1 102000 r 74 goat snp12444-scaffold1474-314478 1 57009873 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778391 Affx-122949130 AX-385265506 1 55915586 TTACTCAGTTAATTTACTCAGGTAATTACTCTGAT[A/G]TCACCATTTTATGTAGCATAGGAGATTGACCAGTT R 2 1 2 1 101000 r 74 goat snp12443-scaffold1474-266951 1 57057795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778015 Affx-122978610 AX-385265131 1 55968340 AAACTGTGGAGAAAAAACCCATCACAGCTGTAACT[A/G]ATGTAAAATACAAGAGATAACTGAGGACTTTCACC R 2 1 2 1 101000 f 74 goat snp12442-scaffold1474-214197 1 57109888 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452513 Affx-122920556 AX-123322846 1 56018601 TAGCCTACCACAACCAGATCTCAGAATTGGAGGTC[A/G]TAGTGGCCTTTCCCTGTGTAATGGCTGACCACAAT R 2 1 2 1 101000 f 74 goat snp12441-scaffold1474-163936 1 57157818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430368 Affx-122937785 AX-123300709 1 56064268 AGTGAAGAATGATCCAGCCCATGATGTTAATAATG[A/C]TGAGGTTAGAAAACCCTGCTTTAAGCTCTTATATT M 2 1 2 1 101000 f 74 goat snp12440-scaffold1474-118269 1 57203991 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788284 Affx-122952635 AX-385275302 1 56100920 TGTTCTTAAACCAAATGCGACCAACCAATTGAGCA[C/T]GTATGAGAACCAGAATAACTGGTCATGACAACAGC Y 2 1 2 1 101000 r 74 goat snp12439-scaffold1474-81617 1 57240702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419416 Affx-122945522 AX-123289764 1 56144191 TTCCATTAGAAGGTAGTAATTAGAGAAAACGAAAC[A/G]TACACTTAACAGTATTTGTTACTTTTAGAAACAGA R 2 1 2 1 101000 f 74 goat snp12438-scaffold1474-38346 1 57285055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773101 Affx-122937790 AX-385260244 1 56180368 CTTCTAGGGCCACTGTAAACTGGAACCTTATCTTC[A/G]TTGATATTTATGGTAAACTTGTATTAAAAAAGTAT R 2 1 2 1 101000 f 74 goat snp12437-scaffold1474-2169 1 57313168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271832 Affx-1111832862 AX-519545616 1 56198096 ATGAGGGGTAATAATAATAGAAGTGCATGTGGAGG[A/G]CAATTACATTTTGATGGGGGAAGGGCCAAGAGATG R 2 1 2 1 201000 f 74 goat 1_56198096_AF-PAKI 1 56198096 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320780449 Affx-122952456 AX-385267540 1 56200120 TGCATATAGGTCTCAAAAACTATGAAACTGAGAAC[G/T]TGAACAAAGTAAAGACTGTTACCTCTCTCTCTGTA K 2 1 2 1 101000 r 74 goat snp609-scaffold1017-548943 1 57341585 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412283 Affx-122950879 AX-123282632 1 56245804 AACCCTAACTCTCCCACAGGAAAAATGTAGAACTC[C/T]GACCTCACTCTCCTTCCACCTCTGATCTACATTTG Y 2 1 2 1 101000 f 74 goat snp608-scaffold1017-503259 1 57387637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794138 Affx-122975813 AX-385281104 1 56277279 TGAGTTAAATGGTGCCTCCACCTCAAGATCTGTCC[A/G]CCAGGAACCTACAAATGTGGGTACATTTGGACAAA R 2 1 2 1 101000 f 74 goat snp607-scaffold1017-471784 1 57419570 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401022 Affx-122959676 AX-123271375 1 56307896 GATTCTTTACCACTAGCTCCACCTGGGAAGCCCAG[C/T]GGTAGTAATAGCTTCTCTTTTTTTCCTCATCCTCT Y 2 1 2 1 101000 r 74 goat snp606-scaffold1017-441167 1 57450345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393930 Affx-122965077 AX-123264285 1 56365921 CAAAGCATTTCAATTTGGCAAGGTTATTTAAACAG[C/T]AAAAATAATATTAATTTTTCTAAGGGTAAATACTG Y 2 1 2 1 101000 f 74 goat snp605-scaffold1017-383142 1 57508982 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431056 Affx-122936643 AX-123301397 1 56400985 TGCGACCTTGGGTTACACCTGAGCAGAACTGCAGA[C/T]GCCTACACAGGTGATGCATAATTCCTCTGTGACCA Y 2 1 2 1 101000 r 74 goat snp604-scaffold1017-348078 1 57544769 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439858 Affx-122930448 AX-123310195 1 56453627 GAACCACTTGCCAAGAAGCCAGTGTTTCTGTCTTC[A/G]CTAGACTATAAGTTCCTGGAATGTATGCACCCTGT R 2 1 2 1 201000 r 74 goat snp603-scaffold1017-295436 1 57597486 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799369 Affx-122940981 AX-385286299 1 56483905 AGTCATGGCCAATATACTATACTCCTAATACTATA[C/T]GTCTCCCAGGAAGTTTATACATTGTGACGATAATA Y 2 1 2 1 101000 r 74 goat snp602-scaffold1017-265158 1 57627853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776455 Affx-122977733 AX-385263582 1 56552928 CTTCTCCTGAGACATCTTTAGAAATAGCAAATTCA[A/G]TCATGCCATATCGATTCCTCTTTCCGACCTCACCA R 2 1 2 1 101000 f 74 goat snp600-scaffold1017-196135 1 57696147 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430085 Affx-122937538 AX-123300426 1 56593759 TTGTCACGGCTTCCAAGCAATGAGGATCTCTGCTG[C/T]GCCACATCACTGCCCAGTGTACAGACTAAAAGCAT Y 2 1 2 1 101000 r 74 goat snp599-scaffold1017-155304 1 57737055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416248 Affx-122948206 AX-123286597 1 56645824 TAGACTGACTAGGCATGGTGGGGAGAGGGGCACAC[A/G]TTTACCTGTAACAAATGAGAGTAGCTCAGACAAAT R 2 1 2 1 101000 r 74 goat snp598-scaffold1017-103239 1 57786867 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396848 Affx-122963259 AX-123267203 1 56675015 TCTTTTTCTTTTTTTTCCACTACAACATAGACAGT[A/G]TAGAGGCACTGTGGGGTTCCAGAGGAGAGGATATA R 2 1 2 1 201000 f 74 goat snp597-scaffold1017-74048 1 57816005 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445290 Affx-122925453 AX-123315627 1 56720318 TTCACAGGCTCTTACAAGTTTGTTATCTCATAATC[A/G]CACCAGGTTAACACTTCCAGAGATACCAGTGTATC R 2 1 2 1 101000 f 74 goat snp596-scaffold1017-28745 1 57862262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782144 Affx-122975175 AX-385269222 1 56762876 AACTGTCAAGATTTAGTCATATTTATTGAGCCCTC[A/G]CTGTATTAAAGAGAATGTATAGTAGTGATAGTATA R 2 1 2 1 101000 f 74 goat snp35158-scaffold4205-266708 1 57905519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446899 Affx-122924708 AX-123317235 1 56834009 ATTATGTACCTTGATGTAACATTCTTTGTGTTTCA[G/T]ATTTTGTTGAGTTTGGAAAGCAGGTTCATGGGTAA K 2 1 2 1 101000 r 74 goat snp35156-scaffold4205-195575 1 57976652 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424108 Affx-122942026 AX-123294454 1 56885348 CTCATTTTAGTCTCAGAAAAGCACTTGTAACTATG[C/T]GCATTTTGAAACAGTCTTGAATGTCTGGTTGCTGA Y 2 1 2 1 101000 r 74 goat snp35155-scaffold4205-144236 1 58027916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403508 Affx-122957632 AX-123273861 1 56940085 AGGCTTAGTCACTGACAATGCAGAACACTCCACTG[C/T]GGCCCGAGCTTTTGTGGCCAGGATGAAGATGTCCT Y 2 1 2 1 101000 f 74 goat snp35154-scaffold4205-89499 1 58083194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445328 Affx-122925424 AX-123315665 1 56969767 GCAGAGTACATAGATATTTTCCATTTTGTCCTTGC[A/G]TTTTGCATCAGGCCATAAGGATGATAGCCAGTTGT R 2 1 2 1 101000 r 74 goat snp35153-scaffold4205-59817 1 58112935 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389865 Affx-122968149 AX-123260222 1 57013033 GAAATAAATTGTTCTGAAGTGTTTTGCCTAACCAA[A/G]GATTTGGAAGAAGATCAGAATTGAAATGTTAGCTG R 2 1 2 1 101000 f 74 goat snp35152-scaffold4205-16551 1 58156502 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380459 Affx-122975735 AX-123250817 1 57036210 CAATATAACCTGTCTTATATTTAAAATAAATTACT[A/G]CACCCAGTTTGTAGTACAGTACTGAAGAGCAATAT R 2 1 2 1 101000 r 74 goat snp37452-scaffold456-5411884 1 58179430 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387858 Affx-122969643 AX-123258216 1 57136000 GTACTCTTGCCTAGAAAATTCATAGACACAGAGAG[C/T]GGAATGGAAGTTTTAGGGAGAGAAGGCAAAATGGG Y 2 1 2 1 201000 r 74 goat snp37450-scaffold456-5312094 1 58280097 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427143 Affx-122939641 AX-123297486 1 57165223 TCTCCAGGGAAATATGATGAGTGAAAACAGCCAAC[A/G]TAGAGTGTTACATAACTGTACTATCCCCTTTATAT R 2 1 2 1 101000 f 74 goat snp37449-scaffold456-5282871 1 58304411 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440530 Affx-122929336 AX-123310867 1 57203069 TCTCAAAGATGACACTAACTTGATCAGTTAACCAC[G/T]ATTTGGAGAATGGCCTCAGCACTGTTGACTTCCTA K 2 1 2 1 101000 f 74 goat snp37448-scaffold456-5245025 1 58342168 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452931 Affx-122920189 AX-123323264 1 57267821 GCACAGGTCGCACGCAGGTTCCCAGCATCTCCACC[A/G]TAAGCGCTTTGGCTGCTCAAGCCCTCGCTTCTCTA R 2 1 2 1 101000 r 74 goat snp37447-scaffold456-5180273 1 58407118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422239 Affx-122944012 AX-123292585 1 57305221 TCCCCTAGTCTTATTTCTGCCTCCTTAAAGACAGT[C/T]TCATTCCTGACATCTGTGGCACCCCCACTATTCTT Y 2 1 2 1 101000 f 74 goat snp37446-scaffold456-5142873 1 58445648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382697 Affx-122973636 AX-123253055 1 57342111 GAAGGGAAAAATAGCAACTTTACACTGGAAAAGCT[A/G]CCTTAACCAAGTGATGGGTCATATTCTCAGTAATA R 2 1 2 1 101000 r 74 goat snp37445-scaffold456-5105983 1 58482700 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415351 Affx-122948782 AX-123285700 1 57389759 TGAACAGGAATATAAACATATGAACAAGTCCAGTC[C/T]AATATATTTCAAAACAAGAAGATTCTTGAGAATAG Y 2 1 2 1 101000 f 74 goat snp37444-scaffold456-5058335 1 58530099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391182 Affx-122967430 AX-123261539 1 57419893 GAAGACTCCCTGTGCCCACCTTTAGCTGCCAGGCC[A/G]CAGTGCTGCTGGCCAAGTCCTGCTCAGAACTATGG R 2 1 2 1 101000 r 74 goat snp37443-scaffold456-5028201 1 58560320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382706 Affx-122973629 AX-123253064 1 57452878 TTTTAGACTCCTATGACCTCCCACAGCTTCCTAAA[C/T]GGCCCTTCAACCACGCTCAGAATTATTTCCCCAGA Y 2 1 2 1 101000 r 74 goat snp37442-scaffold456-4995216 1 58593673 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385730 Affx-122971094 AX-123256088 1 57504377 CTGCTGAGAAGGAACTGATGAGATGTGACATAGAA[C/T]GGGGAAGCAGGATGTCTTTGTTTTGAAATGACAGG Y 2 1 2 1 101000 f 74 goat snp37441-scaffold456-4943717 1 58645840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798938 Affx-122956520 AX-385285868 1 57560141 GTCCAGCTTTCAATTCTCTCACCACTGATTTAATT[A/C]AAGTGACAGGAATGCCAATGCTTTCGTACTAGTCC M 2 1 2 1 101000 r 74 goat snp37440-scaffold456-4887953 1 58701370 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433519 Affx-122935012 AX-123303860 1 57616660 GGGTGGCAATAGGTCAGGCTGTCCACGTGTGCCAC[A/G]TTTCAGACTGCTGCCTTCCTCCTGGCAACTGTCTG R 2 1 2 1 101000 r 74 goat snp37439-scaffold456-4831434 1 58757875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416228 Affx-122948220 AX-123286577 1 57657118 ATGTCTCCATTTAAGTATAATATGCACAATTTAAA[G/T]CAAATGTTAGACATATTTAAAATGTACACTTACGT K 2 1 2 1 202000 f 74 goat snp37438-scaffold456-4790976 1 58798085 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419551 Affx-122945416 AX-123289899 1 57702372 TCGGAATCTCACTAGTGCTCTCAATAGCCTCCCCC[A/G]CACCTGGCCTTCCTGACCAAAGTGAGCACACTGTC R 2 1 2 1 101000 r 74 goat snp37437-scaffold456-4745722 1 58843306 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380765 Affx-122975117 AX-123251123 1 57742551 ACTTAGCACAATGCCTGGCAGATAGGAAAATATTC[A/G]TTAAATAAAATGTGAATAAATTTGCACTCCCATCA R 2 1 2 1 303000 r 74 goat snp37436-scaffold456-4705543 1 58883659 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772015 Affx-122943192 AX-385259171 1 57781932 TGTTAGAGCTCTCCCTGAGTCTGTCATGAGATTTA[C/T]ATTCTTAATCATATGGAGCCCATTTTGGCCATTTA Y 2 1 2 1 101000 f 74 goat snp37435-scaffold456-4666162 1 58923035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375390 Affx-122979214 AX-123245749 1 57831380 AGGAGAGGGATTCTGTCTCAGAATCTCCAGAAAGA[C/T]GCAATCCACTGACACCTTGATTTAAGGATTTCTGA Y 2 1 2 1 101000 f 74 goat snp37434-scaffold456-4616714 1 58972567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781355 Affx-122931444 AX-385268441 1 57860201 TTTATGCACAGTTTCCAAATAACAACAATTTAAGA[C/T]ATAGATATGACCATCCACTTCAGAAAAAAGATAGT Y 2 1 2 1 101000 f 74 goat snp37433-scaffold456-4587893 1 59001370 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800730 Affx-122934506 AX-385287647 1 57933538 AACAGTGAAATATGAAAAGACCTATTCAGATTTAC[C/T]AAAAATCTCCCATGATACCATTATCCATTATATTT Y 2 1 2 1 201000 r 74 goat snp37432-scaffold456-4514556 1 59074768 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773909 Affx-122931037 AX-385261048 1 57965981 ACACTTTCTGTGGAATGTAATTTAGTAAGATGTCC[A/G]TCTAAGCTTTCCTCAACCATTCTTTAGGTCAGATT R 2 1 2 1 101000 f 74 goat snp37431-scaffold456-4482113 1 59107226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415163 Affx-122949399 AX-123285512 1 58019331 TGTTTGTGAAAGTGCTTTATACACTGTAAAACACT[A/G]TACAAATGCTATTTCTTTCTTCTTATGAGTGGATG R 2 1 2 1 303000 f 74 goat snp37430-scaffold456-4428763 1 59160216 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273493 Affx-1111833651 AX-519547109 1 58034921 GTTTTCAGTCTACAAAGTCCATCACGACATTCAGG[A/C]CTCTGGACTGGACTATTAGACTGTACTCTTTCTGC M 2 1 2 1 101000 f 74 goat GoatD01.000586 1 58034921 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38431253 Affx-122937125 AX-123301594 1 58059569 AAAAATTATTTTTAAAATGAATATAAATAATTTTC[A/G]TTATTGTAGCTAAGGCATGAGCTGTGTCCTCAAAC R 2 1 2 1 103000 r 74 goat snp37429-scaffold456-4388525 1 59200339 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773033 Affx-122929414 AX-385260177 1 58115236 ACAGAGGGCTGCTGTTACATGCTAAAAACACGTTA[C/T]AGAGGGCTTCTGTTACTTGTGCCGAGGTTAGAGCA Y 2 1 2 1 101000 r 74 goat snp37428-scaffold456-4332858 1 59256309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413655 Affx-122950121 AX-123284004 1 58182399 TCTCCTTGGAGGTAAACTAATATTGAATATATAAA[C/T]GATGGACTTTGGAATCAGTTCTGAGTTTGAATCCT Y 2 1 2 1 201000 f 74 goat snp37426-scaffold456-4265695 1 59323418 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800912 Affx-122930391 AX-385287827 1 58237595 AAGAGGTCATATGACTGATACTCTGACTCTCTAAG[C/T]GTTTTCCTTTCCTCGATATTCAGCAAGTTTGGCTC Y 2 1 2 1 101000 f 74 goat snp37425-scaffold456-4210499 1 59378737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445392 Affx-122925395 AX-123315729 1 58268365 TATTCTATTCTTCAGCCTCTCATAAATTTACTTCT[A/G]CATATAAGCCAATTAAATTTTATTCATTAGTTGTA R 2 1 2 1 101000 f 74 goat snp37424-scaffold456-4179729 1 59409177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791859 Affx-122920229 AX-385278849 1 58305351 TTTCTAAAATTATGGAAGAACCTTGTGTCCTTTCT[A/G]TTCATTAATTATTGCCAGCAATATTTTGGGGGTGA R 2 1 2 1 201000 f 74 goat snp37423-scaffold456-4142743 1 59446198 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796912 Affx-122924579 AX-385283853 1 58357297 TAGCATCCCAGAAAATACCCATCTTTATTCTGAAA[C/T]ATGATATGCTTGGTATTCAGACTTCTCCCTAGTGA Y 2 1 2 1 101000 r 74 goat snp37422-scaffold456-4090797 1 59498389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432285 Affx-122936324 AX-123302626 1 58414215 AGGATACTCTGTATTTTGCCCCCGTCTGACCTAAA[C/T]GCATCCTGACAGTATCTTCCCCCTCAAATCTTAAT Y 2 1 2 1 201000 r 74 goat snp37421-scaffold456-4033879 1 59555493 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769737 Affx-122957244 AX-385256907 1 58446664 ATGATGAAAGGTAAATAAATGTTCAGCATAATGCT[C/T]AGGGACCTCCTTGAGCTCCAGATATAGTTGTGCTT Y 2 1 2 1 101000 r 74 goat snp37420-scaffold456-4001430 1 59587958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440505 Affx-122929355 AX-123310842 1 58481314 GCTTCCTGGCACTGTAAAATATACTTTAAAAAATA[C/T]AATAATCTTTTGTTCTTTTAGGAAAAAGATTTATA Y 2 1 2 1 103000 f 74 goat snp37419-scaffold456-3966780 1 59622861 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389324 Affx-122968490 AX-123259682 1 58517560 AAAGCTGTTCCAAACAGCAGGCTGTTAGTCCCAGG[A/C]CCTGCCTGATGTCCCAGTACCGCCTCCCCCAGAGT M 2 1 2 1 101000 f 74 goat snp37418-scaffold456-3930534 1 59658933 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786579 Affx-122970246 AX-385273611 1 58547244 CTCTTAATAGGTAAATATGCCCATGGGCTTTTTGT[A/G]CTCCATTTGTGAAGCTATAGTATAGGTTGTCCCAA R 2 1 2 1 101000 f 74 goat snp37417-scaffold456-3900850 1 59688632 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440424 Affx-122929421 AX-123310761 1 58602389 CAATATCACCTTCAGGTTTTATACATATCTTCAAT[A/G]CAGCAGACTTTCGGGACCAGGCAGAGCCTGAGGAC R 2 1 2 1 201000 f 74 goat snp37416-scaffold456-3845705 1 59742488 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450553 Affx-122922473 AX-123320887 1 58655432 GATGTAGACAAAAGAAAAACACATACACAAAATTC[A/G]CTAAATTAACTGATTAATTGAAATAAACATAGAAA R 2 1 2 1 201000 r 74 goat snp37415-scaffold456-3792662 1 59794887 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396878 Affx-122963237 AX-123267233 1 58684281 CATTCTTGTTACTTTTTTTTCTTTTCCAGAGTTTA[C/T]AGAATTGAAAGGAGAGAATCAGTTGGTAATTTCTC Y 2 1 2 1 101000 r 74 goat snp37414-scaffold456-3763813 1 59823879 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398409 Affx-122961633 AX-123268764 1 58742561 TTTCCATCACCCTCCATACATGTCTTCCTGAGCCT[A/G]TCTCTAAACTGAATATTACATCTTTCTACTTCTTT R 2 1 2 1 201000 r 74 goat snp37413-scaffold456-3705533 1 59884268 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271833 Affx-1111832863 AX-519545617 1 58782018 AGGCTTGACAGTTGTCAGGAAAGGTTTTCCTGGGA[A/C]GAGCTCCGACGGCTCTCCTGCCTTGGTTCAGCCCG M 2 1 2 1 101000 f 74 goat 1_58782018_AF-PAKI 1 58782018 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454008 Affx-122919431 AX-123324341 1 58797469 GTGTTTTGAGGTAGGTAAGGGCATTTCCAGAGAAG[A/G]GGACATGGTTCTCCAAAAGTGAGTGGACGCCCAAA R 2 1 2 1 101000 f 74 goat snp37412-scaffold456-3650625 1 59939542 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391420 Affx-122966763 AX-123261777 1 58844891 TTTGTGTAGGGCACTGAGAGATAAGAGCAGGAAAT[A/G]CTGGGAAAAAGAAGACACATTTCCAATCTCTAGGG R 2 1 2 1 101000 f 74 goat snp37411-scaffold456-3603203 1 59987517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775411 Affx-122949509 AX-385262542 1 58898384 AACACATTGATCCCTGCATCCAATAGCAAGTCCTC[A/G]GTATATATCCACCCAGTGCTTGTGTGTATATATCC R 2 1 2 1 101000 f 74 goat snp37410-scaffold456-3549710 1 60041106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765124 Affx-122973558 AX-385252683 1 58929231 TCTCTCGCCAGGGAAAGATGAATGATTGAATAATA[G/T]CTTTTTTAGGCCCCCTGCCTCAACAAGACAGTCAG K 2 1 2 1 101000 f 74 goat snp37409-scaffold456-3518863 1 60072299 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448913 Affx-122923170 AX-123319248 1 58994299 ATCCTTCCTGAGGAAGAAAGAGTGAACCACATTGC[A/G]TCTGTCACTTCGGTTGTTTTCTCACTTCACTGATA R 2 1 2 1 101000 r 74 goat snp37407-scaffold456-3453795 1 60137712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385333 Affx-122971659 AX-123255691 1 59026527 GGGGACCCTGCTTATAATAGCGGTGACTCAGCACC[A/G]CCTTGCAGATCTTTCCCTCTTTCAGCTCCTTACAG R 2 1 2 1 201000 f 74 goat snp37406-scaffold456-3421567 1 60170819 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414145 Affx-122949698 AX-123284494 1 59055126 GCTGATCTGAGTACCCCTTTCTTTTTCTTTCCCAA[C/T]GCCTAAGGGAAGAATCAAGGTGGTCTTTCTGGTGG Y 2 1 2 1 101000 r 74 goat snp37405-scaffold456-3392968 1 60199074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794614 Affx-122956980 AX-385281576 1 59090896 TTGACCTGGTGTGTTGACTCAAGATTCCCACTCCC[A/G]CTGCAGCTAAATTTTGCACTTTTCATGTCAAACAT R 2 1 2 1 101000 f 74 goat snp37404-scaffold456-3357198 1 60234782 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278488 Affx-1111836362 AX-519551971 1 59096342 TTCCCTTTCTGGGAAGCACTCTAATATAACGGAAA[A/G]TTTTGAAATTTGAAATCTTGCTTTCTAGTTCTGCC R 2 1 2 1 101000 r 74 goat Random2.2K-64 1 59096342 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422927 Affx-122943038 AX-123293273 1 59140875 CAGTTTGCATAATCCACACCCTGTTGTGTCTTACT[A/G]TTCAAAGAGGGAGCATTTCTATAGCAGAGTAACCA R 2 1 2 1 101000 r 74 goat snp37403-scaffold456-3307219 1 60284002 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447014 Affx-122924549 AX-123317350 1 59181352 TTTAGAGAGAAAATGGGGAAATGTGGAACTCTGAA[C/T]GACAAAAGGGATTTATACCAAAAGACACTGAGATA Y 2 1 2 1 101000 r 74 goat snp37402-scaffold456-3266742 1 60323049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433545 Affx-122934994 AX-123303886 1 59211823 TCTTATCCTAGATCTGTGCTGGTAATATCCCTACA[G/T]AAGAATCCACCAACAGACCTGGGGTCTTAATGGCA K 2 1 2 1 101000 f 74 goat snp37401-scaffold456-3236271 1 60353585 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423752 Affx-122942851 AX-123294098 1 59247772 CATTTATGGTAGCTCTGCTGGCACCAGAATTTTGC[G/T]AGCTAGAGCACTGAGCTAAGTTACCCAGTAAAGGA K 2 1 2 1 202000 r 74 goat snp37400-scaffold456-3200322 1 60389735 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416843 Affx-122948108 AX-123287191 1 59279202 CTACAATGTTAACAGGTTTGGAAAATGTATTTTGC[A/G]TCTTTAGAAAGTGGGAAAGATTGAGGACAAGAGGG R 2 1 2 1 201000 r 74 goat snp37399-scaffold456-3168892 1 60421729 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442819 Affx-122927708 AX-123313156 1 59355179 AGCAACTTAGCATGCAGGATGCATGCTGCTCAGGA[G/T]TCCTCAATACCGTTTATTTATGTATTCCACTTTAA K 2 1 2 1 201000 r 74 goat snp37397-scaffold456-3092915 1 60498241 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429087 Affx-122938273 AX-123299429 1 59383709 GAATTGAGTCTGAAATTGTTTCCAGAACCTAAAAC[A/G]TAAATCATATCTTAAATAATCTCATTTAATCCAAA R 2 1 2 1 101000 f 74 goat snp37396-scaffold456-3064385 1 60526698 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278501 Affx-1111836369 AX-519551984 1 59397299 GTAAAATGTGAAGTGTAGATGTATAACAGATAAGA[A/C]AGGCAGCCATTTGTATAAGCTTTGACTATGTAATT M 2 1 2 1 101000 r 74 goat Random2.2K-66 1 59397299 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378229 Affx-122976914 AX-123248588 1 59414390 ATCACTAGCCTTCATTGTAGTGTCTCTGTCACAAA[C/T]GTGACTTATAATTCAAGGGCTTTGCTGGTGGCAAT Y 2 1 2 1 101000 f 74 goat snp37395-scaffold456-3033704 1 60557330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434235 Affx-122934835 AX-123304576 1 59451059 ACATGACTCCTCTTCCACTACACTATGATCTGGTT[A/C]GGGTGACAATTCCGTCTTCACTCTTGTGACCCCTC M 2 1 2 1 201000 r 74 goat snp37394-scaffold456-2997035 1 60592222 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433491 Affx-122935034 AX-123303832 1 59496193 AAGACAATAATGGAAAAGAGAAAGGTGGATGGGCA[A/G]TTTTGAAAGGAAGTTGATAGAGCTTGCATATGATG R 2 1 2 1 101000 r 74 goat snp37393-scaffold456-2951901 1 60637464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417107 Affx-122947475 AX-123287455 1 59554060 CAACTTGGGCACGTTCTCTGGCAACCAAAATGTCA[C/T]GATGAAGCACCCCTGCCATTTTGTAGTCAGCTCAA Y 2 1 2 1 101000 f 74 goat snp37392-scaffold456-2894034 1 60695589 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397255 Affx-122962357 AX-123267610 1 59602657 TCAGTCACTGGAAGATAAGTAATCACTGCAGGTAA[C/T]AAGACCACATCATTGCACATCAGTACCAACCCCAC Y 2 1 2 1 101000 f 74 goat snp37391-scaffold456-2845437 1 60744409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787298 Affx-122972397 AX-385274323 1 59637232 TCCATTGTGAATATCTTTAAATAATGGTACAATGT[A/G]CAGTGATTTTCATTGTAGTTGACAATGCAAACCCC R 2 1 2 1 101000 r 74 goat snp37390-scaffold456-2810862 1 60778794 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792183 Affx-122963159 AX-385279168 1 59666182 TCCTTAGTTAAATCAAAAGATAATTATTGAGCAAG[C/T]ACTACTAATATTACCTTTAGTAACTGCTGTTACTT Y 2 1 2 1 201000 f 74 goat snp37389-scaffold456-2781912 1 60807676 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425715 Affx-122940766 AX-123296061 1 59696656 ACTTTAAAGCATGCTCCTAATTGGGTGTACTTGTG[C/T]AGTATCACTTTTGGAGAGTCTAGATATGGGGGAAT Y 2 1 2 1 101000 f 74 goat snp37388-scaffold456-2751438 1 60837934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411120 Affx-122951904 AX-123281470 1 59772319 TAACATTCTAGATTTTCACCTCTGTCTGGATTCTT[C/T]TGCAAACACAGGTTTTCATCAATTCCTTACTTTTC Y 2 1 2 1 101000 f 74 goat snp37387-scaffold456-2675775 1 60913576 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389093 Affx-122968581 AX-123259451 1 59810654 GGAACAAAATTTGAAATTCAGTCTAAGATCACATG[C/T]AAGCAAAAATGTAATTTGTGTGTATATCTGTCTTA Y 2 1 2 1 101000 f 74 goat snp37386-scaffold456-2637440 1 60951762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434057 Affx-122934194 AX-123304398 1 59840914 AGGAATCAAAGCCGCCGCACGTAAAGTCGGATGCG[C/T]ACTCCCAAGGAGACAGAGAGGTCCCAGAAAAAAAA Y 2 1 2 1 201000 r 74 goat snp37385-scaffold456-2607180 1 60981960 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779616 Affx-122948836 AX-385266718 1 59895630 TGATGTTCCATAGTTGAGTTACTGACATTATCAAT[C/T]TTGGACCCTAGCTTAGACTCTGTAAATGAAGATCA Y 2 1 2 1 101000 r 74 goat snp37384-scaffold456-2552464 1 61036720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418208 Affx-122947057 AX-123288556 1 59931711 CCAGTGACCTCCTTTCACCAGTGAACAGGATGATT[A/G]TTCTGAAAATGTATTCCACATGTCCAGGAAAGATG R 2 1 2 1 101000 f 74 goat snp37383-scaffold456-2516383 1 61073550 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406885 Affx-122955637 AX-123277236 1 59986622 ACAAGCTTTCTATTTTAAAAAGATCACTGCTTCCT[A/G]TATTGACAATACACCATGACAAATGCAAGAAAGAA R 2 1 2 1 303000 r 74 goat snp37382-scaffold456-2461472 1 61128560 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435135 Affx-122933682 AX-123305475 1 60039077 TAGAAGGTGGCCATGCTAAGAAGTGGGAAAGCTGA[G/T]CAGGAATGGTGTTTTCAGTGTGTAGAATGGGAGTG K 2 1 2 1 101000 r 74 goat snp37381-scaffold456-2409017 1 61180801 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278349 Affx-1111836376 AX-519551835 1 60075044 TCAGAAGAGATCTCAACCATTGAGAATTACTTGCA[A/C]TTTGGTGCTATATTGTATGTCAAAAACCCTTTTTC M 2 1 2 1 101000 f 74 goat Random2.2K-67 1 60075044 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320788225 Affx-122961431 AX-385275244 1 60082074 CATTTTAGTGGGGCGTGGAGAAAGTGGAAACTAAG[C/T]ATTAACTTTAAGGATACGATTTGGATTGATTAGTA Y 2 1 2 1 101000 f 74 goat snp37380-scaffold456-2366020 1 61224187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278363 Affx-1111836383 AX-519551849 1 60092245 TCTTCGCAGGTAGGAAAGCTTAGGACTTCCCTAGC[A/G]GTCCAGTGGTTAAGACCTCGTGCTTCCAATGCAAG R 2 1 2 1 202000 f 74 goat Random2.2K-68 1 60092245 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429781 Affx-122938239 AX-123300122 1 60129151 ATGAATTTAGGACTGATGACTGAATGTCACAAGTG[C/T]GTCGCCCTTTGGAGGCACAGAGCCTATTTCCACTG Y 2 1 2 1 101000 f 74 goat snp37379-scaffold456-2318943 1 61271085 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781750 Affx-122948154 AX-385268832 1 60215694 AATGGAGTATTGAAAAGAAACAAAGCTGAAACGCT[A/G]TTTACATTTGAGGTGTTTTCTTAAAACAGTCTTTA R 2 1 2 1 101000 f 74 goat snp37377-scaffold456-2232400 1 61357198 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426742 Affx-122939867 AX-123297088 1 60258228 AATTGTTATTTACACCTAGCTAGGAGTTCTGATGA[C/T]GAGACCAAAAGCAAAAACTTGGTATAATTCCAGTG Y 2 1 2 1 101000 f 74 goat snp37376-scaffold456-2189866 1 61400985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451446 Affx-122921159 AX-123321779 1 60307458 ACCAAGAAGGCAGAGATAGAAGCTGCTTCAGATGA[C/T]GTAGTGAAGGGGCCCAGGCTGCCGATTAGAAGAGC Y 2 1 2 1 101000 f 74 goat snp37375-scaffold456-2140636 1 61450126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426533 Affx-122940194 AX-123296879 1 60363839 CCATAAAGATGATTTTTATTATATTTTGTTACCAT[C/T]GAATTAGAAACACCATTCACAAAGTTAAAATACAA Y 2 1 2 1 101000 r 74 goat snp37374-scaffold456-2084255 1 61506587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410437 Affx-122952396 AX-123280787 1 60405511 AGACACTCTGAAGCTGCGGGACAGGAAATTTAAAT[A/G]AGTTCGGTTTATGAGAGAGTTGAACTGTGTTCGGG R 2 1 2 1 202000 f 74 goat snp37373-scaffold456-2042583 1 61548197 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783948 Affx-122963605 AX-385271002 1 60437049 TTTCAACTTCAATATACTGTCATTGCTTTCTAGCT[A/G]CCCAATAAGTGTTGCTATAATTATTTCCAGTAACC R 2 1 2 1 101000 r 74 goat snp37372-scaffold456-2011045 1 61579557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431211 Affx-122937158 AX-123301552 1 60483160 GAGATTATATAGGAAAGATAGAAGTCATGCTACAA[C/T]GGGTAAATCAGTATGTCTATTTTTTATGTTTTTGA Y 2 1 2 1 101000 f 74 goat snp37371-scaffold456-1964934 1 61626298 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430183 Affx-122937357 AX-123300524 1 60555306 GTCGTGTGCCTAATAATGGAAATAACCTGTTCAGC[A/G]CTTTTCATATTTTTTAGAAAAGGTTGTCTGCATAC R 2 1 2 1 101000 f 74 goat snp37369-scaffold456-1892788 1 61698980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804370 Affx-986696537 AX-385290972 1 60571846 TCTCTCTCTTCATCTTCTGTCCTACACTACCCCCT[C/G]CTCCCTCAATAAAATAGCAAACTTGAAAGATCAGT S 4 1 2 1 600010 r 74 goat 1_60571846 1 60571846 Ancestral_priority_1043 ancestry 0.628 recommended IMAGE 10K 10K ancestral 320803838 Affx-986696539 AX-385290574 1 60571880 TCCTCCCTCAATAAAATAGCAAACTTGAAAGATCA[C/G]TAAATGAGATTTGGGAGAAAACTCTAGAAATTTAT S 4 1 2 1 600010 f 74 goat 1_60571880 1 60571880 Ancestral_priority_1043 ancestry 0.696 recommended IMAGE 10K 10K ancestral 320804374 Affx-986696541 AX-385290975 1 60571892 AAAATAGCAAACTTGAAAGATCAGTAAATGAGATT[G/T]GGGAGAAAACTCTAGAAATTTATAAATATTTTCAC K 2 1 2 1 600010 r 74 goat 1_60571892 1 60571892 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320804376 Affx-986696543 AX-385290977 1 60571919 ATGAGATTTGGGAGAAAACTCTAGAAATTTATAAA[C/T]ATTTTCACTGTATGCTTTATGATTATAAAGTAACA Y 2 1 2 1 600010 r 74 goat 1_60571919 1 60571919 Ancestral_priority_1043 ancestry 0.618 recommended IMAGE 10K 10K ancestral 38388562 Affx-122969176 AX-123258920 1 60603923 TTGGACTTCTCTGAGCATTGATGGGAAAGACTGGC[A/G]TTGAGCTCTGCTATACCAGACTGAGTAGACTGAGT R 2 1 2 1 101000 r 74 goat snp37368-scaffold456-1844171 1 61748438 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414446 Affx-122949949 AX-123284795 1 60659955 AGTGACAGATACAGGCTGCATGATAAGAATGGGGC[A/G]CCCTCCAAATCTAAGCAGAGAAAGTTAAAGAAGGA R 2 1 2 1 201000 r 74 goat snp37367-scaffold456-1788139 1 61804794 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779948 Affx-122942882 AX-385267047 1 60752249 AATAATACATGCATTTATGCCAACTCTAAGCCAAA[C/T]ACTGGATTGCACATTAAAGACTGAAAGATGAATAA Y 2 1 2 1 101000 f 74 goat snp37365-scaffold456-1695845 1 61897520 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414401 Affx-122949984 AX-123284750 1 60799586 CCACAAGAAAGAGGATCGAGTCAAGAGGACGGTTA[C/T]AAAAATAGAGAGAAAGGGAGAGCGAGGAGGACAAA Y 2 1 2 1 101000 f 74 goat snp37364-scaffold456-1648508 1 61944890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397180 Affx-122962415 AX-123267535 1 60830950 TGGGACACCCACACTGAAGGTCACAGGGGCAGAGT[A/G]CAATGCAGAAAGACTAAACTTTGATTTGCTAATGA R 2 1 2 1 101000 r 74 goat snp37363-scaffold456-1617144 1 61976563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770635 Affx-122972904 AX-385257799 1 60878587 ATCTTCCCTCAAGCTTCCATACAAAGTGAAACCTT[A/G]TATTAATCACTTTTTCCAAATGAGTTCTTAATGGA R 2 1 2 1 101000 f 74 goat snp37362-scaffold456-1569507 1 62024537 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431936 Affx-122935981 AX-123302277 1 60934300 CAGTTTCTAACAAGATACTTCCATAATGCTGTATG[C/T]ATAACAATTATCTTTTATTTAAATATCTGTACAAT Y 2 1 2 1 101000 f 74 goat snp37361-scaffold456-1513794 1 62080632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790279 Affx-122944796 AX-385277283 1 60972778 CTAAGATGATGGAATCATTTGTAGACATGAAATGA[C/T]GAATCATTCACATAGGGAACCCTTGGTTCTAATTT Y 2 1 2 1 201000 f 74 goat snp37360-scaffold456-1475316 1 62119095 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788326 Affx-122944569 AX-385275344 1 61020700 CTAATATGTAGGTTAGGGAAAGGAAAACACTGGAT[A/G]TAATATCTTGTAAATAATACACCTCACAGACATTA R 2 1 2 1 101000 f 74 goat snp37359-scaffold456-1427394 1 62167010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449705 Affx-122922540 AX-123320040 1 61050632 TATGTCTATAGATAGACTTTCAAGGCCCCTCTTCT[A/G]CCTCTGTAGCTCCTGTCTGTGTCCATGACTTGATT R 2 1 2 1 101000 r 74 goat snp37358-scaffold456-1397462 1 62197061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386922 Affx-122970006 AX-123257280 1 61079347 CCATTCACCTCTTTCTTGCTCATCCCAGAAGCTCA[A/G]TAGAGCTCCAGGGCTCTTTAAAAAATCTGCTTAAA R 2 1 2 1 202000 r 74 goat snp37357-scaffold456-1368747 1 62225958 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803442 Affx-122951090 AX-385290272 1 61113649 TTATTTTTTAAGTCTACACTAGATATTGAGGTCAT[A/G]TATTAAAATGAAGGCAAGGCACATGATCTGCTGCC R 2 1 2 1 101000 r 74 goat snp37356-scaffold456-1334445 1 62260177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424449 Affx-122941785 AX-123294795 1 61163027 TCTTCATTCTTTCTCTGGATGAGTCCTTTAGAAAG[C/T]GCTTTCTTCTTGAGACCCATGTTCTCTCTTCTGGT Y 2 1 2 1 101000 r 74 goat snp37355-scaffold456-1285067 1 62309238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799512 Affx-122961189 AX-385286442 1 61214143 AGGATTCAGTCAATCAGCTGTCCCTAGTTTTTAGC[A/G]AATAAAAACAGACAACTAACAGTGTTTATTCCTTC R 2 1 2 1 201000 r 74 goat snp37354-scaffold456-1233951 1 62360114 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393848 Affx-122965152 AX-123264203 1 61243471 ATTTATACAGACTCAGCCATAGTCTTAATTTCAGC[C/T]TTACTCACTGGCTCATACTTGTTGAAGATGGTAAA Y 2 1 2 1 101000 f 74 goat snp37353-scaffold456-1204623 1 62389587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445005 Affx-122926642 AX-123315342 1 61286803 CCAGATACTATTTAACTCAAAAACTTTTGGCACAT[A/G]CCTATTATCATCTTCCAGAATACAGTCTTCAGAGA R 2 1 2 1 101000 r 74 goat snp37352-scaffold456-1161291 1 62433181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278376 Affx-1111836391 AX-519551861 1 61290289 GTTTGTAGGGTCAGGGACCAGTGATACAGAGCAGA[C/G]CACGGGAAAGTGTGGGGAATAAATATGAAACAAAA S 4 1 2 1 101000 f 74 goat Random2.2K-69 1 61290289 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320772121 Affx-122937647 AX-385259277 1 61323177 TTCCTTTGCAATGTTTGAGATTCTGAAAATAAGAC[A/G]TACACTTTATTGTGGCTTTCTTGACATAACCAACA R 2 1 2 1 101000 r 74 goat snp37351-scaffold456-1124917 1 62470137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272607 Affx-1111832864 AX-519546320 1 61334489 TGAAACTTGATACAACTACACTTGTACCACAGTCT[A/G]TGCCTATGGGATTCCACACTGAAGACAGGAAAGCT R 2 1 2 1 101000 r 74 goat 1_61334489_AF-PAKI 1 61334489 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38391162 Affx-122967444 AX-123261519 1 61360407 ACTTCTGAGGTTTGTACTCAAAATACCTTTATCAC[A/G]TCTTTAGTACAAAGCTGCAGACATTAAGAAAATAC R 2 1 2 1 101000 f 74 goat snp37350-scaffold456-1087687 1 62507128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274709 Affx-1111834376 AX-519548295 1 61439233 AACCAGGCCAATGAACCATTTCTGCAGGAGTT[A/C]TTTCTGCTCCCCAAAGGTTCTAAGCATTTTTGATG M 2 1 2 1 101000 r 74 goat GoatD01.032542 1 61439233 A C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38419465 Affx-122945484 AX-123289813 1 61449683 GCCTGTCTGTCAGCATCCCACAGCTCTGCCACTGT[A/G]TTTGAAGCTTGGCTTCAGTGGATCTTTGAAGACTG R 2 1 2 1 101000 r 74 goat snp37348-scaffold456-998411 1 62596510 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446443 Affx-122925968 AX-123316779 1 61482729 ATCTATCACAATTCTGTGTCTCTCTCTGAATGATA[C/T]ATGATCAGTGATGCTTGTTTTGATTTATCCATAGT Y 2 1 2 1 101000 r 74 goat snp37347-scaffold456-965365 1 62630286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426050 Affx-122941104 AX-123296396 1 61535586 GGTTGTCAGTGTGTCAAATATTTTGAGCAGAAAAA[C/T]GATATTTAAATGCCAACAACAAACACACTCAAAGA Y 2 1 2 1 303000 f 74 goat snp37346-scaffold456-912508 1 62682637 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391092 Affx-122966826 AX-123261449 1 61570292 TTCCCTCACAGCCCCATATGCTTGCTCAGTTTTCA[C/T]TCCCAGTTCTCACAAACCTTTCTCCATCAGCTGCC Y 2 1 2 1 201000 r 74 goat snp37345-scaffold456-877802 1 62717358 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770670 Affx-122926369 AX-385257834 1 61604197 AATGTAGACCAGCTATGATAATTCATTGTCTTCTC[A/G]TTAAGAATTGGCCTTTTCAAAATAATCACGGCTGC R 2 1 2 1 101000 f 74 goat snp37344-scaffold456-843897 1 62751446 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777171 Affx-122952789 AX-385264294 1 61643291 AGGAGGAAATATATGAGTACTAGATCTTCCTGATA[C/T]GTTTATTCTTTAGAGCTTATATTTAGATTATAAAC Y 2 1 2 1 101000 f 74 goat snp37343-scaffold456-804803 1 62791453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417470 Affx-122947182 AX-123287818 1 61687429 TACGTGGGGAGAAGATTGTCACTTAAACTGTGTCG[C/T]AACTGATTAAACTTGAGGGAGGAGGCAGTCCTTCC Y 2 1 2 1 101000 f 74 goat snp37342-scaffold456-760665 1 62835455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410865 Affx-122952606 AX-123281215 1 61726664 ACATTTTTATATTGTTATCACAGGTGAATATATGG[C/T]AAATATCATTGTTTAGCTTGTTTATAAACTTCAAG Y 2 1 2 1 101000 f 74 goat snp37341-scaffold456-721430 1 62875600 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773664 Affx-122964837 AX-385260804 1 61757280 CACTATTAAGGTCTACTGGTGTGAATAACAAATTA[C/T]ATCATCTTGCTACTCAGCAAGAGTAAATTTAAAAT Y 2 1 2 1 101000 f 74 goat snp37340-scaffold456-690814 1 62906322 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278560 Affx-1111836400 AX-186382722 1 61763615 CTTCTTTTTCTAGAATGAGAGGAAAGCAACATTCC[A/G]ACACAGACTAGTGATTTCTTTGTTGGTGTTTATTA R 2 1 2 1 101000 r 74 goat Random2.2K-70 1 61763615 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402230 Affx-122959149 AX-123272583 1 61799793 CTAACTCTCCAATTGTGATCTCATGGAGACATTCC[A/G]TTGTACTCAGGGCCCCTCTAACTCTGAGGTATACA R 2 1 2 1 102000 r 74 goat snp37339-scaffold456-648301 1 62949235 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383123 Affx-122973260 AX-123253481 1 61866404 GTTCACTCTGGGGACTATTGTTTTCATAGGCTCTG[C/T]ATTACTGGAACCACTCACACACACACTTTCTTGTT Y 2 1 2 1 101000 f 74 goat snp37338-scaffold456-581690 1 63016100 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788774 Affx-122955916 AX-385275789 1 61907537 TTGAATTTGTGTTTGAGAAGTTGTTTAGCACTGAT[A/G]TTTCATACTCCAGAAACCCAGAGAAGACTGTCCTG R 2 1 2 1 101000 r 74 goat snp37337-scaffold456-540557 1 63056899 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434149 Affx-122934905 AX-123304490 1 61937729 CTTCATCTTTTCCTATTATAGACACATTTTCTCCA[C/T]AAGGCAAGGAACATGGCCACTTGTGGCCCTGAATT Y 2 1 2 1 201000 f 74 goat snp37336-scaffold456-510365 1 63087371 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382749 Affx-122973598 AX-123253107 1 62031369 GACGGAGTGCCAGGCAGAAGCTATGGCACCTTTTA[C/T]GGCTTAGTTTCAGGAGTCAGATAGCATCACTTCTG Y 2 1 2 1 101000 r 74 goat snp37334-scaffold456-416725 1 63181941 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391424 Affx-122966759 AX-123261781 1 62064419 CACAAAATAAATGGGTCAGGGCTCTCAAGGTAGTC[A/G]CTGGCCCTTGGTATAGTCCCTCAGTCATCTTGGGC R 2 1 2 1 101000 f 74 goat snp37333-scaffold456-383675 1 63215144 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440443 Affx-122929405 AX-123310780 1 62143344 CTTTTTGTCACTTCAGCAGTGTGCTTGAAAATTTA[C/T]TTCTGTGTACTTTTTAATCCACTGGTTTAGTTGCT Y 2 1 2 1 101000 f 74 goat snp37331-scaffold456-304750 1 63295215 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445661 Affx-122926146 AX-123315998 1 62195546 TGGGGAGGGGATGGGAGACTTTTCCAAATCAGTAA[C/T]GTCAGTGAGACTGTTGGTATTGATTTTTGGTCCTG Y 2 1 2 1 101000 f 74 goat snp37330-scaffold456-252548 1 63348656 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773861 Affx-122958911 AX-385261001 1 62226929 TGAGATGGAGAATCACAGAATCTAAGCTAGACTAA[C/T]GATTCTCAACTGCAGTTGCCCAGTAGAATCATCTG Y 2 1 2 1 202000 r 74 goat snp37329-scaffold456-221165 1 63378629 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272436 Affx-1111836404 AX-519546162 1 62240760 GCAGATACTCAAAACCTACATGGCTTATGAGTAGA[A/G]GAGCAAACGGAAGATGGTCTAGTTAGTTGATTCCA R 2 1 2 1 101000 f 74 goat Random2.2K-71 1 62240760 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402942 Affx-122958177 AX-123273295 1 62282472 ACAAGACTTCCTTCTTTGAAATCAGCTCTAATCTA[C/T]GACACTCCCCATTCTGACTTAGTTAATATGAACAG Y 2 1 2 1 101000 f 74 goat snp37328-scaffold456-165622 1 63434689 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437087 Affx-122932192 AX-123307425 1 62317947 TATGCTTTTTGCCCTCTTCTCCTGCAAGAACAGTC[A/G]TCACAGGAAGTGGCCTCCTGGTTTTCAGACTTCTT R 2 1 2 1 303000 r 74 goat snp37327-scaffold456-130147 1 63470301 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445266 Affx-122925471 AX-123315603 1 62363422 AAAGAATAGGAAATTAGGGTGAATTGTCACTTGGT[A/G]CATTTCTGTTTTGTGTGGGTGGGCTTTTTTCTTCT R 2 1 2 1 101000 f 74 goat snp37326-scaffold456-84672 1 63515259 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798784 Affx-122925775 AX-385285714 1 62398934 AGCTGCTGAGAATTCAGGGTTAATTTGCCTAACCA[C/T]AGGGCATGATGTAGTCTATGAAGGTTAATATATTA Y 2 1 2 1 101000 f 74 goat snp37325-scaffold456-49160 1 63550877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770518 Affx-122931268 AX-385257683 1 62433863 TTGAATGCTTACTAGATACTCGCCCTTCAAATATA[C/T]GTGATATAATTAATCTTTACCACACCCTTGAATAT Y 2 1 2 1 201000 r 74 goat snp37324-scaffold456-14231 1 63586237 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783252 Affx-122964673 AX-385270317 1 62455794 ATGTACAAAGTGACATTTGTATGTGCTTTATATAA[A/G]CATGTGCTTCCCAATTAACTTTGTCTGGTCACTAT R 2 1 2 1 201000 f 74 goat snp28579-scaffold306-893870 1 63608252 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418425 Affx-122946530 AX-123288773 1 62490647 GATTAAATTTGAGGCTACTTGTGTGTCTGCAGAGC[C/T]TCAGTGATCTGGAACTGGTTTGAAAACTGAGGTTA Y 2 1 2 1 102000 f 74 goat snp28578-scaffold306-859017 1 63643118 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393605 Affx-122965369 AX-123263961 1 62627971 TGTCGGAGCTTTCAGGAGGAAAGGCCCTTTGATGG[C/T]GTAAAATGTGGGACTGGGTAGAAGTTAAAACTAGA Y 2 1 2 1 101000 r 74 goat snp28575-scaffold306-721693 1 63781802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768565 Affx-122966205 AX-385255745 1 62674431 TATATACACGACTGCTGTTTAAAAGCATTTCAAAG[C/T]TCATTTAGCAATGGCTTCTCCTAAGTGGTGTGGGG Y 2 1 2 1 101000 r 74 goat snp28574-scaffold306-675233 1 63828436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435231 Affx-122934084 AX-123305571 1 62708603 AGGAGGGGGTTGGGCAGCTCCCGAAAGTAAAGCTT[A/G]CAGAGAGAGCCCACACAGTGGATGTCCTGGAGGTA R 2 1 2 1 201000 f 74 goat snp28573-scaffold306-641061 1 63862822 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432318 Affx-122936301 AX-123302659 1 62759584 TTTCAAGTGAATCAAAGGGAATGGAATAAGATGAA[G/T]AAGAGACAAGATGAATCAAGAGGTTCCAGAGAGTC K 2 1 2 1 101000 f 74 goat snp28572-scaffold306-590080 1 63913968 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785260 Affx-122950048 AX-385272305 1 62836461 AGCCTGGCAGACCATCATCCATGGACACAAAACTA[C/T]AGCTGGACCAATCTTTTGCATAAATAGATAACAGT Y 2 1 2 1 101000 f 74 goat snp28570-scaffold306-513203 1 63990873 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788474 Affx-122943713 AX-385275491 1 62867930 TAGATCTGCATGGATTCCTCCAATTCCCACTATTA[C/T]AGCCTCTCCTACTAGTTTCAGCACTATTCTCCCCT Y 2 1 2 1 101000 f 74 goat snp28569-scaffold306-481734 1 64022844 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789896 Affx-122969371 AX-385276903 1 62928988 GTGATTCTAACAATCAGCCAGTCATTATCATGATT[C/T]CTGCAAGTGTTGGCTCATCTACCCAACAGAGAGGT Y 2 1 2 1 101000 r 74 goat snp28567-scaffold306-420676 1 64084001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799655 Affx-122938168 AX-385286584 1 62959364 GGGAATTGTTAGTAAGTGCACTGAAAGTACAGGTT[A/G]TGGTAGATGTGACAACTACTTGTTGAGTCAGATTA R 2 1 2 1 101000 f 74 goat snp28566-scaffold306-390300 1 64114373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448703 Affx-122923858 AX-123319039 1 63048400 AATAGAATTTGTAAAGAAAATATAATTTACCAATA[C/T]GACGCACAAAGTTCTATAAGTTTTAAGAAAACTGA Y 2 1 2 1 101000 r 74 goat snp28565-scaffold306-301264 1 64204122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381719 Affx-122974699 AX-123252077 1 63179280 CATTCAAGCCCTACCTTTGTTTTGGTTCTGAACAT[A/C]TGTTTCCTCCTCAGTAGCAGTGACCAGTTCCATTT M 2 1 2 1 101000 r 74 goat snp28562-scaffold306-170384 1 64336345 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789488 Affx-122947108 AX-385276498 1 63209040 CCCTTGTTAAGTAAACAACTTGGTAGAAACTCAAA[C/T]GCATACACGTGGTGCCTCTTGTGATATTTGTGATG Y 2 1 2 1 101000 r 74 goat snp28561-scaffold306-140624 1 64366087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404587 Affx-122957358 AX-123274939 1 63247002 CACATTTTCTGTCAGTTATAAGACAAAAGTTAGCC[A/G]TTTAAAATATTAAAATTTTCTTTTTCTGAAATGTG R 2 1 2 1 103000 f 74 goat snp28560-scaffold306-102662 1 64404566 C T 1 parentage parentage not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433528 Affx-122935007 AX-123303869 1 63282387 ATTTTCCCCACCTGGTGTTGCATTCTCAGGGTAGC[A/G]GAGCTGTAGCTGAGCTGAGAGGTGATTGAGAGGGG R 2 1 2 1 201000 r 74 goat snp28559-scaffold306-67277 1 64440251 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382332 Affx-122973890 AX-123252690 1 63365876 GCATTATTTTCACTCATTCCTATTATGAAAGCATC[A/G]CTATGTTAAATGTTCTTGTACATCATCATTTTTAA R 2 1 2 1 101000 f 74 goat snp2241-scaffold1069-462570 1 64524325 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427712 Affx-122939282 AX-123298055 1 63409343 AATTATAACCATTAAAATTACAACTTTATATTTGC[A/G]TGTGGTGAAGGACTCTGAGGAATTGTCAGAATAAA R 2 1 2 1 201000 f 74 goat snp2242-scaffold1069-506037 1 64568172 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274040 Affx-1111833969 AX-519547644 1 63459407 TCAGCAGAAATGAGGACCCTCTCTTTTGGACCTCC[A/G]TTGTACATCTCAGTCCATCTGCAGCACCAGCACAT R 2 1 2 1 101000 r 74 goat GoatD01.012088 1 63459407 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38439208 Affx-122931033 AX-123309545 1 63465928 GTAGCTCACAATCTAGTACAGAAATGAATCCATGG[C/T]TATGTATCCACTGAAGAAAGGGCTCTGCAAGGGTT Y 2 1 2 1 201000 f 74 goat snp2243-scaffold1069-562622 1 64625165 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426952 Affx-122940413 AX-123297297 1 63510325 CCAGCTTTCACAGCTACATGTCTGTGTTGTCTAGA[C/T]CACTGATTGGTAGGTTTCTTTCTTAACTCGTCTCT Y 2 1 2 1 102000 r 74 goat snp2244-scaffold1069-607019 1 64670312 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784994 Affx-122953511 AX-385272041 1 63554283 AAAGAAGCTCTACCTAGCAGAACAAAAGTAGAAAT[A/G]CAGAGAGGTTCAAATTAATCCCAGCAGAAAAGGCA R 2 1 2 1 101000 r 74 goat snp2245-scaffold1069-650977 1 64714301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400671 Affx-122960341 AX-123271026 1 63603000 ATGAGGTCTGTGTGTGTGTATGTGGGGTTGCTTAA[A/G]GATTTGGACTTCTCTGAATGTAAATACTGATTTGA R 2 1 2 1 303000 r 74 goat snp2246-scaffold1069-699694 1 64762989 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398243 Affx-122962197 AX-123268598 1 63637948 GTAGGAGCTTTAAAAAAAAAGACATTCCTCAACAG[C/T]TCATGTTTGTCGTTTTAAGTTTACTTCGAAACTTC Y 2 1 2 1 201000 r 74 goat snp2247-scaffold1069-734642 1 64798036 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393575 Affx-122965393 AX-123263931 1 63679693 TCGGTCTCAGCTCCATCGGCATACGTTTCATCCTC[C/T]AGGGCACACTCTGTGAGACCAGAAATAAGGGGCAG Y 2 1 2 1 101000 r 74 goat snp2248-scaffold1069-776387 1 64839355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404170 Affx-122957693 AX-123274522 1 63771780 AAGGAGAAATAATCAAATGAAACAGATAAATAGAC[G/T]AAAATTCTATCCCCATTCCTCCCTCCCCTACCTTT K 2 1 2 1 303000 f 74 goat snp2249-scaffold1069-868474 1 64931597 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271835 Affx-1111832865 AX-186269674 1 63835619 GCTAAGTCGCTTCAGTTGTGTCCAACTCTGTGCAA[A/C]CCCATAGATGGCAGCCCACCAGGCTTCCCCGTCCC M 2 1 2 1 103000 f 74 goat 1_63835619_AF-PAKI 1 63835619 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392524 Affx-122966111 AX-123262881 1 63855152 GACCCAATACCAAGACCTCCCTCTTAGGAGCTCTG[C/T]TCGGAATTGGGCCCCTCGTCTTCTGGTATTATGTT Y 2 1 2 1 201000 f 74 goat snp2251-scaffold1069-951846 1 65013742 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395277 Affx-122964081 AX-123265632 1 63902744 TCAAAAGGCTTGTGACAAACTGAAGGGAGAATCCT[A/G]TACAGCCAGCTGTGGGGAGGAAACAAGGACACACA R 2 1 2 1 101000 f 74 goat snp2252-scaffold1069-999438 1 65060940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766288 Affx-122959549 AX-385253677 1 63945104 TATCCCCCTTCTTAAGGAACAGTCCAGCTGTCTGT[C/T]GCCCAGGCTACCCATTCAATCATTAACACTCAGTA Y 2 1 2 1 101000 f 74 goat snp2253-scaffold1069-1041798 1 65103480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789626 Affx-122938085 AX-385276635 1 63977904 TATTAAGTAATGCTTAAGAGTATGAGTTTCATCAT[A/C]ATAGGTTGGATTTGAATCCTGCCATCACCTCCCAA M 2 1 2 1 101000 r 74 goat snp2254-scaffold1069-1074598 1 65136411 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403559 Affx-122957589 AX-123273912 1 64030909 ATTCATTCACCAAATACTTTTACCATATGCTGGGT[A/G]CTGCTCTAGGCACCAAGAATACAGCAGTGAACAAA R 2 1 2 1 101000 f 74 goat snp2255-scaffold1069-1127603 1 65189519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278417 Affx-1111836413 AX-519551902 1 64063079 ACTCAAATGTAAAAAGAATATCTCCACGAACAAGA[A/G]CAGAATTGCAAAACGGTTCTGGGTTTCAGGTCTGG R 2 1 2 1 101000 f 74 goat Random2.2K-73 1 64063079 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381854 Affx-122974188 AX-123252212 1 64084680 GGCTCCTGTGTGCTGGTGCCTCTCCACCCCCGCCC[A/G]TCTCCATCCTGGTTTTGGCTTTCCTAGTCAGACTT R 2 1 2 1 101000 r 74 goat snp2256-scaffold1069-1181374 1 65243966 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787277 Affx-122970158 AX-385274302 1 64118786 TAGAGGATGTAGAAAAGTGGGTAGTTTTCTGATTG[C/T]CAGCATGGAGTCATAAACAACATTAGATGTTGGAT Y 2 1 2 1 101000 r 74 goat snp2257-scaffold1069-1215480 1 65278049 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394992 Affx-122964243 AX-123265347 1 64153301 AATACTGATGAGGAACATACTTTGATATTGAGAAC[G/T]CCATTTATAAATAATTTGTACACTTGTTACTGGTT K 2 1 2 1 101000 f 74 goat snp2258-scaffold1069-1249995 1 65312612 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802047 Affx-122924030 AX-385288952 1 64183874 TTGAAAACTTCAGCATGATGTAATTGCATGTGGTT[A/G]CAAAAATTCCCGAAAGTGCCCAGAGGGCAAAGGGT R 2 1 2 1 201000 f 74 goat snp2259-scaffold1069-1280568 1 65343528 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451118 Affx-122921386 AX-123321452 1 64240460 ATATGATAAGCCAACATGTATTGCCAAATTCAATC[G/T]TGAAAATTAAAATCCTTTCCTATAAGATCAATAGC K 2 1 2 1 101000 f 74 goat snp2260-scaffold1069-1337154 1 65401072 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377448 Affx-122977526 AX-123247807 1 64292116 TTTTGTAAATCCAAGATCATTTTCAGAAATAAGTA[G/T]ACAAATTTTATTTTCACATTAGCTGTAAAGTTTTT K 2 1 2 1 101000 f 74 goat snp2261-scaffold1069-1388810 1 65453193 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772397 Affx-122977465 AX-385259550 1 64325436 ATAACATCAGTAGCTATGATAAGTTAAATGAATAT[A/G]CAATGCAATACCTAATGCAACCCTGTTTAAAAAAA R 2 1 2 1 101000 r 74 goat snp2262-scaffold1069-1422130 1 65486489 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384384 Affx-122972219 AX-123254742 1 64354038 GGACAAGGTTTAACATCCTTCCCCAAACACACAAA[C/T]ATAAACGGTTGTAATGAATGAAACTGTGGTTTCAA Y 2 1 2 1 201000 r 74 goat snp2263-scaffold1069-1450732 1 65515102 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392883 Affx-122965740 AX-123263240 1 64429992 GATTTACACTTCTGGACTTTTCTTCATCTTCAAAA[G/T]AAGCTGGTGAACTGGATAAGCTGCCTTCCAGATCA K 2 1 2 1 201000 f 74 goat snp2264-scaffold1069-1526686 1 65591382 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411147 Affx-122951884 AX-123281497 1 64463238 TGATGGTCCTTTTGCCACATAATATATGTTCACAC[A/G]TTTTGGGAATTTGGATGTCAACATTTGGGGAGGGA R 2 1 2 1 201000 f 74 goat snp2265-scaffold1069-1559932 1 65625021 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444151 Affx-122926791 AX-123314488 1 64527467 ATTAAATATGAGTGGGCTAAATAATCTATCAAAGA[C/T]AGAGACTGACAGACTGGATTAAAAAAAACAACACA Y 2 1 2 1 201000 f 74 goat snp2266-scaffold1069-1624161 1 65688829 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377188 Affx-122978196 AX-123247547 1 64580736 CAAGATATGAATCTAGTCTTTTGTTTCTAGATCAG[C/T]GGCTTAATCTAAAACCTATGCCCTCTGGGCTAGCT Y 2 1 2 1 101000 f 74 goat snp2267-scaffold1069-1677430 1 65742188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784733 Affx-122955407 AX-385271781 1 64626257 ATGTACCACAGAGAAACTCAATCTACCTTCTTACA[C/T]GGCCATTGATTTCATTCATCCAGCTACAGGGAAGC Y 2 1 2 1 101000 f 74 goat snp2268-scaffold1069-1722951 1 65787668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418737 Affx-122946221 AX-123289085 1 64664986 GTCTTCTCTATAGTCTCCCTCTATTTTCTTCAGCT[C/T]CCTGTTACCACAGAGGGCAGATGACACACAGAGAA Y 2 1 2 1 201000 f 74 goat snp2269-scaffold1069-1761680 1 65826455 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414064 Affx-122949765 AX-123284413 1 64704332 ATACTGCCCCCTTTTGCTCACTCTACTTCCAAGAA[C/T]ACTGGCCTTGCTTCTATCTGAAAACATATCAAGGT Y 2 1 2 1 201000 r 74 goat snp2270-scaffold1069-1801026 1 65868141 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423671 Affx-122942333 AX-123294017 1 64772579 AATTTCAGCTTTGTGTGTCAAAGATGGCAAGAAGG[C/T]GTCACCAGGTTTGTACTGAATCATGAGTTAAGTTC Y 2 1 2 1 101000 r 74 goat snp2272-scaffold1069-1869273 1 65936272 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451347 Affx-122921260 AX-123321680 1 64890702 ATTTCCACTTCCAATTGAAATAACACAATGTGTCT[A/G]TCTACAGAACTTCACATTCTGATTGTCTTGTACTA R 2 1 2 1 101000 r 74 goat snp2274-scaffold1069-1987396 1 66053211 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380677 Affx-122975179 AX-123251035 1 64921155 ATCTCAGACCCATGCTGCGTGTTACTCAAGGAACA[A/G]CTGTAGTAAGGTGACAAGTGGATGGGGGGCAAAGG R 2 1 2 1 102000 f 74 goat snp2275-scaffold1069-2017849 1 66083953 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397989 Affx-122961802 AX-123268344 1 64978949 TCATTCATCAGCACCTCTCTCTATCATTCATTCAT[G/T]AAGACATGACCCAGTTTTCTTTTCTCTAATTATAT K 2 1 2 1 101000 f 74 goat snp2276-scaffold1069-2075643 1 66141335 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416174 Affx-122948262 AX-123286523 1 65019963 TCTTCCAGAATCAACATTCAACTATTCTAAATTCT[A/G]CAGGAATAGATCTACGATACCATCAAAGGCTACTG R 2 1 2 1 101000 r 74 goat snp2277-scaffold1069-2116657 1 66180855 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390647 Affx-122967144 AX-123261004 1 65082834 AATACTCTACTGCGGCTTTTCAAACTGGAGGTCTA[G/T]CACAAATGCAGACTGACTCAGAAGGTCTGGGGTAG K 2 1 2 1 101000 f 74 goat snp2278-scaffold1069-2179528 1 66244206 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408306 Affx-122953774 AX-123278657 1 65137519 CTGGCCTAACTGATCCCTATATTATTACAGGTGAC[A/G]TCAAGACTAGTACCTGGAGTTAGGAAGGTGAAGGA R 2 1 2 1 101000 f 74 goat snp2279-scaffold1069-2234213 1 66299505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400487 Affx-122961291 AX-123270842 1 65175804 AGTTTGCATCCCACAGAGAACACTGAGGGGAAGGA[G/T]AACAGACCCATGTAGCTTTGGGAAGGAGAAGTGGC K 2 1 2 1 101000 r 74 goat snp2280-scaffold1069-2272498 1 66338189 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384894 Affx-122971925 AX-123255252 1 65209278 TGAGTATCTGCTGGGGTGCTCCTTCCAATGAGGGC[C/T]CAGCACCCTCTGCTAGTGTGACTACTGGAGAAGCA Y 2 1 2 1 201000 r 74 goat snp2281-scaffold1069-2305972 1 66371968 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377483 Affx-122977501 AX-123247842 1 65262045 AGAAATGCCTTGTCTACCTCTGCCTGTTCTGGAAC[A/G]TAACCTCTTAGAAACAGAAGCCAGGAAGTCTGGCA R 2 1 2 1 101000 f 74 goat snp2282-scaffold1069-2358739 1 66425008 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802919 Affx-986696082 AX-385289816 1 65311203 TAATATAATATGCAGTTAATGTTTAAATTTCCTAG[A/G]TTGTTCCATAGTATCATAGTACCAGTTGTGTCTGA R 2 1 2 1 600010 f 74 goat 1_65311203 1 65311203 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 38411125 Affx-122951900 AX-123281475 1 65311936 GAGATGAACAGTGGGGTTGAGGGGCTAATACGTTA[C/T]ACAGGGAGAGCAAGACAGACCTCTCCAGGACATAC Y 2 1 2 1 101000 f 74 goat snp2283-scaffold1069-2408630 1 66475102 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454304 Affx-122919258 AX-123324637 1 65342910 TGCTCCTCGTCTTCAGTGACGTCCCCTTCCTTTGA[A/C]AGACTCTCTTATAGGCTGTGGTTCTGCCTGTCTCA M 2 1 2 1 101000 r 74 goat snp2284-scaffold1069-2439604 1 66506209 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383793 Affx-122973194 AX-123254151 1 65372143 AGACACCTGCAGTTGCTAACAAAAATTCCCAGTGT[A/C]TGCTTTGCTTGCTAATTAGGGGAAACTTCATTTTA M 2 1 2 1 101000 f 74 goat snp2285-scaffold1069-2468837 1 66534875 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421004 Affx-122944557 AX-123291351 1 65429177 TCCACAGTGGAAGCAAAAGTTTTACTGGAAACGGA[C/T]GCAAAATAATTTTGTCTCCCTTGTGGCTCAGGGGG Y 2 1 2 1 101000 f 74 goat snp2286-scaffold1069-2525871 1 66591903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781010 Affx-122924480 AX-385268097 1 65472649 TATAAAATTTCCAAAGAGTGATCATTTGATTACCA[C/T]GAGTCTGTTCGTGCTAATCAGAAATTACATACAAC Y 2 1 2 1 101000 r 74 goat snp2287-scaffold1069-2569343 1 66635689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784399 Affx-122955900 AX-385271448 1 65520470 GCATGGTGTCTTGTACATCATGGACTCACTATCAA[C/T]ATTTATTAATTTGAAAGAGATAATTGGACTGAGTC Y 2 1 2 1 101000 f 74 goat snp2288-scaffold1069-2617164 1 66683561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397760 Affx-122962524 AX-123268115 1 65558639 TGACAGGATCAATGGATTCCACATAATGCCACCAG[C/T]GTCTGGGAACAAACAGAACCTGAAAACCAAACAAA Y 2 1 2 1 101000 f 74 goat snp2289-scaffold1069-2655333 1 66721772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791293 Affx-122956123 AX-385278287 1 65568833 AAATCAAGCTACATACATGACTCCTAAACTTTCAT[C/T]GCAAGTCCTTAATTCTCTTCTACTTACCACTAAAT Y 2 1 2 1 101000 r 74 goat snp39045-scaffold495-3419 1 66731850 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278609 Affx-1111836425 AX-519552088 1 65605289 TTAGATGTTAATTATTTGCCACTGACAGACATGCG[A/G]ATAGCACGGACATTTTGTTTTACCAATGAAGGACA R 2 1 2 1 201000 r 74 goat Random2.2K-75 1 65605289 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797871 Affx-122924639 AX-385284809 1 65605655 TGGGGAGAATGACAGTTTAAAAATAGGGTTGAAAG[C/T]TCCACAGACAAGATTCAGAGAATCAATCCTTTAAT Y 2 1 2 1 101000 f 74 goat snp39046-scaffold495-40241 1 66769027 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278622 Affx-1111836431 AX-519552101 1 65606257 CTCTCCAGCACTGGCAGAGCCATGTACAGACAACC[A/G]TTTTCCAGAACATTGTGGTTATCTATTTCTCTCTC R 2 1 2 1 101000 r 74 goat Random2.2K-76 1 65606257 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468274978 Affx-1111834523 AX-519548560 1 65620903 CTTGATCTCTGGGAATTAGATTGTGAAGAAGTGGA[A/G]GGGCTTGCAACAACAAGCACTCAGATCTTACAGAC R 2 1 2 1 101000 r 74 goat GoatD01.039620 1 65620903 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38442233 Affx-122928299 AX-123312570 1 65641056 ATTGGGAGTCAGACCTGGGTCTGAATCTTAGCTTT[A/G]CCTGTTAGCACTTGGGCAAGTTTTTTATGTTTCCA R 2 1 2 1 201000 r 74 goat snp39047-scaffold495-75642 1 66804853 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420393 Affx-122944931 AX-123290740 1 65763844 TTCTCCCCTTCTCCAACTTCCCTTTGTAGTGAAAC[A/G]CTATACTAAATAGCCCCATATACTAACAACCATTC R 2 1 2 1 201000 r 74 goat snp21794-scaffold214-98624 1 66929430 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441202 Affx-122929530 AX-123311539 1 65834281 GACAAATGTCAGGAGGAAAGAAGAGTGTCCTGCAG[C/T]AGGGTTTTCCTTCCCAGACCTCACCCCCCATGAAA Y 2 1 2 1 201000 f 74 goat snp21795-scaffold214-169061 1 67064618 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415181 Affx-122949003 AX-123285530 1 65877066 TAGATTAAGGGCCAGGTCAAGTGCTCAACTCCAGA[C/T]GAGTGTGCAAGGGTCACTTTCTGGACATTTGGACC Y 2 1 2 1 201000 r 74 goat snp21796-scaffold214-211846 1 67107054 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382702 Affx-122973632 AX-123253060 1 65936581 TGAAAGGGTGGCAGGAATGTCCATGCAGCATGCTT[A/C]TGCACTCATGCAGCCCATATGGCCTCATACAGAAA M 2 1 2 1 201000 r 74 goat snp21797-scaffold214-271361 1 67166164 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452338 Affx-122920653 AX-123322671 1 65969649 GTGCATGAAGCCGGGGTGGACAGACAGGTGTCCCC[A/G]TGGAGTGACTGAGTGAAGAGTCCACCCTTAGTTGA R 2 1 2 1 101000 r 74 goat snp21798-scaffold214-304429 1 67199102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439304 Affx-122930961 AX-123309641 1 66013425 CTCCACATCCTTGCCAAAAGTTATTTTCTGGGGTT[A/G]TGTGTGTGTGTTGATAATAGCCATCAAAAATTGAG R 2 1 2 1 202000 f 74 goat snp21799-scaffold214-348205 1 67243090 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278462 Affx-1111836437 AX-519551945 1 66042005 ATAATCAAACATGCTTAATATCCTTTCCTGACTCC[A/C]TGTCACCTTTCAGCTATAAATTCTTACTGTTTTCT M 2 1 2 1 101000 f 74 goat Random2.2K-77 1 66042005 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38379083 Affx-122976320 AX-123249442 1 66045298 AGAAATGATGTCATAGTGGCAAAGCTACTGACACA[G/T]CTGCAATGCTGGGCAATCCTTGCCGTCTGGCTTCC K 2 1 2 1 101000 f 74 goat snp21800-scaffold214-380078 1 67303006 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782428 Affx-122975595 AX-385269503 1 66080503 TTAAGTTAATAATGAAAATGGGTCTTTTATTTATG[C/T]GATAATGTATTTATGATTTAGCTCTTCACCATTGG Y 2 1 2 1 201000 f 74 goat snp21801-scaffold214-415283 1 67339400 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403713 Affx-122958033 AX-123274065 1 66133191 GGAGAGAGGAGGCTTTGTACCTGAATGATAGGGAG[A/C]TACATACTCTCATTTCCAAGACCAGAAGAGGGCAC M 2 1 2 1 101000 f 74 goat snp21802-scaffold214-467971 1 67392726 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408368 Affx-122953730 AX-123278719 1 66205454 ACTCCCGACACCTGGAAGGCCAGGTCAAGACAGCA[A/C]TGGCCTCAGATCTCAAGAAATCAGTCCACTCACCA M 2 1 2 1 101000 r 74 goat snp21803-scaffold214-540234 1 67464956 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414425 Affx-122949965 AX-123284774 1 66245177 CCAGGTCTTAATAGATGCTAAGATCCCTGTGCAGA[C/T]GCAAAGGTTATGAATGAAGAGAAAGCTTCAGTAAA Y 2 1 2 1 101000 f 74 goat snp21804-scaffold214-579957 1 67504649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443392 Affx-122927393 AX-123313729 1 66304743 TCAAGTCTCAGCCTTCTCTGTAACTGCGTGTGCTC[A/G]TCGATGTTGTTGCTGTTATTATTACTGTTGTACTA R 2 1 2 1 201000 f 74 goat snp21805-scaffold214-639523 1 67564002 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438338 Affx-122931338 AX-123308676 1 66389067 TTGAATGCATCAAGCCTAATAATTAGTCTCCTCCC[G/T]CCCTTTCAAATGCAGGCATACCCTCAGCATGCTTC K 2 1 2 1 101000 f 74 goat snp21806-scaffold214-723847 1 67648071 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410311 Affx-122952487 AX-123280661 1 66446999 TTTTCCAAATCCCCTTCTAATTCATCCTATATCTA[A/G]CACCTTAACCTGGGTGGTAGTACTAAAGTAATTTG R 2 1 2 1 102000 r 74 goat snp21807-scaffold214-781779 1 67706153 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410789 Affx-122952666 AX-123281139 1 66547337 AAATGTGGGACTGTGGGTTAGACAGCATCAGTTCA[A/G]TGTTAGATGTCCTGATTTTAAGAACTGCGTTGTGG R 2 1 2 1 201000 r 74 goat snp21809-scaffold214-882117 1 67806759 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447186 Affx-122925002 AX-123317522 1 66578949 CAAAGTAGGCCCACATGGGTTCCTCACCTCCAGAT[A/C]GTCTTTGGAGAGACCGTAACCACATAGTTACCCGT M 2 1 2 1 201000 r 74 goat snp21810-scaffold214-913729 1 67837823 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420598 Affx-122945252 AX-123290945 1 66628549 CCCATTCTGTTAACAGCTCTCCTGCTTTCCTTTCC[C/T]CTCCCCAAGTACCATAACCTAATAAAACTTTTCCT Y 2 1 2 1 201000 r 74 goat snp21811-scaffold214-963329 1 67888110 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271738 Affx-1111832866 AX-519545532 1 66664038 TTCTGCTTCTAGAAAATACTTTTTTTCCTCTCCTT[A/G]TATAGAGACGCAATGGGAAATCCCTTGTAAGGGAA R 2 1 2 1 101000 r 74 goat 1_66664038_AF-PAKI 1 66664038 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396949 Affx-122963178 AX-123267304 1 66664738 CAGGCAATTTTATTGTGCCTTTTAGAAATCACAGA[A/G]GTAATTCCTGCCTACTATTTAAAAAATTCAAGCTA R 2 1 2 1 101000 f 74 goat snp21812-scaffold214-999518 1 67942956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411700 Affx-122951542 AX-123282050 1 66704327 TCAGGCCCCGTGATCAAGGATCACCCAGAAAAGTT[C/T]AGTGCTTATTAATATGTTCCCAGGATAACTCCATG Y 2 1 2 1 101000 r 74 goat snp21813-scaffold214-1039107 1 67982353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405278 Affx-122956858 AX-123275630 1 66747182 GATACTGCTACATATTCACCAGAATGGCTAAAATA[C/T]AAAGTCTGATAATGCTGGGGGCTGGAGCTGACAAA Y 2 1 2 1 202000 f 74 goat snp21814-scaffold214-1081962 1 68023217 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433058 Affx-122935751 AX-123303399 1 66786445 CAACTACCTCTATTTCTCCTGCAAATCAGTGAGGT[A/G]AGGCTGGTAGGATAGATTACCCTTGTAATGGTGAC R 2 1 2 1 101000 r 74 goat snp21815-scaffold214-1121225 1 68062939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433027 Affx-122935774 AX-123303368 1 66818758 CTAACCAGAACCAGACACAGTGTGGCAAGATGCAG[C/T]AGGAATTCCATTAGGGTTGTTCTTTGAAGCCAAGT Y 2 1 2 1 202000 r 74 goat snp21816-scaffold214-1153538 1 68095526 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795100 Affx-122930369 AX-385282059 1 66859940 GTGCTAAATCATATTTCTTGGGAGTTGGCCAAGCT[A/G]CAAGTTTTCTTAGGACAGATCCTTCTCAATCATTC R 2 1 2 1 101000 f 74 goat snp21817-scaffold214-1194720 1 68137187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379147 Affx-122976725 AX-123249506 1 66891193 AAAGTACAGGGATGTAATCAAATGGTTCTCAAATT[A/G]TGCTTATTTATTTATAACTCTAATTTGAAAAGAAG R 2 1 2 1 101000 f 74 goat snp21818-scaffold214-1225973 1 68169324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773699 Affx-122973049 AX-385260839 1 66961583 CATTATTATTACTATCGTTATTAACAAGAGACCAT[C/T]TCAAGAAGTAGAGATGTTCAGCTTAGACTGGAACT Y 2 1 2 1 101000 r 74 goat snp21819-scaffold214-1296363 1 68240008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396423 Affx-122962998 AX-123266778 1 67002224 TGATGGGTTTGCTCTTCACCTTGTGGATGGAGGGT[A/G]CTTTGTTACCAAAGAAACTGTCAAAACAATAAATA R 2 1 2 1 201000 r 74 goat snp21820-scaffold214-1337004 1 68280531 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415300 Affx-122948820 AX-123285649 1 67070477 ATACTGGAAAGCCCTTAGAAAAGCTGAAGAGATGC[A/G]TGAGTGCAGGGCATGTTGATTGTTAAGTGAATGCA R 2 1 2 1 201000 r 74 goat snp21821-scaffold214-1405257 1 68346543 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404203 Affx-122957671 AX-123274555 1 67113279 CCAAGTCCCACAAAGCAGCAAGAACAGAATAGTCA[C/T]GAGGACTTGCAAAAGCAGGAGCTGAAATTTGGGCT Y 2 1 2 1 101000 f 74 goat snp21822-scaffold214-1448059 1 68389643 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439143 Affx-122931079 AX-123309480 1 67147675 TTCTGCTTAGCCCTGGCTTTGGAAAGAAAGGAATC[C/T]GCAGAAATGAACAGCTAGATTTAGGCAGGTGACCC Y 2 1 2 1 101000 f 74 goat snp21823-scaffold214-1482455 1 68424048 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782354 Affx-122973773 AX-385269430 1 67191238 TTCCTTCCTAAGTCTTTTCTGAGTTCCTATGGAGT[A/G]TATTCTGCTAGGTGGGATCGGAAGCTGGAAGCATG R 2 1 2 1 101000 f 74 goat snp21824-scaffold214-1526018 1 68467517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773184 Affx-122959885 AX-385260327 1 67225171 AAGGCCTGGGGTATAAAATACTGGTGTTTCTGTGA[C/T]GTTTCATAGTCTCTGATTCCAACCTTAAAGGAATC Y 2 1 2 1 101000 f 74 goat snp21825-scaffold214-1559951 1 68501358 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790906 Affx-122963887 AX-385277903 1 67256589 TCAGGAATGCAAGGGTTAATTCAACATAAGCCTAA[A/C]TTTATAATTCTTCAGATGGATTTCATATCCCTAAT M 2 1 2 1 101000 f 74 goat snp21826-scaffold214-1591369 1 68532846 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439009 Affx-122930360 AX-123309346 1 67286967 TTCAGGATACGTAGGCAGATGTCCTTCCAGCAGAC[A/G]TAATGTGGTGGGTTAACCCATCACTGGTACCAAGT R 2 1 2 1 201000 r 74 goat snp21827-scaffold214-1621747 1 68563815 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419338 Affx-122945650 AX-123289686 1 67319659 TCTTCCCTGTTAGCCCTTTTCTGTGGGATATAGCC[A/G]CAGTGTTCTCCCTACCTCCTGGGTCCACATTGTTG R 2 1 2 1 101000 f 74 goat snp21828-scaffold214-1654439 1 68596518 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403496 Affx-122957641 AX-123273849 1 67377660 ATCTTCCTGCTGGGCTCTCTCTGGGACTCCAAATC[A/G]CCAGAGGATGGTAGAGGTGAATGGAAAGTAAAAGA R 2 1 2 1 101000 r 74 goat snp21829-scaffold214-1712440 1 68655798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447677 Affx-122924634 AX-123318013 1 67435848 ATTAAAAGCAAGGTTTAAATGTGATACACTGTATT[A/G]TCAGCAATGCATTGAAATAGAGGGGGCATTCACAG R 2 1 2 1 303000 f 74 goat snp21830-scaffold214-1770628 1 68714339 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444321 Affx-122926738 AX-123314658 1 67471068 ACACCAGACCTACACACCCACGCACCACTCTCCAT[A/G]CCTTTCCTTGCTCTCTCTTGCTCTTTAGCACTTAA R 2 1 2 1 101000 r 74 goat snp21831-scaffold214-1805848 1 68749745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273719 Affx-1111833800 AX-519547331 1 67492232 GCCAGCAGCAGCCTTGGGTTGTCAGGAAGAAAGCC[A/G]CCCTGGCTGAGTCTGCAGGCCCAGGAGTGTCCTGA R 2 1 2 1 202000 f 74 goat GoatD01.005508 1 67492232 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38422923 Affx-122943041 AX-123293269 1 67527307 CATCACTCCCTACCCTTCCACCCCAGCTCTCCATC[A/G]CACATGACTGGGATTCCCTCCTCCCCTAAACACAC R 2 1 2 1 101000 r 74 goat snp21832-scaffold214-1862087 1 68806469 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393698 Affx-122965252 AX-123264053 1 67556171 TCAGGTGGCACGTCACAGTAGTTCACTGGGCTCCC[A/G]GTGGCACTGGCGGACCCCTGACTGAAAATCCTCCA R 2 1 2 1 201000 f 74 goat snp21833-scaffold214-1890951 1 68835371 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383182 Affx-122973216 AX-123253540 1 67605120 AATCTTTCTGAGCCTCGGTTACTTTATGTGTAAAG[C/T]GAGACGGATGCTCCCGATCTCACAGGGCTTCTGTG Y 2 1 2 1 201000 f 74 goat snp21834-scaffold214-1939900 1 68884756 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383355 Affx-122972669 AX-123253713 1 67621377 CATATTTGCCTTTTCTTCCCTTTTTTCAGGATGGA[C/T]GATGGCCGACTCTTGGACTACCTTATGAATCATGA Y 2 1 2 1 101000 r 74 goat snp21683-scaffold2121-3990 1 68902117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771677 Affx-122956525 AX-385258835 1 67650746 AAATTATTAATGGAAAAAGGGATGATTTCATTGAT[G/T]ATATTGTGCTATTCTTTAATAACTTTCACCAGTCC K 2 1 2 1 101000 r 74 goat snp21684-scaffold2121-33359 1 68931435 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801234 Affx-122962334 AX-385288147 1 67694725 AACAGGGGATAAGGTCAGATAATTTGATTCAGATA[C/T]GGAAAGAGAGAGGCCTTAAAGGGCCCTTCAGGAAG Y 2 1 2 1 101000 r 74 goat snp21685-scaffold2121-77338 1 68975331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383925 Affx-122972973 AX-123254283 1 67729189 CCATTTCCTGACTTGCCCGCAGCCCTCCCAGCTTG[C/T]GGTGCTAAGGAACAGAAAACACCTGCCGAATAACA Y 2 1 2 1 102000 r 74 goat snp21686-scaffold2121-111802 1 69009452 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799870 Affx-122956366 AX-385286796 1 67778715 AGGCAGGAAAACAAATGAGCTATCATCACTGTAGC[A/G]TTACACAACCTTGTAACAACTTCTTTCTTCCCAAG R 2 1 2 1 101000 f 74 goat snp21687-scaffold2121-161328 1 69059264 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790090 Affx-122955745 AX-385277096 1 67838295 TGGGGAACGCTGAGGAGACTAAAAGTTAGGGAACA[C/T]AGCCTGCTTCCAAAGTACTCTGTGGGTCCACAGCA Y 2 1 2 1 101000 r 74 goat snp21688-scaffold2121-220908 1 69118889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795561 Affx-122951856 AX-385282516 1 67906075 CATCTAGGGGTTTGTTTGGAAAACGTTGCACAAGA[C/T]GACTTAGGAGCGTGTGAAAACGCTGCATGTTAACC Y 2 1 2 1 101000 f 74 goat snp21689-scaffold2121-288688 1 69188596 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399735 Affx-122960453 AX-123270090 1 67950877 ATCAAATAAATCCTTCTTTTCAGAAATGAGGGAAA[C/T]GAGGACCAATTCTTCTTGGCCTAACTGCTTCATAA Y 2 1 2 1 101000 r 74 goat snp21690-scaffold2121-333490 1 69233394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433064 Affx-122935746 AX-123303405 1 67981884 CTACGATTATTATTCCTTGGGTTGGCTGCTCAGCT[C/T]CTCAGCGTCATTTCCCCTTTGGGTGGGAAAGTTCT Y 2 1 2 1 101000 f 74 goat snp21691-scaffold2121-364497 1 69264501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387630 Affx-122969860 AX-123257988 1 68026721 TTGTTACAGCCTAAAAGTTCATTCTCCAGAGAGGA[C/T]GAACCAGAGGGACTTCCAGCTACTGCAATGTGTAG Y 2 1 2 1 101000 r 74 goat snp21692-scaffold2121-409334 1 69309431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431219 Affx-122937152 AX-123301560 1 68068637 AGATACAAGTTCGGTGTCCTTGGGCTCAGGAACAC[A/G]CAGGACATCCAGTGTCTGTTTTTAGAGAATGAGTT R 2 1 2 1 201000 r 74 goat snp21693-scaffold2121-451250 1 69351198 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414560 Affx-122949388 AX-123284909 1 68108755 ATTCAATGTGCTTCATCTTTGTCCTATGAGTTCTA[C/T]TGATGAGACTTGATCCTCCAGAAATAATCCTGCAA Y 2 1 2 1 101000 r 74 goat snp21694-scaffold2121-491368 1 69391863 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408028 Affx-122954296 AX-123278379 1 68161546 GCAATTTGAAACGGAAAAAGTTTAAATTAAATTGC[A/G]GAGTCAAAAAGTTTCTCATCGATTATAATAGTGCT R 2 1 2 1 101000 r 74 goat snp21695-scaffold2121-544159 1 69444822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401337 Affx-122959265 AX-123271690 1 68219891 ATAATAAGACCTAGAAGAATAAAGTAGAAGCGAGG[A/G]TACAATTTCACTCCCATATTTAAGAAAACTGAGGT R 2 1 2 1 201000 r 74 goat snp21696-scaffold2121-602504 1 69503729 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774169 Affx-122930703 AX-385261306 1 68267325 ATTAATTGGGACATTTCTGTCATTAACTGAATCAA[C/T]ATTTTGGATCACCTGATATGTATATGCAATACTAC Y 2 1 2 1 101000 f 74 goat snp21697-scaffold2121-649938 1 69551262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770553 Affx-122924018 AX-385257716 1 68329351 CCAAATATGCTAGATATCTTCTCTGGGTCTTTAGT[A/G]TTCACAATGACCCCATATCGGTCTTTCTTTGAGAC R 2 1 2 1 102000 f 74 goat snp21698-scaffold2121-711964 1 69613576 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397152 Affx-122962437 AX-123267507 1 68359699 ATCCTTTTGCTGTTCTATTTCTGTTGAAGAATAGA[C/T]GCAGTTAGACAATACAAACGTGTGCCTGTACAAAG Y 2 1 2 1 101000 r 74 goat snp21699-scaffold2121-742312 1 69643804 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778041 Affx-122921481 AX-385265157 1 68391302 AAATAGTAGCAGATTAAATGTTAAAAAGGACATAA[A/G]GTTTTATGACAGTCTATTAAATGATCTTATTTTAA R 2 1 2 1 101000 f 74 goat snp21700-scaffold2121-773915 1 69675342 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408506 Affx-122953714 AX-123278857 1 68426134 AGCAAACTCAACCACTGAACTCTGCACTTTGAAAC[A/G]CTGAGCTCAAGCACTTTGTTTCAGTTATCTTCCCA R 2 1 2 1 102000 f 74 goat snp48245-scaffold682-3672712 1 69699837 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434909 Affx-122934324 AX-123305249 1 68454826 AACCCCTTTGGAAAATAATTCCAACAACACAACCA[G/T]CAGAGTGACATATACTGTCTAAGACTCAACTAAAT K 2 1 2 1 101000 f 74 goat snp48244-scaffold682-3644020 1 69728740 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402110 Affx-122958684 AX-123272463 1 68517225 AAATTTTGAAACAGGCCCCATGAACTTATCCAGGG[C/T]ATTCCCCATTTGTGAATCCCCCTCAGTGAATCTGA Y 2 1 2 1 201000 r 74 goat snp48243-scaffold682-3581621 1 69772114 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776207 Affx-122957383 AX-385263335 1 68601050 CAAGATAATCAAGGCTTCAACCATATTTCCTTGAA[C/T]GGAGCACAAAAGAATAGGGACATGATTAACATGGA Y 2 1 2 1 101000 r 74 goat snp48242-scaffold682-3497796 1 69857675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790050 Affx-122937565 AX-385277056 1 68650129 AACACAAACCAAGTCATTAACAAAAGCAATAAGTC[A/G]TAATAAAAGTACTAGCTCAGTCTAAAAACACATTG R 2 1 2 1 101000 f 74 goat snp48241-scaffold682-3448717 1 69907075 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794528 Affx-122947894 AX-385281491 1 68695780 ATCTTTCAATTGATGATTCCTATTTAATCTGTGGC[G/T]AAAACCTTGAGCCAATGGGAAACCATATAGCAGAG K 2 1 2 1 101000 r 74 goat snp48240-scaffold682-3403066 1 69952918 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448278 Affx-122924180 AX-123318614 1 68734572 GAAAAGCCAAATTTCTTATATTTCTTTCAGCTAAC[A/G]GCCAGTTTCCATAGCTGAATTAAAGCACTTGTAGC R 2 1 2 1 101000 r 74 goat snp48239-scaffold682-3364274 1 69992232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387357 Affx-122970477 AX-123257715 1 68786662 TCAAAGGTTTGTGTATTTCAGTGTATATAAATTTT[A/G]CCTTAAGAAAGAGAGTGCTGTCAAAAACAAAAATA R 2 1 2 1 101000 r 74 goat snp48238-scaffold682-3312184 1 70045429 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378226 Affx-122976916 AX-123248585 1 68856752 TTTTCTTCTTATATTGCTTTTTTCCTCCTTACCCC[A/G]TGAAGATATTTTAAGAATATGTTTTTGTCTCTTAG R 2 1 2 1 201000 r 74 goat snp48236-scaffold682-3242094 1 70115785 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450764 Affx-122921842 AX-123321098 1 68963139 CCCCTCAAAAAGCCAGTGCACATTTTAGGGATGAA[C/T]TTGACTCAAGACAAGGGTATCCAGTAAAGCCTAAG Y 2 1 2 1 101000 f 74 goat snp48234-scaffold682-3135707 1 70222494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383790 Affx-122973196 AX-123254148 1 68994805 CTGTCCCCTAGGTCTAGGTCTGGCTAAATATAATC[A/G]ATGTTCATTATACAGGTGGGGAGAGAATGAATGGG R 2 1 2 1 101000 f 74 goat snp48233-scaffold682-3104041 1 70254185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396375 Affx-122963033 AX-123266730 1 69023345 GAGGGAGGAAAAAAAGACTCAAGGTTTCTTGGTTT[A/C]TTTTTGGTTTTGAAGACTTGTGGACCTTAAAGATA M 2 1 2 1 303000 r 74 goat snp48232-scaffold682-3075501 1 70282735 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375483 Affx-122979143 AX-123245842 1 69057177 TTTGCTATGCACGTATGTCTTAGTGTCTTTGCCCT[A/G]TGATTTCATTTGGATCAATTCCTAGAAGTGAATTT R 2 1 2 1 101000 f 74 goat snp48231-scaffold682-3041669 1 70316497 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424020 Affx-122942090 AX-123294366 1 69092486 AAAAAATGTTTTTTGGTGAATGATGGCAGAGCTAA[C/T]ACATCTCAGAATTATATTTTATAAGGGGGATACCA Y 2 1 2 1 201000 f 74 goat snp48230-scaffold682-3006360 1 70351246 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772217 Affx-122951461 AX-385259373 1 69152598 GTGACACATACAGATAAGCATGTATAGTCTGAAAG[C/T]TAAGGACTGAGGTCAAACCAAAGGACTGCCAATGA Y 2 1 2 1 101000 r 74 goat snp48229-scaffold682-2946248 1 70411133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278471 Affx-1111836442 AX-519551954 1 69169838 GCACTCCTGAAATGCACACTGGTTGGCACATACAC[A/G]AGGATATCTACGAATAAATCAACTGAACAGAGACA R 2 1 2 1 101000 f 74 goat Random2.2K-78 1 69169838 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 463650045 Affx-1110091925 AX-515130960 1 69175701 GACACCAAAATCTGAGAATGCTCAAGTTTCTTATA[C/T]AACAGTATTTTCATGTAACCTATAAGTACCCTCCC Y 2 1 2 1 101000 f 74 goat 1_69175701_AF-PAKI 1 69175701 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396716 Affx-122962810 AX-123267071 1 69191601 CTAATAGAAACTCTCCTCCCTCTAAAACCTACTCA[A/C]GTGTGCTTGGAAGACCAGCTGCCTGGCATCACCAG M 2 1 2 1 202000 r 74 goat snp48228-scaffold682-2907245 1 70450345 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438753 Affx-122930820 AX-123309090 1 69222175 CCTGAATCAGTAAATATAGGACCAGTTAAGAAGGA[C/T]GTGGAAGATCAAACTGCCACATTCAGCTCTTATGC Y 2 1 2 1 201000 f 74 goat snp48227-scaffold682-2876671 1 70481541 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273773 Affx-1111833832 AX-519547384 1 69236173 GTAATGTCTCCAAGATGCTGCTGTTATCACTTGCC[A/G]CACACAGCTCGGGGACTTCTCTGCAGTGTCCTTCC R 2 1 2 1 201000 f 74 goat GoatD01.006351 1 69236173 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320792374 Affx-122959395 AX-385279355 1 69273915 AGAGGTTAGATGAGGTCAGATATGGGAACGTAAGA[A/G]GTGCCAGTAAATATCCCACATTGCCTTCCCCTTTT R 2 1 2 1 101000 r 74 goat snp48226-scaffold682-2824931 1 70533390 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417105 Affx-122947477 AX-123287453 1 69321170 TTTTCAAGGTCATACAATGATTGTTCTTCTTTTCT[C/T]TCATGGAATAGATTGTCATGGGATAAAGACTGGTC Y 2 1 2 1 101000 r 74 goat snp48225-scaffold682-2777676 1 70580574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768056 Affx-122949680 AX-385255263 1 69350358 TCTAAGAATTAGGTCAGGTTTCTTGTAGATCTTGT[C/T]ATATTGCTCTTTGGAATTTAGCCAGAGGAAAGAAA Y 2 1 2 1 101000 f 74 goat snp48224-scaffold682-2748488 1 70609833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785638 Affx-122952197 AX-385272680 1 69393766 ACTCAAGGAGGAACTGGCCAATGCTGAATACTCTC[C/T]GGAAGAAATGCCTCAGCTCACAAAACACTTATCAG Y 2 1 2 1 101000 f 74 goat snp48223-scaffold682-2705080 1 70652117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804386 Affx-986696553 AX-385290984 1 69424217 ATGAATCTTCTATATAATCATTGTTCACATTCTAT[C/T]ACAGTGTTAATGTGTCTTTTATTGATTCATGAGTG Y 2 1 2 1 600010 r 74 goat 1_69424217 1 69424217 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 38411590 Affx-122951614 AX-123281940 1 69426829 TATATCATAAAATATCCAGTGTTCAGCTTTTGACT[A/G]TCATAAAAAATCTTTTTGTATAGTTTGGATTCACT R 2 1 2 1 101000 f 74 goat snp48222-scaffold682-2672017 1 70685244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416518 Affx-122947772 AX-123286866 1 69473904 AGGATTAATAAAGACCCTCAAAGTCCCCTTTTACC[A/G]TGCCCTCCATTCCTCCTCTCTAGAGGTAACTATTA R 2 1 2 1 102000 r 74 goat snp48221-scaffold682-2624942 1 70733094 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433093 Affx-122935722 AX-123303434 1 69525239 TAAAAGAATGAAGAAGCTTTCATGTAACTGTATAG[C/T]AACACAGAGTTATCGCCAAGATGTGTTTTAAAATA Y 2 1 2 1 101000 f 74 goat snp48220-scaffold682-2573607 1 70784310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790180 Affx-122946516 AX-385277184 1 69563504 GTAAGATAGTACAGTCATTACTTCTGACTGAAATT[A/G]CTTCTTTAACTGGAGTTGAAAGTATAATTTCTTCC R 2 1 2 1 201000 r 74 goat snp48219-scaffold682-2535342 1 70823016 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409216 Affx-122953164 AX-123279567 1 69600148 TCCCTAATCTGTTAATTAAACATGTATATTGATTT[A/G]TATTTTCTAACATCACAATAGAACTTTCAGATAAC R 2 1 2 1 101000 r 74 goat snp48218-scaffold682-2498698 1 70860032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798716 Affx-122977533 AX-385285647 1 69699429 GATCCATTTCCTAAGAGTAAAAATTCTCAGTCCAA[C/T]AGTAAGAGCTGAATAATATAGATTATGGTATATCC Y 2 1 2 1 101000 f 74 goat snp48216-scaffold682-2399417 1 70959363 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414588 Affx-122949366 AX-123284937 1 69772766 AAAAAATACAGTTAACAACAAGGTAAAAACTAGTA[A/C]GCACAAATACAAGTCAGTAATAATCCCCTCTTCAA M 2 1 2 1 101000 f 74 goat snp48215-scaffold682-2326080 1 71032143 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790646 Affx-122944355 AX-385277648 1 69811501 TAATCTTATCTAATTATTTTAGAGCTCACCAAGGT[C/T]CAAGTCTCTCACTTTGTTAACTCCAAATATTTTTC Y 2 1 2 1 101000 f 74 goat snp48214-scaffold682-2287345 1 71070880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278660 Affx-1111836449 AX-519552138 1 69866677 ACCACATATTAGTCCCAGGTCTTCCCCTAAGGCTG[A/G]TAAGAGTTGATAAAACTAGTTGAGCTGTTCCCTAT R 2 1 2 1 201000 r 74 goat Random2.2K-79 1 69866677 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450625 Affx-122921998 AX-123320959 1 69871820 AAAAAAGCAAACATCTGGCATACAGATTTGAAAAA[C/T]CTCGTTTGCATAATTATGCCTGAAAACCTCAAGAA Y 2 1 2 1 101000 r 74 goat snp48213-scaffold682-2227026 1 71131354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386901 Affx-122970037 AX-123257259 1 69914341 TCCCTGTGAAGATGAAATCAAAAGGTGCTGTAAAA[C/T]GCTGCACAGATAGGTCTGCATTTGCCGGAGAAGAA Y 2 1 2 1 101000 f 74 goat snp48212-scaffold682-2184505 1 71174076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800309 Affx-122976659 AX-385287232 1 69980397 TTCTCCTTCCTGCATGGGCTACTTGTGCTCTGACT[A/G]TATGATCAACTCTCGCCTATCCTATGAAACTCTCC R 2 1 2 1 101000 f 74 goat snp48210-scaffold682-2118449 1 71240423 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775141 Affx-122919731 AX-385262273 1 70044618 TTATTTAAGCCTTGCTCTGGAGCTTTATGAAACAC[A/G]TAGCTCTATCCCTATATACAGATGATGATATAGAC R 2 1 2 1 101000 f 74 goat snp48209-scaffold682-2054228 1 71304469 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419491 Affx-122945465 AX-123289839 1 70077240 CCTTGCCATCAGACTGTTCAACTTACTGCCTATTC[C/T]TTATGTTAGTCATCTAGTGTCCTCCCCATCAGTGT Y 2 1 2 1 101000 r 74 goat snp48208-scaffold682-2021606 1 71337510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380519 Affx-122975689 AX-123250877 1 70125775 TGAGGTCTTACTGCTCCCAGATGTTCTCTGTAGAC[A/G]GAGCAAGGGTACACATGTATATGTAAACACATATT R 2 1 2 1 101000 f 74 goat snp48207-scaffold682-1973071 1 71386721 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382409 Affx-122973829 AX-123252767 1 70159046 GTTTACAGATTCCCAGCCTGGGATGAAAAACATGC[A/G]CTTTTGTTTTCTACCCATTCCTATAATTATGATTT R 2 1 2 1 201000 r 74 goat snp48206-scaffold682-1939800 1 71419997 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446780 Affx-122925311 AX-123317116 1 70197774 ATTCAAATCAGTATTAAATAGGGATGTAAGTCTTC[A/G]TGTGTTTACCAAAAGGAAGCACTGTCCAAACAGTG R 2 1 2 1 201000 f 74 goat snp48205-scaffold682-1901072 1 71458498 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395093 Affx-122964168 AX-123265448 1 70230794 ACAGGTGATAGTAGGGTGATGAAGTAGGGATTTGA[A/G]CTCAGCACTGACTATGAAGTATAAAAAGCCTGTGA R 2 1 2 1 101000 f 74 goat snp48204-scaffold682-1868052 1 71491970 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416596 Affx-122947644 AX-123286944 1 70260917 ACTACTGTCTTTTGGAGTAGAAGGGGAGGGGGTCA[A/C]CCATCTGAGTGTATGGAAACGTAACATCTAATTTC M 2 1 2 1 201000 r 74 goat snp48203-scaffold682-1837929 1 71522286 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389288 Affx-122968519 AX-123259646 1 70293905 TCTCCTACACCCCCACCTTTGCAAATAAATCCTCT[C/T]CTAATTATCCTATCTTGGGTGTGCCCTCTGCTTCC Y 2 1 2 1 201000 r 74 goat snp48202-scaffold682-1804941 1 71555348 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453744 Affx-122919613 AX-123324077 1 70332779 CAGAACAGAAGTAGAGTCACAGAAGCTTCACCCAA[C/T]TGGGGGAAGAGCATCTGAAGCAAGTCAGAATTCTT Y 2 1 2 1 303000 r 74 goat snp48201-scaffold682-1766067 1 71594202 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436707 Affx-122932321 AX-123307045 1 70362256 CGGGGGACCTTCCAGTGGCCTGGGAGGGCACTGCT[A/G]CTTGAGTTTACTGTGGGTGGGAGGGAAAGGAGGGT R 2 1 2 1 202000 f 74 goat snp48200-scaffold682-1736590 1 71624048 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797233 Affx-122920403 AX-385284172 1 70442654 CAGGGGGTGGAAAGGGATGTGTGGTTTTCAGACAG[C/T]AGAGCAGGTAAGAGGTCAGCATTCTACACCAAAGG Y 2 1 2 1 101000 r 74 goat snp48198-scaffold682-1656192 1 71704361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447758 Affx-122924574 AX-123318094 1 70472305 TTTTTATGCACTTTAAGCTATTTTGATGCCAGCAC[G/T]TTTAGATGTGGCTGACTTGAAGGAAAATAAAGTTG K 2 1 2 1 201000 r 74 goat snp48197-scaffold682-1626541 1 71734212 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388187 Affx-122969432 AX-123258545 1 70506872 ATGCTTAGAGGGAGAAGGCTCCATTCTCGGCACTA[C/T]GCCTTCTCCTTTCCCAGTCTCGCAAATACATTCAG Y 2 1 2 1 201000 f 74 goat snp48196-scaffold682-1591974 1 71768727 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426787 Affx-122940546 AX-123297133 1 70556101 TCACTCTGTAATTACACTATTCTAAGACATTAATT[A/G]CCTTCATTTCTTTGTTCACCTTCAGTCTTTGATTG R 2 1 2 1 101000 r 74 goat snp48195-scaffold682-1542745 1 71817758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393527 Affx-122965794 AX-123263883 1 70587638 CACTCAAATCTCACATTTCAATTTCTATTTGACTG[C/T]TAACTTCTATTTTCACATCTTTCTTGGAATAGAAA Y 2 1 2 1 101000 r 74 goat snp48194-scaffold682-1511208 1 71849228 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408469 Affx-122954429 AX-123278820 1 70630569 TATGATGAGATTTTATTTCCTGGCAAATCTGATCT[A/C]GTCTCACAAACGTATACAATATATTAGACTTCTGT M 2 1 2 1 101000 r 74 goat snp48193-scaffold682-1468277 1 71891984 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427011 Affx-122939846 AX-123297356 1 70661229 TTGTCATCCTGCCACAGAAACACGTCCTTAGTCTC[A/G]AATAAATGATGACAGAAAAATCATGAAAATCTTTT R 2 1 2 1 303000 r 74 goat snp48192-scaffold682-1437617 1 71922692 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414663 Affx-122949308 AX-123285012 1 70692257 AAAATGGAAATAATCCACTTGCCCCACCTACCTCA[C/T]AGGACTATTATAAAAATCCCAAATACACTATGTAT Y 2 1 2 1 201000 r 74 goat snp48191-scaffold682-1406589 1 71953985 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446065 Affx-122925825 AX-123316402 1 70745316 ACCATAGTGACAGGTCACACTGACTTAATGGGTAA[C/T]GCTGCACTAAGAAACTGTCCTCAACGGTTTCTTAT Y 2 1 2 1 101000 f 74 goat snp48190-scaffold682-1353530 1 72006567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787814 Affx-122930630 AX-385274837 1 70793556 GAAAGTAGCTCATTTCTGAAAGTTAACCTTTAGCC[C/T]AGGTGTAAAATAAATGGTGCCAATATTCTTTATAA Y 2 1 2 1 101000 f 74 goat snp48189-scaffold682-1305290 1 72054882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379512 Affx-122976080 AX-123249870 1 70862843 AAAGCTCTGCACACACCTGCAGGGAGCTGGGAGGA[A/G]TAACAGTCTGGCCGGGACCGTGCCCAGGTCCAGCA R 2 1 2 1 201000 r 74 goat snp48187-scaffold682-1236003 1 72124350 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768929 Affx-122946949 AX-385256104 1 70901205 GATTTATTTCTGCTTAGTGAATTTCCAGATCCGAA[C/T]GCGCTCTGTTCATCAGCTAAGTTTGCTTTGGTGCC Y 2 1 2 1 101000 r 74 goat snp48186-scaffold682-1197641 1 72162789 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382527 Affx-122973796 AX-123252885 1 70940810 TCAAGCTCAGATGGCGCTTTAAGTCTCCTGGTCTT[A/C]GGAGGCAAGTGCAGTAGAGATGGCCACTTCGCATC M 2 1 2 1 101000 f 74 goat snp48185-scaffold682-1158036 1 72202437 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431205 Affx-122937163 AX-123301546 1 70982194 GGGCAAGACTGAGAATCCTAGCAGCCCAAGTCCCA[C/T]GCAAACCCCAGTGAGAACAAAGTCCTTAGCTCATA Y 2 1 2 1 101000 r 74 goat snp48184-scaffold682-1116652 1 72244279 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797256 Affx-122927493 AX-385284195 1 71018566 CCAGTTTCCAGCATGTTTCTATATAAATTAATGAG[C/T]ATCTAAAAGTGCTCGACCTCAAAGGGTGTGGAGCC Y 2 1 2 1 101000 f 74 goat snp48183-scaffold682-1080280 1 72280800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399480 Affx-122961187 AX-123269835 1 71050602 CAGGAGGCCTAAGCCCCACAGCTGGTCTTTCCTTC[A/G]CCCCTCAGAGATCCCTGAGAATCACTATTGGAACT R 2 1 2 1 101000 r 74 goat snp48182-scaffold682-1048244 1 72313467 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390737 Affx-122967914 AX-123261094 1 71079408 TATGCCCCTTTCTCAGCTCACAGCCATACCTAGGC[C/T]ACACTGCCATGGCAGGCCCTCCTAACACTCATCTA Y 2 1 2 1 101000 f 74 goat snp48181-scaffold682-1019438 1 72342278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415332 Affx-122948796 AX-123285681 1 71118650 TTCATTCATCAATATTTATTCAGATTCTACTATAC[A/G]CTACCATGGGTAAAGCCCTGGGAAGAAGATGAATA R 2 1 2 1 101000 r 74 goat snp48180-scaffold682-980196 1 72381104 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424872 Affx-122941332 AX-123295218 1 71172860 GTAATCTTTCCCTCTGGAGAGGCCTTCTCCGAAAA[C/T]ACTCACTTGAAGGTATCTGTGCTGAATTAACCATC Y 2 1 2 1 201000 r 74 goat snp48179-scaffold682-925986 1 72435994 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394215 Affx-122964898 AX-123264570 1 71202981 TTGCTGCTGTAGAAACACCAAAAGCAATGTGCTAA[C/T]AAGAAAACACTGAGGTTATTCTTACTGCAGTAGGG Y 2 1 2 1 101000 f 74 goat snp48178-scaffold682-895865 1 72466181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791274 Affx-122955476 AX-385278268 1 71253456 TCATGCTTTCCTCACTCAATGGCTTCTACAAGAAA[C/T]ATACAAGACTCCCAGTTACAGGAACGCCAGCTCCA Y 2 1 2 1 101000 f 74 goat snp48177-scaffold682-845390 1 72515827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411464 Affx-122951806 AX-123281814 1 71365207 CAAGCCAAATGATGACAGCCAATAATAATCTTACC[A/G]TTTATTACAAAAAATATTTTTGAAGTCTAAAAGGA R 2 1 2 1 103000 f 74 goat snp48174-scaffold682-733639 1 72626619 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376880 Affx-122977822 AX-123247239 1 71409224 CCCAGGCCTGACCACACCTGAGTCAACAGATAAAA[C/T]GGAGTTCCAAATTCTGTGAGTTGTGGACTCCTAGG Y 2 1 2 1 101000 f 74 goat snp48173-scaffold682-689622 1 72670911 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387678 Affx-122969825 AX-123258036 1 71472190 AAAAACTGAGGAAAGCTAAAGTTATACTGTACCCT[C/T]GAGATGCTGCTGCTGCTGCTGCTGCTGCCAAGTCG Y 2 1 2 1 101000 f 74 goat snp48172-scaffold682-626656 1 72734515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420093 Affx-122945100 AX-123290441 1 71503823 ACCCAGGGCCTTTTAGGAAGTTTTCCCATATTGCA[G/T]AACATTTCTCATCACTGTGGGCCTATCTCATTCTT K 2 1 2 1 101000 f 74 goat snp48171-scaffold682-595023 1 72766967 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779373 Affx-122948231 AX-385266477 1 71544324 CCTAAAAAAGTACAGTACTAGAGTCATCCCACCAA[C/T]GTAAGCTTGTCCCATCAAATCAATATGACCTGAGG Y 2 1 2 1 101000 f 74 goat snp48170-scaffold682-554522 1 72807513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399538 Affx-122961144 AX-123269893 1 71586317 TATCTATACTTACATTTCTATACTCTATACTTAAG[C/T]GAATCCCACTTTCTCATTAATCTCCTCCATGAAAA Y 2 1 2 1 101000 r 74 goat snp48169-scaffold682-512529 1 72849370 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404589 Affx-122957356 AX-123274941 1 71624522 TTGAGAGAGACTGACCTGCCTCTGGGTGACGAGCA[C/T]ATGAGCCATCATTCCCTCCCCTATAATTTTTTGTC Y 2 1 2 1 102000 r 74 goat snp48168-scaffold682-474324 1 72887778 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423008 Affx-122942978 AX-123293354 1 71685316 ATTTAGCTGGGCATAAAAGACTTGTTAAAACATGT[A/G]TTTCAAGACCCCATTCCCAGAGGTTCTGAAGGAGC R 2 1 2 1 101000 r 74 goat snp48166-scaffold682-413530 1 72949108 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407334 Affx-122955296 AX-123277685 1 71721421 CAGCCGCCCACCCAAAAGCTCTCTGGTCTATTCTA[C/T]ACCCCCATCCTTTTCTAACTGGGCCTTGGATGGAT Y 2 1 2 1 101000 r 74 goat snp48165-scaffold682-377425 1 72984206 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271840 Affx-1111832867 AX-519545622 1 71756259 CTTCTAAGATTTTCTCTCTATCATGGATTTTGAAC[A/G]ATTTGATTATGATGTTCTTTGATGTAGTTTTCTTC R 2 1 2 1 101000 f 74 goat 1_71756259_AF-PAKI 1 71756259 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426800 Affx-122940536 AX-123297146 1 71775633 ACATACAGACCACATCAGGAAATTTCACTCTGGGG[C/T]AGAGTGATTTACAAAGCCTGTTCAGAAGTGGAGTC Y 2 1 2 1 201000 r 74 goat snp48164-scaffold682-323213 1 73039055 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393610 Affx-122965364 AX-123263966 1 71806871 TATGGAGCCGGCAATGGGTTTTATTCCATAATCAG[A/G]GGCATGAAATAAATACCACATGATTTTTCTAAAAC R 2 1 2 1 101000 f 74 goat snp48163-scaffold682-291975 1 73068736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800079 Affx-122977083 AX-385287002 1 71866962 TTGACCCAATCACATACAAGGATGGAGTTTAATTC[A/G]TTATTTCAATCAGGTTTTTGGCAAGAAATGAACAG R 2 1 2 1 101000 f 74 goat snp48162-scaffold682-231884 1 73127143 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772390 Affx-122976713 AX-385259543 1 71896115 TAGCATCACTAGCAACTTGAGTCCTCAAAAAATTA[C/T]GGGAAGAAACCAAAGGGAGAGATCCTTTAAGAAGA Y 2 1 2 1 101000 f 74 goat snp48161-scaffold682-202731 1 73156401 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783958 Affx-122951190 AX-385271011 1 71948142 CTTATATCCCATGAAGATATGCCAAGCTTATCTTG[C/T]GGATTAATGTATTTCACTGGGTCACCATCCCGCCA Y 2 1 2 1 201000 r 74 goat snp48160-scaffold682-150704 1 73208538 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385742 Affx-122971082 AX-123256100 1 71977889 TGCCCTGGAACTCCACGAAGGGCTACTGTGCTAGC[A/G]TGGAGAAAGGGGAGGGGTGATCTGTAGGAGAGATG R 2 1 2 1 201000 f 74 goat snp48159-scaffold682-120957 1 73238431 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434406 Affx-122934682 AX-123304747 1 72010708 CTCTTCCCCATGCTTGTCGTCTCTGGGTCCCAAGA[C/T]GGCTAGTGTGACTGCAACAGTATGTCCACATTCAG Y 2 1 2 1 102000 r 74 goat snp48158-scaffold682-88138 1 73271739 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426335 Affx-122940271 AX-123296681 1 72042764 TCTAAACAGCCTTTGTTGTTTCTGCTCCTTCAGCC[C/T]CTCTAAGTCAAAGAAGTAGAATCGAAAGCAAGGCC Y 2 1 2 1 201000 r 74 goat snp48157-scaffold682-56082 1 73303581 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436847 Affx-122932211 AX-123307185 1 72094585 GCATGCTCAGAAATATTACTTAGGTCAGCCAGTTC[C/T]AGGACCTTCTACACAGGGAGCGAATCTCACCCCTT Y 2 1 2 1 101000 f 74 goat snp48156-scaffold682-4261 1 73354985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776680 Affx-122941565 AX-385263806 1 72102137 GTATGTGAATTAATCCTTGGGATTCCTTGGCTCAA[C/T]TCAGTAAACATTCCATGTACAACTTTCACCAGGTT Y 2 1 2 1 101000 f 74 goat snp37621-scaffold462-3192 1 73362608 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418487 Affx-122946445 AX-123288835 1 72148345 ATGAAGGGCTTAATTTGCTGGCTCATTGGTCTCAC[A/G]TGCTCAGCTGTGGCACTCAGCCCCTTAGGCTTGCT R 2 1 2 1 101000 f 74 goat snp37622-scaffold462-49400 1 73409116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773359 Affx-122974262 AX-385260501 1 72190864 TTTGGTTTAAACATAAAGGCATGGACTGATGAAAC[A/G]ATCATTGTTTTTCCTAAGAGAGCTGCTCACTCCCA R 2 1 2 1 101000 r 74 goat snp37623-scaffold462-91919 1 73451660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396132 Affx-122963401 AX-123266487 1 72245839 GAGGCTAAATAATTTGTGGGAAGGAGTGTGTCAGA[A/G]TAAAGCCTGGAAAGAGGGGATAATACAGAGAAAAG R 2 1 2 1 101000 f 74 goat snp37624-scaffold462-146894 1 73506227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432359 Affx-122935872 AX-123302700 1 72276786 GTAACAAACAAGGAAGACCAGAACGGCACGGCTTA[C/T]GAATGCAAAACCACCTGGACATATGAAGGGCCACA Y 2 1 2 1 101000 f 74 goat snp37625-scaffold462-177841 1 73536861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452663 Affx-122920329 AX-123322996 1 72308903 TAATTTGACTCTAGTCTCTCTAGGACATTAACCTG[C/T]GGATCTACATTACAGGATCATCTAAAGCCAAAGCA Y 2 1 2 1 101000 r 74 goat snp37626-scaffold462-209958 1 73568724 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380004 Affx-122975606 AX-123250362 1 72340351 GCAGTGTCCCCAGTCATGACAAAAGTGTACCCAGA[C/T]AATACTAAATGTTCCCTGTAGTCCATGGGGTGGTG Y 2 1 2 1 201000 f 74 goat snp37627-scaffold462-241406 1 73599757 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388055 Affx-122969533 AX-123258413 1 72361615 TCCTGCACTTTTTCCTTCTGACTGGGTTCCTGAAT[A/G]CACTTGGCAATTCATGTGCCACTGTGGGGTTAAGT R 2 1 2 1 101000 f 74 goat snp36345-scaffold435-3913177 1 73621248 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384637 Affx-122972157 AX-123254995 1 72393676 AAAAAATAAAAAAAAAATAAAATAAGTATGTCCTA[C/T]AACTACACATCATTCCTAGAAACACCCTCTTAATT Y 2 1 2 1 101000 r 74 goat snp36344-scaffold435-3881116 1 73653694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797684 Affx-122959480 AX-385284623 1 72426761 ACAATCTAAATATCCATCAATATGACTGTCTTCAA[A/G]ATTATGATACATTTAGAGAAAGCATATTTGTGCGG R 2 1 2 1 101000 f 74 goat snp36343-scaffold435-3848031 1 73686838 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390474 Affx-122967602 AX-123260831 1 72521150 AATATACATCAAAAGGAAATGAAATGCATAGGCTG[A/C]TTACCAGGGGCAATTTTAAGAACCAAAATTGGCCC M 2 1 2 1 103000 r 74 goat snp36341-scaffold435-3753642 1 73782563 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448095 Affx-122924321 AX-123318431 1 72619709 ACTGAACCAGGAAGCAATGCTCCATTTCCAGTCCC[A/G]TTTCTTGACAAACTCACATTTGTTGAGAAATTACT R 2 1 2 1 102000 f 74 goat snp36340-scaffold435-3655083 1 73881816 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785707 Affx-122964634 AX-385272748 1 72650400 ATACCCATTTTTAAGCATTCAGCTTTTCAGTCATC[C/T]AGGAATTATAAAATGATAGGTTTTATGCTTCTCAC Y 2 1 2 1 101000 f 74 goat snp36339-scaffold435-3624392 1 73909458 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435161 Affx-122933663 AX-123305501 1 72678946 CTTCCATTACCATCTCCCTGCTCAGAACATCATTA[C/T]ACATGCATTAGAGAAGTCTGATAATTATAAGTTGT Y 2 1 2 1 101000 r 74 goat snp36338-scaffold435-3595846 1 73937614 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438597 Affx-122930941 AX-123308934 1 72752294 TCTCTCATAAGCAGATGTTACCCTTACCAAAGTCT[A/G]TCTGGAGAGAATCATAAATAATGGCAGGATGGAGA R 2 1 2 1 101000 r 74 goat snp36337-scaffold435-3522498 1 74012046 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416807 Affx-122948137 AX-123287155 1 72784147 CTCATTTAAAAATGTTGAAAACTAAGTAAAAATGT[A/G]TTTAGTTACTGTGCTGGCCAACAAAATTTATCTGT R 2 1 2 1 101000 r 74 goat snp36336-scaffold435-3490645 1 74053122 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441705 Affx-122929157 AX-123312042 1 72818307 TGCAAAAAAAAAAAAATATGTGAGAGAACTGTTTG[C/T]AGGCATCTGACCCCTGAAAATAGAATAACACAAGA Y 2 1 2 1 101000 r 74 goat snp36335-scaffold435-3456485 1 74087508 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387708 Affx-122969805 AX-123258066 1 72888997 ATCTCAGGGGATGAGACCCAGGCATCAGCACTTTG[C/T]AAAGCTTCCTGGGTGATTCCAGCGTGCAGTCAAGA Y 2 1 2 1 202000 f 74 goat snp36334-scaffold435-3385795 1 74158555 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402485 Affx-122958589 AX-123272838 1 72918171 GGGAAGTCCTTGGATTTTAAAATAGAATGGTTTTA[C/T]GACAATATCCAGAGGTTGAGAAATTGATTCATCAA Y 2 1 2 1 201000 r 74 goat snp36333-scaffold435-3356621 1 74187538 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407035 Affx-122954941 AX-123277386 1 72962359 TACCAACATGTCTGGCACTTAGTAAGTATTCAATA[C/T]AAGTCTGATAAATGAAAAAGCAAATGAATGAACCA Y 2 1 2 1 201000 f 74 goat snp36332-scaffold435-3312433 1 74232035 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778106 Affx-122970597 AX-385265221 1 73057096 CCTAAAATGAGTTGTAGCTGGAGGATTCCTAAGGG[A/G]GTATAATCACAGCTTAACAAAATGCATCTCTCCAA R 2 1 2 1 101000 f 74 goat snp36330-scaffold435-3217696 1 74327193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445480 Affx-122925205 AX-123315817 1 73089480 GAAGCATTGGCATACGTTTGCTCTTAAAAGCAAAG[C/T]GAAACGGCCTCCCAGCCTCCCTTTCCGTAATTGAT Y 2 1 2 1 101000 f 74 goat snp36329-scaffold435-3185312 1 74358744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396091 Affx-122963428 AX-123266446 1 73119303 TACAGAGCTAATCTCAGCCTCTCAGACTCTGGCAA[C/T]GGTATTGAGATACATCCATGTCAGTTGAGCTTCCT Y 2 1 2 1 201000 r 74 goat snp36328-scaffold435-3155489 1 74388558 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408785 Affx-122953373 AX-123279136 1 73154493 GTCTGGAAGAATTTAGCTATAGAGGAAGGAATAAT[A/G]AAGTAAATGAGAAAAATTTCAAAAGGCAGAAAGGT R 2 1 2 1 101000 f 74 goat snp36327-scaffold435-3120299 1 74424239 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391286 Affx-122967348 AX-123261643 1 73202926 TTCCCTCATCTTCTTTCCCCTGCTCAGCTCAATTT[A/C]AGGGCCCATTTCAAGAGCTATTACTATGTGTCAGA M 2 1 2 1 101000 r 74 goat snp36326-scaffold435-3071866 1 74472653 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453297 Affx-122920370 AX-123323630 1 73244555 GCAGTATATCCTACTAGGAAGGTGTTCAATAAATC[A/G]TTGATAAATGAATAAATGACTTTATATATATATAT R 2 1 2 1 103000 f 74 goat snp36325-scaffold435-3030237 1 74514357 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771957 Affx-122926000 AX-385259113 1 73290159 AAGCTGAAGGTTGGCATTGTTTGTATCACTATACA[G/T]ATGAGAAAAATAATCATAGGGATGTTTTTAAAAAC K 2 1 2 1 101000 r 74 goat snp36324-scaffold435-2984633 1 74559984 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383932 Affx-122972967 AX-123254290 1 73336822 CTTCGATCTGATTCATAAGGATTGGAACATTTCTA[C/T]AAGAGGTTTTTTAAAATAAGGACATGGTATAAATC Y 2 1 2 1 101000 f 74 goat snp36323-scaffold435-2937970 1 74607091 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798593 Affx-122925913 AX-385285526 1 73378618 TGCCTCACAGACACGCTGTGTCATGAGAGTTGATG[C/T]ATATGAGTGTTTTCTAAACTATACAAACCAGAGGC Y 2 1 2 1 101000 f 74 goat snp36322-scaffold435-2896174 1 74648851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798740 Affx-122968616 AX-385285671 1 73413442 ATAATAGCATTTCTGGGTATATTAATATTCAGTTT[A/C]TATTAATGCAAGCTCCCTTTGAGCCTCTAAATTCA M 2 1 2 1 101000 r 74 goat snp36321-scaffold435-2861350 1 74683564 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389190 Affx-122969078 AX-123259548 1 73450627 AAAAAAGAAAAACAAAATAAAACAAACCACTACTT[A/G]GGATGTTATCAACACCTGTCAATGAATCTTATCTT R 2 1 2 1 101000 r 74 goat snp36320-scaffold435-2824165 1 74720744 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444132 Affx-122926805 AX-123314469 1 73496492 AAAAAAACTTCCTCAAGGTCAAAAAGTCCAATGCC[A/G]TTTTTATGATACTGTTACCTTAGACTGACTCAAAG R 2 1 2 1 201000 r 74 goat snp36319-scaffold435-2778300 1 74767507 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445528 Affx-122925170 AX-123315865 1 73531690 TGTTTGGTAAAAATTAGACTACTCCAGCACACTTA[C/T]AGGGGGCTTTCCAGGTGGCTCAGTGGTAAAGAAGC Y 2 1 2 1 101000 f 74 goat snp36318-scaffold435-2743102 1 74800717 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396490 Affx-122963539 AX-123266845 1 73589997 TCTCCATATTTGTTTTACAGCATTTCTATTTTTTT[A/C]TTTCTTCAGCCATCAAGTAAACTATACAAGGCTAA M 2 1 2 1 101000 r 74 goat snp36317-scaffold435-2684795 1 74859693 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802697 Affx-122973369 AX-385289596 1 73658212 CCACAATACAATTCTGCTAAAGTTCTACTGAAATT[A/G]TATCAGGTCACCGGCTAGGATAGAAGAGAACTATT R 2 1 2 1 101000 r 74 goat snp36316-scaffold435-2616580 1 74928047 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775623 Affx-122944438 AX-385262754 1 73696677 CGCTCTAACTACAGACTGACTTTCAGCTCATTCAC[A/G]TTTTCCTGGGATCCAAGTGGTTGTTATGACTAAGT R 2 1 2 1 101000 f 74 goat snp36315-scaffold435-2578115 1 74966614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431520 Affx-122936230 AX-123301861 1 73731070 CAAACTTCTGAAAGACAGAGAAAATGTTAAAATGA[C/T]ACAAAGAAGGTACAAAGACACAGGAAACACAGGCA Y 2 1 2 1 103000 r 74 goat snp36314-scaffold435-2543722 1 75000666 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778378 Affx-122937878 AX-385265493 1 73766386 TATTGAGTACATTAAAACAGATTCATTTTACTGTC[A/G]TGAGACAAATGTGACTGTATATGAGCATATGAAAT R 2 1 2 1 101000 f 74 goat snp36313-scaffold435-2508406 1 75036320 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320791324 Affx-122931152 AX-385278317 1 73822337 CCAGAAGACTCACATATTTAACAGATAACTATAGC[A/G]CTTCCCTCACTGTTGTGAAGTAGAGTCTAAATCAC R 2 1 2 1 101000 r 74 goat snp36312-scaffold435-2452455 1 75092836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403730 Affx-122958021 AX-123274082 1 73853746 TGTGGCACCTGGTGTTCTTTTGCAAGTTGAGACAG[C/T]ATATCATATTTTTATTGGATTGACAGGAGACTAGC Y 2 1 2 1 101000 f 74 goat snp36311-scaffold435-2421046 1 75124168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781636 Affx-122967171 AX-385268720 1 73920672 TAAGATGAATATGTCTGGAGCCTTGAGCATTCACA[C/T]ATCAATGCAGTGAATAATAATGTCCTCTATTTGCA Y 2 1 2 1 202000 r 74 goat snp36310-scaffold435-2354120 1 75191822 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447238 Affx-122924963 AX-123317574 1 73976158 GCATCTTAGCAACAGTGATTTTGAGATAGCTATTC[C/T]GTTGAGATCTCAGATTATCAGAGGGTCAAATCTGA Y 2 1 2 1 101000 r 74 goat snp36309-scaffold435-2298634 1 75247307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405738 Affx-122956514 AX-123276090 1 74025414 CTTCATCTTTCTGTATTTTCACTCAATCACTTCAC[A/G]TCGCAGTCATACAAAACTACTCACAATTCCACAAA R 2 1 2 1 101000 r 74 goat snp36308-scaffold435-2249378 1 75297350 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792010 Affx-122967361 AX-385278998 1 74062963 TTATTACTCTCAAGCTCTCCTTAAAAACGTTCACA[G/T]CTTTCAGTAAAGCAGTCTATCTTTACGACTAGGGT K 2 1 2 1 201000 f 74 goat snp36307-scaffold435-2211829 1 75335548 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273512 Affx-1111833661 AX-519547127 1 74094908 TGTCAAGTGTGTTGTAGAAGAAAAAGGTTGAGAGT[A/G]GTGCTAGTCAGTCACTCACTTGGCCGCCCTCATTT R 2 1 2 1 201000 f 74 goat GoatD01.000912 1 74094908 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38417102 Affx-122947480 AX-123287450 1 74113885 ATTTCCATTCAAAGAGATCTATATTCCCCTTTTAA[C/T]GTTCTCATTTAGGGCTCAGATTAGCCAGTTAATAG Y 2 1 2 1 101000 r 74 goat snp36306-scaffold435-2160907 1 75387515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415668 Affx-122948554 AX-123286017 1 74178773 CTGGGGGGAGTAGGGGCAATATTATCTTCCAAATA[C/T]ATACTTGTTTTCCTAGCTGTAAAATGGGGGTGAAC Y 2 1 2 1 101000 f 74 goat snp36305-scaffold435-2096019 1 75453165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434116 Affx-122934932 AX-123304457 1 74229734 TCATTTAGATTTTTTCACAAATCCCCTATCTCCCA[C/T]TCCACATATTTCTTGAACTTCTGAATTCCCATAGC Y 2 1 2 1 101000 r 74 goat snp36304-scaffold435-2045058 1 75505344 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450925 Affx-122921777 AX-123321259 1 74262516 ACTGGAGTCTGGAGGCAGGCAGGAGGCTTATCCTG[A/G]TATGCAGCTAAAGGCTTGACTTCTGTTAACTGGTT R 2 1 2 1 101000 r 74 goat snp36303-scaffold435-2012276 1 75538131 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271740 Affx-1111832868 AX-519545534 1 74292981 AAGCCAAAAAAGGAAAAAAAAAAAAAAAGCCCTCA[A/G]TATTACCATGACTTTCTGCTTGGAGTTTGTGGCAA R 2 1 2 1 101000 r 74 goat 1_74292981_AF-PAKI 1 74292981 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38381650 Affx-122974754 AX-123252008 1 74307126 GGCCGTGGAGGAAAAGCTACTTGCTTAAGGCCTCG[C/T]ATCTGGTAAGAGCTTAAACTGGGATTTGAACCATG Y 2 1 2 1 101000 r 74 goat snp36302-scaffold435-1967666 1 75583449 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412591 Affx-122951297 AX-123282940 1 74336626 TCATGCTCCTGTTAGAACTCAAGGTCATATGACAA[C/T]CCACCATTTCTCTCGAGTGTCTGGTTGCATGCAGA Y 2 1 2 1 101000 r 74 goat snp36301-scaffold435-1938166 1 75615308 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804390 Affx-986696557 AX-385290985 1 74346592 GAAAGTCATCATCTCTCCATCACATCATCCACCCT[A/C]TCTCTTAAGGTATCTTTCTCTTCCATATACCCTGT M 2 1 2 1 600010 r 74 goat 1_74346592 1 74346592 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 38440140 Affx-122929686 AX-123310477 1 74387098 TTGGATTCCAATACTCCCTGTGGCCTTTAGGGCTG[C/T]GTTATCCCTGGGGAGGGAGCAGGGGGGATTGCCTC Y 2 1 2 1 101000 f 74 goat snp36300-scaffold435-1887694 1 75666071 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421306 Affx-122944095 AX-123291653 1 74422435 ACCAGTTGAATTCCTCTTATTCTCATTCAAATAGT[A/G]TAATTGTTAATTATTGTTGATTTTGAGACTGTAGG R 2 1 2 1 101000 f 74 goat snp36299-scaffold435-1852357 1 75701019 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278710 Affx-1111836473 AX-519552188 1 74425506 TGAGATGAGTGCAGTTGTGTGGTAGTTTGAGCATT[C/G]TTTGGCATTTGGAGGGTGGAATCCTTCAAGGTCAT S 4 1 2 1 101000 r 74 goat Random2.2K-83 1 74425506 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429960 Affx-122938070 AX-123300301 1 74463567 AAAGGAAGACGTGAAGGGACCCTTCTATTTACTTC[A/G]TTTGTCTTATTTAAATAAATGAGAGAGCCTATTAC R 2 1 2 1 101000 f 74 goat snp36298-scaffold435-1811225 1 75743955 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404147 Affx-122957085 AX-123274499 1 74504259 GAGCACGTCATAAAGTTGTTTGGCAAGGGGTTGTG[C/T]AGGGTGAAGGCTTTCCAGGAAGAAAGACCAGTTAA Y 2 1 2 1 101000 f 74 goat snp36297-scaffold435-1770533 1 75784797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452119 Affx-122920833 AX-123322452 1 74550603 ATCCTATTCCTTAGCAACTCTTTCATTTTCCTTTC[A/G]TTTGGATATTTGTCAGACTCTGCCTGCAATGCAGA R 2 1 2 1 101000 r 74 goat snp36296-scaffold435-1724189 1 75831874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420817 Affx-122944675 AX-123291164 1 74579244 CCTGATTTGAGGGAGGGCAGAAAGGTTTTCTCAGC[C/T]AAACCTACACCAACAACATACAGTGTCTGTGCTTC Y 2 1 2 1 101000 r 74 goat snp36295-scaffold435-1695548 1 75860412 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433358 Affx-122935134 AX-123303699 1 74609953 CTGACACAATAGTCAAGCATCTCCTCTAAATTAAC[A/G]TTGAACAAATATTTAAAGGCTATGATATTTAACCA R 2 1 2 1 101000 f 74 goat snp36294-scaffold435-1664839 1 75891278 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379194 Affx-122976301 AX-123249553 1 74683286 CAGAGAACATCAGCTCAGCTAGAATGTTCCAAATC[A/G]TCTCATTGAGCTTGGGCGGTTGGGAGGACTGGGCC R 2 1 2 1 101000 f 74 goat snp36292-scaffold435-1591506 1 75964790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412016 Affx-122951745 AX-123282366 1 74713118 CTATGTGGCCTGAAACAAGCTAACATCTGTCATTA[A/G]CCCTCTCAAAAAGACAAAAGAAATGAGCAAAATAG R 2 1 2 1 101000 f 74 goat snp36291-scaffold435-1561674 1 75995421 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430297 Affx-122937277 AX-123300638 1 74742740 TGGATCATTTACAAAAGGAACGTAACCCCAGTATT[A/G]ATTCAAAGTATGTCTGTCTTTGGGAGATTTAGAAT R 2 1 2 1 101000 r 74 goat snp36290-scaffold435-1532052 1 76026237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795633 Affx-122935565 AX-385282588 1 74791222 GAATGGGAGCAACCAAGAATAAAGGAGATTTTTGT[A/G]TTCTTTTCCTGTTATAATACAAGAAGTTATTACAC R 2 1 2 1 101000 f 74 goat snp36289-scaffold435-1483570 1 76074658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790657 Affx-122941201 AX-385277659 1 74826682 CCTGACCTGCCAGATCTACCACAGAGGGTTAATGT[A/G]AGGATAAATTGAGTAAAACTTTATGTAAGGTTTTT R 2 1 2 1 101000 f 74 goat snp36288-scaffold435-1448110 1 76110684 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452100 Affx-122920848 AX-123322433 1 74864724 TGATGGACAACAAGATAGGAATAAAATTTTATACA[A/C]TCTTTGGTTTCATATTCATACATTCTGTTTTCTTT M 2 1 2 1 101000 r 74 goat snp36287-scaffold435-1410068 1 76149014 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450034 Affx-122922835 AX-123320369 1 74894153 TTGGTTAAGGATGATTTTCATGAACCAGCCTAGAA[C/T]GGAGAGGAAATTAGGAAAACATTTAGATCCATGCC Y 2 1 2 1 101000 f 74 goat snp36286-scaffold435-1380639 1 76178528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406402 Affx-122955224 AX-123276754 1 74964501 TCTTTTGCCATCTTCTCAGATGTTGAGTTCCTGGT[A/G]TATAAAATACTTCAGGTAAAAGAAGGATAAAAACA R 2 1 2 1 201000 r 74 goat snp36285-scaffold435-1310291 1 76247873 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413818 Affx-122949892 AX-123284167 1 74997845 TTTATGTTGATTTTAAAACATTGACAGAAACCACC[A/G]TACATTTCTTCAGAAATTTAAAGTAAAACTAAAAC R 2 1 2 1 103000 f 74 goat snp36284-scaffold435-1276947 1 76281318 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382672 Affx-122973657 AX-123253030 1 75040457 AAGTTGACCAACCTTCCCATGAGGCCTAAGAGAGG[C/T]GACTACAAAACTGTCCCATAGGGCAATGTCCAGTG Y 2 1 2 1 201000 r 74 goat snp36283-scaffold435-1234335 1 76323863 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397482 Affx-122962080 AX-123267837 1 75150738 AGATCACAGATGCATGCCGGAACAGTGGTTCAGTG[C/T]GGATGTAGTGGGTTTGAGGGGAATGGGAAACTGTT Y 2 1 2 1 201000 f 74 goat snp36281-scaffold435-1124054 1 76435841 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429888 Affx-122938125 AX-123300229 1 75183623 TTCACAGTGTGCATTCTAAAGGCCCAGAGAAGTCA[C/T]GTAGAAAAAAGATAACTTTTAAACTTAGTATTTTG Y 2 1 2 1 101000 f 74 goat snp36280-scaffold435-1091169 1 76469291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437387 Affx-122932438 AX-123307725 1 75217332 CAACTTTGCGCCAGGCAACTTGCTAGGCACACCAG[C/T]ACACGCCAGTGGAAAATACAGATTACATTTTGCTG Y 2 1 2 1 101000 r 74 goat snp36279-scaffold435-1057460 1 76502985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779474 Affx-122958704 AX-385266577 1 75277533 CATGATATGTGACCCAGTTATAGACAATGAGACAC[G/T]AGATAAATATGCTATAGGGACACTGATTATAGGAA K 2 1 2 1 101000 f 74 goat snp36278-scaffold435-997259 1 76562542 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416241 Affx-122948210 AX-123286590 1 75310672 TAAGAAATGCTTAGTGTCCAGACCTATTTTGAAGA[C/T]GGAATCAATTTGAAGCATTTCCTGATGTAGGAAGT Y 2 1 2 1 101000 f 74 goat snp36277-scaffold435-964120 1 76595944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799257 Affx-122926763 AX-385286187 1 75350194 TGTATTATGATAGTTTAGTACAAACCATCTCTACT[A/G]TATCCATTTCCCCAGGCTGCCATAGCACATTACCA R 2 1 2 1 101000 r 74 goat snp36276-scaffold435-924598 1 76635763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794079 Affx-122936272 AX-385281046 1 75387094 AGAGACTCAGGATGTTTTACAAGACTACTCTTTGT[G/T]CTGTAATAATAAGTTATAAGCGAAGATGCTTGTTA K 2 1 2 1 101000 f 74 goat snp36275-scaffold435-887698 1 76672891 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386242 Affx-122970968 AX-123256600 1 75450109 ACATTGAGCAATGCAGAACTGCCCCACATAACTTC[A/G]TAATAAAAGAGTAGGTACAGGAAAACTAAACAGAG R 2 1 2 1 201000 r 74 goat snp36274-scaffold435-824683 1 76744885 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412045 Affx-122951721 AX-123282395 1 75496238 ACAAAGCAGGACAAAGAAAGAGAGTGATAGGGTCT[A/G]TTTTGCATATAGTGATCAGACAGGTCTTTCCTGAT R 2 1 2 1 201000 r 74 goat snp36273-scaffold435-778554 1 76791560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444348 Affx-122926718 AX-123314685 1 75529107 GTCCTCGTACACAATTTTATTAACATCTGTTATAG[C/T]AGCTGACATTTCTAAACGCAAGATTTGCTCCTGAA Y 2 1 2 1 101000 f 74 goat snp36272-scaffold435-745685 1 76824494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432323 Affx-122936297 AX-123302664 1 75596679 TATGTTGCTGTATGTATTTCTTTCACTGTCGTTTA[C/T]GTTTTAATCAATGGGAGTAAGTCTTCCCAGGCTCT Y 2 1 2 1 101000 r 74 goat snp36271-scaffold435-678113 1 76891711 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432577 Affx-122935523 AX-123302918 1 75633520 AGTGAAAAGTCAAAGTGAAGTCGCTCAGTCGTGTC[C/T]GACTAAAAGCCTGTGCATCATGGAACGGACGTGAA Y 2 1 2 1 202000 r 74 goat snp36270-scaffold435-641272 1 76928550 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420098 Affx-122945096 AX-123290446 1 75682393 TAAGTTGAAACCTACCAGTTCTGGTTCCCGGTTAG[A/G]CCCTGGATGAACTCTTTACTCCCTCACAACCCTCT R 2 1 2 1 101000 f 74 goat snp36269-scaffold435-592399 1 76977227 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424725 Affx-122941672 AX-123295071 1 75712798 TTTGGCTCTGAGGCATGTGATTTTAAACTATGATG[A/C]TTAATTAATTCCATGTGCCACCTAGCTCTGGAGAG M 2 1 2 1 101000 f 74 goat snp36268-scaffold435-561994 1 77007576 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412637 Affx-122950798 AX-123282986 1 75776005 GAGAAGCTCAATATAGATTCATAAAAAAGGCAGAT[A/G]TCTGGCTATCAGGTTTCTCCACGATGTCATAATTA R 2 1 2 1 101000 f 74 goat snp36267-scaffold435-498787 1 77070767 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794360 Affx-122945163 AX-385281324 1 75812333 GAAATACCCAAACACTGTTGTTTAAACTAAACTCT[A/G]TTGAGTAATGGAGATGACGATGATGAGGTTGATTG R 2 1 2 1 101000 r 74 goat snp36266-scaffold435-462459 1 77107216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775931 Affx-122971868 AX-385263062 1 75851896 CCCTGGATTAGGAGTTTAAACTGCTCTTTCCATCT[G/T]CACCTGAATCTCCTCCTGAACTCTGAAGCTCCACT K 2 1 2 1 101000 f 74 goat snp36265-scaffold435-422896 1 77146955 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380836 Affx-122975065 AX-123251194 1 75889584 AGAGGTATAATAATGAAATCAACACTGCAGTAACG[G/T]TAAGGGTGACCCTGGGAGCTCACGGGAAGAATGGA K 2 1 2 1 101000 f 74 goat snp36264-scaffold435-385208 1 77184631 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801223 Affx-122972497 AX-385288136 1 75932511 GATTCATATAAGAATTCTGCAAGGTAGGTGAGTAA[C/T]ATTCACATTTTATAGATGCAGAGGTATGTATCTTT Y 2 1 2 1 101000 r 74 goat snp36263-scaffold435-342281 1 77228344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423320 Affx-122943182 AX-123293666 1 75962021 TTTCCTGTGACAAAGGTCCATTTGAATTGAAGCAA[A/G]TAAGTTGACTATATGTTGCCAAAGTTACCTCTCCT R 2 1 2 1 101000 r 74 goat snp36262-scaffold435-312771 1 77257661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789027 Affx-122926371 AX-385276040 1 75995323 TATTAATATGAAAAATTGTACAAATGTTAGTAGAT[A/G]CTGTCATTAAATATATCCCCAAGACCCATGTCCTC R 2 1 2 1 101000 r 74 goat snp36261-scaffold435-279469 1 77290761 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403889 Affx-122957495 AX-123274241 1 76047056 CTGAGTAATGTTATGATAACTTGAATTTTGCAGGC[A/G]AACCTTTGAAAATGACCCCCCAAAAATAACAGTGA R 2 1 2 1 201000 f 74 goat snp36260-scaffold435-227736 1 77340586 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787783 Affx-122927959 AX-385274806 1 76102928 AATGTAGCTGCCTGCAATGAATTTTATACTGATTT[C/T]GAGCAAGAAATCATAATTAGTTAGCAAGAAATTTC Y 2 1 2 1 101000 f 74 goat snp36259-scaffold435-171864 1 77396503 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771450 Affx-122932085 AX-385258608 1 76136354 AAAATTCTATTGGATAATGCTATTCTAGAAAACAT[A/G]CATCTGATACATGCTGACAAAAAAGCAAAACAAGA R 2 1 2 1 101000 r 74 goat snp36258-scaffold435-138438 1 77430308 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278539 Affx-1111836477 AX-519552021 1 76176900 GTTTTGTAATGATTGTTACTGGTCTAACTTTTGGG[A/C]TAAACTCCAAAGTGTGTTTAATGGTTACAGATTAT M 2 1 2 1 101000 f 74 goat Random2.2K-84 1 76176900 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784023 Affx-122950181 AX-385271076 1 76195604 GAGAGAGTAAGGACAAGGCTACGCCTCATGATACA[C/T]AGTGTTTCATAGGCGTAACAGTCATTCATGAGCCA Y 2 1 2 1 101000 r 74 goat snp36257-scaffold435-79188 1 77489358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450670 Affx-122921914 AX-123321004 1 76227018 ACAAATGAACTTACGTACAAAAGAGGAAGAGCCTC[A/G]TAGACTTAGAGAACAAACTCATTGCCAGGGAAACA R 2 1 2 1 201000 f 74 goat snp36256-scaffold435-47774 1 77520913 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438757 Affx-122930816 AX-123309094 1 76279644 ATGCAGAGAGAATCCCACGTGATGGCAGAGGCAGA[G/T]ACTGGAGCAGTGCAGTCCCAAGCCAAGGAATACCA K 2 1 2 1 102000 f 74 goat snp40497-scaffold519-4753 1 77574156 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395218 Affx-122964488 AX-123265573 1 76316438 AAATGGGCATCAGGCCTCATTGCACAATGCTGTTT[A/G]CACTGACCCAGTAAACAGAGCAGACAGATAGGTAA R 2 1 2 1 201000 r 74 goat snp40498-scaffold519-41547 1 77611068 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772288 Affx-122969188 AX-385259443 1 76359145 GCCAGGGCTAAATACTGTAGTTCATTTCAACCATT[A/G]TGCCTGAGAGCTAGGCTAAATTGTTTGTGAAGGTT R 2 1 2 1 101000 r 74 goat snp40499-scaffold519-84254 1 77653355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278728 Affx-1111836482 AX-519552205 1 76365055 TTTCTGTGCCTTGTCCTGGCAAACACTTAATACAC[A/C]CGATGTTCAGGTGTTTAAAAAGGCTTTTTCTCACC M 2 1 2 1 101000 r 74 goat Random2.2K-85 1 76365055 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769002 Affx-122957405 AX-385256177 1 76404400 TTCTAGGCTAGATTTTACTCCAAAACTAAATAAAG[C/T]AGGTAATTAAGGCAACTGGCTTGATGATTGTAGTA Y 2 1 2 1 101000 f 74 goat snp40500-scaffold519-129509 1 77698457 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401201 Affx-122959334 AX-123271554 1 76434159 AAAAAGAATGCCTCTATTTTCCTTTGGAGAGCCAC[A/G]TTCTTCCATTTAGTGCAAATAGCTTAAGTGGAGCT R 2 1 2 1 101000 r 74 goat snp40501-scaffold519-159268 1 77728602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775788 Affx-122938129 AX-385262919 1 76481545 AGAGAAAAGACAGAATAAAACCTGAGTCACATAGG[C/T]GGCATTCCCAGTCTTAAACTCTGAAAGAAACTGAA Y 2 1 2 1 101000 r 74 goat snp40502-scaffold519-206654 1 77776240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387794 Affx-122969698 AX-123258152 1 76510500 CCCCAAAAATTTAAAGTAAAAATCAGGCAGAAATA[G/T]ATGAAGAAACCTCAAACAAAATGGTCATAAGCTTT K 2 1 2 1 103000 r 74 goat snp40503-scaffold519-235609 1 77805126 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376785 Affx-122977954 AX-123247144 1 76547263 GAACAGTTTGGAAATCTCTGAAATCCTGTCCGGGT[A/G]CTCACCGCCTTAGTTCTCACCTTCAGTAGAAACAT R 2 1 2 1 201000 r 74 goat snp40504-scaffold519-272372 1 77842002 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779387 Affx-122947100 AX-385266491 1 76602329 TGCAAAGGGAACCTGCCGCACAACATGCCATATCC[A/G]TTTTCAGAGGGTGTCAACACCCTCCTTCCCACACC R 2 1 2 1 202000 f 74 goat snp40505-scaffold519-327438 1 77897755 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444133 Affx-122926804 AX-123314470 1 76636903 TTTTTTTTTTTTATAATATTGTGATGTTTGTACTT[A/G]TGTATTTGTTCCACTTCCTCATTAGATGGTCCCCA R 2 1 2 1 101000 r 74 goat snp40506-scaffold519-362012 1 77932506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783099 Affx-122959690 AX-385270166 1 76665636 TTTCATTTAGTCATTCATTTATTGAGTCAACATAC[A/G]TTAGTTAAGCACCTCTTATGTGCTATTATGGGTGG R 2 1 2 1 201000 f 74 goat snp40507-scaffold519-390745 1 77961097 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415955 Affx-122948429 AX-123286304 1 76703029 ATGGACTGTGCTTCAGAAATGAGAATAACTCTTTT[A/G]TTTTTGTTGTTTGTGCTTTTAATTCATTTTATTGA R 2 1 2 1 103000 f 74 goat snp40508-scaffold519-428138 1 77998494 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476152 Affx-1251763655 AX-586011584 1 76724779 GAGAAGACAGAGTAATTTGTTTCAAATTAAAGAAT[-/TAAAAAAAAAAAACTAACGATGGGGAGAGGGAAAGATGGCAAAAAAAAATAATAATAAAAAAAAAATAAAAAAAAAAATA]AAAAAAAAAACTAACAAAAGAGAGATACATCATTT - 8 1 4 1 20000 f 74 goat SV_325 1 76724779 - deletion junction SV-TF-chip 539476408 Affx-1251763655 AX-586011812 1 76724779 GAGAAGACAGAGTAATTTGTTTCAAATTAAAGAAT[-/TAAAAAAAAAAAACTAACGATGGGGAGAGGGAAAGATGGCAAAAAAAAATAATAATAAAAAAAAAATAAAAAAAAAAATA]AAAAAAAAAACTAACAAAAGAGAGATACATCATTT - 8 1 4 1 20000 r 74 goat SV_325 1 76724779 - deletion junction SV-TF-chip 562165422 Affx-1251763655 AX-606940833 1 76724779 GAGAAGACAGAGTAATTTGTTTCAAATTAAAGAAT[-/TAAAAAAAAAAAACTAACGATGGGGAGAGGGAAAGATGGCAAAAAAAAATAATAATAAAAAAAAAATAAAAAAAAAAATA]AAAAAAAAAACTAACAAAAGAGAGATACATCATTT - 8 1 4 1 20100 f 74 goat SV_325 1 76724779 - deletion junction SV-TF-chip 562165522 Affx-1251763655 AX-606940933 1 76724779 GAGAAGACAGAGTAATTTGTTTCAAATTAAAGAAT[-/TAAAAAAAAAAAACTAACGATGGGGAGAGGGAAAGATGGCAAAAAAAAATAATAATAAAAAAAAAATAAAAAAAAAAATA]AAAAAAAAAACTAACAAAAGAGAGATACATCATTT - 8 1 4 1 20100 r 74 goat SV_325 1 76724779 - deletion junction SV-TF-chip 562165555 Affx-1251763655 AX-606940966 1 76724779 GAGAAGACAGAGTAATTTGTTTCAAATTAAAGAAT[-/TAAAAAAAAAAAACTAACGATGGGGAGAGGGAAAGATGGCAAAAAAAAATAATAATAAAAAAAAAATAAAAAAAAAAATA]AAAAAAAAAACTAACAAAAGAGAGATACATCATTT - 8 1 4 1 20100 r 74 goat SV_325 1 76724779 - deletion junction SV-TF-chip 38391613 Affx-122966590 AX-123261970 1 76800713 TCAAGGGGTTGGGTTCCAACTATGGAAGATCTAAG[C/T]AGAACAGGTAAGGCAGGGTGGGACCTGAACCCGCC Y 2 1 2 1 101000 f 74 goat snp40510-scaffold519-525822 1 78095314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444145 Affx-122926795 AX-123314482 1 76855354 CTCCTCCCTAGTTTAAGCAGTGGAGCCCCTTAGAT[A/G]GAAAGCAGAATGGTGACTGATGTCAATGACATGGG R 2 1 2 1 201000 f 74 goat snp40511-scaffold519-580463 1 78150398 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441390 Affx-122928848 AX-123311727 1 76917656 TTCCAGGCAACTCTAATATTCCATCCCATTATGAA[G/T]AAAGTTTCTCAACTCTCCTATACAATCTCTTTTTA K 2 1 2 1 101000 f 74 goat snp40512-scaffold519-642765 1 78212977 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423426 Affx-122942612 AX-123293772 1 76956378 GTGATGGGAAGCAATATAATAGTGCCTTCAGAACA[A/G]CTGGAGGACAGAAACTCTCTGTCCTTCAAGAGTGG R 2 1 2 1 101000 f 74 goat snp40513-scaffold519-681487 1 78251755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420450 Affx-122944891 AX-123290797 1 77013781 ATGAACAGAGCGTTGCATAGCACCTAGCACAACTA[G/T]AAACACAACTTTACTGCTATTGTTATTGCCAAAGA K 2 1 2 1 101000 f 74 goat snp40514-scaffold519-738890 1 78308976 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404477 Affx-122956726 AX-123274829 1 77070091 TTGGGTTATAGCACAAGCATGAATAAAATACTATG[A/G]AATATTCTATTCTATAAGAACTCAGGCCTCACCAA R 2 1 2 1 201000 r 74 goat snp40515-scaffold519-795200 1 78364229 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773385 Affx-122926686 AX-385260527 1 77101471 AATGAATAAGAATGATAAAAGCTTAGTGGAATTAA[C/T]GTAAATGACTGCATTTCTGATAAAACATTAACTAT Y 2 1 2 1 101000 r 74 goat snp40516-scaffold519-826580 1 78395598 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425388 Affx-122941559 AX-123295734 1 77156340 ACCGCAGCTGGAAAGGAGTCTGCCCCCAAAACAGA[C/T]ACTTAACAGTCACATACTTTGAAGATGAAAACCAG Y 2 1 2 1 201000 r 74 goat snp40517-scaffold519-881449 1 78451066 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442386 Affx-122928008 AX-123312723 1 77227346 GAACCTTCCATAACCCCATTAAAAGGTGGAGTCTA[C/T]GTCCCTTGCCCTTGAACTGGGTGAGTCTTTGTGAC Y 2 1 2 1 202000 r 74 goat snp40519-scaffold519-952455 1 78522449 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272559 Affx-1111832869 AX-519546275 1 77250630 CAGCCATTTTATAAATGGAGCCCTGATATGGTTCC[A/G]AATAGGGGTCACTAAGTGGATGTTTACAATCACTG R 2 1 2 1 201000 f 74 goat 1_77250630_AF-PAKI 1 77250630 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423080 Affx-122942936 AX-123293426 1 77257614 CCTTAAGTACTGGATACCATGGAGTCTCAAAAGTT[A/G]CAGAATTATGCTGAGCAATGCAATGAAATGAGTAA R 2 1 2 1 201000 r 74 goat snp40520-scaffold519-982723 1 78553169 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433448 Affx-122935064 AX-123303789 1 77303017 CCTGTCCTCATTGTCATCAAAATAGCAACAACACC[A/G]CCCCCCTTAAATGACACATCTTCATCTGTAAATGA R 2 1 2 1 201000 f 74 goat snp40521-scaffold519-1028126 1 78598658 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381265 Affx-122974482 AX-123251623 1 77351908 AGTAAGGAAACCGAAGAAGAACGCTGAGGGTGAGA[C/T]ATGAAGATGCAAATTCAGCCTACTGAGCTTTGGGT Y 2 1 2 1 101000 f 74 goat snp40522-scaffold519-1077017 1 78647446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273569 Affx-1111833676 AX-519547182 1 77395837 TTAATTAATTAAGTGATCACTTTAGTTGAGGCAGC[A/G]TACACTAGCTTACCAGACTGTTCTGCAGTCTTGGA R 2 1 2 1 101000 r 74 goat GoatD01.001203 1 77395837 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38421437 Affx-122943952 AX-123291784 1 77468750 AAGTCCCAAGGAGAGTAAAATGCCGGTTGAAGGAA[C/T]GCTGGTCTCCATCTCACCTCCACCAGTAAGCAAAC Y 2 1 2 1 101000 f 74 goat snp40524-scaffold519-1193859 1 78763443 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387817 Affx-122969678 AX-123258175 1 77539828 ATGAATGCCCTGTAGAACAATGGCAAAAGCACTGA[A/C]CTGGAATCAGGTGACTGGATTCGGTCCTCCGCTCT M 2 1 2 1 101000 f 74 goat snp40526-scaffold519-1264937 1 78834527 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430378 Affx-122937779 AX-123300719 1 77608390 TTGAACCCACCTCTGGTGTCTAGGTCACCTGACTG[A/G]TCCCATGATTTTTCCACCCAGGGAGGAGGCCCTGA R 2 1 2 1 201000 r 74 goat snp40528-scaffold519-1333499 1 78903068 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402799 Affx-122958287 AX-123273152 1 77714581 CTCCAGTAAAAATATTTGCACATATACCACCCTCA[A/G]TATTTGCACACACATTATAGTAGTGTGCACTGCAC R 2 1 2 1 101000 r 74 goat snp40530-scaffold519-1439690 1 79009885 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386752 Affx-122970131 AX-123257110 1 77746001 GTGCCCTATGAGGTAGATTCTATTACTATCCTCAT[C/T]TTAAGTAACAGACAGGACAGGTTTCTCTGCTAATA Y 2 1 2 1 101000 r 74 goat snp40531-scaffold519-1471110 1 79041355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414419 Affx-122949969 AX-123284768 1 77786902 ATGATAATGATTTAGGAGGACTCACATATGAAAGA[C/T]GGTCTTGTGGGGAGATACAGGAGAGAAGGGGGATG Y 2 1 2 1 101000 f 74 goat snp40532-scaffold519-1512011 1 79082101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778109 Affx-122949302 AX-385265224 1 77818649 GAAAAGAGGAATGTGATTACCCAGCTTGATTCATA[A/G]TGCTGGCATTGGGAATATATCTTCACTAAGGCCTT R 2 1 2 1 101000 r 74 goat snp40533-scaffold519-1543758 1 79113853 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420533 Affx-122945304 AX-123290880 1 77868938 CCTTGCAACACACCTGAAATGTCTTGAAGGCAGAA[C/T]GGGAGTTGAACAGTGTGGCAATCATATTATTTTTA Y 2 1 2 1 201000 r 74 goat snp40534-scaffold519-1594047 1 79164135 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425402 Affx-122941549 AX-123295748 1 77905331 ATTAATACAAAGGCTTTCTGATCACAGAAAATACT[A/G]TACTAACTCATTTAATCCTGATAGCAGCTTCTACC R 2 1 2 1 201000 f 74 goat snp40535-scaffold519-1630440 1 79200563 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443187 Affx-122927599 AX-123313524 1 77937442 TGCACACTTGTGGCTCAGAAGCAAGGCCCTTAGCC[A/G]CTATTCTATACCACCCCCAAAAGATGAAAGGGCAG R 2 1 2 1 101000 r 74 goat snp40536-scaffold519-1662551 1 79233377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428516 Affx-122938757 AX-123298858 1 77985840 CTGTCATTTGCGTTGGGCCTTTGGTACAAAGCTAT[C/T]CTACCTTCCTGTTTTAGTGACTCACCCTTTAACTC Y 2 1 2 1 101000 f 74 goat snp40537-scaffold519-1710949 1 79281700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802819 Affx-122921649 AX-385289718 1 78026255 CTTCACTGAAGGAGGAAAGGCTTCAGCATCACTAA[A/G]GAAATGGCCTTCTAGAAAGGCAGGCGCTAAAGCAG R 2 1 2 1 101000 f 74 goat snp40538-scaffold519-1751364 1 79322063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419858 Affx-122945373 AX-123290206 1 78109262 GTCAGCAGCGAGAGGAGGGAGGATGGATTAGAGAC[A/G]AGAAATAAAGAAGGGCTGCAGTTGGGAGAATGCTC R 2 1 2 1 101000 r 74 goat snp40540-scaffold519-1834371 1 79404791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452799 Affx-122920232 AX-123323132 1 78160686 TATGGCAATGAAGGAATGTTAATATTCCTAAAGAG[C/T]AGAGCTAATCTTTTCGTTATCTTGTTAACCTTGTA Y 2 1 2 1 101000 r 74 goat snp40541-scaffold519-1885795 1 79456413 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391711 Affx-122967508 AX-123262068 1 78215896 AGAGAGATGAGGGGTTGGGGTCTCACTGCACTGGA[C/T]AGATACGGTGGGCAGAATTGATTCTCTGAATTAAG Y 2 1 2 1 101000 r 74 goat snp40542-scaffold519-1941005 1 79510272 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435362 Affx-122933587 AX-123305702 1 78278435 CATTTTCTGGAGCATGAACTCCAGGTGATGTCCAG[A/G]GGGGTTGAAAGGCAACCATAGAGAAGCCAGAAGAA R 2 1 2 1 101000 r 74 goat snp40543-scaffold519-2003544 1 79573703 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440188 Affx-122930708 AX-123310525 1 78329291 GGCCAAGATAGATTGGATTAAACTAGGACTAAAGT[A/G]CAGTCCATCCTAAAGGAGATCAGTCCTGGGTGTTC R 2 1 2 1 101000 f 74 goat snp40544-scaffold519-2054400 1 79625006 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392452 Affx-122966166 AX-123262809 1 78363975 GGTCAGTGTATTGAAGGGGTAACTGACCTCCTTGG[C/T]GCTCCTGGAGAGGAAAGAGACAAACAAGCCCATGA Y 2 1 2 1 101000 f 74 goat snp40545-scaffold519-2089084 1 79660095 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397888 Affx-122961960 AX-123268243 1 78394495 GCTAACACTACATATTTCTAGATTTTTCTAAAGCT[A/G]CAGTAATTAAGACAATGTGGTACTGGCATAAAGAT R 2 1 2 1 101000 f 74 goat snp40546-scaffold519-2119604 1 79690853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378104 Affx-122977149 AX-123248463 1 78436088 TGCCTCCTTCTGAGTACATTCTTCACAAGACACTT[A/G]TCACACTGTATGATAGCTCTGTCTGTTTTCCGCCA R 2 1 2 1 101000 f 74 goat snp40547-scaffold519-2161197 1 79732428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446920 Affx-122924693 AX-123317256 1 78468000 TCCTAACTGTAGCATCTAACTCAAGAATCTCCGAG[A/G]TTTCATGGAGGAGGCAACACTTTACCTGGGTACAG R 2 1 2 1 101000 f 74 goat snp40548-scaffold519-2193109 1 79764338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777347 Affx-122963464 AX-385264469 1 78531869 AGCATGGAGAAGAGACTGAAATTGAGGGCAAATTC[A/G]TTTTTTGTCTGTGGCTCCCAAGGGTTTGGTACTGT R 2 1 2 1 101000 f 74 goat snp40549-scaffold519-2256978 1 79830482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780032 Affx-122978382 AX-385267131 1 78583997 GGCAGACAGGAAAACACATCTCAGATGACTTAGAC[A/G]AAATCTGCTTGACATGTTTCTTCTCTTCTAAAATC R 2 1 2 1 101000 r 74 goat snp40550-scaffold519-2309106 1 79882334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444645 Affx-122926921 AX-123314982 1 78612850 GAAATAAAAACCAGTTACATTTAGCTTCTAGAGAA[C/T]GAAGTCCAAAAGAAACCAAAAAAAGCAAAAGCAAA Y 2 1 2 1 201000 f 74 goat snp40551-scaffold519-2337959 1 79910816 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413588 Affx-122950575 AX-123283937 1 78661072 TTCATCAGGTATCTGGTTACTGGGTCCCCTTGTAC[A/G]TGAAGTGGGGGGCCTGGGTGTTCTCTGAGGCCTAG R 2 1 2 1 101000 f 74 goat snp40552-scaffold519-2386181 1 79959352 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383417 Affx-122973484 AX-123253775 1 78704593 TCTTTGGGGCCAGGGTCCTGCTTCATCCTCATCAG[C/T]ACTCCTACGACTCCTACAGACTACTCCAGCGTCTC Y 2 1 2 1 101000 r 74 goat snp40553-scaffold519-2429702 1 80003247 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398996 Affx-122960948 AX-123269351 1 78742319 GTTTCTGGATCACTGTGGTGGGTGGGGCAAGCCCA[C/T]AGGAGTGGTATACACACCCAGCTGGGTTGCAGGAG Y 2 1 2 1 202000 f 74 goat snp40554-scaffold519-2467428 1 80041350 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394852 Affx-122964771 AX-123265207 1 78802453 ATGTATTTTAAAACTATGTGTGCTCCCTAGTTAAA[C/T]ATAGCAATTATTACATTTTGATTTTGAAAGACCTC Y 2 1 2 1 201000 f 74 goat snp40555-scaffold519-2527562 1 80101813 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768798 Affx-122927943 AX-385255975 1 78831074 AGTAAGAACACGCGTTTTTGTTGAAATAATAAATT[A/G]CCTCTCAGACCAGTTTTGAGTCACTTTTTCTTGTT R 2 1 2 1 101000 r 74 goat snp40556-scaffold519-2556183 1 80130048 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449906 Affx-122922331 AX-123320241 1 78876147 GGGAAGCCCCAGCTAAGGGCTCCTGCCTCAGTGAA[C/T]AAGAACGCTCCAGGGCTGCACAGTGAGCCCCTAGG Y 2 1 2 1 101000 f 74 goat snp40557-scaffold519-2601256 1 80175337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435212 Affx-122933629 AX-123305552 1 78924122 TATACTGACAGTCCTTCTGAAGCCTGATCTAAAAT[A/G]TTCTTTCTTTATTTTGATTTTTGGCCATGCCATGG R 2 1 2 1 103000 f 74 goat snp40558-scaffold519-2649231 1 80223186 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424254 Affx-122942462 AX-123294600 1 78970576 TCTACCACCTGCCAAGGAAAACACTCTAATACTTC[A/G]TGTTCCCTCACAGCCACACCCGAGTATAGCAAGGG R 2 1 2 1 101000 f 74 goat snp40559-scaffold519-2695685 1 80269514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773208 Affx-122933045 AX-385260350 1 79059624 ACATGTGAGTGTCAGGAAGCATGCATCAGAAAGAC[A/G]CATAGAGATGCTTTCTGTTTAGGCTGTGTTTTGTA R 2 1 2 1 101000 r 74 goat snp40561-scaffold519-2784733 1 80358831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438604 Affx-122930936 AX-123308941 1 79125312 CAAGGCTATAACTTGGCTGGGGCCCTTTGCCTCTC[A/G]CTCTTCCTTTCTCTTTCTCGAGCTCCTACCCTCAC R 2 1 2 1 201000 f 74 goat snp40562-scaffold519-2850421 1 80424852 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785248 Affx-122933104 AX-385272293 1 79154035 AATTTACTCAAAAACACAGGAGGAGTCACTGCCTT[A/G]CTCCATCTCCAGGGAGTAATTTAAGCAGGTGTATC R 2 1 2 1 101000 r 74 goat snp40563-scaffold519-2879144 1 80453271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782024 Affx-122942267 AX-385269102 1 79189232 TGATATACCTAGAATGGTAACTTCTAAGAGGTGAC[A/G]TTTGAGACAAGACAGAAATGTTGAGGAAGTAGCTA R 2 1 2 1 101000 r 74 goat snp40564-scaffold519-2914341 1 80488803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379838 Affx-122975814 AX-123250196 1 79231615 CAATTATTGTCACTACCAGTAAAGCTTGTTGGAAG[A/C]GTTAGCTCCAGTCTCAAAGTTGGAATCAGCTTTAG M 2 1 2 1 101000 f 74 goat snp40565-scaffold519-2956724 1 80531379 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779696 Affx-122954547 AX-385266796 1 79273093 TTGATGTTTTGATTTCAGTGGTTCCACCCTCCAGT[A/G]CAAGTATATCAGGTACCCTTAGTAAACCAGAGTCT R 2 1 2 1 101000 f 74 goat snp40566-scaffold519-2998202 1 80572979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771338 Affx-122937279 AX-385258496 1 79308226 CTTTCATAACCATAAAAACAGGAGCTTTACAACAG[C/T]GAAATAGCTGAAGTATACAGGCTGAAAATTGAGAA Y 2 1 2 1 101000 f 74 goat snp40567-scaffold519-3033335 1 80605911 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416467 Affx-122947810 AX-123286815 1 79359959 CTCTGACATGGCCCAGCAAGAAAAGCACATTCTTC[A/G]TTCCCAGCACCTTGCAGGCAGATCACAGCTCAAGG R 2 1 2 1 101000 f 74 goat snp40568-scaffold519-3085068 1 80657428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423205 Affx-122942713 AX-123293551 1 79420306 CAGAGCCTGAGAATACACAGATATTTATACTATGT[A/G]CCACCATTTTCAAAGCCCCACCACAGCCTTTATTG R 2 1 2 1 201000 f 74 goat snp40569-scaffold519-3145415 1 80717398 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382677 Affx-122973654 AX-123253035 1 79480067 AGATCAGGTCTGAACTGACAAAACCAAAAAGACAG[C/T]GCAGAAGTGGAATTACAACAGAGTAAGAGATCAGC Y 2 1 2 1 101000 r 74 goat snp40570-scaffold519-3205176 1 80777306 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447129 Affx-122924462 AX-123317465 1 79545505 TTTCCTTATGTTTAAAATAGGGTTGTTTTTGTTTT[A/G]CCTTTTATCAAGCTGAAGAAAATTTCCTTCTAGCC R 2 1 2 1 101000 r 74 goat snp40571-scaffold519-3270614 1 80842684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785388 Affx-122958726 AX-385272433 1 79601377 TGAAAGTTTATTGAATGGATCACTAGTACTATGTG[A/C]TTAGTACAATAACATAAACAATTAAAGTTACATTA M 2 1 2 1 201000 r 74 goat snp40572-scaffold519-3326486 1 80898157 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794827 Affx-122934679 AX-385281787 1 79630901 ACAACAGGAAATGTTATAGCCCTCATTTGAAACAG[C/T]TGGAGAAGAACTTGTTCACCTTCATGATGATACAA Y 2 1 2 1 101000 r 74 goat snp40573-scaffold519-3356010 1 80927229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803444 Affx-122953920 AX-385290274 1 79675929 AGGTTGAGTGAAAAGTCTTATAATTTCACAAATAC[G/T]GTTTTTTTTGACCCTTGATCTGCTAGAAACCTCAT K 2 1 2 1 101000 r 74 goat snp40574-scaffold519-3401038 1 80972456 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272613 Affx-1111832871 AX-519546324 1 79766752 TATATACCCTTCAGAGGGTGACACTTGTGCCCCAC[A/C]TTGGACGTTTCTGAGCCCCAGTGTCTCTCAGGGGT M 2 1 2 1 202000 r 74 goat 1_79766752_AF-PAKI 1 79766752 C A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38388088 Affx-122969507 AX-123258446 1 79790980 TTGTAGGAAAAATTAGAAACAGAAGTCATTTTAAC[A/G]TTATTAGCAGCATCACCATGCTTGCCCGTAGACAG R 2 1 2 1 101000 r 74 goat snp40577-scaffold519-3516089 1 81089634 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448364 Affx-122924111 AX-123318700 1 79826718 TTTCTTAAGATCCTGTACTGCTATCTGTCATAACC[A/G]CTTTGTAATATATTGTCACGTTTGATTGAATGCTG R 2 1 2 1 101000 f 74 goat snp40578-scaffold519-3551827 1 81125519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401632 Affx-122959595 AX-123271985 1 79877966 AGTTTAGACTCTGACCTCCCCACTTGTCCAGTTCC[A/G]TCCTGGAGGGCTCACAACTCAAGGAAGCCAGACTC R 2 1 2 1 201000 r 74 goat snp40579-scaffold519-3603075 1 81177161 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432835 Affx-122935379 AX-123303176 1 79914627 AATTGGATTTTTAAAGTATTTACATAGAGCCAAGA[C/T]AGAGTTTGAATATCTTTGAAATCTGCATTTTTTTT Y 2 1 2 1 101000 r 74 goat snp40580-scaffold519-3639736 1 81213960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775092 Affx-122946297 AX-385262224 1 79948007 GCTTTACAGAATTAGAATGGGAAAACTTCAATGCA[C/T]GGCATGGTCTAGTTAGAATCACTTTTTAAAACGAC Y 2 1 2 1 101000 r 74 goat snp40581-scaffold519-3673116 1 81247509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784657 Affx-122920614 AX-385271705 1 79995375 CAAAAGGAGATTACCATCAGCATTATTCTGCAGGG[C/T]AGTTCAGCTGTGTCCCAACTGTACATTCCACTAAA Y 2 1 2 1 101000 f 74 goat snp40582-scaffold519-3720484 1 81295048 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804398 Affx-986696565 AX-385290988 1 80041436 TTTAATAGGATCTCAGAAAAGTACAGGTTCCGGGT[C/T]CTATAATGAAGATTGCGTGCAGCCCTAGCTTTTCC Y 2 1 2 1 600010 r 74 goat 1_80041436 1 80041436 Ancestral_priority_1043 ancestry 0.714 recommended IMAGE 10K 10K ancestral 38376315 Affx-122978358 AX-123246674 1 80044184 GGAGAAACCAGTCTCAGGTACTTTATAGGCTACAA[C/T]GAGAAAGGGGGGCAGAGCCCTCATCTGGAGAGTCT Y 2 1 2 1 102000 f 74 goat snp40583-scaffold519-3769293 1 81344743 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445408 Affx-122925381 AX-123315745 1 80111844 CCTTTCATCCTTCCTAAAGGTTTTCTTTCCCATTC[A/G]TCACCTTTCTTCCTCTTAAGCCACACATCATTCGT R 2 1 2 1 201000 r 74 goat snp13275-scaffold1510-59490 1 81410879 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384077 Affx-122972859 AX-123254435 1 80148940 AGAGGGAGAAATGTCAGCCAGGTTGGTGGGAAGTG[A/C]TGAGAGATGTAGAAGATAGGGCTGGAAAAAACAGA M 2 1 2 1 101000 r 74 goat snp13276-scaffold1510-96586 1 81448069 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782152 Affx-122968416 AX-385269230 1 80179857 GTTAACTGACTTCTGTGGGTGGGAATATTCTTCCA[C/T]GCGTGGGACTTTCCTACATAAGGCAAAATGTTTAG Y 2 1 2 1 101000 f 74 goat snp13277-scaffold1510-127503 1 81478348 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799811 Affx-122965773 AX-385286737 1 80232251 ATTATGAATAACAGTTACAATAAGTATTACAAATA[C/T]AGTTATTTAAATGTGCAGATTTAACGGACATGACA Y 2 1 2 1 101000 r 74 goat snp13278-scaffold1510-179897 1 81530768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399074 Affx-122960888 AX-123269429 1 80280032 CTGGAGATTATTATTTGGGTTGGCTGAGACAGGTC[A/G]TAATAGAGTCAGAGAAAAAAATGTATAAGGAGCTA R 2 1 2 1 101000 f 74 goat snp13279-scaffold1510-227678 1 81579399 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376319 Affx-122978355 AX-123246678 1 80323862 CTTGGACAAGGCATATACCTTCAGCCAGGATGAGT[A/G]TCCTTGGAGGAACTCAAGCCCTTGGCTTCTCCCAG R 2 1 2 1 101000 f 74 goat snp13280-scaffold1510-271508 1 81623853 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452354 Affx-122920639 AX-123322687 1 80355816 ACTAAGAAAAGGCTTCCAGTTGGCTTCCAGCTAGA[A/C]TCTGAAGGAAAGGAGGGGCATTCCTCATGTATAAA M 2 1 2 1 101000 f 74 goat snp13281-scaffold1510-303462 1 81656425 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436778 Affx-122932266 AX-123307116 1 80390812 CCCACTCCCTTCCAGTGCACGTCTTTTAAATATTC[A/G]TTTTTATTAATTTTTTCTGTTATTCTGTATTTTTG R 2 1 2 1 103000 f 74 goat snp13282-scaffold1510-338458 1 81691562 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278763 Affx-1111836500 AX-519552236 1 80401095 GCTGGACCGTTAACAGTGGTCTCCCAATGTACTCC[A/C]GAGGGTACAATGGCATACCTCCTTACACTCCTGGC M 2 1 2 1 101000 r 74 goat Random2.2K-88 1 80401095 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38423446 Affx-122942597 AX-123293792 1 80433539 GCATATATTTAAAGAGTACAACTTGATAAGTTTTT[A/G]CGTATGTGCACAGCCCCTAAACAATCAACACAGTC R 2 1 2 1 101000 r 74 goat snp13283-scaffold1510-381185 1 81734720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388699 Affx-122968990 AX-123259057 1 80498452 CACCATGATAAAGTTTAAAGGAGGGTCTAAGTGGA[A/C]CAGAGTCAGGAATGGACTAGGTAAGGTGGCGCCGG M 2 1 2 1 101000 f 74 goat snp13284-scaffold1510-446098 1 81800692 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278775 Affx-1111836506 AX-519552248 1 80521830 GTTAAGGTAAAACCCAGACTGAGCGACTGATACTT[C/G]AGGATAGATTGTGAGTTGGGAGGTTTTGTGGATGT S 4 1 2 1 101000 r 74 goat Random2.2K-89 1 80521830 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402252 Affx-122959131 AX-123272605 1 80547878 CTAAATCCTTTAACTGATTTATAATTTCTATTTTA[A/C]AGTCTTTGACTGCTAATTCAAATATCTAGGTCATC M 2 1 2 1 103000 r 74 goat snp13285-scaffold1510-495524 1 81850290 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780599 Affx-122948475 AX-385267689 1 80595266 ATCCTAAGTAAACACAGTAAACATCCTGGGGCATC[A/G]TTCCACCAGATTATTTCCCAAGGTTACTAGTCAGG R 2 1 2 1 101000 f 74 goat snp13286-scaffold1510-542912 1 81892350 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771621 Affx-122957416 AX-385258779 1 80632615 ATTATTCAAGACCCAGTTTGGGCGTATCTGGGAAC[A/G]CTTGTCTGACTTGCTAACACAGTCCGTCATTCTCT R 2 1 2 1 101000 f 74 goat snp13287-scaffold1510-580261 1 81929681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387089 Affx-122969875 AX-123257447 1 80678366 TTCCCTGTTCCTGTCCTTACAGAAAGAAAAAACTA[C/T]AAAACCTAGACATGATATGAAAAGCTACCTGAAGA Y 2 1 2 1 101000 f 74 goat snp13288-scaffold1510-626012 1 81975635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772423 Affx-122921077 AX-385259575 1 80734048 ATACCATTTGATAATGATTCTGCTTTTCATACATT[A/G]CTGATTTCTATTTACTACTATTTCACAGATTTTTG R 2 1 2 1 101000 f 74 goat snp47745-scaffold672-21949 1 82033847 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445469 Affx-122925213 AX-123315806 1 80777028 GTCCCACATTCACCACTGCATTCCTAGTGCCTAGT[A/G]CAATGCCGGACACACAATCAGTACTCATTTACTTA R 2 1 2 1 201000 r 74 goat snp47746-scaffold672-64929 1 82077018 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447125 Affx-122924464 AX-123317461 1 80807791 CTAACTAAGGGAGGATGCTTCCAGCCCTTGCCCAG[C/T]GGTATGGCCTGCATCCATTCCAATTGGTGGGCCCC Y 2 1 2 1 101000 r 74 goat snp47747-scaffold672-95692 1 82107763 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432920 Affx-122935312 AX-123303261 1 80841003 CTACTTTTGGAAAAGGGGAGGTGGGGGCAGGGATA[C/T]GGCAGCACTCAGGATCTGGAATCTGTAGAGGGAAT Y 2 1 2 1 201000 r 74 goat snp47748-scaffold672-128904 1 82141063 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384126 Affx-122972819 AX-123254484 1 80927720 GACAGAAAGCAGGGAGTAGGGATGGGGATTAACTG[A/G]GATGGTACTGGGGCAAGGCTTCCTTATTGAAGGGT R 2 1 2 1 101000 f 74 goat snp47749-scaffold672-215621 1 82227732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437793 Affx-122931688 AX-123308131 1 80959691 CATCTCCAGGCTGGAGCAAGGCTGGAAGGTCTGGT[A/G]TCTTCTAGACCCTTCTAGCTTAGCTCCCCACAGTG R 2 1 2 1 101000 r 74 goat snp47750-scaffold672-247592 1 82259715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781827 Affx-122937318 AX-385268909 1 80992799 GGCATTTTCCTATCTGTTCTTATATTTTATTCAAA[C/T]GCCATACTAATAAAAATAGTAGCTGACATTTTTGA Y 2 1 2 1 101000 f 74 goat snp47751-scaffold672-280700 1 82292922 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783472 Affx-122920967 AX-385270535 1 81054482 AACAATATAAGTGATAGCCACTAAGAGCATTTCAC[A/G]TTAATGCTTCTATTCAAATGTACTCATAGAGTTTG R 2 1 2 1 101000 f 74 goat snp47752-scaffold672-342383 1 82354644 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441983 Affx-122928440 AX-123312320 1 81089544 ATTGTTTATTTTAACACCAATTTAAATTCTGATGA[C/T]AGCTGGAACCACTCTTTCATTCTTCTGCATTTATT Y 2 1 2 1 201000 f 74 goat snp47753-scaffold672-377445 1 82389814 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386495 Affx-122971138 AX-123256853 1 81124467 CAGACCACAATCACAGGTGCCCTCGAAGAGCAGAG[C/T]GGAGGATGCCACACAGATTGTGCCAGTGGTGTTCT Y 2 1 2 1 201000 f 74 goat snp47754-scaffold672-412368 1 82425110 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418234 Affx-122947040 AX-123288582 1 81181298 TGTCCCCACAGTAGGATCGGGGGCTCAACTAGGCA[C/T]GAGAGACTCCAGAAGATGAGGGAAAAGGCCTGGCC Y 2 1 2 1 201000 r 74 goat snp47755-scaffold672-469199 1 82481926 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408273 Affx-122953802 AX-123278624 1 81289909 ATGCTCTTGTGGCTGAGAAAGGGTAGATGATGTAC[A/G]ACTGAGAAACTGCTGGATTTCTTTCTTTTGGCATT R 2 1 2 1 101000 f 74 goat snp47757-scaffold672-577810 1 82590887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409195 Affx-122953179 AX-123279546 1 81330330 GTGGAAGCCACACCAGGAAACAAGACGGTGGCAGA[C/T]GCTTTTCCTTATGAAAGATACCAAACATACATTGA Y 2 1 2 1 201000 r 74 goat snp47758-scaffold672-618231 1 82631410 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273593 Affx-1111833689 AX-519547207 1 81368940 CCCCTCAGGGCCATGCCACGACTTTCTAGGGACCC[A/G]GCACTCAGAGGTGCCCTCTAACCTTACCTTCTTCT R 2 1 2 1 201000 r 74 goat GoatD01.001650 1 81368940 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320782339 Affx-122919800 AX-385269416 1 81376183 AAATATTTTTAAACATAGTTTAGAAAGAAATATAA[A/G]TAGAAAATCAGACCTGTGGTTCCATATTATTGATT R 2 1 2 1 202000 f 74 goat snp47759-scaffold672-664084 1 82677468 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430717 Affx-122936900 AX-123301058 1 81407438 CTACTTTTGCGTTCCAGTTCCCTATAATGAATGGG[A/G]CATCTTTTTTGAATGGGAAAGGCTAAATAAATAGG R 2 1 2 1 201000 r 74 goat snp47760-scaffold672-695339 1 82709138 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775750 Affx-122927190 AX-385262881 1 81449061 GCTATAACGCTGGACTGACAAGGTAAAGAGTTCTT[A/G]TTTTCTATTGGCAACCTATAGAAAAATATAGCAGT R 2 1 2 1 102000 f 74 goat snp47761-scaffold672-736962 1 82750046 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375765 Affx-122978596 AX-123246124 1 81534263 AGTTTTATATAGTGTAAGCATTCATTTTGTCTTTT[A/G]CCCTCCCCCTTCTCCTCCCCTCTGGGAGTTCCTAA R 2 1 2 1 101000 f 74 goat snp47762-scaffold672-822164 1 82835853 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411045 Affx-122951959 AX-123281395 1 81575663 CCACCATCATCCCTCGCTGTCCTCTCTCCTAGGGA[C/T]ACTCAAGAGTTGCAGTTCTCTCCATGGTTTTCAGG Y 2 1 2 1 101000 r 74 goat snp47763-scaffold672-863564 1 82878435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408975 Affx-122953911 AX-123279326 1 81626228 CAAACATAAAATAAAACATAAAAGCAGCAGCAAAC[A/G]CAGACACTGCCCCTTCCTTTTCTTTCTAAAGGCAG R 2 1 2 1 101000 r 74 goat snp47764-scaffold672-914129 1 82928530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396212 Affx-122963356 AX-123266567 1 81660214 GAATTAACTATTGTGTCATAAACCTACTAGTCAAT[A/G]CACTTTTTAACTATTTTAACTACTTTGTCAAAAAG R 2 1 2 1 101000 f 74 goat snp47765-scaffold672-948115 1 82963227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769153 Affx-122971631 AX-385256328 1 81714668 GCTTCTCTTGGGAGTAAAAATCAATGTTTTTACAA[C/T]GATTCACAAAGGCCCTATGTGATTTGGCCCCAACA Y 2 1 2 1 101000 r 74 goat snp47766-scaffold672-1002569 1 83017553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476153 Affx-1251763656 AX-586011585 1 81754622 GATGATCCAGTGGATGCTGGCAGGTTGATCTCTGG[-/TTCCTCTGCCTTTTCTTTTTTTTTTTTTTTTTTGAATTTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCCTCTGCCTTTTCAAAATCCAGCTTGAACATCTG - 4 1 4 1 20000 f 74 goat SV_333 1 81754622 - deletion junction SV-TF-chip 539476409 Affx-1251763656 AX-586011813 1 81754622 GATGATCCAGTGGATGCTGGCAGGTTGATCTCTGG[-/TTCCTCTGCCTTTTCTTTTTTTTTTTTTTTTTTGAATTTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCCTCTGCCTTTTCAAAATCCAGCTTGAACATCTG - 8 1 4 1 20000 r 74 goat SV_333 1 81754622 - deletion junction SV-TF-chip 562165442 Affx-1251763656 AX-606940853 1 81754622 GATGATCCAGTGGATGCTGGCAGGTTGATCTCTGG[-/TTCCTCTGCCTTTTCTTTTTTTTTTTTTTTTTTGAATTTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCCTCTGCCTTTTCAAAATCCAGCTTGAACATCTG - 8 1 4 1 20100 f 74 goat SV_333 1 81754622 - deletion junction SV-TF-chip 562166075 Affx-1251763656 AX-606941484 1 81754622 GATGATCCAGTGGATGCTGGCAGGTTGATCTCTGG[-/TTCCTCTGCCTTTTCTTTTTTTTTTTTTTTTTTGAATTTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCCTCTGCCTTTTCAAAATCCAGCTTGAACATCTG - 8 1 4 1 20100 r 74 goat SV_333 1 81754622 - deletion junction SV-TF-chip 562166407 Affx-1251763656 AX-606941815 1 81754622 GATGATCCAGTGGATGCTGGCAGGTTGATCTCTGG[-/TTCCTCTGCCTTTTCTTTTTTTTTTTTTTTTTTGAATTTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCCTCTGCCTTTTCAAAATCCAGCTTGAACATCTG - 8 1 4 1 20100 r 74 goat SV_333 1 81754622 - deletion junction SV-TF-chip 38409237 Affx-122953148 AX-123279588 1 81832461 TAACCAGGAAGAGGTCCTCACCCAAAGCACCATTC[C/T]AATGAGGTCAAACCCTACCGGGCTAGGGAGAAAAT Y 2 1 2 1 101000 f 74 goat snp47768-scaffold672-1120362 1 83136052 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795783 Affx-122946411 AX-385282736 1 81861044 AAGGAAAGCCAGAAAATGCTGTAACATATAAATTC[A/G]TTATTTAAAAATAACTAGAAAACCATATTTAACAT R 2 1 2 1 303000 r 74 goat snp47769-scaffold672-1148945 1 83164730 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406690 Affx-122955779 AX-123277042 1 81952013 AGACTGGAGAGGAGGACAGAGATATGATAGTAGAG[C/T]AGGCTTTGTTTGTTGTGTTTATCTATATAACTGTG Y 2 1 2 1 101000 f 74 goat snp47770-scaffold672-1239914 1 83256784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423372 Affx-122943140 AX-123293718 1 81984059 GAAAAAGAACAATACTCAGTAAAATTTTCAAAGTG[A/G]GTAAACACCACTGGAATTTCTTATGTAAAGTCCTA R 2 1 2 1 101000 r 74 goat snp47771-scaffold672-1271960 1 83289135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423964 Affx-122942136 AX-123294310 1 82034205 TGGTTAAAGCAGTGAGTATGTGGTACTTGAGCTGC[G/T]ATCTGCTCCCTCTCAGCTCAGTGTAAAGGAAGCTC K 2 1 2 1 101000 f 74 goat snp47772-scaffold672-1322106 1 83339114 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772491 Affx-122922099 AX-385259642 1 82084311 CCTTAATCTAACCTGATGTTTACTGCTGTAAAACA[A/G]TAACTAGTTCATTTCTTGAGGTTCCCTTGGAAATA R 2 1 2 1 202000 r 74 goat snp47773-scaffold672-1372212 1 83389374 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423832 Affx-122942789 AX-123294178 1 82187091 ATCGATACAGCAATGGAGAGTAAATTAGATGAAGA[C/T]AGGCAGGCTGACCACCTGCCAGCAGTTGTCACAGT Y 2 1 2 1 101000 f 74 goat snp47775-scaffold672-1474992 1 83493210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796674 Affx-122974831 AX-385283620 1 82229911 TTTTTAAAATTCACTTTAAACTCTTGGACTGTGTC[A/G]TATCAGCATGATTCAGTCAGCTTCATTCTTTTTAA R 2 1 2 1 201000 f 74 goat snp47776-scaffold672-1517812 1 83536073 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446558 Affx-122924843 AX-123316894 1 82289847 TACCCGGAACTCTCCTGATCATCGTCCTTCCTCTT[C/T]GCATTCCTCCTTGTCCGGAGGAGGATACACTCATA Y 2 1 2 1 101000 f 74 goat snp47777-scaffold672-1577748 1 83597154 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780506 Affx-122947373 AX-385267597 1 82353267 TTGTGGTAACTTGCTTCTTCTGCAGTTTTATGGCC[A/G]CATTTTCTACTATAGTTCACTTTATTCTGTAGAGC R 2 1 2 1 101000 f 74 goat snp47779-scaffold672-1641168 1 83658324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453579 Affx-122919761 AX-123323912 1 82387617 GGGGCCTCCCCAGAGGGAGATGCCATCACCTGTGC[C/T]GCAGTCTGCCAGTGGGGCACCAGAAAGCTTATCTG Y 2 1 2 1 303000 f 74 goat snp47780-scaffold672-1675518 1 83692690 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409459 Affx-122954076 AX-123279810 1 82433467 GTTTTTTCATTCTGAGCTCTAATTGAAACCACAGC[A/G]TGGGAACTGGTTGGCTCTTCTCTTATATACATTAT R 2 1 2 1 101000 f 74 goat snp47781-scaffold672-1721368 1 83738821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420988 Affx-122944567 AX-123291335 1 82465962 CTCTGCAGCAGCACAAAGGAAGGCTAACCCTTTCA[A/G]GATTTTTCTCATTTATCCTTTCTCATTTTTTTCAA R 2 1 2 1 101000 f 74 goat snp47782-scaffold672-1753863 1 83771283 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271741 Affx-1111832872 AX-519545535 1 82502089 CCTCCTAGGAACCCAGGTAAGTCCCCAGTCAAGGG[A/G]GTTAGAGAATATTTCTTTTCTGACTCAGTCCCCTT R 2 1 2 1 101000 r 74 goat 1_82502089_AF-PAKI 1 82502089 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38407444 Affx-122954793 AX-123277795 1 82510938 AGCCTCATTACACAGATAAAAAGGTGTAGGAGAGC[A/G]GAAATACAGCCATTTTTATGTTTATAAATATCCCA R 2 1 2 1 101000 f 74 goat snp47783-scaffold672-1798839 1 83816268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783241 Affx-122948745 AX-385270306 1 82550727 TAAATGAAATCAAGAATGTTCAGGAAAATTTACAA[A/G]CTAGATTCACTGTATATATAAGTAGCAAGGCAAGG R 2 1 2 1 101000 r 74 goat snp47784-scaffold672-1838628 1 83856230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440009 Affx-122929782 AX-123310346 1 82585211 TCTTTAGGTTTCCTCAGAAACAAAGGCGACAGTAC[A/G]CCTCGGTAAGCATGGGATATGAAATGTGAAAAAGA R 2 1 2 1 101000 f 74 goat snp47785-scaffold672-1873112 1 83890709 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398080 Affx-122961728 AX-123268435 1 82615869 GGAGGAATAGACAAGATACGCTGTTTTGCAGTGCT[A/G]AATTGAACAGGTTAGAGGGGAAACACTTTCTGTGG R 2 1 2 1 101000 f 74 goat snp47786-scaffold672-1903770 1 83921759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792282 Affx-122956729 AX-385279264 1 82655484 AACCAAAATCTAAGGAAAAGTCTGAGTTTCATGGT[A/C]TATTCTTTAGGGCCACTTTTGAATGCATTAACTAT M 2 1 2 1 101000 f 74 goat snp47787-scaffold672-1943385 1 83961402 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424044 Affx-122942074 AX-123294390 1 82717260 CACAACAACACAATACATAGTAGCTATTCATGAAC[A/G]TTTCTTCAAAAAAAAATTGAAATTCTTAAACTTCA R 2 1 2 1 103000 f 74 goat snp47788-scaffold672-2005161 1 84023147 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419843 Affx-122945810 AX-123290191 1 82747321 CACAGTTTTAACTCTACATTTATATATGTGAGTCT[A/G]TGATTAGTGCCTTCTCTCCCAGACTATATGTTTCC R 2 1 2 1 101000 r 74 goat snp47789-scaffold672-2035222 1 84053515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775872 Affx-122973088 AX-385263003 1 82788521 GTGCTCTTAAAGGTCCGTTTCCCTATCTTCAATGA[C/T]AGTTAATGAGGGCACAGACCACTAATAAGCAGTTT Y 2 1 2 1 101000 f 74 goat snp47790-scaffold672-2076422 1 84094923 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445237 Affx-122925493 AX-123315574 1 82850318 AAAGTGTTGAGTACAGTTCCTGGCATATGTAATCC[A/G]CTGTTAATTCTAATACTCAGCACCATGCCTAGTTC R 2 1 2 1 101000 r 74 goat snp32733-scaffold377-2162683 1 84159545 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394922 Affx-122964311 AX-123265277 1 82894811 AAGGAGACAGAGCCAGAAGTTGCTCTACCAACTGC[A/G]CTCGGATCACCAAGTGCTGTTTCTGCAGAACTTAG R 2 1 2 1 101000 f 74 goat snp32732-scaffold377-2118190 1 84204295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419598 Affx-122945997 AX-123289946 1 82933056 ATCCATAATGGGTTACGGGCCATCTGAGCCCTCAG[C/T]GACACAATGGGCTGGTATTTCCTGAAGTGGAGAAC Y 2 1 2 1 201000 r 74 goat snp32731-scaffold377-2079945 1 84243041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777744 Affx-122929536 AX-385264862 1 82963120 GTTTCCATAAACCAGAGGAGAGAAAAGTGCTTGGA[A/G]CCATCATTATAAACATGACACATCTGTTTTTAATA R 2 1 2 1 101000 f 74 goat snp32730-scaffold377-2049881 1 84272976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378989 Affx-122976392 AX-123249348 1 83010594 TTCAAAATGCTGAATTTCTTTAGAATGACACATTT[A/G]TTGAGAAGAAAAGTGCTAAGAAGAACGAAAAAAAA R 2 1 2 1 101000 r 74 goat snp32729-scaffold377-2002407 1 84320980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275432 Affx-1111834798 AX-519549005 1 83012073 GATTCATTTATATATTGTCC[A/G]TGTGTGCACTGCAGCCTCAGAGTTTGGTCATTCCA R 2 1 2 1 102000 r 74 goat GoatD01.053406 1 83012073 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38444753 Affx-122926370 AX-123315090 1 83047000 TGAGTTTAGCATTATGCTGGAAATGATTTTGATGC[A/G]TATAACACAGCTATAAAAAGAACAATAGGAAGAGA R 2 1 2 1 101000 f 74 goat snp32728-scaffold377-1966001 1 84357740 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770574 Affx-122941269 AX-385257738 1 83078742 ATCTGGTTTCATCATTCTGAAAATTCCTCATTGAA[A/G]CCATCCCTGTGGAATAGGAATCTATTCCAAGAATG R 2 1 2 1 101000 r 74 goat snp32727-scaffold377-1934259 1 84389437 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450122 Affx-122922766 AX-123320457 1 83139374 GGGGGATGAAGAGGATACTATGTCACCCAGAGGAT[A/G]CGTCCACCCACCTTGTTGTCTATAATGTAAAGCCT R 2 1 2 1 101000 f 74 goat snp32726-scaffold377-1873627 1 84444836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429523 Affx-122937844 AX-123299865 1 83168412 GGGGAACTTAGGGAGCAAGACTATATCAAGTCAGA[C/T]GCTTTTTTGCTGAAGCACAAGTGGTAAGAATGGGA Y 2 1 2 1 101000 f 74 goat snp32725-scaffold377-1844589 1 84474198 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428911 Affx-122938917 AX-123299253 1 83229154 GCCTTATCTTGCCCATAATTATACAGAAGTCAGAT[A/G]CAGGTTTATGCTAAAAGCATGTACTGTTATCTTTC R 2 1 2 1 101000 f 74 goat snp32724-scaffold377-1783847 1 84535011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775004 Affx-122966516 AX-385262136 1 83267332 AAAAGCACTGTTGCCTTACATCTACAGACCATTCC[A/G]TGTCTTATAAAGGAAAAAGGCAATCCAGTACAGAT R 2 1 2 1 101000 f 74 goat snp32723-scaffold377-1745669 1 84573896 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442454 Affx-122927953 AX-123312791 1 83306160 GGAGAACTCACTAGGTACCAAGCACCATTAGAGAA[C/T]ATATGTTATTTTGATTTTTACAACAATTCTGTATG Y 2 1 2 1 101000 f 74 goat snp32722-scaffold377-1706841 1 84612681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778315 Affx-122938412 AX-385265430 1 83373524 TTTGTATCTGAAGAAGGCTTGTGGCCTACATGCCC[A/G]CTTAAGATATAGTGAAAATAACTTGGAGGATAGTT R 2 1 2 1 101000 f 74 goat snp32721-scaffold377-1639477 1 84680880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453718 Affx-122919631 AX-123324051 1 83406572 CAACCTCAGTATTTCCATTTATAAACAGAGAATAA[C/T]AATACCTTCCTTATAGATTTACTCTAAGGATTAAA Y 2 1 2 1 102000 f 74 goat snp32720-scaffold377-1606429 1 84714032 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452992 Affx-122920117 AX-123323325 1 83436546 CCAAAGTTGGACAGACTTTCCAAGTCATAGTACAC[G/T]CAGTATGATCCCTATCATAACCTTCACAGAAATAT K 2 1 2 1 101000 f 74 goat snp32719-scaffold377-1576455 1 84744046 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788205 Affx-122926048 AX-385275224 1 83466558 AGCTAGTAACTGGACTAAAGTTCTCCTGCTCTTGC[A/G]AAATGGCGTTTAGGCTGCTATGTTATTGTGATCCA R 2 1 2 1 101000 f 74 goat snp32718-scaffold377-1546443 1 84774026 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407921 Affx-122954378 AX-123278272 1 83498599 GAATTGTGCTTCTTCCATTTCATCCTTGTGGTTAA[G/T]GAATCCTACAGTGGACACCTGGTCTTGCACCTGGG K 2 1 2 1 201000 f 74 goat snp32717-scaffold377-1514402 1 84806521 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437167 Affx-122932131 AX-123307505 1 83540100 CCCCAGTATAGGGAATTATTAAATAAATTATAATA[C/T]GTCCATATGATGGGATAGTACATAGCTATTAAAAA Y 2 1 2 1 103000 r 74 goat snp32716-scaffold377-1472901 1 84848216 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451836 Affx-122921464 AX-123322169 1 83575251 ATGCAGAGAAGTTGAGCTCCTTGTCTTCAGTGAGC[A/G]GCAAAGTGAGGACTGTAAGCTTGTCAGATCCCAGG R 2 1 2 1 101000 r 74 goat snp32715-scaffold377-1437750 1 84883332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408181 Affx-122954199 AX-123278532 1 83642225 TCTTAGAATTTCACACATTGCTTTGCCACATGGCT[A/C]GTGGAATCTTACTTCCTGGATCAGGGATTGAACTC M 2 1 2 1 101000 f 74 goat snp32714-scaffold377-1370776 1 84951808 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792147 Affx-122940854 AX-385279132 1 83723561 TTTGATTCATGTGCTAAATCAAACGTATTTAAGAA[G/T]ATGATTTCCTACTCCTGTTCCTTTTCAATATTTTC K 2 1 2 1 201000 f 74 goat snp32713-scaffold377-1289440 1 85033007 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383315 Affx-122972697 AX-123253673 1 83762267 AGAGACAAAGACAGAAAGTGAACACAAGCTGAGCA[C/T]GAAGGGCCCACTTCATCCTGAGGAGGAGGAGAGCC Y 2 1 2 1 101000 f 74 goat snp32712-scaffold377-1250734 1 85071523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392441 Affx-122966176 AX-123262798 1 83790824 TAGGTGGGCGGAGATTTCTAATAAGTACCTTTACC[A/G]TGTGATACACTAGATACACTAAAGCCAATCCTGAG R 2 1 2 1 101000 r 74 goat snp32711-scaffold377-1222177 1 85100080 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785066 Affx-122938576 AX-385272113 1 83833574 ATGATGGTCAAAATAATCTTTCAAAAGTCAGGGGA[C/T]AACCTTATCTCAAGAGAAAAATACTGTCCAGTGAC Y 2 1 2 1 101000 f 74 goat snp32710-scaffold377-1179427 1 85143025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402687 Affx-122958353 AX-123273040 1 83897021 TCAGTGAGTGCTCTTGTGTACCCACTGGGGCTCAC[A/G]CCCAGTGAATTTCAGACATCCTTCCCCCTGATGTG R 2 1 2 1 101000 r 74 goat snp32709-scaffold377-1115980 1 85206665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424495 Affx-122941749 AX-123294841 1 84000468 AGTTTCCCTTGCATATCTGTCCTTAGTCCGAGCCT[A/G]GTCCCTATACTAATACTGAAGAAATGTAATGAGAG R 2 1 2 1 201000 r 74 goat snp32707-scaffold377-1012533 1 85310982 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773836 Affx-122967371 AX-385260976 1 84044508 GAACTAGTTTAGGGCCAGAAATTGTTCATTCTTGA[C/T]GGCTTCATTCTTATCTGCTTTTCCCCTATTTATTT Y 2 1 2 1 101000 f 74 goat snp32706-scaffold377-968493 1 85355276 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428231 Affx-122939432 AX-123298574 1 84073683 CCAGAAGAGTGTGGAAGTGAGGTGAACATGCTCAG[C/T]AGAGGAACTAGAAGGAACATGGGTGAAGAAGGCAA Y 2 1 2 1 101000 r 74 goat snp32705-scaffold377-939318 1 85384075 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791438 Affx-122969251 AX-385278429 1 84116774 ATTATAGGTCAGGCTTGAACAAATAAAACATGATT[A/G]CTGGCTTCATGATACTTCCTAACTAGTGTATGGGA R 2 1 2 1 101000 r 74 goat snp32704-scaffold377-896227 1 85427816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441555 Affx-122928694 AX-123311892 1 84176499 TCTGTTCTAAAAATCTAGATTTTTTTTGTTTACAA[C/T]GGAACCAAACCAAAGTCAATACAGTGCAAAAATAA Y 2 1 2 1 103000 r 74 goat snp32703-scaffold377-836502 1 85488116 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428675 Affx-122938642 AX-123299017 1 84278687 TTGGACATTGTAGCTTAAGTCAAATCTGCTTGAGA[G/T]CCAAATGAGAATAGGAATTTGACTAAAAAGAAGAG K 2 1 2 1 101000 f 74 goat snp32701-scaffold377-734314 1 85591981 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796317 Affx-122959375 AX-385283267 1 84309368 AATGGTAATCTCAGTCGCTATGGTGTTTGAACCTG[C/T]AGGCTCTGAAAGGATTTACTCTTTTTTCACAAAGA Y 2 1 2 1 101000 f 74 goat snp32700-scaffold377-703633 1 85620551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402604 Affx-122958418 AX-123272957 1 84365886 GAGCGCTCTCTGTTGCAGGAGAGCAAATGGAACAA[C/T]GGAGGCCAGGTTTTCCAGGCATCATCAGTCTGTTC Y 2 1 2 1 101000 f 74 goat snp32699-scaffold377-647115 1 85677444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770612 Affx-122978188 AX-385257776 1 84410677 GAAAGAAGACCATTCTCAAGTGGATTTAAATTAAG[C/T]TCCACTTCTTGAAGGAGGGAATGTCCACATATATT Y 2 1 2 1 101000 r 74 goat snp32698-scaffold377-602324 1 85722569 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401072 Affx-122959639 AX-123271425 1 84448640 GTAGTGAGTTCAAACCACTGAGACACTGCTTAGGA[C/T]AAGGCTGAGGGAGATTGCTTAAGTAAATACTCTTT Y 2 1 2 1 101000 f 74 goat snp32697-scaffold377-564361 1 85761063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787058 Affx-122954851 AX-180660639 1 84482457 CTTAAATTGAATTCACTGAAGCTTTGTGGTAAATA[C/T]GCTTTTTTTCCGCTCATAGCTTTTCTCTAACCATG Y 2 1 2 1 101000 r 74 goat snp32696-scaffold377-530544 1 85794880 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434136 Affx-122934916 AX-123304477 1 84639344 CACAGAGCTGCTGTGAAGCTACAAAAGTAAAAGCC[A/G]CCATTCATCAAACTCTGAATCTGGGCCAGATTTCG R 2 1 2 1 101000 f 74 goat snp32693-scaffold377-373657 1 85954509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398508 Affx-122961554 AX-123268863 1 84676181 ACACAGTTCATGATAGCCTCATCTTTTGGAGTCTA[C/T]TTAATTCTCCAGCCTTATGTCTTCTAGCCTCCTTG Y 2 1 2 1 101000 r 74 goat snp32692-scaffold377-336820 1 85991395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429097 Affx-122938265 AX-123299439 1 84726553 GGAGACATAAACCATTTTCTTGATAAAATGATTAC[G/T]CACAGAAATTTAAAATACAGAAACAACATTTTCAT K 2 1 2 1 101000 f 74 goat snp32691-scaffold377-286448 1 86043145 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788921 Affx-122936218 AX-385275936 1 84770244 TGTAGACATTATGGAAATCAATTGCTTTTTATAGC[A/G]GTTCTCAAAGTATATTTGTTTCAGTTATAGGTCCT R 2 1 2 1 101000 r 74 goat snp32690-scaffold377-242757 1 86086606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389884 Affx-122968134 AX-123260241 1 84799541 AACATTGTTAATTTTCTTAGGAAACCCTTTTTACA[C/T]AGATGGACAAAAAAATTTTAAGCAAATTATCAGAG Y 2 1 2 1 201000 f 74 goat snp32689-scaffold377-213460 1 86116181 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440389 Affx-122929628 AX-123310726 1 84837074 AAAAGCGGGGAGACAGACAGAGAAGCGGGTGATGC[A/G]AGAGGAAGGAGTTGGAACTGAATAATCTGAAAGAT R 2 1 2 1 101000 r 74 goat snp32688-scaffold377-175927 1 86153178 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379525 Affx-122976072 AX-123249883 1 84870962 TTTTAAATTTAATTTTAAGGAACTGGCTTGCATGA[C/T]CATCAAGAACAGTCAGTCAGAAATCTGTAAAGCAG Y 2 1 2 1 101000 r 74 goat snp32687-scaffold377-142039 1 86187098 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400138 Affx-122960706 AX-123270493 1 84906630 CAATAGCAAGAATTTTAAGGAGGCTGCTGAGATAA[C/T]GCAGGCAAGCAATGAGAACCAGAATCAAGGTGCTA Y 2 1 2 1 201000 f 74 goat snp32686-scaffold377-106371 1 86223391 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775156 Affx-122968974 AX-385262288 1 84988811 CCTCATTCTAATACATTATCCATACTCCTCCAAGG[A/C]TGATTTTTCTAAAACCCTAATCTGATTCTATATAA M 2 1 2 1 101000 f 74 goat snp32685-scaffold377-24190 1 86308506 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430620 Affx-122936969 AX-123300961 1 85073309 ATGCTATTGACAACTTTTCCCTCTTATTATTTATT[A/G]TTGTTTTGTACCTGGCTTTTATTCCTCCTTCAATG R 2 1 2 1 101000 r 74 goat snp48461-scaffold689-60209 1 86399897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444239 Affx-122927226 AX-123314576 1 85112692 AGAATGATGATGCCAAACTGAAAAGCACATACCCC[A/G]TCTAAAGGGGTGGACATTACTCAGGTCCAACCAAG R 2 1 2 1 102000 f 74 goat snp48462-scaffold689-99592 1 86439698 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774714 Affx-122979203 AX-385261848 1 85168222 GACAATAAAGATACAATGTCAGAGATAAGCACAAT[A/G]TCCAGTGATATGGATAGTTCAGTAAATTATGTATT R 2 1 2 1 201000 r 74 goat snp48463-scaffold689-155122 1 86495591 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770924 Affx-122921706 AX-385258087 1 85201142 GAGATTCTGCACTTTGAGAGTTTAAAATTGTCAGA[C/T]GAAATCATCAATTGAATACAAAACTACAATGTAAC Y 2 1 2 1 101000 f 74 goat snp48464-scaffold689-188042 1 86529269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767250 Affx-122927168 AX-385254531 1 85257032 CAAGCATGAATTTGTTGTGTAACACTTCAGTTCAT[A/G]CATCTGTTAATTTACTACATATAATGTGCAAATAT R 2 1 2 1 101000 f 74 goat snp48465-scaffold689-243932 1 86584934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449173 Affx-122923534 AX-123319508 1 85287025 GGAGATCTGAGAGAACAAAAGATACTCTTTAACCA[C/T]GGCCCAGGCAAGGAGGCATTCACATCTGCCACCCA Y 2 1 2 1 101000 f 74 goat snp48466-scaffold689-273925 1 86615554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405371 Affx-122956310 AX-123275723 1 85396740 TTTGCATTTCCACATAACAGAACTCTTGCCTTCTG[C/T]ACACTGACTATTTCCTCATCCTTTATATTCCACCC Y 2 1 2 1 101000 r 74 goat snp48468-scaffold689-383640 1 86726067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792939 Affx-122965267 AX-385279917 1 85453955 GGAAAAAGAAGATTCAGACATATTATCTCTCTCCC[A/G]TAACACAACAGTAAAACTGTTGGCATGATCTGTGT R 2 1 2 1 101000 r 74 goat snp48469-scaffold689-440855 1 86783809 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790003 Affx-122927194 AX-385277009 1 85507180 GTGCCTGGCAATGTTTGCTTACTGGCTGACTTATT[A/G]CTCTCTACTCCATAATCTTGCACACAACAAATCAC R 2 1 2 1 101000 r 74 goat snp48470-scaffold689-494080 1 86836696 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423689 Affx-122942899 AX-123294035 1 85536648 TGATATCCTACTAGATGGGTTCATTACACTAAGTA[C/T]GGAGAATTAAAAGGGCAAGTTCTACCAAGAAATAT Y 2 1 2 1 101000 f 74 goat snp48471-scaffold689-523548 1 86866171 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447955 Affx-122923774 AX-123318291 1 85568683 AAGGCTGTAAATTACTTCAAGTAGTTATCCACAAA[C/T]ATTAGTGGCTGTCTATACATGTTGGCTGCTGAACT Y 2 1 2 1 101000 r 74 goat snp48472-scaffold689-555583 1 86897921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434329 Affx-122934738 AX-123304670 1 85635619 CCTAACCTTAACCTGGATAACTGGTGGCCATTCCG[C/T]GGACTTCTAGCATATCAGATATACATTACCAAGAT Y 2 1 2 1 101000 r 74 goat snp48473-scaffold689-622519 1 86964109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416962 Affx-122948015 AX-123287310 1 85672458 GGCTCCCCATTTTACTCTAGAGCCACACCCTTCCA[A/G]TGCCTCTTCGGCTAAGGCAATCTGGCTCCTACTCT R 2 1 2 1 101000 f 74 goat snp48474-scaffold689-659358 1 87001193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771050 Affx-122961530 AX-385258210 1 85703281 ATGGCATCTGTCTTACTGCGGCTCTTTCCAAAGCC[A/G]CACTAACTGCAATGCTACCTTCTCCACCAACTGTA R 2 1 2 1 101000 r 74 goat snp48475-scaffold689-690181 1 87032144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790210 Affx-122931915 AX-385277214 1 85750268 GAGTTTCTCACTGAACAGGTATATCCTTGTTGGGG[A/C]GAAGGAAACCAGGATGATTGGATCATACCACCATT M 2 1 2 1 101000 f 74 goat snp48476-scaffold689-737168 1 87078969 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422858 Affx-122943091 AX-123293204 1 85779983 CCTTCCTTCCAAAGACCATCACCTCTGTGCCTGCA[G/T]CAGTCACCACTAGAAATCTACAAGGCTTAAGAAAC K 2 1 2 1 201000 r 74 goat snp48477-scaffold689-766883 1 87106738 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432613 Affx-122935496 AX-123302954 1 85808941 GAAATGAGTTGTCACGCTGTCCCACTTCACACCCA[C/T]GAAGGAGAAGAACAGTAAAAGTGGTCACACCACAC Y 2 1 2 1 201000 r 74 goat snp48478-scaffold689-795841 1 87135732 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781578 Affx-122978651 AX-385268662 1 85846879 TAAACTCTATGTGGGGTTTTAGGGACAACTGTTTA[C/T]GAATGCAAGCATTAACAAATACAGAAACTGTAACA Y 2 1 2 1 101000 f 74 goat snp48479-scaffold689-833779 1 87173544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770974 Affx-122971499 AX-385258137 1 85899646 GCTTTAAGATATACTCCTCTACATGAACAAAGGGA[C/T]GTTTATTCTGAAAATCTAAATCATACATGAATATG Y 2 1 2 1 101000 f 74 goat snp48480-scaffold689-886546 1 87225330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804371 Affx-986696538 AX-385290973 1 85904559 TCATTTCTTAAGGATAATATTTTAGCATCTATTAA[C/T]TTCAGCATCTATTAATATTTTAGCATCTTTCTAGG Y 2 1 2 1 600010 r 74 goat 1_85904559 1 85904559 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 320792455 Affx-122952932 AX-385279436 1 85981002 TGTACGGCACAGTACTGAGTGATGGCATCACTGCT[A/G]TTTGCCAATCCTGTTAAGATCCAGCACTCCCATTT R 2 1 2 1 101000 f 74 goat snp48482-scaffold689-967902 1 87307131 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453187 Affx-122920458 AX-123323520 1 86020950 GATGTTGCTGCCACCACCAGAATAGATTCTCCAGC[A/G]TCTCTTTATCTCACTTGTTCCAGATCCTGAGCAGG R 2 1 2 1 101000 f 74 goat snp48483-scaffold689-1007850 1 87347598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799899 Affx-122936221 AX-385286825 1 86050656 GTAGATGAGTTTGATGGTTTCACAGAGTTATGACC[A/G]AAACATTCCAGTGTTAGTGGTTAAAGGAATAGAGT R 2 1 2 1 101000 f 74 goat snp48484-scaffold689-1037556 1 87376742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444476 Affx-122926532 AX-123314813 1 86148154 TATAATAGCTAGTTATGGCAAACCTGGTTAGAAGC[A/C]GATTTCTTCATTCCAAATCTGATTCTGAATCCTGG M 2 1 2 1 101000 f 74 goat snp48486-scaffold689-1135054 1 87473937 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421948 Affx-122943820 AX-123292295 1 86204394 TGATGTTTACACCTTTTATAAATGATGTCTCTTGA[A/C]TAGGGTTAGCAAGTACTGTGTATACAAATATAAAT M 2 1 2 1 101000 r 74 goat snp48487-scaffold689-1191294 1 87530249 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802527 Affx-122970344 AX-385289431 1 86257263 TACACTCCAAAACTAGCATAACTGTCCATCTGTCT[A/G]TTTCTGCTCTTCTCCATATCTGCTGTGTGGTGACA R 2 1 2 1 101000 f 74 goat snp48488-scaffold689-1244163 1 87582608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435825 Affx-122932830 AX-123306164 1 86288098 GTTAATATTTATTCATTTTCTCTTTATTTCCCCCA[C/T]GATGCTATGACTGTTACCATGTGTTATCACTTCTT Y 2 1 2 1 101000 r 74 goat snp48489-scaffold689-1274998 1 87613463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799377 Affx-122921480 AX-385286307 1 86317307 AGAAAAAGCTAAAGGTCAATAGAATCATTGTGGAC[A/C]CCATGCCTTGTCTACTGTTTGTCATTTTGAGTATG M 2 1 2 1 101000 r 74 goat snp48490-scaffold689-1304207 1 87642468 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416003 Affx-122948390 AX-123286352 1 86349215 CTTTTACTTTATTTTATTAACTTTTAAATGTGAAT[A/G]CTTTTATTGTATAAAACGCTTAAAAATTTCTGCAT R 2 1 2 1 101000 r 74 goat snp48491-scaffold689-1336115 1 87670327 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431691 Affx-122936779 AX-123302032 1 86395836 GTTTAATGTGTCAAGAATATAATAGCATAGTTTCT[A/C]TAGTTTGGGTCTCAGGCCACCTGCATCAGGAAGGG M 2 1 2 1 201000 f 74 goat snp48492-scaffold689-1382736 1 87716802 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794864 Affx-122960122 AX-385281824 1 86425495 CCCAAGTTAGAAAGTTGGGAAGAGTCATGACTACT[C/T]TCTTCAATGTCTTCATCCAGTCAGTCACCAAGTAT Y 2 1 2 1 201000 r 74 goat snp48493-scaffold689-1412395 1 87747146 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463660402 Affx-1110097185 AX-515141214 1 86442752 CTCTCCCTCACTGCAGTCTACTCAGTCCTGGTGCC[A/G]CAGCATGGGCACCCATGTCCCAGATGCTAGCATTG R 2 1 2 1 202000 f 74 goat GoatD01.051133 1 86442752 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38435628 Affx-122933774 AX-123305968 1 86486082 GATGGCAGCAGGACAGTCTGTTTGTTTGCTCACCA[C/T]GGGAAGGAGCTAAGTGTCAGGGCTTGCAGCTGCCT Y 2 1 2 1 101000 f 74 goat snp48494-scaffold689-1472982 1 87807773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802520 Affx-122946465 AX-385289424 1 86516757 GCTAGTAATCTCTAGTTACTGGGCATGTGGCCCCT[A/G]CTCAATTCCTATTGGTCTTCCTAGACCGACATGAA R 2 1 2 1 101000 f 74 goat snp48495-scaffold689-1503657 1 87838642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777244 Affx-122932992 AX-385264367 1 86545447 TTTAAGCTGCAGGTAAAAGGCAAATGGATCTAATT[A/G]TAAGAGAAAGTTTTACAATTCAAAATGCACTAAGC R 2 1 2 1 101000 f 74 goat snp48496-scaffold689-1532347 1 87867105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782897 Affx-122942784 AX-385269967 1 86597150 TTCAAGGCATTCACAGTCTGTTACAAGAGGACAAG[C/T]AAGCAGGTACTATCAATACTGCATGATAGGTGCAT Y 2 1 2 1 101000 f 74 goat snp48497-scaffold689-1584050 1 87918800 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417844 Affx-122946785 AX-123288192 1 86627540 AAAAGTGGCGGTACTTGCCAGATTATGGGGACATT[A/G]TTGATAAACTTCACACTGAGGAAATGAAAGACTAG R 2 1 2 1 201000 r 74 goat snp48498-scaffold689-1614440 1 87949422 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379828 Affx-122975821 AX-123250186 1 86661189 GTCACTGACTGGCATTACTACTTGTGCATTGCAGG[C/T]GTGAACTCAGTCAGCCAAGATCCACATGTTGGTTG Y 2 1 2 1 201000 r 74 goat snp48499-scaffold689-1648089 1 87983013 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414858 Affx-122949151 AX-123285207 1 86717835 TTCTCCACTTCTGATAGGAACCTTCTCTATTGATG[C/T]GTAACTTTTAGGCAAAGGCCAAATTTACCGGAGCT Y 2 1 2 1 201000 f 74 goat snp48500-scaffold689-1704735 1 88039569 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407222 Affx-122955381 AX-123277573 1 86754857 ACATGTCCTTGGCATGCTTTTTAAGTCATACATCA[A/G]CCATTCCTCTATATAGCCTCTGAAGTTGAACTTAA R 2 1 2 1 101000 f 74 goat snp48501-scaffold689-1741757 1 88076628 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388008 Affx-122969570 AX-123258366 1 86784620 GGCTTCACTATTAAAAACATAGTTCCTTCCATGCC[A/G]CACTCTGTTTCTGAGGTGCATGACTGAGTTATCCA R 2 1 2 1 101000 f 74 goat snp48502-scaffold689-1771520 1 88106525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380492 Affx-122975709 AX-123250850 1 86815677 GTGCACACAGAGCAGACACTTATTTCAGATCCATT[C/T]TGAGTACAAATAGACTGTTGCCCTCCTAATTGAGT Y 2 1 2 1 101000 r 74 goat snp48503-scaffold689-1802577 1 88137621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420178 Affx-122945568 AX-123290526 1 86852312 GTGGCATATTAGTACCATGGGATACAATACAGCAA[C/T]GTAAATGAATAAACTGCAGTTCTGCCACAACATGT Y 2 1 2 1 101000 f 74 goat snp48504-scaffold689-1839212 1 88173828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781771 Affx-122941743 AX-385268853 1 86943152 GGTTAAAGTGTTAAGGAAAGTACCAAAACATGGGC[A/G]TCCTAATATCCCTGCTCTCATGAGTTTATTTAGCA R 2 1 2 1 101000 f 74 goat snp48506-scaffold689-1930052 1 88263467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765261 Affx-122974742 AX-385252796 1 86994434 AATATTGAACTAATAGTGTAATTTTGAAAATTAGA[C/T]GAGTGAAATCACTTGAGAATGAATGATAAGCCCTA Y 2 1 2 1 201000 f 74 goat snp48507-scaffold689-1981334 1 88314924 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412564 Affx-122951320 AX-123282913 1 87035856 TAAGATAGATAGCTGTGTCAAGGAGACATTAAGAG[G/T]GTTGCAGGGTAGAGATATAGAGTAGCAGAAGCGCT K 2 1 2 1 101000 r 74 goat snp48508-scaffold689-2022756 1 88356720 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452286 Affx-122920693 AX-123322619 1 87102509 ATTGTTGGCTCCGTACTTATAGAAATTTTTCCAGA[C/T]GGTGTGGAAGGGCTTTAACATATCCATAGTTTAGA Y 2 1 2 1 101000 f 74 goat snp48510-scaffold689-2089409 1 88424002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400255 Affx-122960138 AX-123270610 1 87146410 CTGGCTGGAGTGAATTATGAAGGCACAAAATTAGG[A/C]GGCAAGAGAGGTAGACAGGCTCCAAGGCTGTGAGA M 2 1 2 1 101000 f 74 goat snp48511-scaffold689-2133310 1 88467909 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427189 Affx-122939603 AX-123297532 1 87178401 AAAACAATTTCTAGAGCATAAACTTCCATAGTCAC[A/G]GTTTCTTAAAATCAGTTTGCTTGACAGCTTACATC R 2 1 2 1 101000 r 74 goat snp48512-scaffold689-2165301 1 88499826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452223 Affx-122920799 AX-123322556 1 87232472 ATGCCAGTACCAGCTCAAATATTGAAAGGGGTTTT[A/G]CATGATTTGACCTTGATGGTGTAGCTGAGACTTGT R 2 1 2 1 101000 r 74 goat snp48513-scaffold689-2219372 1 88555090 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320786239 Affx-122947334 AX-385273274 1 87285145 ATTATTTAACTACTTTTCAGAGTTTGACTCAATGT[A/G]CATATATGAGAATGCTTTACCAGGGAATCCTCAAA R 2 1 2 1 202000 r 74 goat snp48514-scaffold689-2272045 1 88607732 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451769 Affx-122921513 AX-123322102 1 87325829 TTAGAAGGGAAACTATTTGAATAAATACCAAACAG[C/T]AAATAGTTTTAAATAAAAATAAGCAATGCTAATTC Y 2 1 2 1 103000 f 74 goat snp48515-scaffold689-2312729 1 88648508 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419381 Affx-122945619 AX-123289729 1 87384307 ACACAGTGGATGCTCAGTACTTCTTTCAACTGAGT[C/T]AACAGTCCTGAGACTTGACAAGGGAGATCCAATGA Y 2 1 2 1 101000 r 74 goat snp48516-scaffold689-2371207 1 88714498 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769192 Affx-122933217 AX-385256367 1 87420712 CTTTGTGAGTTGGTAGTGGTGATGTTGAAACCTCA[C/T]GAGGTTTGACCACCAGGTTTATTTGGAATTTTTCC Y 2 1 2 1 101000 r 74 goat snp48517-scaffold689-2407612 1 88751395 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399132 Affx-122960664 AX-123269487 1 87459390 TTACTCTTTCTAAATTTAGCTATTGGCAAACAGTT[A/G]CTCTTACATCTAATTAAATTTGGTAAGACTTTCCA R 2 1 2 1 101000 f 74 goat snp48518-scaffold689-2446290 1 88790472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798629 Affx-122933339 AX-385285561 1 87552429 AAAATGCTGTATAGCACAGTAGCATTTTATACATA[C/T]AAAAGAGGTAAACTTTTATTCTTGTAATATTCCAG Y 2 1 2 1 202000 r 74 goat snp48520-scaffold689-2539329 1 88884470 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773590 Affx-122958086 AX-385260730 1 87590720 TTTTGTAAGAACAATTTAACCTCGAGCTCTATACC[A/G]TATAAGACTTTCTTGTTCTTCAATCAAAGGTGGCA R 2 1 2 1 101000 r 74 goat snp48521-scaffold689-2577620 1 88922721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444363 Affx-122926707 AX-123314700 1 87632932 AACTTCATGGACTGTTTGCTAGTTTGCTTAGCTAT[C/T]GGTTACTCTCTCCAAATGTACTGGCAGACAAAAAC Y 2 1 2 1 101000 f 74 goat snp48522-scaffold689-2619832 1 88965345 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400957 Affx-122960116 AX-123271310 1 87677945 ATACAGTGTGGAAGTGTGGATGAGCAGGCTTAGGC[A/G]GGCTGACGAATGATTCCAAGGGCTTTAGAGACTCT R 2 1 2 1 101000 r 74 goat snp48523-scaffold689-2664845 1 89010341 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770478 Affx-122956146 AX-385257644 1 87758748 GCACAGAGATGATCCTTATCAGTGGAGGACTGTGA[G/T]ATGAGATGACAACACCCTATGGGTTCAGACAAACT K 2 1 2 1 101000 r 74 goat snp48525-scaffold689-2745648 1 89092240 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434574 Affx-122934118 AX-123304915 1 87802980 AGTTGTCCAGAGCTCTGAAATTGTCCTCAGTATTG[C/T]TCATGCACAGACAATGGATGTACTATCCTCTCCTT Y 2 1 2 1 101000 r 74 goat snp48526-scaffold689-2789880 1 89136936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453339 Affx-122919961 AX-123323672 1 87837359 TGTGGGGCAGCCCCCATAGGTGCTTCAGGTTCCAG[C/T]ATTGTGATGGATGAACACTCTTTGCAGAACTCAGG Y 2 1 2 1 101000 r 74 goat snp48527-scaffold689-2824259 1 89171089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399663 Affx-122960511 AX-123270018 1 87911540 ACAACTCATGAGGAACCAAATCCTGCCACCTGACA[C/T]GGATGAGCTTGAAAGATTGTCCCTCAGTCTAGACG Y 2 1 2 1 101000 r 74 goat snp48529-scaffold689-2898440 1 89245781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427756 Affx-122939246 AX-123298099 1 87940819 GTCATTGACCATAACCCTGCCATCTAATGAATTAA[A/G]GAATTTCTATTTGCTTGTGCCCATGCATTATTTTT R 2 1 2 1 101000 f 74 goat snp48530-scaffold689-2927719 1 89275015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383273 Affx-122972729 AX-123253631 1 87973848 AGATATTAAGCTAGTGCTGAGAAATGTATCTTTTC[C/T]AAGGTGTTAGCTCAAGGTAGCCAAAGACTATACAA Y 2 1 2 1 101000 r 74 goat snp48531-scaffold689-2960748 1 89307578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423684 Affx-122942322 AX-123294030 1 88013865 TTGCCATGTTCAGTTCTTTCACAGCATGTAGAAAG[A/C]AGAGGGGAGTCCCCTGGTGCCTCCTTTCTGACATC M 2 1 2 1 303000 r 74 goat snp48532-scaffold689-3000765 1 89348366 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404274 Affx-122957046 AX-123274626 1 88064968 GGGATTTGGGTACAGATTATACTAGGGTTCATTAC[A/G]TTATTCCCTACATTTTGAAGTCTGTTTGAACATTT R 2 1 2 1 101000 f 74 goat snp48533-scaffold689-3051868 1 89399920 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423124 Affx-122942906 AX-123293470 1 88098853 TTTCTTCTGCCTTCCCAGATATCCCCCAGGCTACC[G/T]AATATCCTTTATTAACCTATTTCAGTGAAGACTAG K 2 1 2 1 201000 r 74 goat snp48534-scaffold689-3085753 1 89433588 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384271 Affx-122972308 AX-123254629 1 88128695 TCCTGAACCCCAGAATCTGAGTCAGAGGGAGAGTT[A/C]TAGAAGGGGAACAGAGTAGAGAAAGTTGATACTTC M 2 1 2 1 201000 f 74 goat snp48535-scaffold689-3115595 1 89463514 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432932 Affx-122935302 AX-123303273 1 88162582 TTGGGTCTTAATTCTGACCTCTTCTTCTGACCTAC[A/G]GCTATCCACATTCTAACATGAGGTTACCCTAAACT R 2 1 2 1 201000 r 74 goat snp48536-scaffold689-3149482 1 89497379 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786033 Affx-122976141 AX-385273069 1 88254361 TCTCAAAGCAAATATGCTGCAAAAATACAAACAGA[C/T]GAAAAGCAAACGTGCTGCTGTTTTGTATGTAGCTT Y 2 1 2 1 201000 f 74 goat snp48538-scaffold689-3241261 1 89589169 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442813 Affx-122927712 AX-123313150 1 88288787 AAGGAATAGATAGGATATTGAGCCTTCAATTTTGA[C/T]TTGAAACTCCAGTTATTCTTCTTCCAGGGCTTTGT Y 2 1 2 1 101000 f 74 goat snp48539-scaffold689-3275687 1 89623652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436872 Affx-122933238 AX-123307210 1 88331549 ATAAAATTTGCCACCCACCCATTTTCTGACACTAA[C/T]GGTTATTTCAAAAGGAGTCACTTAGTAATTTGTGG Y 2 1 2 1 101000 r 74 goat snp48540-scaffold689-3318449 1 89666343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385754 Affx-122971073 AX-123256112 1 88378087 CCATCATGTCCTCTGCCCTTCTTCTCTCATCACAT[A/G]CTTCCAGCTCTGTCTTAATTTTTGGCCTTCCCTCA R 2 1 2 1 101000 r 74 goat snp48541-scaffold689-3364987 1 89714012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381282 Affx-122974468 AX-123251640 1 88428426 CGTGGGCTCCCAGAGGCCTCTGGACTGGCCTGGTC[A/G]CCTACAGATGGGCACCTGGGATATGGTGTTTGCCA R 2 1 2 1 103000 r 74 goat snp48542-scaffold689-3415326 1 89763695 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773268 Affx-122931267 AX-385260411 1 88472429 GACATAGATGGCTTTGCTAATCAGTGGGAGAAAGA[C/T]AGAATATTCAAAACCTGTGTAGGATAATTATCCAT Y 2 1 2 1 101000 f 74 goat snp48543-scaffold689-3459329 1 89808282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442252 Affx-122928285 AX-123312589 1 88516578 TTTTATGTTGCTAACAAAGAGAAGCCCAGTGGCAG[C/T]GCACACTGTGGCATTTGCTTTGGGTTTTAAAGACA Y 2 1 2 1 201000 r 74 goat snp48544-scaffold689-3503478 1 89852361 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411795 Affx-122951263 AX-123282145 1 88549465 AGCTCCTATGGAACTGAAAAGCAAAAATATACTTG[C/T]AAAATAAATACAAATTCCAAAACTGATAAAGTTCA Y 2 1 2 1 101000 f 74 goat snp48545-scaffold689-3536365 1 89884997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780419 Affx-122963118 AX-385267511 1 88559852 TAGTAGGTATCTGGAATATATGAATCTCTAATAAA[A/G]AGACCCAAACCTTTCAGGAAGTTCTCTCATGTTTG R 2 1 2 1 102000 r 74 goat snp26306-scaffold276-1558 1 89895197 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437895 Affx-122931665 AX-123308233 1 88630384 TATTGTGTGCATGTGTATGTGTTTGCTTTAAAGCA[A/G]GGAGACTACTGGGGTTCTGTTCTGTATACGAGTGA R 2 1 2 1 101000 r 74 goat snp26308-scaffold276-72090 1 89966221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768481 Affx-122964321 AX-385255661 1 88678918 TTATTGTTTTTAATAAGCTCTACAGATATCTGTGT[A/G]TACCTTTCTGTGAAAGATATATTTTGCATTAGTGC R 2 1 2 1 201000 f 74 goat snp26309-scaffold276-120624 1 90008487 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795879 Affx-122968537 AX-385282831 1 88709256 AGAAGATTGATCTGATGTTGATGTGCGGAGGAGCT[A/G]TATATTTACATCACCTTCCATTAGTGGGAAATGAT R 2 1 2 1 101000 f 74 goat snp26310-scaffold276-150962 1 90038519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271742 Affx-1111832873 AX-519545536 1 88732772 AACACTAATCAGAAGAGACTCCCTGTGGCCTCTGC[A/G]TTTGCTCAGTACACCCCCGGCCATCCTGGGGGTTG R 2 1 2 1 202000 r 74 goat 1_88732772_AF-PAKI 1 88732772 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320767491 Affx-122979068 AX-385254755 1 88766967 TGTCTCTGCTCTTAACATAACTCACTGATGAAAGC[C/T]GACTATTGTCGGCATTTTTATGGGCTATGTATAAA Y 2 1 2 1 101000 f 74 goat snp26311-scaffold276-208673 1 90096310 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274036 Affx-1111833967 AX-519547639 1 88767344 TGCAGATGCTCAAAGTCTTTCTTTCATATAATGCG[A/G]GTTTGAAAGCTTTTCCATAAGTCATGTCAAATGGT R 2 1 2 1 101000 r 74 goat GoatD01.011992 1 88767344 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320786254 Affx-122939688 AX-385273289 1 88799789 GTCCTTCCTCTGTGGAAAGACCTTAGTGTTTTATC[A/G]TCCTTCCATTCAGGAAACTTTACCTCTATAAAGCA R 2 1 2 1 101000 f 74 goat snp26312-scaffold276-241495 1 90128829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771252 Affx-122960456 AX-385258410 1 88862532 ACATTAACAACAGTGGGTGTGTAGACACTGCATAT[A/G]ATAATAATGCTATTAAATTCACTTTTTTTATCTGA R 2 1 2 1 202000 r 74 goat snp26313-scaffold276-304238 1 90191647 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448470 Affx-122923628 AX-123318806 1 88912946 GGATGCAATAGCTCACAGGAAGCTACAGAGGAGAA[C/T]GCCAGGGGCATACATTGCTAAAGAGGAATTGAATG Y 2 1 2 1 201000 f 74 goat snp26314-scaffold276-354652 1 90243406 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438691 Affx-122930867 AX-123309028 1 88963238 CATTTATTTAAAATAGTTTTAAATATCAGTTTCTA[C/T]GCTGATGACTTCTAAATATATAATCTAAAGAATGC Y 2 1 2 1 101000 r 74 goat snp26315-scaffold276-404944 1 90294667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781412 Affx-122953947 AX-385268497 1 88997027 ACTTTCAATTCATTTAAACAAATTCTATGAAAATA[C/T]GATATTCTGCCATTCAAGGACAGATTATTGTGTGA Y 2 1 2 1 201000 f 74 goat snp26316-scaffold276-438733 1 90330182 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382948 Affx-122973374 AX-123253306 1 89029471 ACATTAAAAATGCCAGGGTGGTGACTTTAGACTTT[A/G]TTCTCTGGGAAAATGAGAATCACCAAATTCTAATG R 2 1 2 1 101000 f 74 goat snp26317-scaffold276-471177 1 90364079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430643 Affx-122936952 AX-123300984 1 89084143 ACTTATTTAAAATGACAGTGTTACAATCCTGCTAC[G/T]AGGTTGTAAAAAATTATTGCTTGTATGTATTTTGT K 2 1 2 1 101000 f 74 goat snp26318-scaffold276-525849 1 90418475 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408059 Affx-122954271 AX-123278410 1 89186913 TCCTAAGTAATAAGAATCTCAAGGAATTCGAAGTT[A/G]TAACATATGAGAGCTTCTCACATGGGAGATTTAAA R 2 1 2 1 201000 f 74 goat snp26320-scaffold276-628619 1 90522295 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394031 Affx-122965000 AX-123264386 1 89236473 GAGAGAATTATCCAGATTTCATCCCTTTGCAGATC[A/G]TCCTTCAGATCATCTGATTATGGTTTTCCTCTGCC R 2 1 2 1 101000 f 74 goat snp26321-scaffold276-678179 1 90571978 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779645 Affx-122979072 AX-385266747 1 89276824 GCTCGACAAACTGTGAATGGCTTCTTATATCATTC[A/G]CATTGAAAATCTAAGCCCACAGTGATGTGTAAAGC R 2 1 2 1 101000 r 74 goat snp26322-scaffold276-718530 1 90613037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776331 Affx-122924290 AX-385263459 1 89399881 ATATCTGTTTTAACATAAGTAATTGCAAAACTATC[G/T]CTGAAAAAATGAGTCCATCTAGAGTTAAATAAAAG K 2 1 2 1 101000 r 74 goat snp26324-scaffold276-841587 NW_017199709.1 12632 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773740 Affx-122955047 AX-385260880 1 89450821 CCCCAGTTCCAATAAACTTAATCTATCACAACTGA[C/T]AGTATATGATTTCTGAGACCAAGTTCTAAAAAGCA Y 2 1 2 1 201000 r 74 goat snp26325-scaffold276-892527 1 90790907 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383652 Affx-122972524 AX-123254010 1 89479582 ACTCTGTATCTGGGCTTCTTTCTATTCCATACAGA[C/T]GTAATCTGATCACTTTCCCTGGCTAGAACAGTAGT Y 2 1 2 1 101000 r 74 goat snp26326-scaffold276-921288 1 90820159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386329 Affx-122970881 AX-123256687 1 89511858 TGTAATACCATAAACAGGTTAAAGTAAAAATCTTA[C/T]GAGATTATGGGAAGGAAGAGACCAGTTCTAGGGGG Y 2 1 2 1 201000 f 74 goat snp26327-scaffold276-953564 1 90852445 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448983 Affx-122923114 AX-123319318 1 89548153 AAAACTGCCTTTCAGCAAGGAGTTTCAGAAAAGAT[A/G]CATGAATGAGGAGCAAAGTGAGATGCTTTCATTTT R 2 1 2 1 101000 r 74 goat snp26328-scaffold276-989859 1 90888912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785189 Affx-122962015 AX-385272234 1 89578619 TATACTGAGCAATATCCTAAGAATTTTGCATACTA[C/T]GGCACATGTAATCCTTAAAACAACTTAATGCAACC Y 2 1 2 1 201000 r 74 goat snp26329-scaffold276-1020325 1 90919369 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380079 Affx-122975550 AX-123250437 1 89609794 AACAAATGTACTACATTGCTATAAGATGTTAATAA[C/T]AGGGAACTTTGTGTTGGGAGCTGAGGGAACTGTGC Y 2 1 2 1 201000 f 74 goat snp26330-scaffold276-1051500 1 90950522 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418775 Affx-122946190 AX-123289123 1 89641809 ATAAAGTGCACATTTATTTGCAAATTGGGAAATTC[A/G]TCTTACATTACTCAGAAAGGGGGGAAAAAAGACAT R 2 1 2 1 201000 f 74 goat snp26331-scaffold276-1083515 1 90982717 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790359 Affx-122922629 AX-385277362 1 89699062 AATTCCTGTTTCTATATCCTTAAAAATCTGATAGA[C/T]GAAATGGGAGATTGAAGAGGACTAAATTTATTTAT Y 2 1 2 1 201000 f 74 goat snp26332-scaffold276-1140768 1 91039777 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426885 Affx-122940469 AX-123297230 1 89740466 AGAATATATTTAATACTAAAAGGCTATATAATAAT[A/G]CTATAATGCCACAAACATTGTAAAACTTCTACCAC R 2 1 2 1 101000 r 74 goat snp26333-scaffold276-1182172 1 91080697 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275543 Affx-1111834868 AX-519549115 1 89779351 CAATGATGAGTCTCAGACTGCAGTGTGTTTCTGAG[A/G]AAGTTTTGACCAGGCTGATGGGAAGCCCTTGGGCA R 2 1 2 1 101000 r 74 goat GoatD01.057124 1 89779351 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38432597 Affx-122935507 AX-123302938 1 89787698 TGCAGCGTAGTTTCACAGTAGGAAGGAAAAATTAT[A/G]TATTATTATATATTGTTATATTTTATACTCACTTT R 2 1 2 1 103000 f 74 goat snp26334-scaffold276-1229404 1 91127894 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418788 Affx-122946182 AX-123289136 1 89829495 GTAACAAAGGTGTTCCTCCAAGGTAGTAAACAACA[G/T]CTGCACTCAAGGCCTTCACATTGTTGAACAAAATG K 2 1 2 1 101000 f 74 goat snp26335-scaffold276-1271201 1 91169789 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453949 Affx-122919476 AX-123324282 1 89887496 AGTTTGCATTTTTGTTTCAAATACATAGAGTTAAA[C/T]AGTGATGCATTTCCTTGTTCCGACATAGAACAACT Y 2 1 2 1 101000 r 74 goat snp26336-scaffold276-1329202 1 91228808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444261 Affx-122927211 AX-123314598 1 89927427 AGTTGTCCAAGAGATTCTATCTCATAGGTCTCCGC[A/G]TATACTTTAAAGAGAGCATTGCATTTTTAACCTTG R 2 1 2 1 201000 r 74 goat snp26337-scaffold276-1369133 1 91269366 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795506 Affx-122953868 AX-385282460 1 89997600 AGGCTTTGTCAAAATAACTTCTTAGAAGTTTCAAC[A/G]CTATTTACTTGAGAGTCACAGAACACTAATATATG R 2 1 2 1 201000 r 74 goat snp26339-scaffold276-1439306 1 91339816 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791169 Affx-122924554 AX-385278164 1 90038692 TTTGCATTCTAGCAAGAAAGTAAGGAATTACTAGA[C/T]GAAAATATAGGTTGTGATGGGAACCCAGATAAGTA Y 2 1 2 1 201000 f 74 goat snp26340-scaffold276-1480398 1 91381905 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410442 Affx-122952392 AX-123280792 1 90090652 CATGTATCTCTTTCTATTCATCAGGTAATCTCTAG[A/C]TGATTTTACCTCCATTTATCTTTGCCTTTAAAGTA M 2 1 2 1 101000 f 74 goat snp26341-scaffold276-1532358 1 91434455 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789573 Affx-122926965 AX-385276582 1 90136982 TTATGGTAGCTGGATTAACCCAATTATTTTTAGGA[A/G]GTTAAGGGAAACTGCATTTGGAGAACATCATCCTT R 2 1 2 1 101000 r 74 goat snp26342-scaffold276-1578688 1 91481575 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767402 Affx-122975249 AX-385254675 1 90169147 TTCAGTTTCTTGCTTGGATTCAAACAAGAGGGGCA[C/T]ACTTTCTGCTTCTAACAAGTTGCTGAAATTTGAGC Y 2 1 2 1 101000 f 74 goat snp26343-scaffold276-1610853 1 91513077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385930 Affx-122971562 AX-123256288 1 90206227 TTGCTAAAATGTTGAAATACTTTCACAATGGCAAA[C/T]AGCCACTGCCTTGATCCTCCTGAGAGCTCCCACTG Y 2 1 2 1 101000 f 74 goat snp26344-scaffold276-1647933 1 91550566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444011 Affx-122926897 AX-123314348 1 90258423 GGATACCATCTAAAGTTACTTTAACGTTTCTAACA[C/T]GTAAGAGAAAAAAACAAATACAACTTTCTAGTTTC Y 2 1 2 1 103000 f 74 goat snp26345-scaffold276-1700129 1 91603605 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434768 Affx-122933894 AX-123305109 1 90290978 ATAAAATGCCAAGTCATTTTTCCCCAACCATTCTT[A/G]TTGCTACAGTGAACCTCTTCTTATTGTGTGTATTC R 2 1 2 1 101000 r 74 goat snp26346-scaffold276-1732684 1 91636763 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421685 Affx-122944416 AX-123292032 1 90332048 AGCACTCCAAAAATCCAGCATTAAACCTTTGGAAA[C/T]GCAAGTCAACTTGTAATATAATATCTGGCAATAAC Y 2 1 2 1 101000 f 74 goat snp26347-scaffold276-1773754 1 91677713 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400266 Affx-122960130 AX-123270621 1 90409499 CTGTAGAAATTAATAAGAAACTGAACTGCAAATAA[C/T]GCACTGGAGGCTTATAGCTAGGGGTCTACTGCAAA Y 2 1 2 1 201000 f 74 goat snp26348-scaffold276-1851205 1 91756049 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798078 Affx-122957616 AX-385285014 1 90448152 AGAGAAAGGACACCACAAACTATAAAATAAATGAG[A/C]GGATAAAAACTCTGATCATGTAAGGAAAGTCACTG M 2 1 2 1 101000 f 74 goat snp26349-scaffold276-1889858 1 91794697 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426180 Affx-122940583 AX-123296526 1 90501621 GTGTGTTTATGGTATGAATATCTGAACAAATGAGG[C/T]AACAGAAGGCAACACCAACACACTAAGAGCAGAAT Y 2 1 2 1 201000 f 74 goat snp26350-scaffold276-1943327 1 91848526 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437267 Affx-122932001 AX-123307605 1 90531895 ATTGTATTCATTCAGAAAGTAGTCATAAAATACTA[C/T]AGACCTAAAATCATGCTTGAGTCTGGAAAAGCAAT Y 2 1 2 1 101000 r 74 goat snp26351-scaffold276-1973601 1 91878929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451561 Affx-122921699 AX-123321894 1 90582130 TACACTAAAAAAGTATGCACAGACACACACAAATA[G/T]AGTGTGCCATTAGTATGGTAAGTAAGATAGATGAA K 2 1 2 1 201000 r 74 goat snp26352-scaffold276-2023836 1 91929208 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380222 Affx-122975479 AX-123250580 1 90622625 CTTCCACCCTCACTTTTTCCCCTCTCTCCTTTCCT[A/G]ATACAATTCTTTCTTCCCTCACGCTTTACTTTCTT R 2 1 2 1 201000 r 74 goat snp26353-scaffold276-2064331 1 91970698 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388781 Affx-122968929 AX-123259139 1 90657448 ATCATAGCAAATATATGTGGTCATCTGGTACAATT[C/T]TGACCAATGAGATATAAATATTCATTCATCGGTGA Y 2 1 2 1 101000 f 74 goat snp26354-scaffold276-2099154 1 92006317 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765442 Affx-122921261 AX-385252943 1 90690383 TCTAACCAGACACACTAATTATGAGAAATAGAATC[A/G]GATATCAGATATGATGTCTTTAATGAATAGCAGAG R 2 1 2 1 101000 f 74 goat snp26355-scaffold276-2132089 1 92037773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416550 Affx-122947677 AX-123286898 1 90728360 CTACAAGTGTTAATGCAGGACTATTCACTGACTTA[C/T]AAAATATTTAACACATTATTGTGGTATAATTTGTA Y 2 1 2 1 101000 f 74 goat snp26356-scaffold276-2170066 1 92075525 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448160 Affx-122924268 AX-123318496 1 90821110 AAAAGCAAAAAACATGCCATATCATGAGATAAACT[A/G]CACTGCTGTCATGATTTTAAAATAAAATACTGAAT R 2 1 2 1 101000 f 74 goat snp26358-scaffold276-2262816 1 92169330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789905 Affx-122977023 AX-385276911 1 90873881 CACATCGACCTTTCCAACATAATCCCTGTTGTATT[A/G]TTTATCTATACTTTTTCAACTAAGAAACAAAATAA R 2 1 2 1 102000 f 74 goat snp26359-scaffold276-2315587 1 92222825 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779782 Affx-122943458 AX-385266882 1 90906735 CCTTGTTTTGGAATACCATCTCTGTGCCTTTTTAA[A/C]TTGCCAGTTTTCTATTATACCTTCAAGACCCAAGT M 2 1 2 1 101000 f 74 goat snp26360-scaffold276-2348441 1 92256307 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387178 Affx-122970620 AX-123257536 1 90971281 ATTTGTGAAATAACAGAGGATGAGTATGGATGAAT[A/G]ACCAAGGGGATTAATGCTGATTTTATTTAAATGAT R 2 1 2 1 201000 r 74 goat snp26362-scaffold276-2412987 1 92321401 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380833 Affx-122975068 AX-123251191 1 91001747 ATGTTTACGTATTCTGGACTCCATCAGCGAAGCCA[A/G]GAGAAATGTAACTGTCATCTGCACTAGGCACTTAT R 2 1 2 1 101000 f 74 goat snp26363-scaffold276-2443453 1 92352247 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445735 Affx-122926093 AX-123316072 1 91055733 TTTACCATCTGAGCCACCAGTGTTTTCTTAAACTG[C/T]AATAAATCACACCCATTCATCTGACTACATGCTGA Y 2 1 2 1 202000 r 74 goat snp26364-scaffold276-2497439 1 92406788 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436062 Affx-122932706 AX-123306401 1 91119950 ATTGAGGGAAGGCAGATGAGTGTTGTTGAATCAGA[C/T]GGTTCCTAATATCAAAAAATTTCAGAAAGTCAAGA Y 2 1 2 1 101000 f 74 goat snp26365-scaffold276-2561656 1 92471764 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440588 Affx-122929290 AX-123310925 1 91157153 TAAGGCGGTGATTTACAGATCATTTAGTCTGGCCT[A/G]TTCTGGGGTAGACAGGAGACCCTTGGTGATTAGGT R 2 1 2 1 201000 f 74 goat snp26366-scaffold276-2598859 1 92509032 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803844 Affx-986696542 AX-385290576 1 91162282 TACATCAAAAACTTTACCCAGCTGTCTTGGTCTTA[C/T]GCCCTCACCTGGCAAGATGTATTTGTCATCCTGGG Y 2 1 2 1 600010 f 74 goat 1_91162282 1 91162282 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320803847 Affx-986696544 AX-385290578 1 91162327 TGGCAAGATGTATTTGTCATCCTGGGGTCCACTAC[C/T]ACCCCAGAGAAAAGAAAGGCCATTTGGGCCGCAGC Y 2 1 2 1 600010 f 74 goat 1_91162327 1 91162327 Ancestral_priority_1043 ancestry 0.544 neutral IMAGE 10K 10K ancestral 320769682 Affx-122927585 AX-385256852 1 91187368 TTGTTTTATATTGCTAGTATTGAGGTCTCCAGAAA[C/T]ATTTGCCTGAACTGCTCTGCACATAGAAGTTGTTG Y 2 1 2 1 101000 r 74 goat snp26367-scaffold276-2629074 1 92539331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399472 Affx-122961193 AX-123269827 1 91218201 AGCCCATAGATACAGAAACAACTGCCTCCCCCTTC[A/G]CAGGTGGTATTATCACCCTTGTATTAGCAGCTGGA R 2 1 2 1 201000 r 74 goat snp26368-scaffold276-2659907 1 92570207 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782606 Affx-122950768 AX-385269679 1 91249657 TCATCAGAGAGATGTGTATAGAATAGAAGACAAGC[C/T]GGACCTGTGCCCATTCACATAAATGACCCTTGTTT Y 2 1 2 1 101000 r 74 goat snp26369-scaffold276-2691363 1 92601685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793779 Affx-122964128 AX-385280751 1 91296330 AAGATAAGCCTACATTGTTTCTTGTGTCTGTAAGT[A/G]CTGAATTATTCATATGAATCCTTCAGAGCAGCCTT R 2 1 2 1 101000 f 74 goat snp26370-scaffold276-2738036 1 92645086 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787165 Affx-122949044 AX-385274191 1 91355992 ATGAGAAAATGTGATGTTTCTTGTAAAGAGGGACT[C/T]GATTCTTAATTACTGTTTTCTCTAAACTAAAAATT Y 2 1 2 1 101000 f 74 goat snp26371-scaffold276-2797698 1 92705385 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439762 Affx-122930520 AX-123310099 1 91393520 GAATTTAGTAACAACAAACTTTGTGATGTTCTTCC[A/G]TACCATGGTTTGAAGTATGTGTTATAATGCACAGG R 2 1 2 1 101000 r 74 goat snp26372-scaffold276-2835226 1 92743160 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271847 Affx-1111832874 AX-519545630 1 91393638 ATGTATGGTGTGAGAGTTGGATCATAAAGAAGGCC[A/G]AGCACCAAAGAATTGCTGTTTTTGAACTGTGGTGT R 2 1 2 1 303000 f 74 goat 1_91393638_AF-PAKI 1 91393638 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791694 Affx-122944101 AX-385278685 1 91438326 ACATCACTAGGAACTCTTTACCGTCCCTATGTTAC[A/G]CATATAAATTATAGCCAAATGATATCCATATTAAC R 2 1 2 1 101000 f 74 goat snp26373-scaffold276-2880032 1 92789231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796380 Affx-122932564 AX-385283330 1 91496816 TTAGTCATTCTATTAAACCACTGTTGATCTTACAT[A/C]TTAGCTTCTCACCTACATAATAATCATCTTGCTAG M 2 1 2 1 101000 r 74 goat snp26374-scaffold276-2938522 1 92847698 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794162 Affx-122924096 AX-385281128 1 91574844 ATTTAATGCATTAAATTATATGCTATAAGAAGAAA[C/T]ATGGCTATTCACTTCAAGTTAAAAAATGAACAGGT Y 2 1 2 1 101000 r 74 goat snp26376-scaffold276-3016550 1 92926166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794820 Affx-122962363 AX-385281780 1 91606571 TGAGACAAATTACACATGATGGCTTTGCAATCTGG[A/G]TAAATGACAGGTTCAGGTGGATGTGCAACTTACAA R 2 1 2 1 101000 f 74 goat snp26377-scaffold276-3048277 1 92958344 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771019 Affx-122936733 AX-385258181 1 91640853 GAAACAAAACATAGAAAGTGTCATGGAAATGTTTA[C/T]AAGCTTCTGGATTCAAGCCTTGATATAATATTTTT Y 2 1 2 1 202000 r 74 goat snp26378-scaffold276-3082559 1 92992347 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439419 Affx-122930237 AX-123309756 1 91695865 TTCTCAAAAAAACTCCTGAAATCAAGCAGATGAGG[C/T]ATATATTGGAATCCTGCTATCAGATCACCTTATTG Y 2 1 2 1 101000 f 74 goat snp26379-scaffold276-3137571 1 93048412 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388952 Affx-122968810 AX-123259310 1 91736866 ATTGGCATAGACAGAATGCTTCATAAACAGAGGTA[C/T]GCATATTTAATCTGTGAATTACTAAGGGACCTTTG Y 2 1 2 1 101000 f 74 goat snp26380-scaffold276-3178572 1 93089584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432669 Affx-122936051 AX-123303010 1 91781411 CTGACTGTTTAATGCAGACCAGGGGACTTTCTTGA[C/T]GACTGCCTTCCATGAGAGGGAGGCAACTTCCCATG Y 2 1 2 1 101000 f 74 goat snp26381-scaffold276-3223117 1 93134172 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435419 Affx-122933547 AX-123305759 1 91810480 ACTGAGCTCCGGGTCTCCTGTTACCTGCTGAGACC[A/G]TACCCTTGTAGGCCAGAGAATCTAATGGAGTGAGG R 2 1 2 1 101000 r 74 goat snp26382-scaffold276-3252186 1 93163309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420067 Affx-122945120 AX-123290415 1 91854319 TGCTGCACTCTTTCCCTGCCCTCTTTACCCAACAG[C/T]GTTTGAGGTAAACTGACTGTAAAAGGTTCCTAAGG Y 2 1 2 1 101000 r 74 goat snp26383-scaffold276-3296025 1 93206953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770731 Affx-122943343 AX-385257895 1 91895885 TTCCAAGCATTTAATCAAAGACTTTGATATTAAGC[C/T]GATATTTCTTGGCTCATTGCTATCAGGTTGGTCTT Y 2 1 2 1 101000 r 74 goat snp26384-scaffold276-3337591 1 93248874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388657 Affx-122969107 AX-123259015 1 91925780 GTATTACACTCCCACCACCCAGGTGCTCTGCTTTG[C/T]AGGAAAGACTTCAGGCTTCCTACCAGACAGTACAA Y 2 1 2 1 202000 r 74 goat snp26385-scaffold276-3367486 1 93278915 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770836 Affx-122945647 AX-385258000 1 91990839 AGATCAAATGGGACCACTTCAGTACACTTTAAAAA[C/T]TGAGTTCTTTGGACATCACAAGCATATTTTCCTTT Y 2 1 2 1 201000 f 74 goat snp26387-scaffold276-3432545 1 93343467 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784732 Affx-122922753 AX-385271780 1 92030140 TTCAGTGGAGAAGATTCATCTCTATAAGTATAAGA[C/T]GGGATAACTCAGTTGGGCTAAAGGACTTACTTATG Y 2 1 2 1 101000 r 74 goat snp26388-scaffold276-3471846 1 93382581 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426306 Affx-122940292 AX-123296652 1 92063017 AATGAACAAGCTAATTTCATATAGAGATAAAAATG[C/T]AATGCAGGAGATAACCAAGGGGATGTAAGACAATA Y 2 1 2 1 103000 r 74 goat snp26389-scaffold276-3504723 1 93415460 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406480 Affx-122955169 AX-123276832 1 92108674 GAAAAAGAATATGATGGAGAGGAAATGGTAAGAAA[C/T]CCTGTAGGTAATTTAAATTAGTTTTAAGATCCAAT Y 2 1 2 1 101000 f 74 goat snp26390-scaffold276-3550380 1 93461237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387595 Affx-122970256 AX-123257953 1 92153669 GTTATATATATTTATAATGATATATGACTTTGAAA[G/T]AAATCATCAGAAGACTCATAGCCCACTAAGAAAAT K 2 1 2 1 202000 f 74 goat snp26391-scaffold276-3595375 1 93506393 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409411 Affx-122954132 AX-123279762 1 92184941 AATTAAAGGCAGACTTTCTCAAAATGCATTAAAAA[C/T]GAAAGGAAGCACACAGCAGCCACAAAAAGATACAT Y 2 1 2 1 303000 f 74 goat snp26392-scaffold276-3626647 1 93537993 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402036 Affx-122958736 AX-123272389 1 92277447 ATGATACCATTCACTCTTGTACATGTATCTATACA[C/T]GTACATACATAGACTTTCTCCTTCCAAAAGTAATT Y 2 1 2 1 101000 r 74 goat snp26394-scaffold276-3719153 1 93631840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452651 Affx-122920338 AX-123322984 1 92311069 TTATTACTCCTTATTCAGTACGTTGGGAAGTGTGC[A/G]CCATGTGTGTGCTACCTTAGGAAGCTTTTTATTAA R 2 1 2 1 101000 f 74 goat snp26395-scaffold276-3752775 1 93665360 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771739 Affx-122941532 AX-385258896 1 92365620 CCTGGATTTTATTAGAATCAGTGAGATAATACATG[C/T]AATATACTTTACAACATCTTATATGTAGTAAACAC Y 2 1 2 1 101000 f 74 goat snp26396-scaffold276-3807326 1 93719435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398633 Affx-122961464 AX-123268988 1 92423943 TGAGTACATAAATAAGCAAACAAACAAAGCAGTCT[A/G]GGGGTATGGTAAAGAATTGATATTGTCCCCAGTAC R 2 1 2 1 201000 r 74 goat snp26397-scaffold276-3865649 1 93780028 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439535 Affx-122930113 AX-123309872 1 92466570 CCTTCAAAGCCACTGTCTCCCTATAAATCAGCAAG[C/T]AGAAGGAACATGTCTGACAAAAATCCTGTCTCTCC Y 2 1 2 1 101000 r 74 goat snp26398-scaffold276-3908276 1 93823282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796070 Affx-122979030 AX-385283022 1 92513153 CATAAAAGTTATCTACTCAGAGGTGAGGCAGGAAT[A/G]CTATTCAGGTCTAAGACCAGGCCCAATCTCCTCAT R 2 1 2 1 101000 f 74 goat snp26399-scaffold276-3954859 1 93868739 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799913 Affx-122936812 AX-385286839 1 92569963 ACAGAGTTAGGAAAAAGAGTAGTGAGAAAAATCTG[C/T]GAGAAGTGTTATGATAGGATGATTCAAGGCACTAC Y 2 1 2 1 101000 r 74 goat snp26400-scaffold276-4011669 1 93924525 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442995 Affx-122928185 AX-123313332 1 92637780 GATGTTGTACAGTTTAGAAGAACCTAGTCCAGTTT[A/C]GCAACAGTGACTTCCAAACTCATGTCCTCTACTGT M 2 1 2 1 101000 f 74 goat snp26401-scaffold276-4079486 1 93992564 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798183 Affx-122936984 AX-385285118 1 92676550 CCTCCAAAGAAACGTCAGTGTTTCCTCAAATCAAT[A/G]CCATGAACCAGTTCAAGGGTGCAAAACTTCTCCTA R 2 1 2 1 101000 r 74 goat snp26402-scaffold276-4118256 1 94032221 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278843 Affx-1111836540 AX-519552314 1 92696418 TGGCATAATAACAGAATGCTCTTTTCATTCTGAAA[A/C]AGGACTAACTCTTTACATTAAAGTGCAAGAAAATC M 2 1 2 1 101000 r 74 goat Random2.2K-96 1 92696418 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794976 Affx-122973006 AX-385281936 1 92705755 CTCCTGTTGTTTTTCTTCTTGATACTGCAAAATCA[G/T]CCCAATATTAGTCATTCACCTAATAAAAACTTATG K 2 1 2 1 101000 f 74 goat snp26403-scaffold276-4147461 1 94061238 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274868 Affx-1111834543 AX-519548452 1 92751185 TGTGCAACCAACTAACCTGCAGGGGTGAATGCCTG[A/C]GTCCTCCAGTCACTCTCTGCCCACTTCACGACCCT M 2 1 2 1 102000 f 74 goat GoatD01.040952 1 92751185 C A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320785126 Affx-122952659 AX-385272172 1 92759921 CAATCATGGTAAGAACCCGCAGAGGGAAAACTGGT[A/G]TCAGGAGACGTGAGAAGAAAACACTGTTCCATTTA R 2 1 2 1 101000 r 74 goat snp26404-scaffold276-4201627 1 94115584 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278674 Affx-1111836547 AX-519552152 1 92792868 TCCAGAGATCTTATTAAAGGTTGTAGGAGGTGAGA[A/C]ATGTTGATGGAAAAGTGAATAAAAACTTAAAAGAT M 2 1 2 1 101000 f 74 goat Random2.2K-97 1 92792868 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396866 Affx-122963244 AX-123267221 1 92796145 CCTGGAATGAACAACCCCACTGTGTCCAGCACAAT[A/G]TCCTGCACCCCAGCACCCCTTTCTGTGCACATCAT R 2 1 2 1 202000 f 74 goat snp26405-scaffold276-4237851 1 94151712 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421992 Affx-122943788 AX-123292339 1 92858762 GTGGGGAATGGGCCTTATACCTGTTTCAAGCCCAT[A/C]CAGAAATCCTAAGCAATTTTCCAAAATTTAACTAA M 2 1 2 1 101000 r 74 goat snp26406-scaffold276-4300468 1 94214610 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427606 Affx-122939363 AX-123297949 1 92887827 TAACTACAAGGACTAGACAGCAAAGCCTATGAGAA[C/T]GCCATGAAGTGTGTTACAGACAAGATTCTGAAACA Y 2 1 2 1 101000 f 74 goat snp26407-scaffold276-4329533 1 94244276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433512 Affx-122935017 AX-123303853 1 92918028 AACTTGCAAGCTCAAAGAAAGGGTAGGGCACAGAA[G/T]AGCAGCCTCATTCTCAGTGTGCTCACAACAGGCCC K 2 1 2 1 101000 f 74 goat snp26408-scaffold276-4359734 1 94275913 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765052 Affx-122959489 AX-385252621 1 92998541 TGCAGTGATCCATAAACTATTTTCAGCCTTTCTCA[A/G]TCAAGATCTGGTAGTCCTTAGAGAACACTGACTTA R 2 1 2 1 101000 f 74 goat snp26409-scaffold276-4440247 1 94356598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278688 Affx-1111836555 AX-519552166 1 93020108 AAACCAAATTGTGATGAAAATAATATGTATCTCAA[A/G]TATTAGTTTACAGTACTCAAAGTTAAAAATGTTCA R 2 1 2 1 101000 f 74 goat Random2.2K-98 1 93020108 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320788305 Affx-122958836 AX-385275323 1 93034024 ACCATAGAGAAGTAACACTCCTTTTCAGGGAAATT[A/G]CAGTGCCATCCAAGATATTGGTAGAACTACAGAGC R 2 1 2 1 101000 r 74 goat snp26410-scaffold276-4475730 1 94392080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409781 Affx-122952980 AX-123280132 1 93071444 GTCACATTCCCATCTCAGTTGCACTCTCAGACACA[C/T]GCTCATGAAGTACAGTGGAAGGTGCACTGCCAGCG Y 2 1 2 1 101000 f 74 goat snp26411-scaffold276-4513150 1 94429539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407811 Affx-122954554 AX-123278162 1 93103943 GTGGGTAGAGGGGACTATCTTTGCGGCCTCTGTCT[G/T]TAAGAGGAGAGTAAAAAGCAACTACCACCTGCAGT K 2 1 2 1 201000 f 74 goat snp26412-scaffold276-4545649 1 94459068 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770274 Affx-122938683 AX-385257440 1 93133307 AGTGAGAGAACTCCTCCTCCCACATAGGAAGTCTT[A/G]TACCCTCCTTTAAAAGTCACTGCCATAATAAGCAA R 2 1 2 1 101000 f 74 goat snp26413-scaffold276-4575013 1 94488764 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417346 Affx-122947728 AX-123287694 1 93190358 AGAGTTCTTGACTCGAATTCTCGGGCAAGAGAGGA[A/G]CTGCCTCAGAGGAGGACTGTGTCTGCTTTTGCTTT R 2 1 2 1 101000 f 74 goat snp26414-scaffold276-4632064 1 94546464 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412955 Affx-122951049 AX-123283304 1 93242618 GGGTTGGATTTTTTTCATTTTTGGAAATGACTGTT[A/G]TATGAGAAAGAACTTTTGAATAATTGCTTTTAGGA R 2 1 2 1 201000 r 74 goat snp26415-scaffold276-4684324 1 94598872 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392539 Affx-122966100 AX-123262896 1 93315922 TGGTTGGGAATCTTCTGGTCTCTTGTGTCAGTAAA[C/T]ACCCAAGTCCAAGTAGCTTAAACACAAAGGGGCAG Y 2 1 2 1 101000 f 74 goat snp26416-scaffold276-4757628 1 94671245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773173 Affx-122944150 AX-385260315 1 93355497 AATGCCAAGTGTTTCTCCCTAATCTTCAGTAGTCA[A/G]GAGCCAAAATCAAAGGCTTGGATTCATGGGACCAT R 2 1 2 1 101000 r 74 goat snp26417-scaffold276-4797203 1 94710861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778496 Affx-122943411 AX-385265610 1 93391262 ACTGCTCCTTTCCATCATCACTGTGGGCCAGAAGT[C/T]TGGCAGCTATAGCAAAAATAGGGCCAGAATCCCAT Y 2 1 2 1 101000 f 74 goat snp26418-scaffold276-4832968 1 94746690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788121 Affx-122933942 AX-385275141 1 93429561 TTATTGGACAAGGCCCAATGTGACATTTGTTTCAG[A/C]GCTAGAGATATAAAAGAGTCTACTGTGAAGGTTAC M 2 1 2 1 101000 f 74 goat snp26419-scaffold276-4871267 1 94785046 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425084 Affx-122941246 AX-123295430 1 93461828 GCTATCCTGTGGTGTGTGTGGTTGGGCAAATGAAA[C/T]TTAAAAGAAAAGCCAAGGCTGGTCACAGCAGAGAG Y 2 1 2 1 201000 r 74 goat snp26420-scaffold276-4903534 1 94817358 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413526 Affx-122950621 AX-123283875 1 93496663 AAGAATCAAGAAGGGCCTTGTGGTGCCCAAGTCCA[C/T]ACACAAAAGAATTAAAAGCCCAAACAAACAAAAAC Y 2 1 2 1 101000 f 74 goat snp26421-scaffold276-4938369 1 94852412 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421071 Affx-122944242 AX-123291418 1 93546246 AAATATCTGACTTGTCCACAATCCTGAATATTCTA[C/T]ACTCAACTCAAGAGTGACAATGAAGGTACGGCCAG Y 2 1 2 1 101000 r 74 goat snp26422-scaffold276-4987952 1 94901997 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776880 Affx-122975532 AX-385264004 1 93581234 CCTATTCCCACATTCTATATTGATATGTTCTAGCC[A/G]TCTGGAGTGAAGCATTCGCTCACTCACACTGGAAC R 2 1 2 1 101000 r 74 goat snp26423-scaffold276-5022940 1 94936886 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775353 Affx-122922746 AX-385262484 1 93616757 ATAGCTTATGTTTTATGAGTGATTACAAGTTTCTT[A/C]ATGACTCCCAAAGAAAAACCCAAGCCTAATAAAAT M 2 1 2 1 101000 r 74 goat snp26424-scaffold276-5058463 1 94972442 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798866 Affx-122965777 AX-385285796 1 93665166 ATGACCTGAAGTAACACAAGAAGACCTGTTCCATA[C/T]GAATTACAGATCCATTAAAACAGAAGGGTTTCTAT Y 2 1 2 1 101000 f 74 goat snp26425-scaffold276-5106872 1 95021266 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376335 Affx-122978343 AX-123246694 1 93693812 TGAGAGATAGGTCAAAATAACATCATTGTTGGAAC[A/G]TTACAGTCAATATGATTTTTAAAAGTATGAATGAA R 2 1 2 1 101000 f 74 goat snp26426-scaffold276-5135518 1 95050067 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767294 Affx-122953847 AX-385254575 1 93781901 AGAAGGAATGCCTGAACTGGAATTAAAGAACAACA[C/T]GACTATGTAGTTTTCTTCATATCAAAACTGGACAT Y 2 1 2 1 101000 f 74 goat snp26427-scaffold276-5223607 1 95138092 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448885 Affx-122923263 AX-123319220 1 93814451 TACTCTGGATCAGACATATTGGGTAAAATTGACAA[A/G]CAAAACAGAAAGATGATTTCTGCTCTGATGGTGCT R 2 1 2 1 201000 f 74 goat snp26428-scaffold276-5256157 1 95170617 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446886 Affx-122925228 AX-123317222 1 93850996 AACTTAAGTGTGTCACCGGCAAACTTGTGCAGCTC[A/G]CTGTTGGTTGGCTTTCCCCAGCCCTGCAGCTGGAA R 2 1 2 1 101000 f 74 goat snp26429-scaffold276-5292702 1 95206948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376940 Affx-122977776 AX-123247299 1 93915599 TAATGGTGAGCTGTTCAGGTTTTCTCTTTCAATTT[C/T]ATTGACATATAACTAACACAACAGCACTGAATAAG Y 2 1 2 1 201000 r 74 goat snp26430-scaffold276-5357305 1 95272425 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411722 Affx-122951526 AX-123282072 1 93947690 AGTTCCCAGTCCTATCTCTGCGGAAGCTGAAGTTA[C/T]AAAGTTATGTCTGCATGCCATCTCAGAATTGCAAA Y 2 1 2 1 101000 f 74 goat snp26431-scaffold276-5389396 1 95304851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786940 Affx-122951602 AX-385273969 1 93980043 TACTTAGAGCTAGTGGACTTGTTTCCATATGCTAT[A/C]TGTAAGCCTGGATTCAAATAATAGAATAAGGCTTA M 2 1 2 1 201000 r 74 goat snp26432-scaffold276-5421749 1 95337361 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419836 Affx-122945815 AX-123290184 1 94026823 ACTAAGAGAGAAAAATGATAGTGCTTTCCTGTACT[A/G]CCAGCTGTTGGACATTCTTTTTGATGGTTAATATT R 2 1 2 1 101000 f 74 goat snp26433-scaffold276-5468529 1 95383818 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272615 Affx-1111832875 AX-519546326 1 94041880 GCTATGAAAGGAGGAAACTGAGGTTCCTCAGATTG[A/G]GGATATTAGTTTTCCAAAAGTGGTGAAAAGATCAG R 2 1 2 1 201000 r 74 goat 1_94041880_AF-PAKI 1 94041880 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795163 Affx-122964997 AX-385282121 1 94078292 GACAAACAAAGCTTTTGAAGTATTTAAGGCACTGA[C/T]ATAATGTTTGATTTGGTTTTATCCACTTCATTTGC Y 2 1 2 1 101000 f 74 goat snp26434-scaffold276-5519998 1 95435489 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416759 Affx-122948184 AX-123287107 1 94138237 ACATCTCTGGACCTCAATTTCCTCATGTATAAAAA[C/T]ATGAAAGTGAATGGCTCGTTGTAAAAGAGTGCATA Y 2 1 2 1 103000 r 74 goat snp26435-scaffold276-5579943 1 95495879 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796273 Affx-122933796 AX-385283223 1 94190862 TTGGCTGTAAGTTTCCTTGCAGCAAATACAAAGAA[A/C]GTAAACCAGCTACATGATTCATAAGATAAAACATA M 2 1 2 1 201000 r 74 goat snp26436-scaffold276-5632568 1 95548614 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772677 Affx-122928503 AX-385259824 1 94239394 TTCTAGAACTTTATAGTTGTTATAGTAATTTCCTT[C/T]AAGGTAAGGTCGATATAACTTATCTCTCCTTCCAA Y 2 1 2 1 101000 r 74 goat snp26437-scaffold276-5681100 1 95597525 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399081 Affx-122960883 AX-123269436 1 94270966 ATTGATTTAAAAAAAACCACCCAAAACTCTTGTCT[A/G]TTTGTTTTCTTAGTTTCTTCTGTGCTCATCCCTTG R 2 1 2 1 101000 r 74 goat snp26438-scaffold276-5712672 1 95629099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413757 Affx-122949940 AX-123284106 1 94309968 CTATTTGTTAAAAATTTCCTTCTTTGAATCTTAAA[C/T]GTCTCTTAGTTGATTTAATTATTGAAGTCCGCCAG Y 2 1 2 1 101000 r 74 goat snp26439-scaffold276-5751674 1 95667724 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439872 Affx-122930049 AX-123310209 1 94382869 ACTCTGAAGCAGTCTGCAGTTGCAACCTGGCCCAG[A/G]ACAGCTGAAGCCCCATTATGAAAAATGTTATCTTT R 2 1 2 1 101000 r 74 goat snp26441-scaffold276-5824575 1 95740928 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770477 Affx-122959851 AX-385257643 1 94423258 TATCTGTCCTACAGGCTGCTAGAATACTGCTGTCT[A/G]CTCCTCTCTGTAGTCCTATAGCTCAACCTTCCTTC R 2 1 2 1 101000 f 74 goat snp26442-scaffold276-5864964 1 95781176 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409376 Affx-122954156 AX-123279727 1 94507503 TTCCACACAGGCAAAGCAGTGTTCGACTGAGCTCA[C/T]TGGAAAAGTCGTAACTGCTTATCTCTGGGAAGAGA Y 2 1 2 1 101000 r 74 goat snp26444-scaffold276-5949209 1 95864728 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410639 Affx-122952080 AX-123280989 1 94587913 GTAACATCTGTATAGAAAAGAGTTAGAACCAGTAA[C/T]GGCAATTTTACTAAAATTATGATGAAAATGCAAAA Y 2 1 2 1 101000 f 74 goat snp26446-scaffold276-6029619 1 95945242 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418992 Affx-122946060 AX-123289340 1 94620426 TTCTGCTGCTGAACAATAGGATCTTCGCAAATTCC[A/G]TGCCACAAATTCAGCAATAACGTTTGGGATCGAAT R 2 1 2 1 101000 f 74 goat snp26447-scaffold276-6062132 1 95977695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419346 Affx-122945645 AX-123289694 1 94663893 CCTACCCTCTGTCCTTGTGTAGAGAAAAAACTTCA[C/T]AGAGAAACACCCCTATGTTTGTCTACTCTCCAGTT Y 2 1 2 1 101000 f 74 goat snp26448-scaffold276-6105599 1 96021061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787049 Affx-122957306 AX-385274077 1 94696407 CACAAACTCACAGAATTTTCTTCATTAGCATTTTC[C/T]TGAACTATGATGTGGAGTGCTGTGATGTGGACAAC Y 2 1 2 1 101000 f 74 goat snp26449-scaffold276-6138113 1 96049885 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395698 Affx-122963731 AX-123266053 1 94796824 TCTAGATCAGCAATTTCTCATAAATCATTGGAACA[C/T]GGAACATGAAACAAGAAGAAGAAATCAGGAATTCA Y 2 1 2 1 101000 f 74 goat snp26451-scaffold276-6238530 1 96150950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387219 Affx-122970587 AX-123257577 1 94844914 CTGCATGAAACACAGAGTCTTAACTACTGGATTAC[C/T]AGGGAAGTTCCCATGATGTATACTTTGATTACAAA Y 2 1 2 1 201000 r 74 goat snp26452-scaffold276-6286620 1 96199432 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781399 Affx-122977005 AX-385268484 1 94901451 GTTACCTGAGGGGTATGGGTGTGAGGGATAAATTG[A/G]GAGACTGAATTGGCACGTATGCATGGCTATATATA R 2 1 2 1 101000 f 74 goat snp26453-scaffold276-6343157 1 96256638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401699 Affx-122959547 AX-123272052 1 94978247 CATCAGAGCATATGCAGAGAATCCATTCCTTGGCC[A/G]TGGCCATCCTAAGACTTAGCCTAGCAAGCACATGG R 2 1 2 1 201000 r 74 goat snp26455-scaffold276-6419953 1 96334092 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425108 Affx-122941229 AX-123295454 1 95007910 CACACGCATGTGGCCAGGTATGTGAGATGACCCTC[A/G]TGTACCATCTCTCCATCCAGCTCCCTACTGTCCAG R 2 1 2 1 101000 r 74 goat snp26456-scaffold276-6449616 1 96364460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418581 Affx-122946373 AX-123288929 1 95038583 CTCAACTAGAGTGGTGTCCTCACTCCTTGTATATC[A/G]CTCTATTTTTTTTTTATCATGGTTCTTGTCTCCAC R 2 1 2 1 102000 f 74 goat snp26457-scaffold276-6480289 1 96398563 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425403 Affx-122941548 AX-123295749 1 95108722 GAGCCAGGCACAACAACCAAGGATAACCACCTGAT[A/G]CAGGAGTGCACATGGAAACCGTGAAGAGCAGTTGT R 2 1 2 1 101000 f 74 goat snp26459-scaffold276-6550428 1 96468553 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452709 Affx-122920299 AX-123323042 1 95140184 GGAAGGACTTTAAGGAGGCAGAATTTGAACTGGAC[A/G]ACAAGATAGGTTTTAGACAGAGGGAAGTGGGGGGC R 2 1 2 1 201000 r 74 goat snp26460-scaffold276-6581890 1 96500113 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272451 Affx-1111835351 AX-519546177 1 95189909 GGACATGTGTTAAAAATGCACATTCCCTGTCTCCA[A/G]CCCCAGAATTTCTGATGTAGTGTGACAGGACCTGG R 2 1 2 1 101000 f 74 goat Random2.2K-100 1 95189909 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800344 Affx-122954575 AX-385287266 1 95234236 GCATTGAATGGAAGTATTCCCAGGACCTTTAAGAT[A/G]TGAAGCTGGTCTGATGTACATCTGGAGCAATAAAT R 2 1 2 1 201000 r 74 goat snp26461-scaffold276-6675942 NW_017189517.1 9999612 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377953 Affx-122977205 AX-123248312 1 95273319 GGGGAAGATTTCAACAGGTGAAAAGGAAGGAGGAA[C/T]AGAGAGGCAATGTTAACAGCATGCTATCAGGGAGT Y 2 1 2 1 101000 f 74 goat snp26462-scaffold276-6715025 1 96635727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411206 Affx-122952363 AX-123281556 1 95305311 TACCAGTTACGTGATGGCTGAGTTTCAGTCTCTCT[A/G]TACCACTGCCCACCTCTGAGGCTTGTTAACGTTTA R 2 1 2 1 201000 f 74 goat snp26463-scaffold276-6747017 1 96668034 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449971 Affx-122922884 AX-123320306 1 95338965 TTTTCCAGTGCAAAGTACAGAGCTATTGTTTTCAA[A/G]TCAAGACTTCCTTGATCAATTTAAGCAAAACCACT R 2 1 2 1 101000 f 74 goat snp26464-scaffold276-6780671 1 96701692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404591 Affx-122957354 AX-123274943 1 95377851 CTGAATGGTAATGAAAAATTGTGCTGACAATAGAA[A/G]AAATAAGTATATTCAAATAAGTTATTCATTTTTAA R 2 1 2 1 101000 f 74 goat snp26465-scaffold276-6819557 1 96740910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771457 Affx-122938996 AX-385258615 1 95433621 TTTTAAATGCTTCTCTGAAATCAGACATCAAAGTC[G/T]TCTTTTTGGAGTCCTCATTTTCTCCAGGTAGAATT K 2 1 2 1 101000 r 74 goat snp26466-scaffold276-6875327 1 96796711 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417794 Affx-122947380 AX-123288142 1 95470528 GGATGCAGCGGGAGTTTGGAATTAGCAGATGGAAA[C/T]TACTATATAAAGGATGGATAGACAAGGCCTAGGAT Y 2 1 2 1 101000 r 74 goat snp26467-scaffold276-6912234 1 96833797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433032 Affx-122935770 AX-123303373 1 95537305 CACAGACCGTGAAGGAGCTGTTGTTACACACAGTA[C/T]GGATCCCCTCAATGTTGAAAAGTTCAGCATGAAAG Y 2 1 2 1 101000 f 74 goat snp26469-scaffold276-6979011 1 96901245 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403367 Affx-122957792 AX-123273720 1 95599505 ACACTGAGACACATCTGTTCAAGTGAATCATGTAC[G/T]AGCTCAACTGACTCATGTAGCAGGGATAAGAAATT K 2 1 2 1 101000 f 74 goat snp26470-scaffold276-7041211 1 96964371 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775378 Affx-122943665 AX-385262509 1 95633878 TAGTGATTTTTAATGACCATAAAATGGCAAGCACC[A/G]TGAGAATTGTATTCTGAAAACATGGTTCTTGCTTC R 2 1 2 1 101000 f 74 goat snp26471-scaffold276-7075584 1 96997427 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411068 Affx-122951942 AX-123281418 1 95668644 GGTTGGTCAGTTTCCTACATAGGTGTCCTTCCACC[C/T]ACCTCCACTGGGTGGGGGAAGAGGGTGACTAAGTT Y 2 1 2 1 101000 f 74 goat snp26472-scaffold276-7110350 1 97032543 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792323 Affx-122928781 AX-385279305 1 95699311 AAGTCAAAGGTATACCAGCTTGTGGGCTGTTTAAC[A/G]TGATTTATGTTACAAGAGCTTTGTAAATATATGTT R 2 1 2 1 101000 f 74 goat snp26473-scaffold276-7141017 1 97063520 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453561 Affx-122919773 AX-123323894 1 95739321 ATAACACTAGAAGCTGAATTGAGTTGGACTAATAA[C/T]GACAAGCTATAGCAGAAAGCAACTAGACTTGAATC Y 2 1 2 1 201000 f 74 goat snp26474-scaffold276-7181027 1 97103252 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418570 Affx-122946382 AX-123288918 1 95796085 GCTTATGTTCTAGAATCAGAAATTCATCCACCTCA[C/T]GTGCTTTATCTATTCTGCGATCTCCTGATAGTCGC Y 2 1 2 1 101000 r 74 goat snp26475-scaffold276-7237791 1 97160638 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408636 Affx-122953482 AX-123278987 1 95827435 GAATGTGGCACATCTTTTCATGGTTCTGTGTCTCC[A/G]CAAGTGCTGTCTCCTTCCTCAGAATGCTTCTCCCA R 2 1 2 1 101000 f 74 goat snp26476-scaffold276-7269141 1 97192383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438729 Affx-122930838 AX-123309066 1 95860266 TTTCCTTCCCCCGCGTAGTGCGTGCGTTTCCGAGC[G/T]CAGGGCGGAGATAGTCGCTGACCCCTGCTGTGAAG K 2 1 2 1 101000 f 74 goat snp26477-scaffold276-7301972 1 97224989 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381774 Affx-122974301 AX-123252132 1 95932336 AAAAGGATGAATAAAACTTCATTTCTGCCTCCAGA[C/T]GGTAGCTTCATTTTTCATTTTTATTGGTTATAGAT Y 2 1 2 1 101000 f 74 goat snp26478-scaffold276-7374042 1 97297113 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386231 Affx-122970976 AX-123256589 1 95980351 GTGGATGCAGCAGTTAGGATATTTTTTTTTCCTGA[C/T]GGTTGTCTATTCTTTAAAGGCAGGGCTGTCTAGAG Y 2 1 2 1 101000 r 74 goat snp26479-scaffold276-7422057 1 97345143 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395390 Affx-122963966 AX-123265745 1 96020679 TAGAAGACAAAAAATGATAAAAGCAACTTTAACTA[C/T]AATAAACAGGGATAAATGTGAAGATGTAAAATATG Y 2 1 2 1 101000 f 74 goat snp26480-scaffold276-7462385 1 97385386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765568 Affx-122946004 AX-385253048 1 96051039 GATTAGGGAGAACAAAGCTGGCAAAAGTGGCATCA[C/T]GCCACAAATTCACTTTAGCCATATTTAGTGCAAAC Y 2 1 2 1 101000 f 74 goat snp26481-scaffold276-7492745 1 97415960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410500 Affx-122952188 AX-123280850 1 96110722 CGTACTAGAGAGAGGGCAGGAATTAGACTGATTGA[C/T]GGGGACTATCAGACTATCTGATAGTGCACTATCAG Y 2 1 2 1 101000 f 74 goat snp26482-scaffold276-7552428 1 97475669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401054 Affx-122959652 AX-123271407 1 96161019 AATGTCTTGATGGTGTCCTATCTGTGGTGCCTGTG[A/G]TGTTGTCCAACGCTAAGTATATTATTCAAAATAGT R 2 1 2 1 101000 r 74 goat snp26483-scaffold276-7602725 1 97526489 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387163 Affx-122970630 AX-123257521 1 96273650 CACCTGGGAATAGCTGTCCTGTGGGATTGACTCCC[A/G]CTGGAGAAATGAGACTAGTCCCTATCACTGTCCAC R 2 1 2 1 101000 r 74 goat snp26485-scaffold276-7715356 1 97639400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779722 Affx-122931142 AX-385266822 1 96305674 GGGTAGTGACACAAACTGGCATTTCTTGAAGTTTT[A/G]TCAAATGTCCCCACATTTCATGGTTTTATGGATTA R 2 1 2 1 101000 r 74 goat snp26486-scaffold276-7747380 1 97671099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386018 Affx-122971497 AX-123256376 1 96338441 TAACTGATGTAGTTTGGTTGCTTATGTTTTTTATG[C/T]CTTCACACTGTTCTAGAAGGCTGTGCAAATGGTAA Y 2 1 2 1 101000 r 74 goat snp26487-scaffold276-7780147 1 97704458 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384238 Affx-122972367 AX-123254596 1 96395839 TATTAAAGGAAATGATGCATAATAAGCACTTGACA[C/T]AGTGTAGACACTGATATTTTATGATCTTACCATCC Y 2 1 2 1 101000 f 74 goat snp26488-scaffold276-7837545 1 97762011 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444095 Affx-122926832 AX-123314432 1 96440200 GGAGGCATATAATGGATTGCCTAGATTAATTAATT[A/C]TTTAGGTGCTGCAAAATGAATGTGTTCTAATTCCC M 2 1 2 1 202000 f 74 goat snp26489-scaffold276-7881906 1 97806337 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779892 Affx-122929540 AX-385266991 1 96475287 ATGGTACAAATAAGAAATATCGAACAAAAAGCACC[A/G]TTTGTGTTCTGAGACACCTATTCAGATTTCAAACC R 2 1 2 1 101000 r 74 goat snp26490-scaffold276-7916993 1 97840365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425601 Affx-122940922 AX-123295947 1 96504996 GGAACTTTTGGGTGCTAATATATCCTGGCTCTTAA[C/T]CTGGGTGATGGTTTCATGGGAGTGTTCATTTTATG Y 2 1 2 1 201000 f 74 goat snp26491-scaffold276-7946702 1 97870267 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399835 Affx-122960256 AX-123270190 1 96549595 AAAATCACTCTTAAAGTGTCTGACTGAATGAATCA[A/C]ATTTTACAAATAAATATCTGTCAAAGGTGCAATTA M 2 1 2 1 101000 f 74 goat snp26492-scaffold276-7991301 1 97914078 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272617 Affx-1111832876 AX-519546328 1 96556498 CATAGTACTTGTGATTTACGATCCATATCTTAAGA[A/G]TGTTGAGTAGGAAGTTTTGTGTTTCCTGAAATCCT R 2 1 2 1 101000 r 74 goat 1_96556498_AF-PAKI 1 96556498 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795117 Affx-122973360 AX-385282076 1 96597496 CATCCTAATTTCTACAAGCTTCATATCATGTGATA[C/T]GAGCAGTTAAACCACTAGACTCAATTCTGAAAAAC Y 2 1 2 1 101000 r 74 goat snp26493-scaffold276-8039202 1 97961756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424208 Affx-122942499 AX-123294554 1 96627154 CCAGAGGGGTTCTCTGTGAAGCAAACCTTTCAACA[A/G]TTGCCTGTGATTTAGTTCAGTTCAGTTCAGTCACT R 2 1 2 1 201000 f 74 goat snp26494-scaffold276-8068860 1 97991597 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276470 Affx-1111835357 AX-519549982 1 96654492 TATTGATACTTGACATTTTCCATAATAAAAAGGTA[A/G]CCCAGAGTAAAACATAATACACTTATCAAACAATG R 2 1 2 1 101000 r 74 goat Random2.2K-101 1 96654492 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417995 Affx-122946670 AX-123288343 1 96665188 TAACTTGCATTGATTCCTGTTGAATGGGAGAGCTA[C/T]GAAAGTCAAACTCAGTTTGTCTACAGGGTCACATG Y 2 1 2 1 101000 f 74 goat snp26495-scaffold276-8106894 1 98031155 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433872 Affx-122934422 AX-123304213 1 96697446 TGACTTACTTTGACTGCAGTCAGCCCCGATGAAGC[C/T]AGGAAGGCAGTCACAGGTTCCAATCATGGTGTCAC Y 2 1 2 1 201000 r 74 goat snp26496-scaffold276-8139152 1 98064098 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428277 Affx-122939398 AX-123298620 1 96760186 TCTCCTTCTGATTTTAAACAAGACTGCTTTGGATC[A/G]CTTCACAGGCAAAAAGTTCACTTGCCATTAGTTGT R 2 1 2 1 101000 r 74 goat snp26498-scaffold276-8201892 1 98127175 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410502 Affx-122952186 AX-123280852 1 96812544 TAAGGTCATGTCCCTCCCAGGTCAGGCTGCAGGTT[A/G]TTATAGGCTATTGAGTCCCTGTTGCTTTGCCTCAA R 2 1 2 1 101000 r 74 goat snp26499-scaffold276-8254250 1 98179823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432333 Affx-122936288 AX-123302674 1 96947709 GACAAAATACCTTCACTGTGGAGAAAAATCATTTG[C/T]AAGTTATCAGTTTTCTACAACTTCTACACCTTTAC Y 2 1 2 1 101000 f 74 goat snp26502-scaffold276-8389415 1 98314148 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409822 Affx-122952950 AX-123280173 1 96980351 ATATGAGAGGTCACACTGTAAATTGTACTTCTTTG[C/T]GGATCTTGTTCAAAAGAGTTGGAAAGCTTCTGAAT Y 2 1 2 1 101000 f 74 goat snp26503-scaffold276-8422057 1 98346991 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381815 Affx-122974272 AX-123252173 1 97074803 GACTCAGAAATGTTTTACAAATTGGCTTCAGCCTA[C/T]GAATCTTTAAAATTTATGGTCATATTTGCTTTACT Y 2 1 2 1 201000 r 74 goat snp26505-scaffold276-8516509 1 98441832 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391434 Affx-122966752 AX-123261791 1 97204521 TTTAATTAAAAACACCTGGCCCATAAGTACTGCTG[C/T]ATTACCATACTAGATTTCAAAATACTCCTTTATAC Y 2 1 2 1 101000 f 74 goat snp26507-scaffold276-8646227 1 98572362 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428999 Affx-122938848 AX-123299341 1 97252334 CTGTAACAAACCGAGCAGTTTAAACAACAGAAATG[C/T]ATTGTCTCTCAGCTCTACAGGCTGGAAGCCTGAGA Y 2 1 2 1 201000 r 74 goat snp26508-scaffold276-8694040 1 98620472 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766213 Affx-122960271 AX-385253612 1 97309292 TAAATCAAACTTTGGATCACCTCAGACCATGTGAC[A/G]TTCACATATGTAGACAAAATTAGTTTAGCCTTTCA R 2 1 2 1 101000 f 74 goat snp26509-scaffold276-8750998 1 98677572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417608 Affx-122946873 AX-123287956 1 97345953 TATGTATATTTATGAGATAGGACACAATTAGAAGA[C/T]ACATTTAACTTGTACTTTTTTGGAAACCATACTTT Y 2 1 2 1 101000 r 74 goat snp26510-scaffold276-8787659 1 98714199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780678 Affx-122929964 AX-385267768 1 97378633 GGCTGACAGCAATCTATTGAAAATGCATTTCAGAC[G/T]ATCATTTTTCCAGTCTAATTTACTCTTAATAAAAT K 2 1 2 1 101000 f 74 goat snp26511-scaffold276-8820339 1 98747074 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398702 Affx-122961854 AX-123269057 1 97412844 GGATAAAAAAAACCAATAACCTAGCCCTGAAGAGA[C/T]GGAAAGGGGGAAAAGTAGTCAGAAACACAAATAGA Y 2 1 2 1 101000 f 74 goat snp26512-scaffold276-8854550 1 98781565 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797399 Affx-122962120 AX-385284338 1 97627715 TGGAGTATTTTAGGTAAGTTCAGCCTAGCCTGATG[G/T]TATATGGGTTAGCAATAGCTCTGCTTCATTGTTGA K 2 1 2 1 101000 r 74 goat snp26517-scaffold276-9069421 1 98992253 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387788 Affx-122969703 AX-123258146 1 97670214 TATTGAGAAAAGAGCATTTAAAAAAATTTTTAAGA[C/T]GTTTTTTATGCAAAAGAGAGCTAAAAGCTACCCTT Y 2 1 2 1 103000 r 74 goat snp26518-scaffold276-9111920 1 99035156 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387388 Affx-122970424 AX-123257746 1 97712111 TTTAGAACACTTCAAATATTAATATTTCCAAGGCA[C/T]ATGTGTTGTGTCTCATTCTAATTGCCCTTTCTCTA Y 2 1 2 1 101000 r 74 goat snp26519-scaffold276-9153817 1 99076878 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428783 Affx-122938413 AX-123299125 1 97767429 ACTGGCCAGCACAGAGCGTGCAAGTGTCAACACAG[C/T]GGTGAAGTTGATATAATGGTTAAGTCCAGCAAGAA Y 2 1 2 1 101000 r 74 goat snp26520-scaffold276-9209135 1 99132489 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397346 Affx-122962298 AX-123267701 1 97797689 CATAAGACAGAGCATATGGTGCCCCCAAAATGATG[C/T]AGGGAATAAATGCTATTGAATTTAGAGGAATGGAG Y 2 1 2 1 101000 r 74 goat snp26521-scaffold276-9239395 1 99162718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791150 Affx-122945749 AX-385278145 1 97863426 CTAAGTATCCCTCTATCATAAAAAGCATTTTTACA[C/T]GATTGCTGGCAAAAGTTATACTTCTGATAGGTTCA Y 2 1 2 1 101000 f 74 goat snp26522-scaffold276-9305132 1 99227577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400767 Affx-122959880 AX-123271122 1 97921128 CTCCTGGCTCACAGGCTTGCCAACAGCAGGAGAGA[A/C]GTGAGAACTGTCAGATTTTTCCTCTCTACTCACTG M 2 1 2 1 101000 r 74 goat snp26523-scaffold276-9362834 1 99285884 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419756 Affx-122945877 AX-123290104 1 97952018 AGACCTTTACACCATGGGCTGTGTGCTTCCTCAGT[C/T]ACTTCAGTCGTGTCCAACTCTTTGTGACCCCACGG Y 2 1 2 1 101000 f 74 goat snp26524-scaffold276-9393724 1 99316827 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796800 Affx-122962563 AX-385283743 1 97995639 ACATTTTATTACCTGAGAATGTCTGATAATGATGC[A/G]TTAAGATGTGCAGCATATATGAGCTACATTGGGGT R 2 1 2 1 101000 f 74 goat snp26525-scaffold276-9437345 1 99360577 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276328 Affx-1111835362 AX-519549861 1 98018826 TGTTCTCTCCCAATTCCCAACCAGGTTCTTAAAAA[A/T]AGAATGAAAAAAAAAAAAAATCCCTAGGGTGATTT W 4 1 2 1 101000 f 74 goat Random2.2K-102 1 98018826 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418927 Affx-122946512 AX-123289275 1 98102587 TACTTATATCTTTTTTGCCCCCAACTCCTCTTTCC[A/G]CTAGAGATATCACCAAACTCCATCTTTTCCACAAT R 2 1 2 1 201000 r 74 goat snp26527-scaffold276-9544293 1 99468042 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788708 Affx-122941604 AX-385275724 1 98196876 AGGCAGTGTCAACAATAGAGCAGGTGTTGAATAAA[C/T]ACTGGTTGAAAACGACATGCCCATTGAAAAAGCTT Y 2 1 2 1 101000 f 74 goat snp26529-scaffold276-9638582 1 99563005 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415094 Affx-122949451 AX-123285443 1 98263154 CATCAACTATATATAGTTCTTTAGCCATGATGTGG[A/G]CAAAATAGCTCATCTATCTACTTGGGGTCGATATA R 2 1 2 1 101000 f 74 goat snp26531-scaffold276-9704860 1 99628781 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382060 Affx-122974927 AX-123252418 1 98300631 GAGACAGAGCATACTTTTAGGGATCTAAGGTTTCC[A/G]CAGAGGTCTCAGTTCTAATTTCTCACTTTGAAAAG R 2 1 2 1 101000 f 74 goat snp30205-scaffold332-1463418 1 99666864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385051 Affx-122971831 AX-123255409 1 98330312 TAAAATCATAAGGGATTTGATTTAGTATAGAAGTA[C/T]AGAAGCTGTCAAAGAACTCTGGTCTTTTGAATAAA Y 2 1 2 1 101000 r 74 goat snp30204-scaffold332-1433737 1 99696374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431178 Affx-122937184 AX-123301519 1 98361459 TTACATTTTGATAATATTATAGAATCTCATGAACA[C/T]GTGCTTGAATTTAATTAAAAAACCTTATTGATAGA Y 2 1 2 1 101000 f 74 goat snp30203-scaffold332-1402590 1 99727700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452768 Affx-122920255 AX-123323101 1 98410127 TCCACTGGAATATGTCAGAGACTGAGAAAACAGTC[A/G]CCAAAGCTTGTCTCTAAGCAATTTCCACATATTAA R 2 1 2 1 101000 r 74 goat snp30202-scaffold332-1353922 1 99776399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385320 Affx-122971669 AX-123255678 1 98457712 ACATATCCTGCATTCTGACCATTACTGACCTCTCC[C/T]CTAGGTATCTAATGCACCACAGGTTCATTTTAAGC Y 2 1 2 1 201000 r 74 goat snp30201-scaffold332-1306337 1 99824531 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391904 Affx-122966953 AX-123262261 1 98511688 CTGACAGATAAAAAGATATCTCTGCAAAGTTCTAA[C/T]GGAAGAGCATTTCAGGTAGAGAAAAACTAAAAAGA Y 2 1 2 1 101000 f 74 goat snp30200-scaffold332-1252361 1 99879308 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771776 Affx-122946898 AX-385258933 1 98546397 GTTTCACAACTGCTAAATAATCCTATTGGGACATC[A/C]CTTTGTTAATGAGATAAATAGTAATCTAACCGTGG M 2 1 2 1 101000 r 74 goat snp30199-scaffold332-1217652 1 99914986 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438517 Affx-122931203 AX-123308855 1 98620925 TGTTTATTTAAAGATAACAGTATTGATGTAATATT[A/G]CATTCTTTATCAAGTGTGGCAGTCTCCCCCAATCA R 2 1 2 1 101000 r 74 goat snp30197-scaffold332-1143124 1 99991863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427304 Affx-122940147 AX-123297647 1 98673867 TGCACATATATTAATATTCATCTTATTTGCAAGAA[C/T]GATTAATTGTTATCAGCAGACAGGGACTCTAAAAG Y 2 1 2 1 101000 r 74 goat snp30196-scaffold332-1090182 1 100044856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782943 Affx-122942934 AX-385270014 1 98703635 TATAGGAAACCACACAAAAATACATACTTCTCTTC[A/G]ATTCTAATTTCTAGTATAACAATTTTCCCAATATT R 2 1 2 1 101000 f 74 goat snp30195-scaffold332-1060414 1 100074281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399050 Affx-122960909 AX-123269405 1 98749524 AATATGATAGCTATTTTTAGTTTTAGAGCTCTTTC[A/G]TTCACTTCCTACTCACTTCTTGCACAGGTCCCAGA R 2 1 2 1 101000 r 74 goat snp30194-scaffold332-1014525 1 100120292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396842 Affx-122963264 AX-123267197 1 98797269 AAGATCAGTTAACAAAAGCAGCAGACAATATAAAC[C/T]ATTTTTAGTTAGCTTTTTTGAATTCATTTCTTTAA Y 2 1 2 1 101000 f 74 goat snp30193-scaffold332-966780 1 100168322 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383687 Affx-122972495 AX-123254045 1 98881949 GGACTACTAAACAAAAAGTTGACTTGGGAGCCCAA[C/T]GGTGTCTCACTCATTTCTGGTGATCCTGGAATATC Y 2 1 2 1 303000 f 74 goat snp30191-scaffold332-882100 1 100243780 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419018 Affx-122946043 AX-123289366 1 98939212 AAAGGACCCCTGCTGGGTTCAGAGAGAGCTAAATT[A/G]CATTCATAAAGGAAATCAGAATGAATTTTGTTAAT R 2 1 2 1 101000 f 74 goat snp30190-scaffold332-824837 1 100301088 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396363 Affx-122963043 AX-123266718 1 98971419 TTAAGTAAATATTAGTTCCAGTTTTTCAATTGGCC[A/G]AACATCATTTTGTATTCCTGGTAAGCTATTCAGTT R 2 1 2 1 101000 r 74 goat snp30189-scaffold332-792630 1 100333304 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414058 Affx-122949770 AX-123284407 1 99021773 GACTTCTATGTGAATTATCTCTACATACAAGAAAC[A/G]TCTCTGATTATGTTGTACTCTTATAAGTTCAGTTA R 2 1 2 1 101000 f 74 goat snp30188-scaffold332-742276 1 100383617 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406025 Affx-122955492 AX-123276377 1 99063921 GTTAGCAAAACATTAGCAAGGAAAAGGAGCTGTGC[A/G]GTCTGAAGGCAGAAGCCACCTGAAGCCTGGTAGGG R 2 1 2 1 101000 f 74 goat snp30187-scaffold332-700128 1 100426578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433406 Affx-122935099 AX-123303747 1 99092942 CAAGAATCTATTTGGAATATAAAAATCTGTAAATA[C/T]GTAGAGTAATAGCTTGGAATCAAATTGCCTAGGTT Y 2 1 2 1 101000 r 74 goat snp30186-scaffold332-671107 1 100456200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396338 Affx-122963063 AX-123266693 1 99128985 CTACCTGATTTTCAGTTCTTACTATCTCTCTTTGA[A/G]GACATTTTTTCAAAGCTTTACTGCGAATAGATGAC R 2 1 2 1 101000 f 74 goat snp30185-scaffold332-635064 1 100493318 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380163 Affx-122975967 AX-123250521 1 99159735 ATTATGAGCCACCACTTAAGAATTTGTCCACACTT[C/T]ATTTTTATTATGATCCATGTTAAATGCTACTGTTG Y 2 1 2 1 201000 r 74 goat snp30184-scaffold332-604314 1 100524380 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783757 Affx-122976209 AX-385270813 1 99190885 GTATAAACTAAAGGAAATAGAGAATACCAAAAGGA[C/T]ACATATTGTGGACTTCTTACTAACCTTTGCAAATG Y 2 1 2 1 101000 f 74 goat snp30183-scaffold332-573164 1 100555676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446054 Affx-122925833 AX-123316391 1 99224987 GCAAAGAAAGGAAATCAAAAATTATTTCTACATTC[A/G]TAACTCTGGAAGAACTTTTGCTGGAATAAGAAACA R 2 1 2 1 101000 r 74 goat snp30182-scaffold332-539062 1 100590961 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393831 Affx-122965164 AX-123264186 1 99273949 GAGGGACCAAGGAAAAGAGAGAATAGTGAGAGTGT[A/G]GAGGAGAGAGAGAAGATAGGGTGTGAGAGTGTAAA R 2 1 2 1 101000 r 74 goat snp30181-scaffold332-490100 1 100639919 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441469 Affx-122928755 AX-123311806 1 99314044 GCAATAGCACGTTGGAGTTCCATAAACTCGAAAAA[C/T]GGAGCCCATGGAGGACATTGCTGAGCTCCTGAACT Y 2 1 2 1 103000 f 74 goat snp30180-scaffold332-450005 1 100681774 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405322 Affx-122956829 AX-123275674 1 99346035 AGAAATAAACATAATTTAACATTGTAGTAAAGAAA[C/T]AGGAATAAAGAAAATGTTTGGCCTGGAAGAGCTAT Y 2 1 2 1 101000 r 74 goat snp30179-scaffold332-418014 1 100714073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789235 Affx-122948634 AX-385276246 1 99399193 ATTTAAGACATTTTGATGGTCTTAATCTCACTAAC[A/G]CATAGATTTTTCATTTCACGTTTAGTCCAATACTC R 2 1 2 1 101000 f 74 goat snp30178-scaffold332-364856 1 100768105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272568 Affx-1111832877 AX-519546283 1 99427524 TAGAGAAAACTTACAAAGTGCCAGATTCCATGTAA[A/G]TTATTATGATAATGATTTCTTCTAATTGTTCTTGC R 2 1 2 1 101000 f 74 goat 1_99427524_AF-PAKI 1 99427524 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320790122 Affx-122974281 AX-385277128 1 99444157 CTCTTCTAATCCTTATATGGTTAAATTTATTATTT[G/T]AGAAGCCTGTTGTAGTAAAATTCTTTAACATTAAG K 2 1 2 1 202000 f 74 goat snp30177-scaffold332-319892 1 100813411 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380379 Affx-122975337 AX-123250737 1 99492139 AAAAGTGTTTTCATGGCATTATCTCTTTTGATTAA[C/T]AGAAGACCCTTCATTTGACCTATTCTGTCTTTATC Y 2 1 2 1 101000 f 74 goat snp30176-scaffold332-271910 1 100861790 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423034 Affx-122943405 AX-123293380 1 99521903 AAGTCACTTTCCCCTGGGGCATTTGCTGATTCTTA[A/G]GAGAGGGAAGAGTTTGATAATACTTGCTTTGCCCA R 2 1 2 1 201000 r 74 goat snp30175-scaffold332-242146 1 100888418 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771481 Affx-122952511 AX-385258639 1 99571306 AACTTTAAACCTAACCTATGATAGATTTTATATGC[A/G]TATTATTAATAGAAGCTTTAAGTGCTGGGAGAACT R 2 1 2 1 101000 r 74 goat snp30174-scaffold332-192743 1 100937622 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795439 Affx-122965457 AX-385282395 1 99615013 TCTATTCATTCAGTATCCAAAACTTTTTCATAGCT[A/G]TTTGCCTGTAATCTATGGTTCTGGTATCATTTAAA R 2 1 2 1 101000 f 74 goat snp30173-scaffold332-149036 1 100982156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776742 Affx-122920594 AX-385263867 1 99698840 CTTTCATCTCAAAGGGCAACCTGTGGCAAGATCAA[C/T]ATAAGACTGAGGGAAACTTCTGGACAAGCAGACAA Y 2 1 2 1 202000 r 74 goat snp30171-scaffold332-65209 1 101065184 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437573 Affx-122931879 AX-123307911 1 99760334 ATGTCTGTACTTAAAAGAGGTTTCAATATTTTTCC[A/G]TTATTGATATTTTTAGTAAGACTGTTCCCATAATG R 2 1 2 1 101000 r 74 goat snp30170-scaffold332-3715 1 101127527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795712 Affx-122948060 AX-385282665 1 99790416 CATTGTCTGCTATCACATGACTACAGAGTAGTGAA[A/C]ACAGCATTTAAACCCAGTTGTCTATCTGCTTTCAG M 2 1 2 1 101000 f 74 goat snp11326-scaffold1409-832959 1 101158863 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393720 Affx-122965236 AX-123264075 1 99848865 CTAAATCATAGGACTTTTATTGGGTCACATAATTA[C/T]GTCTCTGTTTCCATTTTGGGGGGATTCTATTGACT Y 2 1 2 1 201000 f 74 goat snp11325-scaffold1409-774510 1 101218319 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410937 Affx-122952044 AX-123281287 1 99890505 ACTACCTCTTTCCCCTAATCACACTGCATTTGAAC[A/C]AGAGCAATGATATCTGACATTTTCAAATGCTCAAT M 2 1 2 1 201000 r 74 goat snp11324-scaffold1409-732870 1 101261462 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780059 Affx-122974334 AX-385267156 1 99923271 CACTATCACTTTTGCAGGAAAGACTAGAATAAGCT[A/G]TTTTTCACAGATCTAATAGAGAAAATATGAGTGTC R 2 1 2 1 201000 r 74 goat snp11323-scaffold1409-700104 1 101294434 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799881 Affx-122949463 AX-385286807 1 99952088 CAGATGGGACATCAGTTTTACCATCATTCAGATTT[A/C]TCCCCACATTAACCCTTGATGAACTAATGACTGTC M 2 1 2 1 101000 r 74 goat snp11322-scaffold1409-671287 1 101323092 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380549 Affx-122975290 AX-123250907 1 100058091 ACTCAAAAATGCCTCAGATGCATTTTTCCAGTAAA[C/T]GTTTTATTAAAAAGAATGTATCCTTTATAAAGAAC Y 2 1 2 1 103000 f 74 goat snp11320-scaffold1409-565284 1 101430324 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775154 Affx-122973816 AX-385262286 1 100087841 ACTAACACTTTCATTTTACCTTTGTATCCTGAGGT[A/G]CTTCTGTGTCTCTTAGTATCACTTACTCCATTTTT R 2 1 2 1 101000 f 74 goat snp11319-scaffold1409-535534 1 101459994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776155 Affx-122966846 AX-385263283 1 100135816 AGTTTTGAACTTGACTGGTTTCCTAGCATCCCACT[A/C]TATTTCTAGCAAGCTTTGACCTTTACATTTTTAGA M 2 1 2 1 101000 f 74 goat snp11318-scaffold1409-487559 1 101509454 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386819 Affx-122970101 AX-123257177 1 100170030 ATTACAGTTAGAAATTAAAGAGCTGAGTAAACTAG[C/T]AGAGTTGAGTGATGGGAAAGTGAAAGTGAAAGTCA Y 2 1 2 1 201000 f 74 goat snp11317-scaffold1409-453345 1 101543519 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793752 Affx-122941188 AX-385280724 1 100213869 CATAGCCTAGGAAATGCCTAGCAGAGTAATCAATA[C/T]GTGATAAGCTCATATTGATACAGTGTCATGTTTAA Y 2 1 2 1 201000 r 74 goat snp11316-scaffold1409-409506 1 101588073 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439360 Affx-122930281 AX-123309697 1 100291525 TATTGAAAAATCATTTAAAACTGTAATATGAATCC[A/G]CAAACTTTCTTTGATGAGCACTTGGTCTTGTGATA R 2 1 2 1 101000 r 74 goat snp11315-scaffold1409-331850 1 101666979 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417515 Affx-122946946 AX-123287863 1 100329005 ACCTGCCGTGTACTCTGTCCAATATCCCTTTTCCA[C/T]AAATATCAGCATGGCTAGCACCATCATGGGCATTC Y 2 1 2 1 101000 f 74 goat snp11314-scaffold1409-294370 1 101703986 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439525 Affx-122930122 AX-123309862 1 100390890 TTCCCTGATCTCAAAAGTCTAACACTAAATGCCTC[A/G]TAAATGCTAAATCAAATGACACTTTCTCTGTCATC R 2 1 2 1 101000 f 74 goat snp11313-scaffold1409-232485 NW_017214269.1 24061 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781989 Affx-122963164 AX-385269069 1 100432606 TATAGAACAATTCAACTAAACTTTCTATCATTCTA[C/T]GTGGGTCTGACAATTTTAATGAATAGCTGGGCAAA Y 2 1 2 1 101000 r 74 goat snp11312-scaffold1409-190769 1 101808411 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803264 Affx-122959801 AX-385290113 1 100507100 GTGTTTCTTCTATTCCAATCACAAACACAAAACAG[A/G]ACTCAAATTCAATCATGCCAAAAGCTCTGGGATTT R 2 1 2 1 201000 r 74 goat snp11311-scaffold1409-116275 1 101881767 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377977 Affx-122977617 AX-123248336 1 100554270 GATAAAAATAATTACATAATTTGCCCAAAGTCATG[C/T]ACTTAATAGTCACAGTAATGCTTGTTGATATTCAG Y 2 1 2 1 101000 r 74 goat snp11310-scaffold1409-69105 1 101928176 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377988 Affx-122977608 AX-123248347 1 100625726 AAGTTAATTAATATCATTTAACAAATGAGACAACT[G/T]AAGGCCATTTGAGAAGAGCTAGAGATGGAGCCAGG K 2 1 2 1 101000 f 74 goat snp16781-scaffold1758-299848 1 102000881 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801466 Affx-122946686 AX-385288375 1 100668969 TTGCCACAATAGTAACATTTTCTGTGCCTGCTAGA[C/T]AATTTGCATTAAAACCTTAATATGATCAGATTTTG Y 2 1 2 1 101000 f 74 goat snp16780-scaffold1758-256605 1 102044394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779375 Affx-122950895 AX-385266479 1 100720126 CTTTCCCATTCTATATCCATACAGTTAAAATAATA[C/T]GATCATCTTAAGTCATATTTAGTAAACTTTCTTTT Y 2 1 2 1 101000 f 74 goat snp16779-scaffold1758-205448 1 102094214 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794455 Affx-122934815 AX-385281418 1 100752309 TGAATAAAGTCTAAATCTGTTTTCATCTCAGCCAT[A/C]GGACCTACATTAGAGTCATACAAAATAGTTCCTTT M 2 1 2 1 101000 f 74 goat snp16778-scaffold1758-173265 1 102127057 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396103 Affx-122963420 AX-123266458 1 100780930 ATGGAGCAGTGTAAAGGAATATCACAAAGTTAGGA[A/G]AGAAAGAGAAAACGTGATTAATCACTCTGCTATTT R 2 1 2 1 101000 f 74 goat snp16777-scaffold1758-144644 NW_017197173.1 3959 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411470 Affx-122951802 AX-123281820 1 100822114 TCTTGATTTTCACTAAACACATAATAAATAGATTT[C/T]GTTATGAATTAAAAAACAAGATAACTCCATCTGAG Y 2 1 2 1 303000 r 74 goat snp16776-scaffold1758-103460 1 102199061 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768149 Affx-122960279 AX-385255348 1 100858117 TGATAGTTTAGGTCAGGTGAAAATTGAGATTTGAT[C/T]ATTGAATTTACCAGTAAAAAACTTGTAGGAACTTT Y 2 1 2 1 101000 f 74 goat snp16775-scaffold1758-67457 1 102235149 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453193 Affx-122920454 AX-123323526 1 100894370 AACAGGCCTCATTTCTCTCTTCACTAACCTCCTTT[A/G]TAATTCTCATCAGTATTTTCACTGTTCTTGCAATT R 2 1 2 1 101000 f 74 goat snp16774-scaffold1758-31204 1 102271564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801074 Affx-122961050 AX-385287988 1 100929642 TAAAATTTTAACCATCTGGTACATATAATTCCATG[C/T]ATGTACACAGACTCATCTATTTATCCTAGCTCAAA Y 2 1 2 1 101000 r 74 goat snp23565-scaffold2379-3969 1 102511470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387466 Affx-122970361 AX-123257824 1 100982960 AGAATCAGCTCCATAACCAAGGCCTCCCACCCCCA[C/T]CCCTTAGGTTCCTTAAGCCCAGACACCTAGGACAA Y 2 1 2 1 201000 r 74 goat snp23566-scaffold2379-57287 1 102566207 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799490 Affx-122974613 AX-385286420 1 101013357 TAACTCTGTCTGAAAATGTGAGGCCTCAGTCCTTG[A/G]CTCTTTGAATGTGCTTTCTGGCCACTCCTTACAAA R 2 1 2 1 101000 f 74 goat snp23567-scaffold2379-87684 1 102596487 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792326 Affx-122970325 AX-385279308 1 101045550 TATATTGCAAAAATTGTACAAGTCATCAAAGCAAG[C/T]GAGAAATTTCTCATGTATTAATGGAAAATCTTACC Y 2 1 2 1 201000 r 74 goat snp23568-scaffold2379-119877 1 102628257 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444883 Affx-122926269 AX-123315220 1 101088190 TTAACTGGGAAAGCATTCATTTATTTAGGCTAAAG[G/T]AAAAATCAAGTCTCTATTGGTAAATGGTTGGATGG K 2 1 2 1 201000 r 74 goat snp23569-scaffold2379-162517 1 102670601 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378855 Affx-122976523 AX-123249214 1 101120147 TGTCTCCTAATTTAGAGTTTTCAAAACATAGGAAA[G/T]ATTTATTATTTTCTGTTTGGCTAGAGAACAAAAAG K 2 1 2 1 103000 f 74 goat snp23570-scaffold2379-194474 1 102704110 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440966 Affx-122928991 AX-123311303 1 101150938 CCTTTCCTCCCCACCTTCCTCACTTCTCTGCCAGT[A/G]TCTCCTGCACTTGAAGCATGGTCTACCTGCACTGA R 2 1 2 1 101000 r 74 goat snp23571-scaffold2379-225265 1 102734131 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384003 Affx-122972914 AX-123254361 1 101176005 TATGCATCTGTCTTTGTCAATTTTGCCCAAGAGAG[C/T]CACCTACTAGAAATAAGATATTGCTTTAGTAATAG Y 2 1 2 1 101000 f 74 goat snp6965-scaffold1257-239 1 104174879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422086 Affx-122943587 AX-123292433 1 101266392 CTAGTCTGTAGCTTGACCCAGTTCGTGTCCAGAAG[A/C]CTTCTCCTGTGACTGTGTGCTTCTTTTTACTTCAA M 2 1 2 1 101000 f 74 goat snp6966-scaffold1257-90626 1 104084475 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786601 Affx-122920958 AX-385273633 1 101318645 ATATATGAAGACAAATTCTACAAGCTTTCACTGCT[A/C]TGTCCTTCATCTATGATTATATGTCCTATGTTCTT M 2 1 2 1 101000 r 74 goat snp6967-scaffold1257-142879 1 104031749 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793671 Affx-122944697 AX-186719019 1 101371482 AGTAATTCATTAGTATTACTAATGTACTGTCCTGG[C/T]AGGAGAGCATACAGTAGGCTTTTAATAAATGTTGA Y 2 1 2 1 201000 r 74 goat snp6968-scaffold1257-195716 1 103978156 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411589 Affx-122951615 AX-123281939 1 101400148 ACAGAGAACTGAGCAAAGAAGTGTTTGTTAAAGGA[A/G]CAAATAAAGAAATGAATACTATTTCAGTTTTTCTA R 2 1 2 1 101000 f 74 goat snp6969-scaffold1257-224382 1 103949486 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421442 Affx-122943948 AX-123291789 1 101446612 AAGCCCAGTAGAAACAGGTTCAAGAAGCACTAAAA[C/T]AGTGATCCATCAGACTACAAAATGGGAGAGGCTTA Y 2 1 2 1 101000 f 74 goat snp6970-scaffold1257-270846 1 103907140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439927 Affx-122930009 AX-123310264 1 101515524 TGGTAATCATAATAAAATATTATTGTGATAGGGAA[G/T]AACAAGTCTGACCCCATATTAGACCCTTTCCTTTT K 2 1 2 1 103000 r 74 goat snp6971-scaffold1257-339758 1 103840418 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384277 Affx-122972304 AX-123254635 1 101558427 GAAGTATAGCAGTGAGGATGATCTTGACTGGATCT[A/C]GGTGTAACTTTCAGGGTTGTCATCTGTTTGTTTCT M 2 1 2 1 101000 f 74 goat snp6972-scaffold1257-382661 1 103797477 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421771 Affx-122944352 AX-123292118 1 101597885 AGGCAGCTAGTGATAATGTAGGAGGTGGGGTGCCT[A/G]CTGGAAAGTCCACCATAGTGAGTAGAAAAAAAGAT R 2 1 2 1 101000 r 74 goat snp6973-scaffold1257-422119 1 103757944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276349 Affx-1111835372 AX-519549881 1 101629228 TTGATATTTACTAACTTGAAAATGAGAGCTTGACA[A/C]ATATTTTTTTCTTTTGTCCTTAGAAAGGTGTATTT M 2 1 2 1 201000 f 74 goat Random2.2K-104 1 101629228 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437926 Affx-122931640 AX-123308264 1 101635571 GCTGTCAATCACTCTGTACCACTTAATTTGTGGCA[A/G]AAATGACTTGACCTTCATTTTCAGAAAAATTGTCA R 2 1 2 1 101000 f 74 goat snp6974-scaffold1257-459805 1 103720380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413557 Affx-122950599 AX-123283906 1 101668450 TTGCATTGCAGAAATAAATCCCCTTCAGCTATGAT[A/G]TATAATCTGACCAATTAACTGTTGAGTTAGTTTGC R 2 1 2 1 201000 r 74 goat snp6975-scaffold1257-492684 1 103686836 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794317 Affx-122926406 AX-385281281 1 101714367 TTGCTAGTGAACAATTTATTATACCTGAAAAATCT[A/G]TTCTTGATCAATAATGTATTTTCTCAAACACACTG R 2 1 2 1 101000 r 74 goat snp6976-scaffold1257-538601 1 103640088 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790660 Affx-122975211 AX-385277662 1 101757470 AAGATACCTTAAGTAGTTAGTAGAGCTTTGCTGAA[C/T]GAAAACCTCAGTAAAATGCAAACGTAACAGGTGTG Y 2 1 2 1 101000 r 74 goat snp6977-scaffold1257-581704 1 103597193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769451 Affx-122950470 AX-385256621 1 101813056 TATTTTCATGTAATTATTTTTCCCATCCATATTAC[A/G]TTTAATGTGCTCATCTGTTTTCACAAGAAAGTAAG R 2 1 2 1 202000 f 74 goat snp6978-scaffold1257-637290 1 103541242 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800099 Affx-122957660 AX-385287022 1 101842821 AACCCTATCAGTTTCTCACAGTGAATGTAGAGCAA[A/G]TAAATCTCTCATGCTTTTGACAACACAAATAAAGC R 2 1 2 1 101000 f 74 goat snp6979-scaffold1257-667055 1 103511221 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425625 Affx-122940902 AX-123295971 1 101872057 TAAACTCAGATGCACAGTTAGTCAGTGTTGTAAAA[C/T]GGACACTAGGTCAACTCAACTATAAATTCTGAGGA Y 2 1 2 1 101000 f 74 goat snp6980-scaffold1257-696291 1 103481804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799631 Affx-122977588 AX-385286560 1 101910090 TATGTTGTGGTTTCTGTTTCAGCAATACAGCTTTT[C/T]TAGAGCCAAATTTTTGTAGCTACATATTGTTAAAT Y 2 1 2 1 101000 f 74 goat snp6981-scaffold1257-734324 1 103443466 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272455 Affx-1111836713 AX-519546180 1 101941444 TGAAAGTGAATTCGCTCCGTCATGCCCGACTCTTT[A/G]AGACCTCATGGACTGTAGCTTACCAGGCTCCTCTG R 2 1 2 1 103000 f 74 goat 1_101941444_AF-PAKI 1 101941444 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437842 Affx-122932092 AX-123308180 1 101945943 CATATTGTTTCTGACCTTACTAATTTTCAAAAGTA[A/G]CAGAAAAAATGCAAATAGAGAAAAGAACAGTCCCT R 2 1 2 1 202000 f 74 goat snp6982-scaffold1257-770177 1 103407638 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799862 Affx-122977085 AX-385286788 1 101987942 TGAATTTCAATTAATGATTTCTGTTGGTTTCAATC[A/G]TTCTTATTAAATTGATCTCAAATACTTATGATGGT R 2 1 2 1 102000 f 74 goat snp6983-scaffold1257-812176 1 103365326 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418269 Affx-122947013 AX-123288617 1 102063360 CAAGTAGAAATCCTGAATTTTTTGGTTTTCTTTTA[C/T]GGAATAATAAAGGTTTGTTTGTTGTTATTTGATTT Y 2 1 2 1 303000 r 74 goat snp6984-scaffold1257-887594 1 103288682 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400728 Affx-122959911 AX-123271083 1 102100621 GGAACAGCAACAGGGTTTGGTGAGAGAAAAAGAAG[C/T]AATTTTACTGGAGAGAAACTTGGCAGACATCACAC Y 2 1 2 1 101000 f 74 goat snp6985-scaffold1257-924855 1 103251264 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402188 Affx-122959177 AX-123272541 1 102141402 TTGATCTATTCAAGATAAGTGGATTCAGCACCTAA[C/T]GTTGAATTGGCAGACATGGCATTGATAAATCTGAC Y 2 1 2 1 101000 r 74 goat snp6986-scaffold1257-965636 1 103210408 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399681 Affx-122960498 AX-123270036 1 102184497 CCTTCTTATTCCAGCACCTTAGACCACTCGGCCAC[A/G]CTACCTCCCATTATAGCTTTCTGTTTTAGAAAACA R 2 1 2 1 201000 r 74 goat snp6987-scaffold1257-1008731 1 103166950 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798317 Affx-122939953 AX-385285252 1 102286494 ATCAACTGTATTTATATTGTAGTAAATATTCTGAT[A/G]TCTCCAACTCTAAGCCATAGTCATGTGTATCTTTC R 2 1 2 1 101000 r 74 goat snp6988-scaffold1257-1110728 1 103064675 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417375 Affx-122947705 AX-123287723 1 102319345 AAGGCAGACTGAGCATGGATCAACAGGGAAGCCAA[C/T]AAGAAAATATTTAAATAAGGAAGGAATGACAGACT Y 2 1 2 1 101000 f 74 goat snp6989-scaffold1257-1143579 1 103032015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798038 Affx-122952376 AX-385284974 1 102354075 AGCCTTTTACACTTTTTCAGTTCAAGTGTTCTCCA[A/G]AATTGCTGAATTCAGTGAAAGCAGCCTAATGTTAG R 2 1 2 1 201000 r 74 goat snp6990-scaffold1257-1178309 1 102996619 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442456 Affx-122927951 AX-123312793 1 102389546 AGAGACAGGTCTGTATGGAGAGTATTACCTTAAAC[G/T]AGTGGGAAGGCATAGCTAGCCTTCAATAATTTCTC K 2 1 2 1 101000 f 74 goat snp6991-scaffold1257-1213780 1 102961211 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403157 Affx-122958093 AX-123273510 1 102435910 TTCCAAATATTAGACATATATAGAGAGATGCAAAA[C/T]GCAATTCAACCACAGTATTAAACCTTGGCCATCAC Y 2 1 2 1 101000 r 74 goat snp6992-scaffold1257-1260144 1 102914890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387883 Affx-122969625 AX-123258241 1 102493999 CTGTTTGGCACTTTCTATTTATTCCTTATGCTACA[G/T]CCAGAGTGATCTTTCACAAAACAAATATTATTCTC K 2 1 2 1 101000 f 74 goat snp6993-scaffold1257-1318233 NW_017192230.1 13525 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404793 Affx-122956669 AX-123275145 1 102526031 TGTTCAAGAGTTCTCAATTAATATCTGAATCTATG[C/T]ATTATGTCTCATTTGGCCTCCAAGGTATTCCAGGG Y 2 1 2 1 101000 r 74 goat snp6994-scaffold1257-1350265 1 102819448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796654 Affx-122973434 AX-385283600 1 102569430 ATTATCAACAATTATAGTACTTGTCCCTATTATCC[C/T]TATGATGAATACACAAGCATTACAGCATTGCTTGT Y 2 1 2 1 101000 r 74 goat snp6995-scaffold1257-1393664 1 102775573 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393022 Affx-122965644 AX-123263379 1 102610519 CTCCTTCTGTGCTCACTCTACAATCTTTGTCTTGG[C/T]AATCTCATGATCTCTTTAATACCAGTGTGTTTAAT Y 2 1 2 1 101000 r 74 goat snp46637-scaffold65-82482 1 104194587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442749 Affx-122927840 AX-123313086 1 102697159 TGTTCTATTTTCTCTCGTAGTGGGAAAGCATCGCC[A/G]TTCAAGTCACATAAACATATGTGCAAAGCTGGGTT R 2 1 2 1 101000 f 74 goat snp46639-scaffold65-169122 1 104282287 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424194 Affx-122942512 AX-123294540 1 102774805 AAGCTATTAAAATGTTACACTGTCATTTGTTTCCA[A/G]ATATCTTTAACACCTCCTTTCATACTTCAGTGACA R 2 1 2 1 101000 r 74 goat snp46640-scaffold65-246768 1 104363174 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428178 Affx-122939028 AX-123298521 1 102803378 GTGTTCTTCAAGAGAATTAATAGGCCAGGCATAGC[C/T]AGAGGAAACTCTTCAGATAAAGAGACATTTAAAAC Y 2 1 2 1 101000 f 74 goat snp46641-scaffold65-275341 1 104391750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379979 Affx-122975624 AX-123250337 1 102845039 GTGAATCTCTATGTGTTACATCTGGTTTATGTGGG[C/T]AAAACTTCAGGATAACTCAAAAGATGATTGTGACC Y 2 1 2 1 101000 f 74 goat snp46642-scaffold65-317002 1 104433935 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394343 Affx-122964662 AX-123264698 1 102875009 ATTTTCCTCAGTTATATAGGTGAGAAGGGGGAGGC[A/G]TTAAACATCATAATGAATACTAAGGACTATAAGTT R 2 1 2 1 201000 r 74 goat snp46643-scaffold65-346972 1 104464784 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787176 Affx-122941687 AX-385274202 1 102915602 TTCTTAATAGCCTTTCATCTCACTTACAAAAGAAA[C/T]GTCTATCACTCAATGAATTCAGATCATATCATTCT Y 2 1 2 1 101000 r 74 goat snp46644-scaffold65-387565 1 104506940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453291 Affx-122920375 AX-123323624 1 102949121 TATGGTATTTTCTACACAAAACAAGTACTATGTTC[G/T]AGGTAGAAGTTAATTGAGATCATATTTGGCTTATT K 2 1 2 1 101000 r 74 goat snp46645-scaffold65-421084 1 104541287 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276384 Affx-1111835390 AX-519549912 1 102958686 CTACAGTTTTGTCTTTTCGAAAATGCCATGCAAAC[A/G]AAATGATTTGTAAATATATGCCTTTTCAGACAAGC R 2 1 2 1 101000 f 74 goat Random2.2K-107 1 102958686 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778136 Affx-122952574 AX-385265251 1 103031962 CTATATTCTGCGTGTTCTTATGCATTACAAAATAT[A/G]TCCACATCAAGAACTTTCATAGAATTTGTGCCACT R 2 1 2 1 101000 r 74 goat snp46647-scaffold65-503925 1 104625709 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788710 Affx-122928336 AX-385275726 1 103062902 TTTCCAGACCAAAGTTAAAAGAAAAGACAAGTTAA[C/T]GGTAACTGAAGTGTCTAAATTCGTGGAAATTTAAA Y 2 1 2 1 101000 f 74 goat snp46648-scaffold65-534865 1 104657505 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453107 Affx-122920027 AX-123323440 1 103093925 AGAATCTTGAAAATAGGTTTAAGTTTATTATAATT[G/T]TGCATTTGCTGCAAGAAAGGAGGATAGTGTTCATG K 2 1 2 1 202000 f 74 goat snp46649-scaffold65-565888 1 104689293 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383661 Affx-122972516 AX-123254019 1 103133040 AGTGTTGTGGGTGTTACATTCATGATGGCCCACAG[A/C]TGAGAGAGAGAGAGTTAAGAGATAGAAATAGAGGT M 2 1 2 1 101000 f 74 goat snp46650-scaffold65-605003 1 104729579 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429430 Affx-122938510 AX-123299772 1 103166746 AATGCAGCAATTTGGATTAACCCCATACCCATTAC[A/G]CTGAGTAAAATAAATAAGACTAGAAAATTTACATC R 2 1 2 1 201000 r 74 goat snp46651-scaffold65-638709 1 104762755 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794304 Affx-122963229 AX-385281268 1 103220400 GCTCAAGGCCACATACTTAATTAGTAGCAAAGATG[C/T]ATCTAGAATGAAGTTTCCTGACTTCCAGTCCATTT Y 2 1 2 1 101000 r 74 goat snp46652-scaffold65-692363 1 104816114 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404202 Affx-122957672 AX-123274554 1 103250664 AGTGGAAGAAATACCACTTGATGGATAAGGAAAAT[A/G]TGTTCTCTAAATACAATGGAGTCACTTGACTGCCA R 2 1 2 1 101000 r 74 goat snp46653-scaffold65-722627 1 104846416 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423087 Affx-122942930 AX-123293433 1 103287344 ACAGTTTCCAGAAAGCATATTATCCATAAATACTT[A/C]ATGAATTGATTTACTATGATTTTAAGAACACTGGG M 2 1 2 1 101000 r 74 goat snp46654-scaffold65-759307 1 104883367 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786681 Affx-122974895 AX-385273714 1 103352668 GATACTATAAATAAATTTAACTACTTTCCAGTTAC[A/C]TAAGGAATTTAAAAGCTTAAAAGTTAGGGTAATGT M 2 1 2 1 201000 r 74 goat snp46655-scaffold65-824631 1 104949406 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775272 Affx-122946893 AX-385262403 1 103398431 TCTAGGTGATTCATGGACACATCAGAGTACGAGAA[C/T]CACTACTCTACAGAAAAAATAACCCCCATTTAAGT Y 2 1 2 1 201000 r 74 goat snp46656-scaffold65-870394 1 104992417 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443652 Affx-122927201 AX-123313989 1 103438369 ACCATTCACAAAATAAACTGTCAAAAAATTTCTAG[C/T]AGCTTTTCCCTCCTCCCAAATCTATCAAAAATAAA Y 2 1 2 1 101000 r 74 goat snp46657-scaffold65-910332 1 105032208 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428446 Affx-122938812 AX-123298789 1 103467000 GAGCACATAGAAAATGAAAAGCCAAAACTTCACAG[C/T]AGCTATTTTTGTGTGTGCTAAGTTGCTTTGGTTGT Y 2 1 2 1 201000 f 74 goat snp46658-scaffold65-938963 1 105061986 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416768 Affx-122948177 AX-123287116 1 103508963 TGGAAGCCACCAATTCAAATATGGAAATCAACACT[A/G]CACACTGAGATTATTTTGTTCTAAGTTCACCATCA R 2 1 2 1 101000 f 74 goat snp46659-scaffold65-980926 1 105104279 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788772 Affx-122972269 AX-385275787 1 103549287 TGATGTCTTAGATCAGCACTTTTGAAACCATTTTA[A/G]CAGTAAAGCCATTTTATCAAAAAATCTCCTACACA R 2 1 2 1 201000 r 74 goat snp46660-scaffold65-1021250 1 105142293 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441616 Affx-122928648 AX-123311953 1 103580318 ATGACCACCAACTAAACTTAATAGACTAATCTGCC[A/G]TGTGATTTGAGGGTGCAGCAGAAAAACAAATAAGA R 2 1 2 1 101000 f 74 goat snp46661-scaffold65-1052281 1 105174455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450514 Affx-122922501 AX-123320848 1 103632606 AACTGTAAAACTTTATGTTACAAATAGATTCATAA[C/T]GGTTTTAAGATAAACCTCTTGGGAAGAAAAAATGT Y 2 1 2 1 101000 r 74 goat snp46662-scaffold65-1104569 1 105228884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436923 Affx-122933197 AX-123307261 1 103664741 GTTTTATCATAATTTTTTCTCACCAATTTTATTTC[G/T]TATAGGACATCTAGATTGCTTCATACGGTTCACCA K 2 1 2 1 201000 f 74 goat snp46663-scaffold65-1136704 1 105261369 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431891 Affx-122936012 AX-123302232 1 103718868 CACTATAATTTTTCCAGGAATCAGAGATCAAGATG[C/T]GATCCTGAAAGCTTCCAGAGGTACATTTAACAAGA Y 2 1 2 1 201000 r 74 goat snp46664-scaffold65-1190831 1 105316122 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276393 Affx-1111835395 AX-519549921 1 103732995 ATGCTTAACAAGATATAAGTAAATTGAGCACAGCT[A/G]TATATGTGAAAAAGAAAATATACCATGAAGAAGTA R 2 1 2 1 101000 f 74 goat Random2.2K-108 1 103732995 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384444 Affx-122973100 AX-123254802 1 103769606 CGAGAGTGAAGTGAATAAAGATCCAAGAAAATGCA[G/T]CCCGTGTCTTTGTGGTAGCTTCTCTGTACCTTGTC K 2 1 2 1 201000 f 74 goat snp46665-scaffold65-1241569 1 105366950 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429563 Affx-122937815 AX-123299905 1 103801231 CAAGTTTAGATAAGTTATGTTTTTCTTTTTTAAAC[G/T]AAGTTGCTAAATATTTTTTCAAAGGGACTTCTCTT K 2 1 2 1 303000 f 74 goat snp46666-scaffold65-1273194 1 105397841 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769090 Affx-122952408 AX-385256265 1 103830056 TGTCTCCTTTATCTCCTTTGGTACCATTGGCACTC[A/G]TGTCCCCCTTCAAGCCTTTTTGTCCTTTCACTCCC R 2 1 2 1 101000 f 74 goat snp46667-scaffold65-1302019 1 105426753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422118 Affx-122943559 AX-123292465 1 103862840 CTATACCACAACTTTCCACGCTTCAAAACATCAGT[A/G]CAAAAATTGGATATAAGACAGCAGAGGAAAGACTG R 2 1 2 1 101000 r 74 goat snp46668-scaffold65-1334803 1 105460312 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426315 Affx-122940285 AX-123296661 1 103907765 CAGAAGGCCTATGGGACTGTAGCCTAGTCTATAAG[C/T]AAAGATGAATATAAAATCTGAATTATAAAACAATT Y 2 1 2 1 101000 f 74 goat snp46669-scaffold65-1379728 1 105505645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769640 Affx-122951639 AX-385256810 1 103937426 GTTCTAACTCTTGAGGCAGGCATTGTGGAAGGAAT[A/G]TACTCTCCTTACAGGAAATGGCTTTGTGCTCTCTT R 2 1 2 1 101000 f 74 goat snp46670-scaffold65-1409389 1 105536119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441696 Affx-122929165 AX-123312033 1 103968062 GGAGGTCATAATTTTACTTACTAACCATGAGGAAA[C/T]GCTACCAAATGTTAAAGTGGAAAAATACCTTATAA Y 2 1 2 1 101000 f 74 goat snp46671-scaffold65-1440025 1 105567454 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385282 Affx-122972065 AX-123255640 1 104004062 TGAAGACCTGGGGATGAAAAGAGAAAATCAGAATC[A/G]TTATGATGCACATGGCACATAGTTGCCAGTAAAGG R 2 1 2 1 101000 f 74 goat snp46672-scaffold65-1476025 1 105603413 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775061 Affx-122964667 AX-385262193 1 104052633 GACATAATGATGACAATGGAATTCATTAAATTTAG[C/T]GATTGAAATATGTACAGGATGTTACAGGAGCACTT Y 2 1 2 1 201000 f 74 goat snp46673-scaffold65-1524596 1 105651989 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384902 Affx-122972348 AX-123255260 1 104087392 TTCCCAAGATCAGCCAGTGGTCCATACAGCTCAGC[A/G]TGGAAGATGCCTCAAGACACTGGTCAGTTCAAGGC R 2 1 2 1 201000 r 74 goat snp46674-scaffold65-1559355 1 105686917 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320800271 Affx-122942419 AX-385287194 1 104120191 CAGACAGTGTAAATCTAATAGTTTTCACCACAATC[A/G]CCACATGTTAAAAGCAAATAGCATACAAACACAAA R 2 1 2 1 101000 r 74 goat snp46675-scaffold65-1592154 1 105719714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440219 Affx-122930686 AX-123310556 1 104177654 GGACCAAATGAGAGTGACACCTGGCAAACAGCTGG[C/T]GACTGAACCTCCTATTTTATATATCCTGGTTATTA Y 2 1 2 1 101000 r 74 goat snp46676-scaffold65-1649617 1 105777647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389094 Affx-122968580 AX-123259452 1 104232794 CTTCACCCCATCTGGAAGATAACTATCAATCTGAA[C/T]TTCTCTAATCAGTTTGCTCCTGTTTTCTAGCTGAA Y 2 1 2 1 201000 r 74 goat snp46677-scaffold65-1704757 1 105833294 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378183 Affx-122976949 AX-123248542 1 104262462 TTGAGTCCTGGAAATTTGATGAAAAAGTTTTGACT[A/C]TGGGGTACAGTAGGGATCAAAAACTGAAATGCCTT M 2 1 2 1 201000 f 74 goat snp46678-scaffold65-1734425 1 105863983 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428097 Affx-122939090 AX-123298440 1 104309467 TTTGTGTACTTTATAAGTCCTGATCTGTTTCAGAA[C/T]GTTGTTATTTCATCTTCATTTCACCTGAACTCTCT Y 2 1 2 1 201000 f 74 goat snp46679-scaffold65-1781430 1 105911209 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447057 Affx-122924517 AX-123317393 1 104350215 ACGTTGGCCATGAAGAAGGGCAAATTCAGTGGCCA[C/T]GCATTTGATGGGAAACATTACAAAGTCCAGTCCCA Y 2 1 2 1 101000 r 74 goat snp46680-scaffold65-1822178 1 105951949 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783978 Affx-122961953 AX-385271032 1 104420774 GGAGAAGGTGGAGGCAGGTTGGAAATGGAAAACCA[C/T]AGCTGTATACAAACACTACTATAGTAAATGGATTT Y 2 1 2 1 101000 f 74 goat snp46681-scaffold65-1892737 1 106022999 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400505 Affx-122961278 AX-123270860 1 104450543 TCAATTCTGTAAATGCTGAGTAGAAAAGAGCTAAA[C/T]TTTAGAACAGTAACTCAGGGATGATGGCTACGTAT Y 2 1 2 1 101000 f 74 goat snp46682-scaffold65-1922506 1 106052836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272459 Affx-1111836715 AX-519546184 1 104453302 GTACCAGCAAAGTGCAGCCGCTGCTCCTTCACTTG[A/G]ACAAGGGGTATCTCCTCACCACCGCCCCTCCTCAC R 2 1 2 1 103000 f 74 goat 1_104453302_AF-PAKI 1 104453302 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38404110 Affx-122957115 AX-123274462 1 104488780 CATAACTAAGCACTGTGGGAATACTCAATTGACTG[C/T]GCCTAAGACAATAATTTTTTTCATAGGGCAGAAAT Y 2 1 2 1 101000 f 74 goat snp46683-scaffold65-1960743 1 106092190 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770907 Affx-122969619 AX-385258070 1 104549729 CCTACAAATGCCCTCTGTGGCACCCAGACAGGTAT[A/G]TCCTAAAAATACCTTTACCTTGTACACTTAACACC R 2 1 2 1 101000 f 74 goat snp46684-scaffold65-2021692 1 106152827 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412510 Affx-122951362 AX-123282859 1 104611949 GGGTGCTGAAAGGGTAATGTGAATGGACTGAGCAA[C/T]GTAAACGTCAGGCAACAGCTGGTGTGGTAGACTGC Y 2 1 2 1 101000 f 74 goat snp46685-scaffold65-2083912 1 106215675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802631 Affx-122971493 AX-385289532 1 104659384 CTTAACCTCTCAGAGCCTTAATTTCTACTTATGTA[C/T]GTAGATAACACAGTACCTACCTCAAAAAAGTGTCA Y 2 1 2 1 101000 f 74 goat snp46686-scaffold65-2131347 1 106262965 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376171 Affx-122978836 AX-123246530 1 104750455 CTTACGTGTGGTTTTCTTTTTGAAATCTAGGAAAC[A/C]GGAGGACTAGGTTTAGTAAGTGCTTAATCATTTCT M 2 1 2 1 101000 r 74 goat snp46687-scaffold65-2222418 1 106353702 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772291 Affx-122978986 AX-385259446 1 104783969 AAGTTCAAAGTATTATGAAATCAAATATAAAATAA[C/T]ATGGTCTTATTCATTAGCCGTATAACAAAGATTTA Y 2 1 2 1 303000 f 74 goat snp46688-scaffold65-2255932 1 106386642 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375447 Affx-122979170 AX-123245806 1 104830876 TCATGAATGACCAGACATTTCTCTTCTGAGTAGGA[C/T]AGAAGAATATTTCTGAGCTCTCATCCAATGACCTG Y 2 1 2 1 101000 f 74 goat snp46689-scaffold65-2302839 1 106428851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404657 Affx-122957300 AX-123275009 1 104875301 CCTACCTTTCTGTTCCTGGCTTCTCATGTTCTTCA[A/G]CAGATCCTGCACGACATCGTTTATGCATCTCTGTT R 2 1 2 1 201000 r 74 goat snp46690-scaffold65-2347264 1 106473927 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772269 Affx-122934069 AX-385259424 1 104911625 TAGTACCATCTGCAGTCATCATTCTTCAGAAGATA[G/T]CCATTTTGCATATTCTCTTCAGTTTCTTCCCTTTT K 2 1 2 1 101000 r 74 goat snp46691-scaffold65-2383588 1 106510449 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385883 Affx-122971596 AX-123256241 1 104946320 TTCCTTGCATACCTGGTTCTCACACACTTGTACAC[A/G]TGAGGACCTATGTGTCCTGTTGTGATCCCCTGCCT R 2 1 2 1 101000 f 74 goat snp46692-scaffold65-2418283 1 106545999 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407211 Affx-122955391 AX-123277562 1 104979465 CAAAGCCATGTATTTAGTATGAGAGACCCATATAT[A/G]TATTTTAAGAGTTCACCTGTTGTGTTACCTTTAAA R 2 1 2 1 101000 r 74 goat snp46693-scaffold65-2451428 1 106579185 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427391 Affx-122940080 AX-123297734 1 105014852 ACTTGGTTAAAAAAAAGTTAGCACTTATGTGGGAT[A/G]TATGAAAAGAGAAAGAGACTGAGATCAAGCATGGC R 2 1 2 1 201000 f 74 goat snp46694-scaffold65-2486815 1 106614605 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450345 Affx-122922115 AX-123320680 1 105063445 AATTAATTAAAAGTGGGGAAGAGGGATTATGTTTA[A/G]TAACCTGGAAAGCTATATATAGTAATTTATTTAGT R 2 1 2 1 101000 f 74 goat snp46695-scaffold65-2535408 1 106663203 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792811 Affx-122958313 AX-385279789 1 105119453 CTGTCAGAATCCAATTATCTACCTGCCTATTGAGC[A/G]TTCCCATTGGATGTCTCATATGTTTGAGTTCAAAT R 2 1 2 1 101000 f 74 goat snp46696-scaffold65-2591416 1 106720153 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382366 Affx-122973864 AX-123252724 1 105155775 AAGCTGGTACAAGAAAAACATCTCGATTCATATCA[C/T]GTGTATTTTCACAAGATTTGTTGTACAGTTCAAGA Y 2 1 2 1 101000 f 74 goat snp46697-scaffold65-2627738 1 106757188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771980 Affx-122929067 AX-385259136 1 105208609 GGAAGGGAGTTCTCTAAAGATGAATTGCACTTAAC[A/G]TCCTTGTTTTTTCCACAGCCAAACCAATGCGATTT R 2 1 2 1 101000 f 74 goat snp46698-scaffold65-2680572 1 106810286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451325 Affx-122921276 AX-123321658 1 105262165 AATATATTATCTTCTGAGTCTAAAAGGGCTCAGAA[C/T]AGAGATGTGCAGATTCATCTTGAAGACACTGCCTG Y 2 1 2 1 101000 r 74 goat snp46699-scaffold65-2734128 1 106864329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434414 Affx-122934676 AX-123304755 1 105305766 GGAGGAGGATGAGCAACTGTCCCTTTTTGCCTGAG[A/G]AGTTTCCTCAGCACATGGCACTTTCCGTGCTAAAG R 2 1 2 1 101000 r 74 goat snp46700-scaffold65-2777729 1 106906595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434277 Affx-122934778 AX-123304618 1 105343434 CCTTCCTGTGTTAACAGACCGAGATACCAACATGA[C/T]GTTCAAAGTCTTCCATGTTAAAAGTACTGGGGCCT Y 2 1 2 1 101000 f 74 goat snp46701-scaffold65-2815397 1 106944354 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430175 Affx-122937364 AX-123300516 1 105390780 CAATCTCTTGAGTGATAAGCTTCCTTATAAACTGC[A/G]CATCTACCAGTAATGCAGATATGCCTTCAACAAGG R 2 1 2 1 101000 f 74 goat snp46702-scaffold65-2862743 1 106991831 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387773 Affx-122969715 AX-123258131 1 105420634 GTCTGCCATACTGTCTTAAGCTTCCTGTTCTTCAT[C/T]TGCAAATGAGGATAACCATATCTACCACATAAGGT Y 2 1 2 1 201000 r 74 goat snp46703-scaffold65-2892597 1 107021537 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452192 Affx-122920825 AX-123322525 1 105498797 TTGGCAGACTGCTACGTGCAAAAAGCTGCTTGACA[C/T]GTGTCTTGCCTTGGATTTGATTTCTGGAAGGTCTG Y 2 1 2 1 101000 f 74 goat snp46704-scaffold65-2970760 1 107099865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771625 Affx-122919605 AX-385258783 1 105535467 GAAGCAGTAATTGTACCAGTCAATAGGTTTTCTAA[C/T]GTGAATTCTTGACCAGCTTCAATGCTGTTAAGAAC Y 2 1 2 1 101000 r 74 goat snp46705-scaffold65-3007430 1 107136658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775852 Affx-122970025 AX-385262983 1 105583841 TCGTATTTTTATTTCTAAGACAAAACCTTGAGAAC[A/G]GAGCCACTTGGAACAGTAGAAAGAACAGCATCCTT R 2 1 2 1 101000 r 74 goat snp46706-scaffold65-3055804 1 107185022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390949 Affx-122967061 AX-123261306 1 105628109 ACACAGAGCTAACCGCACAGGCAAAAGTCGAGAGG[C/T]GGGAATAGCTTAATTGGGTCTCCTCACAGAGGAAA Y 2 1 2 1 201000 r 74 goat snp46707-scaffold65-3100072 1 107229275 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432807 Affx-122935403 AX-123303148 1 105659998 CCAGCATTGTGTGTGTTAACAAGCCTTGCTGATGC[A/G]TGCTCTCTCTAGTTTGGGAAGCACTGCAGTAGGGA R 2 1 2 1 101000 f 74 goat snp46708-scaffold65-3131961 1 107261417 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382700 Affx-122973633 AX-123253058 1 105715197 AAGAGAAACGTCCACTGAACAAGTAAACTGCGGTA[C/T]GTCAGTGACTTAATGAAATATTCTTCAGGCACCAA Y 2 1 2 1 101000 f 74 goat snp46709-scaffold65-3187160 1 107316338 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426750 Affx-122939861 AX-123297096 1 105756410 ATATGGCTATCACTACATTAAATGTGTTAAAGACC[A/G]CCTCTGAATGCCTCAGCAAAAAATAATAAATGCAA R 2 1 2 1 101000 f 74 goat snp46710-scaffold65-3228373 1 107357625 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786384 Affx-122936500 AX-385273418 1 105830289 TTCTGGTTCACTTACTGATACTTTGACTAGTACTT[A/G]TTTGAAAAATGCTGACATGGAACACGAGAGAATAC R 2 1 2 1 101000 r 74 goat snp46711-scaffold65-3302252 1 107430715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411723 Affx-122951525 AX-123282073 1 105872247 AGTGGGAATTTCAGGCTCTCCGAGCACATGTCCCC[A/G]GGCTTCATTAACCTCCTACTACAACCAGGGCCAGT R 2 1 2 1 201000 r 74 goat snp46712-scaffold65-3344210 1 107473030 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395325 Affx-122964048 AX-123265680 1 105906409 TGTCTCTGTGTGTGTGTGAGTGAGAGATGGTGGTA[A/C]ATAGGGGTAGGGCTGTGCTTTAATTAAGAAATCAC M 2 1 2 1 103000 r 74 goat snp46713-scaffold65-3378372 1 107507496 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382247 Affx-122973953 AX-123252605 1 105937501 TAGCTCAGAATGTTGGCTCTTTATATCAGATTACT[A/G]TTAAAAATCCCCTTGAATAGGTAAGTGTTCCTGAG R 2 1 2 1 101000 r 74 goat snp46714-scaffold65-3409464 1 107538971 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399319 Affx-122961375 AX-123269674 1 105968071 AGCAATACCGTAGAGAAAGTTAGCTGTGCCCGGTT[C/T]TCATGTGTGAGCATGCAGCAAAGCAAACAGATGAG Y 2 1 2 1 101000 f 74 goat snp46715-scaffold65-3440034 1 107568920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396138 Affx-122963395 AX-123266493 1 106001784 AGGAAGAGCAAAGACCTGGTAAGAGAAGACCTTCT[A/G]TACTAAGGAGTTTGGACTTTGGAGTCTCATAAATT R 2 1 2 1 201000 f 74 goat snp46716-scaffold65-3473747 1 107602975 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417403 Affx-122947682 AX-123287751 1 106057794 CTGCAGAATAATGTCCCCATGACAGAAGCTACTGA[C/T]GCCCTAGAGAAGAAAAACCCAATGCAAAAAAGCAT Y 2 1 2 1 101000 r 74 goat snp46717-scaffold65-3529757 1 107657487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797818 Affx-122952854 AX-385284757 1 106114698 AGAGACAGTTTTAAGAAATCATCTTAGTGTAGAGC[A/G]TTTCCACAACAGGTTTACAAAAGAAACAACAAAGT R 2 1 2 1 101000 f 74 goat snp46718-scaffold65-3586661 1 107714492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773425 Affx-122939354 AX-385260567 1 106151314 CCACTTGCAGGCTCTCCTTTAGTGAGACTGCTCCT[A/G]TTGGAACTGTAGCTGGGAGAGTTGCTTCTGGCTGG R 2 1 2 1 101000 f 74 goat snp46719-scaffold65-3623277 1 107752002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394665 Affx-122964373 AX-123265020 1 106202160 AAGAGTCAGTCCACACATGAGTTGAAATAAAACAA[C/T]GATAAAGATATTTTTTTAAAGCAGAAGCAAAAGGG Y 2 1 2 1 101000 f 74 goat snp46720-scaffold65-3674123 1 107802974 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387174 Affx-122970623 AX-123257532 1 106250701 AGCTGCCAGCTAGGTAGGGCCATGGGACATGTTCT[A/C]ACCACATGATACATGTCACTTTCAGGCCTGGGCAT M 2 1 2 1 101000 r 74 goat snp46721-scaffold65-3722664 1 107851656 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378852 Affx-122976526 AX-123249211 1 106279213 CTCTCTAGGATGACAAGAGAAAATAAGACTCTCTT[A/G]TATTTAATGCACAGTTATTTTGGGTTTCAATCTCA R 2 1 2 1 101000 r 74 goat snp46722-scaffold65-3751176 1 107883410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381348 Affx-122974416 AX-123251706 1 106329592 AGTATGATCAAAAATGTTCTTTTTACTGAACAGGG[C/T]GCACAATTCAAAAAATCACGAACATCACTGTTCTA Y 2 1 2 1 101000 r 74 goat snp46723-scaffold65-3801555 1 107931346 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447004 Affx-122924556 AX-123317340 1 106376501 CTGTCCTCATGGGCCCTTTCATCCCACCAGCAAAA[C/T]GTTCTGATTCCTGGCCTCACTGTTCTACATCCAAG Y 2 1 2 1 101000 r 74 goat snp46724-scaffold65-3848464 1 107978889 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407831 Affx-122954537 AX-123278182 1 106422824 TATTAAATTATTACAATAGGCTTTTAACTGTTCTC[A/G]CTGCTTCCACTCTTACTCTTCCCCAACCCCATTTG R 2 1 2 1 201000 f 74 goat snp46725-scaffold65-3894787 1 108027785 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430597 Affx-122936986 AX-123300938 1 106480604 ATAAGCACCCCCAAAGAGCATGTTGTCAGAGTGGT[A/G]CCAACACAAAAAAGAGAATTTAGATGGCCTCGACC R 2 1 2 1 101000 f 74 goat snp58241-scaffold945-12446 1 108096270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430390 Affx-122937769 AX-123300731 1 106511597 GATCTTAGGTTCTGCCACCTAGAACTGTGAGACAA[C/T]GCATTTCTGTTATTCAGTTACCTACCTATTGCGGC Y 2 1 2 1 101000 r 74 goat snp58242-scaffold945-43439 1 108127105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394850 Affx-122964773 AX-123265205 1 106558542 AAACACCATCTCAGGTAACCCTAAGAAAGATGGTT[A/G]TAAGAGGTAAACTTGTCACAGAAAGAGGTAACAAT R 2 1 2 1 101000 r 74 goat snp58243-scaffold945-90384 1 108174596 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446746 Affx-122925335 AX-123317082 1 106644421 CTTCTCTGACCCCTCATCCACATCTCCCTTGGACC[A/G]AGTATGAGCAGCATTATTTAAGTCCCCTATTTCCT R 2 1 2 1 101000 r 74 goat snp58245-scaffold945-176263 1 108259487 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794576 Affx-122955554 AX-385281538 1 106673661 GGAGATAATGCTGCCTCTGTTTCTCCACTAACTCC[A/G]TCTAGAAGTATACAGGAGAAACAACCAGTTCAAAA R 2 1 2 1 101000 f 74 goat snp58246-scaffold945-205503 1 108288773 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375760 Affx-122978600 AX-123246119 1 106703279 CTATATATCATTTATTTGAAAAATATTTATCATTA[A/C]GCATTTGATCTTTTTCATTTCCAACCATATATAGT M 2 1 2 1 101000 r 74 goat snp58247-scaffold945-235121 1 108318988 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776673 Affx-122959332 AX-385263799 1 106778516 ATTTATGCGAAAGATTATTTTACCAAGAAGGGTTC[A/G]TTTCCTAAGTAAGCTGTCACATATTAAACTATTAT R 2 1 2 1 101000 f 74 goat snp58249-scaffold945-310358 1 108393850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450556 Affx-122922470 AX-123320890 1 106836048 GCAGTTGTTCCAACAAAATCTACAGAACGAATGAA[C/T]AGATTGATGAATAAAAGTAGAAAAAGAGATATTAC Y 2 1 2 1 101000 f 74 goat snp58250-scaffold945-367890 1 108451718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275458 Affx-1111834911 AX-519549031 1 106856950 GACTCATCATCTTGTCACTAGCTGCAGTTCCAGCC[A/G]TGCATCAGCGCCCCAGGAGACAAAAAGAGAAGGGA R 2 1 2 1 202000 f 74 goat GoatD01.058473 1 106856950 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320781849 Affx-122967340 AX-385268931 1 106893132 AGGTATAAATATGGTAAAGTCCAATAAGCTTAAAC[A/G]TACAGTTCAGTAAGATTTACATATGAATAACCCTA R 2 1 2 1 101000 r 74 goat snp58251-scaffold945-424974 1 108508730 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780020 Affx-122930981 AX-385267119 1 106965690 TAAAGAAACAAACATTAGGAGAGTATAAAAAATAT[A/C]AGCCTAAATTCTCTCTCTGGGTGATGGGATTACGT M 2 1 2 1 101000 r 74 goat snp58252-scaffold945-497532 1 108582124 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400769 Affx-122959878 AX-123271124 1 106999256 AGAGGATATGGTTGAGGAAGACTTCCAGGAAGAGG[C/T]GATACTTGGGCTGCCTATTGTAGGATAACTTAGTC Y 2 1 2 1 201000 r 74 goat snp58253-scaffold945-531098 1 108616721 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779729 Affx-122945503 AX-385266829 1 107050360 TTTTCTGCACTGATTAAAATGTACTACATATCTGT[A/G]CTGCCCAGATAAGACAGCTTCTAGCCACATGTGTT R 2 1 2 1 101000 r 74 goat snp58254-scaffold945-582202 1 108667531 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448551 Affx-122923427 AX-123318887 1 107080716 AGCACAAAGAGATATCCAATACCACAGTGCAAAAG[C/T]ATCAATTCATCGGTGCTCAGCTTTCTTTACAGTCC Y 2 1 2 1 103000 f 74 goat snp58255-scaffold945-612558 1 108698026 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272461 Affx-1111836716 AX-519546185 1 107080965 GTGTCCAAACAAAACACCAAGTAATAATTAAAGAA[A/G]AAAGGAGGTGATCACAGAAGTAAAGCACAGGAGAT R 2 1 2 1 201000 f 74 goat 1_107080965_AF-PAKI 1 107080965 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38430153 Affx-122937381 AX-123300494 1 107142087 AGGGAAGATATCATTTTAAGAAACGTTTAAAGGCT[A/G]TGTTTTAGCAGGATATGGTGTTTAAATGGATATGG R 2 1 2 1 101000 r 74 goat snp58256-scaffold945-673929 1 108761210 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411364 Affx-122952247 AX-123281714 1 107176872 TCATATAAAGTGAAAATACAAAAGAAGAGTCTTTT[A/G]GGAGTAACTTTCTTACCACAAGTGGTTTTATATTC R 2 1 2 1 102000 r 74 goat snp58257-scaffold945-708714 1 108795931 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414874 Affx-122949141 AX-123285223 1 107235351 TAAAAAAAAAATCCTTTAATAGATCCAAAGAAAAA[G/T]AAGGCACAATTTGAAGGTTTGTGTGGATTCTACAT K 2 1 2 1 102000 r 74 goat snp58258-scaffold945-767193 1 108854471 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800456 Affx-122932989 AX-385287377 1 107277667 TTTGAGATTATATTCCCTGACAAGTACCTGGTAGG[C/T]AACTATTTTATGTGACTACCATAGGTACAGAAACC Y 2 1 2 1 101000 f 74 goat snp58259-scaffold945-809509 1 108897412 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399332 Affx-122961367 AX-123269687 1 107321577 ATATGTGAGTGTATGTGTATGTGCACACGTGCGTG[C/T]GCTTGTCTTACCATCCCAATCTAAATGCTTTGTGC Y 2 1 2 1 101000 r 74 goat snp58260-scaffold945-853419 1 108941244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785780 Affx-122942972 AX-385272820 1 107376995 CATTTGGATTATTTTCAGGCTTATGCAAAAGGTAC[A/G]TATAGCAATGAGGCTGAGTGTACTCACCAAAAACT R 2 1 2 1 101000 f 74 goat snp58261-scaffold945-908837 1 108997025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436868 Affx-122933241 AX-123307206 1 107445093 CTGGTGACCAAGCCTGCACTGGCTATGTCAGTCAG[C/T]AAAAATAATATATTTTCTTCTGAAAATTAATCACA Y 2 1 2 1 103000 f 74 goat snp58262-scaffold945-976935 1 109066339 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794782 Affx-122922915 AX-385281742 1 107485400 TGACTCCATAGGTACTGAAAGCTACTGAAAATGGC[A/G]TAAAACTTTGGAATAATTCATTGCTGTGTAAGTAA R 2 1 2 1 101000 f 74 goat snp58263-scaffold945-1017242 1 109106705 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451184 Affx-122921336 AX-123321518 1 107582547 TTCCATGGCAACACAGCAGAGTAAATATTTAATAA[A/C]CATTGGTTCAATGTTGCACACATATTGTGAGGCTA M 2 1 2 1 201000 f 74 goat snp58265-scaffold945-1114389 1 109209428 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383429 Affx-122973475 AX-123253787 1 107642933 ACATGGAAGAAATAGTCTTTAGAAAAGGACAGCAG[G/T]AGTTGTTTGAAAAACAGTTAAAATGCAACTCAAAA K 2 1 2 1 101000 f 74 goat snp58266-scaffold945-1174775 1 109269954 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396183 Affx-122963375 AX-123266538 1 107675447 TATTATTTTATTTTTATTTTTTGCTCTCTATGATC[A/G]TTTATATTCCATATGAATTTAAGACAGCTTTATTT R 2 1 2 1 103000 r 74 goat snp58267-scaffold945-1207289 1 109303461 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411290 Affx-122952301 AX-123281640 1 107716349 TCTATGCCCAGGGCTCTCTGGAGCAGTGCCCACAG[C/T]GGCTCAACATTCTTCCAAGGAACATGGATGGATGG Y 2 1 2 1 101000 r 74 goat snp58268-scaffold945-1248191 1 109344406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451058 Affx-122921431 AX-123321392 1 107751739 GTCACTAGCAGACACCTGGTTCAGAGTAAGAGCTC[C/T]CTTTACCAGGTGACATCGATCTGTCTGTGGGCTAA Y 2 1 2 1 101000 r 74 goat snp58269-scaffold945-1283581 1 109379955 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769089 Affx-122940041 AX-385256264 1 107781884 ACTTGATTATGAAATTATGTAGAAGTTATAAGAAA[C/T]GTATATTTGAGGAGTTACTTAGCTTGGTCATGAGA Y 2 1 2 1 101000 r 74 goat snp58270-scaffold945-1313726 1 109409915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437131 Affx-122932157 AX-123307469 1 107823894 AGTGTATTTATACTGGAGGGACATAGGCAGGTCAT[A/G]CCAAACATAGTCACTCTTTTCTTAACATTTAAAAT R 2 1 2 1 101000 f 74 goat snp58271-scaffold945-1355736 1 109452264 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431830 Affx-122936096 AX-123302171 1 107875997 ACAGTGGGATATTTGTCATGCCCAGTGGTGGGAAT[A/G]CCACTGCTTCTCTCAGTCCTGTCTTCTCTCTCCTG R 2 1 2 1 101000 f 74 goat snp58272-scaffold945-1407839 1 109497716 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411581 Affx-122951622 AX-123281931 1 107963683 CTGCATTGCAGGCAGATTCTTTACCATCTGAGCTA[C/T]GGGGAAGTCCACAAAGGAACCTCCGTGCTCTTGCC Y 2 1 2 1 303000 r 74 goat snp58274-scaffold945-1495525 1 109586270 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426713 Affx-122939888 AX-123297059 1 108002313 AGCTGCTGAAAGATAAATAACATGCCTTGTTGATT[A/C]TTGTCCAGAAAAGGGCAGACTGGATGCCGGCCACT M 2 1 2 1 201000 r 74 goat snp58275-scaffold945-1534155 1 109625403 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768607 Affx-122948263 AX-385255787 1 108061414 AAATACACCAGACAATGTGTAAAGCCTTCTTAAAT[A/G]TGGATGTGATTTGGAACTGATTTGTAATTGTATTA R 2 1 2 1 101000 f 74 goat snp58276-scaffold945-1593256 1 109690340 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397001 Affx-122963142 AX-123267356 1 108091945 AGTTATGGCTGCATCTTTGCCCCATTTTCATGTTA[A/G]TATCAATATCCACCACTTGAAAAACAACACCAAGG R 2 1 2 1 201000 r 74 goat snp58277-scaffold945-1623787 1 109721132 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772926 Affx-122974665 AX-385260070 1 108165663 GTCCTTCACTTGTTTTACTAAGAATTGATGTCATT[A/G]TACTTTGGACCATCTTTTCTCTACTAAATCTACAT R 2 1 2 1 201000 r 74 goat snp58279-scaffold945-1697505 1 109794886 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404663 Affx-122957295 AX-123275015 1 108206386 TGTTTATGCTGCTCTTTTTTTTCTCTGTTCTTTTT[A/G]CTGGAATGTTTCCTTTCTTTTTCTACACCTTTGAT R 2 1 2 1 101000 r 74 goat snp58280-scaffold945-1738228 1 109835798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377963 Affx-122977197 AX-123248322 1 108227014 GGTGTAAAGATGAAGGCATTTGGGGGGATGTAATG[C/T]GATTTATAAATGGAAGCCTTAAATGGGGGAGGGTA Y 2 1 2 1 101000 f 74 goat snp38090-scaffold4745-95947 1 109855360 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775533 Affx-122925310 AX-385262664 1 108262127 AAGTTGTTTTCTTATAATGTACAATGCCATAGGTA[C/T]AGAAGTTTCTAGATCCCTTCTCTCCCCTTTCTGGC Y 2 1 2 1 101000 r 74 goat snp38089-scaffold4745-60834 1 109890327 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786964 Affx-122971093 AX-385273993 1 108292150 TCTGAAAGAGTATTCTGGGAAATGAGTCTGAAAAG[A/G]TAAGTGGTATCCAACAGTGGGTGGCCTAGATGTCA R 2 1 2 1 201000 f 74 goat snp38088-scaffold4745-30811 1 109920528 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783269 Affx-122952956 AX-385270334 1 108328216 CCTGCCTTATTTTCATTAGTGATTTTCTGCATCAT[A/G]CCCATGCGTCATCCAGACAGGATTACTTCAAGCTC R 2 1 2 1 101000 r 74 goat snp25508-scaffold263-5156 1 109966062 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773443 Affx-122961507 AX-385260585 1 108378971 TTCTATTTTTAGTATGTGTAGCATGAATTCTACCA[G/T]TGGAAACAGCAGCTTAAAATGGGCACCATTCCCAT K 2 1 2 1 101000 r 74 goat snp25509-scaffold263-55911 1 110017241 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409335 Affx-122953076 AX-123279686 1 108480880 TCTATGATTTCATACCGTTAACAATGAAAAGAAAG[C/T]GTAAATGACTTATGAGAACAAAGACTTTATTTCAA Y 2 1 2 1 101000 f 74 goat snp25511-scaffold263-157820 1 110117679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771159 Affx-122925227 AX-385258319 1 108518734 CAGGTCTTATGAAAACAAGGGAACCTTGTCAAAAC[C/T]TTATATTTTGTTTAGTAAACATTATTTAAGAAATT Y 2 1 2 1 202000 r 74 goat snp25512-scaffold263-195674 1 110155473 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413315 Affx-122950186 AX-123283664 1 108587905 ATTGGAGATTGCTATCCCAGGAGGGAGAAGCGGAA[C/T]ACCCTTGGGGCTTGTGCTCTAGTCCATTAGGCCCT Y 2 1 2 1 101000 f 74 goat snp25513-scaffold263-264845 1 110225650 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774758 Affx-122938347 AX-385261892 1 108662572 TAATGAGCACTACTTTAAAATTTGAGGGATTTTAC[A/G]TAAAGATGCATATTCTCTGCTTTTCTGTACAAGTC R 2 1 2 1 101000 r 74 goat snp25514-scaffold263-339512 1 110302016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774804 Affx-122962658 AX-385261938 1 108701041 GCATTTGTCCTATGAAAATAAAAGCACAAGTTCAC[A/G]TAAAAACCTGTACACTAATATTTACTGCAACTTTA R 2 1 2 1 102000 f 74 goat snp25515-scaffold263-377981 1 110340492 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443862 Affx-122927516 AX-123314199 1 108736980 GAAAATGAGAGAGAAGCCATCTGAGTCTGTTTTAC[A/G]TTCCTTTAAATTTTGCTTCAAATAACACTTTTTTA R 2 1 2 1 201000 r 74 goat snp25516-scaffold263-413920 1 110376570 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424470 Affx-122941768 AX-123294816 1 108803157 CTGATAAGAAGTGCAAGAAGCCCTGCCACAGACCA[A/C]GTGATGCTAGAGCCATGTCCACCCCAAGAAGTCCT M 2 1 2 1 101000 r 74 goat snp25517-scaffold263-480097 1 110442872 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428011 Affx-122939155 AX-123298354 1 108849810 TCAAGGATTTTTGTTTATATTTTGTTTTTAATGTT[C/T]CCTTTGCAATCTAAGAATTAGAATCATTAAGACTA Y 2 1 2 1 101000 r 74 goat snp25518-scaffold263-526750 1 110489500 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442391 Affx-122928004 AX-123312728 1 108890711 CATGAAATCTAACCTGGGATGCAGGGAGGCAGGAC[A/G]TGTCCTGTGGTGAAAGTGAAGGGAAGCATGGATTA R 2 1 2 1 101000 r 74 goat snp25519-scaffold263-567651 1 110530773 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410139 Affx-122952804 AX-123280489 1 108919616 GGCTTCATGATCCAATACACAGGTGAGCTGCTGCT[A/C]CTGGCTTCAGCCCTGAATTCTCTTCAAGGGAAAAA M 2 1 2 1 201000 f 74 goat snp25520-scaffold263-596556 1 110559332 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417590 Affx-122946888 AX-123287938 1 108960127 TGCCTCTCCCAGGGTGACGGCTGCAGGATGGTGCT[A/G]TGGTAAAGTAGGCAGGGAGGGAGATATGGGTCTTC R 2 1 2 1 202000 f 74 goat snp25521-scaffold263-637067 1 110599971 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385330 Affx-122971661 AX-123255688 1 109055568 AGCCAGTGACTCTAGTCGGGCTGATTGTGTTAACA[C/T]AATCCAGAGCTCACCTCAGAACTGAGGTCCAGCCA Y 2 1 2 1 101000 r 74 goat snp25523-scaffold263-732508 1 110695471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385371 Affx-122971632 AX-123255729 1 109096434 GGAAGGACAGACCCTTCTCACCAATGTGTCAGCAA[C/T]GGTCTGGGGGGAGTCTCTGGGGCCCAGAACTGAGA Y 2 1 2 1 101000 f 74 goat snp25524-scaffold263-773374 1 110736508 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406120 Affx-122956204 AX-123276472 1 109125670 CATGGTGTCTGGCACCTCGCATGCAGTCCTTGGAC[A/G]CACAAATGAAGGAGAGGAGTGCAGATCCCATGCTT R 2 1 2 1 101000 r 74 goat snp25525-scaffold263-802610 1 110766262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276458 Affx-1111835429 AX-519549971 1 109126162 AGGTTTTCACCCAGTTAAAACTGAAAAACAAATCA[A/C]ACACACACACACACACACACACACACACACAAACA M 2 1 2 1 303000 f 74 goat Random2.2K-114 1 109126162 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415015 Affx-122949029 AX-123285364 1 109210559 TCAGGGAAAGGAAGCTTGGAGAGTTGCTTACTTTC[C/T]AAATTTGAAAAATAAGAACTTCCTGGGTTTATAAA Y 2 1 2 1 303000 r 74 goat snp25526-scaffold263-887499 1 110851415 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445539 Affx-122925162 AX-123315876 1 109256497 AATGAGACAATATGTGTAAAGTGCTTCACACCACA[C/T]GCAGCACATAACGAATCCTCAATAAATGAACATTC Y 2 1 2 1 201000 r 74 goat snp25527-scaffold263-933437 1 110893983 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773451 Affx-122953620 AX-385260593 1 109285218 AAATTCATATCCCTGCAAGAAACTCCTACTTTCCT[A/G]TCCCCAACACCACCATTAATTGACAACACTAAGGA R 2 1 2 1 101000 r 74 goat snp25528-scaffold263-962158 1 110922640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803206 Affx-122930500 AX-385290065 1 109328920 GAAATAAGATAGATTTTACAAATACAAGCCTAGCA[C/T]GGCAACCTGCGTTCTATGTACCTTCTCTGTATATA Y 2 1 2 1 101000 r 74 goat snp25529-scaffold263-1005860 1 110964225 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276620 Affx-1111835435 AX-519550130 1 109338632 GACAGGTATGCACTTACAAATAACTAACTTTAAAC[A/G]CCAATGAGATTCAGTTCTATTATCAGTCACTCACT R 2 1 2 1 101000 r 74 goat Random2.2K-115 1 109338632 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800403 Affx-122956449 AX-385287324 1 109427054 GACAACTCCCAAATGTTCTGCCAACTAAATCACTA[C/T]AAATATAAACTGGTTCATAAAACTCCTAAAATGTC Y 2 1 2 1 101000 f 74 goat snp25531-scaffold263-1103994 1 111063662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416997 Affx-122947988 AX-123287345 1 109465902 AGATAGATTCAGGGAAGATAGGTGAGGAATGACAG[C/T]GTCTCCTCGATCCCAGGCTGTGGGACCACGGATTC Y 2 1 2 1 101000 f 74 goat snp25532-scaffold263-1142842 1 111103048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420447 Affx-122944893 AX-123290794 1 109515915 AGAGCTTGATCTTTATTCTAAAAACAATATGAAGC[A/G]CTGAATCTGTTTTGTTCAGAAGAGTGACCTGAACA R 2 1 2 1 101000 f 74 goat snp25533-scaffold263-1192855 1 111153490 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776373 Affx-122936471 AX-385263500 1 109563944 TTGGTTCTTGCACTTATCTTTCAGTATAAAGCAGC[G/T]CATTCATTCTCTTCTCTTCAACCAGCACCTCTGCA K 2 1 2 1 201000 r 74 goat snp25534-scaffold263-1240884 1 111201788 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780530 Affx-122974079 AX-385267621 1 109599694 ACATCTCATTCCAAAGGGTATGAAATAGAACCTAA[A/G]TCTTATTAGCTTCAAGGCCCTTGCTTTTGCCATGA R 2 1 2 1 101000 r 74 goat snp25535-scaffold263-1276634 1 111237824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411706 Affx-122951536 AX-123282056 1 109628240 TAAGATAGACTACAGAGGGACGTAGAGTGAAACTA[C/T]GATAGGACAAATCCTAGGTGACCACACTTAGTTAA Y 2 1 2 1 101000 f 74 goat snp25536-scaffold263-1305180 1 111267033 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389933 Affx-122968097 AX-123260290 1 109696167 ACTGTCCTCTGAATCAATCTCAAATATGTCACTGA[A/G]AGAAATCAGACATCTCTGAAATCATGCTATATCTT R 2 1 2 1 101000 f 74 goat snp25537-scaffold263-1373107 1 111334972 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786867 Affx-122934931 AX-385273896 1 109782549 GGTGAGAATTGAGAATTGGAGTATGGGGAACCTGT[A/G]TGGTTATTAAAAGTAATAATTAAGTCCTACTCCAG R 2 1 2 1 101000 r 74 goat snp25539-scaffold263-1459489 1 111448954 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430308 Affx-122938237 AX-123300649 1 109822677 GCTGGCGATGGAAGGAAACACCAACACTGCAGAGT[A/G]GTTTGAATCTTTGTATTTTAACTCCTCGCTTTTTA R 2 1 2 1 103000 f 74 goat snp25540-scaffold263-1499617 1 111489728 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271720 Affx-1111832829 AX-519545516 1 109839943 TAATGAGAAGAATAATTCATAAAATAAAGATAGCT[A/G]AAAATCAATTTGATTGGGAAATACCTGGGCTGATA R 2 1 2 1 101000 r 74 goat 1_109839943_AF-PAKI 1 109839943 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38417080 Affx-122947500 AX-123287428 1 109855040 AATGTTGGGTACAATAGAAAGATTTTTTTTTAAGT[A/G]CAATACTCTATAAGAAAGTAATGACTACTCAGGCC R 2 1 2 1 101000 r 74 goat snp25541-scaffold263-1531980 1 111521337 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434792 Affx-122933877 AX-123305133 1 109899091 TGCTTCAGAAATGTTAGTAATCCTCAAAGTTCTCC[A/G]TTGTTTAACACACCAGTGGGAAAGGATTATCTCCC R 2 1 2 1 101000 r 74 goat snp25542-scaffold263-1576031 1 111574344 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430727 Affx-122936892 AX-123301068 1 109930416 TTTTAAACATAGCCTCTGTTTCAATATTCTTTTCC[A/G]TTTATAGTTTTTTGTTCATTTATGGTTTCTCATTT R 2 1 2 1 202000 r 74 goat snp25543-scaffold263-1607356 1 111605789 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804402 Affx-986696569 AX-385290991 1 109960672 CCTTCCAGCGCGTAAGCTGGGCCTCGGTCTTACAC[G/T]GGCTAACCAAACTTAACACCAGTGTTCAGATAGCT K 2 1 2 1 600010 r 74 goat 1_109960672 1 109960672 Ancestral_priority_1043 ancestry 0.55 neutral IMAGE 10K 10K ancestral 38410631 Affx-122952088 AX-123280981 1 109968624 TGTAAGTTTCCTGTCAAGGTATCTTTTTAAAGAGG[C/T]GACTCTGGATGGGATGTAGGTGAGATCAGATAAAA Y 2 1 2 1 101000 f 74 goat snp25544-scaffold263-1645564 1 111643988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783215 Affx-122946578 AX-385270281 1 110005953 CTATGCCCTGGTGATATTTGATCACCTTGGCCTGC[A/G]TTTCAGGAAGAATCCTATTAGGCTGGGTTAGCCAA R 2 1 2 1 202000 f 74 goat snp25545-scaffold263-1682893 1 111681527 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402392 Affx-122959022 AX-123272745 1 110052644 GCTTCTCCAGTTTCTTCCATTTCTGCCCTTATATT[A/G]CTGGAAAAATGAAAGTCTCCTCCTGCAAAATGATG R 2 1 2 1 101000 f 74 goat snp25546-scaffold263-1729584 1 111728323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771236 Affx-122935388 AX-385258394 1 110084522 CTTACAGAATGCTTGCTGGTGATGATAACAGCAAA[C/T]GTTTTAGTGTGTGAGAAGCACCGCTTTATTGGGGT Y 2 1 2 1 101000 f 74 goat snp25547-scaffold263-1761462 1 111760712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795091 Affx-122922922 AX-385282050 1 110123141 GATTCTTTAAGGAAAGTATCATACTAAACAAACGG[A/G]CAAAAATGGATCAAAGTACCATGCTGCAGATTCTG R 2 1 2 1 101000 r 74 goat snp25548-scaffold263-1800081 1 111809578 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437614 Affx-122931850 AX-123307952 1 110168450 CATTTGTGAGAAGACTAGTTAATATAGAAAATTAG[C/T]AAATCAAGAAAAGTATCAAAAGTATATTATTTAGA Y 2 1 2 1 101000 f 74 goat snp25549-scaffold263-1845390 1 111855035 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775633 Affx-122957138 AX-385262764 1 110214956 ATAGCAAGTGTGGGGCATCAATTCACCACTATCTA[C/T]CTCAAATTTCTCTACAGATTATTGCTATCAACCAA Y 2 1 2 1 101000 f 74 goat snp25550-scaffold263-1891896 1 111901781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770557 Affx-122978540 AX-385257721 1 110263574 AAGGCCTCAAGAGGCATGAACAGACTAGACTCATA[A/G]ATATCGTAAAGAGTCATATTACAGCCACCTCATCA R 2 1 2 1 101000 f 74 goat snp25551-scaffold263-1940514 1 111950316 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388661 Affx-122969104 AX-123259019 1 110294474 GGGTTGAACTTTAAAAATGGGATGTCCCATCTTGA[C/T]ACATTGCTAATAAAAACAAGATTATGACTGTTCGC Y 2 1 2 1 101000 f 74 goat snp25552-scaffold263-1971414 1 111984607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377374 Affx-122977640 AX-123247733 1 110327037 CATCTGTTTTCCTTGAGCCAGAAAATCACACAACC[A/G]CTTAAGAATATAAGAATTTCTATACCATTTGACAG R 2 1 2 1 101000 f 74 goat snp25553-scaffold263-2003977 1 112017210 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405942 Affx-122955558 AX-123276294 1 110363427 AGTCAACCAGGATGCTTTAAGAAATATTGACAAGG[C/T]GGGGGCCCATCTCCAAAAGTTCTGAAGCAATTGGT Y 2 1 2 1 101000 f 74 goat snp25554-scaffold263-2040367 1 112053639 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404842 Affx-122956629 AX-123275194 1 110404927 GGATCCAGCCTGGCACACTTTTCATTCAAGGACTA[C/T]GCATCCTGAGGCTGAAACTAATGATCCTCTTTACT Y 2 1 2 1 201000 f 74 goat snp25555-scaffold263-2081867 1 112089593 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796278 Affx-122974993 AX-385283228 1 110443900 TGATAGGCTGCATTCTTATATACTCATTAATAGAC[A/G]CATATTCTTATATTGAAAGTGTCAATTGAAAAATT R 2 1 2 1 101000 f 74 goat snp25556-scaffold263-2120840 1 112128637 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424638 Affx-122942173 AX-123294984 1 110494155 CTAGAAACCAGCTACTGGTCTACCTCAAGAAGAGG[C/T]AATCCATGGTCTGCCTTTGAATGCCAATAGCTTCC Y 2 1 2 1 101000 r 74 goat snp25557-scaffold263-2171095 1 112179032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799272 Affx-122954901 AX-385286203 1 110539975 TGGGGTTGCCTGACATCACAAAGATAAGGAATAGG[C/T]TCAGTCTCATTCTTGCTAAATTGAGTCAGTATCTG Y 2 1 2 1 101000 f 74 goat snp25558-scaffold263-2216915 1 112225044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383696 Affx-122972487 AX-123254054 1 110571570 ACACTAAAGCCATAAATGAAAAAGTTTAAAAATTG[C/T]ACTGCAAAAAGACTGTAAGAGCGATTTTACAAGAG Y 2 1 2 1 101000 r 74 goat snp25559-scaffold263-2248510 1 112256671 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797658 Affx-122920589 AX-385284597 1 110605907 AAGGGAGAGTGAAAATCGAAGGGTGGTTGGAATCC[A/G]TTTAAACTGAAGGGATCACCAACTTGAAGTCATGT R 2 1 2 1 101000 f 74 goat snp25560-scaffold263-2282847 1 112290825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382723 Affx-122973617 AX-123253081 1 110663697 CATTCTAGTAAGAGGAGCTGTTTGAAGAGTTTAGA[C/T]ATCTAATTTTCTTTGAGTAGATATTTAGATGAAAG Y 2 1 2 1 101000 f 74 goat snp25561-scaffold263-2340637 1 112348685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793529 Affx-122968093 AX-385280505 1 110694450 TCTGTGGCCACAGTATACTGGAGGTACAATTTGGG[C/T]GGTCCATAGTTTCATAGGCAAAAAGAAGTTTGATT Y 2 1 2 1 101000 f 74 goat snp25562-scaffold263-2371390 1 112379926 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441843 Affx-122929047 AX-123312180 1 110752468 GTCTCAATTTACTTATTTCCCTATTCTTACAAACT[A/G]CTGACCTGTGTTATCTGTTGTTCAATGCCTGAAAA R 2 1 2 1 201000 f 74 goat snp25563-scaffold263-2429408 1 112439098 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413646 Affx-122950538 AX-123283995 1 110870010 TTTCATCATCAGCTTTATAAGCATCACTTTATGAT[A/G]CTAAATTCATTTGAACTTAACATTCAAAAGTGCTG R 2 1 2 1 103000 f 74 goat snp25565-scaffold263-2546950 1 112558348 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794623 Affx-122976749 AX-385281584 1 110921584 AAATGTTAGAACACTCCAATTTTTTTGTAAGAGAG[A/G]CAAAAAATGGCTTCTATGGTTAACACTGAACTTTT R 2 1 2 1 101000 r 74 goat snp25566-scaffold263-2598524 1 112610676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772031 Affx-122949803 AX-385259188 1 110956660 GTATTGTACTCCATAGCTAGTCACCTTGAAAAAAT[A/G]TTTAAATATATTGTCTCTACATCTTCACCTACATT R 2 1 2 1 201000 r 74 goat snp25567-scaffold263-2633600 1 112645538 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780495 Affx-122943068 AX-385267586 1 111005625 TTTTGAGAAAAGATTTAGAAGTTGTAGAATGCAAA[C/T]GTACAGACTCAGAACAAGATCAAGCTGGACCTTCT Y 2 1 2 1 101000 r 74 goat snp25568-scaffold263-2682565 1 112695128 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412536 Affx-122951341 AX-123282885 1 111057463 GGTATCAGCATTTGTGTGGGAAGAAGTAGAGAAAA[A/G]GCACGCAGGCTTCTGTTAACTCTGAGCAAGGAAGC R 2 1 2 1 201000 f 74 goat snp25569-scaffold263-2734403 1 112747530 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764665 Affx-122937435 AX-385252300 1 111126935 CTTCTGTTCCCATATACTCTACTTTCCCTCCGGTT[A/G]CAACATATATTCTTAACCTTTTGTGTGTGTGTTGT R 2 1 2 1 101000 f 74 goat snp25570-scaffold263-2803875 1 112819660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417713 Affx-122947446 AX-123288061 1 111159418 TGTCATTCTCAATGCAACATTTATCGCATTGGGTA[C/T]GTCTAAGCAATCCAGAAGGCTCATGCCACACATCA Y 2 1 2 1 102000 f 74 goat snp25571-scaffold263-2836358 1 112852198 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773651 Affx-122935061 AX-385260791 1 111193557 GCTACGGTATAAACCTTAAAGGCTTTGTGTTGGAA[C/T]GGCCCAGTTATGGCTTAGATCTCTTCTACAGCTCC Y 2 1 2 1 101000 r 74 goat snp25572-scaffold263-2870497 1 112886368 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433580 Affx-122934968 AX-123303921 1 111244752 CTGGATGAGACAGATTCTGTGATTGGACTGCATTC[G/T]ACCACCTTCATCCATAAATATATTTTGGTTTTTGA K 2 1 2 1 101000 f 74 goat snp25573-scaffold263-2921692 1 112938093 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445441 Affx-122925356 AX-123315778 1 111280185 TTCGTTGTTCTCAAACAGTATACAAAAGTTGTCCT[A/G]TAGACAAAGCCGTATTTATGATTTATAACATAAAT R 2 1 2 1 101000 r 74 goat snp25574-scaffold263-2957125 1 112973498 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414397 Affx-122949987 AX-123284746 1 111316932 TGTCAAACAGCCTTTTTGTCCTTCCCTTCCTGTTT[A/G]CTTGTCCATGTGTCCCCTCCTCTGTGCAGCCTTGT R 2 1 2 1 102000 r 74 goat snp25575-scaffold263-2993872 1 113010373 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779296 Affx-122949718 AX-385266400 1 111347053 TTGATCAAGCCTGTTTGTTGCTAGGGTAATAATCT[A/G]TATTAACTGGAAGTTCACATGGCAACATCATCTCT R 2 1 2 1 101000 r 74 goat snp25576-scaffold263-3023993 1 113040102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798212 Affx-122946409 AX-385285147 1 111384917 AATTCTGAACACAATACTATGGATGAGTATAAAGA[C/T]GACATTAAAATAGGAAATAGTCTTTAAAAGCATAG Y 2 1 2 1 101000 r 74 goat snp25577-scaffold263-3061857 1 113077614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795863 Affx-122960016 AX-385282815 1 111416969 GCAAGAAACAAAATGAGTAAGACCCACATAGCTTC[A/G]TGCCACATCTGAACACTCAATTTGTCTCTCCCTCT R 2 1 2 1 101000 f 74 goat snp25578-scaffold263-3093909 1 113109501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380542 Affx-122975669 AX-123250900 1 111460195 CAGTTATGGGAACTCTTTCCTACCTACAAATGCTG[C/T]ACCCAAACTCACATCACATAAACTAAGCATCACAC Y 2 1 2 1 101000 r 74 goat snp25579-scaffold263-3137135 1 113153335 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387432 Affx-122970390 AX-123257790 1 111525567 GGGTTACCTTCATATGGGCATCCTCTGTGTGCAAG[C/T]GGCTCCCTCACTTCTCATTTTGAGTTGCCCCTGGC Y 2 1 2 1 101000 f 74 goat snp25580-scaffold263-3202507 1 113218662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777686 Affx-122934503 AX-385264805 1 111577655 TTCGGTATGAAGAATCACAATTTGTTCCTTGAAAC[A/G]TGGAGATGAGTCATTAGTAGCTGAATTTGATCAAA R 2 1 2 1 101000 f 74 goat snp25581-scaffold263-3254595 1 113270622 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434752 Affx-122933906 AX-123305093 1 111610854 TTGAAGCAACTTGGAAATTATTTTTAGTAAACTAG[A/G]CTTTGATGTTGTGGTTTATGTTTTTCTTCTAAAAT R 2 1 2 1 101000 r 74 goat snp25582-scaffold263-3287794 1 113304084 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394606 Affx-122964419 AX-123264961 1 111653657 ATCACTGGATTGGAGATAAAAACATGGGGGGAGGC[A/G]TACATGGGGAACACCCTGATGGCGGTGGCAGTCAT R 2 1 2 1 103000 f 74 goat snp25583-scaffold263-3330597 1 113347813 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429340 Affx-122938579 AX-123299682 1 111699042 AATTTTGCTACCCTCCATCTGTATTTTTGGTAATG[C/T]AATCAAAAATTTCTGGTTGACTGAATTCAATTTTC Y 2 1 2 1 201000 r 74 goat snp25584-scaffold263-3375982 1 113393304 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420238 Affx-122945073 AX-123290586 1 111728971 AGAGATTGACAGTGGTGGGAAACTACACTCCTGCC[A/G]TGAACTCTCTCTGTGGATTTTTAAAAAAGAACCTA R 2 1 2 1 101000 f 74 goat snp25585-scaffold263-3405911 NW_017191590.1 8076 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393488 Affx-122965823 AX-123263844 1 111763681 TTTTAAATGAATCATTTAAATAGCTGACTGTTAAA[C/T]AGCCTGTGTCCGCTAATTCTCCCTTCTAACTTCCC Y 2 1 2 1 201000 f 74 goat snp25586-scaffold263-3440621 1 113460657 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765050 Affx-122937157 AX-385252619 1 111848799 AGTAACAAAGTCATCAGGTCTAGAAAAAGGAAGAT[A/G]TTTCTCTTTCTAAAGCTACATTACTCTTTTGCTTG R 2 1 2 1 101000 f 74 goat snp25588-scaffold263-3525739 1 113546508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789924 Affx-122961472 AX-385276930 1 111913477 TTTGCCAATACTACCACTAACTCTTTCATATTACC[A/G]TGAATATACTGAAATTACTTGCATTTAGAAATGAA R 2 1 2 1 101000 f 74 goat snp25589-scaffold263-3590417 1 113612516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802085 Affx-122946745 AX-385288989 1 112000320 ATTTTCTGTTTTGAGCTACAGCTAAGACTGCTCCT[A/G]CATCTGGTTTTCTGCTTCAAAACTTTTATTCCTAT R 2 1 2 1 101000 f 74 goat snp25591-scaffold263-3677260 1 113699599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775059 Affx-122957628 AX-385262191 1 112031135 TTAAAAATAACTTACTTAAATCTACCCAATCAGAT[A/G]TCCCCTTAAAAGATATCCAAATTCTTATTTCTGCA R 2 1 2 1 101000 r 74 goat snp25592-scaffold263-3708075 1 113731458 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380356 Affx-122975354 AX-123250714 1 112070197 GAACTTTGGAATGAAATGGTCTTCTTCAGTAAACA[C/T]ACTTAAAATCTGAAAAGAATATAAGCAAATGCTAT Y 2 1 2 1 101000 f 74 goat snp23439-scaffold236-4492 1 113770884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800793 Affx-122968212 AX-385287709 1 112132712 TCTCATTAAGCTCAAAATAAAGTCCTCATCAAGAC[A/G]TCTACGGCCTTCCATGAGATGCTTTCTTTTGCCTT R 2 1 2 1 201000 f 74 goat snp23440-scaffold236-67007 1 113853175 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792643 Affx-122925358 AX-385279623 1 112165187 GATGGAAATGTCTCTCTTAGAGGTAGAAGAATTTT[A/G]CTAGGTAATTTCACAGAAGTTATTCCTGTCTTAGG R 2 1 2 1 101000 r 74 goat snp23441-scaffold236-99482 1 113887304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389876 Affx-122968141 AX-123260233 1 112201651 CCCACTGGAAAAGCTGTAGTGCCCTGTTGGAGGAC[A/G]CATGTGAGACATACTCTGGGACTTCCTAGAAGGTC R 2 1 2 1 101000 r 74 goat snp23442-scaffold236-135946 1 113923292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447828 Affx-122923910 AX-123318164 1 112270731 AAGATGGTGCTTCTGCAGCCATTTGTGAATGAGTG[C/T]AGGGTGGCAAAAAAACTTGCAGCTCAGCAGATGTC Y 2 1 2 1 101000 f 74 goat snp23443-scaffold236-205026 1 113992906 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443263 Affx-122927492 AX-123313600 1 112301140 AGATGAAAAATGGGGCTGGGGAGGACTTGAATCTC[A/G]GAGGGAAAAATCAAAGCAAAGGCTCTGGTTGTGTC R 2 1 2 1 101000 r 74 goat snp23444-scaffold236-235435 1 114023567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403071 Affx-122958517 AX-123273424 1 112348741 AGCCCTCATGGAAATGTCAACTGTACCCTTCAGCT[A/G]ATATTCTGAAACAATGGGAAAAGGACCTTTTTACA R 2 1 2 1 101000 f 74 goat snp23445-scaffold236-283036 1 114070740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413802 Affx-122949904 AX-123284151 1 112377629 ATGTGTAACTTTCATAATTAAAACCCCTCTTCACT[A/G]TAGAGTCTGCATGCATGCATACATGTTCAATCAGT R 2 1 2 1 101000 r 74 goat snp23446-scaffold236-311924 1 114099496 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784020 Affx-122967250 AX-385271073 1 112414563 TGAAGGAATACCTGTAATCAGTAAAACCTACTCAA[G/T]CCCTGATCAAACATAAGATTTGCAAATATTTTCTC K 2 1 2 1 101000 r 74 goat snp23447-scaffold236-348858 1 114136324 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387474 Affx-122970355 AX-123257832 1 112456928 GCTGTTTTCTTTCAAGTAATGAAATAAGTGAACAT[A/G]AAAGAGGAGGCCAGGTTAAAAACAGAAGGGAAGCT R 2 1 2 1 201000 f 74 goat snp23448-scaffold236-391223 1 114178820 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271721 Affx-1111832830 AX-519545517 1 112457804 AAAATCCAGCCCAGGTTGATCTGCTCTGTTGATTG[A/G]TGAAGAGAAACTGACCTACAGCTTGAAGGAGAAGC R 2 1 2 1 101000 r 74 goat 1_112457804_AF-PAKI 1 112457804 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38427602 Affx-122939365 AX-123297945 1 112490962 CAACAGTAAAATTTTGCTCTGTGCTTCTGGAGGAA[C/T]ACCCTACAACAGAAAACCAAAAATTAAAAAAAAAA Y 2 1 2 1 101000 f 74 goat snp23449-scaffold236-425257 1 114212902 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423875 Affx-122942306 AX-123294221 1 112533553 ACTAAGGAAATGTTGATTTTAAGACTTTAAGAACG[C/T]ACAGTTGTGTTAGAGCTGTTCCCATCCACACCTCT Y 2 1 2 1 101000 r 74 goat snp23450-scaffold236-467848 1 114255882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396684 Affx-122962834 AX-123267039 1 112563299 GGTCGCAAAGAGTAGGACACGACTGAGTGACTGAA[C/T]AACAACGCGCACAACCAGTTTTCAATTTTCTCATC Y 2 1 2 1 101000 r 74 goat snp23451-scaffold236-497594 1 114285701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390818 Affx-122967850 AX-123261175 1 112574839 TTTTTGCCTGCTAGCAGAACAATCCAATGGTAAAA[C/T]AGCAGGAGGGAAAAGGAAAGGAAAAAAAAACCCTG Y 2 1 2 1 201000 f 74 goat snp403-scaffold1009-1550238 1 114297514 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402309 Affx-122959087 AX-123272662 1 112614027 AACGTGACCAAAACTCATGCATATACAGATAATCA[C/T]GCCTTTCTGTGTACCAGCGAATCAGAGGTTTTTTT Y 2 1 2 1 101000 f 74 goat snp402-scaffold1009-1511050 1 114336981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406567 Affx-122955098 AX-123276919 1 112655499 TATGGGCATTATTTTCATTACTTTTGAACTGTAAC[A/G]ATTCTGGTGCCCAGTAATTAGTAGCAAATGTAAAA R 2 1 2 1 101000 r 74 goat snp401-scaffold1009-1469578 1 114378951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399368 Affx-122961341 AX-123269723 1 112721894 AAAGTGACCACTGCTTTCTCCTTCCTTCCTTCAAT[A/C]TTTCCTGCCTCCCTGCCTTCTTTTTCTTGAGTCAA M 2 1 2 1 303000 r 74 goat snp400-scaffold1009-1403183 1 114445151 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773189 Affx-122947625 AX-385260332 1 112791564 GCTTTTGTAAAATCCAGTTAGTGGTTAATAGACCT[A/G]TCTAACTTAGGCTTTGCACTTCTCATACGTATTCT R 2 1 2 1 201000 r 74 goat snp398-scaffold1009-1333513 1 114514997 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433421 Affx-122935087 AX-123303762 1 112823404 AGATTTGGAAGTGACAAGAACATCATGAGAAAAGC[A/G]TGAGAAAGAATGCATTGCTAAGGAGTTCTGTGCAA R 2 1 2 1 201000 r 74 goat snp397-scaffold1009-1301673 1 114546836 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422494 Affx-122943309 AX-123292840 1 112930287 TTAAAGAGTCGGGCACAACTGAAGCAACTTAGCAT[A/G]CAAGCACATACATAAGACAAGGAGAAAAAAGCTCC R 2 1 2 1 303000 r 74 goat snp395-scaffold1009-1194790 1 114654763 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406677 Affx-122955787 AX-123277029 1 112960571 CACATATATGCTGAGCTCATGAGTAAGAGGCATGA[C/T]GTGATTTGTTTCACTTTTAGTCAGAACACAAAATT Y 2 1 2 1 101000 r 74 goat snp394-scaffold1009-1164506 1 114685459 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392078 Affx-122966378 AX-123262435 1 112998395 GCACAAATTTGTTTAAACTTGTTTCCTTAATTTAC[G/T]AGAGTCATTACTCTGTGCCAGTAAGAGCATATTCT K 2 1 2 1 101000 r 74 goat snp393-scaffold1009-1126682 1 114723104 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790194 Affx-122973824 AX-385277198 1 113060421 CTTTTTGCCTCTTCATATTGTTTATACTATTCATG[A/C]TGGAGGGTAGTCCTTGGAAAAGGGACCTATAATCT M 2 1 2 1 102000 r 74 goat snp392-scaffold1009-1064656 1 114785123 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423921 Affx-122942270 AX-123294267 1 113100521 CATCTTAGTAAAATATTTTTTGAATAGAAGAGTTT[A/G]CAGCAAGAGACAGACAGCTGGGAAAGGAGTTACCA R 2 1 2 1 103000 r 74 goat snp391-scaffold1009-1024556 1 114826280 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401373 Affx-122959235 AX-123271726 1 113146255 GAGAGGAAGCTGACAGGTTCTGACCAGCATGATGT[C/T]AGCTCCAGTCTTCTCTCAGAAAGCCAAGTCCTGAC Y 2 1 2 1 201000 f 74 goat snp390-scaffold1009-978822 1 114872015 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425946 Affx-122941185 AX-123296292 1 113175449 GTAAAAAATTATAATTGTCTGAAGGAGGATGCAAG[A/C]GAATTTGGGGGATCTGGAGATGGAGAACAACATAT M 2 1 2 1 101000 f 74 goat snp389-scaffold1009-949628 1 114901320 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776860 Affx-122944134 AX-385263984 1 113207793 CTTGTTAAAGGTTATTAAGTGTTATGTCCTCTAAA[C/T]GATTTATCCATCACAGCAGAAACAGGAATACCAAG Y 2 1 2 1 101000 r 74 goat snp388-scaffold1009-917284 1 114933911 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444389 Affx-122926596 AX-123314726 1 113248142 GCAAACCAAACAGCACACCGTAGCTATAGTTGTTA[C/T]GTGATTGTTTTTTAATTGCTGTAGGAGCCTGTTCT Y 2 1 2 1 101000 f 74 goat snp387-scaffold1009-876935 1 114974732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276658 Affx-1111835455 AX-519550168 1 113285837 GCTGCACATAACTGCCTAGGAAGCAAATGTGTGCA[A/G]TTCATAAGACCACCACCAATATTGACTCTTTCCTT R 2 1 2 1 101000 r 74 goat Random2.2K-118 1 113285837 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396951 Affx-122963176 AX-123267306 1 113338591 CTCAACCAGTGTCTCTTAACCCAAGAGCCAATTTT[A/G]TTTTCTTTCATACATTTTCTTCTAAGATAATGGGC R 2 1 2 1 103000 f 74 goat snp386-scaffold1009-786486 1 115064979 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798894 Affx-122935879 AX-385285824 1 113379010 CTTCGTATTTTTGTCACTTAATGAAATACTTGTTA[C/T]GTAGTAGACTCCATCAAAAAGAATGTCTGAATGGT Y 2 1 2 1 101000 r 74 goat snp385-scaffold1009-746067 1 115105280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794653 Affx-122959953 AX-385281614 1 113411999 CTTGCTTTTGGAATTCTAATCTTTAGCAACAATGC[A/G]TCACTTAACTAACTTCCTTCAGTATCCTTCCAGTA R 2 1 2 1 101000 r 74 goat snp384-scaffold1009-713078 1 115138277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782562 Affx-122977130 AX-385269636 1 113466015 GTAAATTCTCCTACATATATTGGTTTGTTAATTTT[A/G]CATATTATTCGTTGAACATTTTCTGGGGAAAAGAT R 2 1 2 1 101000 r 74 goat snp383-scaffold1009-659062 1 115192345 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387117 Affx-122970663 AX-123257475 1 113523164 GTTGATGAGGATGTCATTTGTTGCTTCTATTTGTC[A/G]CAGGCACAGAGCTGGGGCCTGGAGGTGAGCTCAGA R 2 1 2 1 101000 f 74 goat snp382-scaffold1009-601913 1 115249959 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276528 Affx-1111835462 AX-519550039 1 113548317 GGAACAGTACCGTGCATTATGTGGTCCTATGATAC[A/G]ATGAGTGGCACAGATGTGGGCTGGTAGGACCAGGA R 2 1 2 1 101000 f 74 goat Random2.2K-119 1 113548317 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785035 Affx-122947390 AX-385272082 1 113581625 ACAAACAAATTAATGAAATAGATATTCTCATTTCA[C/T]ATAAAATCACAGTGTCGGGTGAGTTCTGTTCTGTC Y 2 1 2 1 202000 f 74 goat snp381-scaffold1009-543452 1 115308758 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379356 Affx-122976159 AX-123249715 1 113650049 GCAAGTTTTGATATTTCATTCCTGCCCTTTACAAC[A/G]ATGTTGGTGAAGAATGAGCATTAATTAAGCAATAG R 2 1 2 1 101000 f 74 goat snp379-scaffold1009-475028 1 115377569 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276543 Affx-1111835469 AX-519550053 1 113670826 TTATCCCTTTTGTGGCCCTGAATTGTGAGGGAAAA[A/G]AATGATAGTATTCCCACCTCAAATGTATTAAAAAA R 2 1 2 1 101000 f 74 goat Random2.2K-120 1 113670826 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386308 Affx-122970896 AX-123256666 1 113696159 GAGGGAGTGTTATGACTTCTGTCGGTTTCCATAAT[A/G]CAGTAGAAGAATAACTTGCTAGCTTCCAAGCAGAG R 2 1 2 1 101000 f 74 goat snp378-scaffold1009-428918 1 115421806 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393317 Affx-122965955 AX-123263673 1 113728652 CAACCTTTTAAGTTCTGCCTAAATGTTACTATTAC[A/G]TCCATTATATTTTATGTTCACTGGTTGATATTACT R 2 1 2 1 101000 r 74 goat snp377-scaffold1009-396425 1 115456614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421859 Affx-122944285 AX-123292206 1 113764573 AAAATGAATTTTGAAAAGAAAATGTATGTCTTGTG[C/T]TAAGTATTTCAATCTTGACTCTTCTCCCTTTCACA Y 2 1 2 1 103000 r 74 goat snp376-scaffold1009-360504 1 115492907 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796342 Affx-122935113 AX-385283292 1 113845590 GAGTAGCTAATTCAGATTTGCTAGTGAGAATCTGT[A/G]CTAGTAAAGCAAAGAGGATACATGAGCACTGGGTA R 2 1 2 1 101000 f 74 goat snp374-scaffold1009-279487 1 115574426 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402839 Affx-122958256 AX-123273192 1 113901792 AATTTTACAGTGAAGGATCTACTGTGTGCAGTGCC[A/G]TGGGCTGCAGGGCAAATTCTGGCCCTGACATTCGG R 2 1 2 1 101000 f 74 goat snp373-scaffold1009-223285 1 115631113 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399776 Affx-122960301 AX-123270131 1 113937631 TCTTTTATATCCATTGCAATCTGTGTTTTACCTCA[C/T]AAATTCTTGAAAATACTCTTGGGACTATCATCAAT Y 2 1 2 1 101000 r 74 goat snp372-scaffold1009-187446 1 115664752 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785845 Affx-122952398 AX-385272882 1 113975281 TAGGAGAAATATAGAACAAGAATTATTCTACTATC[A/G]TGAAATAAACTGAATCATCATTTTAATATTTTTAC R 2 1 2 1 202000 r 74 goat snp371-scaffold1009-149796 1 115703280 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445615 Affx-122925105 AX-123315952 1 114065642 TGATTATCTGTGACCTTTCTAATGTTCTCATAACC[A/G]CTGTATTTTGTTTGTCTTTTTAACTCAGCAAATTC R 2 1 2 1 101000 f 74 goat snp370-scaffold1009-59435 1 115796286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793129 Affx-122940246 AX-385280107 1 114115182 TGTTTTTCTTCAGCTCAATTTAAGCACTTGAAGGA[C/T]GAAAAATAACTCCATGACTATCACAAATGAAAACA Y 2 1 2 1 101000 f 74 goat snp369-scaffold1009-9895 1 115846519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794769 Affx-122962840 AX-385281729 1 114149354 CATTTCTTTGCCTCACCTTTGTATGGAAAGTTGAC[G/T]AGCTTATGCCAGGTCAAATTAGTGGCTATGGTCAA K 2 1 2 1 101000 f 74 goat snp26955-scaffold285-1887635 1 116040333 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422545 Affx-122943266 AX-123292891 1 114196154 AAGGAAACAAGCTATGCTGTGTATTGATTTGTATC[G/T]ACACCATCTCTTGAAATTTTAGCCTCTGTGGTATG K 2 1 2 1 101000 f 74 goat snp26954-scaffold285-1840835 1 116088951 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797542 Affx-122972467 AX-385284481 1 114270879 AACTTAACAACAAGCCAAAAATCAGCTTCTTCCCT[C/T]TTAGACTTAATCTGATTAGAGAACATTTACCAAAA Y 2 1 2 1 101000 f 74 goat snp26952-scaffold285-1766110 1 116165633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425783 Affx-122940713 AX-123296129 1 114301189 ATAACAGCAAGAGCTGATCTGATCACAAGCTTGAG[A/G]CTAATAGAAAAATTAAAAGGTCACTGTCCAGAAAT R 2 1 2 1 101000 f 74 goat snp26951-scaffold285-1735800 1 116196617 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800954 Affx-122937909 AX-385287869 1 114336385 CAATCATCACACACGCTATTTTTTCACTTCTTCCA[A/G]TAGAGAATTTTATTAACACACTCTGAGAACAACCA R 2 1 2 1 101000 f 74 goat snp26950-scaffold285-1700604 1 116233205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418116 Affx-122947126 AX-123288464 1 114369375 AATGAGATCTCTGTTAAAATGAGTATCCTTTGACC[A/G]CTTGTGGTCACTGGATACCAAAATCAGAGAAAGTA R 2 1 2 1 101000 f 74 goat snp26949-scaffold285-1667614 1 116265923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384548 Affx-122973018 AX-123254906 1 114434694 GATGCTCTAGATATAGTCCATCAGTTGTCTGATCC[A/G]TTTTCAAAAACATATATGACAAAAATACCAATGAA R 2 1 2 1 101000 f 74 goat snp26947-scaffold285-1602295 1 116331047 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397197 Affx-122962401 AX-123267552 1 114485164 TACAGGCATATAATGTTTAAGCTGAATTTAAAAAA[G/T]AAAGTTGAATATTCTATTGCTATGCCTTAGAATTT K 2 1 2 1 303000 f 74 goat snp26946-scaffold285-1551825 1 116381966 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407941 Affx-122954363 AX-123278292 1 114542772 TAAGGGAAGCCCAAGAATAGTGGAATGGGTAGCCT[A/G]TCCCTTCTCCAGCGGATCTAGCTATCAGAGAAGCC R 2 1 2 1 103000 r 74 goat snp26945-scaffold285-1494217 1 116439901 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397218 Affx-122962385 AX-123267573 1 114584958 GATGAAATTAACAAAGCTCTTGACAACATTAAAGT[A/C]TTTCTTCAATTACCTTTTTAAAAATTTGGACCAAT M 2 1 2 1 102000 f 74 goat snp26944-scaffold285-1452031 1 116481720 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377459 Affx-122977518 AX-123247818 1 114630349 TTGTTTTAATACAGTGTTGTTCTACCAACGGTGTG[A/G]TGGAAAAACACAAATGATCTTTTTGGTCAACCCAG R 2 1 2 1 102000 f 74 goat snp26943-scaffold285-1406640 1 116527022 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392931 Affx-122965705 AX-123263288 1 114689226 TTTTCATTGTATATCGATCTCAAGGAACAGGAGAT[A/G]CCAATTCACATTAGAAAAGTTGTACCAGTTATTCG R 2 1 2 1 101000 r 74 goat snp26942-scaffold285-1347763 1 116586299 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792344 Affx-122966685 AX-385279326 1 114741608 AAAATAAAATAGCAATCATAATCCGCTTTCAGCTC[C/T]TATTTGATCTCTCTTCTCACCTTCAAAGGTCAAAT Y 2 1 2 1 101000 r 74 goat snp26941-scaffold285-1295381 1 116638791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409471 Affx-122954065 AX-123279822 1 114780998 AACTGTAGTGTTTTTCACCCTTAGGTGTCTTGAAT[A/G]CCCAAACTTTTCTGAGACTTCCACGAGACAAATTG R 2 1 2 1 101000 f 74 goat snp26940-scaffold285-1255991 1 116678181 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773186 Affx-122953226 AX-385260328 1 114814129 CTGTTAAAAAGATTGAAACTGTTGCAAGGTCAACG[C/T]GGTGGAGAATCCTTGCTGAGGGATAAGTAATATTT Y 2 1 2 1 101000 r 74 goat snp26939-scaffold285-1222860 1 116711379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399796 Affx-122960287 AX-123270151 1 114863779 ACCTCGGGAAGGAGTCTGCCATATTCATCATTGCC[A/G]TGGTGAAATAATTATCATAGTGTAAGTAACTAAGT R 2 1 2 1 101000 r 74 goat snp26938-scaffold285-1173210 1 116761086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416202 Affx-122948241 AX-123286551 1 114900273 AGAAGTCCAGAGTCAGTTTTAACCTCCCAGTCCCC[A/G]CTTCCTTGCCTATGAAATATGGATAAGAAAGATGA R 2 1 2 1 101000 r 74 goat snp26937-scaffold285-1136716 1 116797191 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425682 Affx-122940861 AX-123296028 1 114939106 CTTACCTGAGGAAGTTACCGTCTTTTCCCTTCCTT[A/G]TAAACAGCAGGTATTTAATGATGGATCCTTGTACA R 2 1 2 1 201000 r 74 goat snp26936-scaffold285-1097883 1 116835961 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420592 Affx-122945257 AX-123290939 1 114971515 GTGAGGGTAACACCTGGGCAGCTATTTAATAGTCT[A/C]GTGGTGTCTGCACCAAGAAGGTGGTGATGCAAATG M 2 1 2 1 101000 f 74 goat snp26935-scaffold285-1065474 1 116867779 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774493 Affx-122923853 AX-385261628 1 115005901 ATTTGATGAAAGCTAGTCTCTCTCCAGGAAAGTTC[A/G]CAAAATGTGTGGATATTCGGAATGCTCCCTACAGC R 2 1 2 1 101000 f 74 goat snp26934-scaffold285-1031088 1 116902566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271804 Affx-1111832831 AX-519545592 1 115032820 TCGCTTCAGTTGTGTTCGACTCTTTGTGACGTTGT[A/G]GACCACAGTCCGCCAGGCTCCTCTGTCCATGAGGC R 2 1 2 1 103000 f 74 goat 1_115032820_AF-PAKI 1 115032820 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387161 Affx-122970632 AX-123257519 1 115072113 GCCTTCTGAAACTCTTCTGTGAGTGATGAGTGAGA[C/T]ACTTCTGCCAACTGTTTAAAAACACACATCCAACA Y 2 1 2 1 101000 f 74 goat snp26933-scaffold285-964876 1 116969120 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423995 Affx-122942111 AX-123294341 1 115101339 GCCAGAGTCAGGAGGTAAGAACAGAAACACTTGCT[A/G]TGGTGGAGTAGGGGGCACATCAGAGCGTAAGTGTT R 2 1 2 1 101000 f 74 goat snp26932-scaffold285-935650 1 116998709 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786325 Affx-122960205 AX-385273359 1 115182980 TTCTATTGCTGATGATCTCTTTGCTTATATTTTTC[A/G]TTTCTTCGTATATCAGTTTCGTATTTTGTGTTTGC R 2 1 2 1 101000 f 74 goat snp26931-scaffold285-854009 1 117080492 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383742 Affx-122972450 AX-123254100 1 115232611 GTGATGTCACCAGAGAGACACTTTCATTGTGCCCC[A/G]TCTTCTTTGCTTTTGTGTCCCTTCCCCTCTTCTTC R 2 1 2 1 202000 r 74 goat snp26930-scaffold285-804378 1 117129970 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421429 Affx-122943958 AX-123291776 1 115289443 TACAATAGAATTAGTTAACCAAGAGGGAAACAAAC[A/G]CAGGGGTTGATTTCCTCGGTGAGAAAGGCAGGTTA R 2 1 2 1 201000 f 74 goat snp26929-scaffold285-747546 1 117186670 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767533 Affx-122934202 AX-385254790 1 115374236 AGTAGAGAGGTTAGGTTCATGTAAAAATGTAAGCT[A/C]TACTACAAATTGTATGGAAACATTGAACTGAGAAT M 2 1 2 1 101000 f 74 goat snp26928-scaffold285-662753 1 117271956 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796094 Affx-122966130 AX-385283046 1 115408441 GTTCCATAATAAAAGAAAGTAGGCTTTAATAGGAT[A/G]TTATATTTATTATTTAGTTCAAGATGCACCCTTTT R 2 1 2 1 201000 r 74 goat snp26927-scaffold285-628548 1 117305769 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791190 Affx-122960848 AX-385278185 1 115440428 ATTTCTGCTCAGCCAAGTGCAAAAGACATTAGCCT[A/G]TTCATCACAAATCCATCTTCCTTATTTTGATTACA R 2 1 2 1 101000 f 74 goat snp26926-scaffold285-596561 1 117338322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777754 Affx-122921240 AX-385264872 1 115470542 CCTCTGCGGCAAAATAGCATCAACCCTACTTTAGT[A/G]TAGTTATAGGCTCACTACTCCATTTATCATCACTT R 2 1 2 1 101000 f 74 goat snp26925-scaffold285-566447 1 117368427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775024 Affx-122955029 AX-385262156 1 115502604 AGATATAGGTTAAGATATGGATATGGGTAAAGACA[C/T]AGATATAGGAAGACATAGATATCAGTTCAGTTCAG Y 2 1 2 1 101000 r 74 goat snp26924-scaffold285-534385 1 117400400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442026 Affx-122928407 AX-123312363 1 115548951 CACCAAGGAAGTGCTGCGTGATAGACATCTTGAAG[C/T]AGGAAGCCACAAAGTGAACCCCAAGACCCAAAGAG Y 2 1 2 1 201000 f 74 goat snp26923-scaffold285-488038 1 117447153 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398111 Affx-122961708 AX-123268466 1 115601201 AGATCAACTCCCCTAGACGAGGAGTCCCTGATTCT[A/G]CTTGAAATTGCTTTCCTAGACCTCTGGTTCCAGTC R 2 1 2 1 101000 r 74 goat snp26922-scaffold285-435788 1 117499075 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440483 Affx-122929372 AX-123310820 1 115635139 ACATTTTAATTAAAAATAAAAAACCTCTTCGCTTA[C/T]AAACTCTACATAATTCCACCAATGCCTGCAGCCAC Y 2 1 2 1 101000 r 74 goat snp26921-scaffold285-401850 1 117533249 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384568 Affx-122973002 AX-123254926 1 115670525 ATGGTGAGACATGGGATGTACACTGACACATATTC[A/G]TATATGTATATATGCATGTTTACACCATGAGCAGA R 2 1 2 1 103000 f 74 goat snp26920-scaffold285-366464 1 117568940 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800466 Affx-122945726 AX-385287386 1 115732389 ATTTCATAGGGAGGAATTATAGAAGATTAGTAACC[G/T]CCTAAATTACATTGGTCTTACTGTTGGCTAGTGAA K 2 1 2 1 101000 r 74 goat snp26919-scaffold285-304600 1 117626656 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396491 Affx-122963538 AX-123266846 1 115801338 GTCTAGGTAGGCTTTCATCTCAGCTTCCCAGAGAG[C/T]AGCCAAGGCTCCTGTTTTTAAAGATCTGCAAGTAA Y 2 1 2 1 201000 f 74 goat snp26918-scaffold285-235651 1 117697041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420932 Affx-122944996 AX-123291279 1 115872235 TTTAAAAATAAAATTTCAACTAGGAAAAAAAGGGT[A/G]TCACTGACAAAAGTTTTCTTGATAAAACTGGGCAG R 2 1 2 1 101000 r 74 goat snp26917-scaffold285-164754 1 117768269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776504 Affx-122973065 AX-385263631 1 115903579 TGGTGTATCTGCAGGAGTGTACTTCATTTCACTAA[C/T]AATAGACTGGTGCTGTAACTCAAGCATCAAATCAA Y 2 1 2 1 101000 f 74 goat snp26916-scaffold285-133410 1 117799739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418998 Affx-122946056 AX-123289346 1 115966310 ACGATGTTCATGGAGTATCGTCTGTCTGAAATAAT[A/C]CTGGTTTTTAGCTTGCCTTTTCACTATTGTTCAAA M 2 1 2 1 101000 f 74 goat snp26915-scaffold285-70679 1 117862647 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383222 Affx-122972768 AX-123253580 1 116057118 GAAAATGTTTATTAAGGCATTTCTAGAGTGTATTT[A/G]TAGAACTGCTACTCAATCTCTACAGAATAATTCCA R 2 1 2 1 101000 r 74 goat snp27138-scaffold29-20030 1 117952805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447172 Affx-122924427 AX-123317508 1 116125609 CGAGTTCTAGTGTCCTCTCACAACACACACTCACA[C/T]GTGTTGTAGCTCTCTTGGGTGTGACTGCATAGACA Y 2 1 2 1 202000 r 74 goat snp27140-scaffold29-88521 1 118021451 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404415 Affx-122956774 AX-123274767 1 116177880 AGGTTGAGGAAGCAACTGTGACAATCCGTTAATCC[A/G]TCAAAATCAGTAGAAAACACAAGCAAAAGAAATAT R 2 1 2 1 101000 f 74 goat snp27141-scaffold29-140792 1 118072995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783403 Affx-122968649 AX-385270466 1 116217126 ATTAGGATTATTATGAAGGAACTGTCTTTTGAATC[A/G]TTTTGAAGCTAAAGAAATCATAAACCAGTATTTTT R 2 1 2 1 101000 f 74 goat snp27142-scaffold29-180038 1 118112217 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775692 Affx-122977427 AX-385262823 1 116247820 ACCTCACAGTGTCTTACCCTTAGTAGGAGCTGTGT[A/G]ATGTCATGTTTACGGGATTGGTTTCAAGGGCCCTG R 2 1 2 1 101000 f 74 goat snp27143-scaffold29-210732 1 118142843 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273587 Affx-1111833708 AX-519547201 1 116300609 TTCATCTGTATCAACTGCTGCTGCGATGTGATGGC[A/G]TGCAGAGAGGGCGGCTGCATCATGGCCCCCGAGCG R 2 1 2 1 202000 f 74 goat GoatD01.002114 1 116300609 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38431259 Affx-122937120 AX-123301600 1 116301222 TAATGAAGGTTATTTCCTGAAGGATCTTTGCATTT[A/G]CTGTCTATAAAGGACTATAAAGGACTAAAAATTAC R 2 1 2 1 101000 r 74 goat snp27144-scaffold29-264134 1 118196341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400199 Affx-122960184 AX-123270554 1 116330643 GTAAAGAGCTCAGTGGCTGAGAGTGTAGAGATTCT[C/T]ACCCTCAAATAGTCAGACTCTCTGGGCTTAGATCC Y 2 1 2 1 101000 r 74 goat snp27145-scaffold29-293555 1 118225947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801773 Affx-122968615 AX-385288681 1 116361703 GAAGTTAAAGGTAGGAATGTATAATTTATCATTGG[A/G]GTTCTTTTAGATGGACAACTGACTCTGGAGATTAG R 2 1 2 1 101000 r 74 goat snp27146-scaffold29-324615 1 118257096 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766813 Affx-122937403 AX-385254138 1 116429857 GACTGATAATTATGTACTGTAACCAGGAGCAGCTG[C/T]GTATATTTCCTTATTCACAAACCACACTAAGAAGT Y 2 1 2 1 202000 f 74 goat snp27148-scaffold29-392769 1 118325492 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400824 Affx-122959799 AX-123271179 1 116496266 AAAATAATACAGGGAAGCCGTAATTTCCACTCTGT[A/G]TTTGGGAAACGTAAGCACACAACATCTACTTAGTC R 2 1 2 1 101000 r 74 goat snp27150-scaffold29-459178 1 118392885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404359 Affx-122956817 AX-123274711 1 116526061 GCTTTTAACACAGTGCCTAGGATAAAGATACTCAA[C/T]GGATGTCAATTCATTATGATAATTTTGAGGGGGGC Y 2 1 2 1 101000 r 74 goat snp27151-scaffold29-488973 1 118422707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419341 Affx-122945648 AX-123289689 1 116559452 TAAGTCTCAGGGAGGTTGAGTATCACCAATTAATC[C/T]TAATGGAGAATGATTTCTATTTTGTTCATTTACAC Y 2 1 2 1 101000 f 74 goat snp27152-scaffold29-522364 1 118456097 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423307 Affx-122942633 AX-123293653 1 116595496 CAAGAACATATAAATCCCATTGCATGGGAAATCCT[A/G]TACGAGGGCCAACCATTTGAATATGTACTATGTAC R 2 1 2 1 101000 f 74 goat snp27153-scaffold29-558408 1 118492153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420319 Affx-122945016 AX-123290666 1 116636809 TGTTGGCTCCTCTGTTCTTGCATCATCCTAGTCTA[C/T]GCAGAGTGCAGAAATTCTCAATTGCAACATTATTC Y 2 1 2 1 101000 f 74 goat snp27154-scaffold29-599721 1 118534679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398730 Affx-122961831 AX-123269085 1 116667758 TAGTACTATCTGCTTGTTTGAGTATTTGACAAATC[A/G]TGGGTAATAATTCTAAGCCTTGGTCAGAACTTTTC R 2 1 2 1 101000 f 74 goat snp27155-scaffold29-630670 1 118565708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377889 Affx-122977252 AX-123248248 1 116703793 TCTCCTTGGGACTGGAATTCACAGAATTCTCTACA[C/T]GATCACACCTGTGGCTCCAAGAGGGGGGAAATGGC Y 2 1 2 1 101000 f 74 goat snp27156-scaffold29-666705 1 118600327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770964 Affx-122951102 AX-385258127 1 116735413 CATCGTTTCTCTGAGGTCCAGGAATCTTTTTAAGC[C/T]ACCCTAGGTGATTCTTAAACACCAGTAGAGGCATC Y 2 1 2 1 101000 f 74 goat snp27157-scaffold29-698325 1 118631978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446813 Affx-122925287 AX-123317149 1 116766846 TGTGTTCCCTGTATTGGCAGATTCTTAACCACTGG[A/G]CCGCTAGGGAAGTCCTAATTATAGTTTTAAATGGT R 2 1 2 1 303000 r 74 goat snp27158-scaffold29-729758 1 118663522 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792760 Affx-122954824 AX-385279739 1 116814544 AAAGCAGGTGGAGTTGGTTTGAATCTTTCTGCAGC[G/T]TCTCGAGTTTTTTTAATGGATCCAGTAAGTAATTT K 2 1 2 1 101000 f 74 goat snp27159-scaffold29-777456 1 118712082 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426047 Affx-122941106 AX-123296393 1 116864170 AAATATAAATAAATAAATGACATTTAAAAAAAGAA[G/T]AACCACAAGCTCCTATCTACATAGTTGAATTTTCA K 2 1 2 1 103000 r 74 goat snp27160-scaffold29-827082 1 118761957 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416895 Affx-122948070 AX-123287243 1 116910899 AAGTGAAAGTGGATGGTGTGTTACAAAGTTTGGCT[A/C]GAGTTCAGGGTACATTGCATGTGAGAATTATATGA M 2 1 2 1 101000 f 74 goat snp27161-scaffold29-873811 1 118808657 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395676 Affx-122963749 AX-123266031 1 116947095 ACCATGGAAGTCCTACAACAGTTTTAGATGTCCAC[A/C]CAGTGAGCAGCGATGGTGGAGCGTGTTTAGAATAT M 2 1 2 1 101000 f 74 goat snp27162-scaffold29-910007 1 118845656 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416940 Affx-122948034 AX-123287288 1 116996190 GTTGAAAACAGTTGACTGAAGTCAGAAGGACAATT[A/G]TAACCTCTAAAAAATTAAAAAAAATTTTTTGAGGC R 2 1 2 1 101000 f 74 goat snp27163-scaffold29-959102 1 118894841 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397253 Affx-122962359 AX-123267608 1 117040977 TGGAAGTCTTCTTATTACTCCACTTTCTTGAGAAA[A/G]GAGCTCTGTTAAGGGTCTAGCTCTTCCTGCTAAGT R 2 1 2 1 101000 f 74 goat snp27164-scaffold29-1003889 1 118940979 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446810 Affx-122925289 AX-123317146 1 117104293 TTCAAATTCTTCTCTTAGTTGCATTTATTCACTCT[A/G]CTACAGTGTAACTCACTTTTATATAGGGCTTGCAG R 2 1 2 1 101000 f 74 goat snp27166-scaffold29-1067205 1 119005729 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386789 Affx-122970918 AX-123257147 1 117136085 GCAAGCCACAAAGTCTGTCTAGATGTTTGTGTGTG[C/T]ATAGGAGGGACAGCCTTGGTGGATGGGGAGTTGTT Y 2 1 2 1 101000 f 74 goat snp27167-scaffold29-1098997 1 119038932 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787351 Affx-122965851 AX-385274376 1 117166805 AGATTGGTTCATGGTTGCAAGACAAAATTAAAAGC[A/G]TACTTTGCTGTTAGGGAGTCAAGATAACATCAATA R 2 1 2 1 101000 f 74 goat snp27168-scaffold29-1129717 1 119069591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449591 Affx-122923217 AX-123319926 1 117253511 AAAAACCACCCCAAACAGGGAATTGTTTACCCAGA[C/T]GGAATAAGTCAAGTCAAAGGTAACTGAAACTAGTG Y 2 1 2 1 101000 r 74 goat snp27170-scaffold29-1216423 1 119156679 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799249 Affx-122922723 AX-385286179 1 117292248 TTATTTCAAAACTGAAAGTAAGTTACAAGAAATGC[A/G]TAAGGAAGCATTGTAGTTTCAAATAAATGCAAAGT R 2 1 2 1 101000 r 74 goat snp27171-scaffold29-1255160 1 119193521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399406 Affx-122961242 AX-123269761 1 117328942 AGTATTTTCATATGTGTTATTTCAATTTATGTTCA[C/T]GACTACCCAGTAGATATAGGTACTATCCTTTTCTA Y 2 1 2 1 101000 r 74 goat snp27172-scaffold29-1291854 NW_017211682.1 14321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436998 Affx-122933139 AX-123307336 1 117380044 TCACTTTCTTCTTCTCTCCTTTTGTCTCCCTGCCC[G/T]ATTTTGACTGACACCCCCCCTCAAATTGCCTATTG K 2 1 2 1 102000 r 74 goat snp27173-scaffold29-1342956 1 119276500 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376746 Affx-122978945 AX-123247105 1 117436656 ACATGCAGAGGGACACAAAATTCAGGCAGGATTGT[A/G]GGGAAATAAGGATTTTAAAATGAGATTGTTAAAGA R 2 1 2 1 101000 f 74 goat snp27174-scaffold29-1399568 1 119333356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408938 Affx-122953939 AX-123279289 1 117468272 TTGGGTGGAGAGAAAATTTTTTGAGGAAATAATTA[C/T]GCCTAATTTCCCAGAATTAAAGCAAGGTTAAATAA Y 2 1 2 1 103000 r 74 goat snp27175-scaffold29-1431184 1 119365068 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441425 Affx-122928822 AX-123311762 1 117501325 ATCCATTTTAAATGTCAATGTTTTAAATTCATCTC[A/G]TCTAGTTTGAAATGTCAGTGTCATTCAATTGCTTT R 2 1 2 1 101000 r 74 goat snp27176-scaffold29-1464237 1 119398757 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428425 Affx-122938827 AX-123298768 1 117546970 CAGGTGAGTTGAATTCTAAGGGTAAAATGGAGTAT[A/G]TATTTCCTCAGTTCAGTTGCTCAATTGTGTATGAC R 2 1 2 1 201000 f 74 goat snp27177-scaffold29-1509882 1 119445912 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394797 Affx-122964815 AX-123265152 1 117583016 GACTTCTTATATTTTAGCTAAGGGTTGTGAATCTT[C/T]CCTACAAATGGCAAGATAGTAAATATTTTAAGATT Y 2 1 2 1 201000 f 74 goat snp27178-scaffold29-1545928 1 119482417 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429780 Affx-122938240 AX-123300121 1 117624753 ATTTCCTTATTTCTTCTGAAACCCTGTAATTATAG[C/T]GGAATTTGATCTATTCTCCTCCTGTTCTAGGATAG Y 2 1 2 1 101000 f 74 goat snp27179-scaffold29-1587665 1 119524632 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438363 Affx-122931320 AX-123308701 1 117693350 TGACTATACTCCACTTTATTCATTCTATTATTTAT[A/G]TTTCTGTGGTTGACTGTCTCTCTTTATGCCACTGC R 2 1 2 1 101000 r 74 goat snp27180-scaffold29-1656262 1 119596928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415753 Affx-122948936 AX-123286102 1 117735663 TTTTGAAACATACCTTTCAAAGTTGGGGAGGAGAA[A/C]ATGCCCTTTCACAGCAGACTGATCCAACTTTATGC M 2 1 2 1 101000 r 74 goat snp27181-scaffold29-1698575 1 119638383 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452681 Affx-122920316 AX-123323014 1 117781370 AGTACTATTTTAGATTTTGGAGCTATGACAATATG[C/T]AAGATAAAATCCCTGCCTTCAACAAGCTTATCAGT Y 2 1 2 1 201000 f 74 goat snp27182-scaffold29-1744282 1 119684625 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410283 Affx-122952509 AX-123280633 1 117818144 TATACAGTCATGTTTCTTAAAGAAATCCTGTGGTC[A/G]ATCCTTTGCTGCTAATTAATCTCTCTTAGTAGATT R 2 1 2 1 101000 r 74 goat snp27183-scaffold29-1781056 1 119722041 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378930 Affx-122976438 AX-123249289 1 117850292 GACAGATTGTACAAATTAACATCCCCATTAGTAGC[A/G]TATGAAAAGTCAAAGTGATAGTCACTCAGTCATGA R 2 1 2 1 101000 f 74 goat snp27184-scaffold29-1813204 1 119754434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786311 Affx-122941233 AX-385273345 1 117888781 CTGAGACACATTGTATAGAAGAAGTAAAGTAGTGA[C/T]ATCAATGATTCTTTAATATAGTAAATTATCATTGT Y 2 1 2 1 201000 r 74 goat snp27185-scaffold29-1851693 1 119793784 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382224 Affx-122973984 AX-123252582 1 117927174 TGTCTCTCTTCTACCTTTCACCAAACCCCAAAGAT[A/G]TTAGATGTTAGTTATTAAGGGTTGTTTAAGCATAA R 2 1 2 1 201000 r 74 goat snp27186-scaffold29-1890086 1 119832489 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271807 Affx-1111832832 AX-519545594 1 117945786 AAGCAAACCGAGGCACCATGGTAAGAGATAGATAC[A/G]AAGTGTCTTACTTTTCAATAAAGAAAACACATAGA R 2 1 2 1 101000 f 74 goat 1_117945786_AF-PAKI 1 117945786 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320775191 Affx-122961658 AX-385262322 1 117956673 AACAATGGCTTAACTACTGTGGTTCAGAATGATCC[A/G]TCTTATTCCACTCATTTATGCTATTCCTGTTGGAA R 2 1 2 1 101000 f 74 goat snp27187-scaffold29-1919585 1 119861809 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802777 Affx-122963620 AX-385289676 1 118021713 AGACAAATCCACAAATACAGAATCATGAATAATAA[A/G]GATCAACTGTGCCAAAACCCTTACTGCTCCTAATA R 2 1 2 1 101000 r 74 goat snp27188-scaffold29-1984625 1 119928850 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383494 Affx-122973428 AX-123253852 1 118055872 AAAAAAAGAAAAGTATGAGATATGATCATTCATGA[G/T]AGCCTGGATGATCTCTGAAGTCCTTTCCAACTTGG K 2 1 2 1 201000 f 74 goat snp27189-scaffold29-2018784 1 119963723 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770355 Affx-122936536 AX-385257521 1 118133288 TCTCTGAACACCCTGCCTGTGGGCATATATAAAAT[A/G]CTCACTCTTACCTAATAAGACCTGAAATTCTATAT R 2 1 2 1 101000 f 74 goat snp27191-scaffold29-2096200 1 120042039 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450326 Affx-122922130 AX-123320661 1 118168385 TTTGTATAGTTCTTTTGCTTAGTGACTGCATTATT[A/G]TTATTTTGTCTCCTTTGTTTTCCTTTGCTTCAGCA R 2 1 2 1 303000 f 74 goat snp27192-scaffold29-2131297 1 120077695 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784426 Affx-122942024 AX-385271475 1 118214800 CCATTTTTAGAGAGAAGATAACTGGAAAGGTCCAA[C/T]CTATTGGATCTTTTTCTTAGGATTAGGACCAACCT Y 2 1 2 1 201000 r 74 goat snp27193-scaffold29-2177712 1 120124419 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439267 Affx-122930989 AX-123309604 1 118248260 TGGAAACAATCAATGGGAGAAATTCTTGTGCTGTT[A/G]TTCTTTTGTTCATAGTCAACTCAATTTCTTTCAAA R 2 1 2 1 201000 r 74 goat snp27194-scaffold29-2211172 1 120157911 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764844 Affx-122937259 AX-385252443 1 118300479 ACTTTTTCTTCTCTACACAGATGATGGGGTGAGAG[C/T]ACATTCTAGGCCTAGGGAATGGTAAGTATCCCATT Y 2 1 2 1 101000 f 74 goat snp27195-scaffold29-2263391 1 120209874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784623 Affx-122958656 AX-385271671 1 118360605 TGGCTCTTCATATGCCCTGATCCCTATAATTTTTC[A/G]ATCTTGTTGTCTCACCACCATGTTGATTCTACATT R 2 1 2 1 101000 r 74 goat snp27196-scaffold29-2323517 1 120270412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804406 Affx-986696573 AX-385290995 1 118381310 CATTCGCTGGTGTGGCTCGCCATCCTCTGCATTGT[C/G]GCTAATATTTTGCTTTACTTTCCTAATGGGGAAAC S 4 1 2 1 600010 r 74 goat 1_118381310 1 118381310 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 38405463 Affx-122956035 AX-123275815 1 118413261 ATCCAACAAATAAATGAAAGAGAATTCTTTCTTCT[A/G]TCTTTAAAGCCCAAATCTTTTCCACTGCACTATGT R 2 1 2 1 101000 r 74 goat snp27197-scaffold29-2376173 1 120323597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416469 Affx-122947809 AX-123286817 1 118493069 AAAATGAGTAAACACCTTATGCCGGATTCAGTTTT[A/G]CAATTTGCAATCTCAGCTCTCCACTGTCATTAGAA R 2 1 2 1 101000 f 74 goat snp27198-scaffold29-2455981 1 120405168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476157 Affx-1251763660 AX-185682401 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 4 1 4 1 20000 f 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 539476412 Affx-1251763660 AX-586011815 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 8 1 4 1 20000 r 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 560378498 Affx-1251763660 AX-605230913 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 8 1 4 1 20000 r 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 562165977 Affx-1251763660 AX-606941386 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 8 1 4 1 20100 r 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 562166139 Affx-1251763660 AX-606941547 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 8 1 4 1 20100 f 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 562166237 Affx-1251763660 AX-606941645 1 118522444 GTGACTGCAGCCATGAAATTAAAAGACGCTTACTC[-/CTTGTAAGAAAAGTTATGGAGGAGAGGGAAAGATGGCGGAAGTTATGACCAACCTAGATAGTATATTCAAAAGCAGAGAC]ATTACTTTGCTGACTAAGGTCCGTCAAGGCTATGG - 8 1 4 1 20100 f 74 goat SV_375 1 118522444 - deletion junction SV-TF-chip 38403534 Affx-122957611 AX-123273887 1 118531770 CACAGAATTTCACTAATGCTTCCTAAATCATGCCA[C/T]GTTCTGGTGTGACCATATTCTTCAGAAAATAACTT Y 2 1 2 1 101000 f 74 goat snp27199-scaffold29-2494682 1 120444417 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420590 Affx-122945259 AX-123290937 1 118565327 GGATTTGTGGAGTTCACAGTATAAGGAAAAGGGCA[G/T]ATATACAAACAAACAAGTTATAAAACAACATGATA K 2 1 2 1 101000 f 74 goat snp27200-scaffold29-2528239 1 120478571 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396589 Affx-122962906 AX-123266944 1 118638327 ACAGCTGTGTAAGAAAAGAAATGAGAGAGAGAAAA[C/T]GGAAGAAAAAAAATTACTTCAGGATGTAAGTTGAT Y 2 1 2 1 102000 f 74 goat snp27201-scaffold29-2601239 1 120551161 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404937 Affx-122956433 AX-123275289 1 118676534 TCAAGTTACTTAGATCTCCAGATTTCTGTTTCCTC[A/G]TCTGTAAAATGGGAAGGATGTTACTTCCTTATAGA R 2 1 2 1 303000 r 74 goat snp27202-scaffold29-2639446 1 120589055 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408173 Affx-122954206 AX-123278524 1 118707412 TGCTTTGAAATATAAATTTAGGGAGTTTTTGCTAA[G/T]CATAATTTATAAAGGCAAATATTTCTCCATTTAAT K 2 1 2 1 101000 f 74 goat snp27203-scaffold29-2670324 1 120619878 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771001 Affx-122946000 AX-385258163 1 118761754 TAAAACAAGTAAATAGACTGTTCTGTGTCTACTAC[A/G]TTTGTCTTGATTTCTCTAATAAAAAAGGCTTTTGT R 2 1 2 1 101000 f 74 goat snp27204-scaffold29-2724666 1 120682320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792599 Affx-122963058 AX-385279580 1 118800641 GGGGGTGGGCAGGGCTCGGTAGAGAACATTTTGTC[A/G]TATCTGTTTTTCATCTTTGTGTCATGCCATCTGCC R 2 1 2 1 101000 r 74 goat snp27205-scaffold29-2763553 1 120722058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390301 Affx-122967721 AX-123260658 1 118830647 GACTACTCTCTGGGCTTTCAGGAAGAGGTGAAATT[A/G]AACTGAGTCTTCAAAAATGATAAAGTTTCATTTAG R 2 1 2 1 101000 f 74 goat snp27206-scaffold29-2793559 1 120752761 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398485 Affx-122961575 AX-123268840 1 118860711 ATTACTTGTATAAAGACAGACATAGAGCAATGGAA[C/T]GGAAAAGAGAGTCCAGCAATAACCTTTGTGTATTT Y 2 1 2 1 101000 r 74 goat snp27207-scaffold29-2823623 1 120784516 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780361 Affx-122960732 AX-385267456 1 118927884 TTAAGGCATTATGGCATTCAACTAAAATATGCCTA[C/T]AAGCCAGCCAGTTGCCTTTTTGATACTCTGGGGGT Y 2 1 2 1 101000 r 74 goat snp27208-scaffold29-2890796 1 120852507 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276550 Affx-1111835473 AX-519550062 1 118946303 GTTCAGCTGCTTAGCAGCATTAATTCCATAGCAAC[A/C]AAATTCCATCTACATTCCTAACTTTTCTTTGCCAT M 2 1 2 1 101000 f 74 goat Random2.2K-121 1 118946303 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38387759 Affx-122969726 AX-123258117 1 118979763 TCTGTGGTCAAAGAATGAGAAATCCAGCTGCTTCT[A/G]TTGCTGCAGTAGATTTAGAATAAAAGCTCTAATGT R 2 1 2 1 201000 r 74 goat snp27209-scaffold29-2942675 1 120904588 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404655 Affx-122957301 AX-123275007 1 119021606 CCTATTTGCTAGTTATGGATCTTTAGCCCAAGGGG[C/T]AGGCTTCTGGGCTGGCACCCTTCTAGTGACCTACG Y 2 1 2 1 101000 f 74 goat snp27210-scaffold29-2984518 1 120946554 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786005 Affx-122961891 AX-385273041 1 119057467 GGAACCATTTAATTCTAAAATCCCATAGCTAAAAG[C/T]ACATCTTTTAAGAAAAGTATATTTTAGAAATGTAT Y 2 1 2 1 201000 r 74 goat snp27211-scaffold29-3020379 1 120984438 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433350 Affx-122935141 AX-123303691 1 119087221 TTCCGATTCGTCCGTCTCCCCCAATGATGACATAC[A/G]CTGTCATCATTTTCTTGTGTTTTCTTCCAGAGAAT R 2 1 2 1 303000 f 74 goat snp27212-scaffold29-3050133 1 121014512 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430426 Affx-122937745 AX-123300767 1 119120079 TACTTCTGTTCAATAAAACATCAATTAAGCAAATG[C/T]AGAAGAAACACTTCATTGCATTTCTATATTTCTAC Y 2 1 2 1 201000 f 74 goat snp27213-scaffold29-3082991 1 121048869 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451136 Affx-122921372 AX-123321470 1 119167801 AAGACCTAAATGAAATACTTTTGGTATCTTGAACT[A/G]TTGGGCTGTGTGGACTAGAGGGAAGACACCAGAGG R 2 1 2 1 201000 f 74 goat snp27214-scaffold29-3130713 1 121097376 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771683 Affx-122965096 AX-385258841 1 119199195 TCTTATTTTGATTAGGTCACATTGTATAATGGCCC[A/G]TTAGCTTTGACTTTCAGGACATGATAATAAAATGC R 2 1 2 1 101000 f 74 goat snp27215-scaffold29-3162107 1 121129312 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387323 Affx-122970503 AX-123257681 1 119230177 TATGATAAATGAATTCTATTTACCTTTCCTTTGTT[A/G]CATCTGTTTACTCTTTCATGGATGTTTGCTTCATT R 2 1 2 1 101000 r 74 goat snp27216-scaffold29-3193089 1 121158151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410664 Affx-122952762 AX-123281014 1 119264585 ACCTCTTTTTTCTTCATCTCTTATATTCAATTCTA[C/T]CAATAATTTTGATTCCTCCTTTTAAGTCTCCCTAA Y 2 1 2 1 101000 r 74 goat snp27217-scaffold29-3227497 1 121192649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449253 Affx-122923471 AX-123319588 1 119317996 AAGGGTGAATATTTGCTAAACAATAAAATTATTGC[C/T]AATTTCATCTGACTCAAGGCAGGCAGTTAATACTC Y 2 1 2 1 101000 r 74 goat snp27218-scaffold29-3280908 1 121246295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419976 Affx-122945188 AX-123290324 1 119365743 GTAGCACTTGACACTATAAACAGAGATATCAAATA[C/T]ACTCATTTCATCTTCATAAGAATTTCAAACCCCTG Y 2 1 2 1 101000 f 74 goat snp27219-scaffold29-3328655 1 121293822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453828 Affx-122919552 AX-123324161 1 119429385 TGATTGTTGTTTGCAATGCATTGATTCAGGCATGG[C/T]AAATGCAAATATATCTATATTTAGGAGGCAGTAAA Y 2 1 2 1 101000 f 74 goat snp27220-scaffold29-3392297 1 121358705 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393217 Affx-122965493 AX-123263574 1 119490301 GCCTAGGGTGTTCCTGATGCTCTCTCCCAGCATCC[A/G]CATTAGAACTCATGATCAGGTAACCTTCATTCTGA R 2 1 2 1 101000 r 74 goat snp27221-scaffold29-3453213 1 121420959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417051 Affx-122947521 AX-123287399 1 119535994 TTGTTTCTGCCTTGGACTTTACAATCTACTGATTA[C/T]GGGATATGCCTTGTTCCAGGGAATCTGTGTACAGG Y 2 1 2 1 201000 f 74 goat snp27222-scaffold29-3498906 1 121465951 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394996 Affx-122964240 AX-123265351 1 119612931 CCTCAACAGGTATGTAGGATCCACTGTCTCAGGTT[C/T]GATACCCCCAGGCATCTCACACTTGCCTAATCTAA Y 2 1 2 1 201000 r 74 goat snp27224-scaffold29-3575843 1 121544152 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419062 Affx-122945808 AX-123289410 1 119663884 AGCACCATGTAGATGTGTATACATATGTATACATA[C/T]ATTTGCATGTATTGCATTTACTTAGTGCTTACTCT Y 2 1 2 1 103000 r 74 goat snp27225-scaffold29-3626796 1 121595226 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786302 Affx-122966660 AX-186931094 1 119733838 ATTTGTATTGTCATAAAGGTACAAAAGTTCTTGGC[A/G]TATTGGATAATAAACAGTTTTGGTGTGATTTGTGC R 2 1 2 1 101000 f 74 goat snp27226-scaffold29-3696750 1 121666874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782327 Affx-122945025 AX-385269404 1 119800880 AGCAACCAAGCACACATAGCTTCAAGTCAAGTCCA[C/T]AAGACTCCCCTTCCCACAAAACGGTGATCTCCTCA Y 2 1 2 1 101000 f 74 goat snp27227-scaffold29-3763792 1 121734383 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405642 Affx-122956586 AX-123275994 1 119879452 GTGCTACCAGTTAAGACAGGGAACATACAAGAAGG[C/T]ACCTAAGGTAAAATCAGTTTTGTTTTAAATCTGTT Y 2 1 2 1 101000 f 74 goat snp27229-scaffold29-3842364 1 121812783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790405 Affx-122956111 AX-385277408 1 119946308 TTTTAAGCACAGGCTTACTGAGTCTACAGTACTTC[A/G]TTACACCATACTAATTTCATACAGGTCATCTAACT R 2 1 2 1 101000 f 74 goat snp27231-scaffold29-3909220 1 121879669 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380752 Affx-122975127 AX-123251110 1 120003170 ATTCACCATTCAGGAAGGGGCTAGACACCTCCAAA[C/T]GGGAGTTAAAGGTATAAGCTTGCCTGACTTACTGG Y 2 1 2 1 101000 r 74 goat snp27232-scaffold29-3966082 1 121936805 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800146 Affx-122965714 AX-385287069 1 120043093 AATTGTCGTTAGTTTACACTTACTTGATTGTTTTA[A/C]AGATAGATTTCGGCCTTGTTAATACTCTGCCACTC M 2 1 2 1 101000 r 74 goat snp27233-scaffold29-4006005 1 121977146 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802429 Affx-122970457 AX-385289333 1 120083352 GTTTTGTTGAATATCTACAGCATGCCAGATAAGTG[C/T]AGACACAAATAAAATTCCCCTTAATATAGTTCTGG Y 2 1 2 1 101000 r 74 goat snp27234-scaffold29-4046264 1 122016851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411557 Affx-122951641 AX-123281907 1 120140330 AGGCTTTCTACAATGATTAAATGTGTCAATTCATA[C/T]GAAAGGACTTAGAACAGTGCCTTAGAATTAATTTA Y 2 1 2 1 201000 f 74 goat snp27235-scaffold29-4103242 1 122073434 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411098 Affx-122951921 AX-123281448 1 120179602 ACATAGATGGTGATACACTCATTCAGTGGAATTCT[A/G]CACTGCAATGAAAAATTACTGTTTGCAACCACATA R 2 1 2 1 101000 f 74 goat snp27236-scaffold29-4142514 1 122112797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406598 Affx-122956255 AX-123276950 1 120208994 GATGGGGCGCAAAAAAATGAAAGGGATGTTGTGAA[C/T]AGTGTCCAAAAAGTGACAACACTTGGTGGCAAATG Y 2 1 2 1 101000 f 74 goat snp27237-scaffold29-4171906 1 122141743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769588 Affx-122959459 AX-385256758 1 120317123 TGTTCTAGGAAACATTTGAGTATGTTCTGCCAGTG[C/T]ATGATATTTGGATCTGTTCTTATTCTGTGTATGTT Y 2 1 2 1 101000 f 74 goat snp27239-scaffold29-4280035 1 122252351 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391703 Affx-122967513 AX-123262060 1 120356741 ATATTTATCTCAGCTATCTGGGGCCAGTTTCCTGT[A/G]TCTTGTCTTTTCATATCCCCCTAAGCTCCTCAGTG R 2 1 2 1 201000 r 74 goat snp27240-scaffold29-4319653 1 122294386 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788327 Affx-122932141 AX-385275345 1 120370639 CAAAACTTTTTGTTAATCTTCATAAATGACTTATA[C/T]GAGCAAAGTAAATCTTGGATAATAAAAGCTGAATG Y 2 1 2 1 101000 r 74 goat snp14652-scaffold1590-683424 1 122325202 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793217 Affx-122969594 AX-385280195 1 120426454 CTTACTGGTTTCAAGAAATTAACCTGGAAATTATT[A/G]TGTCATTCCATGATAATTATACAATCCAGAATCTA R 2 1 2 1 101000 f 74 goat snp14651-scaffold1590-627609 1 122380371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427783 Affx-122939776 AX-123298126 1 120458177 TAGCAAAATAAATTTCCAGAAAGAGTTTTGTACTC[A/G]TAGAAATCAATTTTCCCAATGTAATAAACCAGCCT R 2 1 2 1 101000 r 74 goat snp14650-scaffold1590-595886 1 122411571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389890 Affx-122968129 AX-123260247 1 120493043 ACTAACCCACTGTGACACCACCCTGTTACCTCACC[A/G]TCAACCAATGAGAGGACTATGCATGAATTGATCAA R 2 1 2 1 101000 r 74 goat snp14649-scaffold1590-561020 1 122447646 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787716 Affx-122932713 AX-385274739 1 120542757 AGATAACTTAGGAGATAACTGTATTCAAAATGTTG[C/T]AATACAGACTATTCTTTACTCAAAAACATGTCAAA Y 2 1 2 1 101000 f 74 goat snp14648-scaffold1590-511306 1 122506755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404627 Affx-122957325 AX-123274979 1 120600162 ATACAATTGAATATTTCTTTCTCCTTTGAAAGATT[A/G]CAAACAGGTCAACCTGTTGTTGTACCACGTTAAAG R 2 1 2 1 103000 r 74 goat snp14647-scaffold1590-453901 1 122564348 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411613 Affx-122951595 AX-123281963 1 120658886 AATAACCAGAATGGGAATGACATTGTACTTCTCAA[C/T]AGCAGCACAAGTTGCTCTAAGAGAAATGAATAATG Y 2 1 2 1 101000 f 74 goat snp14646-scaffold1590-395177 1 122623602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440398 Affx-122929619 AX-123310735 1 120690904 GGCACACTTAGTGGCATTTTTCTAAGATTATTCCA[C/T]GCAACTTACTCATGATAATAGTAGTATAGTCATAT Y 2 1 2 1 101000 f 74 goat snp14645-scaffold1590-363159 1 122655516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428262 Affx-122939410 AX-123298605 1 120724276 AATTATTGAGGCAGAAGATTCTGCATCATTCTCCA[C/T]TGAATGCAGACTGGCTGACTCTTCAGATGTTAAAT Y 2 1 2 1 202000 r 74 goat snp14644-scaffold1590-329787 1 122688253 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775027 Affx-122953115 AX-385262159 1 120760763 GAAAGAGAGGAAATAAAAACCTACTCATTAGCAAA[C/T]ATAAGCTATTTCTTTTGGAAAAGGAAGGATATTTC Y 2 1 2 1 101000 r 74 goat snp14643-scaffold1590-293300 1 122724539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379192 Affx-122976303 AX-123249551 1 120827698 ACCATGGATAAGCCACAGTTTCTTCATTTATAAAT[C/T]ATGCTGTGGAACATAACTCAATTAAATTAAATAAC Y 2 1 2 1 102000 r 74 goat snp14642-scaffold1590-226365 1 122791525 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394526 Affx-122964530 AX-123264881 1 120858649 CATATGAAGAAAGGAATGATGAAGAAAATAACTAA[C/T]GATTCAAGAATGTGTCACAATTTATCCGACTCTGG Y 2 1 2 1 101000 r 74 goat snp14641-scaffold1590-195414 1 122822407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403077 Affx-122958512 AX-123273430 1 120900385 CTAACTCTGGTTGGTATCAGAATTGAACTAAATTG[C/T]AGAATACCCAGCTGGTGTCACAGAGAATTGTTTGA Y 2 1 2 1 101000 f 74 goat snp14640-scaffold1590-153678 1 122864426 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380423 Affx-122975305 AX-123250781 1 120946741 CTGAGTTGATTTTTGTCTTTTCTAGTGTTTCTTAT[A/C]GATTGAACTGCAGAGCAGGGACACACTTTGTCCAC M 2 1 2 1 101000 f 74 goat snp14639-scaffold1590-107322 1 122911826 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398579 Affx-122961501 AX-123268934 1 120987096 ATTATACTCCCCTTCTATAGAAAAAGCAGCAAACT[A/G]CTGAAAAGAGTACTTCCATTAAAAAGCAGAAGCAT R 2 1 2 1 201000 r 74 goat snp14638-scaffold1590-66967 1 122952220 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271724 Affx-1111832833 AX-519545520 1 121035617 TAAATGAAACCTCAGATTATGAAGCCAATTAAGGT[A/C]AAAAAAATTAGTGTAAGAAGCTGCATGTCATGATT M 2 1 2 1 101000 r 74 goat 1_121035617_AF-PAKI 1 121035617 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387908 Affx-122970456 AX-123258266 1 121048966 GCTACAGAAGTGAAATAATTGGGGCAAATGATGGC[A/G]TTAATCAGCAGATTCTCTACCTGGAGAGGAATTCT R 2 1 2 1 101000 f 74 goat snp14637-scaffold1590-5097 1 123015156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417922 Affx-122946724 AX-123288270 1 121098939 TCCTCTTAGGAAAATAATGTAACTCTCTGCTAGAT[A/G]TAAAACAGAAGAAAAGATGTGGCCATTTCCAAGCA R 2 1 2 1 101000 f 74 goat snp16955-scaffold177-1087146 1 123067362 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803168 Affx-122933351 AX-385290031 1 121136119 AACGCATAATCATTCCAAAATGATTAAGTTTGAAA[C/T]AAATACTTAAACATTTCCAGTAATAATTGTTTATT Y 2 1 2 1 201000 r 74 goat snp16954-scaffold177-1049966 1 123104454 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406322 Affx-122955455 AX-123276674 1 121166200 TCTCTTAATATATGCTTCTGTGGTGATCCAGAAGA[C/T]AATGCAATAATAAAAATATTTATGGGAGCAGATGT Y 2 1 2 1 201000 f 74 goat snp16953-scaffold177-1019885 1 123134772 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777781 Affx-122941442 AX-385264899 1 121204522 AAAAAGTTATGTACTACATCTATTTTGTTCTATTC[G/T]ATATTTGGAAGCATGTAAGTCTTCTGTAATATAAT K 2 1 2 1 101000 f 74 goat snp16952-scaffold177-981563 1 123173848 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406622 Affx-122955831 AX-123276974 1 121233953 GACTTCAGATCTCAAAGGATTGAAATTATTTGTCA[C/T]ATTTTCTCTGACCACAGTGAAATCTAGAAGGAAAA Y 2 1 2 1 303000 f 74 goat snp16951-scaffold177-952132 NW_017207670.1 4161 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799731 Affx-122977405 AX-385286658 1 121316305 ATACTCAGTCTTTTATTGTATGAATTAATTAGCAT[A/G]AAGTCATAATTTTGACTCTTTTGTGAATCTAGTAC R 2 1 2 1 101000 r 74 goat snp16950-scaffold177-869780 1 123284237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388155 Affx-122969457 AX-123258513 1 121346925 TTCGACTATAATAAATCTTCCTTGCAGGAGATTTT[A/G]CTATGACATATATACTAGCCTACTTTCAGTGAGAC R 2 1 2 1 101000 r 74 goat snp16949-scaffold177-839160 1 123315079 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276724 Affx-1111835487 AX-519550234 1 121389214 GATTTAAAAGGAGGAAGGAAGGGGATGATGCCATT[A/G]TTCTTTGTATGTAGTTGTAGCATGATACATGGGCA R 2 1 2 1 201000 r 74 goat Random2.2K-123 1 121389214 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409881 Affx-122952907 AX-123280232 1 121405734 AAAGAAAAGTGCTGTTTGTATTGTTTCTGTTTAAA[C/T]GAAGGAGAAGGAGTCGTGTCCAGTATGGAGCAGAG Y 2 1 2 1 202000 f 74 goat snp16948-scaffold177-780351 1 123373118 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437765 Affx-122931709 AX-123308103 1 121447986 CATTTCTTACTTGCACCTATAAATAAACCAAGCAC[A/G]CATATTTTTTAAAACAAGCTACAAGAAACAAAGCA R 2 1 2 1 101000 f 74 goat snp16947-scaffold177-738099 1 123415504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441711 Affx-122929152 AX-123312048 1 121479956 CTTAGTTTCTCACGGTTCTCACCATCTCCCCTCCC[A/G]CAGTCAAAACCAGATCCTGTTAACACTGACGACAC R 2 1 2 1 101000 r 74 goat snp16946-scaffold177-706129 1 123447547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443994 Affx-122926911 AX-123314331 1 121574699 TCTTATTAACTGTGATACTGAGAATATAATAGACA[C/T]AGGTGAGGTCTGTATGGGTTCTGTTAATGGCAGGG Y 2 1 2 1 201000 f 74 goat snp16944-scaffold177-611386 1 123542876 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433746 Affx-122934505 AX-123304087 1 121607128 CAAATAATATAATCATTCTGATTTCAGTATTGATC[A/G]TCTGGTGATATCTGAATTTGGTAACTGGAGATATA R 2 1 2 1 102000 r 74 goat snp16943-scaffold177-578957 1 123575192 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436693 Affx-122932332 AX-123307031 1 121664137 AAGATTCAGAATTTTGACATTTCTTTTTATTTTTA[C/T]ATTGCTTTTTACACAGTAAAATTGAAATGAGCTAA Y 2 1 2 1 103000 r 74 goat snp16942-scaffold177-521948 1 123632639 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409203 Affx-122953172 AX-123279554 1 121703953 TTTTTTATTGTATTGGCCTCCTGGTGAGAATTTAA[C/T]GGGAATGGATCTGCAGAAAACTTATTTTGGTTAAT Y 2 1 2 1 101000 f 74 goat snp16941-scaffold177-482132 1 123673382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450505 Affx-122922509 AX-123320839 1 121739933 AATGTGTAATAAGGAAACTGCAAGAAAGATTCTTT[C/T]ACCTGCAGAAATAAAATTCCTTTATTTGAGAGTAA Y 2 1 2 1 101000 r 74 goat snp16940-scaffold177-446152 1 123709920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437361 Affx-122931931 AX-123307699 1 121864474 TCTGAAAAATAGCTTGTTGAAGAGCATTACTAATT[A/G]CATCAATCTCTTGGGGCTACATGTTGTTAAAAATC R 2 1 2 1 201000 f 74 goat snp16938-scaffold177-321611 1 123836018 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423194 Affx-122942720 AX-123293540 1 121896227 GATTTGTGTTCTTTTATTATTAAAGACCTGGTTGA[C/T]AATGAAGAGAGGTTCAATAATTAGCCCAGAAATAG Y 2 1 2 1 101000 r 74 goat snp16937-scaffold177-289858 1 123868225 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434557 Affx-122934132 AX-123304898 1 121943419 AGACAAAAATCGCTTACACAGGACTGGCGATGTTC[A/G]TTGGAGAGAAGTGGACAGACTTGAGAGCTTTTCTA R 2 1 2 1 101000 f 74 goat snp16936-scaffold177-242666 1 123915386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426559 Affx-122940173 AX-123296905 1 121974254 ATGTCATATTTATCTCCTTCAATTCTCATTAAACT[A/G]CTCTGCTCACAGTAGAATTTAAGCTGTATTTTTAA R 2 1 2 1 101000 f 74 goat snp16935-scaffold177-211831 1 123946108 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424474 Affx-122941764 AX-123294820 1 122020403 AAGTTAATTAAAAACCTGAGATGAAATAAAATATC[C/T]AAAGATGGTTCTCTGGCTTCTTATTTTTAGGACTG Y 2 1 2 1 201000 f 74 goat snp16934-scaffold177-165682 1 123992775 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769169 Affx-122954586 AX-385256344 1 122050419 TTTTGCTCCTCTTTCTCAAGTTTTAAACATTTCCC[A/G]CTAGCATCCCTGTTCCAGGCTTTTCATTTTTCTGT R 2 1 2 1 101000 f 74 goat snp16933-scaffold177-135666 1 124023566 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784672 Affx-122963313 AX-385271720 1 122092899 CCACTTGAATTTCATTCCAGGAAGTAACACAAACT[A/G]CAGAGATAGTTGTGTATACTTTTGTTTGTCAGAAA R 2 1 2 1 201000 f 74 goat snp16932-scaffold177-93186 1 124066756 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801886 Affx-122937937 AX-385288793 1 122133651 GAAGAGAGGGATAATCTATGATTGAATAGCCAAAA[C/T]GACATGATTCCTTTTTGCCCAGTTTGTGCAGAACT Y 2 1 2 1 101000 r 74 goat snp16931-scaffold177-52434 1 124108131 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381621 Affx-122974774 AX-123251979 1 122163298 TCACTCTCAGGTAATGGAATATCTTCCAGTCATTC[A/G]TGTATATTAAGATAATTTTTAAAGATAGTTTTATT R 2 1 2 1 101000 f 74 goat snp16930-scaffold177-22787 1 124137808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451993 Affx-122920927 AX-123322326 1 122233791 GGGCCTTATCTCAAAGCAATATTTTCAAAAGTTTG[A/C]TGCACTGGACTTTCCTATTACACAGTAAAAAATGT M 2 1 2 1 101000 r 74 goat snp25854-scaffold266-3258613 1 124180025 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801284 Affx-122930928 AX-385288196 1 122266559 GGCCAGATGCCATTTATCCTCTAATAACTCTTTAG[C/T]GGAAAAATTCAGCACTAAGAGAAAAATATGTTAGA Y 2 1 2 1 201000 r 74 goat snp25853-scaffold266-3225845 1 124213199 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434003 Affx-122934238 AX-123304344 1 122296181 CAAGATCCCTAGGAATATGAAAATATATAAATGAC[A/G]CTTTTCATCAGCACCACCTGTGTCACAAAGAGGAT R 2 1 2 1 101000 r 74 goat snp25852-scaffold266-3196223 1 124243258 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423313 Affx-122942628 AX-123293659 1 122353075 GTTTCTTCCAATATAAGATATAAATAAATAAACAG[C/T]AAACTCTAGTTGGGAACTATTTCATTGCATGGTTG Y 2 1 2 1 103000 r 74 goat snp25851-scaffold266-3139329 1 124298595 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798089 Affx-122940680 AX-385285024 1 122382460 GACATTACCAAGTTTTTGGCTCTTGCCCAGTCTAA[C/T]AGGTAAAAAATTGTGTTGCAGTGCAGTTTTAATGT Y 2 1 2 1 101000 f 74 goat snp25850-scaffold266-3109944 1 124328326 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779636 Affx-122966950 AX-385266738 1 122424034 TTGGGTTCTGAAACTAAGCATCTAGATCAGTTGCT[A/G]TTCTTTTCTTTCAGTGGTTGTGTTTCAGTTTCATT R 2 1 2 1 201000 r 74 goat snp25849-scaffold266-3068370 1 124370469 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425231 Affx-122941007 AX-123295577 1 122469927 CATTATGATGTGAAAAATCCATCAGCTGAAGCTGA[C/T]CCAGAACTGGATTAAGATAAGGACATTAAACCATA Y 2 1 2 1 101000 r 74 goat snp25848-scaffold266-3022477 1 124416139 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399506 Affx-122961168 AX-123269861 1 122509026 TAACAAATTCCAGAATTTATCATTTATATATGTTT[A/C]TAATCATCTTCCCAACTCAGGCTAAAAAGCCTTGC M 2 1 2 1 101000 r 74 goat snp25847-scaffold266-2983378 1 124455396 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434974 Affx-122933838 AX-123305314 1 122548666 GGTATAATTCAAATGTTCTATTTTTTCTATTTCTT[A/G]CAAATTCTCTTCAGGATACAGAAGGTGATAAAACT R 2 1 2 1 101000 r 74 goat snp25846-scaffold266-2943738 1 124496094 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433520 Affx-122935011 AX-123303861 1 122581667 CTTTCTAGTTACTTTGCATAATAGTTTGCTTTGTT[A/C]GCCAAGTTTAACTGTACAAAACAATCTTATTTTCT M 2 1 2 1 101000 r 74 goat snp25845-scaffold266-2910737 1 124529280 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402283 Affx-122959109 AX-123272636 1 122618296 TATTTCTGCATTGCATAAAACTTTATACATTTTCT[A/G]TAAATGATGATGCTTGGTGTATGCGTTGTTAGAAA R 2 1 2 1 101000 r 74 goat snp25844-scaffold266-2874108 1 124565261 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437674 Affx-122931777 AX-123308012 1 122664834 CCCCGTGTTGTACAATACCAAGCCATCTTGATTAA[C/T]GTAGCTTTACAGGTAGTGTTGAAGTTGAGTAGTTT Y 2 1 2 1 101000 f 74 goat snp25843-scaffold266-2827570 1 124611483 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402754 Affx-122958324 AX-123273107 1 122698863 GAGTGAATGTACTCCTACCCAGTATTATAAGAGAG[C/T]AGGTGACAGATAAAGAGGGACTGCTAATAGGAAGA Y 2 1 2 1 101000 f 74 goat snp25842-scaffold266-2793541 1 124645776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777644 Affx-122930146 AX-385264763 1 122749603 TTACCATGATGGCCTTTATGTCTCTAAATCTGGCA[A/C]TAGCCATGTACTATCAATTTCATCTCCCAAGCAGC M 2 1 2 1 101000 f 74 goat snp25841-scaffold266-2742801 1 124696182 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383096 Affx-122973281 AX-123253454 1 122802107 TATTGCCTAAACCACTTGCTCTTATTAATCAACCC[A/G]CTTGAAAAATACAACAAAATATCCCTAATTTTAAA R 2 1 2 1 101000 f 74 goat snp25840-scaffold266-2690297 1 124748552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449007 Affx-122923098 AX-123319342 1 122842771 AAGCTATCAAAAGGAAAAACACATGCATAACTGCT[A/G]CCTCACTTGCCCTTGCCCTTCTTGCTCTCCCTGGG R 2 1 2 1 101000 r 74 goat snp25839-scaffold266-2649633 1 124789007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410806 Affx-122952650 AX-123281156 1 122890862 CATGTGAAAGCTATTTGAGTTTGTTGAAAGAGATA[C/T]GTAATATAAGTTCAAGCTGCTCTTTTTATTTCTGG Y 2 1 2 1 101000 r 74 goat snp25838-scaffold266-2601542 1 124836595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426846 Affx-122940499 AX-123297191 1 122920561 TTTTTAAGTTAAGCAGATTTATGAGAAATATTGTA[A/C]TTTTTGGCTGGAATAACAGTTTTGGTTCAAGCTCA M 2 1 2 1 102000 r 74 goat snp25837-scaffold266-2571843 1 124866999 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769886 Affx-122974707 AX-385257055 1 122951902 AACCCTGAACCCTCGTGAATATGCATGAGTGCAGC[A/G]CAGTTAGACAGAATATTGGCTGCAAGGTAGAAGCA R 2 1 2 1 101000 r 74 goat snp25836-scaffold266-2540502 1 124899199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400652 Affx-122960358 AX-123271007 1 122985327 AAAATGAAATGGGATCTTCAAAAGGCAAGTCCTCT[A/G]TCACTGGAGATGCTTAAGCACAGAATGAAAGCATT R 2 1 2 1 101000 r 74 goat snp25835-scaffold266-2507077 1 124932532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410423 Affx-122952409 AX-123280773 1 123024303 TACCTTCTAAACCTTTGCCCCTTTCAGAAAGGAAA[C/T]AGTGGCTACCTCTATAATATCTGCTTCAGCTTTTC Y 2 1 2 1 201000 r 74 goat snp25834-scaffold266-2468101 1 124971657 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779277 Affx-122966376 AX-385266381 1 123057179 TTAATCACAGCTTTCTTTCCCATTGATTTTGGGAA[C/T]AGCTATAAACTCCACCTTTATCTTATGTTGTCAGT Y 2 1 2 1 202000 f 74 goat snp25833-scaffold266-2435225 1 125003697 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776142 Affx-122941287 AX-385263272 1 123121250 GTAAGGCACCTATATTTGATCACATTTTACGATAG[C/T]AGGCTAATGAATACCCTTCAATAGAGCAGAATGTT Y 2 1 2 1 101000 r 74 goat snp25832-scaffold266-2371154 1 125067107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442001 Affx-122928425 AX-123312338 1 123178145 CTATATCCTTTGGTGAGAATGGACTTTTAGGAGAA[C/T]GAAAGATTAAAATGAAGAGATTAGTTGAAGATACC Y 2 1 2 1 101000 f 74 goat snp25831-scaffold266-2314259 1 125124047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416229 Affx-122948219 AX-123286578 1 123223584 TACTTCTCTGTCAAGTCAAAATTGCTCTCTATGGT[A/G]TCATTTCCAGAAAAATAACTATGGGATGAAGTACT R 2 1 2 1 101000 f 74 goat snp25830-scaffold266-2268820 1 125169503 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436734 Affx-122932301 AX-123307072 1 123260964 TCCCTCCTGGATCATTTCCATCAGCTACAGACAAA[C/T]GTGATCTGGTGTCTTCCATATTTAACTCTCCTCCA Y 2 1 2 1 101000 r 74 goat snp25829-scaffold266-2231440 1 125207289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773667 Affx-122965151 AX-385260807 1 123369820 GTTTCCAATAGCATCTGCAGGCTCTCAAATTTGTC[A/G]TTCCTTCTCCCTAGAATTCTCTGAGCTCTAGACTC R 2 1 2 1 101000 f 74 goat snp25827-scaffold266-2122584 1 125316857 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439138 Affx-122931083 AX-123309475 1 123439457 GACTGAGCGACTGAATTGAACCAGATAAAATGGTG[C/T]AGGAAATGAGTGTAAATTCAAAGTCACGAAGAAAT Y 2 1 2 1 201000 r 74 goat snp25826-scaffold266-2052947 1 125386355 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390280 Affx-122967736 AX-123260637 1 123485061 GGGTGTCTGGGAGGTGGATATATGGCTTGTACTCT[A/G]TGGGCTTTGCAGGTAGGAACTTGGTGGGCAGGTGG R 2 1 2 1 101000 f 74 goat snp25825-scaffold266-2007343 1 125431929 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796680 Affx-122930637 AX-385283625 1 123516406 AAGTTGGGACTTAAAGGCAAAGACAAAAGAGACGA[C/T]AGGACACTATCCTTGAGGTACTTGCTGAGATCCTA Y 2 1 2 1 101000 f 74 goat snp25824-scaffold266-1975998 1 125463671 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449249 Affx-122923473 AX-123319584 1 123549273 TTTCCTACTACTAGCTGTGTGATCATTTGGAATCT[A/G]TTTTCATCTGTAAAATGGCAGTAATCTTGCCTGTT R 2 1 2 1 101000 f 74 goat snp25823-scaffold266-1943131 1 125496583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375808 Affx-122978563 AX-123246167 1 123614451 TACACTTTGAAGACCGCTGATTGAGAATAGGGATA[C/T]GACAAAGAGCTGTTGTGAACTCAAGAATGCTCTGA Y 2 1 2 1 101000 f 74 goat snp25822-scaffold266-1877953 1 125561884 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463688289 Affx-1110107313 AX-515168538 1 123634970 CATAGTAAGTATTGGATTGGTGAAGCAAAAATACC[A/C]AAGCCAAGGGATCTCTGATTCTCTAGACTTCCTCT M 2 1 2 1 201000 f 74 goat 1_123634970_AF-PAKI 1 123634970 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38453026 Affx-122920092 AX-123323359 1 123672498 CATACATTCAGCAAGTATTAAACAAGTGCCTGCAA[C/T]ATGCTAGGCACTGTACTGAGTGCTGAGGATCCAAT Y 2 1 2 1 201000 f 74 goat snp25821-scaffold266-1819906 1 125620409 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783391 Affx-122920873 AX-385270454 1 123713016 TGGGCTTGATGTTTCTCTAATAGAAAAACAAAGTC[A/G]TGTAAGCAAAGAGTCATTTTTACAAGTTTAAAAAA R 2 1 2 1 101000 f 74 goat snp25820-scaffold266-1779388 1 125661326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795240 Affx-122968249 AX-385282198 1 123800765 TAGCAAAGAGTTGGTTTATTCTCATGCTAAGTTCT[A/G]TCCTGAAATTAATATCTGAAAGTGGTCCCCAGAAA R 2 1 2 1 101000 r 74 goat snp25819-scaffold266-1691639 1 125749280 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435095 Affx-122933714 AX-123305435 1 123847304 AAAAAGAAGGGGAAAAAAGCAAGGTAATAGGATCA[C/T]GTAGGACCTTGTTGGCTCTTTTATGGACTCTGGGC Y 2 1 2 1 101000 r 74 goat snp25818-scaffold266-1645100 1 125795901 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781158 Affx-122947850 AX-385268243 1 123925237 ACAAGTTCTGGGTCAAATGATCTATTCTGCCTGCC[A/G]TTCTTTAAGCATTCAATAGGGCCACTGTATTTTTA R 2 1 2 1 101000 f 74 goat snp25816-scaffold266-1567167 1 125874006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802892 Affx-122978098 AX-186977875 1 123963534 TGCAAACACTGTGAAACAAGGGATTTACTAATAAA[A/G]TTATTATGTGGCCACTAAATATTATGTTGATACAT R 2 1 2 1 201000 r 74 goat snp25815-scaffold266-1528870 1 125912185 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428250 Affx-122939418 AX-123298593 1 123995551 TTCCTGGGCCCAGCCTTATATGGAACAGTGGAGAC[A/G]TGGACCTTGACACTTGTTTGATTATATGACTCTAG R 2 1 2 1 101000 r 74 goat snp25814-scaffold266-1496853 1 125943991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415461 Affx-122949167 AX-123285810 1 124056440 TCAGTTTCACATTATGAGCTTCTTCTCACCATCTA[A/C]ACCTTCTCTAGTGGCTAATGTTGCTGCTCTGCAGT M 2 1 2 1 101000 f 74 goat snp25812-scaffold266-1435964 1 126004373 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398896 Affx-122961023 AX-123269251 1 124097886 GCTTCTTTCTATCATGAAAACAAATACAACTCAGT[G/T]TGCAATCAACTAACTCCTGAGGGTCTTAGGCTCTC K 2 1 2 1 101000 r 74 goat snp25811-scaffold266-1394518 1 126046344 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447035 Affx-122924534 AX-123317371 1 124143094 ATCCTCCCACTCTGGCAGAAACAAGGTTACATCCT[A/G]TAGAAGAGAACACAGAATACTCACTTAAGAAAATC R 2 1 2 1 201000 r 74 goat snp25810-scaffold266-1349310 1 126091255 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409431 Affx-122954115 AX-123279782 1 124211012 AGCAGAATTGGACCGAAGCAGAGAACTACAGAAAC[A/G]ACTGAAACAGACAGAGAAGCTATGATCCTTGGAAA R 2 1 2 1 101000 f 74 goat snp25809-scaffold266-1281392 1 126159397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414288 Affx-122949596 AX-123284637 1 124276659 TTTCATACTAAAGGCACTACTAATATACAAATATC[C/T]TATTAACATTTGGAGAAACTCTTAACATTTAGCAG Y 2 1 2 1 101000 r 74 goat snp25808-scaffold266-1215745 1 126224885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442227 Affx-122928303 AX-123312564 1 124339628 TCAACCCACCACACATACTTCAGGGTGACTCCTAT[C/T]AAATTTCACTAGTATGGGGAGTATGCAGTGTGTAT Y 2 1 2 1 101000 f 74 goat snp25806-scaffold266-1152776 1 126288313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388533 Affx-122969198 AX-123258891 1 124387492 GATTTGTCTGATGAATCTTCCACCACGATCATCGG[A/G]ATATCGCTACTTATGTGTACATATGTGAAGCAACA R 2 1 2 1 101000 f 74 goat snp25805-scaffold266-1104912 1 126336392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406696 Affx-122955775 AX-123277048 1 124422883 TATGTAGAAAAATTCTTTTAAAATATGAACTCAAA[C/T]GAGGAGTCATCAAGGGAAGAAAACTGATATAACTA Y 2 1 2 1 103000 r 74 goat snp25804-scaffold266-1069521 1 126371812 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436327 Affx-122933252 AX-123306666 1 124484447 TAATTAAAATATAGTGCAGATGCAGAAATAGGGCA[A/G]TACAGGGTTTCACAGGAGCACAGACATGACAAATT R 2 1 2 1 201000 f 74 goat snp25803-scaffold266-1007957 1 126434640 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408367 Affx-122953731 AX-123278718 1 124603296 TGGAAATGGGGAACCTATCTGGGAAAATGGCCCTC[A/G]GGTAGTCTTTAGCTCCACTAAAGTCAGTCATACAC R 2 1 2 1 101000 r 74 goat snp25801-scaffold266-889108 1 126551137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273982 Affx-1111833932 AX-519547587 1 124616291 TCCTTTGCCGCTGGAGCCTTGTCCCAAGCAAAATT[A/G]TTTGTTCCCAGTTTTGTGAACTGTACAGTCTAGGT R 2 1 2 1 202000 r 74 goat GoatD01.010903 1 124616291 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437786 Affx-122931694 AX-123308124 1 124643070 AGCACGTTAATACAGCCCTGCTGTGGCATGTTCTT[A/G]TTGTTCAGTCGTTAAGTTATGTCCTGTTCTTGGCG R 2 1 2 1 103000 f 74 goat snp25800-scaffold266-849334 1 126590513 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384233 Affx-122972371 AX-123254591 1 124683449 GGGGAAATGTCATCTGCCCAGGAAGGAGAGGAAAC[A/G]TATTTGGGGAGTCACAGCTCACCTCTGGCATAGGT R 2 1 2 1 102000 f 74 goat snp25799-scaffold266-808955 1 126630832 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798908 Affx-122935200 AX-385285838 1 124713236 GTTTTTTCTGTGAAAGACATGATAGTAAATATTTC[C/T]GATTTTGTGGATGGAAACTACTTAACTCTGCCTTG Y 2 1 2 1 101000 r 74 goat snp25798-scaffold266-779168 1 126660500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789881 Affx-122922826 AX-385276888 1 124748543 TCATCTGAAGTGAAAGCAGATCAGAGGAGATTCAT[A/G]TGGATTGTGGTTGTTTGCAATCCCGGTGAAAGATG R 2 1 2 1 101000 f 74 goat snp25797-scaffold266-743861 1 126696327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444050 Affx-122926864 AX-123314387 1 124797258 CTTACCGATATCCAAGGAGTTATTGAAGTGGTTCC[A/G]TTCAGAAGAGAATTTTTTGCATGCTTATGGTTGAT R 2 1 2 1 101000 f 74 goat snp25796-scaffold266-695146 1 126745796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773518 Affx-122960361 AX-385260659 1 124832092 TGAAATCATAAAAATGGCATGGCAGATAGTTATAT[A/G]TTAGCCCTCAATGGGTCTTGAAGACCTCATTAGAA R 2 1 2 1 101000 r 74 goat snp25795-scaffold266-660312 1 126780546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447062 Affx-122924513 AX-123317398 1 124883357 CATTGTATAAAGGCAACATACTTTTGATACCCAGC[A/G]AGAAGCAAGAAAAGAACTCAGAGATAGTCTTGCCC R 2 1 2 1 101000 f 74 goat snp25794-scaffold266-609047 1 126831533 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773104 Affx-122938509 AX-385260247 1 124923677 ACTGCCAACATTGTGTTTTACTAGGAAAATTTCAA[C/T]CCATGACTATTCAGAGCTTTCCGTTTAGTTCATCT Y 2 1 2 1 101000 r 74 goat snp25793-scaffold266-568727 1 126872579 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408560 Affx-122953675 AX-123278911 1 124964034 GGCTATGGAATGGGGGTGGTACACTTAATACCTGC[C/T]TCCCAACATTAGAGGATGAATTGGTTTCACGTAAA Y 2 1 2 1 101000 f 74 goat snp25792-scaffold266-528370 1 126913220 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410306 Affx-122952491 AX-123280656 1 125002753 ATGAGGAAGAAGTTTTAATGAAAAAGATATGTTTT[A/G]TTAACTCAGAGGAGAATCCTTAGAACTGTGTGATT R 2 1 2 1 101000 r 74 goat snp25791-scaffold266-489651 1 126952028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771596 Affx-122964927 AX-385258754 1 125032239 AGTCTCCATATGCCTATTTGTGACTCATTCTCTGC[A/G]TGAATAATATCACAAGTATAAATGTCTATCTCTTC R 2 1 2 1 101000 f 74 goat snp25790-scaffold266-460165 1 126981505 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423579 Affx-122942402 AX-123293925 1 125091647 TCGCTCTGAATTGATTGCAAACTAAACAGAAGTGC[A/G]CGTGTCTTACAGGTCTTTTGTTGTTTAAGCAAAAT R 2 1 2 1 101000 f 74 goat snp25789-scaffold266-400757 1 127040891 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398187 Affx-122962645 AX-123268542 1 125126749 TTTTCCTTTCTTTGAGCCAAAGCAATAACAGTAAG[C/T]AGTTTTTTGGTGCTTCAGAGCTGTGTTTCATTGTT Y 2 1 2 1 101000 r 74 goat snp25788-scaffold266-365655 1 127075969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436016 Affx-122932742 AX-123306355 1 125170430 TTTGACTTGAACCCACAGGACTGAAAATAAAATGA[A/G]CTCAGACTGTAGAAGGAGGCTGTAAGCAAGCAAGG R 2 1 2 1 202000 f 74 goat snp25787-scaffold266-321974 1 127119577 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772617 Affx-122956960 AX-385259765 1 125210642 GAAAGCCACGAGTCTCCTAGACTTATAAAATTTAC[A/G]CATCAAGGATGTCAAAGAGGTCCTCTATGATGTTT R 2 1 2 1 201000 r 74 goat snp25786-scaffold266-281762 1 127159995 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448981 Affx-122923115 AX-123319316 1 125284118 TGAGAAGGACATTTCCCCATATGCTTTCTGCTCCC[A/G]TTTTCTTATTTAATATCTTACCACCCTCCTCAACT R 2 1 2 1 101000 r 74 goat snp25785-scaffold266-208286 1 127230859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423852 Affx-122942772 AX-123294198 1 125332086 TGGCTTGGGGTTCCCAGGCCCATTGCCCTTGGAAT[G/T]TGGGTTACTTATGAGATAGCACTGACCAAATGCAG K 2 1 2 1 101000 r 74 goat snp25784-scaffold266-160318 1 127280688 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380984 Affx-122974681 AX-123251342 1 125386322 GCAACCTAGTTCCTGACAAGATGGAAAGATGAACA[C/T]AGGATCCTTCCCCCTCATTGCTTCGTTCATAGTAG Y 2 1 2 1 101000 f 74 goat snp25783-scaffold266-106082 1 127334851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448658 Affx-122923344 AX-123318994 1 125416460 GCTTCTCCAGTCTGCCTCTGCTTGGAGGTTGAGAT[A/G]CCTCAACAGGGGCCAAGGCCATGAAGCCCCCAGGA R 2 1 2 1 103000 f 74 goat snp25782-scaffold266-75944 1 127364980 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443531 Affx-122927775 AX-123313868 1 125464043 TGGCCTGGATCAAGGTAGAGACTGCTTCACAAGAC[A/G]CTGTTGATGGTTCGCTTTGACTTGTTATAATCGTA R 2 1 2 1 101000 r 74 goat snp25781-scaffold266-28361 1 127412067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440479 Affx-122929376 AX-123310816 1 125498689 ACAGGCAGAGAATCGGAGTTACCTAGGCAAAATCC[A/G]TGCCAGGGAGCAAGGTCAGCGCGTTCGAAGGCTGG R 2 1 2 1 101000 f 74 goat snp11826-scaffold1438-1284450 1 127446515 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792894 Affx-122949208 AX-385279872 1 125574632 TAACGATACATGAATGAAGGCAATGTCTCTTCAGT[A/G]ACTTAACTGATTATGAACTTAAATTGTCACCCATC R 2 1 2 1 101000 f 74 goat snp11825-scaffold1438-1208507 1 127522708 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385366 Affx-122971637 AX-123255724 1 125609910 ACTTGTTTGTTTAAGGGGCAAGGGCACAAGTAACC[G/T]CTTCTTTGTGCTGGTCCTGTGTGAAGCACTTGAAG K 2 1 2 1 101000 f 74 goat snp11824-scaffold1438-1173229 1 127558025 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802385 Affx-122944002 AX-385289289 1 125663188 ATGGTAGACTAATATAAACGTAGCTACAGGCAGCC[A/G]CATTTGCAGCTTCAATGCCAGATACAGTATCTTTA R 2 1 2 1 101000 f 74 goat snp11823-scaffold1438-1119951 1 127610396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775377 Affx-122934156 AX-385262508 1 125698770 GTCTCTAATCCACTGGTATTTAACTAAAGTTAGCT[A/C]AAATAATTCCCCTCATTCTGTGGAAAACCTAATGC M 2 1 2 1 201000 r 74 goat snp11822-scaffold1438-1084369 1 127645635 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418988 Affx-122946063 AX-123289336 1 125730109 GTAACTTCAGGACCAGACCTCACACCTCCTCCCCA[A/G]TCTAAGAAGGTAGCACCATAATTCTAGCCTTCACT R 2 1 2 1 101000 r 74 goat snp11821-scaffold1438-1053030 1 127678022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454064 Affx-122919388 AX-123324397 1 125769618 TGTGTAACAGGTACTAGACACCTTAGTCTAAACAA[G/T]TGTATGAGAGATTTGGCTTGAGGTGACCCAGGAGC K 2 1 2 1 201000 f 74 goat snp11820-scaffold1438-1013521 1 127718415 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399164 Affx-122960640 AX-123269519 1 125804966 ACAAATTCCACTGGATTTATTCTCTTGGTCAGAGT[A/G]CTCAAAGTCCAGACTGGAATCAAGAACTGAGAAAT R 2 1 2 1 101000 f 74 goat snp11819-scaffold1438-978173 1 127754149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385025 Affx-122971861 AX-123255383 1 125853679 ATGAAATTTCTGCTCCTTTAATCTTTGCAAGCTGC[A/G]TAAAGTGGAAAGCAAAATTCTCCCCTAAAATAGAA R 2 1 2 1 101000 f 74 goat snp11818-scaffold1438-929460 1 127802923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417290 Affx-122947241 AX-123287638 1 125885480 TGTGTTGCAGCGCTTGCACCTGGACAAATGTCTCC[A/G]TGGGCAACAAAATACGAAGAAAGTACAAGAGACTG R 2 1 2 1 101000 r 74 goat snp11817-scaffold1438-897659 1 127834801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419015 Affx-122946045 AX-123289363 1 125936999 AATCCCCCAGCCTTGGCTCTTGGAATCCTCAGGCA[C/T]ATCCCTCTGACCTTGCTCAGGACCTGCAATCCAGT Y 2 1 2 1 101000 r 74 goat snp11816-scaffold1438-846140 1 127887216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396100 Affx-122963422 AX-123266455 1 125981722 CAAAACAGATTAAACCCTTAAAGATGGATGCCCAG[A/C]TCCCACAGCTGAAGACATCCTGCAGTAAAGCAGTG M 2 1 2 1 101000 r 74 goat snp11815-scaffold1438-801417 1 127931852 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445494 Affx-122925195 AX-123315831 1 126015056 TCACCCGTTCATCCTCCCTGGGACTCTGAGGAGAA[C/T]GTTGGATAACATGAGGGATACTTTGAAAATAATAA Y 2 1 2 1 201000 r 74 goat snp11814-scaffold1438-768083 1 127963519 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429811 Affx-122938190 AX-123300152 1 126067658 TCCCAGTGTGCTGCGTCTTCCGGGCCAGAGTACCC[C/T]ATTTGTCCCCATCCCCAGCTCATTCCCATCCCTAT Y 2 1 2 1 101000 r 74 goat snp11813-scaffold1438-715481 1 128016064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415204 Affx-122948984 AX-123285553 1 126131419 CTGCTCTGGATAGCTTTTCCTACAAGGCCCTGTGG[C/T]GTAGCTGATCTGTCCCCACCACACACACACACAGG Y 2 1 2 1 101000 f 74 goat snp11811-scaffold1438-651720 1 128080007 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271812 Affx-1111832834 AX-519545598 1 126138111 TCTTCTTAAGTTAGCATATCAAATAAATGACCTCA[A/G]TTCTAGAACTTACTTAATTTAATTAACTGTCACCC R 2 1 2 1 101000 f 74 goat 1_126138111_AF-PAKI 1 126138111 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320778348 Affx-122934389 AX-385265463 1 126160729 CCATGTGTTTTGGCCATGTTCACAGAGTTAGGAAC[A/G]TTGGAGCTGGTACTTGAAGCCAAATCATCCTGATT R 2 1 2 1 101000 f 74 goat snp11810-scaffold1438-622410 1 128109455 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440249 Affx-122930662 AX-123310586 1 126222287 GACCTGGTGACCCATTTGGTGGCTACAGCTGGAAA[C/T]GGAGCAAGACACATGGCAGACTCATCCATTAAAGA Y 2 1 2 1 101000 r 74 goat snp11809-scaffold1438-560852 1 128171721 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381135 Affx-122974566 AX-123251493 1 126262831 CTACACGTGCATCCAATGTTCTCTGTTCCCATTAG[C/T]GGCACCTAATTAGCAGTAATCCAATTAAGCCTGGT Y 2 1 2 1 101000 r 74 goat snp11808-scaffold1438-520308 1 128209609 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438047 Affx-122931546 AX-123308385 1 126299714 ATAAGTCCATCACTGGTTGAGCATTGCCTTTGGGG[A/C]TAGGCACTTCTGGGCTGCCCCACATAAACAATTGA M 2 1 2 1 101000 f 74 goat snp11807-scaffold1438-483425 1 128246318 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790775 Affx-122973806 AX-385277776 1 126385530 CAATCCATCCGGTTCTCCAAGAGCTAATCAAAAGC[C/T]GCATGTGCAATGATTTATCTTCTGCTCATCTTCCA Y 2 1 2 1 101000 f 74 goat snp11805-scaffold1438-397609 1 128332279 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770724 Affx-122979110 AX-385257888 1 126429075 ATAAAAATGTATCACACATTCGCTACCCTCTAGAA[C/T]GAAGTTGATAGCAAAAGCCACAAAGGTTTTATTTA Y 2 1 2 1 101000 f 74 goat snp11804-scaffold1438-354064 1 128375725 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424186 Affx-122942518 AX-123294532 1 126492454 GAGTTCCTGGAATGAAGGCATAGTATCCTAAGTCA[G/T]CTAGAAACTGTCTCAAGCCAAACATTTGAAGGTCC K 2 1 2 1 101000 f 74 goat snp11803-scaffold1438-290685 1 128439507 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421133 Affx-122944197 AX-123291480 1 126525306 GGTGCTCTTCTAGGCCCTAGGGGAACCTCAGTGAG[C/T]GAAGCAGATTAACATCCCTGTTATTATGGAGCATT Y 2 1 2 1 101000 r 74 goat snp11802-scaffold1438-257833 1 128472620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408961 Affx-122953921 AX-123279312 1 126559305 CAGAGTTTTGAGGATTAAATGAGATCACCTGTATG[C/T]GCTGTTAGCACAGTGACTGACCCACAGTGAAGTCT Y 2 1 2 1 101000 r 74 goat snp11801-scaffold1438-223834 1 128506679 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439847 Affx-122930456 AX-123310184 1 126610922 GAACAGGGTATACTGCCAGGAAATGGGGCTCCCTG[C/T]GCTTAGGAATCATGTGCACCTGGCTTTGCATCTTT Y 2 1 2 1 101000 r 74 goat snp11800-scaffold1438-172217 1 128566484 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416813 Affx-122948131 AX-123287161 1 126644443 AAGTAACATTTCCAGGAAGCTGATATTACTCACTG[A/G]CAGGTTTCTGGGAAAGGATGGAGCCTGTGGTCATG R 2 1 2 1 101000 f 74 goat snp11799-scaffold1438-138696 1 128600199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793551 Affx-122962926 AX-385280526 1 126726793 AAACTGGCAGGCAAAGATGGTCTCCTTTTTCATAG[C/T]CTTGATTACATGTTGAGCCCTATTCTAGGACGTTA Y 2 1 2 1 102000 f 74 goat snp11797-scaffold1438-56346 1 128676575 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778750 Affx-122960030 AX-385265861 1 126761244 ACCCCCATATAGGTCAAATATTCTAGCAAGAAAGT[A/G]TAGCAATCATGAACACATATGCCATGATATATCAT R 2 1 2 1 101000 r 74 goat snp11796-scaffold1438-21895 1 128710957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440507 Affx-122929354 AX-123310844 1 126785109 ACAGCTCATGGTATAAACTGGAGTTTAAGTTATTT[A/C]GTTGCTAGAACAGAGAAAAGAGGAGAATTGAATCA M 2 1 2 1 201000 f 74 goat snp24410-scaffold2473-1871 1 128735061 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791506 Affx-122968090 AX-385278497 1 126828395 GGCTCCTTATGGGTCTCCATGAAGCCTGACATGCC[A/G]TCATTGAAGTTTATGTTACTCTGGACAAAACATCA R 2 1 2 1 101000 f 74 goat snp24411-scaffold2473-45157 1 128778251 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431208 Affx-122937161 AX-123301549 1 126878282 CTGATACTAAATCACTTTTGTGGGTGTTGCAGAAT[C/T]TGGGGTGTCCAGAGTTTAGGGAGGGGCATAAACAT Y 2 1 2 1 201000 f 74 goat snp3462-scaffold1105-1973710 1 128848272 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440300 Affx-122930218 AX-123310637 1 126910700 CACATCTTTTCATTTCCATCATCCCTTGGTTCACA[A/G]ACACCTTCAAGCTTCTGTTCTGTGCTCTGAGACCT R 2 1 2 1 101000 f 74 goat snp3461-scaffold1105-1941292 1 128881789 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379805 Affx-122976236 AX-123250163 1 126961918 TTAGTGAGCCCCTATGCTTTTAAACTTTTGCATAT[A/G]CAGAGTTAGTTAGGTTAGGCTATGCTATGATGTGG R 2 1 2 1 101000 r 74 goat snp3460-scaffold1105-1890074 1 128932771 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421019 Affx-122944548 AX-123291366 1 126990549 TAGCACACCCCACAAATCTTAAGTCAAATATTATG[C/T]GTTTCCCCCATCCCAATCTCTAGCTTAGAGGAAAG Y 2 1 2 1 201000 r 74 goat snp3459-scaffold1105-1861443 1 128961014 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777990 Affx-122946224 AX-385265106 1 127023559 GTGCCTCAAAATTGAGTTACTCAATTTGCAATTTG[C/T]GGACACAATACTCAAACATTTACAAGTGAGCAAAA Y 2 1 2 1 101000 r 74 goat snp3458-scaffold1105-1828433 1 128993746 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775375 Affx-122972862 AX-385262506 1 127074054 TGAGCTAAAACTCCGTCTTGCCCGCTAAATGGTTA[C/T]GAATTTAAGTGTTTATCCTTCCCTACAATCCTACA Y 2 1 2 1 101000 r 74 goat snp3457-scaffold1105-1777938 1 129045102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770395 Affx-122956170 AX-385257562 1 127107655 ATCCTTGCTTTCAGAGAACTTGATGTTGCTATTGA[A/G]TCAGTCATTTCAAGAGTGATGAAATTCTCTCACGA R 2 1 2 1 101000 r 74 goat snp3456-scaffold1105-1744337 1 129078685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427532 Affx-122939511 AX-123297875 1 127137282 GAGTCCTGCCATAGAACAAAGCCATCAGGAGGAAA[C/T]GAAACAAGGGTTTGGAAGGACTTGTTTTAGAGCTG Y 2 1 2 1 201000 r 74 goat snp3455-scaffold1105-1714710 1 129108226 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799362 Affx-122938962 AX-385286292 1 127175486 TGTTTTATTGTTCCTTTGATTCATAAGCAACCAAG[C/T]ATTGTTTCTCAGGTACTCATTAGCATGTCTTAATC Y 2 1 2 1 101000 r 74 goat snp3454-scaffold1105-1676506 1 129146430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423459 Affx-122942588 AX-123293805 1 127249346 GAAAGAAAGGGGTGGTGGGTGGTGGTGGGAGAATT[C/T]ACTGCTATTGCTGGGTCCTGTGAAGCAAGGTCCTT Y 2 1 2 1 101000 r 74 goat snp3453-scaffold1105-1602646 1 129220979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441024 Affx-122928945 AX-123311361 1 127315297 GGTTTTCTTAATTTTTTTCTGAAAAATGACAGTCA[A/C]GTTTGGAAACTTCTGGTGTTTGGAATTAGGTTGCT M 2 1 2 1 101000 r 74 goat snp3451-scaffold1105-1536695 1 129287209 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398147 Affx-122961683 AX-123268502 1 127355351 CACTTTGTTCATGTCTCAGGGCTGTCCAAATTCAT[C/T]ACTGTTTTGTGATAACCACATCACATAGGTGTCCG Y 2 1 2 1 101000 r 74 goat snp3450-scaffold1105-1496641 1 129327673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401283 Affx-122959870 AX-123271636 1 127384052 GAATGTTTGTGCTTCTCCAGTTCCTACCTAGGGCG[A/G]TTAAGAGGTGGTCTCACACAGCGGTCATATCACTA R 2 1 2 1 101000 r 74 goat snp3449-scaffold1105-1467940 1 129356087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774450 Affx-122974841 AX-385261586 1 127431105 GGTCGCATTAAGGTGGCTCCTGAATGCTCTCTGTA[C/T]GAGGTAGATTCCATCACTCCATTATACAGAGAAGG Y 2 1 2 1 101000 f 74 goat snp3448-scaffold1105-1420887 1 129402132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769943 Affx-122967425 AX-385257112 1 127505387 ATGTTGATTTTAGTATTGCTGTAAGTTTCACAGCA[G/T]ACATAATCCAGGGCATGATGGAAATCCTAAAGAGA K 2 1 2 1 101000 r 74 goat snp3447-scaffold1105-1346605 1 129475511 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381942 Affx-122974123 AX-123252300 1 127541961 CTCATCCCACATCTGCAAAGGAGGAATTACTCTTC[A/G]TACTTCTTTAGATGAGGAAATTAAGGCCAAGTGGT R 2 1 2 1 101000 f 74 goat snp3446-scaffold1105-1310031 1 129512966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401280 Affx-122959872 AX-123271633 1 127591732 ACCCAACTTTACAGATCAATGAGGGTGTCATTGTC[C/T]ATTTCTCTCCGCTTGTCTCTGGGGCAAAGAAAGGT Y 2 1 2 1 201000 f 74 goat snp3445-scaffold1105-1260260 1 129562610 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447481 Affx-122924345 AX-123317817 1 127640552 AATAGCTAAGGAACTCAATGCAATGAGAGACCTCA[A/G]ACATGGCATGGACTTTACACATTGGTGTGGACATT R 2 1 2 1 101000 f 74 goat snp3444-scaffold1105-1211440 1 129611514 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791025 Affx-122929224 AX-385278021 1 127704874 ATATATACATAAGTTGATCGTGTAGCAGTTGCTAA[C/T]AAGACACTCAATTCTAACATTGCTTTCCCTTTCAA Y 2 1 2 1 101000 r 74 goat snp3443-scaffold1105-1147118 1 129672870 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413186 Affx-122950330 AX-123283535 1 127758399 GGCAGTCAGAGGCTGGTAAGCGGACCATTGGAGGA[C/T]GAACAGGAGTTAGCAAGGTGCCGAGCTGGGGAGTC Y 2 1 2 1 101000 f 74 goat snp3442-scaffold1105-1093593 1 129726382 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778749 Affx-122946966 AX-385265860 1 127802752 GTGAGATTTATATTTATGGGGTAAAACACGTTTAT[A/G]CTTTATAGATGCATAATGACATTTGAATATCATGT R 2 1 2 1 101000 f 74 goat snp3441-scaffold1105-1049240 1 129770913 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416805 Affx-122948138 AX-123287153 1 127867176 TGCTCTGTTTATGGGGTTTTAGTTCATGACTAGGG[G/T]TTGACAGTGACAGCACCAAGTTCTAACCACTGGAC K 2 1 2 1 201000 f 74 goat snp3440-scaffold1105-984816 1 129835578 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387770 Affx-122969717 AX-123258128 1 127902575 ATGGCTTGAGGATGTAACACAAGCCAATCAAAGCA[C/T]AGAAACCCAGAGTTCACCCTGCAAGAGCATCCTGA Y 2 1 2 1 201000 f 74 goat snp3439-scaffold1105-949417 1 129871123 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780482 Affx-122960338 AX-385267573 1 127985256 TTTGGTATTTGTGAGGCTCCTGGAATCAAACCTCT[A/G]CAGGTAATGAAGGTGAACCCTAATGAAAAGTTACA R 2 1 2 1 101000 f 74 goat snp3438-scaffold1105-866736 1 129955047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768358 Affx-122921197 AX-385255538 1 128036519 ATAGCACCTGAACTTCATTCACTACCTGTCAGAAA[C/T]AACCTCCAGTGAGTTGAGACAAATAAGAAAACTTT Y 2 1 2 1 101000 f 74 goat snp3437-scaffold1105-815473 1 130006675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778786 Affx-122958833 AX-385265895 1 128090087 TTTGGAAAGTAAGAACAGCTACTAGTCCCCAGGTA[C/T]GGATAAGTTGGCTGAGTGATAACACTTGGTCACAA Y 2 1 2 1 201000 r 74 goat snp3436-scaffold1105-761905 1 130060016 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785560 Affx-122934211 AX-385272604 1 128144081 AGACACAAACTTCTAGAAATATACTCAGAGACCTA[C/T]ACCAAGAAGTACTACAATCAAGTTTTTGAAAGAAC Y 2 1 2 1 101000 f 74 goat snp3435-scaffold1105-707911 1 130113992 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452901 Affx-122920210 AX-123323234 1 128179561 AATACTAATAGAAAAAGCTAGCAATATATTCCATG[C/T]AATCTATGTTGATATATTAAAGAAAAATAGGTAAA Y 2 1 2 1 103000 f 74 goat snp3434-scaffold1105-672431 1 130149544 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792971 Affx-122928094 AX-385279949 1 128315980 CACTCACAGCCTGTAAACTGGAGAGAAGAGAGATG[C/T]GTTTACCCAGAAGGCTTTACTGTGGTTTAGGATAC Y 2 1 2 1 101000 f 74 goat snp3432-scaffold1105-536012 1 130287224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451634 Affx-122921613 AX-123321967 1 128377110 TACAGGAAGGGATTTGGCTGTTCAGCATGTGGTAA[G/T]AGAAGGAGGTGGCAGGGGATGGAAGTCCTCAGCTC K 2 1 2 1 101000 f 74 goat snp3431-scaffold1105-474882 1 130348195 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774996 Affx-122946039 AX-385262128 1 128452746 AATACTTCAGGCTTTCGACTGGTATTTAGGAAGAC[A/G]TTAGTAATGAAGTGGTGGTTCAGAGACTGTCATTC R 2 1 2 1 101000 r 74 goat snp3429-scaffold1105-399246 1 130422701 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404186 Affx-122957683 AX-123274538 1 128535812 CCTTTCTCCGCTCTGCTGTGGAGGTCTCAGCCCTG[C/T]GAGTCTGAAGGAACTGTGCTTGGCATTCCTCTTTC Y 2 1 2 1 101000 r 74 goat snp3427-scaffold1105-316180 1 130505864 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396655 Affx-122962856 AX-123267010 1 128601696 GTACTGTAGATGGCATGGATTCCCTGATGATAAAC[A/G]TTAAGTCGTTACTGTTTTCAGATGAATGAAATCTT R 2 1 2 1 101000 f 74 goat snp3426-scaffold1105-250296 1 130572253 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403540 Affx-122957606 AX-123273893 1 128665888 TGAGAGCTCTGCAAATCGGAGTCAGTCACTGAACA[A/G]AGTGAATAAAAGTGGCAGGCTCCCAGGGCTCCGCA R 2 1 2 1 101000 f 74 goat snp3425-scaffold1105-186104 1 130635602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272537 Affx-1111832835 AX-519546255 1 128682158 AGTGTGCTCAGTTGTGTCTGACACTTTGCAACCTC[A/G]TGGACTGCAGCCCTCCAGGCTCCTCTGTCCATGGG R 2 1 2 1 103000 f 74 goat 1_128682158_AF-PAKI 1 128682158 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395564 Affx-122963850 AX-123265919 1 128698173 TAAGGATTTTTACCTACCTCCTGTCCCTGACACTG[C/T]GAATTCTCCTCTGGAGGCAGAGTGGCTGGCAGGCA Y 2 1 2 1 101000 f 74 goat snp3424-scaffold1105-153819 1 130668188 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413715 Affx-122950075 AX-123284064 1 128729907 GTAAAAACCTGTTGCTAAGACTCACTGCACTTTAA[A/G]GAGGCACTAGAAACCACTTTAGAAGTGTCTGGAGG R 2 1 2 1 101000 f 74 goat snp3423-scaffold1105-122085 1 130700297 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802803 Affx-122934241 AX-385289702 1 128764101 CCCTCTTTCAGGTCTCATGGGAGAACTTCCTGCCC[C/T]ATCCTTTTTAGTTGAGCACAACCATAATCATCACT Y 2 1 2 1 101000 f 74 goat snp3422-scaffold1105-87891 1 130734757 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393949 Affx-122965063 AX-123264304 1 128800091 GGCGTGCTCTTCCCAATTTGACAGGACTCTTGGTA[G/T]CTCCTCAGCAACATGTTTGGAAACACTGTTGGTGC K 2 1 2 1 101000 f 74 goat snp3421-scaffold1105-51901 1 130770932 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772039 Affx-122939404 AX-385259194 1 128848028 AAGAAAAATGATCTATGATTCTCATAGAGAGAAGA[A/G]CTGAGAATATGTAGTCTATTTCATTAAAAATAGTG R 2 1 2 1 201000 r 74 goat snp3420-scaffold1105-3964 1 130818247 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782029 Affx-122964156 AX-385269107 1 128853926 TCTGAATATTCCTTGGCCCACAGGAATGAACCCAT[A/G]CTTATTAACAGCTTCTGCTTTCCATATGTCTGAGG R 2 1 2 1 101000 f 74 goat snp34570-scaffold4083-25330 1 130824043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396789 Affx-122962757 AX-123267144 1 128894857 GCCATCCCTCTTTTGACATCGGTATAATATTCTAT[A/G]CTATAGCTGTACTACAATTAATTTAGTCATGCCTT R 2 1 2 1 101000 f 74 goat snp23083-scaffold230-4296149 1 130868713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448546 Affx-122923431 AX-123318882 1 128948377 TCAGTGTCTCTTACATAGAAAATGGAAAGAAAAAT[A/G]AAAGCTTCTACAAAAAAATTAGATGGCATTTAAAA R 2 1 2 1 201000 r 74 goat snp23082-scaffold230-4242629 1 130923008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417469 Affx-122947183 AX-123287817 1 129013502 TTCTCCTATGTGACAGCAAAGGCTGATGCTGATGC[A/G]TTTTCTGTTTTGCGTACCTTTGCTTTAAACACACA R 2 1 2 1 201000 r 74 goat snp23080-scaffold230-4177504 1 130999816 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766182 Affx-122947195 AX-385253583 1 129083350 GTAGAACTGGGCAGAAAGTATAAAAGAAAGTGTAG[C/T]CTGTTATTATCCTTATCTTATAAAGCTAGTAGTAG Y 2 1 2 1 101000 f 74 goat snp23079-scaffold230-4107656 1 131069752 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779813 Affx-122961742 AX-385266913 1 129115113 AGAACTGGCAGGGAAGTAGGAGAAACATTTTAATA[C/T]GTATTCCAACTAAATAGACTGCCTGAGTTAGACAC Y 2 1 2 1 201000 f 74 goat snp23078-scaffold230-4075893 1 131102595 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775674 Affx-122954419 AX-385262805 1 129147921 CTGAGCTTAGGACTTCAATAAAGCTTTTTGGGAGA[C/T]GCAGTTCAACCCATAGTAATATTTATAAGCAATAC Y 2 1 2 1 101000 f 74 goat snp23077-scaffold230-4043085 1 131136061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789831 Affx-122941686 AX-385276838 1 129180349 GGTGACCTCTTATTTTCTACCCTTATTTTACCTTG[C/T]CCCTGTTTTCTCGCTGACTAATGTTTTGTGTGTTT Y 2 1 2 1 101000 f 74 goat snp23076-scaffold230-4010657 1 131168311 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423509 Affx-122942554 AX-123293855 1 129233480 AAGATGATAAGAAGCAGAAGAGCATGCCAGGCAGA[C/T]GGGACAATGTATATGAAGCTCCTAAGTTGGACAAG Y 2 1 2 1 201000 r 74 goat snp23075-scaffold230-3957526 1 131222828 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792519 Affx-122958686 AX-385279500 1 129267668 AAATGATTCAGCTTCTCAACTGAAAAGAGCAGAGC[A/G]TTAAACCAAGCATGGTCTCCCTTGTAAGGGTGGAG R 2 1 2 1 101000 f 74 goat snp23074-scaffold230-3923338 1 131258128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803917 Affx-986696579 AX-385290625 1 129286054 ATGAAGATATTTTGGACGACTAAATAATGTTTCCC[A/G]TTTACTCAGCTAAACAGATCATTATTATGGACAGG R 2 1 2 1 600010 f 74 goat 1_129286054 1 129286054 Ancestral_priority_1043 ancestry 0.606 recommended IMAGE 10K 10K ancestral 320804414 Affx-986696581 AX-385290999 1 129286068 GACGACTAAATAATGTTTCCCGTTTACTCAGCTAA[A/G]CAGATCATTATTATGGACAGGTATTGATCGTCACC R 2 1 2 1 600010 r 74 goat 1_129286068 1 129286068 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 320803925 Affx-986696583 AX-385290632 1 129286150 GCTTTGGACTCTGAGAAACTCCTTACATTTTTTAT[A/G]TATAGACGTTGTTGCCCACTAGGAGCACAATCCCC R 2 1 2 1 600010 f 74 goat 1_129286150 1 129286150 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 320804424 Affx-986696591 AX-385291009 1 129286180 TTTATGTATAGACGTTGTTGCCCACTAGGAGCACA[A/G]TCCCCTCATCTTCAGAGGAGTTTATGTGCAGCATC R 2 1 2 1 600010 r 74 goat 1_129286180 1 129286180 Ancestral_priority_1043 ancestry 0.606 recommended IMAGE 10K 10K ancestral 320803945 Affx-986696593 AX-385290651 1 129286575 GCCTTCCTCTGACTTTGTCTGGTAGTACCTATTTC[C/T]AGAGTCAGCTCCCCTGACCTCATTAAGCTGGGCTC Y 2 1 2 1 600010 f 74 goat 1_129286575 1 129286575 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320804428 Affx-986696595 AX-385291013 1 129286579 TCCTCTGACTTTGTCTGGTAGTACCTATTTCTAGA[A/G]TCAGCTCCCCTGACCTCATTAAGCTGGGCTCTGTT R 2 1 2 1 600010 r 74 goat 1_129286579 1 129286579 Ancestral_priority_1043 ancestry 0.466 neutral IMAGE 10K 10K ancestral 38450796 Affx-122921816 AX-123321130 1 129303982 GCTGCTTCAGAAGTTTGGATTTCTGTCAATCTACA[A/G]TGGCCAGGTAAAGTAAATGAAAAAAAAAAAAATGT R 2 1 2 1 101000 f 74 goat snp23073-scaffold230-3887024 1 131295570 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774653 Affx-122950763 AX-385261787 1 129382079 ACCTAGGCTGTCTGATTCCAGAGCAAATAACCACT[A/C]TTCTGTGATCTTACTGCTATGAAGATGTCATAAAC M 2 1 2 1 101000 f 74 goat snp23072-scaffold230-3808927 1 131374326 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276346 Affx-1111835291 AX-413837232 1 129434939 A[A/G]TCACTACGAACAAAGCTAATGGAGGTGATGGAATT R 2 1 2 1 103000 r 74 goat INRA-CHI1-PIS2 1 0 T C 1 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region PIS PIS-variant SNP associated with polled intersex syndrome multi-breed 320791267 Affx-122937260 AX-385278261 1 129445690 TTACTCTTCCAAATAACGTCACAGTTAGGAATCTT[A/G]CATCTTTTTATTACTTTTGTCAAGGTGGCCTTGTA R 2 1 2 1 101000 r 74 goat snp23071-scaffold230-3745316 1 131438712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400380 Affx-122960014 AX-123270735 1 129502861 AATAGTTTTCAGATTTCGTGGTCATCATGAGATTC[A/G]TGATAAACATTTTTGGCAAGAATACCACATAGAGT R 2 1 2 1 103000 f 74 goat snp23070-scaffold230-3688145 1 131496198 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451057 Affx-122921432 AX-123321391 1 129535097 AGCATACAGTCCATGGGGTCACAAAGAGTCAGACA[C/T]GACTGAGCGACTTTTACTTTTTAGTGAGGCTAACC Y 2 1 2 1 103000 r 74 goat snp23069-scaffold230-3655909 1 131528543 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782179 Affx-122972966 AX-385269257 1 129564489 ATTTTAAGTATGTTTTGCTGTGATAAGATCCCTAA[C/T]GAATATCCCAAGTATTTTAGGATTAGGACTGCTAG Y 2 1 2 1 101000 r 74 goat snp23068-scaffold230-3626517 1 131557973 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412392 Affx-122951453 AX-123282741 1 129602469 TTACCTCTCAGTCATCAGTTTTTTCCTGAGAGTAA[G/T]TTCTTAACAAATCAGCTTCATGAAATCCTTGGCTC K 2 1 2 1 101000 r 74 goat snp23067-scaffold230-3588537 1 131596098 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442452 Affx-122927955 AX-123312789 1 129682502 TGAATATAATCCCTACAGTTTCTACTCCTCAGAGC[G/T]CAGGTCAGGAAGGACTGAACATTTCTTTCTGCTGT K 2 1 2 1 101000 r 74 goat snp23065-scaffold230-3508504 1 131675988 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381463 Affx-122974980 AX-123251821 1 129770149 GATTTAGAATTTAGCAGACACCATATCCTCACTCG[C/T]GCTCAGAAGCGCTCTGCTCAGTGCTCCTGTGGCCC Y 2 1 2 1 101000 f 74 goat snp23063-scaffold230-3420857 1 131763512 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773482 Affx-122958922 AX-385260624 1 129811814 TGTTGCACTCTAAAATTCACGTTCTTTTTACTAAT[A/G]CATTTGCACATGTAGAGTATTTAGAGACTTTAAAA R 2 1 2 1 101000 r 74 goat snp23062-scaffold230-3379192 1 131805668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786858 Affx-122951705 AX-385273887 1 129894158 AAAGGCCCTTAACTTGCATAACCCACTCTTGCTTA[C/T]ACTTTGTCATCTTTTGCTCTAGCAATATTCTACTG Y 2 1 2 1 101000 f 74 goat snp23061-scaffold230-3296848 1 131888025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390717 Affx-122967931 AX-123261074 1 129936450 GCCCTGAGTCACAGAGCAGAGTGCTGAGTGGGTCT[C/T]GAAGGACATGGGGAAAACCAGCAGTCACTTCCTAT Y 2 1 2 1 201000 r 74 goat snp23060-scaffold230-3254556 1 131931194 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793834 Affx-122938065 AX-385280803 1 129975195 TGATGATTTCAGCATGGACCCTGAAGAGAATGGAC[A/G]TTCATGTTTCCAGCGGAGCCTGATGACAGCTGGGA R 2 1 2 1 101000 f 74 goat snp23059-scaffold230-3215811 1 131970293 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276615 Affx-1111835504 AX-519550125 1 129977048 GTAAGCATTGTGTCTCGTTGGATACAATGTGGTAT[A/G]AATAATACTACTACTAAGTACCAATGTAAAGAGTG R 2 1 2 1 101000 f 74 goat Random2.2K-126 1 129977048 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435073 Affx-122933728 AX-123305413 1 130023268 AAGTGAGAAAGTCTTGCCAACAGCTAGATAGAAGA[C/T]GGTGACTCCAGTCATACAGCCACAAGGAAATTCTG Y 2 1 2 1 101000 f 74 goat snp23058-scaffold230-3167738 1 132018470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414114 Affx-122949732 AX-123284463 1 130075544 TTTTCACAAGTGTATACTTACGTCAAAACTTAATT[A/G]TACAATTTAAAGTGTACAATTTAAATACATACACT R 2 1 2 1 103000 f 74 goat snp23057-scaffold230-3115462 1 132071474 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401117 Affx-122959398 AX-123271470 1 130171599 TGAGGTATGAATATATAATAATCCCCATCCTTTCA[C/T]AAATAATGAATATCAACATACGTGGGGTAGCTTAA Y 2 1 2 1 102000 r 74 goat snp23055-scaffold230-3019407 1 132167788 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448299 Affx-122924164 AX-123318635 1 130211629 CACTAGTAATTAGGAACCTCCTATACATTAAAAGA[C/T]GCTTACTCCTTGGAAGAAAAGTTATGACCAACCTA Y 2 1 2 1 103000 f 74 goat snp23054-scaffold230-2979377 1 132207904 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424030 Affx-122942084 AX-123294376 1 130281185 AAATTTCCAGCTTGGATCTGGTAGACAGGGCCTGA[A/C]GATTAACTGACAGCCAACAGACTAAGTGGAGAAGA M 2 1 2 1 201000 r 74 goat snp23053-scaffold230-2909821 1 132277390 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376732 Affx-122978956 AX-123247091 1 130312990 ATAACAAGAAACTTAGGACTGATTCAACAGATTAA[C/T]ATCCAAGTAAAATATATTCAGCAGAGAGTAATGAA Y 2 1 2 1 101000 r 74 goat snp23052-scaffold230-2878016 1 132309208 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787554 Affx-122961466 AX-385274578 1 130349762 TAATATTTAATTCTCTGCTCTAATAAATTTTAGTG[C/T]CTTCTAAGTCCATGTCATTGCTTAAAAAATAAAAA Y 2 1 2 1 101000 r 74 goat snp23051-scaffold230-2841244 1 132346261 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411882 Affx-122951197 AX-123282232 1 130395222 ACTTTTTGGTACAAAAAGAGAAAAACTAATTTAGG[C/T]AGATCTCTTAATCTTATTTCACCTATAATTCATAT Y 2 1 2 1 201000 r 74 goat snp23050-scaffold230-2795784 1 132391733 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784251 Affx-122921193 AX-385271302 1 130471776 ATGTATATCTTAATCTTTGAAATATACTGCAAAAT[C/T]ATATTCCAAGAAGGTAGGAGAAATTGCTTTCACAA Y 2 1 2 1 101000 r 74 goat snp23049-scaffold230-2719230 1 132468894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390233 Affx-122967772 AX-123260590 1 130504607 CCTTAGCTTGTGTCCAACTACTGTTTGTGACTGAG[A/G]TGCCAAAATAGACAGATAAGAAAACATCTCTTTTA R 2 1 2 1 101000 f 74 goat snp23048-scaffold230-2686399 1 132501737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417419 Affx-122947221 AX-123287767 1 130544819 TTCATAGCAGGCACCACAGACAGGCCATGGGGTGG[C/T]ACAGAACCAGGGCACTGAGGAACATGTTGTGGGAA Y 2 1 2 1 101000 r 74 goat snp23047-scaffold230-2646187 1 132542375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378585 Affx-122976588 AX-123248944 1 130586709 TTAGTGGCTCTTGGAGCAGCTGGTTTGCCTTGATT[A/G]CCTTACTGGCTGAATTCTACTGATAACACCTGTGT R 2 1 2 1 201000 r 74 goat snp23046-scaffold230-2604297 1 132584726 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387313 Affx-122970511 AX-123257671 1 130622723 ATCTAATTACTGCCTATTTTCTAGGCCCTGACCCT[A/G]TCTTACCTCTCCTATGAAGATTGCTATGGAGGTCA R 2 1 2 1 201000 r 74 goat snp23045-scaffold230-2568283 1 132621078 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419655 Affx-122945954 AX-123290003 1 130680983 GATCACAAAGAGGAAGAAAATGTCTTTCAGTCTGA[C/T]GGGAAATAAGTAGATGCATGTGTAGAATTAACTCT Y 2 1 2 1 201000 r 74 goat snp23044-scaffold230-2510023 1 132678692 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387840 Affx-122969657 AX-123258198 1 130737951 AGACTAGCAGTGTATTTATTTTTCTTTTTCAGTCC[A/G]CTTGCAATATATTTCTTAGTGTACACTTTACAGAC R 2 1 2 1 201000 r 74 goat snp23043-scaffold230-2453055 1 132736269 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444606 Affx-122926949 AX-123314943 1 130770195 CTCATTATGTGCAAAGCCCTATTATTTGCAAAGTC[A/G]CTATTTTCTGTTATTAAGCAGTTATCAGCTACCTG R 2 1 2 1 101000 r 74 goat snp23042-scaffold230-2420811 1 132768890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275521 Affx-1111834949 AX-519549093 1 130823139 TCCCCATTCATATCTGCAGTTTCCAGAACTGAAGT[A/G]GACTATCAAGAATCCATTTGAGAAGGAAGCATGGA R 2 1 2 1 201000 f 74 goat GoatD01.059663 1 130823139 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434870 Affx-122934357 AX-123305211 1 130825807 TACCACTTTTGAGGATAAAATCCAAACCACTATTC[C/T]CTGTATCCACCTGACCACCTGCGCCTGCCCCTGCA Y 2 1 2 1 101000 f 74 goat snp23041-scaffold230-2365199 1 132825442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779987 Affx-122933175 AX-385267086 1 130854753 AGTTACCAAACCTCAAATTTTGATGATTTCCCTTC[A/G]CGGGAAAGGTCATTATTTTGTAAGAAACCACTGAA R 2 1 2 1 101000 f 74 goat snp23040-scaffold230-2336253 1 132854651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393092 Affx-122965592 AX-123263449 1 131005765 TAGCTACAGGTGATGAGTGGGGGTGGTGGCGGTGA[C/T]GGGGGGCGGGGGAATGTACTGTCAGCCCGAGACTG Y 2 1 2 1 103000 f 74 goat snp23037-scaffold230-2185241 1 133004084 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386134 Affx-122971409 AX-123256492 1 131095400 TTCCAGGGCTAGTCTTGGCCAGAAGTGGATGGTAA[C/T]GGAGCTGAGGCCAACTGCAGGGGAGAAGCACCGTG Y 2 1 2 1 101000 f 74 goat snp23036-scaffold230-2095606 1 133093227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781594 Affx-122958871 AX-385268678 1 131144390 CTGGGAGGATGCCAATGGTTTCTATAAATTTCTCA[C/T]AGAAGAATGAGTGAGTATGATAGTTAATTTTATGT Y 2 1 2 1 101000 f 74 goat snp23035-scaffold230-2046616 1 133142464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394457 Affx-122964581 AX-123264812 1 131203099 CTGTGAAGAATCTCGGTTTACTAACTGATCTGAGT[A/G]GTGTGTTATATCTACATAATCAATTTAGCAATACT R 2 1 2 1 101000 f 74 goat snp23034-scaffold230-1987907 1 133202007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426711 Affx-122939889 AX-123297057 1 131255363 ATAGATACAGATATAGATATAGATAAGATATAAAA[C/T]GTCACACTTGCAGGCAGAGGTGTGTTTGTAATTGC Y 2 1 2 1 103000 r 74 goat snp23033-scaffold230-1935643 1 133254186 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429229 Affx-122937922 AX-123299571 1 131290392 CTTTAGGAGAGCACTGTGGGTGGAGTCAGCTAAAT[A/G]CCCAGTAAGTGGCAAGAGGAAGGACGCAGACTGAG R 2 1 2 1 101000 f 74 goat snp23032-scaffold230-1900614 1 133289412 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380845 Affx-122975448 AX-123251203 1 131327388 GTTTCAGATTTACAGTAAAGTTGCACAGATAGCAC[A/G]ATGAGTTCTCATACACCCCACTGTCTCCACTAGCA R 2 1 2 1 101000 f 74 goat snp23031-scaffold230-1863618 1 133326277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801383 Affx-122954151 AX-385288294 1 131383827 TATGAACACCTGTACAAATGCATTCTTGCACATAC[A/G]TGTATGTTAGGGTATGGCATTTTTAGAAACAGAAA R 2 1 2 1 101000 f 74 goat snp23030-scaffold230-1807179 1 133383315 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416975 Affx-122948006 AX-123287323 1 131423872 TATTGCCCACCTGGCCCCATATACGTTTGAATTGG[C/T]AACCTTAGGCAAGATTTCCTCTAAGGTTTTACTAC Y 2 1 2 1 102000 f 74 goat snp23029-scaffold230-1767134 1 133423420 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272469 Affx-1111832837 AX-519546191 1 131450616 GGGGAAACAATGGAAACAGTGAGAGACTTTACCTT[A/G]GGGGCCTCCAAAATCACTACAGATGGCGACTGAAG R 2 1 2 1 103000 f 74 goat 1_131450616_AF-PAKI 1 131450616 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38422601 Affx-122943733 AX-123292947 1 131464397 AAAAGTTAACTATTGGCACTAACAAGAGAGAAGAA[C/T]GAACTTCAAGAAAAATGTAAATGGTCACAGAAGGT Y 2 1 2 1 201000 f 74 goat snp23028-scaffold230-1726609 1 133464390 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396452 Affx-122962977 AX-123266807 1 131504660 GAGAATAAAATAGAATGGTAGGGAGAGGCATGAAC[A/G]TCAGAGCAAAATTTTCCCTGGGTCCCCTGTCAGCA R 2 1 2 1 101000 f 74 goat snp23027-scaffold230-1686346 1 133504793 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434934 Affx-122933868 AX-123305274 1 131542606 CATCCCAAGATGACACTGATTTCTTCCTGGCAACA[C/T]TGTAATGAAAGACAAGCCAGCACTCACATAAGATC Y 2 1 2 1 201000 r 74 goat snp23026-scaffold230-1648400 1 133543054 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438846 Affx-122930769 AX-123309183 1 131571886 TTGCCCTTTGGAAAATGTGTTGAATTTGGGGGAAA[C/T]GATTTAGGAGGAAGTCCCAGTGAGAAATGATGATG Y 2 1 2 1 101000 r 74 goat snp23025-scaffold230-1619120 1 133572464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420742 Affx-122944760 AX-123291089 1 131626865 AGATACCCAAATAAAAGAGGACAATGTGGACTCCC[C/T]GAATGGCCTAACTGCTGTATAGCAATCCTAGAACA Y 2 1 2 1 101000 f 74 goat snp23024-scaffold230-1564141 1 133627527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408825 Affx-122954025 AX-123279176 1 131737480 CAGGAGACACTCCTGGCTGGAGTCAGTCTCTCTCT[A/G]TCCTCCAATTCTTCCTCTCTGTCACCACTCCTGCT R 2 1 2 1 101000 f 74 goat snp23021-scaffold230-1453526 1 133737751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803434 Affx-122939385 AX-385290265 1 131769671 CACTTTTTAGTTCTGTTTGGTCTGAAGATTTTCTT[A/G]CATATAAAACATGAGATTTAGAGGTGGCATTTGCA R 2 1 2 1 201000 r 74 goat snp23020-scaffold230-1421335 1 133769875 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403779 Affx-122957986 AX-123274131 1 131850019 TCAGTTCAATTGAAAACAAAACCTTCTTGTGTTCT[A/G]TTGGATCAAGCCAAGCCTTCTTGTGGGTCATCAGT R 2 1 2 1 101000 r 74 goat snp23018-scaffold230-1340987 1 133848471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801310 Affx-122954218 AX-385288222 1 131908517 CCTTTCATATCCTGGCTGCCCATAAATGACCTCGA[A/C]TGTTTCCAGCAATGCTCATTGTAATTCTTTTTAAT M 2 1 2 1 101000 f 74 goat snp23017-scaffold230-1282489 1 133907258 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443889 Affx-122927063 AX-123314226 1 131961617 TTTATGGCTTCTGAGTTTCGTGTCGTCATTACTAT[A/G]CATACATTGTCTCTATGGTTTCTTTTAGTATTTTT R 2 1 2 1 101000 f 74 goat snp23016-scaffold230-1229389 1 133959006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777746 Affx-122927039 AX-385264864 1 132030081 AAATTGTGGAAGAGAAAAGACAAGTCTGCAGAACT[A/G]TTGTACAATGATTTATATCCAAATCTAGACTGATG R 2 1 2 1 101000 f 74 goat snp23015-scaffold230-1160925 1 134026984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399380 Affx-122961329 AX-123269735 1 132086882 GAGACTGGTCAGCACAGTCCTGGGCACACATGGAC[A/G]CTGAGTCAGTGTGTGGTCCCCAGATTGGCTAATGA R 2 1 2 1 202000 f 74 goat snp23014-scaffold230-1104124 1 134082080 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449992 Affx-122922869 AX-123320327 1 132141988 GTTAACATACAAACTTAACACTTGACTTGAGGCAA[C/T]GTAACAGCATGCCACAATACTAATGTAATGGAGAG Y 2 1 2 1 101000 f 74 goat snp23013-scaffold230-1049018 1 134136722 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779382 Affx-122963884 AX-385266486 1 132191826 CTGACACATGGAGATTACATAAGGTTCACAGCAAA[C/T]GGACCAGTAAAGGCATTAACAAGAAAATGCAAGGA Y 2 1 2 1 101000 r 74 goat snp23012-scaffold230-999180 1 134186305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442872 Affx-122927666 AX-123313209 1 132233830 ACATCATTTTAGGGTTGGAAAAAACCGAAGTGACT[A/C]GACAATCTGCACACAGCTGGCACAGCATGTCTTGC M 2 1 2 1 101000 f 74 goat snp23011-scaffold230-957176 1 134228496 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415661 Affx-122948560 AX-123286010 1 132291560 TCTAAAATGGGACTGAAAACCCTATTATTAGTTTT[A/G]CCCTTTCTTGGTTTCATTTTACAATATCTGAACAT R 2 1 2 1 202000 r 74 goat snp23010-scaffold230-899446 1 134286400 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275300 Affx-1111834823 AX-519548875 1 132300059 TTGCTCCATTTCCTTCACCTTTTCCTCTATTTTTC[A/G]CATTGGAACCAAAAATAAATTTTTAAAGCTCATAG R 2 1 2 1 303000 f 74 goat GoatD01.055148 1 132300059 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382124 Affx-122974472 AX-123252482 1 132354993 TGCTGATTCGATTCTTGAAAGGATGTTGACTGTCC[A/G]TTGTCAGGTGGTAGGGGGAGGTGCTGTGTGGCCAA R 2 1 2 1 101000 f 74 goat snp23009-scaffold230-836013 1 134348470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396921 Affx-122963202 AX-123267276 1 132386140 TTCAGTTAAATTTGAACCAGCTTAAAAAATGCAGC[A/G]CCGTGTGCTCACTGTGCTCACCCCATCCTCACGCC R 2 1 2 1 101000 f 74 goat snp23008-scaffold230-804866 1 134379200 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380161 Affx-122975969 AX-123250519 1 132426265 TTTATTCACCTCTGTTTTAGAGTTCCGTAAACTTG[C/T]AGTTAAAAGAGCAAACCTGGAATGCCCTTTCCCCC Y 2 1 2 1 101000 f 74 goat snp23007-scaffold230-764741 1 134419132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416105 Affx-122948312 AX-123286454 1 132456001 GAAGGAAATTTCTCCAAGATCAGGGTGGGAAAGAG[C/T]AGATTCATTTAATCATTTACTCATTCAACAAATGT Y 2 1 2 1 101000 f 74 goat snp23006-scaffold230-735005 1 134448822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795422 Affx-122964357 AX-385282378 1 132488373 TTCTGAATAGCAAACAGTAACAGCTGCTTGGTACA[C/T]GCTTATTTGACTAATGGAATAAAATATGCTGACAT Y 2 1 2 1 101000 f 74 goat snp23005-scaffold230-702633 1 134481510 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381858 Affx-122974185 AX-123252216 1 132550535 GGGGCTGGGAGCATGGAATGAGGGGGTGAATCTGA[A/C]GCAGCCCACTTCAATCTTCTATTTCACAAGAAAGG M 2 1 2 1 201000 f 74 goat snp23004-scaffold230-640471 1 134543743 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437862 Affx-122932073 AX-123308200 1 132588244 CAACAGATAGATTTGTCCTGGTTTATAAACCAGAA[C/T]GAAGGGAGAAAAGAGTTTTTACAAACTGCCAAGAA Y 2 1 2 1 101000 f 74 goat snp23003-scaffold230-602762 1 134581196 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275254 Affx-1111834684 AX-519548831 1 132615543 AGGCTACAAGAGGCCCTAGAGAGGAGCACTGCAGT[A/G]GTTAGGAGTTAGTAAAGGGTTTCTGGCACAATGAA R 2 1 2 1 101000 r 74 goat GoatD01.045838 1 132615543 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38394504 Affx-122964547 AX-123264859 1 132631554 TAGAGGCACCTTTAAACTGAAATCTTGAAAGATGA[A/G]TGTTTTCAGTAAACTCACATTTCTCATCTACCCTT R 2 1 2 1 201000 r 74 goat snp23002-scaffold230-559452 1 134624235 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421237 Affx-122944118 AX-123291584 1 132692696 ACACTTCTAGATACAGGCATCCACTGCCTCCGAAG[C/T]GGCACATCCTAACTGAAAAGCTCTAACTGCTCCGA Y 2 1 2 1 101000 r 74 goat snp23001-scaffold230-498310 1 134684117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799836 Affx-122921565 AX-385286762 1 132744490 TAGATATTGTGGTGGGAAGGGAGGTTACATTACTT[A/G]TGACTCTGAATGAAGTTTTACAGCCCAAAAGTAGA R 2 1 2 1 101000 f 74 goat snp23000-scaffold230-446516 1 134736026 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764753 Affx-122919405 AX-385252367 1 132808626 AAACAAGGCCCGTTCTTCCGTAACTTTGACTTTCT[A/G]TGGACAAAATTTATCTCTTTGCTAGATAATACAGC R 2 1 2 1 101000 f 74 goat snp22999-scaffold230-382380 1 134800898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452424 Affx-122920584 AX-123322757 1 132840309 ACAGTCTACCCAGAAAGAAGATTGATTCCATGTGG[C/T]AGCGAAGAAGTCTGGCTTGGCAGTCACCCTGGCCT Y 2 1 2 1 101000 f 74 goat snp22998-scaffold230-350697 1 134832638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452527 Affx-122920546 AX-123322860 1 132897256 TGTGCCCCTTCCCAGCTGTCATAAGTGTGCATGAG[A/G]CCGTGCTAAGTCCCCAGTGCTCGTGCGGGAGTTGC R 2 1 2 1 101000 f 74 goat snp22997-scaffold230-293750 1 134890090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276778 Affx-1111835516 AX-519550287 1 133010643 TTAAACCAAAAACCCCACAGTGAGAATAGAAACTT[A/G]TTTGGTACTTGTAACTACCTGCCTTGGAGAAGAAA R 2 1 2 1 101000 r 74 goat Random2.2K-128 1 133010643 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403169 Affx-122958084 AX-123273522 1 133012042 CCACGTGGGTGTCTCTTTCCTTTCCCAAACTGCCC[C/T]GGGGTGTTCTGGGGCAGCATCATTCACACGGAAAC Y 2 1 2 1 102000 f 74 goat snp22994-scaffold230-178964 1 135005898 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403090 Affx-122958502 AX-123273443 1 133042518 GCATAGCAGTCCATTCCCGACGTTTATGAATTCTG[C/T]AGTTCGACCTAACCTTTCCTCACCTTCTGCAACGC Y 2 1 2 1 101000 f 74 goat snp22993-scaffold230-148488 1 135034718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383795 Affx-122973193 AX-123254153 1 133075319 TCCCATTGGCCCAGCACATGCCCAAGGAAAGAGAT[A/G]TTTCCTGAGGCACTTGTTGAAATCGTTTTTGCTAT R 2 1 2 1 101000 r 74 goat snp22992-scaffold230-115687 1 135065110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381928 Affx-122974134 AX-123252286 1 133105727 ACTAGAAATGACCATTCTAGTGGTTTCCCTTAACT[A/C]GGGAACCTAGGGAGATTTAGAAGCTGTTCTGTTTT M 2 1 2 1 101000 r 74 goat snp22991-scaffold230-85279 1 135095900 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379390 Affx-122976137 AX-123249748 1 133135910 AAAATTTATGTTGTGAGTGTGAATCAGTACCAAAA[C/T]ATTAATATTACTGCTGCCATCCTTAGGGCACTAAC Y 2 1 2 1 101000 f 74 goat snp22990-scaffold230-55096 1 135126105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445557 Affx-122925150 AX-123315894 1 133184002 CAGAATCCCAAAACTTTCTTGCTTTTTATTTAAAG[A/G]CTTGTATAGGTATATATTGGGCTTCCCTGGTAGCT R 2 1 2 1 101000 r 74 goat snp22989-scaffold230-7004 1 135174495 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439624 Affx-122930626 AX-123309961 1 133201624 GATAGTAATAGAGCAGTGAACTTGGGGCTCTTTCT[A/G]TTTAGCAATTGCTTTACATACATTGGGCTTCCCTG R 2 1 2 1 201000 r 74 goat snp48965-scaffold699-939219 1 135204267 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384719 Affx-122972057 AX-123255077 1 133253330 AATTTCTCAGTTGCCTAAGAAAACAGTAAGCAGCT[A/G]GGAAAAGCCTTATCCCTTTCCTTCAGAGCAAAGCT R 2 1 2 1 101000 f 74 goat snp48964-scaffold699-887513 1 135255901 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436915 Affx-122933203 AX-123307253 1 133288345 GTGAGTCTGAGCTGGGGTCCAATTTCTCAGGCCAC[A/G]GTGATGCTACTGGGGGAGACACTACCCCTACATCC R 2 1 2 1 101000 f 74 goat snp48963-scaffold699-852498 1 135292903 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412175 Affx-122951066 AX-123282525 1 133318650 TACACAACATACTCCTCATAAATATTATAAGACAT[A/C]CAGCGAAATGCTAATTTGTATGCTTTTCAGTAAGT M 2 1 2 1 101000 f 74 goat snp48962-scaffold699-822193 1 135323768 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422446 Affx-122943347 AX-123292792 1 133373749 GTTGGAGCACATTCTCTCTCTACATACTTTTCTGC[G/T]AATCTTTTAAATGCACATTAAATTTAAAGTCCACT K 2 1 2 1 101000 f 74 goat snp48961-scaffold699-767094 1 135378111 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423002 Affx-122942983 AX-123293348 1 133410875 CAACTGCTCTTTATGTGTGTTGGATTTAGGGGGGT[G/T]TTCATAGTTATATTAATGTTCGAACTAGATTCAGC K 2 1 2 1 201000 r 74 goat snp48960-scaffold699-729968 1 135414107 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774620 Affx-122927418 AX-385261754 1 133470119 GGTGAATAAAGGCCTACAAGAAGGGATGAATGAGT[A/G]TAGGCACAACCTCAAATTAAAGAAGTTTAGACCAA R 2 1 2 1 101000 f 74 goat snp48959-scaffold699-670724 NW_017198025.1 17773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409343 Affx-122954181 AX-123279694 1 133513697 CTTGGTTCGAAATTCAAAATGTACAAAATAATAAA[A/G]AGTGAAAAATGTCACCTCACCCATGTCCCAGGCAC R 2 1 2 1 102000 r 74 goat snp48958-scaffold699-627146 1 135519152 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451148 Affx-122921364 AX-123321482 1 133590475 GCTGAGCCACTGGGGAAGCCCTGTTCCTCCCTGAC[A/G]TCTCCACAAAGAACCTGATGCAGTCACTCGGGACC R 2 1 2 1 101000 r 74 goat snp48956-scaffold699-550368 1 135595758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426055 Affx-122941101 AX-123296401 1 133622514 AAAACCTCGTCCTTGAGGGATGTCCCCAGGAAAAA[A/G]ACAATGATCTCAGATTCCTTGATGGGCAAAGAGAA R 2 1 2 1 101000 r 74 goat snp48955-scaffold699-518329 1 135628029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419264 Affx-122946257 AX-123289612 1 133691112 GTTTTATGAATTTGGGAGTGGAGGGCCCGGAGAGG[A/G]TGTTTTTTCTTGAACCGTGGGTAACAAGTAGAAGT R 2 1 2 1 201000 r 74 goat snp48953-scaffold699-449731 1 135695117 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770124 Affx-122926459 AX-385257291 1 133727678 TTTACTGACAAACGTACATGCTATCTCTTTCAAAT[A/G]TTGAGAGCAGCATAATTCATTCAAATCTCTTCTTG R 2 1 2 1 101000 r 74 goat snp48952-scaffold699-413165 1 135732399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442674 Affx-122927893 AX-123313011 1 133761215 AACTTAGGAATTATTTATAAACTTCGGAGGGATTT[A/G]TAGTATAATTATTAAGGAAGGAAGGAAGTCTTTAT R 2 1 2 1 303000 f 74 goat snp48951-scaffold699-379628 1 135766400 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451202 Affx-122921324 AX-123321536 1 133800252 TCTGCTACAACAATATCAGGAAATTTCACATAAAA[C/T]AGTCCTAGGAGTGTAGTCCCCATAGAGGTGGTTCT Y 2 1 2 1 201000 r 74 goat snp48950-scaffold699-340591 1 135805374 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416861 Affx-122948094 AX-123287209 1 133829157 GTTTATTTTTTAGGGGATTCTTGTGTGAGTCACTT[A/C]TTTTGTTAACTCTGTCTTCATACTAGAAGTATTTT M 2 1 2 1 201000 r 74 goat snp48949-scaffold699-311686 1 135833985 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406419 Affx-122955210 AX-123276771 1 133881094 CCTGAGAACATGTAGCAAGTGGGAGGCAGGCCTCT[G/T]GTTCTCAGTCATGTGCTTTGTCCACCCCAGAGGCT K 2 1 2 1 201000 r 74 goat snp48948-scaffold699-259749 1 135885973 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392968 Affx-122965678 AX-123263325 1 133915359 TCTAGCCTCATCTGTTGATACTTGCCTATTTATAA[G/T]CCTGGCTTCAGTCTTCTTAAATTACAGTGTAAACC K 2 1 2 1 201000 f 74 goat snp48947-scaffold699-225484 1 135918715 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788584 Affx-122930040 AX-385275601 1 133944266 CCTTCTCTTTTATACATTATTCTTTATGAGGTTGT[A/C]GGAAAGATAGGATATTATTTAGTCCACTCTGTGTT M 2 1 2 1 101000 f 74 goat snp48946-scaffold699-196577 1 135947715 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272471 Affx-1111832838 AX-519546193 1 133973968 ACATTTTATTGGGCTACAATAACCCTAAACTGAGC[A/C]TCTCCTGAGCTCAGAGCCCTGTGTTGAAGATGCAG M 2 1 2 1 201000 f 74 goat 1_133973968_AF-PAKI 1 133973968 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413138 Affx-122950365 AX-123283487 1 133978557 AGTGTAACTACTTTGAGTGGAGAGATATTATAGGC[A/G]TGCAGCAGGAGCCTCCCACCCTCTTCTCTCCATGA R 2 1 2 1 101000 f 74 goat snp48945-scaffold699-162286 1 135981948 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780076 Affx-122941878 AX-385267174 1 134016241 AGCGTCAGCATCTTCCTTGACCCTGTTTAAAATGT[A/G]CATTCCCAGCACTCACAGCGAACTTACTGAATCAG R 2 1 2 1 201000 r 74 goat snp48944-scaffold699-124602 1 136019303 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386280 Affx-122970939 AX-123256638 1 134060498 CAAATCCCCTCCTCAATGGCAGGCAATTGTCTTTT[A/G]GCCCTCTCTTGGGATTATCACACTGTAAATTCCAC R 2 1 2 1 201000 r 74 goat snp48943-scaffold699-80345 1 136064580 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389521 Affx-122968291 AX-123259879 1 134122869 CTCATATCCCTTTTCTCCCCTCTTCCCTGGAACCT[A/C]TTCCCAACCTGAGGTCCCATTTCTATGCCCAGCTC M 2 1 2 1 303000 r 74 goat snp48942-scaffold699-17974 1 136128514 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783736 Affx-122919489 AX-385270792 1 134144946 ATCATATAGCGTTTGCCTTTTAGGGACTGGCTTAT[G/T]TCGCTTAGCAGAATGTCTTCAGAATTCGTCTATGT K 2 1 2 1 102000 r 74 goat snp37475-scaffold458-4004 1 136225466 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441174 Affx-122929551 AX-123311511 1 134191760 CAACCCAGTATTATGGGGTCCTGGCTCAATGTGGC[A/G]AGCACTGCACTCATTGATGGTGGTAAACAATGCAT R 2 1 2 1 101000 r 74 goat snp37476-scaffold458-50818 1 136272847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440192 Affx-122930706 AX-123310529 1 134249106 GCACCCCAACATTAAAGTAATTAAATAAACAGATA[C/T]GTTTGTTCATTCACTTACTGCCTATTTTCCCCATT Y 2 1 2 1 101000 r 74 goat snp37477-scaffold458-108164 1 136330861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436842 Affx-122932215 AX-123307180 1 134301684 GGTTTGCTTCTCAGGAAATCATTTAATTTTTATAA[C/T]AGTTTGTTTCCTTATCTATAAAAGGAGGGCTTGAC Y 2 1 2 1 201000 f 74 goat snp37478-scaffold458-160742 1 136380977 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431522 Affx-122936229 AX-123301863 1 134338891 CAACATTATTCTTTTCTTTAAGCATCTTAAAGCAT[A/G]TTGCTAAAAAATAATCCTGTGGCATCTACTCTACT R 2 1 2 1 101000 r 74 goat snp37479-scaffold458-197949 1 136419816 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775663 Affx-122927305 AX-385262794 1 134425682 CAAAACAGTTCAGTGGCTAACCTACAATTAATCCT[C/T]TGAAGTTTTCTTACTAGAATGAAACATGAGTTTTA Y 2 1 2 1 101000 f 74 goat snp37481-scaffold458-284740 1 136507519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409352 Affx-122954174 AX-123279703 1 134471183 CAGGACTGATTTCCTTTAGGCTGCCTACATAGCTG[C/T]AAACATATGTGACCTTTATCAGGACTGATGCTTTT Y 2 1 2 1 201000 r 74 goat snp37482-scaffold458-330241 1 136552939 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404499 Affx-122956710 AX-123274851 1 134481587 CTATTTTCCTCCATCCTCTTCCTACAGGAAAAGAA[C/T]ATGAAACCCAGAAGCTCAGCACGCGAATTTAGAGC Y 2 1 2 1 202000 f 74 goat snp55184-scaffold848-520062 1 136574462 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386317 Affx-122970889 AX-123256675 1 134511268 GTTCCTGGTGGCAGTGCCTAAAAGTACTGCTGAAG[C/T]AAAAGCAAATTCACTCTGGAGGAAAAGTTCTTTTT Y 2 1 2 1 101000 f 74 goat snp55183-scaffold848-490381 1 136604119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773302 Affx-122963566 AX-385260445 1 134540117 ATGAACAACTCTTTAGCTCTTACTCCAGCAGCATC[A/G]TGGAGTTGTATTTATAGCCTCAAACTTTCACATCA R 2 1 2 1 101000 f 74 goat snp55182-scaffold848-461532 1 136632416 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276678 Affx-1111835535 AX-519550188 1 134591452 TTATTCCTCTAACCACACTGTAAGCTCAGCTCTGA[A/G]AGAGGATGAGGATTATTGAGTCACACAGCAATTAC R 2 1 2 1 101000 f 74 goat Random2.2K-130 1 134591452 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320773510 Affx-122945640 AX-385260651 1 134602152 CACTGATTTTGGCTTCCCTGACTTGGCAGAGAGGT[A/G]ACTTGTGAGCTGGTGCATGTACAATTTTTTATCTT R 2 1 2 1 101000 f 74 goat snp55181-scaffold848-399497 1 136694945 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400147 Affx-122960700 AX-123270502 1 134682326 AAACTCTAACTTGCTGACAGCTTGTTGTGGGGAGA[A/C]AGCTGTAAAACTTTGAAATTTTTGGTTTATTTCAA M 2 1 2 1 201000 r 74 goat snp55179-scaffold848-319323 1 136775752 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769672 Affx-122963713 AX-385256842 1 134730851 TCCCCATTGATTTTCTAAACCTGAGGGAAGGTATT[A/G]CTATTATAGTTTAGTTTGAGTGTGGGGTTAAGCAG R 2 1 2 1 202000 r 74 goat snp55178-scaffold848-270798 1 136824715 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401124 Affx-122959392 AX-123271477 1 134808550 ATTTTTAAAAATATTGATGCCCAGCTCACACCCCA[C/T]AGTACATCAGCATCTCTGAGTGTGGGACCCAGGCA Y 2 1 2 1 102000 r 74 goat snp55176-scaffold848-193099 1 136903242 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387372 Affx-122970466 AX-123257730 1 134870382 ATTTAGAGAAACGTACCACAGAGGGGGAGGGGGAG[C/T]TGGGTATTAATCACCAGTACTGATGGCAGCACAAA Y 2 1 2 1 201000 r 74 goat snp55175-scaffold848-131267 1 136965713 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383427 Affx-122973476 AX-123253785 1 134932459 GCTTCCTGGTAGAGGGACTGGGGCCTGTGTTGTGG[A/G]TGGAGCTGGATCTTGTTCCTCTGATGGGCATTGCC R 2 1 2 1 202000 f 74 goat snp55174-scaffold848-69190 1 137028313 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771871 Affx-122957801 AX-385259027 1 134984769 GGCAGAGATAAGATTCAAATACAGAGTGACTTCAG[A/G]ACTCATGTCTGGTGTAACACTTACCCATGGGGCTG R 2 1 2 1 101000 r 74 goat snp55173-scaffold848-16880 1 137081138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450202 Affx-122922292 AX-123320537 1 135029781 CCCACATTGCAATTGCTTATTTACCTGTCTGGAGG[C/T]GCCTTACAGCAAGGACTCTTTCTTTCTCCTTCTTT Y 2 1 2 1 101000 r 74 goat snp414-scaffold1010-28033 1 137123894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779456 Affx-122931976 AX-385266559 1 135100432 TCTGTCACTATACTGAAAAGGATGCTAGCTGATTT[A/G]TTAATGAACTCTCAGATTATTAAATATGTCATGCC R 2 1 2 1 201000 r 74 goat snp415-scaffold1010-98684 1 137195527 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789347 Affx-122951589 AX-385276357 1 135137336 TTACCAAGTACAGAGAGGAGGGTTTTTAGACAGGA[A/G]TGTGGTTAATTCACATGTTAGCAGATGAACAGATA R 2 1 2 1 101000 f 74 goat snp416-scaffold1010-135588 1 137232670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388632 Affx-122969124 AX-123258990 1 135173099 CCTGCTGTTATCTCATGGGGATGGTCTGGAAGAGA[A/G]TGAGGAGCTCCAGTGAGCTTCTGGGGTGGAGCCAG R 2 1 2 1 101000 f 74 goat snp417-scaffold1010-171351 1 137268823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771513 Affx-122961540 AX-385258671 1 135214569 GGTGAGCAGCTTGGCAGTAGACCCAATGAGCTTAT[G/T]CTCCAGGCTCTCTTTGAGGTCTAGAGAAACATCAA K 2 1 2 1 101000 r 74 goat snp418-scaffold1010-212821 1 137310626 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395012 Affx-122964227 AX-123265367 1 135260650 TGCCTGGGAATTAATTGAGTGGGATGAAATCCTCA[A/G]ATCCTCAGGTCTAGGAGACAACCACCTCTTGTAGC R 2 1 2 1 101000 f 74 goat snp419-scaffold1010-258902 1 137356557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382698 Affx-122973635 AX-123253056 1 135314149 ATTTCTCTGCTAGAGCTCTGCAAGTCTTTCTCATG[C/T]TCTGAGACATCACATTTTCTATTCTTGAAGTCCTA Y 2 1 2 1 101000 f 74 goat snp420-scaffold1010-312401 1 137405419 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410818 Affx-122952641 AX-123281168 1 135370939 TTTACCATGCAAATGTATGCAAATAAGAAAATAGT[A/G]TTCTTAGCCAAGTGCATTAGCACCTATTTCTTTGG R 2 1 2 1 101000 r 74 goat snp421-scaffold1010-369191 1 137461470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802924 Affx-986696084 AX-385289820 1 135395880 ACATAACAGGGGGCCATCCCTGATCACCTTCCTCT[A/C]AAAGGAATTAACTTAGGGCTCCAGTTAACAGTCTC M 2 1 2 1 600010 f 74 goat 1_135395880 1 135395880 Ancestral_priority_1043 ancestry 0.534 neutral IMAGE 10K 10K ancestral 320800273 Affx-122933693 AX-385287197 1 135418063 GTTTGCCCCTACTCTACAATGTCTGAAGTCTTTAG[C/T]AGAAAATTTGAAGGCTAAGGGCCGAAATCACTTGA Y 2 1 2 1 202000 f 74 goat snp422-scaffold1010-416315 1 137509150 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396894 Affx-122963224 AX-123267249 1 135466364 TAACAAATATTTGTAAAATGTAAAGGAATAAAACA[G/T]CATGACCAAATGGGTCAAAGTTGTTTCAAAACTCA K 2 1 2 1 103000 r 74 goat snp423-scaffold1010-464616 1 137557930 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428087 Affx-122939098 AX-123298430 1 135512746 GATTGTGCAACTTGTCCAATTCCAAGGCCATCCAG[C/T]AAGCTAACAGCAGAGCCGCATTTGAATTCACATTT Y 2 1 2 1 201000 f 74 goat snp424-scaffold1010-510998 1 137604549 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275387 Affx-1111834768 AX-519548961 1 135520262 TGATGGAACTGGAGGCCCGCCTCCCAATTCCTAGA[A/C]GTTACATCTCTGTCCCTTCTTCACTGCAGCTGGGT M 2 1 2 1 101000 r 74 goat GoatD01.052126 1 135520262 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38433420 Affx-122935088 AX-123303761 1 135570066 ATCACCTAAAACCACTCCTGATCTGCAGCCAGCCA[C/T]GAATCTTTCATCAATAAGCTCTCCTGTGGTTCATG Y 2 1 2 1 101000 r 74 goat snp425-scaffold1010-568318 1 137662082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412393 Affx-122951452 AX-123282742 1 135646359 ACCTTCCCTCAGATCCCCACCTTACTGCTTCTCCT[C/T]TCATCCAGGATTGACCCTGCCAATCATAAATGTCA Y 2 1 2 1 101000 r 74 goat snp426-scaffold1010-644611 1 137738561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788934 Affx-122955575 AX-385275947 1 135681113 AGCAGTTTTAAACTATTCACTTTATGGCTTCTCAT[A/G]ACTTCTTTCCACTTAGTCACACACTCCAACTGATT R 2 1 2 1 101000 f 74 goat snp427-scaffold1010-679365 1 137773402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432453 Affx-122935804 AX-123302794 1 135718707 TTAACTGAGTTCATGGTGAGGTGAGCACAAGCAAG[A/G]CAGAACCAGGAGAAATAAGTAGCAGAAAAGAAAGA R 2 1 2 1 201000 f 74 goat snp428-scaffold1010-716959 1 137811059 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435429 Affx-122933486 AX-123305769 1 135781523 GGACGGACCTTTGCAGTAGTCCAGAGAATATGATA[C/T]GGGGCTTAAGGTGAGGGTTATAATAAAGACTAGCA Y 2 1 2 1 101000 f 74 goat snp429-scaffold1010-779775 1 137874506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381695 Affx-122974718 AX-123252053 1 135837954 CTAATCTGTCAATGTTGAGAAATAGAATTAATGAG[C/T]GGACTAAGGATCTTCTCCTACATGGAATCTGTGAG Y 2 1 2 1 101000 r 74 goat snp430-scaffold1010-836206 1 137931757 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447941 Affx-122923784 AX-123318277 1 135875385 TAAGGCAGCTGACTTTCCTTTTCATAGCCAGGCTC[G/T]AGCCCAGCTCAAAAGAATAGTAAAAATAACAGCTA K 2 1 2 1 201000 r 74 goat snp431-scaffold1010-873637 1 137969108 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793303 Affx-122933467 AX-385280281 1 135906396 CAAAACAGTTCTTTCCTCAAAAAATCTTATCCTCA[A/G]AACAGATCTGCTCCCTCACCATCATTATCCCTATT R 2 1 2 1 101000 r 74 goat snp432-scaffold1010-904648 1 138000817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409493 Affx-122954049 AX-123279844 1 135946067 TTGGGCCTGAATCCACACTTTGTTCTTGTTGCGTA[C/T]GTGCTCGTAAAACCAGTTTCTGTGCCTGAGTCTGG Y 2 1 2 1 101000 f 74 goat snp21243-scaffold2074-35471 25 41907407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387299 Affx-122970523 AX-123257657 1 135993048 GGCCAGCCTCGCCACTGTGATGGTTACTGAACAGC[C/T]GGACTCTGCGTTTACAGACCCAGGGTGTGCTCAGC Y 2 1 2 1 201000 f 74 goat snp21244-scaffold2074-82452 25 41951912 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402831 Affx-122958262 AX-123273184 1 136041433 TTTTTCCCATCAAATAAAAACAAAATAAATATTCA[A/G]CCTGGGATTTAAGTCAACATAATACAAAATGAGAG R 2 1 2 1 103000 r 74 goat snp53685-scaffold819-57603 1 138047555 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428203 Affx-122939453 AX-123298546 1 136095034 ATGCCCTGGATCAAATTAGGGCATGACTAAAGAGT[A/G]CAACTGCTCTCAAGTGAAGCTCCTCTGGGTACCCC R 2 1 2 1 201000 r 74 goat snp53686-scaffold819-111204 1 138099764 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384935 Affx-122972326 AX-123255293 1 136157770 GCCCTCTGCCCATCTCTAAGGCAGGTCAAAGTCCA[A/G]CGTTCATTAGTTGAGCTCAAATTCTGCTGACATTC R 2 1 2 1 101000 r 74 goat snp53687-scaffold819-173940 1 138163195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386071 Affx-122971456 AX-123256429 1 136211746 GCAGCTCCCTGAGGACCGCCTTTCCTATTCCTCAG[C/T]AAGGACTGCATGCTAAATGCCTCCTTAGAGGAGAA Y 2 1 2 1 202000 f 74 goat snp53688-scaffold819-227916 1 138217396 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441578 Affx-122928678 AX-123311915 1 136284233 AGGTAAACTCAAGTTTAAAAGAAACTCTTTCATAA[C/T]ATTGGCATAGATACACTATCATGTGTAAAATAGTG Y 2 1 2 1 103000 f 74 goat snp53690-scaffold819-300403 1 138292030 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476159 Affx-1251763662 AX-507596443 1 136293073 ATAAATTTATTTATTTTAATTGGAGGTTAATTACT[-/TTAAAATATTGTATTGGGGGCTCCGGAGGGAAAGATGGCGAAAAATAAATTGTGGAATGTCAAAAAAAAAAAAAATAAAA]TAAAATATTGTATTGGTTTTACCATACATCAACAT - 8 1 4 1 20000 f 74 goat SV_379 1 136293073 - deletion junction SV-TF-chip 539476414 Affx-1251763662 AX-586011816 1 136293073 ATAAATTTATTTATTTTAATTGGAGGTTAATTACT[-/TTAAAATATTGTATTGGGGGCTCCGGAGGGAAAGATGGCGAAAAATAAATTGTGGAATGTCAAAAAAAAAAAAAATAAAA]TAAAATATTGTATTGGTTTTACCATACATCAACAT - 8 1 4 1 20000 r 74 goat SV_379 1 136293073 - deletion junction SV-TF-chip 562165086 Affx-1251763662 AX-606940498 1 136293073 ATAAATTTATTTATTTTAATTGGAGGTTAATTACT[-/TTAAAATATTGTATTGGGGGCTCCGGAGGGAAAGATGGCGAAAAATAAATTGTGGAATGTCAAAAAAAAAAAAAATAAAA]TAAAATATTGTATTGGTTTTACCATACATCAACAT - 8 1 4 1 20100 r 74 goat SV_379 1 136293073 - deletion junction SV-TF-chip 562165974 Affx-1251763662 AX-606941383 1 136293073 ATAAATTTATTTATTTTAATTGGAGGTTAATTACT[-/TTAAAATATTGTATTGGGGGCTCCGGAGGGAAAGATGGCGAAAAATAAATTGTGGAATGTCAAAAAAAAAAAAAATAAAA]TAAAATATTGTATTGGTTTTACCATACATCAACAT - 8 1 4 1 20100 f 74 goat SV_379 1 136293073 - deletion junction SV-TF-chip 562165985 Affx-1251763662 AX-606941394 1 136293073 ATAAATTTATTTATTTTAATTGGAGGTTAATTACT[-/TTAAAATATTGTATTGGGGGCTCCGGAGGGAAAGATGGCGAAAAATAAATTGTGGAATGTCAAAAAAAAAAAAAATAAAA]TAAAATATTGTATTGGTTTTACCATACATCAACAT - 8 1 4 1 20100 r 74 goat SV_379 1 136293073 - deletion junction SV-TF-chip 320781069 Affx-122955414 AX-385268156 1 136294294 AATTTGACATTAGTTTTGCCTGATGCAGAAGCCCA[A/C]TTTCTTCCCATTACCTGTTTTGTGAGTTTGTTCTC M 2 1 2 1 101000 f 74 goat snp27914-scaffold2997-194539 1 138308231 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379451 Affx-122976093 AX-123249809 1 136341865 CAAATTTCAAAGAGTAAAATTTATTCATCTCGAGA[C/T]AAGACAAAGTCAGAGTTACATTTGCAATTCATTAT Y 2 1 2 1 101000 r 74 goat snp27913-scaffold2997-146968 1 138356136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402635 Affx-122958393 AX-123272988 1 136420438 TTGTCCACCAGCCCCACACCTGCATTCTAGAACAG[C/T]GTAGATCTCAGGTTTACCTCTGAATATATTATGGC Y 2 1 2 1 101000 r 74 goat snp27912-scaffold2997-68395 1 138432806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405209 Affx-122956905 AX-123275561 1 136455683 GTCCCAGCACCCGGTGATGTCTCCTACCCTTGGAA[G/T]TGGCAGCCCCAAGAGGGAGTCGTACTTTACTCAAG K 2 1 2 1 101000 f 74 goat snp27911-scaffold2997-33150 1 138469529 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432918 Affx-122935313 AX-123303259 1 136486915 CTTCCTGTGTAAGTGTGAGGATGGATGCATTTTAT[G/T]ATAATGCTAGTTCTCACTCTTGGGTTTTTAAAGTT K 2 1 2 1 101000 f 74 goat snp27910-scaffold2997-1918 1 138500754 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790535 Affx-122932451 AX-385277538 1 136505765 CAGAAATTTCGTTTTAGACGTTTATCTTGTGAGAA[G/T]GGTAATGAACGGAAGTAGAGCGATGTTTCTCCTTC K 2 1 2 1 101000 r 74 goat snp8576-scaffold1309-1459353 1 138519063 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423505 Affx-122942557 AX-123293851 1 136534729 TCCTACTGATCCTTGAACAAGAGCTTTTGGAAAAT[A/C]GATCAGAGATGTTTGCTGCTACTGTTGCTGCTAAG M 2 1 2 1 201000 f 74 goat snp8575-scaffold1309-1430389 1 138548003 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441416 Affx-122928829 AX-123311753 1 136574710 ATATGGTAAATATCAGTAGCTATTAGTCACATAAA[C/T]GAAAGCTGGTCCTCAGTTTGTAAAGGGATCCTGAG Y 2 1 2 1 201000 f 74 goat snp8574-scaffold1309-1390408 1 138568103 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421338 Affx-122944070 AX-123291685 1 136623744 TAAATGGGCTAAATGCCTTTTTTTGGAAGGTTAGT[G/T]TAAGGAGAGAATGAAGCCTGGTATGTAAAGTGCCC K 2 1 2 1 101000 r 74 goat snp8573-scaffold1309-1341374 1 138617473 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391974 Affx-122966518 AX-123262331 1 136706417 ATGTGATTGTTTTCTCTTTTGCTTCCTGTAAACAA[C/T]GGTCTACCAAAGAGAAATCAGAGCATTTCACCAGA Y 2 1 2 1 101000 r 74 goat snp8572-scaffold1309-1258701 1 138701430 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385364 Affx-122971639 AX-123255722 1 136748205 TCACTCACCTAGCAGGTATGGGATTTGATTTTATC[A/G]TGATTGATCCCCTCCTACTGTTCTGCTGCAGTTTC R 2 1 2 1 303000 r 74 goat snp8571-scaffold1309-1216913 1 138743182 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434177 Affx-122934882 AX-123304518 1 136801943 TGGCTCACATCTGAGGGCTGTTAATTGCTGATGAC[G/T]GTGACATCCTTAAGTTTCTTGAGTAGGGAGTGGTG K 2 1 2 1 201000 f 74 goat snp8570-scaffold1309-1163175 1 138797866 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780168 Affx-122947759 AX-385267265 1 136839784 AAAGACACTGACAGCCTAAGATACTTTGCAGATTT[A/G]CTGCATTTTCAGCGAAAGAACAGTGGCTCCCTATT R 2 1 2 1 101000 r 74 goat snp8569-scaffold1309-1125334 1 138836636 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406106 Affx-122956215 AX-123276458 1 136955655 GTGCCATGTGCCCCATGTGTATGATAAGCCAAGAT[G/T]GTGATTTTCTTTGAATTGCTGGTTTTTGGTAGTTA K 2 1 2 1 201000 r 74 goat snp8567-scaffold1309-1009463 1 138952998 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790475 Affx-122976999 AX-385277478 1 137007904 GCTGAGAGGAAAGAGAGAGGTATCTTTTCTAGAGT[A/C]TGGAATTTGTGAATGATAACTAGTTTCATGTAACT M 2 1 2 1 101000 f 74 goat snp8566-scaffold1309-957214 1 139005293 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272473 Affx-1111832839 AX-519546195 1 137034442 CATAGATTCCAGCCCACCAGGCTCCCCAATCCCTG[A/G]GATTCTCCAAGCAAGAACACTGGGGTGGGTTGCCA R 2 1 2 1 303000 f 74 goat 1_137034442_AF-PAKI 1 137034442 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446805 Affx-122925293 AX-123317141 1 137093647 AATACCTGTAACGTAACCCTTTTTCTATCAATCTT[G/T]TCTAAAACAGTATATTGTTATAATTAGTGTCCACT K 2 1 2 1 303000 f 74 goat snp8565-scaffold1309-871471 1 139092420 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771440 Affx-122974265 AX-385258598 1 137172068 GTTTACTACAAAATGATACTGTGACAAATAACATC[A/G]TTTCCATAAATCACCAGGTGTCTGTCTTCCCAAAG R 2 1 2 1 101000 r 74 goat snp8564-scaffold1309-793050 1 139169588 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784171 Affx-122969409 AX-385271223 1 137218819 TTCAGTTTGTGGGGAGACAGATGAAATGGTGCTTC[A/G]TGGTTTGGGTTTCCTAAAAGAAAGGGAAGATATTA R 2 1 2 1 101000 f 74 goat snp8563-scaffold1309-746299 1 139216743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse317 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320772020 Affx-122941694 AX-385259176 1 137285746 GCCCCAAATTTAGAAACATGAAGCTATTAAGACAT[A/C]CTTGACCCCTAAAATATCTTTTGAGTTTCCTGGAC M 2 1 2 1 101000 r 74 goat snp8562-scaffold1309-679372 1 139283581 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse318 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410584 Affx-122952124 AX-123280934 1 137318510 AACTGTCCCGTAGTTAACTTCGAAAAAACCAAAAC[A/G]CCCTCTGTGCGGGAAGGCCCCGCGGTCCCACACTT R 2 1 2 1 101000 f 74 goat snp8561-scaffold1309-646608 1 139317139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse319 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38439062 Affx-122930319 AX-123309399 1 137354861 TGGGCACCACTTGGATAAAGCCATGTGAATGAGGC[G/T]CTCTACAACTGCCCCAAGCCCACGCTAGGCCACAG K 2 1 2 1 101000 f 74 goat snp8560-scaffold1309-610257 1 139354044 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse320 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38421016 Affx-122944550 AX-123291363 1 137386709 TGAACCAAGGAGTGATGTGGGAAGCCAGGGCCCAG[A/G]AAAGTTTCCAAGAACAACCTGGTGAGGGTACTGGC R 2 1 2 1 102000 r 74 goat snp8559-scaffold1309-578409 1 139385717 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse321 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320770761 Affx-122960304 AX-385257925 1 137445103 CTTCCATTATATGGATGGGAATGGATGCTCTAATC[A/G]CTGAGAAAAAGCAATCCTACCCACAAGTTTACATT R 2 1 2 1 101000 f 74 goat snp8558-scaffold1309-520015 1 139444127 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse322 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38392389 Affx-122966224 AX-123262746 1 137488373 GAAGCTGAAGTGAACATCAATGCCAGGAGAGAAGG[A/G]TGGGTCTTCGAAGGCACGCACTCAGCAGTAGCGCC R 2 1 2 1 101000 f 74 goat snp8557-scaffold1309-476745 1 139486766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse323 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410601 Affx-122952110 AX-123280951 1 137516937 TGACCCTGAAAAGATAAACAAGTTTAAAGCCTGTC[A/G]CATTCATTCATTTTTAGGTCTAGTTACCCCCGTGG R 2 1 2 1 101000 f 74 goat snp8556-scaffold1309-448181 1 139515537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse324 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38377000 Affx-122977731 AX-123247359 1 137582393 CCCCTCACGGTTGGGGAACAAATTGCCTTCTGTAG[C/T]AGTAAGGGTCCCAGGGCATCCCCAGGGTCCCCAGC Y 2 1 2 1 101000 f 74 goat snp8554-scaffold1309-382725 1 139582025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse325 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320802254 Affx-122946497 AX-385289158 1 137628443 ACTTGACTGAAAGTCATAAAATGCTATAAAGACAA[C/T]AATATAAAGAAATCCATTCTTCCCTAACTATGCCC Y 2 1 2 1 101000 r 74 goat snp8553-scaffold1309-336675 1 139627942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse326 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38432986 Affx-122935263 AX-123303327 1 137701495 CCTTCAGACAAGGGTCATGTATTGAGACCCAGGTA[C/T]GGTGTGACTACAATATTTGGAGGGGCCCAAGTATT Y 2 1 2 1 201000 f 74 goat snp8552-scaffold1309-263623 1 139701259 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse327 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410843 Affx-122952619 AX-123281193 1 137765601 CCTGTCCAACATCTAGTTCTGTGATTTTTCATGGC[C/T]ATTTCCTGTCAAGTTCTCTAAAGTGAATTTCTAGC Y 2 1 2 1 201000 r 74 goat snp8551-scaffold1309-199517 1 139765433 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse328 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38380437 Affx-122975297 AX-123250795 1 137794316 TGTCACTGGTCTCGGTACAGAGAGCGCCTCGTCAC[A/G]TCCTCAAGTCCAGCCTTTCATTCCCCGGAAACGAG R 2 1 2 1 101000 r 74 goat snp8550-scaffold1309-170802 1 139794306 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse329 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38433147 Affx-122935679 AX-123303488 1 137846228 TCTTTCATATCCAGTGCTAATAATAAGGGGAGATG[C/T]GATTGATTGTGGAAGGTCCTGCCTCAGGTATATCA Y 2 1 2 1 101000 r 74 goat snp8549-scaffold1309-118890 1 139845521 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445718 Affx-122926105 AX-123316055 1 137876678 TACAGGGGAAAATGGCTTAGTTTGTCATTTAAAAA[C/T]AAAACTGCCTTATTGCCAATGACCTTCATAGCAAC Y 2 1 2 1 202000 f 74 goat snp8548-scaffold1309-88440 1 139875525 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse330 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38436723 Affx-122932310 AX-123307061 1 137922493 GATGCCTGCATGATTATACACACGTGCACTCTGGC[A/G]CTTACAGAAGAATGCACACACGTGCACATGATCTC R 2 1 2 1 201000 f 74 goat snp8547-scaffold1309-42625 1 139921398 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse331 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38412522 Affx-122951352 AX-123282871 1 137961901 GTTATATATATAGACTGATCAACTGGTCCCGGTTT[A/G]CCTGAGAATTCTGGTGTTAGCCTTAAAAATTCAGT R 2 1 2 1 101000 r 74 goat snp8546-scaffold1309-3217 1 139957414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse332 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38425441 Affx-122941522 AX-123295787 1 137975026 GAAAGGTAAGGAAAGGGCGCAGTGCGTGGAATGAC[G/T]CGGGCTCTTAAGATCAGTGCTGATAAGGAGACCCT K 2 1 2 1 101000 f 74 goat snp4724-scaffold11542-14597 25 42007035 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse333 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38428021 Affx-122939148 AX-123298364 1 137991024 ATGCTGATGAACATTTGCAATGCAAGGGTGGGTCA[C/T]GGAGGGGTGCCTGTGGCCACCAGGGCAGGGACCAG Y 2 1 2 1 101000 f 74 goat snp27437-scaffold292-1261810 1 139961892 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38436766 Affx-122932276 AX-123307104 1 138020133 TCTTCATCAGGGCCCACAGGGACTTGAATCTTTTG[C/T]TTAGAAATCCACAGGAAAAACATCTGACACTGGCA Y 2 1 2 1 201000 r 74 goat snp27436-scaffold292-1232701 1 139990820 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse335 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38402585 Affx-122958435 AX-123272938 1 138076107 CCCTCTCAGGGAAGAAAAGGCTCTCCCTCTTTGTC[A/G]CTTATGCTTTCTTCCATTCTTCTCTCTCTGGCTAC R 2 1 2 1 201000 f 74 goat snp27435-scaffold292-1176727 1 140047297 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse336 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320785275 Affx-122963610 AX-385272320 1 138110014 TCTCCCTGTCTTTCCTACAAGTACTATATATTTTA[C/T]GATAACCAAACAACCCTAGTTCAGGAAGAAAAGTT Y 2 1 2 1 102000 r 74 goat snp27434-scaffold292-1142820 1 140081733 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse337 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38453169 Affx-122920470 AX-123323502 1 138142122 GTTGAGTGAGCATTGCGATAATGTGTGTGGTGACC[A/G]TTGAATAAGAAACAGTGCAGGCAACAAAGCGGCGT R 2 1 2 1 101000 f 74 goat snp27433-scaffold292-1110712 1 140113796 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse338 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38424205 Affx-122942502 AX-123294551 1 138172279 TGGTTGGCTTGCTCGCCTCTGTGGTCAGGTGTCAG[C/T]TCCCTCTGGATAGTGAAGACACAGACTGTTCCCAG Y 2 1 2 1 101000 r 74 goat snp27432-scaffold292-1080555 1 140141842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse339 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38420349 Affx-122944965 AX-123290696 1 138216211 CCATATTTATGCACAGACACACCATTTCTTTGACA[C/T]GTCTAAGTGACAAATAGATGTCACTTTGTCTAAGT Y 2 1 2 1 101000 f 74 goat snp27431-scaffold292-1036623 1 140185652 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse340 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38392900 Affx-122965728 AX-123263257 1 138275303 CGTGAATTCCAATGAGGATATCGAGGATGGAGCAT[A/G]TCTGAAAGTAAAGCATCTTTAAATATATAATGCAT R 2 1 2 1 101000 f 74 goat snp27430-scaffold292-977531 1 140244752 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse341 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320768621 Affx-122963127 AX-385255801 1 138375750 TTTCAAAAAGAGGGGAGATGAAGGGAGGTCTTAGT[C/T]GTTATTGGATAACCTAGAATCAGAGTCAAAGTCAT Y 2 1 2 1 101000 f 74 goat snp27428-scaffold292-877084 1 140345224 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse342 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320788214 Affx-122942099 AX-385275233 1 138417308 ATATTCTATAAGGAAACATTGAAGAATGCACACCT[A/G]CATAACACACCATGATCATTTTTTATTTGAACCTT R 2 1 2 1 101000 r 74 goat snp27427-scaffold292-835526 1 140387562 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse343 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38385442 Affx-122971316 AX-123255800 1 138465188 TTATGTATTTTGGTGCAAGTCCATGGTCAGATATC[C/T]ATTGCTGACTTTTTATATATTAACTATCCCTGAGA Y 2 1 2 1 101000 r 74 goat snp27426-scaffold292-787646 1 140434838 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse344 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38423196 Affx-122942719 AX-123293542 1 138498480 TTCCTAGAAGTCAGTCTCTTTGGGTAAGTTTTGCC[A/G]TCCAGCTGGGCTGTGGAACAAGAATAAGTAGATTG R 2 1 2 1 101000 r 74 goat snp27425-scaffold292-754354 1 140468063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse345 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410686 Affx-122952744 AX-123281036 1 138533195 GAAACGTTTCTGAAAGAGGAACTATGAAGTGGGAA[C/T]TGAATGATTTGTATCTATTATTCAGCTTGTCTTAG Y 2 1 2 1 101000 f 74 goat snp27424-scaffold292-719639 1 140502732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse346 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38453110 Affx-122920024 AX-123323443 1 138591460 GTCAATAAAGCAGAAGTAGATGGTTTGTCCTTTGC[A/G]TTAGCATAATGGGATAGTCTGGTTACAAGAAAGGT R 2 1 2 1 201000 r 74 goat snp27423-scaffold292-661374 1 140559740 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse347 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38383926 Affx-122972972 AX-123254284 1 138627525 GCTCTCCAGCTCTAGGTTCATCAAGCACTGTCCAG[C/T]GTAACTTCTGCAATAATGGAAACCCTTTCAACTCA Y 2 1 2 1 201000 r 74 goat snp27422-scaffold292-625309 1 140596042 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse348 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38420614 Affx-122945239 AX-123290961 1 138674421 TAGTTTTGTTTACAGAGTTGCAATCCAACATGCCT[A/G]CTGATCCATTAATCGGGGGTGACAGTGACCCAGGG R 2 1 2 1 101000 f 74 goat snp27421-scaffold292-578413 1 140643058 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse349 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38432912 Affx-122935317 AX-123303253 1 138710283 CTTTGATAATAAGACACCCTATTATTTTATGTGCC[A/G]TTTTATGTGTTTTTAACAAAGAAAAGATACAGAAG R 2 1 2 1 103000 f 74 goat snp27420-scaffold292-542551 1 140678900 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse350 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38397060 Affx-122962732 AX-123267415 1 138740524 AAAATCTCTGGGTGCTCAGTTCCTTATATGTTGGG[A/C]TGGCCAAAAAGTTCATTTGGGTTGTTAATAAGATG M 2 1 2 1 101000 f 74 goat snp27419-scaffold292-512310 1 140708752 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse351 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38447484 Affx-122924091 AX-123317820 1 138794764 AGAGACCAACACAGACAAATTAAAAGGCCAACAGA[C/T]GAGAGAAACTAAAGAAAGCACAAGGGAATCAGGTT Y 2 1 2 1 101000 f 74 goat snp27418-scaffold292-458070 1 140763357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse352 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38383459 Affx-122973453 AX-123253817 1 138865579 AGGTGGACCTGGAGAGACTTTGTTCATTAGAATTC[A/G]CTTGAATTTTTGATTCTTGTATTAAAGTCTATTTT R 2 1 2 1 201000 r 74 goat snp27417-scaffold292-387255 1 140843053 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse353 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320775306 Affx-122943006 AX-385262437 1 138917290 CTTTGGCATCAACCACAGGCAGACAGGAGAAACTC[A/G]TGGGTCAGGGTAGGAGGTTTACTCTTTCATGTATC R 2 1 2 1 202000 r 74 goat snp27416-scaffold292-335544 1 140894087 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse354 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38397915 Affx-122961939 AX-123268270 1 138947073 TGACTCTCACATCAGTGAGTCTCACAGGAAAGCCG[G/T]CTGGGCTCTGGTCATTACCTGCTGACCATCACTCA K 2 1 2 1 101000 f 74 goat snp27415-scaffold292-305761 1 140923846 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse355 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38412196 Affx-122950942 AX-123282546 1 138996059 AACTCAGTGCCTGTCCTCAGGGAGATTCCAGGCAA[C/T]GAAATAGTTCACGGTCCTCACTGCTGCCCAGGAGA Y 2 1 2 1 102000 f 74 goat snp27414-scaffold292-256775 1 140972331 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse356 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38400609 Affx-122960386 AX-123270964 1 139041683 GGCTGATTGGAAGGAAGAGGTGTCTGTCAAGGTCC[C/T]GGAGGAAGAAGTCCATGAGCTAAGTTGAGCAGTAG Y 2 1 2 1 201000 r 74 goat snp27413-scaffold292-211151 1 141017992 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse357 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410643 Affx-122952777 AX-123280993 1 139075264 CCAAAGGGAAGCAGCATGTGGGTCAGCTGCTCGTC[A/G]CACCTGGTTAAGCTGTTTCAGCTGGGTGTACTTGA R 2 1 2 1 101000 r 74 goat snp27412-scaffold292-177570 1 141051692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse358 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38398543 Affx-122961528 AX-123268898 1 139109166 CATTGCCTAACAACCATCATGCCAAGGAACCTGGC[A/G]TATTCTTTTCTCATAATGGAAACTTTCCTTTTAAA R 2 1 2 1 201000 r 74 goat snp27411-scaffold292-143668 1 141087410 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse359 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320792879 Affx-122949814 AX-385279857 1 139144711 TTAATAACTATGATCCCTAAGTTCCGTCTACTTGT[A/C]TCCATGAACTTCCTTGCTTCCGAAGTTTAATTCTC M 2 1 2 1 101000 r 74 goat snp27410-scaffold292-108123 1 141123033 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse360 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38400602 Affx-122960390 AX-123270957 1 139177402 AAACATATCAAATGCAGTTTTATGTATTTAATATG[A/G]TTTCAATAAGATTCAAATACATTTTTATGTTGAGA R 2 1 2 1 103000 f 74 goat snp27409-scaffold292-75432 1 141155587 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse361 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38439915 Affx-122930016 AX-123310252 1 139207085 CCTAGTGCTCTCATGGTAAGTGACCTGGGTTCCAC[A/G]GTGGGGTCACGTGAGGGGGGCAGCACGATCAGATC R 2 1 2 1 101000 f 74 goat snp27408-scaffold292-45749 1 141185777 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse362 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38418661 Affx-122946322 AX-123289009 1 139244110 TTGAATGGTCTGGTATTGAGAATTCTGTAGTTCCC[A/G]TCATGTGACCAGAGTTGGGAGGGAATCCGGTGGTG R 2 1 2 1 101000 f 74 goat snp27407-scaffold292-8724 1 141221804 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse363 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38436262 Affx-122932546 AX-123306601 1 139258064 ATTATCCAAGGAGAATGGGCTCCTGGGCACTGTGT[C/T]TTCAAGTGAGAAAGCAGTGATATGGGAAAACAGAC Y 2 1 2 1 201000 r 74 goat snp40269-scaffold514-5131 1 141236847 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse364 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38422796 Affx-122943209 AX-123293142 1 139316127 CCTCGAAACAGCACACCTGACTTACAGGTGCAGAC[A/G]CTACTGTCAGACACCTGGGGTGAACTGTCTGAGGC R 2 1 2 1 101000 f 74 goat snp40270-scaffold514-63194 1 141294910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800355 Affx-122947711 AX-385287277 1 139370104 TAGATGCTCAAGATGTACCCATGCATCGAAGAACC[A/G]TAAATTAAGGATATTCACTGCTTACATATGTGAAC R 2 1 2 1 101000 f 74 goat snp40271-scaffold514-117171 1 141349092 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402848 Affx-122958251 AX-123273201 1 139422228 GCATTGGTCATTTTTGATCTCCCTGGGTCATCTTG[A/C]TGTTCAGCCAGGGTTAAAGTCACTGTGCTGTCTAA M 2 1 2 1 201000 r 74 goat snp40272-scaffold514-169295 1 141401573 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273890 Affx-1111833876 AX-519547498 1 139425875 CACCAGCTCAGGCTGCAGAGGAGAAAGAAGGAAGG[A/G]CTCTGTGAACTGGCCCAGAATTTTTGCCTCTGGAC R 2 1 2 1 202000 r 74 goat GoatD01.008855 1 139425875 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437679 Affx-122931773 AX-123308017 1 139454003 AACAGTGGCTTCCAACTAAACTCTGCTATGCCATC[A/G]TTTGGAAGTTGTCTCCCCATTTCAGAGATGTTAAA R 2 1 2 1 101000 f 74 goat snp40273-scaffold514-201070 1 141433682 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409072 Affx-122953344 AX-123279423 1 139539276 TCATTCCTTTTTCTTTCTGGCTAATATTCCACTAA[C/T]GGATGTTCCATTGTCTGGCCATGTCCCGTGGTTAG Y 2 1 2 1 201000 r 74 goat snp40275-scaffold514-286343 1 141519187 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272522 Affx-1111832840 AX-519546240 1 139541154 CCTGAGCCTGGCAGGACCAGCGCATCCTCAAAAAG[A/G]CGGTGGTCAGACAGCTTATCAGCTATGCACAGAAA R 2 1 2 1 102000 r 74 goat 1_139541154_AF-PAKI 1 139541154 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276713 Affx-1111835553 AX-519550223 1 139558608 AGAGCCCACTCCAGGGAGCATTTAGCCACTGGGGA[A/G]CCTCTCCTCCCAGCCCAGCTGTGAACCTCAGAATT R 2 1 2 1 202000 f 74 goat Random2.2K-133 1 139558608 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391652 Affx-122966561 AX-123262009 1 139588375 ATTAAAACGCAAAACCAGAGCACAGACCCTGATGG[C/T]GCCAAAGACACAGTGGTGAGAACATCACCTGAAGA Y 2 1 2 1 201000 r 74 goat snp40276-scaffold514-335442 1 141568586 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403371 Affx-122957789 AX-123273724 1 139633165 GTCCATGGGGTCACAAAGAGTTGGACACGACTTAG[C/T]GACTGAACAACACAAGTCACTTAAGGATCAGAAAT Y 2 1 2 1 103000 r 74 goat snp40277-scaffold514-380232 1 141612835 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448936 Affx-122923152 AX-123319271 1 139737108 ACGTTTCTGCTCATCCCTGGCTCCCTTACCCGTGA[C/T]GTATATGTTGAAGGAGTCACAAAAGCACCTCTGGA Y 2 1 2 1 201000 r 74 goat snp40279-scaffold514-484175 1 141716330 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383755 Affx-122972440 AX-123254113 1 139765868 GCACAAACACCCACAAAACCCTCACTCTGCCTGTC[G/T]GCTTACTCAGAGGCTCCTTCTGCTTCGTCAGGAGG K 2 1 2 1 201000 r 74 goat snp40280-scaffold514-512935 1 141746337 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395886 Affx-122963621 AX-123266241 1 139812547 ATTCCTGCCTCTCTACTTTTCTCTCTGTGCCCCAG[C/T]GGCATCATTTTCTCTCACAAACACACCCAAATCAT Y 2 1 2 1 101000 f 74 goat snp40281-scaffold514-559614 1 141792726 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410078 Affx-122952848 AX-123280428 1 139844549 TGAGACTAACAGCTGCCCACCCTATGGGATTCTTA[C/T]GAAGGACAACGAACGCAGTATGTCTGCAAGTTTCC Y 2 1 2 1 201000 r 74 goat snp40282-scaffold514-591616 1 141824597 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423018 Affx-122943418 AX-123293364 1 139894079 CATGGGTTCTGCATCCTCGGAGGCAGAGAGCTGGC[C/T]TCATAGCTCGTACTCGATAAACAGTGGTTTGCAGG Y 2 1 2 1 101000 r 74 goat snp40283-scaffold514-641146 1 141864810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453768 Affx-122919595 AX-123324101 1 139934921 CTTTTTTTTATGAACTGTGATTTTGTAAGAAAACA[C/T]GGTATTTCCTCCGGAATGAGTAATGTGCACATCAT Y 2 1 2 1 101000 r 74 goat snp40284-scaffold514-681988 1 141905709 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425448 Affx-122941518 AX-123295794 1 140031637 TGTCCTGTGGCTGAAACACATCAGCACAAACTTGG[C/T]GGTTTAAAACTACACAAATCGATCATCGTACATGT Y 2 1 2 1 101000 r 74 goat snp40286-scaffold514-778704 1 142002582 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768291 Affx-122961659 AX-187158319 1 140064692 AACCATGGCTCACAAAGAATGCAATATTGTTGTCC[A/G]TTCTCTGAATTAAGTTGAGATGTAAGTGACATTTA R 2 1 2 1 101000 f 74 goat snp40287-scaffold514-811759 1 142035966 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418317 Affx-122946973 AX-123288665 1 140161533 GCATCAGCTTGAGAATTAAATGCTTCCAAAGCTTC[A/G]TACGTGTGACATGGGAAGGAAAGACACCAGATAAA R 2 1 2 1 201000 f 74 goat snp40289-scaffold514-908600 1 142132966 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799760 Affx-122923627 AX-385286687 1 140203316 CAAGACAAAATAAACTCACATTAGAATAACATATC[A/G]CAAAATGTTGATAAGAGTATAGAGAATTAAGAACT R 2 1 2 1 101000 f 74 goat snp40290-scaffold514-950383 1 142174751 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442101 Affx-122928356 AX-123312438 1 140245191 GAGGGTGATTCAGAGAGAGACGCCCACACCACGCC[A/G]GGCACAGGGTTAGCAGTGGCCATGGGCTTCCCCCA R 2 1 2 1 303000 r 74 goat snp40291-scaffold514-992258 1 142215445 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394471 Affx-122964570 AX-123264826 1 140320986 AGAGCCGGGGACAGGACCCTGCACGCATTCCCCTC[A/G]GCCGTGCCTCTGGTTCTCCACTCTTCCATCAGCTA R 2 1 2 1 101000 r 74 goat snp40293-scaffold514-1068053 1 142289169 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426935 Affx-122940428 AX-123297280 1 140415818 TCTTTGAAACTGGATATTCTTACACTTTTCCCTGC[G/T]GTGGTGGTGTGAGTTCCAGGTGTCTGTTAAGAGCC K 2 1 2 1 201000 f 74 goat snp40295-scaffold514-1162885 1 142385069 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385398 Affx-122971346 AX-123255756 1 140447513 AAGTACCATGGATGATGACCCCTCCCCAGGGTGGG[C/T]GGTGGCTTCTGGGGGATGAGTTTAGAAGAGACTTG Y 2 1 2 1 303000 r 74 goat snp40296-scaffold514-1194580 1 142416711 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769605 Affx-122961252 AX-385256775 1 140493157 TCAGCACAAGCGGTAATTTTGAAAGCAGGGGTAAC[A/G]CTAGAAAGAGAGTCCACTCTTGCAGGGTTATGTTT R 2 1 2 1 101000 r 74 goat snp27918-scaffold3-21710 1 142462719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403406 Affx-122957764 AX-123273759 1 140535710 TGTCTATCTCCCCACCAGAATATAAGTCCCAGGTA[A/C]GTGTTTGTTGTCTGTCTTCCCACTAGAATTAAAGT M 2 1 2 1 102000 r 74 goat snp27919-scaffold3-64263 1 142505324 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423886 Affx-122942296 AX-123294232 1 140579857 GAAAAGGGAAAAGGAAACCCTGAATTCATCACCAG[A/C]TGATATAAATGTTCATTTCTACTTTACCACAGTTT M 2 1 2 1 101000 f 74 goat snp27920-scaffold3-108410 1 142548452 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392561 Affx-122966081 AX-123262918 1 140643356 TTATTTCCCACTGGGGGACATTCAGGTAGCTTCTA[C/T]TCTGGTTTTTGCAGCAGTAGATAACGCTGTGGTAA Y 2 1 2 1 101000 r 74 goat snp27921-scaffold3-171909 1 142600261 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412797 Affx-122950490 AX-123283146 1 140682501 ATGCAAGAAAATGTGTCCTTTGCACTTTTGAGACC[A/G]AGTGTGCTTTTAAATGGGGCCCCTTGGCAGCCAGG R 2 1 2 1 101000 f 74 goat snp27922-scaffold3-211054 1 142638865 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393018 Affx-122965647 AX-123263375 1 140728323 CAATCAATAGGACAGAGGCCCTGGAGTTTGTAATC[C/T]GGTTCCTTAACATCATAAAGTTACATCACCTGTCT Y 2 1 2 1 101000 r 74 goat snp27923-scaffold3-256876 1 142684760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449500 Affx-122922626 AX-123319835 1 140760441 TTCAGGATGCCCCAGCCCTCTTCAGGACGGGAGTC[C/T]CCCCGCCACTGAGAGCCCAGTTTAAAGGTTACCCT Y 2 1 2 1 101000 r 74 goat snp27924-scaffold3-288994 1 142716767 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476160 Affx-1251763663 AX-586011589 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 8 1 4 1 20000 f 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 539476415 Affx-1251763663 AX-586011817 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 4 1 4 1 20000 r 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 562165249 Affx-1251763663 AX-606940661 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 8 1 4 1 20100 f 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 562166082 Affx-1251763663 AX-606941491 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 8 1 4 1 20100 r 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 562166268 Affx-1251763663 AX-606941676 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 8 1 4 1 20100 f 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 562166316 Affx-1251763663 AX-606941724 1 140769047 CTTCACCCATCCATCTGTTGATGGGAATCTAGGTT[-/GCCTCCATGTCCTATCTATTATATATATATATTTTTTTAAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]CCTCCATGTCCTATCTATTATAAATAGTGCTGCAG - 8 1 4 1 20100 r 74 goat SV_380 1 140769047 - deletion junction SV-TF-chip 38431318 Affx-122937074 AX-123301659 1 140790014 ATGATACTGGGTGTTAATGCTGTCCTCTAGGGCAC[A/G]GATATTTACATGTCTGTTTCAGTGTGTTGTAACTT R 2 1 2 1 101000 f 74 goat snp27925-scaffold3-318567 1 142746200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448357 Affx-122924118 AX-123318693 1 140840457 TGTGTCTGGCAGAGGAACTGCCTTTTTCAAATTCC[A/G]CCAAAGTTGCACTGTTGTGTTGGCAGATGGATCAA R 2 1 2 1 201000 f 74 goat snp27926-scaffold3-369010 1 142796576 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405118 Affx-122956973 AX-123275470 1 140930277 AACCTGGACATCCATAGGATTTCACACTTATTCTC[C/T]AGGAACTGCCAACAGGCGGCCCACCCTGCTGGAGC Y 2 1 2 1 101000 f 74 goat snp27928-scaffold3-458830 1 142887188 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405248 Affx-122956879 AX-123275600 1 140979606 TCCATCCATCCAGCACATCTCTGAGCCCTTGCCAC[A/G]TACCAGGTGTTGTTCTGCATATCTGGGATCCACAG R 2 1 2 1 101000 r 74 goat snp27929-scaffold3-508159 1 142933758 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276879 Affx-1111835566 AX-519550388 1 140986624 CAATGTTGGCAAAGAGATTGGAGCAGTGAAAAGCC[A/G]GCGACTGTCAGAATGCTAGACCCTTGCTCTTTGAG R 2 1 2 1 101000 r 74 goat Random2.2K-136 1 140986624 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320787072 Affx-122929242 AX-385274099 1 141015296 GGCCCTCTCTCTTAAAAATGTTTAATAGACTCTTT[G/T]TAAGAGTAGTTTTAGATTCGCAACAAAATTGAGTG K 2 1 2 1 101000 f 74 goat snp27930-scaffold3-543849 1 142969566 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773071 Affx-122929769 AX-385260214 1 141054410 GAAGCTCAGTCTCACAGACTTAATTTGTGTTCAAA[C/T]GAGATCTGGATAAGTGTTGCTCCCCTAAAAGAGGG Y 2 1 2 1 201000 r 74 goat snp27931-scaffold3-582963 1 143008578 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273977 Affx-1111833963 AX-519547582 1 141099375 TCATTTTCAGAGCTGCCAAGATTAAATGAAGTAAT[A/G]TACCAGCACAGACCATCTGCAGCTAGCAGGCACTT R 2 1 2 1 202000 f 74 goat GoatD01.012317 1 141099375 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38410514 Affx-122952178 AX-123280864 1 141102428 CCAAATCTCTCCTTTTAATGCTGTATTTTTGCTTT[A/G]TTTCTATTAACTTTTAATTACCCTGAGATAAACAT R 2 1 2 1 201000 r 74 goat snp27932-scaffold3-630981 1 143053173 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429128 Affx-122938005 AX-123299470 1 141132454 CACAGCATCTTTTCCAGAGACTCCTGCATCCCTCC[A/G]TCCGATCCTGCCCAGCAGAAAGGACACTGCTGAGT R 2 1 2 1 102000 f 74 goat snp27933-scaffold3-661007 1 143083234 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429401 Affx-122938531 AX-123299743 1 141173769 CCTCAGTATCTTTCAGCTCAAGGATAACAGCACCA[C/T]GAGGTTCCTGATAAGAAAGGGCTGCATAGCTCTGG Y 2 1 2 1 101000 f 74 goat snp27934-scaffold3-702322 1 143124704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787153 Affx-122972486 AX-385274179 1 141205239 AATACCTATATTTTAGAATGCTGGTCCACGTGACA[C/T]GCGAAATAAATGCATCTGCATATATTGGGAGTGTT Y 2 1 2 1 101000 f 74 goat snp27935-scaffold3-733792 1 143155775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425710 Affx-122940771 AX-123296056 1 141260937 CCACATGCACACAGACACACACTCCCAGACAAGAA[C/T]TGTGGCTGCAACCACTCATGGTCATGCCAGGGACA Y 2 1 2 1 201000 r 74 goat snp27936-scaffold3-789490 1 143210901 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276889 Affx-1111835571 AX-519550398 1 141264582 GAATTTATGGCATGCCAATTAAATCTTAATTTTTT[A/T]AAATGCCTTTCAGAAAGTATCTCCTGACCAAAAGA W 4 1 2 1 103000 r 74 goat Random2.2K-137 1 141264582 T A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419180 Affx-122945721 AX-123289528 1 141332981 TCTCTTCCCCTGTGAAGTTCCTTGACATGTGTGTG[C/T]ACATGCTATTAACATCTATTTTATATATACAGATA Y 2 1 2 1 103000 f 74 goat snp27937-scaffold3-861534 1 143283606 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424922 Affx-122941293 AX-123295268 1 141373140 ACTTCAGTTGGTACTTCTTTATGGGGGCTGGTGGT[A/G]AAATTGTAGGTGAAATATGACGCACAGGTCAGCCA R 2 1 2 1 101000 r 74 goat snp27938-scaffold3-901693 1 143324182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276770 Affx-1111835580 AX-519550279 1 141398879 TAGATTTAAAACCGCTCTGATTGGAGAGCCTGGAA[A/G]TTAAAAATTAAGTTAACCTGAAGAATGCATTCCAG R 2 1 2 1 101000 f 74 goat Random2.2K-139 1 141398879 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427330 Affx-122940126 AX-123297673 1 141443923 CACTGTTGCTTTCTCACCCAGCCCCCAGCTTCTGG[C/T]ACAAGGAAGGTGAGTGGGGTCATGACCAGGATGGA Y 2 1 2 1 103000 r 74 goat snp27939-scaffold3-972476 1 143394463 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409178 Affx-122953192 AX-123279529 1 141491749 TCCTTGTTAACATTTTGCCATATTTGCTTGTGTAC[G/T]CCATGCATGTCATCATTTATCCATTTGTTGACATC K 2 1 2 1 201000 r 74 goat snp27940-scaffold3-1020302 1 143443612 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402357 Affx-122959049 AX-123272710 1 141512827 GGGGCTAACAGTGTTGCAGAGGGGCTCTGAAATTA[C/T]AGTACTGTTTCTCGTCAAACTGCTACTTATTCACT Y 2 1 2 1 101000 f 74 goat snp21323-scaffold2083-3122 1 143465553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419854 Affx-122945375 AX-123290202 1 141570967 GCATTTCCTTGAACCCACTCAAAACATTACTCAAG[C/T]GGCCCTTTCCCCTACTTCTCAGGAATCAGGTGGCA Y 2 1 2 1 101000 f 74 goat snp21324-scaffold2083-61262 1 143524189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408480 Affx-122954420 AX-123278831 1 141609200 GTTGAAAATTTCTTCATTGCTTAATTCATGGGCAC[C/T]GTTTGTGAACGCTTCTGTGAGCAGCTGAGAGAAAG Y 2 1 2 1 201000 f 74 goat snp21325-scaffold2083-99495 1 143562895 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430315 Affx-122938233 AX-123300656 1 141641238 TGAGATGATATCTCTCTACTGTCCTCTGTTTCAAA[G/T]AGTCAGTCCAGTTCATAGACTTTTCCCTCCAGTAT K 2 1 2 1 101000 f 74 goat snp21326-scaffold2083-131533 1 143592279 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449045 Affx-122923067 AX-123319380 1 141689926 TGAAACTCTCTGTGGCTCAACGTGTTGTCAACGTC[C/T]AAGAATGTTCCAGGGCCACATGGAGAGGCAGTGCC Y 2 1 2 1 101000 f 74 goat snp21327-scaffold2083-180221 1 143641237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400168 Affx-122960682 AX-123270523 1 141727421 GGAGCAGTGTGTGTGCAGGGAGGCACTCCTGTGGC[A/G]CAGTGACGGGAATCCTCCAACATCCAGATTGGATT R 2 1 2 1 101000 r 74 goat snp21328-scaffold2083-217716 1 143678723 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381294 Affx-122974459 AX-123251652 1 141756443 GAGACAGGAGAGAGACGGATAGATTCAGAGACAGA[C/T]GGAGCTCTCTGGTGCATCCTCCTGTAAGGGCATGA Y 2 1 2 1 101000 f 74 goat snp21329-scaffold2083-246738 1 143707820 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400409 Affx-122959990 AX-123270764 1 141797136 CTCCTGAAACAAAATTCCTGTGTTAATTTGACTTC[C/T]CCAGTACATGCAGCTATACAGTTCTCGTCTTTACA Y 2 1 2 1 101000 f 74 goat snp21330-scaffold2083-287431 1 143749941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453826 Affx-122919554 AX-123324159 1 141914329 GGAAGATGCACCATGTACCTGGATTTAATTTCCTA[A/C]TTGCATTTTAAAAGGCAATTCTTCATATCTACAAA M 2 1 2 1 201000 r 74 goat snp28928-scaffold3111-232523 1 143867864 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399107 Affx-122960865 AX-123269462 1 141983550 ACCCTCTTCCAGCCTCTGATCCCCCAAAGGGAGGT[A/G]CTGGACCCTCAGGGGAGCCGAGCTCATGAGCAGTA R 2 1 2 1 303000 r 74 goat snp28927-scaffold3111-163302 NW_017204900.1 9611 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392075 Affx-122966379 AX-123262432 1 142016282 TCTGTAACCCCAAGTTAATTCCGAAGTCCCTTCAC[A/G]CATCCTCCCGCGGATGAGTAGCAGGCCCCACGGAG R 2 1 2 1 101000 f 74 goat snp28926-scaffold3111-130570 1 144265013 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271816 Affx-1111832841 AX-519545603 1 142041543 CACTTTCCATTTCTTATTCTGGGGTTCATCAGGAG[A/G]AAACCACCCCCATCCTCATGCTCTCATGGGCCTGT R 2 1 2 1 101000 f 74 goat 1_142041543_AF-PAKI 1 142041543 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413454 Affx-122950676 AX-123283803 1 142045578 GGTACTGGTGCCAGTCTTCTGGAGTTCAGAAATGC[A/G]AGAGTACACTTCGGTTGCTTTAAGCCATCAGTTCT R 2 1 2 1 101000 r 74 goat snp28925-scaffold3111-101274 1 144294155 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771212 Affx-122927531 AX-385258371 1 142082475 TTGTTGCTCTTCTGCAAGAGTTGAGTTTTGAATAT[A/G]TTCACCATGCCAATTCTCAATTTTTCCCTCTTTGG R 2 1 2 1 101000 r 74 goat snp28924-scaffold3111-64377 1 144330717 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415488 Affx-122948700 AX-123285837 1 142128895 ACCCAATGAATAGAGGAGCAGACGAGAGGCCACAC[A/G]ATTTGCTCAGAAGCCAGGAACTCCGGGAGCTGAAA R 2 1 2 1 101000 f 74 goat snp28923-scaffold3111-17957 1 144376801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412842 Affx-122950456 AX-123283191 1 142157746 ATCCTTGGGAAGAGCCAACCCATGTCCTAAGACTT[A/C]TGAATATTTCCCACAGGCAGGTGGGGGCAGGTCCT M 2 1 2 1 103000 f 74 goat snp59164-scaffold971-10795 1 144397617 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414800 Affx-122949220 AX-123285149 1 142233618 AATATGTCCCATTCATTAGCTAATAAGCAATACAG[C/T]GGATCGTCCCATCCAGGAATAAAAGCTTCATCCAC Y 2 1 2 1 201000 f 74 goat snp59166-scaffold971-86667 1 144513690 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781509 Affx-122969919 AX-385268594 1 142272452 AATGCTGTTGCACCTCAGTTGATATGATTTCACAT[A/G]TTTTCTATCTTACATTGTCAGTGGAATTAATCGCA R 2 1 2 1 101000 f 74 goat snp59167-scaffold971-125501 1 144553336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442558 Affx-122928518 AX-123312895 1 142302374 CTTCCTTCCCCTCCCAAGCTGCAAAGAATGGTTTT[A/G]TCCCAACAGTCATAGTTGCTGCCACAGCCACTGTG R 2 1 2 1 101000 r 74 goat snp59168-scaffold971-155423 1 144583805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380444 Affx-122975748 AX-123250802 1 142358371 AACCAGGCACATGTGACTGTGACAATATGTCCTGC[A/G]ACCCCTGGATCCGCATGAACGCCCCTACCTATTGT R 2 1 2 1 101000 f 74 goat snp59169-scaffold971-211420 1 144639015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435555 Affx-122933383 AX-123305895 1 142413380 TGTTAAGCATCATCAGCCGCGTCCACCAAGCAGCA[A/C]GGTCACGGTCAGCCTGCTGGAGGGGATGAGGAGAG M 2 1 2 1 103000 f 74 goat snp59170-scaffold971-266429 1 144694701 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422127 Affx-122943553 AX-123292474 1 142493459 CGTTGACTGGACACAGCCAGCTTCCCCTGCCTCCA[C/T]GGAGGCTTAGGAGTTGCTTCTTAAATATTTAATGG Y 2 1 2 1 103000 r 74 goat snp59171-scaffold971-346508 1 144774353 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444973 Affx-122926667 AX-123315310 1 142538563 AAAGTAAAATTAAAAACAAAGATTCAATTGATTCC[A/G]TTGCAGTTAGATGTAGTTGAAGAAAGAACTAGTAA R 2 1 2 1 101000 r 74 goat snp59172-scaffold971-391612 1 144818903 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416887 Affx-122948077 AX-123287235 1 142589723 CCCATGGACTGCAGCACACTTGGCTTCCCTGTCCA[G/T]CATCAACTCCCAGAGCCTGTTCATTTATTAACAGC K 2 1 2 1 103000 r 74 goat snp59173-scaffold971-442772 1 144869800 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378739 Affx-122977032 AX-123249098 1 142629300 CTCTGGCCCCACTGTCCCACCATGTGTGCCCTTTG[A/C]CTCAACTGTGGTCTCTGCAGAGCACTCCTTGCACT M 2 1 2 1 102000 r 74 goat snp59174-scaffold971-482349 1 144909427 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432778 Affx-122935427 AX-123303119 1 142659820 ACCGGGAAAGGAACATTTTTTTTTTTTGCAAGACA[C/T]AGTCAGTCATGTTGTAAAGAAGAGTTTGACACATT Y 2 1 2 1 201000 r 74 goat snp59175-scaffold971-512869 1 144939665 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378628 Affx-122977113 AX-123248987 1 142694340 TGAACCGTAAAGGAAAGTAGACGCATGCGCCCCCC[A/G]CGTTCACAGCAGCACTGTTTACACTAGCTAAGGTA R 2 1 2 1 303000 f 74 goat snp59176-scaffold971-547389 1 144974871 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428622 Affx-122938681 AX-123298964 1 142752193 CGTGGAGTGGGCCAGGGTCAAGCGTTCACAAGGGA[C/T]GCCCCCCGCCCTGGACACACACAGAGTTCAGCCAG Y 2 1 2 1 101000 f 74 goat snp59177-scaffold971-605242 1 145032410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378322 Affx-122977344 AX-123248681 1 142801516 GACCCCACACACAGGCCATGGCAAGTCCTGTCCAC[A/G]TGGCTCAGAGCCCAGGAGCCCCTCGAGGCTGCGCC R 2 1 2 1 101000 f 74 goat snp59178-scaffold971-654565 1 145081289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392940 Affx-122965699 AX-123263297 1 142834375 TGTGCTCCCCAGGACTCAGAAGCCAGAAGTCCTTC[C/T]TTCTTCCACAGACACCCTGGCCTGGGCTTCAAGGG Y 2 1 2 1 102000 f 74 goat snp59179-scaffold971-687424 1 145113328 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450984 Affx-122921733 AX-123321318 1 142862899 ATAGTCTTGTTTGCCCACTATGGCTGTGCCACCCA[A/G]TGCTTGGTGTGCTGAGCTGAATGGTGTCTCCACAA R 2 1 2 1 201000 r 74 goat snp59180-scaffold971-715948 1 145141134 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793679 Affx-122942476 AX-385280651 1 142916438 GAGTGAAATACTCAGTGAGAACTCAAACACCGGCA[G/T]AGTCGCTGGAGAGTTCGGTTCTAGTCCATGGAGAC K 2 1 2 1 101000 f 74 goat snp59181-scaffold971-769487 1 145191476 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392684 Affx-122966418 AX-123263041 1 142964084 TGAGGGACTAACATTCTCACTAGAATTCTGCATCC[A/G]GTGAAGACATTCTTCCATAGGAAGAGGAAGCGGGC R 2 1 2 1 101000 f 74 goat snp59182-scaffold971-817133 1 145239454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440221 Affx-122930685 AX-123310558 1 142997989 CCGTCTGGCCATCCCTACTGTGGACATCAAACCCA[A/C]AAGTTGAAAACCCCCTGGACATGCTGGTCATCTTT M 2 1 2 1 101000 r 74 goat snp59183-scaffold971-851038 1 145273759 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798466 Affx-122954942 AX-385285399 1 143131758 AAAAGCTTTTAGACTCTGGCTCTGTTTCAAGGGCA[C/T]AGATTTAAGATGACTCCCGATCTTTCTCCATGTAG Y 2 1 2 1 101000 f 74 goat snp59185-scaffold971-984807 1 145407619 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398396 Affx-122961642 AX-123268751 1 143214056 GGCAGGCTGCCTGGACCTCCCTCCAGCACTTCCCT[A/C]GGTGGAACCTACCAGAAGTCAGCCCAGGACGAGGT M 2 1 2 1 101000 r 74 goat snp59186-scaffold971-1067105 1 145490320 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432934 Affx-122935300 AX-123303275 1 143242847 TCCCAGTTCGCAGGGGTGCACTGACAGCTCTTTGT[A/C]GGTTCTCCTCTCTCCTCCTGACTTCTCAGTGCTTG M 2 1 2 1 201000 f 74 goat snp59187-scaffold971-1095896 1 145520670 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449800 Affx-122922418 AX-123320135 1 143344660 TAAACTATAAAACATTTCAGCTGGTATTAGACCAG[C/T]GTTAACAGCGCCAGCTCTGGGGAAGATCTAGAATG Y 2 1 2 1 101000 f 74 goat snp59189-scaffold971-1197709 1 145622448 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798238 Affx-122956713 AX-385285173 1 143399821 TAACACATTGGAGGCATACTTTGGCAGAGGTAATG[A/C]CTCCCAAGGATGCTGAGAACATAATATTTGATGGG M 2 1 2 1 201000 r 74 goat snp59190-scaffold971-1252870 1 145685638 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804403 Affx-986696570 AX-385290992 1 143400881 TCTGCCCGAGCAGAAATGCGTGAACGTATCTGAGT[C/G]CATCTAGAACTAATGCTCCAGGGTCAGATTTTCTC S 4 1 2 1 600010 r 74 goat 1_143400881 1 143400881 Ancestral_priority_1043 ancestry 0.772 recommended IMAGE 10K 10K ancestral 38377721 Affx-122977393 AX-123248080 1 143443682 ATTAAATTTATGTGGAAGGAAGAAAGCAAGGCTAA[G/T]CCTGAAGTCTCTGAAGTGAGTTCCTTGAGGCCAGG K 2 1 2 1 101000 r 74 goat snp59191-scaffold971-1296731 1 145728897 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385374 Affx-122971630 AX-123255732 1 143521433 CCTAACAAGTGCACGCATGCTTTTTGGTTTTCCCA[C/T]GTGCATAGCCCGTCTGGAAGGAATTTCAGGGTGTG Y 2 1 2 1 101000 f 74 goat snp59192-scaffold971-1374482 1 145806577 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443428 Affx-122927368 AX-123313765 1 143554685 TAGAGAAACAGAAAACAAAAGAATAAAATTGAAAA[C/T]GAGAAAAGCCAGATAAGAATGACCAGGAAGACAAT Y 2 1 2 1 103000 r 74 goat snp59193-scaffold971-1407734 1 145839443 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800488 Affx-122973944 AX-385287408 1 143628286 CACCATCAAGTCTTAAATACTTCTGGACAAAGACC[A/G]TTGCCAACTGTACAAGATTAAAATGTGAATGACCT R 2 1 2 1 101000 f 74 goat snp22395-scaffold2210-27252 1 145909196 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414335 Affx-122950032 AX-123284684 1 143742243 TGTTCTCTGTGATGCTTGTAAGCTTTATCATTAAT[A/G]ACATTTTTGCCTTCCATGTACACGGAAACGACAGC R 2 1 2 1 101000 r 74 goat snp22398-scaffold2210-141209 1 146019858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424911 Affx-122941301 AX-123295257 1 143803889 AAACTGCATCTGTGTTCCATGTGAATGTGAAATGG[C/T]CCTGATCCTTTTTTTCTGACGGGGACAGAAAAGAA Y 2 1 2 1 101000 f 74 goat snp22399-scaffold2210-202855 1 146081892 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276781 Affx-1111835585 AX-519550290 1 143848171 GAATATGTGATCCTGAGTCCAGCCAAAGCCAGTCT[A/G]CAAACCTAAGCAGCAGCTGTCAGCAGACGTGGAGG R 2 1 2 1 201000 f 74 goat Random2.2K-140 1 143848171 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415203 Affx-122948985 AX-123285552 1 143858387 TGTTTCTGGGCATCAGTCACTGCTTGTGACCGACA[A/G]CTAGCATATTTGATAGAGAAGGAATGTTGAGAAGG R 2 1 2 1 101000 r 74 goat snp22400-scaffold2210-257353 1 146136046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444181 Affx-122927270 AX-123314518 1 143907757 CCCACATTCAGTGTTGTTGGGAGGAAAGGTCTCAG[A/G]AGAACCACAGTCACGGTCCTGACCAATGCCTGCCG R 2 1 2 1 101000 f 74 goat snp22401-scaffold2210-306723 1 146184948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424860 Affx-122941340 AX-123295206 1 143959775 AACATGTAAAAGACTGAGGTTCCTGTGAGGGGTTG[A/G]GTGGCACCTATAAACATCTGCCCAAAGATTAATTT R 2 1 2 1 201000 r 74 goat snp22402-scaffold2210-358741 1 146238663 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376024 Affx-122978399 AX-123246383 1 144014937 AGGCTCACAGGTGGAGCTGCAGTGCAGTGCTGCCC[A/G]AGTCCCGATCCTGCCAGAACCCAGACGTAGCATTT R 2 1 2 1 101000 r 74 goat snp22403-scaffold2210-413903 1 146294100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382449 Affx-122974225 AX-123252807 1 144050869 TTCAGAAACCTGAAATTCAGCTCTGAACAGTCACC[A/G]CTCCAGCTTCAAGGGTGATACATAGTGACCAGTGT R 2 1 2 1 101000 f 74 goat snp22404-scaffold2210-449835 1 146330700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378394 Affx-122976797 AX-123248753 1 144112284 GTGTTTGTTGAGCCATTTTTAAGCCTATACAGTCC[G/T]CTGTGCTCTGGTTGGGACCAGAGACTCGAGTGGGA K 2 1 2 1 101000 f 74 goat snp22405-scaffold2210-511250 1 146395126 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766525 Affx-122961086 AX-385253885 1 144142073 TCCTGGTTCACATCGCGGATTACATTATCAAATAA[C/T]GTATCATAACAGATCAAGCTGGAAAAAACATTCTT Y 2 1 2 1 101000 f 74 goat snp22406-scaffold2210-541039 1 146425331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778363 Affx-122968912 AX-385265478 1 144171376 CCATGTGCTCTCTGACATTAGTTGGTAAAATGTGC[A/G]TAATATTGCAGATTGTACCAGCTATTTCACAAGAG R 2 1 2 1 101000 f 74 goat snp22407-scaffold2210-570342 1 146454808 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803904 Affx-986696572 AX-385290616 1 144193528 TTAAGTTACCTCTGAAGATTGCTAAAAATAGCCAC[A/G]GTATACAGAAATGGTCTGGTATTGTATTAAACTTT R 2 1 2 1 600010 f 74 goat 1_144193528 1 144193528 Ancestral_priority_1043 ancestry 0.668 recommended IMAGE 10K 10K ancestral 320767726 Affx-122948059 AX-385254959 1 144236918 TGACTCATTCATCATGGAATGGGAAATAAAGGACC[A/G]TAGTAGACAATTTATGTGAAAGCACAGAAAGATAC R 2 1 2 1 101000 f 74 goat snp22408-scaffold2210-635884 1 146519136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787393 Affx-122956628 AX-385274418 1 144278669 TAGAAATAATGCAAGGTGATTAGCAATGCTAGGAT[A/G]TGTCTGTAAGATTTACCTATTCATATAATCATCAC R 2 1 2 1 101000 f 74 goat snp22409-scaffold2210-677635 1 146561256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769851 Affx-122928605 AX-385257021 1 144339450 CCTTTCCAATAAGGACTGACACATCTATTCATCCA[C/T]ATTGGAAATCTTCCTCCTCCTCTAGCCTAAGGGAG Y 2 1 2 1 201000 r 74 goat snp15149-scaffold1619-19073 1 146701519 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430734 Affx-122937510 AX-123301075 1 144433512 GTGTGAACTGTCTAGCTCTGTTCCAGGAGCCCATT[A/G]TTCCTGAAGAACCTCCTCCAAAAGACTCCTTGACC R 2 1 2 1 201000 r 74 goat snp15152-scaffold1619-113135 1 146795979 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797069 Affx-122951501 AX-385284009 1 144459107 ATAGCATATTTTCATTAGGGGTTATCAAGTTTTCC[A/G]CTGATAGAAAGTTTAGAGAGCAGAGCAAAGTACCA R 2 1 2 1 101000 r 74 goat snp12298-scaffold1461-17289 1 146821420 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421195 Affx-122944151 AX-123291542 1 144488312 TTCATTGGGAAGGGTCCTGGTCCCCAACACCACAT[A/C]CTCTTCACCTTTCTTCCCTTAGCCAGGGAACATGC M 2 1 2 1 101000 r 74 goat snp36351-scaffold436-1810 1 146851572 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770466 Affx-122921019 AX-385257632 1 144521193 CAGTACTGGAAGCCCCTGATCAGTTTTCATATCTG[C/T]GACCACAGTGAACTGTGTTCGGCTTCATTGGCAGT Y 2 1 2 1 102000 f 74 goat snp36352-scaffold436-34691 1 146884606 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272539 Affx-1111832842 AX-187183534 1 144546271 AACTAGTAGAGTCTTACAGTCATGGCTCACCCTCC[A/G]TCTGAGGGCAGCGGGCCCCACTATGGGGAGCAGAA R 2 1 2 1 102000 f 74 goat 1_144546271_AF-PAKI 1 144546271 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412524 Affx-122951350 AX-123282873 1 144557873 CTCAAATAGGAAATGACTTCTGCCCTGTTGTCTAA[A/G]GAGAGGCTTCAGGGAACAGCAGAAAAGGGTTACGT R 2 1 2 1 101000 f 74 goat snp36353-scaffold436-71371 1 146921283 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378152 Affx-122976973 AX-123248511 1 144601558 AGCTGAGATGACATTTACTGCATAGCTAGGAGACC[A/G]TGATCTCACCGACAGAAACGTTACTTCTTTCTTTC R 2 1 2 1 101000 f 74 goat snp36354-scaffold436-115056 1 146964989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397239 Affx-122962370 AX-123267594 1 144643092 CTGCACTGCAGATACAATCTTTACTGACTGAGCTA[C/T]GAGGGAAGCCCATGTATTGTAGTAAACTGTACATA Y 2 1 2 1 303000 r 74 goat snp36355-scaffold436-156590 1 147006487 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385570 Affx-122971845 AX-123255928 1 144673829 GCTCTTCCACCTTCAGATTCACCCGTATGCACTTC[A/G]CTTGGTCCTATCGTGGTCTGTAATCAATTATTTAT R 2 1 2 1 101000 r 74 goat snp36356-scaffold436-187327 1 147038064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797702 Affx-122925507 AX-385284641 1 144733106 TTGTGACTGTATAACATAAGTGTCCACAGTATAAC[A/G]TGTCTGCAAATTATCCCAATCATAATATACATTTT R 2 1 2 1 101000 f 74 goat snp36357-scaffold436-246604 1 147097270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442961 Affx-122928213 AX-123313298 1 144770436 CTTTATGTCACTGTAAGAAAAGGCATCATTTCAGT[A/C]GTCTTTGAGGTGCATGGTCTTTCCACCTGAATTCC M 2 1 2 1 101000 r 74 goat snp36358-scaffold436-283934 1 147134672 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429243 Affx-122937910 AX-123299585 1 144842391 ACTCACATGTTATCATAGGATACCCTTGACATCCA[C/T]TTATTCAGAGGATGTGGGGTGGGAGTCACAGTTTG Y 2 1 2 1 101000 f 74 goat snp36360-scaffold436-355889 1 147207614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445259 Affx-122925476 AX-123315596 1 144874530 ACATTATGCATGATATTAATATATGATAAAGGATC[C/T]GTGGAAAAGTGGAAAAGCACAAGCGTGCCATGCAA Y 2 1 2 1 101000 r 74 goat snp36361-scaffold436-388028 1 147239720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446304 Affx-122925646 AX-123316640 1 144965888 CAAAAGTACTGGCATTAGGGCTCCTTCCCCTTCCC[A/G]TATTCCCTCTTTTCTAGATTATTAGGTACCATACA R 2 1 2 1 101000 r 74 goat snp36363-scaffold436-479386 1 147331232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382499 Affx-122973817 AX-123252857 1 145001694 TGGGAAGCAATGGAAAGGCAAGTTGCTCTCCCCTT[A/G]TCCAACAATGATCTTAACTTTCTAGATATACGATC R 2 1 2 1 201000 r 74 goat snp36364-scaffold436-515192 1 147365588 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387080 Affx-122969881 AX-123257438 1 145037345 CCCGTTCCTCTGAGGTCACCCTGATCACTCTGTTC[C/T]CAGATCGCAAAATTACCGTGACCTCTGCCACACAT Y 2 1 2 1 101000 r 74 goat snp36365-scaffold436-550843 1 147401327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450152 Affx-122922741 AX-123320487 1 145075408 CCTTGGTGAATTGGTAAAGTTTGAAAGATCTGAAA[G/T]ATAACTGTGTAATCATTTAATCTTTGTGGAAGATA K 2 1 2 1 101000 f 74 goat snp36366-scaffold436-588906 1 147439114 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427205 Affx-122939590 AX-123297548 1 145115074 GTTTTCTATCTCTCTGTAACAAATTTCCAAAAGCA[C/T]AGCTGCTTTAAACAACACCCATTTATTACATTACA Y 2 1 2 1 101000 f 74 goat snp36367-scaffold436-628572 1 147478744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442459 Affx-122927948 AX-123312796 1 145154668 AGGGAGGTGCTGTCTCTAGGGAACTTTCTATCCCA[C/T]GCTTCAAAGTATCATATATGTCTGGAACTCCTTGA Y 2 1 2 1 101000 r 74 goat snp36368-scaffold436-668166 1 147517992 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38407744 Affx-122954987 AX-123278095 1 145207697 AGAACTAAGGTGATGATGCCCATAAATGCTCAGCA[C/T]GGGGCTGGGCACCCAGCTGTGCTCAGAAAATGTTA Y 2 1 2 1 101000 f 74 goat snp36369-scaffold436-721195 1 147571154 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800188 Affx-122968626 AX-385287111 1 145239224 TCTCTGAGGATTCATCCTGGTTTGCTCTCAAACAT[A/G]CTCATGTCTACTGTTGATTTCCGTTCTAGGAACCT R 2 1 2 1 101000 f 74 goat snp36370-scaffold436-752722 1 147602702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406216 Affx-122956124 AX-123276568 1 145268152 TGATTGTCTGTTTCACTCTTCCACTGGAATGAAAG[G/T]TCAATAAAAACAGAAACCCTGCCTGTCTCCTTCAC K 2 1 2 1 201000 f 74 goat snp36371-scaffold436-781650 1 147631984 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386143 Affx-122971403 AX-123256501 1 145326929 GGCTCTGTTCTCAAAAGTCCCACTTTCTCTCTCAC[A/G]TCCTCAGTCCCCTAAGACCTAGCCTTTGAATTCAG R 2 1 2 1 101000 r 74 goat snp6737-scaffold1244-1457031 1 147692948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443508 Affx-122927794 AX-123313845 1 145362221 TGGTTGTTTAAATTTTATTTTAAAAGCGAAGAGCA[C/T]GGAGGATTTGACAGCTAAGTTCTCAGTTTCATGAT Y 2 1 2 1 101000 r 74 goat snp6736-scaffold1244-1421739 1 147728303 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388240 Affx-122969791 AX-123258598 1 145403049 ATCTTCGGGGCTTGACTCAGTGTCTGGTCCATAGA[A/C]GGACTTCCAAAAATATTTGTTGAATAAGCCACAGA M 2 1 2 1 101000 f 74 goat snp6735-scaffold1244-1380911 1 147769259 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412519 Affx-122951354 AX-123282868 1 145467271 TGGGGAAGAGGGTTGTGAGGTGGAAAAGGAAATGG[C/T]AACCCACTCCAGTATTCTTGCCTGGAAAATTCCAT Y 2 1 2 1 101000 f 74 goat snp6734-scaffold1244-1316689 1 147834039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411715 Affx-122951530 AX-123282065 1 145521550 ACACAGCTGGCCCTATTGCTCCAACTTCCTCTTCC[A/G]TCACTCTCTGCCATGGTCTTCTTCACCAACCAACT R 2 1 2 1 201000 r 74 goat snp6733-scaffold1244-1262410 1 147888174 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771990 Affx-122927006 AX-385259146 1 145589611 AATATTATCTAACATGGGGACTCTCAAATGCTATC[A/G]TGCTTAAGAATTACCCAGAGAGCTTCTTAAAATGC R 2 1 2 1 101000 r 74 goat snp6732-scaffold1244-1194349 1 147956450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383199 Affx-122972787 AX-123253557 1 145623967 GATTACTTCTTTTTCTTTCCTCCCGCCCTTCCCCC[A/G]CTGTCCCCACCTGGCCTAAATGCTTATACACACTT R 2 1 2 1 303000 r 74 goat snp6731-scaffold1244-1159993 1 147990515 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440593 Affx-122929288 AX-123310930 1 145655990 TGATCTATAGTACAGAGGTAGTGCTGAGGATCAGC[A/G]TCTGAAATTTAGAGACTGCCTCACTGCCTGTATTT R 2 1 2 1 101000 r 74 goat snp6730-scaffold1244-1127970 1 148022658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379306 Affx-122976200 AX-123249665 1 145717128 CAGTGACAATACTGAGATCCTGCAGCAGGCCAGCA[C/T]GTGACCCACATGGACAAACCCAAACCCAACATGCA Y 2 1 2 1 101000 r 74 goat snp6728-scaffold1244-1066832 1 148083864 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450106 Affx-122922778 AX-123320441 1 145783167 ATCTCCCCCCGCAGGACCCTGCTGAAAAGCAGATG[C/T]GGTTTCTGCTCCCTGGCTCATTTTGCCTTGTGCAT Y 2 1 2 1 101000 r 74 goat snp6727-scaffold1244-1000793 1 148149528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450897 Affx-122922201 AX-123321231 1 145813249 TGGCTCCAATCCAAAGCACACTCAATTTCAGAACA[C/T]GCCTCCCCAGATCTTACCACGCCGAATCCTCTCGG Y 2 1 2 1 101000 f 74 goat snp6726-scaffold1244-970711 1 148179447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383246 Affx-122972749 AX-123253604 1 145886802 TTTCAGGTGGACAGCACAGGGACTCAGCCACACAT[A/C]TTCATGTATTGGTTCTTTACAATCTCCCCTCCTTC M 2 1 2 1 101000 r 74 goat snp6724-scaffold1244-897158 1 148252735 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452420 Affx-122920588 AX-123322753 1 145937514 TTTCATGTTTAATTTAAAAATTTGTTTTACAGTAC[C/T]AAGAAATGGTTGATGTAAACTATGTTTTGAAATAT Y 2 1 2 1 103000 r 74 goat snp6723-scaffold1244-846446 1 148310403 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430899 Affx-122936867 AX-123301240 1 145979871 GATCCAATGGCACCATCTCAGCTACGCTCACCAGG[C/T]ACTGCCTTCTTTACCATTCCCACCACACTCATCAC Y 2 1 2 1 101000 r 74 goat snp6722-scaffold1244-804089 1 148352257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433074 Affx-122935739 AX-123303415 1 146008373 TTCCACCGTCTGAGAGCCTGGGGAATGCCACTTAC[A/G]CTATCCCGTCTTCAACATTCAGAGAACACTGCCCA R 2 1 2 1 201000 f 74 goat snp6721-scaffold1244-775587 1 148380537 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403735 Affx-122958019 AX-123274087 1 146039340 TGGGGCTTTGAGATGATTCAAAACATGTTTCTCTT[A/G]TTTAAAAAATTTTGTAAATGGGACTTTCCCTGTGA R 2 1 2 1 303000 r 74 goat snp6720-scaffold1244-744620 1 148413501 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420475 Affx-122944872 AX-123290822 1 146071676 ATCACTGGAAATGCAGAGTGAGCCATCGGGAGGTC[A/G]CAGAGGGTGAGGCCAGGGGTCACCCAGCAGGAAGC R 2 1 2 1 101000 f 74 goat snp6719-scaffold1244-712284 1 148445116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385124 Affx-122971775 AX-123255482 1 146105414 TCCTCACAGAGATGCTGCAGCTGGGTTGGGGTGAC[C/T]TAAGTCATCAGGCAGTGCTGGGACCAGCAGGATAC Y 2 1 2 1 101000 r 74 goat snp6718-scaffold1244-678546 1 148478665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399425 Affx-122961230 AX-123269780 1 146147156 TCTGTTAAACATGTGCCCAGCTCTCAGTTAGCTCC[A/G]CATGGTCTCTTCTGCTCCCTTTGTTTGAGCTGTGT R 2 1 2 1 201000 r 74 goat snp6717-scaffold1244-636804 1 148520480 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405135 Affx-122956962 AX-123275487 1 146190197 AGGGAGGAAGTTTACCAAACGCTGTTGGCCACTCT[A/G]GGCACGCTCATCACCAGGCAGGAAAACAGAAGTGT R 2 1 2 1 101000 f 74 goat snp6716-scaffold1244-593763 1 148563929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790931 Affx-122945366 AX-385277928 1 146248669 ATGCCTCCTGGGAAACGGTTTAGGATTTTACGGTC[A/G]TGGTAACTTAAGCTTGTAGATTTCACTAAATCAAT R 2 1 2 1 101000 f 74 goat snp6715-scaffold1244-535291 1 148622833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414601 Affx-122949357 AX-123284950 1 146295731 TGTGCTCCCTGCAGTGCTGGCCACCACACACTGGC[C/T]TCAGCCCTAAGGAGGCTACTGACGTGTAGACGCGA Y 2 1 2 1 101000 r 74 goat snp6714-scaffold1244-488229 1 148670021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412691 Affx-122950760 AX-123283040 1 146331824 AACAGTGAAGATATATGAGTATGTATGACGGAGTC[A/G]CTTTGTTGTACAGCAGAAACTAACACAATATTTTA R 2 1 2 1 101000 f 74 goat snp6713-scaffold1244-452136 1 148706944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781024 Affx-122921754 AX-385268111 1 146405538 CATCTTAACCATCTCCTACATCTACCTGGCACAGA[C/T]GCTGTCAATATTCCCCTACTCTAAATTACCCTAGA Y 2 1 2 1 101000 f 74 goat snp6711-scaffold1244-378422 1 148780410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452972 Affx-122920155 AX-123323305 1 146462126 CCTTCCTCTCCTATATTTCAGATAGACTCTGTACC[A/G]CTGAGCCACCTGGTACCCTTCCCTTCGCTCTCTTT R 2 1 2 1 102000 f 74 goat snp6710-scaffold1244-321834 1 148837415 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436629 Affx-122932498 AX-123306967 1 146504701 TTCACCTGAAACTATCTTAATATTGTTAACTGGCT[A/G]CACCTCAATAACAAAGTAAAAAGCCTGAAAAAATA R 2 1 2 1 101000 f 74 goat snp6709-scaffold1244-279259 1 148879955 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802235 Affx-122952092 AX-385289139 1 146534752 GAGCTTTAAGCTAGCTTCGGGCTTCCTTTGAAATA[C/T]AGAGCATTCCTGCAGGACTATATAGACGCACACAG Y 2 1 2 1 101000 f 74 goat snp6708-scaffold1244-249208 1 148910087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427917 Affx-122939226 AX-123298260 1 146591028 TCAGACAAATGTTGGAAAACTGATCACGACCACGG[C/T]GCAAGCAATGGCTTCTAGAAGATGAAAATACCATA Y 2 1 2 1 101000 f 74 goat snp6707-scaffold1244-192932 1 148966329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803911 Affx-986696576 AX-385290620 1 146674504 GTCCTTGAACTGCGGGATCTAATTGCTTTGATAGA[G/T]AAATGACAGGGGTGAAGCAGGGGCCAAAACTCCTC K 2 1 2 1 600010 f 74 goat 1_146674504 1 146674504 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 38404112 Affx-122957113 AX-123274464 1 146713017 AGATTTGGCTTAAGGTGGCTGCAGATTCCTTCCTC[C/T]TAATGGACAAGTGGAATTTTATATTCCTCCCTTGA Y 2 1 2 1 101000 r 74 goat snp6704-scaffold1244-70943 1 149089077 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424422 Affx-122941804 AX-123294768 1 146808163 AACAGTGTTTAAAGAGCATTTGGCCCTCCAGTCGT[C/T]GTCCTCAGCCTTTAAAGCTGAGAGACAAACCCTCC Y 2 1 2 1 101000 f 74 goat snp29563-scaffold320-1673275 1 149183747 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418642 Affx-122946338 AX-123288990 1 146867272 CAGCCCATGGGGTCACAGAGTCAGACATGACTTAG[G/T]GACTAAACCACCATCCACTTTAATAACCTCATGAA K 2 1 2 1 103000 r 74 goat snp29562-scaffold320-1614166 1 149242626 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452257 Affx-122920770 AX-123322590 1 146897255 GAATTGAAGAACGTGTCTAACTCTGGATGTCAACT[A/G]TCATATCCACCTTCATGTTCACAGCCGGGCATGGA R 2 1 2 1 101000 f 74 goat snp29561-scaffold320-1584183 1 149272940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382816 Affx-122973559 AX-123253174 1 146929656 TCTTATGGAAGGCCACTGTTGAAAAGCCTCAAAAA[C/T]GTGATCTTCATTCCAGGAATTTATTCATTGCATGG Y 2 1 2 1 101000 f 74 goat snp29560-scaffold320-1551782 1 149305587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453774 Affx-122919591 AX-123324107 1 146973824 TAAGTGGCTAGTAGAAAATTTTAAATTACACATTC[A/G]CTTCTTCACATTTGTGGCTCACCTCATGTTTCTGT R 2 1 2 1 101000 r 74 goat snp29559-scaffold320-1507614 1 149349691 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439380 Affx-122930266 AX-123309717 1 147020690 CGACCTGAAAGCTGAGACAGGTAAAGATGAGGGCA[C/T]GATGCCAGATGTGGAGATGAAACACAGCGAGAGGC Y 2 1 2 1 201000 f 74 goat snp29558-scaffold320-1460748 1 149396646 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436968 Affx-122933162 AX-123307306 1 147062954 ATCCCACTCCCTCCTCCCAGTGTGACTGCGTTACA[A/C]AACACGGATCAATAAACTGTCATGTCCAGGTTGGA M 2 1 2 1 101000 r 74 goat snp29557-scaffold320-1418484 1 149439377 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386115 Affx-122971423 AX-123256473 1 147219943 CTCTGCACATGGCCTGCTCATGTACCAACAGACCA[C/T]GGCCCAGAGACTCTTTGGGGAGCAGAGATTGTTTC Y 2 1 2 1 101000 f 74 goat snp29553-scaffold320-1261495 1 149596828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272541 Affx-1111832843 AX-519546258 1 147259623 AAACTTTTTTGTTTGTTTGAAAGAAAGTGTTAGCT[A/G]CTCAGTCATGTCTGACTCTTTGGGATAGCGTGGGC R 2 1 2 1 303000 f 74 goat 1_147259623_AF-PAKI 1 147259623 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38397331 Affx-122963298 AX-123267686 1 147260103 CCCTCCGTCACCCACCCCCCAGGAACTCTGGAGAG[A/C]GTCCAAGAGAGGTGTTTCCATTTGGTGGAAATCTC M 2 1 2 1 101000 r 74 goat snp29552-scaffold320-1221335 1 149634299 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377236 Affx-122978158 AX-123247595 1 147298119 CCCAAAGCAGAGGGCATTGAGAAGAAAGCAGGGGC[C/T]GAAACCCACATGGGAATTCCCAGTGGCCACTGAGG Y 2 1 2 1 101000 r 74 goat snp29551-scaffold320-1183319 1 149672725 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438003 Affx-122931579 AX-123308341 1 147329636 ATGAGCTGAAAGACATCTCCACTAGTCCTAGGGAA[A/C]GTACAAACTCGGGTGGGTTTCCTTTCCAGCCTTAT M 2 1 2 1 101000 f 74 goat snp29550-scaffold320-1151802 1 149704230 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427215 Affx-122939582 AX-123297558 1 147360186 GGGGTCCATTCCTTGATGGTCAGTCTCACCACGTT[C/T]TTTCCCTCTTCCACCCATCCACTGATGTACTGAGC Y 2 1 2 1 101000 r 74 goat snp29549-scaffold320-1121252 1 149735173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780543 Affx-122968069 AX-385267634 1 147389485 GATCAGAAAATGTGTTCACGTCTTGACCCTGCCCT[A/G]TCCTCGACCAAGATACCTGATTCAGACAGACCCCC R 2 1 2 1 101000 r 74 goat snp29548-scaffold320-1091953 1 149764529 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423170 Affx-122942740 AX-123293516 1 147436985 GCCACATCACGCCACTCCCCAGCTTTCCCATCACA[C/T]AGCCTTCTCTGCCTGTCCTTTTCTGTCTCCTATAA Y 2 1 2 1 101000 r 74 goat snp29547-scaffold320-1044453 1 149809199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797372 Affx-122941951 AX-385284311 1 147476863 CTGGAGAGTGGGGCACCACTCATTCAACCAGAAAA[C/T]CGGAAAGAGCTCTGATCCAGAAGCCTCTCAATGAA Y 2 1 2 1 202000 r 74 goat snp29546-scaffold320-1004575 1 149849592 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449627 Affx-122923192 AX-123319962 1 147526282 TAGACTCCCAAAACAGCCAGCGCTCTGCCCCTTGA[C/T]GATGAAGTCAATCTTTCCCTGGGTTCATAGGTTTA Y 2 1 2 1 303000 r 74 goat snp29545-scaffold320-955156 1 149899346 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387909 Affx-122970455 AX-123258267 1 147563120 AACCTTCTAATGCTCCTCACACTTCACTTTACTTG[C/T]GATTCTCAAGCCCATTATAAGGCTATTCATACTGG Y 2 1 2 1 101000 r 74 goat snp29544-scaffold320-918318 1 149936710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429422 Affx-122938515 AX-123299764 1 147593387 GGTCTGCCTGCTCTACAGGGTCTCTTGCTCATCTA[C/T]GTGGAGACAGGAAGCCAGGATCAGAGAGGGTGAGT Y 2 1 2 1 101000 f 74 goat snp29543-scaffold320-888051 1 149967013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791008 Affx-122946118 AX-385278005 1 147626104 AATCCCTCTAAAGGCAACAACAGTCACAATGCTAT[A/G]TGACATTATAACTTCAGGCACAGGAATAATTCAAT R 2 1 2 1 101000 f 74 goat snp29542-scaffold320-855334 1 149999627 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396686 Affx-122962832 AX-123267041 1 147663352 TCCAACAAAGAAGGACAATGTTATCTTAAAAAGAA[C/T]ATTCAGTATTCCCTAAACTACGGCTTTGATCTAAC Y 2 1 2 1 101000 r 74 goat snp29541-scaffold320-818086 1 150037066 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441056 Affx-122928920 AX-123311393 1 147704741 ACCCCCACCACCTGCTGACCATCAGAGGTTCATCA[C/T]GTGCTTTGATGGTGACAGCCCTGGAAAAGGACACG Y 2 1 2 1 101000 f 74 goat snp29540-scaffold320-776697 1 150078563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389121 Affx-122968559 AX-123259479 1 147744657 CTGAGAGCCATATGATCCTTCCAGATCGGACAAAG[C/T]AATGAGAAATAGAGAATGCCATCAAGTTCAGAGAT Y 2 1 2 1 101000 f 74 goat snp29539-scaffold320-736781 1 150118910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433289 Affx-122935208 AX-123303630 1 147801281 TAGTGATATTTCAGGGAATTGCACAAGAAAAGTTA[C/T]GGTAAATTACTGATTATAACTCATATAATTAAAAG Y 2 1 2 1 101000 f 74 goat snp29538-scaffold320-680157 1 150175723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786494 Affx-122922661 AX-385273528 1 147833361 GTTTTGATGGAAGAAAGCTTCCAGGAGGTTTCACA[C/T]GGCACGAAGATAAAGATATGGCTCCTGAAAAGCAA Y 2 1 2 1 101000 f 74 goat snp29537-scaffold320-648077 1 150207831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276955 Affx-1111835603 AX-519550463 1 147882442 GAGAGAAATAGCTAGAGAGAAACTCAGAAGTCCCA[A/G]TCCAGAGAATTGTGACTCTTCTGTTAAGGCAGGCA R 2 1 2 1 101000 r 74 goat Random2.2K-144 1 147882442 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786979 Affx-122965797 AX-385274007 1 147929662 GCAGGTTAACAAGAGGAAAACAGAAGGGTATTAAC[A/G]TGTGTAGTTTGTACATACATGGGAAATACCAGGGC R 2 1 2 1 202000 f 74 goat snp29535-scaffold320-551776 1 150305283 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776145 Affx-122973463 AX-385263274 1 148048360 ATCCGTCCATGCATTTTCCATTAGGCATAGATGCA[A/C]GTGCGTGGATTCCTTTGAGTATCAAGTAATACTCT M 2 1 2 1 202000 f 74 goat snp29533-scaffold320-433078 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435383 Affx-122933573 AX-123305723 1 148080530 GCCCAGAACATGTGAGCAGTTTCATTGCATGTATC[A/G]TGCCAGGCGAAGTTTTTAAATGGCTTCTTTGAAGT R 2 1 2 1 101000 r 74 goat snp29532-scaffold320-400908 1 150457102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389907 Affx-122968115 AX-123260264 1 148111764 TACATTATACAATTAAAAAGTTTAATAATTGAAAG[A/G]GCTAATATCCAACTACACTAATGTGATTTTTTAAA R 2 1 2 1 101000 r 74 goat snp29531-scaffold320-369674 1 150488663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768323 Affx-122941093 AX-385255503 1 148143653 TGCAAGACCAAAACTCTATAGTTATACATATGATT[A/G]TGAATATGTTATATTGACAGCCTGGGTGTCTCAGA R 2 1 2 1 101000 r 74 goat snp29530-scaffold320-337785 1 150520518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394633 Affx-122964399 AX-123264988 1 148256884 ACTTAAAACCTCAGAAGAATGGTCCAACCATGGCA[C/T]ATTGCTGTTTCTTTTCAACAAATCATGCAAAATGA Y 2 1 2 1 101000 f 74 goat snp29528-scaffold320-224554 1 150635131 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430993 Affx-122936688 AX-123301334 1 148291881 ACTGAAGTGGAATTCAAGTTTGTGTGTCCTGTCCT[A/G]TTTCTTGGCCTTTCCTCCTGAGAAATTCTTCATTT R 2 1 2 1 202000 r 74 goat snp29527-scaffold320-189557 1 150669945 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439100 Affx-122931115 AX-123309437 1 148383848 TTAGATATATAAGATAGCTTTTTTAAAACATAAAT[A/G]CTCTGTATTGAACAACTCATTTTAACATAGCTTGT R 2 1 2 1 101000 r 74 goat snp29525-scaffold320-97590 1 150761309 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437132 Affx-122932156 AX-123307470 1 148424629 TCTTTGCAAAAGTATACGTGGACCTCAGTACGTCC[A/G]TTACAGCTTGGCCTTTATCTCATTCCTAATTTTTG R 2 1 2 1 10000 r 74 goat "ins-del_015;snp29524-scaffold320-56809" 1 150801933 T C ins-del_015 1 preexisting CNV preexisting recommended GoatSNP50 chip candidate gene ou candidate region PIS 10.1371/journal.pone.0086227 38450206 Affx-122922289 AX-123320541 1 148478485 CAAACGCTCACTTGTTAATACTCACTTGTTTCTCC[A/G]TGTTTCAGGTAGAATGTTCCTCCCTTTAGGCCGTT R 2 1 2 1 101000 f 74 goat snp29523-scaffold320-2953 1 150856109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433619 Affx-122934595 AX-123303960 1 148483663 CTGACTTAATTGGTCTGTGATGGGCCCTGGGCATC[C/T]GTACTGGGCAGCCAAGACAGAGAACTCTGGGTTCA Y 2 1 2 1 201000 f 74 goat snp21980-scaffold2163-2126 1 150859549 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770568 Affx-122962690 AX-385257732 1 148574464 TAGGCCTACCAAGAGGGATTGAGACCTGCTGAAAG[A/G]CGTCCTATGAGTAAGTATGTAAGCTTACAAGGTAG R 2 1 2 1 101000 f 74 goat snp21983-scaffold2163-92927 1 150948608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445775 Affx-122926063 AX-123316112 1 148626429 ACAGCATAATTCCTGGAAAGCATTTATGTCCCCCC[A/G]TGTGGGGAACAGACCTTCAGCCCTGCCATAGCCCA R 2 1 2 1 201000 r 74 goat snp21984-scaffold2163-144892 1 151000629 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425531 Affx-122941457 AX-123295877 1 148657624 CTGCAAAACTGGTCACCAAATCCTGCCAGGTAGGA[C/T]GCACGATTTAGAGGGGCACAAGCCTGCTGTGTTCC Y 2 1 2 1 101000 f 74 goat snp21985-scaffold2163-176087 1 151031573 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798119 Affx-122941428 AX-385285054 1 148707231 CAGTAATGGAGGGAAAAGGGTGAATAGAAAATGGA[C/T]AAAAATATTGTGTATCAGCCATGATTCATCTCCAT Y 2 1 2 1 101000 f 74 goat snp21986-scaffold2163-225694 1 151081229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436780 Affx-122932264 AX-123307118 1 148743092 CTATGAAGGGCAAGTATCTGGATTGGTGGCTAGAG[C/T]ATTTATTGTGTACAGGGTTCCCACCTGGGATTTCC Y 2 1 2 1 101000 r 74 goat snp21987-scaffold2163-261555 1 151117036 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408744 Affx-122953404 AX-123279095 1 148778498 AGCAACCTCCTCCCTTTGCTGATAATCACTCTGCA[C/T]ACCCCTTGCCCCTTCACCCTGAAAGCGTTTGCCCA Y 2 1 2 1 101000 f 74 goat snp21988-scaffold2163-296961 1 151165203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409479 Affx-122954058 AX-123279830 1 148811530 TTGATGTTCAAAATATGTATTTACATGCATGCATT[A/C]TGGTCTCCACTTTATAGAGTAGAAGACTAAGACCT M 2 1 2 1 101000 r 74 goat snp21989-scaffold2163-329993 1 151197865 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391696 Affx-122967580 AX-123262053 1 148853218 CATCTCAGGTTTAAATCTTTCCCCCAGAACTAGAC[A/G]CTGACTCAAGAATGGTCTAAACAGCCCTTCCTCAA R 2 1 2 1 201000 r 74 goat snp21990-scaffold2163-371681 1 151239390 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451871 Affx-122921062 AX-123322204 1 148896183 TCAGAGGACTTTCCCCAGTTCAGTAATCAGCAGGA[A/G]TTTATCTAACTGCATGATGCCAGCCATGCTGACTA R 2 1 2 1 101000 r 74 goat snp21991-scaffold2163-414646 1 151283056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406380 Affx-122955406 AX-123276732 1 148926402 CCAAGACCACCATGTACAGTTGCTCAGGTTGTGCA[C/T]AATGCAACATATAGCCATTGGGTTATGGTGCCTCT Y 2 1 2 1 201000 r 74 goat snp21992-scaffold2163-444865 1 151313160 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430093 Affx-122937531 AX-123300434 1 148971281 TTTAAACAGACCCCGAGTGGGAAAACAGGTCAACA[A/G]TGAAAGCTGTTGCTGGAAGTTCAAGGTCACCTTGG R 2 1 2 1 201000 r 74 goat snp21993-scaffold2163-489744 1 151358235 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390131 Affx-122967999 AX-123260488 1 149022417 CTGTGGACTGTAGGATGCTAGCAGTATCCCTGGCC[C/T]CCACCAAATCCCAGGAGTGTCTTCCTAACCGTGAC Y 2 1 2 1 103000 r 74 goat snp21994-scaffold2163-540880 NW_017191234.1 13885 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421882 Affx-122944270 AX-123292229 1 149037907 GATCTTGCAGGAAAGCAAAGCACACAAGCACGCAC[G/T]GCTGTGCACACACGCAAACCTTTACCCCGGGGCAG K 2 1 2 1 202000 r 74 goat snp12152-scaffold145-841841 1 151374628 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446621 Affx-122924796 AX-123316957 1 149067676 TAGATCTCAAAATGTCAGATGACTTTCCAGATCTA[C/T]GAAGTATCTGAAGTTCGCAGGTCTAACAGCCAAAA Y 2 1 2 1 101000 r 74 goat snp12151-scaffold145-812072 NW_017205255.1 12913 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429221 Affx-122937927 AX-123299563 1 149111957 TGAGATGTGGATGGAGAAGTTTCTGTGCTAACAAT[A/G]ATCGATAAATCTGAAGGGTTCATTTTAGCGGGGAA R 2 1 2 1 101000 f 74 goat snp12150-scaffold145-767791 1 151473795 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395011 Affx-122964228 AX-123265366 1 149143491 ACGGCCCTCCATACCTTTATATCCTTATACTTTTT[A/G]TATAAATGCTTCAGTCTGTGCCCTCTGGTTGCTTG R 2 1 2 1 201000 r 74 goat snp12149-scaffold145-736257 1 151505265 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439211 Affx-122931031 AX-123309548 1 149182752 TAGGCATCCCATCACACGGATGATTCTATGGCAAC[A/G]CAGCGGGGACAGTTCAATTGAAATACTCTTAACTA R 2 1 2 1 101000 f 74 goat snp12148-scaffold145-696996 1 151545083 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435830 Affx-122932827 AX-123306169 1 149238996 TATTGGTTTGCTATCAACATCAAACAGGAGAACAC[A/G]TGTAAAGCTGCTGGGACAGGGCATGGCACATGGTC R 2 1 2 1 101000 f 74 goat snp12147-scaffold145-640752 1 151602067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388356 Affx-122969342 AX-123258714 1 149282601 CCTCGCTCTCCTTCCAAACTTGTCTTTTCTCGGGG[C/T]GACCCCAGGGTGCTGACAGGGAAATTTGGATGAAG Y 2 1 2 1 101000 r 74 goat snp12146-scaffold145-597147 1 151646075 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421372 Affx-122944044 AX-123291719 1 149365535 TTCCCACAACCATGAAAGGCATCATAGCTCCACAG[C/T]ATCGCAATCCCCGTCCAGATGGTCCAGCCCTGTAG Y 2 1 2 1 101000 f 74 goat snp12144-scaffold145-514213 1 151727335 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774748 Affx-122955242 AX-385261882 1 149414958 GAGAAAATTAGCATATTTCAATTTACAGATAAATG[C/T]GAAATTAGCTTATTGATTAAGGGCTAAATTAGTTT Y 2 1 2 1 201000 f 74 goat snp12143-scaffold145-464790 1 151776312 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379857 Affx-122975799 AX-123250215 1 149450102 ATGACCCCCATCAGTCAGGGAACTTTGACTGGAAG[C/T]GCGATAACCTTTGTGGATCCATACTTCACCGAGTC Y 2 1 2 1 201000 r 74 goat snp12142-scaffold145-429646 1 151811805 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439631 Affx-122930620 AX-123309968 1 149494557 CTCTGAATTGAAAAGGATCGAATAGTGCTATTCGG[C/T]GTGTCCAAGGACAAGTAGCAGCTCCATCCCCTGGC Y 2 1 2 1 101000 f 74 goat snp12141-scaffold145-385191 1 151856454 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794626 Affx-122927704 AX-385281587 1 149525918 TTCTTTAGGGAGTTTGGCTCATGTTGAGTTTGGGG[C/T]GATTAAAAACAGTAAGGAGTGAACACGGAGTCTCC Y 2 1 2 1 101000 f 74 goat snp12140-scaffold145-353830 1 151889129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400884 Affx-122959754 AX-123271237 1 149584567 GTATTGGATGGGGCTGATATAGAATGTTTCCCTCA[C/T]GGCACCAAGTTCTGCTGGGTAGTGCTACCCTAAGA Y 2 1 2 1 201000 f 74 goat snp12139-scaffold145-295181 1 151949029 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802616 Affx-122944609 AX-385289517 1 149620463 ATTCTGGATTTTTTTCTCCTAGAAATCATAAAGAA[G/T]AATACCATTATCTTGACCACAAAGGAAAAAAGTTT K 2 1 2 1 101000 f 74 goat snp12138-scaffold145-259285 1 151985193 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427966 Affx-122939192 AX-123298309 1 149652912 GGGAAGTCAAGACAGTCTGCACGCTGACCTCTATG[A/C]GAGGCACATACAGGGTGTTCCAGGCCATCAGCTGG M 2 1 2 1 101000 f 74 goat snp12137-scaffold145-226836 1 152017708 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408753 Affx-122953398 AX-123279104 1 149703271 AAATTGAGAAAGGGCTTATGTGGACACAGCAGTAC[A/G]TTGCCATCTCACCAAACAAACAAGTTCGTTAAGAA R 2 1 2 1 201000 r 74 goat snp12136-scaffold145-176477 1 152068247 A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793245 Affx-122939786 AX-385280223 1 149736946 GTTCTGCAACATAAACCCAGTCAGGACTGTCACTG[C/T]GGTTTTCAGGATCTTAAATAAGTCCCTAGGGTACG Y 2 1 2 1 101000 f 74 goat snp12135-scaffold145-142802 1 152102117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377159 Affx-122978217 AX-123247518 1 149805738 CAGTGGTTGCCAGATAGGAATGGGGGCCCAGTGTT[A/G]CCTGATCATCGGATTTAAAAAAAATAAAAATTTTG R 2 1 2 1 101000 f 74 goat snp12134-scaffold145-74010 1 152170948 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272595 Affx-1111832844 AX-519546308 1 149807157 ACACATTGTGGGGACAGCCGGAAGAAAAGTGATGC[A/G]TCCTTTCCCTCTTTCGTGGACTTTCCAGGTGGCTC R 2 1 2 1 201000 r 74 goat 1_149807157_AF-PAKI 1 149807157 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320768079 Affx-122919685 AX-385255283 1 149924303 AGAGGTCCAGTGTAAAACTTAGTTTCCTGAGCCAA[C/T]GGGGAAGAGCGCCAAGTATACCCGAAATCCAGAAG Y 2 1 2 1 101000 f 74 goat snp37579-scaffold46-3395473 1 152300137 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802075 Affx-122951891 AX-385288979 1 149960852 GTCTAGGTTTTCATTCTGTGTATCAGAGAGCAATA[C/T]ACTCCTGTAAAATTAAATATGACAGCTTCTCTGTT Y 2 1 2 1 101000 r 74 goat snp37578-scaffold46-3358924 1 152336132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773790 Affx-122948830 AX-385260930 1 150017950 TGGCTGCCCTAGCAAATGAATATATTGGGCTAATG[C/T]ACTTTCCAGACACTTTGTGGAGAATCACAGACTGT Y 2 1 2 1 101000 f 74 goat snp37577-scaffold46-3301826 1 152393440 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776290 Affx-122973693 AX-385263418 1 150047598 AAACGTAGATTTAAGAGTGACTGTGATGAAGTTCC[A/G]TATCAATGTATGAAGAAAGTTGGAAACCAGTTAAA R 2 1 2 1 101000 f 74 goat snp37576-scaffold46-3272178 1 152423873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781867 Affx-122972998 AX-385268949 1 150083903 TTCAAAAGCCATGTGTTAACAGAAACCATTTGACA[C/T]AGGTTACAGCATCATAGTTTCTGAAATCTTTGGCA Y 2 1 2 1 101000 r 74 goat snp37575-scaffold46-3235873 1 152460114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276827 Affx-1111835606 AX-519550336 1 150129185 GAGTCCGTCATAATGGAACTGGGCAGGTTGGTAAC[A/G]GAGATGTGATCCTTGAAAGCTATTTAAAATTTTGA R 2 1 2 1 101000 f 74 goat Random2.2K-145 1 150129185 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398599 Affx-122961489 AX-123268954 1 150136519 AACATACATTCCCAAATAGCCTTCCAGAAAGACCA[C/T]AGCAAAATTCAGTCCCTCCAGCAGAAAAAGCATTC Y 2 1 2 1 101000 r 74 goat snp37574-scaffold46-3183257 1 152512656 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276975 Affx-1111835613 AX-519550483 1 150146496 AGCTCCTTTCAACCCTGCTTGGGACTCCGTTTGAG[A/C]TGAGTTCCGATAAATTCACCGTTCGTCCTCCTCCT M 2 1 2 1 101000 r 74 goat Random2.2K-146 1 150146496 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383192 Affx-122972793 AX-123253550 1 150190500 CCTTGAAATCCATAATTAGAGATTAAATCATTTAT[A/G]TACGTTCTGATACTGTGACGTTCTCCCAAACATTC R 2 1 2 1 101000 r 74 goat snp37573-scaffold46-3129276 1 152567105 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392587 Affx-122966062 AX-123262944 1 150223746 AGTGTTTTTCAAGAAAAAGTGGTCAGCCTTTGAGC[C/T]GCTTAGTGACCCATGGCCTCTGATTGCATGACTCC Y 2 1 2 1 101000 f 74 goat snp37572-scaffold46-3096030 1 152600356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414704 Affx-122949276 AX-123285053 1 150265965 AGTACAGACATTCATGCCTAGGTACTATCCTTGGT[A/G]CTTAAATGCAGTTGATCCTTGAACAGCATGGGAAT R 2 1 2 1 101000 f 74 goat snp37571-scaffold46-3053811 1 152642766 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393284 Affx-122965445 AX-123263640 1 150312623 GATTTACTGTTCCCTTCTCCAGTGGACAACGTTTT[A/G]CCAGAGCGAAAGTACCTGAAGAAATACTGTGCCGA R 2 1 2 1 101000 r 74 goat snp37570-scaffold46-3007153 1 152689514 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413674 Affx-122950107 AX-123284023 1 150344609 CCTTTGTGGCTATAGGTGCAGTCTCAGGTGGGAGG[C/T]GCCCTTGAAATTGTGTGATGTTGGTGACCGAGGCA Y 2 1 2 1 101000 r 74 goat snp37569-scaffold46-2975167 1 152721678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407798 Affx-122954563 AX-123278149 1 150373752 TCTAGCCTAATATAAAATTCAGTGAATGCACTCTC[C/T]GTGGGCTAGAATAAGACGCACCTGAAAATGTTGTG Y 2 1 2 1 101000 r 74 goat snp37568-scaffold46-2946024 1 152751405 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384237 Affx-122972368 AX-123254595 1 150433892 TGAAGCTCACAGTGAGAACCATTGTGGGGACTGAT[G/T]ATGTTTGCACATATGCAGATCTTCCTTGCTGTTTT K 2 1 2 1 101000 r 74 goat snp37567-scaffold46-2885884 1 152811692 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449925 Affx-122922918 AX-123320260 1 150472573 ATAATACTTAGTTTAGGCTTTAAGATCTTCTAAAC[A/G]TTATCTTTTACAAAGGATTCCCCATTATTTTCTGC R 2 1 2 1 101000 r 74 goat snp37566-scaffold46-2847203 1 152850179 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416667 Affx-122947590 AX-123287015 1 150508565 TAAGTTACCTGGGGCTTAGCTGTGATTTCATTCCC[A/G]TCTCTGTGCCTGGGCAACTTGCTGGCATCTGCTCC R 2 1 2 1 101000 f 74 goat snp37565-scaffold46-2811211 1 152884271 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436732 Affx-122932303 AX-123307070 1 150552092 CATTGCCCCCTCCCTGCACGTGTTAATCCCCATCC[A/G]TGCTTTAAGACCCAGCTTCCGTGTTACGTGGGCTG R 2 1 2 1 201000 r 74 goat snp37564-scaffold46-2767684 1 152927226 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790895 Affx-122942157 AX-385277892 1 150592421 GTTAACTGAGTGCTTGTTTGGACCTCCTGAGCCAA[C/T]GTTCTCAGATCTCCCAGCTGTTTCCACCTAAGTCG Y 2 1 2 1 101000 f 74 goat snp37563-scaffold46-2727355 1 152968447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770240 Affx-122942170 AX-385257406 1 150622162 CAAAACTGGTTATTTTTCCTCAAGGCAATAAAGCT[A/G]TAACCTTGTGTGTTATCTTCTCCATAAACAGAACA R 2 1 2 1 101000 f 74 goat snp37562-scaffold46-2697614 1 152997668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450713 Affx-122921883 AX-123321047 1 150665603 CCATCTTGATCAAAGCTCTCTACATGCTAATTATT[A/G]TTCTGATTAATATTGTAATTATTATTGAAGAAGGG R 2 1 2 1 101000 f 74 goat snp37561-scaffold46-2654173 1 153040045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432964 Affx-122935278 AX-123303305 1 150724692 GCATAGAGCAAGAAGAAAAGGTGCCCGAGTCCAAA[C/T]GTCCCAGGAGACATTGAAGGCACGCGTGATCAATG Y 2 1 2 1 101000 f 74 goat snp37560-scaffold46-2595084 1 153099091 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277003 Affx-1111835627 AX-519550511 1 150824408 CTTCCCGTGGCAGAGGTACCCTCTCAAAGAAAAGC[A/G]TTTTAGGTAATTCATGTATAAATTAAAAGTGTAAC R 2 1 2 1 201000 r 74 goat Random2.2K-149 1 150824408 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791857 Affx-122927155 AX-385278847 1 150843914 GACATCAGCTGTGTCATGCTGGGCATTCCAATACT[C/T]GGAGTGCGTTGGCACATTTAAAGGACTTGGAGGCT Y 2 1 2 1 101000 r 74 goat snp37557-scaffold46-2475862 1 153217991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381799 Affx-122974285 AX-123252157 1 150876734 TTTTTTCTGCCCTGAGATTCCTCTTCTTCTGAAAG[C/T]GGCTTTGTTCCCACAGTCCAGCTGTGTGATTTCCA Y 2 1 2 1 201000 r 74 goat snp37556-scaffold46-2443042 1 153251756 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779990 Affx-122973328 AX-385267089 1 150914623 AAGAGGTCAGAGTCAATCTCAAAGACGTTGGCTTA[C/T]GTGCTACTCATAAACATTGCTTAGAGCCAACATTT Y 2 1 2 1 101000 r 74 goat snp37555-scaffold46-2405153 1 153290013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375979 Affx-122978430 AX-123246338 1 150963379 ATGGTGGAATTTTCCACGGGTTATGTGATGTGTGA[C/T]GACATCATCACTAATTAATGTGTGCTCAGATACTC Y 2 1 2 1 101000 f 74 goat snp37554-scaffold46-2356397 1 153339072 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387552 Affx-122970291 AX-123257910 1 151012727 GGTCATTTGCAGTGTCTAACGTCCTGTCCTTGCAG[C/T]TGGGCCTCAGAACCCCCGGTGGTTACCTGAGTCTC Y 2 1 2 1 101000 f 74 goat snp37553-scaffold46-2307049 1 153388796 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429805 Affx-122938194 AX-123300146 1 151098952 TACCTGCTAAATGAGGAACGCTCAGCTGCACTTTT[C/T]TCCTGAATGTGGCGTGGTTGCAGCTCGTTATTTTG Y 2 1 2 1 101000 f 74 goat snp37551-scaffold46-2220824 1 153474222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435771 Affx-122932873 AX-123306110 1 151225269 TGCCCAAAAGAAAGACCTTATTTCTCAGACTCCCA[C/T]GTGACTGAATTCTGACCAGTGAGGTATACGCAGAA Y 2 1 2 1 101000 f 74 goat snp37548-scaffold46-2094507 1 153598765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397493 Affx-122962071 AX-123267848 1 151256141 GGGGCAGATTCTTTACCAGCTGAGCCACAAGGGAA[G/T]CCTGTAGTAAGGGCAGTACTCGCTGAATAAACATG K 2 1 2 1 101000 r 74 goat snp37547-scaffold46-2063635 1 153629960 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395684 Affx-122963743 AX-123266039 1 151305295 TGGTCAATGCCTGACGACCCTAGGGGGTGTTCTCT[C/T]GCCCACAAGCCTGACCACATTCTCCTGCTCTGGGC Y 2 1 2 1 101000 f 74 goat snp37546-scaffold46-2014481 1 153679766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378849 Affx-122976528 AX-123249208 1 151342083 TGGCATCTCAAGTTGCCCTGGGTGCCCCAGCGCAG[C/T]GACCAGGAGCCAGGAAGGGAAGAGCTGCCTTCATC Y 2 1 2 1 201000 f 74 goat snp37545-scaffold46-1977693 1 153716818 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785112 Affx-122950911 AX-385272159 1 151371167 CCCTCCGTGCTGACCAGGGGCTCTCTGCGGTCTTC[A/G]CTCAGGCCCTCTAAAGGTTAGAGGCCTAAAGGTTA R 2 1 2 1 202000 f 74 goat snp37544-scaffold46-1948609 1 153745989 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452938 Affx-122920184 AX-123323271 1 151403609 TTACCACGACTGTCCAGTAGGTATTATTATTCTCA[C/T]TTTGCAGAGAAGAAAGCTGAACTTAAAAGACACTG Y 2 1 2 1 103000 r 74 goat snp37543-scaffold46-1916167 1 153778150 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401140 Affx-122959380 AX-123271493 1 151440752 TGTAAAAGGATAATTTGGAGTGAAGAAAACAGAAC[A/G]TCTAAAGAGAATTTAAGACAAGATGGCACCACACA R 2 1 2 1 101000 r 74 goat snp37542-scaffold46-1879024 1 153814773 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792364 Affx-122967377 AX-385279345 1 151500405 CCAGTTACGAGTACCTCCTAAATTTCTGGAACTAA[C/T]GTGTTAGGAAAATCTATAGATTTAACGTAGCCCAG Y 2 1 2 1 101000 r 74 goat snp37540-scaffold46-1819371 1 153874172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448322 Affx-122924146 AX-123318658 1 151559875 GGCTGACAGAATTTTTAAAATTCTCCAGATGGTCT[C/T]GGGTAATTAAGGTGGTAATAACAAGAGTTCTCTAT Y 2 1 2 1 101000 r 74 goat snp37539-scaffold46-1759901 1 153934390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401360 Affx-122959244 AX-123271713 1 151614435 GAATTTTTTGTTCTCAGTGCTCTGCTCAGTGACAG[C/T]ATACTGCTGATGAGAACTTTTAGGGTAAGTCCATT Y 2 1 2 1 101000 f 74 goat snp37538-scaffold46-1705341 1 153967041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402783 Affx-122958301 AX-123273136 1 151669166 CTGTAACTTTTGTACCGCGTCTCGTTTTCAAAGCC[A/G]CGTGCAGAAGCGCTGCTCTCGCTCCTGGAAGCTCT R 2 1 2 1 101000 f 74 goat snp37537-scaffold46-1650610 1 154022794 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423904 Affx-122942282 AX-123294250 1 151701785 TTGCTTCCAAGGTCAGGGACACGGATCCCTTGAGC[A/G]TAGAACACCACTGTATATGGTTTCAGTTCCGCCTC R 2 1 2 1 101000 r 74 goat snp37536-scaffold46-1617991 1 154055390 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435541 Affx-122933395 AX-123305881 1 151748940 TGCATATTATATAGAGGAAAATATATTTTGCTTTA[A/G]TTTAATATCCTTACATGTACAACCCACTAAGAGTC R 2 1 2 1 101000 r 74 goat snp37535-scaffold46-1570836 1 154103353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427755 Affx-122939247 AX-123298098 1 151789185 GGAGTAAAGTGCAGTCTGCAGGCAGCATCCTAATC[C/T]GCTTTGCACTAGAGCTGCAGTCTCTTTTCCTAGGT Y 2 1 2 1 101000 f 74 goat snp37534-scaffold46-1530591 1 154143950 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793892 Affx-122971607 AX-385280861 1 151837502 TCCTGTACTTTAAATGTTGATCAATTAAGTTGAAT[A/C]GGAATTATTACCTTTGTTTCTATCAAGTAAAAATG M 2 1 2 1 101000 f 74 goat snp37533-scaffold46-1482274 1 154192252 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276878 Affx-1111835634 AX-519550387 1 151856897 ATGAAACCCACGAGGAATTAATGGTCCAGCTCAAC[A/C]CCCGCCTCCCCCCCCCCCCACCCCCCGGCCGGTGG M 2 1 2 1 101000 f 74 goat Random2.2K-150 1 151856897 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38440922 Affx-122929024 AX-123311259 1 151904749 GCAGGGTTGTTGATGTGAACATTAGGCCTTTTGAT[C/T]TCTGCAGCTGTGTTCTAGGTGCTTAGAATACACCA Y 2 1 2 1 101000 f 74 goat snp37531-scaffold46-1415027 1 154260025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379178 Affx-122976314 AX-123249537 1 151991828 TATATCCATCAAATCAATTTTTAGGAAAGTTTTTC[C/T]CTGTCAGTAATACTTACTGATTGTCCTTCACTTGC Y 2 1 2 1 101000 r 74 goat snp37530-scaffold46-1327948 1 154347914 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392405 Affx-122966211 AX-123262762 1 152035178 TTAGTTCACAGCAGTATCTCTGATCCTTCCACAGC[A/G]TTCTTTCTTGTCTCCACTTCTCCGTATTTACACGT R 2 1 2 1 201000 r 74 goat snp37529-scaffold46-1284598 NW_017214946.1 17626 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769473 Affx-122939640 AX-385256644 1 152064114 GTAGACTAGGGCAGCAGATTTAAACAGAAAACTCT[C/T]GTTCCTTGCAGTTCAGGTTTTTTCTCTCCTCTCCT Y 2 1 2 1 101000 f 74 goat snp37528-scaffold46-1255662 1 154420128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377108 Affx-122978255 AX-123247467 1 152094847 CTAGTTTTTGAGAGGAGGCAGCAGGGGAGCCTGCC[A/G]TGGGGATAGCAGGCGTTTATTGAGCACGTACTTCG R 2 1 2 1 303000 f 74 goat snp37527-scaffold46-1224929 1 154450823 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791521 Affx-122938838 AX-385278512 1 152174942 ATGAACTAAGTGATATAAGTCATGTTGCTCATCGA[C/T]GCTTTTCTTGGCATATTCTAAGCCTGCACCTAGAA Y 2 1 2 1 101000 f 74 goat snp37525-scaffold46-1144834 1 154531335 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391293 Affx-122967342 AX-123261650 1 152216029 CCTTGCTTTTCTTCTTTTCCGTGTGATAACGTTTA[C/T]GTGTATGAATTTCCTCTGCGTGCGGTTTTGGTGGG Y 2 1 2 1 101000 r 74 goat snp37524-scaffold46-1103747 1 154572098 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439802 Affx-122930490 AX-123310139 1 152247982 CTGCGCACAGCTTCTGAACCTGAAAAGAGAGCGCA[C/T]GAAAGTTAGGGAATCAGAGTGTGTTATAAAAGTAA Y 2 1 2 1 101000 r 74 goat snp37523-scaffold46-1071794 1 154605226 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432498 Affx-122935582 AX-123302839 1 152286686 ACTGTGTTCTCATCCCTTTCTTCAGCAAGCATTCT[A/G]TCCAGTGAATTCTTTATTTCTTCTCACTTAAAACT R 2 1 2 1 101000 f 74 goat snp37522-scaffold46-1033090 1 154645750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798710 Affx-122957134 AX-385285641 1 152329746 TCAACTGCCATCCTAATCTAGGCAACATTCACAAA[C/T]GTCAGATTTTTTAACGTAAAAATTACTGTAAGATA Y 2 1 2 1 101000 f 74 goat snp37521-scaffold46-990030 1 154688706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272545 Affx-1111832845 AX-519546262 1 152361551 CTGCACGTGGGGGTGTGGAGCGGGGTCGGCACTTC[A/C]TGCTGGTAGCCAGACGTCCAGAAGTCTCCAGGGTC M 2 1 2 1 202000 f 74 goat 1_152361551_AF-PAKI 1 152361551 T G 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38390573 Affx-122967202 AX-123260930 1 152376840 TTGTCACGCCTGAAACAAGGGACCTGGACTAGACC[G/T]CTGGTCGGGGAACTGGATCCCATATGCCGCAAGTG K 2 1 2 1 101000 f 74 goat snp37520-scaffold46-942936 1 154735424 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277039 Affx-1111835647 AX-519550546 1 152417645 CGAGTAACTGACCAGCACTCCCACGAGTCTAAGTC[A/G]ATTGCCAAGAAGTCCGTTTTTCTCACCGGGACCAC R 2 1 2 1 101000 r 74 goat Random2.2K-152 1 152417645 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395303 Affx-122964064 AX-123265658 1 152440649 AGGCTCCCGTCTGTTGGCATATTTGTGGCATGGAT[A/G]TTGCTGGAATTCTCAGAGTGCTGGGGTGCAGGCAA R 2 1 2 1 101000 f 74 goat snp37519-scaffold46-879127 1 154799871 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769944 Affx-122927077 AX-385257113 1 152471353 AATCTGTTATTTGGGAAAAGCCAAGTTCAACGAAC[A/G]TAGCAGTAGTCTTGACTTAACAGTGTCTGGAGAAT R 2 1 2 1 101000 f 74 goat snp37518-scaffold46-848423 1 154830369 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803919 Affx-986696580 AX-385290627 1 152480696 AGATTGGGAGCGGTCTGTGACCTTGTGTGTGAGCT[A/G]ACTGGTGAGCCAGAAAGGGGTGGGCATGGAGGAAG R 2 1 2 1 600010 f 74 goat 1_152480696 1 152480696 Ancestral_priority_1043 ancestry 0.51 neutral IMAGE 10K 10K ancestral 38398038 Affx-122961764 AX-123268393 1 152503967 CTCTTTTGTTTGCTTGCTTGCTGGCTTCCTATCTG[C/T]ACCCTGACCCCACCCCAGTAAAGTTCTTACTTTAC Y 2 1 2 1 303000 r 74 goat snp37517-scaffold46-815809 1 154863243 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772367 Affx-122977300 AX-385259520 1 152534794 AGATTCAAGAAGTAGGGGGGAAAAGCTGGGAAAGA[C/T]GAAAAAGATAGGGAGCCATTATATTAAGCAAAATG Y 2 1 2 1 101000 f 74 goat snp37516-scaffold46-784982 1 154893878 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773757 Affx-122958504 AX-385260897 1 152566524 CAACTCTTTCTTGATTCTTATTGATAACTGTGTAC[A/G]TGAAAATTCTAGCTTTTGATGTGGTCTACATTGTA R 2 1 2 1 101000 r 74 goat snp37515-scaffold46-753252 1 154925648 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407279 Affx-122955336 AX-123277630 1 152626228 CAGCAACAATGAGTCAGCGATTTGGACTCTGAAAG[C/T]TCTTTATCTGCAGAATGGGGAGAGTAAAACTTGCT Y 2 1 2 1 101000 f 74 goat snp37514-scaffold46-693548 1 154985531 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398728 Affx-122961832 AX-123269083 1 152669904 ATGTCTTCCGAGAAAGCATTTACAGCTTCTGTTTA[C/T]GTGGCATCAGAGCCACCTGAAGACTTGTCCTCTGT Y 2 1 2 1 101000 f 74 goat snp37513-scaffold46-649872 1 155035179 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380770 Affx-122975114 AX-123251128 1 152701473 GATAACAGGTGGCCTGGGCTGGCCCTCACCACATG[C/T]ACTATGGAGCAGAGCCTTGTTCGGAAGCTGGTAGA Y 2 1 2 1 101000 r 74 goat snp37512-scaffold46-618303 1 155067257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382077 Affx-122974912 AX-123252435 1 152733464 TTGTTCTTCTCCGACTTATGTCACTCAGTATGACC[A/G]TCTCTTGGCTCATCCGTGTTGCTGCCACGGGCACT R 2 1 2 1 101000 f 74 goat snp37511-scaffold46-586312 1 155099731 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417208 Affx-122947305 AX-123287556 1 152764079 CCCTTTCCTGCCAAGACTCATTCATCCTTATCCAC[A/G]GACTGGATCCTACCCCTTACAGCTTCAGCTATGGT R 2 1 2 1 101000 f 74 goat snp37510-scaffold46-555697 1 155130941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402402 Affx-122959014 AX-123272755 1 152811098 TTAAAGTCTTAGCAGGAAACCTCGGGGTGCTGCTC[A/G]TAGGAAGCCCACTAACAGAGGCAACTAAAAACCAA R 2 1 2 1 201000 r 74 goat snp37509-scaffold46-508678 1 155178697 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779218 Affx-122952310 AX-385266322 1 152867863 TAATGAAAGCATTGCCTGTTGACAACATACACTGT[C/T]CTATCTCTACTGAGAAATGACTTCGTTCTTAACTC Y 2 1 2 1 101000 f 74 goat snp37508-scaffold46-451913 1 155231686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419686 Affx-122945931 AX-123290034 1 152911628 CATGTGTTTCATGGACCATGATAAATTGCCATTGC[A/G]TTGTCATTGAATCTGTTTTGCCTTTTTTCAGTAGT R 2 1 2 1 101000 f 74 goat snp37507-scaffold46-408148 1 155275220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449289 Affx-122923017 AX-123319624 1 152950925 ACCTTTATTCTTGTGCTGTGTGCAGTGTTAACATC[A/G]TCTCCTGCTCTCCATATGATCTGTTCCTGGGGGTG R 2 1 2 1 101000 f 74 goat snp37506-scaffold46-368851 1 155314464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449523 Affx-122922607 AX-123319858 1 153004715 ATTTGTGGCCAATTACAATATTTCATTAACTTCTT[A/G]ATTGGGTAAGTATTTAATGTATTCCTACTATGTGC R 2 1 2 1 101000 r 74 goat snp37505-scaffold46-315061 1 155367936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780746 Affx-122938074 AX-385267836 1 153101257 CCACAGTATATGAAAATGCCTGAGTTTCATTGTAC[A/G]TTTGTACTTTTGCTCCAAGCAATGACTAAAAAAGC R 2 1 2 1 101000 f 74 goat snp37503-scaffold46-218519 1 155464693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276919 Affx-1111835654 AX-519550427 1 153231240 CGCTGCTTGGGTTTTCTTGATAGGCAACACGCAGC[A/C]TAGCAGAATGCTGGCCTTTGATGCCCTGCCTGCAG M 2 1 2 1 201000 f 74 goat Random2.2K-153 1 153231240 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791352 Affx-122961857 AX-385278345 1 153236133 AACGAGGCCTTTGTGCTTTCCAGGTTAAGGAGAAA[C/T]AGAAAGTAGATTTAGGACGCAAGGAGGCTCCATGG Y 2 1 2 1 201000 r 74 goat snp37500-scaffold46-83643 1 155601607 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453516 Affx-122919808 AX-123323849 1 153328131 ATCCTCAATCAACGAAGGCTTTGAACTTTAAAGAC[A/G]CAAACTGGGTCATATGGAAATGACAAGATCCTCCC R 2 1 2 1 101000 f 74 goat snp59780-scaffold993-8256 1 155693663 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783754 Affx-122960173 AX-385270810 1 153376351 TTAAAAAGCAACAACACACGTACTTTTTAACAAAG[C/T]ACAAGTAGGCATTCAGCTCTCCAGATTCATCATCT Y 2 1 2 1 101000 r 74 goat snp59781-scaffold993-56476 1 155741583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401839 Affx-122959437 AX-123272192 1 153410264 GCAGATAATCATTCACAGTTCTGTGGGGCTTGGTC[A/G]TTCTTGAAATGATCAATGAGAGCAAGCTAAATACT R 2 1 2 1 201000 r 74 goat snp59782-scaffold993-90389 1 155775871 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447267 Affx-122924942 AX-123317603 1 153449969 CCTCCTGCACAAACTGGACCCCACGAGGACAAACT[A/G]GAGCCGTGTCTGTGTCTCCCTGCCCCCAGTCTTGA R 2 1 2 1 101000 f 74 goat snp59783-scaffold993-130094 1 155816589 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378240 Affx-122976904 AX-123248599 1 153500331 GGAAGAGTTGGTGGTCGTGAAGGTTGCTCAGTCAC[A/G]TCCGACTCTTCGTGACCCCATGGCCTACACAGTCC R 2 1 2 1 103000 f 74 goat snp59784-scaffold993-180456 1 155864994 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451281 Affx-122921308 AX-123321614 1 153539790 TACTTGAATTATTCAGGTATTCAGAAAGGGAACGC[C/T]GATGTCATTAGCATAGAGAAAGTCATGATATAAAT Y 2 1 2 1 101000 f 74 goat snp59785-scaffold993-219915 1 155904219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796398 Affx-122939635 AX-385283348 1 153572961 AAATAAAACATATTTCATAAAGGCTATGAAAACAC[A/G]ATAATGAGATAAATTATTCTAGTCATCTTGCTTTA R 2 1 2 1 201000 r 74 goat snp59786-scaffold993-253086 1 155936546 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448269 Affx-122924187 AX-123318605 1 153602983 GCTGCAGGCCGTGGGGCTGCAGAGTCGGACATGAC[C/T]GAGCGACTGAACGCCAGCAATTCAGAATACTTGCA Y 2 1 2 1 103000 r 74 goat snp59787-scaffold993-283108 1 155966732 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407052 Affx-122954928 AX-123277403 1 153648499 TCAGGCGTTTTATCCTCAAAGTTCATCTGAAAGAG[A/G]GGGTGGTGGTGGAATCTCACACTTAGCCAGTCACT R 2 1 2 1 101000 f 74 goat snp59788-scaffold993-328624 1 156012971 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414143 Affx-122949699 AX-123284492 1 153680889 AATCAACTTAGCTCTGACTCACCCTGCTGTGCTGC[C/T]GGGAAATTTAATCACAGTTACGACGTGATTGTAAC Y 2 1 2 1 101000 r 74 goat snp59789-scaffold993-361014 1 156045121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792854 Affx-122941862 AX-385279832 1 153722582 TAGGTTAAAGGAAATTAAATCAGTTGAAAGGGAAG[A/C]AGTGTCTGTTAACGTAACTGGAAGTATTGGCACAT M 2 1 2 1 101000 f 74 goat snp59790-scaffold993-402707 1 156087056 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429664 Affx-122937660 AX-123300005 1 153794202 AAACTTGAAATTTTATAAATTTCATTTTCATGATT[A/C]ACCTTAACCTTGACCATCTAGTTTTTAATAGAATT M 2 1 2 1 101000 r 74 goat snp59792-scaffold993-474327 1 156159567 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377466 Affx-122977513 AX-123247825 1 153824356 GCTGTTCCGTGGAAATGTTGGCAGAAACACACAGC[A/G]CTGCATAGATGTCTCCCGCGAGCGGCTGTCTGTAC R 2 1 2 1 101000 f 74 goat snp59793-scaffold993-504481 1 156190026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787863 Affx-122924287 AX-385274886 1 153859829 TCGTTAATTCAGTTTTGCCACACTTGTAGTTACTG[A/C]ATTGGAACAGGTCATTATACATTAGAAGGTGGTGC M 2 1 2 1 101000 f 74 goat snp59794-scaffold993-539954 1 156225837 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384677 Affx-122972130 AX-123255035 1 153901676 TTACGTATAGAATGGGCAGGCAACAGAGTCATAGC[A/G]TAGCACAGGGAATCTAATCTCCTGTGATAAATGAT R 2 1 2 1 101000 f 74 goat snp59795-scaffold993-581801 1 156268114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383449 Affx-122973461 AX-123253807 1 153933663 CTGCAAGAAGGCGATGGTCAGGCTGAGAACTCAGG[C/T]GTCCTGACCTGCTGTGATTTTCCCCTTAGCATCAA Y 2 1 2 1 201000 f 74 goat snp59796-scaffold993-613788 1 156299930 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788459 Affx-122957966 AX-385275476 1 154032197 TTTTTTCTATTTTAGGCAAATTTGACTTTTAAAAA[C/T]GTTTGACAACTGAAAAACGAATTGAAGCACCAGAT Y 2 1 2 1 201000 f 74 goat snp59797-scaffold993-712322 1 156398759 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441450 Affx-122928768 AX-123311787 1 154075604 CTGTAGGGAACAGAAATGCCACTCTTAAGGGCTCA[A/G]CTGCAGACCTAGACAGCCTGGGACTGAGTGCTCAA R 2 1 2 1 101000 f 74 goat snp59798-scaffold993-755729 1 156442380 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392193 Affx-122966290 AX-123262550 1 154108246 GGCTAAATGAAGATAGTAATTATTTGTATTTGGTA[C/T]GTATGCCCTCATGAACACCATTATATTTTAATTCA Y 2 1 2 1 101000 r 74 goat snp59799-scaffold993-788371 1 156475240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792438 Affx-122931699 AX-385279419 1 154137128 CGAGCGCATGCTTGGTGAATACTGTAAGCAAGTCA[A/G]TTCTGCTGGGCATTCTTTACCGATATTGTGGGCAT R 2 1 2 1 101000 r 74 goat snp59800-scaffold993-817253 1 156503947 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411381 Affx-122952233 AX-123281731 1 154181285 CTGGCCATTCTCGGTAGGTCTTGTTGAAAAGCCCC[A/G]TGAAATTCTACTCTGAAGCATGAATTAAGGAGATT R 2 1 2 1 102000 r 74 goat snp59801-scaffold993-861410 1 156549080 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276928 Affx-1111835659 AX-519550436 1 154197112 ATTTGGAATTGACACTACTTTACTCCTTCAAGGAT[A/G]AATGCTTTAAATTGATTTCAATTTTTTCTTAATTG R 2 1 2 1 101000 f 74 goat Random2.2K-154 1 154197112 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408770 Affx-122953385 AX-123279121 1 154211708 TATTGGAATTTGATTCATTCCTCTGTATATAGACG[C/T]GTTTCCATATCCACAAAATAATAGAATGTTAGAAC Y 2 1 2 1 101000 r 74 goat snp59802-scaffold993-891833 1 156579680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431707 Affx-122936767 AX-123302048 1 154244153 AAAAGGTTTGTAGGTCAGGCTCAGAGGGCTTCCTC[A/G]TCTCCGAAATCTGGGTGACCCAGAAAGACTCCACG R 2 1 2 1 201000 r 74 goat snp59803-scaffold993-924278 1 156612798 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790236 Affx-122960182 AX-385277240 1 154288393 GGAAGATGCAAGACCTGTATTCACTGATGTGAGCG[C/T]GCTACGTAAGCATATACTTTTCTCGCCCTCAAGTT Y 2 1 2 1 101000 f 74 goat snp59804-scaffold993-968518 1 156657013 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799278 Affx-122925336 AX-385286208 1 154346557 CTATTAACCATGGAAGGATACGTTATAGGGAAGGC[A/G]CCTTAATGAGCTCAGAGACCTCCGTTTATCCTCAA R 2 1 2 1 101000 r 74 goat snp59805-scaffold993-1026682 1 156714363 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410483 Affx-122952202 AX-123280833 1 154377317 GAAAGCCAATTCCTGCCTTACCGCCACTGGATTTC[A/G]CAGACACTGGGAAAGTCACGTAACTCTAGAAAGCA R 2 1 2 1 101000 r 74 goat snp59806-scaffold993-1057442 1 156745800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434977 Affx-122933836 AX-123305317 1 154407601 AGTGTTGCCCTGAGCTCTTTCATGTCATCGCCACA[A/G]AACTGTAAGCACACAGTTATCTCACCCTCGTCATC R 2 1 2 1 201000 r 74 goat snp59807-scaffold993-1087726 1 156776150 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404740 Affx-122957236 AX-123275092 1 154444699 CTGAACTCAAATCTTCCAGGGTCTTCCGTGTTCTC[A/G]TGTGGACTGCCCCTTTCCAGCCCCTAAAGCAGCAT R 2 1 2 1 101000 f 74 goat snp59808-scaffold993-1124824 1 156814393 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450654 Affx-122921973 AX-123320988 1 154477212 AGTTTCTTCCAAGAAATACTCCTGAAGAAAAAGCT[A/G]TAACAGATTTGTGTGTAGGAAAATGACAAGCTAGG R 2 1 2 1 101000 r 74 goat snp59809-scaffold993-1157337 1 156847333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395161 Affx-122964115 AX-123265516 1 154521982 CAGCATTTTCTCAAAAGCCTAAGGAGTGAGGTGTT[A/C]GTCACTCAGTCGTGTCTGACTCTTTGCAACCCTGT M 2 1 2 1 101000 f 74 goat snp59810-scaffold993-1202107 1 156892864 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444682 Affx-122926445 AX-123315019 1 154559993 GGAAAATCAGGTAATTACCAGTGAAATAAGGACTG[C/T]AAGCTGTAGATTACTCTCAGGAAACATTTTCTGAG Y 2 1 2 1 101000 f 74 goat snp59811-scaffold993-1240118 1 156930332 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768257 Affx-122965483 AX-385255438 1 154607056 TTCTGAAGAATGTTAACCACTTTGGTCGTCCTGAG[A/C]CACATGCCAAGCCCAATTAATTTCCCAATTTTGAG M 2 1 2 1 101000 f 74 goat snp59812-scaffold993-1287181 1 156977663 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793068 Affx-122924125 AX-385280046 1 154639837 TACTTTGCAAGAGGTGTGTAATTAAGCAGGACCGT[A/G]TTTTTTCAGGTGTTCACGAATATATTTTTAACCCC R 2 1 2 1 101000 f 74 goat snp53422-scaffold809-29101 1 157013272 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419393 Affx-122945609 AX-123289741 1 154677530 TAGCACTCTTCGTCTCCTGCCCTCATGAGACAAAA[A/C]TTATAAAGCGTTTTTAGGCTTGTACTGTGTAAAGA M 2 1 2 1 201000 r 74 goat snp53423-scaffold809-66794 1 157050828 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438876 Affx-122930744 AX-123309213 1 154784514 ATTTTTCAAAACATCTGTAACAATTTTTTTTAGAA[C/T]GGCTCTGCTGGGTGAAGGTATCCACGTTTAATTTG Y 2 1 2 1 201000 f 74 goat snp53425-scaffold809-173778 1 157154991 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392521 Affx-122966114 AX-123262878 1 154815506 ACCAAAAAAGAACAGTCCAGCTAAAGAAGTGGTCT[C/T]GGTTTTAGAAGCAGCCACCTCATGTCCCAGTTTTT Y 2 1 2 1 101000 f 74 goat snp53426-scaffold809-204770 1 157185801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380017 Affx-122975597 AX-123250375 1 154898732 ACTCTCCCGCTCTTGGGCTTAGATCCAGAGAAAGT[A/C]GGAATTTGAGATGACAGGCAACTCCTGTTTTGTTT M 2 1 2 1 101000 r 74 goat snp53428-scaffold809-287996 1 157268892 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376026 Affx-122978397 AX-123246385 1 154928905 ATTAAGGACAACAAATTGTATTCTTTAGTTCTTGC[A/G]TCCTCTAAAAGTCTCAAAAGCAAACTTCATGCCTT R 2 1 2 1 101000 r 74 goat snp53429-scaffold809-318169 1 157299737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272599 Affx-1111832846 AX-519546312 1 155042557 TTGAATCTCCGTGTTTCTTCATGGTAACTGTGGAG[A/G]AAATGATCTTGGACAGAATTAAGTGGGCACAGGTG R 2 1 2 1 101000 r 74 goat 1_155042557_AF-PAKI 1 155042557 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 350603090 Affx-1002479389 AX-413837288 1 155256793 ATATGAACACACACTCAGCCAAATGCAATTCATTA[C/T]AGGAACGCAGTTTACAATCATGTTGAGATATTATG Y 2 1 2 1 101000 f 74 goat 1_155256793_RH-map 1 155256793 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603186 Affx-1002479390 AX-413837372 1 155299798 GCAAGTCACACAAAATACATTCAAACTATATAATC[G/T]TGACTGAGGAATCAATATCAATCCCTTTGGTAAAA K 2 1 2 1 101000 r 74 goat 1_155299798_RH-map 1 155299798 G T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603188 Affx-1002479391 AX-413837374 1 155347735 CAATGTGATGGGTTAAATTGGGAATTTCCAAGATG[C/T]ATATTTTAATAGTTGCTTCACACTGGTGATGCCTG Y 2 1 2 1 101000 r 74 goat 1_155347735_RH-map 1 155347735 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603096 Affx-1002479392 AX-413837294 1 155384297 CTTGCTTCCCTGATGGCTCAGATGGGAAAGAATCC[A/G]CCTGCAAGGTGGAAGACCTGGGTTTGATCCCTGGG R 2 1 2 1 103000 f 74 goat 1_155384297_RH-map 1 155384297 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603098 Affx-1002479393 AX-413837296 1 155519634 TAGTGCCATTTAAATCTGGGTTGGTTTTCACTAGC[A/G]TTGCAGGAGAAGAAGGGTTTCAAAGCAGATGTATC R 2 1 2 1 101000 f 74 goat 1_155519634_RH-map 1 155519634 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603100 Affx-1002479394 AX-413837297 1 155559180 AGGTGGATCGAAATCACCACAGTGTACACCTTACA[C/T]GTATATGTTATATGTCAATAAAATCTCAGTACAGC Y 2 1 2 1 101000 f 74 goat 1_155559180_RH-map 1 155559180 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603102 Affx-1002479395 AX-413837298 1 155575234 GCAGCTGGTCTGGAGTCTACACTTTGAGACTAGAG[C/T]TTAGTTTATCACAAAGTTAAGAAAGATCACTCTGA Y 2 1 2 1 101000 f 74 goat 1_155575234_RH-map 1 155575234 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603104 Affx-1002479396 AX-413837300 1 155662486 ACAGCTGGCTAGGAGAAAATTCAGCAATTGCTTTC[C/T]AGGCCAGCTACACCCCCAAATTGTCAAAGCTTCTT Y 2 1 2 1 201000 f 74 goat 1_155662486_RH-map 1 155662486 C T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603199 Affx-1002479397 AX-413837384 1 155722058 GGGGGGCAGAGGGAGAGAAGCAGAGTCTAAGTGTC[A/G]TGACACAAGTGGAAGAAGAGTCATTTATTTAGTAG R 2 1 2 1 101000 r 74 goat 1_155722058_RH-map 1 155722058 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603108 Affx-1002479398 AX-413837304 1 155831223 ACCTTTTCTGCCTCCTGAGAAACCTGTATGTGGAT[C/T]AAGAAGCAACAGTTAGAACCAGACATGAAACAGCA Y 2 1 2 1 303000 f 74 goat 1_155831223_RH-map 1 155831223 C T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603203 Affx-1002479399 AX-413837388 1 155920183 TAAGAGGAAAATAATGACATTCCAGACATATCAAC[A/G]AAATCATGACCTCCTGTCACCTTTCAGAAACTCAA R 2 1 2 1 400000 r 74 goat 1_155920183_RH-map 1 155920183 G A Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468277086 Affx-1111835673 AX-519550593 1 156353835 GGTCACAAAGAGTCAGACAGGCCTGAGCGACTCTC[A/G]CTCACTCACTCTGATTTTCTGCATCTGAGTTCAAA R 2 1 2 1 101000 r 74 goat Random2.2K-156 1 156353835 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276964 Affx-1111835678 AX-519550472 1 157187893 CTCAAAAAAAACCCTCAAACTTAAGACAAAAACTG[A/G]TAACCTTCAGTTCAGCTCAGAAAATTACACACACA R 2 1 2 1 201000 f 74 goat Random2.2K-157 1 157187893 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320803509 Affx-986696087 AX-385290328 1 157379917 GTGGCGGATGTATTCCCTATGAAGAAGCTCTCTTC[A/T]TGTCAAAACCTTTCCAGACAACCAAATGTTTGATT W 4 1 2 1 600010 r 74 goat 1_157379917 1 157379917 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 320765479 Affx-122974531 AX-385252974 1 TGAAGGGATGCATAGTGATTGACCTTAGGGCAGGA[C/T]GAAATTGGACAGAATTAATAGAAACCTTATATAAG Y 2 1 2 1 101000 f 74 goat snp19065-scaffold1917-222828 5 9412898 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405647 Affx-122956581 AX-123275999 1 GGGCAGTGTGTTGGGGACATTGGCTAGGGTGTATG[A/G]CTAGGATGGGGCAGAGGGCTGAAGTAGCTTCTTGG R 2 1 2 1 201000 f 74 goat snp4303-scaffold1134-142270 25 36460678 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602987 Affx-1002479334 AX-413837230 1 CCAAAGCAAAAATAAGAAAAATAAGGGTATAACTC[A/G]A R 2 1 2 1 10000 f 74 goat "INRA-CHI1-PIS1;ins-del_011" 1 "0;129424781" A G ins-del_011 1 preexisting CNV preexisting not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region PIS 38441951 Affx-122928573 AX-123312288 2 1982 CAGAGGGAAAGCCACAGATTCCTTGATCCACGTGA[C/T]GGGAAGGGTGACACTGCTGCTAAAGCACGGGCGGA Y 2 1 2 1 303000 r 74 goat snp38036-scaffold474-1982 NW_017189900.1 3631 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271857 Affx-1111833160 AX-519545640 2 14356 TGGTGAAATCAGCAGTGTCCTCAGTCAGGACTGAG[A/G]TGTTACACCACTTGTTCTGGTGTAAGAACCTGGGG R 2 1 2 1 101000 r 74 goat 2_14356_AF-PAKI 2 14356 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320804419 Affx-986696586 AX-385291004 2 14633 CGAGCCCCAGGCTAGCTGCTCCTGAACCTCATCCA[A/C]CATTCCTAGGTAAAACACCCGGATATGAGCAAAGA M 2 1 2 1 600010 r 74 goat 2_14633 2 14633 Ancestral_priority_1043 ancestry 0.66 recommended IMAGE 10K 10K ancestral 38391700 Affx-122967516 AX-123262057 2 35123 GTACTTATAGATTCTCCACAGGGGAGTCAGTCCTC[A/G]ACTGGAGTGGGGGCATACAGTTCCGTTTTCCTCCC R 2 1 2 1 303000 r 74 goat snp38037-scaffold474-35123 NW_017189588.1 54672 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380593 Affx-122975258 AX-123250951 2 64813 GTTTCAAGAGCCCTTTTGGGGCTCAGGTAGGAAAG[C/T]GGGATTTCTCTTGAGACGAAGCACTGGAAAAGGGC Y 2 1 2 1 101000 f 74 goat snp38038-scaffold474-64813 NW_017189588.1 24983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397634 Affx-122962621 AX-123267989 2 100362 AGCTATACTGCTAACTTGTGGGAGAGGGTGTGCTT[G/T]TATTTTTCCCCAGGGTGCTGCATTACCAATTTGGA K 2 1 2 1 101000 r 74 goat snp38039-scaffold474-100362 NW_017197087.1 1590 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395609 Affx-122963814 AX-123265964 2 167028 ATGGACTTTGAAGAGTAGCATCTCTTCATGTAACC[A/G]AGATAAGAATATAAGTGAAAGGGGAAAGAAACTAG R 2 1 2 1 101000 f 74 goat snp38040-scaffold474-167028 2 136405967 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399627 Affx-122961077 AX-123269982 2 231997 AGGAAAGCTAATAAGAAAACATCTGGTGGTCTCAT[C/T]AGCTCTTCCACAGTTTGTGGCTTTTGTTTTATGTA Y 2 1 2 1 201000 f 74 goat snp38042-scaffold474-231997 2 136340323 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376614 Affx-122979046 AX-123246973 2 348087 GAGAACACTGAACCAAAAAACTCTGACTGGACCTC[A/C]CTCAGGACTGTATAGGAGAGCAGCCTCATCGTGTA M 2 1 2 1 101000 f 74 goat snp38043-scaffold474-348087 2 136224720 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402538 Affx-122958471 AX-123272891 2 382955 TGCAGTGGACCACTTCCTACATTAACTCTGCATAC[A/G]TCATCAAATAAGATGAAAATTAAATAAAATTCTCA R 2 1 2 1 101000 f 74 goat snp38044-scaffold474-382955 2 136190741 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377730 Affx-122977386 AX-123248089 2 427937 AAATCATAAATATAAGCTTATTTAGAGCATGGTTT[A/C]TTGATATCAGCCTAAAGAGATGTTAGGAACAAAAT M 2 1 2 1 101000 r 74 goat snp38045-scaffold474-427937 2 136144554 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799712 Affx-122927198 AX-385286640 2 483824 TTTTCATAGATCAGAAGTATGATGAGCGTGGCTGA[G/T]CTCTAATTAGGGCCTCAAAACAAAATCAATGTGTT K 2 1 2 1 101000 r 74 goat snp38046-scaffold474-483824 2 136086650 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276982 Affx-1111835687 AX-519550490 2 491452 TACTTTCCAAAGGCAGAGAAAACCCTTCTTGGAAG[A/G]GGGAGCCCCGAGTCCCGAGCTTACCGTTTCCATCT R 2 1 2 1 102000 f 74 goat Random2.2K-158 2 491452 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437046 Affx-122933103 AX-123307384 2 554191 GATTGCTTGCATTTAAAGTACCACTTTTATATCTA[C/T]AAGGGCACTCCAATTTTTGTGCAATCAATACATAT Y 2 1 2 1 101000 f 74 goat snp38047-scaffold474-554191 2 136014197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387733 Affx-122969745 AX-123258091 2 590016 TTCCTGTGAAAATAGGTCTCTCTCTCATGTGTATG[C/T]AACCTATCCTGGGTGACAGATTACAAAGCAAATTA Y 2 1 2 1 101000 r 74 goat snp38048-scaffold474-590016 2 135977152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378872 Affx-122976511 AX-123249231 2 631056 GACTCAGGCTGGCAGGCATAATCACGGATAACACA[C/T]GGACAAGTTCCAAAGACATGAATTTGGTGTTTGAG Y 2 1 2 1 201000 f 74 goat snp38049-scaffold474-631056 2 135936180 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428835 Affx-122938369 AX-123299177 2 683983 TTGTGGGAGGGGAGAAGCAATATAGTAGGGACCCA[C/T]GTGTTTAGCAGGGGACTCAGATGTAGAGGGGAATA Y 2 1 2 1 201000 f 74 goat snp38050-scaffold474-683983 2 135882177 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 coat-colour SNP associated with coat colour multi-breed 38413308 Affx-122950190 AX-123283657 2 772637 CACAGCATCACTTCTGATACAACCAGCTCTGAAGA[G/T]GTGGAGGAAAGCTGCTGAGAAGCAGCAAGCGTCCT K 2 1 2 1 101000 f 74 goat snp38051-scaffold474-772637 2 135792964 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427396 Affx-122940077 AX-123297739 2 814959 ATGTTGATTGTCTTTAATTCAATTAGGTTATTTAG[C/T]GAATTTCCACCTAGGAAATAAAGGGGCAGGGGCAT Y 2 1 2 1 201000 f 74 goat snp38052-scaffold474-814959 2 135749923 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796907 Affx-122965299 AX-385283849 2 858281 AAGATAAAGTGAAGATTAGTTATGATTGTGAAATA[C/T]GTCAGTTGAAAGATCTATAGCACAGCTAAAATACT Y 2 1 2 1 101000 r 74 goat snp38053-scaffold474-858281 2 135706661 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403915 Affx-122957478 AX-123274267 2 911352 CCATAAATGGCATGTGAAGGAAGACAGAGGAGGAA[A/G]AGAAGATTTGCCTAGTGCCCCTGGGAGGGTCAAAA R 2 1 2 1 103000 f 74 goat snp38054-scaffold474-911352 2 135653317 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397213 Affx-122962389 AX-123267568 2 1002815 GCCAGTTGCAATATTAGAATTCCTGTGCTGGTAGA[C/T]AGGCTAGGATGGAGCCTCTTAGCTAGGGGGATGGT Y 2 1 2 1 101000 f 74 goat snp38056-scaffold474-1002815 2 135565544 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778054 Affx-122955885 AX-385265170 2 1055039 CTATGATGTGTGAAGGAATTCACTACCCAGTGACT[A/C]TCTTCTGATACAATGAAATGATGTATTAAAGAAAA M 2 1 2 1 201000 r 74 goat snp38057-scaffold474-1055039 2 135513238 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804421 Affx-986696588 AX-385291006 2 1090376 CGCAATAGTCACTGAGTCCGAGGGGAGCCGAGAGG[C/T]AGCCAACACCCCGGGAGCGGTCGCGACAGTCACTG Y 2 1 2 1 600010 r 74 goat 2_1090376 2 1090376 Ancestral_priority_1043 ancestry 0.454 neutral IMAGE 10K 10K ancestral 38421095 Affx-122944224 AX-123291442 2 1099357 GGGTCACTTAGACATTTTCTGGAATTCTGTTGTGA[C/T]GTAACTGTGGTATTTTGGGGAGCATCTCTTTGCAC Y 2 1 2 1 201000 r 74 goat snp38058-scaffold474-1099357 2 135468712 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399307 Affx-122960530 AX-123269662 2 1133378 GTGAGAATAGCTAAGAATTCTTGAAGAGAGAAAGA[C/T]GTACTTTACAAGACACACGTAACTACTGTAATTAA Y 2 1 2 1 101000 r 74 goat snp38059-scaffold474-1133378 2 135434648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386621 Affx-122970231 AX-123256979 2 1165920 ATCCCAGCCGAACACCAGGGAGCGGGTGCTTTGCA[C/T]AGGCTTTAAAATAGAACTGCCAAGGCAGCTTGATG Y 2 1 2 1 101000 r 74 goat snp38060-scaffold474-1165920 2 135402296 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767957 Affx-122976169 AX-385255172 2 1263606 AATAGGATTCTAGACCAGTGCCAGGTTTTGTACAT[C/T]ATTTTTAGTGAAACAGGTTTACAGACTACATTTAC Y 2 1 2 1 101000 f 74 goat snp38061-scaffold474-1263606 2 135304194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386532 Affx-122970731 AX-123256890 2 1355472 CTGCTGCATCACCACCCTCAGGTCTTGGCTCAAAT[A/G]CTCCTTCCTCAATGAGATCTTCCTGGACCTCACCC R 2 1 2 1 101000 f 74 goat snp38062-scaffold474-1355472 2 135211669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443322 Affx-122927448 AX-123313659 2 1405504 CTTGGAAATCAGAAAACCACTTGCACTAGCTAAAT[A/G]CCTTTATCCAATGGAATCATAAATTTCTATTACAA R 2 1 2 1 101000 f 74 goat snp38063-scaffold474-1405504 2 135161171 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776454 Affx-122976360 AX-385263581 2 1485062 TAGGTTAAAGATCTTAGTCTTTATGTTAAGAGCAA[C/T]GAGGAACAAGTGGAGAGCTTTATTTAATGGAAGCA Y 2 1 2 1 101000 r 74 goat snp38065-scaffold474-1485062 2 135081120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445676 Affx-122926137 AX-123316013 2 1514043 CATGGCTGGCAAATAATGGGAGAGTATCTCTCAGG[C/T]TCCCCCCTAAAAGGGTGTTTAGCCACAGGATAACA Y 2 1 2 1 201000 f 74 goat snp38066-scaffold474-1514043 2 135051585 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415646 Affx-122948573 AX-123285995 2 1600819 TTACTCTACTAGTGCCTTGAATCTCTTTGACCCTC[A/G]CTGAATCTGTTTTTGTACATCTACAAACTTTTCCT R 2 1 2 1 101000 r 74 goat snp38067-scaffold474-1600819 2 134963693 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386201 Affx-122971357 AX-123256559 2 1634633 TAACAATCTGTCAGATCACGAGTTGGTAAGCTCAC[A/G]TTTGTAAAATGCGTGGCCTGTGTACCTTGAGTCTA R 2 1 2 1 101000 r 74 goat snp38068-scaffold474-1634633 2 134930016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273872 Affx-1111833904 AX-519547480 2 1656849 AGAGGTGGCGGTACAGATCCACGTGGGGGCTGTCA[A/G]CGCCGAAGGAGGACCCCGGGGGGAAACACAGCTTC R 2 1 2 1 202000 f 74 goat GoatD01.009963 2 1656849 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382885 Affx-122973418 AX-123253243 2 1741591 CATTGGAGATTGAAGAAAGTGAGATGAAAAGTGTA[C/T]GCCTTTTCTCAGGGTCCCTCAGCCAGACAGTGATG Y 2 1 2 1 101000 f 74 goat snp38070-scaffold474-1741591 2 134823736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438943 Affx-122930409 AX-123309280 2 1791989 TTTGAAGGCAGGAGTTACTGAGAAGGAACCTGTAG[C/T]TGGCTCCCTGCTCCCTGTTCAATTCTCTGTTCATG Y 2 1 2 1 101000 f 74 goat snp38071-scaffold474-1791989 2 134773103 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391226 Affx-122967398 AX-123261583 2 1832926 AGGCACCCTCAAATGGAAGCGACAACCTTTTTATC[A/G]CCTAATCTTGGAAATGATATTTCATTCTGCCAAAG R 2 1 2 1 101000 f 74 goat snp38072-scaffold474-1832926 2 134733162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401810 Affx-122959461 AX-123272163 2 1928042 GACAAGAAAAAAGGGCTGGAGATGGGCCTTCCTTC[A/G]TGGGAAGCTACAGGCCTGAAGGGCCCCTGCCCAAG R 2 1 2 1 101000 f 74 goat snp38074-scaffold474-1928042 2 134636556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429580 Affx-122937805 AX-123299921 2 2039417 TTCATCGAGTGCTCCCTGAGGCTGGGAACGGATGA[C/T]GAAGGGTCAATACGCCCAGCCTTGAGGCATTCAAA Y 2 1 2 1 303000 f 74 goat snp38076-scaffold474-2039417 2 134525302 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780220 Affx-122947169 AX-385267316 2 2081972 ACTGAAAGACTTGCCTTGTTTGGATTTGAAGAGCT[A/C]GGTGAGTCAGAGGAGGTTGTTTCTTAATCTGTATG M 2 1 2 1 101000 r 74 goat snp38077-scaffold474-2081972 2 134486511 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416211 Affx-122948234 AX-123286560 2 2141670 CATCCCTCCATCCATCCAGTCTTCCCTTACACAGG[A/C]GTCTGTGGCTGCATGTCTTACTGAGTCAGTAAGGA M 2 1 2 1 201000 r 74 goat snp38078-scaffold474-2141670 2 134426851 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393366 Affx-122965919 AX-123263722 2 2196842 CCTTGTGTCCACTGGGGTAGTGCCCCTGCATGCCC[A/G]CAATTCTTCCCACAGGGACTCCTTGATGGCTGCCT R 2 1 2 1 101000 r 74 goat snp38079-scaffold474-2196842 2 134371874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767380 Affx-122966430 AX-385254653 2 2256208 TCTCCACCATGGGAAAATGCTGGTGACAAATGAAT[G/T]CTGCATAATCTTCTTAATGTGGCAGTTTTCCATTT K 2 1 2 1 101000 f 74 goat snp38080-scaffold474-2256208 2 134321282 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794199 Affx-122973697 AX-385281165 2 2361272 TATATACATGTGTGTATGCAGTTCTGTGCAGTTAC[A/G]TACATGTGTAATTTCATGTGACAGTGACCACATGA R 2 1 2 1 202000 f 74 goat snp38082-scaffold474-2361272 2 134217722 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428305 Affx-122939377 AX-123298648 2 2407871 TGTTTCCACCCCACTGAACAAACAGGCTCAGATGA[A/G]TTACAAGACTCCTTTCACCCAGCTTGTTAGGGGAG R 2 1 2 1 201000 r 74 goat snp38083-scaffold474-2407871 2 134170650 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444127 Affx-122926808 AX-123314464 2 2447852 TACTTTATTTGATGAAGAACACTGCAAATATGAAA[C/T]ATTACAATCTCACTTACCAGATCACTCAGTGTTGA Y 2 1 2 1 101000 r 74 goat snp38084-scaffold474-2447852 2 134130843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413786 Affx-122949917 AX-123284135 2 2485892 TGTGACTCTTGATTCACAATCGAGGGAGTTGGAGA[C/T]GAAAGGAGGGCAGTAACATTCCCATATGACAAGTG Y 2 1 2 1 101000 f 74 goat snp38085-scaffold474-2485892 2 134091501 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778741 Affx-122949587 AX-385265852 2 2541566 TATTTCATAAGCAGAATGCCCAACCAAAAGAAAGC[A/G]TTCTAGAAGAATTAATGTCACATAGGGATTAGAAT R 2 1 2 1 202000 r 74 goat snp38086-scaffold474-2541566 2 134034468 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421565 Affx-122943852 AX-123291912 2 2573831 TCAGTTTTTCATCTTCTTCTTTGTTGCTTCAGCTT[A/G]TTAATTTTACTCCAGAGCTCTCCCAAGACAATTTT R 2 1 2 1 201000 r 74 goat snp58419-scaffold948-993256 2 134002375 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412909 Affx-122950406 AX-123283258 2 2624821 TGTATATATTATGATTTTTTTTTCCAAATTGGTTA[C/T]ACCAATTTTGATTCTCACTAAAAGTATAAGGAATA Y 2 1 2 1 103000 r 74 goat snp58418-scaffold948-942266 2 133950218 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442758 Affx-122927750 AX-123313095 2 2654670 CATAGCAGCCCTCTTCCAAGGGTAATCAGAGGCAC[A/G]TTTACAGGGAATGGGATATCTAAGCCTTAAAGAAT R 2 1 2 1 101000 r 74 goat snp58417-scaffold948-912417 2 133920474 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432096 Affx-122936479 AX-123302437 2 2688074 CCTGTGGGTTGTCAGAGAGCACTACAAGGTGCAAA[G/T]AGTTTACACCAGATTCAGTTCTTCAGTGCATATGC K 2 1 2 1 101000 f 74 goat snp58416-scaffold948-879013 2 133885555 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439073 Affx-122930309 AX-123309410 2 2719168 GTAACTGTCACGTGTTATTGGTGTGCATGTACAAC[A/G]TGTATGAGAGTGTGTGTATGAACGTGCAGTTGGTA R 2 1 2 1 101000 f 74 goat snp58415-scaffold948-847919 2 133854521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427998 Affx-122939167 AX-123298341 2 2749602 CGTGTTGCCAAGGACCAAGCTCTTCCTAGGGTCTT[A/G]CAGAATTAATACTGCCTTGTGTCCACCATTTGTCA R 2 1 2 1 201000 r 74 goat snp58414-scaffold948-817485 2 133823726 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272030 Affx-1111833165 AX-519545796 2 2782624 AATTGCCTCATCTGTTCAACTTAAATTATTTAAGC[A/G]GAAGGATTTCCCTGGTGGTCCAGTGGCTAAGACTC R 2 1 2 1 101000 f 74 goat 2_2782624_AF-PAKI 2 2782624 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320802261 Affx-122974017 AX-385289165 2 2823278 TGGCTGACATTTCACAGCTGTGGAATTAAGCAAAT[A/G]TAATTTGCAGATCCTCTACAAGGTTTAGTAATAAA R 2 1 2 1 101000 f 74 goat snp58412-scaffold948-743809 2 133749920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791023 Affx-122930705 AX-385278019 2 2863486 CCCTGATGCACCTTTCCGCAGGCTCATTTAAACTT[A/G]TTAAATCAACTCTTGTCCCCACTTTGCCCTGCCTA R 2 1 2 1 201000 r 74 goat snp58411-scaffold948-703601 2 133708844 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408040 Affx-122954286 AX-123278391 2 2895745 TGCTGCAGCAGGTGCTCCATCTTCACATGTTGGAA[C/T]GTACATTCTGATGCTTCTTTTATTGTATAGAGAAT Y 2 1 2 1 201000 r 74 goat snp58410-scaffold948-671342 2 133676381 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379360 Affx-122976156 AX-123249719 2 2932291 TCTAAAGATGAAAAAGTTTTCAAATCACAGAATGG[C/T]AATAAATAACCATAAACAATCTCTTATTTCTTTTT Y 2 1 2 1 101000 f 74 goat snp58409-scaffold948-634796 2 133639875 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791765 Affx-122936257 AX-385278756 2 2978432 TCACCCAGTCTGTAGTTTGTTTTTCATCGTATCTA[C/T]GTGAGTTTTTGCATAGCAACCATTTTGGGTTTTTT Y 2 1 2 1 101000 f 74 goat snp58408-scaffold948-588655 2 133592012 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421447 Affx-122943943 AX-123291794 2 3012471 TTCCATATATAATTTGAGAACAAAAGGGGAGACAG[A/G]AAGAATGAGTTAGAAGAAACGTATGTGAGAGTGGG R 2 1 2 1 101000 r 74 goat snp58407-scaffold948-554616 2 133557239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451906 Affx-122921032 AX-123322239 2 3051820 AAATATAATGTCTGCACATCCAACCTAAAGAATAT[A/G]TGGATTTACATGGATTTGAGAATCGAAGAGAGGGC R 2 1 2 1 101000 r 74 goat snp58406-scaffold948-515267 2 133520292 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380149 Affx-122975975 AX-123250507 2 3085660 AGCTGTAGGTGTACAACAACAGCTCTGGCCTCCCA[A/C]ACTGCCTGCTGTGGTCCCTAGCTGTTGGACATAGA M 2 1 2 1 201000 f 74 goat snp58405-scaffold948-481427 2 133486315 A C 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765008 Affx-122964287 AX-385252582 2 3121017 TGGTTGTTTGGTACAGATATAAATACAAATTGCAG[A/G]GACATGTATTATGTAAACTGGTAAAAAAAAAAAAA R 2 1 2 1 101000 f 74 goat snp58404-scaffold948-446070 2 133454858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431346 Affx-122937053 AX-123301687 2 3178888 TTCCTTTGATTCATTTACTGAGGGTTACCCCAAAT[A/G]TTATGAACTTCTCTGTCTAGGCCAATGGGTAAAAT R 2 1 2 1 201000 r 74 goat snp58403-scaffold948-388199 2 133397948 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403795 Affx-122957974 AX-123274147 2 3222036 GGACCAACTACTTAACTTCTCTGAGCCTCACTCTT[C/T]TATGTTTAATTGGGAAAAACTGAGGAACTGCCTGA Y 2 1 2 1 303000 r 74 goat snp58402-scaffold948-345051 2 133356489 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424514 Affx-122941734 AX-123294860 2 3251090 TACGCTGTTCCCAGGCAAGTGTGCCCCCACCTCTG[A/C]ATCATGCCTCACTGAAGACCCCTCATGGAGCATCT M 2 1 2 1 101000 r 74 goat snp58401-scaffold948-315997 2 133327263 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404250 Affx-122957063 AX-123274602 2 3305696 GACAGCAGGAAAGTGGAAAGTGTTTCAAATTTACA[A/G]CAAAATTCTCATATGCACACAAGTACAGCAGGTGG R 2 1 2 1 201000 r 74 goat snp58400-scaffold948-261391 2 133270846 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448634 Affx-122923366 AX-123318970 2 3337443 GTTGCAGTCTAAGCCTGGTGCATAGCTGCTGTTTC[C/T]GCGACCTTCACTTCCCATTATACTCGGAAGTCCCT Y 2 1 2 1 101000 r 74 goat snp58399-scaffold948-229644 2 133237923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804423 Affx-986696590 AX-385291008 2 3405670 GGCTCCATCAGCAGCATATAATAGATAGAACTGAT[A/C]ATTTCCTGAACCTTTCCAGCAAATCTGAGTTTTCA M 2 1 2 1 600010 r 74 goat 2_3405670 2 3405670 Ancestral_priority_1043 ancestry 0.654 recommended IMAGE 10K 10K ancestral 320803943 Affx-986696592 AX-385290649 2 3406468 CTCACACTAATCGAAGAAAAGCAGAGAAAGTCGAT[A/G]CTATATGACATCACTTATATGTGGAATCTTAAAAA R 2 1 2 1 600010 f 74 goat 2_3406468 2 3406468 Ancestral_priority_1043 ancestry 0.544 neutral IMAGE 10K 10K ancestral 320767772 Affx-122956429 AX-385254999 2 3417224 TGTCAGCCTCATAGGATAAGTAGAAAATGTTTCCT[A/C]TGCTTCTAGTTTATGGATGTAATTATGAAAATTAT M 2 1 2 1 101000 f 74 goat snp58397-scaffold948-149863 2 133166106 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803946 Affx-986696594 AX-385290652 2 3421931 CCTGGAGGGTCCTGGTGAGTGGTCATGACGGAAGA[A/T]CCTGCCCCACCCCGCCCCCAGACCCTGCCACCCAT W 4 1 2 1 600010 f 74 goat 2_3421931 2 3421931 Ancestral_priority_1043 ancestry 0.464 neutral IMAGE 10K 10K ancestral 38439386 Affx-122930262 AX-123309723 2 3482109 TAAATAGAAACTAGCCTAAAGTAGAAAGGAAAGAA[C/T]GGCACAAAGTTAAAAGCACTGAGAGGCGAAACACT Y 2 1 2 1 101000 r 74 goat snp58396-scaffold948-84978 2 133108815 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786608 Affx-122956461 AX-385273640 2 3521685 TTATGTAGCAGAAGGTAAAATGTGTATTTTATATA[A/C]ATTTTCTCTAATTCTCATGATGGCCTGATAGGTAG M 2 1 2 1 303000 f 74 goat snp58395-scaffold948-45402 2 133069358 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401920 Affx-122958824 AX-123272273 2 3563671 GTGATAAATATTTAACAGCATTTATTTAGTGAAGG[A/G]GATGATATACTTTAAAAAAGGTATAGAAATGTAGA R 2 1 2 1 101000 r 74 goat snp58394-scaffold948-3416 2 133027554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387942 Affx-122970020 AX-123258300 2 3572292 CCTTCAATTAGTATAAAGAATAAGAACAAAACAAC[A/G]TAGAAAAAGCAGTAAAAACAGAAAAGCCAAAATTA R 2 1 2 1 103000 f 74 goat snp9808-scaffold1350-344637 2 133003589 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397738 Affx-122962539 AX-123268093 2 3602401 CAACATGGGATGAGTTACAACAAAGTGATTTCACA[C/T]GCCACATTATTTTGTTTAGATTTTCAGTAGTTCGC Y 2 1 2 1 101000 f 74 goat snp9807-scaffold1350-314528 2 132973320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397842 Affx-122962467 AX-123268197 2 3636598 ACTGGAAACACTTGGGGCCAGGGCTTTATCACCAG[C/T]AGGGTTATAGTGTCTCTACCAGAGCTCTTTACCCA Y 2 1 2 1 201000 r 74 goat snp9806-scaffold1350-280331 2 132939114 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802311 Affx-122962191 AX-385289215 2 3684835 GCCTATACTTAGTTATACTGACTCTGCACCTTTTG[C/T]AAAACAATGTTCCCTCTAGCCTGAAGTATACAGGA Y 2 1 2 1 101000 f 74 goat snp9805-scaffold1350-232094 2 132891058 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392029 Affx-122966473 AX-123262386 2 3719323 GCAAAAATTTCAGTAAAGAACATTTATCAGAAACA[C/T]AGAATAAGTATTACATTTAATGTTATTGCATTATT Y 2 1 2 1 101000 f 74 goat snp9804-scaffold1350-197606 2 132856325 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423414 Affx-122942621 AX-123293760 2 3821212 TGGAGCTCTGGCATGTTTCACACATGATGAAGTGG[C/T]GGTCAGTCTCCTGCAGGCTGTGAACAGAGAGAACA Y 2 1 2 1 101000 f 74 goat snp9802-scaffold1350-95717 2 132752709 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423739 Affx-122942860 AX-123294085 2 3875461 TATAAACTCTTAGGTTTCCAGCAGCTTTATCAGAT[A/G]ACTTAGGAAGGAAGGCTTACCTCATCAGTACAGAA R 2 1 2 1 101000 r 74 goat snp9801-scaffold1350-41468 2 132698754 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433794 Affx-122934466 AX-123304135 2 3908725 GTCAGTTGTCAGAATCTCTAGGTTGATCTTCTCTA[C/T]GATTTATCTTTATTTTGCTAATGTTTCTGTCTACA Y 2 1 2 1 101000 f 74 goat snp9800-scaffold1350-8204 2 132671435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416906 Affx-122948062 AX-123287254 2 3922626 GCCTCCCAACCTTGCAGTTGCCCACACTCCCCGTC[A/G]CCCACCCTGTGTGGTTTTCTCTGCTGTACTTGTTT R 2 1 2 1 101000 r 74 goat snp19013-scaffold1910-120802 2 132656324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386151 Affx-122971397 AX-123256509 2 3967148 AAGGATGAATTTTTTTGACTCAGAACCTCAGGCTT[C/T]GCCTAGGGTGGGTAGGAGAGGGGACTCATCCATCA Y 2 1 2 1 101000 f 74 goat snp19012-scaffold1910-76280 2 132611713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449317 Affx-122922998 AX-123319652 2 4005445 AGGATTGGCAGCCAGCTCAGGGAGGGAAAGCAGAA[G/T]CCATGGGCTTACAGCTGGCAGGCCCTCTCAGTGTG K 2 1 2 1 201000 r 74 goat snp19011-scaffold1910-37983 2 132572867 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387060 Affx-122969899 AX-123257418 2 4040490 CTAATGATCTTGTAAGTAACACGTTCTGTCTGGTC[C/T]CGATACACACTAGAAGCTCGACTATGGGGATGGTT Y 2 1 2 1 101000 r 74 goat snp19010-scaffold1910-2938 2 132537168 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426032 Affx-122941118 AX-123296378 2 4086276 ATAAGAAAAGTGATCCTATAGAATTGCACGACCCT[A/C]GGGTTTCTTCCCTTGGGGGAACCATACTGAATGCT M 2 1 2 1 101000 f 74 goat snp13900-scaffold1540-42749 2 132487140 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386552 Affx-122970716 AX-123256910 2 4122276 CTAATAAAGCACTGGTACTCAGTCCTTCCTGGGGA[A/G]CTCAGACTCACACACTGTTCTGATTTTTGTCTTTA R 2 1 2 1 101000 r 74 goat snp13901-scaffold1540-78749 2 132449957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427810 Affx-122939753 AX-123298153 2 4178836 CAGTGGCCCCTAGAATCTTTCCAAACGTGAGTTAA[C/T]GTCCCTTTGGGACATTCCAGGCATGTGAACTTTGC Y 2 1 2 1 102000 f 74 goat snp13902-scaffold1540-135309 2 132392378 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438982 Affx-122930381 AX-123309319 2 4218446 CGGCCCCCAGCCATGGTCCTGGGGGCTCACCCCCA[G/T]CTGTTCCATGTTGCCCTCAAAAGGGCCGTTGTCCC K 2 1 2 1 101000 r 74 goat snp13903-scaffold1540-174919 2 132352924 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444269 Affx-122926777 AX-123314606 2 4235195 TGAGACAGTGAGCCAGCCGACCCCACCTCCTGCAG[C/T]GGTGATGCAAACACAAAGCCTCCATGTGCACAGGC Y 2 1 2 1 101000 r 74 goat snp21081-scaffold2062-610374 2 132336227 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442449 Affx-122927956 AX-123312786 2 4264913 ACAGCCCTTCTAGAGTCTGCATGTGGTTACGCCTG[C/T]GGGGGAAAGTGCAGGTACTGGTTTCCTGGCCCTAC Y 2 1 2 1 101000 f 74 goat snp21080-scaffold2062-580656 2 132306704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424456 Affx-122941779 AX-123294802 2 4302703 AGCAATAACTTTCTCACTCTTATTTGTTTAGTTTT[C/T]TGTGCATTAATTTTGCCCCAAGTGGTTCAGGAGCT Y 2 1 2 1 101000 r 74 goat snp21079-scaffold2062-542866 2 132268439 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413653 Affx-122950532 AX-123284002 2 4337349 ACATCAGTAACTCAGGTTGCCGTTGCCATTTCAGA[A/G]CATCTGGAGGATGCCAGTTCCTTTTTCATTATTTG R 2 1 2 1 101000 f 74 goat snp21078-scaffold2062-508220 2 132232685 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801869 Affx-122972088 AX-385288776 2 4385201 TATTGAAGAATCGTTGCATTCTGGGATATGCAGAT[A/G]TGTGAGATTCAAAGTGTGTATAGAGAGATACATGA R 2 1 2 1 101000 f 74 goat snp21077-scaffold2062-460368 2 132185267 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380802 Affx-122975090 AX-123251160 2 4442615 CTCCCGCATCCACGGCAGACATTGATGGTGGGTCA[C/T]AGCACGTCCATGGTGGGAGGCTGAAGGGTCAGATA Y 2 1 2 1 201000 f 74 goat snp21076-scaffold2062-402954 2 132128046 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419616 Affx-122945985 AX-123289964 2 4480198 GGGTTTTCACTCCCTGTGGATTCCCCAAGCACACA[A/G]CTCTCTTATTCTGGGCTCACCCACCTGGCCAACAC R 2 1 2 1 201000 r 74 goat snp21075-scaffold2062-365371 2 132090228 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421210 Affx-122944141 AX-123291557 2 4539754 AGTAAGTGAAACTAGGTGGCGGGAGACAGGGGCAT[A/G]GATTGTGTTCCCTAAAATGAGCCACTGGGGTCCTA R 2 1 2 1 101000 r 74 goat snp21073-scaffold2062-305815 2 132030791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447889 Affx-122923818 AX-123318225 2 4570173 GTAGGCTCACCAAATGTGCCACTGTGGTGAGGGAC[A/G]CTGAGAGTGAGGGAGGCTGTGCATGTGTGGGGACA R 2 1 2 1 101000 f 74 goat snp21072-scaffold2062-275396 2 131999783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414097 Affx-122949743 AX-123284446 2 4607367 CATATGCTGCTGTCTGTTGCTGCTTTTCTTTGGGA[C/T]GTATACAGTCTGTGATAAAACAGCCAGAAAATACA Y 2 1 2 1 201000 r 74 goat snp21071-scaffold2062-238202 2 131962036 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409348 Affx-122954177 AX-123279699 2 4641694 TTAGGAACGAGGAAGAAACGAGAGCAATTTGTGCC[A/G]TAAATGTGGAAGGGCCTGTGTCTTACTATCTCGTC R 2 1 2 1 101000 f 74 goat snp21070-scaffold2062-203875 2 131927238 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401891 Affx-122958846 AX-123272244 2 4691933 CTTCTCATCTAGCTCGCCTTTTTGAATTCCAGTCT[A/G]TTTGGTGGGTACTCAATAAAATACGTTGAATGAAT R 2 1 2 1 101000 f 74 goat snp21069-scaffold2062-153636 2 131877071 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410114 Affx-122952824 AX-123280464 2 4772544 GCCTGGTGTTGGAACCTTGGCATATGGAAAAACCG[C/T]GGAGGAGAACCAATTTCTGTAGCCATGGTGATGTT Y 2 1 2 1 201000 f 74 goat snp21068-scaffold2062-73025 2 131796669 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377881 Affx-122977258 AX-123248240 2 4801415 GGACTTCAAGTTGGAGAGGAAAGCACAAAGCTTGC[A/G]CCAGTGCCACACTATGACCCTGGAGAGAGGACAAA R 2 1 2 1 101000 f 74 goat snp21067-scaffold2062-44154 2 131767824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426291 Affx-122940304 AX-123296637 2 4845448 TCCAAGAGTCCTTATAAAAGTTTCAGCAATCAAAA[C/T]GTCTATCTGATCAAGCATTCTTATGTAAATCAGGC Y 2 1 2 1 101000 r 74 goat snp21066-scaffold2062-121 2 131724032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380560 Affx-122975282 AX-123250918 2 4871485 TTGCCAGATGCAGGGCTGCCTCCAGATGAAATATG[C/T]GATGCTCTGAATGCTGGATTTGAATGTCAGATAAG Y 2 1 2 1 101000 r 74 goat snp6587-scaffold1235-25817 2 131695475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406744 Affx-122955739 AX-123277095 2 4951357 CTGGAAGGATTTACTGGTGTCAAGGCTGCCCCAGG[A/G]CAGATGGCCAGGGTGGTCAGACTTCCTGCTGTCCC R 2 1 2 1 202000 r 74 goat snp6589-scaffold1235-105689 2 131617753 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437258 Affx-122932009 AX-123307596 2 4990894 CAAGGAGAGTGACGAGAGCTGGCATAAGCCCGGGC[A/G]TGGAGGTTAGCCCAGATGGCATCTGGGTTGCAGTA R 2 1 2 1 101000 r 74 goat snp6590-scaffold1235-145226 2 131579265 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382920 Affx-122973393 AX-123253278 2 5051283 CCACCCCAATTCTGACCGTTGAAGCATAACTTTTC[A/G]TTACACTTCCAATTTTTTTTATTATGACCTTATAA R 2 1 2 1 103000 f 74 goat snp6591-scaffold1235-205615 2 131521228 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792593 Affx-122942567 AX-385279575 2 5102369 TTTAACTTAAACAACCTCACAGTCACCTGATAACA[G/T]AATCATCTTTGTCATACCAATATTCAAAAAGTCAT K 2 1 2 1 101000 f 74 goat snp6592-scaffold1235-256701 2 131470107 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392603 Affx-122966051 AX-123262960 2 5141643 CGGTGGCAGGCTGCTTAGCCCCAGAGGTGCCCAGG[A/G]AGCCTCCATGTGTGTCTGAGGAAGCTGTCCAGGAA R 2 1 2 1 101000 r 74 goat snp6593-scaffold1235-295975 2 131430509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277129 Affx-1111835694 AX-519550635 2 5164716 CCTTGGCCTGAAACGTCCCACCCCTCTGCCTCCCG[A/C]GTCTTTGCCAGCCTACTCCTATTCATTGTTTATGA M 2 1 2 1 101000 r 74 goat Random2.2K-159 2 5164716 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796448 Affx-122959129 AX-385283398 2 5207127 CCCTGAAATAGTTTTTGGCAATTTGTCCAGTTTTA[G/T]TCTTATTTTTGGAGACGAGGATATGCTGACTTCAG K 2 1 2 1 101000 r 74 goat snp6595-scaffold1235-361459 2 131365898 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780354 Affx-122961806 AX-385267449 2 5241773 TATACCAATAATGAGGTAAACATATGTACATTAAC[A/G]TTCAATAACTCTGTTTTTGGAAAAGTAGTGTGTTT R 2 1 2 1 201000 r 74 goat snp6596-scaffold1235-396105 2 131330554 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376272 Affx-122978756 AX-123246631 2 5273170 CAACCAAGCTTGGGAGCAAAAGCAAATACATTTGC[C/T]GGATGCAGACTCTTTGGCCCACAGCAGAGTTCTTT Y 2 1 2 1 101000 r 74 goat snp6597-scaffold1235-427502 2 131298940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389114 Affx-122968564 AX-123259472 2 5312888 GCAGAAGAGTACAATGCCTTCTTCTACTCGCTGGT[A/G]TCCCAGGACACACAGGAAATGGCTTACTCAACCAA R 2 1 2 1 201000 f 74 goat snp6598-scaffold1235-467220 2 131260855 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271875 Affx-1111833173 AX-519545658 2 5328081 GAGAACCACAGGGAAGCCTGGAGGCAGAAAGGACC[A/G]TGGCACAGACCCTTGGGTGATCCCAGGGAGAACCT R 2 1 2 1 102000 r 74 goat 2_5328081_AF-PAKI 2 5328081 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38417802 Affx-122947372 AX-123288150 2 5343497 GGAGCAAAAAGCACGTGGGTTGTGACCACAAGTAA[C/T]GTGATTGATTTCTCATTTTTAAACTCTTTTAATTT Y 2 1 2 1 101000 f 74 goat snp6599-scaffold1235-497829 2 131230620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791286 Affx-122924169 AX-385278280 2 5385459 GGGAAAAAAGCCCTAATAATGAACCCTATGCTTCT[C/T]AAATCATTCAGGTGGCTCCATCTGGTATCATGGTC Y 2 1 2 1 101000 r 74 goat snp23434-scaffold2358-26243 2 131188027 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786350 Affx-122958542 AX-385273384 2 5417964 CCCAAATTCAAGATAAGCACACAACCAAGAGTCAT[C/T]AAACATGGAGGAAAAACACAACCGTGAAAGCGGCA Y 2 1 2 1 202000 r 74 goat snp19057-scaffold1914-6163 2 131155931 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766022 Affx-122929241 AX-385253441 2 5446756 ACTCTAGGGGCTTTACATCTATTGTTCTCTATTTG[C/T]ACAATAATCTACAGAGTGTAATATACCTCCCGTAA Y 2 1 2 1 101000 f 74 goat snp19058-scaffold1914-34955 2 131127068 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421805 Affx-122944324 AX-123292152 2 5485076 GGTACAGCCTGAAGCCTGGGCAAGCACAGCAACCC[A/G]TCCTGTGGGTGACCCCTTTCTCTGGGTGCCTTGTA R 2 1 2 1 201000 f 74 goat snp19059-scaffold1914-73275 2 131090120 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782394 Affx-122933240 AX-385269470 2 5517984 CCTGTCACTCTTAAATCTGGCCCAGCTTGGACCAA[C/T]GACCTATGTGAGTCACCTTATCCATACATAATGGC Y 2 1 2 1 101000 f 74 goat snp20929-scaffold2050-369335 2 131041723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792360 Affx-122949058 AX-385279341 2 5549545 AATTATTTTCAGAAATCAAAGTTTAATGACTTGGT[A/G]CTTTGACAGTCACAATACAGGTGCAAATGTCAAAA R 2 1 2 1 101000 r 74 goat snp20928-scaffold2050-337774 2 131010655 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277009 Affx-1111835700 AX-519550517 2 5557403 TGCAGGTACGTGAGAAACCACACAGATGAGTTAGA[A/G]CACCGTAGGTCCGGATCCATATGACTACCTCCTCG R 2 1 2 1 101000 f 74 goat Random2.2K-160 2 5557403 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793716 Affx-122950343 AX-385280688 2 5584236 AGTGAGCCAGAATGCGTATCAGGTCTGCCAAATCC[A/G]TATGAACAAACATACATGTAGGTTCTAGTCGTCTA R 2 1 2 1 101000 r 74 goat snp20927-scaffold2050-303083 2 130976321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380532 Affx-122975679 AX-123250890 2 5646001 AAAGATTCATGGAATGATAACTCTGGCTTTTTAGA[A/G]ATGGGGAGAAGACATTAGTATTATCCATGTAAAGC R 2 1 2 1 201000 f 74 goat snp20926-scaffold2050-241318 2 130914376 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385194 Affx-122971723 AX-123255552 2 5691962 GTCCATTTAAATTTACTACAGTGACTGATGTTTTG[A/C]ATTTATTTCCTTTATTTTGTATTTCTTCCCTTCCC M 2 1 2 1 303000 f 74 goat snp20925-scaffold2050-195357 2 130868973 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380932 Affx-122975012 AX-123251290 2 5801467 GGAAACTAACCCTGAGGCCAGGCTTCTTCAAACTG[C/T]GGGTTAGGAAATCAGTTCTGTTGAGTGGATGAGGA Y 2 1 2 1 201000 f 74 goat snp20922-scaffold2050-85852 2 130759736 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392429 Affx-122966192 AX-123262786 2 5836510 TCAGTCTTGGCAAGACTAGTCTTGTGATGATGGAT[A/G]TTGGTTTTCTCATCCATAAAATGAGAATAATAATC R 2 1 2 1 103000 f 74 goat snp20921-scaffold2050-50809 2 130724554 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400707 Affx-122959929 AX-123271062 2 5897847 AAAATCTGAACCGTCTTCTAAAGTCGACCTAAACA[C/T]ACACCCAACTTCCTGAATCCAATTCAGAGGTGTTT Y 2 1 2 1 101000 f 74 goat snp40701-scaffold520-288891 2 130659415 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384743 Affx-122972039 AX-123255101 2 5954016 GGCTTGGTGTTTACTGGGTGTGATGGGCAAAATCA[C/T]GGCCTCCTAGAGATGTCCATGTCCTAATCCCCGGA Y 2 1 2 1 101000 f 74 goat snp40700-scaffold520-232722 2 130606349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402572 Affx-122958445 AX-123272925 2 5998395 TGAATCTACTTTCGTTTTTTCTTTTTAATATTCTA[C/T]ATGATTTCAGGTTTCATTTCTGACACCTTGGTGGT Y 2 1 2 1 103000 r 74 goat snp40699-scaffold520-188343 2 130562043 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400721 Affx-122959917 AX-123271076 2 6042334 GTCACAGCTGCGTTCTGGTTATGTTACGGCTGCTG[C/T]TATGACTGCTGCATCAGCCAGAAGAGAGGCTGTGT Y 2 1 2 1 303000 r 74 goat snp40698-scaffold520-144404 2 130516971 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418419 Affx-122946536 AX-123288767 2 6086234 GGGATTGAGCAGAGGGCAAGCCCCAAGCAGTAAAG[C/T]GAAGTTCCTGGTTAGTAAATGGAAGCACTCCCCAA Y 2 1 2 1 101000 r 74 goat snp40697-scaffold520-100504 2 130472249 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450665 Affx-122921918 AX-123320999 2 6139761 CCTTTACTTTCCAGGGGAGTAGTACAAGGATGTCC[A/G]CCAGATCGTAATCTAGCTAGAAGCCTAATCTCTGT R 2 1 2 1 101000 r 74 goat snp40696-scaffold520-46977 2 130418727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773697 Affx-122937667 AX-385260836 2 6169441 ACAGAACTTAATTCATGTGTCATTAGTACAGTTGC[A/G]TCGTTGAGTTAGAACATGACATGACCGAGAAATGA R 2 1 2 1 101000 r 74 goat snp40695-scaffold520-17297 2 130388704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426375 Affx-122940244 AX-123296721 2 6189525 TTGCTGCCTAGGATGCTCCCTTCTGGTACAGAGGA[C/T]GTGAGGTTTACACCCAGAGACTCCTCAGATCAGGA Y 2 1 2 1 101000 r 74 goat snp38176-scaffold479-94944 2 130359220 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780977 Affx-122976727 AX-385268064 2 6228410 CAGGAGAATGAGAGGAAAAGAATTTAGTATGAGCA[C/T]GCTCCACATCTATGCATACCCCAGTTGTAGCCCTA Y 2 1 2 1 101000 f 74 goat snp38175-scaffold479-56059 2 130319063 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767604 Affx-122958109 AX-385254854 2 6276967 AGTTCCACCTTTGAAACCACTTCTAGAAACTTCAC[A/G]TTCTTAGTTTATAGACACTGAGCTTTTTGGCTTGC R 2 1 2 1 101000 f 74 goat snp38174-scaffold479-7502 2 130269662 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378600 Affx-122976578 AX-123248959 2 6287492 TCCACCATTCTATCAAGGTAGCTTCTCCCTCTGGA[C/T]GGGAAACCATGTCTTCAATTCTTATTCTTTTAATA Y 2 1 2 1 201000 r 74 goat snp14410-scaffold1572-692179 2 130259429 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421139 Affx-122944192 AX-123291486 2 6326521 ATCTGGTAAAAGCAAGGTGGGGCTCACTAGTCACA[A/G]TCTACCCTCCCCTATCAGCAAAGGAGAGAGCTCTG R 2 1 2 1 101000 f 74 goat snp14409-scaffold1572-653150 2 130220175 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785206 Affx-122928079 AX-385272252 2 6382855 ACATAGCTGTAATATTCATCAGTCTTTACTATAAA[C/T]AAGTTACTTTTTCGTTCCATCAGTTTAGGACTTGA Y 2 1 2 1 201000 f 74 goat snp14408-scaffold1572-596816 2 130163229 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795743 Affx-122927580 AX-385282696 2 6469408 CTAGGCTTGTATCTGATGCCATTTGGAAACAAACT[A/G]AAGTGTTAGCTATTCCTAAAATAGTTTTATCTATA R 2 1 2 1 101000 f 74 goat snp14407-scaffold1572-510263 2 130066629 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391413 Affx-122966770 AX-123261770 2 6503532 TCTTCACAGAAAATGGTGGCTGAAAAGAAAAGGAT[G/T]AACAGCTGGAGTAAAGTTACAATATAAGGAAAGAA K 2 1 2 1 101000 f 74 goat snp14406-scaffold1572-476139 2 130031994 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392848 Affx-122965765 AX-123263205 2 6532834 ATCTCTTCCAGCTCTATCATACTAGAATTCCTCAG[A/G]ATGTTGATGGATGGAGGCTCATCCTGCTAATATAA R 2 1 2 1 201000 f 74 goat snp14405-scaffold1572-446837 2 130002813 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443430 Affx-122927366 AX-123313767 2 6616297 TACTTCTCCAGATACTTTATCCGATCCTTGGAGTT[A/G]TACTATACTGTGTTGCCAGAAAAAAAAGCAGTGAT R 2 1 2 1 101000 r 74 goat snp14404-scaffold1572-363374 2 129921528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438931 Affx-122930419 AX-123309268 2 6669096 GTTTTTTGTCTTTAAATTCTCATTACACCTACAGC[A/G]CTTTGTTGTTATTTAGTCATTAAGTTGTGTCTGAC R 2 1 2 1 201000 f 74 goat snp14403-scaffold1572-310575 2 129868770 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438530 Affx-122931196 AX-123308868 2 6699059 AATGATACCAAGTAGCCCTAAAGTATTACTTCAAG[C/T]GACACAGGAGCTACAGCAACTGAGGGGAAAGATAA Y 2 1 2 1 101000 f 74 goat snp14402-scaffold1572-280612 2 129833950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse392 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38399272 Affx-122960555 AX-123269627 2 6732389 CAGCTACCTAGCCAAGCACAGACTCAGAAGCTGGC[A/G]TTTATTTGGGGCGTGAAGGAGTAACGTGTGGCCGG R 2 1 2 1 101000 r 74 goat snp14401-scaffold1572-247282 2 129800081 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432605 Affx-122935501 AX-123302946 2 6761737 GAGTCTCATTTTATCCTGAGTCATCCAAAATTACT[A/G]CAATCCACAGAACAACATTTGATTGTCCGCTGCAC R 2 1 2 1 201000 f 74 goat snp14400-scaffold1572-217934 2 129770781 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413806 Affx-122949901 AX-123284155 2 6815851 GTCTCCAAGAAAGTGCATGAATGGTTAAGGCAAAG[C/T]ATGCCGCTGGTATTGGCATGCTGCAAAATGACTTG Y 2 1 2 1 101000 f 74 goat snp14399-scaffold1572-163820 2 129718047 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse393 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38423628 Affx-122942368 AX-123293974 2 6860840 ATCTCTCAAGTGGCTTTTATATACTGAAAGCTCAC[A/G]CATTCATATCTATAGTCCAGACCTAGGATAGCCAA R 2 1 2 1 101000 r 74 goat snp14398-scaffold1572-118831 2 129672023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436762 Affx-122932279 AX-123307100 2 6890467 TTTGTCTGACACTATTTAGCCCCCAGCTTTTATTC[A/G]TCCTTATAACAACACCTCCTTAGCCCAAGTTTGGA R 2 1 2 1 201000 r 74 goat snp14397-scaffold1572-89204 2 129642335 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse394 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468273836 Affx-1111833848 AX-515586065 2 6920977 CCTACTGCAG[A/G]GATCACTGCCTACCTTCCATTATTTGTGCCTATTC R 2 1 2 1 101000 r 74 goat GoatD01.007141 2 6920977 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320776701 Affx-122963986 AX-385263827 2 6923032 AAACTGTGGAAGAATTCACGGAAGTCCTGCTTGTT[A/G]CCATATGGCATAAGTCAAATACTGGAAAGTGGCAG R 2 1 2 1 101000 f 74 goat snp14396-scaffold1572-56639 2 129609623 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791764 Affx-122976923 AX-385278755 2 6975646 ATTATTAGCAGCTAAGAGAGTGGCTAAATTATTTT[C/T]ATATTTTTTGTTATCATTGGAACATTATTCACTGA Y 2 1 2 1 201000 r 74 goat snp14395-scaffold1572-4025 2 129556696 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450055 Affx-122922818 AX-123320390 2 7081216 GGGGTAGGGATGAGGTGGGGGCAGCAGGGAAGTTT[A/G]TATAACTATATTCTTCTTGTCCCTGGGCCATCCTT R 2 1 2 1 101000 r 74 goat snp12485-scaffold1478-361135 2 129451522 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse395 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38400497 Affx-122961284 AX-123270852 2 7125710 GTGAGCTGAACTATATATGCTGTTACTGGCCAGAC[A/G]TTGGGACAGGAATAGCTAGATTTAGAAAAAAAAAT R 2 1 2 1 103000 f 74 goat snp12484-scaffold1478-316641 2 129406161 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse396 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38379132 Affx-122976738 AX-123249491 2 7177958 ATCTTGAGTTCTTACACATTAAGGAAAAGGCCATA[C/T]ACAAAAGAAAAAAAATTCTGAAAAGGCTAATAATC Y 2 1 2 1 103000 f 74 goat snp12483-scaffold1478-264393 2 129354308 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse397 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38443828 Affx-122927541 AX-123314165 2 7236823 GGTATGTCCTGGTTTAAAGAAACAATATTTTTACC[A/G]TCAGTGAAATCACTGAAGTAATAAACAGTTTTTAC R 2 1 2 1 101000 f 74 goat snp12482-scaffold1478-205528 2 129294879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse398 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38449630 Affx-122923190 AX-123319965 2 7270442 TAATCAAAAGAGTATTTCTCTTCCTTATAACATTT[A/G]TAAAACTGTATTTCTTTCCATGTTGCCAAACAAGG R 2 1 2 1 103000 r 74 goat snp12481-scaffold1478-171909 2 129261508 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788132 Affx-122949264 AX-385275152 2 7312610 ATTTCTATATAAGTATGTATGTAACTAATAGTTGC[A/G]TATTCATTATCTTGAGTTAAAGAGAGAAGCATTCT R 2 1 2 1 201000 f 74 goat snp12480-scaffold1478-129741 2 129220004 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse399 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320776479 Affx-122972832 AX-385263606 2 7361654 GTGATGTTCTGGGAGGCTTCTTTTGATAAAAGGCG[C/T]AAGAAGGTCATCTGAGTAATGGCTGCATTAGGTGA Y 2 1 2 1 101000 f 74 goat snp12479-scaffold1478-80697 2 129170679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse400 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320771508 Affx-122936476 AX-385258666 2 7404620 TAATTTCCAATGGCAAATTCTTCCCACTGGATTGA[G/T]AGTTGGTCATAATATTTGCTTGGAGTGATGCCTCA K 2 1 2 1 101000 f 74 goat snp12478-scaffold1478-37731 2 129127940 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse401 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320771226 Affx-122945547 AX-385258384 2 7441725 AAAATCTAACCTATTATTGAGTCATTTTAATTGTT[A/G]CAGTTAAAGCAGAAAATTGGGATGATCCCTTGGGG R 2 1 2 1 101000 r 74 goat snp12477-scaffold1478-626 2 129090917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431728 Affx-122936750 AX-123302069 2 7442917 TCTCCTCATTGTACGCAGATGCTTTACTGTCTGAG[C/T]TACCAGGGAAGTCTCATGCTTAGGGCTGTGACAGA Y 2 1 2 1 303000 r 74 goat snp23361-scaffold2337-467 2 129078196 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441125 Affx-122929589 AX-123311462 2 7485214 ATGTTTTAAAAAGTTTCACAGTCTAGCTCTAGCTC[A/G]TATTAAGGGCTGGGTCTAGCATAACTTGACTTTTC R 2 1 2 1 101000 r 74 goat snp23362-scaffold2337-42764 2 129035927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396088 Affx-122963429 AX-123266443 2 7548918 TGTGTCTCAGAGCTGTGACATTCACAAATTCTATC[A/G]CCAGTGATAATTTTTTTTTCCCCATTCCCTAACTC R 2 1 2 1 101000 f 74 goat snp23363-scaffold2337-106468 2 128970647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse402 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38447033 Affx-122924535 AX-123317369 2 7581467 GTTTGTCCACAGCAGTTATGAAAACCTAGGTATTT[A/G]TGATAACCACTATTTCTGAGTTGGTCATTGCTTTT R 2 1 2 1 101000 f 74 goat snp23364-scaffold2337-139017 2 128937631 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404701 Affx-122957264 AX-123275053 2 7618206 CCCAGTGCAAACTTTTATAATGTGCTTGGATAAGT[G/T]GATGGTGGGCATGAGACCATTAGTTTTGCTTTAGA K 2 1 2 1 101000 f 74 goat snp30384-scaffold3341-1197 2 128901152 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793830 Affx-122958082 AX-385280800 2 7658415 ACATAACAGCATTCTATTTGTGTCACTGGCAAGAA[G/T]CCCTACTTGACTTCAAGCTTACACAAATAGACAGA K 2 1 2 1 101000 f 74 goat snp30385-scaffold3341-41406 2 128860692 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450381 Affx-122922088 AX-123320716 2 7684459 CTCTCTGCCCAGTCCTGCTTCCTATAATCCTGGGC[A/G]TTATCTCTCACTAAATCTCTTACACAACTAACTTC R 2 1 2 1 101000 r 74 goat snp32359-scaffold367-2390405 2 128832750 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse403 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38432102 Affx-122936475 AX-123302443 2 7778906 TCATATGGACAAGGAAAACTGTTTGTGTATACTTG[C/T]GTATATTCTCAGAGAAAACAGAGTTTGGAATTCAA Y 2 1 2 1 101000 f 74 goat snp32357-scaffold367-2295958 2 128738034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416830 Affx-122948118 AX-123287178 2 7812010 AGAATTCATTGAGCCAAACATTTCCAGTTTGCAAG[C/T]AGCTCTATAGGCAATTTGGAACTTGCATTAGACTT Y 2 1 2 1 201000 r 74 goat snp32356-scaffold367-2262854 2 128704135 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse404 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468277163 Affx-1111835711 AX-519550669 2 7825934 GTGGAGGTGTAGGTTATAGGGTATACGTGTGTCCA[A/G]TTTTAGTAGAAATTGATCAGTTTTCCAAGTTCAGC R 2 1 2 1 101000 r 74 goat Random2.2K-162 2 7825934 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272951 Affx-1111833180 AX-519546637 2 7844574 AGGGCAGCAGGTATTAATTTGCTGAGAAGTAAGGA[A/G]ATTGGCGGGCCTGGAGGAACCCTTCCAGTGCTGAT R 2 1 2 1 101000 f 74 goat 2_7844574_AF-PAKI 2 7844574 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320764617 Affx-122975530 AX-385252259 2 7854510 ATGCACACTGAAATTACAATATGGGGGGTTGTTAT[A/G]TAGGATTAATTTGGCTTCAAACTCTCCATGAGTTT R 2 1 2 1 101000 f 74 goat snp32355-scaffold367-2220354 2 128660747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426213 Affx-122940363 AX-123296559 2 7903842 TCTGATCGCAAGGTAGACTCCTTACATAAACAGAC[G/T]CACTGATAATGCCGATTCAGGGTGGCCCTCTCATC K 2 1 2 1 101000 f 74 goat snp32354-scaffold367-2171022 2 128611465 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453482 Affx-122919837 AX-123323815 2 7961292 GCTTTCTTAATCTCTGTATTAGTATTATTCTCAGT[A/G]TTAATACCATGACTGAAAGCACAATGTTTGTAAAG R 2 1 2 1 101000 r 74 goat snp32353-scaffold367-2113572 2 128552956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397398 Affx-122962260 AX-123267753 2 8020297 CATCTTTAGTCTATAATTTGAAAAAGTGAAAAATA[C/T]AGGTCTGGCTTTACCAGTGGTCTGTATTAGAGTTA Y 2 1 2 1 102000 r 74 goat snp32352-scaffold367-2054567 2 128493546 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385873 Affx-122971604 AX-123256231 2 8050333 ATTGAGCAGATGATATAGATATCTTGGCCATTAGA[C/T]ACTAAATGCTAAATATTGTATGCAGCATTCAAAAT Y 2 1 2 1 101000 f 74 goat snp32351-scaffold367-2024531 2 128465987 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441246 Affx-122929498 AX-123311583 2 8079680 ACTAACACAACATTGTAAAGCAACTATACCCCGAT[C/T]TATAAAAGAGAAGGAAGAATGAGGAGTAGATGCTT Y 2 1 2 1 201000 r 74 goat snp32350-scaffold367-1995184 2 128436637 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441566 Affx-122928685 AX-123311903 2 8114946 TTTAGGCTGCTTAATCTACTTTTATACTTTCTTGT[A/G]TCTTTACCGAAAACTTGTTATTGCAACATACATAC R 2 1 2 1 101000 r 74 goat snp32349-scaffold367-1959918 2 128401320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388128 Affx-122969479 AX-123258486 2 8149415 ATCTCAGTATTCACACATTGGCCCAATAGGTAAGG[C/T]CCTGCTGCTTCCAAGTTTCAGACTAGCTGGGAACT Y 2 1 2 1 101000 f 74 goat snp32348-scaffold367-1925449 2 128366699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417410 Affx-122947227 AX-123287758 2 8193088 GCCAGTGCATGGTTTATCAGATTCTCTTTCTTCCT[A/G]TCACTATGACTGTCACTGTTTCTGCTAGAAGTTGC R 2 1 2 1 101000 f 74 goat snp32347-scaffold367-1881776 2 128322932 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778335 Affx-122932295 AX-385265450 2 8234709 CTGAAGGTTGGGTTGGATGTGTCAGTTTCTTAAAA[C/T]GAGACAACAGTGAAGTTCGACACGTTGACTGACTA Y 2 1 2 1 202000 r 74 goat snp32346-scaffold367-1840155 2 128280578 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405486 Affx-122956015 AX-123275838 2 8271302 TCGAGCCAGTTCCACCACGGCAGATTGAATACCAC[A/G]TGCATACAGCAAACGTAAGTGGAATGAGAGCAATC R 2 1 2 1 201000 r 74 goat snp32345-scaffold367-1803562 2 128243655 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385126 Affx-122971774 AX-123255484 2 8319728 AATCCAGGAGCACACACATTTTATCCTATAGGAAG[C/T]ACAAAAGACTGCAAAAAAGAGGATGTGAAACTGCT Y 2 1 2 1 102000 r 74 goat snp32344-scaffold367-1755136 2 128194520 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791917 Affx-122965776 AX-385278907 2 8363892 GACTGACAGAATCAGATCTCCTCTTGTAAATGATC[A/G]TGCATTTGTTATCAAAATCTTCTTTTTGTTCTCCT R 2 1 2 1 101000 f 74 goat snp32343-scaffold367-1710972 2 128150167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428705 Affx-122938471 AX-123299047 2 8394154 GGAGAAATTCAATAGGCTACCTTTCCTTAGGAACA[G/T]ATACTGGGGACAATTTCAGTGTTGTCCTCTTAACT K 2 1 2 1 101000 f 74 goat snp32342-scaffold367-1680710 2 128127436 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438622 Affx-122930922 AX-123308959 2 8446342 TTATTTCACCAAAATTAAATAGAAAAAATCCTAAA[G/T]CTCAAAAAACTGAGCAGGAGTTGTTGAAAAGGCTT K 2 1 2 1 102000 r 74 goat snp32341-scaffold367-1628522 2 128076370 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405675 Affx-122956560 AX-123276027 2 8479380 TCCCAAAGCATTATGTTAAGAAGGCAACTGAGGCC[A/G]TAACTGGAGACAGTGGAAAGAAAACACCTTGATCT R 2 1 2 1 101000 f 74 goat snp32340-scaffold367-1595484 2 128041937 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427247 Affx-122939558 AX-123297590 2 8508167 AGAAGCCAAGAAATTATTTGCATAAAAATGAATAG[A/C]TTTCCCTTCTCTTTGGTGGAAGAGAAATGACTCTT M 2 1 2 1 201000 f 74 goat snp32339-scaffold367-1566697 2 128012457 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408217 Affx-122953845 AX-123278568 2 8551307 AGCATTTGTGATCCTTAGAATTTACTTTCCTCTAC[A/G]TACCTGCCTTTGAACTGTGGTATTGGAGAAGACAC R 2 1 2 1 101000 f 74 goat snp32338-scaffold367-1523557 2 127968606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443960 Affx-122927009 AX-123314297 2 8585568 ATCATCAAAATGAATGAACTGCTATACTTTGTACA[C/T]AGCTTCTGGCAGCTTCGTTATTGACATGATTTATC Y 2 1 2 1 101000 r 74 goat snp32337-scaffold367-1489296 2 127934583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429183 Affx-122937960 AX-123299525 2 8624930 TGAATATGAACCCCATTCAGCCTTTTTGAACATTG[A/C]TGTGAGGTTGCCTTTGTCTGAAGTGCATATTCTTA M 2 1 2 1 201000 r 74 goat snp32336-scaffold367-1449934 2 127894750 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433677 Affx-122934554 AX-123304018 2 8659455 AGTATGACACAGTTTTGAATTTTCCTCTGAGCACT[A/G]CTTTAGCTCTATTCTATACAGTTTGGTATATTGCG R 2 1 2 1 201000 r 74 goat snp32335-scaffold367-1415409 2 127858924 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425854 Affx-122940659 AX-123296200 2 8697046 ATCAAAGTTATTATTCTTGTCATTTTCTCATCTTC[C/T]GCATCTCTCCAAATACTTATATTAATATATTTTAG Y 2 1 2 1 101000 f 74 goat snp32334-scaffold367-1377818 2 127821438 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410950 Affx-122952034 AX-123281300 2 8743010 ACATATACTCAAATATATGTGTGGAACTGAGGTTC[A/G]TGGAACTAAGTATCTGTGTGTGTGGTGCAGGAAAA R 2 1 2 1 201000 f 74 goat snp32333-scaffold367-1331854 2 127775131 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277049 Affx-1111835718 AX-519550556 2 8754453 GAGGGGCCATGGAGGACCTCTCTCATGGACCTCGT[A/G]CCTGCCCAGGCCCAGCCTAGTATGCAGCAGCATTC R 2 1 2 1 202000 f 74 goat Random2.2K-163 2 8754453 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778521 Affx-122934691 AX-385265633 2 8797993 TGCTGGGTAAATACAGAGAAAATCTAGTTGTTATT[A/C]TCCACAGAGAATCTCTAAAATGACTAAAGTAGTCC M 2 1 2 1 101000 f 74 goat snp32332-scaffold367-1276871 2 127719723 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274343 Affx-1111834146 AX-519547938 2 8839041 GCATGCATACATGTGA[A/C]GAGTCGGCTGCAGGACAAGACTGGAAACAAGCAGT M 2 1 2 1 102000 r 74 goat GoatD01.021443 2 8839041 G T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320793301 Affx-122974918 AX-385280279 2 8858042 CTTTTATATCAATTTCTAACCACTTGAACTTCAAT[A/G]TCTATGGTAGTACCCATATACCAAGACCCTTAATG R 2 1 2 1 101000 r 74 goat snp32331-scaffold367-1216822 2 127659675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395819 Affx-122963637 AX-123266174 2 8911065 TAGTGCTTATACTTATTATTATGTAAATATTTCCG[C/T]GTCACTCTATCCATATATATGCGTAGGGGTTTTGG Y 2 1 2 1 101000 r 74 goat snp32330-scaffold367-1163799 2 127607931 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791758 Affx-122925666 AX-385278749 2 8972537 CAGTTAGCTCTAAACATATGTAATAAAGTAAACAG[C/T]GATTCCTCATCCCTCAGACTTCCACATCCAGCTTT Y 2 1 2 1 101000 r 74 goat snp32329-scaffold367-1102327 2 127545933 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444267 Affx-122926778 AX-123314604 2 9014226 AGTATACAGTGTCATTTTCCCCCAGTAAAGGAAAC[A/G]CAGGAACTATCTTAATAGGATTATGTTGAGGAATA R 2 1 2 1 201000 r 74 goat snp32328-scaffold367-1060638 2 127504003 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406808 Affx-122955691 AX-123277159 2 9052981 GTGGTACAGACAGAATCCTGTGGTAGGCAGAATAA[C/T]GAGCCTCCAAAGATTCCCATATATAATCCCCAGAA Y 2 1 2 1 202000 r 74 goat snp32327-scaffold367-1021883 2 127464085 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416826 Affx-122948122 AX-123287174 2 9107165 TTGCTGATAATTTGACATTTTCTATTGTCATTTAT[A/G]GCTGAGACTTGATAGTTTGTCTGGTAGAATGCTGA R 2 1 2 1 101000 r 74 goat snp32326-scaffold367-967699 2 127409679 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780954 Affx-122954763 AX-385268041 2 9171721 ATTCAAAATGATGTGAGGCAGAATATTATCATATA[C/T]GATTTTAATCAAACCAGGAGACTAATTGGATCCAT Y 2 1 2 1 101000 r 74 goat snp32324-scaffold367-903143 2 127344546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776910 Affx-122927242 AX-385264034 2 9202260 GGTGAATATTCTTGTAACTAGAATGTGATCAAGTG[A/C]TGACATAGAAATATGGTTACTTCACAAGAAATTTT M 2 1 2 1 101000 f 74 goat snp32323-scaffold367-872604 2 127313560 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435265 Affx-122934057 AX-123305605 2 9240831 GTTTGCACACTTCTTTTAAAGTATCCCTGAGGTTT[A/G]CACCTGAAAGGATGTTTGTTTGTAAAAAGGAGGGG R 2 1 2 1 101000 r 74 goat snp32322-scaffold367-834033 2 127271173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796514 Affx-122963939 AX-385283462 2 9280023 GTCTCTATGTTTCCAGTGTAAAATCTCTATAACTT[A/C]TCAGTGGAAAAAAGGAATGTGTACTCAGTACTTGA M 2 1 2 1 101000 f 74 goat snp32321-scaffold367-794841 2 127233928 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444039 Affx-122926875 AX-123314376 2 9315663 ATTAAAGATTTATCTTTTGCTCACAGTACATTCCT[A/G]CCTTTTTTGTTATAGATTAGTTGATCATGTAAATG R 2 1 2 1 101000 f 74 goat snp32320-scaffold367-759201 2 127197718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430703 Affx-122936911 AX-123301044 2 9352731 CTTGTGTCTTTCTTTAGAACTTAACCATCACACTA[C/T]GGTTATGTTTTAAATTTGTGGCAAATGGCAACATG Y 2 1 2 1 101000 f 74 goat snp32319-scaffold367-722133 2 127160014 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776345 Affx-122929519 AX-385263473 2 9409673 TGATGTAGGATTCCTCTAATATCCATAGGATATAC[C/T]AATATTTGATCAAATTTGGGCCACGATACAAATCT Y 2 1 2 1 201000 r 74 goat snp32318-scaffold367-665191 2 127102303 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438937 Affx-122930415 AX-123309274 2 9452580 GGGGTTTCCAATCAGGAGAGAAAAGATATTTTGTC[A/G]AATTCAAAAGAACTTGATTTATGAGACATGGACAT R 2 1 2 1 201000 r 74 goat snp32317-scaffold367-622284 2 127058786 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795806 Affx-122960454 AX-385282759 2 9491535 TTAGCAACTTGAAGATTTTTAGCACAGCAGCCAAG[C/T]AAAGATCACATCCATATATTTGATACATAAAAGAC Y 2 1 2 1 101000 f 74 goat snp32316-scaffold367-583329 2 127020034 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440202 Affx-122930698 AX-123310539 2 9522671 TAGGAAGTTCCAGCGTGGCTTCAACCACTACGAGG[C/T]ATGACTCGAGGTAAATAAGAACTTCTCTAGGAATA Y 2 1 2 1 201000 r 74 goat snp32315-scaffold367-552193 2 126988708 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406969 Affx-122955053 AX-123277320 2 9578428 TCCTTTACAACTTTTGTTCATCTTCTGGCTTTGAC[G/T]AGTGTGGTGTTTTTTATTTATACATGGGTTTTTCA K 2 1 2 1 101000 f 74 goat snp32314-scaffold367-496436 2 126933301 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802873 Affx-122958315 AX-385289771 2 9610581 GACCCCTGTAAAACATTTAGAAACGAAACTGTATT[A/C]CTCTTGTGAAATGTTACTATTATATTCTCCACTGC M 2 1 2 1 101000 f 74 goat snp32313-scaffold367-464283 2 126902269 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379859 Affx-122975797 AX-123250217 2 9643635 CCTTCCTCTCCCTGTTCCATTCATCTAGAAGCTAC[A/G]TGCTAACTACCCTTAGTAAACCCTGGCAAAACACT R 2 1 2 1 101000 r 74 goat snp32312-scaffold367-431229 2 126869525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798096 Affx-122968917 AX-385285031 2 9681041 TTTTTTTTTTTCTCAACTAGGTTTCTATATCATAA[C/T]GCTTGAGGGGCTAATTTAAAATTAAACATTTGCCA Y 2 1 2 1 102000 r 74 goat snp32311-scaffold367-393823 2 126831472 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387793 Affx-122969699 AX-123258151 2 9716637 GTAGTTGATTGTCTTTGGTATGACTTGTATAGTTA[C/T]GTCAAAGTTCTTCTAATAATCCTGACCTTTTCCCC Y 2 1 2 1 101000 r 74 goat snp32310-scaffold367-358227 2 126795606 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793949 Affx-122937180 AX-385280918 2 9751656 CAGAAAGAACTTTGGGGAATACAGAAAGTATTTAA[C/T]AGTTAATTATCTTATAATTTAGTAGCTGGAAAATT Y 2 1 2 1 101000 f 74 goat snp32309-scaffold367-323208 2 126760563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393946 Affx-122965065 AX-123264301 2 9781755 TGCCCCTGCATTAGGTAAGCCCTTGTGACTTTTGC[G/T]AGCCAGTGAAACATGAGCAGCAGTGTAGGTGGAAG K 2 1 2 1 101000 f 74 goat snp32308-scaffold367-293109 2 126730371 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424113 Affx-122942022 AX-123294459 2 9811038 TGTCCCAGTTCAACAATAAATTACATGATTAGCTA[C/T]AGTTGACTGGCTGACACATCTCTTACATTTCCTGG Y 2 1 2 1 101000 r 74 goat snp32307-scaffold367-263826 2 126701201 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797080 Affx-122968337 AX-385284020 2 9840527 TAGATGTCTTTCTGCAAGGACCAAAGGGCATCCTC[C/T]AGTCGTTCCACCTTTTTCTGCCCTGTTTTTTTTCC Y 2 1 2 1 101000 f 74 goat snp32306-scaffold367-234337 2 126671339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797377 Affx-122937159 AX-385284316 2 9893647 CATTTTTAATTTCTCATATTTAAAAACCAGTCTTT[G/T]GATCCCATTTACAAAGACTAAATGGCAGCAAATCC K 2 1 2 1 202000 f 74 goat snp32305-scaffold367-181217 2 126618270 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790769 Affx-122971553 AX-385277770 2 9922741 AAGTATGTTTGCAGATGCTTATTTCCCATAATTAA[C/T]GTTTTTACGTATTTTAATTTACACTAGAACTGTAA Y 2 1 2 1 101000 f 74 goat snp32304-scaffold367-152123 2 126589289 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791082 Affx-122929983 AX-385278077 2 9996677 CTAAACTGCATTTCCTTCATAATCTCATGTTTAAA[C/T]ATTATTTACTTTTATGACCACTCCCTATTAGATGT Y 2 1 2 1 101000 r 74 goat snp32303-scaffold367-78187 2 126513704 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798302 Affx-122964372 AX-385285237 2 10088461 GTGGCAGAATCATTTGCATGAATTGGCTTTGGTCT[A/G]TCTGTAATTTAATTCATCTGTTCTGCTTTTCAGTG R 2 1 2 1 101000 f 74 goat snp20609-scaffold203-13498 2 126406723 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413821 Affx-122949890 AX-123284170 2 10139425 GAAAATTACATGTTGATGGATTGGTCCTCTACAAG[C/T]TCAGCTTCATTTGAACTTTCAGTACCCTTTATCTG Y 2 1 2 1 101000 f 74 goat snp20610-scaffold203-64462 2 126356623 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764572 Affx-122966469 AX-385252227 2 10198377 CTTAATCACCTGGCTACTTATTTTCTAGTGTCTGT[A/C]GTATATAGGGATTTCAAAAAAAGCTATTGAATTTA M 2 1 2 1 102000 f 74 goat snp20611-scaffold203-123414 2 126300578 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421964 Affx-122943807 AX-123292311 2 10226914 TCATTTGCAGGTAATCACTTCATTGTGACTGCACA[C/T]GAGAATTCTTGGAGTACTTTAAAAAAAATACCAGT Y 2 1 2 1 101000 f 74 goat snp20612-scaffold203-151951 2 126272265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410085 Affx-122952843 AX-123280435 2 10284408 GTATTTACATTTAGGTCTTTAGACTGAATTTTCAA[C/T]GTTGTGACTTTATTCTTTTCTATAGAGAGTTAGTT Y 2 1 2 1 202000 f 74 goat snp20613-scaffold203-209445 2 126213162 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426201 Affx-122940373 AX-123296547 2 10331892 TTACTTTGGAACTACCTGAGCATAATCTTGGGAGA[C/T]GCATTATTGTAAAATTCTTTGGGTGGAATTGGTTT Y 2 1 2 1 101000 f 74 goat snp20614-scaffold203-256929 2 126165777 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791212 Affx-122973254 AX-385278206 2 10371625 TGGACACAAGAGGCTTAACTAAGAGTGAAGTTTTG[C/T]ACATATAAGTTTACTCTTCATCCAAAATAGGGAAA Y 2 1 2 1 101000 f 74 goat snp20615-scaffold203-296662 2 126125981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277064 Affx-1111835725 AX-519550571 2 10404168 ATTTGCTATATAATACTCCACTAAGTTGATCTAGT[A/G]AATTTTATGTAAGCATTCCTTCTAGATTGTTCTAT R 2 1 2 1 101000 f 74 goat Random2.2K-164 2 10404168 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376014 Affx-122978406 AX-123246373 2 10450322 GGAGGTCTTCTAGATTTCACACTTTGCCCTGTATA[C/T]GTAGTTGATCATCTTCTGCCATCCTGTGACTTCCT Y 2 1 2 1 101000 f 74 goat snp20617-scaffold203-375359 2 126046961 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383776 Affx-122973206 AX-123254134 2 10535534 TCTTGAGAGAATAGGGACAAAACTTTACTGAGAAG[C/T]ACAAACCTTGAAGGATCATTCAGACCATTGTGAGA Y 2 1 2 1 101000 f 74 goat snp20619-scaffold203-460571 2 125960704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464112637 Affx-1110318147 AX-515588612 2 10555813 AAGGTGGGATCTGTCCAAGATTTCCTCACTAGTGC[C/T]CCCTAATGTTAATTCCATATTGACTGTTTAAAGGT Y 2 1 2 1 201000 r 74 goat 2_10555813_AF-PAKI 2 10555813 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789964 Affx-122949823 AX-385276970 2 10566734 TGGGCCTGGTGTAACACACTCTATAACATATTCTA[C/T]GGAAGGGGTTCCCAAAACTTGCTCTCAGAAGCTTA Y 2 1 2 1 102000 r 74 goat snp20620-scaffold203-491771 2 125930651 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383972 Affx-122972937 AX-123254330 2 10599262 GAGACTGTGTAAAGATCTTATTCTCAGCATTGGCT[A/G]CACAGTAGAATTATCTATGAAAAAAAATTAATATG R 2 1 2 1 101000 f 74 goat snp20621-scaffold203-524299 2 125894120 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792725 Affx-122970223 AX-385279705 2 10633795 GAATATTCACATTTGATTCCACCTGGCTTGGTTCA[C/T]GAAAGATGATGCCATCTTGCTTACAGTTTTCCAGT Y 2 1 2 1 101000 r 74 goat snp20622-scaffold203-558832 2 125859788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380721 Affx-122975147 AX-123251079 2 10665796 ACGGCAGACAAGGATACACAAGAAAAAAAGAACTG[C/T]AGGCAAATATCCTGATGAAAGTGAAAGTCACTCAG Y 2 1 2 1 101000 r 74 goat snp20623-scaffold203-590833 2 125826093 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438739 Affx-122930832 AX-123309076 2 10701900 AGAAAAAAGCGAAATTAGGGAATGTGGATAAGATG[A/G]TAGAGAAGGGAGACCCCAGGCTTCCTTCCTTGATC R 2 1 2 1 201000 f 74 goat snp20624-scaffold203-626937 2 125789374 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797997 Affx-122944808 AX-385284933 2 10741595 GCAATGATGGTACACGAGACAAAGAAGTACATACT[A/G]TAAAGGGATCAATCTAACAAAGACATAACAATTAT R 2 1 2 1 101000 f 74 goat snp20625-scaffold203-666632 2 125749572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777144 Affx-122938306 AX-385264267 2 10780857 ACGTGCCCTGGACACATATCAGAGAATCTCAGTTT[A/G]CCATTCTTTAGTTACATATCTTGAATATATTTTGA R 2 1 2 1 101000 f 74 goat snp38134-scaffold477-23223 2 125295495 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792514 Affx-122973519 AX-385279495 2 10850108 GGAACATAGAATAGGCAATGAAAGAAGACAGCCAC[A/G]GTTACTCTCCGAAGCCTCAGGAATTGTACGAAGGT R 2 1 2 1 101000 r 74 goat snp38135-scaffold477-92474 2 125226552 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403786 Affx-122957980 AX-123274138 2 10881635 CTGTGGCCCATTATCATTAATTTTCTTGGAATTGA[C/T]GAAAATTCTTTCAACTCAATTTCCCAGATACCGAT Y 2 1 2 1 101000 f 74 goat snp38136-scaffold477-124001 2 125194906 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433931 Affx-122934295 AX-123304272 2 10921940 TCTATGGTTCAGTTCCCCAAAGTGCAAAGCAGAGA[C/T]AATAATAACAGCTATTCAATTGTTTTAAGACTTCA Y 2 1 2 1 201000 r 74 goat snp38137-scaffold477-164306 2 125153768 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788387 Affx-122959723 AX-385275405 2 10966886 AAGAACAATTATTGAAAAACAAGTTTGATGTTTGG[C/T]AGATACAAAATTTATGTAATAGAACTTCATCGTTA Y 2 1 2 1 101000 f 74 goat snp38138-scaffold477-209252 2 125108100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431093 Affx-122936616 AX-123301434 2 11007018 ACATGAAAAAGTAGAAACTAAGGTAGAACTGGACA[C/T]GGAACATCAGACTGGTTCCAAATAGGAAAAGGAGT Y 2 1 2 1 103000 f 74 goat snp38139-scaffold477-249384 2 125067794 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787003 Affx-122955229 AX-385274031 2 11038227 GAAATCAAATCCATGGTATGGAGAAAGAGAAACAG[C/T]GACTTGAAGATGTTGTTTCTAACAATAATCATAGT Y 2 1 2 1 101000 f 74 goat snp38140-scaffold477-280593 2 125035805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765652 Affx-122948891 AX-385253119 2 11073581 GTCCATTCTTAGGGCCATTGTACCTAAATTAACAA[C/T]ATTTTCCTGCACATATACTTCCACAGTATTCCTAT Y 2 1 2 1 101000 f 74 goat snp38141-scaffold477-315947 2 125000258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412074 Affx-122951698 AX-123282424 2 11118209 CCTCAAATATACTATTTCCCTGAAGAAATGCACAT[A/G]CATACACATGCACACACCTCCTTTTCCCTTTCTCA R 2 1 2 1 303000 f 74 goat snp38142-scaffold477-360575 2 124955059 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771077 Affx-122925769 AX-385258237 2 11149852 AGAATATAATTAATACCGTCTACTTCCCATGGTAT[C/T]CTCTCAGCATCTTATGGCACTTCCTTCTACCAAAG Y 2 1 2 1 101000 r 74 goat snp38143-scaffold477-392218 2 124923022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407345 Affx-122955286 AX-123277696 2 11194776 AGGTGGAATGTAACAGAATGTTCCCCAATATGCAA[C/T]ACTGGCAGTAGTGAGAGGAGGAGGAAAAATAAAAA Y 2 1 2 1 101000 f 74 goat snp38144-scaffold477-437142 2 124876410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769138 Affx-122970570 AX-385256313 2 11249300 TTTATTAAATCACAGAATCTTTCATAAAAACCTAT[C/T]GACACCTTTAGGGACTAGTAACCAGAGTGATAGGC Y 2 1 2 1 101000 r 74 goat snp38145-scaffold477-491666 2 124821928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783430 Affx-122952996 AX-385270493 2 11284903 GTACACTGTATGGTATCTTAACTTCATTAAGAATA[C/T]GGAGCTGGAAAGGTCCTCATGATAATCTAAGTGAA Y 2 1 2 1 101000 r 74 goat snp38146-scaffold477-527269 2 124785838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771616 Affx-122974213 AX-385258774 2 11313776 ACATATAAGCACAGACCTGATGAAGCTGATAAACT[A/C]TAATTTCATCATTAATTACAGTTTATGTAACTTTT M 2 1 2 1 201000 r 74 goat snp38147-scaffold477-556142 2 124756936 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425368 Affx-122941574 AX-123295714 2 11350192 AAGACTGTCTTCAATGCTTAAAACTCAATATAGAA[C/T]ACATTTCCAAAACTGTATTGAGCCACTTGGATGAC Y 2 1 2 1 103000 r 74 goat snp38148-scaffold477-592558 2 124720482 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439548 Affx-122930102 AX-123309885 2 11400822 AAGGAACATGTGATTTAACTGTACTTTTAAAAGAT[A/G]TCATCCTTATAGTAAGTTTTCTGAGACTTAATCAT R 2 1 2 1 101000 r 74 goat snp38149-scaffold477-643188 2 124669062 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447846 Affx-122923898 AX-123318182 2 11485925 CTCCTTACATGGAAATTGCTCTGTACATGTTTATT[A/G]TTGGGTACAGGAAATATTTCAAAATAAATAAACAT R 2 1 2 1 103000 f 74 goat snp38151-scaffold477-728291 2 124583779 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446326 Affx-122925628 AX-123316662 2 11525983 TTTCACAGGCTAAATATAATTTAATTTGTACCCTG[C/T]ATTTCTTACATCTAATTTTTAAAATACTTCTCTTT Y 2 1 2 1 103000 f 74 goat snp38152-scaffold477-768349 2 124545216 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784952 Affx-122933003 AX-385271999 2 11576444 TTTACCAAAAGGAATAACATTAAGATATCTTATTG[C/T]AAGTCAGGGAAAAGATGATCAATTATTACATTCCC Y 2 1 2 1 101000 r 74 goat snp38153-scaffold477-818810 2 124494451 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769145 Affx-122946135 AX-385256320 2 11612200 AGCATTTATATGTTCCTGTCAGTTTATAGCTCCAG[A/C]GTTTTTTTTTCTCCAAGTAAGCAGATCTCAGTTGT M 2 1 2 1 101000 r 74 goat snp38154-scaffold477-854566 2 124460462 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789805 Affx-122956218 AX-385276812 2 11619032 AAGTAATTGAATGGAGGTACACATAGTTTTATAGG[C/T]GGATATTTGAGTATGATGATTTTTTATAATAGTAT Y 2 1 2 1 101000 f 74 goat snp35278-scaffold422-2805090 2 124091544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415755 Affx-122948934 AX-123286104 2 11651262 AAAATTCATGTTTAAAATACAGAGCTTTAGTGTTT[C/T]ATAAATAGCCAGTGGTGTACAAGTAAGTTCAATTC Y 2 1 2 1 101000 r 74 goat snp35277-scaffold422-2772860 2 124058527 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797128 Affx-122922243 AX-385284068 2 11704450 TACTTTTTGTATAAAAAACTTACCAAGAATTGATA[C/T]ACTTATATTGCATGGCAGCAGCAGCACCCTAAAGT Y 2 1 2 1 102000 r 74 goat snp35276-scaffold422-2719672 2 124005988 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383091 Affx-122973730 AX-123253449 2 11737631 ATTTTTATCAAGTGAAATCTGTGCATGTATGGTTT[A/G]CTACATAATCCTGCATATAAGTACAAAGATCGTAT R 2 1 2 1 102000 r 74 goat snp35275-scaffold422-2686491 2 123971307 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439909 Affx-122930020 AX-123310246 2 11776715 GAAATGTGTAGCCACTGTAGTCAGAATAAGGACCT[C/T]GGGGTTGGGTAAAATGAAGTATTTCCTTATAATAA Y 2 1 2 1 201000 f 74 goat snp35274-scaffold422-2647407 2 123933366 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420288 Affx-122945038 AX-123290636 2 11857269 AAGAATACATAAAAAATTCATTATTTTTTGCTTCC[A/G]TTCAACACAAATGTAATAACTTCTAGGTTATTATT R 2 1 2 1 103000 r 74 goat snp35273-scaffold422-2566853 2 123850676 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779203 Affx-122973986 AX-385266307 2 11915280 GTGTCCTCTTGTGTAGACATTGTGATGGAATACCC[A/G]TATCTTCCTCCAGAAATCAGGCAGTTGTTACTCCA R 2 1 2 1 101000 r 74 goat snp35272-scaffold422-2508842 2 123792265 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804435 Affx-986696602 AX-385291017 2 11946563 AGAAGGGAGGGGAAGACAGAGGCCCAGCCAGGGCG[A/G]GAGAAACACTTGTGGTCACACAGCACGTCTCCCGT R 2 1 2 1 600010 r 74 goat 2_11946563 2 11946563 Ancestral_priority_1043 ancestry 0.64 recommended IMAGE 10K 10K ancestral 320803896 Affx-986696568 AX-385290610 2 11946590 CCAGGGCGGGAGAAACACTTGTGGTCACACAGCAC[A/G]TCTCCCGTCCCAGGGACAGAGTGGGGGTCCAGGGC R 2 1 2 1 600010 f 74 goat 2_11946590 2 11946590 Ancestral_priority_1043 ancestry 0.536 neutral IMAGE 10K 10K ancestral 38388665 Affx-122969101 AX-123259023 2 11951138 TATATTAGTATATATAAAATTGTATGTACATAGCT[A/G]TATTTGCTATTGTCTTAATGCCTGCTGATCTTTTC R 2 1 2 1 101000 r 74 goat snp35271-scaffold422-2472984 2 123756825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410531 Affx-122952164 AX-123280881 2 11983265 TTCAGACCTTCACTAGAGAAATAGTGAAATTAACT[A/G]TCATAAAGACATGACCCAACTTCAACAATTACAAA R 2 1 2 1 101000 r 74 goat snp35270-scaffold422-2440857 2 123724414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801181 Affx-122963816 AX-385288094 2 12016946 CATTCCTTTTATGGTGAATAACCATATTTTAAACA[C/T]AATTTTCATTGCATTGAGTTAAAAGGTCAGGTGAT Y 2 1 2 1 101000 r 74 goat snp35269-scaffold422-2407176 2 123690593 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603205 Affx-1002479400 AX-413837390 2 12045678 ATTTCGCCTGGGGCATGTCATGGGGGATTGTTGCC[A/G]TTTGAATGCTGTGGTTCCATCCTTTAGGGCCCTCC R 2 1 2 1 101000 r 74 goat 2_12045678_RH-map 2 12045678 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320786468 Affx-122948896 AX-385273502 2 12059257 ATATTAAAGGGACACTAGAACTTGAGAGAAATACA[A/G]TGACCTTCCCAAAGCCACATGGTTGCCAAATGGTG R 2 1 2 1 102000 r 74 goat snp35268-scaffold422-2364865 2 123649091 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603114 Affx-1002479401 AX-413837309 2 12072547 AATTACTTCTCTGGCACTGGTTGTCGAGAGTGAGC[C/T]GGTCCATTTTTCTCTTTTATTACTACTGAATTTCA Y 2 1 2 1 102000 f 74 goat 2_12072547_RH-map 2 12072547 C T 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603116 Affx-1002479402 AX-413837311 2 12088359 TCGAGGCATTCCACCCAGCTAATTGGCTAAAGAAG[A/T]GGCAGAGGTGGAGGGTTGCAAGAGGGTTCAGAATC W 4 1 2 1 102000 f 74 goat 2_12088359_RH-map 2 12088359 T A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38400907 Affx-122959737 AX-123271260 2 12089124 GTTCACTGCCCCAAATTTCACTGAGCCATGAGTGG[A/G]TGTAGGAGAGGTGCAGAGGATCAAGCAAACCAGTA R 2 1 2 1 201000 r 74 goat snp35267-scaffold422-2334998 2 123619112 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776456 Affx-122953231 AX-385263583 2 12122560 TGCTGAATTGAAGTGACCAGACATAATAGACTATA[C/T]GATAAACAAAAATTTCTAGTATGGAAGAGGCAAAA Y 2 1 2 1 201000 r 74 goat snp35266-scaffold422-2301562 2 123585520 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603118 Affx-1002479403 AX-413837313 2 12136097 GACAGCAGAGACCCTGAAAGGCTTTGAGGACTTTG[C/T]CTGTCAGGGAGAAGCATCCTCAGGAAGTCTGGGCT Y 2 1 2 1 102000 f 74 goat 2_12136097_RH-map 2 12136097 T C 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38449811 Affx-122922409 AX-123320146 2 12152671 GTAGTTGATGTTCTTGGAGTCACTGCTACAGCAAA[G/T]CACTTGATAAGAAAGGAAAGAATTAAACCAAAGCT K 2 1 2 1 101000 f 74 goat snp35265-scaffold422-2271451 2 123554880 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277087 Affx-1111835735 AX-519550594 2 12184609 CCACTCTCAGGGTTAAGAGATGACTGGAGTGGGAT[A/G]CCTTGGTTTCCCCTAGGTAGGTAGATAACGTGTCT R 2 1 2 1 201000 f 74 goat Random2.2K-166 2 12184609 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789560 Affx-122948199 AX-385276569 2 12205856 GAAAAATGGGGTAAAGGGTTAATGATACTGCTCTG[C/T]ATTTGCATGTTATATGAAGACTATACACTGCAGAT Y 2 1 2 1 101000 f 74 goat snp35264-scaffold422-2218266 2 123501327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789589 Affx-122946281 AX-385276598 2 12235357 CCTGAAGTTAAATGTTCAAGTAAATTAACAATCCT[A/G]TTGTTTTTCTCCAAGCAGGCACCTATCTTTCCTAG R 2 1 2 1 101000 r 74 goat snp35263-scaffold422-2188765 2 123471696 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603120 Affx-1002479404 AX-413837315 2 12258123 ACTGAAATTTGAATTTCCTATAAAGGTCACATCAT[A/G]AAATAATATTCTCTTAATTATTCTTTCAATCATTT R 2 1 2 1 101000 f 74 goat 2_12258123_RH-map 2 12258123 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38416012 Affx-122948382 AX-123286361 2 12269075 AAATTGTTCAAGAAGAGTGAGTGAAGAAAACAACA[C/T]AAATCTGGGAAAACCTGGCATGTTAGAACAGGAAG Y 2 1 2 1 201000 f 74 goat snp35262-scaffold422-2155047 2 123437327 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377640 Affx-122977869 AX-123247999 2 12303237 TCAAGGTAATAACCTATAAATGAGAAAAGGGTTAA[A/C]CATCATATTTGAAGTCAACATGGGGGTCTCTGAGG M 2 1 2 1 201000 f 74 goat snp35261-scaffold422-2120885 2 123403908 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425526 Affx-122941460 AX-123295872 2 12340491 AGAGCAAAATAAAAATAGTTTAAGTTCACTGGAAG[C/T]CCCTCCAGGCAGCTTCCACATCCTTTGGTGACCGC Y 2 1 2 1 303000 f 74 goat snp35260-scaffold422-2083631 2 123366371 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375394 Affx-122979212 AX-123245753 2 12387543 CACTAAATGTTTCTCTGAAATTCAAATTTAACTCC[A/G]TGCCTTCTATTTTATCAGGAAACCCTGGGATTAAA R 2 1 2 1 101000 r 74 goat snp35259-scaffold422-2036579 2 123318510 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789694 Affx-122970479 AX-385276702 2 12423729 TTGTTTCACATACCTAAATATCTTCATCCCTATGA[A/C]TCATGTAGAAGAACACAAGAATACGGAACACACCA M 2 1 2 1 101000 r 74 goat snp35258-scaffold422-2000393 2 123282206 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603122 Affx-1002479405 AX-413837316 2 12437740 CTGGACACAGGCATGAGATTGCAAGTCCTGTCCTC[A/G]GGCACCTGACCCACCTCCAGGGGGTCTCCTCCAAC R 2 1 2 1 102000 f 74 goat 2_12437740_RH-map 2 12437740 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320802116 Affx-122961938 AX-385289020 2 12501855 AAGCTTGTTGGAAGGGTTTATGCATTCAATTGAGT[A/G]TGGTCTGAAGACATTAATTCCAGAAGCTTGGATCA R 2 1 2 1 101000 r 74 goat snp35257-scaffold422-1922267 2 123203232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790687 Affx-122973567 AX-385277689 2 12536781 ACTAATCCTTATAGCCAGAGAAGAAAGAGTCATGG[A/C]GTTTTTTTTGGCCAGACACTTAAGAAAAATCCATG M 2 1 2 1 101000 f 74 goat snp35256-scaffold422-1887341 2 123167289 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603216 Affx-1002479406 AX-413837400 2 12548235 AGAAAACTGAGGTCCCAAGAAGAAAGAGGCTGGAC[C/G]AAAGAAACCCAATAGGATGGTGGCAGAGGAAGGAG S 4 1 2 1 400000 r 74 goat 2_12548235_RH-map 2 12548235 C G Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38401213 Affx-122959326 AX-123271566 2 12589967 TGCATCCATATAAGAAGGTGAGGCTAAAGAGGCTG[A/G]GAGAGAATATTTGTTGGAGGAAGTTGTCTTGGGTT R 2 1 2 1 101000 f 74 goat snp35255-scaffold422-1834155 2 123113401 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603127 Affx-1002479407 AX-413837321 2 12591366 AACTCAGAATCCCTCTCTGCTGCCCAAATGCCATA[C/T]TCCCCAGACCCACCCATCTCAGGCTGTCAGGGCCT Y 2 1 2 1 102000 f 74 goat 2_12591366_RH-map 2 12591366 C T 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38404551 Affx-122957385 AX-123274903 2 12627491 GAGCAGACTCCAACTGTAAACATCTGGAACACCTT[A/G]CAGGTAATTTCAGCTGGCTATCATCCCTGTATACC R 2 1 2 1 101000 r 74 goat snp35254-scaffold422-1796631 2 123076849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603129 Affx-1002479408 AX-413837323 2 12676503 TTGGAGGGCCAGATCGCTGATGACTGTGACATCCT[C/T]GTTTACTGATATGGCAAGAGATATTCCATTTCTCA Y 2 1 2 1 103000 f 74 goat 2_12676503_RH-map 2 12676503 T C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38377126 Affx-122978241 AX-123247485 2 12677845 TATCTCTTGTCAATAGAAGATGGTTTCCTGTAGGA[G/T]ATAACTAATAACTTTATAGAATTTGGGGATGTAAT K 2 1 2 1 101000 f 74 goat snp35253-scaffold422-1746277 2 123026128 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452023 Affx-122920906 AX-123322356 2 12707034 GTAACCATTCCATTCTTCAGGGGACCTTCCTGACA[C/T]AAGGATTGAACATGGGTCTGTGATAGTTTAGATGC Y 2 1 2 1 101000 r 74 goat snp35252-scaffold422-1717088 2 122996917 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603131 Affx-1002479409 AX-413837325 2 12708429 TCAGAAAAAGAAGGAGACCAGCACTTTACAGGACC[A/G]GATCACCTTTAATGAGGTGAGAAGGGGCCGCGATC R 2 1 2 1 400000 f 74 goat 2_12708429_RH-map 2 12708429 G A Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603590 Affx-1002479410 AX-185150951 2 12722993 TCAATACCACAGTTCAAAAGCATCAATTCTTCAGC[A/G]CTCAGCTTTCTTTATAGTCCAACTCTCACATCCAT R 2 1 2 1 303000 f 74 goat 2_12722993_RH-map 2 12722993 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38419214 Affx-122945694 AX-123289562 2 12738270 AAAAAAGATTCAGTATTGTTAATTATAGTCATCAT[A/G]TTGTATATTACATCTGTTGGGCCTGATTTTGAGTT R 2 1 2 1 101000 r 74 goat snp35251-scaffold422-1685852 2 122965745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422413 Affx-122943373 AX-123292759 2 12771576 GATAGTGTGTGATTAACTGCAAAAACTAATTGATT[A/G]CTGTAAATTATATAATTGAGTTTGTAGTGAGCCTT R 2 1 2 1 101000 f 74 goat snp35250-scaffold422-1652546 2 122932668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449013 Affx-122923093 AX-123319348 2 12845217 TGAGTCATTGTAATACCCTCCTAACAAATCTCCCT[G/T]CTTCCATGTTGCCCCTACTCCTCCTCACAGCCGCC K 2 1 2 1 101000 f 74 goat snp35248-scaffold422-1578905 2 122861067 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770289 Affx-122928981 AX-385257455 2 12877003 ACAAAACTCTCAGTGACATACTGAAGACTGGAAGG[C/T]AGGTCTCCTAACTTCTGGCTTGATACTCTTTACTT Y 2 1 2 1 101000 f 74 goat snp35247-scaffold422-1547119 2 122825920 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400354 Affx-122960034 AX-123270709 2 12916721 CATTTAGAAATCAAAAAACTGTGAATAGTACAATG[C/T]AAATAATGAGCATTTTACAATAAACTTCACTGACA Y 2 1 2 1 101000 f 74 goat snp35246-scaffold422-1507401 2 122786230 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275456 Affx-1111834909 AX-519549029 2 12927607 ATATTTGTTCTGGAAACTGGAACACACAGATAAGG[A/C]AAGCGCCTGACATTGGAACTGCAGAATAAATTTGC M 2 1 2 1 101000 f 74 goat GoatD01.058445 2 12927607 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 350603650 Affx-1002479411 AX-413837788 2 12947664 GACCTCTCAGAGTCTCAGCACTGATCTCAATTAAT[A/G]TATGTCTGGGCATTTTTCTCCTATCTTTCCACTCC R 2 1 2 1 102000 r 74 goat 2_12947664_RH-map 2 12947664 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38436643 Affx-122932486 AX-123306981 2 12969544 AATCAAACTGCTACAAAAGTCCATCCATCAATTTA[G/T]CACAAAGGTAAAAACAAGATTAGAGACAGAAGAGT K 2 1 2 1 101000 f 74 goat snp35245-scaffold422-1454578 2 122733503 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603134 Affx-1002479412 AX-413837328 2 12976611 ATGGAGCACTTACAGTCTAAATGGGAACTGATTCT[C/T]TTTGAAGGACTCAAATGGGGTAAAAATGATACATT Y 2 1 2 1 101000 f 74 goat 2_12976611_RH-map 2 12976611 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320783404 Affx-122961992 AX-385270467 2 13004256 TTTGATAAAATACTTAGCACTCCTTAGTCACTTGA[A/G]TAAATAATATATATGCTAACAGTTATAATGAAGGA R 2 1 2 1 202000 r 74 goat snp35244-scaffold422-1419866 2 122698394 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782923 Affx-122935455 AX-385269993 2 13040923 TGATTCAGATCATCCAAATACTTCTAAGCTTAGAC[A/G]TTTGGTAAATCCTTCATCTCTCTTGATAGACATTC R 2 1 2 1 201000 r 74 goat snp35243-scaffold422-1383199 2 122661413 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272937 Affx-1111833157 AX-519546623 2 13058359 TTGAGGGAGAGATGAGCCTGAGGGTGAAGCTCCGG[A/G]ACCAGGTAGCTTCTCTCCCTGCAGACTTGCTGGGA R 2 1 2 1 202000 f 74 goat 2_13058359_AF-PAKI 2 13058359 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450181 Affx-122922308 AX-123320516 2 13072027 CTCAGCTAACTAGTTACCCCTGTTCAAGGCCACCT[A/G]CCCTCACAGACATTTTACAGACTCTGCAACCCACC R 2 1 2 1 101000 r 74 goat snp35242-scaffold422-1352095 2 122630391 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433819 Affx-122935166 AX-123304160 2 13127893 ATTCTGGAGAATCAGAAAACTGAATTCTAACACTC[A/G]CTGTGTAAACTTATGTCTCATCACTTGTCCGTTTC R 2 1 2 1 101000 r 74 goat snp35241-scaffold422-1296229 2 122573997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445740 Affx-122926089 AX-123316077 2 13161369 ATAATAGCTTTTTGTGTTGTTTGTCTCCCCAGGGA[C/T]GCTAACATGATTAGTATTACCCAGTCATGATAGAG Y 2 1 2 1 201000 r 74 goat snp35240-scaffold422-1262753 2 122540040 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442829 Affx-122927701 AX-123313166 2 13191492 TATTTCCAGTTTACATCCGGAGTATTTATTTCTCG[A/C]GACTGACTTTTCAACATAGTATTTTCAGGTATATT M 2 1 2 1 101000 f 74 goat snp35239-scaffold422-1232630 2 122509551 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427579 Affx-122939474 AX-123297922 2 13226022 TGTCTCCTGAACTTCCCTCCTTCCACAGATGCATC[G/T]AATGTAAAGTAATTCAAGTCACCATAGCTGGAATT K 2 1 2 1 101000 r 74 goat snp35238-scaffold422-1198100 2 122475008 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423248 Affx-122942679 AX-123293594 2 13259224 TTTTTTATTGTATGCCTTTTTATTTTACTTTTGAT[A/G]TGGTCTACACATACAACTTTATTTGAAGCAAATCT R 2 1 2 1 101000 r 74 goat snp35237-scaffold422-1164898 2 122442874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448370 Affx-122924107 AX-123318706 2 13302225 ATTATTGAGTTTTAAGAAGTCCTAGTTTCTCAGCT[A/G]TTAAATGAAAGTTAAAATGGCACTTATTTCATTGA R 2 1 2 1 101000 f 74 goat snp35236-scaffold422-1121897 2 122400178 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783458 Affx-122970339 AX-385270521 2 13331929 AATAAAGTACAATTGATACATTTATCAAGACAGAC[A/G]TCTCTTCCACACATACTGTTCTCCTTCCCTGGACA R 2 1 2 1 101000 r 74 goat snp35235-scaffold422-1092193 2 122370400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777105 Affx-122965198 AX-385264228 2 13361462 TAAAACATGTAATTTCACTTGAAAAAAATTGGTTT[A/G]TACAAGTTTAACTGAATAAAACAACTTAGAAACTT R 2 1 2 1 202000 f 74 goat snp35234-scaffold422-1062660 2 122339862 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394975 Affx-122964267 AX-123265330 2 13419975 AACTCTACGCAGTAGGTAACTGCCAATTTAACAAG[C/T]GGAAAACACAGCAGCTGCACACAGACTGTTCCGTG Y 2 1 2 1 101000 f 74 goat snp35233-scaffold422-1004147 2 122280511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786561 Affx-122926780 AX-192223468 2 13453075 TGTGCTAATGTCAAATTCTCTTATTAGATTTTAAG[A/C]GCCCCACTTCCTAAGGTTTCAGATTCTTCTTTTTA M 2 1 2 1 101000 r 74 goat snp35232-scaffold422-971047 2 122247122 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772150 Affx-122958675 AX-385259305 2 13511640 CTGCTATACAGATACTTCTAAATTAGCTGTAAAAT[A/G]TACATAGTATAGTACAATAGCCATCAAGTTCAAAT R 2 1 2 1 101000 r 74 goat snp35231-scaffold422-912482 2 122187918 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423642 Affx-122942356 AX-123293988 2 13544177 CCAAATAAATAAATATTTAAAAATAAGGCTACAGA[C/T]ATCTCTCCAGTATCATAGAGCATCAGAGCTTCAAG Y 2 1 2 1 101000 r 74 goat snp35230-scaffold422-879945 2 122155160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444482 Affx-122926527 AX-123314819 2 13575248 CACACACACACACAGAGTTCAGAGATGTGTGTTTT[A/G]TTTCAGTCATGCACATGTGTATTTTATAAGGAACT R 2 1 2 1 201000 r 74 goat snp35229-scaffold422-848874 2 122123523 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425043 Affx-122941864 AX-123295389 2 13628520 ACCTGGGAAGCCTCCATATGCTCACTTAGTGCTTT[A/G]TAAACTGTGAAAGACAGCCTCAGTGTACCACTGGA R 2 1 2 1 101000 r 74 goat snp35228-scaffold422-795602 2 122070058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389667 Affx-122968717 AX-123260025 2 13674323 ATAGGGCGCACACATAGCAGACCCACTGAAGGGCC[A/G]TTTAACATTTTACGTCATTCTCTTGGACCTTGGAA R 2 1 2 1 101000 r 74 goat snp35227-scaffold422-749799 2 122024147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437950 Affx-122931621 AX-123308288 2 13714712 CATAGAAAAGACATCACACACATACATGTATTTAT[A/G]CATGTATATTACAGTTGTTAGTGATAAACATCTAT R 2 1 2 1 103000 r 74 goat snp35226-scaffold422-709410 2 121984442 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766019 Affx-122957756 AX-385253438 2 13757148 CATTTGAAAATTAACAGGCTCACACTCGCTCTCCA[C/T]GACCACCAGTTCTCAGTATTACCTATTTGGGACTG Y 2 1 2 1 101000 f 74 goat snp35225-scaffold422-666974 2 121941747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441584 Affx-122928673 AX-123311921 2 13795481 TCATAGACGATAAAAACAATACTTGCAGGGAATAA[C/T]GTAAGGCACATGATCAGCTGGGTATTAGAGACTCC Y 2 1 2 1 201000 f 74 goat snp35224-scaffold422-628641 2 121902761 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383276 Affx-122972726 AX-123253634 2 13828899 CCAAGTTAAATTTAAATTCTACATCTTCCTGACTA[C/T]AAATTCTATTAAAAACATTAACCTCCATGATGAAA Y 2 1 2 1 101000 f 74 goat snp35223-scaffold422-595223 2 121867744 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420651 Affx-122944828 AX-123290998 2 13874248 TTTACAACCCTTCAAATGCACACCCATCCCTTTAG[A/G]ACAAGGCACTGGAAATAATTTGCAGGGCTGTTTAT R 2 1 2 1 101000 f 74 goat snp35222-scaffold422-549874 2 121822529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407795 Affx-122954565 AX-123278146 2 13904903 TTCCAGACCCAATTCCAACAGGGGTGTGTTCCTCA[C/T]ACCAACAGGCCAATTCTTCCCCACACCAACAAGCA Y 2 1 2 1 101000 f 74 goat snp35221-scaffold422-519219 2 121791284 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793067 Affx-122947817 AX-385280045 2 13933883 ATAAACAGATGTGAATTTTTGTTTCTACGTAATAG[C/T]ATACATGAAGGACATTGTAATCAGCCATTCCAGGA Y 2 1 2 1 101000 r 74 goat snp35220-scaffold422-490239 2 121762401 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785771 Affx-122934314 AX-385272811 2 13964453 TCAAAGAAATCAAAGTAAGTCTCTCTACCCAATTC[A/G]CACAAGCCTTCATAATCACGTGTTTCACAGCATGC R 2 1 2 1 101000 r 74 goat snp35219-scaffold422-459669 2 121731857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392240 Affx-122967573 AX-123262597 2 14038058 TATTATAAAGACTAATTAAATATAGAAATGTGATA[C/T]GTAAACATAGGGAAAATATATATTGAGTGAATTAG Y 2 1 2 1 101000 r 74 goat snp35218-scaffold422-386064 2 121657035 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419387 Affx-122945613 AX-123289735 2 14119591 GAAAACAGAAGTGCTCGTTGCAAGGGAAGTGAATT[A/G]TGCAGAGGTAGGATTTGAAATGGTTGAAACAGCAG R 2 1 2 1 101000 f 74 goat snp35216-scaffold422-304531 2 121574732 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387044 Affx-122969912 AX-123257402 2 14152428 TTGAACTTTCAAAAGTTCTCAGGTATATCCTCTGC[G/T]AGTGAACTATGCAGACTTTGAGTGCAAGCCTCTGC K 2 1 2 1 101000 r 74 goat snp35215-scaffold422-271694 2 121542012 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409464 Affx-122954072 AX-123279815 2 14215380 TTTGTGGACTGACACACACACTGAAATTGAATGGC[A/G]CACTTAGACACTACGCTATTAGGACTCCATCAGTC R 2 1 2 1 201000 r 74 goat snp35214-scaffold422-208742 2 121478323 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421361 Affx-122944053 AX-123291708 2 14264594 ACACCTGTTTCAGCTGGACTGAGAAACAGCACGCT[A/G]TCTAAAGGGGGCTACAATGGGCTGGATAACCGACA R 2 1 2 1 101000 f 74 goat snp35213-scaffold422-159528 2 121428472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391839 Affx-122967003 AX-123262196 2 14299056 AGAGAAGTTTCTTTTAAGTACTTGTCTTCATATAG[C/T]GCCACGTGGCTGTGGTGTACTTAGGAACACCAGGA Y 2 1 2 1 101000 f 74 goat snp35212-scaffold422-125066 2 121393848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790778 Affx-122951696 AX-385277779 2 14360228 AAGCATCTTTAAATAAACCACTGGCATATTAATGG[A/C]AAGACCAAGCAATGGAATAGAACAGAAAGCCCAGA M 2 1 2 1 102000 r 74 goat snp35211-scaffold422-63894 2 121332462 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396010 Affx-122963487 AX-123266365 2 14392269 AAAATATTTACACTCAATCATAGCCAAATTAACCC[A/G]GGGGTAGCTACTAATACTATCAATAAATTTGCAAA R 2 1 2 1 201000 f 74 goat snp35210-scaffold422-31853 2 121300176 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793727 Affx-122937029 AX-385280699 2 14420827 ATAAATTCTTGTTTGGATGTTATTCTTTTCTCAAG[C/T]GTAAGTATGAAATGTACTTTCACCAGTGCTATAAG Y 2 1 2 1 101000 r 74 goat snp35209-scaffold422-3295 2 121271182 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796169 Affx-122962559 AX-385283120 2 14466134 GGCAAAATGTCCTGGTTTTACTGAATATGTTTACC[A/G]TGTGAATTATTTCTCCCAAGCAGTCATTTTACAAC R 2 1 2 1 101000 f 74 goat snp38200-scaffold480-41913 2 121225739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786305 Affx-122943522 AX-385273339 2 14496839 CCTGTGTTAGACAATATTTGAAAAGGAACTACTCC[A/G]TTTAGAAAATGATAGTAATATCTTTTTGCCCTCCT R 2 1 2 1 101000 f 74 goat snp38201-scaffold480-72618 2 121194945 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797660 Affx-122940835 AX-385284599 2 14528450 AAAAATAGCAGCCAAAACTCAGTTACCCAGAGTAC[G/T]TACTAGTTAGTTAGGAGGTAATGCTATTTTCCCAA K 2 1 2 1 101000 f 74 goat snp38202-scaffold480-104229 2 121163020 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388422 Affx-122969278 AX-123258780 2 14560881 GCTATAATTTAAATTAGTTTAAAATTCTATAAATT[A/C]TCCATCTTCATTTTGGGAAAGCAGTTTATACATAT M 2 1 2 1 103000 r 74 goat snp38203-scaffold480-136660 2 121130831 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775726 Affx-122933615 AX-385262857 2 14680037 GATTTTATTAAAAACACCATTGCACCCATATTTCC[A/G]TCAGCATCTTCAGGTATAATGCTTTAAAAGACTTA R 2 1 2 1 101000 r 74 goat snp38205-scaffold480-255816 2 121009124 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420834 Affx-122944661 AX-123291181 2 14730503 GAGCAGTTCCCACCACATTATGAACTTAATGCTAT[G/T]AAATATGCAGTTTTAAAAAATAAGAGCTTCTCTAT K 2 1 2 1 103000 f 74 goat snp38206-scaffold480-306282 2 120958554 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783798 Affx-122966723 AX-385270854 2 14799346 CTGGGAAAAAAATATCTTGACCTCTTTCCACCAAG[C/T]AGTGATACTGAAAGCCACAAGATAATAAACGTTAG Y 2 1 2 1 101000 f 74 goat snp38208-scaffold480-375125 2 120888954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442046 Affx-122928395 AX-123312383 2 14851284 CTGAACAGAATTATGTTCAAAAGACAAAACATTTT[A/C]TTGACTTGGAGAGATTACAAAGCATGCCAAACAGA M 2 1 2 1 101000 r 74 goat snp38209-scaffold480-427063 2 120836881 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401037 Affx-122959666 AX-123271390 2 14883818 AATTTGACATGTCTCTCTGCCTTCTTTGCTCCAGT[A/G]CTAATTAAAATAGTCAATAAAACAATGTCACCACT R 2 1 2 1 201000 r 74 goat snp38210-scaffold480-459597 2 120803899 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388571 Affx-122969539 AX-123258929 2 14926744 TAGAAATCTCCTGGAGTAGACCAGATCTTAAAGTT[C/T]ACTTAGTGATAGGAGTAGTACCATTGCTGGTAGTA Y 2 1 2 1 101000 r 74 goat snp38211-scaffold480-502523 2 120760917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440687 Affx-122929916 AX-123311024 2 14963911 CAAAGTTTTCCTATTAAAGACAGAAAGAAATGGAA[A/G]TGGTGCAGACAGCCCAAGGGTTTTTATTTCAAGTT R 2 1 2 1 101000 r 74 goat snp38212-scaffold480-539690 2 120724003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415620 Affx-122948594 AX-123285969 2 15001699 AATATAGGAGGTACGGCAGAACAAGATAGCAAGAA[C/T]AGTTCAGTTTTCTGGATGTACAACTGAGATGCACT Y 2 1 2 1 101000 f 74 goat snp38213-scaffold480-577478 2 120686207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416748 Affx-122948193 AX-123287096 2 15064308 AAGTTTCTGTTTAGACAAGTATTCCAGTAGCTACC[A/G]GCATCACAAAAAGACAACCAGATTTTTAGGTGTTT R 2 1 2 1 101000 f 74 goat snp38214-scaffold480-640087 2 120623377 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775405 Affx-122943253 AX-385262536 2 15142350 TTTTCAAAACAGCGGCAGATAAGCAGCAAATTTAA[C/T]GTCAGGAAAAAGGCTGCTAGAGATAGACTTATTAA Y 2 1 2 1 101000 r 74 goat snp38216-scaffold480-718129 2 120544313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277232 Affx-1111835746 AX-519550738 2 15174359 GGCAATGAAGTTGGATGAAGAATGAGGGAGAAGGT[A/G]GAGGAGAAAATAACACTGGTGTTTTGTAACATGGG R 2 1 2 1 101000 r 74 goat Random2.2K-168 2 15174359 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789629 Affx-122921099 AX-385276638 2 15178463 AATAGCTATGAAAAAGTAAAGGGGTCATTTTGAGA[A/G]AATCAGTGATATCCAAAAGATAACATACTAATTTC R 2 1 2 1 101000 f 74 goat snp38217-scaffold480-754242 2 120507788 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432310 Affx-122936306 AX-123302651 2 15215485 ACTAGAAACACGAAAATTACAAAGGGAAAAATCTC[A/G]TTGGAAACCGCAAATATACAGTAAAAGCAGTTAAT R 2 1 2 1 202000 r 74 goat snp38218-scaffold480-791264 2 120471386 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382430 Affx-122974240 AX-123252788 2 15251410 AAATACATTCTTTCTCTGATTTGGGGCTCTGCTGC[A/G]CATCTCCACCTTCTCTATTTTTAGCTTTGCTCATA R 2 1 2 1 103000 f 74 goat snp38219-scaffold480-827189 2 120435074 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395940 Affx-122963580 AX-123266295 2 15301931 ATTTGCAAAAATGTGTACAAATAGAGTGAGTAATG[A/C]TGAAAGTTGTGAGTGCTTTGTACAAAAGTCTTTAA M 2 1 2 1 101000 r 74 goat snp38220-scaffold480-877710 2 120382890 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433338 Affx-122935151 AX-123303679 2 15330570 ACAGTCTGCTGTGTATTGAATAGATTATTGTTTGC[A/G]TTTTTTAAAGAATTGATCAGTTTTATCTAAGCTGT R 2 1 2 1 102000 f 74 goat snp38221-scaffold480-906349 2 120353569 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413497 Affx-122950643 AX-123283846 2 15371216 GAAGCTGCCTCAGTAGTTTCTAGCTCCCTTTGAAG[A/C]TTGCAGGAAAGAGGAAAGATGTGGGAGGAAATCAG M 2 1 2 1 101000 f 74 goat snp38222-scaffold480-946995 2 120313096 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383998 Affx-122972918 AX-123254356 2 15449492 TTTGATTAGTGTAAATCAAATTGCTACAAACTGTT[C/T]TCTGAACCAACACTAGGCTGTTTCAGATGTGCATT Y 2 1 2 1 101000 f 74 goat snp38223-scaffold480-1025271 2 120234133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391075 Affx-122966838 AX-123261432 2 15539512 GACTAAGCACTCACTCAAGCGAGTAGAAGTTAAAC[C/T]ACTCTGCATTAGAAGTTATCAAGAATGTAAAGATC Y 2 1 2 1 101000 f 74 goat snp38225-scaffold480-1115291 2 120143928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272556 Affx-1111833161 AX-519546272 2 15558544 CCAGCCTGGTTAGGATTTGGGGAGGTGGGAAGGCC[A/G]ATGGGTAAACACGTTTGGTGCTTGAGTTTCTGTGT R 2 1 2 1 101000 r 74 goat 2_15558544_AF-PAKI 2 15558544 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320792487 Affx-122920457 AX-385279468 2 15579213 TTACTTATTATCTTATATGTTATTCAAAATAAAAC[G/T]AATGAAAGTTTTCAGTGAATTAAGAGAGAGTAAGT K 2 1 2 1 202000 f 74 goat snp38226-scaffold480-1154992 2 120103519 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402332 Affx-122959070 AX-123272685 2 15627719 GTGCTCTATTACGTTGGAGTTTTATCTACCCAGTG[A/G]GGTCAGATTCAGATAGCCCAGGGTTACCTGTTTTA R 2 1 2 1 101000 f 74 goat snp38227-scaffold480-1203498 2 120056888 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804440 Affx-986696607 AX-385291021 2 15638266 AAGGCCGCCTCCGTCATCTCCTCCAGGGTCGGGTC[C/T]TTGGTGTGGTCTTGCTGAACATTATACTTCATGTC Y 2 1 2 1 600010 r 74 goat 2_15638266 2 15638266 Ancestral_priority_1043 ancestry 0.626 recommended IMAGE 10K 10K ancestral 38442292 Affx-122928255 AX-123312629 2 15656877 AAGTTAAGAAGAAGCTAGGAGAAGTTAGGTTTTTA[C/T]GTTGAGTTTCTTTCATATACATAGGCCTATTCTTA Y 2 1 2 1 101000 f 74 goat snp38228-scaffold480-1232656 2 120027050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800441 Affx-122920856 AX-385287362 2 15711031 TGTCCTCAATATGTTGTGATATTTTTACACTGTGT[A/G]CTTTCTAATACCAATTATTACCTCTTATAATAATG R 2 1 2 1 101000 f 74 goat snp38229-scaffold480-1286810 2 119971255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404307 Affx-122957024 AX-123274659 2 15769357 CATTTTCATACCTCTCAGTTCTTTAAGGCAGAATC[A/G]TGTAATTTTGATGTTGCCTACAAAATATCAACAGA R 2 1 2 1 201000 r 74 goat snp38230-scaffold480-1345136 2 119911460 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779980 Affx-122921052 AX-385267079 2 15821023 AACAGAAAAACTCTAAAGCCCTTAGTCCATGTTGC[A/G]CAAAGAACTTCAAAGGTTTCAATTAATGGTGTGTA R 2 1 2 1 101000 r 74 goat snp38231-scaffold480-1396802 2 119858895 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410453 Affx-122952382 AX-123280803 2 15858625 AGATGGTTCACTGCTGTATTCTCTGTCCCTAGAAC[A/G]TTGCTTGTACATCAGAGGCTCTGTTGTGTCCGACT R 2 1 2 1 201000 r 74 goat snp38232-scaffold480-1434404 2 119820777 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435886 Affx-122932782 AX-123306225 2 15914252 TGAGTCCCTGGAGAAAGTTTCATTTATAAACATAC[A/G]TTTTAATCCAAATCAAGCACTAATCATTTACTTTG R 2 1 2 1 201000 r 74 goat snp38233-scaffold480-1490031 2 119765322 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794726 Affx-122963871 AX-385281686 2 16004340 TTTGCAAAATCTTTGGGACAATTTACCAAACAATC[A/G]TATTTTATGTTCAACAACTTGGCTTGCCCAATAAA R 2 1 2 1 101000 r 74 goat snp38235-scaffold480-1580119 2 119674072 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451072 Affx-122921419 AX-123321406 2 16035023 AATATTAAAACTGGAAAGGATGTCAGAGTTTATCT[A/G]TTTGAACTTTCTCATTTTGATACAGGAAAAGCTTT R 2 1 2 1 101000 f 74 goat snp38236-scaffold480-1610802 2 119642477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383551 Affx-122972611 AX-123253909 2 16088516 GGCTTTAGCCCAGTAAGCATTAGGGTGGTTTGCTA[C/T]ACAGTAATTGATAAACTCTTCCATTGGTTGCTTTT Y 2 1 2 1 101000 f 74 goat snp20673-scaffold2035-483220 2 119587953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422093 Affx-122943580 AX-123292440 2 16125266 AGGGAGGTTATTCCTGTTGACCTTTGACTTGACCC[A/G]TGAGTAAAAAGCCATTAGACCCACAGTGAAAAGAA R 2 1 2 1 201000 r 74 goat snp20672-scaffold2035-446470 2 119551023 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398865 Affx-122961048 AX-123269220 2 16163462 TTATAGCACATTTTGCTTGGTCATTGGCTGAGGCC[A/G]CCCAAAGAAGGGCATGACCTGAGCTCCAAAGCTGA R 2 1 2 1 201000 r 74 goat snp20671-scaffold2035-408274 2 119512977 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425193 Affx-122941038 AX-123295539 2 16240406 CCCTACATGACTTTGGGCAGCTATCCCCTTTCTTC[A/G]TCTACCTGTGTAAAGCTGGCCAAAGGTGAACCAAG R 2 1 2 1 101000 r 74 goat snp20669-scaffold2035-331330 2 119435049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793033 Affx-122954307 AX-385280011 2 16286652 CTAAAGTAAATAAACTTCCACCCACCTAGACAGTA[C/T]GCTTTTTGATTGCTGATGCAAGACAATCTCAGTAA Y 2 1 2 1 101000 r 74 goat snp20668-scaffold2035-285084 2 119388571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409594 Affx-122953564 AX-123279945 2 16333103 AACATGAAAAGATCATCAAGGAGTTTAGCTCAGAT[A/G]TGATGAGAACTCAGGACAGCCTATGGAAAGTCACC R 2 1 2 1 201000 f 74 goat snp20667-scaffold2035-238633 2 119342183 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439210 Affx-122931032 AX-123309547 2 16396894 CCAGTGACACACGCCCCAGGAACTTCCCCTCAAGA[C/T]GCTCCCTGCAAGGTGCCTTACAGGTATATCTGTTG Y 2 1 2 1 101000 r 74 goat snp20666-scaffold2035-174842 2 119278302 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776183 Affx-122924015 AX-385263311 2 16440937 ACTTTCTGTAGAAATCTTCACCATGGAAAATAGTA[C/T]ACTTCACATTTTCTTTAGTTATGTCACAGATGAGG Y 2 1 2 1 101000 r 74 goat snp20665-scaffold2035-130799 2 119233059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404362 Affx-122956815 AX-123274714 2 16483515 GCCAATTAGAGCATGGACTAATGAGACTAATATCA[C/T]GGCCTTCCTGTTGTCTAACTGGCTCTAATATAGAT Y 2 1 2 1 101000 f 74 goat snp20664-scaffold2035-88221 2 119190328 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434207 Affx-122934856 AX-123304548 2 16515514 ACATTTGGATTTAATCCTAAATTAGGTCACAAGAT[A/G]GAGAACTTCAAGCACAAAATTACGACATGATCAGA R 2 1 2 1 101000 f 74 goat snp20663-scaffold2035-56222 2 119157831 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769610 Affx-122966341 AX-385256780 2 16545571 CTTTTACCTGTGATGCTATCAAAGGACATAGATGC[A/G]TACGTGACAAGGTCAAACAAATGCATCATGGTAAA R 2 1 2 1 101000 f 74 goat snp20662-scaffold2035-26165 2 119125743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771711 Affx-122973954 AX-385258868 2 16574820 GTGAAAGGATGGTCCTTGTTTAAATTTTTCAGCAT[A/G]CTTTACATTTTGTATTAGAGTCTCTGACAAGACAG R 2 1 2 1 101000 f 74 goat snp6771-scaffold1245-1331909 2 119096414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438221 Affx-122931445 AX-123308559 2 16632478 ATTTATGGGAAGTCAGGCATGAAGGTGGGATATCA[C/T]GCTCCATTTTTTAACCAGGGTGACAGCTGGTCCCA Y 2 1 2 1 101000 f 74 goat snp6770-scaffold1245-1274251 2 119038965 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775836 Affx-122975625 AX-385262967 2 16688259 CAAAACAGTACATACAGCTCAGAGGTGGTTCATTT[A/G]TATCTGAGTATTTTGTCCATGCACTGAACATCTTA R 2 1 2 1 101000 f 74 goat snp6769-scaffold1245-1218470 2 118983524 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782303 Affx-122944321 AX-385269381 2 16726644 AGATTGAGTATATATTCATACTTGGTTATATCTGT[A/G]TAAACAAACCCAGGAAAGATAGGCAAGAAATATTA R 2 1 2 1 201000 r 74 goat snp6768-scaffold1245-1180085 2 118945168 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768981 Affx-122942001 AX-385256155 2 16763147 ACACAACATGATCAAATTATGTCTCCAAATGCATC[A/G]TAAAAAATGTTGCCCCAGTTGCTAAAATAGCAGGT R 2 1 2 1 101000 f 74 goat snp6767-scaffold1245-1143582 2 118907890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394268 Affx-122964720 AX-123264623 2 16799114 GTACTAGTTCAAATTAATATACCCCTCAGGATTGA[C/T]CCATTCTGCCACCTCAGAATCAGGGTGGATGATAA Y 2 1 2 1 201000 r 74 goat snp6766-scaffold1245-1107615 2 118872126 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790914 Affx-122966187 AX-385277911 2 16846202 TTCTCCTCCTTTCCTTAGAACATCTAGGTGATCCC[C/T]GGCTTTTGGCTTATCCTAGAAATTTTAATATTTGA Y 2 1 2 1 101000 f 74 goat snp6765-scaffold1245-1060527 2 118823344 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415740 Affx-122948499 AX-123286089 2 16883658 ATTACTATGGGGCTACGGACAAAGATTCATCTTCC[A/G]TAATTTCTTCATGCTGACATATGGCGCCATACTCT R 2 1 2 1 101000 f 74 goat snp6764-scaffold1245-1023071 2 118785699 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443506 Affx-122927796 AX-123313843 2 16944545 CTGAAACCGCCAGACATGCTCTCCTCTCAGAACCT[C/T]TGTCTTCTTCCTCTACCTGAAACACACCTCAGGCG Y 2 1 2 1 101000 r 74 goat snp6763-scaffold1245-962184 2 118725384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438566 Affx-122931167 AX-123308904 2 16973362 ACAACCAAAATACACACCTCAGTAATCCTACACTG[C/T]AAAGTGAATCTGGCAAACTGCCCTGTCCAAAAATA Y 2 1 2 1 101000 f 74 goat snp6762-scaffold1245-933367 2 118696657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414660 Affx-122949310 AX-123285009 2 17031741 TTCATCAGCTATCTATACAGCCTGGCCTTCACTTC[A/G]CTCATCTCTGGTAAAATGTTATCTTATCATTTTGT R 2 1 2 1 201000 r 74 goat snp6761-scaffold1245-874988 2 118637437 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773435 Affx-122957342 AX-385260577 2 17063411 AACAGGGACATGTAAGTATGAAAATGTGAAGTATA[C/T]TGGCCTACCAGGCTAATTTCTCTTAAACATCAGGA Y 2 1 2 1 101000 r 74 goat snp6760-scaffold1245-843318 2 118605720 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277255 Affx-1111835757 AX-519550760 2 17100962 GGACAGGAGTTGAGTCGCAGCGTCATGGAGTTGAC[A/G]TCATCCCCGAGGGTGACTGCAGTGAAGAAAATGCT R 2 1 2 1 101000 r 74 goat Random2.2K-171 2 17100962 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415278 Affx-122948837 AX-123285627 2 17114501 AGGAGGATGCGGGTGAGTAGAGGACTGACTGGAAA[C/T]GGCAACATGGGAATTTTTTAATAGCATTTTACATT Y 2 1 2 1 101000 r 74 goat snp6759-scaffold1245-792228 2 118554621 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778275 Affx-122936670 AX-385265390 2 17146719 GGCAAGCGGCCTTGGTAGGAACACTTTGCATTCCA[C/T]GCTTCCAGTGCTTCTAGATGGAATCATTTTGTTCA Y 2 1 2 1 201000 f 74 goat snp6758-scaffold1245-760010 2 118522296 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766000 Affx-122947332 AX-385253422 2 17181135 GTGATACTTGAAAAATGCACTCTATCATTTTAAGC[A/G]TAGCTCTGAAATCGCTGGTTTGAAGTGGAGCATAT R 2 1 2 1 101000 f 74 goat snp6757-scaffold1245-725594 2 118487659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779596 Affx-122925039 AX-385266699 2 17239352 TGAGCTAAAGAAATTGTTAAAGGGTGGAGAAAGGG[A/C]GAGGAAAATTGATTTTTAGCCTAATTTTACAAAAA M 2 1 2 1 101000 f 74 goat snp6756-scaffold1245-667377 2 118429137 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402313 Affx-122959085 AX-123272666 2 17268893 TCCAGGTGGAGGGCACAGCTGGAGGCTTTCAGGTG[C/T]GAGTCTTCCTGCTGGGTTGGAGAAACAGCAAGGAG Y 2 1 2 1 201000 r 74 goat snp6755-scaffold1245-637836 2 118398903 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801237 Affx-122958199 AX-385288150 2 17303120 CCTCTCCTCCAGCAAAACTGTACTTATTTCTGGTA[C/T]GGTTTTGCTGCTATTTTGCAGGGCCTCTCATCTCC Y 2 1 2 1 101000 f 74 goat snp6754-scaffold1245-603609 2 118364651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800424 Affx-122952508 AX-385287345 2 17333864 TGAAGGGAATGGGCAAAATGGCAATGAGAACAATA[C/T]GCTATTTACCTGCATTGTGAAACTCATAAATGACA Y 2 1 2 1 101000 f 74 goat snp6753-scaffold1245-572865 2 118333891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767509 Affx-122977075 AX-385254771 2 17366746 TCCTGAAACAGAGCTTTCCTGGAAAAGAATTTGAT[A/G]CTTTATTCATGTTAAGAATAACTTCATGGGATAGC R 2 1 2 1 101000 f 74 goat snp6752-scaffold1245-539983 2 118300553 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770251 Affx-122967816 AX-385257417 2 17431727 AAAGACAGCTTCTAATTGACAATAATAATTCCAGG[A/C]ATCAGTCAACTATTTTAAGATGAAATTGTCCATAA M 2 1 2 1 101000 f 74 goat snp6750-scaffold1245-475002 2 118235182 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794747 Affx-122935406 AX-385281707 2 17461494 ACATTTCTTTTTATGGATATGACATTTATGAAACC[A/G]TACCTTCCACATAAAGAGTGGCTGTTGAGGTAGCT R 2 1 2 1 101000 r 74 goat snp6749-scaffold1245-445235 2 118205513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425245 Affx-122940996 AX-123295591 2 17503370 GTGAAATTGTAAAACAAAACAAAAACCAAACACAC[A/G]TCTAAACCCAAGTGTAAGGATTAATATGATCTGCA R 2 1 2 1 101000 r 74 goat snp6748-scaffold1245-403359 2 118163607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779061 Affx-122976430 AX-385266166 2 17563283 TATTTCTGATATTTAAATCCTAGAGGATATCAATT[A/G]TTTCAAATTCCTGTGCTTGTTTTTGGTGGTAAATT R 2 1 2 1 303000 r 74 goat snp6747-scaffold1245-343446 2 118103687 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413500 Affx-122950641 AX-123283849 2 17600289 AAAAGAATTAAAAAATGGGCTTGATTCTTTAAAAA[C/T]AAAACTTTTCCATGCTAGGGCAGGTACTACCCTAG Y 2 1 2 1 102000 r 74 goat snp6746-scaffold1245-306440 2 118068654 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434607 Affx-122934093 AX-123304948 2 17639395 AGTAACATTTAGAGATGCCAAGATTTAAATGTGTC[A/G]TCATAATACTTAAAAAAATAATTACCAATTGGAGT R 2 1 2 1 102000 f 74 goat snp6745-scaffold1245-267334 2 118029550 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405298 Affx-122956846 AX-123275650 2 17675376 TCATTTTCTGCAGAAACACGGAAATAGTATGGAAC[A/G]CCTTCTAGCAGGTCACTGACTCTGAGGATCTGACG R 2 1 2 1 201000 f 74 goat snp6744-scaffold1245-231353 2 117993569 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445229 Affx-122925499 AX-123315566 2 17705903 CATCCTGAGAAAGCCTCGGCATTGCCTCTTTGTGG[C/T]TGGAGATTATAATCACCGGTTGCTCTTCTCTGACC Y 2 1 2 1 101000 r 74 goat snp6743-scaffold1245-200826 2 117963025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770412 Affx-122967346 AX-385257578 2 17746617 CCAGCTATCTTTCTTTGAGGAAATTTATGTTAATT[A/G]TCATCACCATAATAATATATTAGAGCTGTCCTATT R 2 1 2 1 101000 r 74 goat snp6742-scaffold1245-160112 2 117922101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770173 Affx-122963611 AX-385257339 2 17792534 CTCTTTACATGCTGAAAAAATGTGAGGCTTGGATA[C/T]AGGTTTGCATAGTACAAAACAAAGTCACTACACGT Y 2 1 2 1 101000 f 74 goat snp6741-scaffold1245-114195 2 117876444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407850 Affx-122954521 AX-123278201 2 17833841 TTAATTCCTAACTTTAAAATTAGCTGTTAGTTTCC[A/G]TAGAGACCTCAGTTGAGTATATAAATTCCCTGCTA R 2 1 2 1 101000 r 74 goat snp6740-scaffold1245-72888 2 117835976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448244 Affx-122924205 AX-123318580 2 17869603 GAGAGACAGAAATGATTTTGATTATAAAATGAACT[A/C]GTGACTTGAAATTTATTAGAGAAGTGACTGAAACT M 2 1 2 1 101000 r 74 goat snp6739-scaffold1245-37126 2 117800298 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799791 Affx-122973611 AX-385286717 2 17899205 AAGAACGTACCATTCACCTACTTAGGTATCTCATT[A/G]ACATAATGAGTGATTGTGTGTCCTTATGTAACTTC R 2 1 2 1 101000 f 74 goat snp6738-scaffold1245-7524 2 117770942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409357 Affx-122954171 AX-123279708 2 17935302 GGAGCAGACATCAACTGTCTTGCTGTACCAGAACC[G/T]AGTACTCTTTCTCTTCTTCCAGTTTCTGCCTATGT K 2 1 2 1 101000 f 74 goat snp27453-scaffold2926-28474 2 117729264 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440850 Affx-122929258 AX-123311187 2 17997502 GCACATCCAACTGCCACTGCCCCCGCCCCAGCATC[A/G]CCACCTTACATTCCCAGACTAGGGATACCCCAGGT R 2 1 2 1 101000 r 74 goat snp27454-scaffold2926-90674 2 117666477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776425 Affx-122929623 AX-385263553 2 18046932 GAATGTATAGCTGAGGCAGGGGGTGTGGATAATCA[C/T]CCCTGAATAATTGAGGTTTATAGTCCTTTATTCCC Y 2 1 2 1 101000 f 74 goat snp27455-scaffold2926-140104 2 117620627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425945 Affx-122941186 AX-123296291 2 18089670 ACAGGTGGCAGATGGCATGAACATTATTACAGAAG[A/C]TGGAAAAATGGCAACTTGTATTTGGTAACAATGCT M 2 1 2 1 201000 r 74 goat snp27456-scaffold2926-182842 2 117578123 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277195 Affx-1111835789 AX-519550701 2 18104378 TTAAATGCACGTCAGTATAATGCTTTCCGGAACAC[A/G]TCACTTAAAAATGAAGGTCTGGTCCATAGGGGACA R 2 1 2 1 101000 f 74 goat Random2.2K-175 2 18104378 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450400 Affx-122922072 AX-123320735 2 18107006 TTCCTCCTTGCAGAAGGCACTTGTCGATAGGAAGT[A/G]CCCTCGGGCCATTATGAATATCTCAATTTAGAAAT R 2 1 2 1 101000 r 74 goat snp19176-scaffold1928-359491 2 117561261 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420566 Affx-122945277 AX-123290913 2 18172327 TCCGAGGAAATGAGGATGCTCAGAGACAGGGGGAT[C/T]ATTTTTCTGGGATGTGACTGTGGATTCTTGGCTCC Y 2 1 2 1 101000 r 74 goat snp19175-scaffold1928-294170 2 117496316 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272025 Affx-1111833162 AX-519545791 2 18222596 GAGTAAAAGTGGCTCAGTTGGGTCCAACTCTTTGC[A/G]ACCCCCATGGACTATACAGTTCATGGAATTCTCCA R 2 1 2 1 303000 f 74 goat 2_18222596_AF-PAKI 2 18222596 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38399778 Affx-122960299 AX-123270133 2 18257948 TTTGAGAATTCTCAGCTTGTTGCCTCATTCTGGCC[A/G]TGAGACTTTTACACATATCACAATATTTCCCATGA R 2 1 2 1 201000 r 74 goat snp19173-scaffold1928-208549 2 117410718 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423234 Affx-122942690 AX-123293580 2 18292712 ACAATTTGGTGGCTGGGCAGGGCTGCTGGATGGAA[G/T]CTGGAGCCTCTCTGTACCTGAAGCTGTGCTGTCTC K 2 1 2 1 201000 r 74 goat snp19172-scaffold1928-173785 2 117378270 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406306 Affx-122955468 AX-123276658 2 18335234 AACATCATCCTAAACTACCCTTCAGCAACCAGTCT[A/G]TATTCCATTATCTCACTTTGTTCTTTTTTTATAGC R 2 1 2 1 101000 f 74 goat snp19171-scaffold1928-131263 2 117335396 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383785 Affx-122973200 AX-123254143 2 18368687 CTTAATATGAAACTCACTACCTGCTTACTCTCCCA[C/T]GAGTAAGCAGGCATGTAGTCAGGCTCCAGGACAAT Y 2 1 2 1 102000 r 74 goat snp19170-scaffold1928-97810 2 117301265 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413657 Affx-122950119 AX-123284006 2 18410166 CTGTAGATATTTGTGTTTATTTCTTACTGGAGAGA[C/T]GTTACATATAAACAAAGCAGGACTATCTCGGAGGG Y 2 1 2 1 101000 r 74 goat snp19169-scaffold1928-56331 2 117250799 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452039 Affx-122920894 AX-123322372 2 18458997 TGAAATCAGAAGATCAGATACAAAGAAAAGTAAGG[C/T]GGTACCAGCCTAGCATGAACGCTTACTGAAGATTC Y 2 1 2 1 101000 f 74 goat snp19168-scaffold1928-7500 2 117186963 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420894 Affx-122944614 AX-123291241 2 18471639 AAAGTGCAGAAACAAAGAGAAAATCCTGTCTTCCC[A/G]TGTGGTTTGCACAGGACCATGTGAAGGGGAAACTG R 2 1 2 1 201000 r 74 goat snp9464-scaffold1341-4775090 2 117174374 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803980 Affx-986696611 AX-385290675 2 18519995 ACTTGAGTATAATTAATAAGCATATGCACAAAATG[A/G]ATGGGATATTTTCATCCTGGCCAATTACAAAAGAT R 2 1 2 1 600010 f 74 goat 2_18519995 2 18519995 Ancestral_priority_1043 ancestry 0.762 recommended IMAGE 10K 10K ancestral 38386243 Affx-122970967 AX-123256601 2 18587913 AGCTGTAGGATCTATTCAGCAATAGCGGATTGTCT[A/G]TGTCTGATTTTTGCAAGTGCCAAAAATTACTGTCA R 2 1 2 1 101000 f 74 goat snp9462-scaffold1341-4658816 2 117058374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789954 Affx-122932947 AX-385276960 2 18621912 AACTGATATAAGCCAACAATTCAGAATAAGTTGGA[C/T]AGATAGGTGGAATACAGTACTGGAGGATTATCAAG Y 2 1 2 1 101000 f 74 goat snp9461-scaffold1341-4624817 2 117024160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791063 Affx-122972672 AX-385278058 2 18679157 CTGAAATCAATAAGCAGAGGTGAGTACTTTGAAGG[C/T]GAGTTTAAAAGAAATACATCCTAAAACCAGAGGAC Y 2 1 2 1 101000 r 74 goat snp9460-scaffold1341-4567572 2 116966655 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776722 Affx-122936064 AX-385263847 2 18708565 ATTTTACCCAATCATTTTTGGTATTTGAACATTTT[C/T]CTTGTTTTCTAGTTTTATGTTCTCATATTTATTTC Y 2 1 2 1 201000 r 74 goat snp9459-scaffold1341-4538164 2 116937231 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782235 Affx-122962797 AX-385269313 2 18742843 ATTTGTGGTTTTTTATCCAGTTCTGTATGGAAAGG[C/T]GATGTTGTAAAATCATTCCTTTCAGTTCAGTTGCT Y 2 1 2 1 201000 r 74 goat snp9458-scaffold1341-4503886 2 116902752 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775886 Affx-122975777 AX-385263017 2 18778999 GTGTGTTAAGTGAATGATTAATCACAGAAAGTGTC[A/G]CAACTATTTATACCTTACTGTATGAACCCTTATAC R 2 1 2 1 101000 f 74 goat snp9457-scaffold1341-4467730 2 116863672 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437465 Affx-122932381 AX-123307803 2 18818401 TGAATTTTCTCCAAATAATTAAATGGTTCTTTCGT[A/G]TTGGTCAAATAACTTCTGGAATATTTTAACTCTTT R 2 1 2 1 101000 r 74 goat snp9456-scaffold1341-4428328 2 116826814 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398329 Affx-122962130 AX-123268684 2 18865362 GGAATGGTCTGAACCTGGTCAAGGTCATTTTCTAC[A/G]TTTGCAAATGTATTTTCCAGGCCAGGTTCAAGAAT R 2 1 2 1 101000 f 74 goat snp9455-scaffold1341-4381367 2 116780072 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391184 Affx-122967428 AX-123261541 2 18910083 TTTGGAGTCAAAATAATACTAAAAAGGGATGTGCC[A/G]CTTAGGAGAAAATTGTATGGTGTTTTACAGTGTAC R 2 1 2 1 101000 r 74 goat snp9454-scaffold1341-4336646 2 116736007 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415888 Affx-122948479 AX-123286237 2 18971444 GTGAAGGAGTGTGTCTGCGACGGAGTTCACAGAGA[C/T]GGCTTATCAGTCCACATAAGCAGGACATCCAACCG Y 2 1 2 1 201000 r 74 goat snp9453-scaffold1341-4275285 2 116676692 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801049 Affx-122971387 AX-385287963 2 19000085 TGTTGTGAAGAGAATGTTCCAGAGTGTAGCATTTA[A/G]TATGAAGACTGGTAGCTGTCTAGTCTCTTGAGCCA R 2 1 2 1 101000 r 74 goat snp9452-scaffold1341-4246644 2 116648294 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792963 Affx-122943189 AX-385279941 2 19037704 TGACCTTCATCCTACGACATTCCCAGTGTATATTT[C/T]ACATACATTTTGCCTCAGATTTGGTGTTATGTGGA Y 2 1 2 1 101000 f 74 goat snp9451-scaffold1341-4209025 2 116610363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780825 Affx-122941577 AX-385267914 2 19088198 AATCAGGCTATGTGAAGTCTGAAGCACTTTGGTTC[A/G]TTAAATTGTTTATTATGAGCACTAAAACTATGGTG R 2 1 2 1 101000 f 74 goat snp9450-scaffold1341-4158531 2 116559639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802637 Affx-122966374 AX-385289538 2 19120923 TAGTAAGGGCTCCAGACACATCAGTTGTTGTTAGC[A/G]TGAATTGTTAACCTAAAACGATCAGTCTAAACTGA R 2 1 2 1 101000 f 74 goat snp9449-scaffold1341-4125806 2 116526246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427758 Affx-122939244 AX-123298101 2 19150176 TCTTCTCTGCATAAACATGTTCCTGAGAGATTAAA[C/T]ACGTATACTGTTGCTCAAACTCAGTATAATTTCTG Y 2 1 2 1 101000 f 74 goat snp9448-scaffold1341-4096553 2 116497235 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795643 Affx-122928304 AX-385282598 2 19207518 TGAAAGCAGAGCATTTAATATTCTAAGGGCAGACA[C/T]TACTCCTTGGTGAGTCTTCAAAAATCTTGTCACCT Y 2 1 2 1 101000 f 74 goat snp9447-scaffold1341-4039211 2 116439301 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803511 Affx-986696088 AX-385290330 2 19235203 CGAATGTGCCATCTTAGATAGAGCACCCCATTTGC[G/T]GCCATATGTGCTATCTGAAATAACACATTATGGTA K 2 1 2 1 600010 r 74 goat 2_19235203 2 19235203 Ancestral_priority_1043 ancestry 0.644 recommended IMAGE 10K 10K ancestral 38441653 Affx-122929197 AX-123311990 2 19247028 AGAAAATGAGTGATTCTGGAGGGGCAAACAGAAGG[C/T]ATTAAGTGCAGGATGTGTCGGGAGGTACTGTGGAG Y 2 1 2 1 201000 r 74 goat snp9446-scaffold1341-3999701 2 116398611 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436714 Affx-122932317 AX-123307052 2 19294426 TGAGTTCCCTCTGCAAGAGACATCTCTGCAGCAAA[C/T]AGCAAGCAGGGCTCCCAAGCCTGCATGGGACTCAG Y 2 1 2 1 202000 r 74 goat snp9445-scaffold1341-3952303 2 116351188 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376214 Affx-122978805 AX-123246573 2 19363701 ATTCCTTCTTTGGGTTATCATATATACATATCTCA[C/T]GAGACCTTACTCTAATCCCCTCCTTTTTTCAAACA Y 2 1 2 1 101000 r 74 goat snp9444-scaffold1341-3883028 2 116280966 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394356 Affx-122964652 AX-123264711 2 19402720 TTCTGGGAATAGCCTTGGTTAGCAATTGCTCATAA[C/T]GTCAATGCTTTTGGAAACTTTTTACAGTCATTTTA Y 2 1 2 1 101000 f 74 goat snp9443-scaffold1341-3844009 2 116241683 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795615 Affx-122926863 AX-385282570 2 19465202 ATCTGGTCAGTCAACAGTTTATTGGGCCTCTACTG[C/T]GGTCCAGAAAGTATTCTAGGCCCAGAGGACTGTGG Y 2 1 2 1 101000 f 74 goat snp9441-scaffold1341-3781527 2 116177800 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774049 Affx-122950319 AX-385261187 2 19495299 TGCAAAGCTTTGGAAGGGATATATCTGCCCTCAAG[C/T]AGAAACCTTTAGCTTCGGTTACGGTGAATGAGAGA Y 2 1 2 1 101000 f 74 goat snp9440-scaffold1341-3751430 2 116147866 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411812 Affx-122951251 AX-123282162 2 19533990 GACTAAATGAGACATTTTATATATATAGTAGCAAA[C/T]AGTCATAGGTACATTTCATTTTGAAAGTCCCATCT Y 2 1 2 1 101000 r 74 goat snp9439-scaffold1341-3712739 2 116109140 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387415 Affx-122970405 AX-123257773 2 19597303 GACATGGAGGCACAGAGATGTTATGAGATCTGCCC[A/G]TAGGGAGAGTCATGGAGATTTCTGAGTCCCAGTCT R 2 1 2 1 201000 r 74 goat snp9437-scaffold1341-3649426 2 116047767 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424689 Affx-122941703 AX-123295035 2 19655961 ACCTTGCTTAATCTTACTAAGATTGTCAGATCACT[A/C]TAGTCATTTACTCTTCACCTAGCAACCAAACAGAG M 2 1 2 1 101000 f 74 goat snp9436-scaffold1341-3590768 2 115988958 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452612 Affx-122920484 AX-123322945 2 19699707 TTCAGGCTTCTTTGGGATGGCCCTTTCATAGGCCT[A/C]GTCATAGCAACTAGAGACACGTGATGGAATCAGAG M 2 1 2 1 101000 r 74 goat snp9435-scaffold1341-3547022 2 115945347 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383506 Affx-122972644 AX-123253864 2 19743426 AGTTCCCTCTTATCAAAGCAAATTCACTGTCAGTT[A/G]TTTTGGGGGTTCCCTTCAGCTCTGATGAATTAACA R 2 1 2 1 102000 f 74 goat snp9434-scaffold1341-3503303 2 115901609 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393555 Affx-122965408 AX-123263911 2 19791655 AGTAGTTCATGTTCTACATGTTTATCCCAAATCAA[C/T]GGATGTCTGTATGGGAGAAACCAGGTTGTGGTAGG Y 2 1 2 1 201000 f 74 goat snp9433-scaffold1341-3455074 2 115853237 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787163 Affx-122953772 AX-385274189 2 19841633 CCATTCGCAATGATCATTGGAATCCTTTCATGTGA[C/T]AGTACATTTTTTGGAAGATAGAGATTCTTCTTTAT Y 2 1 2 1 101000 f 74 goat snp9432-scaffold1341-3405096 2 115802847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411544 Affx-122951652 AX-123281894 2 19888749 CCTACTGAACTAGATGCACTGGTATTTGGCCATCT[A/G]TATACCATTCTTACTACACAAATGACCAATGATGA R 2 1 2 1 101000 r 74 goat snp9431-scaffold1341-3357980 2 115755506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769437 Affx-122964537 AX-385256607 2 19926465 TGAGTGCCTGCTACATGCTAATCACTGTGCTAAGC[A/G]TTTAATTCTTAGGAACTCACTTAATCCTTATAATA R 2 1 2 1 102000 f 74 goat snp9430-scaffold1341-3320264 2 115717349 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375434 Affx-122979181 AX-123245793 2 19958674 ATCAGGGCAATGTCTGTTCTGTTCTTTATTTAGAA[G/T]CTCTGTAAACTACATAAAGGATGAAAAAGAAGACT K 2 1 2 1 101000 r 74 goat snp9429-scaffold1341-3288055 2 115685115 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785205 Affx-122968165 AX-385272251 2 20017456 CAAACCTCCCCAGACAAGATTTAATTCTCAAATAC[A/G]TTTAGGTAGGCACTGGATGTATCTACCAGTGCATC R 2 1 2 1 101000 f 74 goat snp9428-scaffold1341-3229273 2 115625877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389538 Affx-122968278 AX-123259896 2 20048676 TTCGCGGAGTATGGAGCCGCCACCCCCTCCAGCGC[G/T]ATCCGCACGAATTTCAGCACCAAGCAACTGACAGA K 2 1 2 1 101000 r 74 goat snp9427-scaffold1341-3198053 2 115594972 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426206 Affx-122940369 AX-123296552 2 20080790 AAATTCTTTGTTTATAAGTCTCAGTTCTCCTTCTC[A/G]GCTTCTAGGGATTCTCTTTTGAAATGTTAATGGGG R 2 1 2 1 101000 r 74 goat snp9426-scaffold1341-3165939 2 115562519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443582 Affx-122927330 AX-123313919 2 20139526 TCCCAAATGCCATGGTTCCTTGTAGATGAAGGAAA[C/T]GCAGCACCAGTTCTGGTCTCTCAAGCCTCCAGGCT Y 2 1 2 1 101000 f 74 goat snp9425-scaffold1341-3107203 2 115502970 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409568 Affx-122953587 AX-123279919 2 20180419 TTCTCACTAAGAGAGCCACCATCAATGCCCAAAGA[C/T]ATCCAGCTGGCTCTTTAGATGGATGGGGTTGGGGT Y 2 1 2 1 101000 f 74 goat snp9424-scaffold1341-3066310 2 115461828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804446 Affx-986696613 AX-385291026 2 20214453 AGGCAAAAAAAAATTCCTTAAAAAAAAACAAAAAC[A/C]AAAACAACTAGATCCTATTTACAAAACATGCAAAG M 2 1 2 1 600010 r 74 goat 2_20214453 2 20214453 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 38446383 Affx-122925585 AX-123316719 2 20236668 AAAAGTCAACAAAAAGAATATTTTACTTACATTAA[C/T]GGGAAAGCAAAAAATGGAAGTGTCATGGCAAGTCT Y 2 1 2 1 201000 f 74 goat snp9423-scaffold1341-3010061 2 115405486 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379732 Affx-122975875 AX-123250090 2 20297198 ATTTTCCTCATCCTCACTCTCATTAAGAAAATAAA[C/T]ACAATCAGAAAACAATTCGAATCACCTACCTATAA Y 2 1 2 1 101000 f 74 goat snp9422-scaffold1341-2949531 2 115344023 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408864 Affx-122953997 AX-123279215 2 20328738 TCTCCTCTGGTTCCTCTATGCCAGATGCTTGTTCA[A/G]TCACTGGGTCTGTCTGCTCTGTATCTGGTATTTTG R 2 1 2 1 201000 f 74 goat snp9421-scaffold1341-2917991 2 115311902 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398610 Affx-122961481 AX-123268965 2 20391461 CTGAATTTCCCTCTTTCTTAGATGAAACTCCATCT[A/G]CATGAGTAGACAGATCCAACAGGTACCCGTAGGCC R 2 1 2 1 101000 f 74 goat snp9419-scaffold1341-2855268 2 115248741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425130 Affx-122941213 AX-123295476 2 20445133 TTAATTCTTAACTCACACTAAAATATTTATCTATT[A/G]TGTATGGTGCAGGCTTTGGGACATGATTCTCCTGT R 2 1 2 1 101000 r 74 goat snp9418-scaffold1341-2801596 2 115195002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776776 Affx-122950049 AX-385263900 2 20496916 ACCACTGAGAAAAGGCAATGAAACATGAAGATAAG[C/T]AAACAACTGCCTTCCAGTCTGTAAACCAGTTCCAT Y 2 1 2 1 101000 r 74 goat snp9417-scaffold1341-2749813 2 115143037 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769993 Affx-122970423 AX-385257160 2 20556666 TATTGTACCAAGGATATCACAGAAATTATCTCAAA[C/T]GCATAAGGTAGGCATTATTTTTATCCTAAATTAGA Y 2 1 2 1 101000 r 74 goat snp9415-scaffold1341-2690063 2 115082740 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783953 Affx-122929724 AX-385271007 2 20589364 CAGGCGTGCACTATCTTTGCAAATAAAAAGCTCAC[A/G]TACACAGACTATACACTGCATCCTGCTTTCCCTCA R 2 1 2 1 101000 f 74 goat snp9414-scaffold1341-2657365 2 115050192 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379990 Affx-122975615 AX-123250348 2 20622014 GAGAGATGCTAGGACCCTCCATAAAATGATCAAAT[A/C]AGGCCTATTCAATCAATGTCTCTAGAGCTAAAGAA M 2 1 2 1 101000 f 74 goat snp9413-scaffold1341-2624715 2 115017403 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770270 Affx-122954636 AX-385257436 2 20651655 GTAGCATTTTCTTCTGCTAGAAATGTCAGAAAAAT[A/C]TTCCTAGAAAAGGAGACCCTCAAGGTGAGTCAGAA M 2 1 2 1 101000 r 74 goat snp9412-scaffold1341-2595074 2 114987844 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795993 Affx-122967324 AX-385282945 2 20717799 GAACAAAAATGTCGATGCATAGTAACGACTATTTT[C/T]GGCATATGCAGAATGGAAGGTGCTTAGGAAGATGG Y 2 1 2 1 101000 r 74 goat snp9411-scaffold1341-2528930 2 114921116 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464112246 Affx-1110321707 AX-515588223 2 20778482 AATAGTGTGTTAGTTTCTGGTGTACAACAAAGTGA[C/T]TCATAGATATATTCTTTTTCATATTTTTTTCCATT Y 2 1 2 1 103000 f 74 goat 2_20778482_AF-PAKI 2 20778482 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449244 Affx-122923477 AX-123319579 2 20789696 AAAGGGGAAGATCCACAATATCAATAGGTGGCAGG[C/T]GCCAAGTGTGTTGCTGGTAGATACAGTGGAGTATC Y 2 1 2 1 101000 f 74 goat snp9409-scaffold1341-2457033 2 114847930 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426781 Affx-122940550 AX-123297127 2 20821438 CAAATCGATTTGAACCACACTAAATCCTAGACCCA[C/T]ACTGAAACAAAACTGGTGTGTGACAAGCAATTGTT Y 2 1 2 1 101000 r 74 goat snp9408-scaffold1341-2425291 2 114816028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793565 Affx-122962331 AX-385280540 2 20876780 GATAATAATGAGTGCATGTGTCTCCAACAGCTTTT[A/C]GGAAAAGGTACAATGTTCTATATGTAAACTAGTGG M 2 1 2 1 101000 f 74 goat snp9407-scaffold1341-2369949 2 114760586 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391519 Affx-122966661 AX-123261876 2 20910714 GCAGAGTAATCATATTGTGAGAAACACCAGGCTTA[C/T]GTAGTAACAGCTGTTGCAGTTATCCATGCCGACTT Y 2 1 2 1 101000 f 74 goat snp9406-scaffold1341-2336015 2 114726573 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375395 Affx-122979211 AX-123245754 2 20969690 ATCCCAAGGATTCTCTATCCTCCTTTTCCTTTGTA[A/G]TAATGGAGCTGTGGCCAGGATGAGACTTCCCCCTT R 2 1 2 1 101000 f 74 goat snp9405-scaffold1341-2277039 2 114667500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444801 Affx-122926337 AX-123315138 2 21013309 AGCCCTATCCAATATATTTCAAATTATATTCAAAC[G/T]CTAATCTATTCATGGTAAGGCTATTCCTGTTTTAA K 2 1 2 1 101000 r 74 goat snp9404-scaffold1341-2233420 2 114623860 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770485 Affx-122975931 AX-385257651 2 21062750 TTGTTAGCCTTTCATAAATATGTAACCTTCAAAAA[C/T]GTTTCAGAAAAAGCCCTTCACAAACAGAGATGACA Y 2 1 2 1 101000 r 74 goat snp9403-scaffold1341-2183979 2 114574536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769030 Affx-122919968 AX-385256205 2 21114637 AGTGTAAATCACAAACAATAGAAAGACACAAGAGA[C/T]CTTATTACTCTAAGAGCCATTTTTAGCACTGCTTA Y 2 1 2 1 101000 f 74 goat snp9402-scaffold1341-2132092 2 114522555 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771427 Affx-122947383 AX-385258585 2 21143621 ACAGAGAAGGGACACTGCCCGGCTCATTGGTACAT[A/C]TAGTGAAGCAAGCAATCATAGCCTGCTAGTTTTTC M 2 1 2 1 101000 f 74 goat snp9401-scaffold1341-2103108 2 114493366 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432469 Affx-122935606 AX-123302810 2 21191530 GAATGAATGTTTGATTGGTATTCTTATTTACTTGA[C/T]ATGCAAAAAAAAAAAAAAAGCCCCACCCCCTACCT Y 2 1 2 1 201000 f 74 goat snp9400-scaffold1341-2055199 2 114445522 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781415 Affx-122922143 AX-385268500 2 21225157 TCCTACTTTACAGATTACTGAAAGGATTAAATACT[A/G]TATGTAAAAGACTTAAAACGGTCTCCAGCATATGA R 2 1 2 1 201000 r 74 goat snp9399-scaffold1341-2021572 2 114411359 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798582 Affx-122962009 AX-385285515 2 21355434 AGACTTTCTGAACAAGATGACTTCCCTCTTTTTAA[C/T]GGACCAGACTGCTGCTCATTAAGTACAGGAAGGTT Y 2 1 2 1 101000 r 74 goat snp9397-scaffold1341-1891295 2 114281189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794358 Affx-122956693 AX-385281322 2 21402215 GACTACAAAACCTTTTTTCGATGTCACCACTGCCA[A/G]TTAGCAGCAGTGAACCCCAGTGAATGCTGGGAACC R 2 1 2 1 201000 r 74 goat snp9396-scaffold1341-1844514 2 114234150 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389859 Affx-122968154 AX-123260216 2 21452954 TTTTTGAGTTATATGCAGAAAGAACCTGAAATAGC[A/G]TCTCCACTGCAATCTGTTTTCAATTAGCTCTGTTG R 2 1 2 1 101000 f 74 goat snp9395-scaffold1341-1793775 2 114184193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275289 Affx-1111834817 AX-519548864 2 21534277 CTTCTCATCTGGGCAAACTTATAGGTTTGGATTCA[A/G]CACTGCAGTGTGGTTCAAACCTGCAGTGATCGAGT R 2 1 2 1 101000 f 74 goat GoatD01.054658 2 21534277 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38435544 Affx-122933393 AX-123305884 2 21548148 TTTAAAAATAATCTCAGAAACAGAGAAATTGAGAA[C/T]TAACATCACACTATTCTATGTCCTGCTAATATAAA Y 2 1 2 1 101000 r 74 goat snp9393-scaffold1341-1698581 2 114089174 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415996 Affx-122948395 AX-123286345 2 21577895 TGAGGTGGAAGTAAGCTTAAGTTAAAAAACCAAGG[C/T]TCATATGCCAGGGACACAGTGAGCACAGAGGAGAA Y 2 1 2 1 101000 f 74 goat snp9392-scaffold1341-1668834 2 114059505 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451988 Affx-122920931 AX-123322321 2 21623112 CGGGGACACCTATATAGATGGAGTTAAGTAAAGGA[C/T]ACTATAGAAAGGGAAAATGAAGGCATTTCCATACA Y 2 1 2 1 101000 f 74 goat snp9391-scaffold1341-1623617 2 114014282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799945 Affx-122974621 AX-385286871 2 21657592 GTAAGAAATTTGAAAGTTAATGGCAAATTTCAATC[A/G]TTCATTTCATTAAGTTTCATTTAGTTTCTCACCAG R 2 1 2 1 101000 r 74 goat snp9390-scaffold1341-1589137 2 113979647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396003 Affx-122963493 AX-123266358 2 21694759 CACATGGCAATAATTTTGTTGGCAAATTTAAATGC[A/G]TCTGTTCAAATTATTATTTTTAGTACCAAAGTTAA R 2 1 2 1 101000 f 74 goat snp9389-scaffold1341-1551970 2 113946180 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772088 Affx-122955085 AX-385259243 2 21751380 ACAAACAAAAAGGTTAAGTAAGAGACATACAGATA[C/T]ATGTGACCATTCACTCTATTAAAGCCAAAATAAAC Y 2 1 2 1 101000 r 74 goat snp9388-scaffold1341-1495349 2 113889645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423896 Affx-122942288 AX-123294242 2 21781949 TATGACTGAAATCCATCGCGGGGGTCGCTTCTGCT[A/C]GGATTCTTGTCTTCGTGTGTGTGTATGTAAACATT M 2 1 2 1 201000 f 74 goat snp9387-scaffold1341-1464780 2 113859367 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432560 Affx-122935536 AX-123302901 2 21839525 GGGATGCAGGTGGCTAGAGCAAAGCAAGGAGTTTA[C/T]GGTGGCAATGGAAAGAGACCCAATCCTAAAGGAAT Y 2 1 2 1 101000 f 74 goat snp9386-scaffold1341-1407204 2 113801692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413718 Affx-122950072 AX-123284067 2 21888833 TTACCTATATGATGGGTAAAGTATCTAGAGGTCTG[A/G]TGAAACAGTGGGGTCTTCTTTAGTTCCCAACAGGA R 2 1 2 1 101000 f 74 goat snp9385-scaffold1341-1357896 2 113752088 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382171 Affx-122974026 AX-123252529 2 21940595 CCTCTTCTCTCCTGCTACCTAGGAAATGATCTAAT[A/C]TTTCTCACTTCACAGAGAAAATGTAAGTCATCTTG M 2 1 2 1 101000 f 74 goat snp9384-scaffold1341-1306134 2 113700309 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770211 Affx-122945518 AX-385257378 2 21998988 AAGAAAAACAGATTTGAAGTGAACCAGCAGGAAGT[A/G]TATTTCACTTTGCTATAATTTCTAAACCAATATTA R 2 1 2 1 101000 f 74 goat snp9383-scaffold1341-1247741 2 113640964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437641 Affx-122931804 AX-123307979 2 22043100 ACCTATATTTTTAAGTTTCTCCTTCACTCTTTTCC[A/G]CTCTCCATATAAACATATAACTAGTGCCGAAAACA R 2 1 2 1 101000 r 74 goat snp9382-scaffold1341-1203629 2 113596387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773138 Affx-122936645 AX-385260281 2 22088868 AAGAAACTGAGAATTATGGGTTGAATAAATTTGCT[A/G]TCTAACTAATGATAACAATTCACATTTAAGTGCAT R 2 1 2 1 101000 f 74 goat snp9381-scaffold1341-1157861 2 113550311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412191 Affx-122951055 AX-123282541 2 22143982 ATTTAACAGCTTATCCTGCCTTTCTTGTACAAACC[A/G]TGCTTTGGGGGTAACCAAACAGCTAACAAGAGAAG R 2 1 2 1 101000 r 74 goat snp9380-scaffold1341-1102747 2 113495459 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796683 Affx-122964454 AX-385283628 2 22182319 TAAAGATACAGCCCTTTGATAGGAGTCCTCAGATT[A/G]CAGATGGACTCCTAGGCCTTTTCATCCGTTCTCCT R 2 1 2 1 101000 r 74 goat snp9379-scaffold1341-1064410 2 113457148 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774301 Affx-122934500 AX-385261437 2 22280188 GTAAGCAATCATACTCTGAAAGGTCCCTGGTTTTC[A/G]TCTCTTACAGGTCTGCAAATTTCTCAGAAGCTAAA R 2 1 2 1 101000 f 74 goat snp9377-scaffold1341-966541 2 113358912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381060 Affx-122974620 AX-123251418 2 22309389 GTTCTCTAAATCATGAGAGCCTGGGCAAAAAAGGA[A/G]CACAAACCAGTCAAAAGGGGAGAATTTTTCTCTGT R 2 1 2 1 101000 f 74 goat snp9376-scaffold1341-937340 2 113323200 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419397 Affx-122945605 AX-123289745 2 22347876 ACACAGTGACAGCATTTTCTGCAGGACGGTGGCAC[G/T]AGAACTGGTGACAGAGAGGGGAAGAGTTCGAGGAC K 2 1 2 1 201000 f 74 goat snp9375-scaffold1341-898853 2 113284441 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438158 Affx-122931461 AX-123308496 2 22393150 AATGGAAGCATGGTGCTTTAGGCACAGGATCACCA[C/T]GGAAGTCTCTCTTTTGTCTTTTGACTTTGCTTATT Y 2 1 2 1 303000 f 74 goat snp9374-scaffold1341-853579 2 113239463 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431268 Affx-122937111 AX-123301609 2 22430265 ACTGAAGAACGGAAACAGGGCTCATTTTCTCTTCT[C/T]GCCTTTCCCCCCTTCTCTCTCCTCATCTTCCTCTT Y 2 1 2 1 101000 f 74 goat snp9373-scaffold1341-816464 2 113202022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798018 Affx-122938301 AX-385284954 2 22467769 AGCCATACAGCTGTGGGTGAAGCAGCTGTATGATA[C/T]CCTGCCTTCCACATCGTCAACCAAATTGTCTGTTC Y 2 1 2 1 101000 f 74 goat snp9372-scaffold1341-778960 2 113163921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419816 Affx-122945832 AX-123290164 2 22525683 GCAAGCTACCAATGTGATGTAACTGAAAGTAGAGA[C/T]AGGAAGAGATATACAGTAGGGAGTCATCAGATAGC Y 2 1 2 1 101000 f 74 goat snp9371-scaffold1341-721046 2 113105599 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789872 Affx-122936206 AX-385276879 2 22572067 ACAATAGAGGAGGATGAGGCAAAGGGAGTTAAGAA[C/T]GTTTGAAAATGGAATGAAACGTGGAGTTGAGGGTA Y 2 1 2 1 101000 f 74 goat snp9370-scaffold1341-674662 2 113058875 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425763 Affx-122940729 AX-123296109 2 22668308 CGTTTGGCTTTGCATCTGCAGCCTGTAGCTATGCC[A/G]TTCAGTTCAGTGTTTGGTGCATAATTGGACCTTGA R 2 1 2 1 201000 r 74 goat snp9367-scaffold1341-578421 2 112962549 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383890 Affx-122973121 AX-123254248 2 22722562 CTTATTCATCTCAAGTGCACAGAACTTAGATCCCT[A/C]GTTACTTGTAACTGAATTAAAAAAAAGAAAAAAAG M 2 1 2 1 103000 f 74 goat snp9366-scaffold1341-524167 2 112908119 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399971 Affx-122960828 AX-123270326 2 22778039 TTTAAGTGGACACTGAGACACGCAGCAGAGAAGGA[A/G]GCAGCGGCTCATAGGAGGGTTTTGCGGACTTGCAA R 2 1 2 1 201000 r 74 goat snp9365-scaffold1341-468690 2 112852824 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411322 Affx-122952278 AX-123281672 2 22821640 AAAATCAGTGGCTCCAAGGAAGATACTTTTGTCCC[A/G]TTTTGTGACACTGTAATTGACCAGCTTGCTCAATA R 2 1 2 1 201000 r 74 goat snp9364-scaffold1341-425089 2 112808948 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442037 Affx-122928400 AX-123312374 2 22855529 GCCCTGTGCAATGGGCTTTGCATTTCTTTTCACTG[C/T]GGCTATTTAGGAGATATAATGAAATCATCAATAAG Y 2 1 2 1 303000 r 74 goat snp9363-scaffold1341-391200 2 112774990 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404330 Affx-122957005 AX-123274682 2 22892354 CATTGCATTTAGTCATGTTTCTTGAAGTCTTCCAT[A/G]TACTAGAAGCTTCTCTGCCTTTTAAATCATGACTT R 2 1 2 1 101000 f 74 goat snp9362-scaffold1341-354375 2 112738399 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429296 Affx-122938610 AX-123299638 2 22921789 TCACACAGCTCGTAAGAAGCAGACCTCAGTCAAGG[C/T]CTATCCAACCCAAAGCCCATGTTCTTAGTCCCTAT Y 2 1 2 1 201000 f 74 goat snp9361-scaffold1341-324940 2 112708489 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421623 Affx-122944472 AX-123291970 2 22952405 TCTGAAGAACTGTCCTAAAAGAACTAAACATGTTT[A/G]TTGTTGCTTAAGAGCTTCAGAGATAGGATGCTAGG R 2 1 2 1 101000 r 74 goat snp9360-scaffold1341-294324 2 112678034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420987 Affx-122944568 AX-123291334 2 22981313 ATGTTTTCTTTATTTCTTGACTCTGCTTCTCAGAC[A/G]TGTGTCCTCTGAGTTGCAGACATTCATCTGTCATC R 2 1 2 1 101000 r 74 goat snp9359-scaffold1341-265416 2 112649225 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395492 Affx-122963892 AX-123265847 2 23037427 GCCATTCTCTCTCGAGCACCTCACATGATAAGAGA[C/T]AGAAAATACCACCTAAAGACATACAGGTATGTGTG Y 2 1 2 1 102000 f 74 goat snp9358-scaffold1341-209302 2 112593115 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277209 Affx-1111835796 AX-519550715 2 23053013 CAGTTAGCTTCATCCAATGGGAGGTTACCAGCCAG[A/C]AGTCTAGAGGAAGGAGAAGAAGAGTAAGGCTGGGG M 2 1 2 1 202000 f 74 goat Random2.2K-177 2 23053013 A C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446043 Affx-122925841 AX-123316380 2 23081441 CCCTTTATGTTTCTCTAATAGCAATAATATGCCTG[C/T]AGACTGAAACAAAAGCACTTAGGCTATTGTCTCAG Y 2 1 2 1 201000 f 74 goat snp9357-scaffold1341-165288 2 112548991 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379011 Affx-122976373 AX-123249370 2 23121853 TTAAGTAAATCTAGTATTTTTCTTCTAAATGTATA[C/T]TAAATTTCTCAAATTAGATTTATTGGATTGATTTC Y 2 1 2 1 202000 f 74 goat snp9356-scaffold1341-124876 2 112508579 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424251 Affx-122942464 AX-123294597 2 23154612 CAGGAAGGCTGGGTAACAAGAGCTAGTATCCCAAG[A/G]GAGCCAGGCAGAAGTGCTTTCAGTTTGATGACCTA R 2 1 2 1 201000 f 74 goat snp9355-scaffold1341-92117 2 112475925 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273724 Affx-1111833763 AX-519547336 2 23194919 GTGAGAATATGCAGCCCTTCACCTGAAAGCTGCAG[A/G]CAGATTTACTTGAATTCCGGAAATATGGTGGTTAA R 2 1 2 1 201000 r 74 goat GoatD01.003848 2 23194919 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386854 Affx-122970073 AX-123257212 2 23203793 ACCCCGCATGGAGGGTCATACTTACTTCTCATTGG[C/T]GATACCCTCTGAGCAGAGTAGTATTAACTCTCATC Y 2 1 2 1 201000 r 74 goat snp9354-scaffold1341-42936 2 112426682 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451819 Affx-122921477 AX-123322152 2 23240701 TAAGATATAAAAAGGTTTGAGTTCGTTTGTATCTC[C/T]ACAAAGATAAACCCTTTCTCTGAAACAAACATGTA Y 2 1 2 1 101000 f 74 goat snp9353-scaffold1341-6028 2 112389314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443714 Affx-122927150 AX-123314051 2 23256815 ACTCTTTAAACAGCTTTGAGATATAGGAAAGTTCT[A/G]TCTCTAGTGTCCCTCGCCACTCTTGTCGCTCCTCC R 2 1 2 1 201000 f 74 goat snp26534-scaffold2760-100572 2 112372574 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769875 Affx-122925112 AX-385257044 2 23309379 ATACATTGACTGTGGTCCATTTTGACTTAGCAGTT[A/C]TAATTATCTGACAGCAGATAATTGAGAGGTTATTG M 2 1 2 1 101000 f 74 goat snp26533-scaffold2760-48008 2 112319729 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804448 Affx-986696615 AX-385291027 2 23313711 AAGCAGCTTCTAAAAAGCCCTTCTGCCTTCTAGGA[A/G]TACATTATATTCAGGGGATATCTGGGATCTCTAGC R 2 1 2 1 600010 r 74 goat 2_23313711 2 23313711 Ancestral_priority_1043 ancestry 0.64 recommended IMAGE 10K 10K ancestral 468272026 Affx-1111833163 AX-519545793 2 23328927 CTGGAATGCCATCACCTCTACTAGCTTTGTTCATA[A/G]TGATGCTTCCTAAGGCTCACTTGACTTCACATCCC R 2 1 2 1 103000 f 74 goat 2_23328927_AF-PAKI 2 23328927 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320776007 Affx-122938640 AX-385263137 2 23354524 CTTAGCAATGGTTTAAATTCATGATTAACAAGTCC[A/G]TAATAGTTAAATCCTGAGTAGAAGATACTTCACAC R 2 1 2 1 101000 f 74 goat snp26532-scaffold2760-2863 2 112274662 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389271 Affx-122969016 AX-123259629 2 23358490 ACGTTTCTTAGTGCAGGCTTTCTAATCGCTAACAC[A/G]CAGGTTACTGTCTGTCTGCTAGCAACAAAGTACAC R 2 1 2 1 101000 f 74 goat snp29696-scaffold3212-1004 2 112270835 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397533 Affx-122962040 AX-123267888 2 23535963 CTCTACTAAGCACCCAAACTGTGTGCTTTCTTAAA[C/T]GTAAGAAAAGCAAGAAGCCGTGCAGAATCTAGGAT Y 2 1 2 1 102000 r 74 goat snp29700-scaffold3212-178477 2 112093291 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414696 Affx-122949283 AX-123285045 2 23568400 GACATCCTTGCCTCATTACCTACCATGCCCACCCC[A/G]CACTCTAGCCAAATTTCTGTTGTTTTCCAAACACA R 2 1 2 1 101000 r 74 goat snp29701-scaffold3212-210914 2 112060340 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390902 Affx-122967099 AX-123261259 2 23607634 AAGAAAAAGGCAATCGGAGAAAGATGGAAGGAGAA[C/T]GGAAAAAGGAGAACAGTGAGTGGAGATGGGCCATT Y 2 1 2 1 101000 f 74 goat snp29702-scaffold3212-250148 2 112020942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447333 Affx-122924890 AX-123317669 2 23700090 ATACTTTAGACTTCCATTTTCAGTTTGTCAGTTCC[G/T]ACCAAAAAAATCTGGGGAGAAATGACATCTTAACA K 2 1 2 1 101000 f 74 goat snp29704-scaffold3212-342604 2 111929443 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418005 Affx-122946662 AX-123288353 2 23786385 CATGAAAAAGTCTGGTGGGAACAAAGGAACAGAGA[A/G]AGTCAAGACTATGGAAACTGGATCTTTTATGTTTC R 2 1 2 1 101000 f 74 goat snp57704-scaffold928-51669 2 111842521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376420 Affx-122978078 AX-123246779 2 24090600 TAATTCCTGTTACAAAGTTACTTCATGGTCCTTTT[A/G]TGCCTGTGCCACTGTATGCAAGCTTATCTGAATGA R 2 1 2 1 101000 r 74 goat snp57710-scaffold928-355884 2 111537915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774115 Affx-122925350 AX-385261253 2 24125480 AGCAGAGTGCTTACTACATATCAGGTATCGTGTAA[A/G]ACACTTACACTATCTCTAATCCTCTTACCAAAACC R 2 1 2 1 101000 f 74 goat snp18657-scaffold1882-999231 2 111503287 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774263 Affx-122959271 AX-385261399 2 24187269 TTAACTCTCGCTTCCAAAATTTTGTGGGATGAAGA[G/T]TAGGGATGATGTCCACTGAAAATCTCAATTTAAAT K 2 1 2 1 101000 f 74 goat snp18656-scaffold1882-937442 2 111441636 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799936 Affx-122953595 AX-385286862 2 24227815 TGGTAATCTTTTTCACTGTACAGTGCCGACTCTGA[C/T]TACTCCCTGTGGATATTTCTTAGCTAAAAATTAAT Y 2 1 2 1 101000 f 74 goat snp18655-scaffold1882-896896 2 111400608 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393629 Affx-122965307 AX-123263984 2 24257222 AATTTTGTGGCTGTTAGCTGCAAATTAGAGTTCAC[A/G]TATGGCACATTGTTGCCAACATGCATCCTCTTCAG R 2 1 2 1 101000 f 74 goat snp18654-scaffold1882-867489 2 111371307 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802615 Affx-122972463 AX-180660645 2 24297182 ATGCATGATCATATAGTTCTGATCAAATTAGTATA[A/G]TCTTTTATGAAGTAAGTTAGCAATTTGTTTTTTTT R 2 1 2 1 201000 r 74 goat snp18653-scaffold1882-827529 2 111334490 A G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452168 Affx-122921241 AX-123322501 2 24389923 TTATGGCCTGTCTAAGCTGGTAGTACAGAAAGCAG[C/T]GGTGATTTAGGATGTGGAATTGAGGGAGACTATAA Y 2 1 2 1 101000 f 74 goat snp18651-scaffold1882-734788 2 111246283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476164 Affx-1251763667 AX-586011592 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 4 1 4 1 20000 f 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 539476419 Affx-1251763667 AX-586011821 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 4 1 4 1 20000 r 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562165680 Affx-1251763667 AX-606941089 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 f 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562165712 Affx-1251763667 AX-606941121 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 f 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562165724 Affx-1251763667 AX-606941133 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 f 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562165838 Affx-1251763667 AX-606941247 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 r 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562165951 Affx-1251763667 AX-606941360 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 f 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 562166377 Affx-1251763667 AX-606941785 2 24402029 GAACTGTTATGGGAGGGTTAAAGGAGGAGATCCAA[-/ACATTTAATGACTTTTTTTTTTTTTTTTAAATTTTAAAATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CATTTAATGACTTTTAAAAGACTTTTATTTCCTGA - 8 1 4 1 20100 r 74 goat SV_197 2 24402029 - deletion junction SV-TF-chip 320780846 Affx-122946609 AX-385267934 2 24424909 TTGTGTTTTCCTATCTTGCTTGAAATGCCACCTTT[A/G]CCTATCTCCCAGAGAAAGCAATAATATGACTATCA R 2 1 2 1 101000 r 74 goat snp18650-scaffold1882-699802 2 111211281 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274738 Affx-1111834467 AX-519548324 2 24468858 CTTCCACAGCTTCAGAGAAAACCTCAGGCAAAGAC[A/G]TGTAGACAGGGAGCGATGGAAGGTG R 2 1 2 1 101000 f 74 goat GoatD01.036983 2 24468858 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38393935 Affx-122965074 AX-123264290 2 24483094 TAAAGTTCCTTTTAAGGAGATAAAGAGAAGGAAAG[C/T]GATGATTTCTGCAGTGTGATTTTGTGATGGTCTGT Y 2 1 2 1 101000 r 74 goat snp18649-scaffold1882-641617 2 111152051 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772379 Affx-122962182 AX-385259533 2 24550719 CTAGGAGAAACAGGGTAACAAGGGCCATGTTTTCC[A/G]TATAAAAATCTCTTCACTAGAATATGAGGACTTCA R 2 1 2 1 101000 f 74 goat snp18647-scaffold1882-573992 2 111087165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788897 Affx-122935805 AX-385275912 2 24585412 CATGACAAGAGTTATCAGCGTTAACAGTTTTTATA[A/G]GAACTGTGCCAGTGCCATGAGTTGAAGTGTAAGAA R 2 1 2 1 101000 r 74 goat snp18646-scaffold1882-539299 2 111052769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775771 Affx-122950946 AX-385262902 2 24617359 CTTGCAACAGAGAGGTAACACACAAATATGCAGGA[G/T]GTGATGGCGAAGCAAAGTTGCAACCATCTGCGTGG K 2 1 2 1 101000 f 74 goat snp18645-scaffold1882-507352 2 111022333 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438293 Affx-122931393 AX-123308631 2 24675161 ATTGAGGCAACGTGCTGCAACTATCGAAGTCCGCA[C/T]GCCTAGAGCCCGTGCTCCACAAGAGCAATCACTGC Y 2 1 2 1 101000 f 74 goat snp18644-scaffold1882-449550 2 110963992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411366 Affx-122952245 AX-123281716 2 24865131 ACTTAGTTGTAATGATTAACTGTCTGCTATGTCAT[A/G]TGCTAAATGCTGGGAGGATTGTCTCCTCCCACCCC R 2 1 2 1 201000 f 74 goat snp18641-scaffold1882-259580 2 110773087 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785671 Affx-122948273 AX-385272712 2 24898294 AAAATCTGATCTGTGGTCTAGATCAGATAGATCAC[A/G]TCTGATCAGTGGTCTACTTTTTCACTGAAGACAAT R 2 1 2 1 201000 r 74 goat snp18640-scaffold1882-226417 2 110739735 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409560 Affx-122953593 AX-123279911 2 24941452 TAACCAAACAATGCTTCCATATTATTATTACATCA[A/G]TACACTTAGAACAGCACAGGTTCTAAAAGGTAGTA R 2 1 2 1 103000 r 74 goat snp18639-scaffold1882-183259 2 110696724 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803995 Affx-986696619 AX-385290688 2 24970721 CCCGGGTATTAATAATTGTGGGGGGGCCAGTCCAT[C/T]GATTTCCTTTTAGATACTGGGGCAACTTACTCTGT Y 2 1 2 1 600010 f 74 goat 2_24970721 2 24970721 Ancestral_priority_1043 ancestry 0.552 neutral IMAGE 10K 10K ancestral 320791431 Affx-122976227 AX-385278423 2 24974323 GGCTGTTTTCTGTGTCCAAACTTGGTTCTCCCTGG[C/T]CAACGCTGTATTTGTCAGTTACTTCCACAGAAATG Y 2 1 2 1 101000 r 74 goat snp18638-scaffold1882-150388 2 110665073 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443471 Affx-122927823 AX-123313808 2 25003729 CTCTGCATTGGCAGTACGGAATCTTAACCACTGAA[C/T]AGCCAGGGAAGTTCCCCCGATAATTTTTATGATCT Y 2 1 2 1 103000 r 74 goat snp18637-scaffold1882-120982 2 110635585 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408303 Affx-122953777 AX-123278654 2 25045382 CAGAGATGAGTCTTTGAGTCTTAAGGTCCTTTAAA[A/G]GCCTATTATCTATTGGTCTGAAATGGTTCATGAGG R 2 1 2 1 101000 r 74 goat snp18636-scaffold1882-79329 2 110593841 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777792 Affx-122919981 AX-385264910 2 25091626 AATGCTCTCTATGACATCATTTTTCTTTCTAAGCA[A/G]TCTCCTGAGATAGGTAACTGTAACATTCCTAGCAA R 2 1 2 1 201000 f 74 goat snp18635-scaffold1882-33085 2 110547883 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451661 Affx-122921593 AX-123321994 2 25135148 AGGCATTCCTGAAAAAGGAACCCAGTGAGCTCCAT[A/G]TTGGGTGCCGGTTTGGAGTGTCAATGCTGGTAATT R 2 1 2 1 101000 f 74 goat snp33253-scaffold39-1061865 2 110504424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448404 Affx-122923677 AX-123318740 2 25167125 TAAACAATACTTGTTTGGGGTAGTCTCTAGGGTTC[A/G]TTACGAAGAAGCAGGAGGCACCTGTGCCCTCCCCC R 2 1 2 1 101000 f 74 goat snp33252-scaffold39-1029888 2 110472431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434543 Affx-122934143 AX-123304884 2 25223409 CTTTTTTTATAAAAAGCCTTTTTTTTTTTTAGTAT[A/G]ATAAAGCCTGTACTTTTTCTAAAGAAATCTCAACC R 2 1 2 1 101000 r 74 goat snp33251-scaffold39-973604 2 110415651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390125 Affx-122968003 AX-123260482 2 25273333 GACCCAGAGGAAATAAACATCCTTATCAATGAAGA[C/T]GAAGGGACACAGAGCAGAATCTGAACAGACAGGCC Y 2 1 2 1 201000 f 74 goat snp33250-scaffold39-923680 2 110364556 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396167 Affx-122963779 AX-123266522 2 25313919 GATAGGTATCAACTGTCTAGGTTCCAGCACTTTTG[C/T]GAACACATGTCATGTCACTTGGCAGTCATGGTATT Y 2 1 2 1 101000 f 74 goat snp33249-scaffold39-883094 2 110323206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449823 Affx-122922400 AX-123320158 2 25360592 GTTTATTGAATATTATGATGAATAGCTGAGAAAAG[C/T]GATGGAATCTATTTAAAATTCTTTCTAAACTCTAG Y 2 1 2 1 101000 f 74 goat snp33248-scaffold39-836421 2 110276338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410897 Affx-122952071 AX-123281247 2 25417261 AGGAGCTCAGCCTAATCCAGAATAAGCAAATGGCA[C/T]AGTAAAGTAGGTGCCCCAGACTCCTGTCAGCATAT Y 2 1 2 1 101000 r 74 goat snp33247-scaffold39-779752 2 110219595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797614 Affx-122920506 AX-385284553 2 25461019 TGTGTGTATATTTGTGTAACTGTATTTCTGTGAGA[C/T]AGATAATAGAAAGTGGAGCCTGTGACTCAAAAGAT Y 2 1 2 1 101000 f 74 goat snp33246-scaffold39-735994 2 110175934 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447075 Affx-122924501 AX-123317411 2 25510613 TCAGCATTTCCTTTCCTAAAGCTAATGGCAAGTAA[C/T]GACAAAAATCCTTTGAATCTATTTGGTTTCAGAAT Y 2 1 2 1 101000 f 74 goat snp33245-scaffold39-686400 2 110125645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445607 Affx-122925111 AX-123315944 2 25565983 TGATGCAAGTGCAGAGGGGACTCACATGAATTAGA[C/T]GGTCCCTGTCTATAAGAAGACTGAGATCCTGATGG Y 2 1 2 1 101000 f 74 goat snp33244-scaffold39-631030 2 110070349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402365 Affx-122959042 AX-123272718 2 25607905 TAGTCTTTTATTAGAATATTGTAGACAAGAGCCCA[G/T]AAGGGGTTGTCTGTATGGAAAAATGAATCTGGCAT K 2 1 2 1 101000 f 74 goat snp33243-scaffold39-589108 2 110028734 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800799 Affx-122923337 AX-385287715 2 25643693 AGCCGTCAGGGAAGCCTAGCAAAGAGCAGTATGCA[C/T]AATTTATAACCCAACTATACCAACCCTGGATGTTT Y 2 1 2 1 101000 f 74 goat snp33242-scaffold39-553320 NW_017213515.1 3838 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404004 Affx-122957196 AX-123274356 2 25702056 TACTGTATTCAAATTTTAATGTATTTCTAAGAAGC[A/G]TTTTGTTACAGTTACCAGTCATTCAGATGGATTAT R 2 1 2 1 101000 r 74 goat snp33241-scaffold39-494957 2 109933805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409284 Affx-122953113 AX-123279635 2 25739445 TCTAATCCAACACCATAGTATTTATTCATCTTTTC[A/G]CTCTTTTCAAATTATAATCTCTAGTCCCACAGTGA R 2 1 2 1 101000 r 74 goat snp33240-scaffold39-457568 2 109896294 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432377 Affx-122935860 AX-123302718 2 25771696 TTAAAACACTTTTAAGGCAGCCTGATTTAAAGGAG[C/T]GGTACTTTATTATGAGTACAGAGAGATCGTTCAGG Y 2 1 2 1 101000 r 74 goat snp33239-scaffold39-425317 2 109864045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791732 Affx-122969600 AX-385278723 2 25804305 TTTTTATTATAAGATACAGTGCTTGTATTTCTTTT[C/T]GAACAGTTAACTCTCTAAGATACGGAATTGCTTGA Y 2 1 2 1 202000 f 74 goat snp33238-scaffold39-392708 2 109831402 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377633 Affx-122977874 AX-123247992 2 25870395 TTTCTCAATGACTTTGGTAATATGTTTATTAAATA[C/T]AATGGTTTTTCCTGTGTTCTTTTACTTCCAGCACC Y 2 1 2 1 201000 f 74 goat snp33237-scaffold39-326618 2 109764483 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272029 Affx-1111833164 AX-519545795 2 25876254 AAATGAAGTCTTTAATTTATTTATAATATATTTCT[A/G]GAATTTTGGCCCTATTTACTTATTTTTTTGGTTAC R 2 1 2 1 303000 f 74 goat 2_25876254_AF-PAKI 2 25876254 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440806 Affx-122929827 AX-123311143 2 25924958 CCCAAAGTTTCTGCAGTAGTTGGCAGCATGGGAGA[C/T]GTGGCTTCAAGCTCAGTGCTGTTGCTGCTCTGGTT Y 2 1 2 1 201000 f 74 goat snp33236-scaffold39-272055 2 109709093 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413691 Affx-122950094 AX-123284040 2 25988237 AGTAGCTTGTTTCTTATTTTTCCTGTTTTATCAAC[C/T]GTCTATAGATATAGTTGAGTATTTTTTTCAGCTGA Y 2 1 2 1 101000 r 74 goat snp33235-scaffold39-208776 2 109645287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447286 Affx-122924928 AX-123317622 2 26095191 AAAGATGTCCCCATATGCAAGGCTCTTCTGATGTA[C/T]AGAGACTTAAATCTCTCGTTCTGATAACTTTATTT Y 2 1 2 1 201000 r 74 goat snp33233-scaffold39-101822 2 109538325 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453386 Affx-122919924 AX-123323719 2 26145829 TCCTTCCTTAGAAAGCTAATAAGAATTCAGAAAAA[C/T]AACCAAATGAATCAAGAAAAAGAAAATTTGTGGAT Y 2 1 2 1 303000 f 74 goat snp33232-scaffold39-51184 2 109486693 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788412 Affx-122935638 AX-385275430 2 26192385 AAACTTTGCATCAAGTCAGAAATTCCACAAGGACA[A/G]TTCCTCTCTTGTCTCCCAGGATTTGCTCCTACTAT R 2 1 2 1 101000 r 74 goat snp33231-scaffold39-4628 2 109439511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424274 Affx-122941992 AX-123294620 2 26222010 TATTCCCGCTTTTAGGAGCTCACACTTTAGAATAA[C/T]GTGCTGTTCTTGATAGAATCATAATAAATTCCTAT Y 2 1 2 1 101000 r 74 goat snp28227-scaffold301-24898 2 109409326 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425839 Affx-122940672 AX-123296185 2 26252553 AACTGCGTCGGTAAGTGACAGTCTTTCATCACAGT[A/G]CTTACAGCGCTGCGGGCACTCCCTTTAACATCAAG R 2 1 2 1 101000 f 74 goat snp28228-scaffold301-55441 2 109378804 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438992 Affx-122930374 AX-123309329 2 26287493 GGAGACATGAGCGATGAGAAGGACTGCCCTACTCA[A/G]CCCTTTCAGTGTCCCAGTTGGCAGTGGCAATGCCC R 2 1 2 1 101000 f 74 goat snp28229-scaffold301-90381 2 109343874 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778124 Affx-122954794 AX-385265239 2 26319244 CTTCTTGTTCTTAGATTATTTCCCGCTAGAAATAT[A/G]CAGTCATTTGTTACTATTTCCAAATGTTGGAAATT R 2 1 2 1 101000 r 74 goat snp28230-scaffold301-122132 2 109312198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779214 Affx-122920812 AX-385266318 2 26363717 GCAAGGTCAGGCTAGTCAAGTCATCCTGAGCTAGG[C/T]AAGCCTTAGCTTAAAGCTTGAAGGATGCCTTTTTA Y 2 1 2 1 201000 f 74 goat snp28231-scaffold301-166605 2 109267092 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410310 Affx-122952488 AX-123280660 2 26404366 ATCAACTACAAAAAAGAAAGAAGAAAGAACAAAAT[A/G]CAGTTAGATAGAAGATTTCAAGCACCTGAGGAATG R 2 1 2 1 101000 r 74 goat snp28232-scaffold301-207254 2 109226837 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434589 Affx-122934109 AX-123304930 2 26434990 CATATCCTGAAATGCAGTGGGAAGTGCTGAGGCTG[C/T]AGGCGCTAATATGTACCACCACCTCCTCTCCCCTG Y 2 1 2 1 201000 r 74 goat snp28233-scaffold301-237878 2 109196137 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777736 Affx-122921005 AX-385264854 2 26477425 CTCATTGCTTTGGAACGGATGGTCTGTAAATCCTC[A/G]TGTTTTTCTCCTCAGGTTACAAGATGAGAAGAAAG R 2 1 2 1 101000 f 74 goat snp28234-scaffold301-280313 2 109153361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382997 Affx-122973334 AX-123253355 2 26523499 TTTAGTTACAGAGCTGCACATGGTAGGACATCAAG[C/T]GATTTTTAAAACTAGGATGAAAAATTAACTTTTTA Y 2 1 2 1 101000 f 74 goat snp28235-scaffold301-326387 2 109107749 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383586 Affx-122972584 AX-123253944 2 26552508 CTTATATTGTCCAATAGCTTTACATAGGAAACCCC[A/G]TTTCATAACCCATGGAGTCTCAAAATTGAGCAATT R 2 1 2 1 202000 r 74 goat snp28236-scaffold301-355396 2 109078871 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394209 Affx-122964903 AX-123264564 2 26680865 TCTAAATGAAAGGGGAAAATACGCAAAAGCCTTGC[A/G]CCCGACTTAATTCCTAAAGCCCCAAACTGGCTGCA R 2 1 2 1 101000 f 74 goat snp28239-scaffold301-483753 2 108949553 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781548 Affx-122952879 AX-385268633 2 26750049 AAGAGTTGGCAAACTTGTTCTGTAAAGGATTTTTA[C/T]GATTAGCAGGTCATATGCTCTTTCCCAACCACTTA Y 2 1 2 1 101000 r 74 goat snp28241-scaffold301-552937 2 108879578 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452220 Affx-122920801 AX-123322553 2 26778595 AAGAAAAATACAATCTGTATTCTTCTGCCTTAAGC[A/G]GGCCATTTCGACACATGCTACAACATGGACGAACC R 2 1 2 1 201000 f 74 goat snp28242-scaffold301-581483 2 108851469 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390156 Affx-122967981 AX-123260513 2 26820799 CAATTGCCTTAAGGACTGAGCATAAACTAAGACGT[A/C]GTGAAAGCAGTGCAATGAGAATAATTCCCAATTTG M 2 1 2 1 101000 f 74 goat snp28243-scaffold301-623687 2 108809347 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400681 Affx-122959947 AX-123271036 2 26899897 CTAGCAAGGCAAAGAAGGTTTTTCACAGCCAGGAG[C/T]TAACACTTAGCTAATACCTCTGGCCATAAAGGAAC Y 2 1 2 1 201000 r 74 goat snp28244-scaffold301-702785 2 108730242 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376090 Affx-122978902 AX-123246449 2 26960357 AGCTGTGCATTTTAATTCCCTTAAATACCTACATC[C/T]ACAAAGGGTCCTTATTTGGGACTCGGACGGTAGAA Y 2 1 2 1 201000 f 74 goat snp28245-scaffold301-763245 2 108668880 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393348 Affx-122965932 AX-123263704 2 26991603 ATGTCCTTATATACCCCACACACCATAAATAAAAT[A/G]TATTCTTTTAAAAGTTGAAATTTTAAAAATTTTAA R 2 1 2 1 103000 f 74 goat snp28246-scaffold301-794491 2 108637631 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439818 Affx-122930475 AX-123310155 2 27056082 GGCTCTGGGCAGCAGGTGAGAAGTGCCCAAATATT[A/G]CAGATAATGAGGGTTTCCTGGCCAAAGGAGAAGGG R 2 1 2 1 201000 f 74 goat snp28247-scaffold301-858970 2 108572819 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426972 Affx-122940398 AX-123297317 2 27088641 TCTTGACCTTGCAAAAGGCCAAGACTGAAGAATGG[C/T]GTTATGCTTTCATTCTCTCTCTCTCTTATTACTTA Y 2 1 2 1 101000 f 74 goat snp28248-scaffold301-891529 2 108539916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776772 Affx-122963271 AX-385263896 2 27119802 CCTCTTTTAAGAACTTGGAAGTTCACTCTGAATTG[C/T]GTGAGGTTTCCTTTTTAGCATTTCCAGTAAATTGT Y 2 1 2 1 101000 r 74 goat snp28249-scaffold301-922690 2 108508756 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431717 Affx-122936758 AX-123302058 2 27188817 TTGATCTTATTCTTAGGAAATAGTCACATATTTTT[A/G]CCCCAATAGGGGGTATTAATCCTTCTTATGATTTT R 2 1 2 1 201000 f 74 goat snp28251-scaffold301-991705 2 108439393 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382435 Affx-122974236 AX-123252793 2 27237315 GGAACTTAGAAAGTCTCCAGGAGAAAACAGGGAAC[C/T]GATTACATCCCAGTGAGGTCATTCTCTAGCGGAGC Y 2 1 2 1 101000 f 74 goat snp28252-scaffold301-1040203 2 108390615 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386369 Affx-122970851 AX-123256727 2 27269489 GCTGCTTCCTGCAGTTACTGTGTCCCTGATGCCTG[C/T]GGAACCAGTTCTTTATACTAGATGATATCTGTTAC Y 2 1 2 1 101000 r 74 goat snp28253-scaffold301-1072377 2 108358429 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769980 Affx-122934984 AX-385257147 2 27305188 TATATAGTGAAGAAATATCAACTATTATAATTAGT[A/G]TTTGTAATCAGTATTTCCCCAGAGAAGAGACTGAC R 2 1 2 1 102000 r 74 goat snp28254-scaffold301-1108076 2 108321831 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425113 Affx-122941225 AX-123295459 2 27342106 TCACTTAAAAAAATTAAATCTAGGTTATTTTGTAC[A/G]TGTCTTGGTTTTTGAAATTTGGTTTCATAGCGTCA R 2 1 2 1 101000 r 74 goat snp28255-scaffold301-1144994 2 108285024 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793516 Affx-122929510 AX-385280493 2 27395248 TTTGTTTAATCACTGTTTATTGCTTAAAGGCCAAC[A/G]CCACCATTTCTTTCAATATCCGAGGCTATAATTCT R 2 1 2 1 101000 r 74 goat snp28256-scaffold301-1198136 2 108231591 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445898 Affx-122925948 AX-123316235 2 27454522 TGAACAGTTGCTGGCATAGGCTGAGAGACATTACC[A/G]TGCAGCCGAGGGATGCATATAGTCCTGAGCTGGCC R 2 1 2 1 101000 f 74 goat snp28257-scaffold301-1257410 2 108172539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789906 Affx-122969776 AX-385276912 2 27486005 TTGTTATTAATATTTCAGATATCCAGAGAAGTCTG[C/T]AAAGTACCATAGACCCACAGGCTCATCACTGAGAT Y 2 1 2 1 101000 r 74 goat snp28258-scaffold301-1288893 2 108140602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399933 Affx-122961262 AX-123270288 2 27535246 TGAAGAGTGCTTTGCCATGGAGGATAGCGCCAACC[C/T]GGACCCAGCACTGTACCTGAACAGGGAGAGGGTGA Y 2 1 2 1 101000 f 74 goat snp28259-scaffold301-1338134 2 108090986 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410597 Affx-122952113 AX-123280947 2 27606970 ATCTCCATAACAAACTCCCGGGATTTGTGTTTTAC[A/G]TCTCAGGCAGAACTTCTCTATGATTAAATCCTTCA R 2 1 2 1 101000 f 74 goat snp28261-scaffold301-1409858 2 108019331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414891 Affx-122949127 AX-123285240 2 27676938 AGGCGAACTCCTGCGTCACTGATCTCTCCTCTTGC[A/G]CTTTCTCCTGCCAGCAAGGCTTAGCAATTTCACAG R 2 1 2 1 101000 r 74 goat snp28263-scaffold301-1479826 2 107949432 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796217 Affx-122975115 AX-385283167 2 27707065 TATATTCAGATCCAATTTTGACTATGTAATCTAGC[C/T]AAGCATTGTGGACCAGGAATGCCACCTGTCACTTC Y 2 1 2 1 101000 r 74 goat snp28264-scaffold301-1509953 2 107918889 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449282 Affx-122923022 AX-123319617 2 27749738 ATATCACTACCCACATTCATTACAGGCCTACTTGA[C/T]AGCTGAGAATGGAGGGAAAGAAGAAAGTGAAAAGG Y 2 1 2 1 201000 f 74 goat snp28265-scaffold301-1552626 2 107876198 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776705 Affx-122942655 AX-385263831 2 27780804 TCCTCCATCATTCTCCTTAACATGCGTCACCACCT[A/G]CGCATTCAACAAGTATATTCCCTATTGATTCTTAT R 2 1 2 1 101000 f 74 goat snp28266-scaffold301-1583692 2 107844502 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797613 Affx-122920578 AX-385284552 2 27815996 CAACATTTTTTAATCTCCTAGTAAAAGATATTAAC[A/G]CTTTCTCCTTCAAAGTATTAATATTTATATAACCC R 2 1 2 1 101000 r 74 goat snp28267-scaffold301-1618884 2 107809338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399865 Affx-122960233 AX-123270220 2 27851203 CTCTATCTGCTACAGTAGAGAGAAGAGACCTGAAG[C/T]AGCAAGGCGGAAGCAAGGAGGCTAATAAATGGGCT Y 2 1 2 1 101000 f 74 goat snp28268-scaffold301-1654091 2 107774475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277358 Affx-1111835808 AX-519550862 2 27860194 CACAATGCGGCACGGTCCTCATGGCCTTAGGGGCC[A/G]AGTACCACCCAGGAGGGCTGAAATGAAGCTCTTGA R 2 1 2 1 102000 r 74 goat Random2.2K-179 2 27860194 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388095 Affx-122969502 AX-123258453 2 27882439 GATGGCTTTATAGATAGGTTGGAGAAGGCAATAGA[A/G]CTTGAAGAGATAGGAAAGTTAAGCATAATATCACC R 2 1 2 1 201000 r 74 goat snp28269-scaffold301-1685327 2 107742417 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397216 Affx-122962386 AX-123267571 2 27928562 GCTCACTTTGAGCAAGTCATCACTCTCTCAGCCTC[A/G]TTCTTCTCATTTGTTAAAAAAGAAACAAAATCAAA R 2 1 2 1 103000 f 74 goat snp28270-scaffold301-1731450 2 107696322 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418020 Affx-122946651 AX-123288368 2 27972191 TCTCTTTGTCTCCTATTATGCTGCCAGGGAAGCCC[A/G]TTCTTAACTGCAGTTTTATAAAATTTTAAGTCTCT R 2 1 2 1 202000 r 74 goat snp28271-scaffold301-1775079 2 107652040 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802799 Affx-122951237 AX-385289698 2 28010061 CGGCCCATCTCTCCACTGCATATGGTATTTTGCAG[C/T]ATGCTATTTCTTTCCTAACCTTATAGCTGATTTAA Y 2 1 2 1 101000 f 74 goat snp28272-scaffold301-1812949 2 107614319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417646 Affx-122946846 AX-123287994 2 28098982 TTTAAAGCTCAGTCCAGAGGGCTTACTGCTCATAC[A/G]CAGACATCCATGTGTAAGAGCAGTGGGGCCACTGA R 2 1 2 1 101000 f 74 goat snp28274-scaffold301-1901870 2 107525609 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272394 Affx-1111834090 AX-519546122 2 28127682 GCCACAAGGACAGTCCCAGCGCTCCTGCTGGTGCT[A/G]TGAGGCTGGCGATATAGCGCGTGATGGCAAACACG R 2 1 2 1 201000 r 74 goat GoatD01.017662 2 28127682 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38388815 Affx-122968903 AX-123259173 2 28164414 TCATTTACTAATAATCAATGCAAAACTTATCAAAT[C/T]GAAAATATGAATGAAAAGCTACAGAATTTAGAGAA Y 2 1 2 1 101000 f 74 goat snp28275-scaffold301-1967302 2 107460103 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387843 Affx-122969654 AX-123258201 2 28197923 AAAGCATCATGGTTGCTTCCAAGTTTTGGCAGTTT[A/G]TGAACCAACTTGCTATAAACTTTGGTACGCAGGTT R 2 1 2 1 303000 r 74 goat snp28276-scaffold301-2000811 2 107427013 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783795 Affx-122954819 AX-385270851 2 28240937 AAGCTATGCACGCAATAAAATGATGTATGTAACTA[C/T]AGAATATCTCTCCTCTCATCCAGGTCAGTGAGCAA Y 2 1 2 1 102000 r 74 goat snp28277-scaffold301-2043825 2 107383516 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408688 Affx-122953443 AX-123279039 2 28278008 GGAGATATGTGTCTTCATTACAAATAAATTTAAGA[C/T]GCCATTTCACTTTTCTTTTTTTCTGGGAAACCTTT Y 2 1 2 1 201000 f 74 goat snp28278-scaffold301-2080896 2 107346689 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394319 Affx-122964681 AX-123264674 2 28322657 GTGAGTTGTTCAGACTGGACTTCCACTCTGGGAAA[C/T]GGAGGCTTGGCTGTAAATTCACAGCTCGGAGCATC Y 2 1 2 1 201000 r 74 goat snp28279-scaffold301-2125545 2 107301198 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436003 Affx-122933496 AX-123306342 2 28351527 TCATAACCCTTCTAAATCATTCTGGCCCCCAGGAC[A/G]TGGAAATTTCTATAGAGGCATGGCCAGAGAGTAGC R 2 1 2 1 101000 r 74 goat snp28280-scaffold301-2154415 2 107272277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784052 Affx-122939390 AX-385271105 2 28397373 GAACATATTACAGATATGGAAGTAGACATTTATCA[A/G]TGACAACGTAACACATACCTTCTGTAATATTTAGA R 2 1 2 1 101000 r 74 goat snp28281-scaffold301-2200261 2 107226601 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377038 Affx-122977704 AX-123247397 2 28426584 GTGTATTCTGGATAAGTCTTCAATAATGCCCCAAC[G/T]AAAACATAATGCTCACCTTTTAGGCTGTGCAATTT K 2 1 2 1 101000 f 74 goat snp28282-scaffold301-2229472 2 107197498 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433034 Affx-122935768 AX-123303375 2 28457576 TGTACATAAGTGCTCATAACAGCTTTGTTTATAAT[A/C]GCCCCAAGCTGCAATTGACACATGTCCTTCAGTGG M 2 1 2 1 201000 f 74 goat snp28283-scaffold301-2260464 2 107166216 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772090 Affx-122924348 AX-385259246 2 28487431 TGAAAGTGTACAGTGAACAGAAGATTTAAAACATG[A/C]TAAGCTACACTATCAAAAAACTAACCTTACTTTGA M 2 1 2 1 101000 f 74 goat snp28284-scaffold301-2290319 2 107135993 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412659 Affx-122950783 AX-123283008 2 28533364 ATGGTGTTGTATATTATATATAATATGTTATATGC[A/G]TAATACTGTATGTAATATGCTCTACACATACACAT R 2 1 2 1 103000 r 74 goat snp28285-scaffold301-2336252 2 107088777 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277375 Affx-1111835817 AX-519550879 2 28605200 TGGGTCCAAAAGTCACCTCATTAACATAGCAAGAC[A/G]CCTTGACCACTCTCAACACTTAGGGAATTCTCAGG R 2 1 2 1 101000 r 74 goat Random2.2K-180 2 28605200 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795149 Affx-122935692 AX-385282107 2 28640418 AGAATCTAGTATAATACCTCTGAAATTATACTCTA[A/G]GGAACTTGGACCCGAGGGAAAATCCATATCAATGG R 2 1 2 1 101000 r 74 goat snp28287-scaffold301-2443306 2 106982245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769131 Affx-122929740 AX-385256306 2 28736535 CTTTAAATCAGCACATTATCATAGGAAATAGTTTC[A/G]TTATGTCTTTCAAACATGAGTAGCCAAATGTTTTG R 2 1 2 1 101000 r 74 goat snp28289-scaffold301-2539423 2 106883985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404007 Affx-122957193 AX-123274359 2 28821420 GGAAGAAATTCCAGGCCTAAGAGGTAATGTGAGTC[A/G]TCCATGGCTACTTAAGAGGCAGTCAGTGGTAAATC R 2 1 2 1 101000 f 74 goat snp28290-scaffold301-2624308 2 106796556 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448250 Affx-122924201 AX-123318586 2 28883680 CTTCATTTTTTGCTAGAGAATAATGGGTTTAGAGG[C/T]GATTTTATATGTAAATAGCAATTACACTATTTTTC Y 2 1 2 1 101000 f 74 goat snp28291-scaffold301-2686568 2 106733947 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771925 Affx-122936466 AX-385259081 2 28918563 TATCACTGATCTCTCATTTAGCTAGGTTCTGAATC[G/T]AAGATTTGTCAGTGATTTTTTCACTTTCTCTTTCC K 2 1 2 1 101000 f 74 goat snp28292-scaffold301-2721451 2 106698779 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796790 Affx-122947148 AX-385283733 2 28951977 AATGCTTTGCCCATTAGAGTTACTGTTTGTTTGTA[C/T]GGTTTCAGACTAAAATTTGCACAGGAAAACTTAAA Y 2 1 2 1 101000 f 74 goat snp28293-scaffold301-2754865 2 106663852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790725 Affx-122953503 AX-385277726 2 29000164 CCATCTCATTTACAATTCCATCTCCAAATAGATTT[A/G]TTCTCCTTAGGTACTATCTTAATTTCTTTCTTGCC R 2 1 2 1 101000 r 74 goat snp28294-scaffold301-2803052 2 106616920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418067 Affx-122946615 AX-123288415 2 29042056 TACTTGAAACAAATGTTCAATAAACGATAGCTATC[A/G]TCATGTTTTTGTTGGTGATACAGTGACACCATCTC R 2 1 2 1 101000 r 74 goat snp28295-scaffold301-2844944 2 106582843 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800559 Affx-122932701 AX-385287478 2 29076720 ATTTTCCATTTTTTTCATTAGTGTAATTACGCTAC[A/G]CTGTCTTTTAAAATCCAGGTAGTATACACATTGTG R 2 1 2 1 101000 r 74 goat snp28296-scaffold301-2879608 2 106547508 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381157 Affx-122974550 AX-123251515 2 29119743 TTACTTCGAGGACTAAAACTTGTTAATCACACATC[A/G]TTTAAGAGGCACAGTCACAAGCTGATTTGGAATTA R 2 1 2 1 101000 r 74 goat snp28297-scaffold301-2922631 2 106504205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779749 Affx-122936309 AX-385266849 2 29162313 ATCCTTACAAAATTGTGTGCCTTGGATAACAATTC[A/G]TATTTAAACACTTGAATATTCTCAAGATATGCTTT R 2 1 2 1 201000 r 74 goat snp28298-scaffold301-2965201 2 106461674 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407783 Affx-122954958 AX-123278134 2 29192831 TGCCATCTATATCAAAAAGCATTCTTCACAGAAAT[A/G]TTGCACCTTCAATTTCAGAACAAATTCAACTTCAG R 2 1 2 1 101000 f 74 goat snp28299-scaffold301-2995719 2 106431151 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439727 Affx-122930546 AX-123310064 2 29227530 ATTCTATTCAACTTTTTATTTATATATATCCAGGT[A/G]TTCTGTCTTAGTTTAATAGGCAAGTCTCGGGAAGA R 2 1 2 1 103000 r 74 goat snp28300-scaffold301-3030418 2 106396459 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439120 Affx-122931097 AX-123309457 2 29287557 TATTTTTAAGTGATAAATGCAAAACATGAAGTGGT[A/G]TGTATATAGAATATTATTAATGTGAAAAAAATTAA R 2 1 2 1 101000 f 74 goat snp28301-scaffold301-3090445 2 106335919 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776125 Affx-122974264 AX-385263255 2 29366924 TTCTGAGTTGGTCTTCTCTCCAAAATTTCTTACAC[A/G]TATTCCAAGGCAGGATGTTTAAACTTGTGCCCTGA R 2 1 2 1 101000 r 74 goat snp28303-scaffold301-3169812 2 106256975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803028 Affx-122921162 AX-385289904 2 29414684 TCATGGGTGAAGGAAAATGTAGTAAATATTGTGTT[A/G]TTTATGCTTACATTCTGAACACAGGTGTTTATTTT R 2 1 2 1 201000 r 74 goat snp28304-scaffold301-3217572 2 106209711 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775344 Affx-122932708 AX-385262475 2 29475382 CAAAATCATAAAGTCATGGGGCTGGAACAGATATT[A/G]CACTTAATTTGTATGTCTTTAGAATTCATACTGAA R 2 1 2 1 101000 f 74 goat snp28305-scaffold301-3278270 2 106149352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420594 Affx-122945255 AX-123290941 2 29511984 ATAAAAAGAACATTTTTTTTTGCCTTTTTCACTGT[A/G]TTGATTATTGCACTTAGGGTCAAAAGCAATTAAAA R 2 1 2 1 101000 r 74 goat snp28306-scaffold301-3314872 2 106112393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776904 Affx-122964095 AX-385264028 2 29559883 AGTAAACTTTCACTAATACTTCTGGATTTTCTTCT[A/G]TCAGTAGAGATAGTTGAACATTTACTAGTTTTCAG R 2 1 2 1 201000 f 74 goat snp28307-scaffold301-3362771 2 106064276 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801187 Affx-122932087 AX-385288100 2 29638690 AATTAAGCAGATTTCTTAACCTCTCCTAATCTTAA[C/T]ACATTCTCATGCATTTTGGGCCTCTCAGAGTAGTG Y 2 1 2 1 101000 r 74 goat snp28309-scaffold301-3441578 2 105985158 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402890 Affx-122958216 AX-123273243 2 29669421 ATCTTGTAAACAGATCTAACAACTAGATACTTTCT[G/T]CAAGGGACTGTATGAGATAAAGCAAGGGGTTCTCA K 2 1 2 1 201000 f 74 goat snp28310-scaffold301-3472309 2 105954585 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451992 Affx-122920928 AX-123322325 2 29698435 TCTTTCTTGGACCTTGATTTTTAATAACTTTGGAT[A/G]CATCATCACAGAATGCCTAGTCATTTTGAAAGTTG R 2 1 2 1 101000 r 74 goat snp28311-scaffold301-3501323 2 105925075 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425678 Affx-122940864 AX-123296024 2 29749143 CAAGACATTATGTGCTCCTGAATGAAGAACACACT[A/C]TCAGACAGTCAGACTGGGGGTGAGACAAGTGAAAC M 2 1 2 1 101000 f 74 goat snp28312-scaffold301-3552031 2 105874461 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774541 Affx-122964347 AX-385261675 2 29789318 TGAAGTAACTTAGCAAACAAGGATAGCATATTCAT[A/G]TTTCTAATACAAAATGATAGAAGTGAAATAGGACA R 2 1 2 1 201000 r 74 goat snp20364-scaffold202-12575 2 105834834 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375387 Affx-122979216 AX-123245746 2 29834873 CTGCCTGCATCGTGGTATCCTGTCAACAGACAAGT[A/C]GGGCTGAAATTCACCCGGGGCTCCCTTTAGCTACC M 2 1 2 1 102000 f 74 goat snp20365-scaffold202-58130 2 105789735 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416933 Affx-122948039 AX-123287281 2 29884743 AAAACTTGACTTTTTCTACTAAAACATTGTTATTG[C/T]TAGGATATTATTAGGAAATATTGTTAGGAGTAAGC Y 2 1 2 1 101000 r 74 goat snp20366-scaffold202-108000 2 105726840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382579 Affx-122973755 AX-123252937 2 29971596 ACTGCCTGGTAAACACCCGGTGGGCAAGGAGGTAA[C/T]TTTGCTCCCTAAAGAGCCCTCAGGGGACAGCACAC Y 2 1 2 1 101000 f 74 goat snp20368-scaffold202-194853 2 105640228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429703 Affx-122937626 AX-123300044 2 30003699 GTCTCCTTCCTCTTGAAAACTATGTTCTGCTCATG[C/T]AGTTTTCCAGAATAAGTATTAATAAAATTTGTGTT Y 2 1 2 1 101000 f 74 goat snp20369-scaffold202-226956 2 105608109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407801 Affx-122954560 AX-123278152 2 30032239 TCAGAAAGCAGGAAATTAATTTTTGAAAAATCCTT[A/C]AAGATTTCTTTGAAGTCTGATATAACACCACCTCT M 2 1 2 1 101000 r 74 goat snp20370-scaffold202-255496 2 105579556 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396211 Affx-122963357 AX-123266566 2 30083794 TGTTATTTCTAGATGCATAAATTATACAAATTATC[C/T]AGCAACTGTGTTAAAGATAAATACAGAATGACTAC Y 2 1 2 1 101000 r 74 goat snp20371-scaffold202-307051 2 105530523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377289 Affx-122978118 AX-123247648 2 30112887 ATAGAAGGAAGGAAGGGAGTGAGGAAGGAAGGAAA[C/T]TGAGAAGGAAGGTAACATACTCCAGGCTTCCTCCC Y 2 1 2 1 303000 r 74 goat snp20372-scaffold202-336144 2 105501498 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409777 Affx-122952983 AX-123280128 2 30142673 ACAATATAAATGCTGTGATGGAATTTTTATATAGA[C/T]ATATTTGATTAATAAAACTACCAATGAAACTTTTC Y 2 1 2 1 101000 f 74 goat snp20373-scaffold202-365930 2 105471694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800087 Affx-122919822 AX-385287010 2 30241667 TAGTTATTTATACTGATGGCTAATGTAATGTTGAT[A/G]TAAGTTGTAACATCACAGTGAAAAAGGAAAAGAAG R 2 1 2 1 101000 r 74 goat snp20375-scaffold202-464924 2 105372893 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787992 Affx-122939617 AX-385275013 2 30276961 TTCAGTCAATCCTATCTAGAGCTTCAAACTGAAAC[A/G]TATTAGTCCTTGATTTACTCACATCTTATTAGATC R 2 1 2 1 101000 f 74 goat snp20376-scaffold202-500218 2 105337093 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277400 Affx-1111835830 AX-519550904 2 30299373 CTGGTGGTCGCAAAGAGTTGGACACGACTGAAGCG[A/G]CTTAGCACTCACTGATGGCAAACAAGGAGATATGG R 2 1 2 1 101000 r 74 goat Random2.2K-182 2 30299373 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320772603 Affx-122970125 AX-385259751 2 30317420 TTTACATTAGTTGTATGGTCATCCCTTTCTTTCCC[A/G]TTACTCCTGGTCAGTGAATGTGTCATAGGATATTT R 2 1 2 1 101000 f 74 goat snp20377-scaffold202-540677 2 105296587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435751 Affx-122933276 AX-123306090 2 30352453 TTGTGACACCAGAATAGTATTGCAATCTACACTTT[A/G]TTACTTCCTCCAGATATTTGGTCAATTTACTTTTT R 2 1 2 1 102000 f 74 goat snp20378-scaffold202-575710 2 105260699 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430155 Affx-122937379 AX-123300496 2 30381311 GATTTATATTTCAGAAAAGGTAGATGACTAAACAA[C/T]GACATCACTTCAAGAGAAAACTAGAAGTCCTCCCA Y 2 1 2 1 201000 f 74 goat snp20379-scaffold202-604568 2 105231638 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418077 Affx-122946607 AX-123288425 2 30423898 CTCAAAGGATGCAGGTTACATATGAAGTAAGCACC[A/G]CCATCTTGAAGTGATGCAAGTTGTACCTCAAGCTC R 2 1 2 1 101000 f 74 goat snp20380-scaffold202-647155 2 105190080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771783 Affx-122960661 AX-385258940 2 30475419 ATTCCTGTGACTATTTCTAACCAAATCCAAAGGAA[C/T]AGCACATTTCTCAATGAATAGTATCTTTCCAGAAT Y 2 1 2 1 101000 r 74 goat snp20381-scaffold202-698676 2 105138526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772194 Affx-122968437 AX-385259349 2 30515869 TTATTTTTCTGTTCAATATTAACAATAAGGGGATA[A/G]TGGCTCCATCTGCCTTAAAGTCTCAGTTCTGGTTT R 2 1 2 1 101000 r 74 goat snp20382-scaffold202-739126 2 105098059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797958 Affx-122935634 AX-385284894 2 30549993 TTTAGCCTCAGAAGTAAGTATGAAAGTACTTACCT[A/G]TTAAAATATCTAATACTTACCAGAAGTAAGTATTA R 2 1 2 1 101000 f 74 goat snp20383-scaffold202-773250 2 105064044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444900 Affx-122926256 AX-123315237 2 30591074 ACTTAGTGAATTATAAACACTGTTGAAGATTTTCA[C/T]GCAAAGAGTCATAGTGTTTTTATTTTTTATAGTAG Y 2 1 2 1 201000 f 74 goat snp20384-scaffold202-814331 2 105023660 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453848 Affx-122919538 AX-123324181 2 30627300 AGGGAAATAGATCTTTTAACTAGGGTATGGAAAAA[C/T]GAACAAACAAACAAATGCAGTTTTCCCTCTAGCTG Y 2 1 2 1 303000 f 74 goat snp20385-scaffold202-850557 2 104987617 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800086 Affx-122950218 AX-385287009 2 30656798 GTTGTGATAGTACCAGAAGCATCATTTAACTTTAG[C/T]ATTTGATAAAATGCAAGAACGATTACATTACAATA Y 2 1 2 1 101000 f 74 goat snp20386-scaffold202-880055 2 104958327 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782160 Affx-122921051 AX-385269238 2 30725442 GTAATGTGAATGCAACTAAACAAGTCAAAGACAGT[A/G]CCAAGATTTTTACACTGTTTCTTATTTAAATATTA R 2 1 2 1 101000 f 74 goat snp20387-scaffold202-948699 2 104888421 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425554 Affx-122941440 AX-123295900 2 30787968 TTGACTTCCGTTCCTATTCTTTACCCACTTTTTTC[A/G]TTATTTAGATATGATCATATATATTATCACCTTAG R 2 1 2 1 201000 r 74 goat snp20389-scaffold202-1011225 2 104825666 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441350 Affx-122928877 AX-123311687 2 30828999 GCACTGAAGACATCACTGTCTGTGGGTCAGAGACT[A/G]TATGTGTGGTGCTGAAGTTATGCTGTGGGAAGAGA R 2 1 2 1 101000 f 74 goat snp20390-scaffold202-1052256 2 104784167 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802831 Affx-122974367 AX-385289730 2 30875155 ACTTTTAAAATTTGTTATCTTCACTGAGACTAAGA[A/C]CTTCTTGATTTACACAAACTTGATTGACCTAAATA M 2 1 2 1 101000 r 74 goat snp20391-scaffold202-1098412 2 104738420 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415597 Affx-122948615 AX-123285946 2 30907194 AGGTAGGTACATTTGTTTTGTTTGTATTTTTAAGA[C/T]GGGGAAGGGGACCATCCATTTTTCCTCTTAACTAG Y 2 1 2 1 102000 r 74 goat snp20392-scaffold202-1130451 2 104706077 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796729 Affx-122936983 AX-385283674 2 30935873 AGGATTATATCTTCATTTCTTTGTAGCTGGAATAA[A/G]CTCTGATTATAGCCTTGAAGAGATAGATGAAAAGG R 2 1 2 1 101000 r 74 goat snp20393-scaffold202-1159130 2 104677398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788354 Affx-122978348 AX-385275372 2 30984112 GAATCCTCTATATTTGGCATATGGTGCTCTTCTAT[A/G]CACCAGTGTGCTTGCCTATCAGTGTATTTTATGCT R 2 1 2 1 101000 r 74 goat snp20394-scaffold202-1207369 2 104629496 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430953 Affx-122936828 AX-123301294 2 31042640 AGCTTTGGACTCCACAGGTTTTCTTTCATTTCAGC[G/T]AATTCCTCAGTTTGGAAGCTTCTGACTGCAGAAGA K 2 1 2 1 201000 r 74 goat snp20395-scaffold202-1265897 2 104570837 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445622 Affx-122925098 AX-123315959 2 31080893 TCACAGTCTTTTCTTTAGCTAAGAGAACATTGTGC[A/G]TTTCATTATTTTCTCTCTTCTGTTTTTCCCTTCTG R 2 1 2 1 303000 f 74 goat snp20396-scaffold202-1304150 2 104532616 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272939 Affx-1111833166 AX-519546625 2 31149945 CCAATTCCACACGGTCATTCAAGCTCCAGTGTGGC[A/G]CGTGATGCTGGCCCAGGAACTGCGCTCTGGTTATT R 2 1 2 1 102000 f 74 goat 2_31149945_AF-PAKI 2 31149945 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320771468 Affx-122948473 AX-385258626 2 31153427 AAAGCCAGGGGCACTGGGGACAGAACGTCTTTGAA[G/T]AAAACAATCTTATTAGTAGATGGCAGACTTTTCAC K 2 1 2 1 102000 f 74 goat snp20398-scaffold202-1376684 2 104460619 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784046 Affx-122956137 AX-385271099 2 31198489 TGGATTCTGGTCTCTGGATCCATCTTTAATAAATG[C/T]GTTGACAAGGTATTAAAACAAGATGTATATGTTTT Y 2 1 2 1 101000 f 74 goat snp20399-scaffold202-1421746 2 104415201 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790294 Affx-122949539 AX-385277297 2 31233071 TTGAAAGAGGAGACTAAATAGGAAGTCAGCTCATC[A/G]TTTGACTTTGAACTTAATTTCTGATTATGAGCCTC R 2 1 2 1 101000 f 74 goat snp20400-scaffold202-1456328 2 104380558 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425638 Affx-122940893 AX-123295984 2 31281996 TTAGCTCAAATAATGAATATAATTCTCTCCCAGAG[C/T]ACTGAAGAATATATTTTATTCCATTGTACATATAA Y 2 1 2 1 101000 f 74 goat snp20401-scaffold202-1505253 2 104330959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407937 Affx-122954366 AX-123278288 2 31313241 GATCACTGACAGCCATCTGTGCCTGGCCCCAGGCA[C/T]GGGCTCTCCTAGGATATGTCTACACTCACCTGTTG Y 2 1 2 1 102000 r 74 goat snp20402-scaffold202-1536498 NW_017205466.1 9452 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422048 Affx-122943612 AX-123292395 2 31350756 ATGATGCTAGACGAGAGGCTTAGAACTTCCCTAGC[A/G]TCTTCAGAGGGAGCATGGCCCTGTGGCACCTTGCC R 2 1 2 1 103000 f 74 goat snp20403-scaffold202-1574013 2 104261755 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431822 Affx-122936102 AX-123302163 2 31383002 ATATATTGACTCATTTTAGGTATAGACACATGCAT[A/G]TGCATGTACAAACACACACGCAAAGAAAATTTATG R 2 1 2 1 201000 f 74 goat snp20404-scaffold202-1606259 2 104229987 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406399 Affx-122955227 AX-123276751 2 31419671 TAGTGAATGACCCAGTGTTTTACCTGTCAGTCACC[A/G]TGAACTACTTTACAAAACAGGCTTAACAGCTCATA R 2 1 2 1 101000 f 74 goat snp20405-scaffold202-1642928 2 104192169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399978 Affx-122960824 AX-123270333 2 31486141 ACACATTCTTTCTGACTATCCCCATCAAACTCTGG[C/T]GTACATATTACTTTGTTCACTTTGTGTACATCTGT Y 2 1 2 1 201000 r 74 goat snp20406-scaffold202-1709398 2 104124026 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277413 Affx-1111835836 AX-519550917 2 31542578 GGAAGCTGGCCAGATGTGTCCCCAAGGAGTGGAGC[A/G]GAGACCCATCTTAGTATTCCTTGCTGTTGGGGCCC R 2 1 2 1 201000 r 74 goat Random2.2K-184 2 31542578 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793364 Affx-122937955 AX-385280342 2 31544059 AATGATAATACCATATTCCTGTAAAACACTGCCAC[A/G]TCTAACAAAAATGTTTGCTTGTTCCGAATTCCCAG R 2 1 2 1 201000 f 74 goat snp20407-scaffold202-1767316 2 104065937 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453951 Affx-122919474 AX-123324284 2 31594197 CTGAATTCTAAATAATGTTTAATTTAACTTTAATC[A/G]ATTCAGGAAAGATATGTTAGGTGTTTCCCTGTTCC R 2 1 2 1 101000 r 74 goat snp20408-scaffold202-1817454 2 104015122 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423048 Affx-122942964 AX-123293394 2 31637569 TCTTTAAAGTTTCTAGATTTTTCCTTCTGCCTCTT[C/T]ATTCATAAATTGTGTCTAGAGAGCTAAGTTTTTGA Y 2 1 2 1 201000 r 74 goat snp20409-scaffold202-1860826 2 103970833 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416545 Affx-122947751 AX-123286893 2 31666728 ATAAGTGACTACATGTGAACTTGGTATCTAAGACT[A/C]GAGTTTCTTAATCTTGGTACTATTGACATTCTCAG M 2 1 2 1 101000 f 74 goat snp20410-scaffold202-1889985 2 103941658 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430009 Affx-122938029 AX-123300350 2 31706593 ACTTGAGAGATAAAAATCAGCAGAATTGTTGAGTT[A/G]CATATTGTGGAATTGTGTCTATTCCATCTTGGGCA R 2 1 2 1 101000 r 74 goat snp20411-scaffold202-1929850 2 103901999 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446305 Affx-122925645 AX-123316641 2 31821130 AAATTATCTGCAAATCACAACTCTTTTATATATTC[A/G]CAAAGCCACATGCACTCCATTTTACAGATAATTAA R 2 1 2 1 201000 f 74 goat snp20413-scaffold202-2044387 2 103787285 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443420 Affx-122927374 AX-123313757 2 31867325 TTGCTTAGTGAAAGCATTGATTCAATAATATGAAT[A/G]TTTTAGAAGTTGCAGTAAGAAAGATAATTTTGGTT R 2 1 2 1 101000 r 74 goat snp20414-scaffold202-2090582 2 103740766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277300 Affx-1111835842 AX-519550804 2 31886910 AGTTGATCACAGTAGAAAGTTACGCTGATCAACTG[A/G]GGCAAAATGTTAGCTTACTGGAAGGATTACTGCTG R 2 1 2 1 101000 f 74 goat Random2.2K-185 2 31886910 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406127 Affx-122956199 AX-123276479 2 31901285 AACTAGACTCACTGTCTGGTCATATTATACCCCCA[A/G]ACATTTCAGACTCAACTCCTCCTTCTTTCCTTTTT R 2 1 2 1 202000 r 74 goat snp20415-scaffold202-2124542 2 103706954 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781401 Affx-122967844 AX-385268486 2 31933165 ATGCAGCTGGCTTCAAGTGCTATAGAGTATTTCCT[A/G]CCTTTCTTTTCTAGTGAAATTTTGTTCTGAAACTA R 2 1 2 1 101000 f 74 goat snp20416-scaffold202-2156422 NW_017193395.1 9921 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443713 Affx-122927151 AX-123314050 2 31994759 TAAAGGAAGTGAAAGTTATTTCCCTTGAGAAACTT[A/G]AGGAAAGTCAAAACAACTGATGACTAGTAAACAAG R 2 1 2 1 101000 r 74 goat snp20417-scaffold202-2218016 2 103608433 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439846 Affx-122930457 AX-123310183 2 32030485 AGCACTTAAAAAAAAAAATCTCCTTTCAGTGATTC[A/G]CCATGTTTCTTCCTCTGTAGATTGCTGTGCATTTG R 2 1 2 1 101000 r 74 goat snp20418-scaffold202-2253742 2 103572499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423783 Affx-122942828 AX-123294129 2 32072413 AACCCAGTTTGAGATCCACGTCCCCATATCTATTC[A/G]TAGTACCATATTGGATTTATAAACTGGAATGCTAT R 2 1 2 1 201000 r 74 goat snp20419-scaffold202-2295670 2 103530507 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426539 Affx-122940189 AX-123296885 2 32164663 CTTGTGCACAACTAACAAAGTATGCTGGCCTAAGG[C/T]AAAATTGGTTTGATACCCACAACCATATCTTTAAA Y 2 1 2 1 101000 f 74 goat snp20421-scaffold202-2387920 2 103437938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447982 Affx-122923751 AX-123318318 2 32199276 TATCATCTGTTTTTCCTTTTAAGAGCAATCTGGAA[C/T]GAGGAATCCTTGTTAAATAGAAAATCTTTCTCAAC Y 2 1 2 1 101000 r 74 goat snp20422-scaffold202-2422533 2 103402209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774546 Affx-122959037 AX-385261680 2 32232271 AATAGAGATCTCTGAGGCCTAGAACTGCAGTGATA[C/T]GGAGTTTGTCCTGATACATAGTTTGTTTGCAATTC Y 2 1 2 1 101000 f 74 goat snp20423-scaffold202-2455528 2 103369518 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412969 Affx-122951039 AX-123283318 2 32261918 CTTCCAACTTCATCCCTTCCCCCATCACCTGAAAG[G/T]CAACCAGAAATTAAGTGAGAGAGAAAAATATATCA K 2 1 2 1 303000 r 74 goat snp20424-scaffold202-2485175 2 103339913 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802534 Affx-122978533 AX-385289438 2 32347509 ATTAAAAATATGTAGATTAGAAAGCATCAGAGTGC[A/G]TCACACAGAGTAATGGCAAAAACTGTTCTGTGAAA R 2 1 2 1 101000 r 74 goat snp20426-scaffold202-2570766 2 103253948 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38408924 Affx-122953951 AX-123279275 2 32435308 GCAGCCTCGCTGTTTGCAGAGCTTGCCTTCTCTTT[A/G]CCTCTTAAGTGCCCCTGGTAGGTTTCTAACACACA R 2 1 2 1 201000 r 74 goat snp20428-scaffold202-2658565 2 103165917 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449177 Affx-122923530 AX-123319512 2 32479052 GGGGAAAATGACAGGTCATTGTATTCAGACCTCTG[C/T]ACCTAATGCATGCTATTGCCAGACAGTTTTATTAT Y 2 1 2 1 101000 r 74 goat snp20429-scaffold202-2702309 2 103122276 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413893 Affx-122949839 AX-123284242 2 32514108 TTCTAAATCAGCAGGAAGGATTTCTGGAGGAGATA[C/T]GCTTTCAGTCCTCATTAATTGGAAATTGCTATTTT Y 2 1 2 1 101000 r 74 goat snp20430-scaffold202-2737365 2 103087153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421102 Affx-122944218 AX-123291449 2 32577071 GAAAGTTTGATTGCAACGGCAAGCTAGAACACTTT[A/G]GATGTGCAGGGTATTGATTTCTCTCCTGTATTTAT R 2 1 2 1 201000 f 74 goat snp20431-scaffold202-2800328 2 103023823 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416334 Affx-122947902 AX-123286683 2 32650568 CCTTCTGAAATTCTTTCTAGGTCCCCACAGGGAAG[A/C]GTAGCCTCAAGCTTTTAGGTCTCAAGGAAACCTAA M 2 1 2 1 201000 r 74 goat snp20432-scaffold202-2873825 2 102949909 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798527 Affx-122937384 AX-385285460 2 32712944 AGAGAAAACTTGGCATTATATAACACTTAATCTCA[C/T]TAAGAAAATCCTTGAACTTGATTTAATGACTTCCT Y 2 1 2 1 201000 f 74 goat snp20433-scaffold202-2936201 2 102885234 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768287 Affx-122955097 AX-385255468 2 32751804 TAATTCCAGACTTCCATTTTAGTAAAAAATATCAA[C/T]AAATATCTCTGCAAAGGTAAGCTGACAATTAGAAA Y 2 1 2 1 201000 f 74 goat snp20434-scaffold202-2975061 2 102845972 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443002 Affx-122928180 AX-123313339 2 32794454 CTCAGTCCTGAGCAGAATCTCAGTTTGGGTCTCTT[C/T]ACCCAGCTTTCCCAGAGGTGGGTACTTGAGATGGG Y 2 1 2 1 101000 f 74 goat snp20435-scaffold202-3017711 2 102802805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414602 Affx-122949356 AX-123284951 2 32840232 TTAAAACATCATAATACTCTGTGTTAGTAAAGGTA[C/T]GAGCTAATGATGTCCTATACTACTGGTATGAACAT Y 2 1 2 1 101000 r 74 goat snp20436-scaffold202-3063489 2 102756860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275313 Affx-1111834721 AX-519548888 2 32846783 CGAATTAAGGACAGA[A/G]CAACAAAAGGGAATGATATTATTTCCTCTGGCATC R 2 1 2 1 102000 r 74 goat GoatD01.048752 2 32846783 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38392511 Affx-122966121 AX-123262868 2 32890637 ATGCTGGCTCATCCAAAGTGGAGAAATGTCACAAA[A/G]TACAGTGGACATTCAAATAAGACCCTAGAAAGAAT R 2 1 2 1 101000 f 74 goat snp20437-scaffold202-3113894 2 102701624 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783197 Affx-122954325 AX-385270264 2 32946608 CCCTCAGCTTCTCACCCTGAAGAAACCATTATCAT[A/C]TTTCCAAAGGCAGATCAAAACAAGTCTTCTGATGC M 2 1 2 1 101000 f 74 goat snp20438-scaffold202-3169865 2 102645060 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439504 Affx-122930140 AX-123309841 2 33005151 CAATCCAATTTTTATCCTCCTCATTCTCTTCTGCC[A/G]CATTTAGTTGCTCCCATTTTCCTAGTCATGAGCAT R 2 1 2 1 101000 r 74 goat snp20439-scaffold202-3228408 2 102586512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387449 Affx-122970376 AX-123257807 2 33036845 GCTTATCCACACCTCAACCTCTCAGTGATTAAAAT[A/G]CACTGTTTTATTTTTCATCATTTTCTCCTCATCAT R 2 1 2 1 101000 f 74 goat snp20440-scaffold202-3260102 2 102555274 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395767 Affx-122963675 AX-123266122 2 33078729 TCTGTGATTCTCAAAATCTGCTTTTGTTTCCCTGA[C/T]GTTAAAATTGTTCACTTTGTTTTTTAAATTCTAAA Y 2 1 2 1 101000 f 74 goat snp20441-scaffold202-3301986 2 102512882 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451721 Affx-122921549 AX-123322054 2 33107752 TTACAAAAACAATTAATGTCTCTTTATTAAGACTG[A/C]AAATTACAGAAAGAACAGAGTAAAATCATATATGA M 2 1 2 1 101000 f 74 goat snp20442-scaffold202-3331009 2 102483886 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386704 Affx-122970167 AX-123257062 2 33154775 TTAGCTCACTGTTTTGTTGAGAAAGAATTTTAGAT[A/G]TATTTTCATAGAAATCAAGGGAACTTTCTGGCTGA R 2 1 2 1 101000 f 74 goat snp20443-scaffold202-3378032 2 102436136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419321 Affx-122945660 AX-123289669 2 33184314 ATGAGAAATGGCAAGAGGAAACTACCCTTTAAGAG[C/T]AATTTTATCTTTTGGTATTTTGATAGCATTTCTCA Y 2 1 2 1 201000 r 74 goat snp20444-scaffold202-3407571 2 102406685 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795537 Affx-122942642 AX-385282492 2 33256929 AAAATAACCTGTATAAGTGTTTCTTTAAATTTACC[A/G]CAAAGGGTCTTCCCAAGGTTTTTCAAGAAAAGCAG R 2 1 2 1 101000 r 74 goat snp20445-scaffold202-3480186 2 102333094 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407854 Affx-122954518 AX-123278205 2 33310736 AGCAGAAAAGTTTAGGACAGACAAATTATATTTGG[C/T]AGCTTCTGATACTATCCAAGTTCTACTTTATATCA Y 2 1 2 1 101000 r 74 goat snp20446-scaffold202-3533993 2 102278806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387959 Affx-122969608 AX-123258317 2 33340585 ACTATAGCCCACCAGGCTCCTCTGTCCTTGGGATT[C/T]TCGAGGCAAGAATACTAACAAGGTGGAGATCAAAT Y 2 1 2 1 103000 r 74 goat snp20447-scaffold202-3563842 2 102249009 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409075 Affx-122953341 AX-123279426 2 33391710 CAGAAGGAAATCTTTTGAGGACAGTTTTCCAGCAG[A/G]CTACAGTCCATAAGATTGCAAAGAGTCCAGCACAA R 2 1 2 1 101000 f 74 goat snp20448-scaffold202-3614967 2 102197905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778965 Affx-122942470 AX-385266072 2 33421587 AGCCATGCTAAATCATTTTCCTCACTCTCCTGGCC[A/G]TCTTCTTAACTCAGAATGCTCGACAATTCACACAG R 2 1 2 1 101000 f 74 goat snp20449-scaffold202-3644844 2 102167399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407797 Affx-122954564 AX-123278148 2 33467023 GATACATTGTACAGAACGAGCCTGCTAAACTCTAG[C/T]GTGGAATAGGAGTGATGGCTAGAGGCTCAGTGTGG Y 2 1 2 1 101000 f 74 goat snp20450-scaffold202-3690280 2 102121974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376374 Affx-122978111 AX-123246733 2 33495634 CTTCAGTCTACTGACATCACAGCTGAAAGAGCAAC[A/G]CTTTAAGAAAATAAGTTACATCATGTCCAGCTAAG R 2 1 2 1 101000 f 74 goat snp20451-scaffold202-3718891 2 102093838 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275433 Affx-1111834893 AX-519549006 2 33498633 TGATACTATAAGGGAATGGGGACATATGATGAATA[A/G]TCTGGAATAGACCTAACTGCAGTGTAACAGTAAAC R 2 1 2 1 101000 f 74 goat GoatD01.057667 2 33498633 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38424446 Affx-122941788 AX-123294792 2 33534104 GTGTTTGGGATGAACTTACATTTATGCAGAGTTCC[A/G]CAGATAATCCCCCAAACTTCTTTTACCATTCTTTG R 2 1 2 1 101000 r 74 goat snp20452-scaffold202-3757361 2 102056875 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391245 Affx-122967381 AX-123261602 2 33575666 GAATTACCAATCACATTTCCTGATCTTAACTATTC[A/G]GAATATTGTTTGTTTAGTGATGAGGACTGACGTTT R 2 1 2 1 101000 r 74 goat snp20453-scaffold202-3798923 2 102014915 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418870 Affx-122946120 AX-123289218 2 33616977 TGGGCAGGGCTTCCAGTGCCTGCAGTAAAAGGAGC[A/G]CCACCTTTAGCTAGCGTAGGTTCAGATCTCCTTGA R 2 1 2 1 101000 r 74 goat snp20454-scaffold202-3840234 2 101972863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403902 Affx-122957486 AX-123274254 2 33661557 CTCGTCTGCTATGGTAGGTAACGGACCTAACACAG[A/G]CTCTACCCTTCTCTGCCTCTTTCCTTGTCCTTGTC R 2 1 2 1 201000 f 74 goat snp20455-scaffold202-3884814 2 101928187 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397026 Affx-122963119 AX-123267381 2 33751806 AAGACCCTCAGCCAATAGCCACGTCGACCACCTGA[C/T]AGGTGAGTAAAGGAACATTCAGACAACTCCAGCCA Y 2 1 2 1 101000 r 74 goat snp20457-scaffold202-3975063 2 101837681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272941 Affx-1111833167 AX-519546627 2 33769581 TTGTAGGTTTGATCCCTGGGCTGGGAATATTCCCC[A/G]GAGAGGGGAATGGCAACCCACTCCAGTATTCTGGC R 2 1 2 1 103000 f 74 goat 2_33769581_AF-PAKI 2 33769581 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781826 Affx-122976288 AX-385268907 2 33826497 AAAACCATATGGGAAAGTATCATTTTCTACTTAAG[A/G]GTGCAAAAGGAGATAAGACAGAAAGAAACCTTAGT R 2 1 2 1 101000 r 74 goat snp20458-scaffold202-4049754 2 101762205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774310 Affx-122930860 AX-385261446 2 33857071 TGCACATTTATTACAAAAGGAGCCTGGGAGGTCAT[C/T]GGGATAGAAGCTCTTACCAGTGATTATCTGTAAGT Y 2 1 2 1 101000 f 74 goat snp20459-scaffold202-4080328 2 101731485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375522 Affx-122979115 AX-123245881 2 33885702 AACTGCCTTGTAAACATGGAGAGGGTTCAGCTTTT[A/G]TAAGAAACAGATACAAAGAAATGTGCTAAATTAAG R 2 1 2 1 101000 f 74 goat snp20460-scaffold202-4108959 2 101703006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415972 Affx-122948415 AX-123286321 2 33957354 GTCTTCCAAACGTTATCAGGAGCTTAAACTTACCA[C/T]ACCACATAATAAGATTTGAAGATTTACTGAGGCAA Y 2 1 2 1 101000 f 74 goat snp20461-scaffold202-4180611 2 101631420 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277453 Affx-1111835857 AX-519550957 2 33993750 ATTAGCCAGGCCATTTCCCAATTACCTCCCAAATG[A/G]AAATTCTTAAGATCAGCTGATGGCCTTTAAGAAAA R 2 1 2 1 201000 r 74 goat Random2.2K-188 2 33993750 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778962 Affx-122954192 AX-385266069 2 34009670 CTTCAATAATTATGAAATAACTTCAGGATAGAAAT[A/G]TAGAAATGAGCCATCAGAATAGTTTCCTTCAATTA R 2 1 2 1 101000 r 74 goat snp20462-scaffold202-4232927 2 101578608 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376903 Affx-122977805 AX-123247262 2 34056139 TGTGTAGAGTTCCAAGAAAGATAAAGAAACTCTGG[A/C]TCTGTTCTTAGTGTTCAAGGACCAAAATGTCAGGA M 2 1 2 1 201000 r 74 goat snp20463-scaffold202-4279396 2 101531982 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412470 Affx-122951394 AX-123282819 2 34138308 TGATTTTTACTCCTTAATTTTAATCTCTAACTAGT[A/G]CTTTAAAAAAAGACCTGATATTGCTGTTAAGCTTT R 2 1 2 1 101000 r 74 goat snp20465-scaffold202-4361565 2 101449954 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408700 Affx-122953437 AX-123279051 2 34179885 AACAAACTTGCATTTTGAGGGAAAATATGAGCATC[G/T]AGCTTCATATGTATAATATTTCCTCTCTATAAACA K 2 1 2 1 201000 r 74 goat snp20466-scaffold202-4403142 2 101407580 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442470 Affx-122927939 AX-123312807 2 34235387 AAAAATCACTATTGTATTTATGCCCACTGTACTTA[C/T]AAAAGAAGCAGTACAAACATAACAATAATCAAATA Y 2 1 2 1 101000 f 74 goat snp20467-scaffold202-4458644 2 101354401 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426116 Affx-122940631 AX-123296462 2 34267256 TGAATGTAGAGCCATCAGACTTTGGTTAAGGATGG[A/C]ATGCAGAATGTAGGAGAAAAAAGAATTGAGGATGA M 2 1 2 1 101000 r 74 goat snp20468-scaffold202-4490513 2 101322139 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433539 Affx-122934998 AX-123303880 2 34298010 CCCTTCTGTAAAGAAAAAGGGAAAATAATCAAGAA[C/T]AGGTTGCAGGGAGGTAAATCATCTTTGGTCACTTT Y 2 1 2 1 103000 r 74 goat snp20469-scaffold202-4521267 2 101289991 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413832 Affx-122949882 AX-123284181 2 34346143 GGGAAAGTAAATCTGAACAGTACTATGGGTGAATT[A/G]TTGACAATATAGGCCTCCACATGGGATAAGACTTT R 2 1 2 1 101000 r 74 goat snp20470-scaffold202-4569400 2 101241639 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794559 Affx-122950542 AX-385281521 2 34377872 TATCTAGAATATTTCAGGTTATACAGAGTCCTCTG[C/T]TCACTGTCACTAACTACCATAAAAATTTAAAGTAT Y 2 1 2 1 101000 f 74 goat snp20471-scaffold202-4601129 2 101209900 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771806 Affx-122976409 AX-385258963 2 34434249 CACTAATGAGCAATGGGTGCAGAAGGTGTTAATTA[C/T]GCCACACTAAGATTCAAGAAAAAGCCCTAGTGAGC Y 2 1 2 1 101000 r 74 goat snp20472-scaffold202-4657506 2 101153073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447363 Affx-122924866 AX-123317699 2 34462993 TTAAAAACCCTAGGCAGGGGGTACCTGAACAGAAA[C/T]GAAGAAAATTTAAACATATACAAATAACTACCACT Y 2 1 2 1 103000 f 74 goat snp20473-scaffold202-4686250 2 101124263 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435964 Affx-122933523 AX-123306303 2 34494905 TAAGGTTTCAAGACAGGATGGGATCAGAGAATAAG[C/T]GAAAGGATTAGCCATGGAAAAGAGAAATGTCATTT Y 2 1 2 1 101000 f 74 goat snp20474-scaffold202-4718162 2 101092154 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797928 Affx-122943282 AX-385284866 2 34523534 GGATAAACTCCAAATAAACACAAGAAGTTTTCTTG[C/T]GCACTTGACAATTGCATAAGAAAAAGATACCTTTG Y 2 1 2 1 201000 f 74 goat snp20475-scaffold202-4746791 2 101063498 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429883 Affx-122938130 AX-123300224 2 34583522 GACTATTCCAGTTTTCAAAGTATACTGATTCAGAC[A/C]TAAAGTAGGAATGATTACTTCTGAAACTAAAGCCT M 2 1 2 1 101000 r 74 goat snp20476-scaffold202-4806779 2 101002974 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783183 Affx-122954992 AX-385270251 2 34629474 TACCTGGATATATCTGAAGGCTAGAGTTTGGAAAG[C/T]AGAATGCTCACATCTAATATTTATGAGGTTTAGCA Y 2 1 2 1 101000 r 74 goat snp20477-scaffold202-4852731 2 100955498 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429086 Affx-122938274 AX-123299428 2 34688003 TGTTGTAAGGAGAACCCAGGGTTCCTGAGCTATGC[A/G]GCAATGTTACAGACAACAATTCTGTTGGCTTTCTT R 2 1 2 1 101000 r 74 goat snp20478-scaffold202-4911260 2 100896884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444185 Affx-122927268 AX-123314522 2 34727610 TAAAAGGTTGGAAATTGCCTAAATGTCCACAGAAG[A/C]CAGGATTGCTTGGTAAGATACTGTTTCCATCATAT M 2 1 2 1 101000 r 74 goat snp20479-scaffold202-4950867 NW_017189798.1 8887 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446437 Affx-122925973 AX-123316773 2 34761336 CAAGTGTCCTAACATCCTCAGGGGGAGTTCCCAGG[A/C]GTTAGGGCTTTATCTGGAGCCTGAGGCAGAAGCTG M 2 1 2 1 101000 r 74 goat snp20480-scaffold202-4984593 2 100822989 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793471 Affx-122934519 AX-385280448 2 34819703 CTTTACTTTCATTTTTTCAGATGATTTTGGCTATC[A/G]TAATTCTATATGCATTTTGAGGTCAACTTTTTTAC R 2 1 2 1 101000 f 74 goat snp20481-scaffold202-5042960 2 100763616 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791806 Affx-122932213 AX-385278796 2 34857281 AATAGGGTCTGTGAAGGAGGAATTCTGAAATTATA[C/T]GGTATGCTATTTGAGTATAGATTTGCTCTGTCCAA Y 2 1 2 1 201000 f 74 goat snp20482-scaffold202-5080538 2 100725382 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437866 Affx-122932070 AX-123308204 2 34904461 CTCACTGTTTATCTGTGATCTCACTGCCATGTCTC[A/C]CACTTCTCACTATCTGCTCTGGTCCTGGATTGCCT M 2 1 2 1 101000 f 74 goat snp20483-scaffold202-5127718 2 100677900 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776956 Affx-122919296 AX-385264080 2 34944422 GAGTGCATCAAGGCATCAAGGGAGTGCCATGAACA[C/T]GCACTTGAAATTCTGTGGTGCTCCTTGGTACCTAT Y 2 1 2 1 101000 r 74 goat snp20484-scaffold202-5167679 2 100637722 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790643 Affx-122923223 AX-385277645 2 35005799 GCCTCTCATTGGAGCACAAAATAGCAGGGCAAAAT[A/C]TTGCCTTTGTGCTCAATTCTAGGCTGCTCTGGGTC M 2 1 2 1 201000 r 74 goat snp20485-scaffold202-5229056 2 100576372 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275410 Affx-1111834881 AX-519548983 2 35032693 AAAAGTGGTCTAATTAATGTGAGGCTTATTATATC[A/G]CTTTTGTTAACGGATATTTTTTTTAACTGCAGTTG R 2 1 2 1 101000 f 74 goat GoatD01.057374 2 35032693 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38435602 Affx-122933793 AX-123305942 2 35059794 ATCTTAGTAATGCCAGGGTGTTCCTGAGTCACTGC[C/T]GATGCAGCACTGGAACCCAGTTCCCCAGTATCCCC Y 2 1 2 1 101000 f 74 goat snp20486-scaffold202-5283051 2 100522464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424100 Affx-122942031 AX-123294446 2 35101095 GGCTACTTATTTCCACATAGCAAATCTCTCAAGTT[A/G]CTTACTTTGAAACACGTTTTGCAAAATATTTGTTT R 2 1 2 1 101000 f 74 goat snp20487-scaffold202-5324352 2 100480795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793272 Affx-122943174 AX-385280250 2 35180973 CCCTCAAAAACCACCCTGAGGAAATCAGCCCAGAA[C/T]TACTCTGAGAAATTTAATATGCCTAGTGATGACAC Y 2 1 2 1 101000 f 74 goat snp20488-scaffold202-5404230 2 100400834 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384327 Affx-122972263 AX-123254685 2 35215758 ATGGAAATCAATTTCACACTACTCAGTTTACACCC[G/T]GTAGCTGTTATTTTCATCTGCCCATGATCCATACT K 2 1 2 1 101000 f 74 goat snp20489-scaffold202-5439015 2 100365286 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777084 Affx-122944466 AX-385264207 2 35248799 TCAAAGACAGGTTTAATTATGGTTACAGAAGATAA[C/T]GAAAATAAACAGTCTGATGAAAAGACGAAGAAATG Y 2 1 2 1 101000 r 74 goat snp20490-scaffold202-5472056 2 100332038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417043 Affx-122947527 AX-123287391 2 35282403 CTGCTAGGCTCTTAATGCTGGTTAGTTCATGGCCA[G/T]TCCCTTATCAAATACATTAAAAGGTCCCACATTGA K 2 1 2 1 101000 r 74 goat snp20491-scaffold202-5505660 2 100297701 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790740 Affx-122957346 AX-385277741 2 35319957 CAACTGAAACGACCTGCTCAATCTGGCAAGTGACC[A/G]TGGCTAATATGTTCTTTATCTTTTGCCCAAATTCT R 2 1 2 1 101000 f 74 goat snp20492-scaffold202-5543214 2 100259785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802561 Affx-122957167 AX-385289463 2 35350185 TTTTAATTTGTATCTATGCATAATAACCATCAGAT[A/G]TATTATTAGTAGTTATGCTAGTTGAAGGGGAAAAT R 2 1 2 1 102000 r 74 goat snp20493-scaffold202-5573442 2 100229661 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789815 Affx-122940134 AX-385276822 2 35394123 TCTTGTTTCAGCTACGAAAAGGCTATGATGGATGC[A/G]TTTTGTCCCAGATGTCAAACTCCTTTCTCAGACAG R 2 1 2 1 101000 f 74 goat snp20494-scaffold202-5617380 2 100185685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793133 Affx-122975766 AX-385280111 2 35437282 TTAGAATTTATGCTCAGATTATAATGTTATTCATA[G/T]TGAAAATAAACTTATTTCAGTAGACTACAGTGAGA K 2 1 2 1 101000 r 74 goat snp20495-scaffold202-5660539 2 100142592 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439060 Affx-122930321 AX-123309397 2 35466386 CTTGGTAATAAAATATGTATGAGCGTGAGAGATAC[A/G]TGTGTGCCTGCATACATCTTCATAGTGGGTTGCAT R 2 1 2 1 101000 f 74 goat snp20496-scaffold202-5689643 2 100114020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404463 Affx-122956736 AX-123274815 2 35496099 ATAGTAAATTTCTTGAGGGTGGGGCCCATGTCTTA[C/T]TGCCTTTACCTCTTTGGTGCTTGATACTCAAATAC Y 2 1 2 1 201000 r 74 goat snp20497-scaffold202-5719356 2 100084334 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379980 Affx-122975623 AX-123250338 2 35526186 GATGCTTCATCCTTCTTCACAAGAGCTGTATGGCT[A/G]TGTTTGAACTCTTTTGTGCCCAACCAGAATAAATC R 2 1 2 1 101000 f 74 goat snp20498-scaffold202-5749443 2 100054123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395705 Affx-122963725 AX-123266060 2 35578590 GATAAAATAGTTACTACTTCAAAGGGGAACTGTGA[A/G]AATGAAATAGGACAATACTAATAAAATATTGAACA R 2 1 2 1 101000 f 74 goat snp20499-scaffold202-5801847 2 100001684 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422693 Affx-122943659 AX-123293039 2 35613199 CCATTCCTAGCTATCAGGCCAGGAGAGGAGCAGCC[A/G]TTTCCCACAGTAAACGACTTTGAAAGTCACTGAAC R 2 1 2 1 101000 r 74 goat snp20500-scaffold202-5836456 2 99966960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401693 Affx-122959551 AX-123272046 2 35655662 AAATCAGCTTCTTTGAAACGCATACATATTGTCTA[C/T]GGCCATACCACCCTGAACACACCCGATCTCGTGTG Y 2 1 2 1 201000 f 74 goat snp20501-scaffold202-5878919 2 99923715 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428992 Affx-122938852 AX-123299334 2 35696001 GATGCAACTTGATTTCGTGACTGGAGGATCAGGAG[A/G]CCAGCCTCTTGCTCTCTTCAACTCCCCCTTTTCTA R 2 1 2 1 201000 f 74 goat snp20502-scaffold202-5919258 2 99883303 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446912 Affx-122924699 AX-123317248 2 35740004 AAGAGGAAATGGAGTTGGGCTTTGGAAAATTCGTG[A/C]AGAAGGGTGTCCGGGGTTGAACATGAAGTTCAGCT M 2 1 2 1 101000 f 74 goat snp20503-scaffold202-5963261 2 99838931 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796779 Affx-122929492 AX-385283722 2 35773283 AAGTAATAGAAATATGCAGTAAAGTAGTAAATAAA[C/T]AGGGAAAAGATGTTCCCAAATTCCTTACCAACTCA Y 2 1 2 1 101000 r 74 goat snp20504-scaffold202-5996540 2 99805583 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379330 Affx-122976179 AX-123249689 2 35841742 ATTTAAACCATTTCCAAGTAATGTGTGTGTTAGTC[A/G]TTCAATTCTGTCCGATTCTTTGTGACCCTCCATGG R 2 1 2 1 303000 f 74 goat snp20505-scaffold202-6064999 2 99737387 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412762 Affx-122950513 AX-123283111 2 35905794 GCATGATATTAGGTGCAGTCGGAGGTTAAAAGTAC[A/G]CTCGTGGTCCAGCCCTCAAGCAACCTAACTTACAC R 2 1 2 1 201000 f 74 goat snp20506-scaffold202-6129051 2 99676334 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789491 Affx-122920577 AX-385276500 2 35940001 ATCGTAAAGCGTGATGGATTTCCGCTATGGGTTGG[A/G]CTCTCAAGTCACGATGTAAGTCTTGTTTTGTTTTC R 2 1 2 1 101000 f 74 goat snp20507-scaffold202-6163258 2 99641830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388495 Affx-122969225 AX-123258853 2 35969172 CCGGGGTCTCCTGCATTGCAGGCAGATTCTTAACC[A/G]TCTGAGCCACCAGCGGAGCAAGCTACTTTTTTCTT R 2 1 2 1 103000 r 74 goat snp20508-scaffold202-6192429 2 99614930 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425143 Affx-122941203 AX-123295489 2 35999709 TCACACATGAAAATTTCTTAACCCATCCCCTCCAT[C/T]AGCTAAAGACCCTTATTAAGAAAACAGAGGCAATT Y 2 1 2 1 201000 r 74 goat snp20509-scaffold202-6222966 2 99584398 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796708 Affx-122977673 AX-385283653 2 36052714 AATATTGTCAGAAAGTCAGTTTTTTCCAACTTGAT[A/C]TATTAATACAATACTATCCCAGTTAAAATCACAGC M 2 1 2 1 103000 f 74 goat snp20510-scaffold202-6275971 2 99533154 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380409 Affx-122975316 AX-123250767 2 36108592 TTAGTGATCCTGATATATACTATGTGTTTGCTTGT[A/G]TGTTTATTGCCTGTCTCTCCCCACTAGAAAGTAAG R 2 1 2 1 103000 r 74 goat snp20511-scaffold202-6331849 2 99477456 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409070 Affx-122953345 AX-123279421 2 36139983 ACAACATACTGATTCAGTATTTGTATAAATGATAT[C/T]CCGTCTAAAGTTATTATAAAATAAAGGCCGTATTT Y 2 1 2 1 101000 r 74 goat snp20512-scaffold202-6363240 2 99445837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452648 Affx-122920341 AX-123322981 2 36186025 AAGTGATACAAAATAACTATACATGTTAATAAACA[C/T]GTTATTTACTTCCTTTTTATTTGGTTTTCACTCCT Y 2 1 2 1 103000 r 74 goat snp20513-scaffold202-6409282 2 99399864 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382751 Affx-122973596 AX-123253109 2 36226056 TTTGTTGCCTCTGTTTGTAAACTGTTGCTTCTCAG[C/T]AAACTGGTGAACCCACAGTGTTCAACAGTGTCTAT Y 2 1 2 1 101000 f 74 goat snp20514-scaffold202-6449313 2 99359602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776409 Affx-122931333 AX-385263536 2 36290778 ATTTACTAGAAATGAATACTCTAAAAATACCTTTT[A/G]CTGCCACACATACTCATAGATAATTATATGCACAT R 2 1 2 1 101000 r 74 goat snp20515-scaffold202-6514035 2 99294795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272994 Affx-1111833168 AX-519546675 2 36305963 AATAATAATGGCTGGAATCATCATTGCTTTCAAAG[A/G]CTTGTTTTTATATACTATTCCTATGAAACTTATTC R 2 1 2 1 101000 r 74 goat 2_36305963_AF-PAKI 2 36305963 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38431102 Affx-122936610 AX-123301443 2 36339205 TAAAGTTTATCATTGCCTTTAGTTCTTCGTTTTGC[A/G]CAAGAATAGAAAGGAGATAGAGAAACATTTTTAAA R 2 1 2 1 101000 r 74 goat snp20516-scaffold202-6562462 2 99245758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780314 Affx-122928009 AX-385267409 2 36380990 GGCCTTCCCAGAACACTTAATTTTGCCTTTTCTTA[C/T]ACCTAACCTCTAGAACTCTATCCCATTATCTTATT Y 2 1 2 1 101000 f 74 goat snp20517-scaffold202-6604247 2 99203996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420896 Affx-122944612 AX-123291243 2 36426211 TGTAATTTGATTTGATATTTTGTGTTTTATTCAGA[C/T]GAGAAATTTATGCTCTAACATTATCCTGTGATATT Y 2 1 2 1 103000 r 74 goat snp20518-scaffold202-6649468 2 99159260 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402503 Affx-122958575 AX-123272856 2 36458471 ATATGACGAAACCAAGGCTTAGAAATGTTTGGTTA[C/T]ACAGCTAATTAGTTGTCAGAACTAGAATTCAAACT Y 2 1 2 1 201000 r 74 goat snp20519-scaffold202-6681728 2 99126765 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399673 Affx-122960504 AX-123270028 2 36506892 TCAGTGAATTCCATAGGAAGGACGTCCCTTAAGAT[A/G]CAGGCAGTTGTGGGGTTGACTTCCCACACTTTCAT R 2 1 2 1 202000 f 74 goat snp20520-scaffold202-6730149 2 99079439 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443222 Affx-122927571 AX-123313559 2 36540529 CCAGGATTTCTGGAACAGACGTTTAGAAGGCTCCT[A/C]ATGCATGCTCATTTCAGGCAAAAAGACTAATTTTG M 2 1 2 1 101000 f 74 goat snp20521-scaffold202-6763786 2 99045881 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421945 Affx-122943822 AX-123292292 2 36574598 ATCTACTCGGCACGCTCCATTTCCCATCTGGCCTA[C/T]GGCACAAGACACTGGTTCTAAGACACAGAAGTTCA Y 2 1 2 1 101000 r 74 goat snp20522-scaffold202-6797855 2 99012202 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437781 Affx-122931698 AX-123308119 2 36605069 AAGTAGTTCTTAAGTGACCTGCTACTCAAAAATAC[C/T]TATTCTTCCAGGCTAACAGGAATATACTCCTGATT Y 2 1 2 1 102000 f 74 goat snp20523-scaffold202-6828326 2 98981872 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392953 Affx-122965690 AX-123263310 2 36636654 AAAGTCAATAAAACTGCAGTCAGTAGCCACACAAG[C/T]GTAAGGACTTACATACATTAATTCATCCAGTCCTA Y 2 1 2 1 101000 f 74 goat snp20524-scaffold202-6859911 2 98950015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431342 Affx-122937057 AX-123301683 2 36676832 GAGGAATTAAAAACATTTCACTGCAACAACCAGTA[C/T]GGCAGGCACATTTCTTTTTAGCCTTGAAAAGATGT Y 2 1 2 1 201000 f 74 goat snp20525-scaffold202-6900089 2 98909716 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376532 Affx-122978000 AX-123246891 2 36765061 CTTCGGCCAGCATTCCAGGCCTACCAACACCTTCA[C/T]AGATACCAGGATTCGGGGTTCCTTTCCCTGTTTCA Y 2 1 2 1 201000 r 74 goat snp20527-scaffold202-6988318 2 98820992 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780697 Affx-122958644 AX-385267787 2 36809018 TTTGCTGCCCTCTCCTGTGAGAGAGTTATTCTTCC[C/T]TTCTCCTCCTCTGACATCAGCTTTGGCCATGTGAT Y 2 1 2 1 101000 f 74 goat snp20528-scaffold202-7032275 2 98776658 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412018 Affx-122951743 AX-123282368 2 36845781 ATGCCCACTTCGATCTGTAAAAGCCACTCTAGAAA[C/T]GCACAAAGGCTGACACCTTGTACAGAAACTCAAAG Y 2 1 2 1 101000 f 74 goat snp20529-scaffold202-7069038 2 98739480 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791975 Affx-122971352 AX-385278963 2 36881880 ATATTAACAATTATCCTGGTATCACTACGCATATA[C/T]GAAACACAATATGCTAAGAAGGCCATGGGCACATT Y 2 1 2 1 101000 r 74 goat snp20530-scaffold202-7105137 2 98703367 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435083 Affx-122933722 AX-123305423 2 36929680 CAAGGGCCCAGTGGCAGCTTCCACCGTCAGATCAC[C/T]TCTGCACTGTGATTTCGGATCTTGCCCAGATGCCT Y 2 1 2 1 101000 r 74 goat snp20531-scaffold202-7152937 2 98655675 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434908 Affx-122934325 AX-123305248 2 36963788 CCAATAAATGATACACCATTTCCTGGTGCCATTTA[C/T]AGATGCTTCTTGCCTCTTTCTGTTCTTTGGGATGA Y 2 1 2 1 202000 f 74 goat snp20532-scaffold202-7187045 2 98621593 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769466 Affx-122921333 AX-385256636 2 37000211 CCTTATTATAGGCAGAAGTCTGCTGTGGGGAAAAC[A/G]GCTAACAGGCATGGAACACTAGGTATCAAGCATTG R 2 1 2 1 101000 f 74 goat snp20533-scaffold202-7223468 2 98584491 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410242 Affx-122952544 AX-123280592 2 37037705 GGGTACCAGATGCTATGGAGGAGGCTGGGCCACTT[C/T]TGTGTACCCTAGTTGGTGTAAACTTGCATAAACCT Y 2 1 2 1 101000 r 74 goat snp20534-scaffold202-7260962 2 98546727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415607 Affx-122948605 AX-123285956 2 37072481 CTCCCCAATCCCTTTTTCTCCACCTGAACCCTGTA[C/T]ACGTAATCAACTATCCTGAATCTTTTATCATTTTA Y 2 1 2 1 201000 r 74 goat snp20535-scaffold202-7295738 2 98511498 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435653 Affx-122933347 AX-123305993 2 37127885 AGTCTGCCTCGTTCACAGATACACGTACAGAACCC[A/G]CAGCAGCTTGTGGCACACGGCTGTCACTCAAAACA R 2 1 2 1 201000 f 74 goat snp20536-scaffold202-7351142 2 98455805 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451208 Affx-122921319 AX-123321542 2 37180259 ACTCTCCTCGAAACTAAACCTAAATGATCACTTTA[A/C]ATACACACCTGTGACACTTACCTTTTAAAATAAAC M 2 1 2 1 101000 f 74 goat snp20537-scaffold202-7403516 2 98403545 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387586 Affx-122970263 AX-123257944 2 37223899 GACAGGTTCTCTGAATCTTGAGGCGGAGACTAAGA[C/T]ATGAGGACATCTATGTTCTGAACTGACGTGAATGC Y 2 1 2 1 101000 r 74 goat snp20538-scaffold202-7447156 2 98359931 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434488 Affx-122934623 AX-123304829 2 37258712 TCTAGACACTCATGCCCTTTTCAAGACCGATTAAA[C/T]AGATGTTTAAAACCATCCCCTGCACTGACTCTGAA Y 2 1 2 1 201000 f 74 goat snp20539-scaffold202-7481969 2 98325130 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784629 Affx-122959583 AX-385271677 2 37302617 AACATGATTGAAAATCTTCCAAATGCATTTCAGTG[A/G]ATTTAGACCCAATATGTTAAATGTTAAATAAAAAA R 2 1 2 1 101000 f 74 goat snp20540-scaffold202-7525874 2 98281341 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454314 Affx-122919248 AX-123324647 2 37349805 TGAATACTGTTTCCTTCCTTTATCATTGATTACCC[A/G]TATTTATGATCATTAAAAATAATTACTTTCATTAA R 2 1 2 1 103000 f 74 goat snp20541-scaffold202-7573062 2 98233660 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443665 Affx-122927189 AX-123314002 2 37404070 TAATTTTAATCTTCAATACACCTCATTTTAAAAGC[A/G]TTATTTTACTGATTTATTTTACAGTTGTAGCTATA R 2 1 2 1 303000 f 74 goat snp20542-scaffold202-7627327 2 98179812 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773648 Affx-122970940 AX-385260788 2 37434134 CACATATGGTTTTACAAAGAAAAGCTGATAGTCTA[G/T]AAAACTGAGGTGTATTTCAGACATGGACCATGTTA K 2 1 2 1 101000 r 74 goat snp20543-scaffold202-7657391 2 98149684 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398951 Affx-122960982 AX-123269306 2 37482462 CCAAAGAATAAGGTAAATATGGCCAAGATTATCAG[C/T]AGTTGGGGAAACCTACTGCTTATTTAACTTCTATG Y 2 1 2 1 201000 f 74 goat snp20544-scaffold202-7705719 2 98100277 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453986 Affx-122919447 AX-123324319 2 37523201 AGAGGATAAAAATATTCTTGAGTAACAGGTAGATC[A/G]TATACTTTAGAGACAATAATATGCTTTTGTTGTGG R 2 1 2 1 101000 r 74 goat snp20545-scaffold202-7746458 2 98059129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436537 Affx-122932928 AX-123306875 2 37580290 AAACATTGGCATCTCTAAGAATGAAGACTTTGACT[A/C]TGTCTCCTTAAAATTTCCCATGGCCAATCTTCACA M 2 1 2 1 101000 r 74 goat snp20546-scaffold202-7803547 2 98001738 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429807 Affx-122938192 AX-123300148 2 37636633 GGAATAATTTCACCCAAAATAAAAATGCATGCCAC[A/G]TCCATATTTGGCTTCATAATACCATTCTCCACCCA R 2 1 2 1 101000 r 74 goat snp20547-scaffold202-7859890 2 97944603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383981 Affx-122972932 AX-123254339 2 37683010 ACTCTTTGCAGCCCATCCCTGGGTCAGAACCACTG[A/G]TGGGTGGTGCTGGATAGTGAACATTTCATAGATAC R 2 1 2 1 101000 r 74 goat snp20548-scaffold202-7906267 2 97898190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401178 Affx-122959351 AX-123271531 2 37727792 TTTTTTCTCAGCATTTCAGATCTTCCCCTAGCAGG[C/T]ATCGAGCCAGTGCCCCCTGCATTTAACCACTGGAC Y 2 1 2 1 101000 f 74 goat snp20549-scaffold202-7951049 2 97853236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395334 Affx-122964041 AX-123265689 2 37785781 ATAACATTTCAGCTTAGTCTTGAAGGAGGGTCCAT[A/G]TTTGTCAAATGAAGAGAAATGAACAGAAGTTCTAG R 2 1 2 1 201000 f 74 goat snp20550-scaffold202-8009038 2 97794532 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403252 Affx-122957879 AX-123273605 2 37825614 CTAATCATTGTCTAGACTTTGCAGTCCTTTGCTTT[A/C]TGCTACCCAGACCAGAAAGACATTGGAGGTGGCAA M 2 1 2 1 101000 f 74 goat snp20551-scaffold202-8048871 2 97754701 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382313 Affx-122973905 AX-123252671 2 37854250 TGAGTCACAACGAGACTGAGATGCAAGCAAAGAAT[G/T]AGATAAGACTCTGAGATCTCTGAGAAATTCTCTTT K 2 1 2 1 101000 f 74 goat snp20552-scaffold202-8077507 2 97725984 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421774 Affx-122944349 AX-123292121 2 37897703 ATGTTTTCTGGGTTTAATGGTGCCAGTTTTTCCCT[A/G]TTAGTTTGTACACTAGAGATGTCCTAACTACTAAT R 2 1 2 1 201000 r 74 goat snp35725-scaffold430-16360 2 97680926 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435613 Affx-122933785 AX-123305953 2 37932531 GTACAAAGGAGTTGAAAATTACTTTTAAAAGCAGT[A/G]TTTTCTTCTTAGCATATTTTAAACTTAGATGCCTG R 2 1 2 1 101000 r 74 goat snp35726-scaffold430-51188 2 97646041 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445371 Affx-122925410 AX-123315708 2 38021900 GTCCTCTTTAAACCTCTAATTTCTAATAATTCCAC[C/T]CTCTCTTCTTTATTGTTTAACCCTTAGGTGTATAG Y 2 1 2 1 101000 f 74 goat snp35728-scaffold430-140557 2 97555856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394137 Affx-122965322 AX-123264492 2 38115717 AGCCACTCACCAATATCCTTAGATTGCTCTCCCAC[A/G]TGAAACAAAAACCTTATAATTAAATACATCTTTTG R 2 1 2 1 201000 r 74 goat snp35729-scaffold430-234374 2 97462217 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425254 Affx-122940988 AX-123295600 2 38145018 CTTTATTATTTATAGCAAGTAAGGTGAACACAAGG[C/T]ATCTTTCAGAAAGCAGTGTCTGAATTCCATAAATT Y 2 1 2 1 101000 f 74 goat snp35730-scaffold430-263675 2 97432386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387930 Affx-122970436 AX-123258288 2 38195434 CTGACCTTTTGTGATTTCAGGAACCATGTTTTATC[G/T]CCTGATAAACTAAGCACTTAACTACCAAGGACTAG K 2 1 2 1 101000 f 74 goat snp35731-scaffold430-314091 2 97381681 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795726 Affx-122954253 AX-385282679 2 38240297 CCCTGATCTCCTTCTCCTATTAATTTACTATTTCT[A/G]TATCAGAGCTTAGCATCAATTCCTGTGTTTGTGAT R 2 1 2 1 101000 f 74 goat snp35732-scaffold430-358954 2 97336286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400506 Affx-122961277 AX-123270861 2 38282415 GAGTGTAGCGCAAATAAAGACACTGGAACAATTAA[C/T]GCTTTTGGCTAACACTTTCAGAGCATTGGAATTGA Y 2 1 2 1 101000 f 74 goat snp35733-scaffold430-401072 2 97293948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426334 Affx-122940272 AX-123296680 2 38321789 TGCTCTCTGAACTTTCTAATCTACTCTTACTTAAA[C/T]ACTCTATATTTTTCTGCTATTACTTTGAATATTTA Y 2 1 2 1 101000 f 74 goat snp35734-scaffold430-440446 2 97253762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431607 Affx-122936162 AX-123301948 2 38355908 GAAATAAAGTAGGTTTTGTTAACAAAAAAGAACGC[A/G]TTATAACTGGTCACTACAGGGCTGACCCTACTCAA R 2 1 2 1 101000 f 74 goat snp35735-scaffold430-474565 2 97220885 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791184 Affx-122940416 AX-385278179 2 38396717 TAGGTTCTTAATCTCACTTTTTATTAAATTATGTC[A/G]TTATATCAATCAGAGTTTAATTGGGAAAATAGAAA R 2 1 2 1 101000 f 74 goat snp35736-scaffold430-515374 2 97173553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397100 Affx-122962702 AX-123267455 2 38447279 TCACAGTGTCTAGTGGGTTTACTAGATAAAAATAT[C/T]ACTTCCTCTTCAGTCTTCATAATAGTTTTCAAATT Y 2 1 2 1 101000 f 74 goat snp35737-scaffold430-565936 2 97122218 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777487 Affx-122969985 AX-385264607 2 38480056 ACCAAGCTTCAATATGAGTAGGAACTGCAAGGATT[A/G]TCTTTTTATAAAGAAAGGGTTAAATATGGAAATGT R 2 1 2 1 101000 f 74 goat snp35738-scaffold430-598713 2 97089483 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792761 Affx-122953052 AX-385279740 2 38510335 CCAAAATTTGTTTTTTTGCAAAGACTAAGATAAAC[A/G]TTTGGTAAGAATGATGAAAAAAAAGTAAAAAGGCA R 2 1 2 1 201000 r 74 goat snp35739-scaffold430-628992 2 97059349 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389065 Affx-122968602 AX-123259423 2 38539242 TCGTCTGATGACTGGGTGACTATCACCATCTTGAG[C/T]ACATTATTTCCTGAATTCTTTACTCCTATGAGAGA Y 2 1 2 1 101000 r 74 goat snp35740-scaffold430-657899 2 97030383 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798465 Affx-122954641 AX-385285398 2 38586943 ACAAACAAATGTGGTTCTTTGCAATTGAGCTGATA[A/G]TCTTTTCTTTTTTGTCCAAGTTTCAAAATTTTCTT R 2 1 2 1 201000 r 74 goat snp35741-scaffold430-705600 2 96981949 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439751 Affx-122930528 AX-123310088 2 38637710 CTTTTGATTTTCTAAACTACGTGCAGTTTTCTGAC[A/G]TCTGGGGTCCCAACCATTAATCTGGTACATAGTAG R 2 1 2 1 201000 f 74 goat snp35742-scaffold430-756367 2 96931211 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772339 Affx-122948814 AX-385259492 2 38671739 GAAATCTGTTTTTCTTCCATAGGAATGAGCCTACC[A/G]TCATAAGAAGCTTTAAAGCATTACAATAAAGAGGG R 2 1 2 1 101000 f 74 goat snp35743-scaffold430-790396 2 96897229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791428 Affx-122954335 AX-385278420 2 38704613 AGAAACACTCTGACAAAGGGTCTCAGCATAAATAG[C/T]AGCTCCACGTTTCAACTTACATATGGAGTGTTTTC Y 2 1 2 1 101000 f 74 goat snp35744-scaffold430-823270 2 96864003 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785269 Affx-122937242 AX-385272314 2 38735494 TATATTTTCTTAATCCTAATTGCCAAAATGTATGT[A/G]TTATTCACTGTTGTTTTCAAGGGTTTTCACCAAAA R 2 1 2 1 101000 r 74 goat snp35745-scaffold430-854151 2 96832550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781920 Affx-122961701 AX-385269001 2 38764334 ACAGATGGGAACTACCTCTCCAACTTCAGGTCTAT[A/G]TTTATTTCACAATTAGATTTTCTCTTGAAGAAACT R 2 1 2 1 101000 f 74 goat snp35746-scaffold430-882991 2 96803667 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782985 Affx-122946212 AX-385270054 2 38794674 AGCGCTGTTGGAAGTAAAGAGTTTGAATGTGGAAT[A/G]TTCTGATTATAACAAGAAGCTCTCTCCCAGCCTCT R 2 1 2 1 201000 r 74 goat snp35747-scaffold430-913331 2 96773222 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272033 Affx-1111833169 AX-519545798 2 38859332 AAGTTTTGTATTTTTCCATAAGACCCTGTGGAAAA[A/G]CCCAAATGAACTTTTGGCCAATCCATAATTCAGGG R 2 1 2 1 202000 f 74 goat 2_38859332_AF-PAKI 2 38859332 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395660 Affx-122963761 AX-123266015 2 38873291 AAAAGAAAAAATAATCATGATGGTTCAGATGTTTC[A/G]TTACCCAATATCTGTACACACTTTTTTAACATCAA R 2 1 2 1 101000 r 74 goat snp35749-scaffold430-991948 2 96694209 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787623 Affx-122962369 AX-385274646 2 38917780 CGACTGGAAAGGTGTTGAGTCTTCAATCTTTAAGG[A/C]TGAATTAGTCTAATGGTTTTCAACTTTTAACCAAT M 2 1 2 1 101000 f 74 goat snp35750-scaffold430-1036437 2 96648888 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381414 Affx-122974364 AX-123251772 2 38969800 CCTCATCTACAGCCTTATTCATTTAAAGTCCCTGA[C/T]ACCCTAAACAAAGGGTTAGCCACTGTCTGTCTGCT Y 2 1 2 1 101000 f 74 goat snp35751-scaffold430-1088457 2 96597292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438795 Affx-122930806 AX-123309132 2 39025170 AAATCCCAAAAGGGATATTGTGCCATTGATAAGTT[A/G]AGCAAGATTATCACTCTAAAAGTGGCAATTGGAAA R 2 1 2 1 101000 f 74 goat snp35752-scaffold430-1143827 2 96541734 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398514 Affx-122961549 AX-123268869 2 39055396 AAGTGACATTTAGGCAAAAGATAATATTTCATCCC[A/G]TCTTTAAATATTCTTTAAAATTTACATGAAACCCC R 2 1 2 1 101000 f 74 goat snp35753-scaffold430-1174053 2 96510054 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386543 Affx-122970723 AX-123256901 2 39099584 CCCAGAGGCTCACAGTGTATGCTTCCTGTGATATG[C/T]GGTATATGTTCATTATTCTTAACTAAATCCCCCCA Y 2 1 2 1 201000 r 74 goat snp35754-scaffold430-1218241 2 96465873 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403591 Affx-122957567 AX-123273944 2 39149920 AAATTTCTTGCAGCAGTACCCAGCCCAACGTGCTG[C/T]ATCTAAGAACACCACAGAGGATGATTTCTCCAGGA Y 2 1 2 1 101000 r 74 goat snp35755-scaffold430-1268577 2 96414918 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400056 Affx-122960769 AX-123270411 2 39195020 TTGTAAACACCCTGACACAGACTTCTACAGGTCTG[C/T]ACTAAGCCAGTGACAACAGAGCGGAGAGCAGAGTC Y 2 1 2 1 101000 r 74 goat snp35756-scaffold430-1313677 2 96369193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428123 Affx-122939069 AX-123298466 2 39231241 GTCCTTATCTTATAAGTTTATTTTAAATAAGGAAA[C/T]GTTTGGTTTTAACCAAAGAAGAGAGGCAGACAGAC Y 2 1 2 1 103000 r 74 goat snp35757-scaffold430-1349898 2 96332945 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776088 Affx-122969130 AX-385263218 2 39262825 TCTTGATTTACCTTGTTTTGGTTAGATAAAGGCAA[C/T]GATACAGCTATTGCATAGAAACTTGTGCTTATAAA Y 2 1 2 1 101000 r 74 goat snp35758-scaffold430-1381482 2 96301415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392370 Affx-122966241 AX-123262727 2 39292529 GGTAAATGAGTAGCCCTTATATAGAATGTGTGATG[C/T]AATTGTCCTGACAGGTATCACATGCTACTTTTCTT Y 2 1 2 1 101000 r 74 goat snp35759-scaffold430-1411186 2 96271372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783936 Affx-122952752 AX-385270990 2 39323575 ATGTGCCTGGGCCACATGTGTGGAAACATCAAAAA[C/T]GTTTGACAGATTGGTGACTTATTTTTAATATATTG Y 2 1 2 1 101000 f 74 goat snp35760-scaffold430-1442232 2 96240392 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410332 Affx-122952471 AX-123280682 2 39352989 TTATCAAAATGCCTTGTAGGCAAAAGAGTTTGTGG[C/T]AAGCAGTTATCCTTCAACGTTCTGAGTAAGTGTGA Y 2 1 2 1 201000 f 74 goat snp35761-scaffold430-1471646 2 96210916 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446491 Affx-122925049 AX-123316827 2 39389197 TTTAAATGATAGGTTTATAGGATATCATATCATTT[A/G]CTCATTATAGACATTGGTTCATCTCAGACTGCCTG R 2 1 2 1 101000 r 74 goat snp35762-scaffold430-1507854 2 96174706 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425484 Affx-122941489 AX-123295830 2 39445008 AAGCACTGTCTATTTCATCCAGCTGACATTGAAAA[C/T]AAGAATTTCAGTTGGTGGATACTAATTAGTGCTTT Y 2 1 2 1 101000 f 74 goat snp35763-scaffold430-1563665 2 96116792 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406415 Affx-122955213 AX-123276767 2 39476023 TCTTTGTGTGAGAAGTTGCTGCATGCTGCAGAAAT[A/C]TGTGGCTGGGCTCTCAAGATGGCCTATTTAAGGCC M 2 1 2 1 101000 f 74 goat snp35764-scaffold430-1594680 2 96085310 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397069 Affx-122962725 AX-123267424 2 39507406 TATGCACATTTTTATATAAGTATCCTGCTAATTTG[C/T]GTAGATTTTCTTAGTCTAGTTGTACATACATTTTT Y 2 1 2 1 101000 f 74 goat snp35765-scaffold430-1626063 2 96053874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400402 Affx-122959996 AX-123270757 2 39548324 TTGTCTTTGGACTTCTTATAAATGGAATAATATAG[C/T]GTGTATATGTTCTACTTTGTATTTAGCTCCTCTTA Y 2 1 2 1 201000 r 74 goat snp35766-scaffold430-1666981 2 96012797 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389421 Affx-122968367 AX-123259779 2 39583290 CTCAGTGAAACATCTAGCATGTGGTAGATTCCTTA[C/T]AATTGTTAGTTCCTCTTGCCTCCTCCTGTTCATCC Y 2 1 2 1 101000 f 74 goat snp35767-scaffold430-1701947 2 95977318 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441770 Affx-122929106 AX-123312107 2 39618406 AAGGAATACCTAATATATTGGTAAAATTGAGAAGA[C/T]CTTGATATTTACTGACAAAGTTTTGCTTTTCTGCT Y 2 1 2 1 101000 r 74 goat snp35768-scaffold430-1737063 2 95941703 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796523 Affx-122951386 AX-385283470 2 39652066 GTAATACAAATGTTATCAGTAATACAAATAAAAAT[A/G]TTTCAAGCTCTACAGAAGTCATCAGGAATCATACC R 2 1 2 1 201000 f 74 goat snp35769-scaffold430-1770723 2 95908294 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384413 Affx-122972196 AX-123254771 2 39685127 GCTGTTGGCACAGAGCAGTGGTTGCTTCATTCAGA[C/T]GCCTTGTTTGCCACTGGAAATATCCCAAGTCTCTA Y 2 1 2 1 201000 r 74 goat snp35770-scaffold430-1803784 2 95875195 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801752 Affx-122948973 AX-385288660 2 39736166 GAACATAGTTTATATGTACAAGGAGCCCATGAAAA[C/T]GGCTTCAGTGTTGATCCTCACATTAATCCTGTTTT Y 2 1 2 1 101000 r 74 goat snp35771-scaffold430-1854823 2 95824151 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442440 Affx-122927964 AX-123312777 2 39779458 CTGCAGATGCTTTCATTTCATACATCATTCACACA[C/T]GCAGCAATTACAAATTGGTAAATGACCTCATGTTA Y 2 1 2 1 101000 f 74 goat snp35772-scaffold430-1898115 2 95780890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429205 Affx-122937940 AX-123299547 2 39813896 TCCCTTCTCTGTCTATATGTCACTGTGTCTAATAC[C/T]AGTAACAACTGGAGTGTGGGGAACAAAGTCAGAAT Y 2 1 2 1 101000 f 74 goat snp35773-scaffold430-1932553 2 95746474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783174 Affx-122926772 AX-385270241 2 39846258 TTTGACAGTAGTAACTCTTCCCTAATTGAATCAAT[A/G]CATATTCCAGAAATACATGAAAGATATTTTATAGT R 2 1 2 1 201000 r 74 goat snp35774-scaffold430-1964915 2 95714105 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804023 Affx-986696633 AX-385290707 2 39897741 GGTCTATAAAGATACAAGATATCCTCCTGAAGTCT[C/T]TGTGCAATTTGAAGCTCTGATACTTGTAGAAGTAT Y 2 1 2 1 600010 f 74 goat 2_39897741 2 39897741 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 320804468 Affx-986696635 AX-385291038 2 39897774 CTCTGTGCAATTTGAAGCTCTGATACTTGTAGAAG[A/T]ATAAATGCTACAAACTTATAAAACATCACCTGAGA W 4 1 2 1 600010 r 74 goat 2_39897774 2 39897774 Ancestral_priority_1043 ancestry 0.736 recommended IMAGE 10K 10K ancestral 320804032 Affx-986696637 AX-385290716 2 39897803 TAGAAGTATAAATGCTACAAACTTATAAAACATCA[C/T]CTGAGAGTTTACTTGAATTTCTTCTAAATTCATTA Y 2 1 2 1 600010 f 74 goat 2_39897803 2 39897803 Ancestral_priority_1043 ancestry 0.744 recommended IMAGE 10K 10K ancestral 320803964 Affx-986696603 AX-385290663 2 39897825 TTATAAAACATCACCTGAGAGTTTACTTGAATTTC[C/T]TCTAAATTCATTAAGTTTTGTAAATTTTAAACATT Y 2 1 2 1 600010 f 74 goat 2_39897825 2 39897825 Ancestral_priority_1043 ancestry 0.668 neutral IMAGE 10K 10K ancestral 320804441 Affx-986696608 AX-385291022 2 39897832 ACATCACCTGAGAGTTTACTTGAATTTCTTCTAAA[C/T]TCATTAAGTTTTGTAAATTTTAAACATTAAGCTCA Y 2 1 2 1 600010 r 74 goat 2_39897832 2 39897832 Ancestral_priority_1043 ancestry 0.446 neutral IMAGE 10K 10K ancestral 38385483 Affx-122971282 AX-123255841 2 39920056 TGTCAGGACTGCCTCACCAGCCAGTCACAAATGCC[A/C]TTTGTAGTAGTTAGTAATTTAATTCACCCCTTTAT M 2 1 2 1 201000 r 74 goat snp35775-scaffold430-2038713 2 95639510 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277461 Affx-1111835862 AX-519550965 2 39971726 TAGAGAACCATGTTATTTTGAGTCAAAATTTGAAT[A/C]ATGTTGAGACCATGGTATGCCTGACAGAGTCCCTC M 2 1 2 1 101000 r 74 goat Random2.2K-189 2 39971726 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320772996 Affx-122960006 AX-385260140 2 39992525 TCAGCTTTATATTTGGTTGGGGCAATTCTAGAACA[C/T]GCTATGTTTTAAACTAGAATAGAACTTGTATAATT Y 2 1 2 1 201000 r 74 goat snp35776-scaffold430-2111182 2 95566849 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446751 Affx-122925331 AX-123317087 2 40026991 GACAGGTCCTCCAAAGGCAGTGTCCTGCCTACTTC[C/T]CATGTCTGATTTCTGTTACTCTCTTCATGAATACT Y 2 1 2 1 201000 r 74 goat snp35777-scaffold430-2145648 2 95531913 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419152 Affx-122945743 AX-123289500 2 40077889 AAAATTCTTCTAAGAATGTTCTGCATATTTGGGAA[A/G]TAAAGGGAAGAAACAAAAGAAGGAAAGAAGGAAGG R 2 1 2 1 201000 f 74 goat snp35778-scaffold430-2196546 2 95481091 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438728 Affx-122930839 AX-123309065 2 40112579 TTAACCATGTCAAAACTTAGATTAGATTTAGAATG[C/T]ATATGCCAATGTTATTATTATTGTTACTGTGTTAG Y 2 1 2 1 101000 f 74 goat snp35779-scaffold430-2231236 2 95446389 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415352 Affx-122948781 AX-123285701 2 40157121 TATCACTCAGCTACAAGAGTTATCTGCTTAAAAAG[C/T]AAGCATTTTAGCACATTTCAAAATACACTGTAAAA Y 2 1 2 1 101000 f 74 goat snp35780-scaffold430-2275778 2 95402215 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404191 Affx-122957679 AX-123274543 2 40208540 AATTGGATGGTTTTTAAGAGAACAATTTGTTTGAC[A/G]TTAAGGAGAGTACTATTCAAATACAGCCTATTGTC R 2 1 2 1 101000 r 74 goat snp35781-scaffold430-2327197 2 95350707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449952 Affx-122922897 AX-123320287 2 40237572 CTCATCCACCACTCCCCACAACCCTTGATATCTTG[C/T]ACCTGCCTACCTTCAGTAAGAGTCCCTTCCCTCTC Y 2 1 2 1 201000 r 74 goat snp35782-scaffold430-2356229 2 95321043 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441153 Affx-122929565 AX-123311490 2 40274436 TCTACAGGCAGCCTAATTTGGGCAAACTAGCCATG[C/T]ACATGAATCAGCACAAAGAGCAAACCAAGCAAAGG Y 2 1 2 1 201000 f 74 goat snp35783-scaffold430-2393093 2 95283743 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776432 Affx-122937244 AX-385263559 2 40332616 TAAGTAAGCAACATGCTTCCCTAAGTACTCACTGT[A/G]CTATATACTGCCATTATATTCTAGCAATCTTGTTT R 2 1 2 1 101000 f 74 goat snp35784-scaffold430-2451273 2 95224366 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777297 Affx-122968395 AX-385264419 2 40366938 GCCAGACACCTGGCACATCAAGGTGTAATTGATTT[C/T]GCAGAAACATATCACTATTTTTATAGTAAATATTT Y 2 1 2 1 201000 r 74 goat snp35785-scaffold430-2485595 2 95188716 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796909 Affx-122965811 AX-385283851 2 40407850 GGGACTCTAGTAACCCAATAGATTATAACAAATAA[C/T]AACTCCATCAAATTTCAATTTACTGTTGCATAACA Y 2 1 2 1 201000 r 74 goat snp35786-scaffold430-2526507 2 95147540 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796730 Affx-122944333 AX-385283675 2 40447630 ATCATTATACTTCCTGAACTAGTAGCAAGAAATTG[C/T]GGTTATTATGCTGTTAATGTGTATTGTTATTATAT Y 2 1 2 1 101000 f 74 goat snp35787-scaffold430-2566287 2 95107414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445452 Affx-122925346 AX-123315789 2 40521144 CTTCCTTGACTTGGGTTTTAGTAAAATAACCAGCT[A/G]CTGTCTATCTCCATTTATTTTTGTTCTCAAGCCAG R 2 1 2 1 101000 f 74 goat snp35789-scaffold430-2639801 2 95033026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775894 Affx-122968743 AX-385263025 2 40564292 TGCTGTTTCCATAAACTTTGATGCCTGAAGCACTT[A/C]TTAGTAAATATCTCACACTAAATACTTTCCAAAGA M 2 1 2 1 101000 f 74 goat snp35790-scaffold430-2682949 2 95014476 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792775 Affx-122942227 AX-385279754 2 40593417 ACAGCTGAAGTAAATTCATATCATGAACTCTGTTC[A/G]ATTATTTCTAACAATAGAGTACATACTGAAACAAA R 2 1 2 1 101000 f 74 goat snp35791-scaffold430-2712074 2 94984853 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787724 Affx-122925206 AX-385274747 2 40629104 TGCAGTGTTTGGTGTACTTCTGCTGCCAGACAGAC[A/G]TACACTTATTTGAAAAAATTAGTGCCTTCTCTTTT R 2 1 2 1 201000 r 74 goat snp35792-scaffold430-2747761 2 94947889 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800224 Affx-122933417 AX-385287147 2 40658477 CTTTGTATTGTATATCCTGAGTGCCATTCCTAAAA[C/T]GAGTCTCTTTTTGTAAATCTTCTACCTTAAAGATA Y 2 1 2 1 201000 r 74 goat snp35793-scaffold430-2777134 2 94918739 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764740 Affx-122954077 AX-385252356 2 40744737 TTTTAGCCTGGCTAACTCCCTTACCATTTCTAAGC[A/G]TAGGTTGTAGCTTTGAGACATCTCCTACTAACTAT R 2 1 2 1 101000 f 74 goat snp35795-scaffold430-2863394 2 94831940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793935 Affx-122952056 AX-385280904 2 40785387 AGCAGCAGGTGACATAATTTTGACTGAACCAATTT[C/T]ATGATCTCTGAGCATGTCTCAAGGTTGTCTGGCAC Y 2 1 2 1 101000 r 74 goat snp35796-scaffold430-2904044 2 94790995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378765 Affx-122977012 AX-123249124 2 40817723 CTCTGGAAAAGAACATTTAGAAATGTGCATTTTTC[A/G]TGAAACATGACAAGAAGCTTAAATCATTCAGTTGG R 2 1 2 1 101000 r 74 goat snp35797-scaffold430-2936380 2 94758625 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800552 Affx-122956906 AX-385287471 2 40891946 TAATGTTTCACCTGTTCCTGGATGAATATAACTTC[A/G]TAGGAATTTATAAAGAAATCTATAATAAAAGAAAT R 2 1 2 1 202000 r 74 goat snp35799-scaffold430-3010603 2 94683791 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445154 Affx-122925557 AX-123315491 2 40930787 AATATCTTTAATTAATAATATAGCATCCCTTGTGG[C/T]CATAAAATAATAGAGGGTTTCCAGGCTTTAGATGT Y 2 1 2 1 101000 r 74 goat snp35800-scaffold430-3049444 2 94644751 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405472 Affx-122956027 AX-123275824 2 40999463 ACATGTTTGTTGGATGTCACTTGGTGCCCAGCACT[A/G]TAATCGACTGGGGAGTTACTGTTGAGTAGAGAAAA R 2 1 2 1 201000 f 74 goat snp35801-scaffold430-3118120 2 94574689 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413774 Affx-122949927 AX-123284123 2 41075092 CATATTTCATTTCCATAAGGCAGGGTATTTGTTCA[C/T]AGAAAACAAAATATAGTCCTTACATGAATATGAAG Y 2 1 2 1 101000 f 74 goat snp35803-scaffold430-3193749 2 94487562 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426357 Affx-122940256 AX-123296703 2 41106568 GAAGCCTTTTAGACTCACCCCTGTCCTTATCAGAT[A/C]TTTTTTTCTCTGAATGCCTTCTGTATAATAGTACA M 2 1 2 1 202000 r 74 goat snp35804-scaffold430-3225225 2 94455800 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406704 Affx-122955769 AX-106754664 2 41136969 GAAAATATTTATTAAAAAAGATAATATTTTGAGAA[A/C]GTATGGAACAGATCAGGGGTTCTCCATGTGTCCAA M 2 1 2 1 103000 r 74 goat snp35805-scaffold430-3255626 2 94424997 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442540 Affx-122928532 AX-123312877 2 41182351 CTCCATTTGAACTCTCATCTAAAGTATCACCAGCT[A/G]CCTGCCTTAGCGCTGCTGTGAAGGGAGGGGAAGGG R 2 1 2 1 101000 f 74 goat snp35806-scaffold430-3301008 2 94379580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434722 Affx-122933930 AX-123305063 2 41234887 AATCAGAAGTCTGTGACTATTGACTATGCAAACTG[C/T]ACTTCTAATTTAAAATATTTCTACCACTAACCATT Y 2 1 2 1 101000 f 74 goat snp35807-scaffold430-3353544 2 94326419 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443259 Affx-122927495 AX-123313596 2 41274752 TTCACGTGTAAAAGAAGAGGAATAGAGGTTGATAA[C/T]GACTAAGTTTTCTTTTGGAGTTATAGGATTCAGAC Y 2 1 2 1 101000 f 74 goat snp35808-scaffold430-3393409 2 94286616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779578 Affx-122979224 AX-385266681 2 41315838 CAGGTGATTCAGATGCTGTTGATCCCTGGAATACA[C/T]GGTTAAGTAAAAGCCTGCATCATAATTGTTATTAA Y 2 1 2 1 101000 f 74 goat snp35809-scaffold430-3434495 2 94245581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424221 Affx-122942488 AX-123294567 2 41360219 TTCTGTAAGTGAAAAGCAAAGAATTCTCGAGTACA[G/T]ATGCTTATGGCAAAAAGCCGTTTAGTATTGACTCC K 2 1 2 1 101000 r 74 goat snp35810-scaffold430-3478876 2 94200904 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272034 Affx-1111833170 AX-519545799 2 41375513 GTCTATGGGGTCGCACAGAGTCGGACACATCTGAA[A/G]GGACTTAGCAGCAGCATCAGCAGGAGTGGGGGGAG R 2 1 2 1 303000 f 74 goat 2_41375513_AF-PAKI 2 41375513 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396755 Affx-122962780 AX-123267110 2 41413058 ATGTTTCCTTAGTGCTGTTCACATTCTGAGCTGCT[A/G]TTCCAGTTCACCTTCCGGGGGATTGCCATCTAGAC R 2 1 2 1 101000 f 74 goat snp35811-scaffold430-3531715 2 94147104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429277 Affx-122937882 AX-123299619 2 41481929 CTCCTGTAACAGAAAGAAGAGAGGCATCCTTATCA[C/T]GAGAGATAGGGAATTTAGGGGCAAGGAGGCTACAC Y 2 1 2 1 101000 f 74 goat snp35812-scaffold430-3600586 2 94077731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786180 Affx-122930848 AX-385273216 2 41516404 ATAAATCATGGGAACAAAGCTTATTTAACACATAT[A/G]TTTTCTCCATAAGGCATATCACACCTCTTTGCACA R 2 1 2 1 201000 f 74 goat snp35813-scaffold430-3635061 2 94043301 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769948 Affx-122931252 AX-385257117 2 41597384 AAGCTCTGCTTTTGTTTTCTAGTCTAGTAACTATC[A/G]CTTACAAATTAGCAATTACCTGGAAAATAACTCTA R 2 1 2 1 101000 f 74 goat snp35815-scaffold430-3716041 2 93964958 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410797 Affx-122952658 AX-123281147 2 41627393 TCTTGCTTATCCTCAATTTCTAACTATCTCAAAGC[G/T]AGGCACATTTCTATTCTTAAATCCTTGTCTCTCAA K 2 1 2 1 101000 f 74 goat snp35816-scaffold430-3746050 2 93934492 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386646 Affx-122970211 AX-123257004 2 41676881 GAAGCAAACAGAATACTGCATGATGCAAATCTCAG[C/T]GAACTCAGCTAACATGGTTTCAATGTGCTGAAAAT Y 2 1 2 1 101000 f 74 goat snp35817-scaffold430-3795538 2 93884687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440580 Affx-122929296 AX-123310917 2 41742638 GGATTATCTAAGCCTGCTTTTTCCTTCTTTTTTAA[C/T]CTTCCTTTTAACTATTGAGTTTTTTGCTATCAGTG Y 2 1 2 1 303000 r 74 goat snp35818-scaffold430-3861295 2 93818985 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419266 Affx-122946256 AX-123289614 2 41771612 AGCTGAAATTCTTTTGTCCTTTACCTTTGTCTTTA[C/T]GCACTGACCTGTTTTAGAGGAGAGCTTCTAAGCAG Y 2 1 2 1 101000 r 74 goat snp35819-scaffold430-3890269 2 93789542 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423274 Affx-122942659 AX-123293620 2 41804405 CTCAGAAATAACTCAGAAAATATATGTCACCTATA[C/T]GTTCTGCTTTATCTCTAATTATTTTACTCTGATCT Y 2 1 2 1 101000 f 74 goat snp35820-scaffold430-3923062 2 93756828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433609 Affx-122934949 AX-123303950 2 41853235 GAAATCAGAGTACTGTTTACCCATGACCAAGTTAA[C/T]ATTGGCAATGGAGCAGGATTTAACAAAGTGCAAAA Y 2 1 2 1 101000 f 74 goat snp35821-scaffold430-3971892 2 93706738 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383930 Affx-122972969 AX-123254288 2 41927941 AAGTGTAAGACCACCACCTAATATATTTTCAGTAA[C/T]GGATACTATCAACCTAGTGGCATTTGTCTATTCTG Y 2 1 2 1 101000 r 74 goat snp35822-scaffold430-4046598 2 93631361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443120 Affx-122928089 AX-123313457 2 41975791 ATGAATTTCGAGGAAACACAAACACTCAGACCACA[G/T]CAACTTCCGTAAATTAAATCTCTCTACTATGGATA K 2 1 2 1 201000 r 74 goat snp35823-scaffold430-4094448 2 93582986 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376794 Affx-122977947 AX-123247153 2 42030189 CAAATTGCAAACTGCAAGGCCATCAGTAGAATGTT[A/G]GAAGAAAATATGAGAATTTCTATCAATGGTATTTT R 2 1 2 1 101000 f 74 goat snp35824-scaffold430-4148846 2 93528909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408090 Affx-122954718 AX-123278441 2 42075063 GTGACTTTTATTGTCTCCTTCCACTGTGCGTACAC[A/G]TTTGCAGAAGACATAAATCTTGTAAGTTCAAATAC R 2 1 2 1 101000 f 74 goat snp35825-scaffold430-4193720 2 93483750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789236 Affx-122936217 AX-385276247 2 42115165 TGATTTTTTTAAGACACAATTACTTCTCAGATCCA[C/T]GGTTTTCTCATATTAACAGTGTAAAATTCTACCCT Y 2 1 2 1 101000 r 74 goat snp35826-scaffold430-4233822 2 93443554 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277471 Affx-1111835867 AX-519550975 2 42115997 TTTTCTGCTGCCTGACAGTGGGGCATGTTTCACTC[A/G]TTAATGTTGGTGATACGTTACATTGTTAGTGAAAG R 2 1 2 1 201000 r 74 goat Random2.2K-190 2 42115997 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441506 Affx-122928727 AX-123311843 2 42157210 GCTCTGCATTAACTCATAGAGTCCTGCACCTTGTC[A/G]TTAATAAAATATTGATAAAATATATGAAGTCTCCT R 2 1 2 1 103000 f 74 goat snp35827-scaffold430-4275867 2 93401647 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387553 Affx-122970290 AX-123257911 2 42199576 AAACTGTAAACCTTTTGATCCAGCAATCTAACTTA[A/G]GATAAATATACTAGAGTGCTACTTATATGTGTGCA R 2 1 2 1 101000 r 74 goat snp35828-scaffold430-4318233 2 93359280 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38421494 Affx-122943909 AX-123291841 2 42267863 CAAGAGGTGGAGGTTAATAAGAGGCTGAGAGTAAG[C/T]GGAAGTAGGGGACATGAGGTCTTTTTTAAACCCCT Y 2 1 2 1 201000 f 74 goat snp35829-scaffold430-4386520 2 93291212 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441654 Affx-122929196 AX-123311991 2 42298529 ATGGAAGGGAGGACTAATATCATTGCCCTTAGCAT[A/G]CTGGTGAAAACCTTTTCTGTCTGGGGAAGAAAATA R 2 1 2 1 101000 f 74 goat snp35830-scaffold430-4417186 2 93259671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797477 Affx-122978571 AX-385284416 2 42394814 GTGACTACCTGAATCCATGACAGTCAAAATGGCTG[A/C]TTTGATTAAATGTTCAGCATTTTCTCCTATCATTC M 2 1 2 1 103000 f 74 goat snp35832-scaffold430-4513471 2 93162614 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774239 Affx-122947440 AX-385261375 2 42426853 CTGTGCCACTGACAAAGAGTTTCCTAGATAAAGGA[C/T]GCCTGTGTTTCAAGTAAGAATCCCATATTTAACTG Y 2 1 2 1 201000 r 74 goat snp35833-scaffold430-4545510 2 93130554 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446522 Affx-122925025 AX-123316858 2 42467079 AGATCTTGTATGTAGCAGAGAGTTGTATTTTACTC[A/G]TTTAGATAATTTGAAATATATTGGTTTTAACTTTA R 2 1 2 1 101000 f 74 goat snp35834-scaffold430-4585736 2 93089728 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277479 Affx-1111835871 AX-519550982 2 42469391 CACAAGATTCCTTTTTCTGTGCTGTTTAAACATGT[A/G]TATTCAGAAAATGCTTCTTTTTTCTAGCCTCCAGA R 2 1 2 1 101000 r 74 goat Random2.2K-191 2 42469391 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418930 Affx-122946510 AX-123289278 2 42514382 CCTGAGATTTTATGTAGTCAGGGAGATGGAAAACT[A/G]TCTTTGGCAGTACTTTTCATATCTGTTGTTCATGC R 2 1 2 1 101000 f 74 goat snp35835-scaffold430-4633039 2 93047095 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780207 Affx-122935409 AX-385267303 2 42548057 TTAATGCCCATTTTGAGGAACACTTAGAACCTAGG[C/T]AAAATGCACATTTGCACTGGAAAAATTGTTTTTAT Y 2 1 2 1 202000 f 74 goat snp35836-scaffold430-4666714 2 93013306 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437173 Affx-122932127 AX-123307511 2 42608189 ACTAACTTTGAGAGGATACACAACCTAAAAACGTG[C/T]AGAGGCAGAGCCCAAACTCAAATGTAGCCTAGGTC Y 2 1 2 1 101000 f 74 goat snp35838-scaffold430-4726846 2 92952278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799333 Affx-122953758 AX-385286263 2 42639424 AGGAAAATTCACTTTCCTCTCAGGAAATGACATTG[C/T]ATTTTCCACTATTTTGAAAGTAACTCTCAAGAGAT Y 2 1 2 1 101000 f 74 goat snp35839-scaffold430-4758081 2 92919766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445151 Affx-122925559 AX-123315488 2 42707073 ACGTGAAAACCCTACATGGAAGACAGTTATGAATC[A/G]TCCCCAGCCCAGAGCTGTTTGTCACATGGGCACTG R 2 1 2 1 101000 f 74 goat snp35841-scaffold430-4825730 2 92853420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446825 Affx-122925278 AX-123317161 2 42740982 ACTTTGCCAGTGTAATGCCAAGAAAACTAAAGAAA[C/T]GTGATTCCTGTATTTCTAAACTATATGAGAATATA Y 2 1 2 1 101000 f 74 goat snp35842-scaffold430-4859639 2 92818792 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452907 Affx-122920206 AX-123323240 2 42774065 GGGACTTGAACCTTAGAAGAAGGCTCCACTTGCAA[C/T]CTGGCCCTAAGCAAATGTTGGAGACCTCTAAATCA Y 2 1 2 1 101000 r 74 goat snp35843-scaffold430-4892722 2 92785254 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794160 Affx-122969725 AX-385281126 2 42805234 AATAGGAATCATTAATGATTCTGATTTACAAAATA[C/T]ACTTCTGATTCATTTTAATTGTAGACTTCTACATG Y 2 1 2 1 101000 r 74 goat snp35844-scaffold430-4923891 2 92753669 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794341 Affx-122943591 AX-385281305 2 42836231 ATTTCATTGAACATCTCATCTAAAATTTACTATTA[G/T]AACAATACAGATTATTATTTTCTCCCCTCAAGGAG K 2 1 2 1 101000 r 74 goat snp35845-scaffold430-4954888 2 92722472 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769350 Affx-122975534 AX-385256521 2 42902914 CTTTTCGGCCAACCCAGTAAAGGAGAGTAAAAGCC[A/G]TACAGTTTTAGCATAATGGTTTTCAAACCTGAATT R 2 1 2 1 101000 f 74 goat snp35846-scaffold430-5021571 2 92655987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787773 Affx-122941790 AX-385274796 2 42953791 GAACTGACAGGAAATACGCTCTCATTTGCCAACAG[C/T]GCAGGTGTTCTAAAGGGCTTAACACCATTTATAAT Y 2 1 2 1 101000 r 74 goat snp35847-scaffold430-5072448 2 92605285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778189 Affx-122935277 AX-385265304 2 42990505 GGGTGATTGATTAGAGCCACACACCTCTACCAAGC[A/G]TATGAGTCACACGGATTCACTTAGGTAGGGCTGGA R 2 1 2 1 101000 f 74 goat snp35848-scaffold430-5109162 2 92568784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397951 Affx-122961914 AX-123268306 2 43020751 CGCTTTGCAACTGCAGGATTAACTGAGACACAACT[A/C]AACAGACTTCACCGCGTGTTCTGTTCTCTGGGGGA M 2 1 2 1 101000 f 74 goat snp35849-scaffold430-5139408 2 92538509 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406079 Affx-122956236 AX-123276431 2 43112527 GCTCCTCAGAACCCAGGCAAGAGAAGCTGAGGCCA[C/T]GAGAGTGCAGAGGAAAGCTCACGAATGGTGGAGAA Y 2 1 2 1 202000 f 74 goat snp35851-scaffold430-5231184 2 92446759 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434483 Affx-122934626 AX-123304824 2 43148641 CAATGCTAACAGCTCTATGAGGTAAGGTCTGCTAG[A/C]ACACAGCAGAGGCAGAACCCAAACCCAAGTCTGCC M 2 1 2 1 102000 f 74 goat snp35852-scaffold430-5267298 2 92410652 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394084 Affx-122964960 AX-123264439 2 43182645 ACTGAAAATGAACACGGTAAAACTCTCTTACATTC[A/G]TTTGATTTTTACAACTCTGTTAGCTAGAGATTCGT R 2 1 2 1 101000 f 74 goat snp35853-scaffold430-5301302 2 92377332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394335 Affx-122964670 AX-123264690 2 43231632 AGACATGCACGGTCAGTGACCTTTATCATTACTAC[A/G]GATGTTCACGTATCCAACCCATATTCAACTTGAGG R 2 1 2 1 101000 r 74 goat snp35854-scaffold430-5350289 2 92328726 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398764 Affx-122961441 AX-123269119 2 43281163 ATGCCTCCACCTTTCTAATAGCTTAAACACGTTTC[A/G]TAAGGCTCCCAAAAGCTCCTGTGAGATTGGGCATC R 2 1 2 1 101000 f 74 goat snp35855-scaffold430-5399820 2 92278252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406918 Affx-122955612 AX-123277269 2 43322140 AATATGTCAAACACATATTACAAAGCTTAGGTAGA[C/T]GTGACATATAAGATATTTTAAGAAGTTTGTTTTAA Y 2 1 2 1 101000 f 74 goat snp35856-scaffold430-5440797 2 92237240 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444891 Affx-122926263 AX-123315228 2 43371038 CGTCTGGCCTGCTTCTTAACGTGTATCATGCACAA[C/T]GCAGTCAGGTTAGTATCTGGGAACTTTTTGTGTAC Y 2 1 2 1 101000 r 74 goat snp35857-scaffold430-5489695 2 92188113 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385225 Affx-122971698 AX-123255583 2 43425016 CAATTACTATTCGCTCTTCTAGTGGGTATTGAACA[A/G]AAGGAGAAATGTTCAAGGCAAGCAGAGGGACAGAA R 2 1 2 1 101000 f 74 goat snp35858-scaffold430-5543673 2 92133390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418447 Affx-122946477 AX-123288795 2 43471344 ACTTTTTAGGAGCCATGTAAGATAATCTCAGAACT[A/G]TCTGCTTGGGAAGACAGATGTGTCCATTGGCTTCT R 2 1 2 1 101000 f 74 goat snp35859-scaffold430-5590001 2 92086984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396343 Affx-122963060 AX-123266698 2 43535923 AGACAGGAGACCACGGGCAGAGAGAGAGGAAGAGG[C/T]GGTGCTGGGCCTCAGACACCAGGCCCCACCATCAT Y 2 1 2 1 201000 r 74 goat snp35860-scaffold430-5654580 2 92021930 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430845 Affx-122937430 AX-123301186 2 43572735 TCTGTCATAGAGCTTTTGGAGAAGGAACCTTAACC[G/T]CTTTTAAGATGAAGATACCCAAGAGGGTTGAAAAG K 2 1 2 1 101000 f 74 goat snp35861-scaffold430-5691392 2 91978396 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385341 Affx-122971654 AX-123255699 2 43609395 TCTCCCTAGCTTTCTTTCATTTTTACCTTCTCCAG[C/T]ATTAACGTCAGTCTTAGTAACCTAGTGTCTGTCTT Y 2 1 2 1 201000 r 74 goat snp35862-scaffold430-5728052 2 91941739 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445142 Affx-122926168 AX-123315479 2 43641007 AAGCCTCAAGCCTTGGTGACCTCTCATCTAGCAGC[A/G]CCTGCCAACGCCTCTACTGGGCTTGGTGATTAGCT R 2 1 2 1 101000 f 74 goat snp35863-scaffold430-5759664 2 91909947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390483 Affx-122967595 AX-123260840 2 43678657 TGTCCACACCTTTTTTGTTTTCAGAACACATGAAG[C/T]AGTTTTCATTTCCTGATTTTTGTTTGTGTGTTATT Y 2 1 2 1 101000 r 74 goat snp35864-scaffold430-5797314 2 91872039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776201 Affx-122974889 AX-385263329 2 43708849 CCCCTAAATAATGAAAGATCCAGATATCTAATGAG[C/T]ATTCCCATTTTTATGTCATTGTCCCAATTTGTACA Y 2 1 2 1 101000 r 74 goat snp35865-scaffold430-5827506 2 91841263 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798678 Affx-122929386 AX-385285610 2 43747822 ATAGGATTATTATGCTCAACTTTGAAAAGAACAAA[A/G]CTCCATACCTCTGCTCATGCAACTGGATTTAAATA R 2 1 2 1 101000 r 74 goat snp35866-scaffold430-5866479 2 91802567 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783669 Affx-122941590 AX-385270728 2 43816831 CCTTGGAACTCCAGGAGCCTGTGCCTTTGTGTGGG[C/T]AAAGAGGATCTTGGAGGAGTTTTGCTGTGATTCTG Y 2 1 2 1 202000 f 74 goat snp35867-scaffold430-5935488 2 91733250 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408084 Affx-122954723 AX-123278435 2 43847021 AGAGTCATGTAACGATACCTCCACCAGAAAAAGAG[C/T]GATAAGTAGAAAACAAAGGAGGGAAGAAATTATGT Y 2 1 2 1 101000 f 74 goat snp35868-scaffold430-5965678 2 91703092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375560 Affx-122978754 AX-123245919 2 43878223 CCTTAGGAGTCCTTGGCAACTATATCACTGCTGGT[A/G]CATATGGGACTGGGGGTCAACCAAAACTCTAACAC R 2 1 2 1 101000 f 74 goat snp35869-scaffold430-5996880 2 91672001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464125649 Affx-1110328481 AX-515601526 2 43981903 TTGGGGTAGTGACTACATGAGGCCTAGAAACACTG[A/G]ATGATCTACCTAATATCACTGAGCAGATGGTGAGC R 2 1 2 1 101000 f 74 goat 2_43981903_AF-PAKI 2 43981903 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413851 Affx-122949869 AX-123284200 2 43983251 CTAACCCTGCCTTTGAGAAAAGGCCTATATATGTA[C/T]GGGGACTGGCCAAAAAGTTCATTTGGGTTTTTTGG Y 2 1 2 1 303000 f 74 goat snp35871-scaffold430-6101908 2 91567259 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408346 Affx-122953746 AX-123278697 2 44077559 TAAATATCTAAAAATTTAAAAAACACAATAGAGGT[A/G]CCAAATTGCCTCTATGAGAAAGCAGTTAAGAGGCT R 2 1 2 1 101000 r 74 goat snp35872-scaffold430-6196216 2 91472555 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776993 Affx-122928509 AX-385264117 2 44116718 GGTTCAAATCCTACCTGTGTTGTAAATCCCTGCTA[C/T]GCTGCCCTTACTTATACTGACCTGAAACTCTTTTA Y 2 1 2 1 101000 f 74 goat snp35873-scaffold430-6235375 2 91433082 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412225 Affx-122950920 AX-123282575 2 44156829 GCAATACCCAAGACAGATTGCTGGAGAGAAGTTGC[A/G]TGTTTCACTCATTGCACAGGGATTGCCGTAAGTCA R 2 1 2 1 101000 r 74 goat snp35874-scaffold430-6275486 2 91394032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274711 Affx-1111834378 AX-519548297 2 44159602 CTAAAATGACCCCACCCATTGTTGGCAAGGATGAA[A/G]AGAAACATGCTCTCATATCCTGCAGGTGGGAATAT R 2 1 2 1 201000 r 74 goat GoatD01.032694 2 44159602 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38446124 Affx-122925780 AX-123316461 2 44218475 AATGTATCTGCAACCCCCATTCCTGAACTTGAGTG[C/T]AAGCTCACAAAGTTTGAGTGGCCCTATAGGCCTGT Y 2 1 2 1 201000 r 74 goat snp35875-scaffold430-6337132 2 91331837 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379899 Affx-122975767 AX-123250257 2 44278025 AAAGAAACTTAGAATCCCCATACCTCCCCAGTCAT[A/C]TCCTGGGCCTTAGGATTTAATGCTGCTAGGGCTGT M 2 1 2 1 101000 r 74 goat snp35876-scaffold430-6396682 2 91271860 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418889 Affx-122946106 AX-123289237 2 44322480 CTAATCCTTTCTTCCCCCAACCTCCTCACCTCTGA[C/T]GACTATCTGTTCTCTGTATTTATGACTCTGTTTCT Y 2 1 2 1 201000 r 74 goat snp35877-scaffold430-6441137 2 91226656 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421778 Affx-122944346 AX-123292125 2 44352486 GGAGGTTCCTGTGCACCAAAAGATCTTTGTTGTCT[A/G]TGCAAAACTTTTCCTTAATAAAATGGGTCTGTCGA R 2 1 2 1 101000 f 74 goat snp35878-scaffold430-6471143 2 91198462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407887 Affx-122954494 AX-123278238 2 44408766 GGCCTGAAGACAGCACATCAGCCTTCACAGGGACG[G/T]TCTCAGTTTGGCTGTGCAGCTTCTCTCGTCTGTTC K 2 1 2 1 101000 r 74 goat snp35879-scaffold430-6527423 2 91141638 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388962 Affx-122968803 AX-123259320 2 44458924 AGATGATAATAATTATTATGCAGTTTCTTCAGTGA[C/T]GCCAAGAGATGGGGCTTAGAGCAGTGCTTGTCTCT Y 2 1 2 1 201000 f 74 goat snp35880-scaffold430-6577581 2 91090041 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429410 Affx-122938523 AX-123299752 2 44511635 CTCAACTCTGAAGAAGTCTTTCAGGCTCATTTGCT[A/G]CCAGACTCCGAGGTGAGAGCTTGCACCTTCTGGTT R 2 1 2 1 101000 f 74 goat snp35881-scaffold430-6630292 2 91037521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423185 Affx-122942728 AX-123293531 2 44578450 CTTATAATGGAGAACAAAACAAACACAACAGAGGA[C/T]GGGAATCTGAACCACACATGACAGAGAGAATACTA Y 2 1 2 1 101000 r 74 goat snp35882-scaffold430-6697107 2 90970031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790788 Affx-122930591 AX-385277788 2 44611261 GCTTTTCAATTTGTTGGTATCTCAAAATGTAGTTT[A/G]TGGATTTATTCTGACATATAATTATATCTTATGGT R 2 1 2 1 201000 r 74 goat snp35883-scaffold430-6729918 2 90936555 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767301 Affx-122956501 AX-385254582 2 44645817 GGGGTATGTCTTGGTGCAAAATTTGAGCATTTCTT[C/T]AGTTGGTTTTTGTGTTTACTTTGAGCCCTTGTTCT Y 2 1 2 1 101000 f 74 goat snp35884-scaffold430-6764474 2 90901562 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443348 Affx-122927427 AX-123313685 2 44696134 TGAAAGCTATCATATTTATTATTCATTGTATAGTG[C/T]AACTATCAGAGCTAATATAATATAGCAAGTTGCTT Y 2 1 2 1 201000 f 74 goat snp35885-scaffold430-6814791 2 90850726 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768616 Affx-122951266 AX-385255796 2 44726153 ATCTGTGAAAGTCCCTTTGCCATTTTATTAGAGTT[A/G]TTCAGAAATGAATAGGATACTGAATCCAAACATGG R 2 1 2 1 101000 f 74 goat snp35886-scaffold430-6844810 2 90820760 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439512 Affx-122930132 AX-123309849 2 44760631 TTAGATCACTTCCAGCTTCAGTATTCACTAACACT[A/G]CTGTGCTGGTTCAGTGTTCATGGGGCGTTCCCACT R 2 1 2 1 101000 f 74 goat snp35887-scaffold430-6879288 2 90786563 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771827 Affx-122978739 AX-385258984 2 44822496 CTTTAACATCGCAAGAAATCAGATGGCTCTCAGAG[A/C]AAACTGGGCCAAATGTATGAAACGGCAAACTTTTC M 2 1 2 1 101000 f 74 goat snp35888-scaffold430-6941153 2 90725269 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389641 Affx-122968737 AX-123259999 2 44859339 TAACACTCAATATTCAAAAAACACCAGATCTATCC[C/T]GGAACATGCTGGACTTTAAAAAATTTCACCCAATC Y 2 1 2 1 101000 r 74 goat snp35889-scaffold430-6977996 2 90687996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449847 Affx-122922380 AX-123320182 2 44898230 AGGAAAACTGCAGTGAAGGGCTTGAGCTTTCCATC[A/G]TGTCACCGGGAGCTTGAATGGTTGCGAGGCTGACA R 2 1 2 1 101000 f 74 goat snp35890-scaffold430-7016887 2 90648886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433613 Affx-122934946 AX-123303954 2 44942512 ATGCATACCAAAAATAGAAACCTGCTGGCTTAAGC[A/G]GTGGAATTTCTGTTGTTTGCAGGATGCTCCTGTAA R 2 1 2 1 102000 r 74 goat snp35891-scaffold430-7061169 2 90604757 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385646 Affx-122971167 AX-123256004 2 44974092 CACTGTGATGGCTTCTCTCATTGCGGAGCACAGGC[A/G]CTATGTGCGTAGACTGCAGTGTTGTGACTTATGGG R 2 1 2 1 101000 r 74 goat snp35892-scaffold430-7092749 2 90572822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443638 Affx-122927285 AX-123313975 2 45019575 GATAAAGCTTCATTTTTGAAGTGTTGAAGCTGTGC[C/T]CCCATTCAGTTGTGGCAGGAGAGGAGATTAAGGTA Y 2 1 2 1 201000 f 74 goat snp35893-scaffold430-7138232 2 90526947 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792567 Affx-122934585 AX-385279548 2 45063618 TATATTTTGAAAAACTGCCACAAACAAGTCTGCAC[A/G]ACTGAATCCATAACATATGAAACTGTGCTGTGACT R 2 1 2 1 101000 f 74 goat snp35894-scaffold430-7182275 2 90484832 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448412 Affx-122923673 AX-123318748 2 45100582 CACCTCAAAATTCAAAGCCCAGCCCTCCTACAAGC[C/T]GTAGGATCACTGCCCAAATCATCATCCTTAAATAC Y 2 1 2 1 101000 r 74 goat snp35895-scaffold430-7219239 2 90447878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775697 Affx-122954979 AX-385262828 2 45132670 GCGAGTTTCTCAAGAAGATAAGAGTCTCCGGATGA[C/T]AGCACAGTGGTCATGCCTCAGATGGCAAGTTTATG Y 2 1 2 1 101000 r 74 goat snp35896-scaffold430-7251327 2 90415243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425912 Affx-122941615 AX-123296258 2 45177365 CAGAGTCTGCCACATTTTTGCTCATCACTTCAGGT[A/G]ATGTGACCCTTCCAGGAGAAGCACACCGGTGGATG R 2 1 2 1 101000 f 74 goat snp35897-scaffold430-7296022 2 90370453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414725 Affx-122949263 AX-123285074 2 45218300 TTGTGGCCTGGACTGAAGGGGTGCCACACATTGCT[C/T]CTGGACATATTTTTTCTTTCATTCTCTCCTGTGAG Y 2 1 2 1 201000 f 74 goat snp35898-scaffold430-7336957 2 90329083 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385213 Affx-122971709 AX-123255571 2 45271308 GCCACAGTCGGACATGACTAAGCAACTGAACTGAA[C/T]TGAACTGAATCCTCAAATAAGAGAACCCCAAAGAA Y 2 1 2 1 103000 r 74 goat snp35899-scaffold430-7389965 2 90275805 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450768 Affx-122921838 AX-123321102 2 45330956 TTTATAGCAAAAGGATCACCTAGATGTACTATGCT[A/C]TCCTTCACTTTTTTCACTTACATTATGAGATATTT M 2 1 2 1 101000 f 74 goat snp35901-scaffold430-7449613 2 90215983 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401575 Affx-122958885 AX-123271928 2 45364005 TTCAAGGCGAAAAATGCTTAGACGGATAATTTAGA[G/T]TCATGTAACAAAAAACTGAGAAAAGAAATAAACTG K 2 1 2 1 201000 f 74 goat snp35902-scaffold430-7482662 2 90182903 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768213 Affx-122947030 AX-385255399 2 45421072 TTCTCACACATACACTCACCTTCTGTTCAGAAACC[A/G]TCTACATGCCTAAACCATTTTGTTCCTAAGAGACG R 2 1 2 1 101000 f 74 goat snp35903-scaffold430-7539729 2 90125741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422284 Affx-122943488 AX-123292630 2 45453744 TCTAGAGAGCCTGCCCATAAAAAAATCAGACATGT[C/T]AAGTAGGATAAACTCTTAAGACTGGTGAAGATATG Y 2 1 2 1 102000 r 74 goat snp35904-scaffold430-7572401 2 90093207 A G 1 parentage parentage neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402544 Affx-122958467 AX-123272897 2 45487167 TGGCACTGGGTGCTCGAAGTAATTCACATTCCTTA[C/T]GACAGTACAGTACTGAATATTCATTGGAAGGACTG Y 2 1 2 1 101000 f 74 goat snp35905-scaffold430-7605824 2 90059650 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401059 Affx-122959648 AX-123271412 2 45530706 GCGACTAATATATTGATTTTTCCTATGTGCCCAGT[A/G]CTATGCTTAACATCTTACATGGCTACTTTATTTAA R 2 1 2 1 101000 r 74 goat snp35906-scaffold430-7649363 2 90016630 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412416 Affx-122951432 AX-123282765 2 45575595 TTTCACTTCACTTTAATTTTCTAAGCATAGTTGCT[A/G]CAAGGTTGGTAGTTTATTTATTGGTTGGTAGTTTT R 2 1 2 1 101000 r 74 goat snp35907-scaffold430-7694252 2 89971659 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386438 Affx-122970796 AX-123256796 2 45610184 TTTGATTAAGAAACTTTCTCAGTCTTCCCACACAG[C/T]AGACACTGAACTACTGAAATGTGTTGTGGCTAGAA Y 2 1 2 1 101000 r 74 goat snp44980-scaffold614-16023 2 89934967 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793235 Affx-122977078 AX-385280213 2 45666342 GTTATAATGCTAGCCTCACAAGACATCATCAAAAT[A/G]CTGATTCATACTTGACTAAATAAGCCACATATTAA R 2 1 2 1 101000 f 74 goat snp44981-scaffold614-72181 2 89877592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391476 Affx-122966718 AX-123261833 2 45714248 GAACATTCAGAGCCGGGTATGTTCCTTACAGACTC[A/G]CACTGGGGGCAGGCCTGAAGCAGCACAGTCTCCAT R 2 1 2 1 101000 f 74 goat snp44982-scaffold614-120087 2 89829393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796832 Affx-122959038 AX-385283775 2 45744376 CAAAATGTCTTGCTCAAAAACGTGATGTGATGAAT[A/G]TAATGAATACCTACAGTGAACAGGTAATATATACT R 2 1 2 1 101000 f 74 goat snp44983-scaffold614-150215 NW_017216733.1 8797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788191 Affx-122938397 AX-385275210 2 45786268 ATTTATTTCAATGACTCCAGGGAAAGAAGTTAGAG[A/G]AATAGCCCAAGATGTATATCTTTGGTGTATTTTTT R 2 1 2 1 201000 f 74 goat snp44984-scaffold614-192107 2 89755211 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397655 Affx-122962605 AX-123268010 2 45852501 TCTCATCAGAAACTAATGTGTAACTACTGAGAAGG[C/T]GATTAAAGGGAAATCCATTTCACAGCCTTAGGAGA Y 2 1 2 1 101000 f 74 goat snp44985-scaffold614-258340 2 89688135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795011 Affx-122932766 AX-385281970 2 45901099 AGCTGAATTATTTAAGGTGTACCCTAATCAGGAAC[A/G]TTCACATGCTCTCCTCTGGTGTCCAGGCATCTGAT R 2 1 2 1 101000 r 74 goat snp44986-scaffold614-306938 2 89639217 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438454 Affx-122931249 AX-123308792 2 45942450 GATGAGGTAGGCAAGGAGAATCAAATAAATGGGAT[A/C]GGAACCTCTGAAAGAATTTGGGCCATAGAAACTGG M 2 1 2 1 101000 f 74 goat snp44987-scaffold614-348289 2 89597429 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405708 Affx-122956536 AX-123276060 2 45978331 TCCACCCTTGGTCTCCACAGTCTCTTCTCAGTAGG[C/T]AGTGGTTCTTTAAAAGACACCAGTTAACATCCTCC Y 2 1 2 1 101000 r 74 goat snp44988-scaffold614-384170 2 89560917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766891 Affx-122948301 AX-385254209 2 46029607 TATGCAAAGCTTGAGAGATTTGGGCTCAAAAAACC[A/G]TCCTATTTCCAGATGTATCGCTAAAAGTAATTTTC R 2 1 2 1 101000 f 74 goat snp44989-scaffold614-435446 2 89509394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408390 Affx-122954490 AX-123278741 2 46072979 CTCACTATTCCCCAGTACAAACCCACATTCATATC[A/G]TGTCAGTTATTTCACTGGGCTCCATGTGAGCTCCA R 2 1 2 1 201000 r 74 goat snp44990-scaffold614-478818 NW_017210027.1 15005 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773201 Affx-122971350 AX-385260344 2 46116901 CAATGTAGCAATACATACCCAGAGCCCTTTTGAAA[C/T]GAGATTATCACACTCAAATGTAATTTGTAAGTGTA Y 2 1 2 1 101000 f 74 goat snp44991-scaffold614-522740 2 89423023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798517 Affx-122976095 AX-385285450 2 46149879 GGATTAATTCATTTCAGTAGTAGTGTCCTCCAGTC[A/G]TGAACATAGAATGTTATTCCAGTTATTTAGGTCTT R 2 1 2 1 101000 f 74 goat snp44992-scaffold614-555718 2 89389007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795213 Affx-122966093 AX-385282171 2 46191290 ACTAGTGCATCGTTTACTGCTCTAAGGTCTGTGCC[A/G]TTCCATAGTCCCCATTTGGCGTAACAACTGGCAGA R 2 1 2 1 101000 f 74 goat snp44993-scaffold614-597129 2 89347568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786760 Affx-122959819 AX-385273791 2 46241550 TCTGTAAAGTGGTTCAATAACACCCAGCCTGCCCA[C/T]ACCCTGGGTCATTGTGACCATCCAATAGAGGCTTG Y 2 1 2 1 102000 f 74 goat snp44994-scaffold614-647389 2 89297235 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420209 Affx-122945544 AX-123290557 2 46271377 CTGTGATGACCACTACAGGGTTGAAATGGAGTTAT[A/G]CTTTATATTTAAGAAAAGTCTTTGACCTGAAGAAC R 2 1 2 1 101000 f 74 goat snp44995-scaffold614-677216 2 89267646 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424120 Affx-122942017 AX-123294466 2 46328925 CAAGTCATTACTATTTTCTCTTCCTCCAGAAGCTA[G/T]AATTCACTGTGCATGTCTGGAGCAGCTGAAATGTG K 2 1 2 1 101000 f 74 goat snp44996-scaffold614-734764 2 89209005 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436892 Affx-122933223 AX-123307230 2 46375179 CCTAAACTCACTTTTTGTCCTTGTCAGTAAAAGCC[C/T]TACCCCAAGAGTGGAGAAGGCTCCCAGATGCATGT Y 2 1 2 1 101000 f 74 goat snp44997-scaffold614-781018 2 89162749 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421307 Affx-122944094 AX-123291654 2 46434995 ACGACTGAGCAAGTGAACAAGAACTCCTCCATTTA[C/T]AGTTTCCTCCCTTCTTTCCTCCCCAAGAGAAGGTT Y 2 1 2 1 101000 f 74 goat snp44998-scaffold614-840834 2 89102570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379153 Affx-122976720 AX-123249512 2 46475441 CAGATAAGCCTGAAGGTACCAGTGCTTTTTATCAC[A/G]CCATACGAAGAAGCAGTCAACATAGGGGGGAAAGA R 2 1 2 1 201000 f 74 goat snp44999-scaffold614-881280 2 89062338 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422133 Affx-122943549 AX-123292480 2 46506807 CTTGAGCTCTCTGAAGGCCTCCTTCAGAGAGGACA[C/T]GTTGTCCACAGCAGCACAAGGTTTGGAGTGTAGCC Y 2 1 2 1 201000 r 74 goat snp45000-scaffold614-912646 2 89030877 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800103 Affx-122927950 AX-385287026 2 46541845 GAGCGAGGGCAAGCATTAGGAAACCTGACATAAAC[A/G]TCAGTCTTCAGTCTTACATCAGGTTGCATGGGGCT R 2 1 2 1 101000 f 74 goat snp45001-scaffold614-947684 2 88995710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796302 Affx-122950376 AX-385283252 2 46591587 TGGGTTAGATGAAAGTATTACTAAGGAATGCTGAG[C/T]GGTAAGAACAACTCACTAACCAGCAAGGTAATGTG Y 2 1 2 1 101000 r 74 goat snp45002-scaffold614-997426 2 88947298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272037 Affx-1111833171 AX-519545801 2 46612012 GAGGTCTCAGAGAGCCCACTGCTAGCTCTCTCAGA[A/G]AAGGAGAAAATCCATCCAGGACCTGTTCCTGGAGC R 2 1 2 1 201000 f 74 goat 2_46612012_AF-PAKI 2 46612012 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38447530 Affx-122924057 AX-123317866 2 46631049 TGGCTCATGCTCTCCTTTCACCTTCAAAGCAGCCA[C/T]GACCAGCTGAGTCCACTCCAGTCTCTCTCAAGATG Y 2 1 2 1 101000 r 74 goat snp45003-scaffold614-1036888 2 88907329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443296 Affx-122927466 AX-123313633 2 46663587 ACTTTGGAAACAGACCTTTCACTCAAAGAGCTTCA[A/G]TCTAATCGGGAGACAAGATATACAGAGATTAAAAG R 2 1 2 1 101000 f 74 goat snp45004-scaffold614-1069426 2 88877558 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385656 Affx-122971158 AX-123256014 2 46700296 ATAGGCAAGAATAGAGGTGGGAAGAAGTGCTGCTG[C/T]GGTGCAGAGAGGAACAGATGACTCAATATACATTT Y 2 1 2 1 201000 r 74 goat snp45005-scaffold614-1106135 2 88840531 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434489 Affx-122934622 AX-123304830 2 46747780 GAAATAACACAAGTCTGATCAAGCCTAGGATTGCT[A/C]GGAAAATTTGCATATAAAGAAGAAAAACTGAAACT M 2 1 2 1 101000 f 74 goat snp45006-scaffold614-1153619 2 88792846 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802508 Affx-122935417 AX-385289412 2 46786734 AAGCCCAAGAGGGAGCAAGACGGAACACAAGAACT[A/C]GCATCACCAGACGATCTGATACTGCTTCAGGCAAT M 2 1 2 1 202000 r 74 goat snp45007-scaffold614-1192573 2 88753035 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782942 Affx-122961030 AX-385270012 2 46819899 CCAAGATAATCAGACTCAACTCTAGATCCCTATTA[C/T]GTTAATAAAGAATGCAAATTAAAAATTGTTTTAAT Y 2 1 2 1 201000 r 74 goat snp45008-scaffold614-1225738 2 88719911 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430133 Affx-122937398 AX-123300474 2 46866127 TTGAGTCCAGGCTTCCCTTCTGTGAAATGTAACAA[C/T]GATATCTACTTTGCAAGTGCTAGAGTAAAGGAGAC Y 2 1 2 1 101000 f 74 goat snp45009-scaffold614-1271966 2 88673028 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801885 Affx-122974937 AX-385288792 2 46895698 GTGGGGTGGTGAGAAGGAAAGTAACTAAAAGATGG[C/T]ACCACTTTTACTTTTATCTCACTCATTATAAAAAT Y 2 1 2 1 101000 f 74 goat snp45010-scaffold614-1301537 2 88643657 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395747 Affx-122963692 AX-123266102 2 46931197 CAGCCTGGACTCTAGCAGGACCAGGGACCAATGGA[C/T]AAGGGAAAACCACTCCATCTCTGTAAAGCCCCCTC Y 2 1 2 1 101000 r 74 goat snp45011-scaffold614-1337036 2 88609588 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451104 Affx-122921395 AX-123321438 2 46969465 CATGCAGCCTTTTCACAGGTCACGTACTTTCCCAA[C/T]AATTTCAGGTGGGGATAAGGAGAGAGCTTATCAGT Y 2 1 2 1 201000 f 74 goat snp45012-scaffold614-1375304 2 88570994 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412046 Affx-122951720 AX-123282396 2 47005652 CTCAGAAAAAAAAGAATTTCATTTTTTTTGATTAT[C/T]ATTTGAGTCAACACTTTTAGGCTAGATCAAAGATG Y 2 1 2 1 101000 r 74 goat snp45013-scaffold614-1411491 2 88534802 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438514 Affx-122931206 AX-123308852 2 47037815 TAATGAAAATTATTCTAATTCTATGACAGCCAAGA[C/T]AAATACATGGAAAAGTATAGTATCTGATAATGTTC Y 2 1 2 1 101000 f 74 goat snp45014-scaffold614-1443654 2 88502642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796828 Affx-122977808 AX-385283771 2 47074706 TTGCCTTGGGTGAGTTTCCAGTCTGTGTGCAAAGA[C/T]GGTGAACCCAGTTAGAGCCCAGCAGACTAAGTTGA Y 2 1 2 1 101000 f 74 goat snp45015-scaffold614-1480545 2 88465944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416531 Affx-122947761 AX-123286879 2 47108500 ACATGTGCATGAATTATACTCAACGAATGAATGAA[C/T]GCCAAAGCAGCTTTTCCAACTGTGCATTCAATCAC Y 2 1 2 1 201000 f 74 goat snp45016-scaffold614-1514339 2 88431526 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795751 Affx-122959060 AX-385282703 2 47150216 AGAGCAAATATAAGCTAGTGGAAGAGAGAATTATG[C/T]ACAATATTCAGTACAACATTCCACTTCCATTCTAG Y 2 1 2 1 101000 f 74 goat snp45017-scaffold614-1556055 2 88389725 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787484 Affx-122932249 AX-385274509 2 47289469 TTGCAGTGATTTTTCTGCATAAATAAGCATATATA[A/C]ATGAATATTCTGTTCCCCTATTATACTATATGTAC M 2 1 2 1 201000 f 74 goat snp45019-scaffold614-1695308 2 88316891 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402406 Affx-122959011 AX-123272759 2 47323586 ATGAAAAACAGAAGGAAGAAATCAAAGCCTACCTT[A/C]TCCTAAGGGTCAGCACTTTGCAGAAAAACATCTAT M 2 1 2 1 101000 r 74 goat snp45020-scaffold614-1729425 2 88282576 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426380 Affx-122940239 AX-123296726 2 47364272 TCTTTCTCCCCAAATCAGGGATGTCTTGCCACTTG[C/T]ATTCAATGTGGTACTACAATTTCTGTGTTTGTGTG Y 2 1 2 1 201000 r 74 goat snp45021-scaffold614-1770111 2 88241914 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391235 Affx-122967390 AX-123261592 2 47424580 CATTCAACTTTGAGAAACTTCATATTTTAATTCAT[A/G]CTGTGATATCCCCTATATTAATTTCCTTCCCTAAG R 2 1 2 1 101000 r 74 goat snp45022-scaffold614-1830419 2 88180760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798296 Affx-122926196 AX-385285231 2 47485233 AAGAGTGGTAATATTTAAACTCATATATAGGAACC[A/G]CTTAAACTTGGGTTAGTGAGTTTTTGTTGTTTCTT R 2 1 2 1 201000 f 74 goat snp45023-scaffold614-1891072 2 88119907 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446670 Affx-122924761 AX-123317006 2 47529255 TGAATTTCTTTTTTGATTTTCATTTCAAGGTAACA[C/T]GCAAAGTAGTTCACAGTATTTCACAGAAATTAATG Y 2 1 2 1 101000 r 74 goat snp45024-scaffold614-1935094 2 88075674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387325 Affx-122970501 AX-123257683 2 47575459 GTACAATGACCAAGTCCTATCCACCACAGGGACAA[C/T]AGGAAGGAATTCTCCCCATAAAGCCATTTTATAAA Y 2 1 2 1 101000 r 74 goat snp45025-scaffold614-1981298 2 88029308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447486 Affx-122924090 AX-123317822 2 47680897 GATTATACTAAGTCCCTGTTTCTGCAGCATGCTCT[A/G]CTCAAATGTAGAATGATTGACTACCATCGATGGTT R 2 1 2 1 201000 r 74 goat snp45027-scaffold614-2086736 2 87925046 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277389 Affx-1111835887 AX-519550893 2 47687080 ACTTGCCCTGAGCAGCTGTTAAAAAAATGTTGATC[A/G]TATTGCGCACTGGCCCTGTGTCCTTTATTGCAAGG R 2 1 2 1 101000 f 74 goat Random2.2K-195 2 47687080 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424724 Affx-122941673 AX-123295070 2 47719790 TAAGAGACTTGAGGAACTGGTAGGATTTAGACAGG[C/T]AAAGACGATAGGCAGAAAAAGAGCATAAGCAAACA Y 2 1 2 1 101000 f 74 goat snp45028-scaffold614-2125629 2 87885647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410211 Affx-122952567 AX-123280561 2 47769871 AAAAGAGAAAGAAAAAGCAAGCTGGGAAGAGGTGG[C/T]GAGACTGAGAAGAAGGCAGGATTGCGGACAGCAGT Y 2 1 2 1 101000 f 74 goat snp45029-scaffold614-2175710 2 87836299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435872 Affx-122932794 AX-123306211 2 47818057 TTCTCCTTTACCATTTGTAGCTGTGTGACCTTATG[A/G]TCTTGTGCTGTTTATTATTTCTTTAAACTGTATGA R 2 1 2 1 101000 f 74 goat snp45030-scaffold614-2223896 2 87787710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433379 Affx-122935120 AX-123303720 2 47857010 AATAGGAGAAGACCTAGTTTGGGGCACGGCTGAAA[G/T]AGGACCTTGGCCCAGCAATCAGGGTAGCAGATAGG K 2 1 2 1 101000 f 74 goat snp45031-scaffold614-2262849 2 87748256 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769395 Affx-122972365 AX-385256566 2 47885761 TTGCAATCATAAATACAACTGCAATGAACATCCTT[A/G]TATGTGTGGCCTCATGTACTGGTACTTTAATTTCT R 2 1 2 1 101000 r 74 goat snp45032-scaffold614-2291600 2 87719396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771385 Affx-122928744 AX-385258543 2 47929683 AATTGACTCAAATGAATCTCCTTTTTTTGTGATGT[A/G]TCTGAAGAACATCTTATTCTTAAGTCATCTTCGTC R 2 1 2 1 101000 f 74 goat snp45033-scaffold614-2335522 2 87675465 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396057 Affx-122963451 AX-123266412 2 48014756 GCTGGCTGAGACAGAGGATGTCTTAGCATCAACCA[C/T]GTTGGACCGATGGTCAGTGACCACAAGGTACTTCA Y 2 1 2 1 101000 f 74 goat snp45034-scaffold614-2420595 2 87591464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427239 Affx-122939564 AX-123297582 2 48061965 TAGTGATGGCGGAAGTGATGGAACTAAGAGGGAAG[A/G]ACATGGCCTCTCTATATCTTGAGGCTGCTGAACAT R 2 1 2 1 101000 f 74 goat snp45035-scaffold614-2467804 2 87546146 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784966 Affx-122951533 AX-385272013 2 48115375 ATTTATTCTTTTTCCACATTGATAACTTTATATGC[A/G]TTTGGAATGCCAAAGATGCCCTTGTTATTTGAGTG R 2 1 2 1 101000 r 74 goat snp45036-scaffold614-2521214 2 87492171 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783445 Affx-122925318 AX-385270508 2 48149912 GTCCCCTGGAGTATTCAGTGGAAAAGTATCTAGAG[C/T]GGTCTTCATTAAGGAACACAACTAATTTCTCTTAG Y 2 1 2 1 101000 f 74 goat snp45037-scaffold614-2555751 2 87457291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796324 Affx-122975795 AX-385283274 2 48209052 CTGTCACTGTGTTTCCAAGCAGACCATATTCTCTA[G/T]GAGAGTAGGGACTGTGTCAGCTGTTTTAACTTTAG K 2 1 2 1 101000 f 74 goat snp45038-scaffold614-2614891 2 87397241 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406619 Affx-122955834 AX-123276971 2 48266328 AATTAAAAAATAGAGTTCATTTACAAAAGTCATAC[A/G]CCCATAATTTAAAGTAGGAGACTAATAGTCTATTG R 2 1 2 1 101000 r 74 goat snp45039-scaffold614-2672167 2 87340876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443872 Affx-122927507 AX-123314209 2 48322309 GTATTCCAATTATAGGTGAGTTCCAAGTTTGGTGG[C/T]ACTTTTTCTGGGTTTTACTTTTCCTGAATATATTG Y 2 1 2 1 101000 f 74 goat snp45040-scaffold614-2728148 2 87285131 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453119 Affx-122920016 AX-123323452 2 48413882 TTTCTTGCTGAACTCTCATTACATCCTACTGAGGT[C/T]GCTTCTGTGTAAGTGTGTAACCATCACTAGACTGC Y 2 1 2 1 201000 f 74 goat snp45041-scaffold614-2819721 2 87193106 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394656 Affx-122964380 AX-123265011 2 48445858 CCTATGAACTGGGAAGGGGGCACACATTGCAGCTT[A/G]TAACATCAGATGAGTCTAAGAGGGATCTCCAAGAA R 2 1 2 1 101000 r 74 goat snp45042-scaffold614-2851697 2 87160376 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423696 Affx-122942893 AX-123294042 2 48496589 GAGCCATTAATAATGTCACACCTGTAGCCAATGAC[A/G]CCATGCAATCAACAGATATTTGTGCTGTCACCTGT R 2 1 2 1 101000 f 74 goat snp45043-scaffold614-2902428 2 87109034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384074 Affx-122972861 AX-123254432 2 48525554 GAATATTCATATATTTCATCACATTTTCAAAAGGA[G/T]CAGACCCAAAAGTGTTAAGTACTGATATGAACCAA K 2 1 2 1 101000 r 74 goat snp45044-scaffold614-2931393 2 87080026 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401352 Affx-122959251 AX-123271705 2 48583647 GAGAGTTGCATTCCATATCTCCCTCAGTATTAGGT[A/G]TAAGACTTGATCTTTTAAAATTTCCACATGAGGAA R 2 1 2 1 101000 f 74 goat snp45045-scaffold614-2989486 2 87021794 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395775 Affx-122963670 AX-123266130 2 48659112 AAATTGTTTCATGGAAAAAAAGACAGAAATCAGAT[A/C]TTTACTAATATTTTCTACACTAGTGAATGACTTCA M 2 1 2 1 303000 r 74 goat snp45046-scaffold614-3064951 2 86944782 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779746 Affx-122950759 AX-385266846 2 48700248 TCTGGGAGCGACAGATGTGTACTTTTATAGCAGCT[A/G]TTACAACAGGTACTAAGAAAAACTATATACTACAT R 2 1 2 1 101000 f 74 goat snp45047-scaffold614-3106087 2 86903671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449490 Affx-122922633 AX-123319825 2 48763309 TTTTAAAAGAAAAAGGGGACCTTGACTACCAACAG[A/C]GTTCTGGATATTTGGAGGGGTTTCCTAGAGATATT M 2 1 2 1 101000 f 74 goat snp45048-scaffold614-3169148 2 86840346 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376788 Affx-122977952 AX-123247147 2 48799099 CACCTTCCCACTTGCAAAAGCTAACAGACAACCTC[A/G]AGTTTAATAGTGCTAATCTTTCTCCTGTGTTAATC R 2 1 2 1 201000 r 74 goat snp45049-scaffold614-3204938 2 86804591 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802978 Affx-122929955 AX-385289863 2 48837285 ACCTTATAAAAAAGAAGCCTAATATGAGCTTCAAA[C/T]GTTTTGCCTCTAAGGCATCATGCTGTGCAATGAGC Y 2 1 2 1 101000 r 74 goat snp45050-scaffold614-3243124 2 86765750 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767407 Affx-122924416 AX-385254680 2 48867411 TATGCCTGATTCATACTGTATAGGTTTGCATAGAG[C/T]ATATGTCTATTTGTGTTTAGGTCTAGGTTATTTTC Y 2 1 2 1 101000 f 74 goat snp45051-scaffold614-3273250 2 86736774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389396 Affx-122968382 AX-123259754 2 48900174 ATCCTTTCTAAGAGAAATAAAAACATAAGACATTG[C/T]ATTTTGCTTCTAATACCATTTCCAGTGACTTCTTC Y 2 1 2 1 101000 r 74 goat snp45052-scaffold614-3306013 2 86703349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385257 Affx-122972082 AX-123255615 2 48931964 AATCAGAGGCTCCCTTTTACTAATTCTGTAAAAAA[C/T]AAGTTTCATGGAAAATTGGAAGGACATGTACTATA Y 2 1 2 1 102000 f 74 goat snp45053-scaffold614-3337803 2 86670706 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794799 Affx-122958252 AX-385281759 2 48961191 GGAACTGGAACTTCGTCTGTGAAAGCCTCATCAAG[A/G]CTATTTCCTAATCACTGGGCTGTGCCGTAGTTCTG R 2 1 2 1 101000 r 74 goat snp45054-scaffold614-3367030 2 86639686 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404471 Affx-122956731 AX-123274823 2 48992986 TATATGTTCTTAAAAATCTGTGTAGAGACTTCCCC[A/G]TCTCAAAGTGATAAATTAGGTAAAAACGGAGCAGC R 2 1 2 1 201000 r 74 goat snp45055-scaffold614-3398825 2 86607808 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379102 Affx-122976759 AX-123249461 2 49025350 GCTCAGGGGAGGGCACTGGAAGGAAAAGGAGCAAG[C/T]AAAGTTAAAAAGAGAACATTAGATATTGTCAGTTT Y 2 1 2 1 101000 f 74 goat snp45056-scaffold614-3431189 2 86575378 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789743 Affx-122961669 AX-385276751 2 49054573 ATTTGTTTCTCTTCACCACCAAACTCACACTTTAC[A/G]TCTCTTTTTGTATGATTCCCCCCCCCTCCTAATTT R 2 1 2 1 101000 r 74 goat snp45057-scaffold614-3460412 2 86546161 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391941 Affx-122966925 AX-123262298 2 49095874 TCTATTCAATCCACCACACAACCCTATTCAATCTC[C/T]ACAATATTTCTAAATTCCAGCACTTTTCCTCGTTT Y 2 1 2 1 101000 f 74 goat snp45058-scaffold614-3501713 2 86505299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802321 Affx-122944059 AX-385289225 2 49143218 TTATGCCCTGTGTAAGATACTGAAGGAAGTATTTG[C/T]GCATTTAGTACTCATTTCAGATGTTGTTGTTGTTT Y 2 1 2 1 101000 f 74 goat snp45059-scaffold614-3549057 2 86457569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429290 Affx-122938615 AX-123299632 2 49173461 ATACATATATCCTTATCTCTGGAGTCTGTGAATAC[A/G]TCCCCTACAAAAAGGATTTTACAGATGTGACAATG R 2 1 2 1 101000 f 74 goat snp45060-scaffold614-3579300 2 86426484 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274707 Affx-1111834375 AX-519548293 2 49218335 CTGCTCCACCATCTTGGCCCATCTCCCTGTATGCC[A/G]GCAGTCTTTGTACTCAAAGGCACATGTAGTAAGAA R 2 1 2 1 101000 r 74 goat GoatD01.032527 2 49218335 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320776641 Affx-122960154 AX-385263768 2 49218485 TTATGTGAAAGACTACACTTCGATATGAAAAGGAT[A/G]GCACCAAAGCTCTAACTCTTGGTAAGCTCCCTTAC R 2 1 2 1 101000 r 74 goat snp45061-scaffold614-3624324 2 86382766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787258 Affx-122926878 AX-385274284 2 49289159 GGGACTCTTTCCATACAATGCCATAGTGATTATCC[A/G]CTGCAAATGAAACGTAAGTTGCTGCTGAGCCTAAA R 2 1 2 1 101000 r 74 goat snp45063-scaffold614-3694998 2 86311180 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423342 Affx-122943163 AX-123293688 2 49345370 ATGGATGAGTTGCAAATGTGTGCCTTAAGGTTTGA[C/T]AAAATTTAACATTTTATAATATATTTGTGTCTATT Y 2 1 2 1 103000 f 74 goat snp45064-scaffold614-3751209 2 86255319 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426722 Affx-122939882 AX-123297068 2 49418638 ACCAAGAGACCCATGAGCAGGCACAAAGCACTTCC[C/T]GCACTGGTTCAACAGTGTGTGGGCCACAGCTGCCC Y 2 1 2 1 101000 f 74 goat snp45066-scaffold614-3824477 2 86180485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382879 Affx-122973423 AX-123253237 2 49501153 ATAGCATCAGGACTATAGAGGTATAGTCTATATAC[G/T]CTTCTGTACACAGAATTTAAAGCGATTCCTCTACT K 2 1 2 1 101000 r 74 goat snp45068-scaffold614-3906992 2 86097707 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401366 Affx-122959240 AX-123271719 2 49583222 CATATCAAGTACTTGTTTTCCTGCCATTTTCAGTG[C/T]CTAGAAAGGGCATATTTTTGTCTTATCATTGATGC Y 2 1 2 1 201000 r 74 goat snp45070-scaffold614-3989061 2 86014728 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405927 Affx-122955568 AX-123276279 2 49622498 GAGGAGTATAAATGCCTGTGTGATTAAACAGAAAG[C/T]AATATATATGGTAAAGGAAGAGAATGGGGCTTGCT Y 2 1 2 1 101000 f 74 goat snp45071-scaffold614-4028337 2 85975024 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777217 Affx-122964394 AX-385264340 2 49657617 ACTTATGGAGTTAAACTAGCATCATACACCTCATC[A/G]TCACAGACCACTGTCCAGTACAAAAACGCACTGGT R 2 1 2 1 101000 r 74 goat snp45072-scaffold614-4063456 2 85939487 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785062 Affx-122977739 AX-385272109 2 49700254 AGTTACAGATGGTTCCTAGTGCTACTAGCACCTTT[A/G]TCTTCAGTCATGTTAAGTATCATTTTGTTAACATT R 2 1 2 1 101000 f 74 goat snp45073-scaffold614-4106093 2 85897114 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407730 Affx-122954998 AX-123278081 2 49761085 AGGATAAATTCAAAATAACCACTGAAGAAATGGCA[C/T]GAAGATGTAATTCTTTCCCAAGGGAAATTGTAAAG Y 2 1 2 1 101000 f 74 goat snp45074-scaffold614-4166924 2 85836653 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442843 Affx-122927690 AX-123313180 2 49823620 CTTAGGAGAATGAGGGTGCCTAACAATATCAAGTA[C/T]GGAAACATACTTAAAATGAGTCAAAATACATTGCT Y 2 1 2 1 101000 f 74 goat snp45075-scaffold614-4229459 2 85773923 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437358 Affx-122931934 AX-123307696 2 49870863 AAGGTTCCTGCATAGGGTACTTACTGTATTGGAAA[G/T]AGTGAACTGAATCTCTGTCTGTTTGTTCAACATTG K 2 1 2 1 101000 f 74 goat snp45076-scaffold614-4276702 2 85730023 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774194 Affx-122940305 AX-385261331 2 49921754 GCCTTAGTCTTGTCTTAATCATTATATTTAATCTG[C/T]AGAGTTAACTACTTATAGGCCATGATAACCATTTT Y 2 1 2 1 101000 r 74 goat snp45077-scaffold614-4327593 2 85678679 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400100 Affx-122960735 AX-123270455 2 49959567 ATATAGAAGAAGAAAAAAAAAAGGTAAGAAAATCT[A/G]CTACATAAGGGGAAAGCCACTGACACTGTTTGTGG R 2 1 2 1 101000 r 74 goat snp45078-scaffold614-4365406 2 85640919 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774992 Affx-122946470 AX-385262124 2 49993846 TGAGAGAAATCTGACAAGCAATGTCTTAATTCAGC[A/G]TTTCTCAAGCTATACTTGGTGGACCACCTGCATCA R 2 1 2 1 101000 r 74 goat snp45079-scaffold614-4399685 2 85606559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400795 Affx-122959823 AX-123271150 2 50044163 AAAAGAAAGAAAGAAATCGTATCTTCTGTCCTATT[A/G]TGATGATTTTCTAACAAATTTTATGTCGTTTGTCA R 2 1 2 1 101000 r 74 goat snp45080-scaffold614-4450002 2 85556239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798585 Affx-122948556 AX-385285518 2 50076965 AGGGGGCCAGATTCTATGGTGTTTCAAGGATGGAA[C/T]ACCATCCTTGAGAGCAGTGTATTGTTATTTGTCTA Y 2 1 2 1 101000 f 74 goat snp45081-scaffold614-4482804 2 85523522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393646 Affx-122965293 AX-123264001 2 50112086 TTGATTTTTGCAAAGTTTGGACTCATACTTCATTT[A/C]GAATCAAAATATCTAGAAATAAAGGATGGCAATGG M 2 1 2 1 101000 f 74 goat snp45082-scaffold614-4517925 2 85488590 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801350 Affx-122943310 AX-385288262 2 50173875 ACTTTTTTCCTAACCTTAACATGTTTACTTGGGAA[C/T]GCAATTTTCCTTTTTGTTCCTCTGTCCCTCATCTC Y 2 1 2 1 101000 r 74 goat snp45084-scaffold614-4579714 2 85427224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767159 Affx-122932971 AX-385254444 2 50277879 ATTTTTCAAAAATTTGAGGGCTTAAACCAATAAGC[A/G]TTTTTAAGCAAGTGACTTTAGTTATTAAGTTGTAT R 2 1 2 1 102000 f 74 goat snp45086-scaffold614-4683718 2 85323011 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391753 Affx-122967477 AX-123262110 2 50319514 ACATTTTAATATTAAAGCTTCCATCTTAAAAAAAA[G/T]CTTCTTTCAAACTACTTAACTCTGTTGTTAATTCA K 2 1 2 1 201000 f 74 goat snp45087-scaffold614-4725353 2 85280615 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436552 Affx-122932917 AX-123306890 2 50369754 AACAACATCCAAATAAATATAAAATATCCAAATAA[A/G]ATATCAAACTGTGAAACCATCAATAATGTGCTTTT R 2 1 2 1 101000 r 74 goat snp45088-scaffold614-4775593 2 85230072 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799988 Affx-122960722 AX-385286912 2 50453234 AAATGTCTAAGAGTTGGTGGTTGTACCATGTCTGA[C/T]GGCTAGGCATTTATAAAGTGTGAATAATATCACCT Y 2 1 2 1 101000 f 74 goat snp45090-scaffold614-4859073 2 85146308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397439 Affx-122962115 AX-123267794 2 50489402 CCTCTAAATCCTCTAAATGTTACTCAAGATTAAGG[C/T]AAACCAGCAGAGAGTTATATCCTTAAATAATAGTC Y 2 1 2 1 201000 f 74 goat snp45091-scaffold614-4895241 2 85110014 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778172 Affx-122967540 AX-385265287 2 50538568 TTCCAATGTTAGCATAAAATCCATGAGCTATAAGA[C/T]CCAAGAGTTCAGGATCATGTTTATGATCCTAGTTT Y 2 1 2 1 101000 r 74 goat snp45092-scaffold614-4944407 2 85060101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797979 Affx-122946233 AX-385284915 2 50568810 TTAAAGAAGTTAGTTTATTGACATTCAAAGTAATT[A/G]TTGATAGGTCTGCCTTTTTTGTCATTTTATTCTTT R 2 1 2 1 101000 r 74 goat snp45093-scaffold614-4974649 2 85030894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443596 Affx-122927318 AX-123313933 2 50597421 GAAAGAACAACTTAAACAAGTAGCATTGTCAATCA[C/T]GGCAGCTGACAGAAAAGGCCCTTGCATTCAAGATC Y 2 1 2 1 101000 f 74 goat snp45094-scaffold614-5003260 2 85001970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388431 Affx-122969271 AX-123258789 2 50641010 GTACCAGAGGTCAAATGTTAAAATCCTTTTCTTAG[C/T]AAGAGGCACTATAGCATCACCTGCAACAGTCAACA Y 2 1 2 1 101000 f 74 goat snp45095-scaffold614-5046849 2 84958168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778616 Affx-122933960 AX-385265727 2 50683519 TAGGTTTTGAACATAATTTAAAAGCCTATACTTGA[A/G]CACAGTTTATCTCAGATATGTATTAGGCTTGTCTC R 2 1 2 1 201000 f 74 goat snp45096-scaffold614-5089358 2 84915910 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774331 Affx-122941936 AX-385261467 2 50733875 AAATACACTGGGTCCTAAACTATAGTAAAATGAAA[C/T]GTTTGGAGACTGACTTCTCTTTACTTCTTGTCCTC Y 2 1 2 1 101000 r 74 goat snp45097-scaffold614-5139714 2 84865134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775074 Affx-122924274 AX-385262206 2 50762417 TGAAAATATCTCCATTATTTTGCAACTCTGAGACA[C/T]CGCCAGTATCATTGCAAGATTTGGCTTGTGTACAC Y 2 1 2 1 101000 r 74 goat snp45098-scaffold614-5168256 2 84836372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420059 Affx-122945127 AX-123290407 2 50793280 ACTCATTCTGAGTCCCCTATTTTTCTCTTCCTCAT[A/C]TTTTCTGTTCTCTGCTCCCGTGTATTTTGCAGCTA M 2 1 2 1 201000 r 74 goat snp45099-scaffold614-5199119 2 84805046 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437560 Affx-122931890 AX-123307898 2 50828279 ATTAATAGATAGTTTGAGACAAGAGGCTACTTAGA[C/T]TCCTTTGATGAGAAGATGCATCAGCTTACATCTAA Y 2 1 2 1 201000 f 74 goat snp45100-scaffold614-5234118 2 84769148 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405564 Affx-122955953 AX-123275916 2 50880997 ATCCTCCTATTCTATCATGGGCCCATGACAATGCT[A/G]TTGGAAAATTACATATTAGAAATATGTTATGGCAA R 2 1 2 1 101000 f 74 goat snp45101-scaffold614-5286836 2 84716395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768147 Affx-122966524 AX-385255346 2 50924812 CCTCGGCTATTTCCTGTCCTCAAGAAGCCAGTAAT[A/G]TGTATAAGAATCATTTGACTTATCAGAAAGGAAAA R 2 1 2 1 101000 f 74 goat snp45102-scaffold614-5330651 2 84672572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798961 Affx-122919551 AX-385285891 2 50965438 GGCTGGATCTAAGTACATATGGGCTTATGTAAAAA[G/T]ATAAGCCCATTTTTCTAGCCTCAGATTCATTGTTC K 2 1 2 1 202000 r 74 goat snp45103-scaffold614-5371277 2 84631388 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382229 Affx-122973967 AX-123252587 2 50997520 TTGACTTTCTGCTGCATTTTACAACTACTCCCCAA[C/T]GTGCTATCCTCAGAGGTGATAAAGGAGAGCTGTTT Y 2 1 2 1 101000 r 74 goat snp45104-scaffold614-5403359 2 84599266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376931 Affx-122977782 AX-123247290 2 51028229 TTAAATAACACAATAAATAAGATCTATTTCTCTTT[A/C]GTTTTCTCACCAATCACTTCCAAGCCCCCTTTGTT M 2 1 2 1 101000 r 74 goat snp45105-scaffold614-5434068 2 84567954 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418148 Affx-122947102 AX-123288496 2 51122889 CAGATAATTCTTGTGATTGGAGAGAGAGACATAAT[A/G]CTTGGGATCCTGGCATAGCCAATTCTGGAACTACA R 2 1 2 1 101000 r 74 goat snp45107-scaffold614-5528728 2 84471749 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776216 Affx-122946722 AX-385263344 2 51166566 ATGTATAATTCTTACCCTTAGTAACAAAAACATAA[C/T]GTCTGGCATAATACATGTATTACAGAAATCCCTGT Y 2 1 2 1 101000 r 74 goat snp45108-scaffold614-5572405 2 84427386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444573 Affx-122926970 AX-123314910 2 51242109 CAGATCTACCCCTTCTAAGGACAATATTGTGCATC[A/G]TTGTGGATTTGGGGTTTTTAGAATATTCATGCTAA R 2 1 2 1 202000 r 74 goat snp45109-scaffold614-5647948 2 84351553 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409378 Affx-122954155 AX-123279729 2 51299755 CTTCCTCCCCTCGCCTCTCTTTCTCCCTCTCTGTC[C/T]CTCTCTTTCACTCTCTCTCTTCAACTTCCTCCCAC Y 2 1 2 1 103000 r 74 goat snp45110-scaffold614-5705594 2 84293840 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432156 Affx-122936420 AX-123302497 2 51328455 ACACAGTTAGTATGTTCGGTTGCCATAAGACAAAT[A/G]GCCGTAAGATTTTAAAATATCAAAGTGATAAGCTA R 2 1 2 1 101000 f 74 goat snp45111-scaffold614-5734294 2 84265213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379499 Affx-122976465 AX-123249857 2 51397404 TATAAAAGAAGGAAGTCAATGGCCATGTTGACTTA[C/T]GTAACAGACACCTTTATCCATCGTTAACAGGAAGT Y 2 1 2 1 101000 r 74 goat snp45112-scaffold614-5803243 2 84197477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476167 Affx-1251763670 AX-586011594 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20000 f 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 539476422 Affx-1251763670 AX-586011823 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 4 1 4 1 20000 r 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562165407 Affx-1251763670 AX-606940818 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 f 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562165673 Affx-1251763670 AX-606941082 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 r 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562165897 Affx-1251763670 AX-606941306 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 r 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562165961 Affx-1251763670 AX-606941370 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 f 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562166363 Affx-1251763670 AX-606941771 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 f 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 562166514 Affx-1251763670 AX-606941923 2 51411098 ATTTGCATTTCTTTTGTATAAGTCATGTGGACATT[-/ATCTAACTTCACATTTTTATTTTTTTTTATTTTTTATTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCTAACTTCACATTTTTAAGTTTGTGTAATCAGTA - 8 1 4 1 20100 f 74 goat SV_268 2 51411098 - deletion junction SV-TF-chip 320774689 Affx-122923819 AX-385261823 2 51450299 TTTCATTTCTTGATTGTTTCAAGGTGTCTTGGGGA[C/T]GACTTGCCCTTAAATAACTAATTATCAGCAAAGGA Y 2 1 2 1 101000 f 74 goat snp45113-scaffold614-5856138 2 84146457 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401325 Affx-122959275 AX-123271678 2 51497393 CGCTCATATTGCTGAGATTTTCCAACTTCCAGTAC[A/G]AGGTTGTTTCCTCTTTCTTCACTTCCTTTTTGGAA R 2 1 2 1 101000 f 74 goat snp45114-scaffold614-5903232 2 84099434 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444479 Affx-122926530 AX-123314816 2 51554046 TCTAGAATCCATCTTCCCTATCTAACTCTGCACCA[A/C]CCTGGCTCTGTGAATGAATTACCACTGTCAGAATC M 2 1 2 1 101000 r 74 goat snp45115-scaffold614-5959885 2 84042705 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413328 Affx-122950175 AX-123283677 2 51605907 GTGTCTTGGCACCTGTGGCTTATTTAATATCAGCC[A/G]TGGAATGTGACACCTTCTCTACCCAAGTACAGATC R 2 1 2 1 101000 r 74 goat snp45116-scaffold614-6011746 2 83990661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429680 Affx-122937646 AX-123300021 2 51636892 CTATTTTATTACCTGATTTTCTTCCCATTAACACT[A/G]TAGAGCAACCCTTTTTTTTTCTTGTTAATACTTCG R 2 1 2 1 201000 f 74 goat snp45117-scaffold614-6042731 2 83959937 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271873 Affx-1111833172 AX-519545656 2 51694566 AAATTCTCTCTTCTTTAGCCTCTTCACTAATACTT[A/C]TCTTTATTCTCTTCCTGAATAGCACTCTTTTCCAG M 2 1 2 1 101000 r 74 goat 2_51694566_AF-PAKI 2 51694566 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401725 Affx-122959526 AX-123272078 2 51720295 ATTAGGTCATCTTGGTGTCCCTACCTGTAGCATAG[C/T]ACCTAGATAGACCCTCAATTAAACACTTGTTGAAT Y 2 1 2 1 101000 f 74 goat snp45119-scaffold614-6126134 2 83875630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413686 Affx-122950097 AX-123284035 2 51764849 ATTGTTAAAGAAAACCCTGAATAGCTTTCATTTCA[A/G]TTCAATATACAATTGACTCTTAAACAACTTATGGT R 2 1 2 1 101000 r 74 goat snp45120-scaffold614-6170688 2 83831049 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783616 Affx-122939905 AX-385270675 2 51808420 ATCTAATTTATCTCGTCAAGGAGTATATACTCTTA[A/G]TGGGAGGAAGCAAGATACCGTATGAAATATGGCAG R 2 1 2 1 101000 r 74 goat snp45121-scaffold614-6214259 2 83786519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421480 Affx-122943919 AX-123291827 2 51897206 GAGTAGAAGTGAAGGGCCAACCTGATTGCTTTTTC[A/G]TGCTGATTTCTTTCTCCCAACTTTCTTTAACCCAG R 2 1 2 1 101000 f 74 goat snp45123-scaffold614-6303045 2 83696977 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450762 Affx-122921844 AX-123321096 2 51930790 TTCTCCATTTGGCATTAATCCTCCGGAGCTACTCC[A/G]TCCCACGTTGTTCCTTCCCGTCTCTGAATTCCTAT R 2 1 2 1 101000 r 74 goat snp45124-scaffold614-6336629 2 83663025 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381820 Affx-122974269 AX-123252178 2 51973442 AGAAAAGGAACATTTTTTTTCACAAGAAAGTTCAC[A/G]CATTTTCTTCTTTTCATCCCCTAGATTCTCTTGTC R 2 1 2 1 102000 r 74 goat snp45125-scaffold614-6379281 2 83621089 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789171 Affx-122969982 AX-385276183 2 52003993 TTGATTATCTCTCTGTGATTCAGTGTATATTTTCA[A/C]CTCCTCCTCCTCCAAAGTGTTTTCCTGTTATATAA M 2 1 2 1 101000 r 74 goat snp45126-scaffold614-6409832 2 83590083 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452717 Affx-122920293 AX-123323050 2 52042080 CTAGCACCACATGGTGAATACCAAGAACAGAAGAT[A/G]TCATGGCTCCAAAATCTTCATGTCTAGGAGACAAA R 2 1 2 1 101000 f 74 goat snp45127-scaffold614-6447919 2 83551158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397211 Affx-122962390 AX-123267566 2 52118426 AAATAGCTTATATTTAATGTGTCTGCTCTACTGAG[C/T]TTGGAGTGGCGATCAGAGGGACTGAATTGTGAAGG Y 2 1 2 1 201000 f 74 goat snp45128-scaffold614-6524265 2 83474726 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780874 Affx-122978974 AX-385267961 2 52188063 TAATCTTATATCAGATAGATATAAATAATGAAGCT[A/G]CTTTGATACAAATGAATTCAAGAGACCTCCAATGC R 2 1 2 1 101000 r 74 goat snp45130-scaffold614-6593902 2 83404148 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448285 Affx-122924175 AX-123318621 2 52249005 CTGAAGCTGAAAGAGCAATGTGACCAATCAATAAT[A/G]TCTACATGGGATTTGGATGAGAAATGGTGGTGTAT R 2 1 2 1 101000 f 74 goat snp45131-scaffold614-6654844 2 83343747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376521 Affx-122978008 AX-123246880 2 52310902 TGTTCATTTCCACAGTCTTATGTGAAAAATTCTTG[C/T]AGGTAAAATTGTCCTGTTGCCTCAAAGCTGCATTT Y 2 1 2 1 101000 f 74 goat snp45132-scaffold614-6716741 2 83281592 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785848 Affx-122957568 AX-385272885 2 52374939 ATATCATTAATACAGTGACAAGAACCTATTACATC[A/G]TGAAACTCTCATAAAGGATATGGTATCTGCTTCCA R 2 1 2 1 101000 r 74 goat snp45133-scaffold614-6780778 2 83217087 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393048 Affx-122965624 AX-123263405 2 52408988 CTATTTCTAAATATAAGAATTGCTAGTTTATCCTT[A/G]CTCACAAGAGGTCTTCCAGTCTGAGCTTTAACTTG R 2 1 2 1 101000 r 74 goat snp45134-scaffold614-6814827 2 83183043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778293 Affx-122931505 AX-385265408 2 52441508 GGCTATTAACAAATGCATTAATTGGTGTGAGTTTT[A/G]TAGTTCTAGAATAGTCTAACAATAAATTAGCAAAC R 2 1 2 1 201000 f 74 goat snp45135-scaffold614-6847347 2 83150403 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403461 Affx-122957719 AX-123273814 2 52513109 TGGGTCCTCCAGTTTTCAAACCTGTTAAGTTTTCA[C/T]GACACTAGTTTATCTTAGACTTTCTTCCTAGCCCT Y 2 1 2 1 101000 r 74 goat snp45136-scaffold614-6918948 2 83078328 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397366 Affx-122962284 AX-123267721 2 52545755 TCCATGGGCAGAGGAGGCTGGCAGGTTACAGTCCA[C/T]GGGGTCATGCAGAACTGGGCATGACTGAGCACAGG Y 2 1 2 1 103000 f 74 goat snp45137-scaffold614-6951594 2 83045579 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444501 Affx-122926512 AX-123314838 2 52581798 AGATCAAACTAATATGCATGGAGGGTGTTATATTC[A/G]CAGCTTTGGGGACCAGTAAAGCTCCCTTTATTTAA R 2 1 2 1 101000 f 74 goat snp45138-scaffold614-6987637 2 83009690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384929 Affx-122972331 AX-123255287 2 52612547 GCCTCACTTTATATTTAATTATTATTCTTGTGTCT[A/G]TTTTGAGTTCATTTCAACTGCATGAATGTCCACCT R 2 1 2 1 101000 r 74 goat snp45139-scaffold614-7018386 2 82978940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438873 Affx-122930747 AX-123309210 2 52673629 GAAGGACTCACCATCAAGAGATTTTGAACAAAATA[A/G]CTAGTAATCATTTATCTATAATATATCTTTCTACA R 2 1 2 1 101000 f 74 goat snp45140-scaffold614-7079468 2 82917773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792538 Affx-122962281 AX-385279519 2 52709609 GAGTAGGAAGGAATAAGGTTGATTCCATAGGAATA[C/T]GTTTATTAGATTTAGTTAGCTAAGCAAATCTTCTT Y 2 1 2 1 201000 r 74 goat snp45141-scaffold614-7115448 2 82881682 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397910 Affx-122961943 AX-123268265 2 52739097 TTTTCCCAGATAGGACAAGCAATTGTCCTCTCTCT[A/G]CTCCAGACAGAAACTATCCCATTTTCCCCAACACT R 2 1 2 1 101000 r 74 goat snp45142-scaffold614-7144936 2 82851762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408862 Affx-122953999 AX-123279213 2 52775088 ACCACTGCCCAGAGTTTTCTCCTGCTCAGTGGCTT[A/C]TGGTATATAAATGCTGTGAATATATATTCTCTTGC M 2 1 2 1 101000 r 74 goat snp45143-scaffold614-7180927 2 82816920 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795440 Affx-122962234 AX-385282396 2 52808940 ACTGGAATTGGTTAGAAATGAAATTGCATGAAATT[A/C]GATTATCTCATGGTTCTCAGAACTTTGAGCTGCTG M 2 1 2 1 101000 r 74 goat snp45144-scaffold614-7214779 2 82783113 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775022 Affx-122971695 AX-385262154 2 52846967 GAAATATGCTATTATGCCAAATCAGATTATGCTGA[C/T]GGAGACTTATGATTTAGGAAATTCTTGATCCAAAA Y 2 1 2 1 101000 r 74 goat snp45145-scaffold614-7252806 2 82744833 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439950 Affx-122929990 AX-123310287 2 52912903 GTGTGTGGAAACTCCACAGACAGATACTGTATTTG[C/T]GAGAAACTCATTTCCGTCCCCTGGAAAGATCTTCT Y 2 1 2 1 201000 r 74 goat snp45146-scaffold614-7318742 2 82677792 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418730 Affx-122946272 AX-123289078 2 52959294 GCAAAGTGAGGAAAATGTTGAAAATTATCTTCATT[A/G]CTTCCAGTCTAATGCCTTTCAGTCTCATTTACTGA R 2 1 2 1 101000 r 74 goat snp45147-scaffold614-7365133 2 82631223 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382065 Affx-122974922 AX-123252423 2 52999372 AATTGCTGTCTGTAATAATACTTTTCCATTGACAC[A/G]CACTTACTAAATAATATGTAAAATACTGACACCTA R 2 1 2 1 101000 f 74 goat snp45148-scaffold614-7405211 2 82590752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428646 Affx-122938662 AX-123298988 2 53040419 TCTGTGGAATTCTCCAGGCAAGAAAGTGGGTTGCG[A/G]TTTCTTTCTTCACCTGTATAAGATAACCGCAAGTG R 2 1 2 1 103000 r 74 goat snp45149-scaffold614-7446258 2 82549904 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778930 Affx-122954544 AX-385266037 2 53096066 CTATTTCTAGCACCCTGATAATGTGACATTAATTA[C/T]AAGGGAAAGTTATTCCATGTTTTGCAGTTCTACCT Y 2 1 2 1 101000 r 74 goat snp45150-scaffold614-7501905 2 82493860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383132 Affx-122973255 AX-123253490 2 53149428 AGTAGACGCAAAACAAACTGATAAAGGTGAAAGTT[A/G]TGTTTATTTTTAGAATGTTAATTTTTTACGTTTTC R 2 1 2 1 201000 r 74 goat snp45151-scaffold614-7555267 2 82439765 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396926 Affx-122963198 AX-123267281 2 53183441 TAGGAAATCCATGAGGGTAATCTTGGGCTAGTGGG[C/T]TTGGAAATGAACCACATGAATTAGCACTTGTAAAT Y 2 1 2 1 201000 r 74 goat snp45152-scaffold614-7589280 2 82404191 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427110 Affx-122939667 AX-123297453 2 53213961 CTTGAAGACAGATGTCAGAACTATAGGATGCTAAA[C/T]GAACATAAACTTCAAATGAAGAACAATTATTTTCA Y 2 1 2 1 101000 f 74 goat snp45153-scaffold614-7619800 2 82373282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785157 Affx-122951689 AX-385272203 2 53277046 GGAACAGTTGTGCAGCTGTTAAAATAGTTTTCTTT[A/G]CTCCTCACCCTCCTGGATCACTTGATTTTAAATCC R 2 1 2 1 101000 r 74 goat snp45154-scaffold614-7682885 2 82310056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799906 Affx-122936130 AX-385286832 2 53335134 TTTTTCTCTCTTTTCTACCAGACTTGAGCTGGTGC[A/G]TGTAGGCCTAGAGCCATATTGTGATCATAAGAACA R 2 1 2 1 101000 f 74 goat snp45155-scaffold614-7740973 2 82251613 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412474 Affx-122951391 AX-123282823 2 53423416 TTTCATATACTTGATTTTTGTTTTTTCTCATTCAT[A/G]GTATTGATCTCCTTCTGATGTTTGCTGATCATTAG R 2 1 2 1 101000 r 74 goat snp6936-scaffold1252-1139021 2 82163173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389649 Affx-122968731 AX-123260007 2 53472858 CCTCTCACCTTCCTCTCTCCCTCATCCCTCTATTT[C/T]TTATCCTCCTCTTCTTAAACCCTGAACCCATAGAA Y 2 1 2 1 101000 r 74 goat snp6935-scaffold1252-1089579 2 82112356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795837 Affx-122960573 AX-385282790 2 53516747 AGCATGCATATATGCATACAAGGCGCTGCTGGTTA[C/T]AGATGCTTTAATTTTGATGGATCAGTCAGTGCAGA Y 2 1 2 1 101000 f 74 goat snp6934-scaffold1252-1045690 2 82069126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392161 Affx-122966313 AX-123262518 2 53549737 ATGTCTTATTCACATTTCTGACACCAAATTAAGCT[A/G]TTATTTGCTTGGTAAATGTAAATTATTATCTGTAT R 2 1 2 1 101000 f 74 goat snp6933-scaffold1252-1012700 2 82035483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802865 Affx-122939344 AX-385289763 2 53623212 TAATGCATTAATATGTTCTTTCAAAAAAAGAGATA[C/T]AAATCCTTTCAGTAATTTTCAATCTCATCCATTCC Y 2 1 2 1 201000 f 74 goat snp6932-scaffold1252-939225 NW_017189834.1 21377 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429123 Affx-122938009 AX-123299465 2 53661960 GAATACAGATAAAATGACTTAGCTTGAAAGCAACT[A/G]CAGTGGTTCAGAGGACCGTGAAACCAGCCTGATCT R 2 1 2 1 201000 f 74 goat snp6931-scaffold1252-900477 2 81934232 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782561 Affx-122971533 AX-385269635 2 53696969 CCTTACCACTATACCACCTAGAAAGCACCTATTGT[C/T]GTAATGTCCTAATTTAAGAATTGTTCCAAACATGT Y 2 1 2 1 101000 f 74 goat snp6930-scaffold1252-865468 2 81897944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792482 Affx-122940710 AX-385279463 2 53761441 CATGTCACATAATTACACAATGTGATTATATGTAA[C/T]GGAATACTAAAAGTATGCATATGCCTTGCAACTTT Y 2 1 2 1 201000 f 74 goat snp6929-scaffold1252-800996 2 81833717 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415368 Affx-122948768 AX-123285717 2 53795934 ATAGGCTCATACCCAAAGCAGGCAAAAACCTCTAG[C/T]AGTTCTTAGGCAGAACTGTCAGCTCCTCCCTGTTT Y 2 1 2 1 101000 f 74 goat snp6928-scaffold1252-766503 2 81799511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454292 Affx-122919267 AX-123324625 2 53836098 GTTGGTTAGTGTTTGTCTTTGAAATCAATATGAAC[A/G]TTAACCCATATACTAAACTGCAGTATTTTCAGCTT R 2 1 2 1 101000 r 74 goat snp6927-scaffold1252-726339 2 81758826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799968 Affx-122933719 AX-385286894 2 53875171 TTTTCTTTCTATGAAAAAAATGTCCAAGTATAAAA[C/T]GAAGATTATAGATTCCCCTTGTTTGCTACACAGAA Y 2 1 2 1 201000 f 74 goat snp6926-scaffold1252-687266 2 81719281 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802010 Affx-122957096 AX-385288914 2 53921424 GAAATATAGTAAGTAATCCACTTGGAATTCTCACC[A/G]AATTTCCCACCTTCCCAAGTAGTTGTTTCTCAGGC R 2 1 2 1 202000 f 74 goat snp6925-scaffold1252-641013 2 81672794 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795497 Affx-122939471 AX-385282452 2 53963404 TCTTGGATGGACAATATTTAAATCATAGGGAATTG[C/T]GCATGAACATCAAAACTCCTGGTCTCTCCTGAATT Y 2 1 2 1 101000 r 74 goat snp6924-scaffold1252-599033 2 81630726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789679 Affx-122931080 AX-385276687 2 53997579 CTACTCTTGTTCACACTCTTCAAGGTGATCTCATA[C/T]ATACTAAGGATTTTACCTCTGAATTGATGAACCTG Y 2 1 2 1 101000 f 74 goat snp6923-scaffold1252-564858 2 81596581 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789385 Affx-122976672 AX-385276395 2 54039764 TTTGTTAGAGGTTTGTTAGTAACAAAATCAATGCT[A/C]GTTTAATATAAAAGTAATAACATTGGGTGGGGGAA M 2 1 2 1 101000 r 74 goat snp6922-scaffold1252-522673 2 81554327 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378363 Affx-122976823 AX-123248722 2 54071466 TAGTACCTTTGAAATAAATAGCAAGAATCACAACA[C/T]GTCTTTCATGCATTTTTGCTGTACTTTTGCTCCTT Y 2 1 2 1 101000 r 74 goat snp6921-scaffold1252-490971 2 81522614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277580 Affx-1111835920 AX-519551079 2 54111276 GATATTTACAATATTTCTCTTTAATAAGGCCCAGA[C/G]TCCCTGAACAGAAGGCAATTCCTATTCCTGGGATA S 4 1 2 1 101000 r 74 goat Random2.2K-200 2 54111276 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418022 Affx-122946649 AX-123288370 2 54128337 ATTATAAAGCAAGGGTCTAGAAGAATCCACAAGTG[A/C]CCAATAAACTTGGATATGGTACAACATCTCAAATA M 2 1 2 1 101000 f 74 goat snp6920-scaffold1252-434100 2 81464961 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392534 Affx-122966104 AX-123262891 2 54159875 TTGCATCTCTCTCGCTTTTTCAACGTATAAAAAAG[C/T]GACAATAAGTAGTATTCAAAGTAGAGAATAATGCC Y 2 1 2 1 101000 r 74 goat snp6919-scaffold1252-402562 2 81433336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786775 Affx-122925333 AX-385273806 2 54207692 AAAAAGTAAACATGAGACTCAGGAGTGAGAATAAG[A/G]ACACAGTTCCTCTAACAATGTATACTTACAATGTT R 2 1 2 1 101000 r 74 goat snp6918-scaffold1252-354745 2 81384918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445981 Affx-122925885 AX-123316318 2 54241618 GAGAAGGATAAGAAAATATGGCTCATTTGTATATC[C/T]CAGGCTTTGCCAATAAAACAAACAGCAGCTAATTT Y 2 1 2 1 201000 f 74 goat snp6917-scaffold1252-320819 2 81351117 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421883 Affx-122944269 AX-123292230 2 54283483 GTGTATTTTTATCATGTTAAAATATATATTATATG[A/G]CTAAAAACTGGTAGGTAGTGTTATATATGTGTATA R 2 1 2 1 103000 r 74 goat snp6916-scaffold1252-278954 2 81309204 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436335 Affx-122933244 AX-123306674 2 54322409 CTGCCACAGGTGGTACCAAGCTTTCATTTCTCAAA[C/T]AACATTTCCACTATTCACTTTAATTCTCATCATAC Y 2 1 2 1 101000 f 74 goat snp6915-scaffold1252-240028 2 81270118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794828 Affx-122967126 AX-385281788 2 54402235 TAATTGAAAAGATATGAACTATTAATAAAATTATT[A/G]TGATTATCTCTGGGTAAGAGGTGATTTGCTTTTAA R 2 1 2 1 202000 f 74 goat snp6913-scaffold1252-160202 2 81189709 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783691 Affx-122967770 AX-385270749 2 54433732 AACCTGATATGATATCAACATCTGCAATATTATTG[C/T]AACTTTCAACTCAAACCCTTTGCAAAGTCTGGTAT Y 2 1 2 1 201000 f 74 goat snp6912-scaffold1252-128705 2 81159155 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783350 Affx-122951052 AX-385270414 2 54488939 GTTTTATATAACGAGATAGCTTGCCATTTCACACT[G/T]TATTTCTCGGTTTTGAATTTGCTTAGAGCAATGAG K 2 1 2 1 101000 r 74 goat snp6911-scaffold1252-73498 2 81102675 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416038 Affx-122948362 AX-123286387 2 54554491 AAAAGTCAAGTAGGTAGAAGGTAGAGGGGGGAGCC[G/T]AAACAGTCATCAACTCCCCAATAACCCTTCCTTCT K 2 1 2 1 201000 r 74 goat snp6909-scaffold1252-7946 2 81037069 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791808 Affx-122969392 AX-385278798 2 54587667 CATAATTGGATATATGTGTTGGAGGGAAGTTAAAG[C/T]AGGTTTTAAGTAAGCCTGGATATTAGATGATTTCT Y 2 1 2 1 101000 f 74 goat snp57652-scaffold923-1754168 2 81004029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779944 Affx-122977590 AX-385267043 2 54621724 TTTCTGTGACCTATAGTCCTTCCTCAACTGGGTCT[A/G]CATTTTCTAATACACATCTCTGGAAGCAATCTTTT R 2 1 2 1 101000 f 74 goat snp57651-scaffold923-1720111 2 80969983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413717 Affx-122950073 AX-123284066 2 54677744 CAGATTCTCCCTGGGAAGCCCTGTAGGGGATCCTG[C/T]AGGCCCTTTTGGTGTTCTAACTGTTCTGTTTTGCT Y 2 1 2 1 101000 r 74 goat snp57650-scaffold923-1664091 2 80913718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794263 Affx-122923805 AX-385281228 2 54728485 TGTATTTTCCCAATTTTTCCAAGATAAATCTGAAA[C/T]AATTAGGAGAGAGACATTGAAAGAATGCACTATGT Y 2 1 2 1 101000 r 74 goat snp57649-scaffold923-1613350 2 80860914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442703 Affx-122927871 AX-123313040 2 54839809 TGGGGAAACTCTAGTGTTTTAGCTTCCCAGACTCC[A/C]AGAGCTCTCTCACACTCAAGGAGACAGCTGGAGTC M 2 1 2 1 102000 f 74 goat snp57646-scaffold923-1502026 2 80748288 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447603 Affx-122924003 AX-123317939 2 54883820 ATCTGGGAATCATTCTTGTTAAAAGGGAGATAGCT[A/G]TTGTGGAGAAGGAGGTTTTTATACAGTGTGGGAGA R 2 1 2 1 101000 f 74 goat snp57645-scaffold923-1458015 2 80706117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772058 Affx-122942458 AX-385259213 2 54917783 TTTTTAATAGGACAAAAACTATAACTTTCAATTTG[C/T]ATGAGAATATCTCCTAAGGATTTACTCTTCTTTCA Y 2 1 2 1 101000 r 74 goat snp57644-scaffold923-1424052 2 80671961 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401485 Affx-122958952 AX-123271838 2 54996585 AAGACCCTTAAGGATGTAGAAATCACAAGACAGAA[A/G]GACTCTCCATCTTAGCATTATTAACACCTGGAGAA R 2 1 2 1 101000 f 74 goat snp57642-scaffold923-1345250 2 80592997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393593 Affx-122965378 AX-123263949 2 55028971 TACCTTCTTTTTCTAATACAGAACACTTATGTAAT[A/G]CTATGAAAAATAAATGTACCTAGTCAGTGTGTGGG R 2 1 2 1 201000 f 74 goat snp57641-scaffold923-1312864 2 80560144 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427913 Affx-122939674 AX-123298256 2 55103172 AACATTTATATTCAAAAGACTGCATTTTCTGGCTA[C/T]ATGCAATAAAACTAAAGTCAAATAATATATTAAAC Y 2 1 2 1 101000 f 74 goat snp57639-scaffold923-1238663 2 80485095 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800495 Affx-122963114 AX-385287415 2 55133367 AGAGGAAATGGGGAACAAGATTATTGAAGATAAAT[A/C]TGCATCATAACTTATGAAGAAATACTCAGAGATGA M 2 1 2 1 101000 r 74 goat snp57638-scaffold923-1208468 2 80455012 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271877 Affx-1111833174 AX-519545660 2 55186669 TTACATAAAGCATTTCTCTTAATCCTCATAGGTTT[A/G]TAGACTACATGCAACTGAAAAACAGTTTATAGAAA R 2 1 2 1 201000 r 74 goat 2_55186669_AF-PAKI 2 55186669 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445781 Affx-122926058 AX-123316118 2 55248555 ATATGAAAGTTGATTCCCTTAAGCCAGTAGTTCCT[A/C]AAGTGTGGTCCCTGGAATGACCTACAGGATCAGAG M 2 1 2 1 101000 f 74 goat snp57635-scaffold923-1093280 2 80340205 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450993 Affx-122921726 AX-123321327 2 55282545 GAGATGAGTGAACATTAATCTCAGAGATGACCAGA[C/T]ATTAACACTTTTCCCATATATAAATCATACTAATG Y 2 1 2 1 101000 f 74 goat snp57634-scaffold923-1059290 2 80305901 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393066 Affx-122965612 AX-123263423 2 55337590 ATAACAGGAATCTTCTGTTCTGAGTGACTCACTGA[C/T]GAAAAAATAATCAGTTCAGTTGTGGAAACAACATT Y 2 1 2 1 101000 f 74 goat snp57633-scaffold923-1004245 2 80249583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453802 Affx-122919572 AX-123324135 2 55382454 TTTTTTTTAACTTTTTTTAATTGAAAATGTTGTTT[A/G]TAGTTAAATATACTAATAGCTCCAAGTGGAATCCC R 2 1 2 1 101000 r 74 goat snp57632-scaffold923-959381 2 80203102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801905 Affx-122975853 AX-385288810 2 55420189 ATCTTCTTATATTATCTTTATACTGTCTTGAAATA[A/G]TACTCATTAATGGTATGTGTTTTTATTGTTGTTTA R 2 1 2 1 201000 f 74 goat snp57631-scaffold923-921646 2 80165005 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776650 Affx-122947987 AX-385263777 2 55465221 TATATTAAAAGGTTCCAATATTTCAAAAATTACTT[C/T]AAATGGCTGTTCTATCCTGGATAATTTATGGCTCT Y 2 1 2 1 201000 f 74 goat snp57630-scaffold923-876614 2 80118803 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382501 Affx-122973815 AX-123252859 2 55497500 GTTTCATCAAGTACTGCCAATAATGGTCTAAGTAA[G/T]ATTGTGTTTAAAACATTAGAAATGCAAGATGGCAT K 2 1 2 1 101000 f 74 goat snp57629-scaffold923-844335 2 80086225 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778559 Affx-122971076 AX-385265671 2 55541797 TATAATTTGTTAATATGCCTCTCTCTGAGTCATGT[A/G]TTAATAGAAAAAGGTGGATGTGATTTGGGGAATTA R 2 1 2 1 102000 r 74 goat snp57628-scaffold923-800038 2 80042086 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438574 Affx-122931161 AX-123308912 2 55609153 AGTGAAAAGCTGCATGGAAGAGCTAGAATATCTAG[C/T]CTTTGACAAGTCTTTTAGAATTATATGACTCTTTA Y 2 1 2 1 201000 r 74 goat snp57627-scaffold923-732682 2 79973792 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772063 Affx-122926147 AX-385259218 2 55699944 TTCAGAGAGATACATGTGCTCTTTTGAATAAGCTT[A/G]CATCACCACATTCACTTCAGTTACAAAGGCATTCA R 2 1 2 1 101000 r 74 goat snp57625-scaffold923-641891 2 79883160 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425408 Affx-122941545 AX-123295754 2 55734512 AATAAACAAACAAACAAAAACTCTAGACAAACTTT[A/C]TAAAAGAATGTCAAAAAGTAAGAAACATCAGCAAT M 2 1 2 1 201000 r 74 goat snp57624-scaffold923-607323 2 79848729 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785425 Affx-122960644 AX-385272470 2 55778124 AAAAGGAAATAACAAAATCTGTAGAACTCATTGAT[A/C]TGTTCATTATCTTGATGTGATGATGACTCACAGAT M 2 1 2 1 101000 r 74 goat snp57623-scaffold923-563711 2 79804576 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423817 Affx-122942801 AX-123294163 2 55815455 TCCTTCTTCTCCTTCACTAGTTCCTCTTCATGCAA[C/T]ACATATGTTCAAGTCTCTTCCAGTCCAATAATAAT Y 2 1 2 1 101000 f 74 goat snp57622-scaffold923-526380 2 79767454 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396898 Affx-122963220 AX-123267253 2 55850195 ATAGAATAATCCACACAAGAATTAGGGAAAGATTC[A/G]TGGGACTAAGACTACACTTAAATGTTCCCAGGATA R 2 1 2 1 101000 f 74 goat snp57621-scaffold923-491640 2 79732325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430832 Affx-122937440 AX-123301173 2 55889891 AGTTTGTTATAGTAGAATAACTCATCAGGTAGCAG[A/C]GACCAAAAGGAGTCCCAGAGAATATGAGGATTAGA M 2 1 2 1 101000 f 74 goat snp57620-scaffold923-451944 2 79692151 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437698 Affx-122931760 AX-123308036 2 55918982 TTGGCCACTTTCTTTTTGACAAATGAATTTGAAAT[A/G]CATTTTAAAATGTATGCCAAAATAAAGACGGAAAT R 2 1 2 1 201000 r 74 goat snp57619-scaffold923-422853 2 79663793 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421855 Affx-122944287 AX-123292202 2 55958727 CATATTGTCTTTACAGAATATTGAGAATAAGATGA[C/T]AGAATAAAGTTTCCTTTTTAAAAAGAAAAAATACT Y 2 1 2 1 103000 f 74 goat snp57618-scaffold923-383108 2 79623520 T C 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38446454 Affx-122925075 AX-123316790 2 55998172 TGTACTAAAATTCTTCTCAGAGTACCATCCATGGC[C/T]GCCTCTTCTATGTGGGAGTGGTCCCCAACAACAGT Y 2 1 2 1 101000 f 74 goat snp57617-scaffold923-343663 2 79584150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798709 Affx-122972514 AX-385285640 2 56051910 TCATAAAATGTAAGAAGTGCTATGACTGCTAATAG[C/T]GATAATAAAACTCTAATGCTGCCTTTTATAACACA Y 2 1 2 1 101000 r 74 goat snp57616-scaffold923-289925 2 79530542 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391385 Affx-122967270 AX-123261742 2 56123310 ATGGTTTAAAAGAGATAAAGTAGGAAAACAGAAGA[G/T]AAATATAACTCCCTAACAGATAGCACACATTCCCT K 2 1 2 1 101000 r 74 goat snp57615-scaffold923-218525 2 79458037 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437078 Affx-122932668 AX-123307416 2 56161659 TATGTATCTCACTCCCAGAAGACAGAATGAGAGAA[C/T]TGAGCTTTTAAAACTCATTTCCATAGTGTCTTGCT Y 2 1 2 1 202000 f 74 goat snp57614-scaffold923-180176 2 79419831 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442492 Affx-122927922 AX-123312829 2 56229103 CAAACAGTTCAAACAGTTACTAATCAGGGCCTGGA[C/T]GGAATGCAGAAACAAAGGAAAGTCAGTCAAGAAAC Y 2 1 2 1 101000 f 74 goat snp57612-scaffold923-112732 2 79352699 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794823 Affx-122960781 AX-385281783 2 56264972 AATAATTTTTACTTTGATTCCTGACTTAACATAAA[C/T]GTGTCTTTCTGACTTAAAATTCTCTTAACTGTGTA Y 2 1 2 1 101000 r 74 goat snp57611-scaffold923-76863 2 79316404 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384197 Affx-122972400 AX-123254555 2 56305844 CAAAATTATTAAAAAGAAGAAACTTGTTTCAGACT[A/G]TACAACAGTTAATAAGACAGAATCTGACCCAGGAA R 2 1 2 1 101000 r 74 goat snp57610-scaffold923-35991 2 79275525 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777649 Affx-122931615 AX-385264768 2 56335824 TGAGGAATCCAAGAAAAATGTTACCATCCATGTTA[A/C]CAAAATTCAAGTGCTTTGAAGAGCCAACTGGAGGC M 2 1 2 1 101000 r 74 goat snp57609-scaffold923-6011 2 79244950 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797577 Affx-122924777 AX-385284517 2 56527900 ATCAATATCAACACAGGTTGAAGTTTCAAAGCAAT[A/G]CTATAAGTAGCACTAGTTCTAGAAAGATACTCTAA R 2 1 2 1 101000 f 74 goat snp51422-scaffold752-1500030 2 79055047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385903 Affx-122971581 AX-123256261 2 56581717 TTACAGTATTTTACATATAATAAATGTTCTATGCC[A/G]CTAAATTTTGACTTAGGTTAGCAAAAACATGATGC R 2 1 2 1 101000 r 74 goat snp51421-scaffold752-1446213 2 79001194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452940 Affx-122920182 AX-123323273 2 56647888 TAAATATTTGTTATTATTGCTGTAAGATTAATGTA[C/T]AGCTAATCAGCACTATAAGATATAAGCCACATAGA Y 2 1 2 1 101000 r 74 goat snp51419-scaffold752-1380042 2 78934409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375905 Affx-122978482 AX-123246264 2 56865047 TCTTAATGTCTAGACCTCAGTTTCTTAATCACCAA[C/T]GGGGAGGGTGTTCTCTCAGTTAATGAGTGCTTCAA Y 2 1 2 1 201000 f 74 goat snp51414-scaffold752-1162883 2 78714809 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376657 Affx-122979013 AX-123247016 2 56903205 GTTCCATTAAGATGTCCAAAACCATACCACAACTT[A/G]CATGCTAAATACACAGTAATTTAATTCCTTACATT R 2 1 2 1 101000 f 74 goat snp51413-scaffold752-1124725 2 78676239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794796 Affx-122961915 AX-385281756 2 56999432 ATTTTCCTTTATGAAACTAAAAGGTGGGAACTTAT[A/G]CCTTGGCATTAGAGGAAGGAAAATAGAGGGAAAAT R 2 1 2 1 201000 f 74 goat snp51411-scaffold752-1028498 2 78579104 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780181 Affx-122935413 AX-385267278 2 57041573 TGCTGAGAAAGTTGTAATTTAAAACTCTTGAAGTG[C/T]ATTTCTCCCAGTATTGTGAGAATTTTCTCATACTG Y 2 1 2 1 201000 f 74 goat snp51410-scaffold752-986357 2 78536483 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450961 Affx-122921750 AX-123321295 2 57148434 AAATTTTTCTTTGTCTAATTCCTTCATTTTAACAA[C/T]GAGAAGGAAGTAGAAAGGAAATTTGAGAGTTCAAT Y 2 1 2 1 303000 f 74 goat snp51408-scaffold752-879496 2 78429748 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383779 Affx-122973204 AX-123254137 2 57181104 ATAGACTAGACCAAAAAAGAGCAGAAGTGAAGTGG[C/T]GTAGGAATAACAAGAATCAGACAGAAGTAAGTCAG Y 2 1 2 1 101000 f 74 goat snp51407-scaffold752-846826 2 78396746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765401 Affx-122937518 AX-385252908 2 57250321 TCACCTTAGCCACAAATAAGGCATTGGAAAGGAAG[A/C]ACATTAACAGAGTTGATGTGTTTCATAACGTTGGC M 2 1 2 1 101000 f 74 goat snp51406-scaffold752-777609 2 78325684 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783435 Affx-122925420 AX-385270498 2 57281550 TGACTAACATGGCAGAGCTCTAAGGGACAGGGTCA[G/T]CACTTAAAATTCCCCTTCTTAATCATGTCTGTATC K 2 1 2 1 101000 f 74 goat snp51405-scaffold752-746380 2 78294380 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769839 Affx-122971817 AX-385257009 2 57313136 TGTGAGTTCCTGTAGAATTACATCCAAAATATTTG[C/T]AAAGTTTGCTGTGAGCTCAGGAAGCATTTCTCATT Y 2 1 2 1 101000 r 74 goat snp51404-scaffold752-714794 2 78262680 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448451 Affx-122923643 AX-123318787 2 57360631 TGTGTTTTGGAATTTATGAGTGCAACCTGTGTGTC[A/G]TAACAGCAAGCAGCTGAGGCCTTGAGTCCCTCACT R 2 1 2 1 201000 f 74 goat snp51403-scaffold752-667299 2 78214820 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795574 Affx-122921825 AX-385282529 2 57405723 CATCCATGTTGCAGCATTTAATATTAGCACAGTCT[A/G]CAGAGGCAAAATATTATGATTATAAGATTACTGGT R 2 1 2 1 201000 r 74 goat snp51402-scaffold752-622207 2 78169517 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409214 Affx-122953165 AX-123279565 2 57453196 TTAATCTAATATTGTGGAGAGAACCATGTGTGTGG[A/G]TTGTCATAGAGCAGACTCGCGTCATTTTGTGTATG R 2 1 2 1 101000 f 74 goat snp51401-scaffold752-574734 2 78121068 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401489 Affx-122958949 AX-123271842 2 57558876 GCAATTATCCTATTTTGAGTGTGCTATCTGTTTCC[C/T]GTTGGGACTCTGACTGATACACGTATTGCTCAAAA Y 2 1 2 1 102000 r 74 goat snp51398-scaffold752-469054 2 78014805 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379921 Affx-122975750 AX-123250279 2 57605771 GTTCTAATTTAGAAAAAAATCATTCACAAATTAAT[A/G]TATTTTATTAACAAATTCTCTAGGACACACAGATT R 2 1 2 1 101000 r 74 goat snp51397-scaffold752-422159 2 77968109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395067 Affx-122964187 AX-123265422 2 57637509 AATGGCAGAGAAATATTATAAAGGGATATATGAAC[A/G]TGGGCAAAATAAATGTTTTTTACAGATGTAAATAA R 2 1 2 1 101000 f 74 goat snp51396-scaffold752-390421 2 77936563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436160 Affx-122932623 AX-123306499 2 57672496 TGCTCACTATGCTGAGCACACAATAGGTTCTCCCT[A/G]TTGTGGGAAGTACATCCTTCAGGGCCAGAAATTTT R 2 1 2 1 202000 r 74 goat snp51395-scaffold752-355434 2 77901048 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779035 Affx-122928530 AX-385266142 2 57701497 TGAACCAGTATTTTTGATTCTAGGAATTCATTTTA[C/T]AAACATACTCACAAATGTACTGAAGAAATTCAAGG Y 2 1 2 1 201000 r 74 goat snp51394-scaffold752-326433 2 77872012 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802343 Affx-122941775 AX-385289247 2 57845095 TTATAGTGGCATATTCATGGGTTCTTGAAATGGAA[C/T]ATTACACTATGGAGACTGTGAAGACATCAAATGCA Y 2 1 2 1 101000 r 74 goat snp51391-scaffold752-182835 2 77729937 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385887 Affx-122971593 AX-123256245 2 57884885 TCTTTATAAGCCTTAGTAAATATAGGGGAGATTTT[A/G]CAATTCTAACACTAATAGTTACAGAGAGTCTAAGA R 2 1 2 1 101000 r 74 goat snp51390-scaffold752-143045 2 77689851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451568 Affx-122921694 AX-123321901 2 57932132 TAATTTCATGAGACTTGCTTTGTGATAAGTGCTTT[A/G]TTGTGGTGGTGTGGAACTAAATCCTTAATATCTTG R 2 1 2 1 201000 f 74 goat snp51389-scaffold752-95798 2 77642573 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433968 Affx-122934264 AX-123304309 2 57979492 CAGAGACTAGGGTTCAGGAGAGAGCAGTGGAAGCA[A/G]AGACTTGGTAGGAGCTTAGGTCTCCAATCCAGGTG R 2 1 2 1 101000 f 74 goat snp51388-scaffold752-48438 2 77595035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423553 Affx-122942425 AX-123293899 2 58013150 CCAGCATTTAGATGTGGGATTCATTCCAACTTTCT[A/G]CGTTTCACAATGATGTACAAACATTTCACATTCAT R 2 1 2 1 101000 f 74 goat snp51387-scaffold752-14780 2 77561293 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452764 Affx-122920258 AX-123323097 2 58033267 TAATTAATGGTACTAGAAAACAGGTTGTGGTTATC[A/G]TTTTCAGGGGATACTGACTGGGAGAGGGGAGCATC R 2 1 2 1 101000 f 74 goat snp29136-scaffold312-7998425 2 77527360 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782959 Affx-122934080 AX-385270028 2 58062303 CAACCATAGACTTTCTAGTCCCACATCAAACTTCT[C/T]AAAACCTCACATTTCCTTTGCATTTGATTCATCTT Y 2 1 2 1 201000 r 74 goat snp29135-scaffold312-7969389 2 77498468 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793193 Affx-122955520 AX-385280171 2 58096165 AGAACTTTACTGTGAACACACGAGCAGTCTGTAAC[A/G]TAATAAAAGATTAACTCTACATGAAGAAATTTAAT R 2 1 2 1 201000 r 74 goat snp29134-scaffold312-7935527 2 77464180 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794816 Affx-122971736 AX-385281776 2 58135484 GTTTTTATGACCATAGAATCCTTTTTTGAAGTATA[C/T]GTTATGACTAGGATCCAACAGAACATATTTAAGAA Y 2 1 2 1 101000 r 74 goat snp29133-scaffold312-7896208 2 77423976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429484 Affx-122937876 AX-123299826 2 58176416 GCTCCACTAGGGCATCAGTCTGTCATGGAGTCTGA[A/G]CTTCCTTGCTGTTTCCCCCCAGGAAAAGCAGTGGA R 2 1 2 1 101000 f 74 goat snp29132-scaffold312-7855276 2 77381573 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397894 Affx-122961955 AX-123268249 2 58223741 TTCCAGATATATTTAACATAGAAGCTAAAAGGTTT[A/G]CCTATGGAGTGTTTAATGGATAGGAAAGTGCCATA R 2 1 2 1 201000 f 74 goat snp29131-scaffold312-7807951 2 77334304 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397496 Affx-122962069 AX-123267851 2 58264847 TACAGGCCCTGGACAACACATTCCTTCCCAAGTCA[C/T]GCAATTGTACCTCATTTCCCAAACAGAGCTGTGAA Y 2 1 2 1 201000 r 74 goat snp29130-scaffold312-7766845 2 77293465 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389305 Affx-122968505 AX-123259663 2 58302257 CATAGCATCTCAGGAACCAAGACTCTCAGCTGTAG[C/T]GAACTGGGATGGAACAGAGCTAGAAGGGGTTGCAC Y 2 1 2 1 101000 f 74 goat snp29129-scaffold312-7729435 2 77255473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772035 Affx-122935727 AX-385259190 2 58345058 TGGATATAGCCAAAATGATTCCATAAGCTTGGTTT[C/T]CCCTTTAATGACATAAAAATATACAATTTTAAATT Y 2 1 2 1 201000 r 74 goat snp29128-scaffold312-7686634 2 77212026 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380872 Affx-122975055 AX-123251230 2 58376723 TTGTAATGAAGACTGCTTAAATGCCTTTTGAAATC[A/G]TTTATTTCTAGACTTTGCAATATGTTCTCCCCATT R 2 1 2 1 101000 r 74 goat snp29127-scaffold312-7654969 2 77180581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765490 Affx-122951954 AX-385252980 2 58407176 TCCTGGTTATATGCCCACAGGCATGTCAGCAGTAA[C/T]TAATATAATTATAGATGATAAAGGAACTTGTTCTC Y 2 1 2 1 101000 f 74 goat snp29126-scaffold312-7624516 2 77149729 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423694 Affx-122942895 AX-123294040 2 58442591 ATCTGGACCCTTTGAGAATAGGAAGCCTGGACAAT[A/G]TGCATGAGACTCAGTACCAAGGCTTAAGCTGTTGG R 2 1 2 1 101000 r 74 goat snp29125-scaffold312-7589101 2 77114472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375599 Affx-122978724 AX-123245958 2 58474309 GTATATGCCTACTGATACATTAGACATTAAGAAAG[C/T]GTATGTTTATTGACTTTCCCCTTTTGTAAAGAAAT Y 2 1 2 1 101000 f 74 goat snp29124-scaffold312-7557383 2 77082457 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443362 Affx-122927417 AX-123313699 2 58503496 AGTCCTAGAGATTGGGGGTCAAAACCCAGGGTCTT[C/T]GAGGCTTTGTCTCTATTAACAATAGCAAACTGATA Y 2 1 2 1 101000 r 74 goat snp29123-scaffold312-7528196 2 77051734 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423549 Affx-122942428 AX-123293895 2 58542113 TGTTATGTTTCACAGAAAGGTAAATATAATTTTAG[C/T]GGGAATAAGGAATTTGCCTGTGGTGACACAGCTAA Y 2 1 2 1 101000 r 74 goat snp29122-scaffold312-7489579 2 77012676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426547 Affx-122940183 AX-123296893 2 58586417 CATGACATGTTCTGGGCTCATCTTATGGTTTCCCT[A/G]CCTGGTCCAGGAATTACCATTTTTCAGATAAGGAC R 2 1 2 1 101000 f 74 goat snp29121-scaffold312-7445275 2 76968211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436177 Affx-122932612 AX-123306516 2 58656910 CAGCCATATGATACTATATCAATATATTGGGTTGG[C/T]CAAAAAGTCCATTTGGGTTTTTATGGAAAACCCAA Y 2 1 2 1 103000 f 74 goat snp29119-scaffold312-7374782 2 76900055 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378340 Affx-122976839 AX-123248699 2 58720656 CACATCACTCCAGTTGGTTTCTCCCACTCTATTCA[A/G]AGAATCACACTTCCTTAATCTACTTTCCGAAATAG R 2 1 2 1 101000 r 74 goat snp29117-scaffold312-7311036 2 76836735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799745 Affx-122936511 AX-385286672 2 58773322 ATGGTAGCATGTCCTACCCATCACCTCTGTAAGAA[C/T]AGAGCGTAACAGCCTGCAACCCAACAAGCTTAAGC Y 2 1 2 1 101000 f 74 goat snp29116-scaffold312-7258370 2 76784357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783341 Affx-122975983 AX-385270405 2 58815990 CTTCATGTATTTGGAACAACAGTATACTATTACTA[C/T]CTTGTCACTGAGTTATACTAACCTTCCTAATCTCC Y 2 1 2 1 101000 r 74 goat snp29115-scaffold312-7215702 2 76741631 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799635 Affx-122965334 AX-385286564 2 58866098 CTGCAAAAGTAATAGTGCCTCAACTTCGTTTGGAC[A/G]TGGAGTCAAGAATTATTAGGTCTGCCGTTTTGCTT R 2 1 2 1 101000 f 74 goat snp29114-scaffold312-7165594 2 76691062 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798428 Affx-122972992 AX-385285362 2 58899670 GGAATGTGTACCCCTAAGAAAGGGGCACAAAATCA[G/T]GCAGTCTGTACACCAAAGATTAAAGGGAGCTCTTG K 2 1 2 1 102000 f 74 goat snp29113-scaffold312-7132022 2 76657142 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379292 Affx-122976210 AX-123249651 2 58991053 CTTTGAGAAATGACTGACTAGCCTAGCTTATCAGG[C/T]AGTACGTGTAAATGAGCTGTGGCATCTCTCACTCT Y 2 1 2 1 101000 f 74 goat snp29111-scaffold312-7040639 2 76565702 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396546 Affx-122962940 AX-123266901 2 59025325 GGACTTCTCAGCCTTAAGTATCAATTGCTTAAACC[A/G]TTTGGGCTTGAGTTTTTGCCAGTTGCAATAAGGAT R 2 1 2 1 101000 f 74 goat snp29110-scaffold312-7006367 2 76534098 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418538 Affx-122946408 AX-123288886 2 59053954 TTACTTGCTTGGTGCATCATTTTCATTCAGGTTGC[A/G]TAACCTCTATGAACTCTGGTTCTCTCCCCTGTAAG R 2 1 2 1 101000 r 74 goat snp29109-scaffold312-6977738 2 76506885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787854 Affx-122922317 AX-385274877 2 59089532 TTTGATTTGCTCTAATTAGTTAACCTCTCTTCAGC[A/G]TCTTAGGACACAGCTAAAAGGGCCTGGGCATTGGA R 2 1 2 1 101000 r 74 goat snp29108-scaffold312-6942160 2 76471665 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797540 Affx-122964644 AX-385284479 2 59150553 ATCTAGAGGAAGTGTGTTAGTAGCAAAGTTGCGTC[A/G]TTACAGAGTGTCTTAGAATCCATTAAACATAATTA R 2 1 2 1 101000 f 74 goat snp29106-scaffold312-6881139 2 76410390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773511 Affx-122925533 AX-385260652 2 59183719 GTTTGTTTTGTTACCAAGTGTCTATGCTAATCTTA[C/T]GAGTTTTCAATAGAACCATGAACTGTAATGTACCC Y 2 1 2 1 101000 r 74 goat snp29105-scaffold312-6847973 2 76377069 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776681 Affx-122927635 AX-385263807 2 59214448 TATTTACAAAAGGAAGTACTATTTAATAGCCTGCT[A/G]TGTTCCAAGGTACCAGGGATAAAATGGAGAACAGA R 2 1 2 1 101000 r 74 goat snp29104-scaffold312-6817244 2 76345944 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422573 Affx-122943754 AX-123292919 2 59243578 TCCAAGCGAGTTGTTCTAGCAGCCTTGGATCACTT[A/G]TCACTGCTTTTGTTTTATGAGAGAATGAAATTGGA R 2 1 2 1 101000 f 74 goat snp29103-scaffold312-6788114 2 76315899 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383812 Affx-122973180 AX-123254170 2 59308395 GTCCTACTTTAATACAAAACTGCTAGCCTCATGCT[A/G]CCTTCAAAATTCATGCATGAGAAGAGGATTGGCTG R 2 1 2 1 101000 r 74 goat snp29102-scaffold312-6723297 2 76251140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378434 Affx-122976770 AX-123248793 2 59342752 GAAGGCAGTAAAAATTAGTATCTATATAATGTGCG[C/T]GCGCACACACACGCACACACACACACACACACACA Y 2 1 2 1 303000 f 74 goat snp29101-scaffold312-6688940 2 76216437 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764873 Affx-122942764 AX-385252470 2 59373805 AGGTAAACCCACTGCTTTCGCAAGCAAACTGACAC[A/G]TCAGATGAGGCCTTGCATATCTTTACATAAATGCT R 2 1 2 1 101000 f 74 goat snp29100-scaffold312-6657887 2 76184991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403360 Affx-122957798 AX-123273713 2 59443457 TTTTGACTTATGGAGTGAAGCGATCCACAGAATAG[A/G]AGGAGATTAGAAAGTGGATTCAGGATTCAGCAGTG R 2 1 2 1 101000 f 74 goat snp29098-scaffold312-6588235 2 76114582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392513 Affx-122966120 AX-123262870 2 59499927 TTCCATTTGGTGGGGCTTTTGGCATCTGTAAGACA[A/G]CTCAGGAAATATGCATCAGATACAGCTATTCTAGG R 2 1 2 1 101000 f 74 goat snp29097-scaffold312-6531765 2 76058179 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435305 Affx-122934024 AX-123305645 2 59586689 ATCCCAAATGTTTTTATTTATGTATGAAGATTTTC[A/G]TCTTATTTAATGTTTCAGAAAATAAAAATGTTTTG R 2 1 2 1 303000 r 74 goat snp29095-scaffold312-6445003 2 75971172 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426007 Affx-122941135 AX-123296353 2 59620378 TTGTTGATTTTCACAGCTTTCTGTACGTTAGCATG[C/T]GGATGAGAGATTGTGGACTTACAGTAGGTATCCCC Y 2 1 2 1 201000 f 74 goat snp29094-scaffold312-6411314 2 75936797 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386254 Affx-122970957 AX-123256612 2 59696364 GTTCCTTCCCCTGTCAATTCCATGATACATATATT[A/G]CAGAGTTAGTTTGGAGTGCTTCTGTGCTTGAAATA R 2 1 2 1 201000 r 74 goat snp29092-scaffold312-6335328 2 75862260 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393498 Affx-122965816 AX-123263854 2 59807554 TGGAGTTGGTGGGCTTTAAAAATGATATCTTTTAC[A/G]TATACGTCTTATTTCAGTTGGTATATTCTCTGGTG R 2 1 2 1 101000 r 74 goat snp29090-scaffold312-6224138 2 75750874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798590 Affx-122967257 AX-385285523 2 59839804 TATGGGAGAGATTATTATATTGATGCAGGTGGATA[C/T]GGGAATTTGAGAAGCTTGGAAGGTATCTTTTTATA Y 2 1 2 1 101000 r 74 goat snp29089-scaffold312-6191888 2 75718572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274356 Affx-1111834153 AX-519547951 2 59851009 GTTTTTAGGATCTGCCGGGGTACCCATGCTA[A/G]TGTCACAGCTGCAGAGAGTCTTGGTAGATGTGCCT R 2 1 2 1 101000 r 74 goat GoatD01.022037 2 59851009 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38414509 Affx-122949530 AX-123284858 2 59934396 TTAAGTCCAGGGTGTAGGAGGGAGGGGCTGGGATT[A/G]TGAACTACAGAGGGAGGGAAACCCCTATGAAGTGA R 2 1 2 1 101000 r 74 goat snp29087-scaffold312-6097296 2 75623436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770300 Affx-122944471 AX-385257466 2 59967721 TAAATTGTAGTTTTTTGATTCCCTTCACTAGAAAG[A/G]TGGGAGCTGTCCAAGGTCTGTGTCTAACAGCTTCC R 2 1 2 1 101000 r 74 goat snp29086-scaffold312-6063971 2 75590291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799934 Affx-122968672 AX-385286860 2 60010451 CATTCATCTAGATGTCTGTAGTAGCCTATCACTGG[A/G]TCTTGCTGCCTTTGATCTCATACTTCTATTACAGA R 2 1 2 1 101000 f 74 goat snp29085-scaffold312-6021241 2 75547552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400477 Affx-122961298 AX-123270832 2 60052187 CCAGTACAAGCTACTCCATCACTTCTCCTGGACCA[C/T]AGCACCAGGCTGCAAATGTTCTACTGCCTTCTAAA Y 2 1 2 1 101000 r 74 goat snp29084-scaffold312-5979505 2 75506956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431492 Affx-122936247 AX-123301833 2 60183033 AATGTACAGAGTCAGGCAGTAGAGGGCTTCCTGGG[C/T]AGTGCTATGATAAAGAATCTGCCTGCCCGTGCAGA Y 2 1 2 1 101000 r 74 goat snp29081-scaffold312-5848659 2 75374015 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393436 Affx-122965863 AX-123263792 2 60253866 GAAAGCTGGACAGTTTTCATAAACAAGGGGAAAAC[C/T]ATAAGCAGAGTAACACTTCTGTTCCAGAGATTCCT Y 2 1 2 1 201000 f 74 goat snp29079-scaffold312-5777826 2 75302263 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388543 Affx-122969190 AX-123258901 2 60283115 TGTATTTAATATACATCATTGAGGAAGTCTATCAG[C/T]GGGAAAGCAAAGCTGACATCTGTCCCTTGCTCACA Y 2 1 2 1 201000 f 74 goat snp29078-scaffold312-5748577 2 75272920 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790197 Affx-122948789 AX-385277201 2 60314015 ATCACTAATCGTAGTCTCTTCCAAAAGGCCTAGAA[C/T]AGTTTTCTAATGGTTTATTAAGATGTAATTCACAT Y 2 1 2 1 101000 f 74 goat snp29077-scaffold312-5717677 2 75242067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272044 Affx-1111833175 AX-519545808 2 60383582 GAGAGTCCCTTGGACTTGAAGGAGATCCAACCAGT[A/C]CATCCTAAAGAAGATGAGTCCTGGGTGTTCATTGG M 2 1 2 1 303000 f 74 goat 2_60383582_AF-PAKI 2 60383582 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395696 Affx-122963733 AX-123266051 2 60560139 ATGCATTTAGCCTCCCTGACCACCCAGAGTCTGGC[C/T]TTATCTGACTTACCCAACAGCACCTTCCTGGTCCT Y 2 1 2 1 101000 r 74 goat snp29071-scaffold312-5471553 2 74997841 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795158 Affx-122929331 AX-385282116 2 60601796 CTATTAGCTTGTTTGGGATATGGAATAAATGTAAC[A/G]TGGTTTCCACCCTTAAGAGTCAGGAAAAAGAGCAC R 2 1 2 1 101000 r 74 goat snp29070-scaffold312-5429896 2 74955919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393844 Affx-122965155 AX-123264199 2 60701500 GGATTCATCTTTTCATATCTGCAAAATTGGTTAGC[A/G]CTGGTTTGTCTGCTCTCCAGCTCCTCGAATTTTGT R 2 1 2 1 201000 f 74 goat snp29068-scaffold312-5330192 2 74855875 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440499 Affx-122929359 AX-123310836 2 60738400 GTGTGGCAGTGCTGCTGCTAAGTGAAGTGAAAGTC[A/G]CTCAGTTGTGTCCGACTCTTTGCGACTCCATGGAC R 2 1 2 1 103000 f 74 goat snp29067-scaffold312-5293292 2 74820096 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769792 Affx-122966139 AX-385256962 2 60778590 GATAGTGTTAAGATTTGCCAAAGCTTGGTAGCAAG[C/T]GCAGGGATGTCCTTTTTTATTATGCTCTAATCTGG Y 2 1 2 1 101000 r 74 goat snp29066-scaffold312-5253102 2 74779956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425235 Affx-122941003 AX-123295581 2 60819618 GGCAGAAACGTTTCACCTGGTTGGTTAGGTGGGTG[C/T]GTGCACGTTCCCTTGATTTAAGTTTTAAACAGCTG Y 2 1 2 1 101000 f 74 goat snp29065-scaffold312-5212074 2 74739088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798513 Affx-122924301 AX-385285446 2 60848954 CTCACAAGATGTTATGCTTAAATGTTTACCATAAT[A/G]TCATATTTCCATCCCTTTTCTATATTCATGAATAA R 2 1 2 1 101000 r 74 goat snp29064-scaffold312-5182738 2 74709928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410846 Affx-122952617 AX-123281196 2 60885744 GGGCGCCGTGAGAAACTGGGCAAGGGTGGGGTGTG[C/T]GGAGCATAACAAGTCTACATTTAAATCGACTCTGT Y 2 1 2 1 101000 r 74 goat snp29063-scaffold312-5145948 2 74673435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411397 Affx-122951853 AX-123281747 2 60989657 TTCTCTGTTTAATGTGGGGAAAGGCTTCTGTAATA[C/T]GTAACTTTATAGTCTTAAAAGAGTTTTATTAATTG Y 2 1 2 1 101000 f 74 goat snp29061-scaffold312-5042035 2 74569557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771735 Affx-122944088 AX-385258892 2 61018642 TCAGCGCTTAGTTATAGTTAGAAGCTGTGGTTTCT[C/T]ACTTAGGATTAGTTAACATTGATTGCATTTTTAGC Y 2 1 2 1 101000 f 74 goat snp29060-scaffold312-5013050 2 74540558 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427970 Affx-122939189 AX-123298313 2 61064660 AACCCAGCATTAGACCAAGCTTCGCAGGTTAAGGG[C/T]ATAGTCCTCTGTAAGTCTGCCCTCACTTCTAATCA Y 2 1 2 1 101000 r 74 goat snp29059-scaffold312-4967032 2 74494366 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787711 Affx-122974684 AX-385274735 2 61096167 ATCTTTATATTTCTTTATCTCTATAGGAATGAGCT[A/G]GTGATTGGTGACAAGGAAGATCTTATGGTACATTT R 2 1 2 1 101000 r 74 goat snp29058-scaffold312-4935525 2 74463016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781238 Affx-122934693 AX-385268323 2 61130879 CTCTGAAAAGACACAGTAGAATAAGTAGTTACAAA[C/T]AGAAATAAAAGCATTCAGAAGTCATCAGATCCTAC Y 2 1 2 1 101000 r 74 goat snp29057-scaffold312-4900813 2 74428149 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408488 Affx-122954414 AX-123278839 2 61199421 AGTTTGGGTACAGAATTCTAGGTTAATATTCCTTT[C/T]TCCTCAAAACGTTGGTAAAACAGTCCCGTTCTCTT Y 2 1 2 1 101000 r 74 goat snp29055-scaffold312-4832271 2 74358892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277604 Affx-1111835932 AX-519551103 2 61213938 TTATCATCTGGGGATTTTCTCTTTTACATGGTTCT[A/G]CATGTGAATAGGAGCAGTTTCAAAACTCATCTTCA R 2 1 2 1 101000 r 74 goat Random2.2K-202 2 61213938 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443325 Affx-122927446 AX-123313662 2 61255148 CATAACTAATTTCATGAGACAAGTATTATCTTCAA[C/T]TGTACCCAAAGAAACTGAGGCTCAGAGAGGTTAAC Y 2 1 2 1 201000 f 74 goat snp29054-scaffold312-4776544 2 74303103 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277617 Affx-1111835939 AX-519551116 2 61258502 TTTGCTGGAAAAAAGTAATCAGCAGATTCATATGT[C/G]TCATTGCCCTACTATTAATTGCGTCAATCTATCAG S 4 1 2 1 101000 r 74 goat Random2.2K-203 2 61258502 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446834 Affx-122925272 AX-123317170 2 61318340 AGACAGCTAAAGCACCAGTTATCATCCCTATTTTA[C/T]GAATGAGGAAACAGATGCAAAGAGAGGTTGAGGAA Y 2 1 2 1 201000 f 74 goat snp29053-scaffold312-4713352 2 74237990 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380235 Affx-122975469 AX-123250593 2 61349804 TAATGTAACACCTGATGATCAATAAAGGCTACTGT[C/T]TCCAGTTTCCTTTGAAGTCAGTTGTGGCTCTGGGA Y 2 1 2 1 201000 f 74 goat snp29052-scaffold312-4681888 2 74206337 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401303 Affx-122959855 AX-123271656 2 61381640 TAGAGGAATTTTTATGATTTGTCATGGGAGAAACA[C/T]GGCACAATAAATATTTCAGTAGGCGAAGAAGCTGC Y 2 1 2 1 101000 f 74 goat snp29051-scaffold312-4650052 2 74174246 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442465 Affx-122927944 AX-123312802 2 61425189 ATTTTCTCTTTGGCTGGGGCTGACCCCTTTACCTC[A/G]GAAGCTGGCTGGACCTCCTGCCTGCCTAATGCTAC R 2 1 2 1 201000 r 74 goat snp29050-scaffold312-4606503 2 74130609 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399195 Affx-122960618 AX-123269550 2 61523111 TTCTTCAATTTGTTTACAGTATGAATTGCTCCGCA[C/T]GTTGCTGTGTTCTGTGGGAAGGTGAGCTCAGTAGT Y 2 1 2 1 201000 f 74 goat snp29047-scaffold312-4508581 2 74031915 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441583 Affx-122928674 AX-123311920 2 61609408 AAAAGCCCAAGTTCGTATTGAAGAGTTCCTGGGAA[C/T]GTTCCTCTTTCTTTGCAAGTAAAGGCTCCGTGGTC Y 2 1 2 1 101000 f 74 goat snp29045-scaffold312-4422284 2 73944892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379637 Affx-122975953 AX-123249995 2 61640178 TTTTTGTTCTTGGTAATTTAGATGTGAAACCTCTA[C/T]GGAGCTATCATGTGAAATGATACTGGGTGGTTGTG Y 2 1 2 1 101000 f 74 goat snp29044-scaffold312-4391514 2 73914081 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453786 Affx-122919583 AX-123324119 2 61685422 TTTGAAATACCGAGCAGACTGTGTAAAGCAAGCTG[C/T]GGAGGTTGAGCAGGGCAATACCAGGGTAGACTGTT Y 2 1 2 1 202000 r 74 goat snp29043-scaffold312-4346270 2 73868842 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386689 Affx-122970179 AX-123257047 2 61727979 ACAGTGAGGGAGGGGAGAGCAGAAGGAAGTTGGGA[C/T]GGAGACTTGCTAGGCTCCAAGGCCCTGGGAAATGC Y 2 1 2 1 201000 r 74 goat snp29042-scaffold312-4303713 2 73826139 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781739 Affx-122952424 AX-385268821 2 61756885 CACTGAAGTCAGTACCACTGACCCAACCTTATCCC[A/G]TTTGATTCTGCTTCCTTCCATTATCTGGCTCTCTG R 2 1 2 1 101000 f 74 goat snp29041-scaffold312-4274807 2 73797458 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401735 Affx-122959518 AX-123272088 2 61805160 ATGGATGCAAAGGTCCAGAGGTGGAAACAAGTTGT[A/G]TGTGGTTACAGCAAGCTCAGTATGTTTGAGGGACA R 2 1 2 1 101000 r 74 goat snp29040-scaffold312-4226532 2 73749070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405128 Affx-122956967 AX-123275480 2 61838305 AACCAAAAATATTATGCAGGTCCCACTGACTCCCT[A/G]TAATTTATTTCCCTTTTCCCAGATGACACAGAAAT R 2 1 2 1 201000 r 74 goat snp29039-scaffold312-4193387 2 73715670 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782329 Affx-122962774 AX-385269406 2 61871285 GTCCTTTTCAGAGAAATGACTGTCACAGGTCCTAG[C/T]ATCATGCCCACCATTGAGCATGAGGAAAGGAATAC Y 2 1 2 1 101000 f 74 goat snp29038-scaffold312-4160407 2 73682816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798889 Affx-122933635 AX-385285819 2 61918897 CAATAAAAAGATGGAATAGAACCAAACCAGGCACA[C/T]GTTCTTAAACTTCTAACTCTAGCAGCTAAGTTTAG Y 2 1 2 1 101000 f 74 goat snp29037-scaffold312-4112795 2 73635031 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800788 Affx-122963322 AX-385287704 2 62011645 ATGTTATAAGCAACCAACTACTGACTTGATTTTTA[C/T]AGATAATTGGGACACGTGATTAGCAAGTGTTCTAG Y 2 1 2 1 201000 r 74 goat snp29035-scaffold312-4020047 2 73544201 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410426 Affx-122952406 AX-123280776 2 62050252 TTGGCTACAGGAACTGGAAGAGAAATAAAGCCTTC[A/G]CCACAGCCCTGGGCCCTAGCAGAGCCCACAAGACT R 2 1 2 1 101000 f 74 goat snp29034-scaffold312-3981440 2 73505509 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388377 Affx-122969325 AX-123258735 2 62084085 ACTCCTGGAAATGGCGTGAAAGGCCTGAGACTAAG[A/C]GCAGGAGGATTCACTGACTAGGTCCTTCAGAGGCC M 2 1 2 1 101000 f 74 goat snp29033-scaffold312-3947607 2 73471510 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402822 Affx-122958269 AX-123273175 2 62116396 CACCATGCCCAGGAAACCATCTGATTGCTCTCCAG[C/T]GGGAAACTAAGGTCATATAACAGAGATCCCTCTAA Y 2 1 2 1 101000 r 74 goat snp29032-scaffold312-3915296 2 73439252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441854 Affx-122929039 AX-123312191 2 62162547 TTGGCCTGGCGTGAAATTGGGGTGAGAGAGGTGCA[C/T]GAGGGAGGCTTCTCCAAGGAGGAGCACCTGAACTG Y 2 1 2 1 102000 f 74 goat snp29031-scaffold312-3869145 2 73392957 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413356 Affx-122950150 AX-123283705 2 62204980 CCTACTTGAATATCAGGACTTGCAAAGGCATATCC[A/G]CCTTAACAGAGCTTGGTGAGACAGATACTGACCTA R 2 1 2 1 101000 f 74 goat snp29030-scaffold312-3826712 2 73350236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800120 Affx-122930730 AX-385287043 2 62241434 ACACTCAGAGTGCAGATTTCTGTTTTCCTAAATTC[C/T]TGGAGTAATTTTAATCCAGAGCTTTCCATCCTAGA Y 2 1 2 1 101000 f 74 goat snp29029-scaffold312-3790258 2 73313928 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801134 Affx-122948641 AX-385288048 2 62304449 GAACATCATTTCTGTTTGTAGTAAGTCATGTCTCT[C/T]ATTTTTTTCCAGCCCTAAGAATGATCAGATAATTG Y 2 1 2 1 101000 r 74 goat snp29027-scaffold312-3727243 2 73251606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431314 Affx-122937078 AX-123301655 2 62338280 AAGGATTAGGTGCTTTGAGTGAATGGCTGTGAATG[A/C]GTTGTCTATACTCCTGGTGGGTGGTATACAAGCTC M 2 1 2 1 101000 f 74 goat snp29026-scaffold312-3693412 2 73217728 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274396 Affx-1111834175 AX-519547989 2 62367870 GAGGTGAGGGCAGGC[A/G]GATGGATGAGAGAGTGAAGCCCTTGCTGCAGGTGG R 2 1 2 1 102000 r 74 goat GoatD01.023402 2 62367870 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38444938 Affx-122926695 AX-123315275 2 62433293 GACCCATGGGTGGTAGAAAGAAGAACCGTAGTAAA[A/G]CATGCTGTAGGAAAGCAGGCAGATGTGACTTTAAC R 2 1 2 1 101000 f 74 goat snp29024-scaffold312-3598399 2 73125173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438167 Affx-122931841 AX-123308505 2 62462003 GAAGATTCCGAAGCTGAGTGAAATAATTTCCCCAA[G/T]GTCCTACAGCTGGGATCTGAGCTGAGTTGGGATCT K 2 1 2 1 101000 f 74 goat snp29023-scaffold312-3569689 2 73096413 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409314 Affx-122953090 AX-123279665 2 62497324 ATTTAAGATTGGAATCGAATAGTTTCAAATGTTGC[G/T]CCTTCACAAAGGCATGTTATAGCTGGGGCATAGCA K 2 1 2 1 201000 f 74 goat snp29022-scaffold312-3534368 2 73060217 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777714 Affx-122967903 AX-385264833 2 62556317 GCCAACCTGAGGACATCCGTCACTCTTAATGACCT[A/G]CACTTAGATCCTTTGTCTTATTTGGCCTCACCTGA R 2 1 2 1 101000 r 74 goat snp29021-scaffold312-3475375 2 73001391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413233 Affx-122950244 AX-123283582 2 62589986 CTAACTGTTTTGACCTGGAAGCCTTCCCTTAACCC[A/G]TAAAACTGCTCCAAAATGAAACGTTTATAGTAAGT R 2 1 2 1 201000 r 74 goat snp29020-scaffold312-3441706 2 72967159 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385090 Affx-122971800 AX-123255448 2 62627330 CCACCAGGGAAGCCTATGGTCATCCTTAGGGGACC[A/G]TTATTCAGCCTACCACAAGGCCTCACAAGTGTATC R 2 1 2 1 101000 r 74 goat snp29019-scaffold312-3404362 2 72929660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393135 Affx-122965554 AX-123263492 2 62693027 CTGTCAGTCTCTCTGCATCTGGCTTAGCTGGGCTC[A/G]TTGTATGTTTATGTTTAGTCTTTTCAAAGACATCT R 2 1 2 1 101000 f 74 goat snp29018-scaffold312-3338665 2 72862670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793343 Affx-122979120 AX-385280321 2 62727765 AGTTAATCCTTTGTGTCTGTTTCCCATCAGTGAAA[C/T]GACTAATAGCTAATCCTAAAATTATAAGAGTTACT Y 2 1 2 1 102000 f 74 goat snp29017-scaffold312-3303927 2 72828002 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416655 Affx-122947600 AX-123287003 2 62764321 CCCCATGCTGATGGATGAGATCGTATTGTAACTAT[G/T]TCAAGTTTAAATGGGCCTCTTCTAGTGCGGTCTAG K 2 1 2 1 101000 f 74 goat snp29016-scaffold312-3267371 2 72791269 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382415 Affx-122974250 AX-123252773 2 62899824 GTCTCTGCACACTGGTGTCTGGGGCCAGGTTCTTG[A/G]TCCTCCAGTGGACAAGGCCATGTCCAAGGATGGCT R 2 1 2 1 101000 f 74 goat snp29013-scaffold312-3131868 2 72654293 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272046 Affx-1111833176 AX-519545810 2 62903668 GTCTCTGTGTCACTTTTCCATTGCTAGTACTATTT[A/G]TTATGGTGATCTGTCATCAGTGATCATTAAAGTCA R 2 1 2 1 101000 f 74 goat 2_62903668_AF-PAKI 2 62903668 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38390265 Affx-122967749 AX-123260622 2 62941697 GGCCTCTAGCAGTCCCCACACACTTACCTTTAAGA[C/T]GGTTTTCTCATATATCCTCATGCAGAACAACTCAT Y 2 1 2 1 201000 r 74 goat snp29012-scaffold312-3089995 2 72612512 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801508 Affx-122945842 AX-385288417 2 62973288 ATCTACAGGATTAGAAATGTGTATCCATTGTACCA[C/T]ACAGGTGTGCAGATGCAGTCTCATTATGTTAATTT Y 2 1 2 1 101000 f 74 goat snp29011-scaffold312-3058404 2 72580063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424803 Affx-122941383 AX-123295149 2 63016835 TTTTGTCCTAAGTGCAACTTTTCATATCTTGATCA[C/T]TACTTATTTAGTTCTCTCCTACCTACTTTTATATC Y 2 1 2 1 101000 r 74 goat snp29010-scaffold312-3014857 2 72536075 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429249 Affx-122937905 AX-123299591 2 63060593 AAACTGGAGCCATGAAAGTCACTGACCAAGCAAGG[C/T]AGTCAAGGAATGAAAGTTTTCAAGCAGGCAGCTCT Y 2 1 2 1 101000 r 74 goat snp29009-scaffold312-2971099 2 72492168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274432 Affx-1111834193 AX-519548024 2 63066909 AAATATGGATGGGTCTACTTCTGGGCTCTCTGTTT[A/G]TTTTCATCATACAGTTGCAGTTTGTCTATTACTGC R 2 1 2 1 201000 r 74 goat GoatD01.024847 2 63066909 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38410456 Affx-122952379 AX-123280806 2 63114624 CCCATTTTCAAACTTGTGGGTATCATTTAGGTACC[A/G]TTCTATCCCTATCTTGATTCCACCATAAAAATGCA R 2 1 2 1 101000 r 74 goat snp29008-scaffold312-2917068 2 72437966 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775465 Affx-122953289 AX-385262596 2 63152315 TTTCCTGACTGTATATATAATATGTGGACTGGAAA[G/T]AGAAAAAGCATCATCAGGTATCTTTAATACCTGGG K 2 1 2 1 201000 f 74 goat snp29007-scaffold312-2879377 2 72400241 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428708 Affx-122938468 AX-123299050 2 63221579 CCCCAAATTTCCCAATCTTCTTTCTCATAATAGCC[A/G]TCTTCTCTGCATTCCCACTGCCATGACCCTAGCTC R 2 1 2 1 101000 f 74 goat snp29005-scaffold312-2810113 2 72330619 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791210 Affx-122934323 AX-385278204 2 63272054 ATTGACTTGGGAGGAACAAATTTAATCCATTCTGC[A/G]TAGAATCATGTCAAGCAATCCAATTGTTTATCCTG R 2 1 2 1 101000 f 74 goat snp29004-scaffold312-2759638 2 72279617 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273859 Affx-1111833860 AX-519547469 2 63305057 GACACCTGCAGAGCCCACACCTAGGGCGCTGCTAA[A/C]CACACAAAAGCTCCATCGGCATGCCCTCTGGCATT M 2 1 2 1 202000 r 74 goat GoatD01.007953 2 63305057 C A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427865 Affx-122939711 AX-123298208 2 63313199 TATTAGAGTTGGAATATTATAGCATACAAACCATA[G/T]AGTGAAGAGAAAGTATGATTTTTTTTACATATTTT K 2 1 2 1 101000 f 74 goat snp29003-scaffold312-2718493 2 72238502 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443431 Affx-122927365 AX-123313768 2 63360750 GACAAAAAGAGTGTTTCCAGCCCCAGTGTGCTTAC[A/G]ATGCTTATTGACCTGAAAGTAACAAATGGGATTCA R 2 1 2 1 201000 r 74 goat snp29002-scaffold312-2670942 2 72190846 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277531 Affx-1111835959 AX-519551032 2 63370656 TCTTCCTCCTTACCATCTCCCACTTCCTCTTCCTC[A/G]GCCAGTCAGTAACTCTTCTTGCCTGTTCACCTGAT R 2 1 2 1 103000 f 74 goat Random2.2K-206 2 63370656 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407597 Affx-122954652 AX-123277948 2 63389280 AGGAAGTTGGGGATGGGTCAGGAAGAAAAAGTCAG[C/T]ACAGGGACCTAAGGCAGGAAATATCTTTTCTCTCT Y 2 1 2 1 201000 r 74 goat snp29001-scaffold312-2642412 2 72161945 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430374 Affx-122937782 AX-123300715 2 63419343 GAGTTTTCCTCCCTGTCCTTCACTGGAGAAGCTTA[A/G]GAAAGCAAAGACCACATGGAGACCAGGCTGAGAAA R 2 1 2 1 201000 r 74 goat snp29000-scaffold312-2612349 2 72131584 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395535 Affx-122963860 AX-123265890 2 63451720 GTTCTACTTTAATTAAAGGAATGGAACTCTTTAGG[C/T]AGCCTCTGCTGATTTTTGCCCCCAAAGGTGCTTTT Y 2 1 2 1 201000 f 74 goat snp28999-scaffold312-2579972 2 72099365 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801312 Affx-122970407 AX-385288224 2 63498901 TTCCCACGTCTGCTACACTGATTTCCTTCACTAAA[C/T]GTTTTTGTTATCTTACAGGTATATTTCTTATTCCA Y 2 1 2 1 101000 f 74 goat snp28998-scaffold312-2532791 2 72052215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436585 Affx-122932891 AX-123306923 2 63535592 ACTTTGGCAATGAAATGTTGAGTAGAAGGAACATG[C/T]GTAACTTTGGGGCAGAAACTTGTAGAGCTAGGACA Y 2 1 2 1 101000 f 74 goat snp28997-scaffold312-2496100 2 72017171 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771219 Affx-122948741 AX-385258377 2 63565353 GAAAAGTATGACATTGATGTATTTCTGCAATAAGT[A/G]TATTATAAATTTTATGAAAGCAAGTACTTCATTTT R 2 1 2 1 201000 r 74 goat snp28996-scaffold312-2466339 2 71986939 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397334 Affx-122963295 AX-123267689 2 63594428 GCGCCATATCTTTGCCGTCATTAAGAATAATTCCC[A/G]TGTGGATCATTTCTAAACTGCATGGTGAATGATGC R 2 1 2 1 101000 f 74 goat snp28995-scaffold312-2437264 2 71957937 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397895 Affx-122961954 AX-123268250 2 63655062 ACTGCCTCCAATTGTTACAGATCTGTGGGACTTCA[C/T]AATGCAAGCCCCTCTGGCTACCAGAGCCAGGCAAT Y 2 1 2 1 101000 f 74 goat snp28994-scaffold312-2376630 2 71898393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379862 Affx-122975794 AX-123250220 2 63697834 TGGCTTTTGAATCAGTTACTAACATCCTCAATAGC[A/G]TGTCAGCCAGGCTCCTCAAAGCACATCCAGATTGT R 2 1 2 1 201000 f 74 goat snp28993-scaffold312-2333858 2 71856532 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383917 Affx-122972979 AX-123254275 2 63735710 CTAACAAACTTGTAACTAGCAAAGTGAGGCATCAT[A/G]TATTAACTTAAAAGCTCGTTAGGGAGGAATCTAAA R 2 1 2 1 101000 f 74 goat snp28992-scaffold312-2295982 2 71818689 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435816 Affx-122932838 AX-123306155 2 63766999 TCTCTGTAGGAGGGAAAAAACTAAGTTTTTCCTTT[A/G]CATAAGGTGATATTCACAAGTTCCGGATATAGGAC R 2 1 2 1 101000 r 74 goat snp28991-scaffold312-2264693 2 71787806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768513 Affx-122965054 AX-385255693 2 63807004 GACTAAATCTATGTCATCAATAACTAAAGACAGCA[C/T]GGAAACTGAAATTTACTCTGGTTAAATGTGGGAGA Y 2 1 2 1 101000 r 74 goat snp28990-scaffold312-2224688 2 71747890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793932 Affx-122959775 AX-385280901 2 63842790 AGTGGACTAATGAGACCATTCCACAGGTCAAGGAA[C/T]GTTGGCTTTACTCTAAGGGCAATAAGAAGCCATGG Y 2 1 2 1 101000 f 74 goat snp28989-scaffold312-2188902 2 71711943 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432073 Affx-122935882 AX-123302414 2 63887192 TTGTCATGAAGCAGCAGCTGGCCTGCAACTGCTCT[A/G]TCTTCCTCTGGATTCTTCTTCACTTCTTCCGACTC R 2 1 2 1 103000 r 74 goat snp28988-scaffold312-2144500 2 71667364 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402875 Affx-122958228 AX-123273228 2 63924393 TTAAGGGACGACCCCTAGACTGTATGAAGTGCTCC[A/G]TTTCACAGACAAAAACTTGAAAAATCATCCATATA R 2 1 2 1 101000 f 74 goat snp28987-scaffold312-2107299 2 71630166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791348 Affx-122921622 AX-385278341 2 63958833 CATAAAACTCTGCCTTGCTCATCATGGAGTGCAAA[C/T]GTACTAATACTGGTTCCCAAAGCCATCAATTATTT Y 2 1 2 1 101000 f 74 goat snp28986-scaffold312-2072859 2 71596022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776816 Affx-122941158 AX-385263940 2 64019032 TCAGATTACTTGCCAGCCACAAAAGGATGGAAGAA[G/T]CTACTTAACCTACCTCTCAGGTAGGGAAAGGTACT K 2 1 2 1 101000 f 74 goat snp28985-scaffold312-2012660 2 71536261 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449135 Affx-122923564 AX-123319470 2 64071361 TCTTTTTCAAATTCTTTTTTCACATCTACCTTCTG[C/T]ATGCTATCAAACTATACCCGCAGGCTTTCTGGTCT Y 2 1 2 1 101000 r 74 goat snp28984-scaffold312-1960331 2 71483844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378763 Affx-122977014 AX-123249122 2 64106561 CAGACAGAAGCACAGAACAGGCTCCACAGGCCAGC[A/G]TGAGAGGCCCAGACAGGAGCACAAATGTCCCTTCT R 2 1 2 1 101000 r 74 goat snp28983-scaffold312-1925131 2 71448503 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401700 Affx-122959546 AX-123272053 2 64177372 TTTCTGGGCCAGCCTTCAGAGGCAGCTATGGAGAG[C/T]GAATGAAGCAACTCCTGGTGAGAATTCCTGTAGGT Y 2 1 2 1 101000 r 74 goat snp28981-scaffold312-1854320 2 71377086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453133 Affx-122920005 AX-123323466 2 64219527 CAGCAGTTCCTCTGCAAGAGCTAACATGGTTTTCT[C/T]AAGCACTTTTCACAGCGAGGCCAAGCCCGAGTCTA Y 2 1 2 1 201000 f 74 goat snp28980-scaffold312-1812165 2 71334920 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795123 Affx-122924260 AX-385282081 2 64255830 CTTCAGAAAATTTCATTGATCTCTCTGAGATCAGA[C/T]GGAGAAAGTGGAAATTGCCTGTCATCTGAGGTCAT Y 2 1 2 1 101000 r 74 goat snp28979-scaffold312-1775862 2 71298789 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411740 Affx-122951513 AX-123282090 2 64288024 ATTGGTGCTAAAGAGGAAATTAAAACATGGGAATG[C/T]GATTTTAAATAGGGTGATCAGCTAGGGTTCACTTA Y 2 1 2 1 201000 r 74 goat snp28978-scaffold312-1743668 2 71269051 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409120 Affx-122953309 AX-123279471 2 64368256 TCAAAGATATGGCCAATGGTCTTGGAGGAAAACTG[C/T]GCAAATATAAACCAAATAGGTCTATGATCCAAGAT Y 2 1 2 1 101000 f 74 goat snp28976-scaffold312-1663436 2 71188590 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401077 Affx-122959636 AX-123271430 2 64423893 AGCAGAAGCTAATACAGCACTGTAAAGCAACTATA[C/T]GCCAATGAAAGTTGAAAATAAAAAGGCTCTATAGT Y 2 1 2 1 201000 r 74 goat snp28975-scaffold312-1607799 2 71132300 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412004 Affx-122951753 AX-123282354 2 64454675 GCTGAGGAATTCCACCTGTTTCTTAAGCTTCTTAC[A/G]CCTCCTTCCCTAGCACACCCACTGTCGGGTTTTTC R 2 1 2 1 101000 f 74 goat snp28974-scaffold312-1577017 2 71101173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802318 Affx-122944404 AX-385289222 2 64505087 CTTTGCAACAATGGGAAACATATTTATTGTTGGAA[C/T]ATAGTCATCAGAAGGACTCAAGAGAGAGTTTTTTC Y 2 1 2 1 101000 r 74 goat snp28973-scaffold312-1526605 2 71050922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452013 Affx-122920913 AX-123322346 2 64534003 TATTTTTGAAGAGGATTAGACCGTAGAGGAAAGTT[A/G]CGTAGATCCACATGCCATGCCCCACCACCATGGCT R 2 1 2 1 101000 f 74 goat snp28972-scaffold312-1497689 2 71022241 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769403 Affx-122921551 AX-385256574 2 64566787 TTCAAGATTATTGCAATGGAGTTCAACTCTGTTGC[A/G]ATGGAAAAGAAAGACTGAGTTCAAGTTCAAACACA R 2 1 2 1 101000 r 74 goat snp28971-scaffold312-1464905 2 70989341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406892 Affx-122955633 AX-123277243 2 64609700 AGCTTAGCGACTAGACAACAACAACAACAATTACA[C/T]GGCTGCCCTAATGTACTCTGTTTCCTGACAAGTAG Y 2 1 2 1 101000 r 74 goat snp28970-scaffold312-1421992 2 70945992 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774978 Affx-122968740 AX-385262110 2 64643424 CCCTGTGATTTATTAGTTATGAATTTATTGACTTT[C/T]GGCTAGTTTAAGCATTTCTATTTTTTCTGTCTTCT Y 2 1 2 1 101000 r 74 goat snp28969-scaffold312-1388268 2 70912285 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778816 Affx-122977641 AX-385265925 2 64686168 CAGGTATTGAGGGTATAGAAATCTTTGAAGAAATA[C/T]AGAGTATTTAGAAATGCCATGACAGAAAAAAATTA Y 2 1 2 1 101000 f 74 goat snp28968-scaffold312-1345524 2 70869028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793899 Affx-122965273 AX-385280868 2 64719752 TTCACTTTCTCGAAGACTTTACTCCCACAAATAGA[C/T]GTCTCTCTCCTGAATTATCAGTTTCCCTCTTTCTA Y 2 1 2 1 201000 r 74 goat snp28967-scaffold312-1311940 2 70835426 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401224 Affx-122959318 AX-123271577 2 64835485 TGGGTCTCCTGCACTTCAAGCAGATTCTTTACCAC[G/T]GAGCCACCAGGAAAGCCTCCTGCTAAGTATATAGT K 2 1 2 1 103000 f 74 goat snp28964-scaffold312-1196207 2 70718428 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770128 Affx-122941016 AX-385257295 2 64869482 ACACCGTCTCCACTGTCTATTACCGTACCGGTCAA[C/T]GTCCGTTCTCCTACTTGTCTGGAGGTCCAAGATGC Y 2 1 2 1 201000 r 74 goat snp28963-scaffold312-1162210 2 70684097 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405491 Affx-122956011 AX-123275843 2 64920230 GCTCTCTCCCTTTTTCTTCTTACAAGGCCACTTAA[C/T]GCCATCATGACAACCCCACCCACAAGGGCCCCATC Y 2 1 2 1 101000 f 74 goat snp28962-scaffold312-1111462 2 70633353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410410 Affx-122952419 AX-123280760 2 64962732 TAAAACCTCAGTTGTGCCTGGAGTTGTGTCCAAAT[A/G]CTTGGGGGTAACAGTACTTGAATGACAATTTCCCT R 2 1 2 1 201000 f 74 goat snp28961-scaffold312-1068960 2 70576844 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398410 Affx-122961632 AX-123268765 2 65006561 TTGTTCCAGTGGTCAGTAAATAGCATAAGATTTGC[A/G]CAGTTCATTGGCTCCAACTCAATTTGAGTGGTGTC R 2 1 2 1 101000 f 74 goat snp28960-scaffold312-1025131 2 70532761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403259 Affx-122957874 AX-123273612 2 65035464 ATAAGACAGCCACCAATTGCTTCGTTTTGCAGTGG[C/T]AACCCCCAAGCTCCAGCTCAAAGATCATGATTAAA Y 2 1 2 1 101000 f 74 goat snp28959-scaffold312-996228 2 70503828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403774 Affx-122957989 AX-123274126 2 65069570 GCTTTGCATAACTGCCTGCAATGCTCACAGTGCCG[A/G]GTCCAATGCACCAGCAGACCCTTGATGAGATTGTC R 2 1 2 1 101000 r 74 goat snp28958-scaffold312-962122 2 70469582 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791872 Affx-122921814 AX-385278862 2 65105361 GAGCCATGTGACTTCCTTTGAGCCATGGGATTTTC[A/G]TGGATGAAGAACACATCTTAGGGATGCTAATTAAT R 2 1 2 1 101000 f 74 goat snp28957-scaffold312-926331 2 70433740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449798 Affx-122922419 AX-123320133 2 65136116 AGCTAATACTTCTGAAAGTGGTGGTGGGGGAGAAA[C/T]AAGAGGCTTCCTTCAGGAATGCTTTTTTCCATATT Y 2 1 2 1 101000 f 74 goat snp28956-scaffold312-895576 2 70403144 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790514 Affx-122924969 AX-385277517 2 65165444 CCTCTAAAAGAGCAATTTGTATTCTGGGGTCGTTC[A/G]TAGACCTAGAAATCCTGCATTAGTGCCTTGACGTT R 2 1 2 1 101000 f 74 goat snp28955-scaffold312-866248 2 70373403 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417312 Affx-122948160 AX-123287660 2 65198383 AGCTACCAACTTCCCCAATTTTGGAAACACATAGG[A/C]GGGACATTTCTGGAAGTAAATGGAGGAAATTTGAG M 2 1 2 1 201000 r 74 goat snp28954-scaffold312-833309 2 70340297 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779543 Affx-122973477 AX-385266646 2 65237763 ACAAAATGAAATGTATATGACCTTAACAATAAAAG[C/T]ATGTACTTAGCACAACCAATGACATAGATCTAAGA Y 2 1 2 1 101000 r 74 goat snp28953-scaffold312-793929 2 70300716 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446729 Affx-122924715 AX-123317065 2 65294014 GCCTTGAACACATTTCATGGACTAGAAATCACAGT[A/G]ATTCTGTATGTACTGGCTTCTCATATGGGTAGTTA R 2 1 2 1 101000 f 74 goat snp28952-scaffold312-737678 2 70243743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415458 Affx-122949170 AX-123285807 2 65391758 CCAGTCAATCCTTACCTAAATTCCTTGTATTACAT[A/G]CATCACAGGAAATGCCACAACCTTAAATAATCATA R 2 1 2 1 101000 f 74 goat snp28950-scaffold312-639934 2 70144175 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277660 Affx-1111835962 AX-519551159 2 65408928 ATTGAATCTCTAAGGCGCAAACCTAGACTTTCAAT[A/G]GACTTGTCTATTCCTATGTTGCCAAGAGAAAGACA R 2 1 2 1 101000 r 74 goat Random2.2K-207 2 65408928 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779756 Affx-122923221 AX-385266856 2 65471262 ATACTTTAACATGGATAAAAACCAACCTATTAATA[C/T]CAAGATCCTGTTTCTGTTGTGCCTAACCTTGTGAG Y 2 1 2 1 101000 r 74 goat snp28948-scaffold312-560430 2 70064421 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769338 Affx-122945476 AX-385256509 2 65513840 GATATAGTTTGTAGACATCTAAAACAAATCCTTCC[A/G]TTACCTGCGTTCTTTGGAGGAAATATGGCAAGAAA R 2 1 2 1 101000 r 74 goat snp28947-scaffold312-517852 2 70021550 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272945 Affx-1111833177 AX-519546631 2 65546821 CTGGAGAGTTACAGTCCATGGGGTAGCAAAGAGCT[A/G]GACAAGACTAAGCAACTAAGCAACAACAACCACCA R 2 1 2 1 303000 f 74 goat 2_65546821_AF-PAKI 2 65546821 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433452 Affx-122935062 AX-123303793 2 65550249 TGCAAGCCATGCCAAGCCATGGATACTTCTCAAGG[C/T]AGAATTTCATTTGGAGTTTTTCATACATAACACAA Y 2 1 2 1 201000 r 74 goat snp28946-scaffold312-481443 2 69985860 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381922 Affx-122974138 AX-123252280 2 65639215 TGCATGATCCCCCACCCTAAGATTCTTTAGTCTGA[G/T]CCCCATGCAGAGTGACTGCAATTAGAAACTGAAGA K 2 1 2 1 202000 f 74 goat snp28944-scaffold312-392477 2 69904026 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415033 Affx-122949016 AX-123285382 2 65673171 GACTCCAGAGATTTGGGGTCTGTTTCCAGCTTCAC[A/G]CTCACAAATGGTGGTGTTTACAACAAAGCAGTGAT R 2 1 2 1 600000 r 74 goat snp28943-scaffold312-358521 2 65673171 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797266 Affx-122949016 AX-385284205 2 65673171 GACTCCAGAGATTTGGGGTCTGTTTCCAGCTTCAC[A/G]CTCACAAATGGTGGTGTTTACAACAAAGCAGTGAT R 2 1 2 1 101000 f 74 goat snp28943-scaffold312-358521 2 69872867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432741 Affx-122935454 AX-123303082 2 65717949 ACATATACCCTGGAGCTAAACATAACATTCACTGC[A/G]TCAGAAAAATAAACAGTAAAAAAATTGAAAATAAA R 2 1 2 1 101000 f 74 goat snp28942-scaffold312-313743 2 69827755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781598 Affx-122977820 AX-385268683 2 65762790 GCACTACAAATTGGATAAAGTTCAGGGAACAAAAA[C/T]ACAGTACATGGTTCTTACCTGTACTCAAGTAACTT Y 2 1 2 1 101000 r 74 goat snp28941-scaffold312-268902 2 69783060 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785651 Affx-122945718 AX-385272693 2 65803156 GACAACCATTTATCAGATGTCAACAAAGGATTAAG[C/T]TACTTTGATATTTTAATCATGCTGACACATTGAGA Y 2 1 2 1 101000 r 74 goat snp28940-scaffold312-228536 2 69709286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390958 Affx-122967054 AX-123261315 2 65834158 TAGATCACAAGTACTTGCATTTCTGTTTATGATGT[A/G]AAGGTTTATTTAATTAATGCTATTTGTCCCCAGAA R 2 1 2 1 101000 f 74 goat snp28939-scaffold312-197534 2 69678133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277669 Affx-1111835966 AX-519551168 2 65870239 GCTTTTAAAGTATGCAAATACATATAGTATTGCAT[A/G]TAGTCTGGTGGTAGTGCATTCATAATCACTGCTGA R 2 1 2 1 101000 r 74 goat Random2.2K-208 2 65870239 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386863 Affx-122970066 AX-123257221 2 65876782 ATAAGTAGAGTTGGTGGCTGGCATACCATGTGCTA[C/T]GCTTGAAATGGACATGAGTTTGAGCAAGCTCCAGG Y 2 1 2 1 101000 f 74 goat snp28938-scaffold312-154910 2 69637271 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381736 Affx-122974329 AX-123252094 2 65919343 TCTTTTAAAGAAATTTGGTACAAAATATGCAAAAC[A/G]TACTTTCAAGTATTAAGGAAAGACATTGACATAAT R 2 1 2 1 101000 f 74 goat snp28937-scaffold312-112349 2 69594632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799581 Affx-122931327 AX-385286511 2 65953131 GAGATTACAATACTTGAAGAAAAAGCATTGAAGAG[C/T]GGAGATATGATTGAAGCTTTTAAGATGTTAAAAAG Y 2 1 2 1 101000 f 74 goat snp28936-scaffold312-78561 2 69560363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801817 Affx-122929945 AX-385288724 2 65984375 AGAAATGTTCTCTAAAAATTAGGGCAAGAGTTCAC[A/G]TATAGGAAAACAAATTTAGAGACCTGCCTTTTAAT R 2 1 2 1 101000 f 74 goat snp28935-scaffold312-47317 2 69528597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392925 Affx-122965708 AX-123263282 2 66024363 AAAGAAGAAAGATCTTTTCAGTTTCTCAGTACATC[A/G]TTACAGAAGGAAATGCTTTAATATAAAAGAGTAAC R 2 1 2 1 101000 f 74 goat snp28934-scaffold312-7329 2 69487994 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386583 Affx-122970695 AX-123256941 2 66051262 TTAAAGGTCAGATCTGTTTTCTTCTCAGCAGCTGC[A/G]TGGGAATTGCTCATCTTGCAGTTCTTGTATGGGGT R 2 1 2 1 101000 r 74 goat snp4619-scaffold1148-19471 2 69460254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394728 Affx-122964329 AX-123265083 2 66080483 TGGGTTAGTGTACAAGATTGTTCAAGAACACTCAG[G/T]TAACTCACAGGTAACTCATGGTGCATACACAAAAA K 2 1 2 1 101000 r 74 goat snp4620-scaffold1148-48692 2 69431025 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401692 Affx-122959552 AX-123272045 2 66135910 CTGGGTACCACCAACCACACTCATTCCCATCCTTT[A/G]TTCTGATCCTTTTTGAAGATGGTTCATTTTAGACC R 2 1 2 1 201000 r 74 goat snp33515-scaffold393-1569489 2 69380444 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398403 Affx-122961637 AX-123268758 2 66189431 CCACATTGCACACATAGGTAAGTATGATGATATTA[C/T]GGTAAAAAAATACAAATATATTTGTTATTCAGCAT Y 2 1 2 1 102000 f 74 goat snp33514-scaffold393-1515968 2 69326768 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429426 Affx-122938513 AX-123299768 2 66258183 TAATATAAATGTGTGCAGGAGGGGAGACTGGTGAG[A/G]TGTTGAAGATGCAGTCTTTCATGCAGACACTGCTA R 2 1 2 1 201000 r 74 goat snp33512-scaffold393-1447216 2 69256077 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411477 Affx-122951797 AX-123281827 2 66297978 GTCCTTATTTTGTCTAAGCTAAGAGGATTATTTTA[C/T]AGCTGTTGGGATCTAAGTTAAGGGCATTAATTAAA Y 2 1 2 1 101000 f 74 goat snp33511-scaffold393-1407421 2 69216272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790281 Affx-122953020 AX-385277285 2 66338397 TGTGTGTATCTGGTACCCCAAGCATATAAAGAGCA[C/T]TCTATTTTCTCCACATAGAAAAATATCCATGTAAA Y 2 1 2 1 101000 f 74 goat snp33510-scaffold393-1367002 2 69175497 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790027 Affx-122971401 AX-385277033 2 66391499 CAGCTTATATATCTCTTTCATTATGATGCCATAAT[C/T]AAAGAATTCCCAGCACAAACATCACTAAGACCAGT Y 2 1 2 1 101000 r 74 goat snp33509-scaffold393-1313900 2 69122162 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452802 Affx-122920230 AX-123323135 2 66469526 ATTACCACTGAGAGTAGTACACTTAAAAATTCTAG[C/T]GGTACACTTAAAAATTATGTTTATGTTATGCATAT Y 2 1 2 1 103000 f 74 goat snp33508-scaffold393-1235873 2 69043186 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779394 Affx-122927974 AX-385266497 2 66527722 ACACAATTTGCAAACATAAATGTACTTAATTAGGA[C/T]ATTAGAGAAGAAAGGATGGACTGTGAGACAGTACT Y 2 1 2 1 101000 r 74 goat snp33507-scaffold393-1177677 2 68983592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775523 Affx-122975414 AX-385262654 2 66559149 AAATACACCTTGTACAGTGTGTGAAATTTTAGCAC[A/G]TCAATTATCCTATAAAGTTATTGGAAGGAAAAATG R 2 1 2 1 102000 f 74 goat snp33506-scaffold393-1146250 2 68949902 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784556 Affx-122941941 AX-385271605 2 66609319 AACATTAAATAATCGAGCCAAAATATAATTAAACT[A/G]TATTAGGTATGAGGCCAGAGGTTAACTAGAAAACA R 2 1 2 1 101000 r 74 goat snp33505-scaffold393-1096080 2 68899004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784811 Affx-122931186 AX-385271858 2 66658443 AGGCAATACCTAGTCTATGTACTAAAGATACAAAA[C/T]ATCCTCACTCATTTAGTTCAGAATTCAGTGGGGGA Y 2 1 2 1 101000 r 74 goat snp33504-scaffold393-1046956 2 68849941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385118 Affx-122971779 AX-123255476 2 66728262 TCTAGCTTCTATTCTCTCTGACAGCCCTTCAACAC[A/C]CAAGATGCATATTATTCTCCCTGTATTTTGCCAGG M 2 1 2 1 201000 r 74 goat snp33503-scaffold393-977137 2 68780003 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774489 Affx-122922519 AX-385261624 2 66768518 ATGTCCATATGATAAAATTTGAGTGAAAAATTATT[A/C]AAGATCTCTTTTAAACAGACTTACCCTGTCCAAGG M 2 1 2 1 201000 f 74 goat snp33502-scaffold393-936881 2 68741278 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451708 Affx-122921560 AX-123322041 2 66823703 TGACAGTTTTTATAAATTTCAGTACCTGCTAATTT[A/C]TTTTCAATGTTAATTTTCTTTCTTTTCACAGACAA M 2 1 2 1 103000 f 74 goat snp33501-scaffold393-881696 2 68685595 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423239 Affx-122942687 AX-123293585 2 66872937 AAACACTTAAAATCCTTGGATACTTCTCTGTATAG[C/T]AGACATATAAACAATTACCTTATAATTATTATATT Y 2 1 2 1 101000 f 74 goat snp33500-scaffold393-832462 2 68636115 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376665 Affx-122979006 AX-123247024 2 66921383 TTACCTACTCAGCTATGGAAAGCCCAATTGAGGAA[C/T]AGGGAGGTCAGAAAAGGCTTCAGATGATGCATGAC Y 2 1 2 1 101000 f 74 goat snp33499-scaffold393-784016 2 68587464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412846 Affx-122950453 AX-123283195 2 66960317 CATTTTAGCATGGAGAAAAATGATAATGGATACTA[C/T]AATCAATCAGGAAAAAATGCTGAATTGAGATAATA Y 2 1 2 1 101000 f 74 goat snp33498-scaffold393-745082 2 68548056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277680 Affx-1111835971 AX-519551179 2 66977348 TATATAATAAATAAAAAAAAACTAATTTATTCAAT[A/G]ACATCAATTTGTGGGACTGGATTCCCTGTAACCCA R 2 1 2 1 101000 r 74 goat Random2.2K-209 2 66977348 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38420909 Affx-122944603 AX-123291256 2 66995227 TTAAGTTTGATCTCTACTCTGGGTAAATAATCCCA[G/T]TACCAATCACAATATGGTAGATGCCCATACAGTAA K 2 1 2 1 101000 f 74 goat snp33497-scaffold393-710172 2 68513464 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449360 Affx-122922732 AX-123319695 2 67039545 CAGAAATCCCCAGGGACTCATACAAAGAATAGCAC[A/G]TCAAGGTTGAGAATAGAGACACACATTTTTGTTGA R 2 1 2 1 201000 r 74 goat snp33496-scaffold393-665854 2 68469281 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776594 Affx-122946488 AX-385263721 2 67099305 TGTTTTCTCCTCAGAGACTCTATATATAAACTACA[C/T]GCCCTGTTGCTATGAGCTGATCTTCTAAAACTGAT Y 2 1 2 1 101000 r 74 goat snp33495-scaffold393-606094 2 68409822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777179 Affx-122964731 AX-385264302 2 67142738 TGTTATACGCTGGCTGCTATCAAGGAAAGTCTTTT[A/G]CAAGATTGGATGTAGAAGAGAGCAACATGAAGTAA R 2 1 2 1 101000 f 74 goat snp33494-scaffold393-562661 2 68366283 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277569 Affx-1111835978 AX-519551068 2 67171584 ATGCCATGATCTTCATTTTCTGAATATTGAGCTTT[A/C]GGCCAACTTTTTCACTAAACTGGCTGACCCACAAA M 2 1 2 1 303000 f 74 goat Random2.2K-210 2 67171584 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38400536 Affx-122960442 AX-123270891 2 67202240 ATAAACATTAAACCTGAGATTCCAGAGAGATGATG[A/C]GTCCTTTGTAGTTAAACCTCATTCCCTTCTCAGAA M 2 1 2 1 101000 r 74 goat snp33493-scaffold393-503159 2 68306047 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407207 Affx-122955801 AX-123277558 2 67240896 ATCATAAGTATTTTATAAATTAATGAACAAATGAA[C/T]TGTTCTCAAATCAGGTAGTAGTAAGATGCTCCAAA Y 2 1 2 1 103000 r 74 goat snp33492-scaffold393-464503 2 68272364 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775497 Affx-122964660 AX-385262628 2 67272667 GTGATACATAGATAAATCATTTTTCATACGACTTG[C/T]CTCATGTTTAAATAGGAATAAATTCCCAGTTCAGT Y 2 1 2 1 101000 r 74 goat snp33491-scaffold393-432732 2 68240615 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424421 Affx-122941805 AX-123294767 2 67312516 GTGAGTGTGAGGCTACCCTGAGGCCTCAGGAATTG[A/C]TTTTCTCTTTTCTACTTCATTTTTCGATAACTATC M 2 1 2 1 303000 r 74 goat snp33490-scaffold393-392883 2 68200223 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408196 Affx-122954190 AX-123278547 2 67352833 AGATCAAACAAAGATATGATAAGAAGAGGAAATTA[C/T]AGAGGAACCTCCATCATCAACACAATTATAAAAGT Y 2 1 2 1 101000 r 74 goat snp33489-scaffold393-352566 2 68160558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277583 Affx-1111835985 AX-519551082 2 67368096 TGATTTTCACCAAGAGTTATCTCATTATTTAAAAC[A/G]ATGAATTGATTTGAAATAATAAGTACTAGTTGAAG R 2 1 2 1 101000 f 74 goat Random2.2K-211 2 67368096 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418171 Affx-122947084 AX-123288519 2 67399880 AAAATCTTCAGTTTAATTTCTGTATTGGGCTTTCC[C/T]AAGCTATTCAGTTTGAAACATGATTTTTATACTCA Y 2 1 2 1 101000 r 74 goat snp33488-scaffold393-305519 2 68115265 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414719 Affx-122949267 AX-123285068 2 67445881 GTATGAAGATTTTGAGGCAAGTGCTTAGAAAGTTC[A/G]TATAAATAAAGGAAAATGTTTATAGCTGGACAAGA R 2 1 2 1 103000 f 74 goat snp33487-scaffold393-259518 2 68068705 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780998 Affx-122965277 AX-385268085 2 67516860 TATTGTTCTTACTTAGAAAACAGGGACACAAAATG[C/T]ATTGTTGGATGTAGTTGACAAGAAGAAAAATTTAT Y 2 1 2 1 101000 f 74 goat snp33485-scaffold393-188539 2 67994515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393645 Affx-122965294 AX-123264000 2 67547728 CAATCCTAGATGATATTATCTTAAGAAAACAAATT[A/C]TTTGTCCCCAAATCAAAATGGGATAAACATGTATA M 2 1 2 1 101000 r 74 goat snp33484-scaffold393-157671 2 67963376 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397903 Affx-122961949 AX-123268258 2 67584099 AAATTTTATCTAGAGAAAAGGAAAACAAATATATA[C/T]GATGGGAGAGGAATGCCCAGAACTGGTTTTAACAA Y 2 1 2 1 103000 r 74 goat snp33483-scaffold393-121300 NW_017211749.1 6609 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783670 Affx-122965683 AX-385270729 2 67646005 GATACTCTTAGTTAAAATCTGATGTTGAATATTCC[A/G]TTCATTAATACCAATAAAGTATTCTTTCTTTTTTG R 2 1 2 1 201000 r 74 goat snp33482-scaffold393-59394 2 67865613 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797386 Affx-122979061 AX-385284325 2 67679646 GACTTATTGTCTCCATGAGCTTCATGATATTTGAG[A/C]AGCATGGGTTGAAAGTGATACTCTCCCTAGGAAGC M 2 1 2 1 101000 r 74 goat snp33481-scaffold393-25753 2 67830853 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448165 Affx-122924265 AX-123318501 2 67732659 TAACTGAGCAGGAACCCTATGGGGCCTTCCCAAGA[C/T]AGATGCCTCCTTTATATCCACTACTGTAGCTCCTC Y 2 1 2 1 201000 r 74 goat snp5762-scaffold1203-27161 2 67654392 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427893 Affx-122939690 AX-123298236 2 67824766 CTGATACTTCATCAAACCAGTTCATGCTAACAGCC[A/G]CCTGGTCTCCTGCATAAGAACAGCAGACCTCCAAT R 2 1 2 1 101000 f 74 goat snp5764-scaffold1203-119268 2 67561016 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445990 Affx-122925878 AX-123316327 2 67863884 GCCCAGATACCCTCATACTCCCACTATGTTTCTGA[C/T]GATAAGATATAGGGAAAAGAGAAAGAAAATTTCAG Y 2 1 2 1 103000 f 74 goat snp5765-scaffold1203-158386 2 67522364 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417358 Affx-122947718 AX-123287706 2 67901509 AACACTCAAAATGGAAGTTCAGAGAGATGAACCTT[A/G]CATCATCAGTTCCACTCCAACCCAGGCAGGGAGAC R 2 1 2 1 101000 f 74 goat snp5766-scaffold1203-196011 2 67484141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773471 Affx-122967526 AX-385260613 2 67967266 ATTTATGATATGTACCATTAATATGGGTACATATG[C/T]ATTGGGAACAGCACCTTATCTCTGTGATCCAATTA Y 2 1 2 1 101000 r 74 goat snp5768-scaffold1203-261768 2 67417205 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390461 Affx-122967611 AX-123260818 2 68004298 AATCTCCACACTGCATCCTCTGTCTTGCTAGAAAC[A/G]TAAGAGGGCAAGGTGCAGAGAATCACGCCAGTGGA R 2 1 2 1 101000 f 74 goat snp5769-scaffold1203-298800 2 67379951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476169 Affx-1251763672 AX-586011596 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 4 1 4 1 20000 f 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 539476424 Affx-1251763672 AX-586011825 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 4 1 4 1 20000 r 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562165303 Affx-1251763672 AX-606940714 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 f 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562165597 Affx-1251763672 AX-606941008 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 f 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562165872 Affx-1251763672 AX-606941281 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 r 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562165907 Affx-1251763672 AX-606941316 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 f 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562166089 Affx-1251763672 AX-606941498 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 r 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 562166365 Affx-1251763672 AX-606941773 2 68029277 CTTATCAGTAGCCATAGCTTAGAGTTGAATCCAGC[-/CAATCTTTTTTTTTTTTTTTTTTTTTTGCCCTGTCTTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCTCT]AATCTGTTTTTAAATCTATGCCTGCAACCATGCTA - 8 1 4 1 20100 r 74 goat SV_311 2 68029277 - deletion junction SV-TF-chip 320771716 Affx-122925526 AX-385258873 2 68067133 GGTGCTCACATTGCCTTTTAAGTTGACTTTTAAGT[A/G]TATGTCTAGGCCTGTCTCATTTCATCATCTGTTTG R 2 1 2 1 101000 r 74 goat snp5770-scaffold1203-361635 2 67316229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416044 Affx-122948357 AX-123286393 2 68104760 TGCTGTCTTCTGGTCCAGCTGATTGAATTGCTACC[A/G]TAACTCTTACAACTTTTTCCTCCTCTTTTTACCTT R 2 1 2 1 101000 f 74 goat snp5771-scaffold1203-399262 2 67278490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272947 Affx-1111833178 AX-519546633 2 68106110 CAGGAAAAAATGATGGAAATAAAGAAAGGCAGTAA[A/C]GACAAAACAAATTGGAATATCAGTACTAACCAGAA M 2 1 2 1 101000 f 74 goat 2_68106110_AF-PAKI 2 68106110 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320764763 Affx-122931851 AX-385252376 2 68193798 TGACAGAAAAGGTGGCTTACACTCTGCTTTCTACA[C/T]TGGATTCTATGAAGGCACTTTATCTCAGAGATAAC Y 2 1 2 1 101000 f 74 goat snp5772-scaffold1203-488300 2 67188121 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277723 Affx-1111835990 AX-519551222 2 68270375 CTGATTTTAGTACTCTGAAAAATAAATGTATTTGA[A/G]TATATGGAATGAGTATACCTTTATCATAATAGCAA R 2 1 2 1 101000 r 74 goat Random2.2K-212 2 68270375 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381447 Affx-122974339 AX-123251805 2 68290722 ACCTTCTGAATAGAGAAAACATGGATTTGCTGATC[A/G]TAGTTCAGTGAACTGTATGTTGGCCCTCACACCTC R 2 1 2 1 101000 r 74 goat snp5774-scaffold1203-585224 2 67092459 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435908 Affx-122932767 AX-123306247 2 68325531 AAGGGTAAGGCCTCAGAAGGCTCCAGAAAGGAAAA[C/T]AACCTTTACCTTGAATTTTGCAGGGTTGATTCTGA Y 2 1 2 1 101000 f 74 goat snp5775-scaffold1203-620033 2 67057322 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440650 Affx-122929941 AX-123310987 2 68354969 CCTTGGCAGGGCTGTTTCTCTGCAACTGCTCTTCA[C/T]GGTGAAGCCATTTCTGAAAATGGCTCGGTTTAGCA Y 2 1 2 1 201000 f 74 goat snp5776-scaffold1203-649471 2 67027055 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399988 Affx-122960815 AX-123270343 2 68392864 TCTGGGGCCAGAAAGCATTACCTTTGGCACTACCC[A/G]CTACCTTGGTGCGCTGCTGCACCTGATGGACTTCC R 2 1 2 1 101000 f 74 goat snp5777-scaffold1203-687366 2 66989113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398268 Affx-122962178 AX-123268623 2 68493471 GACATTTCTGCCTCAGTTTCCCCATCTTGCAAAGA[C/T]GAGTAAATGATCACACCCTTATTGTGAGAATTGGG Y 2 1 2 1 201000 r 74 goat snp5780-scaffold1203-787973 2 66889063 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774559 Affx-122946885 AX-385261693 2 68547846 TCAATTAAGCTTTCTGTCTGCACTTTCTACTTCTT[A/G]TCAGTAACCTGACTGACTCTCTTCCTTGCCCCTTT R 2 1 2 1 202000 f 74 goat snp5781-scaffold1203-842348 2 66835438 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383286 Affx-122972719 AX-123253644 2 68571803 TATGTGACCGAAATATCTAATCCCTAAGGGAAATA[C/T]AAGAATTAAAATATGTAAAGCAATTTTTGAAAGGG Y 2 1 2 1 101000 f 74 goat snp2208-scaffold1067-793682 2 66812408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381119 Affx-122974578 AX-123251477 2 68610098 CCACAGTAGAATTCACTTCCCTGTTACTTCCTGTT[A/C]GTCATGGACAAGTGACTTGCTTTAGCCCACCAAGA M 2 1 2 1 101000 f 74 goat snp2207-scaffold1067-755387 2 66773833 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435994 Affx-122933502 AX-123306333 2 68645434 AATGAAAGATTTGAGGAAACTAGGGAGTGACATCA[C/T]AGCATAAAATAGAATGAATCATCAAGGATAGGCTG Y 2 1 2 1 101000 f 74 goat snp2206-scaffold1067-720051 2 66738708 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441151 Affx-122929567 AX-123311488 2 68679509 TTGATTTATTTGATTCATAGTCGTTTTCATCTGGC[A/G]TCCAAGGTCTGTAAATCACCACCAGGGGGCCCCGA R 2 1 2 1 101000 f 74 goat snp2205-scaffold1067-685976 2 66704034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426434 Affx-122940818 AX-123296780 2 68731290 AGGTCTGAAGCCCAGCACATGTCCAGCAAGGGGGA[C/T]GGTGGTCAAGCCCAGATGTGGGATAGTATCTTTCT Y 2 1 2 1 101000 r 74 goat snp2204-scaffold1067-634195 2 66651654 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407098 Affx-122954891 AX-123277449 2 68760463 TGAAACTGGGTTAAACCATTAGTCTGGGGATTCTG[C/T]GTTACTCAGTGTATCTTAGCTTATCCTGACAAATA Y 2 1 2 1 201000 r 74 goat snp2203-scaffold1067-605022 2 66622515 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406855 Affx-122955658 AX-123277206 2 68801803 GGGAGAGTCACATGGTGCCTTAACCTCTGCGATGA[C/T]GCACAATGTAAGTACCTGCCCATTCTCAGGACCAG Y 2 1 2 1 101000 r 74 goat snp2202-scaffold1067-563682 2 66580532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785408 Affx-122942358 AX-385272453 2 68840006 CTGGGAACACACCCATAGTTAGACAAGTTGGGCTT[A/G]TTACTGGTTGTAGTGAAGGAGACCACACAGCAGTG R 2 1 2 1 101000 r 74 goat snp2201-scaffold1067-525479 2 66542383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453233 Affx-122920422 AX-123323566 2 68878365 AATACATAGTATATACCCCTTAATCTACTAAGCTA[C/T]AACATCTAAAGAATTGTGAGTTCTGAAGCACATCT Y 2 1 2 1 101000 r 74 goat snp2200-scaffold1067-487120 2 66503797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769051 Affx-122938437 AX-385256226 2 68919385 TAAGCCAGATGATAGAATGGCGTTTTGACGTGGGA[A/G]TTGTGGAATGACTGACAATGTCTTTTGGTAACTGC R 2 1 2 1 101000 f 74 goat snp2199-scaffold1067-446100 2 66463045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777373 Affx-122929592 AX-385264495 2 68961673 AGTATAAAAGTCTGAATAATAAGCATCAGAGTTCT[C/T]ATTTGCTCACAGGAAACACATTTTCATAGAAAAAT Y 2 1 2 1 101000 r 74 goat snp2198-scaffold1067-403812 2 66420680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387933 Affx-122970027 AX-123258291 2 68999875 CAGAAAAGATGTTTGTTTTGCATTTTTAAATCAGA[C/T]ATTCACTTCATAGACACAGACACAGTCTAGTTACT Y 2 1 2 1 201000 f 74 goat snp2197-scaffold1067-365610 2 66382460 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785493 Affx-122961505 AX-385272538 2 69039446 TGAAAAAGAGGAATGAAGCATAAATTCAGGAGGTA[C/T]AATAGCCAATTAAGAAAAGTTACAAAAATGTAAGG Y 2 1 2 1 101000 r 74 goat snp2196-scaffold1067-326039 2 66343010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406351 Affx-122955433 AX-123276703 2 69093966 ATATAGATGTAATCACAGTGGACCAAGAGGACAAG[C/T]ACACGTTTTAGAAATGGTGGAGAAGTGAACAGAAA Y 2 1 2 1 101000 f 74 goat snp2195-scaffold1067-271519 2 66288260 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381619 Affx-122974775 AX-123251977 2 69136095 ATATTTCACATGGCAAGACTGTGGAAGGCCACAAA[G/T]ATCGTGGAAAGCCACACAGGCCAGAAGTGTCCTTT K 2 1 2 1 101000 f 74 goat snp2194-scaffold1067-229390 2 66245314 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405559 Affx-122955958 AX-123275911 2 69167683 CTCTCAAGAGTTTTCTCCAACACTACAGTTCAAAA[G/T]CATCAGTTCTTCATATAACAGGATGTAAATATAAA K 2 1 2 1 303000 r 74 goat snp2193-scaffold1067-197802 4 82560227 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442399 Affx-122927999 AX-123312736 2 69198245 ATCATTCGTAAGCACTTTCTTTCCTTCATTTTTCT[A/G]CAAGAGCAAATGAACTTCACACACAGAAGAAGGGC R 2 1 2 1 103000 r 74 goat snp2192-scaffold1067-167240 2 66182991 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389572 Affx-122968791 AX-123259930 2 69234218 GTTTTTGCTAAGGCTCTCACCCTCTGTTCCCATTC[A/G]TCCTCCACACAGACCTACTTCAGCACACCTTGCAT R 2 1 2 1 201000 r 74 goat snp2191-scaffold1067-131267 2 66146801 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793468 Affx-122938031 AX-385280445 2 69269215 AACCCATGGACAAAGCACTTAGCACGTAATAATAA[C/T]TACAGAAAAGAATATCAATGCCAAAACCTTGATAC Y 2 1 2 1 201000 r 74 goat snp2190-scaffold1067-96270 2 66111043 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277730 Affx-1111835993 AX-519551229 2 69300503 ATGGGCATCAAAAAATATCCCTCAATCAATTACAA[A/G]TCACAGTGGTCCTTGAATTCAAGCATGCATCAGAA R 2 1 2 1 101000 r 74 goat Random2.2K-213 2 69300503 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432641 Affx-122935474 AX-123302982 2 69303854 TGATCTTTCCTGGTACCCAGGAGAAGCTCAGTAAA[C/T]AAATGAATGAGGCTTGACATCACCTGACAGTTCTA Y 2 1 2 1 101000 f 74 goat snp2189-scaffold1067-61631 2 66075722 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773723 Affx-122974716 AX-385260863 2 69360775 GCTAGGAGATGCACCATCCACAAAAATTTATGTAG[C/T]ATTTCTCACAGGTGGTGCCAATGCTCCAGCCTCAT Y 2 1 2 1 101000 r 74 goat snp2188-scaffold1067-4710 2 66019056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406377 Affx-122955409 AX-123276729 2 69387190 CCTAGATTGCTACATACCCCTGGACCAAATCCCCC[A/G]TGCAGCAGGACATCAACAATTAATAAGTTTTAAAA R 2 1 2 1 201000 r 74 goat snp7023-scaffold1259-670446 2 65983307 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418686 Affx-122946305 AX-123289034 2 69430770 ATCCAGGTATTTGCTCTTAGTTTTGTTTTTCCTCT[A/G]CAGGTATAGATGCATCTTTCTTGGTCACAGATTTG R 2 1 2 1 101000 r 74 goat snp7022-scaffold1259-626866 2 65939605 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425355 Affx-122941583 AX-123295701 2 69490482 TTTTAACAAGGAGACAGTGAACTCTAGGCTCAGAA[C/T]CTTCAGCAGGAAATGTCAATACTAATGGTTAACTG Y 2 1 2 1 101000 r 74 goat snp7021-scaffold1259-567154 2 65879215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402945 Affx-122958175 AX-123273298 2 69575303 GGAAAATAGAGGCTGCCTTTTGCTGGGCGGAACAC[A/G]CTGCACATACAAGAATGGCAAGATTGCTGGTGACC R 2 1 2 1 101000 r 74 goat snp7019-scaffold1259-482333 2 65793662 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412444 Affx-122951413 AX-123282793 2 69604325 CCAGATTCACTCAGGCGGAGGCCTCGGTGATTTCC[A/G]CTTCTACTTTGGTGTTCCTGCTTTTTCTTGAACGT R 2 1 2 1 101000 r 74 goat snp7018-scaffold1259-453311 2 65764664 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377096 Affx-122978266 AX-123247455 2 69639845 CCACTCCCACCACAGAATGGAGAGAAAAACAGGGA[C/T]GGATGGAGAAGGTTCTATGACTCAGTGTTCTTGAT Y 2 1 2 1 101000 r 74 goat snp7017-scaffold1259-417791 2 65728563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277743 Affx-1111836000 AX-519551242 2 69661318 TATTACACCTAGCTTTTTAAAAGTTATGTGAAATC[A/T]GATCTTTAAAGACTCTTTTTGGCTACCTCAATGTC W 4 1 2 1 201000 r 74 goat Random2.2K-214 2 69661318 T A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785733 Affx-122926046 AX-385272774 2 69679386 TTTTGAAACTTTCTGTTAGACACTAGACATTGTTA[A/G]TTGCCTATTAAATGACCATCAGCTTTTTTCCTCTT R 2 1 2 1 101000 r 74 goat snp7016-scaffold1259-378250 2 65688851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384531 Affx-122973033 AX-123254889 2 69713409 CTGAGTCTGGAATCTGTTCTGATAAAATCTGTTAC[A/G]AAATCAGGACATTCTGCTTTGGAGTTTTCCAAAAT R 2 1 2 1 101000 f 74 goat snp7015-scaffold1259-344227 2 65654524 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800643 Affx-122923844 AX-385287562 2 69751256 GAATCACTGGAAAGCGTTAAAAAAGAACATAAAGC[A/G]TATATTGGAAGGGCCAGTAGAGGCCTGTAATTAAC R 2 1 2 1 101000 r 74 goat snp7014-scaffold1259-306380 2 65616915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411091 Affx-122951925 AX-123281441 2 69799239 GAGGAGTTTTTGATCTCAGAAAATGTCATTTGAGG[A/C]TGTGAATTAGGGCAGGAGGGAGAAAAGGGGCTTCT M 2 1 2 1 201000 f 74 goat snp7013-scaffold1259-258397 2 65568639 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453904 Affx-122919497 AX-123324237 2 69862032 ACCACATTGTTAACAAACTATACTCCAGTATAAAG[C/T]AAAAATTTTAAAGAAGGATTAATACCAAGTATAGG Y 2 1 2 1 103000 f 74 goat snp7012-scaffold1259-195604 2 65507038 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780500 Affx-122952111 AX-385267591 2 69904771 AGCAAAAAATAAACTTTGGTTGGGTTAAGGCATAG[C/T]GATTTCACTATCAGTTTTTTACTGTATGACCTGGC Y 2 1 2 1 101000 r 74 goat snp7011-scaffold1259-152865 2 65463691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272452 Affx-1111834269 AX-519546178 2 69924229 ATAAAACTGCAGCTGTAGTGTGTAACAGATGAAAT[A/G]AGGTCTGTATTTCTCAGATGTAACAGAGCCAAGAG R 2 1 2 1 101000 r 74 goat GoatD01.028299 2 69924229 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320773136 Affx-122949083 AX-385260279 2 69955025 ATCTTGTACAGTTTTTTCCTAAGTCCCACTCAGAC[A/G]CTTTTATCTCCAGAACACAGATCTGGCTGTTACTT R 2 1 2 1 101000 f 74 goat snp7010-scaffold1259-102611 2 65412105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405129 Affx-122956966 AX-123275481 2 69989844 GTTCAGGAAGTCACTTTGAGATTCAGATGGGAGAG[A/G]TGACCCCTCCTCTCTGTTTCAGGTTGGACCTGCTC R 2 1 2 1 101000 f 74 goat snp7009-scaffold1259-67792 2 65377471 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394134 Affx-122965325 AX-123264489 2 70035830 CTGAGTTCTGTACTTCCTCCAGAGCCCATATTTCC[G/T]CTTTCTCATACGTACTGGTCTGGAGTATCCTTTGA K 2 1 2 1 101000 r 74 goat snp7008-scaffold1259-21806 2 65331443 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433259 Affx-122935233 AX-123303600 2 70075677 ACTGTGTAAGGGCAGCACAAGCATAGTAAATGTGC[A/G]TTATGGGGAAGGGAAGGTGAGCCTTGAAAAATGAA R 2 1 2 1 201000 f 74 goat snp50895-scaffold739-17942 2 65291372 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432910 Affx-122935319 AX-123303251 2 70107799 GGTACCCCTCTCTACTCACATGCCAATGTAACAAG[C/T]GCTACTTGAGCACCTGCTGTCTGCACAGGCCTGCC Y 2 1 2 1 101000 f 74 goat snp50896-scaffold739-50064 2 65259090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424424 Affx-122941803 AX-123294770 2 70165000 TCAGACATCTTAGACTTGGGCTTCCCTCATGGCTC[A/G]GTGAAAAAGAATCCGCCTGCCAATGCAGGAGACAC R 2 1 2 1 103000 f 74 goat snp50897-scaffold739-107265 2 65201626 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392477 Affx-122966148 AX-123262834 2 70266783 CGTTTAAAATCTATGCTATTGAAACTGCGTGTTTT[A/G]TTTTTACCTTGAGGAGCTTGTCTGAGAAGCAGCAA R 2 1 2 1 201000 r 74 goat snp50900-scaffold739-209048 2 65085810 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275074 Affx-1111834582 AX-519548655 2 70298542 ATTTTTTAAAAATTCTGTTTCACTGCAGGTATC[A/G]AGGAAAATCCCTTCCTATAAGGGACTGCATTCCAG R 2 1 2 1 101000 r 74 goat GoatD01.042215 2 70298542 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447115 Affx-122924472 AX-123317451 2 70322777 TTCATATCAAAGCTGTGTGCAGCACAGCAATTGTC[A/G]TCCAAGAAAAGAGGCTGAGAAATGTGTCCTGACTG R 2 1 2 1 202000 r 74 goat snp50901-scaffold739-265042 2 65029503 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375415 Affx-122979196 AX-123245774 2 70390078 TGGAGGCCCTGACAACCTATGTGTTCCGAACCAAG[C/T]GAGTCCCAGTTGCAAACTGTAAAGAAATTTTTTTC Y 2 1 2 1 101000 r 74 goat snp50902-scaffold739-332343 2 64961307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433409 Affx-122935096 AX-123303750 2 70438795 GGTCATTTACAGGAGAAGTTTGAGAATCACATGAA[C/T]AGCCAGGAAATATATCAGAGTTGGAAAATGCTGCG Y 2 1 2 1 101000 f 74 goat snp50903-scaffold739-381060 2 64911682 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277628 Affx-1111836007 AX-519551127 2 70454143 GGGGCTGGAATCCTGTCTCGCTCGTGGAATCCCCA[A/G]CATGTGGCCCGTGGCCTGCTGGCATATAGTAGGCT R 2 1 2 1 202000 f 74 goat Random2.2K-215 2 70454143 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785041 Affx-122973833 AX-385272088 2 70492831 GTCATCCATTATACATGTGATCCTTCTGAATCTTA[C/T]GGACTTTACAAATGTGATCCATATAAGCCTCCTGT Y 2 1 2 1 101000 f 74 goat snp50904-scaffold739-435096 2 64857563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428829 Affx-122938373 AX-123299171 2 70526170 ATGCAGGGCCTGGTGAGACTGATGCGAGTAGGGAA[C/T]GGGTGAGAGCCAGGGTGCTGCAGGCTGAGGAACGG Y 2 1 2 1 101000 f 74 goat snp50905-scaffold739-468435 2 64824467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425420 Affx-122941535 AX-123295766 2 70575971 AGACTTGATGCTTTTGACTTAATGGCTTTTCCCCA[A/G]CTTTTAATGACACAAGCTGCCCACACTGTGTTCAG R 2 1 2 1 201000 r 74 goat snp50906-scaffold739-518236 2 64775729 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764374 Affx-986696789 AX-385252086 2 70651049 TGTAATGCACTTGAATCATCCTGAAAGCAAACCAC[C/T]CCCCACCCCGAGTCCATAGAAAAACTGTCTTCCAT Y 2 1 2 1 600010 r 74 goat 2_70651049 2 70651049 Ancestral_priority_1043 ancestry 0.55 neutral IMAGE 10K 10K ancestral 38413858 Affx-122949863 AX-123284207 2 70674112 CCAGCAACATCCAGGCTCCACATCAGCCACTCCTC[G/T]ACCCAGGTGCAGAACCCTCCTTCCTGAGTCCCACC K 2 1 2 1 201000 r 74 goat snp50908-scaffold739-616377 2 64676775 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272949 Affx-1111833179 AX-519546635 2 70741104 GCTGATTGCTGCCAACTTCATTTCTTAGACTCACT[A/G]GCCCATGCCAAAAAAGAATTAGGATAATGAAAGAT R 2 1 2 1 101000 f 74 goat 2_70741104_AF-PAKI 2 70741104 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38419822 Affx-122945827 AX-123290170 2 70885459 GCTCTAAGATAGTACCCAACTCCCAACCACATTCT[A/G]TCCTTTGTTCCTTCTCTTATGACAAATATCTGGAG R 2 1 2 1 101000 f 74 goat snp50911-scaffold739-827724 2 64464441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417480 Affx-122947174 AX-123287828 2 70914765 ATTTCTTTTACCTTATTTACTTGTTTGTTTTCACA[C/T]AGTAGTGCAGAGCTATAAAGATAACCATGTGGCCT Y 2 1 2 1 101000 r 74 goat snp50912-scaffold739-857030 2 64435110 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397795 Affx-122962500 AX-123268150 2 70949333 GACAGATAGTTTGTTTTTTATTCTCAATATTTTGG[A/G]CAGGTAAAACCACTGAGCCCTACTCTGACCTATAG R 2 1 2 1 101000 r 74 goat snp50913-scaffold739-891598 2 64402682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421514 Affx-122943892 AX-123291861 2 71032432 GCTTTATGTATTAACTAACCCCTAGTTTAAATCCA[C/T]GTAGTAGGAGTTTTAAGTAGTCTTTATCCAGCAGC Y 2 1 2 1 101000 r 74 goat snp50914-scaffold739-974697 2 64319017 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277654 Affx-1111836019 AX-519551153 2 71181491 AAAATGGCTTGGCTTGAAATAAATGCTTAGATATT[A/G]ATACATCTTTTTACTTCACAATTGGGGTGAATTAT R 2 1 2 1 101000 f 74 goat Random2.2K-217 2 71181491 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424687 Affx-122941705 AX-123295033 2 71196688 CACCCAACCACTGAGGCTACAGTTTTTTTGTTTAC[A/G]TGTAGACTTGGCAAATAAATAAACTTACTTTACCT R 2 1 2 1 101000 r 74 goat snp50916-scaffold739-1138953 2 64156446 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396774 Affx-122962767 AX-123267129 2 71301416 CGAACCCTTCCTCTAGACCTGGTCTTACTCCCTGG[A/G]AGGAAATGAGGCCCCTGAACAATCACTTCATGGCT R 2 1 2 1 201000 r 74 goat snp50918-scaffold739-1243681 2 64051966 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798739 Affx-122958102 AX-385285670 2 71341027 GTAGGTTTAAGGGGACCTTTCCCACGAATAGTATA[A/G]TATAAACTTTCCCCTATGCAGCTGAATATTCTGTC R 2 1 2 1 101000 f 74 goat snp50919-scaffold739-1283292 2 64011775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790553 Affx-122979165 AX-385277556 2 71369877 TGGCCCCAAGAAGGATGTGAGGAAGGTTATCTGAA[C/T]GGGAACTCACCCATTGCTGGGCAATTCAACAAGTC Y 2 1 2 1 101000 r 74 goat snp50920-scaffold739-1312142 2 63983334 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438707 Affx-122930855 AX-123309044 2 71401866 CTACCCTGTTCTTTCTGTGTCCTGACCAGAAGCAG[C/T]GCTCCTGGGATACAAGGTGCCCACTGCCTTGGGAT Y 2 1 2 1 101000 f 74 goat snp50921-scaffold739-1344131 2 63951421 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410858 Affx-122952610 AX-123281208 2 71444302 GGTTGTTATCTCTGGGAAAGAACTTGCACTCCCCC[A/G]CTTCCTAGATGCGAGTCCTTGGGAGGCTACTAGGC R 2 1 2 1 201000 r 74 goat snp50922-scaffold739-1386567 2 63909121 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426444 Affx-122940810 AX-123296790 2 71515777 CTGTAAGGCTAAACTCGCCATCACCTTGGTTGCCT[A/G]CTGGAACCACTGGATCCCAGAGGCTGTGAGCTGGC R 2 1 2 1 101000 f 74 goat snp50923-scaffold739-1458042 2 63842159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443620 Affx-122927300 AX-123313957 2 71554889 AGAGATAAAGATACCGAAGGGAAGGGGGTCAGGAT[A/G]GGGAAGATGAACTATCTATAGGCTGTGAAAATGAC R 2 1 2 1 101000 r 74 goat snp50924-scaffold739-1497154 2 63802470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408177 Affx-122954202 AX-123278528 2 71613938 AGGAGACATTAGCATCTTCATCTTAGAGATAAGGA[C/T]ATTGAGGTTCAGAGAAGTTAAGTACATTGCCCAAA Y 2 1 2 1 201000 f 74 goat snp50925-scaffold739-1556203 2 63742595 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783461 Affx-122973085 AX-385270524 2 71647037 GTAGAAACAATGGCTAAAAGCATACATATGTGCAC[A/G]TGCACACACATGGGCACTCGCAACAGCAGAAGGCA R 2 1 2 1 102000 r 74 goat snp50926-scaffold739-1589302 2 63709602 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398505 Affx-122961556 AX-123268860 2 71680370 AGAAGACCCTGGTTCAATTCCTGGGTCTGAAAGAC[A/C]CAGGTAGGTTTTGTTATTAGGTACATAGTTGTTAC M 2 1 2 1 201000 r 74 goat snp50927-scaffold739-1622635 2 63676472 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432089 Affx-122936485 AX-123302430 2 71709679 ATACATCCAACAGTCAAAATGAGTCTAGTGATCAC[A/C]CATAAGTTTCTTTATGTTTCTTTGTTATCCATTCC M 2 1 2 1 101000 r 74 goat snp50928-scaffold739-1651944 2 63647095 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420385 Affx-122944937 AX-123290732 2 71787531 CGCGGTAGCTGCCCAAGGAGGTACTTGCTGTTCAA[C/T]GCACTTGGCAGGGGAGGGGGGTGTTTTTCATGAGT Y 2 1 2 1 201000 f 74 goat snp50929-scaffold739-1729796 2 63569262 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420371 Affx-122944947 AX-123290718 2 71836233 CGCTTCTGGGCCGATGTGGCTTGTTTCACCACTAA[C/T]GAACTGGGAGCTTCTGTTTCCTGATTTGAGTTATG Y 2 1 2 1 201000 f 74 goat snp50930-scaffold739-1778498 2 63520783 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400281 Affx-122960118 AX-123270636 2 71869010 CATCTAGGAAAAATTATTTGGGTAGGGATGGCTAC[A/G]TGAAAGTGTTGACTGAGCCTGAGTCCCTGATGGGA R 2 1 2 1 201000 f 74 goat snp50931-scaffold739-1811275 2 63488287 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435731 Affx-122933292 AX-123306070 2 71916786 ATAGCCGAGGTCTCTTTTCTTGGTTTTAATGACTC[C/T]AAGACCTGAGCCCTTGCTACCGTGTCCCTTTTGCT Y 2 1 2 1 101000 f 74 goat snp50932-scaffold739-1859051 2 63440697 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394051 Affx-122964986 AX-123264406 2 71959246 TGAATGAATGAGTAACTGAATGACCCAGAGAGGGC[A/G]CATTGTGAGTTCAAGGAGGGCTGGAGCTGTGTCCC R 2 1 2 1 201000 r 74 goat snp50933-scaffold739-1901511 2 63398419 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387893 Affx-122969618 AX-123258251 2 72001345 TGTTTAGATTACTGGTACAGGGTGACCCTGAAAAG[C/T]GGAGCAACTCAATCTGTTTTATCATTGTTTTTATA Y 2 1 2 1 101000 r 74 goat snp50934-scaffold739-1943610 2 63359612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419464 Affx-122945485 AX-123289812 2 72032730 AGCCAAGAGTCTGCCCTCCCCTGGGGGCTCCACTG[C/T]ATGGCTGTGTGGAGGCTCCTGACAGTGTTCTCCCA Y 2 1 2 1 103000 r 74 goat snp50935-scaffold739-1974995 2 63328166 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401342 Affx-122959261 AX-123271695 2 72061814 CCAGGAGCCAGCGCACTTATATCCCCCAGATGTGA[C/T]CTCTGGAATTTCTGTGATTTATCACCGACCAGGAA Y 2 1 2 1 101000 r 74 goat snp50936-scaffold739-2004079 2 63299561 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382859 Affx-122973527 AX-123253217 2 72094564 CTTGTGGCTTCACATTTATCATCTAACCCCTCGAA[G/T]CCTCTCAAAAATCCTGCAAAGCAGAAATGGTCATC K 2 1 2 1 201000 r 74 goat snp50937-scaffold739-2036829 2 63267006 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387628 Affx-122969861 AX-123257986 2 72125759 AAATGACCAATAGCATCCAAAGCCTGGTCTGGGAG[A/G]TGACATGGATAATCAATCAGAGCTTGCTATTTTTT R 2 1 2 1 201000 r 74 goat snp50938-scaffold739-2068024 2 63235752 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411438 Affx-122951823 AX-123281788 2 72158779 AACTGGATGGGGTCTACTTCTGTGTAGGAGGAAGC[A/G]TAAGGAGGCAACTGGACCTCCAGTGGCCCACAGTC R 2 1 2 1 101000 f 74 goat snp50939-scaffold739-2101044 2 63202379 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277681 Affx-1111836033 AX-519551180 2 72222414 TCATTCCTTGAGCTGATTTTTAAGAAGTCAGGGAA[A/G]GCAGGTTTGGAAACCACAAGTAGATTAGAGTAGTG R 2 1 2 1 201000 f 74 goat Random2.2K-219 2 72222414 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38404402 Affx-122956784 AX-123274754 2 72233077 TGTCTGTAAAATCCTCTGCTTGCTACACGGTATGA[C/T]AGTAAAGCCTGTTCTAATTTCAGAATTGTGAAATG Y 2 1 2 1 101000 f 74 goat snp50940-scaffold739-2175342 2 63127711 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419972 Affx-122945191 AX-123290320 2 72275030 CTGTGAGTCCTCTGTGGATCCTATTTGAGCTGGGG[A/G]GCTGAAATGTATACTCACACTGATCAGTCATGGAG R 2 1 2 1 101000 r 74 goat snp50941-scaffold739-2217295 2 63085795 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449461 Affx-122922656 AX-123319796 2 72354575 TCTGTATCAGTGAGGAGTTAGAATACCAGAATACT[C/T]AGGCAAGGATAAAAACTGGGTTATATTTATCATCA Y 2 1 2 1 101000 r 74 goat snp50943-scaffold739-2296840 2 63005515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405352 Affx-122956323 AX-123275704 2 72383398 TTTTCTGATTAACGTTCCTACCCCCAAAGTGAACA[A/C]GTTTACCTTTCTAAATGTTATCATGATTTTACTTT M 2 1 2 1 201000 r 74 goat snp50944-scaffold739-2325663 2 62976401 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775317 Affx-122935459 AX-385262448 2 72433384 TCAGAGTCTGTCCTCAAACAGCTTGTAGTTTTAAC[A/G]GCTCATCACAAATTGTTCACACTCATTGCAGACGT R 2 1 2 1 101000 f 74 goat snp50945-scaffold739-2375649 2 62927005 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378806 Affx-122976560 AX-123249165 2 72473660 CCTGTGTATCTCAATATTCTGCCCCAGATGGAGAT[A/G]CCCAATACTCTGCAAGCTCATCTGTGGAATGGATA R 2 1 2 1 101000 r 74 goat snp50946-scaffold739-2415925 2 62886830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429220 Affx-122937928 AX-123299562 2 72504593 TCCAAGTGGCAGACAGAGCATAAATAGGCTTTGGA[A/G]TCAGACAAAACTGGGTTCAAAACATGGCACCACCG R 2 1 2 1 201000 f 74 goat snp50947-scaffold739-2446858 2 62855907 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444951 Affx-122926684 AX-123315288 2 72552910 ATCTCACTCCCCTTTGAGTCTGGATTAAATTCCAC[A/G]TGGGCGTTAATAGCATGGCACTACCCTCCACTGTC R 2 1 2 1 201000 r 74 goat snp50948-scaffold739-2495175 2 62805125 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447439 Affx-122924378 AX-123317775 2 72614430 CAGTTTCTAGACACATGGAGCCTCTGGGATGATCA[C/T]TGAGCAGCTACCTCCACGCTCTGCACAAGGGACTT Y 2 1 2 1 201000 r 74 goat snp50949-scaffold739-2556695 2 62743242 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384044 Affx-122972883 AX-123254402 2 72662391 TTCATCTGACTGCCTTGTCGGCAGACTTGTGTCTT[A/G]CTCATCACTCAATGCCAGCCTCTTGCACTAGTGCC R 2 1 2 1 201000 f 74 goat snp50950-scaffold739-2604656 2 62695143 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383232 Affx-122972760 AX-123253590 2 72691503 AGCGTCGATGAAATCAATACAGAAAAAGTGCTCTC[A/G]TTATCCAGACCTTCTTGCTGTCCAACCTAGAGACT R 2 1 2 1 201000 r 74 goat snp50951-scaffold739-2633768 2 62665972 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399829 Affx-122960261 AX-123270184 2 72723206 GATAGTAACAATTTTAGGCTTTGCAGGTCAGGAGA[C/T]GAAATCAAGCAAGCCTAAAGATTTTAAACCCCCAA Y 2 1 2 1 201000 r 74 goat snp50952-scaffold739-2665471 2 62634414 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764386 Affx-986696795 AX-385252095 2 72762561 CCGAGGGGGCGGGGACTCGTCTGACTACGGGAGCC[A/G]AGAGGCCCCTTCGTCTACTGTTCGAGCGTTTCCTT R 2 1 2 1 600010 r 74 goat 2_72762561 2 72762561 Ancestral_priority_1043 ancestry 0.5 neutral IMAGE 10K 10K ancestral 320764389 Affx-986696797 AX-385252098 2 72765215 GGATCCAGTAGCTGCGGGATGGCCACCCTGTCTCC[A/G]TATCATCGCGGCCATTGCTCTCCTTGTCCATGATG R 2 1 2 1 600010 r 74 goat 2_72765215 2 72765215 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 38404973 Affx-122956408 AX-123275325 2 72767314 TGCCTGATCCTCCAATTATGCTGTTTTTGACATAT[A/C]CTTTCCTAATATTCCTGAGAACATCAGACTTAAGA M 2 1 2 1 201000 f 74 goat snp50953-scaffold739-2709579 2 62590230 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423099 Affx-122942922 AX-123293445 2 72813170 CTTTAGGATGGGGAAGATGGAGGGAAGGTGGAAGA[C/T]GAGGTTATGGGGCAACAGGGAGACAGGAAGGGGTC Y 2 1 2 1 103000 f 74 goat snp50954-scaffold739-2755435 2 62543550 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377928 Affx-122977223 AX-123248287 2 72860745 CACGGGAATTCCTAGGATATATTTTGAATCATAAA[C/T]GATACAGTTTTGGGGACAGACTGGATGGGAGTGTG Y 2 1 2 1 201000 f 74 goat snp50955-scaffold739-2803010 2 62495384 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419091 Affx-122945788 AX-123289439 2 72893150 TCAGTGATATTCATTGAACACACACTGTGGTGCTC[A/G]GCTGTGCGCAAGGCTTCAGGGTCTCCACTGGGTGT R 2 1 2 1 202000 r 74 goat snp50956-scaffold739-2835415 2 62462627 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442073 Affx-122928377 AX-123312410 2 72939737 AGCTCTCTGGGAGAGCATACTGATCTTATCTCAGC[A/G]CTGCTCTTTGTCCACCTGGACCTCTCGATTTCCCA R 2 1 2 1 101000 f 74 goat snp50957-scaffold739-2882002 2 62415399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428938 Affx-122938895 AX-123299280 2 72979788 TAGGAGATCCTTTAAGTGAAGTAAGGGAAGAGATA[G/T]ACTGGATTATATTGTACCCTCTTCAACAGATGTTG K 2 1 2 1 101000 f 74 goat snp50958-scaffold739-2922053 2 62372366 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451555 Affx-122921705 AX-123321888 2 73040794 GCAGTCATGGCCAAAGACTCTTCCTGATCACTCCT[C/T]CATCTCAGGGACATGAAATGCAGAAGAATGAGTGC Y 2 1 2 1 201000 r 74 goat snp50959-scaffold739-2983059 2 62311273 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434620 Affx-122934008 AX-123304961 2 73095009 TCTCTAATAAATAATAAAAGAAAAGGGCTTGTGCT[A/G]TTCATCAGGTTTGGCCTCTGGCTTTTTGTCCCTTA R 2 1 2 1 101000 r 74 goat snp50960-scaffold739-3037274 2 62257081 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773162 Affx-122961382 AX-385260305 2 73139265 TTTATACATGTATTCACTCCAGTGATAAATACTTT[C/T]AGGGCTTACTCCACTGCACTTTTATACAGTGGTTT Y 2 1 2 1 101000 r 74 goat snp50961-scaffold739-3081530 2 62214684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380376 Affx-122975340 AX-123250734 2 73194831 GTATGGTCGTGGAGATATGAGCTCTCTGGAAAAGA[C/T]GAAGGATTTCATGTTTGAAATATGTGTAGTTTCTT Y 2 1 2 1 101000 f 74 goat snp50962-scaffold739-3137096 2 62161334 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450077 Affx-122922799 AX-123320412 2 73224983 TGATTTGATTCTTCTACTGTCTGGTGGCTGTAATC[G/T]AGGAGAAAGATCCTTGCATGCCCCTGGGAGGACAG K 2 1 2 1 101000 f 74 goat snp50963-scaffold739-3167248 2 62131096 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426044 Affx-122941108 AX-123296390 2 73254115 AAAGGGCAACATCCCTAATTAAGAATAATGTGCAT[A/G]TGGGTTGGGGGAGGAGAAAATCCTGGGTAGGAGAG R 2 1 2 1 201000 f 74 goat snp50964-scaffold739-3196380 2 62101714 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395096 Affx-122964166 AX-123265451 2 73307257 ATTGATTGAGCATGTACTAAGTGCCAGAAACTCTC[A/G]TGAAACTTGCATTTATGTCAGACAGTGATAGGATG R 2 1 2 1 202000 f 74 goat snp50965-scaffold739-3249522 2 62048346 G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427743 Affx-122939256 AX-123298086 2 73338241 GTGGCTAAACAACAACAAGAAATGTAGGTCTCACC[A/G]TTGTAGTATCTCAGGCCACTTACTGAATGCTAGTG R 2 1 2 1 201000 r 74 goat snp50966-scaffold739-3280506 2 62016888 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396812 Affx-122963285 AX-123267167 2 73370160 TTAAAAAGCACAGAACTAGATTCCAGTTTATGGAA[G/T]CCTTGTTTCCTGTGCTGTGCTTTGCTTAATGTGCA K 2 1 2 1 303000 f 74 goat snp50967-scaffold739-3312425 2 61985992 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442290 Affx-122928256 AX-123312627 2 73417551 ACTGGTGGCCAGCATATTTGCAGCATCTGGGCTTG[C/T]ACATTTCTCACCAAAAAGACTTATTCTGAAAATTT Y 2 1 2 1 101000 f 74 goat snp50968-scaffold739-3359816 2 61937811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464149787 Affx-1110336939 AX-515625459 2 73434957 CCCTGAGTGTCTCCCTGTCTGACAGGAAGTCTGGC[A/G]TCACTAGGGACAGACTGCTAGCCGTCCACACCCAA R 2 1 2 1 202000 r 74 goat 2_73434957_AF-PAKI 2 73434957 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320782184 Affx-122930990 AX-385269262 2 73448426 GCTGATTCTATGAATCTCAAATGCTCTTTCATCAA[C/T]GTACTTTCTTTAAAAGTCTGGTCAAAAAAATATTG Y 2 1 2 1 101000 f 74 goat snp50969-scaffold739-3390691 2 61906773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441062 Affx-122928916 AX-123311399 2 73481464 TCAGAGACAGAAAAACTCAAATAACATCCAATACA[C/T]AGATCCAACTAGGAGGAAACAGAGTGTCCCTTAGG Y 2 1 2 1 201000 f 74 goat snp50970-scaffold739-3423729 2 61873515 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390101 Affx-122968019 AX-123260458 2 73525128 GATGGTGATGCTGGCAGAACAACCAGTTGGTGCCA[C/T]GAATATTTTTGAAAATGTTATTTTTAAGGCAATAT Y 2 1 2 1 101000 f 74 goat snp50971-scaffold739-3467393 2 61829352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385846 Affx-122971001 AX-123256204 2 73559972 TCAGTTTCATCAGCTGTCCAGTCGAGAGCTTATAA[C/T]GAGCTATTTGGAGACAATTCTCATCGGATTTCTCA Y 2 1 2 1 101000 r 74 goat snp50972-scaffold739-3502237 2 61793750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405624 Affx-122956600 AX-123275976 2 73589011 CAGATTTTGAGGGCAGAACATGAGGGCTGGTTGCA[A/G]TTTTAAAATATAACAGTGAAGCTATATCTCATGGA R 2 1 2 1 303000 r 74 goat snp50973-scaffold739-3531276 2 61764236 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405422 Affx-122956274 AX-123275774 2 73637216 GCTGAGGAAGGTGGCCAGGGGCAAGTGAAAACACC[A/G]CACAACTTTCCTATTATTTTTAATTTTTCTTCTTG R 2 1 2 1 103000 f 74 goat snp50974-scaffold739-3579481 2 61715599 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385611 Affx-122971193 AX-123255969 2 73666511 TAAAATCTTGCTAAAATATTTAAATCAAGCCTCCA[G/T]AACTCCACTGCCCTGCCTTATGGAGAAATGAAACA K 2 1 2 1 201000 f 74 goat snp50975-scaffold739-3608776 2 61686696 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789460 Affx-122923482 AX-385276470 2 73699729 AGGCCCATCTGATGATATTCAAGGTTATCAGAGTT[A/G]TCAAATCTGACAGGCTAGAATCAGATTCTACTTCT R 2 1 2 1 101000 f 74 goat snp50976-scaffold739-3641994 2 61653519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444689 Affx-122926439 AX-123315026 2 73735978 TTCTTGTACTCTTTACTATAACAACAATGGAGTAT[A/G]CATTATTTTATAAATGAGGAATTCACACATTCCTG R 2 1 2 1 101000 f 74 goat snp50977-scaffold739-3678243 2 61616437 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395386 Affx-122963969 AX-123265741 2 73784262 TGAAGTTTTTTTAAAAGGGAAAAGGAAAACCTGAA[C/T]TTTGGCTACTGGACACGATTTTAAATAGTGGAGGG Y 2 1 2 1 101000 r 74 goat snp50978-scaffold739-3726527 2 61568062 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779376 Affx-122925229 AX-385266480 2 73824119 ATAGCACTGAAGAAGACAAACAACAGCATTATACA[A/C]AGTCTCCATAGCACAATACCATTTATATAACCTAA M 2 1 2 1 201000 r 74 goat snp50979-scaffold739-3766384 2 61530481 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415980 Affx-122948409 AX-123286329 2 73854331 AGAGTCTTCATGCATGTTTGTGTTGGCTGGAAAGG[C/T]AAAAGAAAGTTCTGGGGAGCAATGACAAGTGTTAG Y 2 1 2 1 101000 f 74 goat snp50980-scaffold739-3796596 2 61500541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442886 Affx-122927655 AX-123313223 2 73908515 TGAGATGGCCATTCCCCAAAACAGAAATAACATCT[A/G]CTAAATTCATGGGTTACAAGTGTGAGAGGACTGAC R 2 1 2 1 101000 r 74 goat snp50981-scaffold739-3850780 2 61446673 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782646 Affx-122929483 AX-385269718 2 73945811 AAAAGAGATGTGTGAGTCAGCTCATATACAAACAC[C/T]ATTGCCTTGACCTTGATTTAGACTTCACTACTGTT Y 2 1 2 1 101000 f 74 goat snp50982-scaffold739-3888076 2 61409473 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794981 Affx-122920156 AX-385281941 2 73975159 TTATCTCTTATCACAACTTTTAGACTCTGTATATC[A/G]TACTTCTTATAGGTAGGACCCTTTGTTTCAGCTGC R 2 1 2 1 101000 r 74 goat snp50983-scaffold739-3917424 2 61381941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422481 Affx-122943319 AX-123292827 2 74028245 ATAAAACAATTATGAAAGATAGAATGGATTGGTTT[G/T]CCAACAAGCAATGTCTCTTTTAGTTTGGTTTAACT K 2 1 2 1 101000 r 74 goat snp50984-scaffold739-3970510 2 61330100 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779227 Affx-122976522 AX-385266331 2 74079151 TTTTTGTTAGTATGTTCACCCTTTTATTAGAGATT[A/C]TCTGTTACTCTGTTCATGCATTTCTTGGGTATCAA M 2 1 2 1 101000 r 74 goat snp50985-scaffold739-4021416 2 61278699 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418085 Affx-122946602 AX-123288433 2 74193632 GCATTGCTTCCTTCATTCATTCACTCAGAAATATT[A/G]CTTGAGTGACAATTACATGGCAACCATTATGTTAG R 2 1 2 1 101000 r 74 goat snp50987-scaffold739-4135897 2 61162780 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434839 Affx-122934381 AX-123305180 2 74222312 TTCAAAATTTGCCCAATTCTCTTTTCAAATCTCAC[A/G]TTAACTACAGAAACTATTAAAAAAAATGTGGCTCC R 2 1 2 1 201000 f 74 goat snp50988-scaffold739-4164577 2 61132999 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421142 Affx-122944191 AX-123291489 2 74255050 AGGCTATAGTCCACGGGGTCACAAAGAATTGGACA[C/T]GACTCAGTGACTAAGCACCCACAGAAATACTTTAA Y 2 1 2 1 103000 r 74 goat snp50989-scaffold739-4197315 2 61100116 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378560 Affx-122976606 AX-123248919 2 74300904 TAAACCCAAAATGGTTTTCACTGAACATCCAGCAC[A/G]TTCACTGCCTACTGCTGTGTGTGTGAGAAACACCA R 2 1 2 1 101000 f 74 goat snp50990-scaffold739-4243169 2 61054036 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448878 Affx-122923267 AX-123319213 2 74353178 CATTCTATATTGAGCACCTACTATGTGATCTCACT[A/G]TGATAGCTGCTAGTATGATGTGAAGAATAAAAAAT R 2 1 2 1 101000 r 74 goat snp50991-scaffold739-4295443 2 61002127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784155 Affx-122926693 AX-385271207 2 74381812 AAATGTTTCTTTCTCACAAGGACTAAAGAAAAAAT[A/G]TTCAACTGTTTCATAAGAATTCTATAAGAGATATA R 2 1 2 1 101000 f 74 goat snp50992-scaffold739-4324077 2 60972832 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438736 Affx-122930834 AX-123309073 2 74447312 AAATACCAAATTTAAAGAGTGCATGAATTTGCCTC[C/T]ATTGGCAGCAGATACTTCTCTTCATATTCTAGATT Y 2 1 2 1 101000 r 74 goat snp50993-scaffold739-4389577 2 60906345 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421760 Affx-122944361 AX-123292107 2 74559084 TGTCTCCTTCACTGGACTCCCATGAGCCCTGGCCC[A/G]CTCGGTTCCTCACTGTCTTACCTAAGATCCTGCAA R 2 1 2 1 101000 r 74 goat snp5724-scaffold1200-98182 2 60785935 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435527 Affx-122933406 AX-123305867 2 74610006 CAAACATGTCCTGTTCTCATCTTACCCCTTCTAGT[C/T]CTCTGTAAAACTCACTCTTGCCCAAAATGCCTAAG Y 2 1 2 1 201000 r 74 goat snp5725-scaffold1200-149104 2 60734487 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449990 Affx-122922871 AX-123320325 2 74639062 GTTCCAGTTTATTCCCATTTATGCCAGTGGGAAAT[A/G]CAGACTTTTTTGTTTTGTTTTAATCTTTGTGCAAA R 2 1 2 1 101000 f 74 goat snp5726-scaffold1200-178160 2 60706615 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421090 Affx-122944227 AX-123291437 2 74694355 GAAAATATTAAACTTTATCCAGGAACATAAAGAAC[A/G]TTGGAATATCTATGTCCTTGGATTCTCTCCCAAAT R 2 1 2 1 101000 f 74 goat snp5727-scaffold1200-233453 2 60652583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795890 Affx-122963530 AX-385282842 2 74724702 TTGTCCTAGATGATAGAGTTGGCCTGAAACTCTTT[A/C]TAGTGAATACTTTTCATGGGATCTTGATAAGTAAA M 2 1 2 1 201000 r 74 goat snp5728-scaffold1200-263800 2 60622450 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403097 Affx-122958497 AX-123273450 2 74755422 TTAGTTTCATCACATTCATGTTTTTCAGTAAGAAC[A/G]ATTGAGGAAGTGCAGAACAAAATAGATAAGAGCCA R 2 1 2 1 101000 r 74 goat snp5729-scaffold1200-294520 2 60590806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383620 Affx-122972550 AX-123253978 2 74865907 TTCAGCAAATCTTCAATAAGTAAATCCTTTAAGCC[A/G]TGCATGGACTACAGCCTTGTCTAACTCAAAGAAAC R 2 1 2 1 201000 f 74 goat snp5732-scaffold1200-405005 2 60481669 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390580 Affx-122967198 AX-123260937 2 74909377 TCATTCCCTTCTAAGCACATGGTAAGATTACACTC[C/T]CACTATTGTCTAAAAGCTTTGTCCAGAGTGTGCAA Y 2 1 2 1 101000 r 74 goat snp5733-scaffold1200-448475 2 60437925 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431039 Affx-122936655 AX-123301380 2 74956006 GAGAGCTGATTCAGCAACCCAGGATATATGCAAAT[A/G]GCCAGGAACACAGGAAGTTGAGTGAATCAGTAGCG R 2 1 2 1 101000 f 74 goat snp5734-scaffold1200-495104 2 60390982 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801206 Affx-122938059 AX-385288119 2 75040487 GTAAACCAACTTTACTTGACGGTTTTATGTAAACT[A/G]TACACTAGGACATCTTTTATAATTGTTGCTTCTCC R 2 1 2 1 101000 r 74 goat snp5736-scaffold1200-579585 2 60307101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277820 Affx-1111836039 AX-519551317 2 75103598 ATGTTCGTGCAACACACACACACACACATACACAC[A/G]CAGTAGTATATTTACATAAGAACATTAGTTATACC R 2 1 2 1 201000 r 74 goat Random2.2K-220 2 75103598 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433531 Affx-122935005 AX-123303872 2 75161006 TTGTTTTAATAGAATAGTCCACTCTTCTGCAAAAG[C/T]GGAATTCTGCATTCATTACCCCAAGATTTGACTTT Y 2 1 2 1 101000 r 74 goat snp5739-scaffold1200-700104 2 60184268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783274 Affx-122940544 AX-385270339 2 75194523 TCATCTGCAAAATAGCGATTAAAATATTCACTTTA[C/T]AGAGCTGTTGTAAAAGTCAAGTGTAACATCCAGTT Y 2 1 2 1 101000 r 74 goat snp5740-scaffold1200-733621 2 60150769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435471 Affx-122933452 AX-123305811 2 75249617 TCTGATGGTGATTTCTGTAGGATTGACATTGCCCA[C/T]GGATAAGATGGCAGCATCACCGAACATCAGCGTGA Y 2 1 2 1 101000 f 74 goat snp5741-scaffold1200-788715 2 60095964 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416429 Affx-122947835 AX-123286778 2 75284673 TTTATCCTTGAAAATCCTCCCTCATCCCTGCAAGG[A/G]GAACCATGCCAGAGCTCCATCCAGCTATATTTAGA R 2 1 2 1 101000 r 74 goat snp5742-scaffold1200-823771 2 60061820 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785413 Affx-122929479 AX-385272458 2 75352845 CACACTGGCTCCACACAACACTTATTGGGTCAAGG[A/C]TCTTAATCTTAAAAATCCAGACATATCCCAGACTT M 2 1 2 1 101000 f 74 goat snp5744-scaffold1200-891943 2 59993893 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442347 Affx-122928036 AX-123312684 2 75386956 AACAGAAAAACACAGAGGGCCCTGCTTAGTGTGTC[A/G]CAAGTTTTTTAATAAATAAACTATAAGTACAGAAA R 2 1 2 1 101000 f 74 goat snp5745-scaffold1200-926054 2 59957813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447196 Affx-122924994 AX-123317532 2 75419507 ACACTGTATAAAGTGTATAGGAGAGTCCCAGTAGA[A/G]ACCTGTGTATAACATTTTGTGCTCATTTCCAATGT R 2 1 2 1 101000 f 74 goat snp5746-scaffold1200-958605 2 59925675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415855 Affx-122948860 AX-123286204 2 75478034 GATCATTTGGCTTTGTTTGGAAAAGTCACGAATTC[A/G]TTGCATGACTCTGGTAAAGAATATCTCTAAGCATC R 2 1 2 1 201000 f 74 goat snp5747-scaffold1200-1017132 2 59866883 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417909 Affx-122946735 AX-123288257 2 75527198 ATGAAATCAACAGAAGGCTGGCTCCACAAGACAGG[C/T]GTTCTTTTCTATTCCACAGATTTATCCCAAGTTCC Y 2 1 2 1 201000 r 74 goat snp5748-scaffold1200-1066296 2 59817204 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445688 Affx-122926126 AX-123316025 2 75564972 TCATATCAGGGAGTGGTCACCCACAATAGTGAAAG[A/C]TACAGAGAGGGTTGGAAATAAGAGTAGTCATAGAA M 2 1 2 1 101000 f 74 goat snp5749-scaffold1200-1104070 2 59779036 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799845 Affx-122933709 AX-385286771 2 75611747 TGCTAGACATCACTTCAAAGAACTGTGGGTTCTGG[C/T]ACAATTCTGTGTTGCCCAGTAGAAATGTTACATTT Y 2 1 2 1 201000 f 74 goat snp5750-scaffold1200-1150845 2 59732329 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414099 Affx-122949742 AX-123284448 2 75632484 AGGCCAAATAAACAGAAACATCAGAGTTTGGAAGA[A/G]AGAAATATTTATTGCAGGGACAAGCAAGAGAACTG R 2 1 2 1 201000 r 74 goat snp12713-scaffold1489-7310 2 59709393 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441098 Affx-122928892 AX-123311435 2 75669154 TTACACAAGGGCAAGATAACATTGTGTTCATGGCT[A/G]TAGTTCTGGAAACTAGGAGAACACCTACCTGCAGT R 2 1 2 1 101000 f 74 goat snp12714-scaffold1489-43980 2 59672826 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788349 Affx-122947385 AX-385275367 2 75707810 CAGGAGACTCAGGGAATCAACAAATCAGGCAACAG[A/G]TTTAAGGTAATGCCCATCAGTTACAAAAGGTAATT R 2 1 2 1 101000 f 74 goat snp12715-scaffold1489-82636 2 59634164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794114 Affx-122930190 AX-385281080 2 75753111 AGAATCCCTAGGCCAAAAGACACATGATGAGCAAA[G/T]ATCCGGAAATCAAACAGATGCTACAAAAATGCTTT K 2 1 2 1 101000 r 74 goat snp12716-scaffold1489-127937 2 59588829 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388608 Affx-122969144 AX-123258966 2 75790087 TGCATTTTATTCTCACTTGAGTCACCTAAGTTTAG[C/T]GGAATTTAGTGATGGGCGAGGTGCCTTGCTAGGTT Y 2 1 2 1 201000 f 74 goat snp12717-scaffold1489-164913 2 59551834 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386516 Affx-122970744 AX-123256874 2 75819978 AAATTATTGCATCCCATTCCCTCCCATTTTTTCCC[C/T]GTTTCCAAGCCATGGCTGGATACTATGGAGTTATC Y 2 1 2 1 201000 r 74 goat snp12718-scaffold1489-194804 2 59521345 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437583 Affx-122931872 AX-123307921 2 75852885 ATTTAGTAGTATTTCCATTTGTGTTATCTTTTGGC[C/T]ACTTTCCCTTTGATTTTCTCCTTACATGACATTTT Y 2 1 2 1 101000 r 74 goat snp12719-scaffold1489-227711 2 59488128 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398795 Affx-122961417 AX-123269150 2 75886910 GTTTGCATTATCTTCTGGCCAAGAGGCCTGTTAAC[A/G]TTTTTATGGCTCTCTTCCTAGATAAATGTCTATCA R 2 1 2 1 303000 f 74 goat snp12720-scaffold1489-261736 2 59454223 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377538 Affx-122977463 AX-123247897 2 75922769 CTTCTGTCTGCTCTTGCCTCTGGCTCTGGTTCTGT[G/T]CTTCTAGTGGCAATGGAAGCAGAAAGAGGAGAAAG K 2 1 2 1 101000 r 74 goat snp12721-scaffold1489-297595 2 59418283 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398297 Affx-122962154 AX-123268652 2 75953962 GACCCACTGTCATAGTTTAGAATCTGGGTTGGGGA[A/G]AGGAAGTGAAAGCTAAATGTGTAAACAGACGCTCC R 2 1 2 1 101000 f 74 goat snp12722-scaffold1489-328788 2 59386836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789963 Affx-122971791 AX-385276969 2 75984810 TCCTTGAAATTATATCAAATTCAGAAGAATGATCC[C/T]CTTCTGTGCGTCTATTAGCAATGCCTTCTCTTTTG Y 2 1 2 1 101000 r 74 goat snp12723-scaffold1489-359636 2 59355109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389783 Affx-122968223 AX-123260140 2 76066973 TGGTATTGCTGTTGTGTCCATGATAGCTTCCTAAG[C/T]ACCAGATTGAATTTTATAAAATGGATGCACCTCTT Y 2 1 2 1 101000 f 74 goat snp12724-scaffold1489-441799 2 59272708 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770066 Affx-122933256 AX-385257233 2 76106617 GTATGAGCTGCATAGACTGTAAAGCACAAAACACC[A/G]TGTATTTTCTTACTCATGATTACAAAATAATATGA R 2 1 2 1 101000 f 74 goat snp12725-scaffold1489-481443 2 59233125 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427700 Affx-122939290 AX-123298043 2 76152899 TAATGGTCTTCTTTTTCTGGGTCACATGCTAGGCT[A/G]TGTGCATCTCGGGAGAAAGGCTGAATCTTTCTTCT R 2 1 2 1 101000 f 74 goat snp12726-scaffold1489-527725 2 59187081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771276 Affx-122966690 AX-385258434 2 76186963 AGGATGAAAATTTAAAGTGAGTTACTAAATTACTG[C/T]ACCTTGTACTAAATTATCTTGCTGGGTGGCTCAGT Y 2 1 2 1 101000 r 74 goat snp12727-scaffold1489-561789 2 59152756 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385444 Affx-122971314 AX-123255802 2 76199285 AAAGTGGTAGCTGTGTAGTCATTGCAGAGGGAAAT[G/T]AAACCATTCTGATCAAGCCTGGGCCCATGTTTACC K 2 1 2 1 101000 f 74 goat snp10170-scaffold1365-163 2 59141544 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408983 Affx-122953905 AX-123279334 2 76243808 AGCAAACATATATTGTAAACAAATTTACATCCATA[A/G]TGTATGTACTGGGAAGTGATATACTTAAGTATTCT R 2 1 2 1 101000 r 74 goat snp10171-scaffold1365-44686 2 59097291 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390290 Affx-122967729 AX-123260647 2 76291876 GAGGCAATATATCATATTTTATTTGTGTGTTGTTT[C/T]AGAATTTTTCTGTCTCATTTGAATATCCAAATTAG Y 2 1 2 1 303000 r 74 goat snp10172-scaffold1365-92754 2 59049081 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393656 Affx-122965286 AX-123264011 2 76321425 CTGACAGTAAGGAAGTATAAAATAACAAATATAAT[A/G]TTGTTTATATTTAGAATAAATATGTTTCATTTTCT R 2 1 2 1 303000 r 74 goat snp10173-scaffold1365-122303 2 59019692 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400091 Affx-122960742 AX-123270446 2 76352711 TATAACCAACTTCATAATGAATAGTTAATATACCT[A/G]TGATTATTATGGTGTGGCATTTAGGTCAGATGTAC R 2 1 2 1 101000 r 74 goat snp10174-scaffold1365-153589 2 58988406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412541 Affx-122951337 AX-123282890 2 76429319 TCTAAAAGTTGTTTAATTCTTGAAGTATCCACTTC[C/T]ATTTATAAAAAGGAGATAAAACCACAAACTTCAGA Y 2 1 2 1 103000 r 74 goat snp10175-scaffold1365-230197 2 58910051 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454049 Affx-122919400 AX-123324382 2 76472987 TTTTTAACTTGATCAAATGTCTATCTCAGAAAGCC[A/G]CCGAAATCATTGTATTAGTCATGACACTTTAAAAT R 2 1 2 1 101000 f 74 goat snp10176-scaffold1365-273865 2 58866517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421558 Affx-122943858 AX-123291905 2 76544072 CCTTGCTGCTCCTGACCTGCATTTCTTGCAGCTTA[C/T]TCCAACAGTAAGCACTTTTCTAAGACTTTTATGCT Y 2 1 2 1 201000 r 74 goat snp10177-scaffold1365-344950 2 58792202 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453883 Affx-122919511 AX-123324216 2 76573965 GATCAAATTTTAATGAAACAATTCAGAGGAAAACC[A/G]TCATCTTACTTCAAAAATTGTTTTCACTGAAAATA R 2 1 2 1 101000 f 74 goat snp10178-scaffold1365-374843 2 58762094 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403212 Affx-122957907 AX-123273565 2 76605098 ATATTGTGCATTTATTTTTTCCAGTGGGCACATCA[G/T]CCAAGGAAAATGGGGAAAGATAAACTGTTCTTTCC K 2 1 2 1 201000 f 74 goat snp10179-scaffold1365-405976 2 58730558 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778085 Affx-122925721 AX-385265201 2 76638010 ATTTCATATTTTCTTTTGTAACACTGTAGTTGATA[C/T]AGCTACAAGTATCTGGATGGTTTGAATTTTATTTG Y 2 1 2 1 101000 r 74 goat snp10180-scaffold1365-438888 2 58697080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787086 Affx-122971616 AX-385274113 2 76702890 ATAAAGAAGTCTTCAGAAACTGATAGTTACAAAGA[A/C]AAAAAGCTTAAAATATAATCCTCAGAACAGGCTTT M 2 1 2 1 202000 r 74 goat snp10182-scaffold1365-503768 2 58631403 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384869 Affx-122971942 AX-123255227 2 76742544 CCAACACAGTTTGATGGGGTCTGAAACAAATCTGG[A/C]GGGTGGTTGAAATGCTTCAAGGACAGAGATCTTAT M 2 1 2 1 101000 f 74 goat snp10183-scaffold1365-543422 2 58591736 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789357 Affx-122952368 AX-385276367 2 76789177 GTTTGTTTTTCTTCCCAATAAACACCTCCAAATGA[C/T]AAGCTTATTAAGTGAAAAGTTGTCTTTTTCCAATG Y 2 1 2 1 201000 r 74 goat snp10184-scaffold1365-590055 2 58543572 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399624 Affx-122961079 AX-123269979 2 76820044 TATTTCTTAGACAATAAAGCTTAATAGCTAAGATG[A/G]GACTATACTTTTTTTCCAACCCTCAACAAAAGGAT R 2 1 2 1 101000 f 74 goat snp10185-scaffold1365-620922 2 58512757 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772782 Affx-122950260 AX-385259927 2 76857184 GAAGTGTTTAGTACTGATATAACTAATCTTGTGTT[A/C]TGCAGTTAGTTAGCTGAAGAGCATGTGGATGATTC M 2 1 2 1 101000 r 74 goat snp10186-scaffold1365-658062 2 58475967 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409590 Affx-122953567 AX-123279941 2 76898018 AAAAGTATTGGCAAAGCAAAGTATCTCAGGAGTTT[G/T]CTCAAACTCATGTCCATTGATTCTAGGATGCCATC K 2 1 2 1 303000 f 74 goat snp10187-scaffold1365-698896 2 58435561 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784223 Affx-122977347 AX-385271274 2 76928993 AAAGTCAGCACCATCCTCATTTTTTAAGCACCTGC[A/G]GTTCATTTGTAGTCTAGTCTTTATAGTGTAAGCTC R 2 1 2 1 101000 f 74 goat snp53913-scaffold82-9558262 2 58396183 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793639 Affx-122955667 AX-385280612 2 77011194 CTCTTGTTCATCTTTTTGTCTAATTAATCTTCACA[C/T]GGGCACAAAGTATCAGGAAAAGTCACTATTGATTG Y 2 1 2 1 101000 r 74 goat snp53911-scaffold82-9476061 2 58313482 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386926 Affx-122970002 AX-123257284 2 77062774 GAAAAGTAATGGTTCAGAGGCATTGAGAACAAGAT[C/T]TGAGAAGGGCAAGAAAGCAAAGATGAAAACAGAAA Y 2 1 2 1 101000 f 74 goat snp53910-scaffold82-9424481 2 58261366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766596 Affx-122940589 AX-385253951 2 77091627 ACCTGTATAGAAATCAGAATTTTGGCAGCTGAATT[C/T]TTTTAAAGATAATGTAAGAGGAAAGGAGTTGCTTT Y 2 1 2 1 202000 f 74 goat snp53909-scaffold82-9395628 2 58231626 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795976 Affx-122964953 AX-385282928 2 77129133 ATGTAGGGTAAACAGGACTGCTTAGCAGCCCAGAT[A/G]TAAGAGCAAAAGGGTGAAGCTAAAAGAAAAATCTA R 2 1 2 1 101000 f 74 goat snp53908-scaffold82-9358122 2 58193182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797257 Affx-122944734 AX-385284196 2 77177078 TCTTTGTAGTACTATTTGGAAAGTGTTTGGATATT[A/C]TTTACCCCTCAACTGTGAGGTGAGATAATCAGACT M 2 1 2 1 101000 r 74 goat snp53907-scaffold82-9310177 2 58144736 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782630 Affx-122919393 AX-385269703 2 77213792 TAATAATTGCCATGAACTTGCTCTAATGTGCACTT[A/G]AGTTTATTAAATCATGACTATGACACTATTGTCTG R 2 1 2 1 201000 f 74 goat snp53906-scaffold82-9273463 2 58106672 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419377 Affx-122945621 AX-123289725 2 77296037 CTCCACATCAGTCACCCCAGCCAGAAAGCCTGGAC[C/T]AGGAAGACAAGCTCCCAGACTGTCTGGCATTTAAG Y 2 1 2 1 101000 r 74 goat snp53905-scaffold82-9191218 2 58022967 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438340 Affx-122931337 AX-123308678 2 77331140 AATGTCATGTTCATTGAGAAATGCCTGGCAAATAG[C/T]AGGTGCTCAATGCATATTTTTGCATAAATAAAAAT Y 2 1 2 1 101000 f 74 goat snp53904-scaffold82-9156115 2 57987640 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379698 Affx-122975903 AX-123250056 2 77369556 CCTAGTTGAGATTAGTAAAAGGCCTACACACATCA[C/T]GACATACTTGATATGAGATACACATAGAACAATGA Y 2 1 2 1 101000 f 74 goat snp53903-scaffold82-9117699 2 57949384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413508 Affx-122950634 AX-123283857 2 77414372 GAAAGACTAGTTTAGGATACATTGAAATACGACAT[A/G]TTAAGGGGGAATGAGGTGGCATCCCCCTTTACTAG R 2 1 2 1 201000 f 74 goat snp53902-scaffold82-9072883 2 57903331 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412795 Affx-122950492 AX-123283144 2 77463420 GAGCATAACTGGTAAAAAATATTTAAAAACCAATC[A/G]CTTGGTCTCTAAAGGGAATTTCCTGATGGTACAGT R 2 1 2 1 101000 r 74 goat snp53901-scaffold82-9023835 2 57853837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399111 Affx-122960861 AX-123269466 2 77492357 CCCTTGGCAGTGATTTAGGACAGCCTGGGTGACCA[C/T]TTGCTAGGTGCACTTCAGGAGTTATGTTGTAAGCA Y 2 1 2 1 201000 r 74 goat snp53900-scaffold82-8994898 2 57824899 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789149 Affx-122972536 AX-385276161 2 77526531 CCTGCTTTTTGATTACATTGCTTAAGTAATTCATC[A/G]TCAATGTTTAATTGATACGATTTGATTTATTCCTG R 2 1 2 1 202000 r 74 goat snp53899-scaffold82-8960724 2 57790959 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375828 Affx-122978548 AX-123246187 2 77677829 CAATGTAAGTCATCCCCATTTTCTGTATTTTCTCA[C/T]TGATGATACTTTTGCAAACTGCATTTCCTTGTCTT Y 2 1 2 1 101000 r 74 goat snp53896-scaffold82-8809426 2 57634828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423232 Affx-122942691 AX-123293578 2 77710833 ATTTCTCTACCTTAAACTGTGACAAATGATTTCCA[C/T]GGCATTTGGTGAGGATTAAGTAAGAAAAATTTTTC Y 2 1 2 1 101000 f 74 goat snp53895-scaffold82-8776422 2 57601453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776933 Affx-122928032 AX-385264057 2 77751123 AAAACCAACTTTGTGAATGGGGAATATCCAGAAAG[A/G]TTAAATAACAGTTTTCTGGGAATTAAACCCTTTGG R 2 1 2 1 101000 f 74 goat snp53894-scaffold82-8736132 2 57560650 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780823 Affx-122973130 AX-385267912 2 77783786 AGCCCAAAGGAGGAAAAGCTTCCCAGAATGTAAAC[G/T]ACTGGATGTCGAAGACTCAAGCTGTCTTTCTCTGA K 2 1 2 1 101000 f 74 goat snp53893-scaffold82-8703469 2 57527247 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779573 Affx-122963087 AX-385266676 2 77819577 TAACCTCAAAAATATCACAAATGTCTGTCATCTAG[A/C]TTAATATCTATGTTGCTCCTCAAATCGTGGTCTTA M 2 1 2 1 101000 f 74 goat snp53892-scaffold82-8667678 2 57491653 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453982 Affx-122919450 AX-123324315 2 77859599 AGCCTGATTCTCCTACCTGACTGCTGAGTATCACT[A/G]GTAAACTTTCTGGCTGCTACCGGATCAAGTAGTTT R 2 1 2 1 101000 r 74 goat snp53891-scaffold82-8627656 2 57451936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802475 Affx-122974601 AX-385289379 2 77890254 CTCCTAAGTGACCAAGTCAGTTGTGTGCCAGACAT[A/G]CCAACTTGGGCCTAAACTCAGCAGCTATTATTGAG R 2 1 2 1 101000 f 74 goat snp53890-scaffold82-8597001 2 57420976 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436329 Affx-122933250 AX-123306668 2 77928954 TTTTCCCAGTGAGAGGAACTCTCTCAGGCCAGAAA[G/T]TTCCCTCTTGGCTCTAAACAGAGTCATCTTGGGAG K 2 1 2 1 201000 r 74 goat snp53889-scaffold82-8558301 2 57382166 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435741 Affx-122933285 AX-123306080 2 78000720 TTGTATTTGAGGAGTGCATTCTCACTGCCTCTCTC[A/G]TTGCTCAATTAAAAGCGTGTCACTGACACTTCAAA R 2 1 2 1 201000 r 74 goat snp53887-scaffold82-8486535 2 57310071 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435679 Affx-122933330 AX-123306018 2 78079128 ACCATCCCCAGGGCTGGAGATATAGAGACACAGGG[A/G]CTTCAGCTTTCTTTACATGGAGTTCAGCGCTTCGG R 2 1 2 1 101000 f 74 goat snp53885-scaffold82-8408127 2 57231905 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443693 Affx-122927167 AX-123314030 2 78138114 AGTTTTGAGAGCTGTTATGTATTCTGCATATAAGT[A/G]CTTTATTAGATATGGGATTTGCAAATATTTTCTAG R 2 1 2 1 303000 r 74 goat snp53883-scaffold82-8349141 2 57172530 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428910 Affx-122938918 AX-123299252 2 78168315 GTGGTCAGCTCTCTTTTCTCTGTTCACTAGCTGTG[C/T]ACCCCAAGCATGTTTCTTACCTTCTCTGTGGCTGG Y 2 1 2 1 101000 r 74 goat snp53882-scaffold82-8318940 2 57142128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795171 Affx-122925613 AX-385282129 2 78198827 TAGAGCTGCCTGTTTGACACAGTGGAAAGTATTTC[G/T]AATTCTCTTTTGTTAGATAATGTTTATAGCTGCTA K 2 1 2 1 101000 f 74 goat snp53881-scaffold82-8288428 2 57110982 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434055 Affx-122934195 AX-123304396 2 78229602 ATAAGTTCCTATACTGGTGCAATTTCTCAGGAGAA[C/T]GAATTGGATGCAATAATGCCCATCACTTAACAGTG Y 2 1 2 1 101000 r 74 goat snp53880-scaffold82-8257653 2 57080219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381191 Affx-122974540 AX-123251549 2 78262221 TGGACTTCAAGGCTATTAGTGAGTTTTCTTCTCAC[A/C]TTTTCCAGGACTCTGGGAATATCAGACCCACTTAT M 2 1 2 1 201000 r 74 goat snp53879-scaffold82-8225034 2 57047510 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379915 Affx-122975754 AX-123250273 2 78317594 CCCTGATTAGCAGCTTTCAGACTCAAGGAAGTTCA[C/T]GGAGGCTGGAGTCTGTTCCTTAACAAATAAGAAAC Y 2 1 2 1 101000 f 74 goat snp53878-scaffold82-8169661 2 56991086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384736 Affx-122972044 AX-123255094 2 78363113 GTACATAATTTTTGCATGAAGTGTTCTACATCTAG[C/T]GTGCATTTTAAACTCACAGTACACCTCAGTTCAGG Y 2 1 2 1 101000 r 74 goat snp53877-scaffold82-8124142 2 56945164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793873 Affx-122944961 AX-385280842 2 78408332 CAAAGGACATGGGCTTTAGACTCATGCTGGCTTCA[C/T]TGACAATTCCAACTTCTCCTGTGCTGGGTACATGA Y 2 1 2 1 101000 r 74 goat snp53876-scaffold82-8078923 2 56899901 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380980 Affx-122974683 AX-123251338 2 78474361 GAACAGTCGGGGTCTCAAGGGGAGACAGAGCCAAC[A/G]TGAGAGGTTTGGTGAGGATTCAGTGAGGGTCTGAT R 2 1 2 1 202000 f 74 goat snp53875-scaffold82-8012894 2 56832967 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431333 Affx-122937064 AX-123301674 2 78503105 GTCACTCCTCAGCTGATAAGCTTTCCCTCTTCCAC[A/G]TTGTGCTTCCAACCAATTTGAGTTCCTCAAGCTGA R 2 1 2 1 101000 r 74 goat snp53874-scaffold82-7984150 2 56804227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450894 Affx-122922203 AX-123321228 2 78554510 TTTCTTTCTTGTTAGCAAACATTTGCTTCCCTAAA[C/T]GTGTGCCCACCCATCCTGCTGCTGTTGCTAAGTCG Y 2 1 2 1 101000 f 74 goat snp53873-scaffold82-7932745 2 56752608 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437467 Affx-122932379 AX-123307805 2 78585480 GGGCCAGTAGGTGGCTGAAATTTGAGAGGTCAGGC[A/G]CCAGAGAAAAGGGAACCATCAAGGAAAAGCCCCAC R 2 1 2 1 201000 f 74 goat snp53872-scaffold82-7901775 2 56726811 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797166 Affx-122954322 AX-385284106 2 78681084 CAGATATTTGTGAAAATACTGATATAGCTATACAC[A/G]TATTATCATAGATACAAATGCACCAAACACAATCA R 2 1 2 1 101000 f 74 goat snp53870-scaffold82-7806171 2 56629384 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795474 Affx-122960288 AX-385282429 2 78765117 TAGCCCTTATATTATGTAGAGGATTTTAAAAACTG[C/T]AAACATTTTATTTAACATTTGAGGATATCATACCT Y 2 1 2 1 103000 r 74 goat snp53869-scaffold82-7722138 2 56544211 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272359 Affx-1111833959 AX-515629181 2 78807129 TATTCTCCTCACCCAGCAATCAACCAGAAAGCCAA[A/G]TGTCCTCCCACCCTCTTAATCACAGATCT R 2 1 2 1 101000 f 74 goat GoatD01.011623 2 78807129 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320778699 Affx-122953740 AX-385265810 2 78811930 TAGCAGAAACACCTGGGGTGCTTAATAAAAATGCA[C/T]ATTTTAAAAGCAATCTTCGGTGTTGGACTTTAGGA Y 2 1 2 1 201000 r 74 goat snp53868-scaffold82-7675325 2 56497170 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767416 Affx-122926486 AX-385254689 2 78844910 ATGTATTTTTGAAGCATATGTTGAGCACAGCCTCC[A/G]TTACTGCAAGGCTGAGATAGTCCTGACCAAGACAG R 2 1 2 1 101000 f 74 goat snp53867-scaffold82-7642345 2 56464269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423255 Affx-122942673 AX-123293601 2 78879754 CTGTATGTACAAGGACCAAGAACGCCTGGTTCACA[A/G]TTATTTCCCTAAAATCTACCACAGTGTGCCTCTTA R 2 1 2 1 201000 r 74 goat snp53866-scaffold82-7607501 2 56429505 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419148 Affx-122945746 AX-123289496 2 78916756 GTAGTGCATATATCCCGTTTTCCCTTGAGACACCC[G/T]TATGTGATATATTCAGTCTAAGATGTTCTCTGGGG K 2 1 2 1 101000 r 74 goat snp53865-scaffold82-7570499 2 56391639 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433234 Affx-122935251 AX-123303575 2 78954290 GATTGAGACAATGAAAAACAGAATTATACTTTGAA[C/T]ATTTCTGCTTAACCTGGGTAAGTGGCTAAGCCATA Y 2 1 2 1 101000 r 74 goat snp53864-scaffold82-7532965 2 56353830 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403576 Affx-122957577 AX-123273929 2 79042768 CCTTTCTCTAGTAGGGCAGGGGACACAGATTAATT[A/G]CCCTAGTCATCAGGTGGGGCCAGGTAGAAGACAGG R 2 1 2 1 101000 f 74 goat snp53862-scaffold82-7444487 2 56264300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379432 Affx-122976105 AX-123249790 2 79086341 TGTTTTTACTAAAGAGAAAGAAAAATAGATGGTTG[A/C]TTTTTTTCCTCACCTCCCACCTCCATACTTAAATG M 2 1 2 1 103000 r 74 goat snp53861-scaffold82-7400914 2 56220815 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441095 Affx-122928894 AX-123311432 2 79128300 GGATGGCCCTCTAACTTTGGGCATTTACTGTGTTA[C/T]GGGCATCAGCTGATGTATTTTACAAAGGAAAAGAG Y 2 1 2 1 101000 f 74 goat snp53860-scaffold82-7358955 2 56178372 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385871 Affx-122971606 AX-123256229 2 79174353 TGGTACTCCCACCCCTAGACAGGCCTCCTGTGTTC[A/G]TGTCACCATCTCCAACACCATTTATTTCCTTCTCT R 2 1 2 1 101000 r 74 goat snp53859-scaffold82-7312902 2 56132365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784706 Affx-122931938 AX-385271754 2 79228831 ATATCTACTCAAATCAAATGAATGATTATGTGTTG[C/T]GACCACCTCAGAATCAAAGACTGATCATTATTATT Y 2 1 2 1 101000 r 74 goat snp53858-scaffold82-7258424 2 56077674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385267 Affx-122972076 AX-123255625 2 79370528 ATCACTTCCAGCCTGTGGGGTTTTCACCCTGTTAC[A/G]TGGGGATGATGACACATGGTCTGCAGAGCATCATA R 2 1 2 1 201000 f 74 goat snp53855-scaffold82-7116727 2 55935305 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433640 Affx-122934581 AX-123303981 2 79407462 CACACTACTCTAGAGACTAGAAATGACATTGTTAA[A/C]AGGCCCAAGTCTTATGTATGCCTGCTTCTTGGACA M 2 1 2 1 101000 f 74 goat snp53854-scaffold82-7079793 2 55898047 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410064 Affx-122953220 AX-123280414 2 79455249 GAATGAAAGTTTTCGGTCTTTCCTCCCATATCATC[A/G]CTTCCAGCTAGAATGATAGAATGTATCAGATAGAA R 2 1 2 1 101000 f 74 goat snp53853-scaffold82-7032006 2 55850416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416946 Affx-122948029 AX-123287294 2 79486248 CCTAATTTTTATTGGTGGTCCTCATCCTTTCCTCC[A/G]CTTCCTGGGAACTACAGATCCTCTCACTTTTAAGT R 2 1 2 1 101000 f 74 goat snp53852-scaffold82-7001007 2 55819134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376963 Affx-122977760 AX-123247322 2 79546300 AAATGAGTTGAGAACAATACCAGAAAGTTGAGACA[C/T]GCATGCCAGGCAGTTTTCTGGCCTTGTTCATCAGC Y 2 1 2 1 101000 f 74 goat snp53851-scaffold82-6940955 2 55759905 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385578 Affx-122971839 AX-123255936 2 79580931 AAGGCTTTGTGAATTGTGTTCAGAAATTTTGACAA[C/T]AAACACACATACACAGTCCCTTCAAATAAGAAAGA Y 2 1 2 1 201000 f 74 goat snp53850-scaffold82-6906324 2 55725024 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431246 Affx-122937131 AX-123301587 2 79700884 ATGACCTTGGGCAAGTTACTTAACCTCACTGTGCC[G/T]CATTTGTCTCATCCATAAAGTTGGGAGACAGTAAT K 2 1 2 1 201000 r 74 goat snp53848-scaffold82-6786371 2 55603686 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389503 Affx-122968305 AX-123259861 2 79732255 TAAATCTATGAGCTTAAAAAAAAAATGTATCTCCA[C/T]CTTCATAGTTTTAGGTTAACCTCTAAAACTTTTCC Y 2 1 2 1 103000 r 74 goat snp53847-scaffold82-6755000 2 55572148 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787830 Affx-122957655 AX-385274853 2 79762925 AGACTATTATAGTTTAAAGACAGTTATATCAGAGA[A/G]CAGATTTCCTACCTTAAGTATATACCACTCACTAT R 2 1 2 1 101000 r 74 goat snp53846-scaffold82-6724330 2 55541474 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428480 Affx-122938787 AX-123298823 2 79828627 AAGTAAGCATGCATGATGCTTGAGCAAGCGATAGT[A/G]AGAGCCTGTCAAATTGGAGACATCTTTGATAATGT R 2 1 2 1 101000 f 74 goat snp53844-scaffold82-6658628 2 55474924 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791935 Affx-122935069 AX-385278925 2 79861381 CAAATAACCTTTCTAATTCTGCATACATTCCTGTG[G/T]CTGTACATTTACATTACTGGAGTCTCCGGTGCCAC K 2 1 2 1 101000 r 74 goat snp53843-scaffold82-6625874 2 55446489 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787938 Affx-122951971 AX-385274960 2 79895602 AGTCATGATCTCAAAATGCAAATCCTACTTTGACC[A/G]CAAATTTGGGATGGAACTATGAGCAAGTCATCTCA R 2 1 2 1 101000 f 74 goat snp53842-scaffold82-6591653 2 55412218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390922 Affx-122967085 AX-123261279 2 79945380 ATGGGTTGTAGCTTATTCCCTCCAGTTGATCATTT[A/G]TAAGACGCTCAGACTTTTAGTTTGAACTCAAATGG R 2 1 2 1 101000 f 74 goat snp53841-scaffold82-6541875 2 55362547 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793453 Affx-122947476 AX-385280430 2 79977499 GAAACGCTGACGTTGATACCATGGTCAGTGAAAGC[A/G]TTTCTGAAAAGGTCATATTTGACTCATGTAAATAT R 2 1 2 1 101000 f 74 goat snp53840-scaffold82-6509756 2 55329383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379689 Affx-122975910 AX-123250047 2 80115168 ATAATTTCATTTCACAACCTCCTTCTTCAGAGCCC[A/G]CATTTCATTTCAATGGTACTAAGTTTTATTCCTGG R 2 1 2 1 201000 r 74 goat snp53837-scaffold82-6372087 2 55191223 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803340 Affx-122944728 AX-385290176 2 80148673 CTGCTTTCAAATTGGGCAATTATAGAAACACTGAT[A/G]GAGACACATCTCTGCTAATTTACATATGCATGGCA R 2 1 2 1 101000 r 74 goat snp53836-scaffold82-6338582 2 55157767 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423175 Affx-122942736 AX-123293521 2 80200334 ATTATGCCACCTGCAAATGTCAGTCATCTAAAGAG[C/T]ATAGACTCTCCTTTTCATCCTTTATCATTTGCCAT Y 2 1 2 1 101000 f 74 goat snp53835-scaffold82-6286921 2 55105932 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436717 Affx-122932315 AX-123307055 2 80234085 AACTAAGAAAAGCATTTCATCCCATCACTTCAGGG[C/T]AAATAGAAGGAGAAAAAGAGGAAGCAGGGATAGAT Y 2 1 2 1 103000 f 74 goat snp53834-scaffold82-6253170 2 55072012 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769828 Affx-122920141 AX-385256998 2 80262853 AAAGCAAGCAAATTCCAGGTGAATACAATTTAATT[A/G]CTATTTATTCTTTATTGTAAACTATGAAGTAATCA R 2 1 2 1 201000 r 74 goat snp53833-scaffold82-6224402 2 55043068 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406353 Affx-122955431 AX-123276705 2 80294106 TGGGATTCTCCAGGCAAGAATACTGGAGTAGGTTG[C/T]CATTTCCTTCACCATCTAGAGCAAAGGTCTATTTT Y 2 1 2 1 303000 r 74 goat snp53832-scaffold82-6193149 2 55008222 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390186 Affx-122967804 AX-123260543 2 80331509 GATTTGTGAAGAGTAAAAACAAAAGGAATTATGTT[A/G]TGTTAGCATCTCTATCCCCTTCAGTATCATTGCCA R 2 1 2 1 101000 r 74 goat snp53831-scaffold82-6155746 2 54970376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445525 Affx-122925173 AX-123315862 2 80381700 AAAATGTTAAACAAAATGTCCAACAAGTGAGTTAT[A/G]GTTAAATAAAACATGGTTTACCTTAGCAATAAAAA R 2 1 2 1 101000 r 74 goat snp53830-scaffold82-6105555 2 54919053 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777286 Affx-122948270 AX-385264408 2 80414439 AGATGCATCTCAGATTTAAGCTGAATAACCAAGCC[A/G]TGTAAAATACCTCAACTATTTGCTAGTATTCAGAA R 2 1 2 1 101000 f 74 goat snp53829-scaffold82-6072816 2 54885900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791231 Affx-122938961 AX-385278225 2 80505441 AAGTCTGGTGGGCATCAATACACATCTAGTTATTT[A/G]TATAGCATCTGTAGAGATGGAAATTTACCATGTTC R 2 1 2 1 201000 r 74 goat snp53827-scaffold82-5981814 2 54793987 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779442 Affx-122923671 AX-385266545 2 80578936 AAATGACAGTGCAAATGGTATTTCCATACAGTAGA[C/T]GTTTTTGACCAATGTCCACATTATTTAACTGAATT Y 2 1 2 1 101000 f 74 goat snp53825-scaffold82-5908319 2 54720521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277724 Affx-1111836057 AX-519551223 2 80584628 TTAGAAAATCTCACTTAGAGATACTGGTTAGTTAT[A/T]AACTGCTATACAGAAGGAATTCAATTAAAGAGGAT W 4 1 2 1 101000 f 74 goat Random2.2K-223 2 80584628 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468277738 Affx-1111836064 AX-519551237 2 80611131 GTCTTGGATGTTGTTATTTTTGTTAGAAAGAATGG[A/C]CAGGAGATGACAGAGATTTTGAACTTCTCTCCACC M 2 1 2 1 101000 f 74 goat Random2.2K-224 2 80611131 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38442867 Affx-122927670 AX-123313204 2 80868153 GGACAATTTATGAAAGCATACCTTTTTCTTGAGTA[C/T]AACAGAGGGTTAACACTGCACATCAACTAGGTGAA Y 2 1 2 1 201000 f 74 goat snp53820-scaffold82-5619102 2 54423577 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783940 Affx-122945753 AX-385270994 2 80972831 CTGAATTTAATCATGCTACAACTGATAGATATAAG[A/G]AAAGCTGACAAATAGTAAGGACCAGTCAAGTGCTT R 2 1 2 1 101000 r 74 goat snp53818-scaffold82-5514424 2 54319222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464147516 Affx-1110339546 AX-515623200 2 80985878 CTCAGAATTAGCTAATTCTTCAATTGAGGCAAGGT[A/G]TACAGTAATGGAGTCCTATCCCATTCTCTTTATAC R 2 1 2 1 101000 f 74 goat Random2.2K-226 2 80985878 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320798455 Affx-122969835 AX-385285388 2 81006441 GCTGCGAAAATGCACTTTATTGCTAAACAAAAGTG[A/G]TGTAAATTAACATCCTGGATTGGTCTACAGTCATC R 2 1 2 1 101000 r 74 goat snp53817-scaffold82-5480814 2 54285519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786054 Affx-122945935 AX-385273090 2 81042782 AAGAAAAGAAAGATAATAATCATTTCTAACTGTGG[A/C]TTATAATGTTTTACAGGACAGTATTTTCATTTTGA M 2 1 2 1 101000 f 74 goat snp53816-scaffold82-5444473 2 54249419 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785871 Affx-122946065 AX-385272908 2 81080576 CCTATCAAATATCTCTTGGAAAGTTTGAAACACAT[A/G]AGGAATATGTATTTCACATTGCCTCACTACTTAAG R 2 1 2 1 101000 r 74 goat snp53815-scaffold82-5406679 2 54210954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402324 Affx-122959076 AX-123272677 2 81115463 AAATGAGACTATAGATAGGATTTAGGGTTGCAGTC[A/G]CAAGAATGAGAAAGAATTGTGACGATACATAGAAA R 2 1 2 1 101000 f 74 goat snp53814-scaffold82-5371792 2 54175531 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796616 Affx-122959906 AX-385283562 2 81146786 TATGAGGAACCTAGTTCTCTCTGGTCTAGTTAACA[G/T]CTAGCTTTGCCTGGATTCATTAGTTTTTTTCAATT K 2 1 2 1 101000 f 74 goat snp53813-scaffold82-5340469 2 54146205 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438400 Affx-122931291 AX-123308738 2 81204062 CATCAGAGGGAAAGTACCCTTACTAAGGTCACATG[C/T]GAGAAAGAAGGAAGGGTAGTAGGGAAAGCCCTCCA Y 2 1 2 1 101000 f 74 goat snp53812-scaffold82-5283193 2 54088309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427194 Affx-122939599 AX-123297537 2 81256073 TTTTTATTCTTTCTGTTCTTCACAGCTCCTTTGCC[A/G]TTTGACACCATTTGGGTGTTTACTGTCTTCTTACC R 2 1 2 1 201000 r 74 goat snp53811-scaffold82-5231182 2 54034947 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779333 Affx-122921860 AX-385266437 2 81312552 TACCACTTAAGCAAATTATAAAAGATTGCTTTACT[A/G]TACAGCCCTGAAATTTCTTGTTTAAAAATGGAAAA R 2 1 2 1 201000 r 74 goat snp53810-scaffold82-5174703 2 53978071 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767858 Affx-122936786 AX-385255078 2 81361639 ATCACATCTTCAAATAGCCTAATTTCATATAAATT[A/G]CATTTAATCTGTGTCAGGGTACTTTGTGCTAGGAC R 2 1 2 1 202000 f 74 goat snp53809-scaffold82-5125616 2 53929225 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400577 Affx-122960410 AX-123270932 2 81416370 ATAGACTTAATGTCCTAAATCCAACACACATAAGA[C/T]GAGGAAAAATAACAAATTACTAATAGATAACTGTT Y 2 1 2 1 101000 f 74 goat snp53808-scaffold82-5070885 2 53873960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789125 Affx-122938225 AX-385276138 2 81456453 GAGTAGCTATCAGGTCAGCCAGATGTCTTTGTAAC[C/T]TGACTGAGTATTCAAATATATTAAGGGAAAGGACC Y 2 1 2 1 101000 f 74 goat snp53807-scaffold82-5030802 2 53833344 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449362 Affx-122922730 AX-123319697 2 81502186 AGTTTTACTCTCAACTTTTCTTCAAAAATTATCCC[A/G]CAAAGATCATGATGAATCTAAAGATATCTAGCTTC R 2 1 2 1 101000 f 74 goat snp53806-scaffold82-4985069 2 53787625 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273003 Affx-1111833181 AX-519546684 2 81545553 TCTCGAAAGGATCTCACTGGACTGTGTCCACTGCC[A/G]TTTTCAACCACTTTCCATAGCAGTGTGTCCTAGAC R 2 1 2 1 101000 r 74 goat 2_81545553_AF-PAKI 2 81545553 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38380705 Affx-122975159 AX-123251063 2 81607276 AAAGGGACTAATGAAAGAGTTATGAGACAGATGTG[A/C]ATAGCTCTGATATTTTAAACATTATGACACTGCAT M 2 1 2 1 101000 f 74 goat snp53804-scaffold82-4879979 2 53678844 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766969 Affx-122952465 AX-385254268 2 81645592 TTTTAAATATGATATTGATTTTCAAAAATGTGTAT[A/G]CATTTTGTAATGTATGATGGTACATTTTTTCTTGG R 2 1 2 1 303000 f 74 goat snp53803-scaffold82-4841663 2 53641244 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449833 Affx-122922391 AX-123320168 2 81680302 AACCTTAGTAGTAAATAAAATATTTCACGAATATC[A/C]CCTATTTTTTAGTTCCAATTCACTTCATTTCCAGG M 2 1 2 1 101000 r 74 goat snp53802-scaffold82-4806953 2 53606043 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416440 Affx-122947827 AX-123286789 2 81787463 TTTCTTCACCCCAGCCTTTACTGAGTTCCTTCCAG[C/T]TCTCTTTATTCAACTTTAGTGCTTTGATCAGTTCA Y 2 1 2 1 201000 r 74 goat snp53800-scaffold82-4699792 2 53497947 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382226 Affx-122973969 AX-123252584 2 81856799 AAAGCAACGACAACCACAAAAAGACTATATACGGC[A/G]TTTGCTTTAAAAATAGGGTCCTTTTTTTTTGAAAA R 2 1 2 1 303000 r 74 goat snp53798-scaffold82-4630456 2 53428311 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440223 Affx-122930683 AX-123310560 2 81908735 CATAAATTTGAGAATTATGATAATTAATTAGTCAC[G/T]AGTTTTCAACAGTGCAGCACCTGGAAAGGAGAAGG K 2 1 2 1 202000 f 74 goat snp53797-scaffold82-4578520 2 53375946 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273559 Affx-1111833690 AX-519547173 2 81953220 ATACCTGACACTTCAAATACAAGATTATATGCTTG[A/G]CACTAAAGGTACAG R 2 1 2 1 101000 f 74 goat GoatD01.001658 2 81953220 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802168 Affx-122966174 AX-385289072 2 81983795 GCCAATCAACATGAAACAAAACTTCAGCTTTGGAA[C/T]AATTTTTCTTATCCACACATATGCCTATTATAAGT Y 2 1 2 1 101000 f 74 goat snp53795-scaffold82-4503460 2 53299302 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277774 Affx-1111836082 AX-519551273 2 82025322 CATGACCATGAAAAAATGGTGCCTTAGTAATCTTA[A/C]TAAAATAAACATTTAATAATGATGCTCCACTACTT M 2 1 2 1 101000 f 74 goat Random2.2K-227 2 82025322 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376671 Affx-122979001 AX-123247030 2 82147574 ACAGAGAGGGATTTAGCCATATATATATTAATGGA[C/T]AAAGAATGAATCTCAAAAATACACAAGCAACTCTT Y 2 1 2 1 303000 r 74 goat snp53792-scaffold82-4339681 2 53135416 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768301 Affx-122941592 AX-385255481 2 82176664 GTTAAACAAACATTTCTGAGGGTAAGGGAAGAGAA[A/C]TCTTATATGCAGCATTTGCTAAACTTTCTTCACCA M 2 1 2 1 101000 f 74 goat snp53791-scaffold82-4310591 2 53105683 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766622 Affx-122976050 AX-385253973 2 82230748 CATTCACATTAATAGTGTGTGGCTTGCAATTGATC[A/G]CTTTATAAGCTGAAAATTTGAACAATTTATGAAGT R 2 1 2 1 101000 f 74 goat snp53790-scaffold82-4256507 2 53051414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788409 Affx-122929072 AX-385275427 2 82281432 CATTTTTTTAAGACCCTTTAAAAGCTTTCATTGCT[A/G]TTTTTTCATCCTTGGCATCTTGTCTTCATTCCCGA R 2 1 2 1 202000 f 74 goat snp53789-scaffold82-4205823 2 53000462 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379069 Affx-122976329 AX-123249428 2 82382033 CCCATAATTACTCTGAATGAATAAAAATAGTGGCA[C/T]GCTCTTGAAAATGTCAACACTCTTAACACTTAAAT Y 2 1 2 1 101000 r 74 goat snp53787-scaffold82-4105222 2 52896278 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277802 Affx-1111836096 AX-519551300 2 82464505 ACCTTGTAGAATTATGGAAGGATACAATAAAAGGA[C/G]GGCTTCCCAGCTGGCTCAGTGGTAAAGAATCTGCC S 4 1 2 1 101000 f 74 goat Random2.2K-230 2 82464505 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438474 Affx-122931234 AX-123308812 2 82476534 ATTTGTTCTAATTTAGGGGTGGGAAAGGCAGCAAG[G/T]TTCCGTGGAAATCTGAAATACTGAGTCAAGCAATG K 2 1 2 1 101000 r 74 goat snp53784-scaffold82-4010721 2 52797791 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446905 Affx-122924704 AX-123317241 2 82523695 GGAAAACATCAAATAAATAGCCCTTCACAAGAAGA[C/T]ATGCTCTTTCTTTATTAAATCCACAGTCATAAGCA Y 2 1 2 1 101000 r 74 goat snp53783-scaffold82-3963560 2 52750593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441760 Affx-122929115 AX-123312097 2 82559467 CATGCATTAGCAGGCAGATTCTTTACCACTAGCGC[A/G]GTTGCCTGTAAATCATGAAACCCTTTACCATTTCT R 2 1 2 1 201000 r 74 goat snp53782-scaffold82-3927788 2 52713419 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420709 Affx-122944784 AX-123291056 2 82647596 GATAAAGAATTCTGTGAACAAAGCTAAGGTCAAAC[A/G]CAAACTCTGTGCACAAATACTCTCTATAGATCTTT R 2 1 2 1 101000 r 74 goat snp53780-scaffold82-3839659 2 52624330 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777959 Affx-122954990 AX-385265075 2 82701760 GTTCTGTTTAATTAGAGGCTATAAACACTACATTG[C/T]ATGGCCAATGAGAACCAAAACCTATCCCATAAAAA Y 2 1 2 1 101000 r 74 goat snp53779-scaffold82-3785495 2 52569307 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399985 Affx-122960817 AX-123270340 2 82740545 TATGCCATATTGTGTTTTAAAATTCTGCTATAAAA[C/T]GCTTTCTTATTTGAAGGATTTAAAGTGACTAGAAC Y 2 1 2 1 201000 f 74 goat snp53778-scaffold82-3746710 2 52528717 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795791 Affx-122968761 AX-385282744 2 82776004 GTTGGCAGGGGAGAAGTTAGGATGTGAAGTAATTT[A/G]TTTGGTACAAAATGTGAATAACTAATTTAGTAAGT R 2 1 2 1 201000 r 74 goat snp53777-scaffold82-3711251 2 52492623 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437952 Affx-122931619 AX-123308290 2 82815190 AAGGAACATATATGTAAACCACTGATTCTCTAAAC[A/G]TGCAGCATTTAGTAGTATGCTTATAAGGCATAGGA R 2 1 2 1 101000 r 74 goat snp53776-scaffold82-3672065 2 52452934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420459 Affx-122944883 AX-123290806 2 82894667 AGATGTTGACCTTGTCCTACAAAAATTTTTGGATT[A/G]TAGTGCAACTATTTTGTTTTTTAAGAGTAGAAGTT R 2 1 2 1 103000 f 74 goat snp53774-scaffold82-3592588 2 52372711 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414198 Affx-122949658 AX-123284547 2 82934971 TGCAGGCTTTACCATCTGAGCCACGAGGGAATCCC[A/G]TCAGATGCCAACACTCAGCTATTTTGGTATCACAA R 2 1 2 1 101000 r 74 goat snp53773-scaffold82-3552284 2 52331939 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402932 Affx-122958185 AX-123273285 2 82988735 TCTGCATTCTCCTCAGCTCCAGGCAAGCCTAGCTG[C/T]AATCTTCCTTTCTTAACTGTGACTATGGAAAATTT Y 2 1 2 1 101000 r 74 goat snp53772-scaffold82-3498520 2 52277252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782854 Affx-122964577 AX-385269924 2 83030853 AATAGTGGATGGTTGTTTACAACCAGTCACCATCA[C/T]TGAACATTCTCCTTTATCTTGTTACTCTCCTATGT Y 2 1 2 1 101000 r 74 goat snp53771-scaffold82-3456402 2 52234338 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769878 Affx-122926387 AX-385257047 2 83118030 GCTTTTGGCTGAAGAAGAAGTTAAAAGATAAGGTT[A/C]GGGGCTGCTTTTAGGGCAGATCATGAAGATCAGGT M 2 1 2 1 101000 r 74 goat snp53770-scaffold82-3369225 2 52147226 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277952 Affx-1111836100 AX-519551447 2 83126326 TTGATATAAACCCTCTAATTCACATCATTGACTTT[A/G]TTCTTATTTCTGCCCAGGTCATTCTTCTCAATGCT R 2 1 2 1 101000 r 74 goat Random2.2K-231 2 83126326 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435573 Affx-122933371 AX-123305913 2 83296024 ATGTTAAATGTTCAATAAATACTGTAAACTGGTGG[C/T]GTGCATTTTTTCTTTTTGCTATCCATTATCAAATG Y 2 1 2 1 103000 f 74 goat snp53766-scaffold82-3191231 2 51966551 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780745 Affx-122948153 AX-385267835 2 83324851 TTTAAATACTGGAGAACCACAAACATGCTATACCA[A/G]AAAAGTATAGAAAATGCATTTAAGATGAAAAAAGG R 2 1 2 1 201000 r 74 goat snp53765-scaffold82-3162404 2 51937773 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451313 Affx-122921282 AX-123321646 2 83361523 CTCATTCTGGTGTTTTGCATTTTCCTGATTATTAA[C/T]GACATTGAGCATCTTTGCTTGTCCTATTGACAATT Y 2 1 2 1 303000 f 74 goat snp53764-scaffold82-3125732 2 51900162 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434659 Affx-122933980 AX-123305000 2 83395760 AGTCAACTTTCTTCATTTTACTTCATTTGAATTTT[A/G]CTGCTTCTCATATGGGAAAAATGCCATGAATCAAG R 2 1 2 1 101000 r 74 goat snp53763-scaffold82-3091495 2 51866025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453079 Affx-122920049 AX-123323412 2 83431583 ATTTCTCTTTCATGTAATTCAGGAACTTGATTAGG[C/T]GAGCTGAGAAATATCATGATGGCTTTATTTCTACT Y 2 1 2 1 101000 f 74 goat snp53762-scaffold82-3055672 2 51830355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784005 Affx-122919397 AX-385271059 2 83483666 GGAAACAGATCCAATGTCTCAAACCAAACAAAAAT[A/G]TCCCAAACACCAAAATAACCAAAATGTATACAGGC R 2 1 2 1 201000 r 74 goat snp53761-scaffold82-3003589 2 51779754 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425772 Affx-122940721 AX-123296118 2 83519956 CATTATCTGGAACAATACAACCTCATTGAATTTGG[C/T]AGAACCGAAACTTTGAAACCTTGTAAATATCCATC Y 2 1 2 1 101000 r 74 goat snp53760-scaffold82-2967299 2 51742981 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774242 Affx-122953918 AX-385261378 2 83553505 CAGACCCTCTCTCTGGAGAATTGGATCAAGTGATA[C/T]AGGGATGTTTCAAAGCATCTGTAAATAAAAATTGT Y 2 1 2 1 101000 f 74 goat snp53759-scaffold82-2933750 2 51709385 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439092 Affx-122931121 AX-123309429 2 83592836 TCGGATACACAGACTGGGGTAGATTTTGTGATATA[C/T]AGACATTTAGAAAAAGAAAAAATAAGAAAATTATT Y 2 1 2 1 101000 f 74 goat snp53758-scaffold82-2894419 2 51670082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415775 Affx-122948920 AX-123286124 2 83683286 TGATATTATTCCAAGGCCTGATACTGCCTTCACAA[C/T]AGTCATGAGCGTTCTGTCATCCTCTATCCTCCTAG Y 2 1 2 1 101000 f 74 goat snp53756-scaffold82-2803969 2 51579633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434040 Affx-122934206 AX-123304381 2 83741640 GAAAGAAAGTTTCCAAATGTTCTAAACAACCATAC[A/G]TCAATCATTATTTCAGGAACTTTGCAGAGCAACTT R 2 1 2 1 101000 f 74 goat snp53755-scaffold82-2745615 2 51521378 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791927 Affx-122970999 AX-385278917 2 83794987 ATTGAACTGTGTTTACAGTTTGAAATTTAGATTGT[A/G]TCTAGTTTTCCTTCTTTATAGATAATACTGCAACG R 2 1 2 1 101000 r 74 goat snp53754-scaffold82-2692268 2 51467330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451067 Affx-122921424 AX-123321401 2 83824310 CTCTTCCTGTTTTTCAGGCCAAAAGCAGAAGAGTC[A/G]TTGTTTTTCTTTTTCCTTTTACTGTCATAAATATC R 2 1 2 1 103000 f 74 goat snp53753-scaffold82-2662945 2 51437701 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795936 Affx-122971699 AX-385282888 2 83971566 CTTCCAGCCAAGTAAACCCTTAGTGTGTAAAGAGA[C/T]GTTTTACTGTTGCACATGGGTTAGTTTCTGCATTT Y 2 1 2 1 101000 f 74 goat snp53749-scaffold82-2515689 2 51284288 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396858 Affx-122963249 AX-123267213 2 84030527 CCAGGTAAAGTAGAAAGCATTTCTTTACTGTCACT[A/G]CAGTGCTCTAGGGGGGGAACTTTAGCTTAAGTGTG R 2 1 2 1 201000 f 74 goat snp53748-scaffold82-2456728 2 51225625 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438775 Affx-122931381 AX-123309112 2 84060189 TTTCTAGGAATTTAAATGCAAGAACACCTCATTTA[G/T]CTGATATTGTTGGAGATGAGCTCACTTATGTGAAT K 2 1 2 1 101000 r 74 goat snp53747-scaffold82-2427066 2 51196000 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801088 Affx-122974310 AX-385288002 2 84090440 ATATTTTCTTTCAACTCCTCTGCCTCAGAATTTTA[A/G]TTATTTTCATGGTCTAGTAATAAGGATGCTAAGGT R 2 1 2 1 102000 r 74 goat snp53746-scaffold82-2396815 2 51165564 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415580 Affx-122948629 AX-123285929 2 84122854 AGTGTGACAAAGCCATGGCTAGATACAGGCTTTCT[A/G]TTTACTAATCTAGTTCAACACATGCGTGTGCACAC R 2 1 2 1 201000 r 74 goat snp53745-scaffold82-2364401 2 51133391 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273005 Affx-1111833182 AX-519546686 2 84157714 TCTCTGAATGTAGTGGAGAGCTTTCACTGTTTTTT[A/G]ATTTATATCGTATTGATACTGTTTTGTATATCTGA R 2 1 2 1 201000 r 74 goat 2_84157714_AF-PAKI 2 84157714 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38375930 Affx-122978464 AX-123246289 2 84223200 TCTGCAATAGAATTCTTAAATATTGAAGCCAATTA[C/T]ATTTTTTAAATATGGCATGATCATGTCAACCACCC Y 2 1 2 1 101000 r 74 goat snp53743-scaffold82-2264055 2 51032777 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380537 Affx-122975674 AX-123250895 2 84264521 AAGCTTACCTTCTTGTGGGGGAAAATACACAAGAA[C/T]GAAATAAGTGCATGGTACTCTGTGGTACATCAGAT Y 2 1 2 1 101000 r 74 goat snp53742-scaffold82-2222734 2 50991635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448377 Affx-122924102 AX-123318713 2 84322756 AGTTATGGGACCAAGGCTCTTGTGTGCCTGTGATG[A/G]TCTGTACTGGCCCTGTTAATATCTCTTTACTGATG R 2 1 2 1 101000 r 74 goat snp53741-scaffold82-2164499 2 50932050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440421 Affx-122929604 AX-123310758 2 84365569 TAGCTTTCTTTTTCAGGCTCTTCAATTGTGATCTT[A/G]TAGAAAATGTTTACTGGTTTAGTTTTATAGTTTGT R 2 1 2 1 101000 f 74 goat snp53740-scaffold82-2121686 2 50888737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396496 Affx-122963534 AX-123266851 2 84402781 TGGCCAGACCTAAGACATGTGCCCACCCAGCCATC[C/T]AAACCTTAGATTCTCTTAATAGGAATGAAGTGTTC Y 2 1 2 1 101000 r 74 goat snp53739-scaffold82-2084474 2 50851918 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407415 Affx-122955236 AX-123277766 2 84436175 ACAATTTTTTTTTGCCAGTGTTCTCATTGTTTTTA[C/T]GGAGGATTAGGTTTTTGGAGGTCCTTACTTAGCCA Y 2 1 2 1 303000 f 74 goat snp53738-scaffold82-2051080 2 50818489 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796743 Affx-122925211 AX-385283687 2 84524509 TGTGGATATCTGGGGACAGAAAAGTCCAGAAAAAA[C/T]GAATATAGTGCAAAGACCTTAAGTCAGAATGTCTG Y 2 1 2 1 101000 f 74 goat snp53736-scaffold82-1962746 2 50730732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771278 Affx-122932424 AX-385258436 2 84572535 ACCTTGTCAAACAGCTTTAAGAAATCTAACTTACT[A/G]CTGATTTCCCAACAGATAGAACTGTCAGGGGAAAA R 2 1 2 1 201000 r 74 goat snp53735-scaffold82-1914720 2 50682994 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415705 Affx-122948526 AX-123286054 2 84610459 CAGTGACTGTAGGGCACAAAGAGGGAGATGGTTGG[C/T]GAACCTGCCCAAGTTTGGGATTTGACATGAATGGT Y 2 1 2 1 201000 r 74 goat snp53734-scaffold82-1876796 2 50644673 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426756 Affx-122939856 AX-123297102 2 84666330 AAATCCTTTGTTTAGTAAACATTTGAATGCCTTGT[A/G]CGTGCACATTCCCATGTCTGACCTCAGTCATGGAA R 2 1 2 1 201000 f 74 goat snp53733-scaffold82-1820925 2 50587642 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415097 Affx-122949449 AX-123285446 2 84713509 TCCTGTCTCACTTCCCATTTATCCTGCATATTCCC[A/G]TTATCCTTTTTAAAACAGCAATTTAGCATAATTAT R 2 1 2 1 101000 f 74 goat snp53732-scaffold82-1773746 2 50541377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393647 Affx-122965292 AX-123264002 2 84745367 CTTCTTGTCAGTTATTTATTGCCTTGTGAATAGAT[A/G]CTCTAAGACAGAAGTTGTAAGCATTTCTGTAAAGG R 2 1 2 1 101000 f 74 goat snp53731-scaffold82-1741888 2 50509206 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777338 Affx-122939736 AX-385264460 2 84774247 TCTTCATAAATATGCCTTTGCTCGGCTTAGCTACT[A/G]TTGCTCTTCCTTAGATTGCTATTCATTAAGTAAAT R 2 1 2 1 101000 f 74 goat snp53730-scaffold82-1713008 2 50480326 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793221 Affx-122944449 AX-385280199 2 84833313 TGCCCTTGGAAATTGCCACATATTCTCCCTGACAA[C/T]ATGATTTCTCAGTAATTTAGGATTGAATCCTTTTC Y 2 1 2 1 101000 f 74 goat snp53729-scaffold82-1653942 2 50420213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421607 Affx-122944483 AX-123291954 2 84883896 TGTCCTAGCAAATAAGGTGCTATATGTGCAGTCCT[A/G]CCTGATACACAGCAAGTGCTCCATGAAATTAGCTG R 2 1 2 1 101000 f 74 goat snp53728-scaffold82-1603359 2 50369633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421845 Affx-122944296 AX-123292192 2 84930611 TAAAATTTATTATTTATCATTTTACTCTAGTCTGT[A/G]TTCCTAGTGGTACAGTGTCAGCCTCTTTCTTCAGA R 2 1 2 1 101000 r 74 goat snp53727-scaffold82-1556644 2 50323989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792415 Affx-122935336 AX-385279396 2 84973754 AATTTACTGTTGGCTAAAGGGGCAAACATCAATGC[A/G]TTTGACAAGAAGGATCGACGTGCTCTGCACTGGGC R 2 1 2 1 101000 f 74 goat snp53726-scaffold82-1513501 2 50281528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798156 Affx-122943430 AX-385285091 2 85006571 ACCATAGGGATATCATTGGCCAATGACCTATTTTT[A/G]CTAGTATTAGTATTAGCATTTTCTTTTCCCCTTGG R 2 1 2 1 101000 r 74 goat snp53725-scaffold82-1480684 2 50248184 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383075 Affx-122973742 AX-123253433 2 85038731 GTGGGTAGACTGCAGGCCCCTTCACAGCTCTGGGA[C/T]GGGTGTTTTTGTCCTGAGGGTAGGTGCTCACCTCT Y 2 1 2 1 101000 r 74 goat snp53724-scaffold82-1448524 2 50216323 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427223 Affx-122939576 AX-123297566 2 85104816 TAGATCTGTCAAGTTTTCTTTCAAGGAACAAAAGG[A/G]TATATCATAAGGAGCTTGTTTCCTGGACTGGGGAC R 2 1 2 1 101000 r 74 goat snp53723-scaffold82-1382439 2 50150342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381653 Affx-122974752 AX-123252011 2 85203721 TCCCCATGGCTCTGGGCTCCACAGAGGGAGATGGC[A/G]TGGAGGGACCTCTCTGTGAAGTTGCTGGGAGCAAT R 2 1 2 1 102000 r 74 goat snp53721-scaffold82-1283534 2 50051321 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448356 Affx-122924119 AX-123318692 2 85234005 TCCTGGACATTTTCCACAGGTGAGTTGGGATGGAT[A/G]AGTGTCAGTCACTGTTGTTCTTGGAGTGGGGCACT R 2 1 2 1 101000 f 74 goat snp53720-scaffold82-1253250 2 50020983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277824 Affx-1111836107 AX-519551321 2 85287737 TACTCAATTATTTCTGGTATCTTGCTGTTGCTGCT[A/G]CTGCTAAGTCGCTTCAGTCGTGTCCGACTCTGTGT R 2 1 2 1 102000 f 74 goat Random2.2K-232 2 85287737 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449052 Affx-122923061 AX-123319387 2 85375465 ACAGAGATCCCAGCAATAAACCCACACTTACATGG[C/T]CAGTTGTCCATAACAAAAGAGGCAATATATACACT Y 2 1 2 1 201000 r 74 goat snp53717-scaffold82-1111790 2 49883481 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791119 Affx-122974875 AX-385278114 2 85412248 ACTGTTCTCTCTGGAAGATGTTCTTGATTCTAAGA[C/T]ATTTTCCTCCCACTCAACCCTACCCCACATTTCAT Y 2 1 2 1 101000 r 74 goat snp53716-scaffold82-1075007 2 49846445 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409077 Affx-122953340 AX-123279428 2 85462071 TAATCTACAGGGTCTAGGGATTTGAGGTCTAGAGT[G/T]TGAGTTAAGGGCCTCTGATCTAGAATTCTACAGAC K 2 1 2 1 101000 f 74 goat snp53715-scaffold82-1025184 2 49795662 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400384 Affx-122960011 AX-123270739 2 85498564 TCTTTGCTCTTTTTTTCACCTTCCTGTCTTCTGTT[A/G]TATTGAGTTCTTTAACATTTCATCTGGCTAAGAAG R 2 1 2 1 201000 r 74 goat snp53714-scaffold82-988691 2 49758283 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420643 Affx-122944834 AX-123290990 2 85548976 TGTCTAATATATAAATTAATTGAATGGGTTGGTTT[A/G]TATTTTAAGTGTTTTTTCCTCTAAAATTAGAAAAC R 2 1 2 1 103000 r 74 goat snp53713-scaffold82-938279 2 49707566 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437397 Affx-122932430 AX-123307735 2 85581732 AATGTCTCCCTGTTTAACCTCAGCTGGGACCACAT[A/G]TGTAACACAACTCAAATTGCCAAATGAGGAATTAG R 2 1 2 1 201000 r 74 goat snp53712-scaffold82-905523 2 49674400 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385811 Affx-122971030 AX-123256169 2 85636938 GCCAAGGTGGAGGCTATGGAAGCTTTTCCTAAAAC[G/T]CAATCAACTTGAAGCAAGAAAAAAGTTCATTAATA K 2 1 2 1 101000 f 74 goat snp53711-scaffold82-850317 2 49618813 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778233 Affx-122977667 AX-385265348 2 85668217 TTTTCCAAAACAGCCACTTGTTTTCACTGTGCTTA[C/T]GTTTAAAAGCATATAGAGATTTAAACTATTACAGT Y 2 1 2 1 102000 f 74 goat snp53710-scaffold82-819038 2 49587445 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387828 Affx-122969668 AX-123258186 2 85707883 AGAACACTACCCACAACAGAACCACCTGAGGCCTC[A/G]TCCTTGACCCGCTGAATCATATTCTCTAGGGAACA R 2 1 2 1 101000 r 74 goat snp53709-scaffold82-779372 2 49547565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390656 Affx-122967136 AX-123261013 2 85771307 GTTTCTGGATAAGCCTTGTAGAATATTAAATATTT[A/G]TCAGAAGATAATTAGTCACTCAGTCAATAGGATTT R 2 1 2 1 201000 f 74 goat snp53708-scaffold82-715948 2 49483714 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378354 Affx-122976830 AX-123248713 2 85800307 GCACAACCTCTTACAAACCATATGGAAGGACTTAC[A/G]TGTCATTTCCTAGCATTTTTCAGAGCCTGGATTTC R 2 1 2 1 101000 f 74 goat snp53707-scaffold82-686948 2 49454586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402801 Affx-122958285 AX-123273154 2 85839919 CTGCCAAAGCAATTTAGATCCCACACAGAATGCAA[C/T]GCTCAACCATGCTGCAAGAAAAAGACAATTTCTAA Y 2 1 2 1 101000 f 74 goat snp53706-scaffold82-647336 2 49414873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435874 Affx-122932793 AX-123306213 2 85869473 TGAAGACACGAGCTTGTTTCTGTCCCTCAGAGACC[A/G]TTTTCCATAATGTCCCAACACAGTGAGGAAGTGGA R 2 1 2 1 101000 r 74 goat snp53705-scaffold82-617782 2 49384851 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772759 Affx-122939595 AX-385259904 2 85900066 AAATCAGAAGTTCTTGACTCAATCTAGGATGACTC[A/G]TAGGTTTCTGGCTTGAATGAAAGGTGAATGGAAAT R 2 1 2 1 101000 f 74 goat snp53704-scaffold82-587189 2 49354050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394355 Affx-122964653 AX-123264710 2 85955490 GACATGACTGAGCGACTTTCACTTTCATAGCTTGC[A/G]CTTTTTAGCATTTGCATCAACGATGAGAACGCACA R 2 1 2 1 201000 r 74 goat snp53703-scaffold82-531765 2 49298424 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453323 Affx-122919974 AX-123323656 2 86009871 GCTTGAACCCCAGTAGATGCCATTCTCCTTTGTTA[C/T]AAACTTAAATACACTCTGACTCCCTCTCCTGCCTT Y 2 1 2 1 201000 r 74 goat snp53702-scaffold82-477384 2 49242718 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382371 Affx-122973859 AX-123252729 2 86040675 ATTAACTGTATATTTCTGCCTCATTCTTTCTCAGG[C/T]TCAGAAACCTTGTCAGAGACTATTGATGTTTACCG Y 2 1 2 1 201000 r 74 goat snp53701-scaffold82-446580 2 49211808 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424690 Affx-122941702 AX-123295036 2 86074192 AATCCTAGGCAAGGAAGATAGGCATAATCATAGGC[A/G]CACACTGGAACATGGGCAGGATAGGGTTCCCCTTG R 2 1 2 1 101000 f 74 goat snp53700-scaffold82-413063 2 49178247 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378720 Affx-122977046 AX-123249079 2 86129436 ACTTGAAAAGTCAAGGCTTAGGATTTTAAATGATC[A/G]TCAAGTGCTAGTAACACTAAGCCACAAATATGACT R 2 1 2 1 101000 f 74 goat snp53699-scaffold82-357819 2 49124528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427128 Affx-122939654 AX-123297471 2 86173736 GTGGAGCTTCTGATCAGCCAAAAATTGAAAGATAC[A/G]TAGATAAGAAAAGGTCTAGATTTAGTTTAAGGAAA R 2 1 2 1 101000 f 74 goat snp53698-scaffold82-313519 2 49080451 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397130 Affx-122962677 AX-123267485 2 86218377 AACACAAATAATTTAAAATGCATTAAGTAGGAACT[A/G]CCCCCTTGGACTTAAACTAACTTATAAACTTTACC R 2 1 2 1 101000 r 74 goat snp53697-scaffold82-268878 2 49035761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769961 Affx-122943179 AX-385257130 2 86247887 GAGAATAGTTCAGGTATTTCAACATTCCAAAAAGC[C/T]TTACTGAGTAAGTTTCTTAATTAGCTATTTCTTGA Y 2 1 2 1 101000 f 74 goat snp53696-scaffold82-239368 2 49005956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417579 Affx-122946897 AX-123287927 2 86291250 TTTGTCATCGAGGAAGGCCATCAGTAGGGTTTATG[A/C]TTTTGGGGATGAGTCTGGAAGTGTTCTAGAAGCTA M 2 1 2 1 101000 f 74 goat snp53695-scaffold82-196005 2 48962165 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802671 Affx-122959601 AX-385289570 2 86343095 TTTGATATAAGGACCACTTCTGTGGATTAAAGTAG[C/T]ATTTTCCAAATAGTGTTTTGCTGCAGGCTGTTCCC Y 2 1 2 1 101000 r 74 goat snp53694-scaffold82-144160 2 48909742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386676 Affx-122970187 AX-123257034 2 86383519 ACGTGACACCCATCCTAACAAGCACAATCAGCGTG[C/T]ATGAACGAAGTAGCTACTATGTACCTTAGTAGGCA Y 2 1 2 1 101000 r 74 goat snp53693-scaffold82-103736 2 48868443 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394732 Affx-122964868 AX-123265087 2 86434485 AAGAACTTATCAAAGCTAGCCTCACTCTTCATGAG[A/G]CATCATACCATTAAGTGCTATAGGGGATGTAAAAG R 2 1 2 1 101000 f 74 goat snp53692-scaffold82-52770 2 48816564 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437555 Affx-122931895 AX-123307893 2 86496223 TATTCTAAGAATTTAATGAGATAGGCTATGTAAAG[C/T]ATTTAGCATAGTGCATGGCTCAGATGAAGTGTTCA Y 2 1 2 1 101000 f 74 goat snp40299-scaffold515-8869 2 48753642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797161 Affx-122967104 AX-385284101 2 86534788 TGAACTCTAAATAGCTAATTGGGGCCCAAACACAT[C/T]ACCTAGCAAATGATAAAGTGACGACAGAACAACAA Y 2 1 2 1 101000 f 74 goat snp40300-scaffold515-47434 2 48714578 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376777 Affx-122977960 AX-123247136 2 86643951 CCTATCATCACTCCTCCCTGGCATGTGTGTATACA[C/T]GCTCTTCTGAAAGTCTTTGCTTGAACCTGACCTCA Y 2 1 2 1 101000 r 74 goat snp40302-scaffold515-156597 2 48599600 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789393 Affx-122974195 AX-385276403 2 86701489 GGCTTATAAACCCACACTGGATTGCTAGTTTCAGA[C/T]AGTGTCTCTGGGAGTCAGGCTTTTTGAATACACAT Y 2 1 2 1 101000 f 74 goat snp40303-scaffold515-214135 2 48542876 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272956 Affx-1111833183 AX-519546642 2 86720368 TACCATCCGTCAATAGGACATAAGAGGGCATGGCA[A/G]CCCACTCCAGTATTCTTGCATGGAGAATCCCCATG R 2 1 2 1 102000 f 74 goat 2_86720368_AF-PAKI 2 86720368 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38384255 Affx-122972354 AX-123254613 2 86743215 TAACTTTACCTGCCATATATTTGTATACTCCTTCA[C/T]TTCTTGCTTTCAGAATTTTAAAGATGCTATCTGGC Y 2 1 2 1 101000 f 74 goat snp40304-scaffold515-255861 2 48501026 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783029 Affx-122948736 AX-385270097 2 86788978 CCTGCCTTTGTTTATGCCATTGCTTCTATCTGTAA[C/T]AATCTCTTCTACTCTGTAAAACCCTACCACCCATC Y 2 1 2 1 101000 f 74 goat snp40305-scaffold515-301624 2 48454182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448768 Affx-122923313 AX-123319104 2 86821973 TGAAGTCCTTCAGCCATCTCAGCCTCCATCATTCA[A/G]TATTGATTTCTTCATATCTACTTCTGGAAACAAAA R 2 1 2 1 201000 r 74 goat snp40306-scaffold515-334619 2 48420403 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401095 Affx-122959416 AX-123271448 2 86857555 AATCTGTTAGAACAAGTTCAGCAACATTACAGGTA[C/T]ATGAATGTACAAAAATCAATTGTATTTTTACATCT Y 2 1 2 1 103000 f 74 goat snp40307-scaffold515-370201 2 48384610 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779219 Affx-122951306 AX-385266323 2 86890641 GAGAATTTCTAAACTTTTCTGGTTCAAAGCAAAGA[C/T]TCATGGACAGAGATGAAAACTGTCTAAAAGAATGA Y 2 1 2 1 101000 r 74 goat snp40308-scaffold515-403287 2 48351477 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274923 Affx-1111834578 AX-519548505 2 86906803 TAACATGCTTATAATGAACATCAAATCTTCCTTGC[A/G]CAGGAAAAAAGCTTGCTTTCCTAGCTGCCCTCAAT R 2 1 2 1 201000 f 74 goat GoatD01.042123 2 86906803 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38429275 Affx-122937884 AX-123299617 2 86929525 AACTTTTATTATAAGAACTCAAAAACATATATCTG[C/T]GATTTGATTCAGTACCACAGCAAATGTATTGCTTT Y 2 1 2 1 101000 r 74 goat snp40309-scaffold515-442171 2 48313080 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803016 Affx-122947898 AX-385289893 2 87018695 ATCTCGATCTACTATGGGGGTAGATCAGATTCTAA[G/T]CTGGTCCTACTCCTATCTGTTCTTGCCTCCAATGT K 2 1 2 1 303000 r 74 goat snp40311-scaffold515-531341 2 48223232 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801419 Affx-122959357 AX-385288328 2 87083089 TTTTCTATAACATTCACTCTGATCCCTTGGATGCA[C/T]GAAGTAGCAGCTACTAAAAATGAGAGATGATCCAA Y 2 1 2 1 101000 f 74 goat snp40312-scaffold515-595735 2 48158615 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424645 Affx-122942167 AX-123294991 2 87120714 AAGAGGGTAGAAACCTACTTCCTTTTAAATGCTGT[G/T]TTTGCATTCTTAAAACAAGAAGCAGAGAAACTTTG K 2 1 2 1 101000 f 74 goat snp40313-scaffold515-633360 2 48121013 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770380 Affx-122959841 AX-385257545 2 87152712 TAGTCAAGAAATCTCTGACTTTGTATTATTGGAAA[C/T]AAAAGTTGTTAGCACAGACCCCCTTCTAAAAGACA Y 2 1 2 1 101000 r 74 goat snp40314-scaffold515-665358 2 48088038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783355 Affx-122970658 AX-385270419 2 87195086 TTACAGTTCAAGGTTAATTACTGTATACCTTGAAT[A/G]TAATAAGTAAAAATGATCTGCTGCTTTTTTTATTC R 2 1 2 1 101000 f 74 goat snp40315-scaffold515-707732 2 48045652 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448072 Affx-122924338 AX-123318408 2 87228879 ATAAAAACAAGGAATGGTAATCACAAAATTCAAGA[G/T]CAGGGTTACATCTGGGGAAAGTCAATGGAAAAGAG K 2 1 2 1 201000 f 74 goat snp40316-scaffold515-741525 2 48011875 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427009 Affx-122939847 AX-123297354 2 87314015 CAGACATGACTGAAGTGACTTAGCACAGACACATG[C/T]AAATACTTCTCTCGATCCAAGGGCTACCAACATAA Y 2 1 2 1 101000 r 74 goat snp40317-scaffold515-826661 2 47926410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424398 Affx-122941821 AX-123294744 2 87343304 AAGCAATCAGTTTTTCCTTTTCATATATGCATATA[C/T]AAATAACTGGAACAAGCACAATAAAAATAAACAAT Y 2 1 2 1 103000 r 74 goat snp40318-scaffold515-855950 2 47897143 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787511 Affx-122975164 AX-385274536 2 87374883 CTCAAAATATAATTATCAATGGATTACCTATTATG[C/T]ATTCAGAATTATGCCAGAGGGTGAGAGGAAAGCAA Y 2 1 2 1 101000 r 74 goat snp40319-scaffold515-887529 2 47866299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800170 Affx-122943468 AX-385287093 2 87430542 GTCAGCCATGACTCTGATTTAAGGAGACATGCATT[A/G]CAGAGGTTTCCTTTTATTGTGGTTTATTTCTAGCA R 2 1 2 1 101000 f 74 goat snp40320-scaffold515-943188 2 47810857 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420445 Affx-122944895 AX-123290792 2 87460411 TCTCATGGTGCTTTAGCTTACTATTTTAGGAGTCA[C/T]GTTCAATTTTCTTAAAATTGTTATTTTATGAAAGA Y 2 1 2 1 101000 f 74 goat snp40321-scaffold515-973057 2 47780742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783384 Affx-122945358 AX-385270448 2 87520254 TCAAACCTGAGAAGGGGTTGTGAGAACTCTGATGT[A/G]TCATCAATCAACCAGAAGTTCACCTGGACTTACAG R 2 1 2 1 101000 r 74 goat snp40322-scaffold515-1032900 2 47720658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784519 Affx-122921896 AX-385271568 2 87551902 TAACTAGTCTACCTGTGTCCCTGCCATGGTTTCAT[A/G]CAATGATGAATCCTTTTTCTAGATATCTGTATTAT R 2 1 2 1 101000 f 74 goat snp40323-scaffold515-1064548 2 47688513 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443147 Affx-122928067 AX-123313484 2 87689572 TTACTGAACCTTACAGCAAAGCTCAATTAACTGAA[C/T]GAAACAGGGAGAGAAAAGCTCCAATCTGGTACCCG Y 2 1 2 1 201000 f 74 goat snp40326-scaffold515-1202218 2 47550145 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274185 Affx-1111834093 AX-519547786 2 87715701 CCCAGGTGGGGCATGTCTTCAGACGCTGGAAGAGG[A/G]TCGCTGGAGGCCCTCCAGGTGGCTGCAGCGATTCC R 2 1 2 1 202000 f 74 goat GoatD01.017843 2 87715701 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38392532 Affx-122966106 AX-123262889 2 87731825 ATTTATCTTTGGTTCCAATTAGGTGAATTCATTGC[A/G]CTCTTGAAGGATCCAGGATAATCAAAATCACCAAG R 2 1 2 1 101000 f 74 goat snp40327-scaffold515-1244471 2 47507659 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769174 Affx-122935139 AX-385256349 2 87861362 ATTCCTAGAGAATAGATGATGGAGAATAATAAGCT[A/G]TGTTGAGTTGGCAATTTTTGTACTTCTGTGTGTAC R 2 1 2 1 101000 r 74 goat snp40329-scaffold515-1374008 2 47376193 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787248 Affx-122927062 AX-385274274 2 87911848 AGGTAGCCCAAATTAATCGCCGTTGTGCCTTTGCG[C/T]ACCCCTAAGACACCATTTGGAGACAAACGTCGAGT Y 2 1 2 1 101000 r 74 goat snp40330-scaffold515-1424494 2 47325778 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382361 Affx-122973868 AX-123252719 2 87949534 AGAAGAGGAGGTGCCTACCCCAAGGAGGAAGGAGG[A/G]CTGTGAGGGATAGCAGGGACCCCAACTCAGAATTC R 2 1 2 1 101000 r 74 goat snp40331-scaffold515-1462180 2 47289117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410176 Affx-122952593 AX-123280526 2 87981570 TGCTTCAGTTGCTTACAGGTATCGGACACTAACAT[A/C]AAGATTTGGGACAAGCTTTTATGTGTTTTACCATC M 2 1 2 1 101000 f 74 goat snp40332-scaffold515-1494216 2 47256764 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428913 Affx-122938915 AX-123299255 2 88019313 ACTCTTCACACGAATGTCATAGCCTTCTCTGTACA[G/T]GGCTTGTTCCTCATCTAGGATGCAGACTATTGGAG K 2 1 2 1 101000 r 74 goat snp40333-scaffold515-1531959 2 47219005 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770881 Affx-122923991 AX-385258044 2 88075911 ATTCAAGAAGGAGTCTCTTAGAGGATGTTCAGCCC[A/G]TATGAACTCAGTCTCCAAAATGGAAACGTTGTAGA R 2 1 2 1 101000 r 74 goat snp40334-scaffold515-1588557 2 47162616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413650 Affx-122950535 AX-123283999 2 88105132 GCCCAGGTATGTGGTCAAATGTTATTCTGGATGCT[G/T]CTGTGAAATATTTTTGCAGCAGTGGACTTTGTATA K 2 1 2 1 101000 r 74 goat snp40335-scaffold515-1617778 2 47133149 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430694 Affx-122936916 AX-123301035 2 88136799 GGGCTTGAGAGTCATAAGGAACTCTGGCCTGCGTA[C/T]GTCTGAGTTTTGACAGCCAAGGAGCCGCTGAGAAA Y 2 1 2 1 201000 f 74 goat snp40336-scaffold515-1649445 2 47101160 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776557 Affx-122944951 AX-385263684 2 88169278 TCTGAAAAGAGAGCTTGAAGAGCCAATTAAGAAGT[A/G]TGCGCTGCTCACCTAGAGTAACAAAGAGTTAGGGA R 2 1 2 1 101000 r 74 goat snp40337-scaffold515-1681924 2 47068691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798452 Affx-122930788 AX-385285385 2 88222598 TTTCTGTGCTCCGTGGAATTCCTCCCTGATTCTTA[C/T]GTAGATTACAACACTCCAGCTTTAGAAAACGCTGC Y 2 1 2 1 101000 f 74 goat snp40338-scaffold515-1735244 2 47014933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393828 Affx-122965166 AX-123264183 2 88286330 TTTTTATCAACCACAAACATGCATTTATGCCAAAG[A/G]GAAAAACTTGGCCTCTATTCAAAATAAGTATGCTG R 2 1 2 1 101000 r 74 goat snp40339-scaffold515-1798976 2 46951347 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379852 Affx-122975803 AX-123250210 2 88329053 TGCACATTCAAAATGCTATTTAAATAAAAATTCCT[A/G]TATGAACGATTTCTCAGGGAAGGCCAAATATGCTT R 2 1 2 1 101000 r 74 goat snp40340-scaffold515-1841699 2 46908778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449959 Affx-122922892 AX-123320294 2 88377461 CCAGTGCCTACCTTAGCTCCTGGCAGGCAGGCATA[A/G]TGATACAGGTTTGAGTGAAAAAACAAAGTCATTTA R 2 1 2 1 101000 r 74 goat snp40341-scaffold515-1890107 2 46860385 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392551 Affx-122966089 AX-123262908 2 88470401 AAAGCAATCTATCCAGTCTCAGTGCTCTAGTGTGA[C/T]AGGTCTGAAAGACAAATTTTCACAGTTCAGAAATC Y 2 1 2 1 101000 f 74 goat snp40343-scaffold515-1983047 2 46767949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797079 Affx-122939893 AX-385284019 2 88550183 GCTATATTCGTTGTAGTTTTTGCCTGGGCAAAACC[A/G]AAATGATCATCCAGTGAACCGTGAGTGTGCTAACT R 2 1 2 1 201000 r 74 goat snp40345-scaffold515-2062829 2 46688231 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796476 Affx-122958026 AX-385283426 2 88583586 AGACCTAGAGCCCAGGATTATAACAATAGAGGTAC[A/G]CAGGCCATTCCATGTCTTCTAGAATGACTAGGGTG R 2 1 2 1 101000 r 74 goat snp40346-scaffold515-2096232 2 46654836 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414122 Affx-122949713 AX-123284471 2 88617508 TTATTAATTCTGGGCAAACCTGCTAGTGCTTGTCA[C/T]GCATAGAAACTTACCTTTACTATTGCTTAACTGTA Y 2 1 2 1 101000 f 74 goat snp40347-scaffold515-2130154 2 46621273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381106 Affx-122974585 AX-123251464 2 88647204 GACTTTGCCTTCAAGGTGCACAGCAACCCCTTTAA[C/T]GAAAGGAATTTTATTTTACTCCTTCTCTCATCCAG Y 2 1 2 1 101000 f 74 goat snp40348-scaffold515-2159850 2 46591510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789610 Affx-122963092 AX-385276619 2 88683770 AAGGTATTCACACCAAAATGCTACAGGTGAGGGAA[A/G]TAAAATTCATCTCTCTATACACTGTTGACATGACT R 2 1 2 1 101000 f 74 goat snp40349-scaffold515-2196416 2 46554551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421208 Affx-122944142 AX-123291555 2 88716965 AATAGGTGTAGAGAACTGATGGAGAATTTCACTTT[A/C]ACACTTCCTATAACAAGTTACCAAGTGCTAAGAAT M 2 1 2 1 101000 r 74 goat snp40350-scaffold515-2229611 2 46521803 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379517 Affx-122976076 AX-123249875 2 88774320 GGGTCGATACAAGTTGCATACAGATTTCTCTCATC[A/G]GCCCATCTAACTCATGTGACCTTTTTTGTGTGTGT R 2 1 2 1 201000 r 74 goat snp40351-scaffold515-2286966 2 46463937 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438088 Affx-122931517 AX-123308426 2 88843534 AGGAACTGAAGGAACAGATTTACATTTCCCCAATA[A/G]CACACACTGGAACACTGTTCACTGAGGAAAAAAGT R 2 1 2 1 201000 r 74 goat snp40352-scaffold515-2356180 2 46394892 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452092 Affx-122920855 AX-123322425 2 88942310 TACTCTGTTTAATCTTTATAATAACACTATAAGAT[G/T]GATGGTAATCATTGCTGAGTAGAAGAAACAGGCCC K 2 1 2 1 101000 r 74 goat snp40353-scaffold515-2454956 2 46295556 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441944 Affx-122928577 AX-123312281 2 88975434 GCAAAGTTGATGAGAACTGGGACTTTCTGTGCTGT[A/C]GTGTGTGTCTCCGCAGAGCGACTGCTAGGACGGGA M 2 1 2 1 201000 r 74 goat snp40354-scaffold515-2488080 2 46262345 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436261 Affx-122932547 AX-123306600 2 89010456 GATCCAGAGGCCTATATCAGTATCTGCAAAATAGC[C/T]GAAAGATATTGTCTGTTGATGGGTACACAGGACTT Y 2 1 2 1 201000 r 74 goat snp40355-scaffold515-2523102 2 46227038 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436903 Affx-122933212 AX-123307241 2 89055111 ATCTAAAGATGGGCTTTTAATTGATCTAGACAGAG[C/T]AACGGGCATTTTGGCTTTCCCTGCTCTGAGAACAA Y 2 1 2 1 201000 f 74 goat snp40356-scaffold515-2567757 2 46182401 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779973 Affx-122978915 AX-385267072 2 89120226 GAACCTCTTGAACTTGTAGTTGATGTCAGAAGTGA[C/T]GATGGTTTGTAGACTGTTCTCTAACTCTGTTGTGT Y 2 1 2 1 101000 f 74 goat snp40357-scaffold515-2632872 2 46115411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788566 Affx-122977630 AX-385275583 2 89158591 TTTTAAGGGAAATGATGTTAATATTAACTCGTTTT[A/G]TACTTCCAGTACATCTTTTCCTAAGCTATCGTTTA R 2 1 2 1 201000 f 74 goat snp40358-scaffold515-2671237 2 46076686 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415213 Affx-122948977 AX-123285562 2 89208794 GCATCCGACATCAGAGGAGTGAGCCACTGAACACC[A/G]AGAGCTCTGGTTCCAGATGTCAAGAGTCAATGTTT R 2 1 2 1 201000 r 74 goat snp40359-scaffold515-2721440 2 46025751 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407050 Affx-122954930 AX-123277401 2 89248860 ATTGTAAAAGTCAACAAGATACTCATGATCTTTAG[G/T]TCAATGGATAAATTCAAATACTCACTCATATAACG K 2 1 2 1 101000 r 74 goat snp40360-scaffold515-2761506 2 45985196 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271884 Affx-1111833184 AX-519545667 2 89279385 TAAATCTGGTCCCTAAGAAAAGTAACAATAATCAC[A/G]CTGTGGGAAAGTAAATAGTAATAACATAAAAGCTG R 2 1 2 1 101000 r 74 goat 2_89279385_AF-PAKI 2 89279385 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320773277 Affx-122957171 AX-385260420 2 89285652 CACACCAGGAAATTCCCAAACCAATGACTTTGTTC[A/G]TGCTATGTCTTCTTTAACGTCCTCTCCCCATTCTA R 2 1 2 1 101000 f 74 goat snp40361-scaffold515-2798298 2 45947717 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375756 Affx-122978603 AX-123246115 2 89360334 TGGGCTTTGGTCAGCTTCTTTAATCCATAGGTTTA[C/T]GTTTTCCACAAATGCTGGGGTGTTTTCAGCCAATA Y 2 1 2 1 101000 f 74 goat snp40363-scaffold515-2872980 2 45872586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447039 Affx-122924531 AX-123317375 2 89390361 AGTCCATGGGGCTGCAAAGAGTTGGACATGACTGC[A/G]CAACTGAACAACAACAACTACAGTGGCATCCCTAG R 2 1 2 1 303000 f 74 goat snp40364-scaffold515-2903007 2 45841987 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799411 Affx-122930372 AX-385286341 2 89426439 ATTAAACTTCCCACTCTTTTCCTTATAACGCCTTC[A/G]TTCCCAGTTTTCAGTAGAATCCACCTAAATAAAAT R 2 1 2 1 101000 r 74 goat snp40365-scaffold515-2939085 2 45805950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417549 Affx-122946920 AX-123287897 2 89462711 TGAAGAACCTGCTCCTCAATTCCTTCTGCCCTAGA[A/G]GTAAAGAAATACTCATCAGAAATGTCTTCATTGTG R 2 1 2 1 201000 r 74 goat snp40366-scaffold515-2975357 2 45759214 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424970 Affx-122941920 AX-123295316 2 89495458 AATGGGATGTTATTTCTTCCCTTATGAAATGGTTC[A/G]TTCTGTAGAAAATTAGTATTTGCTTAATAGATGCA R 2 1 2 1 201000 r 74 goat snp40367-scaffold515-3008104 2 45726362 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412760 Affx-122950515 AX-123283109 2 89541763 CTGTGCTGGCGCCGGTTGGTGGTCAGGGCCACAGC[A/G]ATATTGTCCCACGCTTTCCAAACTTCCCCTTGGCC R 2 1 2 1 101000 r 74 goat snp40368-scaffold515-3054409 2 45680250 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409341 Affx-122954182 AX-123279692 2 89633305 TCTTTGCTATATATCTTTTCAGTTGTAATCGAGCA[G/T]ATGGTTCAGGTTGTAAGCAGTGTTATAATGAAGGT K 2 1 2 1 101000 r 74 goat snp40370-scaffold515-3145951 2 45588278 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394723 Affx-122964334 AX-123265078 2 89676227 TCTGACTATGTCTTTGTGTGTTTGCTGTGAACACA[G/T]CCTAAGCTGTGTGCATCGCATCCACTCGATTCAGT K 2 1 2 1 101000 r 74 goat snp40371-scaffold515-3188873 2 45544997 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406634 Affx-122955823 AX-123276986 2 89714710 ATGTACCTATCAAATCTGTAGAACACACAACTCTC[A/G]AAGAAGCAGCTGATGTTTAGCATTGGATCATGATT R 2 1 2 1 101000 f 74 goat snp40372-scaffold515-3227356 2 45506182 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424462 Affx-122941774 AX-123294808 2 89751880 TGGTCTTAACACAAAGGACTTACTTTCTGATCTTA[C/T]GCTGAGGGAATTACAATAACCCTCTAGGTGATTGC Y 2 1 2 1 101000 r 74 goat snp40373-scaffold515-3264526 2 45468678 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792224 Affx-122956567 AX-385279208 2 89848019 TAAACATTAGCTGTTAATAAACATAGTAACGATAC[A/G]ACTAATACCAGACACTGGAGTCTGTCAGTTGGCTT R 2 1 2 1 101000 r 74 goat snp40375-scaffold515-3360665 2 45372685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410207 Affx-122952571 AX-123280557 2 89880101 CCAAACCCCCCCATGGAAATGAGTGATTTGAGAAA[C/T]AATGACAGGTTCCCTAAGGAGTTTGGGGGTTGTTT Y 2 1 2 1 102000 r 74 goat snp40376-scaffold515-3392747 2 45340052 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435636 Affx-122933769 AX-123305976 2 89909698 AGATTCACACCAAGACTGTCTACCTCTCCATGCTT[C/T]GCACTTCACCCTGTTGTCTGTGGACTGTGGGGGGG Y 2 1 2 1 101000 f 74 goat snp40377-scaffold515-3422344 2 45310168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426668 Affx-122939923 AX-123297014 2 89986086 TGCTTAAACTTGACATTGACATCAAAGGGTATGTA[C/T]GTTATGCCCAGAAGATATGAAGAATGAGAAATAAG Y 2 1 2 1 201000 f 74 goat snp40379-scaffold515-3498732 2 45233753 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774929 Affx-122966728 AX-385262062 2 90026166 CATCCCCTGTTAGGAAGAAACACTATATTGTCCCA[A/G]TCCTTGGAGAAAGGCGAAAACTGACATAGCCATGG R 2 1 2 1 101000 r 74 goat snp40380-scaffold515-3538812 2 45193248 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414274 Affx-122949605 AX-123284623 2 90054824 GTTCCCTGAACACGTCTATAAACTTCCTTCCATCT[C/T]CAGCCCTCTACTGTTCTCGTTTCCTTTACCTGTAA Y 2 1 2 1 101000 f 74 goat snp40381-scaffold515-3567470 2 45164557 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797171 Affx-122950831 AX-385284111 2 90095157 GTTTCTTTTATTGGTGTATACCTTGGAAGCAGTCT[A/G]CTACCTCTTCTCCTAAATGTGTGGCATTTGCAAAA R 2 1 2 1 101000 f 74 goat snp40382-scaffold515-3607803 2 45124216 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788487 Affx-122922364 AX-385275504 2 90130307 GAGACACTAAAGTCAGATTACACAGTTATACTGTG[C/T]AGTCCAAACACCTGAGGGCTGATTTTCTTCCCACC Y 2 1 2 1 101000 r 74 goat snp40383-scaffold515-3642953 2 45089031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390300 Affx-122967722 AX-123260657 2 90193016 GAGGATTAATGTGGTGTTGAGTATTTTTTCGTGTT[A/C]TTTTTGGCCATCAGCATTTCCTTCTTGGATACCTG M 2 1 2 1 101000 r 74 goat snp40385-scaffold515-3705662 2 45026087 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381561 Affx-122974822 AX-123251919 2 90238066 TTGGACACTTTTTGCTTAAATTGCTTGACAACACA[C/T]GGCCAGTTCTATGTAGTGATACTTTCTGCTGAAAG Y 2 1 2 1 201000 f 74 goat snp40386-scaffold515-3750712 2 44980690 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386972 Affx-122969966 AX-123257330 2 90287285 ATGAAATATAACAAATAATCATTAAGTAAATGGTG[G/T]TAAATTCCTAAGCTTTTTTCAGTAAAAAGGCAGAG K 2 1 2 1 101000 r 74 goat snp40387-scaffold515-3799931 2 44931357 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383250 Affx-122972746 AX-123253608 2 90388801 TGAGAAAAGAAAGGATAAAAAACAGTAAAAGCATT[A/G]CCGCTGAGATTTGCTCTAAGGTTCTATTTGGGCTG R 2 1 2 1 101000 r 74 goat snp40389-scaffold515-3901447 2 44829494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397112 Affx-122962692 AX-123267467 2 90437405 CAATTTAAATTTTTTTTAAATTTTGAATAAATTTA[C/T]TTCCATTGCGGTAAAAGAAACAGGTGGCTTGTATA Y 2 1 2 1 103000 r 74 goat snp40390-scaffold515-3950051 2 44780581 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438726 Affx-122930841 AX-123309063 2 90496716 CTAATCTGAAGCAGGTTCGGTTTTGGCAAATTGAG[C/T]AGGTTCTGAAGAACAATTCCAATAATTAATCACTA Y 2 1 2 1 101000 f 74 goat snp40392-scaffold515-4009362 2 44720288 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391807 Affx-122967029 AX-123262164 2 90552515 GTCCCTAAAACTACTTATCTTGACATACTACTTTC[A/G]TTATCTTTTCTTACTGCCCAGTAAGCTCAGTGTTA R 2 1 2 1 201000 r 74 goat snp40393-scaffold515-4065161 2 44664609 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412230 Affx-122950917 AX-123282580 2 90582403 TTGTACATTCTGAAATATTTCAGATAAGCAACACC[C/T]AGCTGTGCAGCTAAGTCAGAGCCATCATTTAAAAT Y 2 1 2 1 201000 r 74 goat snp40394-scaffold515-4095049 2 44634668 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405997 Affx-122955513 AX-123276349 2 90668969 CTGATATAGCCTCTTGTCAGAATGTTTTCACATGC[C/T]TGAAAGAAAATACACACCGTCACAAAGGAAACTAT Y 2 1 2 1 101000 f 74 goat snp40396-scaffold515-4181615 2 44549056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800419 Affx-122926358 AX-385287340 2 90712130 GCTACTTGTTTAATTTCACTCTCTCAGGCTAAAAG[C/T]GGATTTCCCTGAGGTTGTGCATGTTAAAAAATTGG Y 2 1 2 1 101000 r 74 goat snp40397-scaffold515-4224776 2 44505892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445442 Affx-122925355 AX-123315779 2 90820636 TGGATGCCTCATCGCCCATCCCTTGTGGAAACTCC[A/G]GAGAGTAATTTGTGTCAGCGCCTTGAGATGATCCT R 2 1 2 1 101000 r 74 goat snp40400-scaffold515-4333282 2 44396985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773587 Affx-122940468 AX-385260727 2 90856509 CCAGGGATTAGGACGTGATCATGTGTGAAAGGGCC[A/G]CTATTCAGCCTACCGCAGTATTTGAACATAGCTTC R 2 1 2 1 101000 f 74 goat snp40401-scaffold515-4369155 2 44360725 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418320 Affx-122946971 AX-123288668 2 90899457 GTGAAATGTTACCCCCCTCTTCATTCTCCAGAGAC[A/G]TATTGATATTTCTAGCAGGAAAATTTGAAATTGAA R 2 1 2 1 201000 r 74 goat snp40402-scaffold515-4412103 2 44318131 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383671 Affx-122972506 AX-123254029 2 91011936 GCTCTTAAAGAGATTGGGTTTTTATAGTTCACTTG[C/T]ATTAATACTATTTCTAAGGTTTTTATTTAGTGTTG Y 2 1 2 1 101000 f 74 goat snp40404-scaffold515-4524582 2 44205582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781274 Affx-122933826 AX-385268359 2 91047329 CACAGACTCTGGGACATATAAAATCTCATGACTGC[A/G]CTTGGTTCTGAAGTAGTTGAATGTGAGCATTCGTA R 2 1 2 1 101000 r 74 goat snp46058-scaffold631-3250221 2 44168275 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427084 Affx-122939794 AX-123297427 2 91077507 AGCAGGAAAAGAGTCAAATTAGCTAATTACAACTA[A/C]TCAGTAACAATGTAACTTGTACCCTTTCATGTCTT M 2 1 2 1 101000 f 74 goat snp46057-scaffold631-3220043 2 44137739 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424350 Affx-122941932 AX-123294696 2 91109753 GGAATCTTCCATGCTTTCCTGTTCCCTTAAGAGGA[C/T]GCTATATTTTCCTGCTGACCATTCATGAGTCCTCC Y 2 1 2 1 101000 r 74 goat snp46056-scaffold631-3187797 2 44105437 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378302 Affx-122976853 AX-123248661 2 91139544 TCTTCCCAAGTCACCTTTCCCACTCACCTCAAGAT[A/G]TTCTATAATAAAGAACTTTTCTCATCCAAATACCC R 2 1 2 1 201000 r 74 goat snp46055-scaffold631-3158006 2 44075243 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431898 Affx-122936007 AX-123302239 2 91168562 CGTGGTTTATGATTGAGGTCTTACCTCCCCGTACA[C/T]GGAAACAGAGATCCCCTGGAGAAGGAAATGGTAAT Y 2 1 2 1 101000 f 74 goat snp46054-scaffold631-3128988 2 44046373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451532 Affx-122921095 AX-123321865 2 91238976 TTGCTCATACTCAGAGATGGCTGATGATCGGAGCC[C/T]GGGTGACCAGAAGGATAGTGTTTCATCCACAGGTA Y 2 1 2 1 101000 r 74 goat snp46052-scaffold631-3058574 2 43975116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382460 Affx-122974216 AX-123252818 2 91288695 TGATTTTCTAATTAGTTACGTGCATGTAAGAGACA[C/T]GGATGAGAGAGCATCCAGTTTTCCATACACGATGA Y 2 1 2 1 101000 f 74 goat snp46051-scaffold631-3008855 2 43923808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275306 Affx-1111834826 AX-519548882 2 91345014 AGCACACATCTAGATACAACCTAACCACTGAGCAC[A/G]TGCCATTGCAGACCATGGAACCCTGGACACAGGAT R 2 1 2 1 201000 f 74 goat GoatD01.055199 2 91345014 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320772623 Affx-122923694 AX-385259771 2 91346507 GAGAAAACAACAGGAAAGATGTCATGAGCGATACT[G/T]ATGCAGCCAGGTATTGATATACCCATACATGGTAC K 2 1 2 1 101000 f 74 goat snp46050-scaffold631-2951043 2 43865712 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779924 Affx-122972838 AX-385267023 2 91397801 CTTCTGAATCCGAGAACACAATGGTGATTCACTGT[A/G]CGCAGTCTAAGTCCTCAGATGACATCTTCCACTCC R 2 1 2 1 101000 r 74 goat snp46049-scaffold631-2899749 2 43814628 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278008 Affx-1111836128 AX-519551500 2 91458020 TTAAAGGGCTGTCGAATCAGTATGAAAGGGGACAC[A/G]TTGGAGAGATAGTAGGTTGTGATCTGAGAATGAGA R 2 1 2 1 201000 r 74 goat Random2.2K-237 2 91458020 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398490 Affx-122961570 AX-123268845 2 91497700 GAAAGTATTCACAATTGTGATTCTCAGATGAAGTC[A/G]TTTGTAGATTTCTTCCATTAAGTGGCAGGATGAAC R 2 1 2 1 101000 f 74 goat snp46047-scaffold631-2799850 2 43714325 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792728 Affx-122958414 AX-385279708 2 91527465 GATTGTATTCTGAGACAGAAATGTAAAGGAACCAC[C/T]GTTAGTACATGTCTTTCTACCCAGTTCCATCTGAT Y 2 1 2 1 101000 f 74 goat snp46046-scaffold631-2770085 2 43684204 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431097 Affx-122936613 AX-123301438 2 91647172 AGAACCACTACAGAATAATTATACATTGAAGTTTT[A/G]ATAAAGTTTACCAGAGCACACACAGGTTTTCACAA R 2 1 2 1 101000 r 74 goat snp46044-scaffold631-2650378 2 43563981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772312 Affx-122937292 AX-385259466 2 91686390 ATTTTTATATATAGTTTTACAAGGAGAAAATAATT[A/C]TGATAGAAGTACCAAAAATGAGGTTCAAAATAATA M 2 1 2 1 201000 f 74 goat snp46043-scaffold631-2611160 2 43524628 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419178 Affx-122945723 AX-123289526 2 91774725 TCTGCTGAGAGTTAGGAGATATGGATTTTTGTCCA[G/T]CGGATGTGCGTAAGCAGTGGAATGACTTCAATTCA K 2 1 2 1 101000 f 74 goat snp46041-scaffold631-2522825 2 43435892 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272050 Affx-1111833185 AX-519545814 2 91794233 CTTACATGTGGCATGTTAGATGTTTCTAACACTGC[A/G]TAAGTTATTTGCTTATAAGTCTTCCCCATGAGATT R 2 1 2 1 101000 f 74 goat 2_91794233_AF-PAKI 2 91794233 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38424407 Affx-122941814 AX-123294753 2 91804109 GTCCGTTCTGAACCCAGACTCCAGAATGGATTGGT[A/G]CTCACAGGCCTTTCAAGACTCCTGCCTGGAATTTC R 2 1 2 1 201000 f 74 goat snp46040-scaffold631-2493441 2 43406152 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277865 Affx-1111836129 AX-519551361 2 91810949 ACTACTGGGCCTCAGTGTTATAATCCATAAAAGAC[A/G]AGGTTAATTGATCTGTGCAAGTTAACAACTCAACT R 2 1 2 1 101000 f 74 goat Random2.2K-238 2 91810949 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452198 Affx-122920819 AX-123322531 2 91847573 GCATGTTGTAACGTGAGCCATTTTCCAGATCCTGC[A/C]CTGGGGTCTCTTGGGCGATTTTCCCTAGCTGCCTT M 2 1 2 1 101000 f 74 goat snp46039-scaffold631-2449977 2 43362855 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277867 Affx-1111836130 AX-519551363 2 91872886 ATACTCTATCCTTACCACATCCAATATGTAACCCT[A/G]TTAGTATATTAATTAAAAAAAAAACTCTTATTCTT R 2 1 2 1 101000 f 74 goat Random2.2K-239 2 91872886 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403619 Affx-122957548 AX-123273971 2 91909920 GGGAGGGGTGCAGGAGAGCTGTCTCTGTGTACTGT[A/G]TTAGTGGCTGAATTGATATAGGAATAAAATAGAAT R 2 1 2 1 201000 r 74 goat snp46038-scaffold631-2387630 2 43300143 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792989 Affx-122965244 AX-385279967 2 91947048 TCTTCGGCTTTTCTTGTTTAGGTAAATCACTCTCA[A/C]CTGTGATCTTATGTTTGCTTGATGGCTGTGGAGGT M 2 1 2 1 101000 r 74 goat snp46037-scaffold631-2350502 2 43263135 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423046 Affx-122942965 AX-123293392 2 91996682 TTGCAAGCAACCAACTTTCCTTCTATCTCTGACTT[G/T]TCACACCATGTGAATTCAGAACACAGCTCTTGTTT K 2 1 2 1 101000 f 74 goat snp46036-scaffold631-2300868 2 43213335 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416452 Affx-122947821 AX-123286801 2 92034027 AAGAATAGAAACATGTGACTACCATCACCAGGCCC[A/G]TTCCCTAAGCCCAGGAGATAACCTGGATTCCTATT R 2 1 2 1 101000 r 74 goat snp46035-scaffold631-2263523 2 43175543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798194 Affx-122960223 AX-385285130 2 92064323 AACAAAGTGGGTACTGATCTGAAAAGAGAGAACTT[A/G]GTAAATTATTGACAGCCATTTGCAAAACTCATTCA R 2 1 2 1 101000 f 74 goat snp46034-scaffold631-2233227 2 43145422 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447368 Affx-122924863 AX-123317704 2 92161766 GAAGAAAAGTATGGGCCAGAAAGCCCTCTCTGAAG[A/G]CCACTCTGCTCTGATTTCAGAAATACTCCGCTAGT R 2 1 2 1 201000 r 74 goat snp46032-scaffold631-2135784 2 43048552 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416148 Affx-122948280 AX-123286497 2 92190954 CATCCTAAACAGATTTTTGCTGTTCAGCTTCCCCA[A/G]TCCTGACCCTGAGACCTGGTTCCCGAAGGCTCCCT R 2 1 2 1 101000 f 74 goat snp46031-scaffold631-2106596 2 43019352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408309 Affx-122953771 AX-123278660 2 92253405 TGACCATTTCTTTCCAACTCCCAGTGAAACCTTTG[C/T]ATCACAGATGTGCACAAGCATGCTCAGGGCAAGTA Y 2 1 2 1 101000 f 74 goat snp46030-scaffold631-2044145 2 42956774 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441337 Affx-122929427 AX-123311674 2 92339955 TATCTCAAAGACAAAGGGAAAGTCACAGCTGTGAC[A/G]TACTAGAGAACCCAGAAGATTCTTAGATAATTAGG R 2 1 2 1 101000 r 74 goat snp46028-scaffold631-1957595 2 42869977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384136 Affx-122972812 AX-123254494 2 92374806 ACTCCTAATTTCACTATTAAATATGGCAAAGTTCA[C/T]GTAAAAGTTTTAAATCACAAAGCATCTAAGGAAAT Y 2 1 2 1 101000 f 74 goat snp46027-scaffold631-1922744 2 42834912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414294 Affx-122949592 AX-123284643 2 92411522 CTTTAGCGATAACTTATGAGTGAGTTATTCTTTTA[A/G]CATTTTAAAGATGGGTGGGGAGAAAGAAAATTATT R 2 1 2 1 201000 f 74 goat snp46026-scaffold631-1886028 2 42797612 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770403 Affx-122978381 AX-385257569 2 92450284 GTCATCTTTTAAATAGTTATCCAATGAATTTAATG[C/T]ATGTCTAATGTACACAAATTTTGGCCAAAGCTTAC Y 2 1 2 1 101000 r 74 goat snp46025-scaffold631-1847266 2 42758737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400584 Affx-122960405 AX-123270939 2 92487592 AGTGAGGATTGATACTGTTGAATAACTGTTTTTCA[C/T]AAAGATTTTTAAAAGATATTTAAGAGGGAGTTGAA Y 2 1 2 1 102000 f 74 goat snp46024-scaffold631-1809958 2 42721435 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785861 Affx-122964053 AX-385272898 2 92535778 TACATATTAACAATTCTATACCTGTTTGCCTAGTG[A/G]GACCACAGATAAGAGATTTTGTTTCCCAAAGTGAC R 2 1 2 1 101000 r 74 goat snp46023-scaffold631-1761772 2 42673305 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423753 Affx-122942850 AX-123294099 2 92566857 ATACTGACAATTGAGTGTATGAAGGAAAACTGCAA[C/T]CCTAACTTACACCATTTGTAAAACGTATTTATACC Y 2 1 2 1 101000 f 74 goat snp46022-scaffold631-1730693 2 42642387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421499 Affx-122943905 AX-123291846 2 92643867 GGTTATTCTGTTCAACACAATCAGATCTAAGATTA[A/G]TTCCTCAGCCAAACAGGAACAGAAGAATGTGCACA R 2 1 2 1 101000 f 74 goat snp46020-scaffold631-1653683 2 42561298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782242 Affx-122943027 AX-385269320 2 92688735 ACACTGTATAACAAATGTCACCTGAAATCCTCATG[A/C]AGCTAACATGGCTCCCATCATACAAAGTTGGAAGA M 2 1 2 1 101000 f 74 goat snp46019-scaffold631-1608815 2 42515808 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439581 Affx-122930074 AX-123309918 2 92772610 TAGCTACATTCCGAGTCTCAAGCATACATAGCTAC[A/G]TTAAAGTAGACCGTGTTTGCTGTATGCAAGTCCAA R 2 1 2 1 101000 r 74 goat snp46017-scaffold631-1524940 2 42431441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418989 Affx-122946062 AX-123289337 2 92840450 AGGACTCATCGGCCTTCTTCAGCACTGCATCATCT[C/T]AAAGAGCTGGGTCAGCAAGGATCTCTGCAGACAGT Y 2 1 2 1 201000 f 74 goat snp46015-scaffold631-1457100 2 42362687 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433286 Affx-122935211 AX-123303627 2 92902449 AACATAAAGTAACTACTTCAATGCCTAGTATATAG[C/T]AAAGCTCAGGAAACAGCTCTATCATTTCTTATTAT Y 2 1 2 1 201000 f 74 goat snp46014-scaffold631-1395101 2 42301458 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406514 Affx-122955141 AX-123276866 2 92931549 ACTGGGATTATACTTTTTTTTTTCAATTTTCCTCC[A/G]TAAAATAATATCCTTTCTCTTTTCTTATGATTGAA R 2 1 2 1 201000 r 74 goat snp46013-scaffold631-1366001 2 42272358 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393873 Affx-122965133 AX-123264228 2 92971317 ACCTCTTTTGATAACCATTCCAGGCTTTAAGAGTC[A/G]TATTGTCAGAAAATTCTCTCTTTTATCTAGCTTAA R 2 1 2 1 101000 f 74 goat snp46012-scaffold631-1326233 2 42232375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796782 Affx-122968768 AX-385283725 2 93003720 AATTTATGTAGGTATCAGTGACCACTCTTCTTTCT[C/T]TTGGCACAGACTATATGAAAACAATTCTGAGCAAT Y 2 1 2 1 101000 f 74 goat snp46011-scaffold631-1293830 2 42200002 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409792 Affx-122952973 AX-123280143 2 93058861 TGTCTGCCATCAAACTGGCAGAGCTATTTCCTCCA[A/G]ATACAGATCTATCAGCTCATTCTCCAGTTATGGCA R 2 1 2 1 201000 r 74 goat snp46010-scaffold631-1238689 2 42144369 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391086 Affx-122966830 AX-123261443 2 93136268 CCTGATATAGAATGCACCACCAGGGATAAGGTGAC[A/G]CAGCCGGGGCAATGGAGGAAGGCCTCACAAGAGTT R 2 1 2 1 101000 f 74 goat snp46009-scaffold631-1161282 2 42066373 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431068 Affx-122936635 AX-123301409 2 93196856 TCAGAGATGCTGCGCCTTATACTTGAGAAAAGATC[G/T]AAATTTATTACGTTTAATGTTTAATATAAATCACC K 2 1 2 1 202000 r 74 goat snp46008-scaffold631-1100694 2 42003466 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782731 Affx-122932887 AX-385269803 2 93276246 TATGTTTGGAAACACCTGCAGGTACAATTCGTGAC[C/T]AGATGGTAAATGAGCTTGTTCTTAGTTGATCATGA Y 2 1 2 1 101000 f 74 goat snp46006-scaffold631-1021304 2 41924277 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379835 Affx-122975816 AX-123250193 2 93350711 CAGACCTTCTGGAAAATCCCTCCTTGTTATTTCCA[C/T]ACCAAGATAAGCACCGCTGGACGGTCACTCAGCTG Y 2 1 2 1 201000 f 74 goat snp46004-scaffold631-946839 2 41849106 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385588 Affx-122971211 AX-123255946 2 93397645 GCAAGAGAACTGACGTGAGTTGAGCACCTCGAGGT[A/G]CCAGACATCACGCTGGGGGCTTCATCGCCTTCCGT R 2 1 2 1 103000 r 74 goat snp46003-scaffold631-899905 2 41802155 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428725 Affx-122938455 AX-123299067 2 93432452 GAAGGCCAGTTGTGCAGCTTTGCCCATAAAAGGAA[C/T]GTTAGACCAGGCTTTGCAGGGGGAGTCTGCATTCA Y 2 1 2 1 101000 f 74 goat snp46002-scaffold631-865098 2 41767343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781328 Affx-122919965 AX-385268413 2 93501373 TCCAGGTGTTCTGGATCTCCAGGTGTACGAGTTAC[A/G]TCTTCTGGTTACAAATGACAGAAACCAACTCTGAG R 2 1 2 1 101000 r 74 goat snp46000-scaffold631-796177 2 41698550 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436958 Affx-122933170 AX-123307296 2 93600894 TTGGTTACCAGTCAGGCTCATCCAACCAAGCAATG[C/T]AAGAGCCTGTAAGCCTTAGAGAAGATTCTCCACAA Y 2 1 2 1 201000 r 74 goat snp45998-scaffold631-696656 2 41598002 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386026 Affx-122971489 AX-123256384 2 93641723 TTTTTTACTGAGGTAAAAGTGGTACATACACATTG[A/G]CTTTCTTATCAGCCCTTCTTTGACAGTGAAGGGAA R 2 1 2 1 101000 f 74 goat snp45997-scaffold631-655827 2 41557749 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401620 Affx-122959602 AX-123271973 2 93686489 TACTCCTTTTCCACACAGCTGCTGTTTTCTGATGA[C/T]AGGAGGGCAGTTGCAGCTAGCTGTTTCCTTCCAGT Y 2 1 2 1 101000 f 74 goat snp45996-scaffold631-611061 2 41513049 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413561 Affx-122950595 AX-123283910 2 93719529 CTACTTTTACCAAGGATTTGGACAAATGTGCAAAA[C/T]ATACTGCAGTTTTTTAAAAAGTGACTTATGGGGCT Y 2 1 2 1 101000 f 74 goat snp45995-scaffold631-578021 2 41479909 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441880 Affx-122928627 AX-123312217 2 93774178 TTAACATTTTGGTCAAGCTACTTGGTACTCAAGCT[A/C]TCTGGTGCTCAAGTGACTGTGAATTATTTTTGGCT M 2 1 2 1 101000 r 74 goat snp45994-scaffold631-523372 2 41425178 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776888 Affx-122953942 AX-385264012 2 93822320 GAAATATAATTTGTATGTGAAATTAGATCATTAGA[C/T]CTAGTAGAAAGTGCTTATAGATATGACATCCTTAA Y 2 1 2 1 101000 f 74 goat snp45993-scaffold631-475230 2 41377173 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437604 Affx-122931857 AX-123307942 2 93899772 ATATTGACATCACATGACTTTTGTTCTAATACACT[A/G]AGAAGTCCACAGATTTTCTGCCCCACCCCACCGCC R 2 1 2 1 201000 f 74 goat snp45991-scaffold631-397778 2 41298683 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439743 Affx-122930534 AX-123310080 2 93950220 TAGAGCATCTCTGTCCAGGAAGAGCTCTCTTTGAT[C/T]ACCCCAACTCCATAGGAAACTTGTTTTCCTAAAAA Y 2 1 2 1 101000 f 74 goat snp45990-scaffold631-347330 2 41247854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399180 Affx-122960628 AX-123269535 2 94026224 TACCATGTTTCAACCTGAAGCTCCAGTTTCCTTGC[A/G]TTTATATTTTAGAATGTGTTGAGGGGCAACGGGGA R 2 1 2 1 102000 f 74 goat snp45988-scaffold631-271326 2 41173494 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428360 Affx-122938976 AX-123298703 2 94055097 ATTGTTTGGGACTAGATTTCTGCAAAAAATAGGAG[C/T]AGTGAAAGTAAAGCAAAAATGTAAAAGGCAAGTAG Y 2 1 2 1 101000 f 74 goat snp45987-scaffold631-242453 2 41146618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404658 Affx-122957299 AX-123275010 2 94098226 CACTGTTAGGTGGGCAATTATAAATCCTAAGAAAT[A/G]TCATGACCCTTGGGCAGTAGTTAGTTCAGGCTACC R 2 1 2 1 101000 f 74 goat snp45986-scaffold631-199324 2 41103320 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378339 Affx-122976840 AX-123248698 2 94188695 TAAGCTTAGCACTCGAAGCACCACCAAAAGGAAGT[A/C]GCTTCAGGCAGGCTTCCTTTGACCCCCTGTGGCTT M 2 1 2 1 101000 f 74 goat snp45984-scaffold631-108855 2 41013140 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447918 Affx-122923798 AX-123318254 2 94243087 CATGATACCTGTTCTCTGGATATACCACGATACAT[A/G]CAATATGTGCTAACCTTTAATGCTTCTCAGTTGCA R 2 1 2 1 101000 r 74 goat snp45983-scaffold631-54463 2 40958782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766084 Affx-122935350 AX-385253500 2 94278541 AAGGTATATTAATAATTCTTTTCTGACTATAAAAG[C/T]AACATGTGCTCTTCACCAAAAATTTAGGTAATATT Y 2 1 2 1 202000 f 74 goat snp45982-scaffold631-19009 2 40923045 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432468 Affx-122935607 AX-123302809 2 94308188 TTTCTCCATGTTATTAAAACTGTCCGATAAAGGCA[C/T]GAGGGAAGAATATTCAGTCGGAATTTTAGAATATG Y 2 1 2 1 101000 r 74 goat snp30957-scaffold341-3069205 2 40893203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443056 Affx-122928138 AX-123313393 2 94354968 TGGCCTGGATAATTCGCTGTTGCAGTGCTGACTCG[C/T]GCACAGTAGGGCACTGGCAGCATCCCCAGCCTCCA Y 2 1 2 1 101000 f 74 goat snp30956-scaffold341-3022425 2 40846902 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384954 Affx-122971915 AX-123255312 2 94387324 CCTAAACCATCCCAAGCTGATGAGACCTCCAGAGA[C/T]GTAGCTGCACCATCTCCTTGGTCACAGTGTTCCAG Y 2 1 2 1 101000 f 74 goat snp30955-scaffold341-2990069 2 40814521 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450315 Affx-122922140 AX-123320650 2 94474101 GAGCTTTCTCAGGGGCTCATGGGTGGCAGGGCTAG[A/C]GAACTCTTAGTGTGGAATGTCTGCAAGAAAGACAT M 2 1 2 1 101000 r 74 goat snp30953-scaffold341-2903292 2 40728614 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397105 Affx-122962697 AX-123267460 2 94513392 AAAACCCAGGGCTCCTCCCTATAGCCGCTGTGTCC[A/G]TAACGGTGGGAGCCCCAGCTGGAGCTTGGTAATAA R 2 1 2 1 303000 f 74 goat snp30952-scaffold341-2864001 2 40689314 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464154871 Affx-1110343241 AX-515630492 2 94536131 GACTTTTTACAACCTGTGAATTGTTTACAGACCCC[C/T]CAACCAGGAGAGGCACAAAGCTTAAAGCATCTTAA Y 2 1 2 1 303000 f 74 goat 2_94536131_AF-PAKI 2 94536131 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320797314 Affx-122978914 AX-385284253 2 94594383 TAGTTTAGATGCTTTGTTCTGCCTTGTGATTTATG[C/T]ATTTAAACTTCCATTTAAGAAGTTATTCTTCTTTT Y 2 1 2 1 201000 f 74 goat snp30951-scaffold341-2783010 2 40607741 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770901 Affx-122928082 AX-385258064 2 94672352 TTTACTTCCCTCTTCTATTTATTCTACCTGCCAAA[G/T]AATTAACCAAATAAATCATTAGAACTGGCAGGGCC K 2 1 2 1 101000 r 74 goat snp30949-scaffold341-2705041 2 40529671 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377304 Affx-122977692 AX-123247663 2 94738446 GTGATGTTGGGGTCCAATCCATTTAAAGGGCAGAG[C/T]AGAAGATGCACTGTGACACCTCACCCTGAAATGAT Y 2 1 2 1 101000 r 74 goat snp30948-scaffold341-2638947 2 40463650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272261 Affx-1111833646 AX-519546000 2 94760522 TCCATCAACTTCTAAACAATCATTATATGAATGCT[A/G]TTTCTGCAGATATTATCTTCTCAACTTTTCCACTA R 2 1 2 1 201000 r 74 goat GoatD01.000345 2 94760522 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320790956 Affx-122928519 AX-385277953 2 94767347 TGGCAGCGAAGGAAACACCTAAGCTAGAGTTAAAA[C/T]GCAGAGAGCCTGCATGTTAGATTGATTCATGCAGT Y 2 1 2 1 101000 r 74 goat snp30947-scaffold341-2610046 2 40435000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419020 Affx-122946042 AX-123289368 2 94802243 GTAAGAAAGCATTGTGTTGCAATGTATTGGCATCA[A/C]TTTTTTGTCTTAGCGGCACATAAAATAATGGTATA M 2 1 2 1 101000 r 74 goat snp30946-scaffold341-2575150 2 40400640 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780553 Affx-122937601 AX-385267644 2 94838399 CAATGTTTAGTTCTGAGTCAATTAAAGAAGATACT[A/C]TTTTTGACCTAATCTTTGTGATAGCTGGAGAAATT M 2 1 2 1 101000 f 74 goat snp30945-scaffold341-2538994 2 40364170 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415702 Affx-122948529 AX-123286051 2 94888037 TCTGGCTAAGGTTAGCTTTTTAGTTGTTACTGCAC[A/G]TCTCCCGTGTTCACCTGGAGAGCTCTACCTCGAGA R 2 1 2 1 201000 f 74 goat snp30944-scaffold341-2489356 2 40313878 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780813 Affx-122958658 AX-385267902 2 94916727 TCTGAACTAATATCAGCATCAAATAGCATCTGTTC[A/G]CTGTGAGGAGAGAAAATGCACTTTAATTGTAGCAG R 2 1 2 1 101000 r 74 goat snp30943-scaffold341-2460666 2 40285259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435275 Affx-122934049 AX-123305615 2 94973370 CCCCCAGTGTGATGGTATTAGGATGTGGGGCTTTT[A/G]ACAGGCAATTAGGTCTTGGGTGTGGAGCTTTCAGG R 2 1 2 1 101000 r 74 goat snp30942-scaffold341-2404023 2 40228827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452542 Affx-122920534 AX-123322875 2 95011960 GAGAGGCGTCTCTGCTGAATAAAACAGTGGTAACT[A/G]CTTGGATTGACTGGTTGCTACTCACATGAGCTAAA R 2 1 2 1 101000 f 74 goat snp30941-scaffold341-2365433 2 40190142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433816 Affx-122935169 AX-123304157 2 95046104 CTGAGGGTAAGCCACTGACTCCAAGTCTGAGAGAA[C/T]GTAAGTGGCAAAACTGAAGGTATAATTTAGTTCTA Y 2 1 2 1 201000 r 74 goat snp30940-scaffold341-2331289 2 40156073 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783993 Affx-122949978 AX-385271047 2 95137116 TCCATTTCTCAAGATCCATTCTTGCTCATGACTCT[A/C]TTTGGAGAGCTTTTAAACTCTCTGGGAAGCAGAAG M 2 1 2 1 101000 r 74 goat snp30938-scaffold341-2240277 2 40064762 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787559 Affx-122967349 AX-385274583 2 95178937 CAAACCACCTCCAAATATGAAGAAAACTATACTTA[A/G]TAAGTTTCCACTTTTCAGTATCTATCCTGGAGATA R 2 1 2 1 101000 f 74 goat snp30937-scaffold341-2198456 2 40022638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801212 Affx-122944727 AX-385288125 2 95225640 AAACAGATTAAGTATGTACAACTAAACATACTTGA[G/T]AGCTCTGTACAGCTAAACTCTAGTTTATATCATAT K 2 1 2 1 201000 r 74 goat snp30936-scaffold341-2151753 2 39975657 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385890 Affx-122971591 AX-123256248 2 95273606 TTTTTGTTCAAACCACTGTTGGCTCTCAGCTGAGC[A/G]CTGCACCAGCCTCCTAGTTGGTCTCCCTGCTTCAT R 2 1 2 1 101000 f 74 goat snp30935-scaffold341-2103787 2 39927821 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453116 Affx-122920019 AX-123323449 2 95333768 ACAACAAGCACTTTCTACTTCAGCTCCAGCATCTG[C/T]AGTTTATGTGAAGTTTCATTAGGCAGACTTGCTGA Y 2 1 2 1 201000 r 74 goat snp30934-scaffold341-2043625 2 39867478 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446684 Affx-122924750 AX-123317020 2 95371343 CAGATAGATGTCATTTTCCCTCATTTCTGTTCATG[A/C]TGTACAGAACTGTCTAAAACTTGGGGCTTGGGCTA M 2 1 2 1 101000 f 74 goat snp30933-scaffold341-2006050 2 39829778 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452819 Affx-122920745 AX-123323152 2 95420864 CTAACTCTTAGTGGGTCATTCCCATGCATGATCAG[A/G]TAACATTGCTTCAATTTCTCCTCTATTTCTCTACT R 2 1 2 1 101000 f 74 goat snp30932-scaffold341-1956529 2 39779968 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464155209 Affx-1110343409 AX-515630829 2 95465983 TGAGGGAGTCCCTATGACTGGGTCTCCCTAAGACT[C/T]GTCTACCTGGAGGTTTTTATAAAGTTGTCCACCCT Y 2 1 2 1 101000 f 74 goat Random2.2K-242 2 95465983 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449766 Affx-122922444 AX-123320101 2 95470222 AGAGAAAAAGAAAGGTAAAAATTGAATAAACATGA[C/T]AAAAAGGGGATTTATAAGTATATATTAAAAAATCT Y 2 1 2 1 101000 f 74 goat snp30931-scaffold341-1907171 2 39733627 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437104 Affx-122932177 AX-123307442 2 95507495 AGTGTGGTTGTGGCTATACAAGCACATCAAAAAGC[A/G]CAATAGTTTAAGGAGGCATGTGCTGTATGCAAATG R 2 1 2 1 101000 f 74 goat snp30930-scaffold341-1869898 2 39696384 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403726 Affx-122958025 AX-123274078 2 95560745 TCCAGTCACAGAATTCCTAGTCTCTTTTGCTTACT[A/C]TTTTAGGTCAGTATCAACAGAGATTTGCCAGGGCA M 2 1 2 1 101000 r 74 goat snp30929-scaffold341-1816648 2 39643309 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385619 Affx-122971187 AX-123255977 2 95606054 TTCCCTAGAAACTTCATCAGTCAGATTTTTGCTTA[C/T]ATCTCATTGGCCAGAACTTGTTATCTTAACTGCAA Y 2 1 2 1 101000 f 74 goat snp30928-scaffold341-1771339 2 39597309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386073 Affx-122971455 AX-123256431 2 95635448 ATCCATCCACCCTCAAGCAGGAAATGGGATACACA[C/T]ACATACACATTCACACAAAAAAGAAGCATATAGGT Y 2 1 2 1 101000 f 74 goat snp30927-scaffold341-1741945 2 39567926 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445694 Affx-122926122 AX-123316031 2 95686081 CACTATGACTAATACCAAACAGTTATTCAGTGCTC[A/G]TTTGTGCCATGTACATGCCCAACACATTAAACACA R 2 1 2 1 101000 r 74 goat snp30926-scaffold341-1691312 2 39518077 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799693 Affx-122954708 AX-385286621 2 95722475 TGACAGAAAGCCATCAAGGACCCAGAATTGTTCAA[C/T]TCTATTAATGCAATACAAACTTCTAGTTCTACTCC Y 2 1 2 1 101000 f 74 goat snp30925-scaffold341-1654918 2 39482012 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776246 Affx-122927984 AX-385263374 2 95814604 TTTCTTCACCTATACTCAATGTCTTCTGTCATGCT[A/G]TATTGTATACATCTTGAAGACTGCCCTAAATCCTT R 2 1 2 1 101000 f 74 goat snp30923-scaffold341-1562789 2 39388192 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422550 Affx-122943772 AX-123292896 2 95875735 TCCAGTGAAGACTGAAAACTACAGGGAACTAAATA[C/T]AAGGAAGAAGAGCAGTTAATTTTTAAGTTAAAACA Y 2 1 2 1 101000 f 74 goat snp30922-scaffold341-1501658 2 39326410 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383971 Affx-122972938 AX-123254329 2 95931569 AATGACCCATCTATTCTGGGAATGGTGGAAATCCC[A/G]TAAGGAGGAGAAAAAATCTATACCCTCTGCTCCTC R 2 1 2 1 303000 r 74 goat snp30921-scaffold341-1445824 2 39270289 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801376 Affx-122923112 AX-385288287 2 95965775 TTTCAGGTTTGAGCATACCCTACTTTTGAGCATTC[A/G]TTGACAATTTTATTGCTCAATGACAGCGTACCTCG R 2 1 2 1 101000 f 74 goat snp30920-scaffold341-1411618 2 39235925 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794694 Affx-122936844 AX-385281654 2 96010422 CTATACTTATTTTCTGCTTCCTGCTCGCTCCAACT[A/G]GAATTTAAGTTTAGATAGGCAGGGATTGCTGTTGT R 2 1 2 1 101000 f 74 goat snp30919-scaffold341-1366971 2 39191162 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415877 Affx-122948487 AX-123286226 2 96072112 CAATATTTGAAACTGTCATGATTCCTCATCATTTT[A/G]CCTTCAAATATTATTTTTTTCATAGTTACAACATT R 2 1 2 1 103000 f 74 goat snp30918-scaffold341-1305281 2 39128624 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447357 Affx-122924871 AX-123317693 2 96106921 AGAGTAGTAACTTCCTTTTTTTATTCTTTGTCATA[C/T]CCCCAACATCTAAAACAGTGCCTGACATATAGTAG Y 2 1 2 1 101000 r 74 goat snp30917-scaffold341-1270472 2 39093594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795085 Affx-122940714 AX-385282044 2 96175663 GAGTCAAGAGGTCAATTGCAAATATTAGAAAAGCT[A/C]GATGGCACTTTCATGTGCTATCTTCTTGCTATTTG M 2 1 2 1 101000 r 74 goat snp30916-scaffold341-1201730 2 39023691 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432423 Affx-122935828 AX-123302764 2 96350523 CAAATAAGCTGCTTAATTCTTAGGGGGAATGCTTC[A/G]CTGTGAATAAATAAATGATACATTTCTGTGCAAAT R 2 1 2 1 101000 f 74 goat snp30912-scaffold341-1026870 2 38848358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440013 Affx-122929779 AX-123310350 2 96385521 TACCTTCCCCAACCCTGAGCAAGCCTAAGTTGCTC[A/G]TTAGTTAAGTCTCTGATTCCAGGAACTGGAATCAG R 2 1 2 1 101000 r 74 goat snp30911-scaffold341-991872 2 38812821 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790683 Affx-122970095 AX-385277685 2 96426756 GATTTGACTGCAGGAAGTTTATTGGGGGGTGAATG[G/T]TCTTGAGATCAACATTCCCATGGAAAGTAAAGGAA K 2 1 2 1 201000 f 74 goat snp30910-scaffold341-950637 2 38771044 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398650 Affx-122961896 AX-123269005 2 96491145 ATAAGGCTAATAAAGCAAGTAATTCTAAGTGGTAC[C/T]GTATGAGAGAAAGAGATAAAAACTTCTCTAAACTG Y 2 1 2 1 101000 f 74 goat snp30908-scaffold341-886248 2 38705748 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437476 Affx-122932373 AX-123307814 2 96523318 GGGAGAGAAGCAGAATGGAATGAGGCTAGATAGCT[A/G]CAGTGTGCTGTGAAGAACATTATCCCATTGCTGGG R 2 1 2 1 101000 r 74 goat snp30907-scaffold341-854075 2 38673431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768043 Affx-122979002 AX-385255255 2 96559308 TTTCAATTAATTTGGAACTTATGGGTCCTAACAGT[A/G]TTTGAATTTGTCTTAAGTAGGCCACTATTTCTAAC R 2 1 2 1 101000 f 74 goat snp30906-scaffold341-818085 2 38637182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437053 Affx-122933097 AX-123307391 2 96605667 CTATTAATATATTTAGTATTTAATTTGAGGAACTG[C/T]TAGTCTGGGAGATAGAAATATCATTCTAGCTAACT Y 2 1 2 1 101000 r 74 goat snp30905-scaffold341-771726 2 38590648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447430 Affx-122924384 AX-123317766 2 96634795 ACTCATGTAGCAATTTATGACGTGAGATAAACGAG[A/G]TGGCATATAGAATAGTGTACAATTATTCACACACA R 2 1 2 1 101000 f 74 goat snp30904-scaffold341-742598 2 38561526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768510 Affx-122947811 AX-385255690 2 96685393 TGATTAGCAGGGTGAGAGCTTTTGAAGAATAAGGT[C/T]TATATAATCATGCCATGATATCCTTTCTAAGGATA Y 2 1 2 1 101000 f 74 goat snp30903-scaffold341-692000 2 38510758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394911 Affx-122964320 AX-123265266 2 96728443 AAGAAATACCGACCACAGAAGACTAAAAAAACAAA[C/T]GCTAGTTTTCACCAAATGCAAAGGTATTTTGTCTC Y 2 1 2 1 101000 r 74 goat snp30902-scaffold341-648950 2 38469587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436364 Affx-122933059 AX-123306703 2 96766335 TAAGCAGAAAAAAATGATAATAGCCATGCCAGATT[A/G]TACTTCCGTATCGTACGATAGCTTAAATAAATAAA R 2 1 2 1 101000 r 74 goat snp30901-scaffold341-611058 2 38429666 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777265 Affx-122931559 AX-385264387 2 96814045 ATGTGGCACTGAATGTACTGTGTTCTGTATTTGAA[G/T]TAGCTGTACCCACAGGTCTCATGTGTGCTACTAGA K 2 1 2 1 101000 r 74 goat snp30900-scaffold341-563348 2 38381953 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801569 Affx-122967693 AX-385288478 2 96867463 TCTTTCCCTCCCTTTCGGCTAAATAAACTTCTTGC[A/G]CAGCATTCTTTCAAATCTTTTCAATAGCAGTACAA R 2 1 2 1 202000 r 74 goat snp30899-scaffold341-509930 2 38328251 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277869 Affx-1111836131 AX-519551365 2 96924675 ATTGTCCAAAAGCCCACTGAAATGAACAATCATCA[A/G]TGAAATAAGCTAAACAGGTTCAAAACTCATTTAGA R 2 1 2 1 101000 f 74 goat Random2.2K-244 2 96924675 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395163 Affx-122964114 AX-123265518 2 96939361 TGAAAGTCTCTGCCAGGAAGCACATTCTCTGCTTC[A/G]TCATTACACCACTCTGAGTGTCTGAGACGTTTAAA R 2 1 2 1 101000 r 74 goat snp30897-scaffold341-438032 2 38256534 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398936 Affx-122960994 AX-123269291 2 96968765 AAGATGGACAAGCCCTTCAGAGGGATGTGACAGAC[A/G]TCCCAGAAGTCTCCTGTAGGTCAACGCTCTTATGA R 2 1 2 1 101000 r 74 goat snp30896-scaffold341-408628 2 38227108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444112 Affx-122926820 AX-123314449 2 97015451 GTATATTGAATGTTTCCTTTATGAAGGTAAAGCAG[A/G]GAACTAGAATACTAATTCAAACAGCTGTGTTTTAT R 2 1 2 1 101000 r 74 goat snp30895-scaffold341-361942 2 38180319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272052 Affx-1111833186 AX-519545816 2 97036634 AATTTACATATTAACTGGATATTTGACAACGTTGA[A/G]AACTTTTTCGTGATAATCACATTGTGATTAGAGGT R 2 1 2 1 101000 f 74 goat 2_97036634_AF-PAKI 2 97036634 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38419071 Affx-122945802 AX-123289419 2 97051649 ATATATTCTGCCATAAAAACTGATTAAAAAGGAAA[C/T]GAGAATGAAATACCGATTGCTCTAAGTCTCGATTT Y 2 1 2 1 101000 r 74 goat snp30894-scaffold341-325744 2 38144188 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408441 Affx-122954450 AX-123278792 2 97093843 ACGACAGGACTAAATTCTTGGAACTCTGCTTAGGA[C/T]GAACCCTGGTGTCAACTGACCTTTCCATTCCCAAA Y 2 1 2 1 101000 f 74 goat snp30893-scaffold341-283550 2 38102159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409876 Affx-122952911 AX-123280227 2 97164633 CATGAAATATCAGCTGCACTATAAAGAAAGCACAG[A/G]TTTCCAATGATATTGGACATCTAAAAACATCCCTT R 2 1 2 1 103000 r 74 goat snp30891-scaffold341-212760 2 38031197 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424650 Affx-122942163 AX-123294996 2 97207031 TCAGTAAACAAAGGAGAAACAAGTCTAATATTCTC[A/G]TTACTAATAGGCCATATAATTTATCATATTCCACT R 2 1 2 1 101000 r 74 goat snp30890-scaffold341-170362 2 37988136 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767806 Affx-122941665 AX-385255030 2 97235796 CCATAAGAGTCAGATTATGTTTATTTTATGGAAAA[C/T]GTCATTATAATTATGCCATCAAAATACATATTTCT Y 2 1 2 1 101000 f 74 goat snp30889-scaffold341-141597 2 37959157 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451456 Affx-122921151 AX-123321789 2 97294465 GTGTGAGATAAATCAGCAAGGGTTAAAAAATGATA[C/T]TGTACTTGCCTGTAGACAGTCTGTAATGGAAATCT Y 2 1 2 1 101000 r 74 goat snp30888-scaffold341-82928 2 37902089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783063 Affx-122977356 AX-385270130 2 97326964 CACTTTCCCAGATGTATCCAAAGTGGAATAGTATC[A/G]TTTACTTCTCAAAGTCAACCACTGCCCCTTTCACA R 2 1 2 1 101000 f 74 goat snp30887-scaffold341-50429 2 37869849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795913 Affx-122965416 AX-385282865 2 97401699 GAAATTCGAGTTGGTCTCTAGAGACTCCCTGTGGT[A/G]CAGCAAGAGAGCAGAGCTCAATGTGCAGAAGATTG R 2 1 2 1 102000 r 74 goat snp37775-scaffold464-5300048 2 37788459 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440088 Affx-122929721 AX-123310425 2 97448971 TTCTGTAACTCTGTCTAAAATTATATTTTAAATAA[C/T]ATTTAACTAGATAATGTCTTTGCAAAGTAAAGGCA Y 2 1 2 1 103000 r 74 goat snp37774-scaffold464-5252776 2 37740491 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792558 Affx-122958640 AX-385279539 2 97483470 GGTCTTAATAATTTCAAAGAGACCCTCAGATCTTT[A/G]CAAACATTTGTCATTAAATTTAGTTATTAAAAGCA R 2 1 2 1 201000 r 74 goat snp37773-scaffold464-5218277 2 37705885 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399766 Affx-122960310 AX-123270121 2 97518065 TCCTCCCGTGTGTGTCTGTGAATGTCACATCCATT[A/G]TTTACATCAATCCTATTGATCTGTGGTCCCATCAA R 2 1 2 1 201000 r 74 goat snp37772-scaffold464-5183682 2 37671329 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394353 Affx-122964655 AX-123264708 2 97620016 TTTTTGATAACTCTGAAATGAACCTGTTCCCAAGG[C/T]GCTTATTAATGATCATTTGATTGATTTCCCCCTTG Y 2 1 2 1 101000 r 74 goat snp37770-scaffold464-5081731 2 37568963 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793664 Affx-122919438 AX-385280637 2 97674222 GAATTTTGCAGAAACATCTTTCCCATATTATTTTC[A/G]CATATTTTTGCCATAGCAAATTCAAGTGAAAGGTC R 2 1 2 1 201000 f 74 goat snp37769-scaffold464-5027525 2 37514357 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430800 Affx-122937463 AX-123301141 2 97719479 TCTTTCCATGGAATAATAGATTGCTATGCATTTTT[A/G]GTCTACAATTTAAAATAATAACAGGCATAACACTG R 2 1 2 1 103000 f 74 goat snp37768-scaffold464-4982268 2 37469503 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441346 Affx-122928881 AX-123311683 2 97751681 CATGTTACCAAGAAGAATTTTCAGTATAGATGGAA[C/T]GCTGAGAAAGAAAAGGTGTATTTTAAATGAAAAAG Y 2 1 2 1 101000 f 74 goat snp37767-scaffold464-4950066 2 37437223 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792955 Affx-122923360 AX-385279933 2 97795034 CCTGAGTATGGCAGATGCTGTTTAAAAATGGCAAT[A/C]GTGTCTGTAAAGGATATATAGAAAGAGTTCAGAAG M 2 1 2 1 101000 f 74 goat snp37766-scaffold464-4906713 2 37395189 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275203 Affx-1111834651 AX-519548782 2 97843654 CAGGTTTTGAGTTAGTGC[A/G]ACACAGACTGCATTCATTGTGCTGCAGAAAGAGGA R 2 1 2 1 101000 r 74 goat GoatD01.044464 2 97843654 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38448097 Affx-122924320 AX-123318433 2 97844906 CAGGTGGCTATGATTCACTCTAAAACCTGAGAAAT[A/G]TACTTCCTGATTATGAGATAAGAAATGCCGGGCTG R 2 1 2 1 101000 f 74 goat snp37765-scaffold464-4856841 2 37345046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376541 Affx-122977992 AX-123246900 2 97886862 CAGCAAACAATTAAAACATCATTGGACTCCCAAGC[A/G]CATGTGTTTTCTTTCCCTATTTTTATATATGTTAT R 2 1 2 1 101000 f 74 goat snp37764-scaffold464-4814885 2 37303032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422549 Affx-122943263 AX-123292895 2 97922285 ACCAGCTGTTCCTACCGTCTGGAATTCTCTTTCCC[A/G]TATATTTGTATGGCTAGTTCTCTTTTTAAAATATA R 2 1 2 1 201000 r 74 goat snp37763-scaffold464-4779462 2 37267468 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444162 Affx-122926783 AX-123314499 2 97954685 TGTCATCAAGGTGGGTACAGTCTCAATAGTATTCC[A/G]AAATTAGATATGCTAAATTCCTGATGCATCTTCTG R 2 1 2 1 101000 r 74 goat snp37762-scaffold464-4747062 2 37236248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420505 Affx-122944850 AX-123290852 2 98002883 TGAAAAGGAAAAATATAACTTTGTAATGGAAAATC[A/G]TATCAATCATGATCTAATCAAAGTCAACACCACCA R 2 1 2 1 101000 r 74 goat snp37761-scaffold464-4698864 2 37189532 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799548 Affx-122976006 AX-385286478 2 98031783 AGTCTGTAAGAGAGTGTAAACAATTCCCTTTTTTG[C/T]AGCTATATTTGCAGTGTACATTTGACTGTTCTCTA Y 2 1 2 1 101000 f 74 goat snp37760-scaffold464-4669964 2 37160636 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764798 Affx-122923036 AX-385252406 2 98082533 GCTCATATTTATATAAAATTCATAAGTGGTGCACA[C/T]ATATGCAAAACACAATCTAGATGTATTGATGTGTT Y 2 1 2 1 101000 f 74 goat snp37759-scaffold464-4619214 2 37109772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429787 Affx-122938207 AX-123300128 2 98137566 AAATACTTAGTGAATAATAGTAGTAACTGCCACAT[A/G]TGCTTTCTCCAAAAGTTTCTCCCAGTTTGAGAAAA R 2 1 2 1 101000 f 74 goat snp37758-scaffold464-4564181 2 37054277 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454091 Affx-122919369 AX-123324424 2 98178696 ATAACAGTTGAAATAAATTGGTTAAGAGAGAATTT[C/T]GCCCTACTCTCTAAGACTCTGATAAATTCATTGCT Y 2 1 2 1 101000 r 74 goat snp37757-scaffold464-4523051 2 37013178 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424982 Affx-122941909 AX-123295328 2 98271718 AGTTGAGGTAAGTAGAGTAGGTAAGCCTGCCTGGT[G/T]GCTGCTGTTGTTCAGTTGCACAGTCATGTCTGATA K 2 1 2 1 201000 f 74 goat snp37755-scaffold464-4430029 2 36920022 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425018 Affx-122941882 AX-123295364 2 98354546 TTCAACAGGCCCCCTGCCCTCCACCCACTAGATGA[C/T]ATTAACATCTACTCCTCCACTTGATACAGCTAAAT Y 2 1 2 1 201000 r 74 goat snp37754-scaffold464-4347201 2 36837313 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394549 Affx-122964463 AX-123264904 2 98426564 TTTTTACCATTAAAAACAGAACTTTGGATAACTAG[C/T]ATTTTTCATATTAAACTGAAATTTCTTTATTTGGT Y 2 1 2 1 103000 f 74 goat snp37753-scaffold464-4275183 2 36765133 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802863 Affx-122923375 AX-385289761 2 98474007 ATAGGTACTAGTTTTTCTGATCTGGAAAGGAGAAG[A/C]TGTGTTGGTTCTTTGGAAATACGATGATATTCTAA M 2 1 2 1 101000 f 74 goat snp37752-scaffold464-4227740 2 36717032 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782834 Affx-122940572 AX-385269905 2 98522549 TAGTAGGGTTGCTTTTTAGTATGGGAGACTGCTTT[A/G]CTTTGCAAAATCCGTAGGACCAGGGAAGGTTTTAG R 2 1 2 1 101000 f 74 goat snp37751-scaffold464-4179198 2 36667262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775033 Affx-122938841 AX-385262165 2 98552056 TACATAACAGGTACTAATAACTGGAGATAGATGCA[C/T]GTATAATCCAAAATGACCTAAAATGCCTCACAAGA Y 2 1 2 1 201000 r 74 goat snp37750-scaffold464-4149691 2 36637395 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403115 Affx-122958124 AX-123273468 2 98585730 AAACACTGGATCATTTACTAGCATTAATTCCTTTC[A/G]CTTTATTTTGCCCTCATCTATTGAGAGTATGCCTT R 2 1 2 1 101000 r 74 goat snp37749-scaffold464-4116017 2 36603593 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772735 Affx-122961151 AX-385259880 2 98623491 CAAAAAATTAGGACGCATATTCTAAAGAGAACACC[A/G]CTGGCATATCAATCGATAACAAGTTTATGATATCA R 2 1 2 1 101000 f 74 goat snp37748-scaffold464-4078256 2 36566102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437709 Affx-122931751 AX-123308047 2 98655115 CTCAGGGGGAAATTTTTAGCCTACCAAATCATACT[A/G]TAGGAAATAATAAATGTTCCTATTATTATTATTGT R 2 1 2 1 101000 f 74 goat snp37747-scaffold464-4046632 2 36534608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394815 Affx-122964801 AX-123265170 2 98689678 TATTTCTCATCCCTTTATTACTTATGTTGTATTCA[A/G]TCACTCATAGCAAGTTCTATCTTTCCTTAAACTAA R 2 1 2 1 101000 r 74 goat snp37746-scaffold464-4012069 2 36499638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781245 Affx-122954254 AX-385268330 2 98730933 TCTTGAATATAAATATATTAGTAAGATGAATTTAT[A/G]TAGCAAAAGTTTCACAGTATCCAATTAAATATGGG R 2 1 2 1 202000 f 74 goat snp37745-scaffold464-3970814 2 36458709 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437027 Affx-122933118 AX-123307365 2 98790928 AATAGTAAGAGAGTTCTGAAGAATAAGTGTACTTT[A/C]TAAGGTCAATGGGAACTTTGATTTCCCCTAGCAAA M 2 1 2 1 101000 r 74 goat snp37744-scaffold464-3910819 2 36398671 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404314 Affx-122957018 AX-123274666 2 98850163 GGTGGTTAGTAATGGAAAATACAATTAATCTGCAG[C/T]GTGAGAAATGTGGATTCTGTAAAGAATGTTCAGAA Y 2 1 2 1 101000 r 74 goat snp37743-scaffold464-3851584 2 36339334 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801155 Affx-122944013 AX-385288069 2 98900554 ACAAAAGGGATTTCTATTGACTTGACCCTTGAAAA[C/T]GTGTAAGCATTAGATAGGCAGAAAAGGAGTTTAAA Y 2 1 2 1 101000 f 74 goat snp37742-scaffold464-3801193 2 36288785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400778 Affx-122959837 AX-123271133 2 98929089 CCTAAATAGACTACACTCTATCTAGGATGGAGGAT[A/G]CTCTGGGGATGTTCCTGGTCGCCCTGGCTGGTTCA R 2 1 2 1 101000 f 74 goat snp37741-scaffold464-3772658 2 36259855 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444401 Affx-122926586 AX-123314738 2 98977623 CTTTTTTTAGAGCAGGAGAAAAAACAATGGACAAA[C/T]AAAATTTCATCTACACTCCGCCCCTGGCTGAAAAT Y 2 1 2 1 201000 f 74 goat snp37740-scaffold464-3724124 2 36210952 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414286 Affx-122949597 AX-123284635 2 99039624 CTACACGGTGTTCTATGACTTCAAAACAAGATGCT[A/G]TCATTCTTTAAAGAAAGATGTTAAGGATAAAGTTA R 2 1 2 1 101000 f 74 goat snp37739-scaffold464-3662123 2 36149238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794675 Affx-122978923 AX-385281636 2 99071315 CTCTTGAATATTATATTCTAGCAGAGGCAGATGGA[C/T]AGTAAATAATAAAGACAGTAAAATATATTAATATC Y 2 1 2 1 202000 r 74 goat snp37738-scaffold464-3630432 2 36116543 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409661 Affx-122953515 AX-123280012 2 99117704 CAGTTGTGGCACCTTGACTATTGTAAACTGAAGGC[A/G]TTGGAGAAAACAGAAATCGAGAGGTCACTCTTGCT R 2 1 2 1 201000 r 74 goat snp37737-scaffold464-3584043 2 36069966 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799700 Affx-122978427 AX-385286628 2 99148263 TTTCTTCTTTATTAGTTGGAATAGTTTACAAATGC[A/G]TGCCTTTGATCTAGTATTCAGTTACTCAGTGTTAT R 2 1 2 1 101000 r 74 goat snp37736-scaffold464-3553484 2 36039342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416279 Affx-122947947 AX-123286628 2 99193718 ATCAGAAAGTCAGTATTTCTGCATAATTATAAGGT[A/G]TAATTTTTTTCAGTTTATTATATTTGTTTATTTCA R 2 1 2 1 103000 f 74 goat snp37735-scaffold464-3508029 2 35993312 A G 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320799540 Affx-122922957 AX-385286470 2 99268980 TGGTTCCAAAGCCAATGTCCAACTAAAACATTTCC[A/G]TTATATCTTTTTTATCAACCTAAGCTCTGATGCTT R 2 1 2 1 101000 f 74 goat snp37733-scaffold464-3432767 2 35917588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796746 Affx-122948785 AX-385283690 2 99300718 GCTAAGGAATCTAGTATTGAAGTGTAGAACTGTTT[A/G]CTCATTCAGAAATTTCTTAGAAGGTATTACTCAGC R 2 1 2 1 201000 r 74 goat snp37732-scaffold464-3401029 2 35885743 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278017 Affx-1111836132 AX-519551509 2 99307917 ATGTAGAAAACAGGGTGTCCTACAATAGTTTGAAA[A/G]TCACTAGCTATGTAGACCAGAGCTACAAGCTCTTC R 2 1 2 1 101000 r 74 goat Random2.2K-247 2 99307917 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785559 Affx-122957081 AX-385272603 2 99340721 AGATTTGTAGATTTAGTTAGAAATGCCAAGAAACT[A/C]AATGATATTATAGAAAAGGAAAACTAAGAGATGAA M 2 1 2 1 201000 r 74 goat snp37731-scaffold464-3361026 2 35845542 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779128 Affx-122943610 AX-385266233 2 99371410 ATATTAAAAATAGGACTTGTGAAACACCTTCAGAG[A/G]CATATACTATTGCGCTGCTGTTTCTGTCTTGCTAT R 2 1 2 1 101000 r 74 goat snp37730-scaffold464-3330337 2 35814819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441894 Affx-122928617 AX-123312231 2 99402220 ATCAAACAGTACGTTCCTATTCATAGGCTGAACTT[A/C]TTAGGACAGCAAAAATCTGTATTTGAAAAAAAAAA M 2 1 2 1 101000 f 74 goat snp37729-scaffold464-3299527 2 35783785 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789951 Affx-122972915 AX-385276957 2 99435353 AAACAATATGTAAGAACTAGCTGTGAAAACAGAAG[C/T]ATAGGAATGTTACAGCAACTTGTTGAAAATTGTGC Y 2 1 2 1 101000 r 74 goat snp37728-scaffold464-3266394 2 35750575 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435876 Affx-122932791 AX-123306215 2 99477190 ATGACACCTCTATCTTATGAGAATATCTATATTCT[C/T]ACATTAACTTGAAGCTACTTGAAGACAGTAATTCT Y 2 1 2 1 101000 r 74 goat snp37727-scaffold464-3224557 2 35708398 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803360 Affx-122925895 AX-385290195 2 99536268 TATGTACAAACTTGTATTTATGCAAGAATGCATAT[A/G]CATACATATGACTTGTGCCTTTAAAAATGCAAATA R 2 1 2 1 101000 r 74 goat snp37726-scaffold464-3165479 2 35649222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272054 Affx-1111833187 AX-519545817 2 99577748 TCTCTGATTACTCATCAACCATAACTATGCTTAAA[A/G]AAAAAAAAAGTACTGGCCGGGAACTCCTAGTCAGA R 2 1 2 1 201000 f 74 goat 2_99577748_AF-PAKI 2 99577748 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448654 Affx-122923347 AX-123318990 2 99589616 CTGCTTGGTTTAGTCTGAGACATCATCACCAAGCA[C/T]ATAATATCTGAACTGAGGATGTGTAAAGATGTGTT Y 2 1 2 1 101000 r 74 goat snp37725-scaffold464-3112131 2 35595729 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393901 Affx-122965110 AX-123264256 2 99632728 TTCAAGTCTCCCACATGGTGCAGGGCAGCACACTG[C/T]ACTTTTGATAGAAAGCTACATTTCTGCACTATTTA Y 2 1 2 1 201000 r 74 goat snp37724-scaffold464-3069019 2 35552713 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768487 Affx-122924840 AX-385255667 2 99664005 GCATAAAAGTGTAATCTTCCAGTTATTCTACAAAC[A/G]CTGCTGAATTTTTCTGTCATAAACATGAAGATTGC R 2 1 2 1 101000 r 74 goat snp37723-scaffold464-3037742 2 35520826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407626 Affx-122954629 AX-123277977 2 99694412 AAGATCAGAAGTAGGATAGATAGAAACTGATCAAG[C/T]GTATTCACTTAGGGCTTCATCCTTTTTGTGTTGTG Y 2 1 2 1 101000 f 74 goat snp37722-scaffold464-3007335 2 35490029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775089 Affx-122933627 AX-385262221 2 99723793 CTTGATATTAAGTAGAAATGTGACAGAAAACAAAG[C/T]AGTTCTCCAAAAGGTCTTTCTGTAAATTATTGAAT Y 2 1 2 1 101000 f 74 goat snp37721-scaffold464-2977954 2 35460234 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398583 Affx-122961498 AX-123268938 2 99763887 GGTTGCATAATGAATACATACTTTTATGGATATGC[A/G]TTTTATAATGTATTATACCTATTATTAAACTCGCA R 2 1 2 1 102000 f 74 goat snp37720-scaffold464-2937860 2 35420144 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411846 Affx-122951225 AX-123282196 2 99796554 TTCACTCAAGTTCTTTTTTAAATCTCCAGCTATCC[C/T]CTGAATATCTCTAGTTAAGTGTTCCCCATTCATGT Y 2 1 2 1 101000 r 74 goat snp37719-scaffold464-2905193 2 35387494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781765 Affx-122929733 AX-385268847 2 99830473 TGTCCTTATTGGGTCCTCGTCTTTTTTCAGGCCCT[A/G]CTAGGATCACAGTTATTCTTTGCACAAGTGCATCT R 2 1 2 1 101000 f 74 goat snp37718-scaffold464-2871274 2 35353087 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389091 Affx-122968583 AX-123259449 2 99860027 CAGCAGGATCAACATATTAAGTGTGTGCCCATGGA[C/T]GAGGGGTCCCTCCTGATTGCCAATACAAGCTCATT Y 2 1 2 1 101000 f 74 goat snp37717-scaffold464-2841720 2 35323509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790697 Affx-122956993 AX-385277698 2 99896166 ACAGATATGAAGAGAATGCCTGGCTCAGCATAAAG[A/G]GAGAATCTGTAAAGTTCATGGTCATTTTGGGAGAT R 2 1 2 1 101000 f 74 goat snp37716-scaffold464-2805581 2 35287425 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450119 Affx-122922768 AX-123320454 2 99995104 TGCTGAGTCCTGAGCAAGATGTTTTATATGAGTTA[G/T]CCACATTATCAGGAAACATTAACAGTATTAACCTG K 2 1 2 1 101000 f 74 goat snp37714-scaffold464-2706643 2 35186614 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412728 Affx-122950731 AX-123283077 2 100024624 TGGGGAGATCACCTCATCTCTCATGCTGCCATTAA[C/T]GACTTGCATTCCTGAGAGATGGAATAAGCCATTTC Y 2 1 2 1 101000 r 74 goat snp37713-scaffold464-2677123 2 35157157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784758 Affx-122935442 AX-385271806 2 100054061 TGTACTTCACCAATAACACACAGAAGAATCAGCAG[C/T]TGGGCAATTCGATTGTGTTTATTAATAAATAGATC Y 2 1 2 1 101000 f 74 goat snp37712-scaffold464-2647686 2 35128090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772498 Affx-122949094 AX-385259649 2 100112130 GATATGGAGTTACAAAATACATGTGTGAGTTGGAA[C/T]GAATTAGATTCCAGCTATATCACTCATTCTCCATA Y 2 1 2 1 101000 f 74 goat snp37711-scaffold464-2589617 2 35069131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278019 Affx-1111836133 AX-519551511 2 100123406 TTTTATAGGGGAAAATATGAAAACAAAGATTCTTT[A/G]GGTTTTATCAGCTTCAAAGTAAGAAGACTTAGACT R 2 1 2 1 101000 r 74 goat Random2.2K-249 2 100123406 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38411743 Affx-122951511 AX-123282093 2 100153493 CAGGAAATATTCCATTTCTTACTTTGGATACAATT[A/G]TTTAAGCCTATTATCAATCCACATAATTATCTTTA R 2 1 2 1 101000 r 74 goat snp37710-scaffold464-2548254 2 35028221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429171 Affx-122937970 AX-123299513 2 100192855 TTCTCATGCCCAGCATGGTCCAGGAGCTAGGGAAC[G/T]CACACTGAGGCAGGACACACACACATACACACACA K 2 1 2 1 101000 r 74 goat snp37709-scaffold464-2508892 2 34988805 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386250 Affx-122970961 AX-123256608 2 100221477 AATTGATAGGATAGTCCTCCTCCTCGCCTTCCCCA[G/T]AGGGAACTGAGAACACGTACCAGCATGAATATTCA K 2 1 2 1 201000 r 74 goat snp37708-scaffold464-2480270 2 34959833 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784211 Affx-122977937 AX-385271262 2 100263772 AGCATGGAGGTGGTAATTCCAAGGAAACCAAGTTG[C/T]AAGCCTTTTGAAATCAAGAGCTGTGGTTTTCCAGT Y 2 1 2 1 101000 r 74 goat snp37707-scaffold464-2437975 2 34917099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433206 Affx-122935631 AX-123303547 2 100302724 TAGATTATCTTGAGTAGAAACTGCCCTCTAACACA[G/T]ATCTTAGGCTCTCTCCATAGTGCAAATGCATGGAT K 2 1 2 1 101000 r 74 goat snp37706-scaffold464-2399023 2 34878018 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785587 Affx-122943340 AX-385272631 2 100332845 TGCCTTTTTTTAATTTGTGCCAGTTCCTTCTATAA[C/T]ACTGACTTTTCAACGTGCAAATTAGACCTCTTTTT Y 2 1 2 1 101000 r 74 goat snp37705-scaffold464-2368902 2 34847941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383731 Affx-122972457 AX-123254089 2 100364524 TGGGTGAAGGCACAGTGGGACTGTTGGTCTAAGTG[C/T]CCTGCCCTCTTCTGGGGAATGTGGACATGTGACCT Y 2 1 2 1 201000 f 74 goat snp37704-scaffold464-2337223 2 34816296 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443030 Affx-122928159 AX-123313367 2 100413581 CGGAGCGATTATATTGAGGGAGATAACACACTTGG[A/G]GATGTCTCCGTCTCACATCTAGCAATGTAGAAACT R 2 1 2 1 101000 f 74 goat snp37703-scaffold464-2288166 2 34767039 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435902 Affx-122932771 AX-123306241 2 100456116 AAAGTCCATCTCTTTTGGAGATCTTGACACCTATC[A/G]TTAACAAGGTGCAACCTCCTTCGGGATAATTGAGA R 2 1 2 1 101000 f 74 goat snp37702-scaffold464-2245631 2 34724423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380851 Affx-122975444 AX-123251209 2 100512072 TGAATGTCGATAAATAAACTGCTTCTCACCTCTTA[C/T]GCCTGAGAATTCTTCAAAAGTGTATAAATCTAAAG Y 2 1 2 1 101000 r 74 goat snp37701-scaffold464-2189675 2 34668549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788252 Affx-122933497 AX-385275271 2 100579319 AATGCTTTTAAAGGGATTCTGCATTCTAAATAACA[C/T]GTTACGTGTATTAAATGAGTATAGTAATAATCAGA Y 2 1 2 1 201000 r 74 goat snp37700-scaffold464-2122428 2 34600804 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387244 Affx-122970569 AX-123257602 2 100621022 TTCAGGAAATTTATTCTCTTGTGGTTCAGTGAGCC[A/G]TGACGGAGGTGGACTAAACAGATTGAGAATAAATC R 2 1 2 1 201000 r 74 goat snp37699-scaffold464-2080725 2 34558987 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418379 Affx-122946567 AX-123288727 2 100739526 AGCTTCCCAGCAACCTGGCTGGAGGTGGGAGAGTC[A/C]CCTTTCTCTTGAGTTGGTTAGTTCTCTATTTCCTT M 2 1 2 1 101000 r 74 goat snp37697-scaffold464-1962221 2 34438649 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381700 Affx-122974714 AX-123252058 2 100772460 AAAAAGATAGGAAACCACTAAAAGTTTTCAACTGA[A/G]ACATGTAATGGATAGATTTATGTTTTAGGAGGATC R 2 1 2 1 101000 f 74 goat snp37696-scaffold464-1929287 2 34405551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411158 Affx-122951875 AX-123281508 2 100804087 TGGGAATTTGGTACAGACTCAGTGCACAATGGAAG[A/G]GGACAGAACTCCTTACTAGCACATATCTGAAAATA R 2 1 2 1 101000 r 74 goat snp37695-scaffold464-1897660 2 34373809 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450797 Affx-122921815 AX-123321131 2 100857557 TTTGGGAAACTAGGAGGCCCACATCTTTTCTCAGG[A/C]ACCAATTACTTTCTTCTGATAAAACACTCTGGACA M 2 1 2 1 101000 f 74 goat snp37694-scaffold464-1844190 2 34319474 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425600 Affx-122940923 AX-123295946 2 100909155 TTTATTTTTCTCCAAGTAATAATCAACCCACTATG[C/T]TTATGACCCTCCATATCCTAATACTTCATTATGTT Y 2 1 2 1 101000 r 74 goat snp37693-scaffold464-1792592 2 34267492 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795632 Affx-122933598 AX-385282587 2 100946891 TTAATGGAAGTAACCACATGATATTAAATTTTTCA[C/T]CACAACATCTCAGTGAGTTTGATTTAATTGCATGA Y 2 1 2 1 101000 r 74 goat snp37692-scaffold464-1754856 2 34231878 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412104 Affx-122951115 AX-123282454 2 100978803 GCCTCAATTAAATTTTGAGATCTTTTTGTAAATTC[A/C]TATTTGTTTAAATTACCCAGAGCCCCCAGTACAGA M 2 1 2 1 101000 r 74 goat snp37691-scaffold464-1722944 2 34199463 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391938 Affx-122966927 AX-123262295 2 101034410 TTTATTGAAAATGGTGTTCCTTTAGGGTCACTGGG[C/T]TGGGTATAGGGGGGTATAGGGGGGCTTGGCAGGAA Y 2 1 2 1 101000 f 74 goat snp37690-scaffold464-1667337 2 34143535 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395783 Affx-122963665 AX-123266138 2 101068291 TGAGTTCTTGGGGACATCAGGAGAAAAAGTGCAGT[A/G]TTTTGAGAATATTCTGCTGCACTCTCTGAGGCAAA R 2 1 2 1 102000 f 74 goat snp37689-scaffold464-1633456 2 34109047 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451484 Affx-122921131 AX-123321817 2 101128870 CTTAGAGCTCTGAGAATGTTGAAGAGGGTGGAATA[C/T]AGCCCTCCTGTGACTGCCTAGGGAAGACCCTGAAG Y 2 1 2 1 101000 f 74 goat snp37688-scaffold464-1572877 2 34048245 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771491 Affx-122943606 AX-385258649 2 101185219 CTCATACTTAATGATGGCACATGCTCACACATCAC[A/G]TATGCTTTTATCCAGCTTACCAGGACAAACATACA R 2 1 2 1 101000 f 74 goat snp37687-scaffold464-1516528 2 33991834 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406262 Affx-122956096 AX-123276614 2 101305007 CCAGCATTTCAACAAAGAAGCACACAGTAGTTTTT[A/G]TTTTTGTTTTTAACTGTATTTTATCTTTAGATTCA R 2 1 2 1 103000 f 74 goat snp37685-scaffold464-1396740 2 33871234 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412108 Affx-122951113 AX-123282458 2 101341296 TATAGGTTTCCCCTCAAAAGAGAATATTTCTTGAA[C/T]GCCAGGTAGTCAAATAAACAACAAGTAGCCATTTC Y 2 1 2 1 201000 r 74 goat snp37684-scaffold464-1360451 2 33835179 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427032 Affx-122939830 AX-123297377 2 101414148 CACATTGTGATTTTCTTTCTGTTCATTTCCCTCAT[A/G]TCTTAGCTCTTTTGTAGCAAATATCATGTTCTCTT R 2 1 2 1 201000 r 74 goat snp37682-scaffold464-1287599 2 33760715 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797863 Affx-122955898 AX-385284801 2 101475572 TGAAGACAGTTGCAAAAGTGGAGCCTTATAGTTTG[C/T]ACAATGATGTCATTAGATTAAGTACACACCCTTTC Y 2 1 2 1 101000 f 74 goat snp37680-scaffold464-1226175 2 33698972 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788394 Affx-122955099 AX-385275412 2 101539657 TGCGAGATGAAAATCTGTGCTGGGTGGAATTCTAG[A/C]TCACAGTGCTCTAGGCCCGGATTTCTGATTTCTCA M 2 1 2 1 101000 f 74 goat snp37679-scaffold464-1162090 2 33647333 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388224 Affx-122969403 AX-123258582 2 101619982 TCTCTCTAGAATTGTATTCTGTGAACACGACTGAG[C/T]GACAGAACTGAACTGAACTGGTATCCACAAGTTCT Y 2 1 2 1 201000 f 74 goat snp37678-scaffold464-1081765 2 33570051 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784180 Affx-122955032 AX-385271231 2 101663625 TAGTAGTTTTGAAAAAAATCCCACTATCCCTGCCA[C/T]GAGTCATGTTCCTTTTGAAGAAATAGATTTTTAAT Y 2 1 2 1 101000 f 74 goat snp37677-scaffold464-1038122 2 33526002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453190 Affx-122920456 AX-123323523 2 101736145 TGGTTCTGCAGTCAGGCTCTGAACTACAGGCCCTG[A/C]TGCCCATCCGAAACAATGAAAGCTACGAGACAGGG M 2 1 2 1 101000 r 74 goat snp37675-scaffold464-965602 2 33452302 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411721 Affx-122951527 AX-123282071 2 101850008 TCTGCTGGGCACTGGAGAGAAAAAGATAAAAGAGA[C/T]ATGCTTGTTATTTGTCTTCAAGGAGAAGAAACATG Y 2 1 2 1 201000 r 74 goat snp37673-scaffold464-851739 2 33337846 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779171 Affx-122978954 AX-385266275 2 101880096 AAACTCTGGACTTTGGCCCAGGATTAGAAATCAGG[G/T]GTACAAAGTTAAAGCTTGGTTCTATCACTGATTTC K 2 1 2 1 101000 f 74 goat snp37672-scaffold464-821651 2 33307434 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415929 Affx-122948447 AX-123286278 2 101916414 AAGGCTATGAAGCTCACTCCTACTCGTGGTGATCA[C/T]GGGGATTTACAGAAGGCACTGCTGGTGTCTAAGAA Y 2 1 2 1 201000 f 74 goat snp37671-scaffold464-785333 2 33271101 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391197 Affx-122967417 AX-123261554 2 101961129 TGTTTTGAAGATGTGCTGTGTGGAAGCCATGGCCT[C/T]GTCTCCTAAGAGCTCGTCGTCGGGTGGGAATCGCC Y 2 1 2 1 101000 f 74 goat snp37670-scaffold464-740618 2 33225990 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38389263 Affx-122969023 AX-123259621 2 102030898 CTAGTCTCATCTGACCATGTCTGACTGGCAGAACC[C/T]AAGTCTCATCTGGAGCCCTCGCTGCAAATGAAGCT Y 2 1 2 1 201000 r 74 goat snp37668-scaffold464-670849 2 33156454 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443707 Affx-122927156 AX-123314044 2 102062761 AGGAGACAGGGAAAGGTGGAAAAGAGCTGCTGAGG[A/C]GCTGAGAGGGTGAAGAGCAGTGTGTGATCACTGAA M 2 1 2 1 201000 f 74 goat snp37667-scaffold464-638986 2 33125668 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797534 Affx-122958541 AX-385284473 2 102116195 ATAATTAAACAAATTTAAGTAAATTAACAAAAATA[G/T]AAAACAGTCTGGATTCCTTGGATCCAAATTTAACT K 2 1 2 1 303000 f 74 goat snp37666-scaffold464-585552 2 33072275 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431192 Affx-122937173 AX-123301533 2 102157371 GAAAAAAGCCCAGGGGAATACTAAGGCAGGAAAAT[A/G]CGGTGGCATGATGCTGTCTTGGTGAATTTTCTCCA R 2 1 2 1 101000 r 74 goat snp37665-scaffold464-544376 2 33031096 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403500 Affx-122957638 AX-123273853 2 102189975 TGATTTTATTTTTCTAAATTATCTCTGGTCATTTT[A/G]TTAATAGTAAAGGTGATTGACATTGTTTTGAAGTT R 2 1 2 1 101000 r 74 goat snp37664-scaffold464-511772 2 32998465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278023 Affx-1111836135 AX-519551515 2 102199348 TCTTGCCCTCAAGCCCTAATAGGTCAGGAGCAACC[A/G]TCTACAGAGGGTGTTTGTTTATGATATTTGATCTC R 2 1 2 1 201000 r 74 goat Random2.2K-250 2 102199348 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796762 Affx-122923631 AX-385283706 2 102232264 ATTTTCTGGGGAACATACAGAACTCAGTTTTTGTC[A/G]GCCTACTACATATCCCTGAGAGGCTTTCAAGTAAC R 2 1 2 1 101000 f 74 goat snp37663-scaffold464-469483 2 32955586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275383 Affx-1111834766 AX-519548957 2 102250740 ACCAAGCTCAT[A/G]AACACTTTGCAAAGATCAAGCTTGTCTGCCCACAG R 2 1 2 1 101000 r 74 goat GoatD01.052093 2 102250740 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38451972 Affx-122920944 AX-123322305 2 102288703 ATTGCTGTCAATGAACTTACTCCAGTAGCACTTCA[C/T]ATCCCTGATCCCACCAATCAACCAAGACACTTAAA Y 2 1 2 1 101000 f 74 goat snp37662-scaffold464-413044 2 32898616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789042 Affx-122950932 AX-385276055 2 102328243 GAGGGAGCATGTGGGAAAGATCTTGCGAGTATATC[A/G]TACTCTTTCTCATGTATTTCTTTTCCTCCCTCTGC R 2 1 2 1 101000 r 74 goat snp37661-scaffold464-373504 2 32858581 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781313 Affx-122923287 AX-385268398 2 102363761 GGTTTACTTCCTTTCCAAGGAAAAGCCTAATGATA[C/T]GGTAAGGTCCTTTATTAGTCTGCTAAACTTCAGTG Y 2 1 2 1 101000 f 74 goat snp37660-scaffold464-337986 2 32822864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402340 Affx-122959063 AX-123272693 2 102413018 ATGGAAATAGAGGCTAAAAGACTCTACAAAAGCAA[C/T]GAACTCTTTGGAAGTAAGTGTTATTCTACTAGAAT Y 2 1 2 1 101000 f 74 goat snp37659-scaffold464-288729 2 32774094 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767862 Affx-122932990 AX-385255082 2 102462767 TTTCTGCAACCCTTGCAAGAATAAGTAGAGAAATC[A/G]TTTTGGAGTGAATTTATACGTAACGTTCGGAAAGA R 2 1 2 1 101000 f 74 goat snp37658-scaffold464-238980 2 32724392 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278025 Affx-1111836136 AX-519551517 2 102489877 TCAAGGCAGCGGGTGATATGCCCATTTTATAGATA[A/C]GAAAATCAAGACTCAAAAGTTACACTGCTATTAAG M 2 1 2 1 201000 r 74 goat Random2.2K-251 2 102489877 T G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424738 Affx-122941662 AX-123295084 2 102499862 ACTCATTTTGTTGACTTGAATGACATAAAACAACA[C/T]GGATAATGATCAGGAAAAACTAATGTTGAACTGGA Y 2 1 2 1 101000 r 74 goat snp37657-scaffold464-201885 2 32687006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425039 Affx-122941866 AX-123295385 2 102536887 TTGACTTACAGAAAAATGTTCTGTGTGGTTTGGTT[C/T]GAGTACTCTAACTGCTTGCATATCACAGTTAATGT Y 2 1 2 1 102000 f 74 goat snp37656-scaffold464-164860 2 32649270 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410218 Affx-122952561 AX-123280568 2 102572190 AAATTTAATCCAAAATTCTCCTTTCAGACCAGTGG[A/C]TGTTACAAACTTTCAGGACAAATGACTTCATCAAG M 2 1 2 1 101000 r 74 goat snp37655-scaffold464-129557 2 32613597 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407010 Affx-122955024 AX-123277361 2 102640143 AATGTGCATCTGTGACCAAAATTTGAAGCATGTCT[A/G]TAAGAAGAGTATATATTTTAGCAAATGCTCTTAAC R 2 1 2 1 101000 f 74 goat snp37654-scaffold464-61604 2 32544900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444357 Affx-122926711 AX-123314694 2 102669474 ACCTTCTTTCCAGGTGGCTGGCCTCCTGAATAAAG[A/C]AACATTTTCTTTTCCAACCAACACTTGAGTATTGG M 2 1 2 1 202000 r 74 goat snp37653-scaffold464-32273 2 32515348 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774891 Affx-122922075 AX-385262025 2 102699572 GTAATGATCAAGCAGAAATATCAAGTATTAACGTC[A/G]TTTTTAAAAAAGACTGTTTGAAGCACCTCCTGGTT R 2 1 2 1 303000 r 74 goat snp37652-scaffold464-2175 2 32486845 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453912 Affx-122919909 AX-123324245 2 102721476 GTATACCCCAGAGAAGTTAAAGTGCTTATTCGGGT[A/G]TCAGATTTGATAGGAAGATAATTAATTTGCTAAGT R 2 1 2 1 201000 r 74 goat snp33261-scaffold390-334393 2 32464463 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771959 Affx-122959578 AX-385259115 2 102772796 CTCCTTTTTTGAAGTGTCAAACTATAAAGTTTGTG[A/G]AAGCAATACAGCTATCAACTATCAGTGTTATATGT R 2 1 2 1 201000 r 74 goat snp33260-scaffold390-283073 2 32413152 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417626 Affx-122946861 AX-123287974 2 102833860 GCCCTAATGCTCTCCTTAAGTATTTTCTTTAAAAG[C/T]GGCAATTTTTCCACACTCAACAGTTGCACTGTCCA Y 2 1 2 1 103000 r 74 goat snp33259-scaffold390-222009 2 32351650 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426087 Affx-122941075 AX-123296433 2 102874651 ATTTTGCCCATGACCCCTGAAGCATCTGTGTAGTT[C/T]GAAGACCCTGAAGGCCTATCAAGCTTTAGAAACAG Y 2 1 2 1 102000 f 74 goat snp33258-scaffold390-181218 2 32310926 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381926 Affx-122974135 AX-123252284 2 102908817 TTTATCCTTGAAAGAACCTGTTTCACCACTTGCCC[G/T]ATGACGTTATCCCTGTGGTGGTCTTCAATTTCATC K 2 1 2 1 201000 r 74 goat snp33257-scaffold390-147052 2 32276615 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417701 Affx-122947456 AX-123288049 2 102951483 CTATTTGAAAGGGCTCTCACCCTGCCATTTTCCCC[A/G]TCTCTTTCATAGTATCCCCAGTAGGTAAACTTTCC R 2 1 2 1 201000 r 74 goat snp33256-scaffold390-104386 2 32232890 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452107 Affx-122920841 AX-123322440 2 102983353 TTGACTTTAGTGTCTTCTAGTGAAAACCACTAGAT[G/T]AAAGATATCTGAAAGTAGAGACTCATGTCGAAACT K 2 1 2 1 101000 r 74 goat snp33255-scaffold390-72516 2 32200687 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772184 Affx-122940310 AX-385259338 2 103013913 TCCTTCTACTAAGGTTTTGCTTTCCTAACTCACTT[A/G]ATCATAAAAATGCATGGTCATTGTCCTCAAGATTG R 2 1 2 1 101000 f 74 goat snp33254-scaffold390-41956 2 32168959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767530 Affx-122943627 AX-385254787 2 103074084 CACCCTTCATCAAAATCGAGAACTCTGACTCACCC[C/T]GATAGTCATACACAGGATTTAGCCAACCTTCTGAG Y 2 1 2 1 101000 f 74 goat snp16996-scaffold1772-450201 2 32096145 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444498 Affx-122926514 AX-123314835 2 103117116 TCAAGGCAAGTTAGCAATGGAGAGGGTGACAGCCA[A/G]CCTGAAGCAGGCTTTGTCCCCCTTCCTCTGATCTC R 2 1 2 1 101000 f 74 goat snp16995-scaffold1772-407169 2 32052934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419610 Affx-122945989 AX-123289958 2 103162957 CGTCATTAATTCCTCCTACATATTGGGAGGGGGTG[C/T]TTTTGACCTTATATGGCTCACCTGGGGCTGTAATA Y 2 1 2 1 202000 r 74 goat snp16994-scaffold1772-361328 2 32007086 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795538 Affx-122930019 AX-385282493 2 103204257 AGAATGTTGGCTCTTCCCAATTAAACATCGTCATC[A/G]TTGTATCCACAGTAAATGTATGAAAAACCATGGAT R 2 1 2 1 101000 f 74 goat snp16993-scaffold1772-320028 2 31964421 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441659 Affx-122929192 AX-123311996 2 103246504 ATAGACAGTGGTGGGGACTGGTGGGTAACATGAGA[A/G]CTCAAAAAGGGCACAGGTAGCAGCTGCTTGGGAAA R 2 1 2 1 101000 r 74 goat snp16992-scaffold1772-277781 2 31921770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387256 Affx-122970558 AX-123257614 2 103280315 AGTGGTAGATCCTTGTTTGATCCAGGGCACGTGAT[A/G]CCACCTGGTCTTTTAAACAACTGGCCAGTCTCTAC R 2 1 2 1 101000 f 74 goat snp16991-scaffold1772-243970 2 31887770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442678 Affx-122927891 AX-123313015 2 103318888 TAGTCTGCCCGCTTTGGGATGGAAATATCCATCCC[C/T]TCTGCTGCTGGCAGTGTCTGAGATATTGGTGTCTG Y 2 1 2 1 102000 r 74 goat snp16990-scaffold1772-205397 2 31848774 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790693 Affx-122969679 AX-385277694 2 103357228 TGTTTCATGGTGCAGTTGAACGCACCTTAGTCTCT[C/T]GGAGTTTACTTTTTACTCTTACTTGTTTTTGCCAG Y 2 1 2 1 101000 f 74 goat snp16989-scaffold1772-167057 2 31810109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432074 Affx-122935881 AX-123302415 2 103389189 AGTGGGGTACCTGTTATTAGGTTCCAGGACTGCTG[C/T]GACAAGTTGCCACAAACTTGATAGCTGTATATTAA Y 2 1 2 1 101000 f 74 goat snp16988-scaffold1772-135096 2 31777930 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434288 Affx-122934769 AX-123304629 2 103418198 TGATCAATATTTTTCCAAATTTTTATTTCTCTCCT[A/G]CTTGATTTTTAAGAATTTTAGGGCAAATTCCAAAT R 2 1 2 1 101000 r 74 goat snp16987-scaffold1772-106087 2 31750361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392746 Affx-122966010 AX-123263103 2 103451148 GCACAGTTTCAGGGAAGAGTCAGGACACTATTTAA[G/T]AGGATTGTCTTTCTGTCTCCTGCAGTTTACAACTC K 2 1 2 1 101000 f 74 goat snp16986-scaffold1772-73137 2 31717890 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414960 Affx-122949074 AX-123285309 2 103483689 ACCAATAGCTCTAAAGCAGTCAATAAACAACCAAA[G/T]ACTCACAAGACCACAAAATGAACTTATCTACCCAG K 2 1 2 1 201000 f 74 goat snp16985-scaffold1772-40596 2 31685772 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431991 Affx-122935939 AX-123302332 2 103520010 TATTTTAATTCTCACTTGAGTTCTTCTAGAGCCAA[C/T]AAGAATCTCTTCATCCCTGAAAAGCCTGAAAAGAT Y 2 1 2 1 101000 r 74 goat snp16984-scaffold1772-4275 2 31649210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446367 Affx-122925596 AX-123316703 2 103544832 ATGGAAAGCCAGGAGAGCAAAGGTTTTTAATCAAG[C/T]ATCCAAGAAGGACATCAAGGAATTTGTGACCACCC Y 2 1 2 1 101000 f 74 goat snp10730-scaffold138-2121247 2 31624004 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277879 Affx-1111836137 AX-519551375 2 103567956 GATGACAACCTCATGTTGATTTCATTTGGATGTAA[C/G]AGTGTCAGGATTACAGATATAAGAATATATTATAT S 4 1 2 1 101000 f 74 goat Random2.2K-253 2 103567956 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448635 Affx-122923365 AX-123318971 2 103601413 CAGGGACAAGAGTCCACAGATCCATTTTAATAACC[A/G]TAAGTCTTGCTGCTTAAGAGAACAAGGTTCCTTTG R 2 1 2 1 101000 f 74 goat snp10729-scaffold138-2064666 2 31578519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390019 Affx-122968449 AX-123260376 2 103652910 CAGACAAGTTAATTACTGAGGCTAGGACACAGGGT[A/G]AGCACACAAAATGACTGAATCAGAGTAAGCTCCGG R 2 1 2 1 101000 f 74 goat snp10728-scaffold138-2013169 2 31527626 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388401 Affx-122969294 AX-123258759 2 103716461 CCTCCTCAAGGAAAATTATGACTTAGTAGTAAATG[A/G]TTTTGTTTTCTTCAGGATATCTCCTGACAAGAAGT R 2 1 2 1 102000 f 74 goat snp10727-scaffold138-1949618 2 31463392 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417372 Affx-122947708 AX-123287720 2 103751319 AGGGCATTGCTGGATTCAATGGAAACTGGGAACCC[A/G]CAGATGCAAGAAGAACTCTGGGAACAGAGATCAAA R 2 1 2 1 201000 f 74 goat snp10726-scaffold138-1914760 2 31428802 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423998 Affx-122942109 AX-123294344 2 103803766 CACCACTCAGTGTTCACATCTGCTTTGTCAACAGC[A/G]CCACTGATTGAGTACTGTTATATGCAAGGCTTCTT R 2 1 2 1 201000 r 74 goat snp10725-scaffold138-1862313 2 31375952 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409279 Affx-122953116 AX-123279630 2 103836599 GAATCCAGCATTGGAAGAGGAAGCATGGGAGACTG[C/T]AGCAGCTCTGAACTTTTTCCAGGATGGATTTCTGA Y 2 1 2 1 101000 f 74 goat snp10724-scaffold138-1829480 2 31343054 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393484 Affx-122965827 AX-123263840 2 103895990 GTGTGTCCTCCTGCCTGAAGCCTCAGGCTGATGCA[C/T]GAATGCACAGAGTGGACAGGACCCTTGTTTGCACC Y 2 1 2 1 101000 r 74 goat snp10723-scaffold138-1770089 2 31283704 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393241 Affx-122965475 AX-123263598 2 103926941 GATAGTCCTGAGAAGGACTTAAGAGCAGCTCTGGA[C/T]GCCATTATGAGAAAAGAAACAGTACAATCCTGGAA Y 2 1 2 1 101000 r 74 goat snp10722-scaffold138-1739138 2 31252832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440280 Affx-122930638 AX-123310617 2 103965264 CAAACACTTAGAAGTAATCTCTCTTGCCTTACTAG[C/T]TTGCCAAGTAACAAATCTCTGATGGCCTGAGCTAT Y 2 1 2 1 101000 r 74 goat snp10721-scaffold138-1700815 2 31214452 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443452 Affx-122927834 AX-123313789 2 104042175 TCTCCACCCATTCTTTCTCTGGATCTTCAGCAGTC[A/G]TCTAAACTGGGACTGCCACGTGGATACTGGGGTGC R 2 1 2 1 101000 f 74 goat snp10719-scaffold138-1623904 2 31138798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419713 Affx-122945911 AX-123290061 2 104100113 CCAAGAGGTGATTTTATGTCAGTAAGAAACTAGAA[C/T]GATTTGCCTTTGGAATTACTGCTTTGGACAAGAAA Y 2 1 2 1 101000 f 74 goat snp10718-scaffold138-1565966 2 31080674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446667 Affx-122924763 AX-123317003 2 104132764 CCAGTCCCCCAGGGTGACATCTTGTAGACCTGTAG[C/T]GCAATATCACAGCTAGCATGCTGCTGTTTATACAG Y 2 1 2 1 101000 r 74 goat snp10717-scaffold138-1533315 2 31048264 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762263 Affx-986696794 AX-385250455 2 104154096 CCAACTATTTTTATTGGAATGGGCTATTAGGAAAT[C/T]TTCTAGCTATAAAATTTATTTTTAATATAAATTTA Y 2 1 2 1 600010 f 74 goat 2_104154096 2 104154096 Ancestral_priority_1043 ancestry 0.808 recommended IMAGE 10K 10K ancestral 320799847 Affx-122926313 AX-385286773 2 104207828 AGCCAAATTCTGTTTGTATAGCCCGTGAGCTGAGC[A/G]TGTTCATTGCAGTTTTTAGTGGTTAAAAAAAAAAT R 2 1 2 1 101000 f 74 goat snp10716-scaffold138-1458251 2 30972743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768978 Affx-122950945 AX-385256153 2 104238885 GCAGGTATGAAACCTATGAAACTATTAAATAAACC[A/G]TTAAATGTGATTTGTATGATATCAGTGTAATTTGT R 2 1 2 1 101000 f 74 goat snp10715-scaffold138-1427194 2 30941461 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776011 Affx-122959016 AX-385263141 2 104283680 GAGCAAATTAAATCCCTTCTTGGCTTGCTCTCCTC[A/G]TCTGTAAAATGAGCCTGTTGGATTCCGTGATCTCT R 2 1 2 1 101000 f 74 goat snp10714-scaffold138-1382399 2 30896276 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393156 Affx-122965539 AX-123263513 2 104313537 TGATTTTGGAACCCAAGAAGATAAAATTTGTCACT[A/G]TTCACTTCTGAATTAGAACCTCCTCAACCTGCTTA R 2 1 2 1 101000 r 74 goat snp10713-scaffold138-1352542 2 30867737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416450 Affx-122947822 AX-123286799 2 104344625 GGTTTCATTTTAGAGGAAAAGTAAATTCTGCTCTT[A/G]TTTGTAGTTTCCTTTGACAACTGCTTTGCATCTTC R 2 1 2 1 101000 r 74 goat snp10712-scaffold138-1321454 2 30836354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393591 Affx-122965379 AX-123263947 2 104375919 GATTCAAAATGTAAGAGGAAAAGAAAGAAATGGTT[A/G]TGGGGGAGGAAAGAGGAAAGGAAAAGAAAAGGAGA R 2 1 2 1 101000 f 74 goat snp10711-scaffold138-1290160 2 30804985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400403 Affx-122959995 AX-123270758 2 104404575 TGAAATGCCTGAGAAAGATTTCCTAAGGACACAAC[A/G]TGCTTAGCTGCTCAGTCGTGTCTGCCTCTTTGCGA R 2 1 2 1 101000 f 74 goat snp10710-scaffold138-1261504 2 30775849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391555 Affx-122966631 AX-123261912 2 104434968 ATTTCATGGTGACCACTCAGTTGAGACCCTCTCCC[A/G]CTGACCTTCATCTGGATTATTGGAATATCCTCCTC R 2 1 2 1 201000 r 74 goat snp10709-scaffold138-1231111 2 30744625 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398388 Affx-122961647 AX-123268743 2 104464233 CCTGTGTTTCACTTCTGCCATCCTGTTCTCCAATT[A/C]TCCAGGATAACACTCTCAAGGAAACTCCCTGTACT M 2 1 2 1 201000 r 74 goat snp10708-scaffold138-1201846 2 30715364 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769284 Affx-122936455 AX-385256456 2 104507156 TTACAGGATTCTTTTGGTGACATTGGGGGAAAGAA[C/T]GGGTCTTAAGACAATCCTAAATTACTGATTTTTGA Y 2 1 2 1 201000 f 74 goat snp10707-scaffold138-1158923 2 30672472 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375812 Affx-122978559 AX-123246171 2 104545362 GCCAAATACAAGTCAGCTGTAAGCTATTGTAATCA[C/T]ATCAAGCAGGCAGAGTATTAATGACAAAAAACAGA Y 2 1 2 1 101000 f 74 goat snp10706-scaffold138-1120717 2 30634092 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388561 Affx-122969177 AX-123258919 2 104606295 TGAATGTTTGAGCCTATCATTCTGTTACATAAAAT[A/G]TGCACAATTTTTTGTATATCAGTTACACTTCAAAC R 2 1 2 1 101000 f 74 goat snp10705-scaffold138-1059784 2 30572637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771287 Affx-122947348 AX-385258445 2 104649735 CCGAACCAAGTCTGAGTTCATTTTGCAGATCTTAC[A/G]TATGTTCAGTCATCCCATGCACATTGCCCACCGGA R 2 1 2 1 101000 f 74 goat snp10704-scaffold138-1016344 2 30528841 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781795 Affx-122931967 AX-385268877 2 104682190 GGAGAGTGCAGTTCACTAGAGTTTAGGGTTTCATC[A/G]CCTGTTATTTAGTGTTTACTGGGAATATATTCCCA R 2 1 2 1 101000 f 74 goat snp10703-scaffold138-983889 2 30496426 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426755 Affx-122939857 AX-123297101 2 104725034 GTTGCTTTAAAAAAAAAAAAAGATTCAAGCTACCT[A/G]TGGAATTTATGCAAACTTTCATCTCTTCTGTGCAT R 2 1 2 1 101000 r 74 goat snp10702-scaffold138-941045 2 30453742 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783332 Affx-122940117 AX-385270397 2 104756508 TAGGCTTGCCCAAGGACAATTACAGGCAAATTAAA[G/T]AATAATTCTGTAGATGATTGACATCAAGAGAATAT K 2 1 2 1 201000 r 74 goat snp10701-scaffold138-909571 2 30422289 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441643 Affx-122929203 AX-123311980 2 104789717 GTAAACAAAGAGTGAGCAATTGCTCTGTGACTTCT[A/G]TGCTTGAATAGATTAGTAACACCTGCTTTGTCTCC R 2 1 2 1 201000 r 74 goat snp10700-scaffold138-876362 2 30388933 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427180 Affx-122939610 AX-123297523 2 104820135 AGTGTCACTCCCTCAGTGGCCAGGATCAGGGGTAG[C/T]TTTCAGCACATAGGATGGAGCAAAGTTGAGCAGGC Y 2 1 2 1 101000 r 74 goat snp10699-scaffold138-845944 2 30358678 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393350 Affx-122965931 AX-123263706 2 104884230 AATGCTTCATGAAGATTCACAGAGTATATATTTTA[C/T]GTGCTCATATTTGAGGGGTGCTCTAATGCTGACAG Y 2 1 2 1 201000 f 74 goat snp10698-scaffold138-781849 2 30294377 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786238 Affx-122940657 AX-385273273 2 104933092 TCTATCCTACACTCAGTCTGCTATAGGCAAATCCC[A/G]TTTCATTTGTTCCATGGGCATGGCACAAAGATGGA R 2 1 2 1 201000 f 74 goat snp10697-scaffold138-732987 2 30245936 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440366 Affx-122929646 AX-123310703 2 104968473 TGAGAAATATGGGATTACAGAACTGAATCTCATCT[A/G]TGCAGCTGGAGAGAAAAATTAAGGCCTTTAATGTA R 2 1 2 1 101000 f 74 goat snp10696-scaffold138-697606 2 30210498 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399602 Affx-122961096 AX-123269957 2 105001596 CTCTGCAACTTCAGCCTTCCATTCCCCTGCTGCAT[A/G]GGCTATTTCCAGTCTAAATTTATGTAGGCATAATC R 2 1 2 1 201000 r 74 goat snp10695-scaffold138-664483 2 30176189 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790939 Affx-122965011 AX-385277936 2 105092219 CCAAATTTTGATATGTAAAATTAACTGTCACAAGT[A/G]TGGATAGTTTATGTGAGAAAATGGACCCAAAGATG R 2 1 2 1 201000 f 74 goat snp10693-scaffold138-573860 2 30084701 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272927 Affx-1111833148 AX-519546614 2 105105678 ATTATGTCTTAGACTAATGTGGTTAACACTTACTG[A/G]TGAACTGGATATAAAGAATGAAGAAAAAGATTCAA R 2 1 2 1 101000 f 74 goat 2_105105678_AF-PAKI 2 105105678 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426554 Affx-122940178 AX-123296900 2 105126434 AGTTGGGGCTCTTTCCTGGCCCTTGAGCCTGGGGT[A/G]CTGTGGCTAAAATTTCTATCCAGACACCACATCTT R 2 1 2 1 101000 r 74 goat snp10692-scaffold138-539645 2 30050446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423940 Affx-122942252 AX-123294286 2 105170901 GTATGCTCAAGTAACAAAACAGGCTTTGAACTCTT[A/G]TGGGTAGGATGAGGAGGGGGATTTGTGTTGTTCCT R 2 1 2 1 101000 f 74 goat snp10691-scaffold138-495178 2 30005866 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407054 Affx-122954927 AX-123277405 2 105201067 TCATGCAGGTCTCACGGTGCAGCACCAGTGCAAGT[C/T]TGCAGGTGCTGCGGCATGGAAGCAGGAGCAGGTCA Y 2 1 2 1 101000 r 74 goat snp10690-scaffold138-465012 2 29975669 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397618 Affx-122962632 AX-123267973 2 105245026 TTGAGCCTAGGATGCTTGTCATGAAACACATCTTA[G/T]CACCCTGGGACAGAGCTTGAGCAACTGTGGGCAGG K 2 1 2 1 101000 f 74 goat snp10689-scaffold138-421053 2 29930706 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379958 Affx-122975639 AX-123250316 2 105288353 ACCCTGGCTGCTGACCCCACACCAGCTGCCACCAT[C/T]GTTCACTTCAAAGTTTCTGCCCAGGGAATTACACT Y 2 1 2 1 101000 r 74 goat snp10688-scaffold138-377726 2 29887096 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422212 Affx-122944440 AX-123292558 2 105334712 TTCCTGGTTGGCCTGTCTGCCCTGACATCTAAACA[A/G]ATGACCTCTCCCCACTGACATTAGTGAGAGAAGCG R 2 1 2 1 101000 f 74 goat snp10687-scaffold138-331367 2 29840892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434281 Affx-122934774 AX-123304622 2 105368824 AAGAGGAGCATGATGTTTATGATGGTACAATGTGG[C/T]GTGGAGAGTGTGGGCAGGGCAGTCATCTCTGCAGT Y 2 1 2 1 101000 f 74 goat snp10686-scaffold138-297255 2 29806853 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762265 Affx-986696796 AX-385250457 2 105409398 AGTGTCCTCTAGAGGGCAGGCCAATGGGGATCCTG[A/G]TGGCACCCACCACGTGGCTGATGCTGTATGGATTA R 2 1 2 1 600010 f 74 goat 2_105409398 2 105409398 Ancestral_priority_1043 ancestry 0.436 neutral IMAGE 10K 10K ancestral 38409997 Affx-122953272 AX-123280347 2 105436138 AACAGGCAGCTGGAGATCTGCCAGGGTAGGGTGCT[C/T]GAGCCAAGACTCACAGCCTGAACACAATGTTCCTA Y 2 1 2 1 101000 r 74 goat snp10684-scaffold138-229941 2 29740361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414216 Affx-122949647 AX-123284565 2 105475080 TAACAGATTATGGCTGAAGGAGGTGGGGTGGGAGA[C/T]GAGGTCGGGAAGAGAGTCAGGGAACCCGGGCTCTA Y 2 1 2 1 201000 r 74 goat snp10683-scaffold138-190999 2 29701505 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400576 Affx-122960411 AX-123270931 2 105528493 GACTTCAGAGAGGAGTGGGGCTCTCTCCAAGTGCC[A/G]TCCCAGGGCTCTCTCTGGACACACTCACCCTTCAG R 2 1 2 1 201000 r 74 goat snp10682-scaffold138-137586 2 29647881 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418400 Affx-122946551 AX-123288748 2 105560614 GGTCAAGACCAAGTTTTCTCAGAAGCCCAGAGTAA[C/T]GAAATCACAAGATAGGTCACTTCTGGGAGCTGATG Y 2 1 2 1 101000 r 74 goat snp10681-scaffold138-105465 2 29615314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407147 Affx-122954853 AX-123277498 2 105598322 GGTTCTATTATAGATACCTTGTCACAGCATTAATT[A/G]TAGCTATACCTTATCATGTTTAGTGGAAACAGCGT R 2 1 2 1 101000 f 74 goat snp10680-scaffold138-67757 2 29577460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403318 Affx-122957830 AX-123273671 2 105640392 TTTGAGAACTAAATCTGTTTTTGTTTTCACTTGTT[A/C]GAGAACATCTTTATTTCTTCAGCTTAAAAAGCAGT M 2 1 2 1 101000 r 74 goat snp10679-scaffold138-25687 2 29535303 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389617 Affx-122968755 AX-123259975 2 105682934 ACCTGTGGCCTCAATCCCCAAGCCTCTGGAACACT[A/C]TCTCAACAGTCTCAGGGATCTCTCAGCCAAAACTC M 2 1 2 1 101000 r 74 goat snp11350-scaffold1410-16756 2 29492752 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376688 Affx-122978989 AX-123247047 2 105714981 AATCATGCAATTCATACCAATGTATGAATACTCAA[C/T]GTATGAAGCTTTTGACTGTGTGGATCACAACAAAC Y 2 1 2 1 303000 f 74 goat snp11351-scaffold1410-48803 2 29460570 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411374 Affx-122952239 AX-123281724 2 105751449 TCTCTGATGGGTGAGCTACTGTCGGTGAGGCCAAG[A/G]GGGCAGTACTGAGCACAAACATGGGAGCTCAACCA R 2 1 2 1 201000 r 74 goat snp11352-scaffold1410-85271 2 29423755 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783362 Affx-122943213 AX-385270426 2 105792641 AGTGTCCAAGAATAAGGAACTAGTTAAATAAATGT[C/T]GCTGTATCTATACCAGAGAATATAGTGATGAAAAA Y 2 1 2 1 101000 r 74 goat snp11353-scaffold1410-126463 2 29387240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767576 Affx-122943764 AX-385254828 2 105828819 CACAATATAACTATAGATCTATATGAACAGATAAC[A/G]TTAATGGTTAAGTACGAAAAAACAGAATGAATTTA R 2 1 2 1 101000 f 74 goat snp11354-scaffold1410-162641 2 29350964 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781492 Affx-122927291 AX-385268577 2 105860026 CCTAAGAAGGTATAATATCCTTAATCAGATCAAAC[C/T]ATTTCTTGCTACAATAATAGGTTAGTAACACTGTG Y 2 1 2 1 101000 f 74 goat snp11355-scaffold1410-193848 2 29318975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381738 Affx-122974328 AX-123252096 2 105941487 GCTCTTCCCTTCTTCACTTTCCTAAACTTAAAACA[A/G]GCGTCTTAATTCACCAGACTGTCCTGGAAGGATAT R 2 1 2 1 101000 r 74 goat snp11356-scaffold1410-275309 2 29237671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430238 Affx-122937317 AX-123300579 2 105971929 GAACATGACTGGGGCACTGGCTTGGCTTTCCCACT[A/C]TAAGCCTGAAAACTCAAAAGTCCCAGAAGGACCTG M 2 1 2 1 201000 r 74 goat snp11357-scaffold1410-305751 2 29208638 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378156 Affx-122976970 AX-123248515 2 106098084 GCCCCAGCAGATGGGCCCTGGGCAGGAGGGAACCC[C/T]TAGATTAGCTCCTGCTGTGTGAGGACCCTGTCCTG Y 2 1 2 1 101000 r 74 goat snp11359-scaffold1410-431906 2 29105738 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454191 Affx-122919299 AX-123324524 2 106132077 GAAACTGTCTAGGGATCCACCATGAATAACAAAGA[C/T]GCTCCTATCACTGACAAAATTCCAACAATTAAAAG Y 2 1 2 1 201000 r 74 goat snp11360-scaffold1410-465899 2 29071340 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277881 Affx-1111836138 AX-313920127 2 106183966 TAATATCTTCTGTTTCTGTTAGGTCCATACCATTT[A/C]TGTCCTTTATTTTGCCGGTCTTCACAAGAAATGTT M 2 1 2 1 303000 f 74 goat Random2.2K-254 2 106183966 G T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413222 Affx-122950252 AX-123283571 2 106213716 AATGCAGGGCAGGAATAGGAAAGATGCTCTTGGAT[A/G]CTGTCGGTTTGGTCTCTCATTGCAATTAGCCCAGA R 2 1 2 1 101000 r 74 goat snp11362-scaffold1410-547538 2 28989349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386486 Affx-122970759 AX-123256844 2 106272304 TTGTGTGCTTTTCTGTATCTTATTTCAATAACAAG[C/T]TCACACACACACCTACCCCTCTTTCTGTGGAAGAT Y 2 1 2 1 201000 f 74 goat snp11363-scaffold1410-606126 2 28931845 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382888 Affx-122973416 AX-123253246 2 106309507 CAAGAGAAGTGAGACCCCCATCTATCCCAGCAGGC[A/G]TGGGTGTGTGTACATGCACAACACACGTGTAGCAC R 2 1 2 1 303000 f 74 goat snp11364-scaffold1410-643329 2 28894733 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426524 Affx-122940200 AX-123296870 2 106356855 ATTGTAATAAAAAATGAAGGAGTAACTGTGTCCAC[A/G]TGTCTCTGCCTTGTACCAGTGCTGAGAGTGGAAGC R 2 1 2 1 101000 f 74 goat snp11365-scaffold1410-690677 2 28847082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416293 Affx-122947937 AX-123286642 2 106394518 CTCTTTTAGAACAGAAGGTCTAGGGACACCAAATG[A/G]CTCTGTGTCTACAGGACAAGTGTCCCCAGGCCCCA R 2 1 2 1 101000 f 74 goat snp11366-scaffold1410-728340 2 28809348 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794208 Affx-122960629 AX-385281174 2 106410342 GCCAAGTACCAACTCAAAATTGGCTACTTCACAAG[C/T]TGGGTGTCCTAGAACCTACAAGAGGAACGTCCTCT Y 2 1 2 1 101000 f 74 goat snp31725-scaffold3533-12077 2 28793258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432163 Affx-122936415 AX-123302504 2 106440546 TGATGTACACGAACCCACTATAGCAGATGCTGATC[A/G]TATCAAAGCCTCTGAGGAGGAGGGAAACATGCCTG R 2 1 2 1 101000 f 74 goat snp31726-scaffold3533-42281 2 28763060 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405356 Affx-122956320 AX-123275708 2 106496795 AAAATAACTACTACTGCTAACTGAGCAGCGTCACC[A/G]TCTATTTGGTAGCAGCACTCTAATAGAAACTCCTA R 2 1 2 1 101000 f 74 goat snp31727-scaffold3533-98530 2 28707008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421738 Affx-122944378 AX-123292085 2 106525864 ATGAAACCTGGGGTGGTGGGTCGGGTCAGTAGTTA[A/C]TGCACTTAAGTCACTGTAGCCCGTGGAACCTCCAC M 2 1 2 1 201000 r 74 goat snp31728-scaffold3533-127599 2 28678150 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398885 Affx-122961032 AX-123269240 2 106598658 TGCTCAACCCACATCACACATTTATGTTAGCCTGG[A/C]TCCTGCAGCAATGAGTTCACAGCCCTAAGCAGGCT M 2 1 2 1 201000 r 74 goat "2_28604766_AF-PAKI;snp31729-scaffold3533-200393" 2 28604766 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434853 Affx-122934371 AX-123305194 2 106643386 GAACATCTTCCCCACAATTCTCCCCTTTTTCTTGT[A/G]TCATCATTTTCTCCTGTTGTTTACTGAATTATTCC R 2 1 2 1 201000 r 74 goat snp31730-scaffold3533-245121 2 28560445 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409737 Affx-122953021 AX-123280088 2 106674609 CCACACCACAGAGGAGAGCAAGGGGGAGGCTGAAT[A/G]CAAGGGGCTCTGGGTACTTCTCTCCCATCTAAGGA R 2 1 2 1 101000 r 74 goat snp31731-scaffold3533-276344 2 28529243 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414768 Affx-122949244 AX-123285117 2 106738373 GGGGGGATGTGCAGCCCTCAGACAGATTGGAACAC[G/T]GATTGTGGCTCCACCAGGCTCCCTGTGCTTCAGGC K 2 1 2 1 201000 f 74 goat snp31732-scaffold3533-340108 2 28466179 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405528 Affx-122955985 AX-123275880 2 106775939 AACTAGTGCTCAAACCCTGAGCAGATGCTCATCAA[G/T]TGCCATCCTGACTTCCCTCTCCATCTCCATGTCAG K 2 1 2 1 101000 f 74 goat snp31733-scaffold3533-377674 2 28428620 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396389 Affx-122963023 AX-123266744 2 106818470 CGATAGCATGGAGTTGTATTCCGGAAACACTGGGA[A/G]GTGGAGAGGAGAAAGTCATGTAGTTCAGACTTACC R 2 1 2 1 201000 f 74 goat snp31734-scaffold3533-420205 2 28385735 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435422 Affx-122933544 AX-123305762 2 106846311 TATGTGTATGACCACAGGTGTGCATGCGTCTACCC[A/G]CGTGAGGGTACCTGGTATGTATTTGGGATTTTGTG R 2 1 2 1 101000 r 74 goat snp7379-scaffold127-22944 2 28358081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375951 Affx-122978449 AX-123246310 2 106905708 TTTGCTGTTCATGATGTGCTTCCTCTTAGTCTGTT[C/T]CACTTGTTTTAGGCTCTGGGTTCAACTCACATATG Y 2 1 2 1 101000 r 74 goat snp7380-scaffold127-82341 2 28300047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445529 Affx-122925169 AX-123315866 2 106949928 ACCCGAGCTGGAGTGCCTCGACCCTACCTTCACCA[A/C]TTCCTCGGGGGCTGGCCCAACTTCTTCCTTGTTCT M 2 1 2 1 201000 f 74 goat snp7381-scaffold127-126561 2 28255010 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389944 Affx-122968089 AX-123260301 2 106989311 TGCCGCTCTGTTGTCACCTACCTGCAAAGGATGGC[C/T]GGCCTTTCTGAATTGGTTTCCCTCTCTTCCATCAG Y 2 1 2 1 101000 r 74 goat snp7382-scaffold127-165944 2 28215205 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386826 Affx-122970096 AX-123257184 2 107021275 TGATCTTACTGGGATGGCCATGTGTCAGGCTAAAA[C/T]GGAGGGCTCTTTCATTAAGGAGAAGAGGGAGAAGG Y 2 1 2 1 101000 f 74 goat snp7383-scaffold127-197908 2 28183236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453788 Affx-122919582 AX-123324121 2 107081626 TTGTCTTGGCCCCACGGCGTATTGTCTGCCCTGAG[C/T]GCTGTTTGGCCTGGCACCAGCCTGGATTTCCCCAT Y 2 1 2 1 101000 r 74 goat snp7384-scaffold127-258259 2 28122485 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399581 Affx-122961112 AX-123269936 2 107187782 TGGGGAGCTCCTTCTTAACTTGCCTCAAACATACT[A/G]TCTCTGGACACTGTAATCAACAGTGTCTGCTTGTA R 2 1 2 1 101000 f 74 goat snp7386-scaffold127-364415 2 28015754 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801404 Affx-122969735 AX-385288314 2 107242525 CAGCAACACTTATTAAAATCTATATTCCTGGGCTG[C/T]ACCTCAGACCTCCTATAAAGACTCTTCGCCAGAGT Y 2 1 2 1 101000 f 74 goat snp7387-scaffold127-419158 2 27960765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385827 Affx-122971017 AX-123256185 2 107281090 ACCACCATGTGTTTGTGGTGATTTATTGCAGCAGC[A/G]TGGGAAGCTCTTACAGGGAGCAAGGATGGGGCTTT R 2 1 2 1 101000 f 74 goat snp7388-scaffold127-457723 2 27922076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446941 Affx-122924678 AX-123317277 2 107316606 CATCCAGAGCCCTAGGAATTAATCATACCATATAC[A/G]CTAATGGAGAAAACCTAGGTTGTTTAGGGGAAAAA R 2 1 2 1 101000 f 74 goat snp7389-scaffold127-493239 2 27886907 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274028 Affx-1111833995 AX-519547633 2 107345224 AGTCTGCTTCTTGCTGGTTCAAGTTCAGAAACATG[A/G]A R 2 1 2 1 101000 f 74 goat GoatD01.013249 2 107345224 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38432387 Affx-122935854 AX-123302728 2 107383231 GGCCACTGGAAAGGCCTGCCATCCACTGAGTGAGG[C/T]CTCTGTTCCAGACCTCTATCTTTCTCAGCTTCAAG Y 2 1 2 1 101000 r 74 goat snp7390-scaffold127-559864 2 27821153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408538 Affx-122953690 AX-123278889 2 107420335 AACAGACATGACTGGGAGCTGGGAGAGTGGAAGAC[A/G]CGGGCGATCATATCCCCAGACCTTTCTGCTGAGAA R 2 1 2 1 201000 r 74 goat snp7391-scaffold127-596968 2 27784092 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391865 Affx-122966984 AX-123262222 2 107453287 AGTGGAGAAGTGACTAACTTTCTCCCAAAGCACTT[A/G]TTGAATCATAGGGGAATAAGTAAATCAACAAATGA R 2 1 2 1 201000 r 74 goat snp7392-scaffold127-629920 2 27751137 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417426 Affx-122947216 AX-123287774 2 107488861 AAGCTGGCACTATTGTTTAGAAAGAGGGTGGTGGG[A/C]TAATGGACTAGCTGTGTTTTCTCCTGTACGTGGGT M 2 1 2 1 101000 r 74 goat snp7393-scaffold127-665494 2 27715286 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430730 Affx-122936889 AX-123301071 2 107518928 AGAGATAACATTTTCTTTTCTGTCCGTTTTCTACT[A/G]TCTTACCATTCTTTTTATTCTAAACTTTTTTCTTG R 2 1 2 1 101000 f 74 goat snp7394-scaffold127-695561 2 27684644 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378080 Affx-122977169 AX-123248439 2 107559379 GCCCGTTCTTCCCAGTTGGGGTTCTTTTTTGCAGC[A/G]TGAGGGGCAGTGAAGCAGGGGGAGGCTAAGCACCC R 2 1 2 1 101000 f 74 goat snp7395-scaffold127-736012 2 27643520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793583 Affx-122922268 AX-385280558 2 107609221 AGCAGCTAAATAAGCTCACACCTAAGAAATTAATG[C/T]CCTCACCAAAAATACCCTTTCAAAGTTAAAGCTAA Y 2 1 2 1 101000 r 74 goat snp7396-scaffold127-785854 2 27593050 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272978 Affx-1111833149 AX-519546661 2 107624429 GTTATGATGTTCTCAATTAAGGACTGCAAATACTT[A/G]ACCCCTTACAGAGGATTACAGATCTACCAATGAGT R 2 1 2 1 101000 r 74 goat 2_107624429_AF-PAKI 2 107624429 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320773409 Affx-122948092 AX-385260551 2 107645594 GCAAGAATGTAGAAGCTCACAGGATTTGCTGAGTG[A/C]TGAGACCTTCTCTAGCTCAGAGAAAAGTGAAAAGC M 2 1 2 1 101000 r 74 goat snp7397-scaffold127-822227 2 27556862 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277883 Affx-1111836139 AX-519551378 2 107647683 ATTGAATTTTACTTTATCCTAGACACACGGTAGAA[C/G]AGAAACAACAGGGGCCCTGCCATTCTTTCTCAGCT S 4 1 2 1 101000 f 74 goat Random2.2K-257 2 107647683 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320787765 Affx-122953432 AX-385274788 2 107707017 CTTACAGGAAACTAAGGCTTTGAATTACTCTCCTC[A/G]TTTTACACATGTGGTAGCTGAGGCTTCATGAAGCT R 2 1 2 1 102000 f 74 goat snp7398-scaffold127-883650 2 27494061 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410525 Affx-122952169 AX-123280875 2 107765472 CAAGAGCTTTTATTTAGCTGGGTAATTGTGTTTGT[A/G]GAAGTTAGGAATGTTTTTGTTCCAAGCACAGGAGG R 2 1 2 1 201000 r 74 goat snp7399-scaffold127-942105 2 27435626 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381555 Affx-122974828 AX-123251913 2 107810813 GCTTCTGATGCAACATCCTTAGGGGACAAGTAAGC[A/G]TGTGAATACAGCCATTAGAATAAGATGGAATAACA R 2 1 2 1 101000 f 74 goat snp7400-scaffold127-987446 2 27390312 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796205 Affx-122919507 AX-385283156 2 107845502 CAGAGTCTGCTACCGGTGCCTGCATCATCTTTAGC[A/G]TATCATTAACTCCTCAAGTACTCAGGTCATTCACA R 2 1 2 1 202000 f 74 goat snp7401-scaffold127-1022135 2 27354656 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437287 Affx-122931987 AX-123307625 2 107877611 CTTGGTCACTAGACCAGAGTTTATGGTGGGTCACT[A/G]TGCACTGGGGTTACTGAAGAGCTATCACAATGCAG R 2 1 2 1 101000 f 74 goat snp7402-scaffold127-1054244 2 27322496 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785949 Affx-122965387 AX-385272986 2 107915146 TTTATCCTGGGTACTCTTCTGCAAAACCAAACTTC[A/G]TATCTATTGTGGATTCTGGCTATATCAAAGAATCA R 2 1 2 1 101000 f 74 goat snp7403-scaffold127-1091779 2 27284774 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415325 Affx-122948800 AX-123285674 2 107950930 GGATGATCCTAATTTCTACCTCACAAGTGAGAAAA[A/G]CACCAAGCAATGCACTTGGGAAATAATAAGTGCTC R 2 1 2 1 101000 f 74 goat snp7404-scaffold127-1127563 2 27248666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794504 Affx-122975566 AX-385281467 2 107985294 CACCACATTCCAATCCAGTCTCATTTCCTACACTG[A/C]TTGTAATAAATCTAAGTGTAGACCTTGCTCAGGAT M 2 1 2 1 102000 f 74 goat snp7405-scaffold127-1161927 2 27214021 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272384 Affx-1111833875 AX-519546113 2 108014406 GAC[A/G]GCCAGCACAGCTGATGCAGATGCCCCTGCAGCTTT R 2 1 2 1 102000 r 74 goat GoatD01.008780 2 108014406 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802509 Affx-122926681 AX-385289413 2 108030624 TGGAGCACCCCCTGCCAAAATTAGGAATAATTATG[C/T]AATTATCAATCAAAGGAACTCAAAGCTCTTTAAGG Y 2 1 2 1 102000 f 74 goat snp7406-scaffold127-1207257 2 27168418 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798150 Affx-122945529 AX-385285085 2 108059831 AATCAGCAACTATTAACTGGGACATGTTGTTTTCC[A/G]TTAAGCAATATACAAATATTGTTGATCCTGTATAT R 2 1 2 1 101000 f 74 goat snp7407-scaffold127-1236464 2 27138680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436405 Affx-122933026 AX-123306744 2 108096257 AAAGTCTGAGGAGGAGCTCCTGACACATAGCAAGT[A/G]CTTTGTGAGTGTCTGTCATTCTGTTTGAGTTTGTG R 2 1 2 1 201000 r 74 goat snp7408-scaffold127-1272890 2 27102126 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784104 Affx-122948461 AX-385271156 2 108132263 ATTTTATAAGCAAAAAAATCAAGCTGGTAATCTTT[A/G]TCAAATTAATAATGGCATTTTTCTTAACTAGTTTT R 2 1 2 1 101000 f 74 goat snp7409-scaffold127-1308896 2 27066164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400757 Affx-122959887 AX-123271112 2 108195639 GAGAAGAAAGAATGATGTTTTGTATCCTTCTGTAG[G/T]TCCCATGGGATTAAAAAAAAGACTTAAAAGACAAA K 2 1 2 1 101000 f 74 goat snp7411-scaffold127-1372272 2 27002823 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416299 Affx-122947932 AX-123286648 2 108248211 CAAGGTAGGAACCTAAACATATAAGAATTCCACTG[C/T]ATCTGTGAACAAGGAACAGAGAAAATGAAGCTGTG Y 2 1 2 1 101000 f 74 goat snp7412-scaffold127-1424844 2 26949493 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802110 Affx-122929270 AX-385289014 2 108298141 TATTCTATTAACAATAAGAACCAATGGATTTTGAG[C/T]AGGGTCCTGTCATGATCTAAAGAATGTCTTAGTTT Y 2 1 2 1 101000 r 74 goat snp7413-scaffold127-1474774 2 26899421 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431186 Affx-122937177 AX-123301527 2 108335084 TACAAAGGAACTTCTCAAGTCTGCTGTAGGGTTTG[A/G]AATTAACTGAGACTGCAATGAGGAGTTTAAGGGTC R 2 1 2 1 201000 r 74 goat snp7414-scaffold127-1511717 2 26862142 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453709 Affx-122919684 AX-123324042 2 108396783 TGAGAGAAAGAAAAGAACAGAGTGACTTCCTGAGT[C/T]TATGTTTCAGAACAGAATGAAGAAATGTCATAATG Y 2 1 2 1 101000 f 74 goat snp7415-scaffold127-1573416 2 26800016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792950 Affx-122938084 AX-385279928 2 108477285 ATGAATAAAAGTTTGTGGAGGGATGATATGTGTAC[A/G]TATTGTATCAAAGTATGTTCCCTATGAAATTTATG R 2 1 2 1 201000 r 74 goat snp7417-scaffold127-1653918 2 26719342 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401299 Affx-122959858 AX-123271652 2 108508510 TTCATGTAACATATACCTCATGCCTGGGGTTAATC[A/G]CCAGTAGTTCTTGGCAGAATGAAATCTTTAATATA R 2 1 2 1 101000 f 74 goat snp7418-scaffold127-1685143 2 26688338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391677 Affx-122966543 AX-123262034 2 108566090 GCTAAGGACTCTGTCATTATTAGAGCTAAGGAAAA[C/T]GATGCTCAAATTTTAATAAATTATACAAGATCAGA Y 2 1 2 1 101000 f 74 goat snp7419-scaffold127-1742723 2 26631497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776174 Affx-122953761 AX-385263302 2 108597837 GAGCAGTGCAGAAAAATGCTATACAAAGGGACTGC[A/G]TATTTACAAAATATATGACCCATGAAATCCTGGAC R 2 1 2 1 201000 r 74 goat snp7420-scaffold127-1774470 2 26599805 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768024 Affx-122935029 AX-385255238 2 108627298 TGAAATGATAAGTAAAAATAACACTTTCAATTTGT[A/G]TATTTCAGTCATTTTATATGACCTTTTCTTTCATA R 2 1 2 1 201000 f 74 goat snp7421-scaffold127-1803931 2 26569636 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390494 Affx-122967259 AX-123260851 2 108680032 GTCACACCTAGGCAAAGGTTTCCACAGTCTTCAAG[A/G]GCTAGAGTTGTTCAGAGTGAAGGCATGGTCCTACA R 2 1 2 1 101000 f 74 goat snp7422-scaffold127-1856665 2 26516428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790621 Affx-122974733 AX-385277623 2 108746034 AGAGTCTAGAAAACAGGACAGACCTGACAGAACTG[C/T]ATCTGTTTACAAAGTAACAAAAACATTAAATATCC Y 2 1 2 1 101000 f 74 goat snp7423-scaffold127-1922667 2 26449758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452006 Affx-122920918 AX-123322339 2 108782068 GGATGGTTGAATTAATAACATCCTATTATTTTATT[A/G]TTGCATAAGAATTTATAGCTGTGCTGACACCACAC R 2 1 2 1 101000 r 74 goat snp7424-scaffold127-1958701 2 26415367 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449319 Affx-122922996 AX-123319654 2 108811001 TAGCTCTGTGACTCCCAGTAGCCACATACAGACAC[A/G]TATACATATACCTAATATGAATCAGTAGCCACACA R 2 1 2 1 201000 r 74 goat snp7425-scaffold127-1987634 2 26386347 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414770 Affx-122949243 AX-123285119 2 108852120 CTGTGAGAGCTTGACAGAGTGCATAAATCTTCCCC[A/G]TTGGAGACACCAAGCAGTCCCCATGGACAAGGGAG R 2 1 2 1 101000 f 74 goat snp7426-scaffold127-2028753 2 26347511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417322 Affx-122947746 AX-123287670 2 108931927 AACATCTATTCATTACTGAACTTCCTTGGTGGTAC[A/G]TAGGATAAGAATCTGCCTGCCAATGCAGGGGACCC R 2 1 2 1 101000 f 74 goat snp7428-scaffold127-2108560 2 26267626 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383071 Affx-122973744 AX-123253429 2 108973238 CAGTGACGAATGGCTAAAGGATTTTGGTAGTAATA[C/T]TGAACAAAATAATTCATCTCCTTTTCTTCTCATAC Y 2 1 2 1 201000 f 74 goat snp7429-scaffold127-2149871 2 26226372 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789608 Affx-122933352 AX-385276616 2 109032239 AGTAGTAGTAGTAGTAAGAGCTTATTTTTACTGAG[C/T]AGTTACTATGTTCCAGACATGGTTCAGGTGCTTTG Y 2 1 2 1 101000 r 74 goat snp7430-scaffold127-2208872 2 26167025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423388 Affx-122943129 AX-123293734 2 109063319 AAGGAGATGAATATTGATCCCTGTCATTCTATACA[A/C]AGATGCAGCAGATAAAAGGAGCAATCTGAATTCTT M 2 1 2 1 101000 f 74 goat snp7431-scaffold127-2239952 NW_017191778.1 19486 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790829 Affx-122972291 AX-385277829 2 109103312 TCTCAATGCCTTCTTCCAATATGCCGATAATTTGT[A/G]TTTTTTCAGCTGTCATAACAGTGAAAAGCTCAACA R 2 1 2 1 201000 r 74 goat snp7432-scaffold127-2279945 2 26095746 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434930 Affx-122934305 AX-123305270 2 109152789 CTCATGATGCAAAGACACACATGTTAATGTGAAAG[A/G]AGCATATCCACTTACTAAAGAAATAAAATTTTTTA R 2 1 2 1 101000 f 74 goat snp7433-scaffold127-2329422 2 26046119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789007 Affx-122974417 AX-385276020 2 109197254 ATCCCTCATGGCAGTTTCATTGTCATTAAAAGTAC[C/T]GCTCTATTGTGTGTATTCTCTATTCATATTCATGA Y 2 1 2 1 101000 f 74 goat snp7434-scaffold127-2373887 2 26000885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415536 Affx-122948663 AX-123285885 2 109243279 CAGTATACAATTTATACAGGCTACAACAAATTTCC[A/G]CATACATTATTGAACGAAATACTCACAACTGTGTT R 2 1 2 1 101000 f 74 goat snp7435-scaffold127-2419912 2 25955270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775265 Affx-122949522 AX-385262395 2 109274806 AATACTTACTGGACCTTTATTGCCACTTATCATCC[A/G]TCTGCTGATACTAGCCCTTGTTTTATAATCTTGTA R 2 1 2 1 101000 f 74 goat snp7436-scaffold127-2451439 2 25924416 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416930 Affx-122948042 AX-123287278 2 109306023 CAGCCAACTTCTCTTGGCAATTCCAACTTTAAAGC[A/G]TTAGTCCGAAGTCAACCACTTAATTAGAAATTTAA R 2 1 2 1 101000 f 74 goat snp7437-scaffold127-2482656 2 25893732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771891 Affx-122959245 AX-385259047 2 109348394 GACCTGTGGTTTTTCTGGATTCTCAAGTTCATTGA[A/C]TATATTAGACTCACTTAGAGTTGTCAGCATTTCTC M 2 1 2 1 101000 f 74 goat snp7438-scaffold127-2525027 2 25853644 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390491 Affx-122967589 AX-123260848 2 109390055 TAAGAAGAGATTGACTGCAGTGATGGACCCTAGAC[A/G]CTGATTTGGGAAGAAAGGACAGGCAGGAGGTGACT R 2 1 2 1 101000 f 74 goat snp7439-scaffold127-2566688 2 25811948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441552 Affx-122928696 AX-123311889 2 109420203 CACCCTCAGACCATGGGGAAAGAGAAACAGTGAAT[A/G]TCATTCCCACAGATGGCCTGTTGAGAAACCAAAAA R 2 1 2 1 101000 r 74 goat snp7440-scaffold127-2596836 2 25780634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449551 Affx-122923247 AX-123319886 2 109461964 TCCAAAAATGTTGTTCCTGTGACATTCTAGGAATT[A/G]TTGGATAACTCAGTCATAGCCTTGTGGGCCAAATA R 2 1 2 1 101000 r 74 goat snp7441-scaffold127-2638597 2 25738571 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445207 Affx-122925517 AX-123315544 2 109527103 CGATTAGGACCTTTGCTCCCCTGTGTTACTGAAAA[C/T]GGCAGGACTGCAGTGCAGATGCTACCCATTATGAA Y 2 1 2 1 201000 f 74 goat snp7442-scaffold127-2703736 2 25673407 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449050 Affx-122923063 AX-123319385 2 109579566 AACAGAGGAGGTGTCCACGTAATAGAAAAGAGTGA[A/C]CTGGACAAAGACTTCTTCCAACAGTCATACGTACC M 2 1 2 1 101000 f 74 goat snp7443-scaffold127-2756199 2 25622049 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413408 Affx-122950710 AX-123283757 2 109671384 TGTCCATAACCCTTTAATACTTTATCTCTCTAAAG[G/T]TCATTTCCAGTATAGAATGTTATGGTTCTATGGCC K 2 1 2 1 101000 r 74 goat snp7445-scaffold127-2848017 2 25529092 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415763 Affx-122948928 AX-123286112 2 109717823 TATTCCCCCATTCTAAGGAAGTGCTTCCTAACAGC[A/G]CATGATTACAAAAAATTGTCTCAAGAAGTAGTCAG R 2 1 2 1 201000 r 74 goat snp7446-scaffold127-2894456 2 25482634 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434396 Affx-122934689 AX-123304737 2 109748345 GAATTCATTGGCAGTTTTTTCATTATGTTTTTCCT[G/T]GTCCACATATTTCCTTTGGCTTTTTTGGTGGTTGC K 2 1 2 1 101000 r 74 goat snp7447-scaffold127-2924978 2 25451647 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390904 Affx-122967098 AX-123261261 2 109782359 GAGCCACATCTCTTCCGCACATATGTACAAGTACA[G/T]AGTTTATTTATATACTTTCAAGGAACACTTAACCA K 2 1 2 1 201000 r 74 goat snp7448-scaffold127-2958992 2 25417629 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380668 Affx-122975188 AX-123251026 2 109824326 TAAAGGCAGGGATTGCATTGCTTCTGCCTGTTTTA[C/T]ATCTAAATCAAAAGGTTAAGACCAAAAGATTGTAC Y 2 1 2 1 201000 r 74 goat snp7449-scaffold127-3000959 2 25375344 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412734 Affx-122950727 AX-123283083 2 109852935 TGTATGTCAAGATTCATCTTGCTCAAGGGTGAATG[A/G]CATAGTAAAATAAAATCAAATGAAATAAAAATAAG R 2 1 2 1 101000 f 74 goat snp7450-scaffold127-3029568 2 25346689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436922 Affx-122933198 AX-123307260 2 109883401 GAGCAATAATTCAGTTTATGTCATTGTTGTACCTT[C/T]CTCTCTGGAACACAAATTCAAGCAAGCTGGTCCCC Y 2 1 2 1 201000 f 74 goat snp7451-scaffold127-3060034 2 25316263 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411293 Affx-122952298 AX-123281643 2 109933731 TGTGGTGAAATAATTGGTTGAAAAAGACAAATCTG[C/T]AAAATAAATAAATAAGGCGACATTTGACCTTTCAC Y 2 1 2 1 101000 f 74 goat snp7452-scaffold127-3110364 2 25265915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412454 Affx-122951406 AX-123282803 2 109969844 CCTGTTTTGTTGTTTTCTTTATCTGCTCTCACCCA[C/T]GAGGATTCAGAATTCTTTCATACAGTTTTTGTAGG Y 2 1 2 1 201000 r 74 goat snp7453-scaffold127-3146477 2 25229229 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426653 Affx-122939936 AX-123296999 2 110023009 AGTGGTCAGATCTCAGGTCCTTGACCATGGTCAGA[C/T]GTTTGGACTTTATTCTGAGTGCAGTGAGAAGCCAC Y 2 1 2 1 101000 f 74 goat snp7454-scaffold127-3199642 2 25176027 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777051 Affx-122924183 AX-385264174 2 110072664 ATATTTCAAATGTACTATAAGCATACTGAAATAAT[A/G]TAAATAATAGGACTGAAATGATATAAATAGGAGAA R 2 1 2 1 101000 r 74 goat snp7455-scaffold127-3249297 2 25126120 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275310 Affx-1111834828 AX-519548886 2 110105142 TTTCCTCCTCAATCTTCAAGTCTCTCTCAAATGCT[A/G]TTCCCCCA R 2 1 2 1 101000 f 74 goat GoatD01.055426 2 110105142 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38445136 Affx-122926173 AX-123315473 2 110114801 TTATAAAGAGAAAACCTGCTACCTTGTGTAAAAGC[A/G]TGTAAGTAGTAGTAGAGGATAAGGAAAGATAAGTA R 2 1 2 1 101000 r 74 goat snp7456-scaffold127-3291434 2 25085251 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377935 Affx-122977217 AX-123248294 2 110156019 TGCTGTAGTTTTAGAATTAAATTTCAGCTGACAAG[C/T]AGGGCATGTAAGAAGAGAAAGAAGACAATAATGAG Y 2 1 2 1 101000 f 74 goat snp7457-scaffold127-3332652 2 25044407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773631 Affx-122969904 AX-385260771 2 110191114 GTAAAGAAATGTTCGTTTCTGTATCAGAAATTATA[C/T]AATCTCTAAGTAACAAAAGTTATTCCTCCAGAGCT Y 2 1 2 1 101000 r 74 goat snp7458-scaffold127-3367747 2 25009382 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389130 Affx-122968554 AX-123259488 2 110246935 CTTTCAATCTTACAACATTGTATTAGTTTTAGGTA[C/T]ACAACGTAGTGATTTGATTTCTCTGTTGCAGTATG Y 2 1 2 1 102000 r 74 goat snp7459-scaffold127-3423568 2 24952488 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464170848 Affx-1110347652 AX-515646306 2 110248285 ATATGTGGCACCTCTGCTTAGCATTCTTCCCATAT[A/G]CACTCAGTTTCAGTTTTGCTGAGCAGTGGTATGAC R 2 1 2 1 101000 r 74 goat 2_110248285_AF-PAKI 2 110248285 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38414784 Affx-122949233 AX-123285133 2 110283180 TATGTTTTGCCCTCTTGGGAGCTATAATAAGAAAG[C/T]ATCTTATAGGGAGGAGATTAAACCAGTCTCAAATC Y 2 1 2 1 101000 f 74 goat snp7460-scaffold127-3459813 2 24915959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439038 Affx-122930339 AX-123309375 2 110316910 TTTTGGATTAGAGTGTACAGAATTTTAAAAAGGAT[A/G]GGAGGGTTGCAATCATCCTGGAACAAAACAAACAT R 2 1 2 1 101000 r 74 goat snp7461-scaffold127-3493543 2 24882096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425280 Affx-122940967 AX-123295626 2 110358077 ATTCAGCTTTGCCCGCCATATTGGAAAGCTGTCTC[A/G]TGGAGGAAGGGGTGTTGTCCACACGACAAAACGCC R 2 1 2 1 101000 f 74 goat snp7462-scaffold127-3534710 2 24840986 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443407 Affx-122927383 AX-123313744 2 110392122 AGATCTGCATGTAGTCCTACCATTGTGACCTGGCC[A/G]CAAATACAGTGAGAACAGTTGCACTGAAGCAAACA R 2 1 2 1 101000 f 74 goat snp7463-scaffold127-3568755 2 24807290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398538 Affx-122961531 AX-123268893 2 110431871 GAACTGCTGTTTGGACACATTAACTTGCCCCCAGA[C/T]GACTGCGAGTAAGAGGGGAAGCTGTAATCAGACCC Y 2 1 2 1 101000 f 74 goat snp7464-scaffold127-3608504 2 24766973 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439687 Affx-122930578 AX-123310024 2 110467014 TGGGGTTAGGTTGGAAAAGCCACCTGTTTACAGAA[C/T]GATGTGGGAGCTTTTCTGTAGAAATTCCATGGTTA Y 2 1 2 1 101000 f 74 goat snp7465-scaffold127-3643647 2 24731925 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411080 Affx-122951933 AX-123281430 2 110554119 GTTTGTCAGTGTTTCTGTGTGTGAAATTTGAGCCA[A/G]TGGTTTTAGACATATGCATGTGTGAAACAGCTAAT R 2 1 2 1 201000 r 74 goat snp7466-scaffold127-3730752 2 24644687 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408933 Affx-122953943 AX-123279284 2 110588160 AACTTCTAGGCCAATCCAGTAGAGACCCCTTTGCA[A/G]AGCTATAAGTCAGCCATAAGCAAAGCACTTTGCGA R 2 1 2 1 201000 r 74 goat snp7467-scaffold127-3764793 2 24610368 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394679 Affx-122964363 AX-123265034 2 110641252 GTTGGGGCATAGACTTGGATAACTGTGATATTGAG[A/C]TATCAAAAGAGGCTCCTATATCTGAAAGGCTGAGA M 2 1 2 1 201000 r 74 goat snp7468-scaffold127-3817885 2 24557058 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772903 Affx-122968618 AX-385260048 2 110678922 TCTTGAACACTTGTATGTCTCAACAATGAAGACAA[C/T]GCCTGGCACATGCTTGGTGCTTAACAAACACTTCT Y 2 1 2 1 101000 r 74 goat snp7469-scaffold127-3855555 2 24518574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382581 Affx-122973754 AX-123252939 2 110727658 ACATGCACATGAAGACATGGGCAGAAGGAAGAACC[A/G]TCTGTGAGTGGGATGCCTGGGACTCCATTTAAGAA R 2 1 2 1 201000 f 74 goat snp7470-scaffold127-3904291 2 24469582 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777334 Affx-122923846 AX-385264456 2 110777843 TCTGTGCATAGCCCAAATCAGTGCTGGACTCTGCT[A/G]CTCCTCAACACAGATGTGTTGACAAGATGAGGTGT R 2 1 2 1 202000 f 74 goat snp7471-scaffold127-3954476 2 24418472 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801636 Affx-122950068 AX-385288544 2 110867376 TGGCATCAGGAACCTGTGGCTTATTACATGACATA[C/T]GTGATCATTAAAGGAGATTTATTTGGAAATAAACA Y 2 1 2 1 101000 f 74 goat snp7473-scaffold127-4044009 2 24320629 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421892 Affx-122944262 AX-123292239 2 110919212 CAACAGCTTGATGCTAATGAGCCTACTTAATAGCC[A/G]CATTTTCCTCCCCAAAGTCCAGCATCAATACACAG R 2 1 2 1 101000 f 74 goat snp7474-scaffold127-4095845 2 24267325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423464 Affx-122942584 AX-123293810 2 110969858 GTGATCTTTCCCATCTTTGCATCAGGTATTCAAAG[C/T]ATTGGAGCTTCGCCTTCAGTATCAGTGCTTCCGAT Y 2 1 2 1 303000 f 74 goat snp7475-scaffold127-4146491 2 24215685 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789057 Affx-122919403 AX-385276070 2 111020375 GCAGATGTTTGGCCAAGAAAATAGGAGATCATTTG[A/C]GATGAACATTTTTCTGTCCAGTTAAGTTAGGTCTG M 2 1 2 1 101000 f 74 goat snp7476-scaffold127-4197008 2 24164329 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395121 Affx-122964146 AX-123265476 2 111053952 GTGGCTTCTGTTTTGAACTTTTCAAGCACCAACAG[C/T]TGTCTAGCCTCAGGACAAAACATGAAAAACAAAAT Y 2 1 2 1 101000 r 74 goat snp7477-scaffold127-4230585 2 24130443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407588 Affx-122954659 AX-123277939 2 111112737 TTGCTTCTCCCCTGAACTCCATAGTCCATGTGTCC[A/G]CTTGGGTGGTTAATAGCTGTTCCCCACATACCCAG R 2 1 2 1 201000 r 74 goat snp7478-scaffold127-4289370 2 24070689 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443378 Affx-122927405 AX-123313715 2 111197184 GCAAGTTCTGGCGCCAGGCTGCCCAGGTTTGAACA[C/T]TGTCTCTGCCACTGACCCAGTGTGGAGGTCTGATC Y 2 1 2 1 101000 f 74 goat snp7480-scaffold127-4373817 2 23988367 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426931 Affx-122940432 AX-123297276 2 111226826 GATCTTATTAGATACTTTTTTATACTACTGTACCT[A/G]TTAAATCTTGTTTGGCTTGCCTATAACATAGTAAT R 2 1 2 1 101000 f 74 goat snp7481-scaffold127-4403459 2 23957954 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439731 Affx-122930543 AX-123310068 2 111278227 ATTTAACTGTTGCAGATCTGAGGAGACTAAGCAGA[C/T]ATGACCTCTAAATGCTGTGTGATACCCTGGATTGG Y 2 1 2 1 101000 r 74 goat snp7482-scaffold127-4454860 2 23906619 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393759 Affx-122965211 AX-123264114 2 111330478 CAACACATATACACAAACATACATATATGCATATA[C/T]GTATAGTTTAAAATGAGAATCTGTTCACTGGGACA Y 2 1 2 1 103000 r 74 goat snp7483-scaffold127-4507111 2 23854240 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788007 Affx-122919832 AX-385275028 2 111374018 ATGACATACTTCAGAGCTTAATTATATACTCCCAT[A/G]TTCATCTAGGTTTGCTATGCATGCGAGAAATTTCT R 2 1 2 1 101000 r 74 goat snp7484-scaffold127-4550651 2 23807723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436352 Affx-122933068 AX-123306691 2 111434531 ATGGAAATCCTGCCTGGAAATCATCTGACAACATC[G/T]ATAAAGAGCCTTAAGACTGTACATACCCTTGACCC K 2 1 2 1 201000 r 74 goat snp7485-scaffold127-4611164 2 23747345 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414936 Affx-122949093 AX-123285285 2 111463101 CTTTTTAAACTTCCTTACACTCCTGCTGATCCTGT[A/G]GAGGGCTCTACCATCAGTCTCCTTTGCCCTCCTAG R 2 1 2 1 101000 f 74 goat snp7486-scaffold127-4639734 2 23718556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391578 Affx-122966614 AX-123261935 2 111517801 CACAGCTCCTGGGTGGAATGAACCAGGTGAGGAAG[C/T]GGCATCTAGGGATTTTGTGTCAAAGCAGAGAGCCT Y 2 1 2 1 101000 r 74 goat snp7487-scaffold127-4694434 2 23663803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395260 Affx-122964093 AX-123265615 2 111553782 CCTTAATGCTTTGGGTCCTTGCTGAGTGCCCTCCC[A/G]CAGGCAGCCTCAAGTTCTCTTTCTTTCCATGCTGT R 2 1 2 1 201000 f 74 goat snp7488-scaffold127-4730415 2 23627967 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449353 Affx-122922970 AX-123319688 2 111617814 ACTGAGCACGCATGCATGCATGCATCCAATCCACT[A/G]TACTCTCCCAAACACAAAACAGGGAGAGGCTCAAG R 2 1 2 1 101000 r 74 goat snp7489-scaffold127-4794447 2 23563782 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785412 Affx-122944591 AX-385272457 2 111706961 TATTTTAACTATCAGATAGATTATCATTTATATTA[C/T]GGAAGGTTCAATGATGACATTCTGCATTACATTCT Y 2 1 2 1 101000 r 74 goat snp7491-scaffold127-4883594 2 23474109 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411757 Affx-122951500 AX-123282107 2 111744922 TGACTCAAGTCCCAAATCTTTACCCTAAGCTTTGA[C/T]GTTGCCACTTGGGTGTCTAATAAGTTTTCCAAATA Y 2 1 2 1 101000 f 74 goat snp7492-scaffold127-4921555 2 23435930 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441519 Affx-122928717 AX-123311856 2 111779666 TTGGATACTGATTTAGAAATAAGATATAAAATGTT[A/G]CTGTGAGGGCAGTGAAATAATTCTATGTGTAAGAA R 2 1 2 1 101000 r 74 goat snp7493-scaffold127-4956299 2 23401218 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793187 Affx-122965083 AX-385280165 2 111833601 ACTTTTCTTACATTCCCTTCAATTATGGGTTATTA[C/T]AAAATATTGCGTCTAGTCTCTGTGCTATACTGTGT Y 2 1 2 1 101000 r 74 goat snp7494-scaffold127-5010234 2 23347200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422933 Affx-122943033 AX-123293279 2 111904433 TTTGTAGGGCAACATCTAAGCAAGGCAGTTATGTT[C/T]TTATGCTTTTGCACTTGGGGAACATTTTTGTGGTG Y 2 1 2 1 201000 f 74 goat snp7495-scaffold127-5081066 2 23269545 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440696 Affx-122929908 AX-123311033 2 111934280 AAGGCAACAAGCAGACGGGACCCTGGAGTGCAGAA[G/T]AAGGGACATGGGGCATGTGAGTGACACCCAGAGAG K 2 1 2 1 101000 f 74 goat snp7496-scaffold127-5110913 2 23239793 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412748 Affx-122950523 AX-123283097 2 111963489 AGAAGAGAGCAGTGGGATTAAAATAATCTCAGTCC[A/G]AAAATGTTTTGTATGATTCATTATTAAAATGACAA R 2 1 2 1 101000 f 74 goat snp7497-scaffold127-5140122 2 23210349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784446 Affx-122970141 AX-385271495 2 111996291 TGTCTGCATATACCCTGTCTTGAATAAATTCAATA[A/G]TGAATCTCTGAGATTTGCTATTGTTACCCTATCCT R 2 1 2 1 101000 r 74 goat snp7498-scaffold127-5172924 2 23177623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414580 Affx-122949373 AX-123284929 2 112061284 CTAAACAAACAAAAAACCCCAGCAAGCTGAAAATG[C/T]GCCTATTTACAAAATTCTTCATCAAGCTTCATATT Y 2 1 2 1 201000 r 74 goat snp7499-scaffold127-5237917 2 23112754 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800814 Affx-122960488 AX-385287730 2 112093225 CTAATCACTAACAATCTTGGTAAACACGGTACAGT[A/G]TATCATTAATAGCAGAGAACATAGATTTTGCTGCC R 2 1 2 1 201000 f 74 goat snp7500-scaffold127-5269858 2 33591271 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385419 Affx-122971332 AX-123255777 2 112168733 GTAAACAGGCGTCAGGGCTACATTCTTTTTCTTCC[A/G]TGAACCATTTGGATCCTGAAGCCTGAATTTCACAC R 2 1 2 1 201000 r 74 goat snp7502-scaffold127-5345366 2 23005166 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397957 Affx-122961908 AX-123268312 2 112208827 GATAAAAGGATGTATATTACTTTTTGAGGCCTGCC[C/T]GAAAGCTCATCGTGTCTTTCAAAAGAGAAACAGAA Y 2 1 2 1 101000 f 74 goat snp7503-scaffold127-5385460 2 22966840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376434 Affx-122978068 AX-123246793 2 112240815 AAGCCAGCCTCCTTGCCCTTCCTTAAACACCAGTC[A/G]TTTTTGAGCCCACCCAGTCCTCTGGCGTTTGCTGT R 2 1 2 1 101000 r 74 goat snp7504-scaffold127-5417448 2 22935023 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277885 Affx-1111836140 AX-519551380 2 112289093 CCCCTAATCCCACTGTTGCTGGCATCCAAAATAAA[A/G]CAAACTTTCCTTTCTACCAACCTGGCCTCTTTGAT R 2 1 2 1 103000 f 74 goat Random2.2K-259 2 112289093 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791239 Affx-122979186 AX-385278233 2 112294394 CCAACTGCAAGTCATGAGCTAAACAAAAACCATTT[A/G]CTTAGATATTACAGCCAGTCTTTTGGTTGTCATCC R 2 1 2 1 101000 r 74 goat snp7505-scaffold127-5471027 2 22880267 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768609 Affx-122967113 AX-385255789 2 112325450 AAAGAGAACATAAACAAAAATTGAGAAATACAGTG[C/T]GGTACTCCTTACCACATGCTATCATTTTCTGCATT Y 2 1 2 1 201000 f 74 goat snp7506-scaffold127-5502083 2 22849605 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789554 Affx-122950627 AX-385276563 2 112357103 ACTCCTCAGAAGTAAGTACTGAAAATATTCACATT[A/C]TATTTTTAACAGTGTCTTAGAAGAATTGATAGCCA M 2 1 2 1 101000 f 74 goat snp7507-scaffold127-5533736 2 22818077 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771208 Affx-122976413 AX-385258366 2 112436433 AACTCCTGTGAATTCCATCTCCTTAACCGTTCTCT[A/G]CTGTTACCACCATTATCTGCTAGTACAGATCTTTA R 2 1 2 1 101000 f 74 goat snp7509-scaffold127-5613066 2 22737848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388097 Affx-122969500 AX-123258455 2 112493315 CTCTTTGGCAGCATTTAAAACTGGCCTCCCTCTTG[C/T]GTTGGGTGGCTTTCAGGGTTTTGGTTCAGAAAATA Y 2 1 2 1 101000 f 74 goat snp7510-scaffold127-5669948 2 22680948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389328 Affx-122968488 AX-123259686 2 112532443 CACCCAGTGAGGCAGTCGCGCCTCTCCCTGCTGGG[C/T]GATGGTAGCAGTCATGCAGAAGCAGAAAACCTTCT Y 2 1 2 1 101000 r 74 goat snp7511-scaffold127-5709076 2 22641981 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431139 Affx-122936580 AX-123301480 2 112570443 AGAAGGTGTGCCCTGGAGAAGTTCCAGCATTTGTG[C/T]ATCAGGAGACTTAAAATAGCAAACAACAGAAGGAA Y 2 1 2 1 201000 r 74 goat snp7512-scaffold127-5747076 2 22604097 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418238 Affx-122947036 AX-123288586 2 112623877 CTCTGGTTGTTATTATTTTACATTAATTCATAACA[A/G]TGTGTAGAATGCTTGGGGAAGATACAGAAAGGAAC R 2 1 2 1 202000 f 74 goat snp7513-scaffold127-5800510 2 22550801 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379600 Affx-122976022 AX-123249958 2 112654847 TTTTTCCTGCCTATGAGTGGTTTATGTGTCAGATG[C/T]GGTTAAACCCATGGGCTTTATTGCCTCATTTGAAA Y 2 1 2 1 101000 r 74 goat snp7514-scaffold127-5831480 2 22520125 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421897 Affx-122944257 AX-123292244 2 112691228 ATGTAGTTAATTTTCTGTCTTCCTCCACCTAGAAT[A/G]TAACTGTGTAGAAAGAGAAATTTGGCTGTTGGGCT R 2 1 2 1 101000 r 74 goat snp7515-scaffold127-5867861 2 22483507 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407188 Affx-122954821 AX-123277539 2 112726765 CTTGCTCTCGTATCTCCTTTGGCCATATCCTTTTC[G/T]CTTGTCCTTCTCATGCTTTGTAGAAATCCTTAGTC K 2 1 2 1 101000 f 74 goat snp7516-scaffold127-5903398 2 22446414 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271848 Affx-1111833150 AX-519545631 2 112752513 GCTCTCACAAACCTGCTCCACCCATGATTTTGCCA[A/G]TCTCCCAAGATGGCAAATAAATCTTTCCATCGCCT R 2 1 2 1 101000 r 74 goat 2_112752513_AF-PAKI 2 112752513 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440611 Affx-122929974 AX-123310948 2 112756338 GATCCATTTCTTGTTATTCCACCTTCGCCAGGAGT[G/T]AAAGTACTAAAATCAAATTTATGATTTAATATAGT K 2 1 2 1 101000 f 74 goat snp7517-scaffold127-5932971 2 22416240 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394131 Affx-122965328 AX-123264486 2 112785453 TGAAATTTACTGTGATTGTGGGAATGTAATTAACC[G/T]AGGTGAAGAGACAATGGTCACATAAGAAACTTGAT K 2 1 2 1 101000 f 74 goat snp7518-scaffold127-5962086 2 22386580 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778758 Affx-122960891 AX-385265868 2 112823325 CTAGAAATCCACCTTTTCGGGGCTCACTTACTTAT[A/C]TTTCCCAAAGGAGACAGATGTTTTACTGGATTGGT M 2 1 2 1 101000 r 74 goat snp7519-scaffold127-5999958 2 22348757 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393986 Affx-122965036 AX-123264341 2 112854775 TGTAATGTGACCAGGAAATCTAGACATATGTGCTT[A/G]TGTAGGACTAGACAGTGGTTAAGACATATCCAAGA R 2 1 2 1 101000 f 74 goat snp7520-scaffold127-6031408 2 22317281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786842 Affx-122953297 AX-385273871 2 112883485 GCATAAAACAGACTAGAGACAGTGTACTCATTATG[C/T]AAACAAAACTTCAAGATAAATCTTCTTGCCTGTCC Y 2 1 2 1 101000 r 74 goat snp7521-scaffold127-6060118 2 22288714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425201 Affx-122941031 AX-123295547 2 112935878 TGTTTAAAACCTCTGATGAAGGGACCATTGACATG[C/T]AGAGCTCTCAATCACATCCACCATTGCTGGGTCAG Y 2 1 2 1 101000 f 74 goat snp7522-scaffold127-6112511 2 22235955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388868 Affx-122969315 AX-123259226 2 112965575 CATTACGGCTTAAAACCAAATTAAACATAAGAAAA[C/T]AACATAACAGAAAACCATGAGTGAAAGAACAATTC Y 2 1 2 1 202000 f 74 goat snp7523-scaffold127-6142208 2 22206414 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396791 Affx-122962755 AX-123267146 2 113008741 CCAATCGAGTCCAATTCGACTCAATGGACACGAAT[A/C]TGAGTAAGCTCTGGGAGTTGGTGATGGACAGGGAA M 2 1 2 1 303000 f 74 goat snp7524-scaffold127-6185374 2 22163284 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445186 Affx-122925532 AX-123315523 2 113083076 CTCCTATTGATTAGGGTCCATGATCTCTTCCGTAA[C/T]GGATACTTTGGCTTTTTGCCTGCCGGCTAGTATAC Y 2 1 2 1 101000 f 74 goat snp7526-scaffold127-6259709 2 22089011 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415656 Affx-122948564 AX-123286005 2 113114685 CCCATACATCACTGAATGCCATAGTAGGCTTTCCT[A/G]AGGACATGGAAGAATGCCTTCATCCTATCCACGGA R 2 1 2 1 101000 f 74 goat snp7527-scaffold127-6291318 2 22057324 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440834 Affx-122929269 AX-123311171 2 113150619 AATAAGACAGTAATGTTAGACTATGAATCAATTTC[A/G]TTTTGCTTCACAGTTTTCTAAATACAGCCTTCACA R 2 1 2 1 101000 r 74 goat snp7528-scaffold127-6327252 2 22021339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392754 Affx-122966005 AX-123263111 2 113186689 CTTTTAAATACTAATGTTTATGACTTACAGAATGG[C/T]TATCACATCTAGTCCCTGAAAAAACACTTGATCAA Y 2 1 2 1 201000 f 74 goat snp7529-scaffold127-6363322 2 21985033 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435488 Affx-122933437 AX-123305828 2 113229523 TGAGAACATGACCTTTGGGTGATTCCGTACTCTTC[A/G]CATGCCCAGAGAATTTCTACAACTAATCCTGCAGC R 2 1 2 1 101000 f 74 goat snp7530-scaffold127-6406156 2 21942232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769506 Affx-122921533 AX-385256676 2 113261782 TAAACACATGTTAAGCTTGAATTCACTAATAAAAA[C/T]GTTCATGAAAGCATATCACATTCATATAAGATCTC Y 2 1 2 1 201000 f 74 goat snp7531-scaffold127-6438415 2 21910044 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376930 Affx-122977783 AX-123247289 2 113323287 ATTTTTGTCATTTTTATATAAATGTTTTATATACA[C/T]GCTGAGAGGTCTCCTATTAAGTTGGTACAGAAGTA Y 2 1 2 1 103000 r 74 goat snp7532-scaffold127-6499920 2 21848080 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393762 Affx-122965208 AX-123264117 2 113351982 TGTGCCAATAGTGTCCTGCTCATTGGTAGGGGAAG[C/T]GATTGCATCCGGGCAAACAAAACTGTGCCAAATAT Y 2 1 2 1 101000 r 74 goat snp7533-scaffold127-6528615 2 21826745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791972 Affx-122933439 AX-385278960 2 113403831 TATTACTTAGATAAGAATGCTGAAACCTTTGGGTG[C/T]GAAGTTTTAAAATAGACTAGGTTTTTCTCCAGCTA Y 2 1 2 1 101000 f 74 goat snp7534-scaffold127-6580464 2 21774549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382691 Affx-122973642 AX-123253049 2 113460358 ATTCCCTAGACATATCTATCAAATACAGAGGCTTA[C/T]ATTTACCTGTAAAATTGGGAAATATTTAAATTTAT Y 2 1 2 1 101000 f 74 goat snp7535-scaffold127-6636991 2 21717553 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415797 Affx-122948903 AX-123286146 2 113502466 AGGATGAAGAAAAGCCATACAAGCTTAAGAATTCT[A/G]CCACAGGAGGGAGCAAGATGCATGGGGCAAGCACA R 2 1 2 1 202000 f 74 goat snp7536-scaffold127-6679099 2 21674897 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436806 Affx-122932244 AX-123307144 2 113533981 GCCAATAAGGTGAAAGAAATGCCAAAGAAAGACAA[C/T]ACTACAGAAGCCAAAGGAAAAAGTTTTTAAGAAGC Y 2 1 2 1 101000 f 74 goat snp7537-scaffold127-6710614 2 21642658 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390889 Affx-122967111 AX-123261246 2 113566684 TACATCTCTTGCAGTAGTTTTGAGTAAAACCTTAC[C/T]ATTCCAACATGTGATAGAATACTTTTTCTTCAACA Y 2 1 2 1 101000 r 74 goat snp7538-scaffold127-6743317 2 21610311 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452616 Affx-122920366 AX-123322949 2 113599787 CATTTTCCCCTCCTGCCTGAAATGAGACTTAAGAT[A/G]CTGGGACAGAGAGAACAAGTAAGGGATGAAACATC R 2 1 2 1 102000 f 74 goat snp7539-scaffold127-6776420 2 21577734 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428876 Affx-122938339 AX-123299218 2 113660546 ATAAATATAAGTAATCTGATTCTATAGAGAATTTT[A/G]CTTTCATTATTTTCATTTTGATTTATTGAGACCTC R 2 1 2 1 303000 f 74 goat snp7540-scaffold127-6837179 2 21516318 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386397 Affx-122970830 AX-123256755 2 113711378 TGTCTTTCTCCTCTCACAGATATTGTCATTGTTTA[A/G]CCTTCTGTCTAGGTTATTATTATCATCACCAAACT R 2 1 2 1 201000 f 74 goat snp7541-scaffold127-6888011 2 21465466 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798529 Affx-122933391 AX-385285462 2 113741067 CTGAAAATTTGAGTTAGTTTACAGGAGAGGGATCC[A/G]CCCCTAGGGTGTTACATAATAGATGCTTTTCATTG R 2 1 2 1 202000 f 74 goat snp7542-scaffold127-6917700 2 21435388 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417649 Affx-122946845 AX-123287997 2 113791080 TTTCTCCTTTCTTCTCTCTTTTTCAAAAAGTTATA[C/T]ATCAGATTTAGGACAAAGGTGCTTCTCCTCTAACT Y 2 1 2 1 103000 r 74 goat snp7543-scaffold127-6967713 2 21385335 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439555 Affx-122930096 AX-123309892 2 113837007 GAATTTCTCTAAGTCTGTGCATTTCTAAACTTGTA[C/T]AAGCTCTTAATTTTCAAAAGAGTCATTTTCAAGTC Y 2 1 2 1 101000 f 74 goat snp7544-scaffold127-7013640 2 21339798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762277 Affx-986696808 AX-385250466 2 113871749 AATGCTCTCTATGCACCTGCCCTCCTCTGTATGCA[C/T]CCGAGCCACGGCGTCTGGGGTCGCTTCTTCTGTCC Y 2 1 2 1 600010 f 74 goat 2_113871749 2 113871749 Ancestral_priority_1043 ancestry 0.522 neutral IMAGE 10K 10K ancestral 38407481 Affx-122954765 AX-123277832 2 113875009 TCTCATTCTAATTCCTCTTCTTTCCCTTCCATAAC[A/G]CAAAACCAAGGGGTAGAGGATATGAAACTTTGCAG R 2 1 2 1 103000 r 74 goat snp7545-scaffold127-7051642 2 21300495 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802947 Affx-986696095 AX-385289838 2 113907938 TGAAATTGGCGAAGGATTTCCCCATTTTGGAGGCT[C/G]AGCTGGGGTATGCAACACCTAGGTCTGAGAGCAAC S 4 1 2 1 600010 f 74 goat 2_113907938 2 113907938 Ancestral_priority_1043 ancestry 0.574 neutral IMAGE 10K 10K ancestral 320778444 Affx-122949876 AX-385265558 2 113911728 TTTAAAATAAAACCTACAGGGTTCAACCAACACTG[C/T]AGATCTATGCCTGGATGCCTGTAACCACCTTACTC Y 2 1 2 1 102000 r 74 goat snp7546-scaffold127-7088361 2 21263168 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447756 Affx-122924576 AX-123318092 2 114001580 TGAATTCATGGAAGATGGAGTTTCCAAGTTGGGAA[A/C]GCTGAGGAGAAAGGGAAATGAGAAGAATCTCAAAT M 2 1 2 1 101000 f 74 goat snp7547-scaffold127-7178213 2 21172551 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398792 Affx-122961420 AX-123269147 2 114033064 TGCCTAGCACATAATCTGTTTTCCCTGCCTTCATC[C/T]TCCTGGGTATTTTGTAGTAAGTAATGAAAAATTGA Y 2 1 2 1 303000 r 74 goat snp7548-scaffold127-7209697 2 21140519 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411493 Affx-122951782 AX-123281843 2 114062894 ATGTTCTTTATTGCCCCCACCCAAGTCACCAACGT[A/G]CATCCTTAGGATTGTTCAGCTCAAGGCTGAACAAC R 2 1 2 1 101000 r 74 goat snp7549-scaffold127-7239527 2 21109807 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382161 Affx-122974034 AX-123252519 2 114141857 ATGATAAAGAACAGCCAGCAAGACTGGTCTTTCAT[A/G]TTGTTTTTAATTTTTATAAATATATTTACTAAACA R 2 1 2 1 103000 f 74 goat snp7551-scaffold127-7318490 2 21030095 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773266 Affx-122932848 AX-385260409 2 114185315 TATCCACTGCAAGCTGCATGTGACTTTGATTCTAC[A/G]TAGAAACCCTCACTGTAAGAAGAATATAATTATAT R 2 1 2 1 101000 f 74 goat snp7552-scaffold127-7361948 2 20986534 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405880 Affx-122955604 AX-123276232 2 114215351 TTGCACCTATGGAAACTGAGAGGACCAAAAGATCC[A/G]TATTTGAATCTCAGTTCTTTTTTTCCATAGAAAAT R 2 1 2 1 101000 f 74 goat snp7553-scaffold127-7391984 2 20956108 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780223 Affx-122964593 AX-385267319 2 114254886 TTTCTTTGCAATTGTGGTTCCAAGAACTTAAACCC[A/G]TTAAGAAACCATGCTGGTGGCCCTGAGGAAAATGT R 2 1 2 1 101000 r 74 goat snp7554-scaffold127-7431519 2 20915944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431137 Affx-122936581 AX-123301478 2 114313739 CCTTATGAATTTGATTCGTTCTCTCCCAAAACTCT[A/G]CCGTGCGGGAAAAAAAGAATACATAAATGGGTTTC R 2 1 2 1 101000 f 74 goat snp7555-scaffold127-7490372 2 20856819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764612 Affx-122964328 AX-385252254 2 114353075 ACATATTATCCTTATGGCTACAATCTACATTAGGC[A/G]CATGTTAACAAATGTTATCATTCAAAATTATTCTT R 2 1 2 1 201000 f 74 goat snp7556-scaffold127-7529708 2 20816315 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386297 Affx-122970928 AX-123256655 2 114424290 AAAACAGCGACAAAGGGAGGATTTCGGGGTTAGGT[A/G]GGAGTTGCCAAAAGTGGGTCATAGATACCCAGCTC R 2 1 2 1 201000 r 74 goat snp7557-scaffold127-7600923 2 20745163 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767998 Affx-122945409 AX-385255212 2 114459292 TTGTTAGAAGTCAGGTGTGTTAGAAAAAGAAAAAT[A/C]TAAATTATGTAAAGAGAAGCTATCTGTGATCATAG M 2 1 2 1 103000 f 74 goat snp7558-scaffold127-7635925 2 20710088 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443537 Affx-122927769 AX-123313874 2 114513193 CATCAATAGACTGTAAACAGAAAAAAAAAGAATGC[A/G]TGACCTAATAAATGTATGACAAAAATTCATTATTG R 2 1 2 1 303000 r 74 goat snp7559-scaffold127-7689826 2 20656266 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453445 Affx-122919864 AX-123323778 2 114547461 TGAGAGCCAGCCTCTTGGACCAAGGTAGGGAATTT[G/T]CACCCTTCACTTATTTTAAAGTACATACCTCACAT K 2 1 2 1 101000 r 74 goat snp7560-scaffold127-7724094 2 20622167 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275486 Affx-1111834926 AX-519549058 2 114603951 ATTTGCAGTTGAAGTATATGATGAAAATCTAGCCC[A/C]ACGGAGT M 2 1 2 1 101000 f 74 goat GoatD01.059005 2 114603951 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38412042 Affx-122951723 AX-123282392 2 114648407 GTCTATGGAATTGCAAAGAGTCAGACATTACTTAG[C/T]GACTAACATTTTCCATTTTCAGGACACTTGAAAAT Y 2 1 2 1 303000 r 74 goat snp7562-scaffold127-7825040 2 20521428 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788047 Affx-122974105 AX-385275068 2 114701083 TAATCTGCCTTACTCTTATTTAACATACTGAATTA[C/T]ACCTGTTTCAGAAATTACCTCTTTCAACAACCGTT Y 2 1 2 1 101000 r 74 goat snp7563-scaffold127-7877716 2 20468799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398178 Affx-122962652 AX-123268533 2 114755140 CACATCGGGAAATAACTGAGCAAAGCCAAGAGAGC[A/G]TGTTGTGTGTTGGATGTGATGTCACATGGGCAGAG R 2 1 2 1 101000 f 74 goat snp7564-scaffold127-7931773 2 20414760 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773077 Affx-122970321 AX-385260220 2 114793557 ATCTCTGCATAAATTCCCAGAACTGGAATTCCGGT[A/G]TGAAGGAATCTGAAAGTTCAAGATTCTTGATGTAT R 2 1 2 1 201000 r 74 goat snp7565-scaffold127-7970190 2 20376323 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383615 Affx-122972553 AX-123253973 2 114828619 ATGATAGTCTAGTTTTCACAAGGAGAGGACACATA[C/T]GAAGTTATTCAGTTGACTTTCTTTCTGAATTTAAT Y 2 1 2 1 101000 f 74 goat snp7566-scaffold127-8005252 2 20341155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387170 Affx-122970626 AX-123257528 2 114872666 GGCATTCTGTAATGGGTCATCTTGTAAAAAGGAAA[C/T]AAAACAAGAACAAAATAGCAAAGATTTGATAAACC Y 2 1 2 1 101000 f 74 goat snp7567-scaffold127-8049299 2 20296639 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383952 Affx-122972953 AX-123254310 2 114984713 GAAAGGATTAGCTTTGCAGATGCAATCGAGCATCA[C/T]GGTCCTATGGAGCTCAGGGAACTGCTGCTGATGGG Y 2 1 2 1 101000 f 74 goat snp7569-scaffold127-8161346 2 20185700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782516 Affx-122945596 AX-385269592 2 115024015 TCAATGGCTTGTGATGGATAACCTCTGTCAACCTT[C/T]GTGTCAAAGTGATGTTCCCCAGGGATCATCCGGAA Y 2 1 2 1 101000 r 74 goat snp7570-scaffold127-8200648 2 20146405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765501 Affx-122961514 AX-385252986 2 115071872 CTGTTCTTACTAGTCATTCTCTGTGCCCCATTTTC[C/T]ACTCCCTCTTTGGGAGTATATATGATCTTTCTATC Y 2 1 2 1 102000 f 74 goat snp7571-scaffold127-8248505 2 20098635 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421673 Affx-122944425 AX-123292020 2 115103950 GGGTATGAAATAAATAATACATTGTGATACTATTA[C/T]ATGTGTTTTGGTGTGGGGAATTTGCCCCTTTCGTG Y 2 1 2 1 202000 f 74 goat snp7572-scaffold127-8280583 2 20066742 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435913 Affx-122932764 AX-123306252 2 115192820 GGATCAAGTACTGAAAAGAAAGTGATGAGTCACAA[C/T]GTAAGAAAGAAAATATTTTCTGTAGCTCAGTTGAG Y 2 1 2 1 101000 f 74 goat snp7574-scaffold127-8369453 2 19977226 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421534 Affx-122943875 AX-123291881 2 115286607 TTCCTCTGCAGAGAAGCCCACAATGGATCACATAT[A/G]CTCAGTGACCCATCACTTCTCAAGAAGCACTTATG R 2 1 2 1 102000 f 74 goat snp7576-scaffold127-8463240 2 19883068 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447119 Affx-122924468 AX-123317455 2 115312608 CCATCTCTTTTGAAAAAATGAATTTTCCAAAGAAG[A/C]TCACACTCATCCAGCCACCATCACGGCCATCATCA M 2 1 2 1 303000 f 74 goat snp27036-scaffold287-2722095 2 19834813 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398358 Affx-122961671 AX-123268713 2 115379638 GCTCAAGAATAACTGATTAACCATGCCAGTAATTC[A/G]CTGTGTGACTGGGCAAGCCATTGTGTTCTCTGGGT R 2 1 2 1 101000 f 74 goat snp27034-scaffold287-2655065 2 19773571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437013 Affx-122933128 AX-123307351 2 115439012 ATTGGCAAGACGAAGGAGCTGATTATGTGCAGAGA[A/C]AGGGCAGGGTAAAGAAAGCCAGATACCTGGAGGCA M 2 1 2 1 101000 f 74 goat snp27033-scaffold287-2595691 2 19713818 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779013 Affx-122969571 AX-385266120 2 115473672 CAGTTAACAAGCATAAAATGCAATAATGTAGAGTC[C/T]GAGAACTCTTTCTACTCATACACACACAAAAACAA Y 2 1 2 1 101000 r 74 goat snp27032-scaffold287-2561031 2 19679549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395486 Affx-122963897 AX-123265841 2 115620295 ATTTTGTTCTGACCCCATGGGAGTTCTTTTTAGAT[A/G]CCTTTCTAATTCACTCTAATAAACTGGCTGACTAT R 2 1 2 1 101000 r 74 goat snp27029-scaffold287-2414408 2 19532160 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399678 Affx-122960500 AX-123270033 2 115704151 TGAGAAACTTACCTAAATCATAGACCTTTTGAAAT[A/G]CCATGCTCTTTTCTCTCTGCTGAGAAAGTGGAACC R 2 1 2 1 201000 f 74 goat snp27027-scaffold287-2330552 2 19445779 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271850 Affx-1111833151 AX-519545633 2 115739013 GTGACTGCATGATTTTCAAAGACTTAAGCTTCTTT[A/G]CTCTAATTGTTGCTCTACCACCTTCAACACTCAGC R 2 1 2 1 101000 r 74 goat 2_115739013_AF-PAKI 2 115739013 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320778670 Affx-122975738 AX-385265782 2 115809110 ATCATCCACTTGAGGGCAGAATTTGGACTAAAGTT[A/C]TACCTAATCACATAGAATAAAATTACTCTTTATTT M 2 1 2 1 101000 f 74 goat snp27025-scaffold287-2225593 2 19341412 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795253 Affx-122968619 AX-385282211 2 115840152 ATTATCAAGCATGCAGTTGACCTTAAATTTAGACA[G/T]AAATAGCCCTTGCTAAAATTGTAAATGCCATGTCT K 2 1 2 1 101000 f 74 goat snp27024-scaffold287-2194551 2 19310019 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388581 Affx-122969163 AX-123258939 2 115872917 TCAATACTAAGGAACTTGTGAGGGTATTTTGTTGC[A/G]TTTATCACCATGTTATAAAAAACAGGAAGGCATAT R 2 1 2 1 101000 f 74 goat snp27023-scaffold287-2161786 2 19276659 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421699 Affx-122944405 AX-123292046 2 115924204 AAAATCACACTTGAAGTAGCAGGAGGCACTGACAA[C/T]AATGGCCAGAGCCACCAACACAAAGATGCATTTCA Y 2 1 2 1 101000 f 74 goat snp27022-scaffold287-2110499 2 19225099 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443179 Affx-122927605 AX-123313516 2 115976135 ATATTTACTTGTTTGCATCAGTGCTGCTTATATTC[A/G]TAAAAATACTTTTTGAAAAGGGTCAGTGTTGATAT R 2 1 2 1 103000 r 74 goat snp27021-scaffold287-2058568 2 19172913 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389820 Affx-122968190 AX-123260177 2 116012380 AATTTCTAATGAAAATCTTGTATCTAACAAAAATA[C/T]GGATCAACTGTCTAGGTTTAAACATCACAAACAAA Y 2 1 2 1 101000 r 74 goat snp27020-scaffold287-2022323 2 19136580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764411 Affx-986696810 AX-385252110 2 116016800 CGAATCTATGGGTGCTTTACCACCAGGCATTCCAT[C/G]ACCTTCTATGATACCACAAAATTGGAAAATAAAAA S 4 1 2 1 600010 r 74 goat 2_116016800 2 116016800 Ancestral_priority_1043 ancestry 0.732 recommended IMAGE 10K 10K ancestral 320783724 Affx-122951070 AX-385270780 2 116064544 ATATACTCAAGACAACAAATTCCTTTATCTTAAAA[C/T]AATTCCTGATTGTAGCTTTTAAAGATCCCATAAAC Y 2 1 2 1 101000 r 74 goat snp27019-scaffold287-1970159 2 19084906 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382865 Affx-122973522 AX-123253223 2 116093142 ATCATACACACACACACACACACATATACACTTGA[C/T]ATCAGCTAAATTAAAGCTTTACTCACCAAACGAAC Y 2 1 2 1 201000 r 74 goat snp27018-scaffold287-1941561 2 19055336 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798019 Affx-122946628 AX-385284955 2 116157574 GTTTTTATTAGTTTATGTGGAATTGAAGCTATATT[A/C]GCAACTTTTATATTATTAATTTTCTGGAGAGCAAT M 2 1 2 1 101000 r 74 goat snp27017-scaffold287-1877129 2 18990504 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453318 Affx-122919977 AX-123323651 2 116225618 GACCCACAAGGACCTGGTGTAGCCTCAGTCTTCCA[C/T]GGATGTAGGTAATTAAGTTGAGTAGCAAATGGAAA Y 2 1 2 1 101000 r 74 goat snp27015-scaffold287-1809085 2 18922107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799820 Affx-122962250 AX-385286746 2 116351103 CAAAAAGAAAAATTAGAGCTCAGCTCCTTTGTTCA[C/T]GTTCCTCTTTTTAAGAGTGTGGAAAGATCTTTTTT Y 2 1 2 1 101000 f 74 goat snp27013-scaffold287-1683600 2 18799644 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784462 Affx-122939615 AX-385271511 2 116436924 GATTCCTTAATCAACAGAGTCAAAATGACTTCAAA[G/T]AGATTTCTTCATGGGAAAGTTTGGGCGGGAGTACA K 2 1 2 1 101000 r 74 goat snp27011-scaffold287-1597779 2 18713250 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771698 Affx-122959310 AX-385258855 2 116479751 CTGCAGAGCCCAGGAATCTTGGTGATTGTTGAGAG[C/T]GTCTATAGAGAACCTTAAAAGAAAATTAGAAATCC Y 2 1 2 1 101000 f 74 goat snp27010-scaffold287-1554952 2 18670170 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397006 Affx-122963137 AX-123267361 2 116520050 AACAGCAGAGATGGAGGTGTTCATCTTTTGAACTA[C/T]GTTTACATGGAACTGCCCACCAAGTACTCTTTCCG Y 2 1 2 1 101000 r 74 goat snp27009-scaffold287-1514653 2 18629313 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438100 Affx-122931508 AX-123308438 2 116549832 CCTGGGATTCAGCACCACTGCCTCTAGTTCATTAA[C/T]ATGCCAAGTAGTGTGTGGCTGACACACAGGGTTTT Y 2 1 2 1 101000 f 74 goat snp27008-scaffold287-1484871 2 18599451 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777238 Affx-122932223 AX-385264361 2 116596850 TTCTTTATGTTTTTTTTCGCCCTCCATATTCAGAG[C/T]GGATGTTATCTAAGTCTAATTTATTTTCTCTTCAT Y 2 1 2 1 101000 f 74 goat snp27007-scaffold287-1437853 2 18552314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420016 Affx-122945159 AX-123290364 2 116692793 GTACTTGCTGTTGTGCTCAAGAGGTGTGTTCGTGC[A/G]TGCCAGGTCACTTCAGTTATCTGACTCTTGGCTCG R 2 1 2 1 201000 f 74 goat snp27005-scaffold287-1341910 2 18455984 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398672 Affx-122961878 AX-123269027 2 116748892 CAGGATGTCCTTTAAAGAAGCATCACCAAGACTTC[A/G]TTGGGAGGTCTTAGTGATCACTTTTTCACGTGTCA R 2 1 2 1 201000 r 74 goat snp27004-scaffold287-1285811 2 18399806 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375981 Affx-122978429 AX-123246340 2 116784824 AACACAGATCCCAGGAATGACCAGTCACTCAGGAC[A/G]CTTGGAAAACTGAATGGACCCCCACATGGAGGGCC R 2 1 2 1 201000 r 74 goat snp27003-scaffold287-1249879 2 18364052 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273963 Affx-1111833955 AX-519547568 2 116798673 CTGGCTTGATTATTTCTTGTCCCCTATGCTTTTAC[A/G]CTTTA R 2 1 2 1 101000 f 74 goat GoatD01.011549 2 116798673 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382734 Affx-122973609 AX-123253092 2 116816088 ATGAACTAGAAGAATGTATATACTTTGACTCCTTC[A/G]ACACTGGTTTTGGTGTCTTTTGTCTCTTTAGTAAA R 2 1 2 1 101000 r 74 goat snp27002-scaffold287-1218615 2 18332871 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414998 Affx-122949042 AX-123285347 2 116851065 CTCTGAGTGGGAAAAGTCACTGTGGGCAAGGAGAA[C/T]GAGCCTAACAAGAGCCCTTAGAAGTCACCCCTCAA Y 2 1 2 1 201000 f 74 goat snp27001-scaffold287-1183638 2 18297999 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380217 Affx-122975483 AX-123250575 2 116914329 CTGACTTCCCTATTTTTATACAGAGAAATCATTTC[A/C]TATTTTGCCATATCTGAGTTTGGGATCACTTCCAA M 2 1 2 1 101000 r 74 goat snp27000-scaffold287-1120374 2 18234834 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441290 Affx-122929464 AX-123311627 2 116953762 ACAGTCTCCCCGTTTATGATGGTTCCCCATCTGCC[A/G]TGCACACTGCTTCCTTCCAGTGCCCTCATTCAAAC R 2 1 2 1 201000 r 74 goat snp26999-scaffold287-1080941 2 18194691 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776832 Affx-122961015 AX-385263956 2 116999916 TGATGATTCTTTAATTACCTTAAAGGTAACTGTCA[C/T]GGCTTTTTCTGATGTGGACCTTTCGCCTTCTTTTG Y 2 1 2 1 101000 r 74 goat snp26998-scaffold287-1034787 2 18152332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408633 Affx-122953485 AX-123278984 2 117041208 CATTACCATGACCTTATGAATATTTATACTGTTTC[A/G]TGGAAAGAAAGAGGTGACTTAACATTGTAACACAA R 2 1 2 1 101000 r 74 goat snp26997-scaffold287-993495 2 18110804 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274766 Affx-1111834482 AX-519548352 2 117067105 TGCAGAGAGAAGACCTGTGTGTGCTTGCACTTGGG[A/G]TTCCCTC R 2 1 2 1 102000 f 74 goat GoatD01.037908 2 117067105 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443712 Affx-122927152 AX-123314049 2 117078794 TTTGCCTAAAGGGACATTTCAATGTTCAGAAACAA[C/T]GTTTGTAATGATTATAGCACCGCTGCAGAACATTC Y 2 1 2 1 101000 r 74 goat snp26996-scaffold287-955909 2 18072634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380908 Affx-122975028 AX-123251266 2 117137687 AGCATAACTTACTCTGAACCTTCATCGTTGCATGG[A/G]TCTTCACATCTTCACATGGCCTTTCCTGTGTCTCT R 2 1 2 1 101000 f 74 goat snp26994-scaffold287-897016 2 18014109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413504 Affx-122950637 AX-123283853 2 117166297 GATACCTGCCCATCCTCCCTGCTCTCACCCCTCTT[G/T]CCCAAGCTAACCTCTTCACGAAGGCAGTCTTCATC K 2 1 2 1 201000 r 74 goat snp26993-scaffold287-868406 2 17985615 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438901 Affx-122930441 AX-123309238 2 117200911 ACTTACTCATGAAATGAGCTATGCCTGTATGTTAG[C/T]GCCTGTGGAGCTCCAGGTGAGCTGAAGGTGATATA Y 2 1 2 1 101000 f 74 goat snp26992-scaffold287-833792 2 17950977 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382651 Affx-122973676 AX-123253009 2 117235479 AGTCGTTCCATCTTTCCTGATCACATCAGGAAGGG[C/T]GGTGTCTGCCTGTTACAGCAAAAGACAGCAATCAT Y 2 1 2 1 101000 r 74 goat snp26991-scaffold287-799224 2 17916271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376705 Affx-122978976 AX-123247064 2 117275782 CAGATTGATCTTGTTCCGCGAAGTCCTCAAGAACT[A/G]TATGAACTGACATCTCTGATTTGGTAAAGACTGGG R 2 1 2 1 101000 f 74 goat snp26990-scaffold287-758921 2 17876000 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772216 Affx-122945027 AX-385259371 2 117307646 GCCTAATTAGTTTCTAAAAGTATTGGCATGAGTTA[C/T]TGAGTTTAATGGGTGAGGGCGAGAGATGTACTTCA Y 2 1 2 1 101000 r 74 goat snp26989-scaffold287-727057 2 17843807 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408585 Affx-122953658 AX-123278936 2 117353558 AAATTCATGTTTAGAAGTAGAATGGCATCATTGAA[C/T]GTGTACCTTGTCCCGTTATTCTGGAGAGCTGGATT Y 2 1 2 1 101000 r 74 goat snp26988-scaffold287-681145 2 17797570 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425849 Affx-122940664 AX-123296195 2 117384685 AAACAAGAACAACAATTAAGATTATCACTGCTTCC[A/G]TTTAATTCCCAGTTTTTCAGGAGTTTGAGCGGTTT R 2 1 2 1 101000 r 74 goat snp26987-scaffold287-650018 2 17766021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393879 Affx-122965128 AX-123264234 2 117419867 CTTCTGAAACATCAATGGGATTGTGTCAACTCTCC[A/G]CCTAAAACTCTTCCAGGGTTCCCCATCCCTTTCAA R 2 1 2 1 201000 f 74 goat snp26986-scaffold287-614836 2 17730585 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417427 Affx-122947215 AX-123287775 2 117453900 AAATCCCATGTCAATGGATGCTCAGCACTCCCTAG[C/T]CATATAGCTCCGGATTAGGTACTATTGTGCTTAGA Y 2 1 2 1 101000 r 74 goat snp26985-scaffold287-580803 2 17696165 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779631 Affx-122971821 AX-385266733 2 117488585 TTCCATATAAGCAAAGTTTAATGCATGTAATATAC[G/T]AACCTCTTCAAGAATAAAAAGCAGTACTAGAAGTT K 2 1 2 1 101000 r 74 goat snp26984-scaffold287-546118 2 17661316 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389513 Affx-122968296 AX-123259871 2 117544515 GGATCTGGCAAGTTCCTTAACCTGTCTGTGCGCCT[A/G]CTTACTCACCTGTGTATGGGAGAATAAGAGCGTCC R 2 1 2 1 201000 r 74 goat snp26983-scaffold287-490188 2 17605329 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278037 Affx-1111836142 AX-519551529 2 117554114 TCCAAAAATGAGCTTTGTGTGTATGTGCACGTGGC[A/G]TATCTCAAAGGGAGAAGGTTCACAGCTTTCACCAT R 2 1 2 1 201000 r 74 goat Random2.2K-262 2 117554114 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412424 Affx-122951426 AX-123282773 2 117607678 CATCTGTATATTCCCCACTTCCTTTCTTCCTTGCT[A/G]TCTACTTATTGGATAACCTGGGGTCTTTGCCCTAC R 2 1 2 1 101000 r 74 goat snp26982-scaffold287-427025 2 17542418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277890 Affx-1111836143 AX-519551385 2 117629500 TTAAAGAGGAGAACCAGAACGTACACTTGTAGAGA[A/G]GACTTCCCTAGTGGTCCAGTGGTTAAGAATCTGTC R 2 1 2 1 101000 f 74 goat Random2.2K-263 2 117629500 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427598 Affx-122939457 AX-123297941 2 117639980 TGTAGGCTGGAATTTGACACAGATCTCATAGCACT[A/G]TGTAAGCAAGACGGTGACTGCCATTTGTGAGACGT R 2 1 2 1 101000 r 74 goat snp26981-scaffold287-394723 2 17510269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772941 Affx-122972317 AX-385260085 2 117687417 CAAGAAAGATGGTCCACGCAAGTAAGGAAGTGTCT[A/G]CTACTGAAGTTTCCCAAAACCATCCAAATGGAGCA R 2 1 2 1 101000 r 74 goat snp26980-scaffold287-347286 2 17462961 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453565 Affx-122919770 AX-123323898 2 117783936 CTCCTCACCTGAGGCTCTGTTCTCATGGCCTGCAA[C/T]GGTGGCAGAAGCTTCCTGAGGTCTCTCCTGCACAT Y 2 1 2 1 201000 f 74 goat snp26978-scaffold287-250767 2 17366481 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382956 Affx-122973367 AX-123253314 2 117829140 CCCTGAATTCCTGCTGTGACACTGCGTAGAGCAGC[A/G]CTCAATCCTAATTTTCAGCTGGGTGAACTTGTACA R 2 1 2 1 101000 r 74 goat snp26977-scaffold287-205563 2 17321392 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436782 Affx-122932262 AX-123307120 2 117858211 CCGTGTTCAAACATGTTGATTCCCAAGGCAGGGCC[A/G]TGGAATGTGCACCTCTCCTCCCTCCCTTCTTTTAT R 2 1 2 1 201000 f 74 goat snp26976-scaffold287-176492 2 17292393 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443448 Affx-122927837 AX-123313785 2 117903395 CTCATCACACTTGAATCAAAATGACATTTGTTTAT[C/T]TCTCATAAGCAATTTCACTTAAAAGAAGAACTATT Y 2 1 2 1 101000 r 74 goat snp26975-scaffold287-131308 2 17246851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425621 Affx-122940906 AX-123295967 2 117946656 CAATTCAGGCCGTGTGTAAACAGAGAGCAACAGCA[C/T]GGCCCTGGATACCTCAGGTGGTGGTGGAGTTGCGG Y 2 1 2 1 201000 r 74 goat snp26974-scaffold287-88047 2 17203796 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451085 Affx-122921410 AX-123321419 2 117977485 TTTCAAGCCCCTATTATCTATGAGGCTTTACAGAT[A/G]TCATTAAACTAAGTGAAAAGTCAGAAAGAGAAGGA R 2 1 2 1 101000 f 74 goat snp26973-scaffold287-57218 2 17172975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767569 Affx-122923340 AX-385254821 2 118008843 TTATGCATTGCCTAGAATTTCCAGAACAATGCTAC[A/G]TAACAAATCATACAAAGCATCCTAACCTTCAAGTT R 2 1 2 1 101000 f 74 goat snp26972-scaffold287-25860 2 17141029 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420863 Affx-122944638 AX-123291210 2 118056664 GTCTTAACTATCCCCAGATTCTAATGCGAGAATAA[C/T]ACATCCGTGTTTTCTTTGACACGCGGCACCCCTCA Y 2 1 2 1 202000 f 74 goat snp3654-scaffold1113-1450166 2 17092506 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410571 Affx-122952133 AX-123280921 2 118102854 GCATATCGAACGATCAGTAAAAACATGCAAAAGTG[A/G]GAAGGAAAAGGAAAGTAAACGCTGCATTCCCCCAA R 2 1 2 1 101000 f 74 goat snp3653-scaffold1113-1403976 2 17046370 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438772 Affx-122931384 AX-123309109 2 118150389 TTTCTTACTGTCTGTAGGAAAAGGATCTGAAAACC[A/G]AAGGGTGAAATTGCCATTGCCTTGGAGTCCTTGGC R 2 1 2 1 201000 r 74 goat snp3652-scaffold1113-1356441 2 17001811 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379227 Affx-122976275 AX-123249586 2 118193058 TTACTTCCTGATTTATCTATTGGAAAGCTCTTAAT[A/G]ACTGTTTTGTTAGATTTTAAAAAATGCCTATCATG R 2 1 2 1 101000 f 74 goat snp3651-scaffold1113-1313772 2 16959207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440316 Affx-122930209 AX-123310653 2 118225098 AGGTTCACGGAACAGGTGAGTCTGCAAGAAGGTGG[C/T]AATTCTCTGAAGTCAAGAGCAATGGATCTCTCAGC Y 2 1 2 1 101000 r 74 goat snp3650-scaffold1113-1281732 2 16926822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388809 Affx-122968907 AX-123259167 2 118261232 AACTAGCAACTAGAACTTTCATTGCAAGCATTTTG[C/T]GTATCAACCTTATCTCTAGCTTCACATTATTTCTC Y 2 1 2 1 201000 r 74 goat snp3649-scaffold1113-1245598 2 16890744 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435376 Affx-122933578 AX-123305716 2 118296925 CTGGCAGGGAGTGACAGAAGGATCTGTAAACAAAC[A/G]CCAGGTGAACTGAACTATGAATCTTGAACAGGAAT R 2 1 2 1 201000 f 74 goat snp3648-scaffold1113-1209905 2 16856386 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272017 Affx-1111833152 AX-519545783 2 118334565 GAAGCTGAAGCCCCAATACTCTGGCCACCTCATGT[A/G]AAGAGTCGACTCATTGGAAAAAACCCTGATTCTGG R 2 1 2 1 303000 f 74 goat 2_118334565_AF-PAKI 2 118334565 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38439701 Affx-122930566 AX-123310038 2 118338551 TACACAGAGATGCAATGGGGGTAGGGAGGGCTAGG[C/T]AAGATATGGAGGAAGAACCTGCAAATTAGTAGAAA Y 2 1 2 1 201000 r 74 goat snp3647-scaffold1113-1168279 2 16814733 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409167 Affx-122953201 AX-123279518 2 118367405 TTGGCCACTGTCTTAATACTCCATGGTCTAAAAGT[A/G]TGTATGAACCTCTAAAGGACCAATGGAGATTCAGC R 2 1 2 1 101000 f 74 goat snp3646-scaffold1113-1139425 2 16785759 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452877 Affx-122920700 AX-123323210 2 118403559 ATAAGAAATCCTTTCATCCAGGTCCTCTTTGTCCT[A/G]CAAGGAAGAGAGGATGTCTGAGATCTCCGGCTTCA R 2 1 2 1 101000 f 74 goat snp3645-scaffold1113-1103271 2 16749213 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433374 Affx-122935124 AX-123303715 2 118434546 CTGAACATACCTAAATCCTTCCTGAAACCTGTGGG[C/T]TGAATAAATAGGACACAGCCAGGAGCTTTCCTGGC Y 2 1 2 1 201000 r 74 goat snp3644-scaffold1113-1072284 2 16717864 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395026 Affx-122964215 AX-123265381 2 118487400 CCCCAGTTAAAAAATAACATCTGGCCGTGGGGGAA[G/T]CTGAGTAAAATACAGACATGCTCATTCCTTGTCAG K 2 1 2 1 101000 r 74 goat snp3643-scaffold1113-1019430 2 16664622 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390761 Affx-122967897 AX-123261118 2 118519831 GCGGATGCAAGCAGGTTCTGAGCCCTGGAGGACTT[A/G]TTTTGAGGCTGAGCTGTTCTAAACAGCAACTTCCC R 2 1 2 1 101000 r 74 goat snp3642-scaffold1113-986999 2 16632299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414886 Affx-122949132 AX-123285235 2 118597074 GGCCGCCAAGCAACAGACGGAGACACACACATGGA[C/T]GTACTCAGAGACACACAACGCTCGTACACAGACAC Y 2 1 2 1 101000 r 74 goat snp3640-scaffold1113-909756 2 16554578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429078 Affx-122938281 AX-123299420 2 118643526 TACGGAATATAGAATACTAATTCCAAGTGGCGAAA[C/T]GTGAAAAAATAACCTAAAATAAGATAGAAGAACAA Y 2 1 2 1 101000 f 74 goat snp3639-scaffold1113-863304 2 16507044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418646 Affx-122946334 AX-123288994 2 118685664 AATACTCTGGATTATATTGTGACTGCATGTGTTTA[C/T]TGAAACTCATTGAACTGTGCACCCGAAAGGGTGAG Y 2 1 2 1 101000 f 74 goat snp3638-scaffold1113-821166 2 16464989 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401958 Affx-122958797 AX-123272311 2 118717538 TTGGTGCAAACGCACAGGTCTATCACCATGAAGCC[A/G]GCTCATGGGACCAAAGGCAGACAGGGCAGAAGCTG R 2 1 2 1 101000 f 74 goat snp3637-scaffold1113-789292 2 16432431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388768 Affx-122968938 AX-123259126 2 118751449 CAGCTGCCCCCACACACTTACCACACATACACACA[C/T]GTGCATACACGCACACACACACACATCCGTTGGAC Y 2 1 2 1 103000 f 74 goat snp3636-scaffold1113-755381 2 16398480 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381127 Affx-122974572 AX-123251485 2 118784056 CTCTCCAACAGGCACCTCTCTCAGGCCATAGGGGT[C/T]TTGCTGCCTTCACAACTTGCCACACCTTCCCTTTC Y 2 1 2 1 101000 r 74 goat snp3635-scaffold1113-722774 2 16365711 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450467 Affx-122922943 AX-123320801 2 118827286 GTCAGATGGAGAGACCTGAAGTGCTTGTGGAATAC[A/G]GGGCGGGAGACTGGAACTCTTGCAGGACACAGGGC R 2 1 2 1 101000 f 74 goat snp3634-scaffold1113-679544 2 16322347 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794397 Affx-122953925 AX-385281360 2 118873924 TCCCTTTTACTGTATACTAATATACCCTGTGGTGT[C/T]TGTCTTCCCCTCTACAATCCAAATGAATCCCTGAG Y 2 1 2 1 101000 f 74 goat snp3633-scaffold1113-632906 2 16274858 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435504 Affx-122933422 AX-123305844 2 118907102 AGCAAAGCACAGAGCAGTCTTTGGAGCATGGACTA[C/T]AGATTCAGATTTTATTACCTCTACCACTGTGACCC Y 2 1 2 1 101000 f 74 goat snp3632-scaffold1113-599728 2 16241712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439406 Affx-122930247 AX-123309743 2 118937355 CACCACCCTCCAAGCAAGTGAAAACCCCCGGCGAT[C/T]AGTCTATAACAAATATTGACACGAGGGGGAAAAAA Y 2 1 2 1 103000 r 74 goat snp3631-scaffold1113-569475 2 16211260 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424612 Affx-122942194 AX-123294958 2 118974235 ACCTCCATTCTCCTCCTCCTCCACATACGATGGTT[A/G]TCTGGGTGGGTTCCCAAGATCTCCCCCAGCTCTGG R 2 1 2 1 201000 r 74 goat snp3630-scaffold1113-532595 2 16174232 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441982 Affx-122928441 AX-123312319 2 119017426 ATAGAATGGTGAAAGAAATAATTATCGCTACATTC[A/G]TAAGGGAAATGGATAATAATGGCATGTGAATAGCA R 2 1 2 1 101000 r 74 goat snp3629-scaffold1113-489404 2 16132857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278042 Affx-1111836144 AX-519551533 2 119032225 GTTTCATCTTGTGTATTCAAAGAAAATGGTGCTGA[A/C]TGGAATACCCAAGTGGGTTATGTGCCTTCATTCAT M 2 1 2 1 101000 r 74 goat Random2.2K-265 2 119032225 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382595 Affx-122973718 AX-123252953 2 119046372 TCCAATCCAATACCTAAAATCAACTGGTCTGTAAG[C/T]GTTGTGAGGTGAACACTATAAAATGTGGTATAAAT Y 2 1 2 1 101000 f 74 goat snp3628-scaffold1113-460458 2 16103527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398165 Affx-122962661 AX-123268520 2 119177304 TATGCCATTGAGTATGAAATGTTTCCTGAAGCATC[A/G]ACTCAGTGAAGTTTCTGGGTACCTGTGGGGTGTCA R 2 1 2 1 101000 f 74 goat snp3626-scaffold1113-329526 2 15972068 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426856 Affx-122940490 AX-123297201 2 119210849 GAAAGGGTAGGTACATTTAAAATGTCGATAGCTAC[A/G]GAGGATTAGCTCTACTAACTTACATTTCAAACAAG R 2 1 2 1 101000 f 74 goat snp3625-scaffold1113-295981 2 15938173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448179 Affx-122924253 AX-123318515 2 119247191 GTCCTCATTTCCCAGTTTCCACCACACAGATTCCA[C/T]GTCCTCATCATCCAGGTTGGCACTTTTGCCCCATC Y 2 1 2 1 101000 f 74 goat snp3624-scaffold1113-259639 2 15901803 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417430 Affx-122947213 AX-123287778 2 119295645 GTTTTGCAAAATAACACATATTAACATGCATAAAG[G/T]TACTATAAAAATGGAGAAAATTTTAATACCATATT K 2 1 2 1 101000 f 74 goat snp3623-scaffold1113-211185 2 15853549 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427423 Affx-122940056 AX-123297766 2 119331963 AATTTGGTCATTCTAAGCATATATTCCCAAGGAAA[G/T]AATCCGAAACAACTGTGATTAACAATGCATAAGAA K 2 1 2 1 101000 f 74 goat snp3622-scaffold1113-174867 2 15817125 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425592 Affx-122941411 AX-123295938 2 119362637 CTCTCGGGGTCCTGGCAGAATAAATGCCAAAGCAG[C/T]GAAAGGACACATGCACAACCCAGGAACGTATGGGA Y 2 1 2 1 101000 r 74 goat snp3621-scaffold1113-144193 2 15786105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419892 Affx-122945348 AX-123290240 2 119419591 TCTTCACCCAAGGAGACAGTGGAAAGGCATTCAAG[C/T]GAGGTAGCATCAACCACACGGTGCTCTTACAGACC Y 2 1 2 1 201000 r 74 goat snp3620-scaffold1113-87239 2 15728608 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385513 Affx-122971258 AX-123255871 2 119459374 ATAACTCGGATTTTCACATTTCTGTTCAGTCGGCC[A/G]TTTTACCTGCACTCACTTGCGTGTGTGTGGGTTCT R 2 1 2 1 102000 f 74 goat snp3619-scaffold1113-47456 2 15689267 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447858 Affx-122923888 AX-123318194 2 119513161 TCCAGAGCAGTTTCTTCCAGTTTCCTCCAGATAGC[A/C]GGCTGTCTTCCAGGTTATAGTCTTCAGTTTGGCTC M 2 1 2 1 102000 f 74 goat snp43284-scaffold5766-6232 2 15628886 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411890 Affx-122951192 AX-123282240 2 119562766 AGAGGAGCCAGAGGAGGGTGAGCTGGGGTCTGAGC[A/G]GACTTGCAGTCCATGCTGTGAGCTCCCTAATTTTT R 2 1 2 1 101000 r 74 goat snp43285-scaffold5766-55837 2 15579412 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413742 Affx-122950055 AX-123284091 2 119576723 TTGAGGCAGCCAAGGGTGAAGCCCCAATATTTGGA[G/T]GAGTGAAGGTGACCCACTTTGTATGATGGCTCCTC K 2 1 2 1 201000 r 74 goat snp15998-scaffold1684-9957 2 15566111 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415525 Affx-122948673 AX-123285874 2 119606957 CACTGCCTCACTTTCCTTTGATGAATGCTTCTGTC[A/G]TCCCTCCTGTAGGAGGACATTATTTCCATATGGAA R 2 1 2 1 202000 r 74 goat snp15999-scaffold1684-40191 2 15535776 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782161 Affx-122948368 AX-385269239 2 119654843 ATCTTCTGCTACTTAAGGGCATTCTTAATATTTGT[A/G]ATATAAATATTTACTTGGGCTTTTACTTCTAAGTT R 2 1 2 1 201000 r 74 goat snp16000-scaffold1684-88077 2 15487551 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773943 Affx-122934770 AX-385261082 2 119690582 ACCTCAGCTGACTTAATCTTCCATTAAGGTTCTAT[C/T]TGCATAGCCCATGATCTCGAAAGGCTTAGTGTGCT Y 2 1 2 1 101000 f 74 goat snp16001-scaffold1684-123816 2 15451904 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427107 Affx-122939670 AX-123297450 2 119741095 TGCACAGCTTCCAGTTCTGAATCCCAAGCATACAA[C/T]GGTCCCTGAAGGAATTTCTGCACTTCTGTCCTTAG Y 2 1 2 1 101000 f 74 goat snp16002-scaffold1684-174329 2 15399427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418547 Affx-122946401 AX-123288895 2 119785761 CCCAAAACTCATAGAGCCCTGGTTAAAAAACCCAC[A/G]TCTACGAGAAAGAATAGACCTATAATGAGATGATT R 2 1 2 1 101000 f 74 goat snp16003-scaffold1684-218995 2 15354623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438489 Affx-122931601 AX-123308827 2 119807126 GAGAAAACAGTCTGCTGGCTTCTCAGTCTGCATCG[C/T]GGTGGCAGGGAGGTGAGGGCAGGTGCTCCCCCCCA Y 2 1 2 1 101000 f 74 goat snp38585-scaffold4896-36322 2 15332568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446946 Affx-122924675 AX-123317282 2 119839824 GCCATCCTCCTAGCCCCATGATGACCCGTCTACTG[A/G]AAACCTTGACCATGGCCTTTCTCAGCTCAGGGACC R 2 1 2 1 101000 r 74 goat snp38584-scaffold4896-3624 2 15301515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419026 Affx-122946036 AX-123289374 2 119860535 AATTGTTGAGGGATGGGATGGAAGAAGCAGAAATG[C/T]AGTTGCTATGAATAATCGCTGACATTTCTAGAGCA Y 2 1 2 1 201000 r 74 goat snp2519-scaffold1071-506828 2 15281009 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452266 Affx-122920763 AX-123322599 2 119890175 TGTCCTCATTTATCAAACCATAGAGTACCTGAACT[A/G]TACCAGACATTTCTCTTCAAGATCTTATTTAATCC R 2 1 2 1 101000 f 74 goat snp2518-scaffold1071-477188 2 15252241 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442951 Affx-122928220 AX-123313288 2 119937671 TGCAGCCTAAGCAAAGATGCCAAGGAGATCACAGA[C/T]GCCAGAGAGCTTTATAAATGGCAACATTCTGGGCA Y 2 1 2 1 101000 f 74 goat snp2517-scaffold1071-429692 2 15204217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406814 Affx-122955687 AX-123277165 2 119990727 CCTTGGAAATACAATCTTGCTGCGTAGAAACGTGT[A/G]TGTGTGACACACACACAGAGAAGTACACAGACTAC R 2 1 2 1 101000 f 74 goat snp2516-scaffold1071-376636 2 15152105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444142 Affx-122926797 AX-123314479 2 120104480 TTCAGTGAGTAAGCCAGCAACTCTGCATCCTCAGG[A/C]TCAGATGGCAACATGACCTCCTCAGGAATGCCTTC M 2 1 2 1 102000 f 74 goat snp2514-scaffold1071-262883 2 15036122 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277894 Affx-1111836145 AX-519551389 2 120127359 AAGGATAATGTGAATGGAGGTTGCACAGTCATCCT[A/G]AAAAATAGAAAAGAAAGACCGAATGGATCATTATG R 2 1 2 1 101000 f 74 goat Random2.2K-266 2 120127359 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421597 Affx-122944492 AX-123291944 2 120151728 AGGCATTTAAGGTCTACCTGATCTGCCTCCAAGCT[A/G]TCTCCAGTTCCACCTCTTACCATAGATCCTAAATC R 2 1 2 1 101000 r 74 goat snp2513-scaffold1071-215635 2 14988763 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392780 Affx-122965985 AX-123263137 2 120204442 TAGCATGTTAGCTTTATGTCAAAAATCTTCTAGAG[C/T]GCCCATCCCCTCAGGACGTTGAGGTCCATCAGAGA Y 2 1 2 1 201000 f 74 goat snp2512-scaffold1071-162921 2 14935720 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403763 Affx-122957998 AX-123274115 2 120237406 GATCTTAGGGCTCTACTGGTATATTCCTGTATCCT[A/G]TTGGACATAGAGATGCCTCTTAAGAGCAGCCTCAT R 2 1 2 1 101000 f 74 goat snp2511-scaffold1071-129957 2 14902755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420698 Affx-122944792 AX-123291045 2 120266153 GTAAAGTTAGCAAGTAATGATTTTTTTTTTTTCCA[C/T]TGAGGTTTGACCACATTCACAGGTCATTTCTACAT Y 2 1 2 1 101000 r 74 goat snp2510-scaffold1071-101210 2 14874009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423118 Affx-122942910 AX-123293464 2 120298954 ACAAGTCAGTGCTCTGAGAATCAGTGCTCTCACAC[C/T]AGGCTGGGCAGGAAGGACTCCAGGAGGGCTCTGAT Y 2 1 2 1 101000 f 74 goat snp2509-scaffold1071-68409 2 14841182 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426392 Affx-122940850 AX-123296738 2 120347116 AGCGGTATCCCTTTGTCTCCTTCAGATGAGGACCA[C/T]GGAAACACTCACCCTGGGCTTCAGATGCTGTGCTT Y 2 1 2 1 201000 f 74 goat snp2508-scaffold1071-20247 2 14793427 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798476 Affx-122976086 AX-385285409 2 120379025 TACCTGCTGTATCTGTTAGGTCTTTTAGACCCAAC[A/G]CTTATTCTATCAAAGATGAGAGTGGTAAAAAGAAG R 2 1 2 1 101000 f 74 goat snp17729-scaffold1840-11563 2 14757356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775057 Affx-122932128 AX-385262189 2 120424238 GGGTAATTAACTAATAAATAGTTGAACAGAGTTTT[A/G]AAACTATGCTCTTTCTGATACTGCTACTGCTTTTA R 2 1 2 1 101000 r 74 goat snp17730-scaffold1840-56776 2 14712215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765741 Affx-122970351 AX-385253197 2 120453123 AAATAGCGATCCTTTTCTTTCTCACTAATGTCTAA[C/T]GAAGATTTAATAAAGGTCTTACATACACTGATGAC Y 2 1 2 1 101000 f 74 goat snp17731-scaffold1840-85661 2 14684639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434946 Affx-122933858 AX-123305286 2 120496511 GAGGAATAAAAACAAAATCTTCTCTAAGACTGTAC[A/G]TGAAGCAAGTGAACAGAGACTGGAATTCAGGCTGA R 2 1 2 1 101000 r 74 goat snp17732-scaffold1840-129049 2 14641854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381487 Affx-122974960 AX-123251845 2 120559805 AAAGAAAGCAAAAGATAACAAAACTCTTTACAAAG[C/T]ATATCTTTTACACCTTCATTTAGGTTTCCCTCTTG Y 2 1 2 1 101000 r 74 goat snp17733-scaffold1840-192343 2 14578507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438236 Affx-122931434 AX-123308574 2 120608593 CCTTCGTTGATTTTAAACTACCAGTGTGACATCAC[A/G]TAATGCAGAGTTAGGAAGAGATTACAGTAAGTCAC R 2 1 2 1 101000 f 74 goat snp17734-scaffold1840-241131 2 14529555 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777024 Affx-122965809 AX-385264147 2 120696349 CTTGCGAATATAATCCAACTTTCTTAGGGTGGTGC[A/G]CCCAGCCTTTCGTGATCTAGTCCCCATTTACTAGC R 2 1 2 1 202000 r 74 goat snp17736-scaffold1840-328887 2 14443331 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430777 Affx-122937482 AX-123301118 2 120770835 ACTTCTGGTCAACACACTCAGACCCACCCTTAGCC[A/C]CCTGACTCAACAATTCTGTGGAGATACCAGTTTTC M 2 1 2 1 101000 r 74 goat snp17737-scaffold1840-403373 2 14368728 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427915 Affx-122939673 AX-123298258 2 120816129 TGGGGTCCCTGATCACCCCTATGCCTGGAGACTAA[C/T]AGGCACAGGACAAATTCCTAAAGGCACCGCTATGG Y 2 1 2 1 101000 r 74 goat snp17738-scaffold1840-448667 2 14323023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272930 Affx-1111833153 AX-519546617 2 120834877 ATATACTGTGATTGATCTGTTGGGCATTGTTGCTA[A/G]CACTATTTCCTTTATGTCCAGAATCAGTAATCTTT R 2 1 2 1 101000 f 74 goat 2_120834877_AF-PAKI 2 120834877 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412480 Affx-122951387 AX-123282829 2 120853662 AACACTCCACAGAGTGTGGGTCATCTCAGAAGGCA[A/G]GATCAGCCTCCACTCTGAATTGTAACCAGACAACC R 2 1 2 1 201000 r 74 goat snp17739-scaffold1840-486200 2 14285435 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786642 Affx-122923044 AX-385273674 2 120910373 TGTGTTGCAAATCCAGAAGCCAATTGCCTCTTGTT[A/G]CATCCCCCTATCGATGACCCAGAGACCCATCAAAC R 2 1 2 1 101000 f 74 goat snp17740-scaffold1840-542911 2 14228621 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388522 Affx-122969205 AX-123258880 2 120969100 TTGAGGGTATGGGGCTCAGGACAGATACTCTTCCC[A/G]TTCAAATCCGTCTATCACATACTCGCTGGGTGGCT R 2 1 2 1 101000 r 74 goat snp17741-scaffold1840-601638 2 14171204 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392604 Affx-122966050 AX-123262961 2 121034064 ATATATACAGGGCTGTAATGAACTTTGTGGTCCAT[A/G]CTTATCACAACCAATCATTTCCTTAGGATAAATTC R 2 1 2 1 101000 f 74 goat snp17743-scaffold1840-666602 2 14105708 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409581 Affx-122953575 AX-123279932 2 121071860 GAAAAAGAAATATGACATATAATGAAAATGCAGGC[G/T]AAATAAAAGATATCAAATAAAAAAGGGAACCATAA K 2 1 2 1 101000 f 74 goat snp17744-scaffold1840-704398 2 14067775 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388219 Affx-122969407 AX-123258577 2 121106465 AATTCCCTCATCAGTGCTGAACTCTTAAGTGTTCC[A/G]GGGAGAGCAATAGGGATATAGGAAGGAGAGGCTTA R 2 1 2 1 101000 f 74 goat snp17745-scaffold1840-739003 2 14033123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431984 Affx-122935946 AX-123302325 2 121183086 CTTTCCCTTTTCTTTGCCTGCTGAGTTTTCAATCA[A/G]TCTTCAAAGCTCTGTACAAGTGTGGTCTTCTTTAA R 2 1 2 1 101000 r 74 goat snp57678-scaffold925-882815 2 13958321 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392886 Affx-122965738 AX-123263243 2 121226636 GGTTCTACTGTAGACTGAAGAGCTACCTACGCACC[A/G]TCCACTAGCTATAGAACCGCACATTTCTTAATGTC R 2 1 2 1 101000 r 74 goat snp57677-scaffold925-839265 2 13914776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399097 Affx-122960871 AX-123269452 2 121289858 CCAAGCACAACAACCATGGCCTTGCTAGGTCTCAG[A/G]GACCCTTAGTCTTGACTTTCAGATGGTGGCTCAGT R 2 1 2 1 201000 r 74 goat snp57676-scaffold925-776043 2 13852698 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394484 Affx-122964562 AX-123264839 2 121348057 GAGAGTTGATCTGGGTGACTTAGCCTGACATGACC[A/G]TAAAGGGAATTCTGCCAGGCCCCAGACTCCATTTG R 2 1 2 1 101000 f 74 goat snp57675-scaffold925-717844 2 13795103 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377385 Affx-122977631 AX-123247744 2 121381154 CCACCATTAATCCAGGTACTGAGCCTGTCCTGGTG[A/C]TGAGGTTGATACCCGCTGGGATCTGCCCATCTGAC M 2 1 2 1 201000 f 74 goat snp57674-scaffold925-684747 2 13761778 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376167 Affx-122978839 AX-123246526 2 121423580 ATCAATACAGGATGTGGCATGAATGACTGTTGAAT[A/G]TATGAAAGTGAGTGTGGGAAGAGACCCTGGAGGGT R 2 1 2 1 101000 f 74 goat snp57673-scaffold925-642321 2 13720247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419039 Affx-122946027 AX-123289387 2 121467416 GCTGCTCTAGGGGAAATGCCTGGCAGATAGTAGGC[A/G]TGAATGAATGACTACTGAATACTGAGGGAGGGAGT R 2 1 2 1 202000 r 74 goat snp57672-scaffold925-598485 2 13676347 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396234 Affx-122963338 AX-123266589 2 121496441 CACAGAGCAGTGAAAGGAGCCAGATACAGAAGGGT[A/C]CATACTGTGATTCTCTTGATATAACTTGGAAAAAT M 2 1 2 1 201000 r 74 goat snp57671-scaffold925-569460 2 13647358 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444413 Affx-122926578 AX-123314750 2 121537183 CAAAGGACCCATTTCATTTCACAATGCGGCAAATG[A/C]TGCCAGAGGAAGAAGTGTCAGATGCTTGTTACCTT M 2 1 2 1 201000 f 74 goat snp57670-scaffold925-528718 2 13608388 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453088 Affx-122920041 AX-123323421 2 121589528 GGCAGCAACAGAAGCACCTTGGAACTGGTTAGAAA[C/T]GCAAATTCTCGGTCTCCACCTTGGATCTACTGAGT Y 2 1 2 1 303000 f 74 goat snp57669-scaffold925-476373 2 13556112 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412119 Affx-122951105 AX-123282469 2 121619147 AGTAGGGGAACTCGAGCAGAGAGGCGAGACCTTCC[A/G]AGGAGTTGGAGTGGGACGAACTGGGAATGGGTGGT R 2 1 2 1 201000 f 74 goat snp57668-scaffold925-446754 2 13526536 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405009 Affx-122956382 AX-123275361 2 121669214 GACATAGATTTTTTCCTATTTTTGTGGCTCCACCA[C/T]GCTGGGTCTATAATCTCAAGGTGCAAGGAAGCCAG Y 2 1 2 1 101000 r 74 goat snp57667-scaffold925-396687 2 13476890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382969 Affx-122973356 AX-123253327 2 121711062 TTGCTTTAGGTTCTAGGACTAGAAATATTCCCAGC[A/G]AGGCGGAAATAAAGAAAGAGCATGGGCATTAGGAT R 2 1 2 1 101000 f 74 goat snp57666-scaffold925-354839 2 13435239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392119 Affx-122966345 AX-123262476 2 121742020 TTCAAAAGGGAGAAAACCAATCATTCAGGATAAAG[C/T]GTCTTTTCTGTCAAAGACTTGAAGTACTTTCCAAT Y 2 1 2 1 101000 f 74 goat snp57665-scaffold925-323881 2 13404349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798823 Affx-122954144 AX-385285753 2 121771699 CTCTCTAGAAAAAGATTTTGTTAATTACACCTAGT[A/G]TATCCAACTGATATGAACACAGAGTGAATGCACAT R 2 1 2 1 101000 r 74 goat snp57664-scaffold925-294202 2 13374676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382883 Affx-122973420 AX-123253241 2 121859075 CTCAGCGTGGCCCTCCCTGACCCCCAGCTCCACCC[A/G]CTTAACCTCCCCACACATCATCGCTCTCAACACCA R 2 1 2 1 101000 r 74 goat snp57663-scaffold925-206826 2 13287445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781780 Affx-122972813 AX-385268862 2 121899171 CATACCTGATATCCAATTATTCAACCCATTGTACA[A/G]ACAAGGCAATTGAGACTAAGTAGTGAAGATAGACT R 2 1 2 1 101000 r 74 goat snp57662-scaffold925-166730 2 13249460 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789669 Affx-122925160 AX-385276678 2 121935421 CTGTCCCAGTCTAGCAAATATTTAATCCCTTGAGG[C/T]ATGTGTTTTGTTTACTAACTTTCTTCTTTACGTGT Y 2 1 2 1 101000 f 74 goat snp57661-scaffold925-130480 2 13213289 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429225 Affx-122937925 AX-123299567 2 121972121 GCTTGACTTGTACCTTCTCAGTGATGTTCAAGATC[A/G]TTAGAAAATTAGAGCAGGGAGGGGGACTTCATGAA R 2 1 2 1 101000 f 74 goat snp57660-scaffold925-93780 2 13176269 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452634 Affx-122920352 AX-123322967 2 122016360 GTCAGGCAGAGCTGGGTGGCCTACAGCTAACTGGC[A/G]GTGGACAGGCTGCAGGATGGGCTGATAGTGCATTC R 2 1 2 1 101000 r 74 goat snp57659-scaffold925-49541 2 13132455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777669 Affx-122964823 AX-385264788 2 122060736 GACTGAATGGTTGAGAGCAAGAATAAATGCACGCA[C/T]TGAACATACAAGTACGGATTACTGGATGGCAGCAA Y 2 1 2 1 101000 f 74 goat snp57658-scaffold925-5165 2 13087911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388651 Affx-122969111 AX-123259009 2 122066938 TAAAATTCACGGTCCCTCAATCCTGTTAGCAGCCC[C/T]GCAAGGTAGGTTCTGTGGCCCTCTCTTTTTAAGGA Y 2 1 2 1 201000 r 74 goat snp52148-scaffold772-938 2 13078413 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438463 Affx-122931240 AX-123308801 2 122098388 AAACAATTAAGACCAGATCTTTAAGAGCAAGGTCC[A/G]TGGGCAAGTTTGGCCCAGCTGCCTCTTTGCATGAC R 2 1 2 1 101000 f 74 goat snp52149-scaffold772-32388 2 13046973 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277895 Affx-1111836146 AX-519551390 2 122099294 GATAAGGAAAAATGAGGGTGCCAGGATTTGTGATG[A/G]CATCCACTACGGTAGTCAGTGTGGTCGTATTGAGA R 2 1 2 1 101000 f 74 goat Random2.2K-268 2 122099294 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376243 Affx-122978781 AX-123246602 2 122136726 ACATTCTTTCCGATCCCTGGATGTTCACAGTCTAG[C/T]GGGGAAGATGGGAAAATGGCACCGGGGACAGTCAA Y 2 1 2 1 101000 f 74 goat snp52150-scaffold772-70726 2 13008807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762283 Affx-986696814 AX-385250471 2 122166744 CTGAATCATGGTATGTTTAATGAAAGGTGAATGTA[C/T]AAAGAGACTACAGTGAAGACATGTAGCTTTTGACA Y 2 1 2 1 600010 f 74 goat 2_122166744 2 122166744 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 38440292 Affx-122930225 AX-123310629 2 122266053 TTCAAATCCTCCAGCTCCCTGAATCCAGTCCTCCT[A/G]CCCATCCACACTGTCTTTTCTGGGAGTGTAGGGGG R 2 1 2 1 201000 r 74 goat snp52153-scaffold772-200053 2 12882439 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278048 Affx-1111836147 AX-519551538 2 122303331 AGTTCTGGCTTGGGGTCTCTCATGAAGTTGCAGTC[A/G]GACAGTTGTCTCTGGGGTCACCTCTCACCCTTCAT R 2 1 2 1 102000 r 74 goat Random2.2K-269 2 122303331 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320780763 Affx-122932397 AX-385267852 2 122306415 GCAGAAGCAGAACATGAGTGCTTGCATTTGCCATT[C/T]GCGCTGAAATCTTGCACGTGCTAAAACCCACCGGG Y 2 1 2 1 101000 f 74 goat snp52154-scaffold772-240415 2 12842770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429772 Affx-122938247 AX-123300113 2 122338484 ATTCTGCTCTCCAACCAGTCCAGCGGAGGGGCCTC[A/G]TCTATACATACCTGAACTGAGTGACTCCGGTGTCA R 2 1 2 1 101000 r 74 goat snp52155-scaffold772-272484 2 12810236 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393858 Affx-122965145 AX-123264213 2 122368838 AAGGGCAGGGACTGGTCCTTGATCCCGCCAGGCAC[G/T]GCAAGGGAAAGGAGACCCGCGGCAAAGGAAAGCTG K 2 1 2 1 101000 r 74 goat snp52156-scaffold772-302838 2 12779744 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383382 Affx-122973511 AX-123253740 2 122405753 AGCCTCCCTTTTCTTCCTGTGTTCCCCCAGCGCCA[A/G]TTAAGCACTGTGCCAATCTCTGTGACAAAGATTAC R 2 1 2 1 101000 r 74 goat snp52157-scaffold772-339753 2 12743331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783714 Affx-122953015 AX-385270771 2 122456718 TCGATCAGAATCAATTAGAGGATAGATCCGAGGAA[C/T]GTAGAAGGCACAATTCCAGATGTTCCTAGTGATGC Y 2 1 2 1 101000 r 74 goat snp52158-scaffold772-390718 2 12691892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444343 Affx-122926722 AX-123314680 2 122502536 ACAAGAGAAATTGTGAAGATGGGTGAGGTGGACAA[C/T]GGAAAGGCAATGGATGAATGGGTGAGCAGATGGGG Y 2 1 2 1 101000 f 74 goat snp52159-scaffold772-436536 2 12645488 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407851 Affx-122954520 AX-123278202 2 122534178 ACCACCAAAAATAAACTCTGCCAAATATTGGTTGC[A/G]TACACATATGTGTTTATATATATTTATGTTTTTCT R 2 1 2 1 101000 f 74 goat snp52160-scaffold772-468178 2 12614066 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413608 Affx-122950563 AX-123283957 2 122573138 TTCAATTAGTGCATGGTTGGTTGAATCCGTGGAGG[C/T]GGAACCTGCGGATATGGACGGTTGACTGTAACTCC Y 2 1 2 1 201000 r 74 goat snp52161-scaffold772-507138 2 12575052 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395286 Affx-122964076 AX-123265641 2 122616014 TCCCTGACCTCCCAGACAACTCACTCACACACACA[C/T]ATGTATACACACACACGCATACATGCACACACTTG Y 2 1 2 1 103000 f 74 goat snp52162-scaffold772-550014 2 12532035 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408422 Affx-122954464 AX-123278773 2 122644822 CAGATAAGAAGGTCCACAGAAACCTCAGTTCCTAG[C/T]GAGAGGAACCAGCTTTGAGCCCTCTCCACCCGCAC Y 2 1 2 1 101000 f 74 goat snp52163-scaffold772-578822 2 12503309 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383811 Affx-122973181 AX-123254169 2 122688810 GTATCAAGTTCTAAATTTCAGAGTTCATTGACTCA[C/T]AGTATCTCAGAGCTGCAGAGACACTGGTCTAGGCA Y 2 1 2 1 101000 r 74 goat snp52164-scaffold772-622810 2 12459768 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416391 Affx-122947862 AX-123286740 2 122729972 ATAGTCCACCAGCCAAGTCAGGCCTGCCCACGTTA[C/T]GCATGGGCTGCAAGCTGAGAGTCATTTTTAAAGTT Y 2 1 2 1 201000 r 74 goat snp52165-scaffold772-663972 2 12418787 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421155 Affx-122944182 AX-123291502 2 122774023 TTGCCATGGGCTGTGAGCCTCTCAGGACATCAGCA[C/T]GAATCCAGGAAAACACTCATCTTCTGGGAGGACTC Y 2 1 2 1 201000 r 74 goat snp52166-scaffold772-708023 2 12375042 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415667 Affx-122948555 AX-123286016 2 122804270 ACCAAGTCCTTTTCATGAACTATCACTTTCAATCC[A/G]TTTAAGAAGCCTGTGGGGTTGGGGTTACCCTCTGC R 2 1 2 1 101000 f 74 goat snp52167-scaffold772-738270 2 12345538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407531 Affx-122954699 AX-123277882 2 122836304 GACATTATTTTCAGTTAGAAAACTCCTGAAGAAGC[A/G]TGACCTCTCCTGATGAACTAAGCTGATGAGTAGAT R 2 1 2 1 101000 r 74 goat snp52168-scaffold772-770304 2 12313561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391129 Affx-122966796 AX-123261486 2 122866077 GAGAACCATGTTTCATCTAAAAGAAAAAGACAAAG[A/C]GTTAAAATATTATTTTCATTTTTTAAGGTCATGGC M 2 1 2 1 101000 f 74 goat snp52169-scaffold772-800077 2 12283827 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381141 Affx-122974563 AX-123251499 2 122916964 GTCTCCCACATTGCAGGCAGATTCTTCACCACTCC[A/G]CCACCAATGTATAAATCTCTCTCTATGAAAATCTT R 2 1 2 1 101000 r 74 goat snp52170-scaffold772-850964 2 12232894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401293 Affx-122959862 AX-123271646 2 122959134 AAAGCATATGTAAAAGGGAAATATATGGCAAAAAA[C/T]GGTACAAAGATGGGAATAAGGAATATATTGTTTGC Y 2 1 2 1 101000 r 74 goat snp52171-scaffold772-893134 2 12191145 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449443 Affx-122922672 AX-123319778 2 122995842 GGAGCTCAACACTCACCGGCTGGTCCTTTCCCACC[A/G]CTCCCAGCTCTCTTTCCTTGGCGTAGGCCAGTTGG R 2 1 2 1 101000 f 74 goat snp52172-scaffold772-929842 2 12154443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382571 Affx-122973763 AX-123252929 2 123029036 TCCATTAAGTGAAGATTCTATGACCTGGGAATTTA[C/T]GATTCTGGAAGTCAAGGACTATCTGGTTCTAGGAT Y 2 1 2 1 101000 f 74 goat snp52173-scaffold772-963036 2 12121259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802782 Affx-122947256 AX-385289681 2 123090282 CAACCCCTAACTGCTTTCTGACCCTGTTGTTTCAC[A/G]TTTAAATAGGAGGGTGAATACACCTTGCAAAGGGC R 2 1 2 1 102000 f 74 goat snp52175-scaffold772-1024282 2 12060180 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416660 Affx-122947596 AX-123287008 2 123138551 CAGTTCTCCAAGAGCCCCAGGCAGGAGGCAGCAGG[C/T]GAAACTCATTTCCTGGGGTTTATGCCTCCTGCTCC Y 2 1 2 1 101000 r 74 goat snp52176-scaffold772-1072551 2 12010245 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432607 Affx-122935499 AX-123302948 2 123177744 GGATGCATCCCAATATCCTATTTATACCTCCCAGG[A/G]GAGCCTGGGAACTCCACCTGGACAGTCCCCCCTCA R 2 1 2 1 101000 f 74 goat snp52177-scaffold772-1111744 2 11970621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769074 Affx-122920081 AX-385256249 2 123254821 AGTCAATCGGTAAGTACATCCTTTTTTATTGAAAT[A/G]TAGTTGATTTGCCACGTGGTTTTAATTTCTGCTGT R 2 1 2 1 101000 r 74 goat snp52178-scaffold772-1188821 2 11894603 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420551 Affx-122945289 AX-123290898 2 123286034 TTTGCAAACATAAGCCCTAAGCTTACTGTGGGGTG[G/T]AAGTGGAGGTGGAAAAAGAAGAACAGACACTCAAG K 2 1 2 1 103000 f 74 goat snp52179-scaffold772-1220034 2 11863421 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384299 Affx-122972287 AX-123254657 2 123332170 TCTTGTGCCTCCTGCATTGGCGGGTGGCTTCTTTA[C/T]CACTGTGCAACCTGGGAAGCTTAAAAGGAAGATGG Y 2 1 2 1 103000 r 74 goat snp52180-scaffold772-1266170 2 11816801 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407861 Affx-122954512 AX-123278212 2 123375503 TGATTTCTTGGCCTCGGATGCTACCTGGTCCACCA[C/T]GTCAGCACAGCAGGCACAGTTTCTCAGGCTCAGGG Y 2 1 2 1 101000 f 74 goat snp52181-scaffold772-1309503 2 11773023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272932 Affx-1111833154 AX-519546618 2 123447548 AGAAGACTGGGTGGCATTGCTGACTTGATGGACAT[A/G]AGTTTGAGCAAGCTCTGCGAGTTAGTGATGGACAG R 2 1 2 1 303000 f 74 goat 2_123447548_AF-PAKI 2 123447548 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795379 Affx-122930966 AX-385282335 2 123504007 AATTTTAATATATCAATAGTTCAGAGTTTTCTAAT[A/G]CAAAGAACTGTAGCTTCTGGTTCTCCCTGAGTATT R 2 1 2 1 101000 r 74 goat snp47652-scaffold670-6366 2 11643751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476170 Affx-1251763673 AX-586011597 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20000 f 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 539476425 Affx-1251763673 AX-586011826 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 4 1 4 1 20000 r 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562165169 Affx-1251763673 AX-606940581 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 f 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562165479 Affx-1251763673 AX-606940890 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 r 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562165523 Affx-1251763673 AX-606940935 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 f 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562165743 Affx-1251763673 AX-606941152 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 f 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562165783 Affx-1251763673 AX-606941192 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 f 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 562166126 Affx-1251763673 AX-606941534 2 123569219 TAAGTGTTCAAGATGGTCTAACTTTCAAGTTGGCT[-/TTATCATAAACTTTTTTTTTTCATAATTTATTTTTCTTTATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TATCATAAACTTTTCTGATTATACTTTGCCTTTTC - 8 1 4 1 20100 r 74 goat SV_376 2 123569219 - deletion junction SV-TF-chip 38439429 Affx-122930195 AX-123309766 2 123572121 CTTCAGTCTGAAGTAGTCTGCCTGTATCATTCCCC[A/G]CTCCCACCCCACAACGTTTACTTTTCTTAGTCTCT R 2 1 2 1 201000 r 74 goat snp47653-scaffold670-74480 2 11575653 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777101 Affx-122945823 AX-385264224 2 123651037 GCCACTGTGAAATATTTCTTATATAGTTTAAAGGA[C/T]AGATTTGGCCTTCACTTATTTCATTGTATTTAAGA Y 2 1 2 1 101000 f 74 goat snp47655-scaffold670-153396 2 11497091 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392223 Affx-122966267 AX-123262580 2 123688012 TTTGGGGCCAGTTTAAAATCACTAACATAATCTGC[A/G]CCATGGAGTTCTGGGTCATAGTCTCCCAGCTCAGA R 2 1 2 1 101000 f 74 goat snp47656-scaffold670-190371 2 11459478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770953 Affx-122963390 AX-385258116 2 123727230 AATTACTATGCAGAGCTAATGTCCTCAAGGACTAG[C/T]TGGGTTTATAGGGATGGTGAACTCTGCCATATGGA Y 2 1 2 1 201000 r 74 goat snp47657-scaffold670-229589 2 11417637 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796592 Affx-122975250 AX-385283538 2 123764156 TCATGTCATCCCTATAAAGAACACAGTCCAGAGCA[C/T]GGCTCATAATAAGTCATCATTAAATACTAGCATTA Y 2 1 2 1 101000 f 74 goat snp47658-scaffold670-266515 2 11380803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797302 Affx-122936347 AX-385284241 2 123823305 CTTTCTCTTGAAGCTGACTCTCCAGAAGTAGTTAT[A/G]TTGGCCCCATCCAATTGCAAGGGACTGAAAAGTAA R 2 1 2 1 101000 f 74 goat snp47659-scaffold670-325664 2 11321451 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424998 Affx-122941898 AX-123295344 2 123854641 ACAAGCCTCCTTGCCTCCCTCTGAATTGCAGCTTC[C/T]TCACCTGTACACTGGAGGTGACAATGATGGAGATG Y 2 1 2 1 102000 f 74 goat snp47660-scaffold670-357000 2 11289600 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796428 Affx-122929840 AX-385283378 2 123910185 ACTTCCTTAAATTACTCTTTAAGACTTGGTTGGAA[C/T]AGACAGCTTGGAAAACTTCGCAGGTTGGGAAGGGT Y 2 1 2 1 101000 r 74 goat snp47661-scaffold670-412544 2 11233919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413616 Affx-122950558 AX-123283965 2 123946145 CCTTGTCTTCCCAACTGTCTGTATTCTACATCATA[C/T]AAGATTGATAAGCGATACCTCTAACTTGCTTTGTA Y 2 1 2 1 101000 f 74 goat snp47662-scaffold670-448504 2 11197814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413501 Affx-122950640 AX-123283850 2 123975015 GACATAGATTGTTACTAGCGTTTAAACAAGTGATA[C/T]TTGAAAATGCTTAGAAAAGTTCCTGGGGCCAGTCG Y 2 1 2 1 201000 f 74 goat snp47663-scaffold670-477374 2 11168622 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429733 Affx-122937603 AX-123300074 2 124069662 ATCTAGCCAGCTTCATCTCTACAGGGTAATGCATA[C/T]GGTTCAGAGCTCCTTCCCCAAGGACCCCAGTCCCA Y 2 1 2 1 101000 f 74 goat snp47664-scaffold670-572021 2 11073905 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412496 Affx-122951375 AX-123282845 2 124154701 CATTGTCAGGCGGATTCTTTACCACTGAGCCACCT[C/T]GGAAACCCCACAGCTTAGATTTACAGAGAAACTGA Y 2 1 2 1 101000 r 74 goat snp47666-scaffold670-657060 2 10988232 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804473 Affx-986696640 AX-385291042 2 124220951 TTATATTCTCTAAAAGATATAAGGTGTATCAGGTA[C/T]AAGGTATATCAGATATAAGGTATATTCTCTAAAGA Y 2 1 2 1 600010 r 74 goat 2_124220951 2 124220951 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320797485 Affx-122920336 AX-385284424 2 124233522 GTACAGCAGAGAACAAAAGAGAGCACCTATCTTCA[C/T]GAATCTTATATTTTTAGTAGGGAAGCAGTGATTAG Y 2 1 2 1 101000 f 74 goat snp47668-scaffold670-735881 2 10908197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401856 Affx-122959425 AX-123272209 2 124280780 AAACTTGGAATTGGGACAGAAGCTCAAGGGTTCCC[G/T]GAATGGGAAGCAACATTGAGGTTAGAGGTGATTCA K 2 1 2 1 101000 r 74 goat snp47669-scaffold670-783139 2 10862089 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776283 Affx-122973271 AX-385263411 2 124322803 GTCCATTTATAGTCTACTTTCAAAATGTCTCATTC[A/G]CTTTGAAGTGTTAATTTGCTGGTACCAGTGTTTTC R 2 1 2 1 101000 r 74 goat snp47670-scaffold670-825162 2 10820184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397518 Affx-122962051 AX-123267873 2 124365944 GGTGGCTGAGAAGGTGAATCCAGGCTGGAGGAAGA[A/G]GGTCTGAATTGGGGAGCAGAGCTAGGACTCGACTC R 2 1 2 1 201000 f 74 goat snp47671-scaffold670-868303 2 10777397 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794334 Affx-122946541 AX-385281298 2 124395493 ATATTTTTTAAAAGAGGTCAAGAATTTTCAGAGAA[G/T]CAGAATTTTTGGAGATGGAAGGGTCCAATTCCTTC K 2 1 2 1 101000 r 74 goat snp47672-scaffold670-897852 2 10747845 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404426 Affx-122956765 AX-123274778 2 124435980 AATGCCATCAGTGCTCCTACTTGAGAAACCCTGGC[C/T]AAGAGCATGGAACTTGAATGCTTAGGTTGACTCAC Y 2 1 2 1 101000 r 74 goat snp47673-scaffold670-938339 2 10706455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431726 Affx-122936751 AX-123302067 2 124506565 TTCTTTATTACAATTACTCTCTTACTAATACCTTC[A/G]ATAATTTTGACTCTTGTACTGTCCTTGCTAAACCC R 2 1 2 1 101000 r 74 goat snp47675-scaffold670-1008924 2 10635416 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776792 Affx-122968620 AX-385263916 2 124540570 TTGGTTAGGTCAGCACAGTCTTGTTTCTGGGCTTC[A/G]GTTTTATTGGCTCAAAAATTTTTTGTTACCATATT R 2 1 2 1 101000 f 74 goat snp47676-scaffold670-1042929 2 10601277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391612 Affx-122966591 AX-123261969 2 124610126 CACTGAGCCACCTGGGAAGCCCATGAGACAGGACA[G/T]CAGTTTATATAATGCCACCCAAGTGAGACTGAAAG K 2 1 2 1 101000 r 74 goat snp47677-scaffold670-1112485 2 10531540 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419807 Affx-122945839 AX-123290155 2 124641388 TGCCCAATGATAGAGTTCCCTGCCATCTTGGCATT[A/G]GCGTGATCTTACAGGAGTTCTGTGGTTCCCGAGCA R 2 1 2 1 101000 f 74 goat snp47678-scaffold670-1143747 2 10500206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767353 Affx-122930352 AX-385254629 2 124677535 GCCACATCAGAGGGGGTCTATAATTCTTCTAATAA[C/T]AGGGCTCTTGATCTGGTTAATGCACTAGCTACCTG Y 2 1 2 1 101000 f 74 goat snp47679-scaffold670-1179894 2 10463291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380229 Affx-122975474 AX-123250587 2 124718061 CACTTTGATGTTGATATGATCATATTTATTATTAG[C/T]ATGCAACTGAAACCCAACACTTTCTCAGTTTTGTA Y 2 1 2 1 201000 f 74 goat snp47680-scaffold670-1220420 2 10422960 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382645 Affx-122973680 AX-123253003 2 124768983 TTTAATACTCACAGCAACCTTAAGGTAAGTAGAGA[C/T]AGAATTCAAACACAGGCAGTCCAACTTCAGAGCTA Y 2 1 2 1 201000 f 74 goat snp47681-scaffold670-1271342 2 10371129 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789581 Affx-122953753 AX-385276590 2 124806799 AAATCTCTGAAAAGGCCTCTTTGCCATTATCAGTG[C/T]ATAAACATGCTGGGAGAATGCCTGCAAAAACACAG Y 2 1 2 1 101000 r 74 goat snp47682-scaffold670-1309158 2 10332199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435515 Affx-122933413 AX-123305855 2 124835726 ATGGCAAGTTGGGAGGGTGGCGACGGGAGTCCCTT[C/T]GCAGGAGTCCTGTCCCCTCTGGGCCTCTGTTCCTC Y 2 1 2 1 201000 f 74 goat snp47683-scaffold670-1338085 2 10303289 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278050 Affx-1111836148 AX-519551540 2 124881504 CCTAGAAATTCCCTAAGTTTTTATCAGTTTTGGAT[A/G]ATTTTGAATAGCCAGCGATCTTTAATGTACCATCT R 2 1 2 1 101000 r 74 goat Random2.2K-273 2 124881504 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439103 Affx-122931112 AX-123309440 2 124885681 ATGCCAAAGCCTCATCTATTTGTGTAACTTTAGGT[C/T]AGGCTGGGGAGCTGCAAAGGGCCCCTAACAACTTT Y 2 1 2 1 101000 f 74 goat snp47684-scaffold670-1388040 2 10255073 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427549 Affx-122939497 AX-123297892 2 124963602 CTTATCACACTCACAATGTAACATACACACCTAAA[G/T]CCCAAGCTCCAAAGAGGCCACACACCCAGGTTCAC K 2 1 2 1 101000 f 74 goat snp47685-scaffold670-1465961 2 10179462 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796584 Affx-122961115 AX-385283530 2 124997373 CTGGACTCATCAAGCAGCCTTTTTGAATACTTATT[A/G]TATGCTCCTTAATCACTCATCTCATTCTTGCATAC R 2 1 2 1 101000 f 74 goat snp47686-scaffold670-1499732 2 10145818 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434273 Affx-122934782 AX-123304614 2 125092367 GGCAGGCTTGGAAGGATCCAAGCATCCATTGACAA[C/T]ATTCTTGGGTCCCTTGGGTCCTACAAGTAGATGGT Y 2 1 2 1 101000 r 74 goat snp47688-scaffold670-1594726 2 10051234 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449763 Affx-122922446 AX-123320098 2 125133592 CAGATGCCTAGACAAAGGAAATGGAATCTGCTGGA[A/G]TGGGAAGGGGAAATGGGAGGACAAAGAAGGAAGGC R 2 1 2 1 101000 f 74 goat snp47689-scaffold670-1635951 2 10011372 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779940 Affx-122942034 AX-385267039 2 125193122 GACAGAAACAAACTCATAGGTTCAACTGATTCAAA[C/T]GTAACATGATTTACTACGTTCCTATTACATACACA Y 2 1 2 1 101000 f 74 goat snp47690-scaffold670-1695481 2 9952181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774067 Affx-122925030 AX-385261205 2 125244093 TGCATAATCCCTGGTGATTTCCCTACACCTTGACC[G/T]CACCTTCTAAATTAGCTCCTTTGTACATATGACCT K 2 1 2 1 101000 f 74 goat snp47691-scaffold670-1746452 2 9900685 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423749 Affx-122942852 AX-123294095 2 125277229 TCTGTCTAAGCCACGACGAGTGTCTCTAACCCGGT[A/G]ACTCCAGCAGTCTCCTGGCCCACTCCCCTCCGCCT R 2 1 2 1 101000 f 74 goat snp47692-scaffold670-1779588 2 9867466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412742 Affx-122950527 AX-123283091 2 125308567 GTAGACCTGCTGGCTGTGAAGAAAAAGCAAGAAAC[A/G]AAGCGTTCTATCAACGAGGAGATCCACACGCAGGT R 2 1 2 1 201000 r 74 goat snp47693-scaffold670-1810926 2 9836255 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380371 Affx-122975344 AX-123250729 2 125340059 AGGCCGTTTTCACTGCAGGAGGGGGAAGGCAGGAC[G/T]GGCCTTTCATCCACAAGGGGCTTGGAAACAATTTT K 2 1 2 1 103000 r 74 goat snp47694-scaffold670-1842418 2 9804968 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429907 Affx-122938113 AX-123300248 2 125374584 TTTTTAGTCTGCAGTGTCAGCCCTGAGGAGACAGA[C/T]ATGGGAGTAGGCAGCCCTTGAACCTGAGGACCTTA Y 2 1 2 1 201000 r 74 goat snp47695-scaffold670-1876943 2 9769949 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771726 Affx-122969274 AX-385258883 2 125427347 TGGCTGTATCCCAGAAATACACTTATTGGGTCTTA[C/T]GGTACACAGATGTTCAACTGTACACGATATGACTC Y 2 1 2 1 101000 r 74 goat snp47696-scaffold670-1929706 2 9717367 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403316 Affx-122957831 AX-123273669 2 125458128 GCTCCAAGTCTCCGTACAGGCAAGTCGTAATGTTT[A/G]GAAAGATTCATCCCAAGAGATGCTCTTCGGGGGCG R 2 1 2 1 101000 f 74 goat snp47697-scaffold670-1960487 2 9686517 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428115 Affx-122939075 AX-123298458 2 125486718 TGTTCTAAGCCTTTCATTTTCTTATTGACGCTTGA[A/C]AACTATCCTATAAGGCAGGAGCTGTTGTCACCTGT M 2 1 2 1 101000 r 74 goat snp47698-scaffold670-1989077 2 9657402 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393162 Affx-122965534 AX-123263519 2 125522986 AGAAGAAGCAGATCACCAACTCCAGCACGGTGAGC[A/G]GCGCAGTCAAGGACCCACACGGGGACCAGGGCTGG R 2 1 2 1 101000 f 74 goat snp47699-scaffold670-2025345 2 9620945 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422198 Affx-122943502 AX-123292544 2 125599802 AGCAACAAGCTAGGCTTCAGTTCTGTCACTTAAAA[C/T]GACAAGATGACTGGACAAATCTGAGTCTGTAATGC Y 2 1 2 1 201000 r 74 goat snp47700-scaffold670-2102161 2 9544314 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775868 Affx-122928976 AX-385262999 2 125634026 CATTATCAATGCTTATCATCTGACCATTTCTGTGC[A/C]AAGCACAATCCTTCTTAGGACATACAATGAGGGAC M 2 1 2 1 101000 f 74 goat snp47701-scaffold670-2136385 2 9509950 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382648 Affx-122973678 AX-123253006 2 125684923 AGGAAGGAGAACAGGATGGGGCAAGTGCTGATCAC[A/G]TCTTGAGCACACTGATTCTTAAAGAACGCTGGCTA R 2 1 2 1 101000 r 74 goat snp47702-scaffold670-2187282 2 9458759 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387897 Affx-122969615 AX-123258255 2 125717904 ATGGCTGATGGAATATCCCCAAAATGGGAGACAAC[G/T]GGCACTGTTGTTTCTAGCTGTAGACCCTTCTTTAC K 2 1 2 1 201000 r 74 goat snp47703-scaffold670-2220263 2 9425971 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452302 Affx-122920679 AX-123322635 2 125758527 GGCTAAAGTTGGGACAGGTCAAACCTTTCCTGAGA[C/T]CTGCAGGGGGTTCCCACCTCTCCCAACCCTGCACC Y 2 1 2 1 101000 f 74 goat snp47704-scaffold670-2260886 2 9385084 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420888 Affx-122944618 AX-123291235 2 125834008 AATTGTGGTCTTCAATATACAAAATCTTTCAGGTG[C/T]AAATAACAGAATAAAACAGCTTAAACACTTGGGTG Y 2 1 2 1 101000 f 74 goat snp47706-scaffold670-2336367 2 9310575 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430805 Affx-122937460 AX-123301146 2 125844386 ATTCTAGAAAACAGCAGAACCATCCACCCAACTGC[C/T]CAGGCCAAAACCTAAATGTTTTGCTTCCTAGTAAT Y 2 1 2 1 101000 f 74 goat snp8256-scaffold130-7687 2 9299981 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396438 Affx-122962986 AX-123266793 2 125898238 ATTTCATGTTACGGTGGATGAGGACTTAACCTTGC[A/G]TACAAGGCCTACTTCTCCTTGCCTTTTCCTCCCAG R 2 1 2 1 201000 f 74 goat snp8257-scaffold130-61539 2 9245931 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450028 Affx-122922840 AX-123320363 2 125929616 CCCCTGCATTAGAAGGCAGATTCTTAACCACTGGA[C/T]CACCAGATAAGGCCTGACAATAAGTCTTGACAGTT Y 2 1 2 1 101000 r 74 goat snp8258-scaffold130-92917 2 9214815 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400897 Affx-122959744 AX-123271250 2 125971525 TGTGTTTCTCTGTGTCTGTGAATGCATGTCTGGAC[A/C]TGTGTCTCATTTATGTGCAATGAGGGCATGTGTGT M 2 1 2 1 201000 r 74 goat snp8259-scaffold130-134826 2 9172777 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386270 Affx-122970946 AX-123256628 2 126020330 GCCAAAATGAGGGGTGGAGTATGAGATGATGGTGA[C/T]GGAAGGCAATGGAAAACTGAGGAGTCTGTTAAATT Y 2 1 2 1 101000 f 74 goat snp8260-scaffold130-183631 2 9124075 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440065 Affx-122929738 AX-123310402 2 126090340 AAGCCAGTGTCCTGGAAGCCATAGCAACACCCTGG[C/T]GAGAGAAGACAAGACAGGAACTAGAATGGGGTACA Y 2 1 2 1 202000 f 74 goat snp8261-scaffold130-253641 2 9053807 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449742 Affx-122922461 AX-123320077 2 126127554 TATTTAGCCAATGGTCACACAGGCCCTGGCAGGTT[A/C]AGTGGTTTGCATAGAGGCACAGTAAGCTTGGGGCA M 2 1 2 1 201000 r 74 goat snp8262-scaffold130-290855 2 9016846 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278052 Affx-1111836149 AX-519551542 2 126154061 CAAGCAACTGTATTTCTAAGGTGTTTAAGCAGTCT[A/G]TGAAGTAAAGGACTTTTAGAAGTATAAACACCCTA R 2 1 2 1 101000 r 74 goat Random2.2K-276 2 126154061 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437096 Affx-122932184 AX-123307434 2 126161122 AGATTGGCAAGTATCATGGCATAACAGGTGGCTTA[C/T]GTTATTTTTAGGTATTTGCATCACAGGTTTAAATA Y 2 1 2 1 101000 f 74 goat snp8263-scaffold130-324423 2 8983108 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272934 Affx-1111833155 AX-519546620 2 126161417 TGTCCAACTCTGTGTGACCCCATGAATTGCAGCAC[A/G]CCAGGCCTCCCTGTCCATCACCAACTCCTGGAGTT R 2 1 2 1 103000 f 74 goat 2_126161417_AF-PAKI 2 126161417 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38414782 Affx-122949234 AX-123285131 2 126241178 TAAGTTCGAGTCTGTGTATATGTGGGCTTCCCAGG[C/T]GGCTCGGGGGCAAAGCATCTGCCTGCAAATCGAGC Y 2 1 2 1 103000 f 74 goat snp8265-scaffold130-404479 2 8903721 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380950 Affx-122975000 AX-123251308 2 126271269 CTGAATTAGACCTTCTCTGTAGGCTCCAGAAGCCA[C/T]GCCCAGCCTCCTCTAGTTCCTGGAGTCTCCCAGAG Y 2 1 2 1 101000 f 74 goat snp8266-scaffold130-434570 2 8873361 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388593 Affx-122969155 AX-123258951 2 126304799 GAAAGAGAGAGGAATCAAGGTTTTTTCATTTGTGC[A/G]CCCATCATTTGAAGGGAAGATGACCGTCCTTTATT R 2 1 2 1 101000 r 74 goat snp8267-scaffold130-468100 2 8838836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780152 Affx-122955663 AX-385267249 2 126336860 ATACTCATAGACTGCTCTACAAATCCTGAATGCCT[A/G]TTCACTTATTTACAGTGAGAAACGTGAGTGGAAAG R 2 1 2 1 101000 f 74 goat snp8268-scaffold130-500161 2 8807019 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375368 Affx-122979230 AX-123245727 2 126367579 CAGGCAACAGTGTATTGCTAATTGTTTGCTTTGTG[C/T]GGTGTGTCTGCTGCCTGTATAATCCAGTTTTCCTT Y 2 1 2 1 201000 f 74 goat snp8269-scaffold130-530880 2 8776142 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440894 Affx-122929226 AX-123311231 2 126416573 AAAGTTGTTTGTATCTGGCCCGCGGTGATTCTCTG[C/T]GCACGCCTCAGCTGCCAAGGGCAGCACTGGCCAGT Y 2 1 2 1 101000 f 74 goat snp8270-scaffold130-579874 2 8726791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432294 Affx-122936317 AX-123302635 2 126456497 ACCTTTTCTTTCGCCAGGCTGCCTCTTCTAAAGGC[A/G]TTAGGACCACACCACCCTCCACCGACCCAGGCCTT R 2 1 2 1 201000 f 74 goat snp8271-scaffold130-619798 2 8687015 C T 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408094 Affx-122954715 AX-123278445 2 126487270 TGGAAAGGAATGTCTGGGCCTGGTGTGACATCTCC[A/G]CGTCTCCAAGTCCTGTCTCCTCACAGAGGAAAAGA R 2 1 2 1 101000 f 74 goat snp8272-scaffold130-650571 2 8656873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781133 Affx-122966958 AX-385268218 2 126596717 TCACTTATGAGGTCTGCTCACGACTGAGCAGTTCA[C/T]ACATACATTGGCATGTCTAACAGTGACAGATTCTC Y 2 1 2 1 101000 r 74 goat snp8274-scaffold130-760018 2 8547620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385551 Affx-122971229 AX-123255909 2 126632716 CTGCTCTCCCTGGAAATCAGAGCAGACTTGCTGAC[G/T]GCTCTGCAGCAAACCAAGAGGTCCAGAGAGAAGCA K 2 1 2 1 202000 f 74 goat snp8275-scaffold130-796017 2 8511617 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405451 Affx-122956043 AX-123275803 2 126719639 ACAGAGAGAAAGAAAAAGGCCTTCCAGAGGGAAGG[A/G]TAGTAGGAACAGAGAGGGAGCTAGAACAGGCGTGA R 2 1 2 1 201000 f 74 goat snp8277-scaffold130-882940 2 8426507 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412457 Affx-122951404 AX-123282806 2 126751725 GAGGGGAAGGGTGGGAGGGGCAGGTCTTTCTTTGC[A/G]TGAATACAATATGCCACAGCCCACTGCAGCCTTTC R 2 1 2 1 101000 r 74 goat snp8278-scaffold130-915026 2 8394435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767196 Affx-122973409 AX-385254478 2 126835436 TGCTGTCCTCTAGCTTACTCCATTCACCCACAAGC[C/T]ATTCCTTTGCAGACTCACATCCACAATGCAGCGCT Y 2 1 2 1 101000 f 74 goat snp8280-scaffold130-998737 2 8310464 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797337 Affx-122938965 AX-385284276 2 126866350 ATCACTAGCGATGACACTTACATTAAGAAGGCTAC[A/G]GTTGCTATAACACCACACGCATGGTAGGAATGGTT R 2 1 2 1 101000 f 74 goat snp8281-scaffold130-1029651 2 8279708 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803167 Affx-122958443 AX-385290030 2 126896301 TGGGTATATATGTCCTGGACATCAAATTTGTTACT[A/G]TCTTTTAGGTAGTCTTGGTCACATTCTCATCCTTT R 2 1 2 1 101000 r 74 goat snp8282-scaffold130-1059602 2 8249237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413928 Affx-122949812 AX-123284277 2 126925995 GGCTGTCTCCATAGAGGGCTGCTTAGGACCAAGTT[C/T]AGGAAGTAGAATTGTCCTCCCGTAAACAGTGAGCA Y 2 1 2 1 101000 r 74 goat snp8283-scaffold130-1089296 2 8218437 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278054 Affx-1111836150 AX-519551544 2 126927246 CATCTCTAATACCCCCCACCCCTTTTCGTCCCTCT[A/G]TTATAGTGGCTATGTGCCTGCATCCTGCCATAGGC R 2 1 2 1 201000 r 74 goat Random2.2K-279 2 126927246 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427400 Affx-122940074 AX-123297743 2 126962003 GTGTGATGGTGAGATTGTGTGTGTGTGTGCGTGTT[A/G]CAGGAGTGGGACTGTCAATGGGACTTTCTTATTTG R 2 1 2 1 103000 r 74 goat snp8284-scaffold130-1125304 2 8181941 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436728 Affx-122932306 AX-123307066 2 126995453 GCTGGGAAAACTGCAGAGTGGATTCAGTTTCTGCT[A/G]CAAGAAGAAATTGCTGCTGCTGGGGTGAAGGGGTG R 2 1 2 1 101000 f 74 goat snp8285-scaffold130-1158754 2 8148605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378710 Affx-122977054 AX-123249069 2 127034435 AGATGCCGATATGATGAGAGGGGAAGCCTATGGAC[G/T]CTGCGACACTGCAAGGCTCAGTCTTGGCCCTACCA K 2 1 2 1 101000 f 74 goat snp8286-scaffold130-1197736 2 8109563 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388229 Affx-122969398 AX-123258587 2 127066370 AAAGTCAGGGGAGAAGGCACAGGCCACGATGGGAC[A/G]AGGGTCTCCGGTGCTTTCTGCATCAGCCAGGAAAC R 2 1 2 1 101000 f 74 goat snp8287-scaffold130-1229671 2 8077046 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402866 Affx-122958236 AX-123273219 2 127096201 ACAGCAAGTTAAAACCTAGGACTCCAGGTTCCAAG[C/T]TTCTTTTCAAACTTCTGGGCTTCCAGGGGTCATAG Y 2 1 2 1 101000 f 74 goat snp8288-scaffold130-1259502 2 8047008 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795097 Affx-122962653 AX-385282056 2 127183615 AGATGAAATATGGTTTTAAGTCTATCATTAATATC[A/G]TCAGAGTGATAAGAGAAGGTACTGCATCTGTGCAA R 2 1 2 1 101000 r 74 goat snp8290-scaffold130-1346916 2 7960797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784991 Affx-122949784 AX-385272038 2 127222564 ATGAACTTACCTGCCATCAGTAACGATGAATAATG[C/T]TCAGAAATGTAATCGTGTGGCTGCAATCCTATCCC Y 2 1 2 1 101000 f 74 goat snp8291-scaffold130-1385865 2 7922396 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407637 Affx-122954621 AX-123277988 2 127267429 TGTAATAACAGCAGCCCTACCCTCTCCGTGATCCT[C/T]GGGCTCCTACCCCGAACAGGTCTTAGTGAAGCCTT Y 2 1 2 1 201000 r 74 goat snp8292-scaffold130-1430730 2 7877857 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446303 Affx-122925647 AX-123316639 2 127317363 TTTCAAGAGACCCCGCTCCAAAGCTGAAAGAAAAA[C/T]GGAAATGCTGTAAGAAGGAAAACCACCCAACCCCC Y 2 1 2 1 202000 r 74 goat snp8293-scaffold130-1480664 2 7827824 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408921 Affx-122953953 AX-123279272 2 127387562 GCTGAGAAGCTGATGAGTAGACAGCGATCCAAAAA[G/T]TAGAGAAGTGTTGGGAAAACAGTAAGATTCAGACT K 2 1 2 1 101000 f 74 goat snp8294-scaffold130-1550863 2 7757419 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412028 Affx-122951734 AX-123282378 2 127436666 TAGTCAGCTTTCTGTTGCAATTCTAAGTGCCTCCA[A/G]AAAACCACCTTCATTCAACAAGTCAGTCATTCTGA R 2 1 2 1 101000 f 74 goat snp8295-scaffold130-1599967 2 7707478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453214 Affx-122920438 AX-123323547 2 127467806 CCACCTCAGTTTTCCCCAGTAATGTTCTTCTTCTG[C/T]TCCAGGTTCCAAAAATCAGGATCCTACATTGCCTC Y 2 1 2 1 101000 r 74 goat snp8296-scaffold130-1631107 2 7676429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414603 Affx-122949355 AX-123284952 2 127528825 TCATGATAATAATGGTGGTTCCCATTTGGAAAGCA[G/T]CTGTTGGGTGCCAGGCACCACCTGAGTGACTTGTT K 2 1 2 1 101000 f 74 goat snp8297-scaffold130-1692126 2 7615147 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439199 Affx-122931040 AX-123309536 2 127560776 ACATCTGCTTTCCCCCTCCTGAGGGCCTGGGCAGC[A/G]TCTTGGGCTTGGTCATGCCCCAGCACATCACAGAA R 2 1 2 1 101000 r 74 goat snp8298-scaffold130-1724077 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405530 Affx-122955984 AX-123275882 2 127595070 TTATATCACAACATTTTAAAAAGATGGGATTCATG[C/T]GAATGGGAAAAACAATCATATTCTAGAAGAATGAA Y 2 1 2 1 101000 r 74 goat snp8299-scaffold130-1758371 2 7548666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439232 Affx-122931016 AX-123309569 2 127636574 TCTTTGCAATCTTTTTGTAAGATAAGGTGTATTAG[C/T]GGTTTCTGAAGCCTGAATGCTCTGAACAATTTCAT Y 2 1 2 1 201000 f 74 goat snp8300-scaffold130-1799875 2 7506832 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447319 Affx-122924902 AX-123317655 2 127688235 TACAAAGGTTTTGCTGATACTGAGCACTGTAAGGG[A/G]TTCAGCCACCAGACCCTCATTTCCATCCAGGCTTT R 2 1 2 1 101000 f 74 goat snp8301-scaffold130-1851536 2 7455100 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435478 Affx-122933446 AX-123305818 2 127730655 AGTCAGACTGCTCAGGTTTAAATTTATGCTTCCCC[A/G]TCTATTAGCTGTGGCCCCAACATCTCTGGGCCTCA R 2 1 2 1 101000 r 74 goat snp8302-scaffold130-1893956 2 7412880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450433 Affx-122922049 AX-123320767 2 127778030 AGCTCCAGTCTCTCTCTCCCAGGAAGTCACAGATT[C/T]ACTGTGTCAAAGCCAGAATGCCAGGTATGGAAAGC Y 2 1 2 1 201000 r 74 goat snp8303-scaffold130-1941331 2 7365505 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388863 Affx-122969319 AX-123259221 2 127808411 AGGGACCTTGTCTGGCTCACTGTTGAATCTCCAGC[A/G]CCTTCCGTGGTGTCTGGCACACGGTCAGTGCCCAG R 2 1 2 1 101000 f 74 goat snp8304-scaffold130-1971712 2 7335190 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765155 Affx-122975322 AX-385252707 2 127854226 CAGTGATACAACCACTGGGAAAAGAATGCGTTTTA[A/G]TAAGAACAAAGTACACTCCTCAGTACTTACTCAAG R 2 1 2 1 101000 f 74 goat snp8305-scaffold130-2017527 2 7288771 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778406 Affx-122920426 AX-385265521 2 127889740 TTCTGTCTTGGCCTCTGCTTCTCAGAAGACCCAGA[C/T]GATCTCACCTTTTGTGAAAAGGTTGGAAAGTTAAA Y 2 1 2 1 102000 f 74 goat snp8306-scaffold130-2053041 2 7252648 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376638 Affx-122979027 AX-123246997 2 127924893 TGCCTCCCCATATTGCCAGGCAGGCTCTGCATTTC[C/T]CCTGTGTTAGAGGTGAGGAACAACTCAGGCTGTGA Y 2 1 2 1 101000 r 74 goat snp8307-scaffold130-2088194 2 7214762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784828 Affx-122931968 AX-385271875 2 127957397 TTGCTTGTTCGTCCTTAACTTCCCAACTGATTGAC[A/G]TAGAGTTGTTTTTCCTAGCAAATGCAAAAACTTCC R 2 1 2 1 101000 f 74 goat snp8308-scaffold130-2120698 2 7181877 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379257 Affx-122976255 AX-123249616 2 128011373 CCTCACTCCCATCTAAGCCCCAGGCTAAGCCGACA[C/T]GGCCTCAGAAAACTGCTGTCCTAAATTTCTGTTCC Y 2 1 2 1 101000 r 74 goat snp8309-scaffold130-2174674 2 7130582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377208 Affx-122978180 AX-123247567 2 128041157 ATAATGACAAGTTGGCCTTTGTCATCACAGTGCAG[A/G]CCCTTCCACAGGGCTTGGCTTCAAGGAGGGGCTTA R 2 1 2 1 101000 f 74 goat snp8310-scaffold130-2204458 2 7101053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424366 Affx-122941846 AX-123294712 2 128081488 AAAAAAATTTTTTTTAATTATTGTTGTAATATAAT[C/T]TGTATGCAGAAAATACGTAAGTCTTAAGTGTGTAT Y 2 1 2 1 103000 r 74 goat snp8311-scaffold130-2244789 2 7060664 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441917 Affx-122928599 AX-123312254 2 128177212 GATGATACTGAAACCCACTGTTGCAGCAAAAATAG[A/G]GATGAGACTTTTCTTACATTATAATGAGACTTTTC R 2 1 2 1 201000 r 74 goat snp8313-scaffold130-2340513 2 6964062 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403811 Affx-122957961 AX-123274163 2 128219039 CTCAATTCCTCCTGGAAGAGAGGCTGGAGATGATA[C/T]AGATGGATGAGGAAGGAAGATCCAGGGAGAATAAG Y 2 1 2 1 101000 f 74 goat snp8314-scaffold130-2382340 2 6922494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778415 Affx-122952454 AX-385265529 2 128285587 GGGGCCTTTGCATACACTGTACTCTATCTGAAAAG[A/C]TTTTCCTGTATCCTCTTTACCTGGGTAAAGTTAAT M 2 1 2 1 101000 f 74 goat snp8316-scaffold130-2448888 2 6855899 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385666 Affx-122971150 AX-123256024 2 128334778 AGTTTTCACAAATGAGACCAAAGGTTCAACGTCAA[A/C]GTGTGTCTGCTCTGCAGCCATTTCAACAACCCAGG M 2 1 2 1 101000 f 74 goat snp8317-scaffold130-2498079 2 6806893 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407237 Affx-122955368 AX-123277588 2 128381042 GGGACCAATCTTTTAAAGCAAAAAATAGAAATACT[A/G]TTTTACAGAAATACTATTACAGGGAAAATACTTTC R 2 1 2 1 303000 r 74 goat snp8318-scaffold130-2544343 2 6760614 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424182 Affx-122942521 AX-123294528 2 128436469 AAGTGCTAATGTTCTCTGAATGTCAGATGCTGGGT[A/G]TGCTGAGCATCTTCACATGGGAGGTGGGGACTGCT R 2 1 2 1 101000 f 74 goat snp8319-scaffold130-2599770 2 6704939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405287 Affx-122956852 AX-123275639 2 128496122 TGGAAACATATGGAACTCATTACCCTAAGTCGAAG[C/T]GGTCGCTGGCCAGCTGGCAGTTGGTCGGTTTGGGG Y 2 1 2 1 101000 f 74 goat snp8320-scaffold130-2659423 2 6645284 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402398 Affx-122959018 AX-123272751 2 128575684 TGGGTTCATTTCATTTCCCCAATAACCCTATGTAG[G/T]AAAAACTATTATCATCCTTATTTCATAAATAGGGA K 2 1 2 1 201000 r 74 goat snp8322-scaffold130-2738985 2 6566020 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403414 Affx-122957758 AX-123273767 2 128615973 ATTGACGCCACGGAAACTGACAAACGCTACAAATC[A/G]ATTTTTTCCTTTGAGAACCTGCTGTTAAACATTTA R 2 1 2 1 101000 f 74 goat snp8323-scaffold130-2779274 2 6525690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402917 Affx-122958195 AX-123273270 2 128658131 ACAAAAAAGTCCTGAGCATATATGTGCCTGCTACA[C/T]AGAAACCACCATTCTTATTATTCAGTTGTTACCTG Y 2 1 2 1 101000 f 74 goat snp8324-scaffold130-2821432 2 6483527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272936 Affx-1111833156 AX-519546622 2 128665956 AACGACCTTCTGGAGTGCTCACAAGGCTAAGAGGG[A/C]AGAATAAACCTTTTTTTTTTTTCTGATATAAATAC M 2 1 2 1 102000 f 74 goat 2_128665956_AF-PAKI 2 128665956 G T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433383 Affx-122935117 AX-123303724 2 128697450 GGAGATCAGTATAACTGTGAGCCATTATTGTTACT[A/G]TTGTTGTTATTTAGATAAACTGAAAGGAAAATACA R 2 1 2 1 101000 f 74 goat snp8325-scaffold130-2860751 2 6443953 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381133 Affx-122974568 AX-123251491 2 128746670 TGGCGTACCGATGACTTTCTCTTCCAGTCCCCTAA[A/G]AAAACAAGTTTTGTCAGCCTGAGTTCCCCTAATCT R 2 1 2 1 201000 r 74 goat snp8326-scaffold130-2909971 2 6394722 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414385 Affx-122949995 AX-123284734 2 128787850 CAATTTGTGAGCTCTGTATTTTGCAAGTTGTTTAC[A/G]TTTTTTGCCAATCTGATGAGAGAAGAAGATAGGAT R 2 1 2 1 101000 f 74 goat snp8327-scaffold130-2951151 2 6353510 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389849 Affx-122968161 AX-123260206 2 128848143 CCAGGGAGGCCCCACGTCGTATATGCAGTGCTTCT[A/G]TGAACGCAGCCGCAAACCCAGTAACGCATCTACGT R 2 1 2 1 201000 f 74 goat snp8328-scaffold130-3011444 2 6293493 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422565 Affx-122943760 AX-123292911 2 128953125 AATGTCGAGAGGATAAACTCAAGAGAAGTTACCTT[A/G]GCCCTGTTTTTCTAGTCTGTAAAATGGAAGGGTTA R 2 1 2 1 201000 f 74 goat snp8330-scaffold130-3116426 2 6187588 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382153 Affx-122974040 AX-123252511 2 129017744 TCTGAAGTCTGCGCTCTAGCACTGCCCCAGTGCTC[G/T]GCTCACTGCTGGTGTCCCATGTGGTCCTTTGTTTC K 2 1 2 1 103000 r 74 goat snp8331-scaffold130-3181045 2 6122670 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275693 Affx-1111834957 AX-519549262 2 129115753 GAAAGGAATCCATCTCTGCTGTGTTTTCATTAGGC[A/G]CAGACAGAAATTCTAGTGGTTAATGTAACTTCCCA R 2 1 2 1 101000 r 74 goat GoatD01.059919 2 129115753 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38417455 Affx-122947194 AX-123287803 2 129127295 TTCTGATTTCATTTGAAGCCGAGCTACCAAGTACT[A/G]TGCCCAGGGGTTCTACCACATTTTGACTAACCTGG R 2 1 2 1 201000 f 74 goat snp8333-scaffold130-3290596 2 6013043 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444285 Affx-122926764 AX-123314622 2 129168921 CCTGTCTTCAGTCCCATATTACAGATGGGGAAACT[A/G]AGTCACTTGTTCCACTAACTCAAGTAATAGGAGGC R 2 1 2 1 101000 r 74 goat snp8334-scaffold130-3332222 2 5972490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384120 Affx-122972824 AX-123254478 2 129217391 ACCCCCCAGGGGTAACTAATCTGGTAAAGAAGTCA[C/T]GGCCCCCCTGCTGTTCCTGGGAAGCTCCCAACCGA Y 2 1 2 1 101000 f 74 goat snp8335-scaffold130-3380692 2 5924230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399750 Affx-122960322 AX-123270105 2 129302407 CCCCTTCAGATTGGGAGCTGCCTGCAGGCAGTGCC[C/T]GGACTCTGAACAACATGCATTCAGGGCAGGAGGCC Y 2 1 2 1 201000 r 74 goat snp8337-scaffold130-3465708 2 5840648 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425106 Affx-122941230 AX-123295452 2 129358286 TGTGTCTTCTTCTCTCTTTCCTTTTCATCTGGCCC[A/G]TTTCCCATGCCCTCCTATGCATGAGCCAGGTGTGT R 2 1 2 1 201000 r 74 goat snp8338-scaffold130-3521587 2 5786063 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769428 Affx-122937722 AX-385256598 2 129396603 GATCCTTCACTGAAGGGACTCTGACCCTAATAAGG[C/T]GTTCTTAAGTAGAGCTGAAATCTCTCTTTCTGAAA Y 2 1 2 1 101000 f 74 goat snp8339-scaffold130-3559904 2 5747343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396903 Affx-122963217 AX-123267258 2 129425817 GCATCCTGTCCCCAAACCCCACTGCCTGCAGTGCA[C/T]GATGAATTAATATTTTTTTATAAAACCTGTAATTA Y 2 1 2 1 201000 r 74 goat snp8340-scaffold130-3589118 2 5717470 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441644 Affx-122929202 AX-123311981 2 129473505 GCGGGCCTTGCTCCTGAGCATCTATTTGCTGTCTG[A/C]CTTACTCACCTGTGACGAGCAAACACCTTTCCATC M 2 1 2 1 101000 r 74 goat snp8341-scaffold130-3636806 2 5669979 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769453 Affx-122967163 AX-385256623 2 129510150 CAATAAAAGTTTCGTTATTGTCTGAAAATAGCAAA[C/T]GTATTCCTAAAAACTGGATGCAATTTACTATGTAA Y 2 1 2 1 101000 f 74 goat snp8342-scaffold130-3673451 2 5633270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802914 Affx-122924432 AX-385289811 2 129560672 CCAAATATATATACTGTTAGTAAGATTTTCTTCAA[C/T]GGAGGGAATTTAATTGCTGAAAACAGGGAAAGAGA Y 2 1 2 1 101000 r 74 goat snp8343-scaffold130-3723973 2 5582731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433893 Affx-122934404 AX-123304234 2 129597493 CGGGGGGAGAAGACAGGTGCTCAGTTGTTTAAGCC[A/G]TTGGCTCATTCATCCATTTGCCTACCATGTATCAA R 2 1 2 1 201000 r 74 goat snp8344-scaffold130-3760794 2 5547426 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384368 Affx-122972234 AX-123254726 2 129638803 CAGCCAGTGGAAGGAATGCAGACATCTGGCTCCCC[A/G]TGCAGCGTCTGCTCTTCTTGTTGGTGCTAAATCTT R 2 1 2 1 101000 r 74 goat snp8345-scaffold130-3802104 2 5505530 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768391 Affx-122935985 AX-385255571 2 129678539 CTGAACAAACTGCCGTTTCATGGTGGAACGGCTCT[A/G]CTTGGTGCTTCTTACACTGAGTTGAAATCTGCTCC R 2 1 2 1 201000 r 74 goat snp8346-scaffold130-3841840 2 5465752 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428213 Affx-122939446 AX-123298556 2 129709457 AGAGAAAAGAAGGAAAAGAAAGTCTCTCTCCCTCT[C/T]AGCCTACCCCAGCTACACTATCCAGAAATTTTTTT Y 2 1 2 1 101000 r 74 goat snp8347-scaffold130-3872758 2 5434382 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425298 Affx-122940954 AX-123295644 2 129778513 GCACGAAGTGTGCGACACTTTGCGCATTTTCTTCC[A/G]TTTCCCACTTGTCCTTTCTTCAGGATAGGTGTGTA R 2 1 2 1 101000 r 74 goat snp8349-scaffold130-3941814 2 5367649 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432992 Affx-122935258 AX-123303333 2 129818296 CCTCCAGAACGGAGAGAAAGAAGCTTCTGTTGTTT[A/G]AGCCACCCAGTCTAGGGTATTTTTATTACAGCAGC R 2 1 2 1 103000 r 74 goat snp8350-scaffold130-3981597 2 5328234 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377704 Affx-122977406 AX-123248063 2 129869185 TTGGAGATCTACGCTGAAGTTATGTGCAGCCTACA[C/T]GACAAGATATCTGGACTGTGTGTTGAAATAATGCC Y 2 1 2 1 101000 f 74 goat snp8351-scaffold130-4032486 2 5279720 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414536 Affx-122949508 AX-123284885 2 129934389 TGGGTTCCTGGCACTATTTCTGCAAATGTTCTTTA[C/T]GCTTGAAATTATTTCCAGATAAAAAGTGTCTTAAA Y 2 1 2 1 101000 f 74 goat snp8353-scaffold130-4097690 2 5214859 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436077 Affx-122932693 AX-123306416 2 129969898 ACAGTCTTTAACACTAATTACAGTATTCTTTAATT[C/T]CACCTCCATTTCTCCCCCTGGTTTCATCTGCTCCT Y 2 1 2 1 201000 f 74 goat snp8354-scaffold130-4133199 2 5179270 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429092 Affx-122938269 AX-123299434 2 130009324 CAGGATGTTCTTGGGGATGCAGCCTTGAGCAAGAA[C/T]GGTCCCAGCTTTCTTGGGGCTGCTTTAGTCTACTA Y 2 1 2 1 201000 f 74 goat snp8355-scaffold130-4172625 2 5139817 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406574 Affx-122955092 AX-123276926 2 130047736 GGAAAGGTTGAAAAATTTGTTCAAGACTGCACAGC[A/G]AGGCAGTACAGACAGGATTCTCCATCAGACTGAGA R 2 1 2 1 101000 f 74 goat snp8356-scaffold130-4211037 2 5101584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394370 Affx-122964640 AX-123264725 2 130115763 GGCTGTTCAAACAGTACAGCTGGGCTTGAACCCCC[A/G]TATTAGACCACAGAGCCTACTCCCTTAGCTGCCCT R 2 1 2 1 101000 r 74 goat snp8357-scaffold130-4279064 2 5033497 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793460 Affx-122930825 AX-385280437 2 130177873 GTGTGTTATAATTTTTAAGGCAGATGGTAAACCTT[A/C]CTCTATGTCTTGAGGTTTCATCTTGTTGTGGGACA M 2 1 2 1 101000 r 74 goat snp2021-scaffold1059-1431982 2 4970733 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785576 Affx-122979127 AX-385272620 2 130230451 AAAACATTAGTAATCCTTGACTCCTCTTTTCCTCC[A/G]TATCCAGTCGGCAAATTTCTTCAGCTCTACTTTGA R 2 1 2 1 101000 f 74 goat snp2020-scaffold1059-1379404 2 4917390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378796 Affx-122976990 AX-123249155 2 130299246 CATCTGCAAAATAAGGCTGATGATGAACATAAGAG[C/T]ACCTACTTCAAAGGGTTTTGCCAAGGATTAACTAA Y 2 1 2 1 101000 f 74 goat snp2018-scaffold1059-1310609 2 4848689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425659 Affx-122940878 AX-123296005 2 130337330 TAGATGAGGGAACTTAGGAAAAGTACCCTGCACGG[C/T]GCAGGTGCCCAATACGTGCTTGATCCCTGAGTGAC Y 2 1 2 1 101000 f 74 goat snp2017-scaffold1059-1272525 2 4810894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412339 Affx-122950839 AX-123282688 2 130388646 GCCTTCGCCAGACTCCCAGTGCCCCGGGGAGCAAG[A/C]GGAGCAGGGAACTGGCAAACAGGTAGAGGGCTCAC M 2 1 2 1 101000 r 74 goat snp2016-scaffold1059-1221209 2 4759699 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416217 Affx-122948228 AX-123286566 2 130428225 GTGGGAAAAACACACATTCATCTCCTACCATTGCC[A/G]ATCCACCCACTCAAGGCTGCTTCCTTCTTTGTGGT R 2 1 2 1 201000 f 74 goat snp2015-scaffold1059-1181630 2 4720020 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435730 Affx-122933293 AX-123306069 2 130492573 TGTTGCAAGAGGTGATTTTGATCCTGCAGAACAAC[G/T]TCACCCGGCACATCACACGGCTAGAGTTCATCGGA K 2 1 2 1 101000 f 74 goat snp2014-scaffold1059-1117282 2 4655005 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388926 Affx-122968832 AX-123259284 2 130545285 TCCTCTAACACGCGGCTCAGACACCACCTCCTCTG[C/T]GAAGCCCCCTCAGTCAGGACCCTCAAGGCTGTGCG Y 2 1 2 1 201000 r 74 goat snp2013-scaffold1059-1064570 2 4602598 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387650 Affx-122969847 AX-123258008 2 130581204 TGTTACACAAGTTTGGACAGAGAAACATGGGCTAG[C/T]TGTGGGAGGGATTCAAACTGACCACCGGTCTCTCC Y 2 1 2 1 201000 r 74 goat snp2012-scaffold1059-1028651 2 4566773 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377523 Affx-122977475 AX-123247882 2 130627489 CATCACGTTCTGGAGTAGTATCAATGAAGCACATA[C/T]ACATGTATCAAAAAGACAGTCAAAATATTCTTTCC Y 2 1 2 1 101000 f 74 goat snp2011-scaffold1059-982366 2 4521185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798511 Affx-122978152 AX-385285444 2 130673358 TTTAAACCCACAAAGCATTAAGTGAAGATACCTTT[A/C]AGAGATCTAATACTGAATTCTACCTTGAAGGAGGA M 2 1 2 1 101000 r 74 goat snp2010-scaffold1059-936497 2 4475288 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394954 Affx-122964284 AX-123265309 2 130733573 GTTTTCTGGAAATCACACTGACTTCTGAAATAAAA[C/T]AATATTGCAGTGAAAATAAAGGGACATTATAAAAA Y 2 1 2 1 101000 f 74 goat snp2009-scaffold1059-876282 2 4414530 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437292 Affx-122931984 AX-123307630 2 130774690 TTGGAGTGAGTGGGATGGCCCTGTACGTAGCCAGA[C/T]AGGGGTCGTCTTTTCCTGTTATACTTCTGAGTTTC Y 2 1 2 1 102000 r 74 goat snp2008-scaffold1059-835165 2 4373075 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377058 Affx-122978294 AX-123247417 2 130815935 TCCAGCATTTATTTGCCAGGGCGTTTGCATCTGTT[A/C]TTTGACTTAATCCTCACACTGTTCTATGAGGTAGG M 2 1 2 1 201000 r 74 goat snp2007-scaffold1059-793920 2 4331418 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387461 Affx-122970364 AX-123257819 2 130880266 CCCGGGTCTCCCACATTGCAGGCAGACGCCTTACC[A/G]TCTGAGCCAGAAAGGAGGGTATTAATGAGAAATTA R 2 1 2 1 103000 r 74 goat snp2006-scaffold1059-729589 2 4266599 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408286 Affx-122953791 AX-123278637 2 130918440 CTGGGACTCCTAGGTAATTAGTGAATGAAAACTAC[G/T]AATGGGGGTGCTATGTTCTAAAAATCTTAACAGTT K 2 1 2 1 101000 f 74 goat snp2005-scaffold1059-691415 2 4228350 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800121 Affx-122972129 AX-385287044 2 130947979 TAAGTATCTACAAAGTGTGATTTGTTGTCAGAAGG[C/T]GTAGTCTTATTTCAGAGCAAGTTTCAGAAGTTGCC Y 2 1 2 1 101000 r 74 goat snp2004-scaffold1059-661876 2 4198674 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452300 Affx-122920681 AX-123322633 2 130985203 AAGAAAGACAGTGATGAGTGTTTGAGCTAAGTGAG[C/T]GAAAGGGAAACAAGAGTACCAAAATAATATGGTTT Y 2 1 2 1 101000 f 74 goat snp2003-scaffold1059-624652 2 4161427 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379804 Affx-122976237 AX-123250162 2 131014952 TCATACCTGTGGGTGCTTCAGTCTTGCTCTCAGCT[A/G]TGACACAGCTCTAAGGCAGGGCAGGTGTACCAGCA R 2 1 2 1 201000 r 74 goat snp2002-scaffold1059-594903 2 4132246 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391638 Affx-122966570 AX-123261995 2 131102124 TAGCTGGCCTGCGGACCAAAGCAGAAAGGCTCCAC[A/G]GGAAAATGCCTTTTGGAAACACTGGGTTAGAGAAG R 2 1 2 1 101000 r 74 goat snp2001-scaffold1059-507731 2 4044884 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386282 Affx-122970937 AX-123256640 2 131146469 CCATGGTTGAGGATAAAATCTACTTCCTCCAGTCG[A/G]CCTCCAGTCCCCAGTGACCCGGACAGCTCACCCCA R 2 1 2 1 101000 f 74 goat snp2000-scaffold1059-463386 2 4023897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437731 Affx-122931734 AX-123308069 2 131189012 ATGTGCAGGAAGACGACGCTGAAGATGAAGAGCCC[A/G]AGCATCATGGAGAAGGCGCTGGCGTAGTAGGGGTA R 2 1 2 1 101000 f 74 goat snp1999-scaffold1059-420843 2 3981243 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271854 Affx-1111833158 AX-519545637 2 131215364 ATCCTCTCCGGTAGCTGAAGGGTGTGTGGAGTGGA[A/G]GTCAGACCCTTCCTGTGCGGGTGCTGGAGAAAATC R 2 1 2 1 202000 r 74 goat 2_131215364_AF-PAKI 2 131215364 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401153 Affx-122959370 AX-123271506 2 131228065 GTGTGCTCTCACACTGGGTTGACTCCCTGTGTACA[C/T]AGCTCCATTTTTGATCCTAAAAAAGAATTTTGTGT Y 2 1 2 1 303000 f 74 goat snp1998-scaffold1059-381790 16 28891921 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382260 Affx-122973943 AX-123252618 2 131292445 TCCTTTGATGAGGGGATGTCCAACCCGGAAGGAAT[C/T]AGTCCAACTTCTTCATCTGGCACGACCGTGTCCTA Y 2 1 2 1 201000 r 74 goat snp1997-scaffold1059-317410 2 3877149 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417185 Affx-122947321 AX-123287533 2 131325573 AACCTGGGCTCTCTTTCAAAGCACCTGCTAAAGGA[A/G]CACAGAACAGCAGATGCTTTTGAGATGCTCCAAGG R 2 1 2 1 101000 f 74 goat snp1996-scaffold1059-284282 2 3843922 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415522 Affx-122948675 AX-123285871 2 131355119 TTTGCAACAGGCCCATCATCCAGGTAGGTGTTACT[A/G]TCTCCATTTAACAGATAAGCAAACTGAGGCTCAGA R 2 1 2 1 101000 f 74 goat snp1995-scaffold1059-254736 2 3814218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399826 Affx-122960263 AX-123270181 2 131414474 GAGACTGGATGGTTAACTAGATTCATAATCTGTCA[A/C]GTGACCCAATTTGAGGGATGCTGATAAATGAATCA M 2 1 2 1 101000 f 74 goat snp1994-scaffold1059-195381 2 3755879 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381389 Affx-122974382 AX-123251747 2 131469158 AAGCTTGCTTTCTCATTGGTGTGTGTGTGAGTAAA[G/T]CTGACTGTAACAGCTGGGGGCCTCCTTGTCCCTGC K 2 1 2 1 101000 f 74 goat snp1993-scaffold1059-140697 2 3701631 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427842 Affx-122939730 AX-123298185 2 131506543 AACAGACACTGAGGAGGGGCTGACCCAGCATCACA[C/T]GGCTGGACAGTGATAGCTGAGGTTCAAACCCGGGG Y 2 1 2 1 201000 r 74 goat snp1992-scaffold1059-103312 2 3664475 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449744 Affx-122922459 AX-123320079 2 131557232 GCCTGAAAGAGACAAAGTCTTTGAGGGAGGAAAAA[C/T]CATGATCAAGCTGGCCAGGGATGCGTCACTGTGAT Y 2 1 2 1 101000 f 74 goat snp1991-scaffold1059-52623 2 3614876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439772 Affx-122930512 AX-123310109 2 131587507 CCAAGTTGTGGAATGAACTGTGTCCCACAAAAAAC[A/G]CATATGTTTAAGTCCTAACCCCTGTACTTCAAAAT R 2 1 2 1 101000 f 74 goat snp1990-scaffold1059-22348 2 3583972 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422347 Affx-122943445 AX-123292693 2 131616130 TAATGTGGTGCCTATATGCTACCTTAACTGCTTCC[G/T]CTCCCAGCCCCATCTTCCTCAAACTGAGAACATGG K 2 1 2 1 101000 f 74 goat snp22271-scaffold220-6176 2 3557778 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390542 Affx-122967222 AX-123260899 2 131671619 GGACTCCAGGTGAACAGCATAATGGTGACCCTTAC[A/G]GACCTTGCAGGCTCCTTCCTCCTTCTGTTCTCCAT R 2 1 2 1 201000 f 74 goat snp22272-scaffold220-61665 2 3501685 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450173 Affx-122922313 AX-123320508 2 131709295 GGGACCCTCTAAACTTAACCCACTGAATCAAGATC[A/G]CTGTCTAAGTTCTCCAAAGCTGAAGTGGGGACTGA R 2 1 2 1 101000 f 74 goat snp22273-scaffold220-99341 2 3463848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415501 Affx-122948691 AX-123285850 2 131791179 GCAGGCTACAGTGTGTGGGGTCACAAAGAGTCAGA[C/T]GTGACTGAGTGATTAATGCTTTCAGAGAGGAGGCA Y 2 1 2 1 103000 r 74 goat snp22275-scaffold220-181225 2 3381613 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416847 Affx-122948104 AX-123287195 2 131873585 TTCCTTAGTGTCCTCTGTGCTGGGCACCAGAGCTA[A/G]ATGTTAATTCAAAGGGACAGTGCCCCTGCTTCAGG R 2 1 2 1 201000 r 74 goat snp22277-scaffold220-263631 2 3299548 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783807 Affx-122938984 AX-385270863 2 131916378 TGTGATTTCAGGCGATCAGGACTACTGTAAGCGCC[A/G]TCTGTGTCAATGTGATAAAAGAGCTGCCGATTGTT R 2 1 2 1 101000 f 74 goat snp22278-scaffold220-306424 2 3257108 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803530 Affx-986696098 AX-385290341 2 131935537 CCTGGGTTTGATCCCTGGTCAGGGAGCTAAATCCC[A/G]CATGCCATAACCAAGATCCATCACAGCCACAGAAA R 2 1 2 1 600010 r 74 goat 2_131935537 2 131935537 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 38398547 Affx-122961525 AX-123268902 2 131954563 ATCAGATGTACACAAACTCATGGACACAGAGGGAC[A/G]CACACAGAGACACATAGGCACACAGACACACGTGT R 2 1 2 1 101000 f 74 goat snp22279-scaffold220-344609 2 3218098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403366 Affx-122957793 AX-123273719 2 132067519 CATCACTGGAAGCTCTCTCAGATGACTGAAGGGAG[C/T]GTTGTGGTCTTTGCTGGAACAATGAATTCTTTGTG Y 2 1 2 1 101000 r 74 goat snp22282-scaffold220-457565 2 3104361 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395797 Affx-122963653 AX-123266152 2 132149741 ACCTCTCTGTGCCTCGGCTGATTCATTTGCGAGGC[A/G]AAGCAGATTGCCCTTGCCTTTCAGGGACTCACCAA R 2 1 2 1 201000 f 74 goat snp22284-scaffold220-539787 2 3027549 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278058 Affx-1111836152 AX-519551548 2 132152472 TTTTCTTATTTTTTAAAAATATCTTTTATAAATTA[A/G]CAATGTGGAATTTAAGACATACAAAAGAGTGTGTA R 2 1 2 1 102000 r 74 goat Random2.2K-283 2 132152472 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384861 Affx-122971948 AX-123255219 2 132182648 TCAGCAAAAGGCAGCTACCTCTTTGCTGTTCATCA[G/T]AGCTGTCAGTTGGGAGTCTCGGCATCCTGGCATCG K 2 1 2 1 101000 f 74 goat snp22285-scaffold220-572694 2 2995352 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449651 Affx-122922581 AX-123319986 2 132275886 TGGAACAAGAGATAAATAAACTTCCTCACTGAACT[A/G]CTAGGAGAGTAAAAACAGGATGGTATGATGGCATG R 2 1 2 1 101000 r 74 goat snp22287-scaffold220-665932 2 2901895 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437039 Affx-122933109 AX-123307377 2 132319171 TCAGTATCAAATTTTATTCCCTGAAATATCTTGTT[A/G]CATCTGACTTGAAGAGCATCATTCTTGAAAATGAC R 2 1 2 1 101000 r 74 goat snp22288-scaffold220-709217 2 2858654 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434754 Affx-122933905 AX-123305095 2 132348683 AAAGGTAAACTTCCCAAGGGCAATGATTTGTGTGC[A/G]TTTTGTTCCCTGCCAAGGACAGTGCCAAAGACGAT R 2 1 2 1 201000 r 74 goat snp22289-scaffold220-738729 2 2828264 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401301 Affx-122959856 AX-123271654 2 132385634 AGGCTTTTAGAGATCAGGTCTCTGGGGTGAGGAGG[C/T]GGAGGCTTGCCTGCTGCGGGAGCTCTGGCCCTCTT Y 2 1 2 1 101000 f 74 goat snp22290-scaffold220-775680 2 2791684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394605 Affx-122964420 AX-123264960 2 132415222 CTAGGTACGACTTTAAGAGGCAAGGGCCGAAGCTC[A/G]CTCCCAAGACTTAACCAGCATCACCCTGTCTATGA R 2 1 2 1 201000 f 74 goat snp22291-scaffold220-805268 2 2761810 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433482 Affx-122935041 AX-123303823 2 132472942 ATTTGACAAGAGGAGGAGGTGGGGTAGGGTTGGGA[C/T]GAGGGCAGGGAGAGAGTCATTAACTGATTGACTGG Y 2 1 2 1 101000 r 74 goat snp22292-scaffold220-862988 2 2704062 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451377 Affx-122921217 AX-123321710 2 132518561 TTCTCATGGGAAGCTTTTTAGCTGTACACAGACTC[C/T]CTGAGAGTCTTGTCTCTGCCACCCTCTTTACCTTC Y 2 1 2 1 101000 f 74 goat snp22293-scaffold220-908607 NW_017189554.1 39948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404155 Affx-122957079 AX-123274507 2 132555542 TCAAAAAGTTTCAGGTGGCTTCAGGACTTTCCCAG[C/T]GGTCCAGTGGTTAAGACTCTGTGTTTCCAATGCAG Y 2 1 2 1 101000 f 74 goat snp22294-scaffold220-945588 2 2669860 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404200 Affx-122957674 AX-123274552 2 132615813 GCCGGCCTCAGGTTCAGTTTATTGAAAACCACGAG[C/T]GCAGTAGTGTTTCCATTTGTTAGTCATCGTCCAGG Y 2 1 2 1 101000 r 74 goat snp22295-scaffold220-1005859 2 2609074 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404089 Affx-122957133 AX-123274441 2 132657624 TTAATACTATATTTAATATTGCATGTAAAATTATC[A/G]TAACTGAACAATACTGTTACTATGGTGATCTAGGT R 2 1 2 1 101000 r 74 goat snp22296-scaffold220-1047670 2 2566911 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413406 Affx-122950711 AX-123283755 2 132690073 CTGTCCCCATCGTTGCATGGCTGCAGAGCTGTCCC[A/G]TGTCCCCGTGGAGAATGCGGGGGGTTGGACGTGCG R 2 1 2 1 101000 f 74 goat snp22297-scaffold220-1080119 2 2534427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414201 Affx-122949655 AX-123284550 2 132752491 CCCCTCTGTCCGCACAGCACCCACCTTATTTTGGT[C/T]ACTCCCCACAGCCCTCTTCTCACCGGGGCAGTGCC Y 2 1 2 1 101000 f 74 goat snp22298-scaffold220-1142537 2 2472750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411038 Affx-122951964 AX-123281388 2 132808020 AAGGAGGTAATTGAACTACAGTGCTACAAACTCGG[C/T]GAAAGTTAGCCATTATTAATTTGAATTAGATTGTG Y 2 1 2 1 101000 f 74 goat snp27452-scaffold2925-417572 2 2422980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424778 Affx-122941402 AX-123295124 2 132853538 CAGAGCGGAAAAAGACTAGAGCTGTAACCTAGCAT[C/T]GCACAGACAAGGAGAGAGTGTTGCCAATAGACATT Y 2 1 2 1 101000 f 74 goat snp27451-scaffold2925-372054 2 2377168 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419590 Affx-122945386 AX-123289938 2 132899800 GTTTCCCAAAGGAAGAGGCTGCACGGATGTCCTTA[C/T]AGAAGATGCCTCGAGGGGAAGGCTCTGGAATGTCC Y 2 1 2 1 201000 f 74 goat snp27450-scaffold2925-325792 2 2330570 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409507 Affx-122953634 AX-123279858 2 132938668 AGTCTCCCCGGATGGGGCTAAAAATAAGGTAGATG[C/T]GAAAATGTCCACGAAGGAGTCTATGGGCGGAGGGT Y 2 1 2 1 201000 r 74 goat snp27449-scaffold2925-286924 2 2296985 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38428649 Affx-122938660 AX-123298991 2 132985392 TTGTCGGGACCTATGATGGCCACCACGCGGGGCAC[A/G]TAGTGGCTGTAGTCCTCCTGGATGGGCAGGAAGTA R 2 1 2 1 101000 r 74 goat snp27448-scaffold2925-240200 2 2250497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384632 Affx-122972161 AX-123254990 2 133020710 CAAACCCAGGCCTTCCTGGCTCTGAAGTCCACAGG[C/T]TTAATTACGCTAAAGTGCCTGCTCGATAGGGGTTA Y 2 1 2 1 101000 r 74 goat snp27447-scaffold2925-204882 2 2214958 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401384 Affx-122959227 AX-123271737 2 133059731 GCAGAGCTAGAATGGACTGAGAGACCCAGAGAAGA[C/T]TGGTGTGGGCTCTACCCAGGGTAGAGTTTTGAATA Y 2 1 2 1 201000 f 74 goat snp27446-scaffold2925-165861 2 2175518 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450839 Affx-122922245 AX-123321173 2 133125703 TCTAAAGGGCTTTTGCTAAATGTTGTGAATCCAGA[C/T]GTAGATGAGACATAGTCCTTGCTTTTACAGACGAC Y 2 1 2 1 101000 f 74 goat snp27445-scaffold2925-99889 2 2108792 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775450 Affx-122977715 AX-385262581 2 133166886 CAACTCTAAAAATAATGGAATCACAGCATCCCAGC[A/G]TCTCAGAACCATGTGATGTTAGAGCCAAAAGGAGG R 2 1 2 1 101000 f 74 goat snp27444-scaffold2925-58706 2 2067806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444651 Affx-122926467 AX-123314988 2 133196053 GATTTGGGACTTCTGCGGGGAGTGGGGTTTGAGTC[A/G]TTCTGATGGCCACCCCAGTTGAGAGCCATTGGTCT R 2 1 2 1 201000 r 74 goat snp27443-scaffold2925-29539 2 2042758 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387448 Affx-122970377 AX-123257806 2 133228545 TCTCCGGGTTCCGGAGGCCAGAATTCCTCAGGGCC[A/C]TGTTGGAAGAGGCACCTTTCCCCCTACTCCCCAGC M 2 1 2 1 101000 r 74 goat snp1812-scaffold1050-2854 2 2018573 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451191 Affx-122921331 AX-123321525 2 133273009 CTGGGCCATGGGGTGGGACTGAGGCAGGGTGAAGA[C/T]GATAAAAATTTAAGGAGACACTCGCTCTCATGGTT Y 2 1 2 1 101000 r 74 goat snp1813-scaffold1050-47318 2 1974008 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453192 Affx-122920455 AX-123323525 2 133305214 GACGCGCATCTTCATGGGACTTGCCCCCTAGTGAA[C/T]GGAGACAGGTAATTTGCTCAGTGGATCTGCTGGAG Y 2 1 2 1 201000 r 74 goat snp1814-scaffold1050-79523 2 1943318 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379830 Affx-122975819 AX-123250188 2 133339211 ATGAGCATGCTTGAGTCATCAGCACAGGCGGCAAC[A/G]GCAAGAAGCCTGAGCTTCCTTTCCCATCCCGTCTG R 2 1 2 1 201000 f 74 goat snp1815-scaffold1050-113520 2 1908972 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429386 Affx-122938544 AX-123299728 2 133373338 CAAGCCAAAGAAAAATCACACGCAGGAAAACAGAC[C/T]GGAGGGACCCACACCACAGCGGGGGTTTGTCTTTG Y 2 1 2 1 103000 f 74 goat snp1816-scaffold1050-147647 2 1874619 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448994 Affx-122923106 AX-123319329 2 133410959 CGTAGGGTAAGCAGACCCTGTGACCAGGGGCAGGC[A/G]TGGGTGGTCCTCATTAAAGACACCAGACACAGCCA R 2 1 2 1 101000 r 74 goat snp1817-scaffold1050-185268 2 1836674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424997 Affx-122941899 AX-123295343 2 133445185 GCAGCTTGGGGACGGGTGTCCAGAGGAAAAGAGAC[A/G]CCAGCGTTCAAGAGCCTCTTCCTGGAGCCCCATGT R 2 1 2 1 202000 r 74 goat snp1818-scaffold1050-219494 2 1802279 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380865 Affx-122975059 AX-123251223 2 133489874 CTGATCTTGCTGAATTCCCAGATGCCTAGGAGGAG[C/T]GGCTGAGAGAGCAGCCCAAGTATCCCACGCCGTCT Y 2 1 2 1 101000 f 74 goat snp1819-scaffold1050-264183 2 1758801 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444460 Affx-122926543 AX-123314797 2 133519072 CTGGCTGGCACTGAGATCTCATCCAAGGTAATAGG[C/T]ATTTATCTTAGTGTGTTCAGCTGTGGGCTCGATGC Y 2 1 2 1 101000 r 74 goat snp1820-scaffold1050-293381 2 1730027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384990 Affx-122971887 AX-123255348 2 133568735 GAGGCTGAATTGTATTCTGGCTGCAAGGGAAAGAC[A/G]TTGCAGGGTCTTAAGCAGGGGAATTCTCTGACTTG R 2 1 2 1 201000 f 74 goat snp1821-scaffold1050-343044 2 1683916 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403108 Affx-122958129 AX-123273461 2 133635697 TGAAAAGAGCTGTGATTGATCTAGCCGGAGGTGCA[C/T]AAACAGACTCCCACTCCCTCCTGGATTCATCCCAC Y 2 1 2 1 201000 f 74 goat snp1822-scaffold1050-410006 2 1619247 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447727 Affx-122924599 AX-123318063 2 133668127 CGTGCCCCAGAGTCACACAGCTGGTGGGTCAACAG[C/T]GGCCCTCGATAGAACAAGATGTGGAAAGGCCCCAG Y 2 1 2 1 101000 r 74 goat snp15936-scaffold1675-77883 2 1586567 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411608 Affx-122951600 AX-123281958 2 133709501 TGTCACATTCTGATCTAAGGGGAACGTGAGTGTCC[A/G]TTCTGTCTGATTTTGTTCCACGATGTTTTCACATG R 2 1 2 1 101000 r 74 goat snp15935-scaffold1675-36509 2 1546389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412810 Affx-122950479 AX-123283159 2 133758810 GTTTTTAACTGTTTGGTCCAGTAGTGAGTATATTC[A/G]TACTGTTGAACAACCTATCTGCAGAGCTTTCTCAT R 2 1 2 1 101000 r 74 goat snp28313-scaffold3010-12701 2 1499822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441744 Affx-122929128 AX-123312081 2 133790626 TGGCGCAGTGTTCCCTCCGGCTCTGCTTCCCATCG[C/T]GTCTGTGGTCACATGGCCCTCTCACTCCGACTTCC Y 2 1 2 1 201000 f 74 goat snp28314-scaffold3010-44517 2 1467596 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427644 Affx-122939333 AX-123297987 2 133821537 TTTTCAGGGAAAGAGGACCAGAGCTACAGAGAGAA[A/G]TAAAGGAAAACCCAGCCAGGAAAATAAAGGCACAA R 2 1 2 1 101000 f 74 goat snp28315-scaffold3010-75428 2 1436344 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440445 Affx-122929403 AX-123310782 2 133868368 CAGGAGCTCAGGAGATGCTTGTATTCACATGAGAC[A/G]CCAGGAGAGGAGACACCAAACCTCCGTCTGTCAGA R 2 1 2 1 201000 f 74 goat snp28316-scaffold3010-122259 2 1388991 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404569 Affx-122957372 AX-123274921 2 133917624 TCTCGCAAATCTGCAGGTAAGGGGGCTGCAGCACC[G/T]AGATGTTAAGTGACTCACCTGCCCAGCGGAAGTGG K 2 1 2 1 101000 r 74 goat snp28317-scaffold3010-171515 NW_017189527.1 62719 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380555 Affx-122975285 AX-123250913 2 133948996 GCTTAAGGCTGGAGGATCCTTAGAGAGCATCCTAG[C/T]CCAATCCTTCCATTCTCAAATGGGGAAACTGAGGT Y 2 1 2 1 101000 f 74 goat snp28318-scaffold3010-202887 NW_017189527.1 31447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414265 Affx-122949612 AX-123284614 2 133997193 GGCTGCAGCCATCACAGACCCCCACCCGCAGAGAC[C/T]GCATGAACGGAACTGTTTGTTGCTCTGAGCTGCTA Y 2 1 2 1 101000 r 74 goat snp28319-scaffold3010-251084 2 1180107 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771186 Affx-122939957 AX-385258346 2 134032722 CTGTGCTAAGCACTTTGCTTGCAGGAGCTCACACA[A/G]CTCTATCCGTCACAAGGCAGGTAATACTACAATCC R 2 1 2 1 201000 f 74 goat snp28320-scaffold3010-286613 2 1214172 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450706 Affx-122921888 AX-123321040 2 134070125 AGATAATTCCAAAGGAAAGGACCAGCTAGCCAAGC[A/G]TGAGTCAGTCGGGAACAGCTGGTGCACAGGCGCGC R 2 1 2 1 101000 f 74 goat snp28321-scaffold3010-324016 2 1252615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272021 Affx-1111833159 AX-519545787 2 134118994 TATGGGGTCGCACAGAGTCGGGCACGAGTGAACCG[A/G]CTTAGCAGCAGCAGCAGCAGTTCAGCTTGAAAATG R 2 1 2 1 303000 f 74 goat 2_134118994_AF-PAKI 2 134118994 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791848 Affx-122941674 AX-385278838 2 134167673 TCCCGTAAGGATGGAGCCTCCGAGACAGAACAACA[C/T]GGCACAAGCCATTTAAAGCCAAGAAATAGAGTCGG Y 2 1 2 1 202000 r 74 goat snp17515-scaffold1811-66577 2 1350722 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415207 Affx-122948982 AX-123285556 2 134220701 ACCTTCCCTCCAGACGACATCGTCTGTGCCACTGA[C/T]GGCTCGATCAAACAGTGGAGACCAAAGCGCCTGAC Y 2 1 2 1 201000 r 74 goat snp17516-scaffold1811-119605 2 1092805 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785837 Affx-122960035 AX-385272874 2 134250349 GTCTTTGCTAAGGGGTTTTGCGGGGGAAGAAGAAG[A/G]GTATTCAGACAAGTTCATTCTCGTAACAGCCAACC R 2 1 2 1 101000 f 74 goat snp17517-scaffold1811-149253 2 1119190 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398758 Affx-122961446 AX-123269113 2 134350404 TCCCAGATCTAACAGAAGGCCCAGCATCTCCAGGA[C/T]GCCTCTCCACATGGCCCCTGTTCCCCGACCACCTC Y 2 1 2 1 101000 f 74 goat snp17519-scaffold1811-249308 2 1022414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419404 Affx-122945600 AX-123289752 2 134405745 TTTTCACACACGCATGAAGTGGTTTGGGAAGGAGC[C/T]GTCCTCTAGCGCATGGCATAGTAAGGACTGAAGGA Y 2 1 2 1 201000 r 74 goat snp17520-scaffold1811-304649 2 970824 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436396 Affx-122933033 AX-123306735 2 134473411 AATTCAAGACAACTCTGAGGACTCAGCCCCAGAGC[A/G]TCCCGGGGGGTTTCCCAACCCTCAGTGGCCGCTGG R 2 1 2 1 101000 f 74 goat snp17521-scaffold1811-372315 2 906258 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383260 Affx-122972738 AX-123253618 2 134504835 TGTGTTCCTACAACAAGAAACAACTTTCTGCCCCC[A/G]GGGAGAGACCGTTTGACCTCCCCTGCTGGGAACAA R 2 1 2 1 101000 f 74 goat snp17522-scaffold1811-403739 2 876442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452738 Affx-122920278 AX-123323071 2 134561159 CTCCTGTTGGCCCACAGTCTGAGCACCCAGGACTG[A/C]CAAATCACAGCATCTCCGAGTCGGAAGGGGCTTTA M 2 1 2 1 101000 r 74 goat snp17523-scaffold1811-460063 2 820688 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447549 Affx-122924041 AX-123317885 2 134583606 GCTAGGGTACCGCTTCCCAGACGACCCTGAGAGGC[A/G]GGGAAAGGAGGCGGGCCAGAACTGCTAAGCGCCAG R 2 1 2 1 202000 f 74 goat snp25942-scaffold2682-290286 2 797285 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452394 Affx-122920610 AX-123322727 2 134636595 GTCTCGGGCTTTGCACCTCCTGCTGCCCTTCCTGG[C/T]GCTTGGATGCCCCAGACACACCCCTTCTTGTTCTC Y 2 1 2 1 101000 r 74 goat snp25941-scaffold2682-237297 2 744124 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432048 Affx-122935899 AX-123302389 2 134671066 CTGTGAAAACTGAGTTTCGTTCAGTTTCCAAGTGT[C/T]GTGGACTAGGCTTTTGCTCCCGTCCCCACCGGTTA Y 2 1 2 1 101000 f 74 goat snp25940-scaffold2682-202826 2 709406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277908 Affx-1111836153 AX-519551403 2 134696915 TCAAGCCAAAAGTGCCTTTAGGCAGTGGTCCAAAT[A/G]CATGTGTTTTTAATTTATAAATGCCTCCCCCTGGT R 2 1 2 1 103000 f 74 goat Random2.2K-286 2 134696915 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422640 Affx-122943701 AX-123292986 2 134705993 CTGATGATGGTTGCTCTGAGTGATGCTCCCCACCT[C/T]CTTCGTCCCTCTGAGCCAGTGAGAAACTAGAGGAG Y 2 1 2 1 101000 f 74 goat snp25939-scaffold2682-167899 2 674028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426815 Affx-122940521 AX-123297160 2 134768458 CACTTAGCAGAGCAGCTCAGGCTAGAACTACCACA[C/T]GGCCTCATTAGAGGAGGCGTGTAGTGAGGTCACAA Y 2 1 2 1 101000 f 74 goat snp25937-scaffold2682-105434 2 614121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376722 Affx-122978964 AX-123247081 2 134797775 GTAGACTCCCTGGAGTTAGAAATTAGGGGTAGAGC[C/T]ACGTCCGGAGAATAAGAAAGTCTTGAAGGAGAAGT Y 2 1 2 1 201000 r 74 goat snp25936-scaffold2682-76117 2 584235 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416870 Affx-122948088 AX-123287218 2 134839728 CTTCAGACCCCCTTTTAGGGGCCTCCATTCCTGCA[C/T]ATCGGCTCCAGGGAGGACCAGGCCGTGAGCGGGAA Y 2 1 2 1 303000 r 74 goat snp25935-scaffold2682-34164 NW_017189886.1 4624 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278062 Affx-1111836154 AX-519551552 2 134865265 TTTCAGGAACACCAGAGCTCCATCTCTGTTTCTCC[A/G]AAATGCTAAACTGGTGTGGGAGCAAACTCGCACAG R 2 1 2 1 101000 r 74 goat Random2.2K-287 2 134865265 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436803 Affx-122932246 AX-123307141 2 134955186 GTTCAAATGTCTTTGGTGATGGCACTGGGTGTTCC[A/G]GTGAACTAACAGCAGCAGGCATTCAGGTTTTTATA R 2 1 2 1 101000 f 74 goat snp56621-scaffold895-81195 2 450930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420655 Affx-122944825 AX-123291002 2 135156332 TGGAAGAAAATACATGTGGATGTACATGGGACAGA[C/T]GTGGGTCTGTGTGACACTGTATGCATCTGTATGTC Y 2 1 2 1 101000 f 74 goat snp56625-scaffold895-282341 2 250290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777453 Affx-122976208 AX-385264573 2 135188495 TGGTAGAATATGCCACATGTAATGTGGAGCGCACC[A/G]TCTTAGCCATCTTTAAGCTTCGGCTCAGTGGCATC R 2 1 2 1 101000 f 74 goat snp56626-scaffold895-314504 2 224737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434515 Affx-122934603 AX-123304856 2 135223081 AAGTGGAAAGCATCATAACAGCGCCGAGTATGATA[A/G]CAGACTTATTGTGACGACTAAATGAATGTCAAGTG R 2 1 2 1 101000 f 74 goat snp56627-scaffold895-349090 2 181916 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409742 Affx-122953017 AX-123280093 2 135255106 GGCTGTGCAGCCATCGATGCTGTAATTCCAGGACA[C/T]GCTCATCGCCCCCAAATGAGACTTCGTGCCTGTCA Y 2 1 2 1 101000 f 74 goat snp56628-scaffold895-381115 2 149547 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413506 Affx-122950636 AX-123283855 2 135331490 GCTGTCCCCTCCCTAACCCCCTGCTCATCTTTCCC[A/G]CTCACACTGTCCTTGTCCGAGAGGGCAATGATGTT R 2 1 2 1 101000 r 74 goat snp56629-scaffold895-457499 2 90162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390364 Affx-122967677 AX-123260721 2 135369861 TTGATTCTGGTTGGATATTAAATGATTCCAAAGAA[C/T]GTTTTGTTAGGCATAATCAGGGCATTGCATAAATG Y 2 1 2 1 101000 r 74 goat snp56630-scaffold895-495870 2 51534 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428111 Affx-122939078 AX-123298454 2 135409132 TCCTTCTTTTGTCCCTTACAAGGAACATTCTAATT[A/C]GATTGAGGGCCAGCCACACCCATCGTGACCTCACC M 2 1 2 1 101000 f 74 goat snp56631-scaffold895-535141 2 13915 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792507 Affx-122955333 AX-385279487 2 GACATGACTGAGTGACCCATCACCACCAATAACAA[C/T]GATCAGGTCCCATTGTTAAGGCTCCTCTACCTGTT Y 2 1 2 1 101000 f 74 goat snp19062-scaffold1917-98839 4 24436926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762302 Affx-986696833 AX-385250484 3 1965 AGTATAATATTGTCATACATTCCCTGGCCTCAGAT[A/T]TCAATTCTGTTCATTTTTCTTGGTTTTGACTAATA W 4 1 2 1 600010 f 74 goat 3_1965 3 1965 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 38438528 Affx-122931197 AX-123308866 3 23250 TCCAGATGTGGTATGCAGGCTCCTCTCTCATTGTG[A/G]CACCTGGTCAACACACTAGTTGTGCCCAGGGCCTC R 2 1 2 1 102000 f 74 goat snp32075-scaffold361-731478 3 120005149 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392964 Affx-122965681 AX-123263321 3 72885 GGAAACATGACCTCTCCGTAATCTCATTTGCCATT[A/G]TAAGACAGTTATTCATTTGACAAGTGTTTATTGAT R 2 1 2 1 101000 f 74 goat snp32074-scaffold361-681843 3 119954417 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272064 Affx-1111833400 AX-519545828 3 79964 CAATCTCCAAACAAATCTCTACTTATTTCTCCCAT[A/G]AGGTCTTGGTGGCTGGCCAAGCTGACCTGACTGTG R 2 1 2 1 303000 r 74 goat 3_79964_AF-PAKI 3 79964 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403799 Affx-122957971 AX-123274151 3 172416 GCTGACAATTGGACTTCCTTATCCTCCACACCCCA[C/T]GCCAGCATCCTGTCTGTACCCCACACCAGCGGACC Y 2 1 2 1 201000 r 74 goat snp32073-scaffold361-582312 3 119853700 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410253 Affx-122952534 AX-123280603 3 203015 CTCCTCTCTTCTGAAAGTCATTCTCTTGTTTTCTC[A/C]TGCAATGGGGAGGTACAATTGCCTGGCTGAGAAGT M 2 1 2 1 101000 r 74 goat snp32072-scaffold361-551713 3 119823011 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450092 Affx-122922788 AX-123320427 3 246193 AAGGTGGGTATTATATTTAAGCCTGACAATAATGG[A/C]TGACCATTGAAGGTGACAGGATGAATGTCTCTGGT M 2 1 2 1 101000 f 74 goat snp32071-scaffold361-508535 3 119779380 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429764 Affx-122938254 AX-123300105 3 314245 GGGAGGGCTATAGGAAAGAGAGTCCATGGCTTTCC[A/G]TTGGCTGATTCCTTCCCAGAAACTAAGAGGAATCT R 2 1 2 1 101000 r 74 goat snp32070-scaffold361-440483 3 119711529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391813 Affx-122967024 AX-123262170 3 343430 TCGAAGTCCTGTTTTGGGAACCAGGGGTAGAGACT[A/G]ATGTATGATTCTGTATTATCTCACAGATAGCATGC R 2 1 2 1 201000 r 74 goat snp32069-scaffold361-411298 3 119682046 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778893 Affx-122947358 AX-385266001 3 397115 AATATAATCGTGCTGATGACAAAAATTTATTAAAA[C/T]ATAAATATTGCCAGTGAGGATGATTGATAACAAAA Y 2 1 2 1 201000 r 74 goat snp32068-scaffold361-357613 3 119628310 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278064 Affx-1111836155 AX-519551554 3 407597 CACCGTGCTCGATGCCCTGTGAGTGCCCCACAGAC[A/G]AGGATGTCCACTGCCAAGTGTGATTCAGCTGTGCC R 2 1 2 1 101000 r 74 goat Random2.2K-289 3 407597 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413912 Affx-122949825 AX-123284261 3 436705 AATTAAAATCAAAGAGGTTTCATTTGACCACTAAG[C/T]GAATAAAAGAGAGGAGAGAAAGGCTGTTGAGAAAG Y 2 1 2 1 201000 f 74 goat snp32067-scaffold361-318023 3 119587835 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794456 Affx-122924789 AX-385281419 3 522636 CATTAAACATAATATATAGTGACCATCGGAAATGT[A/G]AAATTAGAGTTCCTCTTGGGGAATACAGAATTGAT R 2 1 2 1 102000 r 74 goat snp32065-scaffold361-232092 3 119502245 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388120 Affx-122969484 AX-123258478 3 568238 ATTATCTTGCCTTTAAAAAATCTCTTAATTGTCCC[A/G]CATTCCCCTCCAGACTCATGTCTTTGCTCCTTTTA R 2 1 2 1 101000 r 74 goat snp32064-scaffold361-186490 3 119456680 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409452 Affx-122954082 AX-123279803 3 605675 CTATAAGAAAACAGATATCAGACTTTAAAGATGCT[G/T]CTTTATTGTGCTGTAGGGCTCTATACTAGGCTTTA K 2 1 2 1 101000 r 74 goat snp32063-scaffold361-149053 3 119418788 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434468 Affx-122934637 AX-123304809 3 687920 ACAGAGTAAGTGACTTTTACACACATGCAAATGTA[C/T]ACATATACAAATACTGCATAGAGGTGCTCCCAATG Y 2 1 2 1 101000 f 74 goat snp32062-scaffold361-66808 3 119335778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412653 Affx-122950787 AX-123283002 3 731044 CCAACTTGCATTTTGTTTATTTAGGCTTTATGACA[C/T]ATACTGATATTTCTCCTCTTATTTTTGCAACATTG Y 2 1 2 1 101000 f 74 goat snp32061-scaffold361-23684 3 119292994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275024 Affx-1111834547 AX-519548606 3 739234 CCTGCAGGGTCAGACAGTCGGGTGGTCAAGCTGGG[A/G]TGAGGTCGGCTCTGCTGCTGCAGGAGATGGACCCT R 2 1 2 1 202000 r 74 goat GoatD01.041204 3 739234 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320783902 Affx-122956532 AX-385270957 3 763240 TGCTTTTACTTTATCTTCTATAAAGTGAAGAAATA[A/C]TAGTACCCAGCTCACAGGGTTATAAAGTTTAAATG M 2 1 2 1 201000 r 74 goat snp40756-scaffold522-8413 3 119260783 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768239 Affx-122930651 AX-385255420 3 800826 TTTCCACATCAAACTTTTTGTAATATATTCTACCT[A/G]CCTAGGAATTCATACCAAAAGAGGTGTCACCTAGT R 2 1 2 1 101000 r 74 goat snp40757-scaffold522-45999 3 119222421 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765109 Affx-122945528 AX-385252670 3 895146 ATAGGAAGATGATGTAGGAATATTTTCCATTATGT[A/C]TTCTTTCTAAACTTCTGAACTATGTCAATATAGTG M 2 1 2 1 101000 f 74 goat snp40759-scaffold522-140319 3 119126876 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421590 Affx-122944497 AX-123291937 3 924689 AAGTGAAGAGCGAAGGCTCAGTGGCTTGGTCCACA[C/T]GAGGGGCAAGGAACATTTCTGAGCCTCATACGGTG Y 2 1 2 1 101000 r 74 goat snp40760-scaffold522-169862 3 119098678 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786952 Affx-122946346 AX-385273981 3 977870 TGCACACCCAGAGTTTATGGCCTACTAAGGAACAG[C/T]GGTGATTAGGCAAGTATTTAAACCATGATCAGGAT Y 2 1 2 1 101000 r 74 goat snp40761-scaffold522-223043 3 119045920 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421596 Affx-122944493 AX-123291943 3 1007730 CTGAATGATGGTCATGAAACGTGTCAAGCTCTCTC[A/G]TCACTTGAGGCATGTGGGAGGACTGCACTTCCTCC R 2 1 2 1 101000 f 74 goat snp40762-scaffold522-252903 3 119015999 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437147 Affx-122932145 AX-123307485 3 1068387 CAATCATAACACGTACTCACTGTGTTCACTGCAGA[C/T]GACCGTGCGATAGCAGGGATCTGCCCTACAATGCC Y 2 1 2 1 101000 f 74 goat snp40763-scaffold522-313560 3 118955097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425875 Affx-122940646 AX-123296221 3 1099000 TCAATAATGGCCTAAGGCTTTTTCAACTTCTTCAG[A/G]TCTCTAAGGGGCTTCTAATGCTGTTACTGCCTAAA R 2 1 2 1 101000 f 74 goat snp40764-scaffold522-344173 3 118924291 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454171 Affx-122919314 AX-123324504 3 1127874 CCATTCCAGGCATTCTCTGCAGAAGGGAGTGAAGA[A/C]AACTTCTGTCCAAACTAGAATCTCCAGGATTATGG M 2 1 2 1 101000 r 74 goat snp40765-scaffold522-373047 3 118895423 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786945 Affx-122931290 AX-385273974 3 1176469 AACAGAACACACACTGCAGATAAATATTGCAATCT[C/T]TGAACTTTTCCAGTAACTGTATTTCTCTTAATCTT Y 2 1 2 1 101000 f 74 goat snp40766-scaffold522-421642 3 118846961 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444628 Affx-122926934 AX-123314965 3 1208726 CAAGGAGTCAATTTCCCCTTGTGTTCCTCCCTTGA[C/T]AACAGTGGAAAAACACCCCTGAATCAATATTAAAA Y 2 1 2 1 201000 r 74 goat snp40767-scaffold522-453899 3 118814860 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780946 Affx-122922671 AX-385268033 3 1244943 CAGGTATTCTAAAAAGACTACTTCTGTAACCATTA[C/T]AGAAATTCACAGTAGAGAGTTTTGACCCATTTAGT Y 2 1 2 1 101000 r 74 goat snp40768-scaffold522-490116 3 118778598 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378021 Affx-122977584 AX-123248380 3 1297858 CCAGAGTAACCCAAAGAGGTTTCAACAATCCTTCA[C/T]ATAAACAGGAAAAACTCAGCACAAAATATGGTCAC Y 2 1 2 1 101000 f 74 goat snp40769-scaffold522-543031 3 118725500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388635 Affx-122969122 AX-123258993 3 1334206 TCCATTAAAAGACAAGGGCATGTTTCATGCAAAGA[C/T]GGCCACAATAAAGGGCAGAAATGGTAAGGACCTAA Y 2 1 2 1 303000 f 74 goat snp40770-scaffold522-579379 3 118689653 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277915 Affx-1111836157 AX-519551410 3 1345661 CGTCCATAGCACACACCTATACATAGATCAGCCAC[A/G]TCATCTGTTCATCCTCCCTGATACTCAGCCATCCA R 2 1 2 1 101000 f 74 goat Random2.2K-291 3 1345661 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320765065 Affx-122925568 AX-385252633 3 1366799 CTACAGTATAAGTGTCACTGAAGTTGCCTTTTTTT[C/T]TCTTACTTGTATTATAAAAGGAGCAAACAGAAAAA Y 2 1 2 1 102000 f 74 goat snp40771-scaffold522-611972 3 118657073 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781138 Affx-122943034 AX-385268223 3 1405778 ATTCTGGTCCAAAGAGTTTTCTATAAAGAGGAAAA[C/T]GAGGAAAGAACTCATTCAGGAGGGATACAGAAACT Y 2 1 2 1 102000 r 74 goat snp40772-scaffold522-650951 3 118618059 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790489 Affx-122965942 AX-385277492 3 1445861 TGACATCTGTCTTAGGCCAAAGATTGACCACATAA[C/T]GATTTTTATCTTTGTCTCGTCTATTAAATTAATGA Y 2 1 2 1 101000 f 74 goat snp40773-scaffold522-691034 3 118577946 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797951 Affx-122941002 AX-385284886 3 1493505 TTTCGCTTTCATAAAGTACCTGTGGACAGGAGTCC[A/G]TTTTACTGAAACTTCACTGATTTCTTGGTATTAAG R 2 1 2 1 101000 f 74 goat snp40774-scaffold522-738678 3 118530481 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400432 Affx-122959968 AX-123270787 3 1542525 TCAAGATTCTTCTCACAAGGGCAATTCTGTTTAGC[A/G]TGTTTTAGGCAGGTTGTGGCAAGAAGTTATTTAAT R 2 1 2 1 101000 f 74 goat snp40775-scaffold522-787698 3 118479957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792861 Affx-122931362 AX-385279839 3 1599829 ATGAGTCAGTGAATCTGAGAGATCACATTTGAAGA[C/T]GACCCAGTACACTTTTGAGAAGCTGGAGGTTTTAT Y 2 1 2 1 101000 f 74 goat snp40776-scaffold522-845002 3 118422769 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380272 Affx-122975423 AX-123250630 3 1629362 GGGTCATTTCCACCTTGACGGACAGGACAGGCCAA[C/T]ATGAACGTGCATGTATGAGCTGCACCCCTTGGCCT Y 2 1 2 1 101000 r 74 goat snp40777-scaffold522-874535 3 118392553 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423851 Affx-122942773 AX-123294197 3 1713638 GGGGAGATTAGCTAACTGTGCCAGTGGGTGATTAT[G/T]GCATATCGCTCTGAGAAGAGTACATGTTCCTGCTG K 2 1 2 1 101000 f 74 goat snp40778-scaffold522-958811 3 118306768 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793455 Affx-122934214 AX-385280432 3 1757727 AAGCAACAACAAGGAAAGTTGCAAAGAATTCAATG[C/T]GGATTAGAGTATTATGAAGACTCCTAACTTACGCA Y 2 1 2 1 101000 f 74 goat snp40779-scaffold522-1002900 3 118261861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411432 Affx-122951828 AX-123281782 3 1796484 ATACATGTGTACAGCAGTTTGTGTTCACCTGAAAC[G/T]AACACAGTGTTGTAAATCATGCGTGTGCTGTGCAT K 2 1 2 1 101000 f 74 goat snp40780-scaffold522-1041657 3 118222461 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426510 Affx-122940210 AX-123296856 3 1841681 GTGTTAGGCAAGATACATACATTCTCTGAGAATCC[A/G]TTTCTTCATCTATAAAATGGGTGTAATGATAATAT R 2 1 2 1 103000 f 74 goat snp40781-scaffold522-1086854 3 118177025 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406125 Affx-122956200 AX-123276477 3 1880254 CCATTTTCCCAAAGGACGGAGAGGACAAAAGAGGC[A/G]TTAATAGGACTCGTTGCTGCCTTTTTCTCCCAGTC R 2 1 2 1 201000 r 74 goat snp40782-scaffold522-1125427 3 118137999 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799214 Affx-122952481 AX-385286144 3 1951684 GACATAAAATAAATATAGGTAGAGTCAGTGTGACA[C/T]GCCTCTCAAGTGTCTTCCAACATAAATTTTACTAG Y 2 1 2 1 101000 r 74 goat snp40784-scaffold522-1196857 3 118066229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789446 Affx-122932591 AX-385276456 3 2004670 CAAAGAAGTCTAGTCAATGGAGAACATTTGATTCA[C/T]ATATTGGGACAGATGTTAAGATTTTTTGTTTTTAC Y 2 1 2 1 101000 f 74 goat snp40785-scaffold522-1249843 3 118012823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452603 Affx-122920491 AX-123322936 3 2048588 AAACAAGGCTTGAAAGACTTCATATGCCCCACTTA[C/T]TTGTAGAATCACTAGGGAAATATGTGAAGATCTTG Y 2 1 2 1 201000 r 74 goat snp40786-scaffold522-1293761 3 117967000 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410618 Affx-122952098 AX-123280968 3 2083721 TTGCATTTAATTTATTCTGTGCTCATCTGTTGATC[A/G]TGAATGTGAGAGAGAATTTTTAGACTGTTCTATTA R 2 1 2 1 600000 r 74 goat snp40787-scaffold522-1328894 3 2083721 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777697 Affx-122952098 AX-385264816 3 2083721 TTGCATTTAATTTATTCTGTGCTCATCTGTTGATC[A/G]TGAATGTGAGAGAGAATTTTTAGACTGTTCTATTA R 2 1 2 1 101000 f 74 goat snp40787-scaffold522-1328894 3 117933056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417543 Affx-122946925 AX-123287891 3 2120870 GTAGTTTGAGATGGAGAATTGTCTCCAGCATTTGG[C/T]AGAGTGTGGTTTTACATATATTCTCAATTAGAAAA Y 2 1 2 1 201000 r 74 goat snp40788-scaffold522-1366043 3 117894247 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377522 Affx-122977476 AX-123247881 3 2150216 GCTTTTCTAGAGCAAGCTTTCATATAAACCATTTC[A/G]TTTGAAATCTCCAATTTTCGAGTTGGCTTTAGCTA R 2 1 2 1 101000 r 74 goat snp40789-scaffold522-1395389 3 117864878 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798535 Affx-122951278 AX-385285468 3 2184826 TGATTTTAACTGTCCCTATGTTTCTTCTTAATCTT[A/G]TATTTTGTCCATTCACTTAATTTTACTTTGGGTTA R 2 1 2 1 101000 f 74 goat snp40790-scaffold522-1429999 3 117831305 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417302 Affx-122947232 AX-123287650 3 2235161 CCGCGTGGGTGATCTACAGTCTGGAGAATAATTAT[A/G]CCACAGAAGCTCTCTTACAGGAATGAAAATTCTGA R 2 1 2 1 101000 r 74 goat snp40791-scaffold522-1480334 3 117780616 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413523 Affx-122950623 AX-123283872 3 2329615 AAAGCATGAGTACAATCTCAGGACAGAGGGCACAG[C/T]GTAGGGGGCCATGTGCCACTAGGTTTACAAAAATT Y 2 1 2 1 101000 f 74 goat snp40793-scaffold522-1574788 3 117683870 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392136 Affx-122966331 AX-123262493 3 2361086 AATCATCAACTATGATTGGACTATGAAGTTTAAGA[C/T]GGTCTTTATGAAGTTTAAAGAAAAACTTCATCTTA Y 2 1 2 1 101000 f 74 goat snp40794-scaffold522-1606259 3 117652247 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415574 Affx-122948633 AX-123285923 3 2395582 AGGAAGTGGAGTGCCTTGTGCTTTGTGTTACACCG[A/G]AAGAAAGATCAAATTCACATCCTCATGGGTTTCGG R 2 1 2 1 101000 r 74 goat snp40795-scaffold522-1640755 3 117617165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440243 Affx-122930667 AX-123310580 3 2441361 TCCAAAGGATTATTAAACAAATATTTCCTGCAGTG[A/G]AATCCAAGCCTGAGGTCATATCCTCAGCTGCACTT R 2 1 2 1 101000 r 74 goat snp40796-scaffold522-1686534 3 117570387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784860 Affx-122923125 AX-385271907 3 2475829 GAGGGAAAATATGTTCACTGGGCTTAAGAGAGAAG[C/T]ACCCTGTTGGAGAGGAGGAAGGTCACAGCCTCAGA Y 2 1 2 1 202000 r 74 goat snp40797-scaffold522-1721002 3 117534750 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791165 Affx-122942142 AX-385278160 3 2501137 AGGAATGACAGGGCAGAAAGAGGGTAAAAAGACAG[A/G]ATCTTTGTTGATCTATGAATCATTAAATCAATTTG R 2 1 2 1 101000 f 74 goat snp55780-scaffold865-16545 3 117509571 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383710 Affx-122972477 AX-123254068 3 2534062 ACATGCTATTAAAACTTCTATTATAGGACTTCACC[A/G]TCTTTTATATTAATTTCTTTCTTCCTAGACTGTGA R 2 1 2 1 101000 f 74 goat snp55781-scaffold865-49470 3 117476076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436070 Affx-122932699 AX-123306409 3 2568081 AGGTCAAGGGCTAAGTATATATCTGCAGTTCAAGA[A/G]CGCAGACCAGTTTACAAGGTAGCAATGAAACTCCT R 2 1 2 1 101000 f 74 goat snp55782-scaffold865-83489 3 117440950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272027 Affx-1111833381 AX-519545792 3 2594496 GAGAGATCTCTCGTCATCACTCATCAACAAGAGAC[A/G]TTCCTCTCTCACCTTGTTGCAAAACCTTGGGTCTT R 2 1 2 1 101000 r 74 goat 3_2594496_AF-PAKI 3 2594496 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38436254 Affx-122932551 AX-123306593 3 2601445 GGCTGCTCTTGTATCTCACCTTCACGTTGATTAAT[G/T]TGTTGGGTTGAGGTCCCACTGGAGGGAAACTCAGG K 2 1 2 1 201000 f 74 goat snp55783-scaffold865-116853 3 117407740 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406282 Affx-122922901 AX-123276634 3 2653763 AGGTAGACAATGCCCACAGGGAACAGGAGCTACTC[A/G]TCTTGCCTTTGGAGTCACACATCTCAGCGAACCCA R 2 1 2 1 201000 r 74 goat snp55784-scaffold865-169171 3 117355703 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773979 Affx-122938356 AX-385261117 3 2734085 TTGTACAGCAAAGACCAATCTATTATTTATAACCA[C/T]GAAGAACTCTATTAATTCCCTGTCCTCAAATAGAG Y 2 1 2 1 101000 r 74 goat snp55786-scaffold865-249493 3 117274316 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430697 Affx-122936914 AX-123301038 3 2777708 GAGGTGCAAACAGCTCTCTTCTGCTTCCAGAAAAT[A/G]CATATCTTGCTTTCTTTCTGATTATTAAAATGAAT R 2 1 2 1 101000 f 74 goat snp55787-scaffold865-293116 3 117229873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799509 Affx-122927252 AX-385286439 3 2823843 AAGAAAGTCTAGACTTCTAGGCCCTGAAAGCTCTC[A/G]TAAATAGCATTAGTCCAACAACCCAAGGCTATCTC R 2 1 2 1 101000 r 74 goat snp55788-scaffold865-339251 3 117183527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375788 Affx-122978577 AX-123246147 3 2914052 CCAGTAAGTTTGGAAAAACCTGTGTACTATCCTCT[A/G]TTCCCACTTAAACTTCTAGGCGGGAGTGACAGGGC R 2 1 2 1 101000 r 74 goat snp55790-scaffold865-429460 3 117094720 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377505 Affx-122977486 AX-123247864 3 2958206 CCTCTGGGATAATTTTCCTTTCTCATTTTGTATAG[C/T]GAACTCCTACTCATTCTTCAGATCTCAAAGCCTTA Y 2 1 2 1 101000 r 74 goat snp55791-scaffold865-473614 3 117051881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405789 Affx-122955911 AX-123276141 3 2988548 TCCCCAGTATAAGACTGTTTTTCAGTGCAGGGAAT[A/G]TGAGTTTGACCCTGGTTGGGAAACTAAGAGCCCAC R 2 1 2 1 103000 f 74 goat snp55792-scaffold865-503956 3 117021588 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789424 Affx-122943523 AX-385276434 3 3027242 TCACCCAGGCTGTTTCATTAGCATCGCAATGGGTC[C/T]GTTTGATTCCCTCTTCTGGTTCTAATACAGCAACA Y 2 1 2 1 101000 r 74 goat snp55793-scaffold865-542650 3 116982853 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390731 Affx-122967919 AX-123261088 3 3073323 CCTGGGCGTGTCAGAAGAGATGTCTGTTCCTTGGC[A/G]TTTTGAAGTCCATGGTCCCTTGTCATTTCACAGAG R 2 1 2 1 101000 r 74 goat snp55794-scaffold865-588731 3 116937160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278071 Affx-1111836158 AX-519551561 3 3153024 GCCCCTAGAATCCCTCCTGAAAAGAGAATTTTTAC[A/G]ACCACACATTCGCCAAATTGTCTGTTCCAGGACGT R 2 1 2 1 101000 r 74 goat Random2.2K-294 3 3153024 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275817 Affx-1111835024 AX-519549380 3 3179124 GCGTCCCCCAGCAGATCGCGGAAGCTGCTGCCCTC[C/G]CGCAGCGGCATGGACTCGAGCAGGTGGTTCAGGAG S 4 1 2 1 103000 r 74 goat ilmnseq_rs642262399 3 3179124 C G 1 not_recommended Goat_IGGC_65K_v2 Illumina 468276097 Affx-1111835165 AX-519549648 3 3179289 TCCGTCCCCTCGGCAGGCGGGGCCCGGCTCAGTTC[A/C]ACCTCGGGGACCTCCTCTAGGTCTGAGGACTGGTC M 2 1 2 1 102000 r 74 goat ilmnseq_rs658495597 3 3179289 G T 1 neutral Goat_IGGC_65K_v2 Illumina 38450774 Affx-122921833 AX-123321108 3 3305056 CTCCAGCCTGTGGTCAGAGGTCAGGCAGTTGTAAA[G/T]CTGCACAGGGAATTTCATTCAGGCAGTTACTTTCT K 2 1 2 1 101000 f 74 goat snp55799-scaffold865-820464 3 116705300 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437416 Affx-122932417 AX-123307754 3 3346505 TTAAAAGGAGAGCTGTATATCTACAACACACACAG[C/T]GATCAAGGGCAGGAATCCGCTATTTTAGGGTAAAG Y 2 1 2 1 101000 r 74 goat snp55800-scaffold865-861913 3 116663779 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770479 Affx-122939915 AX-385257645 3 3375550 TAAAGGGGTTTGTAGGAATGAATTAAGTCAGTATA[C/T]GTAAAGCGTTTGGATCTATGTCTGGCTCATGGCAA Y 2 1 2 1 101000 r 74 goat snp55801-scaffold865-890958 3 116634943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376878 Affx-122977823 AX-123247237 3 3410690 CTGAACAATTGGAAAACAGTTTTCACTGACTGAAG[C/T]GGAGGTTCTAAGGGTGGGTGGCTAGGAAGCAGGTC Y 2 1 2 1 201000 f 74 goat snp55802-scaffold865-926098 3 116599562 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453898 Affx-122919501 AX-123324231 3 3515134 CTTCATAAACCAGTCTTCTCATTAAGGAACAGGAC[A/G]TGTCTCTGTTAAAATCTTTTACATCTTTCAGTGAT R 2 1 2 1 201000 r 74 goat snp55805-scaffold865-1030542 3 116495155 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786539 Affx-122975940 AX-385273572 3 3581154 TACTATGTATTGACCTATATTTTAGGCAATCTTCC[A/G]TTTCAGCAAAACACAATGGATCCAAAACTGAATTA R 2 1 2 1 101000 f 74 goat snp48292-scaffold684-4653 3 116129166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375911 Affx-122978478 AX-123246270 3 3614393 ACAGGGATATAAAAGTACCTAAGAGGGCAAGCAGA[C/T]AGTGCATCGCAAGAAGCATTTAAATTGAGAATGAA Y 2 1 2 1 101000 f 74 goat snp48293-scaffold684-37892 3 116096397 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405851 Affx-122955861 AX-123276203 3 3649112 CATCTGTTCTGTTTTAGTGCCAGGGAATTGCAAAA[C/T]GACCAGCAACTCTCACCTCCTGGTTCTGATTGGTC Y 2 1 2 1 101000 f 74 goat snp48294-scaffold684-72611 3 116061501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787453 Affx-122959006 AX-385274478 3 3689889 CTTCTTCAAAAGTCAGTATGTGTCATTCTGGAAGA[C/T]AGACCACTGTCCAGTTAGAGGAAGACATGTCTTCA Y 2 1 2 1 101000 r 74 goat snp48295-scaffold684-113388 3 116021038 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275790 Affx-1111835086 AX-519549355 3 3733664 GTGGGTGTCCCGTTCAGGCGAACCTCTCCTCTTAG[A/G]GCTGGTGGGTCATCACGGGCTTCTGTGAAGCACAA R 2 1 2 1 201000 f 74 goat ilmnseq_rs649524942 3 3733664 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468276206 Affx-1111835220 AX-519549756 3 3733671 TCCCGTTCAGGCGAACCTCTCCTCTTAGGGCTGGT[A/G]GGTCATCACGGGCTTCTGTGAAGCACAAACACACA R 2 1 2 1 101000 r 74 goat ilmnseq_rs665215002 3 3733671 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276089 Affx-1111835236 AX-519549641 3 3735158 CCAATGGCAGGAAGAGTGCCGCCAACTACAGCTTT[A/G]CAGTGAGTTTTCTCTGTTCTCTGGGGCGGCTTAAA R 2 1 2 1 202000 f 74 goat ilmnseq_rs666925188 3 3735158 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468275598 Affx-1111834989 AX-519549168 3 3735189 ACTGCAAAGCTGTAGTTGGCGGCACTCTTCCTGCC[A/G]TTGGGGTTTCTTTGGGTCAGGGATCCGCGGTACAT R 2 1 2 1 102000 f 74 goat ilmnseq_rs637141532 3 3735189 A G 1 neutral Goat_IGGC_65K_v2 Illumina 468276136 Affx-1111835186 AX-519549686 3 3735190 CATGTACCGCGGATCCCTGACCCAAAGAAACCCCA[A/G]TGGCAGGAAGAGTGCCGCCAACTACAGCTTTGCAG R 2 1 2 1 103000 r 74 goat ilmnseq_rs661607006 3 3735190 T C 1 not_recommended Goat_IGGC_65K_v2 Illumina 468276122 Affx-1111835251 AX-519549672 3 3735233 TTTTCCCCGAAGACAAAGATGATGACTGCTTCAGT[A/C]GGAAGTCCATGTACCGCGGATCCCTGACCCAAAGA M 2 1 2 1 101000 f 74 goat ilmnseq_rs668105767 3 3735233 G T 1 recommended Goat_IGGC_65K_v2 Illumina 468275997 Affx-1111835111 AX-519549553 3 3735260 TGTGATTAATAAACAAGCCCCCTTCTGTTTTCCCC[A/G]AAGACAAAGATGATGACTGCTTCAGTCGGAAGTCC R 2 1 2 1 201000 r 74 goat ilmnseq_rs653396172 3 3735260 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468276274 Affx-1111835254 AX-519549818 3 3738469 GGGGCTCACGGTGCGGCCCTCGGGAAAGCCCCAGA[A/G]GAAGTCTAACCTCCCGGTGAGTGGAGGGACTTCGG R 2 1 2 1 202000 r 74 goat ilmnseq_rs668232262 3 3738469 T C 2 neutral Goat_IGGC_65K_v2 Illumina 468275902 Affx-1111835067 AX-519549460 3 3738483 GCCTTGCAGGCAGCGGGGCTCACGGTGCGGCCCTC[A/G]GGAAAGCCCCAGAAGAAGTCTAACCTCCCGGTGAG R 2 1 2 1 103000 r 74 goat ilmnseq_rs647065552 3 3738483 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275955 Affx-1111835091 AX-519549513 3 3738490 GATTGCAGCCTTGCAGGCAGCGGGGCTCACGGTGC[A/G]GCCCTCGGGAAAGCCCCAGAAGAAGTCTAACCTCC R 2 1 2 1 303000 r 74 goat ilmnseq_rs649926286 3 3738490 C T 3 not_recommended Goat_IGGC_65K_v2 Illumina 468276212 Affx-1111835223 AX-519549762 3 3738495 TCCAGGATTGCAGCCTTGCAGGCAGCGGGGCTCAC[A/G]GTGCGGCCCTCGGGAAAGCCCCAGAAGAAGTCTAA R 2 1 2 1 303000 r 74 goat ilmnseq_rs665577468 3 3738495 C T 3 not_recommended Goat_IGGC_65K_v2 Illumina 468275855 Affx-1111835117 AX-519549417 3 3738540 CCAAGTGATGTCTATCTGTCATTCCTCCAGGTTTC[A/G]AATATCAAGTCCAGGATTGCAGCCTTGCAGGCAGC R 2 1 2 1 101000 f 74 goat ilmnseq_rs654226695 3 3738540 C T 1 recommended Goat_IGGC_65K_v2 Illumina 38433334 Affx-122935154 AX-123303675 3 3739524 GCATGGCTGCTACCAATCTCAGGGCTGAAGGCAGA[C/T]GACTCACGCTCTTAAGTTCACCTTCGGGGAATCTT Y 2 1 2 1 201000 r 74 goat snp48296-scaffold684-163023 3 115971776 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275900 Affx-1111835066 AX-519549458 3 3740486 TGGGGGAAGGATCCGCTGAGTCCTGGGGACCCCGA[A/G]CAGCCCAGCAGGACCACGGAGGCAGAGCTGGCGGA R 2 1 2 1 202000 r 74 goat ilmnseq_rs647010203 3 3740486 T C 2 neutral Goat_IGGC_65K_v2 Illumina 468276154 Affx-1111835195 AX-519549704 3 3740488 GCTGGGGGAAGGATCCGCTGAGTCCTGGGGACCCC[A/G]AACAGCCCAGCAGGACCACGGAGGCAGAGCTGGCG R 2 1 2 1 303000 r 74 goat ilmnseq_rs662667530 3 3740488 C T 3 not_recommended Goat_IGGC_65K_v2 Illumina 468275712 Affx-1111835047 AX-519549281 3 3740489 GCCAGCTCTGCCTCCGTGGTCCTGCTGGGCTGTTC[A/G]GGGTCCCCAGGACTCAGCGGATCCTTCCCCCAGCT R 2 1 2 1 303000 f 74 goat ilmnseq_rs644663602 3 3740489 G A 3 not_recommended Goat_IGGC_65K_v2 Illumina 468275877 Affx-1111835055 AX-519549437 3 3740510 CTGCTGGGCTGTTCGGGGTCCCCAGGACTCAGCGG[A/G]TCCTTCCCCCAGCTGGGTGTTTGGTCTGCTGCCGT R 2 1 2 1 102000 r 74 goat ilmnseq_rs645584577 3 3740510 A G 1 neutral Goat_IGGC_65K_v2 Illumina 468275927 Affx-1111835155 AX-519549485 3 3740547 CTCGTGGTCACATTTGGGGCTTCTGTCCTAGGTGC[A/G]CACGGCAGCAGACCAAACACCCAGCTGGGGGAAGG R 2 1 2 1 202000 f 74 goat ilmnseq_rs657425815 3 3740547 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276114 Affx-1111835174 AX-519549665 3 3740862 TCAGCCCCTGCATCCGTGCCCTCTTCCTCCTCCGC[A/G]GATGAGACCCCTTGGTCACTGATGTGGCTGGTCAA R 2 1 2 1 102000 r 74 goat ilmnseq_rs659534114 3 3740862 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275618 Affx-1111834999 AX-519549188 3 3740882 TCAAGAGAAAGCTGGAGGAGTTGACCAGCCACATC[A/G]GTGACCAAGGGGTCTCATCCGCGGAGGAGGAAGAG R 2 1 2 1 101000 f 74 goat ilmnseq_rs638749927 3 3740882 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275731 Affx-1111835057 AX-519549298 3 3740954 ACCCACCCACTTGTCCATTTCAGCATCCAGGTGGC[A/G]ACGAGCCCACAGATGCCGACGTGGAAGAGGCGGCC R 2 1 2 1 102000 f 74 goat ilmnseq_rs645789240 3 3740954 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468276164 Affx-1111835272 AX-519549714 3 3747747 CCCGAAGAAGCAACCAGAATGTGTCCTTTCCACCT[C/G]CCTTTACCTGGCTCTCAGAGGCGGTCCAGCCTTTC S 4 1 2 1 102000 f 74 goat ilmnseq_rs669588432 3 3747747 G C 1 neutral Goat_IGGC_65K_v2 Illumina 468275704 Affx-1111835043 AX-519549273 3 3747748 AGAAAGGCTGGACCGCCTCTGAGAGCCAGGTAAAG[A/G]CAGGTGGAAAGGACACATTCTGGTTGCTTCTTCGG R 2 1 2 1 202000 f 74 goat ilmnseq_rs643881729 3 3747748 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276029 Affx-1111835127 AX-519549583 3 3747769 TGGCCTCTCACCATCCCAGACAGAAAGGCTGGACC[A/G]CCTCTGAGAGCCAGGTAAAGGCAGGTGGAAAGGAC R 2 1 2 1 102000 r 74 goat ilmnseq_rs654993557 3 3747769 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468275821 Affx-1111835026 AX-519549384 3 3747814 CCGACGTGGACACCTCGGACGAAGAAAGCATCTGG[A/G]CTCAGAGAGTGGCCTCTCACCATCCCAGACAGAAA R 2 1 2 1 102000 r 74 goat ilmnseq_rs642369280 3 3747814 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468275647 Affx-1111835014 AX-519549217 3 3747833 CTGCCCTCCCAGTATCTGGCCGACGTGGACACCTC[A/G]GACGAAGAAAGCATCTGGGCTCAGAGAGTGGCCTC R 2 1 2 1 202000 f 74 goat ilmnseq_rs640800213 3 3747833 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468275596 Affx-1111834988 AX-519549166 3 3750000 GCCTGTGTGGAAGACCACGGTCAAGCGCACTTACC[A/G]GGAGTGGCAGCGACCCCGGGGCCTGCAGTGCAGGA R 2 1 2 1 102000 f 74 goat ilmnseq_rs637083966 3 3750000 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276159 Affx-1111835269 AX-519549709 3 3750087 AGCTCCGAGAGCTCGTCTGGTCCAGCAGGCGAGAG[A/G]CCGACCCTCTGCTCTTCTGGACGGGGGTGGCACGC R 2 1 2 1 103000 f 74 goat ilmnseq_rs669419642 3 3750087 G A 1 not_recommended Goat_IGGC_65K_v2 Illumina 468276184 Affx-1111835209 AX-519549734 3 3750099 GCCAGGGCCCCCGCGTGCCACCCCCGTCCAGAAGA[A/G]CAGAGGGTCGGCCTCTCGCCTGCTGGACCAGACGA R 2 1 2 1 103000 r 74 goat ilmnseq_rs663762137 3 3750099 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275830 Affx-1111835031 AX-519549393 3 3750109 CCAGGCTGATGCCAGGGCCCCCGCGTGCCACCCCC[A/G]TCCAGAAGAGCAGAGGGTCGGCCTCTCGCCTGCTG R 2 1 2 1 103000 r 74 goat ilmnseq_rs642583600 3 3750109 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275792 Affx-1111835087 AX-519549356 3 3750121 GGCCGACCCTCTGCTCTTCTGGACGGGGGTGGCAC[C/G]CGGGGGCCCTGGCATCAGCCTGGTCCAGGATCCCA S 4 1 2 1 103000 f 74 goat ilmnseq_rs649545123 3 3750121 G C 1 not_recommended Goat_IGGC_65K_v2 Illumina 468276008 Affx-1111835198 AX-519549563 3 3772277 ATCTTTCCAAGCTCACGGATGAAGAGGCCAAGCAC[A/G]TCTGGGAGGTGGTTCAACGGGACTTCGACCTTCGA R 2 1 2 1 202000 f 74 goat ilmnseq_rs662818451 3 3772277 T C 2 neutral Goat_IGGC_65K_v2 Illumina 320777243 Affx-122966666 AX-385264366 3 3784110 CTGCAGAGAGAAAACTCTCAGGTTATAGACCAATA[C/T]ACTATCAGCTCTGGAAGTGAAACTGGAGATCATTT Y 2 1 2 1 101000 r 74 goat snp48297-scaffold684-207609 3 115926896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447098 Affx-122924485 AX-123317434 3 3828981 ATATGCAACATTAGGGTACCTTAAGCCCTAAGCCC[G/T]CATAGCCAACTGCATTTTTTAAAATTCAGCCCCAA K 2 1 2 1 101000 f 74 goat snp48298-scaffold684-252480 3 115881734 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38447022 Affx-122924543 AX-123317358 3 3874998 CATGAGAATCCCGCTCTGAACTCCTGAGGCAGCTC[A/G]CGGTGGTAGTTTACTCAAAGTGTTTTCTTTCCTCC R 2 1 2 1 201000 r 74 goat snp48299-scaffold684-298497 3 115835715 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425563 Affx-122941434 AX-123295909 3 3922731 TATCTTCACTTGCAGAGCCTAGATCAGGCAAGCTA[C/T]GGGTCAGAGCCCAAAGCACAAAATGTCAAACAGGC Y 2 1 2 1 101000 f 74 goat snp48300-scaffold684-346230 3 115788538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425370 Affx-122941572 AX-123295716 3 3963722 GACAAAGACAGAATCAAGACCTTGGTTTAGGAAAG[C/T]GATAAGCATATGCTGGGTAGAGAATGAGAAGGAAT Y 2 1 2 1 101000 f 74 goat snp48301-scaffold684-387221 3 115747719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794865 Affx-122978186 AX-385281825 3 4000463 TGGAAATGAAGAAAGAAAAACACGCGTCTACTGAA[C/T]GCTCATCACATGCCTAGTGCCGTATTTGAGGCTTG Y 2 1 2 1 101000 f 74 goat snp48302-scaffold684-423962 3 115711253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447762 Affx-122924571 AX-123318098 3 4036443 TTGGAACCCTAAGCACTTCTTTTATTCCACAAAAG[C/T]GAGCAGCTAGAAGGGGAAAAAGGAACAGGTTAGAA Y 2 1 2 1 303000 f 74 goat snp48303-scaffold684-459942 3 115675114 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774075 Affx-122971560 AX-385261213 3 4070559 AAAGCCACTGGTTTAGTTATTCCTATATTTCTCTA[C/T]TAACTGGACTTTAAGACATGGAACGTTGCAAAGGC Y 2 1 2 1 101000 r 74 goat snp48304-scaffold684-494058 3 115641152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419317 Affx-122945662 AX-123289665 3 4127985 CTGTGCCAGAGAACACAGATGGTATGTTTATTGGA[C/T]TGGTGTGACTGAGACAGACATGGTCCCCTTTCTTA Y 2 1 2 1 101000 f 74 goat snp29472-scaffold3194-50498 3 115574011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799097 Affx-122977459 AX-385286027 3 4168641 TCAGTCTCTGGGATAGCAGTGGTTTTACAGGAGTA[C/T]AGGATTGAGATATGGGTTAAAAACAAATGGATTAA Y 2 1 2 1 101000 f 74 goat snp29473-scaffold3194-91154 3 115532674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386488 Affx-122970758 AX-123256846 3 4199898 TTGTTATCCAGCATATCTTAGAACTATTCTTCATT[C/T]CTCAGAAAATGAAGAACTCATTTGAATATAAACCC Y 2 1 2 1 101000 f 74 goat snp14634-scaffold159-8591 3 115495269 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429218 Affx-122937930 AX-123299560 3 4268489 CTGTTTTTTTTTTTTTTAATACTTCCAGCATTTTA[A/G]CTGCTTCTCCAAAAGAAACTAAATCTGAAAAAGTG R 2 1 2 1 102000 r 74 goat snp14635-scaffold159-77182 3 115428879 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376700 Affx-122978980 AX-123247059 3 4330731 TAGCTCTCTTCTCCAGGGCATAGAGGGCTTTTATT[A/G]CTTCACAGAGCTCTAGGAAATGGAGCAGTAAATGC R 2 1 2 1 201000 r 74 goat snp14636-scaffold159-139424 3 115366759 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449537 Affx-122922597 AX-123319872 3 4341142 TTACCACTTTGAAAATACCAGTTACTATCCTAGGT[A/G]CTGAAAATACAAAAATTAATGAGACATAATTCTTG R 2 1 2 1 101000 f 74 goat snp7791-scaffold1280-234365 3 115356129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432046 Affx-122935900 AX-123302387 3 4392244 CTCTTCCTGCTCTCAGAATTTCTAGAAGATTGTCC[A/G]GAGATGCCTGTCAAAGGCACTTCACCATTCATCAC R 2 1 2 1 101000 f 74 goat snp7790-scaffold1280-183263 3 115304435 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801983 Affx-122933841 AX-385288887 3 4447892 AAAATTAGTTAACTCTTAAGAAAACATAAATTAAA[C/T]GCTCTTTAATAGCAAAGTAAACTCCAGTTAAACTA Y 2 1 2 1 303000 f 74 goat snp7789-scaffold1280-127615 NW_017209692.1 415 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773107 Affx-122932854 AX-385260250 3 4500005 TACAAACAACATTTCAGTTAATTGTTGCAAAAGCC[A/G]TTTTGTTACCATTTAGTTCTATTTTACAGATAAGG R 2 1 2 1 101000 f 74 goat snp7788-scaffold1280-75502 3 115171649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277919 Affx-1111836159 AX-519551414 3 4520098 CAAGAGAAACGTGGAAAGACCCACAGTTAACAGTT[A/T]CCAGCCAGTGATGACCCAGGGCCTAGACAGGGCCA W 4 1 2 1 101000 f 74 goat Random2.2K-297 3 4520098 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38405543 Affx-122955972 AX-123275895 3 4536105 GAGATCATTTCATAAGCACTTAAATGAATTATTAG[C/T]ATTTGTTAGTACTTTTTTCTTCAAAGTGGTTTTTA Y 2 1 2 1 101000 f 74 goat snp7787-scaffold1280-39402 3 115140101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795517 Affx-122967740 AX-385282472 3 4565301 GAAAGCATAGGTTTTTATCAAAGCATTCACATTAG[C/T]GCAATTCAGAACAGGTGTCTGATGTTCTCGGCTCC Y 2 1 2 1 101000 r 74 goat snp7786-scaffold1280-10206 3 115110635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797264 Affx-122977757 AX-385284203 3 4579860 TGAAATTATTTTCCAAAGCTGGTGGCAATTCTTCC[A/G]TTTCTATAGAGAAGATATTTGACTTCTTTTTTAAG R 2 1 2 1 101000 f 74 goat snp26961-scaffold2852-4254 3 115090070 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783117 Affx-122938344 AX-385270184 3 4668825 TGTCCAATGAAATAGAAATGGGTTTAGTTTTGATG[C/T]GTGAGTATAACTAGAACCAGTGGGTAGAATATACA Y 2 1 2 1 101000 r 74 goat snp26963-scaffold2852-93219 3 114999672 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425877 Affx-122940645 AX-123296223 3 4747526 GGGATTCAGATGCCCAATATTGCAAATTTGCTACC[C/T]CTGCTCACTGAGGCCTGGGAATGTTCTGCTTTCAG Y 2 1 2 1 101000 f 74 goat snp26964-scaffold2852-171920 3 114920595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769798 Affx-122972974 AX-385256968 3 4776395 ATATATGTGATAGTTGTTTCTTTATAAATTTATTA[C/T]AGTTTATGAATTTATCACCTGTTCTACCTCAGTAA Y 2 1 2 1 201000 f 74 goat snp26965-scaffold2852-200789 3 114891630 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772973 Affx-122949277 AX-385260117 3 4811854 CCAGAAATGCACAAAGGTATCAATAAACACTTCTT[A/G]TACAGCCTCAAGGAAATAGATCTCCAGTTCCATCT R 2 1 2 1 101000 r 74 goat snp50523-scaffold726-27321 3 114844820 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441386 Affx-122928852 AX-123311723 3 4841440 ATGGAGACTTTAAACAAAGCAAAATGTACCATCTT[A/G]ATAATTTATTTCATTTCATATAATGAAATATGAAA R 2 1 2 1 303000 r 74 goat snp50524-scaffold726-56907 3 114814867 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797426 Affx-122975895 AX-385284365 3 4930128 AAATTGCATAAATGAGGATGAATATAGGGACATTC[C/T]ATTGGCTATAGTACATTGATTCTGCTTGCCCAGTT Y 2 1 2 1 101000 r 74 goat snp50526-scaffold726-145595 3 114725763 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782358 Affx-122956739 AX-385269434 3 4967785 AACCTACTAATTTACTCCCACTAAAAACACTATTT[C/T]TTTTCGTGCTTTGCCAAATGAACCATGTTTTATAA Y 2 1 2 1 202000 f 74 goat snp50527-scaffold726-183252 3 114687272 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416794 Affx-122948148 AX-123287142 3 5020991 CAAAACCTTTCTACTTCTGGAGGAAAGACAGTAAA[C/T]TATCATGGGCACAGACCTTTTGAGATTCCCTATTG Y 2 1 2 1 201000 r 74 goat snp50528-scaffold726-236458 3 114633632 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443268 Affx-122927488 AX-123313605 3 5070317 CTTGCATTCTACTTAGACTTGCTCCAGGCTATAAA[C/T]AAGGCTGAATAGTAGGTTGGTTTTAAATGCACTAA Y 2 1 2 1 101000 r 74 goat snp50529-scaffold726-285784 3 114583973 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390139 Affx-122967992 AX-123260496 3 5104250 CTGGAACCTTATCTAATCCAGGTATTAAGTGATTC[A/G]AACCTGTTTACTTCCATTTAATATTTATATTTTGA R 2 1 2 1 101000 f 74 goat snp50530-scaffold726-319717 3 114550200 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272045 Affx-1111833391 AX-519545809 3 5176243 CGCTGTGATGGGGGTCCAAGCACCAGGGCTGACGC[A/G]AGTACCACCGCGGTGCGTCCCGTTTCATGCCACAT R 2 1 2 1 202000 r 74 goat 3_5176243_AF-PAKI 3 5176243 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320801065 Affx-122955869 AX-385287979 3 5191158 AACTCAAGGCTGCTTGTTGGGATCTATCCTGACTA[G/T]CCCAGTGCCTGATCCAAACCACTAGTAAAATATTC K 2 1 2 1 101000 f 74 goat snp50531-scaffold726-406625 3 114462193 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446192 Affx-122925728 AX-123316528 3 5240862 AGACCTGCTGTATATCCTGACACCACTCTGCCTTC[A/G]TAATAAGACTACTATGGAGTTTAGATGAGATCATA R 2 1 2 1 201000 r 74 goat snp50532-scaffold726-456329 3 114412300 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278075 Affx-1111836160 AX-519551565 3 5299648 GCCCCTTACAATGGAAGTGCAGAGTGCTAACCACT[C/G]GACTTCCAGGGAACTCCCACAAATACAACTTTAAT S 4 1 2 1 103000 r 74 goat Random2.2K-298 3 5299648 G C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429404 Affx-122938529 AX-123299746 3 5300314 TGTGCAACCAACATGGTAAATATTAGGTTAAGCAC[G/T]AATCAATGAAATCTCAGAGAATTTTGCTATGAATT K 2 1 2 1 101000 f 74 goat snp50533-scaffold726-515781 3 114352299 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428331 Affx-122939000 AX-123298674 3 5365787 ACCTACCAAAAAGCACACAGTGTGAACAAAAACTA[C/T]GCTGAGCCCTTGGGGCAGTCGCATCTGCCAATTCC Y 2 1 2 1 101000 f 74 goat snp50534-scaffold726-581254 3 114287040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418866 Affx-122946124 AX-123289214 3 5396341 TACTTTTGCCTCAGGGATAGTAGCAGCCCTGAGCA[A/G]TTTTCAGGGATGGGCTCTGAAGCACTGTCCTATAT R 2 1 2 1 303000 r 74 goat snp50535-scaffold726-611808 3 114256474 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787604 Affx-122952086 AX-385274627 3 5443271 GTCGGATAGCAATTATTAACTGAGTGTGCATGCCA[A/G]TTTGGCACTGTATAAATCAGGTTGGATATTGGTAC R 2 1 2 1 101000 f 74 goat snp50536-scaffold726-658738 3 114209131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387528 Affx-122970310 AX-123257886 3 5490011 TGGAAAGATTGTATTGACAATAGACACAAATTCTT[A/G]TACTTTGTTGTATGGGGGAGTAAAGGCTCTACCTA R 2 1 2 1 201000 f 74 goat snp50537-scaffold726-705478 3 114162314 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786075 Affx-122926149 AX-385273111 3 5565183 TTAAGACAGATGAAACACTTAAAGTAGAACATGTC[A/G]TTGCATTTCCTGATCATATGCTAGATCTGATTGTT R 2 1 2 1 101000 f 74 goat snp50539-scaffold726-780650 3 114085817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403447 Affx-122957730 AX-123273800 3 5710826 ATATCCCTTTCTCCCCAAATTCTTCAGACAATCCA[C/T]GAAAGGAAATGATTTGGCTTTTAATTATGCCCTCC Y 2 1 2 1 201000 r 74 goat snp50542-scaffold726-926293 3 113939041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440320 Affx-122930205 AX-123310657 3 5769480 TGACACTCAGTTCTTTTAAAAAGATACCTTATTGG[G/T]ACAGTTCAGAGTCTATTACTAGTAAAGAGGCAAAG K 2 1 2 1 101000 r 74 goat snp50543-scaffold726-984947 3 113879651 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412287 Affx-122950876 AX-123282636 3 5800164 ATTGCTTGTTCTAATTTTCTCTGACTCAGATGGTC[A/G]TTTCCCAGGGCTCTGGAAAGGTCTTTTGTTTCTAA R 2 1 2 1 101000 f 74 goat snp50544-scaffold726-1015631 3 113848189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436255 Affx-122932550 AX-123306594 3 5845187 GTATAGCTGCAATCTGCGCATGCAGGCTCAGTTGT[A/G]CTCAACTCTTTGAGACTCTATGGAACGCAGCCCAC R 2 1 2 1 103000 f 74 goat snp50545-scaffold726-1060654 3 113802845 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801561 Affx-122927454 AX-385288470 3 5873764 TTTGTTATCTGTTCTTGACCAATCTTAAGGAGACT[A/G]TGGTTTAGGATTTGGGCAAGAGAGCGCTTTTAGCA R 2 1 2 1 101000 r 74 goat snp50546-scaffold726-1089231 3 113773571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779252 Affx-122927344 AX-385266356 3 5910490 TTTAAGTACATAATCACGACTTCCTCTGTTGGCTA[C/T]GATGGAGTACAATGAAACAACATATTGCTGCCAAT Y 2 1 2 1 101000 f 74 goat snp50547-scaffold726-1125957 3 113737002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453131 Affx-122920007 AX-123323464 3 5956363 GAGATAATGTGAAGCTCATTTCCAGTCTATAATAA[G/T]AACATGTGTGCCAGGAGGCAGTGTGGTGAAGTGAA K 2 1 2 1 201000 f 74 goat snp50548-scaffold726-1171830 3 113689052 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787842 Affx-122976855 AX-385274865 3 5980654 AAACAGAAAAGTATCACAATGATCAAATTTGCAAA[G/T]AACTTTGTGTGTTTCAGGTTACTAAAGGATGTTCC K 2 1 2 1 101000 r 74 goat snp26119-scaffold2721-225024 3 113664632 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794591 Affx-122942393 AX-385281553 3 6048656 TACATGAATAAGTTGTAGGGCAAAAATTATAAAAA[C/T]ACTTTACAGATATAAGCCATTATTCACCCTATGAG Y 2 1 2 1 101000 r 74 goat snp26118-scaffold2721-157022 3 113597256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390865 Affx-122967817 AX-123261222 3 6080021 AAGTGACTTACTATTCCATTTGCTTGTTTTCTTTG[C/T]AGCAGAACTTAGACCTGTCTTTGGTCTCTGTCTCC Y 2 1 2 1 101000 r 74 goat snp26117-scaffold2721-125657 3 113565061 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803373 Affx-122937307 AX-385290207 3 6132056 GAAGGGACTTCAGTTTAGATTAAGATGGCCTCCTT[A/G]CTTGTTTCTTCTGTTGCTCAATGTCAGAAAGTCGT R 2 1 2 1 101000 r 74 goat snp26116-scaffold2721-73622 3 113514917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406382 Affx-122955405 AX-123276734 3 6174072 GTGTTGGAGGAAGAAGGGCCCATGGCATTCGTTTG[C/T]GGTGTTATGTACACTCATCCTGTCCCCTGAGTTGA Y 2 1 2 1 101000 r 74 goat snp26115-scaffold2721-31606 3 113472304 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434068 Affx-122934185 AX-123304409 3 6215908 TTAATAAGAATTGTTTGCTACATGATCTTATAATG[C/T]ACTACTTTTCTTTTATAGCACTTTTTACACTTTTA Y 2 1 2 1 101000 f 74 goat snp17637-scaffold183-10131 3 113430423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393320 Affx-122965952 AX-123263676 3 6296876 TCATTATCTTCCCTTGGATACAGTCACTGGCTTTC[A/G]TTCCAAAGGCACCCAAGGCTGGTCACTGTTCCTCC R 2 1 2 1 101000 f 74 goat snp17639-scaffold183-91099 3 113350737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397148 Affx-122962440 AX-123267503 3 6347008 TAACCAGGGAGGAAATAAAGCTTATGGCTATGTAG[C/T]GCTGGTCCCCTCACTTCACCAGCAGCAGAAAAAAT Y 2 1 2 1 101000 f 74 goat snp17640-scaffold183-141231 3 113300813 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396198 Affx-122963365 AX-123266553 3 6386394 CAGCTCCAAGTAAAGTGATGTTGAACACCCTGACT[A/G]TACTTAAGTTGTAAGAAATTTCCAAGATGGCCAAT R 2 1 2 1 201000 r 74 goat snp17641-scaffold183-180617 3 113260820 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768916 Affx-122966195 AX-385256093 3 6418968 GGCAGTGCAACTGTTTATAATTGGGTGTGTACCAT[A/G]TATCTTTGTGTGGATGTGCCCTGCAGATTATATGC R 2 1 2 1 101000 r 74 goat snp17642-scaffold183-213191 3 113228064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780340 Affx-122941681 AX-385267435 3 6492695 TTTTAGTTAACTGCTTTTTACCACAAAAATTCTTA[C/T]ATTAAATTTTGCCTGCTCAAATTACTAGTGTGGTG Y 2 1 2 1 101000 r 74 goat snp17644-scaffold183-286918 3 113153820 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274517 Affx-1111834238 AX-519548108 3 6509898 AACCTGTGGGGTTCCTGCAGCTGAAACCCAGAAGC[A/G]TGTGAGAGCCCCCTAAGTCTACAGCTTCTGGAAGT R 2 1 2 1 201000 r 74 goat GoatD01.026962 3 6509898 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770283 Affx-122935374 AX-385257449 3 6536576 AAGTTGTATAGAATACAGATATTCTTCTACAAATA[C/T]AGTAGCTTTTAGATTTGTTATTTTATATTTCACAT Y 2 1 2 1 201000 r 74 goat snp17645-scaffold183-330799 3 113108842 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409994 Affx-122953273 AX-123280344 3 6594362 AACTGGGGCCAACCTCTTTGTTCTTTAAAATCTGA[C/T]GGATTACAAGAAGGTCTTCATCACCCACATTTGTT Y 2 1 2 1 102000 f 74 goat snp17646-scaffold183-388585 3 113050745 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780951 Affx-122920869 AX-385268038 3 6632028 GCTTTCTGAGACAATTTCTGCCATTCAGAGGGTGC[C/T]CTGATGATCACATTTGGATTCTTACAGATATAATA Y 2 1 2 1 101000 f 74 goat snp17647-scaffold183-426251 3 113013005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401003 Affx-122959691 AX-123271356 3 6687585 CATGGGGTTCAAGGAGGGGGAGAGGGAGTTTGTAC[A/G]TAATGGGTGCAAAGTTTAGAGTTATGAGAACATCT R 2 1 2 1 201000 r 74 goat snp17648-scaffold183-481808 3 112957069 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444071 Affx-122926848 AX-123314408 3 6755065 CGCTCAACGGTCTGAGTGTTAAAAACATTCACAGG[C/T]ATGCTTTAAAATCCCCACCCTGACCTGTCTTAACT Y 2 1 2 1 101000 f 74 goat snp17650-scaffold183-549288 3 112889137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389173 Affx-122969091 AX-123259531 3 6789610 TCTGCAGTTTCTCTGTATCCACCATTCTGTATCCA[C/T]AGCCGCAACCAACCGCATATTGTGTATTTACTGTA Y 2 1 2 1 101000 f 74 goat snp17651-scaffold183-583833 3 112854560 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451557 Affx-122921703 AX-123321890 3 6842520 CATGCGCTTGGCAACTAACACAGCCTTCTCTGTGG[C/T]ATCTCACTGAACCTTCATGAAACAGCTGAGGAAAC Y 2 1 2 1 101000 r 74 goat snp17652-scaffold183-636743 3 112802027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403895 Affx-122957491 AX-123274247 3 6880944 AGATTCCCTGGGTACAAAAGCAGGGGCAAGGGTAG[C/T]AGGGGTGAAGGCCAACCAGAATGATTAACCATCCT Y 2 1 2 1 102000 r 74 goat snp17653-scaffold183-675167 3 112763166 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391970 Affx-122966521 AX-123262327 3 6912888 TTACAGAAAAGGGGTTGCTAGATCAAAGAGTAAAC[A/G]CATATGCAATTGTACGAGGTACTGCCTATTCCCCT R 2 1 2 1 101000 f 74 goat snp17654-scaffold183-707111 3 112731681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391840 Affx-122967002 AX-123262197 3 6942994 ACTGGAATTTCATTTACGTCAGGGAAAATGTTTAC[A/G]TGGCAGTTTCTTTGGAAGGCAGTGGCATTTTGTCA R 2 1 2 1 101000 f 74 goat snp17655-scaffold183-737217 3 112701807 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394270 Affx-122964718 AX-123264625 3 6976730 TGAAACAGGTGGTAGAAGAACAACCACTGATCCTA[C/T]AAATGCAAAGAGTAATGACAAGATTGTTCTGTTAA Y 2 1 2 1 101000 f 74 goat snp17656-scaffold183-770953 3 112668041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791841 Affx-122937402 AX-385278831 3 7014209 GAAGGTGGACATCTTCTAAGAGATCATCTAATGAC[A/G]GAGATCCTGATAATTGTCCCAAACCATGAAGACAG R 2 1 2 1 101000 f 74 goat snp17657-scaffold183-808432 3 112631010 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398258 Affx-122962185 AX-123268613 3 7044577 AAGCAGGGTGTTTGGATAGTCACTTAGAAGTTTCT[A/G]CTGCAAAGTAAGGATTGGGAAAGAAAGATTAATTC R 2 1 2 1 101000 f 74 goat snp17658-scaffold183-838800 3 112600146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381010 Affx-122974662 AX-123251368 3 7093613 AGGACTCTGAGGCAGGAAGCTGAGCTGGCCCAGCA[A/G]TGTGCAGTGGAAAGAGGGCTTTCATGGTGGAAAAT R 2 1 2 1 103000 r 74 goat snp17659-scaffold183-887836 3 112550518 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770706 Affx-122947842 AX-385257870 3 7129897 ACATCTGCAGCTTTTTTAGTAATTGTGTGCATCAT[A/G]TTTCTCTGTTAAGTCAGAGTCTCTCCAGCTATCAT R 2 1 2 1 101000 r 74 goat snp17660-scaffold183-924120 3 112514040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390665 Affx-122967129 AX-123261022 3 7193819 TACTACACAGTTGAATATAAGTATCTTTTTTTAAT[A/G]GCTTGAATTTCTCAGATCATCAGTATTTAGAGTCC R 2 1 2 1 101000 r 74 goat snp17661-scaffold183-988042 3 112448237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450597 Affx-122922019 AX-123320931 3 7241455 GAAAGAGAGTCATCAGGATATACAGAAATGGACTG[C/T]GTGCTAAATTATGGCATAAAGGGGAAAAAAAAAGT Y 2 1 2 1 101000 f 74 goat snp17662-scaffold183-1035678 3 112400019 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804072 Affx-986696656 AX-385290742 3 7275293 CCAGGGATGGTCCTTCTGTGAGGCCAACGAGAAGG[A/G]GAAGAAGCCACTGTGGCCATCGGGGAGAGGGTCTG R 2 1 2 1 600010 f 74 goat 3_7275293 3 7275293 Ancestral_priority_1043 ancestry 0.458 neutral IMAGE 10K 10K ancestral 320787330 Affx-122938504 AX-385274355 3 7305057 TGAGGAGATGAGATTGAACAACTTGAGGAGGCTGG[C/T]GAAAGTGGCTGAGGTTCTGTCTTTATATCTTTAAT Y 2 1 2 1 102000 f 74 goat snp17664-scaffold183-1099280 3 112335839 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409064 Affx-122953348 AX-123279415 3 7334204 ATGGGATTTATGTCCTCTAGGTTTTAATTTCAATG[C/T]AGTCAGATTTATCAATCTTTTGTTAATGATCTCTG Y 2 1 2 1 101000 f 74 goat snp17665-scaffold183-1128427 3 112306142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383625 Affx-122972547 AX-123253983 3 7374576 TGACCAATGCTGAGCACTGACCCCTGGGAGGCATC[A/G]CTGCTTCTCCCAGTCTTTCCTCATTTCTGAACATG R 2 1 2 1 101000 r 74 goat snp17666-scaffold183-1168799 3 112265375 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421614 Affx-122944478 AX-123291961 3 7408036 ATGACAAGACAAACAAAAAACTAGACAAACATTTG[G/T]GAAGCCTGATTAAGATAAACAGATATGACAGTCAA K 2 1 2 1 101000 r 74 goat snp17667-scaffold183-1202259 3 112232560 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778627 Affx-122962941 AX-385265738 3 7475270 GGACACGGGGGCTTGTGCATGGTTTTACTATTACT[A/G]TAATTCCCACCCCAATCCTACGCTCCACCACTACC R 2 1 2 1 101000 f 74 goat snp17668-scaffold183-1269493 3 112157042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417446 Affx-122947202 AX-123287794 3 7576409 CAGATCATTATGAATAATTAGGTTAGCAAACAAGC[A/G]TTAATACCAAATATGAATTTAATACTAAATATCAC R 2 1 2 1 101000 f 74 goat snp17670-scaffold183-1370632 3 112055110 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764948 Affx-122964666 AX-385252529 3 7591446 CCAAAGGGATAAAAGAGAAAGGACTTGATCCCTAA[C/T]GGATATGGTGAGTACGAAAGGTTCTGAACTTATTT Y 2 1 2 1 101000 f 74 goat snp17044-scaffold1777-7639 3 112015390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452026 Affx-122920903 AX-123322359 3 7624985 CTGTTCCCATGCATTCAGTACTAAAGTTTCCAGTC[A/G]TGGAGATGCTTCCTCCTTCCCTCCTCTGAGTCTTT R 2 1 2 1 101000 f 74 goat snp17045-scaffold1777-41178 3 111981879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452560 Affx-122920522 AX-123322893 3 7662294 TCTATATATCTTCTCCCCAAGACCTGCTCCAAGAG[C/T]CAACTTAACTCTTTTTATCTCCTGCTAGCTGGGAC Y 2 1 2 1 201000 r 74 goat snp17046-scaffold1777-78487 3 111944041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418762 Affx-122946200 AX-123289110 3 7693631 TTATTAAAGATACTTGGGGCTCTTTCCCATTCTTA[G/T]GTAAACCTTCTTCACCAGAAATAGTGCACACGCTG K 2 1 2 1 101000 r 74 goat snp17047-scaffold1777-109824 3 111912650 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272225 Affx-1111833399 AX-519545972 3 7699659 AAGCCATGCAGGACTTGAAGGCAGCTGAAATCACT[A/G]AAGAGAGCCCAGAGATGGCGGATGGGGAGGGGGAC R 2 1 2 1 101000 f 74 goat 3_7699659_AF-PAKI 3 7699659 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446106 Affx-122925795 AX-123316443 3 7732226 ACAGACCAGCAACTACTAAGGGCTGAGGGGTGACT[A/G]TGGAGGGGGCTGGGGGAATTTGGGAATGATGGAAC R 2 1 2 1 201000 f 74 goat snp17048-scaffold1777-148419 3 111873951 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785917 Affx-122943751 AX-385272954 3 7769340 ATATTTACTTCCCTACCCTAACTCATTCTTCATAT[A/C]TCATCTGAAACCACCTTTTCCCAAGACATCAGAAA M 2 1 2 1 101000 r 74 goat snp17049-scaffold1777-185533 3 111837021 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277923 Affx-1111836161 AX-519551418 3 7778398 CCAGGAATCCACCAAGTTTGCCTGGTTGTCAGGAG[A/C]CCTGAGCTTGGTGGGAAAAGGCGGGGAGAACAGGG M 2 1 2 1 102000 f 74 goat Random2.2K-299 3 7778398 T G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431232 Affx-122937142 AX-123301573 3 7798148 GTAGACCTTAATGTATTAACATTTTATTGTTAACA[C/T]GTCTAAGAGGGTGCTTCTGAACCAGTTGAACACCT Y 2 1 2 1 101000 r 74 goat snp17050-scaffold1777-214341 3 111808346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386110 Affx-122971427 AX-123256468 3 7853474 CCTGCAGCCCTTTCCCCTTTTGCTTTCTTCTGGCT[G/T]GGGCAAAGGCCATCATAGGTGAGAATGAAGTGATG K 2 1 2 1 201000 r 74 goat snp17051-scaffold1777-269667 3 111753373 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799208 Affx-122925123 AX-385286138 3 7891413 TACAAAGTCAGTTGAAATTCTACCACTCATTTGAC[A/G]TCTCTGTTGATGGTATAAAAGAAGAAAAAGCTAGA R 2 1 2 1 101000 r 74 goat snp17052-scaffold1777-307606 3 111715466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435264 Affx-122934058 AX-123305604 3 7943509 TAGTCCCCGCGCGGCGAAGCTGTGTGTGTTTCTAG[C/T]GTCGCAGTGACTGCTGTCGCATCGGGATCTTGATC Y 2 1 2 1 101000 r 74 goat snp17053-scaffold1777-359702 3 111662990 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793175 Affx-122945229 AX-385280153 3 7972983 GTGGGAAGCAGGTGATGACAACCTCTAGCCTTCAA[C/T]GTTAGAACAAAGCCTAAGGTCCAGGTGGTCTAAAG Y 2 1 2 1 101000 f 74 goat snp17054-scaffold1777-389176 3 111633576 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389596 Affx-122968772 AX-123259954 3 8012178 CTCAAGGAAGTCAACTTGTCTTCCATCTTGGGCCT[A/G]TTTGGTTCTATTATCTTATGTCATGTCCTCAGGCT R 2 1 2 1 201000 r 74 goat snp17055-scaffold1777-428371 3 111594078 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397580 Affx-122962002 AX-123267935 3 8066373 GACATCCATGAGACAGTTGGATATGGGGTTTCAAA[C/T]GCAGAAAATAACTGGCTGCCCTGTGAAATTTAGGA Y 2 1 2 1 101000 f 74 goat snp21715-scaffold213-40854 NW_017200692.1 8587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376137 Affx-122978861 AX-123246496 3 8114988 TTGCACAAATTGCCTTATCATTCAATTTTGATCTC[C/T]TAAATTTATAATTCACAAAATAGATGTAGCTCACA Y 2 1 2 1 101000 f 74 goat snp21716-scaffold213-89469 3 111159559 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438743 Affx-122930828 AX-123309080 3 8152220 TTCTTTGGAAACCATGAGCACCATTGTTTACTCCC[A/G]GGGTAGAAAATTCTAGACAATTCTGGGTGAGAAAA R 2 1 2 1 101000 f 74 goat snp21717-scaffold213-126701 NW_017214458.1 12035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422157 Affx-122943533 AX-123292504 3 8186627 CACTGTTGAGGCTGAGTCCTTTTCAGAGGCTCCTT[G/T]CCCTGCAGAGACAAAAGAGGGACTTGGAGAAGCAG K 2 1 2 1 101000 f 74 goat snp21718-scaffold213-161108 3 111233829 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392053 Affx-122966394 AX-123262410 3 8228332 GAGACATGGTATAGTCAAGACCAGTATCCTCAGGT[A/C]GACCATCCACAAATAAGAGGACAACTGCAATTACA M 2 1 2 1 101000 r 74 goat snp21719-scaffold213-202813 3 111275816 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423166 Affx-122942742 AX-123293512 3 8272913 AATCACTTAATAAATATGTAAGATAAAGAAGTCCC[A/G]TGAGCTATGAATCTCCCAAGTGATTAAAGAATAAT R 2 1 2 1 101000 r 74 goat snp21720-scaffold213-247394 3 111325054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384760 Affx-122972027 AX-123255118 3 8336365 AACAAAGTGCAAAGGGAGGTCCTGAGGAGCAGCCA[C/T]GGGGAAGAGGGCCCTGTAGAGAGAGCTAGTGGGCA Y 2 1 2 1 303000 f 74 goat snp21721-scaffold213-310846 3 111389028 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420760 Affx-122944716 AX-123291107 3 8349748 AATCTACTGCTTCTCTCATTCTGCTATTGGTTCCC[C/T]CTAATGGCTTTTCACCTCAGTTATTGTGTTCATTG Y 2 1 2 1 201000 r 74 goat snp29272-scaffold315-1752872 3 111002050 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454110 Affx-122919356 AX-123324443 3 8418625 TGAAAGAGGTTGCTATTGGGCCTCATGTATTTAAA[C/T]GGAATCTGGTTCTCAATGGTAGTCATGGCCTGTGA Y 2 1 2 1 201000 f 74 goat snp29271-scaffold315-1683995 3 110932495 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433860 Affx-122934430 AX-123304201 3 8520732 TAATTATATTAGCCACACTTCTGTGTTTTTCTACT[G/T]TGGGGCAGATGGAGATGGTAAAATCCTTGAGACAT K 2 1 2 1 201000 f 74 goat snp29270-scaffold315-1581888 3 110826227 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395813 Affx-122963642 AX-123266168 3 8682604 TTGTTATTTTTTAAAATGTCAGGATGAACTGTCAC[A/G]TGTATGGCTGTGTTTGTCTTTTGCTTCTCCTGTAT R 2 1 2 1 101000 r 74 goat snp29266-scaffold315-1420016 3 110662506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781022 Affx-122943949 AX-385268109 3 8713914 CACTGAGGTTGACCTCTTTAGGAAATCCTGTCACC[G/T]CAACATTCTCCTCCCTGCTAAAGAATTAGACTAGT K 2 1 2 1 101000 r 74 goat snp29265-scaffold315-1388706 3 110632974 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377763 Affx-122977361 AX-123248122 3 8761572 GCTCACTGCAAAGCCTTTCAGTGGAACAAGGTGGG[C/T]GACGGCTTGGCTTATGAAGATTTCAGTTTCCCCAT Y 2 1 2 1 101000 r 74 goat snp29264-scaffold315-1341048 3 110585048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413522 Affx-122950624 AX-123283871 3 8849859 ACCTTAGGCTCTGAAATTCAAAGAATGACCCCAAC[A/G]AAGCTGAAACTCATACTATAAAAAACATGTTTATA R 2 1 2 1 201000 r 74 goat snp29262-scaffold315-1252761 3 110496588 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403214 Affx-122957906 AX-123273567 3 8883776 GCCACCCAACCCCCACCTGGAAGGGGCAAAGAGAA[A/G]CAAGGGGCAAAGAAGCCAGAGTTTGTGTTTGTACC R 2 1 2 1 202000 f 74 goat snp29261-scaffold315-1218844 3 110462688 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422875 Affx-122943077 AX-123293221 3 8966220 CAAGGAGCTCAAAGTCTAGCATCCAGTGCCTTGTG[A/G]TGAGTGCAGCCCCAGAATCATGCCTGGGATACAAG R 2 1 2 1 101000 f 74 goat snp29259-scaffold315-1136400 3 110380851 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443308 Affx-122927458 AX-123313645 3 9070346 AGAGTGCTTAGGATGTTCAAAAAAAATTTCTCCAA[A/C]GCTCTCTCTGATCCATTCAGAACAATCAGAATCCA M 2 1 2 1 101000 r 74 goat snp29256-scaffold315-1032274 3 110276949 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396575 Affx-122962917 AX-123266930 3 9127193 GTCACTTACAAGATGAAATGAAAAGATTTAAGCCT[C/T]TCTAGATTCAGCCTGCCCTTGACTGTCCATTCTCA Y 2 1 2 1 101000 f 74 goat snp29255-scaffold315-975427 3 110219759 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445763 Affx-122926072 AX-123316100 3 9194582 TTCTCCAAAGGCACTTATCGCTGGCTTTCTGAATT[A/G]CCTTGGCTCATCCCCGTGTTTTATCTCCCCTACAG R 2 1 2 1 201000 f 74 goat snp29253-scaffold315-908038 3 110152428 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441522 Affx-122928715 AX-123311859 3 9262723 GGAGGATTGCCGTAAATATTAATATATGCACATGC[A/G]TTCCAGGATTCAGAGGCGAGGCCTGGTTCTCCTCC R 2 1 2 1 101000 f 74 goat snp29252-scaffold315-839897 3 110084129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386927 Affx-122970001 AX-123257285 3 9296460 AACCTCTGTCCATAGTTCTTCAGGCACTCTATCAG[A/G]TCTCACCATCATAAACATCATCTCCACCACACCTT R 2 1 2 1 201000 r 74 goat snp29251-scaffold315-806160 3 110050535 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388618 Affx-122969137 AX-123258976 3 9358962 CACAAGTGTCCTGAAATGTCCCTGCTTTCAGGGCT[A/G]AGCGGTACTGTAGAATCTCTTCCAGTCTTTTCTCT R 2 1 2 1 101000 r 74 goat snp29249-scaffold315-743658 3 109987902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406775 Affx-122955716 AX-123277126 3 9394836 GATAAGGAGATCTTAATGAAAAGGCTGAAAGTTCT[A/G]CCTAAATGCCATTAGTGCGTGTAGTATTTTTAGTG R 2 1 2 1 101000 r 74 goat snp29248-scaffold315-707784 3 109952453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449142 Affx-122923557 AX-123319477 3 9432476 AAAACTCCTCACCAAGTCTGCATGAGTTAGGACAC[A/G]CAGTTTTAAGGAGCACAGCCCACCATGTTCCTCTT R 2 1 2 1 101000 f 74 goat snp29247-scaffold315-670144 3 109914133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446681 Affx-122924752 AX-123317017 3 9463298 GAGATGGAGAGATTATGCTGGTGTCCAGGAGGCTC[G/T]ATATAATGACAGGGAGGAAGGAAGTTGGAGAGAAG K 2 1 2 1 201000 f 74 goat snp29246-scaffold315-639322 3 109882458 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434846 Affx-122934377 AX-123305187 3 9499083 AGAAGAACACCACAGAGTTTAAAAAATAACTGATA[G/T]ACCTGGAAAAACATTTTGTAAAGATAAACTCTGAC K 2 1 2 1 303000 r 74 goat snp29245-scaffold315-603537 3 109851197 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395258 Affx-122964094 AX-123265613 3 9549347 ATTACCTTAATAAGAATAAAATTTGGAAATAAAAG[C/T]AATAAAAGTCAAAACAAAAAAATTAGCCCTAAGGG Y 2 1 2 1 303000 f 74 goat snp29244-scaffold315-553273 3 109802334 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774548 Affx-122924011 AX-385261682 3 9618383 CTGCATTTACAAGAAAAGAAACTATTACAGAGTGT[A/G]TTGATATTTACAACAAATCATGTATGTTATTTAAA R 2 1 2 1 101000 f 74 goat snp29242-scaffold315-484237 3 109732311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443848 Affx-122927526 AX-123314185 3 9672353 TTTCCTCTTTGTCCGGTACTATTGGCCTTTCCTGG[C/T]GCACAGATGCTACAAAGCAAGGGGAAGTAGATGTA Y 2 1 2 1 101000 f 74 goat snp29241-scaffold315-430267 3 109677329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772912 Affx-122939120 AX-385260056 3 9788047 TCATTCAGTAAAATTCAATCAAACTCTTTACCATG[A/C]TCCATGATGACCCTCAATAGGAAATGCATATCATA M 2 1 2 1 101000 r 74 goat snp29239-scaffold315-314573 3 109558762 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435050 Affx-122933746 AX-123305390 3 9834695 ATATTCATCATGGACACTTTGCAAAATTCAAGAGA[C/T]GGTAGAAATTTATACCGTGAGTTATACCATGCAGA Y 2 1 2 1 101000 f 74 goat snp29238-scaffold315-267925 3 109516602 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446049 Affx-122925837 AX-123316386 3 9875393 AAACATTGGGATTCTTTATGCTTTGTCCTGGAATC[A/G]TCTTTGTTTTCTAGCTACTCTTCCTCTCTCTTTAA R 2 1 2 1 101000 r 74 goat snp29237-scaffold315-227227 3 109476096 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418215 Affx-122947053 AX-123288563 3 9910236 AGCCAGCTAGATACTTGTTGGGGTAACAAAACTAA[C/T]AGTAGGAGCAGATAGAGAAAGTTTCTACTGCTAGC Y 2 1 2 1 101000 f 74 goat snp29236-scaffold315-192384 3 109440956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411035 Affx-122951966 AX-123281385 3 9953630 TTTCCCCTGAGTAGTTTGTTCTCCACCTCCTAAAA[G/T]AATACACTGCACGTGACTCCAAACTGCATGTGTTT K 2 1 2 1 201000 f 74 goat snp29235-scaffold315-148990 3 109396960 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448962 Affx-122923131 AX-123319297 3 9989703 CTTTATCAAATAAATAAAACAGATCAAAGGAAAAC[G/T]ACTCTTTTGGAAACAGATAAATAAGACCTGAAACC K 2 1 2 1 201000 f 74 goat snp29234-scaffold315-112917 3 109360888 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423154 Affx-122942752 AX-123293500 3 10024829 TCCCCTACTGTCTGGCCAGGCACCTTTTCTTCATG[C/T]TGAGGAGTGAGACAAAAGCAACCTTCAAACTAACA Y 2 1 2 1 101000 r 74 goat snp29233-scaffold315-77791 3 109325802 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412836 Affx-122950460 AX-123283185 3 10064906 ACATCTACATCACCTGGAAACTTGTTAGAAATGCA[A/G]CTTCTTGGGCCTCAAGCCAGATCAAATAAACCTGA R 2 1 2 1 201000 r 74 goat snp29232-scaffold315-37714 3 109285126 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402154 Affx-122958651 AX-123272507 3 10094387 ACACTGAGCAAGTCACTAATCTTATGCTTTAACTT[C/T]CTTGTCTCTAAAGTAGAGATATTAGTAGTACTTGG Y 2 1 2 1 101000 f 74 goat snp29231-scaffold315-8233 3 109255390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446900 Affx-122924707 AX-123317236 3 10122051 AAGAAAAGGGGGAGGAAAATGTTCTGAATTATGAC[G/T]ATTTCTCCCATGTCCTCTAACCTCTGATCTCTGGA K 2 1 2 1 101000 r 74 goat snp56497-scaffold89-1084978 3 109138720 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404717 Affx-122957251 AX-123275069 3 10151083 CTTAAGTCCTGTGCACATCTTCTCAAGGTGCTGCT[A/G]TGGTTACTTGTAAGAGATTCGCTGTTACTGATTTA R 2 1 2 1 101000 r 74 goat snp56496-scaffold89-1055946 3 109111988 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793897 Affx-122973075 AX-385280866 3 10234090 CAGGGTGTACTTGTATGCAATTCAAGAGTGTTAAG[C/T]ATGTTGACTTTGTGCAACTAATCTCCAGAACTCTT Y 2 1 2 1 101000 r 74 goat snp56495-scaffold89-972939 3 109035337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783056 Affx-122944596 AX-385270123 3 10304067 TAAGTTCTTCCCAGTGCTCAGATTAGAATACAAAA[G/T]GGTAGAAATGCCTGACTGACAACGTTCTTACCCAA K 2 1 2 1 101000 r 74 goat snp56493-scaffold89-902962 3 108964864 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409860 Affx-122952922 AX-123280211 3 10353865 AGAGCATTTTGTAAGTATGAAGGAGGCCCAGTAGG[C/T]GAACTGTGGACTCTCTCTTGGGAATCTGGTTCTTG Y 2 1 2 1 101000 f 74 goat snp56492-scaffold89-853164 3 108914528 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387409 Affx-122970409 AX-123257767 3 10400624 CTCATTATTTTCAGAACTCCATCATGTTGATGGCT[A/G]CTAGCTTCTCTCAAGACCCTGGAAACCAAGGAAGA R 2 1 2 1 201000 r 74 goat snp56491-scaffold89-806405 3 108869326 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377271 Affx-122978131 AX-123247630 3 10444909 AGCTGAGCCACAAGGAAAGCCCCTATATCTTCCTA[C/T]AGCTCACAAAACAACTGCTCAATACTGACCTGTCT Y 2 1 2 1 101000 r 74 goat snp56490-scaffold89-762120 3 108823572 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417931 Affx-122946717 AX-123288279 3 10477794 TCAATCCCATCATTTATAGCCTAAGAAATAGGGCT[A/G]TGCAGACAGCCCTGAGAAATGCTTTCCAAGGGGGA R 2 1 2 1 101000 f 74 goat snp56489-scaffold89-729235 3 108790706 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272007 Affx-1111833372 AX-189289814 3 10496829 CCTGGAGTTCACTCAGACTCACGTCCATCGAGTCC[A/G]TGATGCCATCCAGCCATCTTATCCTCTGTCGTCCC R 2 1 2 1 303000 r 74 goat 3_10496829_AF-PAKI 3 10496829 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401762 Affx-122959500 AX-123272115 3 10508996 GTTTGTTTGTTTTTATTTGTTTGTGACTACCTTGA[C/T]AATTTTAGTGAAATTTCTCCTTCCCAGCCTTTTAC Y 2 1 2 1 101000 r 74 goat snp56488-scaffold89-698033 3 108760431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780573 Affx-122963025 AX-385267664 3 10561005 TTACCTAGAAAAATTCTTCCACTTTTATATCTCTA[A/G]TTATTTTATACCATCTATTAGTGTAGTGATCATAG R 2 1 2 1 101000 f 74 goat snp56487-scaffold89-646024 3 108708379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436120 Affx-122932654 AX-123306459 3 10590435 GAAGGAGGGGTAAATATTCTGCCTGCACATGTGTT[A/G]CAAAAATGGTCCCAGGGAAGAAAGTAGAGTCATGG R 2 1 2 1 101000 r 74 goat snp56486-scaffold89-616594 3 108678239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379073 Affx-122976326 AX-123249432 3 10623536 GTGTCATCTTCGATTCAAGAAAGAATGTGACTTGA[C/T]AAGAGTCATACAAAGAGGATATTATCAGTTGACAT Y 2 1 2 1 102000 r 74 goat snp56485-scaffold89-583493 3 108644869 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449465 Affx-122922652 AX-123319800 3 10656340 TGTCATAGAATATGCTTCCCTAGTCCATGGAACTT[A/G]CTTCCTTTCTATCAGCCATCTCTGAAAGACTGATT R 2 1 2 1 101000 r 74 goat snp56484-scaffold89-550689 3 108611762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776128 Affx-122938101 AX-385263258 3 10701613 TCCCTAAGAGAGACATCTTTGAGTATCTAGTACAA[C/T]ATTTTCCCATTTCTAGCCCAGAGTATATGAACTCA Y 2 1 2 1 101000 f 74 goat snp56483-scaffold89-505416 3 108565401 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426187 Affx-122940578 AX-123296533 3 10739717 GAAGTCTGGGCTGAGCAATGGAACTAAAGAAAAGA[C/T]GACTTGATGGCCAAATTAAATTTGCTTTGATCCCT Y 2 1 2 1 101000 f 74 goat snp56482-scaffold89-467312 3 108527077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795540 Affx-122932452 AX-385282495 3 10812658 TGCAGTAATATCATGGCCTACTCATTTGCTTCAGG[C/T]TCCTCTGCCTGGCTTAGTATCTTTAGGTATTGTGA Y 2 1 2 1 101000 f 74 goat snp56481-scaffold89-394371 3 108455302 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447282 Affx-122924931 AX-123317618 3 10903897 ACTAACCTCCATGGTATATTAGAAAAGGTCTTTTC[C/T]ATGACCAATTAATTTTCCTACTGTATTACCATAGT Y 2 1 2 1 101000 r 74 goat snp56480-scaffold89-303132 3 108367359 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773978 Affx-122919755 AX-385261116 3 10932583 TAAAAATTGAGGGATAGAAATAAGAATAGAGAGAG[C/T]AATTCAAAACTGTGAGAGCCTTATTGATGATGTTA Y 2 1 2 1 101000 f 74 goat snp56479-scaffold89-274446 3 108338837 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389690 Affx-122968698 AX-123260048 3 10963679 CATATCCTGGATACTTTCGTGAATATAATTTTCCT[G/T]ATATAGCAACTTATACAGTTTTGGAAAGCAAGTAC K 2 1 2 1 101000 r 74 goat snp56478-scaffold89-243350 3 108307563 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796060 Affx-122962207 AX-385283012 3 11006856 CAGCCACATGTTCATCACTATTGATCCTTTAAATT[C/T]TAATTCAGATGCCTCTTTCTTAACAACTTCCCTGG Y 2 1 2 1 101000 r 74 goat snp56477-scaffold89-200173 3 108264470 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406330 Affx-122955449 AX-123276682 3 11055188 AAATCCATGCCTGATGCACACAGAGGCCAAAGAAA[C/T]GGAGATGTCAGAGTATGGAGAAGAGAAAGATTTAT Y 2 1 2 1 101000 f 74 goat snp56476-scaffold89-151841 3 108219133 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394279 Affx-122964711 AX-123264634 3 11084563 CCACATTCACCAGATAAAGCTGCTCAGAACCCAAC[A/G]CTCTCCAATTTCTGGAGGGAGCAGGCAGAGAGAAA R 2 1 2 1 202000 r 74 goat snp56475-scaffold89-122466 3 108189786 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441310 Affx-122929447 AX-123311647 3 11124378 CTGGTGTCCTCAGGCTTGCAGAAATCTTACCTTTA[G/T]ACCTGAGATGTGTGTCTTCCTTGATTTTGGAGTAG K 2 1 2 1 201000 f 74 goat snp56474-scaffold89-82651 3 108149275 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407082 Affx-122954904 AX-123277433 3 11153156 TTTTATACCATTTAATTTGCAAAATTAAAAAGCTG[C/T]AGCAGCCCAGTGTTTGCAGGGATGTGAAAAAATTG Y 2 1 2 1 201000 f 74 goat snp56473-scaffold89-53873 3 108119600 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391902 Affx-122966954 AX-123262259 3 11188244 AAAGTCAACAACCTTTAATTCCTCCTCAAGGGACA[G/T]AGATAATATTCCAAACCATATCCGTGTGCTATTTT K 2 1 2 1 102000 f 74 goat snp56472-scaffold89-18785 3 108084233 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415025 Affx-122949022 AX-123285374 3 11222888 AGTAATATTTCTGCAAGCCTGAGGACACCAGAGGA[C/T]GTTCCACTGAAGTACAAGGCACTTGTTCATGTGAG Y 2 1 2 1 101000 r 74 goat snp16912-scaffold1767-15760 3 108040918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777742 Affx-122968176 AX-385264860 3 11252941 ATTGCATGCACAGAGAGCAAATTGTGTACAGCTGG[C/T]GCTTGAATAATGTGATTTGAGCTACATGACTCCAC Y 2 1 2 1 101000 f 74 goat snp16913-scaffold1767-45813 3 108009942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453881 Affx-122919513 AX-123324214 3 11296990 GCATTTCTCCCCTGCTTTTTAAATATGAGGTCCCA[C/T]ATTTATATTTGGTGCTGGACTCCAAAATTGAGTAG Y 2 1 2 1 201000 r 74 goat snp16914-scaffold1767-89862 3 107965476 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417159 Affx-122947343 AX-123287507 3 11353242 TAGCCCATGGTCTTATTCCAGCCTGTCATCTCTTT[C/T]TGAATGGTCCATAGACTAAGAATGGTTTTATGGCC Y 2 1 2 1 201000 r 74 goat snp16915-scaffold1767-146114 3 107907604 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387407 Affx-122970410 AX-123257765 3 11389734 TGTCTTCCCAATGTCATGTTCCTTGCACTCATACT[A/G]CCCCCAGGGTACTGTCATGTTCCTCACATTACCCC R 2 1 2 1 101000 f 74 goat snp16916-scaffold1767-182606 3 107870714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774084 Affx-122959879 AX-385261222 3 11427176 AGATACACAGAGACACAATCATTCATTACTCACTC[A/C]GGTCAGGTCTACTGTCCTTATAGCCAAGAGTCAGC M 2 1 2 1 101000 f 74 goat snp16917-scaffold1767-220048 3 107834378 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448893 Affx-122923257 AX-123319228 3 11508793 TCCTTGATTGCATGCACGTGTCTAGTGAGCTTGTG[C/T]GTGTTAGTGCACATCTACACACAAGTGTTGGTAGG Y 2 1 2 1 101000 r 74 goat snp16919-scaffold1767-301665 3 107753918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442577 Affx-122928501 AX-123312914 3 11542727 CCAAAGATCGTTAATGCATAAATGTACTAATGTTG[A/C]TCAGAAAGGTGCCTGGCACATGGTTCATGCACAAG M 2 1 2 1 101000 f 74 goat snp16920-scaffold1767-335599 3 107719989 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437399 Affx-122932428 AX-123307737 3 11573513 GCACACAGCTTGTTCACACTGACACAACTATCCAG[C/T]GGCCTGGGAGGAAAGGGGTTTAGCCAGGGAGCTGG Y 2 1 2 1 101000 f 74 goat snp16921-scaffold1767-366385 3 107689696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797301 Affx-122971681 AX-385284240 3 11613006 TCCTGAACAACTGTGCGTGTGGGATCCCAATAAAG[C/T]ACTGTTTCTATATCATCAGCATGCTGCTTGTGCTG Y 2 1 2 1 101000 r 74 goat snp16922-scaffold1767-405878 3 107650659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427406 Affx-122940070 AX-123297749 3 11653379 CCTCCTTCCCTCAGTTCCTCTATTTTCCCTCCTAT[C/T]TCCCCTTCCTACCTTCACAACATTCCTGTAGTACT Y 2 1 2 1 101000 r 74 goat snp16923-scaffold1767-446251 3 107610466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783560 Affx-122971288 AX-385270622 3 11683867 GACTGGAAGAGAGAAAAGGGGGAAGTTTCAGAAGA[C/T]GAGGAGTTTAGGGAACTGAGGTGAGGTTATCAGTA Y 2 1 2 1 201000 f 74 goat snp16924-scaffold1767-476739 3 107579628 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405434 Affx-122956058 AX-123275786 3 11715035 TGGGGCCTCCTTCCAGCCTTACATTTCAGTTCACT[A/G]TCTTCAGCCATCTGGGACATGGCCCTGTTTTTCTT R 2 1 2 1 101000 r 74 goat snp16925-scaffold1767-507907 3 107548331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375927 Affx-122978466 AX-123246286 3 11758923 ACACCCGCTATGCTTCAGAATCATCTATTCAGATT[A/C]TTTTCTAAAAATTATTTGTAAAAACAATGATTTGT M 2 1 2 1 103000 f 74 goat snp37056-scaffold4496-18196 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402782 Affx-122958302 AX-123273135 3 11797945 TGAAAATGGCAACATGTACCATGAACCATACAGCA[C/T]GCTGGATTTACAGAAAATTTTTTTAAGGCGTGTTT Y 2 1 2 1 103000 f 74 goat snp6327-scaffold1223-614225 3 107448791 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774085 Affx-122936868 AX-385261223 3 11835897 ACAAGACATATATCATCTACCATGTCTCCCTTGTA[C/T]GGTCACACCACAAGGACTTCAATTCGTATTTGATG Y 2 1 2 1 101000 r 74 goat snp6326-scaffold1223-576273 3 107410652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792283 Affx-122953516 AX-385279265 3 11881912 AGTTATAGAGCTAATAAATACACCACTCCTTTAGG[C/T]AACTTGGAGGAAACAATCAGGCTTAAGGAGCAGAA Y 2 1 2 1 101000 r 74 goat snp6325-scaffold1223-530258 3 107364229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390590 Affx-122967189 AX-123260947 3 11911621 AGACTCCCACTGTCCTTGAGGTTGTAAAGAAACTT[A/G]CATACTAGCAGAGATGGCAGATGTTATACAAATAA R 2 1 2 1 202000 r 74 goat snp6324-scaffold1223-500549 3 107334523 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801876 Affx-122952507 AX-385288783 3 11947863 AATTTTTGATTTAAGATCCTAGAATCCAAAATTTG[A/C]TACAGGAATGTCTCGACCAATATATATTAATTACA M 2 1 2 1 201000 r 74 goat snp6323-scaffold1223-464307 3 107298085 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398293 Affx-122962157 AX-123268648 3 11992886 CCAGATCTATCTGAGACTGAACCTAACGAATTCAA[C/T]AAAGAGATTCAACAGGCATTAACACTTGAATAAGA Y 2 1 2 1 101000 f 74 goat snp6322-scaffold1223-419284 3 107252718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769268 Affx-122947820 AX-385256441 3 12039298 TATAGGCAACCATGAACTGTACACTGATGATTCGT[A/C]TACATTTACAAATGTATGTCATACTGCAACAAAAC M 2 1 2 1 101000 f 74 goat snp6321-scaffold1223-372872 3 107206026 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424953 Affx-122941270 AX-123295299 3 12096695 CTCGCTCTGATGCTCGAATGCTTGTTAGTTATATC[A/G]CTGGCTCTTCTAGAAAACACGGCAGACAATGAAGC R 2 1 2 1 101000 f 74 goat snp6320-scaffold1223-315475 3 107152091 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801819 Affx-122973508 AX-385288726 3 12153807 CATTTAGAATAAGAACAAAAAATGGCTTAAGATTT[G/T]TCACCTTCTGGTTAATCCACCTCTAGCAGAACCAA K 2 1 2 1 201000 f 74 goat snp6319-scaffold1223-258363 3 107093838 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783330 Affx-122923597 AX-385270395 3 12186613 GGACAAGTATCTACCCAAAAGTCGTGGTCCATAAA[C/T]AGAAAGACTATTTATTTGCCACACAGCCAAAAGCA Y 2 1 2 1 101000 r 74 goat snp6318-scaffold1223-225557 3 107060767 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277927 Affx-1111836163 AX-519551422 3 12207071 CAGATGAATCCACAAACAAGTGCAAACATGTTAGA[A/G]TCAATGGCCATGGAAGACCATGGTCAAAGGCGATG R 2 1 2 1 101000 f 74 goat Random2.2K-300 3 12207071 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38420437 Affx-122944900 AX-123290784 3 12322611 TGAGGAACATGGAAGAAGATTTAGAAAGAGAAGGA[C/T]GGCAGCAAAGCTTTGTGATCTACCAAAGATCTAAT Y 2 1 2 1 101000 f 74 goat snp6316-scaffold1223-89559 3 106924756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387616 Affx-122969870 AX-123257974 3 12389090 TTGGGCCCCTTGTTAGGGTAGGGCCACGTGTGTAT[A/G]CATGTTCACATGATCACAAGTCTGCAGTCATTGTG R 2 1 2 1 201000 r 74 goat snp6314-scaffold1223-23080 3 106857019 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418977 Affx-122946071 AX-123289325 3 12413784 AGATTGATCATCTCCTTGAGCAACAGTTAGGGAAC[A/C]CTGGGAACTACGGAGAAGGGAGCTGTTGTGACGAC M 2 1 2 1 101000 f 74 goat snp30036-scaffold3280-19323 3 106829459 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445962 Affx-122925897 AX-123316299 3 12468394 ACAGGTGGGGGAGATGGAGAGGAAGGTGAGGGCTC[A/G]TGAAGAGAACAAAACATAGCTTGGCTCCTGCACAC R 2 1 2 1 101000 r 74 goat snp55040-scaffold841-2879850 3 106688006 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408432 Affx-122954456 AX-123278783 3 12498381 CATTTAAACATTCAATGATTCTGTGAGGCAGAAAT[G/T]TCCACTGCACAGGTGGAAAACTAAAACTTACAGAT K 2 1 2 1 201000 f 74 goat snp55039-scaffold841-2849863 3 106657436 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778619 Affx-122942991 AX-385265730 3 12543318 TGTGCACTAGACATGGTATATAGCTATATTATCAC[C/T]AAGTACTCTGCAAACAATCTGTGGGAGAAGTGCCT Y 2 1 2 1 101000 r 74 goat snp55038-scaffold841-2804926 3 106611750 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393714 Affx-122965241 AX-123264069 3 12582852 TCAGCAAGCTGCCAAAGAATACAGACAGACCACTA[C/T]GCAAAATTTGGAAAACAATTTGTGACCAAAATGAA Y 2 1 2 1 101000 f 74 goat snp55037-scaffold841-2765392 3 106574152 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400228 Affx-122960161 AX-123270583 3 12625178 ATATAATGGCAGTACTGTGGAAGTGCTCTGGTAGC[A/G]CAGAGGAGAGCCAGCCTAAATGTAAACAGCAACTC R 2 1 2 1 201000 r 74 goat snp55036-scaffold841-2723066 3 106534062 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452630 Affx-122920355 AX-123322963 3 12671268 TTGCAGGACAGGTAATTGGCATCCCAAACTAATTG[G/T]TGACAGAGCAAAGCCTTAAATCCAACACTGGATAA K 2 1 2 1 101000 f 74 goat snp55035-scaffold841-2676976 3 106487295 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451461 Affx-122921148 AX-123321794 3 12727653 AGGAGGGAAGCTATAGGATGGGGTGAGAGGTTGTC[A/G]CTTATGATAGACAGTGAGATGGAAAACCCTGTTAA R 2 1 2 1 101000 r 74 goat snp55034-scaffold841-2620591 3 106432372 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443544 Affx-122927764 AX-123313881 3 12756318 CTTACCCAGAGAAGTTGGCAGAAAAGAGGCAGTGA[C/T]GCTGGCTCTCTCATCCTCCTGAGGGGAGGAGTGGC Y 2 1 2 1 101000 f 74 goat snp55033-scaffold841-2591926 3 106403038 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429827 Affx-122938176 AX-123300168 3 12801360 CTGTGGGTCAAGTAAGTTAAGGCAAGTGACAAGAA[C/T]GTACAAATGTTACTTGTTATTGTCAACATGGGGGC Y 2 1 2 1 101000 r 74 goat snp55032-scaffold841-2546884 3 106357583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431189 Affx-122937175 AX-123301530 3 12861613 GAGAGAGATTATATGCATTTCAGGCCACATTCCAC[C/T]GCCAAAAAGAAATTATCAGCATGGATAATCAAAGG Y 2 1 2 1 101000 f 74 goat snp55030-scaffold841-2486631 3 106297552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464190566 Affx-1110361225 AX-515665799 3 13006322 GTGGATAAACCTAGAGTCTGTCTTATAAAGTGAAG[C/T]CAGAAAGAGAAAAACAGATATCGGATATTAATGGG Y 2 1 2 1 101000 f 74 goat 3_13006322_AF-PAKI 3 13006322 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38422724 Affx-122943260 AX-123293070 3 13047314 CCTGGTTCCTGCACTCCCTTCTCCCAAGGTACTTT[A/C]CACGGTCCTCACTCAGAAGATTCAGGTCTGAATCT M 2 1 2 1 201000 r 74 goat snp55026-scaffold841-2300930 3 106118041 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423595 Affx-122942390 AX-123293941 3 13162187 TACTTCTGAGAGTGAAAGAGGGTGCTGTTAATTGC[C/T]TGAAAGGAAAGGCATGATGGGACACATAGCCACCC Y 2 1 2 1 101000 f 74 goat snp55024-scaffold841-2186057 3 106003511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791774 Affx-122933536 AX-385278765 3 13205200 CCAACTGACCCTCAATTCACCTGTTTTAAAAAGGA[A/G]GTTAATACTTATCCATATCCAGGTGTTTGTTCTGA R 2 1 2 1 101000 f 74 goat snp55023-scaffold841-2143044 3 105960506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797474 Affx-122930695 AX-385284413 3 13240846 CCACTGGGTTCTAACAGGACTAAGATTTGCCATCA[A/G]TTTTATTAGCACCATTAGTATCTGTGTTATTCCTA R 2 1 2 1 101000 f 74 goat snp55022-scaffold841-2107398 3 105925065 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376182 Affx-122978828 AX-123246541 3 13341792 TCACAGTTCACAAGGCCAGGGGCTTGATTAGAACA[C/T]GAGTTCCTTCACCTCCTGGCTGTGGGACTTTAGGC Y 2 1 2 1 101000 f 74 goat snp55020-scaffold841-2006452 3 105824803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449493 Affx-122922631 AX-123319828 3 13372807 AAATTAAAGTGGGGAGGGGGCATCCAGGTCCCAGG[A/C]GACCAAGAGAGCTGGGTCAATCAGCCTGCCTTCAG M 2 1 2 1 201000 r 74 goat snp55019-scaffold841-1975437 3 105793163 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391378 Affx-122967275 AX-123261735 3 13417893 ATGGGCAACAGAGGACAGCAAAGCTTCAATGATGG[C/T]TATCTGTATATTTAACTATATGCATAGATTAAACT Y 2 1 2 1 101000 f 74 goat snp55018-scaffold841-1930351 3 105748965 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407178 Affx-122954827 AX-123277529 3 13487471 AAGATGGGGCCTTCATGCTCCAGCATCCTCTACCA[A/G]GAACGGAAGTCCTTCCTGCAGCCTCATGGCCTTCC R 2 1 2 1 101000 f 74 goat snp55017-scaffold841-1860773 3 105679897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383683 Affx-122972498 AX-123254041 3 13528976 CTATTACTTAGTCGGAAAGTATTTGTATTTGTTAC[A/G]CATTTCCCACTAAATGGAACGTTCTTGTATTCCTA R 2 1 2 1 101000 r 74 goat snp55016-scaffold841-1819268 3 105639432 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384317 Affx-122972272 AX-123254675 3 13571150 ACTCACCAGCGCAGGTAGCAATACATGGCTTCCAC[A/G]TTATAGTACTTGCTGCCTGCAAGGGTGCCCAGCTG R 2 1 2 1 201000 r 74 goat snp55015-scaffold841-1777094 3 105597337 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440714 Affx-122929897 AX-123311051 3 13686718 CCTTCAGCTTCTTTGACCCTGCTTGTCACTGCTCA[A/G]CCAGTATTGCTGAATCATCCTCTTCTCCCTGACCC R 2 1 2 1 101000 r 74 goat snp55013-scaffold841-1661526 3 105481913 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434161 Affx-122934895 AX-123304502 3 13739435 CGTGGCACTTCGCTGGAGGCACCCCTTCCAAAATC[C/T]CATAGACCATCCAACTTTAGTGTGCGGGTGACCAC Y 2 1 2 1 101000 r 74 goat snp55012-scaffold841-1608809 3 105428930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773365 Affx-122960743 AX-385260507 3 13771428 TGCAAAATGATGCCACAGATTTATGGATACATGCA[C/T]AGGTAATAAAAGAATCAAAATGCCAAACACCAACT Y 2 1 2 1 101000 r 74 goat snp55011-scaffold841-1576816 3 105401309 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389166 Affx-122968526 AX-123259524 3 13830541 AGAGGGGCAGAAATGCCCACATCAGCACAGAGACA[C/T]GGAAAGCAGGGAACAGAGGGTCTCGGAGAAAGAGG Y 2 1 2 1 101000 f 74 goat snp55009-scaffold841-1517703 3 105344102 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409317 Affx-122953088 AX-123279668 3 13871074 AAGTTTAAACAGGTCCAAGTCAGAGGTGAATGAAC[A/G]CATGCAAACCCACCCTAAGGGATGGGAGGCGGAGG R 2 1 2 1 101000 f 74 goat snp55008-scaffold841-1477170 3 105303954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437576 Affx-122931877 AX-123307914 3 13942972 AGTCCTAAGGGACCTAGCTCTGGATCTTGTATAGA[C/T]CAATTGCCCATCAAAGTGGACTATGGGGAAGAACT Y 2 1 2 1 101000 f 74 goat snp55007-scaffold841-1405272 3 105232245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793578 Affx-122963208 AX-385280553 3 13973726 AACCAGACGAACTGAGATTAGAAAGAACAAAAACT[A/G]CTCTGGCATAAGGCTGTTCAATTCAGAAGGGATTA R 2 1 2 1 101000 f 74 goat snp55006-scaffold841-1374518 3 105201556 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382154 Affx-122974039 AX-123252512 3 14031339 TACATCCCAACACAGTGATAGATGCAAAAGAAATA[C/T]AAAACCCTAGACTGCATCAGAGGTGATAAAGTGAT Y 2 1 2 1 101000 f 74 goat snp55005-scaffold841-1316905 3 105143741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779798 Affx-122949549 AX-385266898 3 14063962 GGGAAGGAACTCTTGAGATTTCTTTTGTGATTATA[C/T]TATGCTATTTAATGTAATGGAGAATGGCTGATGCT Y 2 1 2 1 101000 f 74 goat snp55004-scaffold841-1284282 3 105111029 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428977 Affx-122938865 AX-123299319 3 14095988 GAATTTAACAATACTGAGCAAAAGGCAGATGCAAA[A/G]GAATACGTACTCCGATTACATAACAGACAGACAGA R 2 1 2 1 101000 r 74 goat snp55003-scaffold841-1252256 3 105078771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766973 Affx-122919255 AX-385254272 3 14134494 AGAAAGAAAAATGGTATAGTGATGAGGAATATTTA[C/T]TCTCAATTCCAATAACCATGTTTAGATCCAAGCCT Y 2 1 2 1 101000 f 74 goat snp55002-scaffold841-1213750 3 105040266 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802488 Affx-122932622 AX-385289392 3 14168763 TCTATACAAGGCAAACCCTTTTCATAAAAAAAAGA[C/T]TCTCAAGAAACCATATTACTATACAATCTAATGAC Y 2 1 2 1 101000 f 74 goat snp55001-scaffold841-1179481 3 105006179 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402631 Affx-122958397 AX-123272984 3 14203126 TTAACAGATACAGTAGGTGATGGGGAAGGGAGATT[A/G]CTTTCTCCTACTGCGCTAAAAGGGGATTTTGCTGT R 2 1 2 1 101000 f 74 goat snp55000-scaffold841-1145118 3 104971804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785079 Affx-122968551 AX-385272126 3 14379661 TTAATAAAATCAGATGAACAGAATGTTGGCAATTG[C/T]GAAATCTGAGTGACAGTTACCTGAGGGTTTATTAG Y 2 1 2 1 101000 r 74 goat snp54996-scaffold841-968583 3 104795782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453492 Affx-122919828 AX-123323825 3 14412584 AGGCTTCCTTAGCCCCTTTCAAACATACTTCCTCT[A/G]TGATAACACTCAACACCACAGTGTAAATGGGTTAA R 2 1 2 1 201000 r 74 goat snp54995-scaffold841-935660 3 104762986 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399300 Affx-122960535 AX-123269655 3 14450123 GAGACTAGCGAGGGGCCCAAGGTGGTCTGCTATGC[A/G]GAAGGAGAGACTGAGGTGGCTCACTGTGATGATAC R 2 1 2 1 101000 r 74 goat snp54994-scaffold841-898121 3 104725644 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427123 Affx-122939658 AX-123297466 3 14501250 GTCTCCTTGTCACACAGGGCCTCAAATTTAGGCTT[C/T]GGATGTTACTTCTAGGTGTGGTTTCAGACAGTCTC Y 2 1 2 1 101000 r 74 goat snp54993-scaffold841-846994 3 104682487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434736 Affx-122933919 AX-123305077 3 14566478 ATGCCTTCCTGTGTCCACTATACGCCCCTCTCACT[A/G]CCAAGATGTGTGCATTCCTATGCAAAGAAAATTAG R 2 1 2 1 101000 r 74 goat snp54992-scaffold841-781766 3 104616958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450128 Affx-122922761 AX-123320463 3 14600266 TTTCCCTCTGAAGAATGGGGAGATTGAACAAATCT[A/G]TGAGGCCTGGTCACTAGAGATCAGTAATAGAGTGG R 2 1 2 1 101000 r 74 goat snp54991-scaffold841-747978 3 104584711 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384609 Affx-122972568 AX-123254967 3 14691296 AAGTGGCTGAAGATGAAATCCTCAAAGTCGTCCAC[C/T]GCGTCGTCATCACCTGTTTCTCTCACTGCCACCTC Y 2 1 2 1 101000 f 74 goat snp54990-scaffold841-656948 3 104495297 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417433 Affx-122947211 AX-123287781 3 14727299 AGAGTCAGATATGACTGACTGAACTGAACTATAGG[C/T]ATTATTTATTCTAGCCAAAAAGTATATCTCTCACC Y 2 1 2 1 201000 r 74 goat snp54989-scaffold841-620945 3 104459198 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786625 Affx-122952682 AX-385273657 3 14757452 CTTTTCTGAATTTTTATAGGAAAGGCTTTCTCATC[A/G]TGAAAGGTTTGGAAAGAATAGAAGACAATAAAGAA R 2 1 2 1 101000 r 74 goat snp54988-scaffold841-590792 3 104428652 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450111 Affx-122922774 AX-123320446 3 14789576 CCCAGTGCCTTCAAACTGCTCTTTCCTATTCCCCC[A/G]GGGCTCCCTCCCTCACCTCCTAAAGATCTCCCATC R 2 1 2 1 103000 r 74 goat snp54987-scaffold841-558668 3 104397583 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798940 Affx-122943327 AX-385285870 3 14851116 GAGGCTTTGCCCAGGGGACAGGATATGGCTTTTGA[C/T]GGTGTGGTTTGCTTTTGTGATGAATGAAAGAGTTT Y 2 1 2 1 101000 r 74 goat snp54986-scaffold841-497128 3 104337585 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799089 Affx-122973400 AX-385286019 3 14883292 GTGGTCTGGATGAAGTGAAACAATACCTGGCTGAC[A/G]CTATTGTTATCATCATTAGACTTATAAAATTCTTC R 2 1 2 1 101000 f 74 goat snp54985-scaffold841-464952 3 104305442 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431956 Affx-122935965 AX-123302297 3 15024088 CTCCAAAGAGATCTTCACCCTGGAATTTCCTGCTA[C/T]GCTAAGGGGTTTGTTGACTTGTGAAGGAGATGGAG Y 2 1 2 1 101000 f 74 goat snp54982-scaffold841-324156 3 104164256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446206 Affx-122925715 AX-123316542 3 15058576 GAACACTGTAATGCCTTTCAGAAAAAATGTTCCTC[A/G]CCATCACAGGCCTTGAGTGTGTCCCACCAAAACCT R 2 1 2 1 101000 f 74 goat snp54981-scaffold841-289668 3 104129630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429483 Affx-122937877 AX-123299825 3 15089091 CTGGGCCATCAGGGAAGTCCCTTAACCTCTCTTCC[A/G]TTTATCAGGCATCTCTTTCGTGTCATGTCCTGAAC R 2 1 2 1 101000 r 74 goat snp54980-scaffold841-259153 3 104098878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434714 Affx-122933936 AX-123305055 3 15182681 CGATTTTTTTTTTTAAATAAAGTGGAAAAAAGTTT[A/G]TTCTTGGAGTCAGAAAGCTTTAACACTTATTTCTT R 2 1 2 1 101000 r 74 goat snp54977-scaffold841-165563 3 104005456 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445865 Affx-122925993 AX-123316202 3 15216847 GTTCTCCGTTTTCCTGGTGCTCAGGTTGGTTGGGC[A/G]AGGTGGTCTCAAGGCCTGGACAGCCTTGTGAAAAA R 2 1 2 1 102000 r 74 goat snp54976-scaffold841-131397 3 103971044 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768666 Affx-122944032 AX-385255844 3 15257792 GATTATTGAAAAAATAAATCGCTCTGCCCAGCAAT[A/G]CTCTGATGCTCGGTAAACCTGCCCTGTCATGTGGT R 2 1 2 1 101000 r 74 goat snp54975-scaffold841-90452 3 103929170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766823 Affx-122976188 AX-385254146 3 15300792 CTCCTTCATTTAGCCTGTGTGTATCACTCTTTCCC[A/G]TAGGTCCAGAATCACCAACACCTCCATCCTTGGAT R 2 1 2 1 101000 f 74 goat snp54974-scaffold841-47452 3 103886063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777434 Affx-122961217 AX-385264555 3 15329551 CACAGTCAAGACTTTGCTGTGAATTATAGTGATCA[C/T]GGATGAACTTTCCTGTGTTTTTTGTTTACTCAAGC Y 2 1 2 1 101000 r 74 goat snp54973-scaffold841-18693 3 103857346 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411773 Affx-122951487 AX-123282123 3 15394793 GATGTTATAAAAGAAGTAAATTTCAAGGTCTACCC[A/G]TTCTGAGAATTGCTCCTGTTGCAGGGAAGCTGCAG R 2 1 2 1 101000 r 74 goat snp24560-scaffold2498-586958 3 103792989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427805 Affx-122939757 AX-123298148 3 15460162 CTCTGAGAAGTTACATTATAAGTTTCAGGCATAGC[A/G]TAATATGTCCCCTTAAAGTGATGCTTCAGTTTGTG R 2 1 2 1 101000 r 74 goat snp24559-scaffold2498-521589 3 103730057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396879 Affx-122963236 AX-123267234 3 15514927 CACAAAGTAGATCATACACCTGGTAATAAGGTTCC[C/T]CACACTGTCTCAAAGGGTACACAGAGGTCACATAA Y 2 1 2 1 101000 r 74 goat snp24558-scaffold2498-466824 3 103675384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395160 Affx-122964116 AX-123265515 3 15550782 TTACCATGGTGACTATCACTGCCACTAAACTAAAA[C/T]ACTATATTCTTCTTAAAAGGGAACACAGTACTACC Y 2 1 2 1 101000 f 74 goat snp24557-scaffold2498-430969 3 103640970 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392649 Affx-122966446 AX-123263006 3 15626524 CTCAGTTTTACCAAAGCCTTACTGCTCATTCACCC[A/G]TATCAGGCTTAGAGAGAGTAAGCCACTGTCCATAA R 2 1 2 1 101000 r 74 goat snp24556-scaffold2498-355227 3 103565769 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464192323 Affx-1110362116 AX-515667538 3 15639658 GCAGAAGCAAGATACCCAGCGGATACAGGAGAGGT[C/T]GGGCAGGAGCACCTACGTGTTTGCGAAAGAGGTCA Y 2 1 2 1 202000 f 74 goat GoatD01.001881 3 15639658 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38420963 Affx-122944585 AX-123291310 3 15657299 CAAAATAGCTTTAAAAAAGTTAATCACCTTAAAAG[C/T]TTGAAATGATGAAACTGCTGCTTATCTTAGAACTA Y 2 1 2 1 101000 r 74 goat snp24555-scaffold2498-324452 3 103535122 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803266 Affx-122973211 AX-385290115 3 15755044 AGATAAAGGAACAGTAATAACTCCCATTTAATTGA[A/C]TACTCCAAAAGCCCAAGAAATAATGAACATTGAAT M 2 1 2 1 101000 r 74 goat snp24553-scaffold2498-226707 3 103437396 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407944 Affx-122954360 AX-123278295 3 15836282 AAATGAGGACACTATCATCTACCACACAGATCAAA[C/T]GAGATAACACAGGTAGAGACCTAGTGAGCACTCAG Y 2 1 2 1 101000 f 74 goat snp24552-scaffold2498-145469 3 103356062 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417623 Affx-122946863 AX-123287971 3 15881880 CCAGCACAAGCCCTAGCCTCCTGGTGTTGCAGGAA[G/T]CAGGACCCCTTCCAGGGCCTAAAAGTGGGCTCTTG K 2 1 2 1 201000 f 74 goat snp24551-scaffold2498-99871 3 103316119 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387351 Affx-122970482 AX-123257709 3 15941147 TAAGTTTCAGAGGCTGAGCTATCTATAATCTTAAG[C/T]TCCTGGAACACAAATACCTCTTATCTCTTGCAAGG Y 2 1 2 1 101000 r 74 goat snp24550-scaffold2498-40604 3 103256760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272187 Affx-1111833377 AX-519545939 3 15974845 AGCAGCCTGGACATGACGTTTGCCAAGCAGGAATC[A/G]CACAGCAAGCTGGACACATATAGATATCCCAAATG R 2 1 2 1 201000 f 74 goat 3_15974845_AF-PAKI 3 15974845 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394388 Affx-122964627 AX-123264743 3 15981349 GATTGTCAGCCTGGCGACCGTGACTCTTGCTGATG[A/G]TCTCCTCCCTGGCTGGCTTAGGGATGGACAGTGCC R 2 1 2 1 101000 f 74 goat snp24549-scaffold2498-402 3 103216182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392009 Affx-122966489 AX-123262366 3 15994564 TTGAGTCTGGGGTGCTCAAGGGATGACCCAAGCTA[C/T]GGTCAGAACAGAACCAGAATTCTGAGGAAGTGCAC Y 2 1 2 1 201000 f 74 goat snp26817-scaffold2813-264011 3 103119670 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412391 Affx-122951454 AX-123282740 3 16043609 ACTCAGGGCACCTGGAAGAGTGCACTTTGTGTCCC[A/G]TATCACATAATACGGGCTCAGTCACACAGCCGTGC R 2 1 2 1 101000 r 74 goat snp26816-scaffold2813-214966 3 103070496 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430541 Affx-122937195 AX-123300882 3 16076652 AATTCTCAGCGTGCACTCTGGATGCAGAGACAGGG[C/T]TCATCTGTGCATTTGGCAAATAAGGCAAGTGTCCA Y 2 1 2 1 101000 r 74 goat snp26815-scaffold2813-181923 3 103037580 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417978 Affx-122946684 AX-123288326 3 16122788 CTACAATTAAAAGAGGGTCATACACACATTCATAA[C/T]GCTAAAGATTAGCCTTTCTGGTCATCTTCTTTTCT Y 2 1 2 1 201000 f 74 goat snp26814-scaffold2813-135787 3 102991921 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442613 Affx-122928473 AX-123312950 3 16158320 CTGGCTGAAGTGCTGTGGTGGGGCAGTCATGAGTG[A/G]TGGGTCTCTGAGGTTTTCTAATCCACAGGGTTATC R 2 1 2 1 101000 r 74 goat snp26813-scaffold2813-100255 3 102956199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396661 Affx-122962851 AX-123267016 3 16203807 TCTTAAACTCTTCCTTATCCCCAGCCCACAGGAGT[A/G]CCCGTCTGTACAGCGCTCCCGGTTCCATCAAGGCT R 2 1 2 1 201000 r 74 goat snp26812-scaffold2813-54768 3 102910341 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786974 Affx-122919930 AX-385274003 3 16234620 AACCTTTCTGTAACGTTTTTTCACTATGTATAAAA[C/T]GGAGGCAGTGGCTTTTCTCGTCTCATAGGATTTTA Y 2 1 2 1 102000 r 74 goat snp26811-scaffold2813-23955 3 102879224 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782064 Affx-122964358 AX-385269142 3 16288425 TTTCTGTAGAGATGATGTTACAGGTGTTTGCACAC[A/G]TCCAAACTCATATTTAGTTATGCATATTAAATATG R 2 1 2 1 101000 f 74 goat snp50663-scaffold73-1092297 NW_017189676.1 23826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424815 Affx-122941375 AX-123295161 3 16319077 CACAACAGAAATGTATGCATATGACACTAAAGCAC[A/G]TGTATGAAGATGCTCATAGCAGCAGAATTTGTAAT R 2 1 2 1 101000 r 74 goat snp50662-scaffold73-1061645 3 102808791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384186 Affx-122972409 AX-123254544 3 16458054 CCCTGACTCTGAGAACCATCTTCTTCCAGCTTCTG[C/T]GCCTGCAAAGACATGAAATGAACACAATAGCAACA Y 2 1 2 1 101000 f 74 goat snp50660-scaffold73-922668 3 102667984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422737 Affx-122943252 AX-123293083 3 16495115 CAGAGTCGGACATGACTGAGCACGCATACACGGTG[C/T]GCTATGGGACCTTTTGCAGACATCTTACTTCTTTG Y 2 1 2 1 101000 r 74 goat snp50659-scaffold73-885607 3 102630509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386292 Affx-122970931 AX-123256650 3 16555503 GCTGACAAACCTGTGCTGCGTGTGTACAGGTAAGC[A/G]TCCTCTGAGAACTGGAGTGGGGCCTTCCACAGAGG R 2 1 2 1 101000 f 74 goat snp50658-scaffold73-825219 3 102570237 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394505 Affx-122964546 AX-123264860 3 16607125 AGAGCTATGAGGAACATGAACAAAAGATCAAGATC[A/G]TATGACACACAGCTCACAGTTCACTGCTTACAAAC R 2 1 2 1 101000 f 74 goat snp50657-scaffold73-773597 3 102518711 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779490 Affx-122948119 AX-385266593 3 16649086 GATTCAATCTGAAGGGTTCTTAGAGTAGCAGCTCT[A/G]TAAAAGATGTTGGTGCACTGACTGAGGTGTTATAC R 2 1 2 1 201000 r 74 goat snp50656-scaffold73-731636 3 102476964 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783740 Affx-122937410 AX-385270796 3 16697698 CGTTTCATATTGGCAGTCAAGGATGAATCAACAAA[C/T]GAAAAATCCTTTGCTTACAACTCACAGTTGCTGCT Y 2 1 2 1 101000 r 74 goat snp50655-scaffold73-683024 3 102428514 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787825 Affx-122954292 AX-385274848 3 16734614 AGAAAATACAAGCATAAATAAGTTATTTTAAGAAA[C/T]AACTTAAAATTCTATCCTCCACAGAAAATCATTTC Y 2 1 2 1 303000 f 74 goat snp50654-scaffold73-646108 3 102393561 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419431 Affx-122945510 AX-123289779 3 16824934 TAGCTCAAGATGGAAACTGAAAGGAAATAGTTTCT[A/G]TCAAACACGTACTGTGTGTAAGCAGTGTGCTGGCC R 2 1 2 1 101000 r 74 goat snp50652-scaffold73-555788 3 102301703 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785932 Affx-122960684 AX-385272969 3 16873032 GAAATGTCAGAGTGTTTTTGGTGGAGAGGGTCTTA[C/T]AGTTATGTGAATAGAGTTACAAAACAGCTTTCTCT Y 2 1 2 1 101000 f 74 goat snp50651-scaffold73-507690 3 102253288 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404239 Affx-122957643 AX-123274591 3 16943228 ATAGACCATGCAAATAATTTCTCCCAGTCTGTTAT[C/T]TGTCAGTTAACTTTGTCATGACATCTTTCACTGAA Y 2 1 2 1 201000 r 74 goat snp50649-scaffold73-437494 3 102178741 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414760 Affx-122949249 AX-123285109 3 16984128 TGGTATCCCCAGTGGTGGTGAGCATACCAGGGAAG[C/T]GATGTGGAACCCAGGCTCTTTCACTACTTCAGGGT Y 2 1 2 1 201000 r 74 goat snp50648-scaffold73-396594 3 102133965 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791284 Affx-122955565 AX-385278278 3 17016512 GGGTCTCAGTCATGTTATAATGCATTATGAGTATT[A/G]TCAGCATTGGGTAAACATCTCAAAGAGGTGCAAAT R 2 1 2 1 101000 r 74 goat snp50647-scaffold73-364210 3 102101194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451270 Affx-122921317 AX-123321603 3 17052405 AGAGTTAATACCACAACTGACCAGAGTAGGTTGGA[C/T]GGAGAAAAAAGGAAGCAGCAAAGGCCTTTGTACAA Y 2 1 2 1 101000 f 74 goat snp50646-scaffold73-328317 3 102065213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780170 Affx-122926320 AX-385267267 3 17092367 AAGTCACATAGGCTTACAACTTATACAATATGATC[A/G]TCAGGGATTGGGAAGGAGTGGTAGCAACTATTGGG R 2 1 2 1 202000 r 74 goat snp50645-scaffold73-288355 3 102024761 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408100 Affx-122954712 AX-123278451 3 17126094 TTTAATTTTTTAAGACTTTGCGTGTATTCGATAAC[A/G]TATAGTAGTTGTCTTTCTGAGTCTCACATGTCACT R 2 1 2 1 101000 f 74 goat snp50644-scaffold73-254628 3 101991367 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424242 Affx-122942471 AX-123294588 3 17159042 TCCATCCATCATTCATTCAAAAGCCTTAATTATAT[A/G]CTTGTGATGTGCAAAGAACTGGGGATACAAAGGAA R 2 1 2 1 201000 f 74 goat snp50643-scaffold73-221680 3 101957547 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771241 Affx-122945301 AX-385258399 3 17201583 AACTCTAAATGTCTATGGTTTTAGGTTACAGTTTC[G/T]ATTTGGAAAATCAGGGTTGGATATGCCTTGTCTTG K 2 1 2 1 101000 r 74 goat snp50642-scaffold73-179139 3 101917553 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406362 Affx-122955422 AX-123276714 3 17234818 CGTCTTTTGCAGACAACGCCCCAGGTGTATAATGG[A/G]CTGATTCATGGCCAGCCAAACCCCATTCCACCTGT R 2 1 2 1 201000 r 74 goat snp50641-scaffold73-145904 3 101883745 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423098 Affx-122942923 AX-123293444 3 17283348 TGGGGAGGCGACTCAGAGCCTTCTCTGGTGTCATC[A/C]AGTCCGTGGAAGAGAGACTTTCAAGACGGAGAGGG M 2 1 2 1 201000 r 74 goat snp50640-scaffold73-97374 3 101835914 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376596 Affx-122979062 AX-123246955 3 17333233 CCTTGCAGATTCTGTGGAAAGAGCTCTGCCTCATG[C/T]CAGATGCTCAAGGACATGTAGGAAAAAGCATTTCT Y 2 1 2 1 101000 r 74 goat snp50639-scaffold73-47489 3 101785868 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408877 Affx-122953986 AX-123279228 3 17377285 GTATATTAATATATAAAATGAGATCTTGGGGACTC[C/T]GTCCTCTTCTGTAAAAAGGGGGGTAAGAGTATGAC Y 2 1 2 1 201000 f 74 goat snp50638-scaffold73-3437 3 101741423 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403493 Affx-122957696 AX-123273846 3 17420803 TAGGAAGAAGAGAAATAAGAAGGGAGGGAGGAAAC[A/G]CACACCAGGGAACCTGCTTAAGATGCTGTACTTGG R 2 1 2 1 201000 r 74 goat snp9904-scaffold1353-39982 3 101309344 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274121 Affx-1111834018 AX-519547724 3 17448212 ATCCTGGAGCTGTTCCGCTCGGCCGCCTACCGCCA[A/G]CCCATCCTCATTGCCGTGGTGCTGCAGCTGTCCCA R 2 1 2 1 202000 r 74 goat GoatD01.014314 3 17448212 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427218 Affx-122939579 AX-123297561 3 17454971 TGCTGGTATGTTCACCTTCTGATGTGGGCTCACTT[A/G]CTAGTTCGTATTTGGTAACTTCTCACTGTGTCCTT R 2 1 2 1 101000 r 74 goat snp9905-scaffold1353-74150 3 101274883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429016 Affx-122938330 AX-123299358 3 17483756 AGATGGCCTTGGACAACAACATCCTCCATCCTACA[C/T]GAGCCGTCAGAATTCAACACCCCATGTACAATTTT Y 2 1 2 1 201000 r 74 goat snp9906-scaffold1353-102935 3 101245273 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394803 Affx-122964810 AX-123265158 3 17565596 AGACCACCTCCCCCCAGTAAAATTCCTCTCAGGTT[C/T]TGAATATCAGCTATGATCAGTTTAGTCAGGCCAGT Y 2 1 2 1 101000 r 74 goat snp9908-scaffold1353-184775 3 101163811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394556 Affx-122964458 AX-123264911 3 17667374 CAAGCACTGGATTTGGAGGTACAAGAGGGAGTGAC[A/C]CAAAGCTACTGGCCTGGGCAAAGGATGAAACCAGA M 2 1 2 1 101000 f 74 goat snp9910-scaffold1353-286553 3 101067737 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407195 Affx-122954816 AX-123277546 3 17725368 ATGAGACATTAGGTAAATAATTCAATCTCAATCTT[A/G]TTTAACTTCAATTTCTTAACCCAAGTGGGGCTAAT R 2 1 2 1 102000 r 74 goat snp9911-scaffold1353-344547 3 101009226 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389830 Affx-122968175 AX-123260187 3 17779786 TGTCTTCCCCCAAACAACAGACAAGCAAACCCTGA[G/T]GCCTCAGGGTAAATATACTTGCCTTCCTGAGGTTT K 2 1 2 1 201000 r 74 goat snp9912-scaffold1353-398965 3 100955778 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378587 Affx-122976586 AX-123248946 3 17837501 CAAGCCATTTGGAGGTGAGCAGAAGGGAGGGAAGA[C/T]GAAGAGATATTTCTGAAAAAGGTGGACAATGAAAA Y 2 1 2 1 101000 r 74 goat snp9913-scaffold1353-456680 3 100897621 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414581 Affx-122949372 AX-123284930 3 17892232 TTGCCCCCATTACACACACTCACTTCATTCTTGCC[A/G]TTTTCATTAGTTCAACATTTGGATCAAAAGGCTCA R 2 1 2 1 201000 r 74 goat snp9914-scaffold1353-511411 3 100842823 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764438 Affx-986696826 AX-385252131 3 17937879 TTTGGAGAACACCTTGGAGGTCCCTCTCAGATTTA[A/C]ATTGTACCTATCTTTTCCTCAGCAAGCAAGTGTAC M 2 1 2 1 600010 r 74 goat 3_17937879 3 17937879 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 468278083 Affx-1111836164 AX-519551573 3 17987172 TCTCTCTGTATAGTTTGGGTAAGTTATATCACCTC[A/G]GTTTTTTCGGCATTCTGTGGTCGTAACAGAATCTA R 2 1 2 1 101000 r 74 goat Random2.2K-301 3 17987172 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397155 Affx-122962435 AX-123267510 3 18010329 AAGGTTAGACCAGTGTATGGAAGACAGAGACTCTG[A/C]GTGAAGACTTTTTCCCAGGCCTCCCTCTGACTCCA M 2 1 2 1 201000 f 74 goat snp9916-scaffold1353-629508 3 100723896 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445409 Affx-122925380 AX-123315746 3 18046498 ATGTTCTTTTTTGCCTTTGCTCCCTGGGTGGTCTT[A/G]TCCTCCTTTGCATTTCTGCTGTTTGCTTGTGCCTT R 2 1 2 1 101000 f 74 goat snp9917-scaffold1353-665677 3 100687387 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384749 Affx-122972035 AX-123255107 3 18119660 AAGGTTAAAACCAGTTTCTACTCCTAAGGCCTGCT[A/G]CATAGCATGCATGTATGCTAAGTCACTTCAGTTGT R 2 1 2 1 101000 f 74 goat snp17385-scaffold180-1209310 3 100613549 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788399 Affx-122923578 AX-385275417 3 18149809 ACCAGTTTTCAGATCAAAACTCCAGAAGTATTGGA[A/G]AGATGCCTATTTACAGGGCTCCCTCAGAAGAGCCC R 2 1 2 1 101000 r 74 goat snp17384-scaffold180-1179161 3 100582878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777035 Affx-122930104 AX-385264159 3 18284158 GCATTATTAAGTGGAAAACTGTTCTGATTTTAGAC[A/G]TAACTGTACTCTTAAACAAAGTATATAATCTGGCC R 2 1 2 1 101000 r 74 goat snp17381-scaffold180-1044812 3 100448021 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435443 Affx-122933474 AX-123305783 3 18315726 GCCGAGGTCATCTTCGAGAAATGTAGTCAGATCTC[G/T]CTGTCAGAATCTACCACTGCCTCCCTGTCCAAGAA K 2 1 2 1 101000 f 74 goat snp17380-scaffold180-1013244 3 100416335 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413381 Affx-122950132 AX-123283730 3 18392023 TGACTGGTTGGTTGTTCACTCTTAAGCAAGAGCTA[C/T]AACCTCAGAGTAGCAAAGCTACTTGTTAGTGCTAG Y 2 1 2 1 101000 f 74 goat snp17378-scaffold180-936947 3 100339710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418603 Affx-122946357 AX-123288951 3 18428123 CTTTGGCCCAGCTGGGATGCTTACCCCCAACCACT[A/G]AACTGAGGCAGCCAGCATGATGAGGCCGTGTCAGA R 2 1 2 1 201000 r 74 goat snp17377-scaffold180-900847 3 100303564 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399666 Affx-122960509 AX-123270021 3 18473971 AGTCTCCTGCCAACCAACAGACATGGCCATCATTA[C/T]ATGACATGTGTGTTGATAGGGGAGGAGGCATTTTT Y 2 1 2 1 103000 f 74 goat snp17376-scaffold180-854999 3 100256454 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451445 Affx-122921160 AX-123321778 3 18555824 TGCATGTATTGAGGGGCTGTTGGGTGCCACATACT[A/G]TGCTAAGAATTCAAAGACACAACATAATCTCTGCC R 2 1 2 1 101000 r 74 goat snp17374-scaffold180-773146 3 100174635 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800599 Affx-122925385 AX-385287518 3 18586293 TGAGTAAAGGGAAGAGACTTTGGGGCCTAACAGAA[C/T]AGAGAATCACAGGAAATCATTCACTCTAGTAATCT Y 2 1 2 1 101000 r 74 goat snp17373-scaffold180-742677 3 100143884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407989 Affx-122954324 AX-123278340 3 18622242 CATGCATTATATGATTACATCTTCACAACAATCCT[A/G]TAAGGGAGGTTCTACTATTACCCACATGTTAAAGA R 2 1 2 1 101000 r 74 goat snp17372-scaffold180-706728 3 100107771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272020 Affx-1111833378 AX-519545786 3 18636994 GGCTGCCGGAGGTACCAGTTAGGGGCCCGAGGGCC[A/G]TGGTGAGCTGTTTCAAAGGAGCAGAGCGCAGCGGC R 2 1 2 1 102000 r 74 goat 3_18636994_AF-PAKI 3 18636994 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320800293 Affx-122939527 AX-385287216 3 18650946 TAATGAATGATGGAGTAGGACAATACTGAGAGAGA[A/G]TAGAGAATATATTCATGGTTCTAGGACTGCGAGAA R 2 1 2 1 101000 r 74 goat snp17371-scaffold180-678024 3 100083865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436116 Affx-122932657 AX-123306455 3 18724451 CCCAAACACTGCCCTTCTCTCTGTGATACCGGGAC[A/G]ATGTCTCCCCAGTGCATTTTTGCCTTCAGCAGCTG R 2 1 2 1 101000 r 74 goat snp17369-scaffold180-604519 3 100010259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397226 Affx-122962379 AX-123267581 3 18777292 ACTTGACAGTAGATACAGAGGTGCAACTGAAACAT[C/T]CTCAGATATTATCCCAGTTTGTTTTTTTTTTTAAG Y 2 1 2 1 101000 f 74 goat snp17368-scaffold180-551678 3 99956996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437806 Affx-122931678 AX-123308144 3 18855200 ATTCACTGAGCACCCTTTCTGGATGTCATATGTAT[A/C]TATGTTACCTGTAATCCTAACATCAGTTCTGTAAG M 2 1 2 1 101000 r 74 goat snp17367-scaffold180-473770 3 99877977 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447707 Affx-122924610 AX-123318043 3 18899920 AAACTGCCTCACCTCCTACCTCTCCACATCACTAG[G/T]GCTCAAACATTGCCCCCTTGTGGTACAGCAGCATG K 2 1 2 1 201000 r 74 goat snp17366-scaffold180-429050 3 99833120 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401098 Affx-122959414 AX-123271451 3 18966716 CAACAGGGTCACCACTTCCCCTCTTGACAACAGCA[C/T]AGATGATGAATACTGAAAGAACATAATTCTACAAT Y 2 1 2 1 201000 r 74 goat snp17365-scaffold180-362254 3 99766411 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400023 Affx-122960792 AX-123270378 3 18999026 ATAAAAATTGATACAATTGATTTTTAAAAATCAAA[G/T]CACTGAAGCCTAATTGATAAAGGTTAGAAACCATC K 2 1 2 1 101000 r 74 goat snp17364-scaffold180-329944 3 99734083 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413025 Affx-122950999 AX-123283374 3 19035500 CTAATGCCTAGGCTCTGGCAGGAAGAAGGAGAGGG[A/C]TAGTGGAATACTCTACACCCGAGTGGGGACCTGGA M 2 1 2 1 201000 r 74 goat snp17363-scaffold180-293470 3 99697929 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439119 Affx-122931098 AX-123309456 3 19123479 TCAGTGTTTTGAGTCTTTATCATTTTATTCATATC[G/T]ATGTTCAGGAATCTTTAATGGCTTAATTTTACTTC K 2 1 2 1 101000 r 74 goat snp17361-scaffold180-205491 3 99609500 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783912 Affx-122969489 AX-385270967 3 19169651 GTGCTACTTTACCTGACTGGAATGCCATTCAAGTC[A/G]GTCAGCTTCATCTCCACTTCACAGGTGACACACCC R 2 1 2 1 201000 r 74 goat snp17360-scaffold180-159319 3 99562497 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779437 Affx-122964899 AX-385266540 3 19209089 GATGATCCCAAATACGAAAATCCAAGTCATTAATA[C/T]ATAAAAAGGAAGTCTTACAGACCTAAAATTATGCT Y 2 1 2 1 101000 r 74 goat snp17359-scaffold180-119881 3 99522928 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443085 Affx-122928115 AX-123313422 3 19239428 GAGAATGATGAGAGGGATCTTGAGAGATGGGACTA[C/T]TGGGGATTGCCAAGGAAAGGATCCTAAGATTCTAA Y 2 1 2 1 101000 f 74 goat snp17358-scaffold180-89542 3 99492564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417521 Affx-122946941 AX-123287869 3 19271082 TCCTCCAACACTCATGAAGTAACAGTGAAGTAAGA[C/T]AGGAAGCTGCAGGATTGAGAAGAACCATGGGTCTT Y 2 1 2 1 201000 f 74 goat snp17357-scaffold180-57888 3 99461379 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378471 Affx-122976674 AX-123248830 3 19314358 GACAATGTGTCAGTTTTGCTTTCACACTTGTAAAT[A/G]TAATGCTGGTGCTAAAGGGAACTATTGATTGATGG R 2 1 2 1 101000 f 74 goat snp17356-scaffold180-14612 3 99409068 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400587 Affx-122960402 AX-123270942 3 19342516 ACAATAGAGTAATAATCCTGTCAATGTTCTCAATA[G/T]ACCACTTTATCAAAAGCAAGTTTATAACAGAAGAA K 2 1 2 1 101000 f 74 goat snp23402-scaffold2345-165737 3 99388787 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381935 Affx-122974128 AX-123252293 3 19401074 CATAGAGGAGAATCCGGCTTTCTCAGGCTGAGTCT[C/T]CGGCTCATTCACCGTCCTCTCAGAAGGCCCCTTCT Y 2 1 2 1 101000 f 74 goat snp23401-scaffold2345-107179 3 99329745 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429817 Affx-122938185 AX-123300158 3 19445161 CAAGTGGGGTGGGTTATGGCAAAATGTGTAGCTGC[A/G]TTTATCTCCCCCCAAACCCAGAAGTTCTACTACCG R 2 1 2 1 101000 r 74 goat snp23400-scaffold2345-63092 3 99285246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425103 Affx-122941232 AX-123295449 3 19480032 ATATATATGTGTGTATATATATGGAGAGAGAGATC[G/T]AAAAGCTACAAGAGTCCTAGGAAGTTACATTCCCT K 2 1 2 1 101000 r 74 goat snp23399-scaffold2345-28221 3 99250573 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446483 Affx-122925056 AX-123316819 3 19531719 CTCCTCTTGAAAATCTAATGAGAGATATAAGCCCC[A/G]TCCTCAGAGAATGCTCAAGTATGTCTGTGCTTTTC R 2 1 2 1 101000 r 74 goat snp50889-scaffold737-1255532 3 99171914 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416760 Affx-122948183 AX-123287108 3 19564394 AATAAGAATGGACCCTGAGTGGTATCTCAGGACTC[A/G]AAGCCTGTGGGTTTCACAGTTACATCCCCATGTTC R 2 1 2 1 101000 f 74 goat snp50888-scaffold737-1222857 3 99139226 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452016 Affx-122920911 AX-123322349 3 19652308 GCTAGTCCCTCTTCCCCTTCCCTGGCAACACCAAC[A/C]AAAAGGCCAAGATAGGTCTTCAGCTATGGAGGAGG M 2 1 2 1 101000 r 74 goat snp50886-scaffold737-1134943 3 99051256 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785291 Affx-122925632 AX-385272336 3 19686388 AGGTGAAAGAGAGGGCTTAGTAACTCCAGATGGCA[C/T]AGGTATTTACTTTGCCAGTTCTGAAGGAAAGTATA Y 2 1 2 1 101000 f 74 goat snp50885-scaffold737-1100863 3 99017096 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800241 Affx-122945250 AX-385287164 3 19715723 GTTTCATAAAGGCAGGGTTCAGATCAATTTTGTTT[A/G]CCATTATACCCCTAAAACAGTCAGGTATTCAATAA R 2 1 2 1 101000 f 74 goat snp50884-scaffold737-1071528 3 98987342 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414369 Affx-122950006 AX-123284718 3 19765405 AACAGTACAGACATTAGAAATGTTAGTTGCCTTTG[A/C]TTCCACAAGGCTCTGAGAGGCTTGGGTTTGCCCTT M 2 1 2 1 101000 f 74 goat snp50883-scaffold737-1021846 3 98938370 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418980 Affx-122946069 AX-123289328 3 19797853 CAGTGTCCATGTCTTTGTCTGCTCTGCTCTACGAG[A/G]GAGATAAGACTTGTCCCACACACGTGGTAGACCCA R 2 1 2 1 101000 r 74 goat snp50882-scaffold737-989398 3 98908213 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439924 Affx-122930011 AX-123310261 3 19845983 TATTTGTCCCTACCCCATCAACTTGCCTAAATTCT[A/G]TTCATACTATAAAGCCAGAGCTCAAGTGCTACCTT R 2 1 2 1 201000 r 74 goat snp50881-scaffold737-941268 3 98859862 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434112 Affx-122934935 AX-123304453 3 19878438 ATAAAACAAGGATTGGAAAATGTTGAATTTTGCAA[G/T]CAGAAGTAAATTCCTGACCATATTATGATAATGGC K 2 1 2 1 101000 r 74 goat snp50880-scaffold737-908813 3 98827409 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387830 Affx-122969666 AX-123258188 3 19927863 GAGTAATAAGCAGGCTTCAGACAGCAGAGGGCCCC[A/G]TTCACCTTGTTAAAGGGCACAAGCTTCATCCTGCA R 2 1 2 1 101000 r 74 goat snp50879-scaffold737-859388 3 98778194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789670 Affx-122926375 AX-385276679 3 19990805 CTTCTTATTTTACTTTTCATTCTACGAACACTCCA[C/T]TGAAGCAGCTTCCATAACAAGCTCACATTGTATAG Y 2 1 2 1 101000 r 74 goat snp50878-scaffold737-796446 3 98715490 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789786 Affx-122970884 AX-385276794 3 20019783 GAAGTAAAGCCCACTGTTACTATATACCCTAAGCT[A/G]TGAGCCTTCATCTCATCAGTAAGAAAGGGCATGAT R 2 1 2 1 101000 r 74 goat snp50877-scaffold737-767468 3 98686329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404394 Affx-122956791 AX-123274746 3 20060829 CACCACCACCAAGGCCGATAGGATCTGAAGTGATA[C/T]GTAAAAGGGATCTAATATACCCATTACCCTCTCCT Y 2 1 2 1 201000 r 74 goat snp50876-scaffold737-726422 3 98645285 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375475 Affx-122979149 AX-123245834 3 20100621 ATAATTCCATGTCTGGGTTTAGAAAAACAAGCACA[C/T]GGCAAGTGATACTGCTCCTCATCCAGGCAGGGGCA Y 2 1 2 1 101000 f 74 goat snp50875-scaffold737-686630 3 98604333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775463 Affx-122955979 AX-385262594 3 20219799 TACTAATTCTTACGTTTCCTGAGATGTGTTTCTGG[C/T]GATTATTCCAATTATCTTTAAGAATGTGTGTGTGT Y 2 1 2 1 102000 f 74 goat snp50873-scaffold737-567452 3 98484513 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430474 Affx-122937250 AX-123300815 3 20275954 GAAAAGTCAGTGGCAAGATAGACGATATAAAAGAA[C/T]AGTAAAGAGCAAGAGCTTTGGATCAAACAGAACCA Y 2 1 2 1 201000 f 74 goat snp50872-scaffold737-511297 3 98428183 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273682 Affx-1111833738 AX-519547294 3 20311446 TGTAGAAGTTCTGTATATTAAATGTACATTTGCTT[A/G]CTATTTTTCTCTTCAATAGAGAATTACCTCCAAGC R 2 1 2 1 201000 r 74 goat GoatD01.003271 3 20311446 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402689 Affx-122958352 AX-123273042 3 20346916 ATGGAAGCCAGAGATACTGTCCTTCCCCTGAGCTT[A/C]CATGGGGCCCTAGAAATTTCTCTATCATTGAAATT M 2 1 2 1 202000 r 74 goat snp50870-scaffold737-440335 3 98357680 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388446 Affx-122969258 AX-123258804 3 20393402 ATTTGCCACTAAAGCATGGTTCCTGGACCAGCAGC[A/G]TGGCATCACCTAGGAGCTTGTTGGAAATGTAGATT R 2 1 2 1 103000 f 74 goat snp50869-scaffold737-393849 3 98310296 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774409 Affx-122962425 AX-385261545 3 20423457 TTCACTTTTGTAATTTAGCTATATACAAATGATGC[A/G]TTACTTTTCTCTTTGTGGGATCTCCTTCCATGAAA R 2 1 2 1 101000 r 74 goat snp50868-scaffold737-363794 3 98281805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783036 Affx-122942542 AX-385270104 3 20471456 TTCAGAAAATAGTACTGTAATTAAAGAGCTAAACA[C/T]GGCTGGTGTTCAAGAAAGTCCATTGAATTTTCTAG Y 2 1 2 1 101000 r 74 goat snp50867-scaffold737-315795 3 98232773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399039 Affx-122960919 AX-123269394 3 20502168 GTCTCTTAACCTTGAAAATCCTTCCTGCTCTCCTC[A/G]TTTCTCACCACTTATCCCAGGACAAACACTGGTGG R 2 1 2 1 201000 r 74 goat snp50866-scaffold737-285083 3 98201775 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425730 Affx-122940754 AX-123296076 3 20555915 TGTTAAGATGGTGTGTGAACCACTCAACTATAATA[C/T]AAAGCTTAAAGGAAAATAGTAAAAGTAACTATAGC Y 2 1 2 1 101000 f 74 goat snp50865-scaffold737-231336 3 98148042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453440 Affx-122919868 AX-123323773 3 20594146 TTTATAATGTTTACTCAGTATGACCCCTGAGAACA[C/T]AGTTGTGTTCTTTTGACGTATTTGGCAAGGTTGTA Y 2 1 2 1 102000 r 74 goat snp50864-scaffold737-193105 3 98109507 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413102 Affx-122950943 AX-123283451 3 20649710 CCTACGCATCTAGTGCGGCATGCCATGCTCTTGTG[C/T]ACAAAAACAAGCAGTGGAAGACCTTCCCTTTGTGA Y 2 1 2 1 201000 r 74 goat snp50863-scaffold737-137541 3 98052775 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377713 Affx-122977398 AX-123248072 3 20682672 ATCTGATCCCTGAATCTATATGTCAGCTCCTTTTT[A/C]GTACTTCAAATGGCACATTTTCAAATCCCTTAACC M 2 1 2 1 101000 f 74 goat snp50862-scaffold737-104579 3 98019711 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394285 Affx-122964707 AX-123264640 3 20769475 ACTTTAACTCAGAACATGTATTATTATTTCTTGAC[C/T]ATCTTTGTCTCTGCATTCCCTCACTCTAATTAGTT Y 2 1 2 1 101000 r 74 goat snp50860-scaffold737-17776 3 97932548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430072 Affx-122937546 AX-123300413 3 20830408 CAATGACCCACAGAGCACCCTCCTTACCCAGGCCA[C/T]GAGGCAGATCTCAGCTCCTCGGCCAGCTTCCCTTC Y 2 1 2 1 101000 f 74 goat snp47051-scaffold659-43058 3 97691794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395826 Affx-122963633 AX-123266181 3 20859358 GTTTAGAAAAGAATAAAGAATACATCTACGGAGTA[C/T]GTTTTATGTTAGGAAAAGGGGACACAGGCATGTTA Y 2 1 2 1 101000 r 74 goat snp47052-scaffold659-72008 3 97662792 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404716 Affx-122957252 AX-123275068 3 20918215 GTCACAAAGCCACACACTGTATGACTCCCTTTATA[C/T]GAAATGTCCAGAGCAGACAAACCCAGAAGAATAAA Y 2 1 2 1 303000 r 74 goat snp47053-scaffold659-130865 3 97604126 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767737 Affx-122952810 AX-385254968 3 20950412 AGAATAAATGAATGTCATCTAGGCTTAGGGAGAGA[C/T]AGTGAGGAAGAGAAAAGTCTAAGCTAAAACTCAAA Y 2 1 2 1 101000 f 74 goat snp47054-scaffold659-163062 3 97571938 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781587 Affx-122973456 AX-385268671 3 21002782 GCCAGAGCTGGAGTCTAGGAACGTTTTAGGTGCAA[C/T]CTGAGAGCAAATGCAGCCCTAACAGAGTTATAGGA Y 2 1 2 1 101000 r 74 goat snp47055-scaffold659-215432 3 97518859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417339 Affx-122947734 AX-123287687 3 21066665 GGGAAGAAGGTGCCAACTGTGTCTAGACCCTACTC[A/C]TTTATTGAGTTTGGTAAGTTTTTGTGCCTCACTTC M 2 1 2 1 101000 r 74 goat snp47056-scaffold659-279315 3 97454325 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790372 Affx-122966112 AX-385277375 3 21104160 TAAAGACAGCAGATTAAGTACATGCATTGTGTTCC[A/G]CTCCCTCGTAGACCTTAACCAAAAGTTAACATTTG R 2 1 2 1 101000 f 74 goat snp47057-scaffold659-316810 3 97416267 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394235 Affx-122964881 AX-123264590 3 21151975 ACCTGTTCGAATGCCTGAGGACATGAATACCACAG[C/T]AAAGCTCCAAGTCAGGTTAAAAGGCTTGGTTCTTT Y 2 1 2 1 101000 f 74 goat snp47058-scaffold659-364625 3 97368452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272192 Affx-1111833379 AX-519545944 3 21155934 GCTAAAAGGAGAGGCAATCTGAGGCAAGAATCAGG[A/G]CTTGGTCTGGAACAAGGCCAGGAGTCTGAGGTTAG R 2 1 2 1 101000 f 74 goat 3_21155934_AF-PAKI 3 21155934 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38444421 Affx-122926572 AX-123314758 3 21193605 TCTTAGAGTTCAGTTATATGGTTTTATATTGTGAT[A/G]TATACATTGTACACATTCTAAAAGTTCTTTTGGTA R 2 1 2 1 101000 r 74 goat snp47059-scaffold659-406255 3 97326485 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421690 Affx-122944412 AX-123292037 3 21228626 AGCTGAATACATGGGCCAGGCTTGGCTAATGCTGC[A/G]TTTCTGAGAAGTGGCCTTGACCATGAGAACTCAAT R 2 1 2 1 101000 r 74 goat snp47060-scaffold659-441276 3 97290881 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453875 Affx-122919518 AX-123324208 3 21263106 ACAGTAGCTTCTGCTAAGGAATGAAGAAAGCAAGG[C/T]GTGATTGATGTCTGCCCACTCACCAGACTGCAGTG Y 2 1 2 1 101000 f 74 goat snp47061-scaffold659-475756 3 97256492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447935 Affx-122923788 AX-123318271 3 21294093 CTCACTAAGTACTTAAAGCACAGTATACTACCCAG[A/C]ATCACTGCTAATGCCTTTTTTCACCTGTGATCTTA M 2 1 2 1 101000 f 74 goat snp47062-scaffold659-506743 3 97225533 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423424 Affx-122942614 AX-123293770 3 21364720 AGACATGACTGAGCACACACAAAGAAGTTGTGGGA[C/T]ACTCATGATAAAGAGTGTCTCCTTGGACTATTTGG Y 2 1 2 1 303000 r 74 goat snp47063-scaffold659-577370 3 97154728 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435065 Affx-122933735 AX-123305405 3 21398118 AAGGACACTCTAAAAAGTAAAGCAACAAATAACAG[A/G]TTGGCCGAATTGACTTCCAATTTATAAGTAGCTCC R 2 1 2 1 101000 r 74 goat snp47064-scaffold659-610768 3 97121334 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392580 Affx-122966068 AX-123262937 3 21438099 TGTGTGATTAAAGCAAACGTCATAAATTCCTGAGG[C/T]AAGAAGATATAAGAACTTCAGAAACTGCCTGGGAT Y 2 1 2 1 101000 f 74 goat snp47065-scaffold659-650749 3 97080527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401668 Affx-122959569 AX-123272021 3 21482315 ATATGAGAACATTTCTTTGGGGAGTACATCATAAA[C/T]AACATAATAGTGTATAAACAGAGTGAAGGGGGAAA Y 2 1 2 1 101000 f 74 goat snp47066-scaffold659-694965 3 97036174 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409476 Affx-122954061 AX-123279827 3 21511827 GGGAAGAGGTAGGAGGCAGCATGTGGCTTCCCAGT[A/G]CAAAATATAGATAGCCACCCAAAACAGGATACATA R 2 1 2 1 101000 r 74 goat snp47067-scaffold659-724477 3 97006774 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434749 Affx-122933909 AX-123305090 3 21549939 GTTAAACACCTTGCCCAGCATCACTCAGCCAGAAG[C/T]AGCAGAATGAAGTCAAAGCCAAGGAAGGCATCCCC Y 2 1 2 1 101000 r 74 goat snp47068-scaffold659-762589 3 96968636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396776 Affx-122962765 AX-123267131 3 21585507 GTCCATTCGATAGTGAAGAAATATTTACAGAGAGT[A/G]TATTTGCCTGGCACATAGTATGTGCTCAATAAACA R 2 1 2 1 101000 f 74 goat snp47069-scaffold659-798157 3 96932930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769907 Affx-122922403 AX-385257076 3 21614550 ATATAGACTTATTTTAGAAGATTAGTGGACCAAAT[A/G]TCTTTCTAATCTTTGGCATACATAGGTGATGGAAA R 2 1 2 1 101000 r 74 goat snp47070-scaffold659-827200 3 96903960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787242 Affx-122973594 AX-385274268 3 21676808 TGAAAAACGGGTGGTAAACGTTTTATCAATACTAG[G/T]CTTCTGGAGCCTGGCAATGGCCTTATATGCTGAGC K 2 1 2 1 202000 r 74 goat snp47071-scaffold659-889458 3 96846692 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796862 Affx-122977010 AX-385283805 3 21730682 TCTTTTGTATATAATAGATAACTCATGGGAACCGA[C/T]GGAGTGACTTTGCAGCAAAGCCTTCCTTTGCTAGG Y 2 1 2 1 201000 f 74 goat snp47072-scaffold659-943332 3 96792816 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448389 Affx-122924094 AX-123318725 3 21762825 GATGGCCTCAATCCAGACCCTGCCCCCTTAACCAC[C/T]CAGTTAACGTGAACGTGACCCACAGCTCCAACCAC Y 2 1 2 1 101000 r 74 goat snp47073-scaffold659-975475 3 96760620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769722 Affx-122927094 AX-385256892 3 21795243 TTTTGTTTTACTGAAACTAATGTGAAAATAAGAAG[A/G]TTTCTTTCTACAAAGATGGCAAGTTATACAAGGAA R 2 1 2 1 101000 r 74 goat snp47074-scaffold659-1007893 3 96727164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795126 Affx-122965845 AX-385282084 3 21852378 AATTGCTTTCACAAGATATAGTAGCATACATCATG[A/C]TTTCACAAGATATAGTATGATAAATTCTCCAGTCA M 2 1 2 1 101000 f 74 goat snp47075-scaffold659-1065028 3 96669569 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770859 Affx-122962347 AX-385258023 3 21892625 CCTAACACTCCTATGAAGGTTTAATCAGTACCTCT[A/G]CTCCAATATCTCGCCACCTTTATTTGGTGAGTAAT R 2 1 2 1 101000 f 74 goat snp47076-scaffold659-1105275 3 96629629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409034 Affx-122953863 AX-123279385 3 21930822 CATTTCCTCTGCTTGTTCCTCTTTCTTCAGTCACC[C/T]TTTCCAAAAGGCCATTCCTCAAGATTCCATCAGTG Y 2 1 2 1 201000 r 74 goat snp47077-scaffold659-1143472 3 96590965 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443130 Affx-122928083 AX-123313467 3 21975667 ATGACTAGAATGCTTTCTTCAAAAATAACAGAGAT[A/G]CAAAGTGAGAAGATGGGCGAGATTAAAGTAATTAG R 2 1 2 1 101000 r 74 goat snp47078-scaffold659-1188317 3 96545958 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778625 Affx-122953605 AX-385265736 3 22017615 GTAACATACTAGGCAAGTTACTGAAGCTCTTTGAA[C/T]ACCCTTTATAATGTCTATAATAAGGATATTTAAAT Y 2 1 2 1 101000 f 74 goat snp47079-scaffold659-1230265 3 96503671 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390143 Affx-122967988 AX-123260500 3 22060696 AGAAATACTTCAAAGTATATTCTGCCTGACTACAA[G/T]AGTAGTTGGCCTAAGAATTCCCTGACAGTCCAGTG K 2 1 2 1 201000 f 74 goat snp47080-scaffold659-1273346 3 96460100 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439523 Affx-122930124 AX-123309860 3 22099700 TGTCCAGAATGCTGTTTCCTCCATCCCCCAGGATA[C/T]GGATAGGGGTTGAGGACCTAATATCGAACTTTACC Y 2 1 2 1 101000 r 74 goat snp47081-scaffold659-1312350 3 96421723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414244 Affx-122949629 AX-123284593 3 22129501 CAGTGACCTTGAAGATGGGGGAGCTGGTGGCAAAG[A/G]TGAAGGCACAAGTGTGGTGAAGAGCTTCAGGTGTT R 2 1 2 1 101000 r 74 goat snp47082-scaffold659-1342151 3 96392020 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788110 Affx-122961370 AX-385275130 3 22168302 TTCCACTTTTCTGTACTTGGAAGAGACCAACATTA[G/T]CTTCTGTTTAGTCCAAGGTATAAAATGATATGCTT K 2 1 2 1 101000 f 74 goat snp47083-scaffold659-1380952 3 96353204 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451476 Affx-122921137 AX-123321809 3 22198443 AAAGCCATTTCCTGGCAAGAGAGAGGACTGTGAGA[C/T]GAGGTATTAGAGTGCTGAAAATTAACAGGAGGAAA Y 2 1 2 1 201000 r 74 goat snp47084-scaffold659-1411093 3 96323103 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395235 Affx-122964476 AX-123265590 3 22227863 TCAGCTGCTCTTAACTTCTATGAATTGCCCTCCTC[C/T]CCTCTGAAGCCCCAGGCTCCTAGTACATCCCTTAG Y 2 1 2 1 101000 f 74 goat snp47085-scaffold659-1440513 3 96293682 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420792 Affx-122944692 AX-123291139 3 22319616 TTACTCATTCTGATTAAGCCTGTTCTCCATATTTA[C/T]GGCCAGTATCTGATGTGTAAATTAGAGACTTTGTT Y 2 1 2 1 101000 f 74 goat snp47087-scaffold659-1532266 3 96201078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787579 Affx-122919816 AX-385274603 3 22351015 ACTCTGTAGCAAGACTGATTTGCGTAAGTAAAATA[G/T]CTTTAGGCTTCTCCTCTCTTTAGCTTAAGTTTCTT K 2 1 2 1 101000 r 74 goat snp47088-scaffold659-1563665 3 96169571 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419166 Affx-122945733 AX-123289514 3 22381404 GAATGGATAGTTAGTGCCAATAACAGCAATGTGGT[A/G]TTGTTTTATCCCTTCTGTAACCTTGCAGATAAAGA R 2 1 2 1 101000 r 74 goat snp47089-scaffold659-1594054 3 96139216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412688 Affx-122950762 AX-123283037 3 22418850 CTGAGGAAAATGCTGTTTTAGTACCATCACCTGGG[C/T]TCCTCTTTCTAGTCACTTGTATAAACATGTGCTAC Y 2 1 2 1 600000 r 74 goat snp47090-scaffold659-1631500 3 22418850 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772043 Affx-122950762 AX-385259198 3 22418850 CTGAGGAAAATGCTGTTTTAGTACCATCACCTGGG[C/T]TCCTCTTTCTAGTCACTTGTATAAACATGTGCTAC Y 2 1 2 1 101000 f 74 goat snp47090-scaffold659-1631500 3 96101707 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449486 Affx-122922635 AX-123319821 3 22450724 TAAGTATTCAAGAATTGTTTGTGTTCCTTCCCAGG[C/T]GAGCCCCTCCCTCCTGATGGATACTTTCATTCACA Y 2 1 2 1 201000 f 74 goat snp47091-scaffold659-1663374 3 96069301 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436186 Affx-122932606 AX-123306525 3 22489522 TTCAATATTTCAGTGTCTAAAAAAGAATATAATTA[A/C]ACTTCTTTCTGATGTGGCCTGTAATTCTCTTTGTA M 2 1 2 1 101000 r 74 goat snp47092-scaffold659-1702172 3 96031091 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433805 Affx-122935178 AX-123304146 3 22534993 AATGGAATGAGGATGGGCCAAAACTCCAAGGGGGC[A/G]CTCAGAAGATGAGCTTAAACTTGTAGATGAAATAT R 2 1 2 1 201000 r 74 goat snp47093-scaffold659-1747643 3 95985020 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424026 Affx-122942086 AX-123294372 3 22577891 AGCTTGCTACTTGGGGCTCCAGGAACGAATCAAGC[A/G]ACAGCTCATAAAAAAAGAGGGTTTTATGATTTTCC R 2 1 2 1 102000 r 74 goat snp47094-scaffold659-1790541 3 95941565 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766177 Affx-122957457 AX-385253579 3 22610490 TAACATCTGGTCTTATAATCTGATACTCTGGGTGC[C/T]TCACTTATGTCTGAATAGCTAGTATGCCTCACCAG Y 2 1 2 1 101000 f 74 goat snp47095-scaffold659-1823140 3 95908052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396959 Affx-122963172 AX-123267314 3 22642105 AACTTCATTATTCCTTTTCTTTGGTGCATACTCTG[C/T]GGCACATGTAAGCACATCTGACTCTCAATACATCA Y 2 1 2 1 101000 r 74 goat snp47096-scaffold659-1854755 3 95876256 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421498 Affx-122943906 AX-123291845 3 22723414 AAGGATGGTGGTATGGCTATTAAACCATGTCTATT[A/G]AAGTCTAGAGCACTTAAAATTCACCTGCTTGCTTG R 2 1 2 1 101000 f 74 goat snp47097-scaffold659-1936064 3 95794259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429188 Affx-122937956 AX-123299530 3 22780229 AAGTAAAGCAAACATAATTCTGTTGTGTTTCCATC[A/G]CTGGCCTAATTCTGAAGGACATTCAATGAAATAGA R 2 1 2 1 101000 r 74 goat snp47098-scaffold659-1992879 3 95736908 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382708 Affx-122973628 AX-123253066 3 22823066 AAAGGAAAGAAAAGAAGGAAGATAGTCTTCTCCCT[A/G]CCTTTCCTCCTCTCCTACGGCTCTGGCATTCGGCT R 2 1 2 1 103000 r 74 goat snp47099-scaffold659-2035716 3 95693458 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409892 Affx-122952901 AX-123280243 3 22857327 GTAGCTCACTTAAAGTTCTTGAGCTAATAGATGGT[A/G]GAGGCAGAGTTTGAACCAAATTCTAACTTTTGAGT R 2 1 2 1 101000 f 74 goat snp47100-scaffold659-2069977 3 95659096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398567 Affx-122961510 AX-123268922 3 22889721 GATAGGCAGCATATCCCTGTGATGAGGAACTGCTG[C/T]ATAGACAGTGGTTTTCTCCTGCTCCTTACCACTTT Y 2 1 2 1 101000 r 74 goat snp47101-scaffold659-2102371 3 95626935 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391715 Affx-122967505 AX-123262072 3 22933035 ACTCCATAAATGCTGTGAGCAGACACTGCTCTAAG[C/T]GCTTTATGTGGATTAATTTTAACCCCCAGAACAAC Y 2 1 2 1 101000 f 74 goat snp47102-scaffold659-2145685 3 95583712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802889 Affx-122959248 AX-385289787 3 22972661 GTCATTCATAACTGGAGGAATGATGAAAACAAATG[C/T]AGTCATTCTTCCTATTATACCACAACCACCCACCT Y 2 1 2 1 101000 f 74 goat snp47103-scaffold659-2185311 3 95543985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390556 Affx-122967214 AX-123260913 3 23027986 AATTTTTTAAGGCTAACAGTATAAAATTATTTCTG[C/T]ACTGTTATTTCTTTGAAATGTGAACAAAGTAATAA Y 2 1 2 1 303000 r 74 goat snp47104-scaffold659-2240636 3 95491610 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414644 Affx-122949324 AX-123284993 3 23121413 CCAAAAAAAGCAAGAGAATTAGAATTTGAATTAAG[A/G]TGGTAGGAATGAATATGAGAGGCATGATATGAAAG R 2 1 2 1 101000 r 74 goat snp47106-scaffold659-2334063 3 95397604 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441336 Affx-122929428 AX-123311673 3 23172950 AAAATGTTGACATTTGGCTTTTAAGTTAGTGTCAA[C/T]TTGCATTTAGAACATAGCAAACATATAGGAAGGAA Y 2 1 2 1 101000 r 74 goat snp47107-scaffold659-2385600 3 95345743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431570 Affx-122936189 AX-123301911 3 23203011 ATCTCTCACAATATAGAGATTATGACTGAGCATGA[C/T]GTCCTGTTCTTACCTGTGGAAGCAAATATCCTTTA Y 2 1 2 1 101000 f 74 goat snp47108-scaffold659-2415661 3 95315608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785046 Affx-122922984 AX-385272093 3 23242604 CGTAACCAGCAGGTTCTTTTCTCGTAGAAACAATG[A/C]TTGTGTGATGGCGTCCTTGTGACCCTTTAGACGGT M 2 1 2 1 101000 f 74 goat snp47109-scaffold659-2455254 3 95275957 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443276 Affx-122927482 AX-123313613 3 23276841 AGGCACCATTATTTTGTAGAAAAGTCTCTGAAAAA[C/T]GACTTAAGACTACTGGTTTTTGGTCCCAGTTCTAC Y 2 1 2 1 101000 r 74 goat snp47110-scaffold659-2489491 3 95241824 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785791 Affx-122942908 AX-385272831 3 23310407 AAAGAATCAGCTACTACCACAGAGAATGTCAGTTA[C/T]ACAGTAATATGAGTAACACGGTGTTGTTGGAACTC Y 2 1 2 1 101000 f 74 goat snp47111-scaffold659-2523057 3 95207934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388374 Affx-122969327 AX-123258732 3 23340370 TTCCCTAAGGACACCCTGTGAATGATGGTGGGGTC[A/G]ATGGGAATTCAGGCTCTCGGGCTCCTCAGGCAGCT R 2 1 2 1 101000 f 74 goat snp47112-scaffold659-2553020 3 95177895 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397092 Affx-122962709 AX-123267447 3 23371002 CCTTCTCAGGTTGGCCTTGAGAACAATAGTACAGG[A/G]CTGTTAAGCCACTGATGACCACCTGCCCTCAAGGG R 2 1 2 1 101000 f 74 goat snp47113-scaffold659-2583652 3 95147501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787389 Affx-122943352 AX-385274414 3 23468125 ATTCTCTCTCTCCATCTATCAGAGCAGCCTAGTAT[A/C]TGATTTCCAGCCTTGTGCCCATCTAAGTCTTGTAG M 2 1 2 1 101000 f 74 goat snp47114-scaffold659-2680775 3 95051123 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386358 Affx-122970857 AX-123256716 3 23516687 CTAAAGCCCATGAAAATGATTGTCCATCCCAATGC[C/T]GTACCAAGGGTGAAAATCTTCAAATATCTCATTTT Y 2 1 2 1 101000 f 74 goat snp47115-scaffold659-2729337 3 95002983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442783 Affx-122927731 AX-123313120 3 23552991 CACCTCCCACATGCAGTCAGCAGGAACCCTGATCT[A/G]AAGGTGTCAGTGATGTAGTTTGGTTTCAGAGCTGA R 2 1 2 1 101000 r 74 goat snp47116-scaffold659-2765641 3 94966933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430171 Affx-122937367 AX-123300512 3 23593613 GAGGGCTCAGTGTGGCCTGTCCCTTCATCTGGCCA[G/T]CATTCCATGGGCCCTTGGTCACATGGATGACAGGG K 2 1 2 1 202000 f 74 goat snp47117-scaffold659-2806263 3 94926825 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444773 Affx-122926354 AX-123315110 3 23635074 ATTGATCTGTCATTTACGGATATGAGATGGTCAAC[C/T]AAGATGGAATTGCAGCTATTACATATTAAAAATGA Y 2 1 2 1 101000 f 74 goat snp47118-scaffold659-2847724 3 94885280 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801832 Affx-122952778 AX-385288739 3 23664213 TCAAAATTTCAAACTGCTTGGTTAAAATCTACCAA[C/T]TGAAGCCCTGGGTTGTCCTAGAGAACATCACAGAG Y 2 1 2 1 101000 r 74 goat snp47119-scaffold659-2876863 3 94855248 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793084 Affx-122962025 AX-385280062 3 23696307 TGAAATGTGAAAGTCAGAACTGTACAGTAATATGA[C/T]GAATCCTTTCATAACGCTGGTATTCTATGAATTTT Y 2 1 2 1 101000 r 74 goat snp47120-scaffold659-2908957 3 94823167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393837 Affx-122965160 AX-123264192 3 23782705 CACCTTCTGAACTTAGATGGTTGTTTCCTTTGAAA[C/T]GTTGTGCTGTACTTAGTCACTCAATCATGTGCGAC Y 2 1 2 1 101000 f 74 goat snp47122-scaffold659-2995355 3 94735771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785263 Affx-122929746 AX-385272308 3 23848965 TAGGATCAGAACCTGACAGGACAAAAACTAATTGC[A/G]TCATTCTCGCAATAGCAATATTAATCAGTATATTA R 2 1 2 1 101000 f 74 goat snp47124-scaffold659-3061615 3 94668956 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272194 Affx-1111833380 AX-519545946 3 23867537 ACTGCATAGCTTGAGAAGTCCAGCACAAAATGAAA[A/C]TGTAGGCCTCTTACTCAAAAATTAGTATGTTCCCC M 2 1 2 1 101000 f 74 goat 3_23867537_AF-PAKI 3 23867537 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413369 Affx-122950140 AX-123283718 3 23911840 ACACCAGGGATTCAAAAGAAAAGTTTCCAATACGT[A/G]TACACTCAAAAGAATGACGGGGCCAATAAAAATAC R 2 1 2 1 101000 f 74 goat snp47125-scaffold659-3124490 3 94605780 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443132 Affx-122928081 AX-123313469 3 23948002 AATAAGTTAATAGACTATTGAAATAGTCCAACAGC[G/T]AACTGAGAGCTTGAACTAGAGCAGGGGCAATGGGG K 2 1 2 1 201000 f 74 goat snp47126-scaffold659-3160652 3 94568902 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409720 Affx-122953033 AX-123280071 3 23979986 CTAGCTAAAAACTTAGATCCCAACTGACCACAATC[G/T]ACCCAAACATCAAGGATCTAAGAGACCAAAGTTTC K 2 1 2 1 101000 f 74 goat snp47127-scaffold659-3192636 3 94536756 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393423 Affx-122965874 AX-123263779 3 24027875 TGCACTCATATTACACAGCTAAACTGCATACTACC[G/T]TCTTTCATATTTTTTCTCCCAAATCTCCCACATGA K 2 1 2 1 101000 f 74 goat snp47128-scaffold659-3240525 3 94488568 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375762 Affx-122978599 AX-123246121 3 24065455 GGGGAGGCAGAGTGGGCAGAGTAGTAGGGAGATGT[A/G]CTCTTAGAATTTCTTGGCCCCTGGGATAGGATGTG R 2 1 2 1 101000 r 74 goat snp47129-scaffold659-3278105 3 94451014 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782018 Affx-122954501 AX-385269097 3 24101130 TTTTAGAAGGGCAGATAAGAAATGACTTACACATC[A/G]CTTCTCTCCACATTCCACTGACTTAGAACTGCGTA R 2 1 2 1 101000 r 74 goat snp47130-scaffold659-3313780 3 94415356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788416 Affx-122927297 AX-385275434 3 24144179 CAAAAAAACGGAGATGAATATTTTGGCAATCCTAA[C/T]GTAAAAAGGGAATGACAAAATCCTGCAGCTGAGAG Y 2 1 2 1 102000 r 74 goat snp47131-scaffold659-3356829 3 94372586 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396472 Affx-122962962 AX-123266827 3 24185398 GGACTGTGCTAGATGCTTCATATGCGTTTGTGTTA[C/T]GACCCTCATTTTATGAGAAAGCTGAGTAACCAGGG Y 2 1 2 1 101000 f 74 goat snp47132-scaffold659-3398048 3 94331545 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782816 Affx-122953543 AX-385269888 3 24229062 TGCTGGGTTTCCTTTGTGTTCCTAATAGGAAACCA[A/G]ACACACCACAAAGTATACCCTTTCTCACTAACCCC R 2 1 2 1 101000 f 74 goat snp47133-scaffold659-3441712 3 94288511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415707 Affx-122948524 AX-123286056 3 24265011 TGGCTGGTACATACTGTCATTCGGGGGCTAGGAGA[C/T]GGAGGGTGGAAGTGAGGGTAAAACCATCTGCTGGG Y 2 1 2 1 101000 f 74 goat snp47134-scaffold659-3477661 3 94252299 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438016 Affx-122931570 AX-123308354 3 24316059 ACACTTTACTGAATGGCTTTTCTTTCCCTGTGGCA[G/T]AAGCCTTCGGGGTCCCTGCTTCACTATGTTTTTGG K 2 1 2 1 101000 f 74 goat snp47135-scaffold659-3528709 3 94201075 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407622 Affx-122954633 AX-123277973 3 24376226 TTCAGTTTCTCCTTCTGAAAATGGGAAAAATAATC[A/G]TGTCCCACAGAGATGCTGGGAGAATTATATAAAAT R 2 1 2 1 101000 r 74 goat snp47136-scaffold659-3588876 3 94140531 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398050 Affx-122961754 AX-123268405 3 24411782 TTCATTATTTGCACTCATTCACATTTATTTCAGAC[A/G]CACATATGATTTGGTAGTACTCTCTTAGTTCTAAG R 2 1 2 1 101000 r 74 goat snp47137-scaffold659-3624432 3 94104790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792589 Affx-122966434 AX-385279570 3 24447361 TTGTTAAAGTGCAATTGAGAGTGCTTTTTCTTTCA[A/C]ATGGTGTGTAAATAATGGTGCCGGTTAAAATCAAT M 2 1 2 1 101000 f 74 goat snp47138-scaffold659-3660011 3 94068980 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429991 Affx-122938044 AX-123300332 3 24506258 AACAGACAAGAGCAGAGCTGCTTGGGAACACTCAA[C/T]GAAAAAGCAACTGTAACAGAAGAGACATGTTACAT Y 2 1 2 1 101000 f 74 goat snp47139-scaffold659-3718908 3 94009660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277932 Affx-1111836165 AX-519551427 3 24514908 ATGAACTCCATCATCACACATGTTATTTCCTTCTA[A/G]GAGGAAACTTGTTAATTTATTTCTTTGGAGATATT R 2 1 2 1 101000 f 74 goat Random2.2K-303 3 24514908 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800226 Affx-122919721 AX-385287149 3 24536748 ATTTCAAATTTCACAAGATTGTACCAGTTAACTGT[G/T]GCTCGTCAGAAACCCTAAAGCTTAGTGGCTGGACC K 2 1 2 1 101000 r 74 goat snp47140-scaffold659-3749398 3 93979076 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385879 Affx-122971599 AX-123256237 3 24629878 GGGAGTGATGCCCTGTAAGTCATTCTGCTTAAGGC[A/G]AGAGGAGACTGTTTTTTCCATTGATGCCGAAGTTG R 2 1 2 1 101000 r 74 goat snp47142-scaffold659-3842528 3 93887784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386731 Affx-122970148 AX-123257089 3 24696956 TAGTGGTTGTACCAATTTACCTTCCCACCAACAGT[A/G]CATGAGTTTTCTTTTCACTTCAGTCTTGCAACTCT R 2 1 2 1 101000 r 74 goat snp47143-scaffold659-3909606 3 93818159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405669 Affx-122956565 AX-123276021 3 24734393 CTCCAAATATAGTCACAGCAGGAGTTAGGGTTTCA[A/G]CGTGACTTTCAGGGGATGGATCATTCACACTGCTT R 2 1 2 1 101000 f 74 goat snp47144-scaffold659-3947043 3 93780301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437017 Affx-122933126 AX-123307355 3 24763345 CCCATAGCCTCTCCTAAAAATTAACCAGGTAGTCA[C/T]TCAGTACCTGTTATTATTTGTTATGCTAAGCCTTC Y 2 1 2 1 101000 f 74 goat snp47145-scaffold659-3975995 3 93751703 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775874 Affx-122936739 AX-385263005 3 24793389 TATCTGGTATGGCTTTTTGCACAAACCAGCTCTTA[C/T]GAAATAGGAATGCCAAAGGTCAGGCACTCAGAATC Y 2 1 2 1 101000 r 74 goat snp47146-scaffold659-4006039 3 93721759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432307 Affx-122936307 AX-123302648 3 24829767 GGAACGTTTAAGGCACAGATCTCTGGACTCCACTC[A/G]GACCTACCCAAACGCATCTCTGTGGGGTGGCTTAG R 2 1 2 1 101000 f 74 goat snp47147-scaffold659-4042417 3 93685570 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431779 Affx-122936708 AX-123302120 3 24885573 CTCTAACCTTTCTCTGAAGTCAGAAGAAATAATAA[C/T]GGTCACGTGTATATGGGGCTCCTTCCACCCCCTCC Y 2 1 2 1 201000 f 74 goat snp47148-scaffold659-4098223 3 93629355 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444933 Affx-122926700 AX-123315270 3 24929562 TGAAACTGAAGTTTCTGGGCCTGTTGGGGGCTGCA[C/T]TACTGTTGTCCCTTTTTATTTATGCTTGAAAGAAT Y 2 1 2 1 201000 r 74 goat snp47149-scaffold659-4142212 3 93585150 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424737 Affx-122941663 AX-123295083 3 24961211 GTATAGACAACCAATCACCCGACTCATCCCAAAGT[A/G]GCCTGTTCCCACACCGGGGAGGTGTCCTAATATCC R 2 1 2 1 101000 f 74 goat snp47150-scaffold659-4173861 3 93553329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772978 Affx-122944845 AX-385260122 3 25028419 GCAAGGATGAATGCAAAGCCCAGATTAGTGATCAA[C/T]AGCATTTACTACTGTAATTATTTATTACCACCATA Y 2 1 2 1 201000 r 74 goat snp47151-scaffold659-4241069 3 93486187 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403675 Affx-122957504 AX-123274027 3 25061122 TGCTGGTAAAGAACCAAAAGAGGGAGGCATTTACA[A/G]TGTTTCACGTCTACTGACATAACGTTACCTTCTTT R 2 1 2 1 101000 f 74 goat snp23724-scaffold2397-22213 3 93453320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388489 Affx-122969228 AX-123258847 3 25091536 TAGCTCTCTTAGCATCAGTTTCCCCAACTTTTGCT[A/G]TTGGTGCCTGTGGCAGAAGCCTGGGAGTTTATAGG R 2 1 2 1 201000 f 74 goat snp23725-scaffold2397-52627 3 93423085 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410492 Affx-122952194 AX-123280842 3 25127978 GCCTTGATACCACAGAAGACAGGTCTCCCTACCCA[C/T]GCCTACCCCCCAAGGCAGGGTCAATCAAGGCAGAT Y 2 1 2 1 101000 f 74 goat snp23726-scaffold2397-89069 3 93386783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782597 Affx-122959572 AX-385269671 3 25168211 ACAAGCAAAAGTACATGCAAATCCTTTGCTTTCTA[C/T]ACAAATGGAGTTTCATATTGTTCAGCAGTTTGGTT Y 2 1 2 1 101000 f 74 goat snp23727-scaffold2397-129302 3 93346132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424705 Affx-122941688 AX-123295051 3 25225286 AAGAGAGATCTGGGGTCCAAGGTTAGAAGAAATGG[A/G]TTTTATAGTCCTTCCTCTCCTCCTACCGGGAGGCT R 2 1 2 1 101000 f 74 goat snp23728-scaffold2397-186377 3 93288682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384785 Affx-122972008 AX-123255143 3 25245278 ATAGAACATGCCTGTCCCTTCCTTGGGACTGCATA[C/T]GTGGTTCATCAAAACCACTCTTCCCTTAAATAACT Y 2 1 2 1 201000 r 74 goat snp47869-scaffold675-11017 3 93269368 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402533 Affx-122958474 AX-123272886 3 25275282 TGAGTACAAACCCACTGTGCTGCCCAGTAAACTTG[C/T]AAATTCTGTACCTCTGACATGCTTTCTATAACTGC Y 2 1 2 1 201000 r 74 goat snp47870-scaffold675-41021 3 93239480 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438160 Affx-122931460 AX-123308498 3 25335685 CATATGTTTTGGACTTTTGTTTTTGAATCACTTTT[A/C]GTTTCTTCTAGAAGTGTTACTGTTTTATCCACTTT M 2 1 2 1 101000 r 74 goat snp47872-scaffold675-101424 3 93178738 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403922 Affx-122957474 AX-123274274 3 25382309 TTGGCATGTCTTGGGCTACTGAAGGGCTTGGTCAT[A/G]CTTTCTGGTCTCTGCTTTCCTCCTTCAGAGGCATT R 2 1 2 1 101000 r 74 goat snp47873-scaffold675-148048 3 93132294 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378072 Affx-122977175 AX-123248431 3 25431366 AAGGGACTTCTACTTGAACAGTCTCCTCAGCCCTC[A/G]CCCTGCTGCCAGGCTGCTGGTGTGGTAGTCATCCC R 2 1 2 1 101000 f 74 goat snp47874-scaffold675-197105 3 93079276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778799 Affx-122963533 AX-385265908 3 25466890 TGGTTTACCCTTCACTTTTGTATATAAGCAATTAT[A/G]TATATGCAAAATATGGATAGGTAGGTACATCTTTC R 2 1 2 1 201000 f 74 goat snp47875-scaffold675-232629 3 93041757 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793266 Affx-122938368 AX-385280244 3 25525676 ATGTCCTTTCTACCTTAGTGAATTAAGAGAATTAA[A/C]TGAATAAAAATTCCCCATAAAATTTTAAGAAGCTG M 2 1 2 1 101000 r 74 goat snp47876-scaffold675-291415 3 92983106 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387328 Affx-122970499 AX-123257686 3 25556409 CATGAAAGTGAGGTCAGGCTATAATTAAAAACTCA[A/C]TGGGCTCTTCACTAAAAACTCTGAAAGACACTGAG M 2 1 2 1 101000 f 74 goat snp47877-scaffold675-322148 3 92952348 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410898 Affx-122952070 AX-123281248 3 25599660 ACCCCTTTTAAAAAGTATAGTCGATTGGCTCCAAG[A/G]ACTGAAACAGAAATGCACTGTGTTCAACTGTGTGA R 2 1 2 1 101000 f 74 goat snp47878-scaffold675-365399 3 92910642 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378197 Affx-122976939 AX-123248556 3 25688805 GACTGACCCTCCTCTAAATAAGAGAGGGTTGGGAA[C/T]GCGGTACAGAGATTCAGAGATGACCACGGTGAATC Y 2 1 2 1 202000 r 74 goat snp47880-scaffold675-454544 3 92822823 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411372 Affx-122952240 AX-123281722 3 25754158 TAGAAATTGGCAAGCCTTATTAAGGTACAGGCTTG[A/G]CCAAAATTGTCCTCCACTGTTTGAAGAGTGGGCTT R 2 1 2 1 101000 r 74 goat snp47882-scaffold675-519897 3 92758128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427213 Affx-122939583 AX-123297556 3 25804796 TAGATCAGCATTCTGAAAAGACTTGCATGCCTCTC[A/G]CCCTCATCCTGATTAGTCATGGCACTTAAAAATCC R 2 1 2 1 101000 f 74 goat snp47883-scaffold675-570535 3 92707466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427782 Affx-122939777 AX-123298125 3 25864085 ACTACTAAATTAATAGAAAATGCCAAATAAGTAGC[A/G]CATCAGTGCTATTGCAGTTTCAGCCACAGCAATTA R 2 1 2 1 101000 r 74 goat snp47884-scaffold675-629824 3 92648489 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397421 Affx-122962245 AX-123267776 3 25898508 CTAAGACTCAACACAGCCAAATAAATACATAAAAA[C/T]GAAAAAAATCCTCCAAAACAAAATAAGGAACTTGC Y 2 1 2 1 303000 r 74 goat snp47885-scaffold675-664247 3 92614002 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389231 Affx-122969047 AX-123259589 3 26018663 CTATAAGTAACTTTTAATTTCCTCTTTATCTTTGA[C/T]CCATGGGTCTTTTCCCCCCAAATTAATGATATTAG Y 2 1 2 1 101000 f 74 goat snp47887-scaffold675-784402 3 92493875 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783880 Affx-122936154 AX-385270936 3 26055504 GTGTAATTCAGTAGTCAGCAAAGGCTTCCCTTATG[C/T]GACATTGCTCTAAATATATTGTTCAGTTTATTTGT Y 2 1 2 1 101000 f 74 goat snp47888-scaffold675-821243 3 92457018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448657 Affx-122923345 AX-123318993 3 26104227 GGGAGCAACAGATGTTCTGTGGAGAGCCCAGCACA[A/G]TCCCCATCCTTGATGCTCACAGTCAGACAGGCAAC R 2 1 2 1 101000 r 74 goat snp47889-scaffold675-869966 3 92407169 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278088 Affx-1111836166 AX-519551578 3 26113319 ATGGCACACTGCATTTTCCAAAAATGGCCTATAAT[A/G]GTATTTCTCATCCTACAAGCTCTTCTAGAACTTTG R 2 1 2 1 101000 r 74 goat Random2.2K-304 3 26113319 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396656 Affx-122962855 AX-123267011 3 26133536 TGAGGCTCCCCTTGATTTCCCCACTTGAATGTGCC[A/G]TCTATTTCTCACTGGTATCCCGACCTCATGGAGCA R 2 1 2 1 201000 r 74 goat snp47890-scaffold675-899275 3 92377814 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429902 Affx-122938116 AX-123300243 3 26183953 TTTGTACTTGTGGGTTTTCCCCACCAGAACTTAGA[A/G]TACTCTGAGAGCAGGAAATTTTTGTCTGCCTTGTT R 2 1 2 1 201000 r 74 goat snp47891-scaffold675-949692 3 92327379 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447496 Affx-122924082 AX-123317832 3 26219766 AAATAAAGGAAAACATCCTCTCCTAGTTTTGTGCA[C/T]ACAACAGAGACAAGCTAAGGAAATAAAAATACACA Y 2 1 2 1 101000 f 74 goat snp47892-scaffold675-985505 3 92291786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386189 Affx-122971368 AX-123256547 3 26249119 AGTGCATAAAACTGGAAACAAAGAGAAATCCCATT[A/G]TATCAGTTAAGATAGAATAAGTTTTGCCAACAATA R 2 1 2 1 201000 r 74 goat snp47893-scaffold675-1014858 3 92262331 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429174 Affx-122937967 AX-123299516 3 26324601 CTACAGTAGTATCAAAAGTAAATTGATACTTGAAA[C/T]GATTTTATTATTTGAAATGATTTTATTAATTTATT Y 2 1 2 1 101000 f 74 goat snp47894-scaffold675-1090340 3 92185137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768868 Affx-122938008 AX-385256045 3 26385287 GTCTTTTCTGCAGATCTGGCACAAGTTTCTTTGAG[G/T]AGATTACATAAATGTCTTGTAGCATTATTCCTGGA K 2 1 2 1 101000 f 74 goat snp47895-scaffold675-1151026 3 92124371 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381587 Affx-122974802 AX-123251945 3 26471855 TATTCTGTTAGGAAAGAGTATTAGAAAGCAGCTAA[C/T]GACAGTCTTTACACTGAATAGTTTTTAACCATTGT Y 2 1 2 1 101000 r 74 goat snp47896-scaffold675-1237594 3 92037016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417271 Affx-122947255 AX-123287619 3 26527131 AGTTTTCTCAAGTATGTTCTAAGCACAGAAGTATC[C/T]AAGTGGGGCCAAAATTCAGACTTGAAAATGTCCTT Y 2 1 2 1 201000 f 74 goat snp47897-scaffold675-1292870 3 91981688 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453605 Affx-122920136 AX-123323938 3 26573366 TGAGACTCTTAAGTTTTATTTATTAACTTTAAATG[A/C]GTTCTTCAAGTGTGATGTTTTTGAGTTCAGTGATA M 2 1 2 1 101000 r 74 goat snp47898-scaffold675-1339105 3 91935510 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407818 Affx-122954548 AX-123278169 3 26625734 CACTGGGAGGTGTGGGACTATCCTAATTTTACAGA[A/G]TAAGAAGCTGAGTGAGAAGAGGAAGCATCAATTTG R 2 1 2 1 101000 f 74 goat snp47899-scaffold675-1391473 3 91882394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786978 Affx-122925508 AX-385274006 3 26661549 TAGAGACTTAACATCAGAAACAAGAGTGCTACTGA[A/G]CTCCTATTTCTTTTCCACATAATTAGCTTTAGGTT R 2 1 2 1 201000 r 74 goat snp47900-scaffold675-1427288 3 91846582 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464198750 Affx-1110365364 AX-515673899 3 26695999 AAGGTACACTCTGATATGTCAGCTGTCACAATGCA[A/G]TTTAACAAAATTGTTTTAAATGAAGTTAAAGACAA R 2 1 2 1 101000 f 74 goat 3_26695999_AF-PAKI 3 26695999 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320780932 Affx-122962104 AX-385268019 3 26750210 TTATGCCCATTTGTTAATGTATATGACTGCTTTCA[C/T]GCTACAGTGGCAAAATGAGTAGCTGTGGCAGGTTG Y 2 1 2 1 202000 r 74 goat snp47902-scaffold675-1515949 3 91757873 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800908 Affx-122955976 AX-385287823 3 26804805 TGCTCCTTCCCTACCACAAGTTTCAGTGAGTCAGT[A/G]TCATTCTAGTGAATCCCACTTTTGATGTTAACTAT R 2 1 2 1 101000 f 74 goat snp47903-scaffold675-1570544 3 91701815 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449575 Affx-122923228 AX-123319910 3 26834961 AGCTAAGAGAATCAGAAGGAGCTTGTAGCCAAAAC[G/T]ACTTTATTGTTCATTTGTTTTTCAAGCTAAAGTTA K 2 1 2 1 101000 f 74 goat snp47904-scaffold675-1600700 3 91671606 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444966 Affx-122926673 AX-123315303 3 26869042 TTCATCTTCACTATCGGAAGCATTTCATTAGTAGT[A/G]CCTGCCTGCGGCACCATGTGCAAAGTTCTCAGACT R 2 1 2 1 201000 f 74 goat snp47905-scaffold675-1634781 3 91637523 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429657 Affx-122937666 AX-123299998 3 26903559 AAATGAAAGAGCTGAGGCTCAGAGTTGTTAGGTCA[C/T]GTGCTCAAGGCCCCAGAGTTAGTAAGTGGCAGATC Y 2 1 2 1 101000 r 74 goat snp47906-scaffold675-1669298 3 91603590 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383778 Affx-122973205 AX-123254136 3 26934483 GCTTTCAAATTTTATGGGATGCAGCTAAAGCAGAA[C/T]GTAGAGGGAGATTTACACGTTTGTATGTAGCGCTG Y 2 1 2 1 101000 r 74 goat snp47907-scaffold675-1700222 3 91572543 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783787 Affx-122930849 AX-385270843 3 26965574 ACATTTCCTAAACTACAAGTGCCATCAGAGTTAAA[C/T]AGTTACCTTTTGGTATACTTTTCTTTTTGTCGTAT Y 2 1 2 1 101000 r 74 goat snp47908-scaffold675-1731313 3 91540861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778719 Affx-122959169 AX-385265830 3 27070003 TCTCAGTTGTAATGAGAGACCAGCAGATATATCAG[C/T]GTTTTACTCTACCTGTTTCCAGTGTCAGTGGCATG Y 2 1 2 1 101000 f 74 goat snp47911-scaffold675-1835742 3 91435770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439166 Affx-122931064 AX-123309503 3 27111429 CCTCTCCTGTTCACTGACTATTTATCACCTGGCTT[A/G]CTTGCCCTCTCTACCTGTCATGATTCCTGGTGACT R 2 1 2 1 201000 r 74 goat snp47912-scaffold675-1877168 3 91394291 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396085 Affx-122963431 AX-123266440 3 27157688 CGTGACCGTTTTGCTCAGCATCAGCCTTGCCAAGA[A/G]CTGGTGGAGCCCCACTGGAGATGAGGTCATTGGTG R 2 1 2 1 101000 f 74 goat snp47913-scaffold675-1923427 3 91347488 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429206 Affx-122937939 AX-123299548 3 27195815 TGTATAAAAATGCGTGCCTGTGCTTTTAGCCCCCA[C/T]AGTTGAAGTCCCTTTATAAAGATGCATCTAAAAGC Y 2 1 2 1 201000 r 74 goat snp47914-scaffold675-1961554 3 91309415 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434613 Affx-122934089 AX-123304954 3 27241018 CTCCTTTTGCTTTTTCTATAAGGTGGGAATAATGA[C/T]GCTAGCGCTATTTTCCTAGAAGTTTGCTGAGAGGG Y 2 1 2 1 101000 f 74 goat snp47915-scaffold675-2006757 3 91264444 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393734 Affx-122965228 AX-123264089 3 27303314 CTGACTCCCACTGAAGCCAGAAACATTCTGTTGCC[C/T]GATCACTGGGGTTGCCCCCATGCATTTAAAGGTCA Y 2 1 2 1 201000 r 74 goat snp47916-scaffold675-2069053 3 91203559 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422308 Affx-122943473 AX-123292654 3 27341252 AATATAATCTGTTCACTAAGTTTGAAGAGATGCCA[C/T]GAAACAGCTGCCTAGGAATGGCACTCTGGAGGCTA Y 2 1 2 1 201000 f 74 goat snp47917-scaffold675-2106991 3 91165377 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779682 Affx-122951264 AX-385266783 3 27372615 GATCAAACCCGCATCTGTTGCAGAATAATGATATT[A/G]TGGCCTTCTCAGAATATCACACCCAAAGTCAGATG R 2 1 2 1 201000 r 74 goat snp47918-scaffold675-2138354 3 91134160 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796352 Affx-122974558 AX-385283302 3 27415028 GGGCCATCTTATCTTAGATGAAGCTAGCTGTGTAC[A/G]TGCCGTAGTGTTTCTCGAAGTGCAGTTCACTTACC R 2 1 2 1 101000 r 74 goat snp47919-scaffold675-2180767 3 91091802 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804486 Affx-986696653 AX-385291047 3 27453924 TGATGCTCAGCGTCTTGGCACAGGTGGCAGGTTTT[C/T]TGCATCCTCTCACCTTTGTGTTTCTCACATGGTGC Y 2 1 2 1 600010 r 74 goat 3_27453924 3 27453924 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 38396035 Affx-122963468 AX-123266390 3 27476125 TCCAGTACTTTCTGACTTGTTTTATGCAATGAACA[A/C]CACCACCAACAGCCAACAGTTATTGAACACTGATA M 2 1 2 1 101000 f 74 goat snp47920-scaffold675-2241864 3 91030637 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397501 Affx-122962066 AX-123267856 3 27504736 GCACTGGGTGAGGGAGAAGAATGGAGTATTAAAAT[G/T]ATTTGGACAAATGAGCGGACTCTGGTGACAAAGTC K 2 1 2 1 101000 f 74 goat snp47921-scaffold675-2270475 3 91002130 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389111 Affx-122968566 AX-123259469 3 27569763 GTGTTACCTTCTAACCCTGGTGGATAGCAATATGC[A/G]CAAGGTATGACCAGCCAGAGAAACTCACCTAAGCT R 2 1 2 1 101000 f 74 goat snp47922-scaffold675-2335502 3 90913204 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401739 Affx-122959515 AX-123272092 3 27607009 AAGGAAAGAGATGACTGCAAAACCATGAGACACCC[A/G]CCTGCTTGTTCATACGCAGAGGTGCCCTCAGCTCT R 2 1 2 1 101000 f 74 goat snp47923-scaffold675-2372748 3 90875949 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449292 Affx-122923015 AX-123319627 3 27679206 GAGAGCTGAGGAACACCACCACTTGCTTGGTAAAA[C/T]AGTTATCAGAAAAGTATTCTAGAAGACAGTGACGT Y 2 1 2 1 101000 f 74 goat snp47924-scaffold675-2444945 3 90803165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777405 Affx-122972164 AX-385264526 3 27713602 TGGGCTTGGTTCTCTTTCTGCAAAGTGGCACTGAG[C/T]AAGATGGCGATCATAATTCTTTCCATTAATAAACA Y 2 1 2 1 101000 f 74 goat snp47925-scaffold675-2479341 3 90768462 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778656 Affx-122953597 AX-385265767 3 27745989 GGCAACACTGCGGACTATGAGACAAGGAGAACAAG[C/T]GGAGGGCACCAAGACCAGCGCAGAATAAATGTAAC Y 2 1 2 1 101000 r 74 goat snp47926-scaffold675-2511728 3 90736196 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425356 Affx-122941582 AX-123295702 3 27793463 TGGTATCAAAAAATGAACCTATGGAGCATCATAAA[C/T]AAAAGAGTAGCATGACTGCATATGTGGGAAAAAGT Y 2 1 2 1 201000 f 74 goat snp47927-scaffold675-2559202 3 90688705 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375926 Affx-122978467 AX-123246285 3 27841491 AGTGATAGAAAACACAGATGTCACAGCAGCAGAGA[C/T]GGCAGGTAGGACAGACACGAGCTAACCTTGTACAG Y 2 1 2 1 202000 r 74 goat snp47928-scaffold675-2607230 3 90640832 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405626 Affx-122956598 AX-123275978 3 27871395 GGGGCTGGAGTATTGAGGGGTGGAAGGGTCTATGA[C/T]GACAAGGTAGTAGAAAGAATTCTGGGAAGAATATT Y 2 1 2 1 201000 f 74 goat snp47929-scaffold675-2637134 3 90610853 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464199324 Affx-1110365661 AX-515674470 3 27896703 TCCTCCAGAAAGCCCTCCTTGGCTTCCTCCAAAGA[C/T]AAGCTCCCTCCCCCCAACCTCCATCATCTCACGGG Y 2 1 2 1 102000 f 74 goat Random2.2K-305 3 27896703 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395461 Affx-122963913 AX-123265816 3 27901633 CAGGCAGCTTCACTAATGATCCCATCAAGACTGCA[C/T]GTGGCAGGGAGGGACAATCCCCCAGGAAAAAATGA Y 2 1 2 1 101000 f 74 goat snp47930-scaffold675-2667372 3 90580733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408056 Affx-122954274 AX-123278407 3 27958173 ATAAAGAGGCTGCTCCTTTCCAGAGCCCAAAATCT[A/G]GTAGGAGCAGAGAGATTATAAAAACAAATAAGCAC R 2 1 2 1 201000 r 74 goat snp47931-scaffold675-2723912 3 90524363 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400447 Affx-122959958 AX-123270802 3 27988740 GTCCAGGCAGTGCCTCTGGGCGACAGAAATCAAAA[G/T]ACACTTTGCAGTACTACGTGATAACATTCAATTCT K 2 1 2 1 201000 f 74 goat snp47932-scaffold675-2754479 3 90493869 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441709 Affx-122929153 AX-123312046 3 28029118 AGAAACTAGGTTTCTGCTGTCTGGTGGACAATGTC[A/G]TTATTATAGCCTAATTCCCCTTGAAATCTCTGGCA R 2 1 2 1 201000 r 74 goat snp47933-scaffold675-2794857 3 90453077 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438800 Affx-122930802 AX-123309137 3 28085684 CAAACAAATGAAGAGAATTTATGCATCCCTACTGA[G/T]ATGAAGTGGTAATTGGGTGGGGGACAGAGTATTTC K 2 1 2 1 101000 f 74 goat snp47934-scaffold675-2851423 3 90399377 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801287 Affx-122952323 AX-385288199 3 28133226 AGTCAGTCATTAATAACTGGATCATCTGTCATCAT[A/G]TGATACGAAAAATAAATTTCCAGCCAAGGCCACTT R 2 1 2 1 101000 r 74 goat snp47935-scaffold675-2898965 3 90351782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772690 Affx-122920058 AX-385259837 3 28171444 GATCCAACCTTACCCACCACAAAGTAGATCACTTA[C/T]GAGAGATGAAACTGTCCACCAAGTACCATAACCAC Y 2 1 2 1 201000 r 74 goat snp47936-scaffold675-2937183 3 90313098 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443549 Affx-122927761 AX-123313886 3 28203846 TATGCATGCAAAATTTCTGGAAGGACACACAAGAC[A/G]CTATCAACAGGGATGGCTTCTAGACTTTAGAAAAT R 2 1 2 1 201000 r 74 goat snp47937-scaffold675-2969585 3 90280105 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277936 Affx-1111836167 AX-519551431 3 28255892 TCCCCGCACACTACTTCCAGCTTCTCTGCCGAGCC[A/G]TGTCCTGTAACCTCCTGGGTCTCCCTTGCTTGTGC R 2 1 2 1 202000 f 74 goat Random2.2K-306 3 28255892 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468277938 Affx-1111836168 AX-519551433 3 28289202 TTGCGCCACACATAGCTTGTGCGTGTGACATGTAC[A/G]AGGTGGTGCGTGTGTGTGTGCTAAGTCACTTCAGT R 2 1 2 1 201000 f 74 goat Random2.2K-307 3 28289202 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391625 Affx-122966580 AX-123261982 3 28317199 CAGGGCACTTGTAGCTTCTGCTTTCTCTCAGATCA[C/T]AGCCTATAGTATGCTAGATAAGGAAGCCAGTCTAG Y 2 1 2 1 101000 r 74 goat snp47939-scaffold675-3082938 3 90166033 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444085 Affx-122926840 AX-123314422 3 28380435 CAGAGTGTTGTTAAGTACAAGTCAATAAAGCTAAA[C/T]AAAACATGTCCTTTAGAGAGTTAAAAACCCCCTTC Y 2 1 2 1 201000 f 74 goat snp47940-scaffold675-3146174 3 90101356 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426417 Affx-122940832 AX-123296763 3 28410342 GAGGGGCATTTTAAGACAATTTTATCTGTTTCTTT[A/G]TTCATCATATACATAATATCTGAAAGCCAACCACA R 2 1 2 1 101000 r 74 goat snp47941-scaffold675-3176081 3 90070651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398659 Affx-122961888 AX-123269014 3 28445157 AGGGTCAGAGGAGTGGACTCTCGGCTAAGCCCACA[A/G]GGGTAACACATGGAACTTCATCCAGCTGACCCTCC R 2 1 2 1 101000 r 74 goat snp47942-scaffold675-3210896 3 90035553 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791104 Affx-122971292 AX-385278099 3 28512379 GATGAGCTGCCAGGATAGGAATATGGACAATAGAA[C/T]GAAAAGAATACTTTGAGGATAATTATGGCAAGATT Y 2 1 2 1 101000 f 74 goat snp47943-scaffold675-3278118 3 89967486 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415799 Affx-122948902 AX-123286148 3 28546443 CAGTTGTCATATCATATCTATGTCACCTGTGTATT[C/T]TGAGATCACACCTGTACCTGCCAATAAACCTGGGA Y 2 1 2 1 201000 f 74 goat snp47944-scaffold675-3312182 3 89933466 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450178 Affx-122922310 AX-123320513 3 28578297 GTATTTCTTAGAAACTATTCTAGTAGTAACCAATT[A/G]TAAGTCTGGGTATATGTAGACAAATAGGTAGGGAA R 2 1 2 1 101000 r 74 goat snp47945-scaffold675-3344036 3 89901645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446806 Affx-122925292 AX-123317142 3 28637431 TGTGACATCTACTAAAATAAATTGATGAGCAGACT[A/G]CATTCTTACACTTTGAGGAAAGGGCCAGAGACATC R 2 1 2 1 101000 r 74 goat snp47946-scaffold675-3403170 3 89842511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454095 Affx-122919367 AX-123324428 3 28670908 GTGTGTGTGTGCTGCATTCCGAATTCCCTGTGCAG[C/T]CTCCTTAATCTGCAGCCTGCTGTCAGTACCTTACA Y 2 1 2 1 101000 r 74 goat snp47947-scaffold675-3436647 3 89808849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792662 Affx-122925738 AX-385279642 3 28715924 AATGATCCATTCTGTGCTTTTGCTGCAGAATCACA[G/T]TCATATGGCAGTCTAATTTCAGGCACTTTTAAAAC K 2 1 2 1 101000 f 74 goat snp47948-scaffold675-3481663 3 89763874 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444061 Affx-122926855 AX-123314398 3 28771119 GAGATCTTGCTCAAGCTCTTTCTCCTTTCTGGGCC[C/T]GAGCCCTGCAGCTGAACATCTAAGGGTTGGTTGAC Y 2 1 2 1 201000 r 74 goat snp47949-scaffold675-3536858 3 89708973 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787492 Affx-122925796 AX-385274517 3 28805573 GTAAGTACTTGTAGATCAGTGTGAAGTATTTCCCA[C/T]GGTAATTTTGTTTGGATTAACAGAATTTGCCCAGT Y 2 1 2 1 101000 f 74 goat snp47950-scaffold675-3571312 3 89674432 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800967 Affx-122975335 AX-385287882 3 28835068 AAAGTGTGAATTTAACCTAAATTTTGTATCTGATG[C/T]GTAAATATTTTCTAACCTTTCTCATTGTCTAAGCA Y 2 1 2 1 101000 r 74 goat snp47951-scaffold675-3600807 3 89644687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434609 Affx-122934092 AX-123304950 3 28881722 CAGGGTCCTCACTAGCAGATCCTCCTGAATCTTGT[C/T]TCTAGGCAATGAATGCCGTGAGTTCCAACTGCCTG Y 2 1 2 1 201000 r 74 goat snp47952-scaffold675-3647461 3 89598649 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426095 Affx-122940644 AX-123296441 3 28929732 AAAAGAAGGAGAGGCCTGGGGTCATTCTTTGGAAA[C/T]GAATGGGCAAGTGGAGTAAAGAATGAAGGGGAGCC Y 2 1 2 1 201000 f 74 goat snp47953-scaffold675-3695471 3 89551317 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425681 Affx-122940862 AX-123296027 3 28985552 TGAACTGAGAGGCCACCAGTTCTACAACTAACTTT[A/G]TTAGTTTGCTAAGGCTGCCATAAGGAATATAACAG R 2 1 2 1 103000 f 74 goat snp47954-scaffold675-3751291 3 89496039 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779899 Affx-122969393 AX-385266998 3 29067209 CCCAGTAGGAAAGACAGATAAGTAATAAGAAACAA[C/T]AGGATCCCATGAGAGACACAAAAGTGTCCAAGTAT Y 2 1 2 1 101000 r 74 goat snp47956-scaffold675-3832948 3 89414322 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408116 Affx-122954252 AX-123278467 3 29116334 GTGAAAATCATGAAAGGAAAAAAAGAAAGCTAACC[A/G]TGGCAGTAACGCACTAAGGTGATCCCCAGTGAGTT R 2 1 2 1 101000 r 74 goat snp47957-scaffold675-3882073 3 89364966 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798638 Affx-122937950 AX-385285570 3 29160713 CAGAGTGTGGAGAAACTGAATCAACACAATTTATT[A/G]TTAGATGAAAGTCAGACGCAGCAAAAAAGAGCAGA R 2 1 2 1 101000 f 74 goat snp47958-scaffold675-3926452 3 89320747 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277940 Affx-1111836169 AX-519551435 3 29205567 CGCTGTTCTTGCTTCATGGCTTGGGAATTGCCAAA[A/G]AAAGCTTACAGCCAGAAGCCCTGGGACAACCAGCA R 2 1 2 1 101000 f 74 goat Random2.2K-309 3 29205567 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38428612 Affx-122938689 AX-123298954 3 29217572 CTGATTTGCAGGACAGTAGAAAGCAGGCAGGGTCT[A/G]CCCATGGTCTCCCCAGGTTTATATTCCTGAGTCCC R 2 1 2 1 201000 r 74 goat snp47959-scaffold675-3983311 3 89264170 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436276 Affx-122932536 AX-123306615 3 29268640 AGTTACACTGAAGAGCCTTTGCTTTTCTTGGTACT[A/G]TTTGTTAGTTCTATCTCCTTCCTCCTGCTGATCAA R 2 1 2 1 101000 f 74 goat snp47960-scaffold675-4034379 3 89213420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272518 Affx-1111833382 AX-519546236 3 29297461 TATAGTCCAACTCTCCCATCCATACATGACTACTG[A/G]AAAAACCATAGCTTTGACTAGATGGACCTTTGTTG R 2 1 2 1 103000 f 74 goat 3_29297461_AF-PAKI 3 29297461 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38416328 Affx-122947908 AX-123286677 3 29321173 TTACAGCTTTTCATTGTAAAATTTATCATGATAAT[G/T]ATTAGTTGATATATCTTATCCTAGGTGGTGCTAGC K 2 1 2 1 101000 r 74 goat snp47961-scaffold675-4086912 3 89160896 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773287 Affx-122963958 AX-385260430 3 29353247 CCGCATTGTGGATTAAATGTAGATCTGAGCAATAA[G/T]GTAATGATATGACTTCAAAAACCTCCCCTGAAAAT K 2 1 2 1 101000 r 74 goat snp47962-scaffold675-4118986 3 89133272 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390659 Affx-122967134 AX-123261016 3 29403522 ACGAGGAATCAGCTTGGGCGTCTTCTTCCTTCTAG[C/T]CCCTCAGGACGAGAGTCCCTCCCTCTTCTTCCTTC Y 2 1 2 1 101000 f 74 goat snp47963-scaffold675-4169261 3 89083478 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798698 Affx-122972888 AX-385285630 3 29463896 TGTAAAAATGTTACCCAGTTGGGCTGTTGGCCAAA[C/T]GGCAAACAATTTACACTTGTCCATGGAAGGATATG Y 2 1 2 1 201000 r 74 goat snp47964-scaffold675-4229635 3 89023520 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432514 Affx-122935569 AX-123302855 3 29495225 AAAATCATAAGAAGCCCAAGGAAAAAGTTTAGATA[C/T]AGAAGAACTAAGTTATGAAAATATATAGATTTTCT Y 2 1 2 1 101000 f 74 goat snp47965-scaffold675-4260964 3 88992051 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772647 Affx-122934073 AX-385259795 3 29546702 TTTGAACCACTCTCTATCAATGTGAACTAAACAAA[C/T]AGGGTGGAGATAGGAAACTATCTCTATCCCTGGAA Y 2 1 2 1 101000 r 74 goat snp47966-scaffold675-4312441 3 88940448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396425 Affx-122962996 AX-123266780 3 29607718 TTTAGATCTGGGGGCTCTACTAAAGATGTTCATCT[A/G]AGGTTACTCAGTAACCCAAGGCTGAGTCTGTCCTT R 2 1 2 1 101000 f 74 goat snp47967-scaffold675-4373457 3 88879524 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794869 Affx-122930366 AX-385281829 3 29628400 TAGATGGGAGTTATAAAAAAACATGTGGGTCTGAC[A/G]TTTCACTCTACCTGTAAGCCAAAAAAGTTAGCCTG R 2 1 2 1 101000 f 74 goat snp43515-scaffold580-4578 3 88858705 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420075 Affx-122945113 AX-123290423 3 29661431 AGAGCAATAAACCTGAAGGTCTAGCAATAGAAATG[A/C]TGCCAAATGAATCAGGGAGAAAGAAATTTAAAAAA M 2 1 2 1 101000 f 74 goat snp43516-scaffold580-37609 3 88825363 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775408 Affx-122948567 AX-385262539 3 29694774 CCCTAGATATAGAAGGGGACTTTGTTCCCGACAAG[A/C]TCCCCATCAAACTTTTTGGGGGATCTTTTTTGTTT M 2 1 2 1 202000 r 74 goat snp43517-scaffold580-70952 3 88792453 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431700 Affx-122936773 AX-123302041 3 29758731 AAAACAAGTAATGTAAAAATACCTGTTACAACCCC[C/T]GCTTCTGTAACAATGCCAGTTGCCTCTTTCTAAGC Y 2 1 2 1 101000 r 74 goat snp43518-scaffold580-134909 3 88728896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382541 Affx-122973785 AX-123252899 3 29818865 GGGCCAGGAGCCCAGGAGGGTGTGAACTAACAAAA[A/G]CAAAATAAGTGTATGTGTACCAAAGAAATGAGGGA R 2 1 2 1 202000 f 74 goat snp43519-scaffold580-195043 3 88668156 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802308 Affx-122942403 AX-385289212 3 29853494 TGGTGAGAATCCAGTCCATTGGAGACTTAATGACT[A/G]TACCAGGTAGACAGTCCAATGGTTTAATCAACATG R 2 1 2 1 201000 f 74 goat snp43520-scaffold580-229672 3 88632930 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396157 Affx-122963383 AX-123266512 3 29930073 CTATATGGTGCAATGGTTAAGAATCTAGACTTTGG[C/T]GTCAGCTATACCTGGTCCTCAAGCCCCAAAAGACA Y 2 1 2 1 201000 r 74 goat snp43521-scaffold580-306251 3 88554321 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380035 Affx-122975584 AX-123250393 3 29964237 TTTATTTCTTGAGACTCTGGGCTGAGCTGAAAGCA[C/T]ATTGGAGGGGCTGACCTTACCTTGATTCTGAAGCT Y 2 1 2 1 202000 r 74 goat snp43522-scaffold580-340415 3 88519330 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377282 Affx-122978124 AX-123247641 3 30025861 AGGCCTGTCTGAGCTGGAGCTTGAGTGGGTTGCAG[C/T]GGCAAAAGATACACAGGACCCTTCACGTGGCAAGT Y 2 1 2 1 101000 r 74 goat snp43523-scaffold580-402039 3 88448719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446415 Affx-122925563 AX-123316751 3 30074010 GCTGTCCACAGTAGGCCCATCATCAGTAGTGCATC[A/G]TTGTTAAACAGATGAATGAGCAAGTGAACTCTTGA R 2 1 2 1 201000 f 74 goat snp43524-scaffold580-450188 3 88400189 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417039 Affx-122947530 AX-123287387 3 30112426 TGTACAGAGAACACAAATGTTGTTGCAGGATGGAA[C/T]AGGAGACTGGGGTTACCGAATTGAAGTTAAAGTCA Y 2 1 2 1 101000 f 74 goat snp43525-scaffold580-488604 3 88361845 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784985 Affx-122958980 AX-385272032 3 30149276 GAAAACAAGATGTGGAGTCAGAAAATAGTTGAAGA[C/T]GAACATTGTAGATAAGGTGGTTGAAGACCATGAAA Y 2 1 2 1 101000 f 74 goat snp43526-scaffold580-525454 3 88325088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436654 Affx-122932479 AX-123306992 3 30180595 CAGTGATCAACTGATTTGCAGAAGAATCTCTGAAG[A/G]TTAACAAGGTTTTTCTTTTTAGAAGAAGTGGGTCC R 2 1 2 1 101000 f 74 goat snp43527-scaffold580-556773 3 88293459 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442369 Affx-122928021 AX-123312706 3 30215704 CATCACCCTGATACCAGAAACCAATAAAGATAGCA[C/T]GAAAAAGAAAATTGTAGGGTCATATCACTGGTGAA Y 2 1 2 1 101000 f 74 goat snp43528-scaffold580-591882 3 88257210 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450136 Affx-122922755 AX-123320471 3 30298510 CAGTTTGATGTGCATGTAGTTTTGTACTGTGTGTT[A/G]TTATCTTTGTTTATGTGATTTGAGTGTGTGTGTGT R 2 1 2 1 101000 r 74 goat snp43529-scaffold580-674688 3 88174479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377379 Affx-122977636 AX-123247738 3 30337693 TCTTCTGTCTAGGATCATTGTACATGCTTTAAAGT[A/G]CATATCTCCCCAACTCCCCAGCCTCCCACCCCTGG R 2 1 2 1 101000 f 74 goat snp43530-scaffold580-713871 3 88134866 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420669 Affx-122944815 AX-123291016 3 30397915 AGATTTTGACAGCAGAAGGGTGTCAGTTTTTCCAG[C/T]GGGGTTGGCTGGGGTGGTAAGTCCATGCCTGACTA Y 2 1 2 1 101000 f 74 goat snp37607-scaffold460-1208717 3 88069189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379901 Affx-122975765 AX-123250259 3 30440599 AGTCACAAGATCAGGGGTGCCAGATACGAGTACAC[A/G]CTCTTTGGAGTGGGCTAAAAAGAGAATTCAGGGAA R 2 1 2 1 101000 f 74 goat snp37606-scaffold460-1166033 3 88025765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385271 Affx-122972073 AX-123255629 3 30490449 AGGAAGAAAAGCAGAGGCCATTATTAGCAGATGCA[C/T]GGTAGGAGTGAGTACAGTTCAGAAAGACCTGCTCT Y 2 1 2 1 101000 f 74 goat snp37605-scaffold460-1116183 3 87974034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423030 Affx-122943408 AX-123293376 3 30520865 ATTTACAGTAACGATAGTCACTGCCACCATAGCTT[A/G]AAAACTTCACATCCATCATCTCCTTTAATCTTGCA R 2 1 2 1 101000 f 74 goat snp37604-scaffold460-1085767 3 87942897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448887 Affx-122923261 AX-123319222 3 30552942 GAGTATCATGTGTTAATTGCTCATGCTGTCCTCCC[A/G]CTGCCTAGAATGCCCTCCTGTTCTGTGCCCTAGCC R 2 1 2 1 101000 f 74 goat snp37603-scaffold460-1053690 3 87910322 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451163 Affx-122921353 AX-123321497 3 30585768 AGCTGTGTCAAATGGATTGATTAAGCTACAGATCT[A/G]TAATTTGCCTGCTGAGATATATGCTGTGACCTGAG R 2 1 2 1 101000 r 74 goat snp37602-scaffold460-1020864 3 87877415 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439660 Affx-122930598 AX-123309997 3 30643238 TAGGGTATATATATTTTTCCCAGGGTGCTGATGGA[C/T]ATGCACTGATCCAGTCACATCTCCTCCCATGAATC Y 2 1 2 1 101000 f 74 goat snp37601-scaffold460-963394 3 87819430 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423079 Affx-122942937 AX-123293425 3 30682678 TCCTGGTGTCAGAACTGAGGCCATAGATGAAATAA[C/T]AAGAAGAAAAATTCCAGTTCACCAGAGCTAGACCT Y 2 1 2 1 101000 f 74 goat snp37600-scaffold460-923954 3 87782696 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384835 Affx-122971970 AX-123255193 3 30737338 CAGTTGATTGGAATCATTTATTCATCAGCATAATT[A/G]CCCACTTTGCACGAGGAGCCTTTCTCCTTTCTTAA R 2 1 2 1 201000 f 74 goat snp37599-scaffold460-869294 3 87727935 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415974 Affx-122948414 AX-123286323 3 30788842 GGATATCAAGAAAGTGGTGGAGGAGGTCTGGGAGG[C/T]AAGAGGAAAGTGAATTCCTGTAAACTTCCAGAAAG Y 2 1 2 1 101000 r 74 goat snp37598-scaffold460-817790 3 87676187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451026 Affx-122921453 AX-123321360 3 30825501 CATCTCTCATTAAAACAGTTGAACTTGAGCATTTC[A/G]TTTACCGATGATGTTTTTGAGAAAATTAAAACAAA R 2 1 2 1 101000 f 74 goat snp37597-scaffold460-781131 3 87639807 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445970 Affx-122925891 AX-123316307 3 30870653 AAGCAGAACAGAAGGACACCCCAGAGGCGACAGGA[A/C]TGTGGGGTGCGATGCATGGAGCTGACTGGATCGTT M 2 1 2 1 303000 f 74 goat snp37596-scaffold460-735979 3 87594496 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408649 Affx-122953473 AX-123279000 3 30903478 GTCCTTCTCCTGGGACTTTATGTTCTTTATGTACA[C/T]GCAACTGCAAGAGCACAAGCATGGCAACACCCACC Y 2 1 2 1 201000 f 74 goat snp37595-scaffold460-703154 3 87561326 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392162 Affx-122966312 AX-123262519 3 30981545 ATAATATAATTTAGGTTTTCTTTGCTGTATTTTAA[A/G]TGGGATCAAAAATTTTGAAGAGGATTTTTCTGTTT R 2 1 2 1 201000 f 74 goat snp37594-scaffold460-625087 3 87482497 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379258 Affx-122976254 AX-123249617 3 31012777 AGGCACAGCAACCAGAACAGAGTCACTCTGCAATC[C/T]AGGGACAAAGGCATGCTGGGCCACAGCCCTGTTCC Y 2 1 2 1 101000 f 74 goat snp37593-scaffold460-593855 3 87451268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425694 Affx-122940782 AX-123296040 3 31044128 GGCCCTAGATGGGAAGTGTTCTGCGTTTCTTAAGC[C/T]GGTTCCTTCATTCATTCTGTAAACATTTACTATGC Y 2 1 2 1 201000 f 74 goat snp37592-scaffold460-562504 3 87419998 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411538 Affx-122951656 AX-123281888 3 31087786 CACCCACAATCTGAGAGCACAGTTTGCTTTCCCTT[A/G]CCTCTGGATTTGGGCTTGTACCCATTACTGTGGCT R 2 1 2 1 101000 f 74 goat snp37591-scaffold460-518846 3 87376548 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451810 Affx-122921484 AX-123322143 3 31123522 TCTGGGCAGGATGGCCTCCCTCCTTGCCAACCCTG[C/T]ACCCTGTTTCATCCTGATACTCCCAGCTCCAGAAT Y 2 1 2 1 101000 r 74 goat snp37590-scaffold460-483110 3 87341066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398444 Affx-122961610 AX-123268799 3 31181998 TTGAAAATAATTCTATTAGTGAAACTCAAACTTAC[A/G]TTAGCTCCTTTAGCAGAATTTCACGTTGCTGCTTC R 2 1 2 1 101000 r 74 goat snp37589-scaffold460-424634 NW_017211741.1 1958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448163 Affx-122924266 AX-123318499 3 31221653 GCCTCTCTGCCAACCCACGAGATTCCCACCAGACC[C/T]CATTCTTGGGCCACTGGTTTCTGTCTGGCAAAGAA Y 2 1 2 1 101000 r 74 goat snp37588-scaffold460-384979 3 87245594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380003 Affx-122975607 AX-123250361 3 31276876 GGAGATAGCCTCCATTTTCCTTGCCCAAGTTCAGG[A/G]AGTTGAGTTAGAGGAGTAGGCAGGTGGAGATTCAT R 2 1 2 1 101000 r 74 goat snp37587-scaffold460-329756 3 87190283 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771811 Affx-122969865 AX-385258968 3 31330854 GCTTTTTGCTTTGAATTCTCAAAATGCAGCATCCT[A/G]TCTCTAACTTCAAAAGAGGTCAATTAGTAGACAGA R 2 1 2 1 101000 f 74 goat snp37586-scaffold460-275778 3 87136133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451336 Affx-122921269 AX-123321669 3 31360161 TGCTTATTGGCAGAGGGGAGGCTCAGATCCAAATG[C/T]GCCTCTCTCCAAAGTCATGAGGTAACCTCCATGAC Y 2 1 2 1 101000 r 74 goat snp37585-scaffold460-246471 3 87106651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438626 Affx-122930919 AX-123308963 3 31443956 TACACACAAAACCTGTCCAAGAGAACAATGCTGCC[A/G]TGCAGAGGACAGTAAGAAAGCAGGGCAGGGAGAAC R 2 1 2 1 101000 f 74 goat snp37583-scaffold460-162676 3 87022692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784913 Affx-122926550 AX-385271960 3 31498517 TTTGGAATCATGAGGGCATTATATTATGTCCCTTA[C/T]AGCTTTATCCCTGAGTCTATTTTGTCATACTCAAG Y 2 1 2 1 101000 r 74 goat snp37582-scaffold460-108115 3 86970991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387254 Affx-122970560 AX-123257612 3 31545686 TGGGTAGGTGCCTCGCCTGGCCTCTGCAGCACAGA[C/T]ACTTGGAACAGAGCCCCTAAACCCCTTAGGGCATG Y 2 1 2 1 101000 r 74 goat snp37581-scaffold460-60946 3 86923796 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775309 Affx-122955983 AX-385262440 3 31618061 GTAGGTTATATGATTGCTTGTTCATTTCTATCTCC[A/G]CTTCATGTACCTCTGTGTCTTAGCATCAGATCTCT R 2 1 2 1 101000 f 74 goat snp25341-scaffold261-1157571 3 86826111 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769626 Affx-122961141 AX-385256796 3 31688141 TTCTTTCCAGAGGACAAAATTTGGCTGTAAATTTC[A/G]TAAAAGTGAAGGCAAAGGGTGAAGTACAATTTGTT R 2 1 2 1 101000 f 74 goat snp25340-scaffold261-1087491 3 86754555 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785006 Affx-122923974 AX-385272053 3 31783185 ACCATTACATAGTGAATGCCAAAGTTGAAAACTGC[A/G]TTTACACAGGATGGTTCCAAAGTTCTTGTACACTG R 2 1 2 1 201000 f 74 goat snp25338-scaffold261-992447 3 86658898 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379848 Affx-122975806 AX-123250206 3 31823088 GGGGCCCACAAGACAGCAAGTCCCTCAGGAAGGAT[A/G]CAGCTGAGGAGGGTTTGGAAGTGAGGCGCCTCTAT R 2 1 2 1 101000 f 74 goat snp25337-scaffold261-952544 3 86618728 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799639 Affx-122949408 AX-385286568 3 31894974 TTCTGTTTTAAGAAGGAAAGCCATGTACTTATATC[A/G]TTTATACACACTGCTGCCAGATTAATATTCCTGAA R 2 1 2 1 101000 f 74 goat snp25336-scaffold261-880658 3 86546808 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798556 Affx-122961037 AX-385285489 3 31937505 TTAAAATTAAACATAGTAGGGCATTTTTTTAGTAA[C/T]ATTCACTACTAGTATTTAGTATAATTTGAAAACTG Y 2 1 2 1 101000 r 74 goat snp25335-scaffold261-838127 3 86504211 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272198 Affx-1111833383 AX-519545949 3 31957556 TTTCCAGTGAGTCAAGTCTTCGCATGAGGTGGCCA[A/G]AGTACTAGAGTTTCAGCTTTAACATCATTCCCTCC R 2 1 2 1 303000 f 74 goat 3_31957556_AF-PAKI 3 31957556 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38441195 Affx-122929535 AX-123311532 3 31967093 GGTTTCAACTCATTTAGAAAACTACTAACAGTACC[A/G]CAGTGCCAGTACATGCTGGTCACATGCCACACCTG R 2 1 2 1 101000 f 74 goat snp25334-scaffold261-808539 3 86474467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453865 Affx-122919526 AX-123324198 3 32008750 ATTTGAGTTTTATTTCCATTTTGTGGAATCTTATT[C/T]TGGGGTCTGGCTTTGTTGTGCAATTGACACAGGTC Y 2 1 2 1 202000 f 74 goat snp25333-scaffold261-766882 3 86432804 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422426 Affx-122943362 AX-123292772 3 32039846 GCATGGTGAGGACGGAATCTCCTGATGGCCAGTGG[C/T]GGGTGGAGGCCCAGCCACCCAGCTTTTACTGAGGG Y 2 1 2 1 101000 f 74 goat snp25332-scaffold261-735786 3 86402597 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390803 Affx-122967863 AX-123261160 3 32068579 CTAGACATTTGCCAAGACAAAAAATTGGGGGAGAT[A/G]TTTTTCAATCTAAAAAAACAATTGTATTAATTTAA R 2 1 2 1 101000 f 74 goat snp25331-scaffold261-707053 3 86373671 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430515 Affx-122937215 AX-123300856 3 32144148 TTAGCACGTATGCATGCAAGGTGGAAATGAGATGA[C/T]ACTTGGAAAGATTTGGAGCAATTCCTGGCATTAGA Y 2 1 2 1 101000 f 74 goat snp25329-scaffold261-631484 3 86296541 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799079 Affx-122938314 AX-385286009 3 32187694 GTCCTAAATCCTTATCTTTTCAGCAGGATGACTCC[A/G]AATTGCAAATATTGCCCAATAGGATTAGTTTCTAG R 2 1 2 1 101000 f 74 goat snp25328-scaffold261-587938 3 86252637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392309 Affx-122967518 AX-123262666 3 32250834 AAATGGAGGTTCATAATATTTGCTATGGTCTGAAC[A/G]TTAGTGTCTTCCCAAAATTCATATGTTAAGTGATG R 2 1 2 1 201000 f 74 goat snp25327-scaffold261-524798 3 86188582 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376823 Affx-122977923 AX-123247182 3 32321234 AGTCAATACAGAGATGAAACCAAAGATGGAAAATA[C/T]ACTGGTTCACTCTAATTAACTTCTGCTGAGGACCC Y 2 1 2 1 101000 r 74 goat snp25325-scaffold261-454398 3 86117458 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392401 Affx-122966214 AX-123262758 3 32371884 TTGCTCTGAATATGCTAATTTCCTTAATGTGCCTG[C/T]GTGCCATGTCGCTTCAGTCATTTCTGACTCCTTGC Y 2 1 2 1 101000 f 74 goat snp25324-scaffold261-403748 3 86067035 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453878 Affx-122919515 AX-123324211 3 32401290 GTTGCCAGGAGTGGGGTACTCTCGAGGTGGAGTGC[A/G]TGGCTTCTCATTACAGTGGCTTCTCTTGTGGAGCA R 2 1 2 1 201000 f 74 goat snp25323-scaffold261-374342 3 86037798 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418924 Affx-122946515 AX-123289272 3 32441749 GCTGTAGCTGTGATTCTTAACCAAGGGGCTTATCA[A/G]AGTCAGGGGAAATTTAGAAGAAACATTCCCACAAG R 2 1 2 1 10000 f 74 goat "023;ins-del_024;snp25322-scaffold261-333883" 3 85996844 A G "ins-del_024;023" 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403747 Affx-122958011 AX-123274099 3 32533999 TGAGGGCCTGCTATATGCTGAGCATCGTTAGCTGA[C/T]GAGCATACAAATCAAATAAGGCATGATTGCTACAC Y 2 1 2 1 101000 f 74 goat snp25320-scaffold261-241633 3 85904780 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396507 Affx-122963526 AX-123266862 3 32580882 AGTCCTATTTTGAGACTCGATCTGATTTTACTAAT[A/G]AATTAATTACCCATTAGTAAGTAAAGTCAAGTCAC R 2 1 2 1 101000 f 74 goat snp25319-scaffold261-194750 3 85856559 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387307 Affx-122970516 AX-123257665 3 32631342 AACACCATTTCCAAATAATAGTACTCTAGGTATTC[A/G]TTCCATCATTCTTTTAGCTTTCAGCCAGAATTTGA R 2 1 2 1 101000 r 74 goat snp25318-scaffold261-144290 3 85805974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435609 Affx-122933788 AX-123305949 3 32669537 CCCAGCTTCTCCTTCTAGGAGAGCAAGAATGAGGC[C/T]GTGTTAGGTCATGCCTTTTACTACCTAGGAGTCCT Y 2 1 2 1 102000 r 74 goat snp25317-scaffold261-106095 3 85768825 G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383196 Affx-122972789 AX-123253554 3 32716037 AAAATTATTGTGGAAGTCCCTCTCTTGTTTAGATC[A/G]TTACAGAATTTCATTCTCCCTTTTGAAGGATATCA R 2 1 2 1 101000 r 74 goat snp25316-scaffold261-59595 3 85722276 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787980 Affx-122926815 AX-385275001 3 32749401 TTAACAGCTATTTCAGGAGCAAGCTTGAGAACATT[C/T]GTACCATTTCCTCTCCACAAAGAAATGACTCCGCC Y 2 1 2 1 101000 r 74 goat snp25315-scaffold261-26231 3 85688470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425769 Affx-122940724 AX-123296115 3 32781675 CCTTACTCAAACCTCACCTGCATTGCACATTGCAG[A/C]GTTGGCAACATTCTCAAACTCTCTAGTTACCATTT M 2 1 2 1 101000 r 74 goat snp30451-scaffold3351-51973 3 85655654 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796826 Affx-122936426 AX-385283769 3 32823822 ACCTCACACTCCATTAAACTCAATGGGATAAAATA[C/T]GTGAAATTCCAATATGACCCACAGATTATGATTTG Y 2 1 2 1 101000 f 74 goat snp30450-scaffold3351-9826 3 85610855 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782933 Affx-122947105 AX-385270003 3 32861779 TTAGAGGAGCAGAGACTAGAGAAATGAGATGACTA[A/G]ATACGAGATGTTGCTATCATTCAGAGAAGTGATAA R 2 1 2 1 101000 f 74 goat snp46868-scaffold654-28032 3 85556043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772422 Affx-122947096 AX-385259574 3 32951624 CACTCATATAATTTTTGTGTAAAGAGGAGTGACAA[A/G]ATAATATTTATTTCAGTGACCACTTCTCCATTTTG R 2 1 2 1 201000 r 74 goat snp46870-scaffold654-117877 3 85465268 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422808 Affx-122943201 AX-123293154 3 33008949 ACATTCAGTCTATAGTATCCCCGGTGCCATTTTCT[A/G]CTGTTGCTCTGGATATACCTGCTCAGCTGAAGTTG R 2 1 2 1 201000 r 74 goat snp46871-scaffold654-175202 3 85406909 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800671 Affx-122934412 AX-385287589 3 33055792 ATTTTGTTAGTTTTCATGATAGTAATAGTAAGAAA[C/T]GAGTCAGGCAATTTATCTCCTCGTCTGTAAAATAA Y 2 1 2 1 101000 r 74 goat snp46872-scaffold654-222045 3 85359533 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784484 Affx-122977464 AX-385271533 3 33089434 AAGAAGCTCACAGTTCTATTAAGGAGATAGGCATG[C/T]AGACTGTAATGCAAGGTTAAAGAGCAAAAACAAAA Y 2 1 2 1 101000 f 74 goat snp46873-scaffold654-255687 3 85325841 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451799 Affx-122921492 AX-123322132 3 33132072 CTGGCAGGCTACAGTCCGTAGGGTCGCAAAGACTG[C/T]GCGACTAAGCACACAGGGCAGCTTGGAAGAGGGAA Y 2 1 2 1 103000 r 74 goat snp46874-scaffold654-298325 3 85282998 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421387 Affx-122944033 AX-123291734 3 33161601 GTTTGCTCTCAGAAGTTAGTAGGTTTGGATGGGAT[A/G]TTGCTTGAAACCAGTTTACTTTGAAGGAAGAGCAT R 2 1 2 1 101000 f 74 goat snp46875-scaffold654-327854 3 85253553 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388677 Affx-122969007 AX-123259035 3 33192392 GACCCTGCTTGGAATTAAGGACAGTCACAAATTTA[C/T]GTTCTGCCTTTCCCCAGTCATGAGCATTTAATGGA Y 2 1 2 1 101000 f 74 goat snp46876-scaffold654-358645 3 85222683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439953 Affx-122929988 AX-123310290 3 33248522 CCCGCTCCCTCTTCTCACATTCGCCTCTCCTTCTC[A/G]TTTCTCTGCTTTGCCTTCACCCTTTCTCTGCTTTT R 2 1 2 1 101000 r 74 goat snp46877-scaffold654-414775 3 85165384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428503 Affx-122938769 AX-123298845 3 33293650 AATAGCCTTCAAAATACTCACAAGAAGGTTTACAG[C/T]AATGAAACAGCAGTTTAAAAAGTCCTGAAATATCT Y 2 1 2 1 101000 f 74 goat snp46878-scaffold654-459903 3 85120156 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791266 Affx-122940159 AX-385278260 3 33348074 ATCAGTTTTAAGTTTTGAGCTTCTGATAACATTTT[A/G]TTGAGCCAAAAGCAGGCACCACAGACCAGAGAGTT R 2 1 2 1 101000 r 74 goat snp46879-scaffold654-514327 3 85065869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377921 Affx-122977228 AX-123248280 3 33388815 CAGTCAATGTACGCTGCAAGGTACATGGGAAGGGG[C/T]AGTGGGAGAATGGACACTTCGACTTGAACCTCGTC Y 2 1 2 1 101000 r 74 goat snp46880-scaffold654-555068 3 85025157 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408612 Affx-122953500 AX-123278963 3 33421585 TGTCTGGTACTCAGGTAACACTGGCTATGAATTAC[A/G]TAAGTCACTGGAGGTATGAACGCAGTGTGAAAACA R 2 1 2 1 101000 f 74 goat snp46881-scaffold654-587838 3 84992393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433594 Affx-122934959 AX-123303935 3 33451459 CTTAACCACTGGACCACCAGGAAATATCACTTCTT[A/C]GAGTTTTGAACCTAAGTCCTGTGTTCTCTTGATTC M 2 1 2 1 201000 r 74 goat snp46882-scaffold654-617712 3 84962474 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387406 Affx-122970411 AX-123257764 3 33492472 TTCTTTCCTGCCTGTGTACCTTGGCTCCTGCTCTT[A/G]CTTCTGGCCCAAATAACCTTACCCCTCTTCTCTGT R 2 1 2 1 101000 r 74 goat snp46883-scaffold654-658725 3 84920760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794916 Affx-122923252 AX-385281876 3 33521333 CTTTTGAGGTAACCTGGACAGTTAGAACTGAATGA[C/T]GGTCATTCATTCTCCTCTATTTAGTGCTACAGTTT Y 2 1 2 1 101000 f 74 goat snp46884-scaffold654-687586 3 84892259 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450058 Affx-122922816 AX-123320393 3 33563672 AAGCTATTTACCTCCTTCCTCCCTCCTCTTTTTCT[A/C]TTTTTGTTGTTGTTCCCAGAAAGACATATTGCGTT M 2 1 2 1 201000 r 74 goat snp46885-scaffold654-729925 3 84849923 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388028 Affx-122969556 AX-123258386 3 33592325 ACCTACATGAGTGATTGTCTGAAATATTATAAAAT[A/G]TACTTGATACAGAATAAGAACTTAGTAATTCTGAT R 2 1 2 1 101000 f 74 goat snp46886-scaffold654-758578 3 84820723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444108 Affx-122926824 AX-123314445 3 33683337 ATGAGAAATAAATGCATTTTTTTAAGGTACTCTGA[C/T]ATTGGGGATTGTTTGTTACTTTAGCAGATTCTAGC Y 2 1 2 1 103000 r 74 goat snp46888-scaffold654-849590 3 84730073 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274689 Affx-1111834366 AX-519548275 3 33701290 GGCTGGGAAACTGAA[A/G]TGGCCCCACATGCTCCTGTGAAGGCAGTGAATGGG R 2 1 2 1 102000 r 74 goat GoatD01.032245 3 33701290 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320768189 Affx-122965559 AX-385255380 3 33739867 TTTCTCTCTCTTCTTGAACAAAATATTTTTAGAAG[C/T]GTTTTCAAAATTGCCAAGCAAAAAGCAAGGAACTG Y 2 1 2 1 201000 f 74 goat snp46889-scaffold654-906120 3 84673014 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782835 Affx-122942701 AX-385269906 3 33776242 AAACACTCAATATTATAAGCTTGTTTCAGAAGATA[C/T]GTGGATATTCTAAATATCTTTAGAATCTAAGAAAC Y 2 1 2 1 201000 r 74 goat snp46890-scaffold654-942495 3 84636519 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771044 Affx-122935781 AX-385258204 3 33820770 TGTATTCAAGTTGTGTTCACCCATTCTGTGGTTTA[C/T]AGTAACCAGTTACATTAGATTTCTTCTTTTTTTTC Y 2 1 2 1 102000 f 74 goat snp46891-scaffold654-987023 3 84591854 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409884 Affx-122952906 AX-123280235 3 33859837 CTGCCTATTTTTCATATAATTTCTGCTTATACATT[A/G]TGGGATTTTGGTACATTTTACATTCTTTGTGCTGC R 2 1 2 1 101000 r 74 goat snp46892-scaffold654-1026090 3 84552819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444972 Affx-122926668 AX-123315309 3 33903498 CAGCTATTCTTGAAACTTGTCTTCTAGGGTCAGGA[G/T]AAGATGTTAGCATAGGAATCTTTCAAGTGGTGAAA K 2 1 2 1 101000 f 74 goat snp46893-scaffold654-1069751 3 84509180 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446270 Affx-122925671 AX-123316606 3 33948157 TGGGCTACAGTCCACAGGGTTGCAAAGAGTAGGAC[A/G]TGACTGAAGCAACATAACACAATAAAACTTTCAGT R 2 1 2 1 103000 f 74 goat snp46894-scaffold654-1114410 3 84464505 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452652 Affx-122920337 AX-123322985 3 33985812 AAAACAACAACAACAAAAAATCTCGAAAAGTTTCT[A/G]CAAACTGTCATGGCATAGCAAACTTTGGTAAGGTG R 2 1 2 1 101000 r 74 goat snp46895-scaffold654-1152065 3 84427455 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277944 Affx-1111836171 AX-519551439 3 34019423 TCTGGCTTTGAGGGCCTGTGGGTCTTAGTTTCAGA[A/G]GACCCACAAGACTGGGAGAAATAGAGACCTCACTC R 2 1 2 1 202000 f 74 goat Random2.2K-311 3 34019423 A G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424857 Affx-122941343 AX-123295203 3 34040199 GATTTTCAAAAATTTTTCTTGTACTTACCAGAACT[C/T]GAGACCAACACAGACATCTACTCACTTAGTAGAAC Y 2 1 2 1 201000 f 74 goat snp46896-scaffold654-1206452 3 84372587 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451903 Affx-122921034 AX-123322236 3 34098168 TAGGTTTAGATTTGGGGCTCTTATAGGGGACATCA[C/T]GGTCTTTGGAGGCATCTGTGATCTGATCCCCAACC Y 2 1 2 1 101000 f 74 goat snp46897-scaffold654-1264421 3 84314585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412128 Affx-122951100 AX-123282478 3 34132776 ATGAATATTTACTAAGAGCCAGTGGGTCAGGCACT[A/G]TTTTAGGTGCTCAGAATACATGGAGGAGTGTGCTA R 2 1 2 1 201000 r 74 goat snp46898-scaffold654-1299029 3 84279599 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453963 Affx-122919462 AX-123324296 3 34167630 ATACAAAAATCACCACCTTTTGTGTTCATTTTCTA[G/T]AAAGGATTTTTTTGTTTTTGACAGAAGTGCCTCTT K 2 1 2 1 303000 f 74 goat snp46899-scaffold654-1333883 3 84244335 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784333 Affx-122965756 AX-385271384 3 34202428 ATATAAATCCGAAGATGTTAGTGAGATTTAGGATA[A/G]TAGGATATATAAGAATTTTGGTTATGGGATAGTGT R 2 1 2 1 201000 f 74 goat snp46900-scaffold654-1368681 3 84208755 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390320 Affx-122967708 AX-123260677 3 34253688 ATGGAATGATAAGCTGTTTGGCATCTTCCCAGTCA[C/T]GCCTTTGCATAAAGAGGGAGATTGGGACTGTCACC Y 2 1 2 1 101000 f 74 goat snp46901-scaffold654-1419941 3 84162741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415361 Affx-122948773 AX-123285710 3 34288551 TGCTGATAAGGCTTGTAGATAGCTATTAAGGATAA[C/T]GTCATTTGGTATAAACATTATTGATTTTAGCTTGG Y 2 1 2 1 101000 f 74 goat snp46902-scaffold654-1454804 3 84127650 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385174 Affx-122971737 AX-123255532 3 34392806 TTCTGTAATGTCCAAATACAGAAAGCCTCACTCAA[G/T]TGTAGATTTTTGTCTTTACAGTCAGCCTTGAAACT K 2 1 2 1 101000 f 74 goat snp46904-scaffold654-1559059 3 84022361 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800031 Affx-122945970 AX-385286954 3 34427081 ATGTCAGTACACAAGCCTGAAGTCTAGGGGAGCAA[C/T]ATATTGCTAGCAAATAAGAAATAACTGTACCTCTC Y 2 1 2 1 101000 f 74 goat snp46905-scaffold654-1593334 3 83987913 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795106 Affx-122927624 AX-385282065 3 34458581 TACTTGTAAGTTTGACATGAATTCCTTACTGTTGC[A/G]TTGTTCTTCCTTGACATCTTTTGTTGTCAATTATA R 2 1 2 1 102000 f 74 goat snp46906-scaffold654-1624834 3 83956545 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421490 Affx-122943913 AX-123291837 3 34503046 TGAATCATGATATTCAACTGAAGAAAATTAAAAGT[A/G]TCATCTTGGCAACCAATAATGAGAAGGTATAATGC R 2 1 2 1 101000 r 74 goat snp46907-scaffold654-1669299 3 83912790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386021 Affx-122971494 AX-123256379 3 34532918 AGATTTATGAGTTTACTTCCTTTTTTTTGCCAAGT[A/G]CCTAATCTTCCTTTGAAAATTGCTTGATTATCCTC R 2 1 2 1 101000 r 74 goat snp46908-scaffold654-1699171 3 83882765 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272199 Affx-1111833384 AX-519545950 3 34538516 TTGCCAAATTCAGAATTAAATTCAAGAAAGTAGGG[A/G]AAACCACTAGACCATTCAGGTATGACCTAAATCAA R 2 1 2 1 303000 f 74 goat 3_34538516_AF-PAKI 3 34538516 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406953 Affx-122955063 AX-123277304 3 34569642 TATAGTGCTGGCTTCTCTATTAGATGCTCAATAAA[C/T]ATGTCTGGAGGAAATTTAATATATTTCCAGACACA Y 2 1 2 1 101000 f 74 goat snp46909-scaffold654-1735895 3 83845924 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396976 Affx-122963161 AX-123267331 3 34605119 CTTTTCATTGCCTTTCAAGGATTTTGTATTTGCAC[A/G]TGGCAACTAGAGAAGAGATGACAGCTTCTAAAGCA R 2 1 2 1 201000 f 74 goat snp46910-scaffold654-1771372 3 83811085 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801887 Affx-122947416 AX-385288794 3 34638803 AACATAGTTGGAGAGATTTCTCTTGGCTCTGTTGT[A/G]GTGGATAGAGAATGTCTTAGGTGATCAGAAGACGT R 2 1 2 1 101000 f 74 goat snp46911-scaffold654-1805056 3 83777169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440814 Affx-122929822 AX-123311151 3 34679195 CTATTAATGTCGCAGTTATTGTTCCTTTATGATAC[A/G]TATTGTAATAAATCTTTTTTTATTATTAATCTATA R 2 1 2 1 101000 f 74 goat snp46912-scaffold654-1845448 3 83736997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785230 Affx-122965008 AX-385272276 3 34731476 CCTTCTTCCCCTTTCTTTAAAATCAAAGGTACTCC[A/G]ATTGTAGACTAAGGAAACTGACTCTCCCAGTGTTG R 2 1 2 1 101000 f 74 goat snp46913-scaffold654-1897729 3 83687752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434355 Affx-122934717 AX-123304696 3 34775568 CTCTTTAATGTCCAGGAAATATTTGATTCCCAGAA[A/G]ACTGCACTGTAGCCCCTGATATAATTTTCTTGTGG R 2 1 2 1 101000 r 74 goat snp46914-scaffold654-1941821 3 83642788 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385652 Affx-122971161 AX-123256010 3 34859131 AAAGACTGCACAAAAAGCTAAAACTGAACCTTATC[A/G]TTTGCTCTCCAGAGATTCTAACACTCCAACTTGAC R 2 1 2 1 101000 r 74 goat snp46915-scaffold654-2025384 3 83559366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407760 Affx-122954976 AX-123278111 3 34905943 GTCTCTGCCAAAATCAACATGAATCAGCCATAGGT[A/C]TACCTATGCTCCCCTCCTTGAACCTCTCCATAAAT M 2 1 2 1 103000 r 74 goat snp46916-scaffold654-2072196 3 83511357 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787839 Affx-122925282 AX-385274862 3 34973592 GACACAAAATTATTCACATTTGTAAACACCATAGA[C/T]GATTTTAGAAGGATTCTAGCTGAGTTAGAGAGTAT Y 2 1 2 1 101000 f 74 goat snp46918-scaffold654-2139845 3 83442371 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435487 Affx-122933438 AX-123305827 3 35025388 TCCAAAATAATTGGGAAAGTTATTCTCTCTTCTTG[A/G]ATGTTGGCTTAGACAGCTGGATACAGTTTTCCTAC R 2 1 2 1 101000 r 74 goat snp46919-scaffold654-2191641 3 83390302 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442906 Affx-122927639 AX-123313243 3 35061779 ATAATTTGATTTGATGTCAAAGTAAAAGCACACTG[C/T]TGACTTATGTGTATGTGTTTTATATAAATAGGAGC Y 2 1 2 1 201000 f 74 goat snp46920-scaffold654-2228032 3 83353816 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416955 Affx-122948022 AX-123287303 3 35097738 TCAAGAAAACTAAAAAAACAAGATAGAAAATGTTG[G/T]GACACAGTAGACCATCAGGCCATTTCAAGATCCAG K 2 1 2 1 101000 r 74 goat snp46921-scaffold654-2263991 3 83317330 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383193 Affx-122972792 AX-123253551 3 35156719 TGATGGAAATAATTGTTTTCTTTTTCCCACAGAAA[C/T]AGACTCATTGAATGCATGCCTTGTTTATTAAAAAG Y 2 1 2 1 101000 r 74 goat snp46922-scaffold654-2322972 3 83257856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442164 Affx-122928311 AX-123312501 3 35186389 GCATCTTTGAACAAAGTCGATTTTGTATTTTTCTT[A/G]CTAATCTTTATACTTTTGATTTCCTTTTCTTGTCT R 2 1 2 1 103000 f 74 goat snp46923-scaffold654-2352642 3 83228108 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769339 Affx-122924037 AX-385256510 3 35221433 AGCTCTTCACATCTACCCTTAGCTCTGCAGAGTTA[G/T]ATATAACTTCACAATTACTTTACTGTCTGGAGACA K 2 1 2 1 101000 f 74 goat snp46924-scaffold654-2387686 3 83193001 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795594 Affx-122975160 AX-385282549 3 35253167 CTCCTCATGGCCAAATTTCTTGCTTAAGCCATTCT[A/G]TATTCCCTTGGCTAGTCATGGTTTCTTACATGGTT R 2 1 2 1 101000 f 74 goat snp46925-scaffold654-2419420 3 83162197 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433924 Affx-122934300 AX-123304265 3 35289018 TAAACATATCTTCCTTTTTAAAAATCAGTAACTGA[C/T]GAGATATATTTAGTGTCAATCATGTTAAACCAAAT Y 2 1 2 1 101000 r 74 goat snp46926-scaffold654-2455271 NW_017199951.1 11865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794669 Affx-122955688 AX-385281630 3 35318224 GTATTGAGATTAATTTTCCTAGAATCTACCATAAT[A/G]CCTAATTCTCAATAAGCAATTTTAGAATGGATGAT R 2 1 2 1 101000 r 74 goat snp46927-scaffold654-2484477 3 83096351 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278100 Affx-1111836172 AX-519551590 3 35322375 TTTATTCAACCCTAAATAATTCAACCTATCTTTTC[A/G]TGGGCCATTTTCTTTGGTCTAATAGGAAATTCAAA R 2 1 2 1 101000 r 74 goat Random2.2K-312 3 35322375 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431634 Affx-122936141 AX-123301975 3 35369406 CTGGGTAGAGAATGAAAAAACACACTTCAGTAACC[A/G]CATTTCTATTGACAGAAGTAATTGGAAGTTTGCAA R 2 1 2 1 101000 r 74 goat snp46928-scaffold654-2535659 3 83044556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803179 Affx-122931305 AX-385290041 3 35400517 CAATAATGTTAATAATCTGAGTCACACATTTATTT[A/G]CTGGTTTAAAGGAAACAAAGTTTTCTGATATATTA R 2 1 2 1 101000 r 74 goat snp46929-scaffold654-2566770 3 83013155 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797585 Affx-122929887 AX-385284524 3 35461132 GCATGACCTTGAAGTACGTTAAGCAACTGCATGTA[C/T]GAAAAGGTGACTTCCAAAATTCATGGCCCTTTCAG Y 2 1 2 1 101000 r 74 goat snp46930-scaffold654-2627385 3 82952150 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441134 Affx-122929582 AX-123311471 3 35511357 TCTGTTGCCTTACTAAACTTCTTTCTGGTTAATCT[A/G]TTGATGTCCGTGGGGTGTTAAAAACTCCTACTATT R 2 1 2 1 101000 f 74 goat snp46931-scaffold654-2677610 3 82901927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451330 Affx-122921273 AX-123321663 3 35527664 AACAGAATTGTTATTCAAATATACCTCAGGCTTAA[C/T]TGCAGATTTACCCTTTGACATAACATATGGATTGA Y 2 1 2 1 101000 r 74 goat snp43590-scaffold582-14146 3 82883735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412080 Affx-122951694 AX-123282430 3 35558017 TTTCCCTTCTCTTTCATTGAGTTTCTATTTTTTCT[A/G]TCTTTTCAATGCCAATCCAAAATATATAATCAACT R 2 1 2 1 201000 r 74 goat snp43591-scaffold582-44499 3 82853631 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803494 Affx-122943928 AX-385290315 3 35607221 TAGTTTTCCAGATTCATGCATACTTGTTTTCCAAT[C/T]CTGACTCAGTGTGTTTTTACTTCAGTTCTGTATGG Y 2 1 2 1 101000 r 74 goat snp43592-scaffold582-93703 3 82803560 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381786 Affx-122974293 AX-123252144 3 35639323 CAAAAATAAAATTTTTACATTTGCAAGAATGAATA[G/T]AACAGAAAAGAAACAGACTTTGAGGTGAATGACTT K 2 1 2 1 202000 f 74 goat snp43593-scaffold582-125805 3 82771183 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409223 Affx-122953158 AX-123279574 3 35674225 CTTTGACATATGATTTTTAGAATTAAAAAACAAAC[A/G]TGATCCAACACATTGCCATTGGGATTCTGTTGCTT R 2 1 2 1 101000 r 74 goat snp43594-scaffold582-160707 3 82735707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394744 Affx-122964858 AX-123265099 3 35719873 ATTCTTCTGATCTATGTGGTTGTTGGCTGGGATAA[C/T]AGAGCAACAGCAGTCTTAGATTCAACTGTGGGTTC Y 2 1 2 1 101000 f 74 goat snp43595-scaffold582-206355 3 82689652 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775374 Affx-122960351 AX-385262505 3 35752482 TAAGGACACCTAAATTCACTGTTTCTCCAGACTAA[C/T]GGCAATAACTTCGGTCTGTCACTTTACTCTCTGTC Y 2 1 2 1 201000 f 74 goat snp43596-scaffold582-238964 3 82656523 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783475 Affx-122930186 AX-385270538 3 35803400 TGAAGAGATCTAAATAAAAGACCCATCTTTATGAA[C/T]GCTTCACCAAACTTTTACTAAACTCTTCTTTCTTA Y 2 1 2 1 101000 r 74 goat snp43597-scaffold582-289882 3 82605682 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432882 Affx-122935342 AX-123303223 3 35838212 TAAAAGACTGGTTGTTCAACTCATAGTTACTATTA[C/T]AAGTGTGTATTTTATGCCTTTGGTCCTAACAGAAA Y 2 1 2 1 101000 r 74 goat snp43598-scaffold582-324694 3 82570793 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395553 Affx-122964247 AX-123265908 3 35895281 ACTTACTTATAGATCTATGTAAAATAATAAATAGC[G/T]AATTTTAAAGACATTAATATGTAGTGTGTTTGTTA K 2 1 2 1 101000 f 74 goat snp43599-scaffold582-381763 3 82516140 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275542 Affx-1111834961 AX-519549113 3 35914102 GTTCCATCAGGTCTCAATCTGCAGTTTTCCAGACA[A/C]CCTCAGACATGTCTAG M 2 1 2 1 101000 f 74 goat GoatD01.060076 3 35914102 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38424358 Affx-122941853 AX-123294704 3 35952253 AAATGATAAATCAAGTTTCTATACTTTCTCACATC[A/G]TTTAATTTTAAAACACAGAATTGAAATGTATTTTT R 2 1 2 1 303000 r 74 goat snp43600-scaffold582-438735 3 82457915 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764424 Affx-986696818 AX-385252122 3 35969269 CTTAAAAATGGTATTTCCTATTCAGAAATTAATCA[A/C]ATTAAATTTGGAAGGAATTTGATCCTAAAGATGGT M 2 1 2 1 600010 r 74 goat 3_35969269 3 35969269 Ancestral_priority_1043 ancestry 0.716 recommended IMAGE 10K 10K ancestral 468277947 Affx-1111836173 AX-519551442 3 36011916 CGCTTGCTTTCATCAGAAGATGTTCACAAAATCAC[A/G]GCAGTTAAGGCAGAAACTTTGGCATCAGAACATTC R 2 1 2 1 101000 f 74 goat Random2.2K-314 3 36011916 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424676 Affx-122941713 AX-123295022 3 36030712 CAGCCAGCGACCCTCAGCACTCTTTGGCTTTTAGA[C/T]GTATCAGTCCAGCTGGGGCCTCCATCTTCATACAG Y 2 1 2 1 101000 f 74 goat snp43602-scaffold582-517194 3 82381273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795430 Affx-122932677 AX-385282386 3 36059562 TTATGTCCTGCTTCCTTCAGTAGTATATGAAGGCA[C/T]GTAGTGATATTCTTCACTATTTTATCTTAAATTAT Y 2 1 2 1 101000 f 74 goat snp43603-scaffold582-546044 3 82352402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798598 Affx-122920130 AX-385285531 3 36098469 ATTTATGCAAGATGATATTATATAGTGAAATAAAA[C/T]ACAGCCTTGTTGTGTCATGGCTTGCCATTTAACAT Y 2 1 2 1 101000 r 74 goat snp43604-scaffold582-584951 3 82313126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772215 Affx-122966462 AX-385259370 3 36145082 GTTCACTGACAAACATTTGACACCTTATCCACTTC[A/G]TGACTGTTCCATGATTGCTTCAATACTATCATACA R 2 1 2 1 101000 f 74 goat snp43605-scaffold582-631564 3 82268189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381397 Affx-122974377 AX-123251755 3 36194076 TACACCGCTCTGTGAACAATTATGAAAACAGAAAA[C/T]AAAATCTTGAGTAGTAGTACCACTTTGGAGAATAC Y 2 1 2 1 202000 r 74 goat snp43606-scaffold582-680558 3 82218791 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793435 Affx-122951073 AX-385280412 3 36270427 TTTGAAATATCATTATTATAGAACTTGAAGTAGTC[A/G]TTTTCACACTTCAATTTTGTTGCTGAGCCAGAGAG R 2 1 2 1 202000 f 74 goat snp43607-scaffold582-756909 3 82142073 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385269 Affx-122972075 AX-123255627 3 36300937 CATGCTACATTTTGGAACTATCAGTCTCTCTCAAA[A/G]GAAATTATAAATCAAATATGCTAATATGTAAAGTC R 2 1 2 1 101000 f 74 goat snp43608-scaffold582-787419 3 82111640 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426266 Affx-122940323 AX-123296612 3 36349407 GTGCCCTGATAAATACTTATACCTAGCTGGCTACT[A/C]TCTAATATGCCCACACAGTTTTGGTCCTGTCCCAC M 2 1 2 1 101000 f 74 goat snp43609-scaffold582-835889 3 82063158 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428824 Affx-122938378 AX-123299166 3 36394559 CCAAAACACCTCTTCTGTCTTTAAAAAACTAAACA[C/T]AGAACTGGCATATGATACGGCAATTCCACTCCTGT Y 2 1 2 1 101000 r 74 goat snp43610-scaffold582-881041 3 82018719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766073 Affx-122962020 AX-385253489 3 36450778 ACCAATTGGAAACACAAAAATCTAAAAGGTTAATA[C/T]TCCAATGGAATACATCAAGAAGTGAACCTTGTGAA Y 2 1 2 1 201000 f 74 goat snp43611-scaffold582-937260 3 81962222 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795672 Affx-122951879 AX-385282627 3 36488368 ATGTTTAGTCAATACATTTCTCTCAGGGATAATTT[A/G]TTCTTTGTTAAATGAAGAACAGTGAAGGCAAGGGT R 2 1 2 1 201000 r 74 goat snp43612-scaffold582-974850 3 81924701 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775526 Affx-122942944 AX-385262657 3 36517197 TTGATGTTTGCAACAGTCCTGAATTCAGATTAAGA[C/T]GAGAGATGTTTGCCTGACAAGGAAACAAGACTAAG Y 2 1 2 1 101000 r 74 goat snp43613-scaffold582-1003679 3 81895836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402645 Affx-122958386 AX-123272998 3 36606841 CCCTAATTTGGATAAGTAATACCTCTAATCCCTCA[A/G]TTATGTCAGTTACAAGTTATATCAAGGAAGCATAA R 2 1 2 1 101000 f 74 goat snp43615-scaffold582-1093323 3 81806198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778472 Affx-122962590 AX-385265586 3 36646518 GTACTTTGTAAGCGTAAGTAACTATTGAAAAGGGA[A/C]TCATTGAATGAATAATCCATCCATGTGTTTTTATG M 2 1 2 1 202000 r 74 goat snp43616-scaffold582-1133000 3 81766469 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771544 Affx-122951178 AX-385258702 3 36716489 GAAAGTAAATATGTGACTTTCTTATAAGAAGTACC[A/G]TTATAAGAAATTGTATAGAAAGAATCTCTCAAGGT R 2 1 2 1 101000 f 74 goat snp43618-scaffold582-1202971 3 81694860 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774801 Affx-122920003 AX-385261935 3 36766020 GTACATTTTTAGGTTGGATCTTCTTTTCCATGTGT[A/G]CATTTGCTTTGTTGTTTCTAATTGTTCATGGTATT R 2 1 2 1 101000 r 74 goat snp43619-scaffold582-1252502 3 81644702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802208 Affx-122977328 AX-385289112 3 36824846 GAATGATCCTTGGCTAGATGCTTATGTCAGGACAA[C/T]AAACTTGAAATATCATGCAGCACTTGCAGTTCAGA Y 2 1 2 1 101000 f 74 goat snp43620-scaffold582-1311328 3 81584393 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440709 Affx-122929900 AX-123311046 3 36909248 CAAATGCCAGATAAATCTACCCCACAAACCAGTTG[C/T]TATAATCATTGCCCTGACCCAAGACCTAAGATGAA Y 2 1 2 1 201000 r 74 goat snp43621-scaffold582-1395730 3 81498859 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437713 Affx-122931747 AX-123308051 3 36917405 TTTTAAACTCAAGCTCTAACAGACTGTAGGTGTCC[A/G]TTTTATTCTTTTCATTAGAAGTAGTTCCTCTGCTT R 2 1 2 1 103000 f 74 goat snp21571-scaffold2102-137705 3 81490846 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772232 Affx-122959340 AX-385259387 3 37014595 ACATTTTACTCCTTTCATTTTTGCTGCCATGCACT[A/C]GAATCAAACTCAGTGAATTAATTTTTTCCTATCCA M 2 1 2 1 101000 f 74 goat snp21569-scaffold2102-40515 3 81392350 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384679 Affx-122972128 AX-123255037 3 37071006 CTCTGTGGAAGTCAGGTCCTGGGGTTCTCCTCTCT[A/G]TTTCTGGGATTTTTAAAAAATGAGGTTTGCAGGTG R 2 1 2 1 201000 f 74 goat snp22465-scaffold222-1353540 3 81342067 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272032 Affx-1111833385 AX-519545797 3 37106836 TAAACAATCAGATTATGAGAAGCATTTCTTAATCT[A/G]TTTTTCTTACATTGTAATCAACTTTTAATTCTGTT R 2 1 2 1 101000 r 74 goat 3_37106836_AF-PAKI 3 37106836 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38424128 Affx-122942012 AX-123294474 3 37231756 TTGGTTGTCGACATGAGAATTGCTAAGACGTAGAC[A/G]TCAATTTCTCAGGGAGGAAAAATACAGAAATATGC R 2 1 2 1 101000 f 74 goat snp22461-scaffold222-1192790 3 81178869 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777547 Affx-122965338 AX-385264666 3 37322030 CAAAGCAGAAAGAGACAGGCTATAAGTTGGGAGCC[A/G]CTTTGCCAGTTTTTCTGAGTAAGGAAACTCTATGC R 2 1 2 1 101000 r 74 goat snp22459-scaffold222-1102516 3 81088564 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386933 Affx-122969996 AX-123257291 3 37407941 ATTTCTTTGTTTAAGGCTCGCACTCTTCTAAAGAG[C/T]ATTTAGATGTGCACTGCAACAGTTACTTCACCTTT Y 2 1 2 1 101000 r 74 goat snp22457-scaffold222-1016605 3 81001841 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388965 Affx-122968800 AX-123259323 3 37447199 AGGTAAAGCAGTGCTTGAAAATTGCTTTCTTAAAA[C/T]GTTGATTTTATGGATTTTAAAATTTTCCTTCTAAA Y 2 1 2 1 103000 f 74 goat snp22456-scaffold222-977347 3 80962409 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791574 Affx-122923292 AX-385278565 3 37492889 ACGTTAACATTGTCACTCTTCCTGATGCTTTTTTA[C/T]AATCTTTTGCCATCATATTCATATAAATTATGTGT Y 2 1 2 1 101000 f 74 goat snp22455-scaffold222-931657 3 80916281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768740 Affx-122956626 AX-385255918 3 37525247 GTGATGCTAGCTTTTGCTTTGCTGTTCAGAATCAC[A/G]TTTTACAAGCCCATCCATTAAGAGATTCTTCCTAA R 2 1 2 1 101000 f 74 goat snp22454-scaffold222-899299 3 80883442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768292 Affx-122952204 AX-385255472 3 37572717 ACTTGCTGAGGGGCATTTACTTGGTAAAGTCATCA[G/T]ATTTTAGATCTGACTTTAGTCTTCGACAAACATTG K 2 1 2 1 201000 r 74 goat snp22453-scaffold222-851829 3 80835937 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376474 Affx-122978040 AX-123246833 3 37601963 CGTTTTATTGCTGTGAAATCCTGTGAAAGAGAAAA[C/T]AAGTCTGGAAGAATATTCAGGTACAACACTGTCAC Y 2 1 2 1 201000 f 74 goat snp22452-scaffold222-822583 3 80806355 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774821 Affx-122921617 AX-385261955 3 37730445 ATAATATCCATATGAGAAGTAGGATTTTTGAAGTA[G/T]TAAATGTAAGTTACTTTGTTCAGTGCCTCTAGTGT K 2 1 2 1 201000 f 74 goat snp22450-scaffold222-694101 3 80675857 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416745 Affx-122948196 AX-123287093 3 37831940 CCCCTTCTCTCTCTCTCTCTCTTATAAGGAGCTTG[C/T]GGAGATTAAATGAGATGCTATACAGGAAGGCCCTG Y 2 1 2 1 101000 r 74 goat snp22448-scaffold222-592606 3 80571972 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431424 Affx-122936521 AX-123301765 3 37898920 GCACTAAATAGGGGAAAGAAACTTTTATGTATTAA[C/T]AAAAATTAGTTCTATATCAAAGCTTTAAAAATCTT Y 2 1 2 1 202000 r 74 goat snp22447-scaffold222-525626 3 80506857 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768819 Affx-122933374 AX-385255996 3 37930325 CTAGGCTTCAATCTTTTATGTATAATATGACAATT[A/G]TGTCTTACAAAAGGCAAATATGAGGGGTAACTATT R 2 1 2 1 202000 r 74 goat snp22446-scaffold222-494221 3 80476865 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420789 Affx-122944694 AX-123291136 3 37959263 CCGAAATATTTTAAAAACGAAATAGATGACTGAAA[C/T]GCCTAAATAATTGACTCAAAGGTTACTTTCTTTAA Y 2 1 2 1 101000 f 74 goat snp22445-scaffold222-465283 3 80447899 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429630 Affx-122937689 AX-123299971 3 38031438 ATTCTGCTTTAGGTGATATTAAGGCTGATGGCCCA[C/T]GGTCCACATTTTGAGTAGCAAAGATTCTAGAAAGT Y 2 1 2 1 201000 f 74 goat snp22443-scaffold222-393108 3 80375226 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793048 Affx-122962650 AX-385280026 3 38109840 CTTCAATAATCTCATGCTCTCTGAGCTACAAATTG[C/T]TGCATTAATTTAATAGGTTTGTCACATTCTTTTTA Y 2 1 2 1 101000 f 74 goat snp22441-scaffold222-314706 3 80296779 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419706 Affx-122945916 AX-123290054 3 38144920 TAGGGAATGTATTTGTTCAACTTGGGCTTCCTCGG[C/T]GACTCAGCAGTGAAGAATCTGCCTGCAATGCAGGA Y 2 1 2 1 101000 f 74 goat snp22440-scaffold222-279626 3 80261738 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397210 Affx-122962391 AX-123267565 3 38209784 GCTTTCAAGGACAGGAAAAAAAAATTCACCAAGTA[C/T]TTTTCAAACCATTATGAAAAATCCCCCCATAATTG Y 2 1 2 1 303000 r 74 goat snp22439-scaffold222-214762 3 80197099 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390442 Affx-122967627 AX-123260799 3 38257075 AATCACTACATTCAGCAGTACAATAAAGGCAGCTA[C/T]AGTCTACTTAAAATTCTCAACTCCATTCATTGAGA Y 2 1 2 1 101000 f 74 goat snp22438-scaffold222-167471 3 80150162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801717 Affx-122949339 AX-385288625 3 38293519 AGGGCCCTGTAAAAGACCCAATGCAATTTAAATAC[A/G]TAATGCACTGAAAGTGCCCCTCACTCACATACTAC R 2 1 2 1 101000 r 74 goat snp22437-scaffold222-131027 3 80113827 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436538 Affx-122932927 AX-123306876 3 38353202 TAAATTTAGATTCTTCATTTTACAACCCTGCAAGA[C/T]GGTAAATGCCTTTCCTATTATGGATATCTTAGCCC Y 2 1 2 1 101000 r 74 goat snp22435-scaffold222-71344 3 80053840 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772763 Affx-122922511 AX-385259908 3 38384297 TTATTTTTAAGAAAGACTAGAGTGAAAATGGATAA[C/T]GTAATTTTTCTAAGAGGATAGGCAGTTTTCCTAAA Y 2 1 2 1 101000 r 74 goat snp22434-scaffold222-40249 3 80024879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378520 Affx-122976636 AX-123248879 3 38416038 AAAAATAAAAATCTGTGTATTTGTGTAGCTTTGTA[C/T]GAATACTATTATAGGGAGAAATGCCATTATAAGGC Y 2 1 2 1 101000 r 74 goat snp22433-scaffold222-8508 3 79993119 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425716 Affx-122940765 AX-123296062 3 38447841 GTGTTGCAAGTCTACTTAGACATAAATCATCTTTG[C/T]GTTTGTGTGTGAGAGAGAGACAGAGAGAGAGCAAG Y 2 1 2 1 202000 f 74 goat snp21085-scaffold2063-155139 3 79959916 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439010 Affx-122930359 AX-123309347 3 38531229 CTTGGATCCCTCCTCAGCCTATGTGCTTGGTGATT[A/G]TAAACAAGCATTACAGTTCTTGGGAAAAGCAGAAT R 2 1 2 1 101000 r 74 goat snp21083-scaffold2063-71751 3 79875903 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444364 Affx-122926706 AX-123314701 3 38587080 ACGGCTAGCCTTCTCCTATTCTCTTTGGATCAGGG[A/G]CTGCTTCTCCTGAAGGTGGCTAGGTTTCGACCTAT R 2 1 2 1 101000 f 74 goat snp21082-scaffold2063-15900 3 79819376 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771780 Affx-122921957 AX-385258937 3 38603587 CAAAATATTCAATTGTGCTAACTGAGGTGATTCAT[A/G]TAGCACTATATTTTTTCTTATGAGTCTTAAAAATT R 2 1 2 1 201000 r 74 goat snp6600-scaffold1236-508 3 79803271 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380941 Affx-122975006 AX-123251299 3 38634418 TGCTTTCCATAACACTTCAGATGAAGACTTGTAGG[C/T]GGATTAATTGTAAAAAGTTGTTTCTTTTGGTTTAT Y 2 1 2 1 101000 f 74 goat snp6601-scaffold1236-31339 3 79769740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773105 Affx-122978384 AX-385260248 3 38758113 TCAGCATCAGAGAAAATGTAGGAATAAGTATGCCA[A/G]TTCAGCAGCCAACCTCTCTTTTGTTAATGTGAAAG R 2 1 2 1 201000 f 74 goat snp6604-scaffold1236-155034 3 79644136 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405809 Affx-122955895 AX-123276161 3 38792547 TGTGACTCCACTCCAAGTATATACTCTAGACACAC[A/G]CATGCTCAATTACACAGATGTTGCTCACATTGAGA R 2 1 2 1 101000 f 74 goat snp6605-scaffold1236-189468 3 79612716 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386919 Affx-122970008 AX-123257277 3 38821456 GCACATTTTTTAAAATCTATTTGACAATTAGCCTG[C/T]ATTATTTCAAACTATCTACATTTTTATTGCATTAT Y 2 1 2 1 303000 r 74 goat snp6606-scaffold1236-218377 3 79584165 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445411 Affx-122925379 AX-123315748 3 38852602 TTTTAACCCACTTAACAAATAATCTTGAAACAATT[A/G]TAGATTCACAGGAAGTTGCAAAGATAGTATAGTGA R 2 1 2 1 303000 f 74 goat snp6607-scaffold1236-249523 3 79552698 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785188 Affx-122952237 AX-385272235 3 38910979 TTGAGAATTATTACCTAAATAAACCTTATTAACAT[A/G]AGATTTACCTGCACCTTTTTTATACCCCTTCAACC R 2 1 2 1 201000 f 74 goat snp6608-scaffold1236-307900 3 79496338 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442484 Affx-122927928 AX-123312821 3 38956482 GTACTTCTGCCACTACTTTGTGCTTAGTTGCTCAG[C/T]AGTGTCCAACTCTTTGTGACTTATATATATATATT Y 2 1 2 1 103000 f 74 goat snp6609-scaffold1236-353403 3 79450839 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396810 Affx-122963287 AX-123267165 3 39011834 TCCAGTAGAATACAGCTGTGTCCTGTCACTCATCC[A/G]TGATTAAACATGTAGTGGTGGTACACATTCTCAGG R 2 1 2 1 101000 r 74 goat snp6610-scaffold1236-408755 3 79396945 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769213 Affx-122920343 AX-385256388 3 39062185 GGTGTAAGGAAAGGTCTGCTACAGCTGCTGTTGCA[A/G]TTACTGACGCGACTGCGAGAATAGAAGCAATGACA R 2 1 2 1 102000 f 74 goat snp6611-scaffold1236-459106 3 79346608 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785818 Affx-122968237 AX-385272856 3 39094937 TTACAGTTACCTGAGGAATCATACTAGAACAAGGA[C/T]GATTATAGCCCTTGGTTGAGATCATGTTTAATTTC Y 2 1 2 1 101000 r 74 goat snp6612-scaffold1236-491858 3 79314238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796685 Affx-122947400 AX-385283630 3 39141947 TATATGTAATATGATATGTTGTTTGATAAATGTTT[A/G]CTCATGCTAATGGAAGACCCTAGATTGTATAGTAC R 2 1 2 1 101000 r 74 goat snp6613-scaffold1236-538868 3 79267264 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396175 Affx-122963773 AX-123266530 3 39193860 ATAGCGGGTCAGAGTTCCTTAAGTGGAATTTAACC[A/G]TAAAAAGGGTAATTTGAATTTATCTAATTATATAC R 2 1 2 1 101000 f 74 goat snp6614-scaffold1236-590781 3 79215406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788746 Affx-122972345 AX-385275762 3 39253735 AATTTTTAAGATATTTGAAAAAAACATGGATTCTC[A/G]TGAATATGAACATCCTCCAGTCTTTGACCATTTCT R 2 1 2 1 202000 f 74 goat snp6615-scaffold1236-650656 3 79155971 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409586 Affx-122953571 AX-123279937 3 39306859 TGCTTGCATTTACTTTTTGTTGTTCTTTTCTTTTT[A/G]CTTTTACTGCATTTGTTCTCAGGGACTGTCAAAGT R 2 1 2 1 103000 r 74 goat snp6616-scaffold1236-703780 3 79101788 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390857 Affx-122967822 AX-123261214 3 39382198 AAATATACACTGAATTTATTCTTATCTGATCTATT[A/G]GCTAGGTTGCTTATTTTTCATTTATTTTCTCACTC R 2 1 2 1 201000 f 74 goat snp6618-scaffold1236-779119 3 79026201 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779737 Affx-122971609 AX-385266837 3 39421778 AAGAGGAACAGCTTAATTTGCCAAAGTCATTAGAG[A/G]TTAAACTTTATCTGGTCCTTAAGTTGTAACCATAG R 2 1 2 1 101000 f 74 goat snp6619-scaffold1236-818699 3 78986488 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777633 Affx-122927791 AX-385264752 3 39469402 AATGTTGGTGCTATGACAAAGATGTACAAGGTACT[A/G]TAAGTATTTTTAATAGGAATTAAAGGATGTCAGGG R 2 1 2 1 101000 f 74 goat snp6620-scaffold1236-866323 3 78937099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785681 Affx-122951092 AX-385272722 3 39481925 TGACTATTAAATGAGTATTAATCTTTCCTTCTCAA[C/T]AGCTGTTTAATCAAGATTTTTCTCTAGGTGGGAGA Y 2 1 2 1 101000 r 74 goat snp56242-scaffold879-1912984 3 78923218 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800270 Affx-122930649 AX-385287193 3 39510953 ATATCCTAGCATCTGATCAGGAACACAAAACACTG[A/G]CTAGTTGAATGCCCACTCTCCTAAACACAGTGCTA R 2 1 2 1 101000 f 74 goat snp56241-scaffold879-1883956 3 78893608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449311 Affx-122923002 AX-123319646 3 39547483 ATAAAAAATTAATTTTAAAAGATTTAAAAGATTAA[G/T]AAAACCTGACATTAGGTCACATGTAACAGTGTGAG K 2 1 2 1 103000 r 74 goat snp56240-scaffold879-1847426 3 78856396 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767836 Affx-122936366 AX-385255056 3 39588658 GCTTTGGGGATTTGGATGAAGAAGAACCTCTCCTA[C/T]ATCAGAGTCCTGTGCCTAGTTACTACCAGAAAAAT Y 2 1 2 1 201000 f 74 goat snp56239-scaffold879-1806251 3 78815388 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412372 Affx-122950814 AX-123282721 3 39618985 TTAGTGAGCATCTGAAACATAGCATCATCATTTAC[C/T]TGGAAGGGGAAAATAGGCCTGTTTTAAATGTAAAT Y 2 1 2 1 201000 f 74 goat snp56238-scaffold879-1775924 3 78784766 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785432 Affx-122937485 AX-385272477 3 39670240 AAGCTTCCTCTGACCTCTGCAGACTTTGTTTAGTG[A/C]CCTTCATCAGTATCCCTTTGATCCTCTGTGCTCTG M 2 1 2 1 101000 f 74 goat snp56237-scaffold879-1724669 3 78733141 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423721 Affx-122942875 AX-123294067 3 39727019 CAATAGTGTTCCTCACCTCTCAAGGTTTCACAGAA[A/G]AGGTGCTGGAAGAGGTGGTGGTAACCATAAAGGTG R 2 1 2 1 101000 f 74 goat snp56236-scaffold879-1667890 3 78676301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377534 Affx-122977466 AX-123247893 3 39756393 CAATGGCATGTTTTCTTGCGGCTAGACTGTGACTG[A/C]ATCCTGTCATTTCATATTTGCAGGCTGCTCCATCT M 2 1 2 1 201000 r 74 goat snp56235-scaffold879-1638516 3 78645053 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416532 Affx-122947760 AX-123286880 3 39790183 TGTTGTCTTCTGAGCATGTACAAAGAAAAATGACC[A/G]TATGGGCTATATTTCTGGCTAGTCTCTTTTAATTC R 2 1 2 1 101000 f 74 goat snp56234-scaffold879-1604726 3 78611056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385183 Affx-122971730 AX-123255541 3 39834683 ACAGGGTCTGTTAAAGGCAAAAAGAGCAAAGCAGG[C/T]GGAGATCAGAGAAGAATTTTACAGGTGTGAGTTTT Y 2 1 2 1 101000 f 74 goat snp56233-scaffold879-1560226 3 78566522 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272035 Affx-1111833386 AX-519545800 3 39849930 AGAAATTCTCTTTACCACTATGTAGAAGAGATCCA[A/G]TGGTACAGTGGCCTATCACCGTCATCAATTTTTTT R 2 1 2 1 101000 r 74 goat 3_39849930_AF-PAKI 3 39849930 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438343 Affx-122931335 AX-123308681 3 39882101 CCTTTTGGTTGTTAAAAACCCTTCCTTTTTCTTGA[C/T]GGGTCTTCTGTACTATTATCACTCTTTGTCTTTTT Y 2 1 2 1 101000 r 74 goat snp56232-scaffold879-1512808 3 78519545 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434312 Affx-122934752 AX-123304653 3 39917972 GAGAAGAGGTGTGTTCAGTGGGGATCTGCTTCTGG[C/T]GGTCTCACCAATGCTCCATTTTACTTGCTTTGAGA Y 2 1 2 1 101000 r 74 goat snp56231-scaffold879-1476937 3 78483085 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398753 Affx-122961450 AX-123269108 3 39951875 ACAAAATCAGATTTGAAAATGAATAGAATAAAAGA[C/T]GTCACAACAAACTGCTAATTTTAAAAAGCCAGCAG Y 2 1 2 1 201000 f 74 goat snp56230-scaffold879-1443034 3 78448708 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414437 Affx-122949955 AX-123284786 3 40016315 AGAAAGACTGCCTTGAAAAATAGTGCAAATAATTC[A/G]TGCAAGTTAAGCTTGGAAAAGCAGAATCTTAAAAA R 2 1 2 1 101000 f 74 goat snp56229-scaffold879-1378594 3 78382963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407145 Affx-122954855 AX-123277496 3 40053449 TTTTCCACTACAGAAATCAAAGCAAAAAAGTTTTC[A/G]TTTTCTCATTAAACTAGAAAACTCATTCAGTCAGA R 2 1 2 1 303000 r 74 goat snp56228-scaffold879-1341460 3 78344760 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788651 Affx-122972549 AX-385275667 3 40100659 ATTCCTCAGTTGTGATCAGAAGATGAGAATAATTA[C/T]GTCCAGCTATAGGCTTGTTTTGTGGGTTAAAGAAA Y 2 1 2 1 101000 r 74 goat snp56227-scaffold879-1294250 3 78296821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386666 Affx-122970196 AX-123257024 3 40141457 TAAGTAGTTTGAGTTGTGATTTAAGTTTTCTCTTT[G/T]TAGTGGCATCCCTACCATTGTTTTTTCTTTCCTGC K 2 1 2 1 101000 r 74 goat snp56226-scaffold879-1253452 3 78255635 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376213 Affx-122978806 AX-123246572 3 40187382 TAAAGAACAAGGAAGTAAATATTTTAGGTTCTGAA[C/T]GCCACAAGGTCTCTGCCAAAACTACTTATTGCTGC Y 2 1 2 1 101000 r 74 goat snp56225-scaffold879-1207527 3 78211486 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275273 Affx-1111834694 AX-519548849 3 40194763 AACTCA[A/G]TTTAGATATCTGAGCTTCAAATACTGCAGGACATA R 2 1 2 1 101000 r 74 goat GoatD01.046382 3 40194763 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802225 Affx-122940554 AX-385289129 3 40274913 CCCTACTTTTTATTAGAAGCAAAGAATTAGAAACC[A/G]TGTTACTTACAAAAGGATTTGCTAGCCAATCTTTA R 2 1 2 1 201000 f 74 goat snp56224-scaffold879-1119996 3 78124736 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396762 Affx-122962775 AX-123267117 3 40309644 AGACTGAATTATTTTTAGAACTTAAAATTTTCTAT[A/G]CTGTGTTCTAAAAAGTATATGCAGGTGACTAGGCA R 2 1 2 1 101000 r 74 goat snp56223-scaffold879-1085265 3 78090704 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774865 Affx-122922381 AX-385261999 3 40371352 ACAAAGACAGCAGACATGCTGAACAGCATCAAATC[A/G]TGTGCAAGGAAGGCCACAGAGTTATACAGAGAGAA R 2 1 2 1 102000 r 74 goat snp56222-scaffold879-1023557 3 78028731 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787772 Affx-122922833 AX-385274795 3 40428048 TTAGCTGCATGGGTTTGGGTTCTGCTTCCTCTTCA[C/T]GGGTTTGGGTCGGTTGTTGATTAAATTGGAATGTT Y 2 1 2 1 201000 f 74 goat snp56221-scaffold879-966861 3 77972270 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427971 Affx-122939188 AX-123298314 3 40469474 GTATCTTTCACTATATGAGACCTTACTCAAATTTG[C/T]AATCTACAGCCACAGATCTCTCATGATCTTGGATG Y 2 1 2 1 101000 r 74 goat snp56220-scaffold879-925435 3 77930440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382578 Affx-122973756 AX-123252936 3 40502514 ATATAACACAGTGCAGCAAGTATATTCCTTCCTCC[A/G]CACATCAGTCATTCAACTATCCATGGCCTTCGTGT R 2 1 2 1 201000 r 74 goat snp56219-scaffold879-892395 3 77896836 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779080 Affx-122977601 AX-385266185 3 40590549 TAATAATAATATTGATATTAACTTGCTCAGTGTCA[C/T]GTAAGTGGTCGAGATTTGAACTCAGGAATTCCTGA Y 2 1 2 1 101000 r 74 goat snp56217-scaffold879-804360 3 77808526 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782960 Affx-122971834 AX-385270029 3 40619440 TAGCACCCCCTCTTCACTCACTGAGTTTTGGACCA[C/T]GTAATACATAAGAACATGTATGTAAATGGTGACCC Y 2 1 2 1 303000 f 74 goat snp56216-scaffold879-775469 3 77779666 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796142 Affx-122953993 AX-385283093 3 40655248 AGAAAGTAGAAAATAATTGCATTAAGTTATTTTGA[G/T]CTGGGTTGAAATGTTAATTTATTCCCACCCAGTTC K 2 1 2 1 201000 r 74 goat snp56215-scaffold879-739661 3 77743009 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380610 Affx-122975246 AX-123250968 3 40687427 AGGCTTCTCACCATCACCAGCAACCATGTGGCTTT[A/G]TTTCAGGGGATTTGTTGCTCCTAGAGCAGCTGAGA R 2 1 2 1 101000 f 74 goat snp56214-scaffold879-707482 3 77711066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380616 Affx-122975243 AX-123250974 3 40735904 GTGTGTATGTGTGTGCACATGTGCACACTCGTATG[C/T]GCAGGCACACACATTTAATTAGAAAAACCAGTTTG Y 2 1 2 1 303000 r 74 goat snp56213-scaffold879-659005 3 77662044 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773920 Affx-122972297 AX-385261059 3 40785725 ACTGACTTTCTTTTATGGTGTGTTCAAAGACTATA[C/T]GAGACAACATACATTCCTTCTGCTCTCATTCAATT Y 2 1 2 1 101000 r 74 goat snp56212-scaffold879-609184 3 77612335 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377017 Affx-122977720 AX-123247376 3 40814459 ATTGCTGGTTTTGTGTGTGTGTGAGTACTCATTCT[A/G]TTCCCAATGGCCTTTGTTTTAATTTTGTGAATTAA R 2 1 2 1 303000 r 74 goat snp56211-scaffold879-580450 3 77583562 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406171 Affx-122956160 AX-123276523 3 40853028 AGAGAGCAGGAAAGTTCAACGTAAAGCAGAGGAAA[C/T]GAGTTTGTTCAAATAAGGCCAAGTTTCATGCATTT Y 2 1 2 1 101000 f 74 goat snp56210-scaffold879-541881 3 77545004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380988 Affx-122974677 AX-123251346 3 40893242 CTCTTAGTAATTAATTTTTTTTTAATATTGTGCCT[A/G]TTGTAGGTGTTAATGCAGACAAGGTTGGAATTGAA R 2 1 2 1 101000 r 74 goat snp56209-scaffold879-501667 3 77504423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430468 Affx-122937255 AX-123300809 3 40947572 AGGGTTATTGTGAGGATTAGCTGTAATGTTATGTA[C/T]GGCATCTGGCTCAGAAGTGCTGAAACGATGGAGGC Y 2 1 2 1 101000 f 74 goat snp56208-scaffold879-447337 3 77449737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277949 Affx-1111836174 AX-519551444 3 41030095 CCTGCCACTACTACTGAGAGCACTGGAAACGATGC[A/G]TGTGAAAAGTAGAAGATAGCATTATTTCTGCTCTT R 2 1 2 1 101000 f 74 goat Random2.2K-317 3 41030095 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797203 Affx-122957389 AX-385284142 3 41062043 GATAAAATAAAAATAATCGATCAATACCTTTCACA[C/T]AGCTATTTATCATCAGTCGATAAGATTAAGCCTGT Y 2 1 2 1 101000 r 74 goat snp56206-scaffold879-332866 3 77333772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377411 Affx-122977558 AX-123247770 3 41090637 TTTTTACAATTGGAGTATATACCTCAGGGGATTGC[A/G]TAACACTTTTTAAATGAACTGAGTTCTAAATCGAT R 2 1 2 1 101000 f 74 goat snp56205-scaffold879-304272 3 77305201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783279 Affx-122972961 AX-385270344 3 41131551 TAATTAGGACTGGCTGTGTTACTTTGCTGAGGCAA[A/G]CCTAGTCTCAACAAGACACAGGCCTAATATATTCC R 2 1 2 1 102000 f 74 goat snp56204-scaffold879-263358 3 77264274 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790572 Affx-122963571 AX-385277575 3 41208730 AGTCTGCTACTAGAAACCAGACAGCAAGAAGCCTT[A/G]AAATAAATCGACCCTTCTCTGGTCATTCTAAATAG R 2 1 2 1 101000 f 74 goat snp56203-scaffold879-186179 3 77186614 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775925 Affx-122952520 AX-385263056 3 41290350 TAGTAACTGAAGCCCTTCCTTGTCTACTAGTTCAA[C/T]ATCTGTGTCATTCATGGATTGTGTTTTCCTCCTTC Y 2 1 2 1 101000 f 74 goat snp56201-scaffold879-104559 3 77104449 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796460 Affx-122925610 AX-385283410 3 41322717 TTGAGTAATATTTTAACTGAAAGTCTCTGACTTCA[C/T]TGATTCTGTTATAATGAACTCAACCAGCATAAAAC Y 2 1 2 1 201000 f 74 goat snp56200-scaffold879-72192 3 77071786 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443893 Affx-122927060 AX-123314230 3 41356367 TTGGATCTTGTCATCCCAAGACGACAGACCTCTTC[A/G]TTTAAAAGGTTAAAAGAGAGATTATCCTGATTCTC R 2 1 2 1 201000 r 74 goat snp56199-scaffold879-38542 3 77037688 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407493 Affx-122954754 AX-123277844 3 41415684 CATCCTTGCACAAAGTTCCACGTCATTAAAGTTTT[A/C]GTCTTTATATATTTAATGAATAAATCAGAAATTTT M 2 1 2 1 101000 f 74 goat snp15520-scaffold164-3351664 3 76968822 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405142 Affx-122956957 AX-123275494 3 41465676 TTTTAAGAACAAAATTTTATACTTTAAGAACAAAA[G/T]CAAAAGACAGTTGCCCAATGTAACCAAACACAGTG K 2 1 2 1 101000 r 74 goat snp15519-scaffold164-3301672 3 76919076 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394968 Affx-122964272 AX-123265323 3 41536334 AATTCAAGAATTATTAGAAATAAAATACTAGAACA[C/T]GCCTTGAGAGATTGTCCATCATCATTTTACATCAA Y 2 1 2 1 101000 r 74 goat snp15518-scaffold164-3231014 3 76847834 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394476 Affx-122964567 AX-123264831 3 41619391 TATTTTCATTCTCTGCACATTAAAGAAAGAGCTTA[C/T]GAACCTATGAAACATGCCAATATGTGCATTAAAGT Y 2 1 2 1 101000 r 74 goat snp15516-scaffold164-3147957 3 76764046 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801446 Affx-122943979 AX-385288355 3 41715167 CTACCCCTCTTCCTTATCTTCTGCAAAATGTCTCA[A/G]CAGTCTGTCCAATGGTGATCCCTCTTTACTTTCTT R 2 1 2 1 101000 f 74 goat snp15514-scaffold164-3052181 3 76665007 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432984 Affx-122935265 AX-123303325 3 41750445 GTAAAGAATTGCTTCTTTGCTTAGCTGCCCCCAGC[C/T]GCTTAGAGCTGTTTGGACTTCATCTTCACCACCAC Y 2 1 2 1 201000 r 74 goat snp15513-scaffold164-3016903 3 76629470 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786958 Affx-122967600 AX-385273987 3 41782700 ATGTATTACTGACATGGGCCAGTTTTAGCTGATTC[C/T]GCCTATCTTTTCTTAAGCTCTAAGTGTTAGAATAA Y 2 1 2 1 101000 f 74 goat snp15512-scaffold164-2984648 3 76597055 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445361 Affx-122925418 AX-123315698 3 41839503 CCTATCACAAATGAGAAAACTGTGGCTTGAAAAGG[C/T]TAACTGAGTTACCTAAAAACACTATGGTTAATATC Y 2 1 2 1 303000 r 74 goat snp15511-scaffold164-2927845 3 76539807 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774077 Affx-122924697 AX-385261215 3 41883348 GATAGAATTAAATAATTCAGCACTGGAATAGTGTA[C/T]AGGAGAAGCATGTATCTGAATTTTGGCAATCGTAT Y 2 1 2 1 101000 r 74 goat snp15510-scaffold164-2884000 3 76495500 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788621 Affx-122934167 AX-385275638 3 41919667 GTTGGTTGATTGTCTAAAATATTCTCTGTCCTCAG[C/T]GTAGCTAAAGAACTGTTCATTCTTCAATTGCAGTA Y 2 1 2 1 101000 f 74 goat snp15509-scaffold164-2847681 3 76459068 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791334 Affx-122973412 AX-385278327 3 42038549 AGAGGCTGAGAAAGAGAATGCTTATTTTAGGTAGC[A/G]CTTTTAAAATACGCTTATTACAAAAGAAGATGAGA R 2 1 2 1 101000 f 74 goat snp15507-scaffold164-2728799 3 76339511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767947 Affx-122970566 AX-188959500 3 42095647 GTATGTTACTATGGTGAGCATTAAACAAAGGAACA[C/T]ATTAAATTTATGTTACACAGTGTCTGGTACATAGG Y 2 1 2 1 101000 f 74 goat snp15506-scaffold164-2671701 3 76281773 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415048 Affx-122949488 AX-123285397 3 42135080 AAGCAACTATACCCCAATTAAAAAACATCCCCCAG[C/T]AAGGAACTGGAGCAAGTGTCATGTATCATAATAAT Y 2 1 2 1 201000 r 74 goat snp15505-scaffold164-2632268 3 76242293 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384565 Affx-122973005 AX-123254923 3 42166500 GCTCTGAATAACAACCCTTCATCACTGACACATTT[A/G]CCTTATTCCTTAAGTGCAGCCGTGGCTAGTTTCAC R 2 1 2 1 101000 f 74 goat snp15504-scaffold164-2600848 3 76210810 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381584 Affx-122974804 AX-123251942 3 42212200 TTGACTTTGAAGCCCTCCATAGAGTCCCAAGGACC[A/G]TCTAGCAAAAGGGAGCCGATCTGAGAGAAGGGGAG R 2 1 2 1 101000 r 74 goat snp15503-scaffold164-2555148 3 76166488 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410764 Affx-122952685 AX-123281114 3 42262089 TTACTTTCCCTCCTCCACCTGGTCACATTTGAGCA[C/T]GTATTCATTATCTCATCTTTCTTTTCTTCTAATAT Y 2 1 2 1 103000 f 74 goat snp15502-scaffold164-2505259 3 76115330 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789331 Affx-122964147 AX-385276341 3 42307012 TTATGTGTCAAGCACGGTCTTAATTGCTGAACATG[C/T]AACAGTGAATGCCACAGAACTATCTGTTCTCATTG Y 2 1 2 1 202000 r 74 goat snp15501-scaffold164-2460336 3 76072374 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782623 Affx-122928856 AX-385269696 3 42337602 AAAATGCATATGATATCATCCATCTGTGTGAATAA[C/T]GGCATAAGAATGAACTCACTGTTAAGAATCACTTG Y 2 1 2 1 101000 r 74 goat snp15500-scaffold164-2429746 3 76041936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422562 Affx-122943763 AX-123292908 3 42370900 TTGCCGACGCTGGACGCAGGATAGGTCCTGATGTA[C/T]GTAAAGGAGTGGTAGGCTTACACTGACAAAGAAAG Y 2 1 2 1 101000 r 74 goat snp15499-scaffold164-2396448 3 76007824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786516 Affx-122942355 AX-385273550 3 42468923 ATGGCTACCCTGGGAAAGTTTTAGTTTTATAAACA[G/T]TTATATTCATGGGCACTAAGATTATTAGGATAAAT K 2 1 2 1 101000 f 74 goat snp15497-scaffold164-2298425 3 75908770 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429583 Affx-122937725 AX-123299924 3 42501568 AAAGGGAAGAGAAATGGAAATAGTGTTGCTGGAAC[A/G]CAAGGATGCTTGGAGCTGTGGAAAAGGGGCCACTT R 2 1 2 1 101000 f 74 goat snp15496-scaffold164-2265780 3 75877446 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381357 Affx-122974408 AX-123251715 3 42530207 CAACTATAAGGTTTAATAATTATTGATATATAAAA[G/T]AAATTGAAGCACTTTGACTAATGTGACCTAGGAAG K 2 1 2 1 102000 r 74 goat snp15495-scaffold164-2237141 3 75848446 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443102 Affx-122928103 AX-123313439 3 42594938 GGCTTTGGCACAGAAGACATTGCAAATGATGCCTC[A/G]TTTGCAATGAGGCATGGACATAAACACTCCTGTAT R 2 1 2 1 101000 r 74 goat snp15494-scaffold164-2172410 3 75782939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786371 Affx-122949865 AX-385273405 3 42669057 TTTCTCATCAAGTTTGGTCTTGTGTGGATCATCAC[A/G]TTAAAGCTTGTTTTTCAGCTTGGTGAAAGCCATGA R 2 1 2 1 101000 f 74 goat snp15492-scaffold164-2098291 3 75708022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794771 Affx-122948821 AX-385281731 3 42698333 TGGCTCATTTAGTGAATAGAAAACTCATCTTCTAG[C/T]AGTATATATGTTTTCACGGAAATAAAATTGGAAAA Y 2 1 2 1 101000 f 74 goat snp15491-scaffold164-2069015 3 75678719 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454060 Affx-122919390 AX-123324393 3 42760113 TTTTAAAAGGCAGTTAACAAAATAATTGTAGTTTT[A/C]TTAACCTCTTTACTTAAAAAAATAGTCAGTGCAGT M 2 1 2 1 303000 f 74 goat snp15490-scaffold164-2007235 3 75617051 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795437 Affx-122970195 AX-385282393 3 42805323 GGAATTCCCTGGAGAACAATGTGTTTATTATATGC[A/G]TCTACAAATGATATTAAGGTGATTTCCTAAGTTGT R 2 1 2 1 101000 f 74 goat snp15489-scaffold164-1962025 3 75572120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412202 Affx-122950938 AX-123282552 3 42867352 CATGCCTTGGGAGCTTCTTCCATGCTTCCACATGC[A/G]CTCACAACTCTCTGGGTACTTGGCCAATGTATTTC R 2 1 2 1 101000 r 74 goat snp15488-scaffold164-1899996 3 75509672 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430749 Affx-122937500 AX-123301090 3 42929033 ACATTAACATGAAAATACACGACCACAACTTAAAA[G/T]CTAGAATAGTAAATTTTTATTTTGTTTGCTTTTGA K 2 1 2 1 103000 f 74 goat snp15487-scaffold164-1838315 3 75447742 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789917 Affx-122975930 AX-385276923 3 42974643 ATTAGAAATACATTCCTTTGTACTTTCTATTTCTG[C/T]ATCTAGAAATCATGCCTGAATCTATTACATTTCTA Y 2 1 2 1 101000 f 74 goat snp15486-scaffold164-1792705 3 75401657 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419439 Affx-122945504 AX-123289787 3 43061010 TGATCCTCTGTTTAGAAAACAAGGGCATCCATGCC[A/G]CAGATGCTTTGATGGTGAGCAAATTACCCTACTTA R 2 1 2 1 101000 r 74 goat snp15484-scaffold164-1706338 3 75317364 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379008 Affx-122976376 AX-123249367 3 43115661 TACCACTCTTACGTCTCCATTTAAAACAATGCTCC[A/G]CTTTCTCTTATTGACACTGACTTTTCTCTCCTTTG R 2 1 2 1 101000 f 74 goat snp15483-scaffold164-1651687 3 75263058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454263 Affx-122919644 AX-123324596 3 43155034 TGTATTAAATATACTAAAGATGTGATTTGATTTCT[A/G]TTCTTTGGTGTGTGAAAATCACTCACTCAGTAATA R 2 1 2 1 202000 f 74 goat snp15482-scaffold164-1612314 3 75223903 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426042 Affx-122941110 AX-123296388 3 43193982 TTGTAAACACTAGCATATTAATTGTACCTATTTTC[C/T]AAAGAGCAGGTCATTATTATTGACATGCTACTGGC Y 2 1 2 1 101000 r 74 goat snp15481-scaffold164-1573366 3 75185301 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784541 Affx-122973072 AX-385271590 3 43290315 TGACTCTTCCAAGTAGCACAAATACATTTCACAAC[A/G]TGATCTTTGATAAGTGTCCAAATGGATTTTAAAAC R 2 1 2 1 101000 f 74 goat snp15479-scaffold164-1477033 3 75088456 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451962 Affx-122920950 AX-123322295 3 43326733 GAAAAGTTGACTCAAAGAATAAAGGTTATCAAACC[C/T]AAAGGTTATATTTTTAAACCAAAGGTTCTTATGGA Y 2 1 2 1 101000 f 74 goat snp15478-scaffold164-1440615 3 75052016 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408576 Affx-122953664 AX-123278927 3 43394000 CAACAGAAGAATTAAGAACTTCAGATAACAGTAAA[C/T]AGTGCATTAGATAAAAATTTCAATCTTCAGGGAAG Y 2 1 2 1 201000 f 74 goat snp15476-scaffold164-1373348 3 74984604 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793773 Affx-122926939 AX-385280745 3 43423086 GCAGCTTAGACTCAAAAGCAAACAGACATAGTTCA[C/T]AAAAATCTCTCATCACCTCAATATCCATTTCTCAG Y 2 1 2 1 101000 f 74 goat snp15475-scaffold164-1344262 3 74955066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418638 Affx-122946341 AX-123288986 3 43474557 ATGACGATAATTTAGCCCACTTGAAGATGAGTACC[A/C]TGCAGTTCCTCCTGCAAGTGAAAGCATCCTGGCAT M 2 1 2 1 101000 f 74 goat snp15474-scaffold164-1292791 3 74903713 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38419735 Affx-122945893 AX-123290083 3 43514929 GGTCAGATGGTCTGGGTTACTTTATTTATAGGAAA[C/T]AGCTAGCATGAACAAGTCAGATAATACAAAGCATA Y 2 1 2 1 101000 f 74 goat snp15473-scaffold164-1252419 3 74863471 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802972 Affx-122929109 AX-385289858 3 43561811 CATCATTTCTTACATCCCTCTTTCATTCCAAGTTT[A/G]TCTCAATTATGCTGAAGAATAATTTTTTTAAGAAT R 2 1 2 1 201000 r 74 goat snp15472-scaffold164-1205537 3 74816599 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766965 Affx-122960160 AX-385254265 3 43618622 CATCAGGAGAGACTATCTTTAGCAAGAAATTTTGT[A/C]TTACCAGTCAATAGATAAAATTTACTGACCAATAT M 2 1 2 1 101000 f 74 goat snp15471-scaffold164-1148726 3 74758949 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398381 Affx-122961653 AX-123268736 3 43649525 ATTGACAAAAGGAAAGCTCAAAGAATGAATATCCC[A/G]CTCTTGCATTAAAATTCCTAAGTTAATGAGACCAG R 2 1 2 1 600000 r 74 goat snp15470-scaffold164-1117823 3 43649525 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780384 Affx-122961653 AX-385267478 3 43649525 ATTGACAAAAGGAAAGCTCAAAGAATGAATATCCC[A/G]CTCTTGCATTAAAATTCCTAAGTTAATGAGACCAG R 2 1 2 1 101000 f 74 goat snp15470-scaffold164-1117823 3 74728152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769575 Affx-122941204 AX-385256745 3 43746023 TTTCTACTCTTGCTTGTTAACTCAGTATTTCCCAT[G/T]TGAAAGATTGACAAGACTGAATAGGCCTCTCTAAA K 2 1 2 1 101000 r 74 goat snp15468-scaffold164-1021325 3 74631714 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449774 Affx-122922438 AX-123320109 3 43787182 CCTTTCCTAATGACCATACTTTGAAGATCAAGAGA[A/G]AAGAATGAAAAATGGCAGCTATGTTAACAGCTAGT R 2 1 2 1 101000 f 74 goat snp15467-scaffold164-980166 3 74590318 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791662 Affx-122967963 AX-385278653 3 43838982 GTCATAAACTGAGAAAGGGCTTCAGTAGAAATGAC[A/G]TATCTTATAACAGGAGTATTACATACCATTGTTCC R 2 1 2 1 101000 f 74 goat snp15466-scaffold164-928366 3 74538470 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397542 Affx-122962033 AX-123267897 3 43890890 AGTGAGATGATTCGCTGTTTCCTAACCACCTAAAA[G/T]CATTAAAGAATGAAAATAGGGTAGCACTGGCCCCT K 2 1 2 1 101000 f 74 goat snp15465-scaffold164-876458 3 74486017 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452381 Affx-122920619 AX-123322714 3 43955403 AATCATACACATTAAACCTTCACACTTGATGCCAA[C/T]ATTTAAAACTGTGGAAACAGATTCTGGGAATATAG Y 2 1 2 1 101000 f 74 goat snp15463-scaffold164-811945 3 74423865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451248 Affx-122921942 AX-123321581 3 43998548 CAAAGTTCACAGGCTTTCAAATCCAGATAGAATAA[A/C]TTTTAGATTACTAAGTGACATTTGTACCTTATTAG M 2 1 2 1 201000 r 74 goat snp15462-scaffold164-768800 3 74380893 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398737 Affx-122961825 AX-123269092 3 44049812 ATGCTCAGGGTGTCCGTCGTCACACCTGCTCTACC[A/G]CCAAAATTTTCCTTTTATTCTCATTCTTTTTACTT R 2 1 2 1 101000 f 74 goat snp15461-scaffold164-717536 3 74329119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380469 Affx-122975727 AX-123250827 3 44086287 TGGCTTGGTTAAATATTCTGGTCCTTCAGGTACTT[A/C]TGCAGACCTCAGAACAAAACACTGGACTGAAGTCA M 2 1 2 1 101000 r 74 goat snp15460-scaffold164-681061 3 74292332 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794707 Affx-122943386 AX-385281667 3 44144130 CTTGTTATAAGATAGGCAGCAAAATCAGTACACAC[A/G]TGGAAAATTAACATTGATAACAAATCCAGCTATCT R 2 1 2 1 101000 f 74 goat snp15459-scaffold164-623218 3 74234315 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450222 Affx-122922276 AX-123320557 3 44199555 GAAGATTAATCAATCTTTTTTAGATTTACATACTA[C/T]AATACCTAATATTTTCCTACATGGAAACACCTGGA Y 2 1 2 1 101000 r 74 goat snp15458-scaffold164-567793 3 74178155 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376779 Affx-122977958 AX-123247138 3 44270264 AAAATAATTCAATTTTAAAACCCACCAGAACATAA[C/T]AAGTGAACAAGTTTGTTTTCCAGGCTCATCAGTGC Y 2 1 2 1 201000 f 74 goat snp15457-scaffold164-497084 3 74107032 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788754 Affx-122939929 AX-385275770 3 44298968 AGAAGAAGGTAGGGTTCCACTTCAAAGGAATGCAG[C/T]GTTCACTATAGTTGAATCATTTGGTTGACAACATA Y 2 1 2 1 101000 f 74 goat snp15456-scaffold164-468380 3 74078372 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441347 Affx-122928880 AX-123311684 3 44329234 GTGCCATAAAACTTTTTCAGGAAGGAATCTGGAAA[C/T]AATGGGGGAAGGAACAGGTCACACAGAACCTTAGG Y 2 1 2 1 201000 f 74 goat snp15455-scaffold164-438114 3 74047864 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392006 Affx-122966492 AX-123262363 3 44369843 CTATGATTTACTGGAGCACGAAAGTTGGACTTCCC[A/G]TTTCCTGTGCATAAACTTGCCTATCTAAGTCTATT R 2 1 2 1 101000 f 74 goat snp15454-scaffold164-397505 3 74007657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419219 Affx-122945690 AX-123289567 3 44433231 TTTCCCAGTAAAACCAAAAGGTTTAGTTTGTTTTT[C/T]AAGTTAAATTCTGGAAAAAGGTGAAAAAAAAAATA Y 2 1 2 1 201000 r 74 goat snp15453-scaffold164-334117 3 73943645 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383462 Affx-122973450 AX-123253820 3 44508071 CGAGATGATTAAAACACTGGTCTGGGCCTCCCCAG[C/T]GAGAGTAAATCTATTAACATTTCCTTATTGACTCT Y 2 1 2 1 201000 r 74 goat snp15452-scaffold164-259277 3 73867638 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393895 Affx-122965114 AX-123264250 3 44578001 TTTATACAGAAAATGTTTATTTTTCTAATAAAAAA[G/T]CAACAATATATTCCCCTGTTCTCTAGTTTGTTCCA K 2 1 2 1 103000 r 74 goat snp15451-scaffold164-189347 3 73797164 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790626 Affx-122942394 AX-385277628 3 44709045 ACTTTCGGATCAAAAATTATATGCAGCTTAAATAA[C/T]GGAAATCCCAACATAGAAAATCCATTACTGTATTT Y 2 1 2 1 101000 r 74 goat snp15449-scaffold164-58303 3 73663707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389329 Affx-122968487 AX-123259687 3 44754515 AATTCATTCAGAATCACAAAGGAGTAAAAGAACTA[G/T]GTGGTCAAAACCATAGCAATGTTAGGAAAATCACA K 2 1 2 1 101000 r 74 goat snp15448-scaffold164-12833 3 73618270 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393282 Affx-122965446 AX-123263638 3 44768442 TTCCGTCATCTTCTTACTCATTCTTTCTCATGGAG[A/C]GGAAGTGAAACAACTGAGGTGTCCGCATTTAATGA M 2 1 2 1 101000 r 74 goat snp29695-scaffold321-5715610 3 73362598 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795257 Affx-122977446 AX-385282215 3 44807117 CAGTACTCCTCCTTCCTTACAGTCTATTTTGTCCT[A/G]TCTTATTCTTCGCAGTTGAGTTCAAATAGCACCTT R 2 1 2 1 101000 f 74 goat snp29694-scaffold321-5676935 3 73322575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785963 Affx-122960627 AX-385272999 3 44887977 GAAGAGTTATTATCAAAATGCAAAGCTACACTCAT[A/G]TTCCTTTCATGGAAGCAGAGTTGAAGATGTGGCTA R 2 1 2 1 101000 r 74 goat snp29692-scaffold321-5596075 3 73239950 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399168 Affx-122960638 AX-123269523 3 44934087 CTGACATACAAGAAAAGGGGAGCCAGCATTAATGG[C/T]GCCACAGTGGAGGGATTTCGGGCAAGAACTACAAC Y 2 1 2 1 101000 f 74 goat snp29691-scaffold321-5549965 3 73193411 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416381 Affx-122947868 AX-123286730 3 44985068 AACTATCCCACCCAGGAGACCACCCATAATTTCAA[C/T]ACCAAGAGCTAATTGTTGTTCAGTTGCTAAGTCGT Y 2 1 2 1 103000 f 74 goat snp29690-scaffold321-5498984 3 73142431 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272039 Affx-1111833388 AX-519545803 3 45013233 AGAAGAAAATATAGAAATTAGAAGGAAAGAAACAT[A/C]AAGACAGATCCATACATTTAGGGGACTTCTTTTGT M 2 1 2 1 102000 r 74 goat 3_45013233_AF-PAKI 3 45013233 T G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449593 Affx-122923216 AX-123319928 3 45046560 CAGCACGTATTTCATATATCTGTACATATGTGCCA[C/T]GTGTGCTATCAAACTTTGGAGAATATTATGAATTC Y 2 1 2 1 201000 r 74 goat snp29689-scaffold321-5437492 3 73080920 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436417 Affx-122933016 AX-123306755 3 45091046 ATAAATACGACACCTGAGCAGATAGACCTGGGGTA[G/T]AAAGGGAGCTCTCCCCGTGAGGCTTGCTCAGGGAG K 2 1 2 1 101000 f 74 goat snp29688-scaffold321-5393006 3 73039121 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385176 Affx-122971735 AX-123255534 3 45173746 GTTGAATAAAATTATCCATTTGTGTATGTCTTCTC[C/T]GAGGTAATAATTTTTCTGAGGGTGAGAAGCAATTT Y 2 1 2 1 101000 f 74 goat snp29686-scaffold321-5310306 3 72955673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785057 Affx-122973027 AX-385272104 3 45234219 TATTAAACTCCTGGTGAGGGACAATTCAACTTTCT[A/G]CTAAGAATTCTAACCCCTTCTGGACACTAGCTCTT R 2 1 2 1 101000 r 74 goat snp29685-scaffold321-5249833 3 72894170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385925 Affx-122971565 AX-123256283 3 45302247 ATTATCTTTCACTTGGCAATTTGATTCCTACAACT[A/G]CCCTGCTATTCATGGAGCCCTGACTTAGACCCCTG R 2 1 2 1 101000 f 74 goat snp29684-scaffold321-5181805 3 72825699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768967 Affx-122960635 AX-385256142 3 45379868 GCTTGAAGCTCCAGTGCTAAGAAATATCATCACCT[A/G]TTTGTCCATCTGAAAGCAAGGTTTATCCTCCTCTT R 2 1 2 1 101000 r 74 goat snp29682-scaffold321-5104184 3 72746713 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436071 Affx-122932698 AX-123306410 3 45441055 TTTAAAAAAAGCGTTATTTAGGAATGGATGTTTTT[A/G]TTTTTGCTCTTCATTATTGACTTGGCTTGATTTCC R 2 1 2 1 101000 r 74 goat snp29681-scaffold321-5042997 3 72685746 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390006 Affx-122968041 AX-123260363 3 45489847 GGGGGGTTGAGAAGTCCTTTTCATGGAAATAAAAA[C/T]GGAGATGAAAGAAAACAGCAGTTCCAATTTTCGAT Y 2 1 2 1 101000 f 74 goat snp29680-scaffold321-4994205 3 72645696 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385826 Affx-122971018 AX-123256184 3 45571454 CCCTAGCCCTTCACTTCTTAATACTTGGTTTTCTT[C/T]GAGAATTCAGTTCAATCATCACCTGCTCAGCTCTC Y 2 1 2 1 101000 r 74 goat snp29678-scaffold321-4912598 3 72563797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415771 Affx-122948923 AX-123286120 3 45612322 CCCTTTTCACCTAACTGGGAATAGAGACCAATTCT[A/G]CTTCCAAAGTAACTCTCACCTTGATCTCAGCATTC R 2 1 2 1 101000 f 74 goat snp29677-scaffold321-4871730 3 72522396 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801213 Affx-122977877 AX-385288126 3 45667981 GGAAGAAGAATAAGTAAACAGGCAGAGTGTCCTGC[A/G]CTAAAGTACACCAGTGTCCTGATAAGAGTTCCAGC R 2 1 2 1 101000 f 74 goat snp29676-scaffold321-4816071 3 72466537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408384 Affx-122953720 AX-123278735 3 45771830 TCAGGCCAAAAGAGTATAAAATAAGACAAAGAAAG[G/T]TATTTACACTTATTCCAATTATCTATTGTTTCATA K 2 1 2 1 303000 r 74 goat snp29674-scaffold321-4712222 3 72362095 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397189 Affx-122962407 AX-123267544 3 45837529 TAGATAATTTGGGGCACTATCAAGGAGAGACAATG[A/C]GATGTACTTGGAAGATAATGGATTTTGGATTTAGA M 2 1 2 1 101000 f 74 goat snp29672-scaffold321-4646523 3 72295657 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412154 Affx-122951081 AX-123282504 3 45880438 ACACAGAGTTGAATATTCCAGTCCACATACTACAT[A/G]TGATAAAGTAAATAGAAAGGTTTTCCCAGAAAAGT R 2 1 2 1 101000 f 74 goat snp29671-scaffold321-4603614 3 72252371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427511 Affx-122939528 AX-123297854 3 45928159 GCCTATGTATGTTGGAATGAAGGAGTGTTCTACTT[A/G]GGTAAAAAGTGGTACATTCCAAAAACATAAGGGGT R 2 1 2 1 101000 r 74 goat snp29670-scaffold321-4555893 3 72200351 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432713 Affx-122936018 AX-123303054 3 45975181 TTAGGAAAGAGTGGTAGTAAAAATGATATACTTTA[C/T]TGAGTGATGTTTTGATCTATTGCTTAATAGCAAGC Y 2 1 2 1 101000 r 74 goat snp29669-scaffold321-4508871 3 72153287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431291 Affx-122937094 AX-123301632 3 46035837 CACCCAACCACTGTGTGTTCAATTTCTGAAATCGT[A/G]CAATCTCCAAAATTTTCCCACTTTAATTTTAAAAC R 2 1 2 1 101000 f 74 goat snp29668-scaffold321-4448215 3 72092458 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390353 Affx-122967685 AX-123260710 3 46070422 AAGGGACTTTCACTAAGTAGGAGTTCATTTTGTGA[G/T]GCCAACCATATCAGAACAGCAGACTGGACAATGTT K 2 1 2 1 101000 f 74 goat snp29667-scaffold321-4413630 3 72057922 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411129 Affx-122951897 AX-123281479 3 46110649 TCAACAAATGTAATGATGCTTGGCGTTCTTCTTGG[C/T]ACTTGGGTTTGGGAAGACAAGTAAGCCATCAGGGA Y 2 1 2 1 101000 f 74 goat snp29666-scaffold321-4373403 3 72017633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775537 Affx-122969822 AX-385262668 3 46165843 AGTAAAGTACATAAACATAGTCTATCCCTTTTAAA[C/T]TCTGTTAAAAAAAACTCTATCTCCTCTTTTGGCTC Y 2 1 2 1 101000 r 74 goat snp29665-scaffold321-4318209 3 71961688 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415408 Affx-122948735 AX-123285757 3 46198025 ACGCTGATTCCACTGAAAGGATTCCTAAAGGTCCA[C/T]TTGCAAACCTTGGAAAGAACACCACAATAGTCTAG Y 2 1 2 1 101000 f 74 goat snp29664-scaffold321-4286027 3 71929307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476174 Affx-1251763678 AX-586011601 3 46202087 CAAGCTTTATTTCTTCTGATTACACAAAATGCAAA[-/TAAGAAAAATCACTGAGGGGGGAGAGGGAAAGATGGCGGATTAAAATTTAAAAAAAAAAATAAAAAAATTAAAAAAAAAA]AAGAAAAATCACTGAATATTTCAGATGAATTGCTG - 8 1 4 1 20000 f 74 goat SV_257 3 46202087 - deletion junction SV-TF-chip 539476429 Affx-1251763678 AX-586011830 3 46202087 CAAGCTTTATTTCTTCTGATTACACAAAATGCAAA[-/TAAGAAAAATCACTGAGGGGGGAGAGGGAAAGATGGCGGATTAAAATTTAAAAAAAAAAATAAAAAAATTAAAAAAAAAA]AAGAAAAATCACTGAATATTTCAGATGAATTGCTG - 4 1 4 1 20000 r 74 goat SV_257 3 46202087 - deletion junction SV-TF-chip 562165064 Affx-1251763678 AX-606940476 3 46202087 CAAGCTTTATTTCTTCTGATTACACAAAATGCAAA[-/TAAGAAAAATCACTGAGGGGGGAGAGGGAAAGATGGCGGATTAAAATTTAAAAAAAAAAATAAAAAAATTAAAAAAAAAA]AAGAAAAATCACTGAATATTTCAGATGAATTGCTG - 8 1 4 1 20100 r 74 goat SV_257 3 46202087 - deletion junction SV-TF-chip 562166102 Affx-1251763678 AX-606941511 3 46202087 CAAGCTTTATTTCTTCTGATTACACAAAATGCAAA[-/TAAGAAAAATCACTGAGGGGGGAGAGGGAAAGATGGCGGATTAAAATTTAAAAAAAAAAATAAAAAAATTAAAAAAAAAA]AAGAAAAATCACTGAATATTTCAGATGAATTGCTG - 8 1 4 1 20100 f 74 goat SV_257 3 46202087 - deletion junction SV-TF-chip 562166355 Affx-1251763678 AX-606941763 3 46202087 CAAGCTTTATTTCTTCTGATTACACAAAATGCAAA[-/TAAGAAAAATCACTGAGGGGGGAGAGGGAAAGATGGCGGATTAAAATTTAAAAAAAAAAATAAAAAAATTAAAAAAAAAA]AAGAAAAATCACTGAATATTTCAGATGAATTGCTG - 8 1 4 1 20100 f 74 goat SV_257 3 46202087 - deletion junction SV-TF-chip 320782234 Affx-122925434 AX-385269312 3 46228202 GGCATTAAGGCCCTTCTGCTTTGAAACAGAGAATG[C/T]AAAGCACTCCTTAGTCCAGCCAGGCACTGATGTTT Y 2 1 2 1 201000 f 74 goat snp29663-scaffold321-4255850 3 71899081 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441700 Affx-122929162 AX-123312037 3 46269546 CTCATCTGGACTAGTGAATTCATCCTTGCATGCCA[A/G]CAAATGACTGTAGCTGGAACAGTGGTGACGTGTTA R 2 1 2 1 101000 f 74 goat snp29662-scaffold321-4214506 3 71857518 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406880 Affx-122955640 AX-123277231 3 46301388 AAGAGGAGAGAATTATTTCCAGAGGAGAATACCAT[A/G]CTATTTTTCTGTAATACCTTTTTTAAAATTTGATT R 2 1 2 1 101000 f 74 goat snp29661-scaffold321-4182664 3 71824970 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419496 Affx-122945461 AX-123289844 3 46338318 CAGTTATTTTCCAGTCAATATATTTGTAAGGTGAC[A/G]AGTCACCCACTCCCATTTTTCAAAGGTTGAGCTGA R 2 1 2 1 201000 f 74 goat snp29660-scaffold321-4145734 3 71788042 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420731 Affx-122944767 AX-123291078 3 46376373 ATTTTTAAAGGACATTGGGGTTCACATTTCTGTTC[A/G]TTTTGTTTTAATTTTTCTCCTTTAACTTAATTTAG R 2 1 2 1 101000 f 74 goat snp29659-scaffold321-4107679 3 71750706 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387964 Affx-122969605 AX-123258322 3 46435238 TTGTAATTTCATAGCTTTTCTTAAGGCATGCCCAC[A/G]TTATATAGACTCCTAGGACCCCAAACCAGAGCCAG R 2 1 2 1 101000 r 74 goat snp29658-scaffold321-4048814 3 71690634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417955 Affx-122946702 AX-123288303 3 46469079 AGATGAATGATTATGATTGGCCAATCCCCTGTCAC[A/G]TGGCCACCACTAATAGGAGGGTGATGGAAAAGCTT R 2 1 2 1 201000 r 74 goat snp29657-scaffold321-4014973 3 71657369 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395629 Affx-122963798 AX-123265984 3 46498154 AAAGCAGAGCATTTCAGGAGGAGGTGATGACCAGC[A/G]TGGAGCTTAGCATGAGACCAGGTCCTGGGCCAAAA R 2 1 2 1 201000 f 74 goat snp29656-scaffold321-3985898 3 71628337 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403703 Affx-122958041 AX-123274055 3 46574052 AAAAGACATACAACTTTGCAAAATTTAATTTTCTC[A/G]CATCCTTGAACTGAAATAGCAAGTCCAGGTTTAGC R 2 1 2 1 101000 r 74 goat snp29654-scaffold321-3910000 3 71552837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412436 Affx-122951418 AX-123282785 3 46609186 TTAAAACTGAAAAAGGTTTTTCATTGTTTTGTGGC[A/G]AGCTTACTGGGTAGCCAGAGCTGGCCTGAACTAAC R 2 1 2 1 101000 r 74 goat snp29653-scaffold321-3874866 3 71517837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415210 Affx-122948979 AX-123285559 3 46638930 GACCAGTGTTTTCTTGACAAAATTTTTATGCAAAT[A/G]TGACTTTAGAACTATGGAAGAATTAATTTTAATAC R 2 1 2 1 201000 r 74 goat snp29652-scaffold321-3845122 3 71490073 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777415 Affx-122953023 AX-385264536 3 46701612 CTTTATTATTACACACCAAATTTTAGTAACTTCTT[A/C]AGTTTCCATTCTGGTGGGTAACACACAGTGCTAGA M 2 1 2 1 101000 r 74 goat snp29651-scaffold321-3782440 3 71428033 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398143 Affx-122961685 AX-123268498 3 46753775 CTGTCCCAGCTTGTTGTTTCTTGTGCATGCATGTT[A/G]AGTCTCTCACTCATGTCTGACTCTTTGCGACCTCA R 2 1 2 1 101000 f 74 goat snp29650-scaffold321-3730277 3 71375476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393743 Affx-122965223 AX-123264098 3 46793902 TAAAAAACTTCTTTGTTTTTTGTTTGCTTGCTGCC[A/G]TCAATGTATTCATAAAAATGTTTACCAGAGAGCAA R 2 1 2 1 201000 r 74 goat snp29649-scaffold321-3690150 3 71335899 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769384 Affx-122943992 AX-385256555 3 46849079 TGCACTTATCCAAGTTCCCATAGATGATTCATGTT[G/T]CCCTATCCAGACTATAATCTCAAGGAAATCATAAC K 2 1 2 1 101000 f 74 goat snp29648-scaffold321-3634973 3 71280967 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792781 Affx-122960941 AX-385279760 3 46878304 GGTATATATGCTGACAGATTGCTCATGATTTTTAG[A/G]TGTTCACAAATAGATGAAACTATTATAATACTAAC R 2 1 2 1 101000 f 74 goat snp29647-scaffold321-3605748 3 71251692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770321 Affx-122972173 AX-385257487 3 46910110 GGTTGTGGGGAAAAAACACCCTTACTGATGTACAA[C/T]AGCTTATATGCTATGTATGAACAAGTGAAGTGAAA Y 2 1 2 1 101000 f 74 goat snp29646-scaffold321-3573942 3 71219932 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277951 Affx-1111836175 AX-519551446 3 46945463 AAAGTAACTGTTACTCAGAGGCTACAAGAGCCAAA[A/G]TTGTTTTTGCTTGTTTAACTTAGTTTTCCGCATTA R 2 1 2 1 101000 f 74 goat Random2.2K-319 3 46945463 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38404611 Affx-122957339 AX-123274963 3 46978631 GGACACTCATCAGAGAGGCACACTGAGGAGCCAGA[C/T]ATTACTTGCTGCTTCAGTGACAAATAGCAACCAAC Y 2 1 2 1 101000 r 74 goat snp29645-scaffold321-3505421 3 71161831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400618 Affx-122960380 AX-123270973 3 47036111 GACCTGGGCTCCATCCTGGCTGTTTTATCAGGCAG[A/C]TGATTCACAGTCATGTTTCCTGCTGTGTCTCTCTA M 2 1 2 1 101000 r 74 goat snp29644-scaffold321-3447941 3 71104053 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432540 Affx-122935549 AX-123302881 3 47077709 CCACCTGGGAAGCCCCAGTAATTAAACATATTCAT[C/T]TCAAAAAAATTATCTGGAAAGCAGGGAGGGGCCTA Y 2 1 2 1 103000 f 74 goat snp29643-scaffold321-3406343 3 71061802 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421841 Affx-122944299 AX-123292188 3 47108410 ACTTCATTGTTTATTAAGTGGGTTAATAAAATACT[A/G]CTTATTCCAAGCTAGGTTTGAATTGAATTCCTCTA R 2 1 2 1 101000 r 74 goat snp29642-scaffold321-3375642 3 71030839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385952 Affx-122971543 AX-123256310 3 47147748 GCTGGTTTAGTCTAGATTTGCCTGTTTGTACAAAG[C/T]ACCAGCTGCAAAGGCCTTGGTAAGGTTCTTGCCCC Y 2 1 2 1 101000 f 74 goat snp29641-scaffold321-3336304 3 70991431 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795221 Affx-122919490 AX-385282179 3 47219287 ATTCTAGTCAGATGCTTTGGGGAGTTTTTTAAAAT[A/C]ATTTTGTTTCAATCTTAACTGCATGCTTTCAATAA M 2 1 2 1 201000 f 74 goat snp29640-scaffold321-3264765 3 70919733 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386204 Affx-122970994 AX-123256562 3 47250405 TCCATGAGTCGTGCTGTGAAGGAACACAGGGAGGT[C/T]TGGCCCTCTGTGTTTCTGCCCTGGAGGTCCATCTG Y 2 1 2 1 101000 f 74 goat snp29639-scaffold321-3233647 3 70888375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401203 Affx-122959333 AX-123271556 3 47279469 CTTTTTGTGGCTATTACTATTCATTTCTCTTGGGT[A/G]TGTACTTAGAAGTGGAGCTGCTGGGTCATAGGAAG R 2 1 2 1 103000 r 74 goat snp29638-scaffold321-3204583 3 70859283 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782946 Affx-122919654 AX-385270016 3 47319420 TCACTGCCAATCAATCAGGTGACTACCATGGTAGC[A/G]TCCTAGTTCTAATTTGAATCTCTGATTATGAGTGA R 2 1 2 1 101000 f 74 goat snp29637-scaffold321-3164632 3 70821809 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452068 Affx-122920872 AX-123322401 3 47355664 CTTAAATATCTATTATCTGTCCAACATCTGTACTG[C/T]ACTTGAGCATCCCTGATGGGCTCATGGAAGGCTAA Y 2 1 2 1 201000 f 74 goat snp29636-scaffold321-3128388 3 70785680 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436314 Affx-122933261 AX-123306653 3 47403482 CGCCTCACCTGCCACTGCTTGTTTATGTCTTTTCC[G/T]CAGGGCTGTAAGCTCTGTGAAGTCAGAGGCTGCTT K 2 1 2 1 101000 f 74 goat snp29635-scaffold321-3080570 3 70737743 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442119 Affx-122928343 AX-123312456 3 47451480 GGCATTTTCTTTCCCAGGTAACTATCTAAGTAAAA[C/T]AAGACAGGGAAATGCATACCAAGGGTCAATGGGGA Y 2 1 2 1 101000 f 74 goat snp29634-scaffold321-3032572 3 70689361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769168 Affx-122977948 AX-385256343 3 47544313 TGCTTATCTAGTATTTGGATGTAGCCTTTGACACT[A/G]TTAACAGGATCATTGGCATTAGTCCAGATGGCAGA R 2 1 2 1 101000 r 74 goat snp29632-scaffold321-2939739 3 70596375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793009 Affx-122961542 AX-385279987 3 47638535 AATTTGGATCACTGTCTTCCAAAGAATAAAGGAAA[C/T]ACTACCCATAATGACCTCAGAAAATTAAATATGAA Y 2 1 2 1 101000 f 74 goat snp29631-scaffold321-2845517 3 70501494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770588 Affx-122957603 AX-385257752 3 47678859 AATGCTTAGTTTGAGTTTCCGTACTTAACTCATTG[C/T]AGACAATTACATGATGATACGGTTATGATACAGAT Y 2 1 2 1 101000 r 74 goat snp29630-scaffold321-2805193 3 70460801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434580 Affx-122934113 AX-123304921 3 47749848 AATGGAAAATGAGCATTGGCTTCAAGTCACCATCT[A/G]CGTTAGCCCCTAACAGAAGGTGAGCCAGTCTTTGC R 2 1 2 1 103000 f 74 goat snp29629-scaffold321-2734204 3 70390569 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410034 Affx-122953244 AX-123280384 3 47779125 CAATTCTAAATAACATTCCAAGCATACAGTTTCTC[A/G]CATTAGAATAAGATTGAACGATAGCTTAATGTTGC R 2 1 2 1 101000 f 74 goat snp29628-scaffold321-2704927 3 70360714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272208 Affx-1111833389 AX-519545957 3 47824803 CAACAGGTACATGAAAAGATGCTCAGCATTACTAA[A/C]CTTCAGAAAAATGCAAATCCTAACCACAATGAGAT M 2 1 2 1 103000 f 74 goat 3_47824803_AF-PAKI 3 47824803 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320782599 Affx-122972940 AX-385269673 3 47877266 GAAACATATGAGATTGAGATCCCTAAATGAAAAGA[C/T]CATGCATAGTTCTTTTCAATATCAGATGATGACAG Y 2 1 2 1 101000 f 74 goat snp29627-scaffold321-2606786 3 70263726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384997 Affx-122971882 AX-123255355 3 47921055 ATTGTATTGGTACCTATTGCCCCACAATACATTCT[A/G]TTATACTTTTTTAAAAGAAGCTCAATTAGGTCTCA R 2 1 2 1 103000 f 74 goat snp29626-scaffold321-2562997 3 70220028 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450060 Affx-122922814 AX-123320395 3 47963595 ATGATAATACAAATCCACACGAGTCAAGAAAATTT[A/G]TTTGTCCTATGCATTATTTCTTGGTTGATGGCCTC R 2 1 2 1 101000 r 74 goat snp29625-scaffold321-2520457 3 70177343 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417412 Affx-122947226 AX-123287760 3 47997775 CTATCCTTATTCCCTCAAGCCTATCCTTCTTTCTC[C/T]CATAGGTAACTATTTTTAAAATTGTGTGTTTATCA Y 2 1 2 1 101000 f 74 goat snp29624-scaffold321-2486277 3 70142982 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781825 Affx-122938618 AX-385268908 3 48061961 ATTAAACCAGTGGTAAGGATGACTTGAGCCCAGGT[A/C]ATAGATTGTGAAGGTGGAATTGATTTTTTTTTTTT M 2 1 2 1 101000 f 74 goat snp29623-scaffold321-2422091 3 70078706 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791036 Affx-122939504 AX-385278031 3 48106764 CAATCTAAGTATGTTTCTAAACAGAAAAAATCCTG[G/T]ATGTGTTAACACTAAATGCTGATATTATATAGCTG K 2 1 2 1 101000 f 74 goat snp29622-scaffold321-2377288 3 70033816 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399716 Affx-122960468 AX-123270071 3 48152000 ATTTTCTTTTTTCCTTTTTTTGCTTTGCTCTGCAG[C/T]AGGTAGAAGCCACAGAGTAAAGGAAACCACGCAGA Y 2 1 2 1 103000 r 74 goat snp29621-scaffold321-2332052 3 69987786 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449544 Affx-122923251 AX-123319879 3 48199413 TAGATCAGGAGGTTCCTGGGAATAACTTTTGTAAA[A/G]ACCTATCAGAAATAAGTGGAAAATAGAAATAATGG R 2 1 2 1 101000 f 74 goat snp29620-scaffold321-2284639 3 69939507 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448396 Affx-122923684 AX-123318732 3 48255064 TCCTCAAGGGTTCCGGAGCTGCCAGAGCAAAGAAG[C/T]AGCGGACTGAAGAAGGAAAGATCGGGTGAAAACTG Y 2 1 2 1 101000 r 74 goat snp29619-scaffold321-2228988 3 69884658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800025 Affx-122962858 AX-385286948 3 48330560 TTGCAAGCCACATTTATATCTTACTCATCTGTATA[G/T]CCCTTTATATTGTCTTTGTATTTAGCTCAAAACAA K 2 1 2 1 201000 r 74 goat snp29618-scaffold321-2153492 3 69808469 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432164 Affx-122936414 AX-123302505 3 48378096 GTTCCTGAGGGAGAAATGGTTCCATGAAGAGACAG[C/T]AAACTGGAAGTTAAGGCAAACCACTTTGAGGCCTC Y 2 1 2 1 101000 f 74 goat snp29617-scaffold321-2105956 3 69760772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435925 Affx-122932756 AX-123306264 3 48434023 GCACAACAGGGCGACAGATACAAGCGGAAAGCTCC[A/G]CTGGGGTATTTTGATTCAATAGCCGGCTTTAAGGG R 2 1 2 1 101000 r 74 goat snp29616-scaffold321-2050029 3 69704954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405603 Affx-122955923 AX-123275955 3 48508033 ACCTAAGTTCTAAAAGTCATAATGGGAGAGCAGTT[A/G]ACTAGATTTCAATCAGTTCTACTTACCCCACAATG R 2 1 2 1 101000 f 74 goat snp29615-scaffold321-1976019 3 69630859 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778290 Affx-122969510 AX-385265405 3 48647322 CCATTTTTTTGTCCTCTGTTAGCTTGTTTTTATAC[A/G]TTCTTTTACTAATCATTAATTGGTTTCCCTAGATT R 2 1 2 1 201000 r 74 goat snp29613-scaffold321-1836730 3 69491100 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766078 Affx-122967619 AX-385253494 3 48685317 TCACCTGTCTCAATCTCACAATCAGTCCTCTCTAT[C/T]CTACTCTAAAACTTCCTGCAAGTGCTACACAGTGC Y 2 1 2 1 101000 f 74 goat snp29612-scaffold321-1798735 3 69452908 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781445 Affx-122929657 AX-385268530 3 48716588 TTTGTGGATCATGTCTTATTTATGAAATAATACTG[C/T]AGAACTTTATCACTTGTAATATTAAGGAATGTTAT Y 2 1 2 1 101000 f 74 goat snp29611-scaffold321-1767464 3 69421249 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381244 Affx-122974498 AX-123251602 3 48760627 AGTCCTTCTTATCCCTCAGTTGACAGAAAAATAGC[A/C]TGTAGTAATTAACTTGGTGCAGCAGCAGAGAAGGG M 2 1 2 1 101000 f 74 goat snp29610-scaffold321-1723425 3 69377191 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412402 Affx-122951443 AX-123282751 3 48808361 CTGGGAAATTTTAGACTTGGCCTATTTTCTTAAGC[A/G]CAATGTAAATAGCTTAATGCTCTACTAGTTACAAC R 2 1 2 1 101000 f 74 goat snp29609-scaffold321-1675691 3 69328998 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440944 Affx-122929007 AX-123311281 3 48866784 AGGAATGGGGAAGGGGGTGACTTGGGTGAGGCTTT[A/G]TAGGTGATGGTTGAGTGATCTTTTAGGGATTGATT R 2 1 2 1 201000 r 74 goat snp29608-scaffold321-1617268 3 69269829 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438634 Affx-122930912 AX-123308971 3 48940882 ACACAGGAACTAATACGGAAGCATCTGGAACAGAA[C/T]ACAAAGGAACCAAAAGTATTTCAAGAAAATCAGAG Y 2 1 2 1 101000 f 74 goat snp29607-scaffold321-1543170 3 69196632 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432896 Affx-122935330 AX-123303237 3 48971043 AGCCTGAAGGAAATGTTGAAGTGAACCATAAGGCT[A/G]TCTCCTGACCGGTGGAACAAATAGTCTGCTTATGC R 2 1 2 1 101000 r 74 goat snp29606-scaffold321-1513009 3 69166198 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798877 Affx-122937061 AX-385285807 3 49058272 TCCCCTCCGTCTTGATATAAAAATTCTAAAACCTG[A/C]GGTAAACCTCTCGCATACACCCTAGCAAAGGCCCC M 2 1 2 1 101000 f 74 goat snp29605-scaffold321-1425780 3 69077420 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377840 Affx-122977291 AX-123248199 3 49143542 ATGGAAAGTGTTTGTTTAGTAACTGAATTTCACCA[A/C]TATACAGTGTCTGTGTGTGAGGGGTTTACTTTGAT M 2 1 2 1 201000 f 74 goat snp29603-scaffold321-1340510 3 69005783 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446228 Affx-122925701 AX-123316564 3 49173968 AGCCAGGCATAGCAAGAACCCAATGTCGACATGAT[A/G]TGAGTACTGGATCACTCATTTCCATCTGCAAACTG R 2 1 2 1 101000 f 74 goat snp29602-scaffold321-1310084 3 68974868 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765702 Affx-122959955 AX-385253164 3 49213328 TGAACAAACTACAAGAGTTTACTTTTGAAGCAGAA[A/G]TATTGCTTCTTCAGGCTCAACACCTTTGATATGTA R 2 1 2 1 101000 f 74 goat snp29601-scaffold321-1270724 3 68935630 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779112 Affx-122923852 AX-385266217 3 49247222 TGAGCATCAAACTTACTAAAAAGTCAGATTTGTCA[A/G]CTCTGTAAAACTTTAGGCCTGTGGTTCATTGCCTC R 2 1 2 1 101000 r 74 goat snp29600-scaffold321-1236830 3 68903434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419304 Affx-122946230 AX-123289652 3 49318111 GAAGCATCTAGGCAGTGTGGGTTGGAGAGGGAAAG[A/C]GGGGTCAAATTTTGGAGGGTCTTAAAAAATAGGCA M 2 1 2 1 201000 f 74 goat snp29598-scaffold321-1165941 3 68832678 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397944 Affx-122961919 AX-123268299 3 49382119 AGAAGACCTTGACAGCTGAGCCCCTCCTCAGCACC[A/G]TGGGGTCTTGCAATGAGCTCCTCTCTAAAGTCTTC R 2 1 2 1 101000 r 74 goat snp29597-scaffold321-1101933 3 68768728 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783286 Affx-122971430 AX-385270351 3 49444092 AAATGTGACTTAAACTATTAAGAAAGATTAGAATC[A/G]TTGCTATTGAGAATGCTGAAATAATTTTATGGCTT R 2 1 2 1 101000 r 74 goat snp29596-scaffold321-1039960 3 68706807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420041 Affx-122945140 AX-123290389 3 49474834 GAAGCACTTTCGTTTATGACCTATGGATACCCTTA[C/T]ATCATCTTCTATTACCTCTTCCCACACACCCTTAT Y 2 1 2 1 101000 f 74 goat snp29595-scaffold321-1009218 3 68676051 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448267 Affx-122924189 AX-123318603 3 49511488 TTTTAAAACTTTATATGCGTTTCCATATAAATTTT[A/G]TAATCAGTTTGTCAAGTTATAAAAACATAAAAATC R 2 1 2 1 103000 r 74 goat snp29594-scaffold321-972564 3 68638919 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443128 Affx-122928084 AX-123313465 3 49551442 TCAGCCAAAACAAACAGAAATGCAATGAAATAAAA[C/T]GCTTTAAAATTATGACTTCAAATATAATGCTGATG Y 2 1 2 1 303000 r 74 goat snp29593-scaffold321-932610 3 68598601 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278109 Affx-1111836176 AX-519551599 3 49604174 CTCTATAAAGAAAATAACAATGTACTTGTAAATGG[A/G]TAAACAAGATATCTTTGAAAGAACCTGTAGCAAAT R 2 1 2 1 101000 r 74 goat Random2.2K-323 3 49604174 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384055 Affx-122972876 AX-123254413 3 49620219 TTAAAGCAAAATAAATCATTAATGTGAAATAGAAA[C/T]GCATTTGAAGTGAATACATAAAATTACTTTAACAA Y 2 1 2 1 303000 f 74 goat snp29591-scaffold321-863833 3 68529544 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797040 Affx-122959815 AX-385283981 3 49668131 GCAAAGCTCTTCCGGAAGACGATGACCATTGATAC[A/C]CTAGAGAATCAGTTGTGTTCAGTTAATCACACCCC M 2 1 2 1 101000 r 74 goat snp29590-scaffold321-815921 3 68480915 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451143 Affx-122921367 AX-123321477 3 49707793 AGAAGAGGCGACGACATTGATTAAAAGTAACAATC[A/G]TTTAAGGAAACAAGGGGTCAGGACCTTTGACTGCT R 2 1 2 1 201000 f 74 goat snp29589-scaffold321-776259 3 68441785 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398798 Affx-122961415 AX-123269153 3 49746826 CTGCCAAGTTTTACATGGCAAATGTATGCTTTTCT[C/T]GTCAGTGTCATCTTCCTCATTACTAACAATATCAT Y 2 1 2 1 101000 f 74 goat snp29588-scaffold321-737226 3 68402418 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788873 Affx-122952046 AX-385275888 3 49781063 TTATAAGAAAGGGTCATTTAATTTGTCCATCATCA[G/T]CAGTACTACATATATAATCTTACAGAAAATAAGTG K 2 1 2 1 101000 f 74 goat snp29587-scaffold321-702989 3 68368303 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381207 Affx-122974528 AX-123251565 3 49830973 TTCTACTCTTAAACACAATTCCTACTGAAATATAA[C/T]GGGGAGCAATCTAGAACAAAGTAACATCAAAAATT Y 2 1 2 1 201000 f 74 goat snp29586-scaffold321-653079 3 68317931 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423830 Affx-122942791 AX-123294176 3 49886261 GAGTTTATAAATGTAATACAGAATTCTCCACTTAG[A/C]AAACAAAAAACATTAATAAAGCTGATAAAAACTTC M 2 1 2 1 101000 f 74 goat snp29585-scaffold321-597791 3 68262076 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451391 Affx-122921204 AX-123321724 3 49929144 TGTCCTAGCTAAGATTTCAAGGTAAAGTGTTCAAG[C/T]TGCTGCTTGGGTTCTTGTGGCTGCTTCCAGTAAAA Y 2 1 2 1 201000 f 74 goat snp29584-scaffold321-554908 3 68219111 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434492 Affx-122934620 AX-123304833 3 49974831 GGCTGCCTGGTGGCAGTGAGACTGTGGCAGGAAAG[A/G]GCATTGTCAGTGTGGGTAATTTTCACCCTGAACAC R 2 1 2 1 101000 r 74 goat snp29583-scaffold321-509221 3 68173255 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779213 Affx-122922047 AX-385266317 3 50007532 TTTGGAAATATACAGAACGAAGCTCGAATAGAATC[A/G]TCTCCACTCACTAGTTTATACTAGCTTCATGAAGT R 2 1 2 1 101000 r 74 goat snp29582-scaffold321-476520 3 68140186 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386191 Affx-122971366 AX-123256549 3 50045880 TATGGTACCATTCAGGGGGAAGTCCGAAGAAGAAG[G/T]TTCCAGAGCAAAATGCACTCATTTATTCTCATCCA K 2 1 2 1 101000 f 74 goat snp29581-scaffold321-438172 3 68101762 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796986 Affx-122945537 AX-385283927 3 50075248 TCGTAACTGCTGTCAAATACAGTTAAGTAAATATC[A/G]TTAGGAAAGAGCTCCGTTAAGAGAAATGCCAATCC R 2 1 2 1 101000 f 74 goat snp29580-scaffold321-408804 3 68072163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405560 Affx-122955957 AX-123275912 3 50113964 CTTTCAAAGGTTCAGTGCTGAAGGTCTCATATTCT[A/G]GGAAACCCCTCAGTCCAAGACAAACTGGTACATTC R 2 1 2 1 101000 f 74 goat snp29579-scaffold321-370088 3 68033400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431674 Affx-122936793 AX-123302015 3 50144249 ACTTGGTCCCACTGCTCTTTATATTATCTCTCATT[A/G]TCTTACCCTAGAGTTGTATCACATTTCCACATACT R 2 1 2 1 101000 r 74 goat snp29578-scaffold321-339803 3 68002652 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765367 Affx-122971746 AX-385252880 3 50175356 AATGAATAAAACAGAACAGAGCACCCAAGAGTTGT[A/G]GGATAATATCAAACGATCTAACATACCAGGAAAAA R 2 1 2 1 101000 f 74 goat snp29577-scaffold321-308696 3 67970317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431062 Affx-122936639 AX-123301403 3 50207434 TACTTTATAATATCTAATTACATATACAATAGGCA[C/T]AATCTGGGACTATAGGAATGTGCAATTTTAATTGG Y 2 1 2 1 101000 r 74 goat snp29576-scaffold321-276618 3 67942376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764786 Affx-122940250 AX-385252397 3 50242134 AATGTGTGTACCATTCCCTACTAAGGCAGGAAACA[G/T]TCTAAAATGCTTCAGCCACAGAAGTTAAAAAAAAA K 2 1 2 1 101000 f 74 goat snp29575-scaffold321-241918 3 67907255 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429928 Affx-122938095 AX-123300269 3 50303632 AGACATGGTGGTGGTGTCAGAGAGAGTGCTTTGGC[A/G]TGTACTGGGAAATCCTATGGACAGAGGAGCCTGGT R 2 1 2 1 101000 f 74 goat snp29574-scaffold321-180420 3 67845229 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779609 Affx-122978349 AX-385266711 3 50345509 CCTCTCTCCAAGAAAATTCCACTCACTTTTACTCT[A/C]GTTGACATGTAAGATTTATAAAAGTTTAATATTTG M 2 1 2 1 101000 f 74 goat snp29573-scaffold321-138543 3 67802888 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393405 Affx-122965888 AX-123263761 3 50386489 TGCATATGAAAATATGCTCAATCTCATTAGCAACT[G/T]AGAAATAATAAGTAAAATGAAAATGAGGCACCACT K 2 1 2 1 101000 f 74 goat snp29572-scaffold321-97563 3 67761345 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772434 Affx-122932753 AX-385259586 3 50460296 ACTTTAACAAATTTAGTAACAAATTTCTCACTGCA[C/T]GCTCTGTTTGTGCTGTAGTAAATGCAGCTTGTTTG Y 2 1 2 1 101000 r 74 goat snp29570-scaffold321-23756 3 67687811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799499 Affx-122925622 AX-385286429 3 50508183 TTCTGAGTTAATAATTATTGATATCTAAGCTACTG[C/T]GTTAGTGCTTTACACAAAGCATTTAATACTGGCAA Y 2 1 2 1 101000 r 74 goat snp195-scaffold1004-24032 3 67640152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444026 Affx-122926885 AX-123314363 3 50542879 TTTAAGGTGCACTCGCAGTGTCTCCTAGACTGTCC[C/T]TAGGGGAAGGAACCCCAGCTGCCCATAGCAGCAAT Y 2 1 2 1 201000 f 74 goat snp196-scaffold1004-58728 3 67605292 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272209 Affx-1111833390 AX-189023032 3 50563539 AAAAACCCTGATGCTGGGAAAGATTGAGGGCAGGG[A/G]GGAAAAAGAGGTATAGAGGATGAGATGGTTGGATG R 2 1 2 1 303000 f 74 goat 3_50563539_AF-PAKI 3 50563539 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448195 Affx-122924240 AX-123318531 3 50576242 CACTTCGTGAACGTGCGATAGAGGAGCAATAGCGA[C/T]AGCCCTCCCCATAACTAGCTTGTGATCCAGGACAG Y 2 1 2 1 101000 f 74 goat snp197-scaffold1004-92091 3 67571921 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420842 Affx-122944654 AX-123291189 3 50608206 CGAGCAGTATGAGCTGGTGAGAGTTCTCATAGTGC[A/G]TCTACAAGCCACTTCTTCTGCAGGCCACCTCTGTC R 2 1 2 1 101000 r 74 goat snp198-scaffold1004-124055 3 67532270 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775851 Affx-122973064 AX-385262982 3 50700682 AAGGGTTGACACTGGAGATTGACACTTCTGCATCT[G/T]TCAGTAATTCTGAACAAGTTTTTCTTTAGCAGTGG K 2 1 2 1 101000 f 74 goat snp201-scaffold1004-216531 3 67439041 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408020 Affx-122954303 AX-123278371 3 50735223 AGCAGAGTGCCCAGAAAATGATGAACACACAATAA[C/T]ATTAGCTAATCTGATTATCACTGACTCTATGAGCA Y 2 1 2 1 101000 f 74 goat snp202-scaffold1004-251072 3 67403724 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427628 Affx-122939345 AX-123297971 3 50790553 TAGGTTTAAGGTTTACACAGCATCAACAATGAAAC[A/G]TAAGTACAACCAAAACTGTACTGCATTAAAATAAA R 2 1 2 1 101000 f 74 goat snp203-scaffold1004-306402 3 67348535 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376487 Affx-122978031 AX-123246846 3 50834433 AGCAACTGATGAGCAGGACTGATGAACAGGAACTT[C/T]AGTTCCTTAGCATTTCAGTCAGCACAGGTTACATT Y 2 1 2 1 101000 r 74 goat snp204-scaffold1004-350282 3 67304843 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277955 Affx-1111836177 AX-519551450 3 50895881 CGTTACCTCATCTAATTCTACCACACCCCAAGGTG[A/C]TTTCTATTATTATCTGTATTTTTCAAGTCAGTAAA M 2 1 2 1 103000 f 74 goat Random2.2K-326 3 50895881 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449447 Affx-122922669 AX-123319782 3 50956852 CAAGGCAGCGATTATGAACACATGGTCTGGAAAAG[C/T]GATCTGAGATCTAGTTCCAGTTTGCAAACTATAGA Y 2 1 2 1 101000 f 74 goat snp207-scaffold1004-472701 3 67181921 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437411 Affx-122932420 AX-123307749 3 50994987 CAAGGGGCTCAAGTTGGGCCCCATGGTCGGCTAGG[A/G]CTCCCCAGTATCTATTCGCCCTCCTTCTGCCCACC R 2 1 2 1 101000 f 74 goat snp208-scaffold1004-510836 3 67143823 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407356 Affx-122955277 AX-123277707 3 51038936 TGGCATTTTCCTGAGTGAACCTTTGGGAGCCCTTG[A/C]ATCCCTTCTGGGATCCTCTGGAAGCGCCTTTGTTG M 2 1 2 1 101000 f 74 goat snp209-scaffold1004-554785 3 67100127 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781194 Affx-122938490 AX-385268279 3 51088754 TGAATTTCAACCCCACAAAAAATATTCATTAAATA[A/G]GCAGAATCATATGGGAGAGTGAACAATGTTCAGCA R 2 1 2 1 303000 f 74 goat snp210-scaffold1004-604603 3 67050343 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440753 Affx-122929867 AX-123311090 3 51121146 TCCCTGCAGCAGTTCCGCTGTCACGCGTGGCACGG[C/T]GATCAAGTAAGACAGATGCAGAGTCTTCCTGCAGA Y 2 1 2 1 101000 r 74 goat snp211-scaffold1004-636995 3 67017922 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768322 Affx-122926195 AX-385255502 3 51159118 TCTTTTTAAATTCTTATGCTGAAAGTTAAGCTTCT[A/G]TCTCTTTTCAAAAGAGATATACAATCACTCTTTAG R 2 1 2 1 101000 f 74 goat snp212-scaffold1004-674967 3 66981540 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435033 Affx-122933758 AX-123305373 3 51194094 ATCTTGGGCTAAAACTGAGCTTCTCTCTGCTTCAT[C/T]ATCCTCCTCTGAGGATTTCATTCAATCATTTAACA Y 2 1 2 1 201000 r 74 goat snp213-scaffold1004-709943 3 66946532 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788254 Affx-122968871 AX-385275273 3 51231658 CTATAACTAGAACCTAGGTCCTCAGGATAAAATCT[C/T]AAGGCTCGTCCACACCAGACCACATTGTCTAGGCC Y 2 1 2 1 101000 r 74 goat snp214-scaffold1004-747507 3 66909070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439390 Affx-122930259 AX-123309727 3 51266129 AGAAAATGAGGCAATTCTATTGTCATGTCTAAAGA[C/T]ACTGCCTCGGGGTCTAATGAGCCCACCTGTAAACT Y 2 1 2 1 201000 f 74 goat snp215-scaffold1004-781978 3 66875699 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377474 Affx-122977507 AX-123247833 3 51312057 TAACACCTGCAATTCCAAATGGTGTGCCATGTGAA[C/T]ATCACAGAAATATTTGAAAGTGGTGATTTTCTTCA Y 2 1 2 1 101000 f 74 goat snp216-scaffold1004-827906 3 66829584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419526 Affx-122945437 AX-123289874 3 51343822 CTGTCTACGTTCTGGCCATTTTCAATTGCACTAGA[C/T]GGCTAGGGATTTGAAATCCAATGAAAGGAAATACT Y 2 1 2 1 101000 f 74 goat snp217-scaffold1004-859671 NW_017197361.1 8021 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388228 Affx-122969399 AX-123258586 3 51376938 TTCTCTCCTCATTTCAATTAACCTTTAGAGAACTT[A/G]CAGGGGCTTCTCAGGTGGCTCAAGGGTAAAGAATC R 2 1 2 1 103000 f 74 goat snp218-scaffold1004-892787 3 66762272 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789830 Affx-122935094 AX-385276837 3 51420321 TAATTTGTCTTAATAGTTGATTCTTCATGTCACCC[A/G]CTTTACCTCAATGCCATCTTATTGGCTACAGATTT R 2 1 2 1 201000 r 74 goat snp219-scaffold1004-936170 3 66718559 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452447 Affx-122920568 AX-123322780 3 51495741 CAGAAACTTAGACCATCTGGGGAGAAGTATGTCTA[C/T]AGGTTGAGGAAGTAAAATGACTTTTTTCTGCTTTA Y 2 1 2 1 101000 f 74 goat snp3256-scaffold1099-48913 3 66437903 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797448 Affx-122951718 AX-385284387 3 51531024 CCCATGCCTTCCTTTACAGAGTTCACCCTAATCTC[A/G]CTGGACAGTTGAGGTAGCTACCAGTTAATTTCTCT R 2 1 2 1 101000 f 74 goat snp3257-scaffold1099-84196 3 66402575 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795336 Affx-122977749 AX-385282294 3 51583255 TCTGTTCACTGTATGCCTCATGTGGGCAAGGTTGC[A/G]TTAGGGTTCATTTAAGGATCAATAAGATAACATAC R 2 1 2 1 101000 f 74 goat snp3258-scaffold1099-136427 3 66349662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804118 Affx-986696680 AX-385290772 3 51635295 GTGTTTGAGGAAAAGAGGGGTCAGAGAGCTTTAGT[A/G]GCCTGAAAGTAAAGATTCTCAAGATTTCTGCTTCA R 2 1 2 1 600010 f 74 goat 3_51635295 3 51635295 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 320804514 Affx-986696682 AX-385291064 3 51635408 GGAATGAAAAGAGAAACAGCCAGCCAGCAACCAGA[C/T]ACTCTGTCATCATTTGTACAAACTACAAGACCATA Y 2 1 2 1 600010 r 74 goat 3_51635408 3 51635408 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 38439077 Affx-122931136 AX-123309414 3 51636958 CCATACAACTGGTCTTTCTACACAAATGTTTCTCC[A/G]TCCTTTTTTTTCTTCTAGTCACCACTTTCCAACCA R 2 1 2 1 101000 f 74 goat snp56514-scaffold890-747830 3 66250196 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804522 Affx-986696690 AX-385291071 3 51667998 TGAAACTATTGCAACATTTTTAATCAGCTATACAC[C/T]GAAATAAAATACAAAGCTTTCTTTAAGAAGTAATA Y 2 1 2 1 600010 r 74 goat 3_51667998 3 51667998 Ancestral_priority_1043 ancestry 0.69 recommended IMAGE 10K 10K ancestral 38405571 Affx-122955948 AX-123275923 3 51703790 TGAAAACACCAAGCAGTTTCATAGTCCAGTAACTG[C/T]CCCTCTTCCTCAGGGGGAAAAAAGCTATCACAGAA Y 2 1 2 1 202000 f 74 goat snp56512-scaffold890-680998 3 66182410 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801736 Affx-122958321 AX-385288644 3 51787233 CCCAGATAGGTCTTTTTAGAGTTTTGAGATACTCT[A/C]GAAATTATCTAGATTTAGAATGATCTAGAAAAGTT M 2 1 2 1 101000 f 74 goat snp56510-scaffold890-597555 3 66098310 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793457 Affx-122972106 AX-385280434 3 51843536 GCCCAGAATTACCAAACTAGCTAAAGAACTCTTCA[A/G]TCTAGTATTTTTTTATCCACGTGTTCAATAATTAC R 2 1 2 1 101000 f 74 goat snp56509-scaffold890-541252 3 66041968 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454241 Affx-122919661 AX-123324574 3 51928836 TTCATTTTAGAGGAGACCTAGAAAATATGGTATTG[C/T]AATTGATGTTTGGAGGTCACTCCTGATAAAACAGT Y 2 1 2 1 101000 r 74 goat snp56507-scaffold890-455952 3 65956182 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796636 Affx-122937217 AX-385283582 3 51964957 TTTTTAAATATTCCTAATGTCATGAAGACTGCTAT[A/G]ATTCTTAAACTGACTTCTATCATAAAACAATCATT R 2 1 2 1 101000 f 74 goat snp56506-scaffold890-419831 3 65919195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416042 Affx-122948359 AX-123286391 3 52025863 CATCTCTTCCAGCTGTGTTCACTTTCAACAATGAT[A/G]TCACCCCAATCCCTTGAGGCACTCAGATTAGAAAT R 2 1 2 1 201000 r 74 goat snp56505-scaffold890-358925 3 65857679 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804142 Affx-986696692 AX-385290791 3 52027301 TGTGACTTAGGACTAATTCCATGATAAGAAAAATA[A/C]TAGTAGCAGCAACTACTGAGTTCCTCTTTTGCTGG M 2 1 2 1 600010 f 74 goat 3_52027301 3 52027301 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320804526 Affx-986696694 AX-385291075 3 52029406 TAAGGATGGATAGGATGAAGGGAGGAAACCGATCA[G/T]CTCATTCTACTACTAAAAATCCTTGCGATGGGCTT K 2 1 2 1 600010 r 74 goat 3_52029406 3 52029406 Ancestral_priority_1043 ancestry 0.692 recommended IMAGE 10K 10K ancestral 38438734 Affx-122930835 AX-123309071 3 52059258 CCTCACCACCTTACCTCTACAGACGACTCTCAGCT[A/G]GTTGGCTCCACCCTCCTGCTCCCTTCATTTGTCAC R 2 1 2 1 201000 f 74 goat snp56504-scaffold890-325530 3 65824345 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453673 Affx-122919712 AX-123324006 3 52124148 ACATGTCAGCAATGCAGGTGAATTTGGAAGAATTC[A/G]CACAGCAGTATTTCTGTCACACTCTAGACATTTAA R 2 1 2 1 101000 r 74 goat snp56503-scaffold890-260640 3 65757557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776318 Affx-122941984 AX-385263446 3 52166853 AAACTTCATTGTTTTGAGCCTGTCTCATGAGCTAA[A/C]CATAACCTTTGACAACATTTCAGTGATACAATGCT M 2 1 2 1 101000 f 74 goat snp56502-scaffold890-217935 3 65714961 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413854 Affx-122949866 AX-123284203 3 52203529 GTAGATTAGAGTTCTCTAAGCCATAAAAGAGCAGG[C/T]GGAGGAGGGCTGAGAGGAGCTACTCCATGCGCAAG Y 2 1 2 1 101000 f 74 goat snp56501-scaffold890-181259 3 65677585 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778954 Affx-122920503 AX-385266061 3 52263791 ATTGCTCCACTGTAAAACCCAAGGCAGAATTAAGC[A/G]TAAAATCAACACATCTGTTGAGTACCTGCAGTGTC R 2 1 2 1 101000 r 74 goat snp56500-scaffold890-120997 3 65617004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781200 Affx-122955594 AX-385268285 3 52358141 TTAAAATTAAATTAGGGAAATTTTATAATTTCATA[C/T]GATTACTCAAGCCCCAAGCCTACCAGTATCAAGTA Y 2 1 2 1 202000 f 74 goat snp56498-scaffold890-26647 3 65522396 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409269 Affx-122953124 AX-123279620 3 52391932 CTGTGGGAATGCAAAGCCCAGCCCATCAATGGCAG[C/T]AGGAATGGCCACTCAAAAGAGGGGAGTTTAAGTTG Y 2 1 2 1 101000 r 74 goat snp1694-scaffold1047-2361794 3 65488387 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385016 Affx-122971869 AX-123255374 3 52421122 GAAACCATAGCCACGTAAGAGTTTTAAGCCCTTCA[C/T]ATATCATTCCGTCACTCCAAGAAGGAAAATATAAG Y 2 1 2 1 101000 f 74 goat snp1693-scaffold1047-2332604 3 65465811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401751 Affx-122959508 AX-123272104 3 52453435 CATTTTCTGCATAGCAGTCCCCATCTTCCTTCTTC[A/G]TTTTGACTACTGCAAACTTATAGTGCCTTTTATTC R 2 1 2 1 201000 r 74 goat snp1692-scaffold1047-2300291 3 65433264 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443305 Affx-122927460 AX-123313642 3 52483983 AGAAGGATTCATGTCTCCATTCTCTGTACCCCTGT[A/G]AAACTAGAATTGTTGAATCATTCTGCTCCATTGGC R 2 1 2 1 201000 r 74 goat snp1691-scaffold1047-2269743 3 65402815 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790494 Affx-122921963 AX-385277497 3 52527335 TCTGGTCCAGGAATAAGAAGGTTTTTTGAGCAGCC[A/G]CAACACCCTCTTTGCTTGCAACTTCTGATCTGTGG R 2 1 2 1 101000 r 74 goat snp1690-scaffold1047-2226391 3 65358878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802530 Affx-122964727 AX-385289434 3 52584704 CTTTTTAATTAGGAGTAAAAGCTAGCAAGTAACTT[A/G]TCAATCCTATTGGAAATCTCACACAAACTTGAGGA R 2 1 2 1 101000 r 74 goat snp1689-scaffold1047-2169022 3 65301469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413917 Affx-122949821 AX-123284266 3 52614961 CTCTACAGATGTAAACAAGGAACACATGTTGAACC[A/G]CATCATTTTGATGCCTCTGGTAGATACATATGGTT R 2 1 2 1 101000 f 74 goat snp1688-scaffold1047-2138765 3 65271258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431451 Affx-122936498 AX-123301792 3 52693621 TCCTTCCACAGGCACCCCTCACCCTGCAAGACAGC[C/T]CTTCCGGACACTGTTATTCATCAGGACAGAAAAGC Y 2 1 2 1 101000 r 74 goat snp1686-scaffold1047-2060105 3 65192724 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768308 Affx-122977243 AX-385255488 3 52733890 GCACTTTTACTCTTCCCCGTGAATTTGAAGAATTC[A/G]TTTCTTGTGTCCTATAGTCCATTATTTTGCCTGTA R 2 1 2 1 202000 f 74 goat snp1685-scaffold1047-2019836 3 65152096 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401257 Affx-122959294 AX-123271610 3 52790898 TAAACCTATTATGACCAAACACTTCAGCAGGCTTT[A/G]AGCAGAAGGTGCTTTCATTTGCTTCCAGAGCACAT R 2 1 2 1 201000 f 74 goat snp1684-scaffold1047-1962828 3 65094698 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421637 Affx-122944460 AX-123291984 3 52825309 TATTACAGACACTGCTTCTCCTCATTCCTGAAAAC[A/G]GGGGGTTGGAGGAGGTAATTCCTTGAGAACAGGAA R 2 1 2 1 101000 f 74 goat snp1683-scaffold1047-1928417 3 65060270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394298 Affx-122964698 AX-123264653 3 52868133 TTATTTTCCTGTACAAAGTTTTGTGCATACTGCTT[A/G]TTCCTTGACCTTACATTCATCTTCTTCTCTAAGAA R 2 1 2 1 101000 r 74 goat snp1682-scaffold1047-1885593 3 65016428 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382376 Affx-122973856 AX-123252734 3 52899763 CATTTTTCAAGGGAGAGCCATACATTTCAAATACC[A/G]TAGATCTGCAAACATTTTCAATGAAATCAAATGAA R 2 1 2 1 101000 f 74 goat snp1681-scaffold1047-1853963 3 64984832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418235 Affx-122947039 AX-123288583 3 52966912 TCTTGTTGGCCTGCATGATATCTTTTGGCTTACCA[G/T]AACAAGTACAAAGGCAAGACAGAAAAAATTTTCCT K 2 1 2 1 101000 f 74 goat snp1680-scaffold1047-1786814 3 64917528 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409964 Affx-122954108 AX-32597095 3 53025113 CTGTGTAATTTTAATTTATCATTAAGTAACACTTC[A/G]CTTTTTAACATAAAGAATTCAGTGTGCTTGATGGA R 2 1 2 1 101000 r 74 goat snp1679-scaffold1047-1728613 3 64858534 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380085 Affx-122975545 AX-123250443 3 53064066 TGTTGTGATAAAACAACCAGCTACACAAAGCAGCC[A/G]CTGGATCTGTGACTTAACACATTTATTTCATTACC R 2 1 2 1 101000 f 74 goat snp1678-scaffold1047-1689660 3 64818942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783127 Affx-122951950 AX-385270194 3 53098362 AACTGAAGGCTCTGGAGTTAAATAATCAGTATAAA[G/T]CCTTGCTTAGAGGCAAAATAATATCTTCTTGATAT K 2 1 2 1 101000 r 74 goat snp1677-scaffold1047-1655364 3 64784122 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392541 Affx-122966098 AX-123262898 3 53139823 AGCTTGCCATTGATTAAGTGGCTTTATTTCTACAA[C/T]AGCAGAGGGTTGGCTCAGATGAGAAGTGGGTAGGC Y 2 1 2 1 101000 f 74 goat snp1676-scaffold1047-1613903 3 64742195 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437774 Affx-122931704 AX-123308112 3 53245194 GGCCATGACAGAGGAGGGTGTGGAAGGTGATGGAA[G/T]AGGGCTGGAACCTGGAAAACAAATTCTACAACTTG K 2 1 2 1 101000 r 74 goat snp1674-scaffold1047-1508532 3 64636477 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435221 Affx-122933623 AX-123305561 3 53366887 CTGGGTCTAAAACTGCAAAAGACCCCAGTGCAATA[C/T]GGAGCTGAGTAGTATGGCTATGTTTAGCGCAGGGA Y 2 1 2 1 201000 r 74 goat snp1672-scaffold1047-1386839 3 64515050 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402947 Affx-122958173 AX-123273300 3 53412936 AAGAGAGGGAAGACTTGTTGCAGAAATTGGGATTA[C/T]GGATAGGTCTTCTCTTTTTGAGAGTTTGAATTTTA Y 2 1 2 1 101000 f 74 goat snp1671-scaffold1047-1340790 3 64468830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390281 Affx-122967735 AX-123260638 3 53441834 CAAGTCACTGGTAGAACCTGGGAGCCTACAGTCTT[A/C]GAATCTAACTGGACTGAATCCAATTGAGTTAGGAG M 2 1 2 1 201000 r 74 goat snp1670-scaffold1047-1311892 3 64440013 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417638 Affx-122946851 AX-123287986 3 53472177 GTGATCCATTCTGTCGGCATAAAACTCAGGCACCC[A/G]CAGAGAACTGACCAGGTGGAGGAAACAACCTATGA R 2 1 2 1 101000 f 74 goat snp1669-scaffold1047-1281549 3 64409786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801975 Affx-122951553 AX-385288879 3 53514860 AGTAAGAAACAAAATCCTTAGGATTTTTTAACTGG[C/T]ATTTCAAGTTCTTGTGAGGATTTTATTTCCACTTA Y 2 1 2 1 101000 f 74 goat snp1668-scaffold1047-1238866 3 64366556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272213 Affx-1111833392 AX-519545960 3 53543437 CAGGCTACAGTCCGCAGAGTCACAGAGTCGGACAC[A/G]ACTGAGTGACTTTCAGTTTCACTACTCTTAGGTGA R 2 1 2 1 303000 f 74 goat 3_53543437_AF-PAKI 3 53543437 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320776029 Affx-122948947 AX-385263159 3 53601620 CTTTTCCTCTTATCAAGATCCACAGTTGGTTCCAC[A/G]TTAAGCCGTGGCACACTCGATGGTAAAAGGATTTG R 2 1 2 1 101000 f 74 goat snp1667-scaffold1047-1152106 3 64279781 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424929 Affx-122941288 AX-123295275 3 53671081 GGAGCTTTTTAAAAATATTTATTCCTAGTACTTTC[C/T]CAGACATGCAGAAGCTATTATGCCCTGGATTCTAT Y 2 1 2 1 101000 r 74 goat snp1666-scaffold1047-1082645 3 64209744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399996 Affx-122960809 AX-123270351 3 53703095 GTTGGTACAGTGAAGCTTTCCTCTTACCCATTTTG[A/C]TGCAGTTGTTCTTGGCTTTGTGCTGCCTGGGGTAC M 2 1 2 1 101000 f 74 goat snp1665-scaffold1047-1050631 3 64177620 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400542 Affx-122960437 AX-123270897 3 53753070 CCCCAGACTCTCACTATTTAAAGTTCTGGTTCTCA[A/G]CCTTGGTTCCACCTAGGATTACCTGAGAAATTGAC R 2 1 2 1 101000 f 74 goat snp1664-scaffold1047-1000656 3 64127518 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404586 Affx-122957359 AX-123274938 3 53787794 GCAAGCAAAACAGTAGAGAAGGAAATTTTAAGGGA[C/T]GTTGATGCCAGTAGTAACTGTAATCATTGTGTGTG Y 2 1 2 1 101000 r 74 goat snp1663-scaffold1047-965932 3 64092456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774010 Affx-122972825 AX-385261148 3 53819460 TACAAATTGTGGTAAATTTTCAATGCCTTATCATC[A/G]TAAGAATCTTTGGCAACACATACATTCACATACAA R 2 1 2 1 101000 r 74 goat snp1662-scaffold1047-934266 3 64060676 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432538 Affx-122935551 AX-123302879 3 53848513 CATGAAAATTACTGTATCAGACTGTGCATCATTTC[A/C]AGAACTTTCTCAAGAAAATGCTGTTATTTTTAAAA M 2 1 2 1 101000 f 74 goat snp1661-scaffold1047-905213 3 64031606 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438653 Affx-122930895 AX-123308990 3 53901807 TTGAGCATTTACCAAGTATCTGACGCTGCTCCAAG[C/T]GCATTATTTCATTTGACCTTCTCAGCACATTTAGA Y 2 1 2 1 101000 f 74 goat snp1660-scaffold1047-851919 3 63977951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790515 Affx-122973647 AX-385277518 3 53933320 GAGCTTGATTTGAGGAAATTTTTGAGATGTTAAGC[A/G]TATTTAATTTTTTAGCAAGAGAGAAATTAGTAAAA R 2 1 2 1 201000 r 74 goat snp1659-scaffold1047-820406 3 63946406 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396523 Affx-122962957 AX-123266878 3 53967993 TGAAACAGGCCTACTAGTGAATCATCACAAATGAC[A/G]CCTTAGAAGCAGGCTTCCTCTAGTTAAACACACAG R 2 1 2 1 101000 f 74 goat snp1658-scaffold1047-785733 3 63911346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777387 Affx-122956824 AX-385264509 3 54018966 TTATATATACCAATAGAAGTAACGAAAATTACTAA[G/T]ACAGTTAACTAACAGTCATTTTATCCAGTCCTGGG K 2 1 2 1 101000 r 74 goat snp1657-scaffold1047-734760 3 63860330 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793686 Affx-122927649 AX-385280658 3 54056151 TTTCCCTTTAAGGTGGTAAAATGAAAGCAATATGC[A/G]TATCAACAGACAATATCTCAGAGGCTTTTAGTGCT R 2 1 2 1 101000 f 74 goat snp1656-scaffold1047-697575 3 63823048 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412054 Affx-122951713 AX-123282404 3 54137042 CGAACAGCAACAGGAGATGCATTTGTGGTTTCCAA[C/T]GTTCCACAGTCTCCCTCATTACTTGACCTCTTCCC Y 2 1 2 1 101000 f 74 goat snp1654-scaffold1047-616684 3 63740963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382111 Affx-122974886 AX-123252469 3 54191488 ATTAATCTGACTTGGACAGCTCCTGGGGATGATTA[C/T]GATCATGGAAGAGGTAAGCTGAATGTGGTATGGAC Y 2 1 2 1 101000 r 74 goat snp1653-scaffold1047-562238 3 63685964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420139 Affx-122946002 AX-123290487 3 54252378 AGCTATCTGGGAGATTGTAATTTGTTGTTTTGGCT[A/G]TTCTTTTCTTTGATGTCACAGGTAATATTCAGATG R 2 1 2 1 201000 r 74 goat snp1652-scaffold1047-501348 3 63624055 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443377 Affx-122927406 AX-123313714 3 54288410 GGGTCTTTACCTGAAGATTCCATGAAAAAAAAGAG[A/G]GGCCTTCTGGGATCAGCCTGAACTGTAGATTTAGA R 2 1 2 1 201000 f 74 goat snp1651-scaffold1047-465316 3 63588184 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394261 Affx-122964723 AX-123264616 3 54317038 TCCGGAAGCAGGCGAACTCCTAGAACGGCCTGAGT[A/G]GAAGAATGCCCAACGGGGAGCAAGCGGGACAAAAC R 2 1 2 1 201000 f 74 goat snp1650-scaffold1047-436688 3 63559551 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436931 Affx-122933189 AX-123307269 3 54357932 ATAGAACAGTAAATCCTCGTGAAGTTTAAAATCTA[A/G]TAAGACAAATATGAAACATATAATTATGCAATTAA R 2 1 2 1 101000 f 74 goat snp1649-scaffold1047-395794 3 63518445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436323 Affx-122933255 AX-123306662 3 54435846 ACAGAACTGTAAGAGGAGATATATTTGGGATATTT[A/C]TGGAAAATATGTTTGGAGGAGGTGGTCTGAGCAAA M 2 1 2 1 201000 f 74 goat snp1648-scaffold1047-317880 3 63440470 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788715 Affx-122924669 AX-385275731 3 54482822 CCCAATAATGACAGACTAGATAACTTGATAATAAC[C/T]GGGAGATTGGACAAAATATACTTTAACTATGTCAC Y 2 1 2 1 101000 r 74 goat snp1647-scaffold1047-270904 3 63393166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447956 Affx-122923773 AX-123318292 3 54538215 ATAGTTTAGAAAGGGGATATCTATTTCTGCCAAAG[C/T]AAAAATTTAATATAAGCTGCATCAAAGTCTAAAGA Y 2 1 2 1 101000 f 74 goat snp1646-scaffold1047-215511 3 63337398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376452 Affx-122978056 AX-123246811 3 54572015 TACCCACTTTCTACTGTTCTGTATAATCTCAGCCA[A/G]ATCGTCTTGCCAGAATTAAGACTCAAAGATAGTGC R 2 1 2 1 101000 f 74 goat snp1645-scaffold1047-181711 3 63303493 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787844 Affx-122958843 AX-385274867 3 54623942 GTGAACTCAGTTCCATTACAGCAATGAAATTCTTA[C/T]AACTCTAGATTAAACTTGATAATTTGTTAGTATAA Y 2 1 2 1 101000 f 74 goat snp1644-scaffold1047-129784 3 63251315 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424974 Affx-122941916 AX-123295320 3 54668385 AAAAAGGAAGACGTAAGAACTACATTATCTCAGTA[C/T]GCAAAAGCATGAGTACACAAATGTTGACTAATATG Y 2 1 2 1 101000 f 74 goat snp1643-scaffold1047-85341 3 63206935 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419426 Affx-122945514 AX-123289774 3 54717382 TAAGCTAATAATTATACTTTGCTTATATTTTGTCA[C/T]AGATAGTTATTTTAGTGTTTTCTTCTGACATGGAA Y 2 1 2 1 101000 r 74 goat snp1642-scaffold1047-36344 3 63157987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405295 Affx-122956848 AX-123275647 3 54769413 AGAAAAGGAAACCATATTTTTACTCTGAGGGTCCA[C/T]AGATTAAAAATATGGATAAATTGTGTGCATTTTCA Y 2 1 2 1 201000 r 74 goat snp18857-scaffold190-14530 3 63102011 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792568 Affx-122930653 AX-385279549 3 54805353 TAATTATAAGAATGAGTATTTTGCTGTGAAGATAA[C/T]TTATAGTGCCTTCCTGGTTTCATAAAGTCAAATTT Y 2 1 2 1 101000 r 74 goat snp18858-scaffold190-50470 3 63065761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391484 Affx-122966713 AX-123261841 3 54839132 ACCAAAATTACAAAAAAACAAAGAAAAACAGATAT[A/C]TTGGACTGCATTAAAGTGAAAAGTTTTAGAACTTC M 2 1 2 1 101000 r 74 goat snp18859-scaffold190-84249 3 63031029 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383631 Affx-122972541 AX-123253989 3 54873629 TATATTAATCTGTTTTTCTTTTCTTAAATAAATCC[A/G]TCCTAGTTGTTTATTCATATGAACCGTGGCGCTGT R 2 1 2 1 101000 r 74 goat snp18860-scaffold190-118746 3 62996559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794970 Affx-122940944 AX-385281930 3 54938851 TACTAAATATATGTTACTGAAACACAGCCACGCTC[A/G]TTCATCTCTTTATTATCTAGGGCTGTTATCACACT R 2 1 2 1 101000 f 74 goat snp18861-scaffold190-183968 3 62931252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379212 Affx-122976287 AX-123249571 3 54997863 TTAAGGCATTGACTGACATTATCAGACTTGTGTTT[A/C]GCAAAGATGCTCAAGCAGCAGTCTGGAAAGTACAC M 2 1 2 1 201000 f 74 goat snp18862-scaffold190-242980 3 62870831 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434044 Affx-122934203 AX-123304385 3 55034533 CAGCAAAGCGCCAGCTGCCAAAGTGAGGAGGACAG[C/T]GCACCATGATGCCTTGTGCAGGGATGGTGGACAGA Y 2 1 2 1 201000 r 74 goat snp18863-scaffold190-279650 3 62834856 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785683 Affx-122961512 AX-385272724 3 55070625 TTACTTCACTGGTCTATTATCGAACTACAAATGTC[A/G]TGCTTTAGGGTGCCTAAGTTGCTGAGAATATTCTG R 2 1 2 1 101000 r 74 goat snp18864-scaffold190-315742 3 62798549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804150 Affx-986696696 AX-385290799 3 55101554 TAGAAGCTGAAGAGGGACAGGGAACTTCTGGTGAA[A/G]CAGAGAAAGCAAAAAACTCCGCACAGGGGACCAAA R 2 1 2 1 600010 f 74 goat 3_55101554 3 55101554 Ancestral_priority_1043 ancestry 0.624 recommended IMAGE 10K 10K ancestral 38438220 Affx-122931446 AX-123308558 3 55134783 GGATCATCCACCAAATCAAAAAAAGATGATTTTTC[A/G]TGCATGTATTGCAGGGCCAGAGTGAATCAGAGGCT R 2 1 2 1 101000 r 74 goat snp18865-scaffold190-379900 3 62734234 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788623 Affx-122944507 AX-385275640 3 55187906 TCTTTCCAAAGGAAAGAAGTAGGGTGTATATGTGG[A/G]AGGATCAGTTATCTCCTCTTCTCGTTGTTAAGATT R 2 1 2 1 101000 f 74 goat snp18866-scaffold190-433023 3 62680684 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803536 Affx-986696101 AX-385290344 3 55218052 AAACATTAACTCAAAATGAGTTACAAAATTAATTG[C/T]TAGAGCTAAAATTATTAAATTTCTAGAAGAAAGCT Y 2 1 2 1 600010 r 74 goat 3_55218052 3 55218052 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 320804154 Affx-986696698 AX-385290803 3 55218106 ATTTCTAGAAGAAAGCTTTAAGACAAAATCTTTAT[G/T]ACATTGAGAAAGGCAGATTTCTTAATAGACTCTAA K 2 1 2 1 600010 f 74 goat 3_55218106 3 55218106 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 320804532 Affx-986696700 AX-385291081 3 55218115 AGAAAGCTTTAAGACAAAATCTTTATGACATTGAG[A/C]AAGGCAGATTTCTTAATAGACTCTAAAAGCCACAT M 2 1 2 1 600010 r 74 goat 3_55218115 3 55218115 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 320796055 Affx-122959175 AX-385283007 3 55246127 AAAGTGGAATGTAAATATGATGGAATATCATTGTT[A/G]TCCTATCTTTCTCCTTCACTCCACAACCATCTAAA R 2 1 2 1 101000 f 74 goat snp18867-scaffold190-491244 3 62621929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426383 Affx-122940237 AX-123296729 3 55281270 AAGTGGCAGGGTCGCACTAATCTCTACATATCATC[A/G]TAACACATGAGAAACTTGTTATTCACAGTCAGTAC R 2 1 2 1 101000 f 74 goat snp18868-scaffold190-526387 3 62588904 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776989 Affx-122941516 AX-385264113 3 55310446 AATAACAAACAAGGGTTAATTCCATCTATTCACCC[A/G]CAGACTTTTTCAGTCCTCCCAGAGCTAATTCGAAG R 2 1 2 1 101000 f 74 goat snp18869-scaffold190-555563 3 62559500 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796803 Affx-122936063 AX-385283746 3 55346089 TTATTTTTTAAAAAGATTACCCAGACTTTCTCACC[A/G]CTGCTGTCCTAAGGGTCAGTACATTGCACAACTCC R 2 1 2 1 101000 r 74 goat snp18870-scaffold190-591206 3 62523564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277957 Affx-1111836178 AX-519551452 3 55364970 ATCACAGGAGTTAAAGTGAAGTACAAGAAAAAGTC[A/G]CTGGAGTTAAAAAGATCAAAGCACTGAGAATCCAG R 2 1 2 1 101000 f 74 goat Random2.2K-329 3 55364970 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778242 Affx-122948478 AX-385265357 3 55397572 ATAGTTTTGCATTGCGTGACAGTATATCCAGTCTG[C/T]ATTTGAAAGATTCTTAATTTAAGATCTGTCATTTA Y 2 1 2 1 101000 f 74 goat snp18871-scaffold190-642689 3 62472223 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403309 Affx-122957836 AX-123273662 3 55429401 TGTTCCAGAAAAGAAACAAAAAAGAATGCTCTTTC[A/G]TGTGCACAGACTCTCCTCTAACCCCAAGCAACTCT R 2 1 2 1 303000 r 74 goat snp18872-scaffold190-674518 3 62440182 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798271 Affx-122925474 AX-385285206 3 55489082 TAGTTAAGACTGGGATATTGATAACCACTAAAGAA[C/T]AAAAGAGTGTTGTGTTATTCAAGATTTGTGCCAGT Y 2 1 2 1 101000 f 74 goat snp18873-scaffold190-734199 3 62382357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786727 Affx-122967494 AX-385273758 3 55535965 GGCTCCCTGGCGGTGGAAAATAGTTAACTATTCAA[C/T]GTTAAACAATGACTTATTTACCTTTTCTTTTTTTA Y 2 1 2 1 201000 r 74 goat snp18874-scaffold190-781082 3 62334677 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442099 Affx-122928357 AX-123312436 3 55576900 GATGAATACAGTCCAATGTACAGCATTGCAAATAC[G/T]CTTCCAAAGCCCTGAGTGATGAAAATGGCAATTTG K 2 1 2 1 101000 f 74 goat snp18875-scaffold190-822017 3 62293567 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417237 Affx-122947283 AX-123287585 3 55616220 AGGCAACATTTATTAATCACTAACGACATGCCAGA[C/T]GTTTTACATCTGTTTACACTGTCTTTGTAGGAGGT Y 2 1 2 1 101000 f 74 goat snp18876-scaffold190-861337 3 62253788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443482 Affx-122927814 AX-123313819 3 55644829 GAAGCAGACTCAGAAGTGAAGATTAAGTTTAAGGC[A/G]GAGATCTGAGCCCCAACAGCTGTCCCCTTCAGGCG R 2 1 2 1 101000 f 74 goat snp18877-scaffold190-889946 3 62224561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419740 Affx-122945889 AX-123290088 3 55678084 CCACCATCCCCCACACAGTCATCTTTACTCATTAC[G/T]ACCTCCTGCTGGTGATCCTTGGAATTGACGGAATT K 2 1 2 1 101000 r 74 goat snp18878-scaffold190-923201 3 62191819 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432701 Affx-122936028 AX-123303042 3 55711868 GGAATAAGACAAGGCCCTTACTTTCAAAGAGCTAA[C/T]GTTCCTCTGTTTACCTTCTTCATGCCATCTACTAA Y 2 1 2 1 101000 f 74 goat snp18879-scaffold190-956985 3 62157608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785453 Affx-122945455 AX-385272498 3 55778331 ACCTTCACAGGTTCCTTGGGGGTTTATGATCCTAG[C/T]AAGGTTAAGAATTGCTGATAATTTGTTCTGTGTTG Y 2 1 2 1 101000 f 74 goat snp18881-scaffold190-1023448 3 62091951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769827 Affx-122935286 AX-385256997 3 55795268 GCACGAGAACCTTTGTTTTATACGGATGTCCCTCT[A/G]TTATATTACCAAGACACCTTAGAATCGAGTTACAG R 2 1 2 1 101000 f 74 goat snp52103-scaffold770-397235 3 62074627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798676 Affx-122950530 AX-385285608 3 55847679 GCAAAAGAATGCTGTAATATGACCCTAACATTCTT[A/C]TCTCCAGGATTGATTGTTTCAACTGGATTTCGTAG M 2 1 2 1 101000 r 74 goat snp52102-scaffold770-344824 3 62022192 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438780 Affx-122931378 AX-123309117 3 55883071 TTCTAGTCAACTCCTGTTAATCCTTCAGATCCCGG[C/T]GTAAATGTCCCTTGCTCCAGGACCCTGGTCCTTGA Y 2 1 2 1 201000 r 74 goat snp52101-scaffold770-309432 3 61986484 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376731 Affx-122978957 AX-123247090 3 55911849 CCCATGAGACCCTAGGAAATTCTCAGGGGCTCCTC[C/T]GTCATTTGTCAATACCCACCACTGTACTTGTAAAT Y 2 1 2 1 101000 r 74 goat snp52100-scaffold770-280654 3 61957865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415635 Affx-122948582 AX-123285984 3 55957733 AGTGCTGAGCTCTGGGCAGTCCAAGGTGGGAAGGC[A/G]TGTAATTCTGGGGCCACATCTCTGCCAATCCAGCC R 2 1 2 1 101000 r 74 goat snp52099-scaffold770-234770 3 61911997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775500 Affx-122927546 AX-385262631 3 55992256 ATCTGCATATGGCCCATAGATTCTAGGAGACTACC[A/G]CGTGTATTATCAACAGCTCTGGTTAAATAATGAGA R 2 1 2 1 101000 f 74 goat snp52098-scaffold770-200247 3 61877694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782443 Affx-122964031 AX-385269519 3 56020799 CTTCTGTTGGATGATGCTGAGTCATGGACAATAGA[C/T]GCTTTGAGTATGAAAGGTCTGGTCATAAAAGACAA Y 2 1 2 1 101000 r 74 goat snp52097-scaffold770-171704 3 61848551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795256 Affx-122953034 AX-385282214 3 56070409 TCAACTTTCATCAACTACACACCCTACACCCTACT[A/C]TATTGTAGGAGAGGAAGGAATATACAATTTGTGAG M 2 1 2 1 201000 r 74 goat snp52096-scaffold770-122094 3 61798436 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444398 Affx-122926589 AX-123314735 3 56115506 TCTTCAGGTTATGACCCCAGAGTCCAGATGACTAC[A/G]TCTCTCATGTCCACTCCACTGACGTCTTCTAACTG R 2 1 2 1 201000 r 74 goat snp52095-scaffold770-76997 3 61753408 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774058 Affx-122972403 AX-385261196 3 56191330 GATCAAAAGGTAATGGCAATGGATGAAGAAAATAT[A/C]TCCTTTTCTAGGTCTTACAGAATTGAGTCTAAGAG M 2 1 2 1 101000 f 74 goat snp52094-scaffold770-1173 3 61677119 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790064 Affx-122924521 AX-385277070 3 56203225 TGTTTATTGCTGTATCCTCAGCATTTAAAACAGTG[C/T]TGAGAACTGAGGTGCATAGTAGGCTCAATCAAAAT Y 2 1 2 1 101000 f 74 goat snp42040-scaffold55-10623 3 61665777 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272215 Affx-1111833393 AX-519545962 3 56226061 AGTTCTTGCAATCTAACAACAAATACTCAGCCGCT[A/C]TACTAACCACTTCTATCAGAGCATGCGCATTTTCA M 2 1 2 1 101000 f 74 goat 3_56226061_AF-PAKI 3 56226061 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38417393 Affx-122947691 AX-123287741 3 56259446 TTTTCTGTGGTTATACTATAACTTAAATTATACTT[C/T]ATCAAATATTGAGGTTTCCAAATTTGAGGCTACAC Y 2 1 2 1 303000 f 74 goat snp42041-scaffold55-66844 3 61608140 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429255 Affx-122937900 AX-123299597 3 56299752 TCCAGGGTGTCCACCAGATGGTTGTATTAAGCTTT[A/G]CAGCTCACCACAGAGATTGTGAGCAGAGCCAGCCC R 2 1 2 1 101000 f 74 goat snp42042-scaffold55-107150 3 61567864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396352 Affx-122963052 AX-123266707 3 56334953 GAATAGGAAGGATGACAGTAGGTGACCTGTAATGA[A/G]TGGGTGGGAGAGCAGTGGGACAGTGGCTCGAGAGA R 2 1 2 1 101000 f 74 goat snp42043-scaffold55-142351 3 61532420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429085 Affx-122938275 AX-123299427 3 56385438 TTTGCGTTCTGCCTAAACCATGGCAGTAGTGAACC[A/G]TCTTGGAGAATGTAAGATGTTTTATACTGCATGAA R 2 1 2 1 101000 f 74 goat snp42044-scaffold55-192836 3 61481872 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424015 Affx-122942094 AX-123294361 3 56436121 CAACCAATCCAGGTTCTCTGATTCCTATACCTGGT[G/T]CAGTGGGGATGAGGGTGGGGGTGGGAATCAAGAAA K 2 1 2 1 101000 f 74 goat snp42045-scaffold55-243519 3 61433065 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429947 Affx-122938080 AX-123300288 3 56472522 CTGCTCAGGGTACTGTTGGAAGCAGTTGGTCTAAC[A/C]GACACATTAAAAAAAGCATCTCCTTCTTTCACTCT M 2 1 2 1 101000 f 74 goat snp42046-scaffold55-279920 3 61396736 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417618 Affx-122946866 AX-123287966 3 56508577 GTGTAACAAATTCCATAAAGATGTAAAAAATGGTC[C/T]ATATCCAAAAATAATGTTTAAAAACCACCCTAAAA Y 2 1 2 1 101000 f 74 goat snp42047-scaffold55-315975 3 61360269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764679 Affx-122956211 AX-385252308 3 56542179 GATAGGACACAATTCAGCCCTCATCAGAAGGCATA[C/T]AGAAAATGTTCAGCAAAGCTAAACTGAAGGTATTT Y 2 1 2 1 101000 f 74 goat snp42048-scaffold55-349577 3 61326258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791941 Affx-122946835 AX-385278931 3 56585330 TTAGTGTAAAATTAACATCAGATTTGGGAACTTGA[C/T]ATGAAAAAAAGAATACGAAACACCTTAGTAATTTT Y 2 1 2 1 101000 f 74 goat snp42049-scaffold55-392728 3 61282858 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427477 Affx-122940015 AX-123297820 3 56626813 CAAAGAGTTGGACATGACTGAGCAACTGAACTGAA[C/T]TGAGCTCCGATTCTATCTGAAAAACATCCATATAC Y 2 1 2 1 201000 r 74 goat snp42050-scaffold55-434211 3 61241642 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380711 Affx-122975153 AX-123251069 3 56679208 CAACTCTTGATCTCCCTCATGACCCTCCTCCAAAA[C/T]AAAAAAATATATAAATGAAGAGATGAATTATAATA Y 2 1 2 1 103000 f 74 goat snp42051-scaffold55-486606 3 61188892 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430168 Affx-122937369 AX-123300509 3 56735393 CCCACATGCTAGTGTTTAATAGTGTCCCCTATTAT[C/T]GACATTCTCCACCAGATTGGGGCATTTATTGCAAT Y 2 1 2 1 101000 f 74 goat snp42052-scaffold55-542791 3 61131465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787787 Affx-122937124 AX-385274810 3 56786645 AATGATGGGTTATTGGTTTCCAGAGTATTCCAATA[C/T]GCTAAAACCCAAGTTAGGAATAATCCACTTGGATC Y 2 1 2 1 202000 f 74 goat snp42053-scaffold55-594043 3 61079565 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801902 Affx-122943960 AX-188760460 3 56831368 CGTTTAGTAATAGATGAAATGGGATTTATGAAAAC[A/G]CCAGATGAGGATGAAACAAGCAATCTTATATGGTG R 2 1 2 1 101000 r 74 goat snp42054-scaffold55-638766 3 61034464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400622 Affx-122960376 AX-123270977 3 56890899 CTTGAGGATGAACACTGAGAATATATTTATTTTCC[A/G]TTTGCTCATGGAGTAGGGTAATTTTGCATTGATTG R 2 1 2 1 101000 r 74 goat snp42055-scaffold55-698297 3 60977101 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400911 Affx-122959734 AX-123271264 3 56962815 GGATGGTTGCTCATAAACCTTTCTGAAGAGCCCCT[A/G]CACTTAATGCTGAATCCACCTCATCTCACCTTCTT R 2 1 2 1 201000 r 74 goat snp42056-scaffold55-770213 3 60903830 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444024 Affx-122926887 AX-123314361 3 57000694 TGAACACTATATTGTTAGTGGATTAGATAGTCACC[A/G]TCTCTTGAAGCTGTCACTTTTTTCTCTATGGATAA R 2 1 2 1 101000 f 74 goat snp42057-scaffold55-808092 3 60866030 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444676 Affx-122926449 AX-123315013 3 57057441 ATGTAACAGGTCACTGCCTATTGATGGTAACAATC[A/G]TATCCACGTCGTATCCAGTGTTATAAAAACTGTGC R 2 1 2 1 101000 r 74 goat snp42058-scaffold55-864839 3 60809300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786426 Affx-122938315 AX-385273460 3 57100117 AGGGGACAAACTGACTGTGGCTGGCATATTTTGAG[C/T]ATTTACTTTTTAGCAAGAACCAAGTAGATGTAGGT Y 2 1 2 1 101000 f 74 goat snp42059-scaffold55-907515 3 60766558 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419212 Affx-122945696 AX-123289560 3 57142821 GCCGCCTTAACTGCATTTTTGTGAAGTAGCTGCAG[C/T]GGCACTTGATAGCTGATTATGTTAATCCTTTAGGG Y 2 1 2 1 101000 r 74 goat snp42060-scaffold55-950219 3 60722674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769404 Affx-122926257 AX-385256575 3 57178049 ACAGCCTACTATATGCTACTCTAAAATTTGAGGGT[A/G]TAAAGCTAAATCAGTTTATGCCCACAAGAAAGTGA R 2 1 2 1 201000 f 74 goat snp42061-scaffold55-985447 3 60687436 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426949 Affx-122940415 AX-123297294 3 57213014 CATAGAAATGTTAGCTTATTTGGCCATCCTTTCCC[A/G]CACGTGGACTTTTTTCTGCTCTAAAGGTAGTCTTC R 2 1 2 1 101000 f 74 goat snp42062-scaffold55-1020412 3 60652451 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378002 Affx-122977597 AX-123248361 3 57258179 AAAAAATAATTTTCCAAAAGTAGAATTTCAGGTAC[A/G]TAACAACTTGATGGGAAAGGCTGTTTGGGGTCTAG R 2 1 2 1 201000 f 74 goat snp42063-scaffold55-1065577 3 60607278 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447565 Affx-122924032 AX-123317901 3 57309029 GGTCTATCAAATGTGCTACCCAACTGGTTATTGAG[C/T]GTATTCTGTGCACTATCTTGAACATTCTCTCTTGT Y 2 1 2 1 101000 f 74 goat snp42064-scaffold55-1116427 3 60556134 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438069 Affx-122931530 AX-123308407 3 57365953 GGCTTGCCAGTTGCCAGTGGGAAGTGAACATAATT[A/G]TGACTTCACAGCTGCTTCTCCTAAAGAAAAAGGTG R 2 1 2 1 101000 f 74 goat snp42065-scaffold55-1173351 3 60499216 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780863 Affx-122973568 AX-385267951 3 57394786 CAGTTATAACCACTTATATACTAACATTAAATTTA[C/T]ATGAAATGATTAACAGTATACAAATAGATGGATAT Y 2 1 2 1 201000 f 74 goat snp42066-scaffold55-1202184 3 60470027 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400706 Affx-122959930 AX-123271061 3 57430158 CACCAGAGGACGAGAGAGAGTGTTTGCTAAACATC[A/G]TGGCATGGAGCATTCTTTCCTCTTGGGTAAGGATT R 2 1 2 1 101000 f 74 goat snp42067-scaffold55-1237556 3 60434201 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426000 Affx-122941141 AX-123296346 3 57503098 CTTCGAGACTTGATTGTAGGTCAACATTAGCATGG[C/T]GCTGTTGGGAGGCTACCATAAGAGTAAAATCAAAG Y 2 1 2 1 201000 r 74 goat snp42068-scaffold55-1310496 3 60360911 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421968 Affx-122943804 AX-123292315 3 57557194 ATGTAAACACTGAACATGATTGCTGAATCATATGG[C/T]AAGAGTATGTTCAGTTTTCTAAGAAACTGCTAGTC Y 2 1 2 1 303000 f 74 goat snp42069-scaffold55-1364592 3 60306913 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413939 Affx-122949804 AX-123284288 3 57606903 AGAATAAAGTTCTTGCATTGGTGAAAGAGGGTGTG[A/G]CCCAGTATATTATTGGAGAATTTAGACATATTAAC R 2 1 2 1 101000 f 74 goat snp42070-scaffold55-1414301 3 60256911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445624 Affx-122925096 AX-123315961 3 57645538 GCAGCAGAAGAGGTTTGATGAGGTAAAGAGAGAAG[G/T]GCAAATGTGGAATTTTTGATTGATTTTAAATTGTT K 2 1 2 1 101000 f 74 goat snp42071-scaffold55-1452936 3 60218387 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798983 Affx-122937633 AX-385285913 3 57675115 ATCTCCACTTAATCACAAACTCCTACAAATTCTAG[A/G]TTTTAAATATTGTTATTTCTCTGACATAGAGAAAA R 2 1 2 1 303000 r 74 goat snp42072-scaffold55-1482513 3 60188791 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434512 Affx-122934605 AX-123304853 3 57722408 TAGCCAAATAAGGTAAGTCATTTGTTATCTGAGCC[A/G]TAAATATTTACATCCACTAGTGACAAATGTATAAA R 2 1 2 1 101000 f 74 goat snp42073-scaffold55-1529806 3 60141029 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384410 Affx-122972198 AX-123254768 3 57783386 TTTCTTTTTAGATTCCACATGTAAGAGATGTCATA[C/T]GAGGACAAATATTCTTTTAGTCAGGAGCTCTAAAT Y 2 1 2 1 101000 r 74 goat snp42074-scaffold55-1590784 3 60079280 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433082 Affx-122935732 AX-123303423 3 57843271 GGCTTTTAATGAAGAACTACTCTAGAAGAAGTATG[C/T]TGCATATAATAAATAATGATGAGCATTAAAAAATA Y 2 1 2 1 101000 f 74 goat snp42075-scaffold55-1650669 3 60019651 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392736 Affx-122966019 AX-123263093 3 57900451 CTTCTCCCACAAAGCCTTTCCTGAGGACCTTCTTG[C/T]ATCTTGCCTTTGCACTTACTGGTAGTTTTCTTTTC Y 2 1 2 1 201000 r 74 goat snp42076-scaffold55-1707849 3 59961512 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784474 Affx-122938591 AX-385271523 3 57933045 TGTCAAATGCCATGGAATGAATACTTTAATTACCC[G/T]AAAATTCATGTGAGGTCAGTCCTTGAAGGAAAATA K 2 1 2 1 101000 r 74 goat snp42077-scaffold55-1740443 3 59928726 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451218 Affx-122921964 AX-123321552 3 57970557 TTTTAAAGAACTGAATGAAGCTGATAATTTGCTGG[A/C]GACTGCTATCTGATTCCCTTAGGAAAAAGTACTAG M 2 1 2 1 101000 r 74 goat snp42078-scaffold55-1777955 3 59890507 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399363 Affx-122961344 AX-123269718 3 58012878 GTTAAATGCCGTCTTCGGGTTCTGTTGCTAAATAA[G/T]GAAGGCGAGCACTGATGTAGAGGCGGAAGTTTCTA K 2 1 2 1 101000 f 74 goat snp42079-scaffold55-1820276 3 59847968 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781498 Affx-122979060 AX-385268583 3 58059077 ATTATAGTGTCATCAAATCATCTCAAATTGGTATA[A/G]AGGAGAAAAGCTCTATACTGATTACAGTGTCTGAA R 2 1 2 1 101000 r 74 goat snp42080-scaffold55-1866475 3 59801799 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792341 Affx-122970550 AX-385279323 3 58089080 CAACTCTGATCTTTTCTATTAAATCCCTTTGTGTA[G/T]GACACATCAAGAATGGTTTTGTTCCTTAGCCAAAT K 2 1 2 1 101000 r 74 goat snp42081-scaffold55-1896478 3 59771806 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420396 Affx-122944928 AX-123290743 3 58131154 ATATGTTTGAATTCTCACAAATTCTCTGATGTTAA[C/T]GGGTGATTCTTTCCATTATTTTATTTTCAACATTA Y 2 1 2 1 101000 f 74 goat snp42082-scaffold55-1938552 3 59729245 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780789 Affx-122921468 AX-385267878 3 58178246 TACAAAAGCTAACTAAAGAGGGCATGCTAAATGCA[A/G]CTCATTGGTTGGTTCTAACAGAGCTTGGAGTTTAA R 2 1 2 1 101000 r 74 goat snp42083-scaffold55-1985644 3 59682120 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405925 Affx-122955570 AX-123276277 3 58212938 GTCAGACAGGACTGAAGCAACTTAGCAGGCATGCA[C/T]GGAGAATGAATGGAACTGTTTCTTAAAGGAAATAA Y 2 1 2 1 201000 r 74 goat snp42084-scaffold55-2020336 3 59647782 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452367 Affx-122920629 AX-123322700 3 58242774 TCTCTCTGTTTTGTCTTGGCCTCTTCTACTTCTCT[A/G]TTCATCTTGGACTGCATCAGTTCAGTTCAGTTCAG R 2 1 2 1 103000 f 74 goat snp42085-scaffold55-2050172 3 59617527 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392824 Affx-122965783 AX-123263181 3 58272530 CAGAAGAATGTGTGTATTCCCCAGTACTCAGCATC[A/G]TTTCCTTGAACACTGAGAGAACATATTAAATGAAA R 2 1 2 1 201000 r 74 goat snp42086-scaffold55-2079928 3 59587578 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775824 Affx-122971465 AX-385262955 3 58303604 TCTGAATCCCTTGTGAGGCTTGCTTAGATCTCAGG[A/G]GAATTTCTCTTAACTAAAATCATCATTGTTTGGAC R 2 1 2 1 101000 f 74 goat snp42087-scaffold55-2111002 3 59556674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404545 Affx-122957390 AX-123274897 3 58346730 GTATACAAATGTCACAATGCAAAAATATATGAAAT[A/G]CAAAATCAGCATCAGACAGGATAAGATCACACTTG R 2 1 2 1 303000 f 74 goat snp42088-scaffold55-2154128 3 59513055 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432706 Affx-122936024 AX-123303047 3 58375557 AAACTAAAAAAAGCAAACCCCTGTCTGGGTGCATA[G/T]GTATGAAAATTATATTGGACAGGTACTGTCTCATC K 2 1 2 1 201000 r 74 goat snp42089-scaffold55-2182955 3 59484224 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424948 Affx-122941274 AX-123295294 3 58455240 ATAAAATATCCTTGTATTCAGCCAGCATATAGTCT[A/G]TTTAATCTTTTTCACTTCCAGGTCACAGTCTTTAG R 2 1 2 1 101000 r 74 goat snp42090-scaffold55-2262638 3 59402827 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789918 Affx-122929533 AX-385276924 3 58507342 ACCAAAAATATTTATGGCTAGTATAATTGAAAATT[A/G]CTGTTTTATAACTGAAACTCAGATTATGTTCTCAA R 2 1 2 1 101000 r 74 goat snp42091-scaffold55-2314740 3 59349314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398141 Affx-122961687 AX-123268496 3 58569030 GTTCTTGATCCCGGAGGCAGGAAAGAAAGTGAGCT[A/G]TTGAGAGAAGACTGCTGTAGAACAAATGCAGTGAG R 2 1 2 1 101000 r 74 goat snp42092-scaffold55-2376428 3 59287427 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438259 Affx-122931416 AX-123308597 3 58657496 TTGCACTGACAACCAAACAATTCTTGTGAATGAAT[A/G]CTGATTATGTATGCACAGCAGTTTATCTAGCACAA R 2 1 2 1 101000 r 74 goat snp42094-scaffold55-2464894 3 59199236 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392024 Affx-122966477 AX-123262381 3 58689508 CAGGTTGATGCATGACAACTGCATGGAGATCAAAT[A/C]CCTGGGCAGGTTGAGGCATCTTGGCTTCCTGAGAA M 2 1 2 1 101000 f 74 goat snp42095-scaffold55-2496906 3 59166962 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447353 Affx-122924874 AX-123317689 3 58718905 GGCATAGATTAAGCTGAAAAAAATGGCACACCATT[A/G]TAGACAAGACTTTCCAAAAGATCTAGAAAACACTC R 2 1 2 1 101000 r 74 goat snp42096-scaffold55-2526303 3 59138103 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435959 Affx-122933528 AX-123306298 3 58765578 CTTGGGAAGATTCAAGAGTCCAATAGCTATTATCT[A/G]TTCTGTCTATCAGAAATGCTCACTTTTCCTAATTA R 2 1 2 1 101000 f 74 goat snp42097-scaffold55-2572976 3 59090785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440080 Affx-122929728 AX-123310417 3 58796038 GATATCAGCAACAGGGCCAGCAATTTCAACATGGA[A/C]AGTGGAAGTCTCATCATTCATAAAGCTGCCAAGAG M 2 1 2 1 101000 f 74 goat snp42098-scaffold55-2603436 3 59059388 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420591 Affx-122945258 AX-123290938 3 58826456 GGCAGAAGTAGAATCCTGGGTCGTCTTTCTGGCAC[A/G]CTGCCTTCCTGATGATCATTAACATAATGCAAAAC R 2 1 2 1 101000 f 74 goat snp42099-scaffold55-2633854 3 59028955 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802639 Affx-122934973 AX-385289540 3 58867316 CTGAATATCAGTACAGGGAATATTCATTCTCTGGT[A/G]AATAGAAATTCATCCTAGAAAATAGCATCATGAGT R 2 1 2 1 101000 f 74 goat snp42100-scaffold55-2674714 3 58987593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395911 Affx-122963604 AX-123266266 3 58900854 CTCTTCGCCAAAGATGAATCAGATTATATTTTGTT[A/G]GCTATTTTGGGGGCAGGGTGGATATATGTATTTTT R 2 1 2 1 201000 f 74 goat snp42101-scaffold55-2708252 3 58953998 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401567 Affx-122958892 AX-123271920 3 58938497 GAAATTATAAATGGAGCAATGGAGCAGTCATCAAG[A/G]ACCCCAGGAAGATAATTATGGGTTGATAGTGGCCG R 2 1 2 1 201000 f 74 goat snp42102-scaffold55-2745895 3 58914688 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384332 Affx-122972259 AX-123254690 3 58974652 TATCTCTCTTAGAAAGTAAGACCCTTATGGAGGCT[A/G]GTAAGTCCCAAGATCTGCAGTTGGCAAGTTCATGA R 2 1 2 1 201000 f 74 goat snp42103-scaffold55-2782050 3 58878587 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396505 Affx-122963527 AX-123266860 3 59022214 TCGTACAATATAAAGTGATTCAGAGTTGGTAGTGC[A/C]GACAGAAACAGATAACTGCCAGAAGGAAATATAAA M 2 1 2 1 101000 f 74 goat snp42104-scaffold55-2829612 3 58831002 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429298 Affx-122938609 AX-123299640 3 59081981 AGAATCTTAAAATACCTGGTTGGCATCTCTTTTCT[C/T]TGTAACAAATAATTCATTTTAGTATACTCTGTGTA Y 2 1 2 1 101000 f 74 goat snp42105-scaffold55-2889379 3 58769802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794483 Affx-122957057 AX-385281446 3 59127894 TAATAGGAAACATGACAAGTCACAATAGAATTATA[C/T]TGTAAATCTAAACCCTACTGTTCACAGCCTTCCCG Y 2 1 2 1 201000 f 74 goat snp42106-scaffold55-2935292 3 58723821 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432628 Affx-122935484 AX-123302969 3 59162319 GAAATCAGTTTTGTCTCTTACTTAATTTATTAAAT[C/T]GTTCCCATGTTCAAAAAGCTAGACTTTTTTCCCTT Y 2 1 2 1 101000 r 74 goat snp42107-scaffold55-2969717 3 58689505 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777249 Affx-122931210 AX-385264372 3 59203121 TGAAGCTTTCTCTACTCATTTCAACCATTAAATGG[C/T]ATAAAAGTAAAATTACCTGTGTACTTTTTAATGCT Y 2 1 2 1 202000 f 74 goat snp42108-scaffold55-3010519 3 58649859 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385639 Affx-122971172 AX-123255997 3 59325353 GGAATTCTTTGGTGGGCCAGTACTTGGGAATCAGT[A/G]TTTTCACTGCGAAAGACCCAGGTTCAATCCCTCAT R 2 1 2 1 101000 f 74 goat snp42110-scaffold55-3132751 3 58529698 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383906 Affx-122973110 AX-123254264 3 59373361 CTGTAGGGTATAGGCAGGCAGCTCAGCAAATCCCA[C/T]GAGATGGGTTAAGGTGATGAGTCCAGGGAAGGACA Y 2 1 2 1 101000 r 74 goat snp42111-scaffold55-3180759 3 58482423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413262 Affx-122950223 AX-123283611 3 59420062 AATTTTACATTAATTATGCCCCTGTATTTTGACAG[C/T]GCTTTTTGTAGAACGCTGAATTTTTACAAAACCCA Y 2 1 2 1 101000 r 74 goat snp42112-scaffold55-3227460 3 58435598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413834 Affx-122949880 AX-123284183 3 59451796 CTTCCTACTGGTAAAGTATAGGTACAAATGCTTCC[A/G]TTGGCACCTCCGCAAATATTTATTAAATGCCTGCT R 2 1 2 1 201000 f 74 goat snp42113-scaffold55-3259194 3 58404560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424799 Affx-122941387 AX-123295145 3 59480622 CATTCTCATTTATTGAGTAAGCCAAAAGAATACCT[C/T]CACATCTGTATGCAAATATTTCACAATTGTGAAAA Y 2 1 2 1 101000 f 74 goat snp42114-scaffold55-3288020 3 58375779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384219 Affx-122972381 AX-123254577 3 59522355 GCGATGTGACCCTGAAGGCATTGTCAACAAACCAG[C/T]GGGTGAGACGTTTCAGTTATAGGAATAAGCGAAAC Y 2 1 2 1 101000 f 74 goat snp42115-scaffold55-3329753 3 58334328 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476175 Affx-1251763679 AX-586011602 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 4 1 4 1 20000 f 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 539476430 Affx-1251763679 AX-586011831 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 8 1 4 1 20000 r 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 562165156 Affx-1251763679 AX-606940568 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 8 1 4 1 20100 r 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 562165207 Affx-1251763679 AX-606940619 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 8 1 4 1 20100 f 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 562166256 Affx-1251763679 AX-606941664 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 8 1 4 1 20100 f 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 562166261 Affx-1251763679 AX-606941669 3 59573202 AGCTTCAGCACCAGTCTTTCCAATGAATATTCAGG[-/ACTGATTTCCTTTATTTATTTATTTATTTTTTAAAATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTCCCACTCTC]CTGATTTCCTTTAGGATGGACTGATTTGATCTCTT - 8 1 4 1 20100 r 74 goat SV_291 3 59573202 - deletion junction SV-TF-chip 38423467 Affx-122942582 AX-123293813 3 59575877 TGTCATCTTATCCCTGACCATCCATTCTTCCCTCC[A/G]CTATTATTTTTAAAAGTTTTTTTTTTTCCATTACT R 2 1 2 1 103000 f 74 goat snp42116-scaffold55-3383275 3 58280826 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432895 Affx-122935331 AX-123303236 3 59607644 CCTATAGGTTTGCTAAGACATGTCAACAGAACTAA[C/T]GCCAATTGCCATTCATATAGTACCTCTTATGTCCC Y 2 1 2 1 101000 f 74 goat snp42117-scaffold55-3415042 3 58249118 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409264 Affx-122953127 AX-123279615 3 59647481 GCTCTGCTTATATTTGTGTGTAATTTCTCATTTAA[C/T]GTGGACAAGTAAAAAGTCCACAGTGCCTGCACTGT Y 2 1 2 1 101000 f 74 goat snp42118-scaffold55-3454879 3 58209445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275091 Affx-1111834592 AX-519548670 3 59658069 CTGAACTAAACTGAGCCACCAGGAGAGCCCAGCAT[A/G]TAGGACTTATGCACAAATGACCTGCAGAAAATACT R 2 1 2 1 201000 r 74 goat GoatD01.042516 3 59658069 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770775 Affx-122933842 AX-385257939 3 59678001 CACTATTGTTTCTGATCAGGAAACATTACAGGAAT[A/G]CCACTATTAGAATGGATGAAAGCAGAAATCTGACG R 2 1 2 1 101000 f 74 goat snp42119-scaffold55-3485399 3 58177723 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407479 Affx-122954766 AX-123277830 3 59720662 GCAATATGAAGCACAAAAGGTCTCAAATTACCTGA[C/T]GTTTATTGTCATTAAATTTTACCACTGAAAGATCT Y 2 1 2 1 101000 f 74 goat snp42120-scaffold55-3528060 3 58135295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443552 Affx-122927759 AX-123313889 3 59757273 CCCCTTTATTTGATTTAAATGCTCATTTTTCAAAA[C/T]GCATCCCTTGACAGTATATTCCATCCCATGATATC Y 2 1 2 1 101000 f 74 goat snp42121-scaffold55-3564671 3 58098157 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385872 Affx-122971605 AX-123256230 3 59797155 AAACTCCAGGAGTCATATACCAGGCATTTTGCATC[G/T]CTGTCAAGAAGTTCCTTCATTTGATCCCACCTACA K 2 1 2 1 101000 r 74 goat snp42122-scaffold55-3604553 3 58058882 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408178 Affx-122954201 AX-123278529 3 59846837 CACTGAGCCACCTAGGAAGCCCTGGACTAACTTAG[C/T]AGAGAGTTAATTTGAGATACATTTGTAGGTAGAGG Y 2 1 2 1 201000 r 74 goat snp42123-scaffold55-3654235 3 58008530 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773957 Affx-122947697 AX-385261096 3 59914644 TTCTGGGAAGTCAGATGACTGAGAAAGGAAGACCT[A/C]GAAGAAGGATATTTCAGTGGTCTGATTTCAAATTT M 2 1 2 1 101000 f 74 goat snp42124-scaffold55-3722042 3 57941793 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787543 Affx-122943600 AX-385274567 3 59956199 TCCAGACCCAAGACATGACTATTTCAACTAGAAGA[C/T]GGTAAAACATCTCTGAGCAAAAGAAACAGTGGAGA Y 2 1 2 1 101000 r 74 goat snp42125-scaffold55-3763597 3 57899693 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277959 Affx-1111836179 AX-519551454 3 59959339 GAACAATGGTTACTATGGCCCTGGACATGAGAGAA[A/C]TAGAAAGATGTTGGTCAAAGGGCACATATTTTTAT M 2 1 2 1 101000 f 74 goat Random2.2K-333 3 59959339 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769009 Affx-122937524 AX-385256184 3 59991756 AATCACAATAATGAGATTTCGGAGAAAAGGAATCG[C/T]GGAAATCACTCAACACTTCCTAGCAATGGGTAATA Y 2 1 2 1 102000 r 74 goat snp42126-scaffold55-3799154 3 57863626 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277961 Affx-1111836180 AX-519551456 3 60013636 AGGGAACAATTTGAGGAACTCTAGAAGAAACCAAT[A/G]AAATATAGGTAGGAAAACAATCTTATGTCAGGTAA R 2 1 2 1 101000 f 74 goat Random2.2K-334 3 60013636 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399471 Affx-122961194 AX-123269826 3 60028741 AGCAATTTATACCCCAGAGCTTTTCAGAAGAGTTA[A/G]TACAATGGCTGTGCATGTCAGAAATGATTTTCTTT R 2 1 2 1 101000 r 74 goat snp42127-scaffold55-3836139 3 57827460 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781013 Affx-122937150 AX-385268100 3 60061917 TGTAGTGGCAATAACTGGTCTGAAAATGACCCTCT[C/T]AAACATTTGTGAACTATCAAGCAGGGACTGAAATT Y 2 1 2 1 101000 f 74 goat snp42128-scaffold55-3869315 3 57795018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438507 Affx-122931212 AX-123308845 3 60098471 ACTAATACTTCTTCCTTTTTTAAAATGAGAAATGT[A/C]TCCTGCTTGGGCTTTAGAGATATGAACTTAAAAAG M 2 1 2 1 101000 r 74 goat snp42129-scaffold55-3905869 3 57757315 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765214 Affx-122978103 AX-385252753 3 60130712 TGTATATAGTTTCTTCATTTGGTTTTTAGAACACC[A/G]CACTCTCTTAGATTTCCTCTTATTTCAATTATTTT R 2 1 2 1 101000 f 74 goat snp42130-scaffold55-3938110 3 57725075 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275117 Affx-1111834607 AX-519548696 3 60153208 GTCAACACTGCAGGGAAGGTGTCAGTCTCAACTCC[A/G]ACTGTCTAAAATGGAAAGTTCACCTGCAGCCCACT R 2 1 2 1 101000 r 74 goat GoatD01.042967 3 60153208 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770591 Affx-122968704 AX-385257755 3 60188447 TGGCATTCTCCTGTTTACTGATGAGTGGTGAACAC[A/G]CAAATTTTGCTCAGCCATAGTAATGAGCAACTAGA R 2 1 2 1 101000 f 74 goat snp42131-scaffold55-3995845 3 57667151 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393803 Affx-122965179 AX-123264158 3 60239826 AGCCTGTACAGATGACACACGCATAAAGAGTTAAA[G/T]ACTCAAGAGTAGTCAAAAGTTGGCCGTTTTATTTT K 2 1 2 1 101000 f 74 goat snp42132-scaffold55-4047224 3 57615564 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780610 Affx-122926040 AX-385267700 3 60268696 GTGTTTTTCTGAACTGGCCCTCAGGTATTTAGGGT[A/C]TGTTGGGTCCTACATCTCTTTGTAAGAGCTACTTG M 2 1 2 1 101000 f 74 goat snp42133-scaffold55-4076094 3 57586611 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394144 Affx-122965317 AX-123264499 3 60305135 GGGATAGACAAAAACAAAGCCAGTAAAAGTACTTG[C/T]ATTATTAGGCTTGGGATCCTGTACATATGCTCTCT Y 2 1 2 1 101000 r 74 goat snp42134-scaffold55-4112533 3 57550226 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779635 Affx-122965052 AX-385266737 3 60334684 GTGTGCAGGTTGAATCAGATTGGCCTTGGTAGGAC[A/G]CAGTCTGTGCTGGTATCGATTAGAATCTCGGGGAG R 2 1 2 1 101000 f 74 goat snp42135-scaffold55-4142082 3 57519074 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769638 Affx-122934418 AX-385256808 3 60383235 AAAAAAATTTTTAACTTTACTCTTCATATTTTATT[A/G]TTTTGTTGTTTTGGCACAAAGGATGACAAGGAAAG R 2 1 2 1 303000 f 74 goat snp42136-scaffold55-4190633 3 57469911 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797024 Affx-122936932 AX-385283965 3 60419793 CTGACAAGTGAAGTAGAATTTTAAGCGTGTCCCAC[A/G]TTTGTTTCATTAACCTTTTTTTCTCTAGAGCCTAG R 2 1 2 1 101000 f 74 goat snp42137-scaffold55-4227191 3 57433219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400269 Affx-122960128 AX-123270624 3 60468095 GGACAGGAGGATGTTAACATGCTGCAACACACTTA[C/T]GCACAGTCCCGAACTTGACAGCAGTAGACAGATTT Y 2 1 2 1 101000 f 74 goat snp42138-scaffold55-4275493 3 57384144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278120 Affx-1111836181 AX-519551610 3 60471020 AAAAAAAAGAACAAATAATAATAATAGCAAGCTAT[C/G]TGGAAGGAATCTAAACTCACTGTTTTCACTGTTTT S 4 1 2 1 101000 r 74 goat Random2.2K-335 3 60471020 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434534 Affx-122934151 AX-123304875 3 60502935 CAGACTTGACTAAGTGACTGAACTGAACTGAATCA[C/T]GTAGGTCCATTCAGAGGATTGAGAAAATGTTTGTG Y 2 1 2 1 201000 r 74 goat snp42139-scaffold55-4310333 3 57348250 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452295 Affx-122920685 AX-123322628 3 60558110 TAGAGAAGAAAAAACTCATTAGTTGTAAGACTTGA[A/G]TGTCCATGTAATAAATGGCTAAATATAACATTTCA R 2 1 2 1 101000 f 74 goat snp42140-scaffold55-4365508 3 57293372 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423208 Affx-122942711 AX-123293554 3 60602762 TTTTACTTAGGTTAAAATAAACAAGGATGAGAACC[A/G]TTGGATTTATCAACATGGAGTACACTGAAGATCTT R 2 1 2 1 201000 r 74 goat snp42141-scaffold55-4410160 3 57248671 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797389 Affx-122949184 AX-385284328 3 60681285 CAACTTAATATTCAACAATTTTTGAGACCCTGAGT[C/T]CTCAGAAAATTTAACTAGGTGATAAACTTCTTTAT Y 2 1 2 1 201000 r 74 goat snp42143-scaffold55-4488683 3 57172140 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786810 Affx-122959052 AX-385273839 3 60723967 TGCTCTTTCTATGTTTTAGGATATGATATTATTGA[A/G]CTTATGCTTTAATATTATTTGAAAACATGGTGTAA R 2 1 2 1 201000 r 74 goat snp42144-scaffold55-4531365 3 57129182 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379434 Affx-122976103 AX-123249792 3 60756302 TCATTAGGCCTCTCATATCCACTTGGGGGCAGTGA[A/G]TCATCCCCAGACTGGGGCATTAAAACTCTTCTATC R 2 1 2 1 102000 f 74 goat snp42145-scaffold55-4563700 3 57096327 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770356 Affx-122968252 AX-385257522 3 60835078 AATCTGGGAATCCTTTGAACTAGATTTTTTTTATC[A/G]TGGGTTTGAATACTTGACCTTTGAACCTGCTTTTG R 2 1 2 1 101000 r 74 goat snp42147-scaffold55-4642476 3 57017014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784273 Affx-122949073 AX-385271324 3 60885655 ATACTGTTAACCAGGCTTATCTTTTACTGGCCTCT[A/G]TCTGGCTCAGACTAATATGATAAAAAGTTTTCCAA R 2 1 2 1 101000 f 74 goat snp42148-scaffold55-4693053 3 56966101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383097 Affx-122973280 AX-123253455 3 60954429 CTCTCCTTATTTACAACTTCTTGGTACCTTCCAGC[A/G]CTCCGTCCATTTCCTTCCCCTCATGCTATAAATTG R 2 1 2 1 101000 f 74 goat snp42149-scaffold55-4761827 3 56895440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779983 Affx-122975796 AX-385267082 3 61003556 AGAAGACACTCAAATTCTAGGAAATAGTCTTGGCT[C/T]TGTTATTTCTCTATTCTTCAGTCATTAATTCTTCC Y 2 1 2 1 101000 f 74 goat snp42150-scaffold55-4810954 3 56846760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397743 Affx-122962536 AX-123268098 3 61041488 GCAACACATGAAAACCTTTGACTTCTCTCACATTG[C/T]AACTATTTCACATAAAAGCAAAGAACAAGAAACAT Y 2 1 2 1 101000 f 74 goat snp42151-scaffold55-4848886 3 56808148 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407161 Affx-122954841 AX-123277512 3 61076132 TGAAGCCTCACTTAAACTAATATAAAAGCAAAGGA[A/G]AAGACCCTGACTTTGGGAAAGATTAAAGGCAGAAG R 2 1 2 1 201000 f 74 goat snp42152-scaffold55-4883530 3 56773531 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789633 Affx-122969598 AX-385276642 3 61107560 ATTATCTAGTGTTTAAGAAACAATTTAAAACATTG[C/T]AATCACAATGAGTTCACTGAATACATTTTGAGCAT Y 2 1 2 1 201000 f 74 goat snp42153-scaffold55-4914958 3 56741635 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438326 Affx-122931347 AX-123308664 3 61148397 CCTAACCAAACATACACCCCCATGGAATGTATTAA[C/T]GCTTCCGTCTGCACCATGTGGGTGAATGTAGGATA Y 2 1 2 1 202000 r 74 goat snp42154-scaffold55-4955795 3 56700488 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429618 Affx-122937698 AX-123299959 3 61205793 TTGTTCATCGCTTTGTAACTGAAGCATTCTGTATC[A/G]CACCAACTGAGAATGGTTTTGTTCCTGCTTCTGAG R 2 1 2 1 101000 r 74 goat snp42155-scaffold55-5013191 3 56642564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448284 Affx-122924176 AX-123318620 3 61234595 TAATCTTCATGCTATACACCTGAAGTCTCTCCTAA[C/T]ATTCTTTTTATGTGATGCTGAATGATACTACACTA Y 2 1 2 1 201000 r 74 goat snp42156-scaffold55-5041993 3 56613869 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411640 Affx-122951575 AX-123281990 3 61327346 CAATTAGTAGTTTTCAAGGTAAAGAACCAGTTTCC[G/T]TCTCACCCTCTCATTTTGACAATTTTTAGGAACTC K 2 1 2 1 101000 f 74 goat snp42157-scaffold55-5134744 3 56519628 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464218132 Affx-1110375202 AX-515693068 3 61361916 TAGGCCAATGTTACATATTCACAATGAATTGTATA[C/T]TGTACAATGTATATTCTGTATCTAAAAAAATGGGA Y 2 1 2 1 101000 f 74 goat 3_61361916_AF-PAKI 3 61361916 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445271 Affx-122925468 AX-123315608 3 61383058 CAGATTCTTTACTCTCTGATCCACCAGGGAAGCCC[A/G]CACATCCATTTCCTTCTTCTTAAATATAAATATGT R 2 1 2 1 101000 r 74 goat snp42158-scaffold55-5190456 3 56464287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794834 Affx-122965430 AX-385281794 3 61386356 TTATCTGTTGCTCTGGCAGCCTGATTTTCCTATTA[A/C]TTCATATGAATTCATTGTAAATTAAAGAAATTAGC M 2 1 2 1 202000 r 74 goat snp21579-scaffold2108-2142 3 56461127 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379187 Affx-122976307 AX-123249546 3 61439592 CTTAAGTAAGTTTTATGGCTCCTGTATGACTTGGA[A/C]TATACCACTGGCAACAATATCCTAATAATTTTTCT M 2 1 2 1 101000 f 74 goat snp21580-scaffold2108-55378 3 56406649 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788490 Affx-122936590 AX-385275507 3 61491968 GAGTCTACCCCCTCTAGTCTAAAAATGATATTACT[A/G]TCACTAGTAAACATAGGTTTCCTAGGCATGTTTAC R 2 1 2 1 202000 f 74 goat snp21581-scaffold2108-107754 3 56353243 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398961 Affx-122960975 AX-123269316 3 61526390 AAAGGTTATATAACAAATTATTATAAATAATTAAT[A/G]TACAGTCATATCTGATTTAAGAATATTTGGTTAAT R 2 1 2 1 103000 r 74 goat snp21582-scaffold2108-142176 3 56318729 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376525 Affx-122978005 AX-123246884 3 61556039 TACAAGTCTTAATTTTGTGTGTGTGATCCCAATGT[A/G]ATTTCTGTCAATCACAATGCCCTAAAAAAAGAATA R 2 1 2 1 201000 r 74 goat snp21583-scaffold2108-171825 3 56288381 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452828 Affx-122920737 AX-123323161 3 61631099 AGTTGGAAATGATCTGAGAAACCATAGATAACTTC[A/G]TTTATATTATACAAAGAAATAAAAACGGATGCCTA R 2 1 2 1 103000 f 74 goat snp21585-scaffold2108-246885 3 56211068 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378454 Affx-122976690 AX-123248813 3 61660450 AGGGCTCTTCTAATCCTTAATCTAAGATCCCTTTA[C/T]AAATTTTTGCAGAGTTCTTCTAATGCCCATAGATC Y 2 1 2 1 101000 f 74 goat snp21586-scaffold2108-276236 3 56182055 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386829 Affx-122970093 AX-123257187 3 61688614 GGGAAAAAGCTGACTGGGTGAAATCCAAATGCCTT[C/T]AGTAGCAGAATGGCAGGAAAGTTGGGAAAGCCATA Y 2 1 2 1 101000 f 74 goat snp24971-scaffold257-12862 3 56152999 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410886 Affx-122952078 AX-123281236 3 61724032 ACTACCAACGTGGGTAGAGTAAGAGAAGTTTTCAC[A/C]TTTTGCCATTTTAAATGTAAGAAAACAAAACACAA M 2 1 2 1 101000 f 74 goat snp24972-scaffold257-48280 3 56117250 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451874 Affx-122921059 AX-123322207 3 61862222 GAGGCTGCATTTTCACCCTCTGAAAGGCTAATGAC[A/G]TCAGACAACTTCGGGTACAAAAGTCTCTTCCCCTA R 2 1 2 1 101000 r 74 goat snp24974-scaffold257-186470 3 55976482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392196 Affx-122966288 AX-123262553 3 61916325 AAGACCCAGAAGCACTGTCCTATATAAGTGATTTA[C/T]ATCACCTCCTCCTGCACTCCTCACTTAGGATGCCT Y 2 1 2 1 201000 r 74 goat snp24975-scaffold257-240573 3 55922300 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425719 Affx-122940763 AX-123296065 3 61957490 ATGATGGGAGAATAAGAGCACTGCAGTAACTATCC[G/T]AGTGAGTGAGAAAAGAGTAATGGCTCTCTCCAGAA K 2 1 2 1 201000 f 74 goat snp24976-scaffold257-281738 3 55881947 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409127 Affx-122953304 AX-123279478 3 61993723 AGGGTAGGGTTGCTGTCAAATGTTTGAATATCTCA[C/T]GGGGATGGGTCTTTCTGCAAACAATAACACAAAAT Y 2 1 2 1 101000 f 74 goat snp24977-scaffold257-317971 3 55845677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429543 Affx-122937829 AX-123299885 3 62050007 TTTAGCATAAAGAGAATTTTTTTGTAGTATAGTTG[A/G]TTCACAATATTGTGTTACTTTCAGGTGTACAGCAT R 2 1 2 1 303000 f 74 goat snp24978-scaffold257-374255 3 55788625 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388440 Affx-122969263 AX-123258798 3 62095554 AGATGACTATTGTACTTTACATTTGCAATGCTAGG[A/C]TCTGTCTAAATACCCACTGAAAGAGATTCAGTTTA M 2 1 2 1 101000 r 74 goat snp24979-scaffold257-419802 3 55743248 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798255 Affx-122927180 AX-385285190 3 62129105 TGTTTTGCTTTTACTTTAAAAAGTAGACACTGCCA[A/G]CTCCATCAAAGTGTAGTTTGCAAAATATGAGATTA R 2 1 2 1 101000 f 74 goat snp24980-scaffold257-453353 3 55710010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274408 Affx-1111834237 AX-519548000 3 62175990 AGAAATTTATCCTTTAGTGTTAACTACCAAGACCC[A/G]GGAAATATTTAACTGCAGAGTAGAAGAAGATGTCA R 2 1 2 1 101000 f 74 goat GoatD01.026894 3 62175990 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320787723 Affx-122926606 AX-385274746 3 62176284 TCCCTTTCATGGGAGTAGGGAGAGAGCAAGACATA[C/T]GTAACAGTCATCATGGCCCATAGAAATTCTGAAAT Y 2 1 2 1 101000 f 74 goat snp24981-scaffold257-500532 3 55662520 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435927 Affx-122932755 AX-123306266 3 62223940 TGTGTCACATCACACTCTTTTTTTCACTCCCCCAC[A/G]TTTTTCTCACAGCTCACAGAACTCAGTCCACGTTG R 2 1 2 1 101000 r 74 goat snp24982-scaffold257-548188 3 55615003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775280 Affx-122973311 AX-385262411 3 62266002 TGAGTCACTGGGGATGACATTGGACACATTTTATT[A/C]TTCCTAAGCCTGAGATCTTAATTTGACTAACAGTA M 2 1 2 1 101000 f 74 goat snp24983-scaffold257-590250 3 55571260 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434095 Affx-122934165 AX-123304436 3 62300492 ACTTAAGTGATTGGTTGACTTGTTTTCCTAAGGCT[A/G]TGCAGATTGGTCTCTTTCCCACTGGTGTTTGCTCC R 2 1 2 1 101000 r 74 goat snp24984-scaffold257-624740 3 55536059 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798670 Affx-122932707 AX-385285602 3 62343648 TCTGTTTCAGGGTGAACACTGGTGTGATTTATACC[C/T]CTTATAAATCACATACTAAGTTTTCAACAGTTTGC Y 2 1 2 1 101000 f 74 goat snp24985-scaffold257-667896 3 55492344 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425401 Affx-122941550 AX-123295747 3 62412212 ACTTTGAGCCAGTTATTTAACTTCCCTATGCTTCT[A/G]TTGCCATAAATGTGAAATACATGTAATGATACAGA R 2 1 2 1 201000 r 74 goat snp24987-scaffold257-736460 3 55423232 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787777 Affx-122960764 AX-385274800 3 62449452 ACGGAGGAGTTAGGCCTCACCTCTTGATCAGAAAG[C/T]GGTTAAGATAATATTGAAGAAAACATGTGAGGTAG Y 2 1 2 1 101000 f 74 goat snp24988-scaffold257-773700 3 55385933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419306 Affx-122946229 AX-123289654 3 62482359 CATACGGTACATTTGCTTTGTACTATTTTCTACAC[A/G]TTTGTTGAAATTTAAAATGAAGAGTAATCATATTA R 2 1 2 1 101000 f 74 goat snp24989-scaffold257-806607 3 55352802 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452586 Affx-122920504 AX-123322919 3 62511638 TTAGTGATTTTCTTAATTCCTTTATCAGACAGATC[A/G]TTTCCTGCGCTTTCCCCTTCAGTGTCTCCCACTGC R 2 1 2 1 101000 r 74 goat snp24990-scaffold257-835886 3 55323960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801158 Affx-122977554 AX-385288072 3 62652617 TGTGCAGCTAGATATTGACTATTATCCTAACTATT[A/G]TCTGACTGACCCCAGTGTCCTGCATTTTCTCCAGC R 2 1 2 1 102000 r 74 goat snp24993-scaffold257-976865 3 55182338 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440786 Affx-122929842 AX-123311123 3 62682937 CTCAGGAGTCTCAGGGAAACAAGAAATGAGAGATT[A/G]TAGAAGAATTAAGATTTTGTTAGGCATGTCCCTCC R 2 1 2 1 303000 f 74 goat snp24994-scaffold257-1007185 3 55151148 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410074 Affx-122952850 AX-123280424 3 62758861 GGCTGGCTCATTGGAACTTGGATTCCAGAGAGTTG[C/T]GCATAGATTCTCATCACTCATGCAGTCTTTCATCT Y 2 1 2 1 101000 f 74 goat snp24995-scaffold257-1083109 3 55074064 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416269 Affx-122947954 AX-123286618 3 62828377 TGTGCCAGAAGAAGGAAAAAAACTGAGAAGAAATT[A/G]CTTCATCAGAATTAAAAGCTTGACCTTAAAATAAG R 2 1 2 1 201000 r 74 goat snp24997-scaffold257-1152625 3 55003964 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398742 Affx-122961822 AX-123269097 3 62877145 TATAATGGCCAGCAATGGTGACATTATTTATACAG[C/T]GGAAAAGCCCATAGTGTAAACATATAAGACATACA Y 2 1 2 1 101000 f 74 goat snp24998-scaffold257-1201393 3 54953622 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425464 Affx-122941504 AX-123295810 3 62957936 TTTCTTTGAAACTTCTATTTGCTACCAGTTTCCTA[C/T]AGAGCTATCATTAAATCCTTTATCAGGGCTTACAT Y 2 1 2 1 101000 f 74 goat snp10420-scaffold1373-55295 3 54870680 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274051 Affx-1111833976 AX-519547655 3 62982439 TGGTTTGAGACTAGTCAGCTTA[A/G]CACATCTGCAGTAAATGAGTCTACCATGCTGTTTT R 2 1 2 1 101000 r 74 goat GoatD01.012499 3 62982439 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320789600 Affx-122971262 AX-385276609 3 63040093 AAAACTCAGCTAAGAAATGGCATCATCAGGAAAGT[C/T]TCTTTTGGACCCTCACCCAGCTTACAAGTGACCCC Y 2 1 2 1 101000 r 74 goat snp10421-scaffold1373-137452 3 54781829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410822 Affx-122952638 AX-123281172 3 63071753 GGTAACCCATAGAAGGCAGCCTCCTGAATCCCAGC[A/G]CAGGACAGAGAAAGAGAAGCAGACTAATGATTTTG R 2 1 2 1 201000 f 74 goat snp10422-scaffold1373-169112 3 54749819 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447673 Affx-122923953 AX-123318009 3 63105880 CACCAGCAACTTTTTCTCTGTCCCAAGTGAGAAAT[C/T]TAACACAGTGGCTCAGATGGTAAAGAATCTGCCTA Y 2 1 2 1 201000 f 74 goat snp10423-scaffold1373-203239 3 54715276 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386967 Affx-122969969 AX-123257325 3 63135959 CAGATGGAATAGCTGTCAGCAGGGAAAGTAGGCCA[C/T]GACCGTGTAAGTACAAGGAGCTGCTCTTTGGGACT Y 2 1 2 1 101000 f 74 goat snp10424-scaffold1373-233318 3 54685736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438672 Affx-122930880 AX-123309009 3 63166445 TTCCGGGGTGACAGTGATGGGCTATAACTGGGTAG[C/T]AGTTACAGGTGTTCCCTTTTCTCAACCATTCATAC Y 2 1 2 1 201000 f 74 goat snp10425-scaffold1373-263804 3 54657521 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433501 Affx-122935024 AX-123303842 3 63197978 ATCAAAGAAAAGAGAAATAAGACATTTTTACATGC[A/C]ATCTCTTGAATGTTGAGGCATACATGGGGGAAATC M 2 1 2 1 201000 f 74 goat snp10426-scaffold1373-295337 3 54625021 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780477 Affx-122959672 AX-385267568 3 63230161 ATGACCCGATAGAATTATTAGGGGCTGCTGTTATC[A/G]TGTAATAGATCTGTGTATATTCTGCATTTTTATCG R 2 1 2 1 101000 f 74 goat snp10427-scaffold1373-327520 3 54593013 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783217 Affx-122964063 AX-385270283 3 63264968 AATAATAATACTTCTCAGGTATTAAGTGGATTGAG[C/T]AAAGTCATGCATCTTGAGCTCAAAATAATAACACA Y 2 1 2 1 101000 f 74 goat snp10428-scaffold1373-362327 3 54558229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425428 Affx-122941530 AX-123295774 3 63319277 TCTGAGTCTCTACTTCTGCTTTGTGACTAAGATCA[C/T]CCATACCAATTTTTTCAGTGGTTTCCTTGTTTTAA Y 2 1 2 1 101000 f 74 goat snp10429-scaffold1373-416636 3 54503497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450943 Affx-122921763 AX-123321277 3 63368370 GTAAGAGTTGGAAGCCATGAAAATAAAGGGGTAAT[A/G]TAAGAGTAGAATTTGAACTGTCAGGTAGTGCGTCT R 2 1 2 1 101000 r 74 goat snp10430-scaffold1373-465729 3 54454410 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432959 Affx-122935282 AX-123303300 3 63399027 TTTTTAAAGAACTGCCAAACTGTTTTCTAAATGCC[G/T]GTACTATTTTATCTTCCCACCAATATGAGAGCTAT K 2 1 2 1 101000 r 74 goat snp10431-scaffold1373-496386 3 54423995 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436591 Affx-122932524 AX-123306929 3 63429802 ATAAAAGTCTTGGCTAAAGTACGTATCTTCAAGGT[A/G]TGAAGCATAAAAACAAAGCTTTTGAGAATGAAACT R 2 1 2 1 101000 f 74 goat snp10432-scaffold1373-527161 3 54393259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385138 Affx-122971765 AX-123255496 3 63471984 ACTTATTTGCAAATGAGTATAAAATCAGCCATGAA[C/T]ACTTGATGGCAAATACCTATCTGCAAAAAATCTCA Y 2 1 2 1 101000 r 74 goat snp10433-scaffold1373-569343 3 54350758 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404525 Affx-122956691 AX-123274877 3 63506716 ATTGGGATGTTGAGAAGACAAATGTAATAACACTT[A/G]TAAAGCACTAAGATTTTCATATAACTTTTTAACTT R 2 1 2 1 101000 f 74 goat snp10434-scaffold1373-604075 3 54315961 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384270 Affx-122972309 AX-123254628 3 63560550 GTGCCCTATGTTCTGCGAAGTTGTATGTCCACATT[A/G]TAATGCTACACATGTAGAAATCAATTGCTAACCAT R 2 1 2 1 101000 f 74 goat snp10435-scaffold1373-657909 3 54261686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779904 Affx-122975403 AX-385267003 3 63602815 CTAGGTCCTAGTATAGGGGCCTGTAACCAGATTCA[A/G]TAAAGGCTTGTTGATGTGTCAATATAAAAATATAC R 2 1 2 1 101000 f 74 goat snp10436-scaffold1373-700174 3 54219080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278123 Affx-1111836182 AX-519551613 3 63626024 GGGTGACTAGAGCAGGGTGACTAAAGCACATCAGC[A/C]CTGCTACAATGTGAAATCTCAGATCACAGAAGATC M 2 1 2 1 101000 r 74 goat Random2.2K-339 3 63626024 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38445799 Affx-122926042 AX-123316136 3 63651442 ATTTTGGAATACGTAGATGTGTATTAAATTTTTTT[A/G]TGACATTACCTAATGTGTTTTTTAACATTTGAAAA R 2 1 2 1 101000 r 74 goat snp10437-scaffold1373-748801 3 54170450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792025 Affx-122930127 AX-385279013 3 63715292 GTGGCACTCTTTTTGCCTTAGGATATATTCCACTA[C/T]AGAAATAACATTAAATCACACTTTTTAAATATTCT Y 2 1 2 1 201000 r 74 goat snp10438-scaffold1373-812651 3 54106574 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800823 Affx-122967290 AX-385287739 3 63808010 TTAAAGTGAATGTTGACCATAAAGTCACACCTGAC[G/T]AGAGTCTTACCAAGGAGAGTTATTTGGCCTTTACC K 2 1 2 1 101000 r 74 goat snp10440-scaffold1373-905369 3 54017849 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391228 Affx-122967396 AX-123261585 3 63848339 AAAGATGATGAAAAAGCATTAAGTGGAATTGGCAA[C/T]AGATTGTCAGTGACCTTGATAATGGCTTTATTTGA Y 2 1 2 1 101000 f 74 goat snp10441-scaffold1373-945698 3 53977455 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272217 Affx-1111833394 AX-519545964 3 63879650 CTCTCACAACAAGAACTATCTTAGAAATTCTTTGA[A/G]AAGACTGATTTCCTAACAGAGAAAATTTTTTCTAT R 2 1 2 1 101000 f 74 goat 3_63879650_AF-PAKI 3 63879650 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38388274 Affx-122969765 AX-123258632 3 63884982 CCACAGAGATCTTTGAGGCTGGTCTGAATAAGGAA[C/T]GAATGCCCAACCCTTGTGATATTCTGTGGGCAGAG Y 2 1 2 1 201000 f 74 goat snp10442-scaffold1373-982341 3 53939312 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454312 Affx-122919250 AX-123324645 3 63923585 TTCACTTGGCTGGCCATGTTTATTTTTTCTCTTTA[C/T]GTCTCCTGTCTAGGATGTGATTAGGGTATTGGCTT Y 2 1 2 1 101000 r 74 goat snp10443-scaffold1373-1020944 3 53900613 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399539 Affx-122961143 AX-123269894 3 63963680 TGCAGAACAGTACCTAATTTACACAGCAAAGTCAA[C/T]GATAACACTTATTTTCTCTTCATATGAAATTTGGA Y 2 1 2 1 101000 f 74 goat snp10444-scaffold1373-1061039 3 53860458 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278127 Affx-1111836184 AX-519551617 3 63991471 CCTACAAAGAGAACAGGAGGAAGGCCAAGGTGGAG[C/G]CAGGCAGCACAGAGAAGTCCAAACACAGAAAGAAG S 4 1 2 1 202000 r 74 goat Random2.2K-340 3 63991471 G C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451611 Affx-122921630 AX-123321944 3 64007599 TCAATTCTGCCATTAAAACAGGTTGCTAGATACTT[A/G]TTCTTCCACTTAGCTAACATTTATGGGTTACATAT R 2 1 2 1 101000 f 74 goat snp10445-scaffold1373-1104958 3 53816397 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786328 Affx-122919573 AX-385273362 3 64077488 GTCCTTTATTCTGGAACTCAAGGCCTTTGTAGTCT[A/G]TCTATATCTAATATTCTGATCATTTCAGTTTTTTA R 2 1 2 1 101000 f 74 goat snp10446-scaffold1373-1174847 3 53746657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437874 Affx-122932064 AX-123308212 3 64110673 AATCATCACTGTCCCTATCACCCTTAATCCTCAGG[C/T]GAGGTTGCAAGAACTAATGGATAAAAAAAAAACTG Y 2 1 2 1 202000 r 74 goat snp10447-scaffold1373-1208032 3 53711863 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422600 Affx-122943734 AX-123292946 3 64146330 AATGCAAAAGGCAGAGGGATAATTAGAATGAAAGC[A/G]TTGCAAAATACTATTCTTATTGGAGAAATGATAAA R 2 1 2 1 101000 f 74 goat snp10448-scaffold1373-1243689 3 53675420 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406548 Affx-122955113 AX-123276900 3 64217184 GAAAAAAGTTACTCCCTTTCTTTATTTCTAGTTCT[A/G]ATAGTCTTGGGAAAGAACTGATTAACATTGTTGGC R 2 1 2 1 101000 r 74 goat snp10449-scaffold1373-1314543 3 53601007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420013 Affx-122945161 AX-123290361 3 64299669 CCCCAGTGGGAGCTGGACTGTGAGAGTGTGTGTGG[C/T]GTTTGTCAGCACGTGGGCTTTGCTGACTCTGGGGG Y 2 1 2 1 103000 r 74 goat snp10451-scaffold1373-1397028 3 53519153 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790461 Affx-122925458 AX-385277464 3 64350177 TAGTCCCTATCTTGCTCAGTCCTACTGATTATCTC[A/G]TCTCAAGATCAAAGACATTCAGACCAATTATGTCT R 2 1 2 1 101000 f 74 goat snp10452-scaffold1373-1447536 3 53467914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414448 Affx-122949947 AX-123284797 3 64394264 TGTTTAGATGTTTCTTTTCAGCTTCAGCCTCCGTC[C/T]CCTCTCCCCATCACAAGCATCTAAGAAAGGCAGCT Y 2 1 2 1 103000 r 74 goat snp10453-scaffold1373-1491623 3 53424142 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788655 Affx-122956918 AX-385275671 3 64423223 TAGATTTTAACCAGAGCACTGAAAGACAAATTCAC[G/T]CCTTGTGGTTGGTTCCTAGTGAGCACTAAAGATGT K 2 1 2 1 101000 r 74 goat snp10454-scaffold1373-1520582 3 53394706 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428449 Affx-122938810 AX-123298792 3 64456639 GAGAGGAGACCACCTTCCACCCCATACTTCAAACA[G/T]ATCTACACCTGGTGAGATTTATTATGCAACAAAAG K 2 1 2 1 303000 r 74 goat snp10455-scaffold1373-1553998 3 53360997 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794983 Affx-122954513 AX-385281943 3 64487158 TAAATTGAAGGAAAATCTATGGAATTATTGTCATG[C/T]GGTATGTGGAAAATGTTTAAAACATAAGAAGCTTT Y 2 1 2 1 101000 r 74 goat snp10456-scaffold1373-1584517 3 53330835 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386421 Affx-122970811 AX-123256779 3 64557505 ATCCAGGTGACAGCGTAACCATGGACAACAAGCAC[A/G]CTAGCAATCAAAATGATCCAGAATATATCTGTATT R 2 1 2 1 101000 f 74 goat snp10458-scaffold1373-1654864 3 53260034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407126 Affx-122954868 AX-123277477 3 64604738 GGGGCTTTGAAATGCACTGCATGACTTCTTTGGCA[A/G]AGGATTTACATCTTATTTGCTTTGCTTAAGCTAAT R 2 1 2 1 201000 r 74 goat snp10459-scaffold1373-1702097 3 53212771 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450646 Affx-122921980 AX-123320980 3 64662665 ACTTTTAATTAGAATCAGGGGAGAAACAAGGTGTC[A/G]TTTCACCCATTCTGCCAGGATAGGATCCTATCTAT R 2 1 2 1 101000 r 74 goat snp10460-scaffold1373-1760024 3 53176780 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406318 Affx-122955458 AX-123276670 3 64698601 GTACTACTGCTTGAATATTCCTTATAAAATGCCAG[C/T]TCATCTCTACCTAATGCCTCTTACTGGCTTCCCTC Y 2 1 2 1 101000 r 74 goat snp10461-scaffold1373-1795960 3 53140851 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453733 Affx-122919621 AX-123324066 3 64730963 TTAATCCCGTATGCTAAAGTTTTCATGTCTAGAAA[C/T]GTCAGCATAAGGAAAACAGCTATAATAATTTAAGA Y 2 1 2 1 201000 r 74 goat snp10462-scaffold1373-1828322 3 53108400 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389851 Affx-122968160 AX-123260208 3 64760891 TCTCTGAGCTCCTCTCTCAGTAATTCAACCCTCTA[A/G]TATTTGACAAGCAACAAGTGTCTGGAGAACAATGT R 2 1 2 1 201000 r 74 goat snp10463-scaffold1373-1858250 3 53079077 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401640 Affx-122959588 AX-123271993 3 64796853 CTTAACCAAGCTGTCAGTAGTCAGGGCTGCCATTC[A/G]TTTTTTTTGCAATCCTTTTCTCTCATTCTTTCTTT R 2 1 2 1 102000 f 74 goat snp10464-scaffold1373-1894212 3 53043473 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786272 Affx-122919775 AX-385273307 3 64859673 CTGGGGCAATTTAACCTATTTATTCTTCTCAATTT[A/G]CCTCTAAGTTTTCAGCTACAACAGGAACACAATAA R 2 1 2 1 101000 f 74 goat snp10465-scaffold1373-1957032 3 52980042 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769232 Affx-122941940 AX-385256406 3 64895958 ATTTGAAGTCACTTTTTTAAAGATAAAGGGAAGTA[A/G]ATTACATTATTTAGTTACTTCTTCCCCACTAAAGG R 2 1 2 1 202000 f 74 goat snp10466-scaffold1373-1993317 3 52943468 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410121 Affx-122952818 AX-123280471 3 64965596 AATGACAAATTTATTGAGCTTTTCAAGTATTTGTT[A/G]GATAGAGATAAAGTATTGTGTAGGAACCAGAGGTT R 2 1 2 1 101000 r 74 goat snp10467-scaffold1373-2062955 3 52873538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415239 Affx-122948954 AX-123285588 3 65004655 CACGTCTAATAAAATCTCTCATGTTTCCAGAGAAG[C/T]AAAAATTCAATTCAATAAACATTTGTAGAGCTCCT Y 2 1 2 1 101000 f 74 goat snp10468-scaffold1373-2102014 3 52834633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432298 Affx-122936314 AX-123302639 3 65069725 CTAAAATCCTATTAAACACTGGAGCACAGACAGCA[C/T]GTTCCTGGGACCCCCTCTAAGTAGTGTAAGACACT Y 2 1 2 1 101000 f 74 goat snp10469-scaffold1373-2167084 3 52769710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424315 Affx-122941959 AX-123294661 3 65125645 GCCTTTCCTACCTGTTCATTTTCCTCCCCAGTATC[A/G]TCCCCTCACTCCTAACCTATCTACCCTAATAGAGG R 2 1 2 1 201000 r 74 goat snp10470-scaffold1373-2223004 3 52713823 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771637 Affx-122941680 AX-385258795 3 65176424 AGAGGAGTTTTCATCTTCTTTGAATACCAGGAAGG[C/T]GAAAGCTTTTCCTGTAAATTCATTTGCCATTTAGA Y 2 1 2 1 101000 f 74 goat snp10471-scaffold1373-2273783 3 52662478 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452444 Affx-122920570 AX-123322777 3 65240670 TCATAGAGGTGAGACCCTAATCCAATTGGACTGAT[A/G]TCCTTATAAGAAAAGAAAGAGACACCACAAATACA R 2 1 2 1 103000 f 74 goat snp10472-scaffold1373-2338029 3 52598136 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427480 Affx-122940013 AX-123297823 3 65301414 CTTTTCATCTCTGTCCTTACTGCATGTGTCTGGCA[C/T]AGGAAAGGCACTAAATAAAATGATTGTTCAATGAA Y 2 1 2 1 101000 f 74 goat snp10473-scaffold1373-2398773 3 52537302 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785165 Affx-122929407 AX-385272211 3 65333324 AATAAAACTGAGTCTATCAAAGATGACTAGATGAT[A/G]CATTATAGACTGCAACTTTACCACTAATTTCAAAA R 2 1 2 1 101000 r 74 goat snp10474-scaffold1373-2430683 3 52505328 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408816 Affx-122954033 AX-123279167 3 65383770 AATAATACCCATCCTGTAATCTTGCTGAGGGATAA[C/T]AAATATCTGTAAAATATCTGGCGGGCTGTCTGCCA Y 2 1 2 1 201000 f 74 goat snp10475-scaffold1373-2481129 3 52455131 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795215 Affx-122975031 AX-385282173 3 65421391 AGGCAAAAGGACTTAATATCTCCAAGCTTCAATTT[A/C]TTCAAAGTAGTCAAGAATAATAATAACCTTAACCA M 2 1 2 1 101000 f 74 goat snp10476-scaffold1373-2518750 3 52417457 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787438 Affx-122977995 AX-385274463 3 65452475 TCGAGCACCCAGTGACCATCAAAATGCCATGTTAA[C/T]ATTTCACAACTCAGATCCACCATCTATTTTGTGGA Y 2 1 2 1 101000 f 74 goat snp10477-scaffold1373-2549834 3 52386974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793944 Affx-122973707 AX-385280913 3 65492185 GTTGGGCCTTACTATCAATGATTTAATTGAATTGA[C/T]GAGATTTATTTCTTTCTTAGTGCAAATAAAATGGC Y 2 1 2 1 101000 r 74 goat snp10478-scaffold1373-2589544 3 52346985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393604 Affx-122965370 AX-123263960 3 65546057 TATTTATTCCCTAGAAGGATGTAGTTTATTTGCAC[A/G]TGGGAAAATCTAGCATATTAACTCATTAGAGCTCC R 2 1 2 1 101000 r 74 goat snp10479-scaffold1373-2643416 3 52292768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788244 Affx-122941145 AX-385275263 3 65633061 ATTTGGAAAAGAAAAGGGGTTGGCAAGTAGAAAAC[A/G]GAACACCTGGCTATTAGGTAATTACTCCTTCCAGA R 2 1 2 1 101000 r 74 goat snp10481-scaffold1373-2730420 3 52204607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450891 Affx-122922205 AX-123321225 3 65702635 GTGCATAATGTTAAGTTTTCTCAACTGAGGGAACT[A/G]GAGGGACCTTGCAGGATGACAGGCTCTCCTGCAGT R 2 1 2 1 101000 f 74 goat snp10482-scaffold1373-2799994 3 52134603 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389853 Affx-122968158 AX-123260210 3 65741050 AAAACATGGGTTAGTATCTTTCCTCTAAATTCATT[A/G]CTATACTTATCCCAGTGGTAAACAGTGAAATACTA R 2 1 2 1 101000 r 74 goat snp10483-scaffold1373-2838409 3 51861918 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770978 Affx-122947401 AX-385258141 3 65774953 GTACATTAAGTTCTTCTAACCATCTCTCTATGCTA[C/T]AATTTTTTAGCTTGTTTCTAACATTTTATACATTA Y 2 1 2 1 201000 r 74 goat snp10484-scaffold1373-2872312 3 52064848 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802053 Affx-122950257 AX-385288957 3 65806441 TTTCTACAAGAGTACTTAAGGAATGATCCTGGAAA[G/T]CTAAAAGCTTTTGATAATAACCAAGCTTTCAAATC K 2 1 2 1 201000 r 74 goat snp11968-scaffold144-5847631 3 51619756 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277971 Affx-1111836185 AX-519551465 3 65842975 ACTCTTGAAGCTATCTGGACATTCATGTTCACTCT[C/G]CCTTGTACCTTAGTGTGTAACAATCCTTCTTCCTA S 4 1 2 1 101000 f 74 goat Random2.2K-342 3 65842975 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418076 Affx-122946608 AX-123288424 3 65847418 CTAATTTGACCTATTTTTTAAAATTCATAGAAGGG[A/C]AGAATTAAGAGTAGAAAAGAGTGGTATTATTCGGT M 2 1 2 1 101000 r 74 goat snp11967-scaffold144-5806654 3 51576804 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401991 Affx-122958770 AX-123272344 3 65898539 TCTCCTTTTCTGACTGCCTTGTCTGCCTCTACCTC[A/G]TGGCAACAAACACATTTCAGGGTGCCTAGTCACCA R 2 1 2 1 201000 r 74 goat snp11966-scaffold144-5755533 3 51525239 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420576 Affx-122945271 AX-123290923 3 65955636 AAAACTGCTGTGTCCCTCTGTTCTCAAATTATTCA[G/T]CAAAAGGGGAAATTCCAACCATTTATCTAGAGCCT K 2 1 2 1 201000 f 74 goat snp11965-scaffold144-5698436 3 51466538 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792351 Affx-122951057 AX-385279333 3 66044770 TATCTAGTGATATTCAGGTCTGACAATAGGGGCAC[C/T]AGTTTCCTATCAAGTGTAAAACTACAATCTCTGCC Y 2 1 2 1 101000 f 74 goat snp11964-scaffold144-5609302 3 51378239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441159 Affx-122929561 AX-123311496 3 66089847 TATGAAGATGTCCATATTTTCAAGTCAGCAGTAGA[C/T]GGGCATTTTACTTCATTCACAAGATTGTTTTTTCC Y 2 1 2 1 101000 f 74 goat snp11963-scaffold144-5564225 3 51332805 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411583 Affx-122951620 AX-123281933 3 66135244 ACAAAAATTATCTAGTTTGGGCTCCCACGTGATTC[G/T]CAGAGAAACATCCAGGTCCTGCTAAATGATGTACT K 2 1 2 1 101000 f 74 goat snp11962-scaffold144-5518828 3 51286127 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794153 Affx-122966447 AX-385281119 3 66204031 TGAAAAATGGAAATTTGAAAATGGCCATTTGATGA[C/T]GGCCTATTTAAGAAGGAGTATTTTTAGGATCAAAA Y 2 1 2 1 201000 f 74 goat snp11961-scaffold144-5450041 3 51217296 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437906 Affx-122931655 AX-123308244 3 66276921 AGTAATAGTATCTAATCCTGTCTTTACAACAATTA[C/T]ATTCAAGTGAAAAAGTCAGTCAAAAAGAGTAAACA Y 2 1 2 1 101000 f 74 goat snp11960-scaffold144-5377151 3 51145176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804502 Affx-986696669 AX-385291058 3 66282835 TTCATCTTTCAGTGTCTTATCTTTTTGCCTTTTCA[C/T]ACTGTTCATAAGATTATCAAGGCAAGACGGCTGAA Y 2 1 2 1 600010 r 74 goat 3_66282835 3 66282835 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 468277973 Affx-1111836186 AX-519551467 3 66329663 AGTGATCATGGTTTAGAGAAATGAAGTGGTTAAGA[A/G]TGAGGGACTGGACAGTTACAGCAGAGTGAAAGGAA R 2 1 2 1 101000 f 74 goat Random2.2K-343 3 66329663 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320804102 Affx-986696671 AX-189342110 3 66344680 CAGACGGAAACCTGCCCAGAAAGAGGAGGAAGCAA[C/T]GCACAGTAAGAGCAGATAGTCCAGGCTGCCCATGG Y 2 1 2 1 600010 f 74 goat 3_66344680 3 66344680 Ancestral_priority_1043 ancestry 0.56 neutral IMAGE 10K 10K ancestral 38415450 Affx-122949177 AX-123285799 3 66361278 CATACCAGACACATATTTACTGCATGCACGCACGC[A/G]TGAAAGACACCAGTCTAGACCCACTGTTATACGCT R 2 1 2 1 201000 r 74 goat snp11958-scaffold144-5292794 3 51059679 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277975 Affx-1111836187 AX-519551469 3 66364459 TGAAATTTTATCTTCTTGCTTTGAGCCCTCACTTG[A/G]GATGGGTTTTTAAAAGCATGATTTTATATATTATT R 2 1 2 1 101000 f 74 goat Random2.2K-344 3 66364459 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789712 Affx-122922645 AX-385276720 3 66405007 TATGTCAGAAGGTGGTAAGGGCAAAGAGAAAAACT[A/G]TAAAGAAGGGAAGCAGGTTATAGACTATCAGGAGG R 2 1 2 1 101000 r 74 goat snp11957-scaffold144-5249065 3 51016019 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771371 Affx-122971904 AX-385258529 3 66446223 TGTAGAAAATATAACATGGGAATCCTGTGCCAAGT[A/G]CTAGATAACTTATCTTTTACTCTATTATTTGCAAA R 2 1 2 1 101000 f 74 goat snp11956-scaffold144-5207849 3 50974797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764546 Affx-122971391 AX-385252203 3 66497979 TTGTTTTTTACTTTTTTATGGTAAAATATCCATAA[C/T]ATAAAATTCACAATTTTAGCCATTATTCAGTTCAT Y 2 1 2 1 303000 f 74 goat snp11955-scaffold144-5156093 3 50922301 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391526 Affx-122966655 AX-123261883 3 66532830 CGTATGTTGTTAGGAAGGGGGAGATAACAAACACA[C/T]GAAGAAATAAATGAATAAAGTAAATTCAGAGAATG Y 2 1 2 1 101000 f 74 goat snp11954-scaffold144-5121242 3 50887622 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275224 Affx-1111834777 AX-519548803 3 66538300 TTACTTGTCCTTTTCAATCCCTGTTTGTCTGCCTG[A/C]ACTGG M 2 1 2 1 102000 f 74 goat GoatD01.052504 3 66538300 T G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38452316 Affx-122920669 AX-123322649 3 66573552 AGGAGACATAGATGCCAGCGTAGGAGGATGGCAAA[C/T]ACTGCAGTGTTAGTAGAGAGATCAGCAGGGGAGAG Y 2 1 2 1 101000 f 74 goat snp11953-scaffold144-5080520 3 50846254 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791531 Affx-122967261 AX-385278522 3 66615773 TGTACACATCAGTTTTCCCACCTTCTACTGTTTAG[A/G]AAAGATTGAGGGCCCCTGGTAGGGATGCCATGTGT R 2 1 2 1 202000 r 74 goat snp11952-scaffold144-5038299 3 50804074 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451704 Affx-122921563 AX-123322037 3 66647107 TAGAGCATAAAGTCTTTGAGAAGAACAGGGAAAGA[C/T]AGGTGGAGAAATACATTCTTCTTATCTGTTATGCA Y 2 1 2 1 101000 r 74 goat snp11951-scaffold144-5006965 3 50772167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376622 Affx-122979039 AX-123246981 3 66680980 AGTGGTGAATTAGCTCCCGGGGTTGTCAACACAAA[C/T]GCAGAGAAAAGGAAGCTGTCATTCTTTTTAAATGA Y 2 1 2 1 101000 f 74 goat snp11950-scaffold144-4973092 3 50738219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411326 Affx-122952274 AX-123281676 3 66722851 CCTCTCGGGTGACAGAGAATGATTCCAGCATTATG[A/C]TCACAATTATAGCAGTACTGTGAGTCAGAAGCCCT M 2 1 2 1 303000 r 74 goat snp11949-scaffold144-4931221 3 50696532 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382108 Affx-122974888 AX-123252466 3 66766433 GTGGACTTGAGTTCAAATTCAAGTTCTAACACTTA[C/T]AGGTTATGTGATCTTGGGCAAGTTAGTTGAGTTCT Y 2 1 2 1 101000 f 74 goat snp11948-scaffold144-4887639 3 50652310 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413415 Affx-122950704 AX-123283764 3 66798528 ATCAAGGTGGGAAACTATGTCAGATATTTTCTCCA[C/T]GGGTAATAAGCATTCATTAATTCCCAAAGAAACCC Y 2 1 2 1 101000 r 74 goat snp11947-scaffold144-4855544 3 50620338 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425087 Affx-122941243 AX-123295433 3 66849673 CTAAAGTCTGTTTTACACAAAATATATTCAAATTA[A/G]CCTTATAATCTCAGGTTCAGAAAAAACTGAAAAAT R 2 1 2 1 101000 r 74 goat snp11946-scaffold144-4804399 3 50568968 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801222 Affx-122926932 AX-385288135 3 66881851 TGTCTACAGGGTTACTTTGAAAAAATCAGGATGTT[A/G]CATTAGTATTTATATTGATTATTCACAACCATATT R 2 1 2 1 101000 f 74 goat snp11945-scaffold144-4772221 3 50536712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272218 Affx-1111833395 AX-519545965 3 66910631 ATAAATTAAGGGAGGTCAGAGGCCATATGTGATCT[A/G]GTCTGTGGATGGGGTCTTATATAAGTAGCTTTGCC R 2 1 2 1 201000 f 74 goat 3_66910631_AF-PAKI 3 66910631 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398825 Affx-122961393 AX-123269180 3 66927020 CATAAGTAATTGGATAATTGAGAATTAACACTTCC[A/G]TACTTTTTTGTTTATGTTTTGTTTAATCATAGCTT R 2 1 2 1 101000 f 74 goat snp11944-scaffold144-4727052 3 50490235 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378875 Affx-122976508 AX-123249234 3 66977058 CACAGGATGACCATTGGTGACCTATGCATGAAGTC[A/G]CTATGAAAATGAAGAATCACATAAACACTGCTGGC R 2 1 2 1 101000 f 74 goat snp11943-scaffold144-4677014 3 50440323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382493 Affx-122973821 AX-123252851 3 67032499 TTGATTCAAGTATAACTTTATATGATGCTGAGTAA[A/G]TGGTCATAAGAACCCATGGGGATATAATGCATGTA R 2 1 2 1 201000 f 74 goat snp11942-scaffold144-4621573 3 50384632 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427831 Affx-122939739 AX-123298174 3 67066839 GTAGAATTCAAGAATTCAAGAGGAAAACAAAAGTA[A/G]GAGACTACAGCTCAGTTTTGACAAAATGCTATTTA R 2 1 2 1 103000 f 74 goat snp11941-scaffold144-4587233 3 50349308 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800239 Affx-122961965 AX-385287162 3 67109825 ATCATTCAAATGGTTCATATTAGTTTTGCTTTACC[A/G]TTTCATTGTAAGAGGGTATCATATTGCCCTGAAAA R 2 1 2 1 101000 f 74 goat snp11940-scaffold144-4544247 3 50305519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423566 Affx-122942413 AX-123293912 3 67167543 ACAATTCACCAATTAAAAATTTTCACCTGAATTAA[A/G]TAACATTAAATAACCAAAAAAAATTAGAAGAATAA R 2 1 2 1 103000 f 74 goat snp11939-scaffold144-4486529 3 50247017 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448964 Affx-122923130 AX-123319299 3 67250068 CCTAACCTGCTGGCCTGCAGAGTCCTACGGGAAAC[A/G]GAATGCTTTTACACAACTGCCTTTCCTGTTAGCCT R 2 1 2 1 101000 r 74 goat snp11938-scaffold144-4404004 3 50158290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416932 Affx-122948040 AX-123287280 3 67313545 AAGAACCTAACTAAGTTACGGTGTATCTGCCTTGA[C/T]GTCTTTGGAATTCTTCATACTTATGTGGATTCCCT Y 2 1 2 1 101000 f 74 goat snp11937-scaffold144-4340527 3 50093997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778115 Affx-122951728 AX-385265230 3 67391508 TTATCTGTCACAATTCTGTAGGCAAGCAGTCCATG[C/T]AGATTCAGCTACAATATTGACCCAGGGCCTCGCAA Y 2 1 2 1 101000 f 74 goat snp11936-scaffold144-4262564 3 50014007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396525 Affx-122962955 AX-123266880 3 67421392 ATCACATGGCTATACCCATCCATTTATTGTAAATT[A/G]TTATTGAGAGAGGTCTAAGAAGAAAAGCCTGGGGA R 2 1 2 1 101000 r 74 goat snp11935-scaffold144-4232680 3 49984428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448355 Affx-122924120 AX-123318691 3 67482326 TGCTATGGATACACATCAGTAGTACCTATTAACCT[A/G]CTACTCTAACCCATTAAGAGGGCAGGCTGGAAGTT R 2 1 2 1 101000 f 74 goat snp11934-scaffold144-4171746 3 49923374 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377528 Affx-122977471 AX-123247887 3 67525041 TTTCCCCGTAAATAACAGCATGGAGCAAATATATC[A/G]CATTCCCAACTTCTTTGAAAAGGCTAAAAATAACC R 2 1 2 1 101000 f 74 goat snp11933-scaffold144-4129031 3 49881475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476177 Affx-1251763681 AX-586011604 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 4 1 4 1 20000 f 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 539476432 Affx-1251763681 AX-586011833 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 4 1 4 1 20000 r 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165087 Affx-1251763681 AX-606940500 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 r 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165331 Affx-1251763681 AX-606940742 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 r 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165408 Affx-1251763681 AX-606940819 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 r 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165431 Affx-1251763681 AX-606940842 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 f 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165504 Affx-1251763681 AX-606940915 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 f 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 562165942 Affx-1251763681 AX-606941351 3 67555392 TACTGATAATGAAAAACTATCAAGCTAATAATTAT[-/AGAACCAGAAAGTGAAAGAGGAAAGATGGCGGAGGAATAGGAATTGAATCGCCAGTCCAAAAAAAAAAAAAAAAATTATG]GAACCATCCATGATAAGTGAAGGATTTCCTGGTAG - 8 1 4 1 20100 r 74 goat SV_309 3 67555392 - deletion junction SV-TF-chip 320799186 Affx-122927025 AX-385286116 3 67586389 CATTTTCCAGTGTGTTGCTGTATAATTCTTCATAG[C/T]AATTTCATGATTCATGATTGCTTGCATTTCTGTGA Y 2 1 2 1 201000 f 74 goat snp11932-scaffold144-4067683 3 49819629 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453059 Affx-122920065 AX-123323392 3 67617695 ATTCTAGAGAGTTTTTTAGGATTTACCCAATTTGG[C/T]GGTTTTATATAAACTGGCTGATGAGAGTCAGAGAA Y 2 1 2 1 101000 r 74 goat snp11931-scaffold144-4036377 3 49786673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277977 Affx-1111836188 AX-519551471 3 67621592 CCTGATGCTGTGTGGACTGTGTTGGGCTGCAATTT[A/T]TTTTGTTCAATTATTTACATGCACTTGGCCAAATA W 4 1 2 1 102000 f 74 goat Random2.2K-345 3 67621592 A T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800895 Affx-122963551 AX-385287810 3 67675866 AAATCCCTGAACTCTAACTAGTCTGGTTCTGAGTC[A/G]TATTAAATCCTATGATCCATGGGGGTGGCCTGAGA R 2 1 2 1 202000 r 74 goat snp11930-scaffold144-3978206 3 49727265 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453327 Affx-122919972 AX-123323660 3 67710970 AGCAATGGTTGCCTTAGCAACTCTTTAATAGGCTG[C/T]GACTCTCAAAACCTGTCTTTTCTAGAGAGTCTTCA Y 2 1 2 1 201000 r 74 goat snp11929-scaffold144-3943102 3 49691854 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381247 Affx-122974496 AX-123251605 3 67773504 TAAAATTTCCCTAGTTCTGTCAAATGCCATTTCTC[C/T]ATGGAGCTTAATTATTTCTTCTTTTTCAGAAGTGA Y 2 1 2 1 101000 f 74 goat snp11928-scaffold144-3880568 3 49629347 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780092 Affx-122930401 AX-385267189 3 67803625 TGCAGCACTTGGTAACTCTGTGATTTCATCATAAC[C/T]CTACTTCAATAGACTCAAAATCAAAATAATAATAG Y 2 1 2 1 101000 f 74 goat snp11927-scaffold144-3850447 3 49598635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424585 Affx-122942213 AX-123294931 3 67848109 AAACAGGGATTATAAAGTTTCATTCAAAACCAAAA[C/T]AATAGGCTATTACATACTAGAAGAATTGAGATTGC Y 2 1 2 1 101000 f 74 goat snp11926-scaffold144-3805963 3 49553302 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767714 Affx-122958067 AX-385254948 3 67877996 GCAGGAAAATGTAAGAGAGGACTTTGTCCCTTTAG[C/T]ATATTCTAGGCCTACGCAGTGTGTAAACAGATGAA Y 2 1 2 1 101000 f 74 goat snp11925-scaffold144-3776076 3 49522555 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274529 Affx-1111834349 AX-519548120 3 67913669 GCATAGAAATCACTTGTCTAAAAAGGAAGGTACCA[A/G]CAAGAGCAGGGGTGGAGGCAGGGCTGCAGGGGGCC R 2 1 2 1 101000 f 74 goat GoatD01.031083 3 67913669 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38388116 Affx-122969486 AX-123258474 3 67929293 ATGGACAATCAATAAAAGGCAGGGGTCCACTCTAG[G/T]TCCAAGACTGGTTGGATTTTCACAGAGCATGAAGC K 2 1 2 1 101000 f 74 goat snp11924-scaffold144-3724779 3 49470479 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449735 Affx-122922465 AX-123320070 3 67998264 TGTCCACTGAGATAAAACAAGTGAGAGTGTTAGTC[A/G]CTCAGTTGTGTTGTGTCCTGCTGTTTGTGATCCCA R 2 1 2 1 103000 r 74 goat snp11923-scaffold144-3655808 3 49401007 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785604 Affx-122921185 AX-385272648 3 68043979 CTATTTCTAAAATTCTAAGTCACAAAGCTTGTTTC[A/G]CATTTTGTTTAATGATTCTAAAGTTAGCCAGACAA R 2 1 2 1 101000 f 74 goat snp11922-scaffold144-3610093 3 49354316 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278137 Affx-1111836189 AX-519551627 3 68087601 TATTGGAAGAGATGCTGACTCTAAGCAGGACTGGA[A/G]GGACAGAGAATTGTGAGAAACGTTGTTCCTGGCTA R 2 1 2 1 101000 r 74 goat Random2.2K-347 3 68087601 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800911 Affx-122954154 AX-385287826 3 68092561 CCAAATAATTCATTTTATATACAACTTTACTATCT[C/T]GATGCCAATGTTATTCTTCCAACTTGCTATGGATT Y 2 1 2 1 101000 r 74 goat snp11921-scaffold144-3561511 3 49305057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431711 Affx-122936763 AX-123302052 3 68134137 TACTTGGAACTTGCTCAGAGGGTGAATCTCAAATG[C/T]ACTCACCACAAAAAGGAAATGGAAATTCTAGGTCT Y 2 1 2 1 101000 f 74 goat snp11920-scaffold144-3519935 3 49273742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771365 Affx-122955956 AX-385258523 3 68164267 TACGATCTGTTTCTCCTCAAGCCACCAAAATTGCC[A/G]TATTTTGTGGGATTATTTTCCCTTCGTTGTGGTCC R 2 1 2 1 201000 r 74 goat snp11919-scaffold144-3489805 3 49243432 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443320 Affx-122927450 AX-123313657 3 68196422 GAAACTCAGCTGACTGAAAAGAGAAATAAATGGTC[A/G]TTTACTTCCATGGTTGATTCTCAGATCTTTACTGT R 2 1 2 1 102000 r 74 goat snp11918-scaffold144-3457650 3 49210658 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410004 Affx-122953266 AX-123280354 3 68247295 GCTATCTATATATCTCTGTCTCTATCTCTACATTA[C/T]GATATCTAACTGCATATTCCTGGCCCAGTTCTGAA Y 2 1 2 1 201000 r 74 goat snp11917-scaffold144-3406777 3 49157484 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783221 Affx-122921163 AX-385270287 3 68277351 TGTAGCAGTTGTCATTTTCTTGGAAATTTGTGATT[A/C]TCTAGGATTCAAAAAGATTGATCCTTCCAGGTCAA M 2 1 2 1 101000 f 74 goat snp11916-scaffold144-3376721 3 49126714 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399207 Affx-122960609 AX-123269562 3 68321829 GTTAAGCAAGATGAAAAAATTCTGTATACCTCTAT[A/G]CAATGATGTGCACATATGATTAACAAAACCGTACT R 2 1 2 1 101000 r 74 goat snp11915-scaffold144-3332243 3 49081495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451767 Affx-122921514 AX-123322100 3 68423843 CAAGGAGAGGGCAGCCAAGAGCAAGAAGTAAACTG[C/T]GTTTTTAAAATGAAAGTAAGGGAAAGTGAAACCAA Y 2 1 2 1 101000 f 74 goat snp11913-scaffold144-3230229 3 48978573 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396311 Affx-122963082 AX-123266666 3 68475868 TAGTGCTTCAGTTCCTTGCTCTTTCCTTCATGATA[C/T]GCCTTAAATAAATACAACATTTATTTATGTCAAAT Y 2 1 2 1 103000 f 74 goat snp11912-scaffold144-3178204 3 48926546 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385326 Affx-122971664 AX-123255684 3 68524246 GGACTCTAGGTCTCCAAAACAGGATGATAAAACAC[A/G]TACACATCCATTTATTTCTGTAAACTCTGGTATCG R 2 1 2 1 101000 f 74 goat snp11911-scaffold144-3129826 3 48878375 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783695 Affx-122976719 AX-385270753 3 68558100 GTACAATATTGCAGTATATTTTTCACTTTCTCTGG[G/T]ATAGCTAATTCCTTAGCAAGCTGCATAGTCAATAC K 2 1 2 1 202000 f 74 goat snp11910-scaffold144-3095972 3 48844113 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384267 Affx-122972311 AX-123254625 3 68604035 AATCTATCGTGTTATAGTTTTTATACTAATTTATT[A/G]TTGAATTCTTGAGAAGATCCTCTATAGTTGAGAGT R 2 1 2 1 201000 f 74 goat snp11909-scaffold144-3050037 3 48796734 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796440 Affx-122971215 AX-385283390 3 68700158 ATGTCTTTCATTACTGTTGCAAACTTGAAAATTTC[A/G]TTCCCTGAGATGGCTAAATCGAGATTTTGAGCTTA R 2 1 2 1 101000 r 74 goat snp11907-scaffold144-2953914 3 48700651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417882 Affx-122946757 AX-123288230 3 68754491 CTCTTCAATGAGTGACATTAAGTAATATGTATGAG[G/T]AATTGCTGAGTTTACTGCTCATTACCTCTTTAAAA K 2 1 2 1 101000 f 74 goat snp11906-scaffold144-2899581 3 48646284 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423228 Affx-122942695 AX-123293574 3 68834817 AAATGAAAGGAAAGGAAACTTGCAAGTAACTGAAG[C/T]AATTAAGGAAAGAAACTGATATTATCTGGTCTAGA Y 2 1 2 1 201000 r 74 goat snp11905-scaffold144-2819255 3 48567748 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423994 Affx-122942112 AX-123294340 3 68868067 TCTTTAGTTCTTCTACATATTTGTTAAAAATTTCA[C/T]GCATGTTCTCAATCTTCTCCTCCATTCTATTTCCA Y 2 1 2 1 101000 r 74 goat snp11904-scaffold144-2786005 3 48535683 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783448 Affx-122923026 AX-385270511 3 68918232 GCTGATTGTCTATATTATGGGACTCATATTCAAAT[A/G]CATTTCTCTCTACCAAACTGCCTAAAGGTATTGAT R 2 1 2 1 101000 r 74 goat snp11903-scaffold144-2735840 3 48485063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389150 Affx-122968540 AX-123259508 3 68971867 ATCATTTTCTGCTTCCTAGATATACAAGTCTGATG[C/T]GTAGCCTGCAAGATTCTGTACAAGAAAAATACCCA Y 2 1 2 1 101000 r 74 goat snp11902-scaffold144-2682205 3 48430850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401823 Affx-122959449 AX-123272176 3 69025806 CACTCCAGATCACTCTGCTGGGCACATGCATCATG[C/T]GGCAGGCAGACCTAGGTGTCAGGTGCAGTGGTTTT Y 2 1 2 1 201000 f 74 goat snp11901-scaffold144-2628266 3 48376340 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402729 Affx-122958342 AX-123273082 3 69056471 ATGGACTGGATATTTTATTGAGAGAATTAATCTGA[C/T]GTGTTTGATTAGATCTAAATCTTCATGCATGTATA Y 2 1 2 1 101000 r 74 goat snp11900-scaffold144-2597601 3 48345568 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377200 Affx-122978185 AX-123247559 3 69096867 AGGTCTTGGCTAAAACACAACTTCCACAGAAGTAG[A/C]GAGAAGCTTCACAAATATCCTAAGTGGACCCCCTC M 2 1 2 1 101000 f 74 goat snp11899-scaffold144-2557205 3 48304460 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790208 Affx-122930993 AX-385277212 3 69128844 TGTTCATCATACAACAAAGACTCAAAGGTAGATCA[C/T]GAAATAATTTTATAGGGCTTGGTAAGTAAGAAATA Y 2 1 2 1 101000 f 74 goat snp11898-scaffold144-2525228 3 48271750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447638 Affx-122923978 AX-123317974 3 69194116 TCTTCCTAATAAGCTTAATTTTTCTATTAACAGCA[A/G]ATAGAATACTACTGGATTACCTGTTGAAGTCTGGT R 2 1 2 1 101000 r 74 goat snp11897-scaffold144-2459956 3 48205079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420647 Affx-122944830 AX-123290994 3 69244695 GCCTTCCTCAGCCAACATGTATGGCATAGCAACCA[C/T]GCCAAGTTCCCCCAAATTGCCAACTCCCTCTCAAG Y 2 1 2 1 101000 f 74 goat snp11896-scaffold144-2409377 3 48153678 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435176 Affx-122933652 AX-123305516 3 69290450 CAAGGTATATCATCATGATTTCATGAATGCTAGAA[G/T]ACGTGGGACTCATGAGTCAGGGGCAAGTGAAAGTT K 2 1 2 1 201000 f 74 goat snp11895-scaffold144-2363622 3 48107740 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439992 Affx-122929796 AX-123310329 3 69347622 TTTAATAAGCATTAAAGCCTAGTAAGCAGTAAATT[C/T]ATCAATTGTTTTTATATTTTCTTAGGGAGAGACAT Y 2 1 2 1 101000 f 74 goat snp11894-scaffold144-2306450 3 48050077 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445401 Affx-122925388 AX-123315738 3 69406580 ATCCCCTTCCTATGAGAAAGTATCCAGGTATATTA[C/T]ATTACAGGGAAAAAGGGTACATTCAAAATGAATTA Y 2 1 2 1 101000 f 74 goat snp11893-scaffold144-2247492 3 47990661 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273595 Affx-1111833713 AX-519547210 3 69426418 GTTAGGTCTGGGATTGGCTGCTTGCCTTCAACCTT[A/G]A R 2 1 2 1 101000 f 74 goat GoatD01.002236 3 69426418 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38406212 Affx-122956127 AX-123276564 3 69454078 CCAATTATTTCCTTCAAGTTGCAGCTTATCTTATG[C/T]TGAACTGCTGCCCTGAGAGCCCAAATGACCCTCTA Y 2 1 2 1 101000 f 74 goat snp11892-scaffold144-2199994 3 47943361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397947 Affx-122961917 AX-123268302 3 69499528 TGTTGCATATTTATATATACCATGATTATACTTAA[A/G]CTTTAAATTTGGGGGTGTTCAATTAAGTAATTTTT R 2 1 2 1 102000 r 74 goat snp11891-scaffold144-2154544 3 47898164 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389814 Affx-122968194 AX-123260171 3 69548410 AGCGGGCAGTAGGCCCACTTACAGGGAGTTGGAAC[A/G]CTTGCTTCCTTGCCTTCTCTCTGGGTAAACCTGAG R 2 1 2 1 101000 f 74 goat snp11890-scaffold144-2105662 3 47849162 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272220 Affx-1111833396 AX-519545967 3 69616332 CTCTTTCATTTGTGAAAGGCTCTCAGAGTTGTGAC[A/C]ATTTTCTGTGTTCAAGGTTATTTTCCTGGTGCTAT M 2 1 2 1 101000 f 74 goat 3_69616332_AF-PAKI 3 69616332 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38408358 Affx-122953738 AX-123278709 3 69628197 AGACCACCTGATGTATTTTCATGTTGGGTGGCATA[C/T]ATATTATTTCATTTTTATATAATACTGAAATATAT Y 2 1 2 1 103000 f 74 goat snp11888-scaffold144-2025875 3 47767613 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793502 Affx-122930314 AX-385280479 3 69760522 GAAGTGAAAATATAGTAATTAAATTGTTGCTATAA[C/T]GAATTATTATAATTATCTGAAGGTTTCTGGCATCT Y 2 1 2 1 101000 r 74 goat snp11886-scaffold144-1893550 3 47635252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777637 Affx-122976900 AX-385264756 3 69800141 CAAAGTAATGTATGTGCTATTTGTTGTTAACAAAG[C/T]AGATATAAAAGAATTTGGGGACTATTTCTTTTCTT Y 2 1 2 1 202000 r 74 goat snp11885-scaffold144-1853931 3 47595636 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406150 Affx-122956179 AX-123276502 3 69829510 GCTTATGTGTGTTAGCTTCCTAGAGGTTCAAGTGT[C/T]TTCAATTAAAAAATGGTCAACACTAGAAAATGTCG Y 2 1 2 1 101000 f 74 goat snp11884-scaffold144-1824562 3 47565691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769793 Affx-122954265 AX-385256963 3 69865419 TGATATCACTGCTTATTGGATGTTTAGTAATAGGC[A/G]TTTGTTAGTTTCAAAAATCACATGGGAAGTTGCCA R 2 1 2 1 101000 f 74 goat snp11883-scaffold144-1788653 3 47529940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446676 Affx-122924756 AX-123317012 3 69908457 CATGGGCTAGTAATTTTTACAAAAGACACTCATAT[C/T]CCTGGAACTCATTAAATATTTGTCAGATGGTGAAA Y 2 1 2 1 201000 f 74 goat snp11882-scaffold144-1745615 3 47486926 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390083 Affx-122968031 AX-123260440 3 69939804 ATAAACTGAAGAAAGGTAATAGAATGATGACATGA[G/T]ACTTAAAGCAGGAACTCCATGTTGCTGAGCATTGG K 2 1 2 1 101000 r 74 goat snp11881-scaffold144-1714268 3 47455575 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439050 Affx-122930329 AX-123309387 3 69978062 GCAGGGTGACTTTAGGCAAGTTACACTTGATCAAT[A/G]TCCTTATCTTTAAAATGGACATAATAATAGTATCT R 2 1 2 1 303000 r 74 goat snp11880-scaffold144-1676010 3 47416956 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795903 Affx-122966039 AX-385282855 3 70016793 AAAACAACAAGAAATGCGTATCTGAAAATGTTACA[C/T]GCATATTTCCATTTTTGTGTACTGATATATTTTTA Y 2 1 2 1 201000 r 74 goat snp11879-scaffold144-1637279 3 47380018 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447058 Affx-122924516 AX-123317394 3 70054532 GAATGTTTCTGAGAGCAGTCTGCTTTGTGTGAGAC[A/G]TTTTAGGTCACATATATTGTCTGTGTTGTTCTCAT R 2 1 2 1 201000 r 74 goat snp11878-scaffold144-1599540 3 47342065 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770434 Affx-122966654 AX-385257600 3 70086056 ACTGCATACATAGTTAAAAGCTCCATGGATATTTA[C/T]GGGATGAATGGTGGATGACTCCTTACCATTGGACA Y 2 1 2 1 101000 r 74 goat snp11877-scaffold144-1568016 3 47310295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433165 Affx-122935665 AX-123303506 3 70114646 GCCATGGGGTGTAAGTAATCAATATGGAGAGGGAA[G/T]TCTCAAATACATTTCATTTTGAGGCTAAAATTATA K 2 1 2 1 101000 f 74 goat snp11876-scaffold144-1539426 3 47283058 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396568 Affx-122962924 AX-123266923 3 70147436 ATTCAGCAATTATATGTTTAACAAAATGTATTGTT[A/G]TCTGAGACTGTAAGAGAAAATTTTGTTAATATTAA R 2 1 2 1 101000 r 74 goat snp11875-scaffold144-1506636 3 47250255 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380307 Affx-122975395 AX-123250665 3 70177181 ACTTCTGTGCATATAGGGGGTATATAACTTCTGCT[A/G]TTTCATTGGCCAAAGCAAGTCACATAAACACTTGA R 2 1 2 1 201000 f 74 goat snp11874-scaffold144-1476891 3 47220492 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802655 Affx-122936658 AX-385289554 3 70207324 CCTAACAATGCTGTGAGTTATATACTATTATTAAT[G/T]CCCTTTCTGTAAATTAGATAACAGAGCACAGATAA K 2 1 2 1 201000 f 74 goat snp11873-scaffold144-1446748 3 47190355 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393384 Affx-122965904 AX-123263740 3 70237588 GAACTCATATTTTGTTTTGTTTTAAATATACAATC[G/T]CCACTGTTTTAAGAAGCTAGATAGAAAAGGTGAAG K 2 1 2 1 101000 r 74 goat snp11872-scaffold144-1416484 3 47159717 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779341 Affx-122954060 AX-385266445 3 70333762 GAATAAGGTTTTACTGTAAAGCTCAAGAGCACTGT[A/C]GGGAAGGTGATATCATCAAGCAATAATGCAGGATT M 2 1 2 1 101000 r 74 goat snp11870-scaffold144-1320310 3 47063686 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403539 Affx-122957607 AX-123273892 3 70406458 TTGAATTTTCTAGTTTTTGGAATAAGGTTTCACAG[C/T]GTGCATGCTAAGTTACTTCAGTGCTGTCCAACTCC Y 2 1 2 1 201000 f 74 goat snp11869-scaffold144-1247614 3 46990737 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422013 Affx-122943637 AX-123292360 3 70462834 AGCGCTTGGCCCTGTTTTGCTTAAGATCTTTTTCA[C/T]TGGGCATCCAATCTATTTTCTTCTGTATGGCTATA Y 2 1 2 1 101000 f 74 goat snp11868-scaffold144-1191238 3 46933038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435743 Affx-122933283 AX-123306082 3 70513872 AGAAAGTCTCTAATTCAAAAGTCCCCTATTGTATA[C/T]TCTCACAGCTTTCTCCATTTTCCTCTCATAGCCCT Y 2 1 2 1 202000 f 74 goat snp11867-scaffold144-1140200 3 46881871 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436226 Affx-122932575 AX-123306565 3 70583249 TGCTCTGTGCACAGATATGCTCTGCCATCATTTTG[A/C]TCTGCCATCCATAAGATACTGACATCATTTCCTTC M 2 1 2 1 101000 r 74 goat snp11866-scaffold144-1070823 3 46812087 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402611 Affx-122958413 AX-123272964 3 70633089 ATTCAGTCTCAGCCAACCTGACAATAAAGTGATCC[A/G]TTTATCCAACACAAGCAGGCAGAGAAGGAGATACT R 2 1 2 1 101000 f 74 goat snp11865-scaffold144-1020983 3 46761419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796154 Affx-122959126 AX-385283105 3 70669452 TTAAAATCTAAGATATAAACTTATACACATAAAAT[G/T]AACTAGTATTTAACTTTGGATATGAGCCCAGTAGC K 2 1 2 1 101000 r 74 goat snp11864-scaffold144-984620 3 46725075 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382942 Affx-122973378 AX-123253300 3 70701465 ACAAGGACCATGCCATTTGCTGTATCAGGTTGTAG[C/T]ACAGTGTCTTGCACACAACTGATAGTAAGTGTCAC Y 2 1 2 1 101000 f 74 goat snp11863-scaffold144-952607 3 46693038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443381 Affx-122927403 AX-123313718 3 70730930 TGCTAAATGCAATTATCAGTAAAACATTCCTGACA[C/T]GAGTTGGCATCAGGAAAGAAAGACAGGGCCATTTC Y 2 1 2 1 101000 f 74 goat snp11862-scaffold144-923142 3 46663626 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780690 Affx-122976703 AX-385267780 3 70763100 GAGACCTTGAACTGGCCAGAGGCCTATTAATGCAC[A/G]TAATTGTTGGGTTGAATAATGAAAACTTGTTGTTG R 2 1 2 1 101000 f 74 goat snp11861-scaffold144-890972 3 46631099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426687 Affx-122939908 AX-123297033 3 70798041 AAACTATAAATATGTTCTAGAAAATAAAATTAAGG[C/T]GATGTGTCCTGTATGGCCATGTATTCTGCCTAAGA Y 2 1 2 1 101000 r 74 goat snp11860-scaffold144-856031 NW_017199931.1 72 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777091 Affx-122946616 AX-385264214 3 70832734 TTCACTGTATCTCAGATACTTGCTATAGTGCTTGA[C/T]GCTTAGAGATGGTTTCATAAATAAACTGAATGCCT Y 2 1 2 1 101000 f 74 goat snp11859-scaffold144-821338 3 46560644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441702 Affx-122929160 AX-123312039 3 70873831 TCCTAAAGTCATGCACCTGAGTAAGTGGCAGTGCT[A/G]TGATTTAATCTAGATCAGGCTGATGCCTTCTCCTA R 2 1 2 1 101000 r 74 goat snp11858-scaffold144-780241 3 46521726 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277980 Affx-1111836190 AX-519551474 3 70877334 CTCTCCACAGGCTGCTTGAGCTCCCTCATAACATG[A/G]AGGCTGGGCTACAGAAGGGAGCATCTCAGAGAGCA R 2 1 2 1 102000 f 74 goat Random2.2K-350 3 70877334 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796948 Affx-122921858 AX-385283890 3 70960497 GTAGCAAAGCCCTCATAATAAATCCATTTACCTTC[A/G]GTTCAGGTTATAGCTTCTTTCCTAAAATGCCAGGC R 2 1 2 1 101000 f 74 goat snp11856-scaffold144-693575 3 46435516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425279 Affx-122940968 AX-123295625 3 70998989 CCACTCTGCTTTGTGTATCTTTCAGTGTCTTCTTA[A/G]CATTTTCTGCATTATGAACTTGGTAGGAGGAATAA R 2 1 2 1 201000 r 74 goat snp11855-scaffold144-655083 3 46396422 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429775 Affx-122938244 AX-123300116 3 71039197 AAATGATTAGACATAGGCTTGAAAGGATTATGTTT[A/G]AAACAAGGAAATCAAGCAGGAAAGTATTTGAAGCA R 2 1 2 1 201000 f 74 goat snp11854-scaffold144-614875 3 46355720 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436953 Affx-122933173 AX-123307291 3 71097324 CTGGAACCAGCATTTCATATTCCTGTAGTAAGCAA[C/T]AGTGGGACTAGACATATTTTCTTGTCTCTATATTA Y 2 1 2 1 101000 f 74 goat snp11853-scaffold144-556748 3 46297462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411335 Affx-122952269 AX-123281685 3 71138052 CACAGAGTCATACAGGACTTAGGGACTGTGCATGC[A/G]TGCACAAACAAATATTGAAAATAATTGGCTTGATG R 2 1 2 1 101000 r 74 goat snp11852-scaffold144-516020 3 46256354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425975 Affx-122941161 AX-123296321 3 71183306 AGGAAAGAAACAAGAATACATCCTGACCTTAAAGC[A/G]TGATGAAGCACAGATGATGTACTGTATGGCCATAG R 2 1 2 1 101000 f 74 goat snp11851-scaffold144-470766 3 46210805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791706 Affx-122955758 AX-385278697 3 71260765 CAAAGAAATACAAGATTAAGCTATGTGCAGTGTGT[C/T]CTTTTATTAAAATCATGGAAATCACTATTGATGCT Y 2 1 2 1 101000 f 74 goat snp11849-scaffold144-393307 3 46126286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375523 Affx-122979114 AX-123245882 3 71321087 TCAACAAGACTAACAGGCTCAAAAACAGATGAAAC[A/G]CAACCAACCACAGAGTTAAACCTCACATATCCTGG R 2 1 2 1 201000 f 74 goat snp11848-scaffold144-332985 3 46065557 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384227 Affx-122972377 AX-123254585 3 71381949 TATACGTCCCCCATCTTAGTAGAGACTAATGAATC[G/T]AACTTAACCTTTTACTGAGCACTTTACCTCATCAT K 2 1 2 1 201000 r 74 goat snp11847-scaffold144-272123 3 46004239 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408505 Affx-122953715 AX-123278856 3 71435758 TTTAAATTGTTCATGTTTTATCTTTACCTCACCAC[C/T]ACTTATAGGTATAATAGAGTAGTCAAATAATGTTA Y 2 1 2 1 101000 r 74 goat snp11846-scaffold144-218314 3 45950462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384445 Affx-122973099 AX-123254803 3 71465271 AGATCCTTTAAAAAGAGGAAGACAAAATGAATGAA[C/T]GAACAAGTAGATAAAAAAATAAATGAAGGATCCCT Y 2 1 2 1 303000 f 74 goat snp11845-scaffold144-188801 3 45920781 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427824 Affx-122939744 AX-123298167 3 71515876 CTTTTTTTAAATATATATAATGAATTTACTTTACA[C/T]GCCAGTGTTCCAAGTATTTTGTTATGATTTTCACA Y 2 1 2 1 101000 r 74 goat snp11844-scaffold144-138196 3 45870111 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778038 Affx-122940527 AX-385265155 3 71546697 AGAGTTGTCTCACCCTAAGGAAGGAAACAGCCTTT[C/T]GTATCATGGTACCAGTCATTGAGGGCTTCATAAGT Y 2 1 2 1 101000 f 74 goat snp11843-scaffold144-107375 3 45838988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412493 Affx-122951376 AX-123282842 3 71625346 TTCCATGTGTTACATAGGTATGGGGGGATGTGTGT[A/G]CCCCACCCTTTTTCTCTTTTAATCTCTCATTCCCT R 2 1 2 1 101000 f 74 goat snp11842-scaffold144-28726 3 45760189 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277982 Affx-1111836191 AX-519551476 3 71632335 GTGGCACCACTGCTCCTGTGGACAAAAAAAACATC[A/C]CCTGCCGTTTCAATGAACAAAGGATGCTGCAGGCA M 2 1 2 1 101000 f 74 goat Random2.2K-351 3 71632335 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796589 Affx-122945781 AX-385283535 3 71662172 ATTCCCAAATAAAAGTTTCAGATCCAGTAAATTAC[A/G]TCTTATACTGTGATAAGAAAAGACTAATGTAGTTT R 2 1 2 1 201000 r 74 goat snp15138-scaffold1615-551675 3 45716037 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420695 Affx-122944795 AX-123291042 3 71710044 CGTGAGTCCTTGCCCTGTCTTCCCTTCTGCACCAT[A/G]CTTGGCAGTCTTTCCCTGAATTCTGTTGTGAAGGA R 2 1 2 1 101000 r 74 goat snp15137-scaffold1615-503803 3 45667972 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801497 Affx-122951661 AX-385288407 3 71743648 AGTTAAACTCTGCAACAACATGCAGTAGTTCTGTT[A/G]GATAATTATTTTGCTGAACTATGTTGCATTTCTGG R 2 1 2 1 102000 f 74 goat snp15136-scaffold1615-470199 3 45634152 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780574 Affx-122973793 AX-385267665 3 71792585 ATATGAAAAATTTGGAAGCACACATCCATCTAGGA[G/T]ATTGCTTGAATGTATTATGATACATCCATATGACA K 2 1 2 1 101000 f 74 goat snp15135-scaffold1615-421262 3 45584499 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380792 Affx-122975097 AX-123251150 3 71825307 TATGAATTTACTGTTTACTTCACATCTATTAAAAC[A/G]TTTATCTGAACTACTACATTGATAAGAAATTGAGA R 2 1 2 1 101000 r 74 goat snp15134-scaffold1615-388540 3 45551137 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801639 Affx-122946864 AX-385288547 3 71856277 GGTGATTTTGTTGATATTCGTGTTGATGATGTTTT[A/C]TTCTTAATGTTTTTGGGGGTTTCCTGTGTTCTCAT M 2 1 2 1 102000 r 74 goat snp15133-scaffold1615-357570 3 45519222 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792491 Affx-122972881 AX-385279472 3 71943703 AGTAAAGAAAAAATACATGGAGTATGTATTTTCTT[A/G]TCTGTTTAAGACAAGGTAAAGTTAGAAAATCATAG R 2 1 2 1 201000 f 74 goat snp15131-scaffold1615-270144 3 45430197 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394727 Affx-122964330 AX-123265082 3 71985375 TAATAATAAAGCTAAAGCATGTTCCTTTTCATACC[A/G]TTCCAGTTCCCCCTGGATACCTTAACAAACTCAAT R 2 1 2 1 101000 r 74 goat snp15130-scaffold1615-228472 3 45390274 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766433 Affx-122933829 AX-385253807 3 72024837 AGATCACTTCTCTTCCATACCTCCTGATTACTAGA[C/T]ATTAGACTTCAACTAAATGCACAAAATAAATAGTA Y 2 1 2 1 101000 f 74 goat snp15129-scaffold1615-189010 3 45350079 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429903 Affx-122938115 AX-123300244 3 72054644 TGCTACCTTGAATTTCAAAGATGAGGTGAGTGGCC[A/G]TTCTTAGGTGGTTATCCCTCCAGTACATATTACAT R 2 1 2 1 201000 r 74 goat snp15128-scaffold1615-159203 3 45318949 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771162 Affx-122949102 AX-385258322 3 72085810 TCTTTGGACCTGGAGAAGCAAAGTATGTATCTAAA[A/G]CTTTTTTAGAAGACAAATTATGACTTTCATGTTTC R 2 1 2 1 201000 f 74 goat snp15127-scaffold1615-128037 3 45287029 C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433735 Affx-122934514 AX-123304076 3 72123325 CAAGATGACTTTGGGGGAAACATTAATTCATATCT[A/G]TGACAAAAAACAGACCTTCAGTTTGTGCCAAGCCA R 2 1 2 1 101000 r 74 goat snp15126-scaffold1615-90522 3 45249665 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771262 Affx-122939412 AX-385258420 3 72205640 TATTTTTGCATTTCCAGTATTGCTGATGGTAAAGG[C/T]GGTAAGGGTGGGAGTTCTAAATTTTTAGATATTTG Y 2 1 2 1 201000 f 74 goat snp15125-scaffold1615-8207 3 45165600 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782073 Affx-122935699 AX-385269151 3 72225962 GCCCATAAGAAGGACTTCTTCTCTACAGTAATGCC[A/G]TTATGATGAATAACTTTGCATGCAAATGAAGTAAA R 2 1 2 1 101000 f 74 goat snp54382-scaffold83-4509273 3 45145295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770934 Affx-122927298 AX-385258097 3 72266966 AGCTGTTTCCTTCAATGTATGCATTATAATTTAAC[A/G]TATTTGGGAAGGTACCATAGAGTGATTTAGAGCAC R 2 1 2 1 101000 r 74 goat snp54381-scaffold83-4468269 3 45103514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382552 Affx-122973777 AX-123252910 3 72305435 TAATCTTTTTAATATTATAACTGAAAAAGAAAAAA[C/T]AATGAGGTGATTTATGTTGGCCTTTGGAGACAGAC Y 2 1 2 1 103000 r 74 goat snp54380-scaffold83-4429800 3 45066094 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412383 Affx-122950806 AX-123282732 3 72336377 CTGGGTGAGTATACTCATAAAGTAAAGGTGTGAGA[C/T]GAAATATATGTAATGGTGTGTGCTGAAATAATTTG Y 2 1 2 1 101000 f 74 goat snp54379-scaffold83-4398858 3 45035114 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272222 Affx-1111833397 AX-519545969 3 72349145 CAATCCATTTTTTTTTTGTGAGAAAGATTGAATGG[A/G]ATAATGTTCTCTTTTTTGTCTCTTTTTCAAAGTTC R 2 1 2 1 201000 f 74 goat 3_72349145_AF-PAKI 3 72349145 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423123 Affx-122942907 AX-123293469 3 72368531 TCTTATTTTCCTAATTTCAAGGGTCTTATGGGAAG[C/T]ATCACAGTGTCTTTCATCTACTGACATTAGTGAAA Y 2 1 2 1 101000 f 74 goat snp54378-scaffold83-4366704 3 45002177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451090 Affx-122921406 AX-123321424 3 72401845 TACTGATGAGTTTCCAGACAAGTTTCAAGATGGAT[A/G]TTTATCATTATCTTCCATGATCTGTTAAGGCTTAT R 2 1 2 1 201000 r 74 goat snp54377-scaffold83-4333390 3 44968737 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429595 Affx-122937716 AX-123299936 3 72443320 GTAATTCACTGTGTATTTTGGAAAAATGTTTAACC[C/T]CTCTCAGTCTCATTTTCCTAATTTTTAGCAGTTAT Y 2 1 2 1 101000 r 74 goat snp54376-scaffold83-4291915 3 44927282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444411 Affx-122926580 AX-123314748 3 72481678 ATCAACAGACATCATGAATTTGTTTAAAAGAATAA[C/T]AGCCTTAGGGTGAAGTTGCAATCTCTGCCCAGTTT Y 2 1 2 1 101000 r 74 goat snp54375-scaffold83-4253557 3 44888292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800485 Affx-122953378 AX-385287405 3 72519423 TTCATAGAATTATTATGAGGAACAAATGGAATATC[A/G]CATGTGTATCAGTGAGTAGAGTGACACCACCAGGC R 2 1 2 1 101000 r 74 goat snp54374-scaffold83-4215812 3 44850765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442700 Affx-122927874 AX-123313037 3 72569588 ATTCATTAAAAGTATAAAAACCTAGAAATAATCCT[A/G]GGATAATGATAATTGACAATGATGCCATTATTCTT R 2 1 2 1 101000 r 74 goat snp54373-scaffold83-4165647 3 44801261 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429351 Affx-122938570 AX-123299693 3 72633085 TGAAAATTGTAATTATATATACACAGAAATGCTAC[A/G]TAATCTGTCCCCTCCTTTAAAACTGAAAGGTGTTT R 2 1 2 1 101000 r 74 goat snp54371-scaffold83-4102150 3 44736997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787907 Affx-122962123 AX-385274929 3 72678225 TTGAGAGCTTCTGAGTTGGTTAGCATATCCACATG[C/T]GAAGAGGGTGGTGCATCCCAAACTCCATGAGGTAA Y 2 1 2 1 101000 r 74 goat snp54370-scaffold83-4057010 3 44691741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409246 Affx-122953141 AX-123279597 3 72739366 TAGGTTAAGAGTAATAGTCCAGCCATAGCTGTTAT[C/T]GTATTGTGAAGCAATGGGACTAATTCTTCAAGTTG Y 2 1 2 1 101000 f 74 goat snp54369-scaffold83-3995869 3 44630053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404194 Affx-122957677 AX-123274546 3 72828891 TTAGGAAAACTTTTAGAAGTGATGACCCTTAGAGA[C/T]AGGACATTCAGGCAGATCTTAGGGGATGTAACCAT Y 2 1 2 1 201000 f 74 goat snp54367-scaffold83-3906344 3 44539574 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416289 Affx-122947941 AX-123286638 3 72862420 ATTTACTCAAAATATTAAGTAATAAATGTATTAGT[A/G]TTCTCTCAGAATGAATTAATGCATCTCTATGTAGT R 2 1 2 1 101000 r 74 goat snp54366-scaffold83-3872815 3 44505951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430735 Affx-122937509 AX-123301076 3 72926786 TTCTGAAATATATCTGACAACTTCTCTAAATTGCC[A/G]TTATTACTTTTTAAAAATCATAAGATGTGTTGTTA R 2 1 2 1 103000 f 74 goat snp54365-scaffold83-3808449 3 44441313 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277984 Affx-1111836192 AX-519551477 3 72938055 TCGCTGGAGACAGGCTTCATGGCTTCAGTTCAGTT[A/C]AGTTCAGTTCAGTCGCTCAGTCGTGTCCGATTCTT M 2 1 2 1 103000 f 74 goat Random2.2K-352 3 72938055 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320775841 Affx-122938791 AX-385262972 3 72960255 ATTTTAGAGTGGCTTAATAAAAGTGGTAGCACTTA[A/C]GTTTTGCAAACTAAGACGGTATTTCAAAAATTAAG M 2 1 2 1 101000 f 74 goat snp54364-scaffold83-3774980 3 44407892 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376450 Affx-122978057 AX-123246809 3 72991369 CCTGAATAAGAACCCCCAAATACCATTTTCATGAA[A/G]ACAACAGAAATGCTGCAGTGTGAGGGGGAGGAATT R 2 1 2 1 202000 f 74 goat snp54363-scaffold83-3743866 3 44376403 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447361 Affx-122924868 AX-123317697 3 73039152 AGTCCATGGAGCTGCAAAAGAGTCAGACACAACTC[A/G]GTGACTAAACAGCAAACTTACAGTAACTTAAGAAA R 2 1 2 1 303000 r 74 goat snp54362-scaffold83-3696083 3 44328121 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782002 Affx-122926438 AX-385269081 3 73135324 GCCTCTCTTGTCTTTCTATATTCATAGGAGAATAT[A/G]CTATAATGAAGGTGGTCTCATCTCTCAGAATTATG R 2 1 2 1 101000 r 74 goat snp54360-scaffold83-3599911 3 44231723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778181 Affx-122952065 AX-385265296 3 73190475 TTCTTGAAGGAGGTTACAGGTACAGATTGGTGCCT[A/G]TGTTATAATTTGTACTGGACAACTCATTTAAGCTT R 2 1 2 1 101000 f 74 goat snp54359-scaffold83-3544760 3 44141902 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772385 Affx-122946883 AX-385259538 3 73240173 GAAAGGGAACTATTATCAATTGATACCATCCTGTA[C/T]GCATACTTGTGCTAGGCACTTTATACATTTTATGT Y 2 1 2 1 101000 r 74 goat snp54358-scaffold83-3495062 3 44092203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392564 Affx-122966079 AX-123262921 3 73273623 TGACAAGACTGCCTAATTTAGGCACTTATTTTTTA[G/T]TAAGCATTTACTATGTGCCACATACCATCAAAAGG K 2 1 2 1 103000 f 74 goat snp54357-scaffold83-3461612 3 44057356 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799359 Affx-122957767 AX-385286289 3 73326652 TTAGCAGTCCACTGACTGCAAAATGTTGTACAAGA[C/T]ACAAAGATGGTCATGAGCCCAATGAAATTACAATG Y 2 1 2 1 102000 f 74 goat snp54356-scaffold83-3408583 3 44003594 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764922 Affx-122966311 AX-385252509 3 73368890 CCTTTAAGTCTAACCAATTCTGTCTCTATGGTTCT[A/C]CTTACTGATTTGCAACCAGGCTGCACCTCATTGTT M 2 1 2 1 101000 f 74 goat snp54355-scaffold83-3366345 3 43974786 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430456 Affx-122937264 AX-123300797 3 73403021 CCATTGAGAATATTGCCCTTGGTGGTCCTGACTTT[A/G]TGGCAAGGGTCTTTGATCCAACCTCCCATTTCACT R 2 1 2 1 201000 r 74 goat snp54354-scaffold83-3332214 3 43940659 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776027 Affx-122957059 AX-385263157 3 73455754 ATTGAATTTAACTGAAGTTGGGACAAGAGAATTAA[C/T]ATTTATTGAGTACCATCAAAAGCTGGAACCAGTAC Y 2 1 2 1 101000 f 74 goat snp54353-scaffold83-3279481 3 43887348 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391377 Affx-122967276 AX-123261734 3 73504414 CTGATTTCCCCATGCTGTCTTTTCTTTGTGTCCTA[C/T]AAGTAGAAGCAAAATTATCAGAGGCCAGGAAATGG Y 2 1 2 1 101000 r 74 goat snp54352-scaffold83-3230821 3 43841202 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425455 Affx-122941512 AX-123295801 3 73558033 TTCTTTCTTTTAAAAAATATTGAAAAGTCGTATAT[A/G]TTTATATCTTAGTATGAGAGGATTTTAAATGCTTA R 2 1 2 1 101000 r 74 goat snp54351-scaffold83-3177202 3 43787687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787565 Affx-122929182 AX-385274589 3 73609489 CCACAGAAGATGATCCAGAAGGAGAGAAGCATTGC[A/G]TAGAAGATGCCCTGTCGGATATCACCAAACAACAG R 2 1 2 1 101000 f 74 goat snp54350-scaffold83-3125746 3 43736453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390116 Affx-122968010 AX-123260473 3 73640686 GGAGGCCAGGAAGAGGGGCAGACACATGATGGAGA[C/T]AGGAAGGAGGGTCAGATTCCAAGACCACATACACA Y 2 1 2 1 101000 r 74 goat snp54349-scaffold83-3094549 3 43705263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407511 Affx-122954739 AX-123277862 3 73689585 TTTGTCTGCCTTGTTTTTAACCAAGCATTTCATGT[A/C]ATTCCAATTTCTCTCCTCTCTTAGTCTATCAATTT M 2 1 2 1 101000 f 74 goat snp54348-scaffold83-3045650 3 43656470 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409239 Affx-122953147 AX-123279590 3 73729809 GCAGAGCCAAAGGGGCAGGCAGCCTAGGACACGTT[A/C]GTGTGCCTTTATCAGCAGCGATTCTGATTTGGGCC M 2 1 2 1 101000 r 74 goat snp54347-scaffold83-3005426 3 43618546 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767782 Affx-122958117 AX-385255008 3 73805718 ATCTAGTGTGGGTGTGGATCAAAGTTCCCAGTGCT[C/T]AAGTTTTATTCTGCTTTACTAACATTGGCAGCCAA Y 2 1 2 1 101000 f 74 goat snp54345-scaffold83-2929517 3 43542371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397520 Affx-122962050 AX-123267875 3 73851066 GGAGCTTTTATTCAGATTATTCTTCTGAATGGAAG[C/T]ATCCTTCCCATTACTGACCCCCTGCTTTTCTGACT Y 2 1 2 1 101000 f 74 goat snp54344-scaffold83-2884169 3 43496497 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414853 Affx-122949155 AX-123285202 3 73884614 GACCTATCTTGCAGAGGATGGGAGTATTTTTGTCA[A/C]GGTATCATAGAAAGAAATTATCTGAATGCTTCTGA M 2 1 2 1 101000 f 74 goat snp54343-scaffold83-2850621 3 43462947 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387172 Affx-122970624 AX-123257530 3 73923851 ATGTTCATTTTTGAATCATGTAAAGAGTATGAAAT[A/C]TACTCTAATGGATAAAAATGATTTTTTTTGTGGAA M 2 1 2 1 303000 f 74 goat snp54342-scaffold83-2811384 3 43423648 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444298 Affx-122926756 AX-123314635 3 73957531 GAGAGATAAGTCACAAGGCGACGTCTTTTCTCTCA[C/T]GTTCCTTCTCCTTCCAGGAGGCCACCCCCTCCAGC Y 2 1 2 1 101000 f 74 goat snp54341-scaffold83-2777704 3 43389916 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414436 Affx-122949956 AX-123284785 3 73996029 ATAAACACAGTTAAAGACTCATTTCCCCAGTTGCA[C/T]GAGCCACAGTCAAGTGATCAGGCAGACACAGAAGC Y 2 1 2 1 101000 r 74 goat snp54340-scaffold83-2739206 3 43353764 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417150 Affx-122947350 AX-123287498 3 74044365 CCTTCAGAATCTGAGTTTGCAATGATGGGGGAAAC[A/G]TTTAGGAAAACTGCTCTGCTCTTTCAGGCAGTGAT R 2 1 2 1 101000 r 74 goat snp54339-scaffold83-2690870 3 43307590 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415337 Affx-122948792 AX-123285686 3 74130356 GCATGCTCTTTCCGTGTTTTAGATGTCTGCCCAAG[C/T]GTCACCTTTGCAGAGAAGCATGCTCTGACAACCGA Y 2 1 2 1 101000 f 74 goat snp54337-scaffold83-2604879 3 43221490 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769522 Affx-122976216 AX-385256692 3 74174497 TAACAAAATTATTTGAACCAAGATGGCTACAAAAC[C/T]GAGCTTGTAGATAGTGGTTGATACAGAATCAGAAG Y 2 1 2 1 101000 r 74 goat snp54336-scaffold83-2560738 3 43177319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440194 Affx-122930704 AX-123310531 3 74216064 CATATAGATTCACTGAGGTTTGTTCTTGTTTAGTC[A/G]CTAAAGTCATGTCCGACTCTTTTGCGACCTCATGG R 2 1 2 1 103000 f 74 goat snp54335-scaffold83-2519171 3 43136449 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772631 Affx-122941506 AX-385259779 3 74260674 ATGAAGCAGCTCTTGGAGGAGGTAATGTATGAACC[A/G]GGTCATGATAGGAATGATGTCCATTCAGACATAAT R 2 1 2 1 101000 f 74 goat snp54334-scaffold83-2474561 3 43091767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788842 Affx-122959715 AX-385275857 3 74305031 AAAGAGATAAAAAACTGACACATTCTGCCAAGAGA[C/T]GCACTGAAGTGTTAATGAAGGTTGCCTTTGGATTG Y 2 1 2 1 101000 r 74 goat snp54333-scaffold83-2430204 3 43046873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791319 Affx-122972705 AX-385278312 3 74340381 AGCTGTCAGTTTTCCCTACCTACTAAGTGATGGAA[A/C]TGGGATCTGTCAAAGGAGTATCAAACACTATACCT M 2 1 2 1 101000 f 74 goat snp54332-scaffold83-2394854 3 43011274 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376895 Affx-122977811 AX-123247254 3 74371575 AAACTGATATTATGTCCAATATTTAAAACCAGTTT[A/G]TAATAGGGGGAACATCTAAATCCTTAATTAAAAAA R 2 1 2 1 201000 f 74 goat snp54331-scaffold83-2363660 3 42979982 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403379 Affx-122957783 AX-123273732 3 74413392 GTGAAGAAGCTGATCCACACACAAACCCATGAATA[G/T]GTGGAGCTTAGTGTGTGACAGGGGTGGTACCACAT K 2 1 2 1 101000 f 74 goat snp54330-scaffold83-2321843 3 42938006 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391731 Affx-122967492 AX-123262088 3 74442832 TGAACATTAAATTTTTACAATAAAAATGTAGGATT[A/G]TGATTCTTTCCAGTATTTTGGTATTTCCAGGATTA R 2 1 2 1 101000 r 74 goat snp54329-scaffold83-2292403 3 42908836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411778 Affx-122951483 AX-123282128 3 74492290 ACATCTGTCTGGCATCTCTAAAATGAAATTTAAAT[A/G]CCAAGCTCACACATCTTGACTTTCTTTTATTTCCG R 2 1 2 1 101000 r 74 goat snp54328-scaffold83-2242945 3 42858734 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436837 Affx-122932220 AX-123307175 3 74549732 AAGGTAAAGGTGCTTAGGGCCCATGAAAGTCACAC[C/T]GTGACCCTGGATGGTCTTGATTATGTTTTCAAAAA Y 2 1 2 1 201000 r 74 goat snp54327-scaffold83-2185503 3 42801082 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431886 Affx-122936055 AX-123302227 3 74581111 AGTAAAAGTAATAAATAAGTGTTGGTCCTTTGGTC[A/G]TGTCCAACTCTTTGCGACCCTATGGACTGTAGCCT R 2 1 2 1 303000 f 74 goat snp54326-scaffold83-2154124 3 42769785 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399066 Affx-122960896 AX-123269421 3 74625870 CATAGTTACACAAAATGAGAAAATACATGGAAATG[A/C]TTTGTGCAAAGGAGGCTCCTGGAAAAGTAAGACTA M 2 1 2 1 103000 r 74 goat snp54325-scaffold83-2109365 3 42725065 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414199 Affx-122949657 AX-123284548 3 74672605 AATATATCAAAAACTTACTTCTTGATCATGTTTCA[C/T]GAGGACTATGGGTTGGCTGAGGCTCTTCGGGCCTT Y 2 1 2 1 201000 f 74 goat snp54324-scaffold83-2062630 3 42678319 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785192 Affx-122970803 AX-385272238 3 74719735 GTTGCAATTCTTCTAAACTACCAAGACTTGTTTTA[C/T]GGCCCAGAATGTAGTCTATGTTAGTGCACTGTTCC Y 2 1 2 1 101000 r 74 goat snp54323-scaffold83-2015500 3 42630367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377894 Affx-122977248 AX-123248253 3 74758001 ACTCTTGACAAACTGCATTGGGAAAAGAAGCCTTC[A/G]TTAATAGTTACTTAGTCTCCCTCACCCCATACCTA R 2 1 2 1 101000 r 74 goat snp54322-scaffold83-1977234 3 42592228 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410422 Affx-122952410 AX-123280772 3 74805955 GAGCCTTAAAGAGCAGTAAAAGCACAGGCATTGGA[A/G]TCAGCAGATCCAGAATTAAAGTTCTGTTCTTGGCA R 2 1 2 1 201000 r 74 goat snp54321-scaffold83-1929280 3 42543811 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396227 Affx-122963345 AX-123266582 3 74836057 AGGAAATGCCTGACACATAGTAATCATAAATAGGT[A/G]TAGACTGCAGTTATGTAGGCTGACTGAAGCATGAG R 2 1 2 1 101000 r 74 goat snp54320-scaffold83-1899178 3 42513590 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420797 Affx-122944688 AX-123291144 3 74893609 AGCCATCCTGGATATTTACTGAATACTCTATTTCT[A/G]CCCCTCTGGCCAGTCAGAAATCAAATGTGTCGCAG R 2 1 2 1 101000 f 74 goat snp54319-scaffold83-1841626 3 42455432 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272223 Affx-1111833398 AX-519545970 3 74919350 AGAATAGAGCCAGATCATTGCTTGTTTAACAAAAA[A/C]TTTTAGTAAGTGTCAAGTTAGTGTTTGCTTTTTCA M 2 1 2 1 102000 f 74 goat 3_74919350_AF-PAKI 3 74919350 T G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406137 Affx-122956190 AX-123276489 3 74941806 ATGAACGAGAAGTCTTTATTAGTTAAAGCCACTGA[C/T]ATAGAGTAATTATTGATTGCAGCAACATCAGCAAA Y 2 1 2 1 101000 f 74 goat snp54318-scaffold83-1793429 3 42406710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784602 Affx-122971199 AX-385271650 3 74994578 TATCTTATCCAAAAACTAAACTATCATCCCTACTT[A/G]CATAATTTTCATTCACTTCTTCTTCAGAGCAAATT R 2 1 2 1 102000 r 74 goat snp54317-scaffold83-1740657 3 42353327 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428257 Affx-122939413 AX-123298600 3 75074520 TGGAAATAGACCCTGGATAGACATTTTGACCCAAC[A/G]CGCATGACATGGTTTTCCAGCAAAATAGAACCCCC R 2 1 2 1 101000 f 74 goat snp54315-scaffold83-1660715 3 42273700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443110 Affx-122928098 AX-123313447 3 75127712 CTGGATATGTTGGAAATAACTGTGTATGAGAATAA[C/T]GTGGGTCAAAATATTTCCATTTAAATATGTACATA Y 2 1 2 1 101000 f 74 goat snp54314-scaffold83-1607523 3 42220541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801317 Affx-122925301 AX-385288229 3 75177745 TAAATTCTGAATGAGAGTAAGTGAACTCAAAGTAA[C/T]AGGAGGGATATTATAAGGCACCACATTTGTGAAAC Y 2 1 2 1 101000 r 74 goat snp54313-scaffold83-1557490 3 42170706 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440482 Affx-122929373 AX-123310819 3 75212644 ATTTATTGATGGTGAAAATTGAAGTCCTCAGAGAG[A/G]TGAAGTTGATTTGCCTAAGATAAGAAAGCTAGAAC R 2 1 2 1 101000 r 74 goat snp54312-scaffold83-1522591 3 42136493 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440535 Affx-122929332 AX-123310872 3 75242099 ACTCTTCTACACAGCAGTCTCTGAGAACTGTCTAA[C/T]AACATTACACCTCTGGATGCATCACCCAATTACTA Y 2 1 2 1 101000 r 74 goat snp54311-scaffold83-1493136 3 42107550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452017 Affx-122920910 AX-123322350 3 75283852 AGTATAACTTTGGACTAGCAACTTGATTTCTCTTG[A/C]TTCAGCTTTCTCATATGTGATGTAGGAATACTGGC M 2 1 2 1 101000 r 74 goat snp54310-scaffold83-1451383 3 42066001 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384057 Affx-122972875 AX-123254415 3 75312772 AGAATATTTTCCTGATCACTTTTTCCCACTCCATC[A/G]TCTTATTCATCCCCCATCAAACATGCAAAAAAGCA R 2 1 2 1 101000 r 74 goat snp54309-scaffold83-1422463 3 42036482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428928 Affx-122938901 AX-123299270 3 75355389 GAATAACCCCAGGGGTAGGATCCATTACGTTCTCC[C/T]TTCTGTGGCTGAGACTGTGCACACCCCCACCTCTT Y 2 1 2 1 101000 f 74 goat snp54308-scaffold83-1379846 3 41994837 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381761 Affx-122974311 AX-123252119 3 75386535 CATCCTGGGCTGGCTCCCTTTCGTTTTAAAACCGC[A/G]GCATATTTTAAAGTTATCAGGGAAAGAATGTTGAG R 2 1 2 1 101000 r 74 goat snp54307-scaffold83-1348700 3 41963557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423889 Affx-122942294 AX-123294235 3 75438669 AAAATCTATGTCATAATAATAATGCTTTCTATCTC[A/G]TGGGATTTATTTTTCAAGGAAAAAATGAGATCTGC R 2 1 2 1 201000 f 74 goat snp54306-scaffold83-1296566 3 41911457 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772930 Affx-122971107 AX-385260074 3 75471752 AAATCCATTATTACCTAATGTCCTTACTGTGTCCC[A/G]TTTCCGTGAATGGATGTTTGTGTTCCTAGGTTTCA R 2 1 2 1 101000 r 74 goat snp54305-scaffold83-1263483 3 41877647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401596 Affx-122958869 AX-123271949 3 75558310 CACCAGGGAGGAATACCACATTCATTGTATGTGTC[A/G]TGTTTAAAGAAAGACTAGGTAGCTGGGTGATTTCT R 2 1 2 1 101000 f 74 goat snp54303-scaffold83-1176925 3 41790683 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770386 Affx-122927975 AX-385257552 3 75605469 GCTTACATGTTGATTGCTAAGTCATTTGTATTCAT[A/G]TCGAAAATGATATCTACTCTGCAGTGGGAAGTGGC R 2 1 2 1 101000 r 74 goat snp54302-scaffold83-1129766 3 41743540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278145 Affx-1111836193 AX-519551634 3 75631736 TTCCTAAAAATTTCACTTACCATTATGAAAATCAT[A/G]AGGAATTATTCATGAACATTATTCTAATGGATGGA R 2 1 2 1 101000 r 74 goat Random2.2K-353 3 75631736 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444632 Affx-122926931 AX-123314969 3 75662559 GTTGGACATTTTGTGTACCTATGAGCACAGTACCC[A/C]TATTTCAATGATATTCAAGTAGATGTTAGAATGAT M 2 1 2 1 101000 f 74 goat snp54301-scaffold83-1072676 3 41686839 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443989 Affx-122926915 AX-123314326 3 75692028 GCCTTAACTCTATCTTGGGAGCGAATGCTGTCTAG[C/T]AGAATGTATATGGGGCTTTTTGAACTAGAAGAACC Y 2 1 2 1 101000 f 74 goat snp54300-scaffold83-1043207 3 41657498 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436144 Affx-122932635 AX-123306483 3 75725476 AATCAAATATTAATTTACACTGTATCCATAGAAGT[A/G]TGGATTTCAGAACTCTGGAAATCCTTCTCTGGCAC R 2 1 2 1 201000 f 74 goat snp54299-scaffold83-1009759 3 41623915 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796149 Affx-122920475 AX-385283100 3 75779045 ACATGTATAGGTACTCTGAAGGCAGATAAACATGG[A/G]TTTTAATCTTGACTTCACTAAACTGTAATTCAGAA R 2 1 2 1 101000 f 74 goat snp54298-scaffold83-956190 3 41569224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451334 Affx-122921270 AX-123321667 3 75824971 CTCACTGGCATGCCCTTGTGAACCAAATACACACA[C/T]GCTAGCAAGTAAAGATACCCACACACAGACACTAT Y 2 1 2 1 101000 f 74 goat snp54297-scaffold83-910264 3 41523616 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453093 Affx-122920038 AX-123323426 3 75875466 ACAGACTCCTTCTATCATCATTAACCTCATTAGTC[A/G]TCCCCAAATGAGGAAAGCCCAGGATGAGCTTTGAG R 2 1 2 1 101000 f 74 goat snp54296-scaffold83-859769 3 41472632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782350 Affx-122932866 AX-187886881 3 75911972 ACTGAGAACTCATATGGGCGTGTGGCTCCCACATC[A/G]CTTACTCAGTCACATAGCCTATGTGATCAGTCTTG R 2 1 2 1 102000 f 74 goat snp54295-scaffold83-823263 3 41435942 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441677 Affx-122929180 AX-123312014 3 75970786 CTGAACAAGTCTCTGGGAGCCTCTTACTTAGACAC[G/T]CAGGACAAGGAGAGACTGGCTTATCTCTATGAACT K 2 1 2 1 201000 f 74 goat snp54294-scaffold83-764449 3 41376935 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391101 Affx-122966818 AX-123261458 3 76032437 ATTGGATAGTTAAATGTTATATCACATCCTGCCAG[C/T]GAAATCTAAGCAAAAATCTATGTATGCAGTATTTT Y 2 1 2 1 101000 f 74 goat snp54293-scaffold83-702798 3 41313589 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796845 Affx-122951208 AX-385283788 3 76063264 GATACCATTATTTTGCAGAACAACTAAGAAATAGG[C/T]AAGTGCTTACCCAACATACTCTAGATGTTCATCAT Y 2 1 2 1 101000 r 74 goat snp54292-scaffold83-671971 3 41282517 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452761 Affx-122920260 AX-123323094 3 76092978 ACTTAGCTCTTTTGTTGGAGGGAAAATTATGAGAA[A/G]AATTATTCCTGTTAAGATTAGGAGACATACTGAGG R 2 1 2 1 101000 r 74 goat snp54291-scaffold83-642257 3 41252908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397103 Affx-122962699 AX-123267458 3 76154266 ATTAAGCTGTTTTGTTTGAAGATAAATCATTTGTC[A/G]GGGTTAATAAGATTATAGATCTCCTAGGTTAAAAC R 2 1 2 1 101000 f 74 goat snp54290-scaffold83-580969 3 41189888 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801352 Affx-122939814 AX-385288264 3 76209578 GTTTTTTTTAATAGCAGGAATTCACATTTGTCAAA[A/G]TAACATAATTTTCTGATTTATAGTTTTTACCAAGT R 2 1 2 1 102000 r 74 goat snp54289-scaffold83-525657 3 41133466 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787412 Affx-122971873 AX-385274437 3 76260075 GTAAATATTTAGATCATCTTTCAGTCTAGCTTAAA[A/G]AATCACATTCAACTTGAAGTTAATATTTGCAACAC R 2 1 2 1 101000 r 74 goat snp54288-scaffold83-475160 3 41082612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403241 Affx-122957888 AX-123273594 3 76323917 TAGGGAAAGGCAAAAGGGACACAAGAGTTGAGCAT[A/G]CTTGGGATAAAACTTCAAAATTTCATTACAGGACG R 2 1 2 1 101000 f 74 goat snp54287-scaffold83-411318 3 41018020 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787978 Affx-122944664 AX-385274999 3 76398899 TAAATTATTGGCAGCATTTCTCTTTTGCCAGTTAA[C/T]GTTTAAGGGCTAACACAGTAAATTTTTTACTGTAG Y 2 1 2 1 101000 f 74 goat snp54285-scaffold83-336336 3 40943705 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410556 Affx-122952145 AX-123280906 3 76434231 GAAAAGCCACACAGCTCTTTCCTGTTCCCTTCTGC[A/G]CCTCCAAGCTCCTTATTAGAGTTGTTTAGTTGCTA R 2 1 2 1 101000 r 74 goat snp54284-scaffold83-301004 3 40908405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380404 Affx-122975319 AX-123250762 3 76484390 TCATTTGCAAATCCCCCATCTCCAAAAACTGTAAC[A/G]TTAGGGTTTAGTGCTACAAATATGAATTGGGGGGA R 2 1 2 1 201000 r 74 goat snp54283-scaffold83-250845 3 40858326 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398390 Affx-122961645 AX-123268745 3 76523602 TGATGAGAAGAGTGCCTGGCACAGAGTAGGCACGG[C/T]ATGTGTGAATTCTCTTCCCCTTGCCTTGTGGCTTG Y 2 1 2 1 101000 r 74 goat snp54282-scaffold83-211633 3 40818782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414479 Affx-122949553 AX-123284828 3 76569755 CAGGGTCACCCTAGACTTTAATATCATCCTCCCTG[C/T]GTGACATTGCACATTAACATGGTCCTGAACGCCAA Y 2 1 2 1 101000 r 74 goat snp54281-scaffold83-165480 3 40772890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392218 Affx-122966271 AX-123262575 3 76599717 GTCTTCGCCGTATGCCTTTTAGTTGGATAAGAAAT[A/G]CTCTTTTTTGTATTAATATGTGTATACAGATGTGG R 2 1 2 1 101000 f 74 goat snp54280-scaffold83-135518 3 40743500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408606 Affx-122953641 AX-123278957 3 76649896 AACTTATTAGTCACTTAACATGTTTCTGTGCCTGC[A/G]TTAGGTAGGGGGAGGTATGCACAAGTGTCCTTGAG R 2 1 2 1 201000 f 74 goat snp54279-scaffold83-85339 3 40692675 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777417 Affx-122952725 AX-385264538 3 76685019 ACTCCGCCATTTGGAGTGGTATTACACGGCTAGTG[C/T]GCGTTAACTACCTATTAGTTAGCTGAATGCCAAAA Y 2 1 2 1 101000 r 74 goat snp54278-scaffold83-50216 3 40658133 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441669 Affx-122929185 AX-123312006 3 76729241 GGCCTCATCACAAAAGGACTTCTTTCCTCTCTTTG[A/G]CTTGGAGTCAGGTTGGGCTTGTGAATGTTTTACAT R 2 1 2 1 101000 r 74 goat snp54277-scaffold83-5994 3 40614702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785772 Affx-122963802 AX-385272812 3 76743803 GGATGGTAGTTTAGATTGGAGATGACTTGCAAGCT[C/T]TTTACCTGGTCCTACACAGGAAAACTTCTCTCTAA Y 2 1 2 1 101000 f 74 goat snp48419-scaffold687-3117450 3 40600219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799269 Affx-122922483 AX-385286199 3 76815353 TTGATATGCATACTAACGCAGAGGTAAACAATGAG[C/T]GTGGGCTTTCTAGCAAGAGAGATTTTAGCTCTTCA Y 2 1 2 1 101000 r 74 goat snp48417-scaffold687-3045900 3 40528381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387881 Affx-122969627 AX-123258239 3 76866319 TAATTTTTTCCAACAGCTCTGTGTGACGGCCAAAG[C/T]GGATATTTTACAGATGAAGAAAATAGGTGCCTGAG Y 2 1 2 1 103000 f 74 goat snp48416-scaffold687-2994934 3 40477345 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439529 Affx-122930118 AX-123309866 3 76909749 GCTGGTTGGAGACAAACAGGATTCGATATTTCAAA[C/T]GCAATTTCATACCCCAAGTATTTCTTCCTCTTTAG Y 2 1 2 1 101000 f 74 goat snp48415-scaffold687-2951504 3 40433828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409712 Affx-122953040 AX-123280063 3 77026193 GAGGGAGGGACCCCAGCTAAGTAGGTAAGCGTGCA[A/G]TTTTGTTGCTGGCAGCCCTTATTGAGGTGGAATAG R 2 1 2 1 101000 r 74 goat snp48412-scaffold687-2835060 3 40316707 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451558 Affx-122921702 AX-123321891 3 77079867 GTGGCGATTGGCTTCTTTGTATGTGAGTGTATAGA[C/T]GTTGAGAGGCTAGAGGATGGACAAGGAGAGCTGGT Y 2 1 2 1 101000 f 74 goat snp48411-scaffold687-2781386 3 40263047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420346 Affx-122944967 AX-123290693 3 77119164 AAGGCCTCCTCACCTTGCCTGAGTTCTTGACACTC[G/T]GTGCTGGGTTTCCCTTCTGGGCAGGTGTCCTTCTC K 2 1 2 1 101000 f 74 goat snp48410-scaffold687-2742089 3 40223260 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454277 Affx-122919278 AX-123324610 3 77149039 GGAGTCACAGAGCTGGACACGACTTAGCAACTAAA[C/T]GAAGGCACTGTGTTTTATGTCATAACGTTAGACAT Y 2 1 2 1 101000 r 74 goat snp48409-scaffold687-2712214 3 40193445 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793982 Affx-122960525 AX-385280951 3 77203072 TGGGGCATTGTCATTTTAAAGCAGTGTTCTAATTA[C/T]AGTGATGTATTTTAGATTCACATTCTGTGATCCAG Y 2 1 2 1 101000 r 74 goat snp48408-scaffold687-2658181 3 40139324 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444915 Affx-122926245 AX-123315252 3 77289716 TCTCTCAGGTTTGTAATGATTAGATGAGTTAATCT[A/G]TGTAAAACACTTGGAATATTCTTGATACAATGTAA R 2 1 2 1 101000 r 74 goat snp48406-scaffold687-2571537 3 40052189 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404139 Affx-122957091 AX-123274491 3 77323767 ATAAGAAGAGAAACAAAGAGCTTATCCCAAAGACA[C/T]AGTTAAATTACAAGAGACATGTGTTCATATACTTG Y 2 1 2 1 101000 f 74 goat snp48405-scaffold687-2537486 3 40017870 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774172 Affx-122965938 AX-385261309 3 77353881 CATTTTTTTGAACAAATATTTCTCCATCTTATTCC[A/G]TAATATCTGTGGAAGTGTTGTAAGGGTTGTAAAAT R 2 1 2 1 201000 f 74 goat snp48404-scaffold687-2507372 3 39987761 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406361 Affx-122955423 AX-123276713 3 77407509 TTAATCTCTCTGGTTCTGTTTCCTCATCTATAACA[C/T]TGGAGTAAATAATACTTCACAGAGCTGTTATATCA Y 2 1 2 1 303000 r 74 goat snp48403-scaffold687-2453744 3 39934094 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389813 Affx-122968195 AX-123260170 3 77442937 ATGAACCGGCATCCAGTTAGGTCATAAGTAAGGAG[C/T]ACAGGGCAGGCTGGGGAGAAGCTTAAACTAGCAGA Y 2 1 2 1 101000 f 74 goat snp48402-scaffold687-2418316 3 39898691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384926 Affx-122972333 AX-123255284 3 77475067 CCACTTCACAGTTGGCTACCGTGGGTGGGTCTTTC[C/T]AGAAAGGCGAAGAGAAACCATACCTCTGGATGGTC Y 2 1 2 1 101000 r 74 goat snp48401-scaffold687-2386186 3 39866341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787631 Affx-122931996 AX-385274654 3 77512318 CTATCTGGTGACAGTTCATTTAAGAAAAGCAGTTA[C/T]AGTTCTTCCAGCTGAGGACATAAGAGAAGAAAAAG Y 2 1 2 1 101000 f 74 goat snp48400-scaffold687-2348935 3 39828337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785499 Affx-122947415 AX-385272544 3 77545279 AAGACCATCAATGGACAACTTTGATGAAGCAAAAC[G/T]AAGTTTATTAGACTTACTACGTGAAGAGTGAACAC K 2 1 2 1 201000 f 74 goat snp48399-scaffold687-2315974 3 39795070 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381694 Affx-122974719 AX-123252052 3 77574657 GAATGAGGATAGCACCAAGGAAAACATAGAGACAC[A/G]CCAGCACTAAGTAATAATGGCATTGCTTGAAATCC R 2 1 2 1 101000 f 74 goat snp48398-scaffold687-2286596 3 39764842 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464228483 Affx-1110380459 AX-515703292 3 77605259 CCTGTCCCGGGATCTTCCTTAGTTCTCTCCTCTAC[C/T]GCGCTCTGCCTCAGCCTTGTTCACTGGTGCCAGCC Y 2 1 2 1 102000 f 74 goat 3_77605259_AF-PAKI 3 77605259 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320790289 Affx-122931788 AX-187869299 3 77610485 AACTAGCATAGCAGGCTGGAAAAAGGATGAACCCA[C/T]GTTACATCACAGCAAAACCATTGACAAAGTGTTGC Y 2 1 2 1 101000 f 74 goat snp48397-scaffold687-2250768 3 39728506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417336 Affx-122947737 AX-123287684 3 77640915 AGACTGTCTGCTGTGTCCCTAAGATGCTAGAACCC[A/G]CATGTACCCGGTTATCTTACTGTAAAATGGAAATA R 2 1 2 1 201000 r 74 goat snp48396-scaffold687-2220338 3 39697587 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451949 Affx-122920962 AX-123322282 3 77674459 TGTTTTTTCTTTTTTCAAAGAACAGAGTAGGAACT[A/C]AGAGGGCAAATAATCAAGGTCATTGACTCCCAATA M 2 1 2 1 101000 r 74 goat snp48395-scaffold687-2186794 3 39664309 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392120 Affx-122966344 AX-123262477 3 77707105 GTCTTACAAAGAAGCTGTACCATTTTCCATTCCCT[A/C]TCCAGAGATATTTAAGGATTTAGTCATTAGGCTTT M 2 1 2 1 201000 r 74 goat snp48394-scaffold687-2154148 3 39631650 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429363 Affx-122938561 AX-123299705 3 77739234 CAGATCTTTCCTAAAGATTGCAAGATCTTTCCATT[A/G]GATATAAATAATTTTTCTTATTTTTTTATAAAAAT R 2 1 2 1 103000 f 74 goat snp48393-scaffold687-2122019 3 39599414 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404771 Affx-122956687 AX-123275123 3 77774236 CAGGTGTTCCAGGAAAAGGTTTTGTGAAATTGATC[A/G]TTTTAGTTACTTTCCATGCTTCTTCCAAAGCAAAT R 2 1 2 1 202000 r 74 goat snp48392-scaffold687-2087017 3 39564311 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451614 Affx-122921628 AX-123321947 3 77818803 AATGAGAAAGGAGGCAGGGTCTATGGAGCAGACCA[A/C]GGAGGGGTAGTTTAATCAAACTTCTCTTCTTAAAG M 2 1 2 1 101000 r 74 goat snp48391-scaffold687-2042450 3 39519734 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391869 Affx-122966981 AX-123262226 3 77879511 AGGAGTCTGCTTTCTGTGGCTTCTTCTTTAGGGTC[A/G]TTAAAGATAGATGGCCCAGGGAGACTCCTTTTGTG R 2 1 2 1 102000 r 74 goat snp48389-scaffold687-1981742 3 39458856 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381590 Affx-122974800 AX-123251948 3 77932953 CTTTATATCATTTAATCCACATAACAATCTGAGGC[A/G]GCAGGTATTAATAGAGCTGAGAGGTACATTTGCCC R 2 1 2 1 101000 r 74 goat snp48388-scaffold687-1928300 3 39406774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408344 Affx-122953747 AX-123278695 3 78048935 TTTCAGAGTGAACCTCATTTTTTTAATGTGTAAAA[C/T]AGAGTTGATAACACTGACCTCAAATGGTTGTGAGG Y 2 1 2 1 102000 r 74 goat snp48385-scaffold687-1812318 3 39290148 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790542 Affx-122920165 AX-385277545 3 78086750 CTCTTGAAGGTTAATAATAGCTACCCCAGAGAGCT[A/G]TTATATGTATCAAATGATGTAATAGGTGTGGAAAT R 2 1 2 1 102000 f 74 goat snp48384-scaffold687-1774503 3 39252378 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387834 Affx-122969663 AX-123258192 3 78144864 CCCAGTATTTCACCCTGCGGAGGCATGTGTGTGTG[C/T]AAACACTCTTGCCCTGGGAGCTTCTCCTTGTTTAG Y 2 1 2 1 102000 r 74 goat snp48383-scaffold687-1716389 3 39194406 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399939 Affx-122961257 AX-123270294 3 78181406 TCCTTACTGATTACAGAGTAAGTACCAGTGCCCTT[A/G]CCACATCCTTGCACCACTGCAGAACCTACCTACCA R 2 1 2 1 101000 f 74 goat snp48382-scaffold687-1679847 3 39158028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798131 Affx-122931957 AX-385285066 3 78219755 CCCAGACTAGAGGGTCTTCAATTGGGGTACCTGAA[A/G]TTAAGGCTATGCAAACCCCCAGAAATAATACACAA R 2 1 2 1 101000 f 74 goat snp48381-scaffold687-1641498 3 39119621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784976 Affx-122961388 AX-385272023 3 78275117 ATCCTTTTGTGTTGAGGTTTCAAATCAACCATCTA[C/T]GAGGCCAGATTACTATAGGTTCTGGAATTTGGGGA Y 2 1 2 1 101000 r 74 goat snp48380-scaffold687-1586136 3 39063732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447933 Affx-122923789 AX-123318269 3 78308144 AGGAAGTCAGCCTATTTCCTAGAGAGAACTGTGGC[C/T]GAGACAAGGCTTCCTGGTGCAGACATGGCTACCCC Y 2 1 2 1 101000 f 74 goat snp48379-scaffold687-1553109 3 39030614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376924 Affx-122977788 AX-123247283 3 78336730 CCTCGCCACAGTGACCCTTGGCGCCTGGAGTATCC[A/G]TTTCTCAAAATGTTGGCCCTGTGGCTTTTTTCCCT R 2 1 2 1 101000 r 74 goat snp48378-scaffold687-1524523 3 39002031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413070 Affx-122950966 AX-123283419 3 78389731 AAGCCTAAAATGTTAGCTTTTCTCTTTTAGCTTCT[A/G]TGCTTTGTCCCTCCCTTGATTTCTCCAGTGCTGAT R 2 1 2 1 101000 r 74 goat snp48377-scaffold687-1471522 3 38949102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423490 Affx-122942568 AX-123293836 3 78431362 ATGAGAACTGGAATTCTGATCTTTTCACATGGGTA[C/T]TCCTTGGGTTAATATTTGTAAAACACTTGAAACAG Y 2 1 2 1 101000 f 74 goat snp48376-scaffold687-1429891 3 38907666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427855 Affx-122939721 AX-123298198 3 78472990 ACTCTTAGCTGGGTGAGAGATCTCTCTCAGTTTTC[A/G]TATCTGTAACAGGTTCAGAAAGTACCTGACCACTG R 2 1 2 1 201000 r 74 goat snp48375-scaffold687-1388263 3 38866070 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386194 Affx-122971364 AX-123256552 3 78559173 CAGTCAGTATTCTCACAGCACTCTTGTGCCCCGCT[A/C]TTTAGTTTCCCTTTCACTGTCTGTCTACTCTCAAA M 2 1 2 1 201000 r 74 goat snp48374-scaffold687-1302080 3 38779227 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389721 Affx-122968674 AX-123260079 3 78594489 GTGTCCTTATTGCTAAAAGTGATGGGGAATAAAGT[A/G]CATGTATGTATGCTTTGATTTGCAGGGCAAAGTTT R 2 1 2 1 101000 r 74 goat snp48373-scaffold687-1266764 3 38743654 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418785 Affx-122946184 AX-123289133 3 78640979 CAGTTCTGCCACTTACTAGTCATGTGACTGTGTAA[C/T]CTTACTGTTATTTAGTGTCTTCATCTGTAACAAGA Y 2 1 2 1 201000 r 74 goat snp48372-scaffold687-1220274 3 38697569 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793877 Affx-122962748 AX-385280846 3 78722316 TTTCCAGATCTGGAAATTAAGGTCAAGAGAAGTTG[C/T]AAGACTTGCCCGTAGTCTTAAAGCTAGTTAATAGC Y 2 1 2 1 202000 r 74 goat snp48371-scaffold687-1138937 3 38615480 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441196 Affx-122929534 AX-123311533 3 78761013 GAGCATTAGTTATGCATCCTTTTTGCTTTGCATTG[C/T]AATAAATGCTGCACTTTCCTACATCACAAACTGGT Y 2 1 2 1 101000 f 74 goat snp48370-scaffold687-1100240 3 38576668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437810 Affx-122932118 AX-123308148 3 78799505 GGCAGCCAGGACCTTGTCTGCTTTGGTAACTGCCT[A/G]TATGCCCCGTGCCTCAAACACTGTCTGGTATAAAA R 2 1 2 1 201000 r 74 goat snp48369-scaffold687-1061748 3 38536884 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778679 Affx-122943710 AX-385265790 3 78838385 CCAAAGTGCTCACACTCACAGGTGCTATGAGGAAC[A/G]TAAACTATAAGTTAGATATATTCTTTGCCCTCAAA R 2 1 2 1 102000 f 74 goat snp48368-scaffold687-1022868 3 38497587 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409844 Affx-122952934 AX-123280195 3 78867639 TTGCTACATCTATGAAGCCTCTAATGTAGTCCCTG[A/G]CACATATTATATGTCAGTTACCTTTTCATTTACTC R 2 1 2 1 101000 f 74 goat snp48367-scaffold687-993614 3 38467823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381266 Affx-122974481 AX-123251624 3 78902836 CTTTGTCCCTTCACATAGTCGCAGGCTCTATTCCA[C/T]GCTCACCCCCTGCACAAAGCACCCCCACCCCAAAC Y 2 1 2 1 101000 f 74 goat snp48366-scaffold687-958417 3 38432783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451001 Affx-122921720 AX-123321335 3 78937808 CATTCATTTTTACCTAACAAACAGTGGTGGTAGCT[C/T]AGTTGTGTCCGCCTCTTTGCGACCCCATGGACTGT Y 2 1 2 1 101000 f 74 goat snp48365-scaffold687-923445 3 38398011 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428107 Affx-122939081 AX-123298450 3 78969176 GGTATTAAATTCCACTGGTGCTCAATGTTTCCATA[C/T]GTAAAAACAGATAATAGATTGATGTGAAGTGTAGG Y 2 1 2 1 101000 f 74 goat snp48364-scaffold687-892077 3 38366653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431590 Affx-122936175 AX-123301931 3 79011807 AAGGACATAAGACCACAGCCCAGGGAAGTGATCAA[C/T]AAGAGTAATTGTTCACTTTCATTACTATAGGTGTT Y 2 1 2 1 101000 f 74 goat snp48363-scaffold687-849446 3 38322981 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784343 Affx-122927177 AX-385271394 3 79051982 ATGCCTTTTGCTTGCATTTTGTCTAAAAGGACTAC[A/G]TTTTCAGAACTGGGAATTATTTACTAATTGCAAAT R 2 1 2 1 101000 f 74 goat snp48362-scaffold687-809271 3 38282790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795268 Affx-122945732 AX-385282226 3 79111751 TTTCACCTGCAATGTTTGTTAAAAGTACATCTCAG[C/T]GCTACTGGATCTGAATCGCTGGGTTTGGGTGGGAG Y 2 1 2 1 101000 r 74 goat snp48361-scaffold687-749502 3 38223142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425754 Affx-122940737 AX-123296100 3 79167467 TCAGTGAATCCCAAATTGACAGAGGCTATATAAAG[A/G]TTGTTGGTGTTCCCACAAAATTCCAGGTATTACTT R 2 1 2 1 101000 f 74 goat snp48360-scaffold687-693786 3 38167041 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442147 Affx-122928322 AX-123312484 3 79196426 GAGACTTTTAAAGTCATCTTAATTACTTGAGTGGC[A/G]CATGGATCACAAATTCTCCAGGGCTTGGCAAGTTG R 2 1 2 1 101000 f 74 goat snp48359-scaffold687-664827 3 38138132 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409368 Affx-122954163 AX-123279719 3 79228242 CTTCTACTCCCTTTGTGCACTATAACTTATTGCTT[A/C]TGTAAAATGTAGATCATTGCAGAGCCTCAGACTCT M 2 1 2 1 201000 f 74 goat snp48358-scaffold687-633011 3 38106422 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442134 Affx-122928332 AX-123312471 3 79269808 TAAGTTCTGGTCCACAAACACTTGCCTGTAGGAGG[C/T]TCAGTACTTGAGAAAGAATTTGTAATAAACCAGAC Y 2 1 2 1 201000 r 74 goat snp48357-scaffold687-591445 3 38063130 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422557 Affx-122943767 AX-123292903 3 79318306 GAAGGATTTGGTGTGCCAGGCTAAGGAATGTAAAG[C/T]ACACACTAAAAGAAATGGCAGTTCAGTTCAGTCCC Y 2 1 2 1 101000 f 74 goat snp48356-scaffold687-542947 3 38014216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409226 Affx-122953156 AX-123279577 3 79349577 AGTTGGGGTGAAGTCACTAAGAAAGTTTGGACCCT[A/G]AGGCCCCTTACCACCATCCCTGTATCTTCAGCAAA R 2 1 2 1 101000 f 74 goat snp48355-scaffold687-511676 3 37982473 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794643 Affx-122927021 AX-385281604 3 79396925 TCCCAGTAGTTCACTATTGTATTCTAAGCAGAATA[C/T]AGAATTGATATTCTTTTATCCCATTATTTTAAATA Y 2 1 2 1 201000 r 74 goat snp48354-scaffold687-464328 3 37935083 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431527 Affx-122936224 AX-123301868 3 79426085 TTGCTCTATAGACACTATGCTATTTTTACATACAA[C/T]GTTAGATTTGATCCTTAGAGTAATCATTCAAACAC Y 2 1 2 1 101000 r 74 goat snp48353-scaffold687-435168 3 37905940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776800 Affx-122975849 AX-385263924 3 79466927 CTCATCACAAAAATGGTTGACTGTTAGAATTCTCT[A/G]TTCTTTATCAGACACCACTGAATACCTACACAACA R 2 1 2 1 101000 r 74 goat snp48352-scaffold687-394326 3 37865097 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450305 Affx-122922147 AX-123320640 3 79532351 AATTAGGGAATACCATCCCTATTTTGTCAGTGATA[C/T]GTATTTTACTTATGTGCCGGGTTTTTTTAATCTGA Y 2 1 2 1 101000 f 74 goat snp48351-scaffold687-328902 3 37799675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428588 Affx-122938705 AX-123298930 3 79574600 GCGCTTGCTGCTGAACTCACCATGTCGGTGTGCGT[A/G]TTTTCTGGAGGGAGAATGACGTGTCAGTATACTAA R 2 1 2 1 101000 r 74 goat snp48350-scaffold687-286653 3 37757452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426441 Affx-122940813 AX-123296787 3 79626650 TTTTCTCTTCTTTTTTGTGTCCAGGGCCAGGTTAC[A/G]CTGCAGTAGCAGTGCTAACACCTCAATGGCTTGGC R 2 1 2 1 202000 r 74 goat snp48349-scaffold687-234603 3 37705429 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438527 Affx-122931198 AX-123308865 3 79659390 TGTGCATTGTGTTTCCTTCTGCTTGGAATTTTCCT[G/T]CCTCCAAATTCTTTCTCTGGATAATTAATACTCAC K 2 1 2 1 201000 r 74 goat snp48348-scaffold687-201863 3 37672593 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415009 Affx-122949033 AX-123285358 3 79694557 TACCAGTGTTTACTGTTAGAAAATGTTTAACCACA[C/T]GAATTAATCATCAAAAAGATGCCAAAGAAACATCA Y 2 1 2 1 101000 r 74 goat snp48347-scaffold687-166696 3 37637367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385393 Affx-122971349 AX-123255751 3 79728713 AATCACTTTGGGCTGGGGTGGATAGCAGAGTTAAA[C/T]GGATTGTTGGGAGACAGTTTTCTATAGCGTCTTGG Y 2 1 2 1 101000 f 74 goat snp48346-scaffold687-132540 3 37603383 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773262 Affx-122961276 AX-385260405 3 79757596 CTTAGCACACATGTAGACGTTTGGAAGCCAGACCA[A/C]CTGGATCTTGAATACAAGGCTAGAGCTGACTACAA M 2 1 2 1 101000 f 74 goat snp48345-scaffold687-103657 3 37574013 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377821 Affx-122977305 AX-123248180 3 79812201 TACTTACTTACTGTGCTTATTTACTTACTGTGAGG[A/C]GCTTACTAATGAAGACCTTGTGGAATTGGAGTCCC M 2 1 2 1 201000 f 74 goat snp48344-scaffold687-49052 3 37518506 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443570 Affx-122927340 AX-123313907 3 79850260 TGGAAGATTTAGTCAGTCTAGGAGGGAAGGGGGCT[A/G]GAGAGTCTGTTAGAACTTTCTAACCAGTTCTCAGG R 2 1 2 1 201000 r 74 goat snp48343-scaffold687-10993 3 37480037 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443903 Affx-122927055 AX-123314240 3 79869480 TTGTGCTCAGCTGCTCATTCATGTCTGACTCTTTG[C/T]GGTCCCAAGGACTGTAGTCTATTGAGCTCCTCTCT Y 2 1 2 1 303000 r 74 goat snp54276-scaffold829-108064 3 37454032 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422488 Affx-122943314 AX-123292834 3 79902662 TGGCTATTATAAACAGTGCTGCGATGAACATGTTC[A/G]CTTATACATTGATTCGGGATTTGACCTTGTGCCTA R 2 1 2 1 102000 r 74 goat snp54275-scaffold829-74882 3 37419725 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401173 Affx-122959355 AX-123271526 3 79934139 ATGCAATACCATTTAAGTACAATGTACAACCTAGA[C/T]AGCATATTGAAAAGCAGAAATATTACTTTGCCAAC Y 2 1 2 1 303000 f 74 goat snp54274-scaffold829-43405 3 37387751 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415000 Affx-122949041 AX-123285349 3 79980416 ACTCTGGTCACAGGCAGAGGTGCAGTGCCCTTTCC[A/G]TTTTCCTGTGATACTGTGACTTTAATAAAAAATAT R 2 1 2 1 201000 r 74 goat snp15923-scaffold167-1887521 3 37485170 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764775 Affx-122964636 AX-385252388 3 80023478 GTAGTCCATAAACAGTTTGCATCAGTATTCTGGTG[C/T]AGGCAGATATACACTTAGGAATCAAAATCTGCCTT Y 2 1 2 1 101000 f 74 goat snp15922-scaffold167-1844459 3 37299576 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278147 Affx-1111836194 AX-519551636 3 80088755 CTTGCAAAATTTGAAAACACTATCAAGTGAAGAAA[C/G]AGAATGAAAAACTATGATACTTACAGGAGGGCCTT S 4 1 2 1 101000 r 74 goat Random2.2K-356 3 80088755 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402009 Affx-122958757 AX-123272362 3 80120019 ATAGAATTTTAGAACTTGGGTAAATCCTGTACATC[C/T]TCTGGCCTTTCTTTTCCCTGTTGAAAAATGAGCAC Y 2 1 2 1 201000 f 74 goat snp15920-scaffold167-1747918 3 37202790 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396824 Affx-122963275 AX-123267179 3 80171223 AATAGAGGTCATAATTCCACTGTCGTTGGACATTT[A/G]TTTCAGATTCAGCATGGTCAGCTATTTTGGTGGTT R 2 1 2 1 101000 f 74 goat snp15919-scaffold167-1696714 3 37151417 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436715 Affx-122932316 AX-123307053 3 80228628 TCTGTCAACTCTCTTAACTCAAACCTCTCTTCTTT[A/G]TGGATGTTCTCCTTGATGTCCAGTTCAGATACAGA R 2 1 2 1 101000 f 74 goat snp15918-scaffold167-1639309 3 37093708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448856 Affx-122923285 AX-123319191 3 80282810 TCTTCGCCTCTAGGACTAATTTAAGAGGTCAGATG[C/T]ATACTGAAAGGGAAGATCTCTAGGAAGGAAGAATG Y 2 1 2 1 101000 f 74 goat snp15917-scaffold167-1585127 3 37039301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769824 Affx-122931074 AX-385256994 3 80333306 GTATTAGCTATGGTGCCTTACTCTTCCATAATAGA[C/T]GAGTGTCATGACCACCAGCTTTGATTCTGTTATGT Y 2 1 2 1 201000 f 74 goat snp15916-scaffold167-1534631 3 36988381 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406707 Affx-122955766 AX-123277058 3 80427040 ACTTTGACAACCTGGAGATAATGTATTACAAGATA[C/T]GTCATTTTTGAATGAGAAGACATGAAACTATTTGC Y 2 1 2 1 101000 f 74 goat snp15915-scaffold167-1440897 3 36893595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448490 Affx-122923469 AX-123318826 3 80479087 CTGCAACCAAAGGAATGAGAGAATACTAAAAAATG[A/G]GCAATCTAGCTTAACCGAAGCCAAAAATATTACTG R 2 1 2 1 101000 r 74 goat snp15914-scaffold167-1388850 3 36842504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272229 Affx-1111833401 AX-519545976 3 80504373 TGGTCAAAATTTCATTTTACTCAGCTAAAACTGTA[A/G]CCCCTTAGAATGAAGTGACTGGCTCTTTAGTGCAT R 2 1 2 1 201000 f 74 goat 3_80504373_AF-PAKI 3 80504373 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320799280 Affx-122971089 AX-385286211 3 80538292 CACAAAAATTTGGGAAGCTACATATGGAGCAGAAG[C/T]AATCTTCTTGTCATTATTTCCGCTAACAAGCAAGA Y 2 1 2 1 101000 f 74 goat snp15913-scaffold167-1329645 3 36783110 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394902 Affx-122964734 AX-123265257 3 80611159 ACTAAAGGAATCCCCAGGGGATTTCCAGCATTGGC[A/G]TGGGTGCAGCAAGCTCGAACCTGAAATCTATGCTG R 2 1 2 1 201000 r 74 goat snp15912-scaffold167-1256778 3 36710282 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383396 Affx-122973500 AX-123253754 3 80664734 GGGATGCAGTCCCAAGGCTGCCTCACACACAGTTA[C/T]GGGATTAATCAAGGAACTCACCGTGTGTTTGTGCC Y 2 1 2 1 101000 r 74 goat snp15911-scaffold167-1203203 3 36656663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442913 Affx-122927634 AX-123313250 3 80734106 TTACATCAAGTTGACCAATACTTGAACTCAAGATG[C/T]TCGAAGTAGTTTATTATAGTTTGCTATTTCTGTAA Y 2 1 2 1 101000 f 74 goat snp15910-scaffold167-1133831 3 36587339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403829 Affx-122957951 AX-123274181 3 80777856 CTCCGTCCCCTGCTCTGTCACTGTCTTCAGCACAG[A/C]CGCCGTGCCTTAGGTGGCAAAGAGCTGGTTCATCA M 2 1 2 1 101000 r 74 goat snp15909-scaffold167-1090081 3 36542899 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424753 Affx-122941649 AX-123295099 3 80807095 ATAGAATAAGAGCATTCCAATACTAGATCTAATTC[A/G]TCTACTTTAGGAATCCCCAAAATTTTTATTCCTCA R 2 1 2 1 101000 r 74 goat snp15908-scaffold167-1060842 3 36513699 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786079 Affx-122966702 AX-385273115 3 80861741 ATTCATAGCACTGTCAAAGGAGACTGTCGTCTGCC[A/G]TGGCAGTATCTTTTAGTATCCCCAAAGGTTTTCCT R 2 1 2 1 101000 f 74 goat snp15907-scaffold167-1006196 3 36459759 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803224 Affx-122976247 AX-385290079 3 80894117 TATGTTTAGAATCTCCCTGCACTTAAAAAATCTTA[C/T]ATAGGTGTGGTTTGTATAAGAAAGATGCTGCATTT Y 2 1 2 1 101000 r 74 goat snp15906-scaffold167-973820 3 36427349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439118 Affx-122931099 AX-123309455 3 80931631 TTGCCTCTACAAGGGGTATTGACAGTGTTTATATT[A/G]TGGCATTGTTATGAAGAAAAAATGAGGTAATATTA R 2 1 2 1 101000 f 74 goat snp15905-scaffold167-936306 3 36389985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795189 Affx-122973639 AX-385282147 3 80975420 TTGCATGTTATAGGGTCAAGTTATTCCAACATCCT[A/G]TACCGTCTATATTATCTTAAACAATAGTAGATTCA R 2 1 2 1 101000 f 74 goat snp15904-scaffold167-892517 3 36346016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399801 Affx-122960283 AX-123270156 3 81008973 AGAGAATCAAGCCCTCCCCACAGAGTGAATGGCAT[A/G]CTTAGTAAATATTCTTCAAATATTGCTGGGTGAAC R 2 1 2 1 201000 r 74 goat snp15903-scaffold167-858964 3 36312405 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768355 Affx-122965044 AX-385255535 3 81060087 ATTTAATGTTAGTACCACTCTATTTCAAATTGTAA[C/T]CCTAACCTTAAACCAAAGGTGGATTTTGTGGCCGA Y 2 1 2 1 101000 r 74 goat snp15902-scaffold167-807850 3 36261316 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385709 Affx-122971110 AX-123256067 3 81092873 CTTTGAAGCAAGTGTCATGCATATTATGTTTTCAG[G/T]ACTTACTCAAATACTATGCTTCTACATAAGAGTGT K 2 1 2 1 101000 r 74 goat snp15901-scaffold167-775064 3 36228252 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449222 Affx-122923495 AX-123319557 3 81123009 GCACCAGGCTCCCTCTTTCTCTCTTTTTCTGGGAA[C/T]GGATTTGATGCAGGGAGAGGGAAATGGCTCTTTAA Y 2 1 2 1 101000 r 74 goat snp15900-scaffold167-744928 3 36197830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425670 Affx-122940870 AX-123296016 3 81153983 ACTAGGAGTGTACATGGCCTGATTTGGGCTTTGCC[A/G]CTAACCTAGTCTATGACCTTAGTCTGTGACCTCAT R 2 1 2 1 101000 r 74 goat snp15899-scaffold167-713954 3 36166694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415386 Affx-122948754 AX-123285735 3 81182577 AATCTTGAATACATTTTAAGGGAAGAGCAGGCCTC[A/C]CTTGCCACCTTGCACTTTTTCCTACATGGAAAAGA M 2 1 2 1 101000 r 74 goat snp15898-scaffold167-685360 3 36138156 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277990 Affx-1111836195 AX-519551483 3 81230869 ACTCTGTAGCAAATATTTCTCAATGTAAGTTGCTC[A/C]AATTCCATTCTATTTCTTTGAACACAATAAGATCT M 2 1 2 1 101000 f 74 goat Random2.2K-357 3 81230869 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394053 Affx-122964984 AX-123264408 3 81237220 TTGGATAAAGAAACTGACCCCTGATGGCTCAGCAC[A/G]TAAAGAATCTGCCTGCAATGCAGGAGACAAAGAAG R 2 1 2 1 303000 f 74 goat snp15897-scaffold167-630717 3 36083582 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381298 Affx-122974456 AX-123251656 3 81285471 CTTTGGATTTAGAGGCAAAGAAATTGCTCCCCTAA[C/T]ATGTTGGATTAATCTGCCCTAGCAACTCAGTTTGG Y 2 1 2 1 201000 r 74 goat snp15896-scaffold167-582466 3 36034750 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779969 Affx-122960265 AX-385267068 3 81322292 TTCCTATTATGGGCCCAGAATTAAATGGGTACCAA[C/T]AGACTGTACGTAGTACACAGAAAGCTACCGTTGGT Y 2 1 2 1 101000 f 74 goat snp15895-scaffold167-545645 3 35998069 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391523 Affx-122966657 AX-123261880 3 81355489 TCCAGAGCAGCAACTGAAGATGAAGATATGACAGA[C/T]GTCAGTGCAAGACAGAAAAGGACTTTGTCTCTTAA Y 2 1 2 1 101000 f 74 goat snp15894-scaffold167-512448 3 35964819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764743 Affx-122964828 AX-385252357 3 81411656 CATTTAATTGAATCTCCTCTGAACTAAAAAGGGCT[A/G]CTATGTCCACTTGTACAGATACCTTAATATCACTG R 2 1 2 1 101000 f 74 goat snp15893-scaffold167-456281 3 35908554 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799714 Affx-122941328 AX-385286642 3 81467208 CCCACAAGAGAAGACACGTGGCTTATACTTAATCC[A/G]TAGACTAAGTAGAGCTTCTCTAGCCAACTTGTTAG R 2 1 2 1 101000 f 74 goat snp15892-scaffold167-400729 3 35852039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771777 Affx-122973919 AX-385258934 3 81538656 AGAGGGGTAAGAGGAAAAGATTGAAAGAAGGGAAA[G/T]AAATTATTTGCAGAATAGTTTCACCAAGAAAAGAC K 2 1 2 1 101000 f 74 goat snp15891-scaffold167-329281 3 35780063 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793789 Affx-122978410 AX-385280761 3 81571539 AAGCAATGATAAAGATGATGTCTGGCAGGGTTGAA[A/G]TTTATTCAAGCCTTGTGCTCCTGGAAAATAGCAGT R 2 1 2 1 101000 f 74 goat snp15890-scaffold167-296398 3 35746846 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278151 Affx-1111836196 AX-519551640 3 81651248 AAACACTATTTCTCACAAGATGATAGTGTTTAACC[A/G]ACATATCTTCACAACACTTTCCAAGATATGACACT R 2 1 2 1 101000 r 74 goat Random2.2K-358 3 81651248 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398054 Affx-122961750 AX-123268409 3 81670173 AGGCAACTGCAAAAGGCTCACTAATAGATCATTGG[C/T]AGGAATCAATGGAACTTTCAAAACAACTGAAATCC Y 2 1 2 1 101000 f 74 goat snp15889-scaffold167-197764 3 35643825 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427569 Affx-122939481 AX-123297912 3 81699472 ATTCTGCTGTCCACCAAAGCCACTGGGTACACATA[G/T]ACTGTATAGGGATGCTCCCACATGAGAACCTCCAC K 2 1 2 1 101000 r 74 goat snp15888-scaffold167-168465 3 35613593 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803540 Affx-986696103 AX-385290347 3 81708893 CTATATAACCCCACCATAATATTACTAAACCTAAT[C/T]ATTTATATCATTATAACCTCCACCATATTCACACT Y 2 1 2 1 600010 r 74 goat 3_81708893 3 81708893 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320784961 Affx-122975762 AX-385272008 3 81732129 GGCAATAAGAGGGGTTGAAATAATCACAGAACTTT[A/G]CGATCCAGTCATTCTCCAAACCAACATGAGACTAA R 2 1 2 1 101000 f 74 goat snp15887-scaffold167-135808 3 35579957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379418 Affx-122976113 AX-123249776 3 81794313 TTGTATTTATGGAGATGCCCCTCCAAACAAAGGGA[G/T]AATGTACTATAATAACATCAGCATAAGCATTCATT K 2 1 2 1 201000 r 74 goat snp15886-scaffold167-73624 3 35517938 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399788 Affx-122960293 AX-123270143 3 81835732 CAGGAAAAAAAGGGAAAGAAGAATATTGTTTCATA[C/T]AACTGCTGCATTTTTGTTTCCTCAGCTCATTGATC Y 2 1 2 1 101000 r 74 goat snp15885-scaffold167-32205 3 35476471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450643 Affx-122921983 AX-123320977 3 81865081 TTATATGCATGTGCATGTGTATGTAGCATGTGTAT[A/G]TATATAATTTTCTCTATCCATTCATGTGATGAATA R 2 1 2 1 201000 r 74 goat snp15884-scaffold167-2856 3 35447280 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773904 Affx-122947488 AX-385261043 3 81939947 GTCAGTGAAATTCAACTTCTCTTAATCCTTTATTT[A/G]CAAGTTTAGGCCCTGAGAAAGACTTTTGTTTAGGT R 2 1 2 1 101000 r 74 goat snp5214-scaffold118-3285247 3 35371152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448133 Affx-122924292 AX-123318469 3 82023212 AAGAGAATCTCAGACCACTCTCATTTATGAAAACA[C/T]TTTTCCTCTAATTTCCATTTTCCATATTCAAAAAG Y 2 1 2 1 101000 f 74 goat snp5212-scaffold118-3201982 3 35288216 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375922 Affx-122978469 AX-123246281 3 82054172 GAGATATAAAGTGCTGTCTGTGAGAGATTAACCAA[G/T]ACCCTGGAAAGTACAGACAAGCCTCAGTGTTTCCA K 2 1 2 1 201000 f 74 goat snp5211-scaffold118-3171022 3 35257406 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772078 Affx-122930709 AX-385259233 3 82112247 TCACATAAGGGAGTAGGAACATGAATGAAATTAGC[A/G]TGATTATCAAGCAGTCCTAAAGTTCTGCTTGAGTT R 2 1 2 1 101000 f 74 goat snp5210-scaffold118-3112947 3 35198755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388808 Affx-122968908 AX-123259166 3 82193636 GTGTCCTACATTGCAATTCCATTCTGACACTATCT[A/G]CCTGGAGTTGAAAAGACCCCACAGGTTAAGGTCTC R 2 1 2 1 201000 f 74 goat snp5208-scaffold118-3031558 3 35116836 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421567 Affx-122943850 AX-123291914 3 82269590 GGAGATGTGTTTACTGTGACTCCCTCCAGCTTGCC[A/G]TGTGATTACAGGTAAATCATCTAACTTCTTGAGGC R 2 1 2 1 201000 r 74 goat snp5206-scaffold118-2955604 3 35040660 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775997 Affx-122970528 AX-385263127 3 82304397 CACTGGACATGGTCATATGCAATTTTATATTGAAT[A/G]TCCCACATGAATCTGAAGTTATTGTGTGTTCCTGA R 2 1 2 1 101000 r 74 goat snp5205-scaffold118-2920797 3 35005840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788310 Affx-122963323 AX-385275328 3 82334863 TATGTCATGGATCTGGTAAAGGAAAATCCTTTACA[C/T]GTGAATACATTTATGCATAAATGCAGTTCACCAGT Y 2 1 2 1 201000 f 74 goat snp5204-scaffold118-2890331 3 34975317 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804515 Affx-986696683 AX-385291065 3 82474191 ACTAATCTAGGTGTTGTGAAAGTATATTGTGGATA[C/T]GGTCAACATGTACAATAAATTGGCTTTAAGTAAAA Y 2 1 2 1 600010 r 74 goat 3_82474191 3 82474191 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 38387029 Affx-122969923 AX-123257387 3 82474590 TGTCATTTGTCCCCACTCCTTTCCATGCCATTTTG[C/T]ATGACAGCCTCTGGGTATTTTCATGCCAATGAGTA Y 2 1 2 1 102000 f 74 goat snp5201-scaffold118-2750604 3 34834404 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449463 Affx-122922654 AX-123319798 3 82524959 AAGCATTATTCAAAAGAATAACAATCAGTGGCACC[G/T]GCATGCAGAGGAAAACTACACAGAGTAAATTAGAA K 2 1 2 1 101000 f 74 goat snp5200-scaffold118-2700235 3 34782555 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784660 Affx-122959385 AX-385271708 3 82600665 CATTAATGATCAAGTTTCACAAGAACTTAGAAGAG[C/T]AGCACATTTTAGCACTCAGTATGGTTATGACAGAG Y 2 1 2 1 101000 r 74 goat snp5198-scaffold118-2624529 3 34702985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447594 Affx-122924010 AX-123317930 3 82699626 CTGTCACTATGAGATGCTACTCTAGGCTCAGATAC[A/G]TTCTCTCTGCCCCTAGAATCATCATTTGTCCAAGG R 2 1 2 1 101000 f 74 goat snp5196-scaffold118-2525568 3 34602967 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408532 Affx-122953694 AX-123278883 3 82773787 AAAATCGAGCAAATCACAATTCCAGTGGATTACTG[C/T]GAGGTTTAATGTCTCCAGTGTCCCAGCCCACTTAA Y 2 1 2 1 201000 f 74 goat snp5194-scaffold118-2451407 3 34528774 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440087 Affx-122929722 AX-123310424 3 82861737 GAACCACTGGCAGTCCACACCCTCCTCATGTCCCC[A/G]TATTTTTACCACTTCATTTAGTCTCTAATTTAGTA R 2 1 2 1 201000 r 74 goat snp5192-scaffold118-2363457 3 34443332 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424683 Affx-122941707 AX-123295029 3 82915477 GGTCTGTGCCAGGCACTGGAGGGAAATGGTAAGCA[C/T]GAGTAGACACAGACCTTACAGTCTGATGGGGAAGA Y 2 1 2 1 201000 f 74 goat snp5191-scaffold118-2309717 3 34389786 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390689 Affx-122967950 AX-123261046 3 82981247 GAGACACTTTTTGTGCTGGAAAACTGGACTCCATT[A/G]CTGTGAATATTTTAACAGATTTTCACAGTTTCTCT R 2 1 2 1 201000 r 74 goat snp5189-scaffold118-2243947 3 34324162 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420544 Affx-122945295 AX-123290891 3 83014857 CCGCGTTGTGATTACCACCACACAGGATAGGGATC[A/G]TTCATTTGTTGTTTTGTTTTGCAAGCCCTTGACAT R 2 1 2 1 101000 f 74 goat snp5188-scaffold118-2210337 3 34289640 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272230 Affx-1111833402 AX-519545977 3 83117470 ACAATTGCACTCATCTCACATGTTAGCAGAATAAT[A/G]CTGAAAATTCTCCAAGCGAGGCTTCAACAGTACAT R 2 1 2 1 303000 f 74 goat 3_83117470_AF-PAKI 3 83117470 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38453047 Affx-122920075 AX-123323380 3 83202449 ACATAGGGTTGTCATTAATCAGAGCATGGAGGGGG[C/T]GTTTCTGATGGTTGAGTGTCTGAGAAGTTTTCACA Y 2 1 2 1 101000 r 74 goat snp5184-scaffold118-2022745 3 34100971 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399248 Affx-122960575 AX-123269603 3 83258540 TGAATGAATGGGTGGATGATTAAATGGTTAGTCAA[C/T]GGGAAGATTCCTGGGCCAGATTCCTGGTCAATATG Y 2 1 2 1 201000 f 74 goat snp5183-scaffold118-1966654 3 34044693 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800968 Affx-122977846 AX-385287883 3 83346185 GTTGTTGTTGGTATATAGCAGAAACACAGCCACTT[A/G]TTGATTCCTTCCTATGTGCCAACACCATGCTAACA R 2 1 2 1 101000 f 74 goat snp5181-scaffold118-1879009 3 33955774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770575 Affx-122937433 AX-385257739 3 83439394 TAGGTGTACCGACACGCATCTCTACCAAGTCGCTG[A/C]TAGCACAGTGCACCTGACTTGGCATGTGTGCTCAG M 2 1 2 1 202000 f 74 goat snp5179-scaffold118-1785800 3 33862642 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784835 Affx-122962232 AX-385271882 3 83484799 ATCTCCTGAAACTAATTAGTGATTTTTACAAGATC[A/G]CTTGTTGTACAGATCAGTATACAAAGGTCAGTTGC R 2 1 2 1 101000 r 74 goat snp5178-scaffold118-1740395 3 33816569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389832 Affx-122968174 AX-123260189 3 83576058 CCTTGGTGCCAGCTCTCCAGTCTCCCAGAGCACGC[A/G]TGTTCCTTTTCTTCCCTTGACCCCTAAGAGCAGCA R 2 1 2 1 101000 r 74 goat snp5176-scaffold118-1649136 3 33726657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275422 Affx-1111834793 AX-519548995 3 83586520 TTGACTTTTTATTTGTTTAATTCCAGTGGTGATTA[A/G]TTCACATAGACTCAAACTGTAAACTCCCTTCCACA R 2 1 2 1 101000 r 74 goat GoatD01.053299 3 83586520 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38380188 Affx-122975505 AX-123250546 3 83766825 AAAACAACTCCAGATCTTAGTGACAAAAAAGTTAT[A/G]TTTCTTCTTTGTTCCGCGTCTGTCAAGGCTTGTCA R 2 1 2 1 101000 r 74 goat snp5173-scaffold118-1458369 3 33537474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381955 Affx-122974113 AX-123252313 3 83813887 AGGTTGGAGAGTATGAATGGAGGAGGAAGGATAAA[C/T]GAGAGGAAGATTGGGGCATCTCATAACTGCTGAAA Y 2 1 2 1 101000 f 74 goat snp5172-scaffold118-1411307 3 33500933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395115 Affx-122964151 AX-123265470 3 83999161 GAAGATTCTTCATTGGCTAGGTGGTATGTGAGTTA[C/T]GGACACAGCATAAAATTCAATCCCTGACCTCACAA Y 2 1 2 1 101000 f 74 goat snp5169-scaffold118-1226033 3 33315513 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442987 Affx-122928190 AX-123313324 3 84070677 CTCAGTGATAACAGGTTGGCTGTGCTGAGAACCCC[C/T]GAGGTACCGAGACTATAATGCCATCAACGAGCCCA Y 2 1 2 1 201000 r 74 goat snp5168-scaffold118-1154517 3 33242187 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377929 Affx-122977222 AX-123248288 3 84102263 ATTCCGGTTCAAGGAGTCATATGGCTCCAATTTTA[C/T]GCATGGCAAATAAGCCATATGGTGTCTCTTTTTGT Y 2 1 2 1 101000 f 74 goat snp5167-scaffold118-1122931 3 33210558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277994 Affx-1111836197 AX-519551486 3 84128924 TATCTTCTGTTTATGGCAACTCCATAAGGTAATGC[A/G]GTTATCATCCTCATTTTATACATAAGACCCTGAAC R 2 1 2 1 101000 f 74 goat Random2.2K-359 3 84128924 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376605 Affx-122979054 AX-123246964 3 84188900 TCTAAGCTTTAGTTGCATCATGAATAAAATTGAGA[C/T]AGTCATAGTTCATACCTGCCCCTCAGCTGTTCTCA Y 2 1 2 1 201000 f 74 goat snp5165-scaffold118-1036294 3 33123644 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408651 Affx-122953472 AX-123279002 3 84243949 TAGCTCTTTTTTTCACCCTCTGGGATCTATCTTGG[G/T]TATCCACAGTAGGACTATGTCCAAGTCTTGAACTC K 2 1 2 1 101000 r 74 goat snp5164-scaffold118-981245 3 33068371 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428931 Affx-122938899 AX-123299273 3 84278101 AATAGATAGTAAAAGCATCTACCTCTAGGGTTATC[A/G]TGGAAAGTTCATCACGTAGTATACTACCCAGGATG R 2 1 2 1 101000 r 74 goat snp5163-scaffold118-947093 3 33034035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432357 Affx-122936271 AX-123302698 3 84331064 TCATTTTACAGATATGAAACCTGAGGTTCAGAGAG[A/C]TAAGTAATTTACCCAAATCACCCAGGTAGGAAGTG M 2 1 2 1 202000 r 74 goat snp5162-scaffold118-894130 3 32981332 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380496 Affx-122975705 AX-123250854 3 84364915 AAGGAGACTGTATTCTAGTAGGAGAAATAGACAAG[A/C]GCACAAATAGCTGTAGGAAGTTACAAGGGTCACAG M 2 1 2 1 101000 f 74 goat snp5161-scaffold118-860279 3 32946937 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769619 Affx-122972175 AX-385256789 3 84421431 GGTCACCCAGAGATCTTTTATCCTCATTCAAGGCT[A/C]TCAAGTATTTTCTGAATAGATAAAGTTGGTGGAAA M 2 1 2 1 101000 f 74 goat snp5160-scaffold118-803763 3 32890373 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433547 Affx-122934992 AX-123303888 3 84519568 AAATACGTGCAGATCAAACATCCTGACAACATATC[A/G]TAGAAATACATCCACGTTTAGCCATTGTGTGGCTG R 2 1 2 1 101000 r 74 goat snp5158-scaffold118-705626 3 32795023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277998 Affx-1111836199 AX-519551491 3 84553966 ATTTTGGTAGTAAAATAATACTGGAATCTTTACAT[A/G]TGCTTCTGTTAATAGCAAAATCTAATAGAACAATC R 2 1 2 1 101000 f 74 goat Random2.2K-360 3 84553966 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320767488 Affx-122976903 AX-385254752 3 84590504 TGGTGATGAGGAATATGAAGAAAGGTTCTGTTACC[A/G]TATCATGAATAAGAGCAAGGTGTCCTGGTGGCTAG R 2 1 2 1 101000 f 74 goat snp5156-scaffold118-634690 3 32724308 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767079 Affx-122944672 AX-385254368 3 84640026 TTGCTATGGAACACTTCCTAAAATGAATGTGCTTG[C/T]ACTGCAAGTCGTCTTCTGCCTTTGCGAGAAGTGGC Y 2 1 2 1 101000 f 74 goat snp5155-scaffold118-585168 3 32674374 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443415 Affx-122927378 AX-123313752 3 84903570 TCTTATGGCATAAATTCAGTTATTCTCACTGCTTC[A/G]TTGACATTTCATAATTGTTGCTAACGTGGTTCACA R 2 1 2 1 101000 r 74 goat snp5149-scaffold118-321624 3 32409999 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394970 Affx-122964270 AX-123265325 3 84970047 TTTTACAGATTATCAGATATCTGTTCAGTGCTCAC[A/G]TTTGCAACCTATCTTTTCAATTTTGTTTTCACATG R 2 1 2 1 101000 f 74 goat snp5147-scaffold118-255147 3 32343273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275438 Affx-1111834801 AX-519549011 3 85036073 A[A/G]GGGGCCTCCCTTCAGGAGATTCACCCCCAGTGGTG R 2 1 2 1 103000 r 74 goat GoatD01.053514 3 85036073 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38423679 Affx-122942326 AX-123294025 3 85054209 TGTCTGTATTCCCTACCCTCCAATAATATAAATAA[A/C]ATGAGGGCAAGGAACACAACTACTTTATCCATAGC M 2 1 2 1 600000 f 74 goat snp5146-scaffold118-170985 3 85054209 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776138 Affx-122942326 AX-385263268 3 85054209 TGTCTGTATTCCCTACCCTCCAATAATATAAATAA[A/C]ATGAGGGCAAGGAACACAACTACTTTATCCATAGC M 2 1 2 1 102000 r 74 goat snp5146-scaffold118-170985 3 32258961 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402708 Affx-122959199 AX-123273061 3 85104995 TGTATCTCCACACTGGAGACACACATGGGTGCTTT[C/T]AGGCGGTCCTTGAGGCTACAGGTGTATATGGGGTA Y 2 1 2 1 201000 r 74 goat snp5145-scaffold118-120199 3 32207475 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401636 Affx-122959591 AX-123271989 3 85146436 TTGACATGCTTGACATTTGGTAAAGAGCTCAGTGC[A/G]TGAGTGAATGAATGAATAGATGCATGACCACAGGA R 2 1 2 1 101000 f 74 goat snp5144-scaffold118-78758 3 32165663 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771390 Affx-122938880 AX-385258547 3 85237081 ATCTTGTTTTAAACAGGAAGCATCGTTGGAACCTC[A/G]TTTTGAGCGCCCCAAACACACACATCCTCTCCTCC R 2 1 2 1 101000 f 74 goat snp8031-scaffold129-2939905 3 32075029 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423095 Affx-122942924 AX-123293441 3 85310866 TTTCTGTCTAATCTGAGAGCAACACAGCCCATCCC[A/G]TTCAGATGACTGACGTGGAGGAGAGAGAAGTTACC R 2 1 2 1 201000 f 74 goat snp8029-scaffold129-2866120 3 32001389 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766505 Affx-122939170 AX-385253869 3 85369297 GTGTGCTGTGCTCTCAAGAAGATAAAAAGGGAGAA[C/T]ATAAAATTATGTACACACAAACAATGATGGATGCC Y 2 1 2 1 101000 f 74 goat snp8028-scaffold129-2807689 3 31942193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782857 Affx-122977578 AX-385269928 3 85398112 ATTACAGCAAAAATCTATAGCCTTTCATAATTTGT[A/G]CATGCTTATCAATACAGAATAATGGGCCCACAGCA R 2 1 2 1 101000 r 74 goat snp8027-scaffold129-2778874 3 31913352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410072 Affx-122952852 AX-123280422 3 85434537 AGGAAGGAATATGAGGTACCCATTCAAACCCTCCT[C/T]CCCATTTTACAGATGAATGACCTAGAAGACATCAC Y 2 1 2 1 101000 f 74 goat snp8026-scaffold129-2742449 3 31876887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411213 Affx-122952358 AX-123281563 3 85463418 TATCCTAGCTGTGGAGTATGACTTCAACCATCAAA[C/T]GTGATAGTCATAACTGCCTTATTAGGGCTGTCGTA Y 2 1 2 1 101000 f 74 goat snp8025-scaffold129-2713568 3 31848276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423742 Affx-122942858 AX-123294088 3 85494508 TGCAGGACTAGTGATGTTGAGCATCTTTTCATGTG[C/T]TCATTACCCATTTGCCTATCCACTTTGGTGAAATG Y 2 1 2 1 303000 r 74 goat snp8024-scaffold129-2682478 3 31817061 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442004 Affx-122928423 AX-123312341 3 85527180 ATCAACCTCCCTGGAAAAAAAAAGACCAAAGCATT[A/G]AAAATATACATACTTGTTGACCCAGCAATTCTGGA R 2 1 2 1 202000 r 74 goat snp8023-scaffold129-2649806 3 31783945 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769815 Affx-122964545 AX-385256985 3 85556071 ACTAGGGAATACAAAGACAATACATCACAGTCTCT[A/G]TCCTCAGGTGGTTCAGATACAAATAATGATACTAG R 2 1 2 1 101000 f 74 goat snp8022-scaffold129-2620915 3 31755908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439812 Affx-122930481 AX-123310149 3 85640881 CATAAGCATTGTTAGGAGTATAGAAATAATACATG[C/T]AAAGCATGGAGAAGGTACATATAATTGGCATCTAA Y 2 1 2 1 101000 r 74 goat snp8020-scaffold129-2536105 3 31671232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388710 Affx-122968982 AX-123259068 3 85674180 TGGGAGTCCAAGATCATGGTGCCAGCAGATTTGCT[A/G]TCTGGTGAGACTCCCTTCTTGGTTCATAGCCGTTT R 2 1 2 1 101000 r 74 goat snp8019-scaffold129-2502806 3 31637873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769108 Affx-122949588 AX-385256283 3 85706810 CCTGTGACGTTATGTTCGAAATCTGAGTACGATTC[A/G]TATTCTGTCAACGTAAATTCAGATTTGCCTCGGGT R 2 1 2 1 101000 f 74 goat snp8018-scaffold129-2470176 3 31605195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418666 Affx-122946318 AX-123289014 3 85744554 AAACTGGGTGTTGAGAGTTAATTAGAGGGTTAGCT[A/G]CTCATGGCACTTTGGATCATCCAAAAAGAAAAGAA R 2 1 2 1 101000 f 74 goat snp8017-scaffold129-2432432 3 31567278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400144 Affx-122960702 AX-123270499 3 85804633 TGGTTCGTCTATAGCGATGCTGAGGTCTCCCAGGG[C/T]GATGAGAGGAACTGGAGTAGAGAGGAAGCTGATAA Y 2 1 2 1 101000 r 74 goat snp8016-scaffold129-2372353 3 31507166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272069 Affx-1111833403 AX-519545833 3 85852238 GTTGTTGTTGTTGTTATTTATAAACTTTCAGTGCA[A/G]TAGTGTGGTTGATGGAAACGTTGAAGAAGTTCCCA R 2 1 2 1 101000 r 74 goat 3_85852238_AF-PAKI 3 85852238 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320802416 Affx-122938399 AX-385289320 3 85860091 TGAGGTCTTGTCCATTCATGCACATACTGAGCAGT[A/C]GAACAGTATTTCCAGCACGTTCTTCCTGATTCCAA M 2 1 2 1 101000 f 74 goat snp8015-scaffold129-2316895 3 31452256 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450421 Affx-122922057 AX-123320755 3 85893431 AGGTACCGGAAAGTCTCTAAAGACTGCAATCAGGA[A/G]AGAGACACAGTAGGTAACCCCTATGCATTCAAGTT R 2 1 2 1 101000 f 74 goat snp8014-scaffold129-2283555 3 31418601 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448925 Affx-122923161 AX-123319260 3 85934818 ATCCTCTCAGTAGCACATGTGGAAACTGAGGCTTG[A/G]AGAGCTTCAGTAACTCACTCAAGACAGCACCACTG R 2 1 2 1 201000 r 74 goat snp8013-scaffold129-2242168 3 31377449 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798219 Affx-122921349 AX-385285154 3 85967072 GAGGAGATCAGGAAGTTTCATACCAAAGTTGCTTC[A/G]TTGTCACAAAAGACCCATTACGGGCATCTTCCTGA R 2 1 2 1 101000 f 74 goat snp8012-scaffold129-2209914 3 31343915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421527 Affx-122943880 AX-123291874 3 86001920 TATATATATATATTTTGTGAATGTTAAATGATCAG[C/T]GGAAGGATCTGTCTTCTAGCAACTGTGTGCTATGG Y 2 1 2 1 101000 r 74 goat snp8011-scaffold129-2175066 3 31309168 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384262 Affx-122972315 AX-123254620 3 86036783 TCTATAATGTTGAGAATGGAGTGAGTGATGGAAAG[A/C]GAGGTAGTTCATGAGGTCAGAGAGTGGACATGGAC M 2 1 2 1 201000 f 74 goat snp8010-scaffold129-2140203 3 31273881 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771732 Affx-122925894 AX-385258889 3 86096751 TTCTTTAGAGTTTAGTTTATGAAGGACATTATTGT[A/G]TCCCTCTATCTCACACAAATAATTATTTCTGGCTC R 2 1 2 1 101000 r 74 goat snp8009-scaffold129-2080235 3 31214080 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433158 Affx-122935670 AX-123303499 3 86154811 CTGAGAGGCGATCACGTATATAGCTGTATCTTCAG[C/T]GGTGAAAGGATGGGAAAAAAGAAATCAGTCTTATC Y 2 1 2 1 201000 f 74 goat snp8008-scaffold129-2022175 3 31155684 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417503 Affx-122947155 AX-123287851 3 86184250 TTGAGCGAGTTACTCCCCATCTCACGACCCCCTTC[G/T]CATCTGCTCAATGGGAAAAATGAAGACTTGCTTTG K 2 1 2 1 101000 r 74 goat snp8007-scaffold129-1992736 3 31126289 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404450 Affx-122956746 AX-123274802 3 86216553 GTCTGAACTATCATCCCTGAGAGGTGTTGGTGACA[C/T]AAGCAGAATAACACATATATTGACTAGGGTCCCTG Y 2 1 2 1 201000 f 74 goat snp8006-scaffold129-1960433 3 31093965 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419117 Affx-122945768 AX-123289465 3 86273908 CACAGCATAATTAAAAGCATGGGCTCCAGGACAGA[C/T]GGCCTGAGTGTGAATCTCAGTTTCATTGCTTATTA Y 2 1 2 1 201000 r 74 goat snp8005-scaffold129-1903078 3 31036186 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783851 Affx-122974798 AX-385270907 3 86348522 TTAGGGAAACCATCTGTTGATCCCTCTGAACTTCC[A/G]TTTCTCACCTTAAAACAGATACTTGATAAATCATA R 2 1 2 1 101000 f 74 goat snp8004-scaffold129-1828464 3 30960624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397244 Affx-122962367 AX-123267599 3 86442489 AGGAAACTAATTCCCCAAATGAAATTAAGTGCTGT[A/G]AGGAAGTGGAAATCAATTCTGGGAAGCTAAACAAT R 2 1 2 1 201000 r 74 goat snp8002-scaffold129-1734497 3 30866511 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419055 Affx-122946016 AX-123289403 3 86480190 TCTCCTGCAGTGGAAAGTGGATTCTTTACCACTAG[C/T]GCCACCTGGGAAATCCTCTAAAAGTCAAGTCATAT Y 2 1 2 1 303000 r 74 goat snp8001-scaffold129-1696796 3 30828800 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798154 Affx-122950630 AX-385285089 3 86515877 CAAAACCCTAATGTAGTGTAAATTGACTTGTAAAT[A/C]TGACCTCTCCTCAACATTTTATCACCTCATGCCCC M 2 1 2 1 101000 r 74 goat snp8000-scaffold129-1661109 3 30793142 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376775 Affx-122977961 AX-123247134 3 86545839 CTCCACCATCCTGAGCCAGCAGCAGGACCACCTTT[C/T]CCTCTGTTTCCCATGGGTCTTTCTGTGTGGCGGAC Y 2 1 2 1 101000 r 74 goat snp7999-scaffold129-1631147 3 30763316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789269 Affx-122938463 AX-385276280 3 86584650 AGGTGAGAAATTAATATTATTTGTAGAAATAGTAG[C/T]ATTATAAAGAATCCAACAAATGCTACCTGAATTCA Y 2 1 2 1 201000 f 74 goat snp7998-scaffold129-1592336 3 30723160 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417698 Affx-122947457 AX-123288046 3 86665212 TCACTTATATGGAGGTTGAGGTTATATTAATAGCT[A/G]TATGTTTTATTTTATTTTATTTTCTTATCCATCGT R 2 1 2 1 101000 f 74 goat snp7996-scaffold129-1511774 3 30642462 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798055 Affx-122938606 AX-385284991 3 86704834 GGGGGCCTGGAAAGAGGAAATGTGTAGCATACAAG[C/T]GTATAAAGGCATGCTACGAAGGTAACAGGCCTTCC Y 2 1 2 1 101000 f 74 goat snp7995-scaffold129-1472152 3 30601707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393343 Affx-122965936 AX-123263699 3 86760388 ATAAGCATGGGATTAGGCAATTGTAAATTATTTGA[C/T]GTAACTCTTATAACAAATTAAGTCCATATCAGGAC Y 2 1 2 1 101000 r 74 goat snp7994-scaffold129-1416598 3 30545149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781281 Affx-122962216 AX-385268366 3 86805660 GCTGTTCATAGGAGTGCTGCTCATAATAGTTTGTG[G/T]GGTATATTCAGACAGTAGAATAACACACAACTAAA K 2 1 2 1 101000 f 74 goat snp7993-scaffold129-1371326 3 30500089 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804521 Affx-986696689 AX-385291070 3 86828983 TCAGGAACAGGTACCTTCTGCTCTTGTCTCTCAGC[G/T]TCCTGGTTCTGTTTTCTGCCTTTCCATGATGCTCT K 2 1 2 1 600010 r 74 goat 3_86828983 3 86828983 Ancestral_priority_1043 ancestry 0.634 recommended IMAGE 10K 10K ancestral 320803542 Affx-986696104 AX-385290349 3 86829073 CATTTTGCAGCATATTATTTAGTGCCCACCATAGT[A/G]TTTAGGCTCTGTGAGTGCCAGGTTTTATCCCTTGG R 2 1 2 1 600010 r 74 goat 3_86829073 3 86829073 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320804140 Affx-986696691 AX-385290790 3 86832348 TCTCAGTGCTTTTCTCTGTGTAGGAAGATGGGTAA[A/G]TCTGGAGTCACGAAAATTCTCTTTTTGAGATGCAT R 2 1 2 1 600010 f 74 goat 3_86832348 3 86832348 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320804144 Affx-986696693 AX-385290793 3 86835948 CTTCCCCTTAACAAATAAACTTTCATCTCAATTCT[A/G]TCAACTATCAATATTTTACCTTTAACCATAGCCCT R 2 1 2 1 600010 f 74 goat 3_86835948 3 86835948 Ancestral_priority_1043 ancestry 0.614 recommended IMAGE 10K 10K ancestral 320804527 Affx-986696695 AX-385291076 3 86835957 AACAAATAAACTTTCATCTCAATTCTATCAACTAT[C/G]AATATTTTACCTTTAACCATAGCCCTTGTAAGGAT S 4 1 2 1 600010 r 74 goat 3_86835957 3 86835957 Ancestral_priority_1043 ancestry 0.662 neutral IMAGE 10K 10K ancestral 320804529 Affx-986696697 AX-385291078 3 86835979 TTCTATCAACTATCAATATTTTACCTTTAACCATA[G/T]CCCTTGTAAGGATGCTGTTAACAAGTCTTGGTCTA K 2 1 2 1 600010 r 74 goat 3_86835979 3 86835979 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 320804156 Affx-986696699 AX-385290805 3 86836677 AGTTTGATTTTTCCATAGGGACCAGCTAAACAACT[C/G]TTTTCAATGAGAGATCTGTAAAAATTTACCAATTT S 4 1 2 1 600010 f 74 goat 3_86836677 3 86836677 Ancestral_priority_1043 ancestry 0.702 recommended IMAGE 10K 10K ancestral 320804533 Affx-986696701 AX-385291082 3 86836680 TTGATTTTTCCATAGGGACCAGCTAAACAACTGTT[C/T]TCAATGAGAGATCTGTAAAAATTTACCAATTTAGC Y 2 1 2 1 600010 r 74 goat 3_86836680 3 86836680 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 320804500 Affx-986696667 AX-385291056 3 86836833 AGAGTGCGAAGGATGCAGCCTTCTCAGGAGCCAGG[A/T]AGCTTACTCACAAATATCGTCTAAGAGAGTAAAGG W 4 1 2 1 600010 r 74 goat 3_86836833 3 86836833 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320804536 Affx-986696704 AX-385291085 3 86839224 AGGAGCCAGTGCCTTGGAGACCAGGTGTACCTTCC[C/T]TCCCGCAGAACCATCTGTCTTTTTCTTTCTCCTTC Y 2 1 2 1 600010 r 74 goat 3_86839224 3 86839224 Ancestral_priority_1043 ancestry 0.562 neutral IMAGE 10K 10K ancestral 38396761 Affx-122962776 AX-123267116 3 86842008 CGTGTTTATTGTTGGGAAGATCACTTTCAGCCCAA[C/T]GAGGTCACAGAGTTGACTTGACATGCTTCCTATCC Y 2 1 2 1 101000 r 74 goat snp7992-scaffold129-1334978 3 30464464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787190 Affx-122957534 AX-385274216 3 86873940 AACCCACTAGCTGCCAAAGCCATGAGTAAAGTGTA[A/C]TTTCAAAAACTAAACCATCTTACCACATAAAGAGC M 2 1 2 1 101000 f 74 goat snp7991-scaffold129-1303046 3 30432699 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396432 Affx-122962990 AX-123266787 3 86903285 GCTCCACCCATGATGAAGCAATAGTAAGGATGTAC[A/G]TCCTGGGATGGGTGAAGAATAAAGGCTATTAATAG R 2 1 2 1 101000 f 74 goat snp7990-scaffold129-1273701 3 30401590 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773758 Affx-122921831 AX-385260898 3 86953510 TACAGAGTAGTTGGTTTAACACAATGAGGTGCCGG[C/T]GAACTTTTAGGATCTAATACATAGGGTAAAGGAGT Y 2 1 2 1 101000 f 74 goat snp7989-scaffold129-1223476 3 30351336 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423934 Affx-122942258 AX-123294280 3 87005453 TTAGTGACTGAACAACAGCAACAATAAAACCACCA[C/T]CTCTTGGATGACTTGTGGAAGTACTTTCCAACATT Y 2 1 2 1 101000 r 74 goat snp7988-scaffold129-1171533 3 30298877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424850 Affx-122941349 AX-123295196 3 87035443 AAAAACCTTGAAAAACTATGAGAGCATCCTTATGC[A/G]TTGCAAGCTCTGTTGCCCCAACCCCAAAATGAATA R 2 1 2 1 101000 f 74 goat snp7987-scaffold129-1141543 3 30266086 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379782 Affx-122975838 AX-123250140 3 87068682 AGATAACAGTCACAATATTGCATGTTGTAACAAAA[C/T]GTAGTGGGAGCATAGATGCCGGAGCAGTAAATCAT Y 2 1 2 1 201000 f 74 goat snp7986-scaffold129-1108304 3 30233474 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781428 Affx-122923121 AX-385268513 3 87202884 CTCTTGAAATCCCTGAAAAGCAGAGTTGATAAGGA[C/T]GACTAGGTTGAGCAAATGTTGACTGAGCCTGCAGG Y 2 1 2 1 101000 f 74 goat snp7984-scaffold129-974102 3 30097401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420025 Affx-122945152 AX-123290373 3 87279428 TGCTCTGGTTGAAGACAGCCAAGTGGAGACAGGGC[A/G]TTAGCCCAGTCTGTGAGCACACCCACCATCCCCCA R 2 1 2 1 102000 f 74 goat snp7983-scaffold129-897558 3 30020133 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278000 Affx-1111836200 AX-519551492 3 87281469 TGGCAAAGGCAACATGCACACAGGCCTACTCAGTA[A/G]TCTAAGCCACGCCTGACTCTTCGTGACCCCACGGA R 2 1 2 1 101000 f 74 goat Random2.2K-363 3 87281469 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415329 Affx-122948797 AX-123285678 3 87311697 ATTTGACAACTGATTTTTTTTTTTCATTCTTATGC[A/G]TTTGTTAACTAAAAATTTCTTATGTGACTGGTTGA R 2 1 2 1 201000 r 74 goat snp7982-scaffold129-865289 3 29987691 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778957 Affx-122951994 AX-385266064 3 87351208 TCAATTTGTCTAAGTCCAGGTGTGGGAAAGGGGGT[A/G]TTAGGATATTTTTAGCTGTAAGTAACAGAAGACCT R 2 1 2 1 101000 f 74 goat snp7981-scaffold129-825778 3 29947139 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443930 Affx-122927032 AX-123314267 3 87410264 GCTTTATGGAGAACACTCTTGAGCTACAGGAAAAG[C/T]AGGTGCTTTTCTTCCTATAGTGCCAAAGCTTCTCC Y 2 1 2 1 101000 r 74 goat snp7980-scaffold129-766722 3 29887519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422181 Affx-122943517 AX-123292527 3 87521500 TTTATAACCCTCTAGAATTTGAAAGATAATTTCAG[A/G]CTATTTCATTTGCCATCACCTCCAACAAACCCAGG R 2 1 2 1 101000 r 74 goat snp7978-scaffold129-655486 3 29777445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804542 Affx-986696710 AX-385291090 3 87547662 TCCTCCTCAGATGCAACCAACCACCAACTTGGGGC[C/T]TTTTTCCCCTCGCCCTGATTGGCCTCTCCCTGTCT Y 2 1 2 1 600010 r 74 goat 3_87547662 3 87547662 Ancestral_priority_1043 ancestry 0.466 neutral IMAGE 10K 10K ancestral 320779688 Affx-122934894 AX-385266788 3 87559569 GGTTGAGTTACACTTGATCCGATAAGGCGAAAATT[A/G]CATATAATCTATATTACTCTTGACCTGATTGTTAA R 2 1 2 1 201000 r 74 goat snp7977-scaffold129-617417 3 29739458 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444315 Affx-122926742 AX-123314652 3 87605552 AGTCACACACACTGACACGGTCATGTACACTCTCA[C/T]GCATAATTTAAACATTAAAAAAGGAAATAGTATCA Y 2 1 2 1 101000 f 74 goat snp7976-scaffold129-571434 3 29692751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450320 Affx-122922135 AX-123320655 3 87671218 TAAATATGGACCAAATAATAGAGAATATTAATGTA[C/T]TGTTAAATTCCTTTGGTTGAGACAATGCTATTGTG Y 2 1 2 1 101000 r 74 goat snp7975-scaffold129-505768 3 29628595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448643 Affx-122923358 AX-123318979 3 87701049 GCTTTATAAGAGATGTGACCAGAATGGGGGCAAGC[A/G]TATCAGTCTAGGTCCAAAAGAGATGCTGCCGTCTG R 2 1 2 1 101000 f 74 goat snp7974-scaffold129-475937 3 29598521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795721 Affx-122967873 AX-385282674 3 87748055 TCAGTTTTCTCATTGGGTAAATGAGGACAATAATT[A/G]CCTTTCCCAGAGTATTGTTTGTAAGTAAGAACACA R 2 1 2 1 101000 r 74 goat snp7973-scaffold129-428931 3 29550286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441548 Affx-122928699 AX-123311885 3 87798259 ACATTTAGCACACTGAGACACTGCCTCCAGCCAAC[A/G]TTTATAAGGAGCCAATTCATTCTGAATACAACATT R 2 1 2 1 201000 r 74 goat snp7972-scaffold129-378727 3 29499801 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387077 Affx-122969884 AX-123257435 3 87839467 GCATTCATGTGGCTGTGCAACTATCTCCACCACCC[A/G]TCTCCTTATTCATCTGCTCAAACTGAAACTGCACC R 2 1 2 1 101000 r 74 goat snp7971-scaffold129-337519 3 29458347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443358 Affx-122927420 AX-123313695 3 87874162 GTGTAGTGAGGTTCTTTTTCTCCCCCAGAGAAAAC[A/G]CCTTGAGCTGGAGATAGGAGGCACTTGCCCCATTG R 2 1 2 1 201000 r 74 goat snp7970-scaffold129-302824 3 29423690 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779967 Affx-122949554 AX-385267066 3 87922310 TCAAAAATGAGTCATCTAGACCTGTACACTCTTAC[A/G]CAATAGCTACTAGCTTCTGGTATGCAGCTAGTCCA R 2 1 2 1 101000 f 74 goat snp7969-scaffold129-254676 3 29373546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398857 Affx-122961055 AX-123269212 3 87955222 TGCCTACCCCATCTGTTGCCCTCCCAAGAGCCCAG[A/C]GATGGAAAGGAACTTTCCTTCCTTCCCTCCGCGAG M 2 1 2 1 103000 r 74 goat snp7968-scaffold129-221764 3 29340589 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445473 Affx-122925210 AX-123315810 3 87984478 TCTGAACCTCTCCACGAGGGCTTCTTATACCTACA[A/G]CCCAGGTTTCTGGGTGGGATGGGGTATTAACTTCC R 2 1 2 1 101000 f 74 goat snp7967-scaffold129-192508 3 29310945 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437206 Affx-122932046 AX-123307544 3 88018361 CACCACCACTGTGCTCCTAGGGCTTCAGATGCCCC[A/G]TAGGGTCCACAGGTTCCCAAGGTTGAAGAGCAATG R 2 1 2 1 101000 r 74 goat snp7966-scaffold129-158625 3 29278563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378084 Affx-122977166 AX-123248443 3 88067897 TGATCGGGAACCTTTCTGGGGATGCTTTACCTGAA[C/T]GAGTTGTTCATTTTCTTTCTGCTTTTGGTGAAGCA Y 2 1 2 1 101000 f 74 goat snp7965-scaffold129-109089 3 29229447 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388823 Affx-122968896 AX-123259181 3 88109119 CCTGTTAGTCTATAGTTCATTTGAGTCTATGTCTC[A/G]TTCCCCATGGTGTGCCCAAGATCTCGCCCTGGGCC R 2 1 2 1 101000 f 74 goat snp7964-scaffold129-67867 3 29188138 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427574 Affx-122939477 AX-123297917 3 88167442 TAGGCTTTGTCGGGGTAAACGTGAGAATATGAGAG[C/T]TTTGCTCTGAAGAAAAGGGACAAGGCTTCTACTGG Y 2 1 2 1 101000 f 74 goat snp7963-scaffold129-9544 3 29129189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420421 Affx-122944912 AX-123290768 3 88185344 ATGTATGATCCAATTAGGGCAGCAGCTGTGCCTAA[C/T]TGGTGCCTCTGTCCTCGACATCTAACACAGTAAAC Y 2 1 2 1 101000 r 74 goat snp16958-scaffold1771-8259 3 29109416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446935 Affx-122924682 AX-123317271 3 88251876 GTCTCCCCTTTCCAACTTGGGAGCCCCTTGATGGC[C/T]GAGAGCCCATCTTCCTGATCTTTGTGCCTCTCCCA Y 2 1 2 1 201000 r 74 goat snp16959-scaffold1771-74791 3 29042366 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381933 Affx-122974130 AX-123252291 3 88289922 TGTTAATAGTAAACAGGAAACCAGCAAGAAGAGAG[C/T]TGGCTGCAGCCCAGTCCCTCTCTCAATTCCGCACC Y 2 1 2 1 101000 f 74 goat snp16960-scaffold1771-112837 3 29004122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405089 Affx-122956992 AX-123275441 3 88321211 CTGGGACAGTTAGCCCAGCCACATGTGAAGCCATC[A/G]GCTGGAACCCAGACTCCTCACTTTTTACATGGATC R 2 1 2 1 101000 r 74 goat snp16961-scaffold1771-144126 3 28972868 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402297 Affx-122959096 AX-123272650 3 88360058 CCTGGCACGCACGAACCACCTGTTGGTTGATGAGC[A/G]CTCTGGGTCCCTAGGTTGGAATCCACCTTCTTCAA R 2 1 2 1 201000 f 74 goat snp16962-scaffold1771-182973 3 28933712 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272234 Affx-1111833404 AX-190537523 3 88372622 AAATGGTTGGATGGCATCACCAACTCAATGGATGT[A/G]ACTTTGAGCAAACTCAAGGAGATAGTGAAGGACAG R 2 1 2 1 103000 f 74 goat 3_88372622_AF-PAKI 3 88372622 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394276 Affx-122964713 AX-123264631 3 88444061 AAAGCAGGCTTGCGGGGAACCAGCACTGGTTTTGT[A/G]CGTCCTCTTTGAAATAGAAGGTCCGTCTCTCCCAT R 2 1 2 1 201000 r 74 goat snp16963-scaffold1771-266976 3 28849694 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278159 Affx-1111836201 AX-519551648 3 88450909 CCACAGTAGAGGTGGGCACTCTGCAACCTGAGAGA[A/G]TTAGTAAAGGAACCCATAGGCTCTAGAGTGGTCTC R 2 1 2 1 101000 r 74 goat Random2.2K-364 3 88450909 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406764 Affx-122955724 AX-123277115 3 88475113 AGCTCCCACAGCCTTGTGTCTCCCTGTCCTGGTCG[A/G]TATGATGAATCTGTACTTTTTGGATCGTCTGTCGG R 2 1 2 1 103000 r 74 goat snp16964-scaffold1771-298028 3 28818703 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433243 Affx-122935245 AX-123303584 3 88520299 CTTGTATTCCTCCGTCCCAGTGCTGAACGAGGAAG[A/G]GAAGGGAAGAGGTGGGGAGGCTGAGGCAGGTGGGC R 2 1 2 1 101000 f 74 goat snp16965-scaffold1771-343214 3 28774213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476179 Affx-1251763683 AX-586011606 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 8 1 4 1 20000 f 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 539476434 Affx-1251763683 AX-586011835 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 4 1 4 1 20000 r 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 562165123 Affx-1251763683 AX-606940535 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 8 1 4 1 20100 r 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 562165532 Affx-1251763683 AX-606940943 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 8 1 4 1 20100 r 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 562165571 Affx-1251763683 AX-606940982 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 8 1 4 1 20100 f 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 562165936 Affx-1251763683 AX-606941345 3 88544482 ATTTTGATTTTTGTCATCTTGTTATGTTTTGTTTC[-/TTAGGCTTTAGTTGTTTTTTTTTTTTAATTTTTTATTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCCCTCCCCC]TAGGCTTTAGTTTTTGCTTGTTTCCTTTCAACATT - 8 1 4 1 20100 f 74 goat SV_345 3 88544482 - deletion junction SV-TF-chip 38447561 Affx-122924034 AX-123317897 3 88562744 GTCCACAGGCTTCTGTGAGGGTGACCTGAGTCCAC[A/G]TGGAAGGAAGTACCTGGCCTGTGGTGGGGCTGGGT R 2 1 2 1 101000 f 74 goat snp16966-scaffold1771-385659 3 28731636 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375449 Affx-122979169 AX-123245808 3 88592908 TGTTCATAATGCTGAACAACGTTGCTTGTACAGTC[A/G]TAAGTCCTGACTGACCGTGGTTTGAAAAACTACTG R 2 1 2 1 101000 r 74 goat snp16967-scaffold1771-415823 3 28702170 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798905 Affx-122976955 AX-385285835 3 88637958 CAGAACTTCCCACACTGTATTATAACTTCTATTTG[A/C]CTATTTCCCTCAGAAGATTGTGAGTGCCTCCAGGG M 2 1 2 1 101000 f 74 goat snp16968-scaffold1771-460873 3 28657196 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803254 Affx-122955117 AX-385290107 3 88692673 TGAGAGAAAACTTGGCGATTTTAATCACACACATG[A/G]GGGTTGGCACACATGAGAATTACAGGTTTGCAGCA R 2 1 2 1 101000 r 74 goat snp16969-scaffold1771-515588 3 28601921 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796723 Affx-122954448 AX-385283668 3 88744487 ATTAAGATTAAATACACTTGTTTCACACAAAAACT[A/G]CATTCTTGACAAATGTTGTGTCAAATTCTAAATGT R 2 1 2 1 101000 r 74 goat snp16970-scaffold1771-567402 3 28550061 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436624 Affx-122932502 AX-123306962 3 88777985 TATCTTTGGTATTATTATATTGATCATGTTCATTA[A/G]AAACACCGAAGAGAAAGCATAGGGCAAATAAAAAT R 2 1 2 1 201000 f 74 goat snp16971-scaffold1771-600900 3 28515997 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464234469 Affx-1110383484 AX-515709204 3 88788145 GAGAGGGTAGAGCCTGAAGCAGACATGCTGGCAAC[C/T]GGAGCAGGTGAGCAGGTGAAAGTGTGGGTTCTGGG Y 2 1 2 1 102000 f 74 goat GoatD01.022479 3 88788145 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38405959 Affx-122955543 AX-123276311 3 88857917 TCCTCCTAGATAAATAAGAAGACATATAGAAGGGC[A/G]TTATTCTTCATTGCCTCCTCATTGCTTGTAATTAG R 2 1 2 1 201000 r 74 goat snp16972-scaffold1771-680832 3 28436538 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447860 Affx-122923887 AX-123318196 3 88897901 TATCTTTTAAAAATTTTTTTCTAAAATTAATTCTT[A/C]ATTTCTTTATTGTGGCTGATAAGAAAGATGAAAAG M 2 1 2 1 101000 r 74 goat snp16973-scaffold1771-720816 3 28397619 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432789 Affx-122935419 AX-123303130 3 89000905 AACAGTCAGGTATCATGTTTACCAAATGATGGTCC[A/G]TACTTTGGAGAAAAAGCAGGGAAGGGAGTTAGGGG R 2 1 2 1 201000 f 74 goat snp16975-scaffold1771-823820 3 28295233 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401500 Affx-122958940 AX-123271853 3 89046550 GATGACTGACCTAAGCACACCCTCGGTGAGGTTCC[A/G]TTCAAATGAGTGGCTCTGGAAGTCAGAGCCTTAAG R 2 1 2 1 202000 f 74 goat snp16976-scaffold1771-869465 3 28250779 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414489 Affx-122949546 AX-123284838 3 89099821 CATAGAAAGTGGCTGATATTCAGGTGTAAGCTCCA[C/T]GTGGGCACTATGTCTGGTTGATGGCTCATCCCTGG Y 2 1 2 1 101000 f 74 goat snp16977-scaffold1771-922736 3 28197345 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406740 Affx-122955742 AX-123277091 3 89129658 ACTCCCTGTGTAACCTTGGGTAACCCACTAAACTC[C/T]TCTGAGTCTTTGTCTGAGATGGAGTGGTCTTACCA Y 2 1 2 1 101000 r 74 goat snp16978-scaffold1771-952573 3 28167490 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273499 Affx-1111833654 AX-519547115 3 89197917 CTGTCTGCAGAAAGGCCTACCAGATTCCACACCAA[A/C]TGCATGCCTAGCCCTAATGCCTGCAGCTTCTGGCT M 2 1 2 1 102000 f 74 goat GoatD01.000714 3 89197917 C A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38411086 Affx-122951930 AX-123281436 3 89217595 GGGCCCCAACTTAAAGTCCCATGGACTCCCCACCA[C/T]GATTCCTTGCTTCAGAAGAGAAACCCGGACCTCTG Y 2 1 2 1 101000 r 74 goat snp16980-scaffold1771-1040510 3 28079529 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412841 Affx-122950457 AX-123283190 3 89282144 CATCACTTCAAACGTTTCCTTTAAAAGCCCTTCCC[G/T]GAAAGCTGTTGGGAGATCAGGTGTTTTGACCATGA K 2 1 2 1 101000 r 74 goat snp16981-scaffold1771-1105059 3 28015171 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410788 Affx-122952667 AX-123281138 3 89313042 TGGGCTACCTCCTCTATCTCTCTGGTTCAGGTCAC[A/G]GTCACCTGAGGTCTGGGTTTTCATATTAGCCTCCC R 2 1 2 1 201000 r 74 goat snp16982-scaffold1771-1135957 3 27984311 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447340 Affx-122924886 AX-123317676 3 89342466 TGCCTTGTTCCCTGCAGTCTCTGCTCAGCTCAGGG[C/T]TGAGAATTGTTGCTGTTGCTGTTCAGTTCCTAAGT Y 2 1 2 1 201000 f 74 goat snp16983-scaffold1771-1165381 3 27955791 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406021 Affx-122955496 AX-123276373 3 89383764 GAAATATGAATGAAAAATAACCCCGAAGAAAAGAT[A/G]CTGAACCTTACAGAAAATCAGGAAAAAGTAAGTGA R 2 1 2 1 101000 r 74 goat snp44030-scaffold595-5911614 3 27914723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446591 Affx-122924818 AX-123316927 3 89418243 CTTAGGGAGAAGGATGGTGTGGCTTCCACTGCCCC[C/T]AGGAGAGCCTGAGAGCCTGCATCCTCACTGGAAGG Y 2 1 2 1 201000 r 74 goat snp44029-scaffold595-5877135 3 27880634 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791183 Affx-122938267 AX-385278178 3 89459966 CATTTCCAATAGTAAATGAAACTAAGGAAATGTAC[A/G]TTCCTTCTCCTCCCTTTATTGGGCACCTTCTGTAT R 2 1 2 1 101000 r 74 goat snp44028-scaffold595-5835412 3 27839261 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278005 Affx-1111836202 AX-519551497 3 89553563 AATCTCTGATTTTAGAATTGCTACAGGAAGGGATT[C/G]GAATTTTGGTAGAATGACCTAATGATCCTTTCAGG S 4 1 2 1 101000 f 74 goat Random2.2K-365 3 89553563 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413994 Affx-122950280 AX-123284343 3 89553914 CAGCTTCACTCTGTGAAATATGAGCATGAACACAA[C/T]GGTGAAGACATGGGGCCCCCTGGGACAGTGTCTCT Y 2 1 2 1 101000 f 74 goat snp44026-scaffold595-5741464 3 27745177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381865 Affx-122974181 AX-123252223 3 89593851 ACATCCTGGAGCTTCTCCTTTGGGAAGCTGTTCTC[A/G]TATCTGCTCTGTCCATCCCCACTCTCATCCCTGCA R 2 1 2 1 201000 r 74 goat snp44025-scaffold595-5701527 3 27704731 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387334 Affx-122970496 AX-123257692 3 89638236 TGGGAGGCCCTGGGAGGCCCTGCTGGGCCTGTCCG[C/T]CCTGAGCCTTCCAGGACTCTTGTGAGGATAGAAAG Y 2 1 2 1 101000 r 74 goat snp44024-scaffold595-5657142 3 27660329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427367 Affx-122940098 AX-123297710 3 89714538 GAGCTGGCTGTCTCTGGATGGATAGAGAAAGTGAT[A/G]CAGTGACACTGATGGATACAGAGAGTGATAAAAGG R 2 1 2 1 101000 f 74 goat snp44023-scaffold595-5580840 3 27583839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787482 Affx-122953243 AX-385274507 3 89749391 AGTTTTCCTTGGGAGAATGAGGGATGAAACAGAAT[A/G]TCATTATTAGCTGACCAGTAATTAATGTTGTGCAT R 2 1 2 1 101000 f 74 goat snp44022-scaffold595-5545987 3 27548591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787571 Affx-122954910 AX-385274595 3 89846008 TTGGTACTCAGGAGGCCAGAGGCAGCTACAATCTC[A/G]TTTCTTGACATGCTCATTACCTCTGTGCTCCAGTG R 2 1 2 1 202000 f 74 goat snp44021-scaffold595-5449370 3 27454000 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429089 Affx-122938271 AX-123299431 3 89935530 TGAGGCACATTTGTTTTTGAAAGCAAGTCAACAGC[A/G]TTACTGGTCTGTGTCCATGCCCATGCCCATGGTTC R 2 1 2 1 101000 f 74 goat snp44020-scaffold595-5359848 3 27364230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377908 Affx-122977237 AX-123248267 3 89974384 GCACTGATCAAATAGGGTCATTCTGAATAATCTGA[C/T]GTTCGGAGCCTCCATGTCTTTGTTTTGTTCTCCCA Y 2 1 2 1 101000 f 74 goat snp44019-scaffold595-5320994 3 27327364 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403751 Affx-122958008 AX-123274103 3 90015480 CTGCCCTCAGTCTTTCCCAGCATCAGGGTCTTAAT[A/G]CTCTTGCCCATATCACACAGCAAGTCAGTGACAAA R 2 1 2 1 101000 r 74 goat snp44018-scaffold595-5279898 3 27285691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454256 Affx-122919650 AX-123324589 3 90059437 TTTTTCTCACTGGAGAATTTTGGTCTTGATGGAAG[A/G]TGGTATCTGAATCAGACCTTGAAGGATAGAACTGT R 2 1 2 1 101000 r 74 goat snp44017-scaffold595-5235941 3 27242111 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789912 Affx-122937762 AX-385276918 3 90088649 TGTTGTAGGAAACCTGTTTAGAAGGAATAGCATAT[A/G]TGAATGACCTAGTCCTGTCTCTTGCCTGCTTAACT R 2 1 2 1 101000 r 74 goat snp44016-scaffold595-5206729 3 27212900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406105 Affx-122956216 AX-123276457 3 90122796 TCATAAGTCAGTACAAGCACAATTAAAGGACTGAT[A/G]CATCTCTACTTTCCTCCCAGACCTACCCACTGCCT R 2 1 2 1 101000 f 74 goat snp44015-scaffold595-5172582 3 27179933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404392 Affx-122956793 AX-123274744 3 90161719 AGACCCAATTACCTCCTCCTGATTGGAAATGATTG[C/T]AAGAGACTTAAATTTGTCAGTTATTAGAATAGCTG Y 2 1 2 1 201000 r 74 goat snp44014-scaffold595-5133659 3 27139985 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439069 Affx-122930313 AX-123309406 3 90191490 AGTCACAGTGGATTACCTATCTTTCAGAGTTGTAG[A/G]TCTGTGAAATTCTAGAAGGCTAGTGGCTCTTCAGG R 2 1 2 1 101000 f 74 goat snp44013-scaffold595-5103888 3 27110185 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404437 Affx-122956757 AX-123274789 3 90225952 TAAGTTCAAAAATTTTTTTTTCTGTTTTATTAACT[A/G]CTATATCCCTGGCCATGAAATTAATGTCTTGTACA R 2 1 2 1 101000 r 74 goat snp44012-scaffold595-5069426 3 27075765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273589 Affx-1111833686 AX-519547203 3 90254623 AATCTTCCTCCAAGCAGTCTCTCTCTTC[A/G]CTAGCTACAGAACACAGTGTTATCTTTTAGTGTTT R 2 1 2 1 101000 r 74 goat GoatD01.001476 3 90254623 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38414175 Affx-122949675 AX-123284524 3 90268693 GGAAGTCAAAATAGTTGTTATCTCTGTGTGAGGAT[A/G]TAGATATGGACTGGAAAGGGGTACAGGGGAGCCTA R 2 1 2 1 201000 f 74 goat snp44011-scaffold595-5026685 3 27031936 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378674 Affx-122977080 AX-123249033 3 90317440 CCACTGGAACATTCTGAATAGCAGTAACACAATCT[G/T]AATAATTTTAACAGGATCATTCTGGCTGCTATGTT K 2 1 2 1 101000 f 74 goat snp44010-scaffold595-4977938 3 26982720 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382986 Affx-122973343 AX-123253344 3 90376195 ACAAATCCCGTTGACTCTACATTCAAAATATATCT[G/T]CAATTTGTTTCTCATTGACTCTTTTAAATCACTAT K 2 1 2 1 202000 r 74 goat snp44009-scaffold595-4919183 3 26923433 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384221 Affx-122972380 AX-123254579 3 90458380 AACTTAAAACCGACCTTTCTACATTCTACATTCGG[C/T]ATTTGAAGCAAATTGGAAAGGTGAAAAAGCTTGAT Y 2 1 2 1 101000 f 74 goat snp44007-scaffold595-4836998 3 26841547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433695 Affx-122934540 AX-123304036 3 90542462 TGGGTAACAGAGCCGCTGGTCTTCTTTCACTAGTT[G/T]CTGAGATTACCACTTTGACTGAGACACTCCAAATC K 2 1 2 1 101000 r 74 goat snp44006-scaffold595-4752916 3 26757648 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278007 Affx-1111836203 AX-519551499 3 90568819 GTCAGTCCTCAGACACAATAGGTTTCATGCTCATC[A/C]AGTATCAATAGTTAATTTCTTCCATTTGGTGATGG M 2 1 2 1 101000 f 74 goat Random2.2K-366 3 90568819 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435266 Affx-122934056 AX-123305606 3 90576796 TCATCAGAACAGGGAGCAGAATGCTTTAGGAAGAG[A/G]GAACATCATGGACACAGTCTCTGAGGTAGGAAAGC R 2 1 2 1 101000 f 74 goat snp44005-scaffold595-4718582 3 26723318 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274527 Affx-1111834275 AX-519548118 3 90624529 GTCTTCCTTTGATGGTTGGGGAAAGCCCTTAAACT[A/G]TGAATAACTCCACAATCTCACCACTTCTCAGATAG R 2 1 2 1 201000 r 74 goat GoatD01.028520 3 90624529 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320781037 Affx-122967794 AX-385268124 3 90668366 GTAACTCTCCCACTGGGGCTTGCTATAAATGCTAT[A/G]CTGCAACTTTTCCCACCATTTCTACCTCCAGTGGC R 2 1 2 1 101000 r 74 goat snp44004-scaffold595-4627012 3 26630847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801152 Affx-122956790 AX-385288066 3 90697354 AATCCCCTACCCTATTCACCATATGGGGCTATTAA[A/G]GGGCTCAAACAGGATGGTGCATGTAAAAAGGCCTT R 2 1 2 1 101000 r 74 goat snp44003-scaffold595-4598024 3 26601650 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776104 Affx-122953271 AX-385263234 3 90748095 TGCTAATCCTGTTTAAATAATCTAATCTGTTTATA[C/T]GTTGACTTTTCCTTCCCATTGTAATGTATGCTCCT Y 2 1 2 1 201000 f 74 goat snp44002-scaffold595-4547283 3 26550959 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405556 Affx-122955961 AX-123275908 3 90804388 AAATGTATGAAATTATTCAAAGGCTCCAGGGAACT[C/T]CAGGGATTGTAAGTCTCTGGAAGCACAGACATGAT Y 2 1 2 1 101000 f 74 goat snp44001-scaffold595-4490990 3 26497412 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430964 Affx-122936819 AX-123301305 3 90838954 TCATACATGGGTTTTGAAGTCCAATGTACATGCGT[A/G]CTAAGTCGCTTCAGTCATGTCCCACTCTGTGCAAC R 2 1 2 1 102000 f 74 goat snp44000-scaffold595-4456424 3 26462960 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402208 Affx-122959162 AX-123272561 3 90878845 AAGAGAAAGGTCCTCCTGATTCAGATAAAGTGGCC[A/G]CTTCCCAACTGAGGAGTCCTAGCCAGGTTGGTGGC R 2 1 2 1 101000 f 74 goat snp43999-scaffold595-4416533 3 26422735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386841 Affx-122970085 AX-123257199 3 90914099 TCTTCCCTTCCTTTCTGAATATTTATGTCTAAAAG[C/T]CATTTGCATAAGTGGGGCTAATCGAGATAGGAACC Y 2 1 2 1 101000 r 74 goat snp43998-scaffold595-4381279 3 26387663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441275 Affx-122929475 AX-123311612 3 90978789 AAAGTATATAATTAGCTTTTTTAGTGCCATCTGCT[A/C]GCGGCGCCGCCTCCTGCTCCTCCCGCCGCCGCCCT M 2 1 2 1 103000 f 74 goat snp43997-scaffold595-4316589 3 26321728 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793213 Affx-122975676 AX-385280191 3 91072473 CTTCTGGTCCATAGTCAGATGCATTATCCATTATG[C/T]CACCAGTCCCATACTTAGATGTTATTCAGTGTAAA Y 2 1 2 1 101000 f 74 goat snp43995-scaffold595-4222905 3 26227487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771375 Affx-122963078 AX-385258533 3 91137720 AAAGAAGAGTATTTCCCTGCTTTAATGTATAATGT[A/G]TAACTGAAAATGTACATGGAAGTAAACTGAGTTGA R 2 1 2 1 101000 r 74 goat snp43994-scaffold595-4157658 3 26161467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423547 Affx-122942429 AX-123293893 3 91193337 GTTTTAGGGATGGGAAGCAGGGTACTTTTAAAGAT[A/G]AGAGTAGAGTTAAGATTTAAGGAATGTAGTAAAGA R 2 1 2 1 101000 f 74 goat snp43993-scaffold595-4102041 3 26105251 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394772 Affx-122964835 AX-123265127 3 91246782 GAGCAAGACATTGAGAAAATATAAGGAATAATGCT[A/G]TATTCCAGGCTAGCAACAGTAAGGCTATTCCCAAC R 2 1 2 1 101000 r 74 goat snp43992-scaffold595-4048596 3 26051693 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395632 Affx-122963796 AX-123265987 3 91320095 CGTGGAGTTACAAAGTCTATAAACCTGAAGCTTTT[A/C]GTGCTTATTTTAGTGTTATAATGGGAAAGCCTACC M 2 1 2 1 101000 f 74 goat snp43991-scaffold595-3975283 3 25978236 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273774 Affx-1111833803 AX-519547385 3 91358010 AGACTCCATCTCAGAGGCGGTGTGGACACAGACAC[A/G]TCATTAACTTTTATGCCTCTGCACCTTTGCATATT R 2 1 2 1 201000 r 74 goat GoatD01.005555 3 91358010 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402454 Affx-122958612 AX-123272807 3 91380236 AGATAATAACAAAAACAGAAAATGCAACATAGTAT[C/T]ACAGACCAAACCTGCACACACTAATGTGCATGTTT Y 2 1 2 1 103000 r 74 goat snp43990-scaffold595-3915142 3 25917969 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445870 Affx-122925989 AX-123316207 3 91415421 CACACTGTGCACGTACCCTAAAAGGGCACTGTGAC[C/T]GCAAGAGGAACAGGATGGACTGTGCAGCCCATGAA Y 2 1 2 1 101000 f 74 goat snp43989-scaffold595-3879957 3 25882478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411653 Affx-122951567 AX-123282003 3 91443952 TCACACTAAATGCACACCCGAGCAGGGGCCTAGGT[A/G]AAGTCATCTGGGTTACCACTTGCACAGGGGGAAAA R 2 1 2 1 101000 r 74 goat snp43988-scaffold595-3851426 3 25853951 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438843 Affx-122930770 AX-123309180 3 91485702 GAAAGGCCTGGAGGAGATGCTCCCACCAGTTAACC[A/G]TGTTTCCTCCAGGTAGAGGAACTGTGGGGAAGGAA R 2 1 2 1 202000 f 74 goat snp43987-scaffold595-3809676 3 25812412 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778927 Affx-122970693 AX-385266034 3 91517967 AAGCACTTAAAGATTTGACATTCAACTGTAGCAGT[A/G]TCTATGTTGGTTAATTTTCTTATGAGCCCCATGAT R 2 1 2 1 101000 f 74 goat snp43986-scaffold595-3777411 3 25782931 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768262 Affx-122977256 AX-385255443 3 91590481 TAACAGGAATATTCTCTAGTGTATGATAATAATAA[G/T]AGTACAGCTATGAGTATCTTGAAGATCAGGGACTA K 2 1 2 1 101000 r 74 goat snp43985-scaffold595-3704897 3 25710155 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274865 Affx-1111834462 AX-519548449 3 91602712 GTGCCTGAGCTGGGCCC[A/C]AGCCTGCAGAGATCGACTGGGTCCATCCAATCCTC M 2 1 2 1 102000 r 74 goat GoatD01.036833 3 91602712 G T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320801503 Affx-122962889 AX-385288412 3 91627336 GATTTTGGTGACTCATTTCTCTAAGTCTTATTCTC[A/C]GTAATATCTTTTGTGAAGTAGGGCTAATAACTACC M 2 1 2 1 101000 f 74 goat snp43984-scaffold595-3668042 3 25672936 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770610 Affx-122921949 AX-385257774 3 91687660 GAAAACAATGGGTTCAATGATATCATACCTATCTA[A/G]TTCAAGTCAGGGAGATTAAAGTGCTTATCCTAGCC R 2 1 2 1 101000 r 74 goat snp43983-scaffold595-3607718 3 25610772 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427555 Affx-122939491 AX-123297898 3 91726316 CAGCAGCAAAAATAAATGTAAATAAGTTAGTCTCA[C/T]GAAAACAATTTGCACTGTGATTATTAGCACATAGA Y 2 1 2 1 101000 r 74 goat snp43982-scaffold595-3569062 3 25571613 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779043 Affx-122971620 AX-385266149 3 91763684 CTTTAAGGCAAGATGTGTTGCTAAGTATAAACAGA[C/T]ATTTGATAATGTTTAAAGTATTGATTCAAAAGGAA Y 2 1 2 1 101000 f 74 goat snp43981-scaffold595-3531694 3 25533756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435999 Affx-122933498 AX-123306338 3 91820783 CCAATGGAAGAAGCATTTAGAGAAAAATCTAAATG[C/T]TTTGCGTTCTGAATGCAAAGCTTCCAGGGTCCTGG Y 2 1 2 1 201000 f 74 goat snp43980-scaffold595-3474595 3 25476546 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424236 Affx-122942475 AX-123294582 3 91860533 CCTGAGAGGCATAGAGCAGTTCCCTTCATCTAGCT[A/G]CTTGTTTTTTAAGTTCTTTATATGTCACAACCCCT R 2 1 2 1 101000 f 74 goat snp43979-scaffold595-3434845 3 25436178 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426450 Affx-122940805 AX-123296796 3 91928599 GAGAAATAAGATGCAGGAGAGACAATAAGGGTTAA[C/T]GGCAGCAGAAAATTTACATGTGTCCATGGAACATA Y 2 1 2 1 101000 f 74 goat snp43978-scaffold595-3366779 3 25377427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273628 Affx-1111833735 AX-519547241 3 91974436 GAACAGCTTCCAGTTTCCACACCTTTTCACATGCA[A/G]CCTTGTAGCCATGCTC R 2 1 2 1 102000 f 74 goat GoatD01.003065 3 91974436 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427263 Affx-122939547 AX-123297606 3 91992725 AGCAAGATAAGAAATGGTAAAAGAAGGCATAAACT[A/G]TTTATGGTGAAAATGGAAAAGGTGATGCACGAGAC R 2 1 2 1 101000 r 74 goat snp43976-scaffold595-3302653 3 25312991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779431 Affx-122972655 AX-385266534 3 92025455 CTTTTATCCAGAATGCATAACTTTAGGGAAATGTC[A/G]TCTTCTTAAAATAAGCCACTTTTCAGTACCCTTTA R 2 1 2 1 201000 r 74 goat snp43975-scaffold595-3269923 3 25280181 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445239 Affx-122925491 AX-123315576 3 92070125 TCTTTACAGAAAATGCAACTAAGGGTAATAACTCT[A/G]CAAGTAAGAAGCAGAAGCAAAATTCAAAAGGAAAA R 2 1 2 1 201000 f 74 goat snp43974-scaffold595-3225253 3 25235510 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437657 Affx-122931791 AX-123307995 3 92106304 TATTGGTTCATTGGTTCTTCTATATCCATACACAA[G/T]CTCACACACACACACACAAAATAATAATATTTTGT K 2 1 2 1 101000 f 74 goat snp43973-scaffold595-3189074 3 25199355 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434146 Affx-122934908 AX-123304487 3 92193503 CAACCAATCAAAATTACAGCAAGAAATATACATAC[A/G]TATACACAGACACACACACATACATATGACATCAT R 2 1 2 1 201000 f 74 goat snp43972-scaffold595-3101875 3 25112029 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432696 Affx-122936031 AX-123303037 3 92228035 CTGAATTGGCTTTAATATTTAGGTCTATCAGTTTG[C/T]AAAGCCTATATTCTTTCCACTAAACTAATGGTCCT Y 2 1 2 1 101000 f 74 goat snp43971-scaffold595-3067343 3 25076519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796480 Affx-122969381 AX-385283430 3 92266607 GACCCTGATCTGAGTGTTAAGTTGTTCAGAACATA[A/C]TTCTCGGATCTCCTATGGGATACAGAGATGAGATC M 2 1 2 1 101000 r 74 goat snp43970-scaffold595-3028771 3 25037442 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783904 Affx-122955325 AX-385270959 3 92297040 GAACCTTTGTTTATGTTGTTCCCACTAGTGGACCA[G/T]CCTTTCTCCCCAGTTTCACATGTTGAAAACATCCT K 2 1 2 1 101000 r 74 goat snp43969-scaffold595-2998338 3 25006938 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415648 Affx-122948571 AX-123285997 3 92358697 CCTACCTGCTCCTTGGAATTTTCACCTGGAGCCTG[A/G]CTGTACGTTAATGACATGTTTATGTGACTGTCCAC R 2 1 2 1 101000 r 74 goat snp43968-scaffold595-2936681 3 24944827 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389157 Affx-122968535 AX-123259515 3 92394866 AGTAAGTCAATCTGCCTTACTGATAGACCCCTGTC[A/G]ACCCCTAAAGGAAGGTGAACTTGCCACAACCAGTT R 2 1 2 1 201000 r 74 goat snp43967-scaffold595-2900512 3 24908534 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383560 Affx-122972605 AX-123253918 3 92437208 ACGTGCTATGAATGTACGCACAAATGCTTGATATG[C/T]ATAGAGCATCTGAAAAGATACATAAGAAATATAAC Y 2 1 2 1 101000 f 74 goat snp43966-scaffold595-2858170 3 24865955 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396509 Affx-122963524 AX-123266864 3 92469643 CCTCAGAGGGAAATCTAACTTCTCAGGGATGTGAG[C/T]GCTGCCAACCCGTCTCCTTCTCCAGCCTCATTTCT Y 2 1 2 1 101000 f 74 goat snp43965-scaffold595-2825735 3 24833505 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449861 Affx-122922369 AX-123320196 3 92517445 GTCTTTTAAGGCAAAACCTTTGGGGTTACCATTAA[C/T]TCCATTTATTTTCCTTCTCTTCTCTAGACATTTTC Y 2 1 2 1 101000 f 74 goat snp43964-scaffold595-2777933 3 24785761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390724 Affx-122967924 AX-123261081 3 92548939 AAGAAGCACTCCCCTTCTTAGTGCTTCTTAAGAAT[A/G]CAATTGCAGTGGTCCAGCTCTTTGTTGCATGAATT R 2 1 2 1 102000 f 74 goat snp43963-scaffold595-2746439 3 24754268 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391860 Affx-122966987 AX-123262217 3 92587541 AATATAAAGTTGTAATCTTTTATTTTGCCTCATGA[C/T]GTAAATACTGATGGTGTAAACTAGGTTAAGATACA Y 2 1 2 1 101000 r 74 goat snp43962-scaffold595-2707837 3 24715682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783578 Affx-122922619 AX-385270639 3 92626068 TCTCCTTCCTGTCTTCCTTTTCAAGCTATGTACCT[A/G]TATGAAATACTTTCCACTCTCCAGAACAAACCCTG R 2 1 2 1 101000 f 74 goat snp43961-scaffold595-2669310 3 24676736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454108 Affx-122919358 AX-123324441 3 92682548 GGGGGAAGTGATCAGAGTAAACTTAAAATTTAGCA[A/G]TTTGTCCTCTAGTAACAAATAGTGTCATGCAGAGT R 2 1 2 1 101000 f 74 goat snp43960-scaffold595-2612830 3 24620121 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407897 Affx-122954397 AX-123278248 3 92726151 TCTGTTTAGAGATACACACTTGGGTGATAAAACCA[C/T]AAAGAAACATATAGACGTGATTGTGTGTCCTTGGT Y 2 1 2 1 101000 f 74 goat snp43959-scaffold595-2569227 3 24581630 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431261 Affx-122937118 AX-123301602 3 92756680 CTTAGAGTAAAGGGTCTGAATCACCATTTTAAAGA[C/T]GAATAAAACTGAGTCTCATAGAAGCACTGTTACAC Y 2 1 2 1 101000 f 74 goat snp43958-scaffold595-2538698 3 24550910 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449612 Affx-122923203 AX-123319947 3 92848267 AATGCCAAAACTTACCCAGATAAATTGTTACTAAT[C/T]ATTCCAGATTTAGCTCTTTGTAGCTCTGAAAAGAT Y 2 1 2 1 101000 r 74 goat snp43957-scaffold595-2447111 3 24457883 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777718 Affx-122950583 AX-385264837 3 92906610 TTATTGCATTAATGAACACCATTTGGTCAAATAAT[A/G]GAAATCCATAACTTTCTATCTCCTTATTTTTATTT R 2 1 2 1 101000 r 74 goat snp43956-scaffold595-2388768 3 24399004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409533 Affx-122953614 AX-123279884 3 92946695 TTCACAATACAGCTCTATCCCCTATTATCTGTGTG[A/G]CCGTAGACTAGATATGGTGCCTCAAATATTTCAAT R 2 1 2 1 201000 r 74 goat snp43955-scaffold595-2348683 3 24358458 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421394 Affx-122943986 AX-123291741 3 92999226 GAGAAAGGTCTTTCATATAGAAGGGGCAGCATGAA[C/T]AATAAATGAATCATAAAGGATTAATCTCAAATTTC Y 2 1 2 1 101000 f 74 goat snp43954-scaffold595-2296152 3 24304803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400867 Affx-122959768 AX-123271221 3 93034131 AATGGAAACAGGCATATAAGGTGTTTGTATTCCTG[C/T]TTGGTTTTAGTTCAGTTAGCTGACCATCATTAATA Y 2 1 2 1 101000 r 74 goat snp43953-scaffold595-2261247 3 24268368 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381989 Affx-122974087 AX-123252347 3 93087569 AGGTTCAATCAGGCCCCCACCTGCTGTGGTACACT[A/G]AGAATCTTAATCCAACAAATTGCTTTAAAATACCC R 2 1 2 1 101000 r 74 goat snp43952-scaffold595-2207809 3 24213902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410666 Affx-122952760 AX-123281016 3 93140340 GACACTGCTTTATATATGTCATATTTTCATATTTA[C/T]ATCATATTCAAATTCACACAACTATCTTGTAAGGT Y 2 1 2 1 103000 r 74 goat snp43951-scaffold595-2155038 3 24160488 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431288 Affx-122937096 AX-123301629 3 93175103 ATTAAAATAAATAAATTTATATTTTAAAAAAATAA[G/T]AAAATTTAAAAAAAATGAAATGCTGCCTCCACTGG K 2 1 2 1 303000 f 74 goat snp43950-scaffold595-2120275 3 24125733 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405573 Affx-122955947 AX-123275925 3 93240915 GGATTCTAAGTAGAATTCAGGCATCTTAACTCCCA[A/G]TTCTGGGCTCCTTCCTACCTCTTCACTAGCCAAAC R 2 1 2 1 101000 f 74 goat snp43949-scaffold595-2054463 3 24061940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396711 Affx-122962814 AX-123267066 3 93278160 GTAAACAGATACAGTGCCCCACCAGTGGGTGCCAC[A/G]TCACTAGAAGCACTCAAACAGAAGCTGAACACCCT R 2 1 2 1 101000 r 74 goat snp43948-scaffold595-2017218 3 24024683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429053 Affx-122938302 AX-123299395 3 93308753 CTCAGGATGCTTCTCTCCCTCATGCTTTTCTGTGC[C/T]CCTCCCCTACCCTGTCAAATGCTAAGACTTGCCCT Y 2 1 2 1 201000 r 74 goat snp43947-scaffold595-1986625 3 23993976 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413985 Affx-122950287 AX-123284334 3 93358363 GCCAGTGCAGGGGAGCGATCCAGAGGTCACCTGTA[A/G]ATGGTTATCAATTTCTGGCTCTGCCTAAAATATAG R 2 1 2 1 101000 r 74 goat snp43946-scaffold595-1937015 3 23944078 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793700 Affx-122930024 AX-385280672 3 93395171 TAATTCATACCAAAGAATCTCAGAAATGGAAAGCA[C/T]TGGAAGTACTTGGGATGCCAGTCTGAGCTTGGTTC Y 2 1 2 1 101000 r 74 goat snp43945-scaffold595-1900207 3 23907313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782180 Affx-122955168 AX-385269258 3 93436125 AAAATGTCTCACCATCAGTGGAGATCCCACATCTA[C/T]TTGAGAACCTTTAAAACGTGAGTGCAATCACAAGA Y 2 1 2 1 101000 f 74 goat snp43944-scaffold595-1859253 3 23866244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464244987 Affx-1110385057 AX-515719609 3 93452848 GATAGGCTTGTACTTGGAGAGCCCTTGGGAGGATG[G/T]TCAGGAGCAAGGCTGCAGTTATTGCATAGGGCCAC K 2 1 2 1 101000 r 74 goat GoatD01.032672 3 93452848 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38446988 Affx-122924642 AX-123317324 3 93481088 GGACACTAACCCAGGTTTCTCTAGACCATGTTGTA[C/T]TTCGTTTATTCATTCAACAAATGCCACACACTAGC Y 2 1 2 1 201000 f 74 goat snp43943-scaffold595-1814290 3 23821463 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417762 Affx-122947405 AX-123288110 3 93510491 CATCACTGCTACCAGCACTTCCTAACCTTCTGATC[G/T]CTATCTCTTGAATTAATACCTGCATACTCTCTATG K 2 1 2 1 201000 r 74 goat snp43942-scaffold595-1784887 3 23791797 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431921 Affx-122935993 AX-123302262 3 93547920 AGGGCACAGAGTAGCAGCATAAGAAGTGAGCCAAA[C/T]GACATAGTGAGTGGGTGGGCAGATGATGTCAGTGG Y 2 1 2 1 101000 f 74 goat snp43941-scaffold595-1747458 3 23754897 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441352 Affx-122928876 AX-123311689 3 93577776 AGGAGCTCACCTTCTCTTTTCCCTTTGGCAGAATT[A/G]CCTTTTGCTTCCCTTGAAAGAAATGGCAACCCACT R 2 1 2 1 201000 f 74 goat snp43940-scaffold595-1717602 3 23725233 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278164 Affx-1111836204 AX-519551653 3 93630347 GAGAGTGGGGGGCAGGCCGTCCACCTAACTTGTAA[A/C]ACCCAGCTTGACTCCTTGAATTTATATCCCAATCA M 2 1 2 1 101000 r 74 goat Random2.2K-367 3 93630347 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422088 Affx-122943585 AX-123292435 3 93645465 TAAGTTTACAAACATTGTTAGCAGCTGAGCCTATT[C/T]TTCAAACCAAGTCTATGAGGAAGGCCAGTAAGTAG Y 2 1 2 1 101000 f 74 goat snp43939-scaffold595-1649913 3 23657044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409880 Affx-122952908 AX-123280231 3 93689765 GGGGCATTGATTCATGCTCACTGGAATGCGTATTT[A/C]TTATGCATTTGAATTTGCCTTATCTATACTCAGTG M 2 1 2 1 101000 r 74 goat snp43938-scaffold595-1605613 3 23612052 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401425 Affx-122958998 AX-123271778 3 93733199 CTTTCCATTGCAACCTCCTCTATTCCCTGCCCCTA[C/T]GGGATCTAATACTCGCTTATCCTTCCCCTTTCTGG Y 2 1 2 1 101000 r 74 goat snp43937-scaffold595-1562179 3 23569065 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272073 Affx-1111833405 AX-519545837 3 93740688 GGGTGTGTGGTGGAGCTTTGTACTGTTTTCTGATC[A/G]CAGAGATACTTTAGCCATTACAGGGCATCCAGAAC R 2 1 2 1 101000 r 74 goat 3_93740688_AF-PAKI 3 93740688 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403295 Affx-122957846 AX-123273648 3 93774072 CATACAAGAGGAGCTATGAACCACATTTGATATTG[C/T]GATGATGTTGTTTAATTGATGAGGAAAGTCAAGTA Y 2 1 2 1 101000 f 74 goat snp43936-scaffold595-1521306 3 23528232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401082 Affx-122959631 AX-123271435 3 93807362 AAAAACAGTAGTGAAATGTTGGAAGGGAGGGGTAT[C/T]GATAGGAGGGAAAATTCTTCCTGATAGCAATAAAC Y 2 1 2 1 101000 f 74 goat snp43935-scaffold595-1488016 3 23494804 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387008 Affx-122969939 AX-123257366 3 93837698 CTCCTGCCTTCTGTCTCCCATTCCATCACACTCTG[C/T]GCTCTGACCATGAGAAGCCACTTCCAGTTCCCCAA Y 2 1 2 1 101000 r 74 goat snp43934-scaffold595-1457680 3 23463397 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386795 Affx-122970914 AX-123257153 3 93866487 AAAGTCTTATCTCATTTGACACCAGGGATCACTCC[A/G]TACTTCTTGAAACTCACACAAATGGATCGCTCACA R 2 1 2 1 101000 r 74 goat snp43933-scaffold595-1428891 3 23434546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417855 Affx-122946776 AX-123288203 3 93911698 CCTTCCCTCTTGAGGTCCATCCTGGCAGCGATTCT[A/G]CCCAAATATCCATTAGTTCATGCAGCAAACCTTCC R 2 1 2 1 101000 r 74 goat snp43932-scaffold595-1383680 3 23389298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431230 Affx-122937143 AX-123301571 3 93961663 GACCAGGCTCTCCTGCCTGTGTGCAGTACGCATTA[C/T]GATATCCATTTTACAGAGGAGAAAAGAGAGGCTGA Y 2 1 2 1 101000 f 74 goat snp43931-scaffold595-1333715 3 23338982 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403745 Affx-122958012 AX-123274097 3 93991763 AACCAAATTCTGGAGAGATGTGCAGACTCAGAAAT[A/G]ACCAAAGGAATTAGAATGAGGTACCAATTTTCACT R 2 1 2 1 201000 f 74 goat snp43930-scaffold595-1303615 3 23309405 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386642 Affx-122970215 AX-123257000 3 94029226 TCTCCATTCATGCACTGCTGCTGACTGTTGCTGAG[C/T]GGGATGCTTTATGCAATCAGAACAGATTCTACCAG Y 2 1 2 1 101000 r 74 goat snp43929-scaffold595-1266152 3 23271713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416917 Affx-122948051 AX-123287265 3 94070259 AGGCTCAATGTTTTCCCTCTGGTGGTTTTAGGACC[A/G]TGGGGTCCTTGCAATGGGGGAAGACACATTCAATA R 2 1 2 1 101000 f 74 goat snp43928-scaffold595-1225119 3 23231181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403373 Affx-122957788 AX-123273726 3 94107052 ATCTGTGCCTTCCCTCTTCCTCGGCCCCGCCACCC[A/G]CCTAGGATCCTGAAGAGTTCTCTCATTTGCCCCGT R 2 1 2 1 201000 r 74 goat snp43927-scaffold595-1188326 3 23194089 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785326 Affx-122945599 AX-385272371 3 94150701 TCCTCTTACCTCTATGGGTAGATATTTTTGTCTTC[A/G]GGATGTTCACTGCTATTAATACAACCCCTGTGCTT R 2 1 2 1 101000 f 74 goat snp43926-scaffold595-1144677 3 23149565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385306 Affx-122971679 AX-123255664 3 94199811 AAGGTAAACAGACTGACCTCTGGGCTTGTGAACTA[A/G]TACAGAGCAAGCCCGGCACTGTTTATGGAGATTTG R 2 1 2 1 101000 r 74 goat snp43925-scaffold595-1095567 3 23100139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790361 Affx-122954281 AX-385277364 3 94254550 AAAAAATAAACATGGAAAGGGGAGGGAAAATGAAG[C/T]ACCACATTTTCCATAAGCAAGTAGAAATTAAACAC Y 2 1 2 1 101000 f 74 goat snp43924-scaffold595-1040828 3 23044316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794775 Affx-122922848 AX-385281735 3 94313884 CTACAACAGAGGCATTCAGGTTGTGCTGTAAGAGT[A/G]TTATAACAAGATAATCCAGTCAGGGAGTCAGCAAA R 2 1 2 1 101000 f 74 goat snp43923-scaffold595-981494 3 22984314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402843 Affx-122958254 AX-123273196 3 94361066 CCCCCTTTTCCCTTGGACATGTGCTTCCCTCCTTT[C/T]TACACAGTAAATTACTATCCACCTTCAGAGCTCCA Y 2 1 2 1 201000 r 74 goat snp43922-scaffold595-934312 3 22937184 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434322 Affx-122934744 AX-123304663 3 94392829 TGAAACACTAGGCTAGAGAGGTAGAACTGAAGACT[C/T]GAAGAGCCTCAAACACAGAAAAGGTCCTTATCAAG Y 2 1 2 1 101000 f 74 goat snp43921-scaffold595-902549 3 22905203 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274354 Affx-1111834151 AX-519547949 3 94406262 GC[A/C]GACTGGATATAGAAATAACTGGGAGCATTATAATC M 2 1 2 1 101000 r 74 goat GoatD01.021831 3 94406262 A C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38408046 Affx-122954282 AX-123278397 3 94487857 CTTGGTCTACCTGTAGGGCAGCCTCACACAGAGCA[C/T]GCATTGCCTCCAGATCTCAGCTCACCACTGTGTCT Y 2 1 2 1 101000 r 74 goat snp43919-scaffold595-807521 3 22793896 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402050 Affx-122958728 AX-123272403 3 94527277 TTTTCTGTAAAGATAAAACTGCTTTAGAAAAAAAG[A/G]AGTAAAATTTAAAAAGTCAATGAGGATAAAAAGTA R 2 1 2 1 303000 f 74 goat snp43918-scaffold595-768101 3 22752789 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391604 Affx-122966597 AX-123261961 3 94559462 GGAAGAGGTGGTAGAATGGAGTTCAGTAGCAAAGA[C/T]ACGAACAGGATGGAACCCACATGCATGGACTAGAC Y 2 1 2 1 101000 f 74 goat snp43917-scaffold595-735916 3 22720527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791660 Affx-122957640 AX-385278651 3 94627299 AGGGCTTATCTTGCCTCAAAACCCTCTCTGACTTT[C/T]AATACTGATTTCCTAGAGGCCTAGGACCTTGGAAA Y 2 1 2 1 101000 f 74 goat snp43916-scaffold595-668079 3 22651673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417949 Affx-122946705 AX-123288297 3 94658879 GCATGCTTTTTCTCAAAGCTGTGTGCCTGGGTTCT[A/C]GACAAGACGGCTCTAGAATTAAACAGATTGAGTAC M 2 1 2 1 101000 r 74 goat snp43915-scaffold595-636499 3 22620059 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446036 Affx-122925847 AX-123316373 3 94695090 ACTGGTGTAGAGAACTGAGTTAAATGAGATAACTC[A/G]TGTGAACATGGTCCACACCCAATCGGTATGCGAGA R 2 1 2 1 101000 r 74 goat snp43914-scaffold595-600288 3 22583863 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451164 Affx-122921352 AX-123321498 3 94724206 TGAGGGAGACCCTGGGAATGATCATGGATGACTCA[A/G]TGTAACCCATCTCTACAGCTGAAAAGACCACAGGA R 2 1 2 1 101000 r 74 goat snp43913-scaffold595-571172 3 22554765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433941 Affx-122934287 AX-123304282 3 94784549 CTGGTTCTACTGTTGACCTGTTTTGTGGATAAAAG[C/T]CACAGTGGCTCTGAGAAGTTAAGTAACTCAACCTT Y 2 1 2 1 101000 f 74 goat snp43912-scaffold595-510829 3 22494275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777664 Affx-122942395 AX-385264783 3 94863569 AAGTACAGAGAACCTAGCAAATGCTTGTATTTACC[A/G]CTGAGATTTAACACACATTGATCTTCTGTCATCTT R 2 1 2 1 101000 f 74 goat snp43911-scaffold595-431809 3 22415856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412774 Affx-122950504 AX-123283123 3 94901080 GTGGGTGGTGCCATGAAGGCTCTCCTACTTGGGGA[A/C]ACAAGGGCAAGAACCCCTTAGACCCCAGGTTCAAG M 2 1 2 1 201000 f 74 goat snp43910-scaffold595-394298 3 22378335 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437067 Affx-122933084 AX-123307405 3 94933191 GCTCAGCATGAACAGAGTTGTGTTAGGAAATCCTG[C/T]GGGACTGGGGGAATCCCAAAGCGGAGGTCCAGGCA Y 2 1 2 1 101000 f 74 goat snp43909-scaffold595-362187 3 22346595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381365 Affx-122974403 AX-123251723 3 94987222 AAAATGCTGGGCTGAGAGGCTCAGCTCCAGGGTCA[C/T]GTTGCTTAGGAAAAGTGAGAGTGACCACCATTAAT Y 2 1 2 1 101000 r 74 goat snp43908-scaffold595-308156 3 22293928 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386070 Affx-122971457 AX-123256428 3 95067190 ATTAAAAATCTAAGCAAATAAATGAAATTGAGGTC[A/G]CACTTTCCTTATTCATAAGCATCTCATTTAAAAAT R 2 1 2 1 101000 r 74 goat snp43907-scaffold595-228188 3 22215352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445241 Affx-122925489 AX-123315578 3 95113344 GGATTGGAATTCCAGTTACTGCACTTGACTGTGTG[C/T]GGCTGTGCACAAGTTACTAATCTTTGTGTGCCTGA Y 2 1 2 1 101000 r 74 goat snp43906-scaffold595-182034 3 22169083 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402460 Affx-122958607 AX-123272813 3 95144888 AACAAAATAAAGCCTTGACTGGAGGGCAGGAGGCA[C/T]GGTCCAGAGGCCCAGCTCTGTCACAGACCTGCTGT Y 2 1 2 1 101000 f 74 goat snp43905-scaffold595-150490 3 22137413 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409561 Affx-122953592 AX-123279912 3 95188532 CAGTCATCAAAGTTAGAGGCTTAGAGCGGTGAGAA[G/T]CCTTGTGGTTCCAGGTTGTCCTTCCTTCTGTACAT K 2 1 2 1 101000 f 74 goat snp43904-scaffold595-106846 3 22093980 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446874 Affx-122925239 AX-123317210 3 95231027 AAATTTTATGTTGTATTTTCATTATCATTCAATGT[A/G]CATGCTTTCTTTCCACTCAGGTCTGTGCTTAACTG R 2 1 2 1 103000 r 74 goat snp43903-scaffold595-64351 3 22050912 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399224 Affx-122960594 AX-123269579 3 95311827 TTTAAAAAGTCTGGTGCCAGGGTGGGCCAGACACT[G/T]TCATACATGATCTCATTTGAATCTTATAACAACAC K 2 1 2 1 101000 f 74 goat snp5260-scaffold1181-397294 3 21970295 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388540 Affx-122969192 AX-123258898 3 95344670 TACTTAGATTTATAAAAGTGATTCGGTTAGTGTTT[C/T]AGTAATACTTCAAAATGTTTCTGTTTATTTTTTAG Y 2 1 2 1 101000 f 74 goat snp5259-scaffold1181-364451 3 21937557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384592 Affx-122972986 AX-123254950 3 95400318 TCTTAGAACTCTGCTTTTAACAAGTAACTCTCTTA[C/T]ATACAATATCTCAATGGATCTCTGTTTTCTATTAC Y 2 1 2 1 101000 r 74 goat snp5258-scaffold1181-308803 3 21881519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 532577586 Affx-1248697226 AX-579216003 3 95408267 AAGGGAGGGAGGAAGGAAAACTAAGAGAGGGATGG[-/CAGGTGGAGGAAGG]GTGGGAAGAGAGAAGGGGTGGCTGGTGTCATAGGC - 4 1 2 1 500000 f 74 goat "ins-del_026;rs659761737" 3 95408267 - CAGGTGGAGGAAGG 5 indels body size 0.476 neutral SV-TF-chip candidate gene ou candidate region SPAG17 562165375 Affx-1248697226 AX-606940786 3 95408267 AAGGGAGGGAGGAAGGAAAACTAAGAGAGGGATGG[-/CAGGTGGAGGAAGG]GTGGGAAGAGAGAAGGGGTGGCTGGTGTCATAGGC - 8 1 4 1 20100 f 74 goat "ins-del_026;rs659761737" 3 95408267 - CAGGTGGAGGAAGG junction SV-TF-chip candidate gene ou candidate region SPAG17 562165770 Affx-1248697226 AX-606941179 3 95408267 AAGGGAGGGAGGAAGGAAAACTAAGAGAGGGATGG[-/CAGGTGGAGGAAGG]GTGGGAAGAGAGAAGGGGTGGCTGGTGTCATAGGC - 8 1 4 1 20100 f 74 goat "ins-del_026;rs659761737" 3 95408267 - CAGGTGGAGGAAGG junction SV-TF-chip candidate gene ou candidate region SPAG17 562165780 Affx-1248697226 AX-606941189 3 95408267 AAGGGAGGGAGGAAGGAAAACTAAGAGAGGGATGG[-/CAGGTGGAGGAAGG]GTGGGAAGAGAGAAGGGGTGGCTGGTGTCATAGGC - 8 1 4 1 20100 f 74 goat "ins-del_026;rs659761737" 3 95408267 - CAGGTGGAGGAAGG junction SV-TF-chip candidate gene ou candidate region SPAG17 562166002 Affx-1248697226 AX-606941411 3 95408267 AAGGGAGGGAGGAAGGAAAACTAAGAGAGGGATGG[-/CAGGTGGAGGAAGG]GTGGGAAGAGAGAAGGGGTGGCTGGTGTCATAGGC - 8 1 4 1 20100 r 74 goat "ins-del_026;rs659761737" 3 95408267 - CAGGTGGAGGAAGG junction SV-TF-chip candidate gene ou candidate region SPAG17 38448146 Affx-122924279 AX-123318482 3 95555443 CATTTATTAGAAGCAGAATACATGTGAAAGAACAC[A/G]TGGGTGGGCTCAGAGAGTCGTGTTTTGGGGGTGAC R 2 1 2 1 201000 f 74 goat snp5254-scaffold1181-153678 3 21725993 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797705 Affx-122935376 AX-385284644 3 95584866 TAATAGAGCTACTATTATTAACCATGGAAACTAAA[G/T]CAATTGAAAAATGGAAGCAGTAACATGTTTATAAT K 2 1 2 1 202000 r 74 goat snp5253-scaffold1181-124255 3 21696060 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406163 Affx-122956167 AX-123276515 3 95711606 GAGGGCCCAGGAGCCAAAGAATGCAAGGATTGCAG[C/T]GCTAGATGCAGAAAAGGCACAGAGTGGGACCCTGT Y 2 1 2 1 101000 f 74 goat snp17513-scaffold181-931146 3 21492044 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786702 Affx-122933100 AX-385273734 3 95776414 ATAGAATTTTCTGAGAGTTCAATAAAAGAATTTGC[A/G]TGTAGTATTAGCTCAGTATCTGAACACATCAAATG R 2 1 2 1 101000 r 74 goat snp17511-scaffold181-866338 3 21426270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415073 Affx-122949468 AX-123285422 3 95806065 AGTTCTGACCATATCTGTTGCAGCCTTGGCATTTT[A/G]TTAAGACCAAAAAATTTCTGGCCCCATATCTCACT R 2 1 2 1 201000 r 74 goat snp17510-scaffold181-836687 3 21396003 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447522 Affx-122924062 AX-123317858 3 95855611 AGTATTTCTAAGGGTACTCCAGGAGCTGGAAAGGA[C/T]ACACAGATTGGTGTTTCGGACTTCCGGGGCAGGAT Y 2 1 2 1 201000 f 74 goat snp17509-scaffold181-787141 3 21346008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793338 Affx-122930439 AX-385280316 3 95928233 GTCATTCTTTGCCAGATCTTGCTAGGTAAATATAA[A/G]GAACCACCAGAGGGTACTTTGATCACATCTGATGT R 2 1 2 1 101000 r 74 goat snp17507-scaffold181-714519 3 21273172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437034 Affx-122933113 AX-123307372 3 96009785 GAAAACCCCACCATCAGAGGGAGACATTGTGTTCA[A/G]AAGAATCAGGCCAAGTCCTGGATGGTTCCCTCGTG R 2 1 2 1 201000 r 74 goat snp17505-scaffold181-632967 3 21191756 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391018 Affx-122966882 AX-123261375 3 96089956 CAGCCCCACGGGGAGCTCATCTCTCCATTTATTAA[C/T]GGGCACTGGATGCGTGCTGTGGAGTGGAGGTGGGA Y 2 1 2 1 101000 f 74 goat snp17503-scaffold181-552796 3 21111062 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448161 Affx-122924267 AX-123318497 3 96132466 CTCACTCTATAGAATGAGCTTCACTCCTCCCATTT[A/G]CAAGTGAGGAAACTGAAGGGAAGTGAAATGACCTT R 2 1 2 1 101000 f 74 goat snp17502-scaffold181-510286 3 21068194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411738 Affx-122951514 AX-123282088 3 96201921 GATCTTAACCTCTGGGAAGTTCAAAAATGTATTCA[C/T]GGAGTCCAGGAACCTCCTGAAATTGAAAAGTTGTT Y 2 1 2 1 101000 f 74 goat snp17501-scaffold181-440831 3 20998727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390008 Affx-122968040 AX-123260365 3 96241073 TCTTGGCCTGGAGAATCTTTCACTAAATTGTGTTT[A/G]TAGCGCTGGCATTTTATGTGGCCAAATGTGTCTAT R 2 1 2 1 101000 f 74 goat snp17500-scaffold181-401679 3 20959314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272238 Affx-1111833406 AX-513054855 3 96245599 GTACGTAATGAGAAACGCTGGGCTGGAAGAAGCAC[A/G]AGCTGGAATCAAGATTGCCGGGAGAAATATCAATA R 2 1 2 1 303000 f 74 goat 3_96245599_AF-PAKI 3 96245599 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394052 Affx-122964985 AX-123264407 3 96270797 TCCCAGAGGTACCACCATCCTAACTATGTTCATCA[C/T]CCCTTGCTTTTTGTGATAGTTTTACCGTATGTATA Y 2 1 2 1 101000 r 74 goat snp17499-scaffold181-371955 3 20929572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403017 Affx-122958560 AX-123273370 3 96322194 TCACTCTGCAAACTTTAGCTCAGGGCAGAGAAAGA[A/G]CTAACTTAGAATGTCTTGCTTTGGAAACTAACTTT R 2 1 2 1 101000 r 74 goat snp17498-scaffold181-320558 3 20877710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408580 Affx-122953661 AX-123278931 3 96399403 AACACAAAACTGGCTTTAGCCTTTGGGGAAGGATC[A/G]CTGGACTCAATTCCCCTCTTTTTCTTCCTTTCTTA R 2 1 2 1 101000 f 74 goat snp17496-scaffold181-243349 3 20802795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411647 Affx-122951571 AX-123281997 3 96431938 CAAACTCTTGCCCACCTTCTCAAGTTTCCCTAGGG[C/T]ATACACTATGTCAGATACTTCTAAACTATCTTCTA Y 2 1 2 1 101000 r 74 goat snp17495-scaffold181-210814 3 20769991 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405000 Affx-122956388 AX-123275352 3 96464065 AGGTGAAGAGACATAAAAATCAACTGGGGAGGTTA[C/T]AAATGCAGATTCCTGAACCCTACTCCATTGATTTT Y 2 1 2 1 101000 f 74 goat snp17494-scaffold181-178687 3 20737431 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778366 Affx-122926066 AX-385265481 3 96493936 TTTACCATACTTCAACTAATTTGATCTGAACTTTA[C/T]GAGTGGTTGATTTTCTATTAATCAATGTAGAAGTT Y 2 1 2 1 101000 f 74 goat snp17493-scaffold181-148816 3 20707461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410188 Affx-122952584 AX-123280538 3 96528053 TTGCTGTCAGATACTGGAAGTCTTCTCGTATGTAA[C/T]AGATGCATAGCTTTTCTGTCCCCTAAAAGGCAGAC Y 2 1 2 1 101000 f 74 goat snp17492-scaffold181-114699 3 20673827 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422296 Affx-122943481 AX-123292642 3 96571122 GAAAAGTGTAGTGGCAATACAAGAAATAGTCAAGA[C/T]AGTGACAAAAGTTATTGCAAGATGGCACACAATAA Y 2 1 2 1 101000 f 74 goat snp17491-scaffold181-71630 3 20630635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399513 Affx-122961162 AX-123269868 3 96603895 TGTGTGGGGGAGGGGATTTGACGCTTGTCACTGAG[A/G]AGGAACGAGGTGCTCCCTGGGACTCTGATTTGTTC R 2 1 2 1 101000 r 74 goat snp17490-scaffold181-38857 3 20598001 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402826 Affx-122958266 AX-123273179 3 96647246 CACCACTCCGCTAAACCAGGTTTCTCTCAGTCCAG[C/T]GTGAGTACACAATCACTGCCTCACATCACAGCCAC Y 2 1 2 1 101000 r 74 goat snp41820-scaffold545-4395 3 20554328 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787118 Affx-122922904 AX-385274144 3 96682192 TTTATGGTCCCAAAGAGTACATGAACTCATCTTAA[C/T]GGGAACATGCTTCTGTTATCATATCCTGCAAATTA Y 2 1 2 1 201000 r 74 goat snp41821-scaffold545-39341 3 20519366 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413780 Affx-122949922 AX-123284129 3 96711777 TTTAAACTGATAAGTTTATGGTAATTTATTACCCC[A/G]TAATAGAAAACTAATACACTCAGCTACTTAGTTTC R 2 1 2 1 101000 r 74 goat snp41822-scaffold545-68926 3 20489667 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278011 Affx-1111836205 AX-519551503 3 96734226 CATGATTCCTTGGTGTATAACTCTCAAACACTCAC[A/G]AACCAGAGCAGAGGTGTTGTGGGAGGGATGGAGTG R 2 1 2 1 101000 f 74 goat Random2.2K-369 3 96734226 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396196 Affx-122963366 AX-123266551 3 96756832 GCCTGGAACATGTTGACATGCTCCATTGAACTAGT[C/T]TCCTGGGGCTTCTCAGAACGACTGCTCTAGTTCAT Y 2 1 2 1 201000 f 74 goat snp41823-scaffold545-113981 3 20443840 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278168 Affx-1111836206 AX-519551657 3 96807888 CTATACTGCCTCACCAGCCAACTGACCCCACGAGT[A/G]ATTTCTTGGGACCCAGTGGGGTCCTAGACCTGTGC R 2 1 2 1 202000 r 74 goat Random2.2K-370 3 96807888 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378269 Affx-122976880 AX-123248628 3 96810078 GTGCTCAAATATTTGCTGAATAAACCAACCTTTGA[A/G]GATGCTTGAGAAAACTTCCGGATGAAGTGAAGCAT R 2 1 2 1 101000 r 74 goat snp41824-scaffold545-167227 3 20390939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799838 Affx-122924317 AX-385286764 3 96845252 CTGTTCTTAAGCCCTGCCTTTCTACTTGTTTTAGT[G/T]TTGCTGTGAATTTATAAATAGTGAAGACCAAAGAA K 2 1 2 1 102000 f 74 goat snp41825-scaffold545-202401 3 20355923 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401957 Affx-122958798 AX-123272310 3 96951426 GAGCCGGGCCTTCGTAGGTCAGCGATTCTTGAGAG[C/T]ACCACCGACAGAAGGCACACACTTCTAGACACTAG Y 2 1 2 1 201000 r 74 goat snp41827-scaffold545-308575 3 20248678 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452235 Affx-122920789 AX-123322568 3 97005899 TTGGAGGCAGACAGCCTAGGTAGTTTGGAAAGTAA[C/T]GTGCTAATCCAGGTCAGAGGAGAGTGAAGAGAATG Y 2 1 2 1 101000 f 74 goat snp41828-scaffold545-363048 3 20193851 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448280 Affx-122924178 AX-123318616 3 97038848 GGTCAGTTTCACTGCAGAGTTCACAGCTATGTTTC[A/G]TTAGGAAGTAGGCTTTGCCTTGTCAGGGGACTGTG R 2 1 2 1 101000 f 74 goat snp41829-scaffold545-395997 3 20161006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409552 Affx-122953599 AX-123279903 3 97069587 TTCTTGCTGTTGTTTTCATTTTCATTGCGCTCTTA[C/T]GATGTGCCAGGCCTTTTATTTAGGTACTGCAAAAT Y 2 1 2 1 201000 r 74 goat snp41830-scaffold545-426736 3 20130107 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396929 Affx-122963195 AX-123267284 3 97104428 AGCTCTTGGTTTCACTAAGGATCATAAAGAAAATT[A/G]CTAATTACATCAAGCACACTGCTTAGAGCTTGGAT R 2 1 2 1 101000 f 74 goat snp41831-scaffold545-461577 3 20094915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450456 Affx-122922953 AX-123320790 3 97174673 CATCACATTGATGTGGGGCCTCTTGCCAGGAGCTC[A/G]TGGAAGACAGTGACATGTGTGGTAGAAAGCACATG R 2 1 2 1 101000 r 74 goat snp41833-scaffold545-531822 3 20022189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424450 Affx-122941784 AX-123294796 3 97228915 AAGGATATGGACACATAGACGCTTTCCGTACAAAG[C/T]GACAGAGCTAGGAACACTATGCTGTCTTAGCCTAA Y 2 1 2 1 101000 f 74 goat snp41834-scaffold545-586064 3 19967898 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379024 Affx-122976364 AX-123249383 3 97270781 TAGAAGGAAAACAATTTTTTTTTTAATTACACAGC[A/G]CCAGAAAACATCTATTATGAAAGAGACACTGAACA R 2 1 2 1 101000 r 74 goat snp41835-scaffold545-627930 3 19925224 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781772 Affx-122973682 AX-385268854 3 97327272 TGAATTAACTTATTTATAGTAAGTTATCAGGACTA[C/T]GTGTGTTTAAAGTCTTATTATGTTGAAATTATTCC Y 2 1 2 1 201000 r 74 goat snp41836-scaffold545-684421 3 19868308 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416119 Affx-122948302 AX-123286468 3 97374853 TTTTGCATTTGGAGTAGCAGACACCTCAAATATTT[A/G]CTAGTTGCCTTCAGGCAGGATATACTGTTTGTTGG R 2 1 2 1 101000 r 74 goat snp41837-scaffold545-732002 3 19819661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430262 Affx-122937301 AX-123300603 3 97404364 AGCAGAACAGAGCAGGTTGCGTCCAGGGAGCCCTA[C/T]TGCCTCACCCTGGTCGTCCTCTTCCTCTTGCTCCA Y 2 1 2 1 201000 f 74 goat snp41838-scaffold545-761513 3 19790100 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395982 Affx-122963511 AX-123266337 3 97444122 CATTAGGGAAGACACCCACTAGGATGGCTTGGCTG[C/T]GCTATTGCACGGCTTGTGGTATGTTAGTTTCCCAA Y 2 1 2 1 201000 r 74 goat snp41839-scaffold545-801271 3 19750714 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438026 Affx-122931562 AX-123308364 3 97472945 AGGGCTTCTCAGTGCAAACATGAAATCTGGAGCTG[A/C]GAGGGGAAATAAGGAGTCCTCTGCCCAGAAGCAGG M 2 1 2 1 101000 f 74 goat snp41840-scaffold545-830094 3 19721842 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768536 Affx-122978499 AX-385255716 3 97513564 CAAGGGAGTTCCATAGCGGCAACATGGAGGAATAC[A/G]TGATTTTGTCTGTTGTCATTTGCTTCATGTCATGA R 2 1 2 1 101000 r 74 goat snp41841-scaffold545-870713 3 19681242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378018 Affx-122977586 AX-123248377 3 97548920 TACTTACACCTGAGATCCTTTGTAGCACTGCGTGC[A/G]CCTGTCAAGCCCTTGAGGCTGTGTCTGCTGGGTCA R 2 1 2 1 101000 f 74 goat snp41842-scaffold545-906069 3 19645276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431569 Affx-122936190 AX-123301910 3 97595579 GAAATTCTTAATGATTCTGCCCAAGTGTTTTCTCT[A/G]TAGAACCTTCCTGACTCTTTCCGTGATTCCTCACA R 2 1 2 1 101000 f 74 goat snp41843-scaffold545-952728 3 19599119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275509 Affx-1111834847 AX-519549081 3 97632732 TATGGTTATCAGCAGAACTTATCTTAATATAGTAA[A/C]CACTGCAGGCTTTCATGTTATTAAATATCCACAGC M 2 1 2 1 101000 r 74 goat GoatD01.056320 3 97632732 T G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437757 Affx-122931714 AX-123308095 3 97653936 AACACAGCCAACTGGAAGCACTGTCAGAGAAGTGA[C/T]AGGACTTCAGGGCCCGAGCTCCCCAGGTACCAGAG Y 2 1 2 1 201000 f 74 goat snp41844-scaffold545-1011085 3 19540309 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392514 Affx-122966119 AX-123262871 3 97691482 GCCATGGGACCAGCAACTGATTTTTCTGGAATCTT[A/C]AAAGAATGCTTAACTGACAGAAACAATTTAACTGA M 2 1 2 1 201000 r 74 goat snp41845-scaffold545-1048631 3 19502864 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423001 Affx-122942984 AX-123293347 3 97765593 CTGAGCCTCCCTAGGCTTGCTGCTGAGAAATCTGA[C/T]GTCATTCTGATTCCTGTGCCTTTGTCTGTGGCTTG Y 2 1 2 1 101000 r 74 goat snp41847-scaffold545-1122742 3 19428646 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418222 Affx-122947048 AX-123288570 3 97844380 TGCCCTTGCCATCTTCCTTTCCCTCTACTCTGCTG[G/T]CAGAAACCCAGATTGGTATTGCCCGCTCCATATGG K 2 1 2 1 201000 r 74 goat snp41849-scaffold545-1201529 3 19351212 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388773 Affx-122968936 AX-123259131 3 97904157 CCGGGAAGATGGAAAGCAGAGGAAGAGAAGGGGAA[C/T]GGGTCTGGCAGGAGGTATAAGATGAATGTCATTTC Y 2 1 2 1 101000 r 74 goat snp41850-scaffold545-1261306 3 19291620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804552 Affx-986696720 AX-385291097 3 97917691 CGTGACTGATTGTCTGCAGCGGCAGCTGGACCAGC[A/G]TTTCGACTGTGGTGACAGCAAAGCCATGCTTGGTC R 2 1 2 1 600010 r 74 goat 3_97917691 3 97917691 Ancestral_priority_1043 ancestry 0.584 neutral IMAGE 10K 10K ancestral 38386690 Affx-122970178 AX-123257048 3 97963917 CATTGGAGAGTTGTAAGTATGCAGAAATATGAGAA[C/T]TGCATTTTAGAAAGGGCAGGATGACTGCAGGATGG Y 2 1 2 1 101000 f 74 goat snp57206-scaffold910-1289981 3 19231991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434016 Affx-122934226 AX-123304357 3 98010026 TTGGTCTCCTCACACTGACTCACCTTAGCAAGGGC[A/C]TGCTTCAAAAATAAAGTGCTAAGGAGGACACCTCA M 2 1 2 1 201000 r 74 goat snp57205-scaffold910-1243872 3 19185914 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396685 Affx-122962833 AX-123267040 3 98042831 GGTGGGGTTAGAGGAACAAGATGCTTTCACTCCCT[C/T]TTCCATTCTGCCCTACCATCCAACCCATTCCTACC Y 2 1 2 1 101000 r 74 goat snp57204-scaffold910-1211067 3 19152554 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415374 Affx-122948763 AX-123285723 3 98122998 ATACTGTAAGAGTTTAGTTACCTGATTCTCCTCTT[A/G]CCAGTCGTTTTCAGGGAGATGAGAATTTTCAGGGA R 2 1 2 1 101000 r 74 goat snp57203-scaffold910-1130900 3 19072180 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431183 Affx-122937179 AX-123301524 3 98154587 AGGCAGAGACGTAATGAGCTGGAGTGGATTCTAGA[A/G]GTGGTAGGAAAGGGCTTGGGAAGGAAGAAAACACA R 2 1 2 1 201000 f 74 goat snp57202-scaffold910-1099311 3 19040670 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418065 Affx-122946617 AX-123288413 3 98211068 ACTGGATGGGGATCAGTCAAGCTCCCTGGACCACT[A/G]TCTCTTTCAGCACACCCTCATGACAGGAGGTGGGG R 2 1 2 1 101000 r 74 goat snp57201-scaffold910-1042830 3 18984248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453503 Affx-122919818 AX-123323836 3 98259388 GCTCTTGCTTGCCTACTAGGATGCAGGAGCTCGAT[A/G]TCTCACTCCAGGACGTGACTTCTTGCTCTAGGGTA R 2 1 2 1 101000 f 74 goat snp57200-scaffold910-994510 3 18937163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781850 Affx-122942277 AX-385268932 3 98313265 GCAGAGTGCTTCTGATTCTGCTGAAGTGTACACAC[A/G]TATTCTTTGCACATTACATTTATACAAAAGTTAAT R 2 1 2 1 101000 f 74 goat snp57199-scaffold910-940633 3 18882405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443207 Affx-122927584 AX-123313544 3 98356402 ACCTAAAGGGTTTATGGGGGCTAGTTGGGTCTCCC[A/G]TTTCCTGGATGTCTGCCTTTGATCATGCTCTGTGC R 2 1 2 1 101000 r 74 goat snp57198-scaffold910-897496 3 18838617 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778992 Affx-122967938 AX-385266099 3 98411389 CTTTGTTAATTTCTTCATTTCGCTTTTCCTTTTGT[A/G]GTTTGATGATTTTCTTCTGTAATATGCTTGAGTTC R 2 1 2 1 103000 r 74 goat snp57197-scaffold910-842509 3 18783832 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451848 Affx-122921078 AX-123322181 3 98446354 ATAGTATACCCACAGTAAATAAAAGGACATTTTTG[C/T]CAGGGTGGGAAAATAGAAGGGTTTGGGGGGAAGGG Y 2 1 2 1 101000 f 74 goat snp57196-scaffold910-807544 3 18747929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417122 Affx-122947465 AX-123287470 3 98531989 CCCCAGACCTAGAAGCCTTGAGGCCTCAGGTGCAT[C/T]CTGTTTGCTCACAGGTCTCAGGCTCAGGTGTCTGG Y 2 1 2 1 201000 f 74 goat snp57194-scaffold910-721909 3 18661955 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401934 Affx-122958813 AX-123272287 3 98570686 CGTGGTGAGGCAGGTAGACACTGTGGCCTCCTACT[A/G]CTCAACAAGTCCTCTGCTGACCCACCTTGGTGGTC R 2 1 2 1 101000 f 74 goat snp57193-scaffold910-683212 3 18623326 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422305 Affx-122943475 AX-123292651 3 98610351 TCTAAGCACTGAACTTGATGGGCTCCCTGAATAAG[C/T]GCAAATAACTGGGAATTTCATGTCTGTTGGTTCAC Y 2 1 2 1 101000 f 74 goat snp57192-scaffold910-643547 3 18583543 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379905 Affx-122975761 AX-123250263 3 98653959 CCCTCATTAGACTGGCTGCCTGGAAACTGGGCTCT[A/G]CCCCTCTGTTCATGCCCTGTCGAGGCCCCCTCACA R 2 1 2 1 101000 f 74 goat snp57191-scaffold910-599939 3 18539528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384364 Affx-122972236 AX-123254722 3 98717449 GGGCCATGATGAGTCCCAAGAAAGGCCTCAGGCTA[G/T]ACCATGAGGGCAGTGAAGTTGGGATCGGTCCTTTT K 2 1 2 1 201000 f 74 goat snp57190-scaffold910-536449 3 18475228 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435089 Affx-122933718 AX-123305429 3 98747328 TTAATTTTTATTCATTTATGACTTAATCAAGATTA[C/T]ATATTAGGATTCCATCACGTTGGGGGAAAGAAGGG Y 2 1 2 1 202000 f 74 goat snp57189-scaffold910-506570 3 18444571 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272077 Affx-1111833407 AX-519545840 3 98783372 ACACAAGCTTAGGCCGTGTGCTAGTGGCAACACTG[A/G]CACAGTCTCATTCCAAACCTTGGCATCATGGCTAG R 2 1 2 1 101000 r 74 goat 3_98783372_AF-PAKI 3 98783372 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426535 Affx-122940192 AX-123296881 3 98798960 TTACAGAGTGGGCCTCTTCCAGGCCTCAGTTCCTC[A/G]TTCAATAGGTGTTGCCATAACCCATGTCTCCTAAA R 2 1 2 1 101000 r 74 goat snp57188-scaffold910-454938 3 18392814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771550 Affx-122943062 AX-385258708 3 98842401 CTTTTTATCACATTTGAAGTTATTATAAGTACAGC[A/G]TCTACTCTGTACTCTGGGCCTAGAGTTTGTTTCAC R 2 1 2 1 101000 r 74 goat snp57187-scaffold910-411497 3 18349415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425376 Affx-122941567 AX-123295722 3 98881711 TGTCACTCCACTGAATGCCGATGCCTCCAGGCGCC[A/G]CACCGCCCTGTTATAGGGGGTTGTCAGCTCAAATA R 2 1 2 1 201000 f 74 goat snp57186-scaffold910-372187 3 18309716 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443463 Affx-122927827 AX-123313800 3 98939077 CTGATGGATGATGAAGCTGGCACTCATTCAAACAG[C/T]AGCTGAGGATTACTAGGATATGGACCCAGTGTGAT Y 2 1 2 1 101000 r 74 goat snp57185-scaffold910-314821 3 18252067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382378 Affx-122973854 AX-123252736 3 99051697 CATGCTCTCATAAAACCACATTCTTATCCTTAGGC[A/G]CACCTAGTTTGTATTAATATAATAATTAGAGTGAT R 2 1 2 1 101000 f 74 goat snp57183-scaffold910-202201 3 18139486 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380190 Affx-122975503 AX-123250548 3 99105752 CTCCCCTGTATCTGTCCTGTGCATACCGCAGCTGA[A/G]CCCTGTTCCAGCAGCTTCCTTGCCTTTGGCCCTGT R 2 1 2 1 101000 f 74 goat snp57182-scaffold910-148146 3 18085741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441187 Affx-122929541 AX-123311524 3 99142971 GGAACGGCTAAGTCAGAAGCTCAGGTCCCAGCCTC[A/G]CCACGACCTCAGAGAGCCCTCAGGCCCTGCAGGCT R 2 1 2 1 103000 f 74 goat snp57181-scaffold910-110927 3 18048402 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436541 Affx-122932925 AX-123306879 3 99176284 ACGAATGAGTGACTCACACACTCTGTACTCTCAAC[G/T]CAGTTGGTTGCTCTGCCAGCCTTCTTCAACTTCAC K 2 1 2 1 201000 r 74 goat snp57180-scaffold910-77614 3 18014645 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452813 Affx-122920750 AX-123323146 3 99245848 GGTCCTGAAACATAGGTATCAGGAATGAAACTTGG[C/T]GTGAGCTAAGATTGGTGAGGTTAGCAGGACCTGAG Y 2 1 2 1 101000 f 74 goat snp57178-scaffold910-8050 3 17944887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424587 Affx-122942211 AX-123294933 3 99280469 GAGCACCTCAAATTGAAAGGTCTCTAAGACCTCTG[C/T]GTCTCCAAAATTCTGTGTCACAGTAGGTGAAATGC Y 2 1 2 1 101000 f 74 goat snp23602-scaffold238-1302314 3 17711754 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403953 Affx-122957447 AX-123274305 3 99309198 ATTGAAGAGGAACACTCAGTAGAGGAGAGCTAGGC[A/G]TAATTTCTGAAGGTGCTAGACTTGATGGGGCAGTG R 2 1 2 1 201000 f 74 goat snp23601-scaffold238-1273585 3 17682727 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424019 Affx-122942091 AX-123294365 3 99350239 GGCCTTTGTCATGACACTAATGGGGTTATTAAAGA[G/T]AAACAGCCCAGAAGACAGTTTGGAAAGTGACTCCC K 2 1 2 1 101000 f 74 goat snp23600-scaffold238-1232544 3 17641832 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783386 Affx-122969043 AX-385270449 3 99382758 ATTCTTTACATATTCTAAATATGAATCTTTTGTTA[C/T]ATGTATTTCAAGTATTTCCCCCCCTTTAACTTCTT Y 2 1 2 1 101000 r 74 goat snp23599-scaffold238-1200025 3 17609732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426452 Affx-122940803 AX-123296798 3 99411427 TTAACATGCATCATGGACCTGTGTCCTTAAAATAC[A/G]CCGGTCCATGAACAAAGGTGTATATGTTGGACTGG R 2 1 2 1 201000 f 74 goat snp23598-scaffold238-1171356 3 17581336 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423425 Affx-122942613 AX-123293771 3 99462841 TGGTGAATGATATGGCAGGTGAACGAGTGAATACA[G/T]GTATGTGGTCACCTGAGCCATTTTCTTTCTCCAGT K 2 1 2 1 101000 f 74 goat snp23597-scaffold238-1119942 3 17529677 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424080 Affx-122942045 AX-123294426 3 99513129 TGAGAAGCCTTGTCATGATAAGTGGTGTGTGTCAA[C/T]AGTTTGCTGTGTGCCAGGGGCAGAGCTGAGTAACT Y 2 1 2 1 101000 f 74 goat snp23596-scaffold238-1069654 3 17479639 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443467 Affx-122927825 AX-123313804 3 99553060 AGCTGTCCTGACCTCCCTGCTGGTCCTTTAACACA[C/T]CAGACATGGTCCTGCCTTTGTACCTTTGGACTTGC Y 2 1 2 1 101000 r 74 goat snp23595-scaffold238-1029723 3 17439965 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451520 Affx-122921104 AX-123321853 3 99603117 GATCCAGCCCTAACTGTAGCTGGTGTCCCTTCCAT[C/T]ATTGTTTGTTGTTGTTTTCCACAAAGGATGAAGAA Y 2 1 2 1 201000 f 74 goat snp23594-scaffold238-979666 3 17388892 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784794 Affx-122972718 AX-385271841 3 99636923 TACAACATAGTCACAATATTTGTTTTATCATTTCA[G/T]TTTGTGAAAAAGAGGCTGGATAGAAACACAACAAA K 2 1 2 1 201000 f 74 goat snp23593-scaffold238-945860 3 17356281 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788180 Affx-122944427 AX-385275199 3 99668575 TTCTGGAGAATGGGAATGCTAATACTAACATTAGG[A/G]GCATTTGAGAAAATCCAGTAAGGTGACTGTAATGT R 2 1 2 1 101000 f 74 goat snp23592-scaffold238-914208 3 17324839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765078 Affx-122933443 AX-385252642 3 99732458 TTTCTAGGTACATCCAAAACCCTGTTCAGTAATCA[C/T]AGGGTCAAACATTAAGTATGGAAACATTTAAATTC Y 2 1 2 1 101000 f 74 goat snp23591-scaffold238-850325 3 17261113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416599 Affx-122947641 AX-123286947 3 99775062 TTTCCACATCATCACTGCAAGAGTACTCTCAATAC[C/T]TGGCTGACATGCCAAGCAACTGAAACCCTGACGCT Y 2 1 2 1 101000 f 74 goat snp23590-scaffold238-807721 3 17217595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451944 Affx-122920966 AX-123322277 3 99804201 GAGATATGGGCAGAGTCCAGGTGTTCCACTTTGGC[A/G]TATATTGGCGTAAATGTGGTATTTTTAGATCCTGA R 2 1 2 1 201000 r 74 goat snp23589-scaffold238-778582 3 17188087 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434744 Affx-122933912 AX-123305085 3 99852658 AGAGAGATGGTTTGCTACAGCCTTTTCTCTTGTAC[A/G]CCTAAGATGAGTAATGTTCCTTGTTGCTGAGGGAT R 2 1 2 1 101000 f 74 goat snp23588-scaffold238-730125 3 17139401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429789 Affx-122938206 AX-123300130 3 99904952 GAAAAGCAGTGAGTAGTGGGCAGGCTAATGTGGCT[C/T]GGCATCTGTCTTTCAAAGGTCTTTCAATACTCTTA Y 2 1 2 1 201000 r 74 goat snp23587-scaffold238-677831 3 17086548 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390103 Affx-122968018 AX-123260460 3 99956120 GTGCAAGACTGACTTGAAGAAAAACACTTGCAAAC[A/G]CAGCTTCTCTGCTTGTTCTATTTTTCTGTGTTGTT R 2 1 2 1 101000 f 74 goat snp23586-scaffold238-626663 3 17035286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274716 Affx-1111834456 AX-519548302 3 99970177 CAACATGGGGGTTTTCACTTCTGAGAAACCGCGGC[A/G]GGT R 2 1 2 1 102000 f 74 goat GoatD01.036647 3 99970177 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320779372 Affx-122973597 AX-385266476 3 99986041 GATCATGTTTGGGATGACACATATTCCTCCTAGCA[C/T]GACATGGTAGTGCGCAGCACTTGATGGATTATTAT Y 2 1 2 1 101000 r 74 goat snp23585-scaffold238-596742 3 17005342 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404847 Affx-122956625 AX-123275199 3 100015933 TCAGCCGGCAGATCAGTTTGAAAGTCAATTATGCA[C/T]AGTTGTTTCATTTCCATTCCTGAAATTATCTTTTA Y 2 1 2 1 101000 f 74 goat snp23584-scaffold238-566850 3 16975367 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422113 Affx-122943563 AX-123292460 3 100076003 TTAACCAAAATATTAAGCTTTGGTTCTTGTTATTC[A/G]TGCACTAAAATCCATTTATGCCAATTAAGATGGTC R 2 1 2 1 101000 r 74 goat snp23583-scaffold238-506780 3 16913410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419887 Affx-122945351 AX-123290235 3 100126947 GTATAAGGTTTATAAAGTTCTCACTCCATACATAA[A/G]ATAGTATAATGAAGGTAGAGTGTGATAAGTTAAAG R 2 1 2 1 201000 r 74 goat snp23582-scaffold238-455836 3 16862712 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429330 Affx-122938585 AX-123299672 3 100158401 CTGCAGTTACTTCTCCACTGAAGTCTAGAACGCCT[C/T]ACAGCCATCCATGACGGTTAGAATTAACCTCTTTC Y 2 1 2 1 201000 r 74 goat snp23581-scaffold238-424382 3 16830260 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386693 Affx-122970176 AX-123257051 3 100189953 CCTTCTCTGTGCAGCTCTCTCATCTCTAACATGCC[A/G]CCCTGTGAACTCTAGCCACCAAGTTCTCCTGACTC R 2 1 2 1 201000 r 74 goat snp23580-scaffold238-392830 3 16799006 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766689 Affx-122925689 AX-385254033 3 100218950 CTAGCAATGCTAAAGAGCAACCAGTGAGCAGTTAG[C/T]ACTCCTTGATTTCATCTAACATTTTATTTCCCCAT Y 2 1 2 1 101000 f 74 goat snp23579-scaffold238-363833 3 16770910 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278170 Affx-1111836207 AX-519551659 3 100234401 CCATTCTATACATTCCAGTTTGCATCAGCTAATCC[A/C]AGACTCCCAGTCCAAACCTCTGCCACCTTTATCCC M 2 1 2 1 202000 r 74 goat Random2.2K-374 3 100234401 G T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443868 Affx-122927511 AX-123314205 3 100264624 CCCAGAACCTAATTTTGCAATGAATGATGAATATC[A/G]CATAGGGTTGTCATCAGGATTAAACAGGAAAATGC R 2 1 2 1 101000 f 74 goat snp23578-scaffold238-318159 3 16725168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446233 Affx-122925698 AX-123316569 3 100296505 TGGGCCAAGGAAGGGGGAAGAGGAAGTGAATGGCA[G/T]AGCACCCTAGGTCTCCTAGCTTCACTGCAGGGACC K 2 1 2 1 101000 r 74 goat snp23577-scaffold238-286278 3 16692635 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776876 Affx-122927996 AX-385264000 3 100343353 CCCCAAAGCACCTTAAGTTTTTCTTGCCTACAAGC[A/G]TGCTTCATCCTCATCCCTCCCTTAGAATACCTTCT R 2 1 2 1 101000 r 74 goat snp23576-scaffold238-239430 3 16646444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421827 Affx-122944310 AX-123292174 3 100386251 AGGATAAGGGGATGGGGATTTATTTACTCCTCTTG[C/T]GAGTACCCCCACACATACATCAAAGCATGTACCTC Y 2 1 2 1 201000 r 74 goat snp23575-scaffold238-196532 3 16603212 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405611 Affx-122956609 AX-123275963 3 100446217 GTCACAGGCATCAGCCCAGAGGCAAATGAAAGGAC[A/G]TTAGGAACTAGGAAGATTCTCTCCACACAGAACAG R 2 1 2 1 201000 r 74 goat snp23574-scaffold238-136566 3 16543852 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785743 Affx-122946014 AX-385272783 3 100495621 AATTTTACAACTCCCACAAAGCCTAATTTCATTTG[C/T]AAAATACACCAGGGAATCCTGGCAAGTTCCTGTGG Y 2 1 2 1 202000 r 74 goat snp23573-scaffold238-87162 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383938 Affx-122972964 AX-123254296 3 100557182 TATACACATTCACAGTGGAAAGCACTGGGCTGAGA[A/G]TGAGCAGCCCTTACCTCTAGCTCTGCTTCTGCCAT R 2 1 2 1 201000 r 74 goat snp23572-scaffold238-25601 3 16457450 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433434 Affx-122935077 AX-123303775 3 100605584 GCACCTGCTGCTGCTTCTTCCTGGAACACCCTATT[A/G]CCTTTCTCTGATGGGCAAATTCCTACTGACCTTTG R 2 1 2 1 101000 r 74 goat snp28607-scaffold3068-430703 3 16409481 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278171 Affx-1111836208 AX-519551660 3 100662067 TGAGTTCCCGAGGAACTGTCCCAAGGCTTCCAGAC[A/G]GACGGGAGGATGGCATCCAGACAGGTCAGCCAGGG R 2 1 2 1 202000 r 74 goat Random2.2K-375 3 100662067 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38445196 Affx-122925525 AX-123315533 3 100664105 TCCCCAAGCACAACCTCACCTGCGGGCTGAGCCCC[A/G]CTTCTCAGAAGGATGTCCACCATTTATTCCTATGG R 2 1 2 1 101000 r 74 goat snp28606-scaffold3068-372182 3 16351762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411391 Affx-122952225 AX-123281741 3 100715960 TGATAGGATGTTCAAACAACTAGCTCAGAGCACAG[C/T]AAGCATCAATTTAGTCATTCCACAAACATTAATTT Y 2 1 2 1 101000 f 74 goat snp28605-scaffold3068-320327 3 16303386 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434187 Affx-122934874 AX-123304528 3 100745676 CCTGTAGGGAAGAGTGAGGATTCCCATATTATAGA[C/T]GAGGACACTGAAGCTTGGGAGAGGCAAAGGAACTT Y 2 1 2 1 101000 f 74 goat snp28604-scaffold3068-290611 3 16273852 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387091 Affx-122969874 AX-123257449 3 100776702 GTTTGATACTGTGAGTGATGCAAACCAGAATTCCC[A/G]TCTCTTCCTCCCCAAATGTCCACATAACATTAAAC R 2 1 2 1 101000 f 74 goat snp28603-scaffold3068-259585 3 16243114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799056 Affx-122971788 AX-385285986 3 100849466 AGAGGAGGAGGCTTTTATTCTAAAGGAATCAATAC[A/G]ATAACTTGAGATGCTGTGCAATGAATGACTGAGGC R 2 1 2 1 101000 f 74 goat snp28601-scaffold3068-186821 3 16170284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453206 Affx-122920445 AX-123323539 3 100899487 TGCTCTTTCACTTTCTGGAAAACCAGTCACTTCCC[C/T]GTTGTCACCTGGCCCCACCAGCTCTCAGGAAGCTC Y 2 1 2 1 101000 f 74 goat snp28600-scaffold3068-136800 3 16120618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406975 Affx-122955050 AX-123277326 3 100932354 CCAGGCAGAGGTCAGGGCAGATGAGGAGGTTTGGG[A/G]CATTTGAGGGTTCTGGAGACCCATGGGGAAGAGGT R 2 1 2 1 303000 f 74 goat snp28599-scaffold3068-103933 3 16087822 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384144 Affx-122972807 AX-123254502 3 101000851 GGGTTGGGCCAATCCTGCGCACACTTGTCCGCAGG[A/C]TTCCCTAGAGAGTGGCCCTGGTCTCTCTGCACTGA M 2 1 2 1 101000 r 74 goat snp28598-scaffold3068-35436 3 16019647 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424400 Affx-122941819 AX-123294746 3 101035027 ACTGGGCCCTGAGGCACAAACTGGAGAAGCAAACT[A/G]CACAAGGTCACAGTCAGGAGATGGGAAGGCTGGAT R 2 1 2 1 101000 f 74 goat snp28597-scaffold3068-1260 3 15985686 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402745 Affx-122958329 AX-123273098 3 101082059 TGGCACTGTCTACCATGCACCTGGAGACCTGTCCA[C/T]TCGTCTCTCCCATTAGATGCGGGGCATCTCCAGGA Y 2 1 2 1 101000 f 74 goat snp14497-scaffold158-544965 3 15938867 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414541 Affx-122949504 AX-123284890 3 101118053 ATGATATGATGGGCAGGTAAAAATGAGAGAGAGGA[C/T]GAGGTTGGAGAGAAGTGAGGGACGTGAAGGTGTAG Y 2 1 2 1 101000 f 74 goat snp14496-scaffold158-508971 3 15902833 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428621 Affx-122938682 AX-123298963 3 101159741 CTTTTTAAGTGGTTGAAAAAAGAATATGCCATGAC[A/G]TGTGAAACTTTAATGCCAATAAAGGTTTATTGGAG R 2 1 2 1 101000 r 74 goat snp14495-scaffold158-467283 3 15862332 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406022 Affx-122955495 AX-123276374 3 101246268 AAGTTTCAGTACTTCTCCAATTTAGCAGTATATTG[C/T]GACAGTTTTTGCTAAAGTAATCTACTTTTGAGATT Y 2 1 2 1 101000 f 74 goat snp14494-scaffold158-380756 3 15775363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787323 Affx-122934740 AX-385274348 3 101307931 TTGAGAGCTTAGTATATGCTAGATGTTGTTCTAAT[A/C]CGTGAACTCATTTAACTCCTTACAATAATCACGTG M 2 1 2 1 101000 r 74 goat snp14493-scaffold158-319093 3 15713913 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272175 Affx-1111833371 AX-519545928 3 101341578 CTCAAACCTTGAGCTAACCAATGTGTTTTTCTTAC[A/G]GAAATGTTTTTCATTAAGCTATGCTAATGAACTAT R 2 1 2 1 103000 f 74 goat 3_101341578_AF-PAKI 3 101341578 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789858 Affx-122920419 AX-385276865 3 101350037 GTAGAGAAAAAGTGAGGGAAAATCATTGATAAATT[C/T]AAGAAAGTTTCAAGAAACCAAATGATGGAATGGGC Y 2 1 2 1 101000 r 74 goat snp14492-scaffold158-276987 3 15672032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781893 Affx-122961034 AX-385268974 3 101381542 AGGCCCTGAGACCCTTCTTCACTCAAATCTTAAGC[A/G]TAGGTCTGATTCTGGAAATGGTCAGAAGGAATTTT R 2 1 2 1 101000 r 74 goat snp14491-scaffold158-245482 3 15640013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409485 Affx-122954055 AX-123279836 3 101431782 GAGGAGTCCAGGGTGACTAGAGGCTGGCATGAGTC[A/G]TGTGGCCAGAGGGTTGTAAACTGAGGCCAGCTTGT R 2 1 2 1 101000 r 74 goat snp14490-scaffold158-195242 3 15590151 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444858 Affx-122926290 AX-123315195 3 101462307 GAAGCTGGTCCAGGCGAGAGAAGCTGGTGCTTAGC[A/G]TGGGGTGCTGGCTATGGGGAAGGAGAGAGATACAT R 2 1 2 1 201000 f 74 goat snp14489-scaffold158-164717 3 15559576 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384106 Affx-122972835 AX-123254464 3 101503398 CCTGAGTGTGACTCTTTGCATCATAGACAGAATGA[C/T]AGGACTGGAAGGTCATTATGCCCCAGTGCCCTCTA Y 2 1 2 1 101000 f 74 goat snp14488-scaffold158-123626 3 15517713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274022 Affx-1111833991 AX-519547626 3 101521601 GTGACACATCTTTCAGTTTGCTTTTCATCTCAGCA[A/C]CAAATGTGACCCTTGTTTGTGGTCAGAGCAGGAAA M 2 1 2 1 101000 f 74 goat GoatD01.012998 3 101521601 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443152 Affx-122928063 AX-123313489 3 101538661 ACGACTGAGTGGCTGAACTGAACTGAACTGAAGCT[C/T]TCCCTAAGACCCTAGGTGCTGGTTGGGAAGACCTT Y 2 1 2 1 101000 r 74 goat snp14487-scaffold158-88363 3 15482609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427288 Affx-122940566 AX-123297631 3 101606209 AGCCCCTCTTCCCTCCTCATTCCCACCCTTGCTTG[A/G]TGTGTTGCTCAGTGCACTTACCTGGTGCGCCAAGT R 2 1 2 1 201000 r 74 goat snp14486-scaffold158-20815 3 15414967 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396464 Affx-122962969 AX-123266819 3 101629223 AGGGCCTTTCCCCAGCGCAGCCTTTAGTGACTAAG[A/G]CACTTTTCCGAGCCCACAGCTGTCTCAGGTGCTCT R 2 1 2 1 202000 r 74 goat snp16199-scaffold1704-2100 3 15390350 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442471 Affx-122927938 AX-123312808 3 101659763 TCAACCCAAGTAAATCCTCTCACAAACATAAGCTG[C/T]GTAAAACAACTCACAGACTGAAAAGTTAGAACAAG Y 2 1 2 1 101000 f 74 goat snp16200-scaffold1704-32640 3 15359969 C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440281 Affx-122930231 AX-123310618 3 101710242 GCTGAGCCCTGAAATCCATGCTACACTCTGAGATC[C/T]ATTGCCCTTCACCCCCAGGCCTCACTTCCCACAAG Y 2 1 2 1 101000 f 74 goat snp16201-scaffold1704-83119 3 15310434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451215 Affx-122921967 AX-123321549 3 101744676 AGAGTCAGGCTTTATCTGACCCTTTTGGTTTACAC[A/G]CAGATGAGGAACCCAGGCCCAGAGAAGGTCACACA R 2 1 2 1 101000 f 74 goat snp16202-scaffold1704-117553 3 15276396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381970 Affx-122974102 AX-123252328 3 101776263 ATAGCTGGTGCCCAGTCCTGGAGAGGTGGTATAGC[A/G]ATGGCACAGAGTTAATAGGATGGGGAGGGGGAGCA R 2 1 2 1 201000 f 74 goat snp16203-scaffold1704-149140 3 15244846 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768811 Affx-122924218 AX-385255988 3 101806921 CACAAATCAGGGGACAGAGTATATATGCAATTATA[A/G]CCAGTTTAATGCCTAATTATTCAATTTTTTCACAA R 2 1 2 1 101000 f 74 goat snp16204-scaffold1704-179798 3 15213013 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407714 Affx-122955011 AX-123278065 3 101864247 ATGTATTATGGGGTATATAACATGTAAAGTGAAAA[G/T]CATGATGACAACACACAAAGAATGGGAAGAGTAAA K 2 1 2 1 201000 f 74 goat snp16205-scaffold1704-237124 3 15155116 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804212 Affx-986696726 AX-385290852 3 101866680 CATCTTCTGTTGAAGTTGGTCTCTGGTCCCCAATT[G/T]GTCTTCTGTCATCACCCCTGGGATCCGGTCTTTGC K 2 1 2 1 600010 f 74 goat 3_101866680 3 101866680 Ancestral_priority_1043 ancestry 0.468 neutral IMAGE 10K 10K ancestral 38412790 Affx-122950495 AX-123283139 3 101894383 TTATATCCTTCAGTTGAGTATTAGTATGAGTATAT[A/G]TGTAGAAACTTTATCTGGTTCACTTTTTCCCATCT R 2 1 2 1 101000 r 74 goat snp16206-scaffold1704-267260 3 15124939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407841 Affx-122954529 AX-123278192 3 101954280 CGATCCTTAATTTGAGTCACTTGTGTCAGATGCCT[A/G]TTCATAGACAAGGCTCAAAACCAAGTCAGAAGGCT R 2 1 2 1 201000 r 74 goat snp16207-scaffold1704-327157 3 15065070 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411377 Affx-122952236 AX-123281727 3 101990115 TTCTACCTAAAATAACTATCCAAAGCTTGCTGGGC[A/G]CTATGCTAAGCACTTCATGGCCATCAAGAGGCATG R 2 1 2 1 101000 f 74 goat snp16208-scaffold1704-362992 3 15028433 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784981 Affx-122957310 AX-385272028 3 102035403 TAACCTTGTAGGAAATTATACTGAGAGAGAGCAGA[A/C]GTTGTGCGAAGAATTAGCAGAAAGAAAAAGGAACA M 2 1 2 1 101000 f 74 goat snp16209-scaffold1704-408280 3 14983536 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452472 Affx-122921001 AX-123322805 3 102067635 CCATCAAACTGTTAATTCTGATTATCTCCAGGGAA[A/C]TGTTACTAAGTAATTTTCACTTTCTACTTTACTGT M 2 1 2 1 101000 f 74 goat snp16210-scaffold1704-440512 3 14951706 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387017 Affx-122969931 AX-123257375 3 102128165 TCTTTGTCTTTTCCTTTTCTCATCAAGAGAAGAAA[C/T]AAGCCTCATAACCACATCAGACACTGAAGATGTAG Y 2 1 2 1 201000 f 74 goat snp16212-scaffold1704-501042 3 14890956 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423021 Affx-122943416 AX-123293367 3 102178799 CTGGCTACTTAAGAACTAAAAATTAAGCTGGGGGC[A/G]AGGCTGTTACGACTTTTCATCCCAAGAAATCAGGA R 2 1 2 1 101000 r 74 goat snp16213-scaffold1704-551676 3 14840121 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382222 Affx-122973985 AX-123252580 3 102235114 AGGATTAAGTTGGGAACCTTTGGCATATGGCTAGT[A/C]TTTAAAGCCGTGAGACTGGACAGGATCATGTAGGG M 2 1 2 1 101000 f 74 goat snp16214-scaffold1704-607991 3 14783297 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781677 Affx-122961617 AX-385268760 3 102284739 GACATGGATTTAAAACCAGTTTTCTGACTCCAAAC[A/G]CAGTTCTCTTTCCATTACATAAAAGAATTTCAAGC R 2 1 2 1 101000 f 74 goat snp16215-scaffold1704-657616 3 14733539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278173 Affx-1111836209 AX-519551662 3 102338775 ACAGATTTAGAGAACAAACTTATGGTTGTCAAGGG[A/G]GAAGAATGGGAAGAAAGGATAGGAAGTTTTCAGTT R 2 1 2 1 102000 r 74 goat Random2.2K-376 3 102338775 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396986 Affx-122963153 AX-123267341 3 102351172 TCTGGGCTTGAGTCCACAGCCCTAACATCCTCAGC[G/T]CTAGGGGATTACACTGCATCAGACGTGATTTAGAC K 2 1 2 1 101000 r 74 goat snp16216-scaffold1704-724049 3 14665805 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382071 Affx-122974917 AX-123252429 3 102416789 GTTAGATACTTTGTGTCTTGTACAGTGCTGATGAC[A/G]TGGTAGATCTTTAACATTTGATGAAATATTTGTTG R 2 1 2 1 101000 f 74 goat snp16217-scaffold1704-789666 3 14600060 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779399 Affx-122966468 AX-385266502 3 102457326 ATATGTCTATTTATTTAGCAGATGTTTATTGAGCA[C/T]TTAATTGTATTCCTGGAAAACATCTGGAAAGGGTC Y 2 1 2 1 201000 f 74 goat snp16218-scaffold1704-830203 3 14559681 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378433 Affx-122976771 AX-123248792 3 102500959 TCTTTAAAATTGCTGTCTCTTTTTCATATTCTATA[C/T]GGAGTAGGTCTTGGCAATGATAAATTTAACTTTGT Y 2 1 2 1 101000 r 74 goat snp16219-scaffold1704-873836 3 14522128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451529 Affx-122921097 AX-123321862 3 102536986 ATGTGTGTCACCTCCAGAAAGAGCTGAATGAATAG[C/T]GTGATTTAGGGCCAAGGCCAGTGTCAGTTACCTTC Y 2 1 2 1 101000 f 74 goat snp16220-scaffold1704-909863 3 14487962 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381932 Affx-122974131 AX-123252290 3 102596366 TAAAATGGCTCACAGAGCCAAAGGAAAAATAGAAG[C/T]AGGTCTTTGGAAGAAATGTGTACCAAAGTGGCTCT Y 2 1 2 1 201000 r 74 goat snp16221-scaffold1704-969243 3 14428392 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390721 Affx-122967927 AX-123261078 3 102628534 AGTAAAATTGAGCCCAAAGGGCCTGAATCCAAGTA[C/T]TGGTAATCTCTCCAGGGCTCTTTTTCTCTCTGGAC Y 2 1 2 1 101000 f 74 goat snp16222-scaffold1704-1001411 3 14396587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384147 Affx-122972804 AX-123254505 3 102672345 CCCTGGGCCGGAACATAGTGTCTATTTCACTTCCT[A/G]AGATAGAAACCGCACAGGGGCCACTAAGAGGTCTC R 2 1 2 1 101000 f 74 goat snp16223-scaffold1704-1045222 3 14353235 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445343 Affx-122926390 AX-123315680 3 102723661 CGCAGCTCTGAGCTTCCATTTCACTTTCACATCCA[G/T]TGGCTGAGTTGATCCTTAGTTGCTCTGCAAGGTGA K 2 1 2 1 101000 r 74 goat snp25493-scaffold2623-30425 3 14301933 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386383 Affx-122970841 AX-123256741 3 102804714 TAATGGTTGAGAAAAAAAAAGCAGGAAATACAAAA[C/T]GTTTGTTACTGCAAGCAATTTTAATACAAAAGTGT Y 2 1 2 1 101000 r 74 goat snp41712-scaffold543-13848 3 14218863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435658 Affx-122933344 AX-123305998 3 102852105 TTCTTCAGACCATGATAAATGCTCTTATATAGGCC[C/T]GTCCTTATGTCAAAACTTATTTTTCCACGAATAAA Y 2 1 2 1 201000 f 74 goat snp41713-scaffold543-61239 3 14171510 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410282 Affx-122952510 AX-123280632 3 102889434 TGCCTATATCCTTAATCGGCTATAAACATTAAAAT[A/C]AATTAGAATAGAGGAACATTCAACCCAGTTGCTCA M 2 1 2 1 101000 r 74 goat snp41714-scaffold543-98568 3 14134132 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407357 Affx-122955276 AX-123277708 3 102935430 CTTCTCCACCTCATCATTTCTTGCCTGTATTGTCA[G/T]AACAGCCTCTTAACTGCTCGCTGAGGCCTCTACTC K 2 1 2 1 101000 f 74 goat snp41715-scaffold543-144564 3 14088330 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779440 Affx-122947837 AX-385266543 3 102982636 ATCCGTTCTGTACCAAGGTAAAAGCTGACTTTGAC[A/G]TTCCCTCTTATCCAATGAAACTCAGATACACCCCA R 2 1 2 1 101000 f 74 goat snp41716-scaffold543-191770 3 14041196 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776017 Affx-122930889 AX-385263147 3 103021079 AAATTCTAAACTTCGAATAACCTTATTGTTACTCA[G/T]CAATAAGATCATTAACTCCCTGAGGAAAGACATCA K 2 1 2 1 101000 r 74 goat snp41717-scaffold543-230213 3 14002666 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432646 Affx-122935472 AX-123302987 3 103051923 CCTTATAGAGAAAAGAGCAGGCAGAGAAGGAACAG[C/T]CACTGGCACACAACCCCTACCCCACACTACCCTGC Y 2 1 2 1 201000 r 74 goat snp41718-scaffold543-261057 3 13971768 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765910 Affx-122962362 AX-385253342 3 103085616 GCAACCTTTCCCTTAAAAATAAACGTCACCCTCTC[A/G]TCATCAGGGTCAGTGACCCTAAATTTGCACAGTGT R 2 1 2 1 101000 f 74 goat snp41719-scaffold543-294750 3 13937948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412730 Affx-122950730 AX-123283079 3 103146486 CTCAGCCCGACATGCCTCTCCATCTGACATGTGTC[A/G]TCAGCAGGGGTCCCCCATTCACCTCTCCAGCGTGA R 2 1 2 1 303000 r 74 goat snp41720-scaffold543-355620 3 13881430 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776424 Affx-122976529 AX-385263551 3 103197258 TCTATTTTGCACTCCTTCTCTGCTCGGATACTACC[A/G]ATTCCATGTGCACACTCTATCCATTCTTTCTCAAA R 2 1 2 1 101000 f 74 goat snp41721-scaffold543-406392 3 13830093 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803548 Affx-986696107 AX-385290353 3 103253439 GGAAGTTCTATGAGGCCCTTTTGCAGATGAGAAAG[C/T]GAGGATCAGGGAATGAGAGTGACTTGTCCAAAGTC Y 2 1 2 1 600010 r 74 goat 3_103253439 3 103253439 Ancestral_priority_1043 ancestry 0.526 neutral IMAGE 10K 10K ancestral 38382546 Affx-122973782 AX-123252904 3 103270593 AGCTGGAAAGACGCGTGGTCCTTGCATTCCTATAG[C/T]GCCCAAACCCAAATCAGTCCTACCATCCTACTATG Y 2 1 2 1 101000 r 74 goat snp41722-scaffold543-479727 3 13757181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375992 Affx-122978422 AX-123246351 3 103304486 CCAAACCAGAATTGTGTCCCCCAAGTTGTGTGGTG[G/T]TGTTAAATGTTCCCTTTAAAATGTGAATTGCCAGT K 2 1 2 1 101000 r 74 goat snp41723-scaffold543-513620 3 13723042 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783068 Affx-122924803 AX-385270135 3 103348119 GCTGTTTCATGGGGGTCTCATGAATCTTCTGCTCT[C/T]GTTTATATTAGCTGGAACGAATGACTCTTTGCCAC Y 2 1 2 1 101000 f 74 goat snp41724-scaffold543-557253 3 13679300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413245 Affx-122950235 AX-123283594 3 103396911 CCAGGGGAATGTGGATGGACAGCTTTCAGCTGAAG[C/T]CATTCTTTCGCTTTCCATTTGGTCACTCATTCAAC Y 2 1 2 1 101000 r 74 goat snp41725-scaffold543-606045 3 13631059 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390960 Affx-122967053 AX-123261317 3 103446745 ATTTGACTTCGGTTCTAGGTGTGTTGGGTTTCCCC[A/G]GTGGCTCAGCAGTAAAGAATCTGCATGCATTGTAG R 2 1 2 1 201000 f 74 goat snp41726-scaffold543-655879 3 13580719 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440538 Affx-122929329 AX-123310875 3 103476676 CGACCAGGTCCTGGATCTCTGGCCCAGGCTCCCTG[A/C]CCCTTCTATTGCATCGTGCCAGCATATCATCAAGC M 2 1 2 1 101000 r 74 goat snp41727-scaffold543-685810 3 13550772 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796821 Affx-122961379 AX-385283764 3 103517378 TCACGTCTTAAGCGTACACTTTGATGACTTTTGAT[A/G]TAGGTGTATACTCATGTAACTGTCACCCCCGTTAA R 2 1 2 1 101000 r 74 goat snp41728-scaffold543-726512 3 13510202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441776 Affx-122929101 AX-123312113 3 103574877 CCTGGCAAAAATACTTATTTTAGGAGTGTATTGCT[A/G]CAGTGGGTAAGTGCCACCGGACATCTGTGATGTCT R 2 1 2 1 101000 f 74 goat snp41729-scaffold543-784011 3 13452491 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383228 Affx-122972763 AX-123253586 3 103668392 TTGGGCTTGGAGTTCTCAAGGGCTCCAGTGATTGC[A/G]CCCACTTTGAAGCACAGAGCGAGTGTAGGCTCAGA R 2 1 2 1 202000 f 74 goat snp41731-scaffold543-877526 3 13358478 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786106 Affx-122923364 AX-385273142 3 103699963 CCACTGAGACTAGCTGACATTTTAACAAGACTTAA[C/T]GAGTGTGTAGAATTTTCATCAATGGAGTGGGGCAC Y 2 1 2 1 101000 r 74 goat snp41732-scaffold543-909097 3 13326794 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439707 Affx-122930562 AX-123310044 3 103763753 TTCCTGTCCAAGTCTTTTGTCCATTTTTAATTGTA[C/T]CTTTTAACACTGAATGCCTGATATTACAGTTTTCT Y 2 1 2 1 101000 r 74 goat snp41734-scaffold543-972887 3 13262497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424918 Affx-122941296 AX-123295264 3 103796023 ACAACTGTCTTTAAAATGAGGATAGTCTCTGCTTC[A/G]TAGGTTTGTTTTTCCTCTGTGCAAGAATTAAATAG R 2 1 2 1 101000 f 74 goat snp41735-scaffold543-1005157 3 13229834 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382049 Affx-122974936 AX-123252407 3 103851374 ATCTAGGAGCTCGGAGTCCAATAGAAAAGACAAAC[A/G]CAATAGACTAAGGGCAAAAATGGCCCCAACTCTTC R 2 1 2 1 101000 f 74 goat snp41736-scaffold543-1060508 3 13177327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401510 Affx-122958933 AX-123271863 3 103896879 GCCAGGCAAGCTTCTAGGCACTTTCCATATGCTGA[A/C]TTATTTAGGTGGGTGCTATGATGAATCCCCATTTT M 2 1 2 1 101000 r 74 goat snp41737-scaffold543-1106013 3 13132448 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387641 Affx-122969853 AX-123257999 3 103995983 ATGGTCCCCTTTTCACAGATGAGAAAACTGAGGCT[C/T]AAGCAGTTAAATAACTTGTTCAAGGGCTTAGAATC Y 2 1 2 1 201000 r 74 goat snp41739-scaffold543-1205117 3 13033085 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782537 Affx-122964429 AX-385269612 3 104038196 GACTGCTAAACATTACTCCTTTGGTGTTGCTCAGC[A/G]TATCTAAATCTAAATTCAGTATCTCATCAAGCCAG R 2 1 2 1 101000 f 74 goat snp41740-scaffold543-1247330 3 12990959 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393884 Affx-122965123 AX-123264239 3 104097023 GGCTCTTCTGGGCTGGGAGGTGGGCAGAACATGAA[C/T]ACTCTCTCTCACTCCCCTCCTCAACAGGCTATGAG Y 2 1 2 1 101000 f 74 goat snp41741-scaffold543-1306157 3 12932089 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444776 Affx-122926352 AX-123315113 3 104210916 TTTAAGATCAGGAAAGGTCTGCTGAAGAGGAATTC[G/T]ATTTGAAAGCAAGACTTTCCTTTTGTTGTGCAAGA K 2 1 2 1 101000 r 74 goat snp41743-scaffold543-1420050 3 12818174 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779494 Affx-122975913 AX-385266597 3 104249799 AAATTTACTCTAGGTATTCAAAATTAACAATTCAA[C/T]TTCTCACTCACTCTTGCCACATTTTAACTGTTCAA Y 2 1 2 1 101000 r 74 goat snp41744-scaffold543-1458933 3 12779321 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410983 Affx-122952012 AX-123281333 3 104279679 GGGCATTGAGTCATTTTGTAAAACAAATGAATATA[C/T]GGGATCCTAGGACTCATGGAAATACCTTTATTGCC Y 2 1 2 1 103000 r 74 goat snp41745-scaffold543-1488813 3 12749199 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385991 Affx-122971517 AX-123256349 3 104333194 CCTATAGCTTTGGATTCCCACCGAGGTTTCCAGTC[A/G]TTTTACTCCTCCCTCCCAAACTGAAGCAGTGTGTG R 2 1 2 1 101000 r 74 goat snp41746-scaffold543-1542328 3 12695463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410342 Affx-122952463 AX-123280692 3 104364018 AACTCTTGAAGTGTTGAGATATTTCTCCTAATGAT[A/G]TCAAGATGGTTGCTGCAGCAGCAGGTGTCAGATGC R 2 1 2 1 201000 f 74 goat snp41747-scaffold543-1573152 3 12664743 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278175 Affx-1111836210 AX-519551664 3 104393730 TGGGGCAGGAGGGTGGGTGGGGGTCAGGCCGCCAC[A/G]ACTCTCAGGAGCAGCAGACTGTGACAAGGGCTCTG R 2 1 2 1 102000 r 74 goat Random2.2K-378 3 104393730 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382146 Affx-122974045 AX-123252504 3 104398672 GCATTGAAGTGCTGACCCCAGGAGAGGGTAAGTGA[C/T]ACGTGAAAGAGGAGAGAAAACCCAGCCTGGGGCTG Y 2 1 2 1 102000 f 74 goat snp41748-scaffold543-1607806 3 12630148 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451159 Affx-122921357 AX-123321493 3 104445083 GCTGGCCCCTGGTGGCCATGGCCTCTGGTAAAGAC[A/G]TGGTGTCCTGGCAAGATCACGAGCTTTGGCAGAAT R 2 1 2 1 101000 r 74 goat snp41749-scaffold543-1654217 3 12583914 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411768 Affx-122951491 AX-123282118 3 104501818 CGCCATGGGTCCTCCATTGCTGCACGGTCTTCAGC[A/G]ATCTCTGCTCTGATTCCCCTGGTTCTCTCCTCCAG R 2 1 2 1 101000 r 74 goat snp41750-scaffold543-1710952 3 12526653 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776720 Affx-122957165 AX-385263846 3 104611898 ACAAAAAACCACGAGCTGTAAGTATCAGCCAGACC[A/G]TTTCAGAGAGGCTGGTAAATTTTGAAAATGGTTAG R 2 1 2 1 101000 f 74 goat snp41752-scaffold543-1821032 3 12417993 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794592 Affx-122926316 AX-385281554 3 104657033 TTCCCCAGTTGTCTAGGTACACTTCTTAAAATGTC[A/G]TAAATATAATTCTCAGGCAATATAAAGTGAACACA R 2 1 2 1 101000 f 74 goat snp41753-scaffold543-1866167 3 12373067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380666 Affx-122975190 AX-123251024 3 104692180 GCCATAGTTTTAGTCCAGGGTCCAGTGCCAGCCAG[C/T]GACTCAGTCTTTACTTGAGCAGGCCACCAAAGTCT Y 2 1 2 1 101000 r 74 goat snp41754-scaffold543-1901314 3 12337511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802825 Affx-122932528 AX-385289724 3 104725260 AAAGGTTTCATCTAATATCTGGGAAGAGATGGCCC[A/G]TGTGGCATGTCCTAAATTAATTATTGTGTGTGTGT R 2 1 2 1 101000 f 74 goat snp41755-scaffold543-1934394 3 12304721 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390093 Affx-122968025 AX-123260450 3 104755902 CCAGGGACCACTGTGTGGAAGCCAGCCTGGCACTG[C/T]GGCTCTGATGGAGCTGGTTCTCCCTAGAGGTAGGT Y 2 1 2 1 101000 r 74 goat snp41756-scaffold543-1965036 3 12274018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438778 Affx-122931379 AX-123309115 3 104786540 AAAGGCAACAGAACGTGGTGCCATGCATCCCCCTT[C/T]TGGGCCTCAGCATCCACATAAACGCTGGAGTGAAA Y 2 1 2 1 101000 r 74 goat snp41757-scaffold543-1995674 3 12243766 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395267 Affx-122964089 AX-123265622 3 104819553 TCTACAAGTACTTTCCTGGGAAGCTGTGTCAGCCC[C/T]GCAATTAGTTCCCTCAATCAGGAAAGCAGCTCATC Y 2 1 2 1 101000 r 74 goat snp41758-scaffold543-2028687 3 12210791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385098 Affx-122971792 AX-123255456 3 104870070 CTGGCTCTTCCAACATTATCTTTCTTCCTCTTCCA[G/T]CATAAAATTCACCCATCCTACATCCTTGAGGAGAT K 2 1 2 1 101000 f 74 goat snp41759-scaffold543-2079204 3 12160476 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385210 Affx-122971711 AX-123255568 3 104911600 CATAGCAATTCTTTGCATTGTCATCACGTACAATT[A/G]TGTGTATGTTTTTGTGTGTGAAATTGTTCTGTCTC R 2 1 2 1 101000 f 74 goat snp41760-scaffold543-2120734 3 12118740 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435837 Affx-122932821 AX-123306176 3 105040213 GAGAGGGACCATGGAGATGGCAGGGAGTGAACAAA[G/T]CTCTCCATTCCCCGTTTACAGGGGCCTCTAGAGAG K 2 1 2 1 101000 f 74 goat snp41763-scaffold543-2249347 3 11990400 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433398 Affx-122935104 AX-123303739 3 105135792 ACAGGCTTTGCCTTCCTCATGCCTACATGGCAGCA[C/T]CAGACATCGTGCTCCTGGGAGATCCCTTTTCTTCA Y 2 1 2 1 101000 f 74 goat snp41765-scaffold543-2344926 3 11894799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444313 Affx-122926743 AX-123314650 3 105173268 ATGAAGATGTTGGAAACCAAAATAAAACTGGGCAC[C/T]GATCTTCTGGGCAGGAGGAAGCCAGGGAGGCTGAA Y 2 1 2 1 101000 f 74 goat snp41766-scaffold543-2382402 3 11857630 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448488 Affx-122923615 AX-123318824 3 105218886 CTTGTGCCCAGGGCACAGTCAGCACTGGATGTGGC[A/G]CAGCTTTAAACTCAAAGTGGGAGAGACAAAGCTCC R 2 1 2 1 101000 r 74 goat snp41767-scaffold543-2428020 3 11812358 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377773 Affx-122977353 AX-123248132 3 105279820 CCATCCAAGAATTCCTTGGGGGAAGGAATGAAGCC[A/G]TATACTCGTAGCCTAGAACAGTCCTGGTACATCGT R 2 1 2 1 101000 r 74 goat snp41768-scaffold543-2488954 3 11751891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439607 Affx-122931149 AX-123309944 3 105319893 TTGAGATTTAGCACAATCGCTGTAGTTCAAGAGCC[A/G]CTCTGTGGTCTCCTCATTTGTTAGTATCAACAGCC R 2 1 2 1 101000 f 74 goat snp41769-scaffold543-2529027 3 11711587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405881 Affx-122955603 AX-123276233 3 105350666 TACCAACAGAATGCTGCTGTGTCCCCAAGGTCTTA[C/T]GGAAATTTTAGTGAAATGCTCCTTTTTATTTTTGC Y 2 1 2 1 201000 r 74 goat snp41770-scaffold543-2559800 3 11680228 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383842 Affx-122973157 AX-123254200 3 105449494 TCTGTGGGCTGTCTGGGGTCACTCGACCTTGGCTG[A/G]GGCCACTTGTGGTCTATGAGGGAGCTAGGCGCTCA R 2 1 2 1 201000 r 74 goat snp41773-scaffold543-2658628 3 11583343 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804562 Affx-986696730 AX-385291103 3 105489744 GAAGCCAGCCCTGACTGTGGGCTGGCTCTGTGTGC[A/G]GCAGCAAGAGAGAGGGCAGTGCGGCTTGAAGTCTG R 2 1 2 1 600010 r 74 goat 3_105489744 3 105489744 Ancestral_priority_1043 ancestry 0.456 neutral IMAGE 10K 10K ancestral 320794650 Affx-122935637 AX-385281611 3 105496693 GAATATAATGTATAGTATTTTACAGAAGACAAGCT[G/T]GTCTGGTATGTAGGTCTGCATGGATATATCGTGTG K 2 1 2 1 101000 r 74 goat snp41774-scaffold543-2705827 3 11536117 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438336 Affx-122931339 AX-123308674 3 105537719 CTTCTCCAGGGACTCGTCTCAACCCAGAGATCAAA[C/T]CTTTGTCTCTCGCATCTCCTGCCTGACTTCTTGCT Y 2 1 2 1 101000 f 74 goat snp41775-scaffold543-2746853 3 11494754 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436754 Affx-122932286 AX-123307092 3 105613279 AGAATACAGCTTGAGAGCCCAGGAGAAACTGGAGC[C/T]AGGACCAGGCCCTTGTTTCATCTTCCATGAGGGGT Y 2 1 2 1 201000 r 74 goat snp41777-scaffold543-2822413 3 11418722 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420199 Affx-122945550 AX-123290547 3 105652675 TAAACCGGAGGCCAGTCTTGCTAAGTTCAGAAGCT[A/G]TTTCTAGCTATTTCTAGAAAGGTGGGCGTCTGAAA R 2 1 2 1 101000 f 74 goat snp41778-scaffold543-2861809 3 11379086 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376893 Affx-122977812 AX-123247252 3 105698672 AAAGGGCTCATCTGCTGGTGCAAGAAGCTGATTCA[C/T]GGAGGGCGTGGTTGCTGGAGAAGGAGGAGAAAGGG Y 2 1 2 1 101000 f 74 goat snp41779-scaffold543-2907806 3 11333285 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407884 Affx-122954495 AX-123278235 3 105764589 AGGGTCCATGTAAGGAATGGAGAAAAACAACTCCT[C/T]GTCTTCTATTCAAATACTTTTCTGCTGTCCTCTAG Y 2 1 2 1 101000 f 74 goat snp41780-scaffold543-2973723 3 11267621 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406639 Affx-122955820 AX-123276991 3 105796523 GCCACAGGAATTAAAAAGTATACAAAAAGTGTAAA[C/T]TGCCTGGCATTCAGCAGGTGACTTCACACCTTAAG Y 2 1 2 1 201000 f 74 goat snp41781-scaffold543-3005657 3 11235698 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452866 Affx-122920709 AX-123323199 3 105864255 GCACAGTGTACACAACAGAGGTTCCCAAAGGGTTA[G/T]TGCTACTAACAGGATGTCCATGGGGGTGAGGCTGA K 2 1 2 1 101000 f 74 goat snp41782-scaffold543-3073389 3 11168070 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418717 Affx-122946282 AX-123289065 3 105896927 ACCAAGCCAGGCTGGAGGAAGGCTGGGAAGATGGC[A/G]TGATGAGCATGGCAGCTTGTGAGTGAATGCAGACC R 2 1 2 1 101000 r 74 goat snp41783-scaffold543-3106061 3 11135541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383502 Affx-122972648 AX-123253860 3 105946848 GAGCAGTTGGTTGATTACTGTCTGCCGAGATAACC[A/G]TCATGATTTTCTGGTACATTTGTGTACACTACCAG R 2 1 2 1 101000 f 74 goat snp41784-scaffold543-3155982 3 11087061 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800342 Affx-122967853 AX-385287265 3 105999110 AAACCATGGCATTTAGATGATCACATATTAATGGT[G/T]GGTAATGCACTACCTTCCAACAAAGCTGACTGTGC K 2 1 2 1 101000 r 74 goat snp41785-scaffold543-3208244 3 11036080 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794902 Affx-122936439 AX-385281862 3 106036746 TTCATCCTTGCTAGAACTGTTCAAGGAACAGTTAT[A/G]TAAGGGAAGATACCAACTAGAAGATCGAAATGTAT R 2 1 2 1 101000 f 74 goat snp41786-scaffold543-3245880 3 10998907 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386553 Affx-122970715 AX-123256911 3 106103811 TGAGTTTGAAGTCCAGCTTTGCCAACTCTAGATGA[C/T]GTTACCTTGGGCAGGACTCTTAACCACTCTAAGAC Y 2 1 2 1 101000 f 74 goat snp41787-scaffold543-3312945 3 10931633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793239 Affx-122966217 AX-385280217 3 106271692 ACACCCCTCCACTGCAGAGCAACTGTTACAAACTT[C/T]ATTGACTTAAACTTCTGATGAAAAGGAATCTGTGT Y 2 1 2 1 101000 f 74 goat snp41790-scaffold543-3480826 3 10766917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377566 Affx-122977442 AX-123247925 3 106313689 GTGTGTTCCAGAGATGCTCCAGGACATGAGCACTG[A/G]CCCTCAGAGAGCTTCCTGAAGCTGCAGTCCCTGTG R 2 1 2 1 101000 f 74 goat snp41791-scaffold543-3522823 3 10725042 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402641 Affx-122958389 AX-123272994 3 106368480 GGAGAAAGAGGTGATTCACATGACCATGCCTAGTT[A/C]GTCATTAGTTTGACACCACCCTCGCTATGCATAGG M 2 1 2 1 101000 f 74 goat snp41792-scaffold543-3577614 3 10670284 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397291 Affx-122962329 AX-123267646 3 106407377 CTGTCATTCAACCCGTAGATTCTGGATGTCTAGTA[C/T]AAAATAGGGGTTGTGTAAATACTTGTTGAGTGGAT Y 2 1 2 1 101000 f 74 goat snp41793-scaffold543-3616511 3 10631274 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795647 Affx-122923079 AX-385282602 3 106436457 TAACCCTTCTTTAATTCCTGATGTTGTCAATTTGT[A/G]CTCTCTTTTTTTGTCATCAGTCACGCTAGAGCTTT R 2 1 2 1 101000 r 74 goat snp41794-scaffold543-3645591 3 10602268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419556 Affx-122945412 AX-123289904 3 106469603 TTGTACATTAGTTCTGTGGCAAGAACTGGGGATTT[A/G]CTAGTTACCAGTGTGAGAGTTGGACTGTGAAGAAG R 2 1 2 1 201000 f 74 goat snp41795-scaffold543-3678737 3 10568666 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387612 Affx-122969872 AX-123257970 3 106542261 TTCCTCTCTTTGCCCCTCTTCCTCATACATAAAAA[C/T]AGAAAAAGCACTGCAAAGAAAAGGCCAGATGATTC Y 2 1 2 1 102000 f 74 goat snp41796-scaffold543-3751395 3 10495582 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272179 Affx-1111833373 AX-519545931 3 106579784 GTATGGCCTAACATATGATGTATCCTGGAGAATGT[A/C]CTGTGTGCACTTGAGAAGAGTATGAGTTCTACTGC M 2 1 2 1 303000 f 74 goat 3_106579784_AF-PAKI 3 106579784 G T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38397891 Affx-122961958 AX-123268246 3 106593421 AACCATTGATATTTCATTGGAATTGTATCAGAACT[A/G]TATTTTACTTTGGGAGTAACTAATTTCTTTCATTT R 2 1 2 1 101000 f 74 goat snp41797-scaffold543-3802555 3 10444299 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379821 Affx-122976223 AX-123250179 3 106633729 CTGAGCCACAGAACGACAAGCATAATAAAATTGTC[A/G]TTTTAAACCACTAAGTTTATGGTGATCTGTTAAGC R 2 1 2 1 103000 f 74 goat snp41798-scaffold543-3842863 3 10403504 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380320 Affx-122975383 AX-123250678 3 106699483 GACACAGACTTTGGAGACAAGGCTAAAAGATTAGG[C/T]GAAGGCCAGGAAGTGGATGATGAGGTGGGTGAAAA Y 2 1 2 1 101000 f 74 goat snp41799-scaffold543-3908617 3 10337000 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794214 Affx-122921986 AX-385281180 3 106739463 TTTGTTGTGCCAGAAACTAAGCAGTGCTCAAAGAA[C/T]GATGCAATATTCAAAAGTACACATGAGCCAGCTTG Y 2 1 2 1 101000 f 74 goat snp41800-scaffold543-3948597 3 10296943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411637 Affx-122951577 AX-123281987 3 106774246 GGTGTCTACTGCTACTTCAGAATGATTTTAGATTC[C/T]ACCCCACCCCCATGAAGTTTCTTCCTATTTTTTAT Y 2 1 2 1 201000 f 74 goat snp41801-scaffold543-3983380 3 10262086 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781233 Affx-122944926 AX-385268318 3 106852182 AAAAATTGAAACTTTTTTCACAATTCAGTTAGTGG[C/T]ATAATTACTTAACCTGAACTCTTTTAGCAACAAAA Y 2 1 2 1 101000 f 74 goat snp41803-scaffold543-4061316 3 10183400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420295 Affx-122945033 AX-123290643 3 106880741 GTATAGGGTAGTGGTTAGGAGCCTGGACTTTGGAT[C/T]CAGATGAAGTAAGTTAAATCTCCTACTTTTCTGTT Y 2 1 2 1 201000 r 74 goat snp41804-scaffold543-4089875 3 10154952 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452682 Affx-122920315 AX-123323015 3 106966316 TTTTCTAGGCAGACAATTATATCATCTGAAAATAA[C/T]GATAGCTTTATTTTTCCTCTTTAATCCTATCATGT Y 2 1 2 1 303000 f 74 goat snp41806-scaffold543-4175450 3 10068570 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378173 Affx-122976958 AX-123248532 3 107023863 TATATTCTATTATTTTTAATATATTTTTAAAAATT[A/G]TCCTTTATTAGTCTTAAAAAAAAACCTAGCTTTTG R 2 1 2 1 103000 r 74 goat snp41807-scaffold543-4232997 3 10010523 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402658 Affx-122958376 AX-123273011 3 107063659 TTCCAGGTCACTTCTGCCCCTGCTGTCTGGTTCTG[C/T]GGTGAGTGAGCGAATCACCGTGCAGAGGGGGTGAA Y 2 1 2 1 103000 r 74 goat snp41808-scaffold543-4272793 3 9970900 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384961 Affx-122971910 AX-123255319 3 107093333 ACATGCTCAGGACTCGCCTGGTGGCTGTCAGTAGG[C/T]GGCTGCAGTGCTTGGGCGGGAAGGACAGAGCTGTT Y 2 1 2 1 101000 f 74 goat snp41809-scaffold543-4302467 3 9941165 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395921 Affx-122963595 AX-123266276 3 107123677 TAAACCTCACTGAACTTGCAACACTTGGCCTGTTC[C/T]GGACCCTCAGGGCTGGGGTGTGCTCAGGACTGGTT Y 2 1 2 1 101000 f 74 goat snp41810-scaffold543-4332811 3 9910480 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782298 Affx-122942166 AX-385269376 3 107212203 CTTTCGGGGTGTCCTCTAAAAATACCACAGGCAGT[C/T]TTCTCTGTGTGCTTGCTCACTCTTTTCCCTTGCGG Y 2 1 2 1 102000 f 74 goat snp41812-scaffold543-4421337 3 9822999 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391665 Affx-122966551 AX-123262022 3 107238060 ATTATACCACACATAGTATCAATATGGTGGTGCTT[A/G]TGAAGGATGCATGTTACCTTACAGCAGAACTGACT R 2 1 2 1 101000 r 74 goat snp10650-scaffold1378-5076 3 9797033 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451304 Affx-122921289 AX-123321637 3 107281325 AGGTAGGCTGTTGGGCTGCCATTTCTGCTGAGTTC[A/G]TTGTGACAGTTCATCCTTTGTTGGTTTCCAACTCT R 2 1 2 1 101000 r 74 goat snp10651-scaffold1378-48341 3 9752840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433257 Affx-122935234 AX-123303598 3 107355424 TCAGGGTATTCTTGTGAGTTTGATCCAGCTTTGGC[A/G]TTGGGGTAGGGTGTCAGATCAATCATGCAAGACGC R 2 1 2 1 101000 f 74 goat snp10653-scaffold1378-122440 3 9678388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791379 Affx-122921562 AX-385278371 3 107389035 TAGCTTGTGTGAATGCTGATATTGAGAAATTTGAT[A/G]CTATCTTGTTCCTAATATTTTTGAAAATCAGTGGG R 2 1 2 1 101000 r 74 goat snp10654-scaffold1378-156051 3 9644394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386822 Affx-122970099 AX-123257180 3 107422236 CGTTTTTACACCCCGGATTTCCTTGGAAACTCAGT[C/T]GTCCCTCTCCATATGGCACTCTCTGTGGTGCTTTA Y 2 1 2 1 201000 r 74 goat snp10655-scaffold1378-189252 3 9610997 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420721 Affx-122944775 AX-123291068 3 107490582 GGTCTCTGCTAGCCCAGTATGGAGCTCCTCTCTTC[A/G]TCAAGATTTTCTTCTGAGGGATACAGACGGGTGCT R 2 1 2 1 101000 r 74 goat snp10657-scaffold1378-257598 3 9542132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768563 Affx-122975896 AX-385255743 3 107551739 TACTTAAGATACTTTGTTTTATACATTAGAGAAAG[C/T]AAAGGGATATAGAGAGTGGTAAGACTTCAATACCT Y 2 1 2 1 101000 r 74 goat snp10659-scaffold1378-318755 3 9480693 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444814 Affx-122926326 AX-123315151 3 107608507 TGGGGTCTCAGGAGTCACCTTTGCATCTATCCATC[A/G]TTTCCAGGAAAGCAGAAGCTAGAGTCTTGCATCTT R 2 1 2 1 201000 f 74 goat snp10660-scaffold1378-375523 3 9423534 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776068 Affx-122956959 AX-385263198 3 107646845 CACACCCAGCTCTACACCATTTTTAATGACTACAT[C/T]GCAATCCTTTGGGTCAATATTCTAAAATTCATTTA Y 2 1 2 1 101000 f 74 goat snp10661-scaffold1378-413861 3 9384899 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439977 Affx-122929807 AX-123310314 3 107675518 CAGTGGCCACTGCAGATGTTAACCCTCTCTCAGAC[A/G]CCACATTCCCTTCTCTCTGAGCAGCTTAATTCACG R 2 1 2 1 101000 r 74 goat snp10662-scaffold1378-442534 3 9356013 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434960 Affx-122933848 AX-123305300 3 107707616 TGTGGACCACTTTTAAAGTCTTTATTTGAACGTTG[A/C]TTCTGTTTTACAGTTTGTTTCTTAGGCCACGAGGC M 2 1 2 1 101000 r 74 goat snp10663-scaffold1378-474632 3 9323556 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404580 Affx-122957363 AX-123274932 3 107779942 CCAAGCTGCTCAGCTGTTCAGCATACTGACTGCCC[A/G]CTCTCACCCTGCACACCCTTATCTAGTTTAAAAAG R 2 1 2 1 101000 r 74 goat snp10665-scaffold1378-546958 3 9254628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411329 Affx-122952272 AX-123281679 3 107811817 ATACCTGGATTGTTGTACTTGGTTCTGGTTGCTGC[A/G]CTGCCCTAAGAACCAGCAGCGTGGGCAGGAAACTG R 2 1 2 1 202000 r 74 goat snp10666-scaffold1378-578833 3 9222802 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404561 Affx-122957377 AX-123274913 3 107847070 AGACACCTGCTGAATTCCGCCTTGTCCAAGTCGTG[C/T]GTGCCCCGTGCATTTTCGCCATTCTGCCTCCTCTG Y 2 1 2 1 101000 f 74 goat snp10667-scaffold1378-614086 3 9188351 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432143 Affx-122936430 AX-123302484 3 107881997 ACCTCGTCCAGGCAACCTTCCCCACTGCCCCTCAG[C/T]AGAGGCTACTGGACTATAAAGCATTTGGCGACACC Y 2 1 2 1 101000 r 74 goat snp10668-scaffold1378-649013 3 9155917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778483 Affx-122935031 AX-385265597 3 107921691 ATGGAGAGGAGCCAAATAAGAATGAAGACCCAGGC[G/T]CGAATGAATCTGGGCGGGACATAAGAAATGTGTTC K 2 1 2 1 101000 f 74 goat snp10669-scaffold1378-688707 3 9116288 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422842 Affx-122943103 AX-123293188 3 107950974 ATTCATTTACATATTTGTCTTAATCACCTCAGGTT[A/G]CTAGAACAAAAACACCTTAGACTGGGTGGCTTATA R 2 1 2 1 201000 f 74 goat snp10670-scaffold1378-717990 3 9086046 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420736 Affx-122944764 AX-123291083 3 107970702 CTTCCTACAGATACCATGGGATTATGCATTAAAAC[A/G]GGAGATCGACACACTCTTTGACCCGGCAACTGCAC R 2 1 2 1 201000 f 74 goat snp32019-scaffold3595-128545 3 9066689 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380319 Affx-122975384 AX-123250677 3 108007017 TTTGGAACGGCAGTTAATTTAGATTTTCCTGTTGA[C/T]GTACACCTGACAGTTCTTATTCCCACATGTGACCC Y 2 1 2 1 101000 r 74 goat snp32018-scaffold3595-92230 3 9030422 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413934 Affx-122949807 AX-123284283 3 108050024 TGCAAGCAAGGAACGTTAGGTCAGCTTGGTTCTCA[C/T]AGGGGACTTGAAGCTGGACTCAGCTGATTTCCAAA Y 2 1 2 1 201000 f 74 goat snp32017-scaffold3595-49223 3 8987512 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427922 Affx-122939223 AX-123298265 3 108081147 CAAAGAGGGTGAGGAGTGTCAGATGCCCCTGGCAC[A/G]TCTGATTTGGCCACCTTGAATGGTAACACGCATCA R 2 1 2 1 101000 r 74 goat snp32016-scaffold3595-18100 3 8956181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804566 Affx-986696734 AX-385291105 3 108102821 AGCAGGCTGTGAGCTGCATTCTGGGGAGGCCATAG[A/G]AAGCTCTTTGAGAGGAGCTTTAGGAGGACTGGATT R 2 1 2 1 600010 r 74 goat 3_108102821 3 108102821 Ancestral_priority_1043 ancestry 0.528 neutral IMAGE 10K 10K ancestral 38392739 Affx-122966016 AX-123263096 3 108107693 ACTCCATTAACCCTCACACTCAGTAGTATCACACC[A/G]CAAAGGTTTATTTCCTGCTTACGCTGCACGTCTGT R 2 1 2 1 101000 f 74 goat snp22160-scaffold219-8347 3 8929232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380225 Affx-122975477 AX-123250583 3 108158019 AGTTTTATGAAAATAAACTAGTTACGTGTGTGATG[C/T]ACTCTTTTCTTTTCCATTCTATACTCTTGTAACCT Y 2 1 2 1 201000 f 74 goat snp22161-scaffold219-58673 3 8878414 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435809 Affx-122932844 AX-123306148 3 108218076 AATCCTGGCTTCAGCCACACTGCGCTCCTGGATCA[C/T]AGACACAGCTGGCCCTTTAAAACCTCTGTCCAGCA Y 2 1 2 1 101000 r 74 goat snp22162-scaffold219-118730 3 8818355 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439268 Affx-122930988 AX-123309605 3 108250343 AGATGATCTGGGTGCGCTGAGAGAATTAGGGATTC[A/G]GCATCTGGAGACCTGTGTCAGTCTTGGCTCAGTTT R 2 1 2 1 101000 f 74 goat snp22163-scaffold219-150997 3 8787382 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428148 Affx-122939050 AX-123298491 3 108280994 CTCCCTGAGGTTAGGGAACCTTCCTCGGCCTTGTA[G/T]CCCCACAGCTGGCTTATTATGGTCTGACACCCGCT K 2 1 2 1 201000 f 74 goat snp22164-scaffold219-181648 3 8756877 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425732 Affx-122940753 AX-123296078 3 108310541 ACCAGGAACATGCCCCCCTGAGAAGGAGATAAACA[G/T]CTCTGGGCTCTAATTCATGGTGTGGCGGGCAACAC K 2 1 2 1 202000 r 74 goat snp22165-scaffold219-211195 3 8727808 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793091 Affx-122943414 AX-385280069 3 108347117 GATGGACAGTCGCAGAGCCTTCATTTACAGGGTGA[C/T]GATGACGAGAGAACAAGTCCAAGTTTACTTGGCAA Y 2 1 2 1 101000 r 74 goat snp22166-scaffold219-247771 3 8691971 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446166 Affx-122925746 AX-123316502 3 108383432 CTTCCCTTCAGCAGTCTTTCCAGGAGTCCCACATG[C/T]ATCCACTTTGTTGTTCAGTTGCTAAGTCGTGTCCA Y 2 1 2 1 201000 f 74 goat snp22167-scaffold219-284086 3 8656432 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404198 Affx-122957675 AX-123274550 3 108419076 CTCTAGTCCCCTGGTTATTCGTTACTCAGTTTGGG[C/T]AGCCTGCCTCTCACTTATCCTGTCTAGTCACTGAG Y 2 1 2 1 102000 r 74 goat snp22168-scaffold219-319730 3 8620937 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451467 Affx-122921143 AX-123321800 3 108449457 CCTTTGCGCTCCTTTGGTCAGGCCTCTTTCCTGGC[C/T]GCACAGAACTTCCCCCTGAGGCTCCCTGGCAGAGG Y 2 1 2 1 101000 r 74 goat snp22169-scaffold219-350111 3 8590964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427341 Affx-122940118 AX-123297684 3 108478556 TTAACTGAGTTCCTGTTTCCAATTATTTATTTTGC[A/G]TTTGAGAAACAAATGCATTATTTGTTTTTTCACAT R 2 1 2 1 103000 f 74 goat snp22170-scaffold219-379210 3 8561839 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398692 Affx-122961861 AX-123269047 3 108524317 GGTCATCCAGGAGCAAAAGCCACCCAAAGAGACAC[A/G]AGGAAGGAAAGTAAAGGCTAGTAAAAACTAGCATT R 2 1 2 1 101000 r 74 goat snp22171-scaffold219-424971 3 8516018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415493 Affx-122948697 AX-123285842 3 108569184 TTCCTGCGTGCTGGAAGAGTGTTAATTGTTATTAG[A/C]GTAATAATCACCAGAATAATTTTAATATAAATCCA M 2 1 2 1 101000 f 74 goat snp22172-scaffold219-469838 3 8471276 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773865 Affx-122946433 AX-189247382 3 108600826 CCCTGGTTATATTGGATGCTAATATTAGGGGAAGC[C/T]GGAAGAAGGGTATACGGGAACTTTATGTACTATTT Y 2 1 2 1 101000 r 74 goat snp22173-scaffold219-501480 3 8439761 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404609 Affx-122957341 AX-123274961 3 108634143 TTGTGTGATGTGGGAGGAGCTGGAAGGAGGTGGCA[C/T]GATTTCTGGCGGTTTCATCTTTGCAGAGAGCTTCC Y 2 1 2 1 101000 r 74 goat snp22174-scaffold219-534797 3 8407402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414869 Affx-122949144 AX-123285218 3 108669231 ATCCATTTCCTTGGGTCATCCTTTTCTGTGTCTCT[C/T]CTTTCTTTCTCATCCAGCCTCCTTGTTCTCATTCT Y 2 1 2 1 101000 r 74 goat snp22175-scaffold219-569885 3 8372344 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414851 Affx-122949182 AX-123285200 3 108707171 TTATTTTACAGTTTTTAAAAAATTCTTTTAAATTT[A/G]TTTAGCAAATAAGTCTAACAAATTTTCATCAGGCA R 2 1 2 1 103000 r 74 goat snp22176-scaffold219-607825 3 8334419 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404302 Affx-122957027 AX-123274654 3 108767340 CAGTTTAGAATTGGGAAGATGATGTCAGACCTAAG[A/G]TTCAGTGATGGGGACTAGGAAAAACCATTGTGTTT R 2 1 2 1 101000 f 74 goat snp22177-scaffold219-667994 3 8274317 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766026 Affx-122961381 AX-385253444 3 108804261 AAGGTATGCTCTCTTATTTTAAAGTTCTGAGTCCA[G/T]ATATTGTTCCCTCTTAAGTATTTGTGTTTATAGTC K 2 1 2 1 101000 f 74 goat snp22178-scaffold219-704915 3 8239694 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278177 Affx-1111836211 AX-519551666 3 108839115 AAAAGACTGTGACGTTCAGGGTGATACTTAAGCAT[C/G]AAGCATTCTCAAAGGTGAATTTCAAGCAGTGCACA S 4 1 2 1 101000 r 74 goat Random2.2K-380 3 108839115 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392322 Affx-122966698 AX-123262679 3 108871088 TTGCCAGAACAAGTTGCCTGACTTGCTTTGATAAA[C/T]GGAAAGATGACCTGATGCAGACGTCTCTGATTTGG Y 2 1 2 1 101000 f 74 goat snp22179-scaffold219-771742 3 8177011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401722 Affx-122959528 AX-123272075 3 108918605 GAAGGCAACTGGTGATTTTGTGCTCAGGGCTGTCA[C/T]GCACAGCAGCTCAGGTTGTGCACTGCCCAACACCA Y 2 1 2 1 101000 f 74 goat snp22180-scaffold219-819259 3 8129403 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274005 Affx-1111833947 AX-519547610 3 108961002 CTGTGGCTTGATATTTCACAGTCTTTGCTGCAGAT[A/G]TTTCCTCTTCCTAAACTGTTTTTTTCACCAAATAT R 2 1 2 1 201000 r 74 goat GoatD01.011258 3 108961002 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38398412 Affx-122961630 AX-123268767 3 108992924 GCGAACTAGGCAGATTGCTTCCTGACTCATGAGAG[A/G]CAACATCCTAACTAGGTCAAGGCTGGGCCTGCACA R 2 1 2 1 101000 f 74 goat snp22182-scaffold219-893578 3 8054668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413577 Affx-122950584 AX-123283926 3 109034992 GGAGATGCTGAGAGAGCAGGACCCCAGGTAAGCCA[A/G]CTATGGTGTCAAGGCCTTTTAATGACCCTGCTCCA R 2 1 2 1 101000 r 74 goat snp22183-scaffold219-935646 3 8012715 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797404 Affx-122948469 AX-385284343 3 109063609 ATAAAACACTCTCATAGGTTCCAGGCAGCATTGAG[A/G]CATGGGCATCTTTGAGGCGCTGTGGTTCTAGCTCC R 2 1 2 1 101000 f 74 goat snp22184-scaffold219-964263 3 7983688 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422314 Affx-122943469 AX-123292660 3 109123595 CAGAAGGTAGAACAAAAGGATAAAAGGAAGAAAAA[C/T]AGGAGAGAAGAGGTTTTTAAAAATTAGAAGACCAG Y 2 1 2 1 202000 f 74 goat snp22185-scaffold219-1024249 3 7924454 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418458 Affx-122946469 AX-123288806 3 109159738 GAAACCACGGCTGCAGTTGAGATTAGAATTTCCCA[C/T]GCGGTTCCTGTTCTTCCTCGTGGCCACGTGGTGCG Y 2 1 2 1 101000 f 74 goat snp22186-scaffold219-1060392 3 7888065 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427323 Affx-122940131 AX-123297666 3 109196014 TTTTCTCTTTGAACCTCACTTACTAAATATCAGCC[A/G]AAATTATAGAGGTTTGTTTGTTTGTTTGTTTAATC R 2 1 2 1 101000 f 74 goat snp22187-scaffold219-1096668 3 7853048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790803 Affx-122934010 AX-385277803 3 109232665 TAATGCCAATGGCCATCGCCTAGGAAAAAAATGAC[A/G]TTTTATCTAAGCTTGAGACTAAAGAGACGAGTATG R 2 1 2 1 101000 f 74 goat snp22188-scaffold219-1133319 3 7816460 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418573 Affx-122946379 AX-123288921 3 109309203 TTCCTGAGCCTCAATTTCCATATCTGTAAAGTAGC[A/G]ACGATAGTAATAGTTCTCAGGTCTGTGAAATAGAA R 2 1 2 1 201000 r 74 goat snp22190-scaffold219-1209857 3 7739171 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448249 Affx-122924202 AX-123318585 3 109347309 TCTGTAATTCTGGTTCATGTGCTTTGTCTTGTTCT[C/T]TGGGAGTTCGGCAAAATCATTCTCTCACTGTTTCA Y 2 1 2 1 101000 r 74 goat snp22191-scaffold219-1247963 3 7700830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389008 Affx-122968643 AX-123259366 3 109376663 TTTTGCTGTGTGGCTTCTTTCAGCATTGTAAAGCT[A/G]TTACTTTGTGCGGCTGCAGGTGGACTGTTCTTGCT R 2 1 2 1 101000 f 74 goat snp22192-scaffold219-1277317 3 7671560 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412731 Affx-122950729 AX-123283080 3 109405945 TATATAAGAAAGTGTCAAAGCTAGAAAAAGATGGA[C/T]GTTATCTCAGTTCATTTTTTTTTTATTGTGGTAAG Y 2 1 2 1 101000 f 74 goat snp22193-scaffold219-1306599 3 7642218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802792 Affx-122921361 AX-385289691 3 109444137 TTCAAGCCAACCAAAGTACTCCTTTAGTGAGTACA[C/T]AGAATTCTTTAAAGGATATTATGTAAACCCTAGCC Y 2 1 2 1 201000 r 74 goat snp22194-scaffold219-1344791 3 7598497 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426260 Affx-122940328 AX-123296606 3 109496699 TGGGCTTTGGAGGCAGGCAAGACCTGATTTTTTTC[A/G]TCCCTGTTCCACACTACCTGTGTGACCTTGGGCGA R 2 1 2 1 101000 f 74 goat snp22195-scaffold219-1397353 3 7546305 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781866 Affx-122931000 AX-385268948 3 109557440 GACTGCCCTTTCCAACAGCGTCTGTTGTAATGGTC[A/G]TGCAGTTTTCTGAATCTAGTAAGAGCCAGGAACTT R 2 1 2 1 201000 f 74 goat snp22196-scaffold219-1458094 3 7485126 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436615 Affx-122932508 AX-123306953 3 109639368 TGCATTTGGAATTTTTGTTTTCATTTTAGACACAT[A/G]CCTGCTAGATTGTTGCACACAGGTTTATGACTGCT R 2 1 2 1 101000 r 74 goat snp22197-scaffold219-1540022 3 7402582 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376114 Affx-122978880 AX-123246473 3 109676619 CCGCAGAACTTTATCAACTGTCTTTCTTGATATCA[C/T]GTCTTTATATCGTTTATTGACATATTTGCCCCTAA Y 2 1 2 1 101000 r 74 goat snp22198-scaffold219-1577273 3 7365026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771314 Affx-122973025 AX-385258472 3 109822076 CCATCAGCGTCACGGACAAGCGTGTCTGCCCGTCA[C/T]GGAGTGTTTGTGTGTTGTTGTCAGCTCACTGCGGT Y 2 1 2 1 102000 f 74 goat snp22201-scaffold219-1722730 3 7217267 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408970 Affx-122953914 AX-123279321 3 109929446 TCCATACATTGGTGTCAGCCACTCAGGATGATGGT[A/G]CATTCTGTGTAGAATGGTTCTGTCACAATCAGCTT R 2 1 2 1 101000 f 74 goat snp22204-scaffold219-1830100 3 7110014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437728 Affx-122931736 AX-123308066 3 109980452 CACGTGTAATTAGAAGTAGAAGCTACTGGAAGGAA[C/T]GCCTTATAGCCGCTGCCCCTGCACCTCCAGATGTC Y 2 1 2 1 101000 f 74 goat snp22205-scaffold219-1881106 3 7060467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419557 Affx-122945411 AX-123289905 3 110073101 TTTACAAGCTTCAATTATTAATTAGTTTAAATGTT[A/G]CTTCTTTCTTCTATTTTCTAGGGGTCTTTGAACTT R 2 1 2 1 303000 f 74 goat snp22207-scaffold219-1973755 3 6968262 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418809 Affx-122946167 AX-123289157 3 110108356 ACCGGGGGCAGAGCCTGACCTGGAACGCTGCCCTT[A/G]TCCTAAGCCAGACACCACTCCTCAGATAGCATGCA R 2 1 2 1 102000 r 74 goat snp22208-scaffold219-2009010 3 6932930 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444656 Affx-122926463 AX-123314993 3 110139196 TGGTCAATTAGTATTTTATTTATAGTGTGGAATAA[C/T]GGTTAGGAGAAAATTGGCATTCCCATGGTGGTACA Y 2 1 2 1 101000 r 74 goat snp22209-scaffold219-2039850 3 6901718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411480 Affx-122951794 AX-123281830 3 110172542 AACTGTCATCCCCTTCATAGATTTCAGCCCTCCCC[A/G]TGGTGAAGATGCTAACTTGACTGATAATCAGACAA R 2 1 2 1 101000 r 74 goat snp22210-scaffold219-2073196 3 6868425 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445599 Affx-122925117 AX-123315936 3 110211996 TCCTTACATGTCTCGTTCCAGACTATAGTAAGTCA[C/T]GATATGTAAGAATATCTCCATCATAACAACTGAAT Y 2 1 2 1 101000 f 74 goat snp22211-scaffold219-2112650 3 6827435 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439205 Affx-122931035 AX-123309542 3 110251841 CTGTTGCTATTTAAGGTGATGTTTAGAGTTCCTAA[C/T]GATGTGCAAAGAAAAAAAAAAAGTGTACACTATAA Y 2 1 2 1 101000 f 74 goat snp22212-scaffold219-2152495 3 6787570 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429804 Affx-122938195 AX-123300145 3 110356767 TGAAGGCAGGCAGCAGTGCCGGCAAGATGAACCTC[A/G]TAGTCTTCCAGAGATAATTAAAGGAAATGACTCTG R 2 1 2 1 101000 r 74 goat snp22214-scaffold219-2257421 3 6681861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405353 Affx-122956322 AX-123275705 3 110402425 TCTCGCACTGGTTGGAAGGAAGCCAACTGCAACAA[C/T]GTGTCTTATCAATTTTGTTTTACACCCAAGAAGCC Y 2 1 2 1 101000 r 74 goat snp22215-scaffold219-2303079 3 6636375 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801542 Affx-122959054 AX-385288451 3 110431911 CACTACTGAAAATATTCAAGGACAAGTTGAATGGC[G/T]CCTTGTCAGAGATGTGATAATAATCAATGCTCAGA K 2 1 2 1 101000 r 74 goat snp22216-scaffold219-2332565 3 6606730 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388588 Affx-122969158 AX-123258946 3 110505218 GGTGGCTGGTTTCACCTGATAACCTGAGGTCCTCT[A/G]CCAAGAAGATCTGTTTTAGATGGAAAGAAGGCTTT R 2 1 2 1 101000 r 74 goat snp22218-scaffold219-2405872 3 6532570 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464248293 Affx-1110390475 AX-515722869 3 110532386 TCCATGGACAAACCCACAATGTACTCACGGCAAAT[A/G]GTGATAAGCTGCTGAGCCTGGAGAGAGGGGACAAA R 2 1 2 1 101000 f 74 goat ilmnseq_rs660465535 3 110532386 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275625 Affx-1111835002 AX-519549195 3 110532565 GGCACACTGAGTAAAATGGAGCGGAACTTTTCCAC[A/G]GCCTCCTCAAACTTGCCGACTGTGGTGAGCTGGTA R 2 1 2 1 101000 f 74 goat ilmnseq_rs639500528 3 110532565 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276130 Affx-1111835183 AX-519549680 3 110533011 AGCTCCTTCACGACCAAGTAGGGGTAACCCAGTTC[A/G]GCCCCTACAAGCAACTGTTCCTGCAGACCTATGCC R 2 1 2 1 202000 r 74 goat ilmnseq_rs661460057 3 110533011 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276243 Affx-1111835239 AX-519549792 3 110533012 GCATAGGTCTGCAGGAACAGTTGCTTGTAGGGGCC[A/G]AACTGGGTTACCCCTACTTGGTCGTGAAGGAGCTG R 2 1 2 1 101000 r 74 goat ilmnseq_rs667085686 3 110533012 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275894 Affx-1111835063 AX-519549452 3 110533800 CAGGGCTATATTTCTCTGCTTACCTGAGTTGGGCT[A/G]GTTCCCTTGGTTGGGGGCACAAAGAACCCATCCTC R 2 1 2 1 202000 r 74 goat ilmnseq_rs646426062 3 110533800 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468275931 Affx-1111835157 AX-519549489 3 110533832 GCTGGTTCCCTTGGTTGGGGGCACAAAGAACCCAT[C/G]CTCAGCTCCACCAGCTGCCCCGGAGGGTATATCCT S 4 1 2 1 101000 f 74 goat ilmnseq_rs657521433 3 110533832 C G 1 recommended Goat_IGGC_65K_v2 Illumina 468276177 Affx-1111835279 AX-519549727 3 110534680 ACCAGCTCAGGAGGAAGCTCCAGATCTTCTTCCAC[A/G]TCCCAGCCACCTCCTTCTTCTTGTCCCTTGCCAAG R 2 1 2 1 102000 f 74 goat ilmnseq_rs671093869 3 110534680 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275925 Affx-1111835154 AX-519549483 3 110534972 GAGGCGCGCTGGCTGCTGACATCGACATTGACACT[A/G]TTGGTACTGAGGGCTGGGGAGAGGATGCCGAGCTG R 2 1 2 1 202000 f 74 goat ilmnseq_rs657418381 3 110534972 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276186 Affx-1111835210 AX-519549736 3 110535000 TTTCTGTCCCTTCGCGCTGTAGGGAAGGGAGGCGC[A/G]CTGGCTGCTGACATCGACATTGACACTGTTGGTAC R 2 1 2 1 101000 r 74 goat ilmnseq_rs663834397 3 110535000 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275584 Affx-1111834983 AX-519549154 3 110536192 GAGAGCCTGAAGGAGACATTTGACCCAGAGAAGGA[A/G]ACAGTGAGTCTTTATGTAAAGTGTCTCTGATTACA R 2 1 2 1 101000 f 74 goat ilmnseq_rs636676154 3 110536192 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276113 Affx-1111835247 AX-519549664 3 110537448 TATCAGAATGCTCTCTACCTGGGAGATGTGTCCGA[A/G]CGAGTGCGGATCCTGAAGAACTGTGGACAGAGTAA R 2 1 2 1 201000 f 74 goat ilmnseq_rs667713149 3 110537448 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468275941 Affx-1111835085 AX-519549499 3 110548134 TCACGCTCTTTGATGTACAGCAGAAGCGGTAACAT[A/G]TCAGATATCCCTATGCAGACAGGTTTATAGTGGGG R 2 1 2 1 101000 r 74 goat ilmnseq_rs649458664 3 110548134 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275911 Affx-1111835146 AX-519549469 3 110558928 CGATCATGGTCCCTGCGGAATGTCTGAACTCCAGT[C/G]CTAGGAAAGCAAAAGGTATACAAAGAAAAATATTA S 4 1 2 1 101000 f 74 goat ilmnseq_rs656488281 3 110558928 C G 1 recommended Goat_IGGC_65K_v2 Illumina 38444088 Affx-122926837 AX-123314425 3 110559650 TCACCCTGGCCTGTACTCCAGTCCCTGGAACCACC[A/G]TGCTCTCTGGCCCCACACGCTTGAGCTTGCCCTTC R 2 1 2 1 201000 f 74 goat snp22219-scaffold219-2460304 3 6477783 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395041 Affx-122964205 AX-123265396 3 110614740 AGACCACAGCCCATGGGAGAAAAGACCACGGCCTC[A/G]CCAGGGAGGCAAGACCCAGGGTCACCAGATGCCTT R 2 1 2 1 201000 f 74 goat snp52716-scaffold790-42071 3 6422063 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789841 Affx-122960001 AX-385276848 3 110659633 TCCAGCTTCTGGATGTGTAGGATTTTCTGAAATGC[A/G]TGGAGTAGACTCAAACTTTTCAGCTTCAACAAATC R 2 1 2 1 101000 f 74 goat snp52717-scaffold790-86964 3 6377130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789327 Affx-122952073 AX-385276337 3 110711320 GGGACAACACATCAAGTGCAGGCAGGGAGAAGATA[C/T]ACGTGTCTACACCCATTTTAACTTCAGTCTCGGAG Y 2 1 2 1 101000 r 74 goat snp52718-scaffold790-138651 3 6325072 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376952 Affx-122977768 AX-123247311 3 110745986 CTCTGCTCTAGGCTGTGAACACACACACACATACA[C/T]GCTAGTCAAGTCAGAAAAAAGAAAGTGGTAGGTGT Y 2 1 2 1 201000 r 74 goat snp52719-scaffold790-173317 3 6290876 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437884 Affx-122931672 AX-123308222 3 110779667 AGAGAATCAGACATGAATGAAGCGACTTATGCCCC[A/G]GAACCTGCTGCAATTATTCAAAACAGCCAGTCCCA R 2 1 2 1 201000 r 74 goat snp52720-scaffold790-206998 3 6258008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424569 Affx-122942224 AX-123294915 3 110825438 GACAGGGTGCCTGTGTTCAATTAAACTGTGCTTCT[G/T]CACACTGCGATCTGAATTTCATATTTTTAAAACAT K 2 1 2 1 101000 f 74 goat snp52721-scaffold790-252769 3 6212113 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379967 Affx-122975634 AX-123250325 3 110872410 GAAGGGAGAGAGTGGAATTGGTTTTTAGACACAAA[G/T]AGATTTCTGCTGGAGGGCTTTCCTGGTCTTTGGTT K 2 1 2 1 201000 f 74 goat snp52722-scaffold790-299741 3 6166245 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385949 Affx-122971545 AX-123256307 3 110933251 GGTAGTGGGGGTGTATGTGTCCTCTAGGGTGGTGG[G/T]GGTCGGGTCATTGATAAAGAGAAATGGATCTTAGC K 2 1 2 1 103000 r 74 goat snp52724-scaffold790-360582 3 6104728 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434041 Affx-122934205 AX-123304382 3 110967860 AGGGGTGGAATTGCTGGGCCAGATGTTAGGTGCCC[A/G]TTAAACTTTATAAGGAACTGGAAGACTGTAAAAGT R 2 1 2 1 201000 r 74 goat snp52725-scaffold790-395191 3 6069589 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774727 Affx-122934482 AX-385261861 3 111045639 ACAGCGAGCACAAATGACCAATGAAATGGTCCTTG[A/C]TCCAAATGATCCATGTGGTATTTCTCCCCGTATGA M 2 1 2 1 101000 f 74 goat snp52727-scaffold790-472970 3 5990538 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411843 Affx-122951227 AX-123282193 3 111157014 GGCTCTCCTACAGCTCTGCCCCTTGCTTAGGAAAA[A/G]TAGCTGGTTGTTTAAACAGTCAAGGTGAAATACAA R 2 1 2 1 101000 r 74 goat snp52729-scaffold790-584345 3 5878885 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278179 Affx-1111836212 AX-519551668 3 111222666 GGTGAGTCACAAGACTGTTAAAGTTTGAGAAGCAA[A/C]GTGTTAAAGGAAGGTGATTTGGGGAACAAAAGAGA M 2 1 2 1 102000 r 74 goat Random2.2K-382 3 111222666 G T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408972 Affx-122953913 AX-123279323 3 111252380 ATTAGCACTGAAACCTACTTCCTGGCAGCCCCATC[A/G]CTCAGATTACTTGCTAATTTTTCTGTTTGCAAAAC R 2 1 2 1 201000 r 74 goat snp52731-scaffold790-679711 3 5784974 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380962 Affx-122974991 AX-123251320 3 111331594 ATGGGGCTGGCTGTCTTCCCTTTGTCTGAAGATGA[C/T]GGTTCTGCCTCATGCCTCCTGCCACGTTCAGCTCT Y 2 1 2 1 101000 f 74 goat snp52732-scaffold790-758925 3 5705906 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427737 Affx-122939261 AX-123298080 3 111371741 AGTTAGCCTGGTGCTTTCAGGTTTCATCCCTGTTG[C/T]AGCGTGTATCCGAATTCCCTCCCTTTTCACCGACG Y 2 1 2 1 201000 r 74 goat snp52733-scaffold790-799072 3 5666704 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412353 Affx-122950828 AX-123282702 3 111420666 GAAAAAAAAAAAAAAAATTGGCAGAATGGAATAAA[A/C]GCCTTAGCAAGGTATGTGGCCTTTGACCTAGCTTT M 2 1 2 1 101000 r 74 goat snp52734-scaffold790-847997 3 5618660 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415545 Affx-122948656 AX-123285894 3 111459414 CAGCCTGGGAACCAGGGAGCTGGTGACACCTTGGC[C/T]AATGAAGGCAGGAGGCTGATCACATGTCTTTCATT Y 2 1 2 1 101000 r 74 goat snp52735-scaffold790-886745 3 5580712 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452333 Affx-122920656 AX-123322666 3 111506485 ATCAAGAAAAATAATAAAATACGAAGCAGTAGAAA[G/T]CCGTAGCTATGTTGCTTTTTCGGTAGTAGTGGCAG K 2 1 2 1 101000 r 74 goat snp52736-scaffold790-933816 3 5533863 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804537 Affx-986696705 AX-385291086 3 111522308 CCCATGACTTCTGTTAGTATCAGCATAATCATACA[A/T]TGTCAAGAGATTCCTAAATCTCGGAAGTCAGGTCC W 4 1 2 1 600010 r 74 goat 3_111522308 3 111522308 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 38379161 Affx-122976714 AX-123249520 3 111549985 CCATAAAGTATGTGAAGCTACTGCGCCAGCAGTGC[A/G]CGGAGGCAGAAGTGAAAGAAGTTTCATCCGCTCAT R 2 1 2 1 101000 f 74 goat snp52737-scaffold790-977316 3 5490907 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418714 Affx-122946283 AX-123289062 3 111598884 CCAGCATCACAGGTGAGACAGAGGCGGAAGTCCAC[A/G]GGGTTTCACAAGACCCCTTCAGAGACGGGGGAACT R 2 1 2 1 201000 f 74 goat snp52738-scaffold790-1026215 3 5441606 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381539 Affx-122974839 AX-123251897 3 111631111 GGACTCCAAGAAAACCTCCGCACCAGTGGTTTTCC[A/G]TCTTGGAGATACATCTGTTCACGTCGCTGCACACA R 2 1 2 1 201000 r 74 goat snp52739-scaffold790-1058442 3 5409301 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392666 Affx-122966431 AX-123263023 3 111659662 AACTGGAAAAATCAAGAAGGGTCTGTGCATCCTGG[C/T]GGGAATAGGTTTTTTCTCCCTTTCTTTTATTTCGA Y 2 1 2 1 101000 f 74 goat snp52740-scaffold790-1086993 3 5380268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777737 Affx-122927589 AX-385264855 3 111693725 ATACCTTTAAAAAGTATATGTGAAATTGGGGTGAT[A/G]TTGAGTGCATTTCAGAGCTGTGTGTTTTATTCTGA R 2 1 2 1 101000 r 74 goat snp52741-scaffold790-1121056 3 5346420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454133 Affx-122919339 AX-123324466 3 111740812 TAGAGATACTGTTTTGTTACTGATTTTTCTCATGT[A/G]TTAAAGTTGTATTTGTGGGAGTTCCCTGGAAGTCC R 2 1 2 1 202000 f 74 goat snp52742-scaffold790-1168143 3 5299683 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464248844 Affx-1110390750 AX-515723413 3 111802936 ATCTGAGGTTATTGATATTTCTCCCTTGATTCCAG[C/T]TGGTGCTTCATCCAGCCTGGCATTTCGCTTGATAT Y 2 1 2 1 103000 f 74 goat 3_111802936_AF-PAKI 3 111802936 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38379981 Affx-122975622 AX-123250339 3 111806829 AACCCTAACACGGAAGTCCCAATTCTGACAACAGA[C/T]GTCACAAGCACAGAGGACGGCAGTTTCCGCACGAG Y 2 1 2 1 101000 f 74 goat snp52743-scaffold790-1234160 3 5233653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801026 Affx-122944751 AX-385287940 3 111843331 TGTCTGCATATACTGTATTGTTCGTGCATCTACAC[A/G]CATGTACCTGTGATTTCACCACCAGTCAGCACTGG R 2 1 2 1 101000 r 74 goat snp52744-scaffold790-1270662 3 5197690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781486 Affx-122978613 AX-385268571 3 111915776 TAACACACATATTCTAAATGATCACATGAAGGTCT[A/G]TGATATTTCTGCATGTGGGTGGCCGAGTGCCCCCA R 2 1 2 1 101000 r 74 goat snp52746-scaffold790-1343107 3 5125372 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419514 Affx-122945446 AX-123289862 3 111982177 CTTGACTAGGGATATTACTGTAAATAAATCATAGA[C/T]GACCAACAAATATGGAGACAAAGAAACCACAAAAC Y 2 1 2 1 101000 f 74 goat snp52748-scaffold790-1409508 3 5058744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387436 Affx-122970386 AX-123257794 3 112072099 TTCCTCAAAATGCAGAGGAACATTATCATTTTACA[A/C]AGGAGAAATAACCTGGGAATTTCTAACAAGAATAT M 2 1 2 1 101000 f 74 goat snp52750-scaffold790-1499430 3 4968078 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426665 Affx-122939926 AX-123297011 3 112126025 TTCTTGGACATGGAGTCTTACAATATAGACTCTTT[A/G]GTGTCTGGCTTCCTCCAATCAGTATTACGATCACA R 2 1 2 1 101000 f 74 goat snp52751-scaffold790-1553356 3 4914517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424200 Affx-122942506 AX-123294546 3 112173594 CTGCATGCTCTGACTCCCTACTCCAACAAAATGCT[A/G]TTGGTATTTTTATTTGGGTCGTATTATATGTATAA R 2 1 2 1 101000 f 74 goat snp52752-scaffold790-1600925 3 4866614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773380 Affx-122955796 AX-385260522 3 112226682 TCAGTGTAAGCCATTAAGACTTTACCATGGAAAAA[C/T]AGCATTTGACCATTCTCTAAGTTTCTCGTGTACTA Y 2 1 2 1 101000 r 74 goat snp52753-scaffold790-1654013 3 4814568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446863 Affx-122925248 AX-123317199 3 112257623 AGATACAGGCTGGTAGGTGCTCCATCAGGCAGCAA[C/T]AGGGGCCCCACGTTGGCCTTCACCCCATCCAGCTG Y 2 1 2 1 101000 f 74 goat snp52754-scaffold790-1684954 3 4783670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418184 Affx-122947074 AX-123288532 3 112290920 GCAAGAAATTTATAATCCCCTTTACACGTGTTTTG[G/T]GTTAGGAAGGAGTGGTGCGGCTTTCGTTCTGGGCA K 2 1 2 1 201000 r 74 goat snp52755-scaffold790-1718251 3 4757984 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444619 Affx-122926940 AX-123314956 3 112332505 GGCCTGGGCTCAGACAGAAACACTTAAGTGCGAAG[C/T]GGGATATGGATTGCACCCCCAGTTCAGCTCCGTAA Y 2 1 2 1 201000 f 74 goat snp52756-scaffold790-1759836 3 4716828 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391565 Affx-122966623 AX-123261922 3 112401794 GTTATAAGCCACCAAGGAGACGCTATGAGAGGCCC[A/C]AAATAAATTCACTTTGCATCATGGCTAACTTCACT M 2 1 2 1 201000 r 74 goat snp52758-scaffold790-1829125 3 4647929 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394171 Affx-122964930 AX-123264526 3 112431368 GTAAGATCTGTATAGAGATATCAAGTTAAAAATGA[C/T]GTCATCAGGATGACCCTATTCCAGTGCTGGTATCC Y 2 1 2 1 101000 f 74 goat snp52759-scaffold790-1858699 3 4618289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410213 Affx-122952566 AX-123280563 3 112439560 GCTGTGAGTGTGGCCTTGGTCAGCCCTTGATGTCT[C/T]CTCTTATTGGCAAACCCTCACACCAGTACCCAGTT Y 2 1 2 1 101000 r 74 goat snp12103-scaffold1447-604691 3 4610152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375887 Affx-122978495 AX-123246246 3 112502839 ACCAGGGGCCCTGGTGCTCACTCCAAGTGCAGCGT[A/C]CACTCCATGCCCAGGGCCTCAGCGGCATTTTCTGG M 2 1 2 1 201000 f 74 goat snp12102-scaffold1447-541412 3 4546390 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442139 Affx-122928328 AX-123312476 3 112568346 CCCATTTGGAATGTGGGTGCTATTCCGTGGATGGG[C/T]ATCCAAGACTGTCAAGGTCTCAGAGCTGGATCGAG Y 2 1 2 1 201000 r 74 goat snp12101-scaffold1447-475905 3 4480801 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767964 Affx-122939486 AX-385255179 3 112613336 GTGCCAAACAGGATGTAACTCACAGCTGAGTTTTC[A/G]ATGAACTTTTTACCTCTTGGACCGCCATGGGAAGC R 2 1 2 1 101000 f 74 goat snp12100-scaffold1447-430915 3 4436243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395113 Affx-122964153 AX-123265468 3 112645987 TCTACTACTCCTGAGGTCCACCCTGAGGCTGCTGT[C/T]GGCAGTTCCTAGAATAGTGACTGGTATGTATAACA Y 2 1 2 1 101000 r 74 goat snp12099-scaffold1447-398264 3 4404617 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447664 Affx-122923959 AX-123318000 3 112687676 GCTCTTTGTGGATCGTGCCAACAGCGACATAGCAG[C/T]GCTAATGTCTCTGGAGATCCCGACTGCCGTCCTCT Y 2 1 2 1 201000 f 74 goat snp12098-scaffold1447-356575 3 4363089 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442976 Affx-122928200 AX-123313313 3 112739878 TGATGGTATGTTCAACATGAGATTCCAGAACCTCA[G/T]AGGGAGGGCATCAGAGATGCTGGGTGATTTTTCTT K 2 1 2 1 101000 f 74 goat snp12097-scaffold1447-304373 3 4310331 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416400 Affx-122947855 AX-123286749 3 112777582 AAGACGGCAAATTAGGCGAATCCCACTTGGTAGGC[A/G]TCTCAGCAGGGTCCCCACGTTGTGCTCAGCCTTCT R 2 1 2 1 101000 f 74 goat snp12096-scaffold1447-266669 3 4272639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421909 Affx-122944247 AX-123292256 3 112825397 TTGTGCTGCGGTTTGCCAGGCAGCATTCTCAGCTC[A/G]TAACTCACACGGTTTTCATTTTATCCTTAACACTG R 2 1 2 1 101000 r 74 goat snp12095-scaffold1447-218854 3 4224922 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784310 Affx-122975151 AX-385271361 3 112859855 ATAGGCTGCAGACCAATTGTACAAAGTGTATCACG[C/T]AATAGCTTCTTTCCCCAACAATGCATTCCACACTG Y 2 1 2 1 101000 f 74 goat snp12094-scaffold1447-184396 3 4183491 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792688 Affx-122970563 AX-385279668 3 112895609 TTCTTTAGGGAAACTAAAGACCAGAAAGCCAGCAG[C/T]TATCCAGTCTGAAACTACAACAAACCAAACTGGTA Y 2 1 2 1 101000 f 74 goat snp12093-scaffold1447-148642 3 4147434 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275347 Affx-1111834848 AX-519548922 3 112901970 TTTCTGCAGTGGTTGGTGTGTCAAGAGAGGCTGGT[A/G]TTGGTGAGTGGTTATGAAGGAGAAAGGATGTGAGG R 2 1 2 1 202000 f 74 goat GoatD01.056345 3 112901970 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38424476 Affx-122941763 AX-123294822 3 112925091 AAGCATTAAGGTAGATCTTGGATTATTTTTGTGCC[A/G]TTCAGAAGAAAAAGAGCAACATCTGACTCTCTGAT R 2 1 2 1 101000 f 74 goat snp12092-scaffold1447-119160 3 4117968 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431708 Affx-122936766 AX-123302049 3 113001783 TAACTCACATAGTCGAATTTTGTGACTGAATTTCC[A/G]TAGCTTTGCCTACACAGCCCACACGGAGATGTTCC R 2 1 2 1 101000 f 74 goat snp12090-scaffold1447-42468 3 4041443 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433435 Affx-122935076 AX-123303776 3 113041653 CACAAAATCCTAACCACTGGACCACCAGGGAAGTC[C/T]CTGACCCATCTCTTTGATGTTCATGCTTCTGCCTG Y 2 1 2 1 103000 r 74 goat snp12089-scaffold1447-2598 3 4001522 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408022 Affx-122954301 AX-123278373 3 113055226 TAAAAAGCTGGTCAAACGTCTTGACGAGGAAGAGA[C/T]GGTTCACTGTGCTGACCGCATCCCCCAGCTAAACT Y 2 1 2 1 101000 f 74 goat snp15829-scaffold1661-10876 3 3989111 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380609 Affx-122975247 AX-123250967 3 113091559 GCCTCCATACCAGAATCTGGCGCAGTTTTCAGTTA[C/T]GGAATCATAGTACCACTTTAATACAAACTCTCTGC Y 2 1 2 1 101000 r 74 goat snp15830-scaffold1661-47209 3 3953039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429619 Affx-122937697 AX-123299960 3 113136222 TGAGCTCAAAGTCAAGCTGCTGAGACACTTTCAAC[A/G]TACAGGCACAGCTGGGGACGTGGACCGGGAACACG R 2 1 2 1 101000 f 74 goat snp15831-scaffold1661-91872 3 3909972 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408632 Affx-122953486 AX-123278983 3 113175811 AATTTGAGATGCCTTTTTCCTTTTCATAGCTGTCC[A/G]CTTGAAACTTAAAAAGACACCTCTCATTATGAAGA R 2 1 2 1 101000 r 74 goat snp15832-scaffold1661-131461 3 3871389 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443155 Affx-122928061 AX-123313492 3 113236371 TCGGCAAGAGGAGGACTTCCGAAGCCGTCCTATGC[A/G]CTTTGAGTTTCAGATTCACGTGGAAGGCAGGCCAG R 2 1 2 1 101000 r 74 goat snp15833-scaffold1661-192021 3 3811056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396853 Affx-122963254 AX-123267208 3 113278981 GAAGGGGGGCCGTATAGCCTCTGATTTAGCCCCAA[G/T]CAGATATAATGTCTCCCTGAAGTTGGCTTGTGCGA K 2 1 2 1 201000 r 74 goat snp15834-scaffold1661-234631 3 3768350 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429575 Affx-122937808 AX-123299917 3 113336914 CAGGTAGACGTCTGTGTTCTCACCTGTCACCCCTG[C/T]GGGCAGCGAGCACCTGGACTTTTATGCATCCGTGT Y 2 1 2 1 102000 r 74 goat snp15835-scaffold1661-292564 3 3711110 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420165 Affx-122945578 AX-123290513 3 113399996 AGCCTTTCAAATGTTGAATCCTGTCGGGTGAGGAC[A/G]CGCCTGGCCTGTTGGTGGGTTTCACGGGCATCCTT R 2 1 2 1 101000 f 74 goat snp15836-scaffold1661-355646 3 3648388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414954 Affx-122949077 AX-123285303 3 113452924 GCTCAGAGGAATGAACTGCTGGGCCCGGAGAAGAA[C/T]GGAGTGACCATGGGGAGCAGGATCTGAGGCAGGAG Y 2 1 2 1 101000 f 74 goat snp24416-scaffold2477-1504 3 3593852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413987 Affx-122950286 AX-123284336 3 113483736 ATCTGTGTCTTTATCTAAGAAATTAACACTGATAC[G/T]ATTAGCTATACAGACTGTGAACTCAGCATTTAGCA K 2 1 2 1 101000 r 74 goat snp24417-scaffold2477-32316 3 3563255 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436926 Affx-122933194 AX-123307264 3 113534897 ATGTCAATTAAAATGGAACTCAGAAGGACGATAAA[C/T]GTATCTTACACATAACATTTTCTGTTTTCATTTAT Y 2 1 2 1 101000 f 74 goat snp24418-scaffold2477-83477 3 3512168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436908 Affx-122933208 AX-123307246 3 113587905 ATAGGCACACAGCAGTGTTCAGGTTTGAATGCCAT[A/G]ACTCAGTGAAGCTGAGTGCTCCCAAAATGCCGCTG R 2 1 2 1 101000 f 74 goat snp24419-scaffold2477-136485 3 3458938 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779239 Affx-122944107 AX-385266343 3 113625758 ACGGGTTCCCAACTGTGATGAAAATGCCCCAGTAG[C/T]AAATGTGATGTTTGCTATTCGTTTGAGAGATTTTT Y 2 1 2 1 102000 f 74 goat snp24420-scaffold2477-174338 3 3425877 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278026 Affx-1111836213 AX-519551518 3 113669696 GAGTGCATCTTACTGTATTACTAACTCCTGGCCTG[A/G]CATATTTGTTAAACTTAATGAAATTGAACTGGGAG R 2 1 2 1 101000 f 74 goat Random2.2K-383 3 113669696 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777507 Affx-122960756 AX-385264626 3 113683257 GCTCTTTATTATGACTTTCCTAGGGTACTGCCCAC[C/T]GAACTCTGTTTACACAGGCTGTGCTTTTATTGTTT Y 2 1 2 1 101000 r 74 goat snp24421-scaffold2477-231837 3 3377935 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418084 Affx-122946603 AX-123288432 3 113713622 ACTTTATAAGGACTTTTTTTCTTTAAAACCCCTTA[C/T]GCTTACGGTTCCTGCAATCAAGGTCAGTTTTTTTA Y 2 1 2 1 101000 r 74 goat snp24422-scaffold2477-262202 3 3347909 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409888 Affx-122952903 AX-123280239 3 113760692 AACACACCTGAAACAGAAGAAAGTGTCAGCAAAGA[C/T]GAAGAGGAGCAAGACTGAAATTTTAGAACAAACAA Y 2 1 2 1 101000 f 74 goat snp24423-scaffold2477-309272 3 3303465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446547 Affx-122924851 AX-123316883 3 113805185 TCGGGAACGATTTGGGGAAGAAAATGTATGACCTT[A/G]CAGCACCCCATGCCCCAGATAGATCCCAGATGGAA R 2 1 2 1 101000 f 74 goat snp4734-scaffold1157-21395 3 3262850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453040 Affx-122920080 AX-123323373 3 113864365 AAGCTGAGCACCACTTCCCATCAATCGGCGCCTGC[A/G]TTTCTTCTGTAAACTGTCAGGATACATCCTTTGAC R 2 1 2 1 101000 r 74 goat snp4735-scaffold1157-80575 3 3209476 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429110 Affx-122938019 AX-123299452 3 113914168 GGAGGTGGGCCTGTCACCACTGTTTATAGCACGGT[C/T]GCCTTGGGAACGCAGGTGACATCCCCAAGAGTGTC Y 2 1 2 1 201000 f 74 goat snp4736-scaffold1157-130378 3 3161113 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400856 Affx-122959777 AX-123271211 3 113943596 CCGGAAAACAGGCAGGCTCCAAGGCAGCTCAGCTG[C/T]ACCCTGCTCTGAAATTGCATGGTCCGACGTGGGAA Y 2 1 2 1 101000 r 74 goat snp4737-scaffold1157-159806 3 3131653 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394253 Affx-122964730 AX-123264608 3 113987287 TGACTTAGCTTATGATGTGGACCTCTCTGTGCTTA[C/T]AAGCTGTGCTTAAAACTCTCAAAACTGACCCACAT Y 2 1 2 1 201000 r 74 goat snp4738-scaffold1157-203497 3 3086863 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385412 Affx-122971337 AX-123255770 3 114024287 GAAAGAGAAAGAATCTTAGCATTCCTCCTCACCCC[A/G]CCTGCACTTAGAGTAAGCTGGCTCCTTAGGGCAGA R 2 1 2 1 201000 r 74 goat snp4739-scaffold1157-240497 3 3059781 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453244 Affx-122920413 AX-123323577 3 114056851 ATTCATGAAGTCCTAGGAAGTCACTGCATGTGGTT[A/G]TGACTGTATTCAACACAGATGAATAAATCTTGTTA R 2 1 2 1 201000 r 74 goat snp4740-scaffold1157-273061 3 3027003 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426848 Affx-122940497 AX-123297193 3 114105865 GTCTAGAATCTGGATTGTTTTTGGACAGGAAGGTC[A/G]CCCCGAGTTGGGATGGTTGGTATGACCCCCCGAGT R 2 1 2 1 101000 f 74 goat snp4741-scaffold1157-322075 3 2978396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378565 Affx-122976603 AX-123248924 3 114123940 TGTCCATCCAGGAGGGGTTCTGGCTGCTCAGATGG[A/G]CGGCGCCCCTCAGGCAGAGGACTTCCTCATTCCGA R 2 1 2 1 103000 r 74 goat snp24633-scaffold2509-84042 3 2960058 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388971 Affx-122968796 AX-123259329 3 114164292 CACATGGCGCTTTTGGGCCAAAATATAGAAGGGCC[A/G]GAGTGTCACTCTCCAGTGTGTCTTCTCAGCTGTAT R 2 1 2 1 101000 f 74 goat snp24632-scaffold2509-43690 3 2919887 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411650 Affx-122951569 AX-123282000 3 114195412 TGTTGTTTCAGGCCATTGGTTTGTAGCGATGTGTT[A/G]CAGAAAGCCGATACACAGTAGGGGCCCAGGTAGTC R 2 1 2 1 101000 f 74 goat snp24631-scaffold2509-12570 3 2889608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272183 Affx-1111833375 AX-519545935 3 114417276 TTCATGGGGTTGTGAAGAGTCAGACACGACTGAGC[A/G]ACTGAACTGAACTGAAATCCTTTGTTCTCAGTGAA R 2 1 2 1 303000 f 74 goat 3_114417276_AF-PAKI 3 114417276 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38429610 Affx-122937704 AX-123299951 3 114441716 CAGCTCACTGCAAGCCAGTCCCCATCTCAAGGTGA[C/T]GTGTAATTCTTCAATTTCCTAACAAGTAACAAACG Y 2 1 2 1 101000 r 74 goat snp29174-scaffold3130-115137 3 2644098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415007 Affx-122949034 AX-123285356 3 114495946 TTTCTTTCTGAATATTCTTTGAGGTATATATCCCG[C/T]GATGAGAAAACCTGAAGAAGATTTCAGGTGCAAGA Y 2 1 2 1 101000 f 74 goat snp29173-scaffold3130-60907 3 2594329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418874 Affx-122946117 AX-123289222 3 114554536 AGGCCACAAGACAGGCGTGGTGAGACCTGCTCACT[A/G]CAAACAGTGTTTCTGGGAGTTTCTCAGATCACCAA R 2 1 2 1 201000 f 74 goat snp29172-scaffold3130-2317 3 2545584 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433003 Affx-122935793 AX-123303344 3 114586405 CTCCTCCTGCCTTCAATCTTTACCAGCATCAGGGT[A/C]TTTTCCAATTTGGGTCTAGTTAGTGTTAATCCTGA M 2 1 2 1 201000 r 74 goat snp24076-scaffold2455-91009 3 2325911 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437018 Affx-122933125 AX-123307356 3 114638801 ATTTGCAAACAACCATGTTTGATTCTCTTCATTCT[A/G]TTAGATATTTTTTAAAAAGAATTAATTTCTGATCT R 2 1 2 1 101000 f 74 goat snp24075-scaffold2455-38613 3 2273358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777730 Affx-122955249 AX-385264848 3 114690399 CCACCCATCTGTCTGGTAGAGCCTAGATTTTTAAA[A/G]CAAGGATCGTTTGTTTCCTCAAAGGAAACTGGGTG R 2 1 2 1 101000 r 74 goat snp17455-scaffold1806-12886 3 2222124 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453424 Affx-122919881 AX-123323757 3 114734749 AAATTTCAGAGTATCATAATGATCATTCAGATAAA[C/T]GTCTAAAGGGGACAAACTTTTTACCTTTCAGCGAC Y 2 1 2 1 201000 f 74 goat snp17456-scaffold1806-57236 3 2177464 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416846 Affx-122948105 AX-123287194 3 114774449 CTGAAGCTGGGATGTTCTGTTGGGACATCTGGAAG[C/T]GTCCTGGCCTCAATTTTCTACCTAAACGCTGAGCT Y 2 1 2 1 101000 r 74 goat snp17457-scaffold1806-96936 3 2149000 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441708 Affx-122929154 AX-123312045 3 114821635 TTTCAGGAGACGACTGTTAACTCCAGGTGCTGCGC[A/G]TTGTCTTCCATGTCTCGACTATTTATCCTGTCTAC R 2 1 2 1 101000 r 74 goat snp17458-scaffold1806-144122 3 2102227 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278183 Affx-1111836214 AX-519551672 3 114845737 ATATGTCTCTTTTTCAAAAGTTAATATTTTTTTGA[C/G]AGAAAAGGATCAGACAACTTGGTTCTTAAGTGTTT S 4 1 2 1 101000 r 74 goat Random2.2K-385 3 114845737 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394875 Affx-122964755 AX-123265230 3 114857097 ACGGGATTTTGTGTGAATATCTCATTTCTCTGGGG[C/T]AAATGCCCAGGAGTAGAGTTGCTGGGTTGCCTGGT Y 2 1 2 1 101000 f 74 goat snp17459-scaffold1806-179584 3 2068482 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427452 Affx-122940034 AX-123297795 3 114891802 GAAGTTGAAGTCCTAAGCACTGGACTGCCGGGGTA[G/T]TCCTTCAAATTGGTTTTTAATACATAACAATTCAC K 2 1 2 1 101000 r 74 goat snp17460-scaffold1806-214289 3 2033691 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395502 Affx-122963885 AX-123265857 3 114927776 CAAGAGAAATGAGTTCCCCCAGTCAGAGGAATGGG[C/T]AAGGGTTGTCTAGGAGCAGGGAACTCTGGTCAGTG Y 2 1 2 1 102000 f 74 goat snp17461-scaffold1806-250263 3 1999955 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432590 Affx-122935512 AX-123302931 3 115015238 TGGGAGCCAGTGATGCCCTGGGGTGGCCAGGTCTG[C/T]GTGCCGAGGGCTCCTGCTCACACAGTGAATGCTCA Y 2 1 2 1 103000 r 74 goat snp17463-scaffold1806-337725 3 1911105 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379985 Affx-122975619 AX-123250343 3 115046839 TGCCTAAGTATATGAGTCCTTATCTCTTAGAAATA[C/T]GCGTGAAGAGGGTACAGAAGAGATTTTATGATGCC Y 2 1 2 1 201000 f 74 goat snp17464-scaffold1806-369326 3 1879688 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425349 Affx-122941587 AX-123295695 3 115095779 AAACCCAACTTCAGTTACTATTCACATTCCCAATC[A/G]TCTTTTGTGTACCTGAAAAACAGCTTGGTCGGGAC R 2 1 2 1 101000 f 74 goat snp17465-scaffold1806-418266 3 1830855 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387371 Affx-122970467 AX-123257729 3 115126034 CCGAAATATTTAATTAAAGAAACAGAAGGGTAATG[C/T]GCAATTTCTTTTTCCCAGAATTGGAGGCACTACCC Y 2 1 2 1 101000 r 74 goat snp17466-scaffold1806-448521 3 1801638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788395 Affx-122958812 AX-385275413 3 115163563 TTTTAAAACTAAACCTTACTCAGTTACACAGAAAT[A/G]CTGTTGTATCTAGAGTAAGTTGAGCTGTTGGTGCA R 2 1 2 1 101000 r 74 goat snp17467-scaffold1806-486050 3 1764231 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446377 Affx-122925590 AX-123316713 3 115207786 AGAAGCCGCATCCTCTGAGGACCTTTCCTTGGCTG[C/T]ACTCTATCCATGTTTGACTACCTCATTAGAAACTC Y 2 1 2 1 101000 r 74 goat snp17468-scaffold1806-530273 3 1719278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769444 Affx-122931958 AX-385256614 3 115257571 TGCAACTAGTCGTCACACCATGTGAGATGCACAAA[C/T]ATTCAGAAGATGAAAGATGTTAAGTGCTGAGGGGA Y 2 1 2 1 101000 f 74 goat snp17469-scaffold1806-580058 3 1669699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445193 Affx-122925527 AX-123315530 3 115308000 TGCAGTTGGGAAGTGGGCAGTGATATGTCCAGGAT[C/T]CAGGCCCCCAGGACTCACCTGTCAGTGATGCTGAC Y 2 1 2 1 202000 r 74 goat snp15827-scaffold1659-217357 3 1507467 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441897 Affx-122928615 AX-123312234 3 115336832 GATGGCTCCTCCCAGCTGCCGCCCCTGGCCTAGGA[C/T]GCAGTGTAGCTCAATAACATGAGCTGATAAGGAGG Y 2 1 2 1 101000 r 74 goat snp15826-scaffold1659-188525 3 1479575 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387694 Affx-122969815 AX-123258052 3 115389897 TTAGCCAAGAAAGAGAAGAAGGTTTTAGCCATCTG[A/G]AGGAGGCCTGTTAAACTCTTGAATGTGGCCAGCTT R 2 1 2 1 101000 r 74 goat snp15825-scaffold1659-135460 3 1425992 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402007 Affx-122958759 AX-123272360 3 115430599 AACACCTGACCACATGTCACACAACCAACCCTTCA[A/G]AGGTTGAATGAAGTGGGCTGGAAGCTTTGCCCCAT R 2 1 2 1 201000 r 74 goat snp15824-scaffold1659-94758 3 1385645 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450817 Affx-122921799 AX-123321151 3 115492211 AGGGACACGTAATAACAACCACAAGGAGATGGCGT[A/C]TCCCATGCACCAGGTGGCTGGAATGATAGACCAGC M 2 1 2 1 101000 f 74 goat snp15823-scaffold1659-33146 3 1327171 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446211 Affx-122925713 AX-123316547 3 115551240 AGGCGTATGCAGAACAGTCCACCCAGCAACAGCAG[C/T]GTACGCAGAACAGTCCACCACCACCAACAGCAGCG Y 2 1 2 1 202000 r 74 goat snp57090-scaffold9081-61950 3 1270209 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767252 Affx-122976355 AX-385254533 3 115593701 CAACATTAAAAACCCACCAGGCACTCTGTGTGAGC[A/G]TGGGAATTCTTCTATAGAACAAATGATCAGAAAAA R 2 1 2 1 101000 f 74 goat snp57089-scaffold9081-19489 3 1228606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403325 Affx-122957824 AX-123273678 3 115689389 CTTAATATGCGTTCACTTTTTGACCAAACGATCCC[A/G]CTTCCAGGAATGCATCCCAAAGGTCGTGGGTGAAA R 2 1 2 1 101000 f 74 goat snp24964-scaffold2564-76100 3 1144810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385553 Affx-122971228 AX-123255911 3 115745279 AGAGAGGGGAAGCTTGTGCGTTAAAAATGACACTC[G/T]AATATCTGGCCTTGGCAACAAGAGGAGTCATCCTC K 2 1 2 1 101000 f 74 goat snp24965-scaffold2564-131990 3 1091568 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428899 Affx-122938926 AX-123299241 3 115896763 TCATCATCTCGGTGTGGAGAAATCAGGATACATAC[A/G]CTGATTGCTCCAAAGAAGACAGAAGGACTACATGA R 2 1 2 1 101000 f 74 goat snp24968-scaffold2564-283474 3 987087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440462 Affx-122929388 AX-123310799 3 115936546 GGTGAGCCTGGCCCTGAGGTGAGGCTGGCCCCTAA[A/G]GTGAGCCTGGCCTCAGGTAAGCCTGACTCCTCAGG R 2 1 2 1 202000 f 74 goat snp24969-scaffold2564-323257 3 949425 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375844 Affx-122978528 AX-123246203 3 115986152 TGGAACTCTGAAAAGTCTTTGAAACCTGGAATGAA[C/T]ATGGTATGTTCCAAAAAAGATTTTCGTTTGCTTCA Y 2 1 2 1 201000 r 74 goat snp24970-scaffold2564-372863 3 905464 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405991 Affx-122955517 AX-123276343 3 116010625 GCTAACCAAAGCCTTTTAAATGGCCGTGAATTCCT[C/T]GGGATCTTGCTGAGAGGCTCTGTCTGTGTGTAAGG Y 2 1 2 1 101000 f 74 goat snp29140-scaffold3125-7445 3 2516863 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408959 Affx-122953922 AX-123279310 3 116103520 GGGGGAGCAAAGTGAATAAGGAAGAAAGAGAAAGC[A/G]TGGAGTGAAGGTTCTGGAACATCGCCCTGACCCAG R 2 1 2 1 201000 r 74 goat snp29142-scaffold3125-100340 3 2431089 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449682 Affx-122922556 AX-123320017 3 116144614 GTGAAGAGAGTGGAAATCGTCAAAACAGAGGCCGG[C/T]GTATGGGATGACGGTTACATAGTTTTAAATGGCTT Y 2 1 2 1 201000 r 74 goat snp29143-scaffold3125-141434 3 2389860 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603594 Affx-1002479413 AX-310998304 3 116167006 AGATATAACAATTATAAATATATATGCACCCAACA[C/T]GGGAGCCCCACAATATGTAAGACAAATGCTAATAA Y 2 1 2 1 303000 f 74 goat 3_116167006_RH-map 3 116167006 C T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38378988 Affx-122976393 AX-123249347 3 116193593 AAAATTATACCTTGATAAAGTGGTTTTAAAATTAC[A/G]TAATTGTTATGCTGACATCTTAACACATCTACAGG R 2 1 2 1 101000 r 74 goat snp11602-scaffold1426-13596 3 776966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447244 Affx-122924957 AX-123317580 3 116223610 ATTACCAGCTGAAAGAAGCCTTGGTTCTCAAACAC[A/G]TCCAGCACCTGTTGAGAGAGAGAGACAAGCTGGGT R 2 1 2 1 101000 f 74 goat snp11603-scaffold1426-43613 3 753303 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436445 Affx-122932998 AX-123306783 3 116260679 AAACCGCCTGGAGGCTGGCCGTGCTATGGAACACC[C/T]GAACTGATAAGACATGGGGCTTATGAACATAGTAA Y 2 1 2 1 101000 r 74 goat snp11604-scaffold1426-80682 3 714754 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603136 Affx-1002479414 AX-185909890 3 116287414 TGTTTCTTGACTTCCTACTTTTGCATTCCAGTCCC[A/C]TATATTGAAAAGGACATCTTTTCTGGGTGTTAGTT M 2 1 2 1 103000 f 74 goat 3_116287414_RH-map 3 116287414 C A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603138 Affx-1002479415 AX-413837331 3 116306750 GAAATTAGAACACTTCCTAACACCATACACAAAGA[G/T]AAACTCAAAATGGATTAAAGACCTAAATATAAGAC K 2 1 2 1 103000 f 74 goat 3_116306750_RH-map 3 116306750 T G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38393842 Affx-122965157 AX-123264197 3 116329221 AAGATCCCTCCCCAAATTAAAAAAAATTAAGCTCT[A/G]GAAGCAAGGTCCAAAATCAGATACCCTCAGCAAAC R 2 1 2 1 101000 r 74 goat snp11605-scaffold1426-149224 3 650730 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603229 Affx-1002479416 AX-413837410 3 116365210 CTAGAGGGGAGAAGGCCCATCAGGCAGTGGGAGAA[A/G]TAATCCACAGCTTCTGGGAGAGGAAATAAGACAGT R 2 1 2 1 101000 r 74 goat 3_116365210_RH-map 3 116365210 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38417632 Affx-122946856 AX-123287980 3 116390536 CGGGGAGTTAGCAGTTGGTCTGTGCAGAAGCCTGC[C/T]GTTGTGGCAGGCTTGGCGTGTTTCCTGTGACTGCG Y 2 1 2 1 101000 f 74 goat snp11606-scaffold1426-210539 3 590753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603142 Affx-1002479417 AX-413837335 3 116437755 CCAGAAGAGACACACAGGAAGTACATTTGGTCATT[A/G]TTACTGTCACTGAAACATATTGCTATCCAGACTAC R 2 1 2 1 101000 f 74 goat 3_116437755_RH-map 3 116437755 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38425350 Affx-122941586 AX-123295696 3 116443446 AGGTGGGTCTTGTCCACAGTTGGCAACACAAGTGT[G/T]GAAGCATCTTTATTGTTGTTTGGTTGTTAAGTTGT K 2 1 2 1 201000 f 74 goat snp11607-scaffold1426-263449 3 537332 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603144 Affx-1002479418 AX-413837337 3 116479323 TATTAGCCACAAACACGCCTGTCCCAGAGACAGAA[A/G]AAAGAACACTAGCAGGACTTCTATCCCCAGGTCAT R 2 1 2 1 102000 f 74 goat 3_116479323_RH-map 3 116479323 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38407840 Affx-122954530 AX-123278191 3 116482810 ATGATTCCGTAGTTGCTTGTGTATTCGTGAGGTTG[C/T]ACCACATCGCCACTAATTCCAGGACATTTCCATTC Y 2 1 2 1 101000 f 74 goat snp11608-scaffold1426-302813 3 498081 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603235 Affx-1002479419 AX-413837416 3 116528611 GCACACTCCAGCCAAATGCATGCAAGGAAGGGTCC[C/T]CTGGGACGCTCTAACCCTTTAGATTTCCAAAGTCT Y 2 1 2 1 101000 r 74 goat 3_116528611_RH-map 3 116528611 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603148 Affx-1002479420 AX-413837340 3 116547139 TCAGGTCGCATATGGATACTATCAATATTGAAATG[A/G]AATTTCAATTATATACAGGAAACAAAAAAGCAAAT R 2 1 2 1 101000 f 74 goat 3_116547139_RH-map 3 116547139 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38378509 Affx-122976646 AX-123248868 3 116554711 ATCGAAACATTTCAACACAGAAAATCAACTGGACA[C/T]GGAAGATAGTATGCAGGAAACGAAGGACAAAAAGG Y 2 1 2 1 201000 r 74 goat snp11609-scaffold1426-374714 3 427607 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408311 Affx-122953770 AX-123278662 3 116566088 GGAAAAGCAGATAAAGTCTAAGAACAGACACGTAA[C/T]GTAAGAAGAGAGAGGGAACGTGGACAAAGCATGAA Y 2 1 2 1 201000 f 74 goat snp36346-scaffold4353-5630 3 412873 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420706 Affx-122944787 AX-123291053 3 116630641 TAAAGTATTTTTTGGAACAAACATTTGAGAACCCA[G/T]CCTTTCTGGAAATAAGACTTCAGTGTCGTGTCGAG K 2 1 2 1 201000 f 74 goat snp36347-scaffold4353-70183 3 349076 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603150 Affx-1002479421 AX-413837341 3 116740369 TTTGTACATACTACAAGCAGGTTTGTTACTTCTAG[C/T]ACTTTTATGCTCTAACAGTTACAAAAAGTTCACCT Y 2 1 2 1 101000 f 74 goat 3_116740369_RH-map 3 116740369 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38400979 Affx-122960100 AX-123271332 3 116743421 TCTCTTCCCAAGTTGACAGCCCCTCAAACCCTCAC[C/T]TGCATTTCCGGGTCCAAACAGCTCTGAAAAGCACA Y 2 1 2 1 101000 r 74 goat snp36349-scaffold4353-182963 NW_017189534.1 37978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603240 Affx-1002479422 AX-413837421 3 116765506 CCTTTTAAAGAGCCCCTACCATCACCCCTCAAGTA[A/G]CTAATGGATATAAACTCACACTAGAGCATTAGTGA R 2 1 2 1 201000 r 74 goat 3_116765506_RH-map 3 116765506 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38452179 Affx-122921232 AX-123322512 3 116773477 CAGGGAAAGACACACTGGGCTGACACTAACCAAAC[A/G]GAACCTGGACTTGCTCTGTCGACATCAGACTCTAC R 2 1 2 1 101000 f 74 goat snp36350-scaffold4353-213019 NW_017189534.1 64315 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603155 Affx-1002479423 AX-413837344 3 116827349 TATAGCCTGTTTAAGTACCACTTGATATAATCATT[A/G]ATGACTAAGAATTTTGATAATAATTTGGTAATGTC R 2 1 2 1 101000 f 74 goat 3_116827349_RH-map 3 116827349 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603654 Affx-1002479424 AX-413837792 3 116867220 AGGGAGTGAGAAATGCTAAAGAGAAAAAGGAAATT[A/G]TAGAGGACAAATAAGGAGTTCAGATGGAGGTCAGT R 2 1 2 1 400000 r 74 goat 3_116867220_RH-map 3 116867220 A G Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603656 Affx-1002479425 AX-413837794 3 116908666 AGACACTGAGTAATTTTCTTGAGGACACACAGCTA[A/G]GAGTATGAGATCCAGGTTCTAAACCCAGACAATTT R 2 1 2 1 201000 r 74 goat 3_116908666_RH-map 3 116908666 A G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603157 Affx-1002479426 AX-413837346 3 116953479 TTCCATGGACAGAGGAACCTGGAGGACTGCAGTCC[A/C]TGGGATCACAAAGAGTCAGATAAGACTGAGTGACT M 2 1 2 1 303000 f 74 goat 3_116953479_RH-map 3 116953479 C A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603159 Affx-1002479427 AX-413837348 3 116998730 TCGGGTTGTAATTCAATAAATGCTCACTGACCTTC[A/G]CACTGTATGGCAGGTTCATCTATATATATTTTCTC R 2 1 2 1 101000 f 74 goat 3_116998730_RH-map 3 116998730 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468278030 Affx-1111836215 AX-519551522 3 117344700 AGCAGGTTTTCAGGGAGGGGGCATGAAATAAACAC[A/C]TCAACTTGCAAAGAGAACCTGGGCATTTACAAGGA M 2 1 2 1 101000 f 74 goat Random2.2K-390 3 117344700 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320804180 Affx-986696711 AX-385290828 3 117776320 CCCCTTGCAAAGGTAAAACCTTTGTTGAGGCAGAC[C/T]TTTCTATGAATCTTAATTTTCTGACATGGGTAACA Y 2 1 2 1 600010 f 74 goat 3_117776320 3 117776320 Ancestral_priority_1043 ancestry 0.554 neutral IMAGE 10K 10K ancestral 320802979 Affx-986696110 AX-385289864 3 118818403 AAGAGTAAGGCTCTAGCAAACCAGTATAAATTAAG[A/G]CCGAGCAGAGTGGGTTTCCATCCATCGCCATGTGC R 2 1 2 1 600010 f 74 goat 3_118818403 3 118818403 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 468278186 Affx-1111836216 AX-519551675 3 118955088 CACGTACTCACTGTGTTCACTGCAGACGACCGTGC[A/G]ATAGCAGGGATCTGCCCTACAATGCCCAGGTGGAT R 2 1 2 1 202000 r 74 goat Random2.2K-392 3 118955088 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272016 Affx-1111833376 AX-519545782 3 119768649 CTGTTGGGCTTCCCTGCCTCTTTCCTGGACCCCTC[A/G]CCAGGCCATTTCCCTCAGAACTGTGGAGTCACTCA R 2 1 2 1 102000 r 74 goat 3_119768649_AF-PAKI 3 119768649 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278188 Affx-1111836217 AX-519551677 3 119986641 GGGATGACTACTGTCTGGTTGTGATGTGAAGGGGC[A/G]CTTTTTCTAGTTTTGATGTGCATGAGGCTACTCTC R 2 1 2 1 101000 r 74 goat Random2.2K-393 3 119986641 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320804545 Affx-986696713 AX-385291093 3 120027299 TTTTCCATTATATTAATTATATTTGATACTTTTGG[A/G]GCTTGCTACTTTTTAGCATCTAGAATCATTTATTT R 2 1 2 1 600010 r 74 goat 3_120027299 3 120027299 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 38426974 Affx-122940397 AX-123297319 3 CCATAAACCTCTGCTTTGCAGAGGGGACTCTATTA[A/C]AATTCATTTATTTCACAACAGTTCTAAATTTCTGA M 2 1 2 1 201000 r 74 goat snp35512-scaffold428-358707 NW_017189517.1 21270534 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789306 Affx-122941634 AX-385276316 4 15471 TTTATCCTCCCTTGTGACACTGGAATACAGAAAAG[C/T]ACTGGTCTTACCATCTCAGTTGGAGGAGAACAGAT Y 2 1 2 1 101000 f 74 goat snp46390-scaffold641-15471 4 119118717 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272120 Affx-1111833430 AX-519545878 4 50909 AAGGTTCATCCACCAAGACTGGCCACAGGCTGGCC[A/G]CATGGGCTTCGGTACAACCAGATGGCAGATTCTTG R 2 1 2 1 101000 r 74 goat 4_50909_AF-PAKI 4 50909 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38381662 Affx-122974745 AX-123252020 4 86784 TTTACAAAGTGTGGCTATGAATACGGCTTTAAACT[A/G]ATTTTAGTTGAAATATTGACTGATTTGTTAAAATG R 2 1 2 1 101000 f 74 goat snp46391-scaffold641-86784 4 119047514 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785183 Affx-122949165 AX-385272229 4 122901 AATAACTACTGCTTGCATGTGATAATAATGTTGTT[A/G]CTGTTTTATTACTCTTAGAGATGCAAAAGTAGATA R 2 1 2 1 101000 f 74 goat snp46392-scaffold641-122901 4 119011329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781215 Affx-122929161 AX-385268300 4 193748 ATGAAAAGGACGTGCAGTAACATACCCAGCAGGGT[A/G]TTTGCCATTGACATCATCAGTAAATGATGGGAAAT R 2 1 2 1 101000 f 74 goat snp46393-scaffold641-193748 4 118939982 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801521 Affx-122938520 AX-385288430 4 274857 AGTGAAAAACTAAGGAATAAAAAGCAAATGAACCA[C/T]TTTAGCAACAGAACTGATTCTTTGTTGCCAACTCC Y 2 1 2 1 201000 f 74 goat snp46395-scaffold641-274857 4 118858148 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779350 Affx-122979026 AX-385266454 4 330180 AATATTGTGTTATGGTTACATAGCACAAAAAGATG[C/T]AATTTTGTATATTAACAAAATATATTGTGGAGAGG Y 2 1 2 1 201000 r 74 goat snp46396-scaffold641-330180 4 118807086 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796869 Affx-122975656 AX-385283812 4 378530 CTACAGTAAAGCACATACACTGGAATCTGGGTCTT[A/C]AAGTTGGCTTCTGCAGAAATCTAAAACAAATATAT M 2 1 2 1 101000 f 74 goat snp46397-scaffold641-378530 4 118757652 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388033 Affx-122969552 AX-123258391 4 427227 ACCAAAGGTAACTACTGGTTTACAGTGGTGATACT[G/T]GTAGAACGGGACATCAATGACAAAAACACCAGAGT K 2 1 2 1 101000 r 74 goat snp46398-scaffold641-427227 4 118708961 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422735 Affx-122943254 AX-123293081 4 461272 TAGTCTGAAATTCACAAATTTATTCTCTTTAAAAA[C/T]AAGGTCTTGAAATATGAAAATACATTAGGTTAGTT Y 2 1 2 1 103000 r 74 goat snp46399-scaffold641-461272 4 118674240 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431295 Affx-122937092 AX-123301636 4 519686 AAATGCAGAGCAGAATCTCCCCTGGAGGCGGTGGA[G/T]GGAGAAAGCAGTGCTAACCTCCAGCTGTGGGCTGG K 2 1 2 1 201000 r 74 goat snp46400-scaffold641-519686 4 118615150 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438295 Affx-122931392 AX-123308633 4 563098 TCTAGATTTTATCCACTACAGTTTCTAAATTCTTT[C/T]TTCCATAGTAAATTATGCCCTTTCAGCCCAAATCG Y 2 1 2 1 101000 r 74 goat snp46401-scaffold641-563098 4 118572114 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278035 Affx-1111836218 AX-519551527 4 578015 CTGTGTTGCTTGTCCAGTTTATTGAGGGCTCTCCC[A/G]GGGTGATGGTGAGGGGTCTGGCCTGGCTCTCCTGA R 2 1 2 1 101000 f 74 goat Random2.2K-394 4 578015 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408767 Affx-122953387 AX-123279118 4 657922 GGCAGAAAAGCTGGGTACTTACTGCTGGTACCACC[C/T]ACACTGCAGCTGCCAGAAGCTGTCAGGCATCTGGA Y 2 1 2 1 201000 f 74 goat snp46403-scaffold641-657922 4 118479343 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792471 Affx-122919951 AX-385279452 4 694292 AGAGTAGATATAAGTATATTGGAGGAAAGTACAGG[A/G]ACACACTCCTAAAATCTCAGGGTGCAAATAAGAAA R 2 1 2 1 101000 r 74 goat snp46404-scaffold641-694292 4 118440178 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405860 Affx-122955854 AX-123276212 4 778594 AGAATATCTTCTTTAAAATAAATTAAACCCTGCTA[C/T]AACTAAAGCTGTCAAATTACTGTCAAATTTTTACT Y 2 1 2 1 101000 r 74 goat snp46406-scaffold641-778594 NW_017211816.1 6897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413829 Affx-122949885 AX-123284178 4 808989 TAATAAATATGCTATAAAACACTACCATAGTCAGA[A/G]CTCAAAAGTTTCACTTTAAAAAATTAAAAACTATT R 2 1 2 1 101000 f 74 goat snp46407-scaffold641-808989 4 118324857 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434221 Affx-122934846 AX-123304562 4 842556 GTGAAGTATATTATCTATAATTATATACTTTCAAG[A/C]TTAAAAATTGCCTGTCAACCCTACAATGTTGACCA M 2 1 2 1 101000 r 74 goat snp46408-scaffold641-842556 4 118291067 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425109 Affx-122941228 AX-123295455 4 905679 TCATTTTGTAAATATCATGGTGCTTAATATTAGAC[A/G]TCTGACCACATCCCACATCTTGGGGAGAATGTAAA R 2 1 2 1 201000 f 74 goat snp46409-scaffold641-905679 4 118226600 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772718 Affx-122950419 AX-385259864 4 958268 CTGCAGGCAAGCAGATACAGGATAAGCCTTTAGAA[C/T]ATCTGCTACAAACTCATTTATATATTTAAGCTTTT Y 2 1 2 1 201000 r 74 goat snp46410-scaffold641-958268 4 118173742 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420235 Affx-122945076 AX-123290583 4 1006943 GTTAAAGTTGTTCACTGATATTCCATTGCAAAATG[A/C]ATTTAACATATTCTCTGAGATGACAGCATATAGGT M 2 1 2 1 101000 r 74 goat snp46411-scaffold641-1006943 4 118124568 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786012 Affx-122935940 AX-385273048 4 1063698 CTAGTGATAACATTCTATCTCCTCAACTCAAGTGT[A/G]TTGCTCCAAACATAAATAACTTTCTCTCTTTTTTC R 2 1 2 1 101000 f 74 goat snp46412-scaffold641-1063698 4 118063801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794750 Affx-122975873 AX-385281710 4 1098932 TATTTGTTGTCTGTATAGACTCAACTGAGTTGCCT[A/G]TTTATATTATTTGTCCATTTTCTGAATCGAATCAT R 2 1 2 1 101000 f 74 goat snp46413-scaffold641-1098932 4 118028473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797111 Affx-122921959 AX-385284051 4 1128987 GTCTGCAGAGTGTCCTACCTGAGGCAAGTCTTCAT[A/G]TGTTAGCATTATGTCATCAGTGTAATGGGCCCACT R 2 1 2 1 101000 f 74 goat snp46414-scaffold641-1128987 4 117998522 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426449 Affx-122940806 AX-123296795 4 1168871 TTGACTTTCTACTAATAGGCATCCTCACAAATAAC[A/C]TTTGATATTAAATAAGTAAAATAAATGAAGAAATG M 2 1 2 1 101000 f 74 goat snp46415-scaffold641-1168871 4 117958301 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416205 Affx-122948239 AX-123286554 4 1278697 ACCACAACTCAATGTTTTTACAGTATTTCTGCCAA[C/T]GGTGAGATTTTTTTCAAAATGATAACCAATATTTT Y 2 1 2 1 101000 f 74 goat snp46417-scaffold641-1278697 4 117851568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771680 Affx-122967090 AX-385258839 4 1327116 GGGGGAAAGAACTTCAATGAATCACTAATGCAGGA[A/G]CTCAAGCTCTAAGTCATTTTCCATTCTGTGCTGGC R 2 1 2 1 101000 r 74 goat snp46418-scaffold641-1327116 4 117803520 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387714 Affx-122969801 AX-123258072 4 1390123 GTTTTTTGCTTTCTTTCTTTCTCCCTTGGTATCTT[A/G]TTTGACTTAATGTACTCTGTGCACATTTACAGGTT R 2 1 2 1 201000 r 74 goat snp46419-scaffold641-1390123 4 117740580 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425538 Affx-122941453 AX-123295884 4 1426922 CGGTATCTAGGCATACACTCTGTGCCCCATTTCAA[C/T]GACCACCCATGCTGCAGGGTTAACTACTATCATGA Y 2 1 2 1 101000 r 74 goat snp46420-scaffold641-1426922 4 117703610 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445158 Affx-122925553 AX-123315495 4 1467834 TTGTTTTACTGTAGTACATATGCTGTCACTCAGCA[C/T]GATAGTTGTTTGTTTTTCTTTTCTTCCTCTTTCTT Y 2 1 2 1 103000 f 74 goat snp15036-scaffold1609-17621 4 117028084 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415905 Affx-122948465 AX-123286254 4 1533006 GTAATCCCACTTACATGAGAAAGAATACTATAAAA[C/T]GTGGTGCTGGAGACAGAGAGGAAGGACTCATATTT Y 2 1 2 1 201000 f 74 goat snp15037-scaffold1609-82793 4 116962964 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392440 Affx-122966177 AX-123262797 4 1573618 CTCTAGGAAGACAGAATATAAACTATAACCAAGAT[C/T]ATCTATTTACTTATCTACCATCTGTCTGTGCATGA Y 2 1 2 1 201000 r 74 goat snp15038-scaffold1609-123405 4 116921321 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452823 Affx-122920742 AX-123323156 4 1606230 CACACTGCTGCAGAGAAATAAGTTCTGCATTTTCC[A/G]TAATACTCCAACTTAAACTGAGCAAAAGTTATGGC R 2 1 2 1 101000 r 74 goat snp15039-scaffold1609-156017 4 116887995 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387790 Affx-122969701 AX-123258148 4 1656659 GCAACACATTTTCTCAGATGCTGCCTTCATACCAC[A/G]TAAATGATGACCATTGAAAAGGAGTATTCACTCGC R 2 1 2 1 201000 r 74 goat snp15040-scaffold1609-206446 4 116837253 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384832 Affx-122971973 AX-123255190 4 1700668 AGGTATCTGCCATAGCATCTGCAAAGTACATTCAG[C/T]ATAAACCTCAGCCACCCCTAGCTCTCTTCCCTTAA Y 2 1 2 1 101000 f 74 goat snp15041-scaffold1609-250455 4 116792793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438828 Affx-122930782 AX-123309165 4 1746324 CCCAAGAGAGCAGCCCAGCTGAGTCCTTGTGATCA[A/G]ACCTCCATCTGTGACTCTGACGCACATCAACTGCT R 2 1 2 1 101000 r 74 goat snp15042-scaffold1609-296111 4 116747580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409649 Affx-122953523 AX-123280000 4 1829476 AAGACTGGAAAACAGGTAACAAAATGGTAATAAGT[A/G]CAAACATATCAATAATAACTGTATATGTGAATGGA R 2 1 2 1 101000 f 74 goat snp15044-scaffold1609-379263 4 116662996 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795186 Affx-122940926 AX-385282144 4 1858062 AATCATTTTCACCTAGTATCAAAAAAATACAGCTC[A/G]AGTGTGCTAGATTTCCCAGCCATTTTATTTCCACT R 2 1 2 1 101000 r 74 goat snp15045-scaffold1609-407849 4 116633694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801305 Affx-122922534 AX-385288217 4 1892217 GCAAATAATATTTCTTCATAGTCTAATTAGTCTTC[A/G]CAGTCTAAAAACCAAAATTTTTATCAGTGTCTACC R 2 1 2 1 101000 r 74 goat snp15046-scaffold1609-442004 4 116599659 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275469 Affx-1111834916 AX-519549042 4 1924240 CAGTGAGATTTCGAAAAATGAGGAAATTAATACAG[A/G]CTGCGGTGGCCAGATAAGACCTTCCAGAAGGGTAG R 2 1 2 1 101000 f 74 goat GoatD01.058735 4 1924240 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38378550 Affx-122976612 AX-123248909 4 1934427 GAGACTCAGAGGTTTCCGGTGAAGCAGGTTGTTTC[A/G]TGGCAGTCTCACAGACTAGAAATCTGTCACAAAAA R 2 1 2 1 201000 r 74 goat snp15047-scaffold1609-484214 4 116557293 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450197 Affx-122922295 AX-123320532 4 1966172 TATCAAGTAAAAAAAAAAAAAAAACAGGAACTTCT[A/G]ACAGCTTAATGATATTCTCTGAAAAGTCTGCACCA R 2 1 2 1 101000 r 74 goat snp15048-scaffold1609-515959 4 116524972 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378583 Affx-122976589 AX-123248942 4 1995442 AAATATACTGTAAAATGAAAGAATTAATTCAAGAA[A/G]CTACAAATTAGAAAAAGTAGAAATTACTATACTAG R 2 1 2 1 201000 f 74 goat snp15049-scaffold1609-545229 4 116495305 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390450 Affx-122967620 AX-123260807 4 2050994 CCGTTAAGAACAGAAACAGCTACGAATATTGAACT[A/G]TGCTTGAGAAAGCCTAAGTTGAGCTAGGAAATACA R 2 1 2 1 101000 f 74 goat snp15050-scaffold1609-600781 4 116440306 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780473 Affx-122934955 AX-385267564 4 2098633 AACTGGACTTGAGGCATTAAAAGCAATTTATCCCT[C/T]GTCCATTAATTTTTGAGATTAGGAATGAAAGGCCC Y 2 1 2 1 101000 f 74 goat snp15051-scaffold1609-648420 4 116393666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415263 Affx-122948847 AX-123285612 4 2128311 CATTCTATGCAAAACAAAGAAATCCTTCAAAAAGA[C/T]TGGCATTTCATTCTGTAAATCTAAATAATAGCTCT Y 2 1 2 1 101000 r 74 goat snp15052-scaffold1609-678098 4 116363592 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421176 Affx-122944165 AX-123291523 4 2173921 AAATCACAAAGTTTTTCTATTGAGAGTGAATGGCC[G/T]AGGCTACATCTTCTGGAGACGGATTGCCTGTTTTC K 2 1 2 1 101000 f 74 goat snp15053-scaffold1609-723708 4 116317336 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411416 Affx-122951839 AX-123281766 4 2179520 TATAGTAACATTAGGTCACTGATGATGATGCTGAG[A/C]TTAAGCTCTGAGCTAAACTGATGACAGACAGATTC M 2 1 2 1 101000 r 74 goat snp34376-scaffold404-1637 4 116311562 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397296 Affx-122962325 AX-123267651 4 2239943 TAAAGAGAAAACAAATCACAATTTTTAAGGACTCA[C/T]AAAATCCAAAACTGAAATTAGAGGACAGAGGAATC Y 2 1 2 1 101000 f 74 goat snp34377-scaffold404-62060 4 116252427 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792527 Affx-122919836 AX-385279508 4 2305591 ACAAAGTAGATCTGGAAAACTTAGGCCAACAGGAA[C/T]GGAGTTACATATATGGAAGGAAACCAGTGTGCACT Y 2 1 2 1 101000 r 74 goat snp34379-scaffold404-127708 4 116185963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382396 Affx-122973840 AX-123252754 4 2335774 TCTCTACACAGGCTTCTTTTTATCTTTAAATGTTT[A/G]TTACTCGTTATTTATTCATTTTTGGCTGCCTCAGC R 2 1 2 1 102000 r 74 goat snp34380-scaffold404-157891 4 116155635 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413362 Affx-122950145 AX-123283711 4 2411378 CCACATGTGCTGGATGAATTGGACATCACTTCCCC[A/G]CTTTTAAGTAATTTTACCTTCAGGGTCTACATCAG R 2 1 2 1 201000 r 74 goat snp34382-scaffold404-233495 4 116079409 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422377 Affx-122943403 AX-123292723 4 2492788 TTTCTTGATGATTCTATCTATTCTCTGCTTTCTTT[A/C]GCCCTAGAAGGAGCTCCTTGTGAGTCTGGGCCCTT M 2 1 2 1 101000 f 74 goat snp34384-scaffold404-314905 4 115997831 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781175 Affx-122957648 AX-385268260 4 2541387 GAAAAGTTGGCCATAATGTCTATCTCAGTATCTGT[A/G]CAGTCTGTAGTGATGTTACACTCTTATCCTGATGA R 2 1 2 1 101000 f 74 goat snp34385-scaffold404-363504 4 115949358 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453539 Affx-122919790 AX-123323872 4 2575720 TGCAGATTCTCTGGGTGGCAGTCCTTGGCCACATC[A/G]TCTCTGTGGCCCTGCAGGAAGAAAGTGGCCCGTGG R 2 1 2 1 101000 f 74 goat snp34386-scaffold404-397837 4 115914847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796364 Affx-122939463 AX-385283314 4 2618688 CCTGTCGTTGGGGCACTGGTCAATTTCAGCTCTGT[A/G]TTCTCACCATGAGGTCCTGCCGAAAATGGTCCTAA R 2 1 2 1 101000 f 74 goat snp34387-scaffold404-440805 4 115871625 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774378 Affx-122959214 AX-385261514 4 2663695 TATTGGAATTCCCTCTTTTTGACCTGTGGTTAGAA[C/T]ATCTTATATTTTTTTTGCCATTGTGAATTGTACTG Y 2 1 2 1 101000 r 74 goat snp34388-scaffold404-485812 4 115826699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383834 Affx-122973162 AX-123254192 4 2746459 GGCTTGTGATGGAACATTTAAATGCAGCCCAGATA[C/T]GGGCTACCAGGTATGTACGTTACACACACTGACAA Y 2 1 2 1 101000 r 74 goat snp34390-scaffold404-568576 4 115747461 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775581 Affx-122953787 AX-385262712 4 2778708 TCTCTTAGTATTTTTATTAATAGTCTGATAAAGAG[C/T]ATGAAGTGTAAGACTCTATTAGTTACTAGAAGAGT Y 2 1 2 1 201000 f 74 goat snp34391-scaffold404-600825 4 115715353 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396140 Affx-122963394 AX-123266495 4 2821408 TTCGAGGTGGGTGGAATGAATTCAGGCCTCCAGAG[C/T]GAGTTACAACTCTGGGCATCGGTTCCTTCTGCTCC Y 2 1 2 1 102000 f 74 goat snp34392-scaffold404-643525 4 115672795 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379864 Affx-122975792 AX-123250222 4 2852086 AGCTTTTTAGTGCTGACCTGCAATTTCCTCTTTGA[C/T]ACCAAAGTTTAGGACTTTTCCTTCCCAAATATTTT Y 2 1 2 1 101000 f 74 goat snp34393-scaffold404-674203 4 115643531 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416548 Affx-122947678 AX-123286896 4 2882774 TATCTTGTTAATAGATTCTGCCTTGGTGGCTCAGA[C/T]GGAGAATCTGTGTGTCATGCAGGAGACCCAGGTTC Y 2 1 2 1 101000 f 74 goat snp34394-scaffold404-704891 4 115612333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452641 Affx-122920345 AX-123322974 4 2913169 GCATGGGGCATCTCGGGCTCACAGTTCCCAAGGAA[C/T]GGCCCAAGGGCCTGCCTGCCTTGGACAGCTTTGTA Y 2 1 2 1 303000 f 74 goat snp34395-scaffold404-735286 4 115581983 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414267 Affx-122949610 AX-123284616 4 2947419 ACTCTTTATTCCCATCTTCTCCATAACAGCCAAGC[A/G]TTAGCTTGGTGTCTCCCTTTGCCTGGCAAAGCAAT R 2 1 2 1 103000 f 74 goat snp34396-scaffold404-769536 4 115547484 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272102 Affx-1111833421 AX-519545862 4 2961725 TTTTAGCAACTCTATTCTCATAAAACATTTTATTC[A/G]GCTGGAAGATGGAGACCATTCTTGAGAAAATACTA R 2 1 2 1 101000 r 74 goat 4_2961725_AF-PAKI 4 2961725 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450066 Affx-122922809 AX-123320401 4 2977990 CTTTTAAATTCAAAATAATATCAGAATTACAGAAA[C/T]GGTGTACTAGTCCAAACAATTCTCATAAGTCCTTT Y 2 1 2 1 101000 r 74 goat snp34397-scaffold404-800107 4 115516473 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791019 Affx-122974484 AX-385278015 4 3027631 AATTCCAGCTCTACAATTTCCTGATTATTCACCAA[A/G]TGGAAGATAGTCTCTGTTTTTCAGCTTTGGATTCC R 2 1 2 1 101000 r 74 goat snp34398-scaffold404-849748 4 115466499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398008 Affx-122961787 AX-123268363 4 3063464 AATGAGTTCAGTTTATTGTTTTTGGTCAACACACA[C/T]AATCAAATTGTTTAAAACCGATGAAAAAGAAATCC Y 2 1 2 1 101000 f 74 goat snp34399-scaffold404-885581 NW_017202663.1 15472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452894 Affx-122920216 AX-123323227 4 3136703 GGGGTCCTTGGCATCCTGGATGAGCCTCTGCAGTA[C/T]GGGGAACACATTTGACCCAAGTCAGGCTCACCTGA Y 2 1 2 1 201000 f 74 goat snp34401-scaffold404-958820 4 115357440 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450929 Affx-122921774 AX-123321263 4 3207022 GTGTCCCCTGCATTGCCAGGGAGATCCTTAACCAG[C/T]GGACCACCAGGGACATCCCTGTTGGAGAGTTTAAG Y 2 1 2 1 201000 f 74 goat snp34402-scaffold404-1029139 4 115286722 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273896 Affx-1111833879 AX-519547504 4 3239273 AGTAGCATGCGGAGGAGTCTGGGGCCTCCCTGCAG[A/G]GGAGCAGGCCATCAGTCTAAGGCGAGTGCCAGGGA R 2 1 2 1 202000 r 74 goat GoatD01.008900 4 3239273 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386622 Affx-122970230 AX-123256980 4 3264319 CCACGAGGAATAGCACTTGTACAGAAGTAGAATAG[C/T]GGTGAGCCCCACATGCCCCCCACCCAGACCCCACA Y 2 1 2 1 101000 f 74 goat snp34403-scaffold404-1086436 4 115229760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391682 Affx-122966540 AX-123262039 4 3300526 TCCAGACCCCATAATCCTCCTCCACCTATTTGATG[C/T]GGTTGGAACAGCCAAAGAACACACTCTAATTAATA Y 2 1 2 1 101000 r 74 goat snp34404-scaffold404-1122643 4 115193529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428948 Affx-122938887 AX-123299290 4 3353363 TAGGATGAAAGCGTGGCATCTTTTATTTTCCCAAA[C/T]AAAACCAGTGCGGGTCAGCGTCACGGAGAGAGGGA Y 2 1 2 1 202000 r 74 goat snp34405-scaffold404-1175480 4 115142465 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428630 Affx-122938675 AX-123298972 4 3399134 TTACCTTGAAACAACTTACGTTTGCATTGTGTTTT[A/G]CTTAGAAATGTGTGAAACAATACCTTAGATTACTT R 2 1 2 1 201000 r 74 goat snp34406-scaffold404-1221251 4 115096853 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445365 Affx-122925415 AX-123315702 4 3469297 GCTGCACCCTGTCTCACCCCTGGAGACAGGCACTC[A/G]CCACTGACGGAAAACTGGATGTTTCAAGTCAGCGC R 2 1 2 1 101000 r 74 goat snp34408-scaffold404-1291414 4 115023051 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776657 Affx-122935662 AX-385263784 4 3608380 TAGATAACTCAGTTATTTCTTTAATAGGTTGTTGA[A/G]AAGATGGCCCAAGATGCCATTTAAATAAAGATGTT R 2 1 2 1 102000 r 74 goat snp34411-scaffold404-1430497 4 114884142 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418681 Affx-122946307 AX-123289029 4 3659583 CATGTTTCTGTACTTCTGAAATGTGTGCATTCTGA[C/T]GGCCCAAGGAAGCCACGGGGAAATCATTGCACTCA Y 2 1 2 1 101000 f 74 goat snp34412-scaffold404-1481700 4 114833710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392039 Affx-122966465 AX-123262396 4 3761348 CTAACTCATCTGCTCTCCTTTTCTGTGATGCTGTA[C/T]GCTTATCTCATCCTCTCTCTCTGACCATTTCCTTT Y 2 1 2 1 101000 f 74 goat snp34414-scaffold404-1583465 4 114730585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773293 Affx-122952479 AX-385260436 4 3861340 ACATATTTGTTTTTATCTGAGGTTTATAAATCTGA[A/G]TGTCCATTCCCTCTGCAGATTTCTTTGGCATTATT R 2 1 2 1 101000 r 74 goat snp34416-scaffold404-1683457 4 114632106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387971 Affx-122969599 AX-123258329 4 3907846 TGTGTATCACATTCCCACCTCCAACATGTATAGTG[G/T]GTGACCATAACACATTTTCATCCCATTCCACAGCA K 2 1 2 1 201000 r 74 goat snp34417-scaffold404-1729963 4 114585621 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426802 Affx-122940534 AX-123297148 4 4002182 TAGTCTGTCTAAATTAAATTTGATGACTTGATGCT[A/G]TATTGGTTAAATGTGGGAACAGAATCCCAGATTTT R 2 1 2 1 101000 r 74 goat snp34419-scaffold404-1824299 4 114490887 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447053 Affx-122924520 AX-123317389 4 4038636 ACACACACACCATTTGATGCTGTGCAACTCACTAC[A/G]TGCGGTTTAATTATGATCTTATCCTGCTGTCTGAA R 2 1 2 1 101000 f 74 goat snp34420-scaffold404-1860753 4 114454701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428696 Affx-122938628 AX-123299038 4 4073559 CATTCCAGACCCCCAGACCACAGACATATGGACCC[A/G]TATAGAAGTTTCCAAAACAATCCTAAAGGGACCAG R 2 1 2 1 101000 r 74 goat snp34421-scaffold404-1895676 4 114419798 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800268 Affx-122920174 AX-385287191 4 4144055 TATTACTCATTTAAAGCAGTCACTTGAAAGGCTGT[A/G]CATATTCATTATAATATGGCAAATGTTCTTTGGAA R 2 1 2 1 101000 f 74 goat snp34423-scaffold404-1966172 4 114340663 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386062 Affx-122971462 AX-123256420 4 4231116 TATAGGATGTAATAACAAGGCCGGTCCTCTGCCAC[G/T]TGCTTCTCCAGCTACAGCCCAAGACTCTGGTTCAT K 2 1 2 1 201000 f 74 goat snp34425-scaffold404-2053233 4 114254639 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275234 Affx-1111834782 AX-519548813 4 4252831 TTCATGCAGGAAAAAAATCCTGCCAACTCTCACCA[A/G]AGCTCACTGCAGGACAGG R 2 1 2 1 101000 f 74 goat GoatD01.052699 4 4252831 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320797874 Affx-122947474 AX-385284812 4 4306277 AAAGGATTTTCCACTCCCAATGAGATGCCTCTGGG[C/T]GCTCTTCCTGCTGTCCCGTGAACCTGCCTTGGAAT Y 2 1 2 1 202000 r 74 goat snp34426-scaffold404-2128394 4 114179121 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802526 Affx-122936312 AX-385289430 4 4337782 TGGAGCTTTTCAAAAAACTAACTAGTTAATTGTCA[A/G]TTGGTTACATTGAGTCTGATTTGTGACATGGGGGA R 2 1 2 1 101000 r 74 goat snp34427-scaffold404-2159899 4 114148116 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278192 Affx-1111836219 AX-519551681 4 4386566 GTTCACTGAATGAATAGATTTTGAGCACCTTTTAT[A/G]TGCTGGACGCTGTTCTTGATGTGGATAACAGCGGG R 2 1 2 1 101000 r 74 goat Random2.2K-396 4 4386566 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38414359 Affx-122950014 AX-123284708 4 4399943 AGTCCTGCTCACTAAGGACCCAATAGTGGTTGGAA[A/C]GTAGTAAAATCAAGAAATCAAAATCAAAAAAGAAA M 2 1 2 1 101000 f 74 goat snp34428-scaffold404-2222060 4 114084740 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414933 Affx-122949097 AX-123285282 4 4470729 AGCGACTTCACTTTCACTTTCAAGATAATCTTACC[A/G]CCTCAGTGTCAGTGGTTTTAATCACATCTTTTTGT R 2 1 2 1 201000 r 74 goat snp34429-scaffold404-2292846 4 114019607 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787746 Affx-122926281 AX-385274769 4 4501539 CCCCAAAGAAGGGTGTTTATCACATTTCATTCATA[C/T]GATTTCAGTATAATTCATTATGATATTTGGCCCTG Y 2 1 2 1 101000 f 74 goat snp34430-scaffold404-2323656 4 113988367 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384582 Affx-122972993 AX-123254940 4 4549023 TAAATAGTGGAGTGTGTGCTGGAAAGAAAGCTGGC[G/T]TTAGGTTTCAATAAACTAGAATTGGAATCCCTGTT K 2 1 2 1 201000 r 74 goat snp34431-scaffold404-2371140 4 113940912 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427495 Affx-122940002 AX-123297838 4 4596695 TGTGCTTGCTCTACCGTGGGAGGTCCTCTAAGAGA[C/T]GTCTTGACACTTGGGGGCCCTGGTTTCTTGTGCAT Y 2 1 2 1 101000 f 74 goat snp34432-scaffold404-2418812 4 113894320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792769 Affx-122933797 AX-385279748 4 4620400 ACAACACATTTAACCACTTGTTTTCAGCCAGATTT[A/C]TGAAAAGCAAAAGGTGGCTTTGGTTTTATTGATCA M 2 1 2 1 201000 r 74 goat snp14556-scaffold1588-32651 4 113863730 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787528 Affx-122954881 AX-385274552 4 4650578 GCATAAATGCAATCTCAAGTAACATGAAAATTAAC[A/G]TGAGAAACTCAGAATCAGCCAAGAAACACTGCTTG R 2 1 2 1 101000 r 74 goat snp14555-scaffold1588-2473 4 113833627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417188 Affx-122947319 AX-123287536 4 4654902 ATGAGATGAAGCGACAGAGTTGCCTGGCCTAGTTC[A/G]CTCTTGCATTATCAAGATCTTCATGATCTAAGTCA R 2 1 2 1 201000 r 74 goat snp56732-scaffold898-750442 4 113829449 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772748 Affx-122933043 AX-385259893 4 4684127 TCTGTAAACTAGGATATTTACACCTCTGGCAAAAA[C/T]GGTGAACATTTCCTAGCTAATTTGCATGTAATCTT Y 2 1 2 1 201000 r 74 goat snp56731-scaffold898-721217 4 113802221 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779623 Affx-122943380 AX-385266725 4 4717296 AGTTTCTTTGGAGAAAGACTAAAGGAATAATTACT[A/G]CATAATTTTGTGGTGGTGTTGCTGAACTCTTACTA R 2 1 2 1 101000 r 74 goat snp56730-scaffold898-688048 4 113767771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787275 Affx-122976935 AX-385274300 4 4752731 TGCTTTTATTTATTCATTGACTTATTTAACAGATG[G/T]ACTTGAGTACATACCTTAGGCTAGAATCTGTCTGG K 2 1 2 1 101000 r 74 goat snp56729-scaffold898-652613 4 113731685 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399221 Affx-122960597 AX-123269576 4 4786480 TTCAAGTGCATGAACTGTTCCCTGTGAAATTCTAT[A/G]CTCTGAACAGTCTCCAAGTTCTTTTTCTGAACTCC R 2 1 2 1 101000 r 74 goat snp56728-scaffold898-618864 4 113697525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386859 Affx-122970069 AX-123257217 4 4823556 TCCTAGGAACCAAGTAACCAGGAGTAGGCTAAAAT[C/T]GAGCACAGGCACTTAGTCATCTTGTAAGTTAGTTA Y 2 1 2 1 101000 f 74 goat snp56727-scaffold898-581788 4 113658702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793180 Affx-122942140 AX-385280158 4 4909528 AAAGAGCATGATCTTTCAACATGATTCTTAGTGAC[A/G]AGAAGGGAGAGAGATTAGGTTAAAGCCTCTGCCTG R 2 1 2 1 101000 r 74 goat snp56725-scaffold898-495816 4 113568350 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792136 Affx-122951584 AX-385279120 4 4962488 ATCCCATGTAACATACCTTCTTCAATCATCCAACA[C/T]GTTCATGTCAAAATGTGATTGGAACATGATATAGT Y 2 1 2 1 101000 f 74 goat snp56724-scaffold898-442856 4 113515130 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274429 Affx-1111834280 AX-519548020 4 4977137 CAGGTCCAGCAGCCAGATGAAAATCCTGAGACCAA[A/C]GCCCAGCGCTGAGGA M 2 1 2 1 101000 f 74 goat GoatD01.028657 4 4977137 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38409021 Affx-122953872 AX-123279372 4 4994037 GTGGAGTATATGGAAAATCTCTGGACAATTTTCTC[A/G]TTTTTTTCTGTAAATCTAACACTGCTTAAAAAAAT R 2 1 2 1 202000 r 74 goat snp56723-scaffold898-411307 4 113483145 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427986 Affx-122939178 AX-123298329 4 5024049 CCACGAGAAGAACTTCTCTTTTTGATTGTTGATTC[A/G]TCTTGGCACAGAAAACATCTCCTTTCTGTGCAAAT R 2 1 2 1 101000 r 74 goat snp56722-scaffold898-381295 4 113452873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278194 Affx-1111836220 AX-519551683 4 5042272 TGGTGGTGGGTGTGTGTTCGGGAGAGCCTCAGAGC[A/G]GTAGGAGAAGTTGCAAGAAAGAACGTTAATGCTCA R 2 1 2 1 101000 r 74 goat Random2.2K-397 4 5042272 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800574 Affx-122932112 AX-385287493 4 5052638 GCAATTTCAACAACAAGGTGCACTTTCTGCCCTCA[A/C]ATAAAATCCAGGAAGTTTATGAAAGCATTGGTGTG M 2 1 2 1 101000 f 74 goat snp56721-scaffold898-352706 4 113424299 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392676 Affx-122966425 AX-123263033 4 5107625 CCACATGCCCAGGAGGGCCCAGCCTCAGCTGAAAC[A/G]TGGCAGTGGGCCTCCTCATTTCATTCTCTGTTCTG R 2 1 2 1 101000 r 74 goat snp56720-scaffold898-297719 4 113365857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401614 Affx-122959607 AX-123271967 4 5151423 CATCTTCAGTGTTGAGTTGACTCAGTAGCTGTGTC[C/T]GCATCCCAGCTTATGGGAAGTGGAAAGATCCAAAA Y 2 1 2 1 201000 r 74 goat snp56719-scaffold898-253921 4 113321775 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411064 Affx-122951945 AX-123281414 4 5214219 CCATTCTCCCCACCACCCCCAGCAATCCTAAATTC[A/G]TTCTCTAAGTCTCTGAGTCTGTTTTGTAGATATGT R 2 1 2 1 103000 f 74 goat snp56717-scaffold898-191125 4 113258575 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779603 Affx-122973537 AX-385266706 4 5256908 GTTACAGTGTACACAGGTGACTTACTGGTAGTGGC[A/G]TTTGCTGCTTTGCTGTATAGAAACATTACTTGAAC R 2 1 2 1 101000 f 74 goat snp56716-scaffold898-148436 4 113214996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442710 Affx-122927867 AX-123313047 4 5294482 GAGCCAAGGGAGGCTACCATGATGTCTGTCCTTGT[G/T]TTTGATGTTGTGAGATGCCCTGTGTGTGAAACTTC K 2 1 2 1 102000 r 74 goat "GoatD01.031682;snp56715-scaffold898-110862" 4 113177481 T G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320796213 Affx-122930109 AX-385283164 4 5351694 GCTAATATTAAGGTGAGGAATACCAGATAAGACTT[A/G]TTTGTATATGATAAAAAATGTGGAAGTAACATTAA R 2 1 2 1 201000 r 74 goat snp56714-scaffold898-53650 4 113120666 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782434 Affx-122973849 AX-385269510 4 5383118 TAGCAGATTTTGCATGGAATAGAACTGGACTGTTA[C/T]GAGTACTTTTCTCATGAGGGAGCTTATTTGCATAA Y 2 1 2 1 101000 f 74 goat snp56713-scaffold898-22226 4 113088818 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401086 Affx-122959628 AX-123271439 4 5423819 AACCTAAAATGGCAGAAAATTAAAGCTAATTTAGG[C/T]GAGATAAAACACCAGGAACAATGTTGGTTGAATAC Y 2 1 2 1 101000 r 74 goat snp18882-scaffold1903-18376 4 113047435 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415791 Affx-122948907 AX-123286140 4 5465713 GTGAATGAACTTCACATGAAGTTTCTCTAATACAA[C/T]ACCATTAAAACATGTATGTTCTTGTTGGAATGAAC Y 2 1 2 1 101000 f 74 goat snp18883-scaffold1903-60270 4 113005525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788665 Affx-122945818 AX-385275681 4 5508328 AGTCTGACTTGTTAGTTTCTGACCTTCAAAATTCT[A/G]CACAAATTTCCAACTGAAATCATTTTCATCCTGAA R 2 1 2 1 201000 r 74 goat snp18884-scaffold1903-102885 4 112963187 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802451 Affx-122974971 AX-385289355 4 5556863 ATTCTAAACCATTATCTCACACAGAAACCCTTCGC[C/T]GTGCCACTCAGGATAGTCAGTTAATTTTTTAACCG Y 2 1 2 1 101000 f 74 goat snp18885-scaffold1903-151420 4 112914344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407018 Affx-122955018 AX-123277369 4 5594982 TGGAACCAGCTGTCCAAAATGCATGGCAGTCAGGG[C/T]CTAACACAGGACCAGCTCCTGGCAGGTGTAGTGGG Y 2 1 2 1 101000 f 74 goat snp18886-scaffold1903-189539 4 112875088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770259 Affx-122920880 AX-385257425 4 5628233 ATGGGAGCGAATCTATTTATAGATCAGAATGCTGG[A/C]TCAGAACAATTAAGGGAATTTCTGTGTGTGCCTAA M 2 1 2 1 201000 r 74 goat snp18887-scaffold1903-222790 4 112841086 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411527 Affx-122951665 AX-123281877 4 5673207 ACCAATTGTTCCCTTTTCACCTCTAAAAATATGAT[A/G]GCATATCAAAGAGGGAGAAGTATTTAAAATCTCTC R 2 1 2 1 101000 f 74 goat snp18888-scaffold1903-267764 4 112798683 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401611 Affx-122959617 AX-123271964 4 5713736 AGCAGGGACTTATTTCTTCTTCTGAAATGACTATC[A/G]TTTTTCCTTCTGTCCTTATCTTGTCAGTTTATGAG R 2 1 2 1 102000 f 74 goat snp18889-scaffold1903-308293 4 112757144 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396336 Affx-122963065 AX-123266691 4 5757228 GGAATAGATGGTTTCTTTTCTGCCAAGTCGAACCT[C/T]TTCTGGGAATATTTGTGCTGAGTGAGCTCCCTGAC Y 2 1 2 1 101000 f 74 goat snp18890-scaffold1903-351785 4 112713071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780222 Affx-122921941 AX-385267318 4 5788006 AAGGAATATCTTGCTTGAAGGGCAATCTTGTTATC[A/G]GAAGGATTTTTACCTGTTATGTAACTTGTTGTTCA R 2 1 2 1 101000 r 74 goat snp18891-scaffold1903-382563 4 112681992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272125 Affx-1111833433 AX-519545883 4 5792170 AGCCTTCCAAGGTCTCCCCAGAAAGCAGCTGTGGA[A/G]TTAAACCGGTGAGCATCCTGGCTGGCCTGCTCAGG R 2 1 2 1 102000 r 74 goat 4_5792170_AF-PAKI 4 5792170 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320780142 Affx-122934474 AX-385267239 4 5829345 ATCGCCGTTGAGATAAAGTCAGATCTGAGGGGCAA[C/T]TTAGTTATATCTGTTTGAGAAGTTGCCCATGCACA Y 2 1 2 1 201000 f 74 goat snp18892-scaffold1903-423902 4 112640532 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802747 Affx-122953710 AX-385289646 4 5868831 TAGTTAAAGTAGAAAATCTGCTTCAACATGTAATT[A/G]TAGACTCAGCCTACGTTGTATCAGGTAGAGTATTT R 2 1 2 1 101000 r 74 goat snp18893-scaffold1903-463388 4 112602700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795882 Affx-122939234 AX-385282834 4 5923414 GCTCTGTGTTGTTTTGACCCTATAGACTTAGGATC[A/G]TTCAGTCCAACTCTTTCATTTCACGGAGGAAAGAA R 2 1 2 1 202000 r 74 goat snp18894-scaffold1903-517971 4 112548209 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429974 Affx-122938058 AX-123300315 4 6021603 GGTGAGAGTGGGGTGGGAGTTGACCGCAGCAAGAG[C/T]GGTGAGACCACTTGCTCTTAGCACTTTTGTAGTCA Y 2 1 2 1 101000 r 74 goat snp18896-scaffold1903-616160 4 112448782 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410486 Affx-122952199 AX-123280836 4 6053872 TTTTCTCCACACCATAGTGAGGGAGCTGCAGGCAC[A/G]TAATTTAATCATGCTCTCTCTTTTCTGAAGAGTCC R 2 1 2 1 101000 r 74 goat snp18897-scaffold1903-648429 4 112416475 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418129 Affx-122947117 AX-123288477 4 6086036 TAGGATTCATGAGAAGCTGTTTGATTTCCCGATTT[A/G]TTTTTGTAGGTGGTGCAGCCAAAAAATTGAATCTC R 2 1 2 1 101000 f 74 goat snp18898-scaffold1903-680593 4 112383547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795272 Affx-122966167 AX-385282230 4 6126119 TATCTTCCAGCCTCTCTGTTGAAAGGACTGAAACA[C/T]GCTAACATCGTGCTACTTCACGACATCATCCACAC Y 2 1 2 1 101000 f 74 goat snp18899-scaffold1903-720676 4 112343638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435367 Affx-122933584 AX-123305707 4 6162680 GTAGGAACTCTGCAAGACATTCTTTTTAAAATAAA[G/T]ACTAGAATCAGTATGGTACTTGAAGTATTTGTTGA K 2 1 2 1 303000 r 74 goat snp18900-scaffold1903-757237 4 112307004 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396955 Affx-122963174 AX-123267310 4 6198643 GAGTTAACAATGAGCTGAGCATATAAACCCTATGC[A/G]GTCTAAAGATGTATAAAGGGTTTGGTGATGATGAT R 2 1 2 1 101000 r 74 goat snp18901-scaffold1903-793200 4 112271030 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414816 Affx-122949207 AX-123285165 4 6247416 ATGGAGGATGGGGTGGCAGAAAGGGTTAGTTAAGG[A/C]GTTTGGGATGGACATGTACACACTGTTATATTGAA M 2 1 2 1 101000 f 74 goat snp18902-scaffold1903-841973 4 112222208 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394233 Affx-122964883 AX-123264588 4 6286491 AACGCTTTTTTCCGAGTTTAGATAATTGCCACAGT[A/G]TCATCCTTCCTTGGAGACAGTAGTCAGCCCCAGAC R 2 1 2 1 101000 f 74 goat snp18903-scaffold1903-881048 4 112183721 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416262 Affx-122947960 AX-123286611 4 6356431 GTTACTGGAACTAGCTTCAGAGATTTGAGCTTATC[C/T]TGTCTTCATTTGGAAAAGAAAACAGATGCGGTTAG Y 2 1 2 1 101000 f 74 goat snp18904-scaffold1903-950988 4 112113336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403846 Affx-122957937 AX-123274198 4 6385362 TGGGCTTTAAGACTGGGCTCCCATGCACAAAGCCC[A/G]TTCCCTGCCATTTTAAGATGGGTTGACCTCCTGTT R 2 1 2 1 101000 r 74 goat snp18905-scaffold1903-979919 4 112084538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378414 Affx-122976784 AX-123248773 4 6420272 TTTCCTAAAGTAGGCTGCCAGGTAAACAGTAGGAT[A/G]CAGAAACTGCTCAAAAATTTTGGCTAAATAAGACA R 2 1 2 1 101000 f 74 goat snp18906-scaffold1903-1014829 4 112049442 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792846 Affx-122923074 AX-385279824 4 6471199 TGGTCAGCAAGTGCATATTTTCTGAGCAAACTAAC[A/G]TATAATGTGAAAAGACTAGTTTTCCCTGTTTCCCA R 2 1 2 1 101000 f 74 goat snp18907-scaffold1903-1065756 4 111998068 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436941 Affx-122933183 AX-123307279 4 6526465 AGAGTGCCAGTGCTGGAGTGAAATGTACCAGTCAG[C/T]GGCTCTGCCACTTCCTTTCCACTCAGCCCCAAGGA Y 2 1 2 1 101000 f 74 goat snp18908-scaffold1903-1121022 4 111942425 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781779 Affx-122967441 AX-385268861 4 6572545 AATACACATAAATTTTCACTGCCTTTGTTGCTGAA[C/T]CAAAAGACTATTCTTGCTATCTTTGAATTAAACTC Y 2 1 2 1 101000 f 74 goat snp18909-scaffold1903-1167102 4 111896405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797127 Affx-122957166 AX-385284067 4 6576842 CACCCCATTTCAGATTAATTTGATCTGTATTTCTA[A/G]CTGTGACTAAAGATTTTAATCCTTTATGAAGTTAC R 2 1 2 1 101000 f 74 goat snp38586-scaffold49-2395 4 111892173 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398432 Affx-122961618 AX-123268787 4 6623456 AACCTCAGAATGACTTTCACTGATATTACCCAGAG[C/T]GGTGATAAATTAATCTCTTAGGCATAGAGAAGAAT Y 2 1 2 1 101000 r 74 goat snp38587-scaffold49-49009 4 111845720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418166 Affx-122947088 AX-123288514 4 6684779 TTGTCATACAGTCCTTAAGGAAGAAGAAAAGGAGA[A/G]AGAAATGTATCGAAATTCATCAGGTTTTTCAGGCA R 2 1 2 1 201000 r 74 goat snp38588-scaffold49-110332 4 111784472 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278197 Affx-1111836222 AX-519551686 4 6692653 GCCTGCCCCACTGGCACAGAGCTTTAAAAGCCATC[A/G]TGCCTGCCCTCTTAACAGTCAAGGACACAGCCCAA R 2 1 2 1 102000 r 74 goat Random2.2K-400 4 6692653 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38411094 Affx-122951923 AX-123281444 4 6717765 TTTTTTGCAGCCCTAGAATGTCAGAGCTAAGGGTT[A/G]CTGACAGAACTGGAATTAGTCCTGGGCTATTACCT R 2 1 2 1 101000 f 74 goat snp38589-scaffold49-143318 4 111751334 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387202 Affx-122970599 AX-123257560 4 6764072 CTAGATATGGGTCCCTGAAAATCAAGACCAAAATG[A/G]TCTGGCTTTCTCTGTCCAGAGGATATCTATGACTT R 2 1 2 1 101000 f 74 goat snp38590-scaffold49-189625 4 111705085 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433256 Affx-122935235 AX-123303597 4 6796192 GGAGAGAAAATCAAGGAGATTATTCATTTACTTAC[A/G]TTTATTCTGAGACTTGGCAAAAGGCATTTTAGTCA R 2 1 2 1 101000 r 74 goat snp38591-scaffold49-221745 4 111673121 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278199 Affx-1111836223 AX-519551688 4 6868190 TTGCATCCTGAACCACCAGCTGAGCACCCACACAT[C/G]AGTCAGTCTGGCTGAGATTAGCCTGGTGGGTCCAG S 4 1 2 1 202000 r 74 goat Random2.2K-401 4 6868190 C G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38426556 Affx-122940176 AX-123296902 4 6875674 CAGAAAATCTCAGAGTCTTTACTTAAGGGAGGAGA[C/T]GGGATGATCGTCTATGCAGGCATGTTCTTCTAACA Y 2 1 2 1 101000 f 74 goat snp38593-scaffold49-301227 4 111592239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430083 Affx-122937539 AX-123300424 4 6933637 AACACTGAATTCCTACATCTACCCCTTTCCCACTG[A/C]TGCCCCCTAGCAAAGGAACAAAGCTAGAGACCAGA M 2 1 2 1 201000 r 74 goat snp38594-scaffold49-359190 4 111534248 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433666 Affx-122934562 AX-123304007 4 6990443 CTAAAGCCACTCTCGACAGGCTGAAGGAGCCAGGC[A/G]GATGGCTGCCCTTGCTAAAGCGACGTGGGAAGGCC R 2 1 2 1 201000 r 74 goat snp38595-scaffold49-415996 4 111477173 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406801 Affx-122955695 AX-123277152 4 7033112 ACATGTACTCCTTCAGTTACTGATGAGTTAATTTC[A/G]TTCTATTCTCAATGACAGACTTATTCTCTGATCCA R 2 1 2 1 101000 r 74 goat snp38596-scaffold49-458665 4 111433737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406323 Affx-122955454 AX-123276675 4 7074160 CGCAATAAATGATGGCATGAATCACCCCTTTCAAA[C/T]ACAGGACAACATCCTGAAGCTCCTTACTTGCAGTA Y 2 1 2 1 201000 f 74 goat snp38597-scaffold49-499713 4 111392557 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795298 Affx-122941748 AX-385282256 4 7125345 GATAATGGTAAAGAACTATCATGTCTAAAAATAGA[C/T]ACTTGGAGCTTAGAATCTGTCAGACCATATGTTGT Y 2 1 2 1 101000 r 74 goat snp38598-scaffold49-550898 4 111340901 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390435 Affx-122967633 AX-123260792 4 7193967 CAGAGACCTATTCTGTCAACTTTCTTCCTCCTACC[A/G]CAAAATGTCGGTGATAGAGGCATTTGTATTATGGA R 2 1 2 1 101000 r 74 goat snp38599-scaffold49-619520 4 111269808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449830 Affx-122922394 AX-123320165 4 7239847 CTCACATGCCATTTTTTATCCTAAAAAACAAAATT[A/G]TACATGTCAGTTTATTCCTTCACTGTTCAGACATG R 2 1 2 1 101000 r 74 goat snp38600-scaffold49-665400 4 111223958 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476438 Affx-1251763688 AX-586011839 4 7256266 TGAACCCACAATCTCATAGTTATACTTACAGGATA[-/AAAAAAAAAAAAAAAAAAAAATGGGAGGGGGGAGGGAAAGAAAAAAAATAAAAAATTAAAATTAAAAAAAAAAATAAAGG]AAAAAAAAAATGTATATCTTAAGTCCCTTTCTCAT - 4 1 4 1 20000 r 74 goat SV_147 4 7256266 - deletion junction SV-TF-chip 560378490 Affx-1251763688 AX-605230905 4 7256266 TGAACCCACAATCTCATAGTTATACTTACAGGATA[-/AAAAAAAAAAAAAAAAAAAAATGGGAGGGGGGAGGGAAAGAAAAAAAATAAAAAATTAAAATTAAAAAAAAAAATAAAGG]AAAAAAAAAATGTATATCTTAAGTCCCTTTCTCAT - 8 1 4 1 20000 f 74 goat SV_147 4 7256266 - deletion junction SV-TF-chip 562166096 Affx-1251763688 AX-606941505 4 7256266 TGAACCCACAATCTCATAGTTATACTTACAGGATA[-/AAAAAAAAAAAAAAAAAAAAATGGGAGGGGGGAGGGAAAGAAAAAAAATAAAAAATTAAAATTAAAAAAAAAAATAAAGG]AAAAAAAAAATGTATATCTTAAGTCCCTTTCTCAT - 8 1 4 1 20100 r 74 goat SV_147 4 7256266 - deletion junction SV-TF-chip 562166133 Affx-1251763688 AX-606941541 4 7256266 TGAACCCACAATCTCATAGTTATACTTACAGGATA[-/AAAAAAAAAAAAAAAAAAAAATGGGAGGGGGGAGGGAAAGAAAAAAAATAAAAAATTAAAATTAAAAAAAAAAATAAAGG]AAAAAAAAAATGTATATCTTAAGTCCCTTTCTCAT - 8 1 4 1 20100 r 74 goat SV_147 4 7256266 - deletion junction SV-TF-chip 562166287 Affx-1251763688 AX-606941695 4 7256266 TGAACCCACAATCTCATAGTTATACTTACAGGATA[-/AAAAAAAAAAAAAAAAAAAAATGGGAGGGGGGAGGGAAAGAAAAAAAATAAAAAATTAAAATTAAAAAAAAAAATAAAGG]AAAAAAAAAATGTATATCTTAAGTCCCTTTCTCAT - 8 1 4 1 20100 f 74 goat SV_147 4 7256266 - deletion junction SV-TF-chip 38389645 Affx-122968734 AX-123260003 4 7303861 GTACGTGCCAGGTACTATATTGGGTTCTGAGGCTA[C/T]GATGAACAAATCTGATAAGGATCTTGCCCTTATGT Y 2 1 2 1 101000 f 74 goat snp38601-scaffold49-729414 4 111159034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782071 Affx-122940733 AX-385269149 4 7335957 TCATAGTACTTTCTTTTTATCTGTATTATGACTCA[C/T]GTCACACTCTTAAGTATTCAAACATTCATGTGAAT Y 2 1 2 1 101000 f 74 goat snp38602-scaffold49-761510 4 111126804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278047 Affx-1111836224 AX-370982909 4 7352975 TGTGAATCAAAGAAGAGCTCGTTGGTGAGGAAGGC[A/G]CGCTAGTGCTCCCGCTCCAGCCCCTCGATCACAGC R 2 1 2 1 101000 f 74 goat Random2.2K-403 4 7352975 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381973 Affx-122974100 AX-123252331 4 7368047 CTTTTTAAGGATTAATGCCTGACTTTAAGTCTTTC[A/G]TGTAACTCTTAAGGAACCTCCACAGCTAGGGACCA R 2 1 2 1 201000 f 74 goat snp38603-scaffold49-793600 4 111094130 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785082 Affx-122943854 AX-385272129 4 7407900 GTTAAGTTCTGTTATTTCTCTGAAACAGTTCACCA[A/G]CTACCTCCTATATATTCCCACTATAATTTACCATT R 2 1 2 1 101000 f 74 goat snp38604-scaffold49-833453 4 111053817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402833 Affx-122958261 AX-123273186 4 7441644 TTCCAGTTTGAGCAGCAGCTTCTGTTTCTTCTTCC[A/G]TCAACCATGGCTCTGCTTCTTTAGTTGAGGATCAA R 2 1 2 1 201000 r 74 goat snp38605-scaffold49-867197 4 111020164 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802883 Affx-122934274 AX-385289781 4 7486400 TACTTAACCTAGGTAATCTTGACAATTCTGCAGGG[C/T]AGGTGGCCTTATCCCTTTTTTATGTAAGAAAAAAT Y 2 1 2 1 101000 f 74 goat snp38606-scaffold49-911953 4 110974470 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278203 Affx-1111836225 AX-519551691 4 7516291 GTCACCTGATAAAAGAAATTCATTTATTTATTCTC[A/G]ATTCAATGTTTGGCAGGAAGCATGAAAATACTGGT R 2 1 2 1 201000 r 74 goat Random2.2K-404 4 7516291 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784277 Affx-122941977 AX-385271328 4 7533989 AGAATGGGCCTTTGGTAAATAACTGACTCTGTGTT[A/G]CTTTTGACCTGTGCTTTATTGAGCTGCACTGGAAA R 2 1 2 1 101000 r 74 goat snp38607-scaffold49-959542 4 110926942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788740 Affx-122919366 AX-385275756 4 7581831 AAGAAAATGCTGGTCTTAGTTGTAATTAAGATACA[A/G]TGGTACAGTGTGTAATTAAAACTAGAATAAACTGT R 2 1 2 1 101000 f 74 goat snp38608-scaffold49-1007384 4 110879395 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434432 Affx-122934663 AX-123304773 4 7611108 AATGTCTTGGAAAACTTGGGGAGCTGTCTGTTCTT[A/G]CATATATCATGTTTCATGGTAAAGCATGATGGGAA R 2 1 2 1 201000 r 74 goat snp38609-scaffold49-1036661 4 110850682 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451958 Affx-122920954 AX-123322291 4 7650476 GCAAAAATGTGAGATGCATACAACGTTCTCAAAAT[C/T]GGCCAAGGTTCAGTTCAGTCCAGTCCAGTCACTCA Y 2 1 2 1 101000 f 74 goat snp38610-scaffold49-1076029 4 110810925 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441936 Affx-122928583 AX-123312273 4 7679220 ACCCATCTCCTAGTCGTGTCTTCCTGGTCAGATTA[C/T]ATCACCTTGAATTTCCACTTACTCACCTGTAAAAC Y 2 1 2 1 101000 r 74 goat snp38611-scaffold49-1104773 4 110781983 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414640 Affx-122949327 AX-123284989 4 7715452 CTCTAGCTTCTGTGGGTTGGAGAATTTCCCCGAGC[A/G]TCTTGCCCGCTCCCCAGTTGTTCCCCTCGGCGCCT R 2 1 2 1 101000 f 74 goat snp38612-scaffold49-1141005 4 110745862 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793294 Affx-122955142 AX-385280272 4 7747711 AGGAAGGAATGCAACTTCTTTTTTTCTAGACAGCT[A/G]TATCTTCTTTGTAGAAGACTATATGGGATATAGGT R 2 1 2 1 101000 f 74 goat snp38613-scaffold49-1173264 4 110713855 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418011 Affx-122946657 AX-123288359 4 7784360 ACAGCAGCCTGGAATGTGCTTTATATTCTTGGGTT[A/C]GTTTTTCTATTTGCACCACAGCCGAAACGGAATGC M 2 1 2 1 201000 r 74 goat snp38614-scaffold49-1209913 4 110677395 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411705 Affx-122951537 AX-123282055 4 7891659 TCATGGACAAAATACACGTGGGTGAAATACGGATA[C/T]ATGTGTATTTCTCCCAGATGGTCTTGGTATCACAT Y 2 1 2 1 101000 f 74 goat snp38616-scaffold49-1317212 4 110570371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775275 Affx-122924849 AX-385262406 4 7935339 CTCACCTCTTCGGTTCTGAGGTCATTCTGTCTCAT[A/C]GTCTATGCGAAGATTAACCTCAATGAGTGCAAATG M 2 1 2 1 101000 f 74 goat snp38617-scaffold49-1360892 4 110525936 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388213 Affx-122969413 AX-123258571 4 7973287 CCACAGTTAAGTAGATCAAAAAACATTCTGAACGA[C/T]AAAGAGGAAAATAAGATACAGCAATGATCGGCCTA Y 2 1 2 1 201000 f 74 goat snp38618-scaffold49-1398840 4 110488027 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795394 Affx-122924354 AX-385282350 4 8002859 AACATAAGGTCCAGAATCTATTAACTTGTGATCCA[C/T]AGCCTTCAAAGCAATTTACGTGCAGTATACATTTC Y 2 1 2 1 101000 f 74 goat snp38619-scaffold49-1428412 4 110458569 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435037 Affx-122933755 AX-123305377 4 8042267 TCTGCAGCTCGTGAGGATGATGACATCATCGATGA[C/T]TGTCTCAAGTGTCATTGAACTTCATGGCATATAAC Y 2 1 2 1 101000 r 74 goat snp38620-scaffold49-1467820 4 110419145 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792105 Affx-122924736 AX-385279091 4 8124777 GAAAGTCCTTGTCATTTATCTTAGAGTTAAGAACC[A/G]TAGCTTGGAGTCTTAGAAATTAGAGATCATTATAT R 2 1 2 1 101000 f 74 goat snp38622-scaffold49-1550330 4 110335944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383334 Affx-122972684 AX-123253692 4 8156285 GGGGGTGAAGGTGAGGAGACAGAAGCCAGATTACA[A/G]TGGATTGGCATGTGAATATTTGTTCAAGTCCTGTG R 2 1 2 1 101000 r 74 goat snp38623-scaffold49-1581838 4 110304399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787421 Affx-122964955 AX-385274446 4 8194109 TCTGAAATAGATACTGATACTTCTCTAAGACATCA[A/G]GAATTATTTACCCCTTTTTTTTGACTAGTGCAGTA R 2 1 2 1 101000 f 74 goat snp38624-scaffold49-1619662 4 110266145 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377055 Affx-122978296 AX-123247414 4 8230472 TATCACAGACCCTTTTGAGAAACCGGAGGATGCTG[C/T]AGACAAACTCTTTAGGGAAATGCATATACACATTT Y 2 1 2 1 101000 f 74 goat snp38625-scaffold49-1656025 4 110229528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447919 Affx-122923797 AX-123318255 4 8267578 ATCTGTGCCTTTAACTTTTAATATACTGAGAAGTG[A/G]CTTCAAGAGTTCATTCCAATTTTCATATCTATTGG R 2 1 2 1 101000 f 74 goat snp38626-scaffold49-1693131 4 110192077 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272141 Affx-1111833441 AX-519545898 4 8293720 CTCATGTGGTTTTAATGTGCATTTCTCTAACTATT[A/C]ATGATGCTGATGGCATTTGGGTGCTTATTGCCATC M 2 1 2 1 201000 r 74 goat 4_8293720_AF-PAKI 4 8293720 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38377654 Affx-122977858 AX-123248013 4 8298732 GTAACAAATGGCATTACTATTTGGTATACAAATGG[C/T]AAGCTGCTATTTGGAAAATCATTGGCAATCTGGGT Y 2 1 2 1 101000 f 74 goat snp38627-scaffold49-1724285 4 110160466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418600 Affx-122946358 AX-123288948 4 8330032 TAAATCTGGTACAGCTCTCTGTCGCTCCTCGCCCA[C/T]GGCATCTGCTCCTGCTTCCAGCACTTCCCTTGTTT Y 2 1 2 1 101000 f 74 goat snp38628-scaffold49-1755585 4 110129300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800609 Affx-122979206 AX-385287528 4 8369249 ATCTGATCTGGAACAGGAACACAGCGAAGCAGCAG[C/T]AGCTTATTGTAGTTAGACTCTTGGTGCTGGAGAGG Y 2 1 2 1 101000 f 74 goat snp38629-scaffold49-1794802 4 110089204 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393625 Affx-122965310 AX-123263980 4 8402887 TTATGAGTGGAAGAGGCTAAAGGAAAGTGAGTGCT[A/G]TGGAGAGATAGGAATGGGGTGCTGAAGGTGCACAG R 2 1 2 1 101000 f 74 goat snp38630-scaffold49-1828440 4 110055580 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791408 Affx-122950804 AX-385278400 4 8437686 AACAGACGTGTGTGAAGGCAGTCGTGGTGATACAC[A/G]TTTCAGAGGAATAGAGGATAGAGAGTTCTGGGAGT R 2 1 2 1 101000 r 74 goat snp38631-scaffold49-1863239 4 110020159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800073 Affx-122959479 AX-385286996 4 8480609 TGTGCATTGCTCCAGGCATCTGGATATAAGCCCTC[A/G]TGTATCTTACCTTCTAGTTCAGAAGACAGAAATTA R 2 1 2 1 101000 f 74 goat snp38632-scaffold49-1906162 4 109976926 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419466 Affx-122945483 AX-123289814 4 8527941 GGAATTAAGCCGGTCGAATATTTTTGAAATAATGT[A/G]TCCCTCTGTACTAGTGATTTGTTCATTTTAATCTC R 2 1 2 1 101000 r 74 goat snp38633-scaffold49-1953494 4 109926139 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387417 Affx-122970403 AX-123257775 4 8579711 GAACTCTTTCAACAGGTATGTTAGAACTGTGAGTG[C/T]ACTACCTTTGATCGTTTTCTCCATGTTTTTCCAGT Y 2 1 2 1 101000 f 74 goat snp38634-scaffold49-2005264 4 109874497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794189 Affx-122955525 AX-385281155 4 8609855 TGGAAGTGTTCATTACAATCGTAAGGTGTTGAACC[A/G]TAACCTAGCCAATGAAAGAACTACTATTTTAGACC R 2 1 2 1 101000 f 74 goat snp38635-scaffold49-2035408 4 109843682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434114 Affx-122934933 AX-123304455 4 8641462 GTGCTGCGCTTTTAAACACCCATCTTTAGTGGTTT[A/C]ACAGAGAAATAATTACTGAAAGAACATCCTTACTT M 2 1 2 1 101000 f 74 goat snp38636-scaffold49-2067015 4 109812035 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785741 Affx-122970741 AX-385272781 4 8673781 ACTGAAGAGTTTTTTTCCTATCACACAACATTTAT[C/T]GTAGTGCTAGGCATAAAGCCAAAACTCTGAAAATG Y 2 1 2 1 101000 r 74 goat snp38637-scaffold49-2099334 4 109779996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376573 Affx-122979079 AX-123246932 4 8702520 ACAAGATTCTAGAGTAGATAAGTGAGAAGAAACTT[A/G]TTGTCATTTCTGTTTTTGTTAACTTGTTCAAGACA R 2 1 2 1 101000 f 74 goat snp38638-scaffold49-2128073 4 109751119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378624 Affx-122977117 AX-123248983 4 8740302 GACAGGAAAGATGATGACGTAACCATGGTAGAGAA[C/T]GCATGAGCTGGGAGAAGAGTAGGAGAAAATATTTA Y 2 1 2 1 101000 f 74 goat snp38639-scaffold49-2165855 4 109713390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278051 Affx-1111836226 AX-519551541 4 8826678 GCTAACTTCAGTAAAACATGCTGTGTAGCCATCCT[A/G]CCATGAGAGCCTTGGGGTCCTTTAAGGTTGGGGGT R 2 1 2 1 201000 f 74 goat Random2.2K-405 4 8826678 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382330 Affx-122973892 AX-123252688 4 8833627 GAAACTAGAAAGTTGGATGACCTTGAGGCAGACAT[A/G]CAAGCAGAGCCTCCCTCCCTGATGGTACAACTTGG R 2 1 2 1 101000 f 74 goat snp38641-scaffold49-2259180 4 109619940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799479 Affx-122929213 AX-385286409 4 8870175 TCTTACCAGAGCAAACAGAGAGATAGTTTAAAATA[C/T]GAATTGCATCTTTTATCTTGCCACTTTCCTCCTGA Y 2 1 2 1 101000 r 74 goat snp38642-scaffold49-2295728 4 109582324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785704 Affx-122959861 AX-385272745 4 8924550 TTTTATGGAAGAATAGCGAGAGGTTCTCTAAGCTC[G/T]CTTGAGTTCCTTGATTTGCTGAAGGTCATGGCTAG K 2 1 2 1 101000 r 74 goat snp38643-scaffold49-2350103 4 109527372 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278207 Affx-1111836227 AX-519551695 4 8938494 CAGTTAGGCCCAGCTAACTGCCCTCTGCTCTCACC[A/G]AGACCCTTTACCCTCCGCTTCCAAAACACGCCCCA R 2 1 2 1 201000 r 74 goat Random2.2K-406 4 8938494 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320802562 Affx-122975989 AX-385289464 4 8960292 TTCAATACTACCACTGGACTTTGCATATAGCAGAC[A/G]TTTGGTTAATGTTCCTTGAACTAAATTTTTAATTA R 2 1 2 1 101000 f 74 goat snp38644-scaffold49-2385845 4 109491040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381642 Affx-122974759 AX-123252000 4 9009396 AGATCAAGTGTGCTCACCCCTACTGTAGGAAAATA[C/T]GAATTCTGCAGTTTGGGGCAGTGTTCTATATTCTC Y 2 1 2 1 102000 f 74 goat snp38645-scaffold49-2434949 4 109441705 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431466 Affx-122936487 AX-123301807 4 9035931 TAAGTATTCTGATGTTGATGTATTCAAAAACAGCA[C/T]TGTAAATGTGAGTTAGCAACAACAACAAAAAAAAC Y 2 1 2 1 101000 f 74 goat snp2240-scaffold1069-433050 4 109391748 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418934 Affx-122946507 AX-123289282 4 9084076 TAACATTTTCAGAACATTTTAAAAAATATTTATTT[A/C]TTTGGGTGTGCTGGATCTTACAAGCCCCTTGAGGT M 2 1 2 1 103000 r 74 goat snp2239-scaffold1069-384905 4 109343657 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396166 Affx-122963376 AX-123266521 4 9182607 CAACCAAAGATTGTATGACAGTGTCATGGTGTCCC[A/G]CTTCCTAAGGCCAACTGAACCCATTTCACTAAGAT R 2 1 2 1 101000 f 74 goat snp2237-scaffold1069-286374 4 109244119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394306 Affx-122964690 AX-123264661 4 9222695 AATCATATTCTCTTTAGGAATGAATTTTTTAGGAA[C/T]GATATCCACAATCACAGGGCAGGGGTAGATATGCA Y 2 1 2 1 101000 f 74 goat snp2236-scaffold1069-246286 4 109204415 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436532 Affx-122932933 AX-123306870 4 9290744 GAAAGTAGTCCAGATGCTCACTGGTATGAATTCAA[C/T]GGTATCATTTATTTGGTAATTATGAGAGGTACCAA Y 2 1 2 1 101000 r 74 goat snp2235-scaffold1069-178237 4 109136736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769653 Affx-122962583 AX-385256823 4 9325842 TTTATACTCTTGGGAGATTAGATATCAGGTTTTAT[A/G]TTTCCACGTAGTTAAATCACCATGCCCCTTATTCC R 2 1 2 1 101000 r 74 goat snp2234-scaffold1069-143139 4 109101618 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394817 Affx-122964799 AX-123265172 4 9376675 GCAATATACATATTTATCAAAACTTTACAATAAAA[C/T]ATCCTTAAAGATGGATTTTAAAATTAGGAGCAAGA Y 2 1 2 1 303000 f 74 goat snp2233-scaffold1069-92306 4 109050057 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437591 Affx-122931867 AX-123307929 4 9436126 GAGATTTCCCATGTACCCTTTGCTTCCCTGCATGC[A/G]TGACTTCCCCCATCATAAACACACCCCTCCTCCAC R 2 1 2 1 101000 r 74 goat snp2232-scaffold1069-32855 4 108990425 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381523 Affx-122974852 AX-123251881 4 9482233 GGAAAGTCTCCTAGGGGAGATCCAGAGGGAGGAGG[G/T]CAAAGCCAAGGTCGTGGGGTAGGTGCTGCGATTGG K 2 1 2 1 303000 f 74 goat snp44424-scaffold603-6640725 4 108943158 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769028 Affx-122937385 AX-385256203 4 9512423 AGTTTTCACCTCCCACCTTTCTTCTTTAAGGGTCA[C/T]GCCACTTTTAATGACTAGAAATAGTTGCAAATGAA Y 2 1 2 1 101000 f 74 goat snp44423-scaffold603-6610535 4 108912533 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402672 Affx-122958364 AX-123273025 4 9544634 ATCAATCGTATAGGGTGACTGTTCAAGCCACATCT[A/G]TCATTTATCACTGGAGAGATCTGTTAGGGCCAAGT R 2 1 2 1 101000 f 74 goat snp44422-scaffold603-6578324 4 108880366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797366 Affx-122948453 AX-385284305 4 9575034 CCCCCTTACCTAAGCTTAGATTTTTATAGATTTGA[A/C]TACAAAAATAGCTACTGCTTTTATCTGATCTGAGT M 2 1 2 1 201000 r 74 goat snp44421-scaffold603-6547924 4 108849963 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433443 Affx-122935068 AX-123303784 4 9605962 AGATGACTTTATAGCAGGAGGCAAATATTACAATC[A/G]CAATTATGTTCTGCAACAGGAAGTAAGTTCTAAAT R 2 1 2 1 101000 f 74 goat snp44420-scaffold603-6516996 4 108819032 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378967 Affx-122976410 AX-123249326 4 9635059 GCTCCTTTGGGCTTGCCATTTATGGAAACTCTTAA[C/T]GGAAAGTGAATTCATGTGTGGATGGGATTTAGGTA Y 2 1 2 1 101000 f 74 goat snp44419-scaffold603-6487899 4 108789915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787606 Affx-122925587 AX-385274629 4 9676896 ATTTTGATAAAAACTGTTCCTGCTCTACTGTGTCC[A/G]TTTTGTTGGGATTTTAAAATTTGGGTATAATTGGC R 2 1 2 1 101000 f 74 goat snp44418-scaffold603-6446062 4 108746887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447814 Affx-122923920 AX-123318150 4 9709013 TTCCTTAGAGTATATGAAAACTCTTACATATTCAG[C/T]GAGGTGATGGAAAGTCAAATTATTTCTAGATCTAT Y 2 1 2 1 101000 f 74 goat snp44417-scaffold603-6413945 4 108714604 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791707 Affx-122931897 AX-385278698 4 9743196 CATTTTTAGTGTAAGAAAATGAACCAGAATAAATA[C/T]GTTGCCAGATACATTTCTCTGAATCTCAGCTATCC Y 2 1 2 1 101000 r 74 goat snp44416-scaffold603-6379762 4 108680532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444987 Affx-122926657 AX-123315324 4 9799836 GAAAAAAATTTTAGGAAGTAAGTCAAGAGAGTGTC[C/T]GTACACTAAAACACTCAGTAAATATTGGTTGAATA Y 2 1 2 1 101000 f 74 goat snp44415-scaffold603-6323122 4 108623866 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437776 Affx-122931702 AX-123308114 4 9849958 AAACCTGCACAGAAAAGAAACCACAGCAGAAAAAC[C/T]GCAGGAGGGCGGGGCTGTGCAGCCAGGCTCAGGCA Y 2 1 2 1 103000 f 74 goat snp44414-scaffold603-6273000 4 108573551 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768771 Affx-122965727 AX-385255948 4 9897210 CATCCTCCTCAGAATTATATATAAATCAAATACAA[G/T]TCCAATCAGAATTCCAAAGATATTTAATTTGATAC K 2 1 2 1 103000 f 74 goat snp44413-scaffold603-6225748 4 108526018 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792065 Affx-122959217 AX-385279052 4 9943987 AATGCCATTTCTGTTAGATCTATATTAGTGTTACT[A/G]TAGTATGTTGTCAAGAGTTTAATGTATTTTAAATA R 2 1 2 1 101000 f 74 goat snp44412-scaffold603-6178971 4 108478905 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428318 Affx-122939009 AX-123298661 4 9978362 CCCCACATCAAGTAGAACTTATTCTTTTTGTACAA[A/G]CATAATTAAAAGTTCAGAATCTATGTTTACAAACT R 2 1 2 1 101000 r 74 goat snp44411-scaffold603-6144596 4 108444453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603161 Affx-1002479428 AX-413837350 4 10047285 CATGGTGGAAAAACTTTCTGAGAGTAGCTATTTCT[G/T]ACCCATCTCACTTGTCAGTGGCTGATGTTGTTTTT K 2 1 2 1 101000 f 74 goat 4_10047285_RH-map 4 10047285 T G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38414767 Affx-122949245 AX-123285116 4 10067567 TGGGAGCTGGTTCCCCTTACTTTAAATTATTCCTA[C/T]AAAAATTTATATAAAGATTAAGGGATCTCACCAAA Y 2 1 2 1 303000 r 74 goat snp44409-scaffold603-6055391 4 108355223 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793271 Affx-122939030 AX-385280249 4 10116756 TGCAAGGAACCCTGAAAATAGATTAATCTCTATAA[C/T]ATGTCCCCAGTCTCAGCCTCTTCCTAGTTTGCTAG Y 2 1 2 1 101000 r 74 goat snp44408-scaffold603-6006202 4 108305526 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430194 Affx-122937350 AX-123300535 4 10145777 AGTCCTCAAGGCACTGAGAGATTTTGCCTAAGGTG[A/C]CCCTGCTGGTGTGGCCAGCCATTCACAGGACAACA M 2 1 2 1 101000 f 74 goat snp44407-scaffold603-5977181 4 108276743 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784832 Affx-122926357 AX-385271879 4 10185729 GCTGTAGTAACTGAGAGAAGCCATGATCTCACTAC[A/G]TGAGTACAAAGTATGTTCCTAACTTAGAAAGGTCT R 2 1 2 1 101000 f 74 goat snp44406-scaffold603-5937229 4 108236346 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603250 Affx-1002479429 AX-413837430 4 10199787 TTTGAGATGCCATGTGACCCACTGACAGGTGGAGA[C/T]AGAGAAAAGTAAAGTGGACAGTAAATATGTATAAC Y 2 1 2 1 201000 r 74 goat 4_10199787_RH-map 4 10199787 C T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38402024 Affx-122958746 AX-123272377 4 10223838 TTGGTGAGGCAGTGTGTAACACAAGAAAGGGAGAG[A/G]GATATGCCCAAAAGGAACATGAGAGAGAAACAAAC R 2 1 2 1 101000 r 74 goat snp44405-scaffold603-5899120 4 108197423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603166 Affx-1002479430 AX-413837355 4 10232070 ATGAGACCTAATTAAACATACCAGGTTTTACACAG[A/G]AAAGGAAACCATAAATAAAATGAAAAGACAACCTA R 2 1 2 1 101000 f 74 goat 4_10232070_RH-map 4 10232070 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38390911 Affx-122967094 AX-123261268 4 10277772 GCAATTGCAGAACAACAGGTATATTCATTTTAAGT[A/G]TTAAAAAACCAGCAACATAAAATACATTTTCTAAC R 2 1 2 1 101000 f 74 goat snp44404-scaffold603-5845186 4 108143041 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414884 Affx-122949134 AX-123285233 4 10318838 TTCTCTGACTTGATAAAAGGAAGAAGTTTGTTGAC[A/G]TCAATGACTGGATATAGGAGGAAGCCCGTAATTGA R 2 1 2 1 101000 r 74 goat snp44403-scaffold603-5804120 4 108101424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794187 Affx-122938807 AX-385281153 4 10400731 TAAAAATACTACTACTACCTTATCAAAGGCCCAGT[A/G]TCCATGAGCTTTGTGCTGAGTCCTTTGGAAACACT R 2 1 2 1 101000 r 74 goat snp44402-scaffold603-5722227 4 108018875 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603167 Affx-1002479431 AX-413837356 4 10411948 CTAGAGAATCCACAGAGGGAAAAAATGTGGTATTA[A/G]AAGTATGAAAAATAAATCAACTGAACATCTTCAAA R 2 1 2 1 102000 f 74 goat 4_10411948_RH-map 4 10411948 A G 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603169 Affx-1002479432 AX-413837358 4 10429139 ATCTGAGACAGAGAAGACAGTTTAACAGTAAACAG[A/G]TCTAGAAAACTAAAGTTTTGTTGATATAAAAAGAA R 2 1 2 1 101000 f 74 goat 4_10429139_RH-map 4 10429139 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603172 Affx-1002479433 AX-413837360 4 10458331 GTTCTTGCCATAACGTAATATTTGAAATATGTTCC[C/T]TATGCAAAATAATAAAAAAGCTATATTTGACAGAG Y 2 1 2 1 101000 f 74 goat 4_10458331_RH-map 4 10458331 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603600 Affx-1002479434 AX-413837750 4 10494906 CAAATTCGTGCATCAGCAGGAGGATTCTTTATAGT[A/T]GTACCACCTGGGAAGTCCTATACAATGCCTATAGG W 4 1 2 1 103000 f 74 goat 4_10494906_RH-map 4 10494906 T A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38385399 Affx-122971345 AX-123255757 4 10504647 CCCACAGAATGCATGAAAGCTGTTTGTGCCGGAGT[A/G]CTACTGGGCATAACACACAATCTCTGGCTTCCTAC R 2 1 2 1 101000 r 74 goat snp44400-scaffold603-5618311 4 107914144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603260 Affx-1002479435 AX-413837439 4 10516519 ACATCTAGCAAAAATACCCTTCAAACATGAAAGCA[A/G]CATAAGGATACTTAGGACAAATGCTGAGAAAATTC R 2 1 2 1 400000 r 74 goat 4_10516519_RH-map 4 10516519 A G Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38401678 Affx-122959561 AX-123272031 4 10538527 CTGGCATTAAAGCCATATCTTACTTTGGCTTGCCC[A/G]CTGAAAATGAGCATGTGTCCTGCGGTCTCTGGATC R 2 1 2 1 101000 f 74 goat snp44399-scaffold603-5584431 4 107880246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768429 Affx-122955059 AX-385255609 4 10573012 GGTCTGCACTCTATTATTTGATAAAATACTGTGGC[A/G]TAAATGTCACTGGGAAGTGGTTAGTCTCATTTCTA R 2 1 2 1 101000 f 74 goat snp44398-scaffold603-5549946 4 107844964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429132 Affx-122938003 AX-123299474 4 10601740 CTCCAGCTATTGTTTTTGGGCAAAAGTCACAAAAC[G/T]GGTTTTTCCCACCTTTACAAGTCCTTCTTAGGTGG K 2 1 2 1 101000 r 74 goat snp44397-scaffold603-5521218 4 107818046 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446015 Affx-122925862 AX-123316352 4 10638467 AAGGCCCCTAACTATAGTAAGCCCTCCTTGTCTGT[A/G]CCAGTTAGGAATACTTTCAATTGCAAATAACAACA R 2 1 2 1 101000 f 74 goat snp44396-scaffold603-5484491 4 107781881 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603176 Affx-1002479436 AX-413837363 4 10666100 CCCAGGGTCATCCCAGTGCACTAGCCCCGAGCACC[C/G]TGTCTCATGCATAGAACCTGGACTGGTGATCTGTT S 4 1 2 1 303000 f 74 goat 4_10666100_RH-map 4 10666100 G C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320789537 Affx-122919655 AX-385276546 4 10696439 ACACAGATGTGCACCTCTGTCAAAACTCTAAGAAT[G/T]TACCCTTAAAAGGATCACATTTTATTGTATATGAA K 2 1 2 1 101000 f 74 goat snp44395-scaffold603-5426519 4 107723838 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603178 Affx-1002479437 AX-413837365 4 10709598 CAAATGAAAAGGCCACACTTGCTCAAAGATACAGC[C/T]ATTTTAACTAGAATAGAGGGAGAAATACAGGGCTA Y 2 1 2 1 101000 f 74 goat 4_10709598_RH-map 4 10709598 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38438776 Affx-122931380 AX-123309113 4 10732937 AGTCCTCTTTTTCCTTATTAGGAAGTCAATGTTGC[A/G]CTGTGCTTAGTCGCTTAGTCGTGTCTGACTCTTTG R 2 1 2 1 101000 f 74 goat snp44394-scaffold603-5390021 4 107686736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278209 Affx-1111836228 AX-519551697 4 10739260 AATAAGGTGTATAGAAAGCCTCATTTTGGAAACTA[A/T]CATAATGTACTTCACTTCTACATTGCAGAAGGGAG W 4 1 2 1 101000 r 74 goat Random2.2K-409 4 10739260 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38400570 Affx-122960415 AX-123270925 4 10772367 AGTGCTTTTAGTTGTCAATTAGAGATAAGTCACTA[C/T]CAGAAATTTATAAAGCATGGAAAGCTTATCTTTTC Y 2 1 2 1 101000 f 74 goat snp44393-scaffold603-5350591 4 107646727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603181 Affx-1002479438 AX-413837367 4 10809126 CCTCAAGTGGCAACAAGAGAAACCCATGAGTTACA[A/G]ATACTGAGCTCTGTGCCACAACTAGAGGGTCCAGT R 2 1 2 1 102000 f 74 goat 4_10809126_RH-map 4 10809126 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38428073 Affx-122939108 AX-123298416 4 10817225 ATTCTTTGGGCCCCAAAGAACTGCCAAAGACAAAA[C/T]GAACTAAACTAATGTCTGAAGGTCCTACACAGCTT Y 2 1 2 1 201000 r 74 goat snp44392-scaffold603-5305733 4 107600681 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603183 Affx-1002479439 AX-413837369 4 10850488 TTGCTGTTTTGTTTTTAGCTGAGGTCTATAACCTT[A/C]TCAAGAACTTAGTAAATAAATGAATTTGTTGATGG M 2 1 2 1 101000 f 74 goat 4_10850488_RH-map 4 10850488 A C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38404648 Affx-122957307 AX-123275000 4 10853480 CTAAATCAAAAGACAGTAAGACTGACATAACTCCC[A/G]CTGCTCCCCTCTAACTTGCTTGCCTGAGTACTCAC R 2 1 2 1 101000 f 74 goat snp44391-scaffold603-5269478 4 107561917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272520 Affx-1111833410 AX-519546238 4 10869594 TATATATTCTTGAATTCTTATATTCTTAGCCACCT[A/G]TAATTTAAAAAACCAAAAAGCCAACAGCAACAACA R 2 1 2 1 201000 f 74 goat 4_10869594_AF-PAKI 4 10869594 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 350603185 Affx-1002479440 AX-413837371 4 10888468 GGGGCAAGTCAAACATAAGAAAATGTCATTGTAAG[C/T]AGGGTCCCAGAGGAGGTGACCCTGCCTAACTGCAT Y 2 1 2 1 101000 f 74 goat 4_10888468_RH-map 4 10888468 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38421545 Affx-122943867 AX-123291892 4 10890231 GGCTTTATGCAGGTTAGGGGAGAACAAATCTTCTA[C/T]GGTTGTGTTTAACCAGTGTTCACACTGCAGCAAAA Y 2 1 2 1 201000 f 74 goat snp44390-scaffold603-5232727 4 107525200 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603187 Affx-1002479441 AX-413837373 4 10987779 GGCAATATTAGAAATTTTCAAATTTTATTCTAGGT[C/T]CATCACTTCTCCTTTCTCCATCCTTTTCAAATTAC Y 2 1 2 1 303000 f 74 goat 4_10987779_RH-map 4 10987779 T C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38402137 Affx-122958666 AX-123272490 4 10990241 ACCAGGGCAGTGTGAGAGTTCCTGTTTCACCACGA[C/T]GCCTCAACTTGTTCAAGTTCCTGAGTGGCTGGGGC Y 2 1 2 1 201000 r 74 goat snp44388-scaffold603-5132717 4 107425852 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799812 Affx-122929621 AX-385286738 4 11125402 CTACCAATGGGAATAAAGAAATCTCAAGGAGGTAT[A/C]TTTAGTGAAGCACCTTCTGACATTATATTCATCGA M 2 1 2 1 101000 f 74 goat snp44385-scaffold603-4997556 4 107291145 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278059 Affx-1111836230 AX-519551549 4 11206800 GTTAATAAACATATGTGCCTTCTAAATCAGAACTT[A/G]AGATACTTTAAGGCTATAAGAGACTTTGTCGTTGT R 2 1 2 1 101000 f 74 goat Random2.2K-411 4 11206800 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320783594 Affx-122978871 AX-385270653 4 11226696 GGGCCACTGTATGCAGCCTGTAGTTCAGGTTGCAC[A/G]TATCTGGCCCACACTGTAATGACCAGGGGAAAGGT R 2 1 2 1 102000 r 74 goat snp44383-scaffold603-4896262 4 107190130 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397351 Affx-122962295 AX-123267706 4 11267629 GAATGCCTTCTCACTCATCTTGTGTCCTTACTGTT[A/G]CTAGGACAAACTTGGAACCTGATTGGTAAAAATAT R 2 1 2 1 101000 r 74 goat snp44382-scaffold603-4855329 4 107149249 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437746 Affx-122931723 AX-123308084 4 11296443 AAAAGAGCATGGCCATACTCAAGCTAGCAAGAGCA[C/T]AGGGGAACGTTCCGTAAGAGTTCGTGAGGGAGAAG Y 2 1 2 1 101000 f 74 goat snp44381-scaffold603-4826515 4 107119712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778803 Affx-122949414 AX-385265912 4 11348100 TGGAACTATTTGCTTTTTTAAAGAGGGACTTTGAA[C/T]GAGTAGACATATGTCAGTTAAGACTTTTCCAGTAT Y 2 1 2 1 101000 f 74 goat snp44380-scaffold603-4774858 4 107068009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379185 Affx-122976309 AX-123249544 4 11390115 AAACATTGATACTTTCAATATCTGTGTCAATTTCA[G/T]ATTTATTAATTTATTTAATGAATATTTATTGATAC K 2 1 2 1 103000 f 74 goat snp44379-scaffold603-4732843 4 107025741 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387076 Affx-122969885 AX-123257434 4 11437185 GCAGGGAACTGCTAGATTCTGTCCCAGGCTATGCT[A/G]CTTTCATTCAATCCTGATTCTCTCTCATTCTCTCT R 2 1 2 1 101000 r 74 goat snp44378-scaffold603-4685773 4 106979258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785711 Affx-122935149 AX-385272752 4 11469364 GTAAGCCATAAAATTTCAGAGTAGGAAAAGAACTT[A/G]AAGAGCTTGATTCACTGATTCTCTCCATTAAAAAG R 2 1 2 1 201000 f 74 goat snp44377-scaffold603-4653594 4 106948974 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418745 Affx-122946213 AX-123289093 4 11506800 ATTGCAACAAATCTGTTTCAAGGGTAATAATCTTC[A/G]TTTGGACAGAATTGAATTCAAGACCTCAGCCTTGC R 2 1 2 1 201000 f 74 goat snp44376-scaffold603-4616158 4 106912214 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382988 Affx-122973341 AX-123253346 4 11535647 CTGCATGGAACTTTATAACTGAAAGAGTGTTTTCC[A/G]CCTGTGGTCTTCACAACAACCCTGTGAGATAGTTA R 2 1 2 1 201000 f 74 goat snp44375-scaffold603-4587311 4 106883445 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397430 Affx-122962236 AX-123267785 4 11568840 TTTTCTTTCCGTCCAATTTCTCAGTGAATTCTGCC[A/G]GTTGTGTGGATAGCTTTAGTCTATCTGCTTCTTTT R 2 1 2 1 201000 r 74 goat snp44374-scaffold603-4554118 4 106849796 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390000 Affx-122968046 AX-123260357 4 11615439 TAATTTCCACTGTACAAAATTCAAAACCTGAGGGA[C/T]GCAGTTTGGTAATTTAGCATTTTTGCTTCATGTGA Y 2 1 2 1 201000 r 74 goat snp44373-scaffold603-4507519 4 106803408 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765173 Affx-122971495 AX-385252724 4 11666429 AGGTAGTTAGGGAAGGCTTTCATTCCTGGGTTCCA[C/T]GGGACTGTGGCAGTATGAAAGATAGTTCTTTGCAG Y 2 1 2 1 101000 f 74 goat snp44372-scaffold603-4456529 4 106750812 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406308 Affx-122955466 AX-123276660 4 11709027 GATGGTCTCAACTAAATTATCATTCTGCTTAAGTT[A/G]TCTGGGTTTTGTTTGTATTTTACTCTCTAGCTTCT R 2 1 2 1 101000 f 74 goat snp44371-scaffold603-4413931 4 106707873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389984 Affx-122968059 AX-123260341 4 11787687 CTATATATAACAGCCCTGATTTGAATTTTTGGTTG[C/T]GTGCAACAGAGATTAACCCTAAATATCTTAAGCCA Y 2 1 2 1 101000 r 74 goat snp44369-scaffold603-4335271 4 106629236 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438151 Affx-122931467 AX-123308489 4 11838720 CCTCCAGCCACACTAGCTTCCTTCCTGCTACTCAG[A/G]CACACCAAGTTTGCTGCAACCTTCCTCCTGTGCTT R 2 1 2 1 101000 r 74 goat snp44368-scaffold603-4284238 4 106577825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424256 Affx-122942460 AX-123294602 4 11900239 CCTTGCAGGTATTTAGCACACTGTGTAACCTCACT[A/G]CTCCTGGAGGAAGCTTACTGAGCAGCACTACTTCT R 2 1 2 1 101000 f 74 goat snp44367-scaffold603-4222719 4 106516034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388821 Affx-122968898 AX-123259179 4 11965939 GAAAGTGACATTAATCATCTACAGTCATTTAGATC[A/G]TAGGGAAAGTCAAGGAAGAGGAATAAACCACAGAT R 2 1 2 1 201000 f 74 goat snp44366-scaffold603-4157019 4 106450121 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441186 Affx-122929542 AX-123311523 4 12007678 ATCTATAGCATTTATCAATGGTTCTCATTCAGCTT[G/T]CTTTCTTTTTGTTTTAGTCCAAAAGTTTCATGGAA K 2 1 2 1 101000 f 74 goat snp44365-scaffold603-4115280 4 106408620 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408250 Affx-122953818 AX-123278601 4 12057510 GAAAAGATTCCATCATTGTTTTCCTAATGAAAGAC[G/T]ACCACAAAAAAAATTGCCAAATCTTTATAAAAGGT K 2 1 2 1 101000 f 74 goat snp44364-scaffold603-4065448 4 106358246 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788543 Affx-122923330 AX-385275560 4 12087312 GTTGAGGATTTAGGCATCCAAAACAAATAGATGCT[A/C]TCATTTTTATATCCTTGAACATACTAAAAAGATTA M 2 1 2 1 101000 f 74 goat snp44363-scaffold603-4035646 4 106328568 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793522 Affx-122943910 AX-385280499 4 12136028 CAGATTAAAACCCAAACGCGTTGAATATACATACA[C/T]AGGCATACACTGCATAAGCCACCCACTGTACATGG Y 2 1 2 1 101000 r 74 goat snp44362-scaffold603-3986930 4 106280166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783515 Affx-122927607 AX-385270578 4 12202170 CAGGGGACATTTATTTCTTAATGAGGACTTCTTAA[C/T]GAGAAACTCTCTAAGAGGACTTGAACCTCCAGATT Y 2 1 2 1 201000 f 74 goat snp44360-scaffold603-3920788 4 106213256 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450833 Affx-122921786 AX-123321167 4 12239582 AATGAGGATTATATCTGGTGACTTTTTTAAATACT[A/G]CGAATTATTAATGTTGAGGGCAGTATATGAAACAC R 2 1 2 1 101000 f 74 goat snp44359-scaffold603-3883376 4 106175767 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415887 Affx-122948480 AX-123286236 4 12286375 TGAGGCCATAGTGATTACCTGGGTAACAAAGTTTA[A/G]TCCCTTTTAGTTCTTGCTGTTACTCTTACTTGAGC R 2 1 2 1 101000 f 74 goat snp44358-scaffold603-3836583 4 106128146 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397031 Affx-122963115 AX-123267386 4 12347417 ATATGAGTAGAAAGAATAAAGTCTAAACTGGAGGC[A/G]TGTAAAGAACTTAAAAGAAGCTCTTCTCTCCAGAG R 2 1 2 1 101000 r 74 goat snp44357-scaffold603-3775541 4 106065896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432180 Affx-122936403 AX-123302521 4 12379084 GACAATCCAAGTGTAACATACTCTTAATTATATCA[C/T]TGGACTTCAGCCCTTCGGATGTTGTCATGGAAATT Y 2 1 2 1 101000 r 74 goat snp44356-scaffold603-3743874 4 106033189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436170 Affx-122932617 AX-123306509 4 12436935 AAAGGCTATAAAATTGACTTAATTCTTCACTGTCT[A/G]TTTAGCTGAAATGTTTATTTAATTTCTAAGTTCCA R 2 1 2 1 101000 f 74 goat snp44355-scaffold603-3686023 4 105967172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789922 Affx-122977052 AX-385276928 4 12485615 ACATTTGCATAGAGTGTTGCCTGAAGGTTTGAGGA[G/T]AGAGCCCATGGCATCTAAATGTTCCCTTTAACATG K 2 1 2 1 101000 r 74 goat snp44354-scaffold603-3637343 4 105918380 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798074 Affx-122934963 AX-385285010 4 12528962 TCACTACCTCTGTGGCCTTGGGTGAACTTACTTAA[C/T]ATCTCTTTGCTCTTGCTTCCTCATCAATAAAACAG Y 2 1 2 1 101000 f 74 goat snp44353-scaffold603-3593996 4 105873295 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424391 Affx-122941826 AX-123294737 4 12590559 GTGTTTTCTTTTGCAAAAAGTTTTGGGAAGATCAT[A/G]CTGTTGGATAAGCAGGAAGAAAAATACTTGTGTTG R 2 1 2 1 101000 r 74 goat snp44351-scaffold603-3532399 4 105812736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769850 Affx-122966911 AX-385257020 4 12663607 TTCTGTGGTACTATAGTATGATGGCAATTTGCTGT[C/T]TAATCTGACAGTATATCTTGGAGCTATTCAAACTA Y 2 1 2 1 101000 f 74 goat snp44349-scaffold603-3459351 4 105739757 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422283 Affx-122943489 AX-123292629 4 12810373 GTTATGTTTCATACCAGGGGATGGATAAAAAATGG[C/T]GAAGATGCTTAGTAATTCTTAGGAGAAAAACAACA Y 2 1 2 1 201000 r 74 goat snp44346-scaffold603-3312585 4 105590883 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278061 Affx-1111836231 AX-519551551 4 12876984 AACAACACGGAGAATAGCTCCTATTGTTTTTGTTT[A/T]GTTTTAACCTCAAAACCCCCAGGATCTACAGACTT W 4 1 2 1 102000 f 74 goat Random2.2K-412 4 12876984 T A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439356 Affx-122930283 AX-123309693 4 12924629 AAGGAGCTGAAAGTGGGTGAGGAACAGAAGGTCAG[C/T]CAGCAACACTGAAATCCAGGAAGTAAGGAGGAAGA Y 2 1 2 1 101000 r 74 goat snp44344-scaffold603-3198329 4 105476408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770323 Affx-122974163 AX-385257489 4 12965640 ACTTGGGCTCCTAATTCTCAGTCCTATGTCTACAA[C/T]ATGATTTAAAGAGCTTATCACATAATATTCAGTGG Y 2 1 2 1 101000 f 74 goat snp44343-scaffold603-3157318 4 105436151 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784619 Affx-122971936 AX-385271667 4 13001863 ATAGTGGAGCCTACCTAGCACAATCTAGGTATTTG[A/C]TTATTTGTTGTTTTGAATGAGTAAACAACTGAATG M 2 1 2 1 101000 f 74 goat snp44342-scaffold603-3121095 4 105399928 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772101 Affx-122930675 AX-385259256 4 13051054 TTCAGGTGGCCCTCAGTTAAACTTTTGTTCAGTTA[C/T]ATAATTCTCATAGATTTCTGAGCTGGCATGAGAGC Y 2 1 2 1 101000 f 74 goat snp44341-scaffold603-3071904 4 105350869 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453548 Affx-122919783 AX-123323881 4 13079789 GGTTAACTATTCAAGCAAATCCCTCTTTGCTACCA[G/T]CATGTCATCATCTTGCATCAAGAACTATCCCACAA K 2 1 2 1 101000 r 74 goat snp44340-scaffold603-3043169 4 105322215 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804567 Affx-986696735 AX-385291106 4 13105755 CAGCCCCTCTTGCTCCAGCACTGCTCCCCTCTGGG[G/T]CAAGGAGTTGTTGGGTACAGGAAGAGCACACACCC K 2 1 2 1 600010 r 74 goat 4_13105755 4 13105755 Ancestral_priority_1043 ancestry 0.598 neutral IMAGE 10K 10K ancestral 38376447 Affx-122978060 AX-123246806 4 13124008 AATAGTGGGGGTGATCAGCCCTCTCACACACCCCC[A/G]CTCCATGACCTCTGCTCCCTGACTGCTAAGGAGGT R 2 1 2 1 101000 r 74 goat snp44339-scaffold603-2998950 4 105277656 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796823 Affx-122947295 AX-385283766 4 13154792 GACTTCTTTTCCTACTAATAGGCAAGACTACATTA[A/G]CTGGACAAACCTCCCTGCTGGAAACAATGAACTTG R 2 1 2 1 101000 r 74 goat snp44338-scaffold603-2968166 4 105247008 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804234 Affx-986696737 AX-385290867 4 13178272 GTAAGAACTGAGGAAGAATGGCAAAGACGTCTGTA[C/T]TCAAGAGACTCTTGAAATAAAACTCTAAGTGATAA Y 2 1 2 1 600010 f 74 goat 4_13178272 4 13178272 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 38437752 Affx-122931718 AX-123308090 4 13204056 ACTATTCTGTCTTTTGCCCTGTCTGGGGAATCCTA[C/T]GGACAGAGAAGCCTGGAGAGCTACAGGGCATGGGG Y 2 1 2 1 101000 f 74 goat snp44337-scaffold603-2918902 4 105197965 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786748 Affx-122937052 AX-385273779 4 13236140 CTCACTCATAAGAAGTCAGGGATAGGTTCAATGTA[C/T]ACTAAGTTGCAAATACCTGGGACATCGCCCACAGC Y 2 1 2 1 101000 r 74 goat snp44336-scaffold603-2886818 4 105165564 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38404851 Affx-122956623 AX-123275203 4 13272654 GGGCTCCCAGGACAGCCAGGAGTACCAGGAGAAGA[C/T]GGAGCTGCAGGGAAGAAGGTAACACTGTTTTCCAT Y 2 1 2 1 103000 r 74 goat snp44335-scaffold603-2850304 4 105128268 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780011 Affx-122945417 AX-385267110 4 13304993 TTCATCTGGGAGACTGGTGCCTCATGGTTATAAGA[C/T]GAGCTATTACCTCTCCAAGGAACAAAAGAAGCAGA Y 2 1 2 1 101000 f 74 goat snp44334-scaffold603-2817965 4 105095520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397511 Affx-122962057 AX-123267866 4 13360516 AAATATCTTCAAATGGATAATGGACTTAATTTTCA[C/T]GTTCAAAATTTGGACTATCAGTAGCATATTTGCAA Y 2 1 2 1 101000 r 74 goat snp44333-scaffold603-2762442 4 105039822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786253 Affx-122967542 AX-385273288 4 13390617 TCTTTTCCCATTTTGTGATAAAGAACCTATTTAGT[A/G]ATGTGGTCATAAGTGGTTAAAGCAGGAGAGAGAGG R 2 1 2 1 101000 r 74 goat snp44332-scaffold603-2732341 4 105009572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379262 Affx-122976251 AX-123249621 4 13433683 GGAGCATCCTTCGCAGGTATTTTTATGAGCACTCA[C/T]TCTGGAATATCCCTGGCAAGGCAGGTACCAAATCC Y 2 1 2 1 101000 f 74 goat snp44331-scaffold603-2689275 4 104966481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769266 Affx-122962079 AX-385256439 4 13474626 AATTAACTATATTCCAAATAATCTATCCTGACTTT[C/T]ACTGGTCAATTCTCAGTTAAGGCTTTAACTGCGGA Y 2 1 2 1 201000 f 74 goat snp44330-scaffold603-2648332 4 104927339 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421839 Affx-122944301 AX-123292186 4 13511263 GACTCTTTTAACTCAGCCACACCTAAGTTGACAGT[A/C]TCTTTTTTTTTATTTTAGCAATTAAACTATAATGA M 2 1 2 1 101000 f 74 goat snp44329-scaffold603-2611695 4 104890875 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783454 Affx-122967977 AX-385270517 4 13542446 AACGAATGGAATCACCATACACGTCCCAACTTGGA[C/T]GAACCTTGAAAAGTAGAAGCAAAGGAACCAACCAT Y 2 1 2 1 102000 r 74 goat snp44328-scaffold603-2580512 4 104858747 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434233 Affx-122934836 AX-123304574 4 13573217 AGCGCAGATCAGCCACCATCTTCTGTGCACGCCCA[A/G]CTCAATCCTGACACAGAGATGGAACTCAAGACATG R 2 1 2 1 101000 r 74 goat snp44327-scaffold603-2549741 4 104828125 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443763 Affx-122927113 AX-123314100 4 13620685 GTACCAATTTAAACTGCCTTCAATACCAATTCCCA[C/T]TGTACCTGTATTTGGATTATGAATATCTTGTGAGA Y 2 1 2 1 101000 f 74 goat snp44326-scaffold603-2502273 4 104780775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449666 Affx-122922571 AX-123320001 4 13650037 CTGCATAAGGAAGGACCACGGCTGTCATGTCCATG[C/T]GTATATTGTTAGGCGGCTCCATAAATATGCGTTGA Y 2 1 2 1 101000 r 74 goat snp44325-scaffold603-2472921 4 104751421 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444585 Affx-122926961 AX-123314922 4 13717914 TTTTTCAGAACTGCCTGATCATTCCTGATAGTTTT[A/C]TGCTGCTTGTTCAGGCTTCTGATTCTATGCTTTAT M 2 1 2 1 101000 r 74 goat snp44324-scaffold603-2405044 4 104684434 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382547 Affx-122973781 AX-123252905 4 13774147 AGAAGATATGATAAATATAGATTGGAATAAATCTG[C/T]ATTTTCAAAACCTGATGAATTTTTAAAAAACTGAA Y 2 1 2 1 101000 f 74 goat snp44323-scaffold603-2348811 4 104628190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405166 Affx-122956939 AX-123275518 4 13847341 ATACCAACTCCTGGCTATAGCTTTAAGATTATATT[C/T]ACCTGTGAGATAAAAGAGCAAATTTACTTTTTATT Y 2 1 2 1 101000 f 74 goat snp44321-scaffold603-2275617 4 104553325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451127 Affx-122921379 AX-123321461 4 13911880 CAGGTTTATACAGTTTGCTTGGGGCAGGGAGTTCT[C/T]TTCAGTTTTTCTTGATGAGGTAGTTCAAGAAGTTT Y 2 1 2 1 201000 r 74 goat snp44319-scaffold603-2211078 4 104487560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378719 Affx-122977047 AX-123249078 4 13942682 CCTGGCTTAAGGTCCTCATTCATAATTGGCTCTAT[A/C]AGATCTAATGAGGAGGACTCAGGCATCTGTCTGTA M 2 1 2 1 101000 f 74 goat snp44318-scaffold603-2180276 4 104456591 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398451 Affx-122961604 AX-123268806 4 13989924 TGAAGAGTATATGGGGACATCAGCTTCAAAGAACC[A/G]TAGGAAAACAACGGGGAAAAAATTGTCCTCTTACC R 2 1 2 1 101000 f 74 goat snp44317-scaffold603-2133034 4 104409559 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798735 Affx-122923140 AX-385285666 4 14044412 TGGTACAGTTCTACGTAAATTGGACAAGCTGGCTT[A/G]CCTTACTCTTCACAAGCTTACATTAATACCGTCAT R 2 1 2 1 101000 f 74 goat snp44316-scaffold603-2078546 4 104354088 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430257 Affx-122937305 AX-123300598 4 14083052 CTTTATAGTTACTGCTTTTTGTGTGTGATGAGTGC[G/T]CATGAAGAGTAATGCTCCCCTCCTAGCCTGTTTGC K 2 1 2 1 101000 r 74 goat snp44315-scaffold603-2039906 4 104315554 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785654 Affx-122949260 AX-385272695 4 14143426 TGGATCAAACTAAGAAAACTAATACCAACAGTCTG[C/T]AGGAGCTAGAACACTATTTCAGGTATCAGATTAGA Y 2 1 2 1 101000 f 74 goat snp44314-scaffold603-1979532 4 104254985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452395 Affx-122920609 AX-123322728 4 14175395 GACTGCACCACTCCCTGGCTTCCATTATCACCTGC[A/G]CTTCTGACTAGCTATAGACTGAAGGAAGGTTTCAG R 2 1 2 1 101000 r 74 goat snp44313-scaffold603-1947563 4 104223190 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802105 Affx-122972252 AX-385289009 4 14224353 AAATTTCTAAGCAAGAATAGCATAATGTGTACTGT[A/G]CTTTCAGAGATAATTACCATCTTTTTAGAATGAAT R 2 1 2 1 101000 f 74 goat snp44312-scaffold603-1898605 4 104174246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393637 Affx-122965301 AX-123263992 4 14282839 CCCTATTAATTTAAATGGTGAGGACTCGTTAAGGT[A/C]TTGGAATGAGATCTGAAGCTCTTAAAGCACAGAGT M 2 1 2 1 101000 f 74 goat snp44311-scaffold603-1840119 4 104115306 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391596 Affx-122966602 AX-123261953 4 14319573 AGCAAATAACACGAGTAGTCTTCTACCCTTTTAAC[A/G]TGAGATCCACAAGGTGAGGTTTCATTGAGGAAGTA R 2 1 2 1 101000 f 74 goat snp44310-scaffold603-1803385 4 104078353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792756 Affx-122967092 AX-385279735 4 14348657 CAGTCAGATCCTAAAGCCTGTGTGTAACATCCTGC[A/G]TCTTCCCAGTTCAACAAACTTCAAAACTTTCCAAT R 2 1 2 1 101000 f 74 goat snp44309-scaffold603-1774301 4 104049548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389546 Affx-122968272 AX-123259904 4 14381942 CACCACAGCTTCTCTCTCAGTACATCAGTTATTGC[A/G]CTTTGGGAGCTGGGTCAAAGGGCCACCCTTTCCAG R 2 1 2 1 101000 f 74 goat snp44308-scaffold603-1741016 4 104016156 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412297 Affx-122950868 AX-123282646 4 14437984 TCCGTGTACTTCAACTCTTTAAAAAAAGGCTTATA[C/T]GCTTTGTATTCATTTTAACAAATTCTAAACATGAA Y 2 1 2 1 101000 f 74 goat snp44307-scaffold603-1684974 4 103958557 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776788 Affx-122967819 AX-385263912 4 14478923 AAAAATGTCACAGTGGGAAGTGTTTTAATATTGAG[C/T]GGTAAATCCCCAGAGGCAAATGCAAAATATATCCA Y 2 1 2 1 101000 r 74 goat snp44306-scaffold603-1644035 4 103915656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446554 Affx-122924847 AX-123316890 4 14528279 TTGTTGGAATTTCCAAATCATTTTCAAAAGAAAGC[A/G]CAGCCCAGTGAATTTTTACATGGAAGGCTGATATG R 2 1 2 1 101000 r 74 goat snp44305-scaffold603-1594679 4 103866505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764624 Affx-122925097 AX-385252266 4 14567440 CAAATAAGTATCTTAAAGGAAGCCGACTGAGAGTC[A/G]TCAGTTTATTAAACCTTTGCGTGAAAAGGTTTAAG R 2 1 2 1 101000 f 74 goat snp44304-scaffold603-1555518 4 103827008 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449141 Affx-122923558 AX-123319476 4 14610615 ATTCACTTCAATTAACTATTCCCATATACTGCCCC[A/G]CACTGGTAGTCTGTTGTATTCTGATAACAAGTCTG R 2 1 2 1 101000 r 74 goat snp44303-scaffold603-1512343 4 103782098 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441836 Affx-122929053 AX-123312173 4 14642251 TTCTTGCATTTTAATAAATTACTTTGTCCTTCAAT[A/G]TAGGTTTTAATCTCTATATTAAAATGTGTTTGATT R 2 1 2 1 101000 f 74 goat snp44302-scaffold603-1480707 4 103750713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379433 Affx-122976104 AX-123249791 4 14698846 AATCTAAAGATTATTTGGGAATGTTGGTTCTTATC[A/G]TAATGACTTGCAATTACTAGAAGTAGAGATTATAC R 2 1 2 1 101000 r 74 goat snp44301-scaffold603-1424112 4 103693324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784521 Affx-122939010 AX-385271570 4 14731947 AAAAATCAAATTGCATCTCAGTAACTGTTTGATTT[A/C]TAAAACACTTAATCAATAGATGAGGCTTATCCATT M 2 1 2 1 201000 f 74 goat snp44300-scaffold603-1391011 4 103659734 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804535 Affx-986696703 AX-385291084 4 14786986 CCTCCTGTTCCCTGATTGGAGCATTTGCCTATGAC[A/G]TCACTGCTCTGTGCCTCTGCAGGCTGCCCTGTCCA R 2 1 2 1 600010 r 74 goat 4_14786986 4 14786986 Ancestral_priority_1043 ancestry 0.416 neutral IMAGE 10K 10K ancestral 320786094 Affx-122942498 AX-385273130 4 14841149 ATTCAAATAGTTTCACTTTTAGGTTAAGCACAATC[A/G]CAGCAATGTCTGACACAGTAAAGAAAGGGCTGTGC R 2 1 2 1 101000 r 74 goat snp44298-scaffold603-1281809 4 103551211 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381734 Affx-122974330 AX-123252092 4 14912777 CCAACAGAAGTCTATAAATAATTATGTATGTCTAT[C/T]TGTTAAAATGTAAACATAAATGTATAGAAAATACT Y 2 1 2 1 103000 f 74 goat snp44297-scaffold603-1210181 4 103478895 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804240 Affx-986696740 AX-385290871 4 14931156 TAAACAGCTTCATCTCTTCATGACCCTCCCTGTTA[A/G]CCAGCGTCACCTTCCTCCCATCCTGAAAACATTAC R 2 1 2 1 600010 f 74 goat 4_14931156 4 14931156 Ancestral_priority_1043 ancestry 0.556 neutral IMAGE 10K 10K ancestral 320797039 Affx-122948590 AX-385283980 4 14955328 TTACTACTTGCCATTTATAAGCTAACTATCATTTG[C/T]ACAATAGCACTATGACATGATAAAATTGGTTTTTG Y 2 1 2 1 101000 f 74 goat snp44296-scaffold603-1167630 4 103436922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404271 Affx-122957049 AX-123274623 4 15028401 GGATAGCAGGAATTGTGTTATACTTTTCCATTTCC[G/T]AGAACACTGAGAGCTCTGACTTTATGACACCCAGC K 2 1 2 1 101000 r 74 goat snp44294-scaffold603-1094557 4 103360894 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379186 Affx-122976308 AX-123249545 4 15057396 TCCCAGCAGTGTTTCCCCAATAAAATCCTGGCATG[C/T]AAATCTCAGAATCTGTTCCTGAAAATCTAACCTAT Y 2 1 2 1 201000 r 74 goat snp44293-scaffold603-1065562 4 103331918 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778474 Affx-122955139 AX-385265588 4 15090046 AACACAAGACTCAGGTAAAGTGTGCAAACTCATAA[C/T]CTTTTAAGAAGAAAAGGAGACATTGTTTTGGCAGA Y 2 1 2 1 202000 r 74 goat snp44292-scaffold603-1032912 4 103299289 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775370 Affx-122936200 AX-385262501 4 15120226 TCACATAATACCCAATACTCTTGGTCCTAAAGAAT[C/T]CCGTGCCCATATGCACATTAAGTCACAATAGAAGA Y 2 1 2 1 101000 r 74 goat snp44291-scaffold603-1002732 4 103268626 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804243 Affx-986696742 AX-385290874 4 15121246 TAGCCCCCACGGACATGAAGATTAATGTGGTCAAG[A/G]GGCGCTGGCAAGGACTTCCACTCACCCGTCGACTG R 2 1 2 1 600010 f 74 goat 4_15121246 4 15121246 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320804575 Affx-986696744 AX-385291114 4 15121252 CCACGGACATGAAGATTAATGTGGTCAAGAGGCGC[C/T]GGCAAGGACTTCCACTCACCCGTCGACTGAATGTC Y 2 1 2 1 600010 r 74 goat 4_15121252 4 15121252 Ancestral_priority_1043 ancestry 0.502 neutral IMAGE 10K 10K ancestral 38377211 Affx-122978178 AX-123247570 4 15188775 CAAATGTTTGAATTTCTGCAATAGTCTAAAGATTT[A/G]TGAGAATAATGAGGTCTTTTTAGGAATACGAATTA R 2 1 2 1 101000 r 74 goat snp44290-scaffold603-934183 4 103199656 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386960 Affx-122969974 AX-123257318 4 15232656 GTCACTCAGTAGGACATTTAAAACACCCTCAGTTC[A/G]TAGCTGCTGCAGTGTCACCATCAACTAGTCAATAA R 2 1 2 1 101000 f 74 goat snp44289-scaffold603-890302 4 103154955 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408168 Affx-122954210 AX-123278519 4 15287123 TCAATGTTTCCACTGAAAAAATTTAAGGCAGTGAT[A/G]CTAATTATGGAATAATAATGTTCAACATGTCATAC R 2 1 2 1 201000 r 74 goat snp44288-scaffold603-835835 4 103099867 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390128 Affx-122968001 AX-123260485 4 15327171 ATTAACAGATTTATTCTCTAATTTTATATGATTGG[C/T]ACAATCAAATTAAAAGGTGAAAACAAATGGTGATA Y 2 1 2 1 103000 r 74 goat snp44287-scaffold603-795787 4 103059400 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788458 Affx-122965025 AX-385275475 4 15371792 GTTATGAGGGAATGCAAACAATACAATGACATGTA[C/T]GTTCAGGAAAAATCCACTAATTAGGGAAAAATTTT Y 2 1 2 1 201000 f 74 goat snp44286-scaffold603-751166 4 103013741 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405446 Affx-122956047 AX-123275798 4 15437030 AATCACTCAATTAGATTTTTTAGCTTGCTTATCAA[G/T]AAAATAGAGAATACATCCATGATTGTGAAAGGTTT K 2 1 2 1 101000 f 74 goat snp44285-scaffold603-685928 4 102947467 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792639 Affx-122939703 AX-385279619 4 15466256 AAAATTAACTTAACCCAGGGGTAAGATTATTAGTG[C/T]ATAATGCTGATCTATTGTCTTGGGGATGTAGTCAG Y 2 1 2 1 102000 r 74 goat snp44284-scaffold603-656702 4 102918076 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445061 Affx-122926226 AX-123315398 4 15504497 TAAAGTGTACAAAGGGTTTTGACATTTGCATGTAC[C/T]TGGGCAGTTATGGTAAACATCAAGATAAGAACATG Y 2 1 2 1 101000 r 74 goat snp44283-scaffold603-618461 4 102879937 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440723 Affx-122929890 AX-123311060 4 15551691 ACCTTGGCTAAACCAACAGTTTTCCTTCAGTGCCT[A/G]ATTTTGAATGATGCTTACAGTTGGCATTCAATAAA R 2 1 2 1 101000 r 74 goat snp44282-scaffold603-571267 4 102832608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379599 Affx-122976023 AX-123249957 4 15603284 ACTGAACCAGTGAACCAGAGGGCCAGAATGACGGA[C/T]GGAAGAGACAACTTACATTTTAGTTATATCTCATA Y 2 1 2 1 201000 r 74 goat snp44281-scaffold603-519674 4 102783799 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423382 Affx-122943134 AX-123293728 4 15632383 GGCATACAGTCCCAGCTTCTCAGTATAATTTAATA[C/T]TACTGAAAATGGTTTATTCATAAAAAATTACCATT Y 2 1 2 1 201000 r 74 goat snp44280-scaffold603-490575 4 102754551 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375687 Affx-122978658 AX-123246046 4 15666907 CCTGGCTGGTTTGACCCTTGATAGCTACCTTGTTT[A/G]CAGTGCTGCCTCCTGAAGCACACTGGGCTCTAATG R 2 1 2 1 101000 f 74 goat snp44279-scaffold603-456051 4 102719412 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273515 Affx-1111833663 AX-519547130 4 15682830 GCAAAGCATTACCATCCTTGCAGATGGGTCTCCTA[A/G]CCCCCAATACATCAGCATACATTTCTGCAGCAGCT R 2 1 2 1 201000 f 74 goat GoatD01.000958 4 15682830 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278063 Affx-1111836232 AX-519551553 4 15708549 GGGGGCTGGGAGTCTCTTTTACTCCCTCTTGCTTC[A/C]CAGGGGCAGCTCCAGAGGCACTGCCGTGGCACATG M 2 1 2 1 102000 f 74 goat Random2.2K-415 4 15708549 T G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399809 Affx-122960277 AX-123270164 4 15712343 CCAAGGGCCTCTTCAAACAATCAGCCTTTAGCAAT[G/T]CACATCTACTTTACAGAGAAACTTGGTCTGCATGG K 2 1 2 1 101000 f 74 goat snp44278-scaffold603-410615 4 102673403 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423043 Affx-122942968 AX-123293389 4 15766945 CAAGACAATTATGCTTGAAAATCACAAACCTGATC[A/G]TTTTTGTTTTCTCTTAAATCAAGCCTCTTCTCATT R 2 1 2 1 101000 f 74 goat snp44277-scaffold603-356013 4 102620010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781310 Affx-122948865 AX-385268395 4 15798371 ATTTTTTGTATTTAGTTTGAAATCTCACCCTGCAC[C/T]ACTTTTGGAATTTCAAGTCAGTTCCCTTTTCCTGG Y 2 1 2 1 101000 r 74 goat snp44276-scaffold603-324587 4 102588036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791644 Affx-122968186 AX-385278635 4 15856059 GACCCTTCCACATATTAAATACTTGACTGAAGTCC[C/T]CACTTTCTGTAGCTTTGGGAATAGTAATATCTAAG Y 2 1 2 1 101000 f 74 goat snp44275-scaffold603-266899 4 102529834 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765905 Affx-122954410 AX-385253337 4 15900923 AAATTTCTTTTATGTTGGCTTCTGCACCCTTTTAG[C/T]ATATCCCCATTTTTTGAATGTCTTTACTATTTTCT Y 2 1 2 1 101000 f 74 goat snp44274-scaffold603-222035 4 102484704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451941 Affx-122920968 AX-123322274 4 15949360 AAGTAAAGGAATTTTCTCCTTTACTCTGTTAAAAA[C/T]ATGAATTATATTATTAAATTTTCTAAGTTTAAATA Y 2 1 2 1 103000 f 74 goat snp44273-scaffold603-173598 4 102435822 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778272 Affx-122953043 AX-385265387 4 15991964 GATATTAAAAGAACAGATTAGGAGAACAACTAAAT[A/G]TATAAATTATTTATATTCTAGGAACTTTGCTGTAC R 2 1 2 1 303000 r 74 goat snp44272-scaffold603-130994 4 102393001 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272255 Affx-1111833415 AX-519545996 4 16021218 TTTATCTCAGTAACACTAGAAGAAAAAATAAAAAA[A/C]CAAAAAATAAAAGCAATTCACAAGACGACTACATG M 2 1 2 1 303000 f 74 goat 4_16021218_AF-PAKI 4 16021218 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320771274 Affx-122923424 AX-385258432 4 16035598 TTGCAACTTTAGAAATATTAAGGCCAGATTAATTG[C/T]AATCTATCAAGAAAGCTCTGTTAACATCTTTGGAT Y 2 1 2 1 101000 r 74 goat snp44271-scaffold603-87360 4 102348308 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426667 Affx-122939924 AX-123297013 4 16064415 AGTGAATGTGTTCATTCCCACTCAGACTTCTCATA[A/G]GAAACAAGTTGGAACAGATAGGAGACATTTAAAGA R 2 1 2 1 101000 f 74 goat snp44270-scaffold603-58543 4 102319752 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391401 Affx-122966778 AX-123261758 4 16102679 CACTCACTTATTCACCTCTTTGAAATTTTGGGTGC[A/G]TTTTGTCTCTTTCATTGGCCTGGCCTTGAATTTTC R 2 1 2 1 201000 f 74 goat snp44269-scaffold603-20279 4 102281199 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403656 Affx-122957519 AX-123274008 4 16182006 TAGTTCATGGAAGCAAGAAGATCTTGCCACATACA[G/T]ACTCCTATACAAAATACTTCCGCCTCAACTGCCAT K 2 1 2 1 101000 r 74 goat snp47971-scaffold676-58949 4 102236845 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791226 Affx-122921988 AX-385278220 4 16237885 AAGATGGATAAAATCAAAGCCAGTCATTCATAATG[C/T]ATTTGCAGTTACACTGCAGCTCATTTTTATTGAAT Y 2 1 2 1 201000 f 74 goat snp47972-scaffold676-114828 4 102179755 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393133 Affx-122965555 AX-123263490 4 16282467 AACTTTACTCTGGAAGATGATACTCACTGCCAGCA[C/T]AATCCTTTGGGCTTCTTCTTGGCAGATGCAGGGGC Y 2 1 2 1 101000 f 74 goat snp47973-scaffold676-159410 4 102134856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774086 Affx-122975011 AX-385261224 4 16323475 AAGTATAAATGCTGTGCCTGTTTACTGGTAAATGA[A/G]AATTAAGAGTCATTGAACTTGCTAAATAAGATTCT R 2 1 2 1 101000 f 74 goat snp47974-scaffold676-200418 4 102093391 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278218 Affx-1111836233 AX-519551706 4 16333343 AAATTCCTTGAGCTTGAAAGTGATGTTCCTCAGGG[A/G]CTATGAGAAGTTAAAGGTGAACATAGCTGCCTCTG R 2 1 2 1 201000 r 74 goat Random2.2K-416 4 16333343 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384940 Affx-122972322 AX-123255298 4 16371546 GTCCCACTTATTTACTGCTTTGTTCCCCATTCCTC[A/G]TGCCTAGAGAAGTACAGTCAGCCCTCCCTACCCAT R 2 1 2 1 202000 r 74 goat snp47975-scaffold676-248489 4 102045063 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424659 Affx-122942155 AX-123295005 4 16401531 CGATGCTGAGGTTTAATTCTCCCTATCCCCTCTAT[A/C]TAGGAGGCATTTCAGAAACAGGGTATGGGGGGAAA M 2 1 2 1 303000 f 74 goat snp47976-scaffold676-278474 4 102014010 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448895 Affx-122923255 AX-123319230 4 16440626 ACATTAGACATTATAAAATTGCTCCCCTAAAAAGA[C/T]AATACTAATTTATCACCTATCACCAGCATTGTATG Y 2 1 2 1 101000 r 74 goat snp47977-scaffold676-317569 4 101974567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378342 Affx-122976838 AX-123248701 4 16481627 GACCAGAAGAGAAGATGTGTTTTTATCTTGGTTTT[A/C]TTTCTTTCTAACTAGTTTACCTTGGGTAGGTCACT M 2 1 2 1 101000 r 74 goat snp47978-scaffold676-358570 4 101934031 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398814 Affx-122961402 AX-123269169 4 16528540 TTTGCATAAAAATCATTCTTCCCTTGGTTCTTCGC[A/G]TGGCTACTTCCATCTCACCCTTCAAGACTCACTTC R 2 1 2 1 101000 f 74 goat snp47979-scaffold676-405483 4 101886905 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274931 Affx-1111834499 AX-519548513 4 16552808 AATGGTCAAGCCCTGTTTCCTTCAGTAACAGGGTT[A/G]ATCTGTTTTCTGGGACAGCTTGTATGGAGAAAACT R 2 1 2 1 101000 r 74 goat GoatD01.038482 4 16552808 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434964 Affx-122933845 AX-123305304 4 16572983 CCTCAGTGTCAAGGAATTGGAGGAGGAGTGATGAG[C/T]AAGAGATGTCTCCCCATGCCATTCCCCACTTCAAG Y 2 1 2 1 202000 r 74 goat snp47980-scaffold676-449926 4 101842219 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420415 Affx-122944916 AX-123290762 4 16603759 TGTTATGTTATGACAGGAGATCCTGGTAAGAAACA[C/T]GAAACTAACAAACCATCACCAAGTGGAAGAATTTA Y 2 1 2 1 303000 r 74 goat snp47981-scaffold676-480702 4 101810839 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445821 Affx-122926026 AX-123316158 4 16644306 CCTATTAATTAATCTAACAGCACAGTTAAAAGTTT[A/G]CCTTAATCACTCATTCCACTGATATCTACTGAAGT R 2 1 2 1 101000 r 74 goat snp47982-scaffold676-521249 4 101770307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397278 Affx-122962340 AX-123267633 4 16677274 CCCAGGCCCTCAAAACCCCTACAATGTACAATGTT[C/T]GCTGCTGATCGTGGTATCTCCTGGGTGGAGTCCTT Y 2 1 2 1 202000 r 74 goat snp47983-scaffold676-554217 4 101740644 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416875 Affx-122948084 AX-123287223 4 16711852 TTGAGTTCAGTTCACCCTGGAATCTTTTCTCGACT[A/G]CAGTAGTGTATTACTGATTAAAATCTGTCCTGACC R 2 1 2 1 101000 f 74 goat snp47984-scaffold676-588795 4 101705619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772334 Affx-122939570 AX-385259487 4 16761218 ATTCTACATATGGCAATTATTTCGAATGTGTGAAA[C/T]ACTGTGGTATATGAAGTATTTTTTCCATCCTTGTG Y 2 1 2 1 101000 r 74 goat snp47985-scaffold676-638161 4 101656681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443517 Affx-122927787 AX-123313854 4 16857236 GATCCTTTAAAGTCGCCCTAACTCAAACACAAAGC[A/G]TCAGCAACTACAGAGTTTGAAATGCAAAAGTGAGT R 2 1 2 1 101000 f 74 goat snp47986-scaffold676-734179 4 101559771 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772446 Affx-122976144 AX-385259597 4 16890852 TTCCATTTCCACTTCAGTGTCTTTAACAGCAATAA[C/T]TGGATGTAGTTTCTTCAAGACATGTCTCATACCAA Y 2 1 2 1 101000 f 74 goat snp55520-scaffold860-11629 4 101526731 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410010 Affx-122953262 AX-123280360 4 16979457 TATGTTTCATTTTGAAATTCCTCTGGAGTTTCTAC[G/T]ACTTGTCTGTAATTCCGACCCCTCGTTATCTTCAT K 2 1 2 1 101000 r 74 goat snp55522-scaffold860-100234 4 101437464 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780890 Affx-122926926 AX-385267977 4 17110413 GCATTTCTTGTAAGTTCATTTCAGTATCTTTATCA[C/T]GGCCCACTAAAGTTGGGATTCAGTTGTAAAATGGT Y 2 1 2 1 201000 f 74 goat snp55526-scaffold860-231190 4 101305967 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389525 Affx-122968288 AX-123259883 4 17194402 CCATGAACCTGGGGAAATGGGGATTGTTTCAGGAT[G/T]TTTTCAGTACTTTACATTTATTGTACACTTTATTT K 2 1 2 1 101000 f 74 goat snp55528-scaffold860-315179 4 101222466 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437301 Affx-122931977 AX-123307639 4 17266126 TTCCATTGAGGTCTGCCTGAAGCTTTCATAAGATG[C/T]ATTTGAACTGCTCCCTTTGGAACTGGCTTTTCAAT Y 2 1 2 1 101000 f 74 goat snp55530-scaffold860-386903 4 101152249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431076 Affx-122936629 AX-123301417 4 17296380 CGAAGTTGAACACAGCACCTGCCTGCGAGTGCTGT[G/T]TCCAACTGACCTCTCTTACCTTAACCCCGGCACAT K 2 1 2 1 101000 r 74 goat snp55531-scaffold860-417157 4 101120685 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396675 Affx-122962839 AX-123267030 4 17359559 TTTTCATATGAAAGAAAGCAGCCAAGCTAGATATC[A/G]TTTTACTGTGCCATTCCCAGGGCTACATCTGTGAA R 2 1 2 1 101000 r 74 goat snp55532-scaffold860-480336 4 101056685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426035 Affx-122941115 AX-123296381 4 17408877 TCCATGGGCTAAGACGGTGATGTTTCCTGGTTCCA[C/T]GGGGCGACAGCATGGATGCCCTGTGTTTGGGACCC Y 2 1 2 1 101000 f 74 goat snp55533-scaffold860-529654 4 101007463 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770884 Affx-122936797 AX-385258047 4 17453664 CACAAATGATATCCATCAAATTGAAAGTCTTAATT[A/G]TAGGTTTCAAAGTGGTGCTCATTTCAGTGAATTAG R 2 1 2 1 201000 f 74 goat snp55534-scaffold860-574441 4 100962814 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780508 Affx-122931866 AX-385267599 4 17575017 ATCAGCAACACTTCCATCAGCTTTCTAGGAATTAT[A/G]CTGATAACCTCCTCATGGGCAAGGCCTCTTCCTGT R 2 1 2 1 101000 r 74 goat snp55536-scaffold860-695794 4 100851080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433998 Affx-122934243 AX-123304339 4 17604118 TAGAGTTGCCGCCATTGGCTTTCTAGTTCTGTTAA[A/G]TGCTGCTATCAGCGTTTCTACTGGGAAGCCCAAAA R 2 1 2 1 201000 f 74 goat snp55537-scaffold860-724895 4 100821533 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409501 Affx-122953638 AX-123279852 4 17643280 TCTCTGCATTGGCCAAATCTTCTCTATCAATTATC[A/G]TTTGGGACTGTGATTATTTCCTATTGTCATAAAAA R 2 1 2 1 101000 f 74 goat snp55538-scaffold860-764057 4 100781800 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402308 Affx-122959088 AX-123272661 4 17703890 TCATGGGATAATTAAAGGGAAACTGATTCAATAAC[A/G]TAGTCTCCTTTTCTACAACAGTAGTGCAAAACATA R 2 1 2 1 101000 r 74 goat snp55539-scaffold860-824667 4 100720169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800432 Affx-122937639 AX-385287353 4 17740983 CTCAATATTGCTTTTATTCTTCTGGAACCAAAATC[A/G]TAAAAGAAAGCCATCATTTTTCTTGATACTTACAG R 2 1 2 1 201000 r 74 goat snp55540-scaffold860-861760 4 100681764 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380565 Affx-122975278 AX-123250923 4 17780775 TGGTACTAGCTACACAATAATGTGAACGTACTTAC[G/T]CCACAGAAATGTACACTTAAAAATGGTGAAAATGG K 2 1 2 1 101000 f 74 goat snp55541-scaffold860-901552 4 100641968 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446226 Affx-122925703 AX-123316562 4 17872419 CCAAGTTTGTGTTTCAACAAAGATAACTTCAGAGC[A/G]CCAAGCTATCTTGGCATTTCCAGGATACTGGTTAC R 2 1 2 1 202000 r 74 goat snp55543-scaffold860-993196 4 100550756 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274953 Affx-1111834511 AX-519548535 4 17910852 CAGTTGGCCCCACTGGCTAATCCCTGGGCTGCCAC[A/G]TGTGCAAGGAGAGTGGGCCACTGGGGAACCAGGAA R 2 1 2 1 303000 r 74 goat GoatD01.039036 4 17910852 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320766318 Affx-122925063 AX-385253704 4 17937215 ATTCTCCTTGGTCTGTACCCTCTCAATCAAAATCA[C/T]ATTTCTTAATTCTTTGCTCTTCAACCTCAGTCTTG Y 2 1 2 1 101000 f 74 goat snp24932-scaffold255-963671 4 100489210 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408525 Affx-122953700 AX-123278876 4 18011955 GATGATTAACATAACATGACACGACATAAAGAGTA[C/T]GAGTCATTCATTTATATGCTTCTGAAATTCAAAGA Y 2 1 2 1 101000 f 74 goat snp24930-scaffold255-888931 4 100413822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423524 Affx-122942448 AX-123293870 4 18040961 CTTTATCAGTTGATAGAGTAACTGAGCATGGAGCC[C/T]GGATGCATGCTGCCTTTTAATATTGATCTCCTGTT Y 2 1 2 1 101000 f 74 goat snp24929-scaffold255-859925 4 100384330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424053 Affx-122942066 AX-123294399 4 18071161 TTGAACTCCTGCTCCTTTAGAGGGGACTCTGCCCT[C/T]ATACCTCCCTTTTGCTTGTGGGTTGCTACACTGGG Y 2 1 2 1 101000 r 74 goat snp24928-scaffold255-829725 4 100354304 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774082 Affx-122937296 AX-385261220 4 18101192 AGAGTTGGATTTGACTGTTTTAAAATTACATGCTC[A/C]TTAACTTGTAATCAGTGCTGTTGGTTTATCACAAA M 2 1 2 1 101000 f 74 goat snp24927-scaffold255-799694 4 100324340 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780557 Affx-122934122 AX-385267648 4 18156621 GCTCATAGTTTACTGTGAAAAGCTAGGTTCTAACG[C/T]ACAACCTCAATTTTGCACATAAGAGCTTCTTGATA Y 2 1 2 1 101000 f 74 goat snp24926-scaffold255-744265 4 100269334 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398057 Affx-122961748 AX-123268412 4 18196040 GTAGATAACTGATAAAATTCTCATGAACCATAGAT[A/G]CTGTTTGGTATGTAGAATTGGATGAAATCACTTAA R 2 1 2 1 101000 r 74 goat snp24925-scaffold255-704846 4 100229568 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417274 Affx-122947253 AX-123287622 4 18251934 GGGTTCTCTGGCAGTTACTTAACCCTCTGTGAAAA[C/T]AGTCACAAGCGATCTTTATTTCTCTACTACTTTCT Y 2 1 2 1 101000 f 74 goat snp24924-scaffold255-648952 4 100173543 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401770 Affx-122959494 AX-123272123 4 18302674 TATCTGACATATCCAGATATAAAGTGTTAATGCAA[A/G]ATTAGGAACTCTCAGGACTGTTGCAAGAGCCTTGG R 2 1 2 1 101000 f 74 goat snp24923-scaffold255-598212 4 100122224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405746 Affx-122956508 AX-123276098 4 18339291 GCTGGAATATTAATGTAGGTTTTTACTTTCATATC[A/G]CAAATACTAATAGAGAAAAGCCTTTCTCAAGTTTA R 2 1 2 1 101000 f 74 goat snp24922-scaffold255-561595 4 100088066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409241 Affx-122953146 AX-123279592 4 18389808 CTTGTGTAGCAATGCCAGGTCTCTCAGCAGGGGGT[A/G]CAGAAGTTACTGGGTCTTCTGAGACCAACAATGAA R 2 1 2 1 201000 r 74 goat snp24921-scaffold255-511078 4 100039076 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449168 Affx-122923538 AX-123319503 4 18420685 CAGGTACCAGCATGTGAACTGATATGAACGTGTCC[C/T]ACTGCTTTCCAGAGTCCAAATCAGATTCCCTTCTA Y 2 1 2 1 101000 f 74 goat snp24920-scaffold255-480201 4 100008197 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410672 Affx-122952755 AX-123281022 4 18451665 CATGTTGTTTTCATGTTGGGTGCTTCTGAATCTGG[C/T]TAATGTGACTTCAACACTGACCCACCTACTCACTA Y 2 1 2 1 101000 r 74 goat snp24919-scaffold255-449221 4 99977178 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417144 Affx-122947354 AX-123287492 4 18558933 GACTGTTTTTCTATTTTAGGTTCATAGGAGGCCTG[C/T]GACCTGAAAGAAATTATCTCCTTGTGCTGCTTTTG Y 2 1 2 1 201000 f 74 goat snp24917-scaffold255-341953 4 99869914 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401928 Affx-122958817 AX-123272281 4 18596248 CTTTTTTCTCCAACACTTTCTTCTAAGTTTGTGTT[C/T]GTTTTAGTGCTAGACTATGGAATGATTTGCCCCTA Y 2 1 2 1 101000 r 74 goat snp24916-scaffold255-304638 4 99832666 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450886 Affx-122922209 AX-123321220 4 18627050 TAGAGCAGTCAGCCCAGAGGTTTTTCGAAAAGTTA[C/T]CAGAATCACTTGGGGAGGTTTGTCAGTCTGCTTAT Y 2 1 2 1 101000 f 74 goat snp24915-scaffold255-273836 4 99801262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388385 Affx-122969307 AX-123258743 4 18691254 TGAAGGCTGTGCCTAGCATGTGGCAATGGTAAGAA[C/T]GGTTGTCGTGTGATGAAAACTCAATATTCACTGGT Y 2 1 2 1 101000 f 74 goat snp24914-scaffold255-209632 4 99736996 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797781 Affx-122929481 AX-385284720 4 18773625 TTTTCATCTCTGTAGACCTTTTATCAACACATCCT[A/C]TGTCAAGACTAACTGTCATACCTATAGAGAGAATT M 2 1 2 1 101000 f 74 goat snp24912-scaffold255-127261 4 99654238 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419523 Affx-122945439 AX-123289871 4 18803080 CATTTTGTTTCCTTTGTTTATTTAGGATGGCTCAG[A/G]AGAGGCTGGTGGACACTAATCTGGCCTCCCATCCC R 2 1 2 1 201000 r 74 goat snp24911-scaffold255-97806 4 99624997 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800642 Affx-122946642 AX-385287561 4 18862978 GGTTAGGAAAGCAAAGCAAAATACTATGCAAAAAT[A/G]CAGTCATTCTCGGTATATTTTGCTTTCTCCATTAA R 2 1 2 1 101000 f 74 goat snp24910-scaffold255-37908 4 99564736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272093 Affx-1111833416 AX-519545853 4 18867752 GATTCCCAACCAGTCACTCCACAGTGGAGGTGAAC[A/G]AGCTGATGAATCACAAACGTAACCACATGGTGCTT R 2 1 2 1 101000 r 74 goat 4_18867752_AF-PAKI 4 18867752 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38444789 Affx-122926345 AX-123315126 4 18924688 GGATTGAGAGAAATTTTATTCCATATACTGTTGCT[G/T]GATATGGCAGTCAACCTCCCTGCCTCCGCATACAG K 2 1 2 1 102000 r 74 goat snp20329-scaffold2013-22977 4 99500206 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405613 Affx-122956607 AX-123275965 4 18965980 TTACAGAAGCTCTATTCCAGGTGCTCTTCCCTGTT[C/T]ACTGCAGTCAGAAGAGATGGGTGCCCTCTTGGCTG Y 2 1 2 1 101000 f 74 goat snp20330-scaffold2013-64269 4 99458739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775287 Affx-122919814 AX-385262418 4 19020368 GGAAACAAAAGAAGAATAACAGGAAAGTCACTAAT[A/G]TTTGCCATCACATGAGTTTTGCAAATGGTTGACTT R 2 1 2 1 101000 r 74 goat snp20331-scaffold2013-118657 4 99403473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426493 Affx-122940222 AX-123296839 4 19051989 AGGACAAAAATTGGCTAGGAAATAAGATAGGGGTC[A/G]TCAGTTAGAAGCTATGTTTAGAATGAATTGTCTAG R 2 1 2 1 101000 f 74 goat snp20332-scaffold2013-150278 4 99372160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450765 Affx-122921841 AX-123321099 4 19100984 AATGCTACTTTATTTTATTTATTTTAGCTAATACT[A/G]TAAAGTACTTATTATAATAGCAAGTTTCGAACAGC R 2 1 2 1 103000 r 74 goat snp20333-scaffold2013-199273 4 99329918 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777550 Affx-122949225 AX-385264669 4 19130087 AGTATGTGCAGCACTACTGTAGAAGTCGGGTGGTT[A/G]TCAGCAGATGCACTCTAAAGGACACAATTCTAAAT R 2 1 2 1 101000 f 74 goat snp20334-scaffold2013-228376 4 99299509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765294 Affx-122942869 AX-385252821 4 19182780 GGGTTGCCATTTAGCTTACTAAATTTATAACTGAC[A/G]TTAAGAAAGGATTTAGTCATGGAAACTACTAATCA R 2 1 2 1 101000 f 74 goat snp20335-scaffold2013-281069 4 99247159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443878 Affx-122927503 AX-123314215 4 19247099 TCCTCGGGTACTGGTCCCACCCAGGTATCCTTAGC[A/G]TGCAGGGAAGTACACAGTGCTCCATCAGTCTGGAA R 2 1 2 1 101000 r 74 goat snp49477-scaffold706-40859 4 99176119 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448772 Affx-122923310 AX-123319108 4 19292133 GTGCTGTCAATCCTTTTTCATTTTAACCACTCTGG[C/T]AAATATGTATATCGTATCTCACTGAGGTTTTAATT Y 2 1 2 1 201000 r 74 goat snp49478-scaffold706-85893 4 99129856 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781068 Affx-122925684 AX-385268155 4 19320690 AAAAAGTATTTCTTTCATTTGACCTTATATCTCTT[C/T]CCACCTGCATACTTTCAGTTTTCTCCCCATTTTTG Y 2 1 2 1 101000 r 74 goat snp49479-scaffold706-114450 4 99100909 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791618 Affx-122979209 AX-385278609 4 19358552 GTAATTGGCATCCTTTTACCAAAAGACATTTAACT[A/G]TTCTTCTACTGCCATTATATAGATCAATGCTTACA R 2 1 2 1 101000 f 74 goat snp49480-scaffold706-152312 4 99063151 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792984 Affx-122970682 AX-385279962 4 19434591 TCAGCCATGGAGAAAGCTTTGACTTTATTATTTAC[A/G]TTATGTGTAAATAGAAAACGCTGTGGATTTATTTA R 2 1 2 1 101000 f 74 goat snp49481-scaffold706-228351 4 98988160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780903 Affx-122947417 AX-385267990 4 19496220 GCATAGCAGGAAATGCAGATAATTTAATGTTCCCA[C/T]GGTCAAAATATTACCAGAAAGGGATAGGAAACAGG Y 2 1 2 1 101000 f 74 goat snp49482-scaffold706-289980 4 98925794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433563 Affx-122934979 AX-123303904 4 19551214 CATGTTCCTTGCCATACTTCAGGCCTAGCACAGTC[A/G]GTAAAGTATCTGCCTGCAATGCATGAGATCCAGGT R 2 1 2 1 201000 f 74 goat snp49483-scaffold706-344974 4 98870393 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785793 Affx-122929335 AX-385272833 4 19598220 TCATTTCTATAACACATGTTTGAAGACATATTTTT[A/C]TTTTCCTCAATTTCCATAATAGTTTGTTGCTTTTT M 2 1 2 1 202000 f 74 goat snp49484-scaffold706-391980 4 98823422 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778764 Affx-122927887 AX-385265874 4 19630123 GACATTAAACCCATCAACCCTCCATTAGGTATATG[C/T]GGGTTTTCTTGTTTGTTGGACTTGTATATCAAACT Y 2 1 2 1 201000 r 74 goat snp49485-scaffold706-423883 4 98790604 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431394 Affx-122936546 AX-123301735 4 19809518 CCCAATTTAAAAAAAAAAAATCACAGTATGTCTTA[C/T]ACTGCTGTGGATTAGTTCATTTCCAAAAGATATGC Y 2 1 2 1 101000 r 74 goat snp49487-scaffold706-603278 4 98609124 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791441 Affx-122942943 AX-385278432 4 19852393 ACCTTATTCTTGCATAAGGATACTTTAGTCTTATC[A/G]TAAATCCCACATCTGGTTTACCCCGGGTACATCTT R 2 1 2 1 101000 r 74 goat snp49488-scaffold706-646153 4 98566016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453036 Affx-122920084 AX-123323369 4 19890084 TTAAACACTTGTTTTCGTGGCTCCCTTTCCACAAA[A/G]CTCTGAACTCCCTCTGCTTCTTGAAGACCAGATGC R 2 1 2 1 101000 r 74 goat snp49489-scaffold706-683844 4 98528350 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375460 Affx-122979161 AX-123245819 4 19918794 TTTGGTCTAAGCAATTCAGAATACAACTTTATTTC[A/G]CTTATAATTCCAGCTTGAATCAAAGCATCTTCTAC R 2 1 2 1 101000 r 74 goat snp49490-scaffold706-712554 4 98498900 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767213 Affx-122965363 AX-385254494 4 19951660 CTATTTCACCTCTGATCAGACACTGTCATTATCCA[C/T]AGGTTTTGCTCAATAAATTCTAAAGGGAGATTTTC Y 2 1 2 1 101000 f 74 goat snp49491-scaffold706-745420 4 98465997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404571 Affx-122957370 AX-123274923 4 19997123 TTCAAACAGATGAGAATTACTGACATTTATATTGC[A/G]TTATGATCCTGATGAACTGAAACAAATACAGTTTA R 2 1 2 1 101000 r 74 goat snp49492-scaffold706-790883 4 98420571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776269 Affx-122938093 AX-385263397 4 20030046 CCTCAACCACATTTCCATGCAAACTTTTATGACCT[A/G]CAACTCCTCCGGACAATCAGATTTTTAGGAGGAGA R 2 1 2 1 101000 f 74 goat snp49493-scaffold706-823806 4 98387749 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420657 Affx-122944823 AX-123291004 4 20076216 GGGACACCGAAGCCATGTGTATCGAGTCACCAGTT[A/G]TCCTAACTGGTGTGTTTGGTCCACTATCCGGCTGA R 2 1 2 1 101000 r 74 goat snp49494-scaffold706-869976 4 98341650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411789 Affx-122951474 AX-123282139 4 20107026 GAATAGAAAGAGAAGACGGTGTGTTATTTTTGTCT[A/G]TAAGAAATGAAAAATCTAATAGGGGGACATAATAG R 2 1 2 1 101000 f 74 goat snp49495-scaffold706-900786 4 98313318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391282 Affx-122967351 AX-123261639 4 20171345 AACTGGGTTATCACAAAAACTATTTCTCCTAAATT[A/G]AGCACATTTGTGTGTGAGTGTGTGTTAGTTGCTCA R 2 1 2 1 201000 f 74 goat snp49496-scaffold706-965105 4 98247331 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790130 Affx-122935777 AX-385277136 4 20206066 AAAATTTGGGACTACTGCAGAAGTAGGAACTATAT[G/T]TGTCCCATGTCATACAAATCAACAGATACTTTTGA K 2 1 2 1 101000 f 74 goat snp49497-scaffold706-999826 4 98211672 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399841 Affx-122960252 AX-123270196 4 20245413 GTGACTTCATCATGACTGATTTCCTGAGGTTCCTC[A/G]CTGGTGATGGGGAAAAAGCAAGCAGCAGGCATACG R 2 1 2 1 101000 f 74 goat snp49498-scaffold706-1039173 4 98172374 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784016 Affx-122921516 AX-385271070 4 20281396 TGAAAATAGAACAATATCTCGCTAAGTGCTCTTGA[C/T]ACAGTAGGACCCTTAATCCATGCTACTGACTACTT Y 2 1 2 1 101000 r 74 goat snp49499-scaffold706-1075156 4 98136101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421075 Affx-122944238 AX-123291422 4 20350156 TGGGAGACAATGAAAGTTTTAAGACAAATTTTTTG[C/T]AAGAGTAAAATATGGATAATATAGTAAAAGCACTT Y 2 1 2 1 101000 f 74 goat snp49500-scaffold706-1143916 4 98067654 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427077 Affx-122939798 AX-123297420 4 20389131 ATATTGTAATTCTGATGAAAGAAAATCATGGTTAC[C/T]GAGTTTCCAAAGGGGAAAAAAATTTAGTTGATATG Y 2 1 2 1 101000 f 74 goat snp49501-scaffold706-1182891 4 98027566 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416734 Affx-122947541 AX-123287082 4 20425882 TCACTCCTTTAATGTTTAAACATCCACAACTGAAA[A/G]CACTTTTTTCTCTGACCCGTTACTGTCTCTATATA R 2 1 2 1 101000 r 74 goat snp49502-scaffold706-1219642 4 97991067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799848 Affx-122946472 AX-385286774 4 20477723 ATGATATTGGGACTATCCTGATCAAGACAGATATG[C/T]AATTGTAAATGACATGAACTTTGTACCTCTCACTT Y 2 1 2 1 101000 r 74 goat snp49503-scaffold706-1271483 4 97939188 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394121 Affx-122965337 AX-123264476 4 20518887 ACTATCTATATTCTCTGGCCCTTTTGATTTACAGC[A/G]CGGAGCAGAAGAGGCAAGGAGAGCAAGATAGTTCT R 2 1 2 1 101000 f 74 goat snp49504-scaffold706-1312647 4 97897298 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409175 Affx-122953194 AX-123279526 4 20570314 AGGTCAACAGAACTACCAATAAGGACAGATAGAAT[A/G]AACAGAATTAGGAATTAAATTTCAAAGATTAAACC R 2 1 2 1 101000 f 74 goat snp49505-scaffold706-1364074 4 97845632 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409403 Affx-122954137 AX-123279754 4 20621111 TATACTGTTCTTCAAAGTGTTTCTATCAACATAAA[C/T]ATGATAGGCAGTGTTTAAGATCTGCCTTTGCTTCT Y 2 1 2 1 201000 f 74 goat snp49506-scaffold706-1414871 4 97794389 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780753 Affx-122954561 AX-385267843 4 20658229 GAAAGATTCCATGTACACATAGAATCTATAATAAT[A/G]AGCAGAAATTCTTTTTAAGTTGCCTTCTGTTTAAA R 2 1 2 1 101000 r 74 goat snp49507-scaffold706-1451989 4 97757468 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380789 Affx-122975099 AX-123251147 4 20706677 TTGCAGTGTGTTGGACCGTTCGTTAGTTGCAGCAT[A/G]TGAATTCTTAGTTGCAGCATGTGGGATATAGATCC R 2 1 2 1 103000 f 74 goat snp49508-scaffold706-1500437 4 97709367 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387158 Affx-122970634 AX-123257516 4 20775814 TTCACCAAAGCCCCCACCCAATCCACGGGCAAGCT[A/G]TATCAGCCTATCCCTGAAAATGGCAGTGTGTCCAC R 2 1 2 1 101000 r 74 goat snp49510-scaffold706-1569574 4 97639751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448541 Affx-122923434 AX-123318877 4 20806121 AGGATAAAATAAGAGGCACTCATTCTCCAGTGCCT[A/C]TCCATGATATATGAGAAGTAGCTGGCAGTAGGCTA M 2 1 2 1 101000 r 74 goat snp49511-scaffold706-1599881 4 97609391 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383609 Affx-122972558 AX-123253967 4 20849470 TTGCACATGAGAAAAAACAGCCCCTTCATCTGGTA[C/T]GGGCTCTTTGACAAATAAACAACTAAGTGTATAAA Y 2 1 2 1 201000 r 74 goat snp49512-scaffold706-1643230 4 97565862 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406827 Affx-122955678 AX-123277178 4 20881677 ATATTAATAATAATGCTTCCTAACCACTTTTTCCT[A/G]TTCCTAGTCAAGACATAAACCACCAGATTTGAAGC R 2 1 2 1 101000 r 74 goat snp49513-scaffold706-1675437 4 97533685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427560 Affx-122939487 AX-123297903 4 20939726 TGGGGGAGGCATTTGCTTCCTGTGGTTGTACCTCC[A/G]CATGCCTCAGTGTTCATCTTTGCATTTCAAACTCT R 2 1 2 1 201000 f 74 goat snp49514-scaffold706-1733486 4 97474219 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407020 Affx-122955017 AX-123277371 4 20972432 GATAATAACACTGGACTCATATGGACAGTATTCAA[C/T]GAACTAATAAACACAAAATGTTTATATAAAATATA Y 2 1 2 1 101000 f 74 goat snp49515-scaffold706-1766192 4 97441582 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801468 Affx-122967521 AX-385288377 4 21010865 GTACTGTATTTATTGATGATATGGCTATAGGTCTT[A/C]TAGGTCTTCTATAAAGTTCCTAATGAGTCTCTGGA M 2 1 2 1 101000 f 74 goat snp49516-scaffold706-1804625 4 97403556 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452924 Affx-122920193 AX-123323257 4 21079806 CAGAAGGAGGTGGAAATGATGGCAACATTTCCTTA[C/T]AGTCTCTGCCTCTGTATAAATGTATACAAAGAAAA Y 2 1 2 1 103000 f 74 goat snp49517-scaffold706-1873566 4 97333214 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407055 Affx-122954926 AX-123277406 4 21111874 TCACCTGCATTTCTGAATTTCCTGTACAGCTGGTG[C/T]GCAAGATGAACTGCAGGATGCTGTACAGTGTCATT Y 2 1 2 1 101000 f 74 goat snp49518-scaffold706-1905634 4 97300876 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409153 Affx-122953212 AX-123279504 4 21143037 GAGAAAGACCAATCTTAAAATATTGTTTGGCGTTA[C/T]GCCCATAACATTTTCATTTTATTCCTTGTTAGTAT Y 2 1 2 1 101000 r 74 goat snp49519-scaffold706-1936797 4 97269729 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448012 Affx-122923728 AX-123318348 4 21201441 AATGCCTTTGAGCCATCTGTAGTGGAGGCCAGTCC[G/T]CTGATGCCACAAACCCTCTATTTGGCAAAATTTAA K 2 1 2 1 201000 r 74 goat snp49520-scaffold706-1995201 4 97211189 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765497 Affx-122960399 AX-385252983 4 21248642 CAAATAAGAGCACCCTAAAAGTGCTTACAAGCTAC[A/G]TTTCTTGATAAACTCAAACAACATATTTTCAGCAA R 2 1 2 1 101000 f 74 goat snp49521-scaffold706-2042402 4 97163384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396106 Affx-122963418 AX-123266461 4 21296683 TCAGGTTTTTTTCTATTCCTTTTGGAAAACATATT[G/T]AAATGCCAAAAATAAATACTAATAAAATAATACCT K 2 1 2 1 101000 f 74 goat snp49522-scaffold706-2090443 4 97114891 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769166 Affx-122932631 AX-385256341 4 21359607 AGGTGTAATGTAACATTATCTTACCTAAAACCAAA[C/T]AGTCTCCTTAAAACTGCATTTTATCATTTCCCTCA Y 2 1 2 1 101000 r 74 goat snp49523-scaffold706-2153367 4 97050876 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796728 Affx-122971755 AX-385283673 4 21410352 AGCATTCTAATCTTCTCTCTTCTTGGTGGCGTGTG[C/T]GTGTATGTGTTCAGCCATGACCAACCCTTGGTGAC Y 2 1 2 1 102000 f 74 goat snp49524-scaffold706-2204112 4 96999642 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272095 Affx-1111833417 AX-519545854 4 21421330 AAAGGCCTCCTAACAATTCACTTTTTAAAACATTA[A/G]GCATCTACCAGTCACACATGATTCCTATCTCAGGA R 2 1 2 1 101000 r 74 goat 4_21421330_AF-PAKI 4 21421330 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38407349 Affx-122955283 AX-123277700 4 21445118 AGCAAAAATTCAGGGTAAAATTTATTTTATTTTTA[C/T]ATCCCAAGAAATCCCAATTATGCCCAAGATCATAT Y 2 1 2 1 101000 r 74 goat snp49525-scaffold706-2238878 4 96964924 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445721 Affx-122926103 AX-123316058 4 21473938 TAATTCAACTGAACTCCAAAACCAGAAAAATTAGG[C/T]ATTTTATTATTTTTCTCTTCAGTGGGGGGGCAAAG Y 2 1 2 1 303000 f 74 goat snp49526-scaffold706-2267698 4 96936265 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786267 Affx-122968782 AX-385273302 4 21504644 ATTTACCAAATAGATTATAATGTGACTCTTCCAAC[A/G]TGAGGCTCATAATTTCCTATCTCAAAGGAGACTTA R 2 1 2 1 101000 r 74 goat snp49527-scaffold706-2298404 4 96905039 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443971 Affx-122926999 AX-123314308 4 21558580 TGTTAGAGGGGAGGAGAGGGGGGAAACACGAAAAA[C/T]AGGCGAAGAAGATTAAGAAGTACAAACTTCCAAGT Y 2 1 2 1 103000 f 74 goat snp49528-scaffold706-2352340 4 96850105 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406625 Affx-122955829 AX-123276977 4 21589563 ATTATTCAATGGATAGTACCATTTAATAATTTCCA[C/T]GGGAAGGGATTCAGCAAGGTTTCCCTTTTTGTTAT Y 2 1 2 1 201000 f 74 goat snp49529-scaffold706-2383323 4 96818744 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433800 Affx-122934463 AX-123304141 4 21619251 CTTTGAAAAGTTCCCTTCCACATCTGTTCTTTTGC[A/G]ATGCAATTCCTCTCCCCAAAGCATTCTAATGTTGG R 2 1 2 1 101000 r 74 goat snp49530-scaffold706-2413011 4 96788691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789468 Affx-122971987 AX-385276478 4 21648311 TAATACAGAATTCTTGAAACTCAAATTATGACATG[C/T]ATAAAATAGGTATGTGTATTTAAAATAAAGTTGAG Y 2 1 2 1 101000 r 74 goat snp49531-scaffold706-2442071 4 96759522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402425 Affx-122958633 AX-123272778 4 21707545 CTACCATGAAGACTTCTACCAGTCAAAAGTGTATA[C/T]GCAAAAAAACCCACGAGTGGATGCACTTCTCAAAA Y 2 1 2 1 101000 f 74 goat snp49532-scaffold706-2501305 4 96700230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414931 Affx-122949098 AX-123285280 4 21743094 CCCTAGCTTCAGTCATATCTAAACATTCCACTTTG[C/T]AAAATATGAACCATTAACCTTGCTTTCCTTAATTT Y 2 1 2 1 101000 f 74 goat snp49533-scaffold706-2536854 4 96664971 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797905 Affx-122953401 AX-385284843 4 21842146 ACAACCACTTAGCAATAATGTAGGTTATTAAAGAA[A/G]TGACTTAAATGCATGCAAAAAGAAAATTTTAAATA R 2 1 2 1 201000 r 74 goat snp49535-scaffold706-2635906 4 96565193 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438804 Affx-122930799 AX-123309141 4 22020690 TGTGGCACATTTTAGTTTTACTTCTAAAAGTTTCT[A/G]TTTCCATATTTACTTTTCCACACTTGCAACCCTAG R 2 1 2 1 101000 r 74 goat snp55987-scaffold87-2297972 4 96385701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452034 Affx-122920898 AX-123322367 4 22078034 TATTCATCAAGTTCAGAAAATACAACTATGAATTC[A/G]TGAATTTAAGTCTTAATCTTATATCCACCCAAACC R 2 1 2 1 101000 r 74 goat snp55986-scaffold87-2240628 4 96327571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405853 Affx-122955860 AX-123276205 4 22115162 TAAGAACTTGAGAATCTATTTGATACAGTCTTCTA[C/T]AATTGGTACATGCTTTACATCACTTAATGATATTT Y 2 1 2 1 101000 f 74 goat snp55985-scaffold87-2203500 4 96290247 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785127 Affx-122924575 AX-385272173 4 22213996 ATATATATGTAGAGCCAGCATATGTGTGTATGCAC[A/G]TAAATACGCTGGCTCTCATGTAGCTAACTCTCCAT R 2 1 2 1 202000 f 74 goat snp55983-scaffold87-2104666 4 96192027 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442345 Affx-122928038 AX-123312682 4 22314248 GGCAAGGAATTTGAGGGTGGTATTAGGACAAACCA[C/T]GGATCCTACTTTTGGAGGGAAGAATATAAGCATAG Y 2 1 2 1 101000 f 74 goat snp55981-scaffold87-2004414 4 96091931 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765880 Affx-122962909 AX-385253318 4 22514508 GATTAAGTAGAGCTATTGTAACTCATGGATTCTCT[A/G]TTACAGAGATATTTCGATGCACATATGCCCATTTT R 2 1 2 1 101000 f 74 goat snp55976-scaffold87-1804154 4 95890757 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429173 Affx-122937968 AX-123299515 4 22584481 GATGCATCCTATTTCTTCATGCTCAAATTTTGTCA[A/G]CCTGAAAATCACTGCTGATGGTGACTGCAGCCATG R 2 1 2 1 201000 f 74 goat snp55974-scaffold87-1734181 4 95819430 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796493 Affx-122958943 AX-385283443 4 22663017 TCTTATACAGTTGCAGTTCTGCTAGTGACTGTTTT[A/C]CACTGTTCATCAATAATTTTGTTCATGTCTCTCTA M 2 1 2 1 101000 f 74 goat snp55972-scaffold87-1655645 4 95740576 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797235 Affx-122936711 AX-385284174 4 22770741 GAATAAAGACAACTCAGCTAACTGAAATGGTAATT[A/G]CCTAGTCAGGGTTTCTGTTGTAGAGTGTCATAATT R 2 1 2 1 101000 r 74 goat snp55970-scaffold87-1547921 4 95630908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441043 Affx-122928932 AX-123311380 4 22807495 GCAGGAGTCAATCATAAGCCCTGGGTCAAGTGGAG[C/T]AGAGGTCAGGAGGAAGATTTCCAGGAGGTGGGTGT Y 2 1 2 1 101000 f 74 goat snp55969-scaffold87-1511167 4 95593474 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775551 Affx-122977204 AX-385262682 4 22854689 ACTTTAAATATACCAAGATAAACTGTTTATGAAGA[C/T]GGTATGAATTCTCACCTAGAAGCTCATATGTGTAA Y 2 1 2 1 101000 r 74 goat snp55968-scaffold87-1463973 4 95545781 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379705 Affx-122975897 AX-123250063 4 22954261 TAGAATTTCTGTCAAAAATGGATTTGTCCTAACTA[C/T]GTTATATGTGAACATCCTGTCATAATCAATTTGTA Y 2 1 2 1 101000 f 74 goat snp55966-scaffold87-1364401 4 95448750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779259 Affx-122936438 AX-385266363 4 22987971 TTACATGTTGCCTGCAATATATTTGCTTGATTGTC[A/G]TTTTCCTCCCTTCTTGAAAAGTATGTAGGTAGAAA R 2 1 2 1 102000 f 74 goat snp55965-scaffold87-1330691 4 95414563 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438799 Affx-122930803 AX-123309136 4 23018211 TGCCCAACAGTAATGTCAGTTTTAGACAAAACAAA[C/T]GTATCACTGAGTAGCTCTGGTGAGGAGTGATGATA Y 2 1 2 1 101000 r 74 goat snp55964-scaffold87-1300451 4 95382322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393479 Affx-122965831 AX-123263835 4 23047211 ACTAAAGTAGGAAAATAATAAACGACGCACATGCA[C/T]GGCTAGATGGCTCACAACTGATGGCTCACGGGGGG Y 2 1 2 1 101000 f 74 goat snp55963-scaffold87-1271451 4 95353271 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430386 Affx-122937771 AX-123300727 4 23096542 TCTTCACCAGTAAGCAGGCTTTGCTGCACAGAGGG[C/T]AAGTGGACCCAAGTTTGGTTCAGTAGCAATGTCAG Y 2 1 2 1 101000 f 74 goat snp55962-scaffold87-1222120 4 95304711 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780680 Affx-122939177 AX-385267770 4 23129459 CTTCTTTGCTTATTACCTATCCTCCCCTTCAAATG[C/T]AAGATCCATGAAGGTAGGACATTTTGGTTTGTTTT Y 2 1 2 1 202000 f 74 goat snp55961-scaffold87-1189203 4 95271808 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429384 Affx-122938545 AX-123299726 4 23173385 TCTAGACTTGACTCTCTGGCAGTCATGAAGGCCTG[C/T]GGTTCTGACTTGGAAACAGTCTTACTATTGGTCAC Y 2 1 2 1 101000 f 74 goat snp55960-scaffold87-1145277 4 95227994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396283 Affx-122963301 AX-123266638 4 23260010 CAATGACTGACTCAAAAGATAGAAAACCTGAAAAA[C/T]ATTACACCAATTAAACAAAACTGATTTTGTAATTA Y 2 1 2 1 101000 f 74 goat snp55958-scaffold87-1058652 4 95140568 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396284 Affx-122963301 AX-123266639 4 23260010 CAATGACTGACTCAAAAGATAGAAAACCTGAAAAA[C/T]ATTACACCAATTAAACAAAACTGATTTTGTAATTA Y 2 1 2 1 600000 r 74 goat snp55958-scaffold87-1058652 4 23260010 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381683 Affx-122974728 AX-123252041 4 23292639 AAAAAGAAAACATTACTATAACTATAAAATTAAAA[C/T]GTCTGGTCATCAGACTCCAACTCACTATGTTTATG Y 2 1 2 1 102000 r 74 goat snp55957-scaffold87-1026023 4 95108186 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789550 Affx-122942553 AX-385276559 4 23332258 AAAATTAGTAATACTACTATTGGAATTGTCAGTCC[A/G]TCTTCCCAGGTTGGTCTCAGAAGCATTTTGCTAAA R 2 1 2 1 101000 r 74 goat snp55956-scaffold87-986404 4 95069962 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436367 Affx-122933057 AX-123306706 4 23365053 ATTACATTAGCCTCTCAGGCCTCAGAATTGATTCC[A/G]CTCCTTCATGATTTTTCAGCCCAAGGGTCCTGCAC R 2 1 2 1 101000 f 74 goat snp55955-scaffold87-953609 4 95038785 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790209 Affx-122931191 AX-385277213 4 23454536 CAGTTTTTTCTATTTGGTAACGAAAAAGCAGAAGA[C/T]AGATACTTTGTTTTTGTAGACCACAGAAAACTACT Y 2 1 2 1 101000 r 74 goat snp55953-scaffold87-864126 4 94948823 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780346 Affx-122967669 AX-385267441 4 23497673 TTTTAAATATGATTGTGCTGAGCCCATAATCTGAT[A/G]TTTTATTACATAAAGATTCCACTGAGAGACATAAA R 2 1 2 1 201000 r 74 goat snp55952-scaffold87-820989 4 94905212 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791698 Affx-122922043 AX-385278689 4 23553756 AAGAACACATAGATCCCATTTTTTCTGAGTTTCAC[A/G]TGTATATATCCATGCCATTCTGATCTGCTTGTTTG R 2 1 2 1 201000 f 74 goat snp55951-scaffold87-764906 4 94849293 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383825 Affx-122973170 AX-123254183 4 23600891 CATCTTCTCTATTTCTCAGTATAATCACTTTACAC[A/G]TTTTCTGTATTACCCATTCACACATGAGTTCAGCC R 2 1 2 1 101000 r 74 goat snp55950-scaffold87-717771 4 94801564 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379204 Affx-122976294 AX-123249563 4 23680822 ACCTTAGGTTCCTATAGAGGAAACTGAAATAATAA[C/T]AAAACCTTTTCATAGTACTACTATAAAAATGAAAT Y 2 1 2 1 202000 r 74 goat snp55948-scaffold87-637840 4 94721323 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798102 Affx-122961905 AX-385285037 4 23836709 GAAAGGTAGGATGAAGCTGTAGGTTTATTAGTATC[A/G]CTTCTGCTCCATTGCTCTTACCCTCATCATAGGTA R 2 1 2 1 201000 f 74 goat snp55944-scaffold87-481953 4 94565266 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418007 Affx-122946660 AX-123288355 4 23911510 GAATAGAAAAAGCTTTTTGGAGGTACAGTTCTGGT[A/G]CTCTTGTCTATAAGAGACTGGAATGTTTATGGGAG R 2 1 2 1 101000 r 74 goat snp55942-scaffold87-407152 4 94490451 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427991 Affx-122939173 AX-123298334 4 23948928 CTCTCTATAAATTTGGTTTTGGACATTTCATAAAT[C/T]CAGTTGTCTGCTGTGCAGTCTTTTGTATCTGGCTT Y 2 1 2 1 101000 r 74 goat snp55941-scaffold87-369734 4 94452603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272262 Affx-1111833418 AX-519546001 4 23952911 ATGACAACAACAGGCTGCAAGATGGGGATTATAAC[A/G]CCGAAGCAAGTGAGAAACAGGAGGTGGTGGTGAGA R 2 1 2 1 101000 f 74 goat 4_23952911_AF-PAKI 4 23952911 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387171 Affx-122970625 AX-123257529 4 23994900 CATTATTGAGCAAATCTTATTTTTGAAAAGGTTCA[A/G]GATGCATTTAGATTACTCAACTTAAATTAATAGAG R 2 1 2 1 101000 r 74 goat snp55940-scaffold87-323762 4 94405984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764557 Affx-122920464 AX-385252212 4 24033953 ATCATGTCTCCAAGGGGTGCCTATAGTCTGCTTTT[A/C]AATTCTTTCTCCATTTTGCTAAGATTTGATCTAAA M 2 1 2 1 101000 f 74 goat snp55939-scaffold87-284709 4 94366434 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418370 Affx-122946574 AX-123288718 4 24108960 AACAACACAAGAAATCACACAGTGAAAGATGACTT[A/G]CAACTTCATAAAAACATGACATTTTAACATTCCCA R 2 1 2 1 201000 r 74 goat snp55937-scaffold87-209702 4 94291163 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799429 Affx-122932375 AX-385286359 4 24141130 TATGGTTGACAAAAATTTTGAGTGCTTTCTAGATG[C/T]GTGAATGTGTGAAAGCTCTTAAACATAAGTATCAT Y 2 1 2 1 201000 r 74 goat snp55936-scaffold87-177532 4 94259033 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777472 Affx-122963694 AX-385264592 4 24173147 ATTCATGTAAGAGTCTACTGTGTACATGTGAAAAT[A/G]CATTTCTAGATAATGTGAGGAACGCTGGCCATCAA R 2 1 2 1 101000 r 74 goat snp55935-scaffold87-145515 4 94227172 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430165 Affx-122937371 AX-123300506 4 24201960 TAAGAGGACTCACAGACCCCAGCATAGCTATACTC[A/G]CAGCTAAAACTTATTATAGTAGAAGGATATAAAGC R 2 1 2 1 201000 r 74 goat snp55934-scaffold87-116702 4 94198220 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278220 Affx-1111836234 AX-519551708 4 24226142 CATTGCCATGGCTGAGCGGTGAAAGGTGAGGGGGA[A/C]GGTTCTTGCATCAGAATGATCAGAATGACCGTGGG M 2 1 2 1 102000 r 74 goat Random2.2K-425 4 24226142 A C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408236 Affx-122953830 AX-123278587 4 24279418 GTGACCCAGGTTGGCACTGAAGTAACATCAGCTTT[A/G]TGAGTCTCAGCCCTGTCTGGCTGGCTGCCCTATGC R 2 1 2 1 101000 f 74 goat snp55932-scaffold87-39244 4 94119902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379743 Affx-122975868 AX-123250101 4 24317444 GGAAGAAATTTTAATGGGCAGTGGGAAGTATTCCT[A/G]CTTGGACTGATAGAGAGAAATGTGTGTAGATGAGT R 2 1 2 1 201000 f 74 goat snp55931-scaffold87-1218 4 94081893 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382326 Affx-122973896 AX-123252684 4 24319537 TTTTCCGAAATGCCTTCGTATCCCCTTAAAAGAGA[C/T]GGAAGGATTCTGCATGTCAAATTTGAAAACTTGTC Y 2 1 2 1 201000 r 74 goat snp59163-scaffold970-900354 4 94079574 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386043 Affx-122971477 AX-123256401 4 24353668 GGGAGGGAGATAGTCAGGGAGTTAGGGGTTGACCT[A/G]TACACACTGCTAAATTTAAAATAAAAAACCAACCA R 2 1 2 1 201000 f 74 goat snp59162-scaffold970-866223 4 94044962 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790543 Affx-122954888 AX-385277546 4 24395421 TAAAGGAAGCTATCACATGCTCTGAATTTCTCTAA[C/T]CACTAGTCACCATCAAATTGATTTATGGTTTGCCC Y 2 1 2 1 101000 r 74 goat snp59161-scaffold970-824470 4 94003030 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386310 Affx-122970895 AX-123256668 4 24432352 GCTCTGAAAAATCTTTGTATTCCCTCTCAGTGGTT[A/G]TGATCCTTTTCTCTGCCAGATGAGTAAGGTTTTGA R 2 1 2 1 201000 r 74 goat snp59160-scaffold970-787539 4 93962664 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434435 Affx-122934661 AX-123304776 4 24485240 CTCCTATATGGCCTGTTCTCCACTCCTGCAGTCTT[C/T]GGGTACAGCTTACACATTTGATTTAGAATTCAGGA Y 2 1 2 1 101000 r 74 goat snp59159-scaffold970-734651 4 93908494 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786581 Affx-122923135 AX-385273613 4 24613072 CCAAGATGAATGACACATTTCTCCTCAAGGAACAA[A/G]AAGTGTTTCAGAAATTGTCTAAATATGTATATATA R 2 1 2 1 101000 f 74 goat snp59157-scaffold970-606819 4 93779941 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786294 Affx-122946595 AX-385273329 4 24678502 ATCTCAATTGACATAGCTTTAAGTTCACTATTTTT[C/T]CCTTCTGCCAGCTCAATCTGATGTTAACCTCCTCT Y 2 1 2 1 101000 r 74 goat snp59156-scaffold970-541389 4 93713834 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433876 Affx-122934419 AX-123304217 4 24749655 ACAGGTGAACAGTGATTAAAGCTGCTAAATCTACA[G/T]AAAGGCTGAGATGATTTTATGTTACAGATGATTTA K 2 1 2 1 101000 f 74 goat snp59155-scaffold970-470236 4 93641786 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401763 Affx-122959499 AX-123272116 4 24829633 TTTTGGATTACTTTCATCTATCCATCCTTTATTTT[A/C]TTGATTTCTTCCCTTTCATGCTAAGAAGATCTACA M 2 1 2 1 202000 f 74 goat snp59153-scaffold970-390258 4 93560613 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416336 Affx-122947900 AX-123286685 4 24868014 TATAAGTACTGAGGTAAAAATTGAGTTGCATAGTC[A/G]TTATGGAATAAAGAATAAAAAGGAACTACAAAGAT R 2 1 2 1 101000 f 74 goat snp59152-scaffold970-351877 4 93521730 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441529 Affx-122928711 AX-123311866 4 24897176 TCAAGTCTGCTGTTTGCTACAGCAGATGATGCCTC[C/T]GTACTGCAGGTGGATTCCACAGCCAAATTGCCTGA Y 2 1 2 1 101000 f 74 goat snp59151-scaffold970-322715 4 93492517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436082 Affx-122932689 AX-123306421 4 24943529 CCTGGGAGCTGACTCATAGTGTTCTCCAGAAGAGG[G/T]TCTTCCCTGAACCAGAGCAGCCTAATTTTCATCTG K 2 1 2 1 101000 r 74 goat snp59150-scaffold970-276362 4 93446261 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772046 Affx-122940939 AX-385259201 4 24981573 ACACTATGTGAATCAAAAGTACCCTGAGAAAGCAA[C/T]AGCATACAAATATACATGGTGAGGCAGTGTGGTGA Y 2 1 2 1 101000 r 74 goat snp59149-scaffold970-238318 4 93408298 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387347 Affx-122970486 AX-123257705 4 25027177 AAATAAGGGAACCTAATTAAAGAGCTAGGAGAACA[C/T]CTGGAAATTCAGTAAATATTACTTAAGATAATAAT Y 2 1 2 1 101000 f 74 goat snp59148-scaffold970-192714 4 93361008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800517 Affx-122932816 AX-385287437 4 25057624 GGAGTTGCAGAGGTTCCTCTTCAAGAAGCAAAGCA[G/T]GATTTTTGCCAGGATTCTTTTTACTTACTCTAGGT K 2 1 2 1 101000 f 74 goat snp59147-scaffold970-162267 4 93330492 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392198 Affx-122966286 AX-123262555 4 25133579 AGCACATGATAAAGATCCCCTTTTTCTTACTATCA[G/T]AAAGATGATTAGACTTTTGCCCATGAGGTTTTGTT K 2 1 2 1 101000 r 74 goat snp59146-scaffold970-86312 4 93253652 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777356 Affx-122936465 AX-385264478 4 25175768 ATTAAATGATATATGTAAATTGCTAGGCCAGGTGA[C/T]AGGCATTTAATTAATTCTCAAACATACTACCTTTC Y 2 1 2 1 101000 f 74 goat snp59145-scaffold970-44123 4 93211468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774770 Affx-122927538 AX-385261904 4 25208004 AAATCTTAAGGAGAGCTGACAAGCAGTATAAATAT[A/G]GCTACTTAAGACACATGAATTAGACGGATTTATCT R 2 1 2 1 101000 r 74 goat snp59144-scaffold970-11887 4 93179239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439703 Affx-122930565 AX-123310040 4 25256495 ATCTTGTTAGCAGATTATTTTTCAAGTGTGTGATT[A/G]AGCGTTCAGCCTAGTGAGGTTGTGGGAGAATGAGA R 2 1 2 1 101000 r 74 goat snp1953-scaffold1055-36505 4 93129454 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793566 Affx-122957185 AX-385280541 4 25314267 GGAAGAACAGCTTTTTTAGTCCTTAGCTCAATGCA[C/T]GTTGAGTTACAGAAATTTGTAGGATCATTCAAGTC Y 2 1 2 1 101000 r 74 goat snp1954-scaffold1055-94277 4 93071607 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789175 Affx-122945245 AX-385276187 4 25353038 CTTTACATTTAGAAGGTATTGATGAAATAGCAAAT[A/G]TCTCATTTGGCACGCACTGAAGACAAGCTAAGAGA R 2 1 2 1 101000 r 74 goat snp1955-scaffold1055-133048 4 93032403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793227 Affx-122976437 AX-385280205 4 25401552 CATATCTCAATTGGAAGGCCTCTTACATTTGTTGG[C/T]ATTTCATTGTTGTATTGGCAGTGTTTTTTTTCTAA Y 2 1 2 1 101000 f 74 goat snp1956-scaffold1055-181562 4 92983834 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391958 Affx-122966532 AX-123262315 4 25464130 TTGCCTACTAGATAACATATTTTGCATATCCACCT[A/G]TATTCTAAAATTACTTATTTCATTTTAGATATAGA R 2 1 2 1 101000 f 74 goat snp1957-scaffold1055-244140 4 92920851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278069 Affx-1111836235 AX-519551559 4 25466137 GCAGGCTCTCCTCTCCCTTGGAATTAAAGCCTCAG[A/G]AGTGAGGCAGCCTCAGTGTGACTGTTGCCCCTGAT R 2 1 2 1 102000 f 74 goat Random2.2K-426 4 25466137 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384297 Affx-122972288 AX-123254655 4 25496972 CATGAGTGACATGAACACTGAAGACACAGTGTTAC[C/T]GAATCAGGAGCAGTAAAATGTAGTCATCATGAAAA Y 2 1 2 1 201000 r 74 goat snp1958-scaffold1055-276982 4 92887868 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424651 Affx-122942162 AX-123294997 4 25536438 TTGGGGGTAGTCTTTCAAGGGTCTTAGATTAATTG[C/T]AAACATGGTGTAAAAGATAGCTTTCATAGTTCCAA Y 2 1 2 1 101000 f 74 goat snp1959-scaffold1055-316448 4 92847933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797608 Affx-122957854 AX-385284547 4 25571694 AAATTGAATATTTTCCTAAGCATCCAGCACATAAA[C/T]AATTCATGTTTCAGCAATGGCCAATCAATAAAAGG Y 2 1 2 1 101000 f 74 goat snp1960-scaffold1055-351704 4 92812560 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796885 Affx-122949561 AX-385283827 4 25682062 CATTGAGCCAAACAAATCTTAAGTGAAAGATTTTC[A/G]CTTAATCTGAAAGCTTTTTTACCCCTAGTAGGAGG R 2 1 2 1 101000 r 74 goat snp1963-scaffold1055-462072 4 92702047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425819 Affx-122940687 AX-123296165 4 25718176 AATGTGAGCCTATCCTGTTTCCCTCTTTTAGAGCC[A/G]TGCTGGCTCACCCACATGCATTAACTTAGAGGATC R 2 1 2 1 201000 r 74 goat snp1964-scaffold1055-498186 4 92665560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417266 Affx-122947259 AX-123287614 4 25798828 TTTCCTAATATACATTGACAGCGAGGATTTATTAA[C/T]GAACCTGGAGTAACTTAAAACATAAATCACCTTAA Y 2 1 2 1 101000 f 74 goat snp1966-scaffold1055-578838 4 92584790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422746 Affx-122943246 AX-123293092 4 25850430 GAGAGAAAATTTTACAAAACATGTCCCACAATGAT[A/G]TATGCCCAGCATGGGGTGGGATATGAAGACGGAAA R 2 1 2 1 201000 f 74 goat snp1967-scaffold1055-630440 4 92533001 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804579 Affx-986696748 AX-385291118 4 25850949 GCCTCCCCCATTTTCTTCTCTGACTAGACCTAAGA[A/C]GGTCCCTGTTTTCGCCCCCTGGTTCCTTGTGTGGA M 2 1 2 1 600010 r 74 goat 4_25850949 4 25850949 Ancestral_priority_1043 ancestry 0.51 neutral IMAGE 10K 10K ancestral 320804259 Affx-986696750 AX-385290888 4 25856966 AGGTTACTCCTCTTCATTTCAGACCTGTGACACCG[C/T]CCCCCTGGGGAGCCTTGCCCCCCCAAGTCTCCCTG Y 2 1 2 1 600010 f 74 goat 4_25856966 4 25856966 Ancestral_priority_1043 ancestry 0.504 neutral IMAGE 10K 10K ancestral 320804263 Affx-986696752 AX-385290891 4 25865271 AGGGAGAGCATCAGCCTCTCCTCTAGGCCCATCGT[C/G]TCCTCTCCGTACTCCCTGATGCCTGTCGTCACTGC S 4 1 2 1 600010 f 74 goat 4_25865271 4 25865271 Ancestral_priority_1043 ancestry 0.492 neutral IMAGE 10K 10K ancestral 320804587 Affx-986696756 AX-385291125 4 25869497 GCCACTGCTCCCACCCACTGCTAGCCCCCCACTTT[C/T]GTTCCACGCCTCCCTCCACAATCCTCAGCCCGCAC Y 2 1 2 1 600010 r 74 goat 4_25869497 4 25869497 Ancestral_priority_1043 ancestry 0.484 neutral IMAGE 10K 10K ancestral 320804276 Affx-986696758 AX-385290898 4 25869700 CCCTGGGTGCCTCCCATCACCTGGTCTGTCTCTGC[C/T]AGGTGACCCTCCTGTCCTGCCACATCAAGAACCTG Y 2 1 2 1 600010 f 74 goat 4_25869700 4 25869700 Ancestral_priority_1043 ancestry 0.47 neutral IMAGE 10K 10K ancestral 320778914 Affx-122930516 AX-385266021 4 25879180 CAAGCACCCTCAAATAAACTGTCTTCTTAATGTTC[A/G]TTATATTTTTCATGACAAAAGTTAAGTACAAATGA R 2 1 2 1 101000 f 74 goat snp1968-scaffold1055-659190 4 92504253 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781265 Affx-122932541 AX-385268350 4 26035188 GATAATTTCTTTTTTAACCCTTGAATTACTAAAGT[A/G]TATTCGTAAGGCACAATAAAGCTTCTAGTAATATT R 2 1 2 1 101000 r 74 goat snp1971-scaffold1055-815198 4 92349061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415301 Affx-122948819 AX-123285650 4 26081495 TGCCCTTGTGGAAGTGGTATAAACTGGGATACTTT[A/C]TAGAATGAGAAGAGACACTATTAAAAATTGGATAA M 2 1 2 1 101000 f 74 goat snp1972-scaffold1055-861505 4 92302579 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423610 Affx-122942381 AX-123293956 4 26147614 CCACTTAAATTTCACACTTGCCTTGTGAAATTTCT[A/G]TGCACCCATGGAAAAAATCCTTTTTGGATTTTTAC R 2 1 2 1 101000 r 74 goat snp1973-scaffold1055-927624 4 92235689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453399 Affx-122919913 AX-123323732 4 26179462 AAGATGAGGAAACAGACATTCAGAGTTAAGTAATC[A/G]AACCAAATATTTGGACCTAAGTCTGCCAGGGTTCA R 2 1 2 1 201000 f 74 goat snp1974-scaffold1055-959472 4 92205975 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402810 Affx-122958278 AX-123273163 4 26254854 GAGAAGGAGAGAACAGTCAGCACTGTTTCCTAACT[A/C]ATGATCCACAGGTAGGGCTACGGTTCAAAGAGGGC M 2 1 2 1 101000 r 74 goat snp14140-scaffold1566-46818 4 92129521 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376106 Affx-122978888 AX-123246465 4 26291208 TTTGGGTTATCAGAAAGTGGTAAACTGCCTAGTTC[A/G]TAGAGAAACGTTTAGGGCCATTTGTGCATACTTTT R 2 1 2 1 101000 r 74 goat snp14141-scaffold1566-83172 4 92092771 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417778 Affx-122947392 AX-123288126 4 26341629 ATAAGCATTGCCTTAGCTTCACAACAACTTCACAG[C/T]AACCCAATAATAGGTACTGTTATTTCTCTCCCTGA Y 2 1 2 1 101000 f 74 goat snp14142-scaffold1566-133593 4 92042268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383408 Affx-122973491 AX-123253766 4 26398407 TACCCTTTTAAAAATGTCAATATGTTTTTTAAAGC[A/G]CCTATTACCAAGCTCATGGACTGAAGAAAAGGAAA R 2 1 2 1 101000 r 74 goat snp14143-scaffold1566-190371 4 91985736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445244 Affx-122925486 AX-123315581 4 26447945 GAATTGTTCTCCTAGGAAACTCTTGTATCTCCTTG[A/C]TTCCTCACTGCTCCCTGCAATCCCCAAATTAAAGT M 2 1 2 1 102000 f 74 goat snp14144-scaffold1566-239909 4 91935431 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272263 Affx-1111833419 AX-519546002 4 26467662 TCAGCTGTACAGGACTCCCAGTACAAGGATGTGCA[A/G]CATCTCCCCAGCCCCTTGTTGATGGGGTTGAACTT R 2 1 2 1 201000 f 74 goat 4_26467662_AF-PAKI 4 26467662 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403076 Affx-122958513 AX-123273429 4 26485346 AATTTTATTTTATTTTGGTTTGTTTGGGGAGACTA[C/T]CAATCACTAAGTCTCAGTTTTAAAAGGTTTTAGAT Y 2 1 2 1 101000 r 74 goat snp14145-scaffold1566-277310 4 91898238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798837 Affx-122923843 AX-385285767 4 26520163 ACATGATAATTTTGATATATCATGGGTTGCTGAGT[A/G]TGAACTAGCTTGAGAGTGAGAAGCTCTTAGGGCTA R 2 1 2 1 101000 r 74 goat snp14146-scaffold1566-312127 4 91863410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382674 Affx-122973656 AX-123253032 4 26549188 ATGCCGTGAGCTGGAATGACTTTTACTCTCTGCTG[C/T]GTCAGCCAAAGACGGTGTTGCTTCACTGAGCTCTA Y 2 1 2 1 101000 r 74 goat snp14147-scaffold1566-341152 4 91834082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780600 Affx-122947729 AX-385267690 4 26593196 GGAAAAATGAATAACATTGATCAAGTACTATCAAG[C/T]GTTGCTCCTTAAAGGGATGGCTTTACCCTTTAGGG Y 2 1 2 1 101000 r 74 goat snp14148-scaffold1566-385160 4 91789356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409393 Affx-122954145 AX-123279744 4 26622502 CATCTCAGTTTCTTAGTGCAGGCAGTTTGGTATAC[A/G]TAGGGGTTACCATCTTGGACCAGCACAAAGGATAA R 2 1 2 1 101000 r 74 goat snp14149-scaffold1566-414466 4 91759869 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777143 Affx-122961362 AX-385264266 4 26653213 GAATGGAAGAAAATTATCAGTTAAACCATACTGAT[A/G]TGGTCTTGATGCAGCAACAGAAATCACACCATATT R 2 1 2 1 101000 r 74 goat snp14150-scaffold1566-445177 4 91728911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425870 Affx-122940649 AX-123296216 4 26697358 TCACTAATAAGAAATGCTGAGTCCTACTCAAAGGC[A/G]TGAATAACAGGAAAACACAGCTGCCTGAATGAATG R 2 1 2 1 101000 f 74 goat snp14151-scaffold1566-489322 4 91684215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431160 Affx-122936565 AX-123301501 4 26732659 GTTCTGGCCAGTTCTGATGGCTCTCCAGAATTCCA[A/G]TTCCAAGTGATTAACAACTCAGTTTCCCTTTCCAC R 2 1 2 1 101000 r 74 goat snp14152-scaffold1566-524623 4 91649103 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771196 Affx-122958421 AX-385258354 4 26766765 GAACAGAAAGTTAGTGGTCTCTAAAACTATTTTTC[A/G]TCTCCCTGGAGTAAAGACTGAACTCAAGATTGAGA R 2 1 2 1 101000 r 74 goat snp14153-scaffold1566-558729 4 91615082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375717 Affx-122978636 AX-123246076 4 26830272 TTCTCATCCCTCTCATCTCTTAATTCTGTCCTTCT[A/C]TGCTCCCTTGTAGTCAAACAACCTTATCTCTATAT M 2 1 2 1 201000 r 74 goat snp14154-scaffold1566-622236 4 91552063 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430161 Affx-122937375 AX-123300502 4 26900341 ATTCATGGTGTTTTATTTCTTCTTTTACATTTTCC[A/G]TCATCTGAGCATGAATTGCCTTGTGTTTTGTTATT R 2 1 2 1 102000 r 74 goat snp14155-scaffold1566-692305 4 91481688 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419292 Affx-122946239 AX-123289640 4 26959284 CCAGTCTCTGTTAACAGTAAAATATTAAAAATCAA[C/T]GTACTGGTCCTTCTACATGACTATGATAACTACTG Y 2 1 2 1 101000 r 74 goat snp14156-scaffold1566-751248 4 91422529 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436362 Affx-122933060 AX-123306701 4 26990652 ACAGTTTCCTCCTCCACAAACACCAAATATTTTCA[A/G]TTTTTTGAGTAGGAGAAAGTAGACCAAAAAGAATG R 2 1 2 1 101000 f 74 goat snp14157-scaffold1566-782616 4 91391045 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801000 Affx-122953803 AX-385287914 4 27021957 TGAAAGAGCAAGATAAAATCCCTAAAAAAATAAAA[C/T]AAATAATTTACCAAATAAAGCTTTAAAACATTACT Y 2 1 2 1 303000 r 74 goat snp14158-scaffold1566-813921 4 91358799 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439774 Affx-122930511 AX-123310111 4 27117949 GGCTGTCTGTACCTACCAGTGAATATCCATGTATC[C/T]CTCAGGCTTCCTTTATAGAGTTGGGGCTGTTGATT Y 2 1 2 1 101000 f 74 goat snp14160-scaffold1566-909913 4 91261102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417787 Affx-122947386 AX-123288135 4 27148091 TAACTATTCTATATTTTACTCAGTAGCAGGGAAAA[C/T]AAAAACATCAAAAAGCAGGCTGTCAGGGCCAAGTG Y 2 1 2 1 103000 r 74 goat snp14161-scaffold1566-940055 4 91231604 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786299 Affx-122924986 AX-385273334 4 27197446 TGATTTCTAGTTCCAGACTATCATGGTCCAAAAGA[C/T]ACTTGGCATTTCAGTCTGCTTAAATTTGCTAAGAC Y 2 1 2 1 101000 f 74 goat snp14162-scaffold1566-989410 4 91181688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796725 Affx-122944816 AX-385283670 4 27262362 AGTTTTTTGTTAGGGCACATTAACATAAGTGGTAG[C/T]GATTAGGCTCTAGCTATCTTCATTCTGCCTTGTTC Y 2 1 2 1 101000 r 74 goat snp14163-scaffold1566-1054326 4 91118129 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782791 Affx-122923640 AX-385269863 4 27291231 TACTAAAAAATTTTTGAAGACTATTTCATGACCCA[C/T]GAAAAAGCTTGCAGTGTAATATAAAGGGATAAAAG Y 2 1 2 1 201000 f 74 goat snp14164-scaffold1566-1083195 4 91089624 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769931 Affx-122969018 AX-385257100 4 27332228 AGAAATTAGAACAAAAAGTCATACATAAGGATGTT[C/T]AATCATTTGGGAACAACTAGATGCCCAGTATTAGG Y 2 1 2 1 101000 r 74 goat snp14165-scaffold1566-1124192 4 91046022 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771060 Affx-122932200 AX-385258220 4 27361501 CCTTATACTTAATATTCAGTCATTAGCATTATTCT[C/T]TCTTCTATGGAAAGTCAACTTCTAACTGCATGAAA Y 2 1 2 1 101000 r 74 goat snp14166-scaffold1566-1153465 4 91016806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430811 Affx-122937456 AX-123301152 4 27395182 GTGAGAAATATTTTGGCAGTTCTTTAAAAATGTGA[A/G]CATTCTCCTCCCATGCAATCCAAAATGACACTCCT R 2 1 2 1 101000 r 74 goat snp14167-scaffold1566-1187146 4 90982874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777514 Affx-122927282 AX-385264633 4 27475171 TTGGTAAGAATCAAGACAAAGGACTTCTATCACTC[A/C]TATCTTAATTCTCCTTCAAGATTTCTTGAACTGCT M 2 1 2 1 101000 f 74 goat snp14168-scaffold1566-1267135 4 90904763 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378947 Affx-122976426 AX-123249306 4 27529509 GTTAACCCTGCTAACAAGCTACTATTCTGTCTCTT[C/T]ACACCACAAAATACCATGTGAAGAGGTGATGGCAG Y 2 1 2 1 101000 r 74 goat snp14169-scaffold1566-1321473 4 90851566 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452461 Affx-122920559 AX-123322794 4 27680846 GGTTGGTGGTACAATTATTGGAAAAACAATTTCCA[C/T]TACAGACTAGAAGTTTCCCCTAGAATGTTCCTTCA Y 2 1 2 1 101000 r 74 goat snp14171-scaffold1566-1472810 4 90701889 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435883 Affx-122932784 AX-123306222 4 27716020 CATGAAGCGTAGCACCTTTCTAAGCTCAGGTTCCT[A/C]TGTGACTGCTCTGGTCACAATCCTGTGAAACCTCC M 2 1 2 1 101000 f 74 goat snp14172-scaffold1566-1507984 4 90665806 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451083 Affx-122921412 AX-123321417 4 27754242 ACATTATGTACCAGCCCTTATCCCTTTTGGCCTTG[C/T]AATAGGGTTATTTATGTGTGTGTCTAATCTCTACT Y 2 1 2 1 101000 r 74 goat snp14173-scaffold1566-1546206 4 90628349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426773 Affx-122940555 AX-123297119 4 27810202 TATGTATATTTTAAATTAATATATGTAAATAATTT[A/G]GAAAAATTCATGAGTGACAACCAAGATTGTTGAAG R 2 1 2 1 103000 r 74 goat snp14174-scaffold1566-1602166 4 90572098 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394044 Affx-122964990 AX-123264399 4 27852726 CAAAGGTTATGTATGTTTTTATCTTAATAGATATT[A/G]CAAACCAAGTTCCTTAGGTGTTACACCAATTTATA R 2 1 2 1 201000 f 74 goat snp14175-scaffold1566-1644690 4 90528269 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418260 Affx-122947020 AX-123288608 4 27897201 AGGGAATCCTTCTCTGACAGGTAATATTTGAGAAA[A/G]TGTAGGAAGACAGATAACCATTATGAAAATATGTC R 2 1 2 1 101000 r 74 goat snp14176-scaffold1566-1689165 4 90483232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395420 Affx-122963945 AX-123265775 4 27949204 AGGCTCACAGTCAGATACAGCTGACCAACTAAATA[A/G]TAAAGCAATAGCAGCACTGGAAAATTCTGTGGTTT R 2 1 2 1 101000 r 74 goat snp14177-scaffold1566-1741168 4 90431756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435131 Affx-122933684 AX-123305471 4 27966272 TAAAACAAGGCATTGTGGTATATCAGAAAAAGGCT[A/G]TGAAGTCAGACAAATCCAAGTATAATCCTATTTAT R 2 1 2 1 201000 r 74 goat snp15440-scaffold1637-10670 4 90407622 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388563 Affx-122969175 AX-123258921 4 28010585 TAATAAATAAGTTCATAGCAAGGCTTTTGTGTGCT[A/G]CTGTTCTTTATCCTGCAGTATCATCAGTCAAATTC R 2 1 2 1 101000 r 74 goat snp15441-scaffold1637-54983 4 90363722 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274488 Affx-1111834322 AX-519548079 4 28023348 CTGACAGCCCCAGCTGCTGTGCTCTGAAACCCATC[A/G]CT R 2 1 2 1 103000 f 74 goat GoatD01.029976 4 28023348 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38397021 Affx-122963123 AX-123267376 4 28093990 TCACTATCTCCTGGAGTTTGCTCAAATTCATGTCC[A/G]TTGAACTGGTGATAGTATCTCAACAGAGATCGTCC R 2 1 2 1 201000 r 74 goat snp15442-scaffold1637-138388 4 90279740 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776608 Affx-122960701 AX-385263735 4 28123552 GTTTTATTTTCAGTTCTTAGCAGAATCAGGACTTT[A/C]GCACAGTTCTTTTATTCCCAGTCACCTGGTCTTTG M 2 1 2 1 101000 r 74 goat snp15443-scaffold1637-167950 4 90249752 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402435 Affx-122958624 AX-123272788 4 28175880 GTGAAAGAAAGTGATTAGAGAAAATTGAGTTATAC[A/G]CAGAGCACCAGTGTGACAAGGCAGGGCTGGCTAGA R 2 1 2 1 101000 f 74 goat snp15444-scaffold1637-220278 4 90196868 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420430 Affx-122944905 AX-123290777 4 28206627 GGTGCAGCCACATACACACAAAAAAACAACCCAAC[A/G]TTTATTATGGAAATAAAAGGTAATATTGAAAAAAA R 2 1 2 1 303000 r 74 goat snp15445-scaffold1637-251025 4 90166278 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450480 Affx-122922934 AX-123320814 4 28263751 TTTACCTTCTTTCCTTATCTCTTTAAAAAGTCCAT[A/G]TTTCTCTTTGATACCCCCAGTGTTTAATGTGGAAG R 2 1 2 1 101000 r 74 goat snp15446-scaffold1637-308149 4 90108709 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403197 Affx-122958063 AX-123273550 4 28320845 GTGAGAAATTCTTGACTGTCCCTAGACTCTAGTAC[A/G]AGGAAGATAAAGAAGGACTTATTGACGGGTTCCGG R 2 1 2 1 101000 f 74 goat snp42201-scaffold552-21764 4 90051034 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788727 Affx-122945089 AX-385275743 4 28354323 TGTGCTTGTGTTGCAGCTTGGCTTTTGGGTTTGGT[A/G]TGTGGAGCAGGGGTAAATCCTTTGCCCTGCTTGGC R 2 1 2 1 202000 r 74 goat snp42202-scaffold552-55242 4 90017067 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382193 Affx-122974008 AX-123252551 4 28440536 AGTGACTGTTTTACAAGAAGAATTTGAAGAGCAAA[C/T]GGTAAAGGGAACTCAGTGGAGATGCTGAGGCTACA Y 2 1 2 1 201000 f 74 goat snp42204-scaffold552-141455 4 89930327 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446575 Affx-122924829 AX-123316911 4 28490723 ACCATTCAGAAACCTGTTAGAAGTTTAGAACATTG[C/T]ATCTTACCCACATCACCTGTGAAGAGTTGTCACAA Y 2 1 2 1 101000 r 74 goat snp42205-scaffold552-191642 4 89880401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402923 Affx-122958191 AX-123273276 4 28538038 AGTTTAAGCAGAAATGGTGACTGGACACAGGCGAA[C/T]AGGGAAGGAAAAATAACTAGAAAATGACACCCAGG Y 2 1 2 1 201000 f 74 goat snp42206-scaffold552-238957 4 89832795 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775090 Affx-122945957 AX-385262222 4 28569884 TACTACAGTTCTTATAGTGGTATGTTATATACTGA[C/T]GTAGTGGTTTATTATGGTAAATAAGAAATTCCAGG Y 2 1 2 1 101000 r 74 goat snp42207-scaffold552-270803 4 89800935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783433 Affx-122950887 AX-385270496 4 28623135 TGAAGAGTCTGCAACATGTCGATCCTCTGTTCTAG[C/T]GTTTCAGTTTGGCTTGGATTTTTGCAAGCAGCTGA Y 2 1 2 1 101000 f 74 goat snp42208-scaffold552-324054 4 89747274 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453383 Affx-122919927 AX-123323716 4 28659466 TGAGCTGGAGAGGAAGGTGAAAGCCTGAAGACAGA[C/T]AGCGCAATGAAGGATAAACACCAAACAGCATTTGA Y 2 1 2 1 101000 r 74 goat snp42209-scaffold552-360385 4 89711942 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787167 Affx-122942733 AX-385274193 4 28710269 GTAACAAACTCATGTTCGAAAGTGTGTCGTAACTC[A/G]TAGTCAGAACTTTGCAAACGCTAACCTGCACAGGG R 2 1 2 1 101000 f 74 goat snp42210-scaffold552-411188 4 89671995 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383032 Affx-122973304 AX-123253390 4 28753818 ATTCCCCCATAATACCCTGCACAGATGTGCAAACA[C/T]AGAGTGATCAATACAGATTTCCTAAATATATTACA Y 2 1 2 1 201000 r 74 goat snp42211-scaffold552-454737 4 89629231 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380287 Affx-122975411 AX-123250645 4 28789230 AATTCTGTCTCATTTCATATTTATTTCTGGGATTT[A/G]GGGGAAGGACTGACAGCCAAACAGCAGCCTTAAGT R 2 1 2 1 102000 r 74 goat snp42212-scaffold552-490149 4 89593811 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476185 Affx-1251763690 AX-586011611 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 4 1 4 1 20000 f 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 539476440 Affx-1251763690 AX-586011841 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 4 1 4 1 20000 r 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 562165816 Affx-1251763690 AX-606941225 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 8 1 4 1 20100 r 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 562165867 Affx-1251763690 AX-606941276 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 8 1 4 1 20100 r 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 562166222 Affx-1251763690 AX-606941630 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 8 1 4 1 20100 f 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 562166402 Affx-1251763690 AX-606941810 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 8 1 4 1 20100 r 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 562166541 Affx-1251763690 AX-606941949 4 28829269 TTTCAGCTCACTGATTCATTCTTTTGCTTCAGATA[-/TTCTGCTGTTGTCCTTTTATTTTTTATTTTTTTTTTGTTTTGGTCTTGCTGTCCTATTCCTCCGCCATCTTTCCCTCCTC]TCTGCTGTTGTCCTTTTAGAGTATTTTTAATTTCA - 8 1 4 1 20100 r 74 goat SV_205 4 28829269 - deletion junction SV-TF-chip 38385474 Affx-122971291 AX-123255832 4 28832474 TTAGAAATCATCCCATGTAGAGAGAAATTTGATGG[C/T]GTGGGCCAAAGAGATGGCATTTTTAGGAGACATGT Y 2 1 2 1 201000 f 74 goat snp42213-scaffold552-533393 4 89550707 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429028 Affx-122938321 AX-123299370 4 28876546 CATCTAAGACCCCTTCCAACCAGGAAGTCTATCTA[C/T]AAAAACTGCGAATGTGGGAGGACATCCTGGAAGAA Y 2 1 2 1 202000 r 74 goat snp42214-scaffold552-577465 4 89506781 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444693 Affx-122926435 AX-123315030 4 28916317 CTAAGATAATAGCTATGTAACTACCTATTCTAGTT[A/G]TTTTTGCTATTGGACCATTTAGGCTATTAGGCTAT R 2 1 2 1 202000 f 74 goat snp42215-scaffold552-617236 4 89466870 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448459 Affx-122923637 AX-123318795 4 28956694 GCTTACTGAATGGGAGTACGTAAATTAGTTGCAAA[C/T]GATATACCCAACAAGGAGCTGATCTAAAATATGCA Y 2 1 2 1 101000 f 74 goat snp42216-scaffold552-657613 4 89426527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272264 Affx-1111833420 AX-519546003 4 28994988 ATGCACCTATTGAAATTCCATATGAAATCTCAGAA[A/G]TGGCCTAAATAAATCATTCTGGAATTTCTGCTATT R 2 1 2 1 101000 f 74 goat 4_28994988_AF-PAKI 4 28994988 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454141 Affx-122919334 AX-123324474 4 29001121 AAACCATCAAGGGAACCAGGACAGTCCTGGGAGTC[A/G]CCTGCATCCTTGAGGTCCTCCCCCAGTGTGGACCA R 2 1 2 1 102000 f 74 goat snp42217-scaffold552-702040 4 89381772 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408810 Affx-122954039 AX-123279161 4 29036708 CCGGCCAGATATTCTCAAGAAACCTGGAGACAGCC[A/G]TGTCCTCCTGCTTACAGGTGATGACCTCATTCAAA R 2 1 2 1 101000 r 74 goat snp42218-scaffold552-737627 4 89346410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769210 Affx-122932380 AX-385256385 4 29065224 CTATTTTATTGCTCACTTTAAAGGAGAAATACTTA[C/T]AGGAATCCCATTATTTTTCAGACAGCATGTTGAAG Y 2 1 2 1 101000 r 74 goat snp42219-scaffold552-766143 4 89317844 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399507 Affx-122961167 AX-123269862 4 29138814 TCAGCAGAAGATGGTGGAGTATGTCTCCTAGCAAC[A/C]GGGATAGTTTACCATTTAACAGTAGGACTGTCTCA M 2 1 2 1 101000 r 74 goat snp42220-scaffold552-839733 4 89244086 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388566 Affx-122969173 AX-123258924 4 29180153 TGAAAGTAAGGTCTTTATTGTCTATTATCTCTCAC[C/T]CTGTGAGACTGCAAGCTCCAAGACAGCAGGCACTT Y 2 1 2 1 101000 f 74 goat snp42221-scaffold552-881072 4 89202682 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418450 Affx-122946475 AX-123288798 4 29235278 AGGCATAGCACTGGAATTAGGACAGACGAGGACAA[C/T]GCAATGGGAGGTGTCCCCAGCAGACAGGAAGGAGG Y 2 1 2 1 101000 f 74 goat snp42222-scaffold552-936197 4 89147630 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426093 Affx-122941072 AX-123296439 4 29289578 GAAAACAGAAAAGGAAGGATTCTATTATTACTAAC[A/G]CAAGAGTAAATGGATAGAGGGAGGTAGCCAACACG R 2 1 2 1 101000 f 74 goat snp42223-scaffold552-990497 4 89093482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444228 Affx-122927236 AX-123314565 4 29324529 TTGTAACAGCGCTACCGACACCCGTGAGACAACAG[C/T]AGCAAACAGCGTCACGAATCTGCACAAAAGGAGAC Y 2 1 2 1 201000 r 74 goat snp42224-scaffold552-1025448 4 89058317 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778857 Affx-122933132 AX-385265965 4 29405212 CTGATCTCTTATTTGGGCCGGCTCATGTGTCCTCA[A/G]ACTAATGTTTCCCAAAATCCTTCTACAACATTTCC R 2 1 2 1 101000 f 74 goat snp42226-scaffold552-1106131 4 88976703 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430464 Affx-122937258 AX-123300805 4 29439437 AAGCAAGCACTGGGGAGGGATATTGTGTTACAGAA[C/T]AGACCTGTCCAATATAATCACACCAACAACAATAC Y 2 1 2 1 101000 f 74 goat snp42227-scaffold552-1140356 4 88941418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436568 Affx-122932903 AX-123306906 4 29480271 GAATGTTTACACATTTATATGAGAAGTCAACTAAC[A/G]TTCATCTGCTACTCAAAAGACTCTCTGTTCCAGAA R 2 1 2 1 101000 r 74 goat snp42228-scaffold552-1181190 4 88900328 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407191 Affx-122954818 AX-123277542 4 29552432 AAATAAGAAGAGCCTATGTTGAGGGATCATGAGAA[C/T]AATTTTTCCTTTTTAATTTATGTTCTTCCTCTGTA Y 2 1 2 1 101000 f 74 goat snp42229-scaffold552-1253351 4 88827571 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396818 Affx-122963280 AX-123267173 4 29565668 AGGGAGTTGTCAATGGGCGTTGTTATGAAAATTCA[A/G]TGAGAAAAGCCTGTAAAACACTTTGCAGAATGGCT R 2 1 2 1 101000 f 74 goat snp3301-scaffold1100-649710 4 88815675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779982 Affx-122940628 AX-385267081 4 29604610 CAAATTATTCATAATTCCTACCTGACCAGGTTGAA[C/T]AGCAGAGAAATACAGTTTTATTAATGTTATATTTA Y 2 1 2 1 202000 r 74 goat snp3300-scaffold1100-610768 4 88776733 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780084 Affx-122941813 AX-385267182 4 29635896 CAATGACCTTTTTCCAGTTATAAAGTTACTTCTCC[A/G]TTACTTGAAAAAAGCCTAGAAAAGATGCATCTTGA R 2 1 2 1 101000 f 74 goat snp3299-scaffold1100-579482 4 88745519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278224 Affx-1111836236 AX-519551712 4 29658726 TTATTATTATTATTATTATTTTCGTTTAAAAGATG[A/G]ATTGAGGAGGAAAGTAATAAAACCGCATGAGAGAG R 2 1 2 1 101000 r 74 goat Random2.2K-429 4 29658726 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468274778 Affx-1111834416 AX-519548364 4 29682721 TT[A/G]GATGTTGGGGTCATCATGCCTGCAGCTTACTCTCA R 2 1 2 1 102000 r 74 goat GoatD01.034617 4 29682721 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38399987 Affx-122960816 AX-123270342 4 29718629 CCCCCTTGGCTAGCGTTCACATGTTTCAAGTAAAC[A/G]TTCATTTGCTTTGTTCTTAATTCATTCTTTCTACA R 2 1 2 1 101000 f 74 goat snp3297-scaffold1100-496749 4 88662934 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450344 Affx-122922116 AX-123320679 4 29764892 AGGGAGAACAGAGCTGGGAAGTGCCGTCTTGTGCC[A/G]TGGGAAGCTGGCTGTTGATTTAGGTGTTTCCAGTT R 2 1 2 1 101000 r 74 goat snp3296-scaffold1100-450486 4 88616629 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402589 Affx-122958432 AX-123272942 4 29814425 TTTCTGTTCTCCCATCGGACTCTTAACTTAGGGAC[C/T]AGGGGCTGTGTCTTCTGTTTTGTCATCAAAGACAC Y 2 1 2 1 101000 f 74 goat snp3295-scaffold1100-400953 4 88566789 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454270 Affx-122919640 AX-123324603 4 29850880 CCTTGTAAAAGGGTGATTGGTGTGTGGTGTCCAGC[A/G]TACAGTCTCACATAATTCGTATTGCTTCCGTCTTT R 2 1 2 1 201000 r 74 goat snp3294-scaffold1100-364498 4 88530471 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404526 Affx-122956690 AX-123274878 4 29880984 ACAGAAATAAGAAAAAGTTGTCTTCTGTTCTGGGA[C/T]GTGTGCTCATAAACGTAGAAATCTTTGGGTGGTGT Y 2 1 2 1 101000 r 74 goat snp3293-scaffold1100-334394 4 88500144 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413033 Affx-122950993 AX-123283382 4 29931485 GATTAAAAAGTAGTACATGGTTATAATATTTTTAC[A/G]CATAGATAATTCTTAGATTGAGTACATGGTCATGG R 2 1 2 1 101000 r 74 goat snp3292-scaffold1100-283893 4 88449459 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791044 Affx-122944292 AX-385278039 4 30025751 AGTCTTAACTGTATCAGTAATAGAATAGACAATGA[C/T]AGATTAAAGAAGAGATTCTACAAATAGTTTTCATT Y 2 1 2 1 101000 f 74 goat snp3290-scaffold1100-189627 4 88354741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390337 Affx-122967697 AX-123260694 4 30087869 CGAATTGGTCGGATGTTGGGGGAGAGAGGAGATGA[C/T]GGGCCATGGCTGTGAAGTGCAGCATTTCAGTCCTT Y 2 1 2 1 101000 r 74 goat snp3289-scaffold1100-127509 4 88292444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415475 Affx-122948709 AX-123285824 4 30117900 CATAAAAGTCTGCATTGTGTGTGATGTGTGAAGTC[A/G]CTCAGTCATGTCCGACTCTTTGTGACCCCGTGGAC R 2 1 2 1 103000 f 74 goat snp3288-scaffold1100-97478 4 88262904 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791610 Affx-122950444 AX-385278601 4 30154093 ATCCACCTATTCTTTCATCTACCTGAATACCTGTC[A/G]TTCATTCTGTCTCCCTGATACACATTCAACAGAGT R 2 1 2 1 101000 f 74 goat snp3287-scaffold1100-61285 4 88226637 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768506 Affx-122958219 AX-385255686 4 30182606 ACTCTGAGATTATTGCTTTCAGTGTAGAATAATTT[C/T]TCTCTTCTTTACAAGAATGCTCAATGGTTATGATT Y 2 1 2 1 201000 f 74 goat snp3286-scaffold1100-32772 4 88198440 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376331 Affx-122978346 AX-123246690 4 30228638 ATGGCACATTGAGAATGCCCAGGTCTCATTGCCTC[A/G]TGGAATTCTGTGCCCTGTGAGGATTATGGTAACAG R 2 1 2 1 201000 f 74 goat snp19229-scaffold1934-283568 NW_017189707.1 14769 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772207 Affx-122948919 AX-385259362 4 30309881 AGGCGGGCAGAATCAAGCCAATCATGCTCTCATCT[A/G]CTTTCTTGATAGGCGGAAGTGTTGTGAAGATACTA R 2 1 2 1 101000 f 74 goat snp19228-scaffold1934-202325 NW_017189707.1 104113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403654 Affx-122957520 AX-123274006 4 30354781 TGTGAATTTCTGTTGCTTTTCTCACTTTCAGAATT[A/G]CCAGAACCTGGGTATCTCACCCACATCTGTTAATT R 2 1 2 1 201000 f 74 goat snp19227-scaffold1934-157425 NW_017189707.1 149604 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426461 Affx-122940797 AX-123296807 4 30443000 ACTTAAGTATGTATAAACACAGAGCCATTTATAAT[A/G]CTGACAAAACTGTTCTGCCAACAAAATAAATAAAA R 2 1 2 1 101000 f 74 goat "snp19226-scaffold1934-69206;snp22340-scaffold2208-51495" 4 87557203 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788767 Affx-122928065 AX-385275782 4 30483955 TAATACCATGAAACTTTTCATTAAACAATGACACC[A/G]TGATCCCTAACACAAGCTCTGCAAATCAGCAAGAT R 2 1 2 1 101000 r 74 goat snp19225-scaffold1934-28251 NW_017189707.1 279588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768342 Affx-122921262 AX-385255522 4 30518639 TTTAGGTAAGGAGTTTGTAAAAGGGTGATATGTCC[A/G]TCTACATAACAGAAATATCAAAGAAGTTAAATCTG R 2 1 2 1 201000 r 74 goat snp10824-scaffold1385-957875 4 87479143 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392786 Affx-122965981 AX-123263143 4 30553925 AAAGTGTCTTCAGTTGTGTTTGACTCTTTGTGACC[A/G]TATGGACTGTAGCCCTCATACCACAAAAGAATAAG R 2 1 2 1 303000 r 74 goat snp10823-scaffold1385-922589 4 87444643 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784254 Affx-122974010 AX-385271305 4 30587319 GGAAGGGTGTTGGTTTGGTGGTTGAGGTCCAGGTA[C/T]GCCTTCTCTTTCGTGGGATGCTTATAGCTCCAGTT Y 2 1 2 1 101000 f 74 goat snp10822-scaffold1385-889195 4 87410994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789572 Affx-122957224 AX-385276581 4 30620298 TATGAGGGAAGGAAAGGCCAAGCACTCTGTATTCT[C/T]TATTGCTGTGTAACGAATTACCCAATATCTTAGTA Y 2 1 2 1 101000 f 74 goat snp10821-scaffold1385-856216 4 87378071 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394907 Affx-122964324 AX-123265262 4 30659535 AAGGGCAAGAATTATATTGGCTTAAAGCAGTCTCT[A/G]CCACACCATTATTATTATTATTTTTTAAAATAATG R 2 1 2 1 101000 f 74 goat snp10820-scaffold1385-816979 4 87338972 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405750 Affx-122956505 AX-123276102 4 30706837 TCCTATTAATTAAATATCTATCTCTGGTCTCAAGT[A/G]TTCCTTTCATATTCAGACTCCAAATTACCTGATTT R 2 1 2 1 101000 r 74 goat snp10819-scaffold1385-769677 4 87291024 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421302 Affx-122944098 AX-123291649 4 30740061 GGTGCTTGGGGCCACACCCCAGGCCAATAATATCA[G/T]AATCTCTGGCGACAACACTCAGCAACAGTATTTTT K 2 1 2 1 101000 r 74 goat snp10818-scaffold1385-736453 4 87260109 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423444 Affx-122942598 AX-123293790 4 30801141 CTACTTCAGACTTTGTTTTCCTGCCACTAATTCCT[A/G]TCTTTGCAGTTTACTTTCTCTAATACTTCTGCAGT R 2 1 2 1 101000 f 74 goat snp10817-scaffold1385-675373 4 87199259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427293 Affx-122940156 AX-123297636 4 30871858 ATAGGATTAGGGGCCCACCACACTCCAATATGACC[G/T]CATCTTATTTTAAGTAGTTCCATCTACAATCACCC K 2 1 2 1 101000 r 74 goat snp10816-scaffold1385-604656 4 87127859 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767066 Affx-122936376 AX-385254355 4 30925186 AACAACTCTGCAACTTTCAGAGTTAAAAGTGGCAG[C/T]ACATGGTTCTACAGATATCAAACATCTTCTTGGAT Y 2 1 2 1 101000 f 74 goat snp10815-scaffold1385-551328 4 87074552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395151 Affx-122964121 AX-123265506 4 30956659 AAACAAGTTTGCAAATAAACCCTGTGCCTGATGCT[A/G]TACCAAACAAAATAATAAAGGACAGAATATTTCCT R 2 1 2 1 101000 f 74 goat snp10814-scaffold1385-519855 4 87043385 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797646 Affx-122957006 AX-385284585 4 30994302 TGAGCTTAATAAAAACAAACTAGTTATTTGAGTTC[A/G]TTTGAACTCAATTGAACCTATAAGAATCTCTCAAA R 2 1 2 1 101000 f 74 goat snp10813-scaffold1385-482212 4 87005252 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375507 Affx-122979126 AX-123245866 4 31042999 CAAGCAGAGCACAGTGGTCTCACTGAGGGATGAAT[A/G]TCTGGAGGAAGCTGAAATAACCAGAATTTACAGGC R 2 1 2 1 201000 r 74 goat snp10812-scaffold1385-433515 4 86956656 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412315 Affx-122950854 AX-123282664 4 31082340 TAAGTTCACACTTGAAAGAGAATGCTAAGCCTAGA[A/C]ATTTACCTCTGAAAGCCACTCTTTCACTTACCACC M 2 1 2 1 101000 r 74 goat snp10811-scaffold1385-394174 4 86917197 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801695 Affx-122935340 AX-385288603 4 31114727 CATTCATAGTTTCCTATTCAGATACTAATATAAAT[A/G]TACATTTAATATAAATGTGATAGTCTACAGTCGCT R 2 1 2 1 101000 r 74 goat snp10810-scaffold1385-361787 4 86884466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793199 Affx-122968802 AX-385280177 4 31171548 TTACATTCATTCCAATTGCTACCTTAATAATGTTC[G/T]TGCTTATTGCTTTTGCTTCAAATGAGTTATCATAT K 2 1 2 1 101000 r 74 goat snp10809-scaffold1385-304966 4 86827831 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426225 Affx-122940353 AX-123296571 4 31208968 ATTACTCCTTGGTATGCAAATATACAAATATATCC[A/G]CTCATTAACAGCTAATAGAATGAAAATTCTTGGAT R 2 1 2 1 101000 r 74 goat snp10808-scaffold1385-267546 4 86789684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278074 Affx-1111836238 AX-519551564 4 31211039 TTTGATCACCTGGCAAGGTGTTATTTTGTTTCTCC[A/C]CTGGAGAGGTACACTGGATTGTCCCCTTGGCATTC M 2 1 2 1 201000 f 74 goat Random2.2K-430 4 31211039 A C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402320 Affx-122959080 AX-123272673 4 31247080 GTAGATTCGTGCCTTAGATCAATGTTTTGACATTC[A/G]CTATTATATTTTAAACTTTTCTATTTCCGTTGGTC R 2 1 2 1 103000 f 74 goat snp10807-scaffold1385-229434 4 86751624 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420122 Affx-122945079 AX-123290470 4 31289988 GTAGGCATCTGCACATGTGAGCCAAATGAGATCAT[G/T]CAAGAGAAACACTCTGCATTATAACCCAGTTGGCC K 2 1 2 1 101000 f 74 goat snp10806-scaffold1385-186526 4 86708973 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781152 Affx-122951329 AX-385268236 4 31322694 GTAACGTAAACACTCAAAAGAGTACTAAAAGAATG[C/T]AAAAGTTAAAATCTTAAAGGAATTACAAAATGGAT Y 2 1 2 1 202000 r 74 goat snp10805-scaffold1385-153820 4 86676892 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781292 Affx-122969731 AX-385268377 4 31369127 AGAAAGGTCACAGTTTTATATCTGGACATCTTTTC[G/T]AAATATTTAAGACACATCCTTAGGTCATTCATGTG K 2 1 2 1 101000 f 74 goat snp10804-scaffold1385-107387 4 86630518 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781909 Affx-122968778 AX-385268990 4 31401836 GTAATATTTTCGCAGGAAGACATATATATTACATC[A/C]TACCAAATAGTATACTTCGATATGGACAATTTATT M 2 1 2 1 101000 f 74 goat snp10803-scaffold1385-74678 4 86597901 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414942 Affx-122949089 AX-123285291 4 31434472 GCAATTTAATCTCAATCCCACCATGTCAAGCTCTA[A/G]CTGGAAATTCAGAAACCTAAAGTAAAGGCTTATTG R 2 1 2 1 101000 r 74 goat snp10802-scaffold1385-42042 4 86564681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442115 Affx-122928347 AX-123312452 4 31473409 TGGTACTTTCAATCAATAATATTGGGAAAATGGCT[A/G]TATAAAAGAAAAATAAACATTGACTCTTTTCTCAT R 2 1 2 1 103000 f 74 goat snp10801-scaffold1385-3105 4 86525132 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406713 Affx-122955762 AX-123277064 4 31486949 GAGAAGCTTTCTGTCTTCTAGAGCATGTACCATGT[A/G]GTTAGTGGGACCTGATAATGTTGCTGCATGATAGA R 2 1 2 1 101000 f 74 goat snp49381-scaffold704-10336 4 86511557 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428223 Affx-122939438 AX-123298566 4 31539164 AGATAGGACATCATGTGAGCAGTGACTTGAAGAAA[G/T]CAAGGGAGGACATTTATATGAATTTGGGGAAGGGG K 2 1 2 1 101000 f 74 goat snp49382-scaffold704-62551 4 86459227 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395249 Affx-122964100 AX-123265604 4 31576628 GATATTTGGTCAATAAAAATGAAATTTAACAGGAT[G/T]GCCAAGTCAGAATGTAAGAGAACATAAATATTAAG K 2 1 2 1 201000 r 74 goat snp49383-scaffold704-100015 4 86421019 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377395 Affx-122977625 AX-123247754 4 31615809 GACAGTCATCCACATACAAAGCTAGTAGAGAGGTT[A/G]AAAAACAAAAGTAGTAACATCATTTATATAATTTA R 2 1 2 1 102000 f 74 goat snp49384-scaffold704-139196 4 86381468 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416125 Affx-122948297 AX-123286474 4 31663504 AAGAGCCTACAATGAGGTAGAGAGACCTTTTCAAC[A/G]TTAACTACTATTACTAATATTTAATAAGGAAAAAA R 2 1 2 1 101000 f 74 goat snp49385-scaffold704-186891 4 86334401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443535 Affx-122927771 AX-123313872 4 31730360 AATGAAATGCAAGAGGGATTCTTCAAAAAGCAATG[C/T]GTCTTTGCTTTTAAGGAAAAATCAGCATTGGTTCA Y 2 1 2 1 101000 f 74 goat snp49386-scaffold704-253747 4 86266862 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435878 Affx-122932789 AX-123306217 4 31763519 CAAAGAGCTTCTCAAAATCACACACATTTCAGAGA[C/T]ACCAACTGAAGCTACATTGCCTAAACATGCATGGC Y 2 1 2 1 101000 r 74 goat snp49387-scaffold704-286906 4 86233773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385915 Affx-122971572 AX-123256273 4 31804844 TATATTCAGTTTATAAAATGTATCCTGTGTATCTG[C/T]CTGCCCCCTTAATCTTCTCTATTGCTGTCAAAGGA Y 2 1 2 1 201000 f 74 goat snp49388-scaffold704-328231 4 86193863 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415069 Affx-122949471 AX-123285418 4 31865464 TATTGGAAACTTTCTTACATAGAGTTAGTAGCACC[A/G]TCCTTTTCCACGTAAATCAAACATTACTGAACTCT R 2 1 2 1 101000 r 74 goat snp49389-scaffold704-388851 4 86132620 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798882 Affx-122950661 AX-385285812 4 31899451 ACAATCACCTTGATAAAGGTTTGGTAGATTATTAA[C/T]AATTATATTAGTTACAATCATCACTCAGAACAAGA Y 2 1 2 1 101000 r 74 goat snp49390-scaffold704-422838 4 86097965 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272266 Affx-1111833422 AX-519546005 4 31916163 GTTCCAGATAGTGGAGAACACTTAGGGAACTGTTT[A/G]CTGGCTGGATCTGTCTCTCTCCTTTTCATTTCCCT R 2 1 2 1 103000 f 74 goat 4_31916163_AF-PAKI 4 31916163 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387968 Affx-122969602 AX-123258326 4 31974506 TTTAAATATTGACAATAATATTTAAAAAGAAAAAA[C/T]GGTACAGATAGCTTGACAGGAATGTGAAGTGAGCT Y 2 1 2 1 103000 r 74 goat snp49391-scaffold704-497893 4 86018173 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405979 Affx-122955527 AX-123276331 4 32023040 TTATATGCTGTTTATTCCTTTTCAAACTGAATGCC[A/G]TAAGAACATTCATTTTATCCATATTTTTTCTAGCC R 2 1 2 1 101000 f 74 goat snp49392-scaffold704-546427 4 85968441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445876 Affx-122925986 AX-123316213 4 32058212 AGGTACCTTAGAGTAATGATATTTTAAAACAGTGG[C/T]CTTATTCTCACAGGTATTAAGTTTTCATTCTTTAA Y 2 1 2 1 201000 r 74 goat snp49393-scaffold704-581599 4 85931997 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434762 Affx-122933898 AX-123305103 4 32116288 AAAAATATCACTGTCATGTAAACAAATGGCTACTT[A/C]TGTGTGTGCAATACCAGAGTGGGTAGCCTTTCCTT M 2 1 2 1 201000 f 74 goat snp49394-scaffold704-639675 4 85875708 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781416 Affx-122951209 AX-385268501 4 32154042 CTTATATCTAACTATTCATTAACAGTTCTGGTGCT[A/G]CATTATGTCTCTATGTCAAAAAAAGTATTTACTGC R 2 1 2 1 101000 f 74 goat snp49395-scaffold704-677429 4 85838794 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783069 Affx-122942699 AX-385270136 4 32261815 ATCCCGAACGCTGTGTCTACTACATTGCTTAAATT[G/T]CTTAAAATTCAGAAAGCATGCAAAAAACCCGTAAG K 2 1 2 1 201000 r 74 goat snp49397-scaffold704-785202 4 85730667 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399530 Affx-122961149 AX-123269885 4 32300443 ACTGTTATGGTATAGTTTTGATCTTCAAGCTCAAA[C/T]GTCTGTTAAAGCCCAGCTGTGAGAAATGATAGAAA Y 2 1 2 1 101000 r 74 goat snp49398-scaffold704-823830 4 85691768 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792037 Affx-122925366 AX-385279025 4 32367344 TACAGTGAGTATTTATTATTCTGATAAGAATCAAC[A/G]TGTGGGTCTCCAGAAATTCTTATGGTAATTTTTTT R 2 1 2 1 101000 r 74 goat snp49399-scaffold704-890731 4 85622669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779409 Affx-122977945 AX-385266512 4 32395918 GATTGTAGTCTGTTGATCTCATTGTCATATAGATA[C/T]GTCTCAAGCAGAATTAGGTTTTGAAATCTGTTGTT Y 2 1 2 1 101000 r 74 goat snp49400-scaffold704-919305 4 85593094 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795922 Affx-122930964 AX-385282874 4 32429998 AGATCAGGTTCTGTTTACATGTCATAGCATAGCTC[A/G]CCAGCTATCTAGTGGACTGGCTAACTTGATAGTTT R 2 1 2 1 101000 f 74 goat snp49401-scaffold704-953385 4 85558996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428865 Affx-122938346 AX-123299207 4 32462367 TCAGTTATGATAAGTGTGCAGATGTGTGCATGTGT[A/G]TATGAAAGAGAGAGATGAATGGAGGGAAATTAAAA R 2 1 2 1 303000 r 74 goat snp49402-scaffold704-985754 4 85526698 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779665 Affx-122933482 AX-385266767 4 32515150 TAAACTGTGTTTCCTACCTTAATAACTGAAGAGAA[C/T]GCTGAATTTAATTACAGATTAGTGAATATAAATAC Y 2 1 2 1 101000 f 74 goat snp49403-scaffold704-1038537 4 85473914 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429816 Affx-122938186 AX-123300157 4 32566445 CTGAGAAAATGGAAAAAGCGATGCAGGGAAGGTAT[A/G]CGATTTTTAGTGGACTTCATATTACACACCATTTT R 2 1 2 1 101000 f 74 goat snp49404-scaffold704-1089832 4 85415707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377966 Affx-122977624 AX-123248325 4 32604848 CTCCGTTCTAGTTTAGAATGGAGTTTCCCCATTAG[G/T]AGGTTAAAAACCAAGTGTAAAAGGTAAAATTAATT K 2 1 2 1 202000 r 74 goat snp49405-scaffold704-1128235 4 85377003 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413423 Affx-122950698 AX-123283772 4 32654716 ACACAGTTGAATTGAAAAATAGTAAAAGGTAAAAA[C/T]ATAAGCAAATAAACAGAACTAGAATGTGTTGATCA Y 2 1 2 1 201000 f 74 goat snp49406-scaffold704-1178103 4 85326894 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417473 Affx-122947179 AX-123287821 4 32689113 TTCAAGTCTCAGAGGAACCAGTGAACCAAGTAAAG[C/T]AGATTATCAAGGCAAGAACTGGCATTATAGAATTA Y 2 1 2 1 101000 f 74 goat snp49407-scaffold704-1212500 4 85292043 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449594 Affx-122923215 AX-123319929 4 32718759 ATCATCTGTATTATAGTTAGGTCAAAATAAGAGAC[A/G]CTTTAGAATGATGTTGGAAACTTAAACAAAGGTTT R 2 1 2 1 101000 f 74 goat snp49408-scaffold704-1242146 4 85261912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778048 Affx-122920845 AX-385265164 4 32761998 TGAGCTATAAATTAAGATATGAATTATGGAATGGT[A/G]TTTGAGAGATGACTGGCAGGATCAAGACTAAGAAA R 2 1 2 1 101000 r 74 goat snp49409-scaffold704-1285385 4 85217679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787997 Affx-122929484 AX-385275018 4 32809343 GTTCTTCACAATAAGCTTTTCATTGTGGCACAGAA[C/T]ATATTTGTACTAATAAGCCCGAATACCTTTAGTCC Y 2 1 2 1 201000 f 74 goat snp49410-scaffold704-1332730 4 85170259 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791519 Affx-122968475 AX-385278510 4 32850546 AGGTTGAACTTCAGTTGATGGCTGCCAAGAGTTCT[C/T]ATTTTAATGTCACACCCAAACCCTAATACAATGAC Y 2 1 2 1 101000 f 74 goat snp49411-scaffold704-1373933 4 85128182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785596 Affx-122959821 AX-385272640 4 32922975 CATAATTAATTGTGTTAGGACACAGAAGTTTGAGG[A/G]TTACCTAAGATATCATCATTATGCTAACAAGTACA R 2 1 2 1 101000 f 74 goat snp49413-scaffold704-1446362 4 85053541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396025 Affx-122963477 AX-123266380 4 32959499 GGCTTGAGATGTCATTTTTCTCTGAAACTTGTTCT[C/T]ATGGGACTCAGCTAAAAGGACATAGCTAAGAATGT Y 2 1 2 1 201000 r 74 goat snp49414-scaffold704-1482886 4 85006985 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789249 Affx-122971393 AX-385276260 4 32995172 ATGTTTCCCTGTTATATAGTCAAAGCATTATTATT[A/G]TAAAGTGAACTTTGCTCTCAGCCTGACTCAAACTA R 2 1 2 1 201000 f 74 goat snp49415-scaffold704-1518559 4 84970958 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414015 Affx-122950265 AX-123284364 4 33048497 GAGGTTAGTTATTGAGGATGCTGAGAGATTATATC[G/T]AAAGAAAATTCTGTATTTATTTTCAAGTATTTATT K 2 1 2 1 101000 f 74 goat snp49416-scaffold704-1571884 4 84917507 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427132 Affx-122939651 AX-123297475 4 33079199 AGAGCTGTGTTATTTGGCTTGCTAATGAAGACAGA[A/G]AGGAAACTCTTTCTATTTTACTGTTAAAAGTATTT R 2 1 2 1 101000 f 74 goat snp49417-scaffold704-1602586 4 84886966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776062 Affx-122974749 AX-385263192 4 33109036 GTAAAAAACGTCCTTTCCTAGTTTTCCTATTAGGT[A/G]TTTAGACTTTTATAGGCACATCTCTCAATTTTTTT R 2 1 2 1 101000 f 74 goat snp49418-scaffold704-1632423 4 84855944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433311 Affx-122935188 AX-123303652 4 33138271 CTAGGGTTAATGAGTCCTGTCTATGTTCTTTTCCT[A/G]TATATGAAATGGTAATCTATGGCAGTGACTCTTAA R 2 1 2 1 201000 r 74 goat snp49419-scaffold704-1661658 4 84826707 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797674 Affx-122958221 AX-385284613 4 33192690 TTGAATCCATCTAATTGAATTTCTCCCAAGCCCTT[A/G]CCCTGTCACCTAACAATCAGCCTGCATCCTCCCTG R 2 1 2 1 101000 f 74 goat snp49420-scaffold704-1716077 4 84764297 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406009 Affx-122955504 AX-123276361 4 33227687 TCTTTATCAATGGCATCTAAATTCATGAGAAATGA[C/T]AAGAATAGAAATGATTTTAATATATTTTGCTTTGA Y 2 1 2 1 101000 f 74 goat snp49421-scaffold704-1751074 4 84729070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388468 Affx-122969243 AX-123258826 4 33265517 AATTTTTCTCCTTTGAGTTTATAGTAGTATTTGTT[A/G]TTTTAATTTACACATATGTGATTACTTGTGAATTT R 2 1 2 1 201000 r 74 goat snp49422-scaffold704-1788904 4 84690571 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441100 Affx-122928891 AX-123311437 4 33300951 GCCTGCATATAGTACTTTTTAAAAGTTAACACATA[C/T]GCTGTGGAAAGGAAACTATGCTCACCTATTTTGTC Y 2 1 2 1 101000 r 74 goat snp49423-scaffold704-1824338 4 84654397 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408704 Affx-122953434 AX-123279055 4 33331743 GATAGATGTTATTTTTAGGTAAATGTTTAGAAGGT[A/G]CAGAATGCAAGTAAGAATTATCAGTGATTTAAGTA R 2 1 2 1 201000 f 74 goat snp49424-scaffold704-1855130 4 84623821 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795344 Affx-122935122 AX-385282300 4 33410643 ACAATATTTTCTCTTCCAGTCTTTGAACCATTAAA[C/T]AGCTCTTCAGTTATTTAGGCCATCTTTAATTTTTC Y 2 1 2 1 101000 r 74 goat snp49426-scaffold704-1934030 4 84544071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275048 Affx-1111834562 AX-519548630 4 33455915 CTGGAAGGCACCCTGAACAGTAAGACCTATGACAC[A/C]CTACACAGACGTTTAACAGTAGAGGAGGCTACAGC M 2 1 2 1 201000 r 74 goat GoatD01.041646 4 33455915 C A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38422847 Affx-122943100 AX-123293193 4 33461191 GACTTCCAAGAATAGAAAATGTCTTATGTCAAGTC[G/T]AAAATATTTACATTTTTCTTAAATTTATAGCTGAG K 2 1 2 1 103000 f 74 goat snp49427-scaffold704-1984578 4 84493728 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767808 Affx-122947504 AX-385255032 4 33509657 TATCTTCTGAGTATTAACCTAGAGCTAGCTACCAA[C/T]GCAAACTTCTAATTTAGCACATCTCGATATAGAAA Y 2 1 2 1 101000 f 74 goat snp49428-scaffold704-2033044 4 84445203 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442923 Affx-122927625 AX-123313260 4 33544664 TATTAGTATATCAGTTACCTATTGCATAAGAAACT[A/G]TCCCAACCCTTAGTGACTTAAAACAACTATAGCCT R 2 1 2 1 201000 f 74 goat snp49429-scaffold704-2068051 4 84409417 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788576 Affx-122919480 AX-385275593 4 33576902 AGTAAACACAAAGAAATCATGGCTTGTTGCAGCCG[C/T]ATATTGATTTCAATGCTCTAGGTTATGTGCAAAAC Y 2 1 2 1 101000 f 74 goat snp49430-scaffold704-2100289 4 84377259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445926 Affx-122925924 AX-123316263 4 33646673 AGAGCACACTATCTAATGGCTCTCATATGTCCACC[A/G]TGCCCACGGACAATTTGTCTTCCGAGTGGAGTGTT R 2 1 2 1 101000 f 74 goat snp49431-scaffold704-2170060 4 84307415 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769531 Affx-122957013 AX-385256701 4 33685152 TGTCATTTAATTACACTACCTCAATATTTTCAACT[A/G]TAAAACAAAAAGTTTGAAATAGATGATGTACATAG R 2 1 2 1 303000 r 74 goat snp49432-scaffold704-2208539 4 84268958 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791140 Affx-122946050 AX-385278135 4 33725251 AGAAAAAGTTCAAGATCCTCTTCACCTTAAATATA[C/T]GTGGACAGAATTGAGGTAAACTTTAGAAAGAATTA Y 2 1 2 1 101000 r 74 goat snp49433-scaffold704-2248638 4 84228554 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411601 Affx-122951606 AX-123281951 4 33761457 TTGTCTGTCTTAGCTAGTCTATCCTGGTTATTGTA[G/T]AAGTTGGCAATAGAAGTGAGAGGATGTCTTTAAAA K 2 1 2 1 101000 f 74 goat snp49434-scaffold704-2284844 4 84192001 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274757 Affx-1111834405 AX-519548343 4 33785474 CATCTGAGCCACCAGGGAAATGAAAAAGGGAGAGA[A/G]GCAAAAGATGACTCCCAAGATCCTGACTGGAGCAC R 2 1 2 1 101000 r 74 goat GoatD01.033795 4 33785474 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443048 Affx-122928144 AX-123313385 4 33792207 GCAGATGTCTATAGACTGACTCTCCCATTGCTACC[A/G]TGTTTGGCCTGTGAGGCAGCTCGGTGATCTGTCAG R 2 1 2 1 101000 f 74 goat snp49435-scaffold704-2315594 4 84160491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435426 Affx-122933488 AX-123305766 4 33855827 ATAAATATCAGTTTATTTGAAAATGCTATCTGGCT[A/G]TTTCAAAGTGGGAGCCCCAAGACCTTTTTTTTTTT R 2 1 2 1 103000 r 74 goat snp49437-scaffold704-2379214 4 84097096 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783581 Affx-122942580 AX-385270641 4 33940541 GTTGGCTGCTATATTAATAACTACTGATATACTTA[C/T]ACAGATTGGCCAATAGATAAATGATACATGGAAAT Y 2 1 2 1 201000 r 74 goat snp49439-scaffold704-2463928 4 84011886 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430337 Affx-122938215 AX-123300678 4 33984008 CATGGTTGGTCTGGTTACAGTTTAATGTATATGCT[A/G]TTTTTTAATGAGGATTTTAAAGAAAATATTTGTTC R 2 1 2 1 103000 f 74 goat snp49440-scaffold704-2507395 4 83968387 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409992 Affx-122953275 AX-123280342 4 34033515 GATTTTTTTAAAGAAGTAATTTCTTCTCACTGAGC[A/G]CTTAGAAATGATAAAGCAACAGCTATATTTGGGAA R 2 1 2 1 101000 r 74 goat snp49441-scaffold704-2556902 4 83919057 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379174 Affx-122976705 AX-123249533 4 34091284 TCTCAGTCCTTCCTATCTTAGCATCCTTTTCTGGG[C/T]CACACTCCTCTTACCTTGTCCTAGCACCCTGGAGT Y 2 1 2 1 101000 f 74 goat snp49442-scaffold704-2614671 4 83861101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441999 Affx-122928427 AX-123312336 4 34123201 AGAAATTGATAAGCATAGTTTCAGGTACCTTCCAC[C/T]TTTCAAGGTGACTAATTTAAAAATGCTTGAGAAGC Y 2 1 2 1 101000 f 74 goat snp49443-scaffold704-2646588 4 83828133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772345 Affx-122920886 AX-385259498 4 34165484 GTATAAAAAGGACAAGGAAGGGTCAAAGTAACTAG[C/T]ACCTTTTATTTTCGCTTACTGTTTGTGCTCATCTT Y 2 1 2 1 101000 f 74 goat snp49444-scaffold704-2688871 4 83785029 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452362 Affx-122920633 AX-123322695 4 34251505 TTTATCCGAATGACATCTTAGCCAGATGTTGAGCT[G/T]TTTGAAAGGAAAAAATCATGTCCTATGTATCTTTA K 2 1 2 1 101000 f 74 goat snp49446-scaffold704-2774892 4 83698823 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452044 Affx-122920890 AX-123322377 4 34315774 TGATTAGCTTCCTTTCTAGTTTGATCTGGGTTGCA[A/G]ATTGCTCAGACCCATTCACTATTGTAAGCATTAAA R 2 1 2 1 201000 r 74 goat snp49448-scaffold704-2839161 4 83633153 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418781 Affx-122946186 AX-123289129 4 34350867 TTTCTATTCTCACAACAGTTTTATGAAGTAGAAAT[A/G]TCATGATCCCCCAAGGAGTACAGGGGGCTTTGACT R 2 1 2 1 101000 f 74 goat snp49449-scaffold704-2874254 4 83597893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404881 Affx-122956474 AX-123275233 4 34385049 AACTAATTTTGATACAGTGTAAAATCTGAATGATA[C/T]ATGATAACTAAATAAGGTGTTTCCAAGGGCCAAAG Y 2 1 2 1 101000 r 74 goat snp49450-scaffold704-2908436 4 83564236 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431854 Affx-122936077 AX-123302195 4 34417236 AAAACCTTACATAAGATAAGGAAAAACAGAGATAC[A/G]TGGCAAAGGGGTATTTGTATCCTTTTCTCCTGCAA R 2 1 2 1 201000 f 74 goat snp49451-scaffold704-2940623 4 83531942 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423618 Affx-122942375 AX-123293964 4 34475790 TAACATAAAATGAACACATTAATCTGTTTTCCTAG[C/T]GATGGAACTTAGAACTTATCCTGAAAAAATTAAGA Y 2 1 2 1 101000 r 74 goat snp49452-scaffold704-2999177 4 83471885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272107 Affx-1111833423 AX-519545865 4 34543491 CTCAAATTGGTTTTTAACCTGAATTTGTCTGAATT[A/G]TATAGATAACCTAGTATTGCGAGGCGGAACTGAAA R 2 1 2 1 101000 r 74 goat 4_34543491_AF-PAKI 4 34543491 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38436620 Affx-122932504 AX-123306958 4 34553691 AATGCAGAGGGCACATCCTTCTTCATTAATTCTTA[A/C]ATGTCTTTGGTTGCAAAGAGGATGTAATGGCTGGA M 2 1 2 1 201000 f 74 goat snp49454-scaffold704-3077078 4 83393354 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424958 Affx-122941927 AX-123295304 4 34584887 AACAGCAGCTATTTACCCCCAATTGAACCTAATGA[C/T]AAAAATTATAAAAGCATAGCTTTGGAAAGGCCCTT Y 2 1 2 1 202000 r 74 goat snp49455-scaffold704-3108274 4 83362371 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411232 Affx-122952344 AX-123281582 4 34627174 TTCCTCTAAAAGTAAGGTTGTTAAGAATGAGAAAT[C/T]GACTTGTCTACTATCAAAAATCTATAAAGTGCTGA Y 2 1 2 1 101000 f 74 goat snp49456-scaffold704-3150561 4 83320160 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779535 Affx-122922478 AX-385266638 4 34666328 AAGGGGCAAAATTCAGTCTAAAGCAATGTGTAATT[A/C]TGCATAAAATAGAAACTAAATACCGGATATTTTCA M 2 1 2 1 201000 r 74 goat snp49457-scaffold704-3189715 4 83280697 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375672 Affx-122978671 AX-123246031 4 34743305 CTAACTAATTAAAGAAGTAGGAGGTCAGATCCTCA[C/T]GAAGCAGTGAGTTCTGCCATGTGGGCTGTTTCCCA Y 2 1 2 1 101000 f 74 goat snp49458-scaffold704-3266692 4 83203377 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453834 Affx-122919548 AX-123324167 4 34791632 CAGAATGATATGGGAGGACAGAGGATACTGGTGAA[C/T]AAGTGGAGCTCTTTCCTGAAAGCTAGACTGGTTTG Y 2 1 2 1 101000 r 74 goat snp49459-scaffold704-3315019 4 83154754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445756 Affx-122926078 AX-123316093 4 34830716 AAGGGAATGGACTTTGAAGAGTTAAATGGTACTCA[C/T]GGACAGAGGAGCCTGGTGGGCTATAGTCCATGGGG Y 2 1 2 1 101000 f 74 goat snp49460-scaffold704-3354103 4 83115872 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785492 Affx-122961058 AX-385272537 4 34860149 GGTTGCCACCTAGACTTATTTGTTATTCTGTGAAA[C/T]GTATAAAACATATCTAGCTTGATTTCAAGCTATGA Y 2 1 2 1 101000 f 74 goat snp49461-scaffold704-3383536 4 83086778 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420841 Affx-122944655 AX-123291188 4 34899804 AGGGTATATTAAATTTAAATATGAATATGATATTT[A/G]CAAAATCCTCTGATGATAAATGCAAGACTCTCCAA R 2 1 2 1 103000 r 74 goat snp49462-scaffold704-3423191 4 83046541 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444139 Affx-122926799 AX-123314476 4 34928305 CAAACACAAAACATTGTGAACATGATATTACCATA[A/C]GCTAACCTTTATATCACTAAAGTTATTTTTATTAT M 2 1 2 1 101000 f 74 goat snp49463-scaffold704-3451692 4 83018019 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411422 Affx-122951835 AX-123281772 4 34958431 GCCCCCATACACAGTGCAATGCAAGTCTGACGGCA[C/T]TTGTGCCTGCAATGTGGTTTGCATCACCTCAAATT Y 2 1 2 1 201000 f 74 goat snp49464-scaffold704-3481818 4 82987664 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787795 Affx-122930451 AX-385274818 4 35018104 TCCAGTTAGACTTTACATATTGCTATTGAAATTTC[C/T]CTCTTCTTTCTCTCCTTGTATACCGACAAGGGCAA Y 2 1 2 1 101000 r 74 goat snp49465-scaffold704-3541491 4 82926525 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435218 Affx-122933624 AX-123305558 4 35062720 TAACTCTACCAATAATCAGTTTTTAAAGAACTCCA[C/T]GACAGAGATAAATACACATTCTGTGTAAAAATTTC Y 2 1 2 1 201000 f 74 goat snp49466-scaffold704-3586107 4 82881691 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444329 Affx-122926731 AX-123314666 4 35121637 TAATTCATAAGTAAGGAACCAGGAAGCTATGCTCC[A/G]TGATGAAATGGTTGAGTCGAACACAACTCCTGAAT R 2 1 2 1 101000 f 74 goat snp49467-scaffold704-3645024 4 82823670 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425595 Affx-122940928 AX-123295941 4 35144237 ATGCCGTCTATTCATAAGATTCATAAAAGAAAACT[A/G]TATATAACTTGTTCCTTAACATGTTGCTGGTTTGC R 2 1 2 1 201000 r 74 goat snp31934-scaffold357-289602 4 82801189 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400104 Affx-122960731 AX-123270459 4 35186024 AACAAAGGAAACAAGGATCAAACCAACAAAACAGC[A/G]TTAAAGAGCTATCAATTCACTGGTCCATGGCTTAC R 2 1 2 1 101000 r 74 goat snp31933-scaffold357-247815 4 82758576 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453477 Affx-122919840 AX-123323810 4 35217169 GGTGCGCTGGCTGGTAAATCTTCCATCTCCATCCG[C/T]GGTTGTTTCTTTTCTTCCACTGCTTCCGGAGGCAC Y 2 1 2 1 201000 f 74 goat snp31932-scaffold357-216670 4 82727473 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395006 Affx-122964232 AX-123265361 4 35247859 GCTTCCTTCAAATTAAATTAAATTAACAAAATTTC[C/T]TTGGAAAGTAGGACCATGGTCCTTCTGTACAAACT Y 2 1 2 1 103000 r 74 goat snp31931-scaffold357-185980 4 82696647 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780688 Affx-122923168 AX-385267778 4 35276755 TGTGCTGGGGTGACTGAAGGTTTTCAGAACCGTTG[C/T]ACAGTTGTTGATCAGCACCTATATCTTTGAAGTTT Y 2 1 2 1 101000 f 74 goat snp31930-scaffold357-157084 4 82668154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379010 Affx-122976374 AX-123249369 4 35335970 AAAAAGGAAACCAGAATCTTCAATAACCATCCCCT[A/G]ATTTTTTTAACTATACCTCCAATTGTTGATTACTT R 2 1 2 1 201000 r 74 goat snp31928-scaffold357-97869 4 82608605 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453254 Affx-122920407 AX-123323587 4 35371691 TGTTATGATGAGTTGTATAGATCTTTTGGTGAGAA[A/G]GGAAATTTTGAATTGAATAACTTAAAATAATATTG R 2 1 2 1 101000 f 74 goat snp31927-scaffold357-62148 4 82572963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442838 Affx-122927694 AX-123313175 4 35402527 TAAGTACAGTATAGATGAAAATTTAAAAATAGGAA[C/T]GGTATGAGTTACCTGAAGAGAATGTCCAGCAGGAC Y 2 1 2 1 101000 r 74 goat snp31926-scaffold357-31312 4 82542219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420369 Affx-122944949 AX-123290716 4 35445234 TGATAAAAGTAGGAAATGAAAGAAGTGGAAAGAGA[C/T]GTAAATACAAGTTAAATGCTGGGTAACTAGGGTTA Y 2 1 2 1 101000 r 74 goat snp31520-scaffold350-11088 4 82495191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800218 Affx-122955206 AX-385287141 4 35499259 GCTGCACACCATGGAAAACTCAGAACTGGGCATTG[C/T]GAATACTAAATTGTAGTCATTAGTATACAAAGGAA Y 2 1 2 1 102000 f 74 goat snp31521-scaffold350-65113 4 82440854 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445764 Affx-122926071 AX-123316101 4 35539531 CTAAACCAGTGTTAGCCTGTACTAATGGGAAACAA[C/T]GGTCAAGGAATCCTAACATATACCAAACACAATCT Y 2 1 2 1 101000 f 74 goat snp31522-scaffold350-105385 4 82400049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453158 Affx-122920479 AX-123323491 4 35597659 TTGACTGAATAACTGCAGAACACGTGCTGAAAAAT[A/G]CAGCTAAGTGATCTCAAAACGCAAGTCAGGTAATG R 2 1 2 1 101000 r 74 goat snp31523-scaffold350-163513 4 82341679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795476 Affx-122963112 AX-385282431 4 35652486 AGTGTTGGGGAAATCATTGATTTCCTTAGCAACTG[C/T]AATTTCAATGAGATTATTGATAGGAAGAAGCCAGA Y 2 1 2 1 101000 f 74 goat snp31524-scaffold350-218340 4 82286598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425209 Affx-122941025 AX-123295555 4 35717882 GTTTCAATAGAAAGTGCAACTTATTTCATCTGAAT[A/C]TTTTAGCCATTGTCACTGGAATTGAAGAGCCATAG M 2 1 2 1 101000 r 74 goat snp31525-scaffold350-283736 4 82227122 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769486 Affx-122972955 AX-385256656 4 35762203 TTTCTGTCTTTTCTTGCAGTCCTTCTGAGTAATAT[A/C]TTTCTCTATACACTTATTCCTGAACAGTTGTCTCA M 2 1 2 1 101000 f 74 goat snp31526-scaffold350-328057 4 82182448 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407767 Affx-122954971 AX-123278118 4 35794926 AGAATTACTGCCCTTTGCTTTTTTTGTAGGCTGTC[A/G]TTTTATTGTATTTGAATCTTTCACCACTGAGCTTG R 2 1 2 1 201000 r 74 goat snp31527-scaffold350-360780 4 82149528 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802344 Affx-122930973 AX-385289248 4 35850307 TGTGAATATTTTCCCTTGTGATCAATGAAATCTTC[A/G]CTTATATCCTAGCCATTATTATTTTCTCATTCCAG R 2 1 2 1 101000 f 74 goat snp31528-scaffold350-416161 4 82094163 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476186 Affx-1251763691 AX-586011612 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20000 f 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 539476441 Affx-1251763691 AX-586011842 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20000 r 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 560378492 Affx-1251763691 AX-605230907 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20000 r 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 562165472 Affx-1251763691 AX-606940883 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20100 f 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 562165577 Affx-1251763691 AX-606940988 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20100 f 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 562165876 Affx-1251763691 AX-606941285 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20100 r 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 562165880 Affx-1251763691 AX-606941289 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20100 r 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 562166399 Affx-1251763691 AX-606941807 4 35908675 CACTGTTAATTATTCCTTTGGTTAAAGCATTCAAG[-/GCCACGGTTAGAATTATTATTTTTTTTTTAAATATTTAACGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CCACGGTTAGAATTAAAATAACATGGGGAAGTTGG - 8 1 4 1 20100 f 74 goat SV_221 4 35908675 - deletion junction SV-TF-chip 38410792 Affx-122952663 AX-123281142 4 35910395 ATCCTTAGAATTTGTGTTGTATAGAATGAACTGAA[C/T]GATGCTGAAAGACACAGATTGGTGAAGACCAAGCT Y 2 1 2 1 201000 f 74 goat snp31529-scaffold350-476249 4 82035959 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405646 Affx-122956582 AX-123275998 4 35939396 AAAAGAAGCCAAAAGGACCTATTACAAATGGGATT[C/T]GGGGATGTTGTTGAATGAAATCCAAATGTATTCAT Y 2 1 2 1 201000 f 74 goat snp31530-scaffold350-505250 4 82007699 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430830 Affx-122937442 AX-123301171 4 35990480 ATGGTCAAAGACATTATAAAGAAAAAGAAAGTAGC[A/G]CTTTTAAAGTAGGTGACTGCAAAATAATTCTCCAC R 2 1 2 1 103000 r 74 goat snp31531-scaffold350-556334 4 81956310 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789376 Affx-122920253 AX-385276386 4 36030853 GTGCTGTTTTTCTTGTAGTCTTTAGCAAATTCTAA[A/G]AAGTACTGGGCGTTTTTCCATTAACCTTAAATAGT R 2 1 2 1 101000 r 74 goat snp31532-scaffold350-596707 4 81916319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804599 Affx-986696768 AX-385291134 4 36042918 GAAATTATGGCATTTAAAATACATAGTGTAGGGAA[A/T]ATTACAATTACTCCTGGGTATGAATATAAGCTCTG W 4 1 2 1 600010 r 74 goat 4_36042918 4 36042918 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 320804301 Affx-986696770 AX-385290918 4 36042973 ATGAATATAAGCTCTGCCTATTAAAATTCATGACA[C/T]TGAAAGGGATTTCCTTCCCCTTTTTTAAACTTCAG Y 2 1 2 1 600010 f 74 goat 4_36042973 4 36042973 Ancestral_priority_1043 ancestry 0.652 recommended IMAGE 10K 10K ancestral 38443084 Affx-122928116 AX-123313421 4 36104166 GCCAGAGTCACTCTGACAAAGTTTTTTCTTGTCTG[C/T]GCAGTAAATGTTGTCCTGTGTATGTTACAAAGTGA Y 2 1 2 1 201000 r 74 goat snp31534-scaffold350-670020 4 81843329 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425969 Affx-122941166 AX-123296315 4 36133138 GGAAATAAATTTATAATGAAAATGAAAGATTAATC[A/G]CTAGTACATACTGAGAATCTATTGAAAAGACTTTA R 2 1 2 1 101000 r 74 goat snp31535-scaffold350-698992 4 81814167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436083 Affx-122932688 AX-123306422 4 36184470 AGGCTAATCCTTCTCACTGTTGTTCAGTGCATTCC[A/G]TCGTTCCAGTTATGTTCCACCCCGCCTCCAGATGC R 2 1 2 1 101000 f 74 goat snp31536-scaffold350-750324 4 81762161 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414289 Affx-122949595 AX-123284638 4 36216955 GACTTCGTAACTGGGAAGGGTTTATTAATCAGTGA[G/T]TTATATGAAAGTTATAAAATTCCATACATTAAAGA K 2 1 2 1 102000 f 74 goat snp31537-scaffold350-782809 4 81729813 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392008 Affx-122966490 AX-123262365 4 36253783 TTTTAAAAATGATACATTATTAAATATTTGATTTA[G/T]CCAGTTTCCTGGTTCATTAAGATGACCACAGAGTG K 2 1 2 1 101000 r 74 goat snp31538-scaffold350-819637 4 81692957 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453357 Affx-122919946 AX-123323690 4 36322323 CCCATCTCTTTAAAAGACTCACACATAAAAATAAA[C/T]GAGAATATATTAAAAGTTTCTAAAGACACTTTTTT Y 2 1 2 1 101000 f 74 goat snp31539-scaffold350-888177 4 81624409 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378023 Affx-122977583 AX-123248382 4 36356997 CCATATGTGGTGCTCCAGGTTTTAGGATTCTTACC[C/T]AGAGACAATTCTCCAAATCAAATACCTAAGAAAGC Y 2 1 2 1 101000 f 74 goat snp31540-scaffold350-922851 4 81589129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416577 Affx-122947658 AX-123286925 4 36398208 TTCCCAACCACATGGCATAACCATATAGATTAGCT[A/G]CAGGGAATCTAGCCAGAGTATTTTTTTAAAACCTA R 2 1 2 1 101000 f 74 goat snp31541-scaffold350-964062 4 81550193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396719 Affx-122962807 AX-123267074 4 36447101 TAGTTCAATGGTGAGTTCAGTGGTAAATCCACAAA[C/T]ACAAAATAACAAACTAGGAACGGGGGCCCAATTCT Y 2 1 2 1 201000 f 74 goat snp31542-scaffold350-1012955 4 81500074 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406718 Affx-122955757 AX-123277069 4 36484917 ACTCATTCTGCTCCTTCATCATCTAATTACGATCT[A/G]TCCCCAAGAGTTATCATACCTTCATCTTTGCCTCC R 2 1 2 1 101000 r 74 goat snp31543-scaffold350-1050771 4 81462199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383645 Affx-122972529 AX-123254003 4 36530756 TCCCTAAATTCATACATTTTACTAATATACTAGTG[C/T]CCAACATCCCAGGTGTGGAATGCTTAGGGTTTATA Y 2 1 2 1 201000 f 74 goat snp31544-scaffold350-1096610 4 81415710 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386855 Affx-122970072 AX-123257213 4 36592696 GCCAGCAGGCTTGGCATATAGAGGGGCTGATTCCT[A/G]GTTCATAGATGGCTAACTCTTCCTTGTGTCTTCAT R 2 1 2 1 101000 r 74 goat snp31545-scaffold350-1158550 4 81353677 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785998 Affx-122968234 AX-385273034 4 36632032 TTTTGAGTTTTAGGAAAATGCCCTATTTACGGAGC[A/G]TAAATTTGTATTGAAGTACATATGTTATGAATATA R 2 1 2 1 201000 r 74 goat snp31546-scaffold350-1197886 4 81313502 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379452 Affx-122976092 AX-123249810 4 36690519 TTATGGCACATCACCGCAAGTAGTTCAGTCCCATG[C/T]GGTGCCCCAGGCAATACTAGCTGATAGCTGAAACC Y 2 1 2 1 101000 f 74 goat snp31547-scaffold350-1256373 4 81254161 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429456 Affx-122938489 AX-123299798 4 36723993 GTCTTTTTTAACAGTGTTTAGTAAATATAAAAATG[C/T]AGGGTCATAATACAATTTATTAGTTCATTAAGCAC Y 2 1 2 1 101000 r 74 goat snp31548-scaffold350-1289847 4 81221306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776916 Affx-122938162 AX-385264040 4 36767099 CTCTGGAAATTCCCTTGCTCATTTGGAGCTCAGGA[C/T]ATTTGGCTCCTTAGCAAGTATACTAATCACTCTCC Y 2 1 2 1 101000 f 74 goat snp31549-scaffold350-1332953 4 81178463 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397801 Affx-122962496 AX-123268156 4 36802568 TATTTTAATATTTATTTTTTAATCCTCAAACATGT[A/G]TAAAGTGTTTCAGATTCTTTCTAAGCCACACAAAA R 2 1 2 1 101000 r 74 goat snp31550-scaffold350-1368422 4 81142808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780269 Affx-122963800 AX-385267364 4 36834548 AGTAGATACCATTAACTCTAAATTTATCTTAAATC[A/G]TTGAATAGTGATGTTCACCAGGGTACTGGTGATAG R 2 1 2 1 201000 f 74 goat snp31551-scaffold350-1400402 4 81111247 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427496 Affx-122940001 AX-123297839 4 36930030 CTCCTGCATTGACAGTCGGCTTCTTCACCACTAGC[G/T]CCACCTGGGAAATCCCTGCATCACAGTAAAAGTGC K 2 1 2 1 201000 f 74 goat snp31553-scaffold350-1495884 4 81015149 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417095 Affx-122947486 AX-123287443 4 36958798 ATGTGTAAAATAATTATATTTAAACAGTTTGAATT[A/G]AAGAACAATACCTAAAATGTCCAGGTATATTATAT R 2 1 2 1 101000 r 74 goat snp31554-scaffold350-1524652 4 80986381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792464 Affx-122948998 AX-385279445 4 36997125 GCACAATAGTTTGAATAGCTATTTTCATATACAAA[C/T]GTTTTCAAATTATTGCAAGTAATGTGAAACTCCCT Y 2 1 2 1 101000 r 74 goat snp31555-scaffold350-1562979 4 80948222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390884 Affx-122967115 AX-123261241 4 37027746 ACGTGCCTTTGACGACTATTCAACCTCTAGTTACC[A/G]TCAACAGTTCTAATTTATATTTCACCCACAAAGGC R 2 1 2 1 101000 f 74 goat snp31556-scaffold350-1593600 4 80917506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777260 Affx-122934929 AX-385264382 4 37084088 TGCAAGGCAGCATAAAGAACACTGGGACAAAATTC[A/G]CTTTCAATTCCCAAACTGTCATTTCCAGTACCCAA R 2 1 2 1 101000 f 74 goat snp31557-scaffold350-1649942 4 80860809 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395892 Affx-122963617 AX-123266247 4 37188218 CCCATGAACTGCTATACATCCAAAGACCATCACAG[C/T]GGGGTAAAAGGAATCCAGTATATTTCATTAGTATA Y 2 1 2 1 101000 f 74 goat snp31559-scaffold350-1754072 4 80755115 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785754 Affx-122922129 AX-385272794 4 37238147 CCACTAGAACTAATCATAAACCCAAAATTTATATA[C/T]AAGCTAACAATAGAGATATATGGCATGTGAAAGTA Y 2 1 2 1 101000 r 74 goat snp31560-scaffold350-1804001 4 80705407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413957 Affx-122950306 AX-123284306 4 37272651 TTTCACATCTGAGATGCAGATGTCACGATAATGAT[A/G]TTCTCTGTGACTTTTACTGAAAACACTGCTATATT R 2 1 2 1 101000 f 74 goat snp31561-scaffold350-1838505 4 80670888 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776439 Affx-122927178 AX-385263566 4 37354466 GTCAAGAGAGCTGTGTAATAGGTGGAGGAACAATA[G/T]AGTAAAAACAAGTGATAAGTTAAAATGAGACTTAT K 2 1 2 1 201000 r 74 goat snp31563-scaffold350-1920320 4 80588062 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412630 Affx-122951268 AX-123282979 4 37408503 CGCACACGCTTGGCCTGGTTCTTAGACCAACAGTC[A/G]CCCCTCCTTGCCTGAATAAAGGTAACCTGTCTCCA R 2 1 2 1 201000 f 74 goat snp31564-scaffold350-1974357 4 80533894 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406805 Affx-122955692 AX-123277156 4 37444987 AAATGTTATCTAATTTATGGTTGCAGTCACTGTCC[A/G]CAGTGATTTTGAAGCCCAGAAGATAAAACCTGTCA R 2 1 2 1 103000 f 74 goat snp31565-scaffold350-2010841 4 80497173 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272268 Affx-1111833424 AX-519546007 4 37453124 TTTCTGTTTTTCCTCTTTTAGATTGTGTAGTTGTC[A/G]CAGAGAATTAAGAACATACAATTTTATGTTGTAAA R 2 1 2 1 101000 f 74 goat 4_37453124_AF-PAKI 4 37453124 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320785687 Affx-122953049 AX-385272728 4 37487049 AATAAAGCATTGTCTTGGACAAAATTACCCTACAA[C/T]GTCTCCAAATGGTTGCCTAGTCTTACTCTAGTGAC Y 2 1 2 1 101000 r 74 goat snp31566-scaffold350-2052903 4 80455037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405173 Affx-122956934 AX-123275525 4 37515285 TTTCATATTGGAAACCAGTGAGTATTCCAAAAACT[A/G]TCAACCATGTGATTTCAAGCCAGACATTGCATTTT R 2 1 2 1 101000 r 74 goat snp58422-scaffold950-12337 4 80424657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780939 Affx-122937550 AX-385268026 4 37593101 GGTGTTCTTGCAGGGAGAGTGAAATTGACCTAGAC[A/G]TGCAGCTAAGTCTGAAGACTGTGGTTTAAAACTTA R 2 1 2 1 101000 f 74 goat snp58424-scaffold950-90153 4 80346808 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386880 Affx-122970055 AX-123257238 4 37644410 CCAGGTTGAAAAATATATGTAATTCCTTTTTGTCC[A/G]TCTAAATAAATATCTTTTCCCTTCCCCTTGTATGT R 2 1 2 1 101000 r 74 goat snp58425-scaffold950-141462 4 80295102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450278 Affx-122922171 AX-123320613 4 37678372 ATGTAAATGCAAAGTGATTGGAACTCTTAAACACT[A/G]TAACTTAGGAATTCCTGACTGGGTGAAAATTTCCT R 2 1 2 1 101000 r 74 goat snp58426-scaffold950-175424 4 80260491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400410 Affx-122959989 AX-123270765 4 37708551 TTTTTCCTCTGAAGAAAACCACCCCCCTTGGTCCC[A/G]CAGTGCCTCATAAGACTCTTCACCCAATGGCAGCT R 2 1 2 1 201000 r 74 goat snp58427-scaffold950-205603 4 80230550 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801737 Affx-122958588 AX-385288645 4 37740118 CAAAATTATAAATTCACACCCTAAAGTACATGCTC[A/G]TACTTTAAGAGAGTGATGACTTGATATTCACAAAG R 2 1 2 1 201000 r 74 goat snp58428-scaffold950-237170 4 80198934 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783140 Affx-122934628 AX-385270207 4 37769154 AATTGTGTATTTCTCAGGGCTATTATGTTGCCATG[C/T]GTGAGCGTTACTTAGATAAAGTGCTATTGAAGAAT Y 2 1 2 1 101000 f 74 goat snp58429-scaffold950-266206 4 80169911 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773053 Affx-122936499 AX-385260197 4 37812407 TTTACTTTATGCACTTCTGTTCAATGAATTCATTC[A/G]CTTCCATGGCTTTAATTAGAGCTCTGACTCCATCT R 2 1 2 1 101000 r 74 goat snp58430-scaffold950-309459 4 80126106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785799 Affx-122975646 AX-385272838 4 37858698 ATGTAGGGTACACATTGTGATTTTGTACTGTGATT[A/G]TAGCATGTTTTATGCTATAATCCTTTATATTAATG R 2 1 2 1 101000 f 74 goat snp58431-scaffold950-355750 4 80079256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439221 Affx-122931024 AX-123309558 4 37894661 TATTCCTAATATTACAATAAAGTTAGTGTTTTTGG[C/T]ACCTCTGCCCCTCCTTTTCTTACTTTGATAGTTAG Y 2 1 2 1 102000 r 74 goat snp58432-scaffold950-391713 4 80042867 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783843 Affx-122959277 AX-385270899 4 37946977 CTCCAGCTCTAAATATGGTCAGTGTATAGTTCAGA[C/T]GTTGATAATGGGTTATGATAGACAGATTAATACAT Y 2 1 2 1 101000 f 74 goat snp58433-scaffold950-444029 4 79989673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403106 Affx-122958131 AX-123273459 4 37983778 TTTTAAAATCTAATAAACATATTTTACACAAGTAG[A/G]AATGATTATTTGCAAAACACGTGAGACTACCATAA R 2 1 2 1 101000 r 74 goat snp58434-scaffold950-480830 4 79953041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773767 Affx-122978663 AX-385260907 4 38017256 ACATATAGGTAATTCTGTTACTATATGCAGAAAAT[C/T]ATAATGAATAGTCATTAATTAAGTGGAGTGGTTAT Y 2 1 2 1 101000 r 74 goat snp58435-scaffold950-514308 4 79910740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796604 Affx-122950673 AX-385283550 4 38046146 ATAGATAAGTATTATGGCTATTCTAAATGTAAAGG[A/C]GTTTACTGTAAATGATGAGGGTTTTGAAGCTGAAG M 2 1 2 1 101000 r 74 goat snp58436-scaffold950-543198 4 79881872 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433589 Affx-122934962 AX-123303930 4 38091052 AACTTGCCTTTAGGAGTGCGTCTGCTGCAGAACGG[A/C]TCACAGCAGCTCTCTGGGATTTGGTCATGTCTAAA M 2 1 2 1 101000 r 74 goat snp58437-scaffold950-588104 4 79836857 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768818 Affx-122976049 AX-385255995 4 38123063 TAGAAGGTTAATAGGAGTGAATGCTTATTGCAATG[C/T]ATCTTCTTTTGTTTGGGTCATCATACAAAGTTTCC Y 2 1 2 1 101000 f 74 goat snp58438-scaffold950-620115 4 79804879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449721 Affx-122922526 AX-123320056 4 38162721 AGCTGTAATGTAGATGTGTTATTTTTATTCAAACA[C/T]GTCAACACAACATAAAACACATAGTAGGTATCTAT Y 2 1 2 1 201000 f 74 goat snp58439-scaffold950-659773 4 79764951 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378101 Affx-122977152 AX-123248460 4 38254272 ATATGCAGTTCTTCTGATGGACTCCCAACAGAACA[C/T]ACTAGATGTACTTAAAAAATAAAACAGTTAAGGTT Y 2 1 2 1 103000 f 74 goat snp58441-scaffold950-751324 4 79677329 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780838 Affx-122968870 AX-385267926 4 38292409 AGTAAGTAATGTATACAAAGCACACAGCATAGTGC[A/G]CGGGGAATATCCAACAGATAATGGCTAGCTGTTAT R 2 1 2 1 102000 r 74 goat snp58442-scaffold950-789461 4 79639197 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422041 Affx-122943616 AX-123292388 4 38335478 AGTATGAGCACTGCATTTAGTATTTTAGTAAGATA[C/T]CTAATTCTTTTATTAATAAAATGGACTGACTTCAG Y 2 1 2 1 101000 f 74 goat snp58443-scaffold950-832530 4 79595353 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426736 Affx-122939872 AX-123297082 4 38396504 GGAAAGGTGAGGGAGGAAGAGAAGAAAAAGAAGAA[G/T]AAGCAGGAGAATGAAAAAGTAGAGAAACTAATATA K 2 1 2 1 303000 r 74 goat snp58444-scaffold950-893556 4 79534172 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770709 Affx-122974573 AX-385257873 4 38453077 CTCTGGGCCACAAGAAGGGACAAAGAGCTATTGCT[A/G]TAATGCAGGTTAGATGAGTGAGAAAAAAACATAAT R 2 1 2 1 101000 f 74 goat snp58445-scaffold950-950129 4 79473106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449502 Affx-122922624 AX-123319837 4 38483738 CATGAAATATAATCCTTTGATATTCTGTTACCTTC[A/G]TGATGTTCAGACCCATTATCATTCACATAGGGGCT R 2 1 2 1 101000 r 74 goat snp58446-scaffold950-980790 4 79442519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448655 Affx-122923346 AX-123318991 4 38521484 TTATTTTAAAATAATCTCAACACAGATAACAAAAC[G/T]AAATAGCTAATTAAAAGTAAACAAATCATGAACAA K 2 1 2 1 101000 f 74 goat snp58447-scaffold950-1018536 4 79405041 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435116 Affx-122933696 AX-123305456 4 38559452 ATACTTGTCCTTTTCCCCATCTCCTTCCTTCTTCC[A/G]CTAGAGGTAAGGGAAGCTTTCCTCTTTAGCTCTTT R 2 1 2 1 101000 r 74 goat snp58448-scaffold950-1056504 4 79365758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450389 Affx-122922082 AX-123320724 4 38594941 TTTGGTAAAGAATGACTGACTGAGGGAAGGAGTGG[C/T]GGAAGATGACATTAGTTTCTAACGTAATAGAACTG Y 2 1 2 1 201000 r 74 goat snp58449-scaffold950-1091993 4 79329692 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410054 Affx-122953229 AX-123280404 4 38633665 TTTATGTGAAAGTTAAAGAAAGAAATCACAGGAAA[C/T]GATAATGTGAAATCTGGTCCATAGAAGTCATTTTC Y 2 1 2 1 101000 r 74 goat snp58450-scaffold950-1130717 4 79290789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779796 Affx-122975865 AX-385266896 4 38690681 ACAGAAGCTTACTGAAAATAGGCTTGTGCAATAGT[A/G]TTTATTTTATTATAACTGTTACAAAAACAAAAGCA R 2 1 2 1 202000 r 74 goat snp58451-scaffold950-1187733 4 79234297 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769659 Affx-122976675 AX-385256829 4 38744179 TGACCTCAGATGACGCATTTTTGTTGACTGATTCT[A/C]TTACTGATGAAAACATCAAGAAGGCTCTTAACTGG M 2 1 2 1 101000 f 74 goat snp58452-scaffold950-1241231 4 79179764 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772260 Affx-122978362 AX-385259415 4 38779015 ATATAAAGAAGCAAATTGTAGATAACGTAGTTAGA[C/T]GGAAGGATCAGTGCCTTGGAATCATTCAGGCTGCA Y 2 1 2 1 101000 r 74 goat snp58453-scaffold950-1276067 4 79144583 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781577 Affx-122979095 AX-385268661 4 38824695 AAAAAAAAAAAAGTAACTATAGGGTTTCCCAAAGT[A/G]TGTTTTGCATTCCCATGATTTCAGGTAAAATGACT R 2 1 2 1 101000 r 74 goat snp58454-scaffold950-1321747 4 79098662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789765 Affx-122975064 AX-385276773 4 38866860 AACACGGCCAAACTATTAGAGGTCCATTTCAAGTG[A/G]TAAATTTTCCTCGCACTGTTTGAAGGGAGAAAAGG R 2 1 2 1 201000 f 74 goat snp58455-scaffold950-1363912 4 79056354 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423705 Affx-122942887 AX-123294051 4 38912730 TATCTGTATCATTTTCTGTTTTTTTGTTGCCTGTC[C/T]ACTTCCCAAGCCTGACTAGTCATGAGATTTGGGAC Y 2 1 2 1 101000 r 74 goat snp58456-scaffold950-1409782 4 79010351 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797664 Affx-122931230 AX-385284603 4 38954717 CCTGTAACCAACAGAGGAAGAGTTGTTAAGCAGCT[A/G]CTATTCCCAGGACATGGTGTGAAGCAACAGACCAA R 2 1 2 1 101000 f 74 goat snp58457-scaffold950-1451769 4 78967601 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433422 Affx-122935086 AX-123303763 4 39018957 GGAAGGAGAACTGGAGGCTAAGCGTACAAAGGCCC[C/T]GTGGAAGGCCATCATCCAAATAATCGGTATAAAAT Y 2 1 2 1 101000 r 74 goat snp58458-scaffold950-1516009 4 78902954 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787082 Affx-122964224 AX-385274109 4 39056277 AATCAGGTCATTTGAAATATAGTATAGCACAACTG[A/C]TATTCCTATGAAAATATTCATAGGAATTCATCAAT M 2 1 2 1 201000 r 74 goat snp58459-scaffold950-1553329 4 78864954 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440740 Affx-122929876 AX-123311077 4 39098862 TTTCAAGTGCAAGAGTAGAAAATATTCTAACTCAG[C/T]AACTGATCTTTTCTTCTTTTTAAACTTTACTTAAC Y 2 1 2 1 103000 f 74 goat snp58460-scaffold950-1595914 4 78822367 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783955 Affx-122977785 AX-385271009 4 39132929 TTATATCATAAGTAATTACTTTGCTAAACTGTAAT[A/G]TTTTGCAACACCCTTGAAGACCATATTTTGTCTTG R 2 1 2 1 202000 f 74 goat snp58461-scaffold950-1629981 4 78787917 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449409 Affx-122922697 AX-123319744 4 39164797 AAATAGTCCATTATTTGGGTTCTGTACCCAATTCT[A/G]CTTCTCCGTGGAGAGGGAGGTTTCAAGCAATGCTC R 2 1 2 1 202000 r 74 goat snp58462-scaffold950-1661849 4 78755419 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395809 Affx-122963645 AX-123266164 4 39200153 GAATGACAAAGATAAATAGTCTTTATTCTTTTCAC[G/T]CAGTGACTTATCTGGAAGACGACATTTATGGTGGG K 2 1 2 1 101000 r 74 goat snp58463-scaffold950-1697205 4 78719143 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278076 Affx-1111836239 AX-519551566 4 39247022 ACTTGTTCTTGTCTCTGAGAGCCAAACTACTGTTA[A/G]TGATCTTCTTTTCAATTCTAAGCATGTTTCCATTG R 2 1 2 1 101000 f 74 goat Random2.2K-433 4 39247022 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781196 Affx-122929360 AX-385268281 4 39254131 GTTGGCATATAGACAACCACCCAATAAGCACTTAC[A/G]CCAACTTAATAGCTAACTCCATGAGCAGGTATGAT R 2 1 2 1 101000 f 74 goat snp58464-scaffold950-1751183 4 78665117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432542 Affx-122935548 AX-123302883 4 39283632 AAGGTGCCAAATCCTCTGTTCCCCCTTCTGCCCAA[C/T]ACATAGTATTACTAGATCTAAAGTGCTGTACTGTC Y 2 1 2 1 101000 r 74 goat snp58465-scaffold950-1780684 4 78635024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773860 Affx-122939657 AX-385261000 4 39313833 GAGATAGGAACTATAACAGTGAATGACACAGTCTA[C/T]AGCAATATAAATATTAACGGTTGATTTAACCAAAA Y 2 1 2 1 101000 f 74 goat snp58466-scaffold950-1810885 4 78604184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425094 Affx-122941238 AX-123295440 4 39400880 AACTTGTCTTCTTCCCCTTCTCAAATGCTAATTAG[C/T]ACTGTTTCTGACCAAACTGGATTTTTAGATGGTGG Y 2 1 2 1 101000 r 74 goat snp58468-scaffold950-1897932 4 78516587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388705 Affx-122968985 AX-123259063 4 39439529 GCATATCAGACAGTTATAATACCCAAATGTTGTGT[A/C]ACTTTTCTAGTTCTATTTTCCTTTCCAAAGCCTCA M 2 1 2 1 101000 f 74 goat snp58469-scaffold950-1936581 4 78477943 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375946 Affx-122978453 AX-123246305 4 39511812 CTAAAGTCAGATATTAGTGTCCTCTGAGTTCATGA[C/T]AATTGAATGAAAAACAGAACTAAATATTGGTGAGT Y 2 1 2 1 101000 r 74 goat snp58471-scaffold950-2008864 4 78405265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773879 Affx-122940871 AX-385261018 4 39558619 ATGGTGCAAAGAAGTGAAATGCAGGTTGAAAACAC[A/G]GCATAAAACACTGCTCTGAGAAAAGTAAATTATGC R 2 1 2 1 101000 f 74 goat snp58472-scaffold950-2055671 4 78358504 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377577 Affx-122977435 AX-123247936 4 39596023 ATAAGTAGGCTGTCTAGGGCTCCTGTGGTAATTCC[A/G]CAGTTTTATCATGGCTCATATTTTCTTCTTTGCCA R 2 1 2 1 101000 f 74 goat snp58473-scaffold950-2093075 4 78319690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398506 Affx-122961555 AX-123268861 4 39680249 TGTTCAGAAAGAGAGTGTGGGGTCACCAGGGAACA[G/T]AGAACACAGAATATGACAAACCTTGAAAACTAGAT K 2 1 2 1 201000 f 74 goat snp58475-scaffold950-2177301 4 78234643 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389808 Affx-122968199 AX-123260165 4 39712193 CTCAAGCTATTGGTGGCCAAGTTGGTACAGATCTC[A/G]TATACCATGATTTCAGTAGTCTTTCCTCTGCTATC R 2 1 2 1 201000 r 74 goat snp58476-scaffold950-2209245 4 78202207 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404767 Affx-122957214 AX-123275119 4 39761273 AGGATATAATTCTAGAATTGGGGTTACTATAATCC[A/G]TAATGGTAGATTGTGGTTACTATAAATAAATCTAT R 2 1 2 1 101000 f 74 goat snp58477-scaffold950-2258325 4 78153202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406694 Affx-122955776 AX-123277046 4 39807929 TTCCTTTTAGAAAAATTTTTGCTGGCCTCTTCTCT[A/C]GTGCTATCCCTTGTAATCACTAAACTATAATATAT M 2 1 2 1 201000 r 74 goat snp58478-scaffold950-2304981 4 78105758 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764655 Affx-122950740 AX-385252291 4 39844058 GGTGTTTGTGTTGCATATATGGTGGTCATGGTGGT[A/G]CAAAGAGATTGTTAATGAACTGTAATTTTGAGAGT R 2 1 2 1 101000 f 74 goat snp58479-scaffold950-2341110 4 78069596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787862 Affx-122921463 AX-385274885 4 39921290 ATTTGTTGGTATTTACTTCCTTTATATGGAATCAC[A/G]TTCCATAAAAGATTCAGGATCATAAAGAGGCTTTA R 2 1 2 1 101000 r 74 goat snp58481-scaffold950-2418342 4 77987318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402592 Affx-122958430 AX-123272945 4 39970616 CACAACTGAATCAGGCAACTAGAAAGAGTTGTTTA[C/T]AGAACTGAGAGGACAAAAGACAGAGAGGCTTTCTT Y 2 1 2 1 201000 f 74 goat snp58482-scaffold950-2467668 4 77936288 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272269 Affx-1111833425 AX-519546008 4 40037513 TGAAAGGCTTGAAAACGTAGTTCTATGTGTTCTAA[A/G]GGCTAAAAAGTGGCACAGAGGAAGAGTGCAAATGG R 2 1 2 1 101000 f 74 goat 4_40037513_AF-PAKI 4 40037513 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320766005 Affx-122934409 AX-385253425 4 40040863 TAGATATGACATAAAACACATTATATATTCAAGTC[A/G]CTATCATTCTTAATTGACAGTAATTCTAGGAATTC R 2 1 2 1 201000 f 74 goat snp58483-scaffold950-2537915 4 77865169 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790721 Affx-122948032 AX-385277722 4 40089283 TGTATGTTTTAGTTATGATTTAAAGAAACTGATTC[G/T]CTTGTCTACATCACAGGAGTATAATGTGTGTTTAT K 2 1 2 1 101000 r 74 goat snp58484-scaffold950-2586335 4 77817220 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275431 Affx-1111834892 AX-519549004 4 40121270 GCATATAAGAAGCCTGCAGTTAGCTTTTGTCACTG[A/G]CTCAAAAAGCTATGTAAATATACATGAGTAAA R 2 1 2 1 101000 f 74 goat GoatD01.057647 4 40121270 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320795340 Affx-122943170 AX-385282297 4 40136612 TGTACTTTGTTTGTGAGTTCAATCTGAGAGTAGGT[A/G]TATAAATTTAACATCAAAATAAATGCTGCTGCATC R 2 1 2 1 201000 r 74 goat snp58485-scaffold950-2633664 4 77769613 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774538 Affx-122935186 AX-385261672 4 40178635 GTTTGGTGGTTAATAGCACATTCCCAACCTGGTCC[C/T]ACTAACCTCTAAGTATTATAAGTATTCTTTCTTGT Y 2 1 2 1 101000 f 74 goat snp58486-scaffold950-2675687 4 77727667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437887 Affx-122931670 AX-123308225 4 40213097 GTGGAGGGAGGTCTGTATGCTTACTGTTCATTGCC[A/G]TATGGGAGATGCTGCCCTGAAGGCTGTTTCAGATG R 2 1 2 1 201000 f 74 goat snp58487-scaffold950-2710149 4 77692775 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443089 Affx-122928112 AX-123313426 4 40248973 TGCACCTAGACAATAATTTTATTTAATTTATCAAG[C/T]GAGATTATCCATGGTCATGTTCCAGAGCAGCAGTT Y 2 1 2 1 101000 r 74 goat snp58488-scaffold950-2746025 4 77655844 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441617 Affx-122928647 AX-123311954 4 40281296 GTTAAGTGCATAGAAATAACCCTTTTAGAAATCAA[C/T]GGCATGGCCTCTTGGGATGAGCCCTGCCCTAGTAG Y 2 1 2 1 201000 f 74 goat snp58489-scaffold950-2778348 4 77623505 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394539 Affx-122964519 AX-123264894 4 40375527 CATAGATTTGACACATATGAGATCTGTGTTAAGGC[A/G]CATTTGCACACATAGAATTTTAAGCTAAACTTCAT R 2 1 2 1 101000 f 74 goat snp58491-scaffold950-2872579 4 77529107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796719 Affx-122967744 AX-385283664 4 40407710 TTTAGTTTCACATGCAAGAAGCACAGAGTTTATTG[C/T]ACCATAGGTTCTAAATTGCTTCTTCACTTTCTTTC Y 2 1 2 1 101000 r 74 goat snp58492-scaffold950-2904762 4 77497120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399361 Affx-122961346 AX-123269716 4 40460628 AGGAAAAAAATGAGAACAGCAGGTTGCATTTTCCA[C/T]GAGGTCAAACTGAAGGGCAGGACTTGAACTTTGAC Y 2 1 2 1 201000 f 74 goat snp58493-scaffold950-2957680 4 77443505 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405274 Affx-122956861 AX-123275626 4 40508729 CCCTCCAGAGCTACCTGTGTACTTTGTCTGCACGT[A/G]CCACTGCTGTTGAATGGTTTGGATTTTTACATGTA R 2 1 2 1 201000 f 74 goat snp58494-scaffold950-3005781 4 77395795 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770922 Affx-122934928 AX-385258085 4 40537236 CAACAGCATTATCTTAACAATGTTTTTCTCCTTTA[G/T]GCCTTTGAGTAGTTCTCTAAATATTCCAAGAAAAC K 2 1 2 1 101000 f 74 goat snp58495-scaffold950-3034288 4 77367320 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788931 Affx-122955434 AX-385275945 4 40590286 GAAGTTATATTATGAAATTAAGAAGGCAGACTAAC[A/G]TAGCATGTTCTATAAAAGTAGCTTATGTCTTGGCC R 2 1 2 1 101000 r 74 goat snp36588-scaffold440-2102239 4 77314256 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444461 Affx-122926542 AX-123314798 4 40658080 GACCTCAGTCCTCAGAATGTTTCTGTTCTTTCCTC[A/G]TACTCAAGCCCTAGGTGTTCTCATTCAGTATCCAG R 2 1 2 1 101000 r 74 goat snp36587-scaffold440-2034445 4 77246996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797276 Affx-122978082 AX-385284215 4 40714641 ATGCTTAACCAGAACCTGCCATCTAATTGTAGATA[C/T]TCTCATTTTTGCATCGCTGCTGAGTATGGTGAGAA Y 2 1 2 1 101000 f 74 goat snp36586-scaffold440-1977884 4 77189779 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453048 Affx-122920074 AX-123323381 4 40758119 TTCACTAAGAGGAGAAAACAGGAAAGGAAAGAAAT[A/G]CTTACTTATATGGGAATTATCCAGCTGATGAAGAA R 2 1 2 1 101000 r 74 goat snp36585-scaffold440-1934406 4 77146832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778503 Affx-122975184 AX-385265617 4 40802861 TATGTTATCTCTGTTCAGTCTTGCATTGTTATTGA[C/T]GTGAGGCCACCTAGTCATTTGACAAATATGAGCCA Y 2 1 2 1 101000 r 74 goat snp36584-scaffold440-1889664 4 77101816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389107 Affx-122968570 AX-123259465 4 40853766 GACTCCGCTATGCATACTCAAAGCAACTGTGAGTA[C/T]GGAAGACACGGGTCCTAAATGGCTCCTTCTGATCT Y 2 1 2 1 101000 r 74 goat snp36583-scaffold440-1838759 4 77050844 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416871 Affx-122948087 AX-123287219 4 40884181 TGGAGTGGGATGCCATTGACTTCTTCAGAAGGGTA[A/G]TGGGGAAGAAGTAATAATACACCAGCTCTTGGGTG R 2 1 2 1 202000 f 74 goat snp36582-scaffold440-1808344 4 77022157 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781293 Affx-122929831 AX-385268378 4 40929723 GTGGACAATGACCATTTAATTTATCTATCAAGGGA[C/T]GTTTGAAGCTCTGAATAGTGTACTGTCAGGAGAAC Y 2 1 2 1 101000 r 74 goat snp36581-scaffold440-1762802 4 76976566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775808 Affx-122944177 AX-385262939 4 40973672 CTGTGGTTTAACACTCTTTCCATTCAGCTTATCAT[A/G]CTTGTTCCAGGCTTTTTGGTTTCATCATTTTTCAT R 2 1 2 1 101000 r 74 goat snp36580-scaffold440-1718853 4 76932726 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401443 Affx-122958985 AX-123271796 4 41003565 TTATAGGGGTTAAGGAATAAACCAAAGAAAACAGC[C/T]CATGTGAAACCAGACCTCATAGATGTTGATCTTGT Y 2 1 2 1 101000 r 74 goat snp36579-scaffold440-1688960 4 76904752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379593 Affx-122976027 AX-123249951 4 41037380 AAAATAATAGGTAAATTCATTGCACAGGGCTCTCC[A/G]TATCCTCAGGTTGTGTATCCTCAAGTTAAGCCAAA R 2 1 2 1 101000 r 74 goat snp36578-scaffold440-1655145 4 76870891 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793678 Affx-122938140 AX-385280650 4 41073778 TAATTTCTTCTGTGTTTATTAGGTGACTTTCTGCT[A/G]CAGAAAATACTTCATTCTCTTATTTATTTGCCCAT R 2 1 2 1 201000 r 74 goat snp36577-scaffold440-1618747 4 76834337 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410326 Affx-122952476 AX-123280676 4 41125187 AAAACATCTATGGAGAATATAAAAAAAGATCTAAG[C/T]GGATGTTTAGATCTGTACTCTGGATTGAATGCAAG Y 2 1 2 1 103000 r 74 goat snp36576-scaffold440-1567338 4 76781636 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407692 Affx-122954580 AX-123278043 4 41171684 CTTAGATTTTTAAAATTATGAATAAGCAAGTTTTG[A/C]TGTATAAAGAGGTAATCCACTAAAGAGTTCACAGC M 2 1 2 1 101000 r 74 goat snp36575-scaffold440-1520841 4 76735131 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792944 Affx-122948452 AX-385279922 4 41241440 TTTGGTTAGGCAGTGATATAGGGGTTGTATACCCT[A/C]GTGGAGTAGGCATTCTATGTTGACAGAAGGATGGT M 2 1 2 1 101000 f 74 goat snp36574-scaffold440-1451085 4 76665327 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379514 Affx-122976078 AX-123249872 4 41281956 ATTTGCTTCTGCAAAGATGAAAATATGAATTGTGC[A/G]TCCACACTATTAATTTGAAGGGTCTCTATTTTTCA R 2 1 2 1 201000 r 74 goat snp36573-scaffold440-1410569 4 76624786 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451436 Affx-122921167 AX-123321769 4 41312444 ATTAGGACCACTGTGAATCTCAGGCGCTCTTTCAC[C/T]AGGTTTTAGACTGATTTGCAAAAAAGCAAAAAGTC Y 2 1 2 1 101000 r 74 goat snp36572-scaffold440-1380081 4 76594239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434061 Affx-122934190 AX-123304402 4 41396081 TAATGAATGATTTCATAGGGACAATAAAGGAAGAC[A/G]TTATTTTAATCTATATTCATATACACAGAACTTAA R 2 1 2 1 101000 f 74 goat snp36570-scaffold440-1296444 4 76510474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375559 Affx-122979086 AX-123245918 4 41487123 GATATATGGGAAAATAGAAATAAAATCTAGTATTT[A/G]TTTAGAACTCAAATGTCCTGGGTTTCATTAACATA R 2 1 2 1 102000 r 74 goat snp36568-scaffold440-1205402 4 76418979 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409360 Affx-122954169 AX-123279711 4 41516890 GTCCCAACCTTGTTTTCCAAGACAAGTCTAACAAC[A/G]CTATGAAAATATTAGTTTGTGTCTCTATGAATAAA R 2 1 2 1 101000 f 74 goat snp36567-scaffold440-1175635 4 76390642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403803 Affx-122957968 AX-123274155 4 41555779 TAAAACCCAAGCCCCACCAGTACCGATGCTGAGAG[A/G]TTTAGGTCAGTTCAGAGGGTGAGGGTTGAATCCCA R 2 1 2 1 303000 r 74 goat snp36566-scaffold440-1136746 4 76351718 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768047 Affx-122937374 AX-338229914 4 41608886 CAAAGACTTGGTGACATTTTTACAGTTGATCTGCA[C/T]GTGAACTTTATGATGTAGGTAGTATTACTAATCTG Y 2 1 2 1 101000 f 74 goat snp36565-scaffold440-1083639 4 76297940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782728 Affx-122924672 AX-385269800 4 41641590 TATCATCAGAGTAGGAATAACATAGACATAATAGG[C/T]AATATGTGCTCAACAAAACCTTAAAATTACATAGG Y 2 1 2 1 201000 r 74 goat snp36564-scaffold440-1050935 4 76265035 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386480 Affx-122970764 AX-123256838 4 41672806 AAAAATGCAAATGTGTGGCATTCAATGAGGTAAGA[A/G]ACTATTGCTTGAAAAGTTTACTTATTTATTCCCTA R 2 1 2 1 101000 f 74 goat snp36563-scaffold440-1019719 4 76233536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411324 Affx-122952276 AX-123281674 4 41715603 GATCTGCAGTTTGTTCAGTCTACAGCTGTGGAACC[A/G]CTAATAGGGAGGACTGACTGAAAAGCTACAGGTGG R 2 1 2 1 101000 f 74 goat snp36562-scaffold440-976922 4 76188377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445915 Affx-122925934 AX-123316252 4 41757641 GGATGTTTAACTGCATCCTTGCCCTCTATCCAGTA[C/T]ATGTCAGTAGCACCTAGTCCCCCCACCATACCTCC Y 2 1 2 1 101000 r 74 goat snp36561-scaffold440-934884 4 76146324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382448 Affx-122974226 AX-123252806 4 41814327 AAGAGGAATTCAACAAATGTTTTCCTGAGCTTTAC[C/T]GGGAAGTCTTTGAAATCATCTAACAGGACATTTTT Y 2 1 2 1 201000 r 74 goat snp36560-scaffold440-878198 4 76089621 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379325 Affx-122976184 AX-123249684 4 41855400 ATTAAATATGGAGAAAGCAAACATTGACAAGAAAT[A/G]TTATCCAATTTATATAATGCTATTATTTATCCTAT R 2 1 2 1 101000 f 74 goat snp36559-scaffold440-837125 4 76047990 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765059 Affx-122930743 AX-385252628 4 41890323 ATTATAATGTAGTGACCTTCTTTATCAGATAAACT[C/T]TAAAAATCCACCTAAAGTACAATGCTGAACAAGAT Y 2 1 2 1 201000 f 74 goat snp36558-scaffold440-802202 4 76012763 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443309 Affx-122927457 AX-123313646 4 41941219 AGTAATGGAAAATTCTGTGCAATGACTCTGTTGCC[A/G]TTTACAATGGATTTTTTTAAAGAGTAAAGGTAAAC R 2 1 2 1 101000 f 74 goat snp36557-scaffold440-751306 4 75962116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776611 Affx-122951438 AX-385263739 4 41990230 ATCCTTTTAAAAAACGGCATTTCTTTAGCTTAAAA[G/T]CATGTATTTTCATAGGATGCTCCTGTCTTTCCAAG K 2 1 2 1 101000 r 74 goat snp36556-scaffold440-702295 4 75913071 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394451 Affx-122964585 AX-123264806 4 42021443 TTTCTAGGCTTCCGCCACGGTTTAATTTTTATCAA[C/T]ATTAGCATTCTTTCCACTTTGGCATTTTGTTCCTT Y 2 1 2 1 101000 f 74 goat snp36555-scaffold440-671082 4 75880763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801781 Affx-122940220 AX-385288689 4 42069211 AGGCTTGTTTAGAGAGTTCATGAAAAGTACTGCTC[C/T]GTATATTGTGCTGTTGTATGGCTGAAGTAACTAAT Y 2 1 2 1 101000 f 74 goat snp36554-scaffold440-623314 4 75833254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796543 Affx-122920347 AX-385283489 4 42151788 AATCTCATCTATGAATGTATTGAATAATACCAAAA[A/C]CAAACAAAAACAGTTAATAGCAAAATGAATTCAAC M 2 1 2 1 303000 r 74 goat snp36553-scaffold440-540737 4 75750403 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386682 Affx-122970183 AX-123257040 4 42180327 GGATTCCAATGAAAAGAAATGTTTTTGCAAACACT[A/G]CCAGGGCTCAGTTGTATGTCATATAGCGGGGAGTA R 2 1 2 1 201000 r 74 goat snp36552-scaffold440-512198 4 75722151 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430729 Affx-122936890 AX-123301070 4 42331724 ATTGAAAACATACTGAAGATTCTCCATGTGCAAAA[C/T]AGAATTGTTTGAAGGTGTCACAAGATGAAAAATAG Y 2 1 2 1 101000 r 74 goat snp36549-scaffold440-360801 4 75570000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401228 Affx-122959315 AX-123271581 4 42363585 GCATTCTGCTTTAGTTAGGATACAGGTCTAGCTAC[G/T]ATAAAAGCAAAATAAATTCAAATGCTTAACAAGGC K 2 1 2 1 101000 f 74 goat snp36548-scaffold440-328940 4 75538181 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404282 Affx-122957040 AX-123274634 4 42410306 TCAGCAATAATGTGTAGTGATGGATAACACAAAAC[A/G]ATTTCCTAATTGATCAGTAGAAATCCCTTCAGAGC R 2 1 2 1 201000 f 74 goat snp36547-scaffold440-282219 4 75491504 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445424 Affx-122925369 AX-123315761 4 42482322 TAAATGCAGATCACTAGGAGATAGGTGCTGTTCTG[C/T]GTATTTTTTATTTTTAAGAAATCTTCCCACTCTGA Y 2 1 2 1 101000 f 74 goat snp36546-scaffold440-210203 4 75419596 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386379 Affx-122970843 AX-123256737 4 42514434 TTAATCATTGTGTTCCAGCAGGATTATGGTGCCAA[A/G]TGCTTTTAGATTTAGAAAAGAGTAAGTCTTAACAC R 2 1 2 1 101000 f 74 goat snp36545-scaffold440-178091 4 75387315 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415786 Affx-122948911 AX-123286135 4 42560242 TGAAGCCAGGGAAGTTAACTTGACAAACTGTATAC[C/T]GCTTATATTGGCATGTGTTGTGCTGTGTGCCATGT Y 2 1 2 1 101000 r 74 goat snp36544-scaffold440-132283 4 75333392 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272113 Affx-1111833426 AX-519545871 4 42577276 CATAGTGTCCAGATGGAATTGAACATGGATAAGTG[A/G]AAAAGAGCAGATCAAGAGCCCATGTCTCTATCAAT R 2 1 2 1 101000 r 74 goat 4_42577276_AF-PAKI 4 42577276 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378357 Affx-122976828 AX-123248716 4 42597109 ACTCAATTTCCTTTGCGTGGTTAGGGAATCCATGC[A/G]CTTTGTGACTTGACTTTGAACTTTCGTGTTTTACC R 2 1 2 1 101000 f 74 goat snp36543-scaffold440-95416 4 75296608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780918 Affx-122924923 AX-385268005 4 42631404 TATATCCCATCCATTGTCACAAGGGGAATCATATA[C/T]AGGGAGAGAATGTGTGAATTAAAGGCAAAATTGAA Y 2 1 2 1 101000 r 74 goat snp36542-scaffold440-61121 4 75262403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425252 Affx-122940989 AX-123295598 4 42682337 GTGCTCTTATCCACTATGTAAGATGCTGCTGCTGA[C/T]GACAATGGTAGTGATAATGGTGATGATAAGGCAAG Y 2 1 2 1 101000 f 74 goat snp36541-scaffold440-10188 4 75211380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388905 Affx-122968849 AX-123259263 4 42706406 CTTATACAGCACAGTGGCAACTTTTACTAGAATCT[A/G]CTCTAAAAATATGACTTTACCAATGTTTTTATTTG R 2 1 2 1 101000 f 74 goat snp49148-scaffold701-13782 4 75185096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778401 Affx-122975682 AX-385265516 4 42748621 ATCCATAGTGATCTGCACATTAAAGAAAAGCATGA[C/T]TGCAGTGCATTAGGCTTTTGATGAAATTCTCAACA Y 2 1 2 1 201000 f 74 goat snp49149-scaffold701-55997 4 75142909 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428894 Affx-122938929 AX-123299236 4 42785895 AGGCTAAGGAGCTGGGGTGAAGAAGAGGGATTATC[A/G]GGGGAAAGAAAAGGTGCAGACATCAACTCAATCTT R 2 1 2 1 101000 f 74 goat snp49150-scaffold701-93271 4 75105253 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439603 Affx-122930058 AX-123309940 4 42819993 TGGAAGCAGGAACAGGAACTCAGGCAGTGACACTG[C/T]GGGGCAGTTTTCAATTATAATATACAAATGGTCCA Y 2 1 2 1 201000 f 74 goat snp49151-scaffold701-127369 4 75071013 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426200 Affx-122940374 AX-123296546 4 42887471 GACGTTTCTCCTTATAGATTTGGTGCCAAACTGTT[A/G]AAACTGATTTTTTTCACTGGTCTTTATCTTCCTTA R 2 1 2 1 101000 r 74 goat snp49152-scaffold701-194847 4 75001538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453420 Affx-122919885 AX-123323753 4 42930436 AATTTAACAAATAGGTTTCTTTCCTAATAACCAAC[C/T]AGTTTACTTAAAACTCACTGTATTTTATTTGAAAA Y 2 1 2 1 101000 f 74 goat snp49153-scaffold701-237812 4 74958656 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426497 Affx-122940219 AX-123296843 4 42977739 AATGGCCTAACTACTGTGGCGGGATGCATGATCAC[C/T]ATTACTAGGCACAGAGGAAAATAAGGGAGTAAGTT Y 2 1 2 1 101000 f 74 goat snp49154-scaffold701-285115 4 74911591 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424367 Affx-122941845 AX-123294713 4 43008687 CAAGTTTGTGCAAAGAAGCATGTAGGACTGAATGA[C/T]CCAGCTGCCTCTGGAAATGTCCGCCCCTTCCTAGA Y 2 1 2 1 101000 f 74 goat snp49155-scaffold701-316063 4 74880894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799953 Affx-122941529 AX-385286879 4 43044637 AATATGCTTTATTCGCAGATTGTAAGCAGGTAAAT[G/T]GGTATTCACACCACACACCTAAATAGAAGCCTGTG K 2 1 2 1 101000 r 74 goat snp49156-scaffold701-352013 4 74844740 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446644 Affx-122924780 AX-123316980 4 43094745 AAGGATTTCTTTTTAAGTAAGTGTCTACAGTTGTG[C/T]AATAATCATCATAATCCAATTTTAGAACATTTAAG Y 2 1 2 1 101000 f 74 goat snp49157-scaffold701-402121 4 74793732 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405651 Affx-122956578 AX-123276003 4 43179323 GAGGGTGTCTTGTGAATCCTGGAATCATGGTGGAC[A/G]TGAGTACTATTCACTTCACTTTTCCTTTTCCATCT R 2 1 2 1 101000 f 74 goat snp49159-scaffold701-486699 4 74707779 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451983 Affx-122920934 AX-123322316 4 43232217 CTTGTCATGTTCCGCATTCTCTAGAGATGATCCCA[C/T]CTCCTTTAAAGACTTCAGTTACCACTTACATGTTG Y 2 1 2 1 101000 f 74 goat snp49160-scaffold701-539593 4 74653854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775673 Affx-122973877 AX-385262804 4 43267276 TAAACGAAACTAAGATTTTATCCTTTGTGGACCTA[G/T]AGGCAGTGAAATGGAGAACTGTTTTCAAAGAAATG K 2 1 2 1 101000 r 74 goat snp49161-scaffold701-574652 4 74618762 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384098 Affx-122972841 AX-123254456 4 43296575 ACCAAGGGGAAAAAAAGACAATCAATAGGTGCCAA[C/T]ATCAAAATTACAGAGATATTAGAATTATTTGATCA Y 2 1 2 1 101000 f 74 goat snp49162-scaffold701-603951 4 74589339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382394 Affx-122973841 AX-123252752 4 43347743 AGAGGACACAAAGCCTTTTTTCTGACCTCTTTCCC[A/G]CTGGTCATTCCATGGCCCTGAAAGTCTCACCTTTC R 2 1 2 1 201000 r 74 goat snp49163-scaffold701-655119 4 74537886 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427426 Affx-122940054 AX-123297769 4 43409242 ACACACTGGGGACAGGAGGTGGGAGATACTGCTGT[A/G]TTATATGGGGCATTTGGGGGAAGACCTCACTGAAT R 2 1 2 1 303000 f 74 goat snp49164-scaffold701-716618 4 74475613 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448990 Affx-122923109 AX-123319325 4 43440881 GCAAAGAAGTAGTGTATTCAAAAGCCTTGAGGAAT[G/T]ACAGAGCATGGAGAGTTTGCAGGGTCCAAGGGACA K 2 1 2 1 201000 r 74 goat snp49165-scaffold701-748257 4 74443741 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406326 Affx-122955452 AX-123276678 4 43492640 AGTAAATGCCAGGTTACTTCTTTTAGGACTTATTT[A/C]TTTTTGGCTGTGCTGTGTCTTCATTGCTGTGTGCA M 2 1 2 1 202000 f 74 goat snp49166-scaffold701-800016 4 74391333 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409423 Affx-122954122 AX-123279774 4 43522645 GAGAGGAAGTGCCACTAAAGAGGAACAGAATAGAC[A/G]TCAGGTACAGTCAGTTCGAAAATTTTGTTATCCAG R 2 1 2 1 101000 r 74 goat snp49167-scaffold701-830021 4 74361310 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453234 Affx-122920421 AX-123323567 4 43620341 TGGTGTCTAGCTCTTTGTGACCCCATGGACTGCAG[C/T]ATGTCAGGCTTTTTGATCACTTTCAGGATTTGATC Y 2 1 2 1 101000 r 74 goat snp49169-scaffold701-927717 4 74263204 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767909 Affx-122945177 AX-385255127 4 43659547 GAGCAGCAAAGGAAAATTCAAAAAGAAGCCACAAA[C/T]AGTGTCGAATTTTAAACTCTGTGTTCAGAAGGAGT Y 2 1 2 1 101000 f 74 goat snp49170-scaffold701-966923 4 74224181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787076 Affx-122956479 AX-385274103 4 43722181 ATGTGTATTGGAGGAGGTCAAAAGTATAATAAATA[A/G]TTTCCTTTCCCCTCACTCTGAGTTTAGCAACAGTG R 2 1 2 1 101000 f 74 goat snp49172-scaffold701-1029557 4 74160816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391806 Affx-122967030 AX-123262163 4 43772543 ACACTTGAACTGAAGGATGCATTCACAAGGGGTAG[A/C]GTAGGAATATTCCATGAAGAGATGATACAAAAGAA M 2 1 2 1 201000 r 74 goat snp49173-scaffold701-1079919 4 74110658 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788922 Affx-122925247 AX-385275935 4 43802533 AATGAGGTGCCCAGAGTTTCATAGGTAGTAACTTC[A/G]CAATAGATTTTGATCAACTAGTATTCTTTTTTTAT R 2 1 2 1 101000 f 74 goat snp49174-scaffold701-1109909 4 74080662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767541 Affx-122970964 AX-385254796 4 43835598 CTTATTTTTCTTCATTTTTGCTTCTACAAACGCAG[C/T]ATGCCCTCATAGTAGTATAGTAATACCTTCTTTAA Y 2 1 2 1 101000 f 74 goat snp49175-scaffold701-1142974 4 74047602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767257 Affx-122925338 AX-385254538 4 43874883 TACAAAACCAGATTCCCATTGGGAGGGAACAGTTA[C/T]TGTATCAGAAGCTGAGAATGGTGTCCACCTGAAAA Y 2 1 2 1 101000 f 74 goat snp49176-scaffold701-1182259 4 74008248 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435536 Affx-122933399 AX-123305876 4 43916112 ATGAATACACACTTTTCACAAGACATGCTATAATG[C/T]AAAATTCTTCCAATCTTCCTGTGTAGACAGACATT Y 2 1 2 1 101000 f 74 goat snp49177-scaffold701-1223488 4 73967107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782483 Affx-122942011 AX-385269559 4 43970228 GAAACTGAAAAGGCATTTGGAATAATTTTTTTATA[C/T]AGTCCACTTCTGAAAGTTTAGCTGTAAAATTATAA Y 2 1 2 1 201000 f 74 goat snp49178-scaffold701-1277604 4 73913208 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784805 Affx-122941833 AX-385271852 4 44018110 AACAAGAAATGGTCCTTTTAGTATCCATTTCCTGA[A/G]TCCCCTGAAAAGGAAATGGATTTCCTACAAGGCAC R 2 1 2 1 103000 r 74 goat snp49179-scaffold701-1325486 4 73865462 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409785 Affx-122952977 AX-123280136 4 44066046 TTGACTTGTGAAACTATAAACTAGCAACACCTTCC[A/G]AAGATCAATATGAAAATAAATTTCAAAGCATATAT R 2 1 2 1 101000 f 74 goat snp49180-scaffold701-1373422 4 73817109 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398993 Affx-122960950 AX-123269348 4 44098574 GGCATCATGCTAAATATGTCACATGAACTCTCATT[C/T]AACTTTCAGAGTAGCCCCAGGAGATACAAATCTAT Y 2 1 2 1 101000 f 74 goat snp49181-scaffold701-1405950 4 73784301 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796444 Affx-122967426 AX-385283394 4 44185014 GCCATTTAAATTGCTACCCATCTTCTGCTATTACT[A/G]TAAAGTACTCTCTAACAAACATCCTCATACAGACG R 2 1 2 1 101000 r 74 goat snp49183-scaffold701-1492390 4 73696976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409621 Affx-122953542 AX-123279972 4 44217641 TAGCAATTCCCTAATGAAATACTGGCCCTGGGCAA[C/T]GACATCAATGGCCACTAACATCACAAAAAAGAGAC Y 2 1 2 1 101000 f 74 goat snp49184-scaffold701-1525017 4 73664231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396067 Affx-122963443 AX-123266422 4 44286312 GCCTTGCTGCTCAGCTTGTGGCCAGCACACCAGTG[C/T]AGCAGCACTGCCTGGTGTCTTTTAGAAATGCAGAC Y 2 1 2 1 202000 f 74 goat snp49185-scaffold701-1593688 4 73594381 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395308 Affx-122964060 AX-123265663 4 44339136 AAAAAAGGGAAGATATAGGATGGCTCTGGTTTTGT[C/T]AAGGTTGTTTTTTAAATCCACACAAGATAAAGAAA Y 2 1 2 1 101000 f 74 goat snp49186-scaffold701-1646512 4 73541571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804574 Affx-986696743 AX-385291113 4 44354376 ATAGGGGTGTTCGACTGGTTGTCCTCCAATTCATG[G/T]GAGTGTTAGTAGGTCTGCTACTAGGATTCAGAATA K 2 1 2 1 600010 r 74 goat 4_44354376 4 44354376 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 320804253 Affx-986696747 AX-385290883 4 44361573 CTGAGCATTGACCATAGAATAGGCCTGGAAGAGTT[A/G]ACATAAGGGTTGTTTGATTTAAACGACCTGGAATT R 2 1 2 1 600010 f 74 goat 4_44361573 4 44361573 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 320804580 Affx-986696749 AX-385291119 4 44363618 CGAATCCTCCAATCATAATAGGCATTACTATAAAG[A/G]AAATTATGACGAATGCATGTGCGGTTACAACTACA R 2 1 2 1 600010 r 74 goat 4_44363618 4 44363618 Ancestral_priority_1043 ancestry 0.716 recommended IMAGE 10K 10K ancestral 38452769 Affx-122920254 AX-123323102 4 44391219 ATGCACCCTCACTATTTGCTGATGGATGGAGTTAA[A/G]CCAGAGCTGGTGATGACAAGGCTACCTTTTTCAGG R 2 1 2 1 101000 f 74 goat snp49187-scaffold701-1698595 4 73488864 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420035 Affx-122945145 AX-123290383 4 44423087 CTGTTGGCTTCTGCTGAAGCACTGATTTGATTAGT[A/G]GCATTCAGTGGAACTACAGACATGAGATGTTGAGC R 2 1 2 1 101000 f 74 goat snp49188-scaffold701-1730463 4 73456635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770826 Affx-122978894 AX-385257990 4 44490242 CCTTCTTCAACACTGACCAAAATTGTAGACTTCAT[A/G]CAAATGATCAAAATGCACTTACCAAAGTAAGACTA R 2 1 2 1 101000 f 74 goat snp49190-scaffold701-1797618 4 73389477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438805 Affx-122930798 AX-123309142 4 44529063 ATTTTTATCAGAATCGGTGGCTTGGGGTCTCCTCC[A/G]CCCACAGTGAGGGAAGGCTGAGCCGAACCTGAATC R 2 1 2 1 101000 f 74 goat snp49191-scaffold701-1836439 4 73350397 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413874 Affx-122949853 AX-123284223 4 44568872 ACTCGACACTCTGTCCAATCCCAAAGAAGAAGAAA[C/T]GGTTCACGTGGCCAAATGTGCATTCTTCAGACAGC Y 2 1 2 1 201000 r 74 goat snp49192-scaffold701-1876248 4 73310800 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797527 Affx-122971381 AX-385284466 4 44602696 TTTGGACATTCAGTTGAGGCTGTAAACAATGAGCC[C/T]GACCTTAATTCAAACACTAGGTGATTATGTTTGAC Y 2 1 2 1 101000 f 74 goat snp49193-scaffold701-1910072 4 73276829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414517 Affx-122949525 AX-123284866 4 44663471 GGAGCGTAGGGAGGCCAGGGCAGAAGGACAATGAA[C/T]GAGAAGAGTTAGTAGATGAGCTCAGACAGGTAAGG Y 2 1 2 1 101000 r 74 goat snp49194-scaffold701-1970847 4 73216548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393199 Affx-122965507 AX-123263556 4 44738239 TCCTCTTTAAAAAATGTATATCAAAGAGAAAAGAA[C/T]AGAAACATTAAGTATTTTGCACTGTGGGAGTACAC Y 2 1 2 1 103000 r 74 goat snp49196-scaffold701-2045615 4 73141882 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436914 Affx-122933204 AX-123307252 4 44777377 CTACTTAAGAAGAAAAGGGTTTATCAGAAAATAAG[C/T]TCCATGAGCACAGAGGCCAGCTTGTTCTCTGCTGC Y 2 1 2 1 201000 f 74 goat snp49197-scaffold701-2084753 4 73102420 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415861 Affx-122948857 AX-123286210 4 44811194 TTGTATGGAGAGTTTGTCCGTTGGGTGAACATGCC[A/G]TCCATCCTGTCCCCCAAGGCGTTGAGTGAGCTCAT R 2 1 2 1 101000 f 74 goat snp49198-scaffold701-2118570 4 73068203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795459 Affx-122962736 AX-385282415 4 44852368 TTAAGCTGGCGGGATGTATTAACATTATTCAACAG[C/T]ACCCTGTTTGTGGACTTCCTCTTTGCTACCAGTGT Y 2 1 2 1 101000 r 74 goat snp49199-scaffold701-2159744 4 73027129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390872 Affx-122967810 AX-123261229 4 44909240 AACTTAATGAAAAATATAACAATCAAAACATCTAA[A/G]ATAAGTACACTCACTACCCATTCCACTAATTCATT R 2 1 2 1 101000 r 74 goat snp49200-scaffold701-2216616 4 72969700 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430545 Affx-122937025 AX-123300886 4 44949544 CAAAAAAAAACAAATCAACAATTTAGTTTGTTTTG[C/T]TCTGTTCCACCAATACAACCAAAGCTGCTAGCTCC Y 2 1 2 1 101000 r 74 goat snp49201-scaffold701-2256920 4 72931108 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453582 Affx-122919760 AX-123323915 4 45016894 CTGCCTGCTAGTTTCTCTAATTCCTAAACCGCACA[C/T]GCATGAGACAGATTCAAGGCATCTTAGCTAATGAC Y 2 1 2 1 201000 r 74 goat snp49202-scaffold701-2324270 4 72864751 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776343 Affx-122968074 AX-385263471 4 45091720 GCACTTACTCAGTGTTTCTAGGCCATGGTTCCTTC[A/G]CTTATAAAATGGGGAGAAGAGTCCCAACCAGTAAA R 2 1 2 1 102000 r 74 goat snp49204-scaffold701-2399096 4 72789884 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272271 Affx-1111833427 AX-519546010 4 45095773 TCTAAACTGGGTGAGACCAATGGTGTTGAAGGGTC[A/C]GAGGAAGGAGTTAATTTTCTGGTTATGTCTTAAAG M 2 1 2 1 101000 f 74 goat 4_45095773_AF-PAKI 4 45095773 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38432971 Affx-122935273 AX-123303312 4 45130748 GTAAATGTCTGGAAATGTCTACTGCAAAACAGTTG[C/T]GAGAAAGAGAGTGAGAGAAACATTTTTTAGCAACT Y 2 1 2 1 201000 f 74 goat snp49205-scaffold701-2438124 4 72749905 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392169 Affx-122966308 AX-123262526 4 45199232 AAATGCCTGGTGGTTATGCTTATTGCCACCCAAGA[C/T]TGCCTCTGGGGAACTTACACACTCTATCAATGATG Y 2 1 2 1 101000 f 74 goat snp49206-scaffold701-2506608 4 72680277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774199 Affx-122960195 AX-385261336 4 45258389 AAGGGCTGAATTCAAAAGCTTTCTGTTCAAAAAGC[G/T]AAGTTTCTCCTCTTCTTATCTTACTGCTGTACTGT K 2 1 2 1 101000 r 74 goat snp49207-scaffold701-2565765 4 72619696 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394682 Affx-122964361 AX-123265037 4 45292967 TGACACCACAATTCTAGTTCTAGGAAAATTTCCAA[C/T]AGATGAAAGGCATATTTGTTCAAAAACTTACTAGA Y 2 1 2 1 101000 r 74 goat snp49208-scaffold701-2600343 4 72585446 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396226 Affx-122963346 AX-123266581 4 45326121 ATCACCCCCCAGACAATGCTCCATCTCCCACTCTA[A/C]ACTTCACCAATATCCTGGTTTTCAACATCATAGGT M 2 1 2 1 101000 r 74 goat snp49209-scaffold701-2633497 4 72541454 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801507 Affx-122954587 AX-385288416 4 45360621 GCTAACTCTGACTTTGTTTTATACTTTAGTACTAA[C/T]AAAATCTGACATCTATTAACTCAAACCTAGCCAAG Y 2 1 2 1 101000 r 74 goat snp49210-scaffold701-2667997 4 72507000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790916 Affx-122921732 AX-385277913 4 45378364 GAGTATACTGAATTTACGAAACTGTATCAAGCTGA[G/T]CTCATACTTTTCATACATCCACTTTTTAGTATGTG K 2 1 2 1 101000 f 74 goat snp4987-scaffold117-1975 4 72488465 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795915 Affx-122946484 AX-385282867 4 45413074 CCTGAAATTTTTGTTAACTTTGAGCATTGGTTATA[A/G]CATTGGTTTTCAGTGACAGGACATAGACTCTCCTA R 2 1 2 1 101000 r 74 goat snp4988-scaffold117-36685 4 72453299 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432394 Affx-122935849 AX-123302735 4 45441758 TTGCCAGAATGAATTTTATTATCTGTAATTGAACC[A/G]TGACTAATACAATAAATGAAATCAGCAGTGTGGTT R 2 1 2 1 101000 f 74 goat snp4989-scaffold117-65369 4 72424614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405758 Affx-122956500 AX-123276110 4 45522178 CTTCTTAAAGTCATGGATTTTATATCAGAAATGGA[C/T]ATTAGAGATCAGCCTCGTCATCAAAGTGGAAAAGA Y 2 1 2 1 101000 r 74 goat snp4990-scaffold117-145789 4 72342981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793629 Affx-122924816 AX-385280603 4 45560486 GGTAAATCTTGGCACTGGTGGCAAATAGACTGATA[C/T]GGCAATTTAACTATAGTAATCATAGAATTTTCAAA Y 2 1 2 1 101000 f 74 goat snp4991-scaffold117-184097 4 72304947 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414649 Affx-122949320 AX-123284998 4 45639441 TCTCAGAGTCTCGCCCCTTTCTGCCGTCATCTGCT[A/C]TAGAAGCTGTGCTGCATTTTCAAGCTCTACTTGAA M 2 1 2 1 101000 r 74 goat snp4993-scaffold117-263052 4 72226163 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386817 Affx-122970103 AX-123257175 4 45698905 GAAAATAGGTCATTTTGATTTATGACCCAGCTATC[A/G]CTAGAAATTCCAGGTGCTTTAGAGACATTTTCTCA R 2 1 2 1 101000 r 74 goat snp4994-scaffold117-322516 4 72166692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440460 Affx-122929390 AX-123310797 4 45740281 TACTTCCAGCTTGGTGTCAATTCTTGTTAAAAGGG[C/T]AACCTTTAGGTGTTAGAATGATAGTGGCATATTGT Y 2 1 2 1 101000 r 74 goat snp4995-scaffold117-363892 4 72125389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421244 Affx-122944112 AX-123291591 4 45800002 GCATAGGTATTCACTAAGCTCCTGACCTCTGTGCC[A/G]GGTCCTTAGGTGAACAAGATGGAAGGTCCTCATTT R 2 1 2 1 201000 r 74 goat snp4996-scaffold117-423613 4 72065859 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787260 Affx-122969222 AX-385274286 4 45844814 AAATGGTATAAAACATCTTATGCAATTTTAAAATC[C/T]TTTATATTTTTGCAATAAAATACCTTTTGATTTCT Y 2 1 2 1 303000 r 74 goat snp4997-scaffold117-468425 4 72020600 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777394 Affx-122978088 AX-385264516 4 45875914 GGATTAACAATTGTGAGAATAGCAAAAAAGTTAAT[A/G]TTTGGAATGACTTGAATAAAGCGATTTTTTCCTGA R 2 1 2 1 101000 r 74 goat snp4998-scaffold117-499525 4 71989455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800142 Affx-122924174 AX-385287065 4 45920848 TCAATTAATGCAAACTTTCTAGATTTTACATGACA[C/T]GATACAATATTAACTCTAAAAGACTGTGGGAAGTT Y 2 1 2 1 101000 r 74 goat snp4999-scaffold117-544459 4 71944424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423447 Affx-122942596 AX-123293793 4 45949887 ACTATAAGAGTAACACTGTAAAATCTTATTAATTC[C/T]AATGGGGCCATGTCTTCACTTAGCCTGTTTCTACA Y 2 1 2 1 201000 f 74 goat snp5000-scaffold117-573498 4 71915245 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446045 Affx-122925840 AX-123316382 4 45987619 AAGAGTCAGACACAACTGAAGCAACTTAGGACAGA[C/T]GGACAGATGAACTAGATGAGAGGGAACCAGGTGTA Y 2 1 2 1 201000 r 74 goat snp5001-scaffold117-611230 4 71877286 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395224 Affx-122964483 AX-123265579 4 46018879 AATACAAAAATGGGAAGAGGAGAAAACTTTTTTAA[C/T]AGGCATTAAAAAACACTCTGGGGAATTTTTTCAAT Y 2 1 2 1 101000 f 74 goat snp5002-scaffold117-642490 4 71845463 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770263 Affx-122927749 AX-385257429 4 46101273 ACTTGTCAAAGGTTACAACAAGTGAAAGGCTAACA[C/T]AAGTTCTGAAAATTGTTAGCTTTTATAATTTGTTA Y 2 1 2 1 101000 f 74 goat snp5003-scaffold117-724884 4 71762650 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776668 Affx-122952592 AX-385263795 4 46130264 ACTCTAGAAGTATAACTATGATCATAAAAATACAA[C/T]GAACCTCTAAATTCACCTATAACCAATCTCAATTT Y 2 1 2 1 101000 r 74 goat snp5004-scaffold117-753875 4 71733694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394581 Affx-122964439 AX-123264936 4 46162620 AGTGACTGAAAAACAACAAAACCACAGAAATTAAA[C/T]GACAGAACAATTGTAACCACAGTTAACATATTTTG Y 2 1 2 1 303000 r 74 goat snp5005-scaffold117-786231 4 71701451 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423454 Affx-122942590 AX-123293800 4 46234541 TTATGATCCTGGCCTGGTCAGCAAGTCAAGTCTAA[C/T]GACAGAATAGCATACAGAAAAACAGAAATTACACC Y 2 1 2 1 101000 f 74 goat snp5007-scaffold117-858152 4 71629534 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794352 Affx-122964450 AX-385281316 4 46267940 GAAGGAAGTATGTTAGCCTAGACTACATGTAAATG[A/G]TTTTTCTGCTCTTGCCTCTCCCTCCCCATTTGAAA R 2 1 2 1 101000 r 74 goat snp5008-scaffold117-891551 4 71596049 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788765 Affx-122978643 AX-385275780 4 46302695 TGTTCATGGACAATTGATCTTATTATTTTTACAGG[C/T]AGTCACCCGCTTCACGGTACCTGATGAATTAGCAT Y 2 1 2 1 101000 r 74 goat snp5009-scaffold117-926306 4 71561084 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387660 Affx-122969841 AX-123258018 4 46334541 TGGTCTAATTGCAGGGAGGGCATAGAAAGAGAGGA[A/C]AGGAAGGGGAGCCAGGGAGACTGCTCTTTCTAGAA M 2 1 2 1 101000 f 74 goat snp5010-scaffold117-958152 4 71529210 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395640 Affx-122963789 AX-123265995 4 46368965 AAACATCTTCCTTGGCTCCCTCCATTACCTCTCCA[G/T]TAATCTTTGAGGAATTACTTCTATTCTTGGAAGAA K 2 1 2 1 201000 r 74 goat snp5011-scaffold117-992576 4 71494659 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791235 Affx-122945200 AX-385278229 4 46415107 TAAAGATGGAATTTTTTGTTATTGATAGATTTAGA[G/T]AAGAGGAGAAACTATAAGAACCTTTTACCTTTTGT K 2 1 2 1 101000 r 74 goat snp5012-scaffold117-1038718 4 71448582 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435155 Affx-122933666 AX-123305495 4 46472632 GAAATCTTGGGCAGCAAGACGAGAGGGTGCAGAGA[C/T]GAGCAGGAGGATGGAGGGTGCAAGGGAAAATGCAG Y 2 1 2 1 101000 f 74 goat snp5013-scaffold117-1096243 4 71390889 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382289 Affx-122973920 AX-123252647 4 46530584 AAAAAGTCTCTCTCCCCCCAGTACACATCAAAACA[C/T]GATAAACCTTATCATGTAGCTCTTATATTCATTCA Y 2 1 2 1 102000 f 74 goat snp5014-scaffold117-1154195 4 71332892 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378037 Affx-122977572 AX-123248396 4 46582345 GGAAAACAGTATAGGAACAGTCTACTAAAATCTTC[A/G]CCAAGAATGCTTTTAGTTTAAGATCTGAAAAATAA R 2 1 2 1 101000 f 74 goat snp5015-scaffold117-1205956 4 71280968 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774560 Affx-122956761 AX-385261694 4 46612646 AAGCAGTTTCCTCGAACCACCATATCATAAACCGC[A/G]TAATAATACTTTTCTCTGATTTCCATTCTGGAATC R 2 1 2 1 201000 r 74 goat snp5016-scaffold117-1236257 4 71250672 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389057 Affx-122968608 AX-123259415 4 46678254 TCTTGGGGCACTAGAGTCCTTTTCTTCTCTTCCTT[A/G]CCATCATATCTTTTTAACGTGATATATATATATTT R 2 1 2 1 201000 r 74 goat snp5017-scaffold117-1301865 4 71185023 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776055 Affx-122960099 AX-385263185 4 46734106 TTACTTATGTCCGGATGTTAGGGTAGCGAATGTCA[C/T]GGAAAGATAAGTCTGAATCAGGTCTTAAGGGATGA Y 2 1 2 1 101000 f 74 goat snp5018-scaffold117-1357717 4 71127942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438869 Affx-122930750 AX-123309206 4 46767316 ATGACCTCACTGTGGTGAACTGGGATATAGCTTAG[C/T]GTGCTAGGGTGAATGGCTTGGGGAAAGGTTTGTTG Y 2 1 2 1 101000 f 74 goat snp5019-scaffold117-1390927 4 71094464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430768 Affx-122937488 AX-123301109 4 46819395 CAAAGTACCATTTTATAATTCCACCAACGATGTAG[A/C]GTCCATTTTCCCTAGATATGTTATCGTTGTATTTT M 2 1 2 1 101000 f 74 goat snp5020-scaffold117-1443006 4 71042384 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777520 Affx-122939737 AX-385264639 4 46877379 TGTGTTTTTTCAACCAGAGTAAAAAGTTACCTCAC[C/T]ATGAACATGGAAGACAGCTCAACTCACAAAGCCAC Y 2 1 2 1 101000 r 74 goat snp5021-scaffold117-1500990 4 70984442 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804261 Affx-986696751 AX-385290889 4 46890119 ACCTTATGACTACTTGACAGTGGTTGCTGAACATC[A/T]TGGCTAATCAATATTGAATTATATATTGCAATTAA W 4 1 2 1 600010 f 74 goat 4_46890119 4 46890119 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 320790999 Affx-122972518 AX-385277996 4 46950271 TAACTATACAGATTCCAATGTAGGAACAAAATGTC[A/G]TCAGCAGTAGTAACAGATGCAATCTTCAAATGCAA R 2 1 2 1 101000 r 74 goat snp5022-scaffold117-1573882 4 70911492 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784350 Affx-122978771 AX-385271401 4 47001393 AGTTCCAGATCACTGACCAAAGTCAAGATCAAATA[C/T]GAAGCTGTCCATTTAAAAAGAGGTCATCTTTAATG Y 2 1 2 1 101000 r 74 goat snp5023-scaffold117-1625004 4 70860114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795064 Affx-122927543 AX-385282023 4 47041199 CAAAGGCAGGATTATCCCATCAGGAAAAAGATGCC[A/G]TGAGATGAAATAGGTGCCCTAATAAAAGCAAAACT R 2 1 2 1 101000 f 74 goat snp5024-scaffold117-1664810 4 70820532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796953 Affx-122922103 AX-385283894 4 47071258 AGTGATTGAACAAGAGGCACATACACTGATTTCAT[A/G]TCTCCTCACTTGTTGAAGAGAACACTCCTCAGATT R 2 1 2 1 101000 r 74 goat snp5025-scaffold117-1694869 4 70790492 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766013 Affx-122975497 AX-385253433 4 47106610 TAGCTCTATTCTGAAGTAGGGCATGATAAGATCCA[C/T]GTATCATATGCCTTATGAAATAATTCAAGAAAAAA Y 2 1 2 1 101000 f 74 goat snp5026-scaffold117-1730221 4 70755209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802024 Affx-122922192 AX-385288928 4 47159063 TCTTTTCATTTTTCTTGACAAATCTAAACATGGTA[A/C]AGGATTTATATGGCAGATAGATAACACAACAAAGA M 2 1 2 1 101000 f 74 goat snp5027-scaffold117-1782674 4 70702058 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396070 Affx-122963442 AX-123266425 4 47187873 CCCCATCACTTCATGGCAAACAGACAGGCAAACAA[C/T]GGAAATAGTGCAAGACTTTATTTACCTGGGTGTGG Y 2 1 2 1 102000 r 74 goat snp5028-scaffold117-1811484 4 70673267 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377246 Affx-122978151 AX-123247605 4 47225853 TGCGTTAAAGGTTATAGAGTTTGGGGCCTTTTAAA[C/T]ACCTGTAGCTGAACATGAGTAATATGATTTGGGGC Y 2 1 2 1 101000 r 74 goat snp5029-scaffold117-1849464 4 70634699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416755 Affx-122948187 AX-123287103 4 47254994 TTTAAAGGTTTTGTTTTAAAGCATTTTCCATATAG[C/T]ATATATGCATTATTCCTGATAGTCTCCACATCCCA Y 2 1 2 1 303000 r 74 goat snp5030-scaffold117-1878605 4 70605754 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791335 Affx-122963054 AX-385278328 4 47288022 CTCAATACAATAAGCCTATTTGACCAGCTTTCTTA[C/T]ACCTTCCATACCAAAGGGCATACCTACCACTATGG Y 2 1 2 1 101000 r 74 goat snp5031-scaffold117-1911633 4 70572499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449048 Affx-122923065 AX-123319383 4 47323189 TTGGATGCTGCTCATTCTGGAAGGGAAGGCTCTCA[C/T]AGACTTCTTGTTATAAGGTATCCAATAGGTAATAT Y 2 1 2 1 201000 r 74 goat snp5032-scaffold117-1946800 4 70537123 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451192 Affx-122921330 AX-123321526 4 47362294 AGATTTAATTGGAAGCCGGTGGGTCTGATGCTCAG[A/C]GAGTGATGCTTCTAAGGTACCTATTGTGGAAGAGA M 2 1 2 1 101000 f 74 goat snp5033-scaffold117-1985905 4 70498581 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430588 Affx-122936993 AX-123300929 4 47407342 TATTAGCCATGGTACTGCCATATTTCAACTTTCCA[C/T]GGTATAACAAGAAAATCATTGCTTTTACTCTGTAC Y 2 1 2 1 101000 f 74 goat snp5034-scaffold117-2030953 4 70454847 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445777 Affx-122926061 AX-123316114 4 47495564 ATGTGCACTAAATATAAGACTATGGGAGGCATTTA[C/T]GCTTCTTATCATGATATCACTATGTTTTGAAAAAT Y 2 1 2 1 101000 r 74 goat snp5036-scaffold117-2119175 4 70364733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399075 Affx-122960887 AX-123269430 4 47538256 TGAATTATTAAACATTTACATCTGACTGGTCACAT[A/G]GTATTGTTTCTCTAAAAGTACACACCATTGATTTG R 2 1 2 1 101000 f 74 goat snp5037-scaffold117-2161867 4 70320842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803161 Affx-122971501 AX-385290024 4 47605452 TAGAGCTGCTTTTCTAGACATTGTATTTAACTTGG[A/C]GTATATAAGACATAAAGTAAGCCAGGGCTGTTTTG M 2 1 2 1 101000 r 74 goat snp5038-scaffold117-2229063 4 70262476 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272272 Affx-1111833428 AX-519546011 4 47628976 CCCTGTTGTTTTGTTTACTCAGGTTCTCCTCTGCA[A/G]GAACCATCTCACCTTGACCCCAACTAACAAGGAAA R 2 1 2 1 101000 f 74 goat 4_47628976_AF-PAKI 4 47628976 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795318 Affx-122976574 AX-385282276 4 47639969 ATTTATTTTATCCAACCAAGTGTCATGGACTTTAG[G/T]CACAGAGGTCCTATTACCAGATGGAAAGTCAGTGT K 2 1 2 1 101000 r 74 goat snp5039-scaffold117-2263580 4 70228051 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777552 Affx-122933764 AX-385264671 4 47678708 ACAAACAAAATCTACACAACTGGGTGAAGCCCACT[A/G]TGGAAATAATTTAGAGCCTATCAGTGCATCCTCTC R 2 1 2 1 101000 f 74 goat snp5040-scaffold117-2302319 4 70131233 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772569 Affx-122974495 AX-385259717 4 47769513 GTATGATCTTAGGCAGGTCAGTTAAGGTCTGGTCC[A/G]TCCTTCCTCTGCTCATGCATAAATGGAGATGATTA R 2 1 2 1 101000 f 74 goat snp31311-scaffold345-7623023 4 70030303 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375540 Affx-122979101 AX-123245899 4 47802445 AACACAAAAGTATAGCATTTTGAGGGGGACAGTAT[A/G]CTAGTGATCAAAGTCAACATCTTAAACTCCATGAT R 2 1 2 1 101000 f 74 goat snp31310-scaffold345-7590091 4 69997263 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385426 Affx-122971327 AX-123255784 4 47837380 CACTAAATTCACAATGGACTTGGATCTTTCAAAAA[C/T]GTTTTTAACTGAACAACTCTTTACTGGCAAACAGA Y 2 1 2 1 101000 r 74 goat snp31309-scaffold345-7555156 4 69962352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802304 Affx-122950626 AX-385289208 4 47900653 AATTTATTTGCCAGGTGTTGAACTCATTAGGTTTA[C/T]ACAATTTAAAGGTGGTAAGTTTTCAACTGTGAAAA Y 2 1 2 1 101000 f 74 goat snp31308-scaffold345-7491883 4 69898188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444287 Affx-122926762 AX-123314624 4 47929698 CGAAAACAAGACAAAAACAAACACACCAAGCACTG[C/T]GGGCCTGCACAGTTCTTTTCTTTTTAGTGCCAAGC Y 2 1 2 1 101000 f 74 goat snp31307-scaffold345-7462838 4 69868879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278232 Affx-1111836240 AX-519551720 4 47961346 GACTAAACAACAACAAAAATTACCATTTGTGAAGT[C/G]CCCACTCCATAAAAGATAGCTGAATGGCAGAAGTA S 4 1 2 1 102000 r 74 goat Random2.2K-437 4 47961346 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391073 Affx-122966840 AX-123261430 4 47984758 ATGTCGATTTTCACTCCTTTTCTTACACTTTATGA[C/T]GGAGAATTGCATTTTCCCGTAAGTGACAGATAGCA Y 2 1 2 1 101000 r 74 goat snp31306-scaffold345-7407778 4 69812824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784372 Affx-122944794 AX-385271422 4 48028845 AGAGCAAAACCATTACAACTGCTTTTTAACTGAGT[G/T]TTTAACTCAATGGAAAGACCAGGTTTTCAAAAAGG K 2 1 2 1 101000 f 74 goat snp31305-scaffold345-7363691 4 69769412 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278235 Affx-1111836241 AX-519551722 4 48031805 TTTGTCCTGGTGAGAGGCTGAAGACTAAGAAAACC[A/G]GGTTAATACAGTTCAAGCAGAGAGACCTGAAAAAT R 2 1 2 1 101000 r 74 goat Random2.2K-438 4 48031805 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452509 Affx-122920972 AX-123322842 4 48080751 CCTGAAAACTTTCAAAGAAAACTTTCACAGAAATA[C/T]AAGCAATCTAGAACAGACAAGACAATTCTCATAAA Y 2 1 2 1 201000 f 74 goat snp31304-scaffold345-7311785 4 69717464 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440997 Affx-122928965 AX-123311334 4 48114220 AGTCAGGCAGATCAGTAGGCAATAATCTAAGCAGT[A/G]GCTTTCTCTATAAGGAAGCGCAGAATGTCAGAAAG R 2 1 2 1 101000 r 74 goat snp31303-scaffold345-7278316 4 69683931 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385828 Affx-122971016 AX-123256186 4 48147408 AATTGCTGGGTAGAAATCTTCTCACCAAGAATGGA[C/T]AGTTTCGCACTAGTGAAACAGATTTTCAAGGGTTA Y 2 1 2 1 101000 f 74 goat snp31302-scaffold345-7245128 4 69651699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378816 Affx-122976552 AX-123249175 4 48179781 ACATTTATTATTATATATTCTATGGATGATTTAAA[C/T]ACGTATTTATGTAAACATGGGCTTTTCTGTTTAAG Y 2 1 2 1 202000 f 74 goat snp31301-scaffold345-7212755 4 69619376 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793203 Affx-122952927 AX-385280181 4 48210870 AGCAGTTTCGATTTAATACTGGCACTTTTTTTCAC[C/T]GCGATCTTGCAGATCCTGTCAGCTTAACTGGGCTT Y 2 1 2 1 101000 r 74 goat snp31300-scaffold345-7181666 4 69588270 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800302 Affx-122960744 AX-385287225 4 48270818 TTAACATGAGTACAGGTACTTATTTCCCAGTATAA[C/T]AGCTGTGTTTTCTAAGTATAATTTTGGAATTTCAT Y 2 1 2 1 101000 r 74 goat snp31299-scaffold345-7121718 4 69527205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393382 Affx-122965906 AX-123263738 4 48304297 CGGGGAGTGAGTAATTCATAATATTATCTGGCCAC[A/G]TCGTCCGTTCACTATTTCAGTGGCTGAAAACCTAA R 2 1 2 1 101000 r 74 goat snp31298-scaffold345-7088239 4 69493551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442192 Affx-122928797 AX-123312529 4 48341174 ACAGCAGAGTGCCACCTCTGGAATCAAACTGACCT[A/G]GCTGTGAATTTTAATTCTGTGTTCTTAACACTATT R 2 1 2 1 101000 f 74 goat snp31297-scaffold345-7051362 4 69456648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451318 Affx-122921279 AX-123321651 4 48374020 CATGACACAAGGCATGTGTCTCGAAGCCAGTTCTT[A/G]TTAGTGAGTGCTGTGGAAACAAGGTGGGTTTTGGC R 2 1 2 1 201000 f 74 goat snp31296-scaffold345-7018516 4 69423953 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438759 Affx-122930815 AX-123309096 4 48412389 AAATTGAGATACACATCAGTAAAACTTGGGTCAAA[A/C]TACTTTTTTCATTTAAATCTCTTAAGCCCCAGAAG M 2 1 2 1 101000 f 74 goat snp31295-scaffold345-6980147 4 69385636 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388827 Affx-122968893 AX-123259185 4 48475270 AGGTGGCACTCATGAAGGAATTCTTTTTTCCTAAT[A/C]TATTAATATTAGCTGACTATGGAGTAGGAAATGGC M 2 1 2 1 101000 f 74 goat snp31294-scaffold345-6917266 4 69322970 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430543 Affx-122937027 AX-123300884 4 48523382 CGTGGACTTACTGCTATAACACTGGAATGTGGGGA[A/G]ACTTTCCACATGAAAATAAAATTTTAGCACCGTTC R 2 1 2 1 101000 f 74 goat snp31293-scaffold345-6869154 4 69274572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785505 Affx-122931960 AX-385272550 4 48558787 AGATCTCAAAGTTTGGGATAAGAGGCAGACCTACT[A/G]TTATAACCAAATTATTCACAGGGACATATGAAAAA R 2 1 2 1 101000 f 74 goat snp31292-scaffold345-6833749 4 69239490 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414307 Affx-122949581 AX-123284656 4 48588819 CTCAGCGCATCTCCCAGAAGAGGGGAGTTAGAAAT[A/G]CATGGAGTGTGACTGTCAGCTTAGAGGCCTTTCCT R 2 1 2 1 101000 f 74 goat snp31291-scaffold345-6803717 4 69209489 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400538 Affx-122960440 AX-123270893 4 48619228 AGATTTCTCCACATAATATCAAACACCCTAAATCA[C/T]ATTTTCACTAAAACAGTCATCTGACGGTCAACAGA Y 2 1 2 1 101000 f 74 goat snp31290-scaffold345-6773308 4 69179248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800130 Affx-122971759 AX-385287053 4 48651867 AAATATGATTCTCAGTTACATGCTAATATTAATGT[A/G]TCTCAAGACAACCAGCTCTCAGGGACCATTAGGCA R 2 1 2 1 101000 r 74 goat snp31289-scaffold345-6740669 4 69148668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452269 Affx-122920761 AX-123322602 4 48689037 AAAAAGATTCTCAGCAGTTCCCCCCAAAATGCCTG[C/T]GTTCTAAAAGAATTACATGAAGAATTAAGGAAATC Y 2 1 2 1 201000 r 74 goat snp31288-scaffold345-6703499 4 69111475 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451642 Affx-122921607 AX-123321975 4 48721716 TTGGGCAATTGAGTCCTAGATTCTGAGACAAAAAC[C/T]TGGGTTCCAGTTCTGGCTCTGTCATTTACTAATCA Y 2 1 2 1 201000 f 74 goat snp31287-scaffold345-6670820 4 69078372 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425248 Affx-122940993 AX-123295594 4 48765436 GCAAATAATAGATTTATTGGTTATTACCTTGTTGC[A/G]TCAGTAGTGATGAAGCACAGTTTCATCAGCATTAT R 2 1 2 1 101000 r 74 goat snp31286-scaffold345-6627100 4 69033701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278237 Affx-1111836242 AX-519551725 4 48793857 CCAGTCTGCAGTCCCAGCTCAGAATTCTGCTCCAG[A/G]ATCTCTGCAGACCTTGGGAAGAAGGGCTGAAGGAA R 2 1 2 1 202000 r 74 goat Random2.2K-439 4 48793857 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795589 Affx-122951358 AX-385282544 4 48806815 TAGAGTATATCTTGAGGAGTCAAACACTCTTTAAG[C/T]GTTTCGTGTTCAGTGTGTTTTCCAGGAGTGTAACT Y 2 1 2 1 101000 r 74 goat snp31285-scaffold345-6585721 4 68993561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449916 Affx-122922925 AX-123320251 4 48837832 CACATTTTAGCCCAAATGTCATTTTCTGAAATGAT[A/G]CCTTCTATAGCTTCCCAACCTAAGCCCTCTTGTTT R 2 1 2 1 101000 r 74 goat snp31284-scaffold345-6554704 4 68962432 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422521 Affx-122943285 AX-123292867 4 48870093 CAGGAGAGATTTTAGCTGTCTTCACTGTTATGGTT[A/G]TCAGACCCTTTCTCTTCACATTAACTTGATTATTT R 2 1 2 1 201000 r 74 goat snp31283-scaffold345-6522443 4 68929920 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433658 Affx-122934568 AX-123303999 4 48901926 CCTATAACATGAGGATAATACCTCACAGGGTTATC[A/G]TATGGGTTAGGTAAGTTATTAATGCATGATTCAGA R 2 1 2 1 101000 r 74 goat snp31282-scaffold345-6490610 4 68898194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409492 Affx-122954050 AX-123279843 4 48985097 TAGTTATTTGTATTTTTTTGTTGTTGTAATTGTTG[C/T]TTATGTATCCTGATACAAGTCGTGTCAGATACATG Y 2 1 2 1 103000 r 74 goat snp31281-scaffold345-6407439 4 68813339 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404324 Affx-122957011 AX-123274676 4 49081017 AAAAGGCATTAGGGAGGTGTGTAGTAAACAAAGAG[C/T]CCATGGTTTTTCATTGTCTGAGTCCTTGCCAGAAC Y 2 1 2 1 101000 f 74 goat snp31279-scaffold345-6311519 4 68717040 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440610 Affx-122929975 AX-123310947 4 49116518 TTTGAGACTCCAATACAATTATTCAGAGGAACCTA[C/T]GTACATGCCATGAAGGAGAAAAGCAGAGAGGTGGG Y 2 1 2 1 101000 f 74 goat snp31278-scaffold345-6276018 4 68684141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278084 Affx-1111836243 AX-519551574 4 49148629 AGGTTGATGGTGAGCTAACAGGGTGTCATCACAGC[A/G]GTTAACATTATCGATCCTTAGTAGCTAGTAGGTCT R 2 1 2 1 101000 f 74 goat Random2.2K-440 4 49148629 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320767936 Affx-122968130 AX-385255152 4 49154243 AAACACACAAAATGAGAATTACAGTCCTAAGGGCA[G/T]AACTCTAGTGCAGGCAGATAACTCCTGAAGTGTAC K 2 1 2 1 101000 f 74 goat snp31277-scaffold345-6238293 4 68646628 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421566 Affx-122943851 AX-123291913 4 49206464 CCGGCTTCCTCTCCGTGTCTCCCTTCAGTGGTTCA[C/T]ATTCAGACCATTCAGTCAGGTTCATCCTAATCAAA Y 2 1 2 1 201000 r 74 goat snp31276-scaffold345-6186072 4 68594388 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767752 Affx-122970476 AX-385254979 4 49237253 TGAAGGCTCTCTCTTGAGAGCACATCTCCAATGCT[A/C]GCTATGCCTTCAGAGAAGTCTACAGAGGATATAGT M 2 1 2 1 101000 f 74 goat snp31275-scaffold345-6155283 4 68563612 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447107 Affx-122924478 AX-123317443 4 49352353 CATAGTAAGATTCTTCCCTGGGGGACTTTAACCTT[A/C]AGTTATGCTTTTATTTCCATACACCTGTTGGAATT M 2 1 2 1 101000 f 74 goat snp31273-scaffold345-6040183 4 68448334 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431256 Affx-122937122 AX-123301597 4 49384144 CCTATTCCACTGGTGATAATGACATAAGTTAGACT[A/G]CAATTTAGTTCCAATAAAACTTGTTTCTTCTTTCA R 2 1 2 1 101000 f 74 goat snp31272-scaffold345-6008392 4 68416324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392530 Affx-122966108 AX-123262887 4 49422061 CCCTTTGCTCTTGAGTCCCAGATGACTCTCTCAAG[C/T]ATTAAAGGTCACCTAACAGACACCAAAACAGTAAT Y 2 1 2 1 101000 r 74 goat snp31271-scaffold345-5970475 4 68379011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451873 Affx-122921060 AX-123322206 4 49458643 ACTCTTCCCCTTACTCCATTGTAGTCTCACAGGTC[C/T]TATTTTGCCAACTCATCAAACATGACCAAGGTTCT Y 2 1 2 1 201000 r 74 goat snp31270-scaffold345-5933893 4 68342480 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781602 Affx-122923202 AX-385268686 4 49495337 TCTGGCAGGATAGCAACTAATCAGAAAGTAGAAAC[A/G]CATAAATGCCGTTAAAATGAGAAACCACTTAAGGT R 2 1 2 1 101000 r 74 goat snp31269-scaffold345-5897199 4 68306024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425074 Affx-122941253 AX-123295420 4 49528341 ATGTTACAGCCTAGATGCTTCCTGAGGCCTCAGGA[C/T]GTTGAAGGCCCCATCAGTTTTCATTTCTGGCTCTT Y 2 1 2 1 101000 r 74 goat snp31268-scaffold345-5864195 4 68272735 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441988 Affx-122928436 AX-123312325 4 49613256 ATTAACCCATTTATGTATGCAACAAATGGATGGAT[G/T]GCAGAGTTGTTCCTGACCTTAGGTCGACCTGACCT K 2 1 2 1 101000 f 74 goat snp31267-scaffold345-5779280 4 68186738 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441624 Affx-122928642 AX-123311961 4 49650828 GGGAACACTTTCCCACCACTTGTCATCACCTGTTT[A/G]TATTACATAAAGAAAATGGATTTACTTATCAGCAA R 2 1 2 1 201000 r 74 goat snp31266-scaffold345-5741708 4 68148435 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413525 Affx-122950622 AX-123283874 4 49688177 GCTCTGCCCTCTGCTGGGCACAGTTCTTGCTTTGC[A/G]GTCTCACATCATGCTCTTTTTAGTTTGACTATGCA R 2 1 2 1 101000 r 74 goat snp31265-scaffold345-5704359 4 68110711 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775234 Affx-122945566 AX-385262365 4 49731300 TTTCAAGTAATACACTTTTGCTCTGTTTTGTGGAC[A/G]CATCTTTCTGATGTACTGTAGGGAAGTTATTCTGC R 2 1 2 1 201000 f 74 goat snp31264-scaffold345-5661236 4 68066673 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786710 Affx-122950797 AX-385273741 4 49822899 AAAATAACTGTGTAGAAAAAGTAGATATAATCTAG[C/T]TCAAGGATGTCTAGAAGAAACTGTTCAGCAACTGT Y 2 1 2 1 101000 r 74 goat snp31262-scaffold345-5569637 4 67974500 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454081 Affx-122919376 AX-123324414 4 49857413 AAGATTGGCACAACTGGACCTCTACTTCAGGAATG[C/T]AATGTGTCACAATATGCAAGATAATGGAAGAGGGT Y 2 1 2 1 101000 f 74 goat snp31261-scaffold345-5535123 4 67939402 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417745 Affx-122947420 AX-123288093 4 49890290 TATGACTATTTGAGATGTTGTACTTTAAAAATGTC[A/G]TGAGAGGTCACCAGTGGGTTCACTCGTGCCCTGAC R 2 1 2 1 201000 f 74 goat snp31260-scaffold345-5502246 4 67906406 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788102 Affx-122933907 AX-385275122 4 49929967 TTTTCATTATGAAATTGTGAATATTCTTTCAAGGA[C/T]GCCGAAAATAAACCAGAAACAAGACTGATTTCTTT Y 2 1 2 1 201000 f 74 goat snp31259-scaffold345-5462569 4 67865656 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448861 Affx-122923281 AX-123319196 4 50021594 CTATTATTATTTTCCTCATTTTTAAAATGTAAAAG[A/C]TAGAACTAATTCTTTACTGTGTATGCCTTCATGTA M 2 1 2 1 101000 r 74 goat snp31257-scaffold345-5370942 4 67773321 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273694 Affx-1111833744 AX-519547306 4 50052309 TATGGTAGAGTTTTCTG[A/G]ACAAAGAAGTTCCTCTCTGGTCCCTTTAAGTGCAT R 2 1 2 1 102000 r 74 goat GoatD01.003392 4 50052309 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38408763 Affx-122953391 AX-123279114 4 50057717 AAAAAATGACATAAGAGAAAAAAAAAAAAACCTCT[A/G]CTGCCTAGGGGAGAAAAAAAAGCATAACTGGTTTG R 2 1 2 1 102000 r 74 goat snp31256-scaffold345-5334819 4 67735504 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801728 Affx-122924845 AX-385288636 4 50086553 CCCCTTGAAAAACCAGTTCTATTAGTTATGATTTG[A/G]CATTGCTTTGCTATCACTGTTCATTTGAAATATTA R 2 1 2 1 101000 r 74 goat snp31255-scaffold345-5305983 4 67706784 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781930 Affx-122933079 AX-385269011 4 50128905 AAATGTGAGATTTGATGTTGATGGGAGACATGTGA[C/T]GTATGATGGAGAAGATTCAATGAAGACTCCGTAGA Y 2 1 2 1 101000 r 74 goat snp31254-scaffold345-5263631 4 67660907 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433541 Affx-122934997 AX-123303882 4 50162188 TTGCCCTGCCAGTGAAGGCTTCCAGGCATTCGCCT[A/C]TTCTGGATCCATGTCACCTTGCCACCTGCCTTTAT M 2 1 2 1 101000 r 74 goat snp31253-scaffold345-5230348 4 67626996 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411104 Affx-122951915 AX-123281454 4 50204462 CATCTTTACCATCCTTGAATACTAGTGACCCCCCA[A/G]CTGTCAATGACCATAAGACCCTTCATGCAGGGGAA R 2 1 2 1 201000 r 74 goat snp31252-scaffold345-5188074 4 67585003 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409632 Affx-122953534 AX-123279983 4 50257096 AACAAATTCTAATAATGTTTTTCTTTTAATTCTGA[C/T]ACCAGTTTATTCATGACACTCTGAGATTCAATTCT Y 2 1 2 1 101000 r 74 goat snp31251-scaffold345-5135440 4 67532413 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389301 Affx-122968509 AX-123259659 4 50285969 AAACAGCAAAGTATTATTCTATCTAGGCATTCAAC[A/G]TAGGTTTATAATATTACAGCAGCAGATAAAACTTC R 2 1 2 1 101000 r 74 goat snp31250-scaffold345-5106567 4 67503659 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802401 Affx-122939735 AX-385289305 4 50330501 GGTAATCATCCTTAATTCTTAAAACTGTTTCATAG[C/T]ATATTTGTAGACATCAGATTACCATTTTCTGGATA Y 2 1 2 1 101000 f 74 goat snp31249-scaffold345-5062035 4 67457742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801288 Affx-122948012 AX-385288200 4 50361272 TAGACTAACAGTTAACCATGCTTGGACTCTTGCCC[A/G]TTTGTCAAAAGGGAGAATTCAAATAAGGAAGTAAG R 2 1 2 1 101000 f 74 goat snp31248-scaffold345-5031264 4 67426357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405883 Affx-122955602 AX-123276235 4 50391488 TTAATACATAATTGGGAAAAAGAAACTGTCTTCCA[C/T]GGTTTTAGGGTTCTACCCCCAAATCTTTTCACAAA Y 2 1 2 1 101000 r 74 goat snp31247-scaffold345-5001048 4 67395710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384535 Affx-122973029 AX-123254893 4 50423589 GAAAAAGTCGCCAATAACTTGGCATATATCTATAC[A/G]GACTTCTTATCTCACCCCACAAAGTAACCAACCCC R 2 1 2 1 101000 r 74 goat snp31246-scaffold345-4968947 4 67363482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441508 Affx-122928726 AX-123311845 4 50463066 GGGAGAGGAAACTGGAACAAAGGGAAAATAATGAT[A/G]CGATATCAGCAAAGCTATAGGCTAGACTAGTATGA R 2 1 2 1 101000 r 74 goat snp31245-scaffold345-4929470 4 67323989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414016 Affx-122950264 AX-123284365 4 50521166 CCAGAGCAAGCTCTGGACCCCTACATTATTATGCA[C/T]ATGTACTTACTGGATAAAATTGCTTGCTAAAGCAA Y 2 1 2 1 201000 r 74 goat snp31244-scaffold345-4871370 4 67265580 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787615 Affx-122936196 AX-385274638 4 50565236 TTTCATGAGGTATCTTATATTTCAAGAGTCTAAGA[C/T]AATACTGAGCACAGAACAGGCCATCACAAAATAGT Y 2 1 2 1 101000 r 74 goat snp31243-scaffold345-4827300 4 67220858 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272118 Affx-1111833429 AX-519545876 4 50595219 TTGAGTGATTTGCAGATATGTTCTTCCAGTCTGCA[A/G]TTTGTCTTTGCAGCCTCTTTGCAGGAGGTACAGAG R 2 1 2 1 101000 r 74 goat 4_50595219_AF-PAKI 4 50595219 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413623 Affx-122950553 AX-123283972 4 50601008 ATGTTCACATCCTGCTCTACTAGAACCTGCAAAAA[C/T]GTTTACACAGCAAGGGGCTTAAGATGGCTAATCAG Y 2 1 2 1 201000 f 74 goat snp31242-scaffold345-4791528 4 67185296 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405280 Affx-122956857 AX-123275632 4 50653289 ATAACCATTGAGCCTTTGTCTATGAATCATATAAA[C/T]ATAATGTTATGAAATGTTTTAAACTTCAGGAAATA Y 2 1 2 1 101000 f 74 goat snp31241-scaffold345-4739247 4 67134435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786684 Affx-122923148 AX-385273716 4 50699275 GGTACCCAGAAAGAAGCAATGAACTTAGATTTTGA[G/T]AAGCAGCAGTTTGTCAAAAACACAAATTAATTTCA K 2 1 2 1 101000 f 74 goat snp31240-scaffold345-4693261 4 67088139 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418579 Affx-122946375 AX-123288927 4 50732553 TTCCCTTGCTTAGGCCTCTAGAACCCTGTCATTTC[C/T]GGTATCTTCTCACTGTTTTAATAGGTAATAAGATC Y 2 1 2 1 101000 f 74 goat snp31239-scaffold345-4659983 4 67054856 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798963 Affx-122976157 AX-385285893 4 50817390 TTTCTCTACAAGAAATTTCTAGAGGCTTAATGGAA[C/T]GTAAAATGACACAGCCACTACGAAAACAGTTTGGT Y 2 1 2 1 103000 r 74 goat snp31237-scaffold345-4575146 4 66972505 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273488 Affx-1111833649 AX-519547105 4 50854217 CTGTGTCGCTCAGCGTGTGTTAGATGATTTGAGCC[A/G]AAGCAGCTGCTGTCGTCTGTCCTGCCCTCTGTTCT R 2 1 2 1 201000 f 74 goat GoatD01.000523 4 50854217 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320774857 Affx-122964542 AX-385261991 4 50857141 GCAATGTTTCTGCCCACCTGGATTTAGGTACTGTC[A/G]TGAGCTTTGAAATTCTGAGATTTTTACCCTATTTG R 2 1 2 1 101000 f 74 goat snp31236-scaffold345-4535395 4 66932452 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447421 Affx-122924391 AX-123317757 4 50994247 TTACATCATTTTTATACAAATATATATTTTCTTAT[A/G]CTTTTTTTTTGTCCTATAAATAGATAATATTGTGA R 2 1 2 1 103000 r 74 goat snp31232-scaffold345-4398289 4 66794118 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396548 Affx-122962939 AX-123266903 4 51027961 CCAGAGAGCCTTATCATATTTGTTGTTGTTCAGTT[A/C]CTAAGTTGTGTCCTCATGGACTGTAGCATGCCAGG M 2 1 2 1 103000 r 74 goat snp31231-scaffold345-4364575 4 66760380 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415477 Affx-122948708 AX-123285826 4 51071852 AGAGATTATTGAAGGCCTCAATGTTCTCAGAAAAA[G/T]AGATGTAACATTTGCTGAGAGCAAGTTGGGGTTAG K 2 1 2 1 201000 f 74 goat snp31230-scaffold345-4320684 4 66717172 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799130 Affx-122974501 AX-385286060 4 51106681 GTATGCTATCCATTTGGTAGAGAATATGACTACTC[A/G]CAGATTTAGTCATATTCTTATGTTAGTGAATCATG R 2 1 2 1 101000 f 74 goat snp31229-scaffold345-4285855 4 66682547 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452353 Affx-122920640 AX-123322686 4 51136366 GTGATACAGAGTTAATATTATGTTATAAAAGTTGA[A/G]CTCAAACTATATTTTCTTTCAGTGGGCCAGCTTGC R 2 1 2 1 101000 r 74 goat snp31228-scaffold345-4256170 4 66652913 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783660 Affx-122945223 AX-385270719 4 51169549 CAAAACTAGAAGTATTCATAACATACCTTCCTACA[C/T]GGAGTTCCAGATAATATCTGTTTCAGGGTTTCTGG Y 2 1 2 1 201000 f 74 goat snp31227-scaffold345-4222987 4 66619559 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377015 Affx-122977721 AX-123247374 4 51228091 GTGTACACCTATTGTAAAGTTAAAGGAGTTGTACA[C/T]GAGAATCATTCTGCTCAGTTTTGCCTTAACATGGT Y 2 1 2 1 101000 r 74 goat snp31225-scaffold345-4164445 4 66561442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453693 Affx-122919696 AX-123324026 4 51277417 TGACCACCCACCCAGTAAATGAAAGCTTTCATGAC[G/T]ATCAGTAGGGCTTCCTTCTTTCCTCTTTTCAAGGA K 2 1 2 1 103000 f 74 goat snp31224-scaffold345-4115119 4 66511959 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775613 Affx-122941671 AX-385262743 4 51327657 TTAATTAGAAATGGTTTGATTTCAAGAAGTAATCC[A/G]TCCAAAAGTATAATCCAGGATTCTCTCAAAACTCT R 2 1 2 1 101000 f 74 goat snp31223-scaffold345-4064879 4 66461708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772290 Affx-122959286 AX-385259445 4 51366784 ATAAAGTATAATAATGTCCTTTATGTTGAGTTAGG[A/G]CTCTGCTGAAGTTCTTCTTTGGCGTCAGTGTTCAG R 2 1 2 1 101000 r 74 goat snp31222-scaffold345-4025752 4 66422056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788656 Affx-122933800 AX-385275672 4 51407578 TATTAACATTCTTCCCCAAAAATAGAAAGCCATGC[A/G]ATTGTAATATTGAAGACAATATGAAATCACTTCAT R 2 1 2 1 102000 f 74 goat snp31221-scaffold345-3984958 4 66380720 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397962 Affx-122961904 AX-123268317 4 51444895 TCTCTTTTATCTCCAAGGATAGATTAATGACAGTA[G/T]CATTTTTATTTGCTGTATTTTTATCTCCAGCAACA K 2 1 2 1 101000 f 74 goat snp31220-scaffold345-3947641 4 66342837 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391000 Affx-122966898 AX-123261357 4 51480502 AGTAACACAAAGGAGAAAATCCATTTCACTATTCC[A/G]CCTCCTTCCCATAGAGCCAAGCATGTAATAGACAT R 2 1 2 1 201000 f 74 goat snp31219-scaffold345-3912034 4 66306893 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434682 Affx-122933962 AX-123305023 4 51592322 GTCACTTCAGTTGTGTCCAACTCTGTGCGACCCCA[G/T]AGACGGCAGTTTCTTAGCAGTTTCACATTATTTAG K 2 1 2 1 101000 r 74 goat snp31217-scaffold345-3800214 4 66214478 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406882 Affx-122955639 AX-123277233 4 51640751 CCTCTTTACACACTAGGTGATATTATCTCTTACTT[A/G]ACTCAGATCCAGGGATGGAGTAGATACAATGCTAA R 2 1 2 1 201000 f 74 goat snp31216-scaffold345-3751785 4 66166018 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406194 Affx-122956142 AX-123276546 4 51686073 GTGAAATAGAAATTTCATTATTTATATTTCACTGA[A/G]TATCACTGAGTGACCAAATCATACAGACTTTTATA R 2 1 2 1 101000 r 74 goat snp31215-scaffold345-3706463 4 66120648 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423110 Affx-122942915 AX-123293456 4 51742523 GCCATAAGGAAAAATAAGGCTGGAACCAAGGATAG[A/C]GACTGATGTTGAGAGCTATTTCATATAAAGTGGTC M 2 1 2 1 101000 f 74 goat snp31214-scaffold345-3650013 4 66064013 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382822 Affx-122973554 AX-123253180 4 51784276 CCTACAAGCTAATGGTGATGAAGAATCATTGTCAA[C/T]GATAAATAACATAAGAGATATCTGTCAGATATACA Y 2 1 2 1 101000 f 74 goat snp31213-scaffold345-3608260 4 66021890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415737 Affx-122948502 AX-123286086 4 51830904 TGTTTAGGGCTTTGGTCTATAGTTTGTTTATTAAA[C/T]AGAACTTTTCTTACTGAGTTATTAGGGTGGGAGTT Y 2 1 2 1 101000 f 74 goat snp31212-scaffold345-3561632 4 65974801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381595 Affx-122974795 AX-123251953 4 51890875 TTATTCCAAACACTAATGCAGTGAATGTATCTGTA[G/T]ATTTCTTTTTGTGTACATGTTTGAGAGTTTTGTTA K 2 1 2 1 101000 r 74 goat snp31211-scaffold345-3501661 4 65914251 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769570 Affx-122937977 AX-385256740 4 51942782 TGTCTTTAACCTAAGAGTGATAGTAAACCATCAAA[A/G]CATTTGGAACTAGGAGATGGCATGATCCAAGTTAT R 2 1 2 1 101000 r 74 goat snp31210-scaffold345-3449754 4 65860149 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381053 Affx-122974626 AX-123251411 4 51972298 CAAATGTACAATAATAGAGAATATATGGTAACAAG[C/T]TATGAATAAATAAACAATAAAATATTTAATGCTTA Y 2 1 2 1 101000 f 74 goat snp31209-scaffold345-3420238 4 65830619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445221 Affx-122925506 AX-123315558 4 52020449 CCACTAGGTGGCACCAAATAGCCATAATTCATAGA[C/T]TGTATCCTAAACCTATACACAAGCCATTAAAAGAT Y 2 1 2 1 101000 f 74 goat snp31208-scaffold345-3372087 4 65782529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436199 Affx-122932595 AX-123306538 4 52071569 GCAGGCGAACAGCTCATTAGCTAAGGAGAAATTAT[C/T]TGAAAATTTCAAAAAGAAATGTTGCCTTCCTTTGG Y 2 1 2 1 101000 f 74 goat snp31207-scaffold345-3320967 4 65730803 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388142 Affx-122969467 AX-123258500 4 52108056 GAGGATACTCGGTTGATTCCAGTACCGCTTTCTGT[A/G]CTTGAAGTTGTTGCATAAGATCTTCTTTTGAAGAA R 2 1 2 1 201000 r 74 goat snp31206-scaffold345-3284480 4 65694126 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450781 Affx-122921829 AX-123321115 4 52147510 AAATTCATTCTGAAGCAATGCTTGTGGAACTTTTC[A/G]TTTAAATTTCCAGCTCTGAATAGTAGTTGACGTCA R 2 1 2 1 202000 r 74 goat snp31205-scaffold345-3245026 4 65654700 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795985 Affx-122969474 AX-385282937 4 52207691 AAGAGGGAAAAGCAAAGTATTACAAAGAGAACAAC[A/G]TAAGTGAAGACAGGGAGATAGTAATCTCACGACCC R 2 1 2 1 101000 r 74 goat snp31204-scaffold345-3184845 4 65594529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439030 Affx-122930344 AX-123309367 4 52242468 TTATTGATTTGTTTTAAATAATGTTGTTGTATTTC[A/G]TTTTCACTCCTTGGCATATATTTCTCCCTTTCCAT R 2 1 2 1 101000 r 74 goat snp31203-scaffold345-3150068 4 65559524 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407488 Affx-122954758 AX-123277839 4 52299811 ATTTGCTGCATTGATGCATTTGGTTTAATCAATCC[A/G]TACATAGCTTCATATAGTGGCTTCAAGCAATGAAT R 2 1 2 1 101000 f 74 goat snp31202-scaffold345-3092725 4 65501354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419777 Affx-122945862 AX-123290125 4 52328554 TTTATACATTGAAGATTTAACTTTTTAATCAAATG[C/T]ATTTATGAGAACAGCATGTGACATCTGAAACTTTG Y 2 1 2 1 101000 r 74 goat snp31201-scaffold345-3063982 4 65471772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406988 Affx-122955041 AX-123277339 4 52369485 CTCCTTCACACTTCACTGAGTGAGATGGAGCCACA[C/T]GCTCTCAGAGCACTTATTAAGCTCTCCTAAGTTCT Y 2 1 2 1 201000 r 74 goat snp31200-scaffold345-3023051 4 65430079 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796325 Affx-122976123 AX-385283275 4 52416094 AATATTTAATTGTTCACCTGTACAGTTAAAATGTG[C/T]ATTATGTTTTGATGAGCACATTTTCCAACTTAACA Y 2 1 2 1 201000 r 74 goat snp31199-scaffold345-2976442 4 65382971 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377686 Affx-122977420 AX-123248045 4 52483432 ATAACAATACAAATTTTGAAAGCGGCAAGGACAAA[A/G]TCAGCAAACCTAGAAACTGCTCATATTGGTATTGG R 2 1 2 1 201000 f 74 goat snp31198-scaffold345-2909104 4 65314160 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378437 Affx-122976702 AX-123248796 4 52578951 ATGTATGTTTCTATGTATCTAAGAATGGGCCATTA[C/T]ACTATCTTCAATCTTCCAAAACTGATAGTCTTAAA Y 2 1 2 1 101000 f 74 goat snp31197-scaffold345-2813585 4 65217527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390548 Affx-122967218 AX-123260905 4 52642617 GAGAGGGAATTTCTCTGTGACTAAGATGCAGCCTT[C/T]AAGAAGAATATGAGTGATTCTCTGACCGTCCCCTC Y 2 1 2 1 101000 f 74 goat snp31196-scaffold345-2749919 4 65152637 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771511 Affx-122934060 AX-385258669 4 52679191 TTTTTTTCCTTTTTAATATGGTAGGACGTGACCTA[C/T]TGAATATAATAAAAGCCTGGCTGATCCCCTTTTAT Y 2 1 2 1 101000 r 74 goat snp31195-scaffold345-2713345 4 65115872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406760 Affx-122955727 AX-123277111 4 52740187 GAATTATTTTACTTGTAAAAGATATTTTGTTTTAT[A/G]ATGTTAGGAGGCTTTGTCATTCAACACTTGAGGAG R 2 1 2 1 101000 r 74 goat snp31194-scaffold345-2652349 4 65054473 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793123 Affx-122978259 AX-385280101 4 52787479 ACTGGCTGGTTCCTGTCTTAGAGGTGAGAACAGTT[A/C]CAAATTCCAAACTATATAGCCTAGGAGTTAACTAG M 2 1 2 1 101000 f 74 goat snp31193-scaffold345-2605057 4 65011823 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786065 Affx-122935829 AX-385273101 4 52839133 ACCAGACCTTGCGTTGTTCTCTGGGTTCTTGATAG[C/T]CTCTTCAACTAGACATTATCAATCTTGAAAATTGT Y 2 1 2 1 102000 f 74 goat snp31192-scaffold345-2553403 4 64958628 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441104 Affx-122928887 AX-123311441 4 52880649 TGCTGGAACTTGAAGCATGTGAGATTTTTGAGTGC[C/T]TGAAAGCTCTCATTTCCAACAGCCCTCTATGGCTC Y 2 1 2 1 101000 r 74 goat snp31191-scaffold345-2511887 4 64915908 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775710 Affx-122927347 AX-385262841 4 52944171 AATAAAATTCACATAGCCTTTCTGATTATGTAGGA[C/T]ATTTGTTTGAAATTCATCACAAGGAAATCAAGTGA Y 2 1 2 1 101000 f 74 goat snp31190-scaffold345-2448365 4 64852573 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783305 Affx-122978322 AX-385270370 4 53003276 TCCAGTGCCTTGAACATGGCAGGATAGAGAAGGAT[A/G]CTGAATTGAATATAAGTATACTGTTTTTCTTTAAG R 2 1 2 1 101000 f 74 goat snp31189-scaffold345-2389260 4 64792607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440792 Affx-122929838 AX-123311129 4 53049545 GTCTCCATGGGATTGTCCTCTTCCTTTTCCAAGTA[C/T]GCTTGCTTCTCAGAGGGACAGGTATTCATTGCTCT Y 2 1 2 1 201000 r 74 goat snp31188-scaffold345-2342991 4 64746286 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272122 Affx-1111833431 AX-519545880 4 53098624 CCCACCTATTGATACTGCCAAACTCATAAAAATGA[A/G]TCTATAAGAAATTTAACATGTTCTCTGTTGTGCTT R 2 1 2 1 101000 r 74 goat 4_53098624_AF-PAKI 4 53098624 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38402894 Affx-122958213 AX-123273247 4 53110509 ACACTGTATTAGTTCTATTCCTCTGGAGAACACTA[A/G]TACACACTTCCCAATAGAATCCTATGTATCTGGTG R 2 1 2 1 101000 r 74 goat snp31186-scaffold345-2282027 4 64685331 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775062 Affx-122960462 AX-385262194 4 53143088 AAAAGGTACCTTTCTATAATATCTTAGTGCTAAAT[A/G]CTAAGTAACAGTGGTTTCTGCTAGGACAGGAGTCA R 2 1 2 1 101000 r 74 goat snp31185-scaffold345-2249448 4 64651751 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401461 Affx-122958971 AX-123271814 4 53200250 TCCACAAATACGTGTATCTGCACAATAGTGAAATT[A/G]CCAGAGGTGGACTTACCTGCAAGAGCCCACTCTCC R 2 1 2 1 101000 f 74 goat snp31184-scaffold345-2192286 4 64594484 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778788 Affx-122947633 AX-385265897 4 53245037 GTCCACAAAACCCTAAAGTTAAAAAGTCCAAAGGT[A/G]TAGCCTATGAAAGGTAAATGAGACCTCTACTCACA R 2 1 2 1 101000 r 74 goat snp31183-scaffold345-2147499 4 64549385 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464297519 Affx-1110411635 AX-515771707 4 53279359 ATGCTTCTGCAGAAAACCCCCAAAGAAGTGGGAGG[C/T]AGGCATGGTATACACTGTAACATCTGACTGAGTCT Y 2 1 2 1 101000 r 74 goat GoatD01.000108 4 53279359 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38409663 Affx-122953513 AX-123280014 4 53313784 GTAAGTATCAGTAGCAGTGGATATTGCTATGCTTT[A/G]TTTTGTCTTACTTGTTTTTAAATTTTATTTTGTTT R 2 1 2 1 101000 f 74 goat snp31181-scaffold345-2078752 4 64479872 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379609 Affx-122976014 AX-123249967 4 53353974 GGGCTTTACTTAAAAGGGATGTTAACCGGCATATC[A/G]TTACAGTCAAAGTCATGTTCTATTCAACTTTAGTA R 2 1 2 1 101000 f 74 goat snp31180-scaffold345-2038562 4 64439198 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771088 Affx-122951490 AX-385258248 4 53408111 TGGATCTTTGCTTCTCTTTATATAAGTAGGTAAAA[G/T]CATAATCAGTCTTTTCTTCTCTAGAAGTGACATAA K 2 1 2 1 102000 r 74 goat snp31179-scaffold345-1984425 4 64383958 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386138 Affx-122971406 AX-123256496 4 53453189 GTTCATTTCTTTCCTTTCAGTCCGTGGTAACCCCA[C/T]GGACTGTAGCCTGCCAGGCTTCTCTGTCCATGGGA Y 2 1 2 1 103000 f 74 goat snp31178-scaffold345-1939347 4 64339146 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784275 Affx-122953504 AX-385271326 4 53501320 TAGGTGAGATCACCTGGGAGCCAAGTTACAGATGA[C/T]GTGTAATCATTTATCTTTAGACTCCCAGCTTTGAT Y 2 1 2 1 101000 f 74 goat snp31177-scaffold345-1891216 4 64290577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768191 Affx-122928191 AX-385255381 4 53579065 AGACTGCAGAATGCATACAGAGTAAATGATAAAAA[C/T]GAGATACAAGCTGTGAACAACTGAAATGTTTTAAC Y 2 1 2 1 101000 f 74 goat snp31175-scaffold345-1813471 4 64212344 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432459 Affx-122935800 AX-123302800 4 53613242 CTTCACTATAGCTCAGAAGGTGAAAGAGGCTGCCT[A/G]TGATGCAGGAGACCAGAGTTCAGTCTCCCGGTTGG R 2 1 2 1 103000 f 74 goat snp31174-scaffold345-1779294 4 64178396 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394667 Affx-122964371 AX-123265022 4 53739951 CACTGACCAAATAAAATTCAAAGCAAATATTCCAG[C/T]AAGTTTCTGGTGCTGTGTATCTCAGGATTCTTCAT Y 2 1 2 1 101000 r 74 goat snp31172-scaffold345-1652585 4 64051781 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388362 Affx-122969338 AX-123258720 4 53777571 CTCTCAAGAGAAAATCAAAGCTAATCTTCATGGTT[A/G]TAATGAAGGATACAAGTAGAAGATTAGTTGGAATA R 2 1 2 1 101000 r 74 goat snp31171-scaffold345-1614965 4 64014176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278085 Affx-1111836244 AX-519551576 4 53827669 CACCCACCCTGGACTGTCTATATACATTTGGACTA[A/G]GAGAGAGAAATAAAGGTGCCTTTTTTTAAACCACA R 2 1 2 1 101000 f 74 goat Random2.2K-442 4 53827669 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413827 Affx-122949886 AX-123284176 4 53829673 ATCCCATGGTGATGGGGCACACGGCATCATGCTCA[C/T]AGGTGCATCCTCGAAGGGGACATAGACTTGAGTTA Y 2 1 2 1 201000 f 74 goat snp31170-scaffold345-1562863 4 63961885 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776298 Affx-122975834 AX-385263426 4 53861993 AAGGGTAACACAGGACTACAAAGACTTTTTAGTTA[C/T]GGTTCCTGTGCTGCTATTAACTCTCATTTTGGCAA Y 2 1 2 1 101000 r 74 goat snp31169-scaffold345-1530543 4 63929133 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792801 Affx-122928048 AX-385279780 4 53893327 CCTTGGTTTTAATGTTGCAAAGGCACTTTCCTAAG[C/T]GGCTACAAGAACAACTGAAGGTCAAACAGTAGAAT Y 2 1 2 1 101000 r 74 goat snp31168-scaffold345-1499209 4 63897877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410135 Affx-122952807 AX-123280485 4 53959158 CTAACTAGGCCCATATAAAAAGGGGAAATGTGGTT[A/C]CAGAAACAGACACACACACCTGAAGAAAGTCATGT M 2 1 2 1 202000 f 74 goat snp31166-scaffold345-1433378 4 63832362 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386788 Affx-122970919 AX-123257146 4 53988154 ACACATGCATCTCTGATAGTAGCAGTTGGGCAAAG[C/T]CCTACACCCATGGGCAGTGGGGTATGTCAGCTTCC Y 2 1 2 1 101000 f 74 goat snp31165-scaffold345-1404382 4 63803539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405190 Affx-122956920 AX-123275542 4 54020875 TGGCATTCAGGATGCTTTCCAGAAGCCTTACATGG[C/T]GACCATGAAGAATTCAAAAATATTTATTTTACTTC Y 2 1 2 1 101000 f 74 goat snp31164-scaffold345-1371661 4 63770347 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410375 Affx-122952443 AX-123280725 4 54072832 GAGCTCATATTCATCAAGAATACAAAAAAACAAAC[A/G]CACATGTTCTCACAGAGAGGGACTGTGGTCTGTGA R 2 1 2 1 101000 r 74 goat snp31163-scaffold345-1319704 4 63718409 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767262 Affx-122972374 AX-385254542 4 54184069 AGGTTACTCAACTACTTTTGACTGGGATTCTGTAG[C/T]AGTCAAGTACTCAGGGTTCAAATGAACCCCAGGCT Y 2 1 2 1 101000 f 74 goat snp31161-scaffold345-1208467 4 63606705 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388916 Affx-122968840 AX-123259274 4 54233057 CACAGGAGAGGGGGTACCCAATAGACGCTGCTGTC[A/G]TCTTCGGGAGAGGAAAGCAGATACTGCCACAGTGA R 2 1 2 1 101000 r 74 goat snp31160-scaffold345-1159479 4 63556935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453151 Affx-122919991 AX-123323484 4 54292215 CTTAAGTAATTTGTGTAATAATTGTTGCATCTATT[A/G]CAGTAACAATAGAAGTTAAGGGCCAGGCTCTGGAG R 2 1 2 1 201000 f 74 goat snp31159-scaffold345-1100321 4 63497280 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441941 Affx-122928579 AX-123312278 4 54340099 GTAAAATGTAAAACTGGAAATGTCGCAAAATCAAC[A/G]TGACCTTTAAAGTGTAACATTTCCCACAATCATTT R 2 1 2 1 101000 f 74 goat snp31158-scaffold345-1052437 4 63448933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445937 Affx-122925916 AX-123316274 4 54369482 TACACAGCAGCACTCAGGTACTATGCAACGAATGA[C/T]GCTCAAGACTGGTTGTTGTTGTTGTTCGGTCACTA Y 2 1 2 1 101000 f 74 goat snp31157-scaffold345-1023054 4 63419480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439789 Affx-122930501 AX-123310126 4 54403819 TGATTGCTCCATTTGAAGAGAAGAAATAATCTCAA[A/G]TCAACCAGGAAAATACCACAGTAAACAGTAAAGAG R 2 1 2 1 101000 r 74 goat snp31156-scaffold345-988717 4 63384618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396485 Affx-122963543 AX-123266840 4 54433095 GTAAAGGGTTATGTCCCAAAAATGTGTATTACCAA[C/T]ATATTAGCATATGAAAAAAAATGTGCCTGGATACT Y 2 1 2 1 101000 f 74 goat snp31155-scaffold345-959441 4 63355062 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445366 Affx-122925414 AX-123315703 4 54468984 AGAGAATTACTGTAAACAAATACAAAAAACATCTA[C/T]GATCTTGTCTACTGTATCAATATGTTCATACAGAT Y 2 1 2 1 201000 r 74 goat snp31154-scaffold345-923552 4 63319200 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398778 Affx-122961429 AX-123269133 4 54515737 TACGCCTACCTTTCAGTGAAGAAGTGTTCATCTAA[G/T]AGAGCCGTCTAGGACACTCATCTTTGCCAGTAGAA K 2 1 2 1 101000 f 74 goat snp31153-scaffold345-876799 4 63272143 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789399 Affx-122970324 AX-385276409 4 54560891 TCAAGTTCAAACTCATTAGCACAGCTTACAAGGTC[A/G]TTTATGATCTCTTTACTCTCAAGCCTCCTCTCTTA R 2 1 2 1 101000 f 74 goat snp31152-scaffold345-831645 4 63226713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377524 Affx-122977474 AX-123247883 4 54592938 TATTATTTACCTTTGTGAAACAACCATCCAAATCA[C/T]TGTGAGCTACTTTCACAGCACAATGGCCAAAGTCA Y 2 1 2 1 201000 f 74 goat snp31151-scaffold345-799598 4 63194138 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434337 Affx-122934731 AX-123304678 4 54640076 TATGGGCTATTAGAAATATGCCAGTGAAAAAAATT[A/C]TCAGTCAAGGATAAACTCAGATTTGACAAACAGAT M 2 1 2 1 101000 f 74 goat snp31150-scaffold345-752460 4 63146475 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439582 Affx-122930073 AX-123309919 4 54673627 TATTCCTGTCATCACAAAATACAGGTGCTTTACTA[C/T]ACTCAATGGTTAAATAAAATGATGGTAAAACTCAA Y 2 1 2 1 101000 f 74 goat snp31149-scaffold345-718909 4 63112987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766836 Affx-122959089 AX-385254159 4 54737922 TAACTTTCAAGAAAATTTAAAATCCCATCCAGGAC[A/G]TGGAAAAGATACAAGACAATGAACTCTTTTCAGGG R 2 1 2 1 102000 f 74 goat snp31148-scaffold345-654614 4 63049788 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428506 Affx-122938766 AX-123298848 4 54781502 TTTAATGTAGCCATAGCAACCACCTATCTTTAACA[A/G]TTTTTGAACTTAAGCATCCAAATGTTTTGCTTCTT R 2 1 2 1 101000 f 74 goat snp31147-scaffold345-611034 4 63006638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452622 Affx-122920362 AX-123322955 4 54816810 GCATTCCCTTTTAAAAATAGTATTTCTATTTTTAG[C/T]ATCCCTTGTTGCTAACTACATTTAATTGGTTGACT Y 2 1 2 1 103000 r 74 goat snp31146-scaffold345-575726 4 62971267 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767822 Affx-122977401 AX-385255045 4 54850822 ACTCCCAATATATCTCAAGTCCACGGGCTTGGGAC[A/C]CACCATATTCACTGCCACCTCAATATTCAAGCCAC M 2 1 2 1 101000 f 74 goat snp31145-scaffold345-541714 4 62936952 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773514 Affx-122946964 AX-385260655 4 54883509 CTGATAACTACAATGTACACAATAGGAGAGTCTGC[A/G]TTAGTAATATGAATGTAACTTTGATCTCATATCTT R 2 1 2 1 101000 f 74 goat snp31144-scaffold345-509027 4 62903046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768661 Affx-122931306 AX-385255839 4 54918796 ATCTGGTAAAAAACTGTAATTGCAAGAATTTCATT[A/C]ATACTATAATAGCAAATCAAATTAATTTCAGATTA M 2 1 2 1 201000 r 74 goat snp31143-scaffold345-473740 4 62867220 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421989 Affx-122943790 AX-123292336 4 54948124 TTCCATTGTATTTATTCTACTGCCTGTATCTGTGC[A/G]TTACCATCTCTAGCTACTGTGGTGACATGCATTAT R 2 1 2 1 101000 r 74 goat snp31142-scaffold345-444412 4 62837823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408331 Affx-122953756 AX-123278682 4 55039965 GCATGGCTTCCTAGCAAACCAATTTAAACAGAACA[A/G]TGAACTTGTAATGCTTAATTTTATTTTTCAGAAAA R 2 1 2 1 101000 f 74 goat snp31140-scaffold345-352571 4 62744258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438572 Affx-122931162 AX-123308910 4 55118975 ATGACGGTGAACAGGTCCCCTTCCCCCACAAAAGT[A/G]CCATAAAGCAATTTAGAATTGTTCATAGGAATTCT R 2 1 2 1 103000 f 74 goat snp31139-scaffold345-273561 4 62665300 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766134 Affx-122978900 AX-385253540 4 55167467 TAGTCTTTTCAAGATAATATCCTTCGGCAGAAATG[C/T]AGATACACCAATGACAGAAATGCATATTTATCAAT Y 2 1 2 1 101000 f 74 goat snp31138-scaffold345-225069 4 62616471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413754 Affx-122949942 AX-123284103 4 55199627 ATTAACATTAGCATCATTACGATGCCATCAGCATT[C/T]CCTGTTTTTCTTGTGCTAAATATTTATTTTGCAAG Y 2 1 2 1 101000 f 74 goat snp31137-scaffold345-192909 4 62586289 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423054 Affx-122942958 AX-123293400 4 55237686 ATGACAGGTCTGTGACTGTGGGTGCAGGAGAATAG[C/T]AAAACTCCAAGACCCTCAGGGTAGACAGAGAAAAT Y 2 1 2 1 201000 f 74 goat snp31136-scaffold345-154850 4 62547278 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432495 Affx-122935585 AX-123302836 4 55286255 GTGTGAGACTGGGTAAGGTGCTTCCACAGACAGTA[C/T]ACAGAACAATGTGAATTTAGTGCTTACGGAGAGAG Y 2 1 2 1 101000 r 74 goat snp31135-scaffold345-106281 4 62496493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771709 Affx-122921960 AX-385258866 4 55333773 AATTTTTGAAACCATATAAAATGTAGATAGGTGAT[A/G]CATAGATACATGATTGCACCAAATAAGATCTACTC R 2 1 2 1 101000 r 74 goat snp31134-scaffold345-58763 4 62447821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788979 Affx-122951920 AX-385275992 4 55388550 AAATGTGTTTGGTAGGGAAAAAATAGTAGCTGCGC[G/T]GTCCAAATCACTCTTAAAAGATACCAAGTTGGCTG K 2 1 2 1 101000 f 74 goat snp31133-scaffold345-3986 4 62392796 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777080 Affx-122951766 AX-385264203 4 55411677 TCATATATTATCAGAGTTACTGCTACTACCAGAAT[A/G]CATTATATTATAAACCTTTCTTCTGTTTCCAGGGA R 2 1 2 1 101000 f 74 goat snp45595-scaffold624-263438 4 62369937 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770898 Affx-122968848 AX-385258061 4 55454105 TTCAGAACATTTACCATAGTTACTCATATCTTTTC[A/G]TTCAAGCCTTGAGCTCTTTCCCTTACCTCAAGCAG R 2 1 2 1 101000 r 74 goat snp45594-scaffold624-221010 4 62328365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436446 Affx-122932997 AX-123306784 4 55500867 TTTGATTAAAAAAAAAGTGTCAAAACAGGTACATA[C/T]AACCAAATATCCTCATCTATTTAATCCAACCTGTG Y 2 1 2 1 101000 r 74 goat snp45593-scaffold624-174248 4 62280326 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429824 Affx-122938179 AX-123300165 4 55547203 GCACATCAGGACTTGTCCCCATTTTTCTCACGTTC[A/G]TATTCCTTATCCTCACGAAAGCCTACACCAGAAAC R 2 1 2 1 101000 r 74 goat snp45592-scaffold624-127912 4 62233783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784739 Affx-122968438 AX-385271787 4 55607592 ATATCGCCAGAGCTATGAAGAACACTCAGATGCCA[G/T]CTTCTCCTCCAGCTTATGGTGGGATAGATATCTCA K 2 1 2 1 101000 f 74 goat snp45591-scaffold624-67523 4 62173242 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439433 Affx-122930192 AX-123309770 4 55650441 TGAAATATCAACAATGCTTTAAAGCAGGAGTTCCC[A/G]ACTTCCAGGATCTAATGCCTGATGATCTGTGGTAG R 2 1 2 1 303000 f 74 goat snp45590-scaffold624-24674 4 62131896 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411435 Affx-122951826 AX-123281785 4 55678598 GAGGAGGGGAGAGAAAGAGAGAAAACTTTGCCTGC[G/T]AGTGGCCTTATTGTAACCCAAACCTTCTTTATACC K 2 1 2 1 201000 r 74 goat snp37245-scaffold453-2289668 4 62103172 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410948 Affx-122952036 AX-123281298 4 55752806 ATTTTAGAGCAGAGAGAAAGAAAACAAAGAATCCC[A/G]TAGAGACAAGATGAGTCAACCAGGATGATGACATA R 2 1 2 1 201000 r 74 goat snp37244-scaffold453-2215460 4 62028713 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385648 Affx-122971165 AX-123256006 4 55786087 GTACTTCCAGTGAGAAAATAAGTTGTAATTACTGA[A/G]ATATGCCCAAGGATGAAATTGTGATGTGAATGTTT R 2 1 2 1 101000 r 74 goat snp37243-scaffold453-2182179 4 61994934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398082 Affx-122961726 AX-123268437 4 55849554 GAATCTGAAGATGTGACTGGGTTGATATAATCTTA[C/T]GATAAAACTAACAGAGAGGGCACTTTTTATGAATG Y 2 1 2 1 101000 f 74 goat snp37242-scaffold453-2118712 4 61930477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380361 Affx-122975351 AX-123250719 4 55883500 CTCATTGAAAGTAAGATGGATAGTTCAAATACTAA[C/T]GTTCAATGGAAAGTTTATAAGATTATTCTTTTGCA Y 2 1 2 1 101000 f 74 goat snp37241-scaffold453-2084766 4 61896241 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793965 Affx-122968842 AX-385280934 4 55931412 AAGTGATCTCCAAGTTAACAGAGTCCAAAATGGTA[C/T]GAAAAATTATCAGCAATTCCACAGGGAATTCTCTA Y 2 1 2 1 101000 r 74 goat snp37240-scaffold453-2036854 4 61848069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409795 Affx-122952970 AX-123280146 4 55989658 TATATTTAAAAATAAAATTAAAGATAAGCTGAAAT[A/G]TTCAAATACTATCTCTGAATGCCACAGTAAATTGA R 2 1 2 1 103000 r 74 goat snp37239-scaffold453-1978608 4 61789027 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272124 Affx-1111833432 AX-519545882 4 56022252 GCAAGCAGATTCTGAGCCACTGGACCACCAGGGAA[A/G]TCCAACTAAGTATCTTTTAAACCCTCACCTGGGCC R 2 1 2 1 101000 r 74 goat 4_56022252_AF-PAKI 4 56022252 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278087 Affx-1111836245 AX-519551577 4 56061967 GTTAGCAACACCTCACAGGCCTAGAATTTTCCACA[A/C]CACCACCAGGTTCATTTGTGGAGGAAGCAGCTTCT M 2 1 2 1 101000 f 74 goat Random2.2K-443 4 56061967 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395064 Affx-122964189 AX-123265419 4 56112700 AGTAGTTGAAGTCTCTTGAGTTCTTAGTATGTGTT[A/G]CTACATACACATTTAAATGCAGAGTTCCAAAGAAT R 2 1 2 1 303000 f 74 goat snp37236-scaffold453-1855566 4 61667263 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379649 Affx-122975944 AX-123250007 4 56164592 TCATTTATTAGCACTGATCACTTGTGTATAGGGAA[G/T]CACTGGGAGGTTCTATTTTTAAACATGTTTGTTAG K 2 1 2 1 101000 f 74 goat snp37235-scaffold453-1803674 4 61614823 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790473 Affx-122945253 AX-385277476 4 56206956 AGCAAAGTGTCAGGTTTTCTCAGGTAGCTGATGGT[A/G]TAAAATCATCCATGCCCTGTGACTTAACAAAAGCC R 2 1 2 1 101000 f 74 goat snp37234-scaffold453-1761310 4 61572239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796911 Affx-122942100 AX-385283854 4 56329054 CTAATGTCTACCAAAATACACACCAAAAAATGGAG[A/C]TTAATCAGTGTCCAAGAGTGAACCCCCATCTGATT M 2 1 2 1 101000 f 74 goat snp37232-scaffold453-1639212 4 61449077 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396767 Affx-122962771 AX-123267122 4 56369778 CTAATAGACATAAACTATCAAATATTTTAAAGAAA[A/C]TTTTCCCTTCTGCTAAGAACAGTGGCGATTCATTA M 2 1 2 1 103000 r 74 goat snp37231-scaffold453-1598488 4 61408302 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400522 Affx-122961264 AX-123270877 4 56411222 TTATGGCCAACATTTATTGGTCTATAAACAGTTGG[A/G]TGATCAAACAGCTAGTCAGTCAGTCAGTTGAGTTG R 2 1 2 1 101000 f 74 goat snp37230-scaffold453-1557044 4 61366093 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795262 Affx-122940060 AX-385282220 4 56454325 CTGAAGGTACATGTAAAAGTCACAACTTTTATCAC[A/G]TGTTATCCCTGATTTTTAAGTAATAGCCATCAGAA R 2 1 2 1 201000 r 74 goat snp37229-scaffold453-1513941 4 61323008 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397827 Affx-122962479 AX-123268182 4 56490224 ATGTTCATCTGTGAAGTCCCTTTTGCCATGTAATA[A/G]GATAACATATTCATAGGTTCCAAGGGTCAGGGTAT R 2 1 2 1 101000 r 74 goat snp37228-scaffold453-1478042 4 61286314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410775 Affx-122952677 AX-123281125 4 56530541 TCCAATATGTGCATTTTGTCAGATGCTAGATCTAC[A/G]TTACTACCAAAAAGTAACAAAATAATAAGAAGCTG R 2 1 2 1 101000 f 74 goat snp37227-scaffold453-1437725 4 61245180 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411598 Affx-122951609 AX-123281948 4 56580174 CTACTCCAGGGCTTTTACACATTTCATTTCCTATA[C/T]TTGGACTGTTTCTTCTCCCTTCTTAATACCCTCCT Y 2 1 2 1 201000 f 74 goat snp37226-scaffold453-1388092 4 61195349 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803157 Affx-122953762 AX-385290020 4 56630089 ACCTAAATTAAATTGGTTATGAATGTCAGTGATAC[A/G]CTAGTGAAGATTAACAAAGAGCTCAGAAGATACTG R 2 1 2 1 101000 r 74 goat snp37225-scaffold453-1338177 4 61145044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452155 Affx-122921658 AX-123322488 4 56671490 ATGGTTATTAAAAAAAGTGGGCATGTGGAAATTTT[A/C]TAGCATGTTCAAGAGTTAATAGAATAGTATAATGT M 2 1 2 1 101000 f 74 goat snp37224-scaffold453-1296776 4 61103045 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797403 Affx-122937093 AX-385284342 4 56715554 GAGAAATAAGTTTATTAAAGGCAAGAAAATCCAGC[A/G]TGAATGGCACTTTACTTAAGACTAAAGGTTACCAA R 2 1 2 1 101000 r 74 goat snp37223-scaffold453-1252712 4 61057609 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799941 Affx-122964481 AX-385286867 4 56751769 AAAATAATAAATCAACTTATATGATGAAATCAAAG[C/T]ATTAACTTGGATTGAGAGGCCAAAGCAGATTTTGA Y 2 1 2 1 101000 r 74 goat snp37222-scaffold453-1216497 4 61021395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405432 Affx-122956059 AX-123275784 4 56786645 TTCTACTCCTTTGGCTATTTCTTTTTCCCTTTTTG[C/T]ACTTCATTCTGAAACCCCAAGACTTATCTCTTAGT Y 2 1 2 1 201000 r 74 goat snp37221-scaffold453-1181621 4 60986663 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442253 Affx-122928284 AX-123312590 4 56826533 ACCTTAGATTTCTCAGACACAAAATGTGGATCTCT[A/G]TTGGGCATGAAGTTTTGTTTTGTTTTTCCCTAACT R 2 1 2 1 101000 f 74 goat snp37220-scaffold453-1141733 4 60944652 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779309 Affx-122973145 AX-385266413 4 56881254 ATCAAGTCTCTGTGAGGGTGAAATGGGATAATACA[C/T]GCAAAATGCTCTCTTCCATGCCTGGTACATGGTAT Y 2 1 2 1 101000 f 74 goat snp37219-scaffold453-1087012 4 60888772 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415059 Affx-122949479 AX-123285408 4 56923762 ACAGCTCTGAATATCCAGAGATTCACATAGTTGGG[C/T]AGAGAAGAGAAGGGGGAGGGAGGAGATAGAGATGA Y 2 1 2 1 101000 f 74 goat snp37218-scaffold453-1044504 4 60847725 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418759 Affx-122946202 AX-123289107 4 56955520 TCTTGAAAATTGTAGCAGCCTCAGTCACTTTGTTT[A/G]CATATTATGGAGTGGTCCCTCCTACCCTCCTTTCC R 2 1 2 1 101000 r 74 goat snp37217-scaffold453-1012746 4 60815642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377596 Affx-122978309 AX-123247955 4 56986417 GTAGTAGCATTCTACATATTGCAGTTGGGGAAGAC[A/G]CCCTGGAGACCTAAAAAAGGGGCAAGTGAGCCATA R 2 1 2 1 201000 f 74 goat snp37216-scaffold453-981849 4 60784687 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434154 Affx-122934901 AX-123304495 4 57025345 AAGGTACATGTCCTATTGGTTTCAAAGAGAATAAA[C/T]GACATGATATACTATCTTAGATTTTTCATTTAATT Y 2 1 2 1 202000 r 74 goat snp37215-scaffold453-942921 4 60745821 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440322 Affx-122930203 AX-123310659 4 57062555 CTTGGCACATGAGCCCTTGCATATATGAGGGATGT[A/G]GGAAAATAAATTAATATAAACTTATTAACATCTAG R 2 1 2 1 101000 f 74 goat snp37214-scaffold453-905711 4 60708843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422749 Affx-122943244 AX-123293095 4 57092454 GATCTTGGATCCAGGATCCAGAAAGGACTTACCAA[G/T]CATTTCCAGAGACAGTGAAATCAGGGGCTCACGCA K 2 1 2 1 102000 f 74 goat snp37213-scaffold453-875812 4 60678669 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428599 Affx-122938697 AX-123298941 4 57123986 CCCACATTGCAGGCAGATTCCTTACCATCTGAGCC[A/G]CCAGAGAAGCCCCAACACTTGTATAATAATATAAA R 2 1 2 1 303000 r 74 goat snp37212-scaffold453-844280 4 60646730 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407952 Affx-122954354 AX-123278303 4 57155269 AAGTTTGTATATATTTGAAGGTTTTGTTGGAGATG[A/C]GAGGTAAAGTGGGATGTATATGTAAATGTAGTGAG M 2 1 2 1 101000 r 74 goat snp37211-scaffold453-812997 4 60614370 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273791 Affx-1111833816 AX-519547402 4 57168749 GGGTCCACAACCGCACTTTGAGTAGCATCATGGTA[A/G]CACATACAACACAGGAGGCTGCAGTAAGTAATTTG R 2 1 2 1 201000 r 74 goat GoatD01.005801 4 57168749 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443011 Affx-122928174 AX-123313348 4 57241362 ACATATCTTTTTTCATTTTTAGAATATACATTACT[C/T]ATTCAAGGAAAATCTGAGAGAGGTAAACTTTCTGA Y 2 1 2 1 201000 f 74 goat snp37210-scaffold453-726904 4 60527825 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406934 Affx-122955078 AX-123277285 4 57297429 AGAACAAAGCGTCCTTTCAAGATTATAACTGGCTA[C/T]AATTTGCCATCAATCAGACTAATTAATCTCCTGAG Y 2 1 2 1 101000 r 74 goat snp37209-scaffold453-670837 4 60470712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423276 Affx-122942658 AX-123293622 4 57330726 GGGTGTGATTTGAGCATGAAAAATTTCTTGAATTC[A/G]CTGAATACATGCTGAACTAGAAATGGAAGAATAAC R 2 1 2 1 101000 r 74 goat snp37208-scaffold453-637540 4 60436733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424917 Affx-122941297 AX-123295263 4 57360890 GACCCAGACTTAGAAGTCATGCAGTGTCATTTGTA[C/T]GTGTTAGAACTTGAGCCCACACTCAGGGGTAGGGG Y 2 1 2 1 101000 f 74 goat snp37207-scaffold453-607376 4 60406329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376463 Affx-122978048 AX-123246822 4 57395923 CGTTAGAGGTCATTCACTATGATCGAATAACTATA[C/T]GTGAAGTTGCAACATTATTGTATAAATAAAGGCTA Y 2 1 2 1 101000 f 74 goat snp37206-scaffold453-572343 4 60371367 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784852 Affx-122977313 AX-385271899 4 57445297 TCAAAGCACAGACTTGGAGAAGTAGTTTTCACTTG[A/G]CACATTTCTCTCCTACACCCATACTTCATGGCAAT R 2 1 2 1 101000 f 74 goat snp37205-scaffold453-522969 4 60321840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439322 Affx-122930948 AX-123309659 4 57487928 GATACTTCTTGGACTCAGTCCCCCAAAAGAAGTGA[C/T]AAACAGGTCTGTGACCTCTGTGTGTGTCCCTTGAT Y 2 1 2 1 102000 f 74 goat snp37204-scaffold453-480338 4 60278944 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793557 Affx-122936225 AX-385280532 4 57521644 TAATTCTAAAAGCCAAAATTTTGATCTCAGTGATC[A/G]TAAAAATTCAAACCTAATGTAAAGACACAGAAAAA R 2 1 2 1 101000 f 74 goat snp37203-scaffold453-446622 4 60245129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778550 Affx-122976698 AX-385265662 4 57553322 TTAAACTCCTGTGTCATGCACCAAAACTTCAATGC[A/G]CTTTATGCAATGAGTGAGCCATTAAAAGGTCTTGG R 2 1 2 1 101000 f 74 goat snp37202-scaffold453-414944 4 60213189 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767996 Affx-122933294 AX-385255210 4 57584999 TGAATGAAGACACTAATCTCCAACACTGGGGTGAA[G/T]ATTATTTCAGGCAAGCACCCAAGGTCTCTTCCAGC K 2 1 2 1 101000 f 74 goat snp37201-scaffold453-383267 4 60181503 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435308 Affx-122934021 AX-123305648 4 57621576 CCTAACTGGCATACTCTAATAGTCTTTACCAGTAG[C/T]ACCTGACCATATAGAAATGAGCAGTTTCCTGTGGA Y 2 1 2 1 101000 f 74 goat snp37200-scaffold453-346690 4 60144983 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405053 Affx-122956348 AX-123275405 4 57685728 TCCATTCCACTCCTATTACAGAAAGAGATAAGAAA[G/T]ACCTAGAAGCTGACCTCCTATTATTTAGGACCCAT K 2 1 2 1 101000 f 74 goat snp37198-scaffold453-282538 4 60080633 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785795 Affx-122954373 AX-385272835 4 57727617 TCTGCCCCTTTACCCATCATGTCAGGAAGAACAGA[C/T]CTGTTGTATTCATCACAATCCAAGCCCTGAGAAAG Y 2 1 2 1 101000 f 74 goat snp37197-scaffold453-240649 4 60039029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790083 Affx-122928124 AX-385277089 4 57757026 CTCAAACCATCAGCCCAACTCTTTCTGGGGAAATG[C/T]AGGAATATGAGCACGTAGTGAAGTCTGCTACTTGT Y 2 1 2 1 101000 f 74 goat snp37196-scaffold453-211240 4 60010119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384838 Affx-122971967 AX-123255196 4 57797726 ATTAAATACTATCCTATATAGGCCTTTGGCCACTC[A/G]ATAATGAGAAGAATGTCTCCCAAAGTGGTTCAAAC R 2 1 2 1 101000 r 74 goat snp37195-scaffold453-170540 4 59968183 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774964 Affx-122940423 AX-385262097 4 57846816 TTAAAGCGCTATCACCATACAAAAACTTATTAATC[A/G]CATTATCACAGTACCTTTTTCAGGACTGGTGTGAT R 2 1 2 1 201000 r 74 goat snp37194-scaffold453-121450 4 59919054 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443497 Affx-122927802 AX-123313834 4 57895285 GGATAGAATGCTTACATTTTCATGTCTTGATCCCC[A/G]CATACTGCCTGTGTTAGTATTTCATTTTTTTTTTC R 2 1 2 1 201000 r 74 goat snp37193-scaffold453-72981 4 59870732 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419894 Affx-122945346 AX-123290242 4 57935056 TTTGGCAGAGTATTTAGAAAAGTGTAAAAGGTCGC[A/G]CTATTTTATATCAAACTAAAAAATGAGGGGACCAG R 2 1 2 1 202000 f 74 goat snp37192-scaffold453-33210 4 59830587 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449180 Affx-122923528 AX-123319515 4 57965462 ACAATGTAAAAGGCCCTAAGACTGAATGTGCTTGC[A/G]TGGAATGAGCTCCTGGCCTGGGAAAGGGAAAGATT R 2 1 2 1 101000 f 74 goat snp37191-scaffold453-2804 4 59800230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440751 Affx-122929868 AX-123311088 4 57986383 AGATGGGCAAGCTGAATAATACCTACCATTGTTGA[G/T]CAGGAAATGTGGTTTGTAAAGTGAGGCACAGGCCA K 2 1 2 1 101000 f 74 goat snp15778-scaffold1654-1545221 4 59779839 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387460 Affx-122970365 AX-123257818 4 58044496 TGAAGTATGGATAATTGTTGTGATTTCAGTCCCTG[C/T]GAAAAGAGACAGGCATTTCAAAGGTAGTAGGAGGA Y 2 1 2 1 201000 f 74 goat snp15777-scaffold1654-1487108 4 59721313 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400958 Affx-122960115 AX-123271311 4 58082927 TTGTGGCCTCATCCTCTTTATCCCTCAGTTCTCCA[C/T]GCACTGTGTTGCTTCGCATTAGTCTATAGATGGGA Y 2 1 2 1 101000 r 74 goat snp15776-scaffold1654-1448677 4 59682790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424289 Affx-122941980 AX-123294635 4 58141816 GAGCAATTTAAAAATTGACACCAGGTGTTCTTTGA[C/T]ACACTTGCGGTGTTGCCTGAAAGGCAGAGAACAAT Y 2 1 2 1 201000 f 74 goat snp15775-scaffold1654-1389788 4 59624355 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796796 Affx-122946372 AX-385283739 4 58173550 CTCTTTAACATCACAGAACCTGAGAAGGACCAGTC[G/T]GTGACTGTGTCCTGTCTAATTCATACTCCTGAAAT K 2 1 2 1 101000 f 74 goat snp15774-scaffold1654-1358054 4 59592409 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420285 Affx-122945040 AX-123290633 4 58207250 GAACCTCTGTCTGTGCAGAAGGTTGGAGAAAGGTC[A/G]CACAGCTTCATTTTTAAAGACAGCTTTCAGTTGTT R 2 1 2 1 201000 f 74 goat snp15773-scaffold1654-1324354 4 59558357 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399880 Affx-122960222 AX-123270235 4 58258865 GTAAGATGGTGGCTTTAGAGACTAGAATTCAAAAG[C/T]GGGACAGTATGGCCTGGTGGGGGGACTGGACAGAC Y 2 1 2 1 101000 f 74 goat snp15772-scaffold1654-1272739 4 59506815 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769499 Affx-122945315 AX-385256669 4 58291326 GAGAAAGAGAGAAAGAATCTCTATCCAGTGTTAAG[C/T]AATTCCTGGTCCATGTTAGGCAATGGGAAGCAAGC Y 2 1 2 1 101000 r 74 goat snp15771-scaffold1654-1240278 4 59474502 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384454 Affx-122973093 AX-123254812 4 58347455 AAATTCTTGTCTTTTTTTTTCATATCCATATATGA[C/T]GGTGTCTAGCAACCCATTATGAAAATCACTTGAAA Y 2 1 2 1 101000 r 74 goat snp15770-scaffold1654-1184149 4 59417362 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782308 Affx-122934659 AX-385269386 4 58437880 AAACAGGGCATCTGCTAAAGACAAATGGAATCATG[C/T]GGCTTCATGGAGCCTACAGATTTTCAACCAGTGAT Y 2 1 2 1 101000 f 74 goat snp15768-scaffold1654-1093724 4 59327642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380064 Affx-122975562 AX-123250422 4 58528448 CCAGCAGGAAATTGGACCCTCTGGAAATACATTTC[A/G]TTGCTGGATTCCTAGAGTCGATAAATTCTGCATGC R 2 1 2 1 101000 r 74 goat snp15766-scaffold1654-1003156 4 59237778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278089 Affx-1111836246 AX-519551579 4 58548723 GGTCAGTTTGCAAAGAAAATTGAGTCCCAAGATAG[A/G]TCTTAGGCTGCTAAAGGAGTAAACAGATGGAAAAT R 2 1 2 1 101000 f 74 goat Random2.2K-444 4 58548723 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431605 Affx-122936164 AX-123301946 4 58567775 GAAGCCTAATGAATGGAAAGGGAAGATAGGAAAAC[A/G]TGACAAGATCGCCCCGGAGACCCCTCTCATGGTTC R 2 1 2 1 101000 f 74 goat snp15765-scaffold1654-963829 4 59198823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391472 Affx-122966722 AX-123261829 4 58623491 ATTATGCAGAAATGCCCTGCTCTGCTTGCAGGCTT[A/G]TAGTTCTCAACAGAGATTTAGGAACCTAGATACTT R 2 1 2 1 201000 r 74 goat snp15764-scaffold1654-908113 4 59142988 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272127 Affx-1111833434 AX-519545885 4 58626247 ATACCTTGCAGTACCTTTCTACAGGCCCCTTATTC[A/G]TCTTTTCTTTCCATTCATCCTTGAGACATCATATT R 2 1 2 1 201000 r 74 goat 4_58626247_AF-PAKI 4 58626247 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38422015 Affx-122943635 AX-123292362 4 58653245 AGAATGGGCTGCTTGAAATTTTAGACAAGTGGCTT[A/G]TGAAGGCCTGCAGGACCTGAGGAAACCAGCCCAGA R 2 1 2 1 101000 f 74 goat snp15763-scaffold1654-878359 4 59113195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448997 Affx-122923104 AX-123319332 4 58683183 AACTAGCCCCACACATCTAGGAGGGACAAATGAAA[C/T]GGTTCTTTACTGAGTGCCTCTTATGTGCCAGTCAC Y 2 1 2 1 102000 f 74 goat snp15762-scaffold1654-848421 4 59084037 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392007 Affx-122966491 AX-123262364 4 58737852 TAGGCTCTGAAGACAGGAGTGCAAACCAGATACAT[A/C]TTGAGGCTCAGTATGACTCAGTTTATGTACTGAAA M 2 1 2 1 101000 f 74 goat snp15761-scaffold1654-793752 4 59029362 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444266 Affx-122927206 AX-123314603 4 58775346 TTTCTGACATGTTCTTAGTAATGTGTTTGCTATCA[G/T]CAGGAAGATGTTACTTCAAATTTGATTCATATTTG K 2 1 2 1 10000 f 74 goat "snp15760-scaffold1654-756258;SV_290" 4 58992122 T G SV_290 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420470 Affx-122944876 AX-123290817 4 58827198 GTTGGAAAAACAATAGCCAACAAAAATCAGCACCT[A/G]TATGTCAGGCAGTATTTCAAGTACATAAAGTATTG R 2 1 2 1 10000 f 74 goat "snp15759-scaffold1654-704406;SV_288" 4 58939928 G A SV_288 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405552 Affx-122955965 AX-123275904 4 58866353 GTCAGACAGACATGCAGTCAAATCCTGGCTTTGCC[A/G]CTTACTAGATGTATAAGTCAATGATAGGTTTAGGT R 2 1 2 1 201000 r 74 goat snp15758-scaffold1654-665251 4 58900427 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798370 Affx-122957498 AX-385285305 4 58895279 TGTACATTCTTAATCTTTAAACTGTGAATTTTAGT[A/G]TTGTTCACCCTGCATATAACACCCCTCCACTGCTC R 2 1 2 1 101000 r 74 goat snp15757-scaffold1654-636325 4 58871508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797347 Affx-122950160 AX-385284286 4 58941218 TAACCTTTTAGTCCATTGTTTCTTAAGATTTTTGC[A/G]TTCATAAACACTAGTTATATCATCTTTTAGGGATA R 2 1 2 1 101000 f 74 goat snp15756-scaffold1654-590386 4 58825379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435832 Affx-122932825 AX-123306171 4 58975013 AATAATTTCCTCTAGAACTCCAAAGGGGCATTCTG[C/T]GCTTAGCTGTTTCTACTCACAGGCCAAATTAGGTA Y 2 1 2 1 101000 f 74 goat snp15755-scaffold1654-556591 4 58792399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427585 Affx-122939469 AX-123297928 4 59008164 GGTTTCTATTAATTATATAAATTAACACATAATGA[C/T]AGCCTTTCTCCATGTACCCTCTGTGAGGAATGATA Y 2 1 2 1 101000 r 74 goat snp15754-scaffold1654-523440 4 58759336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436053 Affx-122932714 AX-123306392 4 59045815 TGTTGAAGATCATGTTTTTCATCATACATTACTCA[C/T]TTACCATTTTGGCTTCTATCCAGCTCTCAGTGCTA Y 2 1 2 1 101000 r 74 goat snp15753-scaffold1654-485789 4 58720509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792581 Affx-122951252 AX-385279562 4 59088312 ATCCAAACATTAAAAACCCCAAAATGATGCTTATC[A/G]TTCTGAATTCTCTTGGCTCACTCTTTGCCTTGCCT R 2 1 2 1 202000 f 74 goat snp15752-scaffold1654-443292 4 58677252 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434841 Affx-122934380 AX-123305182 4 59124243 GTAAGCCTGGAGGACAAGCAAAGGAGGCACTTGGA[C/T]GAAGCCATGGAGATGGAGCCAACTTTCCACAAGCA Y 2 1 2 1 102000 r 74 goat snp15751-scaffold1654-407361 4 58641070 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415115 Affx-122949437 AX-123285464 4 59154921 GCCAGCAGGGGCACAGAGGCCAAAGGAAGCAAAGC[A/G]TGTGAGGACAGCAGGAAGGAGACCAATTTAGTTCA R 2 1 2 1 101000 r 74 goat snp15750-scaffold1654-376683 4 58610546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778020 Affx-122969894 AX-385265136 4 59188425 TTCTGTGTTAGAACAATGAGTGAAAGTGCAGGGCC[A/G]CTGCCAAACTTAGAATTGAAACTATTCAATTGCAG R 2 1 2 1 101000 f 74 goat snp15749-scaffold1654-343179 4 58577268 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431286 Affx-122937097 AX-123301627 4 59220918 CAGATGAGTCCCTTGTGGCTGCAGGCTTCTACTTG[C/T]AGGCCCAGCTGTGTTCTGTTTCGGGGTCTCTCCTG Y 2 1 2 1 101000 f 74 goat snp15748-scaffold1654-310686 4 58544519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779874 Affx-122928439 AX-385266973 4 59274558 TGCCACTTTGCTTTTATGAAAGACCTTCATCAGTA[C/T]CTGTTTTTGCTATTCGAAAGGAATTTTCTCTTTTA Y 2 1 2 1 101000 f 74 goat snp15747-scaffold1654-257046 4 58490818 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770406 Affx-122973995 AX-385257572 4 59369054 TAACTCCATGCCTCAATTCTTTTGGCTATGAAATG[C/T]AACATAAAAATACTGTTGTTCCTATCTCAAGATAT Y 2 1 2 1 101000 f 74 goat snp15745-scaffold1654-162550 4 58395689 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403176 Affx-122958079 AX-123273529 4 59426047 TTGTAGATTTCTCCATCCTTCTTCCCATTCCAGGC[A/G]TCTAAATCAGAACTGAGGCGTGCTTTTGTTTATCT R 2 1 2 1 201000 r 74 goat snp15744-scaffold1654-105557 4 58338592 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410917 Affx-122952058 AX-123281267 4 59474151 GGGATGTTTTATGTATGAAAACTCTTCTGAGGAGG[C/T]AGATGGTGTGGGAAAGGTACATTCCATGCAAGTGT Y 2 1 2 1 101000 r 74 goat snp15743-scaffold1654-57453 4 58289189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440630 Affx-122929956 AX-123310967 4 59523695 ATTTGACTCTCTTAAGGTTAAGTCATCTATAAGAA[C/T]AGGAATTTAGAAAAATATTTGCAAACTCCATCTAG Y 2 1 2 1 101000 f 74 goat snp15742-scaffold1654-7909 4 58238652 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403797 Affx-122957972 AX-123274149 4 59533870 TCTTCACCAGGAAGATACGAATGAGGTCAAACTCA[C/T]GGGGCTATTTAAATTTATGTTACTGCTCGGCTGGC Y 2 1 2 1 101000 f 74 goat snp56814-scaffold9-2636987 4 58226021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775028 Affx-122956198 AX-385262160 4 59698912 TCACCTATGGATTCCCATTACACTGGAATAAAATC[A/G]TACTTTTTCCCATGTCTTACAGTGTGTGTGATCTG R 2 1 2 1 101000 f 74 goat snp56810-scaffold9-2471945 4 58060412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408256 Affx-122953814 AX-123278607 4 59732173 AAGCAGAGGAAGTTCTGACACGCAGACAGAAGGGG[C/T]GCTGTAACCATGGGCTCAAAGATGGTATCGGTGTG Y 2 1 2 1 101000 r 74 goat snp56809-scaffold9-2438684 4 58027103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424774 Affx-122941404 AX-123295120 4 59779404 GCCTGAACAGAATGGGTGCCTGAAAGACATCTGCT[A/C]GAGGAATGAAAAGAGGAAAGGAAGAAAGGAGGAAA M 2 1 2 1 101000 f 74 goat snp56808-scaffold9-2391453 4 57979092 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399567 Affx-122961123 AX-123269922 4 59831556 TGCCTCCTGGTTGACTGCCTTACTGGTTGTTGACC[A/G]CTTGGCAGTGCTTCCTTAGCAGCAGGTGGGGCGAG R 2 1 2 1 101000 f 74 goat snp56807-scaffold9-2339301 4 57926964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767696 Affx-122947944 AX-385254932 4 59885872 AATAATACAGTTAATCAGCAAAGATTGGTATGATG[C/T]GTCCACATCATCGCTAACACACAAATTAAGTTGGC Y 2 1 2 1 201000 f 74 goat snp56806-scaffold9-2284985 4 57872703 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392592 Affx-122966058 AX-123262949 4 59916366 ATTTACACTCACAGCAATCTGTCATTTGGCTGTGA[C/T]GAGTTCTCTCATGAAAAGAGTTCTATGGACTTTTT Y 2 1 2 1 101000 r 74 goat snp56805-scaffold9-2254491 4 57841241 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424529 Affx-122941724 AX-123294875 4 59950455 AGAATTGGAAGGTGCAAGAGCAATCCTTCTTTCCA[C/T]AGGAAGTGGCTTTCAGCCTTAGTCTCCATCTGTGC Y 2 1 2 1 101000 r 74 goat snp56804-scaffold9-2220402 4 57806533 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379971 Affx-122975630 AX-123250329 4 59990147 AGTACTGCTTTCTTAGGGTGATGCAGAAAGACAAA[C/T]AAACCAACAGAACAGAAAAGAGAATTTGCACAAAT Y 2 1 2 1 101000 f 74 goat snp56803-scaffold9-2180710 4 57766722 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450484 Affx-122922931 AX-123320818 4 60019692 TCATTTTCCCATTTGTGGGTCGACTCCCTGGGGGT[A/G]TGGATCTTGACTGCCGCATCTCCACCCCTCCTACT R 2 1 2 1 202000 r 74 goat snp56802-scaffold9-2151165 4 57737126 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426022 Affx-122941126 AX-123296368 4 60055190 CTCACTGGTCAGGTTCCCTAGGAAACAAACTCTGC[A/G]TCAGAGATTTGCATGCAGGAAGCTTACTGGGGAGT R 2 1 2 1 201000 r 74 goat snp56801-scaffold9-2115667 4 57701884 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385649 Affx-122971164 AX-123256007 4 60148472 GTTGGTTCACTGGGGCTTTCTCATGTTCCGAAGCA[C/T]AAGAAGAGAAGTTCTGAGGAGCTGCCTCTGCATGA Y 2 1 2 1 101000 f 74 goat snp56798-scaffold9-2022385 4 57607633 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400077 Affx-122960752 AX-123270432 4 60181098 GACCAGATTCAGACTGCCAGGTCCACAGTGGATTC[A/G]CAAATATCTCAAACACCAGATGATTCTTTTCTGAG R 2 1 2 1 101000 r 74 goat snp56797-scaffold9-1989759 4 57575307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376042 Affx-122978938 AX-123246401 4 60217785 CCTGAATGTTTCCTTCAGTTTAAAAATGAACATCA[G/T]AAACACCATCGTAATGTCTGTAGAATATTTCATTG K 2 1 2 1 101000 r 74 goat snp56796-scaffold9-1953072 4 57538282 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385536 Affx-122971239 AX-123255894 4 60277285 GTGACTCATAGGGGTTCACAGAGGCCCACATTCTT[A/G]TCTGTGAGATGTTGCCTAAGAGAGACATCTTAGAA R 2 1 2 1 201000 r 74 goat snp56795-scaffold9-1893572 4 57477826 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441673 Affx-122929183 AX-123312010 4 60335356 ACTTTGGAAGTATCCATTTAATCCCCTTAATGTAT[C/T]GATTTCCCCAGGTGACACAGAAGAAACAGTGGCTT Y 2 1 2 1 101000 r 74 goat snp56794-scaffold9-1835501 4 57419971 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400733 Affx-122959907 AX-123271088 4 60425892 CATTTTCCTTCTTATTTCAAGAAATGTGTGTTGCC[A/G]TTTCATAGTCTAGAAATACAGCATCTGCCAGCTGA R 2 1 2 1 201000 r 74 goat snp56792-scaffold9-1744965 4 57329454 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781187 Affx-122972405 AX-385268272 4 60459899 GAAGCCTCACGATCAGGAAGCCAGAGGAACTCTGT[G/T]TAAATGGGCTATGCCATTAACTAGTTGTGTGACCT K 2 1 2 1 202000 f 74 goat snp56791-scaffold9-1710958 4 57295461 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439532 Affx-122930116 AX-123309869 4 60559920 AAATTTAAAATTCAGTTTCTCAGTTGTATTAGTCA[C/T]GTCTTGAGTGCTCGCTAGCCATCTGTTGCAAGTAG Y 2 1 2 1 101000 r 74 goat snp56789-scaffold9-1610937 4 57197903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425294 Affx-122940957 AX-123295640 4 60593605 TCAGAACATTTTCACCCGTATCCTCTCATGTTGCC[A/G]TGGAAGGCAAGTAGAAGGAAGGACAAAAGAAAAAT R 2 1 2 1 101000 f 74 goat snp56788-scaffold9-1577252 4 57163734 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429473 Affx-122938478 AX-123299815 4 60657779 GCGTGGCTGACGTCACCTTCTCAGCACAAGGAGCC[A/G]AACTGTCTCAATGTCTGTGGCTCCTTTCTGGAACC R 2 1 2 1 102000 f 74 goat snp56786-scaffold9-1513078 4 57098818 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440912 Affx-122929214 AX-123311249 4 60689489 GCTTTCCTCATGTGATAAAACAAATCCCTAAGAGA[G/T]CCTTTATTTATTACTATTTTTGAATGCGAAGACTT K 2 1 2 1 101000 f 74 goat snp56785-scaffold9-1481368 4 57067302 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387085 Affx-122969877 AX-123257443 4 60781741 ACCCTGGGAGAAGTGGTAGGTGAGTTCTCCACCAG[A/G]CCCCCTCCCTTCCCCCGTTTCCCATTGGTCAGAAT R 2 1 2 1 101000 f 74 goat snp56783-scaffold9-1389116 4 56974507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415356 Affx-122948777 AX-123285705 4 60814365 CAAGAATTTGTGTTCTAGTCAACCACTTACTTGCC[A/C]TGTGACTTTGAACAAGTAATTAATCCTTCTGAGAC M 2 1 2 1 101000 f 74 goat snp56782-scaffold9-1356492 4 56941761 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412622 Affx-122951273 AX-123282971 4 60848391 GAATCTCCCTGTTTGGCAGAGCCTGTGGAGCCACC[A/G]TGCTTGGTCAATGACTAATAGGGTTGGGAGATTAA R 2 1 2 1 101000 r 74 goat snp56781-scaffold9-1322466 4 56907298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278247 Affx-1111836247 AX-519551735 4 60852311 AAAATGTCAAAGTTGTGAAGTAGTCTTAGTTTAGC[A/G]GATCCTTCCTTTCTTATCATCTCTCTTCTTGCATG R 2 1 2 1 101000 r 74 goat Random2.2K-445 4 60852311 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320774590 Affx-122972202 AX-385261724 4 60888665 TAAATAGTTGAGTTGCCTATTAGATTTGTCAAATT[A/G]CTTGCCCCAAAGTTAAACTGAAGTGCATGATAACA R 2 1 2 1 101000 r 74 goat snp56780-scaffold9-1282192 4 56866673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400022 Affx-122960793 AX-123270377 4 60919646 CGATATTTATGCTAAATATTATTTAAAACAATACA[G/T]GTTTACTGTTTCATGTAGACAGAGTAAATTATGCA K 2 1 2 1 101000 r 74 goat snp56779-scaffold9-1251211 4 56835576 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432144 Affx-122936429 AX-123302485 4 61028178 TAGGTAATTTATCATTAATTGGACATCTCAATAAT[C/T]ATAGGCATTATTATACTTTTTATCTTTGTTACTCC Y 2 1 2 1 101000 f 74 goat snp56777-scaffold9-1142679 4 56726750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400562 Affx-122960420 AX-123270917 4 61074240 TTTAACTGGATGCTTCTGCTAAGGTATCTAACCAT[A/G]AGATTTTGTTGTTCACTAAAGCCTTTGACTGTGTG R 2 1 2 1 101000 f 74 goat snp56776-scaffold9-1096617 4 56680674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397938 Affx-122961923 AX-123268293 4 61119589 TTATATACACACAGATGACATTTGCCTCTCTGACT[A/C]GTCCCATTTAGATTTCATACCTTCTTCAGATACTT M 2 1 2 1 201000 r 74 goat snp56775-scaffold9-1051268 4 56634833 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464303591 Affx-1110414694 AX-515777733 4 61162441 TACACAAATTAGTCTAATTAATTATAGAATATATT[A/G]TAGTCACTTGGACCAAAATATGTATATCTCAATCT R 2 1 2 1 101000 r 74 goat 4_61162441_AF-PAKI 4 61162441 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320784244 Affx-122972133 AX-385271295 4 61174663 GAGATTTGCTGTGCTTGGCTTCTTCACATGATCTT[A/C]GTTTGTGGGAGAATTTTGACCTTATTTGATGCATG M 2 1 2 1 101000 f 74 goat snp56774-scaffold9-996194 4 56579650 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450340 Affx-122922119 AX-123320675 4 61213935 CACAAATGCTCACATATAAATCTGTATACACATAC[A/G]TACAGACTGACATATATATGTAGATTGTTTTAATT R 2 1 2 1 101000 f 74 goat snp56773-scaffold9-956922 4 56539290 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409780 Affx-122952981 AX-123280131 4 61315316 TATATTCCTTTTTTTTCATTCATTAACACCCATTC[A/G]TTTTATAAATACTTACCATGTGTCTACTTTGTGTC R 2 1 2 1 202000 r 74 goat snp56771-scaffold9-855541 4 56437824 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379647 Affx-122975946 AX-123250005 4 61359074 TATTTTATAGCTGGTGTGATCCCCCCAGATTCAGT[A/G]CTTCATTTTGATGTACTTCTGATGGATATTTGGAA R 2 1 2 1 201000 r 74 goat snp56770-scaffold9-811783 4 56394562 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452774 Affx-122920251 AX-123323107 4 61401989 GAGCAGTCATCGTGATGCAGGATGCCCCTGGAAAT[A/G]AGGTACGGCCTTGGATAGGATGGCTGGCTTCAAGA R 2 1 2 1 201000 r 74 goat snp56769-scaffold9-768868 4 56351284 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400150 Affx-122960697 AX-123270505 4 61484405 AAACGAATATATTCAAGGAGAAATGAAGCTTTGCA[A/G]TGAGCTTTCACACCTGGGATACCTGCCACCCTGCA R 2 1 2 1 201000 f 74 goat snp56767-scaffold9-686452 4 56268590 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794837 Affx-122943895 AX-385281797 4 61521711 TTGGTTGAGATGACATCAGATTAAAAACTGTTTTC[A/G]TCCTAGGATATTTTTAGAGGCTGTTATTTAAGTTG R 2 1 2 1 101000 f 74 goat snp56766-scaffold9-649146 4 56230892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769911 Affx-122968467 AX-385257080 4 61553901 AAAATGTTTCTTCTCAAAAGTGCCCTCACTTAATT[C/T]GTTATGCCTTAAGAGATAATTCATAGAGTGGCTGT Y 2 1 2 1 101000 r 74 goat snp56765-scaffold9-616956 4 56198839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416854 Affx-122948098 AX-123287202 4 61614821 AGCTAGCATATTTTAGAGATTTCTTCTCCTTCTAA[C/T]GTATCTACTATGTTTGAGGCTCTATAGATCTAAAG Y 2 1 2 1 101000 r 74 goat snp56764-scaffold9-556036 4 56138054 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773025 Affx-122977374 AX-385260169 4 61649062 GCTGGGAAAAGAGGGCACTAAAGTCCTCTTTACTC[A/G]TAACTGATGGGAATTAATTGGGAATGACTTGAAGA R 2 1 2 1 101000 f 74 goat snp56763-scaffold9-521795 4 56104111 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407515 Affx-122954736 AX-123277866 4 61678711 TCAATACATATCATGTTATTTTTAACATCATCATC[A/G]TCACTAGGACTCTAGGTCCCTTTTGTGTGTTATTC R 2 1 2 1 101000 r 74 goat snp56762-scaffold9-492146 4 56073958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445701 Affx-122926118 AX-123316038 4 61711111 AGCCTGGCATGGATGGGAACACTCAGCAGGTGCGG[A/C]GAAAAGAAGATGGGCTTAGACCCAAACCAGGGGCA M 2 1 2 1 101000 r 74 goat snp56761-scaffold9-459746 4 56041179 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375988 Affx-122978424 AX-123246347 4 61747996 GAATAGGCTTTTGAAGAACAAGGAGGATTTCACCA[C/T]GCCCAGAAGAGACAAACACTATATTTCCTGCTGAG Y 2 1 2 1 101000 f 74 goat snp56760-scaffold9-422861 4 56008260 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420402 Affx-122944923 AX-123290749 4 61785332 TCACTCCCTCTTTAACTCTCAGCAACCACTAATCT[A/G]TTCTCCGTTTATAATTTTATCATTTCAAGAAAGCT R 2 1 2 1 103000 f 74 goat snp56759-scaffold9-385525 4 55970667 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414593 Affx-122949362 AX-123284942 4 61829790 ACTGAAGATTTTTAAATGTGGGATGGGTCAGATGC[A/G]GTGATTCTAAAAGCAAAGAGGCCAGTTGGGAGGCT R 2 1 2 1 201000 f 74 goat snp56758-scaffold9-341067 4 55926118 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402962 Affx-122958162 AX-123273315 4 61867626 TTTGGCATTCCGACTTGCTGCTTGGCACTGTGGTG[C/T]TCTGACTGCCCCAAATCCCAGATTTACTGGGATCT Y 2 1 2 1 202000 f 74 goat snp56757-scaffold9-303231 4 55887719 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440743 Affx-122929874 AX-123311080 4 61896526 GGAAGTCACGAGACAGTGTGTTCACTCTAAGCTCC[G/T]AAGACTTTTTCATATGTTTCCCACCTGAGCCTGGC K 2 1 2 1 101000 r 74 goat snp56756-scaffold9-274331 4 55858986 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444777 Affx-122926351 AX-123315114 4 61936314 CAGCAGAATCCGTTCAGAAGGTGACTTCTCAAAAC[G/T]CATCCTTAACTGAGATCAGCTGACAACTCTAAGAC K 2 1 2 1 101000 f 74 goat snp56755-scaffold9-234543 4 55819338 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421131 Affx-122944199 AX-123291478 4 61983364 CTAAGCACGTGGCCCGATGCTAGGCCCCAGAGACA[G/T]AGCAACGAAAACGCCAACACACAGCCTGACCTGAC K 2 1 2 1 101000 r 74 goat snp56754-scaffold9-187493 4 55772367 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770047 Affx-122933081 AX-385257214 4 62013650 TTAAACTTCTCAATCTTGCCGATTATACTCGGATT[A/G]TGTTAGAAAATGTCACTGTCCTTAGGGAATGCACA R 2 1 2 1 101000 r 74 goat snp56753-scaffold9-157207 4 55742198 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782220 Affx-122958047 AX-385269298 4 62045038 ACTATAATAAAATATTTTGGGTAAAGAGCTCTAAG[A/C]TCCATAACCTTAGTTCACTAACAATGTCTTTATTG M 2 1 2 1 101000 r 74 goat snp56752-scaffold9-125819 4 55713981 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413051 Affx-122950980 AX-123283400 4 62111736 TATGATGCATGCTGAAGTTTGAGAACCACTGCTCT[A/G]TTTGAAGCTCCCTCAAATGACTGCTATTTCACAGA R 2 1 2 1 201000 r 74 goat snp56751-scaffold9-59121 4 55647254 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789368 Affx-122923737 AX-385276378 4 62150404 TTGCTTTTGTGCTAAAACAGGTCTCTGTTAAATAG[C/T]TGCAACAGAGACCAAATGGCAGCAACGCATAACAT Y 2 1 2 1 103000 r 74 goat snp56750-scaffold9-20453 4 55608373 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434783 Affx-122933884 AX-123305124 4 62215463 CTAGAAATAATAACTTATATTTATTGAGTCCTTAC[C/T]ATACACTCAGCCTTATGTTATGCTGAGGCAGATAC Y 2 1 2 1 101000 r 74 goat snp11840-scaffold1439-516798 4 55535489 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377176 Affx-122978205 AX-123247535 4 62246227 ATAGAACACGTAGAATGTGAGGCACTAAGTGGGAG[C/T]AGCGTATTAGAAGGAAGCTCCACATTTCTTCCCTC Y 2 1 2 1 201000 r 74 goat snp11839-scaffold1439-486034 4 55504934 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452974 Affx-122920153 AX-123323307 4 62301859 TCATCCTTAATTCCAATGTGACAACTTCAGAGTCA[A/G]TTTCTTGATGGGAGAGCTGAGTTTTGATCTTCCTG R 2 1 2 1 101000 f 74 goat snp11838-scaffold1439-430402 4 55449572 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388066 Affx-122969525 AX-123258424 4 62334810 CCCAAAGCAAGAAACAGCATGAGAATCAGCACATG[C/T]GAATGAGACAAAAACCACAAGTCCAAAAAGGTTTC Y 2 1 2 1 101000 f 74 goat snp11837-scaffold1439-397451 4 55416651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278249 Affx-1111836248 AX-519551737 4 62374615 CTTTAATCCCTTCTAATCCTCGCAGCATCCCTGTT[C/G]TGTCAATGTTTTTCTTCCCTTTTGGTGCAAAGCAC S 4 1 2 1 102000 r 74 goat Random2.2K-447 4 62374615 G C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794760 Affx-122929961 AX-385281720 4 62376552 AGTTATGCATATTCAACTAAATATAAAAGGTATTC[A/G]CTTTCCCTATAACACAGTGACACTTTGTTATATAG R 2 1 2 1 101000 r 74 goat snp11836-scaffold1439-355709 4 55374209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441668 Affx-122929186 AX-123312005 4 62414941 GACTAAATATCATGGATACAAAAATGAGTAAGTCA[C/T]GGTCTTTGTTTCCCAGAAGTCCATTTATCTGAGTG Y 2 1 2 1 101000 r 74 goat snp11835-scaffold1439-317320 4 55335847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418984 Affx-122946066 AX-123289332 4 62444096 GTGAAAAGCAGGTAACATCCAGAGCTAGCAAGTGC[C/T]TGGGTAATGAGATCTCTCCTGAACCACTGGTGAAA Y 2 1 2 1 101000 f 74 goat snp11834-scaffold1439-288165 4 55307713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378693 Affx-122977067 AX-123249052 4 62475826 CAAGATGTGACAAGATGTAGAATATTCAGAACTGG[C/T]AGGAAATCTGTGCTTAGAGCAGCAGAGGCAGGGAA Y 2 1 2 1 201000 r 74 goat snp11833-scaffold1439-256435 4 55275337 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441625 Affx-122928641 AX-123311962 4 62538371 CTGTGTGGATAGCTAGAAACAGAACCTCCTGAGTG[A/C]GAATATCATGGGGGTGGGACTGGGAAGGAAAGAGA M 2 1 2 1 101000 f 74 goat snp11832-scaffold1439-193890 4 55212034 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778128 Affx-122933697 AX-385265243 4 62579161 GTGCTGTTAATATGCATTCATAACATACACCGTAA[C/T]GGCTGTTCTACTCTCTGCTAAGAAAGCATGTTAAC Y 2 1 2 1 101000 r 74 goat snp11831-scaffold1439-153100 4 55171183 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386645 Affx-122970212 AX-123257003 4 62615698 TTTCTTTCCTAACGGAAGAGATGGTGACTAACACC[A/G]CTTAAACATGGTTTTGTTTTAGAGTTCTGTTTTGA R 2 1 2 1 101000 f 74 goat snp11830-scaffold1439-116563 4 55135460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397147 Affx-122962441 AX-123267502 4 62660355 CTATTGATGGACTAGATATTTTCAAAGGAATATTT[A/G]TCTTATTCAGTAAAAATAAAACACAACATTTATTG R 2 1 2 1 101000 r 74 goat snp11829-scaffold1439-71906 4 55091041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793692 Affx-122966338 AX-385280664 4 62693133 AGAACCAAAGAAGTTGGCTATCAATTATTCATAAA[C/T]AGCCATTAATTACCTTTTGGCTTTTGAGGTTTGAT Y 2 1 2 1 202000 r 74 goat snp11828-scaffold1439-39128 4 55058514 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408627 Affx-122953490 AX-123278978 4 62729836 AAATGGCTTCTGAAGGATTTTGTGCAGGTGAGAAA[C/T]ATCTTAAAAGAGATATTAAAACAAAAATTGGTCTG Y 2 1 2 1 102000 f 74 goat snp11827-scaffold1439-2425 4 55021882 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278251 Affx-1111836249 AX-519551739 4 62783676 AAAACACAGAGACGATTCCAGCCCCAACTTTCCAC[A/C]CAAAATGGCTAATGCCAGGTAGTAGAGAAATGCAG M 2 1 2 1 201000 r 74 goat Random2.2K-448 4 62783676 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438535 Affx-122931193 AX-123308873 4 62803109 GGGACAGAGGACCCTCCATGTGGTCCAGATGTATA[C/T]GCGGTTTGGGGCAGGTATAAGACTAAGCTCTAAGC Y 2 1 2 1 201000 f 74 goat snp9657-scaffold1345-298316 4 54953272 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450900 Affx-122922200 AX-123321234 4 62831882 GCTGTCTGCATTTCAGTGAAAGGTGATGGGTGATC[A/G]TGGCAAAGTTAACTTTCAGCAACCTGCTGGGATAC R 2 1 2 1 101000 r 74 goat snp9656-scaffold1345-269543 4 54923274 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381654 Affx-122974751 AX-123252012 4 62866744 AGAGAACTCAGCCCTTATTTATGATGCTGTTTCTG[C/T]AGTAAACATGTGCAAGGCCTCCCAGGAGAGGCCTA Y 2 1 2 1 101000 f 74 goat snp9655-scaffold1345-234681 4 54887711 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449398 Affx-122922705 AX-123319733 4 62897557 CACCTCACTCATGGAAAGAAAAAAAAGCCACTGAA[C/T]GGCTGCATTGTTGAGCTGACCACCCCTGTACCATC Y 2 1 2 1 201000 r 74 goat snp9654-scaffold1345-203868 4 54856951 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418958 Affx-122946085 AX-123289306 4 62946408 GGCCTGCCAAGGCAGGAGCAGCCACCTAGCCCCAG[A/C]GTCTCCTGCAAACCCCATTTCCTATGCCCCTTCCC M 2 1 2 1 101000 r 74 goat snp9653-scaffold1345-155017 4 54808295 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431343 Affx-122937056 AX-123301684 4 62976586 CTCTCCCCGAGCAGCTTTCAGGTTCTGCTGGGCTT[C/T]CTCATCACAGAGACCTAGAAAGGGAACTTGGGTTA Y 2 1 2 1 101000 r 74 goat snp9652-scaffold1345-124839 4 54778358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445492 Affx-122925197 AX-123315829 4 63041887 TCCCTTGGGAGTTCAACCCATGGCAGTGGCCGCAG[C/T]AGCAGTGTCTAGCTTCTGAAAGATAGAGATCAGAA Y 2 1 2 1 101000 r 74 goat snp9651-scaffold1345-59538 4 54713052 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445548 Affx-122925156 AX-123315885 4 63081766 CCCCATGGAACCAAGCAGGACCCTATGGGGCCTTC[C/T]GGGCACAGATCACTCTCCCATATCCTCTGCTTAAT Y 2 1 2 1 101000 r 74 goat snp9650-scaffold1345-19659 4 54672870 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409123 Affx-122953307 AX-123279474 4 63132548 GAGCCTTGGAGGAAGAGGCTTGGAGCAGTCAGGGA[C/T]AGAGGGATTTGAGAAGGCCCTGGCACAATGGGCAG Y 2 1 2 1 101000 r 74 goat snp3271-scaffold11-503068 4 54622882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771926 Affx-122975366 AX-385259082 4 63166547 TTTTTCTTTTGCGCTTACGTTTGAATCACAATACA[A/C]AGCTAATTAAAATAAATGGTTCACAGAGCACAGAG M 2 1 2 1 101000 r 74 goat snp3270-scaffold11-469069 4 54588884 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435955 Affx-122933531 AX-123306294 4 63195275 TTGGGGTACCCAAGGGAGCTGGCAGGGCTTCTGGG[A/C]TGGAGGAAGAGCAGGATCCCAGCCTGGGAGGGAGG M 2 1 2 1 103000 r 74 goat snp3269-scaffold11-440341 4 54560136 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798379 Affx-122957261 AX-385285313 4 63254641 TTTGCCCAAGTCTACTCCTCTGGTAAATACCAGAA[C/T]GTATCATAGTTCAAATGCAATGGAAACTCACTTTT Y 2 1 2 1 101000 f 74 goat snp3268-scaffold11-380975 4 54479524 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377728 Affx-122977388 AX-123248087 4 63296308 TTTTTTCACTCTTTTCAGAGCAGTTTTAGGTTCAG[A/C]GCAAAACTGAGAGCAAGGTACAATTCATCTCTTTT M 2 1 2 1 101000 r 74 goat snp3267-scaffold11-339308 4 54437828 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440671 Affx-122929928 AX-123311008 4 63351609 AGGCACGAACTGGCAACCAAAGAAACCAGGGGTCA[A/C]CCAAGCTCACTAGACTACCCCCAGAGTGCACCACA M 2 1 2 1 201000 r 74 goat snp3266-scaffold11-284007 4 54382115 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414511 Affx-122949529 AX-123284860 4 63417536 AGGAGTGAAGAAACAATGAGTATCTATAAATAATT[A/G]GAAGAGGGCCTAGAATCTTGAGAGCTTTCTGTAGG R 2 1 2 1 101000 r 74 goat snp3265-scaffold11-218080 4 54315182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452209 Affx-122920810 AX-123322542 4 63460404 TGATTTAGTCACTGAGGTGTGTATGTGTTCCAGAC[A/G]TTGTATTAGGCTGCTGTATAGAAAACTCAAATGAA R 2 1 2 1 201000 r 74 goat snp3264-scaffold11-175212 4 54272546 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774858 Affx-122949790 AX-385261992 4 63530344 AACCTGCTAAGATAAATACCACTGACACTTTGGTA[C/T]ATCTCTTTATACATGTATGTTCACACCAATTTTTT Y 2 1 2 1 201000 r 74 goat snp3263-scaffold11-105272 4 54202090 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384976 Affx-122971898 AX-123255334 4 63562367 GGGCAGGCATGAAGAAATAGAGCAAAATTTATTAG[C/T]AGTATGACGTGTCTTAAAAGACCTTACTCCTTAGA Y 2 1 2 1 201000 r 74 goat snp3262-scaffold11-73249 4 54170279 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772376 Affx-122921874 AX-385259528 4 63592365 CTTCACTTCAACTGAATTGAGCCCTATAATTATAA[C/T]CTGTAAAATGAACAACTTGAACTCGACTCTCATCC Y 2 1 2 1 101000 r 74 goat snp3261-scaffold11-43251 4 54140599 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412015 Affx-122951746 AX-123282365 4 63622777 TTCAATCGAGAGCTCTGCATTGGGGTCCACATGTC[A/G]CATTTTAAAGCTCTGAGGTCTCCAGAGAGGTCTCC R 2 1 2 1 101000 r 74 goat snp3260-scaffold11-12839 4 54110432 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414082 Affx-122949753 AX-123284431 4 63660999 AGTGTGTCTGATATGCCAGATGGATGCTTAATGAA[C/T]GGTCTAATGACGAAATCTGACACACCGTATCCGAG Y 2 1 2 1 101000 r 74 goat snp51107-scaffold743-322922 4 54075905 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444916 Affx-122926244 AX-123315253 4 63710702 GTCAGAGATCTGAGGTTCCCCAGAGCTTAGAACTT[A/C]TCTCTTTAAGAGCCTCAATGTCTCACCTGTAAAAT M 2 1 2 1 201000 r 74 goat snp51106-scaffold743-273219 4 54027689 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414894 Affx-122949124 AX-123285243 4 63796760 GCAACTGCAGCGGACTTTGCTTTCTGTGCACTTTT[A/G]TATCTGCCCTCAGTCCCTCATATCCCCTCAGGTCC R 2 1 2 1 101000 f 74 goat snp51104-scaffold743-187161 4 53940976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400550 Affx-122960429 AX-123270905 4 63868157 GTTTGGTCTTAAAGATCAGGGTTCTGGGAATGTAA[C/T]GATTATGGAGATAAATGAAAAAGACTGTTTTTTAA Y 2 1 2 1 101000 f 74 goat snp51103-scaffold743-115764 4 53870305 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429010 Affx-122938840 AX-123299352 4 63911575 GTCTCTGGGCCATTTTGTTCTCTAACTCACAGCAA[C/T]GGGTGCTTCTGATCAATCCTGAGCTTTCCTGTTAT Y 2 1 2 1 101000 f 74 goat snp51102-scaffold743-72346 4 53826837 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278253 Affx-1111836250 AX-519551741 4 63932917 GGAGGATACCATTTAAAAGATGAGAGAATATATGT[A/C]AATTGCCATTTGGCACCAAAAAATGTATATTAAAA M 2 1 2 1 201000 r 74 goat Random2.2K-450 4 63932917 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431432 Affx-122936514 AX-123301773 4 63959179 GACCTGCCATACCCTCCAGCTGATTTGGAAGATGT[C/T]ATCAACAAGTCTGTCATGTGGAATTGACAAGAATG Y 2 1 2 1 101000 r 74 goat snp51101-scaffold743-24742 4 53779937 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451566 Affx-122921696 AX-123321899 4 64011999 GTCCTCTATCTCGTCTGCTGCTGGCTAGCTTCAGT[C/T]GGTGACATGATCTCACACTCACAATTATATGAAAA Y 2 1 2 1 101000 r 74 goat snp28338-scaffold3021-27979 4 53728093 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767208 Affx-122938209 AX-385254489 4 64043533 CAGATATAGTCCTGTTCAGACTGAAGGAAGAATAG[G/T]TCTAAACCCCATCTCTCAATAGCTTTAGAAAGATC K 2 1 2 1 101000 f 74 goat snp28339-scaffold3021-59513 4 53695996 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391203 Affx-122967414 AX-123261560 4 64076886 AGCTTGATGGGCTATCGGGTCGCAACGAGTTAGAC[A/G]CAACTGCGCGACTCAGCACTCACACAGCTGCTAAG R 2 1 2 1 201000 f 74 goat snp28340-scaffold3021-92866 4 53662255 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404099 Affx-122957124 AX-123274451 4 64112177 TTTTGTATACACTTAGGACGTTCTGGTTTATTTAA[C/T]ACTTAGAAATAATTTTTTCTGCTTTGAAATATAAT Y 2 1 2 1 101000 f 74 goat snp53984-scaffold820-3002875 4 53626971 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452001 Affx-122920921 AX-123322334 4 64150995 CCTTGGGTTCACTCTGCAGAGCCAGGCAGGAGGAA[G/T]ACCAGACCCCGAGGTCTCCACTGCCACACAAGCAA K 2 1 2 1 201000 r 74 goat snp53983-scaffold820-2964057 4 53588334 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801776 Affx-122947171 AX-385288684 4 64195214 TGCTGCTGTGCACTCCTTACAAACATCATTTTTGA[C/T]TGTTGCATGAGCCTCATATTTAGTTATTTCCTAAG Y 2 1 2 1 101000 f 74 goat snp53982-scaffold820-2919838 4 53544039 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411962 Affx-122951136 AX-123282312 4 64235944 TCCCTATATCCTGTTGTTCCCTCTTCCTCTAAATC[A/G]CTGGATCTCAGAGTGTAATCCAAGGACCCTAAAGT R 2 1 2 1 101000 f 74 goat snp53981-scaffold820-2879108 4 53505037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386452 Affx-122970784 AX-123256810 4 64295610 TAAATAGTACTGCCAGAAATATTGGGGTGTGTGCA[A/G]TTTTTCAAATGAGTCTCTCTCTCTACTTCTGTTTC R 2 1 2 1 101000 f 74 goat snp53980-scaffold820-2819442 4 53445995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449501 Affx-122922625 AX-123319836 4 64327460 GATATCTGATTTCTCTGGGGAAAGCATGGGGCCTG[C/T]GCAGGTGACAAGTGTTAGAACACATTTCTGTATAT Y 2 1 2 1 101000 r 74 goat snp53979-scaffold820-2787592 4 53413938 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387800 Affx-122969692 AX-123258158 4 64363409 GCACCTCATTTAAGTGACCAACACGCTCTGGGAAA[A/G]CAGCAGATTTAGAGAAGTGCTGTCTTGAGGACCGT R 2 1 2 1 101000 f 74 goat snp53978-scaffold820-2751643 4 53378044 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427271 Affx-122939541 AX-123297614 4 64393515 AGAAGAGGAAGAAGAATAGCAGGTGGTAGACATCC[G/T]AAGTGGCAGAGGAAATTAAACCCAAATAGTGAGTG K 2 1 2 1 201000 f 74 goat snp53977-scaffold820-2721537 4 53347943 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401850 Affx-122959428 AX-123272203 4 64439114 AACCTTATTCTCTGTTTCTCAGTTTACTGTGGTAA[C/T]GTTATCCCCAAGTCACATGATCCTTCTGTACTCAT Y 2 1 2 1 101000 r 74 goat snp53976-scaffold820-2675938 4 53302348 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403501 Affx-122957637 AX-123273854 4 64473148 ATTATGTGTAAGCCAAATATCTTTACCTTTGTTTT[A/C]GTGTTAATTGCTGGTAATTTAATCTCAATTACCTA M 2 1 2 1 101000 r 74 goat snp53975-scaffold820-2641904 4 53267709 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377212 Affx-122978177 AX-123247571 4 64514438 ATTTGAAAATCACGCATGTACTTAGAATTGACATC[A/G]AGATCTTTTCTTTCTCTTACCCTACCACACTAGTC R 2 1 2 1 101000 f 74 goat snp53974-scaffold820-2600614 4 53226407 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779826 Affx-122959804 AX-385266926 4 64545366 AGAAAATAAAATTTTTGCCACAAGGTAAATGAGGA[C/T]GAGGGAACATTCTTCCCTAAAGGTTTCAGAGGGAA Y 2 1 2 1 101000 r 74 goat snp53973-scaffold820-2569686 4 53195156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802871 Affx-122965214 AX-385289769 4 64580087 TTTTGAGCCACGTCATCCTCATCTATCGCATATCC[A/G]TGGACATGGTCGGTAAAACTGAAACCTGTGCCCAC R 2 1 2 1 101000 f 74 goat snp53972-scaffold820-2534965 4 53160648 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801199 Affx-122966682 AX-385288113 4 64608759 CTGATACTCTCAGAGCCAATATCCAATTAGCAAAT[A/G]CTGGATTTTCCTTTTTGTAACTAGTATTTGGCCAT R 2 1 2 1 201000 r 74 goat snp53971-scaffold820-2506293 4 53131795 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795453 Affx-122962794 AX-385282409 4 64639810 ATGGAAACAGGCCTTGGGAATCTATATTTGCTAGC[A/G]TTGAGACACACTGGATTAGGAAACCGTAATGGAAA R 2 1 2 1 202000 f 74 goat snp53970-scaffold820-2475242 4 53101393 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390827 Affx-122967842 AX-123261184 4 64674355 TACCCTAGCACAGGCATTACAGTTTTTCCAGAAAG[A/G]GCCATTCCCAAAGCAGACGGAAGGAAAGGAAGCTG R 2 1 2 1 101000 f 74 goat snp53969-scaffold820-2440697 4 53066432 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443513 Affx-122927789 AX-123313850 4 64728531 AGCACCAGGGTGGAGAGAGAGATCCAAATGGCACC[A/G]TCTGGCCCTGGGGTTGCCGAGCATCTCTGGGAGAA R 2 1 2 1 101000 f 74 goat snp53968-scaffold820-2386521 4 53011787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433090 Affx-122935725 AX-123303431 4 64859479 CATCACTCAGATGACTTTTTCCTGTTCTGAGCATC[G/T]TCCCACCTCTATATTTCATTACAATTGATGGGCAT K 2 1 2 1 101000 r 74 goat snp53966-scaffold820-2255573 4 52880506 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804307 Affx-986696773 AX-385290923 4 64893969 GGAACAAAGCCATCTCTCAGATACATTTAAACTAG[C/T]GACTTCTAACATTTTTGAAGGAGGGAATCTTTTGA Y 2 1 2 1 600010 f 74 goat 4_64893969 4 64893969 Ancestral_priority_1043 ancestry 0.738 recommended IMAGE 10K 10K ancestral 320803565 Affx-986696116 AX-385290366 4 64893971 AACAAAGCCATCTCTCAGATACATTTAAACTAGCG[A/G]CTTCTAACATTTTTGAAGGAGGGAATCTTTTGACA R 2 1 2 1 600010 r 74 goat 4_64893971 4 64893971 Ancestral_priority_1043 ancestry 0.692 recommended IMAGE 10K 10K ancestral 320804238 Affx-986696739 AX-385290869 4 64894227 GTGCAGTGTATGGTACACTTTAGAGACTTCTCACT[C/T]GCGTTTGTGATACCCACCCTAAATATCCCCAAATA Y 2 1 2 1 600010 f 74 goat 4_64894227 4 64894227 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 320804607 Affx-986696776 AX-385291139 4 64894244 CTTTAGAGACTTCTCACTCGCGTTTGTGATACCCA[C/T]CCTAAATATCCCCAAATATGGAAAGTTGTAAATTG Y 2 1 2 1 600010 r 74 goat 4_64894244 4 64894244 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 38395171 Affx-122964108 AX-123265526 4 64906788 TGCACAGTGTTTGGAGGGTTTAAGAAATCTCCTTA[C/T]GCTTTCTGATTTTCATAGTTATTTGACTTATTTAT Y 2 1 2 1 101000 f 74 goat snp53965-scaffold820-2208264 4 52833314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439282 Affx-122930977 AX-123309619 4 64946758 TCTGCAATGGAAGCTCAGTGTCTTAACCACTGGAC[C/T]GCTGGGGAAGTCTCTGAAGTTTATAATTTTTAAAC Y 2 1 2 1 303000 r 74 goat snp53964-scaffold820-2168294 4 52793337 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380145 Affx-122975979 AX-123250503 4 64993214 TTGGTAAACAGTTGATCAGATATCTTTCAAAGCAA[C/T]AGCAACCATGCAGAAATAGCAATTTCAGCAACTAC Y 2 1 2 1 201000 f 74 goat snp53963-scaffold820-2121838 4 52746709 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412874 Affx-122950432 AX-123283223 4 65039738 AGAGTATCAGGTCCCTAGACAACTAGGTGTCTCAC[A/G]CAATGAAAACATCCTTGCTTAGTCCTAAGAACGAG R 2 1 2 1 101000 f 74 goat snp53962-scaffold820-2075314 4 52699515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771222 Affx-122940966 AX-385258380 4 65074920 CCTCTCTCTGATTTTATGCCAGTTTTAGTCTTGGC[A/G]CATGTATGTTTGTAGGTATATTAGCTGTTTCATCA R 2 1 2 1 101000 f 74 goat snp53961-scaffold820-2040132 4 52664349 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782282 Affx-122968071 AX-385269360 4 65114818 AATTGCTGTAAACCTTTAGAAGTAACGTCTTTACC[A/G]TCATATCACAATATTCTGAGTTTATGATAAAAATT R 2 1 2 1 101000 f 74 goat snp53960-scaffold820-2000234 4 52624427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780109 Affx-122957631 AX-385267206 4 65152340 AGGATCTTATGAGACCTAGAGTCTAGAGAATATGT[A/G]CATAATATTAAGACACAAATAGTGGTTTCAGATCC R 2 1 2 1 101000 f 74 goat snp53959-scaffold820-1962712 4 52586776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278098 Affx-1111836251 AX-519551589 4 65195283 CAAAGGGTAAAAGGAGAGTATTGAGATGAATAGGA[A/G]AAACAGAGAGATGGCCATGCCAAGGGAAAAAATAA R 2 1 2 1 201000 f 74 goat Random2.2K-451 4 65195283 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429806 Affx-122938193 AX-123300147 4 65227413 GGATTCTTAGGGGCATGGCTAAAGACTTGTTACTA[C/T]TGTTTGTTATTCATCAATTAATCTGATCAGTGCCT Y 2 1 2 1 101000 f 74 goat snp53958-scaffold820-1887639 4 52511545 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428324 Affx-122939005 AX-123298667 4 65272001 TAACTGCAATTTCCTTTTATTTGTAAAACAGGACC[A/G]TAATTCTCGGATGCTATTGATTCTTTTTATTTTGG R 2 1 2 1 101000 r 74 goat snp53957-scaffold820-1843051 4 52466287 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447989 Affx-122923746 AX-123318325 4 65310203 CACTCTGGCATTTAACTAGAGAATGGATAAACACG[C/T]TGATTATTTACCCAAGCTAGCCCACCAAAGATAAG Y 2 1 2 1 201000 r 74 goat snp53956-scaffold820-1804849 4 52427941 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389398 Affx-122968380 AX-123259756 4 65354642 TCAGGAGCCCTGGGAGCTGGTTCTAGCTCTGACAT[A/G]CCTGCTCAGCGTGATCTTGGGTAAGTTACAACACC R 2 1 2 1 201000 f 74 goat snp53955-scaffold820-1760410 4 52383433 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768179 Affx-122975924 AX-385255372 4 65387527 AAGTGAGGGTTTTGAACTGAAGGATCTTTTAAGGT[C/T]TCTTCAGACTCCAATATTGTCTAGATGTCAGTGGT Y 2 1 2 1 101000 f 74 goat snp53954-scaffold820-1727525 4 52350950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433548 Affx-122934991 AX-123303889 4 65425460 ATTTCCTCAGTTTCTTGATCTAGCATAGTCTCTTC[A/G]CACTTCTCATCCATGTTAACTTTGAGGAGGCCAAG R 2 1 2 1 101000 f 74 goat snp53953-scaffold820-1689592 4 52312640 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780089 Affx-122934991 AX-180660633 4 65425460 ATTTCCTCAGTTTCTTGATCTAGCATAGTCTCTTC[A/G]CACTTCTCATCCATGTTAACTTTGAGGAGGCCAAG R 2 1 2 1 600000 r 74 goat snp53953-scaffold820-1689592 4 65425460 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402743 Affx-122958331 AX-123273096 4 65464897 GGAGGGATGGATATGAATTATAATACTGATTATGC[A/G]TAAGTATAATATATAAATAGAAAGTCTGTGAATCA R 2 1 2 1 101000 f 74 goat snp53952-scaffold820-1650155 4 52272959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417210 Affx-122947304 AX-123287558 4 65515137 TCTCTTTACCCCATGCCCCTCTTTCTGCCAACATA[C/T]CCACTAAAATCTATTCAAGATTTCACAAAGCTCCA Y 2 1 2 1 201000 r 74 goat snp53951-scaffold820-1599915 4 52222985 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409705 Affx-122953045 AX-123280056 4 65572221 AAGGATCAGATGCAAGGGGAAACTGTTTTAAGGAC[G/T]ACACACAAGCACGCTCATGATTCATTCTGCCAAAC K 2 1 2 1 101000 f 74 goat snp53950-scaffold820-1542831 4 52165876 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441285 Affx-122929468 AX-123311622 4 65601501 GAGGAAAGACTGGACAAATACATATTTAGAGCTTT[C/T]TAATAGATGTACAATAGGAAAAATTTCCCAGGTAG Y 2 1 2 1 101000 r 74 goat snp53949-scaffold820-1513551 4 52136614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384062 Affx-122972870 AX-123254420 4 65650258 CAACCCCTTATTCCCTTTCCCTGGAAGTTCTGAGT[A/G]AGGAAGAGAAAGGAAATTAAACTTTCAGTGTAGAT R 2 1 2 1 101000 f 74 goat snp53948-scaffold820-1464794 4 52087927 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800345 Affx-122928375 AX-385287267 4 65691813 ACGAAGAAATACAAGCAAAGAATTCTTGGCATGTA[A/G]AATAAACAGGGATTAATCCATGTGGCAGCACTGTT R 2 1 2 1 101000 f 74 goat snp53947-scaffold820-1423239 4 52046492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793085 Affx-122979236 AX-385280063 4 65747139 GATATTCCATAAGTTAAAATGTCCTTCCTCAGGTC[C/T]TGTAATTGGGTTAACAGGATCTGTCTGAAAGACTT Y 2 1 2 1 201000 f 74 goat snp53946-scaffold820-1367913 4 51990934 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435196 Affx-122933640 AX-123305536 4 65800902 CAACGTCATCAGAACCCAAGCAACCTGCACACTGC[A/C]TTTATGAGAGGCCCTTTCAGAAGGCTTCAGAGGCA M 2 1 2 1 101000 r 74 goat snp53945-scaffold820-1314150 4 51937071 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449935 Affx-122922911 AX-123320270 4 65829794 TCTGGATCACCCTTTAACACAAGGGTAACACTGTA[C/T]GTTCAGGACCAAGACTACTCTTAAGAGATCTGAGG Y 2 1 2 1 101000 f 74 goat snp53944-scaffold820-1285258 4 51907992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385593 Affx-122971207 AX-123255951 4 65872114 TTTCTCCAAAGAGCCTGATTTTTTTTTTTCACATT[C/T]GAGAAAGGTATTTCGAAACCAAGAACTGAATCCTT Y 2 1 2 1 101000 r 74 goat snp53943-scaffold820-1242938 4 51865806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452499 Affx-122920980 AX-123322832 4 65904779 ACATACTGAAACAAATTTTCATCAAGCAATACTTG[A/G]CTTTCATGCACTCTGATGCTTTCTAATTCTTTCTA R 2 1 2 1 101000 f 74 goat snp53942-scaffold820-1210273 4 51833070 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392911 Affx-122965719 AX-123263268 4 66009352 AAGGGAAAACTGTAACTGTTTTGTTCTAGGCTATA[A/C]TACCCATACCCAGCACAAAGTATTCAAGAAACATC M 2 1 2 1 101000 f 74 goat snp53940-scaffold820-1105700 4 51728372 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783090 Affx-122957763 AX-385270157 4 66042343 TTTGACCCTTACCCTGCCTCTAAAATATTAATATT[C/T]TCCACACTATAACTATGTGATCCTTTAGAAATCCA Y 2 1 2 1 201000 f 74 goat snp53939-scaffold820-1072709 4 51695098 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397517 Affx-122962052 AX-123267872 4 66074526 ATATATTCAGTATCATATTTTAATGTAAGTCACTG[C/T]ACTTCCTCTGAACTGATAAATGGAGCTTTGTATCA Y 2 1 2 1 101000 r 74 goat snp53938-scaffold820-1040526 4 51662901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412900 Affx-122950415 AX-123283249 4 66108283 GCCACTGACGAGAGATGATTCCCCGTGTGCACTGG[C/T]GCGATAGACATGCTGGTTTATGGGCCTGACACCTT Y 2 1 2 1 101000 r 74 goat snp53937-scaffold820-1006769 4 51628577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454093 Affx-122919368 AX-123324426 4 66148682 ACTGTGAAGTCGGTAAGAAGGACTTCTCCACTCAA[C/T]GGATAAATGGAAGGCAAGGATCACTTTCCAGAGAA Y 2 1 2 1 101000 r 74 goat snp53936-scaffold820-966370 4 51588107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413393 Affx-122950123 AX-123283742 4 66193991 AGTGAAGGTGGGGTGGTTATGGAGATCTGATGGCT[C/T]CTCCTCTCTCTTTTAGGACTTGGAGTCCCTAAAAA Y 2 1 2 1 101000 r 74 goat snp53935-scaffold820-921061 4 51542800 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422187 Affx-122943512 AX-123292533 4 66227651 CCACGCATGTCTCACGCCATGTAGCCAGCTCTGGT[A/G]ACTATCTTCTTCAAAGTGACAACAAATTCTCTATC R 2 1 2 1 101000 r 74 goat snp53934-scaffold820-887401 4 51509340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423565 Affx-122942414 AX-123293911 4 66258173 CTACCCAACTTAGAAGCATTCTTGAAAATAATAAA[C/T]GGAAATTTAAAAGCACTTTTCATGCTTGACTATGT Y 2 1 2 1 201000 f 74 goat snp53933-scaffold820-856879 4 51478942 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438098 Affx-122931510 AX-123308436 4 66300334 GGTATATATGCCCCACAATTGGGCTTCCCAGTGGG[A/G]CCATACATTTCTGAGAGAAACAATTAGCTTTGAGT R 2 1 2 1 201000 r 74 goat snp53932-scaffold820-814718 4 51436671 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798518 Affx-122969864 AX-385285451 4 66337369 ACCTCATGTCATCCCTTAGATCTAATGTCCTGCAG[C/T]GTTGGTCTGCACAGGGTCATTGGAATAAGTGCCAG Y 2 1 2 1 101000 r 74 goat snp53931-scaffold820-777683 4 51399660 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375592 Affx-122978729 AX-123245951 4 66404911 AGCATGTAGAAACTAAAATGTCCGCATTTCAAAAA[C/T]GGAGAAAACCATGAATCTATGCATCCCGGAGAATG Y 2 1 2 1 201000 f 74 goat snp53930-scaffold820-710141 4 51331639 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427499 Affx-122940000 AX-123297842 4 66441917 CGCTTCACAGCAGCCCTTGCAGCCTCCCTGCTACT[A/G]TCAAGGAGTCAGAACACACTCTCTTCCTTCTCCCT R 2 1 2 1 101000 r 74 goat snp53929-scaffold820-673135 4 51294412 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272129 Affx-1111833435 AX-519545887 4 66517672 TAAATTACAAGAGCTGTTTTTAAATACACTTTTCC[A/G]AGGGCATTCATATGTTTCAAGGAATTCTAATGTGC R 2 1 2 1 101000 r 74 goat 4_66517672_AF-PAKI 4 66517672 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38428710 Affx-122938467 AX-123299052 4 66546117 AACATACAAATAACAGATTTATTACTATCATGGGG[C/T]AAATTACTTCTTACACAAGAACTACTGACTTTGCT Y 2 1 2 1 101000 r 74 goat snp53927-scaffold820-568935 4 51190030 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783121 Affx-122956401 AX-385270188 4 66576167 GAACATTTAAGTAATAAACCTCATCTTATACACAA[C/T]GCATTACTGTGAGGCTCACTACTTACATAAACTAG Y 2 1 2 1 101000 r 74 goat snp53926-scaffold820-538885 4 51160407 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440254 Affx-122930659 AX-123310591 4 66632271 GGGAAATAACCTGTTTTGCAAGCTAATGGGGAAAT[A/G]TTTGATTGTTATCTAAACTCATTTAATCTTGGAGG R 2 1 2 1 101000 f 74 goat snp53925-scaffold820-482781 4 51103312 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772585 Affx-122978136 AX-385259734 4 66674506 CTAACATCCCTTTAATATTTCTAACAAACGACACG[A/C]GTAGTCTTTTTAGAACAGCTGAATTATACTTTAAG M 2 1 2 1 101000 f 74 goat snp53924-scaffold820-440546 4 51060496 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437127 Affx-122932160 AX-123307465 4 66716423 TAATCCCTTTCCCCCTGAGTGCAAGTCAACTTCAA[C/T]GTTTCCTTTCTAATGAGTGAAATGTAGCTGAAGTG Y 2 1 2 1 201000 r 74 goat snp53923-scaffold820-398629 4 51018189 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428165 Affx-122939039 AX-123298508 4 66770064 AGCGGTTTCTGTATGCAGCCATACACCTTCAACCA[C/T]AGCAATAAACCTGATTAAAAAAACAGTGCAATATG Y 2 1 2 1 101000 f 74 goat snp53922-scaffold820-344988 4 50964160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417392 Affx-122947692 AX-123287740 4 66800168 TTTTCAAGAATCCAAGAAAGAAAAATCACAGGCCT[A/G]TAAGAGGAACCATCACCCAGTTGACTTATTGGTTC R 2 1 2 1 101000 r 74 goat snp53921-scaffold820-314884 4 50934057 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431064 Affx-122936638 AX-123301405 4 66878104 ATCAGCCGAGGGAAAGTGAGGGAGGAGATTGGGAG[C/T]GAGGCTGGCATAGCTGAGGCCTGAACAACAAGACT Y 2 1 2 1 101000 r 74 goat snp53919-scaffold820-236948 4 50856371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785543 Affx-122923714 AX-385272587 4 66909104 TCCATAAAATTCACCTCCAGTGAACAAAAGTATGT[A/G]TTCCTCTCATTGACTTGTTATGGGGTTCCCTTGCA R 2 1 2 1 201000 r 74 goat snp53918-scaffold820-205948 4 50825330 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786511 Affx-122941194 AX-385273545 4 67014931 AACAATTGCCCTTTGAGGGTGAAGAGAAGGAAAAG[A/C]TGGGAGGCTCTCTGAATGACCTTGTACTATTCAGT M 2 1 2 1 101000 f 74 goat snp53916-scaffold820-100121 4 50719500 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407471 Affx-122954773 AX-123277822 4 67060883 AATATTGGAACTGAGAGTAATAAAATGAATACAGC[A/G]GGCTCCTCGTGTATGAATGACACTTTCTTCACATA R 2 1 2 1 101000 r 74 goat snp53915-scaffold820-54169 4 50673574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438557 Affx-122931174 AX-123308895 4 67144463 TAAACTGGAAAGTCCTTCAACTGAAAAGGAAAATA[C/T]CCGTAAGGAGAAAGAGGTATAATGTCTAGAAATTT Y 2 1 2 1 101000 r 74 goat snp27698-scaffold295-6418257 4 50588675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422032 Affx-122943622 AX-123292379 4 67191055 GCCAACTTAACTTGCTTTGAATAAACCTCAGAATG[C/T]AACTGGATCTCAGTTTCATTATAAGAAGTTCAATC Y 2 1 2 1 101000 f 74 goat snp27697-scaffold295-6371665 4 50542016 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773427 Affx-122927302 AX-385260569 4 67255864 TCTTTTCTGACCAAGGTATAAAATGACTTTTATGA[C/T]TGACGGTGTCTAAAGCACATATTTTAACATAGCTG Y 2 1 2 1 101000 r 74 goat snp27696-scaffold295-6306856 4 50476893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451728 Affx-122921543 AX-123322061 4 67285333 ACTTCATAGCCAAAATTCTTGAAAGAATGGTCTGT[A/G]TACTGTTCCCAATTTGTTATCTCCCATTTACTCTT R 2 1 2 1 201000 r 74 goat snp27695-scaffold295-6277387 4 50447388 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775784 Affx-122958632 AX-385262915 4 67322759 TTTCTATCCTCTTAAAAGTGTGGAGGCTTATTTCA[C/T]GACCTGGTATGTGGTCTAACCTAGAGAGTGTGTAT Y 2 1 2 1 101000 r 74 goat snp27694-scaffold295-6239961 4 50409964 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376654 Affx-122979016 AX-123247013 4 67353943 AAAAATCGGAGCAAGACATCAGTGACATGGGCTTG[C/T]GCTAGCACCATTTTACTGTCGTTTCTACAGCCCAG Y 2 1 2 1 201000 r 74 goat snp27693-scaffold295-6208777 4 50378802 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275519 Affx-1111834948 AX-519549091 4 67355663 AGCACCAGGTAATTGTATTGTGAACTTCTGGAATA[A/G]TGATATCACACACAAATTTCTTTGTAGAGTTATGG R 2 1 2 1 101000 f 74 goat GoatD01.059651 4 67355663 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38399863 Affx-122960234 AX-123270218 4 67415791 GAAAGTAATCATCCTCAAGAAAACATTCATTTCCT[A/G]CTTTTGCCTAATGGCTTTATTTTGGGGAATCAATA R 2 1 2 1 101000 f 74 goat snp27692-scaffold295-6146929 4 50317057 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395657 Affx-122963764 AX-123266012 4 67465789 TAGTTTTTTTGTTTGGTTGGTTTTTCCCTATTAAA[C/T]GGTAAAGAGGCATGTCTGAGGAGCAAAGCAGACAA Y 2 1 2 1 103000 r 74 goat snp27691-scaffold295-6096931 4 50266798 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788032 Affx-122941965 AX-385275053 4 67511329 GGACTTTGAAAAGGATAAAGCATTAGACAATGTGA[C/T]GCCATAAAAGAAGTATCACAAGGAGTGTCATGTCA Y 2 1 2 1 101000 r 74 goat snp27690-scaffold295-6051391 4 50220900 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397678 Affx-122962587 AX-123268033 4 67563516 TTCAGCTCTCTGGCCAGAGGCTACGCTAACTTTAA[C/T]GGCTAGCCCACCTCACCACAATGTGGACCAAGAGG Y 2 1 2 1 102000 f 74 goat snp27689-scaffold295-5999204 4 50168587 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422471 Affx-122943328 AX-123292817 4 67607748 TACAGGAGGCAACAGAACATTGTAGAGAAGATGTG[C/T]AATTTCGAGTTAGAAATGGATTTGAATTCTGAAAC Y 2 1 2 1 101000 f 74 goat snp27688-scaffold295-5954972 4 50123947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420407 Affx-122944921 AX-123290754 4 67691101 TCGAATTATTAGTTGAGAAAACAACAACATGGATG[C/T]ATCGCATCATCAGGGTATTTCTGTTTGAAAAACAA Y 2 1 2 1 101000 r 74 goat snp27686-scaffold295-5871619 4 50051879 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379874 Affx-122975786 AX-123250232 4 67734864 ATAACTGGGAACATTCCTATGCACAAGAACGTCAT[A/G]CCTTGGCTGGTACCTCCTCCTCCTCTGGTCCTTCT R 2 1 2 1 101000 f 74 goat snp27685-scaffold295-5827856 4 50008124 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799503 Affx-122936370 AX-385286433 4 67796842 AGAATTCTTCATATAAATTTCCAATGTAGTTAATA[C/T]GTATAGCCAGATAAGCTCAGGTCATCAGTAATTTT Y 2 1 2 1 101000 r 74 goat snp27684-scaffold295-5765878 4 49946225 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394834 Affx-122964787 AX-123265189 4 67828621 TCAATAAAAGACTGTATGTTGTGGTGTTTCTATTC[G/T]CAGAAGAAAAAGGAAATCTTTTCCCTAAGCCCTCC K 2 1 2 1 201000 f 74 goat snp27683-scaffold295-5734099 4 49913962 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439645 Affx-122930609 AX-123309982 4 67896381 GCTCTCTCCTCAGGAGAACTCCCAAGTTGGGAAAG[C/T]GTTTCTCAAACTATTGGCTGAAGATCCTTTGTGTA Y 2 1 2 1 101000 r 74 goat snp27681-scaffold295-5666339 4 49845893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384016 Affx-122972903 AX-123254374 4 67925936 TTGTTTCATATATATCATCTTTTTTTGGAGGAAAG[C/T]AAGTTTTAGGCAGAGTGTCAATCCAGCCCCCTGTT Y 2 1 2 1 101000 r 74 goat snp27680-scaffold295-5636784 4 49816148 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790644 Affx-122966299 AX-385277646 4 67979885 CCACTAACTTTGTTTGATTGGTACAAGGGAGAGAA[C/T]ACTGATATTAATAAGGAAGCCCTTAAAGAAACACT Y 2 1 2 1 101000 f 74 goat snp27679-scaffold295-5582835 4 49762293 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448484 Affx-122923618 AX-123318820 4 68008652 TGTAGGGCAAAGATTGCAAGGAAGCCTCTGGCCCT[G/T]GGAGACCCTTGCATGGAGGGGCACCATGGGGTGGC K 2 1 2 1 101000 f 74 goat snp27678-scaffold295-5554068 4 49733591 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772995 Affx-122950116 AX-385260139 4 68045796 ACAGCAGAGTGGAAATATGGGTCTAGAACCATGTA[C/T]ACTTAGACTAGAATTCCTATTTCCTCACTTTTTAA Y 2 1 2 1 101000 f 74 goat snp27677-scaffold295-5516924 4 49696207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426623 Affx-122939959 AX-123296969 4 68074621 CACAGAAAGCTAAAAAGAATTGCCTGCACCAAATT[A/G]TTTGGTATGCTCAAGTTAGGATTTAGATGCAGGGA R 2 1 2 1 101000 r 74 goat snp27676-scaffold295-5488099 4 49667369 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448537 Affx-122923436 AX-123318873 4 68111937 GTGGTTAAACGGTGGCCTGCCACTAAGGCATATAT[A/G]TCCACCTGGAACCTGTGGAATTGACCTTATGTGGA R 2 1 2 1 201000 f 74 goat snp27675-scaffold295-5450783 4 49630142 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436373 Affx-122933053 AX-123306712 4 68171610 CTCCTTTCTTCTTTCATGTTCCTCCCAAATCTCAG[C/T]GGCAGGTTGGCTGCAGAGGGTGGCATTTTGTTGAC Y 2 1 2 1 101000 f 74 goat snp27674-scaffold295-5391110 4 49570420 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777216 Affx-122970142 AX-385264339 4 68215895 TTTAAGACCTGAAAGCTGTGGACTCTGCGTTTCTT[A/G]AGTCGAGGTATATTATGGAATTTCATTTAATATCT R 2 1 2 1 101000 f 74 goat snp27673-scaffold295-5346825 4 49524873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779570 Affx-122927486 AX-385266673 4 68266941 GGATACACTAAACAAGACGATCATTTGTTTTGAAC[A/G]TTAAGGCCCTTTACAGACATGCCAGTTACAGGGTC R 2 1 2 1 101000 r 74 goat snp27672-scaffold295-5295779 4 49472631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446708 Affx-122924731 AX-123317044 4 68304700 CATTATGAAAATTGGTGTGATAGGTGGTACTTCTG[A/C]GTGGAGGCTCAGGGGAGGCTGGAAGGCATAAATGA M 2 1 2 1 101000 f 74 goat snp27671-scaffold295-5258020 4 49435164 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438277 Affx-122931403 AX-123308615 4 68334554 CGCAACCCTGAGAACGAGATGAGCGTCTGCATGCT[C/T]TTACTGCTCACCTATATCTTCATTTCCTTAAAACT Y 2 1 2 1 201000 r 74 goat snp27670-scaffold295-5228166 4 49404596 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414531 Affx-122949512 AX-123284880 4 68391720 TCAGGTTAAACACCAAGTAGAAGAGATAATAATAA[G/T]AAATCTTTACTCAGTCTTCCCAGCATGGACGGATA K 2 1 2 1 201000 f 74 goat snp27669-scaffold295-5171000 4 49347262 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278257 Affx-1111836252 AX-519551745 4 68434947 GTGACTATGTTGTCTTTCCTGGCAGAGGCACAGGG[A/G]GATGCAGAGTAAGGCAGAGCATCATTTCCAGTTGC R 2 1 2 1 202000 r 74 goat Random2.2K-453 4 68434947 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381152 Affx-122974554 AX-123251510 4 68459529 CACTCTCACACTCTAGGCCAGCACACTTACACAGT[A/G]CTGTATGTCAATCATGTCTCATTAAAATTAAAGGG R 2 1 2 1 101000 r 74 goat snp27668-scaffold295-5103191 4 49279373 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409528 Affx-122953617 AX-123279879 4 68605660 AAACACTTTTGCAAAGTACATCAAGGGTTAAAAAA[C/T]GGTAGGAGACACATGGACAAAAGTTATAAACAATT Y 2 1 2 1 202000 f 74 goat snp27665-scaffold295-4957060 4 49132543 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273795 Affx-1111833846 AX-519547406 4 68690678 CTGTAATTAGTATCACTCTATACACTTCCGAAATA[A/G]TAATATTTGAATTGGAATATCTCTGCAGTACAATT R 2 1 2 1 201000 f 74 goat GoatD01.007131 4 68690678 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434399 Affx-122934687 AX-123304740 4 68736961 TTTTTTATCATGAAAAGGTATTTGATTTTGTCAAA[C/T]GCTTTTTCTTTGCCTGTTGAGATACCATGTGGTTT Y 2 1 2 1 101000 r 74 goat snp27663-scaffold295-4825759 4 49000376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770315 Affx-122948959 AX-385257481 4 68788205 GGGCTGATTCATGTGTTTTCACTGTTAAGTCTTGT[A/G]CACATATTCCCATTTTACTAATTGAACATCCTTAG R 2 1 2 1 101000 f 74 goat snp27662-scaffold295-4774515 4 48949114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434174 Affx-122934884 AX-123304515 4 68854464 CGTTGACCTCAAAGAGCTTACACCATATTGACAAG[C/T]GAAATGTATACATACATACACACCCACAAGGCGGT Y 2 1 2 1 201000 f 74 goat snp27661-scaffold295-4708256 4 48882300 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278102 Affx-1111836253 AX-519551592 4 68898772 CCATAAAAATTTGATATCCTTTTTTCCTGGTAATT[A/G]AAATGTGCAAATGGCTAAAACATTATGATTGTTTT R 2 1 2 1 101000 f 74 goat Random2.2K-454 4 68898772 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781251 Affx-122920319 AX-385268336 4 68903053 TTTTAATGTGAAGGAAAGTAACAAGCTATAAGCAA[C/T]AAGAAACCACATGCGCTATATTGGATTCCCGTCTC Y 2 1 2 1 101000 r 74 goat snp27660-scaffold295-4659667 4 48833544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443013 Affx-122928173 AX-123313350 4 68996754 TGGGCTTTATGTACAAAAAAGGTGATGTGTACATG[C/T]GGGGTGGAAAAGTACAGCAGACCATCAAAGTGAAA Y 2 1 2 1 101000 f 74 goat snp27658-scaffold295-4565966 4 48739971 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798993 Affx-122935027 AX-385285923 4 69030962 AGAAAACAGCAAATGTTTATTCATTATCTAATGTC[A/G]TTCACTAATTCTTATTGAAGATGTCATACATTTTG R 2 1 2 1 101000 f 74 goat snp27657-scaffold295-4531758 4 48706340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766920 Affx-122977910 AX-385254233 4 69066817 AGTGTGCAGATTTCTGAAACCTGAGACTAGAAAGG[A/C]TGTTTAGAGGGAGACAGTCCTTCAAATTAAGGTCA M 2 1 2 1 101000 f 74 goat snp27656-scaffold295-4495903 4 48669830 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382675 Affx-122973655 AX-123253033 4 69119055 CATGGAAAATATAGGACTCAGAATCTGTTGGTAGC[G/T]GTGAGAATGGATGCATTTCAGCAGCAGTAATGTGC K 2 1 2 1 101000 f 74 goat snp27655-scaffold295-4443665 4 48616005 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417504 Affx-122947154 AX-123287852 4 69153720 GAAGTGGTCAGCATGATCTTTTACAAATGTAAATC[A/G]TATCTCAGTTCTCAAAACTTTCCAACTTCCTATCA R 2 1 2 1 201000 r 74 goat snp27654-scaffold295-4409000 4 48581073 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396768 Affx-122962770 AX-123267123 4 69188362 TGTATGCTTGTCTTCTCACTGTCTTCTCTTGCCCA[C/T]GGGGTGTAAGCTCCCTGCAACTATGTCCTCTCCTG Y 2 1 2 1 101000 f 74 goat snp27653-scaffold295-4374358 4 48545999 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411862 Affx-122951214 AX-123282212 4 69238525 TTGTTTGAAAGCATCTGTTACCATAACATAGTAAA[C/T]AGTTTTTAAGCCATTTTAGGAACAGCCATCTGTGA Y 2 1 2 1 201000 f 74 goat snp27652-scaffold295-4324195 4 48495521 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391300 Affx-122967337 AX-123261657 4 69284961 TCCTCTCCAGGGGTTTGGAGGTGGAGAGGCTGTGC[A/G]TTCTTAAGGAGGAGGGATGAGGCATGTGGCCCTTT R 2 1 2 1 202000 r 74 goat snp27651-scaffold295-4277759 4 48449330 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393262 Affx-122965458 AX-123263619 4 69324584 AGGGAGCTGGAAATTAGTCCTCTAATGACTTTAAA[C/T]GTCTCTCCTTTCCAATCTGCCTTTCTCAGACTCCC Y 2 1 2 1 201000 f 74 goat snp27650-scaffold295-4238136 4 48409700 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278261 Affx-1111836254 AX-519551749 4 69328818 TCTTCTTTTTTTTTTTTTGGTAAACAATAGCTGGG[A/C]AATAAAAAGGAGTCAATCACAAACCCAAATTTGCA M 2 1 2 1 101000 r 74 goat Random2.2K-455 4 69328818 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272132 Affx-1111833436 AX-519545890 4 69345149 CAGAAAACGGAACTGAGACACAGAAAGGTTAAGTA[A/G]CTTACCCAAGGCCACGCAGCTAAGAAAGCAGTGGT R 2 1 2 1 103000 r 74 goat 4_69345149_AF-PAKI 4 69345149 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389598 Affx-122968771 AX-123259956 4 69354810 CTTAGAATCTGTTTTCCTTGGGGCTCAGAAACAGA[C/T]AATTGCAGAAGAAATCAAACACAACACAGTCTCAT Y 2 1 2 1 101000 r 74 goat snp27649-scaffold295-4207910 4 48378207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795174 Affx-122927592 AX-385282132 4 69388125 CTGTGAACCTGGTGAATTCTTTATCTTGTGAACTG[C/T]AGCACCAAAGAAGTTCATTCTGGGAAGTCAGGGAG Y 2 1 2 1 101000 r 74 goat snp27648-scaffold295-4174595 4 48344811 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765610 Affx-122959629 AX-385253089 4 69439815 AATGGCTATTCAAGACCATAGACAGCAACACGCAG[A/G]TTGTGCACTTTACTCCCATTTCCATGTGACACTCT R 2 1 2 1 101000 f 74 goat snp27647-scaffold295-4122905 4 48293024 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391045 Affx-122966860 AX-123261402 4 69486169 CACATCACATATCCAGCCTTGGAGGTACAGCCTTC[A/G]CTGAAGCCAGTTGATGAACAGTTGCAGAAGGGGCT R 2 1 2 1 101000 f 74 goat snp27646-scaffold295-4076551 4 48245355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450001 Affx-122922860 AX-123320336 4 69534303 CAGATTTCATTTTTACATGCTATAATTCCTCAGGA[C/T]ACCTTTATATTTAGTTAGGACCAAAATGGTCAACA Y 2 1 2 1 101000 f 74 goat snp27645-scaffold295-4028417 4 48196078 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766751 Affx-122954078 AX-385254087 4 69569538 AAGATCCAGAATTCAAGTGATTTGGGCCAAATAGT[A/G]TAGTGGGCATATAACAGATTACCTATATTTGAAAA R 2 1 2 1 101000 f 74 goat snp27644-scaffold295-3993182 4 48160839 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776009 Affx-122978909 AX-385263139 4 69629097 TAGAATCAGAAATTTGACACAAGGAGAAAGACAGG[C/T]AGTTGGATTTTTAATTAAGCCAACCTAAATAATGA Y 2 1 2 1 101000 f 74 goat snp27643-scaffold295-3933623 4 48101126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453260 Affx-122920402 AX-123323593 4 69680676 ATCTCTGGAAGGTTCTGGTAAACAGTGGTTTTTGC[A/G]CTGGGGTACTGGGTGATGGGGCAGGAGAGAAAGAT R 2 1 2 1 101000 f 74 goat snp27642-scaffold295-3882044 4 48049615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415835 Affx-122948876 AX-123286184 4 69714826 GCCTCTAACTTTGAAATGATCTTTGCTTTAGCTTT[A/C]TATCAAAGAGTTTTGATTTGCTACTATACCATGCC M 2 1 2 1 201000 r 74 goat snp27641-scaffold295-3847894 4 48015387 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789607 Affx-122943724 AX-385276617 4 69788637 AGGTAACCACAAAGCACATCCCTGTGTTAAAAAAG[C/T]ACCAAGTATTTACGTCTTCCTTCAAAGATACAGCA Y 2 1 2 1 101000 f 74 goat snp27639-scaffold295-3774083 4 47941467 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404158 Affx-122957078 AX-123274510 4 69865770 AATTTGGAGCTACAAATATAAAAAGATAGAGTTTA[C/T]GCCATGGAGAGAATTTTTCTTCTCAAACAAAAGCT Y 2 1 2 1 101000 r 74 goat snp27638-scaffold295-3696950 4 47864010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453809 Affx-122919566 AX-123324142 4 69908689 ATGACAGCAAAGCCAAGCAAAGAGTGATGGATGTC[A/G]TTCGTAGTCTTGGACTTACTCCATTGGATAAAGGA R 2 1 2 1 201000 r 74 goat snp27637-scaffold295-3654031 4 47820573 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424622 Affx-122942186 AX-123294968 4 69953055 ACAACTGAATGACTAAACACCAGAAAAATAAAAAT[A/G]TCTCTCTGACCTAAAGTTCTTCTCCAGGCATGACT R 2 1 2 1 101000 r 74 goat snp27636-scaffold295-3609665 4 47776311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784150 Affx-122950486 AX-385271202 4 70012554 GTATGATTGTATTTTTTATGACATCACATTTTTTG[C/T]GATTCCTTAAAATGCTTTCTAAAAATTACACTAGT Y 2 1 2 1 201000 r 74 goat snp27635-scaffold295-3550166 4 47714548 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396168 Affx-122963778 AX-123266523 4 70083553 CTAACAGTATTTTCTGCTAAACTGAATGTGGGATA[C/T]GAAGAGAAAGAAGAGTGAAAGATGATTTCTCCGGT Y 2 1 2 1 201000 f 74 goat snp27634-scaffold295-3479167 4 47643673 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804609 Affx-986696778 AX-385291140 4 70115564 ATACAGAAACATCAGCTCATGTGTATATGGTCTCT[A/G]TGTATTGGTTCCTCCAAATTTGTACCAGTGTCTGA R 2 1 2 1 600010 r 74 goat 4_70115564 4 70115564 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 38434457 Affx-122934645 AX-123304798 4 70126584 TGATGAAAATGTGGATATATAGAAAAAATTATTGT[A/G]CTGCTTACAGAAATAAATCCTATGATCCTATTTAG R 2 1 2 1 101000 r 74 goat snp27633-scaffold295-3436136 4 47600308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420089 Affx-122945104 AX-123290437 4 70155961 TCATAGCTGAGTGAAGAATGGATTGAAAAGGGAAA[G/T]TAAAGGGTCAGAGAAATCAGTGAAAAGGCCACTCG K 2 1 2 1 101000 f 74 goat snp27632-scaffold295-3406759 4 47571575 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402181 Affx-122959183 AX-123272534 4 70196244 TGCATTATCTATCTTTAGCAGTAGGGTCTCATTTA[C/T]AACACCTGAAGACAAGCAGATAATTGTTAATAAAT Y 2 1 2 1 101000 f 74 goat snp27631-scaffold295-3366476 4 47531544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786846 Affx-122954385 AX-385273875 4 70228188 TCATTTGAAGCCAACCTTCATATTTTCCCATTAAG[A/C]TATCTAAAGACCAGAGAGGTAAATTTACTTTCACA M 2 1 2 1 101000 f 74 goat snp27630-scaffold295-3334532 4 47503772 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788716 Affx-122975081 AX-385275732 4 70267035 AACATTTCATCAATACATATTTTCATTAATGTATT[A/G]ATATAAAATTGCCAAGTATGCAAAGATAGATGCTT R 2 1 2 1 201000 f 74 goat snp27629-scaffold295-3295685 4 47465673 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789850 Affx-122974253 AX-385276857 4 70300583 TCATGTGTTGAACCACAAGTGTGTAAAGTAGGTTA[A/G]TTCATTCTTGGTAAGATATAAAAAACAATTCAGTA R 2 1 2 1 101000 f 74 goat snp27628-scaffold295-3262137 4 47431819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413433 Affx-122950692 AX-123283782 4 70372389 TCAAAGAGCTCATTTCTTCCTCAAAGTGAATATTC[A/G]TTCTTGGGGAGCAGCTTTTATATGAGGAGGCTCCA R 2 1 2 1 102000 r 74 goat snp27626-scaffold295-3190331 4 47358899 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435711 Affx-122933307 AX-123306050 4 70418737 GAACTGAAAAACTGTGTCAGACAGTTTGTCAGTCA[C/T]GGGGGCTCAGGGGTGCAATGTAATCACAAGCAAAT Y 2 1 2 1 303000 f 74 goat snp27625-scaffold295-3143983 4 47312823 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417501 Affx-122947156 AX-123287849 4 70481098 AATGTCATTGCTGGTTCTGGATTAAGGACTAAGTG[A/G]TTCTTCGCAAAACTCAAATGACTTGATTTGTTGCA R 2 1 2 1 101000 f 74 goat snp27624-scaffold295-3081622 4 47249641 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789415 Affx-122962754 AX-385276425 4 70528220 ATTCAAGAAGCCTAGACTCATTTGGGGTCAGGAAT[A/G]CATTGAGAATGAGTAGTGAAATAAGATTCAGCTAA R 2 1 2 1 101000 f 74 goat snp27623-scaffold295-3034500 4 47202226 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437259 Affx-122932008 AX-123307597 4 70565552 TCACATGAAGTTTTTCTTGTATCAGATCTCCATAC[G/T]ATGCTATATAATATTAATATTTCCTATTTTAAAAT K 2 1 2 1 101000 f 74 goat snp27622-scaffold295-2997168 4 47165506 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376925 Affx-122977787 AX-123247284 4 70594748 GTGGTAACCTGGTCTAATGGATGAGGTTTCCGTTT[C/T]AAGATTTTGGCCCAGAAAACCCATTTCTTTCTGGG Y 2 1 2 1 101000 f 74 goat snp27621-scaffold295-2967972 4 47135957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396206 Affx-122963360 AX-123266561 4 70650010 ATTGCTTTTCTCAAAGCCCAGCAGCAAGACCCTCT[A/G]CTTGATATATTACACAGATGTCCTAGCATGTAAAT R 2 1 2 1 201000 r 74 goat snp27620-scaffold295-2912710 4 47080341 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428697 Affx-122938627 AX-123299039 4 70680625 AATGAGAACAATGTGGTAAAACATGAGGCTGAAAT[A/G]AGTATTAGTGGATTTATTTATCTTTCCTCTTTTCT R 2 1 2 1 101000 f 74 goat snp27619-scaffold295-2882095 4 47049886 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392267 Affx-122967551 AX-123262624 4 70720720 AAGGAGGCAGATCCTGTTATTGCCATCAATCTATA[C/T]GTGCAGAAACCATGGTTTAAGAGAGGCTAGTTAAC Y 2 1 2 1 101000 f 74 goat snp27618-scaffold295-2842000 4 47009127 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789932 Affx-122952832 AX-385276938 4 70756571 CATTTCAATTCAGCAACCTACACAGAACTCACAGG[A/C]GATGAGTTCTGGTTACCTCCTGAGTACAGGTTACC M 2 1 2 1 101000 f 74 goat snp27617-scaffold295-2806149 4 46973425 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769967 Affx-122958839 AX-385257135 4 70788711 ACACAACCCAATAGTGTAGAGGATTAATAAACATA[A/G]AGGTGTTAGTACAGTTCCTCAAATGTAATAAGGAC R 2 1 2 1 101000 f 74 goat snp27616-scaffold295-2774009 4 46941252 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792857 Affx-122970330 AX-385279835 4 70827981 AATTGATGTTATTGAATTACATATGAGAAAAATGG[C/T]ATTAAAATAGGAGAAATAGCACACATCTAGAAAGA Y 2 1 2 1 101000 f 74 goat snp27615-scaffold295-2734739 4 46902113 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390308 Affx-122967716 AX-123260665 4 70868698 CGACTTAAAATAATGAAGCACATTTAAGAATAAGG[C/T]AGTTTCTAACTCCAGCAATAAAATAAGTGCAAAAG Y 2 1 2 1 101000 f 74 goat snp27614-scaffold295-2694022 4 46861447 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440812 Affx-122929824 AX-123311149 4 70915580 AGTTTCCAGGTAACATGCAAAGTCAGAGTCAATAA[A/G]AGAGCTTCACAGCAATCCAAAGAGTGAATCACTGA R 2 1 2 1 101000 r 74 goat snp27613-scaffold295-2647140 4 46813903 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410542 Affx-122952155 AX-123280892 4 70955177 ATCATGGGGATATGCTTCTCTTATAAAACTTTGTG[C/T]ATTTCTGCTAACTCTTTCTGTTTTATCTAACGATT Y 2 1 2 1 101000 f 74 goat snp27612-scaffold295-2607543 4 46773796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385460 Affx-122971303 AX-123255818 4 70991232 TAATTTCAGAGCTGAGACTTGATGATAAAATTAGA[G/T]ACCGAAAAAATAAATTCAGCATCAACTGAGTTCAA K 2 1 2 1 201000 f 74 goat snp27611-scaffold295-2571488 4 46737780 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278106 Affx-1111836255 AX-519551596 4 71027931 CCAAGCCAAGAACATTTTATTTACCAAAACCCTGT[A/G]CATTAACACACTGCCTCCAGGGCTGTGATATTTCT R 2 1 2 1 201000 f 74 goat Random2.2K-456 4 71027931 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415538 Affx-122948661 AX-123285887 4 71044891 TAAAAAAAAAAAAGCCTTATATTCTATTCTGTGCT[A/G]ATCAGCATATTAACTTATCTGTTTCCCCTTCTAGC R 2 1 2 1 101000 r 74 goat snp27610-scaffold295-2517829 4 46683123 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799737 Affx-122954498 AX-385286664 4 71081028 TGGTGTTCATAAACAAAGAATGGGATGCTTTTACA[G/T]ACAAAGCAGGGTTATCAGCAATGTGATGATATTCT K 2 1 2 1 101000 f 74 goat snp27609-scaffold295-2481692 4 46646473 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389341 Affx-122968478 AX-123259699 4 71115479 CTCTTCCCCACTTTCCTTCATCAGCAATCCTTCTA[C/T]ATATATAAAAACTTCCTGTATTTGTTTACTTTTGA Y 2 1 2 1 201000 r 74 goat snp27608-scaffold295-2447241 4 46612156 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800652 Affx-122971116 AX-385287571 4 71153360 CAGAAGAAGTTCAATACGGAGGTACCTTAAAAAAC[G/T]AAATATAGACCTCCCAGATGATTATGCAATCCCAT K 2 1 2 1 303000 f 74 goat snp27607-scaffold295-2409360 4 46574145 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781962 Affx-122941914 AX-385269042 4 71226412 GTATAGACTGTCTGGAGATAAAGCAATCATATAAT[A/G]CCCAAATATATGCTGCCTAGTAAACTCATGTCAGC R 2 1 2 1 101000 r 74 goat snp27605-scaffold295-2336308 4 46511788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439885 Affx-122930037 AX-123310222 4 71300115 GACTTTCAATTAATAAGGTCATTTTGTGGCCTGAC[A/G]TGGTAGTCCAGTCAAACTGATGTCTGTTGTGTGAG R 2 1 2 1 101000 f 74 goat snp27604-scaffold295-2262605 4 46438516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779481 Affx-122931724 AX-385266584 4 71356827 GACGTATATGCATTGTCAAAGTCTATATTCTTATA[G/T]CCCATGCTTTCTTATCATATTCTATGGCAAAGTTA K 2 1 2 1 101000 r 74 goat snp27603-scaffold295-2205893 4 46381552 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278266 Affx-1111836256 AX-519551754 4 71390598 AAAAAGGCAGAAGGCAAAATAATTATCTTGTTATT[A/T]TTGGTACAATCACCTATTACATGTATCCTTTACTA W 4 1 2 1 101000 r 74 goat Random2.2K-457 4 71390598 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438632 Affx-122930914 AX-123308969 4 71418271 TCTCATTCTAGAACTCTGCCATAACCAGTTACATG[C/T]GGCTTCCGCTCTATAGTGGGGAAAGCCTGTACCTT Y 2 1 2 1 101000 f 74 goat snp27601-scaffold295-2144449 4 46319909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411662 Affx-122951561 AX-123282012 4 71462197 CTAGACAGTTCAGTTTCTTAAAAGATGAGCCCTAT[A/G]TTTTCAGACTTAGATTTAAATACTTGTTGCCCTTA R 2 1 2 1 201000 r 74 goat snp27600-scaffold295-2100523 4 46276168 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378373 Affx-122976815 AX-123248732 4 71493822 TAATTAAAATGGAATCTTATCAAATGTAATGGTTC[A/G]GAGGTTGATTTTATTAAAAAATAATGTATTATGGG R 2 1 2 1 201000 f 74 goat snp27599-scaffold295-2068898 4 46244278 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375880 Affx-122978501 AX-123246239 4 71553340 AAATTAGAGTAGCTTGACAAAATTGCTTACTTCTT[A/G]CAGCAACTTCTTACTTCTTACTACTCTGTTTTGGT R 2 1 2 1 101000 f 74 goat snp27598-scaffold295-2009380 4 46182284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452459 Affx-122920561 AX-123322792 4 71581996 CTGCAGAATTCTCCTTGCTCTATTCACATATGTTT[A/G]TCATCTATTTTATATCATTAACTTCAGAATGTTTT R 2 1 2 1 101000 f 74 goat snp27597-scaffold295-1980724 4 46152931 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405407 Affx-122956286 AX-123275759 4 71627518 TCGTGGGATCAAATATTTATTGTCCATAAGCAAGA[C/T]GTACTGTCAGGCTTTTATCTGTGTGTACTTTTCCC Y 2 1 2 1 101000 f 74 goat snp27596-scaffold295-1935202 4 46106953 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786736 Affx-122923584 AX-385273767 4 71659547 AAATTAATCATTGGAGGCATATCACTAAAATTTAG[A/G]TACAGTTGAAGGGAGCAGATTTTATTTACAAATTA R 2 1 2 1 101000 r 74 goat snp27595-scaffold295-1903173 4 46073970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422541 Affx-122943269 AX-123292887 4 71716471 ATGGTTCAGCTGGCTTCCTTTAGGACTTCTGTCCT[A/G]TGGATCAATGGAATTCTCTCTTATGTGTATAATAA R 2 1 2 1 201000 r 74 goat snp27594-scaffold295-1846249 4 46015763 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422210 Affx-122944442 AX-123292556 4 71766496 CAGCATGAGACTTTTAAAAGGTTATGCTTTCAAAA[C/T]GGTTTCAAAGAGATTAGAAATGAGGAAAACCTGCA Y 2 1 2 1 103000 f 74 goat snp27593-scaffold295-1796224 4 45965576 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442462 Affx-122927946 AX-123312799 4 71817680 CTGCTTTTAATTGTGTCTACATGGGCCAATTAGAA[C/T]AGAAATCAACACTTTTGCTATGGATTTGATCAATA Y 2 1 2 1 101000 f 74 goat snp27592-scaffold295-1745040 4 45914871 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450679 Affx-122921907 AX-123321013 4 71857030 GGGACTTTGAAACTGCAGAAATTGAGGGCCTGTTT[A/C]GTACCTTCAAAGATTACAGTATTTATTTAGGAGAA M 2 1 2 1 201000 r 74 goat snp27591-scaffold295-1705690 4 45875777 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379632 Affx-122975956 AX-123249990 4 71888880 AGAACAGAACAGGAACAGAACTCTTTTAGATAGGA[C/T]GGTTAGGGAAAATCACTTGGAGGAGATGCCATCTG Y 2 1 2 1 101000 f 74 goat snp27590-scaffold295-1673840 4 45843682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272281 Affx-1111833437 AX-519546020 4 71901429 TGGAAGCTTTAGATGGAAAATCTGACCAAAGCCTG[A/G]AACATTAAGCTCTGAATGAAGAAACTGAGTTTAAA R 2 1 2 1 101000 f 74 goat 4_71901429_AF-PAKI 4 71901429 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38431606 Affx-122936163 AX-123301947 4 71921816 TCCTTGAAATTTCAAGGTCACAGTTTTCCTGAGTG[A/G]ACCTTTGACTTGATGCATGCATTTAATCCCTGAAG R 2 1 2 1 201000 r 74 goat snp27589-scaffold295-1640904 4 45810414 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407340 Affx-122955290 AX-123277691 4 71989868 TCAAGTTTGGTTATCCTAAGTAAACTCATCAATAA[C/T]GTGAATGTTTTTGCCTAGCCCCTTTTTTCAATATC Y 2 1 2 1 101000 r 74 goat snp27587-scaffold295-1572852 4 45739206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404162 Affx-122957074 AX-123274514 4 72050524 AGCCTTTACATTCTAAAAATTGCAACACACAAGCA[C/T]AGTAAATGTCCTTTTAAAATCTTTCTTAATACTTA Y 2 1 2 1 101000 f 74 goat snp27586-scaffold295-1512196 4 45678400 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450857 Affx-122922231 AX-123321191 4 72095051 TAACTACCGACCATTCATGGGATAGTGATGAAACG[C/T]GCTGGGAATCTAACATAAATTATCTCAACTGATAA Y 2 1 2 1 101000 f 74 goat snp27585-scaffold295-1467669 4 45633080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448006 Affx-122923733 AX-123318342 4 72137279 TACACAGCCCTTCCCACTGCTTTACTCAGTTTGAG[C/T]GTGTGCATGTGCCTGTGTATATTTTTTCCTGCCTA Y 2 1 2 1 303000 r 74 goat snp27584-scaffold295-1425441 4 45590227 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438013 Affx-122931573 AX-123308351 4 72234223 TCGACCCATGGCTCCCTCCTCTGAAAACTTTCCTC[A/G]CTGGGCTTATTAAAGGATTAGCTCACCACCATTAG R 2 1 2 1 101000 r 74 goat snp27582-scaffold295-1328497 4 45493140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411540 Affx-122951655 AX-123281890 4 72265907 TAGTTTATTGAGCACTAATTTCAGTGCTGCCTCTA[C/T]GTTGCCTAACTCTAGGCCCCATGGCCCCACTGAGG Y 2 1 2 1 101000 f 74 goat snp27581-scaffold295-1296813 4 45460953 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382616 Affx-122973703 AX-123252974 4 72306264 CCAGCCCTCAGCTGAGCCATGCCAGTTCCAGAAAT[A/G]CTCTTCTTCTAGATCACCATAAACTAAAATCATCT R 2 1 2 1 101000 r 74 goat snp27580-scaffold295-1256456 4 45420559 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390201 Affx-122967795 AX-123260558 4 72356656 TGCAAAGCGCCGAGCAGACACCAACTCCCCACGTG[C/T]GACGTGACCACACAGATGCACCCACCATCAAAACA Y 2 1 2 1 101000 r 74 goat snp27579-scaffold295-1206064 4 45370007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375542 Affx-122979099 AX-123245901 4 72391477 GGCTCGTAGCTGTTGTTTGTGTACTACTCCTAATA[C/T]ATGAGTCTCTCTCCTAATTCTGAAAAAAATTCAAA Y 2 1 2 1 101000 f 74 goat snp27578-scaffold295-1171243 4 45335889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429691 Affx-122937637 AX-123300032 4 72445428 GCCACTGCATTCCAGCGGCGACTGGGCCTGGAGCC[A/G]CTCTGAAGGACCCAGCTCTAGCCCTGATGCACTTC R 2 1 2 1 101000 r 74 goat snp27577-scaffold295-1117292 4 45282360 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379695 Affx-122975906 AX-123250053 4 72482470 AAGGCTGAATAACATTCCATTGTATGGATGAATCA[C/T]GATATGTTTATCCTTTGCCCGTGGAGGGACACTTG Y 2 1 2 1 103000 r 74 goat snp27576-scaffold295-1080250 4 45245412 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388764 Affx-122968941 AX-123259122 4 72511096 ACAGAGCAAGCCTGAGTCTCAAACTAATCATGTCC[C/T]ACCCCTCAAGACCTTCCTCCCCAGAAAGGCTGTAT Y 2 1 2 1 201000 f 74 goat snp27575-scaffold295-1051624 4 45216744 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435519 Affx-122933411 AX-123305859 4 72542697 ACTAGGGAACCAAGGCCTCTGCTCCCCACTGACAA[C/T]TGATGAGGAGATGGCACCCTCGTGCCACAAGAAGA Y 2 1 2 1 201000 r 74 goat snp27574-scaffold295-1020023 4 45185184 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418124 Affx-122947121 AX-123288472 4 72588505 GTGGGTGCTGAATGAGTGGGCTGCTTGGATCAGAC[A/G]ATTTTAGTTAAGAGGTTTGAGTTGACTGGGGGGCT R 2 1 2 1 101000 r 74 goat snp27573-scaffold295-974215 4 45138617 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780424 Affx-122935364 AX-385267516 4 72620422 GTTGTTGAAGTCTTGAAGTGAGACTGCCAATATCC[A/G]TCTCTATGCCCTAGAACCAAACAGATGCTGGACTC R 2 1 2 1 101000 f 74 goat snp27572-scaffold295-942298 4 45106216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397588 Affx-122961997 AX-123267943 4 72653769 GTTTCAGGTGTACAGCATTATAGTTTGACATCTGT[A/G]TACACTACATTGTGAGTATCATCACAGGTCTTGTT R 2 1 2 1 101000 r 74 goat snp27571-scaffold295-908951 4 45072641 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412294 Affx-122950871 AX-123282643 4 72696361 CCTCGACATACAAGCCACATCTTATCTCCTTACCA[C/T]CACCTACCACTTTTCTTCTGACTGTACAACCCTTA Y 2 1 2 1 101000 r 74 goat snp27570-scaffold295-866359 4 45029756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423687 Affx-122942320 AX-123294033 4 72726252 GGAGCCAGTTATAACATTAGACAAACCAAGAGCCC[A/G]AGGAGAACAGAATAATAAAAAGTGCATTTCTAGCC R 2 1 2 1 101000 f 74 goat snp27569-scaffold295-836468 4 45000196 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787634 Affx-122965306 AX-385274657 4 72759494 TTATGAGATATGTATTTTTACCTCCTGAAAATTAT[A/G]CTTTGACATGACATTTGATCATAAAGTACTTTACT R 2 1 2 1 101000 r 74 goat snp27568-scaffold295-803226 4 44966778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442011 Affx-122928418 AX-123312348 4 72790931 TCAAACTTCATGAAGAAGGCATTGTACAGACTAAA[C/T]GCTTCTTCTATACTTTGCTGAATGTGGTGATCATG Y 2 1 2 1 101000 f 74 goat snp27567-scaffold295-771789 4 44935670 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443388 Affx-122927397 AX-123313725 4 72877276 AAACAAAAGTACTGTGTATACTTCTAGGAAGGCAG[A/C]TTATAAAGAGTGTATTTTATATCAGAAAACCTTTT M 2 1 2 1 101000 f 74 goat snp27566-scaffold295-685444 4 44848584 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790717 Affx-122923144 AX-385277718 4 72907561 GTCAGTGAGTTGACTTTCTCTTTAGAATTTCAAGG[C/T]AGAGGTACAACACTCCTTCTTTCCAAGGATCACTG Y 2 1 2 1 101000 r 74 goat snp27565-scaffold295-655159 4 44818257 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435252 Affx-122934067 AX-123305592 4 72971000 AAAGAGGACCATGACTTTATAATTGGGCAACTATA[C/T]GGAAATAAGAAACAAGATTGTATTTCTAGACTAAA Y 2 1 2 1 101000 f 74 goat snp27564-scaffold295-591720 4 44750738 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789547 Affx-122929300 AX-385276556 4 73008376 ATCTGTTGATAGATTGCTAACAAAGTACTATAGAC[C/T]GAGTGGTTCATAAGCAACATTTATTTCCCACAGTC Y 2 1 2 1 101000 r 74 goat snp27563-scaffold295-554344 4 44713239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796341 Affx-122940691 AX-385283291 4 73037765 AGGTGTATGTCTAATAATTCACATGATGCCTTCAA[A/C]TCTCCAGAAAACCAATAAAAGCAGTGAAAAATCCT M 2 1 2 1 101000 r 74 goat snp27562-scaffold295-524955 4 44686025 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804325 Affx-986696782 AX-385290936 4 73044581 ACAGGCCTGGACAACACGATGTGGTACAAACACAC[A/G]AGGGAAAGGCACAAGCCATCCAAAAAGGAGGAAAG R 2 1 2 1 600010 f 74 goat 4_73044581 4 73044581 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 38430948 Affx-122936831 AX-123301289 4 73082098 ACCAGCAAATATTAAATATCTCTGATACTATCTTA[C/T]GCTTCCCTTGATAGAATAAATATTTGCTCCTGATG Y 2 1 2 1 101000 r 74 goat snp27561-scaffold295-480622 4 44641055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450517 Affx-122922499 AX-123320851 4 73116462 CCAAAGTACTTTGAGTCCACTGAAATTGCTGAAAT[A/G]TTTTCCCAAGTGTTTCTGGACTGGAGAATCCAGAA R 2 1 2 1 201000 f 74 goat snp27560-scaffold295-446258 4 44606707 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414868 Affx-122949145 AX-123285217 4 73185754 CAAATGCTGTTATGAACCTCCACATCGTGATATCT[A/G]TCTGTTCCACACTGGCTACATTTCCCACAAGCAGG R 2 1 2 1 101000 r 74 goat snp27558-scaffold295-376966 4 44536990 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381808 Affx-122974278 AX-123252166 4 73249176 ATAATATGTGCTTTCCAGTGGGAGCTTTTAAAGAC[A/G]CAGACCTCACCACAGAACCTCACTTGGAAGGTACC R 2 1 2 1 201000 f 74 goat snp27557-scaffold295-313544 4 44471910 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400141 Affx-122960703 AX-123270496 4 73294186 GTCAGGGATGGGCTGACTCTGGGCACTATGACTAA[C/T]TGCAATTTTCAATGGATGGGGTGCACGTACCCATG Y 2 1 2 1 201000 f 74 goat snp27556-scaffold295-268534 4 44425927 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464310275 Affx-1110418092 AX-515784361 4 73378247 CTGGAAGCATCACCCACTGCAGTGCACACAGGACC[C/T]CATTGCCCTACCATTTACATGTCAGTATTCCATTT Y 2 1 2 1 201000 r 74 goat GoatD01.053408 4 73378247 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38448019 Affx-122923724 AX-123318355 4 73389390 CTCCAGCCTACCTTCCACACTTTCTATAGCCTGAC[A/G]GTTCTCTCCAATACACCCTTGGTGCTGCCTCTGTT R 2 1 2 1 101000 r 74 goat snp27554-scaffold295-173330 4 44328744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780173 Affx-122932832 AX-385267270 4 73434324 AATTGTTTCAAAAGTGAGGGAGAATGTAGATCTTA[C/T]GATGCTGTTTGCAACTGCTTATTAAATATTGATGG Y 2 1 2 1 101000 f 74 goat snp27553-scaffold295-128396 4 44284387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441845 Affx-122929046 AX-123312182 4 73466481 TTTGGCTCACAACACCTTCCAACATCAGCTGTCAG[C/T]GTATTTATCTGAATTTACTCTCACGTAGCCTCTGG Y 2 1 2 1 101000 r 74 goat snp27552-scaffold295-96239 4 44252069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800489 Affx-122923903 AX-385287409 4 73510016 TTCTAGGACATTTTAGACTTTAGATAGCTCTTCTT[A/G]CATAATGTTGGCATCTCCCACAAATATTTGGCCAT R 2 1 2 1 101000 r 74 goat snp27551-scaffold295-52704 4 44208838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450977 Affx-122921737 AX-123321311 4 73540653 GAGGACATGAGATGCCAAGTCTGGAGAGGGGATGT[A/G]CGAGGAAACATGATCACCATCCCCCAACTTATAGG R 2 1 2 1 101000 f 74 goat snp27550-scaffold295-22067 4 44177937 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387598 Affx-122970254 AX-123257956 4 73581028 AATGGTAAGTTAGGTAGACACACAGGTTATATCCT[A/G]CCTGATGCCCCAGGACACCCTCATTCACCACCACT R 2 1 2 1 101000 f 74 goat snp16190-scaffold17019-299 4 44136425 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442178 Affx-122928806 AX-123312515 4 73587173 ACAGGAGGGACAATTGTGTCCCTATTTTTGGGAGA[C/T]AGCCTCTGAGAAGAAGTGACCTATTATCTTAGACT Y 2 1 2 1 201000 f 74 goat snp39041-scaffold494-6776236 4 44130443 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802797 Affx-122929930 AX-385289696 4 73621110 GCTCACAGTCTGCATTAAAAGTGGGTGCTTGCCTT[A/G]TATTCTACCCCGTAATATATCTTTTTATTTTAGGT R 2 1 2 1 101000 f 74 goat snp39040-scaffold494-6742299 4 44095826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418758 Affx-122946203 AX-123289106 4 73690220 GAGAGCTAAAAGTCATTTGGTTACACATCAGAATC[A/G]CTTTGCATCAGACACAGGCTTTGGAAACAGTTCTC R 2 1 2 1 201000 f 74 goat snp39039-scaffold494-6673189 4 44026632 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423724 Affx-122942873 AX-123294070 4 73755727 TCGCTCCCTTTTTGTTTTAATTTATTTATTTTATT[A/C]GAATATAGTCGCTACACAGTGTGTTAGTTGCTGCT M 2 1 2 1 103000 r 74 goat snp39038-scaffold494-6607682 4 43972323 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431172 Affx-122937188 AX-123301513 4 73799389 TCAGTCATCCTCCTTGGTGGTTTCATCTATTGCTG[A/C]GGAGCTGAGCACATGGAATGTGGAAGTGAGTGAGG M 2 1 2 1 10000 f 74 goat "snp39037-scaffold494-6564020;SV_250" 4 43928380 C A SV_250 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386812 Affx-122970900 AX-123257170 4 73844054 CTTTCTGTCCTCCTGGTATGGGAAGATGTGGGAGA[C/T]GTATTTCCTGCTTTCAGAGGAAAGGAGTGGAAGGA Y 2 1 2 1 303000 f 74 goat snp39036-scaffold494-6519355 4 43883834 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387081 Affx-122969880 AX-123257439 4 73874494 GTGACTTACAAGGGAAGAAACTGAGGCACGAAGCA[C/T]GCAGACCTGCTCTGTGGCTTCCACAGTCCGAGGCG Y 2 1 2 1 101000 f 74 goat snp39035-scaffold494-6488915 4 43853450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400321 Affx-122960057 AX-123270676 4 73909145 AAATGACTGTTTTAGGATGTGTGCATTTTCAACTA[C/T]ACCAAGTCAGCACTTGGGGCTATAAATATCCACTT Y 2 1 2 1 201000 f 74 goat snp39034-scaffold494-6454264 4 43818423 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415224 Affx-122948967 AX-123285573 4 73940178 AGCCTTGTGAGTCAAATCCTCACATGTGCACTTTT[A/C]AACACATCCATAATCATACCTGCAGGACACATTGT M 2 1 2 1 101000 r 74 goat snp39033-scaffold494-6423231 4 43787391 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410547 Affx-122952152 AX-123280897 4 73979274 AGAACAAAGTAAGACCAGGGACAAGGTCCTTGTGA[C/T]GGTCAGGCCTGGGCATCAAAGCCACCCAGAGGCCC Y 2 1 2 1 202000 r 74 goat snp39032-scaffold494-6384135 4 43748046 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418467 Affx-122946461 AX-123288815 4 74022276 AATGAGAAGCGTATGTTGGCCATGCTGCCCCGCTG[C/T]GGCAAGACCTTCGCCGAAAAGATGATGAAGGTAGA Y 2 1 2 1 101000 r 74 goat snp39031-scaffold494-6341133 4 43705022 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453937 Affx-122919486 AX-123324270 4 74064444 CCAAAATTAATATAGATGAAACTTTAAAACATTAT[A/G]TTATGTGAAAGAAGTGTGAATGCTGTATCAGTGAA R 2 1 2 1 101000 r 74 goat snp39030-scaffold494-6298965 4 43662694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447895 Affx-122923815 AX-123318231 4 74097615 GTCTTTCCTACCAGGTCAGTTTTTGGAAAGAGCGC[A/G]AGGTGGCCAAGGCCTGAGCGTGGGGCTGCTCTAGC R 2 1 2 1 101000 f 74 goat snp39029-scaffold494-6265794 4 43629058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386272 Affx-122970945 AX-123256630 4 74130955 CAGACAGACTTTCCGACAGGGTATCCCATGGAGAA[C/T]GAGGTAGGTGCAAACCCAGTGTGGAGAGAGCCATC Y 2 1 2 1 101000 f 74 goat snp39028-scaffold494-6232454 4 43595687 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410821 Affx-122952639 AX-123281171 4 74160985 CAAACTCCGCTGCACCTTCACCAGGTGCATCAATG[C/T]GGCCAAGCCACCACCTCAGTTCCCACTTCCTCATC Y 2 1 2 1 102000 r 74 goat snp39027-scaffold494-6202424 4 43566505 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780558 Affx-122937522 AX-385267649 4 74221663 TGTATAATAAAGACTTTTTGAGCCGGCTTGATCTT[A/G]TAATATAGAGCAAGGAATGGGGATGAGAGTTTAAG R 2 1 2 1 202000 r 74 goat snp39026-scaffold494-6141746 4 43505240 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379381 Affx-122976143 AX-123249740 4 74289424 TACTTATTTGCTCTTTTACTTACTTACTTGGCTGC[A/G]CTGCGTCTTGGTTGTGGCGTGCAGATCTTCAGTCT R 2 1 2 1 101000 r 74 goat snp39025-scaffold494-6073985 4 43437880 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413658 Affx-122950118 AX-123284007 4 74338320 CTGGCATTAGAGCCTGGACATGTGCATCTTTACAA[C/T]TCTCCCAGATTCCCCAGAGATTTGGATACACAGCT Y 2 1 2 1 101000 f 74 goat snp39024-scaffold494-6025089 4 43389000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382269 Affx-122973935 AX-123252627 4 74369157 GCTTACACATGATTGGAAGTGGTTCAAGACCCTCC[A/G]CTGCAGCTGCTTAGTCACTTCATTCATGTCCAACT R 2 1 2 1 101000 f 74 goat snp39023-scaffold494-5994252 4 43358121 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395255 Affx-122964097 AX-123265610 4 74414071 ACTGTCTCCATTCTTTGCCAGAGGCTCCGTTGAGG[C/T]AAATCACCCCAGGTGAGAAGTACGGCCCTATGCAG Y 2 1 2 1 201000 r 74 goat snp39022-scaffold494-5949338 4 43313592 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377627 Affx-122977879 AX-123247986 4 74472414 GTGTGCATGAGACTAAAGGGAATGGAGAAAGGCAA[C/T]GAACTGAGTAGGAGGCTTCAAGCCCCAGTCTGCGT Y 2 1 2 1 101000 f 74 goat snp39021-scaffold494-5890995 4 43256275 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434168 Affx-122934890 AX-123304509 4 74514101 GCCTCACTACCTGTGCCTCCTGCCTCCACAGAACA[C/T]GTCTGCATGGGCACTCTGCACACCCAGCAGGCATT Y 2 1 2 1 101000 r 74 goat snp39020-scaffold494-5849308 4 43214354 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393309 Affx-122965961 AX-123263665 4 74551969 AGATTGAGAATAAGCTGAGATTTACAGCTGAAGAC[A/G]CTGGCAAAGAAAAACAACCCCGAGAAAGGCAAAGG R 2 1 2 1 101000 f 74 goat snp39019-scaffold494-5811440 4 43176771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275049 Affx-1111834656 AX-519548631 4 74607493 AGGCAGAGGATTTAAGGCCCCTCATACATGGTTGG[A/G]GG R 2 1 2 1 102000 f 74 goat GoatD01.044572 4 74607493 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443933 Affx-122927029 AX-123314270 4 74610604 TACTCACTGAATAGAAACTCCAGAGAGCCCAGGTG[G/T]AGGCGGCCAACCTCCCGGACAGTCGGGTACAACAT K 2 1 2 1 101000 f 74 goat snp39018-scaffold494-5752805 4 43118812 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464303820 Affx-1110418528 AX-515777961 4 74704481 AGCCTTGGACAGCAGTAGCATTAAACAATTGCTAA[C/T]GATTATCTTTTACACACGTCTAGAGGACAGTGATT Y 2 1 2 1 101000 f 74 goat 4_74704481_AF-PAKI 4 74704481 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320790995 Affx-122955160 AX-385277992 4 74708960 ATTCATAGGCTATACCTATAACCTACCTCCACTGA[G/T]AATTTTAAACAATCAATACAGGGCCCTGAATCATA K 2 1 2 1 101000 f 74 goat snp39016-scaffold494-5654449 4 43021705 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421782 Affx-122944344 AX-123292129 4 74757465 GAGAAGAATCCCTGACTCCCTCCCCCTATGGGGAA[C/T]TGGCCTGAGAATGATGGAGAAGAGACGTCCTTAAA Y 2 1 2 1 101000 r 74 goat snp39015-scaffold494-5605944 4 42973768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789727 Affx-122950666 AX-385276735 4 74818968 TCAGATATGTTTTCCTTAGTATCTTTGAAAACCTT[A/C]TTTGAAGTCACCCAGATAGTAAACAGCAGAACCAG M 2 1 2 1 101000 r 74 goat snp39014-scaffold494-5544441 4 42912013 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410379 Affx-122952439 AX-123280729 4 74850129 ATGTGTTCTTAATCTCGGAATCCCATCATCTATTC[G/T]CGAGCTCCAGACACTTAGCTTCTCTGCATCCAAGA K 2 1 2 1 101000 f 74 goat snp39013-scaffold494-5513280 4 42880995 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418496 Affx-122946438 AX-123288844 4 74889090 ATTATGATTACGGGGTGGACATCTCCTCCAAACAA[C/T]TAAAGAAACAGTGGTAGAGAAGTCCAGGTTTCCAA Y 2 1 2 1 101000 f 74 goat snp39012-scaffold494-5474319 4 42841551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770044 Affx-122941876 AX-385257211 4 74928898 TTTGAAGCACCTGAAGGGCAAGGGAAACTTAACTT[A/C]TACCTCTTTAGTGTACCCCACTAAACAAAAATCAA M 2 1 2 1 101000 f 74 goat snp39011-scaffold494-5434511 4 42801228 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425449 Affx-122941517 AX-123295795 4 74963390 TCTACCTCGTCTGGTTTACACACTAGGTCAAAGCA[C/T]GAAAACACTGTGGCAACATCAGCATAACTAGTTAA Y 2 1 2 1 101000 f 74 goat snp39010-scaffold494-5400019 4 42765978 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401952 Affx-122958800 AX-123272305 4 75000172 GAGGTAGTGAACATTGAGAGGGGTGCCCAGAGCTT[C/T]CAGTGCCTCAGGGTGGCTGTGCAGCTGCTCCAGGG Y 2 1 2 1 101000 f 74 goat snp39009-scaffold494-5363237 4 42729190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400398 Affx-122959999 AX-123270753 4 75030393 TAGAAATGGAGCTTCAGCAATATTTCTGGGTGGGT[A/G]CAGGCTTCCTGGTGGAGACAGGGCTTGAAATGCTG R 2 1 2 1 101000 f 74 goat snp39008-scaffold494-5333016 4 42699064 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379222 Affx-122976279 AX-123249581 4 75080784 GGTAGATCTAGATCACTGTGGTCAAACATGTTTAA[C/T]GCAGAGAGAGGGTCCCTTTACACCCCAACCTAGTT Y 2 1 2 1 101000 f 74 goat snp39007-scaffold494-5282625 4 42648376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274213 Affx-1111834071 AX-519547813 4 75098832 CTTCAGTTCCCAGGAAGTCCCCCTCTTCACTCTGT[A/G]AGTAGTAACCTCTTGTGAATCTCTTGGACAGAGAG R 2 1 2 1 101000 r 74 goat GoatD01.017031 4 75098832 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38388480 Affx-122969235 AX-123258838 4 75127513 GGATGTTTTCCTGTGAGCCGTTCTGCACCCCAGGG[C/T]AAATGGTTTTACCAAGAAAAGTGAGGGCACCCAAG Y 2 1 2 1 201000 r 74 goat snp39006-scaffold494-5235896 4 42602091 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409273 Affx-122953120 AX-123279624 4 75177435 AGAGAGGGTGGAGAACAGCAGCAAATTACCTGGTA[C/T]ATCATGGAAAGGAGCCTGGATCTACCTCAGCAGGC Y 2 1 2 1 101000 f 74 goat snp39005-scaffold494-5185974 4 42552375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788024 Affx-122968358 AX-385275045 4 75212686 TTGGAAAACAAACATTTTCTATCTTGTCATTTAAC[A/G]TGTTATAATTGTAATTGCATATTTAGTATAATCAT R 2 1 2 1 101000 f 74 goat snp39004-scaffold494-5150723 4 42517344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409316 Affx-122953089 AX-123279667 4 75243838 GTAACCCTCCGCCTCATCCCAACCAGCCTGAGGAG[C/T]GCCTGAAGTCCAAACCAGAAAAGGTCAACAGTCCT Y 2 1 2 1 101000 r 74 goat snp39003-scaffold494-5119571 4 42486023 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798755 Affx-122935018 AX-385285686 4 75281476 ATGCTTAAAATGCAGACATCTGGAAACACTCTGAC[A/G]TGTTACTGTTCTGTTATCTTCTCCAAGGTGACTTT R 2 1 2 1 101000 f 74 goat snp39002-scaffold494-5081933 4 42447965 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436971 Affx-122933159 AX-123307309 4 75343556 CTGGTGACATTCCTACTGCTCCTTCCAAAGACAGC[A/G]TCACTGTTCCCCCGCCTGGAAAGTCCTTCCCAGCA R 2 1 2 1 101000 f 74 goat snp39001-scaffold494-5019853 4 42384515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383899 Affx-122973114 AX-123254257 4 75376457 CGCAAAGAGTCAGACACTGAGTGACTAACACTTTC[A/G]CTTTCAACCTTAGTCTAAACATTTTAGTATAATTG R 2 1 2 1 201000 r 74 goat snp39000-scaffold494-4986952 4 42351583 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439500 Affx-122930143 AX-123309837 4 75405885 AAAATATTAATATTTGGAGAATTCCTTGTAAGATT[A/C]TTGTAACTTTTCCAAAAGTTGGAGCAGAAAGTGGC M 2 1 2 1 101000 r 74 goat snp38999-scaffold494-4957524 4 42322041 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390976 Affx-122966918 AX-123261333 4 75451889 GATCAAACATAAATATAAGTCTTTAGCAAGGAAAA[C/T]GTAAAATTTCATTAGAATTGTATCTCTTAGTGAGT Y 2 1 2 1 202000 f 74 goat snp38998-scaffold494-4911520 4 42274608 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787352 Affx-122946882 AX-385274377 4 75494751 TTGCACTTCTTTGGGGTTTTTAATCCATAGACAAA[C/T]GTTGTAAGTCTAATTTGTTTACTGAGCTTTTTCTG Y 2 1 2 1 101000 r 74 goat snp38997-scaffold494-4868658 4 42231756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273514 Affx-1111833662 AX-519547129 4 75520084 TTGTGTCTCTGATACCATCAGTTCTAAAACAAGAT[A/G]ATGAATCCTTGGG R 2 1 2 1 101000 f 74 goat GoatD01.000935 4 75520084 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447041 Affx-122924530 AX-123317377 4 75527550 CAGTGGGTAGTAGATCGACATTCCAGAAGTATCTC[A/G]CTTGAAGCTCTTTTTCTTGGAAGACTATCTTTCAG R 2 1 2 1 101000 f 74 goat snp38996-scaffold494-4835859 4 42198767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446914 Affx-122924698 AX-123317250 4 75569078 CCAAATTCTACATAATTATTTTGTTTCAGTGCTTA[C/T]GGGTCATCCTATATTTCTTCCTTTTCACTTACACC Y 2 1 2 1 101000 r 74 goat snp38995-scaffold494-4794331 4 42157173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421959 Affx-122943811 AX-123292306 4 75621496 GGTGCTGAGAACAGCAGAATGAGGACAGGACCATT[A/G]CGATGTAAGATCATTCAAAGAAGAGGAAGAAGAAC R 2 1 2 1 101000 r 74 goat snp38994-scaffold494-4741913 4 42104624 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403767 Affx-122957995 AX-123274119 4 75709942 CAAAGAGGGAGACTCTTGGAGACTCTTGGAAACCC[A/G]CTGGTCTCTGGTGCTCTTCCATCTGAACATGGCAT R 2 1 2 1 101000 r 74 goat snp38992-scaffold494-4653467 4 42017506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453398 Affx-122919914 AX-123323731 4 75741057 AAAAGCATAAAAGTGAGAAAGAGCAAAGCAAGCAC[A/G]TTTAGACCACGAGGCCAGATATTTGATTGACCCTG R 2 1 2 1 101000 r 74 goat snp38991-scaffold494-4622352 4 41986300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381812 Affx-122974274 AX-123252170 4 75793887 ACCAAGAACGTGTACATACCTTTGCTCCATCAAAT[G/T]AGTCCATTAAAATAATGTCATTGTTGCATTAGAAT K 2 1 2 1 101000 f 74 goat snp38990-scaffold494-4569522 4 41933245 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804615 Affx-986696784 AX-385291142 4 75805073 AGTCCTGCCCCAAGGCCACAGAAGAGCCCAGTACC[C/T]AAGGTCATCTTGGAAGCTGATGGAGTCCCATTATA Y 2 1 2 1 600010 r 74 goat 4_75805073 4 75805073 Ancestral_priority_1043 ancestry 0.654 recommended IMAGE 10K 10K ancestral 320804616 Affx-986696785 AX-385291143 4 75805269 TATAAAAATTGGCTACTAACCCACAAGAAAGTGTC[A/G]AATTTGCACTGACAGTGCACCTGGGACACTAGCAG R 2 1 2 1 600010 r 74 goat 4_75805269 4 75805269 Ancestral_priority_1043 ancestry 0.648 recommended IMAGE 10K 10K ancestral 38434373 Affx-122934705 AX-123304714 4 75823148 ATGGCAAGGAGTCTCCTCCTTCCCATGGTGGCTCC[C/T]ACTCGCCCTGCCCACTTAGTGCAACATCACAAGCC Y 2 1 2 1 201000 r 74 goat snp38989-scaffold494-4540261 4 41904084 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778767 Affx-122942071 AX-385265877 4 75858585 AAAATGAACAAAACGGTCAGGCATATCTGTTTAAC[A/G]TCTTTTAGAAACAGAGACAGTTATTTTGTTAAAGA R 2 1 2 1 201000 r 74 goat snp38988-scaffold494-4504824 4 41868638 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382880 Affx-122973422 AX-123253238 4 75926298 GAGAGTAGTGAAAATAAATGAACTACGGCTTGATA[C/T]ACAGAAGAATCACAAAAACATAATGATAAGCAATA Y 2 1 2 1 101000 f 74 goat snp38987-scaffold494-4437111 4 41799543 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392255 Affx-122967561 AX-123262612 4 75958386 TGTTGTCTGAGAAGCAGACAACCAAGATGGAATCA[A/G]GCATGCAAGAGATTTATGGAGGTGGGGAATGCTGG R 2 1 2 1 101000 f 74 goat snp38986-scaffold494-4405023 4 41767359 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442553 Affx-122928522 AX-123312890 4 76005925 CATTTTTAGACTCTGAGCTCTTAATAAATGTTTTG[C/T]AATAAAGGAGTCAATGATCAACTCTCAATGGAATA Y 2 1 2 1 101000 r 74 goat snp38985-scaffold494-4357484 4 41720117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797405 Affx-122927345 AX-385284344 4 76061807 ATTCATTAAATGCCTGCAATATACAGGTTGCTAGG[C/T]TAGATGCAGTAAATAAGAAGAAAGTAAGACCCCAT Y 2 1 2 1 101000 r 74 goat snp38984-scaffold494-4301602 4 41664551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413864 Affx-122949859 AX-123284213 4 76092798 TAAAAATTGATTCTTTGGTGTTGAAATTAATAAAA[C/T]TAACCATTCCACTGCTTCCTCAAGGAAGCATTCTT Y 2 1 2 1 201000 f 74 goat snp38983-scaffold494-4270611 4 41633263 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391650 Affx-122966562 AX-123262007 4 76147486 AACAGGAAGTTCTCTCTTAGAGCTGGATAATGCTC[A/G]GAAGTTGCAAATAGGAAAAGTTCAGCAAAAGGAGA R 2 1 2 1 201000 f 74 goat snp38982-scaffold494-4215923 4 41578265 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410454 Affx-122952381 AX-123280804 4 76181187 TTTGAATACACAAACTGATATATTCAACATAAACA[C/T]TGATTTTTTCCAAACACCACATTTTATTTATATTG Y 2 1 2 1 101000 f 74 goat snp38981-scaffold494-4182222 4 41543765 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427368 Affx-122940097 AX-123297711 4 76215949 CAGCATGTGCAATGGAGCTGGCTCTGCTGGTTTTG[C/T]AGTGTTTGTTTTCTTATTCACAGGGAATTTTGTGT Y 2 1 2 1 101000 f 74 goat snp38980-scaffold494-4147460 4 41509053 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768969 Affx-122942967 AX-385256144 4 76247905 TGATGATGGTCAATGGTCAGGCACTGAGGAAATCC[A/G]TTACATAATATGAAATAAGCAAATGCCCAGTGAAT R 2 1 2 1 101000 f 74 goat snp38979-scaffold494-4115504 4 41476685 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381081 Affx-122974605 AX-123251439 4 76292305 GAATTGGGATATTTCAAGAAAAGATGAGAAGTAGT[A/G]GTCATATGCTTGGGAAGTATTGTACTCACAGAAAG R 2 1 2 1 101000 r 74 goat snp38978-scaffold494-4071104 4 41432653 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407896 Affx-122954398 AX-123278247 4 76351821 GAATTCTTGTGAAGATGCTAAAAAATAAAAAACTT[C/T]CTGACAATCCTCAAGAAGACCTTTTTGAACAGAGA Y 2 1 2 1 101000 r 74 goat snp38977-scaffold494-4011588 4 41373062 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419916 Affx-122945329 AX-123290264 4 76387423 CTATAAGTGCTTGCTAGGCTATTTTTACACATATT[A/C]GTAACACCTTACAATGATACTGGGCTTTATGTAAA M 2 1 2 1 101000 f 74 goat snp38976-scaffold494-3975986 4 41337446 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440968 Affx-122928990 AX-123311305 4 76456676 CCAGATACTAGGGACCCGGCCCACATGGAGCAGGT[C/T]CCAGCTTGTGTGGCAGGGTGAACCCAGCTGGATCC Y 2 1 2 1 201000 r 74 goat snp38975-scaffold494-3906733 4 41268254 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404891 Affx-122956465 AX-123275243 4 76498946 GAGTTGTCATTTCATGACCTCTGCATCTTGGCTTA[C/T]GCATATAGGACCCCAGCCTGCCCACCCAGGGATAG Y 2 1 2 1 101000 f 74 goat snp38974-scaffold494-3864463 4 41225913 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392129 Affx-122966337 AX-123262486 4 76530226 TCTACCCATTAAAACTGGTTCTGGAAGATCTTGTT[G/T]TATATAATACCTGAGAGGAAGCATGCATGCCACTG K 2 1 2 1 102000 f 74 goat snp38973-scaffold494-3833183 4 41196651 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388923 Affx-122968834 AX-123259281 4 76559359 TATCTCTCTTCACTGGTTCTATCAAACACTATCAA[C/T]GAGGCACGTTTGAAGAATCTATTTCTGCTTGATCC Y 2 1 2 1 101000 f 74 goat snp38972-scaffold494-3804050 4 41167355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438263 Affx-122931414 AX-123308601 4 76614331 GGGAGCTTCTCAAAAGCCTGTCACCTCTGCTACAG[C/T]ACACCCACAAGAGATTCCCAAATTCACTCTCCAAC Y 2 1 2 1 101000 r 74 goat snp38971-scaffold494-3749078 4 41112927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787035 Affx-122960461 AX-385274062 4 76648666 ACCTGTGGCCATGAGTCCTGAGGCACTCACGTTAG[C/T]TTTTGGTAAAAGAAAGTTTCTCTCTGAGACCACGC Y 2 1 2 1 202000 f 74 goat snp38970-scaffold494-3714743 4 41078489 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779715 Affx-122978278 AX-385266815 4 76681079 TCGAATGTTCCCGTGCTTTTCTTCTGCTCTGCCTC[A/G]TAGCAGAGCTTGGACAAGGGAACTATAGATAAGAA R 2 1 2 1 102000 f 74 goat snp38969-scaffold494-3682330 4 41045755 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437889 Affx-122931669 AX-123308227 4 76768976 CTTGCATTGGCGGGTGGGTTCTTTACCACAGTGCC[A/G]CCTGAGAAGTCCCAGGTGCACAGCAGGGAAGAGTA R 2 1 2 1 103000 r 74 goat snp38968-scaffold494-3594433 4 40951470 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426478 Affx-122940786 AX-123296824 4 76823842 GTGAGTTTTACACCAATCCTTCCCCTATCACCACC[A/G]CTCTCAGGAAGTGAGTGGGTCCTAGTGTTGTCCTC R 2 1 2 1 202000 f 74 goat snp38967-scaffold494-3539567 4 40896334 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780454 Affx-122974588 AX-385267545 4 76876869 TACTAAACTCAAGGGGAAGGTATAATTATCTAAAC[A/G]TATTTAAAAAGGAATGAGACTTAAAGAGGTTAGCA R 2 1 2 1 101000 r 74 goat snp38966-scaffold494-3486540 4 40843833 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402499 Affx-122958578 AX-123272852 4 76911121 TTAGCAAGACCTTTCTTGTGCTTTACTTTAGTATT[G/T]TCTCAAGTTTTACCCATCCCTACTGCCATTAATTT K 2 1 2 1 101000 r 74 goat snp38965-scaffold494-3452288 4 40809927 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768266 Affx-122973159 AX-385255447 4 76952701 TTGTAGGCCATTTCTTTAACTCTGAACCATATTAC[A/G]TTCCCTTATTTTGCATTAATTAAGTGATTTTCAAA R 2 1 2 1 101000 f 74 goat snp38964-scaffold494-3410708 4 40768445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415044 Affx-122949491 AX-123285393 4 77029207 GTATGACAAAGGAATGAAGCAAGGGGAAAATCAGA[G/T]AGGGAGGAAGAGAGGAAAGGTTAAATGGGTGAAGA K 2 1 2 1 101000 f 74 goat snp38963-scaffold494-3334202 4 40691646 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406788 Affx-122955705 AX-123277139 4 77082001 TAGATCTTTATGATAGGTAGAACTCTATTTGAGTC[A/G]CTGTGTTTTATATACCACAGGTTACAGAAATGAAG R 2 1 2 1 101000 f 74 goat snp38962-scaffold494-3281408 4 40638433 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450889 Affx-122922206 AX-123321223 4 77113436 GTTCTTTCTCAATTTCCATTCCCATGAGGTTATCC[A/G]CAGCAAGTCGCTGTTAGTACAGGGTCAGTGTGATG R 2 1 2 1 101000 f 74 goat snp38961-scaffold494-3249973 4 40606649 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385617 Affx-122971189 AX-123255975 4 77148821 GGTCTAGACCGGTCTCAGACTTTGCTGTGTGAAGA[A/G]TTCCAGAAACCTATGGCTTTACACTGAGTCTTTCT R 2 1 2 1 101000 r 74 goat snp38960-scaffold494-3214588 4 40571163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788169 Affx-122954290 AX-385275188 4 77200482 CAAAAAGAGACAGTTCCTAGAGAAAAAGATGAGGA[G/T]CAAATGTACTAACTGTTGGCAAAATAACTGGTCCA K 2 1 2 1 101000 r 74 goat snp38959-scaffold494-3162927 4 40519018 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409599 Affx-122953560 AX-123279950 4 77229070 AAATCAGTTTTCACAAAAGGATGTCACGTCTGATG[C/T]CAGCACGAGTGATCATGTATCTGTCATGAATCAGG Y 2 1 2 1 101000 f 74 goat snp38958-scaffold494-3134339 4 40490605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272282 Affx-1111833438 AX-519546021 4 77244863 GCATCAGGGTCTTTTCAATGAGTCAGTTTTTTTGT[A/G]TTAGGTGGCCAAAGTATTGGAGTTTCAGCTTCAAC R 2 1 2 1 303000 f 74 goat 4_77244863_AF-PAKI 4 77244863 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448528 Affx-122923443 AX-123318864 4 77264208 TGTCCCTAAATGGAGGAGGGAGTCACTAGTTCCCA[C/T]CAGTACTCAACAAGAGAACAATTGGAGTGCTTCCC Y 2 1 2 1 101000 r 74 goat snp38957-scaffold494-3099201 4 40455396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414520 Affx-122949523 AX-123284869 4 77300666 AATGATTGCCAGGCAGAGAACTACTTTCCTACAAG[A/G]TAGGAAGCGCTTACTTAACCTGCTTCTCTTAGTGC R 2 1 2 1 101000 f 74 goat snp38956-scaffold494-3062743 4 40418982 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781800 Affx-122935841 AX-385268882 4 77363605 CTGTATTCTTATATTTTATGTAACTCCACTGACCA[C/T]AGTTCTGCTCTTAATGCAGTTGTTTCAGGTAATTT Y 2 1 2 1 101000 r 74 goat snp38955-scaffold494-2999804 4 40356136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394025 Affx-122965006 AX-123264380 4 77407337 TAGCAGCAAAATTTCCTAATTCAGGTCATTCTCTC[A/G]CCTTGCTTCCTCACCCACCAGACACATACCACAAT R 2 1 2 1 201000 f 74 goat snp38954-scaffold494-2956072 4 40312383 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797422 Affx-122956487 AX-385284361 4 77475175 CTAGGGCTTCTATTAGACAGCAAAATTGTATACAT[C/T]AAGTCATTCTACCTGTTTAAATTCAGAGTGCTAAC Y 2 1 2 1 101000 r 74 goat snp38953-scaffold494-2888234 4 40244807 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447849 Affx-122923895 AX-123318185 4 77523228 GACATTTGGCCTAAGATACTATGCATCTAAAAAGA[C/T]AGTTATATAATATTTACATTAATATCTGACTGCCT Y 2 1 2 1 101000 f 74 goat snp38952-scaffold494-2840181 4 40197135 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425780 Affx-122940715 AX-123296126 4 77568572 CACATTGCATCCCAACTACACCTACAGCAGGGCAC[C/T]CTGTCCTCTCATCCAGGAACCTCTGCCCTCTCCTT Y 2 1 2 1 101000 f 74 goat snp38951-scaffold494-2794837 4 40152146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413420 Affx-122950701 AX-123283769 4 77630671 TCACAGAGGGGTTGCCCACGGGGCAAGCCAGGCCG[C/T]GCTCACTCTCCAGGCTCCTTTGACTCTGGCATCAG Y 2 1 2 1 103000 r 74 goat snp38950-scaffold494-2732738 4 40090080 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428802 Affx-122938398 AX-123299144 4 77667910 CGCCTGCCTCCTACTCAGCTCTGAGGGCATCGGGC[A/G]TGGGGTGGAGATGTCATCTTCCTGGGAGGGTAGGA R 2 1 2 1 201000 f 74 goat snp38949-scaffold494-2695499 4 40052806 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386586 Affx-122970692 AX-123256944 4 77698314 AGAACATCACCAGAACTGAACAGACTGGTCAGATC[A/G]TCTGCATCTGCTCTGATGGCTCATACGGCAAAGGA R 2 1 2 1 101000 f 74 goat snp38948-scaffold494-2665095 4 40022618 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379219 Affx-122976281 AX-123249578 4 77740456 ACAAACACGCTCTACACCTGTAAGACCTAGTATTA[C/T]GGGTAGGTAACTAGGGAATATCCACTACACTAGGA Y 2 1 2 1 101000 r 74 goat snp38947-scaffold494-2622953 4 39980481 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384336 Affx-122972256 AX-123254694 4 77814308 ATCCTAGAATCATACTCACAAGCATGTTTGCTAAG[G/T]CTATAGACTTGTGTCTTCACTCTGATTGTCTGGGT K 2 1 2 1 201000 f 74 goat snp38946-scaffold494-2549101 4 39905588 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380696 Affx-122975166 AX-123251054 4 77846065 TGAGAACAGGATAGAAGAGAAGCTGAGGCTCCATG[A/G]CACTTTCCTTATGGTCGAGTGGTTAAGATTCCAGG R 2 1 2 1 201000 f 74 goat snp38945-scaffold494-2517344 4 39873814 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396334 Affx-122963067 AX-123266689 4 77943964 TTGAAAATAATAAACTTTCTATACATGATACATCC[G/T]ATTTGCAGAATCTGACTCTTTGCAGAAAGGCAGGC K 2 1 2 1 303000 f 74 goat snp38944-scaffold494-2419445 4 39775343 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411780 Affx-122951481 AX-123282130 4 77995040 CAATGGCTAATGGGGAAGATTTGGGACTCACCAGC[A/G]TGAGCCTGAGGAACCAGTGAGAATGCCACGAAGAG R 2 1 2 1 201000 f 74 goat snp38943-scaffold494-2368369 4 39724427 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421629 Affx-122944467 AX-123291976 4 78034765 AAGGCCAGGTGCTGGACAAGTGCTGACAGCTGTCC[G/T]GAATGTGGCATCTTATTTCCTGCAGGCCCAGGTCT K 2 1 2 1 101000 r 74 goat snp38942-scaffold494-2328644 4 39684084 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437175 Affx-122932126 AX-123307513 4 78096158 GTCTATTTCCTCCACTGGAAGAACTGTGATTTCAA[A/G]GACAAAAAGATATCTTAGATTTTTTTTTTAGCCTA R 2 1 2 1 103000 f 74 goat snp38941-scaffold494-2267251 4 39622270 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782680 Affx-122968220 AX-385269752 4 78139181 TATAACACTCTGTTTATTAACACTTAAGTAATTGA[C/T]ACCCTGATTGGAAAGGTTCAGGTTCAAAGTACCAC Y 2 1 2 1 101000 r 74 goat snp38940-scaffold494-2224228 4 39579268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779773 Affx-122946805 AX-385266873 4 78201553 GAAATAGTTGAAATATTGATACTTCAATTCTCTTG[C/T]AGTTCAGCATGACTCTCTCTGCTGAACAAGGCTAA Y 2 1 2 1 101000 r 74 goat snp38939-scaffold494-2161856 4 39516068 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773144 Affx-122947140 AX-385260287 4 78262442 ACAAAATATCAAAATATTTTGCAAAGATTCTTTTG[C/T]AAAAGTAAGACTTTGGTAGAATTACTGAACAGATA Y 2 1 2 1 202000 f 74 goat snp38938-scaffold494-2100967 4 39453690 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382050 Affx-122974935 AX-123252408 4 78343941 GCTGCAAAAGATGGATGTTTCATAGGGCCACAGAC[A/G]TGAACCTCAAGACTCCATTTCTCACATACTGGTGA R 2 1 2 1 101000 f 74 goat snp38936-scaffold494-2019468 4 39371023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408796 Affx-122953365 AX-123279147 4 78382172 ATGAGAAATGAAAATTAAATGAAATAGGTAAACTT[A/G]TAGGATAGAGAAAGTCCTCACGAGTTCCTCTGTTT R 2 1 2 1 101000 r 74 goat snp38935-scaffold494-1981237 4 39332591 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388438 Affx-122969265 AX-123258796 4 78435296 AGCAGAAACTTTATTCTTTCCTGCCCTACCTCTGT[A/G]AACCTGCACTTCTAACTCATTTTCCTTGCTCACGG R 2 1 2 1 201000 r 74 goat snp38934-scaffold494-1928113 4 39278791 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426579 Affx-122939993 AX-123296925 4 78489142 CCTGATCATTCTCTGGACTCTATGGCTACCAGTAA[C/T]GTTACCCCTACAAGTCTCAATTTGAGCACTCTGTT Y 2 1 2 1 101000 r 74 goat snp38933-scaffold494-1874267 4 39225005 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391353 Affx-122967293 AX-123261710 4 78523093 ATAGTCCTAACTGTGGTAATGCTGTGATGTCTAGA[G/T]CAATGCCTTATAGTATAAGTGTTTAAATTATTTGG K 2 1 2 1 101000 r 74 goat snp38932-scaffold494-1840316 4 39191049 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444880 Affx-122926272 AX-123315217 4 78553000 AAATGTGCTCGAACTTAGAATATCATAAAAAGGAA[A/G]GAAACTAAGAAAAGTACCACTTTCAGAACTCAGGA R 2 1 2 1 201000 f 74 goat snp38931-scaffold494-1810409 4 39161475 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377438 Affx-122977536 AX-123247797 4 78584520 ACTGGTCAGACTTCACTCTCCCACATCTACCAGTG[A/G]TGTATCTTTAGTGACTGCTTCTATTTTCTTGAGAC R 2 1 2 1 201000 r 74 goat snp38930-scaffold494-1778889 4 39129943 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392450 Affx-122966168 AX-123262807 4 78636488 TAAGCAGAAGTCTCAGTATATTGCAGTTTGGTGCT[A/G]TTTTCCAAAACTTGTCTATTAATTATAGCCACCCT R 2 1 2 1 201000 r 74 goat snp38929-scaffold494-1726921 4 39077068 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448065 Affx-122924343 AX-123318401 4 78679775 GCTATATTTGTTCTTCTTTTGCCAGGTTCAGTAAA[C/T]GTCTGTTGTTTTGGTACAGATGTTGGACATGATTT Y 2 1 2 1 101000 f 74 goat snp38928-scaffold494-1683634 4 39033583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777498 Affx-122972519 AX-385264617 4 78731696 TCTTGAAAATTCAGATGGAAGATTAGGTTATATTA[C/T]GTAAGCAGATTTTACCCAAAAGTGTAATTCAGAAA Y 2 1 2 1 201000 f 74 goat snp38927-scaffold494-1631713 4 38980560 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412717 Affx-122950739 AX-123283066 4 78776661 CTGAATCTAGGGAAAACTGCCCTACATTCATAGTC[A/G]CCTCTGGGAACAGGGTAATAGTTGATCATTATGAT R 2 1 2 1 101000 f 74 goat snp38926-scaffold494-1586748 4 38936038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768454 Affx-122942754 AX-385255634 4 78819948 ATAGGCTTGAAAGCCTTTGGAAACTGAAGCTTAAG[C/T]TACATATGAAGGATGTACCCCTGACAGCAGCCTTC Y 2 1 2 1 202000 f 74 goat snp38925-scaffold494-1543461 4 38891971 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414166 Affx-122949681 AX-123284515 4 78860043 GACCAGTCAGTGCAACATGTAAGACAAATGCCACA[C/T]GGAACAGTCCCAACTGGACAAGCCATGGACATGAG Y 2 1 2 1 101000 f 74 goat snp38924-scaffold494-1503366 4 38852307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804333 Affx-986696786 AX-385290942 4 78873976 GGACTAGATGATTTCTAAAAATAGGTCTTTCTAGA[G/T]GTGCTTAAAAATAACTGAGATTTATTTTTAATTTA K 2 1 2 1 600010 f 74 goat 4_78873976 4 78873976 Ancestral_priority_1043 ancestry 0.66 recommended IMAGE 10K 10K ancestral 320762304 Affx-986696835 AX-385250486 4 78874059 TACAACAAAATTGTATATGATTCTACAAAATGATG[G/T]TCAAAATTTGTCTAAACAGAACTCCCCACTGTGTT K 2 1 2 1 600010 f 74 goat 4_78874059 4 78874059 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 320764455 Affx-986696837 AX-385252146 4 78874071 GTATATGATTCTACAAAATGATGTTCAAAATTTGT[C/T]TAAACAGAACTCCCCACTGTGTTCTTTCTCCATGT Y 2 1 2 1 600010 r 74 goat 4_78874071 4 78874071 Ancestral_priority_1043 ancestry 0.626 recommended IMAGE 10K 10K ancestral 320774451 Affx-122932775 AX-385261587 4 78890413 CTGGCCGTCTGCTAAAATAAGTGCTCCCTCATCAG[C/T]AGGCTGTTGGGCTGAGATCGATCTACTCAGTCAGG Y 2 1 2 1 101000 r 74 goat snp38923-scaffold494-1472996 4 38821523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775854 Affx-122958577 AX-385262985 4 78921391 GATTCAGACTTGGCACCTTCTTTATATTAGATATG[C/T]GTTTCTTCTGTAACAATCCCACAAGCAGAGAGTGT Y 2 1 2 1 101000 r 74 goat snp38922-scaffold494-1442018 4 38790521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430235 Affx-122937319 AX-123300576 4 78959622 GTCATAGTGCTGGGAAGAACATTTTGCTTCCTTCT[A/G]TTTCCATGCAAGTGGGAAAGGTAGGCAATAGAAAG R 2 1 2 1 202000 r 74 goat snp38921-scaffold494-1403787 4 38752433 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392635 Affx-122966456 AX-123262992 4 79018460 CCTACTCCTTCCACATAGCACCCACACTTGCCCAA[C/T]GCTCAATAATTGTTCTGTTCTCTGAACTCACATGA Y 2 1 2 1 101000 r 74 goat snp38920-scaffold494-1344949 4 38692876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278268 Affx-1111836257 AX-519551755 4 79039928 GCAGGGAGTGTTTGTAGACTTTTGAGGATGTCCCT[A/G]CAAACCGGTTCAAGGTCAGTCTCATGGGACTTTAG R 2 1 2 1 102000 r 74 goat Random2.2K-459 4 79039928 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320768713 Affx-122926839 AX-385255891 4 79072762 TCAATGACAAATGCCTACCCAGTTGTTTTCTAAAA[C/T]GGATTCAACTAAAAACAAGTTCAACTTAAAGTACC Y 2 1 2 1 101000 r 74 goat snp38919-scaffold494-1290647 4 38638627 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783627 Affx-122957979 AX-385270686 4 79110699 AAAGAGCTTAAAGTGAGTTTTCTGAGTTGGCTGCC[A/G]CTGGAAGTAGTTTACAAGGATGGAGTAACACTGGA R 2 1 2 1 101000 f 74 goat snp38918-scaffold494-1252710 4 38601870 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392244 Affx-122967569 AX-123262601 4 79145056 TGTAATTAACACCATCTTTTTTTGTCCCTCACTTT[A/G]TAAATATCTGTTGCTCTCCTGCTTACTTCTCCTGG R 2 1 2 1 101000 r 74 goat snp38917-scaffold494-1218353 4 38567548 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404032 Affx-122957174 AX-123274384 4 79231806 CTGATGAAGAGAGACTGGGAGAAAGCAGGAGAGAG[A/G]AGTCCAGGAGGAATCAGACTCTCAGGGAGGCATTC R 2 1 2 1 101000 r 74 goat snp38916-scaffold494-1131603 4 38480991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429067 Affx-122938291 AX-123299409 4 79271636 CATTGTGTGGTTATAGGCTGACTGAAGGTGACCAC[A/G]TGAAGAGTGCATAAGTACCACTTACCAGAAAAAAA R 2 1 2 1 101000 r 74 goat snp38915-scaffold494-1091773 4 38440240 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375584 Affx-122978735 AX-123245943 4 79337291 GACAATGAAATGCTTCAAGATATTTTGAGAAAATT[G/T]TATCTAGTGAAGAAGCAGAATGTAGCATTTTTATT K 2 1 2 1 101000 f 74 goat snp38913-scaffold494-1026118 4 38374461 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376208 Affx-122978809 AX-123246567 4 79397667 AAGACTTCATTGTTAAAAGTGAGAGGCAAATATTG[C/T]ACCAATGCAGAGGCATGGGTACCAGAAGCCCTAAT Y 2 1 2 1 201000 f 74 goat snp38912-scaffold494-965742 4 38314124 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443599 Affx-122927315 AX-123313936 4 79436770 GGAGGCAGTTTTTGGCTGAGTACCAACCTGTGACC[A/G]TGTCTGAGGAAACTACTGACCTTGGGGAAAGGATC R 2 1 2 1 201000 f 74 goat snp38911-scaffold494-926639 4 38274979 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394230 Affx-122964886 AX-123264585 4 79504324 CAGCCAGACTTCGGGCAGAATGTCTCTCACAAGCA[C/T]GGTATGGGCAAATAGTGTCAGACATCTGTGATTAC Y 2 1 2 1 101000 f 74 goat snp38910-scaffold494-859085 4 38207596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454062 Affx-122919389 AX-123324395 4 79548820 AGACTTTAGCAGATGAGGAAAATCAGACCTGAGCT[A/G]CAGAACTGATATTTTCCACAGAGCATTCTGGCAAC R 2 1 2 1 201000 f 74 goat snp38909-scaffold494-814589 4 38163017 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793761 Affx-122951457 AX-385280733 4 79580514 CTTTAAAAGCTGAAGAGAAGCTGATGGCTTACATA[C/T]AGCAGTCACTTCCTCGTGGTACCTACTATATTTCA Y 2 1 2 1 201000 f 74 goat snp38908-scaffold494-782895 4 38130864 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799113 Affx-122922873 AX-385286043 4 79612954 CATCTACTCTGAACAGGGAGGTCTAGTGCAAGGTT[A/G]TCACCATTTGCTAAATGTTGGACTCTTCAAACTTG R 2 1 2 1 101000 f 74 goat snp38907-scaffold494-750455 4 38098358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446469 Affx-122925065 AX-123316805 4 79657309 AGAGCATTCTAGTTGACCAACATGAAAGATTTATT[A/G]CAAAAAATGCTTTTATCCTCTTTATGTTACTGATC R 2 1 2 1 101000 f 74 goat snp38906-scaffold494-706100 4 38053557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278113 Affx-1111836259 AX-519551603 4 79681707 TAGATGACTGTTAGGCCACAAATTTTAACTGGCCC[A/G]AATCAAAGGCTTTGACCTGTCGTTTTATTGTGTCA R 2 1 2 1 101000 f 74 goat Random2.2K-461 4 79681707 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384037 Affx-122972887 AX-123254395 4 79688873 CAAGAAAGGATACTTACTTGTAAATTGTAGTCTTG[C/T]AGAATTTTAACTAAGGAGTCTCTCAAATTAGGAAT Y 2 1 2 1 101000 r 74 goat snp38905-scaffold494-674536 4 38021975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402507 Affx-122958572 AX-123272860 4 79747692 AAGTAGATCTATCTAGTAGCCATACAAATATGTGC[A/G]TCTGAAGTTTCAGAGAGCTAGCTGCTGAAAGCATG R 2 1 2 1 101000 f 74 goat snp38904-scaffold494-615717 4 37963800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790815 Affx-122944295 AX-385277815 4 79806379 GCCATTTAAAAATGATGTCAAGTTCTGTGTTGCTC[A/G]TCTCCATGAGTATTTGGCAATTTGAATATAGGTGC R 2 1 2 1 101000 f 74 goat snp38903-scaffold494-557030 4 37904453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382621 Affx-122973699 AX-123252979 4 79859442 GACCACTTCCCCACCACCTAATTAAAACACAATAT[A/G]TTGACAAGTTCTTGAGAGAAATGTTCCCATGATTA R 2 1 2 1 201000 r 74 goat snp38902-scaffold494-503967 4 37849896 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771052 Affx-122927396 AX-385258212 4 79889134 TGTGTCCTCACGACTTCTACCTAAATAAAGTGGCC[A/G]TTACATAAATGTCTGGGCTTGAATCCAGTGTGCGA R 2 1 2 1 102000 r 74 goat snp38901-scaffold494-474275 4 37820179 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769647 Affx-122930246 AX-385256818 4 79943079 ATAGAGAAAAAAATTCTAACAGCAGAGAACTAATT[A/G]GCTCCACAGGGACACACTAGACAGGAAGACCAAGT R 2 1 2 1 102000 r 74 goat snp38900-scaffold494-420330 4 37765783 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272283 Affx-1111833439 AX-519546022 4 79955587 CATGATTTTTCCAACGTAAACAAACACCACACAAG[A/G]TGGAACAAATGATTCATTTTTCCTGTGGAATTTTA R 2 1 2 1 101000 f 74 goat 4_79955587_AF-PAKI 4 79955587 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320784307 Affx-122925372 AX-385271358 4 79990179 GTGCATAATTGTTTCCACTTTACAGGTAAGTAAAG[C/T]GGGGCACAGAGAGGACAAAAAAAATCCCTAACATC Y 2 1 2 1 102000 r 74 goat snp38899-scaffold494-373230 4 37718609 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391946 Affx-122966922 AX-123262303 4 80047061 TTTACTTTTTGCTTTCTCTGACATTTGTTTGCACA[C/T]ATGCTCCACTGAGACAGCCTTCCAAGCTTTGTCTG Y 2 1 2 1 101000 r 74 goat snp38898-scaffold494-316348 4 37659232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798475 Affx-122920089 AX-385285408 4 80081906 AAACGTTGTTTACAATGGCTGCATAGTTTTCTATC[A/G]TTTGAACACAGTGTAAATCTTTCCCTGTTATTCAC R 2 1 2 1 101000 r 74 goat snp38897-scaffold494-281503 4 37628472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798166 Affx-122919831 AX-385285101 4 80110427 ACACAATAATAGAAAAATGTACCCATTATGCAGAT[A/G]ATGAAGAGTTGACCATTGTAGGGCACCATCTATCA R 2 1 2 1 101000 r 74 goat snp38896-scaffold494-252982 4 37599953 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776227 Affx-122947727 AX-385263355 4 80149813 ACTGTTTAAAAAGGGTTTTAACCAGAGGGAAAAGT[C/T]CAAACTGATTCCTTCTTATGGGCCCTCTGGGACCT Y 2 1 2 1 101000 r 74 goat snp38895-scaffold494-213596 4 37560549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429576 Affx-122937807 AX-123299918 4 80203709 ACTTGTTCATATCCAGGAAATTTATGGCTGATTCA[C/T]GTTGAGGTTTGACAGAAAACAACAAAATTCTGTAA Y 2 1 2 1 102000 f 74 goat snp38894-scaffold494-159700 4 37506581 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793758 Affx-122953459 AX-385280730 4 80237212 CTGTTTGGGTGCAAAAAACCCTGAAGCAAGGTATA[C/T]TCACACATGGATTGAGGTTTTATAGGGTGAGCTCA Y 2 1 2 1 101000 r 74 goat snp38893-scaffold494-126197 4 37472908 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375444 Affx-122979173 AX-123245803 4 80266190 AAAGGTGCTAAACACGTTTTAAGTAAAGCAATAAA[C/T]GATTACCTTTATGCTCTAAACTGTTGGTATCTTTT Y 2 1 2 1 101000 r 74 goat snp38892-scaffold494-97219 4 37443844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791219 Affx-122956678 AX-385278213 4 80352083 TGAAGTGGCAGATCCATTGCAGGATTACAAATCTT[A/G]CATATTAGCAATGTAGGTTCTAATCAATCTTGCAA R 2 1 2 1 201000 r 74 goat snp38890-scaffold494-11326 4 37358060 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428518 Affx-122938755 AX-123298860 4 80364059 ATCTCATTTACAGAGATTAATTTGAAAAGGTGGGA[A/G]GGGGCTTTCCTGGTTGCTACAGAAAGAGAGTTGCA R 2 1 2 1 201000 f 74 goat snp13652-scaffold1527-551 4 37345719 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405313 Affx-122956835 AX-123275665 4 80416424 TGCAAAAGTCAGAACTATTTTCACAGATGAACATC[C/T]AATCTGTTTTTAAAGTCCCCTGAGGGAAAGATATT Y 2 1 2 1 101000 f 74 goat snp13653-scaffold1527-52916 4 37292940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779794 Affx-122934454 AX-385266894 4 80447975 CAGTATGCCTGGGGTACTGAAATAAATTGGGAGGC[C/T]AAAGGTTAAGTGCCTTTAACAACTAGAGAATTTCA Y 2 1 2 1 102000 f 74 goat snp13654-scaffold1527-84467 4 37261610 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798419 Affx-122942182 AX-385285353 4 80484342 CAAAAAGTTTACTGTCTGGTCCTTGTAATAAAAGA[C/T]TGCTGGTTCCTCATCTAGCCTGTCTCAGGTCCATG Y 2 1 2 1 101000 r 74 goat snp13655-scaffold1527-120834 4 37224192 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773286 Affx-122921985 AX-385260429 4 80550157 CCACTTCACTTCTAAAAAATCATTCTTATTCTTAT[C/T]AAGTGTCCCCAAAAGTGTCATGTTTGTTCATGTTT Y 2 1 2 1 201000 f 74 goat snp13656-scaffold1527-186649 4 37158285 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381169 Affx-122975210 AX-123251527 4 80585378 CAATAGCATAGGTTATGAAATATAAGAGCAGACGT[A/G]TTTGTTCCATGCCTGATGTTGATCCTGTTGAATAT R 2 1 2 1 101000 f 74 goat snp13657-scaffold1527-221870 4 37123723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777970 Affx-122964199 AX-385265086 4 80614741 TCCATTGCTTACTGAAACTAGATTGTTAAAAAACA[C/T]TTGCTAAGTCATGACTCTAGTCATGCTTTCCATCC Y 2 1 2 1 101000 r 74 goat snp13658-scaffold1527-251233 4 37094993 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388404 Affx-122969292 AX-123258762 4 80659977 TCATGGAAGGAAATATTGTTTAATAAAGCTCACTT[A/G]TATTTTTAATATTGTTTATTAGAAGTTCAATTTCC R 2 1 2 1 303000 r 74 goat snp13659-scaffold1527-296469 4 37048937 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417832 Affx-122946794 AX-123288180 4 80697113 CCATAGAGGATAATGAAATTCAGCTATATATTGAT[A/G]CACAAAATTTCCAAATAGACTTTGTCATATTGCAT R 2 1 2 1 101000 f 74 goat snp13660-scaffold1527-333605 4 37010736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425704 Affx-122940775 AX-123296050 4 80733391 CAAAAATGATTTTTCTTTCTGGATGTGCAACTAAA[C/T]GAAGATTCTATCATATAATATATATTTTTATAATA Y 2 1 2 1 103000 f 74 goat snp13661-scaffold1527-369883 4 36972549 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396364 Affx-122963042 AX-123266719 4 80769469 CTAATGACTATCAATTTACAAAGTAGAAACACTCA[C/T]AAACATGACCTACAACTGACAATTGCATAGTTAAG Y 2 1 2 1 101000 r 74 goat snp13662-scaffold1527-405961 4 36936334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413543 Affx-122950608 AX-123283892 4 80799668 ATGCAGCAGTAGAATGGCATTTTTAGGGAAATGCA[A/G]TTATAAAAAAATGAAAACTACATTAAAAAACACCA R 2 1 2 1 103000 f 74 goat snp13663-scaffold1527-436160 4 36905935 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413058 Affx-122950974 AX-123283407 4 80829555 AGTCATTAATATACCTGTTGTATTAATAATTAACT[G/T]GTCAAATCAAAGTAAACCTGATGAATTTAAAGTGG K 2 1 2 1 101000 r 74 goat snp13664-scaffold1527-466047 4 36876049 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433562 Affx-122934980 AX-123303903 4 80869588 TTTATTGGCAAATCTTTAAATCTTGTGTACTTGCC[A/G]TGATTTTATAACAATTCACAATAGATTGAAAATAT R 2 1 2 1 201000 r 74 goat snp13665-scaffold1527-506080 4 36835539 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788952 Affx-122977729 AX-385275965 4 80909294 ATCCCCCCAGAAATCAGTCTCTAAGTCAATAAGCC[A/G]TCATCTAGTATGGAAGATCTGCTTAGATGTTATAA R 2 1 2 1 101000 f 74 goat snp28359-scaffold3027-88649 4 36794937 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398860 Affx-122961052 AX-123269215 4 80945915 GTCCAAAGGGTTGCAGAGTCAGACGTGACCAAGTG[C/T]ACATGCAATGCACACTAGGTAGCAACTATATAAGC Y 2 1 2 1 103000 r 74 goat snp28358-scaffold3027-52028 4 36757101 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419260 Affx-122946260 AX-123289608 4 80986528 TGCTAAGCTTGAAAGTGCTTTTGACTTTCCAACTG[C/T]ACACAATACTCTATTTTGAATTTTATTCTTCCAAA Y 2 1 2 1 201000 r 74 goat snp28357-scaffold3027-11415 4 36715757 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411832 Affx-122951236 AX-123282182 4 81005063 CAACCCCTCTCATATTGTATGTATCACTTATTTTC[A/G]CTTAAAAATGAGAAACAGTGCTCATATTCATAGTG R 2 1 2 1 101000 r 74 goat snp23284-scaffold233-7021 4 36686178 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387438 Affx-122970385 AX-123257796 4 81056965 TAGCTGTAAATTTGGTGCAGCCATGAGAGGAAGAG[A/C]GCTCAGGAGCCTCCTATGTCTCCATCTTAGTTAAC M 2 1 2 1 202000 r 74 goat snp23285-scaffold233-58923 4 36633984 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789616 Affx-122950016 AX-385276625 4 81102100 AATCATATCTCTTCTCCTAGCTAGTCTATACATGC[A/G]TCACTGGGTTTTTCAATTTCTGAATTAAAGAAACC R 2 1 2 1 101000 f 74 goat snp23286-scaffold233-104058 4 36587875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405654 Affx-122956575 AX-123276006 4 81132434 TTTCCTTTGCCTAGTTGTGTTCAACTCTTTATCAC[A/C]ACATAGACTGTAGCTCACCAGGCTCCTCTGTTCAT M 2 1 2 1 101000 f 74 goat snp23287-scaffold233-134392 4 36557203 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780538 Affx-122933673 AX-385267629 4 81187325 ACTACAAGCATGTAGATAATGTTGGTATTTACTTA[C/T]GTATATCTCTCAGGCATTATATTCAGAACACATCT Y 2 1 2 1 101000 f 74 goat snp23288-scaffold233-189283 4 36501286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764622 Affx-122952890 AX-385252263 4 81221600 AGTTAAGAAATTTTTACATTAATATAGTTAGTAAA[C/T]AAGACTATATTCGTAGGACCATAAATAATGGCCAT Y 2 1 2 1 202000 f 74 goat snp23289-scaffold233-223558 4 36465861 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441372 Affx-122928863 AX-123311709 4 81277890 AGGCTGCAATCATGGGGTAGTGGAGGTGATGGTGG[C/T]AACAATGGTGATGACAGGAGTGGTAACAGTGATGG Y 2 1 2 1 101000 r 74 goat snp23290-scaffold233-279848 4 36408658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769658 Affx-122933575 AX-385256828 4 81324706 GGCCTAAGATCTTCATTACACTTGAATATATATCC[A/G]TGAATATATATTAAGCATATATATTAAATGTATGA R 2 1 2 1 202000 r 74 goat snp23291-scaffold233-326664 4 36359863 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796792 Affx-122932855 AX-385283735 4 81427759 AAACAAACAGTCAAAACATAAAAATGCTTTGCACA[A/G]TTCCTGATAGGATTTCACTGAAGCTGTGGTAAGTT R 2 1 2 1 201000 f 74 goat snp23293-scaffold233-429717 4 36256991 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430366 Affx-122937787 AX-123300707 4 81464780 CTTGGTCAAGTTTACTCTCAAAGATATAGGAGCCA[C/T]CTGTCATTTTTCTTCTGTAAAAATTAAGTTTTGAA Y 2 1 2 1 101000 f 74 goat snp23294-scaffold233-466738 4 36220103 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379367 Affx-122976151 AX-123249726 4 81496825 TTTTCCACATCATATGGAAGTTCTAGGCAATGCAA[C/T]AAGAAAAGGAATTAAACTGTATTCAAATTAGAAGG Y 2 1 2 1 102000 f 74 goat snp23295-scaffold233-498783 4 36187567 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435412 Affx-122933552 AX-123305752 4 81526935 GCTCTCATCTGCTTTTCATTCTTCCTAGATCAATG[C/T]ATTTTTCCATTTACTTTTTGAGATCAATATTTTAA Y 2 1 2 1 101000 f 74 goat snp23296-scaffold233-528893 4 36156522 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442866 Affx-122927671 AX-123313203 4 81558926 GAGCATAGAGCTAAGGTCTAAGTAACATCTCCTCT[A/G]CTGCTCAGAACAAATATGCCAGAAACAGAAATGGA R 2 1 2 1 101000 f 74 goat snp23297-scaffold233-560884 4 36124758 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376013 Affx-122978407 AX-123246372 4 81591525 CAGGACTGTTCTGAAAGTAGCCTGAGGTGCCAAAG[C/T]GAAGAAAGACATGCTAGGCCTTTGCTATGTTTGGA Y 2 1 2 1 101000 r 74 goat snp23298-scaffold233-593483 4 36092017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773678 Affx-122977663 AX-385260818 4 81641639 AATTTGGGGATGAGATTGTGAATATTGCAACTACC[A/G]TGTAATAACCATTTGGAATGTTAGCCAAACCAACT R 2 1 2 1 101000 f 74 goat snp23299-scaffold233-643597 4 36041319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433691 Affx-122934543 AX-123304032 4 81672620 GTAAAGGAAGTATAGATGTTTTTCTTGGAGAATAG[C/T]GCAACGTTTGAAATACATTACATATGGAGATAAGC Y 2 1 2 1 101000 r 74 goat snp23300-scaffold233-674578 4 36008837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787700 Affx-122936596 AX-385274723 4 81710642 GTATAATACATATGACTGTGATGCCTTACACAGGG[C/T]AATAATCATAGATGGTATTAGAGTCATTCACTCAG Y 2 1 2 1 101000 f 74 goat snp23301-scaffold233-712600 4 35970419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442363 Affx-122928025 AX-123312700 4 81750111 CTTAATTATCTAGGGTTCAGTGTATACAAAGCGCC[A/G]AATACTGCCTATTGTTCTCCACCCTGAATTTCCCC R 2 1 2 1 101000 r 74 goat snp23302-scaffold233-752069 4 35931113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278115 Affx-1111836260 AX-519551605 4 81757831 CCCTTCCATTCTCATCATTTCTCCTTTACTGCTTA[A/T]GGCCCAGCCATGTCAACAAACCTGCAGTTCTTTCA W 4 1 2 1 102000 f 74 goat Random2.2K-463 4 81757831 T A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789334 Affx-122952367 AX-385276344 4 81806809 AGTTTGAGAGACAGAAGAAGGCAGTGCTTTCAGAA[C/T]GTGAAAGTCAAAAGCATAGAGTTAAGCTGTCCTGT Y 2 1 2 1 101000 f 74 goat snp23303-scaffold233-808767 4 35865105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802687 Affx-122956526 AX-385289586 4 81867271 TCTCCCCTGGGTTTGTTTCTTACAACAATTTCAGT[A/G]CATTAGTACCCTACATCCTGTCATAAGCAATGTAA R 2 1 2 1 101000 f 74 goat snp23304-scaffold233-869229 4 35804464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452751 Affx-122920269 AX-123323084 4 81908310 TGTTTCTGGGGGCTGTACAAGGGATATGATCATTT[A/G]CAAGAGTCACTGAATGTCATTGCACTTAGAGAATC R 2 1 2 1 101000 f 74 goat snp23305-scaffold233-910268 4 35763417 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404538 Affx-122957395 AX-123274890 4 81945017 CTTTTTGTAGATTTCTGTAATATACTGTCCTTTAG[A/C]GGTCTTAGTGACTACAGAGGTAAATCACCAACAAA M 2 1 2 1 101000 r 74 goat snp23306-scaffold233-946975 4 35726521 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773702 Affx-122962791 AX-385260842 4 81989345 GAAATAAATTCACTCAGTCTACAACGTCTGTACTC[A/G]TCCAATTACTAAGATTCAATATGTGTATCTCTGAA R 2 1 2 1 101000 f 74 goat snp23307-scaffold233-991303 4 35681692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410071 Affx-122952853 AX-123280421 4 82031883 CTACTTGAATCAAACCTGTAGATAGTGCTTACAAA[G/T]CATAATATTTTTCGATCTTTTAAAAATGAAAGGGA K 2 1 2 1 101000 f 74 goat snp23308-scaffold233-1033841 4 35641191 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425566 Affx-122941431 AX-123295912 4 82106942 TTAAAAAACTCTCTACTTGTGAGAGGTCTACTCAT[A/G]TTTTCTGTTTTTATTCTTAGAATATTTGCTAGAAT R 2 1 2 1 101000 f 74 goat snp23310-scaffold233-1108900 4 35564934 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393465 Affx-122965841 AX-123263821 4 82154804 GTATTTGGTCACTGTGACAACCAAAGCAATTAACT[C/T]TGACTCCAGTATAATTTGTCTTAATTGATATTGCC Y 2 1 2 1 101000 r 74 goat snp23311-scaffold233-1156762 4 35516888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770838 Affx-122925033 AX-385258002 4 82191042 AAACCTTCTGCTTAGGAAACAATCCATGAGTTGTA[G/T]ATCCCATTTGATTCCCAATTCGATACTTTTCTCTC K 2 1 2 1 101000 f 74 goat snp23312-scaffold233-1193000 4 35480505 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776646 Affx-122966730 AX-385263773 4 82221496 GGAGGTGGGAACTGTGACAACAGCATTTGCACTTC[G/T]GTCATGAAATATTAACAACCAGTGATCTGAAAGAA K 2 1 2 1 101000 f 74 goat snp23313-scaffold233-1223454 4 35450156 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798152 Affx-122966563 AX-385285087 4 82301280 ATCCTCCATAAAACTGATCAAAACATACTTGACAA[C/T]CTCATTGTAAGTAAAAGCAGTCTCCTAGATCCAGC Y 2 1 2 1 101000 f 74 goat snp23315-scaffold233-1303238 4 35369494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405733 Affx-122956518 AX-123276085 4 82336825 CTCTGAAAACTTGGGTTCAAATTCTAGCTCAGTTC[A/G]TACATCAGCTGTGTGATTTTAGACAGATCACTTAC R 2 1 2 1 101000 r 74 goat snp23316-scaffold233-1338783 4 35333893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803436 Affx-122933281 AX-385290267 4 82436747 AAACTAAATTGAAAACTTACTAACTTTTGATCCAT[C/T]ATTCATTTTATTGGTATAAATTCCTCAAATGCCAA Y 2 1 2 1 101000 r 74 goat snp23318-scaffold233-1438705 4 35234023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444841 Affx-122926303 AX-123315178 4 82466808 ATTTTGATTTCCCTTGTGTCAGGAGGTAAATATGA[C/T]TCCGCTCCACAAAGTCCTCAGGGACCCAGGCACCT Y 2 1 2 1 101000 f 74 goat snp23319-scaffold233-1468766 4 35203868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796225 Affx-122952644 AX-385283175 4 82511036 CTGTGTTACTCTAATACTCATAGTCTAGACAAGCA[C/T]GTTTGCTTCCTCTTCTCCATCCTTTCTACTCTCTT Y 2 1 2 1 101000 r 74 goat snp23320-scaffold233-1512994 4 35159810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442836 Affx-122927695 AX-123313173 4 82539892 TGGGGGGAACAGAAGGGCCTGACTATGTGGACACC[A/G]TTGCCACCTCGAAGGCTCTCCCTTCTTCAGAAAAG R 2 1 2 1 101000 r 74 goat snp23321-scaffold233-1541850 4 35130941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438398 Affx-122931293 AX-123308736 4 82579033 CCAATCAAAGCTTTCATCTGATTCTCAAAAGGATA[A/G]GTGGCCTCAAAGACATAACTTTTGTGAGATTTTCT R 2 1 2 1 101000 f 74 goat snp23322-scaffold233-1580991 4 35092246 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422475 Affx-122943324 AX-123292821 4 82608924 AGGATCAAAATTAGACAAAGGTTATAAAGAGGCTA[C/T]AAATTAAATAGACATATTTTCCCACATGGCTAATA Y 2 1 2 1 102000 f 74 goat snp34081-scaffold400-21610 4 35064118 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775812 Affx-122920376 AX-385262943 4 82669077 GAGTACAAGTAATTTGTACAAGAAATTTGAAAGGA[C/T]TGTATTTTAAAAGATCAAACAGTTTTGACAGTTAT Y 2 1 2 1 101000 r 74 goat snp34082-scaffold400-81763 4 35004138 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272284 Affx-1111833440 AX-519546023 4 82712352 ATCTTCAGCACCACCATGAGGGATTTGTCTGGTGT[A/G]CACACAAACGACGCTGTGACTTCCTTGTCCACCCT R 2 1 2 1 101000 f 74 goat 4_82712352_AF-PAKI 4 82712352 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392645 Affx-122966449 AX-123263002 4 82749536 TTATATGTAATCCCACTGCCAGCACCAAGCTCAAG[C/T]GAAAACTTATACAAAATAAAAATATGTATACAAAC Y 2 1 2 1 103000 f 74 goat snp34084-scaffold400-162222 4 34923277 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464315005 Affx-1110420485 AX-515789044 4 82796998 ATAAAATTGCACAGGTTACATGTATGAAAAGAATA[A/C]GAAGTGGTCAAATATTGATACTGCTTCAGTGTCTA M 2 1 2 1 101000 r 74 goat Random2.2K-464 4 82796998 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769270 Affx-122951877 AX-385256443 4 82800465 TAATACTTCCTAGAAAATAGACTGCATTCTGAATT[A/G]TAATGATTCCTTTGTATCACATGAGTAATTTTTCA R 2 1 2 1 101000 f 74 goat snp34085-scaffold400-213151 4 34871914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795297 Affx-122967088 AX-385282255 4 82863917 AGTGAAAAACTAGTAAACAGGAGTAACCGTTATTA[C/T]GTATTTTAGAGACACAGTGTTAGAGATCTTAATAC Y 2 1 2 1 101000 f 74 goat snp34087-scaffold400-276603 4 34808379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382600 Affx-122973715 AX-123252958 4 82981481 CCTTCTTACTGTCACACTGCTTAGCTACCTTTGTC[C/T]ATCTTTTCCTCCAGAGAAGTGACAGAAGCCTGAAT Y 2 1 2 1 201000 r 74 goat snp34090-scaffold400-394167 4 34689737 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770768 Affx-122978702 AX-385257932 4 83056964 TAAAGAGTGTCTATCAGAAACTCATGTCAAGAACT[A/C]AAGTAATAAAAGAACGCAGTTTATTATTTTTATTT M 2 1 2 1 101000 f 74 goat snp34092-scaffold400-469650 4 34613820 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787740 Affx-122949795 AX-385274763 4 83091656 ATCACAGACAGAATCAAATGGAGATTTTGAGAAAG[C/T]GATAGCATCGCCTTGCTTCATTTCCTTGAAAATGG Y 2 1 2 1 201000 f 74 goat snp34093-scaffold400-504342 4 34578989 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393278 Affx-122965448 AX-123263634 4 83184326 CTAGCAACCTATTTCTGGAACTTTTCTGTTTCTCT[A/G]CCATCTCTCTACCTCTCTTTGTCTTCCTCATTCTG R 2 1 2 1 201000 f 74 goat snp34096-scaffold400-597012 4 34486798 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389757 Affx-122968243 AX-123260114 4 83237640 TTGCTATTATTACGCTAATTATTGTGTTTGAGAAC[A/G]TGAGGCACAGAGAGGTTAGGTAACCGCCAATGTCA R 2 1 2 1 201000 f 74 goat snp34097-scaffold400-650326 4 34435790 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418972 Affx-122946075 AX-123289320 4 83283358 CAGATATCCAGTAAGTAAAGTAAAAGTAAGTAAAA[C/T]GTGTAGGAGAAGACAAATGAGAGAGGTGTGATCTT Y 2 1 2 1 102000 r 74 goat snp34098-scaffold400-696044 4 34389972 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275070 Affx-1111834580 AX-519548651 4 83309364 GTGA[A/G]CTTCCTAGAATCTCCTTTTACATTTGAATCTATGA R 2 1 2 1 101000 r 74 goat GoatD01.042191 4 83309364 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770373 Affx-122921467 AX-385257540 4 83331445 AATAGTCACTGGTGAATGAGGCAGATTAAAGAACA[C/T]AGTGGTGAAATTCCTTGTTGTAAAGGACTTTAAAG Y 2 1 2 1 101000 f 74 goat snp34099-scaffold400-744131 4 34343022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437857 Affx-122932078 AX-123308195 4 83370308 CTGTAAAATAGCTGTTTTTTAAATTTACAGAATCA[C/T]GGGAAGTATTTGAAATGCTAAAAGATACATGCTGA Y 2 1 2 1 101000 r 74 goat snp34100-scaffold400-782994 4 34304365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440251 Affx-122930661 AX-123310588 4 83412572 GACATTACTGAGCGATTGAGTACATACACACAAGG[C/T]AGATATTAACAGACAGGTAGATAGATAGACAGGTG Y 2 1 2 1 202000 r 74 goat snp34101-scaffold400-825258 4 34261730 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406099 Affx-122956222 AX-123276451 4 83497741 GCTTTTGACTTCTGAAAAGATTTTTTTCATATGGC[A/G]CTTATAAATTAATATTACCAAAACACATCCTATCA R 2 1 2 1 201000 r 74 goat snp34103-scaffold400-910427 4 34176064 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380082 Affx-122975547 AX-123250440 4 83607587 TCATTGATATGCTACCTTGCTGGTGTTTCAGTGAT[G/T]GCAGAAGAGAGCTAGTGTACCCTATAAATAAATAG K 2 1 2 1 101000 r 74 goat snp34105-scaffold400-1020273 4 34066129 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784292 Affx-122945878 AX-385271343 4 83643973 CAAGTGTTTGGAATACTGGAGAGAACCTGAAAAGT[A/G]TCTGGTCTTGCCATGGGCTCAGGAAAATCAAATCT R 2 1 2 1 101000 r 74 goat snp34106-scaffold400-1056659 4 34029442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447571 Affx-122924028 AX-123317907 4 83681809 GTTCTTAAGAGACTTTTTCCTTTCAGTGTATACTT[G/T]CCACCTCTTGGCCATTTACATGGGTTTAACTATTC K 2 1 2 1 101000 r 74 goat snp34107-scaffold400-1094495 4 33991684 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787921 Affx-122964368 AX-385274943 4 83774748 TAGGAACTTATTTTCTCATTTCATGAGATATTGTG[C/T]AGGCTGATATAGAAAGTATAAAGACTTTTGAAATT Y 2 1 2 1 101000 f 74 goat snp34109-scaffold400-1187434 4 33898389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783613 Affx-122926775 AX-385270672 4 83813604 TCATTGCTTGCATCCATTGTATGGTAATTGTTTAT[A/G]CATTTCTCATCCCATTCTAGTCTGTGACCTCTTGG R 2 1 2 1 101000 r 74 goat snp34110-scaffold400-1226290 4 33859544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383130 Affx-122973256 AX-123253488 4 83945407 CTCAGAATTCTGAAGAAGGAAATAAAATCACAGGT[A/G]TCATATCAGACGATCAGACTGATATGGAAAGAAGT R 2 1 2 1 103000 r 74 goat snp34113-scaffold400-1358093 4 33727902 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427417 Affx-122940062 AX-123297760 4 83987807 ATTTTAGATGGTTTAAATGTTTCACTTTAATTCTG[A/C]AACTGGTAAAACATATAGCATATATAAGAAGATTC M 2 1 2 1 101000 r 74 goat snp34114-scaffold400-1400493 4 33685237 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384515 Affx-122973046 AX-123254873 4 84060379 ATGAACATAAATATCAATATTGGTGTGCTACAATA[C/T]ACTACATAGCCGATAAAAGAGAAATAGAAATTTAA Y 2 1 2 1 201000 f 74 goat snp34116-scaffold400-1473065 4 33614682 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447592 Affx-122924012 AX-123317928 4 84098316 CCTAGTCATAAAGTTATTAGCATGGAGCTATGACC[A/G]TGTAGATGGTAGAGAACGCTGGGGGAGGTACATGG R 2 1 2 1 201000 f 74 goat snp34117-scaffold400-1511002 4 33576800 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420460 Affx-122944882 AX-123290807 4 84251999 AACAAGCAGTGCCTGAACAAAGGAAGGAGGAAAGA[C/T]GCCTCTTGTCACTGAACTGACTGGCTGTACGCTTA Y 2 1 2 1 101000 f 74 goat snp34119-scaffold400-1664685 4 33421446 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402272 Affx-122959116 AX-123272625 4 84299154 TTCAGGAGAAAAGCCAGGAGGACTGTAGCCTAAAA[C/T]AGCATTATGTAAAAAGAAAGCACACACACAAAAGC Y 2 1 2 1 101000 f 74 goat snp34120-scaffold400-1711840 4 33374024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418473 Affx-122946457 AX-123288821 4 84333684 GAATAGTTCTCAGGGAGGAACGCTCTGAAGGAGAC[A/G]TTACAGAAACGGTCTGTTTCCTCAGCAGGTGCTTA R 2 1 2 1 101000 r 74 goat snp34121-scaffold400-1746370 4 33339662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447021 Affx-122924544 AX-123317357 4 84402400 ACATTCTGGAACTTGCAAACAACTGTATTCCCAAA[C/T]AACAAGCTGCGCTCTGTGTGCTTAGGTGCTCAGTC Y 2 1 2 1 101000 f 74 goat snp34123-scaffold400-1815086 4 33271592 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784486 Affx-122926639 AX-385271535 4 84432948 TCAGTTATTTGCAAAGGTATTTGAATGCCTCCTGA[C/T]ACATACCCCAACAGCCTTGTTCTACCTAAACTGTA Y 2 1 2 1 101000 r 74 goat snp34124-scaffold400-1845634 4 33240585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796119 Affx-122920783 AX-385283070 4 84463500 ATCAACTCAATTAGAGATGGGAAAGATGGATAACC[A/G]CACATCCATCAATACACAGGAAGCTTTTTCCTGAC R 2 1 2 1 201000 f 74 goat snp34125-scaffold400-1876186 4 33209992 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771708 Affx-122948695 AX-385258865 4 84538778 GCTCAGGCATGCAAATTAGTAAATTCTGAGTGTCT[A/G]CTAGGTACTAGGATATAAGATTGATAGGACAAGAG R 2 1 2 1 101000 f 74 goat snp34127-scaffold400-1951464 4 33134522 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793876 Affx-122919962 AX-385280845 4 84582639 CTGCTTGTCTATTAATTAATTCTGCTAATTTATTC[A/G]CTGGAAATGAGTCACAAATTAGTAATGCAAAGTAA R 2 1 2 1 101000 f 74 goat snp34128-scaffold400-1995325 4 33090116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413875 Affx-122949852 AX-123284224 4 84664479 AAGCACTTTTTAAATAAAGACTGTCCTCTGATGAT[A/C]GTCATAAACAGTTTTGCCACTAATTAGGCAATACG M 2 1 2 1 101000 r 74 goat snp34130-scaffold400-2077165 4 33009233 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776893 Affx-122958402 AX-385264017 4 84701023 ACTTACAGCTGAAGATATCTAAAGATAAATGTGTA[C/T]ATTCAACAAATGCCTTCAAAGGTTATTTGCATATG Y 2 1 2 1 101000 r 74 goat snp34131-scaffold400-2113709 4 32972873 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773712 Affx-122970562 AX-385260852 4 84750083 CTATGCAAATCCATGAAAGGCAGTATTCTGTTCTA[C/T]GAGAAAATTTATCAGTGGTTATCTGCTGGCTTGGA Y 2 1 2 1 101000 r 74 goat snp34132-scaffold400-2162769 4 32924431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398051 Affx-122961753 AX-123268406 4 84783803 TTTCAATTCAAGGATACAACCTCTTGATAGCTTTG[C/T]GGGCCATTTTAGCCAAGCAGGAAAACAAAAATCAC Y 2 1 2 1 101000 r 74 goat snp34133-scaffold400-2196489 4 32890854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476192 Affx-1251763697 AX-586011618 4 84803021 GTTTTTAACAAACTACTTAAAAATAATTTAAAATT[-/TTAAATACATTCAGGAGGGAAAGATGGCGGAGGAATAGGAAAATATTTAAAAAATGACCAAAAAAAAATAAATAAATAAA]TAAATACATTCAAAATCAATAAGCAGTATGAACTC - 8 1 4 1 20000 f 74 goat SV_337 4 84803021 - deletion junction SV-TF-chip 539476447 Affx-1251763697 AX-586011848 4 84803021 GTTTTTAACAAACTACTTAAAAATAATTTAAAATT[-/TTAAATACATTCAGGAGGGAAAGATGGCGGAGGAATAGGAAAATATTTAAAAAATGACCAAAAAAAAATAAATAAATAAA]TAAATACATTCAAAATCAATAAGCAGTATGAACTC - 8 1 4 1 20000 r 74 goat SV_337 4 84803021 - deletion junction SV-TF-chip 562165076 Affx-1251763697 AX-606940488 4 84803021 GTTTTTAACAAACTACTTAAAAATAATTTAAAATT[-/TTAAATACATTCAGGAGGGAAAGATGGCGGAGGAATAGGAAAATATTTAAAAAATGACCAAAAAAAAATAAATAAATAAA]TAAATACATTCAAAATCAATAAGCAGTATGAACTC - 8 1 4 1 20100 f 74 goat SV_337 4 84803021 - deletion junction SV-TF-chip 562166408 Affx-1251763697 AX-606941816 4 84803021 GTTTTTAACAAACTACTTAAAAATAATTTAAAATT[-/TTAAATACATTCAGGAGGGAAAGATGGCGGAGGAATAGGAAAATATTTAAAAAATGACCAAAAAAAAATAAATAAATAAA]TAAATACATTCAAAATCAATAAGCAGTATGAACTC - 8 1 4 1 20100 r 74 goat SV_337 4 84803021 - deletion junction SV-TF-chip 562166477 Affx-1251763697 AX-606941885 4 84803021 GTTTTTAACAAACTACTTAAAAATAATTTAAAATT[-/TTAAATACATTCAGGAGGGAAAGATGGCGGAGGAATAGGAAAATATTTAAAAAATGACCAAAAAAAAATAAATAAATAAA]TAAATACATTCAAAATCAATAAGCAGTATGAACTC - 8 1 4 1 20100 r 74 goat SV_337 4 84803021 - deletion junction SV-TF-chip 320780291 Affx-122953288 AX-385267386 4 84814495 ATGATCTGGAATTTTTTCAAAGTCCATAGCTCTCC[A/G]TTCAGTAGCAAAATTCCATTATTATTTGAAATGTG R 2 1 2 1 101000 f 74 goat snp34134-scaffold400-2227181 4 32859849 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387558 Affx-122970286 AX-123257916 4 84849084 AAAGGATGGTTACTGTTTCTGCAAGACACAACAAA[C/T]GTCTTACTGAGCTATAACCATGGCTACCATTTGAG Y 2 1 2 1 101000 f 74 goat snp34135-scaffold400-2261770 4 32825885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779334 Affx-122950327 AX-385266438 4 84882926 GCCAGGGAATAAACTGGTCAAATTAAATTGCCAAT[A/G]TTTGAACAAATTCCAAGATGAACCTAGACTGGGTA R 2 1 2 1 201000 r 74 goat snp34136-scaffold400-2295612 4 32791355 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782839 Affx-122953723 AX-385269910 4 84917135 ATATCTACTTTTACATGGACTAATATAAAAATAGC[A/G]TGCATATCACAATAACTCGAGGTTATGATATTTAG R 2 1 2 1 101000 r 74 goat snp34137-scaffold400-2329821 4 32757094 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802274 Affx-122939024 AX-385289178 4 84950268 AAGCGATGCCTGTGCTTCTAGAATAAATCTGTCAA[C/T]AGCATCTGCCATCCCAATCTCCATCTCCACATTTG Y 2 1 2 1 101000 r 74 goat snp34138-scaffold400-2362954 4 32723823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782178 Affx-122949106 AX-385269256 4 84996008 GCCCATTTAACACACTCTCTTGGTCTGATTGTTGC[G/T]ATCCAGATTGTTGAAATCTGGAATAGAATCTATAA K 2 1 2 1 101000 f 74 goat snp34139-scaffold400-2408694 4 32678491 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780888 Affx-122920248 AX-385267975 4 85028761 GGCAGAAAAGGCAAATGCTGCTATGACAAGGCAAT[A/G]TGGATAATGACTCCCCTCTGACTAAAGTTCTGAGT R 2 1 2 1 101000 f 74 goat snp34140-scaffold400-2441447 4 32645746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416553 Affx-122947675 AX-123286901 4 85066503 TATTCCTCCCATTGAAATGCCCTCCCTCATTCTCC[A/G]CTACCTTTTGGAATCAACATATATTTTTTTAAGAC R 2 1 2 1 201000 r 74 goat snp34141-scaffold400-2479189 4 32607929 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384687 Affx-122972122 AX-123255045 4 85143734 GCTCAGTGGTGTCTTCTAATCTCTTCTGTTCCTCC[A/G]CTTTATCCTTCTAATTCTTTCTTTTTATTATCTCT R 2 1 2 1 103000 f 74 goat snp34143-scaffold400-2556420 4 32533639 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272286 Affx-1111833442 AX-519546025 4 85226008 GAATGTCATCCCATATTAAGCCTTACTGAACCATA[A/C]TGCCAACAAGAGTCAATGAACCATTTGGCAAGAGT M 2 1 2 1 101000 f 74 goat 4_85226008_AF-PAKI 4 85226008 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426933 Affx-122940430 AX-123297278 4 85258048 AAGGGAAACATTATTCATGAGGTTTTCAGCACACA[C/T]GGTGGTGCTGGTGGTTTAGTCACTAAGTCGTGTCC Y 2 1 2 1 103000 f 74 goat snp34146-scaffold400-2670734 4 32417579 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395621 Affx-122963804 AX-123265976 4 85304044 AGATGTTTCAGTCCCAGAATTGGTGGATCCTGTGA[C/T]GAGAAGGGGCCTTAGGGTAACTAAAAAGATGACTG Y 2 1 2 1 101000 f 74 goat snp34147-scaffold400-2716730 4 32370744 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412253 Affx-122950900 AX-123282602 4 85339467 TCCTGTCTGCACACCTAGTTCATATTATAGTTATG[C/T]ATGGGGATAGCCTCCTTCAAAATTTCTTCTTGAGT Y 2 1 2 1 101000 f 74 goat snp34148-scaffold400-2752153 4 32334678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784456 Affx-122941071 AX-385271504 4 85359591 AAAATCCTAATAGTTTGGATATTATCCATCTCTAA[C/T]GCTTCCATCCATAACAATTTGGATTTCTTCCTGTC Y 2 1 2 1 101000 r 74 goat snp789-scaffold1021-9749 4 32312509 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448712 Affx-122923850 AX-123319048 4 85389870 AATCCCAGAGCCGTGCGATCCTCCCCCCATCACCA[C/T]GTGACATTAGTGAGAAAGGCGACAGGCGATGTCAT Y 2 1 2 1 101000 r 74 goat snp790-scaffold1021-40028 4 32281906 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774955 Affx-122920046 AX-385262088 4 85431376 ATTCACAACTACTGAATGTATAGACAAAATGTCAT[A/G]TATTTGTGTTGACACATATATAGTTCTCTATATAT R 2 1 2 1 201000 r 74 goat snp791-scaffold1021-81534 4 32240537 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376215 Affx-122978804 AX-123246574 4 85465487 TTAACAGTTCACATCTCTCCCCTGAATCTGACTCA[C/T]AACCAAATGCCTACTCAACACCTACTTAACACCTA Y 2 1 2 1 201000 r 74 goat snp792-scaffold1021-115645 4 32206598 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403348 Affx-122957807 AX-123273701 4 85495641 TAATGGAATAAAAATGCAAACATTAAGAGTCAGTG[C/T]ATGTTAAATATTATCAACAAAAAAGATTATTGGAG Y 2 1 2 1 101000 f 74 goat snp793-scaffold1021-145799 4 32175964 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445785 Affx-122926054 AX-123316122 4 85542051 ATACACATGTGTAATAATCTCCCAATGATTCCAAC[A/G]CATATGTAAACCTGAGAACCCTTCCTGCTCCATAA R 2 1 2 1 101000 f 74 goat snp794-scaffold1021-192209 4 32129620 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396583 Affx-122962911 AX-123266938 4 85570697 CACTTATCAAACCCTTACCCTAAAATAACTTAAGA[C/T]GGGTTATCTACTCATCAGACCCCTACCTTAAAATA Y 2 1 2 1 101000 r 74 goat snp795-scaffold1021-220855 4 32101263 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762314 Affx-986696845 AX-385250494 4 85653355 GACTAGAAACTATCTTACCAAAAACCATTTCACTA[A/G]CCCAAATAAAAATATCTACCACAATCACAAGCCAA R 2 1 2 1 600010 f 74 goat 4_85653355 4 85653355 Ancestral_priority_1043 ancestry 0.766 recommended IMAGE 10K 10K ancestral 38378041 Affx-122977569 AX-123248400 4 85672932 GAGTGAGAGCCTAGAGAGAACAGCAGGGCTGAGAG[C/T]AGAATTCATTTTCTGGGTGAAGGGGAAGCATTTGA Y 2 1 2 1 202000 f 74 goat snp797-scaffold1021-323090 4 31997698 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799771 Affx-122977744 AX-385286698 4 85716478 TCTCTTTTTGTAAATAAAGCCTTCTCTAAATCACA[A/G]TTTATCAAGATCAACTTACTGAATCTAATTTAAGT R 2 1 2 1 101000 f 74 goat snp798-scaffold1021-366636 4 31953951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408300 Affx-122953779 AX-123278651 4 85763552 AACTGGGATGTTGGGTCTGTTTGTTGCTCAGTCGT[A/G]TCTGACTCTTTGTGACCATATGGATGGACTTTGGC R 2 1 2 1 103000 f 74 goat snp799-scaffold1021-413710 4 31907771 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407372 Affx-122955268 AX-123277723 4 85792546 CACAGCTCAACCTTCAAGGATATGCTACAATTAAA[A/C]GGAAATTATGACCACGGCTACTTGGAAATCTTCAG M 2 1 2 1 201000 f 74 goat snp800-scaffold1021-442704 4 31878094 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772913 Affx-122937976 AX-385260057 4 85837976 TCAGACACAACTAAGCCATTAACACGTTCTCGTTC[A/G]CTTTTCAACCTTTAGGAATATGCACTCAGGTAGTT R 2 1 2 1 101000 f 74 goat snp801-scaffold1021-488134 4 31832045 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797227 Affx-122964781 AX-385284166 4 85891617 TTTCTATGGCTACAATTTCCTTTTGTGTACTGTTA[C/T]AGTTTAAGAGTTCTATACAGAACATTTTATGGCTT Y 2 1 2 1 101000 f 74 goat snp802-scaffold1021-541775 4 31777797 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429145 Affx-122937992 AX-123299487 4 85928511 CCAAAGGAAACGGAAAAATGTTTACAAGTGAGCCA[C/T]GGCAGCAATAGGCTGAAAACACATATCTGTATTCT Y 2 1 2 1 101000 f 74 goat snp803-scaffold1021-578669 4 31740807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405786 Affx-122955913 AX-123276138 4 85957357 TTAATATATGCACATGGTTAAAAAAATTAAAAAGT[A/G]CTGAAGGCTTTATCTCTCCACCCTCACCCCTAACA R 2 1 2 1 101000 r 74 goat snp804-scaffold1021-607515 4 31711681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776141 Affx-122921487 AX-385263271 4 86005165 TGAGATCTAATGATAGGATGCTTCTTCTACCTGCA[C/T]ACTTTACCTTCTCATTCCTAGAAACTTATTTATGG Y 2 1 2 1 101000 f 74 goat snp805-scaffold1021-655323 4 31663574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776917 Affx-122978523 AX-385264041 4 86034931 ACTGGATCTTTGCAATTTTATTGAGTGGATCAATT[A/G]CCAAGCTCTAGCCCTTCCCTCTAACCACTTTGCCT R 2 1 2 1 101000 r 74 goat snp806-scaffold1021-685089 4 31633981 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428980 Affx-122938862 AX-123299322 4 86082059 TTCCTCTGTGTGTGTATTTGTTTTAATTTTCCCAT[A/G]CAATCACTTATCCAATTTCTTGATAAATTATCTCT R 2 1 2 1 201000 r 74 goat snp807-scaffold1021-732217 4 31588894 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392923 Affx-122965709 AX-123263280 4 86117011 AATGGAATCTTTGTATTTCTCTTTCTAAAGAAAAC[A/G]ACAGCAACCAAAAAACCCAACTCTGACTCTTTTCT R 2 1 2 1 201000 f 74 goat snp808-scaffold1021-767169 4 31553758 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438116 Affx-122931494 AX-123308454 4 86152818 AAGCTAAACCAGACTGTATGAGGCTCTGTTTTCTC[A/G]TTCATAAAATGGGAATAATAGCAGCACTTCCACTG R 2 1 2 1 101000 f 74 goat snp809-scaffold1021-802976 4 31517838 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792308 Affx-122959095 AX-385279290 4 86191498 CAGACAGTAATAGGAAATCATAGAGAATGTAAAGC[A/G]TTGACAGAATGACAGAAGAGACATCAGACATCACT R 2 1 2 1 101000 r 74 goat snp810-scaffold1021-841656 4 31478750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789959 Affx-122936022 AX-385276965 4 86244084 TCACATAGCATTTACAAACACAAAATTTAACCAAT[A/G]CTATGAAATATAACCAATATTATTCAGCCTGGCAT R 2 1 2 1 101000 r 74 goat snp811-scaffold1021-894242 4 31425833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391264 Affx-122967365 AX-123261621 4 86272713 ATCCTATAACAAGCATGATGGACCCCATCAAAGTT[A/C]GATTCTATTCACATCCTTTATATGGCTTCTATGAA M 2 1 2 1 201000 r 74 goat snp812-scaffold1021-922871 4 31396840 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397525 Affx-122962046 AX-123267880 4 86320833 AATAATAGGCTACTTAAAATATATATCTAGACTTA[C/T]AGACAAGTCTGCCCAGAAAACGGTCTCAATTAAGG Y 2 1 2 1 101000 r 74 goat snp813-scaffold1021-970991 4 31348429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418422 Affx-122946533 AX-123288770 4 86352112 CCCTGCACACTGCTCAATTGTTCCCTGATGCGCCC[G/T]AAATGTGCTGACAACAGCTTTCCTTCATCCGTGCC K 2 1 2 1 101000 r 74 goat snp814-scaffold1021-1002270 4 31318196 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385002 Affx-122971879 AX-123255360 4 86406374 TCGTGCTAGATTTTCAGACAAAAGCAAATATCATA[C/T]ATTATCATTTATATGTGGAATCAAATATTTTAAAA Y 2 1 2 1 101000 f 74 goat snp815-scaffold1021-1056532 4 31263391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785918 Affx-122933065 AX-385272955 4 86439831 CGTTGCCTACATTCTTCAACTGCATTTTCCAAAAC[A/G]CTTTCCACCACCAATTCAAAGCCAACCCCAGTTCT R 2 1 2 1 101000 f 74 goat snp816-scaffold1021-1089989 4 31229873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770256 Affx-122969803 AX-385257422 4 86475937 ATACCTTAAAAATTGGACTGGTGAACTCTAAAAGT[G/T]ACCCTTTGGCCTTCTAGCCCAGTGTGTAACCACCA K 2 1 2 1 101000 r 74 goat snp817-scaffold1021-1126095 4 31193596 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796765 Affx-122964726 AX-385283709 4 86530627 ATATTTTCTTACATGGGAATGTGAAAATTATTATA[C/T]GGGATTAATAGGAAGTCATACAATATTTGTTAAGT Y 2 1 2 1 101000 r 74 goat snp818-scaffold1021-1180785 4 31139195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412169 Affx-122951071 AX-123282519 4 86568151 CCACCTCTGAAATCTTAACTTTAAAGTCCCACCCT[A/G]TGTACAGATTGTCACTCTTCCAGCGCTCTCACTGA R 2 1 2 1 101000 f 74 goat snp819-scaffold1021-1218309 4 31101217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447633 Affx-122923982 AX-123317969 4 86611229 TCCCTTAAAAAGATTACCATTCTTTCAAAACACAA[C/T]AGATTTAAACCATAACTGATTCACTTCCATGACTT Y 2 1 2 1 103000 f 74 goat snp820-scaffold1021-1261387 4 31058187 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784779 Affx-122931692 AX-385271826 4 86647557 TCTTGATATCAAACCAATTTCTACACTGACTTCTC[C/T]TAATCCTCCAAAAGGGATGTCAAAAGGCTGTCCTT Y 2 1 2 1 101000 r 74 goat snp821-scaffold1021-1297715 4 31021342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780742 Affx-122941495 AX-385267832 4 86750784 TTACCTTGCATGCACTTATTCACAATGAATATACC[A/G]CCTTGTGTGTTTTCACAATTTTGTCATCATTCTAC R 2 1 2 1 101000 f 74 goat snp823-scaffold1021-1400942 4 30916000 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780383 Affx-122934798 AX-385267477 4 86785476 ACGTGACAGTAACTTTTGCTATGCTCATTTTACTC[A/G]TTTGGCACAGCCGTCTGATCTCTCTGCCTTTAGAC R 2 1 2 1 101000 r 74 goat snp824-scaffold1021-1435634 4 30881588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406386 Affx-122955402 AX-123276738 4 86865779 TAAAAATTTCATCCTCCTCACTCAGGAAGACTCTG[C/T]ATTTGCCTCCTTGACTTTTGTTGTTGGTTTAGATA Y 2 1 2 1 101000 r 74 goat snp826-scaffold1021-1515937 4 30801239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802395 Affx-122960932 AX-385289299 4 86884543 TCTCTCTACAGTATCTAACACTTCACTACTCTGTA[C/T]GCACATCCTGTGGTGACTTATTCAAACCTCAGTTA Y 2 1 2 1 201000 f 74 goat snp32055-scaffold360-310890 4 30781560 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393469 Affx-122965838 AX-123263825 4 86947057 CGAATAAGAGGGAGAACGGGACAGAAAGCTGGCTG[C/T]GAAGAGATCGTGCAGACTTTGGAAAGGCCACGGTA Y 2 1 2 1 101000 r 74 goat snp32054-scaffold360-248376 4 30719048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410013 Affx-122953260 AX-123280363 4 86978714 TTTGATTTTCCAGTTAAATTATCAAAATTTTCAAA[C/T]AACAGAATTGTTTTTGTTAATAAACTATGACTTAG Y 2 1 2 1 201000 f 74 goat snp32053-scaffold360-216719 4 30686843 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436394 Affx-122933035 AX-123306733 4 87025215 CCAAGCATCATTTTAAAGGAAGAATTCTGTTACTA[C/T]GAGGCGTCCATCATTGTCAGGGATCCTATCCTAAC Y 2 1 2 1 101000 r 74 goat snp32052-scaffold360-170218 4 30640914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771994 Affx-122964846 AX-385259150 4 87060757 AATATATAGCTTCATGATACCAAAGGGCAAAACAG[A/G]AAAGTGGTAAAGAGTTTCAGAATCAGACATACCTG R 2 1 2 1 102000 r 74 goat snp32051-scaffold360-134676 4 30604858 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382514 Affx-122973805 AX-123252872 4 87103187 ATGACAGACTTTAAGGAAGATTATTCCATCTTCTT[A/G]TTTAAAATCCTTATTCTTATCTTTAATATAATTTC R 2 1 2 1 102000 f 74 goat snp32050-scaffold360-92246 4 30561794 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451945 Affx-122920965 AX-123322278 4 87151482 ATTGATTATCCAGAACTCACAAGAGCTAAGGCTCA[G/T]ATTTACATCTACTCATTCCTTGAAATTTGATTAAG K 2 1 2 1 101000 f 74 goat snp32049-scaffold360-43951 4 30512291 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792876 Affx-122963508 AX-385279854 4 87191170 ATTAGTTCATTCCAAAAGAAATAGATCACATGAAG[A/G]TTGGTATATCAATTAATGACACTGAATTTATTGTT R 2 1 2 1 101000 f 74 goat snp32048-scaffold360-4263 4 30474799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766266 Affx-122972017 AX-385253660 4 87206795 TGGAAAGAAGAATAACGGAAGTATTTTCTGAGATC[A/G]TGGCATTTAATATCATAAAGTAGCTAGATGAAGAG R 2 1 2 1 101000 f 74 goat snp20009-scaffold1998-475680 4 30459135 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408160 Affx-122954216 AX-123278511 4 87235444 CCACCCTCTCCATTCTGTAAGAACAGCCTCTCTCA[G/T]CTTCAAAGCAGGCTCCAGCTAAAGCTTTCAGAATC K 2 1 2 1 101000 r 74 goat snp20008-scaffold1998-447031 4 30430731 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780923 Affx-122963682 AX-385268010 4 87269800 CCAATAGCAAGACCTATTTCCCTTATTCTACTTCT[G/T]AATCACTATTTGTGCAATGGAACAATTAATTTCCT K 2 1 2 1 101000 f 74 goat snp20007-scaffold1998-412675 4 30396125 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383991 Affx-122972923 AX-123254349 4 87302323 AGCTATGTTCAGAGAAAGAAAATAACCATGTCCTG[C/T]AGAACAGAAATAACCAATGACCCAGTCTAAAACGT Y 2 1 2 1 201000 r 74 goat snp20006-scaffold1998-380152 4 30363499 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783863 Affx-122979177 AX-385270919 4 87357665 TAAGGATTATGTAAATAGAATCTCCTTCAAATAAT[A/G]TAACTCTATGAGTAAAGGTAGCCTAAAAGTATTAG R 2 1 2 1 201000 f 74 goat snp20005-scaffold1998-324810 4 30307042 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781996 Affx-122948405 AX-385269076 4 87393184 GGGGTTAATAGGTTAAATTAATTGTATAAGGCATC[A/G]CAGTAAGAGTCAGAATTAGAATTTTATTGCATCCA R 2 1 2 1 101000 r 74 goat snp20004-scaffold1998-289291 4 30271648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376196 Affx-122978817 AX-123246555 4 87435369 AGTCTAAAAAAGAACAAATATGAGAGTTATTTAAG[C/T]AGCACTGAGTGAAAACACAGCAAAAAGTGATACGC Y 2 1 2 1 201000 f 74 goat snp20003-scaffold1998-247106 4 30231360 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387395 Affx-122970418 AX-123257753 4 87495878 TGAGAGGCCTCAATGCCTTCCTGAGACACACAATG[C/T]AATCACTTCCTTCTTGATGCTTCCAGACCCTGTCA Y 2 1 2 1 201000 r 74 goat snp20002-scaffold1998-186597 4 30170210 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438984 Affx-122930379 AX-123309321 4 87533347 CTTCTTTAGCTTCAGAAATGTGGCAAGAGCTGTTG[C/T]ACTCATTGCCTTCTGGGAGGAATTTGTTATGGGTC Y 2 1 2 1 101000 f 74 goat snp20001-scaffold1998-149128 4 30132784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278277 Affx-1111836261 AX-519551764 4 87566586 ACCTACTTTTTTAAAAAAGCTTCTCCCCCATAGTA[A/C]CAAAAAAAACTGACTATTCTACACTACTACCACTA M 2 1 2 1 202000 r 74 goat Random2.2K-466 4 87566586 A C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795966 Affx-122959410 AX-385282918 4 87593926 TCTAGAGTTTTAAATGCCTTGCCACAAATATTTAT[A/G]CTTTCACAATTAAGGCAAAGCAAGACAAAGTTTAT R 2 1 2 1 101000 f 74 goat snp20000-scaffold1998-88549 4 30071577 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801271 Affx-122942519 AX-385288183 4 87629057 TAGCAGCAGCAGCTGACAAGCTCAATGAGGAAAAA[C/T]TCAATGAGAAATATACTTAAATGCCTCACCACAAA Y 2 1 2 1 201000 r 74 goat snp19999-scaffold1998-53418 4 30036298 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395646 Affx-122963783 AX-123266001 4 87705568 CTATAATGTATACACACCTGAAATGTTCAAAATAG[C/T]GCCTGAGTCCAGGCTTGATGTGTTGAAGATTGAAA Y 2 1 2 1 201000 f 74 goat snp912-scaffold1024-349093 4 29948853 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764471 Affx-986696847 AX-385252157 4 87720071 AATCACTTTAAACAATTTAGGTCCCTTATGCATAA[C/T]CTTAGTCACTGCTGAACCATTACACTCGATTTCTT Y 2 1 2 1 600010 r 74 goat 4_87720071 4 87720071 Ancestral_priority_1043 ancestry 0.628 recommended IMAGE 10K 10K ancestral 38407736 Affx-122954994 AX-123278087 4 87758165 GTGCCATCAAGAGATAAATATTTCTAGGTAAGTAG[C/T]AATAAAAAATATAAATCTGCCTTTTCCCCCTGATA Y 2 1 2 1 101000 r 74 goat snp911-scaffold1024-296496 4 29895433 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792093 Affx-122922111 AX-385279081 4 87807301 ACTTCTTTTGCTTTTTCCCTACTGAGTTATGTTGG[C/T]AGAGCCTTGAAAGTTGAGCACTGTGTTAAATGAGT Y 2 1 2 1 101000 r 74 goat snp910-scaffold1024-247360 4 29850210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768720 Affx-122936480 AX-385255898 4 87879895 AGAGTTTATTATAGGTTCTATAAACTGTAGGGAAA[C/T]GTGTTTTGAGAGAAATAGGAAGAAGGGAAAGGCAC Y 2 1 2 1 101000 r 74 goat snp908-scaffold1024-174766 4 29777742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778177 Affx-122976650 AX-385265291 4 87931559 TATCTTGACTACTGAGCACCTAACTTTCAGCATTA[C/T]TTATTAATGGGTATTATAAATAGAGTTATTATAAA Y 2 1 2 1 201000 r 74 goat snp907-scaffold1024-123102 4 29725929 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385568 Affx-122971216 AX-123255926 4 87970411 CATCAATGGCACATTACCCATTTTGAAAACTGAGA[A/G]CTGAAATGCATGCATCAATGTCAGTGCTTATTCCT R 2 1 2 1 101000 f 74 goat snp906-scaffold1024-84250 4 29686924 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385134 Affx-122971768 AX-123255492 4 88004210 TGGCTTTGTGTACAAACCATGATCTGGGCTTCCAG[C/T]GAGGTTGATTCCCTCACCTGCTTGATGGTTTTGAT Y 2 1 2 1 101000 f 74 goat snp905-scaffold1024-50451 4 29652495 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423765 Affx-122942843 AX-123294111 4 88057352 CCATTGTAGGCTGGTGGGGGATAGGAGGTTTCTCC[A/G]TGGTGGATACTGACTGGTAGTTCTTGTCCTTCATG R 2 1 2 1 101000 r 74 goat snp7143-scaffold1264-1816508 4 29595888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777074 Affx-122945845 AX-385264197 4 88092897 ACTGAACAACTACAATGTTCCATCTTTCTTTTGAT[A/G]CCTTCACAGTTAAGAAAGCTCAGAGGTGCAATTTC R 2 1 2 1 102000 r 74 goat snp7142-scaffold1264-1780963 4 29561943 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452926 Affx-122920192 AX-123323259 4 88164213 ATGCAGGCCTTTTTCTTCATGGTTTATGATCTGCT[A/G]TATCTCATTTGGAAAATCTTCAAATACAATGAAAG R 2 1 2 1 201000 r 74 goat snp7140-scaffold1264-1709647 4 29493002 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798851 Affx-122940502 AX-385285781 4 88231450 TCTTCATTGTGATGTAGATACAAATATACAGTTAT[A/G]TCATCTTTTCAGAGCCTTATTCTTTTTCAAGGCTT R 2 1 2 1 101000 r 74 goat snp7139-scaffold1264-1642410 4 29426199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403458 Affx-122957722 AX-123273811 4 88270866 GTAAACTGCAAAGTTCTGCATTTTGGGCAGTGTTC[A/C]GGATCTTGTTCACAGGGAGCAGTTTTAAATCAATC M 2 1 2 1 201000 r 74 goat snp7138-scaffold1264-1602994 4 29390697 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419013 Affx-122946046 AX-123289361 4 88301608 CCCATTTTCTTCATAATTACTGATTCTAACAGTTC[A/G]TAGGCTCTTGTCTTGCCTAGAATTATGACATTATT R 2 1 2 1 101000 f 74 goat snp7137-scaffold1264-1572252 4 29359703 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799138 Affx-122921855 AX-385286068 4 88346728 TTTAAGGAGAACCATCTTTGCTGTCTATAATCAGG[C/T]CTATGAGTGAAGGGAGAGTCTGGAGTCATTGAAAT Y 2 1 2 1 101000 f 74 goat snp7136-scaffold1264-1527132 4 29313444 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783813 Affx-122952518 AX-385270869 4 88383187 TGTTAAAAATTTCTGTCTAATAGTGATCAGAGAAT[A/G]TGAACTGAGAGTTCTAGTTTATGACAATTATTCAT R 2 1 2 1 101000 r 74 goat snp7135-scaffold1264-1490673 4 29276932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381576 Affx-122974810 AX-123251934 4 88413492 TTCAGCACAATTTATAAATTTCTATTAAATGATTC[C/T]TTCTCAGTTTCTTTTTCCTTTCAGTTTCCCAATCC Y 2 1 2 1 103000 r 74 goat snp7134-scaffold1264-1460368 4 29245539 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774052 Affx-122972613 AX-385261190 4 88487448 TGTTTTACAGAACTTAGTTGAAAGACTCTCATTTA[C/T]GGGATGTGTGGCTGGCGTATATTACTTAGTTTACT Y 2 1 2 1 101000 r 74 goat snp7132-scaffold1264-1386412 4 29175714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378974 Affx-122976404 AX-123249333 4 88533953 GCACATTATGGAAGATGAACTATGTTATAGCCCCA[C/T]GTAACAAATAATGGTATCCATTTACTCACTGTGTA Y 2 1 2 1 201000 r 74 goat snp7131-scaffold1264-1339907 4 29128448 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397233 Affx-122962374 AX-123267588 4 88584786 TGTTTGAACATTAATTTGTACAGTTTTGCAAGTCT[A/G]TTATACTTATTGAAATGGCTTTGTTCCTTGCCAAG R 2 1 2 1 101000 r 74 goat snp7130-scaffold1264-1289074 4 29077371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272145 Affx-1111833443 AX-519545902 4 88613524 AACTCCTTGGACCACACAAAATAATTTTTCTCACT[A/G]AATTTAAAAAGCAGAATGATCCACAGCCATCTCTG R 2 1 2 1 101000 r 74 goat 4_88613524_AF-PAKI 4 88613524 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38381880 Affx-122974172 AX-123252238 4 88684365 CTGAAGGTTCAAGATCTGACCTGTTGACAAACTCA[C/T]GTTTTAGGTCTAAATATCAGCTGTCTCTCCTCTCA Y 2 1 2 1 101000 r 74 goat snp7128-scaffold1264-1189495 4 28977725 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446627 Affx-122924792 AX-123316963 4 88716341 TATACCATTATTAAAATCAATTTTAGAAAGTCACA[A/G]GCATGCTGTGGAGACCCATCCCTAAATACTTTTAT R 2 1 2 1 101000 r 74 goat snp7127-scaffold1264-1157519 4 28945291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789998 Affx-122951279 AX-385277004 4 88750968 ATTGATAATACAGAGTGTTATTTTTGTCACTGCCA[C/T]TGTGCTACAGGCCAAGCAAAAATCTTTCTAAACTG Y 2 1 2 1 101000 r 74 goat snp7126-scaffold1264-1122892 4 28910175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398810 Affx-122961405 AX-123269165 4 88803600 GGCTTGGGACCCCGAGCCTGATGCTGAGGATAGGG[C/T]TTTGTGGAAAACATTCCTGTCCATGGCACTACACA Y 2 1 2 1 101000 r 74 goat snp7125-scaffold1264-1070260 4 28858018 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441858 Affx-122929037 AX-123312195 4 88881701 ATTTATTTCATGGTTTCAGTCAAGACTCAAGCCAA[C/T]AAGAAAATTGGCAGGGGTTCACAGTCTCAGAGTAA Y 2 1 2 1 103000 r 74 goat snp7123-scaffold1264-992159 4 28772683 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406603 Affx-122955845 AX-123276955 4 88971927 AGGAGGGTTCAAAGCTTGGAATGATGCCACTCACA[C/T]AGCTGACGCTGCCATGCAGGGGCTGTGAAAGGTGG Y 2 1 2 1 101000 f 74 goat snp7121-scaffold1264-901933 4 28684280 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424607 Affx-122942198 AX-123294953 4 89010362 TTTCAGTATTGGCAATTTTAGAATGTGTGCTGGAG[A/C]GAACAATAGGAGAAAAATCACAGACTTTTAGAGCC M 2 1 2 1 201000 f 74 goat snp7120-scaffold1264-863498 4 28646034 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791237 Affx-122941347 AX-385278231 4 89046887 GAAACCCGTGGTGAATTCTTTTGTAATGCAAATAA[C/T]CACCTTTTAATTTATCTGTTTAGTAAGTTGAGCTT Y 2 1 2 1 101000 r 74 goat snp7119-scaffold1264-826973 4 28609327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464318428 Affx-1110422211 AX-515792438 4 89063503 CCTGCAGATAGTATGATCTGCTCCTTAGCACAGTG[C/T]GATCTGATATGAATTTCCTCCACCTTCTCTGCCTT Y 2 1 2 1 101000 r 74 goat GoatD01.011144 4 89063503 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38387961 Affx-122969607 AX-123258319 4 89079111 GATAATTCTTTCCTCTCTGTGTGTTTTAGGTGTCT[A/G]TCATGTGCCAGCCACTGTTCTGAGCATTAGTTTGA R 2 1 2 1 303000 r 74 goat snp7118-scaffold1264-794749 4 28576636 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771428 Affx-122942871 AX-385258586 4 89121883 TGATAGAACCCAGGGAGGTATGAGATATATATAGA[G/T]AGAGAGTTAGATGATAGGTAGCATTATCTATCTAT K 2 1 2 1 201000 r 74 goat snp7117-scaffold1264-751977 4 28533721 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409575 Affx-122953581 AX-123279926 4 89154109 GTATACACGTATATAAATTTTGGCTCATATAGATA[C/T]ACCCCCATATATATAAAATTTGGCTTATGTATTTA Y 2 1 2 1 201000 f 74 goat snp7116-scaffold1264-719751 4 28501449 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382764 Affx-122973979 AX-123253122 4 89200525 TTGAACATTTCCAAGTGATAGGGAATTTAACAGCT[C/T]CTGACACAATTCCTTCCAGTTAAGGACAGTTTGCT Y 2 1 2 1 101000 f 74 goat snp7115-scaffold1264-673335 4 28454545 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452597 Affx-122920495 AX-123322930 4 89250066 CTAGGGTCATTCTGTATATGTTATCTGTTGTTAAG[C/T]AACAAACTGTCTCAAAACTCAGTGGCCTAAAACAC Y 2 1 2 1 101000 f 74 goat snp7114-scaffold1264-623794 4 28403663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445932 Affx-122925920 AX-123316269 4 89342676 CAATGACCCTCATGGTAAACCCTGTCCTTTGCCTT[C/T]AGCAAGGATACCATATCTGGTTCAGTGTAAATTTG Y 2 1 2 1 101000 r 74 goat snp7112-scaffold1264-531184 4 28310096 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432830 Affx-122935383 AX-123303171 4 89378917 ACCCCAACAATGATCCGGGCACCCTGTGGTGTCCA[C/T]GGTGGGAACAGGAGTGTCATTCATAATTTAGAGTC Y 2 1 2 1 101000 r 74 goat snp7111-scaffold1264-494943 4 28273874 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389593 Affx-122968774 AX-123259951 4 89409135 AGGACAGTTCTCCCCTATACTCTTGAGAAGAGGTG[A/C]TTCTCCCACACTTCACTTATCCCAGAGTCCAGTTT M 2 1 2 1 201000 r 74 goat snp7110-scaffold1264-464725 4 28242843 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393995 Affx-122965029 AX-123264350 4 89439642 AACTCATAAAGCTCTCCCAGAAGACCTAGTACATC[C/T]TGGAAAGCCCAGCTAGATGCTTGCCATGGCTGAGC Y 2 1 2 1 101000 f 74 goat snp7109-scaffold1264-434218 4 28212333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443827 Affx-122927542 AX-123314164 4 89514224 TTTTCTACACAGTAACTAGACATTGTAACACCCAT[A/C]TCACAGATTCAGAAACAGATTTAAAGTTAGTTATC M 2 1 2 1 101000 f 74 goat snp7107-scaffold1264-359636 4 28138056 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418684 Affx-122946306 AX-123289032 4 89545485 ACTGGCGTAGCACAAAGACCCCAGTAGAGCGCTGG[A/G]AAAACAGAGGGATGGACTGCTGTGGGCTGAGCTAC R 2 1 2 1 103000 r 74 goat snp7106-scaffold1264-328375 4 28106806 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424526 Affx-122941726 AX-123294872 4 89581193 ACAAAGAGGGCAGACAAAACTGTAATATATACATG[A/C]TAAATTTCATATATATATATGTATATGAATGAAAT M 2 1 2 1 103000 f 74 goat snp7105-scaffold1264-292667 4 28071155 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446059 Affx-122925829 AX-123316396 4 89633807 ATTTCCTTTGTACATGATGAAAGGTCTAGAGGTGG[C/T]AAGTGGGAGGGGCTGGGGAGCAGAGGCCCCTGGAG Y 2 1 2 1 101000 f 74 goat snp7104-scaffold1264-240053 4 28018399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384201 Affx-122972396 AX-123254559 4 89671045 GAATAGTCACTGGATGAATTTCAGAGGTTTGCAGC[A/G]TGGCCAGCAGAGCCCCAAGCTCCCTCAGAGGACAG R 2 1 2 1 101000 f 74 goat snp7103-scaffold1264-202815 4 27981144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393800 Affx-122965182 AX-123264155 4 89700979 TCTAGCTTCCGATAGTATATTCATTTTTATTAACT[A/G]GTTAATTTAAAGCTGGCTTAGAACTGCAATACTTT R 2 1 2 1 101000 r 74 goat snp7102-scaffold1264-172881 4 27952097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405948 Affx-122955553 AX-123276300 4 89736460 TCTAGACAAGTAACGTGGCTACTGTTCCTTCTTAC[A/G]TTTGTCTCCTGGACAGGGAGGGGGCCTGCATGGAC R 2 1 2 1 101000 f 74 goat snp7101-scaffold1264-137400 4 27916586 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793699 Affx-122924786 AX-385280671 4 89791815 TGAACACAGAATCCCAGAAGTTGCTTAAGCACATG[C/T]AAATAATCACCTCGTTTGATCTATACTGTTCTCTA Y 2 1 2 1 101000 f 74 goat snp7100-scaffold1264-82045 4 27861414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446012 Affx-122925865 AX-123316349 4 89831744 GGCAGATGTGGACACGCTGGCATTTGAGAATGGAC[A/G]TATCAGAAAAACCACATAATCAACAGCTGGACAGA R 2 1 2 1 101000 r 74 goat snp7099-scaffold1264-42116 4 27821465 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426775 Affx-122940553 AX-123297121 4 89889600 CTGGGGTGAGCATTTCTGTTTACAGTCTTTTATGC[A/G]TATGCATAATGATCACCCTAGGGAATATGCCTGTG R 2 1 2 1 101000 f 74 goat snp24944-scaffold2551-446847 4 27765279 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439075 Affx-122930307 AX-123309412 4 89918974 AGTCCTTGTTCTCTCTCATACGGTGCATCCTTTCC[A/G]CTCCCATGAGCACTGGCATCGCCCTCGGGTTCTGA R 2 1 2 1 101000 f 74 goat snp24943-scaffold2551-417473 4 27736075 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436442 Affx-122932999 AX-123306780 4 90005102 GCTGGGGTTTTGTGAGCCTGGGAAGAGGCTGTAGC[A/G]TAGAAGGAGGAGAAAGAAGAGATCCTAAGTGAGCC R 2 1 2 1 201000 f 74 goat snp24941-scaffold2551-331345 4 27650106 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402207 Affx-122959163 AX-123272560 4 90039403 GCTCCACAGAAGGAAAGGGAGAGGAGAATCAGCCC[A/G]ATGCTGTTACCGGTCAGCAGTGCTTGCACTGCCGT R 2 1 2 1 101000 r 74 goat snp24940-scaffold2551-297044 4 27615790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409872 Affx-122952913 AX-123280223 4 90084163 CATCTGGATGGAATATGCTCAGGGCAGTAGGCTGC[G/T]CTGTGCTCTCTGCTTCTTCTCCTTTTAAACACTTT K 2 1 2 1 101000 f 74 goat snp24939-scaffold2551-252284 4 27571109 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416954 Affx-122948023 AX-123287302 4 90134661 TTTGGAGACAGATAGATTATAATTCAAAGGTGGTG[A/C]GGTGGTAAAGAATCCATCTGCAAATGTAGGAGACG M 2 1 2 1 201000 f 74 goat snp24938-scaffold2551-201786 4 27520531 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388294 Affx-122969390 AX-123258652 4 90172175 GGGTTGAAACTAAGACCATCTCCCAACAGCTGAAG[C/T]TGCAGCACAAGTCCTCATCTAAGAGAAGACAAAGC Y 2 1 2 1 101000 f 74 goat snp24937-scaffold2551-164272 4 27482448 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438118 Affx-122931493 AX-123308456 4 90206419 ATTGCTGTTGATTATTTTTCTTGAGATTTACAGGG[C/T]ATTTGTGAAGCTTTCATCTCATTTCCATCACACAT Y 2 1 2 1 101000 r 74 goat snp24936-scaffold2551-130028 4 27448102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440689 Affx-122929914 AX-123311026 4 90363844 GAGCTGGGGACAGGGGCAAGAAGGAGACAAAGGCT[C/T]CTGAGCTCAGTAACGCAGGGCCCTGACATCTGAGC Y 2 1 2 1 102000 f 74 goat snp21932-scaffold2156-19824 4 27293141 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413437 Affx-122950689 AX-123283786 4 90441453 AAAAGCAGATTTGTTTTAAAGCCCAATTCAGCAAG[C/T]AACTCTCAATCAGTCTAGTTGAACAGGCTGCTCAA Y 2 1 2 1 101000 r 74 goat snp21934-scaffold2156-97433 4 27218232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393817 Affx-122965573 AX-123264172 4 90473835 AAAGCCAAGGAATGAGGAGGAAATAATGGTTGACT[A/C]GGATGAGATAATGAATTACGAAGCATGGCACACCT M 2 1 2 1 101000 r 74 goat snp21935-scaffold2156-129815 4 27185796 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796114 Affx-122937372 AX-385283065 4 90527034 AGCAGCTGTAAAGCAATTAGCATTTTACAAAACTG[C/T]GGAGTCAAACTGTCACTTATGGTCTTATTGAGACA Y 2 1 2 1 101000 f 74 goat snp21936-scaffold2156-183014 4 27132256 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765851 Affx-122955960 AX-385253295 4 90578040 ATGTTGCCTAGGTCTCTGGAAAACATTAAATATCA[A/G]ACTTATTCTTGTGAAAAAATATCAATTTGTGTTTT R 2 1 2 1 101000 f 74 goat snp21937-scaffold2156-234020 4 27080720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388674 Affx-122969095 AX-123259032 4 90612924 TGGGTGAATCCTTAGCTGTTTTCTAACTTGTTCCC[A/G]TCCCAAAGACCAGATTTGTTAACAGGGCCAGGGGC R 2 1 2 1 201000 f 74 goat snp21938-scaffold2156-268904 4 27046153 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412627 Affx-122951270 AX-123282976 4 90663048 TATATCCCTGAAACCGAGCAAGACTCTGTGGGACC[C/T]TCTTTGGGACAAAAGCTCTTCTGAGTCCTCTGTTT Y 2 1 2 1 201000 r 74 goat snp21939-scaffold2156-319028 4 26995550 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384363 Affx-122972237 AX-123254721 4 90711857 GTTCATCCACACTGTGTGAGTTCTGAGAATTTGTT[A/G]CCATGAACTTCTGTTGTAACCTTGGTTTAGAGTGT R 2 1 2 1 101000 r 74 goat snp21940-scaffold2156-367837 4 26946270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405594 Affx-122955931 AX-123275946 4 90742884 CATTCTCTTCAGTCCGCGTTCCTTTAGGCCTCAAA[C/T]GCCGCTTTCTCAGGAGTTGCTGTCGACCTTCCTTT Y 2 1 2 1 201000 f 74 goat snp21941-scaffold2156-398864 4 26915606 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792992 Affx-122921995 AX-385279970 4 90801765 ATCTTTTCATGACTAATTGGGAGTCACTTTTGTGC[A/G]CGGTTTTGCTTTATATCTTCTGTGGATTATTTTTA R 2 1 2 1 101000 f 74 goat snp21942-scaffold2156-457745 4 26856396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377645 Affx-122977865 AX-123248004 4 90847455 GTCTTTGCTTATAGTTTCCTTGTTTCTGAGTGCCC[A/G]TTCCCCTAAGTTGAGCCAGCCAGTTATGTATTGGT R 2 1 2 1 101000 r 74 goat snp21943-scaffold2156-503435 4 26810586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410068 Affx-122953217 AX-123280418 4 90881322 AAGAACACAAGGGCCTTGGAGTCCAGCAGAGCATC[A/G]TTCTTTGTCTTACGGAATTCAGATACGTGTTGCAT R 2 1 2 1 101000 r 74 goat snp21944-scaffold2156-537302 4 26776840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401468 Affx-122958966 AX-123271821 4 90937440 GCCGTAAGAAGGTCTGGGTGGAGCCAGGAAAGCTG[C/T]GTTTTGTTGCTGAAGAGGTCTCTGGGTGGTGGAAC Y 2 1 2 1 101000 r 74 goat snp21945-scaffold2156-593420 4 26720329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419947 Affx-122945212 AX-123290295 4 90978559 GCAGATTATTTAATAATGTTTCATACTAGAACTTT[A/G]CTTGACTCCCAAAATATTTCATTCTGAAGTTTTAG R 2 1 2 1 201000 f 74 goat snp21946-scaffold2156-634539 4 26679046 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443857 Affx-122927520 AX-123314194 4 91083773 CACGTGGTTCCAGTGCCTGTGCTGACCATCGCTGC[A/G]TTCAGAAAGGAAGCAGCCCACCAGTCCATCTGCCC R 2 1 2 1 202000 r 74 goat snp21948-scaffold2156-739753 4 26572959 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389514 Affx-122968295 AX-123259872 4 91125197 ACAAGTTTAGTCAGTGAGCTCCACAGGTTAGCGAC[G/T]TCTTCAGGCAGAGGGTAGGTGGCAAGGATGGCCAC K 2 1 2 1 101000 f 74 goat snp21949-scaffold2156-781177 4 26531465 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272288 Affx-1111833444 AX-519546027 4 91137679 ATTTATAAATTTTTACCTTGTTTCCATCTCACATG[A/G]TAAGAGTACTGAAAGGTGCTCATATTTCTTATTTT R 2 1 2 1 101000 f 74 goat 4_91137679_AF-PAKI 4 91137679 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449680 Affx-122922557 AX-123320015 4 91161577 CAATCAGAAATAATTTGATTTCAGTCAGTAAGGCC[A/G]TGAACCCAGGCAGGAAGTTATGAGATGAATGAAAC R 2 1 2 1 101000 f 74 goat snp21950-scaffold2156-817557 4 26495172 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794680 Affx-122936578 AX-385281640 4 91194249 GTTCTGTATCTCTGCCTTCCTAGGTCTCATTTTTA[C/T]CATCTTTCAAATAAGGGAACTGGATGGTATAAAAC Y 2 1 2 1 101000 f 74 goat snp21951-scaffold2156-850229 4 26462500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773341 Affx-122921373 AX-385260483 4 91229964 AAGCAATTTACTGATTCCCATGACTACAAAATAAA[C/T]GGAATCCCAAACTGTACCTTAAATCCAATTCAGGA Y 2 1 2 1 101000 r 74 goat snp21952-scaffold2156-885944 4 26426619 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405350 Affx-122956324 AX-123275702 4 91281449 AAATCTGGCCAGCACTGAGATAAATCACACTTCCA[C/T]AGGGGCTATTTTGCCTTTCCTGAAGTGGCCTGCTA Y 2 1 2 1 101000 f 74 goat snp21953-scaffold2156-937429 4 26375046 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399847 Affx-122960248 AX-123270202 4 91329652 TGCTGCAAGTAAGTCTCCTCTTGTCAGACGCAGGC[A/G]GTGACACACATGTCTTTGCAAGGGCAGGGGCTCCT R 2 1 2 1 201000 f 74 goat snp21954-scaffold2156-985632 4 26326716 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399862 Affx-122960235 AX-123270217 4 91367725 GTTTATTTTTGTTATGCTAGCAGCCACTGGTTATC[A/G]TTGAGTAGGACTATTATGTCATAAGGGGTTACCAT R 2 1 2 1 101000 f 74 goat snp21955-scaffold2156-1023705 4 26288117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389883 Affx-122968135 AX-123260240 4 91399077 TCTGTTCAATTTGTTAGCTCTCTTTCTTTGGGTGT[A/G]AGTTCTTTTTGTAACATTAATACCTTTTTCATGTT R 2 1 2 1 201000 r 74 goat snp21956-scaffold2156-1055057 4 26256612 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386722 Affx-122970155 AX-123257080 4 91474242 TCAGTGTTTAAGTATTTGCATTATTACTCACTGTC[A/G]TTTAACTGACCTAAAAGTTTTGGAAATATGTAGTG R 2 1 2 1 101000 r 74 goat snp30213-scaffold3325-331186 4 26192570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395998 Affx-122963497 AX-123266353 4 91512412 GAAAGGGACCATTTTGCCTTTTCTAAGACCAAAGA[A/C]GCTTTTCCCAGAATGTCCCCACTAGCAAGTGTCCC M 2 1 2 1 201000 r 74 goat snp30212-scaffold3325-293016 4 26154546 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400891 Affx-122959748 AX-123271244 4 91579650 TTGGGGGTGGGCAAGGGGTTCCACAAACAGAGGTT[A/G]CAGGCAAGTCACAGAGGCAAGCATGTTATATCTAC R 2 1 2 1 101000 r 74 goat snp30211-scaffold3325-225778 4 26086729 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378500 Affx-122976654 AX-123248859 4 91614056 AACTCTCGAGGTGACTCCAGGACTCCGAGGTGGAA[C/T]AGGCATTACAGGGCACGACCAGGAAACCTGGGTTC Y 2 1 2 1 201000 r 74 goat snp30210-scaffold3325-191372 4 26052339 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406702 Affx-122955770 AX-123277054 4 91709869 AAACCTGGAGAAGCAGTGGCTGACTTGTGATACTT[C/T]GTCCTCAGCTCATGCCAAGGCAGGATGCAAGCAAA Y 2 1 2 1 201000 r 74 goat snp30208-scaffold3325-95559 4 25956685 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796466 Affx-122921693 AX-385283417 4 91753949 TAAAACATTTTAAGTGCCTGAGAAAACATGTAACC[A/G]TACATAAATCCAAAGCTCTGGCTGGCTCTCAGTGC R 2 1 2 1 101000 r 74 goat snp30207-scaffold3325-51479 4 25912638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278279 Affx-1111836262 AX-519551766 4 91770963 GTAAGCCTCAGGCTCTCAGTGCTATGACAGATGCA[A/G]CTCCAAATTGGAATAAAAGCATAAAAAATCTGCTC R 2 1 2 1 201000 r 74 goat Random2.2K-467 4 91770963 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444728 Affx-122926410 AX-123315065 4 91794653 AGTCCTGTCCACATGCCCCAGCCTCCAAAGCTGCT[A/G]TCCTCCCAGCTTCCCCCAGTGTAACCTTCCATGTT R 2 1 2 1 103000 r 74 goat snp30206-scaffold3325-10775 4 25873739 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387976 Affx-122969595 AX-123258334 4 91807344 CTGGATGTGGGGAATAGAAGGCCGGCAGAATGGGA[C/T]GGAGAACCAGAAGAGTCTTAAAGCACAGCTGAGCG Y 2 1 2 1 303000 f 74 goat snp32082-scaffold362-1817 4 25870283 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443726 Affx-122927143 AX-123314063 4 91889219 TCAAATTTCTTATGAGGAGTGAAACTCAAATACCT[C/T]AGACCCAGCTCAAGTCCGAGCTGCACAAAGGATCT Y 2 1 2 1 201000 f 74 goat snp32083-scaffold362-83692 4 25776201 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381768 Affx-122974306 AX-123252126 4 91939722 AGTGCCCATGTGAGTGCAGAAAATGCATGAGATGC[G/T]ATGATCCTTGCCCTCATGAAGGGAGGCAAGAGGAA K 2 1 2 1 201000 f 74 goat snp32084-scaffold362-134195 4 25724749 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437948 Affx-122931623 AX-123308286 4 91973376 ATACTGTATCCCTCTTGCTCAAGTCTACCTCACCT[A/C]GTAGACTTCTCTCTGTCCCTCAGATATGCTGCATA M 2 1 2 1 201000 r 74 goat snp32085-scaffold362-167849 4 25690426 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777814 Affx-122966835 AX-385264931 4 92023324 TTAGTATTAGGGATGAACAAATTAAGGACAGTTTC[A/G]TTTCTAAAAATCTCACAAGGGTGGAAGACAGAAAG R 2 1 2 1 101000 f 74 goat snp32086-scaffold362-217797 4 25640617 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382426 Affx-122974243 AX-123252784 4 92091834 ACCTTTCATTACCTTTCATTGCTTTATTCTTCATT[A/G]TTTTCTTCATTTTCTACTACCATTTAGGTATATAG R 2 1 2 1 101000 r 74 goat snp32087-scaffold362-286307 4 25569852 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442720 Affx-122927859 AX-123313057 4 92135966 ATGCAGGCGGTGCCTTTTTCCATCAGCTGCTTGTA[C/T]GCTGGCCCAAGGGGCAGATGCTGTACATCAATCTG Y 2 1 2 1 101000 f 74 goat snp32088-scaffold362-330439 4 25525719 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441262 Affx-122929486 AX-123311599 4 92171517 GTGGATAATAAAAAAAAGATGGGAGGCTCTTAAGG[C/T]AATTGAAAACAAAAACTTCTAAACGTGTCCTTGCC Y 2 1 2 1 101000 f 74 goat snp32089-scaffold362-365990 4 25490303 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797139 Affx-122920804 AX-385284079 4 92210700 GAAACTAACATATAAGCCACGAAGCCTAAGGATTC[A/G]TTTCCAATTTAAAGTATGTCGCCAGACAAGCTGGA R 2 1 2 1 101000 r 74 goat snp32090-scaffold362-405173 4 25451180 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798539 Affx-122944890 AX-385285472 4 92250838 TCTGACAAGGATTGCATCTGAGGATTAAAATGTCC[A/G]TGGACATACCTCTTAACTCCTCATCTTTTAATTGC R 2 1 2 1 101000 f 74 goat snp32091-scaffold362-445311 4 25410678 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438631 Affx-122930915 AX-123308968 4 92298257 ACTAGACCCGCCACTGCGCCACTCGGTGTGCCCCT[G/T]TCAGAGACTCCTTCTCCTTGAGCACATACTCAGCC K 2 1 2 1 101000 r 74 goat snp32092-scaffold362-492730 4 25363317 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799558 Affx-122922782 AX-385286488 4 92348154 GATTTTGACCTGATACCTGTGTGACATTTTTCAAA[C/T]AGTGTTTCAAAAAGTACTTTGGTGCAGATCCCATG Y 2 1 2 1 101000 f 74 goat snp32093-scaffold362-542627 4 25313057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445811 Affx-122926033 AX-123316148 4 92403827 CACAGGGCATGTTTACATATTGTGTTTGTGTGTGC[A/G]TGTATGTGTCTAAAGAGTTAAGTTAACAAGCTGAA R 2 1 2 1 201000 r 74 goat snp32094-scaffold362-598300 4 25257225 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789986 Affx-122946179 AX-385276992 4 92441052 CCCTTTGTAAAATAGCTGACACTTTACCCAACTGG[A/C]TAGTGACTAGTTTTTAGTAAGTCAGATGATTTACT M 2 1 2 1 101000 f 74 goat snp32095-scaffold362-635525 4 25220228 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799310 Affx-122963639 AX-385286240 4 92471064 ATGAGTGGTCCAAAAAGAAGTACCAAAGGGAATAC[C/T]GAAGGTAGGCAAAAGAATTTCCAGTCAAAGTGACC Y 2 1 2 1 101000 r 74 goat snp32096-scaffold362-665537 4 25190221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379794 Affx-122975829 AX-123250152 4 92502525 GACTGGATATGTGAAGCATGGCTCAGAAGTTTGCC[A/G]CCTATATTTCAAAAGTTCTTCACTCTTTCTCAAAT R 2 1 2 1 101000 f 74 goat snp32097-scaffold362-696998 4 25158660 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442372 Affx-122928019 AX-123312709 4 92538037 TTCAGTGTGGGAACTGTCTGCTGACTTAACTTCAA[A/G]CTTCCTGATTCTTTCCTTGATACATTACCCATCTA R 2 1 2 1 101000 r 74 goat snp32098-scaffold362-732510 4 25123081 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430384 Affx-122937773 AX-123300725 4 92585577 CTTGTCAGAGGGAGGTGGGGAGGTGGGGGAAGAAC[A/G]TACCCCAATAGTGGTTTTCATGAGAGCATGTAGAG R 2 1 2 1 101000 r 74 goat snp32099-scaffold362-780050 4 25074834 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426821 Affx-122940518 AX-123297166 4 92616687 CCTGCAGTCTAATTCTGTAATTGTTTTGCACCTTC[A/G]CTTTGTCACTCCACTAGTTTAGAGATTTTATGTTT R 2 1 2 1 201000 r 74 goat snp32100-scaffold362-811160 4 25043924 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798647 Affx-122944742 AX-385285579 4 92645824 ACATCCTCACCTCTAAATGGTTACTAAATTATTAC[A/G]TTTCTCTCTGAAATTATGAGAGAAAAATTAAACAA R 2 1 2 1 201000 r 74 goat snp32101-scaffold362-840297 4 25014666 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778643 Affx-122937604 AX-385265754 4 92689890 CCATAGATATGTGTTGATTAAGTTATCAGATTACA[A/G]AGGATAAAAACATACTTAAGAGTATCTCACTGGAA R 2 1 2 1 101000 r 74 goat snp32102-scaffold362-884363 4 24970233 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431582 Affx-122936181 AX-123301923 4 92723938 CTCATAAGAAGACACCAGGAAACTAGACTCCAGAA[C/T]CGAGACTGAAGGTCATGAATGACCTCTGTTAGTCC Y 2 1 2 1 201000 r 74 goat snp32103-scaffold362-918411 4 24936308 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433248 Affx-122935241 AX-123303589 4 92757567 GATGTTGGGACAGCACCCTGGGGAAGGGGCAGAGC[A/G]CCTTCAGATTCTCCTTAAGGTCTGTTTCAAGGACC R 2 1 2 1 101000 r 74 goat snp32104-scaffold362-952040 4 24904707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452885 Affx-122920223 AX-123323218 4 92760972 TGGGGTGTGGGTGTTCACACCTTCTGTCCTGGTGA[C/T]ATGGAGCCTCCTCGGCTACTTTTCTGTTCAGTTCA Y 2 1 2 1 101000 r 74 goat snp59342-scaffold976-368940 4 24901461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427909 Affx-122939677 AX-123298252 4 92792182 TGGAGAAAATGGCATCTGCTTTACAATGACTCATT[C/T]AACGGTTAGTTTCCAGGGACAGAGAATAGAGTAAA Y 2 1 2 1 201000 f 74 goat snp59341-scaffold976-337730 4 24875281 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406443 Affx-122955193 AX-123276795 4 92840568 AAGGGACCCCAGGCTTTCAGAGGGGGCGCAGTGTA[C/T]GTGGAAGGCTGCAAGCAGGGGCCTAACAAACCAAA Y 2 1 2 1 101000 r 74 goat snp59340-scaffold976-289344 4 24826975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802141 Affx-122934556 AX-385289045 4 92894052 ACACGACTGAGAAACTCACTTTCACCTTTACTTAC[A/G]TTTACACTGTATGTACATACGCACTGGAATCCAAG R 2 1 2 1 101000 f 74 goat snp59339-scaffold976-235860 4 24772576 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384310 Affx-122972278 AX-123254668 4 92922974 CCCCATCCAGAACTTCCCGTCCCACCTCCCTCCCC[A/G]TCCCATCCCCCTGATCATCTTTTTTAAAGCCCCTG R 2 1 2 1 103000 r 74 goat snp59338-scaffold976-206938 4 24743453 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421207 Affx-122944143 AX-123291554 4 92954103 GAGAAAATGAATGGTATAAATTCAAGCTACACATT[C/T]CCCAGCCAGATGAGTAGTTGCACTCTCTACCTGCT Y 2 1 2 1 201000 f 74 goat snp59337-scaffold976-175809 4 24711981 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412565 Affx-122951319 AX-123282914 4 92988105 CTCCACTTGAAATGGGACCCACTTTTTGGGTTCTC[G/T]ATGTTCTCGTGCTCATTAAGATAAAGGGGCTGGTA K 2 1 2 1 101000 f 74 goat snp59336-scaffold976-141807 4 24677992 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399907 Affx-122960200 AX-123270262 4 93016747 GTTTGCACAGCCATCGAGTCCATGGGCAGGCCCCC[A/G]TGGGCTTTGCACGTCATTTACCTCCTCCTCACGTC R 2 1 2 1 101000 r 74 goat snp59335-scaffold976-113165 4 24649707 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382777 Affx-122973588 AX-123253135 4 93054676 AGATGGGAGCCTGTCCTATTTTTTTCAAAATACCC[A/G]CAAGAAATGCCACCATCTGCTTAGGTAGTCAAATG R 2 1 2 1 201000 r 74 goat snp59334-scaffold976-75236 4 24611761 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444937 Affx-122926696 AX-123315274 4 93085133 TCCATCTGTTCCTACCTTGACAGCCAGCCACTGGG[C/T]GCTCTAATCGCAACTGTACAATAGCTCTGGGCACA Y 2 1 2 1 101000 r 74 goat snp59333-scaffold976-44779 4 24581336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408005 Affx-122954314 AX-123278356 4 93154433 TCCTATTGATGCTTTCAGAGCCTCAACAAGGCCTC[A/G]TTCCCACCCTACAAACAGGGAAGCTTCGTATGCCA R 2 1 2 1 101000 f 74 goat snp4529-scaffold1145-1614968 4 24390402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408601 Affx-122953646 AX-123278952 4 93188675 TCAGACGCAACTGGACAACTAAACAACAGCAACAA[C/T]GGGACACAGAGCATGTAGGCACAGAGAAGTCTCTG Y 2 1 2 1 201000 r 74 goat snp4528-scaffold1145-1580726 4 24355909 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448534 Affx-122923439 AX-123318870 4 93224543 CACGGCTGACACTGAACCCACACCCAAGAACTCAC[A/G]GAGAAGAACACACACATCACGGACTTCGTGGATGT R 2 1 2 1 101000 r 74 goat snp4527-scaffold1145-1544858 4 24320423 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448259 Affx-122924194 AX-123318595 4 93275878 TTGACTTGAGTGAAGAAGCTGATAAAGACCAAGGT[A/C]GTGAACTGAACTCCTGTGTGGGCTCCTTTGCTCTG M 2 1 2 1 101000 f 74 goat snp4526-scaffold1145-1493523 4 24269256 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427870 Affx-122939708 AX-123298213 4 93335425 AGCCTGGCTGGGCTGGAGGCCAAGGCCATCACCGC[G/T]CGGTCAGACTTGGGTGGTAATCCCAATTGGTTTTG K 2 1 2 1 101000 r 74 goat snp4525-scaffold1145-1433976 4 24210458 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439398 Affx-122930253 AX-123309735 4 93364968 CTGCTGAACGAGTGCACTTGTTGGTCTACCAGGCC[G/T]AGGACCCCAGCACAATTCCAGCCAGACAAGAGGAG K 2 1 2 1 201000 r 74 goat snp4524-scaffold1145-1404433 4 24180492 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278281 Affx-1111836263 AX-519551768 4 93441900 CAATTTCAGTTGAGATTGTCATTTTCCTGACATTT[A/C]GTGATTTTTTTTATACAAAGCAACAATATTTTCAA M 2 1 2 1 101000 r 74 goat Random2.2K-469 4 93441900 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416435 Affx-122947830 AX-123286784 4 93451003 GGGCTGGATGGTGTCCCTTACGTGCTCAGCTAGAT[A/G]CCGGACACTTGTGCTCATTGACAGATGTGTGACTT R 2 1 2 1 201000 f 74 goat snp4522-scaffold1145-1318398 4 24094709 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414052 Affx-122949775 AX-123284401 4 93480743 AACATGTCTCCAAACTGGGTGTAGTTTCTCTATAG[C/T]CTCCTTTACCGTATAGAACCAAAGGTCTTCACGAA Y 2 1 2 1 101000 r 74 goat snp4521-scaffold1145-1288658 4 24064961 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411273 Affx-122952312 AX-123281623 4 93510691 AGAAACTCACTAGCGGTAAAGGATGGAACCCCAAA[C/T]TGGAATCCCCTTTCCCTACAGAGTGGTTCTCAGAC Y 2 1 2 1 102000 f 74 goat snp4520-scaffold1145-1258710 4 24035288 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397004 Affx-122963139 AX-123267359 4 93543974 TTAATGCCAGACAATTTCCATAACGAGAAAAGTGC[A/G]TCGCAGTTGTTGGCTCTTTGTTGTCATAGTTGTCA R 2 1 2 1 101000 r 74 goat snp4519-scaffold1145-1225427 4 24001812 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395458 Affx-122963916 AX-123265813 4 93576541 GTGGACACAGCATAGTTACCATGACAGTGACCGAC[C/T]GTAGGAAGTGGACTTACTTCACACCCATGTATGCA Y 2 1 2 1 101000 r 74 goat snp4518-scaffold1145-1192860 4 23969428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454162 Affx-122919321 AX-123324495 4 93610090 ACAGCTGAGCTCTGCTTTTACACCTGTCGGTGGAA[C/T]GTGAAGTGCTGCCTTCTTGGGGGCTCTGCTTAGTG Y 2 1 2 1 101000 f 74 goat snp4517-scaffold1145-1159311 4 23936358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431129 Affx-122936587 AX-123301470 4 93655985 CCCCATTCACCTGAAAACCCCTAAGGAAGGGACTA[C/T]GTCTGAAACAGCTTTGATCCACAGTATAGTGACAT Y 2 1 2 1 101000 r 74 goat snp4516-scaffold1145-1113416 4 23890572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417380 Affx-122947701 AX-123287728 4 93689162 CGTGGCATATTAGGGAGCACGGTGCGTGGGGTGGG[C/T]GTGCTGGGTGTGTGGTGGTGATCAGTGTCAGGTAG Y 2 1 2 1 303000 f 74 goat snp4515-scaffold1145-1080239 4 23857694 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393984 Affx-122965037 AX-123264339 4 93723458 CTCGGGGAAGATGTGAAATGGTGGATGGTGTTGCC[A/G]TCAGGGGAGATGGAAGGAGCAGGAGTCGGCAGTTG R 2 1 2 1 101000 f 74 goat snp4514-scaffold1145-1045943 4 23823195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415145 Affx-122949413 AX-123285494 4 93782089 CCTGGTTAAAGCGTATTGAAGAGTCACTGAGAAGA[C/T]GGGGCTAATGACAATGTGATGTCCTCCTGTCACCT Y 2 1 2 1 101000 f 74 goat snp4512-scaffold1145-987312 4 23764734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430757 Affx-122937495 AX-123301098 4 93827917 AGTCCATTTTCCCTAGCTGTATATGATGGGGCTGT[A/C]GAACTTTCCTCAAAGGGTTCGTGTGAGGTTGAACC M 2 1 2 1 101000 f 74 goat snp4511-scaffold1145-941484 4 23718980 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802143 Affx-122923453 AX-385289047 4 93876626 ACCCCACTTTTAATATTCATTACTGTGGGCTTCAG[A/C]TTTAACCAAGAGGTCTGTTTTTCTCCTTAATCCTA M 2 1 2 1 101000 f 74 goat snp4510-scaffold1145-892775 4 23670187 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272149 Affx-1111833445 AX-519545906 4 93895476 CCATAGAAAGTATTTAGCAAAATTTGAATAAGTGA[A/G]TGGACATGCTCAATGACATCAAATGGGAGAAGACA R 2 1 2 1 101000 r 74 goat 4_93895476_AF-PAKI 4 93895476 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448567 Affx-122923415 AX-123318903 4 93911414 CACCACTTACAGTTAATCAATAGAGCTTGCTGTTT[A/G]CCAATCCTATTTCAGTGTTTTGCCCTTTTCCAAAC R 2 1 2 1 101000 f 74 goat snp4509-scaffold1145-857987 4 23635102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423049 Affx-122942963 AX-123293395 4 93954448 ATTTACATTTTGTCAAACTGACTTTTAAAATGCTT[A/G]TGCCAGTTTATATCCTGACGAACAGTGTCTTGAAG R 2 1 2 1 101000 r 74 goat snp4508-scaffold1145-814953 4 23592079 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435188 Affx-122933645 AX-123305528 4 93985249 CAACCTCTGTGCTATCCACAGTCTTATCTACCCCC[A/G]TGATCAGCCATCAGCAATGAACCAGCGACCCTTGC R 2 1 2 1 201000 r 74 goat snp4507-scaffold1145-784152 4 23561298 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424691 Affx-122941701 AX-123295037 4 94031625 TAATGTAGTTGGGTTGGAGCAGTGTATCTTCAGCA[C/T]GTATTTTCCTTGTACCTTATAAATCCTCTCTGTTT Y 2 1 2 1 101000 f 74 goat snp4506-scaffold1145-737776 4 23515299 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448843 Affx-122923293 AX-123319179 4 94067642 GCACCTTCAAAAACAGAAGAGTGAGTCCCCATGAC[A/G]CTGTTTCAACAATTTTTGTTTCATCTGTATCCTGT R 2 1 2 1 101000 f 74 goat snp4505-scaffold1145-701759 4 23478613 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777981 Affx-122948444 AX-385265097 4 94129904 GGTGCCAGCTGTGCCTCTCATTAGCTGTGTGCAGC[A/G]TACTTGTAATACTTAACGTATTCAGACACTGCTTT R 2 1 2 1 202000 f 74 goat snp4504-scaffold1145-639497 4 23417597 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450975 Affx-122921738 AX-123321309 4 94161303 GCTTTGCCTATTTATTTTTGCCCGTGTGGCTAAAT[A/C]GGATGTCAAGTTAATAGAAAAATTATTTGGTGAAA M 2 1 2 1 101000 f 74 goat snp4503-scaffold1145-608098 4 23385860 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393019 Affx-122965646 AX-123263376 4 94193847 TCCCAAGGTAATTCTTTCATCTAACAAAGGCTGTA[C/T]AATGATTTCCAACAAAGAAGATGTTCAGAATAATA Y 2 1 2 1 101000 f 74 goat snp4502-scaffold1145-575554 4 23353535 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398338 Affx-122962124 AX-123268693 4 94245769 GCAAGAAGAAATTTGCATTATAGTTTTCCATTTTA[C/T]GCCACACACATAAACAGATCTCCTTTAGAGTCAAG Y 2 1 2 1 202000 f 74 goat snp4501-scaffold1145-523632 4 23300985 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451522 Affx-122921103 AX-123321855 4 94309998 CCAGAAATAACTTACCGGGACGCTACAGCTCTGCA[C/T]AGCAAAACCCACAGTAAAATCAAACCTCTTCAGTG Y 2 1 2 1 201000 f 74 goat snp4500-scaffold1145-459403 4 23237013 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784332 Affx-122977555 AX-385271383 4 94366292 GAGGAAAAGCTGTCTCATTAAAAGTAATAGATGTC[A/G]CAGAATTAGCTTCCACTGAAATTTGCCATCACTGG R 2 1 2 1 101000 r 74 goat snp4499-scaffold1145-403109 4 23180925 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444576 Affx-122926967 AX-123314913 4 94412598 GAAGAGAAACTATTTCTGCAAGAATAATCTCACAA[A/G]TTCTCCAGCCTAAAATACTTGGGGGCGGGAGGGGA R 2 1 2 1 201000 f 74 goat snp4498-scaffold1145-356803 4 23134506 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771815 Affx-122928645 AX-385258972 4 94444407 TTCATTTATTATCTATCAAATCCATTCTTAGCCCC[A/G]CTAATCATTAACTGATATATGACTTTCAAATCTCT R 2 1 2 1 101000 f 74 goat snp4497-scaffold1145-324994 4 23102677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792052 Affx-122967079 AX-385279040 4 94476223 CAATGAGTGTTTACTAAGTGAAGAAATTTCTCCTA[C/T]GTTCCTTTCTTTCTAACTATCCTTATTCTGTCCCT Y 2 1 2 1 201000 f 74 goat snp4496-scaffold1145-293178 4 23070814 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442927 Affx-122927622 AX-123313264 4 94515200 CACACCATGCCAGTCGTGCCTGGTAGGCTTTGTTT[C/T]CCAAAGCTCTGTTAATTCAGGGGAAGGACTGGCTT Y 2 1 2 1 102000 f 74 goat snp4495-scaffold1145-254201 4 23032011 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801712 Affx-122968330 AX-385288620 4 94559201 AGAGCAACAGAATGACCTTCCATGACTAATCGATG[C/T]AAACTAATAACTTGCGCTGCTTACATTTACAATGT Y 2 1 2 1 101000 f 74 goat snp4494-scaffold1145-210200 4 22987619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406928 Affx-122955082 AX-123277279 4 94588448 AGGGTAAACTGTGCTCCTTCCTTTGATAGCTCAAA[C/T]ATACTGTGTTCAAATATTTAATAAAAACGCTTGAA Y 2 1 2 1 101000 f 74 goat snp4493-scaffold1145-180953 4 22958335 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404684 Affx-122957278 AX-123275036 4 94620783 AGATGATTGGGCAAGTGGGAAACCATAGCACCCTC[A/G]TTTCACTGAAGAGGAAAACAGGTCTACACAGATAA R 2 1 2 1 201000 r 74 goat snp4492-scaffold1145-148618 4 22926006 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382232 Affx-122973965 AX-123252590 4 94677059 GGGAGCATTTAGGACATAAGCAGAGAATCTTTTCT[A/G]GTCAGAATAATGAAATCAACAAAGAAACCCCCACC R 2 1 2 1 101000 f 74 goat snp4491-scaffold1145-92342 4 22870641 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405599 Affx-122955927 AX-123275951 4 94718254 TACTACAGATATTCAGAAAATTTTAAGAATATAAA[C/T]ATTTTTCAATGGTATTACTAAGGATATAAAAGCTC Y 2 1 2 1 103000 r 74 goat snp4490-scaffold1145-51147 4 22829444 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431348 Affx-122937051 AX-123301689 4 94769005 TCTCACCAGAGCTCTAGTTCTACCTGACCCCTCAT[A/C]TTACTTTTCAGTGACTTTGGGTGTATATGTTTCAT M 2 1 2 1 201000 r 74 goat snp4489-scaffold1145-396 4 22778478 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384773 Affx-122972016 AX-123255131 4 94779475 GCGTGATGTTAATAGTCAAAGCCATGGCAGTGGTC[A/G]AAATGGGCTAGGGAGCTTGTTAAGTAAGAAGGTAA R 2 1 2 1 201000 r 74 goat snp14048-scaffold1559-9975 4 22768046 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401363 Affx-122959242 AX-123271716 4 94813655 AGATATTCCCGTGCAATAAAAGCCTATGCATTCGC[A/G]TACCTGAAGCTTGTGGGAAAAATACATGCATCCCC R 2 1 2 1 101000 f 74 goat snp14049-scaffold1559-44155 4 22734084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789569 Affx-122961166 AX-385276578 4 94848340 ATAGTGTTAAGTGCTTTGAGTGTGATTGGAAATGT[A/G]CAAAGCACAGTTGCCGCTCTGAAGGAGCTCAATTC R 2 1 2 1 102000 r 74 goat snp14050-scaffold1559-78840 4 22699485 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415927 Affx-122948449 AX-123286276 4 94884129 CAGAATGTCCTTCTAGCTGTAAAGTCCCATGATGC[G/T]CTGAAGAAAAAGGGCCATAAAGTACCTGCCACATT K 2 1 2 1 101000 f 74 goat snp14051-scaffold1559-114629 4 22663389 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386198 Affx-122971360 AX-123256556 4 94915938 CGAGAGGTAAATTCTCCCCTAAGTACATCTTTCTC[A/G]TCTTCACTAAACATAGTTATTCTGTTTTTCTGTAT R 2 1 2 1 201000 r 74 goat snp14052-scaffold1559-146438 4 22631304 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382526 Affx-122973797 AX-123252884 4 94958364 ATGTGGCCTAATCTGTTGACGCTCTTGAATTTCAT[A/C]TGGCTGGCCTGGCACAGTGAAATATTTTCCCCTGT M 2 1 2 1 201000 f 74 goat snp14053-scaffold1559-188864 4 22588864 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443701 Affx-122927160 AX-123314038 4 94990429 CAGAAGATCCATTCAGGGATTCTTCTTGTGCTGAG[C/T]CTCTGGTACTTTGTGGTTCTGTGAAACAAAGAAAT Y 2 1 2 1 101000 f 74 goat snp14054-scaffold1559-220929 4 22556379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769470 Affx-122942491 AX-385256640 4 95021003 AGCTCCCAGACTTGCCAATTCTTAGAACAGTGAGT[A/G]CTAAAGAAATTCTAGACACCATAGACAAGAAGTTG R 2 1 2 1 101000 f 74 goat snp14055-scaffold1559-251503 4 22525960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418707 Affx-122946289 AX-123289055 4 95064831 TAACCAGCTGATGTGAGATCATTTTCTTATAGGCT[A/G]TTGAGAAACAGAGCATCTCCTTTGCAATTCTTTCT R 2 1 2 1 101000 f 74 goat snp14056-scaffold1559-295331 4 22486992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416978 Affx-122948004 AX-123287326 4 95093499 TTAGCATCCTGGCTTTAGACACTTCGCCGTGAATA[C/T]ATTAGGCACAACGAAGAAGTAGGTTATCCCCATTC Y 2 1 2 1 101000 f 74 goat snp14057-scaffold1559-323999 4 22458294 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387668 Affx-122969834 AX-123258026 4 95150841 AAATCAAATTCCTCCAAGATTATTTTTATTCAAAA[G/T]AATTTCATAAAAGCCACAAATCTCTTTCTGAATGA K 2 1 2 1 303000 f 74 goat snp14058-scaffold1559-381341 4 22400573 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436743 Affx-122932294 AX-123307081 4 95181615 TTGTATCCCCCAGGGTACCCTGAGTGACACTGTGA[C/T]GCAGCAGTCTGGAATTCTGTCTCCCAGAAAAATAG Y 2 1 2 1 103000 r 74 goat snp14059-scaffold1559-412115 4 22370617 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387397 Affx-122970417 AX-123257755 4 95210719 TTTTAATTAAGCCTCGTGGTATTGGGGTATGGCCT[A/C]ATGTTGCCATGTGGTGTGACACGCGGATCACAACG M 2 1 2 1 101000 r 74 goat snp14060-scaffold1559-441219 4 22340998 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779330 Affx-122930056 AX-385266434 4 95253139 ATATGCAATCAGTCTACTTTGCACATAGCAACTCT[A/G]TTTAGCAAGTCTAGAGTGAATAGCGATAGGATTTA R 2 1 2 1 101000 f 74 goat snp14061-scaffold1559-483639 4 22298665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438015 Affx-122931571 AX-123308353 4 95291483 GGAATGAAACCCATCACTGTGACGGTGTTGAAGAT[A/G]CTGGGAAATTGATACAGATGTGTGGCCTTCATGAA R 2 1 2 1 101000 f 74 goat snp14062-scaffold1559-521983 4 22259565 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422788 Affx-122943214 AX-123293134 4 95329214 CAGCAACAGACCCACAGAGAAGAACGTCAGCTTTC[C/T]TCCTTCACTCTTCTGAGGGTGTAGCAGGGCAGGGG Y 2 1 2 1 101000 f 74 goat snp14063-scaffold1559-559714 4 22221598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420192 Affx-122945556 AX-123290540 4 95369849 GCTTGGTGCCTACTCATGGGCAGACTAGAGGTGGA[C/T]GAGAGGGTCCACTAACCAAGTTTCCCACTGCCATT Y 2 1 2 1 101000 r 74 goat snp14064-scaffold1559-600349 4 22180866 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393457 Affx-122965847 AX-123263813 4 95431226 ACTTTTAGGGACTGCCGTACTCTTCTGCTCGAGGC[A/G]CTTCCGCACTCTGACTGGGGCTTCCGTCGTCATGT R 2 1 2 1 201000 f 74 goat snp14066-scaffold1559-661726 4 22119240 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794333 Affx-122972062 AX-385281297 4 95473833 AGCCTGGCATAAAATCAAGGGCAGCAATCCTAATC[A/G]TTTTTCATGCCAGGACCCCTTGGCATCCTGCAGAA R 2 1 2 1 101000 f 74 goat snp14067-scaffold1559-704333 4 22076193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789205 Affx-122969237 AX-385276217 4 95516074 ATTTGCACTATAAATCCCTTGACTGCAGCTTGTCT[A/G]TACATACATGCAACTTGTTTCATATTTATATGCAT R 2 1 2 1 102000 f 74 goat snp14068-scaffold1559-746574 4 22034983 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411233 Affx-122952343 AX-123281583 4 95551565 TCCAGCTGCCATGAGCTGCACAACGGGGCAAAGAA[C/T]GGTTAGTGCTCAGTCATGGTGCTGACCCCTGAAAG Y 2 1 2 1 101000 f 74 goat snp14069-scaffold1559-782065 4 22000016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375841 Affx-122978531 AX-123246200 4 95583571 TCCTTATTCCCGTCGAATCCTTAGTTATACAGCCC[A/G]CTCTACAACCTCCATCCAGCTCCCCTGAATGTCAT R 2 1 2 1 101000 f 74 goat snp14070-scaffold1559-814071 4 21967802 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417607 Affx-122946874 AX-123287955 4 95627441 GGAAAGACGGGCAGCGGACCACAGAGGGCTTCCTA[C/T]GCCATATGATGGACTTTGGGTTTTGCCCTGAGATG Y 2 1 2 1 101000 r 74 goat snp14071-scaffold1559-857941 4 21923692 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424985 Affx-122941908 AX-123295331 4 95673433 GGAGTCTGGCACTCGCACGCCCACCCCTCAAGCTC[A/C]GACCCTCACTTATCCCCCAGGTCCCGCTCAGCTGT M 2 1 2 1 101000 r 74 goat snp14072-scaffold1559-903933 4 21877057 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399619 Affx-122961084 AX-123269974 4 95706689 TGTCTTCTCACTCTGCCCACTGGATTGCTTTGAAA[C/T]GAATGCTGAATGTCAAATAGGATAGATTTTGAGAA Y 2 1 2 1 201000 r 74 goat snp14073-scaffold1559-937189 4 21843796 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405527 Affx-122955986 AX-123275879 4 95738771 AATGTATATAGAATTCACCACCAGACACTATTGGA[C/T]AGTCTGAAAGAAGTAGGGAATGAAAAATTTTGTGC Y 2 1 2 1 201000 r 74 goat snp14074-scaffold1559-969271 4 21811618 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432326 Affx-122936294 AX-123302667 4 95797519 AGCAGTTGCCTTATTTGGGAAAGTCTACTTGGTTT[A/G]TTCTGATGGGTTCTCCTTAGGTTTGATTTCTTTAC R 2 1 2 1 201000 r 74 goat snp25705-scaffold2645-155523 4 21754720 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784492 Affx-122969626 AX-385271541 4 95827371 TCTTAAACACTGATAGCGGAATAAAATGTAAATGC[A/G]TTTGATTAAAAATGGTCACTTTTGGCTTCTTATCC R 2 1 2 1 101000 f 74 goat snp25704-scaffold2645-125671 4 21725087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384040 Affx-122972885 AX-123254398 4 95873892 GTGTTAGTCAGTGTCTTTCTTTAAAAAATTATAAC[A/G]TTAAATTTTGTCAAATTTCTTATGAAAATCACCAC R 2 1 2 1 103000 f 74 goat snp25703-scaffold2645-79150 4 21678567 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765795 Affx-122941386 AX-385253250 4 95915335 AAGGCCTTTGGAGACGCCTTGCCACTCTTCCATCA[C/T]AATTAGAAAACACTGACATTCAGAGCTGATTTAAA Y 2 1 2 1 101000 f 74 goat snp25702-scaffold2645-37707 4 21637181 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399560 Affx-122961127 AX-123269915 4 95963819 AATTTCAGTGGGCCCAAGTTTCTTCATATGTGGGG[C/T]GGAGCAGGTGGGGGGAAAGAAAGGTATAGTATCTG Y 2 1 2 1 103000 f 74 goat snp46564-scaffold646-10678 4 21588903 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792379 Affx-122932924 AX-385279360 4 95999868 CCTAGTCATAAACCATCGAGAGCAGTGTTCCATGA[C/T]GTTTCAGGTCAGATCTCAAAATTGTAACCTCTAAC Y 2 1 2 1 101000 f 74 goat snp46565-scaffold646-46727 4 21552791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772208 Affx-122956019 AX-385259363 4 96092685 AACAGTTTGTGTCAGCAAGATAAGTTTTTAAAAGC[C/T]CCAAAGGGACTAAGAGATCATCAGGGATGCTAATG Y 2 1 2 1 101000 r 74 goat snp46567-scaffold646-139544 4 21459493 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776198 Affx-122977899 AX-385263326 4 96126083 TGATTGGAAGAGGACACATAAAGAGCAAAAATATC[C/T]TATTTTATCGTGGGACATAAACATGTCAATTTTTA Y 2 1 2 1 101000 f 74 goat snp46568-scaffold646-172942 4 21425582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376475 Affx-122978039 AX-123246834 4 96162823 TTCATCATCGAAGATGAGAAGCTGAGAAAATTCAA[C/T]AGGGGAGATGATGAGACAAGCACTCTCAAACTTCT Y 2 1 2 1 202000 f 74 goat snp46569-scaffold646-209682 4 21388745 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379775 Affx-122975843 AX-123250133 4 96200158 CAATCTTGACATCCACGAGGTGCTCCTTTCAGAGC[A/G]CAGAGACTTCCCAGGGCTTCACCACAACGGCTGCG R 2 1 2 1 101000 f 74 goat snp46570-scaffold646-247017 4 21352048 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788567 Affx-122965333 AX-385275584 4 96232359 GCTGTCGATGCTGGCGCAGAACGTTTCTGATTTTC[C/T]CGACATATATGCACAACCAGAGAACATTTATTTTT Y 2 1 2 1 101000 r 74 goat snp46571-scaffold646-279218 4 21319778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411940 Affx-122951152 AX-123282290 4 96268812 GAAAAACCTGGTATGGACAGTGTTTCTGATTTGAA[C/T]GTTCCCTATCCTATCACTGTAGCCCAGGCCCAGGC Y 2 1 2 1 101000 r 74 goat snp46572-scaffold646-315671 4 21282784 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429024 Affx-122938324 AX-123299366 4 96316278 ATTTCTGTTACTACAGCCCAAGTAGACTAAGACCA[G/T]CCGGCATGTGTGGAATTCCCTTGTGATCTGATTTA K 2 1 2 1 101000 f 74 goat snp46573-scaffold646-363137 4 21235000 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797940 Affx-122951554 AX-385284876 4 96354536 CAAAAATACCCTCGAAAGATGACTGAAAATTATCC[A/G]TGCTCTGAAATATGATTTTCCATGCTCTGAAATAT R 2 1 2 1 101000 r 74 goat snp46574-scaffold646-401395 4 21198187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789490 Affx-122973305 AX-385276499 4 96396661 CTAAAGGCCTTTACTACCACTATCTTGAATAATAA[C/T]GACAATGATTAGAAGTAGTAGTAGCTTATATTAAG Y 2 1 2 1 201000 r 74 goat snp46575-scaffold646-443520 4 21156079 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272290 Affx-1111833446 AX-519546029 4 96422352 CACTGTCACCTGCAGAAAAACTTAGGGTGTGCCTA[A/C]ATGTGGAGAAGCACGAAAGGTGGAGGATTAAGGAA M 2 1 2 1 201000 f 74 goat 4_96422352_AF-PAKI 4 96422352 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389109 Affx-122968568 AX-123259467 4 96433592 CATAAGACAGTAAAACTGCAGAACACTAAAGGAAA[C/T]AAGAATCTCAAAAGCAAACACTGAAAAAGAACCCT Y 2 1 2 1 101000 f 74 goat snp46576-scaffold646-480451 4 21119083 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785479 Affx-122940457 AX-385272524 4 96474296 ACAGATCTAAGAAATAATATAGATCTATGAACATA[A/G]CAGATCTATGAACTAGATCTCCATCATTTACAAGG R 2 1 2 1 101000 r 74 goat snp46577-scaffold646-521155 4 21077666 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403426 Affx-122957746 AX-123273779 4 96502919 AAATGCTACTTCCCTCTGAAATACCAGTTGTCTGT[A/C]TGTTAGATATTTTCTTCTCAGCATTGTTTATAATA M 2 1 2 1 101000 f 74 goat snp46578-scaffold646-549778 4 21048442 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427675 Affx-122939310 AX-123298018 4 96555332 GCTCGAATGATTCACATGAGTATGCAGATGGGGAA[C/T]GATCCCCCCATTTCGCTTAGAAGGGATCTGGAACA Y 2 1 2 1 101000 f 74 goat snp46579-scaffold646-602191 4 20995828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388001 Affx-122969575 AX-123258359 4 96592674 CTTGTTTTAGTTTCTGTTTCCTCCTGCTTAAGAAT[A/G]CCACGAATGTCGCAATAGGAGAAGCACTAAAATCT R 2 1 2 1 101000 f 74 goat snp46580-scaffold646-639533 4 20958056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382138 Affx-122974051 AX-123252496 4 96666888 GCTGGCGTGAGAGTAGACCGGATGAAAAAGACATC[A/G]TAAATCCTAGAAGGGCTGAAGCTGGGTGGCGAGAG R 2 1 2 1 101000 f 74 goat snp46582-scaffold646-713747 4 20883952 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392586 Affx-122966063 AX-123262943 4 96730862 CATTTATTTCATTTTTGTTCCTGAAAGGAACTACC[A/G]CTGGATATACATTCTAAGTTGACATTCTAAGACTC R 2 1 2 1 101000 r 74 goat snp46583-scaffold646-777721 4 20820156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402855 Affx-122958245 AX-123273208 4 96761639 CACTTGGAACTGAAAGTGAGTCTCTCAACCTTCCC[A/G]TCCCTCAGTGACCAGTCTCTAGAGGGCAAGGCAAC R 2 1 2 1 101000 f 74 goat snp46584-scaffold646-808498 4 20789353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405782 Affx-122955915 AX-123276134 4 96806678 CTGAAATGTCATTAGTGCTAAGGATGAGAAATCCC[A/G]CCTTAAATTAGGAACAAATTTGGTTCATTTGAGGA R 2 1 2 1 101000 f 74 goat snp46585-scaffold646-853537 4 20744163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778855 Affx-122946161 AX-385265963 4 96868758 TTGCCTGATTACCCACGTGTTTGCCTCCATTAGTC[A/G]TCCGGTTTAAACCTGGCTGACCAGTACTGCTCGTC R 2 1 2 1 101000 f 74 goat snp46586-scaffold646-915617 4 20681473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404820 Affx-122956646 AX-123275172 4 96920869 TTATCTGAATTATGTCCACAGTCTTAAAAGGAAAG[C/T]AAACTGAACTCCAGTTTAAGCAACATATTCTAAGG Y 2 1 2 1 101000 f 74 goat snp46587-scaffold646-967728 4 20628470 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383407 Affx-122973492 AX-123253765 4 96950142 CTTAAGCCACACACAGTTTTTCAAACTCAAATCCA[C/T]TGACTTGTTAGTCAAGCCAAAAGCCCATAAGTCTT Y 2 1 2 1 201000 r 74 goat snp46588-scaffold646-997001 4 20599458 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398091 Affx-122961720 AX-123268446 4 97012821 CTACTGTGCTTGAGTTGTCCTTTGACACTTTGAGG[C/T]GAGTGACATCCTGCTGTGCCACACTCCACCCCTTG Y 2 1 2 1 101000 f 74 goat snp46589-scaffold646-1059680 4 20536451 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401074 Affx-122959638 AX-123271427 4 97045327 TCACTTTGTTCACAATTTGGCCTAGGCTTATTCCC[A/G]CCCATACTAAGTTAAATGAGCTCAGACATCTACCA R 2 1 2 1 101000 f 74 goat snp46590-scaffold646-1092186 4 20503743 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400744 Affx-122959898 AX-123271099 4 97103754 TGATATGATGCCATCATAATTATGTATTTGTTTGC[A/G]TCTCACCACTAGGCTGCATATCTTTGAAGACAAGA R 2 1 2 1 101000 r 74 goat snp46591-scaffold646-1150613 4 20445788 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396117 Affx-122963411 AX-123266472 4 97166331 TTCCTTTCAGTTTCCTGTCTCCCTCTCTCAGATGC[A/G]TCTCAGGACTTAAAGATTTACTGGGCATTATTCTT R 2 1 2 1 201000 r 74 goat snp46592-scaffold646-1213190 4 20382775 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392459 Affx-122966159 AX-123262816 4 97210352 CTTTTATGATTCCAGCAATTAACTTTCTGCTTGCC[A/G]ATATCTTCATTCATTCTTTATTTTCATAAACTAAC R 2 1 2 1 101000 f 74 goat snp46593-scaffold646-1257211 4 20337886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407031 Affx-122954944 AX-123277382 4 97242285 TCTGATGTCCAAAGTCACACCAACATGGTTGTACC[A/G]CTCATTTGGCTAAATGTCCAGCAATCTGGAAGGAG R 2 1 2 1 201000 r 74 goat snp46594-scaffold646-1289144 4 20306017 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424410 Affx-122941812 AX-123294756 4 97310049 ACCTTTGAAGCTCTGGCTGTGAGGCTGAGGGAGCT[A/G]AGAAGGCATGGTGGAATCCAGGCCAGATGGAGGAC R 2 1 2 1 202000 f 74 goat snp46595-scaffold646-1356908 4 20237739 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418664 Affx-122946319 AX-123289012 4 97362793 CTTCTGTAGATTTTCTGAAAACTGCTTTTGCTCCT[A/G]TGAAGGGGGAAGGAATAGAGGAAATGGAGGAAGAT R 2 1 2 1 103000 f 74 goat snp46596-scaffold646-1409652 4 20185111 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450234 Affx-122922266 AX-123320569 4 97392417 TAGCATTCAAAAGCAGCTTAATGAACAGAAATATC[A/G]ATTAGGGACTGGATTCTGTGGCCAGAAATGAGAAC R 2 1 2 1 201000 f 74 goat snp46597-scaffold646-1439276 4 20155332 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421975 Affx-122943800 AX-123292322 4 97422548 CCCATTTATAGTCACTAGTGGAAAAATAAAACACT[C/T]ACTCCTCTGGCATAAAAATTTAAGTTTACTAAAGT Y 2 1 2 1 101000 r 74 goat snp46598-scaffold646-1469407 4 20125245 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798164 Affx-122923935 AX-385285100 4 97478466 TGAGATTTGCATCAAGATATTTAATATTTACAACT[C/T]AAGAGGTTTGAGTAAATGTTATAAATGAAGCAAGG Y 2 1 2 1 201000 f 74 goat snp46599-scaffold646-1525325 4 20069618 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792494 Affx-122930078 AX-385279475 4 97551913 ATTAAGCACAGCACATATAGTGTAATGAGAAAATC[A/G]CAGTGCTAGTTATCAAAAAATCCAGGCTCCATCCA R 2 1 2 1 101000 r 74 goat snp46600-scaffold646-1598772 4 19993583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396205 Affx-122963361 AX-123266560 4 97599432 GAGAGGAGCTACCCCGGGCTGGAGAGAGACAGATA[A/G]AAATATAGAAACTGTGTTCTTTTCTTCTCTTTCAG R 2 1 2 1 101000 r 74 goat snp46601-scaffold646-1646291 4 19946199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401552 Affx-122958902 AX-123271905 4 97628159 CAACTGTAACATAATGAAGGAAATACTAAGTTTGG[C/T]TCTAAAACAAACTGAAAAATCTTCTGGGTCAATTC Y 2 1 2 1 103000 r 74 goat snp46602-scaffold646-1675018 4 19917402 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439379 Affx-122930267 AX-123309716 4 97644567 TTATATATATCATGATAAAACAAAAAACAATAAAA[A/G]CAAAAAGAAGGTATTAAAAGCAGGCAAAGAGAAAT R 2 1 2 1 103000 r 74 goat snp10499-scaffold1375-13515 4 19884935 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451878 Affx-122921055 AX-123322211 4 97693363 TCCCTAGTGCTGCTGTGCTTTGTAAAACTGGCAGC[A/G]AAGATGCTATTTATATCTTTAATAAAACATTTAGA R 2 1 2 1 101000 f 74 goat snp10500-scaffold1375-62311 4 19835759 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401600 Affx-122958867 AX-123271953 4 97731310 GTTCTGCATTCTTGTTTCCTTTTTAGGTATCATCT[A/G]TATATCCCTTCTCACCTGCCAGCATCTCTCTTTGG R 2 1 2 1 101000 r 74 goat snp10501-scaffold1375-100258 4 19797621 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782720 Affx-122952222 AX-385269792 4 97783464 CAAAGGGCTGCTATGAGGATGAAATACAGAAGTAT[A/G]TGGATGTATTTCTTAAGGGAGTAAAGCACTGTTAA R 2 1 2 1 101000 f 74 goat snp10502-scaffold1375-152412 4 19745116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426635 Affx-122939950 AX-123296981 4 97830383 AAAATATTTATTGGAATATCAAGGAAATTTCAACT[A/G]TTTCAATTCAGAGGTCCCATCAGTCAGTTTATTGA R 2 1 2 1 101000 r 74 goat snp10503-scaffold1375-199331 4 19698124 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278283 Affx-1111836264 AX-519551770 4 97859714 GAGAAGTTGTCTACTAATCACTTCCCAAGCTTTCT[A/G]TTGTAAAAATTATGCTACATGAAGATATTGGAGGG R 2 1 2 1 201000 r 74 goat Random2.2K-473 4 97859714 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446116 Affx-122925787 AX-123316453 4 97886090 CTAAAGATTTGAGAACTTTTCAGACTGTACTTTGC[A/G]GACCAGTCAATATCTCATCAATCCAGCAGATCCTT R 2 1 2 1 101000 r 74 goat snp10504-scaffold1375-255038 4 19642414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802552 Affx-122965195 AX-385289456 4 97920312 AGAAGGACATCTGACCTTAACTCTGAAGGACAGTA[C/T]GGTAACAACCAAAGTAGGTCTTGACACAGTTCTAT Y 2 1 2 1 101000 f 74 goat snp10505-scaffold1375-289260 4 19606878 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404235 Affx-122957646 AX-123274587 4 97952854 TTTGGAGTTGGTGGAGACTCCTCCAAGTCATCCTC[A/G]CTTGGAGGCACAGGATGAGGAAGTCCTCACTCATC R 2 1 2 1 202000 r 74 goat snp10506-scaffold1375-321802 4 19574265 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425938 Affx-122941192 AX-123296284 4 97981683 ACAAGACTTCCTGACTAAACTCTGCCACCTTGTTT[A/G]CTTCTTTGAAAGTTAATCAGACATTTCCTTATTAT R 2 1 2 1 201000 r 74 goat snp10507-scaffold1375-350631 4 19545168 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782186 Affx-122977061 AX-385269264 4 98074997 TAATCTGTTCCTCATCACATTTTTATTGGGAGGGT[A/G]TTAAAATAGCATGTATGAGTGAAAAGCCAAGCAAA R 2 1 2 1 101000 f 74 goat snp10509-scaffold1375-443945 4 19451961 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428298 Affx-122939382 AX-123298641 4 98133947 GGTAATTTGACATTCCTATGCTCTTCCCTTCCCCC[A/G]TCTTCCCTTGCAGTACACTAAGTTTGGTCTCATCC R 2 1 2 1 101000 r 74 goat snp10510-scaffold1375-502895 4 19393677 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434823 Affx-122934801 AX-123305164 4 98167616 GCTGGACTCCTGAGCTAGGGAGCCTCACATGGGGC[A/G]CAGAGCTCTCATTCCTGTGGGAAAACTTCTACAGT R 2 1 2 1 101000 r 74 goat snp10511-scaffold1375-536564 4 19359977 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795827 Affx-122927715 AX-385282780 4 98283003 AAAATCTATGGCTAGCAGTGCCAATCCTTAAAGGG[C/T]AGAAATCAACTCTAGTCTAGTCTTTAAAAACACTT Y 2 1 2 1 101000 f 74 goat snp10513-scaffold1375-651951 4 19244774 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424463 Affx-122941773 AX-123294809 4 98321156 ATTTGATCTACATCATCACCACTATGGAATCGCAC[A/G]TGTCTTCGATAAATTAGTAGGACACAATCCCACTT R 2 1 2 1 101000 r 74 goat snp10514-scaffold1375-690104 4 19205109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765660 Affx-122920978 AX-385253127 4 98407007 TCCAAACCTCTAATTTAAAAGTTCTGCTTTATCAC[A/G]TGCTTGCTATAAATTTAGGAATAACACTCTATCCT R 2 1 2 1 101000 f 74 goat snp10516-scaffold1375-775955 4 19118964 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405403 Affx-122956290 AX-123275755 4 98457293 ACCACTGTAGAAACTGAGTAATTGTCTCTGTGAAT[A/C]TGATTTGAGATGTCAAGTATCCATCTATTTAGAGG M 2 1 2 1 101000 r 74 goat snp10517-scaffold1375-826241 4 19068575 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795765 Affx-122941026 AX-385282718 4 98491488 TAACTAAAAATTGTTTCACTGTATATTGTCTACTG[C/T]ATCCAAGTTATTTATTCCTCTCCATTCTGACTTAT Y 2 1 2 1 101000 r 74 goat snp10518-scaffold1375-860436 4 19034400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408337 Affx-122953751 AX-123278688 4 98533465 CGAGATTTCTGGTCCAGTGGTTTTGAGGAAGGGTG[C/T]GGGGGTGGGGAGGCATAAATGTATATTTCCAATAA Y 2 1 2 1 201000 f 74 goat snp10519-scaffold1375-902413 4 18992274 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398278 Affx-122962170 AX-123268633 4 98567235 ACATATGTGAAAGTCAGCCTACCACAGGCACACTA[C/T]TCTATACATAAATATCAGAGGTAGTACTCATTCCA Y 2 1 2 1 101000 r 74 goat snp10520-scaffold1375-936183 4 18958145 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391351 Affx-122967295 AX-123261708 4 98600410 TTTCTAGCCTAATAGGAAAATGAAGCAAACTCCAG[A/G]AAATAAATATTTTCAACAGTGATATAATCAGGCTT R 2 1 2 1 303000 r 74 goat snp10521-scaffold1375-969358 4 18926519 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387356 Affx-122970478 AX-123257714 4 98635562 TGATATTGTTGGAAAAAAAGGAAGCAATGGAGCAC[A/G]GACTTTGGACTTCTCTCTCTCCCTGGATGTGTAAG R 2 1 2 1 101000 r 74 goat snp10522-scaffold1375-1004510 4 18891214 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778051 Affx-122971411 AX-385265167 4 98679445 AGTTCAAACACTTTGAAATTAGTCCATTTTTATAG[C/T]GATTTTGAACAAATTCAACTTCAAAGAAACATAAA Y 2 1 2 1 101000 f 74 goat snp10523-scaffold1375-1048393 4 18847338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425078 Affx-122941250 AX-123295424 4 98771364 AAACCACCCCAAAGAGAAGTGGCTTAAAATAGCCA[C/T]GATTTGTTGTTTCTCACTATGCTATGGGTTGGCTG Y 2 1 2 1 101000 r 74 goat snp10525-scaffold1375-1140312 4 18754454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449083 Affx-122923604 AX-123319418 4 98816325 ATAGGAAGGATTCGAGACCCTGGATGCAGGGAAAA[C/T]GTGAGAATGGCAAGAGAGGTCTCAGTCAGCCAGAG Y 2 1 2 1 201000 f 74 goat snp10526-scaffold1375-1185273 4 18709467 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421052 Affx-122944520 AX-123291399 4 98844414 CATTCACTGAAAGAACAAATAAATCTTTGAGTGAA[C/T]GCATAATCAGGCCACACTTTTTCCACTTAGAGGTC Y 2 1 2 1 101000 r 74 goat snp2022-scaffold106-12019 4 18681683 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399785 Affx-122960295 AX-123270140 4 98878202 TTATATCTGCAAAAGTTTTATTTCCAAATAAGATC[A/G]CACAGTGAGGGCTTGGGTGAGCATGAGCTTTTGGG R 2 1 2 1 103000 r 74 goat snp2023-scaffold106-45807 4 18647831 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420950 Affx-122944981 AX-123291297 4 98922669 GAGCAGGAGCTAGAAACAAAGTAAGAAATTATTTG[C/T]GAATACTACAAAAGAATTTTAGTTATCTGGAGCTA Y 2 1 2 1 102000 f 74 goat snp2024-scaffold106-90274 4 18603009 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799549 Affx-122970397 AX-385286479 4 98952855 GATCAATATTCCTAAAAGATAGATCAGCAAATAGA[A/C]ACTATTTCCATGTGAGAGTCTCCTCCTTTGTTACC M 2 1 2 1 101000 r 74 goat snp2025-scaffold106-120460 4 18572955 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278285 Affx-1111836265 AX-519551772 4 98968111 ATAACTTATAGAATTTTTGATCCTGATCCACACTT[C/G]CCTTCCCCACAATATCATGCTTGGTTAAAAATATA S 4 1 2 1 101000 r 74 goat Random2.2K-477 4 98968111 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272291 Affx-1111833447 AX-519546030 4 98973553 TTGAGGTTGGTGAAAAGTCATTTAGTGTCAAGCCA[A/C]TGGGATGGACTCCTTGGCCTGGGTCAGTCACCTGT M 2 1 2 1 101000 f 74 goat 4_98973553_AF-PAKI 4 98973553 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320775935 Affx-122923926 AX-385263066 4 98989270 ATACTCAGCTTATTCTCAAGGAGACAAAAGAAAGC[A/G]TTGCTTTCCTTTATTACACCGGAATGGACTTTCAT R 2 1 2 1 303000 f 74 goat snp2026-scaffold106-156875 4 18534197 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765238 Affx-122961018 AX-385252775 4 99050114 ACTTGAGTTGTGTTCTGATTGTTTACAAAATGAAG[A/G]AGGCTTAATAGGCAAAAACTGCCAAGTTAGTATGT R 2 1 2 1 101000 f 74 goat snp2027-scaffold106-217719 4 18472671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797983 Affx-122970665 AX-385284919 4 99104793 TCACTTGCCCACATTCGCATAACTATAATAGTTAG[C/T]GGTGGAAGTGGTATTTGAATGACATATATCAGTCT Y 2 1 2 1 201000 r 74 goat snp2028-scaffold106-272398 4 18419865 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452287 Affx-122920692 AX-123322620 4 99168427 TTATACAACCAAGGGACCATGGGGGAACAGATGCA[A/G]TATACATACAAAATACTCTCATTTGAAAAGGGAAT R 2 1 2 1 201000 r 74 goat snp2029-scaffold106-336032 4 18355680 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380240 Affx-122975464 AX-123250598 4 99220213 CTCTTGATAATGATTGATACTTATGTGAAAGAAGG[A/G]AAATATTCTCAGGGGATGATGTATGATTGGACCTC R 2 1 2 1 201000 f 74 goat snp2030-scaffold106-387818 4 18303193 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278287 Affx-1111836266 AX-519551774 4 99261900 GTAAAGAGTTGAGGATGACTTAGTGATCAAACAAC[A/G]ACATAGGGCTGAATACGTCGTACACTCTGTCCATT R 2 1 2 1 201000 r 74 goat Random2.2K-479 4 99261900 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416009 Affx-122948385 AX-123286358 4 99293666 GGACTGCTCATATTTGATGATGTCTTCAGTGTTTT[A/G]TAGAGGGATAGATACTTGTTGTTCTTGACACCTGA R 2 1 2 1 101000 r 74 goat snp2031-scaffold106-461271 4 18226138 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784807 Affx-122952402 AX-385271854 4 99335818 ACTTGCATCTTTGGTTATATACATAGATTTATAAT[A/G]TAGCTTTAGGAGGGCTAGATGACTGCTGGCATCAC R 2 1 2 1 101000 r 74 goat snp2032-scaffold106-503423 4 18184231 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429103 Affx-122938260 AX-123299445 4 99384670 AAAATAGGCCCCCTTAATATATATTATCTCATTTC[A/G]TCTTTACAAAATCCTATGAGAATGGTAGAATTATT R 2 1 2 1 201000 r 74 goat snp2033-scaffold106-552275 4 18135377 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382127 Affx-122974057 AX-123252485 4 99416680 AGGAGGTAAAAGTGAAATGGGTTGTTGTTCAGTCG[A/C]TCAGTCATGACTCTCTGTGACCCCATGGACTGCAG M 2 1 2 1 101000 f 74 goat snp2034-scaffold106-584285 4 18103371 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406495 Affx-122955155 AX-123276847 4 99454734 GTTTCACAAGCGGGAATAATTAGGGGAAACACTCC[A/G]CAAAGCAAAGTGAGAACACCTTACCAAATGAAAAC R 2 1 2 1 101000 f 74 goat snp2035-scaffold106-622339 4 18065250 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275321 Affx-1111834833 AX-519548896 4 99458637 TCACCCTTGTCCCAGCCCAGTGTTGTAGAATGCCT[A/C]CCCACTGCAGATGTGGCTGAGAGAAACAG M 2 1 2 1 101000 f 74 goat GoatD01.055812 4 99458637 T G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382896 Affx-122973411 AX-123253254 4 99484332 TTTAATGTGTTTGTTTTAACTGATTAGGTAGCTCC[A/G]TGGGTCATAAACACCCTACAAACTTCCCTTCTCTT R 2 1 2 1 101000 r 74 goat snp10825-scaffold1386-14123 4 18025129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396989 Affx-122963150 AX-123267344 4 99535200 CTTAAGACAGTTCTATGGTGACAGACCGGAGAAGG[C/T]GATGGCACCCCACTCCAATACTCTCGCCTGGAAAA Y 2 1 2 1 101000 f 74 goat snp10826-scaffold1386-64991 4 17974057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408381 Affx-122953722 AX-123278732 4 99583790 CCAAGTTCCACCTCCAGAACTAATCACACTTTTCA[G/T]ACTTGGGCAAGAATGGTGAAGGAACCAGGAATTCC K 2 1 2 1 201000 r 74 goat snp10827-scaffold1386-113581 4 17925525 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769288 Affx-122979111 AX-385256460 4 99612951 TTCTAAGCATGTTTAAGTTATGTTAGATATGCCCA[A/G]ATACAACCAGTGATCTGGTTTTCTGCTAGATTAAA R 2 1 2 1 101000 r 74 goat snp10828-scaffold1386-142742 4 17896446 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436544 Affx-122932923 AX-123306882 4 99671642 GGCCAGGGCTGAGAAAACTCCAGGTTTGTGGAACC[A/G]GGAACAGAGGGCTGCAGTGACTGAGAACTGATTGC R 2 1 2 1 101000 r 74 goat snp10829-scaffold1386-201433 4 17837609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422616 Affx-122943719 AX-123292962 4 99703700 CTCATCTGAAAAATGGAGTTAATAGTTGTAGCTGA[C/T]AGAGTTGTTCCAGGACAAAATAATACTATTAATCC Y 2 1 2 1 101000 r 74 goat snp10830-scaffold1386-233491 4 17805523 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438962 Affx-122930396 AX-123309299 4 99760571 GAATGTCTCACTAGACATTCGTGTATGACCTACAG[C/T]TCGCCTGCAAGAATATAGTACTTCCTTATTTTCTC Y 2 1 2 1 101000 f 74 goat snp10831-scaffold1386-290362 4 17748532 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415578 Affx-122948630 AX-123285927 4 99811253 ATCTTTTCCCCTTCGATGGGGACTCCCTTAAGCCC[A/G]CAGAGTTGGTATAAAAGAAAAAAGTGAAAGTGAAA R 2 1 2 1 103000 f 74 goat snp10832-scaffold1386-341044 4 17697597 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451818 Affx-122921478 AX-123322151 4 99840878 AAAAACCAAGAAAGAAAAGCTCTACTCTTCAAAGC[A/G]TATTGGATCTTAGCAACTTTATCTTTAAAGACAGA R 2 1 2 1 101000 r 74 goat snp10833-scaffold1386-370669 4 17667587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452571 Affx-122920514 AX-123322904 4 99876300 CGATTTACTTTTAAATGAGCTCTCATTGATCTTGA[C/T]GCTCCAGCTTCTCCCTGCCATTTTTCTGTCTCCTG Y 2 1 2 1 201000 f 74 goat snp10834-scaffold1386-406091 4 17631720 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426852 Affx-122940494 AX-123297197 4 99971478 AACGCGGCCACAGGCCGACCCTATCGCGACACCGC[A/G]GCCTATCGGTACCTCGTCAAAGCTTTCCGTGCACA R 2 1 2 1 101000 r 74 goat snp10836-scaffold1386-501269 4 17536895 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445232 Affx-122925496 AX-123315569 4 100004169 AATGCATAAAGCTCACTTAATTTGTATTCTACATC[G/T]AGTGATGTTAGTTTATCTTAAAGTATTATTTTTAA K 2 1 2 1 101000 f 74 goat snp10837-scaffold1386-533960 4 17504192 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432070 Affx-122935884 AX-123302411 4 100047859 GTTGTAGCTGCTTCCCATGAACCTTCCCCATCTGA[C/T]GGTCTAGAGACTAGAGACCAGGCTTTTCAAAATTT Y 2 1 2 1 201000 r 74 goat snp10838-scaffold1386-577650 4 17460449 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411321 Affx-122952279 AX-123281671 4 100129736 TGCTATCAACAGAGTTCACAAGGAAAAAGCAAGTG[C/T]ATTAAGAACCACCACCAGTTCCCTGGTCCCAGGTG Y 2 1 2 1 101000 f 74 goat snp10839-scaffold1386-659527 4 17378571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392553 Affx-122966087 AX-123262910 4 100166693 TCTCCTTGAAGTTTTCTTTCTCTAACATTTCTTAC[A/G]CACCTACCTTGCAGAGGACTGGTGTTGCTTATTCT R 2 1 2 1 101000 f 74 goat snp10840-scaffold1386-696484 4 17342069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404298 Affx-122957030 AX-123274650 4 100209478 CCGAGGGATGGAGGCCACCGGGGACAGCCAGGGAC[A/G]TCACCATGACAGACCTACAGCACACTGCAGATGAG R 2 1 2 1 101000 r 74 goat snp10841-scaffold1386-739269 4 17299547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381209 Affx-122974526 AX-123251567 4 100257942 GTCACTGTCCTTCACTTTTAGAGGACAAGTCCATG[A/C]ACTGCACATGGCACAGCACATGTAAAGACTCTGGG M 2 1 2 1 101000 f 74 goat snp10842-scaffold1386-787733 4 17251342 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432159 Affx-122936418 AX-123302500 4 100295814 CCACCTTCTTGATTTCGCAGGAAAGCCCACTCTAC[C/T]CTCAGAAAGTGTGTCATCTACTTGGAAGGGTGAAA Y 2 1 2 1 101000 r 74 goat snp10843-scaffold1386-825605 4 17213526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449306 Affx-122923005 AX-123319641 4 100338953 AACTTGGTGTAACTTATTTTGTACAGTCCTCCCCA[C/T]GGCCCCTGGGGTGGGATTAGATTAGAGATAAAATG Y 2 1 2 1 201000 f 74 goat snp10844-scaffold1386-868744 4 17170731 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378337 Affx-122976841 AX-123248696 4 100388511 TCTCAGTGTGGCTTATCTTGCCTCGAAACCAGCCA[C/T]GTGCAAACCCAGGAGCAAGTGGTATGCTCCCTCCC Y 2 1 2 1 101000 f 74 goat snp10845-scaffold1386-918302 4 17121336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414423 Affx-122949966 AX-123284772 4 100455485 GAACATTAAAGAGATTTGTTTGTTATTCAGTCGCT[A/G]TCATGTCAGACTCTTTTTGTGACCCCACGGACTGG R 2 1 2 1 101000 f 74 goat snp10847-scaffold1386-985276 4 17054400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278128 Affx-1111836267 AX-519551618 4 100493515 AAAACCAAAGACTTTGATGGGGAAAGTGAAAATGA[A/C]AGTCGCTCAGCTGTGTCCGACTCTTTGCAAAGCCC M 2 1 2 1 201000 f 74 goat Random2.2K-480 4 100493515 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320770484 Affx-122946998 AX-385257650 4 100539735 TATGTGAGATGGGTCTGTCTCATTCCTTTTAAAGC[A/G]GATATAAATAGATGCCACACACACCCTCCTAATTA R 2 1 2 1 101000 f 74 goat snp10849-scaffold1386-1069526 4 16970263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787544 Affx-122946598 AX-385274568 4 100589050 TGCACAAACAGACACAGATGATGTATTTCATACCC[A/G]TCTCTTGCAGGATTGCTATATGCCTCTTCAATAAG R 2 1 2 1 101000 f 74 goat snp10850-scaffold1386-1118841 4 16920473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476193 Affx-1251763698 AX-586011619 4 100594226 GCAAATATTGTCTTCCATTGTTTGTGTTGTCTTTT[-/TCTTTTTATTTTTTTTTTTTTTGAAAATTTAAAGTTATATGGAAATCAACAATAACACAATAATAGTGGGAGTCTTTTTC]TTTTGTTTATGGTTTTCTTTTCTCTGAAAGAGCTT - 4 1 4 1 20000 f 74 goat SV_360 4 100594226 - deletion junction SV-TF-chip 539476448 Affx-1251763698 AX-586011849 4 100594226 GCAAATATTGTCTTCCATTGTTTGTGTTGTCTTTT[-/TCTTTTTATTTTTTTTTTTTTTGAAAATTTAAAGTTATATGGAAATCAACAATAACACAATAATAGTGGGAGTCTTTTTC]TTTTGTTTATGGTTTTCTTTTCTCTGAAAGAGCTT - 4 1 4 1 20000 r 74 goat SV_360 4 100594226 - deletion junction SV-TF-chip 562165111 Affx-1251763698 AX-606940523 4 100594226 GCAAATATTGTCTTCCATTGTTTGTGTTGTCTTTT[-/TCTTTTTATTTTTTTTTTTTTTGAAAATTTAAAGTTATATGGAAATCAACAATAACACAATAATAGTGGGAGTCTTTTTC]TTTTGTTTATGGTTTTCTTTTCTCTGAAAGAGCTT - 8 1 4 1 20100 r 74 goat SV_360 4 100594226 - deletion junction SV-TF-chip 562165234 Affx-1251763698 AX-606940646 4 100594226 GCAAATATTGTCTTCCATTGTTTGTGTTGTCTTTT[-/TCTTTTTATTTTTTTTTTTTTTGAAAATTTAAAGTTATATGGAAATCAACAATAACACAATAATAGTGGGAGTCTTTTTC]TTTTGTTTATGGTTTTCTTTTCTCTGAAAGAGCTT - 8 1 4 1 20100 f 74 goat SV_360 4 100594226 - deletion junction SV-TF-chip 562165467 Affx-1251763698 AX-606940878 4 100594226 GCAAATATTGTCTTCCATTGTTTGTGTTGTCTTTT[-/TCTTTTTATTTTTTTTTTTTTTGAAAATTTAAAGTTATATGGAAATCAACAATAACACAATAATAGTGGGAGTCTTTTTC]TTTTGTTTATGGTTTTCTTTTCTCTGAAAGAGCTT - 8 1 4 1 20100 r 74 goat SV_360 4 100594226 - deletion junction SV-TF-chip 320782033 Affx-122956183 AX-385269111 4 100639988 GAGCATGCCAAAGCAAAATGTACAACAACATAGCT[A/G]TATCTCTGGACCACTTTAGGAGTCACAATTATGTT R 2 1 2 1 101000 f 74 goat snp10851-scaffold1386-1169779 4 16869425 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405061 Affx-122957421 AX-123275413 4 100696026 CACACCATAGAAGACAAACACAAAGAGCTCTGGCC[A/G]CACATAGGAAGGACATCTAATCTGATGGAGTTAAT R 2 1 2 1 101000 f 74 goat snp10852-scaffold1386-1225817 4 16813517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440557 Affx-122929313 AX-123310894 4 100760486 CATGTATTTCTAGCCTTTTCTGCTAATTGTTTCAA[C/T]AGTTATTTTTATTTGTTTAAGCTACTTAGATGGGG Y 2 1 2 1 101000 f 74 goat snp10853-scaffold1386-1290277 4 16748566 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401142 Affx-122959378 AX-123271495 4 100841421 GGGTATCAGATACAAGCTCAAGTGGTATCAATAAA[C/T]AAGCTGAGGGCCACTGTTCCTCTGGACATATATTC Y 2 1 2 1 201000 f 74 goat snp10855-scaffold1386-1371212 4 16667342 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432374 Affx-122935863 AX-123302715 4 100884224 GCAGAAAGCCTGAGGACTTACTGGGGGAGGCGGCC[A/G]GGGTCGGGGGAGAAGTAAGATTTCAGCTCACATGA R 2 1 2 1 101000 r 74 goat snp10856-scaffold1386-1414015 4 16623340 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278130 Affx-1111836268 AX-519551620 4 100915908 AAATGGTACTTTATTAGGGGTAGCATATAAGACCC[A/C]AAATATATATCACACCACATTCACTTCTGTGTTGA M 2 1 2 1 101000 f 74 goat Random2.2K-481 4 100915908 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794192 Affx-122925807 AX-385281158 4 100924706 TTCCAAGCTGCTAAGTTTCAGGGTAATTTCTTTAA[C/T]ATCAACAGAAAACTAATACTCCTAGGTATTTTGTA Y 2 1 2 1 101000 r 74 goat snp10857-scaffold1386-1454497 4 16582984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423976 Affx-122942128 AX-123294322 4 100962187 TCTGCAGTGGAAGTGCCGAGTCCTAGCCATTGGCC[C/T]GCCAGGGAATCCTGAAAACAAGCCTAATGAGCAGC Y 2 1 2 1 101000 r 74 goat snp57592-scaffold9213-7093 4 16545078 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451063 Affx-122921427 AX-123321397 4 100975736 CCTCCTAAATGGGAGAATGCACGTACACATATGCA[C/T]ACATATGCACGCACAATGGAATATTACTCAGCCAT Y 2 1 2 1 201000 f 74 goat snp18319-scaffold1859-2117 4 16531551 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442086 Affx-122928367 AX-123312423 4 101007312 GTGGGCACAGTTGCCAATGCCCATCTCTAGCCTCC[A/G]CTCTTCTGATCTATTCCCTAAAGGAGCTCGCTGGC R 2 1 2 1 101000 r 74 goat snp18320-scaffold1859-33693 4 16500211 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386091 Affx-122971443 AX-123256449 4 101038310 ATATAGGACTTTGGAGTTAAAGGGACCTGGGTTTG[A/G]ACCTTGGTTTCATTTTTTTCACCTTACAACGAGAA R 2 1 2 1 202000 r 74 goat snp18321-scaffold1859-64691 4 16469231 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392934 Affx-122965703 AX-123263291 4 101087061 GAAGGCACAAAGGAATGGGTGTTGGACCTGCTTCC[C/T]CTCGGCCATCTGATTGTCCTTTTTTTCTTTGCTGG Y 2 1 2 1 101000 r 74 goat snp18322-scaffold1859-113442 4 16420556 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762303 Affx-986696834 AX-385250485 4 101103731 ATGGAGAGCAACTGGAACTCACATGTATTGTCGAT[C/T]AGATTGCGAAATGGTTGTTGGGCTGCACCCCACAG Y 2 1 2 1 600010 f 74 goat 4_101103731 4 101103731 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 320762307 Affx-986696838 AX-385250489 4 101103803 CCTGCAAGCCCTGTACCTGCCCAGCTTCAAGATCA[A/G]AGAAAGAGCTTGGAGTTGGCGGTGACAAGCATCAT R 2 1 2 1 600010 f 74 goat 4_101103803 4 101103803 Ancestral_priority_1043 ancestry 0.576 neutral IMAGE 10K 10K ancestral 320803573 Affx-986696120 AX-385290370 4 101103813 CTGTACCTGCCCAGCTTCAAGATCAGAGAAAGAGC[C/T]TGGAGTTGGCGGTGACAAGCATCATCGGTTTAATC Y 2 1 2 1 600010 r 74 goat 4_101103813 4 101103813 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320762311 Affx-986696842 AX-385250492 4 101103839 AGAAAGAGCTTGGAGTTGGCGGTGACAAGCATCAT[C/T]GGTTTAATCCAGGGATCCCCAATCTTTTTGACAAC Y 2 1 2 1 600010 f 74 goat 4_101103839 4 101103839 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 38410837 Affx-122952625 AX-123281187 4 101116125 TTGGTCCAAACCAAAGAGCAATCATAACTAATAAA[C/T]AGAATTCAAAGGGACATATGTCAAACAGTTAATTT Y 2 1 2 1 101000 f 74 goat snp18323-scaffold1859-142506 4 16391453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422771 Affx-122943227 AX-123293117 4 101178484 TCCCCAATCTGTGGTCCAAAAAAACAGCAGAAAAA[C/T]AAACACACTTGAATTTTCTAGATTCGAACACTGCT Y 2 1 2 1 201000 r 74 goat snp18324-scaffold1859-204865 4 16328960 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417678 Affx-122946823 AX-123288026 4 101245787 GACATTCATTTTTCTATCATAGCACCCAGCAACCA[G/T]CACAAGGGAGCTCAGTATTTTTAAACTTTAAACAA K 2 1 2 1 101000 f 74 goat snp18325-scaffold1859-272168 4 16261450 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384700 Affx-122972112 AX-123255058 4 101279854 CCCAATTACAGAATGGAATTCGTTAAATCTGGCTT[A/C]TTATTAAAAAATACATTTATGTGACAAGAAGGGGA M 2 1 2 1 103000 f 74 goat snp18326-scaffold1859-306235 4 16227401 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778345 Affx-122928350 AX-385265460 4 101326406 AAAAGAAAATTCCTTTGCTATCAAATAGCTACAGC[C/T]TTGGTGACTCAGCTGAAAAGCCCATTTTAACATGC Y 2 1 2 1 101000 r 74 goat snp18327-scaffold1859-352787 4 16180567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400011 Affx-122960800 AX-123270366 4 101375968 AGAGGGTGGTAGGGTATTTATTCCCTTGAGTCCCT[C/T]CAGCCTGGGTGGCTCTTTTCCCCAGAGCCCTTGGG Y 2 1 2 1 101000 f 74 goat snp18328-scaffold1859-402349 4 16131370 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417361 Affx-122947717 AX-123287709 4 101407340 TATGCTTTCTGAAATCTGTTTCTTGCCCTGCTGAC[A/G]TGACTGTGCCCACAGGAAGACGTTTCTGATCACTG R 2 1 2 1 201000 r 74 goat snp18329-scaffold1859-433721 4 16100241 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452141 Affx-122921671 AX-123322474 4 101450733 AAGGGGCTGGGTGCTCTCCTCCTGCAGATGCAGCC[A/G]TCATGGATGTGGATCAGGGCAGGCCTCTGCCTTGC R 2 1 2 1 201000 f 74 goat snp18330-scaffold1859-477114 4 16056885 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447527 Affx-122924059 AX-123317863 4 101484475 AGGACCATCAACCAGAGGGGCCATCTCTTTTCGGA[C/T]AGAACCGGCCTTTTAACTGGGCAAGCAGATTTTGT Y 2 1 2 1 101000 r 74 goat snp18331-scaffold1859-510856 4 16023169 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464326288 Affx-1110426179 AX-515800234 4 101494746 ATCTTTAAGTAAACAACAGAGAAAACACTTCTGCA[C/T]CTTGTGTCTTTCTGGTTTCCACTGTGTCTTTTTGT Y 2 1 2 1 101000 r 74 goat 4_101494746_AF-PAKI 4 101494746 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320788274 Affx-122974510 AX-385275292 4 101515320 TACCAGCTTAGCTCGATGGTACCCCTTTATCTTCC[A/G]CTGCTTTCCTTCAATGTGTCTGCCATCATTTCATT R 2 1 2 1 202000 f 74 goat snp18332-scaffold1859-541701 4 15992541 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436927 Affx-122933193 AX-123307265 4 101560316 CCCTCTGAGGATCATGCCGGGTTGATTGTCTATGT[A/C]TATTTTCGTCACTGTACTTCCTACAGGTCCATGCT M 2 1 2 1 101000 r 74 goat snp18333-scaffold1859-586697 4 15947709 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272435 Affx-1111834260 AX-519546161 4 101584647 A[A/G]TTCTGCCTGAAGTTCCTCCTTGGTTACAGCTTTCC R 2 1 2 1 101000 r 74 goat GoatD01.028071 4 101584647 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38453942 Affx-122919482 AX-123324275 4 101604174 TGAGATGCACCAGAGGACTGTGAGCGTCCAAGCTG[A/C]AGTCTCCCTTTTCATAAAGATTTCCCGTCCTGTCT M 2 1 2 1 101000 r 74 goat snp18334-scaffold1859-630555 4 15903343 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376277 Affx-122978387 AX-123246636 4 101633193 CCAACAGGAAGTTCCCATCAGGCAGATGGTATTAG[C/T]GCACACGTGTGCCAGAATCCAGCCTTTCAGGGGCA Y 2 1 2 1 101000 f 74 goat snp18335-scaffold1859-659574 4 15874001 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401088 Affx-122959626 AX-123271441 4 101699184 AACTTGTGATTTTCTTTTGAATGAAACCTCATACC[A/G]CAAACATTTTACACTGTTAAAAGGGCATCAAGAAT R 2 1 2 1 101000 f 74 goat snp18336-scaffold1859-725565 4 15807543 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784302 Affx-122946918 AX-385271353 4 101728660 TTTATAGATTCTCAGATTCTAAGATACAGATAAAG[C/T]GAATTGCATAGCATGTATATCTATATGTATTCTTA Y 2 1 2 1 101000 r 74 goat snp18337-scaffold1859-755041 4 15778117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800209 Affx-122935369 AX-385287132 4 101764972 GAGAATCCTTTTCCATAGACTCTTGTTCTTATGTC[A/G]TGGAAGCAAGCTATGTTTCTTCTCTTTTCTCTTGG R 2 1 2 1 101000 r 74 goat snp18338-scaffold1859-791353 4 15741926 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409866 Affx-122952918 AX-123280217 4 101815710 ACATAGAGTCTGACACAACCGAGTGACTAAGCGCA[C/T]GTGCACAGGCATTGTACAGGAAGACCTGCCTAGAT Y 2 1 2 1 201000 r 74 goat snp18339-scaffold1859-842091 4 15690977 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434278 Affx-122934777 AX-123304619 4 101858897 AAAAATGAGAACTTCTACCCATAAACCCTTTTGAT[A/G]TATTTCCCTTTCTAGATAATAGTAATACAATTACT R 2 1 2 1 101000 r 74 goat snp18340-scaffold1859-885278 4 15647883 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416951 Affx-122948025 AX-123287299 4 101913007 TTTCTTGTGTGAAGTATTAATACCTTCACCTCTGC[C/T]CTGAATTCCCTCTCCTCCTCCTTTTTCATGGCCCT Y 2 1 2 1 102000 f 74 goat snp18341-scaffold1859-939388 4 15593630 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408720 Affx-122953422 AX-123279071 4 102006392 GATCAATCATTTCTTAGAAAAGGCAAGAACCTCTA[C/T]GGCAGGAGTTCTTAACGTTTTGGGGTCATGAGAAC Y 2 1 2 1 201000 f 74 goat snp18343-scaffold1859-1032773 4 15500675 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430599 Affx-122936985 AX-123300940 4 102088860 TGAAGAAGGGGTGAGTTGAAGAAGGAGGGATCTTA[C/T]AGATTGAATGGTTTAAAAAACAAACTAACTAAGAA Y 2 1 2 1 101000 f 74 goat snp18345-scaffold1859-1115241 4 15417155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390485 Affx-122967593 AX-123260842 4 102140202 AATGTCTTGTTTCAGGGTTTGTCCATGTTCATTCA[C/T]GTGAATGCAAATACAGAGAGATTTGTAACTTCTAA Y 2 1 2 1 101000 f 74 goat snp18346-scaffold1859-1166583 4 15365423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399312 Affx-122960526 AX-123269667 4 102176302 TTGGACACGACCAAGCAACTGAACAACAACAATGG[C/T]AACCCACTACATTTTATGGCAGACACCCTACATGA Y 2 1 2 1 101000 r 74 goat snp18347-scaffold1859-1202683 4 15328973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793206 Affx-122975301 AX-385280184 4 102222572 TTTCCTCAGTCCTTCACCCTCAAAGTGACAAGGTC[A/G]TAGGAGCACTTTGCGATGGAGTGAGATGATGTTGT R 2 1 2 1 101000 f 74 goat snp18348-scaffold1859-1248953 4 15281159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394329 Affx-122964674 AX-123264684 4 102319307 TCTTCATTTGTAAAATAATGTAGCAGGGTGTGTTC[A/G]TTATCTGTTGCTGTGGAAGAAATTATCTCCAAAAT R 2 1 2 1 201000 r 74 goat snp18350-scaffold1859-1345688 4 15183495 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800819 Affx-122967252 AX-385287735 4 102348289 CCATAATTTTTCAAATTTTCACTTCGTAATGCTGA[C/T]GGAAAATATTTATACACCCAGTACCACCTGCTTTC Y 2 1 2 1 101000 r 74 goat snp18351-scaffold1859-1374670 4 15154738 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795524 Affx-122926567 AX-385282479 4 102384423 TGTGTGTGCATATATGTGTCTCTAGCAGAAGAAAT[C/T]TGGGAATTCCAAGGTGACTACCAAGAGGTTGGGAA Y 2 1 2 1 101000 f 74 goat snp18352-scaffold1859-1410804 4 15118604 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793887 Affx-122962560 AX-385280856 4 102422710 ATCTTGAGTTTTAAGAAGCTTCTGCATTATAAATA[G/T]ATGTAAATTGTATACATCATATTACTTGAGCATAA K 2 1 2 1 202000 r 74 goat snp18353-scaffold1859-1449091 4 15079594 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411604 Affx-122951603 AX-123281954 4 102458240 TTAGACACTGATGGCTAATTTTCCTGTTTATATGA[C/T]GACATGCCTAATCATAAAGTGAATCCCATGTTTAA Y 2 1 2 1 101000 f 74 goat snp43627-scaffold5842-23144 4 15037521 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390097 Affx-122968022 AX-123260454 4 102466642 TTGAGAATTTTTTTAAAAGAAGGGCAACATGATAA[A/G]TTTGTTTCAAATTGCTACAGTTCCTTAAATGACTG R 2 1 2 1 103000 r 74 goat snp5893-scaffold1205-3128185 4 14596647 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398231 Affx-122962208 AX-123268586 4 102700456 CAGGCCCTTTCTAATCCTCAGCTTCCTCATCCTCT[A/G]CGCTATCTGAGTAGCAGACAGTCATTTTCCCTGGT R 2 1 2 1 101000 r 74 goat snp5888-scaffold1205-2894371 4 14369787 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388751 Affx-122968951 AX-123259109 4 102834412 CTTTTCCAACCTGATGAATATGATACAGTTGATGA[C/T]GGAGTAATGTTTGGCAAGGCACTTAATCTCTTACC Y 2 1 2 1 101000 r 74 goat snp5885-scaffold1205-2760415 4 14199311 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382994 Affx-122973336 AX-123253352 4 102865342 TATAACACCTGCTGAATGTGACACACGTCAGTATG[C/T]GGCCCAGTAGGTGAGATCACAATCGGGGAAGTGGT Y 2 1 2 1 101000 f 74 goat snp5884-scaffold1205-2729485 4 14167918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404056 Affx-122957156 AX-123274408 4 102902339 CTGACACTTCTCTTAATGTCTGCCCTGATCCCAGC[A/G]CTTCTGTCTTAATGGTAGCTGCTGGAGACTTCTTC R 2 1 2 1 202000 f 74 goat snp5883-scaffold1205-2692488 4 14130929 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426154 Affx-122940603 AX-123296500 4 102937472 TCATTATTTTCTGAATTTATAAATTTGAGTATTCT[A/G]TCCATACCATCACTTCTTCATCCTTAAAGTGGACA R 2 1 2 1 101000 r 74 goat snp5882-scaffold1205-2657355 4 14095775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419554 Affx-122945414 AX-123289902 4 103025975 AGATCCTGAAAACTTCTAGAGAAAGAAAATAAATG[C/T]GAAAACTTACAAAGGACAAAGGCACATGTTGCCTG Y 2 1 2 1 103000 r 74 goat snp5880-scaffold1205-2568852 4 14006753 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390376 Affx-122967667 AX-123260733 4 103166818 AACTCTGCAACCCATCAGCCGTACCCCTGTTCCAA[C/T]AAGGAGCCACTGCTTTAGGGGCCACTGAAAGGTAT Y 2 1 2 1 103000 f 74 goat snp5877-scaffold1205-2428009 4 13865032 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385678 Affx-122971140 AX-123256036 4 103265072 ATGAATGCCTAAGACTGAAAAATCAAAAGTAGCAA[C/T]GCAAACATTTAGTTTAGAGACAAGGACAGAAACAC Y 2 1 2 1 201000 r 74 goat snp5875-scaffold1205-2329755 4 13766317 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422031 Affx-122943623 AX-123292378 4 103392114 CTGCACAGGCCCATGGCGAAGACAGCTGACAATAA[C/T]GAGGTTCCAAGAACCGGTTGAAAGCCTGCTGCAAA Y 2 1 2 1 201000 f 74 goat snp5872-scaffold1205-2202713 4 13637989 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429730 Affx-122937606 AX-123300071 4 103425001 TTCATCCCTAAAGGGTGTGCACAACCCCATCACTC[A/G]CAAAAATAGACCATGATGCCAAATTAAAATTGCTC R 2 1 2 1 201000 r 74 goat snp5871-scaffold1205-2169826 4 13604422 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406800 Affx-122955696 AX-123277151 4 103453986 AAACAAAAACATGTTAAATTCAAGTCCAATTATGA[A/G]ATAATGATAACAAAAATTACTCATGGACTGTAAGA R 2 1 2 1 303000 f 74 goat snp5870-scaffold1205-2140841 4 13574787 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790976 Affx-122977577 AX-385277973 4 103498170 AAGTTAGCTTTGTAACCTAGCAAACTGTCAGTTTT[A/C]TTTGCTTGAAAATAATGTGTGGTCTCTAATTATCC M 2 1 2 1 202000 r 74 goat snp5869-scaffold1205-2096657 4 13530128 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771917 Affx-122945586 AX-385259073 4 103542561 TTTCAATTTACACTAGTTTCCAGGACAAGAGGGGA[C/T]GGTAGGTGACAATGAGAGGTAAGTTGATAAACAAT Y 2 1 2 1 101000 f 74 goat snp5868-scaffold1205-2052266 4 13485727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442130 Affx-122928335 AX-123312467 4 103601528 ATGGTCATTTTTTAAAAGGCTATGGATATACTGAA[C/T]ATGAAAATCAAGAAACATATCAAGGAGACTAAATG Y 2 1 2 1 101000 f 74 goat snp5866-scaffold1205-1993299 4 13426009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773378 Affx-122937710 AX-385260520 4 103652377 ATATGAATTTAAAAAACCCAGTGAGCTATGTTATA[C/T]GTTATGCCAGGGTGCAAACTATTCACTTTAATCCT Y 2 1 2 1 101000 r 74 goat snp5865-scaffold1205-1942450 4 13376616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774638 Affx-122956915 AX-385261772 4 103681710 AAAAAGAATCAAATATCTATTCTGAAACAGCAACA[C/T]GTATCATCTTAAATTAAGAAAACATTGGATAGATT Y 2 1 2 1 101000 r 74 goat snp5864-scaffold1205-1913117 4 13347102 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386990 Affx-122969951 AX-123257348 4 103736131 CATTGCCCACTCCCTTCAAGTGATGGTTTTAAGAA[C/T]GGATGCTTCTCTACAATCCCCATAAAGGTATACAT Y 2 1 2 1 101000 r 74 goat snp5863-scaffold1205-1858696 4 13292595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412116 Affx-122951107 AX-123282466 4 103781854 CTAATATGGTTGTTGGGTGTATAACTATGTACATG[C/T]GCCCTTGCCAAACCCTCCTCAAACTGATGCAATCT Y 2 1 2 1 201000 f 74 goat snp5862-scaffold1205-1812973 4 13245997 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381999 Affx-122974078 AX-123252357 4 103814501 ACGTCAAGATTCTGTCCACATAAAAAACTGTCTGT[A/G]TCTGTGAATATATTTTCCCATCATGAATTAAATGA R 2 1 2 1 101000 f 74 goat snp5861-scaffold1205-1780326 4 13213265 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788536 Affx-122945064 AX-385275553 4 103859118 GTAGTACATATGTTTGTAAACTAAGCAGATATTGA[C/T]GGTAGGAATACTGGTGGTGTTCTAGTACCTAGAAT Y 2 1 2 1 101000 r 74 goat snp5860-scaffold1205-1735709 4 13168205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386713 Affx-122970160 AX-123257071 4 103978576 GAAGAGCATCCGCATTGTTTGTTATATTTTTTGCC[A/G]TGCCTGGTCTTACTGTGGCATGTGGAATCTGGTTC R 2 1 2 1 201000 f 74 goat snp5858-scaffold1205-1616251 4 13046480 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272243 Affx-1111833408 AX-519545986 4 103996662 GCCAAGAAGATCAACATATTAACTTTGGAAAGAAT[A/G]CTTGAACATACCTGAAGTTGCTTTTTATTTCTTTA R 2 1 2 1 101000 f 74 goat 4_103996662_AF-PAKI 4 103996662 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468274147 Affx-1111834033 AX-519547749 4 104018753 AT[A/G]CTAAGCTCTCAAAAAGAGCACCCAGGGAGACTTGC R 2 1 2 1 101000 r 74 goat GoatD01.015228 4 104018753 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437936 Affx-122931632 AX-123308274 4 104027520 AAAGCTGGAGAGGGACAGGCCTGGAGGGGAGTGAA[G/T]CATAGATAAGGGACCGTGTGAGAGGAGGGAAGTGG K 2 1 2 1 201000 r 74 goat snp5857-scaffold1205-1567307 4 12997189 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389487 Affx-122968318 AX-123259845 4 104077433 CCTATTCATGAAAAAAATTTTCTAGGCCCCAATGG[C/T]CTACACATTCTGCTCTTTTATTTGCACTCCTTAAA Y 2 1 2 1 101000 r 74 goat snp5856-scaffold1205-1517394 4 12947445 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386352 Affx-122970862 AX-123256710 4 104117708 TTGTTAGTCTCCAGTGACAAAAACCTTTGCTGATA[C/T]ATTGCCAGTGCCCACAAGACTGGTGACCCATTCAT Y 2 1 2 1 101000 f 74 goat snp5855-scaffold1205-1477119 4 12907167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788418 Affx-122946115 AX-385275436 4 104206249 TGCTTCTTGGATAAGTATTGTCTTTAGAAGTCATC[A/G]TTTAAAATGTCCATATCTTTTGGAGGAGCAAAGAG R 2 1 2 1 201000 r 74 goat snp5853-scaffold1205-1388578 4 12820444 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794930 Affx-122941493 AX-385281890 4 104238365 TGTTTTTGAGGACAGCATCTTCTAGAATTGGTTCT[A/G]TGATTCTAGTTTGTCTGAAATTGAAGATAATAGGA R 2 1 2 1 101000 f 74 goat snp5852-scaffold1205-1356462 4 12788489 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443112 Affx-122928096 AX-123313449 4 104306059 CCCCCGTGAGTGCTTATTGTCAGGCCTTTTCTTTC[A/G]CTCATCCTCAGTAACTAGTTCACTCTGAACTTAAT R 2 1 2 1 201000 r 74 goat snp5851-scaffold1205-1288768 4 12720920 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382179 Affx-122974020 AX-123252537 4 104388806 GTTTTATAGTAAGATTACCAAACCTGGATGTACTC[A/G]TTCCTGCTACAGGGAGCTAATGCTCTTAGGAGGAA R 2 1 2 1 101000 f 74 goat snp5849-scaffold1205-1206021 4 12639311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278293 Affx-1111836269 AX-519551780 4 104432452 GTTCCCAGAGTGTGAGAGGAGAGAGTCTGGGAAAC[A/T]GAGGACATTGGTTAAAGTTTCTTTTTTCAAAATTG W 4 1 2 1 202000 r 74 goat Random2.2K-484 4 104432452 A T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407298 Affx-122955321 AX-123277649 4 104443953 GTAAGTGGCAGAGTCAAGGTTTAGACCTAGGCAGT[A/G]TGTCTGCAGAGCCTGAGGTGTAAGCATTCTGCAGT R 2 1 2 1 101000 f 74 goat snp5848-scaffold1205-1150874 4 12587079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405240 Affx-122956884 AX-123275592 4 104502295 ACATAAAAAGAATAAGTAGTTTCTTTCATTGTTAT[A/G]CATTACCCCCAAAATTGCTACTTTAAGTCACCATT R 2 1 2 1 101000 r 74 goat snp5847-scaffold1205-1092532 4 12534868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395875 Affx-122963999 AX-123266230 4 104544551 TTGATTCTTGAAAAAATAAGATTCAGAAATCACAG[C/T]GGATCACTATGATACTGCTTTTTAGCATACTCCTC Y 2 1 2 1 101000 r 74 goat snp5846-scaffold1205-1050276 4 12492229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450443 Affx-122922963 AX-123320777 4 104577513 TGACTCAGTTTGCAGTCTCTCTTTAGAATAAGAAT[A/G]TTAAGTATCGGATGCTAACAGTCTCCATACACAGA R 2 1 2 1 101000 r 74 goat snp5845-scaffold1205-1017314 4 12459247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434723 Affx-122933929 AX-123305064 4 104609667 CTAAACATTATCCACCCAGGTCTTCGCCTCAGCGT[A/C]TGCTTCTGAGAAAACCTAAATTAAGAAGAAACATT M 2 1 2 1 201000 r 74 goat snp5844-scaffold1205-985160 4 12426601 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391709 Affx-122967509 AX-123262066 4 104680484 GTCCCCATTTTTAAATGTGTAATCAGAATGGATAT[A/G]CTTAGAATCTGGCCAAACTCAGACCATACGGTAAA R 2 1 2 1 101000 r 74 goat snp5843-scaffold1205-914343 4 12355709 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393666 Affx-122965276 AX-123264021 4 104718981 ATAATCTCTGAGCTCAGGTCATGGAAAATCTTTTA[G/T]CTTCTACTTTTCTTTTTTACAAGAAAAGTCTTGAG K 2 1 2 1 101000 f 74 goat snp5842-scaffold1205-875846 4 12317467 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432392 Affx-122935851 AX-123302733 4 104749225 CTAACCTCTTCTGTTCTAAATTTTTCTTCTATTAC[A/G]TTCCACACAGTCTTTGTTCCCTCTGTCAGGTCATT R 2 1 2 1 101000 r 74 goat snp5841-scaffold1205-845602 4 12287040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445457 Affx-122925221 AX-123315794 4 104862005 GTTTGGTATTCAATAAAAATTTACCAGGAACGCTA[A/G]AAAGCAAGCAAAAAAATTAATCAGAAACAACCCTG R 2 1 2 1 101000 f 74 goat snp5838-scaffold1205-732822 4 12169815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278134 Affx-1111836270 AX-519551624 4 104914172 TGGAGACCTACCAGGGGGTAGAGTTTGCACCAGTA[A/G]AACAACGGAGGCAAGAACAGAGATGAAATTTTTAT R 2 1 2 1 101000 f 74 goat Random2.2K-486 4 104914172 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439342 Affx-122930292 AX-123309679 4 104940302 CTTGCCCACTAAGTCCTCGTGACATACAATGACTT[A/G]CTTGGTGTTATTAACACACATCCTTACAGTGTTTC R 2 1 2 1 101000 r 74 goat snp5836-scaffold1205-654525 4 12090451 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390197 Affx-122967797 AX-123260554 4 104971719 TCCATCAGAAGATGACTTGTGTCTTCATGCTCTTA[C/T]GTTCTTTCTTTAAATATTTTCAAAAATTGCTCTCA Y 2 1 2 1 101000 f 74 goat snp5835-scaffold1205-623108 4 12058855 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394569 Affx-122964449 AX-123264924 4 105002508 AAAATTAATGTGACAGAGCTTAATATTGCCAGTTA[C/T]GGTCTTGGCAGAGTCGGCCCTAGAATTCTCATATG Y 2 1 2 1 201000 f 74 goat snp5834-scaffold1205-592319 4 12027779 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378125 Affx-122977134 AX-123248484 4 105039379 CAAAATGTATTTCTCACAGTTCTGAAAGCTGGAAA[G/T]CCAAGATCAAGGTTCAAGAATGACTGGGTTCTGGC K 2 1 2 1 103000 r 74 goat snp5833-scaffold1205-555448 4 11990909 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439132 Affx-122931088 AX-123309469 4 105070450 AATACAGAAGACCACAAAGAAAAGCTAAGGAAATA[C/T]GAGTATAAAGAGAGCTGTAGGAGGCAGCTGAAAGT Y 2 1 2 1 101000 r 74 goat snp5832-scaffold1205-524377 4 11959800 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770937 Affx-122971782 AX-385258100 4 105191869 GCTCTTTGATCAAGTACTATTCAATGCTTTTGTTG[A/C]GCCTATGACCACTTTTTAACTTATGACATAAACTC M 2 1 2 1 101000 f 74 goat snp5829-scaffold1205-402958 4 11839760 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793365 Affx-122928113 AX-385280343 4 105224038 TAAGAAAACTCCGAAGGGAAGTTCAATGAGCTCAG[C/T]AACAAAATTGATGAAAAGAGAGAAATCTTTACCAA Y 2 1 2 1 201000 r 74 goat snp5828-scaffold1205-370789 4 11806821 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770890 Affx-122951773 AX-385258053 4 105252895 GAAGTGCTTTTAAATCTTTAGAAATGGTAAGTAAC[A/G]TAACCAAGGTTAGTAAAGCTAGTGATAGGGGGAAC R 2 1 2 1 101000 r 74 goat snp5827-scaffold1205-341932 4 11777772 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386917 Affx-122970009 AX-123257275 4 105289846 CACATCTGAACACAAGTAATGCAGAATGATACAGA[C/T]GACATTTTATTTTTAAATTCTTTTAAAAGAAACTG Y 2 1 2 1 101000 f 74 goat snp5826-scaffold1205-304981 4 11740460 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391508 Affx-122966669 AX-123261865 4 105338786 TTGATACATAGGAAAAGTATATATTTAAGGTGTCC[A/G]TTTCAATTCAGTTCAGTTCAGTCGCTCAGTCCTGT R 2 1 2 1 201000 f 74 goat snp5825-scaffold1205-256041 4 11691150 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376127 Affx-122978869 AX-123246486 4 105454372 GTTCTAAATTTTAATCCTAATGATATTGAAATAAA[C/T]GAAATGACTGCTTTCAGTGACTAAAGATGAATTAA Y 2 1 2 1 102000 r 74 goat snp5822-scaffold1205-140455 4 11580449 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438094 Affx-122931513 AX-123308432 4 105495302 AAGAGGCGATAACATTGATCCAAATCACCACCTGG[A/C]TCCTCCAGGGCTGAGGGACTGTGATTACCACAGAA M 2 1 2 1 102000 f 74 goat snp5821-scaffold1205-99525 4 11541870 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794876 Affx-122970370 AX-385281836 4 105535368 AGATGCAACAGATATCTAAACAAGTCATTTGATAC[C/T]GATACTGGTTAGCTGAGCTGTAGACAAGCAAGTTT Y 2 1 2 1 101000 r 74 goat snp5820-scaffold1205-59459 4 11501638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278297 Affx-1111836271 AX-519551783 4 105559823 TTGAGCCTACTCGCTTTTTGGGTCTTCATTTTCTT[A/G]TGGAGACTCTCCTATACATGTAAAACAAAATTTGT R 2 1 2 1 201000 r 74 goat Random2.2K-487 4 105559823 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781900 Affx-122960549 AX-385268981 4 105564423 AGTAAGCTGTGACATCTTCCAAACTATAAACTTTT[A/G]TGACATTTTCTATTTATCAGCATAGTTTGTATGTG R 2 1 2 1 101000 f 74 goat snp5819-scaffold1205-30404 4 11472430 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778581 Affx-122957263 AX-385265692 4 105594136 TTTGAGTCTCAAAAAGTGGAATTAACTTTTCCACC[A/G]TCTCTGTGAGGAAGAAAACTTTAAACTTTTGATGG R 2 1 2 1 103000 r 74 goat snp5818-scaffold1205-691 4 11441976 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377733 Affx-122977384 AX-123248092 4 105603072 TTGCTGTTATTGCTTTATTCTGTTGTCTTAGTTTT[A/G]TTATTTCCCCTCATTCTTTGTCTATTATTTCGCTG R 2 1 2 1 101000 r 74 goat snp15287-scaffold1629-829571 4 11432005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429930 Affx-122938094 AX-123300271 4 105634830 TTAGAAGCCCCTTTTCTCCTCAAGATGCTTTTCAT[A/C]TTCCTCACTCACTCTCTTTGAGAGCTATTATCCTC M 2 1 2 1 101000 r 74 goat snp15286-scaffold1629-797813 4 11400072 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422116 Affx-122943561 AX-123292463 4 105670258 ATTTTAAAAAAGATATGCCCACTAAATCTATATGC[A/G]TAGTAGAGAGAAAGAATGACAAAGTCTCTTATTTC R 2 1 2 1 201000 f 74 goat snp15285-scaffold1629-762385 4 11364371 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764667 Affx-122953323 AX-385252301 4 105722639 ATCATCTGTCAAAGAAGTCAATATCAAGCTTCTTC[A/G]TTCAAAAATTTTACCATTCTCAGAGATTCAACAAT R 2 1 2 1 101000 f 74 goat snp15284-scaffold1629-710004 4 11311936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769036 Affx-122931740 AX-385256211 4 105754797 ATTATAACCCAGTTTCCTTCCACCTCAACTTATCT[A/G]TCTTCCTGTTTGATGAGAGTAGGCAGAAGAAAAAG R 2 1 2 1 102000 f 74 goat snp15283-scaffold1629-677846 4 11279511 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409361 Affx-122954168 AX-123279712 4 105797490 CTGACGCGTCTGCCAGTCACTCTACAAGCCAGCCC[A/G]CAGGGAAGCCCTTGCTTACAATGAATACACTACAG R 2 1 2 1 201000 f 74 goat snp15282-scaffold1629-635153 4 11236924 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444691 Affx-122926437 AX-123315028 4 105847338 GCAGAAGATTTATCTAGATTCTTCTGTGAGTCAAC[A/G]TCAAGGGGAGTAATAGGTCCAGCTTTCTCATACTT R 2 1 2 1 101000 f 74 goat snp15281-scaffold1629-585305 4 11173393 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448304 Affx-122924160 AX-123318640 4 105882800 AATCTTCCTTAATGAAGAATTCCAAATAATAAATG[C/T]AGAAAGAATGGAAGAAATCAAAAATTGCAAATAGC Y 2 1 2 1 103000 r 74 goat snp15280-scaffold1629-549843 4 11137652 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453874 Affx-122919519 AX-123324207 4 105915029 AGTTTGCGCTTTCTGGCAGGAGAGGAGGAAATTTC[A/G]TACCAGGTGAACAGAAAGAGTAAGACTGTCTTCTT R 2 1 2 1 101000 r 74 goat snp15279-scaffold1629-517614 4 11105767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417236 Affx-122947284 AX-123287584 4 105948315 CATCCATTCAACTATTCCCCTCATAAAAAATGACA[C/T]GAGAACCTTGCAATATTTCCAGAATCTTCAACAGT Y 2 1 2 1 101000 r 74 goat snp15278-scaffold1629-484328 4 11070578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476194 Affx-1251763699 AX-586011620 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20000 f 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 539476449 Affx-1251763699 AX-586011850 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20000 r 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562165265 Affx-1251763699 AX-606940677 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 f 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562165697 Affx-1251763699 AX-606941106 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 r 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562166020 Affx-1251763699 AX-606941429 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 r 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562166159 Affx-1251763699 AX-606941567 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 f 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562166179 Affx-1251763699 AX-606941587 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 r 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 562166557 Affx-1251763699 AX-606941965 4 105973221 CGTACGGTGTTAAAAAGTGTTCTAGTTTCCCTTTT[-/TTAAAATGTAGTTGGGGAGAGGGAAAGATGGTGGAGGAATAAAAAAATAAAAAATTTTCAAAAAAAAAAAATAAATAAAA]TAAAATGTAGTTGACCAGTTTTCCTAGCACCACTT - 8 1 4 1 20100 r 74 goat SV_365 4 105973221 - deletion junction SV-TF-chip 38398192 Affx-122962642 AX-123268547 4 105983513 TGAAGTTTCCTTTTTTCTTTTGCGAATCCTCTCTT[A/G]CTTTGTCTCCTCAAAAAGACTTATATATTGATAGT R 2 1 2 1 201000 r 74 goat snp15277-scaffold1629-449130 4 11034858 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440350 Affx-122929659 AX-123310687 4 106015385 AGACAGAATGAAGTCACTATACAATGAACTTCAAG[C/T]AGTAGTCTATCCACTCATTGTAATAGAAAAGTGAA Y 2 1 2 1 101000 f 74 goat snp15276-scaffold1629-417258 4 11002647 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441824 Affx-122929062 AX-123312161 4 106051094 GAAAAGTCGCCCTAGAGATAAGAGACCCAAAGGAA[C/T]GGATATAAAATAAAATGAGAATGGAAAGTACATAT Y 2 1 2 1 101000 f 74 goat snp15275-scaffold1629-381549 4 10966745 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438466 Affx-122931238 AX-123308804 4 106086408 TCAAAACTGGCAGAAAGGCCTTCTGAGGTTTTAAA[G/T]ATCACACCAAGAAGTGATCACATTTTATAAAATTA K 2 1 2 1 102000 f 74 goat snp15274-scaffold1629-346235 4 10931941 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423147 Affx-122942757 AX-123293493 4 106187564 TTTACATGAGCCTTCCACAGCAAGGAATAAATAAA[C/T]AAGGAATAAAAGAATTAGAAAGGTGTTCTTGATTT Y 2 1 2 1 102000 f 74 goat snp15272-scaffold1629-245079 4 10830973 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793212 Affx-122933056 AX-385280190 4 106224878 CTCAGGTCAATCACTGAAACCCATTTATAATCTAA[C/T]TATGAAGCTGTAGGAATGTACCAAGATGGCATTAA Y 2 1 2 1 101000 r 74 goat snp15271-scaffold1629-207765 4 10794232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781330 Affx-122934293 AX-385268415 4 106261548 TGACCAATAAAGCATTGTTCCATAGCTATGCTACA[A/G]AATTGCTTTCCTCAGCATAAGTTCAGTTCAGTTCA R 2 1 2 1 101000 r 74 goat snp15270-scaffold1629-171095 4 10757691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775670 Affx-122965098 AX-385262801 4 106294488 CAATATGAACAGTTTCAGAGGGTCAGATATATTGA[C/T]GCAAGTTATTGTTTTCAGTATATCTTATAACTTCT Y 2 1 2 1 101000 f 74 goat snp15269-scaffold1629-138155 4 10724737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388884 Affx-122968862 AX-123259242 4 106328024 TAATATTCAGCACTGTAATCATGATTTGCTTGTTA[C/T]GATCCCCTGGAGAAGGGAATGGCTACCCACTCCAG Y 2 1 2 1 202000 f 74 goat snp15268-scaffold1629-104619 4 10691369 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768332 Affx-122922529 AX-385255512 4 106370372 TAGAACTAGATTAAAGTTCCTTAGACCATTCATGC[A/G]TTACGGATAAGAAAAATTATTGTTGCTAGTTCTAC R 2 1 2 1 101000 f 74 goat snp15267-scaffold1629-62271 4 10648747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418740 Affx-122946218 AX-123289088 4 106405684 GCAGATGCAGTATGCATTATTTAATTTTCTTTCTC[A/G]TTGGATAAAAGCTGTGATTGTTTGTGCATACAACA R 2 1 2 1 101000 r 74 goat snp15266-scaffold1629-26959 4 10613316 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435286 Affx-122934041 AX-123305626 4 106538367 GAATCACTTCCTATCATGTTTCAATGTAACTATCA[G/T]ACTACAAATGCCCCATGATGTCTGGGAATCTTACT K 2 1 2 1 201000 f 74 goat snp16356-scaffold1725-105625 4 10478364 A C 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278140 Affx-1111836273 AX-519551630 4 106623206 ATTAGCTCATGGTCCTACCTACAACTATAATCTCC[A/G]TGGGGGGGAAAAAAAATCACAAGACTATCTCTAAT R 2 1 2 1 102000 f 74 goat Random2.2K-491 4 106623206 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381821 Affx-122974268 AX-123252179 4 106640422 GCTATTTGGATTTCCTTACAGGATAAGAGAAGCAA[C/T]AGGGCAAACACTGCTTCTCAAAACAGGAGTTGAAC Y 2 1 2 1 201000 f 74 goat snp16358-scaffold1725-207680 4 10375824 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441378 Affx-122928857 AX-123311715 4 106670022 CCTTTTTTTTTTTTTCCTATTTCTTCATCATTAGC[A/G]TAAACCTCAGATACGATCTCTGGATTTTGTTAACA R 2 1 2 1 101000 r 74 goat snp16359-scaffold1725-237280 4 10346324 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781400 Affx-122939351 AX-385268485 4 106699188 AGTGTACTAACACAGCAAAGCTTATTAATAAAAAT[A/G]CTTGAAGTCTTATGAAATATCTGAAAAGTAGAAAC R 2 1 2 1 101000 r 74 goat snp16360-scaffold1725-266446 4 10317241 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426481 Affx-122940233 AX-123296827 4 106731950 TTCTTCAAGTATCGTATCAATTTCTCGAAGGTATG[A/G]ACCATTTATCAACAGCATTCCTGTCTTCAGCAACC R 2 1 2 1 101000 f 74 goat snp16361-scaffold1725-299208 4 10292998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272245 Affx-1111833409 AX-519545988 4 106747832 GGCTCCTTTGTCATAGATTAATTGATCATACATGT[A/G]TGGATTTATTTCTGGGTTCTCTATTCTGTTCCATT R 2 1 2 1 303000 f 74 goat 4_106747832_AF-PAKI 4 106747832 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438303 Affx-122931366 AX-123308641 4 106772042 CCTCTCTGAGTTATTGTTAGAAACTAAATCATGGA[C/T]GCACTCTGATTTTGCATTCCCTTTTTGACTAGCCA Y 2 1 2 1 101000 f 74 goat snp16362-scaffold1725-339300 4 10253048 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417956 Affx-122946701 AX-123288304 4 106810114 AAGTCACAGTTTTCCATAAAAAGCTACTCATCTAT[A/G]TAACTTCATTCTTATCTGCAGATTGTAAATATACT R 2 1 2 1 101000 r 74 goat snp16363-scaffold1725-377372 4 10214409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795935 Affx-122977491 AX-385282887 4 106867607 TGCAATAATTTTAATCTTCACTCTAATTTTTCAGA[C/T]GAAGAAATCAAAGTTTCAAGTTATTATGGAACAGT Y 2 1 2 1 101000 r 74 goat snp16364-scaffold1725-434865 4 10156667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415804 Affx-122948899 AX-123286153 4 106904552 AAGGTTTTATTAAGGTGAGGACATTAATATGTTTC[C/T]AAGAGCTTCTACAAGGTATTAATTATAACTGAAAA Y 2 1 2 1 101000 f 74 goat snp53385-scaffold805-1222667 4 10120115 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376370 Affx-122978113 AX-123246729 4 106934883 GTTTGCAAGGTTGAAATTCAGAGGCCTTCACTGAG[C/T]GCTGGGATCAAGCAAGCCAATTCTCTATGAGTCAT Y 2 1 2 1 101000 f 74 goat snp53384-scaffold805-1192336 4 10090238 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384673 Affx-122972132 AX-123255031 4 106994037 TTCACATCATTACACAGTGTTTTATTATTTTCTAA[C/T]GCTGAATTTTCCTCTCTTCTAATTTTAGCCTCCAT Y 2 1 2 1 303000 f 74 goat snp53383-scaffold805-1133182 4 10031390 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787089 Affx-122969551 AX-385274116 4 107027902 AAGCCATGATAAAAATGGTGTCTAGGTTAAGTCTG[C/T]TGTCTAAAATGTACCATCTACTCTACTGAATGCAC Y 2 1 2 1 101000 f 74 goat snp53382-scaffold805-1099317 4 9997659 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386571 Affx-122970703 AX-123256929 4 107078257 TGATGGGTCAGAGCCACAGTGAAGTCAGACTTGAA[C/T]AGGCATGAAGTTCTGAATAATGTGAAGTTCATCTG Y 2 1 2 1 201000 r 74 goat snp53381-scaffold805-1048962 4 9947905 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378004 Affx-122977595 AX-123248363 4 107116204 TCCCCAGACTAAGACTATAAAGTTATTGAGAAAAC[A/G]TGCACAAATCCACTATATATTCTATCCCCTTTCTG R 2 1 2 1 101000 f 74 goat snp53380-scaffold805-1011015 4 9908657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782587 Affx-122963607 AX-385269661 4 107153473 CCTCAGGCTTTTTCAAGAACTTAACACACTGAGTC[A/G]CTACTTTCTCCACAATTATCAACTTTTCCCTCTCC R 2 1 2 1 101000 f 74 goat snp53379-scaffold805-973746 4 9869786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788681 Affx-122926868 AX-385275697 4 107196539 CACAGGCATTCTTCTTTGCTCATGCAAAGTTGAGG[A/C]AAACAGGTTATGTTTTCTCCAAAGACAACCAGCAC M 2 1 2 1 201000 r 74 goat snp53378-scaffold805-930680 4 9827024 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448601 Affx-122923391 AX-123318937 4 107241775 AACTCTATTAAGATTTCCCCTTTAAAAATGCTTTC[A/G]CAGCTCTTAAGTGTATACTATTATCTTCCATTTGT R 2 1 2 1 101000 r 74 goat snp53377-scaffold805-885444 4 9779867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389029 Affx-122968630 AX-123259387 4 107277134 TACTTATATTTCTACCTCATTCTCTCCCTTACTCC[A/G]TCTCTCTCCTTTTCTTTCATTCTACATATATATTG R 2 1 2 1 103000 f 74 goat snp53376-scaffold805-850085 4 9744677 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776643 Affx-122961470 AX-385263770 4 107306264 TAGTTGGATTTTGATATGAGTTTGAACTTGGACAC[G/T]AGGTAAATGTCATCTTGGGTCAATGACTGACCATT K 2 1 2 1 101000 r 74 goat snp53375-scaffold805-820955 4 9715553 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278142 Affx-1111836274 AX-519551632 4 107308408 ACACTCATTTAAGAATAACTGGTTGTACTGAAGTG[A/G]CATTTTTTATTTGGCTGCACAGTGACACTGTGTGG R 2 1 2 1 101000 f 74 goat Random2.2K-492 4 107308408 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797734 Affx-122976641 AX-385284673 4 107338606 CTATTAAAATTTTCCAGAACTCCTTTATTTTTTAA[C/T]GTAATAATTGCAGTAGCCTAAAGGAATAGGAGACA Y 2 1 2 1 201000 f 74 goat snp53374-scaffold805-788613 4 9683448 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772717 Affx-122974963 AX-385259863 4 107396998 TTTAACATGATCCCACACTTCAGGGTTATTAGCCT[A/G]CTTGGTGCTCCTCAGCACAAGAAGAAAGGAGATTG R 2 1 2 1 201000 f 74 goat snp53373-scaffold805-730221 4 9629051 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800880 Affx-122954204 AX-385287795 4 107427836 GTCTAGTAGTTGTTTTTGATCATAAAGATGACAAA[C/T]ACTCAAAGAAAATCCAAACATTAGAGAAAAATATA Y 2 1 2 1 202000 r 74 goat snp53372-scaffold805-699383 4 9597852 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435182 Affx-122933648 AX-123305522 4 107466910 TGTGTCAAGTGAAAGCATTTCTGATGTTCCAATTA[C/T]CTTCAAGTTTCTTTAAAATATCTATTCTCATCAAA Y 2 1 2 1 101000 f 74 goat snp53371-scaffold805-660309 4 9558792 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419421 Affx-122945517 AX-123289769 4 107555942 ACAGTCAAGCAGCCACTAAACACTGGTGCGACACC[A/G]TCAGATCATTCTGTCAAATTAGACTTCTCTTCTCC R 2 1 2 1 201000 r 74 goat snp53369-scaffold805-571277 4 9469558 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431298 Affx-122937090 AX-123301639 4 107587228 TGAAAGATGGAATGTGGTATACACATACAAAGAAA[C/T]AGTATTCAGACTTAAAGAGAAAGGGGATCCTGATA Y 2 1 2 1 103000 r 74 goat snp53368-scaffold805-539991 4 9438548 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783543 Affx-122973415 AX-385270605 4 107632925 TCAAGCTAGTTAAAGTGAGTGCATATGAAAATAAA[C/T]GTTTTAATATTACCTGATAGAAGTAGCCTCCCCTT Y 2 1 2 1 201000 f 74 goat snp53367-scaffold805-494294 4 9392450 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440855 Affx-122929254 AX-123311192 4 107666795 CAAAAGAATAAAAGTTTTCATTTAGTTAAGATGAA[G/T]AAATGTGCAAAAGCCTTGTTGAGGTTAAAAAGAGT K 2 1 2 1 101000 r 74 goat snp53366-scaffold805-460424 4 9358864 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793036 Affx-122976718 AX-385280014 4 107696816 CCATCAAGGGATCTTGTGCTTTGTGTCTAGGCATC[A/G]TTACCATGCATGATAGATGAATTGAGTTTAAGGAA R 2 1 2 1 101000 f 74 goat snp53365-scaffold805-430403 4 9328805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451371 Affx-122921222 AX-123321704 4 107735579 TCATAATGTCCAGATTAATAGAGGCATGTATTATT[A/G]TAACTATTTTACCCAGAACTCCTCTTGAGCTGATT R 2 1 2 1 101000 r 74 goat snp53364-scaffold805-391640 4 9290299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412598 Affx-122951291 AX-123282947 4 107793087 CCCTGTTCCTCCCAAAAGTTCCTTTGAACCTGAAT[A/G]GAGGTGCTATACAAAGATGGACATTTGGTATCTCT R 2 1 2 1 101000 r 74 goat snp53363-scaffold805-334132 4 9232000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774361 Affx-122976645 AX-385261497 4 107842250 TAGTCAATATGAAGAAAAATCTTTTGTCCTGAAAA[C/T]GGTCATGAAATATTATGCAAAGGATGCTAACGCCC Y 2 1 2 1 101000 r 74 goat snp53362-scaffold805-284969 4 9182562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792296 Affx-122968020 AX-385279278 4 107943372 TTGGGGAAAGATATGAGTAGCACAGAAGACTCTGC[G/T]ACAGGCTTCCAATTGACTTAAAGATTCTCCTGAAA K 2 1 2 1 101000 f 74 goat snp53359-scaffold805-183847 4 9082100 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418192 Affx-122947069 AX-123288540 4 108086796 TTAAGGTGATTCACGTTAACTCATTTTTCTTTCCC[A/G]TGTGTCCTGGGCTTGTATTTTATAAACCAGATAGG R 2 1 2 1 101000 r 74 goat snp53356-scaffold805-40423 4 8939735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393612 Affx-122965362 AX-123263968 4 108124660 CACGCCAGCATTTGGGATCTTACTAACAGCCACAG[A/G]TGCTGTAAGCAAGGGAACAAGGCCATCAAACTTCT R 2 1 2 1 101000 r 74 goat snp53355-scaffold805-2559 4 8902856 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399218 Affx-122960599 AX-123269573 4 108136378 CTTGAGAGACCATGAACTTGAGCATGGGAAAGCAG[C/T]ATTTGTCATCTCTGCCCATCCACTCTCCTAGTTTA Y 2 1 2 1 101000 r 74 goat snp25283-scaffold2601-9060 4 8891513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419139 Affx-122945754 AX-123289487 4 108167714 ACTCTATCTCCACCCCTGGGTTCCCAGACCCGTTA[C/T]GCCCCCTCCTAGGGACAGTGCAAACATAATGGCTG Y 2 1 2 1 101000 r 74 goat snp25284-scaffold2601-40396 4 8860021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776923 Affx-122963737 AX-385264047 4 108196377 CATTAATAATAAATTTCCCATCAGACCTGTAAGTT[A/G]TAATTCTTTTACCTCTGCCCCGAGGAACTTGTTTA R 2 1 2 1 101000 r 74 goat snp25285-scaffold2601-69059 4 8831602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436485 Affx-122932966 AX-123306823 4 108314666 GCCTGGATGCAAAATATGTTTATTTCGGATTGTTC[A/G]TAGTTAGGTCATCTGTTTAATTTTAGGGTTCTGAC R 2 1 2 1 201000 r 74 goat snp25287-scaffold2601-187348 4 8713692 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382758 Affx-122973590 AX-123253116 4 108402661 GACGCCCTTCTTTAAAAGGCTCTTCATTCCCAAGG[A/C]TCTGCCGCATCAAGTCATTTGCCATCCACTCCCCG M 2 1 2 1 201000 r 74 goat snp25289-scaffold2601-275343 4 8625530 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396050 Affx-122963456 AX-123266405 4 108461114 TCAGAAGATGCCCAGAGATAAATATTAAGGAAATA[C/T]AGTCCAGAAAGCTTCCCTGTGAAGCCCGAAGCCTG Y 2 1 2 1 101000 r 74 goat snp25290-scaffold2601-333796 4 8566741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418213 Affx-122947054 AX-123288561 4 108492048 TTCGTGTCTAACAAACATACGCCACATCCTACCAG[C/T]AACTATTCTGGGGACTTCCCTGGAGGCCCAGTGGT Y 2 1 2 1 101000 f 74 goat snp25291-scaffold2601-364730 4 8535805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785811 Affx-122938746 AX-385272849 4 108522161 GCTGGCAGTTACTCTTGAATTTAACAAGATAACCT[A/G]CAGGTGTGGAAACAGCACTTTTTAAAATATTATTT R 2 1 2 1 201000 r 74 goat snp25292-scaffold2601-394843 4 8505674 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769906 Affx-122949782 AX-385257075 4 108557622 TGAAGGATTAGAACACCCATGGGATATTTTTTATA[C/T]GTATCTCCTAATCCGAGATGGATTAGCAGTCCATC Y 2 1 2 1 201000 f 74 goat snp25293-scaffold2601-430304 4 8470376 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799275 Affx-122978847 AX-385286205 4 108589216 TTATAGACTAAAGGGATCAAGAGATACCAAGTTGA[C/T]GAAACATGATCTAGAAGTTTATCATTTAAATTATA Y 2 1 2 1 101000 f 74 goat snp25294-scaffold2601-461898 4 8438501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770766 Affx-122975830 AX-385257930 4 108637875 GAATTACTTGTTGATCAGTCAAACAGTTTCCTGGG[C/T]GTTCCTTAAATGATGCCTCTCTTCATTCAAGAATG Y 2 1 2 1 101000 f 74 goat snp25295-scaffold2601-510557 4 8390136 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401241 Affx-122959305 AX-123271594 4 108667854 AAGGTGAAATAAAGGGACAGACTCGAGCTGTGGGC[A/G]CAGATGTTTCAAACTCATGTCTCCCATCCAAGTAC R 2 1 2 1 201000 f 74 goat snp31087-scaffold3433-338560 4 8359252 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436761 Affx-122932280 AX-123307099 4 108706272 CGACCCCATGGACTGCAGCAGCCCAGGGCACCTAA[C/T]AGGGAAGCCCTATTAGGCGCCAAAGTAATGACCAA Y 2 1 2 1 103000 r 74 goat snp31086-scaffold3433-300142 4 8320709 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402627 Affx-122958399 AX-123272980 4 108742729 GGTTTCAGGCGCTCAGCACAAAAACCTCTATTGGT[A/C]CTTCCAGCCTCAGGGCAATGCTCCCCAGCTTACGG M 2 1 2 1 101000 f 74 goat snp31085-scaffold3433-263685 4 8284264 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419325 Affx-122945658 AX-123289673 4 108852619 GGGTAGAAGTTTTAATTTTTGGCAGAGTCGTTAAC[A/G]CCAGTCTTTGCCTTTAAGATCTGTGCTTTTTCTGC R 2 1 2 1 101000 r 74 goat snp31083-scaffold3433-153795 4 8173751 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428070 Affx-122939111 AX-123298413 4 108892240 AGTTAAGGATTCTTCCAAAATATCCAACCGTGGGA[C/T]GTGAACTTACTCCTAGATTTCCCCAAAGTGCCCTT Y 2 1 2 1 101000 r 74 goat snp31082-scaffold3433-114174 4 8134004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442655 Affx-122927907 AX-123312992 4 108922857 TCCTGGAAAAAAATCAAGAGGGTGTGGGCCCCCTG[C/T]ACTGGGTCCTACTCACTGATGGGGAGGGGGCTCCC Y 2 1 2 1 101000 f 74 goat snp31081-scaffold3433-83557 4 8103475 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383401 Affx-122973496 AX-123253759 4 108966623 TCTGTGTACTGAAAGTTTCATTAAAATTACAATCC[A/G]AAGGTTCTGGGGCTGTGGAATGAATTGGGGATGGA R 2 1 2 1 201000 f 74 goat snp31080-scaffold3433-39791 4 8059287 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797695 Affx-122927696 AX-385284634 4 109051609 ACTTTGGACTCATGTTTCTTCAGACTTTGTGTAAT[A/G]TTTTTTAAATGCTGCACTGAGGGGGTAGAGCAAGC R 2 1 2 1 102000 r 74 goat snp16302-scaffold1718-45096 4 7978490 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453195 Affx-122920453 AX-123323528 4 109081891 GCCAGGTATTTCGGGGGAAATCCAAAGGGCGGAGA[A/G]CTAAGGGACCTTGGCAACTGGATGCTCCTGTGAGG R 2 1 2 1 101000 f 74 goat snp16303-scaffold1718-75378 4 7948436 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400930 Affx-122959719 AX-123271283 4 109151936 GTGAACTGAACTCCGTCTTCCAGGCAGAGGAGATC[A/G]TTAGCTCATCCTGAGGTGTCTGTCGTTTGTGATGA R 2 1 2 1 201000 r 74 goat snp16304-scaffold1718-145423 4 7878599 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799156 Affx-122976607 AX-385286086 4 109189716 CTGAGGCCTGCCTGGCCGCGTTTTTATTACAGTGT[A/G]CAAATCAGGGACTATGCAGGCCGTTAGTAAATATT R 2 1 2 1 101000 f 74 goat snp16305-scaffold1718-183203 4 7840691 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778725 Affx-122940616 AX-385265836 4 109270378 TTACACAGTAAATACTCTTTCAAATCTTTGCAAAA[C/T]GCTCAACAGAAAAACTTATTGCCCAACAGATGCCA Y 2 1 2 1 101000 r 74 goat snp16306-scaffold1718-263865 4 7758065 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272247 Affx-1111833411 AX-519545990 4 109293711 ACGGACTGTAACCTGGCAGGCTCCTCCATCCATGG[A/G]ATTTTCCAGGCAGGAGTACTGGAGTGGCTTGCCAT R 2 1 2 1 303000 f 74 goat 4_109293711_AF-PAKI 4 109293711 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378227 Affx-122976915 AX-123248586 4 109304284 ACTATGCTTAGAAGGATTTTGCTCCACTGTTACCC[A/G]TTCAGAGAAAAGCAAGGATCAGGGGACCAACACCA R 2 1 2 1 102000 f 74 goat snp16307-scaffold1718-297771 4 7723311 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773912 Affx-122922731 AX-385261051 4 109323767 TCAATGTGGTAAAAATGATGAAGATAGTGGTGACA[A/G]TGTTGATGAACTTTAGCATCGTAATAATCCTCTGC R 2 1 2 1 101000 f 74 goat snp18280-scaffold1855-396008 4 6618097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783002 Affx-122976785 AX-385270070 4 109404365 TGCAAGTCATGTCACAGATGGTAATTTTTCAAACG[C/T]ACAAAGAACTCCTATAAAGACCAAAACAAAACAAT Y 2 1 2 1 201000 r 74 goat snp18278-scaffold1855-315410 4 6509798 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452129 Affx-122921680 AX-123322462 4 109492773 TGAAGTTGACTGATGGTGAGGACGATGGATGTCTA[C/T]ATTCCTGCCCTGGTGGGGGAAGAGAATGCGTTCCC Y 2 1 2 1 101000 f 74 goat snp18276-scaffold1855-227002 4 6418954 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421146 Affx-122944187 AX-123291493 4 109564610 TTAGCCTGAGGCCACAACTCTCTCCTTGCCTGCCT[A/G]CCTCTAAGCACAGGACGAGGGCTACCTTGTGCCTG R 2 1 2 1 201000 f 74 goat snp18275-scaffold1855-155165 4 6347304 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278144 Affx-1111836275 AX-519551633 4 109691465 GAACTCAGTAAGGTAGAAGTGACCCTATGTAACTA[C/G]TGAGGCTATGTCAGAAAAAGAAAACAAAATAAAAA S 4 1 2 1 101000 f 74 goat Random2.2K-494 4 109691465 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390089 Affx-122968027 AX-123260446 4 109761528 AGTGGGAACAGTAGAAACAAACACAGCCCTGACCA[C/T]GCTCCAGACCTGTTCTAAGATGTGTTACCTTAGAG Y 2 1 2 1 201000 r 74 goat snp5817-scaffold1204-1492506 4 6115719 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436523 Affx-122932940 AX-123306861 4 109860412 CTCGTCTTTGAGATTCTTCTCTATCCTCCTCTATC[C/T]GTACACAGAGGGTTTCCCTACTGTTTGATAGATTC Y 2 1 2 1 101000 r 74 goat snp5815-scaffold1204-1393622 4 6018143 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414254 Affx-122949621 AX-123284603 4 109923025 AACAAAGCCACAATAATTAAAAACACACAAACAAC[C/T]CTATGGTTCTGGCTCAGGAACAAACCTACAGGTAC Y 2 1 2 1 101000 r 74 goat snp5814-scaffold1204-1331009 4 5955115 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432868 Affx-122935354 AX-123303209 4 109959413 GGCGCTTGGAGGAGGAACAGAATGGAGCTTGTTCT[A/G]CAGAGGGAGTCGAGGGTGTTTTTCAACCTCTCCTT R 2 1 2 1 101000 r 74 goat snp5813-scaffold1204-1294621 4 5918247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278146 Affx-1111836276 AX-519551635 4 109976836 AGGGTACAGAGTGATGCAAAGTATTGGTTTGTATG[A/G]GATAGTCAGGAAAGGCTTCTCTGAGAAGGTGACCA R 2 1 2 1 201000 f 74 goat Random2.2K-495 4 109976836 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435784 Affx-122932862 AX-123306123 4 110020958 ACTGAATTTTAAGTTTAACCCAAATCTGGTCCTCT[A/G]CCGTGCTTTCTGATAGATGAGAAGAGAAGGCCTGT R 2 1 2 1 101000 f 74 goat snp5812-scaffold1204-1233076 4 5856240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394905 Affx-122964326 AX-123265260 4 110057477 CTTACCTGGGACGTGATTGTGCAAGATAAAGCATT[A/G]TGAAATCTTTAGTGCTCACAGTTGAGAGAACCTTT R 2 1 2 1 101000 f 74 goat snp5811-scaffold1204-1196557 4 5820055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802612 Affx-122952867 AX-385289514 4 110109751 AACATTGTCCACTTATAAAAGGCTTTCAAGTAGAA[A/C]GCAGGACATAAATGTAATTTATTTCACTGTATTAT M 2 1 2 1 202000 r 74 goat snp5810-scaffold1204-1144283 4 5768064 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420007 Affx-122945165 AX-123290355 4 110237504 CAGCCCGATCGCTTTTACATCTTATCAGAACCTTG[A/C]GAAAGCCTCATTCGCCTGCTCCTCATCAGGCGTTT M 2 1 2 1 101000 f 74 goat snp5807-scaffold1204-1016530 4 5640592 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386595 Affx-122970687 AX-123256953 4 110322594 TATATGGCAGACAAAGGGGTGAGTCACGTCCCGGT[C/T]GGGATGGAGCAGGATGGTGCAAGGTTTCATCAGCT Y 2 1 2 1 201000 f 74 goat snp5805-scaffold1204-931440 4 5556595 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392955 Affx-122965689 AX-123263312 4 110393376 ATCCATGCTCTTTCTCCTGCAGACTTTTCTTGATC[A/G]TGCTCCGAGTCCTTATGGGGTGGAGCAAAGACAGA R 2 1 2 1 101000 f 74 goat snp5803-scaffold1204-860658 4 5484351 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411551 Affx-122951646 AX-123281901 4 110430057 TGTTCATCCTAAATGCTGAGGGGTGTGATATGACA[C/T]GTAAGAGAGGGTGTGAGCTGAGTGGCTGGGCTGCC Y 2 1 2 1 101000 f 74 goat snp5802-scaffold1204-823977 4 5447663 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438692 Affx-122930866 AX-123309029 4 110459805 TTACTCACAAGAGCAAAATCTGGAAAATGTCCACA[C/T]GTTTAACAAGAAAAAGAGAAGGTAAATAATTTAAA Y 2 1 2 1 101000 f 74 goat snp5801-scaffold1204-794229 4 5417572 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453285 Affx-122920381 AX-123323618 4 110490398 ACAAAATTTTAAAATTTTCACAGAGAAATTGTAGA[C/T]TTCTGAGGAACACTGATACAAACTAATCTAATTTA Y 2 1 2 1 201000 r 74 goat snp5800-scaffold1204-763636 4 5387546 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397438 Affx-122962229 AX-123267793 4 110592386 TAAGGTTCCAAACGCCACTGCTGTGAGGGGGAGCC[A/G]TCACAGATGGCCATGGCAACAGAGCCTCTGCGACT R 2 1 2 1 201000 r 74 goat snp5798-scaffold1204-661648 4 5284383 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412198 Affx-122950941 AX-123282548 4 110628232 AGCAGAGCATGGTTCAGAAGCAGCTGGAGCAGGTA[A/G]CACACGGCTTGGCCAGACAGTCTGCTCTCGATTAG R 2 1 2 1 201000 f 74 goat snp5797-scaffold1204-625802 4 5248467 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379051 Affx-122976344 AX-123249410 4 110753993 TGTCCTTTAAGTGTCATTTATTTATTTGTATTTAC[G/T]CTTTGGAGAATGGTGAACTGTCCTGTAAACACTTA K 2 1 2 1 101000 r 74 goat snp5794-scaffold1204-500041 4 5122339 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443366 Affx-122927414 AX-123313703 4 110785072 CCATTCTCTGCTTTGTTTCCTTCTATTCATTTCCT[A/G]TCTTCTTTGGGTTAATTGAATATATTTTTAGGATT R 2 1 2 1 201000 r 74 goat snp5793-scaffold1204-468962 4 5091177 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382830 Affx-122973548 AX-123253188 4 110867895 GAGACTGCAGTCTCCCATCACCTCACTTCTGCCCC[G/T]ACATGCTGCTCTTTTCCCAGAGACAGAGAAACTCA K 2 1 2 1 201000 r 74 goat snp5791-scaffold1204-386139 4 5007847 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423218 Affx-122942704 AX-123293564 4 110897654 CTGGGAATCAAACCCAGGTCCTCTGCGTTGGGAGC[A/G]TGAAGTCTTAGCCATTACAGCACCAAGGGAATTCC R 2 1 2 1 103000 r 74 goat snp5790-scaffold1204-356380 4 4977824 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386672 Affx-122970190 AX-123257030 4 110930872 ATGGCCATCCTGTTTGTCTCTAAGCTCACTGTCTC[A/G]TTTTCAGAACTTGGTGGGCAGTTGTTTTGTTTATT R 2 1 2 1 101000 r 74 goat snp5789-scaffold1204-323162 4 4944453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415302 Affx-122948818 AX-123285651 4 111036349 CCTTGTCTAGGGACTGCTTTTGTTGTGAGTTGAGG[A/G]GGAACCAAACTGTCGGCAGGCAATAAGTCATCAGG R 2 1 2 1 201000 r 74 goat snp5787-scaffold1204-217685 4 4839020 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432805 Affx-122935404 AX-123303146 4 111093736 TATTGGGAGTTTGTTCTGGGTCACTGGGAATGTTC[A/G]TTATGGCTCTATAAAAATGTTGGTGATGTCCACCA R 2 1 2 1 101000 f 74 goat snp5786-scaffold1204-160298 4 4781134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396996 Affx-122963145 AX-123267351 4 111122236 TTCAGCACCCAAAACGAGCCCAGAAATAAGCAACC[A/G]CACAGACCAATGCAGTACGCAAGGAGAGCGGAATC R 2 1 2 1 101000 f 74 goat snp5785-scaffold1204-131798 4 4754092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441526 Affx-122928713 AX-123311863 4 111178252 ACTGCCCATCAAGAAGCATCACTAGTCAACACACC[A/G]CCAAGTGTGTCCTGTGAGAGAAGGAAAGCTTGACC R 2 1 2 1 201000 f 74 goat snp5784-scaffold1204-75782 4 4698186 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787372 Affx-122934231 AX-385274397 4 111263608 CAGCTGACTAACCAGAAGTCTAAGGAAACACTTGC[A/G]CATCTCAGGAGGTATGGGATGCGAACATTTGCTTG R 2 1 2 1 101000 f 74 goat snp27042-scaffold2876-9475 4 4610737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440780 Affx-122929848 AX-123311117 4 111334657 CCTGTGAATGCAGAAAAGAGAAGGGGCAGGAATCC[A/G]TCTGTCTCCAAGATGCACAGTGTTCAGGAAGCACA R 2 1 2 1 201000 r 74 goat snp27043-scaffold2876-80524 4 4538930 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762313 Affx-986696844 AX-385250493 4 111338450 AGTATTAATACCTAGTCTTCCAGTTAAGAATTTTT[A/G]TAGCACTATTAAATATTTCTTCAAGGATTTTTTCC R 2 1 2 1 600010 f 74 goat 4_111338450 4 111338450 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320773294 Affx-122954386 AX-385260437 4 111367291 AAGTTTGGAACTGTTAACACCATACATCTTATATC[A/G]TTGACTTTCCATAGATCTTCTGAAAAGAAAGCCTC R 2 1 2 1 101000 f 74 goat snp27044-scaffold2876-113158 4 4506126 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278148 Affx-1111836277 AX-519551637 4 111391309 GCACAGGGGCAGACGTTAAAGCTAAGGAGCAGGAT[A/G]GGCCTTTCAACCTAGTCAGGCCAATCCAATTTACA R 2 1 2 1 101000 f 74 goat Random2.2K-496 4 111391309 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380778 Affx-122975107 AX-123251136 4 111398348 GTATTCTCTCTCCTGCATGGAGCACCATGCTGGGG[A/C]AACGATAGAGATGTCACACATACCTGGCGATCGGT M 2 1 2 1 201000 r 74 goat snp26966-scaffold2859-19792 4 4474769 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408386 Affx-122953718 AX-123278737 4 111514263 ATGTCTCCTATTTATAAGACGAGGTGCTATGAAAA[G/T]AGAGGATTGTTTCAAAACCCAAAATGATGTTTATA K 2 1 2 1 101000 f 74 goat snp26969-scaffold2859-135707 4 4356801 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422099 Affx-122943576 AX-123292446 4 111549514 TCTTTGTACCGTTACAATGTAGTTACCATGAAGAC[A/G]GGAACTGAAGCTCTCAGGGGTCGAGTGCCTTGCCT R 2 1 2 1 101000 f 74 goat snp26970-scaffold2859-170958 4 4321707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393957 Affx-122965058 AX-123264312 4 111563778 CCCTTGAGTAACCCTCCCCATCAAGCCTTCACTCC[A/G]CTCCTGTCAGCCACCACTGTACCCTCTGCTGCTGT R 2 1 2 1 101000 r 74 goat snp42422-scaffold5605-48780 4 4307391 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395779 Affx-122963667 AX-123266134 4 111592956 GGTCTCGGGGGGAGAAACATCTCTCCACCAAGAAA[C/T]ATCAGATGTTTCCTTCCACAGGGCTGGAACTCTAC Y 2 1 2 1 201000 f 74 goat snp42421-scaffold5605-19602 4 4277728 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770543 Affx-122929383 AX-385257707 4 111627929 AAGGAGGTAAGAGTGTTCAGCCTTCCAATGATACA[A/G]AAGTTCTTTGCAGCAGAGGAGGTTTTTGCTTTGGG R 2 1 2 1 101000 f 74 goat snp1898-scaffold1053-15272 4 4243192 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801096 Affx-122978866 AX-385288010 4 111665251 TTTCCGGAATGTCAGAAAACATATATTAGTGACAA[C/T]AATCATATACTTTACACGATCTGTGTTCTCTTTCC Y 2 1 2 1 101000 f 74 goat snp1899-scaffold1053-52594 4 4206251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802021 Affx-122921718 AX-385288925 4 111753628 CTATTCTCTTCCAATTCCTTGGAAAGGATTTAGAT[A/C]CTAATGGGGATAAAAGTTGCAAGTAGGTACACAAA M 2 1 2 1 102000 r 74 goat snp1901-scaffold1053-140971 4 4118764 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454040 Affx-122919408 AX-123324373 4 111810220 CTGTACACCCCCAAAGTAAGGGCTACAAGTCCTCC[A/G]AGCCACACAGAGAACATCCTGGGCACCTCAAGATG R 2 1 2 1 101000 r 74 goat snp1902-scaffold1053-197563 4 4062212 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799274 Affx-122953573 AX-385286204 4 111839134 AAATAAAGAGCTTTTCAACAAGAGCTTAAGGATTA[C/T]AGAGATAAGCGTGTGAAGAAAAGTGTGAAACTGGT Y 2 1 2 1 101000 r 74 goat snp1903-scaffold1053-226477 4 4033243 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401656 Affx-122959577 AX-123272009 4 111888692 ACCATTGCCTCCATCTCTAACAGGAAGACAGACAA[C/T]GGCTGGGTTGAGACCTGGAGGTCAGATTTTGCCCA Y 2 1 2 1 101000 f 74 goat snp1904-scaffold1053-276035 4 3983763 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464325614 Affx-1110429532 AX-515799565 4 111949642 CACCATCACCAGGGCCCATTTTAAACCAAGGAAAG[C/T]AACCCACAGCCCCCAGGACAAATCCCTGCCCATCG Y 2 1 2 1 101000 f 74 goat 4_111949642_AF-PAKI 4 111949642 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38421526 Affx-122943881 AX-123291873 4 112002258 AGGCCGTGTCACTCCCAGCGTGGCTCGAGGATTAC[A/G]TAGTGTTCCTTTCCCAAAGGCGACGATGCTCCCTG R 2 1 2 1 101000 r 74 goat snp1907-scaffold1053-389601 4 3874484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413476 Affx-122950659 AX-123283825 4 112038983 GCAGACTTTCAAAGGGAGGAGGACCAGGAACAGGA[G/T]CTCTACCCTCGATCTGTCCCCGTTCTGCCTGAGTC K 2 1 2 1 201000 f 74 goat snp1908-scaffold1053-426326 4 3837029 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767722 Affx-122962469 AX-385254956 4 112069519 GCCAAAGACATGCCGCAGGCAAATGGCATTAATTT[A/G]TCTAAGCCAAAACAGTCATTAGTATGGCTTTAAAC R 2 1 2 1 101000 f 74 goat snp1909-scaffold1053-456862 4 3806475 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796776 Affx-122945784 AX-385283719 4 112099303 TGTCCCAGTGTTGCTTGGAGCTTTCAAATTCTCTA[G/T]CAGGTGATCTAAAGTGGATTCACTGATTCATTACA K 2 1 2 1 101000 f 74 goat snp1910-scaffold1053-486646 4 3776556 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428132 Affx-122939062 AX-123298475 4 112154732 GGTGCCCGGAGCGGAACCTGCTTGGTGACACCAGC[A/G]CATGTATTCTGATGACTCAGAAGGCAAGCTATTTA R 2 1 2 1 101000 r 74 goat snp1911-scaffold1053-542075 4 3721258 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387151 Affx-122970639 AX-123257509 4 112203394 TCCTTAGTCTGCCTGTAGACTCTTGAGTGCCCTGT[A/G]CATGGGTGACAAGTTCAACCAAAGATAAAGTCCCT R 2 1 2 1 101000 r 74 goat snp1912-scaffold1053-590737 4 3673372 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427984 Affx-122939179 AX-123298327 4 112242077 TCAGTTAACATTATAGATTATGTCACCAAGCAGTT[A/G]ATTTAGAGTGTCATTGCTTTGCAGCTTGTATCCTG R 2 1 2 1 101000 r 74 goat snp1913-scaffold1053-629420 4 3634608 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790216 Affx-122922482 AX-385277220 4 112296876 CAACAGTCAATTTTAGGTGGATCATATGCCTAACC[A/G]TAAAATCTAGAATGATGATGGATATATTAATAGTC R 2 1 2 1 101000 f 74 goat snp1914-scaffold1053-684219 4 3579266 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421931 Affx-122943833 AX-123292278 4 112355698 ACCGCATTTCACAAAAGTTTCACAAAATAATACCC[A/G]TCCCAGGAACTGTCTGCACTTGTATTTTCTGTTTG R 2 1 2 1 101000 r 74 goat snp1915-scaffold1053-743041 4 3520714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441020 Affx-122928947 AX-123311357 4 112418416 GTGTTGAGGGCAGTAAGCTTTAGTGATACTGCGTG[C/T]GTGCATGCGTGCTGAGTCGTTTCAGGCCTGTCCGA Y 2 1 2 1 101000 f 74 goat snp1917-scaffold1053-805759 4 3456926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430576 Affx-122937003 AX-123300917 4 112453311 AGCAGAAGAAATGACCACTAATGTGATTTCTGAAA[C/T]TAACGAGAGTCTTCTTTAGGGAGGGAGCTTAGAGA Y 2 1 2 1 101000 f 74 goat snp1918-scaffold1053-840654 4 3422573 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404630 Affx-122957323 AX-123274982 4 112482275 ACATATCATATCGTATAAATGATGGTCAGAAGCCA[C/T]GCACTCTGAGTTGGGGACTCTCTGTTCAAATCAGT Y 2 1 2 1 201000 f 74 goat snp1919-scaffold1053-869618 4 3393563 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273834 Affx-1111833847 AX-519547445 4 112491500 GACCTCTGCAGAGATCAAG[A/G]TTTATTACATTTCTGTGTCTCAGCTGTTATCTTCT R 2 1 2 1 101000 r 74 goat GoatD01.007134 4 112491500 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443213 Affx-122927578 AX-123313550 4 112522172 GAAATGAAAAGCTGCTCAATCAGTGAGATCTGATC[A/G]CTTCTTGTCATTGGCCAGTGATTTCCTCGCATAGA R 2 1 2 1 101000 f 74 goat snp1920-scaffold1053-909515 4 3354380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780191 Affx-122972085 AX-385267287 4 112557290 AATTCAGATTCAAACCTATAAACAGCTGCACTGGT[A/G]TCTATAAATAGCTACATTGTATTTAACCAAAGTCT R 2 1 2 1 101000 f 74 goat snp1921-scaffold1053-944633 4 3321554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441793 Affx-122929086 AX-123312130 4 112633603 TTAGCATATCTTTTTTACTACTAAACTCTTTTAAT[A/G]TTATTAAACTTATAGCTTAACTAACAGCCTTGAAC R 2 1 2 1 101000 r 74 goat snp1923-scaffold1053-1020946 4 3245681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405176 Affx-122956931 AX-123275528 4 112682397 CTCACCACGAGTACCAGAGAGCCATTCCCTTGAAA[C/T]GTAGGACTGTTCTTTGATCCAGAACTGGGTTCAGT Y 2 1 2 1 101000 r 74 goat snp1924-scaffold1053-1069740 4 3196377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436415 Affx-122933018 AX-123306753 4 112721100 TGACCCATGTTCATTCATCAGCTATTCATATAAGT[A/G]CCAACCTTGCTTCTAAATCACAGAAGAAAGCTCTC R 2 1 2 1 101000 f 74 goat snp1925-scaffold1053-1108443 4 3159243 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780955 Affx-122972755 AX-385268042 4 112752034 GGACTGCGTGGCCTCTTTAATAAATTCGAAGCCTC[A/G]TGAACACCATTCTCACTTCGTGAAGAAGCAAAGAA R 2 1 2 1 101000 r 74 goat snp1926-scaffold1053-1139377 4 3128247 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394948 Affx-122964289 AX-123265303 4 112812968 AATCTCGTTTAGTCCATTTGGTGATGCTGTTTCCG[C/T]AGGCTTGATTAGCTTCAAGGACAGTGAAAAATTAG Y 2 1 2 1 201000 r 74 goat snp1928-scaffold1053-1200311 4 3068376 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446778 Affx-122925312 AX-123317114 4 112854118 GAGGCCTCTGCCCAGGATGCACACCCAGCGCTTGC[C/T]GAGTCACTCCTGCTTATATGCAGGGTACTGACCGT Y 2 1 2 1 201000 f 74 goat snp1929-scaffold1053-1241461 4 3027223 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389695 Affx-122968694 AX-123260053 4 112932771 AAATTCAGCTTCTGAATTTCTGAGCTTCTTCATCC[C/T]GGCTTGTATCCCAACTGCAGTGGCTGCCCGGTTGT Y 2 1 2 1 101000 f 74 goat snp1930-scaffold1053-1320114 4 2949686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409157 Affx-122953208 AX-123279508 4 112976174 GGTTAAAATTGTTAAAAGTTAGTTTCAGATTTCTC[C/T]TTACTGATTTATGATCAAATATAAGTGTTTTGTTG Y 2 1 2 1 101000 f 74 goat snp1931-scaffold1053-1363517 4 2909497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798326 Affx-122960393 AX-385285261 4 113043453 CACTAGACCATTTACTGCTGAGGGCAGGAACTCGC[A/G]TACTCTCACTGTTGGTGAAGAGTTAGCTAACTGAC R 2 1 2 1 202000 f 74 goat snp1933-scaffold1053-1430796 4 2842530 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403268 Affx-122957867 AX-123273621 4 113111866 GACCTTCATTCATTCGCTCAAACGTTACCTATTGC[A/G]AAGGGAAGAAGTCCACTAGCAGATTAAATTGCTTT R 2 1 2 1 101000 f 74 goat snp1934-scaffold1053-1499209 4 2775189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397091 Affx-122962710 AX-123267446 4 113141053 TCAAAGGACGCGGTGAGCACAGTGCACTCACTCGA[C/T]GGCACAGCCCACGTTGGGCCCGGTATGCAAGTCCT Y 2 1 2 1 201000 r 74 goat snp1935-scaffold1053-1528396 4 2746300 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395882 Affx-122963625 AX-123266237 4 113243617 GTGATCAGTCATTTAAAAACCTTTCTTCATTCATC[A/G]TCTTATTTTCCCCATGTGGACTATCTCAGTGAACA R 2 1 2 1 101000 r 74 goat snp56264-scaffold8805-4754 4 2645141 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441586 Affx-122928671 AX-123311923 4 113303617 GGGGCAGTGGCTGGTGTGGCCGCGGTGCTGGGAGA[C/T]GGCTTCCAGGGGGCGACATGGGTCCCCCCAAGAGG Y 2 1 2 1 103000 f 74 goat snp19460-scaffold1965-55147 4 2585014 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431339 Affx-122937059 AX-123301680 4 113334440 TTCAGAGGATTACTTTTGAACCTGGCACTTCTGGA[C/T]GGCAAGTAAACCCAGACTCATCCATGTGTGTGTCT Y 2 1 2 1 101000 f 74 goat snp19461-scaffold1965-85970 4 2554216 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278150 Affx-1111836278 AX-519551639 4 113361909 GGTCGGATCTCGTCTGCTATGTGGTGCAGCCAAAA[A/C]CAAAGAAATAAATGAATACTTGCATAGAAGAATCA M 2 1 2 1 103000 f 74 goat Random2.2K-498 4 113361909 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425618 Affx-122940907 AX-123295964 4 113365196 TTCTTACGGATGCAGGAATGTTGTTCCTATTTGGC[C/T]GGGTGCTGAGCATCTTCACTAATTTAGCTGCACCA Y 2 1 2 1 101000 f 74 goat snp19462-scaffold1965-116726 4 2523203 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774093 Affx-122964658 AX-385261231 4 113436637 GAATATGGACCTAAAATAAAAACAGATAAACGGTT[A/C]TTTCTTAAGATGTTAAAGTAAGATAAAAATTGTCT M 2 1 2 1 101000 f 74 goat snp19463-scaffold1965-188167 4 2453038 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398083 Affx-122961725 AX-123268438 4 113490813 GAAACCAAAGATCCCACTGAACACCCAAACCTTCA[C/T]ACAGTTCCCCAGTCTCCTCACTGCGGCCCAGAGCC Y 2 1 2 1 101000 f 74 goat snp19464-scaffold1965-242343 4 2401794 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780731 Affx-122932691 AX-385267821 4 113514257 TTTGCTCATTCATTGTTTATGATACATTTTCATTG[C/T]GCTTGAATGATATTCAGTTAATCAAGGCACAGGAT Y 2 1 2 1 101000 r 74 goat snp38319-scaffold4847-17621 4 2382743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379074 Affx-122976325 AX-123249433 4 113551771 AGATGCAATATTTAAAAATCTAGTATATAATAAAA[C/T]GTGCATTTCACATTAGTGGGGAAAGAGTAAGTTAT Y 2 1 2 1 202000 f 74 goat snp38320-scaffold4847-55135 4 2345608 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278153 Affx-1111836279 AX-519551642 4 113562775 AACGTGCAAGCACATAGCTAGAGGGGCTAGCCCAG[A/G]TGTGCACACGATGGCAGGGCCAACGGCAGGGGTCT R 2 1 2 1 102000 f 74 goat Random2.2K-499 4 113562775 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430291 Affx-122937282 AX-123300632 4 113601120 TGTACCCAGCGACAGTCTGCCCGGGAAGGAGGCTC[A/G]TCTCATCTTAAAGAAGCAGGGGACCAAACAGACGA R 2 1 2 1 101000 r 74 goat snp38321-scaffold4847-104484 4 2297584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395246 Affx-122964470 AX-123265601 4 113654734 GCCGCCGTCAAAATCCTGCTTTTGAGCTGGTCGGA[A/C]GAACGCTGGTATTCCGAAGGCCACTCACAGTTGCA M 2 1 2 1 101000 r 74 goat snp38322-scaffold4847-158098 4 2250260 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388993 Affx-122968655 AX-123259351 4 113770980 CTCAGTGGATCTGTTTTGTATGTTGGACTTCCCTG[C/T]GAGGTTTCCTCTGAAGCGTGTGGTGTCTTTGATGA Y 2 1 2 1 101000 r 74 goat snp20992-scaffold2056-470017 4 2134001 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382067 Affx-122974920 AX-123252425 4 113806205 TTTCAGTCTTGCTCACCCCACGTGCACGCAGCCTG[C/T]ACTCCATGTCAGCTGTGCTTTCCAAGTATATGCGG Y 2 1 2 1 201000 r 74 goat snp20991-scaffold2056-434792 4 2098922 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447373 Affx-122924860 AX-123317709 4 113838709 ATTGTATAAATTGCTTTGGAAAGACACAGCTGCCC[A/G]TTTTATCTCCCCTCAAAGGATCTGTCTGTTGAAAT R 2 1 2 1 101000 r 74 goat snp20990-scaffold2056-402288 4 2066412 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424488 Affx-122941754 AX-123294834 4 113878140 ATCTGGTTCTGAGGTTGATGGGGCCCAGTGATCAT[C/T]CTGGACCTTCTAGAACCTTGATGCTTCTCTGGACT Y 2 1 2 1 201000 f 74 goat snp20989-scaffold2056-362857 4 2027049 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441959 Affx-122928568 AX-123312296 4 113908043 AGTGACCGGTCCAGTCTGAGAGGACAGTGTGTCAG[C/T]GGGAGGAGTCCTTTCTTTCATATGTCTCGTGCAAA Y 2 1 2 1 101000 r 74 goat snp20988-scaffold2056-332954 4 1997388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450272 Affx-122922176 AX-123320607 4 113943774 ATCCTCAAGTGTGGCATATTGAGAAACCAGAGTTC[A/G]GTGTCTAAAGGGGAGTGTCCTTATAAGAGATTAAT R 2 1 2 1 201000 f 74 goat snp20987-scaffold2056-297223 4 1961864 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385168 Affx-122971742 AX-123255526 4 114020152 GCCAGAGCCTTGCTTTCTTGGAGGTTGGCGGCTGC[A/G]TTTGTGAAAATACCTGTAGCGAAAATCCATTGTTT R 2 1 2 1 101000 r 74 goat snp20985-scaffold2056-220845 4 1886015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422598 Affx-122943735 AX-123292944 4 114089311 GAGAGGATGGTGTCATATAAGAAGCATTTTAGAGA[C/T]GTGGATGTAGACACAGGGTGTGGTCCATGCCTGTA Y 2 1 2 1 101000 f 74 goat snp20983-scaffold2056-151686 4 1816351 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382464 Affx-122974212 AX-123252822 4 114139903 AAGTGGTCGGATTCTCAGAGACGCAGAGGAAACTC[A/G]TGGTTGCCAAGGTGGGGAGAGGGGCGGGGAGTAAG R 2 1 2 1 101000 f 74 goat snp20982-scaffold2056-101094 4 1764953 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408349 Affx-122953744 AX-123278700 4 114185583 GGTAGAGTGCCACAGGAACCCGTCTGCTGCCCAGC[A/G]TAATAGCTATGGTAGGGTGGGTCACGCCACCATGC R 2 1 2 1 202000 f 74 goat snp20981-scaffold2056-55414 4 1719317 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430759 Affx-122937493 AX-123301100 4 114228256 TCAGTGTTTATTAAACTACCTATTGTGTGCCTAGC[A/G]TTGTGCCATCAAAAAAAATAAAAAGTGTTACAGAA R 2 1 2 1 102000 f 74 goat snp20980-scaffold2056-12741 4 1676585 A G 1 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38427190 Affx-122939602 AX-123297533 4 114255764 TAAGTTTGTGTGACTCTCTGAATCGCTTGCTGTCA[C/T]CTCAGCAGTCTTCACAGTGTCTTTACCAGGAATGG Y 2 1 2 1 201000 f 74 goat snp20847-scaffold2044-855182 4 1648971 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453344 Affx-122919957 AX-123323677 4 114321536 TGGCTCTCTTATACTTCCAAAATCTAAAAGTTAAA[C/T]GAAATATTCCTTTGAAGTCATCTTTATTGGAAAAC Y 2 1 2 1 101000 r 74 goat snp20845-scaffold2044-789410 4 1583212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405843 Affx-122955867 AX-123276195 4 114350251 AATCATGATAGAATTATGGAAATGCCTCCATTTGT[A/G]CATATTTCACGATCACATACAAACTCGATGTGTGA R 2 1 2 1 101000 r 74 goat snp20844-scaffold2044-760695 4 1554221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476195 Affx-1251763700 AX-586011621 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 4 1 4 1 20000 f 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 539476450 Affx-1251763700 AX-586011851 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20000 r 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 562165269 Affx-1251763700 AX-606940681 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20100 f 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 562165819 Affx-1251763700 AX-606941228 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20100 r 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 562165905 Affx-1251763700 AX-606941314 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20100 f 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 562165988 Affx-1251763700 AX-606941397 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20100 f 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 562166560 Affx-1251763700 AX-606941968 4 114404703 ATCTCTTGATTGGCGTCTGGTGACACAAGTATGAT[-/CAAAATGTAGCACAGGGGGGAGAGGGAAAGATGGCGGAGGAAATTTTAAAATTTAAAAAAAAAATAAAAAAATTAAAAAA]AAAATGTAGCACAATATATATATAAGCTGTGAAAA - 8 1 4 1 20100 f 74 goat SV_373 4 114404703 - deletion junction SV-TF-chip 38423648 Affx-122942351 AX-123293994 4 114466374 ACACAGCAGATGACAATGCCACGTGTAGACGAGCC[A/G]CTGTCACGGGGGAGTTCTCGCTCATCTTTCTCGTG R 2 1 2 1 201000 f 74 goat snp20842-scaffold2044-644572 4 1438969 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797852 Affx-122951541 AX-385284791 4 114503388 ATGATTCTAAGGGTACTTGATGATAAACTCAAATC[A/G]TCCCAGGCATTTTCAACACATTCATTTCTGCTCAT R 2 1 2 1 101000 r 74 goat snp20841-scaffold2044-607558 4 1401747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464335124 Affx-1110430661 AX-515808991 4 114523140 CTGTGGTAGAGTTCCTTCATTTGCTCAGCCTTCAT[A/G]TCTAAGGAATATGACACAACCTGCCAAGTCATCTT R 2 1 2 1 201000 r 74 goat 4_114523140_AF-PAKI 4 114523140 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426028 Affx-122941121 AX-123296374 4 114556716 GCGTCATATTCTGCAAGTTCTAAGTGTAAGCAAAC[A/G]TTGTGTAACTGGGAAACGCCCAACCAAGGCACACC R 2 1 2 1 101000 f 74 goat snp20840-scaffold2044-554230 4 1348638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399245 Affx-122960577 AX-123269600 4 114657935 GAAACCCTCGCCACGCTCTACACCGCTCCACCCCA[C/T]GCACAACAAACCAACCCACAGTTTCGTGTGGTTCA Y 2 1 2 1 101000 r 74 goat snp20838-scaffold2044-453011 4 1257240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375929 Affx-122978465 AX-123246288 4 114700929 CCCTCAGACGTGATACAGAACCTTCTATGGGGACC[A/G]CAGTTCACAGACCCCCCTGGGCCCCCCAAGATAAC R 2 1 2 1 101000 f 74 goat snp20837-scaffold2044-410017 4 1224434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424198 Affx-122942508 AX-123294544 4 114735513 TGTCACTCACCATAAGCGAATTTATCAACATGTAC[A/G]GAATCGGAATACACATGAGAGTTTTAACTGTTTGC R 2 1 2 1 101000 f 74 goat snp20836-scaffold2044-375433 4 1191971 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400285 Affx-122960085 AX-123270640 4 114799477 CACCTGACGACCTGGGATGAAGCTATCACGAGTGC[A/G]TGATCCCCAAAGGCACTCCTGCAAGACGGGAGGTG R 2 1 2 1 101000 f 74 goat snp20834-scaffold2044-311469 4 1133115 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797398 Affx-122952673 AX-385284337 4 114920183 GACTTTTTATACTGCTTTTAAGTCATTTTGGTAGT[A/G]CAGGTAAATTAGGAACCCATTCTACTTAAAACTCA R 2 1 2 1 201000 f 74 goat snp20832-scaffold2044-190763 4 1020488 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445081 Affx-122926210 AX-123315418 4 114964055 GCTGGACAGTGTGACGACAGCATCGCCGTAATTGC[A/G]TCCTGTCCCCACGCCATCCTGCTGGGCCTGTGTCC R 2 1 2 1 101000 f 74 goat snp20831-scaffold2044-146891 4 977273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376674 Affx-122978999 AX-123247033 4 114999710 TTGTATACACATGTGGTGTGTTACATGTGTGCGTG[C/T]GTGTGTGCGTGTGTGCATGTGTACACGTGTGAGTG Y 2 1 2 1 103000 f 74 goat snp20830-scaffold2044-111236 4 942730 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377155 Affx-122978219 AX-123247514 4 115036030 CTGAAAAACTGTCTTCCAGAGTGGCTGTGCGTTCG[C/T]GCCAAGTCACTTCAGGCATGTCCGACTCTCTGCAA Y 2 1 2 1 103000 f 74 goat snp20829-scaffold2044-74916 4 909586 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409904 Affx-122952892 AX-123280255 4 115108601 TGGGTCCTTGGGGTCGGGGCACATTGTAGAAGCAC[A/G]TCAGCGACAAAAGAGAGAAAAGATGTAATCATTTT R 2 1 2 1 201000 f 74 goat snp20828-scaffold2044-2345 4 858890 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452889 Affx-122920221 AX-123323222 4 115114235 AAATGGGACCATTGGAATGGGAGCAGCAACCTCCC[A/G]TCCCACAGTATCTCAGGCCTTGAGTGTGACCGAAA R 2 1 2 1 101000 r 74 goat snp24717-scaffold2522-628716 4 851551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392601 Affx-122966052 AX-123262958 4 115182057 GACTTCCAGCCTCACTACCAAGTGAATCACGTGAG[A/C]AAGGCCGAAGCTGGTTTGATTTTTTGTGCTGTGAC M 2 1 2 1 102000 r 74 goat snp24716-scaffold2522-560894 4 783452 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769050 Affx-122920242 AX-385256225 4 115216900 CCTTAGTTGGATGAAGACGCACATGTTTAAGAAGG[C/T]GACTGAGATGATGAGGATGTGGGAATTTTGTCAGT Y 2 1 2 1 101000 r 74 goat snp24715-scaffold2522-526051 4 750270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410541 Affx-122952156 AX-123280891 4 115252040 TGTGTTCACATGTTAACACCCCTGAAACCAGCGTG[C/T]ATCCTACACCAATAGCGCGTCATCGTTTACCTTGC Y 2 1 2 1 101000 r 74 goat snp24714-scaffold2522-490911 4 715411 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446451 Affx-122925077 AX-123316787 4 115288986 CTGGACTTGTGTGCGTTAAGTGCAGATTGCTCACT[A/G]ATGGGCACGATCCTCACCTGCTTGGTCTGGGAGAG R 2 1 2 1 101000 f 74 goat snp24713-scaffold2522-453965 4 680392 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389117 Affx-122968562 AX-123259475 4 115330846 GTGGGAGAACATTCTATGGAGGATGCCAAGAATCC[A/G]CTGGCAGCTGGAGGTTGCAAGACTGGACTGGAAGA R 2 1 2 1 201000 f 74 goat snp24712-scaffold2522-412105 4 642534 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444279 Affx-122926769 AX-123314616 4 115373814 TTGCCTTCTTCTAGAGCGTATTGTCAGCAGAACCC[A/G]TATCAGAGATGTCAGCGAGGCCGTGGAGACTGAAA R 2 1 2 1 201000 f 74 goat snp24711-scaffold2522-369137 4 600146 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378944 Affx-122976428 AX-123249303 4 115440920 GGTAATTTGTTTTATATAAGCCTAGGAAATAAACC[A/G]CTTTCCAGATCTACTTTCTCCTTAGAAGAAAGGCT R 2 1 2 1 101000 f 74 goat snp24710-scaffold2522-302031 4 534565 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384128 Affx-122972818 AX-123254486 4 115477722 GCTTCACGGAAGCCCACACATGCTGGAGTATGTAG[C/T]GTATCCCTTCTTCAGTGGATCTTCCTGGCCCAGGA Y 2 1 2 1 201000 f 74 goat snp24709-scaffold2522-265229 4 498220 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441238 Affx-122929503 AX-123311575 4 115506942 AATTAATAGTAATTCAATGTATCTGGGTTAAGGTT[C/T]TTCAGAAACTGAGAAAGAAATTATTTCAAGTGACT Y 2 1 2 1 101000 f 74 goat snp24708-scaffold2522-236009 4 469314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380087 Affx-122975544 AX-123250445 4 115537623 CTGGGGATGTTTGTGTGGGTTTCCTACTCACGCCC[A/G]TTTGTCACAGGTGTGTCCGTGGCTCCCTTAGATAA R 2 1 2 1 101000 r 74 goat snp24707-scaffold2522-205328 4 442512 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765121 Affx-122947895 AX-385252681 4 115609878 GTGTAAAATATAGATCTTGGTCCTGTGAAGAAACA[A/G]TTATGAACAACTGACTAGTCACGTAGTGTTCTCCT R 2 1 2 1 201000 f 74 goat snp24705-scaffold2522-133073 4 370795 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794874 Affx-122956667 AX-385281834 4 115655238 TCATGTTCACTCAACTAACGACAAATGTCTTCTAG[A/G]TGCACTTAGGAACCACTTCTGCTCACTGCATCTAA R 2 1 2 1 101000 r 74 goat snp24704-scaffold2522-87713 4 325835 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398006 Affx-122961788 AX-123268361 4 115727811 GAGGTCCATAGGCAGTGGGACCTTGTTCTCCCACC[A/G]CAGGAGCCAGTTTGGACCCAGGCTCGGACCACGCT R 2 1 2 1 201000 f 74 goat snp24703-scaffold2522-15140 4 255223 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382115 Affx-122974884 AX-123252473 4 115771875 ATGCCCTGGCCACTGTAAACAGTGCAGTGATGAAC[A/G]CTGGGATGAACCTTTCTTTTCTAATCAGAATCTTC R 2 1 2 1 201000 r 74 goat snp18259-scaffold1851-28825 4 211277 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402674 Affx-122958362 AX-123273027 4 115815185 TGCCTTATTTTGGGATACCCTAGAAATTAAAGCAG[C/T]GTTAAGCGTAACAATTCCTGCAGCTCTTCCGCGCT Y 2 1 2 1 101000 f 74 goat snp18260-scaffold1851-72135 4 173068 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392650 Affx-122966445 AX-123263007 4 115852329 TCCGTCTAGAACAGACATACTCTGATCACCAGTAC[A/G]TTTTCACTTGGATAAAAATAGAATTCATTTAGCTG R 2 1 2 1 101000 f 74 goat snp18261-scaffold1851-109279 4 135700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278158 Affx-1111836281 AX-519551646 4 115856329 CAGTGAACTGAACTCCTGGGTACACAGTTTCTTTG[A/G]TCAGTTAGGTTCTTACTGGAACTTGAGAGCCTTTG R 2 1 2 1 101000 f 74 goat Random2.2K-502 4 115856329 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378854 Affx-122976524 AX-123249213 4 115884268 AACGATTTATCTAAGTCTTGACCAAAACCTCAGCT[A/G]TACAGAACACGGCTGAGAGCCCAGTGGAAAAAGAC R 2 1 2 1 101000 f 74 goat snp18262-scaffold1851-141218 4 103204 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385230 Affx-122972101 AX-123255588 4 115925391 GTTGGTCACTAGGACCTTCTGCAGTGTATATAAAA[C/T]GCCTTCCAAAATCATCCGCTAAAGAGGTGAAGGCA Y 2 1 2 1 101000 f 74 goat snp18263-scaffold1851-182341 4 62511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278160 Affx-1111836282 AX-519551649 4 116868085 CAGCTGCTATATAATCATGTATTATATAGCAAAAC[A/G]TGGGATGAAGGCAAGAGGCCATGGTGCACAAGAAC R 2 1 2 1 201000 f 74 goat Random2.2K-504 4 116868085 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272085 Affx-1111833412 AX-187122616 4 117691937 GGCTGTAGTCACCATCTGCAGTGATTTTGGAGCCC[A/C]CCAAAATAAAGTCTGTCACTGTTTCCATTGTTTTC M 2 1 2 1 303000 r 74 goat 4_117691937_AF-PAKI 4 117691937 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278321 Affx-1111836283 AX-519551807 4 118968983 TACGACTGAATTGAACTGAACTGAAACTAAAGAAA[A/T]TGGCTAAATGCTTCCATTTAAAGACCTAATATCCA W 4 1 2 1 201000 r 74 goat Random2.2K-509 4 118968983 A T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272088 Affx-1111833413 AX-519545849 4 120216251 ATTAGCATGGAGAGAACAAAAATCTGATTGGTGTA[A/G]ATATGGAAAGAATTGAAGTAGAAAAGTTGGAAATG R 2 1 2 1 101000 r 74 goat 4_120216251_AF-PAKI 4 120216251 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320804311 Affx-986696775 AX-385290926 4 120290244 GCTGAATGAGGAAAGAAAATTATAATTACTGGAAA[G/T]TAGAAAGTAAAACTGTCTTTATTTGCCAGCTAGAT K 2 1 2 1 600010 f 74 goat 4_120290244 4 120290244 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320764489 Affx-986696857 AX-385252166 4 120290258 GAAAATTATAATTACTGGAAATTAGAAAGTAAAAC[G/T]GTCTTTATTTGCCAGCTAGATTCTGTATATAGAAA K 2 1 2 1 600010 r 74 goat 4_120290258 4 120290258 Ancestral_priority_1043 ancestry 0.692 neutral IMAGE 10K 10K ancestral 320764500 Affx-986696863 AX-385252177 4 120290297 TTTATTTGCCAGCTAGATTCTGTATATAGAAAATT[A/C]TAAGGAATCTGCAACCAAAATATGAAAAAATAATA M 2 1 2 1 600010 r 74 goat 4_120290297 4 120290297 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 320762334 Affx-986696865 AX-385250508 4 120567632 CGGAGGCGGGCATGAGACAAAACACCTCTAACTCC[C/T]TGAAACAGCGAGGACTCAGGATCCCTACCCACACC Y 2 1 2 1 600010 f 74 goat 4_120567632 4 120567632 Ancestral_priority_1043 ancestry 0.592 neutral IMAGE 10K 10K ancestral 38396611 Affx-122962890 AX-123266966 5 22890 CATGTCTCCACTCGAGACGAGGACTGACTCCCCTG[G/T]GGAGACTCCAGAAGTACCCCATGATCCATGTCAGC K 2 1 2 1 103000 r 74 goat snp38525-scaffold487-1150834 5 28849 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375413 Affx-122979197 AX-123245772 5 102188 ACTTGCCTGACAGGTTTGTCTGGACTTTTTCTACT[A/G]CACTTGTGTTTGTTTACAACCTCCCACGCGAGAGG R 2 1 2 1 101000 r 74 goat snp38524-scaffold487-1071536 5 108900 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431592 Affx-122936174 AX-123301933 5 234968 TTCATCTCAAGTTTCAGTGCTGGACCCAGGGTTAC[A/G]CTAGAGCCATGGTGGAGAATGTAGTGTGCCTATCG R 2 1 2 1 101000 f 74 goat snp38522-scaffold487-938756 5 242032 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397865 Affx-122962449 AX-123268220 5 267098 GCTCAGCCCCAAATCCTTAGCACCCTGAATGCAGG[C/T]GCTGGAAGGGCCAGCCCCCTTGTGTAGTAGGGACA Y 2 1 2 1 201000 r 74 goat snp38521-scaffold487-906626 5 274017 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272178 Affx-1111833461 AX-519545930 5 276213 CACCGCAGCCTCAGAGCTGCCTCACCAGCACAGAC[A/G]CTCTCCAACCGTAACAACTGGAACTGCATCCATGT R 2 1 2 1 102000 r 74 goat 5_276213_AF-PAKI 5 276213 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320770457 Affx-122952540 AX-385257623 5 319322 ATTGTTGATATATTTATTATCTTGATGGGGGACAC[A/G]TGTTTCCAACCATATCAAATTATACACTTTAAACA R 2 1 2 1 101000 f 74 goat snp38520-scaffold487-854402 5 327050 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388179 Affx-122969438 AX-123258537 5 431566 GCCCAATATTTTGACTCCATGTCTAAAAGTTTTCA[C/T]TAGACCAGACAACTTATTTGAAACAAATGCTTACC Y 2 1 2 1 101000 f 74 goat snp38518-scaffold487-742158 5 439743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799301 Affx-122951475 AX-385286231 5 469026 GAAGCTGGATAGAAGAATGCAGTTATCCATAATTA[C/T]GGCAGAAACATACCAAAGAAGAAGTTGAAGATTTG Y 2 1 2 1 202000 f 74 goat snp38517-scaffold487-704698 5 478263 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454021 Affx-122919422 AX-123324354 5 540200 TCCCTGGATTTCCCAATCCTTATCAGGGAAATAAC[A/G]TCTCCAAGATTCCCTGAAGCTGTTTTGTTAGGTGT R 2 1 2 1 101000 f 74 goat snp38516-scaffold487-633524 5 550031 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401989 Affx-122958771 AX-123272342 5 606053 AGTCCAAAATGGAATATTTTTTCATTCTTGTTTCT[A/G]CATTCAAGGAGGTAGGTGAGGTTACTCACATAATA R 2 1 2 1 101000 r 74 goat snp38515-scaffold487-567671 5 616218 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788540 Affx-122971798 AX-385275557 5 639191 TTGAAAAATGAGCTGAAGACTCACAATGCCAAATA[C/T]GCCCTCTAGTATAGAGTGATGGTGATAATGGGAGG Y 2 1 2 1 101000 r 74 goat snp38514-scaffold487-534533 5 649407 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427339 Affx-122940120 AX-123297682 5 673882 AGGTTTCCCTCTGCCTACACAAAAAGTCCAGACTC[A/G]TTGGCAGAGCATGAAAGACTCTTGTGTGTCTCTTT R 2 1 2 1 201000 f 74 goat snp38513-scaffold487-499842 5 684201 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449554 Affx-122923245 AX-123319889 5 739997 TGTTTCCTTGTCTAGAGAATAACCTGATTGGCTTA[G/T]ATGATTATAAATTGTATTCAGTGACCCTTCAGTAG K 2 1 2 1 101000 f 74 goat snp38512-scaffold487-433727 5 751276 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771201 Affx-122959174 AX-385258360 5 772860 ATCATCTCTTTAAGCATAATTACTCAAGTGAGATT[A/G]TTGCTGAGTTGTTGGCATCCAGGGGCATGTATCTG R 2 1 2 1 102000 r 74 goat snp38511-scaffold487-400864 5 785693 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779172 Affx-122959456 AX-385266276 5 801675 TACTTCCCTGCTTTAGTCTAGGGGACATAGCATTC[A/G]TGTTTACTGGGCATCTTTTGTGTGCCTGGTGACAC R 2 1 2 1 101000 r 74 goat snp38510-scaffold487-372049 5 814257 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795695 Affx-122927920 AX-385282648 5 848039 CAACACATATGGATGCTACAAATGCCACTAAGTGA[C/T]GAAGATGACTAATATTCATAGTTAAAATTCAACCA Y 2 1 2 1 101000 f 74 goat snp38509-scaffold487-325685 5 861055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426553 Affx-122940179 AX-123296899 5 897556 CAATCATGATTAAATTTCAGTTTTGCCCTATGTAA[C/T]GTGACCTTAGGTATACAGCTTAGTAATTCTGGTAA Y 2 1 2 1 101000 r 74 goat snp38508-scaffold487-276168 5 911555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448766 Affx-122923315 AX-123319102 5 942776 ATCATCTGCATATCTGAGGTAAGATGCTGAAGGTA[C/T]TCAATGTTAATTCTGCTACAAAGCTTGCTCTGGAT Y 2 1 2 1 101000 r 74 goat snp38507-scaffold487-230948 5 953004 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771537 Affx-122968405 AX-385258695 5 980933 CTTTCTGGCTCAGAATCTTCCAGTGGATTCTCATT[A/G]CTTTCATAATAAAGTCTAAAATCCACGACATGTCC R 2 1 2 1 101000 f 74 goat snp38506-scaffold487-192791 5 990534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441755 Affx-122929120 AX-123312092 5 1017825 ACATGCTCTCCAGGTCTCCCTTTTCCAAGCGACAG[C/T]AGAGCCTGGTGTAGGCGACGGTCGTCACGAGGAAG Y 2 1 2 1 201000 r 74 goat snp38505-scaffold487-155899 5 1027487 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431965 Affx-122935959 AX-123302306 5 1071689 TAAGTGAGGATTGGTATGATTTCTAAGAAAGTTTT[A/G]TTGGCTTGTGTCTTTTCTAACTTGTTTTGAAAAGC R 2 1 2 1 101000 f 74 goat snp38504-scaffold487-102035 5 1081890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417769 Affx-122947399 AX-123288117 5 1163092 CAGAAAACTCACCCTCATCCCTGCCATCTGTCTGT[C/T]GGCCTGATCTTGGTCTCTTCATCCCCGTATCTAGC Y 2 1 2 1 201000 r 74 goat snp38503-scaffold487-10632 5 1174059 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801173 Affx-122943857 AX-385288086 5 1211298 CACGATCAAACCCTTCTAGAATGTAAGTTATATCA[C/T]CTGAAGTTAATATAAGATCAATGATCTAGACCCCG Y 2 1 2 1 101000 f 74 goat snp33879-scaffold399-2325009 5 1221605 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779298 Affx-122969505 AX-385266402 5 1250915 AGACATTAAGCAATTTGACTGACATCACTAGTAAG[C/T]GTGAAGTTAGTTTTCGAAACTGGCTTGGCTCTCCA Y 2 1 2 1 101000 r 74 goat snp33878-scaffold399-2285392 5 1261542 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440728 Affx-122929886 AX-123311065 5 1286691 ATTCATGATTCATTAGCTTCACGTTGCATTTTATA[C/T]AGTTTCTTATTCAATCAATGTTGGTAATTTTTAAA Y 2 1 2 1 101000 f 74 goat snp33877-scaffold399-2249616 5 1297127 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438449 Affx-122931253 AX-123308787 5 1338422 GGATCAGTTTCCGGAAAGACTGATTCCCCCATGTC[A/G]CTTCTTTCTTGCTCCCGTTTTTCTGGCTGAATTCC R 2 1 2 1 303000 f 74 goat snp33876-scaffold399-2197885 22 21012306 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392811 Affx-122965964 AX-123263168 5 1378732 TCTTCTTTTTGTATTCTATGCCAGTATCCCACATG[C/T]GGGGTACAAGGGGACATTCTTTAATAGCTGTATAT Y 2 1 2 1 101000 f 74 goat snp33875-scaffold399-2157575 5 1388224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783281 Affx-122958920 AX-385270346 5 1435540 TGGTTAAACTTGGGGAAAAACTCAAGTGTGAAGTC[G/T]AGGTAGTTTGGGCCCTAGATCCTAAATAAAAACTT K 2 1 2 1 101000 f 74 goat snp33874-scaffold399-2100767 5 1444916 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464332608 Affx-1110433058 AX-515806509 5 1439425 ACTTTCAGAGCAAAAATAATGTAACTGCAGCTCCT[C/T]TCAAGAGCATGGTGAGTCATTTGGTTGTACAGAGA Y 2 1 2 1 101000 f 74 goat GoatD01.026425 5 1439425 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38440544 Affx-122929323 AX-123310881 5 1470207 AAAGTATAGAAGCTGGCCACAGCTCCAGCTTCTAT[A/C]CTCTATTTCTTGATAAGCTGTAAAAGTAAACTATA M 2 1 2 1 101000 r 74 goat snp33873-scaffold399-2066100 5 1480291 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781489 Affx-122960466 AX-385268574 5 1501010 CTTACAACAAAAATTACTAGTATTCTTATGTCTCC[A/G]TACCGAAAGCAGACAAAAAGCTTTTATCTGCAATT R 2 1 2 1 101000 r 74 goat snp33872-scaffold399-2035297 5 1511491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412566 Affx-122951318 AX-123282915 5 1557865 GGTGGGAGGAGGTCAGAGCCACTCACATCAAAAGC[A/G]CTTTATTAATCAGAAGAGAGCTGGGGACTGGAAGC R 2 1 2 1 201000 f 74 goat snp33871-scaffold399-1978442 5 1568670 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418440 Affx-122946482 AX-123288788 5 1589020 AGCATGACAGTGTGACTCAGACACAGGACAACCTG[C/T]AGGCGAGATCTTGGAAGACATAAGCCATGTAATGC Y 2 1 2 1 101000 r 74 goat snp33870-scaffold399-1947287 5 1599869 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376308 Affx-122978363 AX-123246667 5 1676686 TCTCTGTCCAGGGGATCTGTGGTTCCAACTAGAAC[G/T]ATTCTGGATTTCTCATGAAAAACCATAGCAATCAA K 2 1 2 1 101000 f 74 goat snp33868-scaffold399-1859621 5 1687465 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787234 Affx-122978330 AX-385274260 5 1723169 TCAAATATGCATACTTGATGCTCTGCTTCCATTCA[G/T]CTGTATATTAAGATGCTTTTCAAGTTACTCTCTCA K 2 1 2 1 101000 f 74 goat snp33867-scaffold399-1813138 5 1733976 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779125 Affx-122953213 AX-385266230 5 1836843 TGGAAAAAAATGATCTTATGGTTCCACCATTGTAG[C/T]AATGAGCTAAGGTTTAGGAGCTGTATAATTTTGAT Y 2 1 2 1 101000 f 74 goat snp33865-scaffold399-1699464 5 1847297 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773324 Affx-122925028 AX-385260466 5 1899086 TTGGAAAATGGGCCATTTCCATTCTTATTTTCCAC[G/T]AATTTTCAAAGATATTCCCATAATAGTTCAGCAGA K 2 1 2 1 101000 f 74 goat snp33864-scaffold399-1637221 5 1909651 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796101 Affx-122978170 AX-385283053 5 1939114 TGCATGACAGGCCTAACTTTGTCTTTGAACAAAGA[C/T]GTTGCATCCTGATTTCTGAATGGAAAATACTGTTT Y 2 1 2 1 202000 f 74 goat snp33863-scaffold399-1597193 5 1949073 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392520 Affx-122966115 AX-123262877 5 1969077 TATTGCACTGAGGGATATGTGATGATGTATTAGAG[C/T]GGGCGTTACTGAAGGACTTTTGAATCTGAGAGAGA Y 2 1 2 1 101000 f 74 goat snp33862-scaffold399-1567230 5 1979075 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446155 Affx-122925755 AX-123316491 5 2005940 TTCTGCATGATTATACATTCAATGCATACGTTTGC[A/G]TCAGTTGCTCAGTTGTATCCAAATCTTTGAGACCC R 2 1 2 1 201000 f 74 goat snp33861-scaffold399-1530367 5 2016169 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802876 Affx-122971051 AX-385289774 5 2040781 GCACAGTGCGCTTTGGCATTGCATAATTAGCTCCC[A/G]TTCTCCTATCTCTTGTCCTGACTATCTCTGCTCAT R 2 1 2 1 101000 r 74 goat snp33860-scaffold399-1495526 5 2051367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772249 Affx-122958336 AX-385259404 5 2100804 GAAGCTCACCACTGTTGTGCATTTTGGATATAAAC[A/G]TATTTCACATCTCAAGTAACAGAACTATGGACATC R 2 1 2 1 101000 r 74 goat snp33859-scaffold399-1435503 5 2112670 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432371 Affx-122935864 AX-123302712 5 2133523 AAGAATGTACACTGAATGCTTGCATTATCTGCTCA[C/T]CAACATAAAATAAGCAAGATTTGTTTATATAGAAA Y 2 1 2 1 101000 f 74 goat snp33858-scaffold399-1402784 5 2145620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430228 Affx-122937324 AX-123300569 5 2165226 AGTGCCGTGAAACCGAAATGAGAATTATCCTGAAG[C/T]ACCATAAATGTTTTGAAAAGAAGAATACATAAATA Y 2 1 2 1 101000 f 74 goat snp33857-scaffold399-1371081 5 2177381 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440586 Affx-122929292 AX-123310923 5 2194693 AAATGAAGACTGGGCAAATTGCTGTAACTGAAATC[A/G]CCTTGAACTGATGAGAAACTGCATGCCCCTAATCA R 2 1 2 1 101000 f 74 goat snp33856-scaffold399-1341614 5 2207100 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417834 Affx-122946792 AX-123288182 5 2244014 CACTGTAGTGTAGGAAGCTTCCACACAGAGCTATG[C/T]CAAATTCTTTTAATATTCACCTCAGACTTTTCATG Y 2 1 2 1 101000 f 74 goat snp33855-scaffold399-1292293 5 2258598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397565 Affx-122962014 AX-123267920 5 2282826 ACTGAGTGAGTAAGCATGTCTAAGCACCTGAAGAC[A/G]TGAACAGAAAGGAGAATAACACATACAGAGACTGA R 2 1 2 1 202000 f 74 goat snp33854-scaffold399-1253481 5 2293959 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379423 Affx-122976110 AX-123249781 5 2314647 CAGACTGTTCCCTTTGCTTCTAACTCCCTTCCCCC[A/G]TGTCAGCTCATATCTCCTAGTTCTTGCCTAGGAAG R 2 1 2 1 101000 r 74 goat snp33853-scaffold399-1221660 5 2326548 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797899 Affx-122937490 AX-385284837 5 2460736 CTTTCCTTAGAAGGTCCTTCTAATTCTATATAGCA[C/T]AGTGTCTATGTTGCTTTGTTCAGAGGTGACTACTT Y 2 1 2 1 101000 r 74 goat snp33851-scaffold399-1075571 5 2471520 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432203 Affx-122936384 AX-123302544 5 2493778 AATAGATTCCATTGATATTTTGTTCTGATTGGCTC[A/G]AGCTACTGTCAGTTTTATTGAACAACTCTATATTT R 2 1 2 1 101000 r 74 goat snp33850-scaffold399-1042529 5 2504861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790267 Affx-122946394 AX-385277271 5 2526878 TCAGATCAGAAGGATGTCTATTTATCTTTCAGGTG[A/C]TTGTTTTAAACTGATTCCAAACGCATATATGTGTT M 2 1 2 1 101000 f 74 goat snp33849-scaffold399-1009429 5 2538157 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414474 Affx-122949557 AX-123284823 5 2588950 AAGATGAGATTGCAGAAGGACACAGATCATGTGAG[A/C]CGTTATAGGCCATGATAAGATGCTGAGATTTTATT M 2 1 2 1 201000 r 74 goat snp33848-scaffold399-947357 5 2601724 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780140 Affx-122949360 AX-385267237 5 2647243 AGAATTCATGGTCAAGGCTTGGCAGAACCAGTTCA[C/T]GCATGTTTAGAACAGGCAGCTTTCTTTGTGATGTG Y 2 1 2 1 101000 f 74 goat snp33847-scaffold399-889064 5 2661152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776602 Affx-122925038 AX-385263729 5 2736542 AAATCAATGCACTTAGAGAATAAGCCAAATCAGTC[A/G]TTAAATAAAAGATAGCATTTTCACCCATCTAAACT R 2 1 2 1 201000 r 74 goat snp33846-scaffold399-799765 5 2750802 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800506 Affx-122936040 AX-385287426 5 2785311 AATTATGATATTAGTGGAAATGGTATCACTCAGTG[C/T]GGACTTAGGATATCATTTTATATGCAAAATGTTAC Y 2 1 2 1 101000 f 74 goat snp33845-scaffold399-750996 5 2795956 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773001 Affx-122926737 AX-385260145 5 2814502 GTATGGAGATCAATACGCTTAAAAGATTTATAAGG[A/C]AAAGTGAGATGTTTCTCAAAACAAGTAGGCCTAGA M 2 1 2 1 101000 r 74 goat snp33844-scaffold399-721805 5 2825337 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278165 Affx-1111836284 AX-519551654 5 2832184 CAAGTAATTGGTAGGGAATATCTGTTTCATGAAGA[A/G]AGAATATTCATTTTTTTCTTTATAATATAATTCAA R 2 1 2 1 101000 f 74 goat Random2.2K-511 5 2832184 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390564 Affx-122967208 AX-123260921 5 2845709 GCTTTGCTGTTCTTAGGGGGTGGCATTTGTCTGTG[C/T]GATCCAGATGGCTTTTTAGTTCTTCCACACTTTAA Y 2 1 2 1 103000 f 74 goat snp33843-scaffold399-690598 5 2857312 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383322 Affx-122972691 AX-123253680 5 2896095 CTGGCACAACACCTAAGTCCACCATTCAGAACCCA[A/G]GCACTCACTCCTTGAGCTGCCAGGTATATTGCCAG R 2 1 2 1 101000 f 74 goat snp33842-scaffold399-640212 5 2908117 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272304 Affx-1111833462 AX-519546043 5 2946267 CAGACACGACTGAACAAATGAACTGAACTGAACTG[A/G]ACTGAACTGATGAGACCAGATGCCATGATCTTAGT R 2 1 2 1 103000 f 74 goat 5_2946267_AF-PAKI 5 2946267 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394312 Affx-122964685 AX-123264667 5 2952043 AGGATTTATGCTTTCTGTTGGTAATGGCCAGTTCT[A/G]TTTATTATGAAATAAGTCCTGATAAAAATTGATCA R 2 1 2 1 102000 f 74 goat snp33841-scaffold399-584264 5 2963602 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440012 Affx-122929780 AX-123310349 5 2994494 ATAACAGTGTACTTGGTCTTCTCTCTTGTACATCT[A/C]TTTTTGTAACCCCTATCCAAATGTTCAGAAAGAGC M 2 1 2 1 201000 r 74 goat snp33840-scaffold399-541813 5 3006775 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443969 Affx-122927001 AX-123314306 5 3066672 TGAAAATGGGTATGTCACTTAAGAGAATGGAGAGG[C/T]AATTAGGGGCCAGTTCAGGCAGTACCTGGTAGGAC Y 2 1 2 1 201000 f 74 goat snp33838-scaffold399-469635 5 3080386 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430497 Affx-122937231 AX-123300838 5 3117946 AAATTTTAAGTTTATATAAAATTATACTCTAGCTG[C/T]GAGTGTTGTTGCATATGTTGGAATAGTTTCAGTAA Y 2 1 2 1 102000 r 74 goat snp33837-scaffold399-418361 5 3130943 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794639 Affx-122964265 AX-385281600 5 3163711 GCCAGATCTCTCAGATAGTACTTCTCAAACTATGT[A/G]TGGTAAAAGACTATTTTTCCCCTCTGCATCAGAGA R 2 1 2 1 202000 r 74 goat snp33836-scaffold399-372596 5 3177027 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431481 Affx-122936256 AX-123301822 5 3192218 TAAAGAGCTTTGACAACGTTATATTAAATATAAAG[C/T]ATGGAAGAACTATGTTTACACTGATATGAGGGTCC Y 2 1 2 1 101000 r 74 goat snp33835-scaffold399-344089 5 3205500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426784 Affx-122940548 AX-123297130 5 3233290 CTATAGAGGGATCTAAGAAAAGTGAAAAGAGAGAA[C/T]TAAAGAAATGTAATATGATGAATACTTCCAAGGAG Y 2 1 2 1 303000 r 74 goat snp33834-scaffold399-303017 5 3245241 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435918 Affx-122932761 AX-123306257 5 3276713 AGGCAATGAACAACACAGAAATGAAATTGTAAATA[A/C]AAAGCATTGTGAGGCACAGAAGAGTGGTGCTAGTA M 2 1 2 1 201000 f 74 goat snp33833-scaffold399-259594 5 3288723 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799816 Affx-122931978 AX-385286742 5 3312323 TTAAGGGTTCTCACCTGTGAACAATTACTTGTTCT[A/G]TCAACAGTATTAGAATAAATGGATGGTCTTAGCAA R 2 1 2 1 101000 f 74 goat snp33832-scaffold399-223984 5 3328188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437201 Affx-122932050 AX-123307539 5 3342461 ATCTGTATCAGAATTACCTGAATTGTTCATTGAAA[A/C]TGCTGACAGCTTAACCTCCCCCAGGACAATAATAT M 2 1 2 1 201000 f 74 goat snp33831-scaffold399-193846 5 3358775 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384250 Affx-122972357 AX-123254608 5 3372214 AATTACCAAGATAATCAATCATACAATCACCTTTT[A/C]TTTTTCTGGAAATATCTAATCCAGAAGAAGACTAT M 2 1 2 1 202000 f 74 goat snp33830-scaffold399-164093 5 3388252 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783961 Affx-122967004 AX-385271015 5 3402667 AATTACACATGTTTTGTTTTGATCTGAAGATTATC[A/G]TTCTTAAATTTAAATGTTATCTATTTGGCTACCAT R 2 1 2 1 303000 r 74 goat snp33829-scaffold399-133640 5 3419485 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408682 Affx-122953448 AX-123279033 5 3459064 ATTGGGTAGATTGCTTGTCTCTATTTAACTTAGTC[A/G]TTTTTCTTATATTTTGTCTTTTCCTTCATTTGAAA R 2 1 2 1 101000 f 74 goat snp33828-scaffold399-77243 5 3475878 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404832 Affx-122956636 AX-123275184 5 3487621 ACATGACTACTGGAAAAACCATAGCCTTGACTAGA[C/T]GGACCTTAGTCGGCAAATAATATGCCATGCCCATA Y 2 1 2 1 303000 r 74 goat snp33827-scaffold399-48686 5 3504386 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768557 Affx-122946159 AX-385255737 5 3545385 AAAATTTTCAAAATTTGAGCAAACATCAGTTCTCA[C/T]GGGAACGCATCCAGCTGAAAGTGGTTAGGAGCTTT Y 2 1 2 1 101000 r 74 goat snp19014-scaffold1911-8979 5 3558208 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440682 Affx-122929920 AX-123311019 5 3574084 CTTCACATCAATGTCAACCTTCCCTTGGCAGCTTA[C/T]GCACTGACTTCTGGCTACAGCTCCACCAAGCATAG Y 2 1 2 1 101000 f 74 goat snp19015-scaffold1911-37678 5 3587924 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397276 Affx-122962341 AX-123267631 5 3608837 TACCACAAATCCTACTAGCTCCCAGAATCTTCCTC[G/T]CTGGAAGCCATCTTGACCAAGCAATGCATGTGCTA K 2 1 2 1 201000 r 74 goat snp19016-scaffold1911-72431 5 3623276 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786981 Affx-122941782 AX-385274009 5 3691732 CAAGCTGAAGAGACAAACACAGATACAAAGAGTCA[C/T]AAGGAACCCTTTCCTAAAATTCTACCTTACCAAAG Y 2 1 2 1 101000 f 74 goat snp19018-scaffold1911-155326 5 3707367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423903 Affx-122942283 AX-123294249 5 3842269 TTTGGACATAACTGATGGACAGGCCTTTATCGTTG[A/G]GCCGCAGTGGGACACCTCTGCTCTCTCAACCTTGG R 2 1 2 1 101000 f 74 goat snp19022-scaffold1911-305863 5 3857314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770951 Affx-122935945 AX-385258115 5 3896620 AACTTAGGACGCATGCATACTTAATTGCAGACTAA[C/T]ATTTTAAGAAAATATGAAGTGATAGACCTGCTCCA Y 2 1 2 1 201000 r 74 goat snp19023-scaffold1911-360214 5 3912927 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788569 Affx-122961735 AX-385275586 5 3926484 GACCACAGCCATTACAAAAATGCCCTGCAAATATA[C/T]AGCATTCTGTATTTACAACAACCTGCTTCCCTCCC Y 2 1 2 1 101000 r 74 goat snp19024-scaffold1911-390078 5 3943394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398132 Affx-122961694 AX-123268487 5 3964374 TCAGGTTTTCAATTCGTTTCACAGAAGCTAGTTCT[A/G]TCTAAAAAGGAAGGAAATAACTTTATCAAAAGGAT R 2 1 2 1 103000 f 74 goat snp19025-scaffold1911-427968 5 3981275 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278167 Affx-1111836285 AX-519551656 5 3978285 CATGATCCAGGGGAACCCTCAGGAGAAATGGCATT[A/G]GCAAATGAATGAATAAATGAGAGAGGAATAGAGGA R 2 1 2 1 303000 f 74 goat Random2.2K-513 5 3978285 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418223 Affx-122947047 AX-123288571 5 3998060 AAGACAGATCTTCAGGTCCTAAAGTATGTCTGTTC[A/G]TGTTCCACATGCATTCTAAAGGCTCTGTGAAGCAA R 2 1 2 1 101000 f 74 goat snp19026-scaffold1911-461654 5 4014996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448067 Affx-122924342 AX-123318403 5 4045145 CAAGTGATGCAGACACTACTCAGCCCCAGATCATT[A/G]TTGATTTGAGGAAACATGGGACAAGCATTGCAAAT R 2 1 2 1 201000 r 74 goat snp19027-scaffold1911-508739 5 4062602 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420747 Affx-122944726 AX-123291094 5 4075822 TTCTGCAAGAATTCACACAAAGCTTGCAAGTGAAA[C/T]GGACAGTTATCTTCAAAATCCAAGTGGTAGGGGTA Y 2 1 2 1 201000 f 74 goat snp19028-scaffold1911-539416 5 4093263 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380456 Affx-122975737 AX-123250814 5 4109459 TCAGAATTTCACCTAAAACAAATAATTTTGATACG[C/T]AGGGTAATATATTTAGACACAAGATATGTGAGCTC Y 2 1 2 1 101000 r 74 goat snp19029-scaffold1911-573053 5 4127835 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780072 Affx-122969128 AX-385267170 5 4146591 GTTATAGAGTTTATATGATACATAAAGATAAAGCA[C/T]AGAAAGCATTTGACCTGACATACAGCTAGCATATA Y 2 1 2 1 101000 r 74 goat snp19030-scaffold1911-610185 5 4165404 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388310 Affx-122969377 AX-123258668 5 4188498 TCATTAGAGACACTTTACAGCAGCTTTTACATTAA[C/T]AGTAAAGTGAAGTGTTAGTTGCTCAGTCATGTCCA Y 2 1 2 1 303000 f 74 goat snp19031-scaffold1911-652092 5 4200640 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434118 Affx-122934930 AX-123304459 5 4227973 TGCTTAGAGTGATTTGCTTAAGGCCTCTGATTCTA[C/T]ATCCAGTCAATATTCCATTGGCTACTCATTAAAGA Y 2 1 2 1 101000 f 74 goat snp18733-scaffold1895-555496 5 4255662 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389438 Affx-122968355 AX-123259796 5 4268370 CACTTAATCTTCTCAGTGCTTTCTCTGTCATGTCT[A/G]TTAGAAATCCATTCATTTCTTCTCCTTTCCTTTAT R 2 1 2 1 201000 r 74 goat snp18732-scaffold1895-515099 5 4296024 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385215 Affx-122971707 AX-123255573 5 4297190 AGATGAGTGACATAATTACATTTGTTCCCTTAAAG[C/T]GATGCTTATTCCTAGTAATCAAGGACAAGCTAATT Y 2 1 2 1 101000 r 74 goat snp18731-scaffold1895-486279 5 4325392 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409286 Affx-122953112 AX-123279637 5 4329684 GTATAGAAATTTTCAGGAAACATTTCAAAGCTTTG[C/T]GCCTGGCAAACAGCAGGAGTGGGATTGTAGCTCTT Y 2 1 2 1 103000 r 74 goat snp18730-scaffold1895-453785 5 4357831 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441903 Affx-122928611 AX-123312240 5 4369651 GACTAAGTAGCCGAGGAGATGGTGTTCCTAAAGAA[C/T]GGACATGGATATTTCTGAACCTTTTAAAATTATGA Y 2 1 2 1 101000 f 74 goat snp18729-scaffold1895-413818 5 4398484 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777038 Affx-122960094 AX-385264161 5 4412403 CCTGTGATTCATCCTTTATACTGTTACTTGGTGAT[A/G]TTCTCATCATGTAATTAACTGATTATGTTCCTTTT R 2 1 2 1 101000 f 74 goat snp18728-scaffold1895-371066 5 4441043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772970 Affx-122957779 AX-385260114 5 4523688 AATGAGCCAAATAAAATCGCTGAGCCCTTCTTTGT[A/C]TAACTGCTAAATCAGAACAGCTAATCCATGTTTTT M 2 1 2 1 101000 f 74 goat snp18726-scaffold1895-259781 5 4552766 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779707 Affx-122963450 AX-385266807 5 4576269 AATTATCCTCTTAATTAGTACTGTTATATGTTAAA[C/T]ATATAAAGCTTGTTTAGCTTTAGTATTGTCTCGGC Y 2 1 2 1 101000 r 74 goat snp18725-scaffold1895-207200 5 4605204 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389234 Affx-122969045 AX-123259592 5 4662943 TTGAAACCCTGTGTATTGCTAGTAGGAATGGGAAA[C/T]ATGTAGCCACTATGAGAAAGAGAATATAAGTTCTT Y 2 1 2 1 101000 f 74 goat snp18723-scaffold1895-120526 5 4691919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422220 Affx-122944028 AX-123292566 5 4709049 CATGTTTTGAGGAAGAAACATTTACTGAAGGTTCA[C/T]GTCCTCTTGTGCTTCTTAATTTGAGAAATAGTCCA Y 2 1 2 1 101000 r 74 goat snp18722-scaffold1895-74420 5 4738366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429797 Affx-122938201 AX-123300138 5 4741965 GACCATATGGACGGAGTTCCTCCACTTGTGGGAGA[C/T]TGTGTTATAGTCTTTTTCACTAAGGTTCGTGGGAG Y 2 1 2 1 101000 r 74 goat snp18721-scaffold1895-41504 5 4776686 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401250 Affx-122959299 AX-123271603 5 4795801 TACATAAATAGATTCATATGCCTGCTGTCTTATCA[C/T]GGATGTCTATTTTTTAAAGTCTTTTTGCCTACTTC Y 2 1 2 1 101000 f 74 goat snp27789-scaffold2973-83864 5 4831214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784412 Affx-122951566 AX-385271461 5 4848756 AAATAAAAGTTTGTGCAATAAATGTTGTGAAATTA[C/T]TTCCCACTAAAAAGTAAATAATTGGCAGCCACTTA Y 2 1 2 1 101000 r 74 goat snp27788-scaffold2973-30909 5 4883832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778423 Affx-122919288 AX-385265537 5 4891775 TATTTTAGCCAAAAGGATTAAGTCAACTAAGCACA[C/T]GCTAATTAGAATTTCTAACAATCAGACACAGGTTT Y 2 1 2 1 101000 f 74 goat snp15217-scaffold1622-12011 5 5105723 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772597 Affx-122935779 AX-385259746 5 4924728 AAACATGAGACCATGAAGAGTAAACTACTCTGTAC[A/G]CTTTCGTCAAAGGTTGTCATCAACGTGGACTGAGT R 2 1 2 1 101000 f 74 goat snp15218-scaffold1622-44964 5 5138261 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397646 Affx-122962612 AX-123268001 5 4972341 ACAATCTGTTGATTTGTTTCCATCTTGGTTCTTTC[A/G]TGCCTCTTCTTTCTCAGCTCACACCAGTGTGCAGT R 2 1 2 1 101000 r 74 goat snp15219-scaffold1622-92577 5 5186201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437647 Affx-122931799 AX-123307985 5 5030730 ACGCTTCCTTGTTGCTGGCTGCCACGATGAACTGT[C/T]TGTTGCTGTTGTCCAGTTGTTGAGTCCTGTCCGAC Y 2 1 2 1 201000 f 74 goat snp15220-scaffold1622-150966 5 5244140 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383240 Affx-122972754 AX-123253598 5 5065571 ATTTCCCACAGGAGAAAGGTTTTTAAACCAAAAAT[A/G]TTTTTCAAAACCAGAAGAAAAAAATAAGACAATCA R 2 1 2 1 103000 f 74 goat snp15221-scaffold1622-185807 5 5278802 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441260 Affx-122929487 AX-123311597 5 5102504 GAAACCAGCTTCATTAGAGAAAGGAGATTAGTCAC[C/T]ACCAGGTAGACAGGATTTCTTGGACCGCGCCCTGT Y 2 1 2 1 101000 f 74 goat snp15222-scaffold1622-222740 5 5315383 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408282 Affx-122953794 AX-123278633 5 5145894 TAGGCAGTGATTTTCAGCCCTAAGACGATTTGCTA[G/T]CATCTATGGCTCTTTTTCAAACTGAAGTAGCATCT K 2 1 2 1 101000 f 74 goat snp15223-scaffold1622-266130 5 5358882 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383940 Affx-122972962 AX-123254298 5 5179055 ACATATTCTGGAAGTACCGAAGGCTTGCATATCCC[A/G]TAACTATAAACCCCACCGGGAAGTACATACACCAG R 2 1 2 1 101000 f 74 goat snp15224-scaffold1622-299291 5 5392011 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403616 Affx-122957550 AX-123273968 5 5237155 GAGGATCCCTTCATTTGTCATTCCTTCAGATTCTG[C/T]GGCCAGGGAGCTTGCCGTCAACAGCAGAGAAAATC Y 2 1 2 1 101000 f 74 goat snp15225-scaffold1622-357391 5 5451052 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767395 Affx-122948294 AX-385254668 5 5348475 AGATGGGAAAGTCAGAGGGAAAGAGCGTATAAGAG[C/T]GCTTTACTGCAGTTATCCTTAGAAGATGCCACACA Y 2 1 2 1 101000 f 74 goat snp15227-scaffold1622-468711 5 5562569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390873 Affx-122967809 AX-123261230 5 5410199 AACATACTCTTATTCTATTTTACAAAACTGACCAG[C/T]GTTTGAATTTATAAATGATCATTAAACAGGATATT Y 2 1 2 1 101000 f 74 goat snp15228-scaffold1622-530435 5 5625234 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777519 Affx-122926912 AX-385264638 5 5424311 AAAGTAGCTAGTACTTCTTTTCCCAATTTTAGTTT[A/G]CCTGATATTTGATTAACACAGTCACTACTACCTAG R 2 1 2 1 101000 f 74 goat snp6035-scaffold1213-6500 5 5640982 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774759 Affx-122941896 AX-385261893 5 5474583 AAATTGGTATAAATCAACATGTGTAAAAGAGACTC[A/C]GCCAGAAAACAATGCGAATCTTTGCCATTCTAAAG M 2 1 2 1 101000 r 74 goat snp6036-scaffold1213-56772 5 5688792 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272312 Affx-1111833470 AX-519546050 5 5501967 CCTGGGACCCCTTGCTACAACGCTTGCCCCTGGAC[A/G]AGTGTCTTCTCCAGCAACAAAATCCAAAGAAACTA R 2 1 2 1 303000 f 74 goat 5_5501967_AF-PAKI 5 5501967 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38424267 Affx-122941997 AX-123294613 5 5508027 TTACAAAATATTTTAATACATATATTAAATGTAAA[C/T]GTGTTCTGAAGTATCCTGAGTATAAAGATTGAATT Y 2 1 2 1 101000 r 74 goat snp6037-scaffold1213-90216 5 5722309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776545 Affx-122930055 AX-385263672 5 5545906 ATGTGTATTGCTGATGTGACCAACAGAAGTTTGCA[C/T]GTACTGGAATACACGTTACATTTGCCTTTCCCCTA Y 2 1 2 1 101000 f 74 goat snp6038-scaffold1213-128095 5 5760707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453815 Affx-122919561 AX-123324148 5 5575663 AATGACTTTTGTGAATGGAAAATCTGCATATACTG[C/T]TGCTTCGGCTGGGCCGGTCTTGTGTGGATGGCTCA Y 2 1 2 1 101000 f 74 goat snp6039-scaffold1213-157852 5 5790791 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408996 Affx-122953893 AX-123279347 5 5638113 TTAATACATAAAGTTCACCTAGGAGATCAAGATAA[C/T]GAAACTAATTTTGTTCAGTATGAAAAGAGGAAACT Y 2 1 2 1 101000 f 74 goat snp6041-scaffold1213-220302 5 5854049 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395480 Affx-122963901 AX-123265835 5 5667778 CAGCGTTCAATATGTTAATTTCAGAGTACGTGTGT[A/G]TTGGGGGTAGGAAGGAGCCACACTTGAGTGACCTC R 2 1 2 1 101000 f 74 goat snp6042-scaffold1213-249967 5 5883267 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792618 Affx-122929959 AX-385279599 5 5711854 GCTTATAAGGAACTCACATTTGCAGAAGAGGACAC[A/G]TAAATTGATAAGTACAATACAATAGAGTAGGTGTA R 2 1 2 1 101000 f 74 goat snp6043-scaffold1213-294043 5 5927775 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383668 Affx-122972509 AX-123254026 5 5790406 AGTACATATCTTGATAATAACCTTCTTATAGTATT[A/G]CAAGGAGGCTTAGGTTTAACAGTAATAATTATAAG R 2 1 2 1 101000 r 74 goat snp6044-scaffold1213-372595 5 6008633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791663 Affx-122976238 AX-385278654 5 5820267 TCCTAGAAAACAGACTAGTACCTTGAATACTTTCT[A/G]CACATAGTAGGTATATTTGATAATTTCACCTCTGT R 2 1 2 1 101000 r 74 goat snp6045-scaffold1213-402456 5 6038517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393920 Affx-122965085 AX-123264275 5 5901989 GACTATTAGCAGGACCAGCTGCATTATTTGTAGAG[C/T]CCAGTGCTGAATGAAAATGTGGGTCTCTTTGTTCA Y 2 1 2 1 101000 f 74 goat snp6047-scaffold1213-484178 5 6120398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383146 Affx-122973242 AX-123253504 5 6040291 TTTTCTTCCCCCTTTGCTCTGTCTCTATGTAAAGG[C/T]ATACACACGGCTTCCCTGGTGGCTCAGATGGTAAA Y 2 1 2 1 303000 f 74 goat snp6050-scaffold1213-622480 5 6260315 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772624 Affx-122967662 AX-385259772 5 6101165 TCTGTAACAAAATAGAAACTGTTGTGGAAGAAAAT[G/T]TAATAAAAATATTAGCTAGATGTTGGTTCATGCTA K 2 1 2 1 202000 r 74 goat snp6051-scaffold1213-683354 5 6321852 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772947 Affx-122940298 AX-385260091 5 6137852 GTCTGGTCTAGACATATTAGTATATGTCTAATACA[C/T]ATCTTGTTTCTTAATTCTTGCTCCATTACTGCATT Y 2 1 2 1 101000 r 74 goat snp6052-scaffold1213-720041 5 6358276 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791549 Affx-122960479 AX-385278539 5 6185804 CTATTTTTTGAAAATGAGGAGAACTGGACATGTGC[A/G]TTTAACAAGTAAATGGAACTGATTTCATTCATGGG R 2 1 2 1 102000 f 74 goat snp6053-scaffold1213-767993 5 6404546 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389689 Affx-122968699 AX-123260047 5 6283370 CCCATGCCTTCATATGCCTTCATTGTCTAGTGGGA[C/T]GATGGTGCAAATGAGTGTCAAGGATGGTCTGTTGG Y 2 1 2 1 101000 r 74 goat snp6055-scaffold1213-865559 5 6502219 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796408 Affx-122972245 AX-385283358 5 6325527 TTGCTGAGGATTATTTATTACCGAGATATTTTAAC[A/G]TACACTTTTCTTTTTCCAAGTTGTAAGATGCAGCC R 2 1 2 1 101000 r 74 goat snp6056-scaffold1213-907716 5 6544791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376356 Affx-122978326 AX-123246715 5 6356750 ATACAAGCATGTAAAAGGAACCATATCTTCTTCAA[C/T]ACTATGCATTCAAACCTACCAAAAGCCAAGTAAGA Y 2 1 2 1 101000 r 74 goat snp20363-scaffold2019-183334 5 6575895 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773332 Affx-122952897 AX-385260474 5 6403630 GTAGGTAGGAAGGATAAAGACGTGTAAAGTAGACT[A/G]CAAAAGTCAGTTATGTACACTGTAATTTTTTAAAA R 2 1 2 1 201000 r 74 goat snp20362-scaffold2019-136454 5 6622453 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795766 Affx-122968433 AX-385282719 5 6441582 AAGTGAAGACTCAAACTGCAACCTCCAGATTCAAC[A/G]TCTCATTATTTATTAATCAGGGATGCATATCTAGT R 2 1 2 1 101000 f 74 goat snp20361-scaffold2019-98502 5 6659685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453872 Affx-122919520 AX-123324205 5 6493852 AGAAGGCTTTGTGAAAGGTATATAAGGTAGGTCTT[A/G]TCAAATACTGAAGTTTCAGGACCTCTGAAAACCCT R 2 1 2 1 201000 f 74 goat snp20360-scaffold2019-46232 5 6712761 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434122 Affx-122934926 AX-123304463 5 6524178 TCTCTAGCTCACCAAGACCAATGCTTATAGCTGAA[G/T]AGATGAACAAATTAATATTCATAATCAAGTGTAAA K 2 1 2 1 101000 f 74 goat snp20359-scaffold2019-15906 5 6743295 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278169 Affx-1111836286 AX-519551658 5 6546009 AAATCTGTAACTCACTGACTTTAGCAAACTTGCCT[A/C]TAAGTCTTACCTCTCTCTGTCTCTCCACTTTCTAG M 2 1 2 1 201000 f 74 goat Random2.2K-516 5 6546009 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382018 Affx-122974062 AX-123252376 5 6563698 AATGTGAATTGACATCTCATACACAAAAGCACTGC[A/G]TGAGGGGAATAGCAACTTAGCTTAATGAAGATGTA R 2 1 2 1 201000 f 74 goat snp54018-scaffold822-23515 5 6779068 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425501 Affx-122941478 AX-123295847 5 6606867 GAGATGAACTATTATTGCCAACTAGCGCAGAGCAA[C/T]ATACCTTCTTTATTACAGAATCCGAGAGCACTCCT Y 2 1 2 1 101000 f 74 goat snp54019-scaffold822-66684 5 6821614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788501 Affx-122939637 AX-385275518 5 6656022 GTTACATGTGACCAGTGATAGGATAGGAACAACCC[A/G]CTAGAGGACTTAACTTGAGCATCTTTCACTGTCTT R 2 1 2 1 101000 f 74 goat snp54020-scaffold822-115839 5 6871387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430621 Affx-122936968 AX-123300962 5 6693380 GAATGTACACGGTAAGTAAACCTTAATTGCTCATA[C/T]AGTTGAAAATAATTTTATCATATTGAAAGAAGTTC Y 2 1 2 1 101000 f 74 goat snp54021-scaffold822-153197 5 6909014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786186 Affx-122971245 AX-190704346 5 6724928 ACTTATAACTGACATTTAAGCACTTAAATTTAACA[C/T]GTTTTAGTGGAAATTATCATTTCTATGGGAACCTT Y 2 1 2 1 201000 f 74 goat snp54022-scaffold822-184745 5 6940498 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392570 Affx-122966076 AX-123262927 5 6753483 AAATACTCATTGTTTCTAGAAAGCACCATTCTAAA[C/T]GTACCCAGGCTCCCTCTAAAGTAAAATACATTGAA Y 2 1 2 1 101000 r 74 goat snp54023-scaffold822-213300 5 6970753 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436838 Affx-122932219 AX-123307176 5 6792560 CAAAAAGAAAGACAACCCTGGGTAAGAGCTAAGAT[A/G]GGGTTTCACTGGGGGATCTCACCCTTGATTAGCTT R 2 1 2 1 101000 f 74 goat snp54024-scaffold822-252377 5 7008513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400555 Affx-122960425 AX-123270910 5 6841490 TAGAAACGAAACTGTTCCCAAAGCAGAAATGGAAC[A/G]TGGAGCTCAACTCCCATAGCTAATAAACTGAGGTA R 2 1 2 1 101000 r 74 goat snp54025-scaffold822-301307 5 7057035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404141 Affx-122957090 AX-123274493 5 6878482 TAGTTCCTGTCTCTATCCACCCCCTCACAATGGTG[A/G]CTTGTGTGAACACATTCAGCTGGAGCAGCTGCCCA R 2 1 2 1 101000 r 74 goat snp54026-scaffold822-338299 5 7093779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792705 Affx-122931159 AX-385279686 5 6909588 GCTATTTTCTTCTAGTATGTTTGCTAAGAGAGAGT[A/G]CAAGAGAGAGGATGCACTGATGAGCGTGTTTCATG R 2 1 2 1 102000 r 74 goat snp54027-scaffold822-369405 5 7124196 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789535 Affx-122946201 AX-385276545 5 7012191 CGATGCTTTAATCTTTCACATCACCCACCAACTAA[C/T]AGAGAAACTAGATGTTTAAACAGATGGTTCGGTGA Y 2 1 2 1 101000 f 74 goat snp54029-scaffold822-472008 5 7225957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410251 Affx-122952535 AX-123280601 5 7040791 GCACTCTTAAAGAGCATCCTGACTGGTCCTTTTTT[A/G]ACCCTCTCCTCTCATCTTCACCAAAAATCCCAGGT R 2 1 2 1 101000 f 74 goat snp54030-scaffold822-500608 5 7254631 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768778 Affx-122971069 AX-385255955 5 7085429 ACTTAGGATTTTTTCTTCATGTAACTGCAAGGTAT[A/G]TCATGAAGTTAATGGAAATGGACTTTCCTTTTTTT R 2 1 2 1 201000 r 74 goat snp54031-scaffold822-545246 5 7299303 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385707 Affx-122971112 AX-123256065 5 7126020 ATATTCCTACGTCCGTGCTTCTTTGATTCCAGTAC[G/T]GCAAATAAATGTATAAGCTATGGAAAATTCAAAAG K 2 1 2 1 101000 f 74 goat snp54032-scaffold822-585837 5 7340355 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449669 Affx-122922568 AX-123320004 5 7167583 GCCAACTTTTATCCTCAGAAACTCTCTCTGGTGTT[A/C]GTTTTTATTATCATATCATTTAAGAATTCATAGTG M 2 1 2 1 201000 r 74 goat snp54033-scaffold822-627400 5 7381998 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415812 Affx-122948894 AX-123286161 5 7200417 AGTAGCCTTCAGTATCAAACTGACGTTAGGAACTG[A/G]CTCCTACGTTCGAACTCTTCTCTCCTCTTGATTTG R 2 1 2 1 101000 f 74 goat snp54034-scaffold822-660234 5 7415185 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418655 Affx-122946327 AX-123289003 5 7238973 AAAGAATTAGGACAATTCTACAATTGGGATCAGAA[A/G]ATCACAGCAGAGGCCCACTTCCAGGAAATAATGAC R 2 1 2 1 101000 f 74 goat snp54035-scaffold822-698790 5 7454139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392426 Affx-122966194 AX-123262783 5 7284652 CAAGTAAAAGGGATAGTGGAAATGCATGAAGTATC[A/G]CCCCTTTAAATAAGATAACTTTTTAAAGAGTAGGG R 2 1 2 1 103000 f 74 goat snp54036-scaffold822-744469 5 7499977 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278329 Affx-1111836287 AX-519551815 5 7327312 TCAAATTAACTTTTAAATGTTTTCTATCTTGCAAC[A/G]TGCTTTTGAAATAAATTTTCACCCACAAAAATGTT R 2 1 2 1 201000 r 74 goat Random2.2K-517 5 7327312 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406556 Affx-122955107 AX-123276908 5 7333911 TTCACCAGGGGCTGGGTGCTAACAGATGTGGGTAG[C/T]GATTTGCACTAGGAACACGTGATGGTGTAGAAATG Y 2 1 2 1 101000 r 74 goat snp54037-scaffold822-793728 5 7549368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427968 Affx-122939191 AX-123298311 5 7421904 TGAGAATGTCATTGTACAGGATGAGGATCCTTGTA[C/T]GTCTTAGGGTAAAGGCTAAGTTGCCCTATCAATAA Y 2 1 2 1 101000 r 74 goat snp54039-scaffold822-881721 5 7636070 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800660 Affx-122963690 AX-385287578 5 7456757 CAATATGTTACCAAAGAAATCATGAGCCAGACTTA[G/T]AGACTTCTTTTACTTTTCACCCCTTAAAACAAACT K 2 1 2 1 101000 r 74 goat snp54040-scaffold822-916574 5 7671183 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771408 Affx-122964599 AX-385258566 5 7531528 CCATATGTCTTATGGCTAAAGGCAGACTTTTAGAG[C/T]AAATTATGACATTTTATGTAGCTTTGAAAGAATAT Y 2 1 2 1 101000 f 74 goat snp54042-scaffold822-991345 5 7746988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396765 Affx-122962772 AX-123267120 5 7581676 TTCTTGCCACAAGCATACTGTATTATCAATTTGCT[A/G]TAAGGCTTGGGGAAACTGAAGTGGTCACTTCTTCG R 2 1 2 1 101000 f 74 goat snp54043-scaffold822-1041493 5 7797400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396110 Affx-122963416 AX-123266465 5 7624732 AACTCACTCTTTCTCACACTTAACTCCCCCTGAAA[C/T]GTTCCCTTGTCCAGAAAATTAACAACCTATTTCAA Y 2 1 2 1 201000 r 74 goat snp54044-scaffold822-1084549 5 7841370 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798209 Affx-122923362 AX-385285143 5 7669179 CATTTTCCACTAAGCAACATGGAATTTCCTATGAA[C/T]GACTTCTGTTGATACACACAGGTCTAAAGTGTTTT Y 2 1 2 1 101000 r 74 goat snp54045-scaffold822-1128996 5 7886931 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783938 Affx-122944747 AX-385270993 5 7700098 TGCAGTTTTCAGAAGTTATTGATGAGTGAAAAAGG[C/T]GCACAGAGAGGCGTGACAGTTACTCTGAATATACC Y 2 1 2 1 101000 r 74 goat snp54046-scaffold822-1159915 5 7919116 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781154 Affx-122941913 AX-385268239 5 7744179 CTTCTACCTCTTCTGAAAATGGAAAGGAATTAATA[C/T]GATTATAAACATCCAATCTTCAATCCAGCCACCTT Y 2 1 2 1 201000 f 74 goat snp54047-scaffold822-1203996 5 7965213 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772448 Affx-122942313 AX-385259599 5 7809443 ATACCCGGAATGAGTGTGAAGCAGTTCTGCCAGGC[A/G]TTTGAGTATTATGGAGATGGGACGAAGTACAAGCA R 2 1 2 1 202000 f 74 goat snp54048-scaffold822-1269260 5 8029624 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430858 Affx-122937422 AX-123301199 5 7845430 GGAAGACTTGCAAGAAAGTTGGCAAAGTCTACAAT[A/G]CATTAATCTCTTTCAAAGAAGAAAAACTGCCTCAA R 2 1 2 1 103000 f 74 goat snp54049-scaffold822-1305247 5 8065766 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397396 Affx-122962262 AX-123267751 5 7895598 TGGAATGACCAGTATGAAAATATACCTGACAGTGC[A/G]TTTGAGACTGCTGAGATAAGAGGCATGGTGGACCA R 2 1 2 1 101000 r 74 goat snp54050-scaffold822-1355415 5 8116477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397575 Affx-122962007 AX-123267930 5 7990337 AATCAAAATTGTTTTGCTCACTGAACTCACAGAAA[C/T]AGACTAATTTACCAACTTTGAAGTTTTGTACTGGG Y 2 1 2 1 101000 r 74 goat snp54052-scaffold822-1450154 5 8209663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416244 Affx-122948208 AX-123286593 5 8049761 TGGCATTTTCATTTGAAAACTAAAATATATTATCA[C/T]AGAAACATTTTCATTTCTCTGTGATTGATTTATTT Y 2 1 2 1 103000 f 74 goat snp54053-scaffold822-1509578 5 8268460 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437833 Affx-122932099 AX-123308171 5 8081403 GTTAAAAAGCATAAGCGAGATATTGGGAGATAACA[A/G]TAATTGAGAATGAGATGTGGAAATAGGAGTTAACG R 2 1 2 1 101000 f 74 goat snp54054-scaffold822-1541220 5 8300616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383098 Affx-122973279 AX-123253456 5 8115301 AGTAGTTGTACCAAAAAGCACTATTGTCATTATTC[A/G]TTTACTGGCAATTCTGGAATATTCCTAGACTAGAG R 2 1 2 1 101000 r 74 goat snp54055-scaffold822-1575118 5 8334424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406607 Affx-122955843 AX-123276959 5 8171510 TAAAGCCAAAAGACCTTTAGGAATCATATAATATT[C/T]TTTCTGATTGCTAGTAGGCTGGTGGCAAAGCAAAG Y 2 1 2 1 202000 f 74 goat snp54056-scaffold822-1631327 5 8391671 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391043 Affx-122966862 AX-123261400 5 8201430 GATTTGCTCCAAATTGGAAAGTTACCTTGTGATAG[A/G]AGGACAGAGAGAATGCTATCACCTGCCCCCTAGAA R 2 1 2 1 101000 f 74 goat snp54057-scaffold822-1661247 5 8421801 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397633 Affx-122962622 AX-123267988 5 8251572 TTTTACTCTATTCTAAGTATTTCTAATCATCTGTA[C/T]GTTGATACAGTAACGACCAGGAGAATGTACATGTT Y 2 1 2 1 101000 r 74 goat snp54058-scaffold822-1711389 5 8470845 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797971 Affx-122941398 AX-385284907 5 8282239 GGAATGATTACATGTAGTAATGACTGATAAAATTC[A/G]TAAAAATATCAGTTGATCTAAATTTTAGTTCACTT R 2 1 2 1 202000 r 74 goat snp54059-scaffold822-1742056 5 8501612 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406179 Affx-122956154 AX-123276531 5 8321803 TTGTAACTCTATAGTTTATTTCTTTATACATTCAA[C/T]ATCACATCAACCCTTTGTTAGCATGGCTGACCTTT Y 2 1 2 1 101000 r 74 goat snp54060-scaffold822-1781620 5 8540781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438826 Affx-122930783 AX-123309163 5 8369325 GTCCTGCCTGCAGTGAGTGATGCTGTGCAGGGTGT[A/G]CCAGCTTTCAGTGAACCCACTAAACTGGGCAGCTA R 2 1 2 1 101000 r 74 goat snp54061-scaffold822-1829142 5 8588665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426004 Affx-122941138 AX-123296350 5 8398788 TCAGATACACATACAGTAAAGAATACGAGCAAGCA[A/G]CCTTAGCATAGCATAGCAGAAAATAAGCCTGTGGA R 2 1 2 1 102000 f 74 goat snp54062-scaffold822-1858605 5 8618487 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417998 Affx-122946667 AX-123288346 5 8453316 ACTAGTACAATTTTAAGAGAAACTTTGAAGGGGAT[A/C]TACAACATAAAAATTATTTAGAAAAAATAATTGAC M 2 1 2 1 103000 f 74 goat snp54063-scaffold822-1913133 5 8673872 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771179 Affx-122966845 AX-385258339 5 8489659 AGAAGCTAATGCCTCAGTCCTTGTAGAACAGATGG[C/T]AAGAGACATATGTTACTTGGAACTTTTTTAAAAAG Y 2 1 2 1 101000 f 74 goat snp54064-scaffold822-1949476 5 8710272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776725 Affx-122927219 AX-385263851 5 8551019 AACCAGCCCTGAAAAGCTGTATTACAGGGAAACTT[C/T]AGTTTACTATAATTAGAAATCTATTTTAACCTTAA Y 2 1 2 1 101000 f 74 goat snp54066-scaffold822-2010836 5 8772257 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433981 Affx-122934255 AX-123304322 5 8585026 TGACATTTCTACACAATAGAGTTGTTTTGCTATTG[A/G]GTGTATTTAGTTATTAAATGGATTAGCCTGTCTAC R 2 1 2 1 101000 r 74 goat snp54067-scaffold822-2044843 5 8806800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401381 Affx-122959230 AX-123271734 5 8664523 TTTCTTCCACCTTTTTTAACATATGGCATGTATCT[A/G]TTTAGATGCTTTAGTATCCTTTTCTGCTAGTTCTA R 2 1 2 1 101000 r 74 goat snp54069-scaffold822-2124340 5 8886124 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390985 Affx-122966910 AX-123261342 5 8717404 TAATTCTTTAACTACCTCATAATATAAGAAAACAA[C/T]GAACCCAAATAGACTTTAATTTTCTTTACTCATTG Y 2 1 2 1 201000 f 74 goat snp54070-scaffold822-2177221 5 8938912 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786318 Affx-122941729 AX-385273352 5 8748464 TGATCAGATTCCAGCCTGAAACAGCAAATACTACA[C/T]GGTACAGTAAAGAATGTATCAATGTGGAAAAACAA Y 2 1 2 1 101000 f 74 goat snp54071-scaffold822-2208281 5 8969998 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445582 Affx-122925130 AX-123315919 5 8786012 CAAGGGGAGATCATATTATCTGAATTACCCCTTCA[C/T]ATAAAACCCAAAGGTTGAGCTAATACTTTAAACAT Y 2 1 2 1 201000 r 74 goat snp54072-scaffold822-2245829 5 9007613 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278174 Affx-1111836288 AX-519551663 5 8873575 AATTGTTTAAATCTAGTCTTTAGAGATGACAGGGG[A/G]AAATGTAGATAATTGCTGCTACAATAAATGGAAAA R 2 1 2 1 101000 f 74 goat Random2.2K-518 5 8873575 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395438 Affx-122963932 AX-123265793 5 8878419 CACAAGTTTAAAGTCATCAGCTGGTGACTCAGCTG[C/T]TAGAATGGAAATCAGAACTTTTCAGAGGAAGATGA Y 2 1 2 1 101000 r 74 goat snp54074-scaffold822-2338236 5 9095441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454078 Affx-122919378 AX-123324411 5 8913231 AGGTGCCCCTCTCACTCCTTAATGTGTTCTGCCTC[A/G]ATAATGGCTTGTTGCCAAACACGCTGAATGCTAGT R 2 1 2 1 101000 r 74 goat snp21401-scaffold2087-193717 5 9130582 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402803 Affx-122958284 AX-123273156 5 8943319 ATTCTTTTAAAAAGGGAGAAAAATCTGTTTTGCTC[A/G]TAACTTCCTTTTATATTTTCAAACTTTCAATCTGT R 2 1 2 1 101000 r 74 goat snp21400-scaffold2087-163629 5 9160754 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794765 Affx-122935428 AX-385281725 5 9054226 GAGTTTGTAGAATACTGTTTCACTGGAGAGACTCT[A/C]CTTTGGATGCTCATTTTACCTTATGTCTTGCTTTT M 2 1 2 1 101000 f 74 goat snp21398-scaffold2087-52722 5 9271737 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392345 Affx-122966260 AX-123262702 5 9104934 TAGTTGACAATGTTATCTTCATATACAAAGTGTAG[C/T]ATATTTCCATGAAGGTAGCCCAAAATCAAAGCACC Y 2 1 2 1 101000 r 74 goat snp21397-scaffold2087-2014 5 9314507 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802559 Affx-122951183 AX-385289462 5 9153728 CATTTTCCTTTGGGAATTATGTTCCCAGAAGTGTA[C/T]GGACTCTCACGATGGAAACTGACATGTACCATGAA Y 2 1 2 1 101000 r 74 goat snp19067-scaffold1917-319225 5 9509945 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440778 Affx-122929849 AX-123311115 5 9202798 TGCTCTCCAGCAACTGTCTGCTTGTTGCTGCTGTA[C/T]GTTAGCTCCTGAATCTTGCTTCAGAATAATGCTGG Y 2 1 2 1 101000 r 74 goat snp19068-scaffold1917-368295 5 9558939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396943 Affx-122963183 AX-123267298 5 9236189 ATCAGTTAACAATGGTATGTAAAGTGACAACTGCC[A/G]TCTCTTTTGAAAATATCATATTATGATCATATCAT R 2 1 2 1 101000 f 74 goat snp19069-scaffold1917-401686 5 9592472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441452 Affx-122928767 AX-123311789 5 9253935 CCAACTTGGGATGTTGAGGGTAGTTGTAAGGAGCA[C/T]AGCCTTTGGAGTCAGTTAGTACTCACTTAGAACCC Y 2 1 2 1 101000 f 74 goat snp17482-scaffold1809-4831 5 9621135 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775631 Affx-122935147 AX-385262762 5 9336518 GCTGAATAACAAGATACAATATGTACCAAGGTAAT[A/C]GAATTTTAGCTCTTTAAAGAATCTTACATATCATA M 2 1 2 1 201000 r 74 goat snp17484-scaffold1809-87414 5 9702851 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416183 Affx-122948255 AX-123286532 5 9386435 AGTAATAGCAAAGACACATTTTTTCCCCCTAAAAT[C/T]TAGTCCTTTTCAAGACATGGTGACATGATTTGTTT Y 2 1 2 1 103000 r 74 goat snp17485-scaffold1809-137331 5 9752574 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789203 Affx-122977103 AX-385276215 5 9424858 TATAATAGCTTATTTATCTATTTGCAGAGCTGAGC[A/G]TGTAAGACATTATACTTGAATAAATTCAAGGATTA R 2 1 2 1 101000 f 74 goat snp17486-scaffold1809-175754 5 9791312 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786612 Affx-122956351 AX-385273644 5 9455749 CTTCATTTACCTCATCTAGACAGCTATTCACCTGG[G/T]AAATCCTTCTAAGACTTTAAACTGATTGTATCCAG K 2 1 2 1 101000 f 74 goat snp17487-scaffold1809-206645 5 9822772 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278333 Affx-1111836289 AX-519551819 5 9467864 CCCAAGCATGGTAGTTGTCTGTAAACTGAAGGCCT[A/G]CTTAGAGTTTTCTCTTATCAACCACAAGGCTGTAG R 2 1 2 1 101000 r 74 goat Random2.2K-519 5 9467864 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320802581 Affx-122973557 AX-385289483 5 9501959 CCTTTCAAAGAGTCTCAGACTTTGTCTAGGAAACC[A/G]TTCATGTTCACAGTTGGGAAAATAGGGAATTTTGT R 2 1 2 1 101000 f 74 goat snp17488-scaffold1809-252855 5 9865450 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798690 Affx-122950820 AX-385285622 5 9556923 TTTAATATTTTTTGTCATATCTTACCGTATTTAAT[A/C]GAACATTAACCTCTAAAAAAGTGGCCTTACAAACA M 2 1 2 1 101000 r 74 goat snp34529-scaffold405-4073717 5 9919187 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448108 Affx-122924312 AX-123318444 5 9603941 TGACGCTATAACCTGCATAATGTAGCATATACACA[G/T]AAAGCATTTCTGTTTGTATCTGCAGAGGGTGATTT K 2 1 2 1 101000 f 74 goat snp34528-scaffold405-4026699 5 9966506 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476196 Affx-1251763701 AX-586011622 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 4 1 4 1 20000 f 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 539476451 Affx-1251763701 AX-586011852 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 4 1 4 1 20000 r 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 562165430 Affx-1251763701 AX-606940841 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 8 1 4 1 20100 r 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 562165435 Affx-1251763701 AX-606940846 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 8 1 4 1 20100 f 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 562165500 Affx-1251763701 AX-606940911 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 8 1 4 1 20100 r 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 562165820 Affx-1251763701 AX-606941229 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 8 1 4 1 20100 r 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 562165902 Affx-1251763701 AX-606941311 5 9638065 TGATGGAAATTTTGGGGCTTGCTCTCCTTCCTGTT[-/TGGGAGACTTTTATTTTATTTTATTTTTAGTTTTTTATTTCCGTCCTATTCCTCCACCATCTTCCAATTCCATCCTGTTC]GGGAGACTTTTAAACCCTCTAATTCAATTACCTTC - 8 1 4 1 20100 f 74 goat SV_153 5 9638065 - deletion junction SV-TF-chip 38391064 Affx-122966847 AX-123261421 5 9662168 GCCACATCTTCCTAAGAACATTAATGTTCCATGAC[A/G]TGGTGTTACATGTTTTGGGGTCAAAAGGGTTCAAG R 2 1 2 1 101000 f 74 goat snp34527-scaffold405-3968472 5 10025252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790988 Affx-122924883 AX-385277985 5 9694608 AGAGAAAAAAGGAAATGCCAACTTGGGAAATAACC[A/G]CTTTTTATTAGATTAGGTAATGGGAAAATACACAA R 2 1 2 1 101000 f 74 goat snp34526-scaffold405-3936032 5 10057900 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454003 Affx-122919435 AX-123324336 5 9775143 CAAAAGAGAAAAGCATGACTAAAGGGAATGAATGG[C/T]GAATATGTGAGTAGAATTCAGTTTGAAAGAGGTAG Y 2 1 2 1 101000 f 74 goat snp34524-scaffold405-3855497 5 10137221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412039 Affx-122951725 AX-123282389 5 9846495 TGCTCAGGAGTTAATATAAATTTGGCAATGAATAC[A/G]CTAAAGTAGATCAGAAAATAATTATGTATACTGTT R 2 1 2 1 101000 f 74 goat snp34522-scaffold405-3784145 5 10208480 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444716 Affx-122926418 AX-123315053 5 9886628 GCCCAAGTACTGTGCTTAGATCATAGGATAGATAA[C/T]GGAGGTATGAACCTGAGAGTTGGTAGATGAGAGGA Y 2 1 2 1 101000 f 74 goat snp34521-scaffold405-3744012 5 10248926 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792710 Affx-122950153 AX-385279690 5 9928886 TTTTTTAATTTGGAGAGATTGTGGGGTGACTAATG[C/T]AATCTGTTGGCGCCAGAAGAAATGTTATGTGGTGC Y 2 1 2 1 101000 f 74 goat snp34520-scaffold405-3701754 5 10290789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417636 Affx-122946853 AX-123287984 5 9973946 TTGGTCATAAGTTCACTGTGGAAATTAATTATCCA[C/T]GTAAAAGACTCAACAGAATGCCTAGCACACAGTAA Y 2 1 2 1 101000 f 74 goat snp34519-scaffold405-3656694 5 10336989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780836 Affx-122955645 AX-385267924 5 10072571 TTATTTATAAATGACTAAGAGGTACTAATAGATCC[A/G]TTTCTGTCCCTGAGTAGCTCATAGTATAGTCAGGA R 2 1 2 1 101000 r 74 goat snp34517-scaffold405-3558069 5 10435170 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431469 Affx-122936267 AX-123301810 5 10108099 AAACAGTGTTTTCCCGTGCATGTTATACCAAGTAA[C/T]GATGGCTATAAACTATTTAAGATGGTACAGAAGTG Y 2 1 2 1 101000 f 74 goat snp34516-scaffold405-3522541 5 10470304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787285 Affx-122963290 AX-385274310 5 10148306 GCTCTGCTTACTTAAAAAAATCCAACAACCAACAA[C/T]ATTCTTGCTCTTATGGTAGTTTTACAGATGATATC Y 2 1 2 1 101000 f 74 goat snp34515-scaffold405-3482334 5 10510974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781332 Affx-122959394 AX-385268417 5 10178016 TACGCATTTTTCATGATCTCCATTAAAAATGACAA[C/T]AGCAAGTCTCAAAATATATGAGAAGACAGAAAAAC Y 2 1 2 1 101000 r 74 goat snp34514-scaffold405-3452624 5 10540731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803004 Affx-986696122 AX-385289884 5 10203728 TATTGAGACTGATACTTATATCTACAGCTATCTAT[A/G]ATTTTTAAATGAATTTCTTTATTTTTCAGAATTGG R 2 1 2 1 600010 f 74 goat 5_10203728 5 10203728 Ancestral_priority_1043 ancestry 0.654 recommended IMAGE 10K 10K ancestral 320764521 Affx-986696875 AX-385252189 5 10203748 TCTACAGCTATCTATGATTTTTAAATGAATTTCTT[G/T]ATTTTTCAGAATTGGAAACTCAGATAAGAGTTGAA K 2 1 2 1 600010 r 74 goat 5_10203748 5 10203748 Ancestral_priority_1043 ancestry 0.624 recommended IMAGE 10K 10K ancestral 320764528 Affx-986696879 AX-385252197 5 10203836 ATGTGGACTCTGATTTTAAAATATTAAATACTTTC[A/G]TAACATTAAAAGTGAAGGTTGAGATCCCTCATGTT R 2 1 2 1 600010 r 74 goat 5_10203836 5 10203836 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 38431671 Affx-122936796 AX-123302012 5 10221140 ATAAGTAAATTCTCATATCACTTCCCTGTAGGAAG[C/T]ATCACCTATCAAAAATAACCACTCAGCGTATTTTC Y 2 1 2 1 102000 r 74 goat snp34513-scaffold405-3409500 5 10583762 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451228 Affx-122921956 AX-123321562 5 10281687 AGAGCAACTCATTGTGCAGTTTCTCTCCAGTGAAA[C/T]GAGCTACAGTTTCACAGAGCTAGCTGCTGTTTTGG Y 2 1 2 1 102000 r 74 goat snp34512-scaffold405-3348953 5 10644077 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790007 Affx-122939500 AX-385277013 5 10310410 ATTATCTCTCCATTCTCTCAATTTGGAAGAGAAGA[C/T]ATACACTTGAGTTTCTGTGCATTGGGCTATCATTT Y 2 1 2 1 202000 f 74 goat snp34511-scaffold405-3320230 5 10672828 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785362 Affx-122931042 AX-385272407 5 10434328 AATTATGTAGTTGGAACAACTTTCATCATGCTCAA[C/T]AAACAGCACTATATTGATCATGTGTATAAAATAAG Y 2 1 2 1 101000 f 74 goat snp34508-scaffold405-3196312 5 10797131 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402738 Affx-122958335 AX-123273091 5 10469020 ACAGAACAGCACATTTTAATATATTTTATAACTCC[G/T]ATAACACCTCCTGCAGCATTTTAATTTGTGTGTGT K 2 1 2 1 101000 r 74 goat snp34507-scaffold405-3161620 5 10832744 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433436 Affx-122935075 AX-123303777 5 10516808 TAGAAATTTTTCATTTTTCAAAATCCTTCACATTA[C/T]AGAGTTAAGTTCTAGTTTCTTAGATAACACAGAGT Y 2 1 2 1 101000 r 74 goat snp34506-scaffold405-3113832 5 10880880 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797112 Affx-122926734 AX-385284052 5 10547799 TGGAAGATGGAATGTGAGATAGAATGGAAAACATG[C/T]GTGAGATAGATGTGAGATAGAATGGAAACATGCTT Y 2 1 2 1 201000 r 74 goat snp34505-scaffold405-3082841 5 10912285 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272158 Affx-1111833450 AX-519545914 5 10564538 TTCATCCTCTGCCATCCCCTTCTCCTTTTGCCTTC[A/G]GTCTTTCCCAGCTTGCATTGCTGTGATTCGTTAAC R 2 1 2 1 201000 r 74 goat 5_10564538_AF-PAKI 5 10564538 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38434106 Affx-122934939 AX-123304447 5 10584437 GTCCATGGGGTCATGAAGAGTTGGACACGACTGAG[C/T]GACTTCACTTTCACTAAGATAAAGTATTTAATTCA Y 2 1 2 1 103000 r 74 goat snp34504-scaffold405-3046203 5 10949157 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770162 Affx-122973425 AX-385257329 5 10615067 TTATGAGGTAAGTACTGCGATTACTACCATTTTAC[A/G]TGTGAAGAGCGTTGTTGGGCCATTGGAACTAGGTG R 2 1 2 1 101000 f 74 goat snp34503-scaffold405-3015573 5 10979832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781290 Affx-122969084 AX-385268375 5 10655390 TTCCATACCTCCAGTTAGTCAAGAGAGCCTTATTG[C/T]TAAAAATCCTTGCCTCTGAAGTTAGCCTGTCTAGA Y 2 1 2 1 101000 f 74 goat snp34502-scaffold405-2975250 5 11021445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393409 Affx-122965886 AX-123263765 5 10684878 TGAATGGTGCCTAAGCGTCAGGCACTGTCCCAACC[A/G]CTTTACTTGTGGCATTTTCATTTCATCTTCCCAAC R 2 1 2 1 101000 r 74 goat snp34501-scaffold405-2945762 5 11051719 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800634 Affx-122976982 AX-385287553 5 10744591 ACTTTAGGGCCTAATCTGAGTCATGTTCTGTGTTT[A/G]CAGTATAGTGTGGCTGATATGTACTTTTTTTTTTT R 2 1 2 1 101000 f 74 goat snp34500-scaffold405-2886049 5 11111610 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790526 Affx-122962414 AX-385277529 5 10799280 CATTTTAAGTTATATCTTCTATCAAAAAAAGTTAA[C/T]GTTTGGTCTTTGTCTTGCTGTCAAGAGCTGATTAG Y 2 1 2 1 101000 r 74 goat snp34499-scaffold405-2831360 5 11167116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447688 Affx-122924625 AX-123318024 5 10845868 TGTGATGAGGGACACCTCTATTGAAATGGGAAGGA[C/T]AAATAGGACAATGTGGACAGGTGGTTTGCAAGACT Y 2 1 2 1 101000 f 74 goat snp34498-scaffold405-2784772 5 11214796 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454125 Affx-122919344 AX-123324458 5 10883744 GTTTTGCTTTTATGTCTTTGCATTTCCTAGATTAG[C/T]AAAAGAAAAAAAAAGTGTATTTTTTGCTTTTATAA Y 2 1 2 1 103000 f 74 goat snp34497-scaffold405-2746896 5 11252512 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453265 Affx-122920397 AX-123323598 5 10917098 CTTTCAATGTCCTAGTTTTTCTCCATAGCCATTAT[A/C]TTGTATACTATATATTTTGTTTATTTTGTTTCCTT M 2 1 2 1 101000 f 74 goat snp34496-scaffold405-2713542 5 11286611 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403863 Affx-122957926 AX-123274215 5 10945813 AAGCACTGTGTGAATGCTGTGTGTGCCATTGGTGC[A/G]TCAGTTAAAGCAGCCCTGGGCAACTTTTTACTTAC R 2 1 2 1 201000 r 74 goat snp34495-scaffold405-2684827 5 11315803 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453281 Affx-122920385 AX-123323614 5 10981383 TAGAGCTACTTCTATAAAAGTAAAGCAGTATTTTC[A/G]TAGGAAAGTAATTCAAGGGCTTCTTTCTCTGGTTT R 2 1 2 1 101000 r 74 goat snp34494-scaffold405-2649257 5 11351418 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791803 Affx-122950534 AX-385278793 5 11034120 AGCACACAATGTTCCCTAGATATTGCAAAAAGATT[A/G]TATTGTACTCTGGGAAAACTTTCTAGAATTGAATA R 2 1 2 1 201000 r 74 goat snp34493-scaffold405-2596520 5 11404252 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783081 Affx-122943782 AX-385270148 5 11066517 CTCTTTCTTCCTATATTATGGGAATTTACATATTA[C/T]GCTTATTTTCTTGAGAGATTTATCCATAGGCACCC Y 2 1 2 1 101000 r 74 goat snp34492-scaffold405-2564123 5 11436571 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431814 Affx-122936109 AX-123302155 5 11109812 TCAGCTAGCTAAAGCAATGTGCTCCCAGAATCTTT[A/C]TTTGTATTTACAGCAAGTCAGAAGAGTTAAAAGAG M 2 1 2 1 101000 f 74 goat snp34491-scaffold405-2520828 5 11480739 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396303 Affx-122963088 AX-123266658 5 11168253 CCAAATAGGCATATTATAAGCAAGATTTTGGAAAA[C/T]ATTAATACTTGTAGTCACAAATGGTAGGCTGCATG Y 2 1 2 1 101000 f 74 goat snp34490-scaffold405-2462387 5 11539863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440782 Affx-122929846 AX-123311119 5 11203545 TTTAATGTAACACATTTAATTCCATAGGGCAGATA[C/T]GCTCATGAGATTTCTATTTGCAGACAAGAAACCAG Y 2 1 2 1 101000 f 74 goat snp34489-scaffold405-2427095 5 11576006 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380675 Affx-122975181 AX-123251033 5 11246408 AAATATATACATTCAACTAATTTTATTTTAATACC[G/T]CAATTCCTGTGCCTATATTCTATGGCTTGAAATCC K 2 1 2 1 101000 r 74 goat snp34488-scaffold405-2384232 5 11619476 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431452 Affx-122936497 AX-123301793 5 11286969 TGAACCATGACGCCACACTAGGTAGGAACAAAGTT[A/G]TAGGGAAGAGAAGATATTTTAGCTGTATATTTAGG R 2 1 2 1 101000 f 74 goat snp34487-scaffold405-2343671 5 11659619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792897 Affx-122953810 AX-385279875 5 11316777 TTATTTGGATGTCTTACTAGCAAGATTTAATGTCT[G/T]TCTTTCAACATCTCTCCCCCTGCCTTAAGTTGCAT K 2 1 2 1 101000 r 74 goat snp34486-scaffold405-2313863 5 11690185 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389177 Affx-122969087 AX-123259535 5 11396183 AGCTGAGAAGAAACTCTTAAAGCACTCCTTTCCCA[C/T]GCCTTTTAGAAAAATTATATAAAATGATATTCAGA Y 2 1 2 1 101000 f 74 goat snp34484-scaffold405-2234457 5 11770319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425633 Affx-122940896 AX-123295979 5 11458670 TTATTTCATTCTCATCTTGGTGTATAATCAGCTGC[A/G]TTTAACAGTTTGGGGCTTATTTATTGAGACAAAGG R 2 1 2 1 101000 f 74 goat snp34483-scaffold405-2171970 5 11832772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445920 Affx-122925930 AX-123316257 5 11488966 TTCCATGTTTCCTTTTGCCAAGACTCACAAATAAA[C/T]GAAAAAATGAGAAGTAAATTATACTATTTGACCAT Y 2 1 2 1 102000 f 74 goat snp34482-scaffold405-2141674 5 11863244 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379094 Affx-122976765 AX-123249453 5 11525503 GCCAATGCCTCAATTAGCCCTTGTGTTTTAAGTAG[A/G]GAACTGATTGTTAGACATTGTCCAGCATACCAACA R 2 1 2 1 101000 f 74 goat snp34481-scaffold405-2105137 5 11900470 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448525 Affx-122923445 AX-123318861 5 11554629 CAATTTCCTTTACAGTGCTGTATCAACTGATACTG[A/C]AAAATGCAGGAGAGAAAGTAACATAATCAAAGAGT M 2 1 2 1 201000 r 74 goat snp34480-scaffold405-2076011 5 11927046 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438209 Affx-122931454 AX-123308547 5 11610348 CTAGCCCTGAATAAAGCATTTCTGACGAGATGCTT[A/C]TCTTGAAGAATCTTCTACATCGACTATAACACTGC M 2 1 2 1 101000 r 74 goat snp34479-scaffold405-2020292 5 11982438 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384122 Affx-122972822 AX-123254480 5 11662779 TGCAGTAACAAGGTGGGGTATGACAAAGTAAGTAC[G/T]CCTTTGAGTAAATTGTGCAATCTCACAGTTACTGT K 2 1 2 1 101000 f 74 goat snp34478-scaffold405-1967861 5 12033719 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447976 Affx-122923756 AX-123318312 5 11694287 AGGAAGGGAAAGGCAAATGCTAAGAAATATATGTA[C/T]GCTGGAAGAACAGTACGGATTTATCCACAGTCTCT Y 2 1 2 1 101000 r 74 goat snp34477-scaffold405-1936353 5 12065472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420133 Affx-122946006 AX-123290481 5 11731225 CTTAGGGTATTTCACTTTGATTCATTTGTTTCACC[A/G]CCTTATTACATCAACAGAAATGTTTCAAACAGAAA R 2 1 2 1 102000 f 74 goat snp34476-scaffold405-1899415 5 12102453 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794999 Affx-122921397 AX-385281958 5 11763843 CTCTTCCATTCAAAAGAATTAGTTAAGTCTGTTGA[C/T]GTTTTCCAGTAAATGGACAAGCTGTAATACATGCA Y 2 1 2 1 101000 r 74 goat snp34475-scaffold405-1866797 5 12135270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790041 Affx-122924858 AX-385277047 5 11794285 AGCACTCTGCTTTTAGCCAGCCACAGAGATAAGGC[A/G]TGCAGTCTCAGTAACAGAATCACCTCAATTTAATT R 2 1 2 1 101000 f 74 goat snp34474-scaffold405-1836355 5 12165569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378865 Affx-122976517 AX-123249224 5 11843290 CAACACCAAGGCTATTTAAAAATAGCTTGGTTATC[A/G]TCATATACAGAAAGTTGGCCTTGTCACCTCTATAT R 2 1 2 1 101000 r 74 goat snp34473-scaffold405-1787350 5 12214469 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431804 Affx-122936116 AX-123302145 5 11898967 GCAGTTACTAACTTAAGAATAAGCAAGAGGAGTTC[A/C]AAAAATGAAAGTTTTAGCCTATCTCCTTCGGCCTG M 2 1 2 1 101000 f 74 goat snp34472-scaffold405-1731673 5 12270425 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772888 Affx-122957887 AX-385260033 5 11936101 TCTATACAACTTAGAAAAACTTCATGTAATCATTC[A/G]TTATATCTCAGTGATAATGATGACAATAGCATTCA R 2 1 2 1 201000 r 74 goat snp34471-scaffold405-1694539 5 12307733 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414105 Affx-122949738 AX-123284454 5 11974629 TTACCTTTTGCTTCTAAATAAACTATTTCCTACCA[C/T]GTAACTGTCCTTTAACTGTCTTCTTTTTTTTTGAA Y 2 1 2 1 101000 f 74 goat snp34470-scaffold405-1656011 5 12346052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384988 Affx-122971889 AX-123255346 5 12026106 GGTATCTCTAGAAAAACATGGCCCCATAAGACCAA[C/T]AGAGGATCAGAAATATAGATGTCTGAAAGGTTAAT Y 2 1 2 1 201000 r 74 goat snp34469-scaffold405-1604534 5 12397921 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783942 Affx-122973766 AX-385270996 5 12054956 AATGCCATTCAGAGCAATCATATTTCAGCATGACA[C/T]TAGAAGGCAGCAACTGTCCACCCACAGAATGAATA Y 2 1 2 1 101000 r 74 goat snp34468-scaffold405-1575684 5 12426494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425515 Affx-122941468 AX-123295861 5 12118152 TCACCTTTGTCTACCTAATTATTTACCTTTTAGGA[C/T]ACAATGCTTGACAGTGTCTATTTTACATGTATAGT Y 2 1 2 1 101000 f 74 goat snp34467-scaffold405-1512488 5 12491106 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407220 Affx-122955383 AX-123277571 5 12184026 CTACAAGGAAAGGGAAGGTTTGTAGTCTATGTAGA[C/T]ATTCCCCATATAAAGGAGCCTAAGAGATAATATTT Y 2 1 2 1 101000 f 74 goat snp34466-scaffold405-1446614 5 12556850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800813 Affx-122932858 AX-385287729 5 12240004 TTATATCTCAGACTTAACTATGGTATATGTATGGT[A/G]TAAAGTATGAATATATCTTATCCATACTTTAAGTT R 2 1 2 1 201000 r 74 goat snp34465-scaffold405-1390636 5 12614285 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780472 Affx-122922216 AX-385267563 5 12281369 ATTAAATTCAAAACACAGCAAATTGTACCACTCTA[C/T]GAGAGTGGTTCCTTAACATCACTTCCTATATTGGT Y 2 1 2 1 101000 r 74 goat snp34464-scaffold405-1349271 5 12663231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448505 Affx-122923457 AX-123318841 5 12314446 CATATTACCTCTGGATGCTGGACAGAGAGACGAGA[C/T]GGACAGCTCCCAGTCAGCCACGTGACCACGAAAGT Y 2 1 2 1 101000 f 74 goat snp34463-scaffold405-1316194 5 12696718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786728 Affx-122960790 AX-385273759 5 12360528 TATTCAAGTAAGCAAGGATACCAGGCAATATTCAA[C/T]GGCATTATGTTAAGTAATAAAGAGTGATAGATAGT Y 2 1 2 1 201000 f 74 goat snp34462-scaffold405-1270112 5 12742809 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449505 Affx-122922621 AX-123319840 5 12407672 TTGTTCTAAGTACTAAGAATGTACAACAGACAAAG[C/T]ACTAGAGATTCTGCCCATATGAAAAAGAAAGGACT Y 2 1 2 1 101000 r 74 goat snp34461-scaffold405-1222968 5 12790222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382962 Affx-122973362 AX-123253320 5 12462544 AACACATCTTCGTATATAAGGGATTTGAGCATTCA[C/T]GGATTCTGGTATTTAGGATGATCCTAGGACTAATC Y 2 1 2 1 201000 r 74 goat snp34460-scaffold405-1168096 5 12844157 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388577 Affx-122969167 AX-123258935 5 12508427 AAAAGCAATAATGTTTATTTGGAAGAAAATTTAAA[C/T]GAAAAGAACAATGGGTTGGGTGGAGAACAAAACAA Y 2 1 2 1 103000 r 74 goat snp34459-scaffold405-1122213 5 12889946 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789351 Affx-122976422 AX-385276362 5 12537723 TTTCTGAGGAGCAATGTAAGCAATCCTTCATACTG[C/T]AGGTAGTAAGCAAAAGGTAGACTTTGTAGAGATCT Y 2 1 2 1 101000 f 74 goat snp34458-scaffold405-1092917 5 12919585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801860 Affx-122956039 AX-385288767 5 12588217 AGTATGTTATTACAATGTTTTGAACTTTACTCAAG[C/T]ACCCACTGAATTTTGAATACATAGTCTAAATATGC Y 2 1 2 1 101000 r 74 goat snp34457-scaffold405-1042423 5 12969958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448773 Affx-122923309 AX-123319109 5 12617400 TTTGGTTGAGCCAACATTATGGTGAACCAATTATG[A/G]ATTCTGGAAAATAATAGGGACCATGGAAAGCTTTC R 2 1 2 1 101000 r 74 goat snp34456-scaffold405-1013240 5 12999817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476197 Affx-1251763702 AX-586011623 5 12646294 TGACCCAGATAGCCATAATGGTGTGATCACTCACC[-/TTGAGCCAGACATTTTGTTTTTATTTTATTTTTTTTTTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TGAGCCAGACATTTTGAATTCCTAAGGCCTTGGGC - 4 1 4 1 20000 f 74 goat SV_165 5 12646294 - deletion junction SV-TF-chip 539476452 Affx-1251763702 AX-586011853 5 12646294 TGACCCAGATAGCCATAATGGTGTGATCACTCACC[-/TTGAGCCAGACATTTTGTTTTTATTTTATTTTTTTTTTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TGAGCCAGACATTTTGAATTCCTAAGGCCTTGGGC - 4 1 4 1 20000 r 74 goat SV_165 5 12646294 - deletion junction SV-TF-chip 562165242 Affx-1251763702 AX-606940654 5 12646294 TGACCCAGATAGCCATAATGGTGTGATCACTCACC[-/TTGAGCCAGACATTTTGTTTTTATTTTATTTTTTTTTTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TGAGCCAGACATTTTGAATTCCTAAGGCCTTGGGC - 8 1 4 1 20100 r 74 goat SV_165 5 12646294 - deletion junction SV-TF-chip 562166420 Affx-1251763702 AX-606941828 5 12646294 TGACCCAGATAGCCATAATGGTGTGATCACTCACC[-/TTGAGCCAGACATTTTGTTTTTATTTTATTTTTTTTTTTAGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TGAGCCAGACATTTTGAATTCCTAAGGCCTTGGGC - 8 1 4 1 20100 f 74 goat SV_165 5 12646294 - deletion junction SV-TF-chip 38394848 Affx-122964775 AX-123265203 5 12671367 AGATGATATTGTGAAGTTTTATCTGGTTTTTGTGA[C/T]ATTTTATTGTGAAGTTTATCTGCCCTCTTCAGTTC Y 2 1 2 1 101000 r 74 goat snp34455-scaffold405-959273 5 13054069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795233 Affx-122927255 AX-385282191 5 12700252 CTCAGTTATCTTCTGTTTTAACTCCTTCTTTGTTC[C/T]GTTTATATCATATACTAGAACTTTGAATGTTTATT Y 2 1 2 1 101000 f 74 goat snp34454-scaffold405-930388 5 13084173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796883 Affx-122925861 AX-385283825 5 12733275 AAGAGGCATGTGCTTTTGCTAAAGTATTCTTTGAA[G/T]AACAAGCTCACACCTCCCCTTTTATCCATTTTGTT K 2 1 2 1 202000 r 74 goat snp34453-scaffold405-897365 5 13117368 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771071 Affx-122933169 AX-385258231 5 12816267 TTAAAAGTAAGTTAAGCCCTTGCTTATTCAAACAT[C/T]AAACTGTCAGCATGGAAGTAAATTTAAAACTTATG Y 2 1 2 1 101000 f 74 goat snp34451-scaffold405-814373 5 13201598 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445095 Affx-122926201 AX-123315432 5 12855027 GTATGGACACACAGTACCTCCAACTCCTATAGCTG[C/T]GTTCATTCCAGGAAAAATGATTCTAATTGTCCTTT Y 2 1 2 1 101000 f 74 goat snp34450-scaffold405-775613 5 13240231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768958 Affx-122950852 AX-385256133 5 12901288 TTACTGTGAGTTAATCAAGTCCATCCTGATATAAC[A/C]AGAAACTCTTCTTCTGGTACAATAACTTTCAGTTA M 2 1 2 1 201000 f 74 goat snp34449-scaffold405-729352 5 13287400 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768425 Affx-122965890 AX-385255605 5 12958055 AGCAAAGCATAAATCTGCTTAGGTGCTATGGATAT[A/G]CAGAATCAGATATTTAGCATTCTCCTTTCCTTTCT R 2 1 2 1 101000 r 74 goat snp34448-scaffold405-672585 5 13347337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394816 Affx-122964800 AX-123265171 5 12994692 AAGGAGCAAAATATCAACCATTCGGCTTTACCCAG[C/T]ATGGGGCTGCTAACCCTGTCTTGCTTTGACTTTCA Y 2 1 2 1 101000 f 74 goat snp34447-scaffold405-635948 5 13384774 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438029 Affx-122931560 AX-123308367 5 13029227 CTTCTAAAATGTGTTCAGGATGGTCACAAACTAGA[C/T]GTAGATGCACAGGAGTTAATTTATTCTCCAACACC Y 2 1 2 1 101000 f 74 goat snp34446-scaffold405-601413 5 13419540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278178 Affx-1111836290 AX-519551667 5 13053984 CATTTTTTGTAACAGGCATCTTTGAATGGCAAAAT[A/C]GGAGTGTATGTTTATAGCAACAAATTTTTGGCTCA M 2 1 2 1 101000 f 74 goat Random2.2K-521 5 13053984 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392030 Affx-122966472 AX-123262387 5 13062243 TCAGTAAGCACTACACAGATCCATGATTGGTTGAA[C/T]GAGAGCATTCAGAACTGTGGCTTTGTAGGGTAGAT Y 2 1 2 1 201000 f 74 goat snp34445-scaffold405-568397 5 13452995 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768937 Affx-122943944 AX-385256112 5 13109948 TTTAACAACACCTATTTGCGACTTATCTTGACTAT[A/G]TTCATTTTCACACCAAGTGGCTGGATAATTTGACA R 2 1 2 1 101000 r 74 goat snp34444-scaffold405-520692 5 13500743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418803 Affx-122946171 AX-123289151 5 13157298 ACAACATGGAAAGCATGAGAAGACATCAATTCTGC[C/T]AACAAGCAGTGACTTTGGAGGTAGACTACAAGACT Y 2 1 2 1 201000 f 74 goat snp34443-scaffold405-473342 5 13549093 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429899 Affx-122938117 AX-123300240 5 13193135 AAATTCATATAAAATAAGGAAGGGAGTTGTGCTGT[A/G]TTAATTTATATTTTTCCTATTTCCTACTGCTGACC R 2 1 2 1 103000 f 74 goat snp34442-scaffold405-437505 5 13585671 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426397 Affx-122940847 AX-123296743 5 13237559 CAATTCCTTTTTAAAGACAGTTTCACCAAAGTATC[A/G]TTTATATACAGTAAAATGAATCCATTCTTAAGTGT R 2 1 2 1 303000 r 74 goat snp34441-scaffold405-393081 5 13630138 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272300 Affx-1111833457 AX-519546039 5 13254143 ACCTGGTGAGCTACACTTTTGGGGAAGCAAGAGTC[A/G]GACACAACTAAAGAGACTGAGCACCATTTCATACC R 2 1 2 1 201000 f 74 goat 5_13254143_AF-PAKI 5 13254143 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320770180 Affx-122927022 AX-385257347 5 13322272 TTGTAAACTTCAAATTAGCAAGAATGAAATGTAAC[A/G]CAAAACAACAGCTTGGAATAGATCCATTGTTTATT R 2 1 2 1 101000 r 74 goat snp34439-scaffold405-308368 5 13719164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278180 Affx-1111836291 AX-519551669 5 13358822 TTTGGCAATGTTAAAAAATTTGCCCTACCTAAACT[A/G]CAAATGTTGATTTAATTAAGCAGTATCATCTACAA R 2 1 2 1 101000 f 74 goat Random2.2K-522 5 13358822 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424743 Affx-122941657 AX-123295089 5 13373151 GACTGAGCCTGGATTATATTAGTGGTTCTATAGTA[A/G]CAAAATTGCATCTGGAGACCATACGTACACTTTCT R 2 1 2 1 101000 f 74 goat snp34438-scaffold405-257489 5 13771877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776660 Affx-122932233 AX-385263787 5 13404837 CAGTGATACAAATTTCTGTTCAAATTTTATAAAAG[C/T]GTTTAATTTTAGAATGTAATTGCAGAATTCTGGAT Y 2 1 2 1 101000 f 74 goat snp34437-scaffold405-225803 5 13803158 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794736 Affx-122936075 AX-385281696 5 13441236 TCTTTTAAACGTTTATGTTTCCACCCAAACACATC[A/G]TCAATAGAAAACAAACACTTCCTCTTAACAGAGAT R 2 1 2 1 101000 r 74 goat snp34436-scaffold405-189404 5 13840303 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796340 Affx-122976767 AX-385283290 5 13491910 CTTTGCTGTTTTTATGTATTTCCTTTGTCAGTGAT[A/G]TTGAAAATCAATTTTTACAGTAATGCTGTTATTTA R 2 1 2 1 102000 f 74 goat snp34435-scaffold405-138730 5 13889797 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278339 Affx-1111836292 AX-519551825 5 13516520 GCCAGGAGTCTGCGAATCTCAGGCAAATTTTTAAT[A/C]TCTTTCCCCTCTGCCGTCAGAAGCCCCCGTTCTTT M 2 1 2 1 202000 r 74 goat Random2.2K-523 5 13516520 A C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381286 Affx-122974465 AX-123251644 5 13541555 CTAGAGAGAGAGGGAAAGATGGCGGAGGAATAGGA[C/T]GGGAAGACCACTTTCTCCCTCACAAATTCCTCAAA Y 2 1 2 1 303000 f 74 goat snp34434-scaffold405-89085 5 13940272 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431598 Affx-122936169 AX-123301939 5 13610697 AGAAGTTAGTATAGTAAGATTTCTCCCACTAATAC[A/G]TTTGAGAGCTTCTGGTGCAAATAAAGCAATTATGA R 2 1 2 1 101000 r 74 goat snp34433-scaffold405-19943 5 14008417 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414631 Affx-122949335 AX-123284980 5 13637149 TGGAATACAGAGAGAAACTTGAGCTCTGTAACAGA[C/T]GTACATCTATTCACTTTGGAACACAAATATAATAT Y 2 1 2 1 201000 r 74 goat snp43287-scaffold577-6410 5 14036504 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448918 Affx-122923166 AX-123319253 5 13681883 GAGAGTGACTTCTGTCCCTTAAGAATCACTGGATC[A/G]TTAGTGGCTTATGTTCAGTTCAGTTCAGTCACTCA R 2 1 2 1 101000 f 74 goat snp43288-scaffold577-51144 5 14081951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398116 Affx-122961704 AX-123268471 5 13735826 AAACACTTAAGGATGAAAGGGTGCAGCATATTCAA[C/T]GGAAGGGAGAAATTATTTTGTAAATAAAGCATTAA Y 2 1 2 1 101000 f 74 goat snp43289-scaffold577-105087 5 14136024 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429798 Affx-122938200 AX-123300139 5 13778481 AGTTAGGTGCCCTTATTACATCAATGTAGCATGCA[C/T]GAATTAACAATAGCAAAAAGTAATTTTAAATAGGT Y 2 1 2 1 101000 f 74 goat snp43290-scaffold577-147742 5 14179232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423354 Affx-122943153 AX-123293700 5 13808719 TTTATCCTTTCATCAAATTCCTTGCCCTTGAGTTA[C/T]ATCTTATTTTTGGCTGCTATATTGTCCATTGCACT Y 2 1 2 1 101000 f 74 goat snp43291-scaffold577-177980 5 14210211 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780429 Affx-122976513 AX-385267521 5 13842599 ATCAGGTTTCTTGCAAATAGCCATACAGCTAGCAC[A/G]ACTGTGTGTTTGGGAAGACAGAATAAATAGTCTTT R 2 1 2 1 201000 r 74 goat snp43292-scaffold577-211860 5 14244421 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423917 Affx-122942272 AX-123294263 5 13877097 AGCTGCTCAAGCCCTGGCAGGGGGCTCTATGGGAA[G/T]AACAAGAGAGGACCTGTGCCTTCTCCTCTTGTTGA K 2 1 2 1 102000 f 74 goat snp43293-scaffold577-246358 5 14277388 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394010 Affx-122965018 AX-123264365 5 13908422 ATCTCAACAACTGAATCTCCAGACATCTGGCATCA[G/T]CCTGAACTCAATCAATCAGTAAACCTCAGTTTGTT K 2 1 2 1 101000 r 74 goat snp43294-scaffold577-277683 5 14309146 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476198 Affx-1251763703 AX-586011624 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 4 1 4 1 20000 f 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 539476453 Affx-1251763703 AX-586011854 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 4 1 4 1 20000 r 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 562165342 Affx-1251763703 AX-606940753 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 8 1 4 1 20100 f 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 562165421 Affx-1251763703 AX-606940832 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 8 1 4 1 20100 r 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 562165443 Affx-1251763703 AX-606940854 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 8 1 4 1 20100 f 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 562165512 Affx-1251763703 AX-606940923 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 8 1 4 1 20100 r 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 562166219 Affx-1251763703 AX-606941627 5 13915018 TTCTCTTGTGTCAAGATTGATAAGTATATTTTCTT[-/TGGTCTTCTTTTTATTTTTTTTTATTTTTATTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]GGTCTTCTTTTTAAAATAAACTTATTTTGAAGGAT - 8 1 4 1 20100 f 74 goat SV_168 5 13915018 - deletion junction SV-TF-chip 320796319 Affx-122969964 AX-385283269 5 13938202 CCTGGGTGCTTTGGGGCAAGCAAACTAACTGGATG[C/T]AATCATAATGTATACTTTGCTAGATGAAAAGATCA Y 2 1 2 1 101000 f 74 goat snp43295-scaffold577-307463 5 14338672 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437404 Affx-122932425 AX-123307742 5 13971861 AGTGGTTTGTCCCAACCTTTCATATTTGAGGGTTC[A/G]CAGGAATATCTTCTTTCCAGTGCCCATGGGTATTT R 2 1 2 1 101000 r 74 goat snp43296-scaffold577-341122 5 14372265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431948 Affx-122935971 AX-123302289 5 14001359 AAACAGAACTATCAGGAAGGACATGAAGTAGTGAG[C/T]GATAAAGTAGTGGTATCCTACAGGTCACATGAGCA Y 2 1 2 1 101000 r 74 goat snp43297-scaffold577-370620 5 14401603 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380042 Affx-122975578 AX-123250400 5 14057165 TTATTTTGCTTAGTTATAATGTCTTCCAGGTTCAC[A/G]CATACTGTTACATATGGCAGGATTTTCCTATTTTC R 2 1 2 1 201000 r 74 goat snp43298-scaffold577-426426 5 14457816 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408541 Affx-122953687 AX-123278892 5 14091055 AAGAGTGCTTCCTCATTTCTCCTCCAGTCTATAAT[A/G]TTTTGCAAACAGTCTTATTCCCCATGAGAAAAGGA R 2 1 2 1 201000 r 74 goat snp43299-scaffold577-460316 5 14492047 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422538 Affx-122943271 AX-123292884 5 14127562 TACTAAAAAGGTTGTCAGTGAAAATGATTTGCTTA[C/T]ACAAAGTTACACAAGTTAGTGCAGTTCCTATGTAA Y 2 1 2 1 101000 r 74 goat snp43300-scaffold577-496823 5 14528022 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785879 Affx-122949771 AX-385272917 5 14165337 TCTCATGTCTTACTACTTAACCTCCCTTTTCTGCC[A/G]CCTGAAATTCAGCTTCTACTCACTTCTATACATTT R 2 1 2 1 101000 f 74 goat snp43301-scaffold577-534598 5 14566035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792226 Affx-122969033 AX-385279210 5 14194221 CACAAGTACATTCCCTGCTCTAAATGAGCTAATAG[A/G]AAATCCTGTTCTTGATTAGCTCTGAAAAACTTAAG R 2 1 2 1 101000 f 74 goat snp43302-scaffold577-563482 5 14595781 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438300 Affx-122931387 AX-123308638 5 14236673 GTTGATTGATGGAATGCCAGATAATAGCCAATAGA[C/T]GTAGACTGGAAAAATGTTAGAATCTACTACTGGGC Y 2 1 2 1 101000 f 74 goat snp43303-scaffold577-605934 5 14642989 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275362 Affx-1111834855 AX-515815391 5 14258585 ACATGGGTTCTTAGCTCTAATCTGCAGTGTCTATC[A/C]CTAGCCCATCTTCTGTTGTTTATCCCTA M 2 1 2 1 101000 f 74 goat GoatD01.056684 5 14258585 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320782471 Affx-122973762 AX-385269547 5 14274494 AGAAATTCCGCTAAAATAAATAACAACTCCATAGA[G/T]CTTACCTGTTAAGTAGTAGCATCATTACTTTAGGA K 2 1 2 1 201000 f 74 goat snp43304-scaffold577-643755 5 14680113 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441443 Affx-122928773 AX-123311780 5 14306652 ATTTCCTATGGCTGGAAGGTCCATTGTTCTTTTTT[A/G]TCCCAGTAATTTAACATTTGAATAGGTTTAGAAGA R 2 1 2 1 201000 r 74 goat snp43305-scaffold577-675913 5 14712146 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402026 Affx-122958744 AX-123272379 5 14339212 TTCGCAAGCCAAATCTAGAGAGCAGTTTATGGGTT[A/G]CAGCTATAAAACTTTTTCAGCTTTTGATCTTTTCT R 2 1 2 1 201000 r 74 goat snp43306-scaffold577-708473 5 14744736 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391416 Affx-122966767 AX-123261773 5 14386598 TCCTTGAGTTTAAGAACCAAGCAAGTATCTATCAA[C/T]ATTAGATTCTAATGTGTTTCTAATTTATTAAAACC Y 2 1 2 1 101000 f 74 goat snp43307-scaffold577-755859 5 14791704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278341 Affx-1111836293 AX-519551827 5 14429047 CTTCTTGAATAGATGTTAGCTGGTCTTATTAGGGC[A/G]AATGAAGTCAGGAATGATTTATGTTACCATCTCAT R 2 1 2 1 201000 r 74 goat Random2.2K-525 5 14429047 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433459 Affx-122935057 AX-123303800 5 14473161 TGTGAATGTTACATTTTTGAGTTTGCTGCACTGGA[C/T]GATATCTTAAATTTCACTCCCTTCTCTGGGCAGCA Y 2 1 2 1 101000 f 74 goat snp43309-scaffold577-842422 5 14878228 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378164 Affx-122976965 AX-123248523 5 14504023 CCTTAATATGGGAGAGTGCTTTAAAGATGAAATAC[A/G]TTAAGCACTAAGAAGTTGGGGCCTAGGTCTATCCA R 2 1 2 1 102000 r 74 goat snp43310-scaffold577-873284 5 14909181 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800533 Affx-122955044 AX-385287453 5 14548578 TGGTGTCCTACTAGCTTCCCAGGCTTCAGAAAAAA[C/T]GAAAAATCTGAGTTCTCCCATTATGAGATTTCACC Y 2 1 2 1 202000 f 74 goat snp43311-scaffold577-917839 5 14953370 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452409 Affx-122920597 AX-123322742 5 14616205 TACTGTAATGGAAGAATTCAGCCATCTTATTCACA[C/T]GTAAGATGGGGTTGTGGGCATGTTATGAGGATTTT Y 2 1 2 1 201000 f 74 goat snp43313-scaffold577-985466 5 15023010 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782088 Affx-122931831 AX-385269166 5 14674226 TAACCTCTTTATCACAGAAATGTTTGGGGTTTGGA[G/T]AATTTCACTTTTCATGTCTAGCTAGTATTTATCGT K 2 1 2 1 101000 f 74 goat snp43314-scaffold577-1043487 5 15082482 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787450 Affx-122972225 AX-385274475 5 14729185 ATTTGATGGGCTATAAACAGGGTGTATGTCACAGT[A/G]TTAACACCATGAATGGATGTATATGTACAGAACAA R 2 1 2 1 101000 f 74 goat snp43315-scaffold577-1098446 5 15137822 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800300 Affx-122924031 AX-385287223 5 14782880 ACTAAGATACTCCCAATGCACACATGAGTGTAAAT[A/G]CGAGGGAATACTGTTAGCTCACTGGACACTATTGT R 2 1 2 1 101000 f 74 goat snp43316-scaffold577-1152141 5 15191827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402587 Affx-122958434 AX-123272940 5 14822710 TACTGTTCTCAGGTCTTTCTATGCGTTCTCATTTA[A/G]CCCTCACAACAATGTTATCAGGTAAATTTATTGTC R 2 1 2 1 101000 f 74 goat snp43317-scaffold577-1191971 5 15232284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412827 Affx-122950466 AX-123283176 5 14885298 ATATCATTAACCTGAGACATTTTCTTCTGCTGCTT[A/G]CTTCTACAACTAGTCCTTTATCAGCTTCATCATTT R 2 1 2 1 201000 r 74 goat snp43318-scaffold577-1254559 5 15295488 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771585 Affx-122938137 AX-385258743 5 14921503 AAGTAAGGCCTTCAGCAGAATCTTAGTATGAAAAA[C/T]GGTAACATTAGATACTCCCCAAAACTGAAATATTA Y 2 1 2 1 201000 r 74 goat snp43319-scaffold577-1290764 5 15329809 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446880 Affx-122925234 AX-123317216 5 14951037 ACACCACGTGGCTTATTTAGCTGCTTAGTTGGAAA[C/T]ACCCACAGTTTTACATCCCAAGTCACCTCTGTGGT Y 2 1 2 1 101000 r 74 goat snp43320-scaffold577-1320298 5 15359199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380861 Affx-122975436 AX-123251219 5 15010624 CCTTTGATATTCCCAAATGTAAATTGTCTGGTAAG[C/T]GGCTGAATAAAGGAGATAGCGTTTTAAGGAGAGGT Y 2 1 2 1 101000 r 74 goat snp43321-scaffold577-1379885 5 15417400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399279 Affx-122960550 AX-123269634 5 15069896 CTCCTTATAGCTAGGCAGGACTATTTCAACAACAA[C/T]AAAAAAATCCAGTTTTGCAAGAAGACAGTCTATGA Y 2 1 2 1 202000 r 74 goat snp43322-scaffold577-1439157 5 15477217 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404294 Affx-122957032 AX-123274646 5 15103922 TACAAAATATGTGGTAAGGACATGTAACCAAAAGC[C/T]AGTTTGCCTACTTCATAGTGGGTGGGATGGGGAGA Y 2 1 2 1 101000 f 74 goat snp43323-scaffold577-1473183 5 15511456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380291 Affx-122975407 AX-123250649 5 15177065 GGTCTCTGAATGTAAGACCTCTTTACATAATGTCC[G/T]CACTTATTTTCAATAGTCAAATTTTAATATCGGAA K 2 1 2 1 101000 f 74 goat snp43325-scaffold577-1546326 5 15586506 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768712 Affx-122950069 AX-385255890 5 15224974 TGCACAGTGCTTAATAACAAGGAAATTACATTATG[C/T]GGTTAATACCTAATAAAAGGCATTGCTCATATTAT Y 2 1 2 1 101000 f 74 goat snp43326-scaffold577-1594235 5 15634884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402514 Affx-122958489 AX-123272867 5 15288767 ATGCAATTAGAGCAGTACAAGCAATTAACTTTGCT[A/G]TTTAGTATAAAGTTGAGAGCACTAAAGACTGAAGT R 2 1 2 1 202000 r 74 goat snp43327-scaffold577-1658028 5 15699060 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788433 Affx-122929933 AX-385275450 5 15321722 GTTACTCAATTCTGGCATTGATATTCATATCAATA[C/T]AAGATTTGAAGGAGACATAGAATTATGGTAATGCT Y 2 1 2 1 102000 r 74 goat snp43328-scaffold577-1690983 5 15732018 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452666 Affx-122920327 AX-123322999 5 15355511 CATGTGTTAATATCAGTTATGTTTTTTCTTATCAT[A/G]CTATTGTAAGAATAATATATCAAAATGTCTTTATA R 2 1 2 1 101000 r 74 goat snp43329-scaffold577-1724772 5 15765686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765319 Affx-122940426 AX-385252841 5 15470536 TCTGATTGAATGGTGTAATATGATACAAATACATC[A/G]TATAATGCCTAGCATCTGGTACAGGCACATTTTCC R 2 1 2 1 101000 f 74 goat snp43331-scaffold577-1839797 5 15882095 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787429 Affx-122972218 AX-385274454 5 15522930 TTGCTTCTATTTAGTTTGTGACTTTTGGGATAACT[A/G]TTTATAGGTACATACATCTCTTTTAGCTTAAAAAT R 2 1 2 1 101000 f 74 goat snp43332-scaffold577-1892191 5 15936205 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393435 Affx-122965864 AX-123263791 5 15535777 GCAGTGTAGGGCAAAATGCCTAATGAATGATTCTT[A/G]TCACATCATGGTGAGCTCTACTGCTTCTCAGTATT R 2 1 2 1 101000 f 74 goat snp36630-scaffold443-1619 5 15950639 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394094 Affx-122964950 AX-123264449 5 15619038 GAGCATATATTTTATGTTTCTTTTTGATTATTTTT[A/G]CAGTAACTTCCCAATGCAGGTAGGTTAAAAAAGGC R 2 1 2 1 101000 r 74 goat snp36632-scaffold443-84880 5 16034314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452342 Affx-122920649 AX-123322675 5 15665578 ACCATTGAATCTTTGGGTTGGAGAAGACCTTGACA[C/T]GTTCCAGTCTCAAGTCTAATAACTTTCCCTGTAAT Y 2 1 2 1 101000 r 74 goat snp36633-scaffold443-131420 5 16080623 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770265 Affx-122936769 AX-385257431 5 15712214 ATACTCAATCTACAGAATCCTGTGCTATCACTGTC[A/G]CTTGTCTATATGGCTTCATGAAGACCATCTCCATG R 2 1 2 1 202000 f 74 goat snp36634-scaffold443-178056 5 16127472 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794543 Affx-122939014 AX-385281506 5 15755281 GGTCTGATAAGACTACAGAAACTTTCACAATTCCT[A/G]TCTCTATAATATAGAACTTAGATAATCCCTTCCCT R 2 1 2 1 101000 f 74 goat snp36635-scaffold443-221123 5 16171178 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429256 Affx-122937899 AX-123299598 5 15793252 CAGTAGTTACCCACAGTGTAGACAATGGACTTTTA[C/T]AATTTCTCATATAATGACTGATAGATGTGAACCAG Y 2 1 2 1 101000 r 74 goat snp36636-scaffold443-259094 5 16209854 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278187 Affx-1111836294 AX-519551676 5 15846141 CTTACAAATAAGCATTGGTTATCTGTAAAGTAATG[A/G]GCTTCCTCTGGTAGCTCAGTTGGTAAAGAATCTGC R 2 1 2 1 201000 f 74 goat Random2.2K-527 5 15846141 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278189 Affx-1111836295 AX-519551678 5 15896894 CTGTGAGCATCAAATAGTCACTAGAGACTTCTTTG[A/G]TGATAGAAGGAAGAAAAGTTAAGGTTAAGTTTCAG R 2 1 2 1 101000 f 74 goat Random2.2K-528 5 15896894 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446209 Affx-122925714 AX-123316545 5 15907435 TGGAGAGGTGGCTGATCTGCAGGCTGGGAAAAGAG[C/T]ATGCATGAACTGCAAGTACAGAAGGAAGGGAGAGG Y 2 1 2 1 201000 r 74 goat snp36638-scaffold443-373277 5 16323879 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272301 Affx-1111833458 AX-519546040 5 15943891 GTGGCAACCCCTGGTAGTGGTCATTGTTCTGGAAT[A/G]CTGCTTTCTTAGCTGCCTGATCAGCGGCTTGGTTC R 2 1 2 1 101000 f 74 goat 5_15943891_AF-PAKI 5 15943891 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418300 Affx-122946987 AX-123288648 5 15946143 CATTATCTGGTTAAAAAAGAAATGCAATTATTGTA[C/T]GCCCAAGTAGCAAGCTATTATTTGGCATTGAAAAG Y 2 1 2 1 103000 r 74 goat snp36639-scaffold443-411985 5 16363364 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274810 Affx-1111834507 AX-519548395 5 15947334 AGAAAGCTTTACTGCAGGGCATCAAGCAAGCAAAA[A/G]GGGCATCTCACACTCA R 2 1 2 1 102000 f 74 goat GoatD01.038762 5 15947334 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320783278 Affx-122934597 AX-385270343 5 16004059 AATTCTTTGCTTTAGTGAGCTTAAATGTAAAATCT[A/G]TTTTAGAAACTACATTTAATATTGCTAATGAACCA R 2 1 2 1 101000 r 74 goat snp36640-scaffold443-469901 5 16421629 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417727 Affx-122947436 AX-123288075 5 16048126 CCGGTTCCACCCCATCCCGTGGGCAAACATCAGGC[A/G]TATTGATGTTTTTGCATAGTTGTCTGATAACATCT R 2 1 2 1 102000 r 74 goat snp36641-scaffold443-513968 5 16467185 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767634 Affx-122978578 AX-385254878 5 16090277 GTCCTGAACTTAGTTACTCATTCTCCCGATGTCCT[A/G]TTATAGAATTTCATCATGGCAATGATCTGTTAAGC R 2 1 2 1 102000 f 74 goat snp36642-scaffold443-556119 5 16510062 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790187 Affx-122950734 AX-385277191 5 16122206 ATGGTAGATTGCTTCACAGCTTCTCCACTGTTAGT[C/T]ACTGGTACAAGGTAGAACCCAATTGATTTTATGGA Y 2 1 2 1 102000 f 74 goat snp36643-scaffold443-588048 5 16542470 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393181 Affx-122965519 AX-123263538 5 16152507 AATATAGAAAAGAAATAAAATATTTGACATTAATG[C/T]AAATGCCGTTTCAACCAAGAGCTGGCTCTGTATTT Y 2 1 2 1 103000 r 74 goat snp36644-scaffold443-618349 5 16572585 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398965 Affx-122960971 AX-123269320 5 16214474 TTTTTCAGAGATCAAGGATCATTTTCACTCTCATT[A/G]TTCTGAATTTTTTCTAGGAAGTTGCCTATCTCCAT R 2 1 2 1 201000 r 74 goat snp36645-scaffold443-680316 5 16632368 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413379 Affx-122950134 AX-123283728 5 16248047 ATAAACTTAAGAATGTTTTGATAAGCCATCTGCAG[A/G]GCCAGAGCTCTACATAATCCAAACTCTGCAGTGTT R 2 1 2 1 101000 r 74 goat snp36646-scaffold443-713889 5 16665908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380312 Affx-122975391 AX-123250670 5 16303129 TGGTGAAAAATAGAATTATACCCAATGCTAGGAGG[A/G]AATTAGGGAGGCAGCAAAATCGCTGTAAATTCAAG R 2 1 2 1 101000 r 74 goat snp36647-scaffold443-768971 5 16721921 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770918 Affx-122958804 AX-385258081 5 16332172 ATGCAATTTTATTATGTGTAGGTTTTTATATCCAC[A/C]ACTACTGTCAGGATTCTGAACACATTCCACACCAT M 2 1 2 1 102000 r 74 goat snp36648-scaffold443-798014 5 16751318 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792004 Affx-122964426 AX-385278992 5 16375327 CACAGCTCTGCTTCCTCAGAATTCACTTGCTTGAA[C/T]AGATATCCTAAATGAATATACTACATAAAGCAAAA Y 2 1 2 1 101000 f 74 goat snp36649-scaffold443-841169 5 16794442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403649 Affx-122957524 AX-123274001 5 16406791 TGGATGATTTGAGGAGCTGTAGAAAGGAGGAAAAG[C/T]AGTTCAAATCTAGAAAAACTAACAGAATTATTAAT Y 2 1 2 1 101000 f 74 goat snp36650-scaffold443-872633 5 16827066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452301 Affx-122920680 AX-123322634 5 16436391 TGTAGGATAGAGATATGAGTTGACAATTAATAAGC[A/G]AAGATTCTTTCAGGAAAAAAAAAAAGACGCATAAA R 2 1 2 1 101000 f 74 goat snp36651-scaffold443-902233 5 16856633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383600 Affx-122972564 AX-123253958 5 16486228 GTTAGACCCGTGGGGATGTATCCAGCTCCTGTTTT[C/T]AGAGGATTCTTTTAAAATGCTCATTTTAAAAAATG Y 2 1 2 1 101000 f 74 goat snp36652-scaffold443-952070 5 16907501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787780 Affx-122963724 AX-385274803 5 16524538 ACTAAATAATATGGTAGCAGAGAGAAATACAATGG[A/C]TTTCTCAACAAAGACTGGGAAGGTAGGAAAAGTGA M 2 1 2 1 101000 r 74 goat snp36653-scaffold443-990380 5 16949397 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775196 Affx-122962172 AX-385262327 5 16571266 ACCCACTAGTTTCCAGACATGTTTATTCAACATCA[C/T]GATGATCATATATGCTAATAATATAAATGAATTCA Y 2 1 2 1 101000 f 74 goat snp36654-scaffold443-1037108 5 16996437 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406046 Affx-122955475 AX-123276398 5 16601310 TTGAAGAGTATATATTTATTTCATAAAATAATTTT[A/G]TAGCTTTTCCTCCCACTCAATATTATTTCATCATA R 2 1 2 1 103000 r 74 goat snp36655-scaffold443-1067152 5 17026638 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769782 Affx-122936210 AX-385256952 5 16638543 AAGAATTTAAGTGTAGGATGCAATTTATAATTGGG[C/T]AAGCCTTTTCCCAATTTTGTGGGATAGTATTGTCC Y 2 1 2 1 101000 r 74 goat snp36656-scaffold443-1104385 5 17064069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797198 Affx-122943409 AX-385284137 5 16668800 CGTCTTCTTTCCACAGATTCCTCAGAAGGAGAAAT[A/G]TGACCTAGTCTGTCATCTATGGACAACTTCAACTA R 2 1 2 1 101000 f 74 goat snp36657-scaffold443-1134642 5 17094695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770872 Affx-122977691 AX-385258036 5 16711276 GAAACAGGTCTTTTCAGTTCCCAGTTGACTGTTTT[A/G]CCTGAGAAAATATTCTGTCCATCATTTGGTTTGGC R 2 1 2 1 101000 f 74 goat snp36658-scaffold443-1177118 5 17138082 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405438 Affx-122956054 AX-123275790 5 16740134 TCAGTTTCTTAAGTGCTAAGAAACTTATAGCAGCT[A/G]TACTGAGCTTGTGATCTTAGCACCCTCCATCGATT R 2 1 2 1 101000 r 74 goat snp36659-scaffold443-1205976 5 17167022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447548 Affx-122924042 AX-123317884 5 16773475 TTCTTTTCTACAGATTCTTTCAGTTCATGGTATAA[G/T]CAGTGATATCTACAGTTATATATGTGTGTACAAAA K 2 1 2 1 101000 f 74 goat snp36660-scaffold443-1239317 5 17200334 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766106 Affx-122964559 AX-385253518 5 16806052 TTTTGCACAGGTAGAAAAATTTCCCAGAAGTCATA[C/T]GATTTAGGAATTTTGAGATACTAATATTGGTATCC Y 2 1 2 1 101000 f 74 goat snp36661-scaffold443-1271894 5 17235589 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450585 Affx-122922029 AX-123320919 5 16863668 TGATTAAACATGTACATCATCTCTGACTCCTGTTT[C/T]TGTTTTACTGATTTGTGATATTTATGGTAGTGCTG Y 2 1 2 1 101000 r 74 goat snp36662-scaffold443-1329510 5 17294147 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411518 Affx-122951672 AX-123281868 5 16916022 TGGACATTCCTGAAGCAACTAAGCAGCATTCTATA[C/T]GGAAGAATGTCTCCCAAACCTATCAGTGATCACTC Y 2 1 2 1 103000 r 74 goat snp36663-scaffold443-1381864 5 17346674 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278191 Affx-1111836296 AX-519551680 5 16923227 TCAAGAAGCAAAAGGAAGATCGCTGTAAGTAACAG[A/C]CATACTAGGCGTAGGGATGGGATTGTTCCTTACTG M 2 1 2 1 101000 f 74 goat Random2.2K-529 5 16923227 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38389809 Affx-122968198 AX-123260166 5 16966753 AGGACCCACCTTTATTTAACAAAGCTAACTATCTT[A/G]TTGTGCCAAATATAAATATCAGTGGAAAACATAGA R 2 1 2 1 201000 f 74 goat snp36664-scaffold443-1432595 5 17397867 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442294 Affx-122928254 AX-123312631 5 17021094 TTCTGTAAATTTTCCTAAAATCTTTCTTTTGGAGC[A/G]TCAACTTCACATTGGAAATGCAAACTGACCTGGCC R 2 1 2 1 101000 r 74 goat snp14305-scaffold157-2666725 5 17453016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796505 Affx-122935635 AX-385283454 5 17079707 TATCATAGGATTTTTTAGAGCCTTTAATATTCTAA[C/T]GTTCTTACAGAAAGAAATATTACTGTGTAGCTTTC Y 2 1 2 1 101000 r 74 goat snp14304-scaffold157-2608112 5 17513225 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440037 Affx-122929760 AX-123310374 5 17128954 TGTCGTCTTGTATCCAGTGAGTATGTGTTAAGCTC[A/G]CTATACAGCAGACACCATGCTGTATGGCATGATTA R 2 1 2 1 101000 f 74 goat snp14303-scaffold157-2558865 5 17563212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381733 Affx-122974689 AX-123252091 5 17187161 CAGAATTGCTGCAATTTGATGAAGACATTATTGCG[C/T]ATCAGAATTGCTACAATTTGTAGAGTACTGCAGTG Y 2 1 2 1 101000 r 74 goat snp14302-scaffold157-2500658 5 17621760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792287 Affx-122929893 AX-385279269 5 17217530 TGTTCTTCTAATAAATTAAATCAGCCAGAATGAAA[C/T]ATTTGCTTACTTGATGAAATTTTGGTTCTAGGTGT Y 2 1 2 1 101000 r 74 goat snp14301-scaffold157-2470289 5 17651353 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384936 Affx-122972325 AX-123255294 5 17256214 ACAGAATAGAAATGCAGAACTAGAGCTTGAACGTC[A/G]TAGAAGCCAGGCAGAACAGGTAGTGTAAAGGCAGA R 2 1 2 1 201000 f 74 goat snp14300-scaffold157-2431605 5 17689990 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385027 Affx-122971859 AX-123255385 5 17294104 AAATCATTTTGAAATAAAGTTTTTAAGGGTGTAGA[C/T]GGATGCAGGTCTTTATTATCCAGTATTGCTGAAAC Y 2 1 2 1 201000 r 74 goat snp14299-scaffold157-2393715 5 17728349 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379592 Affx-122976028 AX-123249950 5 17377809 TAATGATTCATTTCTTCAGTCCAGTTTCATAATTC[A/G]TCCAATACAATGCAGTGAAGGGCAGAGAATCTAGG R 2 1 2 1 201000 f 74 goat snp14297-scaffold157-2310010 5 17812744 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417390 Affx-122947694 AX-123287738 5 17407794 AAGAAAACAAAGAGGACATTTCAAGAGATTGATTT[G/T]TCAATGCATGATCCAGTGTATGGTGAGAGGTTCTT K 2 1 2 1 201000 f 74 goat snp14296-scaffold157-2280025 5 17844091 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776304 Affx-122970347 AX-385263432 5 17448053 GGTATTATGACCCTTGATGTCAAACATCTTGAATA[C/T]GTATCCAAACTCTCAGATGCAAAATAAGCTAGCAC Y 2 1 2 1 101000 r 74 goat snp14295-scaffold157-2239766 5 17885832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771971 Affx-122947582 AX-385259127 5 17484048 TAGCAAACCAGCGAGGGTTGGGCTAAGTTTAGAAA[C/T]GCACACCCTTAAAATGATGCTGATTTTTTTCCCTC Y 2 1 2 1 201000 r 74 goat snp14294-scaffold157-2203771 5 17922160 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801992 Affx-122920179 AX-385288896 5 17513145 CACACTATTTCTTATCTTGAAATTCTAACAAAAGT[A/G]CATAGTATCTCAATGATTTTCCCAGATGGAGTTAC R 2 1 2 1 101000 r 74 goat snp14293-scaffold157-2174674 5 17950877 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803151 Affx-122935845 AX-385290014 5 17571379 AGTTGCCATCAGGATTGCGCTGAATATTCTAACAC[A/G]TGTAGCAGTTTGAATAGTGATTACTCCTCCCAAGA R 2 1 2 1 101000 r 74 goat snp14292-scaffold157-2116440 5 18010213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414261 Affx-122949615 AX-123284610 5 17689586 CCCTCATCAAGGTCAGCTCCTCTAGGTCCTCTTCC[A/G]ACAACCAACTGGTTGACATCTTTTAGTGCTTGTTG R 2 1 2 1 201000 r 74 goat snp14289-scaffold157-1998233 5 18127556 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422256 Affx-122944000 AX-123292602 5 17744519 TACAACCTTCTATTTTTTAATAAATGAGGAAAATT[A/C]TCTGGAGAAGTAAAATACTGATGATTAAAAACAGC M 2 1 2 1 103000 r 74 goat snp14288-scaffold157-1943300 5 18183342 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769377 Affx-122956923 AX-385256548 5 17812167 ATACTTTCAAATAATGTGATTGAGTATACTTTATG[C/T]ATTTCCTGTTCTTTGCAAGATTTTTCACCTGTGAC Y 2 1 2 1 101000 r 74 goat snp14287-scaffold157-1875652 5 18251407 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448117 Affx-122924305 AX-123318453 5 17882417 TATTCTTAAGGGTCCTGGAAAGATGATATTAAAAG[C/T]AGTGATAATTATTAAAAAAAAAAAAAAAAAAAAAA Y 2 1 2 1 101000 f 74 goat snp14285-scaffold157-1805402 5 18322515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794300 Affx-122979136 AX-385281264 5 17917339 ATACCAGAACAGTGCCTGCCTATGTGATGAAAACT[A/C]GCACTGCCTCTACTTGCTGCGATTTTACTTTGTGC M 2 1 2 1 101000 f 74 goat snp14284-scaffold157-1770480 5 18357488 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451089 Affx-122921407 AX-123321423 5 17950392 AGGGCATGCCCTCTTTTCCCCTGATATAAACCTTT[A/G]TCTAATTTTAAGTGTAACACCAATCAAATGAGTTT R 2 1 2 1 201000 r 74 goat snp14283-scaffold157-1737427 5 18389725 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428751 Affx-122938435 AX-123299093 5 18021302 AGTAAATACTAATCTCGTCCTTCTTGAATATTCCC[A/G]TTCTCAAGTTCTGTAAATCTTGCATTGTACAAATG R 2 1 2 1 101000 f 74 goat snp14282-scaffold157-1666517 5 18460920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424864 Affx-122941337 AX-123295210 5 18065454 TCAGGATTTTCCTAAAAGTAGAAATATCAAGTCAG[C/T]ATGCCAAGCAGTCATCTTCAGAGCCAAATGATAAC Y 2 1 2 1 101000 r 74 goat snp14281-scaffold157-1622365 5 18494563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275884 Affx-1111835058 AX-519549444 5 18111095 ATCATCAGTCACACGGTTCCGGCAGATCCCTTGAG[A/T]GTGGACGAGAGGATTAAATAGGAGCAGTTGAAGAT W 4 1 2 1 101000 r 74 goat ilmnseq_rs646080217 5 18111095 T A 1 recommended Goat_IGGC_65K_v2 Illumina 38388081 Affx-122969512 AX-123258439 5 18117905 AACAAATTCCTCTCAGTCTCCACTGACCTTGTGCT[A/G]TTTAATCCATCAAAGACTGCTGCTATCCTTTAGTA R 2 1 2 1 201000 r 74 goat snp14280-scaffold157-1569914 5 18554970 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432043 Affx-122935903 AX-123302384 5 18187525 TAGTGGACTCTTTCATATGTTGAAAAAGCAGTAGA[C/T]GTACAGGCTCATTGAGCTGTTAGTTTTTTCAGCAA Y 2 1 2 1 101000 r 74 goat snp14279-scaffold157-1500294 5 18625211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405480 Affx-122956021 AX-123275832 5 18275038 AAAATAAACTAGTTTTCCCAGTTGCTACAGGAATG[C/T]AGTATAGGGGGCATGGTGGGGAGATTTGGAGGTTT Y 2 1 2 1 201000 f 74 goat snp14277-scaffold157-1412781 5 18711563 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435842 Affx-122932817 AX-123306181 5 18325018 AGTATTTAGTTTTCAATGTTAAATTTCATTGAAAT[A/G]CTCTAATAGATGGCAAGGCAGAGTATAGGCCAAGG R 2 1 2 1 201000 f 74 goat snp14276-scaffold157-1362801 5 18761482 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781887 Affx-122945233 AX-385268968 5 18369656 TTGTCTCTCATTTCATTCATGAGTCAAGAAAGGTA[C/T]GAGCAATGACTTTTGATATCGTCTTCTTTACTGGT Y 2 1 2 1 101000 f 74 goat snp14275-scaffold157-1318163 5 18805829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420023 Affx-122945154 AX-123290371 5 18409885 GGAACCACATTGAGGGGTCCACTAGTCCCTACTGC[C/T]ACTGACTTATTGACACTAAAGCAATCAAGTTTCTC Y 2 1 2 1 101000 r 74 goat snp14274-scaffold157-1277934 5 18846686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395856 Affx-122964011 AX-123266211 5 18450759 CAAAAGGTGTTGAATGCAGCGCTTGTAAAGCCATG[C/T]GGAGTGAAATGTCATGGCATAGCTTACAGGGCTCA Y 2 1 2 1 101000 f 74 goat snp14273-scaffold157-1237060 5 18887610 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421836 Affx-122944304 AX-123292183 5 18479815 AGTAAGAAGCGGGACTGACTTGGTGTGCTGGGTCT[A/G]TACAGACAAAAGCATTCTGCTTCCAAAGGAGCCAA R 2 1 2 1 201000 r 74 goat snp14272-scaffold157-1208004 5 18916756 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411177 Affx-122951860 AX-123281527 5 18510813 AGGAGGGCTTTATCTTTTTTGTTCACTGTGGTATT[C/T]CATTGCCTAGAACAGGATGTACTCATATTAGGGAC Y 2 1 2 1 201000 r 74 goat snp14271-scaffold157-1177006 5 18948122 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412464 Affx-122951398 AX-123282813 5 18546775 CATATTCCATTTGATTATTGTAAATATTTGATCTT[A/C]AGTCACTTGACAGTGTTTGTTTGAACTGTGTTTTT M 2 1 2 1 101000 r 74 goat snp14270-scaffold157-1141044 5 18983941 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380475 Affx-122975723 AX-123250833 5 18604264 TAGGACACTACTGAGCAAATAACACACATACATAC[A/G]CATCATGGAAGTGGGGTTGTGTTTCTCCCAGTGAG R 2 1 2 1 103000 r 74 goat snp14269-scaffold157-1083555 5 19041366 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404328 Affx-122957007 AX-123274680 5 18633519 CATCGTCTCCTCCCCTCAGAAGTCAAATAACAGTC[A/G]TCTTAATTGACGTGACTTTTAAAATCAAGAATCAG R 2 1 2 1 201000 r 74 goat snp14268-scaffold157-1054300 5 19070194 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464351742 Affx-1110439057 AX-515825414 5 18638450 CCAAAAGATTGTAGACTTTAAGCATTTAGCTAATA[C/T]CTCTAAGCCCCAGGCTTCTCCTATAAACTGGGGAT Y 2 1 2 1 101000 r 74 goat 5_18638450_AF-PAKI 5 18638450 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320796690 Affx-122932837 AX-385283635 5 18729598 GCTGAATTCAGAATTAAATCTTAACTAGTTCATTT[C/T]GCTGTAGACTTGTGAAAAATGCATGCTCCATAAAG Y 2 1 2 1 102000 r 74 goat snp14267-scaffold157-958221 5 19165860 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274033 Affx-1111833966 AX-519547637 5 18738730 TGTTTGTGATTGGGTGCCCTTAGCATTTTGATTTT[A/G]TAACCTTGAGGCATCTGCAGGCTTGGATTTGGTTT R 2 1 2 1 101000 r 74 goat GoatD01.011966 5 18738730 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407106 Affx-122954884 AX-123277457 5 18777206 AGGATTTTTTTCTGATAAAATCAGATTTATAGCAA[A/C]GATAGTTAGCTGACAGCTCCACATTACTTGGCTTT M 2 1 2 1 101000 r 74 goat snp14266-scaffold157-910613 5 19213942 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446747 Affx-122925334 AX-123317083 5 18827268 GTCGCTGTTGGACCCTCTTTGGTCAATTAGCAGGC[A/G]GTCTCCTGCCAGGCCAGGGAGTAGCAAAGTGCCCA R 2 1 2 1 101000 f 74 goat snp14265-scaffold157-860551 5 19263842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432472 Affx-122935603 AX-123302813 5 18907720 TTCAATTACTATGAGGATTTTGGAGATGAGTGAGA[A/G]ATGAGGTCTGAAATAGAGTCTTGTAGGTAAATGAA R 2 1 2 1 101000 f 74 goat snp14263-scaffold157-780099 5 19342177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390836 Affx-122967836 AX-123261193 5 18939903 TTTGGTTTTAAAAGGTCCCCAATGAAGAGATTTTC[A/G]TTCTCGAAATCCAAAACCTTGTTGGAAATCTCACA R 2 1 2 1 201000 r 74 goat snp14262-scaffold157-747916 5 19374317 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375685 Affx-122978660 AX-123246044 5 18999826 TGCATTTCTCTGATCATTCCATGTGTCCTATCCCA[C/T]GATACAAAGCCCAATTTTTTAAGCTATAGTCTGTT Y 2 1 2 1 101000 f 74 goat snp14261-scaffold157-687993 5 19434932 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769467 Affx-122962413 AX-385256638 5 19043264 ATCTATTTACCCTTTGAATCATTTTTAATTTAACT[C/T]TTAGCACAAATCCTATGAGTTCTTGCTATTCCCTT Y 2 1 2 1 201000 f 74 goat snp14260-scaffold157-644555 5 19478681 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791823 Affx-122920970 AX-385278813 5 19076785 TAAAAAGTGAATAGTTGATCTGATATCCCAAGAAG[C/T]AGTAAATTACCATGGCCTTATGTTTTTAAACGCTA Y 2 1 2 1 101000 r 74 goat snp14259-scaffold157-611034 5 19512408 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434145 Affx-122934909 AX-123304486 5 19128084 TTCAGTATTTTCAAGGAATCAGCACCACTCGCTCT[A/G]CACAATATGCTCCTTTCTTTTGAGAAGAAAAGTGG R 2 1 2 1 101000 f 74 goat snp14258-scaffold157-559735 5 19563816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450462 Affx-122922947 AX-123320796 5 19198567 AAGATAATACAAATATGTGAATTATCCTTGTTTTT[A/G]CTGATACATTACAAAGAGGAAATGATTGACATAAA R 2 1 2 1 101000 r 74 goat snp14257-scaffold157-489252 5 19634110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436029 Affx-122932733 AX-123306368 5 19244402 TCAGGTCTCCCAGGCTCAGAGATGTTAAGTGGTTT[A/G]CTCAATCTGACAAAGCAAGTGGCAGATATAAAATT R 2 1 2 1 201000 r 74 goat snp14256-scaffold157-443417 5 19679840 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397660 Affx-122962600 AX-123268015 5 19297600 AACCCTCCATCTAATGAGCTTGCTCTCTTACCCAC[A/G]CCATCCATCATCTACTGATATCCATTGCTCCACCC R 2 1 2 1 201000 r 74 goat snp14255-scaffold157-390219 5 19733227 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384507 Affx-122973052 AX-123254865 5 19412365 AAAAGAGCATCTTGAGAACAGAGATATAGTACTCT[A/G]TTTTATCCCCATTTTTGTTCCAAGCAAAAGAGAGT R 2 1 2 1 201000 r 74 goat snp14253-scaffold157-275454 5 19848381 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435804 Affx-122932847 AX-123306143 5 19467409 GTGCAGACACAGAAAGAAAACCAGCAAAGAGTTTT[A/G]TAGTTTTGCTATATGCACAGTTTCCAGGGGAGATC R 2 1 2 1 101000 r 74 goat snp14252-scaffold157-220410 5 19902189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413510 Affx-122950633 AX-123283859 5 19499085 GGTGGGCGTTGCGGTTAGGAGGGCACATTAGCAGC[A/G]AGCATATTGAGTCTTCAGATTACCTGGAGCCAGCA R 2 1 2 1 101000 r 74 goat snp14251-scaffold157-188734 5 19934148 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774798 Affx-122974303 AX-385261932 5 19541394 GGAGTGTATAACACATGCAAACATAGATATTGAGT[A/G]AACAGTTGATAAAAATTGCAAGCAGTCTGCGGTGG R 2 1 2 1 101000 r 74 goat snp14250-scaffold157-146425 5 19976541 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441400 Affx-122928842 AX-123311737 5 19578480 GAAGAGGAAAAGTGCCTATGCTCTGTGCGTTTAAA[C/T]TACACTGCAAACATAATTGGAGACAGCGTTTGCAA Y 2 1 2 1 101000 r 74 goat snp14249-scaffold157-109339 5 20015454 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799256 Affx-122925326 AX-385286186 5 19607848 TAATTACATGCTAGTTGCTTTATATACAGTACCTG[A/C]AACATGGTATTAGTCATTTTGGATGATGACAGATG M 2 1 2 1 101000 f 74 goat snp14248-scaffold157-79971 5 20045308 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431596 Affx-122936171 AX-123301937 5 19641065 ATCTCTCTAAATAATGGACATAGTGCATGAACGCT[A/G]TCATGTCTGACTCTTTGCAACCCCATGGGTTGTAG R 2 1 2 1 102000 f 74 goat snp14247-scaffold157-46754 5 20079492 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418090 Affx-122947144 AX-123288438 5 19685347 GTACAGGATTCAGTTGCAGTCAGCATATATTAACT[A/G]CAGATCAATGCAAGAGGCAGTAATTATACACAACA R 2 1 2 1 101000 f 74 goat snp14246-scaffold157-2472 5 20124247 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791892 Affx-122956112 AX-385278883 5 19689030 CATAAATGAATAAATACTGGCTATGTTTTAATAAC[A/G]TCTTATTTATAAAAGCCAGAGACACCTGGATTCTG R 2 1 2 1 102000 r 74 goat snp38501-scaffold486-5603502 5 20143470 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398439 Affx-122961613 AX-123268794 5 19749651 ATTTGAAGTCAATATCATTGTCATCATTTTGAGGA[C/T]AGCAAAGAATAGTTCTTACTTTTTCTTAGTTTTTG Y 2 1 2 1 101000 f 74 goat snp38500-scaffold486-5542881 5 20203977 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393305 Affx-122965428 AX-123263661 5 19782498 AACAGTACTTTCTTGTAACTAAGAACTCTAAACAC[A/G]CATACTTAAAGTGTCAACTAATAAGAATTGCTATT R 2 1 2 1 101000 f 74 goat snp38499-scaffold486-5510034 5 20237382 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379382 Affx-122976142 AX-123249741 5 19873546 GTGATTTAAATACGATGGTATTTTATGATAATTAC[C/T]GTCATTACTGAGCTACTTTTTCCACTGACCATGTG Y 2 1 2 1 101000 r 74 goat snp38497-scaffold486-5418986 5 20329430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416680 Affx-122947581 AX-123287028 5 19902330 AAAAGCAATTTTAACCTAAACATATGCAAAGTATC[A/G]TCAGAAAATAAACAAAAATCCTCAGATGAAACAGA R 2 1 2 1 101000 f 74 goat snp38496-scaffold486-5390202 5 20358348 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398376 Affx-122961657 AX-123268731 5 19966342 GGTACCCTGCAGCTTAGGCTCTCTACTTAGACTGC[A/G]TCTTCCTGGATTGCTCTTTTCCCAGATAACTTGAA R 2 1 2 1 101000 r 74 goat snp38494-scaffold486-5326190 5 20422747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772876 Affx-122959256 AX-385260021 5 20037103 AAAACATGAAGAAACTAGCATAGTGTCTAGAAGAT[A/G]CCAATCACTCCTTAAATGTCACCATTATTTTCATT R 2 1 2 1 101000 r 74 goat snp38493-scaffold486-5255429 5 20495087 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796023 Affx-122962881 AX-385282975 5 20066247 ACCCACTCCCTTCCCCAGACAGTGACAGAGCTTTT[A/G]TACTTCCAGTAAAAAGCCAGGCCTTGTCAATCTGA R 2 1 2 1 303000 f 74 goat snp38492-scaffold486-5226285 5 20524637 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772622 Affx-122949019 AX-385259770 5 20122772 AGTACTTGTGCTTTATTGTGTTAATTACCCAAAAA[G/T]ACCTCTTCTACATACATATTCCCAGATTCTGAGGG K 2 1 2 1 101000 r 74 goat snp38491-scaffold486-5169760 5 20582039 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400316 Affx-122960060 AX-123270671 5 20163337 TCCTTGTGCTACATAAAATGAAAGTAATCAGTGTA[C/T]GCTACAAATGTAGAAACACATATAAAATGCATAGC Y 2 1 2 1 101000 f 74 goat snp38490-scaffold486-5129195 5 20622071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431847 Affx-122936083 AX-123302188 5 20205561 GACATTTGGTCACAATAGACCTGGTCGTATCTAAA[C/T]GTATATTCTGTCTTGTTAGGCTGCCCTCTTGCTAC Y 2 1 2 1 101000 f 74 goat snp38489-scaffold486-5086971 5 20663976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435272 Affx-122934051 AX-123305612 5 20237621 GGCTATATATTCACTTCAGAAGAACAGATGCACAA[C/T]AGAGAAAACACCTTTTGAGACTAAGCCTTCCTCAT Y 2 1 2 1 101000 r 74 goat snp38488-scaffold486-5054911 5 20695898 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435007 Affx-122933813 AX-123305347 5 20273055 AGCAGATTATATTTGTCAGATTATACTGACACACC[A/G]CTGACTTCTTGTATTCTTTCATGCAACTACAACAT R 2 1 2 1 101000 f 74 goat snp38487-scaffold486-5019477 5 20731318 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799663 Affx-122930680 AX-385286591 5 20301872 ACAGAGTTTGCTACTAGTTTCAGATAAACTTTGGA[G/T]AGCATAGCCTCAGGATGCTTCATATACAAAGGCTA K 2 1 2 1 102000 r 74 goat snp38486-scaffold486-4990660 5 20760425 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777398 Affx-122923639 AX-385264520 5 20403368 GAAGTCTAGTGTATATTTCTACAACTTAGAAAATA[A/C]TAGAAACTGTCACCAGAGAGGTGAAAACAAACACT M 2 1 2 1 101000 r 74 goat snp38483-scaffold486-4889164 5 20861799 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273984 Affx-1111833934 AX-519547589 5 20436497 ATTTGTAAATATTACAGACAATGTTCAAAATAATA[A/G]GTTTTAAACTCTTGTGAACACATTATCTATCAGCA R 2 1 2 1 201000 r 74 goat GoatD01.010929 5 20436497 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320778043 Affx-122919401 AX-385265158 5 20461804 AGAAAAATATCTCCAAGTTAAATCTGGAAGAATCA[A/G]CATTGGTTGAGGTAAGAAGGAGAATGACATGGAGA R 2 1 2 1 101000 r 74 goat snp38482-scaffold486-4830728 5 20921004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423431 Affx-122942608 AX-123293777 5 20503921 GAATTAAAAAGAAGAATAAAGCTTATTTTAAACAA[C/T]GAGGGAAAACCGAATAATCTTAAAGTCTATGAATT Y 2 1 2 1 101000 r 74 goat snp38481-scaffold486-4788611 5 20963339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450371 Affx-122922094 AX-123320706 5 20535475 GACTATTGTAAATTTGCTGTTTTTCTTAGATTGAG[C/T]GTCTAATAAGTCCTATGCTTTACACTTGCTCAAAA Y 2 1 2 1 101000 r 74 goat snp38480-scaffold486-4757057 5 20995407 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448172 Affx-122924259 AX-123318508 5 20569305 CCTTAATTTCCTCTTATTTAATTTTCTCAATTTTT[A/G]CAGTTTTGAAATCCTATACCTCTTTGGAATTATCT R 2 1 2 1 101000 r 74 goat snp38479-scaffold486-4723227 5 21029193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385664 Affx-122971151 AX-123256022 5 20629641 ATACAGTTCCACCCAGAAAAAGTAATTCTTGGAAC[G/T]CATCTCAGAGAGGAAGTCTTTCTTGGTCCAACACA K 2 1 2 1 201000 f 74 goat snp38478-scaffold486-4662891 5 21089836 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431433 Affx-122936513 AX-123301774 5 20662634 TGCCAGAAAAGCACTACCAAGTTTATGGAAGACAT[G/T]ACAATTTCTATATAGGATACTGTACACACACACAA K 2 1 2 1 101000 f 74 goat snp38477-scaffold486-4629898 5 21122756 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787998 Affx-122972224 AX-385275019 5 20694142 CTTTCAGTATCAGGTTCTGTGGCGGCAGCAAGTAT[C/T]CAAGGAACTGAGCTCACCATTTCCAAGTAATACCT Y 2 1 2 1 101000 r 74 goat snp38476-scaffold486-4598390 5 21154536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389602 Affx-122968767 AX-123259960 5 20763505 TTTGTCTGAAACTTCCTGCATCTATTCTGGTATGT[A/G]TAAAGAAAGCACCTCCAGTATATATCCCTTTCTTT R 2 1 2 1 101000 r 74 goat snp38474-scaffold486-4529027 5 21225152 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431167 Affx-122937193 AX-123301508 5 20819541 AACAATATGCCCCTCCTCATTTTCCCTTCAGAGCT[A/C]AGTTCCCTGAAGGCTTGTCTATGTCTGCTTTGGCC M 2 1 2 1 101000 r 74 goat snp38473-scaffold486-4472991 5 21281835 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428900 Affx-122938925 AX-123299242 5 20873352 ATAACAAATATCTTTGTAATGAACATGATTTCTCT[C/T]AAATACAAGTCCACTGTTAGCTCCCTACTCCCACC Y 2 1 2 1 101000 r 74 goat snp38472-scaffold486-4419180 5 21336262 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445231 Affx-122925497 AX-123315568 5 20903202 AGTACAATTTCAACTTGCTGTAATTAGGGCTCTAG[C/T]GGGAACTTAGTACTTATAAGCTGTGTGTCTAAGTT Y 2 1 2 1 101000 f 74 goat snp38471-scaffold486-4389330 5 21366121 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401840 Affx-122959436 AX-123272193 5 20932359 GTGAAAGAGGGAAGATACAAGTAAGGGAAGGAACA[A/C]ATATTAATAGAGGAGGTGAGGTTAGAAGGCAAACA M 2 1 2 1 101000 f 74 goat snp38470-scaffold486-4360173 5 21395298 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439566 Affx-122930087 AX-123309903 5 20979633 TTAGGAAGTTTGCTCCAAAGTAAACAAGCCACCAG[C/T]GCACTGGGAAGAATAGACCCTCTTTCCACTCAGCC Y 2 1 2 1 101000 f 74 goat snp38469-scaffold486-4312899 5 21442411 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429245 Affx-122937908 AX-123299587 5 21016446 CAAAGAGTCAACAGCTGAACTGAACCCAAAATCCA[G/T]ACTCTTCCCTACTGTAGGCTTTTGTATCCTTTTCT K 2 1 2 1 201000 r 74 goat snp38468-scaffold486-4276086 5 21479200 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794594 Affx-122951308 AX-385281556 5 21053402 GCAAGATTGCTGTATGATATAGGATTGGACTACTG[C/T]ATTGCTAACCCAACTCTACTATATGTTTCTCCATC Y 2 1 2 1 101000 f 74 goat snp38467-scaffold486-4239130 5 21515678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779540 Affx-122944840 AX-385266643 5 21084333 CATTACTTACATCATGGATGGGCTTTTCAAAGCAC[A/G]GTTCTGTGGTTTACTATTCCTAGGAAACTTGTCCA R 2 1 2 1 101000 f 74 goat snp38466-scaffold486-4208199 5 21547169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421511 Affx-122943894 AX-123291858 5 21132398 GCCAAAGTAAAGAGTAACATGGATATAAATTTGGA[C/T]AAAAAGCCATGCTTCAGGTACACATATTATTTCTT Y 2 1 2 1 101000 f 74 goat snp38465-scaffold486-4160134 5 21595554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272302 Affx-1111833459 AX-519546041 5 21161885 TGGAGGCCTGAATGTTAAAGGAAAACTCCAAAGGA[A/G]CAGTGCAAATAGCAAGATTGCAATTATATTAGAAG R 2 1 2 1 101000 f 74 goat 5_21161885_AF-PAKI 5 21161885 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437095 Affx-122932185 AX-123307433 5 21181072 CTCAAACTAGTGGTCTACTGTGCTTCTTCCAGTAT[C/T]ACAAGGAAACAACTAGAACTTTCAGGTCACCAGGA Y 2 1 2 1 201000 r 74 goat snp38464-scaffold486-4111460 5 21644333 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438079 Affx-122931523 AX-123308417 5 21233085 AAGAAGATACCACATTGACAAATTTCTTTTCAGTA[C/T]GAAATCCACAGATAAAACAAATTTAAATCAGAACC Y 2 1 2 1 101000 f 74 goat snp38463-scaffold486-4059447 5 21696911 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801957 Affx-122965506 AX-385288861 5 21278877 AAAGTGGGGCAAAACCTAGGGGTTCTGGAGATACA[G/T]CTTTATCTCACTGTCATGGTATCCATCTTATTTGT K 2 1 2 1 101000 f 74 goat snp38462-scaffold486-4013655 5 21742999 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452156 Affx-122921657 AX-123322489 5 21324444 TTGGTCATTTTCAGCCTTGAAATCATAATCTTTTT[A/G]CTCTCTATGCCCAGGAAGCATAAAATTGTCTTAAA R 2 1 2 1 101000 r 74 goat snp38461-scaffold486-3968088 5 21788691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770606 Affx-122937091 AX-385257770 5 21363244 ACACAAGAAATCATGACCAAAATAAGAAACCAACT[A/C]GACTAATCCCTTAGGGATTGCTTTGCTTTCTTAAG M 2 1 2 1 201000 f 74 goat snp38460-scaffold486-3929288 5 21827401 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792470 Affx-122922183 AX-385279451 5 21408146 CTTTTTTTTTCCTTAGCAAAATTTCTCTTTCTCAA[C/T]AGCAAAGTCACCATTCAACTACTATTGCAGAAGAA Y 2 1 2 1 101000 f 74 goat snp38459-scaffold486-3884386 5 21872228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380918 Affx-122975021 AX-123251276 5 21441188 CCACCTCTCTAAAATAACTACACACACACAAGGTT[A/G]ACTTAGGATCAGATTCTGGAGGTTTCCAGGCTGGC R 2 1 2 1 101000 f 74 goat snp38458-scaffold486-3851344 5 21905783 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429833 Affx-122938171 AX-123300174 5 21521519 CTGTTACTTGCTATCAAAAAGTTTCAACTAATGCA[A/G]GTAGCTATTACCATCTCGATGAGGCTGAGAAATTA R 2 1 2 1 101000 r 74 goat snp38456-scaffold486-3771013 5 21985656 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393688 Affx-122965259 AX-123264043 5 21568760 AATGCAAATTACCACTCACAAATGAACAAAGGCCC[C/T]GCCACTCACCCCCAGATGGCTCAGCTGCCAGCCTG Y 2 1 2 1 101000 f 74 goat snp38455-scaffold486-3723772 5 22033072 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414312 Affx-122949578 AX-123284661 5 21615386 CCCATTTTAAGCGGAATTCCCTCTCCCACAGTCTC[C/T]CTCTTGACTATTGACAGTCTGTGTTTCAGGAAGCT Y 2 1 2 1 201000 r 74 goat snp38454-scaffold486-3677146 5 22080295 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399072 Affx-122960890 AX-123269427 5 21653979 CTAAGTCCCCTTGGGGGGTGTTCATTATTTTCACT[A/G]CTGACCACTGCTTCTAATTGCCTGAGTTAGCATTT R 2 1 2 1 201000 r 74 goat snp38453-scaffold486-3638553 5 22119201 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785999 Affx-122925564 AX-385273035 5 21689889 TTTGGGCTACTTGGAACACAGTTAATGTGCAGTGT[A/G]CTCTGTTACTAGCATGTATGTTGGGCACACAGTAA R 2 1 2 1 101000 f 74 goat snp38452-scaffold486-3602643 5 22155501 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789772 Affx-122927533 AX-385276780 5 21752962 GTCTAGAAATTTCCATGTGAGCAAAAACTTGCTAC[A/G]CAGTGTCTGATGGTAAACTTTATGTGTCAACTTGA R 2 1 2 1 101000 f 74 goat snp38450-scaffold486-3539570 5 22218723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776968 Affx-122941417 AX-385264092 5 21813062 CTCACCATATCATTTTAAACAGAACTTTCTCTTGA[A/G]ATAACAGTAACAACTAAAGCATACGGAGTGCTATC R 2 1 2 1 101000 f 74 goat snp38449-scaffold486-3479470 5 22279486 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774677 Affx-122974976 AX-385261811 5 21850068 TTTGCATTTTCTGACTTGTTCCTTTACAGAGTAGC[A/G]TTTCAGGAATCCTCATTTTACTTTGACATTTCAGG R 2 1 2 1 101000 f 74 goat snp38448-scaffold486-3442464 5 22316587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410287 Affx-122952506 AX-123280637 5 21905490 TGGGGACCTCCTACAGCAATTGGGACATGTGCCTT[G/T]TGTTGATGTCTGAAACCATAGTGACTGATGTTGTG K 2 1 2 1 201000 r 74 goat snp38447-scaffold486-3387042 5 22372298 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421733 Affx-122944381 AX-123292080 5 21949586 TGTCCCCTTTGTGTGGAAATAGAAGTTTTTAATCC[A/G]CTGGCATAACTTGAAAAACAGACTGAGGGAAGAAG R 2 1 2 1 101000 r 74 goat snp38446-scaffold486-3342946 5 22416667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451317 Affx-122921280 AX-123321650 5 22039701 AGTCTTTGGCTTATTTTAAATTATTGTGTATGGTC[C/T]GAATTGTGGTTGAGCTTCATTCCTTCCATGTGGAT Y 2 1 2 1 101000 r 74 goat snp38445-scaffold486-3252831 5 22506984 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390923 Affx-122967084 AX-123261280 5 22070448 TGATGTGTCAATAGATACCCAGAGGAAGAATGTGG[C/T]GTGAGGAGGAGAGCAAGAATACACAGAAAAACTAT Y 2 1 2 1 101000 f 74 goat snp38444-scaffold486-3222084 5 22537208 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464353962 Affx-1110440192 AX-515827609 5 22087676 GGTTCTGATTTAATTACAGAGGGCTGCAGTCTGAG[C/T]ACTAGAATTTTCAATTACTCCCAGGTGATTCTAGT Y 2 1 2 1 201000 r 74 goat GoatD01.051531 5 22087676 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38406499 Affx-122955152 AX-123276851 5 22102536 GCTCCTTACAAATAAAATTGGGCTAATTCTTATCT[A/G]CCAAGAGAGTCCTGTATTTTGCCTTTATTTTATTG R 2 1 2 1 101000 f 74 goat snp38443-scaffold486-3189996 5 22564964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376485 Affx-122978032 AX-123246844 5 22142163 TAAGAATGTAGGTGCTGTGATTTTGGGCTTCCTAC[A/G]TGGCTCAGTGGGTAAAGAATCTGCCTGCAATGCAG R 2 1 2 1 101000 f 74 goat snp38442-scaffold486-3150369 5 22604355 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428817 Affx-122938384 AX-123299159 5 22176114 TGCAAATGGAAAAAAAAAATTCACAGTCTGCTAGA[C/T]ATTTGGAATTTCATGAAGTTGATGAAAGCGATACA Y 2 1 2 1 101000 r 74 goat snp38441-scaffold486-3116418 5 22638443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424557 Affx-122942234 AX-123294903 5 22229205 GATCCTTCCCTGATTTTCCTTTTCTGAGATGCTAT[C/T]AAGACTTTGTCATAGAAATGTTTCCCTTACTCAAT Y 2 1 2 1 201000 r 74 goat snp38440-scaffold486-3063327 5 22691868 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401444 Affx-122958984 AX-123271797 5 22304894 GTCATAATAAAAATATAAACCCACAATGTTGACGA[C/T]GTGAAGGGTGTCCCCTTAAATGTGATACTCTCGTG Y 2 1 2 1 101000 r 74 goat snp38439-scaffold486-2987638 5 22768298 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404768 Affx-122957213 AX-123275120 5 22343529 AAGTCTTTTCCCTAAATGAACATCTAGGTTGTATG[A/C]ATGGTGATCAGTACAATCATGAGACCAGTTAGCGC M 2 1 2 1 101000 r 74 goat snp38438-scaffold486-2949003 5 22808088 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800096 Affx-122937964 AX-385287019 5 22372709 TTCTGTAACTTGTTTTTTGCCAATAGTAAATTGTA[C/T]TGAGACATGCATTTGCATGTCATACCTTTTCTCAT Y 2 1 2 1 101000 r 74 goat snp38437-scaffold486-2919823 5 22837300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403226 Affx-122957897 AX-123273579 5 22427296 CATGAGATTTACTGCTGGGATGCTGTACATTTGTT[A/G]CCAAGAAACTGGGATCAGTCTTGTACTGAGTATAG R 2 1 2 1 101000 r 74 goat snp38436-scaffold486-2865236 5 22892046 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776713 Affx-122966170 AX-385263839 5 22457228 CGTCAGACTCAAGCAGAATTACAATTCTAATATCT[A/G]CTCATGTCCCCCACATGCCCTCAGCCCTGCCCAGA R 2 1 2 1 303000 r 74 goat snp38435-scaffold486-2835304 5 22922091 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779553 Affx-122957319 AX-385266656 5 22522352 GTCATCCCTGTAATATTTGGTGCGGGAGCTCCTTT[C/T]ATTCTTTAATTTGATAATCTGCAATTATCTGCATT Y 2 1 2 1 101000 f 74 goat snp38434-scaffold486-2770180 5 22987123 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393187 Affx-122965515 AX-123263544 5 22565432 GCGACTCTGTGGACTGCAGCACGCCAGGCTTCCCT[A/G]TCCATCACAGAGTAAAAGTCTGTTTTACTACTGTT R 2 1 2 1 103000 r 74 goat snp38433-scaffold486-2727100 5 23030421 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433157 Affx-122935671 AX-123303498 5 22620403 ATCTAGTATTCTTTATTCTGTTTCTGGTTATACCA[A/G]CATCTGACTCTCGCAGCAAGAAATTCTGTGGTTAT R 2 1 2 1 101000 r 74 goat snp38432-scaffold486-2672129 5 23085273 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392808 Affx-122965966 AX-123263165 5 22669912 GGTAAAATGTCTCTATCTACACGGTTTTATTAACA[A/G]GGATTGAGTTGCACCTGTATAGCATGACATTCTTG R 2 1 2 1 101000 r 74 goat snp38431-scaffold486-2622620 5 23135294 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781244 Affx-122949671 AX-385268329 5 22714358 TTGAAACTGTAGATGAATGCGGAGATGAGAGTTAT[A/G]TAAGTGGGATGAAGCTGGCCTCTAAAAATCCCATC R 2 1 2 1 101000 r 74 goat snp38430-scaffold486-2578174 5 23179267 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765169 Affx-122958451 AX-385252720 5 22749602 CTCTTTGGAGAGCAGTTTGGTACATGTCACATCCC[A/G]TCATACAGAAACTCTCATATGTGCAAAAAACATGC R 2 1 2 1 101000 f 74 goat snp38429-scaffold486-2542930 5 23213882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445218 Affx-122925509 AX-123315555 5 22796142 AGCCATACACCGGATGATACAGATCACAGAATTAC[A/G]CCATTGGGAAAATCATGCATAGTTTCACTCAGTCA R 2 1 2 1 101000 f 74 goat snp38428-scaffold486-2496390 5 23261140 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416087 Affx-122948325 AX-123286436 5 22827361 AGTTCCTGGAAGAAGGTGGGAAAGTCCTAAAGAGT[A/C]TTCATAAAACTCCCCAAGAGCCACTTTCTGTTCCA M 2 1 2 1 101000 r 74 goat snp38427-scaffold486-2465171 5 23292466 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768766 Affx-122932964 AX-385255943 5 22879856 TCAATAACACCTATCAGATTTTTTGTCCATTTATG[C/T]GTCTCAGAACATAGCTTAAGCTGAAAGACACAATC Y 2 1 2 1 101000 r 74 goat snp38426-scaffold486-2412676 5 23345368 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777923 Affx-122978230 AX-385265039 5 22920767 TTCTGCGGGGAAAAAGGAGAGAGTAAACTAAAATC[A/G]TTTTCTTTTGGCTGGTGGTATATTCCTCCCAGTCT R 2 1 2 1 101000 f 74 goat snp38425-scaffold486-2371765 5 23504396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784580 Affx-122928574 AX-385271628 5 22963825 TTTTTTTCTTTGAAAGCACTGAAACCTGGATTTTA[C/T]GGTCTATGCTTTGAATTAATAACAGCTTTTATAGT Y 2 1 2 1 101000 f 74 goat snp38424-scaffold486-2328707 5 23429366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395853 Affx-122964013 AX-123266208 5 22996171 TGGTCAATGAAACCCCACAGTCCTATAGGAAGGCA[C/T]TGTCGCTTTAAATGAGGCTTGCTGTTATATAATTC Y 2 1 2 1 201000 r 74 goat snp38423-scaffold486-2296361 5 23462175 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777680 Affx-122921301 AX-385264799 5 23058006 TTTGAAGGTCTGCAAGCTCTTTGACGATGTCTTTC[C/T]GAATTTGTTTCTGGAGAGATCTTTAGCCCATGATA Y 2 1 2 1 101000 f 74 goat snp38422-scaffold486-2234526 5 23524219 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404399 Affx-122956787 AX-123274751 5 23110876 AGATATCAAGACTGGGATTCTTTCCTGCATTCCTC[A/G]GTAATCAGTGGTTCTTTGGAACCGAGGTGACCAAA R 2 1 2 1 201000 r 74 goat snp38421-scaffold486-2181656 5 23578293 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424084 Affx-122942042 AX-123294430 5 23154515 TGAGCTCCTGTAGGTAGGTTGTCATGTTTCAGCGT[A/C]CCTCCATGCAGATTGATGGGGCGGGGCGGGGTGAT M 2 1 2 1 101000 f 74 goat snp38420-scaffold486-2138017 5 23622867 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427767 Affx-122939236 AX-123298110 5 23201246 GCTTTGTGCTAAGAGCTAGTGATACACTTGGTACC[A/G]TCATCCATTTTTAGCAACGGGATATTCTTTCAACA R 2 1 2 1 101000 r 74 goat snp38419-scaffold486-2091286 5 23669928 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442716 Affx-122927862 AX-123313053 5 23262939 GCCACTGTCAGCTGCCTGGGTGCCAAGAGCTGGGC[A/G]CCTTCATGGTTTCATCCCCTCTCCACCTTCTGCTC R 2 1 2 1 101000 r 74 goat snp38418-scaffold486-2029593 5 23731868 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411009 Affx-122951984 AX-123281359 5 23320582 TATTTAAGGCACTGCTTTTTGGATCTAAACTTAAG[C/T]AGCACTGTTAAAACCTGTGGCATAGCAGTGTATCT Y 2 1 2 1 101000 r 74 goat snp38417-scaffold486-1971950 5 23789518 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278350 Affx-1111836297 AX-519551836 5 23372374 TCCTGCCCCCAGTCCCTCCCAGCATCAGTTAAGGT[A/G]GGTGCAGATATAGTAGCTATTTCTTCTCTTGCTCA R 2 1 2 1 101000 r 74 goat Random2.2K-532 5 23372374 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793161 Affx-122963927 AX-385280139 5 23416676 CCAATAAACTGTACAGTTTTAAGGAAGTCATCCCA[C/T]GGAGTTATCCTTATTATGTAAATTAATAAGGTCAT Y 2 1 2 1 101000 f 74 goat snp38415-scaffold486-1875856 5 23884882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438438 Affx-122931261 AX-123308776 5 23453462 TATGAAACAACAAGTGCAACATATATGAATAGAAC[A/G]ATTCTGACGCACTCATTTGTTTATTCATGTCATTC R 2 1 2 1 101000 f 74 goat snp38414-scaffold486-1839070 5 23922667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427209 Affx-122939587 AX-123297552 5 23489466 GTCTGAAAGGGAGAGACTCCCTCCCCCCAACCCCC[A/G]CCACCACTCTAGTCTTCAAGTAGACTTGGAGGTTC R 2 1 2 1 103000 r 74 goat snp38413-scaffold486-1803066 5 23958700 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419786 Affx-122945854 AX-123290134 5 23521757 CTTCTTGTTGCATCACAGCAGAAAGCACATCAATA[G/T]CTGGCTGTTTTTCTTTTTCTGATGTAAAGGTTGAT K 2 1 2 1 201000 f 74 goat snp38412-scaffold486-1770775 5 23992266 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430227 Affx-122937325 AX-123300568 5 23611817 GAGAGTTACTATAGTAACAGAGAACCCTTGGCCCA[C/T]AGCGTATGTTCACAAAAAGGAAAGTAAATCAATGT Y 2 1 2 1 101000 f 74 goat snp38410-scaffold486-1680715 5 24083291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381618 Affx-122974776 AX-123251976 5 23643961 CCACTGCCCCTCTTTTAAAGCTCAAGTGAGTGTGC[A/G]CTACAGATGCAGCTCTGTATCTTTCTCCCTTAACA R 2 1 2 1 201000 r 74 goat snp38409-scaffold486-1648571 5 24115332 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412789 Affx-122950496 AX-123283138 5 23684184 AATATAAAAATATTTTGTTTAAATATATAAACATA[C/T]ACAAATTGAGATAGAGGCCTGGCCAGCCCCAGGTA Y 2 1 2 1 102000 r 74 goat snp38408-scaffold486-1608348 5 24155506 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379834 Affx-122975817 AX-123250192 5 23727383 AATTATTGTAATATGAATGGAATGTATAAGACTCC[A/G]TCATGTCATATCTATCAAATATCTTCACGTTTAGA R 2 1 2 1 101000 r 74 goat snp38407-scaffold486-1565149 5 24198761 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272573 Affx-1111833460 AX-519546288 5 23747150 TGACTGAGTGACTAACACTTTCTTAGGTTCCCTGC[A/C]AGAATAGTTAAAAAGCTGATGCCTTGGATTAAGGA M 2 1 2 1 201000 r 74 goat 5_23747150_AF-PAKI 5 23747150 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396384 Affx-122963026 AX-123266739 5 23766741 AATACTTGATCATTTTTAATAAGCTTTAATACTTA[C/T]GCAAATACACTTAAGGGGATGTCGCAAGAAATGGC Y 2 1 2 1 201000 f 74 goat snp38406-scaffold486-1525791 5 24237986 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795429 Affx-122923524 AX-385282385 5 23798215 TTCAACTGCTCACAGTTGTTAAGATTCCTTTCAGA[A/G]GCTGTTTTGAAGTCATCTGTCAGCAAGGAGTGGGG R 2 1 2 1 101000 r 74 goat snp38405-scaffold486-1494317 5 24269164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402553 Affx-122958460 AX-123272906 5 23836338 GATTGTTGATCGTTTTGTTGGTGGTGTTGAGGGCT[A/G]CTGCTATTTGTGACATTTCCACAGTAGTGTTGCAA R 2 1 2 1 201000 r 74 goat snp38404-scaffold486-1456194 5 24307745 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278195 Affx-1111836298 AX-519551684 5 23863229 AGCATCTTCCCTCACAAATGTCCCACCCAACTGAC[A/G]TGCCCCTGGGGATACCCTGGAACAAAATAATCAAA R 2 1 2 1 102000 f 74 goat Random2.2K-533 5 23863229 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383181 Affx-122973217 AX-123253539 5 23915701 TTTCAGGATCCCAGGAGGCAGAGACCAGTCAAAAG[A/G]GTTTTGCACTTCCTTTATTCCTATTATACCAGATG R 2 1 2 1 101000 r 74 goat snp38403-scaffold486-1376831 5 24388157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416479 Affx-122947801 AX-123286827 5 23970641 CTGCCCTGATTCCTGGATGTCTTCTTTGATTCTAC[G/T]ACTTCCTCCTTCCCCCAAATCCTCTTTTTGCTCAA K 2 1 2 1 101000 f 74 goat snp38402-scaffold486-1321891 5 24443150 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793763 Affx-122961594 AX-385280735 5 24039773 GGACCATTCTTTAGTTTGAGGAGAGCACAGAAACT[A/G]TTTTGCCTATGTATTCACTGAAATCAGTTTCACAT R 2 1 2 1 102000 f 74 goat snp38401-scaffold486-1252759 5 24513048 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791743 Affx-122940342 AX-385278734 5 24069726 ACATTCTGGGATTTTGGCAATCCAGTGAGTCAATC[A/G]TGCCATGGAACGGCAGGAGCTTAAACAGCTGCTTG R 2 1 2 1 101000 r 74 goat snp38400-scaffold486-1222806 5 24543119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780969 Affx-122944642 AX-385268056 5 24101378 ACTGATCTAAGTAAAAGTTACACATGTGTTTAATG[C/T]AGGTTTCATGCTGGGCTTGATTTTAATTGATGAAT Y 2 1 2 1 101000 r 74 goat snp38399-scaffold486-1191154 5 24574740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800885 Affx-122940994 AX-385287800 5 24154902 GGTTCCATGTAAGTGTGAATTGGAATAAGGTTGTA[C/T]GAGGTATTATTACCCTTTTATATGTAAAGAAACAA Y 2 1 2 1 101000 f 74 goat snp38398-scaffold486-1137630 5 24629064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412601 Affx-122951289 AX-123282950 5 24212634 AGGACTTCCTGTTGCAGGATAGTATGAAGTGAATC[A/G]AGTCGGAATCCAATATCCTTGCCATTGAAAGACCG R 2 1 2 1 101000 f 74 goat snp38397-scaffold486-1079898 5 24687668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797996 Affx-122963723 AX-385284932 5 24304129 GCATCCAAATTTACTAGTAGCAAAAGTCCACTTCT[G/T]GTTCAAAGGCACAACGTCATCCCAGGAATTTTTTT K 2 1 2 1 101000 r 74 goat snp38395-scaffold486-988403 5 24779337 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391134 Affx-122966793 AX-123261491 5 24380092 GTCAAAGATAGGGTGCACATAGGGGTGCAGGGACC[A/G]CATTTTGAGTTGCACTGTTCTGATGACCCTGCCAT R 2 1 2 1 101000 r 74 goat snp38393-scaffold486-912440 5 24855884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397313 Affx-122962314 AX-123267668 5 24414282 TACACAAGTAGAGACAGATGTACACATACATGAAC[A/G]TAGGAAAATATGGAAGGCTACCTGCTAGGTGGTTA R 2 1 2 1 101000 f 74 goat snp38392-scaffold486-878250 5 24890106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774285 Affx-122967369 AX-385261421 5 24494665 GCATTATCTCTATTTACAAATCATTGAGTTAGTAG[A/C]GATTTCACCTCTTACAGAGCAAAAACTTCAAGTAA M 2 1 2 1 101000 f 74 goat snp38391-scaffold486-797867 5 24970993 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780437 Affx-122970379 AX-385267528 5 24626253 CCGGTGTGACCAATACTATCTTGATTTGTCTCCAA[C/T]GATGTACATTTTCTCTAGCATATGATATCTGTCAT Y 2 1 2 1 101000 f 74 goat snp38389-scaffold486-666279 5 25098771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775131 Affx-122921627 AX-385262263 5 24657997 TTTCCAAATATCACTATCACTACTTACTATCCACC[C/T]GTTTCTCTAGTTGCCTCACTCCTGACTCCAGGAGT Y 2 1 2 1 101000 f 74 goat snp38388-scaffold486-634535 5 25130474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444354 Affx-122926713 AX-123314691 5 24689479 AACACCATAGCCTGGATAATGTAAATAAGAAATTA[C/T]GGAGCTATTCCATCATCTTGTGTTCTTAAGAACTA Y 2 1 2 1 101000 f 74 goat snp38387-scaffold486-603053 5 25162042 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399764 Affx-122960312 AX-123270119 5 24748355 GCGGCCCACCTGGGCTGTGGGCATCCCCATTACTA[C/T]GGCTTCACGACTTCAGAGGCAGGAGGGAATAGGCT Y 2 1 2 1 101000 r 74 goat snp38386-scaffold486-544177 5 25220097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375665 Affx-122978676 AX-123246024 5 24836872 ATGGACAAGCTACACCTAAACTTGACGGAGTTGGC[A/G]CTGACAATGAATCATGTACAGAGCTTCTCTGTGTT R 2 1 2 1 101000 f 74 goat snp38385-scaffold486-455660 5 25308047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383311 Affx-122972700 AX-123253669 5 24880947 AGGTCATCTCCTCCCATCCCCCAGTTCCCCCCAAA[A/C]CAAACCACTAAGGACAGGAATCTAGTTTTTGTTTA M 2 1 2 1 101000 r 74 goat snp38384-scaffold486-411585 5 25352432 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385563 Affx-122971220 AX-123255921 5 24917540 TAATAATGAGAAATGCTTATGAGGGTTGTAGATCG[C/T]CATTCCACTCAGGACACACCCACTGCACACCCGGT Y 2 1 2 1 101000 f 74 goat snp38383-scaffold486-374992 5 25388949 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376813 Affx-122977931 AX-123247172 5 24946802 GAGAGACTCTGATGGTGCTAGAGCCCAGCCAGAAT[A/G]CCACCTGCGCCGGACTCTGCCCCTGCCCCGCCCCC R 2 1 2 1 101000 f 74 goat snp38382-scaffold486-345730 5 25418267 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449059 Affx-122923054 AX-123319394 5 25002667 CAGACCAATCTGCCTGTATATCATTTCCAGTCACC[A/G]TTAGCATTTGAGGTGAAGTTCTGTTATACACTCAG R 2 1 2 1 101000 r 74 goat snp38381-scaffold486-289865 5 25474077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762327 Affx-986696858 AX-385250501 5 25035333 TTCTTAAAAGTGATAACAGAGACAGGTCTGAGAGG[C/T]TGAGCAGGGGGCTATAGCTGAGGTGGTCTGCCTGC Y 2 1 2 1 600010 f 74 goat 5_25035333 5 25035333 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 38396370 Affx-122963036 AX-123266725 5 25055831 ATGAAAGGAATCTACTCAGAGTAACCTAGGGAGGC[A/G]TGTTTTGGATTACCTGTTCTTCAAGTCAGTATTTC R 2 1 2 1 201000 r 74 goat snp38380-scaffold486-236701 5 25527980 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394211 Affx-122964901 AX-123264566 5 25148657 CATAGGAGGAGGAAATGTAAGTTCACACAACGTGT[A/C]TTTCTTTAGAAAGATGTTCCTGTTGGCGGATTATG M 2 1 2 1 101000 f 74 goat snp38378-scaffold486-143875 5 25620890 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423570 Affx-122942410 AX-123293916 5 25206461 ATGGACTTGGATCGCTATTTACCACCTGGTGTCTC[A/G]GTCTCCTCTGTGTTCCCCGCTGGCTTCAGGGGGAT R 2 1 2 1 101000 f 74 goat snp38377-scaffold486-86071 5 25678765 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450822 Affx-122921796 AX-123321156 5 25238315 TGCTCCAGAGTGGCCCCTGGGCCAGCAGCAAATAG[A/G]ACAAGCTTTTATAGCCCCAGGGCAGATGTTGGCTT R 2 1 2 1 101000 r 74 goat snp38376-scaffold486-54217 5 25710260 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411073 Affx-122951938 AX-123281423 5 25276368 CCTCATGACAACTCACGTGACATCATAAATGCTGC[A/G]TTCTTGTTCTTGAATTTTACAATTCTAAAAACTTC R 2 1 2 1 101000 f 74 goat snp38375-scaffold486-16164 5 25748363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436934 Affx-122933187 AX-123307272 5 25348305 GGAAATGAGGAAGGGATGGGGAGGGGTCCCAGGCG[G/T]GAACATCTGGGAGACCATCTCTCCACTCTTCACCT K 2 1 2 1 101000 r 74 goat snp17391-scaffold1802-55674 5 25820244 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779416 Affx-122950681 AX-385266519 5 25391371 AGATTATGGTTTTTGTAGAACAAAATGGCCAAATA[C/T]GTCAGCAATTGCATATGGTTCAAGCAATAAATGAC Y 2 1 2 1 101000 f 74 goat snp17392-scaffold1802-98740 5 25863055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444021 Affx-122926889 AX-123314358 5 25462384 TGGCAGATGTGGGCGAAGGAGAGAGGGGCGAGGAG[C/T]AGAGCTTCCATGAGCCCTCAGGGCAGTGACTGTGT Y 2 1 2 1 101000 r 74 goat snp17394-scaffold1802-169753 5 25934769 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451211 Affx-122921970 AX-123321545 5 25569291 GCAAACTTGGGTACACACTTCTCCAGGCAGTTGTA[C/T]GTGAACTGTCACTGCTGACACATCTGTGTACCATT Y 2 1 2 1 101000 f 74 goat snp17396-scaffold1802-276660 5 26041321 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431459 Affx-122936492 AX-123301800 5 25611388 TTTTGTATTTTTGAGGTTTTCTGTACTTTATCTCC[A/G]TCCCTCTCCACCACCATCCCCCAGGGTCCTCACAT R 2 1 2 1 101000 r 74 goat snp17397-scaffold1802-318757 5 26083849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443443 Affx-122927356 AX-123313780 5 25661697 CCAGGTCTTGCTACCAGCAACTCTTGCATTTGAGT[A/G]CCCCTCGCTCCCCCCATCTTTTCATGTCTGACTCC R 2 1 2 1 101000 f 74 goat snp17398-scaffold1802-369066 5 26134296 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275344 Affx-1111834741 AX-519548919 5 25694161 CGGCTGCCTGGAGCCCAAACCTGGGCCCTCTGCGC[A/G]CTCCGCGCTCAGTGCTTCCACCGACTGCAGTTCTT R 2 1 2 1 202000 r 74 goat GoatD01.051001 5 25694161 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320788525 Affx-122938975 AX-385275542 5 25734084 CTGTATCTCAGGGTGCTAACTGTTGCTCTGATCAC[A/G]GAAGGGTAAACAGGTAGCCATTTTATTGAATTTCC R 2 1 2 1 101000 f 74 goat snp17399-scaffold1802-441453 5 26206783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386981 Affx-122969958 AX-123257339 5 25798690 GAGGGATTATGGTCCTTAAACTAATTCATGGCAAA[A/G]TCAAGATTCTAGTTCTGATCTCTCCAAATCCAAAG R 2 1 2 1 101000 f 74 goat snp17401-scaffold1802-506059 5 26272082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780093 Affx-122950404 AX-385267190 5 25828193 CTCCAACAAACTACAGAAGCTGTTTAAGTCTTAAA[C/T]GCAGACTTCCTAAAATTACAATTTCCCAACATACT Y 2 1 2 1 101000 r 74 goat snp17402-scaffold1802-535562 5 26301500 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405884 Affx-122955601 AX-123276236 5 25869765 GGTTCTCCCACATTGCAGACTCCTTACCTTCTGAG[C/T]GACCATTATAGGCTGACAAAAGGTCTCTCCAGGAG Y 2 1 2 1 101000 r 74 goat snp17403-scaffold1802-577134 5 26343253 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396621 Affx-122962880 AX-123266976 5 25899136 GGTCCCCCTTAAAATGCATTAAGTGTAGGTAACTA[C/T]AGCACAATAGCAACTGGAGCTCCAAGAAGGCAAGA Y 2 1 2 1 101000 f 74 goat snp17404-scaffold1802-606505 5 26372618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434107 Affx-122934938 AX-123304448 5 26009025 CCACAGGGAATCCCAAAGAGGTCAGAACTATTCAG[C/T]AAGTGCTACTTGCCTGCCTGACAAGTGATGGCTCT Y 2 1 2 1 101000 f 74 goat snp17406-scaffold1802-716394 5 26482294 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376205 Affx-122978811 AX-123246564 5 26092490 CTGGAAGCTTTACCTCTGGCCGCTGACTCTGAACA[C/T]TGGTTGGGAGAAAGGAGTTGACGCGGTAGGTTGCT Y 2 1 2 1 101000 f 74 goat snp17407-scaffold1802-799859 5 26564974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464356661 Affx-1110441558 AX-515830275 5 26097001 ACGACCCAAGGATGCCCTGCAGACTGCGTCAAGGT[C/T]GAGGCGGCCATATAGTGGCTATATAGTGGCATTCT Y 2 1 2 1 102000 r 74 goat GoatD01.005755 5 26097001 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38415429 Affx-122948720 AX-123285778 5 26168262 TGGATGGTGCATGTGTGGAACTGGACTCGGAATAC[A/G]AGGGTCCGGTCAGTCCCTCGGCTACCCTTGTGATA R 2 1 2 1 101000 f 74 goat snp17408-scaffold1802-875631 5 26640052 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778239 Affx-122919391 AX-385265354 5 26255649 AGCAAGAAGCAAACTTTTGATAGTAGCAATTAACT[A/G]TTACAGTTATTTACAAGAAACCCACTCACACACAC R 2 1 2 1 101000 r 74 goat snp17410-scaffold1802-963018 5 26727278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441232 Affx-122929508 AX-123311569 5 26320406 ATGTGGACACACAGACAGACCTGTCCAGATCCTCA[C/T]GTACATGTAACACAGAGACATTTTCAGCACAATAG Y 2 1 2 1 101000 r 74 goat snp17411-scaffold1802-1027775 5 26792003 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792765 Affx-122962602 AX-385279744 5 26357252 TTAATGCAGAATTAGGGTTCAGAAACATTGATTTA[A/G]TGTGATTTACCCAGGATACATGAGAAGAGGAGACC R 2 1 2 1 101000 r 74 goat snp17412-scaffold1802-1064621 5 26828519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382035 Affx-122974948 AX-123252393 5 26390605 AATAGTGGACACTGAGCACTTACCCTGTGCTAGGT[A/G]CTTTCTGGACATGACAATGACTATGAGAGAGGTAC R 2 1 2 1 101000 r 74 goat snp17413-scaffold1802-1097974 5 26861770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424865 Affx-122941336 AX-123295211 5 26432710 CAGCTGCTATATCATCATTCCTTGTGATTCAATGG[C/T]AGCCATCCCTCCTCCTGGCAAGACTTTGGCTACAA Y 2 1 2 1 101000 f 74 goat snp17414-scaffold1802-1140079 5 26903443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801704 Affx-122971297 AX-385288612 5 26445573 GACCATTATCTCCTTTACTCCTAGGCTCTTACATC[A/G]TGAGAGAAAGTTTCTTGGTTTCAATAACATGGAGA R 2 1 2 1 101000 f 74 goat snp26714-scaffold2809-1587 5 27157257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432035 Affx-122935908 AX-123302376 5 26486952 TAGCCTGGGAGAGAGAAATGCTCTTGTCCCTGGGA[A/G]CTGAAGTCCTCCAGCTTAACTCACAGACAGAGGGG R 2 1 2 1 101000 f 74 goat snp26715-scaffold2809-42966 5 27199533 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429845 Affx-122938160 AX-123300186 5 26516061 AGCAGCAAAAGCCCCAGCCCAAAGTTTCCAGGGCT[A/G]CTCCTCCCCTCTCCCCACCTGCTACCCTTTGAAAA R 2 1 2 1 303000 f 74 goat snp26716-scaffold2809-72075 5 27227105 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803431 Affx-122969328 AX-385290262 5 26559848 TGAAAATTATAGTAACAGTTAGATGCCATTTACAC[A/G]TTATTAGAGCCACAAGAGTTCCAAAGTCTGGTAAC R 2 1 2 1 101000 r 74 goat snp26717-scaffold2809-115862 5 27270630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418843 Affx-122946141 AX-123289191 5 26624323 TGAATATGCATACCTCTGTATATGTGCTGAAGAGA[C/T]GACATTTGTGGGTCCATGAGGGTATGACTGCAGTG Y 2 1 2 1 101000 f 74 goat snp26718-scaffold2809-180337 5 27334001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442014 Affx-122928415 AX-123312351 5 26675612 TGGGGGACCATACTTATTCTTGAAGTCTTCCACGA[C/T]ATCCTGCATGTTCCGCAGCTCCACCTCTAGACGAC Y 2 1 2 1 101000 f 74 goat snp26719-scaffold2809-231626 5 27385593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402441 Affx-122958620 AX-123272794 5 26721834 GGTGGACAGACAGGGCTCACCTTCCTGTCCAGGCC[A/G]TTGGATCTGTTCAGCTTCCTGGGGTCAGAAGCGCC R 2 1 2 1 101000 r 74 goat snp26720-scaffold2809-277848 5 27431775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442082 Affx-122928370 AX-123312419 5 26755821 GGTGGGGGTGGAGGGAGAGGAACTCGCTGTATTGA[A/G]TCCAGAGCAGAGAGCAAGTTGGGCTCAATGCTGGC R 2 1 2 1 101000 r 74 goat snp26721-scaffold2809-311835 5 27465570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380470 Affx-122975726 AX-123250828 5 26785777 CAGAGTATGGGAGATGGGAGGCAGGACGTGGAGGC[A/G]GAGTTGAAAGTGGTTGTGATTTTGCAGTTAGTAGC R 2 1 2 1 101000 r 74 goat snp26722-scaffold2809-341791 5 27495628 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464357083 Affx-1110441775 AX-515830692 5 26786194 GCTGCAGTCACCATCTGCAGTGGTTATAGGTTGTG[C/T]TTGGGCAAAAAGGAAGTTCATCAGGTGTCCACAGC Y 2 1 2 1 201000 r 74 goat 5_26786194_AF-PAKI 5 26786194 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38399033 Affx-122961597 AX-123269388 5 26824028 ATCACGGAGTTCCTTGGGAAAAGCTGGCCCACGCC[G/T]CATTTGCACCCTCCTCAGTTCTCCTTCCATCCCCT K 2 1 2 1 201000 r 74 goat snp26723-scaffold2809-380042 5 27534006 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405145 Affx-122956954 AX-123275497 5 26856351 CCCCCAAATGCTGATCAGCAACTCCCTACCCCAGC[G/T]CGAGCTCCTCCCTGCTTTGCAGGCAGGCCTTTCCC K 2 1 2 1 202000 f 74 goat snp26724-scaffold2809-412365 5 27564742 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427667 Affx-122939315 AX-123298010 5 26901005 CACATCTGTTCCAGGGGCTCTTAACAAAACTAATC[C/T]GAGATTCTCTTTTTCTCTACAAGAGTTCACTTCTG Y 2 1 2 1 101000 f 74 goat snp26725-scaffold2809-457019 5 27607542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387870 Affx-122969636 AX-123258228 5 26937177 ACCTCGGGGGCCATGTACCGCTTGGTGCCCACTCG[A/C]GGGTTGTTGCCAATGTCCAGGTAATCGCTGCCCTG M 2 1 2 1 101000 r 74 goat snp26726-scaffold2809-493191 5 27643315 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380389 Affx-122975330 AX-123250747 5 26973098 ACTCGTCTTTGGGTTCGGGTGTCAATACATCACTG[C/T]ATTTATTTATCCTCCCTCTCTTCCTCATCCCCTAG Y 2 1 2 1 201000 f 74 goat snp26727-scaffold2809-529112 5 27679351 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380896 Affx-122975038 AX-123251254 5 27007029 TATCAGACAGCTAACATTAAGCCCCAAATCTTTCA[C/T]GGCAAATTCAACTCATTTGAGGATGGTGGGAAGAG Y 2 1 2 1 201000 r 74 goat snp26728-scaffold2809-563043 5 27712909 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418676 Affx-122946311 AX-123289024 5 27096609 TGTAAAGAACCACCTAAATGTAAGGGGGAAAATAT[C/T]TTGCTTTTAAATAAAAGAGTAGGAAGAGAAAGACA Y 2 1 2 1 101000 f 74 goat snp26730-scaffold2809-652623 5 27802772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434829 Affx-122934795 AX-123305170 5 27144305 ACCCAGCTTAGAAACACTGAACCGAAAAGCAGGAC[A/G]TTAGGACACGGGCAGTTTTTTTTTTTCCTTTAGGC R 2 1 2 1 201000 f 74 goat snp26731-scaffold2809-700319 5 27850517 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452121 Affx-122920831 AX-123322454 5 27178880 TTACAGAGCATTTTCTTTCCTTTACCTCATCTCAG[A/C]CTCACTAGTGAGGTTAAAGGAGCAAATACTGCTAG M 2 1 2 1 102000 f 74 goat snp40702-scaffold521-32319 5 27884907 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781567 Affx-122967078 AX-385268652 5 27297239 GCTCCATCTCATCTTAAACACCATTTCCTTAGAGG[A/G]GCCTCCTCTGACCACACTAACAAAACACATCCCTT R 2 1 2 1 101000 r 74 goat snp40704-scaffold521-150678 5 28003309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431809 Affx-122936112 AX-123302150 5 27374275 ATGGCTCTGTTTCTCTGAAAAACAGGTTACCTCTT[A/G]CACTAGTTACTTAACCATTAGCTGTCTCCTAGCCG R 2 1 2 1 101000 r 74 goat snp40706-scaffold521-227714 5 28080799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417367 Affx-122947712 AX-123287715 5 27442653 TAGTCACTGTGTTTGATTCATCTTTGTATCAAAAA[C/T]ACAAAAGATACAAAGATGAATATAAACACAGTCTA Y 2 1 2 1 303000 f 74 goat snp40708-scaffold521-296092 5 28147484 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433760 Affx-122934494 AX-123304101 5 27490560 ACACTTTGCTGATGCCTGGGGCTACAGGCTTCTCT[A/C]CTCAGTCTAGATGCATTGTTGCCTACCTCCTCTGC M 2 1 2 1 101000 r 74 goat snp40709-scaffold521-343999 5 28195368 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440864 Affx-122929248 AX-123311201 5 27521185 GGATGTCAGTGATTATTACACCAATACCAGCAACT[A/G]TTACCCAGGGATGATGAAAGGATGACCAGTCATTT R 2 1 2 1 101000 f 74 goat snp40710-scaffold521-374624 5 28226107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407295 Affx-122955324 AX-123277646 5 27591715 TTATGATGGACAGTGTATTTAGATGAAATCCCTTT[A/C]TTTGTCACAAAATTTATCCACTACTTTTTAAAAAA M 2 1 2 1 101000 f 74 goat snp40712-scaffold521-445154 5 28296722 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445748 Affx-122926084 AX-123316085 5 27649486 GGAACTCAGATTCTGTTCGTACCTTTATTAGGGGG[A/G]ACATGGTTCCTGTTCTTTCATGTCCAGTTTATGTT R 2 1 2 1 101000 f 74 goat snp40713-scaffold521-502925 5 28354497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412376 Affx-122950811 AX-123282725 5 27684179 GTGGGGGTGGCATCTGGGAAGGAAAGCAATTCCTC[C/T]TACTCCACCCCTTTCCACCACTGGGACACACAGGC Y 2 1 2 1 101000 f 74 goat snp40714-scaffold521-537618 5 28389240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767285 Affx-122961797 AX-385254567 5 27745812 TTTTCCCCTAGAGTAGTAAATTCAAATGTTAAGGT[A/G]CTCATATTTTATGTATGTTCACTTGTATTTAGAAT R 2 1 2 1 101000 f 74 goat snp40715-scaffold521-599251 5 28451276 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438206 Affx-122931457 AX-123308544 5 27774631 TGGGATGCTATATTTATGGATATATTTATACTTAA[C/T]ACCTCCTATATATCTGGCCTTTGTTAGTACCAGGT Y 2 1 2 1 101000 r 74 goat snp40716-scaffold521-628070 5 28480010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433195 Affx-122935640 AX-123303536 5 27827496 AGACATACTCCTTTGCCAGGAGAAACAGTCCTTCT[A/G]TCTCAGTCTTAAGAATGACTGAAACTTGGACCAAC R 2 1 2 1 102000 f 74 goat snp40717-scaffold521-680935 5 28534039 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448109 Affx-122924311 AX-123318445 5 27881240 TCCATCATGTGGCTTACAGGGAAATATGCCTTCTG[C/T]GAACTCACTGCTACATTTTCCCCTTCAGGTTTGCG Y 2 1 2 1 201000 f 74 goat snp40718-scaffold521-734679 5 28587718 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386550 Affx-122970717 AX-123256908 5 27910583 TGCACAGTGTGGCATGTATGCTTGGGTGCAAAATC[A/G]TCTCGGTTGTGTCTGACTCTTTACGACCTTATGGA R 2 1 2 1 101000 f 74 goat snp40719-scaffold521-764022 5 28616878 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772784 Affx-122941035 AX-385259929 5 27967175 TCACATTTAAATCCTCAACAGCAATTTGGAAGTTA[C/T]GCTTGTGTGATCCTTATGGATCCATCTTTACTCTC Y 2 1 2 1 101000 r 74 goat snp40720-scaffold521-820614 5 28674375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418675 Affx-122946312 AX-123289023 5 28010183 TTATTGTGCATTTTTATTTCTAGGGCTCTGAAATC[A/G]TTGCTTTTGACAGTTTTTGAGTTTTTTTTTTCCAA R 2 1 2 1 101000 f 74 goat snp40721-scaffold521-863622 5 28717811 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405988 Affx-122955519 AX-123276340 5 28053662 TAAACACTTGTAGAACAAAATATTTAGCTATCTTT[A/G]TTATAATTGGTTCTGACTGAAGCAAAACATATAAA R 2 1 2 1 201000 r 74 goat snp40722-scaffold521-907101 5 28761938 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436913 Affx-122933205 AX-123307251 5 28085843 TCAGGTTAAGGTAATAAAAGGAACATTCCATAGGT[A/G]TGGAGGAGGGAAGGGGTGAACAAAATGTTACTAGT R 2 1 2 1 101000 f 74 goat snp40723-scaffold521-939282 5 28794022 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425502 Affx-122941477 AX-123295848 5 28127629 CAGCTCTCAGAAAAGAGAAGCGATATGTGTAACTG[C/T]AGACACAGTATACAATGGGCCAGGAAAAGAGGAAA Y 2 1 2 1 101000 f 74 goat snp40724-scaffold521-981068 5 28836460 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415167 Affx-122949013 AX-123285516 5 28172375 CCCATCAAACGATGAATGACTACATGAAATGTAAT[A/G]TATCTATACAAAGGAATATTATATGGCAGTATAAA R 2 1 2 1 103000 f 74 goat snp40725-scaffold521-1025814 5 28881197 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396993 Affx-122963148 AX-123267348 5 28219803 ACAAAGACATCCAGACTAAAACAAAACAGAACATT[A/G]TCTTGACAACGGAACTGTCAACAGGTGATGGGAGA R 2 1 2 1 101000 r 74 goat snp40726-scaffold521-1073242 5 28929189 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765588 Affx-122938734 AX-385253068 5 28292488 GAATGCATCTGAGATTTTGGATTTGTCTGTTAAAG[C/T]AGCAAGCATTCACCTTAATACAGATGATATTTAAA Y 2 1 2 1 101000 f 74 goat snp40728-scaffold521-1145927 5 29001781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404647 Affx-122957308 AX-123274999 5 28340797 CTGTAGCTGCCATGTGGAAACTAGATTAAAGAAAG[C/T]AGGGGACGCTAGGTGAGGCGCTATGGAAGCTAGAG Y 2 1 2 1 101000 f 74 goat snp40729-scaffold521-1194236 5 29050482 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378169 Affx-122976960 AX-123248528 5 28380392 AATTTATCAAGTTACCTGCAGGGCCACAGCTACAG[C/T]CGCACTTATGTTACTATTACACGGTGAAGCAGTAT Y 2 1 2 1 201000 r 74 goat snp40730-scaffold521-1233831 5 29090156 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403390 Affx-122957774 AX-123273743 5 28424572 AGCTTTAGTAAAGCAAAATAGGTAACAACTACAGA[C/T]GACTACATGCAAGAGTTGAGGCTCTAGAATCACAT Y 2 1 2 1 101000 r 74 goat snp40731-scaffold521-1278011 5 29134436 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391981 Affx-122966511 AX-123262338 5 28459202 ATGAAGGAGCAGATGGGTTCCTTTGAGGAAGGACA[C/T]AGTCAGAAATTCATGCTATTAATTCTTCTCCAAGT Y 2 1 2 1 101000 r 74 goat snp40732-scaffold521-1312641 5 29168240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386774 Affx-122970113 AX-123257132 5 28517836 ATCTAGATTTTTCCAATTTTTAAATATCTCATTTC[C/T]GTCTCTTGACTGCCTGAATTGATTAAGACCTTAAA Y 2 1 2 1 101000 r 74 goat snp40733-scaffold521-1371275 5 29228511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448686 Affx-122923870 AX-123319022 5 28565959 AGTCAGACACAACTGAGCAACTGAAGTAAACTGAA[C/T]TGATGCTGCTGTTATTCCCAAAGAGCAGATTTATT Y 2 1 2 1 303000 r 74 goat snp40734-scaffold521-1419398 5 29277122 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762329 Affx-986696860 AX-385250503 5 28584923 CACTGGGTCCCTGAACGGGGCGCTTTCCTGAGTGC[A/G]CTGTTTCCCGTCCCCATTGCCAAACAACCAAACCA R 2 1 2 1 600010 f 74 goat 5_28584923 5 28584923 Ancestral_priority_1043 ancestry 0.41 neutral IMAGE 10K 10K ancestral 320764498 Affx-986696862 AX-385252175 5 28584933 CTGAACGGGGCGCTTTCCTGAGTGCGCTGTTTCCC[A/G]TCCCCATTGCCAAACAACCAAACCAAAACGTCCAG R 2 1 2 1 600010 r 74 goat 5_28584933 5 28584933 Ancestral_priority_1043 ancestry 0.61 recommended IMAGE 10K 10K ancestral 38434085 Affx-122934173 AX-123304426 5 28597312 AAATAAGCATCATGATAAGAGTTTCCTCATGAGCT[A/G]TTGTGAATATAAAATGAGATACTGTATATTGAATG R 2 1 2 1 303000 r 74 goat snp40735-scaffold521-1450751 5 29308652 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278198 Affx-1111836299 AX-519551687 5 28615547 TCACTCTCATATAGAAACTTGACTTATTTATCACA[A/G]ACATAAATGTCTAACATTAAATATTTGTGTATTCA R 2 1 2 1 101000 f 74 goat Random2.2K-536 5 28615547 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408516 Affx-122953707 AX-123278867 5 28636815 ATGGTTCCAGGTGAACAGCAAAGGGACTCAGCCAT[A/G]CACATGCATGGAGAAGAATGGCAAAAAGAATAGAA R 2 1 2 1 101000 r 74 goat snp40736-scaffold521-1490254 5 29347331 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396626 Affx-122962875 AX-123266981 5 28669800 AGTAAATGATAATGGTGTTTAGAACTTCTTGGTAC[A/G]TTGACATTAATTTACACGTTAGGACTAAAGCTTAA R 2 1 2 1 101000 r 74 goat snp40737-scaffold521-1523239 5 29380339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444493 Affx-122926518 AX-123314830 5 28740939 CTAGGTGAGGTCCCCGGGGCTCTGACAGGGAAAGG[C/T]AAGATTCCCCCACCCAAATGCCCTGTTAGGACAGA Y 2 1 2 1 303000 f 74 goat snp40738-scaffold521-1594378 5 29451583 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764971 Affx-122938696 AX-385252550 5 28814447 TTAGCTGCATGAAAGAGGACCTGGACTAGAGCGTT[C/T]AAGGGATGATTAGGAGAACATAAGAAGAAGCCTTT Y 2 1 2 1 101000 f 74 goat "5_29524772_AF-PAKI;snp40739-scaffold521-1667886" 5 29524772 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412252 Affx-122950901 AX-123282601 5 28848760 AATTTCCCCCCTCCAGCAGAGTCAGGGCAAACTTC[A/C]TAGAGAAGATGGGCTTGGGAATAACTAGTGGCTGC M 2 1 2 1 101000 r 74 goat snp40740-scaffold521-1702199 5 29559231 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409187 Affx-122953184 AX-123279538 5 28881707 CCCATGCAGTAGGGCACAGGGATGAAGAAGACCTC[A/G]CCTATAGCCTCCTATAGCTCCCACCGCCCACAGGA R 2 1 2 1 101000 f 74 goat snp40741-scaffold521-1735146 5 29592330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797519 Affx-122975907 AX-385284458 5 28918028 ATGTTCTTACTGCAACAAAGCGTTTTTTAAAAAGC[A/G]CTCAAGAAGCATTAGTCCAGGTCACCTTGCCTTCA R 2 1 2 1 101000 r 74 goat snp40742-scaffold521-1771467 5 29628478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381178 Affx-122975202 AX-123251536 5 28948507 CACGTCACACACATACACCACATATACCACATACA[C/T]ACCTACACACATCACACACACCACTCACATACACA Y 2 1 2 1 103000 f 74 goat snp40743-scaffold521-1801946 5 29659223 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789796 Affx-122933388 AX-385276803 5 29011563 ACTATTTTCATCTGTTACCTGTTGGCAATATTTGT[C/T]TGTAGAGCATTTTCTTCTGCCACCATATTGGGTCT Y 2 1 2 1 101000 r 74 goat snp40744-scaffold521-1865002 5 29720002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376884 Affx-122977818 AX-123247243 5 29057198 TTTACCAAACAGTCCGGGTCCACTTGGTGAAGCTC[A/G]GCCGGAGAGCGGACTCTTGGAGCTTGCCTCTGCTG R 2 1 2 1 101000 f 74 goat snp40745-scaffold521-1910637 5 29765591 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445900 Affx-122925946 AX-123316237 5 29090906 TTTAGCCAGATGCTTTGCACGTGATAAAAAATAAT[A/G]TCTTTTACATTTTGCTAAAAACCAAAGATTATGCT R 2 1 2 1 101000 f 74 goat snp40746-scaffold521-1944345 5 29799331 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402419 Affx-122958639 AX-123272772 5 29125027 ATCATATGAATAATGGTACAATCAGTCCTTTAGAT[A/G]ACCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT R 2 1 2 1 101000 f 74 goat snp40747-scaffold521-1978466 5 29833399 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278356 Affx-1111836300 AX-519551842 5 29150225 CAAGAGTACTGGAATGGGGTGCCATTGCCTTCTCC[A/G]GTGCTCCAACATACTTGGTTACAAAAATTCCGAGA R 2 1 2 1 101000 r 74 goat Random2.2K-537 5 29150225 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438184 Affx-122931830 AX-123308522 5 29187529 GTGCCCATCAGTCGCTGGAGGGACTCGGAGGATGC[A/G]TCTTTGGCGCCTCCCCCAAGCCGGGCGCAATCTGC R 2 1 2 1 101000 f 74 goat snp40748-scaffold521-2040968 5 29894418 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406223 Affx-122956120 AX-123276575 5 29282027 AGTGAGAGTACATACAACCATCTCACTGTGATGAA[C/T]AATAGGGGAATGATGCCAGCAGATAAAAAATTAAA Y 2 1 2 1 101000 f 74 goat snp40750-scaffold521-2135466 5 29988432 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389391 Affx-122968387 AX-123259749 5 29317810 TGGGGTGCAGAGAGCTTTCAGGTTAGTGAATGCAT[C/T]GGTATGCTGGAAGAGTAGTACACCTCAACTTCATG Y 2 1 2 1 101000 r 74 goat snp40751-scaffold521-2171249 5 30024444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772125 Affx-122964340 AX-385259280 5 29354577 ACAGATTATAAACATGGTTAAGCTCAATTTCTGTA[C/T]AGAAATTAAAACAGCTGAGCCAAGTACTAATTGGC Y 2 1 2 1 101000 r 74 goat snp40752-scaffold521-2208016 5 30062597 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794302 Affx-122971826 AX-385281266 5 29398586 CACTCTTTTCGGACCTTTATAAAATAGCCTAATGC[C/T]ACTATCTGAGGCCAAGCTGAGAAATATAAACGGAA Y 2 1 2 1 101000 r 74 goat snp40753-scaffold521-2252025 5 30107254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387744 Affx-122969736 AX-123258102 5 29448126 CCTATTAGTTTTCCTGTCTTTATTCCTGGTGATTT[A/G]TAAGATGCCACTGTGTATTCTGCATATTAATCCCA R 2 1 2 1 101000 r 74 goat snp40754-scaffold521-2301565 5 30156125 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781660 Affx-122953098 AX-385268744 5 29482430 GCTCACCTTCCCAATGAGTTAAACTAATTTGTGAA[C/T]GTAGATAAAATTCTCATGTAATTAGGAATGCTTGA Y 2 1 2 1 101000 f 74 goat snp40755-scaffold521-2335869 5 30190829 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786421 Affx-122970054 AX-385273455 5 29515888 TATAGCAGAGAGAAGTGAATTCAGATAAAACCAAA[C/T]CTTGGGTTTTTTAGTGTTGTCTCTACTAGGCTCAA Y 2 1 2 1 101000 r 74 goat snp24050-scaffold2447-16234 5 30229301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774903 Affx-122946636 AX-385262037 5 29562377 GGGGACATGAGCCTGCAGCAGATGATACTACAAGT[A/G]TGAGACATGTGTGGATCCATACCATAATAAAAGAT R 2 1 2 1 101000 f 74 goat snp24051-scaffold2447-62723 5 30276323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435112 Affx-122933700 AX-123305452 5 29614124 GGCTGAGGAGAGAAAGAGAGAGAGATTTTAAAAAG[C/T]ATTGGTTACAGAAACTGAGAAGTCTCACTCTGCCG Y 2 1 2 1 201000 r 74 goat snp24052-scaffold2447-114470 5 30325865 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414182 Affx-122949670 AX-123284531 5 29679998 TAAAGTGAACAGGATGGAGTATCTACAAGTGTTCC[A/G]CAGTATTCAGAGTCTGTCTTCAGTGGGGAGTCACC R 2 1 2 1 101000 f 74 goat snp24053-scaffold2447-180344 5 30391958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402680 Affx-122958358 AX-123273033 5 29788165 CAACATTTAAAGCAAAAAAAGGCCAGGAAAGAGAG[C/T]AGGAAGCAACCAAAAGGGTAAAAAGGAAATCAAGA Y 2 1 2 1 101000 f 74 goat snp26005-scaffold2691-365236 5 30500499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394239 Affx-122964878 AX-123264594 5 29818385 AAAACAAAAATCTGTTCCTGTTATTCCACTATGTA[A/C]ATCTCCTTAGTGGCTCCATAAATAATGGCTCCCTT M 2 1 2 1 101000 r 74 goat snp26004-scaffold2691-335016 5 30530766 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389371 Affx-122968453 AX-123259729 5 29864038 AAAATCTATTTCAGCGAGGTGCTAAATTCAGACAG[C/T]AAGTCTGAATCTGCCTCTATTCTACCATCTCCATC Y 2 1 2 1 101000 f 74 goat snp26003-scaffold2691-289363 5 30576461 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396288 Affx-122963099 AX-123266643 5 29910593 GTAAGTGTATCTGGACAGTGCTATAAATACCCAGC[A/G]TTGAAAGCACCCTGGAACATAAGTAATGGAAGAGC R 2 1 2 1 101000 f 74 goat snp26002-scaffold2691-242808 5 30622975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450072 Affx-122922804 AX-123320407 5 29945471 AAGATTTCTTGAGAAGCAACAAATGCTAGCTGGCA[G/T]CAAAGGATAGCTCATCCAGACCCTGAAAGAGCCTG K 2 1 2 1 101000 f 74 goat snp26001-scaffold2691-207930 5 30658085 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410274 Affx-122952517 AX-123280624 5 29987011 AAATGTAGAGTTTAAGAAATAATTAGAAAGATTAA[G/T]CCAGTGGTAGATGGAACTAAAAGGAAGAAAGGATA K 2 1 2 1 201000 f 74 goat snp26000-scaffold2691-166390 5 30699834 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426602 Affx-122939975 AX-123296948 5 30073982 CTAAAGCAGGACCCAGGTCCTAACCCCTTCCAGAG[C/T]AGAAAGACTACTATTGACCTTAGGGACAATCCACC Y 2 1 2 1 101000 r 74 goat snp25998-scaffold2691-79419 5 30787445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434305 Affx-122934757 AX-123304646 5 30103706 TGAAAATATTTCTCTATAGGATGAAGGCCAGGGAT[A/C]TGGAACTAAATGAAACAGTCCCAACTTTAGTTAAA M 2 1 2 1 101000 r 74 goat snp25997-scaffold2691-49695 5 30818669 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765817 Affx-122931633 AX-385253264 5 30134204 AACGACTGGTTTGCACAATCAAGATCTATTTTAGT[A/G]TGTGTCATACCACAAGACAAATATTACTAACCTCG R 2 1 2 1 101000 f 74 goat snp25996-scaffold2691-19197 5 30849700 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413569 Affx-122950589 AX-123283918 5 30183390 GCTGCTCACATGGAATATTCTAGTGTGTTTTCTCC[A/G]CAACAAGGACACTCTCCCAGGGAACCAGCATGCAA R 2 1 2 1 101000 f 74 goat snp10948-scaffold1393-29890 5 30900306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414418 Affx-122949970 AX-123284767 5 30222465 AGTATCCAAGGCCCTTGGTCACAGTGACTAGTCTA[A/G]GAGTGATTAGACTTAACCAGCCTAAGTGCTTCCTT R 2 1 2 1 201000 r 74 goat snp10949-scaffold1393-68965 5 30940176 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781503 Affx-122965461 AX-385268588 5 30292487 TACCTAGTTGTATATTCCTTCAAATATTTTTGTAC[A/G]TTTAAACTCAGAATCCAAAGATTTTTGAGTGTTTG R 2 1 2 1 101000 f 74 goat snp10950-scaffold1393-138987 5 31010202 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419359 Affx-122945634 AX-123289707 5 30366725 ACAACAGTGCTGTGAGAAGCAGTGTACAAATCAGC[A/G]CAATCACCTTGTGGAAGGCATCCTTATCTCTGGGA R 2 1 2 1 101000 f 74 goat snp10952-scaffold1393-213225 5 31086141 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378486 Affx-122976664 AX-123248845 5 30395275 AAGGCATACTTAAAACATTCAGCTCTCTATGTATC[A/G]CAGTTGTGTACCTTTCTGATCTTTATCCTTAAACA R 2 1 2 1 101000 f 74 goat snp10953-scaffold1393-241775 5 31114519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384209 Affx-122972390 AX-123254567 5 30437036 ATTTTCACTTTTCTAATTTTTCAATTTGTTTAACT[A/G]CGTTTCCATATTAAATTATATTGCTCTGTCCCATT R 2 1 2 1 101000 r 74 goat snp10954-scaffold1393-283536 5 31154833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386515 Affx-122970745 AX-123256873 5 30483158 ACTTCTCTCAGCAGCTTCCCTCAGCAGAAGCTGCC[A/G]GAGCCTGCAGGGACAACAAGAGCAGTTGTAGTGAC R 2 1 2 1 201000 r 74 goat snp10955-scaffold1393-329658 5 31201679 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428315 Affx-122939369 AX-123298658 5 30552260 TAACGTCATGTAACCCGTAGCTGGTCCACATAAGT[G/T]AGCTGGACAGCATGCAGATGGCCAGTCACACAGCT K 2 1 2 1 101000 f 74 goat snp10956-scaffold1393-398760 5 31271557 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434071 Affx-122934182 AX-123304412 5 30585288 AATTAACCAGTTATGTCCCTTGGATAGGTCTTGAA[G/T]AGGAGGAAGAGTCTAAGTGACACAGCAGAGAAGAC K 2 1 2 1 201000 f 74 goat snp10957-scaffold1393-431788 5 31305571 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783973 Affx-122920263 AX-385271027 5 30614292 CACAAAACAGCTGTTTTCATTATGTTTGTGAATCC[A/G]TAATTTATTTGTAATGTGTTTGGTAGGTATAGAGG R 2 1 2 1 101000 f 74 goat snp10958-scaffold1393-460792 5 31334752 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse470 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320799121 Affx-122945565 AX-385286051 5 30650224 TGCCAAAATTATTGTACCAAATATAATATTACGAA[C/T]AACGTATAAGGTCATATATGACTCACCAAATCTTG Y 2 1 2 1 101000 r 74 goat snp10959-scaffold1393-496724 5 31415706 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse471 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38402789 Affx-122958295 AX-123273142 5 30681285 CCTCCAATGTATATGTCCTTTCAATCCAAGAATTT[A/C]GTTCTTTCTCTATCCCCCTCAAATTAGATATTATT M 2 1 2 1 101000 f 74 goat snp10960-scaffold1393-527785 5 31446671 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse472 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38386340 Affx-122970872 AX-123256698 5 30726256 TAAAAGGATGCAATTTGGACACAGAAACAGATGTA[C/T]AGAAAATAAAAATGACAAGACACACAGGGAGTAAA Y 2 1 2 1 103000 r 74 goat snp10961-scaffold1393-572756 5 31489870 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795554 Affx-122935703 AX-385282509 5 30771734 ATTAACATACCTTGTATTTCTCACCTGTGGAAATA[C/T]AAATGAAAAGAACCTCTGGATTTAGTTCCAGGAAC Y 2 1 2 1 201000 f 74 goat snp10962-scaffold1393-618234 5 31535900 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse473 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410193 Affx-122952580 AX-123280543 5 30807534 AAGGACATTTGGAAATGTGTAGTCTAAACCCTTCT[A/G]CTTCAAGCTCCAGAGCAAGATCATTTTGTCCTTGG R 2 1 2 1 201000 f 74 goat snp10963-scaffold1393-654034 5 31571529 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse474 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 538942910 Affx-1251531480 AX-585490034 5 30812229 CCTTTGTGCCTTTTCTGATTGCTTCACTTGTATTA[C/T]CCCTGAGGCCCCCTTTGTTCCCGAAGTAGGTTGGG Y 2 1 2 1 400000 f 74 goat SNPs_027 5 30812229 T C SV-TF-chip candidate gene ou candidate region LALBA 538942861 Affx-1251531499 AX-585489985 5 30812424 GGGAGGAAAGGAAAAGTGGGGTGAAATTACTGAAG[A/G]AAGCTAGCAGGCTCAATGTTTCTTTGTTGGTTTGA R 2 1 2 1 400000 f 74 goat SNPs_028 5 30812424 G A SV-TF-chip candidate gene ou candidate region LALBA 538942872 Affx-1251531500 AX-585489996 5 30812436 AAAGTGGGGTGAAATTACTGAAGGAAGCTAGCAGG[C/T]TCAATGTTTCTTTGTTGGTTTGACTGGCCTCTCTC Y 2 1 2 1 400000 r 74 goat SNPs_029 5 30812436 C T SV-TF-chip candidate gene ou candidate region LALBA 538942865 Affx-1251531501 AX-585489989 5 30812466 GCAGGCTCAATGTTTCTTTGTTGGTTTGACTGGCC[G/T]CTCTCGTCCTCCTCTTCCTGGATGTAAGGCTTGAT K 2 1 2 1 400000 f 74 goat SNPs_030 5 30812466 T G SV-TF-chip candidate gene ou candidate region LALBA 538942867 Affx-1251531502 AX-585489991 5 30812545 CCCTGAGGCTTTTTCCACAAATAAAAGGAGGTGAG[C/T]AGTGTGGTGACCCCATTTCAGGATCTTGGGGGGTA Y 2 1 2 1 400000 f 74 goat SNPs_031 5 30812545 C T SV-TF-chip candidate gene ou candidate region LALBA 538942869 Affx-1251531503 AX-585489993 5 30812604 TCTTGGGGGGTAACCAAAATGATGTCCTTTGTCTC[A/T]CTGCTCCTGGTAGGCATCCTATTCCACGCCACCCA W 4 1 2 1 400000 f 74 goat SNPs_032 5 30812604 T A SV-TF-chip candidate gene ou candidate region LALBA 538942879 Affx-1251531504 AX-585490003 5 30812625 ATGTCCTTTGTCTCTCTGCTCCTGGTAGGCATCCT[A/G]TTCCACGCCACCCAGGCTGAACAATTAACAAAATG R 2 1 2 1 400000 r 74 goat SNPs_033 5 30812625 A G SV-TF-chip candidate gene ou candidate region LALBA 538942874 Affx-1251531505 AX-585489997 5 30812697 GAGGTGTTCCAGAAGCTGAAGGACTTGAAGGACTA[C/T]GGAGGTGTCAGTTTGCCTGAATGTGAGTTCCCTGC Y 2 1 2 1 400000 f 74 goat SNPs_034 5 30812697 C T SV-TF-chip candidate gene ou candidate region LALBA 538942883 Affx-1251531506 AX-585490007 5 30813685 TCATTTTTTTCCCACCTGTAACTCCTGCCAGAGTT[C/T]CTGGATGATGATCTTACTGATGACATTGTGTGTGC Y 2 1 2 1 400000 r 74 goat SNPs_035 5 30813685 C T SV-TF-chip candidate gene ou candidate region LALBA 538942885 Affx-1251531507 AX-585490009 5 30814450 GCTAACTCGTCTCTGAGCCCTGGGCCCTGTAGTGA[C/T]GATGGACATGTAAGGACTAATCTCCAGGGATGCGT Y 2 1 2 1 400000 r 74 goat SNPs_036 5 30814450 T C SV-TF-chip candidate gene ou candidate region LALBA 464352735 Affx-1110443188 AX-515826397 5 30814497 AAGGACTAATCTCCAGGGATGCGTGAATGGTGCTC[A/G]GGACATTTGACCCTTGCTCGGTGCCTCTGATAGCA R 2 1 2 1 400000 f 74 goat SNPs_037 5 30814497 G A SV-TF-chip candidate gene ou candidate region LALBA 464359845 Affx-1110443189 AX-515833426 5 30814523 ATGGTGCTCGGGACATTTGACCCTTGCTCGGTGCC[C/T]CTGATAGCACTTTTAATGCAACAGTGCATATTCCA Y 2 1 2 1 400000 r 74 goat SNPs_038 5 30814523 T C SV-TF-chip candidate gene ou candidate region LALBA 538942860 Affx-1251531494 AX-585489984 5 30814534 GACATTTGACCCTTGCTCGGTGCCTCTGATAGCAC[C/T]TTTAATGCAACAGTGCATATTCCACTTCTGTCCTG Y 2 1 2 1 400000 r 74 goat SNPs_039 5 30814534 T C SV-TF-chip candidate gene ou candidate region LALBA 320783939 Affx-122969665 AX-385270992 5 30848822 ATACTCCACAGAATAAATAAGCAATATATTGCTAT[A/G]TTATATTTTCTCTTCCTAGGTCATAGCATGCTAGG R 2 1 2 1 201000 f 74 goat snp10964-scaffold1393-695322 5 31613340 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426075 Affx-122941085 AX-123296421 5 30896769 CTCTCAATTCACCAGCACTGTTCTTTGAGAATTCA[A/G]CATATGTGTTTGTCAGCAGAATTCCTCACTCTCTC R 2 1 2 1 202000 r 74 goat snp10965-scaffold1393-743269 5 31661338 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse475 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320771327 Affx-122967608 AX-385258485 5 30930789 TTTATCAAGTCTTTTATTGATTCTAGATTTTGAGT[C/T]ATATGAATGCTTTCCCCACTACCCCCATGGGTATA Y 2 1 2 1 101000 r 74 goat snp10966-scaffold1393-777289 5 31695495 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse476 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38425026 Affx-122941877 AX-123295372 5 30966107 CCTCCTGATCTGCCCCCACGGGGAGCCCCCCAGGT[C/T]TCCGGAGAAGAGGAAAGGGCTATTGCTTGTACACG Y 2 1 2 1 101000 r 74 goat snp10967-scaffold1393-812607 5 31731258 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771934 Affx-122959816 AX-385259090 5 31007158 TAAAACATCATTTTAGTAAGCTATTTGTGGTTGCT[A/G]TAATACTTCACTAATCTAGTCTCAACCGAACATTT R 2 1 2 1 101000 f 74 goat snp10968-scaffold1393-853658 5 31772434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse477 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320799678 Affx-122938649 AX-385286606 5 31036451 AATCAAGAGCAGTCAAAAGTATCCACCAATTAAGT[A/G]TTTTTCTTTGAAGATATTAATGTGAGGTCTCTGGC R 2 1 2 1 101000 r 74 goat snp10969-scaffold1393-882951 5 31801705 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse478 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38418111 Affx-122947130 AX-123288459 5 31074313 GGCTTAGCAGAGAGGATGCAGATGGATCAAGATGG[C/T]CTCAGGGACTCTGGCCCCTTTCTCTGGGTGATGCT Y 2 1 2 1 101000 f 74 goat snp10970-scaffold1393-920813 5 31839621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426268 Affx-122940321 AX-123296614 5 31104511 GGCAGGCGAGGATAGGAGTCTCTTTAACCAGTCTC[A/G]ATTATTCAGGTAATCCGTCGACAGTCTCACCCATT R 2 1 2 1 101000 r 74 goat snp10971-scaffold1393-951011 5 31869701 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse479 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38424139 Affx-122942552 AX-123294485 5 31137250 TCTGGTGCATATGTTGTTCAGATAAAGAGAAATAA[C/T]AGGCCCTGCCCTCCAAGATTCCAGTTCCAGTTCTA Y 2 1 2 1 101000 f 74 goat snp10972-scaffold1393-983750 5 31902222 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse480 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38396888 Affx-122963230 AX-123267243 5 31218670 ATTCCCATCTGGAGCCAGGGAGGGAGGAGAGAGAA[G/T]TGAGGAATGGCAGGGTGGGATTCAAAACCAGGAGA K 2 1 2 1 101000 r 74 goat snp10974-scaffold1393-1065170 5 31983701 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435699 Affx-122933316 AX-123306038 5 31354847 GTTGGGCGGGCTACAGTCCATGGGGTTGCAAAGCA[C/T]GATGGTGATAATAGTTCCTAACAGCTGTATGAAGT Y 2 1 2 1 101000 r 74 goat snp10977-scaffold1393-1201347 5 32119276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse481 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38384889 Affx-122971927 AX-123255247 5 31366644 TGGGATGATGGGAGTCCTGAGAGCCTTGTGTCTTG[C/T]GGGGTCGGTCCATGGGGGAGAGGAATGTAACAGGG Y 2 1 2 1 201000 f 74 goat snp43251-scaffold576-10875 5 32131174 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse482 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38378093 Affx-122977159 AX-123248452 5 31504569 TTTCTTTTTCACTCAAGAGTCTATCAGGGATCTTG[C/T]ATTGCATTTGATGATGAAAGCCCTGCCATATGGAG Y 2 1 2 1 101000 r 74 goat snp43254-scaffold576-148800 5 32270307 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776189 Affx-122963970 AX-385263317 5 31550071 GACTCTTGGCAGGTCAAGTACATTAATCTATAGCT[A/G]CAGTTAACTTATTAAGAAGGAACTGAGGCAGGAGA R 2 1 2 1 101000 r 74 goat snp43255-scaffold576-194302 5 32317001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse483 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468278358 Affx-1111836301 AX-519551844 5 31551302 CCCCTAGAGCTGTCTGGTGTTCCCCACTTTGTTGT[A/G]TCAGGAAAGAAGAGCTGAGAATGGAGGGTAGAGGA R 2 1 2 1 102000 r 74 goat Random2.2K-538 5 31551302 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320768722 Affx-122927165 AX-385255900 5 31579900 TGATAAAGTCATAGTTCCTTCATTCAAGACATTGT[A/C]GTCAGTTGATTTCTGAGAGGAGATAAGCACATACT M 2 1 2 1 101000 r 74 goat snp43256-scaffold576-224131 5 32347688 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse484 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38399552 Affx-122961134 AX-123269907 5 31667114 TAAAAGATATGGAAACGGTTTATAAGTCACCAAGT[A/G]CTTCAACATGGAAGATACTATTGTCATTACTCTGA R 2 1 2 1 101000 f 74 goat snp43257-scaffold576-311345 5 32435566 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772409 Affx-122920626 AX-385259561 5 31801769 GATGGTCCCAATAGCACTTTTAGATTAAATGGTCA[C/T]GGAAGACCTCTTAGGAGATGACTTGGAAGGTACAG Y 2 1 2 1 101000 r 74 goat snp43260-scaffold576-446000 5 32570974 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse485 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38386208 Affx-122970992 AX-123256566 5 31844953 ATGTCTTTGGCCAGTGCTGTGCTGGGAATTCTGTA[C/T]AGTATCTGGATGATTCTGGGCCAGCCCTAAAAATG Y 2 1 2 1 201000 r 74 goat snp43261-scaffold576-489184 5 32614268 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse486 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410030 Affx-122953247 AX-123280380 5 31887772 TCGGACACGACTGAACAACTTTGACTTTCACTTTC[A/G]CTCAATATTTTCTCATCGGCCCTGAATTTGACCTT R 2 1 2 1 101000 r 74 goat snp43262-scaffold576-532003 5 32656339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378826 Affx-122976546 AX-123249185 5 32013219 TGGTGTGAAGTTAAGCAGCTTTATCAGGGAAAGAG[C/T]GAAGGTATCTGAGACATAACTAAGCAGGGGAACCT Y 2 1 2 1 101000 f 74 goat snp43265-scaffold576-657450 5 32782420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse487 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468272305 Affx-1111833463 AX-519546044 5 32043804 GTGCCCTCATTGGAGGGCCCTTCTGCAAGCTCTGC[A/G]ATGGGCCCAGGAGAGTGAAGGTGATCACTCACATC R 2 1 2 1 202000 f 74 goat 5_32043804_AF-PAKI 5 32043804 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449436 Affx-122922677 AX-123319771 5 32063215 TTTTTTGGCTAGGTACCAACTAGGAGAATACACAG[C/T]GGGTACCACCAATTCAATGGACGTGAATCTGAGCA Y 2 1 2 1 101000 f 74 goat snp43266-scaffold576-707446 5 32832954 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse488 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38417522 Affx-122946940 AX-123287870 5 32092518 GCTTGAAGTTAAAAGGAGAAAACTTTTATTTCATT[A/G]CATAAAATATTATATCTCAGGGTCCGACAGAGTTA R 2 1 2 1 201000 r 74 goat snp43267-scaffold576-736749 5 32861661 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383552 Affx-122972610 AX-123253910 5 32153443 AGTCTAAAGGTATATACATGGTATTTGTTATGTGT[C/T]TCTGTACTTTTTGAACAAGTGGAATATTTAATAAT Y 2 1 2 1 201000 r 74 goat snp43268-scaffold576-797674 5 32921038 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse489 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320789655 Affx-122926167 AX-385276664 5 32202795 AAAGCAAGTATCAGTCTTCCAATTGTTATTTATTA[C/T]ACTATACTAGATAATATAAAAATAGAATTAGAGAC Y 2 1 2 1 202000 r 74 goat snp43269-scaffold576-847026 5 32970509 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse490 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38394381 Affx-122964632 AX-123264736 5 32235854 TAAGTCCTCTTGCATGATCCAGACTATATCATCAC[A/G]TAGTGGCACTTGCTTCCCCACCTCCTACCCAGTCC R 2 1 2 1 101000 f 74 goat snp43270-scaffold576-880085 5 33003770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798134 Affx-122943145 AX-385285068 5 32265249 TTTAGTTTCCTCATATTTGTTGGAATAATTTCTGT[A/G]TAATGTAATTCCCAAGATCATTTAGCTTGTAATCA R 2 1 2 1 101000 r 74 goat snp43271-scaffold576-909480 5 33033334 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse491 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38433561 Affx-122934981 AX-123303902 5 32303550 ATGGGACTGTTCAATGGACTTTCCAAATCAGGGGT[A/G]TCTAAGGGTTCATCGTAAATTGCAGAGTTGTGATA R 2 1 2 1 101000 r 74 goat snp43272-scaffold576-947781 5 33072151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse492 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320797616 Affx-122923940 AX-385284555 5 32332647 TTCATGAAGAAAACAATACATGTGAGACAAGCAAA[C/T]ACATCTTCACCAAATGAAAGTGAATTAAGTGCTCA Y 2 1 2 1 101000 f 74 goat snp43273-scaffold576-976878 5 33101184 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398322 Affx-122962136 AX-123268677 5 32370118 ACATCACCCACACTTCCTCTGCCCAAGCGTAAACA[C/T]GATGTTATCCCTACATCTGCCTGGAGGTGACACGT Y 2 1 2 1 201000 r 74 goat snp43274-scaffold576-1014349 5 33139887 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse493 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320798118 Affx-122975600 AX-385285053 5 32439311 CTATGAAGTGATACAAAACGAATAGAAGCTCCATC[A/G]TTACCATAGAGAAGCTAAACAATTGTCTAAGAACT R 2 1 2 1 101000 r 74 goat snp43275-scaffold576-1083542 5 33210633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse494 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38446550 Affx-122924850 AX-123316886 5 32468931 TGAAATTCCCACCTATCCTCCTTAATCTCCCGCTT[A/G]CCACCTGTTTCAATGTGGAGAAGCAGGAAATGGTG R 2 1 2 1 101000 r 74 goat snp43276-scaffold576-1113162 5 33239455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419102 Affx-122945777 AX-123289450 5 32501198 ATTGTCAGCCAATGTTCTTATTCTTGTTTTCAACT[A/G]TAGGTCAGTCATTCCTTTCTGGGGATAGCTCTTGA R 2 1 2 1 101000 f 74 goat snp43277-scaffold576-1145429 5 33272152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse495 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320803013 Affx-986696127 AX-385289891 5 32504894 CCCTTGACCACCGAGGTACTGTACCTCCCAGCCAA[C/T]GCCTCTTGTGTCCTGGCCAATGACACTTCATTAAC Y 2 1 2 1 600010 f 74 goat 5_32504894 5 32504894 Ancestral_priority_1043 ancestry 0.47 neutral IMAGE 10K 10K ancestral 320764519 Affx-986696874 AX-385252188 5 32505118 TCCCTACCTGACCATTCTGACACCCCAGGCAATGG[A/C]GGACCAAACCCAGTCAACCCACCACCAGAGGGCAC M 2 1 2 1 600010 r 74 goat 5_32505118 5 32505118 Ancestral_priority_1043 ancestry 0.492 neutral IMAGE 10K 10K ancestral 320762345 Affx-986696876 AX-385250516 5 32505142 CCAGGCAATGGCGGACCAAACCCAGTCAACCCACC[A/G]CCAGAGGGCACTAGCTGCAGCTCCCCTGCTCCTCA R 2 1 2 1 600010 f 74 goat 5_32505142 5 32505142 Ancestral_priority_1043 ancestry 0.486 neutral IMAGE 10K 10K ancestral 468273709 Affx-1111833794 AX-519547321 5 32536056 GCAGACGTGTTCTGGCAGGTTTTTTTTCTGAGCAC[A/G]GAGTGCTTCATTTCTACTTTCCA R 2 1 2 1 102000 f 74 goat GoatD01.005381 5 32536056 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802498 Affx-122940089 AX-385289402 5 32550233 ATAGTCTCTCACTAAAAGAATTTATAGAACAAGAA[C/T]AATCTTGTGATTAAAGATTATTTTAATTTAGGAAT Y 2 1 2 1 202000 r 74 goat snp43278-scaffold576-1194464 5 33320813 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse496 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320780484 Affx-122924358 AX-385267575 5 32594485 CTGTCATCTTTCCCTCCCTTATATTTGGCTCAGGG[A/C]GAATAGTTCAGATCCCCACTTAAAGAGTCTGTACT M 2 1 2 1 101000 f 74 goat snp43279-scaffold576-1238716 5 33365253 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410020 Affx-122953256 AX-123280370 5 32640144 CAATAGGTCACCTGACTGTAAGGTTGTTCTCTTGA[A/G]CTTAACATTTTTAGTTTTAGGCAAGGGCCAGAAAT R 2 1 2 1 101000 r 74 goat snp43280-scaffold576-1284375 5 33411113 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse497 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38378794 Affx-122976992 AX-123249153 5 32722546 TTTCAGAGAATATATTTATGTATCTTTTGCCTAGA[C/T]GGGAGAGGAGCAGTCAGCTCAATTTACAGAGTAGA Y 2 1 2 1 101000 r 74 goat snp43282-scaffold576-1366777 5 33492408 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412258 Affx-122950897 AX-123282607 5 32778784 TGACACAGAACAGCGCTTTTTGTAAGAAAGGGCCC[A/G]CACGAATGACAACAGGATTTCCAAGTGCCCCCAAC R 2 1 2 1 101000 r 74 goat snp43283-scaffold576-1423015 5 33547738 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773617 Affx-122965264 AX-385260757 5 32822917 AATCACATGTGCTATGGGACAGCTGGTTCCTTCAG[C/T]GTCTGAGATCATTGTCAGATTACATCTTTTTGTGT Y 2 1 2 1 101000 f 74 goat snp47304-scaffold665-4902 5 33595238 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406731 Affx-122955748 AX-123277082 5 32876057 AGTGAATTCCTTTAATGTCAGCATGCCCTCCAAAG[C/T]GTGTATATTGCCCCTCTTTTTAATTTATTTTCCTC Y 2 1 2 1 101000 f 74 goat snp47305-scaffold665-58042 5 33649076 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440515 Affx-122929348 AX-123310852 5 32919606 GAACAGATGCTATCCTGCAGAGAACCAATTCTACA[A/G]CAAAGAACGACAGTGATGCAGAAAGAGACCATGCT R 2 1 2 1 101000 f 74 goat snp47306-scaffold665-101591 5 33693670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784676 Affx-122967255 AX-385271724 5 32984362 GTCATGGAAAGTTTTTAAGGGGCATATTTTTGTAT[A/G]CTTTTAGGTGGTAGTAATGGGTTTCATTGCTTATA R 2 1 2 1 101000 r 74 goat snp47308-scaffold665-166347 5 33755979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409233 Affx-122953151 AX-123279584 5 33021629 TCAGCTCTTTAATGTCTTGCTTCTCTATAAATTTC[A/G]CAGCCAGTTACTCTAACTATGCAAACATCTTTCCT R 2 1 2 1 101000 r 74 goat snp47309-scaffold665-203614 5 33793519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385158 Affx-122971750 AX-123255516 5 33128912 TCTCAATAAATGGCAACTGTTACTATTATTATTTA[C/T]GTTAATAGAGAAGTCCAAAGTGGAACCATATTCTA Y 2 1 2 1 102000 r 74 goat snp47311-scaffold665-310897 5 33901255 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275396 Affx-1111834874 AX-519548970 5 33142702 GGATTCTGATCCTTATTGAGTCTGAGAGATACAGG[A/C]CTGGTATCCCCAAACTCCTCCAGCTCCAACACTGC M 2 1 2 1 201000 f 74 goat GoatD01.057270 5 33142702 T G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402264 Affx-122959121 AX-123272617 5 33220511 TAAAACTGATCTTCCTGAAACTTAAAAATACCAAG[C/T]ACTTTTTCCAAAGTAGGAAAGTTACCTCCTTGGTA Y 2 1 2 1 101000 f 74 goat snp47313-scaffold665-402496 5 33993843 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796887 Affx-122919830 AX-385283829 5 33272419 TATGAATCTAGCATTTGGGGGCAATAATTTATAAT[A/G]CAGCATCTACTCCTAGATATCACTAAGAGATTTCA R 2 1 2 1 101000 r 74 goat snp47314-scaffold665-454404 5 34046474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403581 Affx-122957574 AX-123273934 5 33344835 TCCTCAGGAATGGCTTCAGAATCCTAGATCTTTCC[A/G]TTACTCACCTGATGCCCTGAGTGCCTGTTGCTATT R 2 1 2 1 101000 r 74 goat snp47315-scaffold665-526820 5 34119539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414177 Affx-122949673 AX-123284526 5 33379404 ATGTAGTAGTGGCAGAAATAGCATTTGTTCTGGAG[C/T]CTTTAGACTCCAAATTCTTTTCTCATTTGATGGCA Y 2 1 2 1 102000 f 74 goat snp47316-scaffold665-561389 5 34154067 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412428 Affx-122951424 AX-123282777 5 33412564 GTCTCTGCTTTTTAATATGCTATCTAGGTTGGTCA[C/T]AGCTCATATCCATATCTATCTGCAAAACAAGAAAA Y 2 1 2 1 201000 r 74 goat snp47317-scaffold665-594549 5 34188399 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766637 Affx-122965339 AX-385253988 5 33442929 CTGCAGGTTAAACATACTCTAATACACTGATTTTA[C/T]GAAAATCAGTATGATTACAAGAGATTAAATGCAGT Y 2 1 2 1 101000 f 74 goat snp47318-scaffold665-624914 5 34218177 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414538 Affx-122949507 AX-123284887 5 33563625 GTATCTTTAGCACAGAGAAACTAGAACTTGATAAA[C/T]ATTCAGTATAAACATATACACACACTGAAGTGAGT Y 2 1 2 1 201000 f 74 goat snp47320-scaffold665-745610 5 34341669 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419498 Affx-122945460 AX-123289846 5 33596723 TAGTGGTTCTCAAAGTGTGATTCCTGAGACCAGCA[A/G]CAAAGGGAATTCTCAAGTTCCACTACAGACTTACT R 2 1 2 1 201000 r 74 goat snp47321-scaffold665-778708 5 34374455 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766244 Affx-122929910 AX-385253640 5 33644202 ATTGTGAATTAATGTTTTCTGAAATTCAAGATGCA[C/T]GTGCAATTATAAGGGAAGACTTTCAGTGATAAACA Y 2 1 2 1 101000 f 74 goat snp47322-scaffold665-826187 5 34423847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411510 Affx-122951678 AX-123281860 5 33673456 GTCTGGGTCCTAGGGAGTTCTGTAGTTAAAAGAAA[C/T]GTTAAGATTTTAAAATTGCAAACAGCTTTGAGACT Y 2 1 2 1 101000 f 74 goat snp47323-scaffold665-855441 5 34453343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399046 Affx-122960913 AX-123269401 5 33743135 CTTCACCATGTGAGCCACTAAATAAGTAAACAAAA[C/T]GTTTCTGCAAATAAACCCTGCAAAACCCAAATTGG Y 2 1 2 1 201000 r 74 goat snp47324-scaffold665-925120 5 34523035 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438324 Affx-122931348 AX-123308662 5 33780018 AATGATTCTAATGCTTCTGAAAAACTGAGTTCATC[A/G]CAGTGAACCAAAGCAGAAACAAGAAACAGATGAGG R 2 1 2 1 201000 f 74 goat snp47325-scaffold665-962003 5 34559800 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398624 Affx-122961471 AX-123268979 5 33842512 AAATGTTGGTAAACATTCTTAGCTGCTATCACTTT[A/G]TGTTTTCCTCTGTGTTTTCTCATCTTCTTCCAGTG R 2 1 2 1 103000 f 74 goat snp47326-scaffold665-1024497 5 34622136 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791000 Affx-122947617 AX-385277997 5 33877671 GCAATGGTTAGGTGTGAATTGAACCCTTGAGCAAT[A/G]TGAAAAACCATCATAACCAGAGGAAACAAGGTACT R 2 1 2 1 101000 f 74 goat snp47327-scaffold665-1059656 5 34657220 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404855 Affx-122956620 AX-123275207 5 33910110 TAATAAACACTCAGTAAATGAAAGAAAGATGCCTC[A/G]CATTTTATAGGAATAACTAATGTGTCTTCCCATTC R 2 1 2 1 101000 r 74 goat snp47328-scaffold665-1092095 5 34684414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406945 Affx-122955069 AX-123277296 5 33957958 TTTCTACATATTTCAGTCCTAAAATGTCAGGTTCA[C/T]GCTATTCAAGAAATATACCTATACTGTACCAATCA Y 2 1 2 1 101000 f 74 goat snp47329-scaffold665-1139943 5 34732671 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404149 Affx-122957084 AX-123274501 5 33998482 TTCCTTTCTTAAGGCTCTCACATACATTTTAGACT[A/G]CATAATTAAAATAAACTCCCACAGTTCATGAAAGA R 2 1 2 1 101000 f 74 goat snp47330-scaffold665-1180467 5 34773194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415939 Affx-122948440 AX-123286288 5 34030756 ATCAAGCAAAAAGTGTCTGGAATTGGTCCAGTAGG[A/C]TTTTAGAAAAGACAGATTAAAGAACAGTCTGAAGA M 2 1 2 1 103000 f 74 goat snp47331-scaffold665-1212741 5 34805399 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405678 Affx-122956558 AX-123276030 5 34088707 TAATTCTTCTGGGTAATTTGTGGCTTTTTCATATG[C/T]TTATGGTCATCTTTATTTGTCCAAAAGTTTCTCCT Y 2 1 2 1 101000 r 74 goat snp47332-scaffold665-1270692 5 34863272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423493 Affx-122942566 AX-123293839 5 34131356 GCAAGTACACTCACATTTCATTGGCCAAAGCAAGT[C/T]ACATGGTCACATGTAACTTCAAACAAGCCCATAAG Y 2 1 2 1 303000 r 74 goat snp47333-scaffold665-1313341 5 34904537 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796748 Affx-122978650 AX-385283692 5 34185139 ATCATAATTAAATGACTAATAGGCTGAAGGTGAAA[G/T]GGACCATTTTGGAAAATGGTGAATTCTCCTTCAGT K 2 1 2 1 102000 r 74 goat snp47334-scaffold665-1367124 5 34958839 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797116 Affx-122948739 AX-385284056 5 34239507 TATAAAATTAATGTTGTTATGAAGAATTTTGTGTG[C/T]AGTTACTGTTCTGCTAGGTATTAGGCATATAATAA Y 2 1 2 1 101000 r 74 goat snp47335-scaffold665-1421492 5 35013633 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438394 Affx-122931296 AX-123308732 5 34295243 AACCTTGTGTCAACTGGTTTCATAATGACACAGTG[C/T]GCTTCAGAAAAATCAAGTCTATAACAATGCAGGTA Y 2 1 2 1 101000 f 74 goat snp47336-scaffold665-1477228 5 35068980 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38383629 Affx-122972543 AX-123253987 5 34333024 CTTCTGCTGGAGTTCAGACTAATAGAACTCAGACG[A/C]CCCTCCTCTTTAAAAATGTATTTAACCAATGTCAT M 2 1 2 1 101000 f 74 goat snp47337-scaffold665-1515009 5 35107087 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775755 Affx-122971439 AX-385262886 5 34367373 ATTGTGTAAGAAGCATATAGGAAAAGTATGACACT[A/G]TGAGAGGCAAATCTTGGGACTCAATTTATACAGAG R 2 1 2 1 101000 r 74 goat snp47338-scaffold665-1549358 5 35141359 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435352 Affx-122933594 AX-123305692 5 34433186 TACATGGAGTGATTCTTCTCTCAATTTGCCAACCA[C/T]TGACATACAACAAACATTTGAGAAACTTCTCACCT Y 2 1 2 1 101000 f 74 goat snp47339-scaffold665-1615171 5 35207690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443557 Affx-122927351 AX-123313894 5 34466262 TTCTTTGGATAATAAAAATATAAATAATACCTATA[C/T]GCTTGAGAACTTTATAGTCTACCAGAGGAGATAGA Y 2 1 2 1 101000 r 74 goat snp47340-scaffold665-1648247 5 35241240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784099 Affx-122965533 AX-385271151 5 34510656 ATCAACATGCTGATATCTTGCAAAGTGCTCCAATG[A/G]AGATATATACATGATGTACCCTTTCTTTTTATGAG R 2 1 2 1 101000 f 74 goat snp47341-scaffold665-1692641 5 35285668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421186 Affx-122944158 AX-123291533 5 34553225 GTTCTAGCTTTTAAGAATCAATTTATATTTCCTTT[A/C]TTGGTGATTCTCTTTTAGGTATTACAGTAATGATA M 2 1 2 1 201000 r 74 goat snp47342-scaffold665-1735210 5 35328498 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380329 Affx-122975376 AX-123250687 5 34597585 AATCTCATCGGATAGCAAAAGGTAAGAGTTAGTCC[A/G]TTATGATGTTTCTGCTTAAATATTAATATTTCTCA R 2 1 2 1 101000 f 74 goat snp47343-scaffold665-1779570 5 35372408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272184 Affx-1111833464 AX-519545936 5 34638160 TTTGATAACATGAGCTGTATCTCTGTCCCTTTCTC[A/G]AGCTGTTTTACCAGTGGTACCTTAAATCTTGGCAA R 2 1 2 1 201000 r 74 goat 5_34638160_AF-PAKI 5 34638160 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454033 Affx-122919413 AX-123324366 5 34696711 GTTGGAAGGTTCTGAGCCTTTCTGTTTGTCTGTGT[A/G]TGGGGATACACTGATTGTTTGTTGAATGTACCTTT R 2 1 2 1 202000 r 74 goat snp47344-scaffold665-1878696 5 35473015 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415150 Affx-122949410 AX-123285499 5 34745541 ATAAGCAATTGAGTTATATGGTTAAGTGATGTTCC[A/G]TCTCTACCAGGGCCTAGTCCCACGTCAAGAGTTGT R 2 1 2 1 201000 f 74 goat snp47345-scaffold665-1927526 5 35522227 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783410 Affx-122971343 AX-385270473 5 34801240 ACTAAAGGCAAACCCCACTCCTGCAATGTTAAAAA[C/T]GTGATACTTTGGTTTTTATGTACAATCTTCTAAAA Y 2 1 2 1 102000 f 74 goat snp47346-scaffold665-1983225 5 35578214 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443634 Affx-122927289 AX-123313971 5 34868852 GTCTTCTTATAGCTAGAGGATTTGGCCTGTGAATA[C/T]GAGTTTTTATTTGCTCAAATGGATTTCTCTGAAAC Y 2 1 2 1 201000 r 74 goat snp16394-scaffold1728-163445 5 35649882 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774948 Affx-122966234 AX-385262081 5 34901536 TTTTCAATTTTATTATACAGCAGTAAATGGTTTTC[A/G]AAAGTGGTATAATAGTTTAAACAACATAATTCAGT R 2 1 2 1 101000 r 74 goat snp16393-scaffold1728-130761 5 35682290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777859 Affx-122953784 AX-385264976 5 34939479 ACAGTTGATGTCCTAAAAGCTGGCACTAACAACTA[C/T]AATAAAAATGCAGCATTTTACTAGGGGATGCTAGA Y 2 1 2 1 303000 r 74 goat snp16392-scaffold1728-92818 5 35721075 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445048 Affx-122926612 AX-123315385 5 34970113 TAATGTTAACACTTTAAAAGAGCATGAAGAAGTAT[A/G]TTTTAATGGATGATGAAAATGTTTCCTTACTCAAT R 2 1 2 1 103000 f 74 goat snp16391-scaffold1728-62184 5 35752730 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418452 Affx-122946474 AX-123288800 5 35025677 ACTTAGCACTGAGCCCCTAGATTGGAACAGCCTCT[G/T]GTTTTTCTCCCTTCCCAAATGAGAAGAATCCCAAG K 2 1 2 1 201000 r 74 goat snp16390-scaffold1728-6620 5 35806949 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407732 Affx-122954996 AX-123278083 5 35051581 AAAGGCATCATTCCATGCTCACTTAAGTATGAGGA[C/T]AGCAGAAACAATTCCTGAATTAGAGTAACCAGAAA Y 2 1 2 1 101000 f 74 goat snp9039-scaffold1329-19185 5 35833443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793431 Affx-122969252 AX-385280408 5 35093328 GGAAAACATATGAAGTTTGCTAAAAGAAGTAACTA[C/T]ATGGCAGGAAAAAGAAGATCTCAGAGAAAGTAATC Y 2 1 2 1 101000 r 74 goat snp9040-scaffold1329-60932 5 35875581 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786602 Affx-122922003 AX-385273634 5 35136750 GGTTAAAACCATGGCTCCAAGGTCTATCCCTTCAG[C/T]GGAACTTTAAACATGAAAGTTCACCTTCTCAGCAG Y 2 1 2 1 102000 f 74 goat snp9041-scaffold1329-104354 5 35918720 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387368 Affx-122970469 AX-123257726 5 35167421 AGGGAACCAAAGAAGCAGAAGTATAAAATCAGAAT[A/G]TCCTATGGTATCATTTTGGACACATGGGCATGCTT R 2 1 2 1 101000 r 74 goat snp9042-scaffold1329-135025 5 35949405 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769360 Affx-122959670 AX-385256531 5 35215957 CTATTTCTATGTTGTAACAAAGTTGAGGAGGCTGT[A/G]TTAAATACATGATAACTGGGATAAAAGACAACAAA R 2 1 2 1 101000 f 74 goat snp9043-scaffold1329-183561 5 35998150 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783178 Affx-122929524 AX-385270245 5 35244759 AATGAGAACTCTAGGAGCAGGCAACTTGACTCTTA[C/T]CAAGTAAGCTGTTGCTAAAACTATTGAAGTTCTGA Y 2 1 2 1 101000 f 74 goat snp9044-scaffold1329-212363 5 36028011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387142 Affx-122970645 AX-123257500 5 35276416 AAATGGTAATGGCAGTAGCAGAATAGGGAAAGATG[C/T]AGAAATGGACAGATGTCAGAGACAAATCTGGAATG Y 2 1 2 1 201000 f 74 goat snp9045-scaffold1329-244020 5 36059625 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386333 Affx-122970878 AX-123256691 5 35314475 AAGGAATTAAGATAGGACCTAGAAAGCTGATAAGG[C/T]GCCTTTTTCTATCAGAACAACACCTGAATGAATGG Y 2 1 2 1 101000 f 74 goat snp9046-scaffold1329-282079 5 36097872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796642 Affx-122941083 AX-385283588 5 35345962 CATTAGCCAGCTATCCCATCAAAACGGCCTTTTCA[C/T]GTCCTAAGTCGAAAAACAATCAACAATTAATTCTT Y 2 1 2 1 101000 f 74 goat snp9047-scaffold1329-313566 5 36127871 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381984 Affx-122974092 AX-123252342 5 35380190 TATGTTTTCTTTCAAAACTTAAGTGTCAAATCATT[A/G]GTCGCTCAGTCGTGTCTGACTCTTTGCAACCCCAT R 2 1 2 1 201000 f 74 goat snp9048-scaffold1329-347794 5 36162380 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385311 Affx-122971675 AX-123255669 5 35450975 ATGCTACAGAGGCCTTTTTTATATATGTGAAAATC[A/G]TACTGTATATGTAATTTGTATTTTACTTAATAAAA R 2 1 2 1 102000 f 74 goat snp9050-scaffold1329-418579 5 36233085 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413412 Affx-122950707 AX-123283761 5 35486795 AAGAAACTTGTTTATATTTGAGCATTTATGGTCAC[A/G]TGGGATTGGGAAGGCCTTCTGGCGTTGTCTGGTTC R 2 1 2 1 201000 f 74 goat snp9051-scaffold1329-454399 5 36268945 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453293 Affx-122920373 AX-123323626 5 35542479 TGTAACATTGATTCCTGGAGCCTTTCAACCTAGTC[A/G]CATTTACCAGGAACACTTCCTAGTTTGTCAGTGTC R 2 1 2 1 101000 r 74 goat snp9052-scaffold1329-510083 5 36325761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278362 Affx-1111836303 AX-519551848 5 35585935 AGCATAATAAAAGGAGAGCAGTGGGAACAAATAAT[A/G]AAAGTCTGGCTTTCCAGCTAAGACCTAGATTGAAA R 2 1 2 1 101000 r 74 goat Random2.2K-541 5 35585935 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38404703 Affx-122957262 AX-123275055 5 35591977 TTGAGTCAGAAACAGGATATACAAAGAAAGATATA[C/T]GAGAAAAATCAAAGACAACTTTTAAAATAAGAAGT Y 2 1 2 1 101000 f 74 goat snp9053-scaffold1329-559581 5 36375399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 coat-colour SNP associated with coat colour multi-breed 320779154 Affx-122961321 AX-385266258 5 35708039 TCTTGTGACTGTCTTACATGGTGATGTCTGTTAAA[C/T]GCTTTTCGTAGTAAATCTGTTTGCATGTAGACATG Y 2 1 2 1 101000 r 74 goat snp9056-scaffold1329-675643 5 36494319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382441 Affx-122974230 AX-123252799 5 35745646 GGCAAAACTGAAGGAGACAATCTAATGATGAGAAT[A/G]TGAAAAAGACATTTGCATGTGTGTTTGATTGAGTG R 2 1 2 1 101000 f 74 goat snp9057-scaffold1329-713250 5 36529393 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783712 Affx-122970150 AX-385270768 5 35791915 GTTGTGCTCACTTGTCCTTGAAGGTAAAACATTTA[C/T]GAGCTGTAAAGAAATACAAGTGAAAAACAACATTA Y 2 1 2 1 101000 r 74 goat snp9058-scaffold1329-759519 5 36576488 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772382 Affx-122947248 AX-385259534 5 35823004 TATAGCTCTAAATCTGTATGTATACTGAACATTGG[C/T]GTAGGCTTAATTAGCATTCATTAAACACTTCAGCT Y 2 1 2 1 10000 r 74 goat "snp9059-scaffold1329-790608;SV_224" 5 36606094 T C SV_224 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765519 Affx-122962055 AX-385253003 5 35869590 GGGTCTTGAACATTGTAAGTCACCCATGATTCTCA[A/G]TATGATTTATTGAGTTGACAAGAAAACAAAACAAA R 2 1 2 1 101000 f 74 goat snp9060-scaffold1329-837194 5 36651381 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387743 Affx-122969737 AX-123258101 5 35969164 TAGCCCATGGGGTAGCAAAGAGTTGAACTTCAGGG[C/T]ATGGCAGAAATGTTAGACTTTATGTGAAGAAGAGG Y 2 1 2 1 201000 r 74 goat snp9062-scaffold1329-936768 5 36750714 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415236 Affx-122948957 AX-123285585 5 36008499 GTTACAATAATTTTAATTTGCATCTGTGTCCCATA[C/T]GCTCTATGATGTTACATACACCTTGCAATTTTTGA Y 2 1 2 1 101000 r 74 goat snp9063-scaffold1329-976103 5 36790974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782096 Affx-122944861 AX-385269174 5 36058910 ACTGAGGGAGAAGAACATGGACATAATACGTCTTT[A/G]TTAATAGTGGTTATTTTGGGTAGGAGTTAAAGGCA R 2 1 2 1 101000 f 74 goat snp9064-scaffold1329-1026514 5 36842333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391937 Affx-122966928 AX-123262294 5 36118073 GCATAAATGTGGTTCTTTTGATCCTTGTTTTTTGT[A/C]ATTTCTACTCTATTACAGAACAGTCATGAGATGAA M 2 1 2 1 201000 r 74 goat snp9065-scaffold1329-1085677 5 36896157 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376318 Affx-122978356 AX-123246677 5 36161080 CCTTGCACACAATTTTAATAACAAAGAAAAACTAT[A/G]TCCAGGGGTCAACTAAATCCTGTATCTATAAAATG R 2 1 2 1 101000 r 74 goat snp9066-scaffold1329-1128684 5 36939144 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437955 Affx-122931616 AX-123308293 5 36202058 TGTGAAAGGAAAAAAGGGCCATGTCTTTCTGACCA[C/T]AGCAAAGTAGAAAAGGGAAGATTAAATAAGCCAAA Y 2 1 2 1 101000 f 74 goat snp9067-scaffold1329-1169662 5 36980714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392098 Affx-122966363 AX-123262455 5 36251305 AAGCTGTGAGCTTCTCACCTGTTACCAAGTTTAAA[C/T]CTCTCAGCTCACAGCATTAGTTGGAACAGAAGGAA Y 2 1 2 1 101000 r 74 goat snp26896-scaffold2844-2833 5 37031306 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768368 Affx-122927875 AX-385255548 5 36289767 CCTCTTGGACTTCCTGAGATGATTTAGAAATGACT[A/G]CATATAAATGTTATTTGATGGCACAAGATGGGATG R 2 1 2 1 101000 f 74 goat snp12728-scaffold149-35530 5 37074793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385928 Affx-122971564 AX-123256286 5 36324830 TCCTTTGGTTTCACGGCTGCAGTCACTGTCTCCAG[C/T]GATTTTGAAGCCAGAGATCAAGTTGGGTTGTGTTA Y 2 1 2 1 103000 r 74 goat snp12729-scaffold149-70593 5 37109938 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394432 Affx-122965093 AX-123264787 5 36353590 ATTAGAATGTTTTTTAAAGCACAGATTTAGGGAGA[C/T]AAATAAAATTTGAAGCTTGTTGGGCCACGGTGGGC Y 2 1 2 1 101000 r 74 goat snp12730-scaffold149-99353 5 37138657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450950 Affx-122921758 AX-123321284 5 36393331 GTCAGAAGATAGGAAGTATTATTGTGGCAAATCCT[A/G]CAGAAGTATTACATAGTAACAATAGTTTGGTACAA R 2 1 2 1 101000 f 74 goat snp12731-scaffold149-139094 5 37179394 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379324 Affx-122976185 AX-123249683 5 36431779 TCTGGAGGTGAGCCCTGCATTTATCTCCTCCCCGT[A/C]TAGAATATCAGGCACATGGTTGGAATTGGGAGCAA M 2 1 2 1 101000 r 74 goat snp12732-scaffold149-177542 5 37217919 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445402 Affx-122925387 AX-123315739 5 36469334 TCTTAAACTGATTTTACTTTTTAGAATTCCTCTTT[C/T]GTAGCTCTTAACTTGTCACACCTGTTGGGCATAAC Y 2 1 2 1 101000 r 74 goat snp12733-scaffold149-215097 5 37256426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432109 Affx-122936457 AX-123302450 5 36516250 ACTACTGTAGAGGCAACTGAAGTATGGCAGTTGAG[C/T]TCAGCCCAGCTGGGATTACTTGTGCTAAATTCCAG Y 2 1 2 1 101000 f 74 goat snp12734-scaffold149-262013 5 37304485 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414455 Affx-122949572 AX-123284804 5 36548646 CAAAGAAGGTAATCATTGAGCTTAGCAAGGAAATA[C/T]GTCTCTGGGTAAGCAGGGGTGTTCTCCAGGTAAGG Y 2 1 2 1 101000 f 74 goat snp12735-scaffold149-294409 5 37340455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417253 Affx-122947269 AX-123287601 5 36601518 ATTCACCCAGAAGGCAAAAATAAGTGTAATGTTTT[A/G]TTATGGTAAGCAGTTTGGCCTAGTTTCAAAGGCTT R 2 1 2 1 201000 r 74 goat snp12736-scaffold149-347281 5 37394583 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378916 Affx-122976449 AX-123249275 5 36653606 GCAGAAAGGACCCCACTAGGGAAAATGCTAACATT[C/T]ACTTTGTCTTTCTCCATCTACCTTCTATTCCAAGG Y 2 1 2 1 102000 f 74 goat snp12737-scaffold149-399369 5 37446624 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773428 Affx-122970134 AX-385260570 5 36689331 ATTGGTGAAGACTCTACTAATCATTTTACTCAGAT[A/C]TACAATTATGTGACATAAAAGAGAACACATTCTTC M 2 1 2 1 101000 f 74 goat snp12738-scaffold149-435094 5 37482167 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779725 Affx-122959017 AX-385266825 5 36767716 ATTCTGTTAACGAAGATAAAGTATTCCAACAATAC[A/G]TTGCATTCTTGGAAGTTTGGAAGCCGAGGGTAGAC R 2 1 2 1 202000 f 74 goat snp12740-scaffold149-513479 5 37559243 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799985 Affx-122950631 AX-385286909 5 36817705 TGCTGAGCTCTTAAGTCATTTGAAACTTGAAAATA[C/T]ATTGGAAATAATTATTTTTGCACATTCTTATTTAG Y 2 1 2 1 201000 r 74 goat snp12741-scaffold149-563468 5 37609251 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766827 Affx-122943936 AX-385254150 5 36858695 GACCTTGGAGTGTCTGGGTTTTGACCAGCTACTCA[A/G]TGAAAACTTGAAGTAGCTCCTCTGTCTCCTCGCAC R 2 1 2 1 101000 f 74 goat snp12742-scaffold149-604458 5 37650260 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397359 Affx-122962289 AX-123267714 5 36895038 CGATAACTACGAAAAATTTATCCAGAATAAGAGTG[C/T]CCGGGAGATCCAGGCCTACATCCAGAACGCTGACC Y 2 1 2 1 101000 f 74 goat snp12743-scaffold149-640801 5 37687125 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395778 Affx-122963668 AX-123266133 5 36966636 TATCTTAGAAGAAACTGTACCTATTCCAATGCCAT[C/T]TGAATTTCTGACACATGCATGCATAATCTACTTTT Y 2 1 2 1 101000 f 74 goat snp12744-scaffold149-712399 5 37759371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438380 Affx-122931308 AX-123308718 5 37058103 ATCAACCCCAATGTAAGCTGTAACCTAGCAGAAAT[G/T]ACAATCATGAAGGTGATATCACCCACCTAAGAGGG K 2 1 2 1 101000 r 74 goat snp12745-scaffold149-803866 5 37850809 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795266 Affx-122921803 AX-385282224 5 37108589 TATACTTCATTCCTTCTTGTATCTGGGAACTTCTA[C/T]GTAGGACCATTCTCATTTTTTTGCCAAGAAATTCT Y 2 1 2 1 101000 r 74 goat snp12746-scaffold149-854352 5 37901045 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388014 Affx-122969565 AX-123258372 5 37163826 TAAAATGCTCAATAAACAATGTTAAGAAAAGGCAG[A/G]AACTTTAATGTGGAGATAGTTATAATCTTAACTTC R 2 1 2 1 101000 r 74 goat snp12747-scaffold149-909589 5 37957640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783015 Affx-122965899 AX-385270083 5 37196676 AACCTTTCCTTCAAGATTATGTACGTTACTATATC[A/G]CTTTTAAATACTTGCACTTACTGTATATATATATG R 2 1 2 1 101000 f 74 goat snp12748-scaffold149-942439 5 37990539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401933 Affx-122958814 AX-123272286 5 37230630 GAGCATGGTGAAGGTGGGTCAGTTTATGATAGGCT[A/G]AAGAGATCGTCAGAAGCTGTGTTCCTCCTGCCTTC R 2 1 2 1 101000 f 74 goat snp12749-scaffold149-976393 5 38024708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381578 Affx-122974808 AX-123251936 5 37259615 CCCATTATTTAGCCAGGTGCTTGGCAACCAGTAAA[C/T]GACTAGTAATAATTTCCCCCAGCATTTCCAGACTT Y 2 1 2 1 101000 f 74 goat snp12750-scaffold149-1005378 5 38053692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797385 Affx-122924493 AX-385284324 5 37354018 TAATTACTGGGTGAATTTGTGATCCAACAGGTTTC[G/T]CCTCAATTACACCTAGAGAACACATCAATTCATTT K 2 1 2 1 101000 f 74 goat snp12752-scaffold149-1099781 5 38149524 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441671 Affx-122929184 AX-123312008 5 37385932 AGCACCAGACCTTCTCATCTGTCAGTTGTCTGTTA[C/T]GTCTGTTCCTTTTATTGCCTGAAAACTCCTTACTT Y 2 1 2 1 201000 r 74 goat snp12753-scaffold149-1131695 5 38181565 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391874 Affx-122966976 AX-123262231 5 37440350 ACCACCAGGAGCTTGTTCATTAGTCCTCTTGAAAG[C/T]GTAGAAAATGTCCAACTATAGGTAGATGGGGCAGG Y 2 1 2 1 101000 r 74 goat snp12754-scaffold149-1186113 5 38237098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272307 Affx-1111833465 AX-519546046 5 37484341 TCCCATCTCTTTCAGATTTTCCCACAGTTTATTGT[A/G]ATACACACAGTCAAAGGCTTTGGTATAGTGAATAA R 2 1 2 1 103000 f 74 goat 5_37484341_AF-PAKI 5 37484341 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38452080 Affx-122920863 AX-123322413 5 37486306 TTGACTATATCTGTCGCTTGGTCATTGCCATACAC[A/G]TTAGCGTAGTGAAGGCTCTGAGAAGTCTTTTAGTA R 2 1 2 1 101000 f 74 goat snp12755-scaffold149-1232069 5 38282736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425519 Affx-122941464 AX-123295865 5 37517925 GCAATCTTAACCTCAGTCATACTAGGTCAGGCATA[G/T]AGATTAAAGAAAAGAAATCTGGCCACCAGGTTTAT K 2 1 2 1 101000 f 74 goat snp12756-scaffold149-1263688 5 38314809 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278364 Affx-1111836304 AX-519551850 5 37524393 CAAGAAAAAAAGATGTTATTTTCAAAGAACTTACA[C/G]TCTAGTAGGAATACAAGGGAGAAAATATCTGCCAT S 4 1 2 1 101000 r 74 goat Random2.2K-544 5 37524393 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278366 Affx-1111836305 AX-519551852 5 37575963 CGCAGAGCGGTGCCAGCCGTCCTTCCCCCACCCCC[A/C]CCTCCTTCTTCAGCCTCCTGAAGACAATCTGTGGA M 2 1 2 1 103000 r 74 goat Random2.2K-545 5 37575963 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399555 Affx-122961131 AX-123269910 5 37607391 CTATAGAGGCATCATCTGTATCTGGATGTTTAAGG[C/T]GAGTGGTTGTTATCTATGAATGGAGAGCCACGTTA Y 2 1 2 1 101000 f 74 goat snp12757-scaffold149-1353154 5 38405695 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453097 Affx-122920035 AX-123323430 5 37674340 TGAGTTTTTAATATATTTTTAGAAAACCAATTGCA[A/G]AGGAAGTCAGTTTACAAGTTTTGTTCTTTTGTATT R 2 1 2 1 101000 r 74 goat snp12758-scaffold149-1420103 5 38473260 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404377 Affx-122956803 AX-123274729 5 37708882 AGGAGGGACAGAATCATACAGGTTGAATAGGAATA[C/T]ATGGAAGAAGAGGGTCTTCTGTTTCTGTTCTAAGA Y 2 1 2 1 201000 f 74 goat snp12759-scaffold149-1454645 5 38507719 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439301 Affx-122930963 AX-123309638 5 37756077 TTGTGTTTCTGGGGATGCCTGAGAAGCACTCTACT[C/T]GAAAATAAACAGCATGATTTTGGTTTCATACAGCT Y 2 1 2 1 101000 f 74 goat snp12760-scaffold149-1501840 5 38555394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442416 Affx-122927983 AX-123312753 5 37813816 CTCAAATCCATATTCTGAACTCTCTGAATCCAGGT[A/G]TGATCCAGACTAGTGGCCGCAGACAGGGTTTAACA R 2 1 2 1 101000 f 74 goat snp12761-scaffold149-1559579 5 38613802 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399909 Affx-122960198 AX-123270264 5 37861027 TTATGTTGCCTAAGTGCCTGAAACAGTGGGTGTTC[A/G]TGAAATGTGCAAGGAGCATTGGAAGAATGAACTGA R 2 1 2 1 201000 r 74 goat snp12762-scaffold149-1606790 5 38661509 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784965 Affx-122920119 AX-385272012 5 37896242 ATATTTGAAATAATTTGGTTACTTCTCCAGGAAGT[A/G]CATACTATTTTTCCCAAAAACTGTTTAGAAAGCAG R 2 1 2 1 201000 f 74 goat snp12763-scaffold149-1642005 5 38697619 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320786505 Affx-122929852 AX-385273539 5 37943297 ATTTAGTTTGTCTAACCTCTGGGTTCATGCACATA[C/T]ATATAATATGCATGATTTCACATACATATGTGTGT Y 2 1 2 1 101000 f 74 goat snp12764-scaffold149-1689060 5 38745515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781015 Affx-122919598 AX-385268102 5 37988022 CAGTCCCCAATATATGACAACTGGATGGTTTGGCC[A/G]CCACAATTAGGATTTTAATGTGATATAACTGATAT R 2 1 2 1 101000 f 74 goat snp12765-scaffold149-1733785 5 38790446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423939 Affx-122942254 AX-123294285 5 38023638 ACCACAAGATTAACAATAACTGGTAACAGTTACTA[C/T]GAAAATATGAAAATAATAGTTAACTATTTAGAGTT Y 2 1 2 1 103000 f 74 goat snp12766-scaffold149-1769401 5 38826483 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401402 Affx-122959212 AX-123271755 5 38056279 AAAAAGAGGCAGGGGTGAGGGGGCCAGTAAGAGAC[C/T]ATTCTTGGCTTCACGACTTGAACATTTCTCTCCTA Y 2 1 2 1 101000 r 74 goat snp12767-scaffold149-1802042 5 38859155 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796496 Affx-122931224 AX-385283445 5 38085153 GCACAGATAGATTTAATCTGGTTTAATTCTATAAA[C/T]ACAAATTTGAGAATCCCTGAAATGAAATTTTCTGT Y 2 1 2 1 102000 r 74 goat snp12768-scaffold149-1830916 5 38887990 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382386 Affx-122973847 AX-123252744 5 38115858 CATGATGAATGCAGATGAAGCAGTCATTTTGATCA[C/T]GACATGACCTTGGGAATGAAAGCCAGGTGTGCCCA Y 2 1 2 1 101000 r 74 goat snp12769-scaffold149-1861621 5 38919029 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394201 Affx-122964909 AX-123264556 5 38153866 GAGAAAGAGAGAAACTGTGAGACTCCTATTTATTA[G/T]ATCAGGATGTAAATTGTTTACTGTGAATATTAGAA K 2 1 2 1 101000 f 74 goat snp12770-scaffold149-1899629 5 38957214 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410510 Affx-122952181 AX-123280860 5 38183672 TAGAGAAGCAGAGTAGTAATTGCATTTCTCCAGTA[C/T]AGAAGTGAGTACAAATTTACAAATTCTTCCAGAAT Y 2 1 2 1 101000 f 74 goat snp12771-scaffold149-1929435 5 38986985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417316 Affx-122948157 AX-123287664 5 38227497 CTTTGCATATCAAGGACATTAACTTTATCTGTTAT[C/T]CGTGATACAAATACTTTCATTCAGTCGTATTTTTA Y 2 1 2 1 101000 f 74 goat snp12772-scaffold149-1973260 5 39031059 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396974 Affx-122963163 AX-123267329 5 38259247 CTTTGGCTCAAAGGTGTTTGGGGTTTTAAATAAAA[C/T]ATGTTAATACCTGACATGGTGTCTTGCAGATAACT Y 2 1 2 1 101000 r 74 goat snp12773-scaffold149-2005010 5 39063099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782669 Affx-122926899 AX-385269742 5 38337458 TATGAAGATTAAAAGACAAAGTACAGAAACTCACT[A/G]CAATTATCTATGATAATTAGGTAAGGAATTCACCA R 2 1 2 1 101000 f 74 goat snp12775-scaffold149-2083221 5 39142559 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418128 Affx-122947118 AX-123288476 5 38411732 TAGGGCCTCTGTCTTCCTCACTGTCCTGACACTGA[C/T]ACTGTTAATAAATTAGTCTTCAACATTTCAAAACT Y 2 1 2 1 201000 r 74 goat snp12777-scaffold149-2157495 5 39217021 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447946 Affx-122923780 AX-123318282 5 38457170 GAAAGAAAGACTAACAATTTGAAGTTTCCAAATAC[A/G]TGGAGTGATAATTCTCCACATATTCCATGAGATTC R 2 1 2 1 101000 f 74 goat snp12778-scaffold149-2202933 5 39262826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388756 Affx-122968948 AX-123259114 5 38501755 TTGGATAAATCAGAGATATATATTTGAGAGTTTTT[A/C]GCATTTATAGCCTTGACACAATAAGATTGCTTATG M 2 1 2 1 101000 r 74 goat snp12779-scaffold149-2247518 5 39307023 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407157 Affx-122954845 AX-123277508 5 38553726 CTGAGATTAAAAAATCTAAATTCTTATGATAATTC[C/T]GGCCAGATGATCAACCAAAGTATATTAAAGCAATA Y 2 1 2 1 101000 r 74 goat snp12780-scaffold149-2299489 5 39359513 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376070 Affx-122978918 AX-123246429 5 38605217 AGTGTAGGGAGAATAAGGTAATTTGGATAATTTTG[C/T]GTGAACATAAAAATTTCATTAAGACTTCTCTGTTA Y 2 1 2 1 101000 f 74 goat snp12781-scaffold149-2350980 5 39410541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794309 Affx-122973251 AX-385281273 5 38647674 CTTGAACAGTCTCATGAACACTTCTTTGAATCTCT[A/G]TCAATTGCCCTGCTTTACTAACTGGAGAAATTTAG R 2 1 2 1 101000 f 74 goat snp12782-scaffold149-2393437 5 39453515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432575 Affx-122935524 AX-123302916 5 38685478 TGCTGAGAATGAAAGACTCCCAACCCACCTGGCAC[A/G]TATGTAATCACATAGATTTTGAACCTGATGTAAGT R 2 1 2 1 201000 r 74 goat snp12783-scaffold149-2431241 5 39492096 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775241 Affx-122944700 AX-385262372 5 38750391 ACTTTAATACACTGATTTAATTTGATCATCACAAA[A/G]CTCTTGTGAGACAAGTAGCATTTACCTCCACTTAA R 2 1 2 1 101000 r 74 goat snp12784-scaffold149-2496154 5 39556882 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778263 Affx-122929753 AX-385265378 5 38818502 TTTTGAATTATAAAGAGCCATATTCCAACAGGAAA[C/T]ATAAATAGTAGTAACCTCTGGCAACTATAATCTAA Y 2 1 2 1 101000 r 74 goat snp12785-scaffold149-2564265 5 39626806 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408463 Affx-122954433 AX-123278814 5 38850688 ATTGAGAATCTATTTCCAAATCTTTCCAGTACAAA[C/T]GAAAGGGTAAGGGAGTAGTTTTCAATCATGTTACT Y 2 1 2 1 101000 r 74 goat snp12786-scaffold149-2596451 5 39659011 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775552 Affx-122935587 AX-385262683 5 38894423 TGAAATAATTATATTGGCTAGTGGCACAGAGGAAC[A/G]TTATGAAAACAGAATCACAATATGTCTGAGAGAGG R 2 1 2 1 101000 f 74 goat snp12787-scaffold149-2640186 5 39697234 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801332 Affx-122955963 AX-385288244 5 38930703 TTTAGGGACATCAAGTTCCTATAAAAAAGTCAGAT[A/G]TAATCAAAATGATTCACAAAGTGTAAGAATTTATG R 2 1 2 1 101000 f 74 goat snp12788-scaffold149-2676466 5 39733551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781085 Affx-122955302 AX-385268171 5 38996654 AACATTGACAAAGAAATATCATAAGAACAAACAAC[A/G]AACAGGAAATTGCATCTTGCACAGCTGGCTTATTT R 2 1 2 1 101000 r 74 goat snp12789-scaffold149-2742417 5 39800510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394174 Affx-122964928 AX-123264529 5 39047682 ATGGAAGAAAGAAGTTAGGAGCCTCATATGCTACC[A/G]TCTTACTCAGTTCCATGTACAGCTCTTTATATACC R 2 1 2 1 101000 f 74 goat snp12790-scaffold149-2793445 5 39857559 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420751 Affx-122944723 AX-123291098 5 39077421 GGCAAGGAAAGAGGGAGGAGGAAACAGGCAGATGA[C/T]GGGTTCATCTTTCTAAATTTTACTCATCAATTACT Y 2 1 2 1 201000 r 74 goat snp12791-scaffold149-2823184 5 39887271 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393563 Affx-122965401 AX-123263919 5 39400443 GTCTGAAGTCCAAATCCTGCCTTTGTGCACCCTGA[G/T]ACAGAACTGTGTCTGCCTAGAAGGAGGTGCACATT K 2 1 2 1 202000 f 74 goat snp5577-scaffold1195-1813787 5 40229186 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415399 Affx-122948744 AX-123285748 5 39436115 GTGTAGTTTGAAAGCTCCTCTAGTAATTCTGAAAA[G/T]TCCTTTCGGTTCTCTTCCATCCCTCTCCCTCTACA K 2 1 2 1 201000 f 74 goat snp5576-scaffold1195-1778115 5 40265435 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428006 Affx-122939160 AX-123298349 5 39578139 CAAAATATATAAGTTCATGGGAACAACTTACATTA[C/T]AATCTATAAATATTATTTGTACTATGCCACTGAGA Y 2 1 2 1 101000 f 74 goat snp5572-scaffold1195-1636091 5 40409737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439601 Affx-122930060 AX-123309938 5 39610286 CATGTAGAAACAACTGAAAAATTTAAGGAGAAAAT[A/G]TTGTGATCCAAGTATATTCTGGCTAGTCTTCCAGG R 2 1 2 1 101000 r 74 goat snp5571-scaffold1195-1603944 5 40441025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278213 Affx-1111836306 AX-519551701 5 40041070 CAAGCATTTTCCAGAAGAGAAAACATATATTGCCA[A/G]TGAATATATAAAGAAATGCTCATCCTTATTAGTAA R 2 1 2 1 101000 f 74 goat Random2.2K-546 5 40041070 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38442143 Affx-122928325 AX-123312480 5 40041604 CTTTAATAATGCTCAACAAGGGATCTATTTAGTCA[C/T]ATGTGCTATAAATAAAGTGATATACTGGTGACATT Y 2 1 2 1 101000 f 74 goat snp5561-scaffold1195-1172626 5 40871415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448723 Affx-122923842 AX-123319059 5 40082511 AATTAACTTTGTACCTCGGTCAAAAATTAGTTGAT[A/C]ATGAAGTATGAGTTTGAATTGTTTATTACATCCCA M 2 1 2 1 101000 f 74 goat snp5560-scaffold1195-1131719 5 40913018 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439576 Affx-122930079 AX-123309913 5 40373042 TACTTAAGAATGGCAAGTCAATCTAATGAACAATT[A/G]CACTTACTCCTGGCTTTCCTATAGCAATAGCACTT R 2 1 2 1 101000 f 74 goat snp5555-scaffold1195-841188 5 41204780 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425423 Affx-122941533 AX-123295769 5 40681465 AAGGAGACAGTTTTCCCAACTAGGGAGGAGACAGG[C/T]GCAAGAGGCCTCTGCTGGTGCCAGGGCTCCAGCTC Y 2 1 2 1 101000 f 74 goat snp5548-scaffold1195-532765 5 41513992 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795741 Affx-122977348 AX-385282694 5 40717523 AAGAACAATGCTTCTGAGGCAGATATATCAATACC[A/G]TAAATTATATTTCTACACTTTTAAATTTTCTCATG R 2 1 2 1 201000 r 74 goat snp5547-scaffold1195-496707 5 41551386 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787750 Affx-122936612 AX-385274773 5 40785341 AAGCATACCATAATGGCAGTACTCTAAGCATAAAC[A/G]TGCCCTCTTTCACAGCTGCACAATTGTCTTAATTG R 2 1 2 1 101000 r 74 goat snp5546-scaffold1195-428889 5 41619228 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415631 Affx-122948585 AX-123285980 5 40859372 CCCAAGAGATGCAGGGTTGGTAGAAAGAACTGAAA[G/T]AGACATTGAAGAAGCTTTCTCCAGATGAGTCTTTA K 2 1 2 1 101000 f 74 goat snp5544-scaffold1195-354858 5 41692570 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405600 Affx-122955926 AX-123275952 5 41044681 CAAACTTGCCTCTCAGCATTGCTTAAGCAGTGAAA[C/T]AATTTCAGAAAATGACTTACCCTCCCTTAATATAG Y 2 1 2 1 101000 f 74 goat snp5540-scaffold1195-169549 5 41881488 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783407 Affx-122937891 AX-385270470 5 41074020 AGCATCCCAGGTATGGCCCAGGTATCTTGAACAAA[C/T]GTACCATTCTCCTTGTATCATGCTCAAATTCTTGA Y 2 1 2 1 101000 f 74 goat snp5539-scaffold1195-140210 5 41910947 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776339 Affx-122932566 AX-385263467 5 41135357 GATCTGAACAGTATGAAAACTCCATTGAAATTTAT[A/G]CTTTCCCTGGCAAAGTTTGCAGAATGGGTCAAATA R 2 1 2 1 101000 r 74 goat snp5538-scaffold1195-78873 5 41973035 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403051 Affx-122958532 AX-123273404 5 41176602 AAGATATAGTTCGGACCGAAGCAGAAAAGGAGAGA[C/T]GACCTCAATGGAGGTAGGTTAGCTTTATTCAGGTA Y 2 1 2 1 101000 f 74 goat snp5537-scaffold1195-37628 5 42019956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450973 Affx-122921740 AX-123321307 5 41206720 ACACTTCATAAACAGAAATGGAGAAGCAACGTAAT[A/G]CAACAATGCTTATGGCATATTTAATACTCCCAGGT R 2 1 2 1 600000 r 74 goat snp5536-scaffold1195-7510 5 41206720 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786752 Affx-122921740 AX-385273783 5 41206720 ACACTTCATAAACAGAAATGGAGAAGCAACGTAAT[A/G]CAACAATGCTTATGGCATATTTAATACTCCCAGGT R 2 1 2 1 101000 f 74 goat snp5536-scaffold1195-7510 5 42050664 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441615 Affx-122928649 AX-123311952 5 41229011 ATCCTCGGTGCCCAGGACAGGGACTGGAACGAAAC[A/G]CATGCTTCATTAAGTGTGGGTTGCGGGTTGCGTGC R 2 1 2 1 101000 r 74 goat snp57564-scaffold920-14682 5 42073513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783539 Affx-122964821 AX-385270600 5 41264173 ATTTCACTGTGTTGCTTAGCAGATAGCCCAGACTT[A/G]TCCTCGGAGCTGCCTCCCTAACTAGTCTCACTGGC R 2 1 2 1 202000 r 74 goat snp57565-scaffold920-49844 5 42108726 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382624 Affx-122973696 AX-123252982 5 41339033 TTTCTTGATTCAAATCACTATTCATTAAGGAAACT[C/T]GAGGTTAAAGTTATTTAACCTCTCTGCGCCAGTCA Y 2 1 2 1 101000 f 74 goat snp57567-scaffold920-124704 5 42183861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794163 Affx-122953333 AX-385281129 5 41384602 CTAGACAGTTTATCATACTGCATCCTGGGGACCCT[A/G]CCTTTGTGTGCAGACTTCACGAAAAGACTAGTCAG R 2 1 2 1 101000 f 74 goat snp57568-scaffold920-170273 5 42229267 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784919 Affx-122939444 AX-385271966 5 41417966 TTTAAAATGAAAATTATAAGCTGCAAAATAACTTT[A/G]TGGGATTATTTTAAGCTTCCTCTCATTGGTTTCTC R 2 1 2 1 101000 r 74 goat snp57569-scaffold920-203637 5 42262510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388211 Affx-122969415 AX-123258569 5 41447356 AACAGAGATAGCAATGGGTAAATATCTGCAAATGC[A/C]TTTCTTTTGGGAACTTATGGCAAGTGTGCTTTTCT M 2 1 2 1 101000 f 74 goat snp57570-scaffold920-233027 5 42292064 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278371 Affx-1111836307 AX-519551857 5 41465774 AGATCTGACCTTTGCATGGAGAGGTCTCCTGCTGG[A/G]TTAGAGTCAGATGAGGAAGTATGTGAAATGTGAGC R 2 1 2 1 101000 r 74 goat Random2.2K-548 5 41465774 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415067 Affx-122949472 AX-123285416 5 41480912 TTGGTTGGAAAATCATCAGAAAAGATGGGAATGAA[C/T]ATGAAAATCTGCTGTTTATGGTTTATTTTAGACTG Y 2 1 2 1 101000 f 74 goat snp57571-scaffold920-266583 5 42325547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799831 Affx-122927390 AX-385286757 5 41529120 CAGAAACAACATTTGACTTAGTTAACTGAATGTCA[C/T]AGTAAATATACTCCAAGCCTTAAAATTACACTGCT Y 2 1 2 1 101000 f 74 goat snp57572-scaffold920-314791 5 42374415 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430927 Affx-122936846 AX-123301268 5 41560154 TATTGAGTCTCCACAACATGGGCATGGGGAGATAA[C/T]AAAGAGCCAAGACTTCTTCCTTCAAGAGTTTTCTA Y 2 1 2 1 101000 f 74 goat snp57573-scaffold920-345825 5 42405691 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773550 Affx-122945231 AX-385260691 5 41601273 TGAGATTCCCTCCTCACTTATCCATCCCACAATAG[C/T]CATCATCTTGACTCTCATTTTTCTCTCTTGCCTTC Y 2 1 2 1 201000 r 74 goat snp57574-scaffold920-386944 5 42446770 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419478 Affx-122945474 AX-123289826 5 41648973 CCAACCTAGAAGAGTCTGATTAGGCTTCAGAGTAA[C/T]ACAAAATCTGTCACTTTCTCACACAAACATAATCA Y 2 1 2 1 101000 f 74 goat snp57575-scaffold920-434644 5 42494415 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278372 Affx-1111836308 AX-519551858 5 41688044 GTTGTCTACTTTTGATGTCATCTTCTTGTCCTGGC[A/G]TTGGTCTTTCCCTGTTATCAGACACTGCTTTAAGG R 2 1 2 1 201000 r 74 goat Random2.2K-549 5 41688044 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427337 Affx-122940122 AX-123297680 5 41700744 CACCATGGGAAAGATGGGTTATTCAATAAATTGTA[C/T]TGGGACAATACTGATCATTTGGGGAAAAGGCATTG Y 2 1 2 1 201000 f 74 goat snp57576-scaffold920-486415 5 42546099 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441079 Affx-122928906 AX-123311416 5 41747270 AACACAGAACTACTAAATCAGAAACTAGGGTGGAA[C/T]CTCTGATTCAGTGGGTTTAGGATGGGTATTGAGAA Y 2 1 2 1 202000 f 74 goat snp33525-scaffold394-26343 5 42592363 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788641 Affx-122938608 AX-385275658 5 41775835 ACTTCTCACTTCACAATCCTCAAATCCTGAAAAGA[C/T]GTAACTGCCACCCCAAAACTGACAGTGCTTTTGCT Y 2 1 2 1 202000 r 74 goat snp33526-scaffold394-54908 5 42621112 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394589 Affx-122964433 AX-123264944 5 41869559 TGATTCTTTAGCTGTAAGTGTTCAGAACACTCTAG[A/G]CTACAGGAATTGAAAGCAATGGTTTAAGAGCATGT R 2 1 2 1 101000 r 74 goat snp33528-scaffold394-148632 5 42715795 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423417 Affx-122942619 AX-123293763 5 41929344 TTGGGTAAATACCTAGAAGTAGAATTTCTGGATGG[C/T]ATGGTAGTTTTGTTTTTAATTCCATGCTGTTTTTA Y 2 1 2 1 303000 r 74 goat snp33529-scaffold394-208417 5 42776354 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454148 Affx-122919330 AX-123324481 5 41965035 GGCTCTGGAGGTCAAATCTTCATGAAGAAGAAAGA[C/T]GATGAAAGAAAAAATTTTAATTTTAATTTAGGTTA Y 2 1 2 1 101000 f 74 goat snp33530-scaffold394-244108 5 42812009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424782 Affx-122941399 AX-123295128 5 42006828 AAAAGAAACTAGAGGCTTCCTTTGTGTTTTATGTT[C/T]ACTTGCCGTAGACAAGTTAAACTGCTGTTAGGTCC Y 2 1 2 1 102000 f 74 goat snp33531-scaffold394-285901 5 42854111 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450920 Affx-122921781 AX-123321254 5 42035475 TGGCGCTATGCTTGAATCCTCTGACTGTAACGCCC[A/G]TATTCTTCATCACCACCTTCCTGTGACTGGAGGTT R 2 1 2 1 101000 r 74 goat snp33532-scaffold394-314548 5 42882788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419799 Affx-122945846 AX-123290147 5 42089316 TGCAGATGTTTATATATTGCTGAGTGGGAAAAAGT[A/G]TCCTCTGATTCTATTCACTTTGCTATACACCTAAG R 2 1 2 1 201000 f 74 goat snp33533-scaffold394-368389 5 42936199 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442738 Affx-122927847 AX-123313075 5 42155846 CTCAAGTTCTTCAACTTCAAAATGGGGATAAGTAA[C/T]ACCAACCTTGTTTGATTTTGTGAGAATTCAATGAG Y 2 1 2 1 101000 f 74 goat snp33534-scaffold394-434919 5 42994733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798619 Affx-122933247 AX-385285552 5 42195986 CCACTCTTACAGAAGTAGTTCAAACACTCCCAACT[A/G]TCACTGCAAATTGCTCAAAATAAATTTCATGGGTG R 2 1 2 1 101000 f 74 goat snp33535-scaffold394-475059 5 43034788 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433322 Affx-122935180 AX-123303663 5 42227363 GGAATGAAAGAGAGGGAAGGAGGAATGGAAGGGAA[C/T]GAGGAAGAAAGAATATTGATTGACACATGAATACT Y 2 1 2 1 201000 r 74 goat snp33536-scaffold394-506436 5 43065970 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386433 Affx-122970800 AX-123256791 5 42285901 GCTCAATTAGAAACAAAACTAAATTCAGAGGATAC[A/G]CTGTAAATTTCTATTATCTCTGCTTCTGTAAGTCC R 2 1 2 1 101000 r 74 goat snp33537-scaffold394-564974 5 43125566 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387240 Affx-122970572 AX-123257598 5 42319954 AGGGATACCAAAATCAGTGTTATACTCCTGAGAAA[C/T]AAGTCTGTTGGGGGAGAAAATGGGAATATATATTT Y 2 1 2 1 101000 f 74 goat snp33538-scaffold394-599027 5 43159888 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405120 Affx-122956972 AX-123275472 5 42362774 TGAACAAAAAGGAAGAAATAAATAAGACTAGCCTT[A/G]TATGAGTCACCTATGTTAATGCAGCAAGCACTAAC R 2 1 2 1 101000 r 74 goat snp33539-scaffold394-641847 5 43205265 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786158 Affx-122941132 AX-385273194 5 42409573 TCCAGGGTTATTATTCAATAATTACTTAGTAAGCA[G/T]ATTCCAATAATAAACATAATTAAGACATTCTTTTT K 2 1 2 1 201000 r 74 goat snp33540-scaffold394-688646 5 43252162 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771882 Affx-122958057 AX-385259038 5 42446840 AGGTATTTCCTCACATCTTAATTCAAAGAAAGATG[C/T]AACTGACAAAGCTTATCCTTCTCTGTTGAATCTGA Y 2 1 2 1 101000 r 74 goat snp33541-scaffold394-725913 5 43289714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768339 Affx-122957621 AX-385255519 5 42491486 TTGAAAAGAAGGTAAAAAGATACTATTACTCATAA[C/T]AATGGTATTGACCATAACACAGGGTGATACATATG Y 2 1 2 1 101000 r 74 goat snp33542-scaffold394-770559 5 43334664 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403022 Affx-122958556 AX-123273375 5 42523718 TCTCGTCCACTGCTTAACAGAATTTTGTCCTAAAA[C/T]GAACATATTTGCTTCAGGTTAAGACAGAAGTACAT Y 2 1 2 1 101000 f 74 goat snp33543-scaffold394-802791 5 43366931 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383294 Affx-122972713 AX-123253652 5 42556574 GACCTTCCACCAACTCACAGTCATCAATTGTCCCA[C/T]AAAGCTTCTTAACTATTTTAATATCTCTAAGATCT Y 2 1 2 1 101000 f 74 goat snp33544-scaffold394-835647 5 43399844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440567 Affx-122929306 AX-123310904 5 42585867 AGTATTAATCATGAGGCCTCTCTCTCATCATTCAG[C/T]GATCATTCATCCCATCAGTGATCACTACTGAATTA Y 2 1 2 1 102000 f 74 goat snp33545-scaffold394-864940 5 43429583 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448750 Affx-122923320 AX-123319086 5 42617460 AAGATTACTTCAAAATATGAATGACACATGGTACT[A/G]TAACTGATTTATTCTCTGAATCTCCAATCAAAGTC R 2 1 2 1 101000 f 74 goat snp33546-scaffold394-896533 5 43460484 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787601 Affx-122939242 AX-370700598 5 42652640 TTTCAGATACACATGGAGGTAGGAAAATACAGAGC[A/G]CATCCAGAGACCTTGAGCAGATCCTTTTAACTGAA R 2 1 2 1 101000 r 74 goat snp33547-scaffold394-931713 5 43496020 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446675 Affx-122924757 AX-123317011 5 42687261 TTCCCGACTTCTCATTTTCCTTCTTCTTTTTCCAG[C/T]CCACAGTCTCTTCACAATTCTAACCCCCTCCACAT Y 2 1 2 1 101000 r 74 goat snp33548-scaffold394-966334 5 43530535 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444405 Affx-122926584 AX-123314742 5 42741698 AGGCTTCACCTTGAATGACAAATGCAAATGACTGA[C/T]GCAGCTGCATGGAATGCTGTGTGGAGAGAGACACT Y 2 1 2 1 101000 f 74 goat snp33549-scaffold394-1020771 5 43586236 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420268 Affx-122945052 AX-123290616 5 42803228 TGTTCATGGCAGAAGTATTCATTTCACTTCTAATT[A/G]TTACCAGGGTTATTGGGATTGTGTGAGGTAAAGGA R 2 1 2 1 201000 f 74 goat snp33550-scaffold394-1082301 5 43649575 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452341 Affx-122920650 AX-123322674 5 42860491 AGGACCCTAAGACATGAAGTAACAGTCAACATTTT[A/C]TTTGTCTAACTAACCACACTGGGTCTCAGGAAAGT M 2 1 2 1 101000 f 74 goat snp33551-scaffold394-1139564 5 43706924 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434996 Affx-122933822 AX-123305336 5 42894484 AGAATAAGAGAGAAGACAGAAACAGAAGTCTTGGA[A/G]CTTTCACTAGAAAAGGTAAGTGGTATAGGGCAGTC R 2 1 2 1 201000 r 74 goat snp33552-scaffold394-1173557 5 43741872 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378898 Affx-122976492 AX-123249257 5 42927763 AAAGAAGGGAGGATGGACCCAGAGAGACATGAGCT[A/C]GGTTATGGTGGTGAGGAGGGGAGAGTTTTTATGAG M 2 1 2 1 201000 f 74 goat snp33553-scaffold394-1206836 5 43775455 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792118 Affx-122928430 AX-385279103 5 42988944 TTGTGTTCACAAAGTTTTCTAACCTGTTGATTCTG[A/C]TACTTTAACTGTAGTCTTCTCACCGTTCCCCATCT M 2 1 2 1 101000 f 74 goat snp33554-scaffold394-1268017 5 43837030 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272188 Affx-1111833466 AX-519545940 5 42992497 CGGAAGGGACAGAGGAGAAACTAACATCAAGAGAC[A/G]TAAACGCCATCTTCATGGTGAGTACCTCACTTCAT R 2 1 2 1 101000 r 74 goat 5_42992497_AF-PAKI 5 42992497 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789023 Affx-122962793 AX-385276036 5 43056289 TTAGCCTCGAAGGAAGAGTTACGTTTTCCTTTGTC[A/G]TCTGTCATAAGGATGAAAAACCATAAGATGAGAAT R 2 1 2 1 101000 f 74 goat snp33555-scaffold394-1335362 5 43904877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429678 Affx-122937648 AX-123300019 5 43112813 TCCCAGTGCCACTAGTTTTAGGGAGGTAGATCACA[C/T]GATACATTAAACAAGTATGAATCTTTGCCCAAGAA Y 2 1 2 1 101000 f 74 goat snp33556-scaffold394-1391886 5 43961680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441601 Affx-122928658 AX-123311938 5 43142247 TGAGGCAATGTACAAAGGTCTGCCCAGGTCGAAGA[C/T]GAAGGGATAAAGACCCCAGGAGGTGTTGATGGGGA Y 2 1 2 1 101000 f 74 goat snp33557-scaffold394-1421320 5 43991250 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433737 Affx-122934512 AX-123304078 5 43198260 TTTTAAAATAAATGCCATGCTTAAAGAATGCCTAT[A/G]CTTACTAAGCTCAGAAAATATTTTCTTCTGTCTCC R 2 1 2 1 101000 f 74 goat snp33558-scaffold394-1477333 5 44047990 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783964 Affx-122940964 AX-385271018 5 43256550 TGTCTACCCGATGTAGGTGAACTGTAAAAGGCTGG[C/T]TTACTTCGTCCCTTTTATGATCCATGGATATCAAA Y 2 1 2 1 101000 f 74 goat snp33559-scaffold394-1535623 5 44105972 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774760 Affx-122971186 AX-385261894 5 43288354 TGTTTTTTGAGCATTGGCTCATGTAAATTTTTTGC[A/G]GTTTTGGTGCCAAATGTAAACAAACTAAAAAACTA R 2 1 2 1 101000 f 74 goat snp33560-scaffold394-1567427 5 44136084 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400753 Affx-122959890 AX-123271108 5 43319468 TGGGAAGAGACTAAAGACATAGAGGCTACTGCTAG[C/T]GACACTGCAGGTCTGAATCACCATGGGTTCAGCCA Y 2 1 2 1 101000 f 74 goat snp33561-scaffold394-1598541 5 44167483 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780764 Affx-122931706 AX-385267853 5 43350076 TAATCCTAGAAACACTTATCAGAGCTGCAAAAACA[A/C]AGCTAAAGAACTAAGGATCTGGACCCAAAGCCAGA M 2 1 2 1 101000 r 74 goat snp33562-scaffold394-1629149 5 44198141 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803226 Affx-122931914 AX-385290081 5 43392555 AGACAAGTCTCAAAAGCCATAAAAAGACCATTTGT[A/G]TAAATGAACAAAGAATGTATTGGTATGTTTATCTG R 2 1 2 1 201000 r 74 goat snp33563-scaffold394-1671628 5 44240623 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395897 Affx-122963614 AX-123266252 5 43447786 TTGGACATGGCATCTGGCCCACTCTCTCTTGAGAA[G/T]AGTTTGCCAGTGAGCCACGTGCTATGTGAGCAAGC K 2 1 2 1 202000 r 74 goat snp33564-scaffold394-1726859 5 44296353 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443746 Affx-122927127 AX-123314083 5 43482236 GACATAATGTAAATCTCTCTTCAAAAAATGAATGC[C/T]ACTGAAATTCAATGAATAAATGCAGAATCAGGTTA Y 2 1 2 1 101000 f 74 goat snp33565-scaffold394-1761309 5 44330787 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448748 Affx-122923322 AX-123319084 5 43514473 ACGACTAGATAAATATTTTCTCTGTTCAAAACTCC[A/G]TTTAAGAAAAAGGCCAAATTCCCTTGGCATTCAAG R 2 1 2 1 101000 r 74 goat snp33566-scaffold394-1793546 5 44363026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774441 Affx-122976893 AX-385261577 5 43564202 GGTTAAATAAATATGCAGGCTTCCTCATGTGGCAT[A/G]CCTAGTGTTCATGAGATTTTAGTTAAATAGAAAAA R 2 1 2 1 101000 f 74 goat snp33567-scaffold394-1843275 5 44413051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775434 Affx-122975684 AX-385262565 5 43601058 AACATTGGCAGACAAAGCTTTCTCAGTAAAACCAT[C/T]TGATGTATTCTTTCATGGTCTTCCTCAGCATCCTA Y 2 1 2 1 101000 f 74 goat snp33568-scaffold394-1880131 5 44450364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791620 Affx-122966937 AX-385278611 5 43639273 GTGTCTGAATTATATCCCACTAAAAAGTATTTATC[A/G]TATTTTATCCTTTATCCATCAATGGGATTTGGGTT R 2 1 2 1 101000 r 74 goat snp33569-scaffold394-1918346 5 44489252 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405682 Affx-122956555 AX-123276034 5 43675086 ATTGTCCCAAATGAAAGTTCTGAGATAGTTTAACA[A/G]ATTACCAACTGACCTTTGCTCATTTGATGACTCTC R 2 1 2 1 101000 r 74 goat snp33570-scaffold394-1954159 5 44525339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393461 Affx-122965844 AX-123263817 5 43711427 AAAGAGCCATGCATTCGATATTTAAGTGGCAAGGC[A/G]CTGATGGGAATGGTTGGGATGTCACAAGGTCAGAT R 2 1 2 1 101000 f 74 goat snp33571-scaffold394-1990500 5 44561414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802148 Affx-122966760 AX-385289052 5 43747465 GTCGATGGTGACTGAGACTGGTGTTTAAAGGGGCA[C/T]GGTTCTTTTGGCCAATATGACAGAGAGAGCTCAGG Y 2 1 2 1 101000 f 74 goat snp33572-scaffold394-2026538 5 44597424 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793028 Affx-122934120 AX-385280006 5 43790550 GGCTAGATTAATACATAGTGATATTTTTGCACATT[A/G]CTAATTTTTTTCACAGAAAAGACCAAACTAATGTA R 2 1 2 1 303000 r 74 goat snp33573-scaffold394-2069623 5 44640779 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382511 Affx-122973808 AX-123252869 5 43826566 GTGTATCTATCTCACTGCCCATGAAATTTCTATCA[C/T]ATTGTATTACCGTCCAGATTTTAAAGGGTTTCCCA Y 2 1 2 1 101000 f 74 goat snp33574-scaffold394-2105639 5 44677090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375546 Affx-122979096 AX-123245905 5 43857283 CTTTGACCCTATCAGGTCAGAGACATAGAGGAGCT[G/T]AGGCCACTTAATCCTTTGTTGCCCTGTTTTGTAAT K 2 1 2 1 101000 f 74 goat snp33575-scaffold394-2136356 5 44707934 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393618 Affx-122965357 AX-123263973 5 43907176 TTTTGAGGAGTAAAGTGAAGGTGGTACAACTTGAG[C/T]ATAGTAAGAAGGGCATGGGTACAAGATGAGGTCAG Y 2 1 2 1 101000 f 74 goat snp33576-scaffold394-2186249 5 44757760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776536 Affx-122968705 AX-385263663 5 43952473 ACTTCCTCAGCTCCTCTCTATTTATGAAAGCTGTC[A/G]TTTCTATATGAAGTTCCTTATTCCTATACCACTTA R 2 1 2 1 101000 f 74 goat snp33577-scaffold394-2231546 5 44802395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394885 Affx-122964747 AX-123265240 5 43994232 CTGGTGGCTCAGGAATTCGGCCTAGCATTACATCC[A/G]TCATTTTCTTCAAATGTCTGTATATTCTCAAAAAA R 2 1 2 1 101000 f 74 goat snp33578-scaffold394-2273305 5 44844705 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398982 Affx-122960959 AX-123269337 5 44032793 GGAACCTGTACTCATTTATATTATGACATATACCC[A/G]TGGGTATAGTGTTCCCTTTAAGATGAAGTAAAGTA R 2 1 2 1 101000 r 74 goat snp33579-scaffold394-2311866 5 44882353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453381 Affx-122919928 AX-123323714 5 44082655 AGAAATGTGTTGAAATCTGGACTTCCTAGGAGCAT[A/G]TCTCTGTGTGTGTGTGAGTGTGTGTACTTAGTTGC R 2 1 2 1 101000 f 74 goat snp33580-scaffold394-2361728 5 44932737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378578 Affx-122976593 AX-123248937 5 44114085 TGAGTGGGTCAGAGGTCCTGGAGAGAGAGGTCTCT[A/G]CTGAAGGTAGAGATTAAGAGGCCATCAGTATATAA R 2 1 2 1 101000 r 74 goat snp33581-scaffold394-2393158 5 44964614 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413820 Affx-122949891 AX-123284169 5 44149409 GTGTTAGTCTCCATTTTATTTCTCAAATGGATTAC[C/T]AGTTTTACAGGGACAGAAACAATTTCTCATACATT Y 2 1 2 1 101000 r 74 goat snp33582-scaffold394-2428482 5 45000189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400515 Affx-122961269 AX-123270870 5 44194779 TTTTATATATATATATTTTTTGCTTGAGGTTTGTC[A/G]TGTTACTGATAAATGGTCACAGTAAGGTGTTGAGG R 2 1 2 1 101000 r 74 goat snp33583-scaffold394-2473852 5 45046609 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441411 Affx-122928833 AX-123311748 5 44225520 CAGATCCCAAAACCCCGAAAGTGTCCACATCCTAG[C/T]GCCCAGAACCTCTGAATATGTGTTATAGGACAAAA Y 2 1 2 1 101000 r 74 goat snp33584-scaffold394-2504593 5 45077180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775738 Affx-122972103 AX-385262869 5 44255456 GGTCAGAAATGAGTAAGATTAAAGATAGAGAACAG[C/T]GACTTTGTAACAAGGATTGATAAAATATCACTTGT Y 2 1 2 1 101000 f 74 goat snp33585-scaffold394-2534529 5 45106620 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783796 Affx-122938870 AX-385270852 5 44312350 ACTGAATGCTCCCAATATTATCATGAGAGCCACTT[A/G]TAGGTGATTTTATTATAGGAAGGAATCATGCATTG R 2 1 2 1 101000 f 74 goat snp33586-scaffold394-2591423 5 45163667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388346 Affx-122969349 AX-123258704 5 44369590 GTTTCTTTTCTTATAGGGTTCCTTTAATAGGACAA[C/T]GCATATTGTGAAACTTCAAGGGGAAAAGAAAGTAT Y 2 1 2 1 201000 f 74 goat snp33587-scaffold394-2648663 5 45221430 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444543 Affx-122926477 AX-123314880 5 44452956 GCTGTATTTTGCTCTATTTTCTTCCTGCTGAGTGT[A/G]CTGAGGAACAGTACAATTTCTGCCTCTTTTCCGCC R 2 1 2 1 101000 r 74 goat snp33589-scaffold394-2732029 5 45305306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395306 Affx-122964062 AX-123265661 5 44500603 TGATAAGATCTGGTTATACAAAATTAGTGGCTTTC[A/G]CTCTCAGTGAGGACTCATCCCTCCTCTATCCCTCT R 2 1 2 1 201000 f 74 goat snp33590-scaffold394-2779676 5 45351424 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422343 Affx-122943448 AX-123292689 5 44538187 TGGTGTGGGCAGAGACGGGAGATGAGAAGCCTTTA[A/G]AATGCACCCAGAATCCCTGCACACGCCCTCCTCTG R 2 1 2 1 101000 f 74 goat snp33591-scaffold394-2817260 5 45388775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784847 Affx-122973541 AX-385271894 5 44578989 CAGTTTCATTGTGCTGTAATATTAATATAAGAACT[A/G]CATATTTCAAAATAATGGTAAAATGGAAGTTGGCC R 2 1 2 1 101000 r 74 goat snp33592-scaffold394-2858062 5 45430324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407866 Affx-122954509 AX-123278217 5 44645507 ACTACAGTGGAAGCTGGGCAGGAGAGTTTCTACTC[A/G]GTGTAGATGGAAACACGGAGCCACTGGAGATTTCC R 2 1 2 1 101000 r 74 goat snp33594-scaffold394-2924580 5 45497028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449419 Affx-122922690 AX-123319754 5 44676409 TAAAGTTTTAAGTAAGCCTGAGCTTATTGCCATGC[C/T]AGATAAGCAAGAAGTTTCATTTCTTCCTCTCAAGC Y 2 1 2 1 201000 f 74 goat snp33595-scaffold394-2955482 5 45527801 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378955 Affx-122976419 AX-123249314 5 44762412 ATTCAAAGGGTTGAGAACCAGGCTCAACTTCTTGA[C/T]GCAATGAGCTGCAAAGTTAGATGCTACGGGCATGG Y 2 1 2 1 101000 f 74 goat snp33597-scaffold394-3041485 5 45614000 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782683 Affx-122931568 AX-385269755 5 44825490 ACCTTTTCTTCCTCTGTCCCTATTCCTCTGTAAAT[A/G]ACTTAGTCATTCAGTACATAAAATAGAAGTGTGGC R 2 1 2 1 101000 f 74 goat snp33599-scaffold394-3104563 5 45677695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376057 Affx-122978927 AX-123246416 5 44877392 TAGTCCAGGTCTGGAAGCTGTCCTGTCAACCAGAT[A/G]CCCTTCCCTTTTACTTGGGGCTGAGAGGAGTAACA R 2 1 2 1 101000 f 74 goat snp33600-scaffold394-3156465 5 45728717 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768894 Affx-122971310 AX-385256071 5 44970654 TCATTCGATATGGAATGTAGAGGTCCAAAGGAAAT[A/C]AAAGAAAAATCTGGCTACAAATTTCTAAGGGGAAA M 2 1 2 1 101000 r 74 goat snp33602-scaffold394-3249727 5 45822437 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446150 Affx-122925759 AX-123316486 5 45001392 GTTTAGAATGACCCCTCCGGGTGCAGTGCTGAAGC[G/T]CTATCTACTGTCCCTGATAGCACACAAGAAGGTCA K 2 1 2 1 202000 r 74 goat snp33603-scaffold394-3280465 5 45853538 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407411 Affx-122955240 AX-123277762 5 45075711 TGAAGGGAAAGACAGGGTCAGCTGAAATGAAATAC[A/G]TATGACAGCAGACATGGGGTCTGTGTAGGCACTTC R 2 1 2 1 101000 f 74 goat snp33605-scaffold394-3354784 5 45928224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415924 Affx-122948451 AX-123286273 5 45119866 CTGAACAGAGGAAAGCAAAATGCCTTAGAACAACA[C/T]ACAGCTGGGTTTGAATTCTAGCTCTAGCACTGACT Y 2 1 2 1 201000 f 74 goat snp33606-scaffold394-3398939 5 45972715 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391950 Affx-122966538 AX-123262307 5 45149442 GTCCGCTGACATTTGAGAAGCACTATAAATACTAG[G/T]GCAGACCAGGAGGATTAACTATGTATTATTTAAGC K 2 1 2 1 101000 f 74 goat snp33607-scaffold394-3428515 5 46001991 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441996 Affx-122928429 AX-123312333 5 45181614 GTATAAGGAAGAGGTGCAAAGGAACTATGTTTCTG[C/T]GGCCTACCTGACTGCTTTGGTTTGGCTGCACATAG Y 2 1 2 1 101000 f 74 goat snp33608-scaffold394-3460687 5 46033951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782407 Affx-122978800 AX-385269483 5 45210327 AATGTAACTTGTGAATAGTTCTCCTTGATACCCTT[A/C]TCTTGGCTAGGGTTTCTCTTGTTCCCAGTATTCAG M 2 1 2 1 101000 r 74 goat snp33609-scaffold394-3489400 5 46062745 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401475 Affx-122958960 AX-123271828 5 45240411 GAAAGCAGATAGTAAGGAATGGGCAACCCTCTTCT[A/C]GGGGCCCAGACTGTCCGGGAGCTTCTGTTGGGAGA M 2 1 2 1 101000 f 74 goat snp33610-scaffold394-3519484 5 46093126 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413181 Affx-122950334 AX-123283530 5 45280687 ATGGCTGCAAAGCACCTAGCGCAGTTCTTGGTGCG[C/T]GGAATAGTGTACAGCTGTTAGCGTCCTTTTCTTTC Y 2 1 2 1 101000 r 74 goat snp33611-scaffold394-3559760 5 46133409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770663 Affx-122925819 AX-385257827 5 45313955 TTTTGATACCAGAAGGTTTATCCCAATTTTGTTTA[C/T]AATATCAAAATGTATAGAAATAGTGCAAATATGGA Y 2 1 2 1 201000 r 74 goat snp33612-scaffold394-3593028 5 46166793 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406847 Affx-122955664 AX-123277198 5 45371352 CCATATCCCTGTACTTTCCTAGAACTCTTGCCTTA[C/T]GCATCCCTCAGGTCAACTGTTTCTTCTGGGTCAGC Y 2 1 2 1 101000 f 74 goat snp33613-scaffold394-3650425 5 46224170 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390880 Affx-122967119 AX-123261237 5 45400683 CAGGCCAGGTCAGTGCTTTGTTCCTCCCTTAGAGC[A/G]TGCTTCGTGGTCTTCCTCGTTTCAGATTTATTTAG R 2 1 2 1 101000 r 74 goat snp33614-scaffold394-3679756 5 46253414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419650 Affx-122945958 AX-123289998 5 45417741 TGAACTCCAGTGGTTCCAAGAAAACCAGATTTTCT[C/T]TGAAATAAGGAAGCAGTTCTTTCTTCTCCCTGACC Y 2 1 2 1 102000 r 74 goat snp23603-scaffold2380-11002 5 46270016 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773185 Affx-122942325 AX-385260329 5 45463145 TATAGTACTTATTATCTGATGATAAATTTTTAAAA[C/T]GATGTCAAGTAAAAGTTCTTAGTGTATTTCACTCT Y 2 1 2 1 303000 f 74 goat snp23604-scaffold2380-56406 5 46315138 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795601 Affx-122925267 AX-385282556 5 45497851 CCAATTTGGTCAGCATTGATTGATCAAAACTGCCA[C/T]AAGTATATTATTCCATTGCCTTGATTATGGGTGAT Y 2 1 2 1 101000 f 74 goat snp23605-scaffold2380-91112 5 46349698 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421261 Affx-122944752 AX-123291608 5 45542756 ATAAAACAAACTTTTGGAAAATGTGAGAACATAAT[A/G]CATGCTTAGCAGATAGCATTGTCGTGGGTGATCTG R 2 1 2 1 201000 f 74 goat snp23606-scaffold2380-136017 5 46394816 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272309 Affx-1111833467 AX-519546047 5 45579589 TACTCTCTACTTGCAGCGTGAGCACTTCTCATTGC[A/G]GTGGCTTTCTTGCTTTGGAGCACGGGGTCCAGGCA R 2 1 2 1 101000 f 74 goat 5_45579589_AF-PAKI 5 45579589 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392770 Affx-122965992 AX-123263127 5 45592371 TTCTTCCCCAGGACACAGGGTAGCACCTTCTAGTC[A/G]TCTCCTATACTAGAGAACCATGGATTTGTTATTGT R 2 1 2 1 201000 r 74 goat snp23607-scaffold2380-185632 5 46443967 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426645 Affx-122939942 AX-123296991 5 45629797 AAACTCTGCAGGGCTCTGTTACTCTCCATCTCTTG[A/C]TTCTCTTTTCCTCGGTCATGGCTGGCTTGGTTCAA M 2 1 2 1 201000 r 74 goat snp23608-scaffold2380-223058 5 46480641 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407648 Affx-122954612 AX-123277999 5 45691618 CAGACGTGTGAGCTCAAACAACTGCACAGGTCCTG[C/T]CACCAGCTGGTGGGGGCTCTGAGAAAACTGCGAAA Y 2 1 2 1 103000 f 74 goat snp19621-scaffold1980-874042 5 46542940 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788876 Affx-122944130 AX-385275891 5 45756176 GTGGGGGCTACCTTTAGTAGATGGTAAATATCCTG[C/T]CACTAAAATCATGAAGCAGGAGGAGTTAGATGTGA Y 2 1 2 1 101000 f 74 goat snp19619-scaffold1980-809484 5 46605890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397928 Affx-122961930 AX-123268283 5 45788547 CAATCTTGTGGGGGTCATATCTACAAACCAAGTAT[A/G]CATGCATGCTCAGTTGGTCCCACTCTTTGTGACCC R 2 1 2 1 101000 f 74 goat snp19618-scaffold1980-777113 5 46638441 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765140 Affx-122920537 AX-385252695 5 45835960 AGTTCACATCCTTCACTGACACCTTGAACAATTCC[C/T]GAATGTCTCATGAGCCCACCAGACACAACATACCC Y 2 1 2 1 101000 f 74 goat snp19617-scaffold1980-729700 5 46685638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432154 Affx-122936422 AX-123302495 5 45886340 TACACGGCCCAGGTGTCCTTACGCTTCTTTGCGTT[A/G]TTGCACCACCTTTGGTCCTTGGCAGTCCAGATATA R 2 1 2 1 201000 r 74 goat snp19616-scaffold1980-679320 5 46736169 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393990 Affx-122965033 AX-123264345 5 45931524 CAGGAAGCACATTGGAAATCAAATAATCACTACAG[C/T]GGGAGACAACGGTTCTACTTTGATAAGCCTTAGCC Y 2 1 2 1 101000 r 74 goat snp19615-scaffold1980-634136 5 46781804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441886 Affx-122928622 AX-123312223 5 45998955 CTATGATTTCAATATGCTCGGAAGAAAAAAAAGAC[C/T]CTGGAGCACTATTATCTATATTTATTCAGGACAAA Y 2 1 2 1 101000 r 74 goat snp19613-scaffold1980-566705 5 46849539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403223 Affx-122957900 AX-123273576 5 46048408 TTATACCCAGCTGTTGATTCCTTGTTAATCACAGG[A/G]AGCTGTGAAAGTCTTTGACATTAGGCTTTATAAAT R 2 1 2 1 101000 f 74 goat snp19612-scaffold1980-517252 5 46899680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444396 Affx-122926591 AX-123314733 5 46078027 GCTGATACAAGCTAAGGATTTTCTCCCCAGAAAAA[C/T]GTTCATATGCGTTTATACCAAAAAGTATCTGATTT Y 2 1 2 1 101000 r 74 goat snp19611-scaffold1980-487633 5 46928805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388288 Affx-122969395 AX-123258646 5 46111848 CATAGGAAGAGTCTGATTTTTCTTCTGACTGAAAG[C/T]AGAAGCCATTGTTGGCTTCTGAACAGAGGAGAGAC Y 2 1 2 1 101000 f 74 goat snp19610-scaffold1980-453812 5 46962628 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796229 Affx-122953836 AX-385283179 5 46169954 GATGGGAAACAGATCTGTCTAGGTGCCATCAAGGC[A/G]TGGAACTGGCCATTAGTAACTCTGCTGAGGTCTCG R 2 1 2 1 101000 f 74 goat snp19609-scaffold1980-395706 5 47020770 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447525 Affx-122924061 AX-123317861 5 46206541 AAGCAACTTTTTTTTTCATAAAGATTGAACTGATC[A/G]TTGAAAGTAATTATTTTAAGCATCAAAGCAATGAA R 2 1 2 1 101000 r 74 goat snp19608-scaffold1980-359119 5 47057388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412946 Affx-122951463 AX-123283295 5 46270333 GGTTCCATGCAGGGTGGCTGAATAAGCTGACCTCC[C/T]CTTGCAGAAGGGGATACACCTCCCTTCTTCTTCAC Y 2 1 2 1 201000 r 74 goat snp19607-scaffold1980-295327 5 47121478 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453587 Affx-122920149 AX-123323920 5 46300801 CATTTTCCTCCTCTGCCCAGGGTTCTGCACCCAAC[A/G]CCCCTCTCCTGTGGTCTCCCCACCTCTCCCTCAAC R 2 1 2 1 101000 f 74 goat snp19606-scaffold1980-264859 5 47150792 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421950 Affx-122943819 AX-123292297 5 46340397 CCAGGAGGGCTGCTACTGCTGCTGCCTTTGCTGTT[A/G]CTATTACTACTACACCACCCCCACCAGCCTAGTGC R 2 1 2 1 101000 r 74 goat snp19605-scaffold1980-225263 5 47190291 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415138 Affx-122949419 AX-123285487 5 46387959 TTAGTGGGGAGTTCCAAAGACAGAAGTTTGATGCC[A/G]TCTCCTAAGGCCAGCTCTACGAAAGCAATGAAAAT R 2 1 2 1 101000 f 74 goat snp19604-scaffold1980-177701 5 47237701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432352 Affx-122936274 AX-123302693 5 46423464 TGCCAGAAGAGTGATTTTTGTAAGTATGAAAATGT[C/T]GGTCTGTCTGCTGCTTTATCTGCCCGTCGGTAACC Y 2 1 2 1 201000 f 74 goat snp19603-scaffold1980-142196 5 47273188 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787266 Affx-122931949 AX-385274291 5 46469180 TTTACAGAGCTTGAAACCAACTGGGTGAGATCATC[A/G]TGGTGCTATGATGAAACCATGAATATCTGCCTTTT R 2 1 2 1 101000 r 74 goat snp19602-scaffold1980-96480 5 47318992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443473 Affx-122927821 AX-123313810 5 46529205 TAAAATAAATCTTTACACTATACCAAAGGTAAGGA[C/T]AGACTTCCCTGTCTAGCCCTAGATGTCACCTGATC Y 2 1 2 1 201000 f 74 goat snp19601-scaffold1980-36455 5 47379202 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452881 Affx-122920698 AX-123323214 5 46570953 CAAACTTATATCACCAACTTAAGATGAACTCCTCA[C/T]CTTCTCATTTTACTTACTTCCTTACATTTTAACAT Y 2 1 2 1 101000 f 74 goat snp37629-scaffold463-5194 5 47420878 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397318 Affx-122962310 AX-123267673 5 46630429 GCCTTAGAAAATATTGTTTTTATCCTACAGAGTAC[A/G]TGACTAAGAGGAAAACAGGAAATGTGACTTACTCT R 2 1 2 1 101000 r 74 goat snp37630-scaffold463-64670 5 47480416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796490 Affx-122938262 AX-385283440 5 46669554 TTCTCTTCTATGTGGGCAAGGCTGCCTTTTCCTTA[A/C]CTTGAAATATTCTTTCCCTGGATTCTGAAGGTCGG M 2 1 2 1 101000 r 74 goat snp37631-scaffold463-103795 5 47519427 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767017 Affx-122941766 AX-385254310 5 46748532 TCTACTGAGTCGTAAACTCCTAGAAAGAAGGGATG[C/T]GTCTCAGACCTCTTTGACACTTTCAAGGTATTTTG Y 2 1 2 1 101000 f 74 goat snp37632-scaffold463-182773 5 47598533 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440158 Affx-122931139 AX-123310495 5 46778067 TTTGTATTCTCTAAGTGAACATCACTATACATCAG[A/G]TCTTTTATTTCTGACTACCTTGCTGAGCTACTTTT R 2 1 2 1 101000 f 74 goat snp37633-scaffold463-212308 5 47628433 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783576 Affx-122928100 AX-385270637 5 46857252 GGGTCTCTAGCTTCCAAGATATCTTAATGTTATTA[C/T]TTTTTAGTGCTTTGTTGCTTGGCTCCTATTACTTT Y 2 1 2 1 102000 f 74 goat snp37635-scaffold463-291493 5 47708141 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802300 Affx-122955656 AX-385289204 5 46915432 GTCTCCACAGAGACACATTTCACTCCTTGATTATA[C/T]ACTTATATCTAAGTTCAAAGCTATTCAACCAGTTC Y 2 1 2 1 101000 r 74 goat snp37636-scaffold463-349673 5 47768456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777172 Affx-122928735 AX-385264295 5 46962938 AGGAGTAAATGTACCTCCCACAACATCTAAAGTCT[A/G]TTAAATGATTTCAAATTCTAGCCTTTAATAGTAAA R 2 1 2 1 202000 r 74 goat snp37637-scaffold463-397179 5 47814995 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783869 Affx-122923143 AX-385270925 5 46995229 TGTTGTTTTGCAAGGGAAGGTTAACACATTATATA[A/C]AACAGTCTGTATTTCCCTCAGGTAATAAGAGAGCT M 2 1 2 1 202000 f 74 goat snp37638-scaffold463-429470 5 47847658 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381210 Affx-122974525 AX-123251568 5 47043951 TCCACTTACACGTTTATGTAACCACTAAACCCGAA[C/T]TGATTTTCCCATATTCCAGCTGTAGCAAATGAATC Y 2 1 2 1 101000 f 74 goat snp37639-scaffold463-478192 5 47892665 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801388 Affx-122951972 AX-385288298 5 47097551 AAATTACATATGGCTTAAAATTACATAATGACTTA[C/T]ACTACGATTTTATGAGACAGTTCTGGTCTAAAACC Y 2 1 2 1 101000 r 74 goat snp37640-scaffold463-531792 5 47946437 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397552 Affx-122962023 AX-123267907 5 47142528 ATTGAAATTAAAGGAGGACAGGGAAGAAGACTAAC[A/G]TGGACTGAGAAGCTGCATGATCTGGGCATTGGGCT R 2 1 2 1 101000 f 74 goat snp37641-scaffold463-576769 5 47991270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784960 Affx-122944162 AX-385272007 5 47174471 TAAATTATTGAGAATTCTTCTCGGCACAGTTTCCA[G/T]AACCAACTCCTATTTACCCTTTTGGCTTCATCCAT K 2 1 2 1 201000 r 74 goat snp37642-scaffold463-608712 5 48023143 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406016 Affx-122955499 AX-123276368 5 47203683 GTTTCCATATGCTCTGCAAGGATGACGCTAATGAA[G/T]CATGAGTCTCCAGTCACTAAGAGCACAGAGCTAAT K 2 1 2 1 101000 f 74 goat snp37643-scaffold463-637924 5 48051210 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799042 Affx-122975519 AX-385285972 5 47242140 AAAGAAATCTATTTTGAGTTGAGCATAGGTTATAT[A/G]CAAGTCCCTGAAAATGAGGCTAACTAAAGTCAGAT R 2 1 2 1 101000 r 74 goat snp37644-scaffold463-676381 5 48087851 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784996 Affx-122931662 AX-385272043 5 47312516 ATCCCATGTAGAGGTTTAAGCTTGTCTGCTATTGT[C/T]CTGGGAAACAAATTGGGAGCTCAGATTTGTACCAT Y 2 1 2 1 101000 r 74 goat snp37645-scaffold463-746757 5 48158561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390732 Affx-122967918 AX-123261089 5 47356861 TCTTCTTAAAACGGCAGCCCAGAAGTCATGCATAC[A/G]GCTACCACTTTTATTGTCAAGAAATGATCATGTGG R 2 1 2 1 101000 f 74 goat snp37646-scaffold463-791102 5 48203182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401970 Affx-122958783 AX-123272323 5 47401453 TTGTGATTTCCCATGGTGACAATCCTGCCCCCTAG[C/T]GAACATTTTGGGAATTTATAGGGGCTTTTCCCACT Y 2 1 2 1 202000 f 74 goat snp37647-scaffold463-835694 5 48247802 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449884 Affx-122922348 AX-123320219 5 47453883 CATATGATTTCATTAATAACATGGTCAGAGTACAC[G/T]CTCTTTGATGCCACAAAGGCTGCCAGCAGTTCAGT K 2 1 2 1 201000 f 74 goat snp37648-scaffold463-888124 5 48300116 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438478 Affx-122931231 AX-123308816 5 47491421 GCTCCTTCAACTCAACACCCAAGAAGGAGCCCACA[C/T]ACCTATGAGCCCATGGAGACGTCGTCATAACCATT Y 2 1 2 1 201000 r 74 goat snp37649-scaffold463-925662 5 48337663 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379322 Affx-122976186 AX-123249681 5 47505647 TGACACTCCATTGCTGAAATGTGGTTGCTGTTTGA[C/T]GCTCCATCCTCCTCTCTTCAAATTGTTCTTTCCCA Y 2 1 2 1 101000 f 74 goat snp40996-scaffold528-920051 5 48351949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274885 Affx-1111834554 AX-519548469 5 47539594 AGCAGCTGCAGGGTGACCAAGGCGCTGGGCTAGC[A/G]GGGGTGTGAATGCCAGAGGCAGCATCCAGTTCTCA R 2 1 2 1 303000 f 74 goat GoatD01.041397 5 47539594 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320769933 Affx-122948476 AX-385257102 5 47549263 GAGAAAAAGCATTTACTCTCAGGGTTCTGAGATTA[C/T]AAGATGCCAGGATTTGCCCCTAATTATAGCTATGT Y 2 1 2 1 101000 r 74 goat snp40995-scaffold528-876435 5 48395365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423575 Affx-122942406 AX-123293921 5 47593428 GGCCTTTCATCAACCCGAGAGCCCCACCTACAGGA[G/T]GCCCTCAGAAAACACAACCTTCACCAACCCTTGGA K 2 1 2 1 201000 r 74 goat snp40994-scaffold528-832270 5 48439270 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791339 Affx-122920068 AX-385278332 5 47625500 AACAGATGTGGTTTGGGTATGCTGATATCCTCTGA[C/T]GAATACGCAATCTAGTCGCTAAGTGAATAATGGAT Y 2 1 2 1 101000 f 74 goat snp40993-scaffold528-800198 5 48471357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797310 Affx-122965704 AX-385284249 5 47688975 TAAAGTCCCTGTTTGGTTAACAAGGAAGTGAGTCA[C/T]GGATGTTGAGTATGTAACAAAGTCTATTTAGGGCA Y 2 1 2 1 101000 f 74 goat snp40992-scaffold528-736723 5 48535097 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445573 Affx-122925137 AX-123315910 5 47812218 TAAAATTAGTGGGAATTGTAAGCAGTGAATAGATC[A/G]TTGTTAGAATGATTTCATCATTAAACATTGTTTAA R 2 1 2 1 101000 f 74 goat snp40990-scaffold528-613480 5 48658225 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411630 Affx-122951582 AX-123281980 5 47860695 TCGACTTTGGTTTCTGGATGTATTAGACTTCGTGT[A/G]CTGGTTGAGATGTGTGTCTTGTAACACAAGATGAG R 2 1 2 1 101000 f 74 goat snp40989-scaffold528-565003 5 48707175 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391689 Affx-122967584 AX-123262046 5 47910283 CTGAAATCAATCACAGAGCCCAACAAATAGAATAT[A/G]CCAGATTTAACAGGTAAGAGAGATGGATCTACATT R 2 1 2 1 101000 f 74 goat snp40988-scaffold528-515415 5 48757112 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416773 Affx-122948173 AX-123287121 5 47948161 TGGAATCTCAACTAGAAATTTAGGCTGAAGTCCTC[A/G]CCACCCTGACTCCCTGATGCCCTTGCATTATGCTG R 2 1 2 1 101000 f 74 goat snp40987-scaffold528-477537 5 48795152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794717 Affx-122959341 AX-385281677 5 48003230 CAAGATAGAACTCTATGGCATCCTGGTATATTGAC[G/T]ATTTTAAGCTGAATGAATTTGAGAAATGACATGTG K 2 1 2 1 101000 f 74 goat snp40986-scaffold528-422468 5 48849266 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406721 Affx-122955754 AX-123277072 5 48074357 TTCCCATAGAGACTTGGAACTGTGGGGCAGCTTAG[A/C]AGTGAAGACTCTTCCCACAGAGCTCCCTAATGGAG M 2 1 2 1 101000 f 74 goat snp40985-scaffold528-351341 5 48920433 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406693 Affx-122955777 AX-123277045 5 48114456 TATAAGCAAACTTTGCTAAAAAGTCATCATTTTCT[A/G]TAGAGAAAAATGGCATACTCATCCTATATGTCTTT R 2 1 2 1 101000 r 74 goat snp40984-scaffold528-311242 5 48960515 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272310 Affx-1111833468 AX-519546048 5 48143879 TTTCTAGAATTCTTGTCTAAATGAAAACACACAAC[A/G]TGTACTTTTAGGGGTCTGACTTCTTTCCCTTGGCA R 2 1 2 1 201000 f 74 goat 5_48143879_AF-PAKI 5 48143879 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423999 Affx-122942108 AX-123294345 5 48164379 GATAATATAAAATTATTTTCTGTGGCTTACAGTGT[A/G]TCATAGTTGAGACATATAGTAGGTTAAGGCAACAA R 2 1 2 1 101000 r 74 goat snp40983-scaffold528-261319 5 49010512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408803 Affx-122954043 AX-123279154 5 48233650 GTAGCGCAGAGAAGTACTTGGCCAGGCTCTCTTCA[C/T]GCCTGTGCTTAAGCTTCCTTCAGCCTGGGATGCCC Y 2 1 2 1 101000 f 74 goat snp40981-scaffold528-192048 5 49080627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791709 Affx-122946650 AX-385278700 5 48287044 TGTTATTGCTAGAAAGAAGCATGCTTACTTGTAGA[C/T]AGTAGTTTTGCTTTTCTTGGGAGACCATATTCTGG Y 2 1 2 1 101000 r 74 goat snp40980-scaffold528-138654 5 49134334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377115 Affx-122978249 AX-123247474 5 48316861 CCCAACGCAGAGTAGGCTGTGCACCACACTTCCCT[A/G]TTCATTTGACTTTGAATAGGCCCTGGGGAATTTTC R 2 1 2 1 101000 f 74 goat snp40979-scaffold528-108837 5 49163933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453592 Affx-122920146 AX-123323925 5 48368776 AAGGGGTGGCAGTCTGGATTTTGTGCTATCTGCAG[C/T]GCTGACTGGCAGCATGTACTTCCAAGAATTGGTTT Y 2 1 2 1 101000 r 74 goat snp40978-scaffold528-56922 5 49216126 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437610 Affx-122931853 AX-123307948 5 48399805 CATATGTCTTGTTTGGATAAATATCTATTCAAGTT[A/C]TTTACCTATTTTTTTGCTGTTGTTAGTTGACAGAG M 2 1 2 1 101000 r 74 goat snp40977-scaffold528-25893 5 49247024 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802780 Affx-122961741 AX-385289679 5 48450529 GGTAATAGGTATTGGATAGGAGAATGTATTTATTG[C/T]TATGTGATGATTGTAAGATTTAGCAAATAAATTTT Y 2 1 2 1 101000 f 74 goat snp21784-scaffold2136-24732 5 49298007 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785833 Affx-122956074 AX-385272870 5 48478347 GTGTCTGGCAAGTAGAGTGATGTACTCTGAGTCCC[A/G]TTTGTATGGCTCTCCACCCTGGGTGGAATTTCTGT R 2 1 2 1 102000 f 74 goat snp52256-scaffold775-15664 5 49338783 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769008 Affx-122958904 AX-385256183 5 48513588 ATTTTTATCACTTCTAGTTGTACAGCCACTTTGGT[A/G]TTGCTCCTATCTCCTAAAGATGAACTTAATTGTAT R 2 1 2 1 101000 f 74 goat snp52257-scaffold775-50905 5 49374538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780895 Affx-122962032 AX-385267982 5 48563987 TGGAGAATAATAAGAAATTGTTAGGAAGAATTTTA[C/T]GAAGAATTGGGAGAAATATAAGCATGCTTAGAAAC Y 2 1 2 1 101000 r 74 goat snp52258-scaffold775-101304 5 49425424 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397867 Affx-122962447 AX-123268222 5 48625533 AACAGTTACATAAGATGACAGATTTGAAAGTGTAT[A/G]CCCCTTCTGACTTCATAAATCATAGCAATTGTGTT R 2 1 2 1 201000 f 74 goat snp52259-scaffold775-162850 5 49487836 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380169 Affx-122975522 AX-123250527 5 48659907 GACTGCCATATCAGATATTTCCATGAAAAGGTTCA[C/T]CTAGGCTTTTGTATTTATTCTTTTGCATTTAAAAT Y 2 1 2 1 101000 f 74 goat snp52260-scaffold775-197224 5 49522432 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430130 Affx-122937400 AX-123300471 5 48691864 CTGCTTCTCGAGTAAACCAGATAAAAACACTGTCT[A/G]CTTTTCAGGGTTCTCAGGGTTAAATGAGGCATTGA R 2 1 2 1 101000 f 74 goat snp52261-scaffold775-229181 5 49555257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396623 Affx-122962878 AX-123266978 5 48722006 GCAGCATCAATTGATCTTTTTGTCTCCTTTCCCTT[G/T]TCTTTGCAGTTGCATTGGTTTTTTAAGCTCCCAAC K 2 1 2 1 201000 r 74 goat snp52262-scaffold775-259323 5 49585534 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378647 Affx-122977099 AX-123249006 5 48755696 CAGGTAATGAATTTACTCTCTATGGCAAGCAAAAA[C/T]GCACAGTTATACCATAATCAAAAAGAAAAATACTA Y 2 1 2 1 101000 f 74 goat snp52263-scaffold775-293013 5 49622046 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433707 Affx-122934532 AX-123304048 5 48807829 CCGAGCGGGCAGTGGACTCTGGATTTCTAGGTGCC[A/G]TGTCTATTGAAGTCACATGCAGAGTTAAGGTGATT R 2 1 2 1 101000 r 74 goat snp52264-scaffold775-345146 5 49673636 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440265 Affx-122930648 AX-123310602 5 48838489 CAAATATTGGGGATCAAAAAAGCATTCTGGAGGCC[A/G]TAAGTACTAAACTGGGTTTTGAAGGATAAGCTAGT R 2 1 2 1 101000 f 74 goat snp52265-scaffold775-375806 5 49704333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445283 Affx-122925459 AX-123315620 5 48913650 CAGCCGCACGACTCCTTCGCACAGCTAACTTTGTG[C/T]ACCCTGCAGCACTCAGAAAAGGAGTTCCATCCACA Y 2 1 2 1 101000 r 74 goat snp52267-scaffold775-450967 5 49781939 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790106 Affx-122972845 AX-385277112 5 48958767 TTTATAAAGTAGCTCATAATTGGCCTGTGTTATTA[C/T]GCTTTTTGTGTCAAAGCATAGTGCAGTATGGAGAA Y 2 1 2 1 202000 r 74 goat snp52268-scaffold775-496084 5 49828239 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767499 Affx-122927773 AX-385254762 5 49012919 CCCTGGCTCTGAGTCCTCTGTGGACCAGGATACAA[C/T]ATAATTTCATGTACTGATCTCAAAATAAAGTTATT Y 2 1 2 1 102000 f 74 goat snp52269-scaffold775-550236 5 49882342 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423938 Affx-122942255 AX-123294284 5 49043332 GGTCTATCCTGACCAATCCATTAAAACTGAGACTA[C/T]AGGCCACCTCCCCTTACACACAGACACTCTTTCCC Y 2 1 2 1 101000 f 74 goat snp52270-scaffold775-580649 5 49912734 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426969 Affx-122940400 AX-123297314 5 49072420 ACGTGCTGAAATAAAAAATATGCATAAATGGCGGT[A/G]TGTGACTAGAGGGTGAAAAATATTAAACAGGTAAG R 2 1 2 1 101000 f 74 goat snp52271-scaffold775-609737 5 49941846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404868 Affx-122956484 AX-123275220 5 49103471 GGGCTGTCACCCTCATGTTTGCCAGGTCTCTGTGC[A/G]TCATTGGAAACTTACATGTGCTTTATTACTACCCA R 2 1 2 1 201000 r 74 goat snp52272-scaffold775-640788 5 49970653 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785614 Affx-122925179 AX-385272657 5 49168219 TTTCAGTCTATATGTACTACATATCTAATACTTTT[A/C]TTAGTTTACTCATGAAGTCACACAGATCTGGTTGC M 2 1 2 1 101000 r 74 goat snp52273-scaffold775-705536 5 50033132 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376252 Affx-122978773 AX-123246611 5 49199090 TAGGATTGTAGTAGGCCTAAATGAGCTGATATTTG[C/T]AAAGCATTTGCAATATTGCCTGTTAAATGATGGGG Y 2 1 2 1 101000 f 74 goat snp52274-scaffold775-736407 5 50064330 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380210 Affx-122975487 AX-123250568 5 49231307 GTACCATGGTCTATCAGGTAGGCTGACTGCAGAAA[C/T]AGTCAGGCCCCTGGAGAAGCAGCGGCTTGGTCTCT Y 2 1 2 1 102000 f 74 goat snp52275-scaffold775-768624 5 50097442 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380495 Affx-122975706 AX-123250853 5 49290230 AGGGGGTATATGACAGATGGTGCTGTTCACTGATT[A/G]CTGATGCCTTTGGTCCTTCGTTTTCATGGGTCGAC R 2 1 2 1 201000 r 74 goat snp52276-scaffold775-827547 5 50156516 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406733 Affx-122955747 AX-123277084 5 49336493 GTGGGCAGTTTCTGGAACCTCCTCTCTGGTCCCAC[A/G]TATACAGCATCTCACACATCTGCCTTCTCAGTTGG R 2 1 2 1 101000 r 74 goat snp52277-scaffold775-873810 5 50202487 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775687 Affx-122939940 AX-385262818 5 49368774 ACAGCCTCATTTGGTCTCTGTCTACCTGGTCGCTA[C/T]AGAAACAAAACTTCATCTAAGACGCCAAGGCAAAA Y 2 1 2 1 101000 f 74 goat snp19147-scaffold1924-344913 5 50234529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799601 Affx-122926490 AX-385286531 5 49427276 ATAATTTGCCTTCTTAAGTGGCAGATATGCTTACC[A/G]TATGATTATGCAGTTAGCTTAATGCTTATTTTGAA R 2 1 2 1 101000 f 74 goat snp19146-scaffold1924-286411 5 50292984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782136 Affx-122931408 AX-385269214 5 49473167 TTTCCCTCCATTCTTTGGGATTATTTTTATGAGCT[A/G]TTAAAGAATATATGCAGATTTCTTCATTATGGAAT R 2 1 2 1 101000 f 74 goat snp19145-scaffold1924-240520 5 50340995 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405026 Affx-122956370 AX-123275378 5 49545588 GAGAGATCTAAATAAAAATTTCTTGGTTTATTTCC[A/G]TAGCACCAACTTTAGGAACACACTGGGACTAGACT R 2 1 2 1 101000 r 74 goat snp19143-scaffold1924-168099 5 50413523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441660 Affx-122929191 AX-123311997 5 49589380 TACACATGGTATGTATTCTATCTTGTTGATTTCTC[C/T]TCTTCTCCTTGGTATAGTTTTCCTCTGGTTACTCT Y 2 1 2 1 101000 r 74 goat snp19142-scaffold1924-124307 5 50456475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428307 Affx-122939376 AX-123298650 5 49650102 TCTTTTGATTAATCTTGCCTTTTGATTTGCATTCC[G/T]AACAAAACCTAACTGAACTACTTACAGTCTTTAAG K 2 1 2 1 201000 r 74 goat snp19141-scaffold1924-63585 5 50517258 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440372 Affx-122929641 AX-123310709 5 49697697 TTCAGATCACATTACAAATTGTCTGTCTTGATGCC[A/G]TTAGAATATGTAGCACCATACAGTTTAGGCCTTTT R 2 1 2 1 101000 r 74 goat snp19140-scaffold1924-15990 5 50565287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790160 Affx-122921394 AX-385277165 5 49729184 AATTGAATGGTCAGTCAGCCATACCCTTAGCATTC[A/G]CTTATGAATACACTTTGTTATTTGTGTGTGTGTGT R 2 1 2 1 101000 r 74 goat snp49857-scaffold712-15398 5 50596853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404982 Affx-122956402 AX-123275334 5 49776617 TCCCTTGCATTTGTTATTACTACTTGAGGGAACTT[A/G]ATTTCTATAGGTTTCCCATCAGTTGTCTAGCTAGA R 2 1 2 1 101000 f 74 goat snp49858-scaffold712-62831 5 50645481 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791211 Affx-122974706 AX-385278205 5 49809705 CTCTTGAGTAAATACTACAAAAGTAATAAACAAGT[A/G]CATGACTCTGGTAGAGCAAATATGGAAATGGAAGA R 2 1 2 1 101000 r 74 goat snp49859-scaffold712-95919 5 50678387 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449707 Affx-122922538 AX-123320042 5 49857130 TTAAACTCTTTATATATAATGCCTCAATATGTCTC[A/G]TTAAGCAACCCTTTGAAATGGTACCATTATCATTT R 2 1 2 1 101000 f 74 goat snp49860-scaffold712-143344 5 50725244 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782232 Affx-122920618 AX-385269310 5 49895169 CCAGGGGATCTGGTTAATTCTTTGCTGTTAAGACA[C/T]GTAACAACTTTGAAGCCAAAATTGTATGTGAATTC Y 2 1 2 1 101000 f 74 goat snp49861-scaffold712-181383 5 50763472 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378529 Affx-122976628 AX-123248888 5 49928457 ATTCGCCGCCAACCCCAGGTTCCAGTCTCTCGCTC[G/T]CTCTCTCTTGATTACTTCTGCTCACTATTCAGCAT K 2 1 2 1 201000 r 74 goat snp49862-scaffold712-214671 5 50796539 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397815 Affx-122962487 AX-123268170 5 49964487 TTTTCAAAGGGCCCAAGAAACACAGATGGGGACGC[A/G]TTTGTGCCAAATGAGAGGAGAAGTGGAAATCAGCC R 2 1 2 1 101000 r 74 goat snp49863-scaffold712-250701 5 50832627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786993 Affx-122935495 AX-385274021 5 49999189 TGTGAACTGCAAATGCTCTGTAATAGGCTAAATTC[A/G]CATGGCAGCATCTGGAGATAATCTAAATGTTCCCC R 2 1 2 1 101000 r 74 goat snp49864-scaffold712-285403 5 50867311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425041 Affx-122941865 AX-123295387 5 50028383 ACAAATATGTGCCTTAACTTTTTTTTCTCCTGGTC[A/G]GAGGTATCTGAATCATGTAAGAAGCATTGGAGCAA R 2 1 2 1 201000 r 74 goat snp49865-scaffold712-314597 5 50896544 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402534 Affx-122958473 AX-123272887 5 50076785 ATTCCAGGAATGGAGACCTGGTTGGTGGGGGGAAC[A/G]TTTATTTGGGGTTTGTTAGGGCTGTAGCCCAGGAG R 2 1 2 1 303000 f 74 goat snp49866-scaffold712-362999 5 50944970 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785746 Affx-122952030 AX-385272786 5 50110615 GTTGGGATCATGATCTACTTGCTCCCTGTGGTTCA[C/T]ATCCTCCTAACTTCTATCCTAGGAAACTGAAGGAT Y 2 1 2 1 101000 f 74 goat snp49867-scaffold712-396829 5 50979552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395576 Affx-122963842 AX-123265931 5 50163484 TAACCACTGGACCACCAGGGAAGTTCCATAAATCT[A/G]TAAACTTTTGATAATTTAAAAATGGGAAATCCAGA R 2 1 2 1 303000 r 74 goat snp49868-scaffold712-449698 5 51033747 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800227 Affx-122923402 AX-385287150 5 50220605 TTCCTCAAAGAACCCTAATTACAAGCTCTTGTAGC[A/G]CTTTGCACTTCTTCATAACACTTATTAAAATTGTA R 2 1 2 1 101000 f 74 goat snp49869-scaffold712-506819 5 51091546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413336 Affx-122950167 AX-123283685 5 50261215 TCTGTACTCTTAAAGCTTCATGGATTTTACTGTTG[C/T]AGCAAATGACTTCCCAGCTCATTTCTCAGGCCAAT Y 2 1 2 1 101000 f 74 goat snp49870-scaffold712-547429 5 51132571 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421912 Affx-122943845 AX-123292259 5 50290313 ACTAGGTAGTACGGAATATAATTTCTCAAAGAGCT[A/G]CTGGCATCTAAAAACTAAAACAAAGCCTTATCTAG R 2 1 2 1 101000 f 74 goat snp49871-scaffold712-576527 5 51161724 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450129 Affx-122922760 AX-123320464 5 50320369 GAGGCCATGCCTTTCAGGTAAAGGGAAGAAAAAGC[A/G]CAAATACCTGCCATGGAAGCTCCTCTGGGAATATC R 2 1 2 1 101000 f 74 goat snp49872-scaffold712-606583 5 51192076 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442550 Affx-122928524 AX-123312887 5 50360869 GGGCCACAGAGTGTTCAAGCAATTTCCCCAGTGTC[A/G]CATAATAGTAAGTGGCAGAGATAGGATTTTAACCT R 2 1 2 1 201000 r 74 goat snp49873-scaffold712-647083 5 51232688 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778918 Affx-122952308 AX-385266025 5 50425282 TTTTCTGTACAAAATTCACATTCTAAGGTCTTGTA[C/T]GTTTCTTGGAGGAGGAATAAACATTTCTGTTCTGT Y 2 1 2 1 201000 f 74 goat snp49874-scaffold712-711496 5 51297438 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442246 Affx-122928289 AX-123312583 5 50464016 TTTAGCATTTGTCTCTATGCTCCCTTGAATTTTTG[A/C]TTTTGTTGCATCATTTCCCATTTTCTTATCTCTAC M 2 1 2 1 201000 r 74 goat snp49875-scaffold712-750230 5 51336065 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399591 Affx-122961105 AX-123269946 5 50507162 GTGCATAGGGTCGCAAAGAGTTGAACATGACTGAG[C/T]GGCTAACACTACCTAACCTATTATGGGCCCCTCCA Y 2 1 2 1 101000 r 74 goat snp49876-scaffold712-793376 5 51380235 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443356 Affx-122927421 AX-123313693 5 50536419 TTCTTGCAGAAGAAAGAGCATATTGGTTGTTGTAT[A/C]GAACCAGCATAGTTCATTTCACAACAACACTGATA M 2 1 2 1 101000 f 74 goat snp49877-scaffold712-822633 5 51408009 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428483 Affx-122938784 AX-123298826 5 50568855 AACCTATCCCTATGACCCCTAGACCTTTGCTTCTG[C/T]CTTTCCAATACAAATATAGGACAAATTCCCTTAAA Y 2 1 2 1 201000 r 74 goat snp49878-scaffold712-855069 5 51434931 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406420 Affx-122955209 AX-123276772 5 50604117 GTTCATATAACCGAAGTTAAAACCTTTGGTATGCT[A/G]AGAATGTTTAACTAGTTATATCTCTTCTGTCAACA R 2 1 2 1 101000 r 74 goat snp49879-scaffold712-890331 5 51470824 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435683 Affx-122933328 AX-123306022 5 50649383 CACCTGGTGAAATTTGCCCAAGGTAATGTAATTAG[C/T]AAGTGATGAAGATGGGAATCTTTCTGGTTTGATTC Y 2 1 2 1 101000 r 74 goat snp49880-scaffold712-935597 5 51516158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428263 Affx-122939409 AX-123298606 5 50685544 ATGTATATGAGAGAGATATCTCATTAAAAACAGTT[A/G]CAGAATAAGGTACTAAACTTCAGCTTGGATATTTC R 2 1 2 1 101000 f 74 goat snp49881-scaffold712-971758 5 51551473 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796787 Affx-122961404 AX-385283730 5 50718989 GATGATTTTACTTCTAAATGATATCCATTTTACTA[C/T]ATGTTGTTAATGTGGTCATATAGGGTGCAGCATCT Y 2 1 2 1 101000 r 74 goat snp49882-scaffold712-1005203 5 51584761 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423332 Affx-122943171 AX-123293678 5 50771276 GAGAACTGGAAACCTGTTTTTCTCTTGTCCACAGT[A/G]TTAAAACTGAAGCATCAAGAGAGTATTAGCAGCAA R 2 1 2 1 201000 r 74 goat snp49883-scaffold712-1057490 5 51636882 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796235 Affx-122919992 AX-385283185 5 50826724 CAAGTCTTTTTTGACTCTCATTGCCTCATATTGTG[C/T]ATTGAAAGAGTTGTTTCAGTCACCAAAGTTTCAAC Y 2 1 2 1 101000 f 74 goat snp49884-scaffold712-1112938 5 51692033 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272193 Affx-1111833469 AX-519545945 5 50827811 TCAGCCAAACCTAAGTATGTATCCATTCTCCTTTA[A/G]CATTTCTCTGGGGGGATGCCAATGGAGGAAGTGGT R 2 1 2 1 202000 r 74 goat 5_50827811_AF-PAKI 5 50827811 A G 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468273747 Affx-1111833786 AX-519547358 5 50831377 GCTGCAG[A/G]CCGTCTGTAATCTTTCTTGTCTTTTGTTGACTCTG R 2 1 2 1 101000 r 74 goat GoatD01.004867 5 50831377 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38376822 Affx-122977924 AX-123247181 5 50868128 CTTCAACTTCATTATAATCATCATAATGTTGTTTT[A/C]TTCTTTTTCTCCCTTATTTGCTTTTATTGTCTTCT M 2 1 2 1 201000 r 74 goat snp49885-scaffold712-1154342 5 51733783 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771516 Affx-122920877 AX-385258674 5 50916964 TGATTAATGTATTCAATCAAGTCTAGTTTACCTAA[C/T]GACAAAATAGTACCTTGAGAAGGGAAATTCAATCA Y 2 1 2 1 101000 r 74 goat snp49886-scaffold712-1203178 5 51783067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377592 Affx-122978312 AX-123247951 5 50953646 CAGGCAAGAATCTTGGTTTATTTAGAGGTGTGACC[A/G]GGGTTAAGTCACATATTCAGTCCAGATGGTCTCAA R 2 1 2 1 101000 f 74 goat snp49887-scaffold712-1239860 5 51820024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381846 Affx-122974193 AX-123252204 5 50986943 ACAAAGGAAAAAACTTTTTTGCCTCTTTAGGTGCT[A/G]TCTTGTCAATGCAACTTAAATTGATGTTTCAAGTT R 2 1 2 1 201000 r 74 goat snp49888-scaffold712-1273157 5 51853604 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410978 Affx-122952014 AX-123281328 5 51032082 TGGACAGAGGAGCCTGGAGCGCTGCTGTCCATAGG[A/G]TCATACAGAGTTGGACAGACTGAAGCTGCTGCTAC R 2 1 2 1 103000 r 74 goat snp48003-scaffold678-407628 5 -1 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438863 Affx-122930756 AX-123309200 5 51083875 TATAAAAAATGCTTAAAACCAGAGAAAAGGGAAAA[C/T]AAACAAAAGCAACAAATACAAACTGATTTGAGACG Y 2 1 2 1 103000 r 74 goat snp48002-scaffold678-355835 5 51949884 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428308 Affx-122939375 AX-123298651 5 51139189 CCTCCAGTCAAAACTCAACCAACCAGAAACAGCAG[C/T]GACACTCTTTCTTCTCAGATCCTCCAGGGAAAAAG Y 2 1 2 1 201000 f 74 goat snp48001-scaffold678-300521 5 52005547 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381629 Affx-122974768 AX-123251987 5 51188657 AACCACTACAGCACAAACACTGAAAACTGCATTGC[A/G]TTTAAGACATTTGTATTATTTTTTTTAAAAAACTC R 2 1 2 1 103000 f 74 goat snp48000-scaffold678-251053 5 52055441 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771999 Affx-122939203 AX-385259155 5 51219795 ACGTGCGGAGCTTATTTAGTCTGATGCAGCCTGTG[C/T]AATATTGTCTTTAAAGTGCTAGAAGAATAAATGAC Y 2 1 2 1 101000 f 74 goat snp47999-scaffold678-219915 5 52086913 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779127 Affx-122973726 AX-385266232 5 51263421 ACCGTTCTCATCACAGACTGCTCATGCTTTTCTAG[C/T]GTAGCCTCCTTGCTTACTTACTAGCTAAGTAATCA Y 2 1 2 1 101000 f 74 goat snp47998-scaffold678-176289 5 52131130 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765130 Affx-122932183 AX-385252687 5 51308185 TTTTGTGAGCAATTCAACTTGCCAATTAGTCCTAT[C/T]GCTCTGTTGAGGGAACAAAGATATTAAACAAAGCC Y 2 1 2 1 101000 f 74 goat snp47997-scaffold678-131525 5 52175504 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768700 Affx-122919521 AX-385255878 5 51355684 GAACTGCATCATCCTGCTGTGGAAAAGGCTTCAGA[C/T]GGTATTGTTGATGGTACTATACATTTGCAAAGAAC Y 2 1 2 1 101000 f 74 goat snp47996-scaffold678-84026 5 52223469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401503 Affx-122958938 AX-123271856 5 51389370 AATCTCAGGCTTTAATTTCTTCCCCAAACAGACAG[C/T]TCACATAGTATTAGTTTGCATTGAATATTTTAGAA Y 2 1 2 1 201000 r 74 goat snp47995-scaffold678-50340 5 52257669 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790631 Affx-122947905 AX-385277633 5 51432080 TGGAAAATAAAAAATCAGGTCATCAATTATGTTGA[C/T]TGCTGCTGACCATGTAAGATGAAGACTGAGAATAG Y 2 1 2 1 101000 r 74 goat snp47994-scaffold678-7630 5 52301179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397257 Affx-122962356 AX-123267612 5 51455046 GCAAACAAGAGCAGCAACATGGTGTGTATGTGTGT[A/G]TCCATGTAAGACAGAAGAAGCGAGAGATGTATCTC R 2 1 2 1 303000 r 74 goat snp33477-scaffold392-5265732 5 52324968 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419291 Affx-122946240 AX-123289639 5 51556604 CCCTCGCATAGAAAAGCGTATCTTACCTTGATGTA[C/T]GCATGTTCATAAGAAATTAGATGAGGACCTCATGA Y 2 1 2 1 101000 f 74 goat snp33475-scaffold392-5164174 5 52428329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439326 Affx-122930305 AX-123309663 5 51592569 TCAAAAAAAGACATTTTTATTATAATAATATAAAC[A/G]CAATAATATATTTCAACAAAGAGAATGAGAGAATG R 2 1 2 1 103000 r 74 goat snp33474-scaffold392-5128209 5 52464317 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452087 Affx-122920859 AX-123322420 5 51649001 GTCCATGGGAGGAGGTGAGTTTAGGATATGTCATC[A/G]TCAACTCTCCTCTTCCACTGCTGTACTTTTTGAAT R 2 1 2 1 201000 r 74 goat snp33473-scaffold392-5071777 5 52520809 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438554 Affx-122931177 AX-123308892 5 51720916 GGAAGGCTATTGTGACATTTCAGAGTAGTCATGCA[C/T]ATTTTCCTGGAGAGAAAATTAATTATAGAACAAAA Y 2 1 2 1 101000 f 74 goat snp33472-scaffold392-4999862 5 52594228 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778996 Affx-122944229 AX-385266103 5 51763007 TGCTCTGAAGTGTTATACATTCAAACTTCAGTACC[A/G]TCATATTATAAATCATGAAAAAGCTTAATAGCTTT R 2 1 2 1 201000 r 74 goat snp33471-scaffold392-4957771 5 52636750 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783345 Affx-122922248 AX-385270409 5 51792002 ATTCTATGTCTTTGACTTAATCCATTTAATCCCTA[C/T]GACTATCCACAGAAATGGATACCTTGTTACATTTC Y 2 1 2 1 101000 r 74 goat snp33470-scaffold392-4928776 5 52665961 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278221 Affx-1111836310 AX-519551709 5 51819972 GGGAACTTACCTACAAGGTTGTCTTGGGTGCTGCA[A/C]CTAGATCTCAGCACCTCAGGCAAGAATCTTGGTTT M 2 1 2 1 101000 f 74 goat Random2.2K-556 5 51819972 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439279 Affx-122930979 AX-123309616 5 51822229 TGCAAAGATAAGAATCTAGGCCATTAATTTCTAGA[C/T]AGTGTCAAGTCATGATCATGGTAATATCAAGATGA Y 2 1 2 1 101000 r 74 goat snp33469-scaffold392-4898549 5 52696385 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788253 Affx-122950782 AX-385275272 5 51856479 GTGGGTGGATGGGTGAAAAAGATAATGAATATCAA[C/T]TATAACTTATACATTAGCAGCAAGTAGTAACTATA Y 2 1 2 1 101000 f 74 goat snp33468-scaffold392-4864299 5 52731092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385424 Affx-122971329 AX-123255782 5 51897844 AGAGAGTGGTGGGGCATACAAACCCAGCCAGCAGC[A/G]CACAACACTTGAAGCACAGAGGGTGAGTCCAGGTA R 2 1 2 1 101000 r 74 goat snp33467-scaffold392-4822934 5 52770249 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399654 Affx-122960519 AX-123270009 5 51933002 GGTTTCAAAAGCCAAAGATAATTATTAGACAAATG[A/G]TCTCAGCAGAAAACCAAGAGGATTGATATCAGTCT R 2 1 2 1 101000 r 74 goat snp33466-scaffold392-4787776 5 52805588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377429 Affx-122977544 AX-123247788 5 52026715 TCCATCTCTTCTGGAAACAGCAGAATGCTTAAATG[C/T]GGTTGAGGACAAGGAGTTGTGGGGGAGTCATGAGT Y 2 1 2 1 101000 f 74 goat snp33464-scaffold392-4694063 5 52900929 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410208 Affx-122952570 AX-123280558 5 52055996 ACTTCAGATTATAATTTACAATAGTGCAGGGAACA[G/T]AGTTTATGGATTGTTTATATTCCTTATTGTACTTG K 2 1 2 1 101000 f 74 goat snp33463-scaffold392-4664782 5 52930625 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451598 Affx-122921641 AX-123321931 5 52115250 TTCTGTAATTGCAAACAACTTTCTCCTAGTCCTGC[A/G]CTAGTGCTTTTTGTCATTTGACTTGACAGGATACC R 2 1 2 1 101000 f 74 goat snp33462-scaffold392-4605528 5 52989788 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788231 Affx-122962737 AX-385275250 5 52147166 TTTGAAGTGATACTCAGTAGCCTTACATTGTTCTC[A/G]TTAGAATGTGCTCTCCATTCCCTAGGAATGTTTTA R 2 1 2 1 101000 r 74 goat snp33461-scaffold392-4573612 5 53022156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453456 Affx-122919857 AX-123323789 5 52192210 TATTAATTTTCTTTAAATTATTTTTATTGGAGTGT[A/G]CTTGATACTGTGTATGAAGAGTCCTTTGGAGAGAT R 2 1 2 1 103000 r 74 goat snp33460-scaffold392-4528568 5 53067116 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392141 Affx-122966327 AX-123262498 5 52231658 TAATACAGATTTTTCTCTCATCTTTGACTTCTCAA[C/T]TAGGAGGGCAGGTGATTTACATCTCCATAATAAAG Y 2 1 2 1 101000 r 74 goat snp33459-scaffold392-4489120 5 53107032 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415061 Affx-122949478 AX-123285410 5 52262827 TATTCTAGGTTTTGCCTACATGAAGAACTCTGAGT[A/G]TTATTATAGATTCATAGTTGGGACCCTAGATGCAA R 2 1 2 1 101000 r 74 goat snp33458-scaffold392-4457951 5 53138546 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771755 Affx-122928712 AX-385258912 5 52306500 CTCCACTCACTCTAGTCTGAATTGCTATACCGCTT[A/G]ATCTGGGCTCCTATGCTAGCAGTTTCTTTCTACCT R 2 1 2 1 101000 f 74 goat snp33457-scaffold392-4414278 5 53181920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442215 Affx-122928782 AX-123312552 5 52353717 GCCTGGCACATGATAACAGTTCTGTTAACACTGCT[A/G]CTACATCAAATCTGTGGCAGTTGGACATCTTATCA R 2 1 2 1 201000 r 74 goat snp33456-scaffold392-4367061 5 53229370 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385774 Affx-122971057 AX-123256132 5 52391129 CAGTTCAAGAAATACAGTACTCTCTTACATTTATG[C/T]GTTCAAATAACAGTTCATGACAAGCTCACAGATAT Y 2 1 2 1 101000 r 74 goat snp33455-scaffold392-4329649 5 53267677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438448 Affx-122931254 AX-123308786 5 52481858 ATCTGCTCTTACTTTTCTGTTTGTGAAACATAACA[A/G]ATTATAAAAATAGTTTATTTCTCTAGATGAAAAAA R 2 1 2 1 103000 f 74 goat snp33453-scaffold392-4238920 5 53359124 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438157 Affx-122931462 AX-123308495 5 52523994 GAGCAGATCCAGAATTTTCCTAGTCCCTATTCTCC[A/G]TGGCTGTCACTTTGCCTATAGGAAGATTGTTTCCC R 2 1 2 1 101000 r 74 goat snp33452-scaffold392-4196784 5 53401975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793815 Affx-122969614 AX-385280786 5 52564714 ACATTATGAGGGATTTAACACAGAGAGCTAAGTGA[C/T]GCAGGAAATAGCTCTGAGTAAGTCAAGATGTGGAT Y 2 1 2 1 101000 r 74 goat snp33451-scaffold392-4156064 5 53444475 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395722 Affx-122963711 AX-123266077 5 52607761 AGAATATACCATGAACCTCATACGGTCTTATATGC[A/G]GATTTCTTTATTATCCTTCCTAAATGTTAATAAGA R 2 1 2 1 101000 f 74 goat snp33450-scaffold392-4113017 5 53487539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772384 Affx-122960656 AX-385259537 5 52638457 TGTTTGAGCTCTGTTGTTTATAAGAGAAAATGTAC[A/G]TGTTGAAATTATTAGCACTGAGGAGTTGGAGAGCA R 2 1 2 1 201000 f 74 goat snp33449-scaffold392-4082321 5 53518099 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431126 Affx-122936589 AX-123301467 5 52694832 AATTAAGATAGGGATAACAGAAAAATAGATTAGCC[A/G]TGACGGGAGTAGGGCCTTCCCTAAAATGTTGCCTG R 2 1 2 1 101000 r 74 goat snp33448-scaffold392-4025946 5 53574455 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377247 Affx-122978150 AX-123247606 5 52729496 CAGAATGTGATTATATGCTTTCCTTAAAGAGGCAA[C/T]GTTAGAGTTCATCTCAAAACTCAAGAATCCTTAAG Y 2 1 2 1 101000 f 74 goat snp33447-scaffold392-3991282 5 53610425 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390992 Affx-122966905 AX-123261349 5 52759491 AACTACTGGATTTCTCCTCCTTCATCTTGAGTGTA[C/T]GGCTCTCCCTCTTATAATCCAGCCTCATGGATTAT Y 2 1 2 1 201000 r 74 goat snp33446-scaffold392-3961287 5 53640419 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777393 Affx-122936053 AX-385264515 5 52801721 CAATTCTCTGATGCTGGAAGTTTATGGAGCCAGTT[A/G]CTCACACTTCCTATATTCCTGGGTTCTAACTGATA R 2 1 2 1 101000 f 74 goat snp33445-scaffold392-3919057 5 53683169 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792436 Affx-122971722 AX-385279417 5 52839121 GAAGGTGACATAGTTAAAGTGCTTAACACAGTAGA[C/T]CTTATATGAAGGTTTTGGCATATTGCTATTAATCT Y 2 1 2 1 101000 f 74 goat snp33444-scaffold392-3881657 5 53720080 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448536 Affx-122923437 AX-123318872 5 52885543 TTACTAACGATAGTAAAGGGCAAGGGCCTGAAAGC[G/T]ACAGTCCTTGCTCTTAAAGGGTATTCACTCACTGA K 2 1 2 1 101000 f 74 goat snp33443-scaffold392-3835235 5 53766954 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452153 Affx-122921660 AX-123322486 5 53020797 AAGGACAAGAGACATCACGAAGGTGAGAGATGCCA[C/T]AATGGACCATGTACCTGGGCAGCCGGAACTGGGCA Y 2 1 2 1 101000 f 74 goat snp33440-scaffold392-3699981 5 53902359 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384019 Affx-122972900 AX-123254377 5 53123829 CCAACCTGAAATGGCTACTAGGAGAGGAAAAGAAA[C/T]GCCCACCTCTTACTACTTCCAAGTTTCCTTTTTAT Y 2 1 2 1 101000 f 74 goat snp33438-scaffold392-3596949 5 54006489 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788659 Affx-122941712 AX-385275675 5 53176940 TTTATAGATCTACTAGCTGACTTTTCATGGATGTA[G/T]CGCTTTTTGTGTGTGTACCTTCTGTAGTATGGAAA K 2 1 2 1 101000 r 74 goat snp33437-scaffold392-3543838 5 54060917 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412568 Affx-122951317 AX-123282917 5 53207613 GCATCTTTAATACCACCCAGAAGGGGGCTTGGGGC[A/G]TTTCATTCCAGTCTTACTAGGATGAAAGTCTAGGT R 2 1 2 1 201000 r 74 goat snp33436-scaffold392-3513165 5 54092095 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797307 Affx-122949829 AX-385284246 5 53244372 CACCTTCTTTAAAATAGTACGTAAAATTCTCATAC[A/G]TTAATCCTCCACCCATTTTACACTGTGCCTTAGTG R 2 1 2 1 101000 r 74 goat snp33435-scaffold392-3476406 5 54128894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780203 Affx-122957440 AX-385267299 5 53284639 AACCATAAGTATTCTGATATGTCCCATTGGGATTT[C/T]TCCATGGCTGTACTGCTTTGTCAACTATCTCAGGA Y 2 1 2 1 101000 f 74 goat snp33434-scaffold392-3436139 5 54169099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381834 Affx-122974258 AX-123252192 5 53325910 GTCTGATTATAACACAAATATTTTCAGAAGGAACA[C/T]GGGAAATGTCAAAAATTGTCAGTTCAGTGAATATC Y 2 1 2 1 101000 r 74 goat snp33433-scaffold392-3394868 5 54209889 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464366363 Affx-1110450022 AX-515839861 5 53350378 CATAAAAATCATTACTTACAATGTATTATAGACCT[A/C]AATATAAGAGCTAAAACTCCAAAATCTTGAATAAA M 2 1 2 1 101000 f 74 goat 5_53350378_AF-PAKI 5 53350378 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38375361 Affx-122979235 AX-123245720 5 53357331 TTCCAGGGAAAAGAGGGCACAGAAGGGTCAGTAGC[C/T]AGCCTGATCCTACTTGGATCATAAAGTCAGATTTG Y 2 1 2 1 101000 r 74 goat snp33432-scaffold392-3363447 5 54241273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418246 Affx-122947031 AX-123288594 5 53412325 TCCTGATGAATTTTACACTTTCCAGGTAGGAAGTT[A/C]TAGACCCTATAAGAAAGCAGCATGGTGAATATTGG M 2 1 2 1 101000 f 74 goat snp33431-scaffold392-3308453 5 54296567 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443974 Affx-122926997 AX-123314311 5 53505262 GAGATCTTGAATATCATGTTAGGCTGCATTTTGAT[C/T]TGTATTCAGTGAAGAAATATGGAAGACTTTGAGCA Y 2 1 2 1 101000 f 74 goat snp33429-scaffold392-3215516 5 54392409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779234 Affx-122921347 AX-385266338 5 53535846 TAGTATCTAACTTGGACTTAATGGTTGTCATTTCA[C/T]GAGGTCTTTTATTATTTCAGAGACCTACTCACACC Y 2 1 2 1 101000 r 74 goat snp33428-scaffold392-3184932 5 54423278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778917 Affx-122978949 AX-385266024 5 53565750 TGCCACCCTTTGATCGGAGGTTTGCCTAGTTGGGT[A/G]TTAACTCTCCTGCCTGAGAATCTCCTGAGCCTCAC R 2 1 2 1 101000 r 74 goat snp33427-scaffold392-3155028 5 54454086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773019 Affx-122937041 AX-385260163 5 53605402 TTTAATTTAATTCAGTATACATTAGAATTGAGTAC[A/G]TATTTCATAGAGCACATCACATAAACGTGCAGGGC R 2 1 2 1 101000 r 74 goat snp33426-scaffold392-3115376 5 54495501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802218 Affx-122971962 AX-385289122 5 53661012 TATGCCATGAAGACTATGTAAAATCATAAAAGGAA[C/T]GCTTACCTTTCTTAGGCGAAGAAAATAAAGGTATT Y 2 1 2 1 201000 f 74 goat snp33425-scaffold392-3059766 5 54551973 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774568 Affx-122959092 AX-385261702 5 53738631 CATAATCTTTAGCTGCTGTGTGCTTTAGAATCACT[A/G]CTTATCCTTCTCCATATAGGTTTATAATTTATAAA R 2 1 2 1 101000 f 74 goat snp33423-scaffold392-2982147 5 54631025 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389921 Affx-122968105 AX-123260278 5 53796113 AAGATATAGTATGCCAATATCTGGGATGCACTTAT[A/G]CTGAAAAATGATTTGTTATTTATCTGTGATCCAGA R 2 1 2 1 101000 f 74 goat snp33422-scaffold392-2924665 5 54690592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770036 Affx-122947314 AX-385257203 5 53855350 TATAGCAGATAGCATGTAGATATCTGCTATGAAAA[C/T]ATAGTAGATAGAAAACAAAGATATCATAGAAAGTA Y 2 1 2 1 201000 r 74 goat snp33421-scaffold392-2865428 5 54748929 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426823 Affx-122940516 AX-123297168 5 53897044 TGAGAATTGCATTGAAACAAAACACCTATAGCAGA[C/T]GACTTAAAAACTGCTTATTTTTCCCTCTTGTTTTG Y 2 1 2 1 201000 f 74 goat snp33420-scaffold392-2823734 5 54790547 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404794 Affx-122956668 AX-123275146 5 53929960 AAAGACATGAGAGCAGCAAAAATCATAGATCCAGG[A/C]CATATTTCAAAGTAGGTACTTTCTCTGGGGCAATT M 2 1 2 1 201000 f 74 goat snp33419-scaffold392-2790818 5 54823932 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792122 Affx-122923560 AX-385279107 5 54003436 GGTCCTTTAGGGAAAAGATCTGTGTTCCAAACAAG[C/T]TACTTTAGAAGATGTGAACTGATAGGCAATTATCA Y 2 1 2 1 101000 f 74 goat snp33418-scaffold392-2717342 5 54898557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450428 Affx-122922053 AX-123320762 5 54058400 GGTCTCTCCTTCCTGCCTCCTTCCCTCCACCATGC[A/G]CACAGCTGCCAAAGAATGGCCACACTGCTCCAGGT R 2 1 2 1 101000 r 74 goat snp33417-scaffold392-2662378 5 54952435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438334 Affx-122931341 AX-123308672 5 54124775 ATTAGAGAAATTCTTTCCTGACATTGGCACTGTCT[A/G]CTCTCTTCTGGGATCTTGCAATAGGCAGATGCCTT R 2 1 2 1 201000 r 74 goat snp33416-scaffold392-2596003 5 55017378 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389200 Affx-122969070 AX-123259558 5 54168470 GCACCTCTCACTCACTCACGCAAAACTCAGTTCTT[G/T]ATTGTCCAGCCACCTCTCTCACCTTGGCCTTTGGC K 2 1 2 1 101000 f 74 goat snp33415-scaffold392-2552308 5 55061052 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451236 Affx-122921951 AX-123321570 5 54219765 CAGTGTGCACAGAGTTTGGTAAAAGTGCATTTTCT[A/G]TGGAGTTTGGGAACAGTGGGTTAGCCATCTGGAAT R 2 1 2 1 101000 f 74 goat snp33414-scaffold392-2501013 5 55112544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770504 Affx-122969719 AX-385257669 5 54285459 GGATAAAAGATATATGGATTGGATAGGAGAAAAGC[G/T]ATAAGCAGGAAGTTATCTGAGAGCAACCAGAGGCG K 2 1 2 1 101000 r 74 goat snp33413-scaffold392-2435319 5 55175909 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441785 Affx-122929093 AX-123312122 5 54315214 ACTCATAGAAACGTTGAGACCTCCACGCTTCTTCT[A/C]GCCCTCTAGTCGACTGTGAGTCCTCCACCTCAGCG M 2 1 2 1 101000 f 74 goat snp33412-scaffold392-2405564 5 55204930 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380112 Affx-122975525 AX-123250470 5 54365665 GTGGTAGCCCCCGAGGGATTCCTAGGGAATTCCTC[A/G]CCTCCCCTCCTTTCCTAGGCTGGTTGGGACTGTCA R 2 1 2 1 202000 r 74 goat snp33411-scaffold392-2355113 5 55254685 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802329 Affx-122927274 AX-385289233 5 54396487 AGGTTTTTGATTCTTCCTTCAAGGAGATAAGGCAG[A/G]GTAGGTATGAATTAGTCGAAAAGGGAAGGGCAGCA R 2 1 2 1 101000 f 74 goat snp33410-scaffold392-2324291 5 55285642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794261 Affx-122940682 AX-385281226 5 54471648 ACCAGAAAAGACAATGAAGTGGAATGTTTTCTACA[A/G]AGGGTGAAAGGATACAGCAGGAGGAAAATACTAAA R 2 1 2 1 101000 r 74 goat snp33408-scaffold392-2249130 5 55360153 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278223 Affx-1111836311 AX-519551711 5 54489139 TCATCAATTTTCAATCTCTTCCAAGAAGCCCACCC[A/C]CCCCAACCCCGCCCCTGGATTCTAGGACTCAGAGG M 2 1 2 1 102000 f 74 goat Random2.2K-558 5 54489139 A C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776384 Affx-122974965 AX-385263511 5 54531739 CAGAACTGCAAGTATTGCATAAAAAAAGCTATACC[A/G]TAAGACACTCACAGAAAAGTGGCTACAAAAGAACT R 2 1 2 1 101000 r 74 goat snp33407-scaffold392-2189039 5 55419984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446710 Affx-122924729 AX-123317046 5 54622275 ATAGGTCTCTTAGATGATGTGGATGGAATAGAGGG[C/T]CAACATCTAGGAAAAGTACAAGGGGTCAGTCAGAA Y 2 1 2 1 101000 f 74 goat snp33406-scaffold392-2098503 5 55510831 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384107 Affx-122972834 AX-123254465 5 54668482 TCCTTAAAATGCTCTTCCACGGTGAAAAATCCCAC[A/G]ATAAGAGATGAACACACTGGGATTGTGAACGACTT R 2 1 2 1 201000 f 74 goat snp33405-scaffold392-2052296 5 55557157 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407013 Affx-122955022 AX-123277364 5 54699797 AGCACCACCCTGGTGATGCACATGAAGGTCTACGA[C/T]GAGAGCGTCCAGCTGGGTGAGGCGGGGCGAGGGCA Y 2 1 2 1 101000 f 74 goat snp33404-scaffold392-2020981 5 55588174 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382369 Affx-122973861 AX-123252727 5 54732418 CAGACAAATTGAAGTGAAAGCCAGAAGTCACTAGA[A/G]GCCATGCAGGAGGTTTAGGATGGTGAACTGGGTGG R 2 1 2 1 101000 f 74 goat snp33403-scaffold392-1988360 5 55620836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278381 Affx-1111836312 AX-519551866 5 54751706 CTATCAGTCGTTTAAGGCTCCTTTCTCCTCCCAGC[A/G]TTTATTAGGTTGAACATATATAATTGCCAATATTT R 2 1 2 1 201000 r 74 goat Random2.2K-559 5 54751706 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392374 Affx-122966237 AX-123262731 5 54772939 AAGTACAATTTGGCATATACTAAGCTGTCAACTCA[C/T]GGTTGCTGGTGTTATTGCATTTGTCCCTGTGGGAT Y 2 1 2 1 101000 r 74 goat snp33402-scaffold392-1947839 5 55661765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379506 Affx-122976459 AX-123249864 5 54830114 ATCTACTTGATAATATAAGTTCTTAAAGTCAAAAC[A/G]TAGAAAATTTTTTAAAAACCTTTGAGTCGTGACCA R 2 1 2 1 201000 f 74 goat snp33401-scaffold392-1890664 5 55718968 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278227 Affx-1111836313 AX-519551715 5 54839547 TCTAATTCTAGGAGAGTTGTTCCCTTTTTGCTATC[A/C]GTCTCTTGGGGGTAACACCACATATTTCACGGGGC M 2 1 2 1 101000 f 74 goat Random2.2K-560 5 54839547 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406563 Affx-122955102 AX-123276915 5 54906361 TAGAGTTCCTGGATCTCTGGGCTGGAACGATTCCA[C/T]GCTGTCCGAAGACTTTCATGAAATGCCTCATCTTG Y 2 1 2 1 102000 r 74 goat snp33400-scaffold392-1814417 5 55791623 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407047 Affx-122954933 AX-123277398 5 54951173 ATAGGAGGGCATACCAGACAGGTAATTTGCAAAGA[C/T]GCAGTCTTATCAGGGAAATCTCTCCCCAAAACTAC Y 2 1 2 1 101000 f 74 goat snp33399-scaffold392-1769605 5 55837438 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415729 Affx-122948509 AX-123286078 5 54986503 TGAGAACAACCACAGGAAGGTCGGAAGAGAGAAGG[A/C]AGAGACAGGAGGCCGGGGTGACTCTCACTCACCTG M 2 1 2 1 103000 f 74 goat snp33398-scaffold392-1734275 5 55874001 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405179 Affx-122956929 AX-123275531 5 55020635 ACAGTGGGCCAGGACGGCCTGAGTAAAAAGTGACC[A/G]CAGCTTCCTATGGCATTACTGTGGATGTCAATAGC R 2 1 2 1 101000 r 74 goat snp33397-scaffold392-1700143 5 55906531 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392353 Affx-122966254 AX-123262710 5 55063997 ATAAAATGTTGTTCACAGAATCAAAAATATTTACC[A/G]TGTTAGCATAACACCAACACTGAACATCAATCTAG R 2 1 2 1 202000 f 74 goat snp33396-scaffold392-1656781 5 55950625 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769110 Affx-122958095 AX-385256285 5 55101337 CCTTCAGCTGAGTGAGCATTCTGCAGACTAATAGC[A/G]GTAGGTGTTGGTTCTTTCTCCCTTTCTTGCACTCA R 2 1 2 1 201000 r 74 goat snp33395-scaffold392-1619441 5 55987675 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439270 Affx-122930987 AX-123309607 5 55144877 TTCTTATCTTCATGGAAGTCTGTGTCTGAGACACA[C/T]ACAGTATTAAGTCAAAAATACAGGGTCGCACGTAT Y 2 1 2 1 101000 r 74 goat snp33394-scaffold392-1575901 5 56031873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391159 Affx-122967446 AX-123261516 5 55177356 GTATTTGTTGAATACATGTAGGGATAGGAAGTAAC[A/G]TGAAAATGAGGAGGATCAGATTGCACTGAATCATC R 2 1 2 1 101000 f 74 goat snp33393-scaffold392-1543422 5 56064876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274326 Affx-1111834134 AX-519547922 5 55257378 CTGCAGCCCCTGGGCAGAACCATCTAGAAGCTGGC[A/G]GGATTGATTTTTCTCCACGTCACAGGGCCTCTGCT R 2 1 2 1 101000 r 74 goat GoatD01.020590 5 55257378 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320777977 Affx-122959613 AX-385265093 5 55272918 CTTTTCCAATTGTTGCAAAGTGCATCTACAATTTT[A/C]TATTACAGATCCACTTTTAAAAGGTTTTCTCTGAC M 2 1 2 1 201000 f 74 goat snp33392-scaffold392-1447860 5 56160923 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377572 Affx-122977439 AX-123247931 5 55376044 CATACACGTAGGAGTTTTTCACCATCCCACTGCCT[A/G]CCTCCCTTCTAAAGGTAACTACTCGTATGGCAAAA R 2 1 2 1 201000 r 74 goat snp33390-scaffold392-1344734 5 56264175 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394242 Affx-122964876 AX-123264597 5 55417202 ACTTCTCTGTACGCTTTCTGCCAAGGGAATGGGGT[A/G]TTTCAACTCTTTCACAAAAAGCACTGGCCTTAGTC R 2 1 2 1 101000 r 74 goat snp33389-scaffold392-1303576 5 56305839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774984 Affx-122944974 AX-385262116 5 55481324 TATAGAAGGGAAGGAATCAGAGTAGAGTTCTGCTG[A/G]ATTAAGTGGACTGGATTGAATTCTCTTTACTCAGA R 2 1 2 1 101000 f 74 goat snp33388-scaffold392-1239454 5 56370462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437240 Affx-122932022 AX-123307578 5 55543199 GGAAAGTTGTCCAGCATGGTGACCACGTGGGAAGG[C/T]AGAGCTGCCCTCTTTGCCCACTCCTGTGAGAGCCA Y 2 1 2 1 101000 r 74 goat snp33387-scaffold392-1177579 5 56432327 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764579 Affx-122927968 AX-385252232 5 55593777 TTTACTCCACTTGAAATGATGCATGCAAGACAATA[C/T]AAGTTCTACATAAGTACAAAAATAGGCTAAATTAG Y 2 1 2 1 101000 f 74 goat snp33386-scaffold392-1127001 5 56483224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407097 Affx-122954892 AX-123277448 5 55645453 ACAGTGGTTAATTAGGACCTTGTAGAAACACCTTT[G/T]CCCAGCCCTTCCTTTGAGGGCAGCGTCCCCATCCT K 2 1 2 1 101000 f 74 goat snp33385-scaffold392-1075325 5 56534906 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440880 Affx-122929236 AX-123311217 5 55702705 AAATCAAGTAGCAGGTCCATGATTCAAAATCTTCC[A/G]ATGCATGTGCTCTTACTGTAAGGTATCAAGGAAAA R 2 1 2 1 101000 f 74 goat snp33384-scaffold392-1018073 5 56592282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420302 Affx-122945028 AX-123290649 5 55742738 CCAGGCTTTCTATTTGGAGCTCCTCCTGTTCTCGT[A/G]CTTCTCTGACACTCAGGTTGTTTCCTCTGCTCCAT R 2 1 2 1 201000 f 74 goat snp33383-scaffold392-978040 5 56632275 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401726 Affx-122959525 AX-123272079 5 55807399 TCCTTTCTAAATCTCTAGCCTCTCTCCACGTCCCT[C/T]ATCAAGTATTTTAGGATGTCTTTGGGAAGCCATTA Y 2 1 2 1 201000 r 74 goat snp33382-scaffold392-913379 5 56697273 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417363 Affx-122947716 AX-123287711 5 55836970 AGCACCAGCAAGATGCCCACAAACAGAGGAGCCTG[C/T]CTGAGGCCTGCTTCTTGCCCTATGGGTGGAATCCC Y 2 1 2 1 101000 r 74 goat snp33381-scaffold392-883808 5 56726936 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402482 Affx-122958591 AX-123272835 5 55890460 ATGCTGCAACTTAGAATCTTCATGCCACAACTAAA[G/T]ATCGTACATGCCATGGTGAAGATCGAATGCCCTGT K 2 1 2 1 201000 r 74 goat snp33380-scaffold392-830318 5 56781111 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769374 Affx-122922580 AX-385256545 5 55921928 GACTGACTTACAGAACTACAAAATTTCTTTAAGGT[A/C]TTTTTTTATCCCCCTCCCTTGGTCCAGCAGGAGGT M 2 1 2 1 201000 f 74 goat snp33379-scaffold392-798850 5 56812171 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402877 Affx-122958227 AX-123273230 5 55972924 GATCTGTTCAGTATGCCGCTACCTCTTCTAGCTGA[C/T]TGCAGTTCTGGCTCAACTCAACCCTCTCTTTAGAC Y 2 1 2 1 101000 r 74 goat snp33378-scaffold392-747854 5 56862768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 coat-colour SNP associated with coat colour multi-breed 38434799 Affx-122933872 AX-123305140 5 56004848 TCTTTCTGCATCTTGTCCAGGATTGATGCCGTCTC[A/G]TTGGCTTTTGGATAATTCTTCATCTGCTGCCGGAA R 2 1 2 1 101000 r 74 goat snp33377-scaffold392-715930 5 56894742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410872 Affx-122952602 AX-123281222 5 56048152 CTTCGCCCCCACGTTATTATGCCCCTATGTAATAA[A/C]ATTTGTTAAAGAGCCTGTGGGACTTTGGGATTGCT M 2 1 2 1 101000 r 74 goat snp33376-scaffold392-672626 5 56937794 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436342 Affx-122933074 AX-123306681 5 56100784 TATGCTCCCCAGCAGAAACAACATGCACACACAAA[C/T]GCACAAACGCTATCCCATGCAGAGCTCCCATTAGC Y 2 1 2 1 101000 r 74 goat snp33375-scaffold392-619994 5 56990814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405345 Affx-122956328 AX-123275697 5 56160164 AGGAGAGAAGCCTTTAATATATGATTATTTTAATA[C/T]AACTGGAAAAACATGGGGTAAAAGTTTAAATAACT Y 2 1 2 1 303000 f 74 goat snp33374-scaffold392-560614 5 57050669 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431919 Affx-122935995 AX-123302260 5 56209048 GATGGGTACAAAAATTTATTCTTCTGAAAAAAATT[A/G]AGTAATTATTCTGTAGGAATTCTCTTATGTGTGCA R 2 1 2 1 101000 r 74 goat snp33373-scaffold392-511730 5 57098635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272197 Affx-1111833471 AX-185192336 5 56282062 CCCGGAGTTCACTCAGACTCACGTCCATCGAGTCC[A/G]TGATGCCATCCAGCCATCTCATCCTCGGTCGTCCC R 2 1 2 1 303000 r 74 goat 5_56282062_AF-PAKI 5 56282062 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791303 Affx-122936534 AX-385278296 5 56284662 GGGAACTACCAGAAAGTAAGTATGAAATGTTTGTC[A/G]TTTATGTACCTAAAAGTTTGAAAATGGAAGCATGG R 2 1 2 1 101000 f 74 goat snp33372-scaffold392-436116 5 57175827 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274431 Affx-1111834281 AX-519548022 5 56369656 AGCTGATGTACAGGTCCTGCAGCTTCAGCTGTACC[A/G]CCATGGGGGTGTAAATGCTACGCAGACCCTCATCA R 2 1 2 1 101000 f 74 goat GoatD01.028696 5 56369656 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38428596 Affx-122938698 AX-123298938 5 56397107 TGGAGGAATAACAGATTAGGAAGACTGAAAAGAGT[A/G]TCCTTCCCTTTAATTAAAATTATTGATTGAATTTA R 2 1 2 1 101000 f 74 goat snp33371-scaffold392-323671 5 57196981 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442400 Affx-122927998 AX-123312737 5 56443343 TAAACAAAAAGTCATGAGAGGGACAGGGGAAGAAG[C/T]GAATGAGAAAGTTATTTAGAGAATAAAATACTAGT Y 2 1 2 1 101000 f 74 goat snp33370-scaffold392-277435 5 57243762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793975 Affx-122952187 AX-385280944 5 56479955 CATTAGTAATGCTTAAGATAGGGCCACCAAGGACA[C/T]ATTTGTCTGCTTCACTTAATTAAAAATTAGGTCAG Y 2 1 2 1 101000 f 74 goat snp33369-scaffold392-240823 5 57279647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773952 Affx-122965249 AX-385261091 5 56526988 TTTTGCATTTGGCATTATTTGGGAAGCAATAATGA[A/G]AGGTAGGTTTCTAAGCAGCTAATGTTCTTTTCATC R 2 1 2 1 101000 r 74 goat snp33368-scaffold392-193790 5 57327477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765619 Affx-122971947 AX-385253095 5 56637105 TGAACTCATAGGAAATAGGAAACTCATAGGAACTC[A/G]TAGGAACTCATAGGAAAATAATGGAGTAATAGTAT R 2 1 2 1 201000 f 74 goat snp33366-scaffold392-83673 5 57439720 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432483 Affx-122935594 AX-123302824 5 56673532 GTCACCATCAGATGACATTAAACTGTTCAAGAGGG[C/T]ATCAGCCTTTCATCCAACTTTATCTACCCTGAGCC Y 2 1 2 1 201000 r 74 goat snp33365-scaffold392-47246 5 57476798 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430492 Affx-122937235 AX-123300833 5 56714066 GATTGCTGTCCAACTGTTTACTGACCCCATGGTCT[A/G]TAGCCTGCCAAGCTCCTCTGTCATATAAAGCTATG R 2 1 2 1 103000 f 74 goat snp33364-scaffold392-6712 5 57517992 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276125 Affx-1111835180 AX-519549675 5 56724702 GGAACTGGAGAGAAGCCACAGGAGGTGAGAGGAAT[A/G]GCAGCCTGCAGCACCACCTGTGCAGTGACTGGGCC R 2 1 2 1 202000 r 74 goat ilmnseq_rs660355352 5 56724702 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276155 Affx-1111835267 AX-519549705 5 56724720 TGCCTATCTGTGGTGCCTGGAACTGGAGAGAAGCC[A/G]CAGGAGGTGAGAGGAATGGCAGCCTGCAGCACCAC R 2 1 2 1 102000 f 74 goat ilmnseq_rs669322912 5 56724720 T C 1 neutral Goat_IGGC_65K_v2 Illumina 468275935 Affx-1111835159 AX-519549493 5 56725017 CCTGAAGTGTCAACTACAGAGCCCTCTGGAGCCAC[A/G]GTTACACGGGGAACAACTCCAGAGCTGGTGGAGAC R 2 1 2 1 102000 f 74 goat ilmnseq_rs657580692 5 56725017 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275783 Affx-1111835082 AX-519549348 5 56725037 GCCCTCTGGAGCCACGGTTACACGGGGAACAACTC[A/C]AGAGCTGGTGGAGACCACAGCTGGAGAGGTGTCCA M 2 1 2 1 102000 f 74 goat ilmnseq_rs649139597 5 56725037 C A 1 neutral Goat_IGGC_65K_v2 Illumina 468275966 Affx-1111835096 AX-519549523 5 56725086 ACCACAGCTGGAGAGGTGTCCACTCCTGAGCCTGC[A/G]GGTTCAAATACCAGCCCCTTCATGCCTATAGAAGG R 2 1 2 1 101000 r 74 goat ilmnseq_rs650402792 5 56725086 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468275676 Affx-1111835029 AX-519549246 5 56726056 TTCTTGACTTTGCATCTTTAATCCTCTCCTGCCAG[A/G]CTCCCTGAGCCCCCTGCCGGATGATACCTTAGTCC R 2 1 2 1 102000 f 74 goat ilmnseq_rs642561036 5 56726056 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276138 Affx-1111835259 AX-519549688 5 56726131 GGACAATGTCCAGGGTGAGGGAAAAGGAGCCATAG[A/C]GATACAGAACACAATCCGTGGGGGCTTGGCGCTTC M 2 1 2 1 201000 f 74 goat ilmnseq_rs668575715 5 56726131 G T 2 recommended Goat_IGGC_65K_v2 Illumina 468276070 Affx-1111835151 AX-519549623 5 56726452 TTGAGAGTGCTGAGATCCTACAGGCTGTGTCATCC[A/G]GCGAAGGAGACGCATTTGAGCTGACTGTGTCTTGC R 2 1 2 1 201000 r 74 goat ilmnseq_rs657253964 5 56726452 A G 2 recommended Goat_IGGC_65K_v2 Illumina 468276228 Affx-1111835232 AX-519549778 5 56726600 ATGAGATGTCCATGCAGGCTTCCTTGGGTAGCCTG[A/G]GAGAGATGTCAGCTTACGTCAGGGAATCTGGGAAG R 2 1 2 1 101000 r 74 goat ilmnseq_rs666666290 5 56726600 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275803 Affx-1111835093 AX-519549367 5 56726778 TGCCTCAATGTGTCTTTGGCTGATGCCAATAGCCT[A/G]GCGATGGTCAGCACCCAGCTTGTCATGCCTGGTAG R 2 1 2 1 101000 f 74 goat ilmnseq_rs650000190 5 56726778 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276025 Affx-1111835207 AX-519549579 5 56726953 CAAGCAACAAAGCTGTCAGCACCAGCAAGATGCCC[A/C]CAAACAGAGGAGCCTGTCTGAGGCCTGCTTCTTGC M 2 1 2 1 102000 f 74 goat ilmnseq_rs663529192 5 56726953 T G 1 neutral Goat_IGGC_65K_v2 Illumina 468275630 Affx-1111835004 AX-519549200 5 56726980 GGGGATCTCACCTGTATATCAGAGATGCAAGCAAC[A/G]AAGCTGTCAGCACCAGCAAGATGCCCACAAACAGA R 2 1 2 1 101000 f 74 goat ilmnseq_rs639759960 5 56726980 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275658 Affx-1111835020 AX-519549228 5 56727673 AAGACCCAGGGCAGACGTAGCCACTGGGTTCTACC[A/G]TGTGGCAGCTGGGGAAGGGGGACTGCTGAGCCTTG R 2 1 2 1 202000 f 74 goat ilmnseq_rs641491076 5 56727673 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468275824 Affx-1111835028 AX-519549387 5 56727711 TAGAACCCAGTGGCTACGTCTGCCCTGGGTCTTCC[A/G]CTCTTGCCCCATTGGTGAGAGCAAACCTCTCCTCA R 2 1 2 1 102000 r 74 goat ilmnseq_rs642542328 5 56727711 G A 1 neutral Goat_IGGC_65K_v2 Illumina 320801490 Affx-122941689 AX-385288399 5 56734400 AGCATTTTCTTGCTCACTGCTTGGATCTGAAAAGA[C/T]GTCTATAGTATTCCATTCACATTAAATTTTTGAGA Y 2 1 2 1 101000 f 74 goat snp12642-scaffold1482-13523 5 57548700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388847 Affx-122968880 AX-123259205 5 56763163 TGCAGTCATGATGAAGTTCTTACATGATCTTAGAT[A/G]TCAGCAAGCACAGTCAAGAGTGAAATGGATCATTC R 2 1 2 1 101000 r 74 goat snp12643-scaffold1482-42286 5 57578180 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419945 Affx-122945214 AX-123290293 5 56804293 GCTCTATTATGGTTAAAAAGTCAATGCAAAAGTTG[A/G]TGAATATCCTCACTATGAAACTCTCTTTCCTCCAT R 2 1 2 1 101000 r 74 goat snp12644-scaffold1482-83416 5 57621275 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406104 Affx-122956217 AX-123276456 5 56852820 TTTGAAGTCTGTTCCTGCACTAGAAATAAACTCTA[C/T]AATATCAAGAGGTTTTGTGTGCTTTGTTCCCTTCT Y 2 1 2 1 101000 r 74 goat snp12645-scaffold1482-131943 5 57670431 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772087 Affx-122938358 AX-385259242 5 56900888 AATGATTTTGGAAATAAGTAAGGATACTAGTAGTT[G/T]ACAAAAAGTTAAAATTGAGACTTAAGTAAAGGTAC K 2 1 2 1 201000 r 74 goat snp56749-scaffold899-773366 5 57721308 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436235 Affx-122932567 AX-123306574 5 56930475 ACAGAGGGGGAAGAGTTGAGTAATTTCATCAGGGA[C/T]GCTATGGTCTGCAAATTCCAAATTATTGATATAGT Y 2 1 2 1 101000 f 74 goat snp56748-scaffold899-743779 5 57747630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784168 Affx-122947381 AX-385271220 5 56967132 AGGCTTGCCATCGTGCTAAATAAAATAGCTAGAAA[C/T]GACTTTCAGGACATCTCTGTCAATCTAAAGTAATT Y 2 1 2 1 101000 r 74 goat snp56747-scaffold899-707122 5 57784623 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274753 Affx-1111834475 AX-519548339 5 56974041 AGGCTGAAGAGGGGGAGAGGGACCTGTCTGATGAC[A/G]GGGAACAAGGGAGCAGC R 2 1 2 1 102000 f 74 goat GoatD01.037422 5 56974041 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320777241 Affx-122929211 AX-385264364 5 57027319 CAATAGTCTCATAAAAGATTAGTATTCAAAAGTAT[A/G]CAAGACTCCTACATCTCAACATGAAAGGAAACAAA R 2 1 2 1 101000 r 74 goat snp56746-scaffold899-646935 5 57978902 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408341 Affx-122953749 AX-123278692 5 57114873 ATCCACTTCTCTTTTACATGGCAGTGTCTTCTGAT[A/G]CCTACATGACAAAAAATGATGTATGTTTTATAGGA R 2 1 2 1 201000 r 74 goat snp56744-scaffold899-559381 5 57922252 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418013 Affx-122946656 AX-123288361 5 57163188 TTGAACCACTCCATTAAAAGTTAAAAAGGAAGGCT[C/T]GTCTCTGAAAACATCCTGCCACAGATATGACTGCA Y 2 1 2 1 103000 r 74 goat snp56743-scaffold899-511066 5 57973866 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762366 Affx-986696897 AX-385250528 5 57207476 TAGTCTATGACTATACCCCCTGAATGTGCCCATCT[C/T]GTCTGAAAAGTCTTCTAAAACTATTGCCCATAAAA Y 2 1 2 1 600010 f 74 goat 5_57207476 5 57207476 Ancestral_priority_1043 ancestry 0.44 neutral IMAGE 10K 10K ancestral 320764562 Affx-986696899 AX-385252218 5 57207477 AGTCTATGACTATACCCCCTGAATGTGCCCATCTT[A/G]TCTGAAAAGTCTTCTAAAACTATTGCCCATAAAAC R 2 1 2 1 600010 r 74 goat 5_57207477 5 57207477 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320764566 Affx-986696901 AX-385252221 5 57207514 CTGAAAAGTCTTCTAAAACTATTGCCCATAAAACT[A/G]TTAATTGGACCTTATTTGTGCTCCCATAACAAGTA R 2 1 2 1 600010 r 74 goat 5_57207514 5 57207514 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 320803019 Affx-986696130 AX-385289896 5 57208370 TCTTTTTTGCTTTCGGGTTGAATCTGGTAGTGAGA[C/T]ACTTAAGCTGAAGGTCAAATTTGTATAGATTAATA Y 2 1 2 1 600010 f 74 goat 5_57208370 5 57208370 Ancestral_priority_1043 ancestry 0.71 recommended IMAGE 10K 10K ancestral 320803595 Affx-986696131 AX-385290388 5 57208386 GTTGAATCTGGTAGTGAGACACTTAAGCTGAAGGT[C/G]AAATTTGTATAGATTAATACACAATTTTCACAAGC S 4 1 2 1 600010 r 74 goat 5_57208386 5 57208386 Ancestral_priority_1043 ancestry 0.594 neutral IMAGE 10K 10K ancestral 320766984 Affx-122970545 AX-385254282 5 57235625 AGTTTTGAGAGAATATGAATAAAGAAATCATTGAC[C/T]GGAACTTTATTTCTTAATGCTACAGATATATGCAT Y 2 1 2 1 101000 f 74 goat snp56741-scaffold899-438629 5 58047688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421921 Affx-122943839 AX-123292268 5 57281230 TATTGCTATCGATAGTGAGGACTCAGTTAATCCCA[C/T]GTAACAGCAATTTTTAAAAACTGTGAGGGCATTAT Y 2 1 2 1 101000 f 74 goat snp56740-scaffold899-393024 5 58092636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782920 Affx-122961989 AX-385269990 5 57353194 GATGACTTTCTTTTCTTGTTCAATTAAAGAAATAT[A/G]CATACTAGAACCAAAATTTAATTGCTATGAAAAGT R 2 1 2 1 201000 f 74 goat snp56739-scaffold899-321060 5 58166544 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375791 Affx-122978575 AX-123246150 5 57405833 ACTTAAGTGAATGTCATTAAATTTTTAGAATTCCA[C/T]GCAATAAATAAAATAGTACATTCTCTGGAGCTACG Y 2 1 2 1 101000 r 74 goat snp56738-scaffold899-268421 5 58220829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397639 Affx-122962617 AX-123267994 5 57479206 CAGACAAGGAAGTGACACTTTCAGGGTGGGAGAAG[C/T]GCAAACCTGGGTCAGGAATCAAGAATGGGAAGTCA Y 2 1 2 1 201000 f 74 goat snp56737-scaffold899-195048 5 58295452 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762374 Affx-986696905 AX-385250536 5 57490972 GTTACAGAATTTTTTCTTCTGGCGGCTATGTCCTA[C/T]GACCGCTATGTTGCCATTTGCAAGCCTTTGCATTA Y 2 1 2 1 600010 f 74 goat 5_57490972 5 57490972 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 38452686 Affx-122920312 AX-123323019 5 57516919 GGTCACCAGAGCCAAGGGGCATCCCTTGTGTGAAC[C/T]CTGTGAGATAACTATCTGTGGTGGGGGCACTACTT Y 2 1 2 1 201000 f 74 goat snp56736-scaffold899-157335 5 58333673 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440468 Affx-122929384 AX-123310805 5 57578672 TCTAGAAAGTTTTTGATTTCTTCATCAAATCTAAA[C/T]GACAGGCTTCCTGGGTGGAGTGTACTTGGTTGTAG Y 2 1 2 1 103000 r 74 goat snp56735-scaffold899-95582 5 58396042 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793332 Affx-122929739 AX-385280310 5 57609620 CGTCTCTCAGACTATAGATTTCATTTTGCCCAAAG[C/T]ACAGTTCGACTCATGACTCTCAGTTGTGTAATTTT Y 2 1 2 1 101000 f 74 goat snp56734-scaffold899-64634 5 58427642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406762 Affx-122955726 AX-123277113 5 57696597 CAGAGTCTGCACTAATAGAAAAAAATTTTTGGTCT[A/G]TTTTTAAAAGTGCATATAGAGTTTGTAATCAGAAA R 2 1 2 1 303000 r 74 goat snp42457-scaffold562-22244 5 58516468 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403300 Affx-122957842 AX-123273653 5 57736927 CTGAGAGGCCAGACCTTTGTCCATCCAAGATGGTG[C/T]GTTGACCAACTCTGTCATCTCCTTGGGTTTCACAT Y 2 1 2 1 201000 f 74 goat snp42458-scaffold562-62574 5 58556893 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391961 Affx-122966530 AX-123262318 5 57781602 CCCATACCTGGGCCTACTGCAAAAAGCTTGAACAC[A/G]GATTTTGAGAAGATGAAGAGAGGGTGTAGATATTG R 2 1 2 1 101000 f 74 goat snp42459-scaffold562-107249 5 58601838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436049 Affx-122932717 AX-123306388 5 57833464 GTACATGACTACTGGAAAAACTGTAGCCTTAACTA[C/T]ACGGACCTTTGATGGCTTTTTCTGATGTTTAACAT Y 2 1 2 1 303000 r 74 goat snp42460-scaffold562-159111 5 58654251 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441739 Affx-122929131 AX-123312076 5 57862701 CAAGCTAGAAACAGCATTTTCCAGCTTTCTCTGAA[C/T]GTAGGCCATGTAACTAAGTTCTGGCCAATGGGATG Y 2 1 2 1 201000 f 74 goat snp42461-scaffold562-188348 5 58683901 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771257 Affx-122936464 AX-385258415 5 57916918 TGAGATGAATTCTTGGAGTTAGCCTTTATTCTAAT[C/T]AAGTGGAACCCCAATCTTTCCTGCTTTTGTACCTT Y 2 1 2 1 101000 r 74 goat snp42462-scaffold562-242565 5 58738640 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789612 Affx-122932094 AX-385276621 5 57951564 ACTATGTATGGGAAGAGACTTCTCACAATTTTACC[C/T]ACTGTATTTGCCTTTAAATCCTAGTAAAATTGAAG Y 2 1 2 1 101000 f 74 goat snp42463-scaffold562-277211 5 58773784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792569 Affx-122958226 AX-385279550 5 58016578 TGGTTTTATGAAACAAATACTATACTTAAAGTCTT[C/T]GTGATTTAGTCCAAGCTCTGTCACATAACTAACTG Y 2 1 2 1 101000 f 74 goat snp42464-scaffold562-342225 5 58839106 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762376 Affx-986696907 AX-385250537 5 58038937 TATTATTCCTCTATATGTGTGTGAATATTCTGCTT[C/T]CTATCCTATGTTGTATTTTTATATTTTCCTTTTTT Y 2 1 2 1 600010 f 74 goat 5_58038937 5 58038937 Ancestral_priority_1043 ancestry 0.562 neutral IMAGE 10K 10K ancestral 320803597 Affx-986696132 AX-385290390 5 58041410 TGCTTTGGAAATGGTATTGATTAAAATTTATAAAA[C/T]GTTCATACAAGATTATGCTATTCTGACACTGAAAT Y 2 1 2 1 600010 r 74 goat 5_58041410 5 58041410 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38403688 Affx-122958051 AX-123274040 5 58073228 GCGAGCATCGTGCAGCGTTTCCCCACTCCCGCAGC[A/C]GTAGTCGCGATGGTAAGGAGAAAGAGAACGACCAG M 2 1 2 1 101000 r 74 goat snp42465-scaffold562-398875 5 58896316 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387045 Affx-122969911 AX-123257403 5 58107532 AATCACGCAGTGATGTGGGGTCTGATTATACAAGC[A/G]GGAAAATTAACTGCAAGGCATAGTTGGGAAGTTGG R 2 1 2 1 101000 r 74 goat snp42466-scaffold562-433179 5 58930515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399324 Affx-122961373 AX-123269679 5 58139145 TATCTCACCCAGCATGACAGGGAGGACACACCAGC[G/T]CAGGAGGTAGACCCAGAGCCCTAAAGTTTGTTTTC K 2 1 2 1 101000 r 74 goat snp42467-scaffold562-464792 5 58961828 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402090 Affx-122958698 AX-123272443 5 58188383 CATGTTACATGCCTGTCTGGGAGAGTCACCAGGAA[C/T]GCTGGCTTTCTGAAGGCTCTGCAGAGACCCAGAAT Y 2 1 2 1 201000 f 74 goat snp42468-scaffold562-514030 5 59011245 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792562 Affx-122953361 AX-385279543 5 58229385 CCAAATGGAGACAAGTTGTTTGTGATCAGATGGAA[C/T]ATGAAAAGGGTGGAGCTCAACCCACTTTGAAGCAG Y 2 1 2 1 101000 r 74 goat snp42469-scaffold562-555032 5 59052317 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772518 Affx-122934442 AX-385259668 5 58268128 AAATAAGGATGGAAGTGTTGAATGGAGGTGGGACT[A/G]CTTTAGTCACTGTGTTCAGGATTAGCATTTTAAAA R 2 1 2 1 101000 f 74 goat snp42470-scaffold562-593775 5 59091840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415633 Affx-122948583 AX-123285982 5 58303806 TGACTGCATTCACCGAAGATGAGAAATTAGGTAGC[A/G]TATGATTGCTAGGGCAATTGCTGTAAGAAATGTTC R 2 1 2 1 101000 r 74 goat snp42471-scaffold562-629453 5 59126341 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444457 Affx-122926545 AX-123314794 5 58336079 CCTGAACACCGGCAACTGAGACCCGCTTGTTACTG[C/T]AGCCACTGGGTGTTGGGGCTGTTTGCTACATGCTA Y 2 1 2 1 101000 f 74 goat snp42472-scaffold562-661726 5 59158656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801351 Affx-122974628 AX-385288263 5 58373095 ACCCAGATTCAGATCACTTCTATCATGAAAGCTGA[C/T]GCTAAATACATGTCAGAAAAAAGTTACTGCCTTTC Y 2 1 2 1 101000 f 74 goat snp42473-scaffold562-698742 5 59195464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396455 Affx-122962975 AX-123266810 5 58408362 TGCCTTAGAACCTCTTTTGAACTGAAATTCAGTGA[A/C]TATAATATCCAAGTAATGTTTTTATAAAAAACAAC M 2 1 2 1 101000 f 74 goat snp42474-scaffold562-734009 5 59231000 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770860 Affx-122928732 AX-385258024 5 58503238 CTAACATAAAGATATTCTGTAAGGCTCAGCTAATC[A/G]TTCACTCTTCCAACCACCTCCTAACTTCAACAGAA R 2 1 2 1 101000 r 74 goat snp42475-scaffold562-828885 5 59326014 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410656 Affx-122952768 AX-123281006 5 58549561 GGGTATCATTAGAGTTTGTAATGTAGCTAATTTCA[C/T]TCCCCTGACCCCTTTTCCCATCTACCTTTTATTGT Y 2 1 2 1 201000 f 74 goat snp42476-scaffold562-875208 5 59372294 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390354 Affx-122967684 AX-123260711 5 58603628 TTGTTGCCTCTCGCAGTATTTTATGGGCCGCTGGA[C/T]GCAAAAAACCCACTCCTGGCCTCCTGTGAGAAGGA Y 2 1 2 1 201000 f 74 goat snp42477-scaffold562-929275 5 59425442 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381111 Affx-122974583 AX-123251469 5 58643763 TATAGGTGAAATGAGAGAAAGAATATTCAAGGTAG[A/C]GGGAGCAGAAGTGTAAAGGCCCTGAAGTGAGAGTG M 2 1 2 1 101000 r 74 goat snp42478-scaffold562-969410 5 59465540 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431107 Affx-122936606 AX-123301448 5 58686698 TTTATAGCCTCATTTCTTTTTATTATTCCCTTTTA[A/C]GTTGGGAATGACTAGATAATGTGATATAAAATATA M 2 1 2 1 201000 r 74 goat snp42479-scaffold562-1012345 5 59509037 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424745 Affx-122941655 AX-123295091 5 58718449 TTGATTGTCAAGTAAGGAAAGAGACCAAAATAGGT[A/G]CCTGATTTAAAATCTGAAAATGCGGAACCTTTATG R 2 1 2 1 101000 f 74 goat snp42480-scaffold562-1044096 5 59540936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431252 Affx-122937126 AX-123301593 5 58811920 CAGGAACTTTCTAGAACATAGCTTCTGTGAATAAG[C/T]AAGTATGGGCATCAGCTGTGTGTACAGTAAAGGGT Y 2 1 2 1 101000 f 74 goat snp42482-scaffold562-1137567 5 59635759 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775589 Affx-122930130 AX-385262720 5 58889429 TAGGATGCTTTAGATCACAAGCCAGCCTATTTGAG[A/G]TTCAGAATGAGACTGGAGTTATGTTTATAACTTGA R 2 1 2 1 101000 f 74 goat snp42483-scaffold562-1215076 5 59715152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777676 Affx-122969396 AX-385264795 5 58921345 AAGAAAAGGCTAAGCTGTTTATAGCATTTTCAAAA[C/T]GCTCATCTCTCAGAGATTTGCCAGCAACAGTGTCA Y 2 1 2 1 102000 r 74 goat snp42484-scaffold562-1246992 5 59745952 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272314 Affx-1111833472 AX-185174800 5 58953494 TGCTTTTGAACTGTGGTGTTGGAGAAGACTCTTGA[A/G]AGTCCCTTGGACTGCAAGGAGATCCAATCAGTCCA R 2 1 2 1 103000 f 74 goat 5_58953494_AF-PAKI 5 58953494 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320776782 Affx-122932072 AX-385263906 5 58980449 TGTAGTATCTTCTTAGTCCTTTCTTTAATATATTC[C/T]ATAGAGAAGAGTAACAGTAAACATAGGAAGGAGCC Y 2 1 2 1 101000 r 74 goat snp42485-scaffold562-1306096 5 59805245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770755 Affx-122946421 AX-385257919 5 59035339 TTCACTAGCTTAGAACGTATATTAGTTTCTATTTA[C/T]GCATAAAAATTTGCCACAAATTAACAGCTTCAAGC Y 2 1 2 1 101000 r 74 goat snp42486-scaffold562-1360986 5 59860281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412996 Affx-122951019 AX-123283345 5 59104393 GAGTTAGGAGGTTTGGAATATATTGGAAAGAGTGA[C/T]GCTTCTCAGCTTTGCTAAAAGTCAGCAGTGTGTCT Y 2 1 2 1 101000 f 74 goat snp42488-scaffold562-1430040 5 59929528 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778395 Affx-122926431 AX-385265510 5 59145344 GGACTACAACTGTAACAAACCTTAGCAAGGTGTCC[A/G]TATTTTCAGAGTCCTCAGAGATGTGTCTTAAAATG R 2 1 2 1 101000 f 74 goat snp42489-scaffold562-1470991 5 59970888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771374 Affx-122975043 AX-385258532 5 59244228 TGTGGTTTCAAAAGGTAACTTCAATACTATTGGTT[A/G]TCAATTTAATGATGGATTCTCAGTTTCTACTCACT R 2 1 2 1 101000 f 74 goat snp42491-scaffold562-1569875 5 60076394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380710 Affx-122975154 AX-123251068 5 59302690 TTGTCTGGCAATAACTTGGGTAGTGAACCTGTGCC[A/G]TTGTTAACTCATGTGGTGCTGACTCCAGCATCAGA R 2 1 2 1 101000 r 74 goat snp42492-scaffold562-1628337 5 60134798 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771247 Affx-122954670 AX-385258405 5 59337754 TGAGAGTCACCACTGTGTATCCTATTCACATGATA[C/T]GTGTGCAAATGAGACAATTATTTACTTAGCAAACA Y 2 1 2 1 101000 f 74 goat snp42493-scaffold562-1663401 5 60169814 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437536 Affx-122931908 AX-123307874 5 59385117 CTTCCTCACACATACCTATAATACTTTTCCCCCAA[C/T]ATTTTTTGCTTTTTATATGACCACAATTTTACAAA Y 2 1 2 1 303000 r 74 goat snp42494-scaffold562-1710764 5 60216850 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437982 Affx-122931593 AX-123308320 5 59427947 ATTTAGAGCCATTGGCTGATCTGGTTGACCACAAG[A/G]GCTGCTTTCCAAACATTTGAAAAAAAAAAAAGGAG R 2 1 2 1 101000 f 74 goat snp42495-scaffold562-1753594 5 60258551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452407 Affx-122920598 AX-123322740 5 59514321 ACACTCTAGAAATTGTTACCTCTCACTTCTGACAC[C/T]ACCCACACCAGCCTATCCATCTCCATGTGTTAACA Y 2 1 2 1 101000 f 74 goat snp42497-scaffold562-1839968 5 60345811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440835 Affx-122929268 AX-123311172 5 59564380 TGGCAAAATGGAAAAGGCATGGCCTGTCTGAAAAC[C/T]AAGACAATGCATTGTTATATAAAAATATGGCAATG Y 2 1 2 1 101000 f 74 goat snp42498-scaffold562-1890027 5 60395812 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434893 Affx-122934337 AX-123305233 5 59599945 CAAACACCTTAACCTGATGCCTGTCATCAAGTTGA[C/T]AATAAATAATAAATATAATTACCATATACAGTAAA Y 2 1 2 1 103000 f 74 goat snp42499-scaffold562-1925592 5 60431276 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783193 Affx-122976576 AX-385270260 5 59632480 CTACTAGGGCAGGTGACATGAAGAATGAAGGTGAG[C/T]GGTGGAGCAGATATTTTAGAACGACTCAGCCATCC Y 2 1 2 1 101000 f 74 goat snp42500-scaffold562-1958127 5 60463806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397781 Affx-122962509 AX-123268136 5 59670181 ATCCCAGAAGGCAGCCTCCAGTTGGGCCTCTGCAG[C/T]GCACTCTACTGGCAGCGGTGAGAAACAAACTCTCG Y 2 1 2 1 101000 r 74 goat snp42501-scaffold562-1995828 5 60501440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449248 Affx-122923474 AX-123319583 5 59703102 ATGAAATGTTAGCCTGACTATAGCTGGTGGAAGCA[A/G]AAGAGGTTTCAGCATGGGTGTTAAAGTGCCATGTT R 2 1 2 1 101000 f 74 goat snp42502-scaffold562-2028749 5 60534377 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774157 Affx-122974593 AX-385261295 5 59764637 GAGCTGCATGAATAAAGAGGGATCAAATTAAGAGA[C/T]GAGTCATAAAAAATGGATTAAGAGTGATATGAGAA Y 2 1 2 1 101000 f 74 goat snp42504-scaffold562-2090284 5 60595370 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775733 Affx-122921181 AX-385262864 5 59794094 GGGCGCCACCTTCTCATTAGTATCCCAGTAGGAAA[G/T]ATACTTCACAGGGAAAGCTTGCTGAAGGTGTCCTC K 2 1 2 1 101000 r 74 goat snp42505-scaffold562-2119741 5 60624771 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431118 Affx-122936597 AX-123301459 5 59837677 TCAGCCACAGGACTCTTTCCCCTCAGTTTGACTCC[A/G]TCTGAAACTTGACACCAAAGGCAAGTAATTTAAGC R 2 1 2 1 201000 r 74 goat snp42506-scaffold562-2163324 5 60668718 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793108 Affx-122960741 AX-385280086 5 59889303 GGGGAGTTTTTCTCCCTCAAGTAAATAAGGAGCTG[A/G]CATGGTAACTCTGCTGTCTAAAAGTCCTCAGGACT R 2 1 2 1 101000 f 74 goat snp42507-scaffold562-2214950 5 60720741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419659 Affx-122945951 AX-123290007 5 59934753 TGCATAAAAACTTGCAAAAAATTCTACATTTATGA[C/T]ACACTATTTATTATATACTTAACCTTTGTATAGTT Y 2 1 2 1 101000 f 74 goat snp42508-scaffold562-2260400 5 60767260 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453140 Affx-122919999 AX-123323473 5 59976863 ATACTCTATTAGAAGCATGTGAGTGTTTCAACTTA[C/T]AACAACCATACCAGCTCTGGATGTTTTATTAAACT Y 2 1 2 1 101000 f 74 goat snp42509-scaffold562-2302510 5 60808810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278229 Affx-1111836314 AX-519551717 5 60013870 TAGTTTCCTATACCATGCAGGCTAGTGTTCAGACT[C/G]CCTTGCAGCTCTGGTCCCATATATGACCTCAGTTC S 4 1 2 1 101000 f 74 goat Random2.2K-565 5 60013870 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786992 Affx-122944531 AX-385274020 5 60107837 CCTAGAGTGATGGTGATATGGTTTTTGACCTTCTA[A/G]ACCAGAGATTTGTACTCTTGTGACTGAAGATATCC R 2 1 2 1 101000 f 74 goat snp42512-scaffold562-2433484 5 60940927 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419428 Affx-122945512 AX-123289776 5 60151110 CCATACTATATCCCACGAGTCCTACTCAAAACAAT[A/G]CCAGGAGCCTCTCCTCACCTCTTCCTCATCTCTCT R 2 1 2 1 101000 f 74 goat snp42513-scaffold562-2476757 5 60984476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770959 Affx-122929118 AX-385258122 5 60222400 TTAAAATATACATCCCTGTGATGTTCTGCTCTTAC[A/G]TTTATACTAAATGAGTATTTGGATATCATTAAACC R 2 1 2 1 101000 f 74 goat snp42514-scaffold562-2548047 5 61056344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399894 Affx-122960211 AX-123270249 5 60293250 TTCTCTTCCATTCTTTAGTCTCTCTCTGTCCCAGA[C/T]GAAAACTACCCACCTACACTTTTCAAAGCTCTTCC Y 2 1 2 1 201000 r 74 goat snp42515-scaffold562-2618897 5 61128408 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386544 Affx-122970722 AX-123256902 5 60363034 AAAATTGAAGCACAGAGGGTCCACACGACTTGCCC[A/C]AGATCACAATATAACCAGTGACAGGGTTGGATTTT M 2 1 2 1 101000 r 74 goat snp42517-scaffold562-2688681 5 61199200 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801518 Affx-122943326 AX-385288427 5 60397315 ATGAGTCACTGCTTGATTTGCAAGTTTCCCTACTT[C/T]AATGATAATATTGAAAGCCCACTAATATTAGTCAC Y 2 1 2 1 101000 f 74 goat snp42518-scaffold562-2722962 5 61232598 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444470 Affx-122926537 AX-123314807 5 60443406 AAAACCTTTTCCAAACACCGTTTTCCTCGCTTTCC[A/G]CATCACCATTAGGAAGCAAGAATTTGTAGCAAAAG R 2 1 2 1 201000 r 74 goat snp42519-scaffold562-2769053 5 61279940 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407762 Affx-122954974 AX-123278113 5 60474664 TCTCTGTGCTGTCCTTCCAATCTGACCCTGCTTCT[G/T]TTCACAGTACCCCATTGTTCTATGTTTCCAGCAGA K 2 1 2 1 201000 r 74 goat snp42520-scaffold562-2800311 5 61311162 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387317 Affx-122970508 AX-123257675 5 60509284 CCTTCTTAGTACCCTTTCAGGGTCACCTACATTAA[C/T]AGCCTTAGTTTTGTGTGTGTGGTCTTCTTGGACTC Y 2 1 2 1 101000 f 74 goat snp21680-scaffold212-1549745 5 61346574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770368 Affx-122934864 AX-385257534 5 60543850 AGTTTTTTTTTTCAAAGTGTATTTCCACTAAAATG[C/T]GACCAACCAAAAAAAAGCCACCAAAAATCAACCAA Y 2 1 2 1 101000 r 74 goat snp21679-scaffold212-1515179 5 61381147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788385 Affx-122976981 AX-385275403 5 60582364 AATCATAAAAGAGACACTTCTGAAACTGGAGGTGA[C/T]TGTATGAAGAATGTATAGAGCTTTGAACACAGATA Y 2 1 2 1 101000 f 74 goat snp21678-scaffold212-1476665 5 61419908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786358 Affx-122930326 AX-385273392 5 60624123 GAGGCAGCCAAATACAGTGATGTGCGCCACAGATA[A/G]GCATTCTCCTGAATGAAGAAACACAAGGAGGAACA R 2 1 2 1 101000 r 74 goat snp21677-scaffold212-1434906 5 61461511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389462 Affx-122968338 AX-123259820 5 60664641 TCATTCTCCTCCCCGATGGAAAGTGTCCTTCCTTT[A/G]CTCTAACTTTGTAGGTACATTATACTTCTTTCTAA R 2 1 2 1 201000 r 74 goat snp21676-scaffold212-1394388 5 61502027 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415762 Affx-122948929 AX-123286111 5 60700858 AATAGTCAGTAAATACATTTTAAGAGAAAAGACAG[A/C]TTATTCCCATGTTTCAAGCACAGGTGAGAAGAGAC M 2 1 2 1 101000 r 74 goat snp21675-scaffold212-1358171 5 61537864 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416820 Affx-122948126 AX-123287168 5 60735787 TCACTGTGGATGACACTGCTAGCAGGTGGCAGAAG[C/T]GGAACAGATACCTGGTTTCCCAACCTTGTGCACCC Y 2 1 2 1 201000 r 74 goat snp21674-scaffold212-1323242 5 61572814 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802974 Affx-122969526 AX-385289860 5 60802668 CCCTGAAGCATTGTCGACAGGGAGCCATTCTGACT[C/T]GAAGTGAAGGATTTGTGATTTGTAGACACCTGGGA Y 2 1 2 1 101000 r 74 goat snp21673-scaffold212-1256361 5 61639499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379745 Affx-122975866 AX-123250103 5 60840166 ATTAATATTTCTGCTAATGGCCCTGAAAAATGTTT[A/G]TGTCAGGAGTAGCCAGACTTGGAGGTAGAACAAGT R 2 1 2 1 201000 f 74 goat snp21672-scaffold212-1218863 5 61676973 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439017 Affx-122930354 AX-123309354 5 60946302 CCCAGCCACAACGCATCCAGGATATGTGATGATGG[A/C]GGGGCTGTTAAGTAGGAAAGCAGCAAAGATGAGAC M 2 1 2 1 201000 f 74 goat snp21670-scaffold212-1112727 5 61783343 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429061 Affx-122938296 AX-123299403 5 60979691 CCAGGTCTTACTCTTCTGTCTCTTTCTCCTGGTCC[A/G]TTTGAAACCCTTGCTCAGGGAGTCACCCTGTTCCT R 2 1 2 1 201000 r 74 goat snp21669-scaffold212-1079338 5 61816698 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397325 Affx-122962305 AX-123267680 5 61028240 TTCAGGGAAAATGCAAAGCTCCAGGTGCGCTGTGT[A/G]TCCCAGGAGCCAAATGCTTAACATGGGCTGTGCCC R 2 1 2 1 201000 r 74 goat snp21668-scaffold212-1030789 5 61865159 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793497 Affx-122929476 AX-385280474 5 61078639 CACTGCAGAGTGACAGAAAGCCTAACATGTTTGAG[A/C]TTAAAATCTGAATCCCTGATGCTCAGACTAATCTT M 2 1 2 1 101000 f 74 goat snp21667-scaffold212-980390 5 61915179 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795773 Affx-122927600 AX-385282726 5 61113285 TAAATAGCTGTTCTACTTCAAATGGATCATTAAAT[A/G]CAAAGCACTGCTTTTTATTCTATCTGGTCATCTTA R 2 1 2 1 101000 r 74 goat snp21666-scaffold212-945744 5 61949834 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394985 Affx-122964259 AX-123265340 5 61170113 CAGAGTTTCCTTCTGTAGACCCTTTAAAACAAATT[A/C]TTTAGTATTGCTCAACTATTTTTCAGCAGCCTCTC M 2 1 2 1 101000 r 74 goat snp21665-scaffold212-888916 5 62006461 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390501 Affx-122967254 AX-123260858 5 61212312 CATCCCCCAGCAGCACCACCAGATGAATGTATCCA[C/T]GCCAATGACCTGCAGCAAGCTCACCAGGAGAACTG Y 2 1 2 1 101000 f 74 goat snp21664-scaffold212-846717 5 62049815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405544 Affx-122955971 AX-123275896 5 61291360 TAGAGTAAATGGAGGTGGAAGTCGAGACTTGTATC[A/G]TTTTAGAGATTCCAGTCAGAATAAGAGAAAATAAG R 2 1 2 1 101000 f 74 goat snp21663-scaffold212-767669 5 62130041 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414843 Affx-122949188 AX-123285192 5 61324687 CATCTTCCCAACTCAGGGGTTGAACCCAAGTCTTC[C/T]GCATTGCAGGGAAGCCCATGAAAATTCTATATTGG Y 2 1 2 1 101000 r 74 goat snp21662-scaffold212-734342 5 62171778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387926 Affx-122970440 AX-123258284 5 61390251 ATCACCTAACACAAAGCTGGACTGGATTTCAGGAG[C/T]ATGTTTCCTGGACAAACTGCAATGAGCTAGTGTGT Y 2 1 2 1 101000 f 74 goat snp21661-scaffold212-668778 5 62238369 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278231 Affx-1111836315 AX-519551719 5 61413051 ACTCTGACAGATACAGTGACAATGAAGAAGGTAAA[A/C]TTCTGTGATGTTAATAAACTATATAATCAAAAAAT M 2 1 2 1 101000 f 74 goat Random2.2K-567 5 61413051 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38414652 Affx-122949317 AX-123285001 5 61455319 ATAGAGCAAGTTGGGCTACTTCTCCTTTGCCCCAT[A/G]CATACCTTTATCTAGTCTACTGTCATAACTCTATC R 2 1 2 1 201000 r 74 goat snp21660-scaffold212-603710 5 62304120 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384540 Affx-122973024 AX-123254898 5 61485215 GATGTATTTTCTCAGAAAACCAGTTAAGTATGGAT[A/G]TCAGTTTCCTTTCTGTGGTCACTTGTTAACAAATT R 2 1 2 1 101000 f 74 goat snp21659-scaffold212-573814 5 62333795 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764853 Affx-122966572 AX-180660632 5 61563662 CTGCACACACAAATAAGTTTTCTTTAGAAACTAGA[C/T]GGATAAAGTACAAAAGCATGAGGAGGTAGAGGTAT Y 2 1 2 1 101000 f 74 goat snp21657-scaffold212-495367 5 62412915 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426718 Affx-122939885 AX-123297064 5 61626177 GTGGAACATTGGGGGATGAATCAACAGTAGCATCC[A/G]GTAAATCAGAAATTACTGACACCTTTGATTGTCCT R 2 1 2 1 101000 r 74 goat snp21656-scaffold212-432852 5 62477444 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272575 Affx-1111833473 AX-519546290 5 61651502 TCACAGTCCCTGAGGAACCACGGCCAAATTAAATA[A/C]TACTTGTTAATTGTTCTGAAGACCAAGATCTGCAG M 2 1 2 1 101000 r 74 goat 5_61651502_AF-PAKI 5 61651502 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38404236 Affx-122957645 AX-123274588 5 61678411 TTTCACTTCTCTTGTTTTCTGTGGCACACTGCTTC[A/G]CTTCCTTATCTCTCTTCTATCCAACTGCTTTGTTG R 2 1 2 1 201000 r 74 goat snp21655-scaffold212-380618 5 62532038 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791162 Affx-122959805 AX-385278157 5 61744989 ATATGTTTTCAAGGTCAAATATATATAGGTCAAAC[A/G]TTTGTTTTAACAGTTGCATAATCCATGGTATAGAT R 2 1 2 1 101000 r 74 goat snp21654-scaffold212-314040 5 62599364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448602 Affx-122923390 AX-123318938 5 61795202 GAATCTTTCTTGAAATAAGTAAAACCCAAAGTCAG[C/T]GAGACATATACCGGGAAGACATATTTTTCTAAACT Y 2 1 2 1 201000 f 74 goat snp21653-scaffold212-263827 5 62649026 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413701 Affx-122950087 AX-123284050 5 61831068 CTATTTTGGAATCCTCTAACTCACATTGACATCCC[A/G]TCACTGTTTCGGAACCTCATTATGGTTTTCTTGCT R 2 1 2 1 201000 f 74 goat snp21652-scaffold212-227961 5 62685497 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775410 Affx-122929365 AX-385262541 5 61917017 TAGTGAGAATTAAAGTGCTTCTTCCACCAAAGGAA[C/T]CCTTGTTCATGCTATTCTTTTGCTTGAAATACCTT Y 2 1 2 1 101000 r 74 goat snp21650-scaffold212-142012 5 62771709 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377708 Affx-122977402 AX-123248067 5 61958551 TCAACATGTTTGAAGGAAGATTTAATAAATGTCTG[C/T]TGCTAGACTGTTAAAAATAATTTCTTTTTACAGTA Y 2 1 2 1 101000 f 74 goat snp21649-scaffold212-100478 5 62812822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779492 Affx-122939742 AX-385266595 5 61997517 TTTCTTTTTTTCTATTAAGTACACTTCATAGAAGC[A/G]TCTAAAATTGAGCAGGGTACCTGTTTCTTTCATGT R 2 1 2 1 201000 r 74 goat snp21648-scaffold212-61512 5 62851833 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772240 Affx-122949827 AX-385259395 5 62026963 TTATCTTTCTGGAGAAATAGGGAGGTGGGCTTAGG[C/T]AAAAGCAATTAGGAATTCAAGTTACTAGTTGGGAA Y 2 1 2 1 101000 f 74 goat snp21647-scaffold212-32066 5 62881256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380248 Affx-122975457 AX-123250606 5 62057095 GGAGAAGAAACTTAAGAAAGGCATTGGCAGCAGAT[A/G]TGACATAAAAAAGCATAAGGTTGCAAAAAAAACTT R 2 1 2 1 101000 f 74 goat snp21646-scaffold212-1934 5 62911630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476203 Affx-1251763708 AX-586011627 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20000 f 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 539476458 Affx-1251763708 AX-586011858 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 4 1 4 1 20000 r 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562165259 Affx-1251763708 AX-606940671 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 r 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562165334 Affx-1251763708 AX-606940745 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 r 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562165551 Affx-1251763708 AX-606940962 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 f 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562165604 Affx-1251763708 AX-606941015 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 f 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562165723 Affx-1251763708 AX-606941132 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 r 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 562166044 Affx-1251763708 AX-606941453 5 62153670 TATATTTATAAAGGATAACCAAGAAGGACCTACTG[-/TATAAGCACATGGAGAGGGAGAGGGAAAGATGGCGGAGGAATACAAAAAAAAAAAAAAAGAAAAAAAGAAGAAAAAAAAA]ATAAGCACATGGAGCTTTGCTCAATGTTTATGAGT - 8 1 4 1 20100 r 74 goat SV_297 5 62153670 - deletion junction SV-TF-chip 320779911 Affx-122944297 AX-385267010 5 62160165 GACAGAAAATGAACCCGGGACAGCAGGAGGAATTT[A/G]TTATAGGCACTTAGTATGGAACCACTGACAAGCGT R 2 1 2 1 101000 r 74 goat snp28706-scaffold310-101037 5 63000047 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776238 Affx-122949398 AX-385263366 5 62210127 TAATGAGTAATGATCTAGCTTTCTCTATAAAATAA[C/T]GCTTGGCCCTGTTCTGGTGATAATCTGATTCTCTT Y 2 1 2 1 101000 r 74 goat snp28707-scaffold310-150999 5 63050026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432118 Affx-122936450 AX-123302459 5 62247038 GGCTGTCAAGTTAGAAACATCTGAAAATGATTTCT[A/G]CAGAAGCGTTGTGGTTCATGCTTTCTTTCAGTGGT R 2 1 2 1 101000 r 74 goat snp28708-scaffold310-187910 5 63086660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386986 Affx-122969954 AX-123257344 5 62306573 GCCTGTCTTCTGGGTCGCCTGACTGAGTTGAGGAC[A/G]TTCAACCATCACCATGCAGACATGCTTATGTCATG R 2 1 2 1 101000 r 74 goat snp28710-scaffold310-247445 5 63145559 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408499 Affx-122954406 AX-123278850 5 62339484 TTGATTGATGAGACCTCATAATTGATTTTCAGATA[C/T]GGGGTTGAGCCACCAGTATTAGTAAAACTTGAGAA Y 2 1 2 1 201000 f 74 goat snp28711-scaffold310-280356 5 63178478 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766313 Affx-122948112 AX-385253700 5 62372487 CTCTAAAAATAGGCAAGACATAAATCTTAGCAAAA[C/T]GTGTTTTATGGTTAGGATTTTGATTAAATAAACCA Y 2 1 2 1 101000 f 74 goat snp28712-scaffold310-313359 5 63211463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779200 Affx-122942969 AX-385266304 5 62403305 GATGGTTGCTGGTGTTGGTTTCTCAGCTCAACCAC[A/G]TCAAGGATTATCTCCCCGAGATCCTTTTGGCCTTT R 2 1 2 1 101000 f 74 goat snp28713-scaffold310-344177 5 63241879 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380236 Affx-122975468 AX-123250594 5 62453579 TGCATGGGATATATCAATCATCAATGACCTCCTAA[C/T]GGCCAAACCTAGTAAATATTTTCCCATCCTAATCC Y 2 1 2 1 101000 f 74 goat snp28714-scaffold310-394451 5 63292675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784536 Affx-122952139 AX-385271585 5 62484772 AATGTCTTGAGTGGGCCTCCCTTACTGATATGGAT[A/G]TTCTCCGTTCAGCCATCCCAAAGGGAGATTAGTTC R 2 1 2 1 101000 r 74 goat snp28715-scaffold310-425644 5 63324006 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38392091 Affx-122966368 AX-123262448 5 62525775 CAGCCATGAAATTAAAAGACTCTTGCTTCTTGGAA[G/T]AAAAACTATGGCAATATAAAGATGAGGATATTCAG K 2 1 2 1 303000 r 74 goat snp28716-scaffold310-466647 5 63365142 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384223 Affx-122972379 AX-123254581 5 62555140 TACCAATGCTATGGTGTCCATCCCCTGCCCAAAGC[A/C]AAGGACATAATATTCTTTCCTCATTTTCTGGCTCT M 2 1 2 1 101000 f 74 goat snp28717-scaffold310-496012 5 63394829 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391746 Affx-122967482 AX-123262103 5 62587149 CAAAGATTTATTTTAGTTTTAATTTTTCTTTTTTA[C/T]AGCATAGTCCCTGAAAGATGTTTGTCGTTCCATAT Y 2 1 2 1 101000 r 74 goat snp28718-scaffold310-528021 5 63427487 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403626 Affx-122957543 AX-123273978 5 62620191 GAAAAGTCATAACTGAGAATGAGAAAGGAATGAGA[C/T]GGATTGAGAGGATGGTACGATGGTGTAGACAGTGG Y 2 1 2 1 101000 f 74 goat snp28719-scaffold310-561063 5 63460551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791254 Affx-122949325 AX-385278248 5 62658589 AGAGATAAAGGCCACATTAAAATCTGAGCCTGCTT[A/G]CTCTTTACCCTTGTATCCTGTTGATTCCTATTATC R 2 1 2 1 101000 f 74 goat snp28720-scaffold310-599461 5 63498948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442930 Affx-122927621 AX-123313267 5 62703503 AGTCCATGCTTTCTCTTCCTGCTTCTGCTCAGGCT[A/G]CCCGATGAAGGCTGGTTCACACCCTCAGGGGTTAT R 2 1 2 1 101000 r 74 goat snp28721-scaffold310-644375 5 63544140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447141 Affx-122924452 AX-123317477 5 62757548 CATATTTCTTTCTCATTGTGTTTTTGTCTTTGTTT[C/T]ATTCTCTTTTATGTTAATGGATTTCTTCAGATACC Y 2 1 2 1 101000 r 74 goat snp28722-scaffold310-698420 5 63579904 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430518 Affx-122937213 AX-123300859 5 62877200 AGGATTTCTAACTGATTATAACACATTTGATAAAG[C/T]AATGGAGCTTTCTGCCCCTTGTTTGGCTGCTCTGG Y 2 1 2 1 201000 f 74 goat snp28725-scaffold310-818072 5 63699995 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783959 Affx-122950775 AX-385271013 5 62946693 CACTTTGTACATTAACTAGTGTAATTCTTACCATT[A/G]CCCTTCATATAGAAATCATCTCCACTTATCAAATG R 2 1 2 1 101000 r 74 goat snp28726-scaffold310-887565 5 63767217 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780184 Affx-122953050 AX-385267280 5 63019427 CTCATTAATCCTCAAGAATCTGATGAACAGAAGGC[A/G]ATATCTTTTGTAATATGGTTATTATGGACTGACAT R 2 1 2 1 101000 f 74 goat snp28727-scaffold310-960299 5 63840132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410338 Affx-122952467 AX-123280688 5 63053597 TAAAACTGTGTTGACTCCAAGTTTACTCATGATTA[A/C]TGATCTCTTCAGGTTTTGTTAGGTTCCTTTTGACT M 2 1 2 1 101000 r 74 goat snp28728-scaffold310-994469 5 63874244 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421617 Affx-122944475 AX-123291964 5 63087613 TGGCATCCTTTTTATTGTCATATTTCTAACACTCT[A/G]TAGAGTGTCTTGTGACATAAGCTCAATAAGAATGG R 2 1 2 1 101000 r 74 goat snp28729-scaffold310-1028485 5 63907786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787977 Affx-122959281 AX-385274998 5 63139411 TTCAAATTTCTCTTCTGCAGGCATGCATATGACTC[A/G]TTACAAGAAATAAGGATTAAATGATTTAATATAGG R 2 1 2 1 201000 r 74 goat snp28730-scaffold310-1080283 5 63959797 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422689 Affx-122943662 AX-123293035 5 63180821 GATATTTTTAGAAGTAATTATATGTAGGGACCACA[C/T]GATATCACGATGATGTAAAAACATTTTTGTAGAGT Y 2 1 2 1 101000 f 74 goat snp28731-scaffold310-1121693 5 64001203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772538 Affx-122929074 AX-385259688 5 63238681 GTTAGAAACATGCAAGAATCTTATGCTATTAATAA[C/T]AGTTTTGCCTACAAATCATTTCTTAAGAATTTTCG Y 2 1 2 1 101000 r 74 goat snp28732-scaffold310-1179553 5 64059153 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439343 Affx-122930291 AX-123309680 5 63275126 TGGGATCCCTCCTGGAGTAGGATAACTGGGAGGAT[A/G]AAGAATCCAGGAACCATAGTCCATTCACCTTGAAT R 2 1 2 1 101000 r 74 goat snp28733-scaffold310-1215998 5 64095273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436193 Affx-122932600 AX-123306532 5 63324587 ATTTGAAAAGAACAACACATTAATGAATGTTGCCC[A/G]CAGAGCTGTCTATCCCTGGGTAGTGCTGAAAGAAT R 2 1 2 1 201000 f 74 goat snp28734-scaffold310-1265459 5 64144693 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428953 Affx-122938883 AX-123299295 5 63397226 TGCTGCCTGCATAGGTGCCTGCAGCTCTGCTCAAA[C/T]GTAGCCCAAGGTCGCATCTTCTCCCCGACTCTGGT Y 2 1 2 1 101000 r 74 goat snp28736-scaffold310-1338098 5 64217662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379910 Affx-122975758 AX-123250268 5 63435746 GTGGAGAAGCACTGCTTGCCCACATACTCATGTGG[C/T]AGGCTTTCTCACCTCCTTCAAATTTTCATCAGAAA Y 2 1 2 1 101000 r 74 goat snp28737-scaffold310-1376618 5 64256286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781072 Affx-122940306 AX-385268159 5 63475565 TTCATATCTGACAGTATCTTCCACCATGTAGGGTA[A/C]AACTTGATCAATCATGTCTGAGAATCAGGCAAGTA M 2 1 2 1 101000 r 74 goat snp28738-scaffold310-1416437 5 64295887 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389882 Affx-122968136 AX-123260239 5 63560589 AATTACTCTTCTGGCAAAGTGCTGCCCAAGGGCAC[G/T]CATATGCTGTCTCCACTTCTCCCCATCACTGATTC K 2 1 2 1 201000 r 74 goat snp28739-scaffold310-1501461 5 64382412 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779654 Affx-122922569 AX-385266756 5 63609364 GAAGCTTTTTCAAAGAGCAGTGTATGAAAAAACAA[C/T]GGAGCTTCGAGGTGTGAATCCAGAGAGTCTTGACA Y 2 1 2 1 101000 r 74 goat snp28740-scaffold310-1550236 5 64431074 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414023 Affx-122949799 AX-123284372 5 63638188 TCTACCAGTTAACAAGCTGTAGAAAGTTTCAGTCC[A/G]TTATTTGTACTTATACTTTGGCCACCTGACGTGAA R 2 1 2 1 101000 f 74 goat snp28741-scaffold310-1579060 5 64459954 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793808 Affx-122964067 AX-385280779 5 63669283 AAGTGAGGCAGAATGTTCCACCCAGAAAGCAAAGG[C/T]AATGGAATTTTATGAGAAAGGGTATGGAGACAAGG Y 2 1 2 1 101000 f 74 goat snp28742-scaffold310-1610155 5 64491873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433211 Affx-122935628 AX-123303552 5 63705445 TTCCTCCTTACCAATCTGTAAAACTTATATGTGAG[A/G]GCCCTTACTTCTGTCATAGGTGGTCAGCAGGAAAA R 2 1 2 1 201000 f 74 goat snp28743-scaffold310-1646317 5 64528242 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391917 Affx-122966942 AX-123262274 5 63753825 TCCATTTTCCACAGTAAATAAGATTATTAGTCAAG[G/T]CAACTGAATATTTCTTTCTTCTTTATTACTGTTTA K 2 1 2 1 201000 f 74 goat snp28744-scaffold310-1694697 5 64576533 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407933 Affx-122954369 AX-123278284 5 63783672 TGCAAAAATCCAAATCCAGAGAAGCAACTTAGCAC[A/C]GAAGCAGAAAGCTATCTTAAGGACATCTGCCCATA M 2 1 2 1 101000 r 74 goat snp28745-scaffold310-1724544 5 64607093 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782106 Affx-122965341 AX-385269184 5 63840321 CTACCTCTGTTGCCAGTTTACTGCTAATATTAGGA[A/G]TTTTTCCTATACTTAGTAATCTTTTAATTACATGT R 2 1 2 1 201000 r 74 goat snp28746-scaffold310-1781193 5 64664389 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418279 Affx-122947004 AX-123288627 5 63872581 AGAGCTGTTTGGAGGTGAGAGTATGGGGGAGATAG[A/G]TGGCTGGAGTGGGTCACATTTAGATGGAGAGAAAG R 2 1 2 1 201000 f 74 goat snp28747-scaffold310-1813453 5 64696876 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794781 Affx-122955016 AX-385281741 5 63941497 TTAAGGGTGTACAGATAAACTAGCATGTGTTCATG[C/T]GACAGTGATAAGGCCAGTGATAATTTTTGAAACTC Y 2 1 2 1 101000 r 74 goat snp28748-scaffold310-1882369 5 64766268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394571 Affx-122964447 AX-123264926 5 63979229 CTGACCTTAACCGCTTTGGCATCCCCCTCCTACCC[A/C]CAAGGCACACAAAAGAGCTGTGCGAAAGTGCTGAT M 2 1 2 1 101000 r 74 goat snp28749-scaffold310-1920101 5 64804814 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781635 Affx-122926645 AX-385268719 5 64013364 TTTTCTTCTTCCTGTCTTATTTCCAGAAACCTGCC[C/T]CTCAACCTCTGATTTTTAAGTCTTACGTGATCTGT Y 2 1 2 1 101000 f 74 goat snp28750-scaffold310-1954236 5 64816648 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278233 Affx-1111836316 AX-519551721 5 64043184 TAAGGCTCACGTTAGATACTTGACTGAACACTGAA[A/G]GATTCTAAATACAGAGCCAAGATAAAAACCCAACT R 2 1 2 1 101000 f 74 goat Random2.2K-569 5 64043184 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791840 Affx-122947764 AX-385278830 5 64068783 TAAAAGAATAACAATTCTACCAGTTGAACATGTGT[A/G]TGTGCTGGTCACTGTCTTATAAGTGCTAATTGTAG R 2 1 2 1 101000 r 74 goat snp28751-scaffold310-2009655 5 64873013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429446 Affx-122938498 AX-123299788 5 64120919 GATGTCTCTCTTAAAGTAACCCTGAAATAATGCCT[A/G]CAGTGGGAGGAGGTCACTGATCTTCTCAAAATCTA R 2 1 2 1 101000 f 74 goat snp28752-scaffold310-2061791 5 64925304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377724 Affx-122977391 AX-123248083 5 64161275 CTGGGCTGTGCCATGTCACAGAAATGTCTAATTAA[C/T]GTAGGTCTTTATTTTGAGGAACTGGTGCTTTTTCT Y 2 1 2 1 101000 f 74 goat snp28753-scaffold310-2102147 5 64965666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272202 Affx-1111833474 AX-519545952 5 64251298 GGGGAGTTCCCTAGTGGTCCAGTGGTTAGGACTCT[A/G]TGCTTTTACTGTTGAGGGTCCAGGTTCAATCCCTG R 2 1 2 1 102000 r 74 goat 5_64251298_AF-PAKI 5 64251298 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278393 Affx-1111836318 AX-519551878 5 64288473 TCTGTCCCCTGTGTTGGCAGGTGGATTATTAACCA[C/G]CAGACCAAGAGGGAGATCCCAGTCCCTGGCTTAAA S 4 1 2 1 103000 r 74 goat Random2.2K-571 5 64288473 G C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38387149 Affx-122970640 AX-123257507 5 64289202 TGCATATTAGGGAAATCTTTCCACACACCTCCAAG[C/T]GTAAGCATTCCCTGTGTCCTCAGTTGCATCGTACT Y 2 1 2 1 101000 f 74 goat snp28756-scaffold310-2230074 5 65094787 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404514 Affx-122956698 AX-123274866 5 64331912 TTAAATCTTAATGTTGGGCTGGGTCAGAGTTCCCA[G/T]ACCAGAGTCATTCAACCTTTAGCCTAGGGGATTAC K 2 1 2 1 101000 f 74 goat snp28757-scaffold310-2272784 5 65137480 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431485 Affx-122936253 AX-123301826 5 64411003 CAGCAAGCGAAGTCTGTCTCCACAGCTGCTCAGTA[C/T]ACCTTGATGCACAAGAAAACTAAAGGGCGCTTAGT Y 2 1 2 1 101000 r 74 goat snp28759-scaffold310-2351875 5 65217407 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394377 Affx-122964635 AX-123264732 5 64445726 TATACCAATTCCATTTCAATAGCTACTTGTTTCAC[A/G]TGCAGATATCAAACTTTTCCATCATCACAGAAAGT R 2 1 2 1 101000 f 74 goat snp28760-scaffold310-2386598 5 65252327 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404061 Affx-122957152 AX-123274413 5 64503270 CTGTGAAAAGAACACCAGGAAAGACCTGCCTACAG[A/C]GGCACCATTGTTTCAGGGTTAAGTGCTGACGAAGA M 2 1 2 1 101000 f 74 goat snp28761-scaffold310-2444142 5 65310529 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421809 Affx-122944322 AX-123292156 5 64535946 CCATGAATAGACATGCTTCTGACAGCTTGCAAGAG[A/G]GCAAGCCCTAGGCCAGCCTCCAGCTTCAGGGCTGC R 2 1 2 1 101000 f 74 goat snp28762-scaffold310-2476818 5 65343478 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394768 Affx-122964838 AX-123265123 5 64565005 GGGTCTGACCTCAGAAAACTAAATAGATGACGTTG[G/T]GAATACTGGGCACTGTTGCTAAGGAGCAAAGGTGA K 2 1 2 1 101000 f 74 goat snp28763-scaffold310-2505877 5 65372239 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426763 Affx-122940562 AX-123297109 5 64617981 CTGCTCTGGCCTCCAGAGATTGGCTACATTCTAGA[C/T]GACTCAGCAGCTGACTGAACATGCATGATCATGTG Y 2 1 2 1 202000 f 74 goat snp28764-scaffold310-2558853 5 65425226 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416377 Affx-122947871 AX-123286726 5 64670902 CTTTAAATGAGTGACTATTTCTACTGTAAGAAAAT[C/T]AAAACACATTCTTGCCATTCTTCAGCTTTGAAAAA Y 2 1 2 1 101000 r 74 goat snp28765-scaffold310-2611774 5 65476286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434520 Affx-122934162 AX-123304861 5 64724351 CATGAACCTATTGCATGGAATGTGGAATCACTTCT[A/G]CTTTGGCATGTGAGGTATTTCTTTTTTTATCTGCA R 2 1 2 1 101000 f 74 goat snp28766-scaffold310-2665223 5 65531731 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273793 Affx-1111833818 AX-519547404 5 64727873 AGAACTCAGACTAGAACTGCAGACTTAAACTCA[A/C]TGCACCTAGCTACCTATGGGATGGATATGATCGGG M 2 1 2 1 101000 r 74 goat GoatD01.005889 5 64727873 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320792702 Affx-122974423 AX-385279682 5 64764874 CTGAATTAGAAAGGAAAAGAATGGATTAAAGAACA[C/T]GATTACAAAGCTCGAGAGACTAGCTTTGCTTCCGT Y 2 1 2 1 201000 f 74 goat snp28767-scaffold310-2705746 5 65573123 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787883 Affx-122965999 AX-385274905 5 64800911 CCTTTCATCTGTGTGTCTTGAGTGGAATCAATCTC[A/G]TGTTCAGCTTCAGGTAGATTGAGTTAGATTTTCTG R 2 1 2 1 101000 f 74 goat snp28768-scaffold310-2741783 5 65609309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788400 Affx-122932146 AX-385275418 5 64830339 TAGAGAGTCAGAGACTCAGGGTCTCATTGATTTTG[C/T]GGACATAGACAAACCCCTTAATCAGTGGGTCCTTT Y 2 1 2 1 101000 f 74 goat snp28769-scaffold310-2771211 5 65639337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278396 Affx-1111836319 AX-519551881 5 64858996 ACACCCCGGCTTATTCCTTCTTCCTGATCTCTATT[A/G]CTGTTAGTGCCTCCTTGTCAGCCAAACCTACCTGG R 2 1 2 1 201000 r 74 goat Random2.2K-572 5 64858996 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397185 Affx-122962411 AX-123267540 5 64874187 GAGAGGTCTGTTGATCAAGGCCAACTTTGATGCTC[A/G]TCTTAAACAACTCTCCTTCTCACTGGCCTTCGACA R 2 1 2 1 101000 f 74 goat snp28770-scaffold310-2815059 5 65682039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417933 Affx-122946716 AX-123288281 5 64940736 AGTGCAGACATAAAGTTCTGTCACTTCTTGTGTGC[A/G]TCCTCTCTCAAGGAACCCTCTCCCAGCACCTGCCC R 2 1 2 1 101000 f 74 goat snp28771-scaffold310-2881608 5 65748852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382738 Affx-122973606 AX-123253096 5 64989432 TCACTTATGCTCTCCCCAAGAGGGGATCACTAGCA[A/G]CTTGTGTGTACAAGGTAGGCTAGGGAGAACACTAC R 2 1 2 1 202000 r 74 goat snp28772-scaffold310-2930304 5 65798371 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802570 Affx-122968424 AX-385289472 5 65034724 ATGGTGAAATTTTATTTCATGTCTTTACACATATG[C/T]AAATATGCCATTTTGAACATATGCTTGGAGGGAAG Y 2 1 2 1 201000 f 74 goat snp28773-scaffold310-2975596 5 65844051 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392798 Affx-122965972 AX-123263155 5 65068067 CCAGCACCCAGATCAGGACCTGGCACAGAGCAGAT[G/T]CTCTAAAATAGTTGTTAAATGAATGATGTATTCTC K 2 1 2 1 101000 f 74 goat snp28774-scaffold310-3008939 5 65878001 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802286 Affx-122922508 AX-385289190 5 65101558 TTTTGTCCCCTTGATCTATCCATTACTGAGAAAGA[C/T]GTACTAAAATCTCCCTAGAGATTTGTCAGTTTTTC Y 2 1 2 1 202000 f 74 goat snp28775-scaffold310-3042430 5 65911846 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438882 Affx-122930739 AX-123309219 5 65130342 ACTTGGTAACTTTTCACAGCTTGGAGTAAGAAGTT[A/G]GGAAAAGTTTTATTTTAAATGGTTTGGGGGTCTTG R 2 1 2 1 201000 f 74 goat snp28776-scaffold310-3071214 5 65940461 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406405 Affx-122955222 AX-123276757 5 65188770 ACCCTCTGAACTTGCCCTTGCCCAGCTTTCTAGTC[A/G]AAACTTCACTGTCTCTTCTATCCCTGTCCTGTTTG R 2 1 2 1 101000 r 74 goat snp28777-scaffold310-3129642 5 65999922 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429741 Affx-122937596 AX-123300082 5 65233719 TTACTCATAAGAGAAAGGATCTGACCAGGGTCTGG[A/G]CCAGAAAGGTTCCAGCGCAGCTGGGCCCAGATGTC R 2 1 2 1 101000 f 74 goat snp28778-scaffold310-3174591 5 66044597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781683 Affx-122934513 AX-385268766 5 65265493 TATTTGCCAGTTGGCACTTGCCCAGTTTTCCAAAA[C/T]AGTCTGTACAAGGAGCACAATCTGTACAAGGAGCT Y 2 1 2 1 101000 f 74 goat snp28779-scaffold310-3206365 5 66076883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384179 Affx-122972414 AX-123254537 5 65341137 AAAAAGTCAACATTCATCACAACAGAATTGAAACC[A/G]TTTCATTACCTTTCCCAGACACAACAGGCATTCAT R 2 1 2 1 101000 f 74 goat snp28781-scaffold310-3282009 5 66153133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400585 Affx-122960404 AX-123270940 5 65387676 TTTTTATGGAGACATTTTTGGAGTCGTCTTCATTA[C/T]GCAGGCATTTATGGAGTCTTTGTTACATGGGCAAT Y 2 1 2 1 101000 f 74 goat snp28782-scaffold310-3328548 5 66199394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410860 Affx-122952609 AX-123281210 5 65435546 GACTCTCCTCACCCTACCCCAGCCACCACCTGGAG[A/G]GCATCCAGCCATCTAGTGGTCAAGATGGAGCCAGG R 2 1 2 1 201000 r 74 goat snp28783-scaffold310-3376418 5 66247713 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799031 Affx-122976133 AX-385285961 5 65480171 GTTATTGTCACATCGAAACACAACAATGACACTCA[A/G]CACATCTGGGAGTCCGACTCCAATGAATTTTCTGT R 2 1 2 1 101000 f 74 goat snp28784-scaffold310-3421043 5 66292335 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377979 Affx-122977615 AX-123248338 5 65523777 GTCCCTGGAGAAGCCATGATGCCAGGTAAGAGAGT[A/G]GAAAATCAATCTGATTGTTAAGGATCTCTCATCCC R 2 1 2 1 101000 r 74 goat snp28785-scaffold310-3464649 5 66336044 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443271 Affx-122927485 AX-123313608 5 65561052 GATGACATGTGTTCTAAAGAAGGTTTCTTATTCTC[C/T]CCTATGCGTTTTACAAGAATTATAGATCTGCATAG Y 2 1 2 1 101000 r 74 goat snp28786-scaffold310-3501924 5 66373229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278240 Affx-1111836320 AX-519551728 5 65612579 GTGCGTGATCTTAATCTATCCTAGCATCACATCAT[A/T]GAGGGTGATGGAGTCAAGATTTTGTGACTGGCTGG W 4 1 2 1 101000 f 74 goat Random2.2K-573 5 65612579 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320782754 Affx-122928271 AX-385269826 5 65617648 TGCTGGATTCTCAGGACCTGACACTGTGCCTAGGA[C/T]ATACATAGTTGAGAGATGTATGATTTGTAAATGGT Y 2 1 2 1 101000 f 74 goat snp28787-scaffold310-3558520 5 66430098 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798360 Affx-122942319 AX-385285295 5 65711379 GAAGACTGTCTGGGTTGGATGACTCTTCAAGCAGA[C/T]ATCTATTTCTTATCCGGCTCTAGGGACACCAGAGT Y 2 1 2 1 101000 f 74 goat snp28789-scaffold310-3652251 5 66524332 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415932 Affx-122948445 AX-123286281 5 65754015 TGGGGCGGAAGACTATTACTTGATGCTTCTAAAGA[C/T]GAATTCCCTAACACAGAACCAGATAATAGCTGCCA Y 2 1 2 1 101000 f 74 goat snp28790-scaffold310-3694887 5 66567994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391740 Affx-122967486 AX-123262097 5 65802767 AGTTTTAGTTTCTAATATTCAAAGCCCCGTCCACA[G/T]TATTCAAAGCTCTTTGTGGGAAATCCTAAATAATT K 2 1 2 1 101000 r 74 goat snp28791-scaffold310-3743639 5 66616878 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434691 Affx-122933954 AX-123305032 5 65837044 AGACTTTCTAGGGAAGGAGAGGAGCCAGTTATTGT[C/T]ATTCTTTTTCAAAAACAGTGTGTTGGATTCTTGGG Y 2 1 2 1 101000 f 74 goat snp28792-scaffold310-3777916 5 66651149 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442110 Affx-122928351 AX-123312447 5 65873389 AAGACCCATGTCTGGCTCAGTGCTGGGTGCAAGCA[C/T]GCAACTCAGTAGCTGATACATTGTTGGTGCTCAAG Y 2 1 2 1 102000 r 74 goat snp28793-scaffold310-3814261 5 66687354 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768698 Affx-122953012 AX-385255876 5 65906689 ATGGTGACATTCTCTCTTAACTGCAATCAGTCCCA[C/T]GAACTTAGCTTTGCTTGATCTATGGGTTTTTCTGT Y 2 1 2 1 101000 f 74 goat snp28794-scaffold310-3847561 5 66721056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389411 Affx-122968373 AX-123259769 5 65936300 GATACAGCAGGGACCCAAGTGGACAAGACTTGAGG[C/T]GGGGAGACATAATATAAACAAATGCATGTTTGAAC Y 2 1 2 1 201000 f 74 goat snp28795-scaffold310-3877172 5 66750646 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439357 Affx-122930282 AX-123309694 5 65977957 CATGTTTGCATATGTGGTGATGCTGGCTGGCAGCT[A/G]CAGGGACCCAGTGCTCATTTTGCTTGGTTTACAGC R 2 1 2 1 101000 f 74 goat snp28796-scaffold310-3918829 5 66792530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422612 Affx-122943722 AX-123292958 5 66051414 TTTTTCCTCCTCCAAAGTGTTGCTATGTCATTGTG[C/T]GCTGAGGGCAACCTGCATGCATTTAACAGTTTACC Y 2 1 2 1 101000 f 74 goat snp28798-scaffold310-3992286 5 66865739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278400 Affx-1111836321 AX-519551885 5 66061080 TTTTTTTTTTTTAGTAATAATTTTTACCTTTCTAT[A/G]CTAATATCTTTTTCATGGAAGGGCACTTTAAATAG R 2 1 2 1 101000 r 74 goat Random2.2K-574 5 66061080 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390512 Affx-122967246 AX-123260869 5 66102999 GGGCAGCCTCCTGCAGCACCCTCTGCCTTGAATTC[C/T]GCCTTACCCAAGCATGATTTTATTAAGATGAGGCC Y 2 1 2 1 101000 r 74 goat snp28799-scaffold310-4043871 5 66917424 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407583 Affx-122954663 AX-123277934 5 66135580 TTTTAGGCAAAACAAAGAGCAGCGCTCTGTGCCCA[C/T]GGAGCTTGCTCTTGGGTGATCTTAGTTTGGGTCAT Y 2 1 2 1 101000 r 74 goat snp28800-scaffold310-4076452 5 66950006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411197 Affx-122952369 AX-123281547 5 66225393 TGAATGACCCAAGGGAGAGCTAGAAAGACTGAGTG[C/T]CCAAGCTGGAAACCACAGTCTTCTATTTACATAAT Y 2 1 2 1 101000 f 74 goat snp28801-scaffold310-4166265 5 67036930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384307 Affx-122972280 AX-123254665 5 66305075 ATCCATCTTCCCAATGTTTACCTGTTAAAATGAAT[A/G]TTTTCATGTATCACTGAGTAAACTATATGCCCTCT R 2 1 2 1 101000 r 74 goat snp28803-scaffold310-4245947 5 67116313 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779679 Affx-122968283 AX-385266779 5 66343962 CTTGCAACAATATTCATTCCCTCTCTATTGAGAAG[C/T]AGTTACATTCCTTTCTTTGTGTGCAGTTCTGGTAA Y 2 1 2 1 101000 f 74 goat snp28804-scaffold310-4284834 5 67155123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428390 Affx-122938954 AX-123298733 5 66397111 TAAATGGTCCCATGACTGATTTTCAGGCAACAATC[A/G]GCTCAAAAAATTACAAATAGCTAGCAATCAATTTT R 2 1 2 1 101000 f 74 goat snp28805-scaffold310-4337983 5 67208231 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379959 Affx-122975638 AX-123250317 5 66426540 GTGTGCTTGATCAGTTTGAGGAACATCAAGGCAGC[C/T]AGGGTGGCTAAACAGAATGAGAGGGTAGATGATAG Y 2 1 2 1 101000 f 74 goat snp28806-scaffold310-4367412 5 67237819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425988 Affx-122941151 AX-123296334 5 66516888 GTCTTTATATAACTATTAAAACAAACAAATAAAAC[C/T]CAACACACCTCTTGCAAAGAAAGCTAAGACTAGCA Y 2 1 2 1 101000 r 74 goat snp28808-scaffold310-4457760 5 67328157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431446 Affx-122936502 AX-123301787 5 66598572 AGAACGGTCACCAAGCAGTCTTCCCACACTGTTCC[A/G]ACTGCCTCCCCACTTCTCAAAGCCTGCAGTCCTGC R 2 1 2 1 102000 f 74 goat snp28809-scaffold310-4539444 5 67409838 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421747 Affx-122944370 AX-123292094 5 66637415 AGAATGCTTCCTTTTAGTGAAATATTCTAGGTCAC[C/T]GATGACAGAAAAGCCAGGTGCTAGGTGGTTGGGCT Y 2 1 2 1 201000 f 74 goat snp28810-scaffold310-4578287 5 67448712 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770402 Affx-122922921 AX-385257568 5 66670319 TAAAGGGTGGGGAAGTACTCTACTTTTTCAGTATT[A/G]CTAGAAATGGTCCTAAGCATGACCCTCATTAGCCT R 2 1 2 1 101000 f 74 goat snp28811-scaffold310-4611191 5 67481464 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417265 Affx-122947260 AX-123287613 5 66699787 TCCTGTATTCCTCTGCTAGCTTCCCTGCTATTTTG[C/T]AATTATGTTGCTTATAATCTAACTGCCTGGTTAAA Y 2 1 2 1 201000 r 74 goat snp28812-scaffold310-4640659 5 67511008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791794 Affx-122949323 AX-385278784 5 66735981 GTCTAGGAAAATTGTCAGTAAGTGAGTTACTAAGG[G/T]CAGTTGATAACAGGATCTTTCAAAATACACTCAGT K 2 1 2 1 101000 f 74 goat snp28813-scaffold310-4676853 5 67547272 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424161 Affx-122942534 AX-123294507 5 66794249 TTGCCTGATGGAGGGTGCCTGTGACGACGTGTTCC[A/G]CTGTGCAAGGGGGCTCGAGGGCATGCTCTGAATAG R 2 1 2 1 201000 f 74 goat snp28814-scaffold310-4735121 5 67605565 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278244 Affx-1111836322 AX-519551732 5 66816576 ACTAGACCTCGAAGGAATGCTCTACCAGTCAAAAA[A/G]GCAAAGGCAGGCACTCTTGGCAGAAGAAATTGCAA R 2 1 2 1 201000 f 74 goat Random2.2K-575 5 66816576 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781628 Affx-122935870 AX-385268712 5 66844021 GGGAAGGAATTGGCAGAAAAGAAGGGAGTTCAGAG[C/T]GAGAGGAGATGATTTCTAACTGAGAAGGGTACCCA Y 2 1 2 1 101000 r 74 goat snp28815-scaffold310-4784893 5 67656166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464373912 Affx-1110453853 AX-515847322 5 66875041 ATGCTACTGCCTGCTTACAACATAATATGATTTGT[A/G]TATGTTATTTGAAATTTTCTAGCAGTCACGTTTTG R 2 1 2 1 101000 f 74 goat 5_66875041_AF-PAKI 5 66875041 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378110 Affx-122977145 AX-123248469 5 66876251 ACAGGAAGCTAAATATTGAAGATGGAATTTGCCTA[C/T]GGCTCCATAGCTATCAAGTGGCAGGGTGGAGATCT Y 2 1 2 1 101000 f 74 goat snp28816-scaffold310-4817123 5 67691110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445252 Affx-122925481 AX-123315589 5 66920183 TCACCATTAGAATGAGAGTTCCCAGTGTGCAGAGA[C/T]GGGATTTGCACCTGGTGGCATCCCCAGTAGCTAAC Y 2 1 2 1 101000 f 74 goat snp28817-scaffold310-4861055 5 67735283 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447668 Affx-122923956 AX-123318004 5 66971547 TTTGAACTTGAATATCCCTTCTCCTTCTGTGTGTT[A/C]GCAGTCCCTGGCCTCCCCTCAAGGAGTGTCCTGGT M 2 1 2 1 101000 f 74 goat snp28818-scaffold310-4912419 5 67786745 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772838 Affx-122921913 AX-385259983 5 67073281 AATTGCAAGGTTAAGTCTCAGTAGTAAATTTATAC[A/G]TTCAAGACCATTTCCAGCTATGCAAAGAATTTCTA R 2 1 2 1 101000 f 74 goat snp28821-scaffold310-5014153 5 67890089 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780675 Affx-122968280 AX-385267765 5 67113079 GGTCAGCAAGAGTCAATTTATACTGTGGTAACAAA[C/T]AACCTCCAAATCACAGTGGCACAATTAACAAAACA Y 2 1 2 1 201000 r 74 goat snp28822-scaffold310-5053951 5 67926083 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394037 Affx-122964995 AX-123264392 5 67141675 CTGTTCAAATCTTATTGTCTCACATCTGGTTTATC[A/G]TGGTAATCTGCTCACAAATCACTCTTCTCTCAGTC R 2 1 2 1 101000 r 74 goat snp28823-scaffold310-5082547 5 67954671 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800589 Affx-122929507 AX-385287508 5 67174079 AGATCATGACAGATATAAAAGCGTTATGTTCATTT[A/C]TAAAATGATGAGGAAGAAACAAGTTGGGCCTTTAA M 2 1 2 1 101000 r 74 goat snp28824-scaffold310-5114951 5 67987054 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381309 Affx-122974446 AX-123251667 5 67217856 TGGAAACAACTTAGCGACTAAGCCACTGCCACCCA[C/T]AGAATTTTTACAGTTCAAATTCCCTCAAGCCTTTT Y 2 1 2 1 101000 r 74 goat snp28825-scaffold310-5158728 5 68030912 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443646 Affx-122927205 AX-123313983 5 67250823 CCTTGAACTCATATCCAGAGATTCTCCCCATCTTA[C/T]ATTCCATGTCCTGGTAAACTGCACCACATCCATTA Y 2 1 2 1 201000 r 74 goat snp28826-scaffold310-5191695 5 68063875 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393289 Affx-122965441 AX-123263645 5 67322821 TATTCAATACATGATATTGACACAATAGCTCAATT[A/G]CAAAGGGAAAAAATCAAATTAGATCCTACTCAATG R 2 1 2 1 101000 f 74 goat snp28828-scaffold310-5263693 5 68136147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443232 Affx-122927563 AX-123313569 5 67352820 CCCAGATGAAGAGAACCCTGGCAGGGGGCAGGCAG[A/G]GGAGGCTGACATGGGAAGCAAGTGTGGCTGAGTTA R 2 1 2 1 101000 r 74 goat snp28829-scaffold310-5293692 5 68166162 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799905 Affx-122955954 AX-385286831 5 67386088 TGCTTTTGTGCCCTTGGATGAGAGGGGTTCGAGAA[C/T]AGAGGAGATGGTGAACTAACACTTAAAGGTATCAA Y 2 1 2 1 101000 r 74 goat snp28830-scaffold310-5326960 5 68199490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784774 Affx-122934877 AX-385271821 5 67424976 AAGCCTAGAATGAAGGAATCATCCAGATAAACCAA[C/T]ATTTGAGAACTGAGCTGGCTGAACTTTCTGATTGG Y 2 1 2 1 101000 f 74 goat snp28831-scaffold310-5365848 5 68238381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782174 Affx-122973261 AX-385269252 5 67466250 CTCTAGCACATTTTTCTCTAGCAGAGACAAAAGCT[A/G]TCAAATGTGTCATTCAGGCATTATCTGGAATGTGC R 2 1 2 1 101000 f 74 goat snp28832-scaffold310-5407122 5 68279634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775425 Affx-122922031 AX-385262556 5 67502193 CTTGTCAGGTGCCTCTTGCATTCACTGATATTTGG[C/T]AAAATGTTTGGCTATGGGCTCAACAAATGTCCACT Y 2 1 2 1 101000 f 74 goat snp28833-scaffold310-5443065 5 68315409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799952 Affx-122960591 AX-385286878 5 67536514 ACAGCCATGGCATCAGTTTCATCTGCATCCCCAAG[A/G]AAGTGACTGACAACTACTTCCATGTCCCCAAGAGA R 2 1 2 1 102000 f 74 goat snp28834-scaffold310-5477386 5 68349595 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413075 Affx-122950963 AX-123283424 5 67569878 GGGTTAGGTGATCCCCCCATGCCACCTTCCCCCTC[A/G]TGGACTGTGCTCTTCTGTCAAGATGGTCAATATGA R 2 1 2 1 101000 r 74 goat snp28835-scaffold310-5510750 5 68382932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453638 Affx-122919739 AX-123323971 5 67614291 TCTCTCACTATAGAGTTGTTTTAATGACCTTGCTT[A/G]TTAACCACTGTTAAGACCTTCCCATTTGGGAGGCA R 2 1 2 1 101000 f 74 goat snp28836-scaffold310-5555163 5 68427675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278246 Affx-1111836323 AX-519551734 5 67657632 GCAGTATAATTGAAGGAAACCCTCAAGGAGTAGGC[A/G]TATTTCTGAGGCATGCATCACCTGCCACAAAGTTG R 2 1 2 1 101000 f 74 goat Random2.2K-576 5 67657632 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791524 Affx-122949006 AX-385278515 5 67662170 TTCAGCTCCAAACTACTTGGACTTTTTTAAAGTTC[A/G]GTGTTAACGCAGCTTCTGTTTTGGTTTTTGTCTGA R 2 1 2 1 202000 r 74 goat snp28837-scaffold310-5603042 5 68475797 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388528 Affx-122969201 AX-123258886 5 67695115 AAATAGCTAAGGTCCATTTCAAAAGAAAAGTTGTC[A/G]TTGCTCAACTGATCATTTTACTCTTTGCTCCTCAT R 2 1 2 1 101000 r 74 goat snp28838-scaffold310-5635987 5 68508663 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398233 Affx-122962206 AX-123268588 5 67762426 AGAATGGTTTGATAGTACTGTTGTGAGTATATGAT[A/G]TGAAAGGGGTACTAGGTAGCATATATTCAATACTT R 2 1 2 1 101000 f 74 goat snp28839-scaffold310-5703298 5 68575388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803599 Affx-986696133 AX-385290392 5 67825443 AGTGTGACCTACATTGTTTTACCAGCAGGGCTTCC[A/T]GAGGCTATTGATTTTGCTGAGAAGCAAGCTGAGGC W 4 1 2 1 600010 r 74 goat 5_67825443 5 67825443 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 38409852 Affx-122952928 AX-123280203 5 67863451 GTTATTTCCAGGCCCAGGCCAGCTAATAGCCATCC[A/G]TTATCCCAATGACAATAAGAGCCTTGATAGGTGAG R 2 1 2 1 101000 r 74 goat snp28841-scaffold310-5804323 5 68676723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409513 Affx-122953629 AX-123279864 5 67893363 GGAGTTCAACCTGGGCAGTTTGATCCAGCCCCACG[C/T]GGTTACCCACCGTGCTCTATCTACGGCTCACAGGA Y 2 1 2 1 201000 r 74 goat snp28842-scaffold310-5834235 5 68706708 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796190 Affx-122935608 AX-385283141 5 67926258 TGTGAAGACGACTTTCATGGTTCCTTCATAAGACT[A/G]TAATAATTTCCGACACTTTGATAGAAAAAATTCAA R 2 1 2 1 101000 f 74 goat snp28843-scaffold310-5867130 5 68739734 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788883 Affx-122921674 AX-385275898 5 67973344 AGCTTTGCTTTTTGACTTTAGTTCATTCCTGAAAA[C/T]GTTACCTCTTAGTGAAAAGATTTTAAAGCAGAAGA Y 2 1 2 1 202000 r 74 goat snp28844-scaffold310-5914216 5 68786574 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431048 Affx-122936649 AX-123301389 5 68009418 TGCTAAATACTTCTTTATTCTTGCCTGATTATACT[A/G]CACTGTTCCTTGGCTCATCTCCACCGCTTTGCAGA R 2 1 2 1 101000 r 74 goat snp28845-scaffold310-5950290 5 68822646 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786324 Affx-122953105 AX-385273358 5 68066504 ATAAAAGTTTGTAAAGTGAAACTGAGGAGAAAGGA[A/G]CTGAAGGGAAGGCAGGGGCACTTAAAAACTCATTA R 2 1 2 1 103000 r 74 goat snp28846-scaffold310-6007376 5 68880150 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382026 Affx-122974955 AX-123252384 5 68108449 GTTTCTACATATATTAAAATATGTAGAATAATGTA[A/G]CTAATTGATTTATAGTCTTTTTCGTATAGGGAAAT R 2 1 2 1 103000 r 74 goat snp28847-scaffold310-6049321 5 68923042 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383644 Affx-122972530 AX-123254002 5 68147151 TGTATGAGGAATGACAACACAACCCTGTACATTGT[A/C]ATCAACACTTGAAACTGACCAACTGAGCTATGCCA M 2 1 2 1 101000 f 74 goat snp28848-scaffold310-6088023 5 68962168 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375995 Affx-122978420 AX-123246354 5 68190601 CTCTCTTCTCATGTAAGAAGAGAGGGACGTGGAGT[C/T]GGAGATGGAAGGTGACATGGAGAGAAGGGAAAATA Y 2 1 2 1 101000 f 74 goat snp28849-scaffold310-6131473 5 69005520 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387454 Affx-122970371 AX-123257812 5 68303026 TGAATTCCTTAGGAGTGAGAAATGGACCTTTATTC[A/C]GAAATGGAGAGAGGAGGAAGGGGGATAGTTTCATC M 2 1 2 1 101000 f 74 goat snp28851-scaffold310-6243898 5 69119673 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384919 Affx-122972338 AX-123255277 5 68334219 CCTGTTGCGGCATGTGGTGTCAAGGGGAAGAACAG[C/T]GGTTTCTGGCCCCAACAAAACCCTGAAAATATGCC Y 2 1 2 1 101000 r 74 goat snp28852-scaffold310-6275091 5 69150811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446189 Affx-122925730 AX-123316525 5 68368902 CTAGTGAGTCCTTTCTTTATGGTCTTTTCCTGTTT[C/T]ACAAAGCATCCTCTGTTTCCAATGACACCAAAGCT Y 2 1 2 1 201000 r 74 goat snp28853-scaffold310-6309774 5 69185399 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398422 Affx-122961624 AX-123268777 5 68401727 AAAGAGTGGGACACGACTGAGCAACTGAACTGAAA[C/T]GAACTGAACTGAAGGAAGAATGCAAGTTTTCCAGA Y 2 1 2 1 103000 r 74 goat snp28854-scaffold310-6342599 5 69219008 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387269 Affx-122970549 AX-123257627 5 68440402 ATCTGGTGAGGAGATGGAGACTTACAGGTGGAAAA[C/T]AACAATAATGGTAGTATCATTTGAGGGGCAGATTC Y 2 1 2 1 201000 f 74 goat snp28855-scaffold310-6381274 5 69257345 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386873 Affx-122970060 AX-123257231 5 68489902 TGCTTAGAGTGCTGCAGGGTACGACATGTGCTGTG[C/T]ATTGCCCAACTCCTGGGGCACCTTTCACTTAGGTT Y 2 1 2 1 202000 r 74 goat snp28856-scaffold310-6430774 5 69306887 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420661 Affx-122944821 AX-123291008 5 68520308 TCTTGTGTATCCCCTTCACTAGGATGTTAGGTCTG[C/T]ATGGTTGGAGACTGTGGTTTGCGCAGGGCTGTCTC Y 2 1 2 1 201000 r 74 goat snp28857-scaffold310-6461180 5 69337616 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427007 Affx-122939848 AX-123297352 5 68551825 GCATGAGTATCCTAGGGCTGCTGTGACCTATTACC[A/G]CAATCTTTGTGTCTTAAAACAATAGAGATATATTC R 2 1 2 1 101000 f 74 goat snp28858-scaffold310-6492697 5 69369038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432496 Affx-122935584 AX-123302837 5 68593078 CTTTTAATCTGAGGGTGTGGGACTTTGAGATATGG[C/T]GCTCACGGCTCATCTAAATACAAACTGCTTCAAAA Y 2 1 2 1 101000 f 74 goat snp28859-scaffold310-6533950 5 69410361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446112 Affx-122925790 AX-123316449 5 68656668 TTGTGCCCGGAAGAGTATCTGAGACCTCGGGGAGT[A/G]CTGTCTCTTCAGTCGTGTCTAACTCTTTGAGACCG R 2 1 2 1 201000 f 74 goat snp28860-scaffold310-6597540 5 69473474 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432137 Affx-122936435 AX-123302478 5 68701091 TCTCCACCCACTCCTTCCCCAATCTATGGAACCAC[A/G]TCTTTTCTGGGCTCAGAGGAGACTTAAGTGCTGCT R 2 1 2 1 201000 r 74 goat snp28861-scaffold310-6641963 5 69517705 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402543 Affx-122958468 AX-123272896 5 68750664 CACATCGTGAATGCTCGGGAAGTACTAGAGTGCTC[A/G]CTGTACAACTGGTTACACAGCTTCCTTTTTCCTGG R 2 1 2 1 101000 r 74 goat snp28862-scaffold310-6691536 5 69567168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384214 Affx-122972385 AX-123254572 5 68864225 CCATAAAGTAAAATGAACCACCCTCCCATCCCCAA[G/T]CCAATTTAGGCAGCCGAAGACAAAAGTTTAGTATG K 2 1 2 1 201000 r 74 goat snp28864-scaffold310-6805097 5 69680939 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409380 Affx-122954153 AX-123279731 5 68895871 ATATTAAAGAGGTACACTTACTAAGCACACCCTGC[A/G]AAGTGTAAGGTGCACAGCTTTACACGAGATATGAC R 2 1 2 1 101000 r 74 goat snp28865-scaffold310-6836743 5 69713653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442670 Affx-122927897 AX-123313007 5 68925209 GAGATGTGAGGTACATTGAAACTGCCAAAATTTCA[C/T]GGGTATTCATCACAGGTAATAAGTAGTGAAGGGGG Y 2 1 2 1 101000 r 74 goat snp28866-scaffold310-6866081 5 69743011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436841 Affx-122932216 AX-123307179 5 68965839 TATTTTTAGGAAATTCAGTAAAATGAGGTTTTATT[A/G]TGAACGTCTCACTCTTTCATTTTTCAGTTTAGGAC R 2 1 2 1 201000 f 74 goat snp28867-scaffold310-6906711 5 69784150 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398036 Affx-122961765 AX-123268391 5 69128759 CCAAAATCGAAGGCACAACATTTATGAGCATTAAA[C/T]GAAAAGTCAGCTGAGCTAAGTAAGGGCTGACAGAT Y 2 1 2 1 201000 f 74 goat snp28871-scaffold310-7069631 5 69947116 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453932 Affx-122919491 AX-123324265 5 69166557 GTTTTGAAACCTGGGAAGTCCCAGGCACATAGAAT[A/G]AGTAGGTCATCCTATACAACCCGTGACAGTCACGC R 2 1 2 1 201000 r 74 goat snp28872-scaffold310-7107429 5 69985342 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450360 Affx-122922102 AX-123320695 5 69258655 CAGTCATGTGCAGGGGAAAGTTGCAGGAGAAACTT[A/G]TAGTTTTCTGAGTTTTCACCATCTCCCCACTATGT R 2 1 2 1 101000 r 74 goat snp28874-scaffold310-7199527 5 70076623 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431173 Affx-122937187 AX-123301514 5 69315153 GACTTGAGGTGAGTCCTGAGCACGAATCACCTGAA[A/G]TTTCCCTCTGAAAAGTTGGTGGAACCACAGTCCCA R 2 1 2 1 101000 f 74 goat snp28875-scaffold310-7256025 5 70133146 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380641 Affx-122975226 AX-123250999 5 69353872 GTGCCTTACAAATATTATTTTATTCCTCATAACCT[C/T]CTTATAATAGAAGGATGATTATCATCCTAATTTTG Y 2 1 2 1 303000 r 74 goat snp28876-scaffold310-7294744 5 70171984 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464375651 Affx-1110454718 AX-515849041 5 69435586 TTCCAGTAAATAGCACTTGCATGCCTACTGTCTGC[C/T]CCCTTATCTTCCCCTCCAGGCTGAGGGTCTGTTGT Y 2 1 2 1 101000 f 74 goat 5_69435586_AF-PAKI 5 69435586 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38451731 Affx-122921540 AX-123322064 5 69466760 AATTTGTCTGACCTTGGGCAAGCCCATTCTCAGGG[A/G]GCCTTGGTTTCCTCATCTGAAAATAAGAACAGAAG R 2 1 2 1 201000 f 74 goat snp28878-scaffold310-7407632 5 70284420 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774305 Affx-122953139 AX-385261441 5 69607178 CCGATACTCACTGTCTCTGCAAAAGCCTAGCATAA[C/T]GGATGCTCAAAAAGCTATTTAGTGAATGAATAAAT Y 2 1 2 1 101000 f 74 goat snp28881-scaffold310-7548050 5 70424314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442314 Affx-122928239 AX-123312651 5 69649148 TTTTCTTTGTGACTTCTCAGTGAACACTTTCTTGA[C/T]GGAATAGTGCTAAAGCTGAGAATGAAAGGGTGATA Y 2 1 2 1 201000 f 74 goat snp28882-scaffold310-7590020 5 70466486 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413067 Affx-122950967 AX-123283416 5 69682626 TCATTCTGGACTTAAAAAAAATTCATATTGCAGTA[C/T]AGTTGAATTACAGTGTTGTTAGTTTCAGGTGTATG Y 2 1 2 1 201000 f 74 goat snp28883-scaffold310-7623498 5 70500098 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796468 Affx-122963808 AX-385283418 5 69715927 GGATGTTTTGTTTCATAATTTAACTAACATGACAG[C/T]GGATAATTATTTTACCATTGGACTTTGACCATTGG Y 2 1 2 1 101000 r 74 goat snp28884-scaffold310-7656799 5 70532925 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416355 Affx-122947886 AX-123286704 5 69776381 CTGAACTTGGTCTCTGATGCTCTCTGGTTGTGTGA[C/T]GCTGGGACAGTCACTGAATGACTCTGTTCTCACCT Y 2 1 2 1 201000 r 74 goat snp32943-scaffold383-8054 5 70593210 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451604 Affx-122921636 AX-123321937 5 69820383 GCTTCACTGCATGTTTATAACTCAACCAATGAGTA[C/T]GCAAACGCAGAAGGAAGAGGTGGGTTGTGCTGGTC Y 2 1 2 1 101000 f 74 goat snp32944-scaffold383-52056 5 70637445 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378650 Affx-122977097 AX-123249009 5 69854979 CTGCTTTACATCAAGGCAGATAATACCATCTAGTA[C/T]GTAGATATTGACACATTTTCCCAAGGGAGACTATG Y 2 1 2 1 101000 f 74 goat snp32945-scaffold383-86652 5 70672319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444074 Affx-122926846 AX-123314411 5 69895669 ACTCTGCACAGTACAGATGGGTAAGGCCCTAGAGA[C/T]GGCTTGGTAGCTTTGAGTCTGTGGGTGAGCCTCTT Y 2 1 2 1 101000 f 74 goat snp32946-scaffold383-127342 5 70711845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399137 Affx-122960659 AX-123269492 5 69928227 GGTGGAGACCGAACACCAGCACGTTGGGTTAAGCC[A/G]TCTAATTAGACAGCTCCATCTCCCGGCTTTATTTT R 2 1 2 1 102000 f 74 goat snp32947-scaffold383-159900 5 70744300 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442635 Affx-122928456 AX-123312972 5 69972329 TTTGGGTCGGAACCCTGGCTGCATTAATGACTAAG[C/T]GAATGCAAGCATGTGACTTCATCTCTCTAGGCCTC Y 2 1 2 1 101000 f 74 goat snp32948-scaffold383-204002 5 70788311 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390816 Affx-122967852 AX-123261173 5 70008210 CAATCTGAACTCAGGTTCACTGGCTCCAGATCAAT[G/T]TCTCTATTTGCCCCAACCATAATGTTTCCTATTTG K 2 1 2 1 101000 f 74 goat snp32949-scaffold383-239883 5 70824246 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797437 Affx-122936364 AX-385284376 5 70037956 GAAAAGAATGATTAGGCAAGGTACCACAAAGCCCA[C/T]AGCAACTAAATGGTGGAAATGGTATGTGAACCACC Y 2 1 2 1 101000 r 74 goat snp32950-scaffold383-269629 5 70854202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278248 Affx-1111836324 AX-519551736 5 70042223 GGAATATCGAGTGGAAAGGACCGAGATGGGAGCAT[A/C]CTTGGTGTGTCCAAGGAGTAGCCAGTGAGCAGTGG M 2 1 2 1 101000 f 74 goat Random2.2K-577 5 70042223 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401497 Affx-122958942 AX-123271850 5 70072332 GTCACTGAGCAAGGGACCCCTGTACTGACATCCTG[C/T]GGGTCCCAGCTGGCAGGAGGCTTTCTTTTCAGTGC Y 2 1 2 1 102000 f 74 goat snp32951-scaffold383-304005 5 70888541 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449407 Affx-122922698 AX-123319742 5 70172178 AGATTTGGGGGCTGTTAGTATAAATAGCATAACCC[A/G]ATCCATCCTGATAAATATAAATGGTATATTAAAAA R 2 1 2 1 101000 f 74 goat snp32953-scaffold383-403851 5 70988119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415858 Affx-122948859 AX-123286207 5 70223966 TCCGTGTATGTCATCCCTCACCCACAGCACTCAGT[A/G]CCCACCAGACATGGCCTTGTTTTGCTGTGTCCTTC R 2 1 2 1 201000 r 74 goat snp32954-scaffold383-455639 5 71035571 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391289 Affx-122967345 AX-123261646 5 70277682 CAATTTTCACTAAAGTGTAAAGTACTCTTGAAAAA[C/T]AAAGGTACACTAAGAGACGTGTGAAACCTTCAAGC Y 2 1 2 1 202000 f 74 goat snp32955-scaffold383-509355 5 71089122 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407141 Affx-122954859 AX-123277492 5 70328901 TCCATGCTATAGATGTAGTCTTTCAAACATGTTCT[A/G]CTAGTTACAGGATTGGGGGATGAGAGCTGGATGTA R 2 1 2 1 201000 f 74 goat snp32956-scaffold383-560574 5 71140318 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424630 Affx-122942178 AX-123294976 5 70421860 GCAGTAAACCACAACTCCCTTGAGAATAACAGCTG[C/T]GGGGAAAACATTAACACCCAGGAGAATACTCATAG Y 2 1 2 1 201000 f 74 goat snp32958-scaffold383-653533 5 71232715 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442521 Affx-122928545 AX-123312858 5 70471384 ACTGTCTCTCAGCTTTTCCACTGAGTAGATTTGGA[C/T]GCTAGGAATTCTCTTGATCTCTTCATCTGTAAATT Y 2 1 2 1 101000 f 74 goat snp32959-scaffold383-703057 5 71282015 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792179 Affx-122972715 AX-385279163 5 70506233 TAATGATTTCTAAGAAATTAATGGCCATGTTTATC[A/G]TGATATCTCCACTGCAAATTGCAGGCACCCCATAA R 2 1 2 1 101000 r 74 goat snp32960-scaffold383-737906 5 71316861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775109 Affx-122964774 AX-385262241 5 70609547 ACGGCTTCTTTAGACACATTCTTCGTACAGTGATA[C/T]GGTTCAGAAGCACAAGAGGGAAAATCCAAATAGGA Y 2 1 2 1 101000 f 74 goat snp32962-scaffold383-841220 5 71421898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275182 Affx-1111834750 AX-519548761 5 70625092 GCTGGAATGGCCCAGCTTGTCACAGGAAGCACATG[A/G]AGACTGCAGCCTCGTTCAGAGGGGGCCTGCCCC R 2 1 2 1 101000 f 74 goat GoatD01.051345 5 70625092 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38421312 Affx-122944090 AX-123291659 5 70649321 GGCAGGACTCCTCCCAGAGGCATTGCCACTATTCT[A/G]CCATTGCTACATACTAAGTTTCCATCTTGGATGTT R 2 1 2 1 101000 r 74 goat snp32963-scaffold383-880994 5 71462532 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389320 Affx-122968494 AX-123259678 5 70684218 GAACTCACAGAAGGTTTTGAGTTTACGGAGTTTGG[C/T]TCCAGAGCCCACATTCTCAATCAGTGTGTCTCATA Y 2 1 2 1 201000 f 74 goat snp32964-scaffold383-915891 5 71496946 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783383 Affx-122948178 AX-385270447 5 70715073 TTGTTCAACCAGGAAGCCAGGAAAACAATGAAACC[A/G]CAGTTTAAGCCTCTAGTGAAGGAGGGAAGGGGTGA R 2 1 2 1 101000 f 74 goat snp32965-scaffold383-946746 5 71527955 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414279 Affx-122949601 AX-123284628 5 70745989 TAGGATGAACCAGATAACCCTGGTTAATGGAATGG[C/T]AGAAAAAGCAATGAAGATCTCTCCAGGGTAATTTG Y 2 1 2 1 101000 f 74 goat snp32966-scaffold383-977662 5 71557457 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444008 Affx-122926900 AX-123314345 5 70797438 GTTCTCAGTACTCTTAGATTAAGCTTGTCAATTAC[A/G]TTGCTCAAATTATTTTTCAATTGTGTTCTATTCTT R 2 1 2 1 101000 f 74 goat snp32967-scaffold383-1029111 5 71608949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278408 Affx-1111836325 AX-519551893 5 70833566 AAGAGGAGGACAATTCAGAGACCCTTACTGACCAT[C/G]CATGTTGGCTGAGTGAGTCTCAGACATTATCTTAT S 4 1 2 1 101000 r 74 goat Random2.2K-578 5 70833566 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416850 Affx-122948102 AX-123287198 5 70847211 CATTTCTTTCTTTCATCTCTTTTCTTTTCTTTTGC[A/G]TCTTTGTTCTCTGGAAGTTTTCCTCACATGTCTGG R 2 1 2 1 101000 r 74 goat snp32968-scaffold383-1078884 5 71659183 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779135 Affx-122927641 AX-314363912 5 70889722 CAGGTACTTACTTAATCTGAGCAATCATAAAAATA[G/T]AAAACATGCATTTAGAAACTGCAAAATATGTACTT K 2 1 2 1 101000 r 74 goat snp32969-scaffold383-1121395 5 71702243 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386930 Affx-122969998 AX-123257288 5 70937806 CAGGAAACATGCAACTTCTGCCTTCCCCTAGGGCC[A/G]CATCTTCTTCAAAGCCACTTGCATGCTAAGTTGTT R 2 1 2 1 101000 r 74 goat snp32970-scaffold383-1169479 5 71750592 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780313 Affx-122937717 AX-385267408 5 70975465 GTTTTATTTTGTTTTGGTGGACAAAAACAACAGAT[A/G]CCAACTCCTAATAGCTTGTAGTCATTGTCCTAAAG R 2 1 2 1 101000 r 74 goat snp32971-scaffold383-1207138 5 71788347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409447 Affx-122954087 AX-123279798 5 71006103 TCAGCCTCTGGACCATCATTCCTGGCCTCCTCTGA[A/G]CACACCCTTGTCGGTGAGTACCCATTTCCAGCACA R 2 1 2 1 201000 r 74 goat snp32972-scaffold383-1237776 5 71818614 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392915 Affx-122965716 AX-123263272 5 71079797 TCCTGATTCTTAAATCACTAAGCGGACCAACAGAC[A/G]GAGCCCACGAGACACATTCTTACAGGCCCTGTTCT R 2 1 2 1 101000 f 74 goat snp6384-scaffold1225-15706 5 71894800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405562 Affx-122955955 AX-123275914 5 71126119 GATAACTATCAGATTTTGATACCTTGGGAAGTCTT[A/G]CCAATTAAATCACATCTAATAAGGGTTCATATTTA R 2 1 2 1 101000 f 74 goat snp6385-scaffold1225-62028 5 71941070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440314 Affx-122930210 AX-123310651 5 71179951 TTCCCTCTAATACCCACTTGGCTCACCCACCCCTC[A/G]CTTCCTTCAGCTCATGGTCACCTACTCCACAAGTT R 2 1 2 1 101000 r 74 goat snp6386-scaffold1225-115860 5 72002876 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449387 Affx-122922712 AX-123319722 5 71209845 GATGTTTTTGAATCCTTATCACCTTCATCGTCCCT[A/G]CTGATATAATTACAGACTTGTCCAAAGCGATATGA R 2 1 2 1 101000 r 74 goat snp6387-scaffold1225-145754 5 72032792 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418151 Affx-122947099 AX-123288499 5 71372342 TGATGGCTAAGTTGGTTGCTGATTATATTACCCCA[C/T]AGCAGAATTTAAAAACAAAAACAAAAACCACTGAA Y 2 1 2 1 101000 f 74 goat snp34156-scaffold4005-143717 5 72193806 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428730 Affx-122938450 AX-123299072 5 71440016 TCTCAGAAACCCTGCTGTTGTGTGATTGCCCCTGG[A/G]TCATCTGGTGAACTTGGACACATAACGTGGACACC R 2 1 2 1 101000 r 74 goat snp34158-scaffold4005-211391 5 72261468 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441243 Affx-122929500 AX-123311580 5 71491573 CCCAGTTCCCACAGGGCCTCCAGATAGGAGGAGAG[C/T]GACAGAATTCTTCAACATCAGGGTTAGAAGGAATC Y 2 1 2 1 101000 r 74 goat snp16796-scaffold1759-626402 5 72310116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383875 Affx-122973133 AX-123254233 5 71527353 GATGGGGCACTTTTGGTGCTAACACCAAGAATGAC[A/G]TACATGTGTTACAGTCAAGGAAACTGAGACCCAGA R 2 1 2 1 201000 f 74 goat snp16795-scaffold1759-590622 5 72341102 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452909 Affx-122920205 AX-123323242 5 71579537 GATGGGGAAACGAGGCTCAGAGAGGCAAATGGCTC[A/G]CCCAAGTTCCCACTGCCAGGAAGTTGGAGAACTGG R 2 1 2 1 101000 r 74 goat snp16794-scaffold1759-538438 5 72393131 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442357 Affx-122928029 AX-123312694 5 71608366 TGACAGCCAACTAGGCTGCTAGTCTAGCACCTCTC[A/C]TCTACAGAGAAGAGCCTTTAAACCCTCAACTCAAG M 2 1 2 1 101000 r 74 goat snp16793-scaffold1759-509609 5 72421963 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404992 Affx-122956394 AX-123275344 5 71652992 ATGTCCAAGAAGCACCTGGCATACAGTTGGTGCTC[A/G]CTAAGGGCTCTTTCCTTCCCTGCAGTAACCCTCTT R 2 1 2 1 101000 f 74 goat snp16792-scaffold1759-464983 5 72466642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437330 Affx-122931955 AX-123307668 5 71695539 AAATTCTGAAACCAGACTGCCCAGCTTTGAATTTC[A/G]TGCTTGGCCCGTTTCCTAGCCCTGTGACCTTGGGC R 2 1 2 1 101000 f 74 goat snp16791-scaffold1759-422436 5 72508643 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447417 Affx-122924394 AX-123317753 5 71725002 GCTAAATGTTCTAAAGGAATCAAGCCAGAAGTCAT[A/C]GAATTGTAAGCAAGCAGATAAGTTATGGGGTCCCC M 2 1 2 1 101000 f 74 goat snp16790-scaffold1759-392973 5 72538406 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395558 Affx-122964244 AX-123265913 5 71763450 ACAAAACCTACCGGCACCATCCTCCTCCAGCAGCC[A/G]CAGTAGACTTGAGCCAATATTATCTTTCCTTGAAA R 2 1 2 1 101000 r 74 goat snp16789-scaffold1759-354525 5 72576756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801883 Affx-122936503 AX-385288790 5 71815928 ATGCTCATTTTCCTAACCTGTAAAACTGGTGATAC[G/T]AGTTCCTGACTCATAGAGTTGTTTTTAACAATAAA K 2 1 2 1 101000 f 74 goat snp16788-scaffold1759-302047 5 72629412 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476204 Affx-1251763709 AX-586011628 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20000 f 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 539476459 Affx-1251763709 AX-586011859 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 4 1 4 1 20000 r 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 562165164 Affx-1251763709 AX-606940576 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20100 f 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 562166183 Affx-1251763709 AX-606941591 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20100 f 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 562166244 Affx-1251763709 AX-606941652 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20100 f 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 562166419 Affx-1251763709 AX-606941827 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20100 f 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 562166465 Affx-1251763709 AX-606941873 5 71838475 AAAATTCATAGAAAAAGGCAATTGAACAAGAATGG[-/TTAAAACAATTTTTTTTTTCTTGGAAATTTTATTTATTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCTTG]TAAAACAATTTTTAAAAAGAAAAAGTTGAGGAATT - 8 1 4 1 20100 r 74 goat SV_319 5 71838475 - deletion junction SV-TF-chip 320778866 Affx-122964171 AX-385265974 5 71848626 GTTGGTCTGAGATTTATGAATCTTTAGAAATCCTG[C/T]AGTAAGTAGCCTTTAGGCTTTCAGCCATTGCTATT Y 2 1 2 1 101000 f 74 goat snp16787-scaffold1759-269349 5 72662228 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454102 Affx-122919362 AX-123324435 5 71906246 AATCAGCCTGCTACATGCTTTCCATCTCATCTCTG[A/G]TACACAGCCTCTAAGATAGTCCCCATGATTCCTGC R 2 1 2 1 201000 r 74 goat snp16786-scaffold1759-211729 5 72720094 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272316 Affx-1111833475 AX-519546052 5 71941838 GAACGGCACTGTTCAACGGAAGTTTCTGCAATGAT[A/G]ATGTTCTAAATCTGAGCTGTTCAGAATGGTAGCCT R 2 1 2 1 101000 f 74 goat 5_71941838_AF-PAKI 5 71941838 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38399160 Affx-122960643 AX-123269515 5 72004015 AGGGAAGAGGCAGGAGGGGAAGGTGAGGGTCTCGG[A/G]AGACTCTGGGAGAAGGCTCTAGACCTTGTCCTGAA R 2 1 2 1 101000 r 74 goat snp16784-scaffold1759-113960 5 72818316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405442 Affx-122956050 AX-123275794 5 72045648 TGCAAGCAGGCAGCTTACATGGCTAAGGTTTCATT[A/G]TCTAATCCATCATAGATCGGCTTGAATAAACCCAT R 2 1 2 1 101000 r 74 goat snp16783-scaffold1759-72327 5 72859752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803034 Affx-122950222 AX-385289910 5 72104264 CTGTATAGAATCAACAAAGACTACTTTACCAGCTC[A/G]TGAATCTGCTCAAGGACTTGCTCAATCACTTCCTA R 2 1 2 1 101000 r 74 goat snp16782-scaffold1759-13711 5 72918907 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445867 Affx-122925992 AX-123316204 5 72172517 CACAAGGGAAAACGAAGGTTCAGACTTGCCCCTCA[A/C]GTGGGGAAACTGTGCGGGTCTCCCTGCCTCTTGTT M 2 1 2 1 303000 r 74 goat snp294-scaffold1007-1177334 5 73383101 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396361 Affx-122963044 AX-123266716 5 72252668 TCTGTTTTCAGCTCCAGCAGATATCTGTGTAGTGC[A/G]TCTGCCTCTTCCCTGTAACAGTGAACATCAAGCGA R 2 1 2 1 101000 f 74 goat snp292-scaffold1007-1097183 5 73406369 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409647 Affx-122953524 AX-123279998 5 72282485 CTGACTCCAAATTCCATTCCTAAGGGCTTCATGGA[C/T]GGAAAGCAGGCGTGTGTGCTCATGGTGAGTGGGCT Y 2 1 2 1 101000 f 74 goat snp291-scaffold1007-1067366 5 73436169 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388165 Affx-122969448 AX-123258523 5 72312439 TCTGCCTTGGGTACCAGATGAGGCATGGCGGCACA[C/T]GGTATTCCAGATTAGGCTATGGCAGTAGGAGATGG Y 2 1 2 1 101000 r 74 goat snp290-scaffold1007-1037412 5 73464167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403471 Affx-122957712 AX-123273824 5 72343269 ATCACACAGTTCAGCTGGTGACGCAGATCTGAACC[A/G]GTTTAAGCATTTAAAAAAAAGCTGTTACAAGGCTG R 2 1 2 1 101000 f 74 goat snp289-scaffold1007-1006582 5 73494428 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375900 Affx-122978486 AX-123246259 5 72373756 GAGAAGACAGTTACGAGCTCAGGGGAGAGGATTAA[C/T]AGCTTCTTATATTCTCCAGGAGAGGTGAGCTGGGC Y 2 1 2 1 101000 f 74 goat snp288-scaffold1007-976095 5 73525258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790107 Affx-122926951 AX-385277113 5 72450908 AAGAAATCATTTATAAATGAGTTTGTTAGATAATG[A/C]TGATGAATGTAGTTTCTGGTTCCCTGAGCTGTTCT M 2 1 2 1 101000 r 74 goat snp287-scaffold1007-898943 5 73602918 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788853 Affx-122947458 AX-385275868 5 72499036 GGAAACATGAGTGACGGTCTGCTTTTTGTCCACCT[C/T]CTCCATGAAACTCTGAACTTCTTTATTTTTTTTTT Y 2 1 2 1 101000 r 74 goat snp286-scaffold1007-850815 5 73650829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395448 Affx-122963924 AX-123265803 5 72536421 CTGGTGAAACAACACCTCCTCCAAGAAGTCCTCTA[C/T]GCCCCTGAAGGGGTTCCCAGAGCCTAGCATCTTTA Y 2 1 2 1 201000 r 74 goat snp285-scaffold1007-813430 5 73688816 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425384 Affx-122941562 AX-123295730 5 72595640 TTGAAATTCATAGCCCAGGGCCTGCCTTTCTCCCA[A/G]TCCAGGTGAGACTGGTTTCCCTTTACCCTGTCCAC R 2 1 2 1 201000 r 74 goat snp284-scaffold1007-754211 5 73748022 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792209 Affx-122957472 AX-385279194 5 72628651 AGAGGGGGGAAAATCCTCTAAATAGACACAGGCCA[C/T]GCTTTCCTCTCTGTTCATCATCCAGGGTGTCTGTC Y 2 1 2 1 101000 f 74 goat snp283-scaffold1007-721200 5 73780967 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446878 Affx-122925236 AX-123317214 5 72684411 TTCTAGGCTGGGCTCTGCCTAAGCCAGCTGGGCCA[C/T]TGCATGCCTGGGACCCCAGACCACTGTCTGTAAAA Y 2 1 2 1 101000 r 74 goat snp282-scaffold1007-665440 5 73833602 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387211 Affx-122970594 AX-123257569 5 72719942 GGAAATTTACTGAGACCCTCCTCTGCCTTTGGTAC[A/C]TGGCTTGCCCATTCATTGCTGAAACCATCCATCAA M 2 1 2 1 201000 r 74 goat snp281-scaffold1007-629909 5 73869002 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416146 Affx-122948282 AX-123286495 5 72753659 GGCCAAATTATACAGTAGTGTTTGCAAACAAATGA[C/T]GATGGGACAGTGTGACTGAGCAATGGTAAAGAAGA Y 2 1 2 1 101000 f 74 goat snp280-scaffold1007-596192 5 73902741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772948 Affx-122957285 AX-385260092 5 72786485 CTGAGGCTCTATGGGATTAGGAGACTGAACCAAAG[C/T]GACTTAGTGGATGAGTGATGAAGTAAGATTTTGAC Y 2 1 2 1 101000 f 74 goat snp279-scaffold1007-563366 5 73935706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766862 Affx-122969732 AX-385254182 5 72816446 TCTCTTGCAAAATGTCTCTTTTGGCTCATGCTAAC[C/T]TGGATTTACGCAGTGGAGAAAATTCTAGGAAATAC Y 2 1 2 1 101000 f 74 goat snp278-scaffold1007-533405 5 73965943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411617 Affx-122951593 AX-123281967 5 72876171 AATCGTGGTGCACCTGTGAAATGGAGCAGGACCCC[C/T]TGGTCCTTGCCCACCCTCCACCCCACCACGTCCTC Y 2 1 2 1 303000 r 74 goat snp277-scaffold1007-473680 5 74025776 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767911 Affx-122945434 AX-385255129 5 73000764 CCCTTGGACACTTTCTCAAGATGATGGTTACCCTG[G/T]AGAACGGTCAGACTTCAAATGCCTGCTGGTTATAC K 2 1 2 1 101000 f 74 goat snp275-scaffold1007-349087 5 74150662 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408655 Affx-122953468 AX-123279006 5 73082246 TAGGGTATGGGTCTTGGGAGATGGGGTAAGGAGAG[A/G]GCAGCTGGCAGGGGCAGAAGAGATGAAGGAAAGAC R 2 1 2 1 101000 f 74 goat snp274-scaffold1007-267605 5 74222499 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442206 Affx-122928789 AX-123312543 5 73145738 ACTGTGCCAGGATTCCCAGGATTCACCTGAGCCTG[C/T]GGCCACCCAGGCAGAGGGAGACACAAACCTTTGCT Y 2 1 2 1 201000 r 74 goat snp273-scaffold1007-204113 5 74286253 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404247 Affx-122957065 AX-123274599 5 73181734 GAGTTGGTCTAGATTTTCAACCTAGAATTCTAAGC[A/G]CAGCTGGGCCATCAACAAGGGTAGGAGGAGAATGA R 2 1 2 1 102000 f 74 goat snp272-scaffold1007-168117 5 74322729 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762360 Affx-986696891 AX-385250522 5 73196909 GTGTCCTTGACATGCAGGTGCCTGAAACTCACTCA[A/G]ACTTAGCTGAGACAAATTGTCACGCTGGTGCCAGA R 2 1 2 1 600010 f 74 goat 5_73196909 5 73196909 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 38431867 Affx-122936067 AX-123302208 5 73216593 CCACGGGCCTTTTTGCTGCGCCTGAGAACACTTCG[A/C]GCTCCTCCTCACCTTTGCCCTCGGCAGGTCCCTCC M 2 1 2 1 101000 f 74 goat snp271-scaffold1007-133258 5 74357529 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436550 Affx-122932919 AX-123306888 5 73270801 ACTGTGAATACTTAAGATTGAGACAGAAGTAGGTA[C/T]TGAGTCCCCTTCGTAGGTCCTGGGGCTAGGGGGCC Y 2 1 2 1 101000 f 74 goat snp270-scaffold1007-79050 5 74410627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278252 Affx-1111836326 AX-519551740 5 73275819 ACAGACTCACGTAAAGCATCAGGATCCCAGTTATG[A/G]TTTAATACAGGGAAGGGTGCAGTTTCCCATCAGCC R 2 1 2 1 101000 f 74 goat Random2.2K-579 5 73275819 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433184 Affx-122935649 AX-123303525 5 73312198 TAAGCACTATCAGACCCTGCATTCTGATTCTTGCT[A/G]TTAGATTTCTGGTTACTTCTGATATATCTATGCAA R 2 1 2 1 201000 r 74 goat snp269-scaffold1007-37653 5 74452011 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392858 Affx-122965758 AX-123263215 5 73346815 GGGGATCCCAAGTGAGATGGGGACATGGCCTTGAC[C/T]TCACTGCACTTGGTTTCCCCATCTGTAAAGTGGAC Y 2 1 2 1 201000 f 74 goat snp268-scaffold1007-3036 5 74486262 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398820 Affx-122961397 AX-123269175 5 73357479 AGACAGCAGTGCTTGCTGTATGCACACACGTGCAC[A/G]CACACATGGACACAGATGGGGGAGAACACAGGCTC R 2 1 2 1 202000 f 74 goat snp182-scaffold1003-7529 5 74496878 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412366 Affx-122950819 AX-123282715 5 73406401 GGGGTAACATGCAACCCGCTCTCTCTGTCACACAC[A/G]CTCACGTGCAGACACACAGTCGGAGACAAAACACC R 2 1 2 1 101000 r 74 goat snp183-scaffold1003-56451 5 74545499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430688 Affx-122936920 AX-123301029 5 73438665 GGAGGGGCAGACTCGAGTCCACCCTGTGGGATCTT[A/G]GGTGTGCAAACCAACGCACAGGACTGAGAACGCAG R 2 1 2 1 102000 r 74 goat snp184-scaffold1003-88715 5 74577831 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405308 Affx-122956838 AX-123275660 5 73492213 CCTCTGATGCAGGTCCTCTCTTTAACCCCATTTTA[C/T]AGAGCCCAAAACTGAAGCCAAGGAAGTTAATAACT Y 2 1 2 1 202000 f 74 goat snp185-scaffold1003-142263 5 74631596 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418763 Affx-122946199 AX-123289111 5 73547896 AGGAGTGAAGGAAATTATAGGTTGGGCAGGGCCCC[A/G]GTATTTCTCAGATGAATTGGGACTCCTGGTTCTGG R 2 1 2 1 101000 r 74 goat snp186-scaffold1003-197946 5 74688334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426341 Affx-122940267 AX-123296687 5 73606754 GGACAGTGGACCCACTGCAAGAGGAACACGCTCAG[C/T]GAAACAAAAGCAAGACCCAGCTGTTTATTTGAGAC Y 2 1 2 1 101000 r 74 goat snp187-scaffold1003-256804 5 74747006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772254 Affx-122953828 AX-385259409 5 73638841 CCAAATTCACTCCTTATTTGAAACCCAGATAACCA[C/T]GATCCAACACTGAAAACAGTTCACAGTTGAAAAAT Y 2 1 2 1 101000 r 74 goat snp188-scaffold1003-288891 5 74779556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419443 Affx-122945501 AX-123289791 5 73673587 CTCACAAGATGATAGCTGGTTTCCTTTTAGCTTGA[C/T]GCAGCAAAAAAGTACAGATCTTCCTCAACTTACAG Y 2 1 2 1 101000 f 74 goat snp189-scaffold1003-323637 5 74814370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768114 Affx-122954908 AX-385255316 5 73727678 CTTTCTCTCCTCGTTAGAACTTAAACTCATTGGGC[A/G]TTATTTAAGCTTTGACTGGCATTGTGTACTTTAGC R 2 1 2 1 101000 f 74 goat snp190-scaffold1003-377728 5 74868285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446092 Affx-122925806 AX-123316429 5 73778806 AGAATGCAAGTTCTCAGAAAGCATAGTCTTTATCC[A/G]TCTTCTATCAAGTTTCTTGAATAAATGAATCAATG R 2 1 2 1 101000 f 74 goat snp191-scaffold1003-428856 5 74919688 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392036 Affx-122966467 AX-123262393 5 73814972 ACAAAAATGGAGCAAAACAAAATCTCAAACAATGA[C/T]GTGGGTATTTTTCTTCCTTTAAGTGAAAATATGTA Y 2 1 2 1 101000 f 74 goat snp192-scaffold1003-465022 5 74956848 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376192 Affx-122978821 AX-123246551 5 73846948 AGCAAACCTATGACTTCCAATGTCAGTACCCTTCC[A/G]CAGAGCATGTCAAGTGCTCCCACTGAAGTCTTTGA R 2 1 2 1 101000 r 74 goat snp193-scaffold1003-496998 5 74988699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274545 Affx-1111834357 AX-519548135 5 73860416 GTAGCTTATCTGCAGGAGCCTAGAGATGCTCTTCT[A/G]GAA R 2 1 2 1 101000 f 74 goat GoatD01.031751 5 73860416 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38440957 Affx-122928997 AX-123311294 5 73876003 GGGTTTTTATTTCATGGTCTCCATTGTGATTCTCT[A/C]TTAAGGAACAAACTAGATTATATTTCAAAGGAACA M 2 1 2 1 201000 r 74 goat snp194-scaffold1003-526053 5 75018424 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782453 Affx-122947934 AX-385269529 5 73882935 ATCCAGAAGAATACCTGGCAAATAGAAGAACTAAA[C/T]AGAAGTTATTGAACTGATAGATTAAGATCCTTAGT Y 2 1 2 1 101000 r 74 goat snp32385-scaffold368-1143239 5 75031756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392296 Affx-122967527 AX-123262653 5 73938048 CAGGCAGATCTTTACCAATTGAGCTACGAGGGAAC[C/T]AGTGAGCTACCAGGGAACCAGTACCTTTTGGCACC Y 2 1 2 1 103000 f 74 goat snp32384-scaffold368-1088126 5 75087691 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278414 Affx-1111836328 AX-519551899 5 73939655 ACACATCCACACTGAAAACTTGGCACAAAATTTAG[A/G]TATTCCCATATCTAGGCACTTTTCATGCATTTTTT R 2 1 2 1 101000 r 74 goat Random2.2K-581 5 73939655 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441356 Affx-122928874 AX-123311693 5 74002419 GTAACTATTAGCATTAAAGTGACATCCACTTTCTA[C/T]ATTCCCTGACAAAATGAAATATTGAGTGTAATCAC Y 2 1 2 1 101000 f 74 goat snp32383-scaffold368-1023755 5 75158434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787929 Affx-122966707 AX-385274951 5 74039859 ATTTGCAAAGAGTTGCCAAAAGATTTGCTTATTTG[C/T]ATTTTATCTTCAGGTTCTGCAGGTAAGCAAACAAA Y 2 1 2 1 101000 f 74 goat snp32382-scaffold368-986315 5 75196442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770786 Affx-122942000 AX-385257950 5 74105594 TTTTTTAGTTTCTAGACAAAGAAGCAATGAATTTG[C/T]GAAGACTGGACAGAACAAAGAAACTTAGTTTTGGA Y 2 1 2 1 102000 r 74 goat snp32381-scaffold368-920580 5 75263264 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787669 Affx-122938387 AX-385274692 5 74142156 ACTTCCTCTAGTAATAAAGCAATTACTAGAGTATT[A/G]CAAGAATGCAGTAATTAGTAAAACACCATTGCTGC R 2 1 2 1 101000 r 74 goat snp32380-scaffold368-884018 5 75300746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417447 Affx-122947201 AX-123287795 5 74189240 ACCACAAACCCTGTATGAAAGAGGTTAGGTGAACT[A/G]TAAGCATGGCTATACATGATAGAATGACCCTTAAA R 2 1 2 1 101000 f 74 goat snp32379-scaffold368-836934 5 75349132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433962 Affx-122934268 AX-123304303 5 74217770 GGTTGTTTGTCTTTCTGGTTTTGAGTTGTATGAGG[C/T]GCTTGCACATGCTGGAAATTAATCCTTTGTCTAAA Y 2 1 2 1 201000 r 74 goat snp32378-scaffold368-808404 5 75378752 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440263 Affx-122930650 AX-123310600 5 74260884 GTTGGAAGGTTCCTTTTCCTAAGGAAATAATTTTT[A/G]TTTCCTGGTGTAGCAATAGCCTGAAATGTCTCCTG R 2 1 2 1 101000 r 74 goat snp32377-scaffold368-765290 5 75422623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449902 Affx-122922334 AX-123320237 5 74320771 AATAGATCTAGAAATCTAAAAATATTTAATGGAAT[A/G]TTACTTTGGCTCAACATAAAAAGCACTTTTTAACT R 2 1 2 1 101000 r 74 goat snp32376-scaffold368-705403 5 75484660 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446202 Affx-122925719 AX-123316538 5 74367681 GAAGGTAGAATTAATGGGGTTGCCTTGTGTAAACT[A/G]CTGCTGTGTCTTTTAATTTCACAGGCTTGTGTCTT R 2 1 2 1 101000 f 74 goat snp32375-scaffold368-658493 5 75532950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430148 Affx-122937386 AX-123300489 5 74401011 TACCCAGGCACCCAAGGGGGAACTGTTACAATAAG[C/T]AAAGTAGTAGTATTTTCAAAGTAAATGTAATAAAT Y 2 1 2 1 101000 f 74 goat snp32374-scaffold368-625163 5 75565957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429528 Affx-122937841 AX-123299870 5 74438340 AGTTACTGCTCCTCAGGCTCACAAAGGCCTGTGAA[C/T]GGTGCCTATTCTCACCAGCCAGCCAGATAGACAAG Y 2 1 2 1 201000 r 74 goat snp32373-scaffold368-587834 5 75604300 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274825 Affx-1111834441 AX-519548410 5 74468970 AACTGCAGGCGGCCCATGCCCCGCAGCATGCCCTC[A/C]GTCAGGTTGCTGAGCTTGTTGTAGCCCAGCTGCAG M 2 1 2 1 202000 r 74 goat GoatD01.036021 5 74468970 A C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468272317 Affx-1111833476 AX-519546053 5 74484460 TGAGGCTTTGGAAAGAAGATGGGATACTGCACCCT[A/C]ACCTGTGCTCAGCGTGTCGGAGAGTCTCAGACTCT M 2 1 2 1 102000 f 74 goat 5_74484460_AF-PAKI 5 74484460 G T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38451337 Affx-122921268 AX-123321670 5 74525282 CTGAACCAGTGACTCTGGGCAAGCCAAAGGGAAAT[A/G]CCACATAATTGGGGCCTAGAAATTTTTAAAGGTTG R 2 1 2 1 201000 f 74 goat snp32371-scaffold368-500892 5 75691217 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795924 Affx-122932563 AX-385282876 5 74571360 TCTCACCTTCACTTTTCTGTCTTGCCATGGGCCTG[C/T]GAATTTTGAATCTTTGGCCCTTCGATCCAAGATAA Y 2 1 2 1 102000 f 74 goat snp32370-scaffold368-454814 5 75736491 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787041 Affx-122925265 AX-385274069 5 74618075 TGTGCCCCTGGGGGTTTCAAGCTATGACAAGTGAC[C/T]TTAACCACATTCTGTTCATAAGAAGAATTTTCGTA Y 2 1 2 1 101000 f 74 goat snp32369-scaffold368-408099 5 75783387 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796462 Affx-122946928 AX-385283412 5 74648493 TAAGACTTTGTCGATCTTTATCCATCACATTTGAG[C/T]ATGTGTATCTGATAACTCAGAAATTTCATTCCTTA Y 2 1 2 1 101000 f 74 goat snp32368-scaffold368-377681 5 75813731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771437 Affx-122955396 AX-385258595 5 74684671 GGGAATCTCAGAAACTTCTTTATGTTGTGGTGACT[A/G]TTTAGTATGTTGGAAAGTTCTAAGAAAGAAATGAG R 2 1 2 1 101000 f 74 goat snp32367-scaffold368-341503 5 75850053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449315 Affx-122922999 AX-123319650 5 74720956 AGCATTGAAGTGATATTTTAAAGAAAATTTCAGAG[C/T]GAATATATCTGAAAAGTTTAACAATGAGATTGGAA Y 2 1 2 1 201000 r 74 goat snp32366-scaffold368-305218 5 75886454 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764558 Affx-986696896 AX-385252213 5 74738693 GTACTGGGCACTCAGGAATGTAGAGGAATTCATGA[A/G]TCACTTGGTGCCCGCATCTGACATTTTCTGGGCTG R 2 1 2 1 600010 r 74 goat 5_74738693 5 74738693 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 38423664 Affx-122942338 AX-123294010 5 74861849 AGTATCGGAACTTAAAAATTTTTCTCTGTCCTTGC[C/T]TTGAAGCTGTAGTATTCACAGGGCAGAAAAACATG Y 2 1 2 1 101000 r 74 goat snp32364-scaffold368-164325 5 76025980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782263 Affx-122953326 AX-385269341 5 74909103 TGTCATATAACCATTAATTTCATAGTCACCTCTGA[A/G]CCAAAAAAGAAGTCATTGGTATACTCTCCATACCA R 2 1 2 1 101000 r 74 goat snp32363-scaffold368-117071 5 76073818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420028 Affx-122945150 AX-123290376 5 74942465 CATTTATTTAACTATTATTATTATTAACTGTTACT[A/G]TGGGTGATTAGCTCAAGGATTGTAATCTCACATGG R 2 1 2 1 103000 r 74 goat snp32362-scaffold368-83709 5 76107155 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422176 Affx-122943520 AX-123292522 5 74990610 TGGTGTAGATAGTTATCATTTATTTCTGTGTTTTA[C/T]GGCCTTGCTGTTTGCTGTTTTCTTCTCTTGACCCA Y 2 1 2 1 201000 f 74 goat snp32361-scaffold368-35564 5 76155531 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419432 Affx-122945509 AX-123289780 5 75021715 CGTGCGTGCACATGTGTGTGTGTGTGTATGTATCT[A/G]TAATTCCATGGCCAAATTCTTTTCTATATGTGGTA R 2 1 2 1 201000 r 74 goat snp32360-scaffold368-4459 5 76187227 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773392 Affx-122971361 AX-385260534 5 75034842 ATGGAATCATTCCATAGGCATTCTTTTGCAATTTG[C/T]TTTTTAAACTCAACTTTCAATTCCTAATATTCAAC Y 2 1 2 1 102000 f 74 goat snp2290-scaffold107-8569 5 76200730 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413862 Affx-122949860 AX-123284211 5 75087746 TTCTGGTTATGTATCCTCAGGCAAATTATTTACTA[C/T]GTTATAGCTCAGTTGGTAAAGAATCCGCCTGCAAT Y 2 1 2 1 201000 f 74 goat snp2291-scaffold107-61473 5 76254368 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795932 Affx-122943379 AX-385282884 5 75118309 TCATTTTCGGATTAATACACTCAGTAGAAACTTGG[C/T]ATATAACCGATGCTCTCTAAATAATAAATACATGA Y 2 1 2 1 101000 f 74 goat snp2292-scaffold107-92036 5 76285146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801444 Affx-122976277 AX-385288353 5 75155030 TAGCTTTTTGTCTTCTTTCTAAAGATTCTTAATAA[G/T]TACAAAGCACATGCTATAATAGCTCTCTCATCTGT K 2 1 2 1 201000 f 74 goat snp2293-scaffold107-128757 5 76321782 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383072 Affx-122973743 AX-123253430 5 75194884 TTCTGGAGCCAAGTTATTCAGATTCAACTCTCAGC[G/T]CTACCACTTAATAATTTTATGAAATTGGATCTAAG K 2 1 2 1 101000 f 74 goat snp2294-scaffold107-168611 5 76361961 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423843 Affx-122942781 AX-123294189 5 75224814 TTTCAAAGGAAAAAACAAAACAACGTCAGCAAAAC[A/G]CAATGAAACACAGTGCAATTAAATTGAATTCTTGT R 2 1 2 1 101000 r 74 goat snp2295-scaffold107-198541 5 76392253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380564 Affx-122975279 AX-123250922 5 75255749 TATATCCTTCCTTAATTGATCATTGTGTAAGGGAA[A/C]GCATTTAAGTTAATTTCTCTAGTGAACAAGAATAA M 2 1 2 1 101000 f 74 goat snp2296-scaffold107-229476 5 76423528 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430657 Affx-122936942 AX-123300998 5 75325365 CCTTTTGAGTGGATCAATATTTAACCATTTCTCTA[C/T]TGATGAATATTTGGTTTTCTTAGGTGTTTTTACTT Y 2 1 2 1 101000 f 74 goat snp2298-scaffold107-299092 5 76493705 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800301 Affx-122949715 AX-385287224 5 75365922 TGCTGCGTTTTGTTTGTACCACCATTTTCCTTCTT[A/G]TAAAAATAATAGGACTTTCTGTGTCTGATCCCTGG R 2 1 2 1 101000 f 74 goat snp2299-scaffold107-339649 5 76534498 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785259 Affx-122953280 AX-385272304 5 75406020 GCAGTACCCAGAACACATCAGGCTCCTAATAAATT[A/G]CATTGATTATCACTAAACATTTTCCTCTGGGAGAG R 2 1 2 1 201000 r 74 goat snp2300-scaffold107-379747 5 76575529 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426824 Affx-122940515 AX-123297169 5 75435047 TCCAAGAACCTTGAGTCATCACTCTTTAGGGTTTA[C/T]GTATGTTGGAGAAGCAGGAGTCCTTCTGCCTTATG Y 2 1 2 1 101000 f 74 goat snp2301-scaffold107-408774 5 76605256 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417537 Affx-122946930 AX-123287885 5 75477983 TTTCATTCACTCATTTCCAGTCTTTCATTATGGTT[C/T]TGTCCCCTCCACTTATAGTAGATTGGGGTGGTTAT Y 2 1 2 1 101000 r 74 goat snp2302-scaffold107-451710 5 76649018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787975 Affx-122927324 AX-385274996 5 75524454 TCTCCCTGACTGTCGCAGATGCAGACTGTTTTCTG[C/T]AAATGCAATTTTTCCATGTGATACATAGGTTGCTA Y 2 1 2 1 101000 f 74 goat snp2303-scaffold107-498181 5 76695775 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410962 Affx-122952025 AX-123281312 5 75570305 AAGGAATCAGATAAGGAGAGAAAGAAAAATGTTTC[A/G]TTTTTGTTTATAGAAGTATACCAAATTGTAGGTTT R 2 1 2 1 303000 r 74 goat snp2304-scaffold107-544032 5 76741999 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451187 Affx-122921334 AX-123321521 5 75606859 CATTGACTTCATATTTTGATAGTTAAATAATTGCA[A/G]TATAATTTGGCACCCTCTCCTCAATTGTTTTAAGT R 2 1 2 1 101000 r 74 goat snp2305-scaffold107-580586 5 76779010 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789617 Affx-122920743 AX-385276626 5 75641694 TTCAAATGAAATGTATTACTATCTATAATCACAAA[A/C]TTCTCTGAAATATACCATGCTTAAACTACCCCCAA M 2 1 2 1 101000 r 74 goat snp2306-scaffold107-615421 5 76814166 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397595 Affx-122961990 AX-123267950 5 75707106 GTAAAGTTTTCAAATTCCTGACACATATTAATCTT[C/T]GGGATTTAGGAACGAGATACCAGAATTCCCAAGAA Y 2 1 2 1 101000 r 74 goat snp2307-scaffold107-680833 5 76880666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400500 Affx-122961281 AX-123270855 5 75758911 TTTATTTCTGTGCCCCTGTGAACCAACCTTGTTGA[A/G]TAGATCAGGTGACAGCTTTTATCTGAAAGTCAGTC R 2 1 2 1 101000 r 74 goat snp2308-scaffold107-732638 5 76932574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401437 Affx-122958989 AX-123271790 5 75837303 GAAGGGGTTCAGTGTCTTTGTTGTCTTCCACTGTG[C/T]GCGGACTTTCTTTGGATTGATTGGCGGTGAGGTAA Y 2 1 2 1 101000 f 74 goat snp2309-scaffold107-811030 5 77011426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789869 Affx-122943824 AX-385276876 5 75893352 AATGCCTTCTGTACACATCTCTTAATTCTGCAAAC[A/G]CAAACACTGGCTGGGAAGCATTGATCTCACATACG R 2 1 2 1 101000 r 74 goat snp2310-scaffold107-867079 5 77067395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400658 Affx-122960353 AX-123271013 5 75925245 CTTCCTTCTTCTCAGTTCCACTTAATGACATCATA[A/C]CCCTCTTCTCAGTCAGGCAAGCCAGAAAGTCATCC M 2 1 2 1 201000 f 74 goat snp2311-scaffold107-898972 5 77099586 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401545 Affx-122958907 AX-123271898 5 75974556 ATCTAGACAAACCCAACAAGCACTAGCATAAAGAA[C/T]TGCAGGCATACAATTGCAGTCACAGTTATACATTC Y 2 1 2 1 101000 f 74 goat snp2312-scaffold107-948283 5 77148891 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442853 Affx-122927680 AX-123313190 5 76030122 GATATTCTAAATTATTTATAAGGTGTATGTTTACT[A/G]CCAGCTGCCTTTTGTTGCAACCAGCCCTGGAGTTC R 2 1 2 1 201000 f 74 goat snp2313-scaffold107-1003849 5 77204473 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792712 Affx-122975085 AX-385279692 5 76077394 TTTGCTACTTCCCAGACAATATGAGAACTTTGACC[A/G]TTTGTACTCCATTTACCTTCCTTCAGCCTTTAAAC R 2 1 2 1 101000 f 74 goat snp2314-scaffold107-1051121 5 77253141 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449385 Affx-122922714 AX-123319720 5 76107703 GGTCCTGTGAGATTTCTCATTAATTCTGGGCCTTA[C/T]GAAAACAGCAGTAGGGAGCCATTCAAAGATTTTAA Y 2 1 2 1 101000 r 74 goat snp2315-scaffold107-1081430 5 77283449 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406487 Affx-122955162 AX-123276839 5 76147776 CAGTAAATGCTGATGTAAAGATCCAGATCATTCCT[C/T]ATTTCCTGAGTCATGTAGCCTGTGAAATGATACTG Y 2 1 2 1 101000 f 74 goat snp2316-scaffold107-1121503 5 77323953 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799493 Affx-122942721 AX-385286423 5 76264815 TTGCCCTGCATTTACTATCTTCTAGTTATTTACAG[C/T]ATTGGTCTGTCTGGAACAGACTGGCCCTGAAAATA Y 2 1 2 1 101000 r 74 goat snp2319-scaffold107-1238542 5 77440566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273915 Affx-1111833929 AX-519547522 5 76278976 CCAAGCAGCCATTGCAAAACAGCACTGGTGCAGCT[A/G]TTGTCATCAGGATTTTAATTCTGCAGTATCAG R 2 1 2 1 101000 f 74 goat GoatD01.010794 5 76278976 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38428437 Affx-122938819 AX-123298780 5 76329631 TGGAGTGATCTCCTAGAGGGGCAGGAATGAGTGGT[A/C]TCTTTCTCTACAGGCTTCTTATGGGGAGACTCTAA M 2 1 2 1 201000 f 74 goat snp2320-scaffold107-1303358 5 77506297 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766015 Affx-122929482 AX-385253434 5 76358748 GATGTTACCTTATCTTGTATACCTGGTATCACTAA[C/T]TTTAGCAACACACGATCCTATAAGATGTGCTTTAA Y 2 1 2 1 101000 f 74 goat snp2321-scaffold107-1332475 5 77536378 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428878 Affx-122938337 AX-123299220 5 76393810 TGGGGAGGTTGATCCTTGTTTGAAAGTGATGATAA[C/T]AGGAGGTTGATAAGACCTGCCCAGGATGGCTGCCA Y 2 1 2 1 101000 f 74 goat snp2322-scaffold107-1367537 5 77571168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453171 Affx-122920469 AX-123323504 5 76457377 AAGCTGCAAGTCAATATTTTTAATGTTACATTTTT[A/G]TTGGTGAAGACACTTGCCAGCAGCTGCTCCTTGGC R 2 1 2 1 101000 r 74 goat snp2323-scaffold107-1431104 5 77634691 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379095 Affx-122976764 AX-123249454 5 76503527 ATTATTGATTATCACCTAGAAGATGGTGCCTTTGC[G/T]CTGTAATATGAAATCAATAAGGAAAATAAACCTAA K 2 1 2 1 101000 f 74 goat snp2324-scaffold107-1477254 5 77681891 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409453 Affx-122954081 AX-123279804 5 76582877 TCTTGGGATGCTCCCTTAGTGGGTTGTGTGGACCA[G/T]CCATTTGTGGTGGAGCTGGCTACTACAATGGATAT K 2 1 2 1 201000 r 74 goat snp2326-scaffold107-1556604 5 77762147 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391474 Affx-122966720 AX-123261831 5 76645076 CTGACATTTAAAGCAAGGTAACATGCTGCCAATGA[C/T]ACTCTATGAGAAATTCTTGTTTATAGTAGAAGCAT Y 2 1 2 1 101000 f 74 goat snp2328-scaffold107-1618803 5 77821879 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380051 Affx-122975571 AX-123250409 5 76744273 GACACTTGATTACATTGTGATAATTGCAGGATGAG[A/G]GCTGTAACAGGACACCTGACTGATAGGGGTTAATA R 2 1 2 1 201000 f 74 goat snp2330-scaffold107-1718000 5 77922470 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797460 Affx-122973249 AX-385284399 5 76793933 CCTAAATCTCACAGTCTTGTACATGTGGTTTAGGG[C/T]TCCATTTCCCTGTAATCCTCATTCCTATATTCACT Y 2 1 2 1 101000 f 74 goat snp2331-scaffold107-1767660 5 77972547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766773 Affx-122945047 AX-385254107 5 76841966 GCCCCACATAAGCTATGAAATGATATACAAATACA[C/T]AATGGGTCTATTTAAATATTCTAGCAAATTAAATG Y 2 1 2 1 101000 f 74 goat snp2332-scaffold107-1815693 5 78021024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770621 Affx-122960844 AX-385257785 5 76877851 TTTTCTATGATGTCGTTTTCCATGGGGCATTTGCC[A/G]TGAGCTTGGTGTCTTCGTTTTCATGTTCACCATTG R 2 1 2 1 101000 f 74 goat snp2333-scaffold107-1851578 5 78056753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450425 Affx-122922054 AX-123320759 5 76935201 CAGAATACCCTGGCATAATCCTTTGTGTTGGAGAA[C/T]ATACAAAATTTCAGATCCCAGCCATTTTCAAATGA Y 2 1 2 1 101000 f 74 goat snp2334-scaffold107-1908928 5 78115600 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404817 Affx-122956648 AX-123275169 5 76983459 GATCTCAAGATAGAACACAAAATAAAGGGGACATA[C/T]GACACAAAAAGTGAATGCCATTATTATTTGATTGA Y 2 1 2 1 101000 f 74 goat snp2335-scaffold107-1957186 5 78164947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778584 Affx-122958357 AX-385265695 5 77049481 AAGCATCAGCAAATTAGTCCTTAGTCACACAAAGT[A/G]CTGTACTCCAAGACATGCTATTATAGTCTATGATT R 2 1 2 1 101000 f 74 goat snp2336-scaffold107-2023208 5 78231579 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423746 Affx-122942855 AX-123294092 5 77078215 ACCTAAGAGAACACGAGGAACTGAGTTTCTCCTGT[A/G]CTTAGGTAGGGGCTGAGGCTAAGACAGTGATTCCA R 2 1 2 1 303000 r 74 goat snp2337-scaffold107-2051942 5 78260269 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793662 Affx-122961924 AX-385280635 5 77113642 AGCAGGTGAACTTCACTTAAGACTCAGCAATAGAA[C/T]TGATAGTTTTGAAACTCTTGGTGAAGAATTAAATA Y 2 1 2 1 101000 f 74 goat snp2338-scaffold107-2087369 5 78295741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393337 Affx-122965940 AX-123263693 5 77169156 TCCTGAAGACATGGAAGGCTCGTGCTTAGGACCCT[C/T]TCAGACTTGGCCCCATGGATCTTTTTTTTTCTATC Y 2 1 2 1 101000 r 74 goat snp2339-scaffold107-2142883 5 78352550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788178 Affx-122927102 AX-385275197 5 77218543 GACTCAGTTTAGTTCTGGGTTTTAATGAGAATATG[A/G]TGGATATTTTATTGGTTGCTTAACAATTAGATACT R 2 1 2 1 101000 f 74 goat snp2340-scaffold107-2192270 5 78402222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278258 Affx-1111836329 AX-519551746 5 77227212 AATTTAACTGCAGAAAACACTAAGGCTTGGCTTTC[A/G]GTTCTTCAAAAGGATTTAAGTTATCTTGTCAAAGG R 2 1 2 1 101000 f 74 goat Random2.2K-584 5 77227212 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452726 Affx-122920286 AX-123323059 5 77250755 GTACTATCAGCAACACCGTCCCCTCAAGATCTTCC[A/G]TTCCTGTTAAGCTTCATTTTCCTTCACTTCTTCTC R 2 1 2 1 101000 f 74 goat snp2341-scaffold107-2224482 5 78434462 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272318 Affx-1111833477 AX-519546054 5 77261845 TTACTAATCTACTGCTACATAACAAAGTACCCCAA[A/C]AAAAAATAAAAAATAAAATAAAAAAAACAAAGTAC M 2 1 2 1 102000 f 74 goat 5_77261845_AF-PAKI 5 77261845 T G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435739 Affx-122933286 AX-123306078 5 77288117 TATAAAAGCTGACAGTATCCCTGACCTTCCTCCTC[A/G]CCCGCTCTCTCTTGGGGGCTAAAGGAGACTAAAGT R 2 1 2 1 101000 f 74 goat snp2342-scaffold107-2261844 5 78473612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777013 Affx-122961698 AX-385264136 5 77323010 GAATATACGTATAAAATGGGTGGATTCTATTGTAT[A/G]TGAATTGTATCAATAAAGCTATGTTAAAAAAAATA R 2 1 2 1 101000 f 74 goat snp2343-scaffold107-2296737 5 78507446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780216 Affx-122921889 AX-385267313 5 77368015 ACAAACAACTTCGCTTTGTTGATCAAAGCCTTGTC[A/G]TGGCAAAGGGGCATGCGTAACTCAGCAAAGCTATG R 2 1 2 1 202000 r 74 goat snp2344-scaffold107-2341742 5 78552857 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768833 Affx-122978799 AX-385256010 5 77425871 GGAAGAGCACTGGTGCTTGACTCAGAGTCATAGTT[A/C]TATGAACATGATGAGTCGCTTAACTTTTCTGAATC M 2 1 2 1 101000 f 74 goat snp2345-scaffold107-2399598 5 78611222 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792192 Affx-122928228 AX-385279177 5 77478886 ACTGTCTTGGAATCTGGGTTCTTCTCTAGAATTAG[C/T]AGTTGGAGAAATTCAACAGTTGGTGGACACCCATG Y 2 1 2 1 101000 r 74 goat snp2346-scaffold107-2452613 5 78664753 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427106 Affx-122939671 AX-123297449 5 77521009 CCAACATTGGTGTTAGTGTCTCTCTTAGTTCTTCC[A/G]CACTGTCAGTGTCTGTTTGCTAATAGGATTATATT R 2 1 2 1 202000 r 74 goat snp2347-scaffold107-2494736 5 78707358 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402325 Affx-122959075 AX-123272678 5 77570128 TAAACTGCAATCAACTGTGTACATTAATATAGTCT[A/G]TAAAAGTTATGTAGCCAAATTTTAAAAAATAGAGA R 2 1 2 1 101000 f 74 goat snp2348-scaffold107-2543855 5 78756383 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448946 Affx-122923142 AX-123319281 5 77598780 TAAACTAGGCATGCATTTATACTTCTGTAAATACC[A/G]TTGCTTATCTGTAGAACTGACGCTGTCCATTTTAT R 2 1 2 1 101000 r 74 goat snp2349-scaffold107-2572507 5 78785505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278419 Affx-1111836330 AX-519551904 5 77625832 GTATCTTTGAGATCTACATAACTGAAACCCCCACC[A/C]AATGGAAGATGTTCCAGCAAAAAGGTTACAGTTCA M 2 1 2 1 201000 r 74 goat Random2.2K-585 5 77625832 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408060 Affx-122954270 AX-123278411 5 77636759 AGTCCTGGTGAAAGAGTGAACTTCCCCACAGAAAA[C/T]ATGACTAGCATTTACATTTTTTGTTGGCAATTTTG Y 2 1 2 1 101000 f 74 goat snp2350-scaffold107-2610486 5 78823415 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789724 Affx-122927567 AX-385276732 5 77684177 ACTGTTTCCCTCCAAAGTCTAAGCAAATAGAGGAA[G/T]ATTAGATTTCATATGGAGTATTTTCAACTTTTAGT K 2 1 2 1 201000 r 74 goat snp2351-scaffold107-2657904 5 78871158 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773560 Affx-122977562 AX-385260700 5 77740956 AATTAACTTTCTGGACAATCTTAATCAGCATTAAC[A/G]TTCAGCGAAAGATCTTAAGTGTACTTGTTAAAATA R 2 1 2 1 101000 f 74 goat snp2352-scaffold107-2714683 5 78928702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425195 Affx-122941036 AX-123295541 5 77801962 ATAGATATAGTAAAATAGGCAGGAGCCAAAATTGG[C/T]CCTCGAGTCACTGTTTGCAGACCCCTTGGCTAGAG Y 2 1 2 1 101000 f 74 goat snp2353-scaffold107-2775689 5 78989634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435580 Affx-122933366 AX-123305920 5 77836051 GGCTACAGTTTGCTAATTCAACTTTTAAAGTATTG[C/T]ATTAAAATATTATTTCTATTGATTATTGAGTATTT Y 2 1 2 1 101000 f 74 goat snp2354-scaffold107-2809778 5 79024630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777227 Affx-122976788 AX-385264350 5 77886180 GCTTGCTCCAAGCATGTATGTAAAGTCAGGATATG[C/T]GACTTCAGTCATTCGTTTCCAAGAGGTCTCCAATT Y 2 1 2 1 201000 r 74 goat snp2355-scaffold107-2859907 5 79076399 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432353 Affx-122936273 AX-123302694 5 77946541 TGTTGTTCTAGCCTTCCAAATCCAGCTAAAGATAC[A/C]CATTTTTAGAAAGGCTTGTTTGAGCCCTCACCTTC M 2 1 2 1 101000 f 74 goat snp2356-scaffold107-2920268 5 79137217 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397104 Affx-122962698 AX-123267459 5 78048101 TCTAGCATATTAGCATTGTACCACAGGCCAGGTAT[A/G]CACAGATCAATTTATTCTGTGACTTCTGTAAACTT R 2 1 2 1 101000 f 74 goat snp2358-scaffold107-3021828 5 79240366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768526 Affx-122924140 AX-385255706 5 78081180 AAGTTTCATTTCGAAGGAAAGGAGCAGTTTTTGTA[C/T]GTACTGGTTGAATGTTATCCTGACTTACAATACAA Y 2 1 2 1 201000 r 74 goat snp2359-scaffold107-3054907 5 79273196 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773844 Affx-122931130 AX-385260984 5 78118187 GTGAAGACGTGTACTCGTGCCCAGCAGATAGAGAA[C/T]TGGTGACTCTGCAATTAAATGAGAGAAATGATACA Y 2 1 2 1 101000 f 74 goat snp2360-scaffold107-3091914 5 79313143 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785969 Affx-122938057 AX-385273005 5 78152318 TTCAGTGTTACTGTAGGGAATATTATTAACCTAGT[A/G]CAGGAATTAAAGCATGATTGTCACATAGTCATCTA R 2 1 2 1 101000 r 74 goat snp2361-scaffold107-3126045 5 79347750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418099 Affx-122947137 AX-123288447 5 78185504 CATGTGAGGATACAGCAAGAAGACAGCTCTCTACA[A/G]TCCAGGAAGAGACAGAAAGAGAGCTCTTACCAATG R 2 1 2 1 101000 f 74 goat snp2362-scaffold107-3159231 5 79381500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792996 Affx-122963177 AX-385279974 5 78250515 ATGCCTTATATATGCTATCAGCAAAATGGCAATTC[C/T]TCAGTTTTTGACCTCCCAAGGGCAAGAATTTAGTC Y 2 1 2 1 101000 r 74 goat snp2364-scaffold107-3224242 5 79445952 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278262 Affx-1111836331 AX-519551750 5 78267410 AGATAGGTCAGAGAGACTGGGATGAAAAAAAGTCA[A/G]CATGCTGACTCTGAAGTGTAGGACCTCACGCAGGG R 2 1 2 1 101000 f 74 goat Random2.2K-588 5 78267410 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386160 Affx-122971390 AX-123256518 5 78338680 ATGTCCAGACTGCAGGACACAGAGCAAAAAAGCAA[C/T]TGCAAACAGGATCTCAGGAAGCAAAGTATCAAAGC Y 2 1 2 1 201000 r 74 goat snp2366-scaffold107-3312407 5 79535357 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379997 Affx-122975611 AX-123250355 5 78394649 TGAGCTCTCTGTGTCATGAAAAGAAAAATAATAAA[G/T]CTGATGTGACTTTCAATAAAAGTGTAGCTCAGTAG K 2 1 2 1 101000 r 74 goat snp2367-scaffold107-3368376 5 79592913 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801806 Affx-122974796 AX-385288714 5 78450639 CCAAATATTTATCTGAGTGAACCATTCTTGGAACA[C/T]GCCAGGTACATGTGCATATTTTGAGAATATCAAGA Y 2 1 2 1 101000 r 74 goat snp2368-scaffold107-3424366 5 79649158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776501 Affx-122944399 AX-385263628 5 78487795 TTACTAAAAAGAATAACCTGCTTCATATCAATATA[C/T]GATAGTTCCTACAACTGTGCTTTTCCAACATCCCA Y 2 1 2 1 101000 r 74 goat snp2369-scaffold107-3461522 5 79686555 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771145 Affx-122947063 AX-385258305 5 78544457 CTTTCCAAAAAATTAGGTTTTGTATTCAAATGGTA[G/T]AGGAATAAAATATGGTGTTATAGCTTGGAGAGAAA K 2 1 2 1 101000 r 74 goat snp2370-scaffold107-3518184 5 79743593 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774725 Affx-122920340 AX-385261859 5 78585453 CTCCTAATTCAGACAATTTCCAGAACATCTGAAAA[A/G]AGCTACAGATTTAGGAAAATTTTACAACAAAAGTA R 2 1 2 1 202000 r 74 goat snp2371-scaffold107-3559180 5 79784623 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413028 Affx-122950996 AX-123283377 5 78621045 GCAACAAAGTTATTTCATATGCCAAATGTCCCCAT[A/G]GATGAGTAAAAAGCAGACATTAAAATTCTTATAAA R 2 1 2 1 103000 f 74 goat snp2372-scaffold107-3594772 5 79820490 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450648 Affx-122921978 AX-123320982 5 78688926 ATCAGTTTACAACTAGGCAAATCCAGAGTCACAAC[C/T]AAGATCATCTTACCAAGAGCAGAAGCTATTGGATA Y 2 1 2 1 101000 f 74 goat snp2373-scaffold107-3662653 5 79888527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441534 Affx-122928709 AX-123311871 5 78736279 GGCCTGACTACCCAGGCAGGCAGAAGTTAAGCAAC[A/G]TCTATAATCTTTAAGTTCAACCCTTGGGGAAAATG R 2 1 2 1 101000 r 74 goat snp2374-scaffold107-3710006 5 79936627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388934 Affx-122968825 AX-123259292 5 78765404 TGTCAAACCCAAAACCATCGTAAGAATGGGAAGAT[G/T]CAGGAAAATACCCTCACCTTAAATAAAGCTACAGA K 2 1 2 1 101000 f 74 goat snp2375-scaffold107-3739131 5 79966180 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420919 Affx-122944595 AX-123291266 5 78805627 GATAAAAAGGGGAAGGGTGCTTTTATAAAGTATTT[A/G]TAATTTTGTTATTATTTAAACTGTTTTATAAAATC R 2 1 2 1 103000 f 74 goat snp2376-scaffold107-3779354 5 80006568 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452071 Affx-122920870 AX-123322404 5 78869844 GCTGGTCCAACTCCCATTATTCCTTCTAAAGAGTC[A/G]GCTTGTGAAAGACAGTTTAGTTGCTTCCTATATAA R 2 1 2 1 101000 f 74 goat snp2377-scaffold107-3843571 5 80071332 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432017 Affx-122935921 AX-123302358 5 78942284 TACACACCACCGGAGTGTCTATTATTTCTGTACTA[C/T]GGATGCTTCAAAATAAAACGATGATAAAGGTTGGA Y 2 1 2 1 101000 f 74 goat snp2378-scaffold107-3916011 5 80140224 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438629 Affx-122930917 AX-123308966 5 78986373 AGGAGTCTTCCATATAAAATCTTCTCTCTTAACCT[A/G]CATTAAGATACATGGCCCCTTCATGGAACCACAGT R 2 1 2 1 101000 f 74 goat snp2379-scaffold107-3960100 5 80184561 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450510 Affx-122922504 AX-123320844 5 79070645 AAAGTCTGTTTTTTCATGGGGTAGCTATTTAGAAG[A/G]GAGGGAGGGTTGAGCGTGAGATGACAGGACTTTGC R 2 1 2 1 101000 f 74 goat snp2381-scaffold107-4044372 5 80268366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390269 Affx-122967745 AX-123260626 5 79121352 TAGAGTCAACACAGCCCTCCTTGGGCGATGCAGCC[G/T]CCTCCGGCTCAAACATGCGTAACTTTTTCAGTGCA K 2 1 2 1 101000 r 74 goat snp2382-scaffold107-4095079 5 80319219 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777319 Affx-122976737 AX-385264441 5 79206910 AGCCCTGTAGAAAGATGAGACTCTTCATGATGAGC[A/G]CTTCTCTAGAGCACTAGTGATAATGATTAATTTCA R 2 1 2 1 101000 f 74 goat snp2384-scaffold107-4180637 5 80404683 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774449 Affx-122966436 AX-385261585 5 79257026 ATGCATTGGTTTAATCACATTCAGTGTATTTTTAG[A/C]TATGATCCTAATTGTACATATTTATAACTAATTCA M 2 1 2 1 101000 r 74 goat snp2385-scaffold107-4230753 5 80455454 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384833 Affx-122971972 AX-123255191 5 79336570 AAATATTGATACAAGCACACCTTGCAAGTCGAATT[A/G]TTTCCAAACCTGGACAACAAGTTCAAATCTGCATA R 2 1 2 1 101000 f 74 goat snp2386-scaffold107-4310297 5 80535292 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394793 Affx-122964819 AX-123265148 5 79378073 CCAGGAAGCCCAAGACTGGTACAATCAATGGCAAA[C/T]TGCAAATTGCTCCTCTCCTCAGCCTATGCTTTGCA Y 2 1 2 1 101000 f 74 goat snp2387-scaffold107-4351800 5 80576979 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404681 Affx-122957279 AX-123275033 5 79420491 TTGCCTTCATCATAGGCAGAGTCTTCAGTACAACA[C/T]TGGCACTGGTGAGGGCATGAGGCTAAACTAGAATC Y 2 1 2 1 101000 f 74 goat snp2388-scaffold107-4394218 5 80619433 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391991 Affx-122966503 AX-123262348 5 79524532 TCAAGCACTGCTGAGACCTGAGCATTAATTATGAG[C/T]AAAGCGTTTAAAAGAGTGCCTGGCACACGTAAGCG Y 2 1 2 1 101000 f 74 goat snp2390-scaffold107-4498259 5 80723549 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447843 Affx-122923900 AX-123318179 5 79566166 TTCTCTCTATGCTCTTCAAGGCAAAACTCCAGATC[A/G]CGAATCTTCTCTCCCTGAGCCTCTACCTGGTCTGT R 2 1 2 1 101000 f 74 goat snp2391-scaffold107-4539893 5 80765343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449102 Affx-122923588 AX-123319437 5 79596033 CTCAAGTGATGGACATCAAATGCTTGCAGCACAAA[C/T]GCTCATGCCCAGGGGCCCCTCAAACATGCACACTG Y 2 1 2 1 101000 f 74 goat snp2392-scaffold107-4569760 5 80795244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418796 Affx-122946177 AX-123289144 5 79632075 AGGGGCAAATCACTTTTCCAAACTTCAAGAACATA[A/C]CATGAAAATGCTCAAAGGGAGCAAGGGGTCCAAGG M 2 1 2 1 201000 f 74 goat snp2393-scaffold107-4605802 5 80831322 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402757 Affx-122958322 AX-123273110 5 79664375 ACTAAGACACAGATTAAGCAAAGTACCTAATTTAG[C/T]AAACAGCCAAGTCAGGATTCTAGTCTTAATCCCTC Y 2 1 2 1 201000 f 74 goat snp2394-scaffold107-4638102 5 80863542 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393222 Affx-122965489 AX-123263579 5 79734410 TCATGATGCCCTACCCCTTATTTTAAACTTTGACC[A/G]TCTCGCCCTTGTTGTTGCTGTTGTTCAGTTACTCA R 2 1 2 1 101000 f 74 goat snp2395-scaffold107-4708137 5 80932600 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272319 Affx-1111833478 AX-519546055 5 79768238 TTTATTGACTATGCCAAAGCCTTTTGACTCTGTGG[A/C]TCACAATAAACTGTGGAAAATTCTGTAAGAGATGG M 2 1 2 1 303000 f 74 goat 5_79768238_AF-PAKI 5 79768238 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406644 Affx-122955817 AX-123276996 5 79797072 TAACATCCACTTATGATGAGTCCACAAGTGGTTCA[A/G]TGAAAACTAGGCAACAGAAGAAACAGAGGTTGGGT R 2 1 2 1 101000 f 74 goat snp2397-scaffold107-4770799 5 80995815 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788315 Affx-122930950 AX-385275333 5 79951065 AATAGCTTATTAAATCAGATATATATTCCATTCAG[C/T]AAAGGTTGATAAGAAATTTCCTATTCTCAGATAGC Y 2 1 2 1 101000 r 74 goat snp2400-scaffold107-4924792 5 81150661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798773 Affx-122930136 AX-385285704 5 79983932 GTTATACTGCAAATATATTCCTCTAATGGATTTCA[C/T]ACTGCTCTTTGTCTTTTATTTACTAAAGCCCTTTC Y 2 1 2 1 101000 r 74 goat snp2401-scaffold107-4957659 5 81183408 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777544 Affx-122966307 AX-385264663 5 80033149 GGAAAATGTGGTCAACAAAAATGGATTGGCTGGTC[A/G]TGTTGCCTAACTAGTTAGTAACTCAGTGTTCTTTG R 2 1 2 1 101000 f 74 goat snp2402-scaffold107-5006876 5 81232813 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797260 Affx-122957258 AX-385284199 5 80088168 AGATTTTTAATTGCCTAAACTCACACACTGACAAG[A/G]TTGGAAGACATGTATACTTCATGCTTTTTCTATTG R 2 1 2 1 101000 f 74 goat snp2403-scaffold107-5061895 5 81286791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785120 Affx-122943726 AX-385272166 5 80152345 TGTACATAAAAGATAATTCACCATCCAGAAGAAGC[A/G]CTCAAGGAACGTCCTCTGTGGTCATCACTAGGACT R 2 1 2 1 101000 r 74 goat snp2404-scaffold107-5126072 5 81352549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445980 Affx-122925886 AX-123316317 5 80183239 TTTTTATGAGTAGTGATTGAATGCAGTTTCTGCCA[A/G]GCAGGGTTGTTAAAGTTGTCTTGACTTTCAGTGTG R 2 1 2 1 101000 r 74 goat snp2405-scaffold107-5156966 5 81383754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430884 Affx-122936878 AX-123301225 5 80224646 TGCCACTGTGTTTGTAGTTTTGGGGATTTGGTATC[A/G]CACCTTTGAACTTCAGAGTACAAAGTGGGGAGAAC R 2 1 2 1 201000 f 74 goat snp2406-scaffold107-5198373 5 81424743 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786370 Affx-122971852 AX-385273404 5 80264804 CTCTTCTTACATGTGCTTCATATTTATTAACTCCT[A/G]TGACTCTCACAACAGTCCTATGCGGTAATTACTGT R 2 1 2 1 101000 r 74 goat snp2407-scaffold107-5238531 5 81465117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794968 Affx-122962134 AX-385281928 5 80293541 TTTCTCTGGTCTTTGCCTATTGTGTCTTTCTGCCA[C/T]ACTGGGCTGGCTATGTATTCTTACTGTGCTGCTGT Y 2 1 2 1 101000 f 74 goat snp2408-scaffold107-5267268 5 81494484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376311 Affx-122978361 AX-123246670 5 80337774 TCCCACATGGAGTTTTTCAGCCAAAACTGTACTAC[A/G]TCACAACACAGCATAGAAAACAGCCTTCCAGGAAC R 2 1 2 1 201000 f 74 goat snp2409-scaffold107-5311501 5 81535871 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381512 Affx-122974862 AX-123251870 5 80379363 TTGCACAGTTTGGCACACACCTCTTTGTCCGCCCC[G/T]GGTCCCTTCACCTTTCAGCAAACCTTGCTCTGGGG K 2 1 2 1 201000 r 74 goat snp2410-scaffold107-5353090 5 81577577 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786135 Affx-122924469 AX-385273171 5 80408985 AGAATAATTGTGTCACCTTATATGTACACAGTGTA[C/T]AAGAATTGGTTATTATGATGGAGATAGGTGTTAAG Y 2 1 2 1 101000 r 74 goat snp2411-scaffold107-5382712 5 81607166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436111 Affx-122932661 AX-123306450 5 80453004 GACCTGTAGAGGTCTTTGATTTAGTAAATGCACTG[C/T]GTGCTGAAGAATGGCACTTTATTCTTCCAGAGAGT Y 2 1 2 1 101000 f 74 goat snp2412-scaffold107-5426731 5 81651160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436736 Affx-122932299 AX-123307074 5 80512378 GGATGATTTCTTATGCATATACTCCTACTCTCCCT[A/G]TTTTACACAAACATAGCCCAGTTCTGCCCTTTCAT R 2 1 2 1 201000 r 74 goat snp2413-scaffold107-5486105 5 81710149 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387651 Affx-122969846 AX-123258009 5 80552285 CAACTGTCTGTGAGAGTTGAAATACAGGAAATAAA[C/T]GAAACTGCACAAAGGCACAAAGGCTGCCTAAATTT Y 2 1 2 1 201000 f 74 goat snp2414-scaffold107-5526012 5 81750251 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444359 Affx-122926710 AX-123314696 5 80618756 TCATTCCCTATATCTATTTAATTTTATATCCCTTA[C/T]GGTTGCCAACATAATTCCTGCCAGAAATGAAGCTG Y 2 1 2 1 101000 r 74 goat snp2415-scaffold107-5592483 5 81816863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793674 Affx-122931965 AX-385280646 5 80665362 GAGGAGTCATCCTGTCTTATACAGCACTACATACC[A/G]CTTGTATTTACCCTTGTGACCTTGTGAAAGCGCTT R 2 1 2 1 101000 r 74 goat snp2416-scaffold107-5639089 5 81861105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404816 Affx-122956649 AX-123275168 5 80712898 AAAGTTGCTTTACCTCTTTGGGTCTCTGTTTTCTC[A/G]TTAGCAAAATTAGCCTGTTAATAGAACCTAACATA R 2 1 2 1 201000 r 74 goat snp2417-scaffold107-5686625 5 81908610 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409297 Affx-122953104 AX-123279648 5 80748078 GTAGAGGAGTACAATGAGCTGCCCAGGGTGACACT[A/C]CAAGGAGGTGACTGGATAGAGGTTCCAAAACAGAT M 2 1 2 1 101000 r 74 goat snp2418-scaffold107-5721805 5 81943848 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794990 Affx-122927222 AX-385281949 5 80821300 ACACAAACCCATGAGAAAATGTAATTCGTAAACAC[A/G]TACGCCAATATAAAAACACTAATGTCCTGGCACAA R 2 1 2 1 101000 r 74 goat snp2420-scaffold107-5795027 5 82017600 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408232 Affx-122953833 AX-123278583 5 80873311 AAATAATGCAGTGATTCTAGAACCAAAGAGATGGC[A/G]CTAAGTTTATGATAGCCGTGTTCTTTGGAAATCAT R 2 1 2 1 101000 r 74 goat snp2421-scaffold107-5847038 5 82070434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435785 Affx-122932861 AX-123306124 5 80907661 ATTAAGTACCCTTTCTTACTGATCATCTCTTCTCT[A/G]CTTGCCAAGGTCATGTTTCATAGGTCAGACGTTTA R 2 1 2 1 201000 f 74 goat snp2422-scaffold107-5881388 5 82104947 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411840 Affx-122951229 AX-123282190 5 80953245 ACACGACTGAGCAACTGAGCACGCACACAGATTAT[A/G]CAAGAGAATAGAATCTCCCCTTAGGAATCAACCAG R 2 1 2 1 201000 r 74 goat snp2423-scaffold107-5926972 5 82150517 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386891 Affx-122970044 AX-123257249 5 80983014 TGATCCCTTTTACCCATGTCTCCCCTCTGGTAACC[A/G]CTATTCTGTTCTCTGTATCTACATGTTTGTTTTTA R 2 1 2 1 103000 f 74 goat snp2424-scaffold107-5956741 5 82180117 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397232 Affx-122962375 AX-123267587 5 81020582 CTTGGAGCCTCTCCTAACTCAAGGCTTCCTGCTAC[A/G]TGAGATAATAAATTTCCTTATTGCTTAAGCTGGCT R 2 1 2 1 101000 r 74 goat snp2425-scaffold107-5994309 5 82217573 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38437897 Affx-122931664 AX-123308235 5 81075141 CATCCTGGTCTATACCCCTGCCTTACATAGCAAAA[A/G]CTCCTTGGCAACACCCTGCAGCAGTTCTTCTCATT R 2 1 2 1 202000 r 74 goat snp2426-scaffold107-6048868 5 82272285 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411558 Affx-122951640 AX-123281908 5 81104193 TTCTAATAATGTGACCTAAATAGCTTGCAAAGACC[G/T]AAGAATTATAAAACCTCTTTCTCTATTTCTTTTCT K 2 1 2 1 101000 f 74 goat snp2427-scaffold107-6077920 5 82301308 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785003 Affx-122937985 AX-385272050 5 81159468 TATTCGAAGTTGGCTTTAATGTCATTGGAGGAAGA[C/T]GGTCTGATAATGGCTTAGAACAGTTCTTACTCAGA Y 2 1 2 1 101000 r 74 goat snp2428-scaffold107-6133195 5 82353482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394542 Affx-122964468 AX-123264897 5 81230239 CCCCTTCTCCTATTGCCCCCAACCAGACGATGGGC[A/G]TCAATTGCCCTAGTTGCACTGAACTACCACAAGCT R 2 1 2 1 101000 r 74 goat snp2429-scaffold107-6203966 5 82424230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375940 Affx-122978457 AX-123246299 5 81268431 CTAGGATGGGTTCACAATGGCAGAGCGTCCTATGA[C/T]GCTCGTGGAGCTGTAAATCAGCAATGCGTGGAGTC Y 2 1 2 1 201000 f 74 goat snp2430-scaffold107-6242158 5 82462498 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402849 Affx-122958250 AX-123273202 5 81309041 AATGTGATGGATAACAATATATTCAGGAGAGAAGA[C/T]AGATTATTAAATTTTAGACTATGAAAAAATCATAC Y 2 1 2 1 101000 f 74 goat snp2431-scaffold107-6282768 5 82503210 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389440 Affx-122968353 AX-123259798 5 81377693 ATTTCCGAGACAGGCCTAAAACTTATTGTCATTAA[C/T]ATAATGCCATCAAATTACATTCACTCAGCGCTGAT Y 2 1 2 1 101000 f 74 goat snp2432-scaffold107-6351420 5 82572037 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409920 Affx-122952881 AX-123280271 5 81415772 TTTTACCTTGTTTAATATTTTCATAGTAGAAAAAA[C/T]GGAACCTGTTGATTTCTTACATTTTATTGTTCTAG Y 2 1 2 1 103000 r 74 goat snp2433-scaffold107-6389499 5 82610125 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777578 Affx-122922687 AX-385264697 5 81470174 GTTATAAATCTAGATTTTTCAGGTTTAAATGAAAA[C/T]ATGTGGTCCTTAATTATAGACAGCTACTGTTTCTC Y 2 1 2 1 303000 f 74 goat snp2434-scaffold107-6443901 5 82664845 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415880 Affx-122948485 AX-123286229 5 81507212 TTTGAGTCGGGTGCTAATTTTGTTTTTCTTATTGA[C/T]AGTGTCAAATATTTTAAAAGGAAATTTACGTAGAA Y 2 1 2 1 101000 r 74 goat snp2435-scaffold107-6480939 5 82701927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762367 Affx-986696898 AX-385250529 5 81517530 CATGCAAATTTTGTATTTACATTCATGCTAAGAGG[C/T]AAAAATGTCTCTGCAGGAGTGGAGAATGAATGATT Y 2 1 2 1 600010 f 74 goat 5_81517530 5 81517530 Ancestral_priority_1043 ancestry 0.722 recommended IMAGE 10K 10K ancestral 320762373 Affx-986696904 AX-385250535 5 81517599 TTCTTCTGAGAAACTTCAGGAGTCTCAGACACATG[A/T]CTATGGTCATGAAGATGCTTCTGTCCCAGCTGGCT W 4 1 2 1 600010 f 74 goat 5_81517599 5 81517599 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 38418331 Affx-122946962 AX-123288679 5 81537111 AGTCAGCTTGAAGGTCAGTAGGTTTGTGGTCCCTC[A/G]GTATTTTTCAGTATCGTTGTTGTTCAATCACTAAG R 2 1 2 1 201000 r 74 goat snp2436-scaffold107-6510838 5 82732716 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403800 Affx-122957970 AX-123274152 5 81576804 ATTTTTAAAGCTCTGTAATTTGTTTCTGGGGTAGC[A/G]TTAGATTGTCTTACGTAAGTCTGCCTTGGTCTTTG R 2 1 2 1 201000 r 74 goat snp2437-scaffold107-6550531 5 82772128 A G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430627 Affx-122936964 AX-123300968 5 81617152 ATATATGCTTTTCCTAATTAAGCCCAATATGTCAC[A/G]TTGGTCCCACAGAAAGGATGGGAAAGATACCATAA R 2 1 2 1 201000 f 74 goat snp2438-scaffold107-6590879 5 82813213 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376241 Affx-122978782 AX-123246600 5 81650947 AAGCTTGGCAAATCAAGGACCACACAGAGGGACAC[A/G]CCTGGAGAAAACTCCCCTCTCACCTCCTACTTCTT R 2 1 2 1 201000 f 74 goat snp2439-scaffold107-6624674 5 82848075 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796712 Affx-122964866 AX-385283657 5 81686493 AGGCCCTTCTACAAGAGGAAATTCAACATCAAAGC[A/G]TTAATTAGGAACAGTCTTAGAATTATCCTAGGGCT R 2 1 2 1 101000 f 74 goat snp2440-scaffold107-6660220 5 82884391 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388185 Affx-122969434 AX-123258543 5 81744988 CTAAAATGTTTTAAAATAACTTCCAAAACCCTTGT[A/G]TAAGTAACAATCAGGCAGAGATGGACCAAGCAGTG R 2 1 2 1 101000 r 74 goat snp2441-scaffold107-6718715 5 82942831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414228 Affx-122949639 AX-123284577 5 81776387 GATAGCATGAGGATGTTTTCTGGGGGCAGGATTTG[G/T]GTTCTGTGGAATAGATCTTTTTTAAAAAATTGTAG K 2 1 2 1 101000 f 74 goat snp2442-scaffold107-6750114 5 82974290 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787718 Affx-122922981 AX-385274741 5 81813996 TGTATTTCAACCTACATGGATCAGATATAAAAAGG[C/T]TTTCTGTGCCTGTCCCCTGATCCAGTGCCAAGGAG Y 2 1 2 1 102000 r 74 goat snp2443-scaffold107-6787723 5 83011955 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409171 Affx-122953198 AX-123279522 5 81867534 AAAGGAAGGCAAATGAAATTACTATCCATGATATG[A/G]ACAACAGTATTTTTTCTTTCAGAAAAGCTAATCTA R 2 1 2 1 101000 f 74 goat snp2444-scaffold107-6841261 5 83066080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396045 Affx-122963459 AX-123266400 5 81906887 AATTATGAAAGGATAAATTGTTCTTATGATGAAGT[A/G]TTTTTGGTTAATTGCCAATGAGCCTTGTAGAGGAA R 2 1 2 1 101000 r 74 goat snp2445-scaffold107-6880614 5 83105952 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789970 Affx-122939970 AX-385276976 5 81945593 TTCTTGAACAAGCAAGCACTAAGATAACCCATTAT[A/G]CAGTTTTATGTAGACACCAAGGACTAGTCAGGTCT R 2 1 2 1 101000 r 74 goat snp2446-scaffold107-6919320 5 83144702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427591 Affx-122939464 AX-123297934 5 81989085 GACATCTATTCTTGCCTATCTTGCCTCCTGTTGCT[A/G]CTGAGAACAACAGTATTTGCGCAGCGATCTAAAAA R 2 1 2 1 201000 r 74 goat snp2447-scaffold107-6962812 5 83188657 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425205 Affx-122941028 AX-123295551 5 82051405 GCAGCAAATGATAAATAATCAAGTGAGTGATGAAC[A/G]TTAAGTACCTTGTAAAATGTTTGTTCATGGGTATT R 2 1 2 1 101000 f 74 goat snp2448-scaffold107-7025132 5 83251997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278263 Affx-1111836332 AX-519551751 5 82136972 TCTGAAGGCCTTTTGAGGCAATTGTGTAAAATACT[A/G]TAACAAGGATTGTTGGAAATATTGAATAATTTCAT R 2 1 2 1 101000 f 74 goat Random2.2K-589 5 82136972 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320765045 Affx-122931743 AX-385252614 5 82190945 GGGTATGAAAATTCTCAGTATTGACCATTCTCTTA[C/T]GAATTCCCTTGACCATAGGTAAAATAATTGCATGA Y 2 1 2 1 101000 f 74 goat snp2451-scaffold107-7164672 5 83392142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428986 Affx-122938857 AX-123299328 5 82257850 AAACGAACAGCTTTGTATTAACTACCCAGGTTTAG[A/G]AAGAGAATTAGATGGTATTCTTTTACTAAGATAAG R 2 1 2 1 101000 r 74 goat snp2453-scaffold107-7231577 5 83459631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443146 Affx-122928068 AX-123313483 5 82310492 ATTCATGTAATGCTTAACTCATGAAAACAATTTCA[C/T]GATCATATGCCAATTTTTATAACTTCTGCATATAC Y 2 1 2 1 101000 r 74 goat snp2454-scaffold107-7284219 5 83513716 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445535 Affx-122925165 AX-123315872 5 82342856 AAAATTTCTCTCAGAAATATTTCAGTCTGAGCCTC[G/T]AAAAGACAAGGACTGGAAATAATTTCTTTTTGTTC K 2 1 2 1 102000 f 74 goat snp2455-scaffold107-7316583 5 83546066 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764966 Affx-122969833 AX-385252545 5 82378012 CAATAGGAATTCAGTGAAAGGCATATAAAAAGAAG[C/T]AATTTAGACAAGGTTTAATATAGGCAATTTAGAAA Y 2 1 2 1 101000 f 74 goat snp2456-scaffold107-7351739 5 83577365 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272320 Affx-1111833479 AX-519546056 5 82474999 ATCATCAGTGTTCTGCTCAAAATCCCTTAATAGTA[A/G]CCAGACTCACTCAGAAAATTTTAAAGTCTATGCAC R 2 1 2 1 201000 f 74 goat 5_82474999_AF-PAKI 5 82474999 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795861 Affx-122948548 AX-385282813 5 82489337 CAGTTAGCTTACTAAATCTCCTGGAGTTTAGTGAG[C/T]GAGGGGAAACATCATGAATACTCCTTTAAGCCATG Y 2 1 2 1 101000 f 74 goat snp2458-scaffold107-7463064 5 83688154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778270 Affx-122923226 AX-385265386 5 82528395 TATTGTTTGAGCTCAATATTATGTGAGATCTATCC[A/G]TCCAGGACCAATCCTAATGTCTGTGGGCTCTGGGA R 2 1 2 1 101000 r 74 goat snp2459-scaffold107-7502122 5 83727378 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434042 Affx-122934204 AX-123304383 5 82564148 TTTTAGCCTCTTGTCTTACTTTTAGGGAATTTAGA[C/T]GTTGAACAATAGGTATTTCTTGATTATATTGAAAG Y 2 1 2 1 101000 f 74 goat snp2460-scaffold107-7537875 5 83763030 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406631 Affx-122955825 AX-123276983 5 82600390 ACTTTTTCTTGAAACACCACTTACCTCCAAGCATT[A/G]AAGACGTCTCATCTAATTTTCTGTTCCGTCACTCA R 2 1 2 1 101000 f 74 goat snp2461-scaffold107-7574117 5 83799492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424828 Affx-122941365 AX-123295174 5 82629729 AATTGTCTCACAGGTGAATTCTTAACCACTGGACC[A/G]CCAGTGAAGTCCCCTTTGCCTTTTCTTCTAGATTA R 2 1 2 1 103000 r 74 goat snp2462-scaffold107-7603456 5 83829305 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426242 Affx-122940340 AX-123296588 5 82694221 GTGGTCACTGATTGTATAACACACAACATAAAATT[A/G]TGAAAAGATTTTCAGTGAATTTTTCTCCTTAACAC R 2 1 2 1 102000 f 74 goat snp2463-scaffold107-7667948 5 83894444 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402618 Affx-122958407 AX-123272971 5 82725017 GGGACTATCTATGTTGGGTTGGGTGTAACCACAGA[A/G]TTAGAAAGGACTGCTACAGGCACCGCTCAAAGGAA R 2 1 2 1 101000 r 74 goat snp2464-scaffold107-7698744 5 83925701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786742 Affx-122936011 AX-385273773 5 82781576 AAAGTGTTAAGAACGTTTTTCTATGCCTTGTTTGA[C/T]GTTTTACCTTACACACAGTGAGAGGAGAAAATATT Y 2 1 2 1 101000 r 74 goat snp2465-scaffold107-7755303 5 83982339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405369 Affx-122956312 AX-123275721 5 82816650 TTTTACAGGAAAATCGCCTATTGTATGAATGAGAG[C/T]AAAGGCCTCAAAATACCTATGTGTGATAGTGAATT Y 2 1 2 1 101000 r 74 goat snp2466-scaffold107-7790377 5 84017320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431738 Affx-122936742 AX-123302079 5 82847971 GGATAAATAGAACAGCAAAGGGATGCACTATTGGC[A/G]TTCCCTGGAAGCTCAGTGCCTTGTCCTTGCAGCAC R 2 1 2 1 102000 f 74 goat snp2467-scaffold107-7821698 5 84048953 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423698 Affx-122942892 AX-123294044 5 82882316 ATTAATTGTCAGTCCTCACCTTACTTGTCCTGTCT[A/G]CAACATTGGAAACTGTTATTTACACTTGTTGTCTG R 2 1 2 1 201000 r 74 goat snp2468-scaffold107-7856043 5 84083368 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452965 Affx-122920161 AX-123323298 5 82912871 AAGAGAGCCACTCCCAGCCCACGGACAAAACCTCA[C/T]AGTGTTAAGAAGGGTGTAATTTATTGAAAACTATA Y 2 1 2 1 201000 r 74 goat snp2469-scaffold107-7886598 5 84113790 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411004 Affx-122951988 AX-123281354 5 82946143 TCTTTTGTAAATATATTGTCATTTGGTAGAAGGAG[C/T]GCAAATCTCAAGCCAAACACACACAGATACCTGAA Y 2 1 2 1 201000 f 74 goat snp2470-scaffold107-7919870 5 84146893 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787757 Affx-122956569 AX-385274780 5 82993462 AGAAATCTCAGAATAAATTCATAAAATATAGATAA[C/T]ATTTGCAAACAGTTCACAGTCCTGAAAATATCAAT Y 2 1 2 1 202000 f 74 goat snp2471-scaffold107-7967189 5 84192630 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441973 Affx-122928558 AX-123312310 5 83046258 AATGAGACAGGGAGCAATTGTAGTAGCATGTTTTA[C/T]GAAGACTCTGAGAGTCTTTTTAAGTGACCCCCAAT Y 2 1 2 1 201000 f 74 goat snp2472-scaffold107-8019985 5 84245431 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425333 Affx-122941599 AX-123295679 5 83092007 GAATCACATGAAATGATTATGTTTAGATCTCTAGC[A/G]TGTCTGGCAACTATAAACACACATATTTGAACATT R 2 1 2 1 101000 f 74 goat snp2473-scaffold107-8065734 5 84291649 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423913 Affx-122942275 AX-123294259 5 83129315 TATAAGATAGAGCCACTGAGACTGATGCTTTCAGT[A/G]AGTAATCCAGACACTTAGGGCATTTTGAGCAACTT R 2 1 2 1 101000 r 74 goat snp2474-scaffold107-8103042 5 84328917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394238 Affx-122964879 AX-123264593 5 83171692 CTCATTTCTTAATTAAGAACTCATTATGTGGTCTT[A/G]TATTTCCTGAATTGTATAAAATTTCTATATCTCCA R 2 1 2 1 201000 r 74 goat snp2475-scaffold107-8145419 5 84371248 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446523 Affx-122925024 AX-123316859 5 83204030 TTGCAAATTAGTAACAGAGGCACAGAGACCATAAA[C/T]GGAAAAGAAAAACATGAGGTCGTTTGGCTACTTCA Y 2 1 2 1 101000 f 74 goat snp2476-scaffold107-8177757 5 84403910 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416256 Affx-122947965 AX-123286605 5 83258680 TAAAGTTTCGTTTGGGTCCAAGAATGACATGGTTC[A/G]TTTCCATGTTAAATGTCAATCTTTTTCTCCCATTG R 2 1 2 1 101000 f 74 goat snp2477-scaffold107-8232407 5 84458229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450753 Affx-122921851 AX-123321087 5 83410810 TGCTAGCATTGTGGAGTTTTCAACTAATTTCTCAG[A/C]AAAGTAAATATACTGTGCCCCGGTTGTATTTAGTG M 2 1 2 1 101000 f 74 goat snp2480-scaffold107-8384537 5 84611189 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801789 Affx-122970773 AX-385288697 5 83457829 ATCTGAATGTGGTGGGGTAGTTTGTTAAAGAGAGA[A/G]GTAAAGGTTTGAGGCAGCTACAAAAGGGAGTGAGA R 2 1 2 1 101000 f 74 goat snp2481-scaffold107-8431556 5 84658427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416033 Affx-122948366 AX-123286382 5 83497572 AGTCTCTGGCCTCTAGGTAATACACTATAGGACTT[A/C]TTCAATTAGTAAATCAATATTGCATATTGCAATAG M 2 1 2 1 101000 f 74 goat snp2482-scaffold107-8471299 5 84697956 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426934 Affx-122940429 AX-123297279 5 83543953 TTTATGCCTTTCTGTGGAGGGAGGGAAATTAAAGC[A/G]TCTACCTTTGTCTAGATTCCAGTAGTTAACAGCTC R 2 1 2 1 101000 r 74 goat snp2483-scaffold107-8517680 5 84744492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777620 Affx-122944936 AX-385264739 5 83623722 AAAGTTGAAAAATTAGATTAATGGCAGATTGTAAG[A/G]GGCCTTGAGTATTATCAGAAATTTGGAGTTTATAA R 2 1 2 1 101000 r 74 goat snp2485-scaffold107-8597449 5 84824038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440420 Affx-122929605 AX-123310757 5 83670177 TATGAACTTATTTCAATAAGAATAATTTAGCAGTC[A/G]TCTCTCAAGTAACATTCATAATATGCAAGGAGATT R 2 1 2 1 101000 r 74 goat snp2486-scaffold107-8643904 5 84870974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418527 Affx-122946416 AX-123288875 5 83735546 AGGGCTCTGTAAGGGCAGGGAGTTTGGAATTTATT[G/T]TATGTCCAGTATAAAGCTTTGAAATGGTTTTATTC K 2 1 2 1 101000 f 74 goat snp2488-scaffold107-8709273 5 84936163 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432728 Affx-122935465 AX-123303069 5 83787187 AGAGTTTGAGACTGTACTTTCAGAGATGAAGAGTA[C/T]AATATCTGAGACAAAAATAGGCTGAATGCGATTAG Y 2 1 2 1 101000 r 74 goat snp2489-scaffold107-8760914 5 84987964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773568 Affx-122945482 AX-385260708 5 83816012 GAATCATGGATTTATCTTAATGTATGTGACCTTTT[A/G]TCTATATCTTAAGAACAGGAACACAAAGCAGCTGG R 2 1 2 1 201000 f 74 goat snp2490-scaffold107-8789739 5 85016718 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446539 Affx-122925012 AX-123316875 5 83847100 TAGCTTGCATGTGTATATGTATGTTTACACATTAA[C/T]ACATGTATAATATGGCATATGAATAACATTATAGT Y 2 1 2 1 303000 r 74 goat snp2491-scaffold107-8820827 5 85048163 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779995 Affx-122977194 AX-385267094 5 83908396 AGGAATGAGAATATGTTCCTTTGGAAAGAGACATA[A/C]TCCAAGCAATAGACTTGATGTTTCTCTTGAAACAA M 2 1 2 1 201000 f 74 goat snp2492-scaffold107-8882123 5 85110005 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775749 Affx-122961210 AX-385262880 5 84051222 AGTGGTAATATCACATGTCAGAATAAAAACTATTT[C/T]TTGTGGGCCTTAACAATGTTCCTAGTATGATTAAT Y 2 1 2 1 101000 r 74 goat snp2495-scaffold107-9024949 5 85254951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403119 Affx-122958121 AX-123273472 5 84088412 GCCCCAGGTTTGGTCAAAATGAACAACTGGGCAGA[C/T]GAAGATTTGAAAAAAATGTTTTTTTTGTTTTAGTG Y 2 1 2 1 101000 f 74 goat snp2496-scaffold107-9062139 5 85292830 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388943 Affx-122968817 AX-123259301 5 84132393 TACCAGTTATTGAACTTGTGCTAGGTTCCAAGAAA[C/T]GGGTAGACAATGACATGCAAAATTGGTGTGGTGCT Y 2 1 2 1 101000 f 74 goat snp2497-scaffold107-9106120 5 85336862 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435297 Affx-122934030 AX-123305637 5 84193840 TATAGTAATGTTTCCTCTAGACTCTGTTTCTTCCC[A/G]TATACCTGCACCCCTAGGAGTTCTTTCCTCATGTT R 2 1 2 1 201000 r 74 goat snp2498-scaffold107-9167567 5 85398316 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378544 Affx-122976616 AX-123248903 5 84218731 AAGATGCCAGAAAATTTATCTTTCATATGTGAAAT[A/G]TATTTTATATGTAAAATATATTCTTAGATATTCAA R 2 1 2 1 303000 r 74 goat snp8884-scaffold1319-23999 5 85423412 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419137 Affx-122922134 AX-123289485 5 84264504 TGAATTTTTTACTTATATGTATATCCACTACCAAA[C/T]TCAGATATGGAATATATCTAGCCTCTTATCAGACA Y 2 1 2 1 101000 r 74 goat snp8885-scaffold1319-69772 5 85468310 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272365 Affx-1111834099 AX-519546094 5 84281343 TGCAGCCAGCTTGTCTCACAGCTGGGCAAATGACT[A/G]CCTGGATCCACAGCATCCCCTAAATCTGGTTATTA R 2 1 2 1 202000 f 74 goat GoatD01.018281 5 84281343 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320789247 Affx-122963461 AX-385276258 5 84306687 GTGCTAACGCCTAGGGGACAGAGTACAGATGACTG[C/T]ATTTTCCAGGTTACCAGGTATAAGAAAAGGCAAAA Y 2 1 2 1 101000 f 74 goat snp8886-scaffold1319-111955 5 85510664 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798708 Affx-122937251 AX-385285639 5 84342454 ACATGAGCCAACCATAACTGCACAGAACGGTGTCT[A/G]TGTTATCAATGTTTGCAATATTGAAAAAAATGAAA R 2 1 2 1 101000 f 74 goat snp8887-scaffold1319-147722 5 85546548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407115 Affx-122954877 AX-123277466 5 84371707 ACAGAACTTCAGTGGGTTAGAGATAGGTAAATAGC[G/T]ATCACACTTATTTTAGGCCCTCAGATAGCATTTTG K 2 1 2 1 101000 f 74 goat snp8888-scaffold1319-176975 5 85575758 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438261 Affx-122931415 AX-123308599 5 84408639 TTTAAGAAACTGATTTCCTGAAAATGTGTGACTTA[C/T]AGAACACTGATAGTGTCAGAATTTTCTCCAGTGAT Y 2 1 2 1 101000 r 74 goat snp8889-scaffold1319-213907 5 85613261 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393434 Affx-122965865 AX-123263790 5 84445362 CCTACATACTATCATGCCTATCACTTTTTATTAAA[C/T]GAATGAAATAAACTCTATACCTGAATAAATGTGCA Y 2 1 2 1 101000 f 74 goat snp8890-scaffold1319-250630 5 85650067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413713 Affx-122950077 AX-123284062 5 84529090 TATATTATCCGAACAGTTATGAAAACATGGGAGGT[A/G]TGGAAAGCATTGACAACCCCCTTTTTCATATTCTT R 2 1 2 1 201000 r 74 goat snp8891-scaffold1319-334358 5 85733766 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415976 Affx-122948412 AX-123286325 5 84578067 AGGACACACAGGGAAATGACGCTGCTGGTGAGGAC[A/G]GAGACAAGTAATTGAATTTATACACACATACACAC R 2 1 2 1 201000 r 74 goat snp8892-scaffold1319-383335 5 85783108 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404837 Affx-122956633 AX-123275189 5 84627499 CTTCTGAGCTCTTAGCTAAGACTCCTGTAATAAAA[A/G]GCAGAATAGCAAGAGAAAAATTAACAAGTTCATTC R 2 1 2 1 202000 r 74 goat snp8893-scaffold1319-432767 5 85833492 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278425 Affx-1111836333 AX-519551910 5 84647755 CTTTGTATGCAGTTTAACAGCCATAGCTGAAGGTA[A/G]CAGCTCCTCTATAGTCAAGGCTTCACCAGTTCTAG R 2 1 2 1 101000 r 74 goat Random2.2K-590 5 84647755 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412963 Affx-122951042 AX-123283312 5 84717917 TTATGCTTCTTTTGGCTTTCCCTTAGTATTCTGTG[A/C]TTTCCTAGGGGCTCAAGAAAAAAGCATGTGGTGAA M 2 1 2 1 201000 f 74 goat snp8895-scaffold1319-523185 5 85924458 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435118 Affx-122933695 AX-123305458 5 84766372 TCTGAATGTTTGTGTGGGACCTCTTTCCCTGGTGG[C/T]TCAGCTGATAAAGCATCCGCTTGCAATGCGGGAGA Y 2 1 2 1 303000 r 74 goat snp8896-scaffold1319-571640 5 85973736 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389293 Affx-122968515 AX-123259651 5 84801604 TCCTGATGTTGTTGATAGCTGCAGGCAAGCATTCT[A/G]CAATTTTCTAAAGAACAAAATCAAGAATTCTCTCT R 2 1 2 1 101000 f 74 goat snp8897-scaffold1319-606872 5 86009352 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796091 Affx-122932788 AX-385283043 5 84831542 TCATTTTTCCTACTTTAAGAAGGTATAAAAAGATG[C/T]GTGTCGTTGTAAAACATATGTGTGCTCATAAGTTT Y 2 1 2 1 101000 r 74 goat snp8898-scaffold1319-636810 5 86040318 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783359 Affx-122957558 AX-385270423 5 84913933 GGCTAAACAGTTAAAATGGACACATGAACACAGAT[A/G]TAAGGCTGTTAAGAATAGTTTCTAAGCTGCTGATA R 2 1 2 1 101000 f 74 goat snp8900-scaffold1319-719201 5 86119339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410946 Affx-122952038 AX-123281296 5 84977694 TTATTTGTAGGCTGAACGTTGAACTAAAACTCTGC[C/T]TTGGTCCGAGCACATGCATCTTTCCCTTACCTCTC Y 2 1 2 1 101000 f 74 goat snp8901-scaffold1319-782962 5 86183316 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272321 Affx-1111833480 AX-519546057 5 84988328 TGTACAGAAGAGTAAATTGTTGACAGGTTCTTCTT[A/C]TGCTATATATGATGTGGTATAACATTATATGAAAT M 2 1 2 1 101000 f 74 goat 5_84988328_AF-PAKI 5 84988328 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389953 Affx-122968082 AX-123260310 5 85011607 TAATCAATATGCTATTGAGGTACATTTTGGAGTGA[C/T]GTAGTCTGAACCCCAATACATGTAACACTTCAATT Y 2 1 2 1 101000 r 74 goat snp8902-scaffold1319-816875 5 86217175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802005 Affx-122975789 AX-385288910 5 85044011 AGGAAAGATGAGACAGTCTAGGAAGTAGTTTCTTA[C/T]CTGTTTTGCTCTTAAGCTTCCTGACCGCTTCTCAA Y 2 1 2 1 101000 r 74 goat snp8903-scaffold1319-849279 5 86249978 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771626 Affx-122970051 AX-385258784 5 85086165 ATGAACAGCCTTTCTCATGCAGTTTGATTGTTTCC[A/G]TATTATGGCTTGGATGGACACATGAAATTATTAGT R 2 1 2 1 101000 f 74 goat snp8904-scaffold1319-891433 5 86292185 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417168 Affx-122947335 AX-123287516 5 85172873 AGAGAAACCTAAAGTAAAGGGAGAGAAATATGAAG[C/T]AGTAATTTGTAAAATGAAGTTTTTTATGTGTGTAG Y 2 1 2 1 101000 f 74 goat snp8906-scaffold1319-978141 5 86381133 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450162 Affx-122922321 AX-123320497 5 85235829 CATTGTTGCTTTGGTGTTTCAGGGTCAGAGACTGA[A/G]TCTTGTTTTAATTTGTTTTAGATCCCTCATCACAG R 2 1 2 1 101000 f 74 goat snp8907-scaffold1319-1041097 5 86445172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387309 Affx-122970514 AX-123257667 5 85267429 AGTTTAGACAAATCTGTATAGTTTGGAAGACTTAC[A/G]TGGTTTCTATCACATTTGTCTCCTTTTCTACTAAC R 2 1 2 1 101000 r 74 goat snp8908-scaffold1319-1072697 5 86476973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401268 Affx-122959285 AX-123271621 5 85309735 AAAGAAGAATGGATTCATCTGTTCTTCCTCATCCA[C/T]CTTCCTGGATTTGCCACAATCTGAAGATGTTTATA Y 2 1 2 1 102000 r 74 goat snp8909-scaffold1319-1115003 5 86519782 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396453 Affx-122962976 AX-123266808 5 85352445 AGACTGAGATGGTGATTTTGAGAAATGTTTTAACT[A/G]CAGCAGGAGAAAGCAAACTATTTCTTTCCTTTAAA R 2 1 2 1 101000 f 74 goat snp8910-scaffold1319-1157713 5 86562505 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409965 Affx-122954107 AX-123280315 5 85355431 TTTGAGACTTCAACTTGGGAAGTTATTGTTTGCAG[C/T]GACAAAAAAGAGCAGCGATTTTCTGTGTGTGTGTT Y 2 1 2 1 101000 r 74 goat snp8929-scaffold1322-1600 5 86565319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434747 Affx-122933910 AX-123305088 5 85404815 CATAAGAAAATGGATACTACTGACTTTACTCCCAG[C/T]GTAGGCTGATCTGAATTTTTACCTGAAATAAATAC Y 2 1 2 1 101000 r 74 goat snp8930-scaffold1322-50984 5 86615106 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800690 Affx-122943275 AX-385287608 5 85443274 GTATTCAGCAGGGAGCTAGGGAGATAAACATGAAT[A/G]CAACTTTATTTTGATGTGTGCTGCTTCCGAGAGAC R 2 1 2 1 101000 r 74 goat snp8931-scaffold1322-89443 5 86654136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447737 Affx-122924591 AX-123318073 5 85510216 CTACGTGGTTCTGAAGTTACTGAATAAGCCATTTA[G/T]AGGCATATTTTATGTATATGTCTTCCTCACATAAG K 2 1 2 1 101000 f 74 goat snp8932-scaffold1322-156385 5 86721819 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377033 Affx-122977709 AX-123247392 5 85539092 TCCTTTGCTACTTTTTTGCAACATTTTTGCAGGAA[C/T]AGTTTTAATTCTGTTTTTACATATATCTGCATTCC Y 2 1 2 1 101000 f 74 goat snp8933-scaffold1322-185261 5 86750725 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435204 Affx-122933634 AX-123305544 5 85573865 CCTTCTCTGACTCCCTGCTTGCATGTGAAAGGAAC[A/G]TTTCCCAGTCCTCTTGCAGTCAGATGGGACCATGA R 2 1 2 1 101000 f 74 goat snp8934-scaffold1322-220034 5 86785489 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784564 Affx-122924165 AX-385271613 5 85616577 CTTGTCACTTGAATTACATTTAATTGGTCTTTAAC[A/G]CTTGATTTTACTGTTGTTCAGAGAAAGGCTGCATG R 2 1 2 1 101000 r 74 goat snp8935-scaffold1322-262746 5 86828397 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445157 Affx-122925554 AX-123315494 5 85648439 ATTAGGATGTCTAGCAGCGTCTCTGGCTTCCATTT[A/G]TTAAATGTCATTAGTACCATCAAAAATATCCCCAG R 2 1 2 1 201000 r 74 goat snp8936-scaffold1322-294608 5 86860215 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781517 Affx-122956590 AX-385268602 5 85679277 AAGCCACATTGTGAACTAGCATCAAGTTTGTAGCT[A/G]TTCATTATCATGACCGTGGTTTTCCAAGATAACTG R 2 1 2 1 201000 f 74 goat snp8937-scaffold1322-325446 5 86891601 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413868 Affx-122949856 AX-123284217 5 85771324 TTTATTTTTTTTTCTTTTTCTGTGGGCTGGAGCTC[A/G]TTTCCCGGAGTCATTTACACTACGGTCACCAATGC R 2 1 2 1 101000 r 74 goat snp8939-scaffold1322-417493 5 86985099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408172 Affx-122954207 AX-123278523 5 85822769 CACACAAGCCAGGATTAGACCATACAGCTGGAGGA[C/T]GCTAGAGCTTGAGATTTTGACTACATTCTCCATGT Y 2 1 2 1 101000 r 74 goat snp8940-scaffold1322-468938 5 87036947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278267 Affx-1111836334 AX-190769965 5 85844523 CCCCTCCAGTATTCTGGCCTGGAGAATTCCATGGG[A/C]ACAACTGAGTGACTTTCATGTGCCTCTTGTGGCCA M 2 1 2 1 303000 f 74 goat Random2.2K-591 5 85844523 G T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408683 Affx-122953447 AX-123279034 5 85872139 CCAGACACCAGTATTAACAAGGCTGGGGTTTGAGG[A/C]TTACAGTGATTGTTGATTCTATGTGACACCTTTAA M 2 1 2 1 101000 f 74 goat snp8941-scaffold1322-518308 5 87086697 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432240 Affx-122936357 AX-123302581 5 85908182 ATCGAATTCAGCCCTTTTTCTCTTTCTTTCCATAT[A/G]TAGTAAATTAATCTGCAAGACTCATATATTCTTGT R 2 1 2 1 201000 r 74 goat snp8942-scaffold1322-554351 5 87122811 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395815 Affx-122963640 AX-123266170 5 85966322 TTTCAGCAAAGCAGAGATCAATAAAATGCAAAGTA[C/T]ATGTTTGAAGAGTCAGTCCAAATTCAATGACCCAC Y 2 1 2 1 101000 r 74 goat snp8943-scaffold1322-612491 5 87182649 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398680 Affx-122961871 AX-123269035 5 86012095 TAGAGGTGGTCATGGCCCTGAATGATAATTCAGCT[A/C]TATTCATCCATTTATTCAACTAATTCAACTAAATA M 2 1 2 1 103000 f 74 goat snp8944-scaffold1322-658264 5 87227704 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774492 Affx-122951524 AX-385261627 5 86041847 AAGATATTAAGTTACATAACCCAAGTGGCTATTAT[A/C]CTATCAAAATGTAGGAATGATTTAACCCTTTATGT M 2 1 2 1 101000 r 74 goat snp8945-scaffold1322-688016 5 87255522 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784208 Affx-122920306 AX-385271259 5 86122302 CAGCACTTGAAGGAATTATTACTTAATTATTTTCT[A/G]TTTTAGCATGCAATGCAACATTTTGACATCAGCTA R 2 1 2 1 303000 f 74 goat snp8947-scaffold1322-768471 5 87336440 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409324 Affx-122953083 AX-123279675 5 86154919 GTTGTCTGTGGAGGTGTGTGAGTTTCTAAAGGGAG[A/C]GTTCAGTGACTCTAGCTTGAATCTCATGTAATTAT M 2 1 2 1 101000 f 74 goat snp8948-scaffold1322-801088 5 87369044 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798220 Affx-122944793 AX-385285155 5 86197224 ATTTCAGGCAAAAGTAGTTTTCTAACTCTATATCA[C/T]GATTCTCAACTTTCTTGTACATGTGTAGATTTTTC Y 2 1 2 1 101000 r 74 goat snp51087-scaffold740-2829307 5 87411492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793442 Affx-122966421 AX-385280419 5 86226951 AATATTCATTAGAAAATAACATACCCTTCATAAGA[C/T]GTGGTTATGCCAGCAACTGAAGAACTATCACAGAT Y 2 1 2 1 101000 r 74 goat snp51086-scaffold740-2799580 5 87441236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779687 Affx-122954768 AX-385266787 5 86262584 TGATTATCTCACAGTCACTTCATTTCCTTTAAAAT[A/C]TGTTCTCATTACACATGAGCTAAGCAGTCTTTGAG M 2 1 2 1 201000 f 74 goat snp51085-scaffold740-2763947 5 87477353 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781872 Affx-122959919 AX-385268954 5 86312770 AGAATTCTTTCAAATGTTACCACATTTATAGGAAC[A/G]TTGGCCTTTGCAGACAGAATTAACCACTGTCCTGT R 2 1 2 1 101000 r 74 goat snp51084-scaffold740-2713761 5 87528638 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438244 Affx-122931428 AX-123308582 5 86353795 AGCCTAAGCCAAGAAGCATTGTCTTCTTAGGAGAA[C/T]GAGGTAAGAACAGAATTTATTTTGGATGTCCCATG Y 2 1 2 1 101000 f 74 goat snp51083-scaffold740-2672736 5 87569684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435694 Affx-122933320 AX-123306033 5 86412830 AACTCTCATTCAACATATGCTTTCTCCCTTTCTTC[A/G]TTTCTTTCCCACCCCTGGCTCTTTTCTCCTACAGC R 2 1 2 1 102000 r 74 goat snp51082-scaffold740-2613701 5 87628491 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278269 Affx-1111836335 AX-519551756 5 86426266 ACTGGAGTGGATTGCCATCTCCTTCTCCAGGAAGA[A/C]TGTAAGGATATCACTATCTTAAGACTAAGTAGATG M 2 1 2 1 103000 f 74 goat Random2.2K-592 5 86426266 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417586 Affx-122946892 AX-123287934 5 86455306 ACATAGAACAATCATTACATAAAGGCAAGGTAATA[G/T]ACACATAGAATCATTTAAAATTTCTACCACAGAAC K 2 1 2 1 101000 f 74 goat snp51081-scaffold740-2571225 5 87671047 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429993 Affx-122938043 AX-123300334 5 86505921 ATTTCCACAAAAATTTTGGTTGATGGCATATCTCA[C/T]AGCCATCGGCTTTGTTTGTTTGTTGTTACTATTTG Y 2 1 2 1 103000 f 74 goat snp51080-scaffold740-2520610 5 87722650 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274376 Affx-1111834219 AX-515859214 5 86544929 ACTATGGTACATTTGCTGCAGCTCAGCTTTCTGAT[A/G]ATCTTGCAGAGGT R 2 1 2 1 102000 f 74 goat GoatD01.025964 5 86544929 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38412689 Affx-122950761 AX-123283038 5 86545229 TATTTCATGAGCTGGGTCTTTTTCCTGGAGTCTCT[C/T]AAAATTATTCAAGAAAAATGAAGATAAATATGTTT Y 2 1 2 1 103000 f 74 goat snp51079-scaffold740-2481302 5 87762049 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799196 Affx-122932218 AX-385286126 5 86578450 AATATTCATCCTTATATCTCAATCCTATTACTTAA[C/T]GACTCCTTTCATATATGTAACAGATTATAGAAAGA Y 2 1 2 1 101000 r 74 goat snp51078-scaffold740-2448081 5 87795224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795521 Affx-122966088 AX-385282476 5 86625348 AAAGTGCCTGCATATTTGCGTATAAACAAATAAAG[C/T]AAAAGGCTTACAGATTTGGGTTGACTTCAAGCCCA Y 2 1 2 1 101000 r 74 goat snp51077-scaffold740-2401183 5 87845100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799600 Affx-122978484 AX-385286530 5 86668614 AAATAAGTTTTAAATACCCTTGCTAATGGTGTCAT[A/G]CATGCGAAGTGGTTTCAGTTGTACCCTACTCTTTT R 2 1 2 1 101000 r 74 goat snp51076-scaffold740-2357917 5 87888587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399760 Affx-122960314 AX-123270115 5 86722483 GCTATGACTCTATATGTTTTCCCCAAATCAATGAC[A/G]CTTTTATTTATAGTTTCCAGTCTTTGAGGGTAAGG R 2 1 2 1 101000 f 74 goat snp51075-scaffold740-2304048 5 87942690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796677 Affx-122978758 AX-191622040 5 86790013 GATTAATTTAGATCAGATAAGCTCAGTGTTAGGAC[A/G]TTGGGCCTGTCAGATAGTGACTGGTCAGAGAAAAA R 2 1 2 1 101000 r 74 goat snp51074-scaffold740-2236518 5 88010006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445591 Affx-122925124 AX-123315928 5 86866910 GTTACCGATTAGATATATGTACACAGAGGCCAAGT[A/G]TGTTGTGGAGAATAAGTGAACCCATACTGCGGGGT R 2 1 2 1 101000 r 74 goat snp51072-scaffold740-2159621 5 88087732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439365 Affx-122930277 AX-123309702 5 86914366 ATCATTAATTGACAGCTTGGTTGGAAATGTAAAAG[C/T]AGACTCTCAATAATTTTTTCATTACAGTTTTGAAG Y 2 1 2 1 101000 f 74 goat snp51071-scaffold740-2112165 5 88135074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435295 Affx-122934032 AX-123305635 5 86947566 TCAAAGCTAAAGAGATCTGAAGGTCATCTAGTGAG[C/T]GACCGTGATGGGGAGACCATTTTCTGGCTATGTTT Y 2 1 2 1 201000 f 74 goat snp51070-scaffold740-2078965 5 88169415 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775329 Affx-122919361 AX-385262460 5 86981634 AATATGATGCTGGTGTGGACTTCTTTGTAGTTCCA[A/G]TTGAACTTGACTGGGTTCATTCTAATACACTAAAG R 2 1 2 1 101000 f 74 goat snp51069-scaffold740-2044897 5 88203831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385121 Affx-122971777 AX-123255479 5 87017848 GAGATGGCCCCATATTCTTAGGTTAAGCTTCTGGA[C/T]ATTTAGGGGTCTATTTGTACCCTTTTGATTCTGAA Y 2 1 2 1 201000 r 74 goat snp51068-scaffold740-2008683 5 88240726 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778708 Affx-122952754 AX-385265819 5 87050443 TAAGAGTTGGGCCAGTTACTCAAGTTCTTCAACTA[C/T]CTATTGCCTACAAAATGTTTAACATGGAATTTGTA Y 2 1 2 1 101000 f 74 goat snp51067-scaffold740-1976088 5 88273642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405960 Affx-122955542 AX-123276312 5 87105223 ATTGTTGAAGGAGAAAAATCATCAGGGAATTAGAA[A/C]TATACTACTTTGAAATGATGAAGGAAAGAAAGTAG M 2 1 2 1 101000 f 74 goat snp51066-scaffold740-1921308 5 88328603 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394575 Affx-122964443 AX-123264930 5 87134540 ACAAACTTCAACCATGAAGGAGGGGGAGGAATGTA[C/T]GTCAGGGACAATTTCCAATCTCAGTCACAAAATTA Y 2 1 2 1 201000 r 74 goat snp51065-scaffold740-1891991 5 88357886 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791926 Affx-122930438 AX-385278916 5 87193988 CAATTCAGAAGCTCATTATCATTAAATAAGGGGTC[A/G]TTATCCCAGGAGATACTATAGAGAAATGTTAGTTT R 2 1 2 1 101000 f 74 goat snp51064-scaffold740-1832543 5 88418021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378827 Affx-122976545 AX-123249186 5 87236004 ATTCTGCATAATGTGAATGAGTCAGAGAAAAACAC[G/T]CTGGTTCCGTCAACAGCAGCTCTTTCTCTTCATGT K 2 1 2 1 201000 f 74 goat snp51063-scaffold740-1790527 5 88460205 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423953 Affx-122942145 AX-123294299 5 87290882 TCCCATTTTCCACAGCTAAAAGATCCCACATGTCA[C/T]GACTAAAGATCTGTGTGTGGCAACTAAGACCCAGT Y 2 1 2 1 303000 r 74 goat snp51062-scaffold740-1735649 5 88514076 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451205 Affx-122921322 AX-123321539 5 87334480 GTTTCTGAAGCAAATTCATGCCTTTTTATCTTCTC[C/T]GTCCTTCCACTGCCAATATTCACTTTTGTGGTACC Y 2 1 2 1 101000 r 74 goat snp51061-scaffold740-1692051 5 88557676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387265 Affx-122970552 AX-123257623 5 87388172 CCCGGCTGCCCCTCTCCATTGAATTCTGGAATTCA[A/G]CCTTGGTGGGAGACAGGGGCTTCTTTCAGACTTTC R 2 1 2 1 103000 r 74 goat snp51060-scaffold740-1638359 5 88611714 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398221 Affx-122962214 AX-123268576 5 87434707 CTATCTGTGGATATGAAATGCCAACTGTGTGTCTC[A/G]TAACTGTTCATTCATATTTATTGCTCCTTCTAAGA R 2 1 2 1 101000 f 74 goat snp51059-scaffold740-1591824 5 88658836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783422 Affx-122946525 AX-385270485 5 87485243 TGCACTCACCTCATTTATTCCTTCATGAGTAAATA[C/T]GTGAGCACTTTCTGTCTGTGATATCCCACGTCATT Y 2 1 2 1 101000 r 74 goat snp51058-scaffold740-1541288 5 88703853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402703 Affx-122959608 AX-123273056 5 87517064 ACCTCAGGCATCTCTCTGGATAGCAGTCTTTTGAG[C/T]AGAGGGAGGCAACAAATTATAACAGAGAACATGGC Y 2 1 2 1 101000 f 74 goat snp51057-scaffold740-1509467 5 88735700 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422323 Affx-122943462 AX-123292669 5 87545603 CATAGCCTGTCATGACAACTTTAGAGTTAAGTATA[C/T]AGACAAAAAGCTGCATTGTAAACGGAGGCCTTTGG Y 2 1 2 1 101000 f 74 goat snp51056-scaffold740-1480928 5 88765443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802666 Affx-122932994 AX-385289565 5 87582361 ACTGGAGGTAAAATCCCGGGACTGTTAACAGAACA[A/G]TCCCAGTTGGCTAGACTGAGGCCAATACTTAATGA R 2 1 2 1 101000 r 74 goat snp51055-scaffold740-1444170 5 88802263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403517 Affx-122957626 AX-123273870 5 87611230 ATGTGGTTAATGGGGTCAAGTGCATGATATTCATT[A/G]TGGCGCAGGACAGCTTGATGAGCCTTGCAAACACA R 2 1 2 1 201000 f 74 goat snp51054-scaffold740-1415301 5 88831202 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768788 Affx-122939139 AX-385255965 5 87655635 AACTGTTTGGTTGAAATAAAACATACGTACTGAGA[C/T]GGACACAGACCATAAGGTGTAACTCAATCAATTTC Y 2 1 2 1 101000 r 74 goat snp51053-scaffold740-1370896 5 88876582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425275 Affx-122940972 AX-123295621 5 87694257 TAGTGGTATAACACAATCTGTTTATTTCTCACTTG[C/T]ATAGAGTCTGATATGGGCCAGGCCATTTTTTCTTC Y 2 1 2 1 101000 r 74 goat snp51052-scaffold740-1332274 5 88915511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781261 Affx-122949899 AX-385268346 5 87725899 ATGAATGGATTAGTCTGAAATTTGAGCTTGTAAGA[A/G]AGTGAGGTGAGGAAGAAAGCTATAAATAGAGGACT R 2 1 2 1 101000 r 74 goat snp51051-scaffold740-1300632 5 88947226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428126 Affx-122939066 AX-123298469 5 87768747 CCAGTGACTGAAAAAGCAATAATTTAAGGTCTGCA[C/T]AAAAACGAAGAAAACCGAATGGGAGTTAACTGTGT Y 2 1 2 1 101000 f 74 goat snp51050-scaffold740-1257784 5 88990079 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320774039 Affx-122967173 AX-385261177 5 87799929 CTTGTTAGTATTGTATCAAACAAATGTTGCATAGA[A/G]TTAATAGAACATTGCTTGTAAATATTTCAGATTTG R 2 1 2 1 101000 f 74 goat snp51049-scaffold740-1226602 5 89021255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278431 Affx-1111836336 AX-519551916 5 87840555 CAAAAGGTTAGAATGAAATTTGCTTGGAATTTCAC[A/G]GAACTACAACCTTTAGTGTCGTCCTGCAGAATTCG R 2 1 2 1 101000 r 74 goat Random2.2K-594 5 87840555 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778952 Affx-122956238 AX-385266059 5 87843544 TTTGAAAAGCACGGCTTTAAGTTACTGAAACTTAT[A/C]TGAATAGACTGAGTGCTTTTTCTGGCTCAGATTTT M 2 1 2 1 101000 r 74 goat snp51048-scaffold740-1182987 5 89064850 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410343 Affx-122952462 AX-123280693 5 87930720 CACCGTCTTTTCCTTGTCTCTTATCACTTTCAAGG[C/T]AATATGCATGGGCATTCTCATTTTTTCCAAAAGAT Y 2 1 2 1 101000 f 74 goat snp51047-scaffold740-1095811 5 89151882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278273 Affx-1111836337 AX-519551760 5 87969152 TCTGGGTATGTATCCAGAGGAGATAAGGTTAAGAT[A/C]TTGAAGAGATACCTGCATCGCCATGTTTTTGCAGT M 2 1 2 1 101000 f 74 goat Random2.2K-595 5 87969152 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438738 Affx-122930833 AX-123309075 5 87974373 CTTGACCATCTTTCAAATCCCCAGGCCCTCTACCC[A/G]CTTCCTCCCAACCCCCAACCCCCTCACCTAATCTA R 2 1 2 1 303000 r 74 goat snp51046-scaffold740-1052158 5 89195957 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383289 Affx-122972717 AX-123253647 5 88004443 AGTAGCACCCAGCTCTTTAAGATTATGCCCTCCCT[A/C]ATTTAGGGGTATCTTTTTATCTTTTAAGTATATTA M 2 1 2 1 202000 r 74 goat snp51045-scaffold740-1022088 5 89226046 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272322 Affx-1111833481 AX-519546058 5 88022737 AAACATTTCAGGATTAACATCTCAAGAAAGAAGTC[A/C]GTTGAGGAGGATATGAGTCTATGAGTGTGTACATT M 2 1 2 1 101000 f 74 goat 5_88022737_AF-PAKI 5 88022737 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320766410 Affx-122962837 AX-385253786 5 88046073 ACTGGAGTATATACCCTGTGCTCATTTTTACTCTT[A/G]TGTGGTTTTACATAGATCATTCAACAGTAAACTTT R 2 1 2 1 101000 f 74 goat snp51044-scaffold740-980458 5 89267755 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451357 Affx-122921251 AX-123321690 5 88102089 TTCACTGTGCTCGTCACCTGCTTCTGGAATGATGT[A/G]TCGACATGTGCCAGACACCTGCCAGGATGGGGCAC R 2 1 2 1 101000 f 74 goat snp51043-scaffold740-924442 5 89323362 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417027 Affx-122947966 AX-123287375 5 88137659 TGAATGTAGACCCGAAATATAATGAGATAACAGAC[A/G]CACTGGTTGTTTTCCTCACACGACAGTCCAGGGTA R 2 1 2 1 101000 f 74 goat snp51042-scaffold740-888872 5 89358394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796973 Affx-122923243 AX-385283914 5 88177818 TTGTTAAATAGTGATGAATAGTGATAACTGCCCTG[A/C]TGGTAGGTGATTAGAAAAAATGCTAGGATAATGAG M 2 1 2 1 101000 f 74 goat snp51041-scaffold740-848713 5 89398740 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426140 Affx-122940613 AX-123296486 5 88232809 GTGTACGGGCAGAACATTTTGACCTGAATGGTTTG[C/T]GGAGGCACCTATTAGCCAAGCTGACTGAACAGATG Y 2 1 2 1 101000 f 74 goat snp51040-scaffold740-793722 5 89453989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414758 Affx-122949250 AX-123285107 5 88265986 AGAGACAAAGTATTTTGAATCACCTAAACAATTCT[G/T]CAAATCAACAACAATAATAATAAAATCTGGGACTT K 2 1 2 1 101000 f 74 goat snp51039-scaffold740-760545 5 89487339 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402442 Affx-122958619 AX-123272795 5 88310318 TATAGAAATAGGCTTCTTTGCTGTGTTAGCTATGA[C/T]ATACAGGACTAAAATTTAAGTTCAACTGCAGTGAG Y 2 1 2 1 101000 f 74 goat snp51038-scaffold740-716213 5 89531205 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395678 Affx-122963748 AX-123266033 5 88345132 CATTCACTCAGCAATTAATATCCCACATCTGCTCC[A/G]TGCAATGTAATATGTCAGGTCAGTGGTAGATAGGA R 2 1 2 1 201000 r 74 goat snp51037-scaffold740-681399 5 89566019 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449494 Affx-122922630 AX-123319829 5 88377818 TTGAATGAATATACCAATAACACACATTGTTAGTA[C/T]AGTAAGGATCCCAAATGCTAAAATTTTACTGGTCA Y 2 1 2 1 101000 f 74 goat snp51036-scaffold740-648713 5 89601025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777574 Affx-122958370 AX-385264693 5 88411672 GCATAACTACAAAACACTCAGAAAGGTAATATTTC[A/G]TCTATTATTCTGATTTGGAAAACTACATGCAAAAA R 2 1 2 1 201000 r 74 goat snp51035-scaffold740-614859 5 89635206 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801787 Affx-122967514 AX-385288695 5 88443267 GCCAGTCTTCATTCTTTTGAGGACTCTGTAGACAG[C/T]ATTTTTTTAGTTTCTGTCTTAGAAGTTTTGGGCTG Y 2 1 2 1 101000 f 74 goat snp51034-scaffold740-583264 5 89667497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768486 Affx-122932109 AX-385255666 5 88499139 CTTGTGCTTTTCAGAGCAATGCTGTAACACACACA[C/T]GTACTAAAAATTATACTGGAATGCCCAATGAAGCC Y 2 1 2 1 101000 f 74 goat snp51033-scaffold740-527392 5 89721779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407540 Affx-122954692 AX-123277891 5 88554088 ATGGGTGTTCCGAGAAAATGCGACAGCAGTAGATG[C/T]AATCACTCTCTTATTCTGAAAAGTTATAAAAACAA Y 2 1 2 1 101000 f 74 goat snp51032-scaffold740-472443 5 89776741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415643 Affx-122948575 AX-123285992 5 88595271 GAGATAACTTGCAAAAGGTTCATGCCCTACTCTAT[A/G]TCACAAGTGATTCTGCACATTTGCTTCTTCATAGT R 2 1 2 1 101000 f 74 goat snp51031-scaffold740-431260 5 89818435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406569 Affx-122955096 AX-123276921 5 88628358 TTCAAGGAATATTTACCAGTAACTCAAGGAAAGGG[C/T]GATGGTAATGTGTTTCATGGTAGTGACAATCATAA Y 2 1 2 1 101000 r 74 goat snp51030-scaffold740-398173 5 89849204 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789586 Affx-122953844 AX-385276595 5 88673570 ATTACCAAATTATTCCATTTGACCCAGATGTGATT[A/C]TAGTAGAATCCACATTCTCCAATATTTATGGTCGA M 2 1 2 1 101000 f 74 goat snp51029-scaffold740-352961 5 89892651 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381728 Affx-122974692 AX-123252086 5 88702519 CTTATTTACTATCTGCATATCTTCTTTGGTGAAAT[A/G]TGTCGGTGTTTTTGTTCATTTTCTAATTAGAGAGT R 2 1 2 1 103000 r 74 goat snp51028-scaffold740-324012 5 89921559 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788572 Affx-122943273 AX-385275589 5 88739695 TATTATTGATATGAAAATATCTCCAAGACGGTTGT[A/G]CAGAATAGTAAAGATGCTATTCTTTTTGAGGAAAA R 2 1 2 1 201000 f 74 goat snp51027-scaffold740-286836 5 89955646 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445883 Affx-122925962 AX-123316220 5 88795533 CTTAAATATAAATAATCATAATAATAAAGCAGAGA[C/T]GATCCAAAACTAAACCAGAAAAAATAAATACAAGT Y 2 1 2 1 101000 r 74 goat snp51026-scaffold740-230998 5 90012167 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795675 Affx-122955393 AX-385282630 5 88828758 TTGAGACAGTGTAGGTCAACTTTGTAAAATAACTT[A/G]TCCTTCCTTCTCTGTTACAGCTCAGATACATTATT R 2 1 2 1 101000 r 74 goat snp51025-scaffold740-197773 5 90046486 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773621 Affx-122931477 AX-385260761 5 88863753 ATATTACAAGATGAATTTTCACCAGATGGTCATAA[G/T]CTGGTATTAAAATGCCAATATAAACTACATAATAA K 2 1 2 1 101000 f 74 goat snp51024-scaffold740-162778 5 90081778 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786716 Affx-122963751 AX-385273747 5 88904394 AATCAACATTCTAGAAATGAGCTAGTCATAGGAAA[C/T]GGTTATGTTTGCAAGACAATAAAATGTATCAGCTA Y 2 1 2 1 101000 r 74 goat snp51023-scaffold740-122137 5 90121504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431702 Affx-122936771 AX-123302043 5 88940487 TATGTACACTACTAATATAGCTCATTCTTCAGTGC[C/T]ACTATCATTGGCCTCATTTCTGTGTGAGCCTGTTC Y 2 1 2 1 201000 f 74 goat snp51022-scaffold740-86044 5 90157928 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437304 Affx-122931974 AX-123307642 5 88977054 TGAGCTCCTGCTTCTTCATATTCAGCATATTTACC[A/G]CTGAACTCAATGCCTTACCCTGCTCACTCAGGTCT R 2 1 2 1 101000 f 74 goat snp51021-scaffold740-49477 5 90194352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774158 Affx-122957946 AX-385261296 5 89024240 GTAGAGTCTATAGGTTTGTAGAATTTCCAGGTCTG[C/T]GGTAAAGGAAGTGAGGGACAAAGTTTAGCAACATG Y 2 1 2 1 101000 f 74 goat snp51020-scaffold740-2291 5 90241292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405689 Affx-122956549 AX-123276041 5 89032770 ATAGAAAGACTTTAAGTCTGCATATTTTCAGGTCG[C/T]GTGTATCTTGGAAAAATAAAGACAGAAATGCTCAT Y 2 1 2 1 101000 f 74 goat snp49212-scaffold702-6140 5 90249608 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399291 Affx-122960541 AX-123269646 5 89066877 AGGAGCACCAGTCTAATACTTTAGAGATTAAGCAT[A/G]TTTGTAATGTATTTTGAACACTGGAGAAGATTGCT R 2 1 2 1 101000 f 74 goat snp49213-scaffold702-40247 5 90283660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792604 Affx-122963158 AX-385279585 5 89114085 GTGCCAGCTATCAGTTTATTGACCCTGAGCTCCAC[A/G]TTCACTTTTGTTGTCTGATCTGTAAATGTGGATCT R 2 1 2 1 101000 f 74 goat snp47384-scaffold666-1627339 5 95447425 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790032 Affx-122946495 AX-385277038 5 89162496 AATTACAAAGCACTCAGAACGGTGCCTGGCACATT[A/G]TAAGGAAGATCTATGTAGATCTGTGTCTTATATTG R 2 1 2 1 101000 f 74 goat snp47383-scaffold666-1578928 5 95495641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411003 Affx-122951989 AX-123281353 5 89248174 AGGGCACTTATCACTTACAACTACATTTCTTTCTC[A/G]TTTTACTTGTTTTTGGCCCACTATTCTGAAAGTTT R 2 1 2 1 201000 r 74 goat snp47381-scaffold666-1493250 5 95581822 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378904 Affx-122976488 AX-123249263 5 89286456 ATACTCAGTTATGCCTCTCAGAATGTATAGAAATA[C/T]AGCAAGGGTACCAAATCCTAATCACAGAAAACAAG Y 2 1 2 1 201000 f 74 goat snp47380-scaffold666-1454968 5 95619570 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409243 Affx-122953144 AX-123279594 5 89332463 GCATTTAGTTATATTTCCACCAATATGGGAATGGT[A/G]CAGAGAGCATTTCTCTGCTATTATGGATATGCTTT R 2 1 2 1 101000 f 74 goat snp47379-scaffold666-1408961 5 95666162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785526 Affx-122949994 AX-385272570 5 89363461 TTTTTATTTTCAGAATCTAGCATGGTGTCTGATAC[A/G]CCCAGATATTTGATACATGTTTGTGGAGCTGAAAT R 2 1 2 1 101000 r 74 goat snp47378-scaffold666-1377963 5 95697011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451138 Affx-122921371 AX-123321472 5 89397302 TGGAACTAATCTAAGTAACAGCCCCAATCACAGTC[A/G]TTTCTGCTTCAGTCTTTGGTGTTAGGCTTCCATAT R 2 1 2 1 201000 r 74 goat snp47377-scaffold666-1344122 5 95730613 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418851 Affx-122946133 AX-123289199 5 89441075 TCTGAACTCTGCATGGCCATTTGGGCCAACGGCAA[A/C]TTTTCTACAGCGTACACAGACATACAGAGCAGCTG M 2 1 2 1 303000 f 74 goat snp47376-scaffold666-1300349 5 95774388 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395394 Affx-122963963 AX-123265749 5 89529649 TTTTCCCACTGGAGAGCCCTGGGGCTGTAGAGTTA[A/C]GCAGAGAAATGAATTATTTGTTTTCATCAAGGCTG M 2 1 2 1 101000 f 74 goat snp47374-scaffold666-1211775 5 95863069 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432710 Affx-122936021 AX-123303051 5 89574111 CATGCTGCAACCAAAAGAAAGCAGAAAGGGAACAA[C/T]AGATTTCAAAAGATGAACAACACACCCCGTTTAAA Y 2 1 2 1 201000 r 74 goat snp47373-scaffold666-1167313 5 95907779 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785417 Affx-122932785 AX-385272462 5 89605006 TCAGAAGCGCTGATGAGGCAGAGAACAGAGAAAGT[A/G]GCTTGACCAGAGACGCAAGAGCTCTGTAAGCTCGA R 2 1 2 1 101000 f 74 goat snp47372-scaffold666-1136418 5 95938450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779458 Affx-122969310 AX-385266561 5 89683259 ATCTTTACATTTTAGTTCAAAAGCTTGACTGAGAT[G/T]CCAGCAATTACCACTTACATTTAATTGTCTAAGAG K 2 1 2 1 101000 r 74 goat snp47370-scaffold666-1058165 5 96016833 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391154 Affx-122967449 AX-123261511 5 89732570 TGTAATAGCGCTTCAGTTAACTTTTTAAACATGGC[C/T]GTTAACCAGTGAAGTGTGAGTCTTATTCAGAAGAG Y 2 1 2 1 101000 f 74 goat snp47369-scaffold666-1008854 5 96065880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416544 Affx-122947752 AX-123286892 5 89768794 AGCTAGATGATCAAGTCAAGAACTACAACTCGGGG[A/C]TTCCCTGGTGGTCCAGTGATAGAGAATTCGCCTGC M 2 1 2 1 103000 f 74 goat snp47368-scaffold666-972630 5 96102019 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446853 Affx-122925257 AX-123317189 5 89825762 AATTGTTAACTGAAACCAAAGCTTCAAGTCATTCC[A/G]TCAATTGGTACTTAAATTCCTCTGCTGGTAAATGC R 2 1 2 1 101000 r 74 goat snp47367-scaffold666-915662 5 96159353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437344 Affx-122931945 AX-123307682 5 89923134 TCTGCAAACCCCAGATTAGCTTCAGCAAATAATCA[C/T]CTTAGCTGGCTTTCTGCTCTACCGTTACTTCATCT Y 2 1 2 1 201000 r 74 goat snp47366-scaffold666-818290 5 96254213 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453954 Affx-122919471 AX-123324287 5 89956313 CCTAGACATTTATATGAAGTTTTATTAACAGTATC[A/G]TATCTAACCTATGGTAAACAGCAGCCACTGATTTT R 2 1 2 1 101000 r 74 goat snp47365-scaffold666-785111 5 96287196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783883 Affx-122976730 AX-385270939 5 90000487 CCTGTACCCAAAATAGTCTCTATACTGTGATTATT[G/T]ATGTTGTGTCACATAAATATACACAGTTCATTAAT K 2 1 2 1 202000 r 74 goat snp47364-scaffold666-740937 5 96331556 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383243 Affx-122972752 AX-123253601 5 90045426 GGGCCACACACACACCTCAAGGGCAGCAAAGTGAT[A/G]CTGTCACGGAGGGAAGGAATTACACCAAGTTTTTA R 2 1 2 1 101000 r 74 goat snp47363-scaffold666-695998 5 96377077 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779524 Affx-122949336 AX-385266627 5 90104066 TTACAAAGCATATTCTCTTATGCTGCTATATTTTA[C/T]ACTAAACAACCCTAATAATCAAGATTAAAGTCATA Y 2 1 2 1 101000 r 74 goat snp47362-scaffold666-637358 5 96436168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412766 Affx-122950510 AX-123283115 5 90137307 GAATCAGCGTTAAGCACTCTTAAATTCACATGTTC[A/G]TTTGAGCCTCTCGGGTCTGCCAACCAGTTGGAAAC R 2 1 2 1 101000 f 74 goat snp47361-scaffold666-604117 5 96470238 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405831 Affx-122955877 AX-123276183 5 90169271 TGCAGATCCTCCTCCTAATCCATCCCCACAGAGGC[A/G]TTTTAACTTCTTTCTTGACTTGTTTTGAAAAGTCA R 2 1 2 1 101000 r 74 goat snp47360-scaffold666-572153 5 96502605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435623 Affx-122933778 AX-123305963 5 90208669 GCAAACAGAAATGGAAACATTACTTTAAAAAAATG[C/T]ATTCCTTTCCAGGAAGATCTGAACAGTGCAGGTAG Y 2 1 2 1 101000 r 74 goat snp47359-scaffold666-532755 5 96542039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384731 Affx-122972048 AX-123255089 5 90261736 GCCTTTCATTGAGCTCCTTGGAGTTTCCCCTGCAC[A/G]TTGCTGTTTAGGAGCACATGTTAAGGATTTGGGAG R 2 1 2 1 101000 r 74 goat snp47358-scaffold666-479688 5 96595092 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453389 Affx-122919923 AX-123323722 5 90361913 TGAGGCAGGTTCCGAGACAGATCAGATGAGGAGGG[C/T]AAGGGAAAGAAGCTGAAAAGATGACTCTTTGGGGA Y 2 1 2 1 101000 r 74 goat snp47356-scaffold666-379511 5 96695139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439682 Affx-122930581 AX-123310019 5 90393111 GGGTTGTCCTTACCTGGTGCTGTGGGTTGTTTACC[A/G]TGAGAGAGAGACAGAGATACCTGGCTCCATTCTAC R 2 1 2 1 201000 f 74 goat snp47355-scaffold666-348313 5 96726329 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376917 Affx-122977794 AX-123247276 5 90442136 GACCAGCTTTTGTAGTATTTCCTGCACTGAGAGTA[C/T]GTCACTCACCAGGAAAGCAAGAAAGGAGTCAATGC Y 2 1 2 1 101000 f 74 goat snp47354-scaffold666-299288 5 96775413 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406921 Affx-122955610 AX-123277272 5 90500671 ACTTTTACTGAAATCACCATACTGTTTGACATTTC[A/G]TTACTGCCTATTTGTAAGATTTTTTGGTACAAGAG R 2 1 2 1 101000 r 74 goat snp47353-scaffold666-240753 5 96834110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432192 Affx-122936393 AX-123302533 5 90538561 GGTTTTGCCATATGGCATGTGGTAAGTTGTTGCAG[C/T]AGGATGAAAGGACACGTGGAAAACTCTGGCCCTTC Y 2 1 2 1 201000 r 74 goat snp47352-scaffold666-202863 5 96872236 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379467 Affx-122976082 AX-123249825 5 90570742 TGTCCTCATGGGCACGATGAATGATAAGCAGACTA[A/G]TAAAAACAAAGGAGAGCTAGAAAAATTCCCTAGTG R 2 1 2 1 101000 f 74 goat snp47351-scaffold666-170682 5 96904583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272323 Affx-1111833482 AX-519546059 5 90586894 AGTGAAAATAAAACTAACAAGTATGTTGAGAGGAA[A/C]GGAAAGAAAGCAAAGAAAAAAATCATAGATATGCA M 2 1 2 1 103000 f 74 goat 5_90586894_AF-PAKI 5 90586894 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38379771 Affx-122975846 AX-123250129 5 90613401 TGAGGTGTGACCACTAGATGGAACCCCTGAGCCCA[G/T]GTCCATGCTGATGCTTTATAAGGAGAGGTGGTGAG K 2 1 2 1 201000 r 74 goat snp47350-scaffold666-128023 5 96948283 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789261 Affx-122964428 AX-385276272 5 90643018 AGAACTGTGGTTTTTAAAAGCCCATAATGTAGAAT[G/T]TACCATCTTAGGCTAATTTACCATCCAGTGGCTAA K 2 1 2 1 101000 r 74 goat snp47349-scaffold666-98406 5 96978712 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387937 Affx-122970024 AX-123258295 5 90688525 ACTGTGAATCCAGGTCTTTGTGAGAACTCAGTCTT[A/G]TGCAAGTTACTTGAACCTTCAAAATGCAGGGGACA R 2 1 2 1 101000 f 74 goat snp47348-scaffold666-52899 5 97020952 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792596 Affx-122927053 AX-385279577 5 90727371 CAACTGAAAAGAAGAATGCATGTACCTAAAAAAAG[C/T]ATGGAAACAATACCTTATTGTGAAATTATTAAAAT Y 2 1 2 1 101000 f 74 goat snp47347-scaffold666-14053 5 97060163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774252 Affx-122963536 AX-385261388 5 90748500 CGGCACAGCCACGAGCACTAAATATTCACTGGCTC[A/G]TAGATCTTCAATAATAGTCCCTGAATTTCTTTGCA R 2 1 2 1 102000 f 74 goat snp56978-scaffold903-6977 5 97131125 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445011 Affx-122926637 AX-123315348 5 90817334 CTTTCCCTTTCTCCTAGGACCTGCTTGTCAACTAC[A/C]AATTTCCCTCTTACCCTTAGCTTCATTTTGCAGGG M 2 1 2 1 201000 r 74 goat snp56979-scaffold903-75811 5 97201888 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386525 Affx-122970736 AX-123256883 5 90849114 TGAACTGAGACAAGTAAAATGATTAACAGTGAAGA[C/T]ACTGATTAGACAGAGCAAGAGCCCAGTAGATGTCA Y 2 1 2 1 101000 r 74 goat snp56980-scaffold903-107591 5 97227891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439718 Affx-122930554 AX-123310055 5 90935916 AGCTGTTTCTTTTAAATGATTTTTAAATGAGAAAT[A/G]TATCTGGGAGCCAGTTACAGTTTGGCTGATTGTCA R 2 1 2 1 101000 r 74 goat snp56982-scaffold903-194393 5 97315438 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798182 Affx-122951032 AX-385285117 5 90987594 GAACCTGACTTGCTTCATGGAATTCTTCCTTTTGC[A/G]TATATACTGCGTCATGAGTATCACTGCAGTTCTCC R 2 1 2 1 102000 f 74 goat snp56983-scaffold903-246071 5 97365311 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435716 Affx-122933304 AX-123306055 5 91028831 ATCTGTGTCTCTACACTGATCTGTGTCCCACTTCC[A/G]CGACTGAAGCCTTTATGCTTTGACCCAGGTGTATG R 2 1 2 1 101000 r 74 goat snp56984-scaffold903-287308 5 97405907 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411636 Affx-122951578 AX-123281986 5 91063138 TTGTAAATGAATTCAAAGCTATTTATTTTATGCCT[A/G]TTGATTTAGGTACATTCCACAGCATTGACAAATGG R 2 1 2 1 101000 r 74 goat snp56985-scaffold903-321615 5 97440697 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784072 Affx-122942678 AX-385271125 5 91094813 GTGACAGAGTGTTTTGGTGGTATTGGGCATACATC[A/G]TACATTTAATACTCTTTTAAGTTATAGGTTTACTT R 2 1 2 1 201000 r 74 goat snp56986-scaffold903-353290 5 97472519 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411467 Affx-122951803 AX-123281817 5 91151715 GTTGAACTCAATAAGGCTAAGCTTTGTGCAGGGAA[C/T]GATGCTCATCTTTGCTCGTGCCCACGTCTGTGTTG Y 2 1 2 1 101000 f 74 goat snp56987-scaffold903-410192 5 97529808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769612 Affx-122941513 AX-385256782 5 91189871 CAGGCCTCAGCACACAACGACTAATGTTAGTTTTC[G/T]TGCTGTGTCGAATCCCCTTAGTCTCCACGTCTTCA K 2 1 2 1 201000 r 74 goat snp56988-scaffold903-448348 5 97567890 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385916 Affx-122971571 AX-123256274 5 91219419 GTGGCCCAGGAGACACAGTGCTGGTTTCTTCAATT[A/G]CAGTGTGGGAAGAGAATGATTTTTTGACACTGAGA R 2 1 2 1 101000 f 74 goat snp56989-scaffold903-477896 5 97597665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278275 Affx-1111836338 AX-519551762 5 91262824 AGGCTGTATAACCAATGAGTACCACATTAAAGATC[A/G]CCAAATCTTTAAAAGATACACCTAGTACTTCACAG R 2 1 2 1 101000 f 74 goat Random2.2K-599 5 91262824 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320802023 Affx-122937416 AX-385288927 5 91271808 AAGATAACCTCTTTCATTTTAGAGGATCTGGATCA[C/T]GTTACAGCTGTACCTAGGCAACTGACCAGCCATGA Y 2 1 2 1 101000 r 74 goat snp56990-scaffold903-530285 5 97650337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423665 Affx-122942337 AX-123294011 5 91302985 AACACACACCTTTGGGCCTATTTGTGTTCAGACCT[A/G]TCCTTTGCTCTTCCCTCCTCAGCTTCTTATTGTGG R 2 1 2 1 101000 f 74 goat snp56991-scaffold903-561462 5 97681489 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431911 Affx-122936000 AX-123302252 5 91422708 AGGGGACACAGGTGTAGCAAAGACTTGGAAGAATT[A/C]TTTGTTAAACCAAGAGAAATAGCTTTCCTGTGCAT M 2 1 2 1 101000 r 74 goat snp56994-scaffold903-681185 5 97801997 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454084 Affx-122919373 AX-123324417 5 91462928 AGTACCTCTGAGAATTGTTTTCACTTTCTGAAAGA[C/T]AATGGGGGACAAAGGACGTGATCACCATGTTGTTA Y 2 1 2 1 202000 f 74 goat snp56995-scaffold903-721405 5 97840405 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416142 Affx-122948286 AX-123286491 5 91488692 TATGACATTTTACAATAGAGAAGTAGAGTCAACAG[A/C]TGTAGTAAATAAATTTATGGTTACCACCTAGACAG M 2 1 2 1 101000 f 74 goat snp22602-scaffold2239-298641 5 97886752 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765570 Affx-122966523 AX-385253050 5 91564436 AAATAAATTTCCAGTAATAAGATTTTCTCCAACTG[A/G]TATATCAATACAGCTGATTTTTGTTAATAAAATCT R 2 1 2 1 101000 f 74 goat snp22600-scaffold2239-222897 5 97963504 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408929 Affx-122953946 AX-123279280 5 91613126 CCCAATAGAGCCTTGAGAACAAAACTTGCCAGCTT[A/G]CATAATATTAAGGAACTCAGTCCTGTCTCTTTGTG R 2 1 2 1 102000 f 74 goat snp22599-scaffold2239-174207 5 98012304 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404978 Affx-122956404 AX-123275330 5 91661845 GTAATATCTGAAATTAAAAACTCAGGGGATATACA[C/T]GATGGAGTATTACTCAGCCATTAAAAAGAATACAT Y 2 1 2 1 103000 f 74 goat snp22598-scaffold2239-125488 5 98061390 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780417 Affx-122921791 AX-385267509 5 91695356 GAAAGATAACTTTGCAAAAAGGATTTTGTTAGTAA[C/T]AGTGGTAAAGTAATGGAGGTTTAAAGTCTCTAGAG Y 2 1 2 1 101000 r 74 goat snp22597-scaffold2239-91977 5 98095595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429306 Affx-122938604 AX-123299648 5 91742116 AAGCTAATGTTGCTAACTGTGATGATGCATGTCCA[A/G]TGAATAACAGTACTAATGTGACAAAGCGACAGTTA R 2 1 2 1 101000 r 74 goat snp22596-scaffold2239-45217 5 98142806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791496 Affx-122932853 AX-385278487 5 91783769 GAGCAGAAGCAACATTATAATGACAGAATTAGATA[C/T]AATTGTCCCCTGATATTTACAGGAGATTGCTTCCA Y 2 1 2 1 101000 r 74 goat snp22595-scaffold2239-3564 5 98183523 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385766 Affx-122971063 AX-123256124 5 91800737 AAGGATCGGGGGGTGGGCAAGTTGGGGCCAGAGAC[C/T]GTGGACCACAGTAACTTCCTGCTCTCCTTTGCTTT Y 2 1 2 1 101000 r 74 goat snp12674-scaffold1486-607537 5 98208521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785734 Affx-122958741 AX-385272775 5 91832593 TGGGATGAAGTAAAGGTGATGTAATGTATGTGATC[A/G]TGTATATGTGGTTACATAAGGTATTGTACCTATCT R 2 1 2 1 101000 f 74 goat snp12673-scaffold1486-575681 5 98241569 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764881 Affx-122928075 AX-385252476 5 91861811 TCAAAGTCCCTGAGATTTTCTTATGGTCCATGTAC[A/G]TCAAATGCCTAATACTCTTACTTAAAATTCTGAGT R 2 1 2 1 101000 f 74 goat snp12672-scaffold1486-546463 5 98270898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408746 Affx-122953403 AX-123279097 5 91911206 TATAGAATAGACACCCAGAATGAGTTTACTGAAAA[G/T]ATGGGGTCACCAGCCTCTTTCTTCTCAGCCCTTCA K 2 1 2 1 201000 f 74 goat snp12671-scaffold1486-497068 5 98319196 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406170 Affx-122956161 AX-123276522 5 91953286 GAACATAACCTCAATAAGAGCACAACTCTCATATG[C/T]GTCTTTTACCACTTAATCCCCCAGAAAATAGAACA Y 2 1 2 1 201000 f 74 goat snp12670-scaffold1486-454988 5 98361317 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425573 Affx-122941427 AX-123295919 5 92024157 CCCTTGATGCTCCCTGCTCCAGTTTCAGCTTCACC[A/G]CCCAGCTCCAAGTCAGGAGTTTCATGGCTATCTTT R 2 1 2 1 101000 r 74 goat snp12669-scaffold1486-384117 5 98431410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406300 Affx-122956067 AX-123276652 5 92079890 AACTTATTTAGGGCAATAGGTAGAAATACAGAGAT[A/G]CAAGTAGACAAAGAGAAATAATGGATATAAATAAG R 2 1 2 1 101000 f 74 goat snp12668-scaffold1486-328384 5 98487960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438179 Affx-122931833 AX-123308517 5 92116974 CTACAGTCCATGAGGTTGGAAAGAATCTGACATGA[C/T]TGAGCACCTAACACTTTCACATAATTTCAGTATTG Y 2 1 2 1 103000 f 74 goat snp12667-scaffold1486-291300 5 98526514 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410405 Affx-122952423 AX-123280755 5 92158267 CAGAGAACTAATATTCAAAAAACAAACACAGTAAG[C/T]AGAGAAAATAATTGTAACCTTAGAGCACATTACCT Y 2 1 2 1 101000 r 74 goat snp12666-scaffold1486-250007 5 98568346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797486 Affx-122924092 AX-385284425 5 92196647 TTTCCAACATAATATCTTCTCCATGACCACAAGCA[G/T]CACATCTTTTGGAATCAATCCTTGAGTAATACCTT K 2 1 2 1 101000 f 74 goat snp12665-scaffold1486-211627 5 98605966 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427118 Affx-122939661 AX-123297461 5 92295801 TGTAGTAGAGAGTTTAAGGAAATGGGTGGGGAGCA[A/G]CAAAATCTGATAAAAGGAAACAAAACAAGGATAGT R 2 1 2 1 101000 f 74 goat snp12663-scaffold1486-112473 5 98705724 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434914 Affx-122934319 AX-123305254 5 92356456 TCACTAAAACTCTGACTGTGATAATAGTCATACCT[A/G]TCTCAAAGAACTGTTATTGTTTTGTTAATAAGTAA R 2 1 2 1 101000 f 74 goat snp12662-scaffold1486-51818 5 98767194 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448680 Affx-122923875 AX-123319016 5 92393428 GTACTTCCCCAAGAGAAATGGAAGAGTATGTCAAT[A/G]CAGAGATAGGTACCTAAATTTTTATAGAAGCTTAA R 2 1 2 1 201000 r 74 goat snp12661-scaffold1486-14846 5 98805158 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797499 Affx-122958456 AX-385284438 5 92440648 AAAACAGATGGATAATAAAAAGGCCAAGTGAATGC[A/G]TATGACTTGACAGGGCATTTCTTTAATCCTTTGAT R 2 1 2 1 101000 f 74 goat snp43893-scaffold593-1071376 5 100698068 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431400 Affx-122936541 AX-123301741 5 92469468 AATCTGCCAAAGATCAACTAGCTCACCTAATACAT[A/C]GGAGAGGGGAGAGGATTCCAGTCAGGAGTCCTAAT M 2 1 2 1 201000 f 74 goat snp43892-scaffold593-1042556 5 100670978 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392398 Affx-122966216 AX-123262755 5 92550937 CTGGAAAAATGGATAGACTAGAAAAAAAAGCTTTC[A/G]TTTAGTGATAGAGTTAGTAGAAATTTAATAACAGA R 2 1 2 1 201000 r 74 goat snp43890-scaffold593-961087 5 100581649 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401829 Affx-122959446 AX-123272182 5 92635892 CTAGAGGCAGAAAGGAGGCTCTGCAGCTACTCCAT[A/G]TTGTTCTAAGTGGAAAGGGTTATGACTTGAGATCT R 2 1 2 1 101000 r 74 goat snp43889-scaffold593-876132 5 100496745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415102 Affx-122949446 AX-123285451 5 92679764 CACTGCTTTCGACTTCCTCATTAGAACAGTAAACC[G/T]CAAAATTTTTCACATTGCAGCACACATGGAAAATA K 2 1 2 1 101000 f 74 goat snp43888-scaffold593-832260 5 100451811 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396834 Affx-122963269 AX-123267189 5 92734904 TACCATATGTTCATGTTTTTGCTTTTGTCACATAG[A/C]GTTATTATATTCCTTTTTCCACATGTTAAATGATT M 2 1 2 1 201000 r 74 goat snp43887-scaffold593-777120 5 100394370 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404055 Affx-122957157 AX-123274407 5 92798538 TTTGGATACCATATGTTTATGTTTTGCTTTTCTAA[C/T]GTAGCATAATTTCAGTCCTTTTTCCACACGTTAAA Y 2 1 2 1 103000 r 74 goat snp43886-scaffold593-713486 5 100328328 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781329 Affx-122922471 AX-385268414 5 92866491 GTAATTTAAGCCTCCAAAACCGGACTGCACTTAGT[A/C]GGTGCTCTAGAAATGTGTTGAATGTTCAAAGGCTG M 2 1 2 1 101000 f 74 goat snp43885-scaffold593-645533 5 100261940 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278278 Affx-1111836340 AX-519551765 5 92950138 AACTTCATGCAAATGATGAGGCTAAAGACTTCAGA[A/C]TTCCTTGGCTTTGACTCCCATGTATTTTTTTTTTT M 2 1 2 1 101000 f 74 goat Random2.2K-601 5 92950138 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451425 Affx-122921177 AX-123321758 5 92956576 AGAGTCTCATTCCACAAATATTTACGGGATCTACT[A/G]CGTGCCGCACACTCTTTTAGATGTTTGGGTTAAAT R 2 1 2 1 101000 r 74 goat snp43883-scaffold593-555448 5 100170789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406737 Affx-122955744 AX-123277088 5 92986513 ACTTAAAGGACACCAAAAAGATACTTTGCTTCCCC[G/T]CTCCCCTTGTCTATACTAGTCTGTTGCTGGAAAAC K 2 1 2 1 102000 f 74 goat snp43882-scaffold593-525511 5 100140908 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801534 Affx-122977688 AX-385288443 5 93020975 GGTGTCTCCAAAGAGGATGCGAATGATAATACCTT[C/T]CTAGATCTGGAGCTACTTCCAAAAATAACCCAAAG Y 2 1 2 1 101000 r 74 goat snp43881-scaffold593-491049 5 100106444 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443074 Affx-122928123 AX-123313411 5 93052542 GAATTAGATTGCAACTAGGCTTCAAGAAATATGAA[A/C]AATGCATTTAAATCTCATCATTGAATGAAAAGAAA M 2 1 2 1 101000 f 74 goat snp43880-scaffold593-459482 5 100075452 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440539 Affx-122929328 AX-123310876 5 93096471 GTTAACGAGGCAACTTTTGGAATGCCCTTATGTTG[C/T]CTAAGGAAAAGGGCTGGTTGCCAAGGGAGATAGAC Y 2 1 2 1 101000 f 74 goat snp43879-scaffold593-415553 5 100031323 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788192 Affx-122940807 AX-385275211 5 93146761 GATAAAGATGTGATTCTTTTTCCCATCTAAGATTA[C/T]AGACCTTCTAAATCCTATTCAGGATCCCTTGGGGA Y 2 1 2 1 101000 r 74 goat snp43878-scaffold593-365263 5 99979645 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447153 Affx-122924442 AX-123317489 5 93187287 GAAATATTTTTTTAAATGAAGAAAATATAAATAAA[C/T]AAATAAATACAATTCCAACCATGTGAAATGAGTTA Y 2 1 2 1 103000 r 74 goat snp43877-scaffold593-324737 5 99938841 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272224 Affx-1111833483 AX-519545971 5 93192235 CTGTGGAGTCACACAGAGTGGGACACGACTGAAGC[A/G]GCTTAACAGCCATGCAAGTGTGGGGAATGGAGTAG R 2 1 2 1 102000 r 74 goat 5_93192235_AF-PAKI 5 93192235 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320765464 Affx-122957026 AX-385252962 5 93243172 AAGGCTACGGCCCTCACCAAACCACCATCTATATT[A/G]CTTGGATTATTCCAGTAGCCTCTCAACTCATCTTT R 2 1 2 1 101000 f 74 goat snp43876-scaffold593-268852 5 99882273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438237 Affx-122931433 AX-123308575 5 93276141 GGTATGTGACAACTTGGCCAGCTCTCGCTCCCTTA[A/G]GTTCTAAAATTGCCTCAAGGCATTTTTGGGAATGG R 2 1 2 1 202000 f 74 goat snp43875-scaffold593-235883 5 99849530 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437953 Affx-122931618 AX-123308291 5 93306307 AGTGGAAATTGGTAACTTAATAGTGCCAAGTCTCC[A/G]CTGGCTATTAAAAGGGCACACGGTGGGTGAGAGGA R 2 1 2 1 201000 f 74 goat snp43874-scaffold593-205717 5 99819492 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447615 Affx-122923994 AX-123317951 5 93340470 CATGGGAGTATATGTGACCATCATATCTACTACTG[C/T]GGGCAGGAATCCCTTAGAAGAAATGGAGTAGCCAT Y 2 1 2 1 103000 f 74 goat snp43873-scaffold593-171554 5 99785222 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772715 Affx-122946222 AX-385259862 5 93368997 AAGATAAGTCTACTCCCTGAATCTACCCGGGAGAA[G/T]CTACCTACCTGTGAAAAGTTACCAGTGAAAATGCT K 2 1 2 1 101000 f 74 goat snp43872-scaffold593-143027 5 99756163 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442344 Affx-122928039 AX-123312681 5 93401605 TTAAGATACTAAAAGTGTGGGAACTCCCTGGTGGT[A/C]CAGTGGATAAGATTTTGCCCTCCCAATGCAGGGGG M 2 1 2 1 303000 r 74 goat snp43871-scaffold593-110419 5 99723618 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786655 Affx-122957102 AX-385273687 5 93438419 CTATTTAAAAACTAAATGTAAGGACTCCCTTCAGC[A/C]AGTAATATCCAAACAGGTACTAAGGGAAGAGGTGA M 2 1 2 1 101000 r 74 goat snp43870-scaffold593-73605 5 99686788 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398892 Affx-122961027 AX-123269247 5 93482469 CAGATGAATGTGGAGTTAATTTAATTAATATCCAT[A/C]TGTTTTGTTCAATTCAGAGTATTCTGAAGACAAAG M 2 1 2 1 101000 r 74 goat snp43869-scaffold593-29555 5 99642510 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775649 Affx-122938045 AX-385262780 5 93513447 TCTTCAATCTTCATAACTGCAACTATCATCAATTC[A/G]TATTTTAAAATCTTAGTCATAATTAAATATGCTTC R 2 1 2 1 202000 r 74 goat snp28633-scaffold308-274286 5 99610616 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418608 Affx-122946353 AX-123288956 5 93548875 AGCATAACAATATACAATTGTTATTTATTGTTATT[A/G]TTGTCATATAGATGTTTATCTCAGTGATGAAACAG R 2 1 2 1 101000 r 74 goat snp28632-scaffold308-238858 5 99573680 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441415 Affx-122928830 AX-123311752 5 93611281 GATGAAACTTATGAAATATTTTATAAATTAAAATT[A/G]CCATGTAAATGAAATGAATAGCATTGCACAGTGGA R 2 1 2 1 101000 r 74 goat snp28631-scaffold308-176452 5 99509933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395079 Affx-122964178 AX-123265434 5 93643684 GGCATTCTCAAAAGGAACACAACTGCTTTGAACAA[C/T]GATGAATAAATTCTTCTTACCTCACCAGGTTACAA Y 2 1 2 1 101000 f 74 goat snp28630-scaffold308-144049 5 99476638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379063 Affx-122976333 AX-123249422 5 93685434 AGTGTGAGTTCTATGGAAAGTGAAGTGAAAGTGTT[A/G]GTCATTTAATCATGTCCAACTCTTTGCAACCCCAT R 2 1 2 1 103000 f 74 goat snp28629-scaffold308-102299 5 99434832 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448132 Affx-122924293 AX-123318468 5 93809820 CCATTATGCCAAAGAATACAGAACAATTACCATGA[C/T]GAGACTATGTCACAGAGGTCAAACACAGCAGCTGT Y 2 1 2 1 101000 f 74 goat snp53179-scaffold80-449962 5 101130227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781067 Affx-122976401 AX-385268154 5 93933284 GACTTTGAATTTTTTATTTACCCTGTTTTTCTGCT[A/G]TTAGGACAGTTACCTACATATTGTATGCACTCATT R 2 1 2 1 201000 f 74 goat snp53177-scaffold80-326498 5 101257555 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414924 Affx-122949103 AX-123285273 5 94043055 AAAAAAAAGGGAACCACAACTTTCCTTCACACCCT[A/C]TTCACCTTTCACCTTCAATCTTTCCCATTGGTCTT M 2 1 2 1 201000 f 74 goat snp53175-scaffold80-216727 5 101366646 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417600 Affx-122946880 AX-123287948 5 94078007 TACTAGGTACATTCGAGCATGGGGATTACACAAGG[A/C]TGTGAACACAGGTAACAGAAACATCCGGGACACTG M 2 1 2 1 201000 r 74 goat snp53174-scaffold80-181775 5 101401688 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775389 Affx-122941199 AX-385262520 5 94135526 GTCACTTGATTGGTCCTGAGGAAATGTCACTTGTG[C/T]AAGGATGTTTAATTATTACCTTCCTCAGAAAACAG Y 2 1 2 1 101000 f 74 goat snp53173-scaffold80-124256 5 101459541 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446816 Affx-122925285 AX-123317152 5 94292519 CTTTAAGTGACTAGATTTTAAAGTAATTTTGTTTC[A/G]TGGGAACAGTAACTAGAAAACACTCTCAGCATCAA R 2 1 2 1 101000 r 74 goat snp14503-scaffold1584-32638 5 102084477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423068 Affx-122942947 AX-123293414 5 94307142 TTTCTGCTCTGGATTTCTCCTAAACATAGTACTTC[A/G]CCTCCAAAAATCCAGTAAAGGGGATGAAACTCTCC R 2 1 2 1 101000 f 74 goat snp20971-scaffold2055-13810 5 102108018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410755 Affx-122952693 AX-123281105 5 94353657 CCCTCCCCCTGTGGAGGTGGTACGGGGGAAGAAGG[A/C]AGGCAGAGGCTCAAGGTAAAGCTGAACCCTCTCTT M 2 1 2 1 101000 r 74 goat snp20972-scaffold2055-60325 5 102154877 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390638 Affx-122967150 AX-123260995 5 94382834 CTACTCCAGGGCCTTAACCTTTCCTATCCCACCAC[C/T]GGCACCACACACAACACTTCCTGCCCGTAGAAGCA Y 2 1 2 1 202000 r 74 goat snp20973-scaffold2055-89502 5 102184157 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401744 Affx-122959512 AX-123272097 5 94418667 CCTGCCCTAGGACCTCTTCCCCTGAAAGCAAGTTA[C/T]ACCCACCCAGCTTTCCCATGAGCCTGGCTCCAGCC Y 2 1 2 1 101000 f 74 goat snp20974-scaffold2055-125335 5 102219590 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448433 Affx-122923656 AX-123318769 5 94478063 TATTAGTTTTATTTATCTTTATTTTTATGTCTAGA[C/T]ACACATCTAGATATATATTTTCTGCCTTGGCAGGG Y 2 1 2 1 103000 r 74 goat snp20975-scaffold2055-184731 5 102278436 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791970 Affx-122935719 AX-385278958 5 94542950 CTCTCTAGACCTGGGATCACTCACCACATTTCTGG[C/T]AATTTGTTCATCCCTGGTGAGCAGCTCATCTCTTG Y 2 1 2 1 101000 f 74 goat snp20977-scaffold2055-249618 5 102343637 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445681 Affx-122926132 AX-123316018 5 94584186 GTTGTACTTTCTCTTCTGGACTGAAATCCCTTTCC[A/G]AGTGAGTACGCATGCTAACATGTGATTATATATGT R 2 1 2 1 201000 r 74 goat snp20978-scaffold2055-290854 5 102385231 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453721 Affx-122919630 AX-123324054 5 94613150 GGAAGACGGGGCTCCCCAGCTGTGCCTCTGCCGCC[A/G]GCCACATCTCCATTTGGGGCCAAAGGGGAAACTCT R 2 1 2 1 103000 r 74 goat snp20979-scaffold2055-319818 5 102414044 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392312 Affx-122967517 AX-123262669 5 94663190 TCCTGGAGCTCCTGGGATGGGCCAGCACTGTCTGG[G/T]CAGCACCCCCTGCAAGCTGCAGAGGCCTGAGGACA K 2 1 2 1 303000 r 74 goat snp2707-scaffold10780-9376 5 102464695 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278441 Affx-1111836341 AX-519551926 5 94669432 CATACCACATTTTTTTTTAGTTTTATGCCCAGTGA[A/G]TAAAGATATTATCTCTGCCTTATGTACCATGAAAC R 2 1 2 1 201000 r 74 goat Random2.2K-602 5 94669432 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320774506 Affx-122976760 AX-385261641 5 94682371 GGAGGGGGGATGTTATCAATCCTGTAGAATCTGAT[A/G]TAGATACGGCAAGGTCACAAGGTAAGATACCATGT R 2 1 2 1 101000 f 74 goat snp51115-scaffold748-9706 5 102482386 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413730 Affx-122950062 AX-123284079 5 94729498 CACTTGTAATACTTCTTTACTTAAGTGGGACCTGT[A/G]TCTTTCCAGAAGAGGAGAGGATGGGAGACAAACAT R 2 1 2 1 101000 f 74 goat snp51116-scaffold748-56833 5 102526672 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411162 Affx-122951872 AX-123281512 5 94762021 AGCACCACTCTGCTAGCCTCTCAGAGCGCATTCTC[A/G]TTCAGTTATAATGGAGGAAGCACAGCTTCTGAGGT R 2 1 2 1 101000 r 74 goat snp51117-scaffold748-89356 5 102559185 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439484 Affx-122930157 AX-123309821 5 94887862 GTTCTGAGGAAAATCTGAGTATCCAGATGTTTTTT[A/G]TCATCTTAGGAGAAAAAAGTCGTTAATTCAAAGCT R 2 1 2 1 101000 r 74 goat snp51119-scaffold748-215197 5 102684909 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422798 Affx-122943208 AX-123293144 5 94931312 CGCCCCAGTGCAGAACCCACTGTGGCTGAGTGAGC[A/G]CTGAGAACAGAGCTCATTCATGGTTCCAATGGTGT R 2 1 2 1 101000 r 74 goat snp51120-scaffold748-258647 5 102728816 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781797 Affx-122972421 AX-385268879 5 95025634 TTCGTTGATGACCTGCACAACCTGAACAAACGCAT[C/T]AGCTTTCTCTACAAACGCTTTAATCGACATGGGAA Y 2 1 2 1 101000 f 74 goat snp51122-scaffold748-352969 5 102823118 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407459 Affx-122954780 AX-123277810 5 95068430 AGTCTCTGTGCTCATTAAAAATGACCTTTTGGAAA[C/T]GAAACAGCTCAAGACTGGGAGGTCCATGTTCCTCT Y 2 1 2 1 201000 f 74 goat snp51123-scaffold748-395765 5 102865142 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382131 Affx-122974055 AX-123252489 5 95103609 TGGGCTGGAAATGGGAATGGGAGGCAGTAAAGGGA[A/G]GGTGGGCTTGGGGTTGTGAGCAGACATGGCTGCGG R 2 1 2 1 101000 f 74 goat snp51124-scaffold748-430944 5 102900900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272345 Affx-1111833766 AX-519546076 5 95110783 GGGGCAGGGGACAACCTGCAGACAGGCAGGGCACA[A/G]CAGGGAGGCTCAGGGGAGGCGAGCGGAGGCCCCCT R 2 1 2 1 202000 f 74 goat GoatD01.003970 5 95110783 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38393364 Affx-122965920 AX-123263720 5 95153072 GATAAATATATTCCTACTGCCCAGCACTGACTCCC[A/G]TCTTCCCACTTTGGTTATCACTGGCTTTTACTGGA R 2 1 2 1 101000 r 74 goat snp51125-scaffold748-480407 5 102947848 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433947 Affx-122934282 AX-123304288 5 95192209 AAAAAAAAAAAAAAAGTGTTAGAGCAAGATTGAGG[A/C]GACCTGGGTACTTCTTCACCAGAGACAAACAGGCT M 2 1 2 1 101000 r 74 goat snp51126-scaffold748-519544 5 102987044 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379764 Affx-122975850 AX-123250122 5 95224466 CGAAGGCTGGACGTCCAGCTCCAGGGAGTTCTGAT[A/G]CCCAGGCTCTGGAGTCCTCTGCGATCCTGAGATGT R 2 1 2 1 201000 f 74 goat snp51127-scaffold748-551801 5 103019030 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799263 Affx-122924519 AX-385286193 5 95300374 TTATTGACACCTTATGTTAATGTGATATACACGTT[A/G]CTATTGATGAAGCCATATAAGTACATTGTCAGCTC R 2 1 2 1 101000 r 74 goat snp51128-scaffold748-627709 5 103095868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441408 Affx-122928835 AX-123311745 5 95336900 TTTTTTCTGTCTTATTTTATGGTATCTGTCCTGCT[A/G]TTTCAGTCTAGTTGTCTTTATTTCTAGTTCCCCTC R 2 1 2 1 101000 r 74 goat snp51129-scaffold748-664235 5 103132789 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419677 Affx-122945938 AX-123290025 5 95398265 GACGGTTGGGGGCCGGGCAGAGGAGGACATGTGAG[C/T]AAAGCCCCCTTTAAAGTTCTTGTGATTAAGCTAAT Y 2 1 2 1 101000 r 74 goat snp51130-scaffold748-725600 5 103193840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400416 Affx-122959983 AX-123270771 5 95445123 CGACACTGTGGCTTTGCTGTCATTTTTCATTCATT[A/G]TTGTTGAAGGACCTAAAACTGTAGGGTATTTATTA R 2 1 2 1 201000 r 74 goat snp51131-scaffold748-772458 5 103240788 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392945 Affx-122965697 AX-123263302 5 95487487 ATCTCCCGGGGGAGGTACCCCAAGCAGCCTGGGGG[C/T]GGGGATTCAGAGAGAAGCAAAGAGAGCAAGTCAAG Y 2 1 2 1 101000 r 74 goat snp51132-scaffold748-814822 5 103283373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376301 Affx-122978368 AX-123246660 5 95533650 TGTGAGCATCAGGAGACACTCAGGCTGATGATACA[C/T]GCATGCTGATGCAATAGACCTCTAGGGGTGGGAGT Y 2 1 2 1 101000 f 74 goat snp51133-scaffold748-860985 5 103329403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444991 Affx-122926654 AX-123315328 5 95564117 TTCAGAATTACTGGGTCGGAAAGAGTGTAGAGTGT[A/G]TGTATGAGTGTGTGTGAGTGTGTGTAAGTGTGTGT R 2 1 2 1 201000 f 74 goat snp51134-scaffold748-891452 5 103359924 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399899 Affx-122960207 AX-123270254 5 95594534 GCAAAGAGTCGGACACGTCTGAGGTGACTGAGCAC[A/G]CACACGCCTCCTGTTACAGGGCAGAGGCCCTGATC R 2 1 2 1 201000 r 74 goat snp51135-scaffold748-921869 5 103388917 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404117 Affx-122957108 AX-123274469 5 95650657 TGTCCTTAAAGCTCCAGGTATTCAGCTTGCCTTTG[A/C]GCAGGTGGGCATTCGATGACCATGGATTGAGTTCA M 2 1 2 1 101000 f 74 goat snp51136-scaffold748-977992 5 103445136 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443331 Affx-122927441 AX-123313668 5 95701540 TTATCGTGTTGAGTGTCTGGCCCAAGGCAGGCAGG[C/T]GCTCGATGCATATTTGCGAGCTGGTGCTCTTATCC Y 2 1 2 1 201000 r 74 goat snp51137-scaffold748-1028875 5 103495707 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453165 Affx-122920473 AX-123323498 5 95755008 ACACTGCTATTTGCAAAAGCTGGATCTGCCCTGGG[A/G]GAGAAGTGGGAAGCGTGCGGCACCTTTGCTTTCTG R 2 1 2 1 101000 f 74 goat snp51138-scaffold748-1082343 5 103548872 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272226 Affx-1111833484 AX-519545973 5 95784797 CAAGCATACGCTTATGGTATAGCAGGGCAGTGCTT[A/G]TCCAAAGTGTCAAAATATGTCCCAATCAAAGGGTG R 2 1 2 1 101000 r 74 goat 5_95784797_AF-PAKI 5 95784797 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38417365 Affx-122947714 AX-123287713 5 95788107 CTGTGAATTTGATGAATGGATTGGCAAGAGAGACC[G/T]CAATTACCAAACACACCAGGGGCTTCCCTGGTGGC K 2 1 2 1 101000 f 74 goat snp51139-scaffold748-1115442 5 103581920 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415339 Affx-122948791 AX-123285688 5 95844482 ATGCACTATCTCTCTCTCTCTGCCCTCAAAATCCC[A/G]CGAGACAGGCATCATTCTATCGCCATCAGACTCTG R 2 1 2 1 201000 r 74 goat snp51140-scaffold748-1171817 5 103638244 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384891 Affx-122971926 AX-123255249 5 95881684 CACCAACACTTTGGACCCAAAGCTGTCTTTCATCA[C/T]GGACACAGTCCTCATAATTGCTCATAAACCGCTAG Y 2 1 2 1 101000 f 74 goat snp51141-scaffold748-1209019 5 103675737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378610 Affx-122976570 AX-123248969 5 95917848 CCCAGCAAAGGAGACCTTCTGGATAGATGGCCCTG[A/G]TCTGTGGTCAGCCAAGTGAAGATCCCACGCAAATA R 2 1 2 1 201000 f 74 goat snp51142-scaffold748-1245183 5 103711870 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778011 Affx-122954223 AX-385265127 5 95994148 AGAGAAAAAGAGAAGGGCTTACCAACTCCCATGGA[C/T]TGACACATTTTTCACTCACTAGATGTGGTACTATG Y 2 1 2 1 101000 f 74 goat snp51144-scaffold748-1321483 5 103787873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407598 Affx-122954651 AX-123277949 5 96035591 GCCTGTGCTGAGAGGCCCAAGGCTAGTGCATCTGC[A/G]CAAGGGCCCCTCTGTCCAAGTTTGGGGCTGCAACC R 2 1 2 1 201000 f 74 goat snp51145-scaffold748-1362926 5 103829943 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398096 Affx-122961718 AX-123268451 5 96081258 CCATCTTCTGAGCCAGGGCAGACAGCAGAAGACAG[C/T]GGAGAAGGCCTTGCACAGAGCTGCAATTGCCTGTC Y 2 1 2 1 201000 r 74 goat snp51146-scaffold748-1408593 5 103875563 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421656 Affx-122944448 AX-123292003 5 96129109 GTGTCTCCTGCTTGGTGGAGCCCAGCAAATCCGAA[C/T]CAGAGCAGACGCTACCCTGAGGGTCACCCCGGGAA Y 2 1 2 1 101000 f 74 goat snp51147-scaffold748-1456444 5 103923118 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381664 Affx-122974743 AX-123252022 5 96163845 ACCAGAAAGGGGGAGGGAGAGGACCAGAAGACAAT[A/C]GGGAGAAGGAAGTTCAGTAAAAAAAATCCCACCTC M 2 1 2 1 101000 r 74 goat snp51148-scaffold748-1491180 5 103957785 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428780 Affx-122938414 AX-123299122 5 96231144 AGTGATGCTGGGAGAAGGAGCAGGCAGTGTGATGT[A/G]GAAATCACAATGGGGTGGGAGAAATGGCCAAGGGC R 2 1 2 1 201000 f 74 goat snp51149-scaffold748-1558479 5 104026265 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451730 Affx-122921541 AX-123322063 5 96271751 GAACTATCCCTTCTAAGTCTGGGAAGAAAACATGT[A/G]TTCACTACACGATTCATGCAGGCCAGACAGTCCCC R 2 1 2 1 101000 r 74 goat snp51150-scaffold748-1599086 5 104066983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379316 Affx-122976192 AX-123249675 5 96318398 TCCCAAATAAACCATGTGCTCCTTGAAGGTGGAAA[C/T]GCTGCCTTATATGTTTATGCAACCCCAAGATGCAT Y 2 1 2 1 101000 r 74 goat snp51151-scaffold748-1645733 5 104112465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408230 Affx-122953835 AX-123278581 5 96346978 GAGGGCAGTGTAGCCACATTCCCCTTCACTGTCCT[C/T]GCCCTGAGCATTGCAAGGTGCTTTCCCAAAGATCA Y 2 1 2 1 101000 r 74 goat snp51152-scaffold748-1674313 5 104140979 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419903 Affx-122945340 AX-123290251 5 96381478 AAAAACCCGATCAGATAAACCTAAGGAGAGAAGCC[A/G]AAAAGATAGTCACTCCATAATAGGCAGTTTCGTGA R 2 1 2 1 101000 r 74 goat snp51153-scaffold748-1708813 5 104175628 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770123 Affx-122956379 AX-385257290 5 96398899 CCCAGAAGACACTGCTATAGCCATGTCTCCTATTC[A/G]TCTTCTAGGAGTCATCTGATTTGTTACCTTGCCAT R 2 1 2 1 101000 f 74 goat snp51699-scaffold76-1286632 5 104193232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383059 Affx-122973753 AX-123253417 5 96440683 TGGGGATTGTCGCACTCATAGGGAACAGTCACCGC[A/C]GTGGATGCTAGCACAGCTAAATCCCCAAGGAAACT M 2 1 2 1 201000 r 74 goat snp51698-scaffold76-1244848 5 104236500 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399742 Affx-122960329 AX-123270097 5 96478316 AGAGCTGTCTCTCTCATATCCTGAAAGCAGAGTTC[A/G]TAAATCCCAGTGGTGTGAAGTGCAGGGGACGACTC R 2 1 2 1 101000 f 74 goat snp51697-scaffold76-1207215 5 104274127 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426278 Affx-122940314 AX-123296624 5 96527448 AGGCCCCAGGTGTCATCCATAGCAGCCGTGAGCAT[C/T]CCAGTGGTCTTTAGGACAAGCATCTTCCTCATCTG Y 2 1 2 1 201000 r 74 goat snp51696-scaffold76-1158083 5 104317848 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278443 Affx-1111836342 AX-519551928 5 96531456 ATTTCTTTCCAAGTCAGACAAAGTACAAATATTTT[A/G]TCTCCAGCACTGTCCAATCCACAAGTCTTTTTAAA R 2 1 2 1 101000 r 74 goat Random2.2K-604 5 96531456 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380819 Affx-122975080 AX-123251177 5 96564176 TGAAACTCTACCTCCTGTGAATTCTTGTATCTTGG[C/T]GTCTGCTTCCAGTAAGGGCAGGAGTCATGGGCTTC Y 2 1 2 1 101000 r 74 goat snp51695-scaffold76-1121355 5 104354519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274083 Affx-1111834028 AX-519547686 5 96571007 TTATCTGGAAGCCCCAGCTTCATGAGATTAGTTTG[A/C]AAGTGCTGCAGAG M 2 1 2 1 102000 f 74 goat GoatD01.015073 5 96571007 T G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320785406 Affx-122973569 AX-385272451 5 96593466 CATTATACCTTTAATGCTACAAATCTAATTACCCT[A/G]TGACCTTATTCTAAGTTCCTACACCAGAATCTAAA R 2 1 2 1 101000 r 74 goat snp51694-scaffold76-1092065 5 104384845 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379021 Affx-122976366 AX-123249380 5 96720600 TCTTCTTTGGGGAGCTGAATTCCCCTCCTCTCCAA[C/T]ACACAAACTGACAAACTTTATTTCCAGTCATACTG Y 2 1 2 1 202000 r 74 goat snp51691-scaffold76-964931 5 104513366 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442410 Affx-122927988 AX-123312747 5 96753647 AGGAGTGCGGCTTGATATACCACTGTGAATTAAAA[C/T]GGGACTCTGGATGCAGACTTAATGTCCTGCAGCTG Y 2 1 2 1 101000 f 74 goat snp51690-scaffold76-931884 5 104546760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387383 Affx-122970428 AX-123257741 5 96787501 TCTGAGCCTCATCTGCAAGATGAGACCATTACCAC[G/T]CAGGGTTCTTATATATTAGTGACAATATATGCAAA K 2 1 2 1 201000 r 74 goat snp51689-scaffold76-898030 5 104580521 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450237 Affx-122922264 AX-123320572 5 96817435 AGATAGTGACTATGTAAAAGTGAATTGATCTGAGC[A/G]CTGCCTTCAGGAAATGGTCCTCTGCTTCTCCTAGT R 2 1 2 1 201000 f 74 goat snp51688-scaffold76-868096 5 104610351 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397603 Affx-122961982 AX-123267958 5 96888865 AAGAATAGCTTTAAAAGGGAAATCAGTGCTGAGAC[A/G]GTGAAGTCCCTTACCCAGCACGCGCCCTGTAGCTT R 2 1 2 1 101000 f 74 goat snp51686-scaffold76-796666 5 104681817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376471 Affx-122978043 AX-123246830 5 96934010 TTCACTCAACAGAGCCCCTCAATCTCCTTCTTCCT[A/G]TACTCCTGTAACACTGAGGGGATCCTTATCTCCCT R 2 1 2 1 101000 r 74 goat snp51685-scaffold76-751521 5 104727166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788702 Affx-122966533 AX-385275718 5 96985650 GTGATAGTAAAGCCACGAGGAAAAGTTGAGAACCC[G/T]AAGGGAGACTATGTAGGGTGAGAACAGTAAAGAGT K 2 1 2 1 201000 f 74 goat snp51684-scaffold76-699881 5 104778868 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415533 Affx-122948666 AX-123285882 5 97015668 TACATTCTAATGTTCATCAATATTGCTCTGTATGC[A/G]TGCGCGCATGCTCAGTCGCTTCAGTCGTGTCTGAC R 2 1 2 1 101000 f 74 goat snp51683-scaffold76-669863 5 104808889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426124 Affx-122940625 AX-123296470 5 97087706 TCTTCAGTCTTTTGGACAGTGCTAAGCATCACCCC[C/T]TGATTTCCCTCTCACCTATCCCTACTTCACCTCCC Y 2 1 2 1 101000 r 74 goat snp51681-scaffold76-597825 5 104881092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789624 Affx-122956272 AX-385276633 5 97116768 CACTCTGGTATACTGTAAGAATGTGGTACAAAAAT[G/T]AACTGATCCCTGTTCTTTCTAGTGAAGGAGATATT K 2 1 2 1 201000 r 74 goat snp51680-scaffold76-568763 5 104910704 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417847 Affx-122946783 AX-123288195 5 97155727 ACTTATCACGGTGATCATTTCACAGTGCGAGCAAA[C/T]GGCCAATCAACAGAGCACAGCTGAAACTAGCATCG Y 2 1 2 1 201000 r 74 goat snp51679-scaffold76-529804 5 104949685 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394264 Affx-122964722 AX-123264619 5 97207120 CCAATAGTCAACCATTTAGAAAAATTAATGGATGA[C/T]ATGTGCCAGCAGCAAAAAAGAATGACCATCACTCT Y 2 1 2 1 101000 r 74 goat snp51678-scaffold76-478411 5 105001387 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436477 Affx-122932973 AX-123306815 5 97239766 GCAAGACATGTACTTAGATGAGTGAAGATGTGTTA[C/T]GGAGAAACCAGAAAGAGGACAGCCAATAAAAACTT Y 2 1 2 1 101000 f 74 goat snp51677-scaffold76-445765 5 105034060 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425542 Affx-122941449 AX-123295888 5 97269325 ACTTTTTTACAGACAACATTATTTTTCAAAAGAAC[A/G]ATGCAGAAAGAGACCTATAACCCAAAATAATAATG R 2 1 2 1 101000 r 74 goat snp51676-scaffold76-416206 5 105063980 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445780 Affx-122926059 AX-123316117 5 97313846 CCCTTATCATCAGCATCTGAGGATTGGAAGGGCTC[C/T]TGCAGATCACATGATGTGAAATCTACCCACCCCCA Y 2 1 2 1 101000 r 74 goat snp51675-scaffold76-371685 5 105108527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793170 Affx-122963350 AX-385280148 5 97346724 TATGGAATTGACATATGATCATTTAAATGAACACA[C/T]GCCCAGCCTGGTACTTTGCATATGACAGGTGTTCA Y 2 1 2 1 101000 r 74 goat snp51674-scaffold76-338807 5 105141398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431980 Affx-122935949 AX-123302321 5 97410065 GCACCTTGGGGCACAGCCCATGGTTTAAAGCAGGA[A/G]CCTGTGAACCAAGGTGAGGCCTCAGGGAGAGCCCT R 2 1 2 1 202000 r 74 goat snp51673-scaffold76-275466 5 105204794 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395025 Affx-122964216 AX-123265380 5 97441708 TGCTACGAGGGAGTAGAGACTTTTAAGAGATCAAG[A/C]GCCTCTCTGAAGACATGACTTGAAATGGAAACTCG M 2 1 2 1 101000 f 74 goat snp51672-scaffold76-243823 5 105236092 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434411 Affx-122934677 AX-123304752 5 97473625 TGTGTGGAGAAACAGGCAGATGCTGCAAGTCAGGG[C/T]ATCCTTCCTTCCTGGAGAACCCCCTGTTAAGTGTC Y 2 1 2 1 101000 f 74 goat snp51671-scaffold76-211906 5 105267854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447656 Affx-122923965 AX-123317992 5 97511787 AGCTGAAATGGTCCCCAAAACCATGGTCTGCACGC[A/G]TTTCTTCTCCCTCAGCAAACACGGATTTCCGTCCT R 2 1 2 1 101000 r 74 goat snp51670-scaffold76-173744 5 105306033 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394938 Affx-122964297 AX-123265293 5 97554355 ACCAAACTTCTTCTGGTGCACACTCTCTATGTCCT[A/G]TGGCCCTTCCATTTGGACCACCTCCCTGACCTTTC R 2 1 2 1 101000 f 74 goat snp51669-scaffold76-131176 5 105348638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401007 Affx-122959687 AX-123271360 5 97590599 GTCTGGAAGGAACAGACTGGAAATGTGGATGAGCC[A/G]CTGGCAGAGGGACAGGCAGTGCAGAGCTTCTTAGC R 2 1 2 1 201000 f 74 goat snp51668-scaffold76-94932 5 105384757 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273920 Affx-1111833893 AX-515873128 5 97607451 CAACA[A/G]AACAGATCTCCTTGCTTATGGGGGGAAACTGCCAA R 2 1 2 1 102000 r 74 goat GoatD01.009628 5 97607451 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38375427 Affx-122979187 AX-123245786 5 97621714 GCAGTACTAGCTATATCGCCGCTGGCTTTACAGTT[A/G]CTTCCAGACATCCTGGGCTTGAAATAAAGACACTG R 2 1 2 1 101000 f 74 goat snp51667-scaffold76-63817 5 105415820 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420756 Affx-122944719 AX-123291103 5 97671154 CCAGGGACTGGTTCCGGGGCCAGCATGGGTCTTCC[A/G]TGGATGCTCAAGTCCCTTATATAAGATGGTGCAGT R 2 1 2 1 201000 f 74 goat snp51666-scaffold76-14377 5 105464946 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404493 Affx-122956714 AX-123274845 5 97751449 CATACTTCCATGGCGGACCCCTTTCATGGTACACC[A/C]GCCGAACCAACAGAAGGTACAACCAGGGTGAACTC M 2 1 2 1 101000 f 74 goat snp23103-scaffold2301-60270 5 105539243 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385106 Affx-122971787 AX-123255464 5 97810898 GCTGCTCTCACCATACCCATACTTCCCCCTCAGAC[A/G]GTGGGCTGCTCTAAGGGACCCCTGAGGTCCCTAGA R 2 1 2 1 201000 r 74 goat snp23104-scaffold2301-119719 5 105595613 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449545 Affx-122923250 AX-123319880 5 97842602 TTTAAATTGGGCTTTCAGAGCCCATTTGGAAGGCC[A/G]GAGCAGAAAATTCTTCTATCTGACAAAGACCATCT R 2 1 2 1 101000 r 74 goat snp23105-scaffold2301-151423 5 105626278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778782 Affx-122929370 AX-385265891 5 97879869 CAGTATTCACGACAAACACCACCTGGTACATGATG[C/T]GTTCCTCTAGAATCACGGTGATCAACTCCAACCCC Y 2 1 2 1 101000 f 74 goat snp23106-scaffold2301-188690 5 105663212 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411974 Affx-122951779 AX-123282324 5 97930804 GGACATACAAAGACCCTGAGGTGGGAAGGCCTGGC[A/G]CGTCCAGCAAAAGCTCAGAGCCTCAAAGGTTGGTG R 2 1 2 1 201000 r 74 goat snp10771-scaffold1383-755892 5 105714166 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383380 Affx-122973512 AX-123253738 5 97972119 GCAGAGCAACTTGTACCGTGCAGGAACAGCCAGTG[C/T]TTCCTAACCCTATTTCACCACAGAGCCTCTTTATC Y 2 1 2 1 201000 r 74 goat snp10770-scaffold1383-714577 5 105755480 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434078 Affx-122934177 AX-123304419 5 98028379 TGAACAGCTCAATTTTCACTTATGCACACATCCAC[A/G]TAAATTTTCCCCTTTAAAAATTATTGATGGGACTT R 2 1 2 1 103000 f 74 goat snp10769-scaffold1383-658317 5 105812631 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404512 Affx-122956700 AX-123274864 5 98071956 CCCGAGCCCCTCTCTATTCTCTTGCAGCTCACTTG[C/T]GTTGGGGTTGGAGACGTATGTAATAAAGGAAAGGT Y 2 1 2 1 101000 r 74 goat snp10768-scaffold1383-614740 5 105854568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425624 Affx-122940903 AX-123295970 5 98131213 TGACATGAGCTGTGTGCAAGGGTTAAGTTATCCCA[C/T]AGACCCTCAGGCCTCTGAGCTGCTCAAGGACAGAA Y 2 1 2 1 101000 f 74 goat snp10767-scaffold1383-555483 5 105913611 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435124 Affx-122933690 AX-123305464 5 98214573 CTGCTGTGTAGCATTGCGCCAGTAGCTACAATGTA[C/T]AGCCAGGAATCTGTTAAGCAAGTGGATCTTGCATT Y 2 1 2 1 101000 f 74 goat snp10766-scaffold1383-472123 5 105996073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423788 Affx-122942824 AX-123294134 5 98261007 GGACTATTAATAAAAGGAAGAAACTAGTTCCCAGC[A/G]TAATGGGTGAAGAAAGAGCCAAAGAAGGCACACGA R 2 1 2 1 101000 f 74 goat snp10765-scaffold1383-425689 5 106041744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272326 Affx-1111833485 AX-185175994 5 98293519 TTTATGGGGTCGCAAAGAGTCGGACACGACTGAGC[A/G]ACTGAACTGAACTGATACTTATTAAATAAAGTAGC R 2 1 2 1 103000 f 74 goat 5_98293519_AF-PAKI 5 98293519 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413521 Affx-122950625 AX-123283870 5 98308076 GACACTGAGTCCCAGGCTTCATGGGTCCTCAGACC[A/G]TGCTCACACATACAACAGGTCTAGGACCCACACGT R 2 1 2 1 101000 r 74 goat snp10764-scaffold1383-378620 5 106096905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409068 Affx-122953346 AX-123279419 5 98348373 ACATATATGTCTAATGAAATAGATGTATGTATATA[C/T]ACATCTCTTCATTTAATCCTCATGGCTAAGTGTAT Y 2 1 2 1 103000 r 74 goat snp10763-scaffold1383-338323 5 106137302 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442745 Affx-122927843 AX-123313082 5 98383623 CCTTTGCCTGCAGCCTCCCTCCGCCAGCAGAGGGC[A/G]TTAGAGAACATTAAAAGGCCGCGTAGTGAGGAGGG R 2 1 2 1 101000 r 74 goat snp10762-scaffold1383-303073 5 106172998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774205 Affx-122969686 AX-385261342 5 98426855 TTTTAAAATTATTGCTGTGACTGCATAAATTTGTC[A/G]TTGTGCTTAATAGCATGCTATGATTGTTTGAACCA R 2 1 2 1 201000 f 74 goat snp10761-scaffold1383-259841 5 106216238 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381856 Affx-122974187 AX-123252214 5 98459448 CTCACAGGGAGGAAGCCTGCAGGGCACAAGGGGAC[C/T]GGCGACAGGAAACCCAGCTTGGTGACAGCAATGAT Y 2 1 2 1 101000 r 74 goat snp10760-scaffold1383-227248 5 106246036 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278445 Affx-1111836343 AX-519551930 5 98520551 GGTCTTGTGTCTCCCTTTGACCAATAGAATGTGGT[A/G]GAAGTGACACTCTGGGACTTCAGAACATAGACCTT R 2 1 2 1 201000 r 74 goat Random2.2K-605 5 98520551 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796092 Affx-122957884 AX-385283044 5 98559003 ACAGACTATGATGTAGTTACAATCTTTCAAAATAA[C/T]TGGTTCATTAAGAAAAATGATCCAAACTGGCCTCA Y 2 1 2 1 101000 r 74 goat snp10758-scaffold1383-127693 5 106345047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435430 Affx-122933485 AX-123305770 5 98597471 TTAGACAGTCCACTAGCCTCTCCCTCTAGGAAGCC[A/G]TTTCCCAAAGCAGGGCTCTGTGACCCCCAGACAAA R 2 1 2 1 101000 f 74 goat snp10757-scaffold1383-89225 5 106384137 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386679 Affx-122970184 AX-123257037 5 98631265 TGGGGGATCACAGGAAGACAGGCTAACCAGGAAGT[A/G]TCCTGTGGGCTAGAATCAGGGAGATGCCAGGACAC R 2 1 2 1 101000 f 74 goat snp10756-scaffold1383-55431 5 106417843 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403901 Affx-122957487 AX-123274253 5 98676557 AAAAAAGAAAGGAAAAAAAAAACAAAAAACAGAGA[C/T]AGTGTTCTTTCTTTAGAATAGAATAGAGCTTGGGG Y 2 1 2 1 101000 r 74 goat snp10755-scaffold1383-10139 5 106463206 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424792 Affx-122941392 AX-123295138 5 98693050 AAATAAGATGTACAGGTTTAAAATTCAAGCAGTAC[A/C]GAAGAGTAAGCAACGCTAAGCAATGATATGGACAT M 2 1 2 1 201000 f 74 goat snp19986-scaffold1996-6255 5 106479948 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776649 Affx-122967159 AX-385263776 5 98738675 CATATTGTATGGTCCTACAGTTTGCTAGTTTCATT[A/G]CATAGCAGAAACGTTTTCCTTAAACATTTGAGGTT R 2 1 2 1 101000 r 74 goat snp19987-scaffold1996-51880 5 106525552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430793 Affx-122937469 AX-123301134 5 98770160 TAGTAGACTATATATTGGAAATATAAAAATTAAAT[A/G]CTACTTAATGGTAGGTAGAATATTATAATTCATTT R 2 1 2 1 103000 r 74 goat snp19988-scaffold1996-83365 5 106556927 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405820 Affx-122955887 AX-123276172 5 98811604 CTTATCTAATGCAAAGATCCCCACAGAATAGTTTT[A/G]TTGACCCTGGATGTATTTAATGGGTTTTTACTATG R 2 1 2 1 201000 r 74 goat snp19989-scaffold1996-124809 5 106598433 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425661 Affx-122940877 AX-123296007 5 98859585 CGCCTTAAACACAGGCCGGGGGCACAGTTCCTCAA[C/T]GCCTGGCTGTCTCCGAATAGGCCTCTGAACCCCTC Y 2 1 2 1 101000 f 74 goat snp19990-scaffold1996-172790 5 106646304 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387004 Affx-122969941 AX-123257362 5 98946961 TCCTGAATTTCTTTGGGCGTTTTTGGTGATAGGTG[A/C]TTGTTTTCAAGAATAGCACGTTGGTTCTCAGTTGT M 2 1 2 1 101000 f 74 goat snp19991-scaffold1996-260166 5 106734515 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779089 Affx-122961116 AX-385266194 5 98986299 GTGCAGTTACGATAGCGGTTTTCTTAGATGATTTC[C/T]TCTTAAAACTGTTTATATTGTATACATCTGTATTC Y 2 1 2 1 101000 f 74 goat snp19992-scaffold1996-299504 5 106773914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430025 Affx-122937582 AX-123300366 5 99063256 CGAGCCAAGCAGTAGTTTCTACAGTTTCTTCTTTG[C/T]GACTTTTGCTAAGGTTTGGGTTCCTCATAGTGTCA Y 2 1 2 1 201000 r 74 goat snp19994-scaffold1996-376461 5 106850758 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790060 Affx-122928477 AX-385277066 5 99119707 TCTTAGCATTGGAATAGATTAGGCTCTGCCTGCAC[A/G]TCTTTGACAGTGATCCATCCAGAGCCAGCAATCTC R 2 1 2 1 101000 f 74 goat snp19995-scaffold1996-432912 5 106907220 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380006 Affx-122975605 AX-123250364 5 99152261 AGGATGTCAGCTGGGTCTGTAGTTTAAAGCTTGAT[A/G]TAGCCAGAGCCCACGTGGGTGCATATTCACTCACG R 2 1 2 1 101000 f 74 goat snp19996-scaffold1996-465466 5 106939743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784642 Affx-122958347 AX-385271690 5 99180953 AAATCATTCCATCCACTCAGACTAACCACTCTTCA[G/T]ACTTATGTCTGTCTTTGTCCATACATTTTTCTGTA K 2 1 2 1 101000 f 74 goat snp19997-scaffold1996-494158 5 106968539 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408555 Affx-122953678 AX-123278906 5 99250675 GCAACAGCTCGACAACCAGGATCTGGCTCCTCGCT[G/T]ATGGGGAACACCTGGGGCCATCACCTGGGCACAGT K 2 1 2 1 101000 f 74 goat snp19998-scaffold1996-563880 5 107030224 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422460 Affx-122943338 AX-123292806 5 99289382 GAAATGATCTGGACGTTTAGAGAGACTGTGCCGAG[C/T]GTCTGTGCCCCAGCGCTGCTGGGTGGGAGGCAGTG Y 2 1 2 1 101000 f 74 goat snp12155-scaffold1450-110289 5 107069761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399856 Affx-122960241 AX-123270211 5 99320626 TTTTTATTTCACTTTCTGTTTTCTAATTTTCTTAT[G/T]AAGACTAAGTACATTTACAGAAATCAGCAATGGTC K 2 1 2 1 103000 r 74 goat snp12156-scaffold1450-141533 5 107101395 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441395 Affx-122928845 AX-123311732 5 99393386 TGTGTCAGGTACACTGAGCCAGCGGACAAGGAGAC[A/G]TGGGGTCAGCTGTGAAGCTGGGCAGCTGAGAGGGT R 2 1 2 1 101000 f 74 goat snp12157-scaffold1450-214293 5 107173759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377349 Affx-122977659 AX-123247708 5 99428561 GTCTCATTGGACACCGGGGTCCAAGGGAGGTTGCC[A/G]GGTTAAGCTGCAGTGTCTGAACTACTGGTCAGTCC R 2 1 2 1 101000 r 74 goat snp12158-scaffold1450-249468 5 107208739 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796554 Affx-122963740 AX-385283500 5 99503928 TGTACTCATTAAATATTAGCTTTCTATAAGAGCCC[A/G]TGATGTTCAGAACACGGAGATCTAAGTTGGCGTGA R 2 1 2 1 101000 r 74 goat snp12159-scaffold1450-324835 5 107283855 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422277 Affx-122943494 AX-123292623 5 99580241 CCAATAAGGCAGATCCCGTCTCTTAGATGTGACCT[A/G]CTGGCGCCCAAGGCAGATGGGTAGCTCAGAGTCTT R 2 1 2 1 101000 f 74 goat snp12161-scaffold1450-401148 5 107360471 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795515 Affx-122932049 AX-385282470 5 99637994 AAAATGTGTTTGGAAAAGGAAGGCCTTTTCTAGCA[C/T]GATGCGTTACCGTAAAATGACACAGCCTCACTCTT Y 2 1 2 1 101000 f 74 goat snp12162-scaffold1450-458901 5 107417156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398492 Affx-122961568 AX-123268847 5 99667103 TTCAGAGGCAATGAGAGGTTCGTAAATCTGCTTCT[A/G]CAGCAAGGCTTCACACCTAGACATTTGGTCTGCTG R 2 1 2 1 101000 f 74 goat snp12163-scaffold1450-488010 5 107446297 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774173 Affx-122976848 AX-385261310 5 99721587 TTTTTTAATTTCATGATGACACTGAAACGTAGGAT[G/T]AAAGTTCTAAAGATGAAGCTGGTAACTTCACAGCG K 2 1 2 1 101000 r 74 goat snp12164-scaffold1450-542494 5 107498021 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378573 Affx-122976596 AX-123248932 5 99773142 GGCAGCTTTCCTTGGTGTCCACCTGGCCTCCACTC[A/G]TCTGATTTCACTCCTGGGCAGCCCTCACACTAGTA R 2 1 2 1 201000 f 74 goat snp12165-scaffold1450-594049 5 107550298 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404386 Affx-122956797 AX-123274738 5 99803558 AGGAGGAAAGGCCTTGAAGGGTAGGTAAGGAGGGG[C/T]ATCTGGAGCCTCAGGACAAAGAGGTAGGATAACTG Y 2 1 2 1 101000 r 74 goat snp12166-scaffold1450-624465 5 107579312 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406087 Affx-122956231 AX-123276439 5 99838150 AGGCCCTCGTCCTCATTCTCAGGGTCGATGTCCTC[A/G]GCCTGCGTGATCCAGTCCAGGTAGCCCTTCAGGTC R 2 1 2 1 101000 f 74 goat snp27784-scaffold297-471761 5 107615021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274551 Affx-1111834361 AX-519548141 5 99858320 AAGTTCTTCTTCAGAATAAGCACAGGCTGCAATAG[A/G]CTATTTTTCCTGTCTCTCTTCTCTAAA R 2 1 2 1 102000 f 74 goat GoatD01.031902 5 99858320 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38392111 Affx-122966353 AX-123262468 5 99890587 CGGCTGCCCAGGCAGGACCAGAGGAAGAGTGGCCA[C/T]AGGAGAAAGGGCAAGTGGACACTGGAAAAATGGGG Y 2 1 2 1 101000 r 74 goat snp27783-scaffold297-419324 5 107667228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413459 Affx-122950672 AX-123283808 5 99972276 GGCCACACGTGGGTTCAGGCCCTGCTGAGGCCATC[C/T]GGGCTCATTCACTTCTATCCAGTTTTTCTCTGGAA Y 2 1 2 1 101000 r 74 goat snp27782-scaffold297-337635 5 107748993 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395511 Affx-122963879 AX-123265866 5 100016630 ACGTACATTGACCAAGGTCGTGAGTGACAGATGTA[C/T]ACACAAGAAAGTCAGAATACAGTCTTCAGAGAAAA Y 2 1 2 1 201000 f 74 goat snp27781-scaffold297-293281 5 107793101 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384631 Affx-122972162 AX-123254989 5 100052198 TGGGTGTCCGCCCACACCTGACACACGCAGGGCTT[C/T]GCTGCCTTTGTCCTCAAGCCTTCAGCAGCATCACA Y 2 1 2 1 101000 r 74 goat snp27780-scaffold297-257713 5 107828724 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439839 Affx-122930461 AX-123310176 5 100082278 CATGCCTTTCTCAATACAGTCATATCTTCAGGGAA[C/T]TGATTGACTCCAGGACCCCCAGGATAACAAAAGTC Y 2 1 2 1 101000 f 74 goat snp27779-scaffold297-227633 5 107858467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441318 Affx-122929441 AX-123311655 5 100127628 CTGAATAATACTCAATATCCTGTAGTAAACCACAA[C/T]GGAAAAGAATATGAGAAAGAAGGCATGTTTAACGG Y 2 1 2 1 303000 f 74 goat snp27778-scaffold297-182283 5 107903798 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385805 Affx-122971035 AX-123256163 5 100176401 TACAGTTACTATAAAACACTGGCACATCCCCGCGC[C/T]GTACAGGGCGGCCCACCAGCCTTTTGTGAGACGTA Y 2 1 2 1 201000 r 74 goat snp27777-scaffold297-133510 5 107952878 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441458 Affx-122928762 AX-123311795 5 100295301 TTGAAGAGCCTGTTGATGACGCCGCTCTTGACTCC[A/C]CTGTCAGAGATGGCTGCACCGTCGGCATTAGGGGT M 2 1 2 1 101000 f 74 goat snp27775-scaffold297-14610 5 108071900 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410322 Affx-122952480 AX-123280672 5 100330212 CTGCCTCCCCTTCGATCTCTGCTGGTTCCGAGTCC[A/C]CGTCTCCCTCCAGGTCATCCTCATCGAACTGGACT M 2 1 2 1 101000 r 74 goat snp20265-scaffold2006-20202 5 108106683 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385956 Affx-122971541 AX-123256314 5 100359180 GATTCTCTGGGCCCCAGTGAGAAGGGGCTGAGAAC[G/T]CAGTGAGCGGTAACTGCTTCATTTCCTGCAGGTTT K 2 1 2 1 101000 r 74 goat snp20266-scaffold2006-49170 5 108135407 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421919 Affx-122943840 AX-123292266 5 100388942 GGCTAACTGAATCAGACCATCTGGGAATGAAGGTC[C/T]TTGTCACCCCAACTGCTTCCCAGCTCTGGTCCCAA Y 2 1 2 1 101000 f 74 goat snp20267-scaffold2006-78932 5 108165237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766504 Affx-122950317 AX-385253868 5 100423783 TATTTGGGAGGCTTTATGTTTTGGTCTCCTGCTTC[A/C]AAGAAAGTACCACTCTAAACCAAGTATTAATACTG M 2 1 2 1 101000 f 74 goat snp20268-scaffold2006-113773 5 108199920 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405871 Affx-122955609 AX-123276223 5 100470876 CTGGTAGAAGCAGTGTCTTGGTCAGGCTCTCAGCC[A/G]TGGCTCTGAACTCACATGATACTGCTCCGGGGGAG R 2 1 2 1 201000 r 74 goat snp20269-scaffold2006-160866 5 108247156 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378929 Affx-122976439 AX-123249288 5 100568344 TCTCCAGTTCATCTGCTCCCTTTGTGAGACCAACT[C/T]TCTCCCAAGCTCACCTGTGGACACTCTTACCCCAA Y 2 1 2 1 101000 r 74 goat snp20271-scaffold2006-258334 5 108343873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450843 Affx-122922241 AX-123321177 5 100644429 TATTGGTCAAAAAGGTCAATCCCTCTCCCGGCAGG[A/C]GGCGAGTCGGAGCTGAAGCTCTGCGGCTACTGGTC M 2 1 2 1 101000 f 74 goat snp20272-scaffold2006-334419 5 108420020 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476208 Affx-1251763713 AX-586011632 5 100648589 TTTTGAGCATTACTTTACTAGCATGTAAGATGAGT[-/GCAATTGTGCAGTAGTTTTTTTTTTTTTTTAATTTTAATTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCT]CAATTGTGCAGTAGTTTGAACATTCTTTGGCATTG - 8 1 4 1 20000 f 74 goat SV_361 5 100648589 - deletion junction SV-TF-chip 560378494 Affx-1251763713 AX-605230909 5 100648589 TTTTGAGCATTACTTTACTAGCATGTAAGATGAGT[-/GCAATTGTGCAGTAGTTTTTTTTTTTTTTTAATTTTAATTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCT]CAATTGTGCAGTAGTTTGAACATTCTTTGGCATTG - 8 1 4 1 20000 r 74 goat SV_361 5 100648589 - deletion junction SV-TF-chip 562165782 Affx-1251763713 AX-606941191 5 100648589 TTTTGAGCATTACTTTACTAGCATGTAAGATGAGT[-/GCAATTGTGCAGTAGTTTTTTTTTTTTTTTAATTTTAATTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCT]CAATTGTGCAGTAGTTTGAACATTCTTTGGCATTG - 8 1 4 1 20100 f 74 goat SV_361 5 100648589 - deletion junction SV-TF-chip 562166001 Affx-1251763713 AX-606941410 5 100648589 TTTTGAGCATTACTTTACTAGCATGTAAGATGAGT[-/GCAATTGTGCAGTAGTTTTTTTTTTTTTTTAATTTTAATTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCT]CAATTGTGCAGTAGTTTGAACATTCTTTGGCATTG - 8 1 4 1 20100 f 74 goat SV_361 5 100648589 - deletion junction SV-TF-chip 562166007 Affx-1251763713 AX-606941416 5 100648589 TTTTGAGCATTACTTTACTAGCATGTAAGATGAGT[-/GCAATTGTGCAGTAGTTTTTTTTTTTTTTTAATTTTAATTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCT]CAATTGTGCAGTAGTTTGAACATTCTTTGGCATTG - 8 1 4 1 20100 r 74 goat SV_361 5 100648589 - deletion junction SV-TF-chip 468278286 Affx-1111836344 AX-519551773 5 100688052 GTGACACTTGATACTAAGTTCCTACCTATCAACGA[A/T]GTGGTGAGTTCAGTCATTTCAAAGGCATAATGAAA W 4 1 2 1 101000 f 74 goat Random2.2K-606 5 100688052 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38405914 Affx-122955577 AX-123276266 5 100736156 TTCTAACACGACCTTGGGGACTTCCTAAGGCACTC[A/G]GGAGAGGCCACCCTGCAGGCCAGGCATGGGGAGAA R 2 1 2 1 101000 f 74 goat snp20274-scaffold2006-426146 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272521 Affx-1111833448 AX-519546239 5 100795869 GTACTAAGTAAAATGGTGAAGATCAGACATAGTAA[A/G]CAAGGACTAGGAGTTGGTGAGAGATATAGCCAACA R 2 1 2 1 201000 f 74 goat 5_100795869_AF-PAKI 5 100795869 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38408840 Affx-122954016 AX-123279191 5 100798026 CTCCTCAATGACACTACCTCTATATTAGAGGGTAA[C/T]AGAAAGCAATACTTTTATCATCAGAGAAATGGACA Y 2 1 2 1 101000 f 74 goat snp28480-scaffold3035-31924 5 108574327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437429 Affx-122932408 AX-123307767 5 100840521 TAAATTATATGAAGTACTTAGCACAGCACCTGGCC[A/G]TCATGTGCAATGAAAGAATGAAGTCCATTGTTATT R 2 1 2 1 201000 r 74 goat snp28481-scaffold3035-74419 5 108617444 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443264 Affx-122927491 AX-123313601 5 100870851 TTTATTTTTAAGAATTATCGTATAGCAGCATTGAC[C/T]TTTTTTCTTTTTGTATACAGTTCTCTGAATTTGTG Y 2 1 2 1 102000 f 74 goat snp28482-scaffold3035-104749 5 108647769 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435853 Affx-122932809 AX-123306192 5 100931130 AGTTCCTCAGGGGCTTTGTGTCCGACTATCCCTGA[C/T]AGTCTATCCCTGATAGATCTTTCCCTGATAGATAG Y 2 1 2 1 102000 r 74 goat snp47462-scaffold6689-76365 5 108708180 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440679 Affx-122929922 AX-123311016 5 100989577 TTCTTGTCACCTTCTCAGCTACATAAATCACAGGC[G/T]ACCACCTCCAGGAAGCCTTCTGCTGTTAACCTATG K 2 1 2 1 101000 f 74 goat snp47461-scaffold6689-17918 5 108764764 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429779 Affx-122938241 AX-123300120 5 101043075 CGTGGGCCACCACACGGCCAGTGGAGAGCACCCTG[A/C]GTGATGAATTTAAGACTTGGGTCTTGATTCCAATC M 2 1 2 1 101000 r 74 goat snp48873-scaffold698-35481 5 108818624 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417325 Affx-122947744 AX-123287673 5 101107987 GTGTCTGGCTCAAAGGAGGCATCTCATAAGCATAA[C/T]AGACATAGTAGAGTCAGAAGTAATAAGCAGTGGGA Y 2 1 2 1 101000 f 74 goat snp48874-scaffold698-100393 5 108883859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441504 Affx-122928728 AX-123311841 5 101188789 ACACAGGAAAGAGAAACCAGACACCAGTGATGATC[A/G]TGGGTAGGAACACAGTGGAGGGGGCAGGGATGGTA R 2 1 2 1 101000 f 74 goat snp48875-scaffold698-181195 5 108964332 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764627 Affx-986696935 AX-385252269 5 101208804 TCCCTAAAGCTTTCCTCCTTCAAATCTTGGATGAG[A/G]TTAGACACTGAGATTTCCTTATGTGTCAGAGAAGA R 2 1 2 1 600010 r 74 goat 5_101208804 5 101208804 Ancestral_priority_1043 ancestry 0.628 recommended IMAGE 10K 10K ancestral 38432458 Affx-122935801 AX-123302799 5 101225206 TACACAACCACTCATTAGCCAGGCCACGGGAATTA[C/T]GATGATTGCCATGGCTAATAATCCCAATTCCCACA Y 2 1 2 1 101000 r 74 goat snp48876-scaffold698-217612 5 109001429 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780743 Affx-122921545 AX-385267833 5 101272889 GGGATTACACCCACTTCACGGGCATGTTGCAAAGA[C/T]GATAAGTGACCTTGGAGGGTAAAGCATTATCAGCT Y 2 1 2 1 201000 r 74 goat snp48877-scaffold698-265295 5 109048924 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419968 Affx-122945195 AX-123290316 5 101317253 ACAAAAATGCTCTCAATATTCAAAAAACCAGAGCA[G/T]AGCTAGGCAAACTCTGGTCTACGGATCAAATGTGG K 2 1 2 1 101000 r 74 goat snp48878-scaffold698-309659 5 109093134 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787239 Affx-122974658 AX-385274265 5 101356476 TATGTACAGGAATGTTCTTCTTCTTAGAAGAGATA[C/T]GCTGAAATTTAAGAAGTGAGGTGTCATGATGTCTG Y 2 1 2 1 201000 f 74 goat snp48879-scaffold698-348882 5 109131458 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785187 Affx-122975313 AX-385272233 5 101397892 GTTGATTAAGATACTGAGCTTAGAGTTGAAGGTGC[A/G]CACATGAGATCTTGAAGCCAGTGGGCTATTGAACT R 2 1 2 1 101000 r 74 goat snp48880-scaffold698-390298 5 109172218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388639 Affx-122969120 AX-123258997 5 101432824 AGATTCTGGTAGCGTCTGGATGATGCCAGAAGGGG[C/T]AAAGTCTGGCCCAGGTAGAGGTGCTGGCAGGTTAG Y 2 1 2 1 201000 r 74 goat snp48881-scaffold698-425230 5 109207190 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790714 Affx-122933948 AX-385277715 5 101474220 CAGTGCTCCAGCTTCATCATCTTATTTAGTACAAA[C/T]ACGTAGTAAAAATGAGAAACGTATGTAAGAAATCT Y 2 1 2 1 101000 f 74 goat snp48882-scaffold698-466626 5 109258593 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432463 Affx-122935611 AX-123302804 5 101517114 GAGGCAGCCCTGACTAAATTATGTTGACTCTATGG[C/T]GAACCATGGGTGCCAAAGATATTAGGTTCTAATCC Y 2 1 2 1 101000 f 74 goat snp48883-scaffold698-509520 5 109301287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439247 Affx-122931004 AX-123309584 5 101549885 CGGGGATGAAGGACTTGCTCTGCTCTCCTGTAGAT[G/T]CCCCCAGAGCAGCATCCAGTGTCTGGCACATGGGA K 2 1 2 1 101000 f 74 goat snp48884-scaffold698-542291 5 109334129 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410949 Affx-122952035 AX-123281299 5 101605679 CACTTCTCTGAAGCCCCTCACCTGGCTTAAGTTGG[G/T]GAGTGATGTCAACTGTCTCTAAAGACACCTCCCTT K 2 1 2 1 101000 r 74 goat snp48885-scaffold698-598085 5 109378932 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430831 Affx-122937441 AX-123301172 5 101649720 TGCTGAGACACTCCTGGAGAGAAGAAACTGGGACT[A/G]TTTCTTCTGAGTGTCATTTACAAAGTTTTATGGTC R 2 1 2 1 101000 r 74 goat snp48886-scaffold698-642126 5 109423413 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786932 Affx-122936327 AX-385273961 5 101720341 GAGACGGTCTCTTTAGCAGTTGCTCTCCAAACCCA[C/T]CTAAAGTTTTACTGATTAACACGAGGGATGTTAGG Y 2 1 2 1 101000 f 74 goat snp48887-scaffold698-712747 5 109494091 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396696 Affx-122962826 AX-123267051 5 101758021 TTCCGAAGCCAAAATGCTGGGTCTTCACCACTGAA[C/T]GCCAGGAGAGGCCAGAAGCAGGGGAGCAGAGGCTC Y 2 1 2 1 101000 f 74 goat snp48888-scaffold698-750427 5 109531976 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405629 Affx-122956596 AX-123275981 5 101843862 TGTGTGGTGCCTGGGAGTTGTCCTCATTGAGAATC[A/G]GGCGTTGCACTGTCAGCTCACCTCTCTGGAGCCCC R 2 1 2 1 101000 f 74 goat snp48889-scaffold698-836268 5 109617413 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431176 Affx-122937186 AX-123301517 5 101875068 CCCACACCCCCTGCATACACCCCAGTACAACACAC[C/T]CCCCCAAAAAACACCTGGAATCTTGGACCTCGGTC Y 2 1 2 1 101000 r 74 goat snp48890-scaffold698-867474 5 109648306 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448041 Affx-122923706 AX-123318377 5 101904593 CCACCCCGTTCTGTTCTTTGATTCTGGGCCTGGCC[A/G]TTGCTCACACCGTTATTAAGAAAACGTTCTCAACT R 2 1 2 1 101000 r 74 goat snp48891-scaffold698-896999 5 109677702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443047 Affx-122928145 AX-123313384 5 101935487 TTTGCTTTGCAAAGGCAGCGCCTTCAAAATTAGAC[G/T]CCCTGTCTCTATTCCCAACCATTTGCCCTCCCTGT K 2 1 2 1 101000 f 74 goat snp48892-scaffold698-927893 5 109708866 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425390 Affx-122941558 AX-123295736 5 101975510 AAAAAGAACCTAGAAGGGCAAAGGGAAATTCTTCC[C/T]ATCCTAGAGGATCAAGAAAAATGCCAACGGCTCTC Y 2 1 2 1 201000 r 74 goat snp48893-scaffold698-967916 5 109749033 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454267 Affx-122919642 AX-123324600 5 102017717 CCCTACACAAACCCCTCCTGTGCAGAAATGTGGTC[C/T]GACAGTCCCACCGGGGCGGGCTGAGCACCCTGTTT Y 2 1 2 1 101000 f 74 goat snp48894-scaffold698-1010123 5 109789751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782721 Affx-122945243 AX-385269793 5 102056504 ATAAACTGCAAACAAGTAGAGAATGGTCATAATCA[C/T]GATCCCTCATAGAGAATGATTCATTCCAAATGAGT Y 2 1 2 1 101000 r 74 goat snp48895-scaffold698-1048910 5 109828561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278288 Affx-1111836345 AX-519551775 5 102073885 TTCCATTTGTCTCTATGTGTAACAAAAGGTTACCC[A/C]AAAATAAAGAAATCGGATCAGTTTCTGGAAAAACT M 2 1 2 1 303000 f 74 goat Random2.2K-608 5 102073885 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394659 Affx-122964378 AX-123265014 5 102093627 TGGGACCGCTGTGTAGTAGGGGGCTACCTTTCTCC[A/G]AAGACGGTGGCAGACACGTTTGAGAAGGTAGTAGC R 2 1 2 1 101000 r 74 goat snp48896-scaffold698-1086033 5 109865705 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278290 Affx-1111836346 AX-519551777 5 102108628 CTTTACCACTAGCGCCACCTGGGAAGCCCATCAAG[A/G]CATCATTTTTCTTAAAATAATAATATTAGAGGCTT R 2 1 2 1 103000 f 74 goat Random2.2K-609 5 102108628 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419456 Affx-122945489 AX-123289804 5 102166218 AGGCTGGCAGGGCTCAGGTGAGAGATGCTGAAGAT[G/T]AGCTGAGGCCTCAGAGGAGGGCAAGGAAAGACACA K 2 1 2 1 201000 f 74 goat snp48898-scaffold698-1158624 5 109938580 T G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377462 Affx-122977516 AX-123247821 5 102213044 TAGACATTCTTTTTTCCATTCAATACCATGTCTTG[C/T]ATAAGTTTACTTTTGTATATGGTGTGAGGTAGGGA Y 2 1 2 1 103000 f 74 goat snp48899-scaffold698-1205450 5 109985903 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381958 Affx-122974110 AX-123252316 5 102256926 CTAATGGATGATTCACGCTGAGTGTCCTGGGAGCC[A/G]TGGGGAAAAAGGAAACAGGTTGGCACACACAGCTC R 2 1 2 1 101000 f 74 goat snp48900-scaffold698-1249332 5 110030041 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803031 Affx-986696136 AX-385289907 5 102268262 CAGACACCTTTTCCCTTTTGGCAGGTGGCTCTTAT[A/G]CCTCCTGCTGCTGGTCCTGTTCTACGGGGTTGGAG R 2 1 2 1 600010 f 74 goat 5_102268262 5 102268262 Ancestral_priority_1043 ancestry 0.596 neutral IMAGE 10K 10K ancestral 38405534 Affx-122955980 AX-123275886 5 102364494 TTCACTGTTCATTAACACAAACTGGGCAACTGAAG[A/G]TTCAATAATCAATAGACTAGAAAAGTCTCCAAAGC R 2 1 2 1 201000 r 74 goat snp48903-scaffold698-1356900 5 110137907 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426642 Affx-122939944 AX-123296988 5 102434263 GTCCACACCCTGCAAAGAGGAATGAGGCATGGTTC[A/G]TATCCTCTGGGGCTTACAAGTTAGCTAAGGGCAAG R 2 1 2 1 201000 f 74 goat snp48904-scaffold698-1426669 5 110207716 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388064 Affx-122969527 AX-123258422 5 102476878 TTCCAGCAGCGTGGTGATGGCTATCTGTCACATCC[A/G]TTTCTAGGAACGCCGTGGAACCAGCCTGGACATAA R 2 1 2 1 101000 r 74 goat snp48905-scaffold698-1469284 5 110250631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444251 Affx-122927217 AX-123314588 5 102528118 AGATCTCCCCCGATATGGCTTCTGAAGGGCTGCTG[A/G]GAAACCCCCAGGGTAGGCAGTGGGGATTTGTCAAG R 2 1 2 1 103000 f 74 goat snp48906-scaffold698-1520524 5 110301636 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417967 Affx-122946692 AX-123288315 5 102566658 GTTTAACATTTATGATGTTTTAATTTTGCAGTGTG[A/G]CTCTATACCCGTAAACCAAAGAGCACACTAATTAT R 2 1 2 1 101000 r 74 goat snp48907-scaffold698-1559064 5 110340686 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410484 Affx-122952201 AX-123280834 5 102631469 CTTTTAAGGAGGACAGTTTTGGAATGGCATTGGTA[A/G]AGAAGGTGCTAAGAATAGCTAATAAGTGAATAAAA R 2 1 2 1 101000 f 74 goat snp48908-scaffold698-1623875 5 110405663 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415885 Affx-122948481 AX-123286234 5 102753822 GCCTTCATCAGCTTCTTGTTTATTCTCATAGTAAG[A/G]AGAGAGGAGATTGGGAATGCCGTGTGCTGTGGAAT R 2 1 2 1 101000 f 74 goat snp48910-scaffold698-1746228 5 110520580 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375479 Affx-122979146 AX-123245838 5 102808594 TTAGGACTGAGGCTGTTAGTTACGAACCGGAACCC[C/T]TCCTCACTCTCAAATACAAGAAAGGTCCCCTGACT Y 2 1 2 1 101000 f 74 goat snp48911-scaffold698-1801000 5 110575334 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801693 Affx-122965204 AX-385288601 5 102856660 TATTTACCATAGACTTGGCATAGTTCTAAGAATTT[C/T]ATATATATTAACTCAGTCTTCACAACTATCCTGTA Y 2 1 2 1 201000 r 74 goat snp48912-scaffold698-1849066 5 110622299 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444238 Affx-122927227 AX-123314575 5 102905491 GACCAAACGTTGTGACTGAGGCAGCCCAACCAAAA[A/G]GACGTACATCTACTCGGTGCCGTGTCCTTCCTCGG R 2 1 2 1 101000 f 74 goat snp48913-scaffold698-1897897 5 110670757 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429896 Affx-122938119 AX-123300237 5 102989548 CTTCATAAGAGATGCTTTTTCATTTCCTATCATAG[A/G]TATGCCTGTCATTTACTATTACAATCCCATATAAT R 2 1 2 1 101000 r 74 goat snp48915-scaffold698-1981954 5 110755697 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453034 Affx-122920085 AX-123323367 5 103067723 TGGTGACACTGAGCAACACTATTCCATCAACAAAT[A/G]GAATGAGACAGCACACGCGAAAGCACCAAACAGCG R 2 1 2 1 101000 f 74 goat snp48916-scaffold698-2060129 5 110834285 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424051 Affx-122942068 AX-123294397 5 103113897 ATGAAAAAGAGTGGGAGCACCATGGCTCCTAAAGC[G/T]TTTATGAAGTCAAGAAGCTCGGAAAGCAAGGGAGG K 2 1 2 1 101000 r 74 goat snp48917-scaffold698-2106303 5 110879447 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381224 Affx-122974511 AX-123251582 5 103164543 TTTTTAAATATGAGTTACATGAGACAGATGTGCCC[A/G]TGCAGTTGTTGTCCAGGTGGGGAGACATTCCTAGT R 2 1 2 1 101000 f 74 goat snp48918-scaffold698-2156949 5 110931023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438976 Affx-122930384 AX-123309313 5 103197356 TTTCAATGAAGCAAGCATGAGAATTTTCATTTTTA[C/T]AGAGAATCACGGGGAAAATTCTACCTCAAAAGAAA Y 2 1 2 1 303000 f 74 goat snp48919-scaffold698-2189762 5 110964320 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419296 Affx-122946236 AX-123289644 5 103249133 TGGACAAACCCCTGAAGCATAAATATCATTAATGC[A/G]CACTTCAAAGTCAAACTCGACTATATCACCCAAGA R 2 1 2 1 101000 r 74 goat snp48920-scaffold698-2241539 5 111017040 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438136 Affx-122931479 AX-123308474 5 103292477 AGCTCTAGTTTCATCTTTTGTCTTTACAAAAAAAC[A/G]CTGAGGTTTGAGGGTGGAAAAAGCCGTATATCCAG R 2 1 2 1 101000 r 74 goat snp48921-scaffold698-2284883 5 111060434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415758 Affx-122948932 AX-123286107 5 103343314 AACCACCATCGTCAGCCCGCTGCCTCTCAGCCCTT[A/G]CTGCTTCATCAGTCTTGCCTGCTCAGAGCTTCCTC R 2 1 2 1 101000 r 74 goat snp48922-scaffold698-2335720 5 111111883 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272292 Affx-1111833449 AX-519546031 5 103352994 TTAAGACTCAAGATAGGAATTTTGTGGGAACAGAA[A/C]CATTCCAACCACAGCAACCACTGTTTCGTGTTTTT M 2 1 2 1 101000 f 74 goat 5_103352994_AF-PAKI 5 103352994 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446476 Affx-122925060 AX-123316812 5 103392015 AGAAATTTCATGTCCCCTTAGGACTGTTAGAACAA[C/T]GCCTGGCGACCAGGAAGTACTCACTAAATGGGTGT Y 2 1 2 1 202000 r 74 goat snp48923-scaffold698-2384421 5 111161053 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418892 Affx-122946104 AX-123289240 5 103423965 ACTATAGAATGTTTTTATTGGCTTAAGACTAGCTC[A/G]CATGCTTCATCCTTGGTAAGGGGCTGGAAGAAGCT R 2 1 2 1 201000 f 74 goat snp48924-scaffold698-2416371 5 111193182 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772744 Affx-122964934 AX-385259889 5 103478018 CCCAGATTTATGTGTAAATAGACCTGTCATAGTGT[A/G]TTGGCCCTATTGCAGTCATCACTGTTAGCTCTACT R 2 1 2 1 101000 r 74 goat snp48925-scaffold698-2470424 5 111247679 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415465 Affx-122949163 AX-123285814 5 103541688 AAACCCCCATTTTGAAGTTCATTCCGGGGTCGATC[A/G]GGCCGTAGAAAATTACTCCCCTACTGTGCCGTACT R 2 1 2 1 201000 f 74 goat snp48927-scaffold698-2534094 5 111311080 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438643 Affx-122930904 AX-123308980 5 103598142 ATGGGTGCCTTTTACCCATGATCTTGGGTTTCTTA[C/T]AGGTGACCCAGCAGTGCTTGTCAGAAATATTAAAT Y 2 1 2 1 101000 r 74 goat snp48928-scaffold698-2590548 5 111367368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410766 Affx-122952684 AX-123281116 5 103726978 TCAGTAAGATGCCACATTATAAGAAACCACAAATT[A/G]GTCCTTTGGCAGCAGTGCCCACAGATATTGTCCCT R 2 1 2 1 101000 f 74 goat snp48930-scaffold698-2719384 5 111496180 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430683 Affx-122936923 AX-123301024 5 103792186 CTCCAGCCTCATTTTATTCTCTCCCGGCATTCCAG[C/T]CTCATCCATCTTCCTATGGTAGCTAACGTGGGCTT Y 2 1 2 1 101000 r 74 goat snp48931-scaffold698-2784592 5 111561549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403837 Affx-122957943 AX-123274189 5 103840495 AAAGCGTGGCTGTTGCTGCTTGGACTCTACAGGAG[C/T]CACGGAGAAGTTGAGATGTGTGGGGAGCAGGGTAA Y 2 1 2 1 101000 f 74 goat snp48932-scaffold698-2832901 5 111610456 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425757 Affx-122940734 AX-123296103 5 103953753 TATTATGGTTCCTTGGAAGACTGTTTGGTTTATGT[A/G]TAGAGATGTTGGGCGGCAGAGAGACAGGGTGTGTT R 2 1 2 1 101000 f 74 goat snp48934-scaffold698-2946159 5 111724595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435315 Affx-122934017 AX-123305655 5 103984768 CATCCATCCCAGCCTTGGAGGGAATGGCCTGCGGG[G/T]GAGCAAGATGCGGGAGAAGGCAGACGATGACTAGC K 2 1 2 1 101000 r 74 goat snp48935-scaffold698-2977174 5 111755696 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386400 Affx-122970827 AX-123256758 5 104046005 ACTTCTGCCCTTGAGGTTTTTGATGGTCAAACTGT[A/G]TAAGGAAATCCAATAAGTCAGTTCTCCGTCATGTG R 2 1 2 1 101000 f 74 goat snp48936-scaffold698-3038411 5 111817018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464397450 Affx-1110465657 AX-515870566 5 104114369 AGGGAGGTGCTCCAGCCTGCAGACCGCAGCCCTAC[A/G]CCTCCCCAAGCCTCAAGGGCAGCCTGGGAAGAGCC R 2 1 2 1 202000 f 74 goat GoatD01.004835 5 104114369 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38403700 Affx-122958043 AX-123274052 5 104117349 GATCCCAGAGAGGCCAGGGCATAAGATGAGGGTGA[C/T]GGGAGACAGACCTGGAGGAACACTTTGTCCTTTTG Y 2 1 2 1 101000 r 74 goat snp48937-scaffold698-3109755 5 111886538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449344 Affx-122922977 AX-123319679 5 104169840 AATCACCGCTGGTGACTGGCCCAGAGTGCAGCCAC[A/G]CACCCTCCCTACCCCATATAGCAGCCATTTAGGAA R 2 1 2 1 201000 r 74 goat snp48938-scaffold698-3162246 5 111938644 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382872 Affx-122973516 AX-123253230 5 104217974 TCCCCAGGCAACCAGTATACACTGACAGGACAAAC[A/G]ATTATTGCTAACTCAACACTGTTGTGTACTTAATG R 2 1 2 1 101000 f 74 goat snp48939-scaffold698-3210380 5 111987474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452475 Affx-122920998 AX-123322808 5 104259714 TTTTGTCCCCTTTTATATTTGTTTATTGTGGGAGG[A/G]TAAATCCAACATGAGCCACTCCCTCATGGTTAAAA R 2 1 2 1 101000 r 74 goat snp48940-scaffold698-3252120 5 112029471 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390293 Affx-122967727 AX-123260650 5 104272207 TCATTATAGGGCCAGTGCTTGTTGCTAAGTTTTCA[C/T]ATCTCCAATCCACTGTGCACCTGGGAGTGCATTAG Y 2 1 2 1 303000 r 74 goat snp12654-scaffold1483-402121 NW_017189770.1 21117 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403432 Affx-122957741 AX-123273785 5 104336470 AAACAAACATCAGTGTTTCACCCCTTCTCAAACCT[A/G]TCCTCTGCCAGTTTCCTCTGTTTCTGAGCAAAATA R 2 1 2 1 101000 f 74 goat snp12653-scaffold1483-337858 5 112121302 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431760 Affx-122936724 AX-123302101 5 104365279 ACATTTACAGTTATGTATTGAGTCATGTCTCCGTG[C/T]TTTAGTCTGAAGGTCATATTCCAAACACAGAAACA Y 2 1 2 1 101000 r 74 goat snp12652-scaffold1483-309049 5 112150129 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278457 Affx-1111836348 AX-272527278 5 104397928 GGGGTGATTCGGGCCCCCAGGAGTCTCGGGCAAAC[A/G]CCTGGAGAGTTTTAATCGGCACAGTTTGCGGGGGA R 2 1 2 1 102000 r 74 goat Random2.2K-610 5 104397928 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380183 Affx-122975510 AX-123250541 5 104426123 CTGCCCAGCAAGGCAGCTGTTCCTGTCCCGTCTTC[A/G]CTGAGATGGAAACTGAAGCCCCGAGAGATTAAGGA R 2 1 2 1 101000 r 74 goat snp12651-scaffold1483-248205 5 112211269 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416057 Affx-122948345 AX-123286406 5 104457257 ATCCGCATGCACTCTAGCCCCGTGTAACCTGAGAT[A/G]TGTTGGAATAGACCGTCCTCCAACTTGAGCGCGTT R 2 1 2 1 201000 r 74 goat snp12650-scaffold1483-217071 5 112241620 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434702 Affx-122933946 AX-123305043 5 104528563 GCACCCGTCACACTTGGCTGGGTCTGACCTCCCCT[C/T]CTAACCTGGCAGCTGGCTTTTCTTCCTTAGCACGG Y 2 1 2 1 101000 r 74 goat snp12649-scaffold1483-145765 5 112306448 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397686 Affx-122962580 AX-123268041 5 104559445 TCCAGTCTTTGTTTCAGCCGCTGAACCGCACTCTG[C/T]CACTGTGTTGCGTTTACGTGATCATAGGTTTCTGC Y 2 1 2 1 101000 r 74 goat snp12648-scaffold1483-114883 5 112334517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446275 Affx-122925668 AX-123316611 5 104665534 AGTGGGGAATTATTTTATGATACTTCATCCAGGCT[A/G]TGGTGAGGTGCTGTTCTTCCCCCAACACAGCATGT R 2 1 2 1 201000 f 74 goat snp12646-scaffold1483-8794 5 112441733 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780426 Affx-122978027 AX-385267518 5 104698413 GTGAAATTTGGAGGTGACTAAGTTGGCTTTCTCCT[C/T]TTAATCATCCTCTCACAAGCCGTGAAGAATTCCCA Y 2 1 2 1 101000 f 74 goat snp49599-scaffold709-23986 5 112475388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382518 Affx-122973803 AX-123252876 5 104731514 CCCTGGGGCTCCTCTAACCTAGGAGGCATATGCCC[A/G]GGTGGTGGGTTCCTCATCTGGCTCAGTTCAGGCCA R 2 1 2 1 102000 r 74 goat snp49600-scaffold709-57087 5 112508458 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379843 Affx-122975809 AX-123250201 5 104777954 CTCACAACTCCTTGTCAAGTGGACCTCCAACCACC[A/G]TCCCCCTGAGTTTCTTCTGAGGTGTCAACCTCTCT R 2 1 2 1 201000 f 74 goat snp49601-scaffold709-103527 5 112555181 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420039 Affx-122945141 AX-123290387 5 104901383 TGTTTTGCGAGAGACAGAAGGGAGGTAAAACCTGC[A/G]TCGTATAATGGGTTTCCCTGGTGGCTCAGTCGGTA R 2 1 2 1 101000 f 74 goat snp49603-scaffold709-226956 5 112678786 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424821 Affx-122941370 AX-123295167 5 104939177 AGCAAAAAATAAAATAGTGCACAGACCTTTAGTAC[A/G]CACAAATGTTAAAGGCAAGGATTATATATTTTCTT R 2 1 2 1 101000 f 74 goat snp49604-scaffold709-264750 5 112716566 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441297 Affx-122929458 AX-123311634 5 104973056 CACTCTTCTGATTAAAAAACTTCATTGATTCCCAA[C/T]GCCTATAAAGTCCCTAAATTTCTAATGAATTTTAC Y 2 1 2 1 101000 f 74 goat snp49605-scaffold709-298629 5 112750370 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791476 Affx-122940741 AX-385278467 5 105002881 GTGTCATTGAACTCTGAGATCAGAAAAAGCATCTA[C/T]GAGAAATTTGGATAAACATGTGAGGAGTTATATGA Y 2 1 2 1 101000 f 74 goat snp49606-scaffold709-328454 5 112780093 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388509 Affx-122969214 AX-123258867 5 105034110 AACATGTTGTCCAGCTCACTGGTGCTCGGGGTGTA[C/T]TTCACTGTGCAGAAGCGGCAAAATCCAAGTTTATA Y 2 1 2 1 101000 r 74 goat snp49607-scaffold709-359683 5 112809172 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429701 Affx-122937628 AX-123300042 5 105071160 TGGAGCTGAGATTGCCATGATCAGCAGTTGTGAGA[C/T]GAGGAAACCCCAGGACCTGGAATGAGAAGCCGGGT Y 2 1 2 1 101000 f 74 goat snp49608-scaffold709-396733 5 112846109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443301 Affx-122927463 AX-123313638 5 105106479 ACGCGGTCCTGTCTCAGCTCCGTCACTCACTAGCT[C/T]GGTGGCCCCAGGCAAATCTTTGAACTTCTTTTATT Y 2 1 2 1 101000 r 74 goat snp49609-scaffold709-432052 5 112881482 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408254 Affx-122953815 AX-123278605 5 105154744 ACAACCTCAAGACCAGGAAATCTTTGTCTCTAAGC[C/T]ACCCGTCAACCACGCCTTTGCGTTCACGCACTCAT Y 2 1 2 1 101000 f 74 goat snp49610-scaffold709-480317 5 112929984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428147 Affx-122939051 AX-123298490 5 105225577 GATGGGCCAGAGGGATGAATGAACGAGGAGATAGA[C/T]GGCTCTTTTGGTCTGCAGACTGAGCTCAGCTGAAG Y 2 1 2 1 201000 f 74 goat snp49611-scaffold709-551150 5 112997433 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392588 Affx-122966061 AX-123262945 5 105265037 TTGGACTTGAATGTCCAACAGGCAGGACAAACCTA[A/C]CAAGCCTAACATGGCCCACAGTGAGCTATCTCCAC M 2 1 2 1 101000 f 74 goat snp49612-scaffold709-590610 5 113036945 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440404 Affx-122929615 AX-123310741 5 105302253 AGTTTAGGTTATGAGGGTTCCTGGCACTCCCTACC[A/G]CCTTCCCTCCATATACACTATCAGTCTGGAATCGC R 2 1 2 1 201000 r 74 goat snp49613-scaffold709-627826 5 113073386 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375987 Affx-122978425 AX-123246346 5 105356206 GGATTGGCAGAGGGGGCGCGAAGGCTCAGAGAATG[C/T]GGAGGGTCTCCCCAGAGGTGATCCTGGAACCGGGG Y 2 1 2 1 201000 r 74 goat snp49614-scaffold709-681779 5 113125430 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430686 Affx-122936921 AX-123301027 5 105450730 ACTTCTATCATCAATATTACCATCAACACTATCAA[C/T]ACCACAACCACCACCACCATCATTATCTCCATCAC Y 2 1 2 1 201000 f 74 goat snp26711-scaffold2806-593794 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377287 Affx-122978120 AX-123247646 5 105528453 GACCTTGGACCAGTGGCTCACCTTCTCTGAGCTTC[A/G]GTCAGCTATCCCATGGATGGCATGGCCATGTGACC R 2 1 2 1 101000 r 74 goat snp26709-scaffold2806-516071 5 113296647 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320771067 Affx-122927703 AX-385258227 5 105577265 TGGGGGACATAAAATGACTAAACACCCAAGGACAC[A/G]TAAGTCAAGATTAGTCTAATTGAGTAGTTAGACTA R 2 1 2 1 101000 f 74 goat snp26708-scaffold2806-467259 5 113344488 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272460 Affx-1111834411 AX-191821404 5 105578461 TGCAGTTGGGTGAACTATC[A/G]CATCCAGGTGTGGCCTGCCTGCAGAAAACAATTCA R 2 1 2 1 102000 r 74 goat GoatD01.034327 5 105578461 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320797439 Affx-122938969 AX-385284378 5 105617170 GTGAATCTACATGTGTGATAAATTCATGTAAATGT[A/G]TACACACAAACCCATTTTTACTGCACTTGAAATTG R 2 1 2 1 201000 r 74 goat snp26707-scaffold2806-427354 5 113384823 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424437 Affx-122941794 AX-123294783 5 105667875 ATTATAATAAATATTCCATTTAAATGTAAAGTCCA[C/T]GAAAAGAAAAACCTAAACATAAGTTTATAGGAAGG Y 2 1 2 1 101000 r 74 goat snp26706-scaffold2806-376649 5 113435720 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451477 Affx-122921136 AX-123321810 5 105712845 TGTGAGTTCGAGTTATGGGAAGAGAAGTGGTGCTC[A/G]TGGTGCTGGCATAAAATATCTCTACGTGAGAAACC R 2 1 2 1 101000 f 74 goat snp26705-scaffold2806-331679 5 113480884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385960 Affx-122971538 AX-123256318 5 105750695 GACGAGGAACCAGGACCTCAGAGTTCTCAGCACAA[C/T]GCTGGCAGCTGGAAGATGGGAACAGTGCATTCAGG Y 2 1 2 1 101000 f 74 goat snp26704-scaffold2806-293829 5 113518085 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436353 Affx-122933067 AX-123306692 5 105792332 TTGGGTGCAGACCTGGCAAGTACTCCTGGTGCCCA[C/T]GGTGCCCTGCAGCCTGGCAGCCCCTTTCCACTTCC Y 2 1 2 1 101000 f 74 goat snp26703-scaffold2806-252192 5 113555452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448402 Affx-122923679 AX-123318738 5 105828300 GTTCAAGCAAAACGCAAAACAAAGGAGCTGCCTTC[A/G]GCTGGCAGACAGGGACACTGCAGAGGGAAAGGAGC R 2 1 2 1 101000 f 74 goat snp26702-scaffold2806-216224 5 113591475 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401349 Affx-122959254 AX-123271702 5 105965222 AAGGAGGAAAGAGAATCAAGAACTAAAACCTCAGA[C/T]GTCTCACAAAGGGCCTGCCATTTATACCCCAGGCT Y 2 1 2 1 101000 f 74 goat snp26700-scaffold2806-79302 5 113726590 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800607 Affx-122977502 AX-385287526 5 105998365 TTCCCTGTCTCATTCCAGAAAAGATTTCCAGCAGC[A/G]TAAAGAAGTTTTAATTCATATGCTACAGGTATTGA R 2 1 2 1 102000 f 74 goat snp26699-scaffold2806-46159 5 113759860 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404281 Affx-122957041 AX-123274633 5 106034109 TGCAGAAAAGGGGGCAGAGCACGTGGGGAGCGTGC[A/G]AGCAGGAACGTGGGGCTCCTCACGAAAGGTCACGG R 2 1 2 1 101000 r 74 goat snp26698-scaffold2806-10415 5 113794220 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272159 Affx-1111833451 AX-519545915 5 106038681 GGCCCCAGTCGTTCTCCAGGTTGGTCCTGTCACTC[A/G]CTCATTCATCCACCCCAGGAATGTTTATTGAGTTC R 2 1 2 1 101000 r 74 goat 5_106038681_AF-PAKI 5 106038681 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437642 Affx-122931803 AX-123307980 5 106064745 AACGTGAAATCAGTGGAGTCAGCAGGCTGGCTGCA[C/T]GTGGGGGCCTTGGAAGGTGGGACATTTGTCCCCAG Y 2 1 2 1 101000 f 74 goat snp30016-scaffold3274-189409 5 113816926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392343 Affx-122966681 AX-123262700 5 106104359 AAACGACTCTCAGTGTCTAGGAGACAAAGATGGCA[C/T]GTGTTCAGAGAAAAACCTGGCTTCTCCTGTCACTG Y 2 1 2 1 101000 f 74 goat snp30015-scaffold3274-149795 5 113856721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450089 Affx-122922790 AX-123320424 5 106147545 CAGGTTTCTGTGATCTGCACATTCACACAGGATGC[A/G]CGTGGAATTCTCCACCACGTCAGCACGATGGGTCC R 2 1 2 1 101000 f 74 goat snp30014-scaffold3274-106609 5 113896622 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385599 Affx-122971202 AX-123255957 5 106282493 CAGACACCCCAGCCTCCAACACTGAGAACAAACAC[A/G]AAGAAGACATGTGCCCAGCATCTGCTCTGGAGCCC R 2 1 2 1 101000 r 74 goat snp29274-scaffold3154-28240 5 114016665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403457 Affx-122957723 AX-123273810 5 106314645 TTCCATGACCAGATTAGCAAATATTTAACCAGATG[C/T]GAACACTCAGTGCTGGCAAGATGGGCACATTTATC Y 2 1 2 1 101000 r 74 goat snp29275-scaffold3154-60392 5 114048663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451971 Affx-122920945 AX-123322304 5 106399967 TCTTGACGTTGGGAAGCTGGTTTCAGCGCCCTGCC[C/T]GGCTCTCTGCTGGGTGGCAGGTGACAGGCGATCTG Y 2 1 2 1 101000 r 74 goat snp52043-scaffold7677-9635 5 114134337 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464399268 Affx-1110466570 AX-515872370 5 106430751 CTCCTGTGGAGGATGGAAAAGGCAGCAACAGGGCT[C/T]CCCCTGCCCTGTCTATATCCCTCGGCCTCTCTTTC Y 2 1 2 1 202000 f 74 goat GoatD01.042622 5 106430751 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38379759 Affx-122975854 AX-123250117 5 106435784 CTTTCTTTTTTTCTAACATTCCCAGCAAATTCTTG[C/T]TAAGACTGTACTGTTAAAGTGGAAATTACAGGGGG Y 2 1 2 1 101000 f 74 goat snp10800-scaffold1384-1417254 5 114530148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797325 Affx-122970883 AX-385284264 5 106487092 CTCCCCCACAAAAAATCCTAACGTTCTAGATTAAA[C/T]GTAAACAATGTCCTCTTAAATGCATGACCGGGCTT Y 2 1 2 1 101000 r 74 goat snp10799-scaffold1384-1365946 5 114477636 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449370 Affx-122922724 AX-123319705 5 106535849 CTCTCAACCCTAGATTGTGATGATGGCGAATGTCA[C/T]GTGCCTTGAGATGAGAGAGGGGTCTGAGCGGACAG Y 2 1 2 1 101000 f 74 goat snp10798-scaffold1384-1317189 5 114430058 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424040 Affx-122942077 AX-123294386 5 106663901 CAGAATGGGACTCTAGTCTGGGCTTCAGCACACAT[G/T]AACTGTGTGACCTTGGGCAGGTCACTGAACCTCTC K 2 1 2 1 101000 f 74 goat snp10796-scaffold1384-1189137 5 114305112 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387285 Affx-122970536 AX-123257643 5 106762138 CTGTCCTTGTGCTGGCCCCAGGTAGCACCTCGCTC[A/G]GTCTGGACCCTTCTGTGTGTGCAGGGCATCGAGCT R 2 1 2 1 101000 r 74 goat snp10794-scaffold1384-1090900 5 114219895 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391428 Affx-122966756 AX-123261785 5 106809983 AACTAATACATTACTACCCAAAAGCCTTGAAGAGA[C/T]GGCCAGGAACCAAGGACAGTGGTGTCTTGTTCACA Y 2 1 2 1 101000 f 74 goat snp10793-scaffold1384-1043055 5 114172320 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406521 Affx-122955135 AX-123276873 5 106857731 GAAGAACCTGGGCTCGTCTTCCGCCCTGGGTTTGA[A/G]GCACAGGCAGCAAAAAGCAGATCTTACCCGGTGAC R 2 1 2 1 202000 f 74 goat snp10792-scaffold1384-995307 5 115510321 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783119 Affx-122973662 AX-385270186 5 106910186 TTTCTCCATTTCTTCCAGTAAAATTAAGCTCCAAA[A/G]ATGAGCAATTTTGCTTTTAGTGCTGAACGAAATGC R 2 1 2 1 101000 r 74 goat snp10791-scaffold1384-942852 5 115467854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392291 Affx-122967530 AX-123262648 5 106941335 TAGCAGAGGGTGGAGGAGGTATGTTCTGAATGTTG[A/G]GAAAATATTTATCCCCAAGGCCAACGACAGACAAT R 2 1 2 1 101000 r 74 goat snp10790-scaffold1384-911703 5 115436762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406524 Affx-122955133 AX-123276876 5 106973484 AAATAGCTCCATTGAGATGTCGTTTACATACCATA[A/C]ACTAGTATGTAACTGGTATGTTTAAACAATGGTTT M 2 1 2 1 101000 f 74 goat snp10789-scaffold1384-879554 5 115404053 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784916 Affx-122949101 AX-385271963 5 107003959 CACTAGTGAAATTTTTCTGCACAAAGTAGCTGGGC[A/G]TTGTTAAATCTGAACATGCACGATGTAAAATCTTT R 2 1 2 1 101000 f 74 goat snp10788-scaffold1384-849079 5 115374655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390135 Affx-122967995 AX-123260492 5 107094012 GCTGCTGTGTCCCCGTGAGCTGTTTAGTGTTTAAG[A/G]GGGGGCAGGTTTCTTAGAGAACCCAGCCCCAGCCC R 2 1 2 1 101000 f 74 goat snp10787-scaffold1384-759026 5 115299207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378829 Affx-122976544 AX-123249188 5 107124639 TGTGGCATTGTGGAGATTTTTCTTTTTGTTCATTT[A/C]TTTATCTTGCTTGATGTTCACTGAGCATTTTCAAT M 2 1 2 1 103000 r 74 goat snp10786-scaffold1384-728399 5 115268419 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434844 Affx-122934378 AX-123305185 5 107230349 CCAGCTCTCCGACAGCTCCAAATGCTGGCAAGGAC[A/G]TGGACCAACCAGAACACTCGTGCCTTGCAGGCAGG R 2 1 2 1 201000 r 74 goat snp10784-scaffold1384-622689 5 115164585 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383478 Affx-122973439 AX-123253836 5 107320833 GTTTGTTCAGCCACTGAAGTGTGACCTTGTAGACC[A/G]TGTGTTTTGGGTGGGAATTATACCCCAAGTACCAA R 2 1 2 1 101000 f 74 goat snp10782-scaffold1384-532205 5 115082295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440884 Affx-122929233 AX-123311221 5 107402299 ACCATTCCTCTAGTCAGAAGTACAAGAGAGATTCC[A/G]GTCAACCTCAACTAAAGCTGATGTTGCCAAGCCTG R 2 1 2 1 101000 f 74 goat snp10781-scaffold1384-450739 5 115003901 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453431 Affx-122919875 AX-123323764 5 107434224 GTTCCATTTCAGTTTTTCTGTTGGCATCTTATCTA[C/T]AATTCTTCGCATTTTTAAAGTAGTTGCCACCAGGA Y 2 1 2 1 101000 f 74 goat snp10780-scaffold1384-418814 5 114971832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393381 Affx-122965907 AX-123263737 5 107490463 ATGGCAAGAGAAGACCAGTTCTTGCCCGGATTTTA[G/T]GAAATTTTGACATTTGGTACTTTTTTTTTTTTGCC K 2 1 2 1 103000 f 74 goat snp10779-scaffold1384-362575 5 114916795 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410201 Affx-122952575 AX-123280551 5 107523634 TCTTATCATCTCACAGAAGGTTAGAACCTGTCCCC[A/G]TCCTGTCACAGGAAGTTAGAATCTATCTTTATTCT R 2 1 2 1 303000 r 74 goat snp10778-scaffold1384-329404 NW_017212681.1 7951 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274959 Affx-1111834514 AX-519548541 5 107538028 GGGCCTCCTGCTGCCCAGGCTGTCACACTCTGCAT[A/G]GTGTAAAAATTAGGGGGGCCACTCCCCAGCTGGTG R 2 1 2 1 202000 r 74 goat GoatD01.039109 5 107538028 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278296 Affx-1111836349 AX-519551782 5 107562959 GGGATGAGTGAGGGGATGAGTGGCTGCATGAATGA[A/G]TGAGTGAGGGGATGAGTGGCTGAGTGAATGAATGA R 2 1 2 1 103000 f 74 goat Random2.2K-614 5 107562959 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450965 Affx-122921747 AX-123321299 5 107636146 TATTTTTAAAACTTTTGGCGAATCTTCTTGCCTCT[A/G]CTGAGTGTTTTTCTCTTGCTTTTGTCTGTTTTCCA R 2 1 2 1 101000 f 74 goat snp10776-scaffold1384-216892 5 114771051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787867 Affx-122945396 AX-385274889 5 107708062 TCACTGCTTTTTACATGTAACTATATCCACAACTC[C/T]ACCTTCCCTTCTTCTGATAAAAGATTGGGCAACTA Y 2 1 2 1 101000 r 74 goat snp10775-scaffold1384-144976 5 114698103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432268 Affx-122936336 AX-123302609 5 107748386 ACCATGAAGGGGCTAAAAAGACAGCCCTTCAACTG[C/T]GGGCTCAGCTCTGTCGGATGGGCCACCTGCTGGCG Y 2 1 2 1 101000 f 74 goat snp10774-scaffold1384-104652 5 114658003 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387995 Affx-122969579 AX-123258353 5 107787195 CCAGACTTGTCCACTCTGCCTGGTCATTGTGTGCT[A/G]TGGTCTGTCTCCCATAGAATCTCAGCTCTTTGGGG R 2 1 2 1 101000 r 74 goat snp10773-scaffold1384-65843 5 114619211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390121 Affx-122968006 AX-123260478 5 107880268 CCAGCCCGTGAACCAAACGCTGGATGCTGCCAACG[A/G]GGGTGTCAGTGCCCACTTCACGGATGAGGAAACTA R 2 1 2 1 201000 r 74 goat snp14413-scaffold1573-144238 5 115530453 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448903 Affx-122923179 AX-123319238 5 107955211 GACCTCCATCTCCTACTTCTTTGGATGGAGCTGCT[A/G]CTGCTGCTAAGTCGCTTCAGTCGTGTCCGATTCTG R 2 1 2 1 103000 f 74 goat snp14412-scaffold1573-69295 5 115601050 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442816 Affx-122927710 AX-123313153 5 107995138 CCCATGTGACTTCACTCTCTAGAATGTCTGGCTCT[A/G]GGTGATGTTATTAGGCCATGTTATTAGGTGCGTAC R 2 1 2 1 101000 r 74 goat snp14411-scaffold1573-29368 5 115644711 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381559 Affx-122974824 AX-123251917 5 108077456 CCCCATCGAGCTACGATACCACTGCGTTAAGAGAA[G/T]AGTTCAAAACACAAAAGAAGTGTGCAAGATGTAAA K 2 1 2 1 101000 f 74 goat snp23854-scaffold2401-52851 5 115724526 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434121 Affx-122934927 AX-123304462 5 108108946 AAAAGAAGGCAGAAGCCGTGGGTTTCTAGTGTTGT[A/G]CATGTTCTAAACAGCAGCCCCAAATGCTTTTTGCC R 2 1 2 1 201000 r 74 goat snp23855-scaffold2401-84341 5 115796351 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385985 Affx-122971521 AX-123256343 5 108226821 GTAGGCATATACGCTCCCAGCAGCAGAGAGAAAAC[A/C]GCACAGGAAGGGTTTCTAGAGAGGAAAGGACAAAA M 2 1 2 1 101000 r 74 goat snp15139-scaffold1618-38721 5 115839398 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793327 Affx-122932062 AX-385280305 5 108280848 GAATAAGAATGACCGCCGTTCCTTTGAACTGATAC[A/G]TAGAGCTGAGCTGAGCACAAAATCAAGCTAAGACA R 2 1 2 1 101000 r 74 goat snp15140-scaffold1618-92748 5 115893270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784364 Affx-122972328 AX-385271415 5 108334644 AGACTCACAGTACAGATGAGTTTGGAGTTGTGATG[C/T]TGGCATTGTTTTCATAAAGACAGTTCTGAATTTTA Y 2 1 2 1 101000 f 74 goat snp15141-scaffold1618-146544 5 115942653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762412 Affx-986696943 AX-385250563 5 108340022 TCAACAAGAGGCTGGCAGGGGCTCAAGCTGCCCAC[C/T]GAGGTGGAGTCAGGGTCCTAGAGGGGACGGCCCAC Y 2 1 2 1 600010 f 74 goat 5_108340022 5 108340022 Ancestral_priority_1043 ancestry 0.424 neutral IMAGE 10K 10K ancestral 320779151 Affx-122976595 AX-385266255 5 108372729 TGTTCCATATAAAATTCTGTTTCACGCCTTTTCCC[A/G]TTTAACCTTAGAACGTTAGCTTGTTCCTGTATTAT R 2 1 2 1 101000 f 74 goat snp15142-scaffold1618-184629 5 115980821 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448631 Affx-122923368 AX-123318967 5 108421288 GGCAACGAAAGACTGAGGCCCTTGGGTTTAATGCA[C/T]GTAAATCAGCTACGACAATTCTCTTGAAGAAAACC Y 2 1 2 1 101000 r 74 goat snp15143-scaffold1618-233188 5 116025461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762416 Affx-986696947 AX-385250565 5 108502201 AGGTGTGCTGAGTGTGAGGGCTGAAGCTCAGGGAT[C/T]CTGAGTGTGGGTCTTTGGGGAGAAGCATCAAAATA Y 2 1 2 1 600010 f 74 goat 5_108502201 5 108502201 Ancestral_priority_1043 ancestry 0.548 neutral IMAGE 10K 10K ancestral 320764647 Affx-986696949 AX-385252286 5 108502377 ATGGTTCAGAAAGAACCTTGTAAGTGGTTTCAACC[C/T]GGTTTCCTATCAAGATCACCTGACCAGTGTTAAGC Y 2 1 2 1 600010 r 74 goat 5_108502377 5 108502377 Ancestral_priority_1043 ancestry 0.552 neutral IMAGE 10K 10K ancestral 38396130 Affx-122963402 AX-123266485 5 108544853 TTCTTTTAGTGAACGCAGTCTGATTGTCTGTCTCC[A/G]TTTTGGGGGGATCCTGGCTGAGAATTGTGTGATGC R 2 1 2 1 201000 f 74 goat snp15145-scaffold1618-356753 5 116152661 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397187 Affx-122962409 AX-123267542 5 108613329 GTTTGGTATTGGAACCACCTGAAGTCAATTAAGGA[C/T]CCACAGAATCAATTATTCTCTCTGGGCTGAAATCA Y 2 1 2 1 101000 f 74 goat snp15146-scaffold1618-425229 5 116220567 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413906 Affx-122949831 AX-123284255 5 108642407 GTTCACGGTGCTTTGGTTTCATTGCCATAGGGGAG[C/T]GGGCAGAAACTCAACTGGAGGCAAGATTTCATTTA Y 2 1 2 1 201000 r 74 goat snp15147-scaffold1618-454307 5 116249705 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421291 Affx-122944730 AX-123291638 5 108700461 GCCAGTGTAGTCAGAGGGTGCTTGTGGGAGACAGA[C/T]GGGAGCAGGAGGGCAGAGCGTGACCTGAGAGGGAG Y 2 1 2 1 101000 f 74 goat snp15148-scaffold1618-512361 5 116308114 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410667 Affx-122952759 AX-123281017 5 108728068 ACAGAGATATCACCAATGCTGTTGGAAGGATTATC[A/G]TCTTGATTTTACAGATGAGGAGACTGACCCTCAGC R 2 1 2 1 101000 f 74 goat snp15812-scaffold1657-664435 5 116336065 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450372 Affx-122922093 AX-123320707 5 108767113 AGCTCAAAGGATAAATGGAAAACAAAGAGAACAGA[C/T]GAGCCGGGCATTCTCCCGACTCTACAGAAACACAA Y 2 1 2 1 101000 f 74 goat snp15811-scaffold1657-625390 5 116375129 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272295 Affx-1111833452 AX-519546034 5 108781988 TATGTGACTCCGTAACTCCATCTTGTGGCAGCTGG[A/G]AGAGCTGGGGCTGAGGGTTGAGGGATGGCACCTAC R 2 1 2 1 102000 f 74 goat 5_108781988_AF-PAKI 5 108781988 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392382 Affx-122966230 AX-123262739 5 108864631 TGCCCAAGAACGCATCACCCCTACCTCGCCCCAGA[C/T]GGTGGGCTCTGGGTCTATGCCACAGGCACCTCCCA Y 2 1 2 1 303000 r 74 goat snp15810-scaffold1657-527872 5 116473495 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382497 Affx-122973818 AX-123252855 5 108896470 GTGTTCATTTAGCTGTCAGTTTGCTTGGCCACGGC[A/G]CAGAGGACTCAAGGGCAGGAGAAAGGGAGGACTCC R 2 1 2 1 101000 f 74 goat snp15809-scaffold1657-496033 5 116505565 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391934 Affx-122966930 AX-123262291 5 108943148 ATTTCTGCAAGACTGCTCTTGCTCTAAGAGGAGCC[C/T]GGATCCTGCTGAAAGCAAACAGCCCGGTGAGCAGA Y 2 1 2 1 101000 f 74 goat snp15808-scaffold1657-449355 5 116552451 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777250 Affx-122961736 AX-385264373 5 108979481 TGTAATTTTCAAGGCAATACAAAAGCAATCGCATA[C/T]ACTAATAACAACAATGTAGCAGCAGAAGCCTCAGT Y 2 1 2 1 101000 r 74 goat snp15807-scaffold1657-413022 5 116589281 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408143 Affx-122954230 AX-123278494 5 109018726 ATGATAAACTCAAATGTAGTGGATTCAACTGCCTA[G/T]TTCTTCAGGAGCCACTGTCACCGAGAGTCCAGAGC K 2 1 2 1 201000 f 74 goat snp15806-scaffold1657-373777 5 116629121 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384334 Affx-122972258 AX-123254692 5 109055588 CGGATGAATTAATCTCCTGCGGCATAAAGACCTCA[C/T]GATGACCCCACCTGCAGTAGCTGCCCCATAAAGGG Y 2 1 2 1 101000 f 74 goat snp15805-scaffold1657-336915 5 116662402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446216 Affx-122925710 AX-123316552 5 109089389 CCTACTGCGCATCTGGTTCCATTCCGTGGAGGTAC[A/G]CAGCCTCCACTTTTCCGTGTCACGTTCATGCACGT R 2 1 2 1 201000 r 74 goat snp15804-scaffold1657-303114 5 116696476 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415768 Affx-122948925 AX-123286117 5 109126422 GGTGCCCTGGAATTAGACTGTAAGGATCTGCACAC[A/G]CTCGTGAAGATACTAAAAACCACTGAACTGTACAT R 2 1 2 1 101000 f 74 goat snp15803-scaffold1657-266081 5 116734104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441692 Affx-122929168 AX-123312029 5 109168208 TGCAAAGATATCAGGAGCTCTTCATGGAGGAAAGC[A/G]CTGTCCCAGGCAGTGAATCCCACATCCTGCGCAGC R 2 1 2 1 101000 f 74 goat snp15802-scaffold1657-224295 5 116776787 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386833 Affx-122970090 AX-123257191 5 109198873 TTACATTCATTACTAAAGGGAGACGCTGGAACGAG[C/T]GCAAAACTGAAGTCTGTCTATACGTTATCTAACAA Y 2 1 2 1 101000 f 74 goat snp15801-scaffold1657-193630 5 116807516 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393178 Affx-122965522 AX-123263535 5 109237211 ATAACTTCCTTGTGACTGTCAGATATAAATGCCTC[C/T]GTCCTTGGGGTTTGCAGAGCAGATATTTCTAGTAA Y 2 1 2 1 101000 f 74 goat snp15800-scaffold1657-155292 5 116845863 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390389 Affx-122968178 AX-123260746 5 109291877 GGTCGCAAGGAGTCGGACACGACTGAGCAACGAGC[A/G]CTTCACTTCACTGAAGGATAACATTCCTACAGGAG R 2 1 2 1 101000 r 74 goat snp15799-scaffold1657-100626 5 116899637 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415405 Affx-122948738 AX-123285754 5 109321445 CTGTGTGCCATCTCAGGTGGTAAAATAAATGCACC[A/G]CATTGCAGGGACACAGACACAGCTTCATCATGGAG R 2 1 2 1 101000 f 74 goat snp15798-scaffold1657-71058 5 116929596 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781213 Affx-122939683 AX-385268298 5 109369751 ATGTCCTTCATCATTACCAGAAGCCAGAAGTCATA[G/T]AATCTGCTCTAGTATGAGTCACCTTACAGCGTTGA K 2 1 2 1 101000 f 74 goat snp15797-scaffold1657-22752 5 116979586 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393076 Affx-122965606 AX-123263433 5 109409502 AAGGTGTCATGTGACCCGCGTGTTGGGCCGGGTGT[A/C]GGGGTGACTTCACACTGGATCCCACACTGCCTAAC M 2 1 2 1 101000 r 74 goat snp3419-scaffold1104-321302 5 117019919 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410746 Affx-122952698 AX-123281096 5 109449917 GAAGGAAGAGGAGTTCCTTAAGAACAATAACAACC[A/G]CCACAGTAATAACTGTGTATAACTTTGTATTTTTA R 2 1 2 1 101000 f 74 goat snp3418-scaffold1104-280887 5 117060343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422085 Affx-122943588 AX-123292432 5 109480591 CTCACCCCAGGTGGCAAGAATCTCAAAGACCATCC[A/G]CAGTATCTCAGCAAAGAAGGAAAAAAGCCGGAACT R 2 1 2 1 101000 r 74 goat snp3417-scaffold1104-250213 5 117088450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418911 Affx-122946092 AX-123289259 5 109517281 AAAATATTAGAGTGTTCTTTTTTATCCCCAATTAA[C/T]GTAGGAATAATCATATCACATTCTCATAATGATCT Y 2 1 2 1 101000 r 74 goat snp3416-scaffold1104-213523 5 117125837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414963 Affx-122949071 AX-123285312 5 109549187 GAGAGGTGATAAGAACTTTCTCTTGGGGCAAGAAC[A/G]TATGACAAGAAGCAAGGAGACGTGTAGAGACACTC R 2 1 2 1 101000 f 74 goat snp3415-scaffold1104-181617 5 117157387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784090 Affx-122953190 AX-385271142 5 109594632 TTCCTCCTTACACTAAAAGGAATTTACTAATGCTC[A/G]TTAATTTTTTGTGGTGTGAATAAATTGCAGGGAAT R 2 1 2 1 101000 f 74 goat snp3414-scaffold1104-136172 5 117202064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792086 Affx-122977265 AX-385279073 5 109642153 TACCTTCTGACATCATGTATCAGCACGCTAAGCAT[C/T]GGCTGAGAAGCAAATAACCTTTCAAGCAGAATGAA Y 2 1 2 1 101000 r 74 goat snp3413-scaffold1104-88651 5 117248547 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779222 Affx-122954358 AX-385266326 5 109743089 CTTATTATGCACACAGAGCAAGCAAACAGAAAAGC[A/C]AAAATTAAATTAGACGGCAGCCTGGAGATGCCCAC M 2 1 2 1 101000 f 74 goat snp12979-scaffold15-526697 5 117337522 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387627 Affx-122969862 AX-123257985 5 109796958 GCGGGCTACATTCCATGGAGTCACAAGAGTCAGAC[A/G]TGACTGAGTGACTAGCTCATTCCACCTACTGACTT R 2 1 2 1 101000 r 74 goat snp12978-scaffold15-472828 5 117390384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799287 Affx-122977642 AX-385286217 5 109825874 CAACATTCACAAAATGCACATTTATTTCAAGTGAG[C/T]ACAGTCACCACGATAGATCATGCAGAAGGCCCGCA Y 2 1 2 1 101000 f 74 goat snp12977-scaffold15-443912 5 117417259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422204 Affx-122943497 AX-123292550 5 109869117 CTGAAGCACGTGGAAGCCCGAGATGCACCTTATGC[A/G]TTCGCTATTATTCTTTGTGTTAGAAGGTTTACAAA R 2 1 2 1 201000 r 74 goat snp12976-scaffold15-400669 5 117457386 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407116 Affx-122954876 AX-123277467 5 109897638 CAGACACTGCAGAAATAGCACGTGTGCAAGCATTA[A/G]CAACGGAGCAGACTCCAGAAGAACCGCCCAGAAGC R 2 1 2 1 103000 f 74 goat snp12975-scaffold15-372148 5 117486496 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445307 Affx-122925439 AX-123315644 5 109932167 TTCTTTGTCTCTCCTCTTCACATGAATATTTATCG[C/T]GAGGAAGGCCCAGCCAGCACGCCAGCGGCCCCATT Y 2 1 2 1 101000 f 74 goat snp12974-scaffold15-337619 5 117521641 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399294 Affx-122960538 AX-123269649 5 110053631 AAGGAAAGAGAGTCCTTGGTCAGCTTGCTGGGAAA[G/T]TGTCCCCTTGGCTGAAGAGTGGGTGGATACTCAGT K 2 1 2 1 101000 f 74 goat snp12972-scaffold15-216155 5 117632862 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795951 Affx-122966128 AX-385282903 5 110086932 AGATAACAGATAGATGATGATGGCACACAGATAGA[C/T]AACAGACTGATGCTAGATACAGATGCATAACAGAT Y 2 1 2 1 101000 f 74 goat snp12971-scaffold15-182854 5 117666597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418931 Affx-122946509 AX-123289279 5 110141988 GGGGTAATCATCTACACCCTGTCTATCCCTCTAAA[C/T]ACTACTCTGAAACCCCGACACAGTGCCTGGAGCAC Y 2 1 2 1 101000 f 74 goat snp12970-scaffold15-127798 5 117721039 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445884 Affx-122925961 AX-123316221 5 110174076 CGAGCACAAAAGTTTCCGAGCTTTGGCTTCCAGAG[C/T]ATCATGTCAGACAAGACCTGGATTCACTCCCGAAA Y 2 1 2 1 101000 f 74 goat snp12969-scaffold15-95710 5 117754742 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430443 Affx-122937732 AX-123300784 5 110235979 TGCCCGAAACGGAGGCAAAATCACTCTCTGCTCTG[C/T]GATGAGAGTCGAGGCTAATTTTATCCCCACTGTGC Y 2 1 2 1 101000 r 74 goat snp12968-scaffold15-33807 5 117814863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430512 Affx-122937218 AX-123300853 5 110292410 GCGTGCACGCCTCAGCTGATCCGCCTGGAATCAGC[G/T]TCCACGCCTTGAAACCTCTCGTGTTTTTCCCCGGG K 2 1 2 1 101000 r 74 goat snp22113-scaffold2180-22525 5 117872641 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442697 Affx-122927877 AX-123313034 5 110353295 GTTGATGGGCTTTCCTTCCCCATCAAGTGAAATAG[C/T]AGCCTGTTATCGGTCAACAAAAAGACGTTTGTGCC Y 2 1 2 1 101000 r 74 goat snp22114-scaffold2180-83410 5 117932089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375690 Affx-122978656 AX-123246049 5 110408532 AAGCAGAAAGAAATGACAAATGTGAGATGAACTGC[A/G]AATAAACTGTGAACAATTAACTATGAAGAACTGTA R 2 1 2 1 201000 r 74 goat snp22115-scaffold2180-138647 5 117980961 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445674 Affx-122926138 AX-123316011 5 110463870 TAAGCTCCAAGAGGAAAAAATAAAATATGAAGAAC[A/G]CTACAGCCATTTAAATACTTTATTACACAATTGCG R 2 1 2 1 101000 f 74 goat snp22116-scaffold2180-193985 5 118032865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802763 Affx-122956956 AX-385289662 5 110506902 TCTGGAATACACCCTATTGAGTTCCTCCAGTGAAA[G/T]CAAATTCCTGGTCTTGGCCTCAGACTGTCAGTCTT K 2 1 2 1 101000 r 74 goat snp22117-scaffold2180-237017 5 118074684 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419169 Affx-122945730 AX-123289517 5 110533033 TAAAAATGATAGCTTGGCTCACAGGAGAAACAGTA[C/T]GTGCATGGCCCGTGGACGTCAGGCCTCCTTTAATC Y 2 1 2 1 101000 f 74 goat snp7077-scaffold1262-10037 5 118110963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440741 Affx-122929875 AX-123311078 5 110620954 TCAGGCACAGAAAATCCTGTGCGTTAAAGTCCCTT[A/G]CTGACCATTCTTTGTTTGCAGTATGGTCGCTTATC R 2 1 2 1 101000 f 74 goat snp7078-scaffold1262-97958 5 118246438 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376490 Affx-122978029 AX-123246849 5 110691148 TTTCCAAGCCTTATCCATTCTTGGGCAAGGCTCCC[A/G]CCTTGGCGGTGACAGCCTCCTATCTTCCTGGCGGG R 2 1 2 1 102000 f 74 goat snp7079-scaffold1262-168152 5 118301420 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428875 Affx-122938340 AX-123299217 5 110743657 GGGTTTCGGCTCTCTGGCCTCTGAGATGGGACTGC[A/G]TTCTGTCTACGGGGTGTGCCTCTCCCAGAATAAAC R 2 1 2 1 101000 r 74 goat snp7080-scaffold1262-220661 5 118353537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792496 Affx-122932235 AX-385279477 5 110797980 AAAACTCATAGCAACATCATACTTCATGGTGAAAC[A/G]CTGAGCACTTTCCTCTGGAGTTCAGAAACAAACAA R 2 1 2 1 101000 r 74 goat snp7081-scaffold1262-274984 5 118407105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454111 Affx-122919355 AX-123324444 5 110861971 CCATTCTGGCTTCATGTGTTCCTTCTGCCCTGCTC[A/G]CCAGGCTCCTGGGACGGGCACATGCGGCCACATGA R 2 1 2 1 103000 f 74 goat snp7082-scaffold1262-338975 5 118466679 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403760 Affx-122958001 AX-123274112 5 110903832 TTTTTTTAGCAATAAAGTGTTCTTAAGGTATGTAC[A/G]TTGCTCTCTAGACATGCACATAGTATGCAGATACA R 2 1 2 1 101000 r 74 goat snp7083-scaffold1262-380836 5 118507888 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449440 Affx-122922674 AX-123319775 5 110954957 TAACAGCACTCAAACAACTAGGAAAAGAATGGAAG[C/T]GGCTCAACGGGATAAAGACTGTGTGTGAAAACTCC Y 2 1 2 1 101000 r 74 goat snp7084-scaffold1262-431961 5 118558584 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377607 Affx-122977894 AX-123247966 5 110992449 TGATCAGGCCTGAACCCCATTCGGAGTCTGAGACC[C/T]CTTGGAAAACGGGGGAGGGGACAGGGCTCACGGAG Y 2 1 2 1 101000 f 74 goat snp7085-scaffold1262-469453 5 118593702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272296 Affx-1111833453 AX-519546035 5 111337928 GGGGCTCAGTAATCATCTCAGCAAGAACGAGTCAC[A/G]CCCCAACAACGAACAAGTGAGCAGCCTGGGACCTG R 2 1 2 1 101000 f 74 goat 5_111337928_AF-PAKI 5 111337928 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278461 Affx-1111836350 AX-519551944 5 111503812 ATTGGGAAATACATCATTCTGGTTCCCTATTCACT[A/G]TAGTACCTTCTCAGGTGAGCAGTAGTTAGTTGTTG R 2 1 2 1 101000 r 74 goat Random2.2K-617 5 111503812 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 464402868 Affx-1110468381 AX-515875929 5 112142244 AGGGACTTGACGACGGTGACAAACTGCAGCAGCCA[C/T]GTGACAGTCACCGCTCCGTGTCCCCTACAGGTAAA Y 2 1 2 1 202000 f 74 goat GoatD01.015571 5 112142244 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320764651 Affx-986696951 AX-385252288 5 112828562 ACTTAGATACTTGGGTGAAGCTAAGGAAACAGCTA[A/G]AAACTTATTATAGTTTACATGGGCCTGTAAATGCT R 2 1 2 1 600010 r 74 goat 5_112828562 5 112828562 Ancestral_priority_1043 ancestry 0.584 neutral IMAGE 10K 10K ancestral 320764654 Affx-986696953 AX-385252290 5 112829169 AAAAGGATTCTAAAAATAAAAAGTTTCTCTTGTGG[C/T]CAAATGAGGCATTTTGTCGGCAGTGTCCTGCTAAA Y 2 1 2 1 600010 r 74 goat 5_112829169 5 112829169 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 468273635 Affx-1111833711 AX-519547248 5 113205026 AGCCTCTCACAGTGCCCGCTCCCGCAGGACAGGTG[A/G]GCTTCCGCTTCCGCCTCTCCTTCTGCAGGAGGAAG R 2 1 2 1 202000 r 74 goat GoatD01.002213 5 113205026 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278302 Affx-1111836352 AX-519551788 5 113489131 GGGACACGGAAGACAAAGGGGACAGCAGATTTAAC[A/G]TCTCCGGTAAGCGATTCTTGACAAATATCTACAAG R 2 1 2 1 101000 f 74 goat Random2.2K-620 5 113489131 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272297 Affx-1111833454 AX-519546036 5 113851836 CTCGGCCATGGCCGGTTCCCCAGACTTCTCCATCT[A/G]CAGCGGGAACTGTTCCCAGAGGGGTGCTGGGTAAA R 2 1 2 1 303000 f 74 goat 5_113851836_AF-PAKI 5 113851836 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 464404651 Affx-1110469283 AX-515877687 5 114105129 CAGGGTCTGCAGTGGGAGGCCATCCTGGCAGGAAG[A/G]CACAAGGGACGCTGGGCAGGAGTCCCCAGACAAGG R 2 1 2 1 202000 f 74 goat GoatD01.055655 5 114105129 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278304 Affx-1111836353 AX-519551790 5 115004333 GTGTGAAAGCAGCCCTACGCTGTGCGTGAAGAGAC[A/G]CGCGTGCTGTGTCCAGTGAAGCCTCATTCGTGAGC R 2 1 2 1 202000 f 74 goat Random2.2K-622 5 115004333 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273845 Affx-1111833852 AX-519547454 5 116281982 CTGCAGAGCAACGGCTGCTC[A/G]GGCCTCCAATCCGTGGTCTTTGTCTAAAGCAGCCT R 2 1 2 1 102000 r 74 goat GoatD01.007349 5 116281982 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468272298 Affx-1111833455 AX-519546037 5 116371807 GAGCTGCAACCATTGGACTCCTGAAGTAAGCACAC[A/G]CGGTGCTCTCTTAGACATCAGTCTCAGCAATCCTT R 2 1 2 1 101000 f 74 goat 5_116371807_AF-PAKI 5 116371807 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278306 Affx-1111836354 AX-519551792 5 117627326 TGGGGTTTAAGAAGCTCAGGCAGGAGAGCTGGCCT[A/T]GCCACCCCATTTCCTGTTCCTGAGACCCCTCGCCA W 4 1 2 1 103000 f 74 goat Random2.2K-625 5 117627326 T A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273858 Affx-1111833889 AX-519547468 5 117907093 GAGCAGGGCTGCAGAGGGAGTGGACGGAGATGCGG[A/G]GGGAGTGGGGACTGTGTTGTGACTGCGGGGCCGTC R 2 1 2 1 303000 f 74 goat GoatD01.009515 5 117907093 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468274471 Affx-1111834312 AX-519548062 5 118555833 GTGCCATCTGGAGAAGGCAGAGTGGAGGGCTAGGG[A/G]TTGAGGGGTGGGTTCAGTGGAGAGGAGTTCCTGCA R 2 1 2 1 303000 f 74 goat GoatD01.029799 5 118555833 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468272299 Affx-1111833456 AX-519546038 5 118976440 AAAAAGCAAAGACATTACTTTGCTGACAAAGGTCC[A/G]TCTAGTCAAAGCTCTGGTTTTTCCAGTAGTCATGT R 2 1 2 1 303000 f 74 goat 5_118976440_AF-PAKI 5 118976440 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392776 Affx-122965988 AX-123263133 6 25231 ACATCATCAATTGTTGCAGTACTCCTGGTGAGAGA[C/T]GACAGTGGCTTGGGCCAGGGTGGTGGCAGTGGCAA Y 2 1 2 1 101000 f 74 goat snp31735-scaffold354-25231 6 484197 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414442 Affx-122949952 AX-123284791 6 54326 CATCTGTGGCTTGGTTAGTCTTCTGGATGATGACT[A/G]TCACCTGGAAGCCTGTTAGAAATGCAGAAATGCCC R 2 1 2 1 103000 f 74 goat snp31736-scaffold354-54326 6 513324 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437220 Affx-122932036 AX-123307558 6 90072 ACACCATACCTATACTTCCAATGCCTTGTATTCAG[A/G]TTGTTATTTGATGTGTATTATCAGTCTTTGGATTC R 2 1 2 1 101000 f 74 goat snp31737-scaffold354-90072 6 549401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272337 Affx-1111833496 AX-519546069 6 164375 GTGCAGCTCGGCCATGTTTTCACCAAACCTGAATC[A/G]GACTGTTGCCCACTGAGCTGCTCTGATATAGGTTC R 2 1 2 1 201000 f 74 goat 6_164375_AF-PAKI 6 164375 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38420220 Affx-122945536 AX-123290568 6 184232 CGTGTGTGGTGATTAAGGCCCTGTTTAATTAGATA[A/C]TTTTACCATCTCTGCAGAGGTGAAAAATAGACACA M 2 1 2 1 101000 f 74 goat snp31738-scaffold354-184232 6 645298 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796582 Affx-122933047 AX-385283528 6 231230 TCTCCTTGCAGCTTCAGGAGGATGTCTCATTTATC[G/T]CAATTACTGCCTGGTAAACACTGCTGACCAAAGGG K 2 1 2 1 101000 f 74 goat snp31739-scaffold354-231230 6 692622 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432615 Affx-122935494 AX-123302956 6 290051 GACAGTTCCTCAAATATTAGCAGCCTGTATCTGTT[A/G]CTGTTTGTGATATGGTTGAGAAATTGTCCCCAGGC R 2 1 2 1 101000 r 74 goat snp31740-scaffold354-290051 6 752376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801550 Affx-122925352 AX-385288459 6 353088 ACTCACACAGGGATAGTTTAACCCAAATTTCAACC[G/T]ATTTAACTTGACTGTTTAAAGGGCCAACATTTTTT K 2 1 2 1 101000 f 74 goat snp31741-scaffold354-353088 6 816392 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393811 Affx-122965172 AX-123264166 6 420831 AACTAGGGTTTATTTCCTTAATATGGAGATGGGTA[A/G]CCAAGAGTTGTGGCCTGAATTATATCCCATCAAAA R 2 1 2 1 101000 r 74 goat snp31742-scaffold354-420831 6 884237 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382563 Affx-122973768 AX-123252921 6 463461 AGTGGGAAACAGATGGACGGAGGGGTTGGGATTAG[C/T]GAATGCAAACTATTATACAAAGGATGAGTAAACAA Y 2 1 2 1 201000 f 74 goat snp31743-scaffold354-463461 6 927062 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415512 Affx-122948683 AX-123285861 6 545755 TGGCCACCACCCCTGACCTCTACCTTATCTGATTA[C/T]GGTTTCAGTGTCTCCAAAAATGCAGTTTTTACCAG Y 2 1 2 1 101000 r 74 goat snp31745-scaffold354-545755 6 1009718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439327 Affx-122930304 AX-123309664 6 602324 GTCTTTTTTTTTTTTCTGTTAACTTATGACTATGA[G/T]ATGCAGAGTAGATTGAATTGCACAGCTTTGCTATT K 2 1 2 1 101000 r 74 goat snp31746-scaffold354-602324 6 1066471 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800764 Affx-122947451 AX-385287681 6 655359 TAATTAAGGGGCTAGAGCAGCTCTGAAGAGAGAGA[A/G]TAAAAGATTGAATAGTATTACAAGATTATATAAGG R 2 1 2 1 101000 f 74 goat snp31747-scaffold354-655359 6 1118891 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437061 Affx-122933090 AX-123307399 6 688912 AGTAGTGTAACACAGAAGGCATCTACTTGGATGCA[C/T]GGTAGCATGGTGCCTGGCCAAGTTTAATTACCCAG Y 2 1 2 1 102000 f 74 goat snp31748-scaffold354-688912 6 1152513 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384340 Affx-122972253 AX-123254698 6 730671 TGTGTTCTTCATTTATTCATTCAACAAATATGAAG[C/T]ATTTAGGATTGGCCAGACACAGTTCAAGGAGCATG Y 2 1 2 1 101000 r 74 goat snp31749-scaffold354-730671 6 1194797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773168 Affx-122948545 AX-385260311 6 785947 GACAGACAAAAGGCTAGGCTTTAGGATTTATAGGT[A/G]TCTCAAAAGCTCATTATGGTCAGCAAGAAACTCCC R 2 1 2 1 101000 f 74 goat snp31750-scaffold354-785947 6 1250595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429394 Affx-122938536 AX-123299736 6 832609 TTGCTGCTCATGGTTCTGCTAACTCTCATTACTTT[A/C]TGTTAGTGTTACTGAATCTAAGCTGTTCTCCTTGC M 2 1 2 1 101000 r 74 goat snp31751-scaffold354-832609 6 1297065 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387910 Affx-122970454 AX-123258268 6 865635 TACATTTTCTATCCTCTCACTTTCAGTCTATATGT[A/G]TCTTTAGGTCTGAAGTGGCTTCCCTATAGACAGCA R 2 1 2 1 303000 f 74 goat snp31752-scaffold354-865635 6 1328827 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278308 Affx-1111836355 AX-519551794 6 880718 GTGACCCTGGAGGTGGGTGTGATGTCATAGTAAAT[A/G]TCATGTGTTCATACTGACATTACTTTATTTGAATA R 2 1 2 1 101000 f 74 goat Random2.2K-630 6 880718 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320773813 Affx-122926870 AX-385260953 6 885962 AATTTATGGTTTCAAGTGTGCATCACTGTGGTCTT[A/G]TAAAAAAATAATGGTTCAGTAACTCTTTAATTTGG R 2 1 2 1 101000 f 74 goat snp18258-scaffold1850-423514 6 1480210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448561 Affx-122923420 AX-123318897 6 938062 TGCTCTCAGCATGGAAATCTTCAATATTAATACAA[C/T]AGGTTTATTGTACTTTTACTTTTTTAATTACTACA Y 2 1 2 1 101000 f 74 goat snp18257-scaffold1850-371414 6 1532051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785910 Affx-122927549 AX-385272947 6 971396 AATAGCAGTCAATTCAACATGGAACCTCAACATCA[C/T]GATGAACACTCCATCAATAATTAATTCCTAAATGT Y 2 1 2 1 101000 f 74 goat snp18256-scaffold1850-338080 6 1566215 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405965 Affx-122955538 AX-123276317 6 1013672 GAAAGCATTAATAATGTTATACACAATATATCAAC[A/G]TCAGTGTTATAGTCTGTTACATCGGTATCTCACAA R 2 1 2 1 101000 r 74 goat snp18255-scaffold1850-295804 6 1608499 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767817 Affx-122974119 AX-385255041 6 1063089 CATTGGAGGACAACTACATTTTGAAAAGAAATGAA[C/T]TATTATACAAGACAATACCTGTTACTATTTATTTA Y 2 1 2 1 103000 f 74 goat snp18254-scaffold1850-246387 6 1658648 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445982 Affx-122925884 AX-123316319 6 1116256 TTAGAAAAAGCTGGGATCACACAACATTAAAAAGG[C/T]AAAATTTAGTCTTTGTCAGGAAGAGTGGGGCTTTC Y 2 1 2 1 201000 f 74 goat snp18253-scaffold1850-193220 6 1711791 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788319 Affx-122950309 AX-385275337 6 1160929 TTTGTGCAAAGAGTTGTACTCAATATGTGGAGTAT[A/G]TGGAAAGGTTTTGACAACACCTCCACAGACTATCA R 2 1 2 1 101000 r 74 goat snp18252-scaffold1850-148547 6 1756523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406931 Affx-122955081 AX-123277282 6 1201806 AGCTAGGTGTGAGAAGAAACGTGGCTTCCAGGCTG[A/G]ATTGGCTTGGCAGTTTTCCTCTATTTTATTAAAGC R 2 1 2 1 101000 r 74 goat snp18251-scaffold1850-107670 6 1797675 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395262 Affx-122964092 AX-123265617 6 1257189 CCCAGCAGAAAGAGAGCCATGCCGATTTCTCTAGG[C/T]GATACGTATTACATGTATCTTAAAATGCCCTACGT Y 2 1 2 1 101000 f 74 goat snp18250-scaffold1850-52287 6 1854104 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442146 Affx-122928323 AX-123312483 6 1345539 TTTCCATAATTGTGTTATTTATCTCTGTTTGCTTA[G/T]ACTTTATTTTTTCCATGTCTTTGGTGATTGCATTA K 2 1 2 1 101000 r 74 goat snp59983-scaffold999-35964 6 1951800 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780033 Affx-122953336 AX-385267132 6 1395105 GATTTTATGGGGGTTAATGAGATGATATGTAAAAA[C/T]GTACAAAATTTGAAAATCCCATACTGATAGAAATA Y 2 1 2 1 101000 r 74 goat snp59984-scaffold999-85530 6 2003532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795151 Affx-122923512 AX-385282109 6 1438392 TACAGTGTTAAGAAACATTCCAAAGTCTGTTTCTG[A/G]TGTCGCTTCCTTCCAGACTCAAGGCTGCCCTCCAT R 2 1 2 1 202000 r 74 goat snp59985-scaffold999-128817 6 2047262 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433538 Affx-122934999 AX-123303879 6 1484900 GCAGTATTTCCATTAGGAGAGACTAAACTGTTATA[C/T]AAAGAAACCCAAAAATGTGGTGACCCCAAAGAAAT Y 2 1 2 1 101000 f 74 goat snp59986-scaffold999-175325 6 2094606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768502 Affx-122933916 AX-385255682 6 1518467 TCACCCATTTGGTAATGCAAGGAATGATAATATTG[C/T]AAAATAGAATATGAGTAATGGAAAGCACAAGTAAT Y 2 1 2 1 101000 f 74 goat snp59987-scaffold999-208892 6 2128119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412486 Affx-122951381 AX-123282835 6 1552910 CAAAGATAGAAATAAGATAGAGACTAGCAGTGCTG[A/C]AGACAGGATGATCTGAGATTATTCCTAATATTAAA M 2 1 2 1 101000 f 74 goat snp59988-scaffold999-243335 6 2162545 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778721 Affx-122952333 AX-385265832 6 1584320 CTGGCCTTGCCTCTGTGTAAACATTTGCCTGATTT[A/G]CTAGCAATTGTTTGCCACCTTTTTATTCAGATACA R 2 1 2 1 101000 f 74 goat snp59989-scaffold999-274745 6 2194700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433060 Affx-122935749 AX-123303401 6 1621541 CTCATGCTGGCCTGTCTTCAGGTCTCTGAAAGAGC[C/T]ATACTCTCACCTTTCAGGAATGCCTTCATATTATC Y 2 1 2 1 201000 r 74 goat snp59990-scaffold999-311966 6 2231932 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778381 Affx-122944180 AX-385265496 6 1657055 ACCAAAATTATAAGGTAGGATCTGCAAAGGTAAAC[A/G]CATTGGGAAAAATCCATTCCTTTACTGAGAAATGG R 2 1 2 1 101000 r 74 goat snp59991-scaffold999-347480 6 2267878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379078 Affx-122976323 AX-123249437 6 1694216 TGTTTAAAGCTGTAGAACTACCCTCTTTTTTAATG[C/T]AATTCTATTCATAATTCAATGGAGAAGGAAATGGC Y 2 1 2 1 101000 f 74 goat snp59992-scaffold999-384641 6 2305576 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38411250 Affx-122952331 AX-123281600 6 1736025 TGTATGACTGCTTATAACCTAGGGCCACAGAGAAG[C/T]AATATGTAGGAACCTGAACCGAAATGTTTTTGAAA Y 2 1 2 1 201000 r 74 goat snp59993-scaffold999-426450 6 2347436 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422720 Affx-122943262 AX-123293066 6 1741481 TATTCACGATAACTAGTGCCTGACCAAGCCACAAC[G/T]AGACTGTGGGGGGCCTTCCAATCATTAGCCAAAGT K 2 1 2 1 101000 f 74 goat snp4846-scaffold1161-283736 6 2352757 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388620 Affx-122969135 AX-123258978 6 1807664 AAAATTGTTTAAGTCTGTGAAGACAGGTATAAAGT[A/G]TGCTTCACTCTGTTATTACTGCAAAAGCATATTTT R 2 1 2 1 101000 f 74 goat snp4845-scaffold1161-217553 6 2418255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443584 Affx-122927328 AX-123313921 6 1851675 GAGTGTAGGTGTTCACCAGACAAAAACCAAAGAAA[G/T]AGCAGAATCAGATTTTGGCTTACCTGTTGCAAGGG K 2 1 2 1 101000 r 74 goat snp4844-scaffold1161-173542 NW_017202586.1 12842 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431134 Affx-122936583 AX-123301475 6 1894738 AATTTTCTCATAAAATGGATTTATCTGTTCTTTTC[A/G]CTTGTTTGCTTTTATTGAGACATAACTGAGGAATT R 2 1 2 1 201000 r 74 goat snp4843-scaffold1161-130479 6 2506358 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445349 Affx-122926385 AX-123315686 6 1974800 ACTTGTTGAACATTTGGGAAAGACTCTGGATGTTG[C/T]AAGGGAGCAAGAGTGAAAGTGAAGCAAAGCTATTA Y 2 1 2 1 101000 f 74 goat snp4842-scaffold1161-50417 6 2586355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384635 Affx-122972159 AX-123254993 6 2013767 ATACCAGACCACCTGACCTGCCTCCTGAGAAATCC[A/G]TATGCAGGTTGAGAAGCATCAGTCAGGACTAGACT R 2 1 2 1 103000 r 74 goat snp4841-scaffold1161-11450 6 2626228 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395720 Affx-122963712 AX-123266075 6 2060276 TATGTTTCTGTTTAAATGGTAGAACAAGACTGTTG[A/C]GTGAGAGAACATGAGAATAAATCACTAATTTAATT M 2 1 2 1 101000 f 74 goat snp37610-scaffold461-34960 6 2685229 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441133 Affx-122929583 AX-123311470 6 2100509 ATGGGTTGTGGTCCTAACAAACTAAACAGAAAATG[A/G]TCACTTTTCTGAAATGAGAGTAGTTTTTAGCTCTT R 2 1 2 1 201000 r 74 goat snp37611-scaffold461-75193 6 2725719 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464409166 Affx-1110471556 AX-515882151 6 2121068 GAAAATCTGAACCCAGAGTTCTTGCACAGTGAGTG[A/G]CAGCTCTTTAATGCCAGGAGCAGTGTGGGCATGGA R 2 1 2 1 202000 f 74 goat GoatD01.006192 6 2121068 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770680 Affx-122952773 AX-385257844 6 2135328 CTAGATTACAACAACTTGGAAGTAAAAATAGAATC[A/G]CAGTTATTATAAACCCATTTTCCTCTTTTCTCTAA R 2 1 2 1 101000 r 74 goat snp37612-scaffold461-110012 6 2760631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393154 Affx-122965541 AX-123263511 6 2180449 TGCCAATGTTCCTTTGGTATTCTCTTAATGCCAAA[C/T]AGATATTGTTTTGAATTTCTGTCAGTCTTCTCCCT Y 2 1 2 1 101000 f 74 goat snp37613-scaffold461-155133 6 2805884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278310 Affx-1111836356 AX-519551796 6 2208063 AAAGCTGTCCAAAAGACTTCTTTTGGTGGTGAAAT[A/G]ATACTTAAAGGTTAAACATAAATTTAGAGAATTGT R 2 1 2 1 101000 f 74 goat Random2.2K-631 6 2208063 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384242 Affx-122972363 AX-123254600 6 2215019 TTTACCGGGAAGGAACGGAGACAAAACTGTGGACA[C/T]GGCAGGGGAAGGATAGGGTAGGACAATTGAGAAGG Y 2 1 2 1 101000 f 74 goat snp37614-scaffold461-189703 6 2840854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776433 Affx-122955862 AX-385263560 6 2245869 TTAAGGAGAAACTAAAGTACTTTAAACTTGTAAAT[A/G]CAATTTGAAATGTTGAAGACAGTTAACTGCCTAAG R 2 1 2 1 101000 r 74 goat snp37615-scaffold461-220553 6 2873688 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791979 Affx-122925851 AX-385278967 6 2304485 ACTAATAAGACAGGTTCCTGGCCCAGAATTCTCTT[C/T]GGTCAGTGACTTGTCACATGCTTCAGACTGGTGTA Y 2 1 2 1 201000 r 74 goat snp37616-scaffold461-279169 6 2926846 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450328 Affx-122922128 AX-123320663 6 2364398 CATTACTTTGCCATGCACCGCTGCTATCTGGGGTC[C/T]GAGTCCTGTGCTTTCTCATCTTGAGTGTGCACAGG Y 2 1 2 1 202000 f 74 goat snp37618-scaffold461-339082 6 2986906 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795415 Affx-122944879 AX-385282371 6 2425075 AACTCAGGAAGATGGGATTTATTATGGTGTGTTCC[C/T]ACCAGAAACACGGTGGAGCAGATCTTGTGGGAAGA Y 2 1 2 1 101000 f 74 goat snp37619-scaffold461-399759 6 3047826 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801557 Affx-122924695 AX-385288466 6 2454886 TATTAACCCATCTGCCTTGTTATATTCTATGTTAT[A/C]TTCATAACAAGTGCCTTGAAAATCTCATTGAGAAA M 2 1 2 1 201000 r 74 goat snp37620-scaffold461-429570 6 3077912 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388397 Affx-122969298 AX-123258755 6 2506796 AGTAATAGGCTCAACTTCTCTTTGTCATCTGCCAG[A/G]TGTACAGAGCAACATCCTAGAACTTAAGAATACCT R 2 1 2 1 201000 r 74 goat snp20348-scaffold2016-29488 6 3294463 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802514 Affx-122946038 AX-385289418 6 2536003 AACTGTGGCAACAGATTCATGGGGTGGCTTACTGA[C/T]GGTGGAAGTTCTTTCTGGAGACTCATTCTAAAGGT Y 2 1 2 1 101000 r 74 goat snp20349-scaffold2016-58695 6 3321029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803400 Affx-122962221 AX-385290231 6 2571274 CATGCTATTAATTTCAGTTGCTAGCAGGATGACAT[A/G]CAATGAAAGATGAAGAAAGGCACTGTGGAAGAGAG R 2 1 2 1 101000 r 74 goat snp20350-scaffold2016-93966 6 3359749 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376723 Affx-122978963 AX-123247082 6 2684490 CAGTCTTCCACTGCAAGGGGCCTGGCTTCCATCCA[C/T]GGTGGAGGAATAATCCTACATACCTTACAGATTGC Y 2 1 2 1 103000 r 74 goat snp4245-scaffold1131-661201 6 3578055 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272528 Affx-1111833501 AX-519546246 6 2697706 TCACACAACCGCACACGTACTTAAGTACTTGATAT[A/G]CTACTTGATTAGGCTAAGTGCTTGAAACCCTCACT R 2 1 2 1 101000 f 74 goat 6_2697706_AF-PAKI 6 2697706 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38434279 Affx-122934776 AX-123304620 6 2722066 ATGAGTTTAAGTATCTGATAGCATGGAATGACAGA[G/T]AATCTGAAAATTAGGTTTTAAGAACAGAAGAAGCA K 2 1 2 1 101000 f 74 goat snp4244-scaffold1131-623625 6 3615807 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407688 Affx-122954583 AX-123278039 6 2759590 TTACATGTACAACAGTTATTGAATTGTTAACCTGT[A/G]CTACCACGAGAAGCAAATTTCTCAGTTTGAGTACA R 2 1 2 1 101000 r 74 goat snp4243-scaffold1131-586101 6 3654783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441182 Affx-122929545 AX-123311519 6 2799996 TTCCCACAGCCCTTCTGTAAGCTCTTCTGATTTAC[A/G]CGCCAGGTAATGGAGTCACCTTCCTGGTGCCAGAC R 2 1 2 1 101000 f 74 goat snp4242-scaffold1131-545695 6 3701959 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767164 Affx-122971163 AX-385254449 6 2828708 ACATCTCAGACCTATCACTTTTAAATTACAGTCTG[C/T]GAATATGATAATGTAATAATCACTTCCTTGACTAG Y 2 1 2 1 101000 f 74 goat snp4241-scaffold1131-516983 6 3728885 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444950 Affx-122926685 AX-123315287 6 2901557 AAAGGAATGGCCAAACAGGTGAATCAGATGAATTA[G/T]AAATCACTATGGTTGTGATAGCTGGACTGTAAAGA K 2 1 2 1 101000 f 74 goat snp4239-scaffold1131-444134 6 3801285 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411327 Affx-122952273 AX-123281677 6 2939447 AACATTGTGGTGAATACCAAGACTTGGGGTGAAAA[C/T]GCAGTAAGGAAGACAGTGGGGCAGTCGTTTAGGAT Y 2 1 2 1 101000 f 74 goat snp4238-scaffold1131-406244 6 3839505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408734 Affx-122953409 AX-123279085 6 2972121 ACAGATAGATAGCAGTGGTCTCCGTGTGAACCAGC[A/G]TAACCTGAGGGGTGGGAGCATCGGCCACAGACACC R 2 1 2 1 101000 f 74 goat snp4237-scaffold1131-373570 6 3872769 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772809 Affx-122924269 AX-385259954 6 3054604 GCAATGAATAATTTTTGTGAAGCTGTCATTTGTTA[C/T]CTTAATTTCTTCTTTAGAGAACTGCATATGTTAAT Y 2 1 2 1 201000 r 74 goat snp4235-scaffold1131-291087 6 3961495 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770476 Affx-122940283 AX-385257642 6 3083435 AGTAAAAATTAAGAATAAAGAGAGACTACTAAAGG[C/T]AACAACACAAAAGCAACTAGTTAGTACCAGAGAAT Y 2 1 2 1 101000 r 74 goat snp4234-scaffold1131-262256 6 3990308 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768965 Affx-122973757 AX-385256140 6 3116474 CCAAGTAATATTGTCCTATTTCATGAATAATACAC[A/G]TCTATTTCTCTCTTCCTAGGTTTTTGCTTTGTTGC R 2 1 2 1 101000 r 74 goat snp4233-scaffold1131-229217 6 4023430 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427605 Affx-122939364 AX-123297948 6 3163924 GCCATCTCCCCATATCATCCACCATCTCCCTGGGA[C/T]AACTGCTTTCCATCACTCCCAGAGAGTTTCCATAT Y 2 1 2 1 101000 r 74 goat snp4232-scaffold1131-181767 6 4079987 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445170 Affx-122925544 AX-123315507 6 3197710 GAGGTGTCAAGAGAGCACCAGGATGGAAGGAGCCT[A/G]TGTCCCAAATGACAGTGTGGAATGAAGTCAGGGCT R 2 1 2 1 101000 r 74 goat snp4231-scaffold1131-147981 6 4114292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767680 Affx-122949406 AX-385254920 6 3261961 GTAGGGGTGTACACAATGCTATACAGCAGATCTTT[A/C]GAGCTTATTCATCTTGATTAACTAGAATTTCATGC M 2 1 2 1 103000 f 74 goat snp4230-scaffold1131-83730 6 4194777 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433439 Affx-122935072 AX-123303780 6 3298931 ATACTCTACATGGCAAAAGAGATTTTGTAGACACC[A/G]TTAAGTTAAGGACATTTAGATGAGAGATGATCCTG R 2 1 2 1 201000 r 74 goat snp4229-scaffold1131-46760 6 4231437 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385581 Affx-122971836 AX-123255939 6 3336946 ATCTCCAGTATTTTCTGACTTAAAGTGGATAATCT[A/G]CTTCTGGAGGTGAGCCCTAACTGACACTTTGAGTT R 2 1 2 1 101000 f 74 goat snp4228-scaffold1131-8745 6 4267111 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408602 Affx-122953645 AX-123278953 6 3366130 AAAATGGTTGAAGAACTCAAACAGGCTTGTGCATC[A/G]TATGGGCCTAAAGCCCAGTACACTAGGCAATTGGT R 2 1 2 1 303000 r 74 goat snp27465-scaffold2927-304597 6 4310648 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431697 Affx-122936775 AX-123302038 6 3420556 AAATAAGAATCTCTAGGGGAAAAGCATCAGGCATC[A/G]TTTTCAAAACTTCCCAGGTGATTCATGTGTTTTTC R 2 1 2 1 103000 f 74 goat snp27464-scaffold2927-250171 6 4365278 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436163 Affx-122932621 AX-123306502 6 3452025 CACCTGGGAGAACCTTCCCCACCTGTACTAGGATG[C/T]AAACACTCTGAGAGTAAGGGTTTTTGTCTCTTTTT Y 2 1 2 1 101000 r 74 goat snp27463-scaffold2927-218702 6 4396329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449686 Affx-122922553 AX-123320021 6 3482450 GTATCTCACAAAGATACCTTTCTATGGGATTTTGT[A/G]GGGGATATGATCCAGGTGACCACATTTCTCATACT R 2 1 2 1 201000 f 74 goat snp27462-scaffold2927-188277 6 4428208 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390082 Affx-122968032 AX-123260439 6 3523198 TAATTTTCCCCCTAAGCACTCCTCCCTTAGCCTCC[A/G]TCCACTGCCTTGAATAGGGAGTCAGGCGAACAAAG R 2 1 2 1 201000 r 74 goat snp27461-scaffold2927-147529 6 4468954 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426914 Affx-122940446 AX-123297259 6 3558936 ATGTTGGTATTTTCCTCTTAGTTTGAATTTTGTAC[G/T]AATTTTCTTTTTAAAATAACCTTTCTATTTTGTGG K 2 1 2 1 101000 f 74 goat snp27460-scaffold2927-111791 6 4504717 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399037 Affx-122960921 AX-123269392 6 3592526 TTGGCAAATTAAACTCTCTGAGCCCCAGTATCCTC[A/G]TCTGTGAAGTGACAGTAATACTTCCTATCTTCAAA R 2 1 2 1 201000 r 74 goat snp27459-scaffold2927-78201 6 4538212 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408200 Affx-122954187 AX-123278551 6 3624918 GACCCGTCCTCCTCTTGCCAAGCTGGGCACCCCTG[C/T]GTGGGGCTGCACACATCCAGAAGAACGAGCCCCTG Y 2 1 2 1 101000 r 74 goat snp27458-scaffold2927-45809 6 4570669 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762396 Affx-986696927 AX-385250549 6 3644698 GGATAGAATAACTAGGTGATATGTTCTTAATTTTT[G/T]GAACAATCTCCATACTGTTTTCCATAGTGACATCA K 2 1 2 1 600010 f 74 goat 6_3644698 6 3644698 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 320764618 Affx-986696930 AX-385252260 6 3644719 TGTTCTTAATTTTTGGAACAATCTCCATACTGTTT[C/T]CCATAGTGACATCATCAGCTTTTAGTAGCAACTGG Y 2 1 2 1 600010 r 74 goat 6_3644719 6 3644719 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 320762403 Affx-986696934 AX-385250555 6 3646718 CTTCTCATATTCTGTAAAATACCTTTTGTTTTGAG[A/G]TGTTTTCCTTCACTATTCAGAATTTTTTACCTTGA R 2 1 2 1 600010 f 74 goat 6_3646718 6 3646718 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 38414852 Affx-122949156 AX-123285201 6 3667906 ATTTGCGCAAGCATTGAGAGACTGAGTGAGAGATG[C/T]GTAGGTGAGTAAGAAAGAAGCATTTGCTCTCAGTA Y 2 1 2 1 101000 f 74 goat snp27457-scaffold2927-2821 6 4613501 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476209 Affx-1251763714 AX-586011633 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 4 1 4 1 20000 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 539476463 Affx-1251763714 AX-586011863 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 4 1 4 1 20000 r 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165150 Affx-1251763714 AX-606940562 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165185 Affx-1251763714 AX-606940597 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165210 Affx-1251763714 AX-606940622 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165357 Affx-1251763714 AX-606940768 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165576 Affx-1251763714 AX-606940987 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 f 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 562165713 Affx-1251763714 AX-606941122 6 3689923 TTGCCTCTTGTGTTTTTTGGTTTCCTCTTATGCAT[-/ATGTTAACTTTTATTTTTTTTTTTTTTAATTTTTTTATTTCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCCGCCATAT]GTTAACTTTTAAAAAATAAATGTTATTTTTAAATC - 8 1 4 1 20100 r 74 goat SV_131 6 3689923 - deletion junction SV-TF-chip 320769025 Affx-122973521 AX-385256200 6 3705960 AGGCAGCTCAACATATCTCACGCTTCTTTCTCTCC[A/G]CACTAATTTTGATTGAGTCCACATCTGAGGGGAGG R 2 1 2 1 101000 f 74 goat snp27337-scaffold2900-35134 6 4651684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802736 Affx-122932361 AX-385289635 6 3758186 CTATTTATTAATATTATCATAGCCCTTGACTGTTT[A/G]TAAGATATTTCCACATCTATCATTTTCCTTAATCT R 2 1 2 1 201000 f 74 goat snp27338-scaffold2900-87360 6 4703353 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384192 Affx-122972404 AX-123254550 6 3788964 AGTATCAATTGCATGAAACATGTAGAAGAAAACCT[A/G]CTAGAAATCAAACTATTAATACACAACTGTCTCTG R 2 1 2 1 101000 f 74 goat snp27339-scaffold2900-118138 6 4734499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401137 Affx-122959383 AX-123271490 6 3825336 AATACATACATAGAATCCTTCCACACCCATTTTTT[A/G]TTAGTAACTATTTCTACTTCCTTTATGAGGAGTAA R 2 1 2 1 202000 r 74 goat snp27340-scaffold2900-154510 6 4770790 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433080 Affx-122935734 AX-123303421 6 3858412 GACTCTAGGCTGCCTTTACGCAAACATTTGCCGCT[A/G]TCCTCAAGCTGTACCCTTGGTTCTATTCTGCCTAC R 2 1 2 1 101000 f 74 goat snp27341-scaffold2900-187586 6 4803684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378255 Affx-122976892 AX-123248614 6 3909488 CAGGCAGGCTTTAGCCTGCTAATGAAGAAGGAATT[A/G]GAAAGGAGAAAAAAATTTAAAGTCTACATTAGAAC R 2 1 2 1 101000 f 74 goat snp18704-scaffold189-977811 6 4854791 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798522 Affx-122926988 AX-385285455 6 3967403 CTCAATTTGGTATAATCCATCAAATCCATCATATA[C/T]GATTCACAAAACTTTAAATGTAGTTAACATTTTAT Y 2 1 2 1 201000 r 74 goat snp18703-scaffold189-919896 6 4912682 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779230 Affx-122950546 AX-385266334 6 4000730 AAAACTTTGCTTTAAAAGACATACCTTCTCTGTAT[A/G]TACAAATGTATTTTCATGTGGTTTCACTCAGGTGC R 2 1 2 1 101000 r 74 goat snp18702-scaffold189-886569 6 4945869 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415902 Affx-122948467 AX-123286251 6 4043062 CTAGAAGAAAACAGTGAATATTTAAATAATTTTTG[C/T]GTAAGGAAAGACTTTCTAAGGATGGCAGAAATCCA Y 2 1 2 1 101000 r 74 goat snp18701-scaffold189-844237 6 4986566 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476210 Affx-1251763715 AX-586011634 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 4 1 4 1 20000 f 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 539476464 Affx-1251763715 AX-586011864 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20000 r 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 562165173 Affx-1251763715 AX-606940585 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20100 r 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 562165214 Affx-1251763715 AX-606940626 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20100 r 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 562165694 Affx-1251763715 AX-606941103 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20100 f 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 562165744 Affx-1251763715 AX-606941153 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20100 r 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 562166062 Affx-1251763715 AX-606941471 6 4070440 ATATAAAGCATGTTATGGGATTATTAGTTATTCTT[-/TTTTTAATTTATTTTTTTTAAAATTTAAAATCTTTAATTCTCCGCCATCTTTCCCTCTCTCCTATTAGTTATTCTTTACA]TGGGAATTTTTTCTGTAGGTATAATACTTATATAT - 8 1 4 1 20100 r 74 goat SV_132 6 4070440 - deletion junction SV-TF-chip 38451296 Affx-122921295 AX-123321629 6 4073579 TGTGGTACTTTGTTACAGCAGTACCAGCAAACTCA[C/T]AGAATCGCCTTGTTCATAATGGAGGGAATTATTAT Y 2 1 2 1 201000 r 74 goat snp18700-scaffold189-813720 6 5018034 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379236 Affx-122976269 AX-123249595 6 4122008 ATTTCTGAGCGTGCACAGCCAGCTGCACACGATCA[A/G]CACGGTCCCAGGTTCCCACTAACGAGCAGCCTTGC R 2 1 2 1 101000 r 74 goat snp18699-scaffold189-765291 6 5065967 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476211 Affx-1251763716 AX-586011635 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 4 1 4 1 20000 f 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 539476465 Affx-1251763716 AX-586011865 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 4 1 4 1 20000 r 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562165877 Affx-1251763716 AX-606941286 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 f 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562165966 Affx-1251763716 AX-606941375 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 f 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562165996 Affx-1251763716 AX-606941405 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 r 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562166291 Affx-1251763716 AX-606941699 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 r 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562166392 Affx-1251763716 AX-606941800 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 r 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 562166562 Affx-1251763716 AX-606941970 6 4142657 TTGTACCCATGTTTGCATGAAGTGTTCCCATAGAA[-/TCACTAATTTTCTTTCTTTTTTTTTTTTTTTTAATTTTAATCTTGCCGTCCTATTCCTCCGCCATCTTTTCCCGTTATCC]CACTAATTTTCTTGAAGTGATCTCTAGTCTTTCCC - 8 1 4 1 20100 f 74 goat SV_133 6 4142657 - deletion junction SV-TF-chip 38396401 Affx-122963014 AX-123266756 6 4157344 CTATGGGTTGAATGCTTGTGTCCCCTCAAAATTCC[C/T]AAGTTAAAGCCCTAATCCTCAAGGTGATGATTACA Y 2 1 2 1 201000 r 74 goat snp18698-scaffold189-729955 6 5101236 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799258 Affx-122949001 AX-385286188 6 4204662 AAAGGTGATGTCTTCCTCTTACCTGAGGCAAACAC[A/G]ATTGGGAGTTGTGAAATTTATACTGATAACTAGAG R 2 1 2 1 101000 f 74 goat snp18697-scaffold189-682637 6 5147912 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387095 Affx-122970679 AX-123257453 6 4270215 AAAATGAGACTGAGAGAGGCTCATTCTTGCCAGCC[A/G]CCTGATTCAACTGAGGTTGTAGAATAGCTTTCACT R 2 1 2 1 201000 r 74 goat snp18695-scaffold189-617084 6 5213448 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446525 Affx-122925023 AX-123316861 6 4352051 ATAAGATCCAAGGCTGGAGACTTCCCCTTAGATGA[C/T]GGCGTTTTTCCAGTACTCTAAACCAGCGATTCTCA Y 2 1 2 1 201000 r 74 goat snp18693-scaffold189-535248 6 5295397 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444853 Affx-122926295 AX-123315190 6 4440548 GTACATTGCATTAATATACATACATTTCTTTACCT[A/G]TCTTGTTTCTGAGCGAGTGAATTGTTTCTAGCTTT R 2 1 2 1 101000 r 74 goat snp18691-scaffold189-446751 6 5383860 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396869 Affx-122963243 AX-123267224 6 4482379 AAGCATGGATCTCATCTTAAAAAGAAAAATCTGTA[C/T]GCCTTGGATCATAGAAACCTTGTTATCTGTTACAC Y 2 1 2 1 101000 r 74 goat snp18690-scaffold189-404920 6 5426581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789039 Affx-122979160 AX-385276052 6 4512913 AGTTTCTCTTAAATGTGTTTCCAAGGTTTTAGAAA[C/T]GGTAGAATCCAACCTATGGAGTACTAAATGCTCTA Y 2 1 2 1 201000 f 74 goat snp18689-scaffold189-374386 6 5456804 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446693 Affx-122924743 AX-123317029 6 4553960 GGAGGGAGAGAAGCACAAGGTTAATAAGCAACTCA[A/G]CCTCTTTTCCTTCTTTCTCTTCTGCTCAGCATCCT R 2 1 2 1 201000 f 74 goat snp18688-scaffold189-333339 6 5498985 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437917 Affx-122931647 AX-123308255 6 4600563 CAGCTGCGTGAGGCGTGGACACTCTGGTGACCTGT[A/G]CTCCCTGAGAACATGGTCACTGACCGTTAGGTAGA R 2 1 2 1 101000 r 74 goat snp18687-scaffold189-286736 6 5545798 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410554 Affx-122952147 AX-123280904 6 4632624 TTAGTATTTTATTTAGAAAAAATCGAGGAACAGCT[A/G]TAGCATTTTGAATGGGAAAGAGACAGGGTGAAAGT R 2 1 2 1 101000 r 74 goat snp18686-scaffold189-254675 6 5579277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403332 Affx-122957818 AX-123273685 6 4665216 CATATTCATGAAGAAGAGGTAAGACTGTTTTGCTC[A/G]TAGACCAATGAGAATGTTGCCCCACCCCCCTCAAC R 2 1 2 1 201000 f 74 goat snp18685-scaffold189-222083 6 5612072 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453149 Affx-122919993 AX-123323482 6 4710077 TTGGCAAAGATAGGCACAGCCAGGCCTAGTGTGTG[C/T]AGCCGTTGACAGATAAACAAGGCCCGATGCTGCAG Y 2 1 2 1 101000 r 74 goat snp18684-scaffold189-177222 6 5657270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795444 Affx-122955881 AX-385282400 6 4753317 GCAAAGTAGTTGGTTGTTAGTAAATCATTCTCGAA[C/T]GACTTAAGCTTATATGCCTTTGTGAACTAGCTCTG Y 2 1 2 1 101000 r 74 goat snp18683-scaffold189-133982 6 5701045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438919 Affx-122930427 AX-123309256 6 4799509 GGTCTAAAAACACCTAATCCCTACCTCCCACACCT[A/G]CAGGGTTAGCCAAAGCTGTCAGGAGTCCTACGTTA R 2 1 2 1 101000 f 74 goat snp18682-scaffold189-87790 6 5747165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464411168 Affx-1110472562 AX-515884134 6 4876249 CTTGCTAGCTTTAGTTCTGTCCTTATTGTGTTAAT[A/G]GAGAGAGTGGCTTCCTATCCTTGAGATGCATTCTT R 2 1 2 1 201000 f 74 goat GoatD01.015342 6 4876249 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38409757 Affx-122953004 AX-123280108 6 4909464 GTGAAGCCCTGCTCTGGTCACTCCTATAACTTCAA[C/T]AAGCAGCTCAACTTATTCTCTTTTTTAAATATAAT Y 2 1 2 1 101000 f 74 goat snp5510-scaffold1193-22066 6 5905384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779044 Affx-122973435 AX-385266150 6 5065035 ACAGTATGGAATTCGTGTCCTCAAAATGCACTTTT[C/T]GTACATTTTTCTAACATACTCAGGCTTCCCAGGTA Y 2 1 2 1 201000 r 74 goat snp5513-scaffold1193-177637 6 6065820 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393089 Affx-122965595 AX-123263446 6 5128896 CCCTACGCCTAAAATACTAATTTACACAGAAATAA[C/T]GGTATTTAGTTCAGTTCAGTTCAGTTACTCAATTG Y 2 1 2 1 303000 f 74 goat snp5514-scaffold1193-241498 6 6131533 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395415 Affx-122963948 AX-123265770 6 5181687 CTGGGAAGCACATCTTTTAATTCTAATTGCTAAAA[C/T]GATAGCCATGTCTATTCTTCCTTTTCATATATTTG Y 2 1 2 1 101000 f 74 goat snp5515-scaffold1193-294289 6 6184536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765969 Affx-122956576 AX-385253393 6 5230594 AGGGTAAAATACCTTTGTGGAATTTGCATCCATTT[C/T]GTTCTTTTTGCTCAGACAGCCAGGGTGTAATTTAT Y 2 1 2 1 101000 f 74 goat snp5516-scaffold1193-343196 6 6233883 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798592 Affx-122960460 AX-385285525 6 5266300 TGGCAAATGATTGAGGTATTAAAAGTCTTAAAACA[G/T]TATGTCACCAATGCGAGTCTCCGTGAGATCACTGT K 2 1 2 1 101000 r 74 goat snp5517-scaffold1193-378902 6 6268947 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273208 Affx-1111833508 AX-519546867 6 5343525 GAAGAACTTTTCTGTGACAAAATGCTGCCCAAGAT[A/C]TCTAAGGCTCCCTTCTCTTTAGACACAGAAGGTAG M 2 1 2 1 101000 f 74 goat 6_5343525_AF-PAKI 6 5343525 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38416164 Affx-122948271 AX-123286513 6 5408209 CCTCTTTCCCCATTCACTGCTAGGAACTGGACAGG[C/T]GCTTTAAGACTTTTCTGCTGCTCCTTACATCTGTC Y 2 1 2 1 101000 r 74 goat snp17774-scaffold1844-6278 6 6415772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421412 Affx-122943971 AX-123291759 6 5474004 ATGTAGTTCATATATAAAAGATAGATTCAGAAACT[A/G]TTTCTGTTGACCCACAAGTAAAAACTATCAGAGGC R 2 1 2 1 101000 r 74 goat snp17776-scaffold1844-72073 6 6482275 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787206 Affx-122933019 AX-385274232 6 5505913 GGTGAATGTTGGATCCTTGACATTCAGTTCCAGCC[A/G]TAGCCCACATTAACCCCTAGTGGTAGCATTAAAAT R 2 1 2 1 101000 f 74 goat snp17777-scaffold1844-103982 6 6514342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787611 Affx-122936299 AX-385274634 6 5571293 CATCTCAAATAAAACATGCATCTCAAGTAAACAAT[A/G]CATCAGCGTTACCTTTTTCTCTTGAAAAGTTTTGT R 2 1 2 1 101000 r 74 goat snp16164-scaffold170-20288 6 6578637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799486 Affx-122979041 AX-385286416 6 5614926 TTACCTTACCATGCTCACAGTTTCTATTGCCATCA[A/G]TGGAGGCAATAAAAGGCAATAGAAGCAAGCGCAGA R 2 1 2 1 101000 f 74 goat snp16165-scaffold170-63921 6 6622409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793490 Affx-122943896 AX-385280467 6 5662317 ATTTGAAGATCCCTATCACTGGGAACATCTTGTCT[A/G]TAGTCCTCGATTAATGTCAGTTCATCTCAATTCTA R 2 1 2 1 101000 f 74 goat snp16166-scaffold170-111312 6 6670641 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278312 Affx-1111836357 AX-519551798 6 5668668 TGACACAGGACAGAGGTTTCCTTAAGATCTGGCAC[A/G]GCTGAAGGTGGGGCTTTCGGCACAGGACAGACATT R 2 1 2 1 201000 f 74 goat Random2.2K-634 6 5668668 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273612 Affx-1111833725 AX-519547225 6 5744939 CATGTATGTACTGATCAGGACTCCACCTAGTACAC[A/G]ACAAAGACTTCTGCAGAGCTCGGTCTGCACACCTC R 2 1 2 1 201000 f 74 goat GoatD01.002544 6 5744939 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38404013 Affx-122957188 AX-123274365 6 5753451 TGGTGGAAGCAAAGAAATCTAGGAAGGGGAATCAA[C/T]AGAGTGGGGAGAGAACCCTAAAATCCCAGTTCTCT Y 2 1 2 1 101000 f 74 goat snp16168-scaffold170-202446 6 6762314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443876 Affx-122927504 AX-123314213 6 5795798 CCAAAAAGGAATGACAGCATTGCTTTGATCAATGG[C/T]AGTATGTTAAGCTGAAGAAGACAACTCCAATTTTA Y 2 1 2 1 201000 r 74 goat snp16169-scaffold170-244793 6 6804847 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802030 Affx-122950926 AX-385288934 6 5842149 AATGATTGAAAGAGTCAGAGTTGACTTACTCTAAA[C/T]GGAGCTAAACAGCACTATAAGTGACAATTCTTCAT Y 2 1 2 1 101000 f 74 goat snp16170-scaffold170-291144 6 6851981 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450439 Affx-122922965 AX-123320773 6 5876124 TTCATAGAATATATTATCTCCCATTCTTTTCTAAA[C/T]GTTGAAGGAACAAAACACAGACAATCATTTCTTCT Y 2 1 2 1 201000 f 74 goat snp16171-scaffold170-325119 6 6884527 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381756 Affx-122974315 AX-123252114 6 5932510 AATCAAGCTGAAACCCTTTAAGAACTGAGGCACAC[G/T]CAAAACCTCTATTGAGATTTCTCTGTGGTGTTTTA K 2 1 2 1 101000 f 74 goat snp16172-scaffold170-381505 6 6940901 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405046 Affx-122956353 AX-123275398 6 5988222 TGGTTAGGACGGTAGATTGTTTTCTGTGTTTTACC[A/G]CTATTGAAAATCATTTTAAAAGGAAAGAAAATGAG R 2 1 2 1 101000 f 74 goat snp16173-scaffold170-437217 6 6995308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398499 Affx-122961562 AX-123268854 6 6018234 GGTCTAAACATGTTCTTATGGTTGGGAGTAAGCAG[C/T]CCACCAGAACTGATTCAAGGAATCTTTAACGTGCC Y 2 1 2 1 101000 f 74 goat snp16174-scaffold170-467229 6 7025074 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782039 Affx-122939979 AX-385269117 6 6054516 TTAGCTGCTTGGCTATTTGTCCTCGTCAGCTTCTT[A/C]GGAAGCATGAGTAACAGTCATCGGTAGCTGCACAA M 2 1 2 1 102000 f 74 goat snp16175-scaffold170-503511 6 7061825 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278314 Affx-1111836358 AX-519551800 6 6073225 TTCACTCTTGATTATGGAAGCAAAGAAGGAACCAC[A/G]AATGAAGAATTGAGGTCAAAGCCCCAGCAGCATCC R 2 1 2 1 101000 f 74 goat Random2.2K-635 6 6073225 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38385005 Affx-122971877 AX-123255363 6 6085156 AGGATATCTCAACAGAAATCTCAAAAACTGAAAAG[C/T]AAAGGGAACAAAAATTGGGCGGAAAAAAGACTATC Y 2 1 2 1 201000 f 74 goat snp16176-scaffold170-534151 6 7092177 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395099 Affx-122964165 AX-123265454 6 6123549 ACCTAGTATTGGGAAAAATTTAAAAGTCAGCTAAT[A/G]CCAATGTTGGTTAGAATGAGGAGTCATGAGAAACT R 2 1 2 1 101000 r 74 goat snp16177-scaffold170-572544 6 7129135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405055 Affx-122956347 AX-123275407 6 6168905 GTAAAGAATATGGAAAAGCAAGAAGTACCAAATTT[A/C]TTTCTTTTTATCTACCTCATATAGGGCTTAACTTG M 2 1 2 1 101000 r 74 goat snp16178-scaffold170-617900 6 7174988 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378334 Affx-122977336 AX-123248693 6 6201455 ACACTGGGGTCCACTTTGGCTCAGCCAGTAGCTAT[A/G]CAGTGTTGAGTAGGACTCTTAACCCCCAGAGCTTT R 2 1 2 1 101000 r 74 goat snp16179-scaffold170-650450 6 7208182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794083 Affx-122930479 AX-385281050 6 6253918 TCTTTCAATGTAATAAAACTGTCAAACTTGCTGGT[A/G]TCCTTGAAGGTTTAGAAATGATATTTGCTTCATAA R 2 1 2 1 101000 f 74 goat snp11296-scaffold1408-4126 6 7264651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799883 Affx-122942096 AX-385286809 6 6285753 GTGAAAGTAAAGCATAGATCTGTTTTTTGTAAAAG[A/G]GAATTAAAGATATTTAGGAATACTTTTAGTCCTAG R 2 1 2 1 101000 r 74 goat snp11297-scaffold1408-35961 6 7297020 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423638 Affx-122942359 AX-123293984 6 6316297 AATTATAATTCTTTCTAAATACTTCAGTGGATTTA[C/T]ATTTTTGCAAGCAGTTTTCACGGGCATTAGGCCTC Y 2 1 2 1 201000 f 74 goat snp11298-scaffold1408-66505 6 7327864 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448014 Affx-122923727 AX-123318350 6 6366163 GAATTGGACATGACTGAAGCGACTTAGCATCATCA[G/T]CAGCAGCAGGGATGGTCTGTAACCATTTACCTTCC K 2 1 2 1 202000 r 74 goat snp11299-scaffold1408-116371 6 7376953 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786578 Affx-122957417 AX-385273610 6 6399744 AAATCTGGTTCATATTTATAGATTTGGCTACTAGA[C/T]TTCTTTCTAGTTTTTCCAGTGTGCTTTTTAATTCA Y 2 1 2 1 201000 r 74 goat snp11300-scaffold1408-149952 6 7410410 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767101 Affx-122933736 AX-385254388 6 6435512 AAGTAAAGACATCAGGAACTGTTGGGATGCAGTGA[C/T]AGTCAATACTCAAAACCTCTTATGGTATTTGGAGC Y 2 1 2 1 101000 f 74 goat snp11301-scaffold1408-185720 6 7444281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425080 Affx-122941249 AX-123295426 6 6474976 TCATCGCTACAGCCTCTCAAATCATCCTATCACTA[C/T]AGATTTGCCTTCTCAATCTGCCCTGCTTAGTAGGA Y 2 1 2 1 201000 r 74 goat snp11302-scaffold1408-225184 6 7483684 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798523 Affx-122959942 AX-385285456 6 6506807 GAGCTTTGAAGAGGGATGAAGAGAATAATAAAATG[A/G]ACTTATTGAGAGAGGTACTAAAATCAAAGATAATG R 2 1 2 1 101000 f 74 goat snp11303-scaffold1408-257015 6 7515664 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783743 Affx-122969891 AX-385270799 6 6540871 CTGTTAATACTGATTTCATTGAGATCATTGTGTCC[A/G]TTAGATGGGAAATGCAGGTAAAAATGCTTTGAAAA R 2 1 2 1 101000 f 74 goat snp11304-scaffold1408-291079 6 7550758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776194 Affx-122943814 AX-385263322 6 6598573 AAGTGTGCTCCATAGATAAGCACTTAGTTGTGTAT[A/G]TAATCTGTAAGCCCTGAAAGTCACATTGTTTTTCC R 2 1 2 1 101000 f 74 goat snp11305-scaffold1408-348781 6 7606792 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409751 Affx-122953009 AX-123280102 6 6631124 TGGATGTGCTACCAGTTCATAGTGTTGAGGCAGTA[A/G]ATGTGATATATAATTGATTCATGAAGCCTTTGCTG R 2 1 2 1 101000 f 74 goat snp11306-scaffold1408-381332 6 7639027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400464 Affx-122961307 AX-123270819 6 6664705 GATCCCTTGTCTCAAACAAGAACGAACTCAGTGCA[A/G]TTTGTGCTTCCTGGTCCCTCTTGGAATCAGGCTGA R 2 1 2 1 101000 f 74 goat snp11307-scaffold1408-414913 6 7672687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272421 Affx-1111834252 AX-519546147 6 6716692 GTTTTGCCACCATTCCCTTGGCCCC[A/G]CGAGAGGTAAGGTCACAAGGCAACCAGTAAAACAT R 2 1 2 1 101000 r 74 goat GoatD01.027587 6 6716692 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38432903 Affx-122935324 AX-123303244 6 6718915 AATTCATGGACTCCCAAAGAGTAAGCACAAAAACC[G/T]AAGGATCTCCCAGATCTGGTCTAGGAGTGTTAATC K 2 1 2 1 101000 r 74 goat snp11308-scaffold1408-469123 6 7727335 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278316 Affx-1111836359 AX-519551802 6 6751503 CCAGGTATTCCTATAGCAAGCGGTCTAGGGCCACA[A/G]TTAGAGAAGGACTGACTTAAAGGGGACCCACCACG R 2 1 2 1 201000 f 74 goat Random2.2K-636 6 6751503 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278318 Affx-1111836360 AX-519551804 6 6755014 AAGTCTGGTTAGAAACTCGGTTTCCATCCAGAAAA[A/G]AAATAGTTGTTTGTTCTCAAGCCAGACCACTTGAG R 2 1 2 1 201000 f 74 goat Random2.2K-637 6 6755014 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412578 Affx-122951307 AX-123282927 6 6790248 CATTGTAAGTTAACATGGCATGAGCTGTTGCTAAA[G/T]CTACCAGGGTCTCCTTCCACCCAGCATTGCCTCCC K 2 1 2 1 101000 f 74 goat snp46120-scaffold635-31540 6 7955787 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428283 Affx-122939393 AX-123298626 6 6850253 AAGTAAGTTATATACATTTTTGCAAGCATTTTCCC[C/T]ACTCTTTTCATAGTGACTTGTAACTTCTCCCATGG Y 2 1 2 1 101000 r 74 goat snp46122-scaffold635-91545 6 8016126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802068 Affx-122971097 AX-385288972 6 6888531 CTAGCAGCTAATGTATTCAACAGGGCAGATGCAGA[A/C]CATATCCATCGTGGCAGAGGGTTCTATTAGACTGT M 2 1 2 1 101000 f 74 goat snp46123-scaffold635-129823 6 8054263 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771318 Affx-122926307 AX-385258476 6 6919777 GCAATGATATTCAAACAAAATGTGAAAAATTTGGG[C/T]TTATGTCCCTTACCTTTAGAAGATAATGGCACAGA Y 2 1 2 1 201000 f 74 goat snp46124-scaffold635-161069 6 8086484 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795972 Affx-122960020 AX-385282924 6 6957551 TATCCATTTAAGCAAAAATATTGTGATTTAAGTTC[A/G]TTTTCTATATGAAATAGGAAGACTGCAAAATTCAA R 2 1 2 1 202000 f 74 goat snp46125-scaffold635-198843 6 8125994 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418578 Affx-122946376 AX-123288926 6 6993314 CTACCAAATGCATCAATCCATGGATTTCACTTTTG[C/T]GGCAATCGTCACTGATAGCTTTCTTGCTTCACAGG Y 2 1 2 1 101000 r 74 goat snp46126-scaffold635-234606 6 8162051 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451235 Affx-122921952 AX-123321569 6 7042385 CTGAACCCTGCCGAGTTCCCTGGCTAGAACATGCC[A/G]TCACCTTGACCTTGCAGATGAACAAAGCCACTGGT R 2 1 2 1 201000 r 74 goat snp46127-scaffold635-283677 6 8211709 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764631 Affx-986696938 AX-385252273 6 7078329 TTGAGGCTGATAGGAAAAGCTTCAAGGAAGAAAAA[C/T]TGAAGTTATATCTTGAAGAGTAAGTAATACTAACA Y 2 1 2 1 600010 r 74 goat 6_7078329 6 7078329 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 38375718 Affx-122978635 AX-123246077 6 7081190 GATGATTTGATGGCTATGTCCATATCCGAAAAGTG[A/C]ATCAAATTGTACACTCTAAGTTTGTACAGCCTCAT M 2 1 2 1 101000 f 74 goat snp46128-scaffold635-322482 6 8244296 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424971 Affx-122941919 AX-123295317 6 7215141 TTATATTTACCTTTTTCTTTGTGGAGTTATGCATT[A/G]TTGAAAAGCAGACTGTACTTGTTTTACGGAATTAA R 2 1 2 1 101000 r 74 goat snp46131-scaffold635-456433 6 8373232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425268 Affx-122940977 AX-123295614 6 7265184 ATTAAGTTTCATATACAGAGTAAACTTATTCATTT[A/G]TAAGGTTAAATCTAAAGTGTACATTTAGGGCAGAA R 2 1 2 1 101000 r 74 goat snp46132-scaffold635-506476 6 8423412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785295 Affx-122963980 AX-385272340 6 7297387 CATCTTTGAAAAATTTTAGACATTCACTCACCTCC[A/G]TTTGTAAATTTCACCTGCAAACTTTTAACCACATT R 2 1 2 1 101000 f 74 goat snp51700-scaffold760-12170 6 8472930 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392873 Affx-122965747 AX-123263230 6 7357474 TTTGTTCTTACAGCCTTTAAACATATGTAAGGACA[C/T]GGCAATATACTCCAGTATTCATGCCTGAAAAATTT Y 2 1 2 1 201000 f 74 goat snp51701-scaffold760-72257 6 8533888 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384676 Affx-122972131 AX-123255034 6 7438269 GCTTTAGCTATTGTATCCATCTAGTGAGCAAGTCA[G/T]CAGATCACTGAAACATGCCACTTGTTTGGTTTCCT K 2 1 2 1 202000 r 74 goat snp51703-scaffold760-153052 6 8614338 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403123 Affx-122958118 AX-123273476 6 7508063 TAAAATTTGATTTCCCAACAACTAGCTTGTCTCAT[A/G]TTCACTTCCAGCACATGCACACACATATAGTACTG R 2 1 2 1 201000 f 74 goat snp51705-scaffold760-222846 6 8682586 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777000 Affx-122972447 AX-385264124 6 7565675 GTTGAGACTACTAGCATCTGGTGGTTAAAGGTCCA[G/T]TATGCTAGTCAGCTTTCTACATTGCATAGGACACC K 2 1 2 1 201000 r 74 goat snp51706-scaffold760-280458 6 8741030 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772867 Affx-122924284 AX-385260012 6 7598943 ATCTCAATGCTTTATAGTTTGTCTCAAATATAATC[A/G]TTGGATACTAAATGGTGTAAATATATTTATTACGT R 2 1 2 1 201000 r 74 goat snp51707-scaffold760-313726 6 8772725 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767739 Affx-122957449 AX-385254969 6 7613489 GCAATGGTACTTAAAGCTTCTGGATTTCACTTCTA[C/T]ACATATAATTGTCTATTAATTAAGAATTCTTTATT Y 2 1 2 1 101000 f 74 goat snp19454-scaffold1964-526 6 9268471 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278320 Affx-1111836361 AX-519551806 6 7677794 GTGGTAGGAAATCATGGAGACAGTGAATTTTAATC[A/G]TATCTTGAAAACTGAATAGGATTTCAATTTTTAAA R 2 1 2 1 101000 f 74 goat Random2.2K-639 6 7677794 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444255 Affx-122927215 AX-123314592 6 7696943 GAGGAGATCTGTCTTTCCTGTTACAGGGAATATGA[C/T]GAAACCTCATTTTCTAAAATATGTAGTTAGAATTC Y 2 1 2 1 101000 f 74 goat snp19456-scaffold1964-83980 6 9352637 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780598 Affx-122974551 AX-385267688 6 7732009 TCTTGCAGTTCTATTACGAATAGTTCTAGGGTTGT[A/G]TCCTCAGAGATTCCCAGCTGAGTTTAATAATGGGC R 2 1 2 1 101000 r 74 goat snp19457-scaffold1964-119046 6 9388916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780535 Affx-122936401 AX-385267626 6 7769818 CAACGACTCCAATTTTAGCGTAGTTTCTAAAAATG[C/T]AACTAATTTGGAATTAATGAAAATTTTCCTTTTAT Y 2 1 2 1 201000 r 74 goat snp19458-scaffold1964-156855 6 9428226 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801655 Affx-122974228 AX-385288563 6 7836609 GTTAAACCACCAATCACATATGTAATAAACACTAA[C/T]TATTTTCCAAACATTAAGCTGAACTTGAATGGGGA Y 2 1 2 1 101000 r 74 goat snp19373-scaffold1958-302086 6 9549745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773041 Affx-122935378 AX-385260185 6 7873027 TTTAGTTCAAATCTGAAATACACATTCCGAAAGCA[C/T]GGTAAAATTTCTCAGAGAATGCATACTAAATATAT Y 2 1 2 1 101000 f 74 goat snp19372-scaffold1958-265668 6 9586619 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770996 Affx-122932787 AX-385258158 6 7913627 TATGCTCCTTTTCTTAGGAAATTACTTTGTGTGAA[G/T]CTTTCATATTTCAGTAGGCAGATTATATGATTCTT K 2 1 2 1 101000 f 74 goat snp19371-scaffold1958-225068 6 9627998 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273278 Affx-1111833518 AX-519546924 6 7926323 ATTTTTACAAAGTGCAATTAATAGGCAAGGCAAAT[A/G]TAGGATGATAGAAGTTTTCCACAGAAAAAAATAAC R 2 1 2 1 101000 r 74 goat 6_7926323_AF-PAKI 6 7926323 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38444610 Affx-122926946 AX-123314947 6 7946652 AATCCACTGATTCCTAGAATGTAGTATTCAGCATT[A/G]CATGAACTGTGAACTTCCAGATGTTCAAGCTGGTT R 2 1 2 1 201000 f 74 goat snp19370-scaffold1958-192043 6 9662177 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783160 Affx-122926017 AX-385270227 6 7976669 TGTATAACTTGAGTAGAAAGACTACTTGTTTGAGA[C/T]AACATGTACACGCAATGACTCATATCCTAGAGAAA Y 2 1 2 1 101000 r 74 goat snp19369-scaffold1958-162026 6 9692160 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391137 Affx-122966791 AX-123261494 6 8034538 TATTTTGATCAGGAATATTTCCTATTGCCTTAATT[A/G]CATGCTTAGTCGCTCAATCATGTCCAACTCTTTGC R 2 1 2 1 103000 f 74 goat snp19368-scaffold1958-104157 6 9749336 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772951 Affx-122975422 AX-385260095 6 8077883 ATTAGTTTTATTCCACAATTGTTTTATCTACTTGA[G/T]CACAAAATTCAAACTCTTGATCATATCTTATTTAA K 2 1 2 1 201000 r 74 goat snp19367-scaffold1958-60812 6 9793076 T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432107 Affx-122936458 AX-123302448 6 8110392 CTACATTTTGTTTGTCCATTTCCTTATTGAAGGAC[A/G]CTTAGGTTGCTTCCAGTTTGGGGAAATAATCAATA R 2 1 2 1 303000 f 74 goat snp19366-scaffold1958-28303 6 9825323 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419238 Affx-122945674 AX-123289586 6 8144193 GATTATACAATGAGAAAAAGGCAACCACTGTTCAG[C/T]GTATTCTTGATCATTTTTCTACAAAGAAGTAAGAC Y 2 1 2 1 201000 r 74 goat snp31088-scaffold344-5399 6 9872044 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401618 Affx-122959604 AX-123271971 6 8175997 ATTCATGGGGTCACAAAGAGTCAGACATGACTGAA[C/T]GACTGAACTAACTAAATAAGCTACCATAATTGGCT Y 2 1 2 1 103000 r 74 goat snp31089-scaffold344-37203 NW_017216331.1 8391 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390750 Affx-122967905 AX-123261107 6 8226906 ATGGGCTTAGAACCCTATCACATTTTTATCTCTTT[A/G]CCACTGCATAGCAGATAGCTTCAGAGAAGGTGATG R 2 1 2 1 201000 f 74 goat snp31090-scaffold344-88112 6 9917478 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436310 Affx-122933264 AX-123306649 6 8311658 CCTACAACAGTAGATAGCACTATCTTTTGATTTTG[A/C]TTTAAAATAAGATTTTGACTTCTAGTTTACATTAA M 2 1 2 1 201000 r 74 goat snp31092-scaffold344-172864 6 10000394 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796529 Affx-122919710 AX-385283475 6 8341303 ATACTTCTGGCCATAGAGCAAGAAAATGATCAGCA[C/T]AGACTCCCCAGGGCAATGTTTTAACTATGACTCTC Y 2 1 2 1 101000 f 74 goat snp31093-scaffold344-202509 NW_017204024.1 1975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389658 Affx-122968724 AX-123260016 6 8395647 GTGTACAGCATAGAAGATGAATTCGTCATCCTCCA[C/T]GATGAATGAGGAACCTGAGGCTCTCTCTGTAGTTA Y 2 1 2 1 101000 f 74 goat snp31094-scaffold344-256853 6 10083795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438512 Affx-122931208 AX-123308850 6 8456089 CTTAAGATACCATCTAAGTTCTAGTAAATTTAGAC[A/G]TTAGACATCTCTTTTGAAGTCTGTGCTGTAAAATA R 2 1 2 1 101000 f 74 goat snp31095-scaffold344-317295 6 10144986 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432512 Affx-122935571 AX-123302853 6 8487885 TTTCAATGCCCAGAACAACCTTATCATCATGACAT[A/G]TTGACATGGGCAGGTGGAAGAGATACAGGCTTTGC R 2 1 2 1 101000 f 74 goat snp31096-scaffold344-349091 6 10177177 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774602 Affx-122962786 AX-385261736 6 8521311 ATTGAAGATAGTCTATAGATATTGAATATGCATGA[C/T]GACTTGAAAACTATAAGAAAGGAACATCACTAAGA Y 2 1 2 1 102000 r 74 goat snp31097-scaffold344-382517 6 10211421 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423270 Affx-122942663 AX-123293616 6 8563804 TCTGTCATTTTATGAGTCCTCTGTCTTCTATCAGA[A/G]TTTTAATTACATTGTTTTCATATTCTGATATAATA R 2 1 2 1 201000 r 74 goat snp31098-scaffold344-425010 6 10254371 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791579 Affx-122975932 AX-385278570 6 8597302 ATATGATTAGAAATTTAGGTGCTCCAAATATAAAA[G/T]AACTGTGGAAATGTTTGCAGCCATTTATAATTCAG K 2 1 2 1 101000 r 74 goat snp31099-scaffold344-458508 6 10288420 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390975 Affx-122966919 AX-123261332 6 8630635 AGATAAATGAGCTGCACAGGTAGATCAGCTCAGTT[A/C]GGTTCAGTTGACCAGTCGTGTCCGACACTTTGTGA M 2 1 2 1 103000 f 74 goat snp31100-scaffold344-491841 6 10322023 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780959 Affx-122920555 AX-385268046 6 8671058 GACTTCAAAATAATCATTGGGAAAACTTGCCATAC[A/G]TTCACTAGAGTCCAGGGCATATCTGAGTCCATCTG R 2 1 2 1 101000 r 74 goat snp31101-scaffold344-532264 6 10362832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769781 Affx-122967168 AX-385256951 6 8722938 GTTTAGGCCAGCATCTGGATAAAGTAGACAATTCT[A/G]TCAGTGGTTAATATGCCTAGCAGAGATAGACTTAG R 2 1 2 1 101000 f 74 goat snp31102-scaffold344-584144 6 10414687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794522 Affx-122934736 AX-385281485 6 8774561 GAAAGTGACTGAATCCAGATGAATGTCAATTCATT[A/C]GTTTATTCAGAACCTATTTGTTACTCTCCTACTCT M 2 1 2 1 201000 f 74 goat snp31103-scaffold344-635767 6 10467125 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430560 Affx-122937015 AX-123300901 6 8805871 AGTGAAGTCATATTACAATTTTTTAATATATTGAT[A/G]CTGTCAAAATTATCCAGATATAGCAGTTTTGTTCT R 2 1 2 1 101000 r 74 goat snp31104-scaffold344-667077 6 10498408 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387096 Affx-122970678 AX-123257454 6 8848750 TGGAATTGTAGGCTAGTATTTTTAATGTACACATC[A/G]TTTAAAAATAATATGTATAAGCATTCATAACCTAG R 2 1 2 1 103000 f 74 goat snp31105-scaffold344-709956 6 10541646 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397489 Affx-122962074 AX-123267844 6 8878779 CTTCCCAAGGGTAAATGAGAACTGCTACCCCTAAT[A/G]TAGAACAGAATACACTTGTTTGACTACCTATAATA R 2 1 2 1 101000 f 74 goat snp31106-scaffold344-739985 6 10572162 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765632 Affx-122938417 AX-385253105 6 8912565 TGATTGTTTCAGCATAATCTTACTGCAAACAAAAA[C/T]AGAAGATTTTACCAACTACTCAACCTAACCAAGGC Y 2 1 2 1 201000 f 74 goat snp31107-scaffold344-773771 6 10607407 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408848 Affx-122954010 AX-123279199 6 8948836 TATTGGCAAACATCTCTAAGCAATGTTGAAATTAC[A/G]TATTAATAGTAGAAAAATTAGAATTAAAAATAAAT R 2 1 2 1 103000 f 74 goat snp31108-scaffold344-810042 6 10643593 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429461 Affx-122938485 AX-123299803 6 9063008 CCGTGGTCTAGTTGTGGTCTCTGGCTCCCATATTA[C/T]GTCCTGTGCCCTAGGCTGTCTTTGTTGCTAACTCA Y 2 1 2 1 101000 f 74 goat snp31111-scaffold344-924214 6 10759124 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793553 Affx-122968412 AX-385280529 6 9108911 ATCACCTCTCAGCCTAAAGGAGGTTTCCAGCCATC[A/G]CTGGCTAACTTTCAAACATCATATTCTTATACCAT R 2 1 2 1 101000 f 74 goat snp31112-scaffold344-970117 6 10805932 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424793 Affx-122941391 AX-123295139 6 9202008 ATTTATTGCAGGTGTTTCTGTTTATAGTTTCTCAC[C/T]CTTTTATGAAATGGTATAGAAAAGCCCACTTGAGT Y 2 1 2 1 201000 f 74 goat snp31114-scaffold344-1063214 6 10900756 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377630 Affx-122977876 AX-123247989 6 9256535 GCTTAGAAACATAAAAAGGAACACAGTAAATTTCA[C/T]GCATAAATGTAGTTATGGAAATCATATGTTTAAAT Y 2 1 2 1 303000 r 74 goat snp31115-scaffold344-1117741 6 10955166 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377496 Affx-122977493 AX-123247855 6 9289885 GCATATTTCTTTCTTATTGAATTATTATCTTTCTG[C/T]ATCCAGATGACACTTCAAAACCCTCACTATTAAGA Y 2 1 2 1 101000 r 74 goat snp31116-scaffold344-1151091 6 10988896 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375534 Affx-122979106 AX-123245893 6 9334892 CATCATGACCTCATCACATATTGATATTTGCCTGC[A/G]CTGTTCCACACTTGTCAAATGCTAACATGCATTTC R 2 1 2 1 101000 r 74 goat snp31117-scaffold344-1196098 6 11034964 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785440 Affx-122946328 AX-385272485 6 9382659 AAGCAGGCTGAGTGGTTGAATCAATAGCTGGAGTG[C/T]ACTCAGTAGAGATTTAAAGACGTGAACTAAATCAT Y 2 1 2 1 101000 f 74 goat snp31118-scaffold344-1243865 6 11083495 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379808 Affx-122976233 AX-123250166 6 9441703 AACCACAGATATATTTTATAATCCTTTTTTCAGCC[A/G]TTCATCTAAAAATTGCCAATCACTCCAGCTTGGTT R 2 1 2 1 101000 r 74 goat snp31119-scaffold344-1302909 6 11137061 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387430 Affx-122970391 AX-123257788 6 9492360 GTGTATTAATTGGAAACAATGTCACATAGGAAAAA[C/T]AGCTCCTTCGGTTTTCTTCCTTCTCTGATCCTAGC Y 2 1 2 1 201000 f 74 goat snp31120-scaffold344-1353566 6 11187013 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800657 Affx-122959783 AX-385287576 6 9521662 TAGAAAAAGTTGACTATTTAATTATATAAAGTCTC[C/T]AGTTTTAATGACTTCACAGCAATTTGCAAATTATA Y 2 1 2 1 101000 f 74 goat snp31121-scaffold344-1382868 6 11215972 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415142 Affx-122949416 AX-123285491 6 9613372 ACTGACTTGTTGAGTGCTAGTTTATTCAGCTGTCC[A/G]TACTGGGTGAGTCACTACAGCTGTTCATTCAACTG R 2 1 2 1 101000 r 74 goat snp31123-scaffold344-1474578 6 11307853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769802 Affx-122940860 AX-385256972 6 9657796 AGGCACAAAAGTTAGTTCTAGTAAACAGGATGGGA[C/T]AGAAGCAGAGTGGTACGTGCAATTTCTCATTTACA Y 2 1 2 1 101000 f 74 goat snp31124-scaffold344-1519002 6 11360536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383221 Affx-122972769 AX-123253579 6 9705253 TGACATTCATATTAAAGAGTTTTGAACCGTAGAAG[C/T]GATGGGTGGCTGAGAAGCTCTACCAGCAAGAAAGG Y 2 1 2 1 201000 f 74 goat snp21377-scaffold2085-181875 6 11547361 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447159 Affx-122924437 AX-123317495 6 9752966 TTTCACTACTGTTGACCCATTCTCCTTGAATATGC[A/G]CTATCCTTAGGGATTACCTGAAATAGGCGAGATTT R 2 1 2 1 201000 r 74 goat snp21376-scaffold2085-134162 6 11595263 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391249 Affx-122967378 AX-123261606 6 9828863 TATATTGTTGATGTTTAACTTCTTCTTCCTTCTTG[C/T]AAACTACTCCCCTCCGCATAATTTATTGACTGTTC Y 2 1 2 1 101000 r 74 goat snp21374-scaffold2085-58265 6 11671730 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800704 Affx-122965385 AX-385287621 6 9870085 ATAATAAAGAGTGACTCCGCTTTTTTGATGTGTGA[C/T]GGTTGACAGTTTCTAAGCCCGCCTTTCTCTTTCTC Y 2 1 2 1 101000 f 74 goat snp21373-scaffold2085-17043 6 11713793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418725 Affx-122946277 AX-123289073 6 9888228 GACCACCAGGCTTGTGGTCAGACAGAGTCCTGGCA[A/G]TAGAATGAGGGTTGCTGTCAGCAAGCAGTGGGTGA R 2 1 2 1 101000 r 74 goat snp30882-scaffold340-3646604 6 11733550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476213 Affx-1251763718 AX-586011637 6 9897690 TTCTAATCACACCTGTGTCCTCCCTCTGCTTCCTC[-/TCTCCTGGCTTTCATTTTTTTTTGTTTTGTTTTGTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CTCCTGGCTTTCAATATGGAAGAAACAAATACTCA - 4 1 4 1 20000 f 74 goat SV_156 6 9897690 - deletion junction SV-TF-chip 539476467 Affx-1251763718 AX-586011867 6 9897690 TTCTAATCACACCTGTGTCCTCCCTCTGCTTCCTC[-/TCTCCTGGCTTTCATTTTTTTTTGTTTTGTTTTGTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CTCCTGGCTTTCAATATGGAAGAAACAAATACTCA - 4 1 4 1 20000 r 74 goat SV_156 6 9897690 - deletion junction SV-TF-chip 562165396 Affx-1251763718 AX-606940807 6 9897690 TTCTAATCACACCTGTGTCCTCCCTCTGCTTCCTC[-/TCTCCTGGCTTTCATTTTTTTTTGTTTTGTTTTGTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CTCCTGGCTTTCAATATGGAAGAAACAAATACTCA - 8 1 4 1 20100 f 74 goat SV_156 6 9897690 - deletion junction SV-TF-chip 562165466 Affx-1251763718 AX-606940877 6 9897690 TTCTAATCACACCTGTGTCCTCCCTCTGCTTCCTC[-/TCTCCTGGCTTTCATTTTTTTTTGTTTTGTTTTGTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CTCCTGGCTTTCAATATGGAAGAAACAAATACTCA - 8 1 4 1 20100 r 74 goat SV_156 6 9897690 - deletion junction SV-TF-chip 562166125 Affx-1251763718 AX-606941533 6 9897690 TTCTAATCACACCTGTGTCCTCCCTCTGCTTCCTC[-/TCTCCTGGCTTTCATTTTTTTTTGTTTTGTTTTGTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTC]CTCCTGGCTTTCAATATGGAAGAAACAAATACTCA - 8 1 4 1 20100 f 74 goat SV_156 6 9897690 - deletion junction SV-TF-chip 38432794 Affx-122935415 AX-123303135 6 9937793 TATGGAGAGTATGTTGTAGACGAAAGCATGCCAGA[C/T]AAGAAGGGGAGTAAATGAAAGCCCTTTGTAGTCAG Y 2 1 2 1 101000 f 74 goat snp30881-scaffold340-3597039 6 11784174 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403437 Affx-122957739 AX-123273790 6 9981762 TGCCCCAGGGCCTTTGCACTTAACTGTTCACTTGG[A/G]AGAAGTGGTCTTCTCCTAGAGGGCCACATTTCTTA R 2 1 2 1 303000 r 74 goat snp30880-scaffold340-3553070 6 11828141 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377776 Affx-122977335 AX-123248135 6 10035288 TGCCATTGTCAGGAAGGACCCTGTGTTATCACTGC[A/G]TATGTAATGTTGCCTTGAGCTAATTGCTCTTTACA R 2 1 2 1 201000 r 74 goat snp30879-scaffold340-3499544 6 11882255 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394647 Affx-122964386 AX-123265002 6 10066724 TTACAGTGTTGTTTCTCAAAGCCCAGTACACAGAA[C/T]GTCTGCATTACTCTCTCTCCTGCAATCGACTGCCA Y 2 1 2 1 101000 f 74 goat snp30878-scaffold340-3468108 6 11914028 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450558 Affx-122922468 AX-123320892 6 10114409 GGACCACATTTCTTTAGCATGAAAGTACCTAGATA[C/T]ACATTTTGAGGGCTTATTACCAATGTGAACTTTGT Y 2 1 2 1 101000 f 74 goat snp30877-scaffold340-3420423 6 11961236 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435449 Affx-122933469 AX-123305789 6 10150733 GTCATATATGCACATCTGCATGCCTTTTAATTTCC[A/G]TTTATATTTATTAGCAATTTCGGTCAGAATTGAAT R 2 1 2 1 201000 r 74 goat snp30876-scaffold340-3384099 6 11997365 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401322 Affx-122959840 AX-123271675 6 10269756 GTCCAGTTTGCAGCTCAACCTCTCTGACCTGTTCT[A/G]TCATAGTGCTAGGATGGCTGCTGTGCCTCTGAACT R 2 1 2 1 101000 r 74 goat snp30874-scaffold340-3265076 6 12116601 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450299 Affx-122922153 AX-123320634 6 10312514 ACCATCCTGGTGTAGCCAGTGTGAAAGGTGGTGGA[C/T]GAAAAGGGATGATTCTAATGAAGAAATTAGTAAAA Y 2 1 2 1 201000 r 74 goat snp30873-scaffold340-3222318 6 12160039 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769763 Affx-122953251 AX-385256933 6 10345862 GAATTAAACCATGAGAGATCATACTTTCATTAGTG[C/T]AAAACAGAAATTAGTAGTAAAAGACCAATTTTGGG Y 2 1 2 1 101000 r 74 goat snp30872-scaffold340-3188970 6 12193214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404356 Affx-122956819 AX-123274708 6 10390058 GGCTGCTGCTTTCACAGATGAGGACACTGAGGTCC[A/G]CAGAGATGGCAATCTGCCTGGTCACACAGAACCAG R 2 1 2 1 101000 r 74 goat snp30871-scaffold340-3144774 6 12237490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797363 Affx-122940475 AX-385284302 6 10425954 CACTGTTCTAAATAACTCACAATGAAGACAAAATT[A/G]CTTCACTAGAGAATTACATTTCTTTTTAATCTCCA R 2 1 2 1 201000 r 74 goat snp30870-scaffold340-3108878 6 12273239 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411955 Affx-122951141 AX-123282305 6 10461641 TTAAGTCCTTTTCAAAAATGTACTGAGCAGATGCA[C/T]TGCTTTTCTGATAATATCCCTTGGAGAACAGAATA Y 2 1 2 1 101000 f 74 goat snp30869-scaffold340-3073191 6 12309347 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440075 Affx-122929732 AX-123310412 6 10492869 TCCAGTAATAGAATGCACTGATAAGGGCCGTTCAA[C/T]AATGCTTATTTAGGCAAATTTTACTTGCATATTTA Y 2 1 2 1 101000 f 74 goat snp30868-scaffold340-3041963 6 12340047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272329 Affx-1111833488 AX-519546064 6 10513422 CACATTTAAGTTTTTTACATATGAAATGGTCAGTC[A/G]GATAGCATCACTGACTCAATGGACATGACTTTGGG R 2 1 2 1 201000 f 74 goat 6_10513422_AF-PAKI 6 10513422 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448706 Affx-122923856 AX-123319042 6 10541956 GGGCCATCCACGGCACAGCCCACACTCGGCATCAC[G/T]ACACAGTACAGCTTTTCCAGTCATCACACTGTCCA K 2 1 2 1 101000 r 74 goat snp30867-scaffold340-2992876 6 12389096 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800442 Affx-122921186 AX-385287363 6 10579073 AAAGCAGTATTAAGTAAATCCTGTGGCAGTTAATA[C/T]GTTAGAAAGCAAACTCAGAATAATTAGAATTGCAA Y 2 1 2 1 101000 r 74 goat snp30866-scaffold340-2955759 6 12426264 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408351 Affx-122953743 AX-123278702 6 10616587 TCAAATAGCTAACTTATAGACCCACATTCTTTGCA[C/T]GATAATCCTCCATGCCCTATTTATTTGAAAGTTTT Y 2 1 2 1 101000 f 74 goat snp30865-scaffold340-2918245 6 12463407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401376 Affx-122959233 AX-123271729 6 10666512 AAAAATTTGCCACTCAGTTTGTGGAAAGTGTGATT[A/G]CCAGACAACCTGATAACCTCTCAGCTCCTTCAAAG R 2 1 2 1 101000 f 74 goat snp30864-scaffold340-2868320 6 12513254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446014 Affx-122925863 AX-123316351 6 10698272 GCTCTGCTTTGTGTGTTATCAAGAAGGAATCTACC[A/G]CCAGAGGAAATTCTACGGGGTATCTCTTTTTCAGG R 2 1 2 1 201000 f 74 goat snp30863-scaffold340-2836560 6 12544858 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447518 Affx-122924065 AX-123317854 6 10748673 GCAGTAATGACATCCACAGCCTCCCTCTGAGAGAA[C/T]GAACAGCAAGAGCAAGATTTAGCATCTCCAGCTCC Y 2 1 2 1 201000 r 74 goat snp30862-scaffold340-2786159 6 12596533 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448436 Affx-122923654 AX-123318772 6 10798863 CATACCTAGCCGGAGAGAGCAAGAGAGGGCGCACA[C/T]GAGGGAGAATGGTGTACTGCCTCCACATTATGACC Y 2 1 2 1 101000 r 74 goat snp30861-scaffold340-2735969 6 12646821 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784465 Affx-122931148 AX-385271514 6 10829359 TATCCATTGTGAATGCTAATTAGAATGCTAATTGG[C/T]GAAAATATAATATTAGTTACCATTTGGAGTCTGTT Y 2 1 2 1 101000 f 74 goat snp30860-scaffold340-2705473 6 12677116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392977 Affx-122965671 AX-123263334 6 10892947 AACACATGACTATGAAATTATGCTGCTCTGTCTTT[A/G]TTCAAACAGTGATAACTCATAAAACTCACTATTCT R 2 1 2 1 101000 r 74 goat snp30859-scaffold340-2641885 6 12741165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430051 Affx-122937561 AX-123300392 6 10921784 CCAGCTTGTCTTTGAAGACCTTTGTACAGGAATAC[A/G]TATTACCTGTACTGTTCATTCATTCATCACACAGA R 2 1 2 1 103000 f 74 goat snp30858-scaffold340-2613048 6 12770304 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278490 Affx-1111836363 AX-519551973 6 10927851 TAATAATAAAAGGACCAATTCATCAACAAAATGGC[A/C]TACTAACCACAACCTGAGTTGTGAAATACACGATG M 2 1 2 1 101000 r 74 goat Random2.2K-643 6 10927851 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413596 Affx-122950570 AX-123283945 6 10952096 TCTGACAGCAATGCAAGCTTCCTCCGTGCCGCCAG[A/G]GCAGGCAACTTAGACAAAGTCGTGGAATATCTGAA R 2 1 2 1 101000 r 74 goat snp30857-scaffold340-2582736 6 12801008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375748 Affx-122978611 AX-123246107 6 10982097 CACTTATTAAAGAAGAAGTTCTAAGAGATACCTTA[C/T]AGAATTTGTCCTGGATCCTTAGGGGAGCTCTATCA Y 2 1 2 1 201000 f 74 goat snp30856-scaffold340-2552735 6 12830983 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402867 Affx-122958235 AX-123273220 6 11035696 GTGGGTAACTGAGAGGTTTGCGTGAAGACAAAGAG[C/T]ATTAGACCTTAAACTGTTGTTTTGGCATGTCCTTT Y 2 1 2 1 101000 f 74 goat snp30855-scaffold340-2499136 6 12884454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448897 Affx-122923183 AX-123319232 6 11096905 GGGAAATTCTCCCCACTCAAATAATGCTATAATGT[A/G]TCAGTATGAGTGTGTATATATGTCAGATTCTGTAA R 2 1 2 1 103000 f 74 goat snp30854-scaffold340-2437927 6 12945770 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397554 Affx-122962022 AX-123267909 6 11141619 AGAGTGTTTTATTCTCCCCATCCCAGGAGAAAACT[A/G]TTGCTCAAAGAAAAGAAAGAGCTCTGAAGGACTTT R 2 1 2 1 202000 r 74 goat snp30853-scaffold340-2393213 6 12989728 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278491 Affx-1111836364 AX-519551974 6 11149962 TCTGCATTGCAGGCAGATTCTTTACAATTTGAGCT[A/C]CAAGGAAGACCTACTTTTTGACATAAGTTCAAGGA M 2 1 2 1 201000 r 74 goat Random2.2K-644 6 11149962 T G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320801729 Affx-122964522 AX-385288637 6 11171501 AAATATATTCTCTACAGATAATTTAGAAATATCCT[C/T]AGTTGATCTCTTCATGAAGTAAGAGATCTCTTCAT Y 2 1 2 1 201000 f 74 goat snp30852-scaffold340-2363331 6 13020321 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275051 Affx-1111834565 AX-519548633 6 11193164 GTGAGTGACCCACCCTGCAGGGTTGCAT[A/G]GTCATTGGGCATGCTGGGCTCAGAGATATGTTTTA R 2 1 2 1 102000 r 74 goat GoatD01.041763 6 11193164 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38392333 Affx-122966688 AX-123262690 6 11210940 GTAAGGCTTTGCATATTTAATTCTCTTTCCAGGCC[A/G]TTTTATAACTTTGTAGAGGTAGAAGTTAATTTGTA R 2 1 2 1 201000 r 74 goat snp30851-scaffold340-2323892 6 13060434 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438496 Affx-122931221 AX-123308834 6 11253242 CATGTACTTTTTTTTTGAGACCTTATCATGTTCCA[C/T]GTACTTTTCCAGCATAATCTTATCTTTGCATCATA Y 2 1 2 1 101000 r 74 goat snp30850-scaffold340-2281590 6 13102291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388170 Affx-122969443 AX-123258528 6 11284353 GTTTTTGTTTTATTTATTTATTTATTTTTGAGAAC[A/G]TATCATTGGCTTGTGTTATATAGAATGCAGCCTTG R 2 1 2 1 101000 r 74 goat snp30849-scaffold340-2250479 6 13133655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278493 Affx-1111836365 AX-519551976 6 11308338 CAATAAGAGGAAGAAATGGACTCATTATGTCTTAT[A/G]AAGTAGTCTATATGAGGGTTACTGGTACCTTTACG R 2 1 2 1 101000 r 74 goat Random2.2K-645 6 11308338 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450528 Affx-122922491 AX-123320862 6 11315450 AAACAGGAGATGTAGAATTCTGTTTACAAGGCCTC[A/G]TCTAGCAAGGGAGGTTGGGAGCTGTAGTCTGCTCA R 2 1 2 1 201000 f 74 goat snp30848-scaffold340-2219382 6 13164696 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448749 Affx-122923321 AX-123319085 6 11346351 TATATATGTGTCCCTAACAGTAGATGGAATTGTCT[C/T]TCATGTTTTAAAAGTTCATATAAATGATATCATAT Y 2 1 2 1 101000 f 74 goat snp30847-scaffold340-2188481 6 13195756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387886 Affx-122969623 AX-123258244 6 11376428 TAGAGGGGGGGGCATGCCAGCAAATTGTCAGATTT[C/T]AGTTCCCCAACCAGGGATTGAACCTGGCTCATGGC Y 2 1 2 1 103000 f 74 goat snp30846-scaffold340-2158404 6 13225850 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778137 Affx-122955934 AX-385265252 6 11420217 CACTTTTCCTTTATAATAGATGGTAGCTTGCCAAC[C/T]GCTTAGTATTAAAAATCAAACTCCAGGAAATGCAA Y 2 1 2 1 101000 f 74 goat snp30845-scaffold340-2114615 6 13269233 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437207 Affx-122932045 AX-123307545 6 11451766 TTGTTTCTGTTACAGTTATAGCAATTTTCACAATG[C/T]GGCCTCCAAACTTGTAACAGATCAGAATGGTGTTA Y 2 1 2 1 201000 f 74 goat snp30844-scaffold340-2083066 6 13301964 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785094 Affx-122949137 AX-385272142 6 11491575 GTTAAAAAAGAAGCTCCAGAAGTTTGTAAAGAAAG[C/T]AAAGGTATTTCTGACTTTATGTTTAGGATTAGATA Y 2 1 2 1 101000 f 74 goat snp30843-scaffold340-2043257 6 13342058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278495 Affx-1111836366 AX-519551978 6 11559350 CAAAAAATGGATGATCATTTTTATTATTTTTTGCG[A/G]TCACAGGATTATAGCTGTTATCTAATGAGAAAAAA R 2 1 2 1 101000 r 74 goat Random2.2K-646 6 11559350 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383969 Affx-122972939 AX-123254327 6 11560452 AGGAATTCAAAGGCTTGCAGTGATATTTGGATTGT[A/G]TTTTTCCTTTACTTTATAATCAAATCATACTAATA R 2 1 2 1 303000 r 74 goat snp30841-scaffold340-1974380 6 13410795 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424190 Affx-122942516 AX-123294536 6 11647114 GAAGAAAGGTGAAATAAATCACTGTCAAGAACAGA[C/T]TTTGTTCCAAAGAACAAAAATAGTCTCTACAAGAA Y 2 1 2 1 303000 r 74 goat snp30840-scaffold340-1887718 6 13498678 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442370 Affx-122928020 AX-123312707 6 11733391 AAGCAGTTACTGACCCATGATGTTCCCTAACATAC[A/G]CACTCACCTTTCTTAGGAATATATGAAATGATTAC R 2 1 2 1 101000 f 74 goat snp30838-scaffold340-1801441 6 13585034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437228 Affx-122932030 AX-123307566 6 11776663 TCAGTTCTGGGCTGGTGGTAGCTCCCTGTAGTACC[G/T]ACATCTTTTAGACTTTCGAGTTTCCTTCTAGAATT K 2 1 2 1 201000 r 74 goat snp30837-scaffold340-1758169 6 13628666 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278332 Affx-1111836367 AX-519551818 6 11809176 CACACTGATGCAAAGCACTTAAAGCAGTCTGGTGC[A/G]AAGGTACTTAATAATTTTTAGTGTAATTATTACAC R 2 1 2 1 101000 f 74 goat Random2.2K-647 6 11809176 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382925 Affx-122973389 AX-123253283 6 11825896 TTTTCTTCTCCTTCAGATTGCCCAGATTAAGAAAT[A/G]CTTCAGTAAGGTGGCAGATTTTTAGTAATTATTTT R 2 1 2 1 101000 f 74 goat snp30836-scaffold340-1708936 6 13678156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403629 Affx-122957541 AX-123273981 6 11857813 CTTATTATCATAAGATACTGCTAGAGAGGTTTACT[A/G]AACCTTTCATATATTTACTGAGCATCTGCATTTTC R 2 1 2 1 201000 f 74 goat snp30835-scaffold340-1677019 6 13710175 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789957 Affx-122930699 AX-385276963 6 11891602 TTTGACAAAAGCTTTGTGCATAAATGTGCTCAATG[G/T]AAGTACTATACCTGTTTGCTTACCAGCCTGGAAGT K 2 1 2 1 101000 r 74 goat snp30834-scaffold340-1643230 6 13743803 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775832 Affx-122962088 AX-385262963 6 11926434 TAGGGAAGAAGAAGGCTAATTCTGATCATTCATTC[A/G]TCCTATCTCATATTTACGTTTCTTTTCTTCTCCAG R 2 1 2 1 101000 f 74 goat snp30833-scaffold340-1608398 6 13777942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801528 Affx-122932357 AX-385288437 6 11957800 AAGGATTCTAACAAATATTTGCACACCAAAGTTCA[C/T]AGCAGCATAATTCATAACAGTCAAAAGGTAGAACA Y 2 1 2 1 103000 r 74 goat snp30832-scaffold340-1577032 6 13809798 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782280 Affx-122960245 AX-385269358 6 11987875 AGCAGTTTTATTTCACAGGGTTTTTGCTCTGGGGG[C/T]ACTTGAATAGTATCAGGACTCTAATATTTAGTGTT Y 2 1 2 1 101000 f 74 goat snp30831-scaffold340-1546957 6 13840009 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394585 Affx-122964436 AX-123264940 6 12017011 ATTCTCTCCTATGCTAATCATGTGAACTGCCATTT[A/G]GCATTGTTAGTAACTGTATCAAGACAAGTTGTTAT R 2 1 2 1 101000 r 74 goat snp30830-scaffold340-1517821 6 13868975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771123 Affx-122960157 AX-385258283 6 12049918 CCTACTAAAGTGAAAGTTTCTTATATCAGTGATTA[C/T]ATATTAGTCACCACTGTGTTCTCAGCAATCAATAC Y 2 1 2 1 101000 r 74 goat snp30829-scaffold340-1484914 6 13901585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420316 Affx-122945018 AX-123290663 6 12121843 TGTGGGCGATGAATTCCGCATTCGAACCCAGGTCT[A/C]GAGGCGGGCTTTGGGGGCGAGGGGCCGCGTTCCTA M 2 1 2 1 103000 f 74 goat snp30828-scaffold340-1412989 6 13973493 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420568 Affx-122945276 AX-123290915 6 12160387 CTAAAGCGGTTGAGCCTGAAGCCCCAGGGACCCAG[C/T]AGCAGCAGCAGAGATGATACACATGATACCAGCCT Y 2 1 2 1 101000 r 74 goat snp30827-scaffold340-1374445 6 14012807 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793783 Affx-122967242 AX-385280755 6 12264321 GACTACAAGTAAATGGCAAGGGCTTTGACTCTAAG[C/T]GGATCTTCCTTCAAACCCTGTTCTGTCACATACTA Y 2 1 2 1 101000 f 74 goat snp30825-scaffold340-1270511 6 14116546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447695 Affx-122924619 AX-123318031 6 12293091 CAAGAATGTTAAACTCATGAGCCAGTTTTATTCTA[C/T]GCTACTCAATAAGTAAATATTGCACTAATGCTGCT Y 2 1 2 1 201000 f 74 goat snp30824-scaffold340-1241741 6 14145434 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412573 Affx-122951312 AX-123282922 6 12325594 CTCCAATATTATCAATAGAAAAACCAAAATTCTTC[A/G]CCTTAATACTAAGACATCCCTTTCATCTGATCCCA R 2 1 2 1 101000 r 74 goat snp30823-scaffold340-1209238 6 14178198 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393998 Affx-122965027 AX-123264353 6 12402233 TTTACTGGCCAGATTGCATAAGGCTAAGTTATGGG[A/C]GCTCTAAAATAAAATAGACAGGAACATCAAGAAAT M 2 1 2 1 101000 f 74 goat snp30822-scaffold340-1132599 6 14254732 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774038 Affx-122928697 AX-385261176 6 12457921 TAGCACCATGCAAACAAGCCTATTTAAACATCTAA[C/T]ACGTTGCACTGTGGTACTATGTGTACTAGTATAGT Y 2 1 2 1 101000 r 74 goat snp30821-scaffold340-1076911 6 14310591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278334 Affx-1111836368 AX-519551820 6 12470889 AGGAAGTCAGGCTGAAATTTAGAACTCACAAAGTG[A/G]GTAATTCCAGAGGATAATTGAAAGTTGACTGTAGT R 2 1 2 1 101000 f 74 goat Random2.2K-648 6 12470889 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779427 Affx-122960637 AX-385266530 6 12506281 CTTGTCTTTATGTGTCTAAACTACTATATCTATGA[C/T]GAAAGGGACACATTTTTATTGCTGTATCTCCAACC Y 2 1 2 1 101000 r 74 goat snp30820-scaffold340-1028551 6 14358997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400814 Affx-122959808 AX-123271169 6 12552612 GCACCCACTTGATAAATAAGAACACATGCATTCAT[A/G]TTTTAGAATCATTTTGCAGCCCACAGAGCAAAACT R 2 1 2 1 101000 r 74 goat snp30819-scaffold340-982220 6 14405578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783935 Affx-122955158 AX-385270989 6 12581283 AGATGATAAATGTTAGCAGATCTATTATATTTAGA[C/T]TAACCAAACTAATTCAAGTTGATCAATGGAAGAAA Y 2 1 2 1 101000 r 74 goat snp30818-scaffold340-953549 6 14434277 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393715 Affx-122965240 AX-123264070 6 12616734 GACTTTTCTATGAATTGCACTCTGAATTACAACTT[A/G]TCACAAAATTGTATTTTAATAATATTATAATATCA R 2 1 2 1 101000 f 74 goat snp30817-scaffold340-918098 6 14469982 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410448 Affx-122952387 AX-123280798 6 12654988 AATCATTGTAATAAACTGCTATTTGATGAACCTAC[A/G]TCACTTTTGATCTGATACAAACAGTTCAGCTCCTG R 2 1 2 1 101000 f 74 goat snp30816-scaffold340-879844 6 14508198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785109 Affx-122929634 AX-385272155 6 12710384 ATAGGTTTCTGTCTGTCCTCTAATTATAGACTGCT[A/G]TCAACTGGTATTTAATTTTTCCAGTGTGCTTCTCT R 2 1 2 1 201000 r 74 goat snp30815-scaffold340-824448 6 14563391 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392679 Affx-122966422 AX-123263036 6 12759842 AATGTGATCAGAACTATTGAGCAGAAATATAGATA[C/T]CCAAGCCTTTTCCATAATCTGAGACATACTGATAA Y 2 1 2 1 101000 f 74 goat snp30814-scaffold340-774990 6 14613402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446165 Affx-122925747 AX-123316501 6 12795147 CCCCCACAAAAAAGAAACCTATATGACCCTGAAAA[G/T]CCTTCTGAATCGTTTGAGTAAAGTAAAATTTTGTT K 2 1 2 1 101000 f 74 goat snp30813-scaffold340-739685 6 14648765 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409685 Affx-122953062 AX-123280036 6 12845505 AACTGACTTATTTCTTTTGATAAGGAAGACAATTG[A/C]GAAAAAGTGTTTTTGACTTAGCTACTCATACATAC M 2 1 2 1 101000 r 74 goat snp30812-scaffold340-689327 6 14699890 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790962 Affx-122935453 AX-385277959 6 12878262 CGGAGTCACTCACGTCTTTCAGTAACTAGTGGCAG[C/T]ACTGGTGATGAAAATTCACCCACCATGGGACTATG Y 2 1 2 1 101000 r 74 goat snp30811-scaffold340-656570 6 14732934 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779755 Affx-122925275 AX-385266855 6 12933674 GAGAAGCTCATCAGTGTGAAAGCCTGATCACCTTC[A/G]TGTAAAATGTGATCCTCTATGTCTGGTGAAAATAT R 2 1 2 1 101000 f 74 goat snp30810-scaffold340-601158 6 14788563 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780195 Affx-122969089 AX-385267291 6 12973831 GGATATGATTTGTGTAAATATTTCACCATTTTATA[C/T]GGCCAATCTTAATTTCTTGTAGCACATATTTTTCC Y 2 1 2 1 303000 f 74 goat snp30809-scaffold340-561001 6 14828734 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272246 Affx-1111833494 AX-519545989 6 13015198 CCGTAGGATGGCACAGGTGATGCAGACAGTCTTCC[A/G]TAAATGTAATTCCCTCCATAAAACTTCCGTATGAG R 2 1 2 1 101000 r 74 goat 6_13015198_AF-PAKI 6 13015198 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38400290 Affx-122960081 AX-123270645 6 13045662 AATTATTCTGATCTTGAAAATTAAGGATGAGAATC[A/G]TGTTTTGTTTGTTGTTGAATCCTAGCACTTACTTT R 2 1 2 1 201000 f 74 goat snp30808-scaffold340-489170 6 14900689 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380834 Affx-122975067 AX-123251192 6 13085229 ATCTTAGCAGTTCTTTGTGCGTCTGTGGTGTCTCC[C/T]GAGTGCCTGGTATCCTGCAGGCATTCTATTCATAA Y 2 1 2 1 201000 f 74 goat snp30807-scaffold340-449603 6 14938224 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408024 Affx-122954299 AX-123278375 6 13135455 ATTAATGAAATGCATAGATAAAATAAAGATGAGTG[C/T]ACTTCTAGGTTCCCTGTGCAAGATCGCAGAATTAT Y 2 1 2 1 101000 r 74 goat snp30806-scaffold340-399377 6 14988387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277621 Affx-1111835941 AX-519551120 6 13150743 AGTTGTCAGAGACCTGGCTTGCAAACAGATCTGGA[A/G]TTCTCTTGAATCCGAAGGAAACTGATGAATAAAGG R 2 1 2 1 101000 r 74 goat Random2.2K-649 6 13150743 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781236 Affx-122930389 AX-385268321 6 13173300 TAATTGGTCTGAGAGAGTGTGGACCCAGAAATATC[A/G]TTCCATGAATCTGTGACACTGTCTTAATGAACTGA R 2 1 2 1 101000 f 74 goat snp30805-scaffold340-361532 6 15026429 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392910 Affx-122965720 AX-123263267 6 13254220 AAGTACTAAATATTAAATGAGAAATTATTACATCA[C/T]AGTCACTTATAATTTTTACACAAAGTAGTTTTGAA Y 2 1 2 1 101000 r 74 goat snp30803-scaffold340-280612 6 15107279 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436081 Affx-122932690 AX-123306420 6 13284643 TTGGCTGTTCTAAATTTTCTCCCAGTCCAGGTCTT[A/G]TTTCCAAATTTATTCAGGAGGTCTGATCCTACCTC R 2 1 2 1 101000 r 74 goat snp30802-scaffold340-250189 6 15137588 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388759 Affx-122968945 AX-123259117 6 13375737 CTATGGAGGATACAGGAAAAGAAACATTCTCCAAA[C/T]GAGTAGTAGTATTCTCTGTAAAGGGGTAGTCCAAA Y 2 1 2 1 101000 f 74 goat snp30800-scaffold340-159095 6 15228960 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780172 Affx-122925725 AX-385267269 6 13404668 GAGCATGAGACATTTTAAGGGATGATGGTGGTAGT[A/G]TCATTTCAATGTAATTTCTAAAATGTTTCGTTTCC R 2 1 2 1 201000 r 74 goat snp30799-scaffold340-130164 6 15258535 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407414 Affx-122955237 AX-123277765 6 13454831 CTTCTCTTTTTTTCCTGTGTGTTTATAATTTGGAA[C/T]CGTTTAAGGTAGCATTTCTCAGAGTATGGAATACA Y 2 1 2 1 101000 r 74 goat snp30798-scaffold340-80001 6 15308985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387751 Affx-122969730 AX-123258109 6 13492644 TGGACCTTATTTTCATAAGAAGCAAAAGCTGTAAG[C/T]CATTGGAAGAAGGACAGCAGTCCTTCTCAGCCCTT Y 2 1 2 1 101000 f 74 goat snp30797-scaffold340-42188 6 15347345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378370 Affx-122976817 AX-123248729 6 13523916 ATAATTTGTGGTGCTACATTCCTTCTGGCTTTATA[C/T]GAACAACTTCTGAAATTATAATGGAAAGTGGTTGA Y 2 1 2 1 201000 f 74 goat snp30796-scaffold340-10916 6 15379583 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398383 Affx-122961651 AX-123268738 6 13563202 CAGTGATCTCTCCCAGTCCCGAGGCATTGAATACC[A/G]TCTATAAACTGATGACTCTCCAAAGTATGTTTCTA R 2 1 2 1 101000 r 74 goat snp40297-scaffold5140-28271 6 15418511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453731 Affx-122919622 AX-123324064 6 13592048 ATTATTATTACTTATATGTTTATTTTATTTCCACC[A/G]TACTTTTCCTGATTTCTACTCACCCTGCTTTTTCT R 2 1 2 1 101000 r 74 goat snp40298-scaffold5140-57117 6 15448067 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796871 Affx-122923760 AX-385283814 6 13604730 TGGATCAGTTTTTCCATGAATCCTGGTCTTAAATT[C/T]GGAATCTTAAAACAGATGTAGAGACTTGCAGAAAA Y 2 1 2 1 201000 f 74 goat snp18671-scaffold1887-1655 6 15460688 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764606 Affx-122942632 AX-385252249 6 13644975 AAAATCCAGGAAGAAAGGCATTCTGGCTTGCATCA[C/T]ATAAAATCTGAAAACTCTACAAATACTAAGTAAAG Y 2 1 2 1 101000 f 74 goat snp18672-scaffold1887-41900 6 15501584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417075 Affx-122947503 AX-123287423 6 13699662 TTCTCTCACAAACCTCTCACTAATCCTGGGCTCTG[A/G]CCTTGCTGCAAGGAAACCCCGGAGGGCCTGGCCTT R 2 1 2 1 101000 f 74 goat snp18673-scaffold1887-96587 6 15556296 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426912 Affx-122940448 AX-123297257 6 13752968 TGTCTTCATTTTGAGAACCCTCAGGCCACCTCCTC[C/T]CTTGTCCAAACTGTTCGTGCAGTAACTCAGTTTAT Y 2 1 2 1 101000 r 74 goat snp18674-scaffold1887-149893 6 15609221 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376565 Affx-122979084 AX-123246924 6 13784538 TGTAGGCTCAGCGGAAGTGCTATATCCATTTTTGC[A/G]TACTACCTTCCACAGCAGCAAATCAGTCCCCAATT R 2 1 2 1 101000 f 74 goat snp18675-scaffold1887-181463 6 15640971 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783906 Affx-122919873 AX-385270961 6 13856347 ATATCCATCTCTCCACTTTTCATGTCAAAACTTAC[A/G]CATTTCTTCCAATCTGTCTTCTTTCCAAGCTTTTC R 2 1 2 1 101000 r 74 goat snp18676-scaffold1887-253272 6 15714153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778067 Affx-122931770 AX-385265183 6 13902634 GAATGGTTATTTAGATATTTTCATACCAAATTATT[C/T]GTATTTGTGAACGTATTTAATAAGAAGTTGCATTG Y 2 1 2 1 201000 f 74 goat snp18677-scaffold1887-299559 6 15760232 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772725 Affx-122954571 AX-385259871 6 13956997 AAACATAGGAAAGAATACATTAGAGATTTAAATAC[A/G]TAGTGGCTTGTTTTTGCTACTGTTTAAATGACCAC R 2 1 2 1 101000 r 74 goat snp18678-scaffold1887-353922 6 15814509 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404784 Affx-122956675 AX-123275136 6 13993039 AAGTGCAGTTTCCAAGACCCCAGGCTGCTGAATTC[A/C]TATTTGTAGAACCTAGTAGCCTCCATTTTAACAAC M 2 1 2 1 101000 r 74 goat snp18679-scaffold1887-389964 6 15851910 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407473 Affx-122954772 AX-123277824 6 14024090 CTGGAGCTTGTGAAACGGATGAACTGGTTCATGAA[C/T]GTAAAGAATGCCCTCTTTCTGCTGGTGAGCTGAGG Y 2 1 2 1 102000 r 74 goat snp18680-scaffold1887-421015 6 15882730 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788142 Affx-122965571 AX-385275162 6 14053165 ATTTTCTTACCTTGACTTCATATCCAGTTGTTCTA[A/G]CAAACTTTGACTTTAGATCTAATAATTTTCAATTA R 2 1 2 1 101000 f 74 goat snp17583-scaffold1822-2306 6 15915782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766606 Affx-122947490 AX-385253959 6 14090958 GAAATAAGATGATTTCATGTTGTCCTTTTTAAAGG[C/T]AGGACAGAGTTTAGACAGAAAATTATTATCAAAGT Y 2 1 2 1 101000 f 74 goat snp17584-scaffold1822-40099 6 15954215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395148 Affx-122964123 AX-123265503 6 14127197 GGTGAAGTCTTCACTTAGAAGTATGTTTGTTTTCC[A/G]TAAAATTTAAAATATACATATATGCCCAGAAGGAG R 2 1 2 1 103000 f 74 goat snp17585-scaffold1822-76338 6 15990382 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776241 Affx-122967967 AX-385263369 6 14198094 AAAATTTCTATGGGAGGTGCCTTTCAGATAAGAAC[A/G]TTTACCAATTGTTTGCTCCTTATCTAAGCTAATTA R 2 1 2 1 101000 f 74 goat snp17587-scaffold1822-147235 6 16062071 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799931 Affx-122974735 AX-385286857 6 14250043 TTTCTGAAACGAAATTTCAGGTTTATGGTCACATT[A/G]CTGTCAGTCTCTCTAATAAAAATGCACACTCGTAT R 2 1 2 1 201000 r 74 goat snp17588-scaffold1822-199184 6 16114494 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784108 Affx-122978389 AX-385271160 6 14305053 GGAAAACTCCACCTTGCATCATTTCACTAACACAT[A/G]CTGCAGTTGATATTCCTAACAGATAACATATTAAA R 2 1 2 1 101000 f 74 goat snp52911-scaffold795-18975 6 16169314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393146 Affx-122965546 AX-123263503 6 14338814 TGCGATGCGGAGGACGAGGCACCTTGGAAAGATCC[C/T]GGGGTGGATCCCACAGCATGAGGGGCGGGAGGAGC Y 2 1 2 1 101000 f 74 goat snp52912-scaffold795-52736 6 16202958 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391823 Affx-122967016 AX-123262180 6 14375460 CACTTTTAAAATAAAGTAGAAGTTGGAGGCAAAAA[C/T]AATGATTGTTGCTATTTCTTGAGCACCTATGAAGC Y 2 1 2 1 202000 f 74 goat snp52913-scaffold795-89382 6 16240035 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397347 Affx-122962297 AX-123267702 6 14405683 TACGTTAATTTCTGATGTGTAAACTTTTATATTTT[A/C]GTTACTGATCTTAAGAAAACAGAGTTTCTCCATCA M 2 1 2 1 202000 f 74 goat snp52914-scaffold795-119605 6 16270771 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441436 Affx-122928814 AX-123311773 6 14436373 CTGCAAGGAAAGGATACATGAATGTTCCTTTGGAG[C/T]AAGTAAACCCGTCAGGATTGGGGACAGAGGAATAG Y 2 1 2 1 101000 f 74 goat snp52915-scaffold795-150295 6 16301985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771764 Affx-122951203 AX-385258921 6 14471222 AGAAATTACACACGTAAAGGAACTAGGGCCTTTAT[A/G]TTCTTGCATAGTTTCCTTCTGTGCATAGTTATTTA R 2 1 2 1 101000 f 74 goat snp52916-scaffold795-185144 6 16337058 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442881 Affx-122927659 AX-123313218 6 14513321 ACACATCAGGAATCTGTACAAATGAATTAAAGTCA[C/T]GGAGGTAGTTTTCTGGGGGTAAGATTGGGGTTACT Y 2 1 2 1 303000 f 74 goat snp52917-scaffold795-227243 6 16379349 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391117 Affx-122966804 AX-123261474 6 14557602 CTGTTGGGTGACATCCATTTCCTTGATGTCCTGTA[C/T]GGTCTTGGATGTGATTGTTGAGTGAGTTTTACCTG Y 2 1 2 1 101000 f 74 goat snp52918-scaffold795-271524 6 16423690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776575 Affx-122949900 AX-385263702 6 14594614 CTATGCCACTGAATACCTTTAGCTCATCTTATACG[C/T]TGTAACTAAAAATATGCATACTGTCACACACTCAT Y 2 1 2 1 101000 f 74 goat snp52919-scaffold795-308536 6 16459877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448590 Affx-122923400 AX-123318926 6 14635436 TTGAATTCCCCTCCAGGCAAACCATCCAGGAGCTG[C/T]TGCAGTGGCATATGGCTTGATAGCAGGCAATGTTT Y 2 1 2 1 101000 r 74 goat snp52920-scaffold795-349358 6 16500436 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446741 Affx-122925340 AX-123317077 6 14669593 ATTATTAGCAACCTTGACTTCAATTTGGTAATACG[C/T]ATTCATCTTTTAAAAATGTCGGTCCCTAAGGCTGA Y 2 1 2 1 101000 f 74 goat snp52921-scaffold795-383515 6 16534455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442741 Affx-122927845 AX-123313078 6 14701121 CAATTTGTAAATTGGGGAACATCTCATCTAGTAGA[C/T]AGAAAGGGACTCTGAGGAACTGCACAAAATGGAAA Y 2 1 2 1 201000 f 74 goat snp52922-scaffold795-415043 6 16565611 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386435 Affx-122970798 AX-123256793 6 14731837 GGGTGGCACGTCCCTTCTTCCTATTTGACTACCTT[A/C]TGTCCAAACACTTAGTTGTGTGGCTAAATTCCTAA M 2 1 2 1 101000 f 74 goat snp52923-scaffold795-445759 6 16597354 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428522 Affx-122938753 AX-123298864 6 14772125 ACTGAATTTTAACTATGTAACAACTTCTTTGGGGA[A/G]TTTTCAAGCATATTTAAAAGGAAGAGAAAATAGTG R 2 1 2 1 101000 f 74 goat snp52924-scaffold795-486047 6 16637583 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412845 Affx-122950454 AX-123283194 6 14814363 ATAATGATATGACAGGCATATATCTGTAATTTTTT[A/C]GCCACATATGGTAATCATAAAAGTTGCAGCTGATG M 2 1 2 1 101000 r 74 goat snp52925-scaffold795-528285 6 16680176 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393732 Affx-122965229 AX-123264087 6 14853214 TTTAAAACTGTCACATATATGCTTATGAAGACTGC[A/G]TATTCTTTCTTTTTCCAAAGGAAGTATGCAATTTC R 2 1 2 1 303000 r 74 goat snp52926-scaffold795-567136 6 16718907 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407726 Affx-122955001 AX-123278077 6 14893863 CTATTTGTATAGATATTCCACTAAATAACCTACTA[C/T]GCCCCTTAAATAAATGTAAAAATCATTTCACTTGA Y 2 1 2 1 101000 f 74 goat snp52927-scaffold795-607785 6 16759520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795349 Affx-122933248 AX-385282305 6 14938062 ACTATTCTTTCTACCCTAAGTAACAACTCTGGTTT[A/G]CTCGGTGACTATCATACAGTAGAGATTTCTGTAAT R 2 1 2 1 101000 f 74 goat snp52928-scaffold795-651984 6 16803224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464424506 Affx-1110475942 AX-515897336 6 14978606 GGGATCAACCTCTGGGGCAGTCACTGCAGATGCTT[C/T]AGTACTGAGAGTCTGGGCTAACACAGGACTCAGTA Y 2 1 2 1 202000 r 74 goat GoatD01.012043 6 14978606 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320788782 Affx-122961739 AX-385275797 6 15013908 AAACAGTATAATGCTTGGCACGTGATAAACATGCC[A/G]CAAATGATTACTTTTCCACCTGTGTCCGAGTAGTG R 2 1 2 1 101000 r 74 goat snp52930-scaffold795-727830 6 16880306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393445 Affx-122965856 AX-123263801 6 15059911 ACTCTGTCCTTGGCTTTAGAGAAATGAACCTGTAG[C/T]CTTTGACCCCCTACAGGTAGGCACTGCCAGACTAC Y 2 1 2 1 101000 f 74 goat snp52931-scaffold795-773833 6 16927196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425499 Affx-122941479 AX-123295845 6 15124236 GAGGAAAGCATTTTATTTATCACTATTATTGCTGC[G/T]AAGTTGCTTCAGTCGTTTCCGACTCTGTGCGACCC K 2 1 2 1 101000 f 74 goat snp52933-scaffold795-838158 6 16991272 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602979 Affx-1002479330 AX-413837225 6 15156394 TTCGTCCATGAACTGCATGAAAGGCCCGCTGCACT[G/T]GGAGCATCGAGCAGCAGGGACCAAGCTGTTGGCTG K 2 1 2 1 202000 f 74 goat UniBern-var1 6 15156394 T G 2 neutral Goat_IGGC_65K_v2 candidate gene ou candidate region PITX2 PITX2-variant SNP in PITX2 gene multi-breed 350602981 Affx-1002479331 AX-413837227 6 15156423 TGCACTTGGAGCATCGAGCAGCAGGGACCAAGCTG[G/T]TGGCTGCCTCCTCGTCCTCCTCCTGTCACCATCCT K 2 1 2 1 202000 f 74 goat UniBern-var2 6 15156423 T G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles PITX2 PITX2-variant SNP in PITX2 gene multi-breed 350603093 Affx-1002479332 AX-413837291 6 15156447 GGACCAAGCTGTTGGCTGCCTCCTCGTCCTCCTCC[C/T]GTCACCATCCTCAGCCGCTGGCCATGGCTTCGGTC Y 2 1 2 1 202000 r 74 goat UniBern-var3 6 15156447 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles PITX2 PITX2-variant SNP in PITX2 gene multi-breed 320801596 Affx-122975172 AX-385288505 6 15162737 TTAAAAAATAAATCTCAGTAGGAGAACTCAGAAGC[A/G]TTTTGGAACACAAATTGGAAGCTACTTATTAAACA R 2 1 2 1 101000 f 74 goat snp52934-scaffold795-876659 6 17029945 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412064 Affx-122951707 AX-123282414 6 15216748 CTGAAGATGATCAAGGGATTGAAGGAAATACTCCC[A/G]CATTCACTACTGCTATAGCAAGCTCCCACTGCTGT R 2 1 2 1 101000 r 74 goat snp52935-scaffold795-930670 6 17083708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796056 Affx-122971452 AX-385283008 6 15263557 GGCTAATCTGGTTATTTTGAAAGTCTGAATTTTCT[C/T]ATAAGATTTCTTAAAGACAGCACAACTGTTGTTTA Y 2 1 2 1 101000 r 74 goat snp52936-scaffold795-977479 6 17130760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445385 Affx-122925400 AX-123315722 6 15305231 AGGGAGAATGTCTATGACCATCCCAAAGACGAAGG[A/G]AGTTAAAAAACATGTTCTGAGCACAGATGACAACG R 2 1 2 1 101000 f 74 goat snp52937-scaffold795-1019153 6 17172602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439875 Affx-122930046 AX-123310212 6 15368104 CCTCACTTCCAAGGACATGCTAATCACTCTGCAGA[C/T]GTTTAGCCTCCTGAACTCCGACAATGGAAACTGCG Y 2 1 2 1 101000 r 74 goat snp52938-scaffold795-1082026 6 17235578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776079 Affx-122972037 AX-385263209 6 15449693 ACCCACAAGGCCAATGAAAAATCTGAATTTAAGTA[C/T]AGTCATCGGGAAGCGGCTCTTCTGTAGACACATGA Y 2 1 2 1 101000 f 74 goat snp52940-scaffold795-1163615 6 17316787 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772286 Affx-122938234 AX-385259441 6 15490196 AAGGTACATGACTATCTCAGGTCACAGTACATCGC[A/G]TTAGGACCAGAATCTAAGTGACCAAGACAGGTGGC R 2 1 2 1 101000 r 74 goat snp52941-scaffold795-1204118 6 17357273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426068 Affx-122941090 AX-123296414 6 15548252 GAAGCAACTTAGCAGCAGCAGCAGGATGCTTTCTG[C/T]AACTTCAGCTATCACTGCCGTCACTGGCACTCAGA Y 2 1 2 1 101000 r 74 goat snp52942-scaffold795-1262174 6 17415336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768017 Affx-122943350 AX-385255231 6 15586763 CAAGTGTCAGTCTCAAAGACAGCTATAATCATCCT[A/G]TTAGCAACTGTCTAGGCAGTAGACACATGGCTGCG R 2 1 2 1 101000 f 74 goat snp52943-scaffold795-1300685 6 17453875 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785309 Affx-122949963 AX-385272354 6 15626125 GAAAATTGGAATTTTTCTCATTGAAATTGCATTTT[A/G]CTATAATTCCATTGAAGTTTTAGAAATGCTTCAGT R 2 1 2 1 101000 f 74 goat snp52944-scaffold795-1340047 6 17493059 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272336 Affx-1111833495 AX-519546068 6 15642402 CTCAGGGGAGTGAACCTGGATGCGCTGCAGGGTTG[A/G]CAGTAGAGCTCAGCCTTCTTCCTCTGGCTTCTGTG R 2 1 2 1 202000 f 74 goat 6_15642402_AF-PAKI 6 15642402 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38408731 Affx-122953412 AX-123279082 6 15701965 GCTGGGATGATTACTATAATGGTCACAAGAAATGA[C/T]AGAGACATTAAAGTACTTAGAACAGAAAAAAAGTG Y 2 1 2 1 101000 f 74 goat snp52946-scaffold795-1415887 6 17567697 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422285 Affx-122943487 AX-123292631 6 15738674 ATGAATTTTCCCAAATGATATTCAGGCCTTTCTTG[C/T]CAGAAAAGGGAATACTTTCTGCTTCATCCATCCTA Y 2 1 2 1 101000 f 74 goat snp52947-scaffold795-1452596 6 17605017 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423700 Affx-122942890 AX-123294046 6 15810347 GGAACAGATGAATTCTTTTCTTTACCCAGCTTCAA[C/T]AGGACAGACACTATCAGACAAAGGGAGAGATATTA Y 2 1 2 1 201000 f 74 goat snp52949-scaffold795-1524269 6 17669579 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776589 Affx-122978726 AX-385263716 6 15865931 TGCTTTCTGTATGAAGGTATTCAGACATGTAATAT[A/C]TACTATATCAGTCATCATCTTTACAACTTTCTAGT M 2 1 2 1 101000 f 74 goat snp52950-scaffold795-1579853 6 17724808 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392213 Affx-122966275 AX-123262570 6 15965178 TTTATAATCTTGACGCTAAGCCCAGATCCGGGAAC[A/G]CAGTAGATATTTAGAACACAGTAGACATTTGTTAA R 2 1 2 1 201000 r 74 goat snp52952-scaffold795-1679100 6 17824226 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420972 Affx-122944578 AX-123291319 6 16016156 GCTCTGTTAATGCAGGACACCCACAGGCAGCTTCT[A/G]GAGAGGGGCTACCGGCGCCCTGTCCTTCTCCTTCA R 2 1 2 1 101000 f 74 goat snp52953-scaffold795-1730078 6 17875056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407996 Affx-122954319 AX-123278347 6 16055561 GCTTAAGCTGTTCACCCAGTCAGTTCACCTTTGAC[A/G]CCACACTGAGTAACAAGAGGGGACCACGTAGTTAT R 2 1 2 1 101000 f 74 goat snp52954-scaffold795-1769483 6 17914871 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419364 Affx-122945630 AX-123289712 6 16151131 AACCCCAAACATATTTATTCTTTCTCACCAGGTCA[C/T]GGTGACTTTGTTTTATTCATTGAGGGTGAGAAAAA Y 2 1 2 1 101000 f 74 goat snp52956-scaffold795-1865053 6 18010768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430826 Affx-122937445 AX-123301167 6 16193298 CTTTAAGAGAACAGCATAAGAAGAGGGTCATGAGC[A/G]TGAAAATGAGTAAGACAGCTATTAGGTCATTAGGA R 2 1 2 1 101000 f 74 goat snp52957-scaffold795-1907220 6 18054099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392607 Affx-122966048 AX-123262964 6 16230871 TTTATTTTGAAGGAAGTTTTCCTAAAGTCAGAATG[C/T]CTCCTGAACTCTGCCTTCCCAGTAATTAAAAAATG Y 2 1 2 1 101000 r 74 goat snp52958-scaffold795-1944793 6 18091733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800898 Affx-122964834 AX-385287813 6 16291289 CATTTGAATTGAGTGAGTGGTACAAACTTTCAGAC[G/T]ATAGCAGGTATCTTTGTTCATGAGTATAGACTCAG K 2 1 2 1 101000 f 74 goat snp52959-scaffold795-2005211 6 18153848 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443898 Affx-122927057 AX-123314235 6 16361903 AGTGCTATAAAAAAACTTCCCAAACTACAAGAAAA[C/T]GGAGGATGACATGTCCATGCCTCAGGGCTTAACAA Y 2 1 2 1 201000 f 74 goat snp52961-scaffold795-2075825 6 18224216 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424884 Affx-122941323 AX-123295230 6 16398458 ATGATTTGATAATCCTGTCATTAAAAGGAATTATC[A/G]TTGATATTATCACTCCCAATGCACGTAAAGTATGC R 2 1 2 1 101000 r 74 goat snp52962-scaffold795-2112380 6 18260353 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785333 Affx-122927137 AX-385272378 6 16437041 CATATTTCGCCTTTTGGATCTTACTGGAATTTTTT[A/G]TCCAAATATTTTTGGTTTGTGGCTAGTTGAATCAG R 2 1 2 1 101000 r 74 goat snp52963-scaffold795-2150963 6 18298877 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411571 Affx-122951630 AX-123281921 6 16521448 GCATGTCATAGCAAGTTAGGCTAAGCAGGGCAGGG[C/T]GTTTACGACATCTACTATATTGATTTCTGTTACAT Y 2 1 2 1 101000 r 74 goat snp52965-scaffold795-2235370 6 18383693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385173 Affx-122971738 AX-123255531 6 16714746 CCCTGCAGGCTTTCTTCTGCCTGCCCAGCTGACGA[C/T]GTTTTTCTGGCTCCAGAAAACTTCCAAGATTGTTA Y 2 1 2 1 102000 r 74 goat snp52970-scaffold795-2428668 6 18579548 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451244 Affx-122921946 AX-123321577 6 16747718 GTCCTTGTTAGAATAATGCAGCTTCAAAGGTCCCC[A/G]CTTACCTCTCCAGTTTCCTGCTCAGTTACTATTTA R 2 1 2 1 201000 r 74 goat snp52971-scaffold795-2461640 6 18612548 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413095 Affx-122950948 AX-123283444 6 16795691 GAAAAGTAAAGCCACAGATTGGGAGAAAATATTTG[C/T]AAAACACATATGCAACGAAGAGATTGAATCCAAAA Y 2 1 2 1 303000 r 74 goat snp52972-scaffold795-2509613 6 18661580 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391163 Affx-122967443 AX-123261520 6 16898004 GAAAGAGAGTTGGAATCTCATAGATATTTACCTCC[A/G]GAGTGTTATGCATGTGTGCTCAGATGTGTCCAACT R 2 1 2 1 201000 f 74 goat snp52974-scaffold795-2611926 6 18764181 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383504 Affx-122972646 AX-123253862 6 16931847 GACGGGTGGATTCTTTACCACTGAGCCACCTGGGA[C/T]ACTCCTTTCCTCTTTGCATCTGAATAATTTCCTCC Y 2 1 2 1 101000 r 74 goat snp49773-scaffold710-2455417 6 18811896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441214 Affx-122929522 AX-123311551 6 16971547 AGTAATAGTAGCTCTTTTTGCTTTTGTCTTGCACT[A/G]TTGGTTAACTCATGAAGCCAAGTCTAAACAACTAT R 2 1 2 1 101000 r 74 goat snp49772-scaffold710-2415717 6 18852009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403698 Affx-122958044 AX-123274050 6 17043213 TTCTCACAACTCTGGGCTCTGAGGGGTTACGAGGA[C/T]GTAGGTTTCCAAAAAAGCATACTTTTAGCAGGGGA Y 2 1 2 1 101000 r 74 goat snp49770-scaffold710-2344051 6 18923158 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414457 Affx-122949571 AX-123284806 6 17108455 GCTGTGAACCTGCTGCACTCTTGCTGTCATATTGG[C/T]GAGAGCATATTTTGTACCCCCCTCTCTAGAGTTCA Y 2 1 2 1 201000 r 74 goat snp49769-scaffold710-2278809 6 18989323 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798230 Affx-122950977 AX-385285165 6 17138984 CATCCAGATTGCCTGTGTTACCATGTCTCCCTTTT[C/T]TCATACACCGATGCAACCCCAGTCAACAGGATTTA Y 2 1 2 1 101000 f 74 goat snp49768-scaffold710-2248280 6 19020032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772886 Affx-122968659 AX-385260031 6 17198078 GAATATCTAGCATTACTTTAACCAATTCTCCTACC[A/G]TCTCTCTTTTAACAAAGGAATATGTTGATGTTTAG R 2 1 2 1 101000 f 74 goat snp49767-scaffold710-2189186 6 19083602 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403569 Affx-122957583 AX-123273922 6 17232625 ACAGTCTACTATGGAGGGGAAAGCTATTGAACTAG[C/T]ATAATAATTCTTTATAACTTTTTCTATGGTTTGTC Y 2 1 2 1 101000 f 74 goat snp49766-scaffold710-2154639 6 19118319 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389024 Affx-122968634 AX-123259382 6 17286854 AAAGATTAACCCCCAACATATAATAGCAGCAATAA[C/T]AACAATAGTGATAACAACTGTACTTTGTGGCTATG Y 2 1 2 1 101000 r 74 goat snp49765-scaffold710-2100410 6 19172415 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438241 Affx-122931430 AX-123308579 6 17331182 GCCCAAATAATAAACAGGATTTCACCTGTTCATCT[G/T]TACAATGTCAGTGCAAAATCCTGCAGGATATGAGA K 2 1 2 1 101000 r 74 goat snp49764-scaffold710-2056082 6 19216857 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784341 Affx-122949329 AX-385271392 6 17404152 TAAAGCTAAGATTATATCCAAGGACATTATAATTC[C/T]TTACAGTGAATAAGGAAAAGCTCTCCTCAAGGGTG Y 2 1 2 1 101000 r 74 goat snp49763-scaffold710-1983112 6 19289823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410830 Affx-122952631 AX-123281180 6 17459324 AAAAAAGGAATTATGGATACCTACTGAAAATACTC[A/G]TGTTAAGAATCCTTTGCCTTTTGCTCATTATAGAG R 2 1 2 1 101000 f 74 goat snp49762-scaffold710-1927940 6 19345046 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793349 Affx-122955753 AX-385280327 6 17529643 ACAAGGGAAAAAAGGAAACCCAGTAATACTTTAAA[A/G]CATGCTGTTGTGCTAAGTCATCATTGTTGCTAAAC R 2 1 2 1 103000 r 74 goat snp49761-scaffold710-1857621 6 19413771 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779187 Affx-122925779 AX-385266291 6 17562497 AAGTAACTTACCTACAAACTGGAACTCAACTTGCT[A/G]CAAATTAGAGATTTCAGCAAATGTGCTGAAGTTCT R 2 1 2 1 101000 f 74 goat snp49760-scaffold710-1824767 6 19446810 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375763 Affx-122978598 AX-123246122 6 17607424 ATGGGTTACAGTCAACAAACACTTTTCCATTTATT[A/G]TCTCATTTGGCCTCATTGGATAACATACAATTCCC R 2 1 2 1 101000 r 74 goat snp49759-scaffold710-1779840 6 19490953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412542 Affx-122951336 AX-123282891 6 17668475 CCAAGTAGCTCTACAATTGTGAGCAAAATCTTAGC[A/G]TTGCAATTAATAATAGGAAAGTAATTCCTGTTCTG R 2 1 2 1 101000 f 74 goat snp49758-scaffold710-1718789 6 19551628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406877 Affx-122955642 AX-123277228 6 17703937 ATATAAAACGCACACCTAGAGTTTGATTTTACTTT[A/G]CTAGTTCTAAACCTCATTTCCTCCTACCGTCCCCC R 2 1 2 1 101000 r 74 goat snp49757-scaffold710-1683327 6 19587633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425028 Affx-122941875 AX-123295374 6 17751202 TTCTCCATGTAATACGTTTGTGTATGTTTATCATG[C/T]GTCTCTGTAGAATTTAAGCTCCAAGCAGTCTGTTT Y 2 1 2 1 101000 f 74 goat snp49756-scaffold710-1636062 6 19635606 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390448 Affx-122967622 AX-123260805 6 17792438 CCAAAGACTCAAATGCCAGTGTTAGTTTCTTTGCC[A/G]CTTGATGGCTCCATTTAATAGCAGCATTTGTGACT R 2 1 2 1 101000 r 74 goat snp49755-scaffold710-1594826 6 19677127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771203 Affx-122945491 AX-385258361 6 17873200 ACGTTTTGTTCTTTTTCTGCCTAGGTAATTATCTG[C/T]AGGAAACTTTCTGGAAAGCTGGTAGAATTTCCACT Y 2 1 2 1 101000 r 74 goat snp49753-scaffold710-1514064 6 19757890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785758 Affx-122977009 AX-385272798 6 17946415 TTCAGTTATTAGCCAGTACCAAACTGATTATACAT[A/G]CCATATTCCATAAAACAGGTGTGTGTTCACACAGA R 2 1 2 1 101000 r 74 goat snp49752-scaffold710-1440849 6 19831079 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790564 Affx-122966800 AX-385277567 6 18002158 TTTGATCATCAAATTAGAAGCTTAAATTACATTTC[C/T]ACATTGAGGTCAGGGCAGTAATATCCAACTGTGGG Y 2 1 2 1 101000 r 74 goat snp49751-scaffold710-1385106 6 19887362 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438147 Affx-122931469 AX-123308485 6 18031353 ACTTCCTCTCAGCCATCTACCCACTTCAGTTATTC[A/G]TGTATCTAGGGTACACAGTTTTTAGCAAAGGAACC R 2 1 2 1 101000 r 74 goat snp49750-scaffold710-1355911 6 19916905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275283 Affx-1111834701 AX-519548858 6 18059400 GACTGCCAGTATTCACAAGGCTGAGACAGTGCAGC[A/G]CCCACAACAGTGTGCTTCATAAGACCACACAACAG R 2 1 2 1 202000 r 74 goat GoatD01.046794 6 18059400 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38381002 Affx-122974666 AX-123251360 6 18078211 ATCTCCTTTCATGGCGTTCCATCCATTCTGGCTTA[C/T]ACTTCTACCCCATCACTGAAGCTGCTTTTGAAAAG Y 2 1 2 1 101000 f 74 goat snp49749-scaffold710-1309053 6 19963419 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428022 Affx-122939147 AX-123298365 6 18115742 ATATCATTAGTCATCAGGAAAATGCAAATGAAACC[A/G]CAATTAAATACCATTACAATGTTCAGTAAATGGTC R 2 1 2 1 303000 r 74 goat snp49748-scaffold710-1271522 6 20001871 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433552 Affx-122934989 AX-123303893 6 18150523 AGCCTTCAGTGACGAAGCCCAGGATCCGGTCACAC[A/G]GGACCTTGCAACAGTAAGAGCAGAACCTGGCATGA R 2 1 2 1 101000 r 74 goat snp49747-scaffold710-1236741 6 20036705 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272252 Affx-1111833497 AX-519545994 6 18150704 TCTTCTGAAACAATCCACTTCTCTCTTAACCTGTT[A/G]CCACTACCATGGTCTATGTATATGTAGTTTCCTCT R 2 1 2 1 101000 r 74 goat 6_18150704_AF-PAKI 6 18150704 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449110 Affx-122923582 AX-123319445 6 18192066 ACTGGGCAGCCACGAGTTACTGTTCAAAATTAATG[A/G]AGCAATAAACATATTTTGAAGTGTAATACCTAGAG R 2 1 2 1 101000 f 74 goat snp49746-scaffold710-1195198 6 20078195 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415756 Affx-122948933 AX-123286105 6 18223823 CTCAAAACCTTTCAATGGTTCCATCTTACTCAGAA[C/T]AAGAAATGAAATTCTTAAAATAATCATTACAGGGT Y 2 1 2 1 101000 f 74 goat snp49745-scaffold710-1163441 6 20110012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398988 Affx-122960954 AX-123269343 6 18279840 CAAAAATAAAAACTTTTTTTCCTTGAATATAAGAG[A/C]TAACACATTTACTGTAGAAAGTTAAACGACATAGA M 2 1 2 1 101000 r 74 goat snp49744-scaffold710-1107424 6 20167260 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417003 Affx-122947983 AX-123287351 6 18313417 CTGGAGATTCAAATGTGGGAATCATCAGCATGAGA[C/T]GATGTTAAAACCACTAGACTAGATAAAATCGCCTA Y 2 1 2 1 101000 f 74 goat snp49743-scaffold710-1073847 6 20201001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415839 Affx-122948873 AX-123286188 6 18352201 TGAGATGTGATGATTTAATGTTACTATAATAAGGG[C/T]ATTCAAGTAACTAAAACATACTCAGATTTTAATAT Y 2 1 2 1 101000 f 74 goat snp49742-scaffold710-1035063 6 20239572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439280 Affx-122930978 AX-123309617 6 18384358 GGAGACACAGTCTGCTGTTGAAAGTAGGTTTTGCA[C/T]AGATTGACTGTTTTTCTTAAAAATTTTAGCTTTAA Y 2 1 2 1 101000 f 74 goat snp49741-scaffold710-1002906 6 20271800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796926 Affx-122968573 AX-385283868 6 18412881 TCCTATTAGAATACAAAGGTCACAATGATATGATA[C/T]GCACAACTGACATTGATATGAAAAACTGTGAATTT Y 2 1 2 1 101000 r 74 goat snp49740-scaffold710-974383 6 20300362 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443087 Affx-122928114 AX-123313424 6 18444762 GAAGGTGAGTTTTATACATGGAAATATAAAATGCA[C/T]CATGCCTATAAAAATAATGTATATAATTTCTTAAA Y 2 1 2 1 303000 r 74 goat snp49739-scaffold710-942502 6 20331587 T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771964 Affx-122961834 AX-385259120 6 18487124 CATTTCTCCTGGCTCAGAAACTTGTTGCGCAATGA[C/T]ATTTAATCATCTCCAACAAACATATATTTGTGAGG Y 2 1 2 1 101000 f 74 goat snp49738-scaffold710-900140 6 20373960 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447270 Affx-122924940 AX-123317606 6 18519376 TTGACATGGTGTTCCTGGGAATGACACAGATGGCC[A/G]TCTGCCTAGAGAAAAAAATCAAGGGCTGGTGAGCA R 2 1 2 1 101000 f 74 goat snp49737-scaffold710-867888 6 20405778 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794595 Affx-122962241 AX-385281557 6 18563565 AATATGTTTATAAAATGATTGACAAATCCTGACTA[C/T]ATTCCAAGGACACAAAGATGAGGAAGATGTGATCC Y 2 1 2 1 101000 r 74 goat snp49736-scaffold710-823699 6 20451972 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394889 Affx-122964744 AX-123265244 6 18609494 GTTTTCTAGACAATATAGCAAGCACCATTCTATGA[A/G]TTCAGCATTTCCTCAGCTCCCCGCTCCCACTCCTT R 2 1 2 1 101000 f 74 goat snp49735-scaffold710-777770 6 20498822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775071 Affx-122969837 AX-385262203 6 18638933 GAAAAACTGAAACCCTACTTATGTAAGCCTCTACT[A/G]CTTGCAATTTTTGATACTTGCAGCCAAAGCAGCCT R 2 1 2 1 101000 f 74 goat snp49734-scaffold710-748331 6 20528183 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396287 Affx-122963100 AX-123266642 6 18668608 ATTGATCCTTATGATTGTTAGAAACCTTCTATTTT[A/G]TCATGCTTTAAAAATTATATCTGAATCAGCATCTT R 2 1 2 1 201000 f 74 goat snp49733-scaffold710-718656 6 20558094 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433951 Affx-122934278 AX-123304292 6 18702260 CTCAATATTTTTAAAATCTGCCCAGTTTACATTTT[A/G]CTTAAAGTACTGCTAACCTTGAAACTAAATTGAAA R 2 1 2 1 101000 r 74 goat snp49732-scaffold710-685004 6 20590027 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402261 Affx-122959123 AX-123272614 6 18769652 AGGTGTGCAGAGCCTTTGAACCATAATACATAGCT[A/G]ATATGTAGAGAAGAAATAAAAGGAAGGGAGAAAAA R 2 1 2 1 101000 f 74 goat snp49730-scaffold710-617612 6 20657521 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798964 Affx-122921038 AX-385285894 6 18856555 CATCATTTCATTAATCCTCATTCAGGGAAGGGGGC[A/G]TTATGTACAAAATCTCAACAGGAAAGGGAAGAGAA R 2 1 2 1 101000 f 74 goat snp49729-scaffold710-530709 6 20745509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781363 Affx-122969887 AX-385268448 6 18900142 TCGAAAATTAAACTATAATCACATACTCCCATTTA[C/T]AGGTTTTACTTATTTTCACATGGTTATTCAGTATG Y 2 1 2 1 201000 r 74 goat snp49728-scaffold710-487122 6 20789804 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453094 Affx-122920037 AX-123323427 6 18954537 CACTTTTCTGTAAGAATGTCATTTCTCTCCTTTTC[A/G]TCTTCAGATTTCTCCTTTAATTGGTTTGGTAGACA R 2 1 2 1 201000 r 74 goat snp49727-scaffold710-432727 6 20844275 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451458 Affx-122921149 AX-123321791 6 18988897 ATACAGTTTTACATCAAGTAACACAAGCTTTGGCC[A/G]TTTTCCAAATTTATACTTTCTTTCCATAGGTACTG R 2 1 2 1 101000 f 74 goat snp49726-scaffold710-398367 6 20878915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429319 Affx-122938594 AX-123299661 6 19033479 CACTGTGATTGGTGCACCAACAGCAACAAGCAGTG[A/G]ACATTAGAACTTTATGGTGCCAACTTCTTTCTAGC R 2 1 2 1 101000 r 74 goat snp49725-scaffold710-353785 6 20923847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774826 Affx-122969146 AX-385261960 6 19066422 CTAATTTACAGTGGTTTCCTAGTCATCAAATCCTG[C/T]GGACCTGTCTCAGATCTCATCAGTCTCTCTGGCAT Y 2 1 2 1 202000 r 74 goat snp49724-scaffold710-320842 6 20956884 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416598 Affx-122947642 AX-123286946 6 19110806 TTTAGAATTGTTCTTTGCAAAACTTAATTTGGTCT[A/C]GGCCATTTCTTATTTTTTCACTCCTCGTTATATAA M 2 1 2 1 101000 f 74 goat snp49723-scaffold710-276458 6 21002010 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768815 Affx-122922240 AX-385255992 6 19145196 TGGAACCATATAAATGATTTCCAAGATATAATACT[A/G]TGTTCTACATTTCTTGTAGTTTATGAAGCAGCAAA R 2 1 2 1 201000 r 74 goat snp49722-scaffold710-242068 6 21036346 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785025 Affx-122931497 AX-385272072 6 19180571 GTCTGATTCTCCAACTTTACTGTTTTTAAGTATTA[C/T]ATTCATCCATGGCAGAGGCTGCTGTATGTTTATTA Y 2 1 2 1 201000 f 74 goat snp49721-scaffold710-206693 6 21071971 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400483 Affx-122961293 AX-123270838 6 19211445 CACAGTTAAGCTGCTCTGCTCTACACTCAAATAGC[C/T]GTCCACAACTGCTGAAAATTGATTTATCCCCAGAT Y 2 1 2 1 101000 f 74 goat snp49720-scaffold710-175819 6 21102981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422320 Affx-122943465 AX-123292666 6 19268603 AACTGCATCCACACAAGGTAAGTATTTTGAAGTTG[C/T]GCTAATTATTTTTGTTTTTAATATACTGTTCCTGT Y 2 1 2 1 101000 f 74 goat snp49719-scaffold710-118661 6 21160026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416956 Affx-122948021 AX-123287304 6 19375398 CCAGATACAACTCCAATTTTTAAAGATAGAGTTCA[C/T]AATTTTTATTCAACTTATCCCTTAAATGCAATAGC Y 2 1 2 1 201000 r 74 goat snp49717-scaffold710-11866 6 21267109 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375622 Affx-122978708 AX-123245981 6 19439848 CACCAAACAACTGAAAAATTAAAGCTCAGTAGGGA[A/C]TAAAAATAGAAAAACATTAATGATATCAGCAGAAG M 2 1 2 1 102000 f 74 goat snp42243-scaffold553-586410 6 21360351 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445075 Affx-122926215 AX-123315412 6 19571776 TTTACTATTAGGACTGCAGGTTCTATGAACTTTTG[C/T]GTACAAGTTTTCCTGTGGATGTATTTTCAAAGGTA Y 2 1 2 1 101000 f 74 goat snp42241-scaffold553-454482 6 21492259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400845 Affx-122959784 AX-123271200 6 19625267 TCAAGCAAGTATTGGACTTTTTGTTTTTGTCTCTC[A/G]GAGTGTTATTTTTATAGATTATACTCCACTAAATG R 2 1 2 1 201000 r 74 goat snp42240-scaffold553-400991 6 21545111 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382362 Affx-122973867 AX-123252720 6 19666966 TTCAAGGCAGGGATAGGTAACTGTTCCACACAAAA[C/T]GAGAAGACAGAACAATGTTTCAAATGAAAGAACAG Y 2 1 2 1 101000 f 74 goat snp42239-scaffold553-359292 6 21588071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439698 Affx-122930569 AX-123310035 6 19696217 GTACAGAAAGAAAACTTTAAGCCTATTAACTTTAT[A/G]ATGGAGGAGAAGAGGGAAACAAAGCCAGCATCAGT R 2 1 2 1 303000 f 74 goat snp42238-scaffold553-330041 6 21617396 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792237 Affx-122929969 AX-385279221 6 19729867 CCACATTCATTCCTTGTAACAAAATATCATATTCA[A/C]AAAATTTTAGTTTTTGTCCCCTTTTCATATAAAAT M 2 1 2 1 202000 r 74 goat snp42237-scaffold553-296391 6 21651093 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789953 Affx-122967347 AX-385276959 6 19763188 CTATGTTGAATACAATTAAATTAACACTTGAAACT[G/T]AAAAACCAAGCTGTTGTGGTAAGCTTGAGATAAAA K 2 1 2 1 101000 r 74 goat snp42236-scaffold553-263070 6 21683723 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379110 Affx-122976753 AX-123249469 6 19799432 TATCTTGAAGGTGTGCATACTTTGTTTTTTTGAAA[C/T]GGCATAAATCTGGAATATTTGAGATTATTCTTTTC Y 2 1 2 1 101000 f 74 goat snp42235-scaffold553-226826 6 21720480 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449293 Affx-122923014 AX-123319628 6 19828038 CGTTACTGGCCAGAAAACATGAGTGAAAGAAAAAA[C/T]ATAGTAGTTCAATTCCCAATGTATATTTTTTTGTT Y 2 1 2 1 101000 f 74 goat snp42234-scaffold553-198220 6 21746391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382252 Affx-122973949 AX-123252610 6 19871886 CCTCAATTTTTGCTGTTACCATATCACTGTACATT[A/G]CAATATTGGTATTTTCAATGACATCTCGGTAGTAT R 2 1 2 1 101000 f 74 goat snp42233-scaffold553-154372 6 21793053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442455 Affx-122927952 AX-123312792 6 19905684 CAGATGCTTAATATTTTGAGTAATCAGAGTGTTTA[C/T]GTGTTAGAATACTGAATCACCATGGCAACCTAACT Y 2 1 2 1 201000 f 74 goat snp42232-scaffold553-120574 6 21827301 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413922 Affx-122949817 AX-123284271 6 19994814 TAGTGCTAGATCTTTAAATACTCATGGCCTGCCAA[A/G]TTTTGATATATAACTGGTTCTAACTTGAGGAGGAT R 2 1 2 1 201000 r 74 goat snp42230-scaffold553-31444 6 21919284 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433960 Affx-122934269 AX-123304301 6 20043700 TTGTAAACCACATTAAGGGATTTGAACTTTGAATT[G/T]TGCTAAAAACAAGGAAAAGCCTTGTATAGAACGTA K 2 1 2 1 201000 r 74 goat snp34149-scaffold4002-17343 6 21968147 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375738 Affx-122978619 AX-123246097 6 20136449 AATGCAGAGGTTGAAATGTTTTAGTGACAGAGCAG[G/T]AACTACTTCTCAGAACTATTTGCAGCAGTTTTTCA K 2 1 2 1 101000 f 74 goat snp34151-scaffold4002-110092 6 22061563 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416271 Affx-122947952 AX-123286620 6 20221291 GGAGCCATTGGGAGTAAAGTAAATTTCTCAAAAAA[G/T]ACAGTGATAAGAAAAAAGGCATAAGGCAGAATCCC K 2 1 2 1 201000 f 74 goat snp46532-scaffold645-27823 6 22146662 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436476 Affx-122932974 AX-123306814 6 20274837 GTTCCCATTCTACTATCATGCTGTTGTCACCCTAC[A/G]CTTTTGTTATTTTTAATGGGAAAATATTTCTAAAA R 2 1 2 1 101000 f 74 goat snp46533-scaffold645-81369 6 22200997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431695 Affx-122936776 AX-123302036 6 20306887 CTTATTCTTCTATGGTTATATCTTTATATTTGCCC[A/G]TGGTTTTGTTTGCCTTTTTTTTTTTTGGCCCATTT R 2 1 2 1 101000 f 74 goat snp46534-scaffold645-113419 6 22233365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379917 Affx-122975753 AX-123250275 6 20438646 ATTCAGAACTGCAGATATGGAGGGCTGACTTTGAG[C/T]ATCAGTAGATTTTGGTCCTGGATTTTGGTCTTGGT Y 2 1 2 1 201000 r 74 goat snp46537-scaffold645-245178 6 22364493 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787191 Affx-122962933 AX-385274217 6 20498961 AAACAGAAGTTTAGGAAGAAGATAATAGAAAAGTT[A/C]TCCTTAACTTTTGGGGCACTAAACTGTTATAGTCA M 2 1 2 1 102000 r 74 goat snp46538-scaffold645-305493 6 22426963 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442360 Affx-122928027 AX-123312697 6 20537176 ATACAGAAAATCCTTGTTGCTTATCTGTTTTATGT[A/G]TAATAATGTGTATCAGTTAATCCCACATCCTGCTT R 2 1 2 1 103000 r 74 goat snp46539-scaffold645-343708 6 22465380 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778130 Affx-122938442 AX-385265245 6 20574224 ATAAATATAAATAGAGCATCAGGAATATAATTTCT[A/G]CTCTCCACAGGAAATAATATTTTGGGGGAAAGAAG R 2 1 2 1 102000 r 74 goat snp46540-scaffold645-380756 6 22502168 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403400 Affx-122957769 AX-123273753 6 20624381 AGCAGCAGAGAGAAGCCAAATGACAGTGTCAGCTC[C/T]GAATCCAGTGGGCTTTGAAGCTAGCTAGCTTTTCC Y 2 1 2 1 101000 r 74 goat snp46541-scaffold645-430913 6 22552318 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774478 Affx-122971958 AX-385261614 6 20673371 TCTGAAATTCACTAGAACAATAATTTATTAAAAAG[C/T]ACCCCGTATGGGTCAGAATAAAAGCTGGTTGTAAG Y 2 1 2 1 303000 f 74 goat snp46542-scaffold645-479903 6 22600590 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272339 Affx-1111833498 AX-519546071 6 20695624 TTTGCAACACAATATAGTTGTACAACTTTTTCATC[A/G]TCCCCACAAATCTCCTAGTGCCCATTTTGGCCAAT R 2 1 2 1 201000 f 74 goat 6_20695624_AF-PAKI 6 20695624 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389243 Affx-122969038 AX-123259601 6 20748728 TACTTCATCTGTTTAAAATTAAATTTCAAGCCCCA[C/T]AAATTGGATACAAAACCATAGCATGATAAACTCTT Y 2 1 2 1 101000 r 74 goat snp46543-scaffold645-555260 6 22675562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779020 Affx-122929069 AX-385266127 6 20777997 GGGAAAAAAGCCCTCAAATAGTGTAACTGAGTGTA[C/T]GATCTGAATATATAAACAGGCAATTAAAATATAGC Y 2 1 2 1 101000 f 74 goat snp46544-scaffold645-584529 6 22705189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781048 Affx-122929929 AX-385268135 6 20810439 GCCGCTAAGGTGAGAGTTTGAACTCTAACACAGTT[A/G]TGAAGAGAGGGCTAGTAAACTTTCCCCCTTAATGA R 2 1 2 1 101000 f 74 goat snp46545-scaffold645-616971 6 22737729 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391177 Affx-122967433 AX-123261534 6 20854750 AATACAGGGATTCTTACTAAACTGACTTAGCATGA[G/T]CCCTGCTACAACTGGACTCTGTACACTGGGGCAAA K 2 1 2 1 201000 r 74 goat snp46546-scaffold645-661282 6 22781684 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778289 Affx-122962193 AX-385265404 6 20886101 TCTTAGTCTGTTTAGACTTGCTATAGCAAATACCA[C/T]GCACTGAATAGGTTATAACCAGCCAAAATCTATTT Y 2 1 2 1 101000 f 74 goat snp46547-scaffold645-692633 6 22812845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762425 Affx-986696956 AX-385250571 6 20905116 CTCAAGTCCCAGGAAATGCTAAGTACTTCTCAGTC[A/T]TGGATCTTAAAGATGCCTTCTTTTGCATTCCTCTC W 4 1 2 1 600010 f 74 goat 6_20905116 6 20905116 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 320764663 Affx-986696958 AX-385252298 6 20906937 CTCAAGCCTATTCTCTACCATCCCCAGCTGGCTAA[A/G]GTTGTTAGACAGGTCACACAGAATTGTGATACCTG R 2 1 2 1 600010 r 74 goat 6_20906937 6 20906937 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 38421255 Affx-122944757 AX-123291602 6 20924241 CTCAGATTAGATTTTAAAATGATGATTGTTAGGCA[A/G]GAGAATCAAATAACTGTATCTCCATGGAAACATAG R 2 1 2 1 101000 r 74 goat snp46548-scaffold645-730773 6 22851841 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414348 Affx-122950023 AX-123284697 6 20957981 TTTCTCTTTTGGTTTTCAGAACATTTTTAAAAGAT[A/G]TAAATTCAAGATATGAGTCTTCTTTTGACTCTATG R 2 1 2 1 103000 r 74 goat snp46549-scaffold645-764513 6 22885652 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395084 Affx-122964176 AX-123265439 6 20998285 GAGCACACTGAAGGAAATATCCCAAGGGCACCCAG[C/T]GATAAACATCAGAGCTAGGATTCATATTGAGACCT Y 2 1 2 1 101000 r 74 goat snp46550-scaffold645-804817 6 22926326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450142 Affx-122922750 AX-123320477 6 21065820 GAAAGCTTTATACATTTTAAGCATAAAATGCATAA[C/T]GTTTATAGGAGACAACTAGAAAATTCATGTTATAG Y 2 1 2 1 101000 r 74 goat snp46551-scaffold645-872352 6 22994317 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383150 Affx-122973240 AX-123253508 6 21098116 CTTTGACTAATAGTCTATTTTCTAGAGAATGTGAA[C/T]AGGAGAAAATTATGGAGTTAATCCAAAAAACCTAG Y 2 1 2 1 101000 f 74 goat snp46552-scaffold645-904648 6 23026678 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394027 Affx-122965004 AX-123264382 6 21144389 TATCTTACACTGACATGAAGTTGTTGTTTCAAAGA[C/T]TGTGTGAGTTTCTTTTCTCCTTCAGAGACTAACAT Y 2 1 2 1 201000 f 74 goat snp46553-scaffold645-950921 6 23072803 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781471 Affx-122959325 AX-385268556 6 21181931 ACACAGCAGTGAGAAGTGCTGCCTTGGGAAATAAG[C/T]ACCTTTCTTATTAAAGTATAGATTTAACAACATTT Y 2 1 2 1 101000 f 74 goat snp46554-scaffold645-988463 6 23110465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775650 Affx-122950241 AX-385262781 6 21224685 AGATCTAGGTAAAATCCTATTTCCTTCAGGAAACA[C/T]AGCTTGAAAAATAATGTAGCTTTTCTTTAAAATTC Y 2 1 2 1 101000 f 74 goat snp46555-scaffold645-1031217 6 23153401 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433278 Affx-122935217 AX-123303619 6 21257572 AGTTTCTGTGTATTGTTTTAAACTGTATTCAGTGC[C/T]GAGGAATGAACAGGAAGGCGCTAATCTCAGAGGTT Y 2 1 2 1 101000 f 74 goat snp46556-scaffold645-1064104 6 23186553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771178 Affx-122966769 AX-385258338 6 21290469 TTTTTAAAATTCTACATGGCAAAATGCGTATACTG[C/T]GCTTCTGCTACCTACTCAAGTTTAGTAATCATCTC Y 2 1 2 1 101000 r 74 goat snp46557-scaffold645-1097001 6 23220147 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409322 Affx-122953084 AX-123279673 6 21327560 TCATCACCCAGGCTCCCAAGCCCACTCCAATGGAA[C/T]ACCAGAAGGGGAAGGACAGGAACGATAGGGTTATT Y 2 1 2 1 303000 f 74 goat snp46558-scaffold645-1134092 6 23258180 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413235 Affx-122950243 AX-123283584 6 21399397 CAGGATCATAGAATAGCCTAATCGGTTGCACCCCT[A/G]AACAGGGCCACAGACTGGCCATAAATGAGTCTCCT R 2 1 2 1 202000 r 74 goat snp46560-scaffold645-1205929 NW_017213563.1 6258 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440815 Affx-122929821 AX-123311152 6 21429594 GTTAGTCAGTATTTATAGAAAGGTTTTTGTCTCTA[G/T]ATCATGAAGGGGCTATAAGGCAGGAACTGCAATGT K 2 1 2 1 201000 f 74 goat snp46561-scaffold645-1236126 6 23361905 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399872 Affx-122960228 AX-123270227 6 21487719 CATGTCATACCTCATATTTATAAAATGTTAAAAGT[A/C]TCACAATATCAAGGGTTGGCAAAAATATAGACTAA M 2 1 2 1 201000 r 74 goat snp30519-scaffold337-29243 6 23417569 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798196 Affx-122934648 AX-385285131 6 21529605 CAATTGGACATATTTAAAAAAGTCCAGTCAGAGAT[A/G]CTTCTCAAAATTAGACAGAAGGAACAATGCACAAC R 2 1 2 1 202000 r 74 goat snp30520-scaffold337-71129 6 23459796 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768829 Affx-122958132 AX-385256006 6 21564361 GGGAAGTACTAAAGAGAAAGGCTTAGGAGTATAAA[C/T]AGAGTTACAGGGTTTACAAGTGTAAATAGGTTTGA Y 2 1 2 1 101000 r 74 goat snp30521-scaffold337-105885 6 23494025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394412 Affx-122964609 AX-123264767 6 21593545 TCAAAATGGACAGATTCCTTAACTAAACAGTTACC[A/G]CAAAACTGGTGTTTCAAGAAAACAAACTGATAACT R 2 1 2 1 101000 f 74 goat snp30522-scaffold337-135069 6 23521611 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379474 Affx-122976482 AX-123249832 6 21644035 CACAAACGTGAACATTTTCATATGAATAACACCTG[A/G]ATAGACATTGGAAATAGTCAAACTACCACCTACTG R 2 1 2 1 101000 f 74 goat snp30523-scaffold337-185559 6 23572583 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781134 Affx-122955245 AX-385268219 6 21806238 TGATCTTTGAACATTAATAAAGTGAATGGCCAGTC[A/G]TCCAATCCAACAGCTAAAAATCATTCATGAATGTT R 2 1 2 1 101000 f 74 goat snp30526-scaffold337-347762 6 23735925 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403693 Affx-122958048 AX-123274045 6 21837736 TCCCGGTCATCTGCCCCCTGCCTCTCTCTGCTCCT[A/G]CCCCTTCAGTACCTCCTGAAGCATCTTTGTTGCCT R 2 1 2 1 101000 r 74 goat snp30527-scaffold337-379260 6 23767528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393983 Affx-122965038 AX-123264338 6 21881015 TCTCTTGTTTTCCTGTGTGACCTTGGTGTGTCCCT[A/G]TAGGTGTGCTGTTGGGTCTCCTCCGTTTGCCTGGG R 2 1 2 1 201000 r 74 goat snp30528-scaffold337-422539 6 23810865 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789296 Affx-122977490 AX-385276307 6 21913344 AGAATTCCCATGTAATATGGGCTCCATAATTTAAA[G/T]ATAGGTTATTTTATGTCTACGAGGGAGAATGAAAA K 2 1 2 1 201000 f 74 goat snp30529-scaffold337-454868 6 23843624 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441446 Affx-122928771 AX-123311783 6 21996682 GGCTTGTGATCAAATAATTTTTGAAAACACTTCCT[A/G]CAGCACAAAACCTTGTACAGACTTTGCATTGTTCA R 2 1 2 1 101000 r 74 goat snp30531-scaffold337-538206 6 23927977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436010 Affx-122933491 AX-123306349 6 22080615 CAGAGTTGTTATAAGTCCAAGGTTTGTAAAACAGT[A/C]TCTCTATAATTGTTTGATCTCAAGTGGCATGTTTA M 2 1 2 1 101000 f 74 goat snp30533-scaffold337-622139 6 24011885 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408980 Affx-122953907 AX-123279331 6 22126042 GGAAAAAGAAAATGAGGAAGCTGCTAGCCAGTCCT[A/G]TCCCTGAGGATCATTTGGCTTTATTTTGATCCACA R 2 1 2 1 101000 f 74 goat snp30534-scaffold337-667566 6 24057337 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383764 Affx-122972434 AX-123254122 6 22160699 ACCACCAGAAATGGGCTGAGCATCCTCTGAGCAAG[C/T]GTATTTTGGAATCTTCATTGTATCTCAGCTTTACC Y 2 1 2 1 101000 r 74 goat snp30535-scaffold337-702223 6 24090592 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791217 Affx-122924498 AX-385278211 6 22199744 TCCAGATACAACTCAAAAACTCAGTAAGATGTACT[A/G]AAGAGCAATTTTATAGGCTCTGGACATCAGCAACA R 2 1 2 1 101000 r 74 goat snp30536-scaffold337-741268 6 24130107 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786662 Affx-122933702 AX-385273694 6 22235092 CTAAACTTTGAGTAGCAGGAATTGGGGGACTTTTA[A/G]TCTCATATAAGGCCATGAGCTTCTTACACAAAATG R 2 1 2 1 201000 r 74 goat snp30537-scaffold337-776616 6 24165778 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273667 Affx-1111833760 AX-519547280 6 22254481 CACGGAGAGACACTGCAGACAGACATGAAGATAAG[A/C]TCAGGGGGCCGCCAAGTCCCAAGATGCGGCCTCAC M 2 1 2 1 101000 f 74 goat GoatD01.003754 6 22254481 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320768352 Affx-122979051 AX-385255532 6 22294690 CTCGCTCATGTTACGCCCTGGGTCAACTTGATGGC[C/T]TATTTTGTCTTCGTGCTGAAACCCAGGATGAAAGA Y 2 1 2 1 201000 r 74 goat snp30538-scaffold337-836214 6 24225528 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384140 Affx-122972809 AX-123254498 6 22339433 AGCTTTTCTGAGAAAAGCAATGGTGAGCTTGGTCT[A/G]TTTAAACCATTTTCTCCCTTTTAAAATGCTACTTA R 2 1 2 1 101000 f 74 goat snp30539-scaffold337-880957 6 24270361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400212 Affx-122960174 AX-123270567 6 22370829 AATATTCCCTGCCCTCATGGAGCTTTAAGAAAGAC[A/G]TAAAACCTAAAGAGCACTCAAGATATTTTAGTACC R 2 1 2 1 201000 r 74 goat snp30540-scaffold337-912353 6 24302281 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419664 Affx-122945947 AX-123290012 6 22393820 CCAGGGCAAAGCAACTGATGAGACATCTAGCTAAA[C/T]GATCCAGGGCCAAGTGTGAGGGCCAGGGTCAGAGC Y 2 1 2 1 103000 f 74 goat snp38133-scaffold476-899162 6 24326176 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395094 Affx-122964167 AX-123265449 6 22472014 CCTCAGTATTTGTTTTTATAGATAAATAGATTCAG[C/T]AATCAAACTTCTTTGCTGTGGCTTTTCCAATCATT Y 2 1 2 1 201000 f 74 goat snp38131-scaffold476-820968 6 24404951 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799317 Affx-122923998 AX-385286247 6 22505773 TATTTGTTGGAAGATCTGTGAATTTGCAGCTGAGA[C/T]GTTCTCCCAGGCAGCGTTTAACTTTGAAGGGTCAC Y 2 1 2 1 101000 f 74 goat snp38130-scaffold476-787209 6 24439041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440310 Affx-122930212 AX-123310647 6 22534569 ATTTGCTGCAAATTACTATTAGCTGATACTAGGTC[A/G]TCTACCTATCCCTATCATCTCCTCTGCTACAGTTT R 2 1 2 1 101000 r 74 goat snp38129-scaffold476-758413 6 24467883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409475 Affx-122954062 AX-123279826 6 22578745 GATGAATTAGAGTATTCTTTATTTGTGGGTACATA[C/T]GGACATCCTTATAATAAAAATTTTAAAAAAGAAAA Y 2 1 2 1 101000 f 74 goat snp38128-scaffold476-714237 6 24512457 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444942 Affx-122926691 AX-123315279 6 22657235 TGATTTTGTTAGATTACTACCGCATGTCATCTGGA[C/T]ATCACTTCATTGGGACAGGTGACTGGCAAGCAGGA Y 2 1 2 1 101000 f 74 goat snp38126-scaffold476-635747 6 24590099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444943 Affx-122926691 AX-123315280 6 22657235 TGATTTTGTTAGATTACTACCGCATGTCATCTGGA[C/T]ATCACTTCATTGGGACAGGTGACTGGCAAGCAGGA Y 2 1 2 1 600000 r 74 goat snp38126-scaffold476-635747 6 22657235 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790870 Affx-122972158 AX-385277868 6 22703219 AGAATATGTACTATGATAATCATGTTACAAAATCA[C/T]GAATATAGAAAAGATAGAAAGACTACAAAATATAC Y 2 1 2 1 201000 r 74 goat snp38125-scaffold476-589763 6 24636644 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796969 Affx-122954872 AX-385283910 6 22777508 CTGTAATTAACTTATGTCTTCCTTTTGGAGAAAGC[G/T]AAACTCAAGAAGTCTTTGTAAGATCATCAAAATTT K 2 1 2 1 101000 f 74 goat snp38124-scaffold476-515474 6 24711581 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409846 Affx-122952933 AX-123280197 6 22823578 TATTTAAAAAGAAAGCTACTGTGTCTAGTTTGTTT[G/T]TCTGATTTCCCCCCAAAATAATTATTCTCTTTTCA K 2 1 2 1 102000 r 74 goat snp38123-scaffold476-469404 6 24757650 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389151 Affx-122968539 AX-123259509 6 22873428 TAAGCCAAAGAAATAAATTCTTAGTCTGTTATGAA[C/T]GTATGATGGTGAGTGTAGGCTGGTCTCTTTCCTCT Y 2 1 2 1 101000 r 74 goat snp38122-scaffold476-419554 6 24807268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382823 Affx-122973553 AX-123253181 6 22928411 GGCATTGGCAACCAATAATGACTGAAGACTTGCCC[A/G]TTAATAAAACAAAGTAAAGCAAAACAAAACCCCTT R 2 1 2 1 103000 f 74 goat snp38121-scaffold476-364571 6 24861987 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394627 Affx-122964404 AX-123264982 6 22958415 ATATCAAGTTGGCCCCACACAGCTGTTCTTATTGG[C/T]AGGGACATCAGAGGTAGAAAATCCTGCCTGAATCC Y 2 1 2 1 201000 r 74 goat snp38120-scaffold476-334567 6 24892495 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437580 Affx-122931874 AX-123307918 6 22991430 TATTGTCTAGGTTTCATGACTCATCAGTGGTGGTA[C/T]AGGAGGAAGGTAGAAAATATTTATTGTTACCCAGG Y 2 1 2 1 101000 f 74 goat snp38119-scaffold476-301552 6 24925487 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388455 Affx-122969253 AX-123258813 6 23023108 AAGAAATACCACCTAGCACAGTGTTTTCTCAAACT[A/G]TGGTCTGCCTACAGAGTAATTTCCTTGAGTGTTTG R 2 1 2 1 201000 r 74 goat snp38118-scaffold476-269874 6 24956614 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780666 Affx-122977461 AX-385267756 6 23060812 CGGTCTACCCCTAGAGGGCTTGGAGTGAGACGATA[G/T]TCTTTAATCAAATCATAACCCGTGTCTTTCTGGAG K 2 1 2 1 101000 f 74 goat snp38117-scaffold476-232170 6 24994400 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401005 Affx-122959689 AX-123271358 6 23123714 ATATACAAATGAAAGTTAGTGATTGTACTCGTTTC[A/G]TTCACTTTTCCTAAGCCACTTTATCTTCCTCACAC R 2 1 2 1 101000 r 74 goat snp38116-scaffold476-169268 6 25057312 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797778 Affx-122970439 AX-385284717 6 23164075 AGCAGACATTAGGACACACTGATTTAGAAAACAGA[G/T]AGCTCAGAGACCTATGTAGAAACTCCCTCTGCCTT K 2 1 2 1 101000 r 74 goat snp38115-scaffold476-128907 6 25097753 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433793 Affx-122934467 AX-123304134 6 23208482 TTCATCCTTCCCTTTCCACAGTTGATAGCACATTG[C/T]AATGTAAGCCTTTGTCTGATGGTTTTACTGGTGCT Y 2 1 2 1 201000 r 74 goat snp38114-scaffold476-84500 6 25140318 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38412109 Affx-122951112 AX-123282459 6 23252906 GTGATGAGTCACCCAGCAGAACCTGAGGCAGGGAG[C/T]GGAGCTGTTTACATGAGTTTGGCCACTCACTGAGA Y 2 1 2 1 101000 r 74 goat snp38113-scaffold476-40076 6 25184541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272340 Affx-1111833499 AX-519546072 6 23269461 CAGAGAGGCATACAGTGGCCAAAATGTTAAGCTTT[A/G]GAGTCAGTCTGTCATGGAGTCCAATTGGGCAAATA R 2 1 2 1 101000 f 74 goat 6_23269461_AF-PAKI 6 23269461 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412930 Affx-122951472 AX-123283279 6 23287643 CAATACCAGCATAGGAAAAAAATTTGTAGAAAAAA[G/T]AAATTGGCCTTTTTCAAGTGAGGTCAATTTCCAAC K 2 1 2 1 103000 f 74 goat snp38112-scaffold476-5339 6 25219293 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411711 Affx-122951532 AX-123282061 6 23302356 ACAGCCAACACCTGCCCCAGGGGGCCAGGCAGCAT[A/G]CAGAGCTGTGAGCATGACCTCCGGTTTAAAGAAAT R 2 1 2 1 101000 r 74 goat snp14188-scaffold1567-424418 6 25233462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411704 Affx-122951538 AX-123282054 6 23336625 ACCAAAGAGTTTGCCAAATTTCCCATAAGAGAAGT[A/G]TTTAGCAGGCCAGATTAAACTTTGCCTTGGCACTA R 2 1 2 1 101000 r 74 goat snp14187-scaffold1567-390149 6 25267769 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393640 Affx-122965298 AX-123263995 6 23368884 GTCCTAGTTATTTTCATCAGAAGCCACTTCAGGTT[A/G]CCACAAAACTTGAATTTTAGTATATTCCGACATCA R 2 1 2 1 101000 f 74 goat snp14186-scaffold1567-357890 6 25300005 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772984 Affx-122964379 AX-385260128 6 23407559 AGAGACCTTTAAATGGGTTACTGTAATAGAGTACT[A/G]AGAATAAAGCAACAAGAGTCAGTGGACGTCAATAT R 2 1 2 1 101000 r 74 goat snp14185-scaffold1567-319215 6 25338666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786023 Affx-122922013 AX-385273059 6 23437356 ATATCTGCTCCTCGGTTTGAAAGCAAAGGCAGCCA[C/T]ATTTCAGCTAGAAATGGAAGCTGTTTTCTAGTCAG Y 2 1 2 1 102000 f 74 goat snp14184-scaffold1567-289418 6 25368248 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449328 Affx-122922989 AX-123319663 6 23476329 CCACACACAGAGTCAGCCTCAGGGAGGGAGGAAGC[A/G]CTCTTGAATACAAACTACCAGGCACACCCAGGCTA R 2 1 2 1 101000 r 74 goat snp14183-scaffold1567-250445 6 25408166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391050 Affx-122966857 AX-123261407 6 23504923 TTTTCAAAACCTAATTCAACTTATTTTGTAACAAG[C/T]GCTTTTTAAAAATATTTACATTTGAATCCAAAAAG Y 2 1 2 1 101000 f 74 goat snp14182-scaffold1567-221851 6 25436859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389179 Affx-122969086 AX-123259537 6 23571234 CACTTGCTGATGTAGAGAACACAGTAGTGCATGGA[C/T]GCATACATGCCTGAGTCAGGCAGGAAGGGGGAAGA Y 2 1 2 1 101000 f 74 goat snp14180-scaffold1567-155540 6 25503606 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799260 Affx-122963947 AX-385286190 6 23646279 AAACACTTCATCCCTAAAGGTATGCTAGCTGGAGC[A/G]TACTGACATTTGTCAAGAAATGATATAGAAAGGCT R 2 1 2 1 101000 f 74 goat snp14179-scaffold1567-80495 6 25577999 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440837 Affx-122929266 AX-123311174 6 23755627 TTCCCCCACTGCAGGTTATCAAGTGCAAGGCTGCA[A/G]TTGCCTGGGAGGCTGGGAAGCCTCTTTCTATAGAG R 2 1 2 1 201000 f 74 goat snp34814-scaffold415-28754 6 26016615 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437918 Affx-122931646 AX-123308256 6 23866747 TTGAGGAATTTCTTACCTAAGGAATGATTTCTTCT[A/G]TTTCATATATGACCAGTGTTTACAGATACCTATGA R 2 1 2 1 101000 r 74 goat snp34816-scaffold415-139874 6 26128154 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385607 Affx-122971196 AX-123255965 6 23902087 TGCTGGAACTCAAACCCAGGTTCTGTCTACAAGCT[G/T]TATTACTACACTTAGAAAAAACAAACTAAAATTCA K 2 1 2 1 101000 f 74 goat snp34817-scaffold415-175214 6 26163649 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381609 Affx-122974783 AX-123251967 6 23938613 ACTGACTTCCTTCCTTGCTTGCTTGTAATTTTTGC[A/G]TTCACAGTTTCCCAGTGTAAATTGTAGTCTTATCT R 2 1 2 1 201000 r 74 goat snp34818-scaffold415-211740 6 26200227 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433524 Affx-122935009 AX-123303865 6 23970185 TTGCTGAGCCACTGGGGAAGCCCTATCTCTTTAAA[C/T]ACAGAGAAAAGAACTATCGAGTTTGAAGTATGTTT Y 2 1 2 1 101000 r 74 goat snp34819-scaffold415-243312 6 26232406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414390 Affx-122949992 AX-123284739 6 24028808 TTTGTGCCGCTGTGTCAGTCTTGATTCAATAGAAG[C/T]ATTTCATTCCACAGAGACAGTGGGTAGCAACTGTT Y 2 1 2 1 101000 f 74 goat snp34820-scaffold415-301935 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392756 Affx-122966003 AX-123263113 6 24059620 AAGAATGGAATGTTTTCCTGCTTTCTTGCCTTAGA[C/T]ATCTTTAAGTTGGTATATATCTTGAATTTGAGGAG Y 2 1 2 1 201000 r 74 goat snp34821-scaffold415-332747 6 26312981 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407814 Affx-122954551 AX-123278165 6 24088676 TAGGCCAGACCAGGGACCCTTGCCTGCACTCTTAG[A/C]GTTCCCTGCAGTTTTTCTTTCTACCAAATAGCACA M 2 1 2 1 201000 f 74 goat snp34822-scaffold415-361803 6 26342268 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397763 Affx-122962522 AX-123268118 6 24120521 GCATTGTCCCCTTTGTCCATCCATTCATCCGTTCC[A/G]TCATGATTGTAGTGTATGCAGACCTGCCTTGATTG R 2 1 2 1 201000 r 74 goat snp34823-scaffold415-393648 6 26374279 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432562 Affx-122935534 AX-123302903 6 24153390 TGGACATATTTAAAAGTCAAATTCCTGGGTGAGGC[A/G]TTTTGATTTTATCTGAACTTGAAACTTTCATGACT R 2 1 2 1 201000 r 74 goat snp34824-scaffold415-426517 6 26406992 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418757 Affx-122946204 AX-123289105 6 24206396 ACCTGTTTGTCTTCTTTGGAAAAAATGTCTCTTCA[C/T]GTCTTCATCCTTCTTAATACTAGAGTGACGGAGGG Y 2 1 2 1 101000 r 74 goat snp34825-scaffold415-479523 6 26460006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426916 Affx-122940444 AX-123297261 6 24241996 TTACAAAGTGGAAAATAGCTGTAGCAGAATCCCTG[C/T]AGTAAACACAATAAGGACTTTTTTCCTGTAATATT Y 2 1 2 1 101000 f 74 goat snp34826-scaffold415-515123 6 26496008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388202 Affx-122969421 AX-123258560 6 24293081 AAGGGAGAGGTGGACCCTGGTTCAGATGGGAAATA[G/T]CCTGTTTACAAGTCTGGACTTTATCTGCCATGCCA K 2 1 2 1 101000 r 74 goat snp34827-scaffold415-566208 6 26546758 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419909 Affx-122945335 AX-123290257 6 24398707 GTCCATGTGGCAAATACATTATCATAAGAGTATGC[C/T]AGAGAGATTTCAGGAACCAGAAAAGAGAAATGAAC Y 2 1 2 1 101000 f 74 goat snp34830-scaffold415-671834 6 26653528 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426636 Affx-122939949 AX-123296982 6 24491012 CAGTGGTACAGTTTGTAAAATTGTACTTCACATAA[C/T]GTCAAAAGACCTTTTCACTGAGAGTTCAAGAATTA Y 2 1 2 1 101000 f 74 goat snp34832-scaffold415-764139 6 26746134 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792018 Affx-122971355 AX-385279006 6 24548865 CTCCCAAATTAGAAAGCTCAGAGCCATTCTGCATT[C/T]CTCTCTCTTACCCAATCTATATATAATTGACTTTC Y 2 1 2 1 101000 f 74 goat snp34833-scaffold415-821992 6 26804333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423925 Affx-122942266 AX-123294271 6 24583397 GAGGTTTGAATGACAATATAGATAAGACAGTTAGT[A/G]TGATTCCTCTTGCTCAGTCACCAAGTTGTCTTTGT R 2 1 2 1 303000 f 74 goat snp34834-scaffold415-856524 6 26839243 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788450 Affx-122942994 AX-385275467 6 24710053 TTTTCATCTTTATAGAAGGAAATGGGATGAGACAC[A/G]TTATGACACAGGTACCTACTAAAAGCCTAAAGTCA R 2 1 2 1 101000 f 74 goat snp34837-scaffold415-983180 6 26964833 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779028 Affx-122929138 AX-385266135 6 24752999 CAACTAGACAACTGTTCAGAACAGGAGGCAAGTAG[C/T]AGTAGTCCCTGTTTGTCAGTAGCTAATTATTTTTT Y 2 1 2 1 101000 f 74 goat snp34838-scaffold415-1026126 6 27008185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788090 Affx-122931215 AX-385275110 6 24814748 TCTGTTTTGTATTTTCCCATTCTAACCACCATCCT[A/G]CTGCTTTTTCCCTACACTGGGATCTTTTTCAGTTT R 2 1 2 1 101000 f 74 goat snp34839-scaffold415-1087875 6 27070068 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454219 Affx-122919679 AX-123324552 6 24862427 AATCCATAGAGGCTTGCTTTATTTTTCAGTTTCAC[A/G]AATCAGGTATATTACCAACTTACAGGTCCATTTTA R 2 1 2 1 201000 r 74 goat snp34840-scaffold415-1135554 6 27117745 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432522 Affx-122935562 AX-123302863 6 24903743 CCTGCTGTCCTTACAGGTCCACTGTCTTAGTGTAG[C/T]GGGCAGAGGCTTAGACTGTTTTTACAGGTAGTCCT Y 2 1 2 1 101000 f 74 goat snp34841-scaffold415-1176870 6 27158856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414682 Affx-122949293 AX-123285031 6 25000003 ATTAGCAGAGAAATTGTTACTGAAAACTCTGTCCA[C/T]GTCTGTGATGCTGAATGAGAATGAGGAGGCCAAGT Y 2 1 2 1 201000 f 74 goat snp34843-scaffold415-1273130 6 27257290 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787202 Affx-122944833 AX-385274228 6 25052954 ATTCACATAGCACTTTCCAGAGTTTGTGTGCTTTC[A/G]TTAATCATATTTCACTTATAAAGTATCCTTTTGTC R 2 1 2 1 101000 f 74 goat snp34844-scaffold415-1326081 6 27310294 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380231 Affx-122975473 AX-123250589 6 25087845 AGTTTTTGCCTTCTGAGAGAACCCTGATTTGGATA[C/T]GGATACAAGAAGAGAAAACCAATTTGGCTGCAGTG Y 2 1 2 1 101000 f 74 goat snp34845-scaffold415-1360972 6 27345209 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391438 Affx-122966748 AX-123261795 6 25118173 CCAATATGTGTGTGTGTATGTGCGTGTGTGTGTAC[A/G]TGTGTATGGAACCAATACCAAGGAATGACAGCGTG R 2 1 2 1 201000 r 74 goat snp34846-scaffold415-1391300 6 27375870 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779731 Affx-122973038 AX-385266831 6 25167678 TAAATCATTCCTAGGACATAATAGTTTTTTCTGTT[A/G]GCATTCAACCATTATTTGAAAGTAAAAAGGTTTCT R 2 1 2 1 101000 r 74 goat snp34847-scaffold415-1440805 6 27426069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765162 Affx-122944064 AX-385252713 6 25200092 TGTAGGGGTTGATAGAAGAGGATAAAGTCAGATAT[C/T]CATTTACAAATACTGTAGCTAATTATCTGTAGTTA Y 2 1 2 1 101000 f 74 goat snp34848-scaffold415-1473219 6 27458857 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779193 Affx-122945303 AX-385266297 6 25233743 AATTATTGTATTTATGAATAATATAATTAATACAT[A/G]TTATTCTTTTGTTTGACTACTCATAGCTCAGTCCA R 2 1 2 1 303000 f 74 goat snp34849-scaffold415-1506870 6 27492535 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409790 Affx-122952974 AX-123280141 6 25279461 ATCAGGCTGAGCTATAGAGCCAATCGCTATGAGCC[A/G]GACTATGGGGAAAGACCATCTCTTTTTTGTACAGG R 2 1 2 1 201000 f 74 goat snp34850-scaffold415-1552588 6 27539918 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381369 Affx-122974399 AX-123251727 6 25318673 AAAATATACTTTGGCTTTAAAAATTTCATGACTTA[C/T]GGCTATTTTGTAAATACAACTGCTTTGTACATTGT Y 2 1 2 1 101000 r 74 goat snp34851-scaffold415-1591800 6 27579191 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437325 Affx-122931959 AX-123307663 6 25359030 TTTTCATTATCTGGTTGAAGACTATCCTACGGTAG[C/T]ATGACAATTATTTTGAGCTGAAGACATTAGAGTTC Y 2 1 2 1 101000 f 74 goat snp34852-scaffold415-1632157 6 27612703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432969 Affx-122935274 AX-123303310 6 25395390 TCGCTTGGAAGCTGGGGTGTTTTGAAATAAATCTT[C/T]AGGAGTTTGCTGTTTGAATATCTCAATCACTGCCC Y 2 1 2 1 101000 f 74 goat snp34853-scaffold415-1668517 6 27648984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386335 Affx-122970876 AX-123256693 6 25453429 TGTGAGTTCATAGACAGGGCGAAATAGATTGCTGC[A/G]GCTGTGTCAAATCTGTGCAGAATACAGATTTGCTG R 2 1 2 1 101000 f 74 goat snp34854-scaffold415-1726556 6 27708244 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784489 Affx-122942420 AX-385271538 6 25515545 CAAGTGACTGAATTTTGACAATAATGCAAAGTGTG[A/C]TGCTTACAGAGGTGACCCATAAAAGATTGAGTGTA M 2 1 2 1 101000 f 74 goat snp34856-scaffold415-1788672 6 27770384 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418548 Affx-122946400 AX-123288896 6 25592179 TTGCTATAAAGTGGACTTGAGGCCCAAGTATAGAC[A/G]CTTAGGTATTCCTATCCAGAATTTTGATTTCTGTG R 2 1 2 1 101000 f 74 goat snp34858-scaffold415-1865306 6 27847844 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425330 Affx-122940931 AX-123295676 6 25629079 TGTACAAACTGGCATCTTCTCACCTACTTTGTACT[A/G]CTTTATCCCATCCTCATGCACTTGACTTTTGCTGT R 2 1 2 1 101000 r 74 goat snp34859-scaffold415-1902206 6 27884880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450570 Affx-122922040 AX-123320904 6 25668680 AGAGATATAATATCTTTCAACTGTGACAAATTTGG[C/T]AACAGAAAAATTTAAAGGAAAACAACTCACAGTTT Y 2 1 2 1 103000 f 74 goat snp34860-scaffold415-1941807 6 27924974 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799250 Affx-122972350 AX-385286180 6 25705039 AGTAGGGAATGGAGGCTTGGAAACCTGTACTTACA[C/T]GGATCTGCTGGTTTAAATCACTTCAAACCTCCCCT Y 2 1 2 1 101000 f 74 goat snp34861-scaffold415-1978166 6 27961577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801897 Affx-122958190 AX-385288805 6 25737878 ATACATGAAGTCCACAAAGGCAGGTGTGATACTTG[C/T]TACTCTCAGCAGTGGCACTGTATCTGTTACACAGA Y 2 1 2 1 101000 f 74 goat snp34862-scaffold415-2011005 6 27994435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394958 Affx-122964281 AX-123265313 6 25774149 ATATGAGAGAACTAGGTTTGGTTTGGATATCAGTT[A/G]TAAATGCATTATTTAAAAAACAGCTTAATAATTAA R 2 1 2 1 101000 f 74 goat snp34863-scaffold415-2047276 6 28030977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409261 Affx-122953130 AX-123279612 6 25804972 TTATTTGGGCCTAATGTAATAAATTTTAAGTGACG[C/T]AAGTCAGTCTAAAAATCTTGATCCAATGACACTGC Y 2 1 2 1 101000 r 74 goat snp34864-scaffold415-2078099 6 28062018 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272341 Affx-1111833500 AX-185174181 6 25825036 GGAAAAGACTCTGATGCTGGGAGGGATTGGGGGCA[A/G]GAGGAGAAGGGGACGACAGAGGATGAGATGGCTGG R 2 1 2 1 103000 f 74 goat 6_25825036_AF-PAKI 6 25825036 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38405705 Affx-122956538 AX-123276057 6 25837598 GAAAGCACAGGGACAGAGGGACCCTGAAATCTAGC[A/G]TCATTAAGACCAATCTCTTATTTTTCTCTCATATT R 2 1 2 1 101000 f 74 goat snp21589-scaffold211-12629 6 28095951 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433053 Affx-122935755 AX-123303394 6 25898159 ATAAGATAAAATACATTTTCCAAACACAGGCATAA[C/T]GATGTCACCTGAAAATTCTGGTTAGACATAAGCCA Y 2 1 2 1 101000 r 74 goat snp21590-scaffold211-73190 6 28156599 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452960 Affx-122920166 AX-123323293 6 25935818 CTATACATATAAGAGATATCATCCAAGAACTAAAT[A/C]AAGAAGGAGTTGTCTTAGAGTAATGTGGTCTGTAT M 2 1 2 1 101000 r 74 goat snp21591-scaffold211-110849 6 28194306 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771394 Affx-122939718 AX-385258552 6 25969563 AGCTTTGCATAGGGCAGACACACAAGTATGTGTTC[A/G]TTGAAAGTAACAAACATTGAAAAGTAGTACTTAGA R 2 1 2 1 102000 f 74 goat snp14498-scaffold1580-21386 6 28226848 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442364 Affx-122928024 AX-123312701 6 26003679 GGCTGATAATAAATATTTTCTTCCTTTATAATCAC[A/G]TAAACTTTTGAATATATGTACATACATTTATACAT R 2 1 2 1 103000 f 74 goat snp14499-scaffold1580-55502 6 28261829 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449778 Affx-122922434 AX-123320113 6 26058676 ATTAACATCCTATTTTTCAAAGTGATATGCCCGCT[A/G]TATACAAACATTTTAACTGATCCTACTGAGATACT R 2 1 2 1 201000 r 74 goat snp14500-scaffold1580-110499 6 28317795 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792819 Affx-122950159 AX-385279797 6 26094911 CTTAGATGACCTGTTTCTGGAGGACAGACATGATG[C/T]TTAATAAAATGTAGAACAGACACACAGTTAATCAT Y 2 1 2 1 101000 f 74 goat snp58966-scaffold968-13458 6 28354282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396481 Affx-122963547 AX-123266836 6 26139009 CAATAGATATTGACTTTTTTCAAGGTTCTAGTGGT[A/G]TACTTGTACAAACAAAGCCTTTGCTCTCAAGAAGC R 2 1 2 1 101000 r 74 goat snp58967-scaffold968-57556 6 28396204 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782415 Affx-122919934 AX-385269491 6 26177943 GTCAGATTCCTATTATTACATAATGGAAGAAGTGG[A/G]ATTCCTAGGAACTTTCTTAATGTGGCCAGATATCG R 2 1 2 1 101000 r 74 goat snp58968-scaffold968-96490 6 28441253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772657 Affx-122929443 AX-385259804 6 26215353 TTGAAAAGGCAAAATGGACATTGCCGAGAGTGCCA[C/T]AAGGATGTTGACTGTTTTAGCTCGTTTAACGTGTC Y 2 1 2 1 101000 f 74 goat snp58969-scaffold968-133900 6 28479368 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793445 Affx-122966889 AX-385280422 6 26287037 TTCTTAGTATAAGTTTTCTCCTCCCATACACCTAG[C/T]AATTTTTCTCATCCCATGGGAGATTAACTTGAAAC Y 2 1 2 1 101000 f 74 goat snp58970-scaffold968-205584 6 28551663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778200 Affx-122945282 AX-385265315 6 26331733 AAATATAAATATTAACCTAATTATGGTAAACATTT[A/G]TGAAAATGTCTTTGAGCTCAATATTGTATCTTACC R 2 1 2 1 201000 f 74 goat snp58971-scaffold968-250280 6 28596618 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428978 Affx-122938864 AX-123299320 6 26364955 AGTATACTTTCCCCAAATGTGCTCATGCTAAGAAC[A/G]TGAATAGACATTGTTCCTCCTGGATTTTCTATTCT R 2 1 2 1 202000 r 74 goat snp58972-scaffold968-283502 6 28630370 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409794 Affx-122952971 AX-123280145 6 26419337 TGGTTAATTTTTCTTGGTGTCTTGCTTAACTTGGT[A/G]TCCTGTGACTAACTGCAAACAACCAGACAGACTTT R 2 1 2 1 201000 r 74 goat snp58973-scaffold968-337884 6 28686137 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786582 Affx-122929695 AX-385273614 6 26469670 TGAAACTAAAATCATAGTAGGTTCTTCTGCTGGGC[A/G]TCAGGGACAAGGATGTGGTGTAAAGTATGTGCAGT R 2 1 2 1 101000 r 74 goat snp58974-scaffold968-388217 6 28736494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777885 Affx-122943257 AX-385265001 6 26507871 AAGTGTAAAGTTGATTCAATCTGTTCTTGATACTC[A/G]CCTTCATATTCACTTTTCTGCCCGCATAATCCCAT R 2 1 2 1 101000 r 74 goat snp58975-scaffold968-426418 6 28773976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799613 Affx-122961662 AX-385286543 6 26544694 AACCCTCTGCATCTAAAAAATTGGGTAAAAGCCGT[A/G]CTTAAATCATATAGCTGTTGGGTAAATATAACAAG R 2 1 2 1 101000 f 74 goat snp58976-scaffold968-463241 6 28811120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278338 Affx-1111836370 AX-519551824 6 26559855 GTACTCAGCTTTGAGTGAGACAGTAAATGCGCTGG[A/G]GGGCTTGAAGTAGAGACGCGACAGGATTCTGCCTT R 2 1 2 1 101000 f 74 goat Random2.2K-660 6 26559855 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443081 Affx-122928119 AX-123313418 6 26637729 CACAGTCACACTGACATTCACTGACGCAGTGTTCT[A/G]TAGTTTAGCTACTATGCCTTAGCCACTGTCAGCTT R 2 1 2 1 201000 r 74 goat snp58977-scaffold968-556276 6 28903049 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387878 Affx-122969629 AX-123258236 6 26696231 AAATATAAGAGGCATGGGTCTCCAAATGATTATAT[C/T]GAACAGTTCACTTGAAAACACAGACACACACAGGT Y 2 1 2 1 201000 f 74 goat snp58978-scaffold968-614778 6 28962901 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418460 Affx-122946468 AX-123288808 6 26759285 CTACGCTGCAATCAAGTCTCAATCAGATCCACTCC[A/G]CCCACAAGCTGCTCACTGTTTCTGAAAAAAGAGAA R 2 1 2 1 201000 f 74 goat snp58979-scaffold968-677832 6 29025606 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801176 Affx-122976709 AX-385288088 6 26790439 AATCCTCATAAGATTTCAGGTAGCCTCCAGCTATG[C/T]TGAAACACTTTTCATACCGTTTCAAAGCTTCCATC Y 2 1 2 1 201000 r 74 goat snp58980-scaffold968-708986 6 29056730 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415782 Affx-122948914 AX-123286131 6 26820944 ATCATTAAAAAATAATCTGTAATTTGATTAACATC[A/G]ATAGGTTATTTAAAAAGTAGTGACTTTTTTCTTGT R 2 1 2 1 201000 f 74 goat snp58981-scaffold968-739491 6 29087661 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798782 Affx-122974820 AX-385285713 6 26849679 GCCTCATAAATAGCAGCACTGTGATAGTGTACCAG[C/T]ACTCTTCAGCTTCTAAGTGCATCAGATATAAACTG Y 2 1 2 1 101000 f 74 goat snp58982-scaffold968-768226 6 29117050 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448107 Affx-122924313 AX-123318443 6 26902957 CTGCTCTGTTAAACATCATGTTTTATTTGGAAAAA[C/T]AGTCATTCTAACTGGTTCTAGCATCAATATTAAAT Y 2 1 2 1 201000 r 74 goat snp58983-scaffold968-821504 6 29170732 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428461 Affx-122938800 AX-123298804 6 26936028 CTGCATCAGATACCTAGTATACCTGATATATTTAA[C/T]ATGAACAAACCCAAATTCTTGGTTTCCTACCCTAA Y 2 1 2 1 201000 f 74 goat snp58984-scaffold968-854575 6 29203826 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766857 Affx-122954846 AX-385254178 6 27042661 TCCCTATCACCAGAGACTAGGAGTCAACACTGAAA[C/T]GGATCTATACAGACTCACTAAAATAATACTTATCT Y 2 1 2 1 101000 f 74 goat snp58986-scaffold968-961208 6 29312449 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784195 Affx-122924022 AX-385271246 6 27076659 ATAAGAGAGCATGAATTGCAGAGAGGTAAGGATAA[A/G]GTGGTTGGGTTAGTGCCTCATTATCCTTGCATCTC R 2 1 2 1 101000 r 74 goat snp58987-scaffold968-995206 6 29346523 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795826 Affx-122923435 AX-385282779 6 27107543 GATCACAGAAGGAGAGACAGTTTTAAGAGCAACAG[C/T]AATAGAGTCACGTCTGGACATGCTGAGTCTCAAGT Y 2 1 2 1 101000 r 74 goat snp58988-scaffold968-1026090 6 29377452 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772098 Affx-122973888 AX-385259253 6 27147319 AGGGCCGAAAATTGTTAGGAATGAAGTACTTCAAA[G/T]CAATATGTTTCCAATTTCCTAAAGGCACCTTCTTC K 2 1 2 1 201000 r 74 goat snp58989-scaffold968-1065866 6 29417869 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377414 Affx-122977556 AX-123247773 6 27205314 TAAAATTATTTGAGGGGGAAAGAGTTGTTACTACT[G/T]AAAGAATATAAAAAATTTAATTCTGCATAGAGGGA K 2 1 2 1 101000 f 74 goat snp58990-scaffold968-1123861 6 29475856 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376201 Affx-122978814 AX-123246560 6 27250020 TGGTGGGCTATAGTCCATGGGATCACAAAGAGTTG[A/G]ACACAACTGACTGGACATATGCACCCACTCTTGTC R 2 1 2 1 303000 r 74 goat snp58991-scaffold968-1168567 6 29520557 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780236 Affx-122951983 AX-385267331 6 27337276 TGAGAAGTAAGTTTGCTTTGAACTTTCTGATTCTT[A/G]TTTTAGATGAAATATCAAATAATAGATAGGCTTCT R 2 1 2 1 102000 f 74 goat snp58993-scaffold968-1255823 6 29607878 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443490 Affx-122927808 AX-123313827 6 27388755 AAGTATTTTTAGTGTATATTACTCTAATCTATGTT[A/G]TTCTCCATGTCAGTTCTACTACTTAATACTTGAGG R 2 1 2 1 101000 r 74 goat snp58994-scaffold968-1307302 6 29659340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765182 Affx-122938997 AX-385252731 6 27431574 AGATTAGAGCCAAGGAAAGATTTGGCAGCCTTAAT[A/G]CTTGTGTAGTATTCATATTTGGAATGGAATGCTTT R 2 1 2 1 101000 f 74 goat snp58995-scaffold968-1350121 6 29702490 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794741 Affx-122969223 AX-385281700 6 27487166 TTAAACCTGTCTTTTGAAGTACAGGCCTCTGATGT[A/G]TGGTCACCATTCTCACTTAGGAAACAGTAATTTTC R 2 1 2 1 101000 f 74 goat snp58996-scaffold968-1405713 6 29759230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787424 Affx-122968083 AX-385274449 6 27543511 GTATTTTTTATCTTGTACTCTTCTACATTCTAACT[A/G]CATACTGACTCCCACGTTTAGAAATACACTAAGCA R 2 1 2 1 101000 r 74 goat snp58997-scaffold968-1462058 6 29815950 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787614 Affx-122970445 AX-385274637 6 27590453 CTTAAACCACCTCAAAACTAGTGTGACCTACATTT[C/T]ATGTTTTTAGGACCATGGTCTCTGAAATTAAATTA Y 2 1 2 1 101000 f 74 goat snp58998-scaffold968-1509000 6 29863156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278340 Affx-1111836371 AX-519551826 6 27612120 CACAAGGAAGGGGTGCTTCAGACACAGTGGCAATG[A/G]AGTCAGCAGGGGCAGGGGGAGGGTAATGGCGCCAG R 2 1 2 1 102000 f 74 goat Random2.2K-662 6 27612120 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38385575 Affx-122971841 AX-123255933 6 27619461 GAGAAGTTAGCGCCATTTAAAGAATAGAAACTCCA[C/T]AAAGAATGAAACGGCACTTCACAAAGACCGTTCAC Y 2 1 2 1 101000 f 74 goat snp58999-scaffold968-1538008 6 29892139 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440722 Affx-122929891 AX-123311059 6 27703450 TACAGACCTCACTGAACTGGGAGATGACAGCCTTT[C/T]TATAGCAAAAGCAGCCTGAGCAGTATCAATGCACA Y 2 1 2 1 201000 r 74 goat snp59001-scaffold968-1621997 6 29976369 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431116 Affx-122936599 AX-123301457 6 27748058 CCAAGATTCTGTCTCTTAAGTCCTTCTCTCATTTC[C/T]ATGCACCAAAGGCCCTTTTCTTCCTTTGCTCCAGC Y 2 1 2 1 101000 f 74 goat snp59002-scaffold968-1666605 6 30020914 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801447 Affx-122928263 AX-385288357 6 27800859 CTCCAAGACAGGAGGGGCAAGGTGATCCTAAAATC[A/G]CCCTACCAGAAGGATTTCTGTCAGCTAAAAGGAGA R 2 1 2 1 101000 f 74 goat snp59003-scaffold968-1719406 6 30073666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411682 Affx-122952001 AX-123282032 6 27866327 TTGGCCCCTCAGAATTCAAAACGTAGGGAAAATTG[C/T]AGCAAAACTGACAGCAGAAATGTTGCCAATGGTTA Y 2 1 2 1 101000 f 74 goat snp59004-scaffold968-1784874 6 30139356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772464 Affx-122949116 AX-385259615 6 27897570 AATAGTGACAGAAACTAGACTTTTGCTGATGAGCC[C/T]ACTATAGAGTATACAGGTGTCAAATTATACTGTTG Y 2 1 2 1 101000 f 74 goat snp59005-scaffold968-1816117 6 30170250 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413239 Affx-122950239 AX-123283588 6 28008827 CTTAAAGGTGGCACTGATACACCTTCACCGACACA[C/T]GTACTTCCTTCAAGAGGCAGGTTCTAAGGGAAAAT Y 2 1 2 1 101000 f 74 goat snp59007-scaffold968-1927374 6 30282274 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802228 Affx-122946174 AX-385289132 6 28058251 AAACATCTATAAGTGCATTATATCATAGAAATGCA[C/T]AAAGGAATGAAAACTGTCTAGATTCAAGTCATATC Y 2 1 2 1 102000 r 74 goat snp59008-scaffold968-1976798 6 30332531 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389819 Affx-122968191 AX-123260176 6 28102440 CAGGCACTTCATACAACACAGCGACAAAAACAAAA[C/T]TATCTTGCAACCAGAGTGAAATAGCAGAATTGTGA Y 2 1 2 1 101000 f 74 goat snp59009-scaffold968-2020987 6 30380872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382478 Affx-122974202 AX-123252836 6 28162984 GTAGTCCTTGAAAATGGTACCATGAATACCGCTTT[C/T]GTTATAATCATTTTTAAACATAACGCTGTTTTGAA Y 2 1 2 1 101000 f 74 goat snp59010-scaffold968-2081531 6 30441024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408339 Affx-122953750 AX-123278690 6 28204085 CCGCTTCAGAAAGGGAAATATAATTATAAATCTAA[C/T]GCTTTTGCTAAGGACAAAGAAGCTTGAAGAATTAA Y 2 1 2 1 101000 r 74 goat snp59011-scaffold968-2122632 6 30482438 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402870 Affx-122958232 AX-123273223 6 28263130 AGTTTACAGAGACAATGATGAAAATTAGAAAGAAA[C/T]CACTGATTAGGTACTTACACGGTGCCAGGGTTACT Y 2 1 2 1 201000 f 74 goat snp59013-scaffold968-2181677 6 30541734 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436881 Affx-122933232 AX-123307219 6 28316337 GGAACAAATTCAATGGCAAAAATTCTTACTGTGGT[A/G]TATTTGAAAAAGTAAAATGAACTTTTAGACAACAG R 2 1 2 1 103000 f 74 goat snp59014-scaffold968-2234884 6 30594292 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798205 Affx-122938016 AX-385285140 6 28397609 CATTTTTCAATTTCAACAGACAGTAAATTTAAAAA[G/T]ATGCAACTGTTCCCTACAATCACGGGGGATTTGAT K 2 1 2 1 102000 r 74 goat snp59016-scaffold968-2316156 6 30673494 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476215 Affx-1251763720 AX-586011639 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 4 1 4 1 20000 f 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 539476469 Affx-1251763720 AX-586011869 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20000 r 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 560378495 Affx-1251763720 AX-605230910 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20000 r 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 562165618 Affx-1251763720 AX-606941029 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20100 r 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 562165755 Affx-1251763720 AX-606941164 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20100 r 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 562165991 Affx-1251763720 AX-606941400 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20100 r 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 562166248 Affx-1251763720 AX-606941656 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20100 f 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 562166361 Affx-1251763720 AX-606941769 6 28399620 TTATTCATTATTCTATTTACACATCTTTCTTTGTT[-/CTATCAATCTCCTTTGTTTTTTGTTTTGTTTTTTTTTTGAGAGGAGCTAACACCTATCCTCCTCAAACTCTTCCAGAACA]TATCAATCTCCTTTGAATCTACAGATTACACAGGC - 8 1 4 1 20100 f 74 goat SV_203 6 28399620 - deletion junction SV-TF-chip 38421562 Affx-122943855 AX-123291909 6 28433270 TGGGTATGAAGATATTTGCTAGTGGCTTAAATATG[C/T]AATGTGATTTTTTATTTAGGCCATATTTTTCAGTA Y 2 1 2 1 101000 f 74 goat snp59017-scaffold968-2351817 6 30709494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785938 Affx-122970788 AX-385272975 6 28471829 CAGAGTTCTATGTGCTGTACAGTAGTAAAAATATA[A/C]TGCTTAGTTTGGTGTAAATGATACCATACTATATT M 2 1 2 1 101000 f 74 goat snp59018-scaffold968-2390376 6 30747854 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420749 Affx-122944724 AX-123291096 6 28511349 TATTAGCTAAGTAATGTAAGTATGATTTTTTCCCC[A/G]TATTTCACCATTTAAGGATTATGCTCTCTGTGTGT R 2 1 2 1 101000 r 74 goat snp59019-scaffold968-2429896 6 30788852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431507 Affx-122936238 AX-123301848 6 28554042 GCATGTTATTTACTCTTCATCACACAGTATGCTTC[A/G]CTAAGGCATCACAACTTGTGTCAGCTTTATTTGGG R 2 1 2 1 101000 f 74 goat snp59020-scaffold968-2472589 6 30831884 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389702 Affx-122968689 AX-123260060 6 28596607 TGTTAGTTTAGAATTTAGATCTAAGTAGTGATACA[C/T]TGTCAATGAATGTAAGACATCAGTTTCATTTCTCA Y 2 1 2 1 101000 f 74 goat snp59021-scaffold968-2515154 6 30874462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448550 Affx-122923428 AX-123318886 6 28639865 TAAAAGAGAGATGCTAATAATCACAGGATTAATGT[A/G]CACATAAAATTAGAAGATATATATTAAGAATTTAA R 2 1 2 1 101000 f 74 goat snp59022-scaffold968-2558412 6 30918054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428121 Affx-122939070 AX-123298464 6 28669076 AATGTGACTTCTAGAACTTGAAACCTCTATTAACT[A/G]CTGTTAACAATTTAAGGGATTAAAAATAATGAATA R 2 1 2 1 101000 f 74 goat snp59023-scaffold968-2587623 6 30947311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766687 Affx-122947551 AX-385254031 6 28763035 GGTTCCAGACAGTTTATCATAGCTTTGAGTTTCAG[A/C]TTTCTCTTCCATTGACAATTAAAGCAATGCTTTGC M 2 1 2 1 101000 f 74 goat snp59024-scaffold968-2681582 6 31041030 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464427210 Affx-1110480594 AX-515900025 6 28776552 CCCAGTCAGAGATAATTCTTTCCTATTAAACATCT[C/T]TAAATTTATTTTATAGTATTTATCACAGACTTCCT Y 2 1 2 1 101000 f 74 goat 6_28776552_AF-PAKI 6 28776552 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449433 Affx-122922679 AX-123319768 6 28792431 AGCAGAGGAAAACTATGTCTAATACTACAGATAAT[A/G]CAATCCATCTAGTAGGGGTTTCCATAAAAATCTGA R 2 1 2 1 201000 f 74 goat snp59025-scaffold968-2710978 6 31070854 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797747 Affx-122920175 AX-385284686 6 28830290 TTCTCCGCAAGAACTTTGATTCACTATTAAATTCC[G/T]TCTAATGAAGATGACTTTGCCATCCCACGGCCATC K 2 1 2 1 101000 r 74 goat snp59026-scaffold968-2748837 6 31108765 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413997 Affx-122950277 AX-123284346 6 28844432 TATTCAGGACATTCTGCTGATGCGGACTAGAAATA[G/T]ACTAAGGAATTGAGATTACAAATACCATCCGAAAG K 2 1 2 1 101000 f 74 goat snp12505-scaffold148-5556 6 31122826 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779499 Affx-122927863 AX-385266602 6 28878176 TAAGGGTCTTCATAAACCTCAGTGATTAGTTGCCT[A/G]CCGGAATATACTATGCAAAGGTAATTTATACACAA R 2 1 2 1 101000 f 74 goat snp12506-scaffold148-39300 6 31156496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789866 Affx-122944286 AX-385276873 6 28912296 GTGTTACAAGGTATTTGAGGTGATTTTGGCTCTTC[A/G]TTGATTAAAATGAGATTCCTTTGGTAGAGCTCATA R 2 1 2 1 101000 f 74 goat snp12507-scaffold148-73420 6 31190970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400299 Affx-122960074 AX-123270654 6 28973752 TTAATAAGGTAGATTCCTGGGCCCCTACTAAATCT[A/G]CCAAATCCACTTTTTGAAAGGAACCGAGGACTTGT R 2 1 2 1 101000 r 74 goat snp12508-scaffold148-134876 6 31252563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443676 Affx-122927181 AX-123314013 6 29006880 TTATTTGAATTTTTTAAAAGTGTAATATGTTCCGT[A/G]TTACTCTAATGGGGATAGAAAAATACGGGGCTATG R 2 1 2 1 103000 r 74 goat snp12509-scaffold148-168004 6 31285442 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392247 Affx-122967567 AX-123262604 6 29052799 AAAGACTCAGGAAAAAATTTTGACCGTCCCCATAA[C/T]TGCACCCAAAAATTTAGATCGAAGGTCTGTTTCTG Y 2 1 2 1 201000 r 74 goat snp12510-scaffold148-213923 6 31331006 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431962 Affx-122935961 AX-123302303 6 29101223 AAAAGGGGAGGAAGAGCTCATGTTATATCAAACAG[C/T]GAGCAGTAAAGTTTTTTATTTCTTTATCCAGAATC Y 2 1 2 1 103000 f 74 goat snp12511-scaffold148-262347 6 31383681 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378412 Affx-122976786 AX-123248771 6 29165070 TTCCATGAATGAGAAATAGCTTTTTTCAAGTCATG[A/G]ATACTTTGGGCTGTTTGCTACACAGAAAAGGTGAC R 2 1 2 1 101000 r 74 goat snp12512-scaffold148-326194 6 31448495 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432166 Affx-122936413 AX-123302507 6 29207870 TACAGGAAAGCCTACTGATGTTGCAAGCGATCAGT[A/G]TGGGGTGGCAAAGCCAGAGCCTTGAAAGAAATGTC R 2 1 2 1 201000 f 74 goat snp12513-scaffold148-368994 6 31491328 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417915 Affx-122946729 AX-123288263 6 29237567 CCAATACATTTATGGCTCAGGGCCTCCTTTTCTTC[A/G]CCAACGAAATGCAGGAGTTGCTATTTAATGAACTG R 2 1 2 1 101000 f 74 goat snp12514-scaffold148-398691 6 31521126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431209 Affx-122937160 AX-123301550 6 29276768 CACATTTGAGCCTTGTTGTGTGGAATGTTCACCAA[C/T]AAATGACAAGAGTGAGCTGCCAGCTCTAGTTCTGG Y 2 1 2 1 201000 f 74 goat snp12515-scaffold148-437892 6 31560558 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798433 Affx-122957194 AX-385285367 6 29329297 CTTGAAGATTAAGTATAGCCTCAATGGATGAACTG[C/T]ACATCTTTTTCAAAAGAAGGTTTTCTGGAGGATAA Y 2 1 2 1 101000 r 74 goat snp12516-scaffold148-490421 6 31613602 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802089 Affx-122940165 AX-385288993 6 29368528 TTGTTGACTTGCTCTTTGCTGAGTGGTGAGAGAAA[C/T]AAGTATTTTTATAAAACCCTAAATTGTGAAAGAAA Y 2 1 2 1 101000 f 74 goat snp12517-scaffold148-529652 6 31653471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785664 Affx-122962148 AX-385272705 6 29401236 CTACATAAGAATCAATGGGAAAAATTAGTTTGAAC[A/G]TTTCATTTTCTCATTTCATGCCACTGGCAATGGTT R 2 1 2 1 303000 r 74 goat snp12518-scaffold148-562360 6 31686224 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439617 Affx-122930632 AX-123309954 6 29432519 TTTTCAAAAAGGAATGGATTAGAATTCTTGGTAAT[A/G]ACAGACTATGTGGAAAGAAAAAGAAACCACATGGA R 2 1 2 1 201000 f 74 goat snp12519-scaffold148-593643 6 31715754 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278508 Affx-1111836372 AX-519551990 6 29479803 AATGCAAGTGTCAATTATAAAATACATAACAGTTT[A/G]GGTATCTTAATTTACCTTTTTGCCTATATTATAAC R 2 1 2 1 101000 r 74 goat Random2.2K-663 6 29479803 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429511 Affx-122937854 AX-123299853 6 29482007 AATACATATTTTCATTTTAAATAAAAAATGATTTA[C/T]AAGTCATTACACATTTGGCTCTTTCAAACTCACTA Y 2 1 2 1 103000 r 74 goat snp12520-scaffold148-643131 6 31765153 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788964 Affx-122925776 AX-385275977 6 29569382 TCCCTTCTGTCTAAATCATTTTAATGTTGCCATGC[A/G]TAAGTAACATTGAAGTATCAGGTATCTTCATGGAT R 2 1 2 1 101000 f 74 goat snp12522-scaffold148-730506 6 31851817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777531 Affx-122931359 AX-385264650 6 29604633 GCAAAAAGTTTATTTGTACCCGTTTCTGTCAAAAA[G/T]TTATCTCATATTCCAAGTCAGTATTGTCTCTGTTA K 2 1 2 1 202000 r 74 goat snp12523-scaffold148-765757 6 31887118 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788902 Affx-122928333 AX-385275917 6 29657406 AGTGGTATCATTCTCTGAGTTCAAGGAGAAAAATA[C/T]ATCACTATATGAGGAGGCAAGAAAATCAACTTATT Y 2 1 2 1 101000 f 74 goat snp12524-scaffold148-818530 6 31940001 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278510 Affx-1111836373 AX-519551993 6 29663534 AAAAACCTGCTTACCCAAAGTGTTCCTGAAAACAG[A/G]CAGGCTTTCAATTCACTTATGAAGCTGCTTGCTTT R 2 1 2 1 101000 r 74 goat Random2.2K-664 6 29663534 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415019 Affx-122949026 AX-123285368 6 29706746 GTATAAAATAAGTAGGGGGCATCTGTAAAACAAAG[A/C]GTATGGAGGCTGATAAAGGCACTCTGTGAGGAGAT M 2 1 2 1 101000 r 74 goat snp12525-scaffold148-867870 6 31990015 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377402 Affx-122977564 AX-123247761 6 29757929 CTCAAAACTGTTAAGTAATTTGCAGGCATCACACG[A/G]CCAGAATGTGACTGGCGTGGTCTTGCACCTGTGTG R 2 1 2 1 101000 f 74 goat snp12526-scaffold148-919053 6 32041452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765726 Affx-122952529 AX-385253187 6 29808067 TACAGAAGATACTCAATGCCTACCACTGAATTGCC[A/G]GAGTTTATTCCCCTGCCTATTGAGGCTATGTGACT R 2 1 2 1 101000 f 74 goat snp12527-scaffold148-969191 6 32091506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464434283 Affx-1110480925 AX-515907038 6 29847420 ATATTGCATGCCAGGGGACTGCAGGTCTGACAGCG[C/T]CCCAGCCCAGCAGGCAGTGGTCTCCCTTCTGTTCC Y 2 1 2 1 303000 r 74 goat GoatD01.042824 6 29847420 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38397793 Affx-122962501 AX-123268148 6 29907050 AATGAAATAAGCTAAGTTTTCCTGACATCAGCATT[A/G]TCTGGGCTAGGCAAAGTCAGCATGCTTACTTCTAT R 2 1 2 1 101000 r 74 goat snp12528-scaffold148-1068174 6 32191213 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377804 Affx-122977318 AX-123248163 6 29956156 TAGCAGCAGCAGCAGAAGCAATGCCTAACTACCTG[C/T]AGAAATAAATAACCAATGTGGTGCACACTGTAAAC Y 2 1 2 1 201000 r 74 goat snp12529-scaffold148-1117280 6 32243636 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378316 Affx-122977350 AX-123248675 6 30061341 TAAGAAAAAAGTCAGTTGAAGGTACTATTGAGCAT[A/G]GAGGAAGAATGCATAGGTCAGGTTGGGAGCAATAA R 2 1 2 1 201000 f 74 goat snp12531-scaffold148-1222465 6 32349183 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385278 Affx-122972068 AX-123255636 6 30114680 TTGCACACATAGCATCCCCCACAGTACAAGGACCA[C/T]GACACAGAAAAGGGTCAAGATATGCAGCACGACGG Y 2 1 2 1 101000 r 74 goat snp12532-scaffold148-1275804 6 32402952 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787416 Affx-122941147 AX-385274441 6 30175051 AAACCTCATAACAGCCATTTTTATTAAGGAGAATA[C/T]TTGTCAGACATTTCCTCTTAATTAGGTAATGCTAA Y 2 1 2 1 101000 r 74 goat snp12534-scaffold148-1336175 6 32464266 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793307 Affx-122923933 AX-385280285 6 30215114 CAGAGAGATAGTAAACTACACTGATTAACAGTACA[A/C]AATCTGAAGTTGAACTCTCTTGGGTTCAAAAGACA M 2 1 2 1 101000 r 74 goat snp12535-scaffold148-1376238 6 32502437 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789392 Affx-122944230 AX-385276402 6 30246187 GCTATACACAATAGTTGTGTACAATATATAAAGTA[G/T]AACACAATAAACTACCATTAAGAAGAATCAAAACA K 2 1 2 1 101000 r 74 goat snp12536-scaffold148-1407311 6 32533499 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434039 Affx-122934207 AX-123304380 6 30292433 TTTGATAGTCCTTTGTTTTCAAATAGAATCATTTG[C/T]GACTCTATGGTATAAATCTTCCCTTATACTCTTCT Y 2 1 2 1 101000 r 74 goat snp12537-scaffold148-1453557 6 32579773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409825 Affx-122952949 AX-123280176 6 30322182 GACAGTCTTGATGCACATATTTTATAATATTGTCT[A/G]TTTTGTCCAGCCTGGAAACTTTCATATAAATAAAC R 2 1 2 1 102000 r 74 goat snp12538-scaffold148-1483306 6 32609503 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774844 Affx-122973404 AX-385261978 6 30351434 ATTATAACTCAAATATTCCTTGATTTCTTTGACCA[C/T]AGAATTGATTCCTGAAGGAAAAATTGTGATATCTG Y 2 1 2 1 201000 f 74 goat snp12539-scaffold148-1512558 6 32639307 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436764 Affx-122932277 AX-123307102 6 30386478 AATATATAATTGTTGATGGAATAAATAAATGCAAT[A/G]TAGTAAATGCTTTAACAGAAGCACTTATTCAATCA R 2 1 2 1 101000 r 74 goat snp12540-scaffold148-1547602 6 32674653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803155 Affx-122939468 AX-385290018 6 30441516 CTCTTATCTAGAAGGTTGCCACTTCATTTCAGTAA[C/T]GGTTTATTTGCTGTGCAGAAAGTTTTTTTTTTTTT Y 2 1 2 1 201000 r 74 goat snp12541-scaffold148-1602640 6 32730351 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404348 Affx-122956825 AX-123274700 6 30470196 GTATTTCATTTAAGGAAAATAATTAATATATGAAC[C/T]CTTAGGATTGCAAGTACTGTTTGGTAATCTCATTT Y 2 1 2 1 101000 r 74 goat snp12542-scaffold148-1631320 6 32759204 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435433 Affx-122933483 AX-123305773 6 30532259 AAATAAATTAAATAATTTTTTAAAAAAGAGAGAGA[G/T]ATCAGCAGTATTTCCATTGGTTCATTGAGTAACTC K 2 1 2 1 101000 r 74 goat snp12543-scaffold148-1693383 6 32820796 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775833 Affx-122961538 AX-385262964 6 30609415 TTTTTAAGTGCATATTACTTCAGCTGTAATTTATA[C/T]GCTACGTGCAACATTTCTGATCATTTCAAAACAGT Y 2 1 2 1 102000 r 74 goat snp12544-scaffold148-1770539 6 32898786 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278345 Affx-1111836374 AX-519551831 6 30628118 ATGGTATAAATACCGAGAGAAGAAACTTTACTCAT[A/T]GGTTTTTAATTGCAAATTATTTCATGGACTTGTTT W 4 1 2 1 101000 f 74 goat Random2.2K-665 6 30628118 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378908 Affx-122976455 AX-123249267 6 30674858 AAATAAGTCCAAAATCTCTGATTTCTAATTCTTCA[C/T]AACTCATTTCCGCTGTTTCAGCTCTTACTGTTCTG Y 2 1 2 1 101000 r 74 goat snp12545-scaffold148-1835982 6 32965897 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802609 Affx-122976911 AX-385289511 6 30704753 GTGTGTGCATGTATACATAAAGGTATGCAAATGTG[C/T]ATGGTTCTTTGCAACAATAGCACAATTAGGAGAAT Y 2 1 2 1 201000 f 74 goat snp12546-scaffold148-1865877 6 32996417 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776135 Affx-122930093 AX-385263265 6 30755045 TAGTAGTTTGTAACTTCATCCATGAGTTTTGTGGT[A/G]CATCTCAGTTTGAACTTGCAGCTGTCTCCTTTCTA R 2 1 2 1 101000 r 74 goat snp12547-scaffold148-1916169 6 33045438 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395654 Affx-122963766 AX-123266009 6 30852258 TTTTTATTTAACTTCTCCAAATCCTGGTGTGAGTG[C/T]GGCTAGAGCTCAGTGGAGACCATCAAGGATTCTAA Y 2 1 2 1 201000 r 74 goat snp12549-scaffold148-2013382 6 33143559 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796837 Affx-122950015 AX-385283780 6 30884819 ATTAATTAAAGAGAGATACTAATATTATCTACTCC[A/G]TGGATTGTAATGAAGAGCAAATCTTTGCTACATGT R 2 1 2 1 101000 r 74 goat snp12550-scaffold148-2045943 6 33176060 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778565 Affx-122957954 AX-385265677 6 30922133 ACAAGTAGAATATGTTGCTTGCAAACCACTGCATA[G/T]AAATAAGATTTGCTCCTCTCATTGTAACTTCCCAT K 2 1 2 1 101000 f 74 goat snp12551-scaffold148-2083257 6 33213605 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447512 Affx-122924070 AX-123317848 6 30957233 AAATGATTACTTCAAATTCATTATAGAAATTTGGT[A/G]CATTGTTGTATACAGTTACCTAAGTGAACACTAAG R 2 1 2 1 101000 r 74 goat snp12552-scaffold148-2118357 6 33249084 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428591 Affx-122938702 AX-123298933 6 30993315 TCCCTATCCTTCTTGCAAATGATATTAACGTGTTT[A/G]TAAGGACGTCTGGTCAAGCTCGTGAGATGTCACAT R 2 1 2 1 101000 r 74 goat snp12553-scaffold148-2154439 6 33285478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768622 Affx-122944605 AX-385255802 6 31037872 TTTTAAAGGGATGAAAGCTTTCATGCAATGAATAA[G/T]AAATTTAAATTTTTTGGTGCTAGTATCATTATAGA K 2 1 2 1 202000 r 74 goat snp12554-scaffold148-2198996 6 33330782 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381997 Affx-122974080 AX-123252355 6 31066648 GTTAGAGAACTTGTTGGAATTCTAGAGTTTCTGGC[A/G]CTATAGATTTCAACTGATTTGTTTTATGCAGAGGG R 2 1 2 1 201000 r 74 goat snp12555-scaffold148-2227772 6 33359675 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799586 Affx-122951191 AX-385286517 6 31122766 AACAGTAACTAAATATGGAGAAAGATTATTCCACT[A/G]CTTCTTGACTTACATTGTCTCTTTTAGGAAGTCAG R 2 1 2 1 101000 r 74 goat snp12556-scaffold148-2283890 6 33416372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384110 Affx-122972831 AX-123254468 6 31180994 ATAAGTTCAAGCTGAAAATGATGACAAATGCTTTC[C/T]AACTCCACTCAGAAATAGCCATGAAAGAATGAAAA Y 2 1 2 1 201000 f 74 goat snp12557-scaffold148-2342118 6 33475320 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427516 Affx-122939523 AX-123297859 6 31221691 GTAAACCCATTATTCAGAGGTTCTCGATAAGAGAC[A/G]TTTCTCCTCTCTCCCAGGGCTATATAGAAATACTG R 2 1 2 1 101000 f 74 goat snp12558-scaffold148-2382815 6 33517310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789984 Affx-122956580 AX-385276990 6 31253764 GGATTCTATACTTATTGATCTAAACATCAATAATT[A/G]TTCTTAAAAGCTTTGGAAGGGTTAGTGTTCTGGTT R 2 1 2 1 201000 f 74 goat snp12559-scaffold148-2414888 6 33550043 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415201 Affx-122948987 AX-123285550 6 31291349 AAATCATCTCTTTGGTCTACTCTATTTGTACCCAT[A/G]TCAACTCCCCCTCAGTTTGGTGCCTGTCAGCCTCC R 2 1 2 1 201000 f 74 goat snp12560-scaffold148-2452473 6 33587806 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404786 Affx-122956674 AX-123275138 6 31363126 AACATTTAAATTTTCACACACTGGACACACTCCTC[A/G]TACTTTGTTAGACTTTGGGGAGAAAATATTTCTAA R 2 1 2 1 202000 r 74 goat snp12561-scaffold148-2524250 6 33660412 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797985 Affx-122920837 AX-385284921 6 31398437 CTTTTCACAAAAATCATATAGTGGCCAAAAAGCAC[A/G]TGAAAAGTTATTCAATACTGCTATCTATTAGAGAA R 2 1 2 1 201000 r 74 goat snp12562-scaffold148-2559561 6 33696024 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794947 Affx-122923280 AX-385281907 6 31466344 TTCCCATCTAGTGAAATTTAGCCTTTAATTTTATT[A/G]TGTCTGAATATTGAATCAATTTAGAAAACATTTCC R 2 1 2 1 201000 f 74 goat snp12564-scaffold148-2627468 6 33765092 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784900 Affx-122960340 AX-385271947 6 31522657 TTTAAAGTACTGAGCATCTTGTGAGTATGGGAAAA[C/T]AGATTCTAAAGTTTTCATATGTATGCACAGATAAA Y 2 1 2 1 201000 r 74 goat snp12565-scaffold148-2683781 6 33821640 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391133 Affx-122966794 AX-123261490 6 31561561 CCACCAAGTGGAAGAAATTAACTACCTGATGACCA[C/T]GAGCATTTAGGTCTGGGAGCCTTAGGAATGATAAT Y 2 1 2 1 201000 r 74 goat snp12566-scaffold148-2722685 6 33860778 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774279 Affx-122977609 AX-385261415 6 31617551 ATCTGCTAAATGGGCAACCCTAGGTACACTGGTCC[A/G]TTCTAACCTTAGAGACTTACATTATATATGCAATG R 2 1 2 1 101000 f 74 goat snp12567-scaffold148-2778675 6 33917687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377163 Affx-122978214 AX-123247522 6 31664274 TCTCTCCTCTCAAAAGAAAAACAATTAACAAAAAG[C/T]AAACCCAGAATATTTTATTTATTCATATCTTCCAT Y 2 1 2 1 103000 f 74 goat snp12568-scaffold148-2825398 6 33964506 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377488 Affx-122977498 AX-123247847 6 31710162 ATCTTGTTCAAATGGCTTTGCATATTCAAGCTCTT[C/T]TAGTGTTCACAATAACCCTATGAGGTAGATATTGT Y 2 1 2 1 201000 f 74 goat snp12569-scaffold148-2871286 6 34009617 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775293 Affx-122976332 AX-385262424 6 31754679 TGGGATTCAGGAATTTCTATGATTATGGCTAATCA[C/T]ATGGGCAAAGAATGACTGTAGACCAGTTCCCACTG Y 2 1 2 1 101000 r 74 goat snp12570-scaffold148-2915803 6 34054242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436135 Affx-122932641 AX-123306474 6 31793838 TCTTCCTACTTTGGTTTTCATTGGCCCAATCCGCT[A/G]CCCCAGGTTCCTTCTTAGACTCGGATTACTTCCTT R 2 1 2 1 101000 f 74 goat snp12571-scaffold148-2954962 6 34093601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783080 Affx-122953316 AX-385270147 6 31838348 ATGTCAAAGGGTGCTAGTTCCCCTATGGTGAGTTT[C/T]TATCCAAGATCCAAACCCACACTTCAAGGTTGGTA Y 2 1 2 1 102000 f 74 goat snp12572-scaffold148-2999472 6 34138098 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395948 Affx-122963575 AX-123266303 6 31880169 CATGTCAATACTATGCAAATAACATTTCATTTTGT[A/G]GGCTGCACCTGAGTAGTTTGTCTTCCAAGTCTTTT R 2 1 2 1 101000 r 74 goat snp12573-scaffold148-3041293 6 34179940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452532 Affx-122920542 AX-123322865 6 31912928 CTAGCACAGCTCAGAGTGCTGTACTCACATGATCA[C/T]ACCTCATCTTGGGATTTTTTACTATGATTACCACC Y 2 1 2 1 101000 r 74 goat snp12574-scaffold148-3074052 6 34212443 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771534 Affx-122976194 AX-385258692 6 31955976 TTTATTATAATGCAGAACTAGACAAAATGAGTTTA[C/T]GCTTTTATGCTAGGCATACATTAAAAACATGAAAA Y 2 1 2 1 101000 r 74 goat snp12575-scaffold148-3117100 6 34257575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397360 Affx-122962288 AX-123267715 6 32005652 TGGTCCCTGTTTCTTTGATTTCTAGAATATTTTAG[A/G]TCAGAATCGATTTTGACTTTACCCTTTCCTTTTTG R 2 1 2 1 101000 r 74 goat snp12576-scaffold148-3166776 6 34307394 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776422 Affx-122944063 AX-385263549 6 32084419 GGCCAGTTGTATAGCTTGATAGGCTTGTTATATAC[A/G]TCAGCTTATCAATACTTAATTTAATAAAATGGCTT R 2 1 2 1 101000 f 74 goat snp12577-scaffold148-3245543 6 34386561 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394576 Affx-122964442 AX-123264931 6 32116034 TTTACTATCTAAATCAGGACCAACTCTTTAGACTT[A/C]GACTAAGTTCAGCAAGCTTACCAATTTTCGTCACA M 2 1 2 1 101000 r 74 goat snp12578-scaffold148-3277158 6 34418818 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768759 Affx-122929558 AX-385255936 6 32146770 AAACCTGACCCTCTCCTAAGTATTTGGATTCCTGC[A/G]AGTTTTCTCAGCTGGCGGTATCTCTGTCTTCAGCA R 2 1 2 1 101000 f 74 goat snp12579-scaffold148-3307894 6 34449796 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399752 Affx-122960320 AX-123270107 6 32181272 TCCCAGAGGACTATTGAAAGTTAATGTTGCTTAAA[C/T]AGCAAAAGAGTCATGGAAATATACTTCCCTCCCCT Y 2 1 2 1 201000 f 74 goat snp12580-scaffold148-3342396 6 34484359 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405643 Affx-122956585 AX-123275995 6 32222609 CGATTATCACCATTATCTTCATTGACATTTTCATC[A/G]TTTATAACATGATTAGAGTGCCTTTTATGTGACAC R 2 1 2 1 303000 r 74 goat snp12581-scaffold148-3383733 6 34526728 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377457 Affx-122977520 AX-123247816 6 32252416 TCTGCAGGACTGGCCCTTGGCCAGCTCCTGGGAGA[C/T]GAGTTCTGAGTCCTTAGAATATCTGTAAGATAAGA Y 2 1 2 1 101000 r 74 goat snp12582-scaffold148-3413540 6 34557816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774738 Affx-122970210 AX-385261872 6 32296635 TCCTCACAAAGCTACTAAAGAAATTTAAGCAATAA[A/C]ATTTCACATATATCAGCTGAAGATAATTCCCTTAC M 2 1 2 1 201000 f 74 goat snp12583-scaffold148-3457759 6 34602486 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431932 Affx-122935984 AX-123302273 6 32365703 TCTCCCAACTCCAATCCTCCTCCAAAAGCTGTGGC[A/G]GAGACTCAAATTTAGGCCACAGTTCTCTCCACAGA R 2 1 2 1 201000 r 74 goat snp12584-scaffold148-3526827 6 34671206 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429687 Affx-122937640 AX-123300028 6 32420831 CTTTTCAGCTAAATATAAATATTTACTTCTTTAAT[A/G]TTTTCTTCATTATTAACTCCTGTTCAGAGAATTAT R 2 1 2 1 103000 r 74 goat snp12585-scaffold148-3581955 6 34726977 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401879 Affx-122958854 AX-123272232 6 32449737 TGGCTTGAGATGAACATGGTAACATGGAAAAGAAT[A/G]CTGTCACAATTAAAATTCTTGGAAATCTAGTATTT R 2 1 2 1 101000 f 74 goat snp12586-scaffold148-3610861 6 34755798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378621 Affx-122976562 AX-123248980 6 32525693 CCTTCAAACAGTGTGTAACATATATCCAGGGCACA[C/T]AGCTAGCACTGGGTTCAACTGAAAATTCACTTTGC Y 2 1 2 1 101000 f 74 goat snp12587-scaffold148-3686817 6 34831119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799914 Affx-122925246 AX-385286840 6 32588064 ATTTCCCTCATGTTCTGAACTCAACCCAACAATAC[A/G]TTTTTCAGTGAAGAGGCAAAGTTATGCATATTTGG R 2 1 2 1 101000 f 74 goat snp12588-scaffold148-3749188 6 34893977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426922 Affx-122940439 AX-123297267 6 32617738 CCACTTCAGAGAGCTATATCTGGTGTATATAAAAG[A/G]CACAGTGAAAAATAAGCACAGTCCTAAGCTCTCAA R 2 1 2 1 101000 f 74 goat snp12589-scaffold148-3778862 6 34924471 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388200 Affx-122969423 AX-123258558 6 32660121 TAAGATGCAATAATCTATTAGCAGTCATTAAAACC[A/G]TAAAGAATATTAATTTATCAGATTATCAGAGCAAA R 2 1 2 1 101000 f 74 goat snp12590-scaffold148-3821245 6 34967343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424608 Affx-122942197 AX-123294954 6 32720242 TGTGGAAGATGGAGAGGAATAATTTGTATATTTCC[A/G]TTCAGTCTAGATCTGATACTCCATCATATTTACTC R 2 1 2 1 101000 r 74 goat snp12591-scaffold148-3881366 6 35030673 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445043 Affx-122926615 AX-123315380 6 32769306 CTGCTTATATTCCAAGCACTAGTTTAAGCATTACA[C/T]GTATAATAGCTCTAATCTCAAAATAACATAGCAAG Y 2 1 2 1 101000 r 74 goat snp12592-scaffold148-3930430 6 35079732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447874 Affx-122923878 AX-123318210 6 32870210 AGAGACTCTGTCTCTTCCGTTCATTCAACTTCAGA[C/T]GTTTAGAACTCAAAGAGGGAACAGCATAGGAAGAG Y 2 1 2 1 101000 f 74 goat snp12594-scaffold148-4031334 6 35181318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420222 Affx-122945534 AX-123290570 6 32921837 CTGGCATAATTTTTTATTTATTTGGAGGAAGAAGA[C/T]AATCTGTAGCTTGTGGAAAAGTGTATGCATTTAGA Y 2 1 2 1 101000 r 74 goat snp12595-scaffold148-4082961 6 35233924 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411600 Affx-122951607 AX-123281950 6 32976660 TTTTAATAAGATTACCTCTTGCATGCAAATCCTTC[C/T]GAAATAAAACTCAGAAAGCCCACTGTTTCTACCTC Y 2 1 2 1 101000 f 74 goat snp12596-scaffold148-4137784 6 35288662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441723 Affx-122929143 AX-123312060 6 33009159 TCAGTCTTGAAGAATAATGTTTGCAGAGTCTTGAA[C/T]AAAATACTGTTCTTTCAGAATTAATGACTGACAGT Y 2 1 2 1 101000 f 74 goat snp12597-scaffold148-4170283 6 35321910 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795904 Affx-122923744 AX-385282856 6 33039929 TGATGGTCAATATCAACTGGATATGAGGCTTGGGG[A/G]AGAAGGTGTTTGTAGATATGAGAAGAAATACTTGT R 2 1 2 1 101000 f 74 goat snp12598-scaffold148-4201053 6 35353321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788390 Affx-122948664 AX-385275408 6 33080776 TATTATAAGGGTAAATAAATGATTAAGGTAATAAC[C/T]TCAGCAGTTAATCGGAGAGAGAATTGGTTGCTTTT Y 2 1 2 1 101000 r 74 goat snp12599-scaffold148-4241900 6 35394526 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437957 Affx-122931614 AX-123308295 6 33111604 TCTCAGAGGTGTGGTAACCACCTGAGACAAGAGTG[A/G]GCCCAGAGCCTGGCACAAGAGAGTTTCATAGTTGC R 2 1 2 1 101000 f 74 goat snp12600-scaffold148-4272728 6 35425838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441370 Affx-122928864 AX-123311707 6 33161232 CTGACTTTGAGATCCTGAAGGCCAGGGATAGCATC[C/T]TATTCTTCCTGGAATTTCCAACCCTTTGTGCTGTG Y 2 1 2 1 101000 r 74 goat snp12601-scaffold148-4322356 6 35476169 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423983 Affx-122942122 AX-123294329 6 33190439 AAAAAAGGGATAGAAAAGTCACATCAAAAAAGACT[A/G]CCAGCACTTTAAAAGGTTAGGGCAAAAGAGGAATA R 2 1 2 1 101000 r 74 goat snp12602-scaffold148-4351563 6 35505421 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777771 Affx-122957945 AX-385264889 6 33231230 CTGTTAAGTTCAGACAGAAGCTGAGAGTGGGACTG[A/C]TATTGTGAACTTCCCCCCAAGCAAAGCAAGAATAA M 2 1 2 1 101000 f 74 goat snp12603-scaffold148-4392354 6 35546251 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776078 Affx-122938011 AX-385263208 6 33261404 AGACATATATCCTGGGGATATGATTATTCTCATAG[C/T]GCAAATTCTAAATCAGGCCAAATAAAGATAAGCCC Y 2 1 2 1 101000 r 74 goat snp12604-scaffold148-4422528 6 35576733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389771 Affx-122968233 AX-123260128 6 33293819 AGATAGCTACTGATCTAGGTCTCATGCAAGCCTTA[C/T]AGTAGGAAAGATGAGGAAAACAAAAGAGCAGAATC Y 2 1 2 1 101000 f 74 goat snp12605-scaffold148-4454943 6 35610683 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799162 Affx-122976330 AX-385286092 6 33328019 CCTCAGAATCAGTTCATTCAATCTCTCACAGAGAC[A/G]TCTCCGATGATTTGATGAGATATTTCCCCCTTCTT R 2 1 2 1 101000 f 74 goat snp12606-scaffold148-4489143 6 35644361 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391407 Affx-122966775 AX-123261764 6 33370611 AAGACCAGGGCTTGAACCCAGGAGAGCCACACTCC[A/G]TCAGAGTCTCCAAGAAAATGTGGAGAAAAGGCATA R 2 1 2 1 101000 r 74 goat snp16801-scaffold1760-13796 6 35688215 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434878 Affx-122934351 AX-123305219 6 33415791 TAAAATGAAAATTATGTGACAGTTATTTTCCTACT[A/G]TATGGATGTGCTTGGAACTATACCCTGGAAAACAA R 2 1 2 1 101000 r 74 goat snp16802-scaffold1760-58976 6 35733825 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797864 Affx-122926237 AX-385284802 6 33468388 GGAAGTAAGCTACTTTATGATAAAGGGAGTTCCAC[A/G]TTTCAGAAAGAAATATTCCTAGTTGGGAATGTATA R 2 1 2 1 101000 r 74 goat snp16803-scaffold1760-111573 6 35785321 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443641 Affx-122927284 AX-123313978 6 33502535 TGATTGATCATGAGGTTTAAGAAACCTCTTCCAGA[C/T]ACATGTTCTTGTTCTCTTACCTCTTGATCTGGAGA Y 2 1 2 1 201000 r 74 goat snp16804-scaffold1760-145720 6 35819359 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402804 Affx-122958283 AX-123273157 6 33547730 CTAAATTTTTTTCTTCTTTCTTTTCTTAAATTACT[A/G]TTTGCTAACCATTCCCTCTCTAGAACAATAGCTAT R 2 1 2 1 101000 r 74 goat snp16805-scaffold1760-190915 6 35859016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278347 Affx-1111836375 AX-519551833 6 33583530 TTCTTGGTTCTTTTTGCACCAGTTATTTCTGAGCT[A/G]CCTTCCTGGAAGGGATGTTTCTTTCCACTTTGGGG R 2 1 2 1 101000 f 74 goat Random2.2K-668 6 33583530 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433495 Affx-122935030 AX-123303836 6 33584091 TCTTAAGTACATGAGTGTGGGACATTATGGGTGTG[C/T]CATAAGGAAAGAAACTGTAGTCTCTTTTTGTCATG Y 2 1 2 1 101000 f 74 goat snp16806-scaffold1760-227276 6 35896333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437594 Affx-122931864 AX-123307932 6 33612630 TGTTTTCACTTTTTCCTCAGCATCTAGACCAGCAC[C/T]GTCCACTAGAAATGTAATGTGAGCCACATATGTAA Y 2 1 2 1 101000 f 74 goat snp16807-scaffold1760-255815 6 35924453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796045 Affx-122921153 AX-385282997 6 33642909 TTAATTTACTTATTCATTCTCCTGGGTTTTTTATT[A/G]TGGTTAGAAAAAACATGCAACATGAGATATACCCT R 2 1 2 1 201000 f 74 goat snp16808-scaffold1760-286094 6 35955623 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395817 Affx-122963638 AX-123266172 6 33704350 TCTCTGCAGAGCCCTGGTGAATGAGCCCATCTCTG[C/T]ATGTTTGCCCCTACTTGCAGAACTTCGTAGCCTTG Y 2 1 2 1 101000 r 74 goat snp16809-scaffold1760-347535 6 36018389 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388045 Affx-122969542 AX-123258403 6 33737096 CATAGCAAATGAAAAGGTAAAAATGCCAAATATGA[C/T]GAATTACATATAAGAAAAAATATGTTTGAAACAAA Y 2 1 2 1 102000 f 74 goat snp16810-scaffold1760-380281 6 36051052 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452228 Affx-122920795 AX-123322561 6 33765608 GTACATACCTTGTATGAATTATCTAAATTCTCAAA[G/T]CAGTGGAAAGCAGGAAGAAGAAACAGTCGTTCAAA K 2 1 2 1 201000 f 74 goat snp16811-scaffold1760-408793 6 36079594 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375889 Affx-122978494 AX-123246248 6 33846824 CTGCCACCTTGTGTGCTGTGCCTATCAGCATCGTT[A/G]CTTCCCATTCTCATCTCTAGAATACTAACCAGAAA R 2 1 2 1 201000 r 74 goat snp16813-scaffold1760-490009 21 2183902 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778671 Affx-122938987 AX-385265781 6 33884847 AACAACTTTGTGAGTTAGCTTTGTGTCATGATTAT[C/T]ACACTGAAACAGCTTACAATATGTTAGTTTGGATT Y 2 1 2 1 101000 r 74 goat snp16814-scaffold1760-528032 6 36199742 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797199 Affx-122978979 AX-385284138 6 33917093 TTTTAAGAAGCATAGAAAAGATCCTAGAAGTAAAT[A/G]TTAAATGTTTCTGGGTGTCCTCTGTTATTCTTTTG R 2 1 2 1 101000 r 74 goat snp16815-scaffold1760-560278 6 36232621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438228 Affx-122931440 AX-123308566 6 34043869 TTCCCTAAAGAAAGGAGAATGGATACTAGGAATGC[C/T]AAAACATCAGTTGTCTACCCTGGTGCTATTGAGAC Y 2 1 2 1 101000 f 74 goat snp16817-scaffold1760-687054 6 36360840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392207 Affx-122966280 AX-123262564 6 34112365 AATCATGCAAGACCTAGAGAACACCATTAAACAAA[C/T]GAATATACATGACTGAGAAGTCCAAACAGGAGAAA Y 2 1 2 1 101000 f 74 goat snp16818-scaffold1760-755550 6 36429649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410457 Affx-122952220 AX-123280807 6 34149710 AAGGCCAAATCAAGAGATGAGATACATCTAAGATA[C/T]GTATTCACCAAAAGTTGGTTCAACCACAAGCAGCC Y 2 1 2 1 101000 r 74 goat snp16819-scaffold1760-792895 6 36467345 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801434 Affx-122941275 AX-385288343 6 34180737 TAATCCTCCCAGTAACCCATAAAGTAGTAATTATT[A/G]TTATTAATATTCTCATTTGAACATGAGGAAAATGA R 2 1 2 1 202000 f 74 goat snp16820-scaffold1760-823922 6 36498331 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273199 Affx-1111833502 AX-519546858 6 34193381 GGTTTCAGGACTAGCAACGGTGGAAATTATTCTAC[A/G]GAAAGAGAGAACACTCTAGATCAAGGGTAGGGGAT R 2 1 2 1 101000 f 74 goat 6_34193381_AF-PAKI 6 34193381 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38442974 Affx-122928202 AX-123313311 6 34261735 AGTTGATTTTTTTCCCCCTGTTTTGGAATGCAAGC[A/G]CTTTTACTGTGAAAGCATCAACTTCAAAGATAGCT R 2 1 2 1 201000 r 74 goat snp16822-scaffold1760-904920 6 36578566 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794414 Affx-122934191 AX-385281377 6 34297163 CTATTTACGGACCATGACAAATCTCAAAGTCCTTA[C/T]ATTCTGTTCAGGATAAGAAAAGCAGAGGTTGTTTG Y 2 1 2 1 101000 f 74 goat snp16823-scaffold1760-940348 6 36614070 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771156 Affx-122966944 AX-385258316 6 34328116 ATTAAATTTGGTTAATCCACCCACTTTCTTAGAGA[A/G]AGGAATACTTCAGACTGTACTACTTGTGGACACAA R 2 1 2 1 102000 r 74 goat snp16824-scaffold1760-971301 6 36645232 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411570 Affx-122951631 AX-123281920 6 34349154 GGCATTTTTTGACAATAAAAGTATATTTTATTTCT[A/G]ATCCTTTCACAAGAAGCAATTTAAGATCTTTAGAA R 2 1 2 1 101000 r 74 goat snp26732-scaffold281-14273 6 36663600 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433755 Affx-122934498 AX-123304096 6 34377762 ATTCACCAGGGTGCCATCTGCAGATTTTTGCTATC[A/G]CTGGCCTGCAAGGGTTTCACTTCCTTTTTCAGCTG R 2 1 2 1 101000 f 74 goat snp26733-scaffold281-42881 6 36692047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443947 Affx-122927017 AX-123314284 6 34418705 TAGATGAGCAACACTGACCTGAGTTAAGACAATGG[C/T]GGCAGAAATGAGGATGAGGAGAGATCTATGAGAGA Y 2 1 2 1 101000 f 74 goat snp26734-scaffold281-83824 6 36732997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448970 Affx-122923124 AX-123319305 6 34450752 TATTCTTAAACATGCTGAGATGAAGGAGCTGGGAA[G/T]CATGCAGGTAGACACAGGCTACGTAGGAAAAGCGG K 2 1 2 1 101000 f 74 goat snp26735-scaffold281-115871 6 36764986 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399302 Affx-122960533 AX-123269657 6 34481947 GATATTTCTTCTGAAATTTTGAGTTCTTATAAAAA[C/T]GTTTCAGTGTATTTTCTTTTTCCAAGTAACAATCT Y 2 1 2 1 303000 f 74 goat snp26736-scaffold281-147066 6 36796108 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771963 Affx-122929449 AX-385259119 6 34522041 TATTTTAAGTCACTATGCTTTGGGATGGTTCATTA[C/T]GAAGCATTTCTGTAGCCAAAGGTAACTAACTAATA Y 2 1 2 1 101000 r 74 goat snp26737-scaffold281-187160 6 36835936 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435056 Affx-122933742 AX-123305396 6 34556008 TCCTCTGACTTTCCAGCCCTGAACAGTGAGAACAG[C/T]GAATCCTCTGCTCAGGAAGCGATGGGCAGGGAGCC Y 2 1 2 1 101000 f 74 goat snp26738-scaffold281-221127 6 36870150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411159 Affx-122951874 AX-123281509 6 34602233 CTGGTTCATAATTAGAAGCTATTCAAAGAGTGACT[A/G]CATTCCAATGATACCACTAACACCCTCAGTGTAAA R 2 1 2 1 101000 r 74 goat snp26739-scaffold281-267352 6 36917015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384638 Affx-122972156 AX-123254996 6 34634824 AATACTACCTACATCAAAGGGCTTTTATGTGGTCC[A/G]CCTGTAATGCAGGAGACCCCAGTTTGATTCCTGGG R 2 1 2 1 101000 f 74 goat snp26740-scaffold281-299943 6 36949865 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771989 Affx-122965283 AX-385259145 6 34667347 CTGAGGGAAGTTTTGTAGTGGAGAACCAATGGTTA[C/T]TGGCAGATAGGTTAAAAATTATTGTAGGAGATATT Y 2 1 2 1 101000 f 74 goat snp26741-scaffold281-332466 6 36982281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397222 Affx-122962382 AX-123267577 6 34708150 GTCCTGTTTGAATTCTAGCCCAGAGGAAAGAGGAA[A/G]CAGGAAAGAGCATTCTAGGTTTCTAAGAAATATTG R 2 1 2 1 101000 f 74 goat snp26742-scaffold281-373269 6 37023063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428194 Affx-122939015 AX-123298537 6 34745411 TCCATTGTCTGGCCATTGTCAGAGCTCTCATAACA[C/T]AGGGAGGAAAAAAATGTCTTAAGAAGATCAGGTAA Y 2 1 2 1 101000 f 74 goat snp26743-scaffold281-410530 6 37060549 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392380 Affx-122966231 AX-123262737 6 34779914 TCTCTCCCTGTCAGTCCCTCTGATACACTACTTAC[A/G]TCATCTTCAGATGGGTTATAGTCTCCTATTTGGCT R 2 1 2 1 101000 r 74 goat snp26744-scaffold281-445033 6 37095270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767539 Affx-122943065 AX-385254794 6 34811407 ATAGGAAATAACTGTTAAAGAAATGCAATCTGTAT[C/T]ACTTCTGTAGAAGACAGCTTAAAAAGGTTTTTTTG Y 2 1 2 1 101000 f 74 goat snp26745-scaffold281-476526 6 37126708 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388263 Affx-122969775 AX-123258621 6 34882078 GGAAATGCACAACTCCTATTTTTCTTCATCTGGTT[A/G]CTACGTTCTATTGCCATATTACAAATTTCAGGCAT R 2 1 2 1 101000 r 74 goat snp26747-scaffold281-547197 6 37198076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379518 Affx-122976075 AX-123249876 6 34966172 GGGAGGGCTTTTCCAAATATTTCCCTCTAATTTAT[A/G]CTGAATTCCTTACTTTTGTTGATGTGATTCAATTC R 2 1 2 1 101000 f 74 goat snp26749-scaffold281-631291 6 37282758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786056 Affx-122930734 AX-385273092 6 35049865 TTCTTTTCTTTAATAACTAGTATGTTGACATGCAA[C/T]AGTGAAGGCAAGACAAAAGATACCTTTTATATTAG Y 2 1 2 1 101000 r 74 goat snp26750-scaffold281-714984 6 37368764 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400567 Affx-122960417 AX-123270922 6 35081977 GTTATATTGCACCTTCCTGAGTTGAACTTTGAAAA[C/T]GGTAGCCACGCAAAATCCCAGAAGGGGTGAACTCA Y 2 1 2 1 101000 f 74 goat snp26751-scaffold281-747096 6 37401587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414798 Affx-122949221 AX-123285147 6 35111079 GAAAATCTTTTAAAATACATGGAACTTATTTTTCT[C/T]GAAATCTGATGAGCTGGCATCAGGAGATGATGTCC Y 2 1 2 1 201000 f 74 goat snp26752-scaffold281-776198 6 37430746 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418294 Affx-122946991 AX-123288642 6 35140586 TAGAGTCAAAGAGATGAATAGGAGAAACCAGCTAT[A/G]TTAAAATGTTCCCTGACCCTGCCAAAAATCAGGCC R 2 1 2 1 201000 r 74 goat snp26753-scaffold281-805705 6 37459874 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448369 Affx-122924108 AX-123318705 6 35210909 CCTTCCCCAGCATTTATTGTTCCTGGATGTTTAAA[C/T]GGTAAGCACTCTGACTGGTGGGTAATGATACCCTG Y 2 1 2 1 103000 r 74 goat snp26755-scaffold281-876028 6 37531231 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779528 Affx-122945617 AX-385266631 6 35249288 TATGAAATAGGTCAACAAGACCTACTGAATTATCA[C/T]GGGGAATTGGATCAGGAGGCTTTAATAATGTCTAT Y 2 1 2 1 102000 r 74 goat snp26756-scaffold281-914407 6 37570018 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416412 Affx-122947846 AX-123286761 6 35289058 TTTCACAGATTTGATGTTTTACATCTAAACCAAGT[A/C]GAGTGCACCCAAAGGATGGCGGATACTCTGGGCTA M 2 1 2 1 201000 f 74 goat snp26757-scaffold281-954177 6 37608512 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448441 Affx-122923651 AX-123318777 6 35334226 AGCATAGATTATAATAATCATAATCAAAGCAAACC[A/G]TGGTGTGAAATAATTTGTAAACTATTTGAGACTAA R 2 1 2 1 101000 r 74 goat snp26758-scaffold281-999345 6 37653431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771510 Affx-122932247 AX-385258668 6 35384267 TCACCTTATGCCAGTCAGAAACTGGCAACTTTAGA[G/T]TTCTTGATTAAACACCTAACTGATAGCATTTTAGA K 2 1 2 1 101000 f 74 goat snp26759-scaffold281-1049386 6 37703575 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420188 Affx-122945559 AX-123290536 6 35426330 GGAATGGAGTGAAAAGTCTGCTCTCAATCGGCCTT[A/G]TTATTTATATCTCTCTTGACTCACTGAAATGCTCT R 2 1 2 1 201000 r 74 goat snp26760-scaffold281-1091449 6 37746029 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774999 Affx-122940570 AX-385262131 6 35459451 TGTTGCCTGACTATACATATTGTCAAACAAAGGCA[C/T]GGAATATTAGGTAACATTCTTGAGGTTCTGGGGTT Y 2 1 2 1 101000 r 74 goat snp26761-scaffold281-1124570 6 37779121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789266 Affx-122936447 AX-385276277 6 35496829 AGTGAAAGAAGTTAAATTATATAACATTTATACAA[C/T]GGGATATTTTTAACACAACCATTAAAATTATGTTG Y 2 1 2 1 202000 f 74 goat snp26762-scaffold281-1161948 6 37816650 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429344 Affx-122938575 AX-123299686 6 35578781 GGTATGGGTGACAGAAGACCTCAAGAGCCTGTTGA[C/T]GTCAGGGTGCGCTCTGATGAGCAGCATCCTGGAGG Y 2 1 2 1 101000 f 74 goat snp26764-scaffold281-1243900 6 37898873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377020 Affx-122977718 AX-123247379 6 35646796 GATCAGAAAATGATATAGTGGAAGGTAAGAAGGGA[C/T]GTCTTACAGCACTACTGACAGTGTACAGTTCTTGC Y 2 1 2 1 101000 r 74 goat snp26766-scaffold281-1311915 6 37966873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770292 Affx-122953010 AX-385257458 6 35696664 CATCTTGGGTTATCAGTAGGCAATTAAGTATAATG[A/C]TGTTTCTGATCTGAACGAGGACAGCAGGTTTAAAA M 2 1 2 1 101000 r 74 goat snp26767-scaffold281-1361783 6 38016838 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401339 Affx-122959263 AX-123271692 6 35771847 AGGTTCCAATGGTTACTGAAAACCACTGTTATTTT[C/T]CCTAAATTATTTGCTTTTGTTTGTTTTTCAGGCAA Y 2 1 2 1 101000 f 74 goat snp26768-scaffold281-1436966 6 38091565 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790242 Affx-122925351 AX-385277246 6 35825633 TTCATCATCGTATATGAAATTGACACTTGATATAG[C/T]CAGAGTCAGGTTAAAAATGCAACCCAAGGTAGAGC Y 2 1 2 1 101000 r 74 goat snp26769-scaffold281-1490752 6 38144878 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771696 Affx-122948406 AX-385258853 6 35865814 ACTTTATCTAAGACACCTTCTGAAAGGTGTCTTTA[C/T]AGATTCTAATAACACCTTCTGAAAGGTTCTCTGCA Y 2 1 2 1 101000 f 74 goat snp26770-scaffold281-1530933 6 38185434 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770636 Affx-122943207 AX-385257800 6 35908910 ATCAAATAAATAGAAATCAGATTGGTGGTCAGGGA[C/T]GGGATTTTGATTTTAAAGGGTCACAGCAAATTTTG Y 2 1 2 1 201000 r 74 goat snp26771-scaffold281-1574029 6 38228930 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397016 Affx-122963128 AX-123267371 6 35954378 CATATCGTCAGGGAAAGTATCGCTAACCACCAAGC[A/G]TCTTTCCTTTTTCTTTGTATTTATCACTTATCCTA R 2 1 2 1 101000 f 74 goat snp26772-scaffold281-1619497 6 38274307 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412002 Affx-122951755 AX-123282352 6 36006994 AGGCTGTCATGGGCAAAGCTTTCATACCATTGGCT[A/G]CAGTTCTGTCACATGATCACATATAGCTGCAAGAA R 2 1 2 1 101000 f 74 goat snp26773-scaffold281-1672113 6 38327501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390051 Affx-122968422 AX-123260408 6 36050641 AGTGGTACAATAATACCAATGCCAAATAAATGCCC[A/G]TAAGTGTGAAAACCTATACCAGTCAAGGGTCATGT R 2 1 2 1 101000 f 74 goat snp26774-scaffold281-1715760 6 38371444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800610 Affx-122968765 AX-385287529 6 36080167 CCCTCCTCTTCTTCCTTTTTAGTTAAAATCAAAAT[A/G]TCTATTGAAGTTTAGAATTGACATCTTGGTGCTTA R 2 1 2 1 101000 f 74 goat snp26775-scaffold281-1745286 6 38400840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278518 Affx-1111836377 AX-519552002 6 36101662 CAAAATGAAAAAGTTATTTGGGGAAACACAACATT[A/G]GACTGGCATATTTTTTCTCAGATCTGTGGTAATGT R 2 1 2 1 101000 r 74 goat Random2.2K-670 6 36101662 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447986 Affx-122923749 AX-123318322 6 36109438 AATAAATGAGTGGCAGGGCAGGGATGAAATGGGGA[C/T]GTCCACGAAACCAGGCACCACTGGGCAATTTTTCT Y 2 1 2 1 201000 r 74 goat snp26776-scaffold281-1774557 6 38431246 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790339 Affx-122966025 AX-385277342 6 36151709 AGAGCCTTCTTCTGGCAACCTTAAGTTGGTGACCA[A/G]CTGTTAGAAATTGTGGACAACAACCTGGATTTAAT R 2 1 2 1 101000 f 74 goat snp26777-scaffold281-1816828 6 38473627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416502 Affx-122947784 AX-123286850 6 36184782 TTTAACCATTAAGCTATAAATGCCCCATGAAATTT[A/G]CTTCCTTTTAAAGCAGCTATTTTACTATTAGTATG R 2 1 2 1 101000 r 74 goat snp26778-scaffold281-1849901 6 38506633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774542 Affx-122936789 AX-385261676 6 36236213 ATAAGGTCACCTCCTCTATCCACCTTATCAACCCA[A/G]TCTCATTAATTGGCACTTCAGCTCTTCTGTGAAAT R 2 1 2 1 101000 f 74 goat snp26779-scaffold281-1901332 6 38558109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441925 Affx-122928593 AX-123312262 6 36269170 TTGCAGAAGTGAGGGGTGTCTTCAAAGGCATGAAG[G/T]GTTCTTACAAGGAAGAGAGGTGTAGTGGACACTTG K 2 1 2 1 101000 r 74 goat snp26780-scaffold281-1934289 6 38590195 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436699 Affx-122932327 AX-123307037 6 36334988 TAAGTGTTTTGAATGCGGTGTCTAATTTTAGTTTT[A/C]GTCTCCTTAGAAACAAGAATTGATAAATTCTAATA M 2 1 2 1 101000 f 74 goat snp26782-scaffold281-2000107 6 38657369 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376883 Affx-122977819 AX-123247242 6 36374073 ATTTCCAATATCTAAATGAGTGGCTGAATTCAACT[C/T]GAAGGATGCTCATTTGGGTAATTTAAATTTTTTTA Y 2 1 2 1 101000 f 74 goat snp26783-scaffold281-2039192 6 38696985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375758 Affx-122978601 AX-123246117 6 36421332 GTGAATGTTCTCTGCAGTTTCTTCCAACTCTAATG[A/G]GCTGAGATTAAAAGAGTAATGAATTTTACAACTAG R 2 1 2 1 101000 r 74 goat snp26784-scaffold281-2086451 6 38742182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389575 Affx-122968789 AX-123259933 6 36451847 GTGAGCCTGTTGTCCTGATTAGATATTCTCCTTGA[C/T]CAGCTGATAAGCTTCTAACACATCCCAGAAAGCTT Y 2 1 2 1 101000 f 74 goat snp26785-scaffold281-2116966 6 38772709 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278353 Affx-1111836378 AX-519551839 6 36491607 TGGAGTATTAAAAATCACCAAGATAGTATAATGGT[A/G]AAAATATTATGACAATATTTAATTCATAATTTTGC R 2 1 2 1 101000 f 74 goat Random2.2K-671 6 36491607 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390990 Affx-122966906 AX-123261347 6 36551034 AGGAGGTACCACTGAGTTTACTTTTACGTGTGAAG[C/T]ATCTTTAGGGAGAACAACATATTAGAAACTCAAGA Y 2 1 2 1 101000 r 74 goat snp26787-scaffold281-2216153 6 38874180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774177 Affx-122939821 AX-385261314 6 36589460 ATCCAAAACCCACATTATGCACAGTGCCTGGGATC[C/T]ATGATAATATTTAGCACAGTTTCCATGAAGACTAT Y 2 1 2 1 101000 f 74 goat snp26788-scaffold281-2254579 6 38913406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435705 Affx-122933312 AX-123306044 6 36643389 TCAAAGATAACCTTGGCTGATTTTTGTGTCTTGTC[A/G]CTGTGGCATCTATCATAAAACCTAACACACTCTTC R 2 1 2 1 201000 r 74 goat snp26789-scaffold281-2308508 6 38967139 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424498 Affx-122941747 AX-123294844 6 36674413 TTTATGGGTATATGCACAAACTTTTAAGAAGTGTT[A/G]CCTTGACACACACTTTGTGATATGCTTGGCTACTA R 2 1 2 1 101000 r 74 goat snp26790-scaffold281-2339532 6 38998199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464437918 Affx-1110482789 AX-515910643 6 36707177 AGCTTGAATATGCACCAAATATTTTAACTCAGGAC[C/T]GGAGTTTGGTTAAATGCTAATAAGATAACCACCAA Y 2 1 2 1 101000 r 74 goat 6_36707177_AF-PAKI 6 36707177 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398937 Affx-122960993 AX-123269292 6 36732355 TTAGTGGGCACAAAGTCAAGAATAAGAGCAGGTGC[A/G]TAAGCCACTGTGGCCTCTTTCCCTAGATCTTTATG R 2 1 2 1 201000 f 74 goat snp26791-scaffold281-2397474 6 39056220 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423602 Affx-122942385 AX-123293948 6 36794061 CCTGACTGTGCTGTGCACAGCCTCTGACTCTTGCT[A/G]CATCTGCAATCTAAACCATTTAATTAGTAATAGGA R 2 1 2 1 201000 r 74 goat snp26792-scaffold281-2459180 6 39118052 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394357 Affx-122964651 AX-123264712 6 36827041 ATAGGCATTATTTGTTTCTCTAGGCATGAATAGGT[A/C]TTTGAATAATAGTGATTTCTAAAGGTAGAAACAAC M 2 1 2 1 201000 r 74 goat snp26793-scaffold281-2492160 6 39150759 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785273 Affx-122938672 AX-385272318 6 36864248 CAAATAAAATAAAGCATGTGTTTAACATATGTAAC[A/G]TAAACATTACATATAGCCTGGTTTTTTTGATAGAG R 2 1 2 1 101000 r 74 goat snp26794-scaffold281-2529367 6 39187840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795434 Affx-122941109 AX-385282391 6 36919135 TATAAAGTAGTTTCTTGGCTTATGAAAAAGCCAGT[A/G]TTGTCTTTCACTGGAAGCACCCCAGTAGTGCCTCT R 2 1 2 1 101000 r 74 goat snp26795-scaffold281-2584254 6 39243101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788283 Affx-122951591 AX-385275301 6 36971395 CATTCTCCGCATGTTACAATAGGATGACTAGAGTT[G/T]GAATTACTCATTCTAAATAGTGATGAGACCTCAAT K 2 1 2 1 101000 f 74 goat snp26796-scaffold281-2636514 6 39295173 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448652 Affx-122923349 AX-123318988 6 37073419 CAGGACTTATGAGAATCAAGTAAAGAAGCTGTGAA[C/T]AGACCATCACTGATAAAAGAAGCTTAGACATAAAG Y 2 1 2 1 101000 f 74 goat snp26798-scaffold281-2738538 6 39397002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431336 Affx-122937062 AX-123301677 6 37113211 TTAAGGATGTTAAACAAATTGAAAAATTCCTCTAG[A/G]GCACCATTCTTTCAGTTTCATAAAACTATTGATGC R 2 1 2 1 101000 r 74 goat snp26799-scaffold281-2778330 6 39437063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762454 Affx-986696984 AX-385250583 6 37135587 TCTCTCCTTTCATTATGCATATTTATAAAATGTCA[C/T]ATGGGTTTATCACTGGGAGATAAGGAGGCAATATG Y 2 1 2 1 600010 f 74 goat 6_37135587 6 37135587 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 320788852 Affx-122944169 AX-385275867 6 37190104 TGCCAAGAGCATTGTACCTTGGTTATATCTGAAGA[C/T]AATATTTTGAAACCTCTATTATTTGCATTATTGCA Y 2 1 2 1 101000 f 74 goat snp26801-scaffold281-2855223 6 39514043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793297 Affx-122954394 AX-385280275 6 37248152 TTTATTTAACCATTATTGATTCATCATCTGCTATG[C/T]GTCAGTTCCAAAGCCAAGATTAGAAGGAGAGTGGT Y 2 1 2 1 101000 r 74 goat snp26802-scaffold281-2913271 6 39573331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432799 Affx-122935410 AX-123303140 6 37325914 CTACAAAATTCCCTCTAGAATTGGCTGAAGATGTC[G/T]CTGTGACTGTTTACATTTTACCGTATTCTCCTGCT K 2 1 2 1 101000 f 74 goat snp26803-scaffold281-2991033 6 39651303 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434467 Affx-122934638 AX-123304808 6 37374272 GAGAAAGTGAAATGACTTGCTGTTTAGCAATGATA[C/T]ATAAAGTACTAAATCTTCATTTTCTATCAACCTTC Y 2 1 2 1 101000 f 74 goat snp26804-scaffold281-3039391 6 39700586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768783 Affx-122944354 AX-385255960 6 37407402 AGCACAATGTAAGAAGTGCCATTCCAGAGGTGAGC[G/T]CAGTTCATGTCAGTAGCACATGTACGAAAGCAGAG K 2 1 2 1 101000 f 74 goat snp26805-scaffold281-3072521 6 39733758 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395164 Affx-122964113 AX-123265519 6 37437326 TAAATTCTAGAAACTTGACAACTAGTATTTTTAGA[C/T]GCTGCTTTGGAAGTGACTCTGAGCTCTCCCTGTTT Y 2 1 2 1 201000 f 74 goat snp26806-scaffold281-3102445 6 39764156 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448577 Affx-122923408 AX-123318913 6 37505405 AACTGAAGCCATCAGGGCCTCCCAGGTGGCGTTAG[C/T]GGTAAATAACCCACTTGCCAGTGCAGAAAACTTAA Y 2 1 2 1 303000 f 74 goat snp26807-scaffold281-3170524 6 39829276 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse498 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320782828 Affx-122949614 AX-385269899 6 37550096 GCATTTCATAGCATCACATCTCAAAGGGATAATGT[A/G]ATTCTGAAGTTTCATCAATGTCAAACCCAATTTAG R 2 1 2 1 101000 f 74 goat snp26808-scaffold281-3215215 6 39874411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse499 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320767580 Affx-122925286 AX-385254832 6 37588975 TTATTTAGTTGGATATTTTTACACTGGAAGAAACA[C/T]AGCAAGATGTAAAATTGCTAGTAATCTAAAGAAAA Y 2 1 2 1 101000 f 74 goat snp26809-scaffold281-3254094 6 39913786 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779486 Affx-122925811 AX-385266589 6 37659068 CTTCTGAGAATAAGTTAAAAGATTTGGACTATGAA[C/T]AGGGAAGATATCTGTCTTCATGGGAACAAAGCTTC Y 2 1 2 1 101000 r 74 goat snp7248-scaffold1268-14447 6 39985135 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse500 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38417728 Affx-122947435 AX-123288076 6 37700309 GACTGTGGTATGAACTGGTTGACTAAATCTCTCTG[C/T]GAAAATATTTTGCCAACTGTGCAGGGCTACAGAAA Y 2 1 2 1 101000 f 74 goat snp7249-scaffold1268-55688 6 40026095 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse501 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38446840 Affx-122925269 AX-123317176 6 37749287 TTATTACTGAGAGACTATATAAAAGTCATCATTGA[C/T]AGCAACAATTGACATCTAAATTCCGATACTAATAT Y 2 1 2 1 101000 f 74 goat snp7250-scaffold1268-104666 6 40075174 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790713 Affx-122972448 AX-385277714 6 37840604 GCAATTTGCCTTCACAAAGTAAGGATAGAAACTCA[C/T]ATACACGGTCTAGTCAAGTTTCATACTGCCTTTCA Y 2 1 2 1 101000 r 74 goat snp7252-scaffold1268-195983 6 40166627 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse502 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38411895 Affx-122951188 AX-123282245 6 37883816 TAGACATCTCTTAAATCCATCCACTTCTGTCCATC[A/G]CTTTTACCACCATCCTAATGCACTCTCCCATTGTC R 2 1 2 1 201000 r 74 goat snp7253-scaffold1268-239195 6 40209422 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse503 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 538942931 Affx-1251531516 AX-585490051 6 37923911 GAGAAAAACTTACCTAGTTGGTATTTTGAATAATA[G/T]TTTGCCATTTGTCCACTGTTGCAAGACTGTCGTTT K 2 1 2 1 400000 f 74 goat SNPs_040 6 37923911 G T SV-TF-chip candidate gene ou candidate region LCORL 538942936 Affx-1251531517 AX-585490055 6 37923960 CACTGTTGCAAGACTGTCGTTTATGTCTTTTTGTT[C/G]ACATTTCTGTGGTCTTCCACGGTGGTCTTTTTCTT S 4 1 2 1 400000 r 74 goat SNPs_041 6 37923960 G C SV-TF-chip candidate gene ou candidate region LCORL 538942862 Affx-1251531495 AX-585489986 6 37924983 GAGACTGTGTTTCTGTTGTTTGCATAAACCAGGTA[C/T]AGAGTTCATTCAAATCATACTTTTTCTGAAAAAGC Y 2 1 2 1 400000 r 74 goat SNPs_042 6 37924983 C T SV-TF-chip candidate gene ou candidate region LCORL 538942793 Affx-1251531472 AX-585489927 6 37924999 TGTTTGCATAAACCAGGTACAGAGTTCATTCAAAT[C/CATACTTTTTCTGAAAA]AGCATTTTTACCGGTGAAACCTCAAGTTCTAAAAG - 2 1 2 1 400000 r 74 goat ins-del_001 6 37924999 CATACTTTTTCTGAAAA C SV-TF-chip candidate gene ou candidate region LCORL 538942829 Affx-1251531476 AX-585489958 6 37925099 GGACTTGCTATTTTGAAGTTATCATTTTCAATGGG[T/TTC]TCTTTTTCTATGAACAGAATTTTCAGCTTCATCTC - 2 1 2 1 400000 r 74 goat ins-del_002 6 37925099 TTC T SV-TF-chip candidate gene ou candidate region LCORL 538942824 Affx-1251531473 AX-585489953 6 37925378 TTGGAAGCTATTTTAATCCTTGACTGCTTATGTTT[G/GTCC]TCCTGACTTTTACCTTTCTGCAAATGGAGCTTATA - 4 1 2 1 400000 r 74 goat ins-del_003 6 37925378 GTCC G SV-TF-chip candidate gene ou candidate region LCORL 538942864 Affx-1251531496 AX-585489988 6 37925811 TCGGTCGAATAATATTCTTGGAAGGTTGAGGTATC[A/G]CAGGCTTGTTCTTGAAAGGTCTAACATATTCAAAG R 2 1 2 1 400000 r 74 goat SNPs_043 6 37925811 A G SV-TF-chip candidate gene ou candidate region LCORL 538942857 Affx-1251531497 AX-585489981 6 37926205 GTCAGTTTTAGGTTTCGGTGGTCTTCCAATTGGTC[A/G]CTTTATCTGTTTCACAACCTGGGGACCTATTTTTT R 2 1 2 1 400000 f 74 goat SNPs_044 6 37926205 G A SV-TF-chip candidate gene ou candidate region LCORL 538942826 Affx-1251531474 AX-585489955 6 37926262 GGGACCTATTTTTTTAGGTCTACCTGGTTTTCTTT[T/TA]AAAGATGAATCAATCATACTGCTTGAATACTCTTT - 4 1 2 1 400000 r 74 goat ins-del_004 6 37926262 TA T SV-TF-chip candidate gene ou candidate region LCORL 538942868 Affx-1251531498 AX-585489992 6 37926529 TGGTTGCTTTTCAGAAGAAAAATCACGATTTGATT[C/T]GGAATTACCAACTGAAGTTAAAGTATATTTGACTC Y 2 1 2 1 400000 r 74 goat SNPs_045 6 37926529 C T SV-TF-chip candidate gene ou candidate region LCORL 538942915 Affx-1251531479 AX-585490038 6 37926957 AAGACTTTTTGGCCATATTTATTGTATCTTCCAAA[C/T]GTTCCACAACAACTTGTAAATTAGAATTCATTGCA Y 2 1 2 1 400000 r 74 goat SNPs_046 6 37926957 T C SV-TF-chip candidate gene ou candidate region LCORL 538942855 Affx-1251531451 AX-585489979 6 37927192 GGTTCTGCTCAAAAGTCCAGGGATATCACTTTTCA[A/C]AGGAGTTTGAGTATTCTCTAATTTTGGATTCTCTT M 2 1 2 1 400000 r 74 goat SNPs_047 6 37927192 A C SV-TF-chip candidate gene ou candidate region LCORL 538942804 Affx-1251531470 AX-585489938 6 37927338 TTTTAAAGCTTTCTGAAAATGCATCAAAAGCCAAG[C/T]TAGTTTCTAAATTATTTAGAGGTAGTTTCAATGAC Y 2 1 2 1 400000 r 74 goat SNPs_048 6 37927338 T C SV-TF-chip candidate gene ou candidate region LCORL 538942827 Affx-1251531475 AX-585489957 6 37927485 GTCTTTGGCAATGATAGAATTGCTCTTTGTCTGCT[G/GAA]AAGAGTTCATCATTGCGCAAAAACTTCCTTGGATT - 2 1 2 1 400000 r 74 goat ins-del_005 6 37927485 GAA G SV-TF-chip candidate gene ou candidate region LCORL 538942794 Affx-1251531452 AX-585489928 6 37927656 AGCTGTGCATTGCAAATAAGGTTTCTTGACGCTTT[C/T]GAAATCTTGTCTGAATAATTTTATTTTCTATCTTT Y 2 1 2 1 400000 f 74 goat SNPs_049 6 37927656 C T SV-TF-chip candidate gene ou candidate region LCORL 538942806 Affx-1251531471 AX-585489940 6 37927681 TTGACGCTTTCGAAATCTTGTCTGAATAATTTTAT[C/T]TTCTATCTTTTTATCATGTTGACTCAGCAATTCCA Y 2 1 2 1 400000 r 74 goat SNPs_050 6 37927681 T C SV-TF-chip candidate gene ou candidate region LCORL 538942918 Affx-1251531484 AX-585490040 6 37927782 GCAAAAGAGAGGTTATTAAATCTCTCAATTTTAAA[C/T]CATTATCTGTATTGCAATCACTGCTAGATAATTTT Y 2 1 2 1 400000 f 74 goat SNPs_051 6 37927782 T C SV-TF-chip candidate gene ou candidate region LCORL 538942920 Affx-1251531485 AX-585490042 6 37927785 AAAGAGAGGTTATTAAATCTCTCAATTTTAAATCA[C/T]TATCTGTATTGCAATCACTGCTAGATAATTTTATA Y 2 1 2 1 400000 f 74 goat SNPs_052 6 37927785 T C SV-TF-chip candidate gene ou candidate region LCORL 538942818 Affx-1251531491 AX-585489949 6 37927850 TTTATAAGGTTTGTCATATCTATTGTTTCTATTGA[C/CTTTAA]TTTTTCATTAATACGATCCATTAAATCTTGAAAAA - 2 1 2 1 400000 r 74 goat ins-del_006 6 37927850 CTTTAA C SV-TF-chip candidate gene ou candidate region LCORL 538942913 Affx-1251531478 AX-585490036 6 37927924 AATTATAGTAGTTTCACCCTTTTCATGATTTGTAG[C/T]ACAATTATTGCTGTCTTCTAAGAGCAAAGAATCAG Y 2 1 2 1 400000 r 74 goat SNPs_053 6 37927924 T C SV-TF-chip candidate gene ou candidate region LCORL 538942807 Affx-1251531477 AX-585489941 6 37928059 TGCTGGTGTCAGAGATGGAGGCTGGTTAATATTTG[C/T]TTCAAGTCTATTATTTTCTAAGGCTGAACACTCCG Y 2 1 2 1 400000 r 74 goat SNPs_054 6 37928059 T C SV-TF-chip candidate gene ou candidate region LCORL 538942928 Affx-1251531488 AX-585490049 6 37928172 GTGATAATGGTGGGGGTGAGGGACTTCGAGATCTA[C/T]AAACATCTTGAAGATTTACCGAAACATCACATATT Y 2 1 2 1 400000 r 74 goat SNPs_055 6 37928172 T C SV-TF-chip candidate gene ou candidate region LCORL 538942925 Affx-1251531489 AX-585490046 6 37928266 AAAGCCTGATTTTGTGGAATGAATGTCTGCTAACA[C/G]TCCAGAACAGAACCTGTGAGAATTGTAACTGTCTG S 4 1 2 1 400000 f 74 goat SNPs_056 6 37928266 G C SV-TF-chip candidate gene ou candidate region LCORL 538942823 Affx-1251531486 AX-585489952 6 37928641 TATGCACAAAGATTCCAAAACTTTGCTTAATGCTG[A/AT]TTTTCCTTTTTCCATTTTAGTAGCTTCCTCTGATT - 2 1 2 1 400000 f 74 goat ins-del_007 6 37928641 A AT SV-TF-chip candidate gene ou candidate region LCORL 38392238 Affx-122967574 AX-123262595 6 37929411 CTTCATCTCAGAACAATTTTCTGTTCTGTGAAGAT[A/G]CAGTAAGATATTTCAGAGTGGGAGGAGGGTTTGTA R 2 1 2 1 202000 r 74 goat snp7254-scaffold1268-284790 6 40254822 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779802 Affx-122978701 AX-385266902 6 37967374 TCCTGATGTGTTCAGGAGTTTTGAGGGAAATTCTC[A/G]CACTGGTTTGTACTGAAGCAGAAGACATACCAGTA R 2 1 2 1 101000 f 74 goat snp7255-scaffold1268-322753 6 40292732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse504 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320769058 Affx-122959291 AX-385256233 6 38014967 TTTCAGTGACTTCAAAGAAGATGACATTTGGTGGA[C/T]AAAGAGAAGTGATTTAGCGCATAAGAAAGGATTAT Y 2 1 2 1 101000 f 74 goat snp7256-scaffold1268-370346 6 40340257 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse505 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38449893 Affx-122922342 AX-123320228 6 38071340 CAAATTTAGTAAAAATCTTATTTATCTAGAGACTA[C/T]GCTTCATTTAATTTCAGTTCTGGCCAAACCCCAGG Y 2 1 2 1 101000 r 74 goat snp7257-scaffold1268-426719 6 40396508 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419723 Affx-122945903 AX-123290071 6 38101262 TTAAATATCAGTCTCCAATTGGGTATTTTCTTATA[C/T]AGGAATATGTTATTGTTTCCTCCCTCCAATGCATG Y 2 1 2 1 101000 f 74 goat snp7258-scaffold1268-456641 6 40426392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse506 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320775893 Affx-122941715 AX-385263024 6 38131017 GAATTTAAATTGCTATCCTGTATTTTGAAAGACAC[A/G]GTGTTTCCTGGTGTAAGATTTGGTTTACTCACCTA R 2 1 2 1 101000 r 74 goat snp57869-scaffold935-9613 6 40455979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse507 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320783562 Affx-122923374 AX-385270624 6 38160849 TTGAAATATGTAATATTTCTACTAACACCATGATT[C/T]TAACTTTGTTATTACGTTTATCTTACTGATCTCAG Y 2 1 2 1 101000 f 74 goat snp57870-scaffold935-39445 6 40485606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392797 Affx-122965973 AX-123263154 6 38199574 GAGAGTTAAGATGTATGTGGGAGCAAGACTGTTCT[A/G]GACCTAGAAGGAAACTGCTCAAATCCTGATCATAG R 2 1 2 1 101000 f 74 goat snp57871-scaffold935-78170 6 40524279 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse508 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38380620 Affx-122975241 AX-123250978 6 38247412 CCCTCCAAAATGTCTTGTTCTCCCTCTAGTTATTT[A/G]TTTAATAGCAGCAAGAACTGATTACATACATTTGT R 2 1 2 1 201000 r 74 goat snp57872-scaffold935-126008 6 40572138 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse509 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38447272 Affx-122924939 AX-123317608 6 38279583 CTCATCCTTAGTGCCAAACAAGCTTTCCTTCTGCT[A/G]TCTCCTCAGCTGGCTATAAGTAATTGACCATCATG R 2 1 2 1 201000 r 74 goat snp57873-scaffold935-158179 6 40604765 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419950 Affx-122945210 AX-123290298 6 38333801 GAATGAGAGGAAGAATGACAGAAAGACAGTCAAGG[A/C]TGTGTTCATCACAGGTCACTGCTGCGGACGATTGA M 2 1 2 1 101000 f 74 goat snp57874-scaffold935-212397 6 40658741 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse510 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38449794 Affx-122922422 AX-123320129 6 38364658 TAATTCCCTCAGGAAGGGGCATGTCATGATAAAAA[G/T]AAACTGATAAGAGTCAAATTTTTTGCTTTGAAATT K 2 1 2 1 101000 f 74 goat snp57875-scaffold935-243254 6 40689544 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse511 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320801944 Affx-122924529 AX-385288849 6 38395125 GTCTGCAGGATGAGTTCCTAGAGGTGGAACTTCTC[A/G]GTCAAAAGATTTGAACATTGATAAATTTTATATAC R 2 1 2 1 101000 f 74 goat snp57876-scaffold935-273721 6 40719722 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781262 Affx-122938833 AX-385268347 6 38420676 GAACTCTTCTTTGCACATCATATTTGATGTGAGCT[A/G]TCAGTACAATATTAACAACCTGGAATTTGGTAAAC R 2 1 2 1 101000 f 74 goat snp7617-scaffold1273-10351 6 40745285 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse512 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320795710 Affx-122975719 AX-385282663 6 38482775 TAGAAGTCAGGAAGAAAGGCTAGTTCTACTTTTGG[C/T]AAAATACGTAAGATGTCTGGATTGCAGGCATAATA Y 2 1 2 1 101000 f 74 goat snp7619-scaffold1273-72450 6 40807481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse513 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38429952 Affx-122938077 AX-123300293 6 38513140 TTAGCCATCTCAAAATCTCATCAAGACAGAGAGTC[A/G]TACCCTACCTTGATCTAGCAATCCCACTTCTGGGT R 2 1 2 1 101000 f 74 goat snp7620-scaffold1273-102815 6 40838651 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382168 Affx-122974029 AX-123252526 6 38550093 TTGATTTTATTTTTTCTGTTAAGACCAGGCTTTTA[A/G]CCAGTTAAATTGCTCTCATTTTTATTGAGTTTTGG R 2 1 2 1 101000 r 74 goat snp7621-scaffold1273-139768 6 40875771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse514 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38430999 Affx-122936683 AX-123301340 6 38591591 AGATGGCAAACAACAAAATGGTACTGCTAATTAGA[C/T]ATCCAATGAAATGTCACATGGAAAGGTTAACTATT Y 2 1 2 1 101000 f 74 goat snp7622-scaffold1273-181266 6 40917327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse515 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38443044 Affx-122928148 AX-123313381 6 38624908 ATTTGGATATGTGTCCATAAATATTTATTGGAAGA[C/T]GGCCACACCCATCTATTTTTATACCCTTTGTGCTG Y 2 1 2 1 103000 r 74 goat snp7623-scaffold1273-214583 6 40948616 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789255 Affx-122955599 AX-385276266 6 38658929 ACTTGCTCTTGACCAATTTTCAAATCAGACCTTTA[C/T]GATTATTAACCCTAAGTGTCTCCCTTCAAGAGCCC Y 2 1 2 1 101000 r 74 goat snp7624-scaffold1273-248604 6 40982644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse516 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320798588 Affx-122946462 AX-385285521 6 38714374 GGTAATTGTTTTCCCTCATGAAATATTACTACCAC[A/G]TACTTGTCACTAGATGATGTAGCCAAGAAGTCAGA R 2 1 2 1 101000 r 74 goat snp7625-scaffold1273-304049 6 41037445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse517 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38425817 Affx-122940688 AX-123296163 6 38722193 ATTGGCAATCACTGGTACTGACAAATAATTTTTTC[A/G]TTTATGTTGAGTTTCCTAGTTTTTGATGTTTCACG R 2 1 2 1 201000 r 74 goat snp54015-scaffold821-1251869 6 41045116 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428796 Affx-122938402 AX-123299138 6 38751371 CAAGTCAACAAAGACAGCTTCGTTTACAGATACTA[C/T]GTTCTTAAAGAAAATGCATTATGTTTTGGTAGGCT Y 2 1 2 1 101000 f 74 goat snp54014-scaffold821-1222691 6 41073728 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse518 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410094 Affx-122952838 AX-123280444 6 38828723 CTGCCAGTGCCAAGAGTCTCCCCACTGTTTACAAA[G/T]AAGTGTTTTCTGATGAATTTTCTTTAGCCATAATA K 2 1 2 1 201000 r 74 goat snp54013-scaffold821-1145339 6 41150643 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse519 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38384604 Affx-122972572 AX-123254962 6 38857480 CCCAGAGGAACCACTTACTTGCTACACTCCTAATA[G/T]AAGTTACTTAGCCTCTTAAGCCTTGGGCTCCTTAT K 2 1 2 1 201000 f 74 goat snp54012-scaffold821-1116582 6 41179776 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769228 Affx-122925711 AX-385256402 6 38915386 ATTTAGTTGCAGGACTGTTGTGTTGTACACAGGAT[A/G]CATGGTATAAAAATAACTCTAGTAGAGATTTTAAA R 2 1 2 1 101000 f 74 goat snp54011-scaffold821-1058676 6 41238907 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse520 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468278523 Affx-1111836379 AX-519552006 6 38932564 TCTTATGAAAATTTATCATAGGGTTTTATTGCAAT[A/T]CATTTCAATTAACGATTTCTCAGAGAACTAGGTTT W 4 1 2 1 101000 r 74 goat Random2.2K-674 6 38932564 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415214 Affx-122948976 AX-123285563 6 38962409 CTGTGCAGAACACACAGAGTTTTTTGCATACAGCC[A/C]GTTATTGTTTCTATAAAGTTGTCAGAGCAATTTTT M 2 1 2 1 101000 f 74 goat snp54010-scaffold821-1011653 6 41285688 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse521 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320800817 Affx-122973666 AX-385287733 6 39059889 ACTTGTTATAATTATGTTTGAAACCAATCTAGATA[C/T]GTTAAATATGTGAATCATTTTAATCTCCACAGCCA Y 2 1 2 1 101000 r 74 goat snp54008-scaffold821-914173 6 41385076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379202 Affx-122976295 AX-123249561 6 39124666 TTCTACTGTAAAATAAAGGGTGGAGACTAAGGGTC[G/T]ACAGACTAAGTCTAAGGAGTCTTTGCTCTTTACTT K 2 1 2 1 101000 r 74 goat snp54006-scaffold821-849396 6 41450679 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse522 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38381297 Affx-122974457 AX-123251655 6 39155448 TAATGGACCTGATTCCCTCTGGGGTCTCAATAATT[C/T]TGCTATTTCAAATGAATGAAGTACTGCCTTCCAAG Y 2 1 2 1 101000 f 74 goat snp54005-scaffold821-818614 6 41481388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse523 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38376234 Affx-122978788 AX-123246593 6 39188065 CATATATTTGTCAAATAAATATAATCTATTAAGAG[A/C]TTTCTAGGAAGGAAAATAGGAAACTACTTTATTCA M 2 1 2 1 103000 r 74 goat snp54004-scaffold821-785997 6 41514012 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273249 Affx-1111833503 AX-519546901 6 39213717 GATAAAAATTTCTGTCTCTTCTTCCTGCTGCTGTG[A/G]ACAAATGCATTAAAATGTATCTTTCTTTCTTTTCT R 2 1 2 1 201000 r 74 goat 6_39213717_AF-PAKI 6 39213717 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446134 Affx-122925772 AX-123316470 6 39280982 TATGTTATTAGGGCAGTTTCTGTCCTGATAATCAA[A/C]TTTTAAAGTGAAAATTAGTTTCATATGTAATTGAA M 2 1 2 1 303000 r 74 goat snp54002-scaffold821-693080 6 41606728 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse524 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38407756 Affx-122954978 AX-123278107 6 39314505 AAGAGAAGATAATGGAAAGCAGGAAACGGACTGGG[C/T]AGCATTTCTAGGTCAGCAGAGGGGTAGCATCATCT Y 2 1 2 1 101000 f 74 goat snp54001-scaffold821-659557 6 41638377 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse525 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320768633 Affx-122961434 AX-385255812 6 39360271 TATGTCATTGAACAAACACAAGGAAGTTTAAAATC[A/G]TACCACAAATTTTTGACTTCCTGTGATGTACAGGG R 2 1 2 1 101000 r 74 goat snp54000-scaffold821-613791 6 41684168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440272 Affx-122930643 AX-123310609 6 39404274 CAAAGAATTTTATGAAGGTGGTAGATGGTTGTGAC[A/G]TCATAAACTGTAAGCATTGAATCCAAAATCTAGTG R 2 1 2 1 101000 r 74 goat snp53999-scaffold821-569788 6 41727639 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse526 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320778208 Affx-122946430 AX-385265323 6 39434354 TCTTTGAGACAATGTAAAGGCTTTTGAGTCTGGCT[A/G]TTGAGGGAACAACTGCTTCATTGCTCGCCCCAGGA R 2 1 2 1 101000 f 74 goat snp53998-scaffold821-539708 6 41757720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse527 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320783109 Affx-122926499 AX-385270176 6 39498305 ATAAATCAATCTACAATGTTTATATTATTATGGCT[A/G]TAAACCTTGATGTCTGGAGATCCATGAAATTATAT R 2 1 2 1 101000 r 74 goat snp53997-scaffold821-475757 6 41821698 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785720 Affx-122933787 AX-385272761 6 39549491 CAATGTTCTCTCTGTTTGTCTACATATAATTTAGC[A/G]TCTTTAAAATGATTCCTTGTATCATATTTTGTTTA R 2 1 2 1 201000 r 74 goat snp53996-scaffold821-424571 6 41873350 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse528 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38438929 Affx-122930421 AX-123309266 6 39578923 ATATTTAAATAACTGGCTAGAGGTCACACAGCTGG[C/T]AAGTGATGCAGCCAGAATGTGAACTGACCACTAAG Y 2 1 2 1 201000 r 74 goat snp53995-scaffold821-395139 6 41902850 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse529 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38394446 Affx-122964590 AX-123264801 6 39641943 AGAGAGGAAGAGGGTGGGATGATTTGGGAGAATGG[C/T]ATTGAAACATGCACATACCTTTTAAAAGCAGAGTA Y 2 1 2 1 303000 r 74 goat snp53993-scaffold821-332119 6 41965951 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791744 Affx-122929727 AX-385278735 6 39681920 AAACATGCTGGGAAGAGTAATGTCATATCTAAAAG[A/G]TTTTGATCCTAGTAGCCTCTTGTGAAGGCATTTCT R 2 1 2 1 201000 f 74 goat snp53992-scaffold821-292142 6 42005965 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse530 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320766380 Affx-122926300 AX-385253759 6 39713419 GCTCAGGATTATTCAAAGAGGAATGCCAGAGAATC[G/T]AAAGTTAATCTTTGACATTCTGGTTTGTGTTGGCC K 2 1 2 1 101000 f 74 goat snp53991-scaffold821-260643 6 42037438 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse531 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320778915 Affx-122957180 AX-385266022 6 39754097 ATGAGGCTGTCTTTCATCTAAACATATCATATGTT[A/C]TGCATCCAAATGAATGTCTTTAAAATCATATACTT M 2 1 2 1 101000 r 74 goat snp53990-scaffold821-219965 6 42078273 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450867 Affx-122922224 AX-123321201 6 39784459 GCTTTGAGCAGTTAAATTACATGAAGATCCATGTG[C/T]GGCAAATCATAGGTTGAAGATGTGTTTTAGCCTGA Y 2 1 2 1 101000 r 74 goat snp53989-scaffold821-189603 6 42108554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse532 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38380030 Affx-122975587 AX-123250388 6 39818505 TTGGAGTCCCTCCAGTGAATTCATTCATGCGATCA[C/T]GACAGCAGAGAATGTCTTTGTGAATCCAGAGGACT Y 2 1 2 1 101000 r 74 goat snp53988-scaffold821-155557 6 42143763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse533 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38377692 Affx-122977415 AX-123248051 6 39856451 GCTTTTGTTCTAGTAGGGGTTATTTTTGTTTAATC[A/G]CTAAGTGGTATCTGACTCTTTGTAACCCCACGGAT R 2 1 2 1 201000 f 74 goat snp53987-scaffold821-117611 6 42181641 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450074 Affx-122922802 AX-123320409 6 39913225 GAAATACAGTAGACTACCCAAACCTCTTTTCTACC[A/G]TATCAGATTTCTTAACCTCAGTCTGCTTCGTATGG R 2 1 2 1 101000 f 74 goat snp53986-scaffold821-60837 6 42239414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse534 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38451339 Affx-122921267 AX-123321672 6 39985100 GTTGTAATCACCTTGCAACTGTGGCTGAAACCACC[A/G]TTGGTCTTTGTTAACTAAAGGGGAGATACTGGCTT R 2 1 2 1 101000 f 74 goat snp5610-scaffold1199-10939 6 42311182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse535 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38392361 Affx-122966248 AX-123262718 6 40015507 TTATGCTGTGAGCTCTAGTCCAGGCAGGTGAGACA[C/T]GAGAAGCCTTCTTGAAGCTTGCACTTTACAGGAAT Y 2 1 2 1 101000 r 74 goat snp5611-scaffold1199-41346 6 42342544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376965 Affx-122977759 AX-123247324 6 40045993 TAGATATATGGAGAAATGTGGGAACCAACAAAATA[G/T]ATTTGTCTTAGTTGTATGACTTCAATTTAGCTTTT K 2 1 2 1 101000 f 74 goat snp5612-scaffold1199-71832 6 42373274 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse536 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38445296 Affx-122925449 AX-123315633 6 40117924 ATTCCTTGTGAAATAATCTTGACTCCGAAAACTAC[A/G]TAATTGATAAATTAAAATTTTCTGAAATCCTCATT R 2 1 2 1 101000 f 74 goat snp5614-scaffold1199-143763 6 42445683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse537 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320802915 Affx-122953937 AX-385289812 6 40187660 GATTTTGAGCCTGATTTTTAAGCTGAAATTCATGA[C/T]GAACCTACTATGCATTAATTGAGTGTATTTGCACA Y 2 1 2 1 101000 r 74 goat snp5616-scaffold1199-213499 6 42515861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397194 Affx-122962403 AX-123267549 6 40218526 ATACAATGTGCATATGAACTGAGTTAGTCCATCTG[C/T]CTATCTTCCAACTCAGACACATCAACTTTCCCCAC Y 2 1 2 1 101000 r 74 goat snp5617-scaffold1199-244365 6 42545736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415032 Affx-122949017 AX-123285381 6 40295190 GGCAGAAAGAAGCAATATCTGATCTGGGTCTCTCT[A/G]TCTCTAAAAACCATGGTCAGGCTAATCTATTTTAG R 2 1 2 1 201000 r 74 goat snp5619-scaffold1199-321029 6 42622661 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442833 Affx-122927697 AX-123313170 6 40450653 AGGAATCTAAACTGGGCTGGGAAACCAATCAAGAT[A/G]ATCACAAGGAAGATGGCAGCATGCTTGTGATGAAG R 2 1 2 1 101000 f 74 goat snp5623-scaffold1199-476492 6 42778317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397371 Affx-122962280 AX-123267726 6 40484715 AATAGCAATTGGATTCCTACACTTTTACTTACTTA[A/G]TTCAGTAGCTCAGTCGTGTCCGACTCTACGATGCC R 2 1 2 1 101000 f 74 goat snp5624-scaffold1199-510554 6 42812309 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787130 Affx-122936387 AX-385274156 6 40548323 ACAATATAAATCCTTAACAAGGTAGATACCATGGT[A/G]TCTGTTTTACTATGAAAGAAACTGAGGTCTTGGAG R 2 1 2 1 201000 f 74 goat snp5626-scaffold1199-574162 6 42875832 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772324 Affx-122974473 AX-385259478 6 40591830 CTAGGACCTGCTAAGTTAGTCTGAGTTCCCGTCAT[C/T]TCTGAACTTGAAGCTCAGTTGTGTGAAGAAGGGGA Y 2 1 2 1 101000 r 74 goat snp5627-scaffold1199-617669 6 42919478 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389366 Affx-122968457 AX-123259724 6 40628318 GAGTGTTATCACTTAATAACCTTGCTACCTTCTTT[A/G]TGACATGGAGGTTGGCTTCCCTTGAGAGCACAGAA R 2 1 2 1 101000 f 74 goat snp5628-scaffold1199-654157 6 42955958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785673 Affx-122932496 AX-385272714 6 40732605 ATTAGAATTGCTGGGTAGAATACTATAAACAACAT[A/G]CCTAGTTAAGAGGTAGAATTCACTAGAATTTTAGT R 2 1 2 1 101000 r 74 goat snp5630-scaffold1199-758444 6 43061877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278357 Affx-1111836380 AX-519551843 6 40751543 TGACCTGAAGATGCAGGAACTTACGTGAAAAGAAA[A/G]GGGCCTCTCTCATGGCTCAGACAGTAAAGAATCTG R 2 1 2 1 101000 f 74 goat Random2.2K-676 6 40751543 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38440299 Affx-122930219 AX-123310636 6 40830947 GCTATGTGGATCCAGCAGTCCAAAGTCATTCTAAA[C/T]ACTCCAAACCCTTGTTTCCCTGGCAGTGAAAAATC Y 2 1 2 1 102000 r 74 goat snp5632-scaffold1199-856786 6 43160722 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408223 Affx-122953841 AX-123278574 6 40874418 CCGACTCAAAAAGTGCTGACTTCCTCTGGTAGGTC[A/G]TCTTATAGGTCTACCTTATACTGCATAAGAGTGTG R 2 1 2 1 202000 r 74 goat snp5633-scaffold1199-900257 6 43204571 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388660 Affx-122969105 AX-123259018 6 40904297 GGCACAAAAGGATGGACTGTTACTCACAGAGCATC[A/G]CCCTTCACAAGGAAACACATGGGCAGGGGATGAAT R 2 1 2 1 101000 f 74 goat snp5634-scaffold1199-930136 6 43235619 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795518 Affx-122948665 AX-385282473 6 40956702 TTATTCTATGTGTAGGGTATTGGGACTGGGACAGA[C/T]AGATTGAAAACCATTCCTCAAGGTTCCATTGACTA Y 2 1 2 1 101000 f 74 goat snp5635-scaffold1199-982541 6 43288081 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782436 Affx-122921908 AX-385269512 6 41257845 AAACAAAGGGGTCAGGTGTTTTTATTCTGCTGTGA[C/T]GCCCTTGAAAAATTGAGATATTCCTTTGAGAGTCA Y 2 1 2 1 101000 f 74 goat snp5641-scaffold1199-1283684 6 43589749 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784047 Affx-122938001 AX-385271100 6 41292834 TTGGAGGAGAGAATTGGCATGGCTGGGAAGAGATA[C/T]GGAAGAAAGGTTTTATCTCTGGGACTAGACAGCAT Y 2 1 2 1 101000 r 74 goat snp5642-scaffold1199-1318673 6 43624691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419110 Affx-122945771 AX-123289458 6 41520851 AAAGACTTAGCACCACGAGGTATGTGGGCAAACCA[C/T]GCAGCTGCAGATGTCTCACACCTGGATCTATATGG Y 2 1 2 1 101000 f 74 goat snp5648-scaffold1199-1546690 6 43853896 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420862 Affx-122944639 AX-123291209 6 41592699 TGCAAATGGCATTATCTCATTCTTTTAAATAAATG[C/T]AATCATCTTCCAAAGGAAAAATTTGTGTGCCCTTG Y 2 1 2 1 102000 r 74 goat snp5650-scaffold1199-1618538 6 43925687 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381048 Affx-122974630 AX-123251406 6 41666037 AGAATAATTTCACGTCTAGAAATGGTTTAACCCAA[C/T]AATGTAGCAAAAATTCTGGCTTATATGTAATTATT Y 2 1 2 1 201000 r 74 goat snp5652-scaffold1199-1691876 6 43998891 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795859 Affx-122974611 AX-385282811 6 41698185 TATTAGCCAAATCTGAGGTCAAATTATGGTCACTC[A/G]CCTTATTAGTCCTAATTCTTGGGCACATCTATAAC R 2 1 2 1 101000 f 74 goat snp5653-scaffold1199-1724024 6 44031201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794753 Affx-122966705 AX-385281713 6 41837813 ACTATACATCAGGCAATTCCAGAACATTTAAATAG[C/T]AGGGCAGAGGTACCACTATAAGAAGCCACTGTGGG Y 2 1 2 1 101000 r 74 goat snp5656-scaffold1199-1863652 6 44170141 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402806 Affx-122958282 AX-123273159 6 41891566 TTACAGGAAAAAAAAAATATTCTACTTTCTGGTAA[G/T]ACAGCAGATGGTCCAGTGGTGAGCACTGAACTGTA K 2 1 2 1 101000 r 74 goat snp5657-scaffold1199-1917405 6 44223969 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770793 Affx-122927426 AX-385257957 6 41958478 TAACAGGTGAGACACTTAAGGCTTCAATAAGATAA[A/G]TATTGTGCCCAGTGTCACGTTAACTAGTCACAGTT R 2 1 2 1 201000 f 74 goat snp5658-scaffold1199-1984317 6 44290824 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278359 Affx-1111836381 AX-519551845 6 41988264 TCAGATGAGGTACATGTGTATAGCATCCTGCACCA[A/G]CTTTGGTACATAGTAGATTCTCAATAAAGGTTAGT R 2 1 2 1 101000 f 74 goat Random2.2K-677 6 41988264 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391501 Affx-122966675 AX-123261858 6 42023440 TGTACCCCTCAGAGCTACTACTTAGAGTCCTGTGA[C/T]GCAGGCACTGATGTAAGCACTTTGTGTAATTATTT Y 2 1 2 1 101000 f 74 goat snp5660-scaffold1199-2049279 6 44356183 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273202 Affx-1111833504 AX-519546861 6 42035155 ACACACTTGCCAGTGCAAGAGACATAAAAGATGTG[A/G]GTTCAATCCCTGGGTCAGGAAGATACCCTTGAGCA R 2 1 2 1 103000 f 74 goat 6_42035155_AF-PAKI 6 42035155 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320784667 Affx-122955399 AX-385271715 6 42063129 CATCTGCAGAACACCGTGTTTACGAAAACCTGTTG[A/G]TCTTTTTGATCAGCCTCCTTGCTCCCTTTATACCA R 2 1 2 1 101000 r 74 goat snp5661-scaffold1199-2088968 6 44395361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411450 Affx-122951815 AX-123281800 6 42092794 TTGACCTACAAAAAGCTAGTGAGTTTTATTTGGGA[C/T]GTATAGAATTAAAGGTGACTCTGGATATTCAGATA Y 2 1 2 1 101000 r 74 goat snp5662-scaffold1199-2118633 6 44424892 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394779 Affx-122964829 AX-123265134 6 42392481 GGAAGCAGCAGGAAGGCTGAAGAAATGTGCTGAAG[A/G]TTACTGAGCTAGTAAATTGCAGATTTGAGGTTTAG R 2 1 2 1 101000 f 74 goat snp5669-scaffold1199-2418320 6 44723975 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416122 Affx-122948300 AX-123286471 6 42427557 CTTTTATTTGAACAAGGCTTTGAAACTGATCAAAT[A/G]CCTGGATTATCTCATTCATTGCTCATCACCCTTTG R 2 1 2 1 101000 r 74 goat snp5670-scaffold1199-2453396 6 44759620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411884 Affx-122951195 AX-123282234 6 42467230 CATTCATCCCATTTGACTGGTCTCATAACAGGAAG[C/T]AAAGTATCCCAAGGGACCAAATGGCCCTCTTATAA Y 2 1 2 1 101000 f 74 goat snp5671-scaffold1199-2493069 6 44799485 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400192 Affx-122960188 AX-123270547 6 42644423 ACTTTAACTGGAACCGTAAATTCAGAGGCATCGGC[A/G]TGGCCAGGCAGTGGGTTACAGCAGGTGATTTAAGA R 2 1 2 1 101000 f 74 goat snp5675-scaffold1199-2670262 6 44976665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786720 Affx-122929917 AX-385273751 6 42710009 CTAAATGTGATCAAGACTATAATGGACCCAATGCC[A/G]CATAAGAGGTACTAAGTATTTGTTCAGAGATCTGT R 2 1 2 1 101000 f 74 goat snp5677-scaffold1199-2735848 6 45042013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422271 Affx-122943990 AX-123292617 6 42760768 GTAGCTGCTGGGTTTGACTTAGCAGCACAGTGATG[C/T]AAAGGTGGTTCTCCTTTTCTTCCCTCATGATTGTA Y 2 1 2 1 101000 f 74 goat snp5678-scaffold1199-2786607 6 45092988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278361 Affx-1111836382 AX-519551847 6 42808051 ATGCACAGTCCCACTCATCATGTACAAAAGGATTG[A/G]TTCATGCACTAAGCTGGGGGATAAAAACGATGCCC R 2 1 2 1 101000 f 74 goat Random2.2K-678 6 42808051 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784063 Affx-122945048 AX-385271116 6 42824957 ACCCTACTGTCTTAAAAAACACCTACTCAGATAAA[C/T]TGTTTCCATCTCCCTGTTGCAGCTAGTTCACATGT Y 2 1 2 1 101000 r 74 goat snp5680-scaffold1199-2850796 6 45156751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402234 Affx-122959145 AX-123272587 6 42860198 ACGTTAGTTGAGATGGGTTAGGTTTCACTGTGCCT[A/G]CAAACAATCCCCAAATCAGTGGAATTTTATTTAAA R 2 1 2 1 101000 f 74 goat snp5681-scaffold1199-2886037 6 45192284 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421750 Affx-122944367 AX-123292097 6 42922711 CTGTTTAGGACCAGTATCAATGGAGTATGTATGTG[A/G]AACCATTCACTTTATTCCGTCTCTGATTCAATTCT R 2 1 2 1 101000 r 74 goat snp5682-scaffold1199-2948550 6 45255805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403145 Affx-122958101 AX-123273498 6 42959257 ATAACTTTGTGTGTCGGGACTGAGTCATAGGATGA[C/T]GGCAGTGACGCTCCACCTACAGTCTGGCTGATGGC Y 2 1 2 1 101000 f 74 goat snp5683-scaffold1199-2985096 6 45293384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775803 Affx-122938664 AX-385262934 6 42997376 AATTTGTCATAGCAAATTGTACCTTTTTTATAATA[C/T]AATTTTACTCTCATGGAGTCCTCTCTGAATCTGTT Y 2 1 2 1 101000 r 74 goat snp5684-scaffold1199-3023215 6 45331924 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388702 Affx-122968988 AX-123259060 6 43036116 ATAAATAGCCTTAGACTGTAAAGAGATCTGTAGCT[A/G]TTGGAGTTGCTGATTGGAAAATGGGTTTAAAATAA R 2 1 2 1 101000 r 74 goat snp5685-scaffold1199-3061955 6 45370898 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798573 Affx-122953453 AX-385285506 6 43076360 GGAGCCAGCTATTGTTTTAATTTACAACAAGAGCC[A/G]CTATTGCTTCTGGAAGTATTAAATATTTTCAGTTC R 2 1 2 1 101000 f 74 goat snp12879-scaffold1498-8679 6 45415346 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775315 Affx-122977432 AX-385262446 6 43115323 TTTTATAATGAGATGATGGCATCTCTACAAGAGAT[A/G]CTAATTTTCCATTTGTGGTGGTGACACTATTTATT R 2 1 2 1 202000 f 74 goat snp12880-scaffold1498-47642 6 45452774 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440762 Affx-122929859 AX-123311099 6 43157354 AGGACAAATTCCTAGAAGAAACTTTGAGTCAGAGT[A/G]TATGCTCATTTCTAAGACTTTTGATGTATTTTGCT R 2 1 2 1 201000 r 74 goat snp12881-scaffold1498-89673 6 45494802 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386556 Affx-122970713 AX-123256914 6 43210112 CAAAATTCAACTTACTCCGAATGACCTGGAGCATC[A/G]CCATGAAGGGTAGAGGGGGAGGGTGACTGGACTGC R 2 1 2 1 101000 f 74 goat snp12882-scaffold1498-142431 6 45547890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443315 Affx-122927453 AX-123313652 6 43258334 TCCCCATTCTGTTCTCCAGGGATTATCTTTGTGAC[A/G]TTTAGAGGAAGTTGAAGGAAAGTAACCACCATCCT R 2 1 2 1 201000 r 74 goat snp12883-scaffold1498-190653 6 45596465 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397813 Affx-122962488 AX-123268168 6 43288657 ATGCTTTTGATAAGAAATATCTTACTGAATTTTCT[A/C]TTTATCTACAAAAACAGCATAGAGTCAGTACTCCC M 2 1 2 1 101000 r 74 goat snp12884-scaffold1498-220976 6 45625400 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787656 Affx-122923700 AX-385274679 6 43330064 GTGCTCTACCTGGCAACAAATTTAGGGACGGGACA[G/T]AATTTGCATGAGGAAAATTTATCAGCCAGCATGCT K 2 1 2 1 101000 f 74 goat snp12885-scaffold1498-262383 6 45666818 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442857 Affx-122927677 AX-123313194 6 43385988 GGAGGGGATTGAAAATCTGCAAAAGGGCAAGAAAA[C/T]GAAAGGAACAACACTGTCATCAAATGCCCGTGGAT Y 2 1 2 1 101000 f 74 goat snp12886-scaffold1498-318307 6 45722762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439859 Affx-122930057 AX-123310196 6 43444445 CAAACTCTCAAGAGGGAAAGAAAACAATTCTCTTC[A/G]GCACTTCCTTATCCACCTCCCCCCATCCTCACCCC R 2 1 2 1 101000 f 74 goat snp12887-scaffold1498-376764 6 45780116 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376956 Affx-122977765 AX-123247315 6 43490419 GTGATCAGATTCAGCCTTTCCAGGCATCTCTGACT[A/G]TATCTGGCGGAGGGGCCGGAAGGGCCAAGGTTGAA R 2 1 2 1 101000 f 74 goat snp12888-scaffold1498-422738 6 45826049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386939 Affx-122969992 AX-123257297 6 43527601 AGTGTTTTTTCAGTGTTTTGCCATTTCACAAAGAT[A/G]TATTTTTATTCACTGTGTTGGGCATTCCAAGGGTC R 2 1 2 1 101000 r 74 goat snp12889-scaffold1498-459920 6 45863398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441222 Affx-122929516 AX-123311559 6 43583813 AGAGCTGGTGGTCTCTCTGGCCGTCCACCTGGAGA[C/T]GACCTGCGTTCCCCCAAAGGGGCAGTTATATAGCC Y 2 1 2 1 101000 r 74 goat snp12890-scaffold1498-516132 6 45919970 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437672 Affx-122931779 AX-123308010 6 43627970 ACAATGGAAAATAAGATTCCAGAGGGAAAGCATGA[C/T]GAACGACTCAACAAACTGTTCAACTGAAGAAACAC Y 2 1 2 1 101000 f 74 goat snp12891-scaffold1498-560289 6 45963557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798694 Affx-122963064 AX-385285626 6 43637248 GAAAGAATTCAGAGGTGGGTATAAGGAAGGGATAA[C/T]GTTTAGGAAAACCTTGCCAATGTGTTTTCAACTTT Y 2 1 2 1 101000 r 74 goat snp52104-scaffold771-4330 6 45972755 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779257 Affx-122954257 AX-385266361 6 43665773 GTGGCTAATTTGGTGTCCCTTTTCTGCAATATGGC[A/G]TTGAAAGTCATTCCTATAAACGAAACCTTCCCAAT R 2 1 2 1 101000 f 74 goat snp52105-scaffold771-32855 6 46001930 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428610 Affx-122938690 AX-123298952 6 43696657 TGCCCGCAATGTGCCCCACAGGCAGACCCCAGTTT[A/G]CATCTAAGCCCTTCTCAATTCCCAAGGAAAATAGG R 2 1 2 1 101000 r 74 goat snp52106-scaffold771-63739 6 46033200 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418170 Affx-122947085 AX-123288518 6 43754531 TCCCTGGTGGGAGAACTAAGGTCCCACATACCTTG[C/T]AGTGTGGCTAGAACAGAACAAAAACTTGAGCACAC Y 2 1 2 1 103000 r 74 goat snp52107-scaffold771-121613 6 46090905 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385670 Affx-122971146 AX-123256028 6 43877924 ATAAATCTGGTCATCAGATGACCAGAATTTATTTC[G/T]CTTACATGTTTGGTCTTGTCCACAGTTCCTGACTC K 2 1 2 1 101000 r 74 goat snp52109-scaffold771-245006 6 46214946 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396721 Affx-122962806 AX-123267076 6 43912067 AAATGAGAACACATATAAACACATACATTCTGTTT[A/G]TTGTGTGCTTGTCTTTTATTGCATGAGGCTAGTTT R 2 1 2 1 101000 r 74 goat snp52110-scaffold771-279149 6 46249736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777416 Affx-122937781 AX-385264537 6 43944582 CATGCTTTGGTGGACAAGGCTGCTTATGGAGGAAC[A/G]TGAAAGATTTTTTTGGGTTGGCTTGAAAGGTAATA R 2 1 2 1 101000 f 74 goat snp52111-scaffold771-311664 6 46282589 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445097 Affx-122926200 AX-123315434 6 43974295 CCTGGCGAGAACCTGCAAGACTGGACAGTTACTTG[C/T]GGTTCATGTGTTAAGGATAAAGTCGTCTGTGTGCC Y 2 1 2 1 101000 r 74 goat snp52112-scaffold771-341377 6 46312352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445654 Affx-122926152 AX-123315991 6 44007285 GTCAGGAGTTTTCTGCTTGCTTGGGAAACCTCCAG[A/G]TTGCTTCTACTGCATAATGAGCAAAAATCAACAAC R 2 1 2 1 201000 r 74 goat snp52113-scaffold771-374367 6 46345544 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411865 Affx-122951212 AX-123282215 6 44055931 TCCTTTATGCTGGAAACTCCCTGTGGCAGAGACCA[G/T]CTAGATGTTCACTGACCCAGATTCCACTTCCTAGA K 2 1 2 1 101000 r 74 goat snp52114-scaffold771-423013 6 46394446 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802695 Affx-122928223 AX-385289594 6 44094303 TTTTTCTAATGCCTAGAAATTAATAATGTAGAAAA[C/T]GATTTTCATAGATGTTCAGAAGAACTTCTTGCAGA Y 2 1 2 1 201000 f 74 goat snp52115-scaffold771-461385 6 46430025 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428058 Affx-122939121 AX-123298401 6 44124080 GCTGGTGAGCAGGTCAGATGGAAATGGGGAGTGTT[A/C]TACTTTCATCCTCCACTTCATTCCTTCCTATATTC M 2 1 2 1 101000 r 74 goat snp52116-scaffold771-491162 6 46459707 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789285 Affx-122943050 AX-385276296 6 44161902 GATGAGTCTTTTACACCCTACTGGTAATTCAGGTG[C/T]AAACTAGCAGTCTATACATTTTCAATAAACAGTGT Y 2 1 2 1 101000 f 74 goat snp52117-scaffold771-528984 6 46496239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781599 Affx-122920730 AX-385268682 6 44217076 CTTTAAAAAAGTATCATTAGGTTGTAACACATTAT[A/G]TAGTAATTTGAGACTTTTATAATGAGCTTAAGGCA R 2 1 2 1 101000 f 74 goat snp52118-scaffold771-584158 6 46551483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425540 Affx-122941451 AX-123295886 6 44285145 AAAAGGAGAAGGGTGGATAAAGAAGAAAATAAATC[A/G]CAGGAATTGTCTGGTAAAATAAAGATTCATCTTGT R 2 1 2 1 101000 r 74 goat snp52120-scaffold771-652227 6 46619342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784166 Affx-122936522 AX-385271218 6 44314748 CTTAATAAAGATTAGTGCTCGAGTGTTGGGCAGAT[A/G]TTTATATTGGTTCAGGGTGTGATTGGTGATGTAGA R 2 1 2 1 201000 r 74 goat snp52121-scaffold771-681830 6 46649320 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388152 Affx-122969460 AX-123258510 6 44359112 CTTCTTGACACTTGCTAATCCTACCTTCAGCAACT[A/G]TTCTTGACTGGTTTCACTGTTGCAGATTTAAGGAT R 2 1 2 1 101000 r 74 goat snp52122-scaffold771-726194 6 46693889 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379493 Affx-122976470 AX-123249851 6 44410192 GATTAGTGGGAACTTCTTGAGGTGACAAGGACAGC[A/G]TGTTTTGTGTGGGTGGGAGAATAAGTGGGAGTAAA R 2 1 2 1 303000 r 74 goat snp52123-scaffold771-777274 6 46744954 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421205 Affx-122944144 AX-123291552 6 44438872 TGTTGACTTTGGGAACAGACAGAAAATTGGGAGGA[C/T]GAGGGGGTCTCTAGCATCATGGACAAATTGGAATT Y 2 1 2 1 101000 f 74 goat snp52124-scaffold771-805954 6 46773590 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393638 Affx-122965300 AX-123263993 6 44476857 TCTAGAAAACAGTAGGCTTTCTTGAACATCTTACC[A/G]TTCTTTCTTTCCTTACCCCACCAATTGGGAACCAG R 2 1 2 1 101000 f 74 goat snp52125-scaffold771-843939 6 46810675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800723 Affx-122949222 AX-385287640 6 44519341 GCAATGCAGTGAGAACAGTTTCATGATGTGAAAAT[A/G]CACTGTGGTATTGCCATGTGAGAACAAGGAGGGAA R 2 1 2 1 101000 f 74 goat snp52126-scaffold771-886423 6 46853080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442970 Affx-122928205 AX-123313307 6 44569251 TGCCTTATCTGTAGGTTCTCCATCTGCTGACAGAA[C/T]ATGCAGATGCAGAGGGCGGCTGTGAATTTCCATGG Y 2 1 2 1 201000 f 74 goat snp52127-scaffold771-936333 6 46902404 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793268 Affx-122939536 AX-385280246 6 44606058 ATTCTTTTGCAGATGTAAAAGTGTACTGTAAAGCC[A/G]TATCCTAGGATGTAGACAGTGTACTGTAAAGGTTG R 2 1 2 1 101000 r 74 goat snp52128-scaffold771-973140 6 46939046 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439194 Affx-122931043 AX-123309531 6 44649197 GGTAACTCAACAGTGCAGTAAGGGAGATAGATATG[C/T]ATGTATTCAGGTGTAATAAATTATTGAAAACTGAA Y 2 1 2 1 101000 f 74 goat snp52129-scaffold771-1016279 6 46982221 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464443080 Affx-1110485489 AX-515915757 6 44694785 CAGAGCAGAGCTAAAATTCTCTCAGATCCATAACA[A/G]GCTACATGAATACCCTTCCATTCTCTGGAACATGG R 2 1 2 1 101000 r 74 goat 6_44694785_AF-PAKI 6 44694785 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38427730 Affx-122939268 AX-123298073 6 44699431 AGGTTTGAGAAGCATTCTTTAAAGACATTGAAACT[A/G]TTTTCCCTTTACCAACAGGGCCTCAGTAGCATACA R 2 1 2 1 101000 r 74 goat snp52130-scaffold771-1066513 6 47032712 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799890 Affx-122921439 AX-385286816 6 44732416 GATCAGTTGGCAATGACTTTCCGGAGCATTGTCTT[A/C]TGAAGGCTTCTGATGGTGTGTTTAGATTCAACAGT M 2 1 2 1 101000 r 74 goat snp52131-scaffold771-1099498 6 47065959 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402374 Affx-122959035 AX-123272727 6 44774781 CCAGGCAAGAGTCACAGCCATTCCGAAAACTTTAA[C/T]GGTTTGACAAATGAGCAATTTATAATCAGCTGCAC Y 2 1 2 1 101000 f 74 goat snp52132-scaffold771-1141863 6 47108866 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770772 Affx-122942684 AX-385257936 6 44806084 GAACAGAATCTAGCACACAATTGGTCCTAAACAAA[C/T]GTGAGTTTCATTTTTACCTTCCTTTGGATCAACAT Y 2 1 2 1 201000 r 74 goat snp52133-scaffold771-1173166 6 47140009 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418561 Affx-122946389 AX-123288909 6 44836351 AAATCCAATACTTTCTCACTCAGCGGGCAGCTTCA[C/T]TGGAGGACCCTGATGGGGTTGCAACTCTCTAATTT Y 2 1 2 1 201000 f 74 goat snp52134-scaffold771-1203433 6 47170181 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379308 Affx-122976199 AX-123249667 6 44886217 GTCTTAATAGTGAAAGAGGATAGTAAGTGACTGCC[A/G]CAATGGATGAAAAAGACTTGCACTTAGGCAAATCA R 2 1 2 1 201000 r 74 goat snp52135-scaffold771-1253299 6 47218095 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773504 Affx-122963673 AX-385260645 6 44925511 GCACCTTTTCTTATGTTCTTGTGACACTCCCTGTG[C/T]GATTCCTTTGCTGTTTGATACTCAATGCTTTTAGC Y 2 1 2 1 101000 f 74 goat snp52136-scaffold771-1292593 6 47257398 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383249 Affx-122972747 AX-123253607 6 44957766 ATAATAAGTTAAATTTGTGGGCGAGCATATTAAAA[C/T]GACGAAATAGAACAGAATAGAAACTCATTGCATGT Y 2 1 2 1 202000 f 74 goat snp52137-scaffold771-1324848 6 47289467 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786900 Affx-122956865 AX-385273929 6 44995471 AAAGTCTAGAGAATAAAATGAGCTAAAGGCCAACC[A/G]TGAACATTGACACACAGAATAAAACAATAGCTTAA R 2 1 2 1 101000 f 74 goat snp52138-scaffold771-1362553 6 47327222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409829 Affx-122952946 AX-123280180 6 45024541 AATGTCTAGATAAAATTGTGTCTTTCGACTAATGG[C/T]GCTTGGAATTTAACTTGAGGTTTTACCACAATAAT Y 2 1 2 1 101000 f 74 goat snp52139-scaffold771-1391623 6 47356219 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438119 Affx-122931492 AX-123308457 6 45064774 TGATTAATTTGGTCAGTATGCCACGTCTCCTCCTC[A/G]GTTAAGGGCTTACACTTTCAGCCTTCTTCACGGGC R 2 1 2 1 101000 f 74 goat snp52140-scaffold771-1431856 6 47396256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801858 Affx-122975882 AX-385288765 6 45098816 TTCTTATTTCTAAAGGTATTTTATGCTATTCATCT[A/G]GTACTGCTTGAAATGAACTTGCAGGAAAGTAAGTA R 2 1 2 1 101000 r 74 goat snp52141-scaffold771-1465898 6 47430369 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278365 Affx-1111836384 AX-519551851 6 45098894 AAGGAACTCCTAGAATGGAAGTGGGAAGCATAGGC[A/G]TGCGTGCTAAGTCACTTCAGTCATGTCCAACTTTT R 2 1 2 1 202000 f 74 goat Random2.2K-680 6 45098894 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320783078 Affx-122957729 AX-385270145 6 45145304 TCAATATTTGAATCCCTGTAACTTGTGAATATGTT[A/G]TCTTATTTGATAAAAGGATTTATAGACATGATTAA R 2 1 2 1 101000 f 74 goat snp52142-scaffold771-1512386 6 47478200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794532 Affx-122943291 AX-385281495 6 45176457 TGAAGGATGATATCATCTTCAAGTAGGAAAGACCC[A/G]TCTAAGATTCAGAAAACAAATCAACCCCACAAAAG R 2 1 2 1 303000 r 74 goat snp52143-scaffold771-1543539 6 47509245 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770276 Affx-122971871 AX-385257442 6 45237340 GCATACAGAACAGCAGAAATGACAGTATACATAGT[C/T]ATCTCCCTCCTGTTGAAAGGTACAGAAAAAAGTTC Y 2 1 2 1 101000 f 74 goat snp52144-scaffold771-1604422 6 47570784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787645 Affx-122949223 AX-385274668 6 45292403 GCCTGTATTAACAAAATCAGTCAGAATAGTGCTGA[A/G]TTCCTGGAAGCAAATGACAATGGAAGCTAAAGTGA R 2 1 2 1 101000 r 74 goat snp52145-scaffold771-1659485 6 47626274 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384302 Affx-122972285 AX-123254660 6 45345134 AATAAGTCCTATAATTTTGTACATGTTGTTTCCTC[A/G]TCAGTCACACATTTTTCCTTATCATTTACCTACTT R 2 1 2 1 101000 r 74 goat snp52146-scaffold771-1712216 6 47681649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414210 Affx-122949650 AX-123284559 6 45382106 AACTTTACAATAGCACTTATTTTTCATTAATCTCA[A/C]TTTCACTGAGACAGGTTCCATTATGTGAGTTACTC M 2 1 2 1 201000 f 74 goat snp52147-scaffold771-1749188 6 47718157 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432205 Affx-122936382 AX-123302546 6 45399891 TTTCTCTGTCATCAGCATCCACATGCCCATAGTTG[C/T]ACCATTCATTCCCTAAATGATACCCAAGAGGTAAA Y 2 1 2 1 101000 r 74 goat snp23942-scaffold241-2178809 6 47735751 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767237 Affx-122949104 AX-385254518 6 45442328 ATGAAGCTGGAGATGGGACTCTGAAAATTACCTTT[A/C]TCCTTTGCCAGCTAATATACTATTAGGTTGTTCAA M 2 1 2 1 101000 f 74 goat snp23941-scaffold241-2136372 6 47779383 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384538 Affx-122973026 AX-123254896 6 45483029 AAACTGAGATTCCCTGAGGTCATCTTGTTCCAAAC[A/G]CATAGTTATTTATTCTCATTTCACTGCAGTGATTT R 2 1 2 1 101000 f 74 goat snp23940-scaffold241-2095671 6 47820057 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764716 Affx-986696988 AX-385252335 6 45532325 CATGATGAGATGTTTGATGGAGCTGGGAGGTCAAT[A/G]AATGCGTTGTTTACAATTTTTATTAGTGGGTGAGT R 2 1 2 1 600010 r 74 goat 6_45532325 6 45532325 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 320775208 Affx-122948376 AX-385262339 6 45534923 GTTCCACTGAAAGTTGGATTTGCTTAAAATTTCAC[G/T]TATGTTAAGAAAGTATCATTATCTGGTGAGCAATT K 2 1 2 1 201000 r 74 goat snp23939-scaffold241-2043777 6 47871724 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428397 Affx-122938949 AX-123298740 6 45581506 AAATAACATATAATAAAATAACAAAATGCCTCATG[C/T]GGAGTTTTTTGTTATAATAGGATCTATAAAGCAGA Y 2 1 2 1 103000 r 74 goat snp23938-scaffold241-1997194 6 47918132 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799385 Affx-122940454 AX-385286315 6 45636938 TAGGATGCAGCTTAAGATGATTAAAATAACAAGAA[C/T]GCCTGTTGAGGTCTGTTCTATTACAGCAAGAAAAA Y 2 1 2 1 101000 r 74 goat snp23937-scaffold241-1941762 6 47972912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376616 Affx-122979044 AX-123246975 6 45666511 TCTGACTCTGTTCTGACATATTAGGAAATGTGTCA[C/T]ATTTGCACCCCAGGCCATTTAAATATCCTTTATCT Y 2 1 2 1 101000 r 74 goat snp23936-scaffold241-1912189 6 48002111 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437402 Affx-122932426 AX-123307740 6 45704214 ACTAAAACCTTTTGGATTTCCTGACAGATATGATC[A/G]TCTTTTGTTATTCATAAGAATTCATTTCTGAACAC R 2 1 2 1 101000 f 74 goat snp23935-scaffold241-1874486 6 48040408 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770172 Affx-122976340 AX-385257340 6 45738088 CCAGTTAGATAACATTCTTCAGTCAATATCATTAT[C/T]TATCAGTGTTATTGTTTGTTTTGTAGCAAGATTTA Y 2 1 2 1 101000 r 74 goat snp23934-scaffold241-1840612 6 48074647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777926 Affx-122972431 AX-385265042 6 45785263 TTCACTTCAAATGGACATGAAAATGTTTTTGAGAT[A/C]GATAAAAAGCTTAGAGATTTTTACAGAAAGCAGTC M 2 1 2 1 101000 f 74 goat snp23933-scaffold241-1793437 6 48122015 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395599 Affx-122963823 AX-123265954 6 45821587 TTCAAAAATGTCTTCCAGTGCCTTTGATCTTATTG[C/T]AGTTTTCACAGTGTCCAGTGACAACCAGATGATAA Y 2 1 2 1 101000 r 74 goat snp23932-scaffold241-1757113 6 48158333 C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408316 Affx-122953766 AX-123278667 6 45854605 TTTCTTAGAGAGAAAGAGAGGATCTCTGTATCTCC[A/G]TTAGAAAGAGGACTTGAGAAATAAAAGCACTGAGA R 2 1 2 1 102000 f 74 goat snp23931-scaffold241-1724095 6 48191533 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782246 Affx-122930624 AX-385269323 6 45910545 TTTCCAGTCCAGATAGTCACACTTCATTAAAAAGA[C/T]TGTGTTGCTTCTCAACTGAAAACATAACAGGAGAA Y 2 1 2 1 101000 r 74 goat snp23930-scaffold241-1668155 6 48247362 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387789 Affx-122969702 AX-123258147 6 45952024 TATTTGCAATTGAAATATAGGCTACATACTGCACA[C/T]AGCAAGTTTAATATTTCAATTTCAGGCATCATAGC Y 2 1 2 1 101000 r 74 goat snp23929-scaffold241-1626676 6 48289571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404413 Affx-122956776 AX-123274765 6 46062932 ACAAATTCAGTGGACACTTAGCAGGCTGTGGGGCA[C/T]CTCATATACTAAAGCTACTTCCTCTCATAACCACT Y 2 1 2 1 201000 r 74 goat snp23927-scaffold241-1515768 6 48402508 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449372 Affx-122922722 AX-123319707 6 46109977 TCTGAAAAATATAGTTCCCTGACTGATCTACAAAA[C/T]AAGGGTGCTGTAGGCTAGGTGAATTATGTGGCCCC Y 2 1 2 1 101000 f 74 goat snp23926-scaffold241-1468723 6 48450528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424885 Affx-122941322 AX-123295231 6 46183819 ACTGATCAATGTTTTCCAATATGATTGTACCATTG[C/T]ACCTTCCCTTCACAGTGTAAGAGAGGTCCCCATGG Y 2 1 2 1 201000 f 74 goat snp23925-scaffold241-1394881 6 48525038 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416792 Affx-122948149 AX-123287140 6 46215203 GTTTCTCTTTGATAAGGTTACAGACAGGAAATAGG[C/T]AGTTAACAAATCAAACTGAAGAATATAATTATTCT Y 2 1 2 1 101000 f 74 goat snp23924-scaffold241-1363497 6 48556914 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421021 Affx-122944547 AX-123291368 6 46250563 CTCTGTTTGCATTACATTTATTTTGCTCATTTTCT[A/C]GTTTTGGGCAATAGAAACTCAGACTAAGACCTTTC M 2 1 2 1 101000 r 74 goat snp23923-scaffold241-1328137 6 48592679 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278367 Affx-1111836385 AX-519551853 6 46273708 TGTACACCTCAAATTGGATTTTTGTCACTTGTAAA[A/C]TCCAAATAATAAAGGTTCCAACATGAACTGTCTGC M 2 1 2 1 101000 f 74 goat Random2.2K-681 6 46273708 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430882 Affx-122936880 AX-123301223 6 46297424 TTTAGACTTTAAAACCTAACAAATAAGGCTGAGAA[C/T]GGTTTTGAGTGAGGAAAAACTTAAGATTTTACTTT Y 2 1 2 1 101000 f 74 goat snp23922-scaffold241-1281276 6 48639789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439420 Affx-122930236 AX-123309757 6 46331477 TTTCTACTTTGTTTTATTGCTCAAGATTTCTCAGG[A/C]TATCTTATGACTATATATATCTATACACTTTCCTT M 2 1 2 1 101000 f 74 goat snp23921-scaffold241-1247223 6 48674011 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399359 Affx-122961348 AX-123269714 6 46374762 CCATTTCTGTTTCAAATTGTCTCCTCAGCAAGAAA[C/T]GATTCATCAATAGTGATATTTCTAGGATGTGAGCT Y 2 1 2 1 101000 r 74 goat snp23920-scaffold241-1203938 6 48718119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390424 Affx-122967641 AX-123260781 6 46425740 CATGTGCCACCATCATTTAAATTACTTGGGATAAA[C/T]AAAATTTTGAAATGTCATTTCTAAAAAATAGACTC Y 2 1 2 1 103000 f 74 goat snp23919-scaffold241-1152960 6 48768998 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385547 Affx-122971232 AX-123255905 6 46487389 TGTCACCCTATCATTTTCAGGAGATTATGCTTTCT[A/G]CTTACTCCCTGGTGGTGTGCTGCAGTCCATAGAGT R 2 1 2 1 201000 f 74 goat snp23918-scaffold241-1091311 6 48830478 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796334 Affx-122962460 AX-385283284 6 46527009 TGAACACGCACTCTCAGTGAGACACTGCTTCATCC[A/G]CACAAACTAGAAGATTGATGCAGGATAGACAAATC R 2 1 2 1 202000 f 74 goat snp23917-scaffold241-1051691 6 48870197 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434271 Affx-122934784 AX-123304612 6 46566578 TAATCATTCAGCACTGTGATTTTATTCTGTGAGGT[A/G]TAGAAAAAACTTTTAATTCATATTCGTATTTTAGC R 2 1 2 1 303000 r 74 goat snp23916-scaffold241-1012122 6 48909801 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381944 Affx-122974122 AX-123252302 6 46616471 AATTAGGATGGAAGACATGAAAAACAGACAGACGG[C/T]AATACTAAAACATTTTTCTATGTCTATGCCCCGAC Y 2 1 2 1 101000 f 74 goat snp23915-scaffold241-962229 6 48959996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799528 Affx-122965175 AX-385286458 6 46652528 ATATATTTGTTTTTAGAGTTAGGAGATGAATGTAC[A/G]TTCCTTAGAAGAGCTACAGAAATGCTTGTGCTTGA R 2 1 2 1 102000 r 74 goat snp23914-scaffold241-926172 6 48997331 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449162 Affx-122923544 AX-123319497 6 46688925 ATCCTTGAAATGTTTTCTTCATGTGGCTTCCAGTA[C/T]GCTTCACTTTTTTGTTTCATTTTTTTCTATTTTAT Y 2 1 2 1 303000 r 74 goat snp23913-scaffold241-889775 6 49034714 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801842 Affx-122947634 AX-385288749 6 46724222 TTCCACCTAACTACAAATGAAGCTGAAATGTGTAT[A/G]TTTTAATTGTGTGCTATGGACAAAGAGAAACTCTC R 2 1 2 1 101000 f 74 goat snp23912-scaffold241-854478 6 49069398 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801931 Affx-122921887 AX-385288836 6 46760284 CTGGAAATCAAGCAGTAGGAGTCATACCACTGTTA[C/T]GTCTCTCTTACTTAAATTTAGGGCTCCTTCTCTAG Y 2 1 2 1 201000 r 74 goat snp23911-scaffold241-818416 6 49105764 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420885 Affx-122944621 AX-123291232 6 46808531 GCGCTTTACTGCTAAAATGATTCTAAATCAAAATG[C/T]AAAGAAGAGGTATTCCTTATTGACCTTTAAATATC Y 2 1 2 1 101000 f 74 goat snp23910-scaffold241-770169 6 49149953 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444886 Affx-122926267 AX-123315223 6 46857254 GCGTTCCTCATGATGTTCTCTGCATAGAAGTTAAA[C/T]AAGCAGTGATAATCTCACCTCACTCTAAAGAGCAA Y 2 1 2 1 303000 r 74 goat snp23909-scaffold241-721446 6 49198696 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409091 Affx-122953328 AX-123279442 6 46908337 GATGTGCTTTAACTGGTGAATAACAATTTTAAACG[A/G]TGTTCTGATGGAAGCAAAGCAGTCTCTTTCCCATT R 2 1 2 1 101000 f 74 goat snp23908-scaffold241-670363 6 49250504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400945 Affx-122959706 AX-123271298 6 46966084 TCTCCAGTATTTAGTTACTGCTGTGTCTGTGCTGC[C/T]TTTTGGGACTAGACTTCTGAAACGGTTTCTTTGGT Y 2 1 2 1 101000 r 74 goat snp23907-scaffold241-612616 6 49308749 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440132 Affx-122929691 AX-123310469 6 46997627 TCCCAGTTCATTCTTCTTTAGACCAATAAGAAAGT[A/G]CAATATACCTAAGTGTCTACACAAAGGTATGTTTG R 2 1 2 1 101000 f 74 goat snp23906-scaffold241-581073 6 49340865 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784121 Affx-122968865 AX-385271173 6 47044407 AATTAGCCGTTCATCTCGGAGTACACATAACTTGC[A/G]TATATATTGCGTGTCAAGCATTACATCTTCATATG R 2 1 2 1 201000 r 74 goat snp23905-scaffold241-534293 6 49388576 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784769 Affx-122922081 AX-385271816 6 47092218 TATGACTTCAAGTTGTGCTTTGACATAAAAATCTT[A/G]TTTATTTTCTTCATATACATTGTATTGCTGTAAAT R 2 1 2 1 303000 r 74 goat snp23904-scaffold241-486482 6 49434549 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395123 Affx-122964144 AX-123265478 6 47127534 TTGGACATTTACTGGCTATCTGATTTTGAATGATA[C/T]GTGTGATTTGTTGGAGATTCCTCTTTTTGTTATAT Y 2 1 2 1 201000 r 74 goat snp23903-scaffold241-451166 6 49470441 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381194 Affx-122974537 AX-123251552 6 47164315 TGTATTAAAGCCAGAGAGCAAAGAAACAAAGCAAC[A/G]CTCTTCAGAAGAATAGAATTCAGAGTCTCACAAAT R 2 1 2 1 101000 f 74 goat snp23902-scaffold241-414385 6 49507882 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409155 Affx-122953210 AX-123279506 6 47237570 TTCTGTAAAAGTCTTTGCTGAGTAAAGGATATAAT[A/G]AAAGTGATGTTGTGATAGGTGTATCCTAATGGGAA R 2 1 2 1 101000 r 74 goat snp23901-scaffold241-341130 6 49581486 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273252 Affx-1111833505 AX-519546904 6 47260010 GTAAACAGAGCAATTCCTTTCATAAATATCAAAAC[A/G]CTAAACAGCTACCCTAGTTCCTAATGTTGAATTTG R 2 1 2 1 101000 r 74 goat 6_47260010_AF-PAKI 6 47260010 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320774314 Affx-122943230 AX-385261450 6 47282510 CATTAGCACTTTATTACCAATAATATGGTTACAAA[C/T]ATTTTTGGTGTCTTGGTAATCATTTGGTCTCTTTG Y 2 1 2 1 201000 f 74 goat snp23900-scaffold241-296190 6 49627140 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784547 Affx-122939131 AX-385271596 6 47316985 AGGTCTCAAACTTTTAGATTCTGGTGGGGAGATAT[A/G]GGGATATACTCATCTTGTGGCCGCCTAAGACAAGT R 2 1 2 1 101000 r 74 goat snp23899-scaffold241-261715 6 49662691 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384491 Affx-122973063 AX-123254849 6 47353748 TTTTGGAGAACACTAATTGGTACTATTGAAATACT[A/G]TATGCTAGTAATAATGTCCTTTTCTTTTTCATTGA R 2 1 2 1 101000 f 74 goat snp23898-scaffold241-224952 6 49699434 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762462 Affx-986696992 AX-385250589 6 47355852 AAACATCAACTCAAGCCTCCAATCAACATAAAATA[C/T]AGCTAAAACACAAGAAACTAGTGCTTATGTATAAG Y 2 1 2 1 600010 f 74 goat 6_47355852 6 47355852 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 38402200 Affx-122959167 AX-123272553 6 47396994 ATAAATCTTTGCAAAAAATAATAAAATGAGATGAA[A/C]TGCAAAGTAGATTGTCTCTGTGTTTTGCCATTTTT M 2 1 2 1 103000 r 74 goat snp23897-scaffold241-181706 6 49741962 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782418 Affx-122978740 AX-385269494 6 47437508 TTCATGCAATGCAAGAATTGGCAAACTATAGAACA[C/T]GTCAAAGCAGGCAAGCCTCCTATTGTATTTTAGTG Y 2 1 2 1 101000 r 74 goat snp23896-scaffold241-141192 6 49780747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792858 Affx-122932686 AX-385279836 6 47480381 AGTAAAAGATGAAACTCTGAGAGGTCAATAAACAC[A/G]TTCAAACTTACACGATTTAAAGATGTCAGATCCAG R 2 1 2 1 101000 r 74 goat snp23895-scaffold241-98319 6 49823477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400932 Affx-122959717 AX-123271285 6 47528553 TGAAAGATACTCCATGTGATACTGAACAAGCTAGA[C/T]ATCTTCTCACTATAAACCTCTGTGGGTTGTTGAGT Y 2 1 2 1 101000 r 74 goat snp23894-scaffold241-50147 6 49872061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382095 Affx-122974898 AX-123252453 6 47561162 TTCATGGAACAGACCTCTCTCCTTGTTAATCATCC[G/T]ATTTCTCTTGCTAACAATGCCTGGTACTCAGTGTC K 2 1 2 1 101000 r 74 goat snp23893-scaffold241-17538 6 49904342 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786022 Affx-122926498 AX-385273058 6 47587889 AGTCAAAACCCTATTTTTAAGTATCAGTGTGACAT[A/G]CACTATGTTGTAAGGTTTCTTTATACTTGCTTCCA R 2 1 2 1 101000 r 74 goat snp26647-scaffold2790-4489 6 49941106 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390687 Affx-122967951 AX-123261044 6 47608548 CCAATGGGTGGTGAAGGGATATATTACAACTCGGT[A/G]ACTTATTAATGTTGGCAAAGAATTATTCAGGAAAA R 2 1 2 1 101000 r 74 goat snp17112-scaffold1789-313255 6 49975308 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775992 Affx-122959144 AX-385263122 6 47647066 ACTAGTACAATATGATTATAACATAGCAGAGCATC[A/G]TTTTCCTGTCTTTGTTAACTTCATGTTTATAGCAG R 2 1 2 1 101000 f 74 goat snp17111-scaffold1789-274737 6 50014925 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425614 Affx-122940910 AX-123295960 6 47724195 GCAGCTGCCTTACCCTTTTATTCCTATTCTAGTCC[A/G]TGCCCTGCATTGTGGCCTAAGTGATCTTCCTAATG R 2 1 2 1 101000 f 74 goat snp17109-scaffold1789-197608 6 50092811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780261 Affx-122942221 AX-385267356 6 47839202 GAAATGACAATGTGCTGCTCTGTAATAGGTCTTCT[A/G]CTTTCTTCACAATAGTCTTTTTATATCGGTGGCCC R 2 1 2 1 101000 f 74 goat snp17107-scaffold1789-82601 6 50208812 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432337 Affx-122936286 AX-123302678 6 47881611 TATCAAACCAGTGACTTTTCAGATACCTCTGATTC[A/G]TTTAATGTAGATTCATTTAGCTTCTAACAAGTGCC R 2 1 2 1 201000 r 74 goat snp17106-scaffold1789-40192 6 50252133 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416521 Affx-122947770 AX-123286869 6 47921348 AAGGTGAAAGTAAAGAAATTTAATGTTACTGGATG[C/T]AAATTTACTCACTAAATTAATTTTTTGGAATATAT Y 2 1 2 1 103000 f 74 goat snp17105-scaffold1789-455 6 50291991 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779638 Affx-122921512 AX-385266740 6 47944843 GTCTTTATTTTGCAGGAAGAGAGAAAAATTCAACT[A/G]TAACAGTGTGTTAGGATGAGACCTACACGGACAGA R 2 1 2 1 101000 f 74 goat snp41819-scaffold544-267102 6 50316301 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417849 Affx-122946781 AX-123288197 6 47993414 TAGAAGTTATAAGCCAGGGAGGTTCTGACATATTT[C/T]GATTTGTGCTGATTTCTCTTTGAGAAGATCATATT Y 2 1 2 1 101000 f 74 goat snp41818-scaffold544-218531 6 50364437 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770409 Affx-122961368 AX-385257575 6 48027579 GAAATGAAAAGGTGGATACTTAATGCTGTCAACGA[G/T]CCCCATTTTTCTCAATTAGACACATTATTTAGTTG K 2 1 2 1 201000 f 74 goat snp41817-scaffold544-184366 6 50398957 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439726 Affx-122930547 AX-123310063 6 48059256 CTTGAGCCTGACAAGATTTATTGTTTCCAACTACT[A/G]TCTCCTGCATTGGGTGTGAATTTCATTCCCATTAA R 2 1 2 1 101000 f 74 goat snp41816-scaffold544-152689 6 50430663 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438416 Affx-122931278 AX-123308754 6 48094016 ACACATCATCAACAAATGGTTCACTGATTTATGGT[C/T]AAGGATGAATTATTAAAACTATCCCCTTCAAAAAT Y 2 1 2 1 101000 f 74 goat snp41815-scaffold544-117929 6 50465490 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786733 Affx-122949231 AX-385273764 6 48139017 ATATCATTTGCTTTCTCAATTTATTATTGTACACA[C/T]ATGGATTTTACTGTTAGGTAACTAGAAAAATAAAG Y 2 1 2 1 101000 f 74 goat snp41814-scaffold544-72928 6 50510087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412652 Affx-122950788 AX-123283001 6 48194883 AATCACCAGCTGTTTGTTTAGTTCTCTCTTTGACA[C/T]AAATTCAGCAAAAATAAAAATAAGGCCTGCTATTA Y 2 1 2 1 101000 f 74 goat snp41813-scaffold544-17062 6 50566064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445322 Affx-122925428 AX-123315659 6 48249709 CCAAAATGGTATTTTCATGTAAAATCCAATACAAA[C/T]CCTGATTAAAACCTAACCAAGCAAAACACTGCAGA Y 2 1 2 1 101000 r 74 goat snp35094-scaffold42-2458825 6 50617818 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425860 Affx-122940656 AX-123296206 6 48278785 CTGTGGTTTTCGTATGTTACAGAGGAGGAAACCCG[C/T]GCTCCCTGGGAAGTTAAATATTGTTAACTGGCAAA Y 2 1 2 1 201000 r 74 goat snp35093-scaffold42-2429749 6 50646915 C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788217 Affx-122966466 AX-385275236 6 48312591 TAATTTTATAATCATCAGCCTAGTAATCTCTATTA[C/T]CAACATTCTAACCTAGTTAATCACTGTATTATATG Y 2 1 2 1 101000 r 74 goat snp35092-scaffold42-2395943 6 50680795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787139 Affx-122971103 AX-385274165 6 48341490 GACAAGACACAAAATGAACAGGGGGCCAAAGAGAC[G/T]TCTTTGAAGTGACATTTACCTGCAAACTAAATGAT K 2 1 2 1 101000 f 74 goat snp35091-scaffold42-2367044 6 50710104 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397661 Affx-122962599 AX-123268016 6 48375102 ATGCTCCTAGAAAAGAGAGTGCCCTCTGGCTCTAC[A/C]TGTCGTCCCCTGTACACGCATACACACAGATACAC M 2 1 2 1 101000 f 74 goat snp35090-scaffold42-2333432 6 50743833 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396873 Affx-122963240 AX-123267228 6 48407107 CAGTCTTTTTTTGTGCCCTACAACGATCAGCAACT[A/C]GTTCTTATGAGGACTGCATAATTATTGTTGTATGT M 2 1 2 1 101000 f 74 goat snp35089-scaffold42-2301427 6 50776156 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405004 Affx-122956386 AX-123275356 6 48438026 CTGTTGGGACCAGGAGCTTTACTTTTATTAAAAAA[G/T]AAATATACTGAAATCATTTTTTGAAAAATAAATAT K 2 1 2 1 103000 f 74 goat snp35088-scaffold42-2270508 6 50806887 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435499 Affx-122933427 AX-123305839 6 48491269 CTATTACAATAAATGCATTAGCCTTCTAGACCAAA[G/T]GAAGCAGCCTATATAAATTTTGTTTTATGAATGAA K 2 1 2 1 101000 f 74 goat snp35087-scaffold42-2217265 6 50860064 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792542 Affx-122974940 AX-385279523 6 48532149 TTTGCATTTTTGTCTAGCATACATATGTATATTCA[C/T]CTATGCCCCAAGTTCTATTTTCCCACTAATGCTTC Y 2 1 2 1 201000 f 74 goat snp35086-scaffold42-2176385 6 50899654 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384274 Affx-122972306 AX-123254632 6 48577994 GGTTAATTTTTTTTTTTACTTTTAATAGATGAATT[A/C]GTTTTGCATCAGAAAGAAGCATTACTGAAAAAAGA M 2 1 2 1 103000 r 74 goat snp35085-scaffold42-2130540 6 50946281 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278368 Affx-1111836386 AX-519551854 6 48594228 GCTCATACACAGAGAGATGTGTCATGCTAAACCTC[A/G]ATAATAAACAAAGCCACTTAAGGTAAGCAGATGAC R 2 1 2 1 101000 f 74 goat Random2.2K-683 6 48594228 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409346 Affx-122954179 AX-123279697 6 48640453 CCATTCAGCTTTTTAACAATGGCTAATAGCAATTT[A/C]GTTGATTTTCAGTTTAGTTCTGCAGCCATTTATTG M 2 1 2 1 201000 f 74 goat snp35084-scaffold42-2068081 6 51009317 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768465 Affx-122927647 AX-385255645 6 48671241 GATACAGTCATTAGCAATATTCAGAAATATTCTGA[C/T]AGCTTTCACTACAATTTCCTTTCCTTTTGTTTAAA Y 2 1 2 1 102000 r 74 goat snp35083-scaffold42-2037293 6 51040169 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391721 Affx-122967501 AX-123262078 6 48737586 TTAATGTAAACCAAATCTACAAGTTCCCTACATCC[A/G]TAGAGCTCCTATTTTAGTGCGAGAAGCCAGATCAC R 2 1 2 1 101000 r 74 goat snp35082-scaffold42-1970948 6 51107813 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395590 Affx-122963830 AX-123265945 6 48833493 CATATTTATTCTCAACTGACTAGTTAATGCGGCTG[C/T]GTCCTGTCTGTCCTCTCTAAGGCCATGTTGAAATT Y 2 1 2 1 201000 f 74 goat snp35080-scaffold42-1875041 6 51204738 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801417 Affx-122930071 AX-385288326 6 48883723 ATTCAAGAAAATTGAATTTCAGTGACTTCATGGTT[A/G]CAAAGTCTCATTATTCAGTTAGAAGTGTGCTTTAG R 2 1 2 1 101000 f 74 goat snp35079-scaffold42-1824811 6 51254637 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433772 Affx-122934483 AX-123304113 6 48913083 CTATGGTAATTGAGATAATGTATAATTCTAGAAGA[C/T]GGCTGATTATTAATAACTTGACAATATAATTATGG Y 2 1 2 1 101000 f 74 goat snp35078-scaffold42-1795451 6 51285255 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438677 Affx-122930876 AX-123309014 6 48948203 ATGGACTTAATGATAGATGGCTTATAAGATTATTG[C/T]GAGAATAAATTTTAAAATTCAAATCATCCAGCATA Y 2 1 2 1 101000 f 74 goat snp35077-scaffold42-1760331 6 51320397 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787050 Affx-122921666 AX-385274078 6 48994843 ATGGTCCAAAAAGTATTGGAAAGCTGCAATCAATA[C/T]TTATATTTAAATAAAAGGGAGATGTGAGGCACAGC Y 2 1 2 1 201000 r 74 goat snp35076-scaffold42-1713691 6 51367433 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386598 Affx-122970685 AX-123256956 6 49042195 GGCTTGTGTCTCTGTGTGCTATAAACTCTAATTCA[A/G]TTTCATATAGGGAACATTCACTCCCCTGCTGAGTG R 2 1 2 1 101000 f 74 goat snp35075-scaffold42-1666339 6 51415707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790469 Affx-122937943 AX-385277472 6 49084596 GGAGTGAAATTACTGAAGAATTTCATGTAGTGGAA[C/T]GATATGGCCTAATGTACACTTCAGAAACAAATTTA Y 2 1 2 1 101000 f 74 goat snp35074-scaffold42-1623938 6 51453989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445383 Affx-122925402 AX-123315720 6 49120348 AGCTAGGGGAAAAAAAGAAGCAATAAAAACAAAAA[C/T]AGCAACCAGCAATAAGCATGATGAAGCAATATACT Y 2 1 2 1 101000 r 74 goat snp35073-scaffold42-1588186 6 51489807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413182 Affx-122950333 AX-123283531 6 49159217 CATCATTTATTTGAATCAGCCAATGTAACCATGTA[C/T]GAACTTAAAAGGGTCAGAATCAGAAAAGGTGATAT Y 2 1 2 1 101000 f 74 goat snp35072-scaffold42-1549317 6 51529013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381391 Affx-122974381 AX-123251749 6 49197917 AAATGATGAGAAAGGCAAAGCAAAGAACTTAAGCA[A/G]AAGAAATCAAAGGTAAACAAATATATGACATATAA R 2 1 2 1 101000 f 74 goat snp35071-scaffold42-1510617 6 51568641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772749 Affx-122927732 AX-385259894 6 49231999 TACTCCTATATTGACAAGGATATTGTGTCTTTATG[C/T]GGAAAAGTTACCTAGTATACTTAAGTATAGATATT Y 2 1 2 1 101000 f 74 goat snp35070-scaffold42-1476535 6 51603714 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799501 Affx-122946492 AX-385286431 6 49277224 CTTCCAGTCCACAATAGCTATAATTAGAGTTGACT[A/C]TGTTCTCCATTTGACCTTGAAGAACCAATAAATGT M 2 1 2 1 101000 r 74 goat snp35069-scaffold42-1431310 6 51648777 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798659 Affx-122943236 AX-385285591 6 49312264 GATTAGAACCCAGATCTCCAAAAACTTGGTTGTCA[C/T]TATTTTGTTTATAAATTCAACTTTGGAAAATATTT Y 2 1 2 1 201000 r 74 goat snp35068-scaffold42-1396270 6 51683946 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774030 Affx-122959483 AX-385261168 6 49371788 ACAGAAAGAATTCTTGAGGGTTTAAATCAGATAAT[A/G]TCATTCTAAGCTTTATAGTAATATGAAGGTCCTCA R 2 1 2 1 101000 r 74 goat snp35067-scaffold42-1336746 6 51745089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790258 Affx-122970045 AX-385277262 6 49404101 AAAACCAGTTTTAATGATTCTAATCTCCTCTTCAT[A/G]TCTGTTTGGATGTAGCTCACTGATAGCCCAAAGTG R 2 1 2 1 101000 r 74 goat snp35066-scaffold42-1304433 6 51777890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388177 Affx-122969439 AX-123258535 6 49441678 CATCCTATGGAATATCACCAAGAAAAAAATGTAGT[C/T]AAAGCAAAATAATCACATTTTTGACCCAAAATATC Y 2 1 2 1 101000 f 74 goat snp35065-scaffold42-1266856 6 51815100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799283 Affx-122948200 AX-385286213 6 49501236 ATTTATTATTCATATGAGAGGTTTAGTAAAACCAC[A/G]CTTTCTGGGTCTTTGGAAAGATTCCCAGCCGGCAG R 2 1 2 1 102000 r 74 goat snp35064-scaffold42-1207298 6 51875509 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418769 Affx-122946194 AX-123289117 6 49591082 TCAAACAATTAACATCCCTGTCATCTCACACAGTT[A/G]CCACTTTATTTCTTTTTAAGCTGTTGTGAGAACAC R 2 1 2 1 101000 f 74 goat snp35062-scaffold42-1117452 6 51966254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388715 Affx-122968977 AX-123259073 6 49625187 ATATACATAAGTGATAATTTAATTCAAAAAAGTTA[C/T]AAAAGAATAAGTATAAAAATTCAGTGTGGAGGCAG Y 2 1 2 1 201000 f 74 goat snp35061-scaffold42-1083347 6 52000487 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445783 Affx-122926056 AX-123316120 6 49656694 GAAGAAATACAAAGGTTTAGAGAGATTGGAATGTT[A/C]GAAAGGACTATTTAAGACCTGTTACACATCCTGAG M 2 1 2 1 101000 r 74 goat snp35060-scaffold42-1051840 6 52032569 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786934 Affx-122930924 AX-385273963 6 49733929 CTTTTTGCCTGAAGCAGAATCTCCAAGGTGCCAAT[G/T]CTGATACAACTTGTAGGGTAATTTCCTTTAGAAAA K 2 1 2 1 101000 f 74 goat snp35058-scaffold42-974605 6 52110326 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273205 Affx-1111833506 AX-519546864 6 49830191 ACAAACATTAAAGCCCTAGGTGTGTCACAGCTCTC[A/G]GGTCTTGGACAGACCGTGTTATAGCTCTTAGACAA R 2 1 2 1 103000 f 74 goat 6_49830191_AF-PAKI 6 49830191 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398829 Affx-122961390 AX-123269184 6 49858790 TATCATTCCTTAAAATATAAATACATTGACCCAGA[C/T]ATCCCTGGAAATAACAAAAGACTTTGCAAGGTCAT Y 2 1 2 1 201000 r 74 goat snp35056-scaffold42-849744 6 52236308 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448691 Affx-122923867 AX-123319027 6 49898737 CTACAGATAGCTGCCTTATGGCCATATTCTAATGT[A/G]TATGTAAGTATATGTACACATACATGTACTGTTAC R 2 1 2 1 103000 f 74 goat snp35055-scaffold42-809797 6 52276570 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783227 Affx-122926202 AX-385270293 6 49929963 CGTAATGGTGAATGAACAGACAATTGAATGAAAAT[A/G]TCAACAGTGTGATTCCAATTGTATAAAGTTTGAAA R 2 1 2 1 101000 f 74 goat snp35054-scaffold42-778571 6 52308869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791047 Affx-122975019 AX-385278042 6 50011448 GTCAGTTTCATATGATAACAGGATATCCATGTCGT[A/G]TAAAGGGATAGAGACTTGGGTTTTGAGTCTGAGGA R 2 1 2 1 101000 r 74 goat snp35052-scaffold42-697086 6 52392203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779827 Affx-122965500 AX-385266927 6 50040174 CTGTGTGATATGGCCTTCTACCTCAACCTAAAGCT[A/G]TTTACGAATGTCTCATCATTAATAAAAGTGAGTCT R 2 1 2 1 101000 f 74 goat snp35051-scaffold42-668360 6 52421450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391985 Affx-122966508 AX-123262342 6 50087916 CCCACAAAGCAGAATCCTCTTTACTTAACATGAGG[C/T]AAACCTCTTCAACTCACTGTCAGAAAGTTAGAAAG Y 2 1 2 1 101000 f 74 goat snp35050-scaffold42-620618 6 52468657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383931 Affx-122972968 AX-123254289 6 50130394 CTATAACAAATATTGTTGAGAGGTTGAGGGAGAAA[C/T]AGATTATAATATGTTCCCTGGATTACATATCTAAG Y 2 1 2 1 101000 f 74 goat snp35049-scaffold42-578140 6 52509132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443000 Affx-122928182 AX-123313337 6 50186340 CCAATTATCTAAGGATGCATTTCTACTCTTAAAGT[A/G]CAATAAACTATATTTGGACACACAAAACTCAAATC R 2 1 2 1 101000 f 74 goat snp35048-scaffold42-522194 6 52573873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802563 Affx-122920526 AX-385289465 6 50221252 GTATATATGAAAGGTTTACAGCACATGCATATTAG[A/G]TAGCTTTTCAGGCATTTAATATTAAGAAGTGATGT R 2 1 2 1 101000 r 74 goat snp35047-scaffold42-487282 6 52609400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792142 Affx-122970875 AX-385279127 6 50267089 TCAGTAACTCTGTGGTGTCATAACCATAAGTGTTA[C/T]TTCCTAATAGCCCCAAACCCAGAAATATTAATTAT Y 2 1 2 1 201000 r 74 goat snp35046-scaffold42-441445 6 52655928 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386316 Affx-122970890 AX-123256674 6 50309445 AATATAATTTTAGCAGTGGATCATATAAAAGAAGC[A/G]CAGTTTCTTTCAAGTCACAACTTCACAGTTAGTAA R 2 1 2 1 101000 r 74 goat snp35045-scaffold42-399089 6 52698895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769372 Affx-122939594 AX-385256543 6 50343195 GCATTTGTCAAAGTTTTAATAAATTTCACATGGGT[A/G]GTATAGGTACTCCAGGTCAGCATAATAGTCTGAAA R 2 1 2 1 201000 f 74 goat snp35044-scaffold42-365339 6 52732905 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385838 Affx-122971007 AX-123256196 6 50375724 CACAAGCATAGATAGTTTTCATCAAGTATGACTTG[C/T]GGTCCAACTATGCTCCGAAGAATTTTAAGAACATG Y 2 1 2 1 101000 r 74 goat snp35043-scaffold42-332810 6 52765988 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395020 Affx-122964220 AX-123265375 6 50408417 CTAATTTTGTCCTTGTGGATGATACTGTCCCTTCT[A/G]TGAATATACTGTGGTGACTTTGACCTTTCTATCTG R 2 1 2 1 101000 r 74 goat snp35042-scaffold42-300117 6 52798943 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383897 Affx-122973116 AX-123254255 6 50450877 TAATATGTTCAAGGGGTTCATTTTCCACCATTTGT[A/G]TGAGTGTGTTTTAACATAATGCCTCTCATCCCTTT R 2 1 2 1 201000 r 74 goat snp35041-scaffold42-257657 6 52840374 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450026 Affx-122922841 AX-123320361 6 50495230 CACATGAACCTGGGGCCTTGAGCATATTCTATTTC[A/G]CAGCTGCATCAAATGTGACTCTGATGTGATTTTAG R 2 1 2 1 101000 f 74 goat snp35040-scaffold42-213304 6 52882205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801307 Affx-122921900 AX-385288219 6 50525121 AGTATAAAAGTTTACATCTAGTGAGCATTAAAGAT[A/G]CTAAAACTAAACATCAGTCTTCATACTTGTTTCAC R 2 1 2 1 101000 r 74 goat snp35039-scaffold42-183413 6 52913027 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416472 Affx-122947806 AX-123286820 6 50576791 CTTGTGTTGTTCACAATATAGCAAGCAGTTTATTA[C/T]TGGCAAATAAATAATTTCACTTTTGAAAACTGAAG Y 2 1 2 1 101000 f 74 goat snp35038-scaffold42-131743 6 52954327 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440177 Affx-122930716 AX-123310514 6 50622421 TACCCACACTCAGCATCTGTGCATAGACACTGATA[A/G]GGGTAATTGTCATGGCAGCCAAAAATGGCAAACCC R 2 1 2 1 101000 f 74 goat snp35037-scaffold42-86113 6 52999944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798471 Affx-122953881 AX-385285404 6 50656116 CTGCATTTGAACTGCCACCCTCTTATGCAGGAGAT[A/G]CAATAACTTTCTGAGGCTTCTGCAGCTTTATATTA R 2 1 2 1 201000 r 74 goat snp35036-scaffold42-52418 6 53033351 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446953 Affx-122924670 AX-123317289 6 50699551 GTAGACCTTGTTTTTCACTCAGGTGGCATATAAAC[A/C]TTCTATCTTAATCAGTCCAGCTGCTGTAACAGAAC M 2 1 2 1 101000 f 74 goat snp35035-scaffold42-8983 6 53077308 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413938 Affx-122949805 AX-123284287 6 50722833 CCTCTGCCCCAGTATTCAATAGCACTGAAGTGGGA[C/T]ACCATTATACATACATCAGTGATGATACCATGTGC Y 2 1 2 1 201000 r 74 goat snp41643-scaffold541-3277890 6 53100757 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407059 Affx-122954923 AX-123277410 6 50786453 TAGAGAACAAAATAATAGATAAAATCATTCTTACT[A/G]GGCAAATTATCAAGGAATTATGCAATTTTGTCAGA R 2 1 2 1 101000 r 74 goat snp41642-scaffold541-3214270 6 53165865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791591 Affx-122968289 AX-385278582 6 50830298 CAGCAAAAAATAACTACACATTTCTCTGCAGCTCC[A/G]TAAAATGGTATATCACCAAAATAATGCATCATACT R 2 1 2 1 101000 f 74 goat snp41641-scaffold541-3170425 6 53209655 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393687 Affx-122965260 AX-123264042 6 50861509 TATTGGAGAATTTTTGACAAAAAAATTAAAATGTG[C/T]CCCAAAGTGTCATGTGAGTACTGCCTAAAGATATC Y 2 1 2 1 101000 r 74 goat snp41640-scaffold541-3139214 6 53240554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423600 Affx-122942387 AX-123293946 6 50890395 GCAAAGCAATCCCTCCTCCTCGGGATGACAGCACA[A/G]CAGCACTGCATATCTGACAGGTGTCTTTGTAGGAG R 2 1 2 1 101000 r 74 goat snp41639-scaffold541-3110328 6 53269689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454044 Affx-122919404 AX-123324377 6 50938792 TTAAAATCTCATTCTCCCCAGGAGATAGGCAATAT[A/G]CATATATATTTTTATTAATTTTTTTGGATTATAGT R 2 1 2 1 103000 f 74 goat snp41638-scaffold541-3061931 6 53315909 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799298 Affx-122977042 AX-385286228 6 50987327 TAAAGGAAACACTCAATAAAGCTTTATTAAATTAA[C/T]GCAGTATACTTGACTTTTGACTCAAAAGCACTTAG Y 2 1 2 1 201000 f 74 goat snp41637-scaffold541-3013396 6 53365364 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400152 Affx-122960695 AX-123270507 6 51027616 TTCAGTGCTTTGCCCTATTAAAAAGTTAATGCTGA[C/T]AGAATGATATGCTAATTGACATTTTCTAACTGATA Y 2 1 2 1 101000 r 74 goat snp41636-scaffold541-2973107 6 53406821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425787 Affx-122940711 AX-123296133 6 51099723 AATATTTCACAGGATAACACTATTTATTATAGGAG[C/T]ACTTCAAAATTGTATGGCTATAGTATACCTTGTAG Y 2 1 2 1 101000 f 74 goat snp41635-scaffold541-2901000 6 53479250 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440016 Affx-122929777 AX-123310353 6 51162173 TACTCACCAGTAGAATACACAGATCAAAGACCCCC[G/T]AGGACCATGCTCACAACATGACCACTAATGCCCAA K 2 1 2 1 201000 r 74 goat snp41634-scaffold541-2838550 6 53541545 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398977 Affx-122960962 AX-123269332 6 51215058 GGTCTACTGAACCCAGTCTATCTTCTCTTCTAAAA[G/T]CCAATGCCTATTCTTAGTTCTAATCTTACTTAAAC K 2 1 2 1 101000 f 74 goat snp41633-scaffold541-2785665 6 53594183 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435790 Affx-122932859 AX-123306129 6 51253701 TGTCTCCAATGAACTTAAATAAAATCTTTTTGGCT[A/C]AGGCCCTGGATTCTTCATTTTAAACAAACTCCACT M 2 1 2 1 101000 r 74 goat snp41632-scaffold541-2747022 6 53633692 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278538 Affx-1111836387 AX-519552020 6 51254728 AGTTACTAGAAGAAATAATCCCTTCGACTTGGAAT[A/G]CAGTCAATGCAGTGTCAAGTTTTGACCCTGCCACT R 2 1 2 1 101000 r 74 goat Random2.2K-684 6 51254728 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384089 Affx-122972849 AX-123254447 6 51291749 ATTTCATGTCAATCTGAGGCAGAAGATAGATGGGC[A/G]TCCAGCCTCCAGGGTAAAGTGGGAAGATGGGCCCT R 2 1 2 1 303000 r 74 goat snp41631-scaffold541-2708974 6 53671465 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414686 Affx-122949290 AX-123285035 6 51325949 GTTTGATACTTTGAAATATAATTAAAATAATAATT[A/G]CCATCCTGAGGTCATGGCTGTCAGAATAAATTTTG R 2 1 2 1 103000 r 74 goat snp41630-scaffold541-2674774 6 53705830 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765227 Affx-122941304 AX-385252766 6 51379885 CTTGGCCCTAAATTCCCTGTTTCTGGTGATAAGGA[C/T]GTCTCTTCCTCCCACTATAAGGAAAGACCTTTCAC Y 2 1 2 1 101000 f 74 goat snp41629-scaffold541-2620838 6 53759652 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385001 Affx-122971880 AX-123255359 6 51438137 TTAGTAAAACATGATTAATTTCTCACTGATTAGCA[C/T]ACTTTGGCTTTTATTTTTTTCATTTGAAAAACCAA Y 2 1 2 1 101000 f 74 goat snp41628-scaffold541-2562586 6 53818604 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794459 Affx-122941390 AX-385281422 6 51471168 TATTAAAAATGAAATAAGCAGCCCAAAATGAAGCC[A/G]CTTGTACAAAATATCACCAAGACTTAATACCTAAC R 2 1 2 1 101000 f 74 goat snp41627-scaffold541-2529555 6 53851670 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781934 Affx-122930114 AX-385269015 6 51500436 ATCCTCACATTTAATTGTGTAAATACTTTAATGAT[C/T]GTGGCTTAGCACACCAATTGACAATTACCCTGAAA Y 2 1 2 1 101000 r 74 goat snp41626-scaffold541-2500287 6 53881355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453811 Affx-122919564 AX-123324144 6 51530904 TATATTTCTCCTGGTTTCTTTTATATTTTTGGTCC[A/G]TGTTAAAGTTATTGAAGGAAACTTATTTATGAGAG R 2 1 2 1 201000 r 74 goat snp41625-scaffold541-2469819 6 53911675 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401191 Affx-122959343 AX-123271544 6 51581437 TGGAATGAGCTGTCACCTTGGAAATACCAACTGGA[A/G]ACCTCTGTGTTGCCATCCTCTAGCCAAGATAATAA R 2 1 2 1 101000 f 74 goat snp41624-scaffold541-2419286 6 53962817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782337 Affx-122930530 AX-385269414 6 51629229 CAAGCTTTGAGCCCAGGTCGTGGAGCCACTACTTG[C/T]AAATGTCTGAGATCATCAGACTAGTTAATTTCTGA Y 2 1 2 1 102000 f 74 goat snp41623-scaffold541-2371494 6 54010666 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440700 Affx-122929906 AX-123311037 6 51698717 ACTTCAAATCAGCCCCACGCTGAGCTAAAATGTCC[A/G]TATATTTTATATCCTCATTTTCATCTATTGGTCAT R 2 1 2 1 201000 r 74 goat snp41622-scaffold541-2302006 6 54078643 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798689 Affx-122921971 AX-385285621 6 51738487 AAAATTCCAGTATCATTTTGGGACTCAGTATCAAG[C/T]ATTGCATAATAAGATGTCACCATTTATAAGTCACT Y 2 1 2 1 101000 f 74 goat snp41621-scaffold541-2262236 6 54119339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449956 Affx-122922894 AX-123320291 6 51797469 TCCTTAATCCTTTTCACACATTAGTAAAGAATCAC[A/G]TGATTAAAATCTTGATTCCTCCATCTGACCTACAA R 2 1 2 1 101000 r 74 goat snp41620-scaffold541-2203254 6 54178733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795856 Affx-122941068 AX-385282809 6 51833576 AGAAAGGAATTCAACCCTACTGACACTTATTTTAA[G/T]ACAGAAATCAGCTTTCCAACTCATGGAACTATAAG K 2 1 2 1 201000 r 74 goat snp41619-scaffold541-2167147 6 54218216 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801946 Affx-122969713 AX-385288851 6 51864328 TTTTTATTCAAAATTTCATATTTCAAATCAAATAG[C/T]ATGATTTCAGCTACGATCAAGTTCCTTTTTCTGTC Y 2 1 2 1 201000 f 74 goat snp41618-scaffold541-2136395 6 54248886 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415876 Affx-122948488 AX-123286225 6 51897112 GAGGAGGGAAAAAAACCCCCAAGTGTTAAAGATGA[C/T]ATCAAGGTTTAAGAGTGCTGGCTGGAAATACCAAA Y 2 1 2 1 201000 r 74 goat snp41617-scaffold541-2103611 6 54282477 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379205 Affx-122976293 AX-123249564 6 51981535 AGACATTGACGTTCAGTGGGAAGATGGTCATATGA[C/T]GAATTGGAGTTATGCACCTGTAAACCAAGCAACAC Y 2 1 2 1 101000 r 74 goat snp41615-scaffold541-2019188 6 54366134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768888 Affx-122965207 AX-385256065 6 52033228 TATTTTCCTTTTAACATCTAAGAATTTTCTTTCAT[A/G]TCCATTGAAATCCCTGACCTAAAATACTTCTGAAA R 2 1 2 1 101000 r 74 goat snp41614-scaffold541-1967495 NW_017198690.1 18956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402609 Affx-122958415 AX-123272962 6 52070615 ATTGGTTGTTCTAATTTTAAAACCATTTTATAGCA[C/T]GTAATTGATCCCATTTCCTTCTCTTTGTGATCTCT Y 2 1 2 1 101000 r 74 goat snp41613-scaffold541-1930108 6 54453522 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775017 Affx-122941098 AX-385262149 6 52115224 CAAAACTATCTTTATAAGAGATTGTTTGAACTAGC[A/G]TTTTCATTTCCCTGGAGGAAGTTTTCCTTCTGAAA R 2 1 2 1 201000 r 74 goat snp41612-scaffold541-1885499 6 54498594 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770073 Affx-122962818 AX-385257240 6 52158086 AAATAGTAGGAGCATGCCATTTGAATTTAATGACT[A/G]TACAACTTCAATCACCAATACTTTCTCAAATTCTC R 2 1 2 1 101000 f 74 goat snp41611-scaffold541-1842637 6 54541395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432375 Affx-122935862 AX-123302716 6 52193617 ATGAGCACATTTGTTTTTCTCCAGAAATTAACCTT[A/G]TGCTATAATTAAGCAATGCTCCTCAGATTTCCCAA R 2 1 2 1 101000 r 74 goat snp41610-scaffold541-1807106 6 54577700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795058 Affx-122957317 AX-385282017 6 52242276 ATGGAGATGTATGATGGGAATAGATTGACATATAC[A/G]TTCTATAGAAGAAACCTTGACAGTGAATAGAATCT R 2 1 2 1 201000 r 74 goat snp41609-scaffold541-1758447 6 54627135 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406214 Affx-122956126 AX-123276566 6 52274759 TGCACATCCATGCTTTTTCTCACATCAGGAGGCAG[A/C]TATTATTTTCTCTGTCCTGAATCTGGATAGGTCTT M 2 1 2 1 201000 r 74 goat snp41608-scaffold541-1725964 6 54659249 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791244 Affx-122967322 AX-385278238 6 52323275 AATAAATTATATATACTATTTCACTTTGAAAAAAT[A/G]CTGACTTTAAGTTTAAGGTAATGTGTTTACATATT R 2 1 2 1 202000 f 74 goat snp41607-scaffold541-1677448 6 54707039 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273207 Affx-1111833507 AX-519546866 6 52338101 AGCAAATTTGGAAAACTCAGCAGTGGCCACTGGCT[A/G]GAAAAGGTCAGTTTTCTTTCCAATCCCAAAGAAAG R 2 1 2 1 103000 f 74 goat 6_52338101_AF-PAKI 6 52338101 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320783697 Affx-122959991 AX-385270755 6 52380151 GTAGGGTATTTTGCTGGAGGATGCCTGGGTTTACA[A/G]CAATCTGAAAGTGAATGTAGTGTTTTGTCCTCTTT R 2 1 2 1 101000 f 74 goat snp41606-scaffold541-1620572 6 54762668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777225 Affx-122967562 AX-385264348 6 52450805 TTCAATTTAACCTTCAGGAAATGGATTTCATAGGG[A/G]CATTAAGCTACCATTCATGTTCATACTTTCTAAAT R 2 1 2 1 101000 f 74 goat snp41604-scaffold541-1549918 6 54833362 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785299 Affx-122932253 AX-385272344 6 52483058 AACACTGAAATATGTTACCACTCTCCTTGATCTGA[C/T]GCTGGATGTCCTATTAATATACTTTTCATAGAACT Y 2 1 2 1 101000 f 74 goat snp41603-scaffold541-1517665 6 54865614 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476218 Affx-1251763723 AX-586011642 6 52510667 GGGTTCAACAATACATGAACCATGAATTCCAGACG[-/TTCAAGCTGGTTTTATTTTTTTTATTATTTATTTATTTATTCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTCTC]TCAAGCTGGTTTTAGAAAAGACAGAGGAACGAGAT - 4 1 4 1 20000 f 74 goat SV_272 6 52510667 - deletion junction SV-TF-chip 539476472 Affx-1251763723 AX-586011872 6 52510667 GGGTTCAACAATACATGAACCATGAATTCCAGACG[-/TTCAAGCTGGTTTTATTTTTTTTATTATTTATTTATTTATTCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTCTC]TCAAGCTGGTTTTAGAAAAGACAGAGGAACGAGAT - 8 1 4 1 20000 r 74 goat SV_272 6 52510667 - deletion junction SV-TF-chip 562165589 Affx-1251763723 AX-606941000 6 52510667 GGGTTCAACAATACATGAACCATGAATTCCAGACG[-/TTCAAGCTGGTTTTATTTTTTTTATTATTTATTTATTTATTCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTCTC]TCAAGCTGGTTTTAGAAAAGACAGAGGAACGAGAT - 8 1 4 1 20100 r 74 goat SV_272 6 52510667 - deletion junction SV-TF-chip 562165628 Affx-1251763723 AX-606941038 6 52510667 GGGTTCAACAATACATGAACCATGAATTCCAGACG[-/TTCAAGCTGGTTTTATTTTTTTTATTATTTATTTATTTATTCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTCTC]TCAAGCTGGTTTTAGAAAAGACAGAGGAACGAGAT - 8 1 4 1 20100 f 74 goat SV_272 6 52510667 - deletion junction SV-TF-chip 562166556 Affx-1251763723 AX-606941964 6 52510667 GGGTTCAACAATACATGAACCATGAATTCCAGACG[-/TTCAAGCTGGTTTTATTTTTTTTATTATTTATTTATTTATTCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTCTC]TCAAGCTGGTTTTAGAAAAGACAGAGGAACGAGAT - 8 1 4 1 20100 r 74 goat SV_272 6 52510667 - deletion junction SV-TF-chip 38382390 Affx-122973843 AX-123252748 6 52519995 AACTGAAAATGACTCCACCCCTCACTGGGCTTCCC[A/G]TGTGGCTCAGTGATAAAGAACCAGCCTGCTAAGGC R 2 1 2 1 103000 f 74 goat snp41602-scaffold541-1480728 6 54903232 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790235 Affx-122951638 AX-385277239 6 52576661 GTAACAGATATGTGTTAGGCACTTAAAACAAACCA[C/T]GAAATGTGAAGTGACTTTCAGTCATTCATTCAGCA Y 2 1 2 1 101000 r 74 goat snp41601-scaffold541-1424062 6 54960045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400466 Affx-122961305 AX-123270821 6 52616699 GTGGATTTTTAAATAACATTAGTATAGAGCATCAA[C/T]ACAGACTTAAATTCAGTTTTTGATTGGGATTATTA Y 2 1 2 1 101000 f 74 goat snp41600-scaffold541-1384024 6 54999837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441036 Affx-122928937 AX-123311373 6 52653114 TCAAAGTGAACAAACACCAAGTGAGAGCCAGGCTC[A/G]CAAAGCCAATTGACTGAACCCAGTCTAACAGTCAA R 2 1 2 1 101000 r 74 goat snp41599-scaffold541-1347609 6 55036616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430098 Affx-122937527 AX-123300439 6 52700026 AATTAACCAAGCGAGTATAAGTCATACAATTGGTA[G/T]AAAAGAAAAAATAATATGCAATGAAGTTGTCTTAA K 2 1 2 1 103000 f 74 goat snp41598-scaffold541-1300697 6 55084024 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444429 Affx-122926565 AX-123314766 6 52731753 AGAGACAGAGGGTACCTCTATGATCTCATACATTA[C/T]AGAAAAGTTTTAAAACACAGAAATGTTAGAAGAAC Y 2 1 2 1 101000 f 74 goat snp41597-scaffold541-1268970 6 55116497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770866 Affx-122944179 AX-385258030 6 52764918 CACACAAGATAATGATTCAAAGAACTGTAAAAGAA[G/T]AATCAAAAGAGTAGTATGTTCCTTAAACCAACCTA K 2 1 2 1 101000 r 74 goat snp41596-scaffold541-1235805 6 55150320 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416957 Affx-122948020 AX-123287305 6 52824662 ACCATAATGATACTAAACAGTATCTCAAGGTAGTA[C/T]GGCTATTAATTGTATGTTAGATCAATAAATATATA Y 2 1 2 1 201000 r 74 goat snp41595-scaffold541-1176061 6 55209895 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773088 Affx-122968942 AX-385260231 6 52876347 TTCCAAATGATGTGTAATGTGAAATATGATAGTAG[C/T]GACTGATTTTAAAAATGGCAGTGCTCAGATATAGC Y 2 1 2 1 102000 r 74 goat snp41594-scaffold541-1124376 6 55263647 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784506 Affx-122942132 AX-385271555 6 52943748 AGACAGAAAGAGAGATTTCTCATATAAGATATTTC[A/G]TATTATTTTTCAAGTTCTTACCAAACTTGAAGTTC R 2 1 2 1 101000 f 74 goat snp41593-scaffold541-1056975 6 55331994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393287 Affx-122965443 AX-123263643 6 52973230 TTACTGACAGCTGATTTTGACATGTAACTTGTGGT[A/C]TCTCACCTAGAAGGACTGAACTTTACTTTCCATTG M 2 1 2 1 101000 r 74 goat snp41592-scaffold541-1027493 6 55361506 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787937 Affx-122949440 AX-385274959 6 53007147 AGAAAAACTTACCCTAGACATCAAATTATTTACTA[C/T]AAAGATTGTACAAACCCAATATCTTACACATTAAA Y 2 1 2 1 101000 r 74 goat snp41591-scaffold541-993576 6 55395509 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387952 Affx-122969613 AX-123258310 6 53071152 GACATGAAAGTTACAGGAAGTCTCTTCTCCACACC[A/G]TTTAATCTCAGAATGTGGAGTATGTACATACTCCA R 2 1 2 1 201000 r 74 goat snp41590-scaffold541-929571 6 55460282 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391728 Affx-122967495 AX-123262085 6 53109337 AAATTGTTTGTTATTTATTGTTGAGTTGACTTTTA[C/T]GGTATGTTTATTTTCTCTTTCAGTTCAAGCACCTT Y 2 1 2 1 201000 f 74 goat snp41589-scaffold541-891386 6 55498619 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410955 Affx-122952031 AX-123281305 6 53152837 ATACAAAAAGTGGCTTGGAATTTTTAAAATGCTTC[A/G]TCCCTGAAACAGGTTAGAAGTTTATCTATTTTTGA R 2 1 2 1 103000 r 74 goat snp41588-scaffold541-847886 NW_017215591.1 16929 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786953 Affx-122963228 AX-385273982 6 53209067 CAGATGGTAGACTATGATGAAGTGCAGTCAGGCTG[C/T]ACTTCAGATACATATAGTTTTGGTAGGGTTTTTCA Y 2 1 2 1 101000 f 74 goat snp41587-scaffold541-791656 6 55599306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412657 Affx-122950785 AX-123283006 6 53264333 TGTTCATGCCTGGTAAAATCTCTTCCCCCCATTTG[C/T]GGTAGGACCTCTGACCTGTTTTTTAGACAATGGCA Y 2 1 2 1 101000 r 74 goat snp41586-scaffold541-736390 6 55655227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782317 Affx-122974633 AX-385269394 6 53299463 CTAATCTTGTGCCTGAGTTTCTCTAGTTTCATATA[C/T]TTCTATGTCTTGCCTTGCTCTCCAGACTCTAGGGG Y 2 1 2 1 101000 r 74 goat snp41585-scaffold541-701260 6 55690449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780322 Affx-122962916 AX-385267417 6 53331946 AAATACTGACTGCCATGATTAAAATTGGTGACTAA[C/T]AATCTAACCAAGGGTTACTTTGTATTGGCCTCCAT Y 2 1 2 1 201000 f 74 goat snp41584-scaffold541-668777 6 55722849 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792556 Affx-122965149 AX-385279537 6 53364486 GCTTATGTGGCATCTGTCTTAGTTTCTATTAAGTA[C/T]AGCTGTGGGCACATACTAACAGATTTTGGTGTGGG Y 2 1 2 1 101000 r 74 goat snp41583-scaffold541-636237 6 55761187 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383489 Affx-122973432 AX-123253847 6 53401539 GGTAGCTACTTTGCCTTTTTTCCTTCCTCACTCTG[C/T]AGCCTTGTATTAAATCAAGGGGTTGATATTCATTT Y 2 1 2 1 303000 r 74 goat snp41582-scaffold541-599184 6 55798620 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770117 Affx-122955263 AX-385257284 6 53443902 TGCAAGAGAAAGAGATTCTCTGACATGCAAGGACA[C/T]GAAAATTATACCACCTAAGTAGTTATCCTGAAAAA Y 2 1 2 1 101000 f 74 goat snp41581-scaffold541-556821 6 55841000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770787 Affx-122977043 AX-385257951 6 53486622 CAATGACTAGAAACACAGTATAGGAGGGTGGTTTA[C/T]GTGTTATGGACAGCATACATTGCTCTGATGATCAG Y 2 1 2 1 201000 f 74 goat snp41580-scaffold541-514101 6 55883702 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445711 Affx-122926111 AX-123316048 6 53516848 GACCAGTAATTATTTTTTTTTTTGCCAAAGATACA[G/T]ATGTTTTTGTTTCTGATTAATTTGTTTCTTTTAAT K 2 1 2 1 303000 r 74 goat snp41579-scaffold541-483875 6 55913943 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378996 Affx-122976385 AX-123249355 6 53565271 TTAGTTTGGGCACTAAGCATCTTTCCAAAGGACAA[C/T]AATAATAGCATCCTCGGGACAACCCTGCTTATAGT Y 2 1 2 1 101000 r 74 goat snp41578-scaffold541-435452 6 55963060 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422654 Affx-122943689 AX-123293000 6 53634775 CATATATAGACATAGCATTATCCAGAAAAATCCAC[C/T]GTTTGATCCATTTTCACTGAGTTTTCATGGAAATC Y 2 1 2 1 101000 f 74 goat snp41577-scaffold541-365948 6 56033687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789748 Affx-122930607 AX-385276756 6 53676109 AGGTAACATTTCTTTGGAATTCAATTAGGTGAAAA[C/T]GAAACATTTTTCAAAAGGTCATAAAATAAAGATAA Y 2 1 2 1 202000 r 74 goat snp41576-scaffold541-324614 6 56075898 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768196 Affx-122938223 AX-385255386 6 53722722 ATATGAGTTACCTCTAATGAAAGATGTTTTATATT[A/C]TTTATATATGTGCAATATGCTTATGATCAATAAGG M 2 1 2 1 201000 f 74 goat snp41575-scaffold541-278001 6 56122592 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786399 Affx-122949053 AX-385273433 6 53824162 GAATGGTATGGGAGATGGAGGACACAAAACAAATG[C/T]ATAATTGAAAATTCTCCTAAGTGCCATTAAGTAAA Y 2 1 2 1 101000 f 74 goat snp41573-scaffold541-176561 6 56222491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791413 Affx-122969944 AX-385278405 6 53853016 GGCAAATGTACGTTCACATCTGTAATGCCAACTAT[A/G]TATTCTCTAAATGTGCACTGTATATATATATCATG R 2 1 2 1 101000 f 74 goat snp41572-scaffold541-147707 6 56251331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449541 Affx-122923253 AX-123319876 6 53900353 CTAAGACTATAGTGGTAATCATATCACAGTAAAAA[A/G]TACATCAAATCAACATACTGTACACCTTAAACTTA R 2 1 2 1 101000 f 74 goat snp41571-scaffold541-100370 6 56298754 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775554 Affx-122953604 AX-385262685 6 53957192 ATCTCTAAACAGACTTTCATTGAGAAAAATCCTAT[A/G]TAAACCTCTTAATTTTCTAGCTTGGCTAATTTGAC R 2 1 2 1 101000 f 74 goat snp41570-scaffold541-43531 6 56355481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802761 Affx-122973023 AX-385289660 6 53987778 TTTATGAACAAGATACACATAAAAGTCCTTCTGAA[C/T]TTCACCCCTGTTTGGGAAAAGTCCTGAATTGCATG Y 2 1 2 1 101000 r 74 goat snp41569-scaffold541-12945 6 56386380 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798211 Affx-122953268 AX-385285146 6 54001940 ACTAGAGATTCAGGACATCTGACCCACAACCTAAC[A/G]CTAATGCTTTCACATATGTCAGAAGGCAGTAGCTT R 2 1 2 1 101000 f 74 goat snp221-scaffold1005-54720 6 56407385 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783846 Affx-122938749 AX-385270902 6 54042701 TGTTTGGTTGTTGTCATGTTCTAAATAGTTCAGCA[G/T]CAAGATTTTAAACCACTATCCCCATTAACTGGAGA K 2 1 2 1 101000 r 74 goat snp220-scaffold1005-13959 6 56448194 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385549 Affx-122971231 AX-123255907 6 54059823 TACCTGAAGTGTGTTTACATTCATGTAACTCACTC[A/G]TGAACTGGGGAAGGACAGATATTGATTGGCAAATT R 2 1 2 1 202000 r 74 goat snp27054-scaffold289-3064 6 56475731 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395021 Affx-122964219 AX-123265376 6 54089115 CCTTTGGCTCTTCCTTTACTTCCCCTAAATATCAC[C/T]AAGTCCTTTAGATTTAATGACCTTATCCCCGTACT Y 2 1 2 1 201000 r 74 goat snp27055-scaffold289-32356 6 56505117 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450293 Affx-122922158 AX-123320628 6 54143030 AAATAAAATTTATTTTTGGTTTTGCAGTAAACAAA[C/T]GGGCTTCAGAAAGGGAAAAGATATTAGTATTAAGA Y 2 1 2 1 103000 r 74 goat snp27056-scaffold289-86271 NW_017196821.1 4209 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771397 Affx-122931438 AX-385258555 6 54194612 AGGGATGTATCAACATGATTGCTAATTTCCTTTTA[C/T]GGAAATGTTTAAATCTCATTGCTTTCCTTCTATGG Y 2 1 2 1 202000 r 74 goat snp27057-scaffold289-137853 6 56613395 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444745 Affx-122926396 AX-123315082 6 54233109 TATGGCTCAAATCAGCAATAATTTAACATTTTTAT[A/G]TTTATGTAATAAACTTTTATGCCTTTACAATTTAA R 2 1 2 1 201000 r 74 goat snp27058-scaffold289-176350 6 56649292 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773430 Affx-122945689 AX-385260572 6 54263982 GGGTGATGTCAGATATGCCATCTCTGAGCTTGAGT[A/G]TGTCATCTCTGAGCCCTAATACTCACTTGATTTAG R 2 1 2 1 102000 f 74 goat snp27059-scaffold289-207223 6 56680140 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381742 Affx-122974324 AX-123252100 6 54321366 ACTCTCTATGAAGCAAAATAGACTTTATTCAAGGA[A/G]ACAGGCCCTTGATAATGTTGTAAATAGTTAATTAC R 2 1 2 1 101000 f 74 goat snp27060-scaffold289-264607 6 56738762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419297 Affx-122946235 AX-123289645 6 54384851 CCAACTCTGATTCTACTCATACTCAACTCCAATTG[C/T]GTTTGCTACTACATCAATATCTTGAGTTTAAGAAT Y 2 1 2 1 101000 r 74 goat snp27061-scaffold289-328092 6 56803216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771572 Affx-122919781 AX-385258730 6 54456831 TTTTGCTTGAAAGCAATAGGTATAGAATCTCTGAG[A/G]AGTTGAACTGTTTACAAGAACACTGCCTGAGGGGA R 2 1 2 1 101000 r 74 goat snp27063-scaffold289-400072 6 56875390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392973 Affx-122965674 AX-123263330 6 54519683 GCTTAGGATGGCCACATTACTGAATTCTGGCCAAC[A/G]TTATGTAACAGAGGTATGATTTGAAACTTATGACA R 2 1 2 1 201000 r 74 goat snp27065-scaffold289-462924 6 56939051 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802016 Affx-122926009 AX-385288920 6 54556698 TCCAGGCTTAATCTAATACTTTGTGGTTATTGATT[A/G]TCCAATTTATGAGAATTAATCCACCATAGGTCCTT R 2 1 2 1 101000 f 74 goat snp27066-scaffold289-499939 6 56976047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783295 Affx-122920891 AX-385270360 6 54586820 TGTGAAGCCCATGCATTGGCTTGCTTTATGAAATT[A/G]CTAGTTTTCTCCTTGTGTAAGTATGCCTTTTTTAA R 2 1 2 1 101000 f 74 goat snp27067-scaffold289-530061 6 57006151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798546 Affx-122961337 AX-385285479 6 54628693 CCTGAAGGATTTGAGACATAAAGTTTATGTCATAA[A/G]AAATACATTTGGGAGAATAGATAAAGGCCAAAACA R 2 1 2 1 101000 r 74 goat snp27068-scaffold289-571934 6 57046273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396923 Affx-122963200 AX-123267278 6 54684985 AAGGTGTTTCTAGCACACTCTAGCTTCTGAATTCC[A/G]CCTGAGACTACACCTAAGTTCCATAACTTTGTTTT R 2 1 2 1 101000 f 74 goat snp27069-scaffold289-628226 6 57104020 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407394 Affx-122955254 AX-123277745 6 54723965 ATCAAATCTTCTAGTTACATCAATTACATCATGAG[C/T]GGGTAAAAATAGGCCTTTTCATCACTACAACTATG Y 2 1 2 1 101000 f 74 goat snp27070-scaffold289-667206 6 57143518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432694 Affx-122936032 AX-123303035 6 54783680 TGTTTGGGATAGAGGAAAGTAGAGAGGAGGCATGA[C/T]GAGAAGGGGGAGATGGAGCTCTTGAGTGAATCAAC Y 2 1 2 1 101000 f 74 goat snp27071-scaffold289-726921 6 57202628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380848 Affx-122975446 AX-123251206 6 54857972 CACTGGTCCCTGTCACTCTGTTGAGCTGCCGCTGC[A/G]TCTCAGACTCTCAGGACTGGTTGTTTGCCTCTCAA R 2 1 2 1 101000 r 74 goat snp27073-scaffold289-801213 6 57277219 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773492 Affx-122954089 AX-385260633 6 54890815 GGAAATAATAGTTACCTGCCTCCTGGTGTCTTTCT[A/G]AGGATGAAATTAAATTACAGGACACTTTTTACAGT R 2 1 2 1 102000 f 74 goat snp27074-scaffold289-834056 NW_017190901.1 5064 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273210 Affx-1111833509 AX-519546869 6 54905847 AATAGCAAGGAGAGGTAAGAAAGTCATAGTCAGTG[A/G]ACAATGCAAAGAAATAGAGGAAAACAATAAAATGG R 2 1 2 1 103000 f 74 goat 6_54905847_AF-PAKI 6 54905847 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454165 Affx-122919319 AX-123324498 6 54931769 CCTATGGTGCTTTTTATTCCCCTTTTCTTTAAAGT[A/G]TGTGCTTTGAAGTCTAGATATAGAGAAAAGAAGAA R 2 1 2 1 201000 r 74 goat snp27075-scaffold289-875010 6 57349745 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272476 Affx-1111836388 AX-519546198 6 54952728 TCCCATATATTGTTTCTTAAATTATACTTTTGAAG[A/G]TGAGTGGTTTTGAGTATTATACCTACATGGAAACT R 2 1 2 1 101000 r 74 goat Random2.2K-687 6 54952728 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38426193 Affx-122940573 AX-123296539 6 54983172 AGCCAAGAGGTACCTGTTCTCAGGTAATTTTGTAT[A/G]CATCTTCAGTAAACTGAGGAATTGATCGTTAATAG R 2 1 2 1 101000 f 74 goat snp27076-scaffold289-926413 6 57402187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452917 Affx-122920198 AX-123323250 6 55018728 CAGGAGGAGGACCAGGGGAGGTGGCAGAAGGTATT[A/G]TGCTGGGTCTTTTAGGTTACATACTATAATCTGAC R 2 1 2 1 101000 r 74 goat snp27077-scaffold289-961969 6 57437726 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803404 Affx-122950789 AX-385290235 6 55049569 TCTCCTTAACCATATGATCATGTATTATTGTGTTA[C/T]AATTTTCTTATATCTTAAGTTAAGCTAACTCCCAG Y 2 1 2 1 101000 r 74 goat snp27078-scaffold289-992810 6 57468649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275123 Affx-1111834706 AX-519548702 6 55128708 AGATGTCTCTAGCTTGAAAAGCTCTTGAATGGACC[A/G]GA R 2 1 2 1 101000 f 74 goat GoatD01.047087 6 55128708 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38453609 Affx-122920133 AX-123323942 6 55136928 AGAGCAAGACCAGTGCCAACTTGGAGCCAGTAGGG[C/T]AGTGCTGGAAACAGGCACTAAACAAGTGAACACCT Y 2 1 2 1 201000 r 74 goat snp27079-scaffold289-1080169 6 57554828 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766058 Affx-122963835 AX-385253475 6 55177801 CCTGAGCCTAGAAATTAAACTATAAATTATAAGTT[A/G]TAGCCAGAGTCTCATGTAAAATGGAAACTTTTTTT R 2 1 2 1 102000 f 74 goat snp27080-scaffold289-1121042 6 57595684 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438122 Affx-122931490 AX-123308460 6 55222086 TGGACTACCTCACTCATCTTTATAATAAAAATATG[C/T]ATTTTACGTACATTCATAATGAACCACCAAGACAG Y 2 1 2 1 102000 r 74 goat snp27081-scaffold289-1165327 6 57640646 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800550 Affx-122977121 AX-385287469 6 55266307 TATCCAGTGTCTTTTATCCTTCATCACAATCTGAG[C/T]ATCTTACCTAGGAAAGACTATAGACATGTTCATTG Y 2 1 2 1 101000 r 74 goat snp27082-scaffold289-1209548 6 57681279 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788885 Affx-122978733 AX-385275900 6 55319895 ACCTATGTACTTTTTGCTCTAAGATCATAAAGTGA[G/T]AGAAGGTACCACAGTTTAAACATAAAGAGGCTGGC K 2 1 2 1 101000 r 74 goat snp27083-scaffold289-1263136 6 57728823 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415519 Affx-122948678 AX-123285868 6 55350592 TCTCCTGCATTGCAGGCAGATTCTTTACCATCTGA[A/G]CCACCAGGAAAGCCTCTCTTTGTTGGAATCAGCAT R 2 1 2 1 103000 r 74 goat snp27084-scaffold289-1293833 6 57758106 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450503 Affx-122922510 AX-123320837 6 55386602 GCTTCTGTCTTGATCATTCCACTGATGGCTCCTAC[A/C]TGTCAGCAGTCCCTTGTAGCTTGTGAAATCTGGTT M 2 1 2 1 101000 f 74 goat snp27085-scaffold289-1329843 6 57793927 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437214 Affx-122932041 AX-123307552 6 55419535 TTATAAAAAGTAAAAAAGAAATTGCCCTCTCCATC[C/T]TACTGCTGGAACATGTGCACCCTTCCCCAGTTTTC Y 2 1 2 1 101000 r 74 goat snp27086-scaffold289-1362776 6 57827231 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390685 Affx-122967952 AX-123261042 6 55451660 TAGTGGCATCTCCTCCAGCCAGCGACAGGACACCA[A/G]ACAGGAAGCTGAAGGTGGGGCTTGGAGGCCCAGGT R 2 1 2 1 201000 f 74 goat snp27087-scaffold289-1394901 6 57859371 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375673 Affx-122978670 AX-123246032 6 55514155 ACAGTTCACCCATTTAAAGTATACAGTATATTTTT[A/C]TGTATTTATAGGGTTGTGGAACCATCGCTGCAGTC M 2 1 2 1 101000 r 74 goat snp27088-scaffold289-1457396 6 57921757 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792830 Affx-122978517 AX-385279808 6 55553261 GGAGATGGCTGAGCAGCCCTTTCTAGAGTTCCTGT[A/G]GGTCTGTTATAAATGAAATTGACTCTCTGGTTCAG R 2 1 2 1 101000 f 74 goat snp27089-scaffold289-1496502 6 57960681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446164 Affx-122925748 AX-123316500 6 55591293 CTCTGGTATTTCAGAGAATGAAGAGGCTGGAGATA[C/T]GCTTCCTTTGGCAAAGATGTGTCCATTGTTCTTCC Y 2 1 2 1 201000 r 74 goat snp27090-scaffold289-1534534 6 57998777 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404208 Affx-122957666 AX-123274560 6 55626053 CTTGAAAAAGAATTTCTTAACATTTCCTTCCTCTC[A/G]AACACTGAGTGGTATTTTGCTAAGGGAATGACTAT R 2 1 2 1 101000 r 74 goat snp27091-scaffold289-1569294 6 58033222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391618 Affx-122966586 AX-123261975 6 55690601 ATGCTTTGAGGCCCAAGGCCCCTTCCTCTGTGCAG[A/G]CTTTTCCCAGTGTCTGCCTGGATTTCTGTAGAAGC R 2 1 2 1 101000 r 74 goat snp27092-scaffold289-1633842 6 58098874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381978 Affx-122974097 AX-123252336 6 55739558 GGCTGGAGTAGTCCATCCTAGTTCCTAGGGGCTGT[A/C]ATACTCACCCCTAGGATTCACTGGGTCTCTAGCAT M 2 1 2 1 101000 r 74 goat snp27093-scaffold289-1682799 6 58147630 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441874 Affx-122928632 AX-123312211 6 55792130 TTGGGTGGAAATGCAGATTCCTGAGTCCTACCATA[G/T]CCCTGTTGAGTTCCTGGGGGTGGGTAGGCTGGAGT K 2 1 2 1 101000 f 74 goat snp27094-scaffold289-1735371 6 58200652 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408503 Affx-122954402 AX-123278854 6 55862952 TATGAGAAATAGCTAATAAAATGGGATAGAGACAC[A/G]CCCAATTTAAGTGCAAACAGCTGTAAAACAACAAA R 2 1 2 1 101000 f 74 goat snp27095-scaffold289-1806193 6 58271760 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383121 Affx-122973262 AX-123253479 6 55921565 TCCCTCCCCTATTATTGAAATCACAACTATATACC[C/T]TCACTCTCAGTAGGTGGGAGGGAAAAGCCATCCTT Y 2 1 2 1 201000 f 74 goat snp27096-scaffold289-1864806 6 58330787 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783149 Affx-122947310 AX-385270216 6 55982686 AATACAACTTGTATTGTACTCAAGCAGAGTACAGT[A/G]TGCATTCAGTCATTTGAGGGAGACTGAACTTGAAA R 2 1 2 1 101000 r 74 goat snp27097-scaffold289-1925927 6 58390681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796051 Affx-122938940 AX-385283003 6 56015974 TCATGTGAAAACAGCAGCAAGCTGATGCGACTCTG[C/T]TGCATCAAAGTACTATATTGCTAAATTTCCTTTTA Y 2 1 2 1 101000 f 74 goat snp27098-scaffold289-1959215 6 58424208 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453923 Affx-122919901 AX-123324256 6 56045128 AGGCTTCCCCATCTTAGTAAACAACAGCTCTATTC[A/G]TCCAGCTGCTCAGACCCAAAACCTTGACTCATTTT R 2 1 2 1 101000 r 74 goat snp27099-scaffold289-1988369 6 58453359 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413924 Affx-122949815 AX-123284273 6 56092650 CACATGACACTTTTCTGCCTTCATAATTTGGTCCA[C/T]CATCACACAAGGAGAAGAAACTTTCCTGGGAGGAA Y 2 1 2 1 201000 f 74 goat snp27100-scaffold289-2035891 6 58501198 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428464 Affx-122938797 AX-123298807 6 56129710 GGCGCCGTGTTAATAAAAGTGAGTTGTAGGGACTG[C/T]GCACCTAAGAGATCCCGCTTATCAGCCCTCGGATC Y 2 1 2 1 101000 f 74 goat snp27101-scaffold289-2072951 6 58538376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443812 Affx-122927074 AX-123314149 6 56185911 TAACCCAAAGTCCATTCCATGAAAGTTCATTGAAC[A/G]TCTTTTCTGAACCATGGACTGAACAAACTGCTGCT R 2 1 2 1 101000 r 74 goat snp27102-scaffold289-2129152 6 58594485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771473 Affx-122962249 AX-385258632 6 56230874 TGTTCGCATCACTGCATATGTCTATATCAGGTTTA[C/T]GTTTCTCTACATAATTACTCGTTTTCATTTATGTT Y 2 1 2 1 101000 f 74 goat snp27103-scaffold289-2174115 6 58638358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397046 Affx-122962743 AX-123267401 6 56266918 ACTTTCACAGATACAGATAATACTCTTAGTTCCTA[C/T]GTGCATATTTCCTCATGCCAGGTGAAAGATCCATG Y 2 1 2 1 101000 r 74 goat snp27104-scaffold289-2210159 6 58674096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788966 Affx-122963904 AX-385275979 6 56301284 CCCTACATCTTGGAGTAAATGGGGCTTTTAAGCAT[A/G]CATCTAATGTACAAATGTGTGTTTGTGCAGATGTT R 2 1 2 1 101000 f 74 goat snp27105-scaffold289-2244525 6 58708410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407325 Affx-122955303 AX-123277676 6 56330049 GCAAGTATTTAGATAGAATATTAGAGGGATTACAA[C/T]ACAGTAGACCCCCAGGACTGCACTTTAAAATCTAC Y 2 1 2 1 201000 f 74 goat snp27106-scaffold289-2273290 6 58736621 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802407 Affx-122953436 AX-385289311 6 56365383 GTAATATTTAGTCTCTAACCTCAGCTTGTCCTTCC[A/G]AAGTAATTCTTGATTCCCACTGAGTAACAGAAATT R 2 1 2 1 101000 f 74 goat snp27107-scaffold289-2308624 6 58772977 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424539 Affx-122941717 AX-123294885 6 56396058 GCTAGAATATGCTCTCTTGCCAGTGAATACCAATG[C/T]GGAGTTATTACAAGTCCCAAATACCATTAAAGAAG Y 2 1 2 1 101000 f 74 goat snp27108-scaffold289-2339299 6 58803620 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776090 Affx-122944421 AX-385263220 6 56428994 ATAACTTGTGTAGATAAGTTGGGGATACAAAGTCC[A/G]TAAAATATTAATTTAGCTGATTTTTAAAAATGTTA R 2 1 2 1 202000 r 74 goat snp27109-scaffold289-2372235 6 58837011 A G 2 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38407123 Affx-122954870 AX-123277474 6 56468903 CCATCAAATAGTAGAAGGCTTTGGGCAGCAGAGGT[A/G]TGTGGATTTTTAAGGAGTGACCGTTTTGCCATGCG R 2 1 2 1 101000 r 74 goat snp27110-scaffold289-2412144 6 58877044 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783018 Affx-122926623 AX-385270086 6 56512164 TAAATGAAGATATCGTCTTCCTTTATGAATTTAGT[A/G]TAATTATTCTACTATCAATGGATATGTTTTTAGTA R 2 1 2 1 201000 r 74 goat snp27111-scaffold289-2455405 6 58920674 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797820 Affx-122934184 AX-385284759 6 56609110 TCCCAAATTTCCCTCCCAAACAGCATGTTAAGCAC[G/T]GAAAGCACATGTCCTATGTGTTCGGAAAGATTAAA K 2 1 2 1 101000 f 74 goat snp27113-scaffold289-2552351 6 59017819 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778959 Affx-122951292 AX-385266066 6 56688892 AGGGCCTCAGAAGATATGTGAATCCCTTTAAGTGG[C/T]GTATGTATGTCCTTACATATTTCTGTGAGCAGCAA Y 2 1 2 1 101000 f 74 goat snp27115-scaffold289-2632133 6 59096273 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433818 Affx-122935167 AX-123304159 6 56721738 TTGTATGCTTCCTTGTTTTACCTTTAAATATGAAC[A/G]TGTTATTCTGGAGTAAAAAAAAAAAACTAAACATT R 2 1 2 1 101000 f 74 goat snp27116-scaffold289-2664979 6 59129005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376740 Affx-122978950 AX-123247099 6 56779588 CTCTGGTCCATTCCGATGGCTGTGGCCACCTCTTC[C/T]ACATCAGCTCCTGTTGCTTCACAGAGGGCACTTAT Y 2 1 2 1 101000 r 74 goat snp27117-scaffold289-2722829 6 59187339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428872 Affx-122938341 AX-123299214 6 56816888 CAAGTGAAGCCACCATGGAAATAGTTTTAAAGAGA[C/T]AATACCCAAATCAAATGAGAAAGAAAACAAGTATA Y 2 1 2 1 101000 f 74 goat snp27118-scaffold289-2760129 6 59224499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395387 Affx-122963968 AX-123265742 6 56871621 GAATCAGCTACAGGAAGATCTGGGAGAAGACTGAA[G/T]CCACAAGGAAGAGCAAGTGCAAATGCCCTGAGGCA K 2 1 2 1 101000 f 74 goat snp27119-scaffold289-2814862 6 59279248 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781340 Affx-122977784 AX-385268425 6 56927977 TAACTACAAGAGTTTCTTATAGATCATTATGAGGA[A/G]TCAGGAGGTGCTTCATCAGCATTAAGCAATTCTTC R 2 1 2 1 101000 r 74 goat snp27120-scaffold289-2871218 6 59336246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446307 Affx-122925643 AX-123316643 6 56976082 GGATGTGTTAGCCGATGCTGCCCCAGGAAAATACC[A/G]TAGACTGGGTGGCATAAACAACAGAAGTTAATTTT R 2 1 2 1 101000 f 74 goat snp27121-scaffold289-2919323 6 59384174 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411302 Affx-122952291 AX-123281652 6 57028161 AACCATTGACTTTGAAAATTTGCATTTCCATTCTT[C/T]TAGTACTAGTTTAAAATAAATGCTTAAATCAGCTG Y 2 1 2 1 101000 f 74 goat snp27122-scaffold289-2971402 6 59436378 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801772 Affx-122960144 AX-385288680 6 57088355 AGGTGAATCATATATGGAACTACATACTCAGGCAA[C/T]AGTGATAATAATTTCTCTAGAGTGAAAACATTATT Y 2 1 2 1 101000 f 74 goat snp27123-scaffold289-3031596 6 59496880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793026 Affx-122948338 AX-385280004 6 57121687 TAACTGATAATTCTGACTAAAGTCTTATTTAAACA[C/T]GATATGTCTAAACATGCAGAAAGTGATTTCTGAAC Y 2 1 2 1 101000 r 74 goat snp27124-scaffold289-3064928 6 59530692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436416 Affx-122933017 AX-123306754 6 57176344 TCTAATATTTGTAATCTCCAAAGGCTGAGGACCCT[A/G]TATTTAGGCATGTCTGTAACTGTATAGAAGTGTAC R 2 1 2 1 101000 r 74 goat snp27125-scaffold289-3119585 6 59585654 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779764 Affx-122975009 AX-385266864 6 57219985 AGAGGTGGTTTTCCCACTATGGTAACAATGGGCTT[A/G]GGTTTTTAACAAGGACTTGACATCTCATGAGGCAG R 2 1 2 1 101000 f 74 goat snp27126-scaffold289-3163226 6 59630010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423796 Affx-122942818 AX-123294142 6 57305061 ATAAAAAAATCATACGATGAAGCACAAATTGGGCC[A/G]TTTTCTCTGGGACTGAATTTGAAGGAAATTATTAG R 2 1 2 1 101000 r 74 goat snp27127-scaffold289-3248302 6 59715678 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398931 Affx-122960997 AX-123269286 6 57338998 GTTTCCAATCCTTTATTTTGTCCTTTTAAAATTCA[A/C]GTGTTTTGTATGCTTAGAAAAAAAGACGTGTATAA M 2 1 2 1 101000 r 74 goat snp27128-scaffold289-3282239 6 59749954 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398266 Affx-122962179 AX-123268621 6 57370521 TTGGTTTACCTGTGATATTATTTCCAAGGCTGCTT[G/T]GCCGTGGAGACGCAGATGCCTCGCGCTCAAAGCTG K 2 1 2 1 101000 f 74 goat snp27129-scaffold289-3313762 6 59781433 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378283 Affx-122976869 AX-123248642 6 57404371 AGGCACACACCACTCCTACAATACATGAACTAAAA[A/C]CAAAATTCTAGTATCTCACCATTCTAACACAAATG M 2 1 2 1 101000 f 74 goat snp40155-scaffold511-5493595 6 59802430 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273212 Affx-1111833510 AX-519546871 6 57406488 GGGAGAAAACAGAATGCTGAGAGAAAAAGCTGTTA[A/G]TGAAGCTTATAGTCCAGTGGAGGATGGCAGACATG R 2 1 2 1 101000 f 74 goat 6_57406488_AF-PAKI 6 57406488 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789166 Affx-122934239 AX-385276178 6 57455903 TACCTCGAGCAGTTGCCTAAGTTGTTCACTGCACA[A/G]AAGTACTCAGCCAATAAGTGAGTGGTAGCTACATT R 2 1 2 1 101000 f 74 goat snp40154-scaffold511-5442063 6 59853974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431373 Affx-122937030 AX-123301714 6 57495022 CACTTCTAATCTAACCTGTATCCAGTTGTTTGTTT[A/G]CAATGGATACGTGTTAGACTAACACCTCTCAAATG R 2 1 2 1 101000 r 74 goat snp40153-scaffold511-5402944 6 59893165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399200 Affx-122960614 AX-123269555 6 57538917 ATTTCTCAAGATCCTGGGGAAGGGAAAATGCTGTT[A/G]CTCCTCACTGTGGACAGCTGCTCCAGGCTGTTTCA R 2 1 2 1 101000 f 74 goat snp40152-scaffold511-5359049 6 59937162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792290 Affx-122952637 AX-385279272 6 57572037 TAAGGGTTGACGGGTGTTAACCATGTGTTATTCAC[A/G]ATGGTTCTGTTCTTTAAACGCTCGACCTCTCCTTA R 2 1 2 1 101000 f 74 goat snp40151-scaffold511-5325929 6 59970295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413812 Affx-122949897 AX-123284161 6 57612087 TAAATACATAGAGTGATTTGTCATTTCTGTTGTAA[A/C]AGAAATTTTCATTTTCTACTCCCAAACTGGGGTAT M 2 1 2 1 102000 r 74 goat snp40150-scaffold511-5285879 6 60010410 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784585 Affx-122960910 AX-385271633 6 57723513 AATGTCAGATTCAAACCCTAGATATCATTATCCAA[C/T]GCTCCACATATTATGGATTCATGATCAGTGAATGC Y 2 1 2 1 101000 r 74 goat snp40148-scaffold511-5174453 6 60121532 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438599 Affx-122930940 AX-123308936 6 57769091 TAAGCTTCATGAGGATAGAAATTTTTATCTGTTTT[A/G]TTCACTTCTATCTTCCTAAGGCCCAGACAATAGTT R 2 1 2 1 101000 r 74 goat snp40147-scaffold511-5128875 6 60167482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378102 Affx-122977151 AX-123248461 6 57825135 TGGGAGTCAAAATGACTACACAGGGTCTCATAGGT[C/T]ATATCAGGGAGTGTCAACTCTATCCCCTAAGCAAT Y 2 1 2 1 101000 r 74 goat snp40146-scaffold511-5072831 6 60223017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765310 Affx-122920351 AX-385252834 6 57887916 GAAAGTGTGTGCGTATTTTCTGTGAAAGGATGCCA[A/G]TGTTTTACCTGATATTGTAGTGACACTTCAGTTAT R 2 1 2 1 101000 f 74 goat snp40144-scaffold511-5010050 6 60286526 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401288 Affx-122959865 AX-123271641 6 57938636 ACATTTTTAGGCACTTCAATGTTTTTTTTCTCTCT[A/G]CCAGTTAAACTTGAAGGTAATGTAGTGCGTATTCA R 2 1 2 1 101000 r 74 goat snp40143-scaffold511-4959330 6 60337471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423335 Affx-122943168 AX-123293681 6 57975561 CTGAGCCACCAGGGAAGCCCGTATGTCACCAGGCA[C/T]GGCCTAGATCAGATTTGTTGAAAATTCAGAGATAC Y 2 1 2 1 101000 r 74 goat snp40142-scaffold511-4922405 6 60374479 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408372 Affx-122953727 AX-123278723 6 58015918 TTTAGGGGCAAGAAATTAAATTTCCTCTCAACTCC[A/G]TGGCTCTTATTTTCTCATGTTATTTTACTGTTTCA R 2 1 2 1 101000 f 74 goat snp40141-scaffold511-4882048 6 60415118 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408728 Affx-122953415 AX-123279079 6 58050059 TGGGAAGGAAAAGAAATAAGGGTTTTCAGCACAAA[C/T]GCAGTAGGAATATCACCCTTGGGTCAGGTCTGGTT Y 2 1 2 1 101000 f 74 goat snp40140-scaffold511-4847907 6 60449142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453429 Affx-122919877 AX-123323762 6 58114278 AAAGTTTAAAAAAATTAGATTTTTTTGTTGCTCAG[C/T]ACAGAAAATCTCATGTCTTCTTTCAAGCTTTTCAA Y 2 1 2 1 103000 r 74 goat snp40139-scaffold511-4783688 6 60513524 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411966 Affx-122951132 AX-123282316 6 58171057 CTCAGTTCCATGAGGGCAGGGATCTGGTTTAGTGA[C/T]GTATCTCTAGCACCTCGAATGGTGCCTGCTAAATA Y 2 1 2 1 201000 r 74 goat snp40138-scaffold511-4726909 6 60570178 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422497 Affx-122943307 AX-123292843 6 58200356 CATTCTGGACTCCAGAGTGCTCCTCTGTCCAGTAA[C/T]GGACTGCTGTGACCTCCTTGTTCTGACTGAGCCAA Y 2 1 2 1 102000 f 74 goat snp40137-scaffold511-4697610 6 60599450 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443507 Affx-122927795 AX-123313844 6 58258121 CTTGTATAAAGGACCTAGAGATCTGGCCTTTCAAA[G/T]CTCTATAGCTGTGGTTCTTGGGGTGGGGGGTGGGT K 2 1 2 1 101000 f 74 goat snp40136-scaffold511-4639845 6 60657059 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436660 Affx-122932474 AX-123306998 6 58320961 CCACAGGAGTTGCCAATGGTCTGCTTCATGAAGTA[C/T]ACCTTGGGACTGACTTCTTGTCCCTTCAGCTCTTC Y 2 1 2 1 201000 f 74 goat snp40135-scaffold511-4577005 6 60719838 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448857 Affx-122923284 AX-123319192 6 58354882 TCACATTTGCAAAGGGCTTTAATTGTTTGCATGAA[C/T]GTCTCAAATGTGTAGCTCCATCCTCTGAATAGGGA Y 2 1 2 1 101000 f 74 goat snp40134-scaffold511-4543084 6 60754247 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771109 Affx-122943955 AX-385258269 6 58409934 GTTGGTTGCAACAGAACAGTTAAGTTTAATTTTGC[G/T]AACTAAAACACACAAAAGAATGTTTGAATGAAAAA K 2 1 2 1 202000 r 74 goat snp40133-scaffold511-4488032 6 60809883 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376712 Affx-122978970 AX-123247071 6 58452914 CCTTTTCTCATGCTAAAGATCTGGCTGTGTCCAGT[A/G]TCGTCCAGCCAAGAAGGTCAGGCAGAAGACAGAGA R 2 1 2 1 101000 f 74 goat snp40132-scaffold511-4445052 6 60852528 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388326 Affx-122969365 AX-123258684 6 58494380 GGAGAGTCAGTTGGCATAATCAGTTTGAGAAGCAA[C/T]GAACTGATGAAAATCTAGAAAGCCTGGAGATAACA Y 2 1 2 1 101000 f 74 goat snp40131-scaffold511-4403586 6 60894165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774476 Affx-122941380 AX-385261612 6 58530060 TTACTGGCTCTCCTCTTAAATTCTATCACCATACC[A/G]TCTAACCCAACAGACATTGTCTCCTTTGATCTGAA R 2 1 2 1 101000 f 74 goat snp40130-scaffold511-4367906 6 60929835 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785637 Affx-122924751 AX-385272679 6 58562735 TTCATGAATGCACTTAATTTTAACCATGAATTTAA[C/T]CTTCTTAAAAAGTGGGGGTTTTATAGCTTATCTTG Y 2 1 2 1 202000 r 74 goat snp40129-scaffold511-4335231 6 60962593 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795348 Affx-122976152 AX-385282304 6 58591614 TTTTTATAACACAGTCAGTCCATTGCTAATACTTC[A/G]TGTCAGCAAATTTAACCAAGGTAACAGTTGGGTCA R 2 1 2 1 101000 r 74 goat snp40128-scaffold511-4306352 6 60991451 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447103 Affx-122924482 AX-123317439 6 58695102 AAATGAAAGCAAAGTCTTGACACTTCTGAAGAATG[C/T]GAAATTTGTAGGAAAACCCAAAGAGGAAATAAAAA Y 2 1 2 1 101000 f 74 goat snp40126-scaffold511-4202864 6 61095251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396018 Affx-122963482 AX-123266373 6 58726236 TCACTGTTCACATCCTTAGGGCTCCTTTTTAGTGG[C/T]GTGGGAACATGCAGTCCTTACCAAGGTAAAGGGAT Y 2 1 2 1 101000 f 74 goat snp40125-scaffold511-4171730 6 61126366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787120 Affx-122940821 AX-385274146 6 58770780 TATCCATAAAAAGAGTCTTTCCTTAACTATCTAAT[A/G]AAAGTTCTGCGATTCCTGCTGTTTGGACCATTCAT R 2 1 2 1 101000 r 74 goat snp40124-scaffold511-4127186 6 61171028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396024 Affx-122963478 AX-123266379 6 58813389 AATGACCTTCAGTAAATTCTCCCAGACAACATTAC[A/G]TAAACAGTGGCATTAATTTTGATGGTCTAAAATGC R 2 1 2 1 101000 r 74 goat snp40123-scaffold511-4084577 6 61213935 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436366 Affx-122933058 AX-123306705 6 58844002 CACAGGGCACTTAAGGCCTTTTCTGCTTCTGACTG[A/G]CCAGACCACATCTGCTATCATCAACTTGCCACCCC R 2 1 2 1 201000 r 74 goat snp40122-scaffold511-4053964 6 61245036 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433706 Affx-122934533 AX-123304047 6 58887167 GTTTTGATTATCCCATGCTGATGCTCAGTGTGGAG[C/T]GAGATGGATTCTCCACAGGAAGGCTTCTCTCTATT Y 2 1 2 1 101000 r 74 goat snp40121-scaffold511-4010799 6 61288659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423337 Affx-122943166 AX-123293683 6 58929851 ATTTTGTTTGTGTATTTAAATAAGGCTGTAGATAG[C/T]GGCATTCATATTCTTTTTATTTTTAATTCTTTTAT Y 2 1 2 1 101000 f 74 goat snp40120-scaffold511-3968115 6 61330588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400427 Affx-122959973 AX-123270782 6 58962278 ATAAAATTTTTTAAAAATTGAAGGGTTAGGTTAAA[C/T]AGGTGATCTTGGAAGGAAAAAAGTTGTCCACCTAG Y 2 1 2 1 101000 r 74 goat snp40119-scaffold511-3935688 6 61362996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379427 Affx-122976107 AX-123249785 6 59004675 CTACTTGAGGAAAGAGTGCCACCTACTGCTCATCA[A/G]CATAACTGGTTACTTTCTCCCTTGAGGTTTTCACC R 2 1 2 1 101000 f 74 goat snp40118-scaffold511-3893291 6 61405346 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395168 Affx-122964110 AX-123265523 6 59038753 ATGTAGTCCACATTTGCATCAAAGTGGTAGAAAAG[C/T]ATATTTGTCTCTACTCTTGTGTGGCCCTGTCTCCC Y 2 1 2 1 101000 r 74 goat snp40117-scaffold511-3859213 6 61439681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416115 Affx-122948305 AX-123286464 6 59081246 AAAAACAGCTTTGTGCATTAGTCCAAGACATACAG[A/G]AAGAAATAACACAGATTTTTTTAAAGTTTTATATG R 2 1 2 1 101000 f 74 goat snp40116-scaffold511-3816720 6 61482648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412814 Affx-122950477 AX-123283163 6 59112809 TGAGTGTGGCCGGAGAAAAGATGTAACCCTGGGAC[A/G]TGCCAATTCTTGGAGGTAAGGGAAATGAGGAATAA R 2 1 2 1 101000 r 74 goat snp40115-scaffold511-3785157 6 61514355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278373 Affx-1111836389 AX-519551859 6 59118528 AAAAGATTTTCATCACTATGAAAGTCGACAAAGAA[A/G]CTATGGCATTTCCTTCCTTATTTATATATAAGTTA R 2 1 2 1 101000 f 74 goat Random2.2K-688 6 59118528 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38420120 Affx-122945080 AX-123290468 6 59157831 CGGTACTTTCAGGTATAAAAGGGGGACAGGAAGGC[A/G]CCAGCCCTCACCTCAAGGAAGGAGACTGGGAAGAG R 2 1 2 1 101000 f 74 goat snp40114-scaffold511-3740135 6 61559529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405366 Affx-122956314 AX-123275718 6 59222392 GTCTAACACCACTTCAGTCCGTTATGTAATCCCCA[A/G]TTTTCCCCCATTTTGACTGTCTCTGCTGTTTATTG R 2 1 2 1 201000 r 74 goat snp40113-scaffold511-3675574 6 61624572 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398874 Affx-122961040 AX-123269229 6 59262193 AATGTGTAGTTGAAAGCATCCAATGAACCAGGTTT[A/C]GGGAGAACTGAATAACTGAACTGCTCTCATTGTCT M 2 1 2 1 101000 f 74 goat snp40112-scaffold511-3635773 6 61664468 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433926 Affx-122934298 AX-123304267 6 59292351 ACAACCTTGACTAATACACCCAGAGAATCTCTACC[G/T]AGCCTGAGAGGGCTTCCCCTGAGTCATCAAGTGTT K 2 1 2 1 102000 f 74 goat snp40111-scaffold511-3605615 6 61694511 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386251 Affx-122970960 AX-123256609 6 59343911 GTTTTGTTTTTCTGTGTGAACTTTAATGTCAACTT[A/G]CCTAGTTCCAGAAAAAAAGACTTATTGGTATTTTT R 2 1 2 1 101000 f 74 goat snp40110-scaffold511-3554055 6 61746078 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400169 Affx-122960681 AX-123270524 6 59436416 GGAAAAACATATTTGGGAGCCTAGTGGTTTGTTCT[C/T]GTACAACATGAGTGCAAAACAAATAATACTTGATG Y 2 1 2 1 101000 r 74 goat snp40108-scaffold511-3461550 6 61838586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445247 Affx-122925484 AX-123315584 6 59518377 CCTCATGGCAGGCTCTATGTGAGGCCTGAGAATCC[A/G]TGGTAAACATAATAGTCCTGACGCTCTATTTGTAC R 2 1 2 1 201000 r 74 goat snp40106-scaffold511-3379589 6 61920274 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406626 Affx-122955828 AX-123276978 6 59608807 AGTTCTGTCTTCCTATGATTGTGTTGTGGTGAAAT[C/T]AATGGGGTTACCTTTCTGCAAGCATTTTTACCAAC Y 2 1 2 1 101000 f 74 goat snp40104-scaffold511-3289159 6 62010755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779522 Affx-122925608 AX-385266625 6 59670026 TTGGCTCCTTCACCAATCCACGATCATCTGTATTT[C/T]ATTTTCTCTAGCTGGAGATCCTCACCATTCCCATC Y 2 1 2 1 101000 f 74 goat snp40103-scaffold511-3227940 6 62072989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429616 Affx-122937699 AX-123299957 6 59715756 AAAATTGGCTTATAATTTTCTTTTATTGCCTTTAC[A/G]TGATTTTGGAGTCAATACTTCACTAATCTCATCAA R 2 1 2 1 101000 r 74 goat snp40102-scaffold511-3182210 6 62119745 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38385165 Affx-122971744 AX-123255523 6 59747039 CATGTACTTCTTCCAAAGAGAGTTTTCCATGATCC[G/T]AAACAACTCAGAGCTTTCTCACAGTTTTTGCAGAT K 2 1 2 1 101000 f 74 goat snp40101-scaffold511-3150927 6 62150968 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402501 Affx-122958576 AX-123272854 6 59818152 GATGCTCCTTTCTTCCACACTGCTGGCTGAAACAG[A/G]ATTCCTGATTCCACATCCAGAAAATGCAAAAGGCT R 2 1 2 1 201000 r 74 goat snp40099-scaffold511-3079814 6 62222870 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274832 Affx-1111834444 AX-519548417 6 59834165 GCTCTCTGCAGGACTATGGAAACTGAGGTCAAAGG[A/G]GAAAGCTTTATAGCCTGCAGCACACTTACAATTGC R 2 1 2 1 101000 r 74 goat GoatD01.036251 6 59834165 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38395446 Affx-122963925 AX-123265801 6 59885446 TTTAATATAGAGTTCAAGGTTACCCCCATAATAAC[A/G]TCACACTCACATTCTAGCTTTTGAAATGTTCTCCT R 2 1 2 1 101000 r 74 goat snp40098-scaffold511-3012520 6 62289903 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446157 Affx-122925754 AX-123316493 6 59935930 AAGGTATCAAAGAAAACTGAGATTTGGAGTCCGAG[C/T]GACTGGAAGAATTGTGGGGTCATTTATCAAAACCA Y 2 1 2 1 201000 r 74 goat snp40097-scaffold511-2962036 6 62339949 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791734 Affx-122953234 AX-385278725 6 59981954 CTCTGGTCTAAAGCCTTGCCACTGTAAGAAAAGGA[C/T]AGTAAATGCATTTTGATTCACATGTGAATTCTGAT Y 2 1 2 1 101000 f 74 goat snp40096-scaffold511-2916012 6 62386041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452662 Affx-122920330 AX-123322995 6 60034963 TGAAGCACTGCTTCAGACCGATTTCAAGAGGGTGC[C/T]AGCCCTTGAAGGGTGCCAGACTGCAAGAGGACACC Y 2 1 2 1 101000 f 74 goat snp40095-scaffold511-2863003 6 62438828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378626 Affx-122977115 AX-123248985 6 60087151 TTGAATTTCCATCATCCCAGAAAAATTAACTGTTA[C/T]GATCTAATCATTGTTAGGGTCAAGCAACATGAAAG Y 2 1 2 1 101000 r 74 goat snp40094-scaffold511-2810815 6 62491347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771304 Affx-122925280 AX-385258462 6 60194889 AAACAGCCTTGAACTAGCTTTCTCGCTTCGCCCAT[A/G]CAAATCCATGAATAACATGGTAATCTCTATTCTGC R 2 1 2 1 102000 f 74 goat snp40092-scaffold511-2703077 6 62598454 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273214 Affx-1111833511 AX-519546873 6 60205735 TTAGTTCCTCCTCGCTATGTGACATCTTCCAGGAC[A/G]AGGGGTCAAATCTGTGTCCACTGCATTGGCGGTGG R 2 1 2 1 102000 f 74 goat 6_60205735_AF-PAKI 6 60205735 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446261 Affx-122925677 AX-123316597 6 60242274 TCAGTTATGTGATCCCTGTAGGCCAGGTCTCATAG[C/T]AAACCATATGCCATTATTCAACCAGACTACTGGGA Y 2 1 2 1 101000 f 74 goat snp40091-scaffold511-2655692 6 62643472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432488 Affx-122935590 AX-123302829 6 60307831 TCTATTTACCATAAAAGCAGTTTCAAGTCACAAAG[C/T]AAAACTCACCTTCTAAAATATATCATTTTTAACAA Y 2 1 2 1 101000 f 74 goat snp40089-scaffold511-2590135 6 62710047 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394945 Affx-122964292 AX-123265300 6 60356655 ACCTATAGAATTTTGAATGTTTATAATGCACTTGT[A/G]TTAACCTGCCTGGTTGTACTCCCTTTTAGTACATT R 2 1 2 1 101000 r 74 goat snp40088-scaffold511-2541311 6 62749473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390939 Affx-122967070 AX-123261296 6 60389433 TAATAAGATTTTAAAGTTTATGCTGTGAAATGGGA[G/T]CAGTATTAACAAGAGAGAAACTTGTTTGTCTCATA K 2 1 2 1 101000 r 74 goat snp40087-scaffold511-2508533 6 62783220 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777354 Affx-122974368 AX-385264476 6 60440291 CAAATTTGTGGTAGAATGTGGATGGAACACTGAGT[A/G]CAATCCTGTTTCAGTGAAATACAAATTTCTAGCCC R 2 1 2 1 101000 r 74 goat snp40086-scaffold511-2457675 6 62834521 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391251 Affx-122967376 AX-123261608 6 60483823 GAGACTATTATTCAGTTTAGCCTCTGGGGGCCCAG[C/T]GGTCTGGAACTTGTCAGAATATCCAGCACACTTTG Y 2 1 2 1 101000 r 74 goat snp40085-scaffold511-2414143 6 62878413 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379214 Affx-122976285 AX-123249573 6 60523238 TGATCAATTATATTCAAAAGTTCAAAAGAGAAAAA[C/T]ATAGGTTGAAAAGTTTGATATGATGCTGGCTGATG Y 2 1 2 1 101000 r 74 goat snp40084-scaffold511-2374728 6 62917823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391701 Affx-122967515 AX-123262058 6 60553915 TAAACTGAATACAGAGGATGACCTAAATCAGAATG[C/T]ACCTCCCACTCCCAGTCCTTTTGTATGTCATGAAC Y 2 1 2 1 201000 f 74 goat snp40083-scaffold511-2344051 6 62949329 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392464 Affx-122966156 AX-123262821 6 60588680 ATAGGTGCATAATAATCTTTTTCACTTCTAAGAGA[G/T]CTCCAGAAAGGGACTTTAAACTCTATCTTGGCATC K 2 1 2 1 101000 r 74 goat snp40082-scaffold511-2309286 6 62985051 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398003 Affx-122961791 AX-123268358 6 60617536 TATTTGGCTAACTGTACCTTCATCTTAGATATTGA[C/T]GTCAAGAAGGAGAGCTCTCCTTTTACCAAAATTTG Y 2 1 2 1 101000 f 74 goat snp40081-scaffold511-2280430 6 63013941 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789638 Affx-122954130 AX-385276647 6 60657087 ACATACAGTTTGACTTTCAGGTAAAATAAAGACAG[C/T]CATATAGCATTAGCTGCAGTAGGAAACTGATGAAA Y 2 1 2 1 101000 r 74 goat snp40080-scaffold511-2240879 6 63053735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775187 Affx-122950131 AX-385262318 6 60713965 TTATTTTTCAGCATTTGATAGCATTTCCATCATTT[C/T]GGAGAGTTTTGTTGGATATGAAAGTAAGGATAGAG Y 2 1 2 1 101000 r 74 goat snp40079-scaffold511-2184001 6 63110211 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793447 Affx-122949070 AX-385280424 6 60759247 TTGAATTGATACCATAGTAACACCTTATATTGTTG[C/T]AACTGTCTTTCTTAGTGAATTCCATTTTTCATTGG Y 2 1 2 1 101000 f 74 goat snp40078-scaffold511-2138719 6 63154609 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403641 Affx-122957531 AX-123273993 6 60855435 TAAACAATCCTGCAATCTCTAGGTTAAATTGTCCC[A/G]ATTTTGTATTTTTCAGGAAGGACTTTGCTATTCCT R 2 1 2 1 101000 f 74 goat snp40076-scaffold511-2042531 6 63249483 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434541 Affx-122934145 AX-123304882 6 60905890 ATAGGCAAAAATTGCATCTTTTTCATTTGATCTGC[A/G]ACAGCACCTTTGTGTATTTGCCCAAGAAGTAGCAA R 2 1 2 1 101000 r 74 goat snp40075-scaffold511-1992076 6 63298730 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793186 Affx-122962552 AX-385280164 6 60948298 CTCAAAAATTAGCTCAATCTCTTCACATTCATTAC[A/G]TGAACTGAGCTAGTAGACACCTTTTTTTCCCCTAA R 2 1 2 1 101000 r 74 goat snp40074-scaffold511-1949668 6 63341408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385315 Affx-122971673 AX-123255673 6 60990865 GTATTTTCAAATTCAAGAGAGAGCCTTAGAAGAAT[A/G]AGAAAGAAGAAAAATGCAGAAGGCAGAATGTAGAG R 2 1 2 1 201000 f 74 goat snp40073-scaffold511-1907101 6 63383763 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445576 Affx-122925135 AX-123315913 6 61049316 AGAGATATCCTTTCTCTACTATCTTTTCTCTGCCT[A/G]CTGACTGGACACTGAGGTCAAAGCTGATCTTGAAG R 2 1 2 1 101000 r 74 goat snp40072-scaffold511-1848650 6 63442701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795303 Affx-122957708 AX-385282261 6 61092351 GAACAAGCTGTTACACTTTAAATTGAGAATAAAGT[A/G]CCAGACCATGTTTCATCATTCTACTTGTGTCCAAT R 2 1 2 1 201000 f 74 goat snp40071-scaffold511-1805615 6 63486112 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783230 Affx-122936404 AX-385270296 6 61152023 GGCAGAACTAAATAAACATAGGAATGAACTAGTGA[C/T]GGTATTATACAAAAGTAAAGACAGCACTGACCTGA Y 2 1 2 1 101000 r 74 goat snp40069-scaffold511-1745943 6 63545248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447154 Affx-122924441 AX-123317490 6 61203225 TTATTGTAGTCACTTCTGCATTGTCATGTAGAAAA[G/T]AATATGGATTATGGAATAAAGACCACTTTCTATTC K 2 1 2 1 101000 f 74 goat snp40068-scaffold511-1694741 6 63597105 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448042 Affx-122923705 AX-123318378 6 61254371 TATTTGTCTCTGATTCATCCTAGGGACTGAAGACC[A/G]TTAACCCTGCTCTATTTTAAACTATTTTAACTTAC R 2 1 2 1 101000 f 74 goat snp40067-scaffold511-1643595 6 63651501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410002 Affx-122953267 AX-123280352 6 61310517 TCAGGTGTACTTTCCAGGGATATTTGTACCTAAAG[A/C]GATGTTTGTGGCCTCCAAAATTCATATGTTGAGAT M 2 1 2 1 201000 f 74 goat snp40066-scaffold511-1587449 6 63707127 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411753 Affx-122951503 AX-123282103 6 61357685 ATGAGATTTCTGCAAAGTCCGTGTTGATATAGCTT[A/C]TTTTAGAATTTATGTAACTCTTCCAGAAAAGTCTT M 2 1 2 1 101000 f 74 goat snp40065-scaffold511-1540281 6 63754510 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435381 Affx-122933574 AX-123305721 6 61390566 AGGGCTGGGGTACATGTGAGGTTTGCTCAGGGGAA[G/T]GAGTGTATTCTGCAAATGAGAGAAGTAGACATGAT K 2 1 2 1 101000 r 74 goat snp40064-scaffold511-1507400 6 63787490 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393123 Affx-122965564 AX-123263480 6 61425323 CATCCAGTTAAATGTCAAGTAAAATGTTACTCTAA[C/T]ACATGAAAGTTATTTGAAATTGTCACTATTTTCCA Y 2 1 2 1 101000 f 74 goat snp40063-scaffold511-1472643 6 63822282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440634 Affx-122929953 AX-123310971 6 61474508 CCACTTATTAAAATATCGGCATCACATACTTAGCC[A/G]CCACCATTTTGCCCCTGGACTACTACTGCAAACTG R 2 1 2 1 201000 f 74 goat snp40062-scaffold511-1423458 6 63870488 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402938 Affx-122958180 AX-123273291 6 61508159 AGTTCTGCCTAAAAGAGATGAGATATAGGGTGTTA[C/T]AATTGATCTAGGCCCTGTTGTAAGGGGATCAGAGC Y 2 1 2 1 101000 f 74 goat snp40061-scaffold511-1389807 6 63903819 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272533 Affx-1111833898 AX-519546251 6 61540367 AGATGGCAGTACTTCCCAGACTGATCTACGAGTCC[A/G]TTGCAGTTCCTGAGCAAATCTCAGATGACCTCTGC R 2 1 2 1 101000 f 74 goat GoatD01.009857 6 61540367 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320791018 Affx-122978607 AX-385278014 6 61543789 GGATTGCAGACAGATTGAATACAGGGTGTAAGAGA[A/G]AGAGTGGAGTCAAAAATGAGAGCAAGATTTGAAGC R 2 1 2 1 101000 f 74 goat snp40060-scaffold511-1354177 6 63939465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380033 Affx-122975585 AX-123250391 6 61585161 TAGAGAGAGAGAGATAGGGAGTTATATAAACCTAG[A/C]TGGGTTCTCAAAGACATTTATCTAGTTGGTGATTG M 2 1 2 1 101000 f 74 goat snp40059-scaffold511-1312805 6 63981514 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420943 Affx-122944986 AX-123291290 6 61616541 CATTCAGTAAACATAAGCAAAGAACTAAGTATCAA[C/T]AGAGATGATTCAGGGATCTCTTTATATGGAAAAAG Y 2 1 2 1 101000 f 74 goat snp40058-scaffold511-1281425 6 64013030 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397043 Affx-122963104 AX-123267398 6 61685992 AGCATTTGAAAGGTTCTTAATCATCTTAACTACAG[C/T]AATAGAAATCAAACTGTTGAACAAGTTACTCTTGA Y 2 1 2 1 201000 f 74 goat snp40057-scaffold511-1211974 6 64083343 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774618 Affx-122971634 AX-385261752 6 61719617 ACACAGAACTACAGCCTTTCAAATACACAAAGAAA[G/T]CTAAAAGATGCTCTATAGTACCTTTCAAAGACACT K 2 1 2 1 101000 f 74 goat snp40056-scaffold511-1178349 6 64119866 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387194 Affx-122970605 AX-123257552 6 61752544 TCATGACGGAACACCCGTATTTTGTATCCTTCCAC[G/T]CAAGGCAAAGCAAGTTATCAAAGTAATAATGGAAC K 2 1 2 1 101000 f 74 goat snp40055-scaffold511-1145422 6 64152774 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376948 Affx-122977770 AX-123247307 6 61796926 AATATTTTATTGTGTGATTGTGTCAATTAAGTCAG[C/T]GGTAATGTCCTGTTGCTAAACATTTAGTTTCTATT Y 2 1 2 1 101000 r 74 goat snp40054-scaffold511-1101040 6 64197436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382090 Affx-122974903 AX-123252448 6 61826989 TACTGATGGTGAAACCAACCAGATGGCAGCCTTTT[A/C]TGCTGGATGTAGGTGACCTCAAGGCTAGGGCTTTG M 2 1 2 1 101000 f 74 goat snp40053-scaffold511-1070977 6 64228064 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771163 Affx-122971733 AX-385258323 6 61855567 AAACAGAATGCATTTAATTCAGATTAAGGACAAAA[C/T]GAAGAGCATTAATTCAGGCACTTAATATTCCAGCC Y 2 1 2 1 101000 r 74 goat snp40052-scaffold511-1042399 6 64256839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401463 Affx-122958970 AX-123271816 6 61903603 CCCTTTTTTTTTTTCTTTCAGGTAGTGTTGACTAA[C/T]ATAAATTATTTCTTAATTTCTCAAAGCAGTTATTT Y 2 1 2 1 303000 r 74 goat snp40051-scaffold511-994363 6 64305304 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398867 Affx-122961046 AX-123269222 6 61942014 AATATTAAAAATAGTTTGATCTTTTTTTGCTTTAT[C/T]CTGAATGATCTACCACACAGAATTAATATCTCTGT Y 2 1 2 1 101000 r 74 goat snp40050-scaffold511-955952 6 64343943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278542 Affx-1111836390 AX-519552024 6 61957289 CCTTTATTTTGCACAAAGCCAATTTTAACTTGAAG[A/G]AAGGTGAGGGAACGGAAACAGATCCCCTAATCTTG R 2 1 2 1 101000 r 74 goat Random2.2K-689 6 61957289 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437772 Affx-122931705 AX-123308110 6 61984096 AATGAGAGATGTTTGTTTAATTAAAAGGAAATAGC[A/G]TGTTCATATGTCTTCAAGACTAAATACAGGAATGC R 2 1 2 1 101000 r 74 goat snp40049-scaffold511-913870 6 64386057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402008 Affx-122958758 AX-123272361 6 62051060 TCACCCTCAAGGCACCACAGCCCATGTTTCTGTAC[A/G]TGAGCTTGTCTCAGTTTATCTCCCCATTGTCTTTG R 2 1 2 1 101000 r 74 goat snp40047-scaffold511-846906 6 64453604 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772812 Affx-122969520 AX-385259957 6 62125742 AACACTCATCTGTAAAATCCTATTTCTCCAGAATT[A/G]CTCTTGAGATAAAACTGTGTATTAATACAGTCTCT R 2 1 2 1 101000 r 74 goat snp40046-scaffold511-772224 6 64528513 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383353 Affx-122972671 AX-123253711 6 62157956 TTTACTAGGACAGAAAAGTTGGGGAAAAAAGATTC[A/G]CAAACATATCCATCCTCTGTGGCCTCTGCTAGATC R 2 1 2 1 101000 r 74 goat snp40045-scaffold511-740010 6 64561782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446527 Affx-122925021 AX-123316863 6 62201240 AGAGATACTATATTTCCTTACCTCCAACGCAAATA[C/T]AGGAAAAAGTCAACAATTAGTAAAGAAGCTTCACT Y 2 1 2 1 101000 f 74 goat snp40044-scaffold511-696726 6 64605093 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396633 Affx-122962871 AX-123266988 6 62231019 CCAATCAGTAGAACACTGTACTCCAATGTTCATCG[C/T]AGCACTGTTTACAATAGCCAGGACATGGAAACAAC Y 2 1 2 1 103000 f 74 goat snp40043-scaffold511-666947 6 64633642 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421829 Affx-122944308 AX-123292176 6 62365821 TTCTGGAATCAGTAACAGAGGTCTTTGTATTTTTT[A/G]CCCTTAAAGAACCAAGTTTTAAATTATTGCTTTCA R 2 1 2 1 102000 f 74 goat snp40040-scaffold511-532145 6 64769030 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770131 Affx-122954624 AX-385257298 6 62416878 AAATCAAGACATGTCTTTCTGAATCATGAAACAAG[C/T]TTACTTGAGGTCATGAGAATTTGTAGTGACAGAAA Y 2 1 2 1 101000 f 74 goat snp40039-scaffold511-481088 6 64820842 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766977 Affx-122929081 AX-385254276 6 62464431 GAAGAAATTTCTAGCAAAAGTGTTAAAAATATATA[C/T]AGTTGCCACTTTATGGTCTTTGCATTTCCAAAAAA Y 2 1 2 1 303000 f 74 goat snp40038-scaffold511-433535 6 64868681 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445388 Affx-122925398 AX-123315725 6 62494048 TAAATTTTTGTTTACCTTAAATTCCATTTCTCTAA[C/T]GAGAAATATCAGATATTCAGTTTCCATTTTGTTCT Y 2 1 2 1 303000 f 74 goat snp40037-scaffold511-403918 6 64902752 T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768367 Affx-122932444 AX-385255547 6 62542890 AGAGTTCTGCCTTTTAGTGAATAATTCACACTTGT[G/T]AAGATCAAAATGCACTTTGAGTGAGTACAAATAGA K 2 1 2 1 201000 r 74 goat snp40036-scaffold511-355076 6 64951977 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451977 Affx-122920940 AX-123322310 6 62575456 GTTATCTACTATTACTGTATGTATCCATCCATAGA[C/T]AACATATTTATGTAGCTTTTTTTTTTGCATATTTT Y 2 1 2 1 103000 f 74 goat snp40035-scaffold511-322510 6 64983461 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424572 Affx-122942222 AX-123294918 6 62633076 AAACAGTGCAGGAGATGTTCAGATAGGGAGCATGG[A/C]TGTTAAAAATGAGTTTTCTCTCATTTACATGTGGT M 2 1 2 1 101000 f 74 goat snp40034-scaffold511-264890 6 65042221 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453965 Affx-122919461 AX-123324298 6 62661739 ACTGGCCTGGGGACAGAAAGGAATGGCATCTGCAT[A/C]TGTCAGGCTTCATTTATTGGGCAACTCAGCACAGG M 2 1 2 1 101000 r 74 goat snp40033-scaffold511-236227 6 65071262 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797754 Affx-122937366 AX-385284693 6 62691874 AACATACTATCATTTCAAAACTACATTAACAAAGT[A/G]ATAAAGTGAAGCCAAATTGCCCTTGGGATAGATGA R 2 1 2 1 101000 r 74 goat snp40032-scaffold511-206092 6 65101680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278545 Affx-1111836392 AX-519552027 6 62719218 TTTTCTTAATCATGGAGACAAACTGAAAATTTTTG[A/C]TTGTTGGCAGCACTAAAAGGAATTGGAATTTTTCA M 2 1 2 1 101000 r 74 goat Random2.2K-690 6 62719218 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431918 Affx-122935996 AX-123302259 6 62728701 ATATAATTGTTCATTCATCAAATATTTATTAAGGA[C/T]ACCCAGGTTCTAGGTACTGTTCTAGAATAGCTATT Y 2 1 2 1 103000 r 74 goat snp40031-scaffold511-169265 6 65138555 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273215 Affx-1111833512 AX-519546874 6 62742869 GGATGAGATAGTTGGATCGAATCACCAACTCAAGG[A/G]GCATGAGTTTGAGAAAACTCCAAGAGATAGTGAAG R 2 1 2 1 101000 f 74 goat 6_62742869_AF-PAKI 6 62742869 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38386473 Affx-122970770 AX-123256831 6 62765353 CCTCAACTTTGAATGAATTGGTTGTTGTGGGTGGT[A/G]TATATTTGGTTGGTGGTGAGTGAGGGGTTGCATGG R 2 1 2 1 202000 r 74 goat snp40030-scaffold511-132613 6 65175792 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396651 Affx-122962859 AX-123267006 6 62810304 CTAAAGGAATGTAACAAACAAACAAACCAGGAAAG[C/T]ATGGTGTCATGATGCCAAGTATTTTGAGAAAGAGA Y 2 1 2 1 101000 r 74 goat snp40029-scaffold511-87662 6 65221196 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396430 Affx-122962992 AX-123266785 6 62937396 TTCACAAATTAGCAGTTATTAGTCAGACTGTACAA[C/T]GCAAAACAAAACAAGTTTAATGTTGCTATACATCT Y 2 1 2 1 101000 f 74 goat snp57966-scaffold94-39331 6 65348867 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449901 Affx-122922335 AX-123320236 6 62991870 TTTTTGGCCACATCCATTTTTATGTCCTTGTTTCA[A/G]TAACTGGCAAATTTTGAAATAGGTATCTAAGAAGA R 2 1 2 1 101000 r 74 goat snp57967-scaffold94-93805 6 65404262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413041 Affx-122950988 AX-123283390 6 63023019 AACCCTAGATCAGAAATCTTGATATGATTTCAAAG[C/T]GTCCATCGTTTAAGCTCTAACCCTAATACTTATCA Y 2 1 2 1 101000 r 74 goat snp57968-scaffold94-124954 6 65443071 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278547 Affx-1111836393 AX-519552029 6 63038504 CATATCTGCCAATGGTTACTTTGCAGAAATATTTA[A/G]ATTACATAAATTAAAGTGCCTGGTATATAATAAAT R 2 1 2 1 201000 r 74 goat Random2.2K-691 6 63038504 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435875 Affx-122932792 AX-123306214 6 63081852 TCAGCCCTCCAAGGGATTTCAATTTGCTAACATCC[A/G]CTGGATCATCAAAAAAGCAACTATCTACTTCTGCT R 2 1 2 1 103000 f 74 goat snp57969-scaffold94-183787 6 65503377 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776622 Affx-122937901 AX-385263749 6 63152755 CATAGGCAAAATTTGGTGAAAAGGAAAAAGGGAGC[G/T]ATTCTTTGCAGAGAACACAGTATACACAGTCACTA K 2 1 2 1 101000 f 74 goat snp57970-scaffold94-254690 6 65573768 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420088 Affx-122945105 AX-123290436 6 63189415 TCTGACAACACCCAGTCCAGTTGGAGTTGGACTGA[A/C]GGAAAAGAGCTCAGAAGGGTCAGATGCAAAGCTAA M 2 1 2 1 202000 r 74 goat snp57971-scaffold94-291350 6 65612806 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414731 Affx-122949258 AX-123285080 6 63227939 GGTCAATTGTTGGTTTCATTTTCCACACCTCACCT[C/T]TCCTGGGACCCTCCCTGACAAGCGTACACACCATT Y 2 1 2 1 101000 f 74 goat snp57972-scaffold94-329874 6 65652075 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397401 Affx-122962258 AX-123267756 6 63265842 CCTAGTATAATAGCCCTTTATTCATAATCTGAATA[C/T]GAGAATAAGCAACCTATATACTAAAGCATTGGTAA Y 2 1 2 1 101000 r 74 goat snp57973-scaffold94-367777 6 65690075 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449011 Affx-122923095 AX-123319346 6 63295688 GCTGCAGAATATTTCTTTCAATAAATAATTGAATA[C/T]ATATGATTCCATTTTCTATCAAGGTGTATAGGCAA Y 2 1 2 1 103000 r 74 goat snp57974-scaffold94-397623 6 65720216 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424301 Affx-122941971 AX-123294647 6 63349990 GAAGTAGGGTTTTAGAGATAGGATTCATCAGCTCC[A/G]TAATTTCTTTGTGAAAGTATATTACCTCCCACAGA R 2 1 2 1 101000 f 74 goat snp57975-scaffold94-451925 6 65775410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800995 Affx-122967341 AX-385287909 6 63402028 AGGAACTGAAGTCACGGCCCTTGTTCTTAAAAATC[A/G]TATAAGGGTCCCAAATCAAAGTAAGAACAATGAAT R 2 1 2 1 101000 f 74 goat snp57976-scaffold94-503963 6 65827615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411530 Affx-122951662 AX-123281880 6 63456147 CCACTTTGGGGTTACATTAGTTTACATTAACTTAG[C/T]AATACTAACAAAACTGAAAATGGGCATTCCTTAAA Y 2 1 2 1 101000 f 74 goat snp57977-scaffold94-558082 6 65880435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443345 Affx-122927430 AX-123313682 6 63502180 TTTGAACACTTTACTTCAATACTCTCATTACTGAG[C/T]ACTGATATCTATGCCTTTTTTTCTAATAAGTGACT Y 2 1 2 1 101000 r 74 goat snp57978-scaffold94-604115 6 65927141 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408742 Affx-122953405 AX-123279093 6 63538337 AGCATCAAATTATGAAGAAAAGGTAAAAGGTATTT[A/C]GGTCAAACCCTCACTCTGTGGCATTTGACATCATG M 2 1 2 1 201000 f 74 goat snp57979-scaffold94-640272 6 65963323 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412412 Affx-122951436 AX-123282761 6 63611702 AAACTCAGCATCTACAAAACACAATGACATGAAGC[A/G]CACACACACAAAGAAAACTAAGGTATATCTGTACC R 2 1 2 1 101000 f 74 goat snp57980-scaffold94-713637 6 66036890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387873 Affx-122969633 AX-123258231 6 63659235 CCAAGGAGGCATCTACATCATCTTTCTAAACCATC[A/G]AAGTTGCTTAGATATGAGTTCTCCACAATATCTCT R 2 1 2 1 101000 r 74 goat snp57981-scaffold94-761170 6 66083493 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398465 Affx-122961588 AX-123268820 6 63695650 CAATTAATTAGCACACGTTAAGTATATCACACAGT[A/G]CCTGACACAATGTAAAAGTCTGAGGAATTTTAGTC R 2 1 2 1 101000 f 74 goat snp57982-scaffold94-797585 6 66115772 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410522 Affx-122952171 AX-123280872 6 63726709 TGTCTTAGAAGTGGTTGAAGCAAAAGACAAGCTGC[C/T]TGACTAAGGTTTTAAAGAGTCAAGTGTGAGTTCTG Y 2 1 2 1 101000 f 74 goat snp57983-scaffold94-828644 6 66146654 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792864 Affx-122929509 AX-385279842 6 63759347 TGAAAAATGAAGACAGTTTTACCAGAGTTTAAAGA[C/T]GTCAGGTATAAATGACTTAATAAAAGGCTTACCAC Y 2 1 2 1 101000 r 74 goat snp57984-scaffold94-861282 6 66181148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401646 Affx-122959585 AX-123271999 6 63793467 AAGAATTGCCCTCCACTTCAGAATTCTCTAAACGG[A/G]AGCAGGCATCAACCCCTGGAAGGGGGAAGCATGCC R 2 1 2 1 103000 f 74 goat snp57985-scaffold94-895402 6 66214156 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781496 Affx-122958863 AX-385268581 6 63825837 TATCACACGCTTCGAAATAAATTTTTAGAGAAACC[A/G]TGTGAGATACTTTGCTCCACTTTCTCCTTTTGTTA R 2 1 2 1 201000 r 74 goat snp57986-scaffold94-927772 6 66247096 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786664 Affx-122928193 AX-385273696 6 63866821 AAGAACACTTTTCACAACTTCTCACAAATGATTTG[A/G]CTTTATTAAAAGTTTCTGGGGGAAAACAGTGCAAA R 2 1 2 1 102000 r 74 goat snp57987-scaffold94-968756 6 66288209 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401997 Affx-122958766 AX-123272350 6 63962235 ACAATCTGCTTCTCCTCTAAAAGCATGGAGAAGCA[G/T]CAAATTATTCTTCCATTCATTTCTTCCATGGAACC K 2 1 2 1 101000 r 74 goat snp57989-scaffold94-1064170 6 66376585 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778761 Affx-122971780 AX-385265872 6 64004559 AGCAAGTAATTCATACCTAACAAACTGAATTTATG[C/T]ACCAACCCATGAATTCTAGCCCTAAATTTGTCTTC Y 2 1 2 1 101000 r 74 goat snp57990-scaffold94-1106494 6 66419574 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445672 Affx-122926139 AX-123316009 6 64035395 TCTCAATGCATACAAGGATAAGTCATAAACAAAAT[A/C]TTTTATTTTAAATATTTTGTGTGGGAAATCTTATA M 2 1 2 1 103000 f 74 goat snp57991-scaffold94-1137330 6 66450372 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396650 Affx-122962860 AX-123267005 6 64068425 TAAACTAAAAAGACTAAACTGGCAATAAAATACAA[C/T]ATCTGATCCTTGATTCAATTCTGAACTGTTCAAAA Y 2 1 2 1 101000 f 74 goat snp57992-scaffold94-1170360 6 66483982 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278382 Affx-1111836394 AX-519551867 6 64081724 AACTCAAAGGATTATTCTTGGTAGGGTTTTAAGTC[A/G]TTCCTTTCAAATATTTCAAATGTTTGACAGAACAG R 2 1 2 1 101000 f 74 goat Random2.2K-692 6 64081724 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396032 Affx-122963471 AX-123266387 6 64097851 TGAATGTTATCAAGATATGGAATTCAGTCATTTTA[C/T]AAGAATGAAAATAAAACATTTACATAAGACTTTAC Y 2 1 2 1 201000 f 74 goat snp57993-scaffold94-1199786 6 66513997 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795048 Affx-122941911 AX-385282007 6 64154072 TTTCACCTGGAGATTTCTTATTCAATGGTTGAAAG[C/T]GAAGGTGGAGTGCTTGGAAAGCCATCTTAACTCCT Y 2 1 2 1 101000 r 74 goat snp57994-scaffold94-1256007 6 66570681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434141 Affx-122934912 AX-123304482 6 64213476 TGTGTCTGTAAGCATAAATAAATTAAAAAGAAGAC[G/T]AAAGGTTTAGCAAGATATTAAAAATAATGGGCACT K 2 1 2 1 201000 f 74 goat snp57995-scaffold94-1315411 6 66629991 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278551 Affx-1111836395 AX-519552033 6 64290890 CACCCTGGTAGTAAAAAGCACAGATCTTTGTTTCT[A/G]ACACCATTCTCCTATGAGAGAAACTAGTAATAAAG R 2 1 2 1 101000 r 74 goat Random2.2K-694 6 64290890 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382166 Affx-122974030 AX-123252524 6 64320710 AAACCAACTTGGTGCCAGCTTGACCAGTATTAAAA[C/T]GAGAGAGATTGAGAAAGAGAAAGAGAACAGAGTAG Y 2 1 2 1 101000 f 74 goat snp57997-scaffold94-1422645 6 66737838 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431467 Affx-122936269 AX-123301808 6 64369900 ACTGGGGAGAACGTAGTGGGGAGGAGCAGCTGTGC[C/T]TGTGTGGCTGTTGGCCTTTGTCTTTTCTCATAGGT Y 2 1 2 1 101000 r 74 goat snp57998-scaffold94-1471835 6 66787294 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403330 Affx-122957819 AX-123273683 6 64408843 CATTCACATTTCTTTGGTCCAAGCAAGACACAGCC[A/G]TGCTTAATTTCAAGGTAGTGGGGAAATGCAGTTCT R 2 1 2 1 101000 f 74 goat snp57999-scaffold94-1510778 6 66826462 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424614 Affx-122942192 AX-123294960 6 64491727 GTATGGTTGTAGGGCAAATTCAAGCAGAGTTCCAA[C/T]GTAATTGGTTCACACTGACCTAACAATAACAACAA Y 2 1 2 1 101000 f 74 goat snp58001-scaffold94-1593662 6 66909519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413541 Affx-122950610 AX-123283890 6 64625727 CTTCTGAAATGTATATCCTAGAGGCCTTTGTCTAG[C/T]GCATATCTATGAACATATAACCACAGAAGGAACTA Y 2 1 2 1 101000 r 74 goat snp58004-scaffold94-1727662 6 67042652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782222 Affx-122941824 AX-385269300 6 64661550 CACATTATCTCTTACAAGGGCCCTTAGTAAAACCC[A/G]ATATAATTGTACTGGTGGCAAACTGGCAATAGAAA R 2 1 2 1 201000 r 74 goat snp58005-scaffold94-1763485 6 67078272 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427113 Affx-122939664 AX-123297456 6 64716700 CAGCTTAGCCCAGTAATCACATTTGTCTACCCAGA[C/T]AGCTAGTCTAATCTCTCAAGCTCCAGGAACCTGGC Y 2 1 2 1 101000 f 74 goat snp58006-scaffold94-1818635 6 67135632 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383571 Affx-122972596 AX-123253929 6 64780940 TCAGAATCAGCAAAGCCAGGTGCTTTTTCAAATCA[G/T]CATCTTCCATACTACAAACCCAACATGGCCTGGTC K 2 1 2 1 101000 r 74 goat snp58007-scaffold94-1882875 6 67199278 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400173 Affx-122960677 AX-123270528 6 64810238 GGAAAGGAAATCAATCCTTAAAGACCTAATGCATG[C/T]GGGGGTGGTGTTTCCCCATCACATCCTCATTTAAT Y 2 1 2 1 101000 f 74 goat snp58008-scaffold94-1912173 6 67228672 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407503 Affx-122954746 AX-123277854 6 64852528 TCATACATTTATTCATTCACTCAGCTCGTCAACAG[A/G]TATTTATTGGTGCCAACAATATGCCAGACTCTATG R 2 1 2 1 102000 r 74 goat snp58009-scaffold94-1954463 6 67271501 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801622 Affx-122958384 AX-385288530 6 64885120 AGGCCCCACCTCAGACCTATTGAATCAGAACCTGC[A/G]TTTTAACAAAGGCCGCAGGTGATTGTACATGCATT R 2 1 2 1 303000 f 74 goat snp58010-scaffold94-1987055 6 67304117 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384452 Affx-122973095 AX-123254810 6 64968894 GGAAAAAAAAAAAAATTCAATGACACTGTCACAGA[C/T]AGCTGGTTCGGCAGGCTTCATTCAGCACCACTGTG Y 2 1 2 1 201000 r 74 goat snp58012-scaffold94-2070829 6 67387931 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408546 Affx-122953684 AX-123278897 6 65020904 GCTCTGCAACCCTGGGTGAGGAACTCAACCTCCTT[A/G]TCCTTCAGTTTCCTCATCTGTAAAATGGAAATGAT R 2 1 2 1 303000 f 74 goat snp58013-scaffold94-2122839 6 67440911 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796563 Affx-122965315 AX-385283509 6 65060425 GATTGTGAATTACCAAACAAGAGGACGGTAAGGAA[C/T]ATAGTAATTAAGAAACCCTAGTTGTCAGGGTAGAG Y 2 1 2 1 101000 f 74 goat snp58014-scaffold94-2162360 6 67480466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382209 Affx-122973998 AX-123252567 6 65111552 TATGACTTCTTTGAGAGAGGGACTCCCTTCTTACC[A/G]TATATCCACATGGCTTCATAAAATTCATATATTTA R 2 1 2 1 201000 r 74 goat snp58015-scaffold94-2213487 6 67530818 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410552 Affx-122952148 AX-123280902 6 65156571 CACACGGGCTTTCTCTAGTTTTGGTGAGGGAGGAA[C/T]AATCTTCATTGAGGTGCCTGAGCTTCCCATTGCAG Y 2 1 2 1 101000 r 74 goat snp58016-scaffold94-2258506 6 67576147 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768248 Affx-122939800 AX-385255429 6 65200898 GTCTAATCCATTTAACATTAGGATTTTGACCATTT[A/G]TTTTTCCTCTGCTGATTAGATCACAGTACACTTGC R 2 1 2 1 101000 r 74 goat snp58017-scaffold94-2302833 6 67620539 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803172 Affx-122969389 AX-385290035 6 65259550 AGATTTCTGTTTACTTGCTTTGGGACAGTTATTTC[A/G]CAGGCCTCCTTTGGCATTCTTCTTGATTTTTCACT R 2 1 2 1 101000 r 74 goat snp58018-scaffold94-2361485 6 67679002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403682 Affx-122958054 AX-123274034 6 65308475 CAAACCCAAGCAGAGGATGCTGTCTACGTGGCAAC[A/G]TGTACACACTGGGGACAGTTTATTAATGGAAACAC R 2 1 2 1 101000 f 74 goat snp58019-scaffold94-2410410 6 67728132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425307 Affx-122940948 AX-123295653 6 65368690 TAAGGAGCCACAGTGATTGTACAGCATATTAAAAA[C/T]ACCAGTCTATGACTATAAAAATACATTGAATGCAT Y 2 1 2 1 101000 f 74 goat snp58020-scaffold94-2470625 6 67788573 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775982 Affx-122965885 AX-385263113 6 65399463 TGTATCATTTTTATTCCTATGAATCTATAGAATAA[C/T]GCCTTTTTAATACCCCAGAATTATAGCCAAAAGCA Y 2 1 2 1 101000 r 74 goat snp58021-scaffold94-2501398 6 67819418 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781911 Affx-122968275 AX-385268992 6 65442263 GAACACAGTGTATGCTATTTATTTTAAACAATGAC[A/G]TGTTTACTCTGTTTCACGATCCAACATTGCGTATT R 2 1 2 1 201000 f 74 goat snp58022-scaffold94-2544198 6 67862134 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436674 Affx-122932463 AX-123307012 6 65542763 TCTTTTCAAGTCCTGTGATTACATTAGGTCCACCT[G/T]TTTCTAAAACCCTCACAACTCCATTTGTGCATGCT K 2 1 2 1 201000 r 74 goat snp58024-scaffold94-2644698 6 67962508 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791359 Affx-122948237 AX-385278352 6 65572523 GTCCCATCAAGCACAGCCTTGCAAACAGTTCAAAG[C/T]AGAATTTTATTATACTCATTTGTTGAGAGTCCTTT Y 2 1 2 1 101000 f 74 goat snp58025-scaffold94-2674458 6 67992875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273218 Affx-1111833513 AX-185498070 6 65673512 GGCTTAAAGCTCAACATTCAGAAAACGAAGATCAT[A/G]GCATCTGGTCCCATCACTTCATGGGAAATAGATGG R 2 1 2 1 303000 f 74 goat 6_65673512_AF-PAKI 6 65673512 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38386877 Affx-122970057 AX-123257235 6 65683835 AAGGACTCTATTGTGGAATTGCTTTGGAAAATTCT[A/G]CAGACCAATTGCACTGCCCAGCCCCTTGGAGACTC R 2 1 2 1 201000 f 74 goat snp58027-scaffold94-2785770 6 68104101 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796133 Affx-122932881 AX-385283084 6 65716444 TGAGCCCACAAAGCTTTAGCCTAAAACTTTGTATG[C/T]ATTTTACAGCACTGTCTGTAGCTTACCCCTATTTG Y 2 1 2 1 101000 f 74 goat snp58028-scaffold94-2818379 6 68136961 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384553 Affx-122973015 AX-123254911 6 65749403 GGGACTTCAGATACTTCCTAAGAAGATGAAACAAC[A/G]TTGTTTTTCGCAGAGTCTGAAGGGATTCTTACACA R 2 1 2 1 101000 f 74 goat snp58029-scaffold94-2851338 6 68170435 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765178 Affx-122973043 AX-385252729 6 65800812 GTTTCTGGGGAAATCTATAGCCCTAGCTCCTCTTC[A/G]CATCCAGCTTACTGGGTAGAGAAGGTATACAGATT R 2 1 2 1 101000 f 74 goat snp58030-scaffold94-2902747 6 68222016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407579 Affx-122954665 AX-123277930 6 65833543 ACACATAAATGCTTGCTGTATGTTAGAAATGGGCC[A/G]TGTATTTTGGCTCTCAGCTTCCTAGTGGCCAAAAT R 2 1 2 1 101000 f 74 goat snp58031-scaffold94-2935478 6 68254822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781782 Affx-122957749 AX-385268864 6 65865489 CATAGTGTAAACACTTACATAGTATTAGAATTTAT[A/C]TGTTTTTCATGTTTACATCTTGAAAGCATGACTCT M 2 1 2 1 101000 r 74 goat snp58032-scaffold94-2967424 6 68286770 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392427 Affx-122966193 AX-123262784 6 65903443 TTTTTAAGGGGAAGAAGAGCCAGAAGTAATAAGAT[A/G]TTTTTTCATAAAAATCTCCCTAAGTTACATAAGTT R 2 1 2 1 101000 f 74 goat snp58033-scaffold94-3005378 6 68324908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398119 Affx-122922353 AX-123268474 6 65934485 GGAGGGATGGTCAGCAGTTGGCCAACAGGAAAATC[A/G]TGGAAGAGCCAGGTAAGCTGTGGTAAGGATGTGGG R 2 1 2 1 201000 f 74 goat snp58034-scaffold94-3036420 6 68356453 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452787 Affx-122920240 AX-123323120 6 65967118 GTCTACTATCTGCAGAGCACTTACTATAACTGTTT[A/G]TGCTGAGAGATGATGACTTAATTGAAACGGCTTCA R 2 1 2 1 201000 f 74 goat snp58035-scaffold94-3069053 6 68389462 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769861 Affx-122954482 AX-385257030 6 66001059 ACACTTTACTTATCACTCCAGTTGGCTAAAGTTAG[C/T]ATTATCCTAGACCAGCAGTTTTCAAAGTATGGGCT Y 2 1 2 1 101000 r 74 goat snp58036-scaffold94-3102994 6 68423518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436510 Affx-122932949 AX-123306848 6 66095987 TGAAGACTCAGAAGTTAGAAATGGATATCCAACTG[C/T]AAATCATTCTATTGGCCCTTGGTAAGGTTATAACC Y 2 1 2 1 101000 r 74 goat snp58038-scaffold94-3197922 6 68515529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394483 Affx-122964563 AX-123264838 6 66199879 CTTAAAGACCTCCCTGGCTGCTGTGTGGAGAATAC[A/G]TGAGAGGTAAAGACATCAGGGTAACCAGTCGGAGG R 2 1 2 1 201000 r 74 goat snp58041-scaffold94-3301814 6 68616641 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393502 Affx-122965813 AX-123263858 6 66235138 TGCTCTGCATTTTCTTTCTTTTTCTGTTAACCTTT[A/G]TGTGGATAATCCACAGAGACACAACTTAATATTTA R 2 1 2 1 202000 r 74 goat snp58042-scaffold94-3337073 6 68651909 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442708 Affx-122927868 AX-123313045 6 66300361 GTCTCCAAATTTTTTTTTTCCAGTTTCTTGCGCCA[C/T]ATCTCAGGACTGGGGTGTGAAGATGAGGTTATTGG Y 2 1 2 1 101000 f 74 goat snp58044-scaffold94-3402296 6 68717757 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402103 Affx-122958689 AX-123272456 6 66351834 TGCCACGACCATGAGCCCGAAAGCTCTAGAACCCA[C/T]GTGCTGCAACAAGAGAGGCCAGCGCAGTGAGAAGC Y 2 1 2 1 103000 f 74 goat snp58045-scaffold94-3453769 6 68769734 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391563 Affx-122966625 AX-123261920 6 66385058 TGCTATTCTTCAGGTTGTCTACCTTTCCTCAGATC[A/G]TATTAACCTAGTTTGTTCCTAGGGGATTTAAAGAT R 2 1 2 1 101000 f 74 goat snp58046-scaffold94-3486993 6 68802867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400691 Affx-122959940 AX-123271046 6 66489189 TAGGGTATTCTCGCGCGAAAAATTTGAAAAACCGG[A/C]GCTTCGGGGTTGGGAGACGTCTAATTGGTTACCTT M 2 1 2 1 102000 f 74 goat snp58049-scaffold94-3591124 6 68906739 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407968 Affx-122954341 AX-123278319 6 66517734 GAGCAGTATCATTTATAATACTATTGCTAGTTGTG[C/T]TGAATTGTCTTATAAATCACATGAAGTAAGTGGCT Y 2 1 2 1 101000 r 74 goat snp58050-scaffold94-3619669 6 68935210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430873 Affx-122937411 AX-123301214 6 66549834 GAAACTACGTACGGAGCTACCAAAGTATGCTAACA[A/G]CATGACGGACTCCAGAGGCTTATCTGGTTCTGTAA R 2 1 2 1 101000 f 74 goat snp58051-scaffold94-3651769 6 68967104 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423770 Affx-122942839 AX-123294116 6 66582754 ATGTGTCTATACTCACTGTCTCCAAGCCTCCTCTC[A/G]TTTTTCCTCAGCCTACTTGCATCAGGCTTTTTGTT R 2 1 2 1 201000 r 74 goat snp58052-scaffold94-3684689 6 68998343 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777391 Affx-122974125 AX-385264513 6 66622844 AGGGAAAGAGATAGTTTCTAGAGGCAACCTGAGGT[A/G]TCTGCCACTATCTGCATGGTGGAAGAAATGTAGGC R 2 1 2 1 101000 f 74 goat snp58053-scaffold94-3724779 6 69045830 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417261 Affx-122947263 AX-123287609 6 66659560 CAGTCCCCTCCCTTCCGCTTCTTGGGATCCCCTCC[C/T]ATGTAAAGTCTGCTTGCGGCCTCCTGTTTCAGGCT Y 2 1 2 1 101000 r 74 goat snp58054-scaffold94-3761495 6 69082559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420513 Affx-122944844 AX-123290860 6 66695600 CAAAGGGGGCCTTATATGGAGACCGTTCTCGGAAA[C/T]GGTTCTATTTCTTTTTGAAACTTATAATAGATGGA Y 2 1 2 1 101000 f 74 goat snp58055-scaffold94-3797535 6 69118877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446135 Affx-122925771 AX-123316471 6 66724861 AATAAAACCGAGGGGACAGAATTCCTTATCGACAG[A/G]AAGTTATGCTTCCACTAGGACATGGCTTTCTCACA R 2 1 2 1 101000 r 74 goat snp58056-scaffold94-3826796 6 69148066 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800927 Affx-122930179 AX-385287842 6 66755919 CCCTGCTGTAATTTGAGGCTTTTAGGCTTCTCATA[G/T]GGTATAAACATCCCTCTATTAATTGAAAACAGTGC K 2 1 2 1 101000 f 74 goat snp58057-scaffold94-3857854 6 69178964 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777493 Affx-122929188 AX-385264612 6 66787974 AATTCTCTGTCAGCAGGAAAACTCCACCGGGCTTA[C/T]GATGTGCAGTTTTCACGCTTGGAGTTTCCTTTATT Y 2 1 2 1 101000 f 74 goat snp58058-scaffold94-3889909 6 69211220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403298 Affx-122957844 AX-123273651 6 66817302 GACCCAAACATGAACACAATGGTCCTTGGCTTTCA[C/T]GACTCCTCACTCCTTAAGGAATAAGGTGACTCTGT Y 2 1 2 1 101000 r 74 goat snp58059-scaffold94-3919237 6 69241329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276050 Affx-1111835139 AX-519549604 6 66848642 CAGTGCCTTTTAAGCTGCAAGAGGGAGAAGTACGC[A/G]TTATTTCTCTGGAGCAGTGTCAGTCCTACTTTGAC R 2 1 2 1 101000 r 74 goat ilmnseq_rs656019149 6 66848642 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468276124 Affx-1111835252 AX-519549674 6 66850943 AATAACCTAGACCACCCATCAACATTCATGCAGAT[A/G]CGCCTTGTGAAGACCATCATCCTGCATCCTCGCTA R 2 1 2 1 101000 f 74 goat ilmnseq_rs668167322 6 66850943 C T 1 recommended Goat_IGGC_65K_v2 Illumina 38427819 Affx-122939747 AX-123298162 6 66853002 CTCAGGTTTCATTTTATGTTTATATTTTTAAGAAG[C/T]ATTGCCATTTGTAATAACCAGGTTCTCTCTGTGTT Y 2 1 2 1 101000 r 74 goat snp58060-scaffold94-3954937 6 69276901 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275668 Affx-1111835025 AX-519549237 6 66864627 AGGCAGAGCAAAAGAAAAGGTGCAGCTTACCCCTC[A/G]AAGCAGTGGGCGACCGTCAGAACCCATTTCTTGGC R 2 1 2 1 102000 f 74 goat ilmnseq_rs642326566 6 66864627 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276083 Affx-1111835233 AX-519549635 6 66864837 AAGGAGCAGGACAGAGGACAGACAGATGTGACTCA[C/G]CGCCAAACCCAACTGGGTGCCTGCATCTTCGCTGT S 4 1 2 1 102000 f 74 goat ilmnseq_rs666783461 6 66864837 C G 1 neutral Goat_IGGC_65K_v2 Illumina 468276140 Affx-1111835260 AX-519549690 6 66864838 GACAGCGAAGATGCAGGCACCCAGTTGGGTTTGGC[A/G]GTGAGTCACATCTGTCTGTCCTCTGTCCTGCTCCT R 2 1 2 1 102000 f 74 goat ilmnseq_rs668594959 6 66864838 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468275949 Affx-1111835167 AX-519549507 6 66867979 GGAACAGGAGCAAGACCAACAGTGGCTTACATTAC[A/G]CTCCAACTGGGAGAGCCTTAATGCAACAACTTTGC R 2 1 2 1 201000 f 74 goat ilmnseq_rs658741356 6 66867979 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275990 Affx-1111835189 AX-519549546 6 66891894 GCCCTCTGAGAAATTCATCAGGGCTACAAACTACT[A/G]ACCTTACCCTAAACCCATCTGCTTGCAGGCCAGCT R 2 1 2 1 101000 f 74 goat ilmnseq_rs661850269 6 66891894 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275729 Affx-1111835056 AX-519549296 6 66891976 TCCTGCCAGCCATCCGCACACACGTGGTGTTCCAC[C/G]GCAGATCTGTGAGCCATCAGGAATGAGGAGGAGTT S 4 1 2 1 202000 f 74 goat ilmnseq_rs645776058 6 66891976 G C 2 neutral Goat_IGGC_65K_v2 Illumina 468275895 Affx-1111835138 AX-519549453 6 66891983 AAACGTGAACTCCTCCTCATTCCTGATGGCTCACA[A/G]ATCTGCCGTGGAACACCACGTGTGTGCGGATGGCT R 2 1 2 1 102000 f 74 goat ilmnseq_rs656001291 6 66891983 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468276340 Affx-1111835288 AX-519549873 6 66892020 CCCCTCCTTTTTTTCCCCACTCAGTGACCCTCTCT[A/G]CAAACGTGAACTCCTCCTCATTCCTGATGGCTCAC R 2 1 2 1 201000 r 74 goat ilmnseq_rs672467829 6 66892020 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275867 Affx-1111835050 AX-519549428 6 66893157 TGAGCTAGAATGTGCAAACCACGAGTGTGTGCCAC[A/G]TGACCGGTGGTGTGACGGTGAAGCCGACTGTATAG R 2 1 2 1 202000 r 74 goat ilmnseq_rs645120099 6 66893157 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276147 Affx-1111835263 AX-519549697 6 66893161 CTGATGAGCTAGAATGTGCAAACCACGAGTGTGTG[A/C]CACGTGACCGGTGGTGTGACGGTGAAGCCGACTGT M 2 1 2 1 101000 f 74 goat ilmnseq_rs669194710 6 66893161 G T 1 recommended Goat_IGGC_65K_v2 Illumina 468275888 Affx-1111835134 AX-169484688 6 66894545 GTCATCTGTGATGGGTTTCCAGACTGCCCTGATAA[A/C]ATGGATGAAAAAAACTGCTGTAAGTACTTATTGGG M 2 1 2 1 101000 f 74 goat ilmnseq_rs655677263 6 66894545 T G 1 recommended Goat_IGGC_65K_v2 Illumina 468275746 Affx-1111834987 AX-519549312 6 66894611 ATGACTGTGTGCTTCAAACACTGTTTACTGGATGG[A/G]CATTCCCAAAGATCTCTCTCCTTACATCCTGGAGA R 2 1 2 1 101000 r 74 goat ilmnseq_rs636938375 6 66894611 A G 1 recommended Goat_IGGC_65K_v2 Illumina 38448573 Affx-122923411 AX-123318909 6 66903127 AGATCTGGTGTCTCACCCCCAAAGACTCAGCTGCA[C/T]ACTGCCCTCCAGTGCCTGGACTTGGCCCCTTGTTG Y 2 1 2 1 201000 r 74 goat snp58061-scaffold94-4005062 6 69326777 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276087 Affx-1111835235 AX-519549639 6 66904929 AATGCTCACCTAGTCACTTCAAGTGCAGCTCAGGA[A/C]GGTGTGTTCTGGCTTCCAGAAGATGTGATGGCCAG M 2 1 2 1 101000 f 74 goat ilmnseq_rs666917056 6 66904929 G T 1 recommended Goat_IGGC_65K_v2 Illumina 468276115 Affx-1111835248 AX-519549666 6 66909345 CTCATGTTCTTTGCTTGCACCATCTTGGTACCAAA[A/G]TGTGACGAGGATACACACCAGCGTATCCCACCTTG R 2 1 2 1 101000 f 74 goat ilmnseq_rs667768032 6 66909345 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276035 Affx-1111835130 AX-519549589 6 66909408 GCATCCATCAGCTGGGAGTCTTCTCTTTTCCCTGC[A/G]CTTGTTCAAACCAACTGTTACAAATACCTCATGTT R 2 1 2 1 101000 r 74 goat ilmnseq_rs655252822 6 66909408 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275865 Affx-1111835122 AX-519549426 6 66909489 GTCCTGTGGCCAAGGTAATTCGGAAAATTTGTATG[A/G]TTGTAGGGCAAATTCAAGCAGAGTTCCAATGTAAT R 2 1 2 1 101000 f 74 goat ilmnseq_rs654723024 6 66909489 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275915 Affx-1111835073 AX-519549473 6 66909520 TATGGTTGTAGGGCAAATTCAAGCAGAGTTCCAAT[A/G]TAATTGGTTCACACTGACCTAACAATAACAACAAC R 2 1 2 1 201000 r 74 goat ilmnseq_rs647482533 6 66909520 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275906 Affx-1111835069 AX-519549464 6 66917415 ATTCATGTGGTGGTAACTCTCTTTGTGACCCCAGC[A/G]ACAGTGTGAATAATTGTAGTAAGTACAGCCTCTGA R 2 1 2 1 201000 r 74 goat ilmnseq_rs647207540 6 66917415 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275782 Affx-1111835007 AX-519549347 6 66923570 ACGGGGACCACGACTGCGTGGATAAGTCCGATGAA[A/G]TCAATTGCTGTGAGTGCCCTGAAGGTTTTCATCTT R 2 1 2 1 101000 r 74 goat ilmnseq_rs640229792 6 66923570 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276150 Affx-1111835193 AX-519549700 6 66923604 ACTTCATCGGACTTATCCACGCAGTCGTGGTCCCC[A/G]TCACACACCCATTCAATGGCAATGCAGCGCCCGTC R 2 1 2 1 201000 r 74 goat ilmnseq_rs662161074 6 66923604 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275878 Affx-1111835129 AX-519549438 6 66923637 CCGTCACACACCCATTCAATGGCAATGCAGCGCCC[A/G]TCTCCACAGCGATGCTCCTCTACGGGGTTGCAATC R 2 1 2 1 202000 f 74 goat ilmnseq_rs655197517 6 66923637 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468276214 Affx-1111835224 AX-519549764 6 66923660 TTCCTGAGTGCTTGCTTCCTCCAGATTGCAACCCC[A/G]TAGAGGAGCATCGCTGTGGAGACGGGCGCTGCATT R 2 1 2 1 202000 r 74 goat ilmnseq_rs665735605 6 66923660 C T 2 neutral Goat_IGGC_65K_v2 Illumina 320768479 Affx-122962420 AX-385255659 6 66974514 GTCTTTCAGACCTCGAAGTCCAACCTTTTCCTAAA[C/T]AGCACTCCTTCCGTTTAGTCACTTCCCATTCTATG Y 2 1 2 1 101000 f 74 goat snp58062-scaffold94-4076449 6 69398775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275875 Affx-1111835054 AX-519549436 6 66992449 AGGATTTGCTTCTCACCACAGCAGGAAAACGAAAA[A/G]CAATGTAGGTGTCTGCATTTTGTTGCATTTTTTAA R 2 1 2 1 201000 r 74 goat ilmnseq_rs645564281 6 66992449 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468275969 Affx-1111835178 AX-519549526 6 66992454 TCAGCAGGATTTGCTTCTCACCACAGCAGGAAAAC[A/G]AAAAGCAATGTAGGTGTCTGCATTTTGTTGCATTT R 2 1 2 1 101000 f 74 goat ilmnseq_rs660329608 6 66992454 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275846 Affx-1111835113 AX-272252796 6 66992496 TCAAGTGTTCACAGTTTAGAAACCAAAGTGAAAAC[A/G]GCAATGTCAGCAGGATTTGCTTCTCACCACAGCAG R 2 1 2 1 201000 f 74 goat ilmnseq_rs653783895 6 66992496 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275822 Affx-1111835027 AX-519549386 6 66992578 CAGGAGGCATTCACCATTCCCAGGACTGACTCACA[C/G]CCCTCTTTTGCAGACTCACAGAAGGATCTACAAGG S 4 1 2 1 102000 r 74 goat ilmnseq_rs642396302 6 66992578 G C 1 neutral Goat_IGGC_65K_v2 Illumina 38412492 Affx-122951377 AX-123282841 6 67013525 AAACACAGAAATAAAAACAAGTCAGGCAGGACAAC[A/G]GGACCGAGGAGCATGTTCCAAATGAAAGAACAAGA R 2 1 2 1 101000 r 74 goat snp58063-scaffold94-4115460 6 69437616 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275839 Affx-1111835036 AX-519549402 6 67018683 CTGCAGCCTGGCCTTTCCCAAGTGCATCAGGGATG[A/G]TGCTGACAGGTATTTTGGAACCAAAAGCATTCAGT R 2 1 2 1 101000 r 74 goat ilmnseq_rs643218186 6 67018683 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275952 Affx-1111835169 AX-519549510 6 67018732 TCACGTACCTCCATCGCCTCGGTTGCTATCAACAT[A/G]TCATGCTTTTTGGCTGCAGCCTGGCCTTTCCCAAG R 2 1 2 1 101000 f 74 goat ilmnseq_rs658807116 6 67018732 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468276287 Affx-1111835261 AX-519549829 6 67018807 TGCCCTACTACACCACACTGACATCTCCCCTCTCC[A/G]TTGTCAAAAGCATGGAAATGGAGAAGTTCCTCAAA R 2 1 2 1 101000 r 74 goat ilmnseq_rs668716411 6 67018807 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275898 Affx-1111835065 AX-519549456 6 67018887 ACTGGCTGTGGGTGATGTTCATGCAGGCACCTGGG[A/G]AGGTAAGAAAATTACATTTAGGAGAAGACACATAA R 2 1 2 1 201000 r 74 goat ilmnseq_rs646887981 6 67018887 A G 2 recommended Goat_IGGC_65K_v2 Illumina 468275987 Affx-1111835187 AX-519549543 6 67054675 GTGTCTGATGTTATTCTTAATACAATTCATAATGA[C/G]GAGAGCACTGTGACATCTGCTGCCCATCCCACCCA S 4 1 2 1 101000 f 74 goat ilmnseq_rs661663919 6 67054675 G C 1 recommended Goat_IGGC_65K_v2 Illumina 468276052 Affx-1111835140 AX-519549605 6 67070142 GCAGGACAATGAGAGCACAGATACATGGAATCAGG[A/G]CCAGCAAGAGGAAACGAAGAATATTCACAGTCGTC R 2 1 2 1 101000 r 74 goat ilmnseq_rs656037355 6 67070142 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276307 Affx-1111835270 AX-169459686 6 67070170 ACATGGGTGATGGCTGCTCTCAGAAGCTGACGACT[A/G]TGAATATTCTTCGTTTCCTCTTGCTGGTCCTGATT R 2 1 2 1 101000 r 74 goat ilmnseq_rs669469752 6 67070170 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276049 Affx-1111835217 AX-519549603 6 67072103 ATTCTCTGTGGGAGACATTACTTGAATGAACATAC[A/G]ATGTTAGCTTGAGAATGGCTTGATTTCCTAGATTA R 2 1 2 1 201000 f 74 goat ilmnseq_rs664532560 6 67072103 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275991 Affx-1111835108 AX-519549547 6 67072123 GCATGGATCAGTAAAGGTGTTAATCTAGGAAATCA[A/C]GCCATTCTCAAGCTAACATCGTATGTTCATTCAAG M 2 1 2 1 102000 r 74 goat ilmnseq_rs652837066 6 67072123 T G 1 neutral Goat_IGGC_65K_v2 Illumina 468275963 Affx-1111835175 AX-519549521 6 67072134 ATACGATGTTAGCTTGAGAATGGCTTGATTTCCTA[A/G]ATTAACACCTTTACTGATCCATGCCTTTTGAACCT R 2 1 2 1 103000 f 74 goat ilmnseq_rs659659872 6 67072134 G A 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275834 Affx-1111835033 AX-519549397 6 67072148 TGAGAATGGCTTGATTTCCTAGATTAACACCTTTA[C/G]TGATCCATGCCTTTTGAACCTGGTTTAATCGACCC S 4 1 2 1 101000 r 74 goat ilmnseq_rs642934508 6 67072148 C G 1 recommended Goat_IGGC_65K_v2 Illumina 468276090 Affx-1111835161 AX-519549642 6 67072178 TATATTAAGTATGAGGGATCTCACATTGGTGGGTC[A/G]ATTAAACCAGGTTCAAAAGGCATGGATCAGTAAAG R 2 1 2 1 201000 r 74 goat ilmnseq_rs657769287 6 67072178 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468276253 Affx-1111835244 AX-519549800 6 67072203 CCTCCAAAATGGTGCCAATTATTTGTATATTAAGT[A/C]TGAGGGATCTCACATTGGTGGGTCGATTAAACCAG M 2 1 2 1 102000 r 74 goat ilmnseq_rs667545042 6 67072203 T G 1 neutral Goat_IGGC_65K_v2 Illumina 468275802 Affx-1111835016 AX-519549366 6 67072209 TAATCGACCCACCAATGTGAGATCCCTCATACTTA[A/G]TATACAAATAATTGGCACCATTTTGGAGGAGGTCA R 2 1 2 1 201000 r 74 goat ilmnseq_rs641001499 6 67072209 A G 2 recommended Goat_IGGC_65K_v2 Illumina 320782259 Affx-122959535 AX-385269337 6 67072258 GAGAGATAGATGGTTTCTGGAGTTGAATCAGTGAT[C/T]TGAATATAGCAGAGTCAAGGTGTCTTGAGTTCTCT Y 2 1 2 1 101000 r 74 goat snp58064-scaffold94-4174193 6 69496944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276144 Affx-1111835262 AX-519549695 6 67072263 TCTGATTGCCTGAGTCCTGCTCATGGGTCAATGTG[A/G]TGGGTCACATCCTTTCCATGACCTCCTCCAAAATG R 2 1 2 1 202000 f 74 goat ilmnseq_rs668953752 6 67072263 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468275779 Affx-1111835080 AX-519549344 6 67072558 AACTGCCACCCAGCAATCTGGAATGATCTACTGCC[A/G]GGAGCCAGCATGGGGAATCCCACCTGTGGCAAAGG R 2 1 2 1 102000 f 74 goat ilmnseq_rs648835223 6 67072558 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275959 Affx-1111835173 AX-519549517 6 67072583 TGCCTGTCAGGCCTCTTCCTCATGACCTTTGCCAC[A/G]GGTGGGATTCCCCATGCTGGCTCCCGGCAGTAGAT R 2 1 2 1 103000 f 74 goat ilmnseq_rs659491889 6 67072583 T C 1 not_recommended Goat_IGGC_65K_v2 Illumina 468276191 Affx-1111835286 AX-519549741 6 67072608 TTCCCTCGAGGCCTGATCTCACCTTTGCCTGTCAG[A/G]CCTCTTCCTCATGACCTTTGCCACAGGTGGGATTC R 2 1 2 1 103000 f 74 goat ilmnseq_rs672305404 6 67072608 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 38443318 Affx-122927451 AX-123313655 6 67141213 AGCAGCCTGCCTCTGAGATCACATGTGGCACACAG[A/G]CCATACACAGCCATGCAGGCAATAGGAGGCATCCG R 2 1 2 1 101000 f 74 goat snp58065-scaffold94-4243148 6 69566353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416273 Affx-122947951 AX-123286622 6 67198796 AAGACAGTCACAACACACTTTACAAATTTATTCCA[C/T]GCAGGACCCATGGGAGACTTTAACAGGACTTATTA Y 2 1 2 1 201000 f 74 goat snp58066-scaffold94-4300731 6 69624021 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432852 Affx-122935365 AX-123303193 6 67250236 AGCATAATGATACTAGTTAATGAGGAATCTGAAAA[C/T]ACCAGATGACTCATGTGTTAACGTGAGTATGCTGG Y 2 1 2 1 201000 f 74 goat snp58067-scaffold94-4352171 6 69675969 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417281 Affx-122947247 AX-123287629 6 67297634 GATTGTCAGGAAGGGGACGAAGCACTCGCTGAAAG[A/G]GGGTGGTGGCCTTGGTGGCTAAGCACCCAAAGAGC R 2 1 2 1 101000 f 74 goat snp58068-scaffold94-4399569 6 69723126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427053 Affx-122939815 AX-123297398 6 67333034 TGTAAGTCCATTTGTTTCCCCTCTGAGCTCTGTTT[A/G]TATGGATCACTTCCCTATCCAGTGGTTCTGCTTAA R 2 1 2 1 201000 r 74 goat snp58069-scaffold94-4434969 6 69758437 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791985 Affx-122966369 AX-385278973 6 67371713 AAGTAAAGGATAAGCATAGCTTATGCTGAGTGGAA[C/T]GTGGATGAGAATTCCTTCTTAGTCCAGAGATCCCG Y 2 1 2 1 101000 r 74 goat snp58070-scaffold94-4473648 6 69796564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384420 Affx-122972189 AX-123254778 6 67403838 CTCAGTGCTGGTCCTTTTCTCCCCGACCCAGCTGC[C/T]AAAACTTGGCAGATACTGCTAACCATGAGGATTTT Y 2 1 2 1 101000 r 74 goat snp58071-scaffold94-4505773 6 69826676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409627 Affx-122953539 AX-123279978 6 67492603 CAAGGAAAGGTAATAAGTAATCTGGATACTTTGCC[A/G]TATAATTTGATATTTTACTAAACATATTTCATTTG R 2 1 2 1 201000 r 74 goat snp58073-scaffold94-4594538 6 69916501 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426249 Affx-122940337 AX-123296595 6 67568572 TCCAGCTTTAACTCTCTCCTTCCTGACACACACTC[A/G]TCCAAAAAAATCGGCAGAAACCCTTGGTGGACAAA R 2 1 2 1 201000 r 74 goat snp58075-scaffold94-4670507 6 69993297 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383639 Affx-122972534 AX-123253997 6 67622550 CCCCAAGAGTTTGAACCTCAGACCTTTCAATCCCT[C/T]GGCTGAAGCTATAAACCACAAATGTGCTTCATGAT Y 2 1 2 1 101000 f 74 goat snp58076-scaffold94-4724485 6 70048414 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275364 Affx-1111834856 AX-519548938 6 67741693 CTGCAGTGTCTCAAATGTCACAAAGCCTATTCTTC[A/G]CCACGTAACCCCTAATGCACAGCTGATTGGTTCTC R 2 1 2 1 201000 f 74 goat GoatD01.056687 6 67741693 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38439957 Affx-122929985 AX-123310294 6 67753278 TAAGTTTAAAACTGTATGTGGGTTTTTTTTTAAGC[A/G]CATGTCATTTCCCTTTCTCTGTCTTTCAGAACCAG R 2 1 2 1 101000 r 74 goat snp58078-scaffold94-4855213 6 70179795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419512 Affx-122945448 AX-123289860 6 67825438 TCTACCCCTCCCCTCCAAAGATGTGGCGTGGAGCT[A/G]TTTCTGATTCAGAATGATTGCAGTGTTTCAGCCAG R 2 1 2 1 101000 r 74 goat snp58080-scaffold94-4927373 6 70253358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427639 Affx-122939337 AX-123297982 6 67868642 CTGTACACTTGCTATTACAACCACACGCAGATGGA[C/T]GAGAACGAGATCGAGGGCAGACATATTTACATCTA Y 2 1 2 1 201000 f 74 goat snp58081-scaffold94-4970577 6 70297210 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447471 Affx-122924352 AX-123317807 6 67957639 AAAACTTTGGGCTCTGTCGTAATAGAAAACTCTTG[C/T]GGGTAGTTGACTGAACTTTCTGCCTGTTCCTAATT Y 2 1 2 1 101000 f 74 goat snp58083-scaffold94-5059574 6 70386549 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445260 Affx-122925475 AX-123315597 6 67996322 GCCCTGTGTGATCTGAGGCAAGCTGTTTCACCTCA[A/G]TAAGCCTCAGTTTCCCCCTCCTTCAAGGCTATTGT R 2 1 2 1 201000 f 74 goat snp58084-scaffold94-5098257 6 70425574 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436808 Affx-122932243 AX-123307146 6 68025618 AAATTTGAATGAGAGCAGCACTGGAGCTCAGGCAG[A/G]CACCCTTTTATTGAGGCATCTCAAAGAAGTGCTGA R 2 1 2 1 101000 r 74 goat snp58085-scaffold94-5127553 6 70454815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409956 Affx-122952855 AX-123280307 6 68066850 TTTTGCTTAGTTTTGTTGGTTTTGTCCTTTCATTT[A/G]TTTATCTTACAATATTTATTGAGTACCTCCTGTAT R 2 1 2 1 101000 r 74 goat snp58086-scaffold94-5168785 6 70496212 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413920 Affx-122949819 AX-123284269 6 68096669 ACCAAAGAACTAGAGGGTTTCCTGTTTTTGGTTTT[C/T]AACATGGATTTTCAATTTTTGGAGAACGAGAAAAC Y 2 1 2 1 201000 r 74 goat snp58087-scaffold94-5198604 6 70525889 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397736 Affx-122962540 AX-123268091 6 68129743 CACGAGGATCCTTTCTGATTTGGTTCTTGGTCTTA[C/T]GCTGGCTTTAAGGCCAGGCTATCCTGCAGAATGAA Y 2 1 2 1 101000 f 74 goat snp58088-scaffold94-5231678 6 70559150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411854 Affx-122951220 AX-123282204 6 68162012 ACAGCAAAGTCCCCTAGACACTCTTGAACAGCCCC[A/G]CGAGATGGGGGCTGCTCAAGATTATGCCCCTTGCT R 2 1 2 1 303000 r 74 goat snp58089-scaffold94-5263947 6 70591611 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387739 Affx-122969741 AX-123258097 6 68196811 ATCTGTGTGCCTAGACCATAAAAGACCATAAAGTA[C/T]AACAATCATTTATTAAAATGCTAATTATTCAGGGG Y 2 1 2 1 101000 f 74 goat snp58090-scaffold94-5298746 6 70626559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421471 Affx-122943926 AX-123291818 6 68241922 TGTTAAAGGACTCAGTTTGCACAGAGAGCTATGCA[C/T]ACACAAACAATTTGATTCACCACCACCTCTGGGTT Y 2 1 2 1 101000 f 74 goat snp58091-scaffold94-5343857 6 70672374 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273270 Affx-1111833514 AX-519546918 6 68304402 TCTTTGAAAACTAAAAAAAGATTAAAATTAGGCTA[A/C]CTTTAGAAGTCAGAAAAGGCTTCTTTAAGGAACTG M 2 1 2 1 101000 r 74 goat 6_68304402_AF-PAKI 6 68304402 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278552 Affx-1111836396 AX-519552034 6 68305243 TCAGAGACTGATGGTGGGGACGTGTCAGAACGACA[C/G]TGGAGGGACAGTTGTGCACCATAAAGAATGAGGAC S 4 1 2 1 102000 r 74 goat Random2.2K-696 6 68305243 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425590 Affx-122941412 AX-123295936 6 68327191 TGTAGAAAACTCCGGAGGAGCTAGTATTTTATTCA[C/T]GATGATTGTGACAGAAATCAGTGCAAGTAATATTG Y 2 1 2 1 101000 f 74 goat snp58093-scaffold94-5429126 6 70758177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382273 Affx-122973932 AX-123252631 6 68357949 CTTCATATTAAGGAAGTTTTCCAAAAGCTGTCATA[C/T]AATACTTAGTGGCCAAAACCAAGCCACATGGCTGT Y 2 1 2 1 101000 r 74 goat snp58094-scaffold94-5459884 6 70788868 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438371 Affx-122931315 AX-123308709 6 68403067 AAAATAATCACCAGGCACTCTGATCCTACAAGGGT[A/G]TGTGCTCTGTCCATACACATGCCCCTGTGGGTTTC R 2 1 2 1 101000 f 74 goat snp58095-scaffold94-5505002 6 70834128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442630 Affx-122928461 AX-123312967 6 68443348 GTTGAGTTAGATTTTATGGTGCCTAGAATATAGTA[C/T]GGAGAAGGCAATGGCACCTCACTCCAGTACTCTTG Y 2 1 2 1 101000 f 74 goat snp58096-scaffold94-5545283 6 70874215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450917 Affx-122921783 AX-123321251 6 68495816 ATGCATAGTCTGAGGAAACCTTTGGGTCTTCTTTC[A/G]TTTTTTTTCAATTACATCAGAGTAGGGTGGAGGGG R 2 1 2 1 102000 r 74 goat snp58097-scaffold94-5597751 6 70927567 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444622 Affx-122926938 AX-123314959 6 68528130 CACTTCTGCCTGAAAAATACATTGCTAATGGATCA[C/T]AGCACAGTGCTCTGCAGAGTCAACGCTTCAGGACC Y 2 1 2 1 101000 f 74 goat snp58098-scaffold94-5630065 6 70959830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774289 Affx-122953111 AX-385261425 6 68557747 ACATATGTATCCTTGTTCTCCAGCCAGGGGTCATA[G/T]AGTCTCATTGTCTTTGTCATTCACAAGACACCCCT K 2 1 2 1 101000 f 74 goat snp58099-scaffold94-5659682 6 70990195 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799510 Affx-122942960 AX-385286440 6 68612251 GTGTTTCTAAATATTTCTTCAGAAAGCAAATTCAG[C/T]AATATTCCATCTCATGTCTTGTCTTCCCCCAGAGG Y 2 1 2 1 101000 f 74 goat snp58100-scaffold94-5714186 6 71044898 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452526 Affx-122920547 AX-123322859 6 68666685 AGCAAACTGATCTCAGGAGGGCCAACCCTGCACCT[C/T]TTAGGGACTAACCCTTCATAGGGACGGCTGTACAA Y 2 1 2 1 101000 r 74 goat snp58101-scaffold94-5768620 6 71099110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436263 Affx-122932545 AX-123306602 6 68697752 AGGATAAAGGCCAAAGGTCAAATTATAATCTACAA[C/T]GGATAACTAAAAATACCAAAAATATATTTACTTCT Y 2 1 2 1 101000 f 74 goat snp58102-scaffold94-5799687 6 71130474 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779836 Affx-122928253 AX-385266935 6 68731943 CAAACAATTCTTCTCTCTCAACTTTATTTACAATT[C/T]GTGACACTTCCTTTTCCACGTCTCACTTAAGAAGA Y 2 1 2 1 101000 r 74 goat snp58103-scaffold94-5833878 6 71164653 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389687 Affx-122968701 AX-123260045 6 68784341 AAATCTTGTAATAGGGAGTAATATTATTAGCCTAA[A/G]TCCTGCTTTGGGGCCCAGAGTTATGGTTTAAAAAG R 2 1 2 1 201000 f 74 goat snp58104-scaffold94-5886276 6 71210057 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435682 Affx-122933329 AX-123306021 6 68898128 ACACGTAAAGGACATAAAGATCTTTCTGGTCACTC[C/T]CTAGTTCCACAAAGAAGCGCAGCAATGAAGCCAAG Y 2 1 2 1 201000 r 74 goat snp58106-scaffold94-6000063 6 71325965 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401755 Affx-122959505 AX-123272108 6 68938118 TCTTTTCCCGTTTCAGGAGTGGTCATTCACTGTAA[C/T]CACCGAATCCCTTTTGGAGACTGGTTTGAATACGT Y 2 1 2 1 101000 f 74 goat snp58107-scaffold94-6040053 6 71366099 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476219 Affx-1251763724 AX-586011643 6 69000804 TTCTTTGTAAATTTCTGTGTAACTTTTTATAATAA[-/TAAAACATTATTATTATTAAGATTTAAAATGTTTTATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTTCCTCTCTC]AAAACATTATTTTTAAGAGGAACCGCTGCCTCAGT - 8 1 4 1 20000 f 74 goat SV_317 6 69000804 - deletion junction SV-TF-chip 539476473 Affx-1251763724 AX-586011873 6 69000804 TTCTTTGTAAATTTCTGTGTAACTTTTTATAATAA[-/TAAAACATTATTATTATTAAGATTTAAAATGTTTTATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTTCCTCTCTC]AAAACATTATTTTTAAGAGGAACCGCTGCCTCAGT - 4 1 4 1 20000 r 74 goat SV_317 6 69000804 - deletion junction SV-TF-chip 562165381 Affx-1251763724 AX-606940792 6 69000804 TTCTTTGTAAATTTCTGTGTAACTTTTTATAATAA[-/TAAAACATTATTATTATTAAGATTTAAAATGTTTTATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTTCCTCTCTC]AAAACATTATTTTTAAGAGGAACCGCTGCCTCAGT - 8 1 4 1 20100 f 74 goat SV_317 6 69000804 - deletion junction SV-TF-chip 562166276 Affx-1251763724 AX-606941684 6 69000804 TTCTTTGTAAATTTCTGTGTAACTTTTTATAATAA[-/TAAAACATTATTATTATTAAGATTTAAAATGTTTTATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTTCCTCTCTC]AAAACATTATTTTTAAGAGGAACCGCTGCCTCAGT - 8 1 4 1 20100 r 74 goat SV_317 6 69000804 - deletion junction SV-TF-chip 562166475 Affx-1251763724 AX-606941883 6 69000804 TTCTTTGTAAATTTCTGTGTAACTTTTTATAATAA[-/TAAAACATTATTATTATTAAGATTTAAAATGTTTTATTTTGATCTTCCCGTCCTATTCCTCCGCCATCTTTTCCTCTCTC]AAAACATTATTTTTAAGAGGAACCGCTGCCTCAGT - 8 1 4 1 20100 r 74 goat SV_317 6 69000804 - deletion junction SV-TF-chip 38402786 Affx-122958298 AX-123273139 6 69033849 CTTTGAAAGTTTTGAAAATTGTAAGTTTCACCACA[C/T]GTGAACATGTAAAATATAACAGGACTAAGAAAGCT Y 2 1 2 1 101000 f 74 goat snp58109-scaffold94-6135784 6 71459875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412921 Affx-122950396 AX-123283270 6 69069888 TTTAAATCTAAAACAGACAGCAAAAACAAGAAACA[C/T]ATCCTAAATCAAAGTCTCACAATCCAGACCTCTTA Y 2 1 2 1 101000 r 74 goat snp58110-scaffold94-6171823 6 71495883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448931 Affx-122923156 AX-123319266 6 69117144 GTTTCTCTCTCTCTTTTTTTTTTTTTTACTTTATG[C/T]ATCTGCAAGGAACTGGAAAGAAATACAAACAATAG Y 2 1 2 1 101000 r 74 goat snp58111-scaffold94-6219079 6 71543593 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394309 Affx-122964687 AX-123264664 6 69161017 TTGAATCACTTTAATACAATGTTACAATTTCTGCC[G/T]TAAACAATTATAATGTCTTTTAAGAAAATTAAGAA K 2 1 2 1 101000 f 74 goat snp58112-scaffold94-6262952 6 71587897 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783346 Affx-122939374 AX-385270410 6 69198397 ATACAATGTTGTAGCACAACTTTATGTAAACTTTA[C/T]GTTTATTTGTATGTAAATCACTAGTACTTGCTATA Y 2 1 2 1 201000 f 74 goat snp58113-scaffold94-6300332 6 71625921 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420161 Affx-122945581 AX-123290509 6 69241950 GAAGTCCACAGAAATGTGGCACCTCTGACTCCCAG[C/T]GCACATGAGAGGTCACATCGCTATGTCCACCCTCT Y 2 1 2 1 201000 r 74 goat snp58114-scaffold94-6343885 6 71669928 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426179 Affx-122940584 AX-123296525 6 69283954 ATTCTGTATCCAAAGAGAGCAGGGAATGTCTAGCA[C/T]GTAGGACATGGCAAATACCCAATAAAAGTTTGTAA Y 2 1 2 1 101000 r 74 goat snp58115-scaffold94-6385889 6 71712561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464457978 Affx-1110493026 AX-515930543 6 69317455 AGACTGGGACTTCTGTTATTCTTGAATGAGTCCCC[A/G]GTAACTTCATACAAAAGGTCCTCTGTAAAATGTAT R 2 1 2 1 201000 r 74 goat GoatD01.005815 6 69317455 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320777139 Affx-122934098 AX-385264262 6 69326638 GCCAGATTTTTGGCTTTCTGGGAGACATAAATTTG[A/C]TGTTGACTTGCATTCCTTCTATCAAGACTTTTTAA M 2 1 2 1 101000 f 74 goat snp58116-scaffold94-6428573 6 71755407 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424913 Affx-122941300 AX-123295259 6 69369235 TCCAAGACCTACTTGTATGAGGATGGACAAAACCA[C/T]GACATTTTGCTGAAGCGAAAGGGCTTTGGGACGTG Y 2 1 2 1 101000 f 74 goat snp58117-scaffold94-6471170 6 71797566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386823 Affx-122970098 AX-123257181 6 69409654 CACTTTGAGAGGAATCCAGGAGAGGAAGTGAAAAA[C/T]GGCAATTCACTTCTCAACTCTGAAGAGGGCTGTAA Y 2 1 2 1 101000 f 74 goat snp58118-scaffold94-6511589 6 71838503 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379597 Affx-122976024 AX-123249955 6 69450147 ATATCACATTTTCTTGTAAAAATAGAATCCTTTAA[C/T]TATTTGATATATGTAGGGTTTGTCCAGACATATTG Y 2 1 2 1 101000 r 74 goat snp58119-scaffold94-6552082 6 71879090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791268 Affx-122919915 AX-385278262 6 69508413 AAGAGTGATTTAGAAGGTGTAATCTCTAAAATTTA[A/G]TGATGGATAAATTTAGTAAACTTGGGATGTAGAGG R 2 1 2 1 201000 f 74 goat snp58120-scaffold94-6610348 6 71937412 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387506 Affx-122970329 AX-123257864 6 69538323 AGTACTGGCTGAATGATTTAGTAAATAAAAAAAGG[C/T]CTACAGCAGAGTGACTTTTTCAATGAAATATATAA Y 2 1 2 1 101000 r 74 goat snp58121-scaffold94-6640258 6 71967098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418263 Affx-122947017 AX-123288611 6 69568217 GGTGTTAACCGTGATTTGTGGCCCTCCGAAGGACC[A/G]CAGTACATTAACAGTGTATCTGTGTATTAAAATTT R 2 1 2 1 201000 r 74 goat snp58122-scaffold94-6670152 6 71996981 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391330 Affx-122967313 AX-123261687 6 69598991 TTAATTGAAATTAATATGAAATCCTCCAGGGTAGG[A/G]GACTTCCCTGGTGGTCCAGTGGTTAAGACTTGGTG R 2 1 2 1 103000 f 74 goat snp58123-scaffold94-6700926 6 72027672 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427351 Affx-122940109 AX-123297694 6 69723260 TGATGTGATTTGGGGTCCAAGACTGACTTTATCAC[A/G]TATGCCCACCAGATTCTTCCCATTTCCGGCAACTG R 2 1 2 1 201000 f 74 goat snp58126-scaffold94-6825195 6 72152395 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434465 Affx-122934639 AX-123304806 6 69763017 AGTTAGGAGAATAAACCTTTCATTCCTTGATGGTG[A/G]ACTGGATGGAATACCCACCACCACCTATACCATTA R 2 1 2 1 101000 f 74 goat snp58127-scaffold94-6864952 6 72192177 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433185 Affx-122935648 AX-123303526 6 69860768 ATGTCTCTGCAATTTCACCATCCGCCATGTAAAGC[C/T]GAGGGGGAGTTGGGTGAAGGTGGATTTGATACTCT Y 2 1 2 1 101000 f 74 goat snp58129-scaffold94-6962703 6 72290258 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451054 Affx-122921434 AX-123321388 6 69906314 GGTCACAAAGAGTTGACCACCACTCAGGAACTTAA[C/T]GACAAATGTTTATGACCTTTTATCTTATGGTGAGT Y 2 1 2 1 101000 f 74 goat snp58130-scaffold94-7008249 6 72335146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413163 Affx-122950347 AX-123283512 6 69937288 TACCATTTTCTTTTCTAAAAACACCTCAATAAAAC[A/C]AAAAACTATGGAAAACACAAAAGTCAAGTCAGAGA M 2 1 2 1 101000 f 74 goat snp58131-scaffold94-7039223 6 72366121 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375642 Affx-122978693 AX-123246001 6 70017021 TGTTTCTGCTTCCTTTTTGTCCTCATCTCCTATTG[C/T]TGCTTCCCCTTCACTCCACTCCAGCTTCACAAGCC Y 2 1 2 1 202000 r 74 goat snp58132-scaffold94-7118956 6 72446014 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447509 Affx-122924073 AX-123317845 6 70067940 GCTTGGATTTGATCATTCAAATTCATGCCTGTTTC[A/G]CTCACTTTCTCTTCTACAACTTGCAGGGTTCAATA R 2 1 2 1 101000 r 74 goat snp58133-scaffold94-7169875 6 72497088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375896 Affx-122978489 AX-123246255 6 70103888 AGCTATTCTGAAGGACCCTTGCACATCCCCAGTCC[A/G]TGTAAGACTGAGGACAATAACACTAGGCCCAGAAC R 2 1 2 1 101000 r 74 goat snp58134-scaffold94-7205823 6 72533307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278388 Affx-1111836397 AX-519551873 6 70135434 ACTGTCAAACACCACACATCTCGTAGCTAAAGGGT[A/G]CAAAGGTCCTCACTTCAAAATCTACGATCTTGTGG R 2 1 2 1 101000 f 74 goat Random2.2K-698 6 70135434 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438504 Affx-122931214 AX-123308842 6 70169162 GATCTAAGAAGTCCTTTGAAGTATGACAACCTCAA[C/T]GGCTTTAGTGCTTAGGCACCATCCAGGCCTCAAAA Y 2 1 2 1 101000 f 74 goat snp58135-scaffold94-7271097 6 72599015 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770095 Affx-122961350 AX-385257262 6 70231525 GCTCTTCTCCAAATCAAGGAGCAAAACCTAACCCT[A/C]TTGTTTGCAATTTTGGGCCAAACATGTCTGATGGT M 2 1 2 1 101000 f 74 goat snp58137-scaffold94-7333460 6 72661900 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402047 Affx-122958730 AX-123272400 6 70265439 GCACAGAGTCTTAACCAAGTACCTGTCCTGAGCTC[A/G]TATCACACTGGCCATTGTGTTGTTACAGAGCTGGA R 2 1 2 1 101000 r 74 goat snp58138-scaffold94-7367374 6 72695645 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275609 Affx-1111834994 AX-519549179 6 70300890 CGGCATGGGATGATGACTGAATCTTCGTCCTCCAC[A/G]ATGACCAAGGAATCTGTCATTCCTAGAGGTACGAA R 2 1 2 1 101000 f 74 goat ilmnseq_rs638012483 6 70300890 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275841 Affx-1111835037 AX-519549404 6 70302479 AAACTTGATCTGGAAATGGAATCTCCTAAGACTGT[A/G]TATAAGGCAGGCGAATCGATTGTGGTCACCTGCAC R 2 1 2 1 101000 r 74 goat ilmnseq_rs643256510 6 70302479 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468275833 Affx-1111835107 AX-519549396 6 70305708 GTTAAAGTCAGTTTTCCTCCCCTTCTGCTGTAGAA[C/G]GGCAAAGGCATCACGAGGCTGGAGGAAACCAAGTT S 4 1 2 1 102000 f 74 goat ilmnseq_rs652546920 6 70305708 G C 1 neutral Goat_IGGC_65K_v2 Illumina 468276146 Affx-1111835191 AX-519549696 6 70305714 GTCAGTTTTCCTCCCCTTCTGCTGTAGAAGGGCAA[A/G]GGCATCACGAGGCTGGAGGAAACCAAGTTCCCGTC R 2 1 2 1 202000 r 74 goat ilmnseq_rs662035189 6 70305714 A G 2 neutral Goat_IGGC_65K_v2 Illumina 468275580 Affx-1111834981 AX-519549150 6 70308752 TTATCTTTATCTGGCTCTTACAAACCTTGAGTCAA[A/G]AGTTCAAAAGTATAGCTCTTCACATCATCTTCATT R 2 1 2 1 101000 f 74 goat ilmnseq_rs636417098 6 70308752 C T 1 recommended Goat_IGGC_65K_v2 Illumina 464452875 Affx-1110493423 AX-515925478 6 70312019 GCAGTCCTGGTGTTGTTGGTGATTGTAATCATCTC[A/G]CTCATTGTCCTGGTCGTCATTTGGAAACAGGTAGA R 2 1 2 1 101000 f 74 goat ilmnseq_rs672064024 6 70312019 G A 1 recommended Goat_IGGC_65K_v2 Illumina 464452878 Affx-1110493424 AX-457120230 6 70312056 TCATTGTCCTGGTCGTCATTTGGAAACAGGTAGAT[A/G]TTTTTTTAAAGAACTAAAAATCCTTACTGATACGA R 2 1 2 1 202000 f 74 goat ilmnseq_rs660380088 6 70312056 A G 2 neutral Goat_IGGC_65K_v2 Illumina 468275923 Affx-1111835077 AX-519549481 6 70312347 CATCTCGAGTCATAAGGCAGCTGCATCGGGTCCAC[A/G]TAAATGTATTCATGTCCATCAGGGCTGATTGATTC R 2 1 2 1 201000 r 74 goat ilmnseq_rs647814964 6 70312347 T C 2 recommended Goat_IGGC_65K_v2 Illumina 320769512 Affx-122951241 AX-385256682 6 70314508 CCAGTCTTCCCTCCTCTTGGATGATATATTAGGAA[C/T]GACCTTAAGGTAACTGATCTCTAGACAGGAATTTC Y 2 1 2 1 101000 f 74 goat snp58139-scaffold94-7416443 6 72745375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276137 Affx-1111835258 AX-519549687 6 70314690 GGATTAAGTCGGTCTCAACCTGTCATGAAAGTAGC[A/C]GTGAAGATGCTAAAACGTGAGTGCTCCTTTTCTGG M 2 1 2 1 101000 f 74 goat ilmnseq_rs668543709 6 70314690 A C 1 recommended Goat_IGGC_65K_v2 Illumina 468276193 Affx-1111835287 AX-519549743 6 70315120 CAGCCACAGCCAGATCCAGTGAAAAACAAGCTCTC[A/C]TGTCTGAACTGAAGATAATGACCCACCTGGGGCCG M 2 1 2 1 101000 f 74 goat ilmnseq_rs672371467 6 70315120 A C 1 recommended Goat_IGGC_65K_v2 Illumina 468276044 Affx-1111835215 AX-519549598 6 70316692 GGTGACTACATGGACATGAAGCAAGCTGACACTAC[A/G]CAGTATGTCCCCATGCTGGAGAGAAAAGAGGTTTC R 2 1 2 1 101000 f 74 goat ilmnseq_rs664392780 6 70316692 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276133 Affx-1111835256 AX-519549683 6 70320163 AGGCCAAAGTCACAGATCTTCACGATTTTCCCTTG[A/C]GCCAGGAGGACGTTGCGAGCCGCCAGGTCCCGATG M 2 1 2 1 101000 f 74 goat ilmnseq_rs668425158 6 70320163 T G 1 recommended Goat_IGGC_65K_v2 Illumina 468276064 Affx-1111835147 AX-519549616 6 70320229 AATGAGGTAGGGGCACGTACACTGCCTTTGGACAC[A/G]TAGTTCGAGTCATGCATGATGTCTCGGGCCAGGCC R 2 1 2 1 101000 r 74 goat ilmnseq_rs656670959 6 70320229 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275992 Affx-1111835190 AX-519549548 6 70324679 ACAGGGTCGATGTCGGGCAGAGGGATGATGTAGCC[A/G]CTATCTGCACTCAGCCTCTGCTCGTCGAGGCCACC R 2 1 2 1 102000 f 74 goat ilmnseq_rs661931429 6 70324679 T C 1 neutral Goat_IGGC_65K_v2 Illumina 468275660 Affx-1111835021 AX-519549230 6 70331382 ATCGACATGATGGACGACATTGGCATAGACTCCTC[A/G]GATCTGGTGGAGGACAGCTTCCTGTAACTGGCAGA R 2 1 2 1 101000 f 74 goat ilmnseq_rs641692739 6 70331382 G A 1 recommended Goat_IGGC_65K_v2 Illumina 320772234 Affx-122957088 AX-385259389 6 70353895 TGATGTACACATTTTAGTAAATCCAAGGGAGTTAG[C/T]ATACTAAACCAGCAGTCATCTAAACCTGTTAGCTT Y 2 1 2 1 101000 f 74 goat snp58140-scaffold94-7455830 6 72784911 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273475 Affx-1111833641 AX-519547093 6 70403831 ACATTGAGTTTGTAACTTGCATCCATACCCAGAAT[A/G]TGACTTTTCTGCAGGCCATCAGAGCCCAAGAGAGA R 2 1 2 1 101000 f 74 goat GoatD01.000208 6 70403831 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320772092 Affx-122977024 AX-385259247 6 70404839 CTAAATCTGGCCATAGAATAGAGAAGCCAACAGAA[C/T]GGAACTAATATAAAGTAGCCAGCCCACAAGTATGT Y 2 1 2 1 101000 f 74 goat snp58141-scaffold94-7506774 6 72836279 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421697 Affx-122944406 AX-123292044 6 70435882 GGTTTTCAAAATCCAGCTTGTAATGTATACAAGCT[A/G]CACCTTCTCCCTTTCTCTCCCATGTCCAGCTTTTG R 2 1 2 1 303000 f 74 goat snp58142-scaffold94-7537817 6 72867672 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388472 Affx-122969240 AX-123258830 6 70549917 GATGATTTACAGGAGAAAGAAGTAGCTTATTGTTC[C/T]ACATATACGCACTGTGAAATTCATCCATCAATGAT Y 2 1 2 1 101000 f 74 goat snp58144-scaffold94-7651852 6 72982256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447462 Affx-122924359 AX-123317798 6 70580335 AAATATTTGATTCTGTTTGGGAGACTGTCCCCTCC[A/G]TTGGTTATCTGAAGTTACTTTCAAAGACCAGACTA R 2 1 2 1 101000 r 74 goat snp58145-scaffold94-7682270 6 73013074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799039 Affx-122952037 AX-385285969 6 70612857 GGATGAATCCCTTCAGTTGAATTCTGTCCCAAAGC[A/G]TTAGTCTTGGGAAAGTCATAGAAAATAGAAAGCAA R 2 1 2 1 101000 f 74 goat snp58146-scaffold94-7714792 6 73045717 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391361 Affx-122967288 AX-123261718 6 70665009 CAGCAGCAGTAGCTCACTGCCTCTGTCCATGTCCT[A/G]TGAGCTGCTGCAGCAATCTCCAGTAGCCTCTTAGG R 2 1 2 1 201000 r 74 goat snp58147-scaffold94-7766944 6 73098798 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769859 Affx-122949434 AX-385257028 6 70710315 GCATGTGACAGGTGTTTACATTATTAAGTAAAAGC[A/G]TTTAAACAGCGACCTCCTTCGTATAAGGGTGAAGG R 2 1 2 1 101000 f 74 goat snp58148-scaffold94-7812250 6 73143653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428718 Affx-122938460 AX-123299060 6 70739283 ATAACAGAATTCACGTTAGGATTTCTTTAAATTGC[A/G]AAGTCCCTTGCTGGATTAAGGACATTACTGAAACA R 2 1 2 1 101000 r 74 goat snp58149-scaffold94-7841218 6 73172491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276296 Affx-1111835265 AX-519549835 6 70744246 GGGGCACACACAATCTGGGCCATAGCACTTCTCTT[A/G]CTCTTGGTGCTCGGTAACATGTGATGACTAATTCA R 2 1 2 1 101000 r 74 goat ilmnseq_rs669256409 6 70744246 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276003 Affx-1111835114 AX-519549558 6 70747255 GAGAAAGCAGAGGCCACAAATACAGGCAATTACAC[A/G]TGCACCAATAAAGGCGGCTTGAGCAGTTCCATTTA R 2 1 2 1 101000 r 74 goat ilmnseq_rs653927630 6 70747255 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275831 Affx-1111835106 AX-519549394 6 70750521 CGGGGTGTGAGGGGAAACCTCTCCCCAAGGATTTG[A/G]CGTTTGTGGCTGACCCCAAGGCAGGCATCACAATC R 2 1 2 1 102000 f 74 goat ilmnseq_rs652137856 6 70750521 A G 1 neutral Goat_IGGC_65K_v2 Illumina 468275873 Affx-1111835053 AX-519549434 6 70756107 GATTTCTTTCTTTCCCTCCCCTTCTGAGAGCAGCA[A/G]AGTAAAGCACAGACGAAGAAGAATAGCTGGCATCA R 2 1 2 1 202000 r 74 goat ilmnseq_rs645259857 6 70756107 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468276334 Affx-1111835285 AX-519549867 6 70756206 CCAAAAGTATTATTGGCGTAACACATGAACACACC[A/G]GAATCATTCACTCTTGCTGAGCTGATAGTCAGCCT R 2 1 2 1 101000 r 74 goat ilmnseq_rs672280002 6 70756206 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276058 Affx-1111835144 AX-519549610 6 70763252 GTCCCTTTTAATCTGGTTAGATGAAGTTCATTTAC[A/G]TATCTACAAAAAAAGAACAACCCATCAGTCACCTG R 2 1 2 1 101000 r 74 goat ilmnseq_rs656209566 6 70763252 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276327 Affx-1111835281 AX-519549860 6 70763304 GGAAGAATTGACATCAGAATTGGACACGTGAAATG[A/T]GTAAGTGCCTCCTTCAGTCCCTTTTAATCTGGTTA W 4 1 2 1 101000 r 74 goat ilmnseq_rs671664904 6 70763304 A T 1 recommended Goat_IGGC_65K_v2 Illumina 468275714 Affx-1111835048 AX-519549282 6 70763355 ATTCTGATGTCAATTCTTCCGTGACATTTAATGTT[A/T]ACGTGAACAGTGAGTAGAACAAATGGTTCCTTATC W 4 1 2 1 101000 f 74 goat ilmnseq_rs644724711 6 70763355 T A 1 recommended Goat_IGGC_65K_v2 Illumina 468276313 Affx-1111835273 AX-519549846 6 70777648 TCGATGGTTGGCTCCGGGAACCCTGCAGCCACGCA[A/C]TGTAGCATGCCATTCACCAGCCTGTCATGTGTCAG M 2 1 2 1 201000 r 74 goat ilmnseq_rs669741195 6 70777648 G T 2 recommended Goat_IGGC_65K_v2 Illumina 468276099 Affx-1111835166 AX-519549650 6 70779463 GAATGTGCTGTCATCAATGGTGCTATAAACCACTA[A/G]TTTTCCAAATGGTGAGACAGATGAGTTTTGGATCT R 2 1 2 1 101000 r 74 goat ilmnseq_rs658674363 6 70779463 C T 1 recommended Goat_IGGC_65K_v2 Illumina 464458934 Affx-1110493535 AX-515931490 6 70781581 TTTTTCTAAAATAAGATGTTTTTAATTTTAGCAAG[C/T]GCCCATTTAACAGAACGAGAAGCCCTAATGTCTGA Y 2 1 2 1 101000 r 74 goat ilmnseq_rs668535829 6 70781581 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276280 Affx-1111835257 AX-519549822 6 70785270 AACAACCTCATTGACTCAGAGTTTCTCATACCACC[A/G]TGGAATCTAACATGATTCCTGGTAGTAACCGGTTC R 2 1 2 1 201000 r 74 goat ilmnseq_rs668445864 6 70785270 G A 2 recommended Goat_IGGC_65K_v2 Illumina 38446269 Affx-122925672 AX-123316605 6 70785589 TCTCCCACTCAGTTGCAATTCCTGGTCTTCTGGAT[A/G]TCTGTTAGAACACTGGGCTAACTCATTTCTAGGGC R 2 1 2 1 101000 r 74 goat snp58150-scaffold94-7887524 6 73219811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275759 Affx-1111835070 AX-519549324 6 70785717 AAGAGACGTGACTCCTGCTATCATGGAAGATGATG[A/G]GCTGGCCCTGGACCTGGAGGACTTGCTGAGCTTTT R 2 1 2 1 101000 f 74 goat ilmnseq_rs647214940 6 70785717 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276173 Affx-1111835204 AX-519549723 6 70790523 TTGCAGGTATGACATCATGAAGACCTGCTGGGATG[A/C]AGATCCCTTGAAAAGGCCAACATTTAAGCAGATTG M 2 1 2 1 101000 r 74 goat ilmnseq_rs663369828 6 70790523 C A 1 recommended Goat_IGGC_65K_v2 Illumina 468273223 Affx-1111833515 AX-519546880 6 70844830 TTTTAATATTTTGAGCTCTGGGAAGTCAAAACCAC[A/G]CTCTTTATCAGGAAAGAGCACGTCATTAACAATAT R 2 1 2 1 101000 f 74 goat 6_70844830_AF-PAKI 6 70844830 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425158 Affx-122941066 AX-123295504 6 70886354 TCCATCATTATTATCATGATAAATCCTCTAGGTCT[A/G]TGACTTCAGCAGACAGCATGTATGCTTATAGAATT R 2 1 2 1 201000 f 74 goat snp58152-scaffold94-7988289 NW_017203438.1 15998 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778738 Affx-122962366 AX-385265849 6 70944700 ACTTAAGTACAATCTAAATGGGCTCTTTGTCAAGC[C/T]GATTCCTATTTGTATAGCTCTGTGCAGTAAACAGA Y 2 1 2 1 101000 f 74 goat snp58153-scaffold94-8046635 6 73379964 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398042 Affx-122961760 AX-123268397 6 70983425 AAATGATTGACTTGATCGTCCTCAGGGAAAAATCC[A/G]TGCTTACCTTGGCATGTGCTTGTGTCTTAGATAAA R 2 1 2 1 101000 f 74 goat snp58154-scaffold94-8085360 6 73418501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781933 Affx-122957615 AX-385269013 6 71017703 TGTAGCATATTTTTCTTCAACTAAATTTCCTATGA[G/T]TCTCACTTCTTTTCTCCCAATCTTCTATAAACAGT K 2 1 2 1 101000 r 74 goat snp58155-scaffold94-8119638 6 73452743 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782778 Affx-122940500 AX-385269850 6 71104781 AATATTTTTGAATGACTCCTTTTCCTTTAACACCC[A/G]CTTATACTCATGCTATTCCCAAATACATTTGATTA R 2 1 2 1 101000 f 74 goat snp11743-scaffold1432-949027 6 73540579 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276105 Affx-1111835243 AX-519549656 6 71116760 TCAAGTGTTGTTCTTTCCACCACCAGGAAGTAGCC[A/C]CATTTGATTTTCATTTCAAAAAAAGGACCTCAGAC M 2 1 2 1 202000 f 74 goat ilmnseq_rs667531652 6 71116760 T G 2 neutral Goat_IGGC_65K_v2 Illumina 468275891 Affx-1111835136 AX-519549450 6 71116801 CTTCCTGGTGGTGGAAAGAACAACACTTGAAAATC[C/G]GAGCAGCACCTCTCGTGTGATTTCCAGGACTGGGG S 4 1 2 1 102000 f 74 goat ilmnseq_rs655911882 6 71116801 G C 1 neutral Goat_IGGC_65K_v2 Illumina 468276222 Affx-1111835228 AX-519549772 6 71116802 TTCCTGGTGGTGGAAAGAACAACACTTGAAAATCG[A/G]AGCAGCACCTCTCGTGTGATTTCCAGGACTGGGGG R 2 1 2 1 201000 r 74 goat ilmnseq_rs666141385 6 71116802 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275845 Affx-1111835039 AX-519549408 6 71116917 CCAGAGTCAGGCTGGAGAATCGGAGCTGCACTGCC[A/G]ACCTGCGGTCCAATCTCCATCAGCTTTAAAAGTTC R 2 1 2 1 101000 r 74 goat ilmnseq_rs643588602 6 71116917 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275708 Affx-1111835045 AX-519549277 6 71116980 AAAAGTTCAGCCTCCTCGCTGGAGTACACAGTGGT[A/G]TCCGTGTCATCAGAATGGTATCCCGACTGGTAGCC R 2 1 2 1 102000 f 74 goat ilmnseq_rs644176015 6 71116980 G A 1 neutral Goat_IGGC_65K_v2 Illumina 464453391 Affx-1110493681 AX-515925988 6 71117080 CAGACTCCTTGCTTTTGCTGGGCATCAGTCCACTG[C/T]GGAAGAGATGGCAACCAAATAAGTTGGCAGAGAGA Y 2 1 2 1 202000 f 74 goat ilmnseq_rs669554547 6 71117080 T C 2 neutral Goat_IGGC_65K_v2 Illumina 468276016 Affx-1111835120 AX-519549570 6 71123023 TCCAGCATCGCATTTGGCACTTCCATCACACATAC[A/C]TGACTTCATCAACTCTCAGCACCATATGCAAAGCA M 2 1 2 1 101000 r 74 goat ilmnseq_rs654438626 6 71123023 A C 1 recommended Goat_IGGC_65K_v2 Illumina 468272472 Affx-1111835231 AX-519546194 6 71127128 AATATTTCCCAGAGCAGGACACCAAAAGACCACAC[A/G]TCACTCTGAATTGTGTACACTCGGTCAAAAATCGT R 2 1 2 1 201000 r 74 goat ilmnseq_rs666644397 6 71127128 A G 2 recommended Goat_IGGC_65K_v2 Illumina 468276148 Affx-1111835192 AX-519549698 6 71127430 CACAGGGACCTGGCAGCGCGAAACATCCTCTTGTC[A/G]GAAAAGAACGTGGTTAAAATCTGTGACTTTGGCTT R 2 1 2 1 101000 r 74 goat ilmnseq_rs662070915 6 71127430 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275621 Affx-1111835000 AX-519549191 6 71129960 CTCACCTTCCGTGATGCCAAAAACTCCATGCCCTT[A/G]GCCACTTGGAAGCTGTAACAGATGAGATGCTCCAA R 2 1 2 1 101000 f 74 goat ilmnseq_rs638944036 6 71129960 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468275787 Affx-1111835009 AX-519549352 6 71137849 TGATTGCCATGTTCTTCTGGCTACTTCTTGTCATC[A/G]TTCTACGGACCGTTAAGCGGGTAACAGAATAATTT R 2 1 2 1 101000 r 74 goat ilmnseq_rs640423402 6 71137849 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275850 Affx-1111835042 AX-519549412 6 71137868 TTAACGGTCCGTAGAACGATGACAAGAAGTAGCCA[A/G]AAGAACATGGCAATCACTGCAGTGCCTACTAGAAT R 2 1 2 1 202000 r 74 goat ilmnseq_rs643706093 6 71137868 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468275785 Affx-1111835008 AX-519549349 6 71140310 TTTTCCCCCTTTCTCAGGCATTGTGCTAAAAGATG[A/G]GAACCGAAACCTAACTATCCGCAGAGTGAGGAAGG R 2 1 2 1 201000 r 74 goat ilmnseq_rs640409229 6 71140310 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468275641 Affx-1111835011 AX-519549211 6 71143988 TGAATGCCACCATGATCTCTAACAGCACTAATGAC[A/G]TCTTGATCATGGAGCTGCAGAATGCATCCTTGCAG R 2 1 2 1 101000 f 74 goat ilmnseq_rs640585759 6 71143988 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275775 Affx-1111835078 AX-519549340 6 71144140 TGTACCACGTGAGGTTCTCAAACATAGTTCTGTCC[A/G]CGGAGCACCACAGAGACACACTCTCCTGCTCGGTG R 2 1 2 1 102000 f 74 goat ilmnseq_rs648134856 6 71144140 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276326 Affx-1111835280 AX-519549859 6 71144187 AGAGACACACTCTCCTGCTCGGTGGGCTGGGTGCC[A/G]GGTTGCAATGTGATTTCAGGACCCCCTGAAATGTA R 2 1 2 1 102000 r 74 goat ilmnseq_rs671110083 6 71144187 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276006 Affx-1111835197 AX-519549561 6 71146873 CTGGCAGCTGGAGACAGAGTGCACCTACCAGCCCA[C/G]GTGAGTAGGACCATGCCCTGTGCCCCTGCTGTTCT S 4 1 2 1 202000 f 74 goat ilmnseq_rs662787102 6 71146873 G C 2 neutral Goat_IGGC_65K_v2 Illumina 468275840 Affx-1111835110 AX-519549403 6 71146947 CAGCGAATGTGACTTGGGGGAGGAACGGCATAGAC[A/G]GTGCACGTCAGTGTCTGGGAAGTGCCGTACTGGTA R 2 1 2 1 101000 f 74 goat ilmnseq_rs653334871 6 71146947 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276149 Affx-1111835264 AX-519549699 6 71148937 ACAGGAAATTACACTGTCATTCTTACCAATCCCAT[A/T]TCAAAGGAGAAACAGAGCCACATGGTATCTCTGGT W 4 1 2 1 201000 f 74 goat ilmnseq_rs669227336 6 71148937 T A 2 recommended Goat_IGGC_65K_v2 Illumina 468275965 Affx-1111835176 AX-390134760 6 71149239 TTTATTTTCTTCCAGAAAAGCCGTTTGTTGCTTTC[A/G]GTAGTGGCATGGAATCCTTGGTGGAAGCCACCGTG R 2 1 2 1 101000 f 74 goat ilmnseq_rs660192572 6 71149239 C T 1 recommended Goat_IGGC_65K_v2 Illumina 38446094 Affx-122925805 AX-123316431 6 71150072 AAGGAATAGTCATAATGACAAAGATTCCAGATAAG[C/T]AATTTGTCAGAGGTTTTCGTTTCATAGGAAAAAAG Y 2 1 2 1 101000 f 74 goat snp11742-scaffold1432-903736 6 73586334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275591 Affx-1111834986 AX-519549161 6 71150662 TTTCAAGGCAGAGCATAATTCTGAAGGCAATCTTC[A/G]CTTACCATGTACCCGGACGAACGTGCTGTTCTTCT R 2 1 2 1 101000 f 74 goat ilmnseq_rs636924423 6 71150662 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275722 Affx-1111834975 AX-519549290 6 71150677 TAATTCTGAAGGCAATCTTCGCTTACCATGTACCC[A/G]GACGAACGTGCTGTTCTTCTTGGTCATCAGCCCAC R 2 1 2 1 202000 r 74 goat ilmnseq_rs635694893 6 71150677 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468275767 Affx-1111835074 AX-519549332 6 71152749 TTCAGACCTCAATGTGTCACTTTGTGCAGTAAGTT[A/G]CATCTTCTTCCATCATCTCTTACCTTTAATTTTTA R 2 1 2 1 101000 f 74 goat ilmnseq_rs647673929 6 71152749 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275885 Affx-1111835059 AX-519549446 6 71152867 GACATTCTCATCTAGATTACAGGTCTCCGTTTATT[A/G]CTTCTGTTAGCGACCAGCATGAAGTTGTGTACATC R 2 1 2 1 101000 r 74 goat ilmnseq_rs646143562 6 71152867 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276183 Affx-1111835282 AX-519549733 6 71155674 ACATAAACAGTGGAGGCCATGTCAGTGTCCTGGTA[A/G]AAGCACTTGTAGGTTCCAGTATCATTTCCAATCAC R 2 1 2 1 102000 f 74 goat ilmnseq_rs671747138 6 71155674 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275796 Affx-1111835013 AX-519549360 6 71155675 CATAAACAGTGGAGGCCATGTCAGTGTCCTGGTAG[A/G]AGCACTTGTAGGTTCCAGTATCATTTCCAATCACT R 2 1 2 1 101000 r 74 goat ilmnseq_rs640680613 6 71155675 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276038 Affx-1111835132 AX-519549592 6 71155807 TCTCAGAGCTGCTCTGATTGTTGGGCCAGAGCCAG[A/C]GCAAGTCCCTCTGACCCCTGAAAAATTCATTCCAA M 2 1 2 1 101000 r 74 goat ilmnseq_rs655505473 6 71155807 C A 1 recommended Goat_IGGC_65K_v2 Illumina 468275780 Affx-1111835006 AX-519549345 6 71161708 CTAGGAAGTGGGCTCCTTACCCACAGAGGCAGCCC[A/G]GGTCTCCACGCAGAGCCACAGAGCAAGGGCCAGCA R 2 1 2 1 202000 r 74 goat ilmnseq_rs640054948 6 71161708 G A 2 neutral Goat_IGGC_65K_v2 Illumina 38433506 Affx-122935020 AX-123303847 6 71202037 AATGTCAGGATCTACGCATGATTTATTTAATACCA[C/T]GGAGCCTATTTTTACAATAAAAAAAGGCTTTAGGT Y 2 1 2 1 101000 f 74 goat snp11741-scaffold1432-851771 6 73638431 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376995 Affx-122977736 AX-123247354 6 71252243 ATCTCCAACTTTACATTTTCAAAACTGAAATTCTT[A/G]CATCCACATCTTGCCAAGTTCCAAATCTCAGTTGG R 2 1 2 1 101000 r 74 goat snp11740-scaffold1432-801565 6 73688563 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407212 Affx-122955390 AX-123277563 6 71295395 GGCATAAGTTATATAGTCTGACGTAACTGGAAGAC[A/G]TGTTTCTTTCCTTTATAATATCAAGCTAGTTACTT R 2 1 2 1 101000 f 74 goat snp11739-scaffold1432-758413 6 73731904 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387360 Affx-122970474 AX-123257718 6 71336157 GTAGTGCATTTCTATCTTTGCTTTGGAAATATTCA[G/T]AGTTAGAAAGACGGTTCTCAGAACATCTAAAAAGA K 2 1 2 1 101000 r 74 goat snp11738-scaffold1432-717651 6 73773180 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398863 Affx-122961049 AX-123269218 6 71372917 CATCTCAATGTCTATTTCGTTGTTTAACCCAAAAG[A/G]AAAGCCTCCAGCAACAATAATACTTAAGAAGCAAA R 2 1 2 1 101000 f 74 goat snp11737-scaffold1432-680891 6 73810194 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383950 Affx-122972954 AX-123254308 6 71404857 TTATGACTGAAACATAAGTGCCTTTCTAAATGTTT[A/G]TGGAGACAGCTAAGCTGACCTTTCAGCAGGAAATT R 2 1 2 1 201000 f 74 goat snp11736-scaffold1432-648951 6 73842137 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278556 Affx-1111836398 AX-519552038 6 71421015 ATATTAAAATCCATCTAAAGTCCTTAAATATAGGC[A/G]GAACAATGTATAAATACTGCAAACTCTTCTGCAAA R 2 1 2 1 101000 r 74 goat Random2.2K-699 6 71421015 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779880 Affx-122962879 AX-385266979 6 71458917 TCACTAGAATACCCATGGGATTGTGATTGTATTAG[C/T]GTTCTTCTTCCTCTCCAGACCATACTAGCCAAAAA Y 2 1 2 1 101000 r 74 goat snp11735-scaffold1432-594891 6 73896533 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452174 Affx-122921236 AX-123322507 6 71493644 CATGTATGATGGTAAAAAGCACTTTGCAGTCAAAC[C/T]GCCCACTAACCTTAGAGTTTTCCCTTACTAACTGG Y 2 1 2 1 101000 r 74 goat snp11734-scaffold1432-560164 6 73930843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389844 Affx-122968164 AX-123260201 6 71525518 GAGAGATTTTTCTCTTATTTCCTTACTTAGAGCAA[C/T]CCAAGAAGCATTAATATTCCTCATGTATTACATAA Y 2 1 2 1 101000 f 74 goat snp11733-scaffold1432-528290 6 73962627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384432 Affx-122972179 AX-123254790 6 71559439 ACATATTAGATGCTTATACACAACAACTGAAAACC[A/G]CATAAAACAAAGCAAGAAACAAGAAAGTATTGTAA R 2 1 2 1 101000 f 74 goat snp11732-scaffold1432-494369 6 73996870 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436795 Affx-122932252 AX-123307133 6 71595243 TGCTCAAAAGAAGAAGAATCAGTACAGATGAGAAG[C/T]AACTACTATTTTTCCTTGTAAATTTCCAAAAGTTT Y 2 1 2 1 101000 f 74 goat snp11731-scaffold1432-458565 6 74033216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792931 Affx-122956594 AX-385279909 6 71641904 AGAATATAGATAAGTCAATGCTGAGGTCTTTACAT[A/G]TATTCACCTGAACAAGCAGGTTGTAGTATTATGCT R 2 1 2 1 101000 r 74 goat snp11730-scaffold1432-411904 6 74080084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446694 Affx-122924742 AX-123317030 6 71698967 CTGAGATGTTTCTCTCTGGTGTATCATAGAGTTGC[A/G]GAACACACAATGTGCCCCAGCTATGCTGTGTTCCT R 2 1 2 1 101000 f 74 goat snp11729-scaffold1432-354841 6 74138059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274573 Affx-1111834302 AX-519548162 6 71739524 ACGAATGCCTGCAGGAAAGATTTTGGACG[A/G]AGTCCAGTTATTAGTAACAGAAAGGTTAAAGTTAG R 2 1 2 1 101000 r 74 goat GoatD01.029542 6 71739524 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38389772 Affx-122968232 AX-123260129 6 71797251 TTCCTGCCTCCTGAGTAAGACTGCTGTGATAAACA[G/T]CTAGTAATGTTTCATGCTTCTTCCAGGTGCTCATT K 2 1 2 1 101000 r 74 goat snp11727-scaffold1432-256557 6 74237862 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409601 Affx-122953558 AX-123279952 6 71885307 TACCGTTCAGGAGGGCAATATTGACTTTATGTGGT[A/G]CTAGTTCCCAGGTGTTTTACCATCTCTTATCAGAT R 2 1 2 1 201000 r 74 goat snp11725-scaffold1432-168501 6 74334337 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278562 Affx-1111836401 AX-519552042 6 71916920 CTTGGCCTTTCTGGTGGCCAGCCCCATCCTGCAGC[A/G]ATGGAGAGTCCTGCTGGAGTCATCTCATTCGAACA R 2 1 2 1 101000 r 74 goat Random2.2K-701 6 71916920 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776946 Affx-122935229 AX-385264070 6 71933661 TGTTGTTCTTTAAATACCTAAGTGGAATAAAAATT[A/G]TTGAGCATAATGAACTTAAAGAGCAAATACAGTGG R 2 1 2 1 201000 f 74 goat snp11724-scaffold1432-120147 6 74383233 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768938 Affx-122948130 AX-385256113 6 71978511 GTCCCAAGCACTGCAGTGAGAGTAAATCCACAGGT[A/G]TAGGTGAAGGAGTCCTACCTGGAGATTATGGGGGA R 2 1 2 1 101000 f 74 goat snp11723-scaffold1432-75297 6 74434229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377976 Affx-122977618 AX-123248335 6 72021377 TTGCTTAGGATCAGATAATCCATGAGAGGTGTATT[A/G]ATTTTTCCTCAGGATTGTAAAGACTACTGAAAATT R 2 1 2 1 101000 f 74 goat snp11722-scaffold1432-32431 6 74474818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402284 Affx-122959108 AX-123272637 6 72145463 AGTGGCAAACACTTCATGCAATATACAACAAATAT[A/G]CCTTTACAGGACATTGATTCAAGGAAAACATCACC R 2 1 2 1 101000 r 74 goat snp2158-scaffold1066-91556 6 74589910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450885 Affx-122922210 AX-123321219 6 72184942 TGAAAAACTGTCCTTGACCCTTTGTGCTAAGACCA[C/T]GAATGAATTTGAAAATGTATCTATGAATTAAATGC Y 2 1 2 1 101000 f 74 goat snp2159-scaffold1066-131035 6 74629157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434250 Affx-122934823 AX-123304591 6 72225383 CACTTGGCATTTTTCTCTTGGCTTAAGCTACTCCT[A/G]TGTCTTCACTTTGCACTGAGGAAGTTTGAATGTAC R 2 1 2 1 101000 f 74 goat snp2160-scaffold1066-171476 6 74670320 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445188 Affx-122925531 AX-123315525 6 72256280 AACTGTGAACATTTTCCAAAGCTAACAGTGGCTTT[A/G]TTCACTTTGTCTATATACACAGAAAAATATCAATT R 2 1 2 1 201000 r 74 goat snp2161-scaffold1066-202373 6 74701544 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766520 Affx-122951850 AX-385253881 6 72305696 TCATCTGTGATTTTTTTCACTCTCAAGAAACTCTG[C/T]ACCTAGCCTCCAACAATTAATCTAAATTGCCATTT Y 2 1 2 1 101000 f 74 goat snp2162-scaffold1066-251789 6 74751248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417547 Affx-122946922 AX-123287895 6 72337990 ATTTCATTTCAACACAGATTAAATTAAAAATGGAG[C/T]GACTGAGTAAAGTTATAACCAGGCAATGACAAGGG Y 2 1 2 1 101000 r 74 goat snp2163-scaffold1066-284083 6 74784159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442615 Affx-122928472 AX-123312952 6 72371834 AATGTATATACATGCATATATCTTTATTCCTACTG[C/T]GGGGAGCAGATCATTACATGCATAAGACAAAATTC Y 2 1 2 1 103000 r 74 goat snp2164-scaffold1066-317927 6 74818685 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380244 Affx-122975460 AX-123250602 6 72421104 TGTGTGTGTGTGTGTGTGTACATTCCCCCAAAACA[C/T]AATTTTTTTGAAGACTAATCTGGAGTGTGTGGTAA Y 2 1 2 1 201000 r 74 goat snp2165-scaffold1066-367197 6 74868090 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428678 Affx-122938639 AX-123299020 6 72451605 CCTAACTCAAAGTCAAAATGTTTCCTTTTTTCTAC[A/G]TGTTCTTATATAACTTTTAAAGTCTACCACTTATG R 2 1 2 1 103000 f 74 goat snp2166-scaffold1066-397698 6 74898573 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425283 Affx-122940965 AX-123295629 6 72488188 GCACTGAGCCATGGTCACTATGTGAAAAGCAGTAC[A/G]TAAGTTTAAAAATTTTGTATATATACCATGAAGCT R 2 1 2 1 101000 f 74 goat snp2167-scaffold1066-434281 6 74935322 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476220 Affx-1251763725 AX-586011644 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20000 f 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 539476474 Affx-1251763725 AX-586011874 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 4 1 4 1 20000 r 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562165271 Affx-1251763725 AX-606940683 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 f 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562165322 Affx-1251763725 AX-606940733 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 r 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562165612 Affx-1251763725 AX-606941023 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 f 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562165715 Affx-1251763725 AX-606941124 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 r 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562165916 Affx-1251763725 AX-606941326 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 f 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 562166346 Affx-1251763725 AX-606941754 6 72497599 AAATGCTCTTCCTTTTGCTTTAAATGCTGGATTTC[-/TACTTGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTTGTCTTTAAAAGATCTCTGGGTTGGGAAGATC - 8 1 4 1 20100 r 74 goat SV_320 6 72497599 - deletion junction SV-TF-chip 320798489 Affx-122925534 AX-385285422 6 72518254 AGATCTGTATATCACATGAATAGTGGCATCTTAGA[C/T]AGGGAAGGGTTTAATGAAATTTACAAATCTGGAGA Y 2 1 2 1 101000 r 74 goat snp2168-scaffold1066-464347 6 74966540 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398468 Affx-122961586 AX-123268823 6 72556353 ATAAATAGCTTAGTCCTTGAGGAGTACATTTAATC[A/G]CTATTGCATATATTTTGTTTTGTTTTCCTTATAAC R 2 1 2 1 101000 f 74 goat snp2169-scaffold1066-502446 6 75005606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793960 Affx-122961028 AX-385280929 6 72588110 CCAATGAGGGATAATTGAATATCATATGTTCAGAT[A/G]CAACATCATTTCACTTGTGTAGAACTTTTTTAGGA R 2 1 2 1 101000 r 74 goat snp2170-scaffold1066-534203 6 75037649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402240 Affx-122959141 AX-123272593 6 72650873 CTCCTAACCAGAACCCCAGGTCCTGAAAACCCAGT[A/G]AGCAAAACTTCTGTAGACAAGTAAAACCTCCTGAA R 2 1 2 1 201000 r 74 goat snp2171-scaffold1066-596966 6 75100819 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794630 Affx-122943229 AX-385281591 6 72710549 TAAAAATCTCATGTTTGGACTCTGGGGTAAATTGG[C/T]AAGGGTAGAATTTGATTCAGTCACAACTGTTAATG Y 2 1 2 1 101000 f 74 goat snp2172-scaffold1066-656642 6 75160735 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392127 Affx-122966339 AX-123262484 6 72748977 TGGAGTATGAAGGGCAAGACTATCATGAAAAAACA[C/T]AAAGTGGGAATGTATAATGGGAGAAATTTCTGCAC Y 2 1 2 1 101000 f 74 goat snp2173-scaffold1066-695070 6 75199259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803047 Affx-986696144 AX-385289920 6 72764602 TGGTACGTATTTTGAGAAAATGGCCGAATGCCTAT[G/T]TCAGTCAGGAATGCCGCGGCCGAGGCCGGCGCTGG K 2 1 2 1 600010 f 74 goat 6_72764602 6 72764602 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320781597 Affx-122974146 AX-385268681 6 72791056 GAGATTTATGTTTCAGCAAATTGTTGAATATATTG[C/T]AACAATAGCAATTTCTTATACAGCCATGACACTCA Y 2 1 2 1 201000 f 74 goat snp2174-scaffold1066-737149 6 75241459 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787336 Affx-122961674 AX-385274361 6 72820512 ATAGAACAAGACATGTTTTATCACAATTACTAGAC[A/G]GAATAAGCCAGACTGTCCCAGATCTATGAGTACTA R 2 1 2 1 101000 r 74 goat snp2175-scaffold1066-766605 6 75270886 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785131 Affx-122961433 AX-385272177 6 72855662 AATCCAGACTTTACACACTCTTTTCTTCTAAGCAT[A/C]AGTTGCATTCTCCAACCAATGAACAGAATTGGCAT M 2 1 2 1 101000 r 74 goat snp2176-scaffold1066-801755 6 75306006 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798962 Affx-122933932 AX-385285892 6 72899284 CATATGTATATATCATGTATCATTATATATTTAAG[C/T]TTTTCTGGATTCTCTCAAGTCTATAAGCTCTTTAA Y 2 1 2 1 202000 f 74 goat snp2177-scaffold1066-845377 6 75350335 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787225 Affx-122951616 AX-385274251 6 72981945 CCTAACTGTATATCTAATAGTCTAAAATATCGACT[A/G]TTGATGTCAACTGAAGTTTGTAGATGGTAGAGCCA R 2 1 2 1 101000 r 74 goat snp2178-scaffold1066-928038 6 75435551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452326 Affx-122920662 AX-123322659 6 73067507 AACCAGCTCCTATTGTTAATACTGGGTCTAATGTT[A/G]CCAGAGTGTCTGACATTTCCAGATAATCTGCAAAG R 2 1 2 1 101000 f 74 goat snp2180-scaffold1066-1013600 6 75521317 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785180 Affx-122923946 AX-385272226 6 73102041 AAACACATTTGGAGAATTACCTGGTAATACTGTTA[C/T]AGATTCACATGTTTCTTAGAAAGATTTCACACTCT Y 2 1 2 1 101000 r 74 goat snp2181-scaffold1066-1048134 6 75556022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769821 Affx-122977980 AX-385256991 6 73133711 TAGTGAGAATGTGAATTTAGTTTAATCTACTTCTA[A/G]TTGAGTAATAAGGACTTCAATCCAAATCTAGTAAA R 2 1 2 1 101000 r 74 goat snp2182-scaffold1066-1079804 6 75587774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800056 Affx-122963133 AX-385286979 6 73165497 TTATTATTATTGATCACAATATCACAAGAAAGGGC[A/G]CAATGTCTATAACAATAGTAGTAATCTCAGGGTTA R 2 1 2 1 101000 r 74 goat snp2183-scaffold1066-1111590 6 75620791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426067 Affx-122941091 AX-123296413 6 73196968 GGTAGGGGAATGATGTTGGCCAGGACACCGTGCTT[A/G]CAGTGCTTGGTGACATCTACCACAGTTCAAGATTT R 2 1 2 1 101000 r 74 goat snp2184-scaffold1066-1143061 6 75652448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785870 Affx-122938710 AX-385272907 6 73247952 TGAAAAGATTGAATAAAGTTATGCACAATACTTAA[C/T]ACTTATTTACAGACATTAATTCAAGCAACTTCCTA Y 2 1 2 1 101000 f 74 goat snp2185-scaffold1066-1194045 6 75704398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408378 Affx-122953724 AX-123278729 6 73291427 ATCCTTTGGCATTTCTAGTATAATCAATATTCCTC[A/G]TGCCTATTTCAGTAATTATTATTGCTTTTATTTCC R 2 1 2 1 101000 f 74 goat snp2186-scaffold1066-1237520 6 75747830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375792 Affx-122978574 AX-123246151 6 73334083 TCCGCTTAAGGTTAATAGTCATGATTATAATGTGA[C/T]GTCATCAATCATAAATTATTTTGCTAGTCAACTAT Y 2 1 2 1 101000 f 74 goat snp2187-scaffold1066-1280176 6 75790588 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768218 Affx-122930158 AX-385255403 6 73406759 CTAGAAACCCTTACCTCAAATTTCTTAAGAAAACC[A/G]CAAGTTGAACTTCCACTTCATATTATTTAATCATA R 2 1 2 1 101000 f 74 goat snp24425-scaffold248-45659 6 75864969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447140 Affx-122924453 AX-123317476 6 73441268 CTCTAAGCTACGTCCAACTAAAATGTGATATGATG[C/T]AAATAATTTATTCATCCAGGAGTCTAGCCATATAT Y 2 1 2 1 101000 f 74 goat snp24426-scaffold248-80168 6 75895912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400170 Affx-122960680 AX-123270525 6 73473843 TCCCTGACAATTTTTAATTGGATATTCATATTGTG[C/T]TCTGCTTGTAGACCAATGCTCTTTAAGGGTTGAGA Y 2 1 2 1 101000 r 74 goat snp24427-scaffold248-112743 6 75929191 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275196 Affx-1111834759 AX-519548775 6 73482924 GTTCATGGCTTTAAAGCCTTTTAGCCTGCAGTGCC[A/G]AAA R 2 1 2 1 101000 f 74 goat GoatD01.051768 6 73482924 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38417709 Affx-122947449 AX-123288057 6 73511410 AATCTACCTTTTTACCCCTCCCATTTGACTCTCTT[A/G]TGGCAATATTATATTGATAAACTACTCTACACTAT R 2 1 2 1 201000 r 74 goat snp24428-scaffold248-150310 6 75966731 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442033 Affx-122928403 AX-123312370 6 73571711 ACAGATACAATTGGTACATATATCATTTGCAAACC[A/G]TAAGTAAAGAAAGTGACCTCTGAGGTTGCCAGGAG R 2 1 2 1 101000 r 74 goat snp24429-scaffold248-210611 6 76028190 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772745 Affx-122952028 AX-385259890 6 73605540 CAAAAGTGAAATACAAACCCCCTTAGTTAGAATGG[C/T]ATGTTTCATTACATTTCTAAATTGTGGGAAATATT Y 2 1 2 1 102000 f 74 goat snp24430-scaffold248-244440 6 76062710 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444195 Affx-122927261 AX-123314532 6 73652781 GTTTTTTGTTACTGTTTTTTAAATCACATCCATAG[C/T]AGCTTGCTCAAAATTTGCATTTAATTCATATTAGG Y 2 1 2 1 101000 r 74 goat snp24431-scaffold248-291681 6 76107667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775558 Affx-122930263 AX-385262689 6 73750979 TAGCAGGAAATATGAAAATGAAGCAGTACTTTCTT[A/G]CATAATCTCTAATTCCCCAAGATATGAAGAAAGTT R 2 1 2 1 101000 f 74 goat snp24433-scaffold248-389879 6 76208155 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382588 Affx-122973724 AX-123252946 6 73782112 TATCAATAAATTCCTAAAATAAATTTGAAGTTAAG[C/T]TGTTATCCTTAGGCCATAATATAATTACACTGTAT Y 2 1 2 1 101000 r 74 goat snp24434-scaffold248-421012 6 76239682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435140 Affx-122933678 AX-123305480 6 73872499 AACATAGTAATGTAGTACATGTCTTCCTCTCTAAT[C/T]TCATCTTGCATCAGTCTACACTTCATAATATTTAC Y 2 1 2 1 101000 r 74 goat snp24436-scaffold248-511399 6 76331912 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402950 Affx-122958171 AX-123273303 6 73926154 AGACCCGAAGCATAAACTGAAAACCAAACTTAAGA[G/T]AAAAACCAGCACTTTGTAATGAGAGAAACCTAGAA K 2 1 2 1 101000 f 74 goat snp24437-scaffold248-565054 6 76385839 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395717 Affx-122963715 AX-123266072 6 73977587 TGGATTGAAGAAGATTTAATATCTTAATATATCTT[A/G]CTCTAGTTGCTGTTTTTTTTATGCCTACCTGGGAT R 2 1 2 1 101000 r 74 goat snp24438-scaffold248-616487 6 76422624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771134 Affx-122923240 AX-385258294 6 74025207 TCTTCCTTACTGTAAACAGTTGAGTCTATGACTCT[A/G]CATGTCAGTTGGTTCTCAAGCTAGAGGAAACATAG R 2 1 2 1 201000 f 74 goat snp24439-scaffold248-664107 6 76470244 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774959 Affx-122936574 AX-385262092 6 74088079 TTAAATTGCAATTCTTGACTTTTATTAATATCACT[A/G]TAGTTCAAAGTCCAAGTGAAAGTGATGAATGGAAA R 2 1 2 1 101000 r 74 goat snp24440-scaffold248-726979 6 76532305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450864 Affx-122922226 AX-123321198 6 74125585 ACTCTTGGTTTATATAGGCAAGCAAGGCGGTTTTG[C/T]GAGGGACTTTCTATAGTTGCACCAATCACGTTAAA Y 2 1 2 1 103000 f 74 goat snp24441-scaffold248-764485 6 76569926 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790777 Affx-122930999 AX-385277778 6 74168996 TAATATAAGGATTTTCTGTGAGTAGGTATAAAACA[C/T]AAATCTTTCTTAGATATGTTGCCAGCTAATGGCTT Y 2 1 2 1 201000 f 74 goat snp24442-scaffold248-807896 6 76613648 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403538 Affx-122957608 AX-123273891 6 74226660 ACTCCTTTAAGTACTCAATTCACTATCAGTTTAAA[C/T]ATCCATTTACTTACCTACTCACAAACACAGAAACA Y 2 1 2 1 101000 r 74 goat snp24443-scaffold248-865560 6 76669568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405428 Affx-122956062 AX-123275780 6 74284963 TACAAAATGAAATGACACACTAAGAATAGAGAGAG[A/G]CATTTTTATAAAAGGAAATTCTTTTAAGTGATAGT R 2 1 2 1 201000 f 74 goat snp24444-scaffold248-923863 6 76729100 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391363 Affx-122967286 AX-123261720 6 74328557 CTATATAATTTCCTAGAGTGATCACTTTAAAAATA[C/T]GGAGAGATGGCAACATTCTCCTCACAGCCTACTAC Y 2 1 2 1 201000 f 74 goat snp24445-scaffold248-967457 6 76776276 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787387 Affx-122922579 AX-385274412 6 74378188 AGCAAGATTGGCTTTGAGTTGATAACTATTGAAGA[C/T]GGGTGATGAATCCATTTCAGCTCATCACATCATGT Y 2 1 2 1 101000 r 74 goat snp24446-scaffold248-1017088 6 76826473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794564 Affx-122921233 AX-385281526 6 74441930 GATTTTTGAGCCAGTCTTTAATATTAGCATAGTAC[A/G]CAACTCTCCTTCCCAGAAAAGGTGGTACTAATCTA R 2 1 2 1 101000 r 74 goat snp24447-scaffold248-1080830 6 76891418 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383733 Affx-122972456 AX-123254091 6 74477995 TCACAAGAAATAGGCTTGAAATAAAAGAGCTGAAG[A/C]GCTTTCATTATGAATGATATCTGGATCTCTTGGTC M 2 1 2 1 101000 r 74 goat snp24448-scaffold248-1116895 6 76927267 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795568 Affx-122950751 AX-385282523 6 74513269 TATAAGCCTCTGTAATTTTGCTATATGTGACAATG[C/T]AGACCTCAGAAGTATGATGTAAATATTTTTTCAAA Y 2 1 2 1 101000 r 74 goat snp24449-scaffold248-1152169 6 76963216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434888 Affx-122934342 AX-123305228 6 74555146 TCCTAATTTGTTTTTAATTCTTTTCTGTTATTTAT[C/T]ATGTAGGACATTGGACACTCCCTAGAGAGCTACAA Y 2 1 2 1 103000 r 74 goat snp24450-scaffold248-1194046 6 77005946 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777206 Affx-122957620 AX-385264329 6 74599630 AACTAGCTAGCTAATGACTAGACAGAAGATATAAA[A/C]TCTTTTCTACTTAAATCACTGCAACAATATCTTAA M 2 1 2 1 201000 r 74 goat snp24451-scaffold248-1238530 6 77050458 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420685 Affx-122944801 AX-123291032 6 74646716 TTAATTAAATTGTGATTAGAAATAGATTTGGGTGA[C/T]ATTGGAGGAATAGCTACTTTAAACACTTCAAAATA Y 2 1 2 1 101000 r 74 goat snp24452-scaffold248-1285616 6 77093453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400965 Affx-122960110 AX-123271318 6 74678146 AACACTGATACTTTAAGTTAGCTAGACCCTGTGTA[C/T]TATCAAATTGTTGGTCTCTAAAGGAATGTATCATT Y 2 1 2 1 101000 f 74 goat snp24453-scaffold248-1317046 6 77124764 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453124 Affx-122920013 AX-123323457 6 74707367 GCATGATTATGCATATGTCAAGACACACAGAATTA[C/T]ACATAACAAAGACTGAACTTTCCTGTGTGCAAATT Y 2 1 2 1 101000 f 74 goat snp24454-scaffold248-1346267 6 77154443 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446359 Affx-122925601 AX-123316695 6 74762491 TAACAAACATCAACAATAGACAAATAAAATTATAC[A/G]TTTGGTATTTACCTAACATCTGCATGTCTATAAGC R 2 1 2 1 101000 r 74 goat snp24455-scaffold248-1401391 6 77209530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793521 Affx-122957662 AX-385280498 6 74799772 GATGGCCACATTAACCTTGTAGTGCAAGTAAGACA[G/T]ATTTTTGAAATACTAATTTCTCCAATAAGGAAAAC K 2 1 2 1 101000 f 74 goat snp24456-scaffold248-1438672 6 77246736 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785170 Affx-122955850 AX-385272216 6 74829520 TTATAATTAGGTAATAGTTACCAAAATTATTGGCA[A/G]TTTTGAGAAAAAATTATACAGTTGGTATGCATAAT R 2 1 2 1 101000 f 74 goat snp24457-scaffold248-1468420 6 77275965 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404489 Affx-122956717 AX-123274841 6 74882325 TGTCAAGGAAGAGTATCTCCTTTGAAAAAGAGTAA[C/T]GTCTATATTGAATATTTGCCATGTGATAAGCGAGG Y 2 1 2 1 101000 f 74 goat snp24458-scaffold248-1521225 6 77329260 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421460 Affx-122943933 AX-123291807 6 74987343 CTATTTGACTATGGAGCCTCACACACTTAATTTCT[A/G]TTTGCAGAACTTGACTCACATTGACCACACATTTG R 2 1 2 1 101000 r 74 goat snp24460-scaffold248-1626243 6 77439194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476221 Affx-1251763726 AX-586011645 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 4 1 4 1 20000 f 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 539476475 Affx-1251763726 AX-586011875 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 8 1 4 1 20000 r 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 562165428 Affx-1251763726 AX-606940839 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 8 1 4 1 20100 r 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 562165766 Affx-1251763726 AX-606941175 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 8 1 4 1 20100 r 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 562165908 Affx-1251763726 AX-606941317 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 8 1 4 1 20100 f 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 562166448 Affx-1251763726 AX-606941856 6 74997153 TTATAGCAGAAAATATTAGTGAACAGGAATATAAG[-/GTAGGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAAATTTAAGATTTTAAAATTAAAAAAAAAAGGAATATAAGC]TAATAAAAATGAAATGGTAACAGAAAATAATGACT - 8 1 4 1 20100 f 74 goat SV_323 6 74997153 - deletion junction SV-TF-chip 38453799 Affx-122919575 AX-123324132 6 75038743 GTAATGGAAGCAAGCAGTTGTTTGCTGGCTTTGTT[A/G]CCAAAAATTGTGAATGGCTAGATTTTTATAAAACA R 2 1 2 1 201000 r 74 goat snp24461-scaffold248-1677643 6 77490672 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381528 Affx-122974849 AX-123251886 6 75072253 TTTAATATTCTGTGTGGACTCAGGATCAAGGAGAG[C/T]GAATTGGTTATTGCTAATTTTTTTACTATTAATGA Y 2 1 2 1 101000 f 74 goat snp24462-scaffold248-1711153 6 77524371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778870 Affx-122957164 AX-385265978 6 75116041 CAAAGTTTAATGTTGGCTTTGCAATGACTTAGAGA[A/G]ACATGCATATATTGCTTGTTTAGTAATCATAAATG R 2 1 2 1 201000 r 74 goat snp24463-scaffold248-1754941 6 77566884 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776687 Affx-122924857 AX-385263813 6 75170597 AAAACTCTTAAGTATCTATACAATTCATGTTTACA[A/C]AGTCAGTCTAAAATTGTACTAGTAGAGCAAGGTAG M 2 1 2 1 101000 r 74 goat snp24464-scaffold248-1809497 6 77622385 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408082 Affx-122954725 AX-123278433 6 75201248 AGACTTGAGCATGGAGAGATCAGTTAGGTTATTGC[C/T]CTAGGGCAGAAGGTAATGAGTGTCTGAATTGAGGA Y 2 1 2 1 101000 f 74 goat snp24465-scaffold248-1840148 6 77652852 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431350 Affx-122937050 AX-123301691 6 75237432 CTATCCTGTCATTTATTAATTCTAAACTCAGGCCT[A/G]CCATCTTGAGAATTTATTTATTACTCATAAGATGA R 2 1 2 1 101000 r 74 goat snp24466-scaffold248-1876332 6 77688803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413865 Affx-122949858 AX-123284214 6 75267130 CCAATGTGCCTGAGGCCAGCATCTCACCACCAACC[A/G]TTCCTGTGGATTCAACACTTATGCTCTAAGGAAGC R 2 1 2 1 102000 r 74 goat snp24467-scaffold248-1906030 6 77718518 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782012 Affx-122942865 AX-385269091 6 75297704 AACTATGATAAATTTAATTTGATAGTAAAGGTCCA[G/T]TCCAAGGATGAGTATTAACAAGCAATCAGAACGGT K 2 1 2 1 101000 r 74 goat snp24468-scaffold248-1936604 6 77749744 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442432 Affx-122927971 AX-123312769 6 75342927 TTCTAAGAAATGTGAATCTTTCTAATTTTGAAAAT[A/G]TTTCTTTCTTTGGAGAATGAACAAACAACGAAATC R 2 1 2 1 103000 r 74 goat snp24469-scaffold248-1981827 6 77795365 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444492 Affx-122926519 AX-123314829 6 75395713 GAACATAAAAAGTGTAATTGTTAAAGGAGGTCAAG[C/T]GTGCCCAGGCTTTGTTATTTGATATCACAGCACAT Y 2 1 2 1 201000 f 74 goat snp24470-scaffold248-2034613 6 77847993 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785633 Affx-122936705 AX-385272675 6 75437604 CCACTTTAGAATACTCTGCTTCTATCCATATTACC[A/G]TAGGTAAGTGAGAACTGACTTTATTACATAGTAAA R 2 1 2 1 201000 r 74 goat snp24471-scaffold248-2076504 6 77889923 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423823 Affx-122942796 AX-123294169 6 75535467 GTCTTAAGTGTTTATGTTTTTCTTAATTCCTTGAT[A/G]GTGAGAAATGATTAACTAAAACATTTGTTAATGAA R 2 1 2 1 201000 r 74 goat snp24472-scaffold248-2174367 6 77987320 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse271 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468278564 Affx-1111836402 AX-519552044 6 75555731 TGCCTAAGCCTTAGTATGGTCATCAAAATACTGAT[C/G]ATCTGAATTCAGACTAGATGTTTCTAAACCGGTGG S 4 1 2 1 101000 r 74 goat Random2.2K-703 6 75555731 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394643 Affx-122964390 AX-123264998 6 75566667 TAGATAGTGAAGCTGAGTACACACATCTTGAAATT[A/G]ATGTTTTAAAAACATTTTCCTGTTTATGGAAGCCA R 2 1 2 1 101000 f 74 goat snp24473-scaffold248-2205567 6 78018184 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377918 Affx-122977230 AX-123248277 6 75597316 CTGTTCAACTTCGGTTCAAAACTGTAGTTAAGTTC[A/G]TTTCTTTGGAACCAAATAAAATGAAAAAGTAACAT R 2 1 2 1 103000 f 74 goat snp24474-scaffold248-2236216 6 78048833 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476222 Affx-1251763727 AX-586011646 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20000 f 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 539476476 Affx-1251763727 AX-586011876 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 4 1 4 1 20000 r 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562165370 Affx-1251763727 AX-606940781 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 f 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562165377 Affx-1251763727 AX-606940788 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 r 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562165409 Affx-1251763727 AX-606940820 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 f 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562166203 Affx-1251763727 AX-606941611 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 f 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562166339 Affx-1251763727 AX-606941747 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 r 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 562166457 Affx-1251763727 AX-606941865 6 75597849 AAATCATTCTGAAACTGGTGATATATTAAAGTTTC[-/TAAATACACCTATAGATCGGAGGGAAAGATGGCGGAGGAAAGATTTTAAAATTTAAAAAAACATAAAAAAATTAAAAAAA]AAATACACCTATAATTCTGATATGTTCTAAAAGAG - 8 1 4 1 20100 f 74 goat SV_324 6 75597849 - deletion junction SV-TF-chip 38442491 Affx-122927923 AX-123312828 6 75648175 TTATTATATCATCATTTCATCACCCAGGAACCTGC[A/G]TTGAGCATGAGATTCTCACTGTATGCAGTATATAA R 2 1 2 1 101000 f 74 goat snp24475-scaffold248-2287075 6 78099933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394652 Affx-122964383 AX-123265007 6 75676925 TTCAGATTTCTAGTTATAAATATATTTAAGGGCTA[C/T]AACATCTCACAGAGCTTCTGTGTTAGAAGCAGACT Y 2 1 2 1 103000 r 74 goat snp24476-scaffold248-2315825 6 78128675 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771069 Affx-122940947 AX-385258229 6 75720398 GGGAGATGGAGTGACAATACAATTTTTTTACAAAA[C/T]GATTTGATATTGAATATGCAGAATTAATAAACCGT Y 2 1 2 1 201000 r 74 goat snp24477-scaffold248-2359298 6 78172617 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417396 Affx-122947688 AX-123287744 6 75756138 TTAATTTCAAACAAGCTAGAGGGGAGACCATCATA[A/C]AGAAATGATGCAAATCTTTAATTAGAAAAAATTAA M 2 1 2 1 101000 f 74 goat snp24478-scaffold248-2395038 6 78208246 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443874 Affx-122927506 AX-123314211 6 75812828 GTTTAGTAAAGAGGTTTCTCTGGAGCTGTTGTACT[A/G]CTTGGTTGCTCCATCTTCTTTTGAGGAAGAGGCTT R 2 1 2 1 101000 r 74 goat snp24479-scaffold248-2451728 6 78265646 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446796 Affx-122925300 AX-123317132 6 75852226 TGTGATTAGTCTTTTTTAAGAAACAGAAGAAAACA[C/T]AATGAGTAATATGGAAACAGGTAAAATTTTTTTGT Y 2 1 2 1 101000 f 74 goat snp24480-scaffold248-2491126 6 78305644 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376942 Affx-122977774 AX-123247301 6 75894354 AGTAAAACTTAAAAATGATAAATTTTGGGAAAATA[G/T]CCAAACCTCTGAAGTAAAACTCAAGTGACAAGTAT K 2 1 2 1 101000 r 74 goat snp24481-scaffold248-2533254 6 78348338 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408723 Affx-122953420 AX-123279074 6 75943148 TGCAGTGTTCTATTCTCTATGTTTTCAGATATTTT[C/T]CAGAAAGAAATGATAACCAAAATAGCAAAACACAT Y 2 1 2 1 101000 r 74 goat snp24482-scaffold248-2582048 6 78398367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794987 Affx-122953654 AX-272333284 6 75977807 TTAATTTAAGCACTCTTGTGGTCTAGAAGAAAACT[A/G]CTTTGCCTCAGTACTCAAATGTATGACCTCCAGAA R 2 1 2 1 101000 r 74 goat snp24483-scaffold248-2616707 6 78433050 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781425 Affx-122940110 AX-385268510 6 76062429 CAAAGATATATAATAAGGATAATATGCTTAATAAC[G/T]AAAAGAAGTCTACTTTGATAGAATCCTAAGTGAAT K 2 1 2 1 101000 r 74 goat snp24484-scaffold248-2701329 6 78517278 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796797 Affx-122971844 AX-385283740 6 76116354 CTACTGAGACTGTATAAGATGGAACTTCACTAATG[C/T]CCGTTTATTTTATTTGGATTGAATTGGCCTACAAC Y 2 1 2 1 101000 r 74 goat snp24485-scaffold248-2755254 6 78573134 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428333 Affx-122938999 AX-123298676 6 76199241 TGGGAGTCGGGACTGGAAGCAGAGGGGCTGGAGCC[A/G]GAGCCAGGTATGAACTAGGGTTTCTATGCTCAGTG R 2 1 2 1 101000 r 74 goat snp24486-scaffold248-2838141 6 78657310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273225 Affx-1111833516 AX-519546882 6 76212340 CGTATGCAAAGAGTTGACTCATTGATGAAGACTCT[A/G]ATGCTGGGAGGGATCGGGGGCAGGAGGAGAAGGGT R 2 1 2 1 103000 f 74 goat 6_76212340_AF-PAKI 6 76212340 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468274740 Affx-1111834468 AX-519548326 6 76218877 AGATGAGGAAATAGGGTGAGACTGGTGAGTGACAG[A/C]ACAGGCAGAAGCCTGCAGAATGGGATTCAAAGCAG M 2 1 2 1 201000 f 74 goat GoatD01.037030 6 76218877 G T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38423400 Affx-122943119 AX-123293746 6 76237641 AACTACAGGTTGTAGTTTTAAAAAATTAATAAGCT[A/G]CTATGGCAGGGGCTGACATCTTAAAGAAGAACTTC R 2 1 2 1 103000 r 74 goat snp24487-scaffold248-2876541 6 78692249 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447345 Affx-122924882 AX-123317681 6 76268797 ATTTATTAATTTTTTTCCCATTTCAGTAGTTGAAC[A/G]TCAGAACACATGGCTTAAAGCAGTACATTTTAGTT R 2 1 2 1 101000 r 74 goat snp24488-scaffold248-2907697 6 78723789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432195 Affx-122936391 AX-123302536 6 76307936 AACTGAAATATAATGAAAAAGATAATTCTCATTTT[A/G]CATTGATATTTTCTTATAAAATTAATGTATACTAG R 2 1 2 1 103000 r 74 goat snp24489-scaffold248-2946836 6 78763081 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431399 Affx-122936542 AX-123301740 6 76360010 TCAGACACAGCTGAGCAACTAACATACATATTCCC[A/G]TGAGAGAACCGAGATTAGTTAATCCCATCTCCCGG R 2 1 2 1 101000 r 74 goat snp24490-scaffold248-2998910 6 78816057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801184 Affx-122934108 AX-385288097 6 76446487 TTGAAATCTGGAAGCCATAGAAAGAATACTGAAAC[C/T]ATTATCAATTGGATTACTTCATATCTCTCTACAGC Y 2 1 2 1 101000 f 74 goat snp24492-scaffold248-3085387 6 78903196 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790586 Affx-122942415 AX-385277589 6 76519217 AGAAATGCCTGAGATGTTAGGTCTTTCCTTAAGTA[C/T]AAATTTACTATTTTAGTCTGATGCAACAATAATAA Y 2 1 2 1 201000 r 74 goat snp24493-scaffold248-3158117 6 78976441 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395320 Affx-122964051 AX-123265675 6 76622277 ACTAATAATTCAATGCTGGAATTTCAAAAGGAGCT[A/G]TACAACAAAGCAGGTCTTTGTGAAACAGAGTACAA R 2 1 2 1 101000 r 74 goat snp24495-scaffold248-3261177 6 79080650 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802722 Affx-122947892 AX-385289621 6 76668935 AACAATCATTATGGAGGTGATACACAGTACTGAAG[C/T]ATCATAGTTTCAAGTCTTTGCAGAGGACAAAGCTA Y 2 1 2 1 101000 f 74 goat snp24496-scaffold248-3307835 6 79128493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772122 Affx-122927064 AX-385259276 6 76749714 ATATAGTCCCTAACAAGAAAGATGAATTTAACATC[A/G]TTATAGTAGATTAAGAAATACAGTAACCCCAAAAC R 2 1 2 1 101000 f 74 goat snp24497-scaffold248-3388614 6 79209818 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320786156 Affx-122942076 AX-385273192 6 76801029 TATTGTCCGATAGATATGTAAAGTCTGCCAAATAC[A/G]TAATTTTTAATTTTCTGGTACATTAATATTTCTGC R 2 1 2 1 303000 r 74 goat snp24498-scaffold248-3439929 6 79262166 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444435 Affx-122926561 AX-123314772 6 76921365 TTTTAACAAATAAATGATGCAACAGGTTTCTTCAG[C/T]CTAAGTTTTTAACAGCTATTAAGTTTTTGGTGGTT Y 2 1 2 1 101000 r 74 goat snp24500-scaffold248-3560265 6 79383630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782964 Affx-122961223 AX-385270033 6 76974481 CATATACCATGATCAAGAAAGATTTATTCCAGGGA[C/T]GCAAGTAATTTTCATTACCTGCAAATCAATTACTG Y 2 1 2 1 201000 f 74 goat snp24501-scaffold248-3613381 6 79437999 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413018 Affx-122951004 AX-123283367 6 77011193 ACACTCTCACCAGGACTTTAGCTACATATTGCTAA[C/T]AAAAAGTTAGAAAACATTTGTAACTGATTGGTTTT Y 2 1 2 1 202000 r 74 goat snp24502-scaffold248-3650093 6 79474329 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433229 Affx-122935613 AX-123303570 6 77047398 AAATAAAATGCATACTGTTAGAAGAGAAGGAATGA[G/T]CAGATGAAGAAAGACAAGAAACAAAAATAAATCCA K 2 1 2 1 101000 f 74 goat snp24503-scaffold248-3686298 6 79510603 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440333 Affx-122929674 AX-123310670 6 77096243 AATGAAAAATTAAAAATAAAATAGTTGCTTTATTA[C/T]GCTTACATCATTTGTAAGTCATGGTGATGAATTTC Y 2 1 2 1 103000 r 74 goat snp27941-scaffold30-18900 6 79560290 T C 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38432643 Affx-122935473 AX-123302984 6 77134685 GGGAAGATGGAGTGGATGTGCTTTACTTATTTCTC[A/G]CACTAAGAACAACTAAAAATATTTGACATGGTAAA R 2 1 2 1 101000 f 74 goat snp27942-scaffold30-57342 6 79599228 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425178 Affx-122941050 AX-123295524 6 77174216 AAGTATTACTGGTGAGAATTTTAAAACATGTAAAA[A/G]TGATGACAGTGGAAAAGAGAAAGTGAAAAGTTTGT R 2 1 2 1 201000 f 74 goat snp27943-scaffold30-96873 6 79639059 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437470 Affx-122932377 AX-123307808 6 77391292 TGTCACAGCAGGGTGTGCATATTATCAAGATATTT[A/G]TTATTGGTTATATTAACATTGGCCACTGGTTAAGA R 2 1 2 1 101000 r 74 goat snp27947-scaffold30-313949 6 79902177 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791404 Affx-122969506 AX-385278396 6 77424068 TCCATACCAACACAAGCATATATACATTACCTTGT[A/G]CTACTTATGGATTATTAGATGAAAGATAAATAAGC R 2 1 2 1 101000 f 74 goat snp27948-scaffold30-346725 6 79935318 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779448 Affx-122928222 AX-385266551 6 77473818 GAAACACTGAGGTATAGGATGAAATGAGAGAATAA[C/T]GGAAACCATTTCAGATGTCTTATTAAAAAATATAT Y 2 1 2 1 101000 f 74 goat snp27949-scaffold30-396475 6 79986173 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse272 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38377842 Affx-122977289 AX-123248201 6 77510393 AAGACCAAGTATTCTTAGACCATCCTTGTGAACAC[A/G]TACATCACAAAATGAAGCATGAACATATAAAAATG R 2 1 2 1 101000 f 74 goat snp27950-scaffold30-433050 6 80013238 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416841 Affx-122948109 AX-123287189 6 77545118 AAAAGAAAAGAAACCTAGATAAAGTAATACAAGAT[A/G]TTTATTGGCTCATGGAATTTAATTTAGGTCAGAAA R 2 1 2 1 101000 r 74 goat snp27951-scaffold30-467775 6 80048034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785635 Affx-122952925 AX-385272677 6 77591033 TCATTTTCTTAATGGGCTATGGAATTAATAAACAT[A/G]CAATGTTAAATAGCCCTTCAAGGTTAAAGTCTGAA R 2 1 2 1 101000 r 74 goat snp27952-scaffold30-513690 6 80078674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788036 Affx-122925070 AX-385275057 6 77626938 CTTTCAACACTATTAAGGACAAATAATACACATTT[A/G]TGGAACAAATCAGTTTGCAGCATCTGATTTTGGTA R 2 1 2 1 101000 r 74 goat snp27953-scaffold30-549595 6 80114517 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422622 Affx-122943714 AX-123292968 6 77656918 TATAGAAAAAGGATAAAAGATAAAACATCTTTAAA[C/T]ATTGATATAGTAACTGACTTGAAAATCTGGATTTA Y 2 1 2 1 303000 f 74 goat snp27954-scaffold30-579575 6 80144179 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406383 Affx-122955404 AX-123276735 6 77688838 TTTAAAAAAGAATTATAATAATTTTTATACAATGC[A/G]TGGACTTACTATCATTCAACCCTTCAGTTATTCAG R 2 1 2 1 101000 r 74 goat snp27955-scaffold30-611495 6 80176716 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386791 Affx-122970917 AX-123257149 6 77733863 TTTCATCCATTCCCAAGGGTCGATGTGTGTGTACC[C/T]GTGTGTGTATCTGTGTTGAGATGAATTCTTATTTC Y 2 1 2 1 102000 f 74 goat snp27956-scaffold30-656520 6 80221731 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408834 Affx-122954020 AX-123279185 6 77811218 CAGTAAACCTGATAAAAATTTCTTATTCTGTGTTG[A/G]CTTTGACCTGATAGTTTATCTTAAATCATTTCTTT R 2 1 2 1 101000 r 74 goat snp27957-scaffold30-733875 6 80298430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse273 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320796807 Affx-122925325 AX-385283750 6 77848033 GTACATTGTAGTTCTTTCATACTTCTAAAATCTAA[C/T]GAACATGAAACATTTTCCCCAGAGGAGCCCATAGA Y 2 1 2 1 102000 r 74 goat snp27958-scaffold30-770690 6 80336432 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447713 Affx-122924607 AX-123318049 6 77877528 TCTGTGGAAACCATATTTTATTACATATTTCTGTT[A/G]CAGCCATTCACTGCTTTCTAATTTGTATTACACAT R 2 1 2 1 101000 r 74 goat snp27959-scaffold30-800185 6 80364362 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383463 Affx-122973449 AX-123253821 6 77907284 CAGAATAGTTTACTTTCCTTTAAAATGAGCAATAG[C/T]ACAGAACTTCAGTTTTTGTTTTTTTCTAGAATTAT Y 2 1 2 1 101000 f 74 goat snp27960-scaffold30-829941 6 80394184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783110 Affx-122964039 AX-385270177 6 77953101 GTCCATCTGCAGAATGATAAATTATATTTGAAAGG[C/T]AAAATAGCCCAAGGCTTCTTCAAGTAAGCTTTAAA Y 2 1 2 1 101000 f 74 goat snp27961-scaffold30-875758 6 80439756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440908 Affx-122929217 AX-123311245 6 78000019 GATTCAAGAGGCCATGTATTTTTCCATTCTTTTTG[C/T]GAACACCCTGAACAGCACCTTGTAACAGAACCTAA Y 2 1 2 1 101000 r 74 goat snp27962-scaffold30-922676 6 80487198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429412 Affx-122938522 AX-123299754 6 78041848 AAAAATCTAGGCAAATGTCACATAGGCTGAGAAGA[C/T]GAGCACTGAAATTTTGCCTCCTGACTATGGCCCCA Y 2 1 2 1 101000 f 74 goat snp27963-scaffold30-964505 6 80529767 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423133 Affx-122942768 AX-123293479 6 78074634 GAGAAGTAGGATGTTTTCGGCAGCACAATTCACTG[C/T]GGTGATAAAAAAATAATAATAACTGAGATAAGCTC Y 2 1 2 1 101000 f 74 goat snp27964-scaffold30-997291 6 80562582 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse274 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320780542 Affx-122928955 AX-385267633 6 78130338 CGTTAGTTTTAACATCCATTATTCCATAATCCATT[A/G]TTAGATGATTGTCACAAAATGATAACCGTCATTTT R 2 1 2 1 101000 f 74 goat snp27965-scaffold30-1052995 6 80618555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394069 Affx-122964972 AX-123264424 6 78178268 TCACTATTTTGTCTAAAAATTAATTTTTACTGCTT[A/C]TATCTTATGTGTTTCTCCCCATTCCATGAAACAAA M 2 1 2 1 101000 r 74 goat snp27966-scaffold30-1100925 6 80666948 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787290 Affx-122933253 AX-385274315 6 78232492 GAGACAAGTTACTTGACTGCAAATCTCATTTTTTC[A/G]TTGTTTTATTTATCATAGTGTTAATAATATTAATC R 2 1 2 1 202000 r 74 goat snp27967-scaffold30-1155149 6 80722486 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382046 Affx-122974939 AX-123252404 6 78264337 TGATGCAGTGCCTTTTGTATTCAGAGAATATACAT[A/G]CATAGTTTTACGTGTGCACACAAATTAACATTTAT R 2 1 2 1 101000 f 74 goat snp27968-scaffold30-1186994 6 80754569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse275 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320783861 Affx-122932383 AX-385270917 6 78379861 ACTTAATTTTTGTAATTTTTGAGTAAATTCCAAAA[G/T]CCTACTGCTAACCTTATGGACCAAAATATGGCAAG K 2 1 2 1 202000 f 74 goat snp27970-scaffold30-1302518 6 80871249 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420500 Affx-122944854 AX-123290847 6 78436051 TCTTCTTTATCTCTCGTTAAACTTTACAAATTTCC[A/G]TTACTATAAGCCTAGACATGACCAACCATATGATG R 2 1 2 1 101000 r 74 goat snp27971-scaffold30-1358708 6 80928252 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447973 Affx-122923758 AX-123318309 6 78468711 AAGTAAGTTTGACAAAGGAGGCTGTATGGTATGAT[A/G]TTAAGAATAGAGTCTATGAAATTAGATATATTGTC R 2 1 2 1 201000 r 74 goat snp27972-scaffold30-1391368 6 80961287 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse276 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320783008 Affx-122927470 AX-385270076 6 78506979 AGAGCATGAACTGAGTATAGAAAAGACCCAGTTCT[A/G]CTCCCAAACATTGGTACTCCTTCACTTTGCTTCAT R 2 1 2 1 201000 r 74 goat snp27973-scaffold30-1429636 6 80999545 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407769 Affx-122954969 AX-123278120 6 78563952 ATCTGATTTTTTTTAACTGTATCTGATTTTTCACC[A/G]TGAAATTAGTATTGCCAACATGTATAGCACTACCC R 2 1 2 1 101000 r 74 goat snp27974-scaffold30-1486609 6 81048838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787836 Affx-122954349 AX-385274859 6 78597373 GAAAGTAACATTCACTAAACAAATACATGATGAAT[A/G]CCTACTTAAATGAATGTTTCTTTGATTAAGCAAGT R 2 1 2 1 101000 r 74 goat snp27975-scaffold30-1520030 6 81082930 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788955 Affx-122922009 AX-385275968 6 78634160 AAGGTTGCAAAGCAGGGAGTGGAGAATTTTGACAG[C/T]ACTAAATAATTCCTGTTTATCTTATGTTAACTCTG Y 2 1 2 1 101000 f 74 goat snp27976-scaffold30-1556817 6 81119678 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406686 Affx-122955781 AX-123277038 6 78708653 CAAAATTCCTAAACAGGGAAGTTTGGGCCATTTCT[A/G]TGTATTAAAAACTTTCAAGGGGCCTTGAGAATTCA R 2 1 2 1 202000 f 74 goat snp27977-scaffold30-1631310 6 81184265 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse277 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468273227 Affx-1111833517 AX-519546883 6 78750467 TCAGACTCATTTACAAGGTAAAGTTTGGATCAATC[A/C]GACAGTTCAACATCTTTCTCACTCTTTTTTGACCT M 2 1 2 1 201000 f 74 goat 6_78750467_AF-PAKI 6 78750467 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389224 Affx-122969052 AX-123259582 6 78758991 ATGGCCATTGCAGTGGCATATTTGTAAAGTAACTA[C/T]ATGTATAGGTTTGTTTCCTAATTCTCTCTTGGTTT Y 2 1 2 1 101000 f 74 goat snp27978-scaffold30-1681648 6 81234384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449570 Affx-122923234 AX-123319905 6 78819485 TCTTACTTGTATTTTTTCCAGATGGCCTTCTGAAG[A/G]CCATCATTTTTCAGCTGTTTGTGAAACAAATGCTA R 2 1 2 1 101000 r 74 goat snp27979-scaffold30-1742142 6 81296323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse278 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38385641 Affx-122971171 AX-123255999 6 78852104 CCATCCATATATTCCATGATTTTCTCTCTATCTAA[C/T]GGTTAGCTGATTCAATAGCAACTCTAATTCCACTG Y 2 1 2 1 101000 r 74 goat snp27980-scaffold30-1774761 6 81329129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278399 Affx-1111836403 AX-519551884 6 78889128 GACCTTTTTATGTGAAGCACCTGATTTTGATAAAG[A/G]TCAGGACTGCTGACCCCCGCGTGACTCTGTATTCA R 2 1 2 1 303000 f 74 goat Random2.2K-708 6 78889128 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320767054 Affx-122975088 AX-385254344 6 78893700 CATTAAGGGCAGTAGCTCTTTTCAGGAAGAGATTA[C/T]GCTAGAACTATTATAAGGGTAAATTCAAGTATTTG Y 2 1 2 1 101000 f 74 goat snp27981-scaffold30-1816357 6 81371504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379048 Affx-122976346 AX-123249407 6 78924159 AAAAGAGACAGGGTGCACATAGGATGAAAAAAGAA[C/T]AGGAAAAATAATTAAAGCAACCTACCTGGTCCTTC Y 2 1 2 1 201000 f 74 goat snp27982-scaffold30-1846816 6 81401376 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407859 Affx-122954514 AX-123278210 6 78971556 ATCCATAGTAGCACAGGTGTCTTCCTTCATCAAAT[A/G]TATCTTGGTTCTATTGGCATTTAGAGCATTCTGAA R 2 1 2 1 201000 r 74 goat snp27983-scaffold30-1894213 6 81446998 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799033 Affx-122928306 AX-385285963 6 79009002 GAACACATCATTTCCGGTAAAGCAGTCTCTTTTCA[C/T]AAGCTATCTCAAAATTAGGTTAAACAAACTTTGGG Y 2 1 2 1 101000 f 74 goat snp27984-scaffold30-1931659 6 81484507 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785247 Affx-122970847 AX-385272292 6 79060435 ATTAAAAAGCAAGCAAATTTCACTACTTCTAATGA[C/T]ATATTTTCACTATATGAAAAGCTAAGATCTCACTA Y 2 1 2 1 201000 f 74 goat snp27985-scaffold30-1983092 6 81536993 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425906 Affx-122941619 AX-123296252 6 79129246 AGTTGTTTATACAGGGGTTGTAATACTGAAATAGA[C/T]AAAAGGAAATACTGATGTATTTCACTGGTAGATCC Y 2 1 2 1 101000 f 74 goat snp27986-scaffold30-2051903 6 81606037 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797870 Affx-122940888 AX-385284808 6 79168154 CCAATGTACTTCTCTAGGAAGCTAGCTAGCACAAA[C/T]GCTAAATGCTTGTTCAATTAGTTGACCAAGATCTG Y 2 1 2 1 201000 r 74 goat snp27987-scaffold30-2090811 6 81645057 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387589 Affx-122970261 AX-123257947 6 79210762 GCAAAGAGTCGGACATGACTCAGCGACTGAATTGA[A/C]CTGATAATGCTCTCAGAATAATTCTTCCTGTTTTA M 2 1 2 1 202000 r 74 goat snp27988-scaffold30-2133419 6 81688698 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772438 Affx-122960821 AX-385259589 6 79266060 AAAGTAGACTTTGTTTTAGACAAAAACATTACATT[A/C]TAAATGAAGAAATACAACTACCTAGACTCTAAAAT M 2 1 2 1 101000 r 74 goat snp27989-scaffold30-2188717 6 81745130 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380566 Affx-122975277 AX-123250924 6 79318962 CAGTTCTGGCAGCTGTCCTGTCCGGATGTATATAA[C/T]GTGCAGTGGAATACATGAAGGATTCATGAAGCATA Y 2 1 2 1 101000 f 74 goat snp27990-scaffold30-2241619 6 81804650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425980 Affx-122941157 AX-123296326 6 79377086 ATTTTTGAGTTCATTCAAGCTGAGCAGTACTTCTT[A/C]TCTTTTGAAATGTCAGGTGGTTGGTCTGAGGAAAA M 2 1 2 1 201000 f 74 goat snp27991-scaffold30-2299743 6 81862810 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795666 Affx-122939027 AX-385282621 6 79418719 AGCTTTCTTTCCTAATAATTCAACAGATTAGGAAT[A/G]TAAAGGAATTTCATCAACATCATAAAGAGCATCTA R 2 1 2 1 201000 r 74 goat snp27992-scaffold30-2341376 6 81904295 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799798 Affx-122956206 AX-385286724 6 79469448 TTCAAAATAGAAGATCCAACTTTTCAAATTGCCTC[G/T]CCCTACTGAGTGCCAGGTGAGACATTAATAATTAA K 2 1 2 1 101000 r 74 goat snp27993-scaffold30-2392105 6 81955740 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780209 Affx-122927013 AX-385267305 6 79507804 GAGGTCTGGGGCTAAACTGGGGATGGAGATCTGAT[C/T]CAGTGTACATATACAATGAAGGAGTCTAAATTTTG Y 2 1 2 1 101000 f 74 goat snp27994-scaffold30-2430461 6 81996285 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse279 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38376586 Affx-122979069 AX-123246945 6 79579734 CTATGCATAAAATATGTGAATAAATGTAACTACAA[G/T]CAGAAAGCAAAGGAACAAATCAGAGCTTGAAAGAG K 2 1 2 1 201000 f 74 goat snp27995-scaffold30-2502391 6 82067071 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786422 Affx-122927258 AX-385273456 6 79624781 TGTCCTTGTCTGTTGGGATACACAAATAAACAATG[C/T]AGTTTTCTAGTACTTTCCTGAACTATGACATTATC Y 2 1 2 1 101000 f 74 goat snp27996-scaffold30-2547438 6 82113961 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445678 Affx-122926135 AX-123316015 6 79699474 AAATGGGGATTGTGAAAATTACAGAAAACTAAGGA[C/T]TAGAGATAATGTAAAATGTGTAATGACCTGAGATG Y 2 1 2 1 101000 r 74 goat snp27997-scaffold30-2622131 6 82190647 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792863 Affx-122978220 AX-385279841 6 79728463 TATTAGCCTAAGATCTTTCCCAATATTAAGTAATG[C/T]ATCTTTTTTCTCTTGTTGTATCTATATTGGTAGAC Y 2 1 2 1 101000 f 74 goat snp27998-scaffold30-2651120 6 82219569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767064 Affx-122955456 AX-385254353 6 79746635 AGAAATCAAGTTTAAAGATAGCAGTGTTGATACTC[A/G]TCCTCCTGAATGTAATAATAAATACTGTAAGATTG R 2 1 2 1 101000 f 74 goat snp36190-scaffold433-12605 6 82237885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse280 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320772159 Affx-122969673 AX-385259315 6 79802352 TCTAATTATGAATATCTAGTAATAAGATAAAATGA[C/T]ATCAAATAATAAGATAAGATGGCATCTAGGACTTG Y 2 1 2 1 101000 r 74 goat snp36191-scaffold433-68322 6 82294794 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770311 Affx-122922966 AX-385257476 6 79832023 ATCCCTCTTTAACTCCATGCTGAAAATGTGGAGCT[C/T]AAAATGGGACTACTCTTAGAATGTAATATGAGTTC Y 2 1 2 1 102000 f 74 goat snp36192-scaffold433-97993 6 82324888 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801797 Affx-122951479 AX-385288705 6 79871327 TTCCTTTTCAATGGTGAAAGGAATATCACATATTA[C/T]GCTCTATAAAGACATGAGTAGTAGAGAAATAACAA Y 2 1 2 1 101000 f 74 goat snp36193-scaffold433-137297 6 82364176 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379150 Affx-122976722 AX-123249509 6 80011267 ACTAAGCCAAAAAGAGGAACTGAATTGGAGGACCC[A/G]CATACCAGATTTTTAAAAATTGTTATACAGGCCAT R 2 1 2 1 101000 f 74 goat snp36196-scaffold433-277237 6 82505537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse281 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38421457 Affx-122943935 AX-123291804 6 80079001 CTGATAATAACTGCCTTATAAACTTGTAACCAAAG[C/T]AGGATTATCCAAATGTTTGGTTCTGGGCCTGGGTT Y 2 1 2 1 101000 r 74 goat snp36197-scaffold433-344971 6 82574479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451786 Affx-122921501 AX-123322119 6 80132082 CCATGTTCTGTCTATCCATATTGTTCACCTACAAT[C/T]TGAGCAAAAGCTATTTAAATTGGGGGAAGTCAGTG Y 2 1 2 1 201000 f 74 goat snp36198-scaffold433-398052 6 82628656 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795990 Affx-122953924 AX-385282942 6 80162527 AATAAGCCTGTGCAAAGTTTTCAGAACTCCACTTA[C/T]ATCAGTTTTTTTTAGACTTAATGTCTATGATTCAA Y 2 1 2 1 101000 f 74 goat snp36199-scaffold433-428497 6 82659561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791953 Affx-122952024 AX-385278943 6 80201296 TTTAACCAGCCCATACAGAGTTTTAAGGCCAAGAA[C/T]GGAGAAGAATTGTATGTAGATAAAATGAGGACTTG Y 2 1 2 1 101000 f 74 goat snp36200-scaffold433-467266 6 82698836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438403 Affx-122931288 AX-123308741 6 80245600 TTGACTATTACTTGACTATACTATTACTATTACTT[A/G]TTTGGCAGAGTAATGCCTCTGCTTTTCAACACACT R 2 1 2 1 201000 f 74 goat snp36201-scaffold433-511570 6 82743388 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440987 Affx-122928975 AX-123311324 6 80294542 GTTTGACTTAGCTGATGAGAAAAAGCAAGTAGGCT[A/G]TTTTCAAAAGACCAACCATTATTCAATCCCTGACT R 2 1 2 1 201000 r 74 goat snp36202-scaffold433-560512 6 82794061 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403780 Affx-122957985 AX-123274132 6 80390108 GAAAAGGAAACCAAAATTAAGATTCAAAAAATGAC[A/G]CAGGAATAACCTTCAAAGAACATAGACACATCAGC R 2 1 2 1 101000 r 74 goat snp36204-scaffold433-656078 6 82889736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376800 Affx-122977942 AX-123247159 6 80422272 GCTAAAAGTATACCTACAAAATAACCTGCAACCCT[A/G]CTCCTGAAGGAAACCACAATTCCAAAAGACATATA R 2 1 2 1 101000 f 74 goat snp36205-scaffold433-688242 6 82922388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse282 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38389958 Affx-122968078 AX-123260315 6 80482270 GTTGACTGGATTCCCCTACGATCCACTTAGTTGTT[A/C]TCACTTTTTGGCTACAATGGCTTATCTTTTTTCTC M 2 1 2 1 201000 r 74 goat snp36206-scaffold433-748240 6 82981447 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385706 Affx-122971113 AX-123256064 6 80521898 GTCACTGCAAAGCATTCACAGTGTATCACTTTCCA[C/T]CCTTGTTATATTCTTTTTCAGAAAAATGAGATATT Y 2 1 2 1 101000 f 74 goat snp36207-scaffold433-787868 6 83022313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421376 Affx-122944041 AX-123291723 6 80553631 CCCAATTATAGAAAGGCAGTGTTTAAAAAAAAAGG[C/T]AGTCAAATTGACCAGTTTGATAGATGTCCACTATA Y 2 1 2 1 101000 r 74 goat snp36208-scaffold433-819601 6 83054831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436250 Affx-122932554 AX-123306589 6 80594073 CTTAGCACTTGCAGCCTGTTCTACTTCAGGCCTCT[A/G]CAGTCAGAAGGAGCCTTTAGGTACTTTCATTAACA R 2 1 2 1 201000 r 74 goat snp36209-scaffold433-860043 6 83096251 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407995 Affx-122954320 AX-123278346 6 80625907 GGGACATACCTGACAAAGCACAAGACACATCACAC[G/T]TGCTTGCGTGTTAAGTAGCTTCAGCCATGTCAAAC K 2 1 2 1 102000 r 74 goat snp36210-scaffold433-891877 6 83127761 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405196 Affx-122956917 AX-123275548 6 80705169 CATAATGAGGTCAAGGCAGCAATCAATGTCTGCTG[C/T]GCTGTCTCCTGTTTCTTGAAAGTACAACTGCTTTT Y 2 1 2 1 201000 r 74 goat snp36211-scaffold433-971139 6 83207820 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse283 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38448446 Affx-122923647 AX-123318782 6 80758174 ATATTCAAAACACATGCATCCAGGATTACATTGAG[C/T]AACAATCTGCACATAAAGTTAAACACTGGAGACTT Y 2 1 2 1 101000 r 74 goat snp36212-scaffold433-1024144 6 83262094 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775593 Affx-122935287 AX-385262724 6 80787787 CCTTTTTATGAATACTCCTTCTGATCCTTTTTTTC[A/G]TCTTTTGTTAGTCCCATTATATGTACATTATATAT R 2 1 2 1 101000 f 74 goat snp36213-scaffold433-1053757 6 83291850 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse284 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38449431 Affx-122922680 AX-123319766 6 80837359 GTTCAGTATTTCCCAGGAAGCATACATGATGGGCT[A/G]TGGGAAAGGCAATCTTTCAGTGTTTTCAATAATAA R 2 1 2 1 101000 f 74 goat snp36214-scaffold433-1103329 6 83341218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785054 Affx-122941330 AX-385272101 6 80896456 TGCCAATATCTTGAAAGAAAATGCCAGAATCAATA[A/C]TTAAGCATTCTTTAACCTCTATAAGATAAACCATT M 2 1 2 1 202000 f 74 goat snp36215-scaffold433-1162426 6 83400743 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764962 Affx-122962516 AX-385252541 6 80926961 TTAGTTGAGCTTTTGCCCATTTCTCTTTGTCAGTG[C/T]GTTCAACCTGCAACTCAACAAACATCTCATTTTCA Y 2 1 2 1 101000 f 74 goat snp36216-scaffold433-1192931 6 83432946 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402037 Affx-122958735 AX-123272390 6 80985023 AGGTTTTTTGTGTGTGTGTAATTTCAAGGCTACTG[C/T]GGTTGAACAGCTACTTTGATAGCTTAGCAGTTAAA Y 2 1 2 1 201000 r 74 goat snp36217-scaffold433-1250993 6 83490974 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409766 Affx-122952992 AX-123280117 6 81014570 CCATCAGTTTGATCCCCAAACAATGAAATGCATAG[C/T]ACAAAAAGAGCTTAACTCTGCACATTTGATCTCAA Y 2 1 2 1 201000 r 74 goat snp36218-scaffold433-1280540 6 83520284 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422354 Affx-122943438 AX-123292700 6 81044577 CTCTTTCCAGTAGTTCATTTCCACAAATTGCAGCC[G/T]AGGGAGCAGGAAAGACCACAGGCGGACCCAGAGAG K 2 1 2 1 101000 f 74 goat snp36219-scaffold433-1310547 6 83550716 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420729 Affx-122944769 AX-123291076 6 81074637 CAGTAGTATCATTATTTTGTAGCTAAGGAATATGA[G/T]CATGGGGGCAGTGATGGCTCATCTAGTCAGAATGG K 2 1 2 1 202000 f 74 goat snp36220-scaffold433-1340607 6 83580897 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393196 Affx-122965509 AX-123263553 6 81108353 AGGCTTTTAATAAGACCAGGCAGATGAAGGTTCAA[G/T]CTCCTGTGCTCTGGACACTTACTTCCTTATATCAC K 2 1 2 1 101000 f 74 goat snp36221-scaffold433-1374323 6 83615197 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse285 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38390611 Affx-122967172 AX-123260968 6 81142637 ATAGTAGACAAAAGGTTAATGTTTGCTTGTAAGAA[C/T]GACACAAAATAGAAAACAGGTATTGACTAAGTGCC Y 2 1 2 1 201000 f 74 goat snp36222-scaffold433-1408607 6 83649734 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse286 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320794914 Affx-122936440 AX-385281874 6 81176060 TTCTGAACAAAATCCTCTCCTGCTGGCATGTTTAT[A/G]ACTCACTAGCATTACCTCCTGTATGCCAGAGATAT R 2 1 2 1 101000 f 74 goat snp36223-scaffold433-1442030 6 83683464 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38431431 Affx-122936515 AX-123301772 6 81206252 TACAAAATTTTGTCCTGAATTCAAGAATTTGAGCA[A/G]TCCTTTGACTACGCATATGATCTTTTCTCAAATAT R 2 1 2 1 101000 f 74 goat snp36224-scaffold433-1472222 6 83714089 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406546 Affx-122955114 AX-123276898 6 81239014 AGAAATTAATCACTTCCTCCTACAAGTCTCTCAAT[A/G]TCTTCAACTATCTCCACCCTTCTTGCTTGTTGCGG R 2 1 2 1 101000 f 74 goat snp36225-scaffold433-1504984 6 83747651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273279 Affx-1111833519 AX-519546925 6 81250711 AACAATTTTATAATGAAATGTCAAGCAGTTAAGTG[A/G]TGTGTGCAATAGAATCAAGATGACTTTTGCTGTAA R 2 1 2 1 101000 r 74 goat 6_81250711_AF-PAKI 6 81250711 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396173 Affx-122963774 AX-123266528 6 81297166 ATTCACTGCTTGCCAGGCTAACACCCATCAATTTG[A/G]AAAACTCTGAAATCCTTCTTGACTTTATGCAAGAA R 2 1 2 1 101000 f 74 goat snp36226-scaffold433-1563136 6 83805503 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439212 Affx-122931030 AX-123309549 6 81328007 AATGTCAAGTGAAAAAAGCAACTCCTAGAAGACTG[C/T]ATATTTGGTTTAGCGCCCTTTATATACTCTGCTGC Y 2 1 2 1 101000 r 74 goat snp36227-scaffold433-1593977 6 83836778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436960 Affx-122933168 AX-123307298 6 81407294 TAATAAAAGACCTAGGTACACTTATTTATCTTAAG[C/T]GTACCTTACTTACATGTAAAAATAGAGCTAATACA Y 2 1 2 1 101000 r 74 goat snp36228-scaffold433-1673264 6 83917206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427221 Affx-122939577 AX-123297564 6 81458232 ATTTAACATCACAAATACAAGAGAAATGAATAAAG[C/T]ACAGCAACATGAATGATTATGTTAAACAAAACAAA Y 2 1 2 1 101000 f 74 goat snp36229-scaffold433-1724202 6 83969304 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379070 Affx-122976328 AX-123249429 6 81547288 CTGGGCTTTTGGTAAAAATTTCCTTCCCCACCTCA[C/T]GTTTTCATTACTCTATGTCTTTGGTTATTTTTAAC Y 2 1 2 1 201000 r 74 goat snp36231-scaffold433-1813258 6 84058501 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391033 Affx-122966871 AX-123261390 6 81585781 TTTCACCACGAAAAGGATTTATCAGGCAAAAAATT[A/G]TTTCCCACCTTGGAATTTAGATGACTTAAAGTTGA R 2 1 2 1 101000 f 74 goat snp36232-scaffold433-1851751 6 84097842 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423824 Affx-122942795 AX-123294170 6 81614567 AGTACTGAGTCCTGAGGTCAGGCCTTCATGAACAT[G/T]GTTGGAAAGCAGCCAACCTACTGAGTTTTGGAGCA K 2 1 2 1 101000 f 74 goat snp36233-scaffold433-1880537 6 84126949 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764734 Affx-122938656 AX-385252351 6 81678042 TCTCAGGATCAAGCCACATGAAAAAGGTGTGTTCT[A/G]TTAACATGATTTATATCTCAGCATTAGCCAGTTAC R 2 1 2 1 101000 f 74 goat snp36234-scaffold433-1944012 6 84191264 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442777 Affx-122927735 AX-123313114 6 81714484 AACTATCTTGATTCACAAATGTAAAATTATGGTTC[A/G]TTAATAAAAATTTAAAGGCAAATAAACTTTATTTC R 2 1 2 1 103000 f 74 goat snp36235-scaffold433-1980454 6 84227696 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386255 Affx-122970956 AX-123256613 6 81748393 GAGAGCTAAAAAAGAAAACTGAGAAGAAATAACTG[A/C]GAAGTAAAAGGAAAATCAAAGTGTAGAGGGTTATG M 2 1 2 1 202000 f 74 goat snp36236-scaffold433-2014363 6 84262013 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse287 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38421792 Affx-122944335 AX-123292139 6 81819089 TTCGTGTTTATTTTAGGTTTATTTTCTCTTCTTTT[A/C]TAGTGTCTTAAAAGGAGAGCTTTCTTATTTTATAA M 2 1 2 1 103000 r 74 goat snp36238-scaffold433-2085059 6 84333659 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794111 Affx-122921129 AX-385281077 6 81848962 GGAAGTCTGAAAGGCTGACAAGTATATGGCAGTGA[C/T]GCACAATTGAAATATGCAATAGAAAAATGCAAATT Y 2 1 2 1 101000 f 74 goat snp36239-scaffold433-2114932 6 84363690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431351 Affx-122937049 AX-123301692 6 81884920 TCTTAGCTGTGATCACATAGTTACATGAAGGATAA[C/T]GTTAGATTTAAACTTGGGATTCCTCACCACCTGGG Y 2 1 2 1 101000 f 74 goat snp36240-scaffold433-2150890 6 84399935 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse288 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38429793 Affx-122938204 AX-123300134 6 81977976 AAGGTAAAAATAAACAAAAGATCCATGCTTAGACA[C/T]GATCAATTGCTTGTCCCCTTCCTCCAGGAAATCGA Y 2 1 2 1 101000 r 74 goat snp36242-scaffold433-2243946 6 84494753 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773242 Affx-122936106 AX-385260385 6 82024869 GGTTAGACTAAGCAGGTGTTTGAACAAAATTACTC[A/G]TCAAATATCAGTTATTAATTTCCGAGTCTGTAAAA R 2 1 2 1 201000 r 74 goat snp36243-scaffold433-2290839 6 84550454 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779534 Affx-122949776 AX-385266637 6 82061120 ATGTCTCTATCATTTGAGCACTGAAATGAATGGTT[A/C]TGTCATTTACTTATATCTCAAAAGCAATGTTCTTT M 2 1 2 1 101000 f 74 goat snp36244-scaffold433-2327090 6 84587097 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse289 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38431202 Affx-122937165 AX-123301543 6 82103759 CCTTACTGGTTAATATTCAAGGTCCTTAGAATGCC[A/G]TTTCTTTTTACCAATACTGTTCCATTATAGCGTGC R 2 1 2 1 101000 r 74 goat snp36245-scaffold433-2369729 6 84630329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789356 Affx-122963438 AX-385276366 6 82144111 CAGAAAAAAAGGTCTCAGCTCAGCTATTGCACAGG[C/T]AGAAGCCTTGGAGGTTCTAATTTAAGAAAATGTTA Y 2 1 2 1 101000 f 74 goat snp36246-scaffold433-2410081 6 84670923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392211 Affx-122966277 AX-123262568 6 82192038 ACAAACTACCCAAATTATGTCTGTCTCCACCCTCA[A/G]TTTCCCATACATTCTGAAATTATCTTCTCTTCCTT R 2 1 2 1 201000 r 74 goat snp36247-scaffold433-2458008 6 84718350 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778852 Affx-122940132 AX-385265960 6 82230438 GTTGCCAAATGGCCCTTACACATCCTCTTGTGTAT[A/G]CACAAGCTCTCATTATGTGTGACAAACGCAGAATG R 2 1 2 1 201000 r 74 goat snp36248-scaffold433-2496408 6 84756937 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse290 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38403876 Affx-122957918 AX-123274228 6 82275459 GTGGCTAATTCTGGGCCTTGGTTTTAGTCTTTCTG[C/T]TATACAAATTAGCAACCATCAATAACTACTGTCTT Y 2 1 2 1 201000 r 74 goat snp36249-scaffold433-2541429 6 84803252 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449740 Affx-122922462 AX-123320075 6 82332256 AAGCAGTGTCTTTTAGATAACAGATGATGATGATA[C/T]AGGGGAAACTTCATTTAAACTGCTTTCAGAACTCA Y 2 1 2 1 201000 f 74 goat snp36250-scaffold433-2598226 6 84859302 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432712 Affx-122936019 AX-123303053 6 82377438 TTATTTTTAAATCACTTCATGGGATATCTGCTTTC[G/T]AGGATTTTGCTGGAGAGCATGATCTTGATGTGTTA K 2 1 2 1 101000 r 74 goat snp36251-scaffold433-2643408 6 84905253 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428657 Affx-122938655 AX-123298999 6 82423194 ACATCTTTACAGCTTTGTTGCCTCATGAAATTGCC[A/G]TTCCTTTATCCTCTTCCTTAAATTTTTAGGTACTC R 2 1 2 1 101000 f 74 goat snp59410-scaffold980-39769 6 85723685 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409208 Affx-122953168 AX-123279559 6 82559703 TGGTCACTTTTTCTTCTCTATTTCCATATATTGAA[C/T]ATACTGATATTATTTTATATATTTTAGTATTTTGT Y 2 1 2 1 103000 f 74 goat snp59413-scaffold980-176278 6 85861248 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse291 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320776654 Affx-122933865 AX-385263781 6 82612388 CCAATAAACAGGCATCCGTGATTCTTAGCAAAGTC[A/G]TATGGGAAAGAATGTTTCTTCGGAGAACAACAGAG R 2 1 2 1 101000 f 74 goat snp59414-scaffold980-228963 6 85913548 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794276 Affx-122977634 AX-385281241 6 82646152 CATATAAAGGGACATGATAGTATTACTATCTGTTA[C/T]GATAATAATTTTACTGTCTTTGTTTTTTTCTGAAA Y 2 1 2 1 201000 r 74 goat snp59415-scaffold980-262727 6 85946764 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383903 Affx-122973111 AX-123254261 6 82677412 TAGCTCAGAAGCAAAAGTCTGCCATCACCTTGATC[A/G]TCAACCCAGCTTGCTGCTTCTTCCCAGTCTTGGGT R 2 1 2 1 102000 f 74 goat snp59416-scaffold980-293987 6 85978529 A G 1 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse292 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320798890 Affx-122967647 AX-385285820 6 82678598 AAAACCTTACTATTACTTTCAGGATCAAATGCTTT[A/G]CTTTGAAGTGTAGTAAGATATTGATATTTCTTATC R 2 1 2 1 201000 r 74 goat snp59417-scaffold980-295173 6 85979715 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse293 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350603665 Affx-122931499 AX-413837802 6 82678888 CATCCTTACCTGTCTTGTGGCTGTTGCTCTTGCCA[A/G]GCCTGTGAGTACAGTAAAGAATTTAGAAGATTCTA R 2 1 2 1 400000 f 74 goat snp59418-scaffold980-295463 6 85980005 A G GoatSNP50 chip SNPs in specific regions/genes CSN1S1 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 38404336 Affx-122957000 AX-123274688 6 82679453 ATGAAAGCAAAAAGTGAAAGAGAAGTCTCTTAGTC[A/G]TGTCCTACTCTTCGCGACCCCATGGACTGCAGCCT R 2 1 2 1 103000 f 74 goat snp59419-scaffold980-296028 6 85980570 A G 1 not_recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 532567209 Affx-122945173 AX-579205702 6 82680594 TTGCATTTTTTTTTTAACAGAAACATCCTATCAAT[A/C]ACCAAGGACTCTCTCCAGTGAGTGTTCTTTTCTGT M 4 1 2 1 303000 f 74 goat "snp59420-scaffold980-297169;snp59995-CSN1S1-ex3-1;SNPs_063" 6 85981710 "A;C" "A;C" 3 not_recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 320781563 Affx-122965474 AX-385268648 6 82681499 TTTACAATTCACAATTTAATTCCTACAGGAAGTCC[C/T]CAATGAAAATTTACTCAGGTTTGTTGTGGCGGTAA Y 2 1 2 1 201000 r 74 goat "snp59421-scaffold980-298074;SNPs_064;UniBern-var4" 6 85982615 "C;T" "C;T" 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S1 10.1371/journal.pone.0086227 320798954 Affx-122966240 AX-385285884 6 82681531 TCCTCAATGAAAATTTACTCAGGTTTGTTGTGGCG[A/G]TAAGTATTATCTACTTCTTCTTCAATGACAAATGT R 2 1 2 1 202000 r 74 goat "snp59422-scaffold980-298106;SNPs_065" 6 85982647 "A;G" "A;G" 2 neutral GoatSNP50 chip SNPs in specific regions/genes CSN1S1 10.1371/journal.pone.0086227 320780399 Affx-122957941 AX-174390636 6 82686324 GAAGTACATTCAAAAGGAAGATGTGCCCTCTGAGC[A/G]TTACCTGGGTTATCTGGTAAAATTTTATTAAAAGT R 2 1 2 1 101000 f 74 goat snp59424-scaffold980-302899 6 85987327 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S1 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 320785113 Affx-122950393 AX-385272158 6 82687681 ATATATTTTTCTCTTTGAATAGGAACAGCTTCTCA[A/G]ACTGAAAAAATACAACGTGCCCCAGCTGGTAATGT R 2 1 2 1 201000 r 74 goat "snp59425-scaffold980-304256;SNPs_068;UniBern-var7" 6 85988705 "A;G" "A;G" 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S1 10.1371/journal.pone.0086227 38385044 Affx-122971835 AX-123255402 6 82690713 ACATTGCTGGTTCCAACATTGCTATGAAAGATCAG[A/C]TCTAAGTTGCCAAAGGAAATGAAAGAACAATTCTA M 2 1 2 1 101000 f 74 goat snp59426-scaffold980-307288 6 85991743 A C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse294 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38412851 Affx-122950450 AX-123283200 6 82692557 TGGTCCTCTAGTCTAGCTATATTTAGACACATTAC[A/G]CTTAGATAATATCAATAATTAAATTGGCTTCAACA R 2 1 2 1 101000 f 74 goat snp59427-scaffold980-309132 6 85994216 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse295 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320771066 Affx-122973645 AX-385258226 6 82693835 ACTGTTTATAGAATATTTTCCATGTGAACATGGAT[A/G]TGGCTGCAGAGAGAACAACAGTGTAGTAGTTGTGG R 2 1 2 1 102000 r 74 goat snp59428-scaffold980-310410 6 85995496 A G 1 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse296 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320778614 Affx-122969566 AX-385265725 6 82693948 TGCAGGACTTGTTGGAGCCCAATCCATTTGATTAT[A/G]CTTGAGTTTATAACTAGGTAGATTATAAAATAAAC R 2 1 2 1 101000 f 74 goat snp59429-scaffold980-310523 6 85995609 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse297 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320782209 Affx-122969125 AX-385269287 6 82694478 TGGACCTGGCAGAAGTTAATGGAGGGTGCAGATTC[A/G]TACGTCTTCATAAAATGTATCTCCCAGCTTCTGTC R 2 1 2 1 101000 f 74 goat snp59430-scaffold980-311053 6 85996139 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse298 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320796084 Affx-122960451 AX-385283036 6 82694935 CTATTTTAAAGGCCAAATGAGGAAGTGGAATAATG[A/G]TGTAATTCACTATCTTTTAGTCTTTGCATCTTTTA R 2 1 2 1 101000 f 74 goat snp59431-scaffold980-311510 6 85996594 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse299 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320774639 Affx-122925923 AX-385261773 6 82694972 GTAATTCACTATCTTTTAGTCTTTGCATCTTTTAG[C/T]GTTCAACAGCTGTAATTCCCCCATAAATGCAAATT Y 2 1 2 1 101000 r 74 goat snp59432-scaffold980-311547 6 85996631 T C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse300 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320798536 Affx-122952944 AX-385285469 6 82706793 TAGAGACTGTGCCTGGGCAAAGGGGTGGATTTTAT[G/T]CTGGAGTTCATCCTGGAAAGAAGGAAAAAAAATCT K 2 1 2 1 201000 r 74 goat snp59437-scaffold980-323368 6 86008407 G T 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN2 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 320789717 Affx-122966021 AX-385276725 6 82707198 AAAAGACTTAAAAAGTTACTCTGAGGTTTATTTTT[A/G]TTTGTTTTAATGGAAACTAAGTCTTAATATGTGTT R 2 1 2 1 202000 f 74 goat snp59438-scaffold980-323773 6 86008812 A G 2 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse302 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38402573 Affx-122958444 AX-123272926 6 82707736 AATTTACAGGTGAAGAAAATGATGTACAGAGAAAC[A/G]TGGAGCCAAGGTTATACAGCTGATAAATGATCAAA R 2 1 2 1 101000 r 74 goat snp59439-scaffold980-324311 6 86009350 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse303 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38397388 Affx-122962267 AX-123267743 6 82708253 TATAAAAATCAAACACAAAATTTTTAAAAATGTAC[A/G]TTTAAATATGAAGGTTTTACCTTATTGATGTGTGT R 2 1 2 1 103000 r 74 goat snp59440-scaffold980-324828 6 86009867 A G 1 not_recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38391027 Affx-122966875 AX-123261384 6 82708778 CAACTTTGCATGCATACCTGTCCCTCAATCACCCT[A/G]TTTTCTCCTTAGGAAAACAAATGATCTCTGATATT R 2 1 2 1 202000 r 74 goat snp59441-scaffold980-325353 6 86010392 A G 2 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse304 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38444710 Affx-122926423 AX-123315047 6 82748317 GTCATAAAAACAAAAGCAGCCCCAGTTTAAGAAGT[A/G]CAGCCTGGTGTAGCTCTCTTAAACTGTACTCATTT R 2 1 2 1 102000 r 74 goat snp59442-scaffold980-364892 6 86050148 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438782 Affx-122931376 AX-123309119 6 82774413 CAGACGGTAAAGCATCTGTCTAAAATGCAGGAGAC[C/T]TGGGTTCGATCCCTGGGTCGGGAAGATTACCTGGA Y 2 1 2 1 103000 f 74 goat snp59443-scaffold980-390988 6 86076276 T C 1 not_recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S2 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 38418052 Affx-122946626 AX-123288400 6 82779273 GAAAATTGGAAGTGCAACCACAACGAAAAAGTATA[G/T]AGAGAGGAATAAAGACCAAAAATCTACACATTCAA K 2 1 2 1 101000 f 74 goat snp59445-scaffold980-395848 6 86081135 T G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38454002 Affx-122919436 AX-123324335 6 82782072 GAGAACCATAGCCTCGGCTCAGAGCCTTGAGGCTG[A/C]GCCTGAAGACTTCCTGCTTAACATCTAGGAAGCCT M 2 1 2 1 101000 r 74 goat snp59447-scaffold980-398647 6 86083934 A C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse305 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38398635 Affx-122961462 AX-123268990 6 82782776 GTTAATCCTCCTTTTCTTCCCTGAAGGAATCTGCT[A/G]AAGTTGCCCCAGAGGTAACTAATTTTCATTCAAAT R 2 1 2 1 201000 r 74 goat "snp59448-scaffold980-399351;SNPs_077;UniBern-var13" 6 86084638 G A 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S2 10.1371/journal.pone.0086227 538942989 Affx-122973451 AX-585490104 6 82783272 GTATCCGTATCAAGGTCCAATTGTTTTGAACCCAT[A/G]GGATCAGGTTAAGAGAAATGCTGGCCCCTTTACTC R 4 1 2 1 400000 r 74 goat "snp59449-scaffold980-399847;SNPs_079" 6 86085134 G A wobble probeset GoatSNP50 chip SNPs in specific regions/genes CSN1S2 10.1371/journal.pone.0086227 38390323 Affx-122967706 AX-123260680 6 82784092 CAGAACAAATATGTACACATTGAAGGATACAAAGA[C/T]TGGATCTGTGCTCGTATACTTTGTCAAAATGCTGT Y 2 1 2 1 101000 r 74 goat snp59450-scaffold980-400667 6 86085957 T C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38402145 Affx-122958659 AX-123272498 6 82786023 TGATCCCTGGCTTGAGAAGATTGCCTGAAGAAGGG[C/T]ATGGCAACCCATTCCAGTATTCTTGCCTGGATATC Y 2 1 2 1 103000 f 74 goat snp59451-scaffold980-402598 6 86087888 C T 1 not_recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38383623 Affx-122972548 AX-123253981 6 82786136 CAAAGAGTCACATAGGACTGAAGTGACTTAGCATG[A/G]AGGGAGGCACAGCCATTAAAAAAACAATGGTTTTC R 2 1 2 1 201000 r 74 goat snp59452-scaffold980-402711 6 86088001 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38400335 Affx-122960047 AX-123270690 6 82786576 CTGATTTTCTTTTTTTTTTCCATAAGGAATCAACA[A/G]AAGTATTCACTAAGGTAAGTAATTTCCTATCAAAC R 2 1 2 1 201000 r 74 goat snp59453-scaffold980-403151 6 86088442 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN1S2 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 320772971 Affx-122961824 AX-385260115 6 82786730 GAAGAAGAAAAGAATCGCCTAAATTTTCTGGTAAA[C/T]TTTTATACAAACATGTGAGCACACTCAGACTCAGC Y 2 1 2 1 102000 r 74 goat snp59454-scaffold980-403305 6 86088596 T C 1 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse306 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320776854 Affx-122959763 AX-385263978 6 82791242 GAAAAAAAATAATAACATTCTGCTAAACTAGTATG[A/G]ATGAGTATGTGTGGGTTCTGTATACAGACATACAT R 2 1 2 1 101000 r 74 goat snp59455-scaffold980-407817 6 86093184 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 snp-genphyse307 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320767829 Affx-122921209 AX-385255051 6 82791406 CACTTTACTTCATACAACCAGCATGTTTGGGGTGG[C/T]GCATCAATAAGACAAATCGCAGAGTATTTCCTGAA Y 2 1 2 1 101000 f 74 goat snp59456-scaffold980-407981 6 86093348 T C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 320782988 Affx-122960441 AX-385270057 6 82817980 TTTAGGACAATCTTTCAGCTGCTGAAAAAATAGCC[G/T]CATAATAATCTCAACCCTTTAGAAATTTGTTGTCT K 2 1 2 1 101000 f 74 goat snp59458-scaffold980-434555 6 86118792 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse308 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38433337 Affx-122935152 AX-123303678 6 82852913 AGTGATCTAACACATTTTTTTTTAATTCTAACAGA[C/T]GCCATTCTATACTGAATTTGGATATATTCCACAAG Y 2 1 2 1 101000 r 74 goat snp59459-scaffold980-469488 6 86155434 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse309 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320788579 Affx-122968481 AX-385275596 6 82896008 GTGTGTGCTCTTTATCAAGCCTGAACTTCTAACTC[C/T]GTGACCCTAGTCTGTAAAACTCAGTTTGCAGGTTT Y 2 1 2 1 101000 r 74 goat snp59460-scaffold980-512583 6 86198530 C T 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38442876 Affx-122927663 AX-123313213 6 82898948 GGAGAAATAGCAATAACCTCAGATATGCAGATGAC[A/G]TCACCCATATGGCAGAAAGCAAAGAAGAACTAAAG R 2 1 2 1 303000 r 74 goat snp59461-scaffold980-515523 6 86201470 G A 3 not_recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38399057 Affx-122960902 AX-123269412 6 82900719 CATTTTTTGATAAACCTTTAAAAGTTAACAATAAA[A/G]AACAAACATTTCATGATATAACCAATGATTGTTTT R 2 1 2 1 201000 f 74 goat snp59462-scaffold980-517294 6 86203242 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 320800979 Affx-122970898 AX-385287893 6 82901201 CACCTTTTGTAAGTTTTAAAGCTTCATATAGATAT[A/G]CCTGGAGACTACTTTCTCACTCCTGATTTCCTATG R 2 1 2 1 101000 r 74 goat snp59463-scaffold980-517776 6 86203724 A G 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 320798338 Affx-122976794 AX-385285273 6 82901438 TTTCTCCCCTTCTTTTTAGCAATATATATTCAATA[C/T]AAATTGAATATAGGTTGTTCATGTTCTTCATTTAA Y 2 1 2 1 102000 f 74 goat snp59464-scaffold980-518013 6 86203961 C T 1 neutral GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38443804 Affx-122927082 AX-123314141 6 82905902 TTTTTGCAGTGCTGTGAGAAAGATGAAAGATTCTT[C/T]GATGACAAAATAGCCAAATATATCCCAATTCAGTA Y 2 1 2 1 101000 r 74 goat "snp59465-scaffold980-522477;SNPs_083" 6 86208883 C T 1 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 38449622 Affx-122923196 AX-123319957 6 82905977 CTGAGTAGGTATCCTAGTTATGGACTCAATTACTA[C/T]CAACAGAGACCAGTTGCACTAATTAATAATCAATT Y 2 1 2 1 101000 f 74 goat "snp59466-scaffold980-522552;SNPs_085" 6 86208958 "C;T" "C;T" 1 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 38434729 Affx-122933924 AX-123305070 6 82905979 GAGTAGGTATCCTAGTTATGGACTCAATTACTATC[A/G]ACAGAGACCAGTTGCACTAATTAATAATCAATTTC R 2 1 2 1 201000 r 74 goat "snp59467-scaffold980-522554;SNPs_086" 6 86208960 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 320793820 Affx-122972546 AX-385280791 6 82906006 TTACTATCAACAGAGACCAGTTGCACTAATTAATA[A/G]TCAATTTCTGCCATACCCATATTATGCAAAGCCAG R 2 1 2 1 201000 f 74 goat "snp59468-scaffold980-522581;SNPs_087" 6 86208987 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 320777525 Affx-122955707 AX-385264644 6 82906041 ATCAATTTCTGCCATACCCATATTATGCAAAGCCA[A/G]TTGCAGTTAGGTCACCTGCCCAAACTCTTCAATGG R 2 1 2 1 201000 r 74 goat "snp59469-scaffold980-522616;SNPs_090;UniBern-var17" 6 86209022 "A;G" "A;G" 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 320778152 Affx-122921659 AX-385265267 6 82906078 TGCAGTTAGGTCACCTGCCCAAACTCTTCAATGGC[A/G]AGTTTTGCCAAATACTGTGCCTGCCAAGTCCTGCC R 2 1 2 1 102000 f 74 goat snp59470-scaffold980-522653 6 86209059 A G 1 neutral GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 38402882 Affx-122958222 AX-123273235 6 82906116 TTTTGCCAAATACTGTGCCTGCCAAGTCCTGCCAA[A/G]ACCAGCCAACTACCCTGGCACGTCACCCACACCCA R 2 1 2 1 102000 f 74 goat "snp59471-scaffold980-522691;SNPs_091" 6 86209097 "A;G" "A;G" 1 neutral GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 38379413 Affx-122976117 AX-123249771 6 82906203 CCATTCCACCAAAGAAAGATCAGGATAAAACAGAA[A/G]TCCCTGCCATCAATACCATTGCTAGTGCTGAGCCT R 2 1 2 1 201000 f 74 goat "snp59472-scaffold980-522778;SNPs_093;UniBern-var18" 6 86209184 A G 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN3 10.1371/journal.pone.0086227 532567196 Affx-122933267 AX-579205689 6 82906784 CTTAGAAAAAAATCATATAGGCTATGAGTTTAAAT[A/G]CATTTTAATTGTATACCAGTGTTGTTGCACTCTAC R 4 1 2 1 101000 r 74 goat "QTLcaseins6.16;snp59473-scaffold980-523359" 6 86209768 A G 1 wobble probeset "not_recommended;recommended" GoatSNP50 chip candidate gene ou candidate region 10.1371/journal.pone.0086227 320772265 Affx-122925726 AX-385259421 6 82907013 ACCTACTTATTAAGAGGAAACTTTCAGAACTTTAA[C/T]GTAAAATATGTCTATTTATTATTTGGATCAATGGA Y 2 1 2 1 101000 r 74 goat snp59474-scaffold980-523588 6 86209997 T C 1 recommended GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 38437282 Affx-122931990 AX-123307620 6 82965046 TTATGCCACAGCTCATATAATTTTCCTAAATGATT[A/C]TGGGAATCAGGAAGGGAAGGGAAGTAGGATGCTTC M 2 1 2 1 201000 f 74 goat snp59475-scaffold980-581621 6 86266392 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse311 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38391193 Affx-122967421 AX-123261550 6 82995053 ATATTCCATAGTTCTTCTAAGTATTACAAAGTTGC[A/G]CCAGTTGTCAAAATGAAAAAAGGCATCATAACAAA R 2 1 2 1 101000 f 74 goat snp59476-scaffold980-611628 6 86296958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776969 Affx-122926575 AX-385264093 6 83033912 CTTCAAATCCTGATCATTTATATGCAACTTCTTAT[A/G]TGGAAGAGGAGATAAAACTAAAATTTCTATTTCCA R 2 1 2 1 101000 r 74 goat snp59477-scaffold980-650487 6 86335455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774150 Affx-122968702 AX-385261288 6 83102610 AGAACTTTTCCTGATCCTCTTGGCCTCATCCAAAG[A/C]TTGGAGACTTTTTATGTCATCAAGAAGAAGAGGTC M 2 1 2 1 102000 f 74 goat snp59478-scaffold980-719185 6 86403944 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse312 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320771575 Affx-122973607 AX-385258734 6 83140158 ACTGATATGAACAAGTGATGCATTGTTCCTTTTCC[C/T]GTGACTGACTTGATTCTTGCTTTCCCTTTCTGAGA Y 2 1 2 1 201000 f 74 goat snp59479-scaffold980-756733 6 86441696 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783016 Affx-122975938 AX-385270084 6 83189194 CCTGTAGTTGAATATGTTCCTGTTACCTTATTTTC[A/G]TACTGGCCAATAGGAGGAAAGAAGGGTCAACTCTC R 2 1 2 1 101000 r 74 goat snp59480-scaffold980-805769 6 86490795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378141 Affx-122976983 AX-123248500 6 83228568 GTTACTTTCAACTTTTATGACATGATCATGAGACC[C/T]GCTGCAGGGGAAAAAAATCGACTTCATCAATTTTA Y 2 1 2 1 201000 f 74 goat snp59481-scaffold980-845143 6 86530449 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse313 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38418905 Affx-122946095 AX-123289253 6 83280940 GAGAAAGCGAAAGTTCTTCATCCTGCCTCAGGAGG[C/T]AGGAAAGGCTTTTCAGGTGACATTTAAAGTCAATC Y 2 1 2 1 202000 f 74 goat snp59482-scaffold980-897515 6 86583042 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389915 Affx-122968109 AX-123260272 6 83315589 TCTAAACTGGAGGCTCCTCCTTAGGCAGCAGTGGC[C/T]CTCAAGTTTCTTGTTCTGCCCAGCAAAGCCCTATT Y 2 1 2 1 101000 r 74 goat snp59483-scaffold980-932164 6 86617703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439487 Affx-122930155 AX-123309824 6 83421411 ACCTCTGGATACAGAGGGCTGACTATCAGACTTGA[G/T]CATTCATGGATTCTGGTATCCATGACGCGTCCTGG K 2 1 2 1 303000 r 74 goat snp59485-scaffold980-1037986 6 86723586 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse314 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38413996 Affx-122950278 AX-123284345 6 83451593 TCTTCCTGCCCACTATGGGCTTTATTTTACTAAGT[C/T]TCTTTGTCCTGTACTCAAATAGAATGATTGGTGTG Y 2 1 2 1 101000 r 74 goat snp59486-scaffold980-1068168 6 86753883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382344 Affx-122973881 AX-123252702 6 83485578 TGGAGGTAGAGTCCACCAGGGTCGCAAAGAGTAGG[A/G]CACAACTGAGCATTTAAGCAGTAGTAAACCATTAA R 2 1 2 1 103000 r 74 goat snp59487-scaffold980-1102153 6 86788148 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398074 Affx-122961734 AX-123268429 6 83518784 TCACTGTGCCAGAATCTCAGGTGCCTGCTTCTGAG[C/T]ATTCCTTGAAAAAGAGGTATTGGGAAGTAAGGACA Y 2 1 2 1 101000 r 74 goat snp59488-scaffold980-1135359 6 86822427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451496 Affx-122921122 AX-123321829 6 83553692 TCCGTGCTAAAGCTGCACATGTCAGGGTCTGTGGT[A/G]TTATAAAGAGAAAATTAGTATTATGACTGTTAAAG R 2 1 2 1 201000 r 74 goat snp59489-scaffold980-1170267 6 86858086 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787442 Affx-122953134 AX-385274467 6 83601195 CCATTATCTAGTGGGAGAATTCCTACATTATTAAT[C/T]TGATATAGGGATCTACCCTTCTGTGGGTAAACAGC Y 2 1 2 1 201000 f 74 goat snp59490-scaffold980-1217770 6 86905715 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394629 Affx-122964402 AX-123264984 6 83648311 GGGTTAGAATATCTTTATAAGGACTTTTTAAGACA[C/T]GAAAGAAAGACATCATGATACAATGGGAAAGAATA Y 2 1 2 1 101000 f 74 goat snp59491-scaffold980-1264886 6 86946899 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385744 Affx-122971081 AX-123256102 6 83691916 GCGAGAAGAAATGAGATGTTGGCCGTATTCCAAAT[A/G]CTATAATCGTCCCATGAATAAATGAGAGTTGATGC R 2 1 2 1 101000 r 74 goat snp59492-scaffold980-1308491 6 86990478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377051 Affx-122978300 AX-123247410 6 83727693 ATTTCTCTTCTCTTAGTCAAATGAGATGATATTTT[A/G]TCTAACGATCCTAGTTGATTTTGCAAAGGTCATTG R 2 1 2 1 101000 r 74 goat snp59493-scaffold980-1344268 6 87026491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse315 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38414578 Affx-122949375 AX-123284927 6 83761149 TTAGGGTTAGGGACCTAAAGCTTGCAGAAGTGAGT[A/G]ACTCTCCTGACATTACATGGTTGGCAAGTGGTATT R 2 1 2 1 101000 f 74 goat snp59494-scaffold980-1377724 6 87059365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse316 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38381750 Affx-122974319 AX-123252108 6 83792644 GATCATTTCAGATGTTGCTCCAGTTCTTGACACAT[A/G]CTTAAAACTCTGCTCTCTCAGATTAAAATGGAGAA R 2 1 2 1 101000 f 74 goat snp59495-scaffold980-1409219 6 87091435 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273234 Affx-1111833520 AX-502851688 6 83819304 CAGCTTTGTTCACAGTCCAACTCTCACATCCATAC[A/C]TGACCACTGGAAAAACCATAGCCTTGACTGGACAG M 2 1 2 1 103000 f 74 goat 6_83819304_AF-PAKI 6 83819304 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38439591 Affx-122930067 AX-123309928 6 83926387 TTTCAACCACAGAAATGTAATGTTTACTCTAATTC[A/G]TTAATAAAGAAAAAAAGCTTCTGGTTAAAAATAAC R 2 1 2 1 103000 f 74 goat snp59498-scaffold980-1542962 6 87224612 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409487 Affx-122954053 AX-123279838 6 83981411 GGGTCATTCTCTAGAAAATGAGATTCAGAAAAAAA[C/T]AGGTTGACATCTCTTTTCATGAGATTGAGCTCAGT Y 2 1 2 1 303000 f 74 goat snp59499-scaffold980-1597986 6 87277378 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378805 Affx-122976561 AX-123249164 6 84037381 TTCAAAGGACTCCTGAAGCAACTTAACTCAATATT[C/T]CAGCCTTTGAGTAGATAAAACTACCTGTACCTTCA Y 2 1 2 1 101000 r 74 goat snp59500-scaffold980-1653956 6 87333480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792150 Affx-122937329 AX-385279135 6 84079917 TGTTCTCAAACGATGTAATTATTTCACATCACACA[C/T]GTGGCTCTAAGCAATGGAACCCAGAGCAATTTGCA Y 2 1 2 1 101000 r 74 goat snp59501-scaffold980-1696492 6 87375339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382012 Affx-122974066 AX-123252370 6 84137740 TAAAAATCTCAGTGGCTTGTAGGGCAGTCATTAAG[C/T]ATCCTTTGTAGGTGTGAGGAGGAGCTGGGCTGAAC Y 2 1 2 1 101000 f 74 goat snp59502-scaffold980-1754315 6 87432628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441000 Affx-122928963 AX-123311337 6 84192693 AAGACAGATGGCATGCTTCTTGCATGGGCAAGGGG[C/T]ATTACAAGGTAACCTGTCCCTGAGCTGACTTAAAT Y 2 1 2 1 101000 r 74 goat snp59503-scaffold980-1809268 6 87486240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772929 Affx-122932069 AX-385260073 6 84227645 AATTAATAACAGAAATGATGAACAGCTCTTTGAAG[C/T]GAGTTTGTTTTGTCCTAGAAATATTGAAATGGAGT Y 2 1 2 1 101000 f 74 goat snp59504-scaffold980-1844220 6 87520973 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427405 Affx-122940071 AX-123297748 6 84268596 ACTATCAATACTGCAGGCTGCTTTGTGCAACATGA[C/T]TTTTGTTCCTGCAAAAACAATGCTTTTGGAATTCC Y 2 1 2 1 201000 r 74 goat snp59505-scaffold980-1885171 6 87562196 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389576 Affx-122968788 AX-123259934 6 84313021 CTTGAACAGAAAAAGGCTGTTTCATAGTAATGGAA[A/C]TTTTGCTCTAGTACACAGGAAACTGGAAAACACAT M 2 1 2 1 101000 f 74 goat snp59506-scaffold980-1929596 6 87607436 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426647 Affx-122939941 AX-123296993 6 84346966 AAACAATCTCTGAAGAGAAAACAAATAGCCAAAAA[C/T]TCAAAGCTGAACTTCAGAATTGGTAACTTGTCTTT Y 2 1 2 1 101000 r 74 goat snp59507-scaffold980-1963541 6 87643025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404988 Affx-122956397 AX-123275340 6 84380353 CTTTTATGAACAAAACAAGTTTGTTAGAAGCTTTT[C/T]CTTCTTTGTGTTTACATGAAGTCTGGTGATGTGAT Y 2 1 2 1 101000 r 74 goat snp59508-scaffold980-1996928 6 87676522 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375789 Affx-122978576 AX-123246148 6 84422150 ACCATATTGGAAAGAGAGAAAGAAAATAAATACAG[C/T]AAATGTTAACAAGTGTGGAATTTGGGTGATATTCT Y 2 1 2 1 103000 r 74 goat snp59509-scaffold980-2038725 6 87717740 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774428 Affx-122971253 AX-385261564 6 84465351 TTACCTAAGATAACTGAGCTTGGCTACTAGTCTAC[A/G]TGGTTGACTATTTTTCCTATAGTTCACTGTGACTT R 2 1 2 1 101000 f 74 goat snp59510-scaffold980-2081926 6 87763555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476223 Affx-1251763728 AX-586011647 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 4 1 4 1 20000 f 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 539476477 Affx-1251763728 AX-586011877 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20000 r 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 560378499 Affx-1251763728 AX-605230914 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20000 r 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 562165719 Affx-1251763728 AX-606941128 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20100 f 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 562166039 Affx-1251763728 AX-606941448 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20100 r 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 562166531 Affx-1251763728 AX-606941939 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20100 f 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 562166558 Affx-1251763728 AX-606941966 6 84500970 TATTACACTCAACACATGATGTGATTTTTTTTATT[-/CTAAAGATAATGTTTTCGGAAAGAAACATGCCACCACAGTTTTTAAAAAAAATAAATAAATAAATAAAATGAAAAAAAAA]TAAAGATAATGTTTTCATTCTTTTTAAAAAAATAT - 8 1 4 1 20100 r 74 goat SV_336 6 84500970 - deletion junction SV-TF-chip 38400305 Affx-122960069 AX-123270660 6 84501582 TTTCCCTGCCTCCAGTGGAGAGGAGATGAGAGAAG[C/T]GCAGAGAAATTCCTCCCACGTGTTCAAGTGGCCAT Y 2 1 2 1 201000 r 74 goat snp59511-scaffold980-2118157 6 87799841 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439437 Affx-122930189 AX-123309774 6 84559123 GCATAGCTATTTGAAACTTCTCCCCTGGTGGTTCA[G/T]CGGGTAAAGAGCATGCCTGCCAATGTAGGAGACAC K 2 1 2 1 103000 f 74 goat snp59512-scaffold980-2175698 6 87856692 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420770 Affx-122944709 AX-123291117 6 84588611 CCCCTTTTCTCTAAACATGAATATGAGCAAAGGCT[A/G]TCACTGGCATCAAGGAGGAGCATATATCAAATCTT R 2 1 2 1 201000 r 74 goat snp59513-scaffold980-2205186 6 87885937 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430131 Affx-122937399 AX-123300472 6 84621575 AGTTGACTTTTCATGGTTTCATTTACCAGTGGTCA[C/T]CTGCACTGGTCCAAAAATGTTAAAAGGCAAATTCC Y 2 1 2 1 101000 f 74 goat snp59514-scaffold980-2238150 6 87918880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403531 Affx-122957614 AX-123273884 6 84650125 CTAGACATTTCTTTTATTACATCTTCATTGTCACC[A/G]TAAAACTGACTCTAGCTTTTTTAGCCCCCATAAAA R 2 1 2 1 101000 f 74 goat snp59881-scaffold996-25451 6 87947726 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768903 Affx-122971413 AX-385256080 6 84681534 AATTTCTTGTTTTCAACTATGAAGTGTTACTATTG[C/T]GAGAGAATTCTGTCTAGGCTAGCTCCATTGTGGAG Y 2 1 2 1 101000 r 74 goat snp59882-scaffold996-56860 6 87977497 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453645 Affx-122919733 AX-123323978 6 84721124 ACAATCTTGTTTTTTTAAATAGGCCACCCCATCTA[C/T]GTGAATGGCACCATTATCCAGTAGTATTCAAACCA Y 2 1 2 1 201000 r 74 goat snp59883-scaffold996-96450 6 88017071 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404368 Affx-122956810 AX-123274720 6 84762610 CTAGTAGAAATCTAAACTGGTGAAAACAGTGCAAT[A/G]TTGATGCAAAGGCTGACAAAGAGGCCAGTGGGAGA R 2 1 2 1 201000 f 74 goat snp59884-scaffold996-137936 6 88058923 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434637 Affx-122933995 AX-123304978 6 84799567 GCTGGAAGACTGGGAAGGGAAAGGAAAGTAGCTGT[C/T]AGATACTAGGATTGTTGCACCAAAAATATAAAGAG Y 2 1 2 1 201000 r 74 goat snp59885-scaffold996-174893 6 88098811 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395243 Affx-122964471 AX-123265598 6 84831381 GCAAGTTGGCATCAGGGTCAGTGCCTCACACAGCA[A/C]TATTTCTCAAACTTTAAAGTATAAATGAATCAGCT M 2 1 2 1 101000 f 74 goat snp59886-scaffold996-206707 6 88129197 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437048 Affx-122933101 AX-123307386 6 84865479 CAGAAAGTAGCTAAACATCCTGTCATAAAGCAAAG[A/G]CTAAATATATTTGGAATATTCAATTAAGATCAAAA R 2 1 2 1 101000 f 74 goat snp59887-scaffold996-240805 6 88163608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448129 Affx-122924296 AX-123318465 6 84895433 TAGGAAATTTTCAACCTACAGGCTTGGCAAAATGA[A/G]TTGATCAACTCTGGAATGATTAAGGGGTCATCAAA R 2 1 2 1 101000 f 74 goat snp59888-scaffold996-270759 6 88193969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382384 Affx-122973848 AX-123252742 6 84943872 TGACACCAAATGGCCTGAAGTCCAGACTGGCTCTA[C/T]GAACACATGCTCCATTACCCAAGTCAGAGACTGGG Y 2 1 2 1 201000 r 74 goat snp59889-scaffold996-319198 6 88242668 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764711 Affx-986696985 AX-385252331 6 84985928 GAGCTGGACATTTTGATAATAAACTGCTTTTCTGA[G/T]GTACAGTTTTCATCAGTACCTTCAGATTGTTTTCA K 2 1 2 1 600010 r 74 goat 6_84985928 6 84985928 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 320762459 Affx-986696989 AX-385250587 6 84994018 TGCAAAATTCAGATTTGAATTGAAGAAAGACTTAA[A/G]TTGAAAGCGGGGAAAACCGCTAAGCCATTCAGGTA R 2 1 2 1 600010 f 74 goat 6_84994018 6 84994018 Ancestral_priority_1043 ancestry 0.528 neutral IMAGE 10K 10K ancestral 38417180 Affx-122947325 AX-123287528 6 84997830 AATCCTCGCTGTGAGCTTAGTCAGGCAACGCCGTG[A/C]GGTCCTAACCGTCTGGGGCTCAGGTAGTGACACTG M 2 1 2 1 101000 f 74 goat snp59890-scaffold996-373156 6 88296909 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764721 Affx-986696991 AX-385252339 6 85018808 ACTGCTGCTGCACTGGGGCTACACTGGTGTGACCC[A/G]TGGTTATGTTACATGAGATTATGCTATGGCTAGGT R 2 1 2 1 600010 r 74 goat 6_85018808 6 85018808 Ancestral_priority_1043 ancestry 0.662 neutral IMAGE 10K 10K ancestral 320762463 Affx-986696993 AX-385250590 6 85018832 TGGTGTGACCCATGGTTATGTTACATGAGATTATG[C/T]TATGGCTAGGTTATGGTTATGTTATGGCTGCTGCT Y 2 1 2 1 600010 f 74 goat 6_85018832 6 85018832 Ancestral_priority_1043 ancestry 0.638 neutral IMAGE 10K 10K ancestral 320762465 Affx-986696995 AX-385250592 6 85018881 TGGTTATGTTATGGCTGCTGCTACAGGTACTGCAT[C/T]AGCCAGGAGAGAAGCTGTTTTATGGCTGCCGTGCC Y 2 1 2 1 600010 f 74 goat 6_85018881 6 85018881 Ancestral_priority_1043 ancestry 0.522 neutral IMAGE 10K 10K ancestral 38390030 Affx-122968440 AX-123260387 6 85063923 CAGAAGTCAGGATTTCTTGTAATACCATAATTGGC[C/T]AAGTATGTATTATGGTGAATTTAATAACTTAGCCC Y 2 1 2 1 101000 f 74 goat snp59892-scaffold996-439249 6 88364237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422352 Affx-122943440 AX-123292698 6 85070017 CTTTGTATAAGATGTAGATGACTGTTTATGCACGT[A/C]CAGCATGTTTATAGTTATTTGGGAGGTTAATGATC M 2 1 2 1 101000 r 74 goat snp7871-scaffold1281-3251602 6 88369661 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 353791386 Affx-293815452 AX-416972589 6 85098211 TTTCTCTTTGAATAGGAACAGCTTCTCAGACTGAA[-/G]AAATACAACGTGCCCCAGCTGGTAATGTTTTATTA - 2 1 2 1 400000 r 74 goat snp-genphyse672 - G INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 99229977 Affx-293815454 AX-180660630 6 85098211 TTTCTCTTTGAATAGGAACAGCTTCTCAGACTGAA[-/A/G]AAATACAACGTGCCCCAGCTGGTAATGTTTTATTA - 6 1 2 1 600000 f 74 goat norsk01 6 parentage parentage 99229978 Affx-293815454 AX-180660631 6 85098211 TTTCTCTTTGAATAGGAACAGCTTCTCAGACTGAA[-/A/G]AAATACAACGTGCCCCAGCTGGTAATGTTTTATTA - 4 1 2 1 600000 r 74 goat norsk01 6 parentage parentage 38440660 Affx-122929936 AX-123310997 6 85112368 TAAATGAAAGTGTTATAAATATGTAGCAGATTTTT[A/G]TTAAATATTTGGGGATGGTGAGGAAAATCAGAGTG R 2 1 2 1 102000 r 74 goat snp7870-scaffold1281-3209251 6 88414059 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454275 Affx-122919279 AX-123324608 6 85175103 TTCTCCTGATTTTATAAAGAGGACTCATTTAGTGG[C/T]ACTGTACTTAGTTTCAAAGATATAAAATCAGGTGG Y 2 1 2 1 201000 f 74 goat snp7869-scaffold1281-3146516 6 88477979 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803053 Affx-986696147 AX-385289926 6 85219931 AAATTGAAATTTTATGATTGATAGTTATTTAAAAA[A/G]TGAAAATGGAAGGTCATGTGGGAAACTTCAATCTT R 2 1 2 1 600010 f 74 goat 6_85219931 6 85219931 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 320764746 Affx-986697006 AX-385252361 6 85219957 ATTTAAAAAGTGAAAATGGAAGGTCATGTGGGAAA[A/C]TTCAATCTTTTCTACCATAGGAATTGATAAGAGCC M 2 1 2 1 600010 r 74 goat 6_85219957 6 85219957 Ancestral_priority_1043 ancestry 0.618 recommended IMAGE 10K 10K ancestral 320762478 Affx-986697008 AX-385250602 6 85220005 TACCATAGGAATTGATAAGAGCCATTCCAAACACT[A/G]TAAGTTGGACAGTGGAAAGGAGAGTTCAGGATGAT R 2 1 2 1 600010 f 74 goat 6_85220005 6 85220005 Ancestral_priority_1043 ancestry 0.652 recommended IMAGE 10K 10K ancestral 320764752 Affx-986697010 AX-173410846 6 85220034 AACACTGTAAGTTGGACAGTGGAAAGGAGAGTTCA[G/T]GATGATGTTCTTGTGGAAGTATAATAGAACAGAGT K 2 1 2 1 600010 r 74 goat 6_85220034 6 85220034 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 320782413 Affx-122927275 AX-385269489 6 85251808 TTATAGCATGTCAGCATACATTGGGTGAAATTTTT[A/G]CTAAATAGAGTATTTTTCTTAGCTGGTATAGAAGT R 2 1 2 1 101000 r 74 goat snp7867-scaffold1281-3069811 6 88548104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394847 Affx-122964776 AX-123265202 6 85285880 AGTCCAAGGAGTTGCAGAGTTGGACATGACTGAAT[A/G]ACTTTTACTTTCACTTCACTTTTCTGTATCATATT R 2 1 2 1 303000 r 74 goat snp7866-scaffold1281-3035739 6 88582504 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409577 Affx-122953579 AX-123279928 6 85328311 ACCAGCTGTTTGTAGAAAATAAATATTGGAAAGTT[A/G]CTAGCAGGGAATTAGTATTCTAAAAAATGATTTAA R 2 1 2 1 201000 r 74 goat snp7865-scaffold1281-2993308 6 88625439 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772599 Affx-122921192 AX-385259747 6 85374944 TTATGTATTCCAGTTAGATAAGATGTGCAGGTGAT[C/T]AGTTTAAAACGGTACCCAGATATCTTGTTATTGCT Y 2 1 2 1 101000 f 74 goat snp7864-scaffold1281-2946675 6 88672148 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406344 Affx-122955439 AX-123276696 6 85415881 CTTTTGTTTCTCTCCTCACCCTTGCCACTAATACC[A/G]GTAAAATTTTCTTTCTGATCGTGAAATAATTCTAT R 2 1 2 1 201000 r 74 goat snp7863-scaffold1281-2905738 6 88713141 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780298 Affx-122958292 AX-385267393 6 85453625 TTATAATATCCTGAGAACAGATTGTTATAATCTCC[A/G]TAACAATTACTTTACCTGTCTGGAAGTTAGAGAGC R 2 1 2 1 201000 f 74 goat snp7862-scaffold1281-2867994 6 88751536 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786479 Affx-122929630 AX-385273513 6 85533016 TCATTTATGATCATCTGTCACTCAGATGAGGAACT[A/G]TTTTTGAGAAAGTTTGTGGATTATTTAAAAGTCTA R 2 1 2 1 102000 f 74 goat snp7860-scaffold1281-2788603 6 88831292 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409491 Affx-122954051 AX-123279842 6 85577331 TGGCAAAGTGGAACTTAACCTTTGGTTCAAAGCCT[A/G]CCTATTCATTCATATATTCACATGCTCTGCTATGC R 2 1 2 1 101000 f 74 goat snp7859-scaffold1281-2744288 6 88875543 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402967 Affx-122958159 AX-123273320 6 85611834 AGAGCTTTCTCCCACTTAGTTGGTAAGCTTAATAA[C/T]AATAGGGGCCATGTCTGTTTTTATTCACTACTGTA Y 2 1 2 1 101000 f 74 goat snp7858-scaffold1281-2709785 6 88910304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442187 Affx-122928800 AX-123312524 6 85651866 GGTTACCTGATAGGCATCCAAGATTTCAAGTAGGC[A/C]TTTGGATATATAAATTTAAACCTCAAAGGAGAAGC M 2 1 2 1 101000 f 74 goat snp7857-scaffold1281-2669753 6 88950363 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770818 Affx-122950717 AX-385257981 6 85688160 ATTCAGAGGTTGCTTCTTTGGTTCATTTTGACTTT[A/G]CCTTAAAATTGTGAGCATATTCCTGGGAAATATCG R 2 1 2 1 101000 f 74 goat snp7856-scaffold1281-2633459 6 88987300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773824 Affx-122928387 AX-385260964 6 85747726 ATTCCATACGAGTGTTTGAGTATAAACATGAGCTG[C/T]ACCTACCTCTTCTGTAAAGCAGACTTCCTGCTCTT Y 2 1 2 1 101000 r 74 goat snp7854-scaffold1281-2573893 6 89046546 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416311 Affx-122947923 AX-123286660 6 85782574 GCACTTTTGATGTGGAATGGAGGGAGAAAAGAACC[A/G]CTGTTGCTGATGCCTTGGCCCATTCCCCCCTTTCT R 2 1 2 1 101000 f 74 goat snp7853-scaffold1281-2539045 6 89081487 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410714 Affx-122952720 AX-123281064 6 85835455 GCCCACTTTATCTTTTAGCAGGCAGAACAGGTTCA[C/T]ATAATTTACTATTCAAACAAAGAAAATGCCTGTAG Y 2 1 2 1 101000 f 74 goat snp7852-scaffold1281-2486164 6 89131907 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403769 Affx-122957993 AX-123274121 6 85867782 ATATAGTTTTACTTCCTGCCTCTGCCTAGAAGCCT[A/G]CTTGCTTCTCTATATCCACTTGCTAGACTCTTCCA R 2 1 2 1 201000 r 74 goat snp7851-scaffold1281-2453837 6 89164238 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418908 Affx-122946094 AX-123289256 6 85931620 TGATGACAACTGATATGGATTTAGAGTGGGGCGGA[C/T]GGGTTAGTTAATCCCTGCTTGTTCACTGGAGGCCT Y 2 1 2 1 101000 r 74 goat snp7850-scaffold1281-2389999 6 89228465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772097 Affx-122921474 AX-385259252 6 85974307 GGCACTTATGGTGGATCTATTTTCTTTGCCATTAG[C/T]GGTTATGAAAAGAAGCTCTATAGAGCCTGAATGAG Y 2 1 2 1 101000 f 74 goat snp7849-scaffold1281-2347312 6 89271507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601393 Affx-1002479923 AX-413835815 6 85980078 TTCTTGTTTGAAGTCATTTCAAATGCAATTTGATG[-/CAA]CGTCTCATCAAGTGCAAGACATTGCAGTTGTAAAG - 2 1 2 1 201000 r 74 goat QTLcaseins6.1 6 85980078 - CAA 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601926 Affx-1002479924 AX-413836309 6 85981181 TGCTAAACCCTAAGCATCAAAAGAAGGGAATATCT[A/G]GACAGTAAGTTACGAAAAAAGGATCCAAGTTCTTC R 2 1 2 1 201000 r 74 goat QTLcaseins6.2 6 85981181 G A 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 538942825 Affx-1251531511 AX-585489954 6 85982608 TTTCACTTTTACAATTCACAATTTAATTCCTACAG[-/GAAGTCCTCAATGAAAATTTACTCAGGTTTGTTGTGGCG]GTAAGTATTATCTACTTCTTCTTCAATGACAAATG - 4 1 2 1 400000 f 74 goat ins-del_021 6 85982608 GAAGTCCTCAATGAAAATTTACTCAGGTTTGTTGTGGCG - SV-TF-chip candidate gene ou candidate region CSN1S1 350601928 Affx-1002479925 AX-413836311 6 85984028 AGCAATATATCTGCTCCAAGAATGTTTTACATAGT[C/T]CAATTTGATCAAGGTTGTTTTTCAAAGTTTTAATA Y 2 1 2 1 201000 r 74 goat QTLcaseins6.3 6 85984028 C T 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 538942836 Affx-1251531512 AX-585489964 6 85986404 CTCAGAGGCAGTAACAATGATTCTCTTTCTTTTAG[-/CAAATGAAAGCTGGAAGCAGTTCGTCAAGTGAG]GTATACCATTTTTATGTTAATTAAGTATCCCAATT - 2 1 2 1 400000 r 74 goat ins-del_022 6 85986404 CAAATGAAAGCTGGAAGCAGTTCGTCAAGTGAG - SV-TF-chip candidate gene ou candidate region CSN1S1 539241947 Affx-1251531560 AX-585780888 6 85986426 CTCTTTCTTTTAGCAAATGAAAGCTGGAAGCAGTT[C/CC/T]GTCAAGTGAGGTATACCATTTTTATGTTAATTAAG - 4 1 2 1 401000 r 74 goat "CSN1S1-F-allele-1-2;ins-del_008;snp59423-scaffold980-301989;SNPs_066;UniBern-var5" "0;6" "0;85986425;85986426" "c;C" "-;CC,T;g;T" GoatSNP50 chip candidate gene ou candidate region CSN1S1 10.1371/journal.pone.0086227 532567200 Affx-1002479337 AX-579205693 6 85987197 TTTTTTTTTTTAAGGAAATTGTTCCCAATAGTGCT[C/G]AGGTGAGATATATTTACTAAATTTAAAATATATTA S 8 1 2 1 101000 r 74 goat "QTLcaseins6.4;SNPs_067;UniBern-var6" 6 85987197 C G 1 wobble probeset "not_recommended;recommended" Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350603035 Affx-1002479360 AX-413837256 6 85987976 TGGGAAGATCCCCTCGAGGAGGGCATGGCAACCCA[A/C]TCTAGTATTCTTGCCTTGAGAATTCCATAGACAAA M 2 1 2 1 103000 f 74 goat CSN1S1-GAFO2O3B2 6 85987976 c a 1 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603033 Affx-1002479359 AX-413837255 6 85988024 GCCTTGAGAATTCCATAGACAAAGGAGCCTGGAGG[A/G]CTATATCCATAGGATCACAGAGAGCTGGGTACAAC R 2 1 2 1 303000 f 74 goat CSN1S1-O1Ac 6 85988024 g a 3 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603036 Affx-1002479361 AX-413837257 6 85988066 CCATAGGATCACAGAGAGCTGGGTACAACTGAGGT[G/T]ACTTAGCACAGCACAGAAAGCAAATCTGTTTTCAA K 2 1 2 1 202000 f 74 goat CSN1S1-EBC 6 85988066 g t 2 neutral Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 539241943 Affx-1251531567 AX-585780884 6 85994929 AAAATTCCATGCTTTACATGTCTTTTCATCTATCA[T/TC/TG/TT]GTCAAACCATTCTATCCAAAGGCTTCAATTGCTGT - 6 1 2 1 401000 f 74 goat "CSN1S1-A-allele-1;CSN1S1-A-allele-2-2" 0 0 "-;C" "C;G" Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 468273457 Affx-1111833630 AX-413837314 6 85994929 ACAGCAATTGAAGCCTTTGGATAGAATGGTTTGAC[A/G]TG R 2 1 2 1 103000 f 74 goat "CSN1S1-A-allele-1;CSN1S1-A-allele-3" 0 0 "-;T" C 1 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 539241949 Affx-1251531570 AX-585780890 6 85995009 GGACAACCTCAAATTGAAGGCACTCTTTCTTCTTG[A/CTTCCTAAATTCCATATATATGTGTTAGTATACTGTATTGGTGTTTTTCTTTCTGGCTTACTTCACTCA/T]GTTCTCCACTGTATTTTAGATTGTGTAACATCCTT - 6 1 2 1 401000 r 74 goat "CSN1S1-E-allele-2-2;ins-del_025" "0;6" "0;85995009" A "CTTCCTAAATTCCATATATATGTGTTAGTATACTGTATTGGTGTTTTTCTTTCTGGCTTACTTCACTCA,T;T" Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 350603024 Affx-1002479354 AX-413837250 6 85997730 TACAAGTGAGTAAAAGAAATGATTGTGAAAATCTT[A/T]CTGAGGATGAACTGACAAATGCATGCATTCTCTTC W 4 1 2 1 201000 f 74 goat CSN1S1-O1-allele-1 6 85997730 A T 2 recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350601852 Affx-1002479927 AX-413836236 6 85998059 GAGATTAGGAAAGAATAGTGTAGTAGGAAAATTAG[C/T]TGGAGAAAAGAGGCTGAATAACTTGGTTTACACAG Y 2 1 2 1 303000 f 74 goat QTLcaseins6.5 6 85998059 T C 3 not_recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601854 Affx-1002479928 AX-413836238 6 85999129 TGCACGAGCAGATCCAGCGAGGCTCCCTTAAGGCC[A/C]CGACTCGCCTTTGCCTGTCGGGCCCCTTAACCGCA M 2 1 2 1 303000 f 74 goat QTLcaseins6.6 6 85999129 C A 3 not_recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601856 Affx-1002479929 AX-413836240 6 86002527 ATAGCACTAGTACCTGAGAGAACTTTCTCAGATTC[C/T]CCTGTCAAGTTCTTCCTTCTCTCAGATAACCAGTA Y 2 1 2 1 201000 f 74 goat QTLcaseins6.7 6 86002527 C T 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 538942927 Affx-1251531514 AX-585490048 6 86006394 ATATTTCCAAGTTAAAATTGAACTTTTATGCTAAT[A/G]TTGAATTAACATTTTGAAAGTATATGGTTTATGAC R 2 1 2 1 400000 f 74 goat SNPs_070 6 86006394 G A SV-TF-chip candidate gene ou candidate region CSN2 350601858 Affx-1002479930 AX-413836242 6 86006797 AATGTCTGCTGAATCATGATCACAAAAAGATGTAT[A/T]TTCTTTAAGAATATCAAAACTATATGCTATTCCCC W 4 1 2 1 201000 f 74 goat QTLcaseins6.8 6 86006797 T A 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 532567219 Affx-1207771851 AX-579205712 6 86007342 TGAGGAGGGGGCATTCACTTTGAAATCCTCTTAGA[A/C/G/T]CTTAAAAATTAAAAAAATAAAATAAGTGAATGAAT N 8 1 2 1 401000 f 74 goat "snp59433-scaffold980-322303;snp59999-CSN2-ex8-2" 6 86007342 A G GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 532567214 Affx-1207771851 AX-579205707 6 86007342 TGAGGAGGGGGCATTCACTTTGAAATCCTCTTAGA[A/C/G/T]CTTAAAAATTAAAAAAATAAAATAAGTGAATGAAT N 8 1 2 1 304000 r 74 goat "snp59433-scaffold980-322303;snp59999-CSN2-ex8-2" 6 86007342 A G 3 GoatSNP50 chip SNPs in specific regions/genes CSN2 10.1371/journal.pone.0086227 350601940 Affx-1002479931 AX-413836323 6 86007588 GTTTGTTATTCTTAGCCAAGTGAGATTATCAAGTT[A/C]CAATTCTGGCTTTATTGTAACTTAATCCCCTTCAT M 2 1 2 1 201000 r 74 goat QTLcaseins6.9 6 86007588 C A 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 532567205 Affx-1207771856 AX-579205698 6 86008016 GAAAGGCCTGGATGGGCATATCTCTCTGGGGCACT[A/C/G/T]CTTTCTGGGGAACAGGCAGAACTTTGGGCTGAGAA N 8 1 2 1 201000 r 74 goat "snp59434-scaffold980-322977;SNPs_071;UniBern-var9" 6 86008016 "A;C" "G;T" 2 recommended GoatSNP50 chip SNPs in specific regions/genes CSN2 10.1371/journal.pone.0086227 538942982 Affx-1251531575 AX-585490097 6 86008047 CACTACTTTCTGGGGAACAGGCAGAACTTTGGGCT[A/C/G/T]AGAAAGGGACAGCACGGACTGAGGAGGAAACATGA N 8 1 2 1 401000 f 74 goat "snp59435-scaffold980-323008;SNPs_072" 6 86008047 "C;G" "A,C,T;T" GoatSNP50 chip SNPs in specific regions/genes CSN2 10.1371/journal.pone.0086227 538942990 Affx-1251531580 AX-585490105 6 86008049 CTACTTTCTGGGGAACAGGCAGAACTTTGGGCTGA[A/C/G/T]AAAGGGACAGCACGGACTGAGGAGGAAACATGACG N 8 1 2 1 401000 r 74 goat "snp59436-scaffold980-323010;SNPs_073" 6 86008049 G A,C,T GoatSNP50 chip SNPs in specific regions/genes CSN2 10.1371/journal.pone.0086227 538942822 Affx-1251531493 AX-413835719 6 86008403 AGACTAGAGACTGTGCCTGGGCAAAGGGGTGGATT[T/TT]ATCCTGGAGTTCATCCTGGAAAGAAGGAAAAAAAA - 4 1 2 1 400000 r 74 goat "ins-del_009;snp-genphyse673" 6 86008403 "-;TT" "A;T" SV-TF-chip candidate gene ou candidate region CSN2 350602998 Affx-1002479339 AX-413837236 6 86013169 TTCAACATTTTTTTCTGTATTTACCTCTCTTGCAA[G/T]GGCCAGAGCCACCAGACAGGCAAGGATGAGGACCT K 2 1 2 1 202000 f 74 goat "SNPs_074;UniBern-var10" 6 86013169 T G 2 neutral SV-TF-chip candidate gene ou candidate region CSN2 38446381 Affx-122925586 AX-123316717 6 86013256 CGTTCACAGTTGGCTTCCTCTGCAGGCTCCACTGC[A/G]ATGAATTCCTGAGGGGTGACTCAGTAGAAATTCCT R 2 1 2 1 202000 f 74 goat "GoatD01.029085;snp7848-scaffold1281-2308363" 6 89311060 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 350601942 Affx-1002479932 AX-413836325 6 86054630 GCTGTTGGCATGAAATCATCTAAATAGAAACCAAT[A/C]CTCTTGCCTTTCTCTTTAACTGTACTTATCGAAGA M 2 1 2 1 201000 r 74 goat QTLcaseins6.10 6 86054630 C A 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601865 Affx-1002479933 AX-413836249 6 86074665 GACATAATCACATGCCTATATTATTACAGTAGGCT[C/T]TCAAATTGATCATATTTCTTCTCTTGCCCCTTCAG Y 2 1 2 1 201000 f 74 goat QTLcaseins6.11 6 86074665 T C 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350603000 Affx-1002479340 AX-413837237 6 86079098 ATCTATTTCACAGGACCAAGTAAGTATGAAGTTCT[C/T]CATTTTTACCTGCCTTTTGGCCGTTGCCCTTGCAA Y 2 1 2 1 201000 f 74 goat "SNPs_075;UniBern-var11" 6 86079098 T C 2 recommended SV-TF-chip candidate gene ou candidate region CSN1S2 539241946 Affx-1251531586 AX-585780887 6 86080969 ACTGTATTTGCTTTTGTTTGTAGAAGATGGAACAT[A/C/G/T]TCTCCTCCAGTGAGGTAAGATACTCTTAGTATCAA N 8 1 2 1 401000 f 74 goat "snp59444-scaffold980-395682;SNPs_076;UniBern-var12" 6 86080969 G "A;A,C,T;T" GoatSNP50 chip SNPs in specific regions/genes 10.1371/journal.pone.0086227 350603109 Affx-1002479342 AX-413837305 6 86085104 GTTTTATCAGAAGTTCCCCCAGTATCTCCAGTATC[C/T]GTATCAAGGTCCAATTGTTTTGAACCCATGGGATC Y 2 1 2 1 201000 r 74 goat "SNPs_078;UniBern-var14" 6 86085104 C T 2 recommended SV-TF-chip candidate gene ou candidate region CSN1S2 350603111 Affx-1002479343 AX-124387046 6 86089401 TGGGATAATGGAATAATTATAATTTCCCTAGAAAA[A/T]AATCAGCCAGTATTACCAGAAATTTGCCTGGCCCC W 4 1 2 1 201000 r 74 goat "SNPs_080;UniBern-var15" 6 86089401 A T 2 recommended SV-TF-chip candidate gene ou candidate region CSN1S2 38438173 Affx-122931837 AX-123308511 6 86096704 ACTGAGTGACTAAGCACACATACACACCATATGTG[C/T]TATGCAGATTTTTTTGAAGTCATATAGCCATTCAG Y 2 1 2 1 101000 r 74 goat snp7846-scaffold1281-2224915 6 89392434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444169 Affx-122927280 AX-123314506 6 86139194 ACAGAGTGCAACGTCTCCATTTGTAATTATTCATA[C/T]AGTGCCCTTCTCTAGTCCCAGGGGCACTAAGGCAG Y 2 1 2 1 102000 f 74 goat snp7845-scaffold1281-2182425 6 89433842 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601867 Affx-1002479934 AX-413836251 6 86157760 TTCTGCTGTGGACCCAATTATTACCACAGAGCTAA[C/T]TGGAAAAGAAGGTAATCAAAGATTCTTTTTATGAA Y 2 1 2 1 201000 f 74 goat QTLcaseins6.12 6 86157760 T C 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601948 Affx-1002479935 AX-413836330 6 86159168 ATGTAGTTTTATTTCTTTTTAAGCAATTTAGAAAA[C/T]TATCTCAGGAATTTTATAGAAAGCAGTCTAATGAT Y 2 1 2 1 201000 r 74 goat QTLcaseins6.13 6 86159168 T C 2 recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38411113 Affx-122951909 AX-123281463 6 86174593 TGTAAATAAATAAGTGGAAGAACCCTGCTAAGAGA[C/T]GTTCAAACATATTAAGCCTGATCCAGGTGGCTTTA Y 2 1 2 1 101000 r 74 goat snp7844-scaffold1281-2147026 6 89469265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 538942848 Affx-1251531447 AX-585489971 6 86199773 TTTAAGGTGCAATGATGAAGAGTTTTTTCCTAGTT[A/G]TGACTATCCTGGCATTAACCCTGCCATTTTTGGTA R 2 1 2 1 400000 r 74 goat SNPs_082 6 86199773 G A SV-TF-chip candidate gene ou candidate region CSN3 350601871 Affx-1002479936 AX-413836255 6 86201554 AAGTGAAAGAAGAGAGTGAAAACGTTGGCTTAAAG[A/C]ATCAACATTCAGAAAACTAAGATCATGGCATCCAG M 2 1 2 1 303000 f 74 goat QTLcaseins6.14 6 86201554 A C 3 not_recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601873 Affx-1002479937 AX-413836257 6 86208101 AATATATAATACAGTGTATAATACAATTTATAATA[A/T]ATATATGATTATATAATATACAGTATTAATATATC W 4 1 2 1 303000 f 74 goat QTLcaseins6.15 6 86208101 A T 3 not_recommended Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350603008 Affx-1002479344 AX-413837240 6 86208947 TTCAGTATGTGCTGAGTAGGTATCCTAGTTATGGA[C/T]TCAATTACTATCAACAGAGACCAGTTGCACTAATT Y 2 1 2 1 201000 f 74 goat "SNPs_084;UniBern-var16" 6 86208947 C T 2 recommended SV-TF-chip candidate gene ou candidate region CSN3 538942842 Affx-1251531448 AX-585489967 6 86209003 CCAGTTGCACTAATTAATAATCAATTTCTGCCATA[C/T]CCATATTATGCAAAGCCAGTTGCAGTTAGGTCACC Y 2 1 2 1 400000 f 74 goat SNPs_088 6 86209003 C T SV-TF-chip candidate gene ou candidate region CSN3 538942844 Affx-1251531449 AX-585489968 6 86209011 ACTAATTAATAATCAATTTCTGCCATACCCATATT[A/G]TGCAAAGCCAGTTGCAGTTAGGTCACCTGCCCAAA R 2 1 2 1 400000 f 74 goat SNPs_089 6 86209011 A G SV-TF-chip candidate gene ou candidate region CSN3 538942854 Affx-1251531450 AX-585489978 6 86209098 TTTGCCAAATACTGTGCCTGCCAAGTCCTGCCAAG[A/G]CCAGCCAACTACCCTGGCACGTCACCCACACCCAC R 2 1 2 1 400000 r 74 goat SNPs_092 6 86209098 A G SV-TF-chip candidate gene ou candidate region CSN3 538942796 Affx-1251531453 AX-585489930 6 86209222 CCTGCCATCAATACCATTGCTAGTGCTGAGCCTAC[A/G]GTACACAGTACACCTACCACCGAAGCAATAGTGAA R 2 1 2 1 400000 f 74 goat SNPs_094 6 86209222 A G SV-TF-chip candidate gene ou candidate region CSN3 538942884 Affx-1251531454 AX-585490008 6 86209263 CAGTACACCTACCACCGAAGCAATAGTGAACACTG[C/T]AGATAATCCAGAAGCTTCCTCAGAATCGATTGCGA Y 2 1 2 1 400000 f 74 goat SNPs_095 6 86209263 T C SV-TF-chip candidate gene ou candidate region CSN3 350603011 Affx-1002479345 AX-413837242 6 86209296 TGTAGATAATCCAGAAGCTTCCTCAGAATCGATTG[C/T]GAGTGCATCTGAGACCAACACAGCCCAAGTTACTT Y 2 1 2 1 201000 f 74 goat "SNPs_096;UniBern-var19" 6 86209296 C T 2 recommended SV-TF-chip candidate gene ou candidate region CSN3 350603117 Affx-1002479346 AX-413837312 6 86209304 ATCCAGAAGCTTCCTCAGAATCGATTGCGAGTGCA[C/T]CTGAGACCAACACAGCCCAAGTTACTTCAACCGAG Y 2 1 2 1 201000 r 74 goat "SNPs_097;UniBern-var20" 6 86209304 T C 2 recommended SV-TF-chip candidate gene ou candidate region CSN3 38415823 Affx-122948884 AX-123286172 6 86226008 CTTTTTACAGGTGGCCTGTGAAGAAGATGGAGTCT[A/G]TAATCCTCCATGAGTGGGAAAAAAAGCATTTGAAC R 2 1 2 1 101000 f 74 goat snp7843-scaffold1281-2095611 6 89521127 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394288 Affx-122964705 AX-123264643 6 86289421 TTCTACACTTAAGGGAGAAAATGAAGATGGCTGAA[C/T]AAGTTACTAGATCCTAAGATCTCCCATCCTTCTAA Y 2 1 2 1 201000 r 74 goat snp7842-scaffold1281-2032198 6 89585747 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381873 Affx-122974176 AX-123252231 6 86340201 TGGAAACTCTATAGGAGGAAGCAGGGAAGTGAGGA[C/T]GCCAGTGAAGAGGCTAGTGTGGAATCTCAGGCTTG Y 2 1 2 1 101000 f 74 goat snp7841-scaffold1281-1981418 6 89636586 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403418 Affx-122957754 AX-123273771 6 86376826 GGCATTACAAGACATAATATCCCCAATATCCTACC[A/G]TGAGTACTTCTACCTTAGGAACAGTGGGATGGGAG R 2 1 2 1 201000 r 74 goat snp7840-scaffold1281-1944793 6 89673395 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793387 Affx-122968205 AX-385280365 6 86412606 AACAAAACAAAGACTACTACACTGGCTTGATCTGG[A/C]GTCCCCGTCTTGGCTGTAATTCTGATAATATTCCA M 2 1 2 1 101000 f 74 goat snp7839-scaffold1281-1909013 6 89709558 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379052 Affx-122976343 AX-123249411 6 86463530 GAAATTATTTTTATATGGAAAAATAGTAATAACCA[C/T]AGGCAGTATCCATTAAATACTTACTACTTGCCAAG Y 2 1 2 1 101000 r 74 goat snp7838-scaffold1281-1858089 6 89760335 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381069 Affx-122974615 AX-123251427 6 86532152 AGGAAATTAGGTGTGTCAGTCTTCCAGCTTCCATC[A/G]CCAAAGCATTTGTTCATCTTCCTTTTTTATAGTCC R 2 1 2 1 101000 r 74 goat snp7836-scaffold1281-1789467 6 89828187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278401 Affx-1111836405 AX-519551886 6 86545603 ACTGACAAGGTCCTGACCAAACAAAGGTTTCTACC[A/G]ATATCCTTCTCTAAATATGCTGTGATTTGACTCAC R 2 1 2 1 101000 f 74 goat Random2.2K-716 6 86545603 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390479 Affx-122967598 AX-123260836 6 86574829 ACCACCATCTGGGAAGGAAATCTATTTACTGCTTG[C/T]ACTTCTTACAGGGATAAAACAAAACATTGTGTTAA Y 2 1 2 1 201000 r 74 goat snp7835-scaffold1281-1746790 6 89871280 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273236 Affx-1111833521 AX-519546889 6 86592865 AGGGAAACACTTAATGTTCACACGTTACTAAAGGA[A/C]ATGATCTGGAGGAGGATATGGCAACCCACTCTAGT M 2 1 2 1 201000 f 74 goat 6_86592865_AF-PAKI 6 86592865 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425607 Affx-122940917 AX-123295953 6 86609696 GATAAAAGGGGGAGGATTATCCTATAGAATGATAA[C/T]AACAGTATCCAAGAGCAGAGATAGAGTAGCAGGCT Y 2 1 2 1 201000 f 74 goat snp7834-scaffold1281-1711923 6 89906524 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787031 Affx-122920784 AX-385274059 6 86639307 GGAGCCACACTGTGTGTTGAAATGATCTGATGACC[A/G]TGGCAACACATGCCTGACCACGTGTAGTTATGCCT R 2 1 2 1 101000 f 74 goat snp7833-scaffold1281-1682312 6 89936278 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770979 Affx-122936848 AX-385258142 6 86669870 TCACCCATGGACAGCTATGCTTCATAAACAAAATA[C/T]GAATGTCTCTGAGACAAGGATCACAAGTGACTTTC Y 2 1 2 1 101000 f 74 goat snp7832-scaffold1281-1651749 6 89966827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278571 Affx-1111836406 AX-519552051 6 86679141 TATTCTCAGTCTATAAATAGCCTCATCCCCCAGGT[A/C]AAAATGAACACACCCAAAGGCTTTTTGTGGGGGTC M 2 1 2 1 201000 r 74 goat Random2.2K-718 6 86679141 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781522 Affx-122929163 AX-385268607 6 86698998 ACACTATACCTTAAATGTTTTATGATAGAGATTGT[A/G]TATTATTTGTTTTGTATCCTCTGTGACTGACACAC R 2 1 2 1 101000 r 74 goat snp7831-scaffold1281-1622621 6 89996745 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401099 Affx-122959413 AX-123271452 6 86774741 TGGGTATTTAGATTGCCTACTCTTGAAAAGTCTCA[A/G]TTTTGTTAATCTACCAATTTGCATGAAAGGCTATC R 2 1 2 1 201000 r 74 goat snp7829-scaffold1281-1546878 6 90073686 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772361 Affx-122942675 AX-385259514 6 86834481 GTCACATTATTTTGAGAATCTTAAATTACCAATTG[C/T]AAACTAATTTGAAAGAATCCATTTGCACATACTCT Y 2 1 2 1 101000 r 74 goat snp7828-scaffold1281-1487138 6 90133710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393520 Affx-122965800 AX-123263876 6 86868879 CAGACAAAATAGACTTTGAAATAGAGGAAGAACTG[C/T]ATTTCGAGGATGCCTTTCCAAAGTAATGTACAGGA Y 2 1 2 1 101000 r 74 goat snp7827-scaffold1281-1452740 6 90168070 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394900 Affx-122964736 AX-123265255 6 86902576 AGCACAGATGTGGAGGTCATAAGGGGAAGCTGGGA[G/T]AATCTGCAGCATATTAATGTGCAGTAATAACATGC K 2 1 2 1 101000 r 74 goat snp7826-scaffold1281-1419043 6 90201821 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802438 Affx-122941037 AX-385289342 6 86934578 CCCCCAAAATGTGACCACTTCCTATCTACCTGCCC[A/G]TACTATCAAAGAAAGATATTCTTACTTCTGGTCCC R 2 1 2 1 101000 f 74 goat snp7825-scaffold1281-1387041 6 90233787 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452152 Affx-122921661 AX-123322485 6 86968766 TTCTTACTTTTCTCCCCTTTGTAACCAATACATAG[A/C]TTGCAAAATAACATAACTCTAATAACTGAATAATT M 2 1 2 1 201000 r 74 goat snp7824-scaffold1281-1352853 6 90267974 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432691 Affx-122936034 AX-123303032 6 87002714 TGCCCATGTTTAAAAACATTCAGTTTCTTCTAGTC[A/G]CAGGCTATATTAAGAAAAAATTCTAAGATGAACAT R 2 1 2 1 101000 f 74 goat snp7823-scaffold1281-1318905 6 90301669 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787404 Affx-122974748 AX-385274429 6 87035438 GAGCTCTCTAACTAATAGCCAGAGAGGTCTGTCTC[A/G]CAGTCTGGCTCTCCACAAAGTTTCCCGAGCTGATA R 2 1 2 1 202000 r 74 goat snp7822-scaffold1281-1286181 6 90334276 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422231 Affx-122944019 AX-123292577 6 87077159 GAAGGACATTTGAGATGTTAGTTACCTGAAGAATG[A/C]TGTTACAGGCGCAAAACACAAATAGGCTCTCGAGA M 2 1 2 1 101000 f 74 goat snp7821-scaffold1281-1244460 6 90376567 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407844 Affx-122954527 AX-123278195 6 87118368 CCACCCTGTGACCTGCTCAGAACCAGGGAGATGCA[C/T]GTAATCATTGCCCTGACTCACCTGTGCACAGTCTC Y 2 1 2 1 101000 r 74 goat snp7820-scaffold1281-1203251 6 90417624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441666 Affx-122929187 AX-123312003 6 87174077 TGAGCTGTGTCATGCTGGGTCATCAAGTTTCTTGA[C/T]GGAAGGAACAAGATATTTCTACTGAGGAGTCATGT Y 2 1 2 1 101000 r 74 goat snp7819-scaffold1281-1147542 6 90473272 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413813 Affx-122949896 AX-123284162 6 87203481 CTATGGAAAAAGCTCACTGAGTAATTGCAGAAAAA[C/T]GAGAGACTTTAAAAAATTGAAACAAAACAAAAAGT Y 2 1 2 1 101000 f 74 goat snp7818-scaffold1281-1118138 6 90502388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795836 Affx-122936757 AX-385282789 6 87260833 CTATGCTAAAATTTCAGACTGAAATTCTTATTCCA[C/T]ACCAAGATGAAAATTTATATGTACTATTTTTACAG Y 2 1 2 1 101000 r 74 goat snp7817-scaffold1281-1060786 6 90559594 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419931 Affx-122945318 AX-123290279 6 87304858 TAAAAACTGGATTGTGAGTTAACAGGAGGTGGGGC[A/G]TGAGAGTGAAGGAGTTCAGCGAAAAACAACCTTCA R 2 1 2 1 101000 r 74 goat snp7816-scaffold1281-1016761 6 90604237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768869 Affx-122963643 AX-385256046 6 87342788 ATTACCACCTGGACAAATATAACAGGATTTCAAAC[C/T]ATCAGCGGACAGTAGGCACTGTCAAGATTTCTCTT Y 2 1 2 1 101000 r 74 goat snp7815-scaffold1281-978831 6 90642617 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385346 Affx-122971651 AX-123255704 6 87372435 ACAAATATGTATTGAGACCTACTCTATGTCAGGCA[C/T]AAGAGGAAGCAGCAGTGAACTCTCAGACAAGCGCT Y 2 1 2 1 201000 f 74 goat snp7814-scaffold1281-949184 6 90673332 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387702 Affx-122969809 AX-123258060 6 87411509 ATTCTTCAAGTGGGAGTCAGCATCCTACTCTGTTT[A/G]GAAATCTGTATATGCTATATAGTGAGATGTTTACT R 2 1 2 1 201000 r 74 goat snp7813-scaffold1281-910110 6 90713008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408860 Affx-122954001 AX-123279211 6 87441654 AAGCATAAGTCCTTAAAGTGTTCTCTTTTTCTGAC[C/T]GAATATCCTCATGTTCTTCTTGCGGATTTGCTGGC Y 2 1 2 1 101000 r 74 goat snp7812-scaffold1281-879965 6 90743655 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423325 Affx-122943177 AX-123293671 6 87510728 CTAGGGAACATGGAAACTATTTATTAAACCCCCCT[A/G]TTTATGATGCCCACCATATTTGCTAAAGCTAGAAG R 2 1 2 1 101000 r 74 goat snp7810-scaffold1281-810891 6 90814164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781465 Affx-122959503 AX-385268550 6 87556576 TTCTTGTCTGACATATAAGAAACATATTAATGTTC[A/G]TTATTACATTTAGTAAGTTGGTATTGTTTCCTTTG R 2 1 2 1 101000 f 74 goat snp7809-scaffold1281-765043 6 90863494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378192 Affx-122976943 AX-123248551 6 87656043 AACATATTAGTCTCCCAGTCTGGCGTTGTCAAGCT[A/G]TGTGATTTTGGATTTGCACGGACACTGGCAGCTCC R 2 1 2 1 101000 f 74 goat snp7807-scaffold1281-665576 6 90964681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410770 Affx-122952681 AX-123281120 6 87702846 TTGACATCAGTTGTTAACAGTAGTATTAAATGTAC[A/G]TAATTTCCACGTTTTTGTTGTTTTATAAAATTTTA R 2 1 2 1 101000 f 74 goat snp7806-scaffold1281-618773 6 91011237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802399 Affx-122939551 AX-385289303 6 87745801 CAATGTCTGTGTAAGTGTGGTGTGGTGACTTCTCA[C/T]GATCTTTGGTGATAAGAATGTTCTTTGGTTGACTT Y 2 1 2 1 101000 f 74 goat snp7805-scaffold1281-575818 6 91054091 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780038 Affx-122946473 AX-385267137 6 87777342 ACTTTGCCTTCATGAGGTTTAAAACATAGTTATAA[A/C]TTCTTTTGAGAGAACTTCCCTAACTATGACTATAG M 2 1 2 1 201000 f 74 goat snp7804-scaffold1281-544277 6 91085634 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791372 Affx-122978344 AX-385278364 6 87821686 TTAATTCTTTAGGTAGTACTCAAAGCTATAAGATA[C/T]GAGTAAGCTCCTCAAGCAGTTTAGATTTTCACTCT Y 2 1 2 1 101000 r 74 goat snp7803-scaffold1281-499933 6 91129975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430266 Affx-122937299 AX-123300607 6 87867416 GTGTTGCCTCCATGCTGATTGATGTATGTGAGTGC[A/G]TTCTCAGTCACTTCAGTTGTGCCCAACTCTGCAAC R 2 1 2 1 101000 f 74 goat snp7802-scaffold1281-454203 6 91176157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392708 Affx-122966402 AX-123263065 6 87899462 ATCTCTTGTCTGAGTGAACACCACCGTTCTCAGTG[C/T]GCAACTGATTTAGATTCTTCTCTTTTTGCAAATAA Y 2 1 2 1 201000 r 74 goat snp7801-scaffold1281-422157 6 91208098 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430912 Affx-122936856 AX-123301253 6 87931309 ATTATCAGACAAACTAAGTTAGAAATCAAAGTCAG[C/T]ATAAATCTAGTGGGAAAAGAACACAAGAATATTTA Y 2 1 2 1 101000 r 74 goat snp7800-scaffold1281-390310 6 91239611 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429650 Affx-122937672 AX-123299991 6 87976824 CCATGGGGTTGCGAAGAGTCAGACATGACTGAAGC[A/G]ACCTTAGCATGCTCGCATGCTTTATCTGTTTTCAC R 2 1 2 1 103000 r 74 goat snp7799-scaffold1281-344795 6 91285169 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436497 Affx-122932958 AX-123306835 6 88022077 TGGGTTCCTAATTTTCTCTATTCTGTCCTTCCCTC[G/T]AGGCCAGCAGAGTAATCAATTATTAAGTGAAAATT K 2 1 2 1 201000 r 74 goat snp7798-scaffold1281-299542 6 91331202 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796596 Affx-122946821 AX-385283542 6 88077411 ATCCTGACTCCACTTGACAAGTGTTCCTCGCAAGA[C/T]AGATGATGCAGAGATTAAGCCAATAAAACTAAAAT Y 2 1 2 1 101000 f 74 goat snp7797-scaffold1281-244208 6 91386844 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433776 Affx-122934479 AX-123304117 6 88112743 ATGTTCTCAAAGAATTAATCCTCCCCATGTGATAA[C/T]AGAAAGTGTTTAGGTCAGAAGAAGTCATAGGGTTA Y 2 1 2 1 201000 r 74 goat snp7796-scaffold1281-208876 6 91422189 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381431 Affx-122974351 AX-123251789 6 88147358 TGGAAATTATCACCGTCCAAAGACCAGCAGGATAA[A/G]ACACGTCAGGAAAGGTGAGAGACCACTAGAGGGCA R 2 1 2 1 201000 f 74 goat snp7795-scaffold1281-174261 6 91457367 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397697 Affx-122962571 AX-123268052 6 88263412 TGGAAGAGACCCTTAATACATGAATTTAGAATTTC[A/G]CCTTGACCAGAAGTTGGAAGAATTCCTGTTTTTTG R 2 1 2 1 201000 f 74 goat snp7793-scaffold1281-58207 6 91571351 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395924 Affx-122963593 AX-123266279 6 88316143 AAGAGGAGAGAGAAAAAGGATGAAAATCAAATGAG[C/T]AGGTTGGGCTAATTGTGAGAAGCTTAGTAACATAA Y 2 1 2 1 101000 r 74 goat snp7792-scaffold1281-5476 6 91624233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385404 Affx-122971341 AX-123255762 6 88338374 TAAGGCAGTTATGAGGAGGACCATGTCTCCACTTG[C/T]GCCGGGGACAGAGGGTGGCAGTCTCCACAGTTTCC Y 2 1 2 1 103000 f 74 goat snp42034-scaffold549-16656 6 91646745 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388876 Affx-122968868 AX-123259234 6 88382855 TGTGCTGAGCTGAGCTGAGTGTGAATTAATCTAGG[C/T]ATTTCTGATGATATGCAGCTACCTTCCAAAGTCCA Y 2 1 2 1 101000 r 74 goat snp42035-scaffold549-61137 6 91691362 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375735 Affx-122978622 AX-123246094 6 88443477 ATACAAAACACAAACATACACACTCTTCAAACAAT[C/T]AGCTCCCTCCGTTTACCTTGTGTTAATGAGCCACA Y 2 1 2 1 101000 r 74 goat snp42036-scaffold549-121759 6 91751464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409251 Affx-122953138 AX-123279602 6 88485041 AAAGCTGTGTCCTGAGTATGCCCTGCTGTTTCAGG[A/G]CCCTCCTTTATTTACACTCTTTTTCTTCCTCCTTT R 2 1 2 1 101000 r 74 goat snp42037-scaffold549-163323 6 91793057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438925 Affx-122930423 AX-123309262 6 88516711 AAAAGGCAAATACTATAAGGGACAGAAAAGATAAC[A/G]CATTTGATTTGAAAATATTTATATGGCAAAAGCTC R 2 1 2 1 101000 f 74 goat snp42038-scaffold549-194993 6 91824722 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773131 Affx-122938837 AX-385260274 6 88548133 TTTTAATGAAAAGGTCTCTAAAGATCAAACAGCCT[A/G]GCCTAGATCTAGGACCCAGTTTGCTGCTAGGTGAG R 2 1 2 1 101000 r 74 goat snp42039-scaffold549-226415 6 91856045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400513 Affx-122961271 AX-123270868 6 88595695 GATGGTTGTCAGGATTAAGTAAATGTTTAGAAAAA[C/T]GCCATTTAGAAAATACCCAGTAATTCTTAATTTCT Y 2 1 2 1 201000 r 74 goat snp41450-scaffold539-1889731 6 91905025 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431761 Affx-122936723 AX-123302102 6 88672175 TTTCTTCAGCAATTCCATTAGGCTTTCTCACTGGT[A/G]TCACTTGGCTGAGTTGCACAATGCCTCAGCCACGT R 2 1 2 1 101000 f 74 goat snp41448-scaffold539-1813251 6 91981444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601297 Affx-1002479939 AX-413835727 6 88683688 TTAGAGGGAAAAAATAATTAATTCTACATTTTAGA[-/GA]GAAAAAAAACACTAAGTCTTGGGGACCCCAACTAC - 2 1 2 1 202000 f 74 goat QTLcaseins6.17 6 88683688 GA - 2 neutral Goat_IGGC_65K_v2 QTLcaseins QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38401878 Affx-122958855 AX-123272231 6 88700790 TTCCGGGTTGTCTGCGTTACTCATGACCTAAAACT[C/T]CTCCCTCCTCAAGAGGTTAGGTCACTTTGAGGATT Y 2 1 2 1 101000 f 74 goat snp41447-scaffold539-1784636 6 92010631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601956 Affx-1002479940 AX-413836337 6 88701993 GGTTATGTGACTTTGGGCAAGTTACTTCACCTTTC[C/T]CGTGCCTCCCACTCTCCACCATAAGATGGGGATAA Y 2 1 2 1 202000 r 74 goat QTLcaseins6.18 6 88701993 C T 2 neutral Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601957 Affx-1002479941 AX-413836339 6 88708206 GACGCACGAGGCAGGAAAGTCCCACCTTTCCCACG[A/C]CGGCACTGAGCAAGCCTACTGCGCAGACACGAAAC M 2 1 2 1 102000 r 74 goat QTLcaseins6.19 6 88708206 C A 1 neutral Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601880 Affx-1002479942 AX-413836264 6 88709540 CTATTCCTCAAATTCCTAAGACTTCCTTCTGTGGA[G/T]TTCGTACTCAGGAGTTGAAGCTGGAACTTCAATGA K 2 1 2 1 202000 f 74 goat QTLcaseins6.20 6 88709540 T G 2 neutral Goat_IGGC_65K_v2 QTLcaseins QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320802989 Affx-122970034 AX-385289872 6 88747021 TACACAGCAATAGAAAATTCGGCAAACTGTTCTCT[A/G]TATGAGCTAGGAGTAAGTTCCCTCACTTGGTCCTT R 2 1 2 1 101000 r 74 goat snp41446-scaffold539-1738405 6 92056817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427517 Affx-122939522 AX-123297860 6 88786160 CTCACCATCTGGTGTCCCTTCCACAGTTGGGCCTC[C/T]GCATTTAACCTTCTAAAAGCCTGTAACACGGCCAT Y 2 1 2 1 101000 r 74 goat snp41445-scaffold539-1699266 6 92095669 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449702 Affx-122922542 AX-123320037 6 88822373 CACCCTTCTCCCACCTCCCTAGGCCGATCATGTAA[C/T]GAAATGAGTTCAAGGCTCTCCAGGCTAAGGTACTG Y 2 1 2 1 101000 r 74 goat snp41444-scaffold539-1663053 6 92131912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441433 Affx-122928816 AX-123311770 6 88868406 GGCACTTTGAAGGTGAGTTTGAGGAGGCCTGTTCC[G/T]CTAGCCCAGCCCACTGGCCCTCCTTTTTTTCTCCC K 2 1 2 1 101000 f 74 goat snp41443-scaffold539-1617020 6 92178768 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381482 Affx-122974964 AX-123251840 6 88916010 ATGTGGCATCTGCGGTGTGGCAGCCTGAGGTGGTG[C/T]GGAATAAGGTGAGGATGGAAAGGGAATTTAAGGTC Y 2 1 2 1 101000 r 74 goat snp41442-scaffold539-1569416 6 92226541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392989 Affx-122965663 AX-123263346 6 88949370 TAATAGTGTTTGCTTCTGTGAGAGGGCATATGGGG[C/T]AGGTGTGGGCCAAGTTAATAAACACTGTGGGCACC Y 2 1 2 1 201000 r 74 goat snp41441-scaffold539-1536056 6 92260024 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438042 Affx-122931550 AX-123308380 6 88990668 CTTGAAAAATTTACATTTCATAAAACCATTATTTA[C/T]GTCAACAGGCAATACAATTATTCTCACATAAAATG Y 2 1 2 1 102000 f 74 goat snp41440-scaffold539-1494758 6 92299933 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436047 Affx-122932718 AX-123306386 6 89025642 GTTAACTTCAGCCGCACATTGCTTTCCTGAAGCTC[A/G]TAACTTCTGGCTTTTAACCGGACACCTGGTTCATT R 2 1 2 1 201000 r 74 goat snp41439-scaffold539-1459784 6 92335367 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393528 Affx-122965793 AX-123263884 6 89058318 GCCACTCTGAACAGGCATAAATGGCAAGTCATTTG[C/T]GTTTCCAGAAACAAAGTCCCACTGCACATAGCTTT Y 2 1 2 1 101000 f 74 goat snp41438-scaffold539-1427108 6 92367977 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770666 Affx-122922367 AX-385257830 6 89112534 CCAAGCCTCCATAGTCATGAACCAATTTCTTAAAA[C/T]AAATCTCTCTCAAAATCCCTCTATGTATATAGAAA Y 2 1 2 1 201000 r 74 goat snp41437-scaffold539-1372892 6 92422056 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273284 Affx-1111833522 AX-519546928 6 89127917 CTTGAATAACAATGTCGAATAAACATGAAGATGGA[A/G]ATAGACATTGTGAAAACTGTAAGGACATCAGGTCA R 2 1 2 1 101000 r 74 goat 6_89127917_AF-PAKI 6 89127917 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395231 Affx-122964478 AX-123265586 6 89157290 AGAGACAATGGCACTAGTCAGCAGGTACCTCCTTC[A/G]CAGAGATCTGGCTCCTAGCCTAAAGGGCTCCTGTT R 2 1 2 1 101000 f 74 goat snp41436-scaffold539-1328136 6 92467252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427466 Affx-122940024 AX-123297809 6 89195250 CACCTTTGTCAACTATGGATCGCTGTGATCAGGCA[C/T]GGAAAGGACACTGGCAGGTGTGGTACATGTAGAAA Y 2 1 2 1 201000 f 74 goat snp41435-scaffold539-1290176 6 92505590 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779366 Affx-122936765 AX-385266470 6 89240731 GAGTAAGTGAAAACAAAACGTGAAATGTCAGCTCA[C/T]GCTGCATTGATTTGTAGCTAATAATGCGCACTTAC Y 2 1 2 1 101000 r 74 goat snp41434-scaffold539-1244695 6 92551747 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399927 Affx-122961314 AX-123270282 6 89270348 ATCTGATTTCACCATGCATGTTTTGTTTTAATGAT[G/T]GGCACACCACTCTAATGAAGAGTCACTATGCAAGC K 2 1 2 1 101000 r 74 goat snp41433-scaffold539-1215078 6 92580787 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777652 Affx-122955671 AX-385264771 6 89302596 CCCGGGGCCTCAACTCTCTATTCCAAAAAAAACTT[A/G]TAATGTTCATCCTCCCAACAAAAACGTCCCTGACG R 2 1 2 1 101000 f 74 goat snp41432-scaffold539-1182830 6 92613115 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780245 Affx-122961774 AX-385267340 6 89340232 ATGCTACTTAACTTCACCTTAGAACAGATGGTGTT[A/G]CTAGGCATATTCAGGGATATGGCAGATGCTGGTCT R 2 1 2 1 101000 f 74 goat snp41431-scaffold539-1145194 6 92650356 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385291 Affx-122971691 AX-123255649 6 89388222 CTTGGTCACCATTTTCAGCCCCACTGGCCTCTGTC[A/G]GCATTGCTAGCATGTCAAACTCTTCATATTTCACT R 2 1 2 1 201000 r 74 goat snp41430-scaffold539-1097204 6 92698960 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791780 Affx-122941658 AX-385278771 6 89433167 TGACAAATAAGAGAGGATAGGTTTAGAAATAATTC[C/T]GGTGTGTCCTCTCAGTTGGCACAAGTATTACCAGT Y 2 1 2 1 101000 r 74 goat snp41429-scaffold539-1052259 6 92743827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429814 Affx-122938188 AX-123300155 6 89475739 CTTCCTGATCCAGGGATTGAAATTGTGTCTCTTTA[C/T]GTCTCCTGGCATAAGAGATCCTAATTTTACAGGTT Y 2 1 2 1 303000 r 74 goat snp41428-scaffold539-1009687 6 92786528 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448977 Affx-122923118 AX-123319312 6 89505201 TGGTTGAAGTCACACATCTTGACACACTGAAATAT[A/G]TTGACTTTTGCTTTCTCTTCTATATGAGGTTCCTG R 2 1 2 1 201000 f 74 goat snp41427-scaffold539-980225 6 92816467 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395785 Affx-122963664 AX-123266140 6 89545291 TTTATTTTAATTTTATTGTGGCATTACTCTGTACT[A/G]TGTCATACATTGGTATGCATGAATGCAAAACATGT R 2 1 2 1 101000 r 74 goat snp41426-scaffold539-940135 6 92856658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408901 Affx-122953969 AX-123279252 6 89598288 ACTTTTTGGCCAACCCAGTAGTATTGTCTGTCACA[A/G]TTGAGTTCTCCAGAAACAAGACTCCCACGTTAGTT R 2 1 2 1 102000 r 74 goat snp41425-scaffold539-887138 6 92909796 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787001 Affx-122963235 AX-385274030 6 89636295 AATGCAAATATTTACGGGAGGCTACTCATCTTACA[A/G]TAAGTAGGCTTTCCATATGTATGTGGAGATTAAAT R 2 1 2 1 101000 r 74 goat snp41424-scaffold539-849131 6 92947776 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789018 Affx-122945681 AX-385276031 6 89671853 AAAAGTGGATTAGCTGCATTGTTTAATGCTATCTC[A/G]TTTGGATCAGTGTGAGTCTGCATTGGCCTTGCCTT R 2 1 2 1 101000 r 74 goat snp41423-scaffold539-813573 6 92983706 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410156 Affx-122952793 AX-123280506 6 89708041 ATAAACTGATTGCCCCTGAGATAACCATGCTGAGC[A/G]TAGGGAATGGAGTGAAGATCCTCCTTTAGGCAGTT R 2 1 2 1 101000 r 74 goat snp41422-scaffold539-777385 6 93019669 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451140 Affx-122921369 AX-123321474 6 89762487 AACCACCTGGACCACCCACCACTTCCAGACATGTA[C/T]GGGAAGTCAGTCGGAAAATCCCAAATAATGGCATG Y 2 1 2 1 201000 r 74 goat snp41421-scaffold539-722939 6 93075400 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797393 Affx-122971475 AX-385284332 6 89806451 CTGAAAAGAAAATTATTCTCATCATCATCAGACAA[G/T]ATTTATTCAACATGCACTTGGGTATGATACAGTAT K 2 1 2 1 101000 r 74 goat snp41420-scaffold539-678975 6 93119275 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785441 Affx-122924067 AX-385272486 6 89856081 CCAAAATATGCTCTTTTAAACGGGCAAAAAGAATG[C/T]ATATTTCTTCACATAACTTTAACAAAAAGGGGGAT Y 2 1 2 1 101000 r 74 goat snp41419-scaffold539-629345 6 93169191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786843 Affx-122977199 AX-385273872 6 89910616 CTCAGTGTCCCTACCTCCCAGGCTGTTAAATATCT[A/G]TGATATCATCCTATGTTAAATGCAATAGCACAGCA R 2 1 2 1 102000 f 74 goat snp41418-scaffold539-574810 6 93223920 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446353 Affx-122925607 AX-123316689 6 90043188 TTTTATTGCTTTAACTGCCCCGTCATTTTTATCCA[C/T]GATGGCTCTCCAATGCAATGTTTTAAGTGAGGAGC Y 2 1 2 1 101000 r 74 goat snp41415-scaffold539-442238 6 93356714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769503 Affx-122923396 AX-385256673 6 90084820 TGGTCATTACACTAAGGGAACACAGACTCTGTACC[G/T]ACATCATAACAGCTGACAGCACAGACTGCATCCAA K 2 1 2 1 101000 r 74 goat snp41414-scaffold539-400606 6 93398426 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417125 Affx-122947369 AX-123287473 6 90121855 TAAAAGCCTCTGTTCTCATTCCTTCAGTTTGTCTC[A/G]TATCTGTCTGTCTCTCTCTGACCTTTTTCTTTGAC R 2 1 2 1 101000 f 74 goat snp41413-scaffold539-363571 6 93435610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278405 Affx-1111836407 AX-519551890 6 90126608 AAAGTCATTGACCTCTGTGTTATGTCTCATAGGAT[A/G]AAAAAGGCAGAAAAAGCTTGTTGTCATCCTTAGTA R 2 1 2 1 101000 f 74 goat Random2.2K-719 6 90126608 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441577 Affx-122928679 AX-123311914 6 90163532 GAGACTGAGAGCAGGTCAAGCAGTCTGGGTGGCAA[C/T]GAACTATGATCAAGGACAAAGAAGAGGAGAACTCA Y 2 1 2 1 101000 r 74 goat snp41412-scaffold539-321894 6 93477032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403421 Affx-122957751 AX-123273774 6 90194421 TCTGACTCTGCTTTGATTTATGTGTTAGCCAGAAC[C/T]AGAAAAGCCCTTCATAACAACACAGGTACTTACAT Y 2 1 2 1 201000 r 74 goat snp41411-scaffold539-291005 6 93508327 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442272 Affx-122928268 AX-123312609 6 90248500 ACAATCCCCTGACAGAAGACCACATAAAACCAATA[C/T]GCTCTCAAATCTTGCTGTGGAGTCAACCTGAAGGT Y 2 1 2 1 201000 f 74 goat snp41410-scaffold539-236926 6 93561024 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278407 Affx-1111836408 AX-519551892 6 90290741 CTTTATCTTGGTACATGTGATTGTTTCAGCTGCCA[A/G]CAGCATTAATGGACTGAAAATCCAAAGATATTAAA R 2 1 2 1 101000 f 74 goat Random2.2K-720 6 90290741 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796544 Affx-122959807 AX-385283490 6 90307076 CATAATTTCTAAAACTCTACCTGCTGTCTTTGTTG[C/T]GATTCAGGGCTGCTATACCACTTTGGAGTGTAATT Y 2 1 2 1 101000 f 74 goat snp41409-scaffold539-178350 6 93619419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767306 Affx-122952924 AX-385254587 6 90346432 TGTTCAGAAAGACACTAAGCATCCTAGGGCTGAGG[C/T]ATATTATGCTATTTTCAAGGGTCATGTGTATGTAA Y 2 1 2 1 101000 f 74 goat snp41408-scaffold539-138994 6 93658836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449322 Affx-122922993 AX-123319657 6 90394947 GAGCTGTTTCTCACATATTTCTTATTAAAAAGAGT[A/G]CGGTAGAGGAAACATTTTAAAGCACTTTGAAATGC R 2 1 2 1 201000 f 74 goat snp41407-scaffold539-90479 6 93706638 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419745 Affx-122945886 AX-123290093 6 90505282 TGCCAAGAGGTTAGCATAATGCCGAGCATGTCGTA[C/T]GTGCCTGACGAATGTTTATTTAAAAAGTACAATTT Y 2 1 2 1 101000 f 74 goat snp4469-scaffold1143-680238 6 93816114 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380852 Affx-122975443 AX-123251210 6 90546624 CTCTCTGAGAACACTCCTGATTCTTACTCACCACT[C/T]CCACCATCACCACAATTTTCTAATGACTAAGTATA Y 2 1 2 1 101000 f 74 goat snp4468-scaffold1143-638896 6 93858147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792541 Affx-122937919 AX-385279522 6 90586915 AGGCAAGCACAAAGCCAGCCAGGCTTAGATGAAAT[A/G]CACACTGTTTGCTAAATGGCCGTGGTGTTTTGAGG R 2 1 2 1 101000 f 74 goat snp4467-scaffold1143-598605 6 93899141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420243 Affx-122945070 AX-123290591 6 90630129 ATAAACGGCAGCAGCAGAAGGCCTAGGAGTTCCCA[A/G]TCTGGGAGATCTCTGCTTCCTCAGTCTTCCAGAGA R 2 1 2 1 201000 r 74 goat snp4466-scaffold1143-555391 6 93942330 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779740 Affx-122955175 AX-385266840 6 90661713 GTTGTTTTCAGTTTGGGGTATTGTGATTGACAGCA[A/C]CTTCTTCCCTCATGAGCAAATATTGCTTGGGTTGC M 2 1 2 1 101000 r 74 goat snp4465-scaffold1143-523807 6 93973861 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415159 Affx-122949403 AX-123285508 6 90765427 ACAATCACTTCATGAAGGTGGAGAGGGAGCAGTTC[A/C]AGCACGACTACTGTCGAACCCTGTTATCTCATACA M 2 1 2 1 201000 r 74 goat snp4463-scaffold1143-420093 6 94078100 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413378 Affx-122950135 AX-123283727 6 90817084 AGTCCTTACCCTTTGATTATAATCAACTCTTTATA[C/T]GTCCGCCCCCTCATAGCCTGTGAGCTCTCCCACTG Y 2 1 2 1 103000 f 74 goat snp4462-scaffold1143-368436 6 94130124 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774228 Affx-122959127 AX-385261365 6 90856846 ATCTCTGGTTCTCACATACCAACAGGATAAAATTA[G/T]ATACCTTTAATAAAAGTGCTTAGGCTCTACTGCAA K 2 1 2 1 101000 f 74 goat snp4461-scaffold1143-328674 6 94169915 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382399 Affx-122973837 AX-123252757 6 90906599 GATATCTCAGCCTCACCTAGATGACTTCTTCGGGT[A/G]TGTTGACAGCAACTTGTGATCATCTAGGCACTTCT R 2 1 2 1 101000 r 74 goat snp4460-scaffold1143-278921 6 94219862 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440877 Affx-122929239 AX-123311214 6 90954350 GCATTCATTCACTTAACAGAATTTTTTAAACATCT[A/G]CTCTATGCCAGACATTTTTCTGAGCACTGAATACC R 2 1 2 1 101000 r 74 goat snp4459-scaffold1143-231170 6 94268080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802369 Affx-122973441 AX-385289273 6 90984012 ACCTTTGCCATCACTCCATCATCCCAATACATACA[A/G]TAGTTTCCCTAAGTGTTTAGAATGCCCACTCACCT R 2 1 2 1 101000 f 74 goat snp4458-scaffold1143-201508 6 94297562 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439186 Affx-122931049 AX-123309523 6 91042623 GTACAGAACAAAAGAAATGTTTCTTTCCACTTCCT[A/G]AGAAGCATTTTTGAATTATGAAAACCTCAGTATCT R 2 1 2 1 201000 r 74 goat snp4457-scaffold1143-142897 6 94356420 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776928 Affx-122962769 AX-385264052 6 91071169 CACAAATTGTCTATACTGAACACTTCTACCGTCTA[C/T]ATTTTTGGCCCATAGAAATTGCCTCCCTGTGAGTA Y 2 1 2 1 101000 r 74 goat snp4456-scaffold1143-114351 6 94384925 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401340 Affx-122959262 AX-123271693 6 91109382 TATCTAATGTTCAAATCCATCCTACCTTATGCTAC[A/C]GGGATGGCCTAGTCAGGTGTCAATCAAGCGTTCCT M 2 1 2 1 201000 f 74 goat snp4455-scaffold1143-76138 6 94423117 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799491 Affx-122964461 AX-385286421 6 91145301 AATGCTGCTGACCTTGCATAATAATTTTTCCCTTA[C/T]AACATATTAATTATTGTTCTGGCACCTCTGGCCTA Y 2 1 2 1 101000 r 74 goat snp4454-scaffold1143-40219 6 94459436 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453926 Affx-122919899 AX-123324259 6 91180953 CTGTAGGAAATGACCCACACCCACTCCTGTACTTG[A/C]TGCTTTAAAGAAACTATCTGGGTGGGCTCAGGTCT M 2 1 2 1 101000 r 74 goat snp4453-scaffold1143-4567 6 94495194 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781950 Affx-122930430 AX-385269031 6 91237016 TGTCCATATCATTGATGTTAATCTAGCTCACAGCT[A/G]CTTTTCACTATTCTTCTAAAAGCATAATGATTTTC R 2 1 2 1 101000 f 74 goat snp19320-scaffold1951-51397 6 94551442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425101 Affx-122941234 AX-123295447 6 91271049 AGAGAAGAGGCCTTTTAAAATCAGTTCCAATGAGG[C/T]GGTTCCCTGGGAATTCTGAATGTTGATGGGAACAT Y 2 1 2 1 201000 r 74 goat snp19321-scaffold1951-85430 6 94585913 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394912 Affx-122964319 AX-123265267 6 91315559 TCCTGAAATGAAAACAGTTGCAAATTATTTTGACA[C/T]GTACTTAGTGTGTTTTGTGTCTCTGAAGGTAGCAT Y 2 1 2 1 101000 r 74 goat snp19322-scaffold1951-129940 6 94630919 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390602 Affx-122967179 AX-123260959 6 91346618 GTGTGTAAAGGACTTTGAGCCTAAGGTTTAGTGGA[A/G]TTGAAAGTTACACATCTAAAAGGTGATGCCAAATG R 2 1 2 1 101000 f 74 goat snp19323-scaffold1951-160999 6 94661877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278409 Affx-1111836409 AX-519551894 6 91347477 CCCTTCAGCTAGAGAAGCGACTGCCTACCAATGGC[A/G]CCTTCACACAGCCCTGCAGGAGCTCACCTTGGTGA R 2 1 2 1 102000 f 74 goat Random2.2K-721 6 91347477 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791433 Affx-122925339 AX-385278424 6 91383058 AAGTCTTGTTCTATACAGGAAATATCTGACATGTC[A/G]TGTCCATATTCATCTCATTGTTGGGATTTGAAGGC R 2 1 2 1 101000 r 74 goat snp19324-scaffold1951-197439 6 94698397 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401146 Affx-122959376 AX-123271499 6 91416430 CATGAAATTATTTATCATCCCCCTTAGAATCAGAA[G/T]TTCTCTTTCTTCTCTATGATTTTTCTACACGGTAT K 2 1 2 1 303000 r 74 goat snp19325-scaffold1951-230811 6 94731572 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443650 Affx-122927202 AX-123313987 6 91511073 ACTTATGTTAAAATATAATGCTATATAATACTTCC[A/G]ACCATTCAAAACTAGATAGCATGGCTTACTGAATA R 2 1 2 1 101000 r 74 goat snp19327-scaffold1951-325454 6 94827100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404224 Affx-122957653 AX-123274576 6 91551718 CCCTTGGCCTAACTGGGCCCCTACCTGGGACTCTC[A/G]TGCTACCCAAGTTCACCCTCCAGAAATCAGCACTC R 2 1 2 1 101000 r 74 goat snp19328-scaffold1951-366099 6 94868112 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278579 Affx-1111836410 AX-519552058 6 91576002 AAAAATGGGACTAATGATGGAGACTATGTTTTTCT[A/G]ACTGGAGAAGACAATTACCTTAACTTTTCCAAGAT R 2 1 2 1 101000 r 74 goat Random2.2K-722 6 91576002 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403911 Affx-122957481 AX-123274263 6 91580420 CATAAAAGTTTCCAATAAAATTTGTTTTAGATACT[C/T]GCAATAAAACATTCTTTGCTTGCCTCTTAGCTCCA Y 2 1 2 1 101000 r 74 goat snp19329-scaffold1951-394801 6 94897010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386267 Affx-122970948 AX-123256625 6 91614825 ATGTGCGAGGACTAATGATGGCCCGGGGCCTGGGA[C/T]TGGCGACGAGCTGTGCTTGGGAAACAGTCAGAGGT Y 2 1 2 1 101000 r 74 goat snp19330-scaffold1951-429206 6 94932402 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436244 Affx-122932559 AX-123306583 6 91645351 AGACTCCCTACTCTCGGCTTCCCAGTAAGTTTAGC[A/G]TTGAGAGAAACTCATGGAAGTTTAGGGAGAGGAGA R 2 1 2 1 101000 r 74 goat snp19331-scaffold1951-459732 6 94963107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453504 Affx-122919817 AX-123323837 6 91677741 CTGGTTTCTAAGTGTCTAAAGAAAGACCTTATTCC[A/G]TGAAATACATTTTTTGGACATTCATGTGATCTCTG R 2 1 2 1 101000 f 74 goat snp19332-scaffold1951-492122 6 94995511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387836 Affx-122969661 AX-123258194 6 91711763 TTCATGCTTTAGCAAAATTGTTCTCATCAGTAAAA[G/T]CCTTGTCTGAATTATACGTTTCTTTGAATGTAGTA K 2 1 2 1 101000 r 74 goat snp19333-scaffold1951-526144 6 95029782 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273286 Affx-1111833523 AX-519546930 6 91712964 TTGCAGGGTAACTGTGTAGCTCTTCATCACACAGG[A/C]TGGACAGCATTTTTTGATGATAGGAGCCAAACAAC M 2 1 2 1 101000 r 74 goat 6_91712964_AF-PAKI 6 91712964 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38441715 Affx-122929149 AX-123312052 6 91746422 TTATCTTATATTTTCATTTAAAGGTAATCAAATCC[C/T]GTATGCATAGGGTTTGAGGTAGGCTATGTGTGCAC Y 2 1 2 1 101000 r 74 goat snp9903-scaffold1352-2650363 6 95065806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409205 Affx-122953170 AX-123279556 6 91785387 GAGGACAGGACAGATATCTGTTTTTAGATGGTCTT[A/G]TATTTTGATATATTAGTGATACCAAGGTTATATAT R 2 1 2 1 101000 f 74 goat snp9902-scaffold1352-2611398 6 95105044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408782 Affx-122953375 AX-123279133 6 91825476 TTTTTGTTTTCACCATTGTTAACAATGTAGAAAGT[A/G]TACTTGCCAGGATTTCAAAATCAATTTGAATTTAT R 2 1 2 1 101000 r 74 goat snp9901-scaffold1352-2571309 6 95144406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418571 Affx-122946381 AX-123288919 6 91922278 AACCATGAGGAAAACCTGTAAGGGAGTTTGGGAAA[C/T]GTCCATTTTTAGCTTTTTCTAGCACGCAAAAGACA Y 2 1 2 1 101000 f 74 goat snp9899-scaffold1352-2474507 6 95237741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401045 Affx-122959659 AX-123271398 6 91973070 ATTTGAAACTCAATTGACAGAGACTAAAACAAAGA[C/T]AGTCATTATATTACAGTTCTTAAAATGTGCATTGG Y 2 1 2 1 101000 r 74 goat snp9898-scaffold1352-2423715 6 95288815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428793 Affx-122938404 AX-123299135 6 92017807 TCTCAGAGCCCTTTGGCTGCAAGTTCCTACTAGCA[A/C]TGATTTCCAGAGGTCTTGGCAGGCTGTGTAAGCCA M 2 1 2 1 101000 f 74 goat snp9897-scaffold1352-2378978 6 95333419 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417129 Affx-122947366 AX-123287477 6 92054489 GGTTTGTTATTTATTAGTAGTAGCAAAAAGTACAA[C/T]ATTTTCTTAGTCCTGCTTAAAACATCATCTAATAC Y 2 1 2 1 101000 r 74 goat snp9896-scaffold1352-2342296 6 95370112 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772228 Affx-122977678 AX-385259383 6 92087376 AAGTTAACAACAGTAGTACACAAGTTTTGTGGGCT[A/G]TGGAATAATGGTCGCTCACATCTTCCCATTACTGG R 2 1 2 1 101000 f 74 goat snp9895-scaffold1352-2309409 6 95403210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786212 Affx-122947297 AX-385273247 6 92138914 ATTTCTGCTAAAAATATGTGTCATTTTTCCTAAAG[C/T]GCCCTTTCCTTTGCCCTCTACTGTATTTTGAAGAC Y 2 1 2 1 101000 r 74 goat snp9894-scaffold1352-2257871 6 95454706 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381464 Affx-122974979 AX-123251822 6 92170100 AAGATAAAAATAGCAAAACGACTCACTACTTGTGC[A/G]TTCCCAGAAAGAGAAAGGTGAATCGAGGTTTAAAG R 2 1 2 1 201000 f 74 goat snp9893-scaffold1352-2226685 6 95487331 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400149 Affx-122960698 AX-123270504 6 92222898 ACAACCTGATTTTTTAAATGGACCTAAGACCTTAA[C/T]AGATACCTCACCCCAAATGAAGAATATGTATAATC Y 2 1 2 1 201000 f 74 goat snp9892-scaffold1352-2173887 6 95539069 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445254 Affx-122925479 AX-123315591 6 92304909 TTAGCATTCCAGACAGAGAGATCTCAGTTAGAACC[G/T]AGTTTCAGGCTGATAAGCCAGATCCTCAGGCAGCA K 2 1 2 1 201000 r 74 goat snp9891-scaffold1352-2091876 6 95623196 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801910 Affx-122938955 AX-385288815 6 92353866 TTGTGAAGGTGAGGGTAATCACTATTCTACACTTG[C/T]AAAAGTTATTTTTTGCCAATCAGGGCTGTATAAAG Y 2 1 2 1 201000 f 74 goat snp9890-scaffold1352-2042919 6 95673548 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383437 Affx-122973470 AX-123253795 6 92392023 CCACAGATTTAACAACTGCAGGTCTTATAATACTG[C/T]AGTACATATATTTTTTTTAATCCACATATAAGTGG Y 2 1 2 1 103000 f 74 goat snp9889-scaffold1352-2004762 6 95711661 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789086 Affx-122960667 AX-385276099 6 92456638 CCTTGGAGAGTTCAGACCTCATAAAATTCACATAT[A/G]ATTTCTGCTGACAGCAAATTAATATAGATTCAAAT R 2 1 2 1 101000 f 74 goat snp9888-scaffold1352-1940147 6 95777545 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765526 Affx-122946730 AX-385253010 6 92501014 ACCTGCATTTGATAAAACATTAACTTTGTTCTCTG[C/T]GTAAATAAAATGGTGGCTCTCCAGGTGCACCTGCT Y 2 1 2 1 101000 f 74 goat snp9887-scaffold1352-1895771 6 95822843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453807 Affx-122919568 AX-123324140 6 92540250 GAAACTGGGAATAAGGGTCCTTTGGGAATAAATTA[C/T]AGCACTGGTACTCTAGACAGTAGATCTGTTATAAT Y 2 1 2 1 101000 r 74 goat snp9886-scaffold1352-1856535 6 95862319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773148 Affx-122925155 AX-385260291 6 92611018 AACTACTTTAGTCTACCATTAGTGAGTAATATAGT[C/T]AGCCCCCACAATGTTTAAGTTAGTGAAGAAATGGA Y 2 1 2 1 101000 r 74 goat snp9885-scaffold1352-1785767 6 95932409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789812 Affx-122948640 AX-385276819 6 92642913 AGTTGGAGAACTATTACAATTGATTCACAATAGGC[A/G]TAGTATTTTCTGTGTTAAAACTACCTAAACTGCAA R 2 1 2 1 101000 r 74 goat snp9884-scaffold1352-1753872 6 95964303 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772225 Affx-122921893 AX-385259380 6 92690096 ATTATTGTTATGTCATCATTATCCAAAAGAAGTGT[A/G]TTTATATAAGATTCCATAATTTCATATTTTCATTT R 2 1 2 1 202000 r 74 goat snp9883-scaffold1352-1706689 6 96013396 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401469 Affx-122958965 AX-123271822 6 92751924 CTGACTTACATTATGGTTGAAGAAATGGTGATAAG[A/C]TTGGATTTAGTAAGAATACTCCAGACCCTCAAATC M 2 1 2 1 101000 r 74 goat snp9882-scaffold1352-1644861 6 96076212 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789241 Affx-122962993 AX-385276252 6 92826883 CAGGACATTATGAGATACTTATACATTAGCACAGA[A/C]GAATTGTGTCTTCTTTCATTTGCTGGTGTCATGGA M 2 1 2 1 101000 r 74 goat snp9881-scaffold1352-1569902 6 96151594 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406203 Affx-122956133 AX-123276555 6 92907534 AAAGAAAACAGCCCCATAATTGGGTACTGAGCTAA[C/T]AGTTGGGAAGTAGCTCAAGAAGATGAAAGGAAGGT Y 2 1 2 1 202000 f 74 goat snp9879-scaffold1352-1489251 6 96234686 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392757 Affx-122966002 AX-123263114 6 92947590 TACATTCAGAATAAATGAAATGACGAGATGTTAAG[C/T]GGGTAGAATGATCCCTAGCTGGACTCTCACCTGTA Y 2 1 2 1 101000 r 74 goat snp9878-scaffold1352-1449195 6 96274732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429381 Affx-122938548 AX-123299723 6 92979177 GATCTGGGTTTTTAAAAACTGGGTTGCTGGTTGCC[A/C]TTCTTGTGAGGGCTATGCAATGAAAACATCAGTAT M 2 1 2 1 201000 r 74 goat snp9877-scaffold1352-1417608 6 96306278 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788660 Affx-122966435 AX-385275676 6 93013459 CTGGAAACCAAGTAGACCAAACAGGGTAAGAAGAG[C/T]GAAAATATTAAGGTGTAACTAGAAATACTTAAAAA Y 2 1 2 1 101000 f 74 goat snp9876-scaffold1352-1383326 6 96339593 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402106 Affx-122958687 AX-123272459 6 93067225 GCCCTTCTCTGAATTCTCCAGCCTAGTCACAGCGA[C/T]GATACATAAAATATTGGAAGTTTGAGAACTGAAGT Y 2 1 2 1 201000 r 74 goat snp9875-scaffold1352-1329560 6 96393473 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792872 Affx-122941950 AX-385279850 6 93098222 AAGGATTTCCACATAATGAATGGTAGTTATAAGGG[G/T]CAAGTGTTGGTGGAGCTAGAAAAGACTTTTTGTCT K 2 1 2 1 101000 r 74 goat snp9874-scaffold1352-1298563 6 96424327 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408132 Affx-122954239 AX-123278483 6 93143445 CAGGGTTCTTTCTCAAGTCTCTGCGTGCATGTGTT[A/C]GTTGCTCAGTTGTGCCCGGCTCTTTGCAACCCCAT M 2 1 2 1 101000 f 74 goat snp9873-scaffold1352-1253340 6 96470025 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414938 Affx-122949092 AX-123285287 6 93174494 CTTACCGACTTGAAAACTGCAAAGGAAAGATATTT[A/G]CAAAAGATGAAGCGTGTCATTGTGTTCCTTTTTTC R 2 1 2 1 101000 r 74 goat snp9872-scaffold1352-1222291 6 96501544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415638 Affx-122948579 AX-123285987 6 93230491 TGAGAGAGTCTTTCTGAATCATCATAAACCTGAAT[G/T]AGAAAAGGGCTGAGTTTTATACAGCTTAACTTAGG K 2 1 2 1 101000 f 74 goat snp9871-scaffold1352-1166294 6 96557544 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382053 Affx-122974933 AX-123252411 6 93271146 AAACAGAAGAGACAGAATAACCATACAGAACCCCC[A/G]TCTGATGTTTTGATTAAGCCTTGGTGAGGATGTGA R 2 1 2 1 101000 r 74 goat snp9870-scaffold1352-1125639 6 96598371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421007 Affx-122944556 AX-123291354 6 93322577 GGGAAACGTCTGCACACCCCCACATGCTCACCAAC[A/G]CCAGGGACCAGTGCCCGAGGCATTTCCTCTTTTCC R 2 1 2 1 101000 r 74 goat snp9869-scaffold1352-1074208 6 96649422 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464470989 Affx-1110499642 AX-515943445 6 93349772 TCATTGTAGTAGGGGGACAGCCATTGATCTTGGTG[A/T]CAGTTGACTGATACTTTTAAAGCATTTTCTATTAG W 4 1 2 1 202000 r 74 goat Random2.2K-726 6 93349772 A T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417851 Affx-122946779 AX-123288199 6 93360140 AAGTCAGAAAGAAAATACGAGAGGATGCTCTGCTC[A/G]TGATTCAACAGTAGCAGGGGCGGTAAAGACAGGAT R 2 1 2 1 101000 f 74 goat snp9868-scaffold1352-1036645 6 96687011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454274 Affx-122919637 AX-123324607 6 93400720 CTTACTTTAAGGAGATGTATGTTGAAGTATTTAAG[C/T]GTGTCAGCAACTTTCAAATTGTTCTTCAGCAGCCC Y 2 1 2 1 201000 f 74 goat snp9867-scaffold1352-996065 6 96727903 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426149 Affx-122940607 AX-123296495 6 93429960 TAATTCAATCCAGTAGCATTATTGCTTCAACCACA[C/T]GTATCTAGTGGGTAACATATGACTCACCAAAGCGT Y 2 1 2 1 101000 r 74 goat snp9866-scaffold1352-966825 6 96757224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802658 Affx-122955461 AX-385289557 6 93476928 TCAGAGGTCAATTGGAATTTTTGGTTCTTAAGTGC[C/T]TCTAAATGTACCATTAAATAAACTTGGGCACCATC Y 2 1 2 1 101000 f 74 goat snp9865-scaffold1352-919857 6 96804893 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376811 Affx-122977933 AX-123247170 6 93531203 GAGACAGTCAGGAAGAATAAACTTTCCTTTCAGAA[G/T]ATTGAGGATCAGAAAGAAAGTGTTCCTTGAGTGCG K 2 1 2 1 101000 r 74 goat snp9864-scaffold1352-865582 6 96858925 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406355 Affx-122955429 AX-123276707 6 93567095 CTTGGGACTGTGTGAAGATTGGATCAGTTTATGTA[C/T]GTATCAATACAAATCTTTATTGTGGTATCTGGAAC Y 2 1 2 1 101000 f 74 goat snp9863-scaffold1352-829690 6 96895191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448393 Affx-122923686 AX-123318729 6 93619286 CTGATGAGATGAGATTCTGCTCCTCTACCTTATTC[A/G]TTTTCAGCGCTAACTAAAGCAATTGACAAGTGTGT R 2 1 2 1 201000 r 74 goat snp9862-scaffold1352-777499 6 96947441 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445769 Affx-122926068 AX-123316106 6 93668905 CCCCAAAGGGGAGCGTCTGTAAGTAGTGGGGAGGC[A/G]TTGAGGAGTGTTGGCAGTGGAGTAACCATATCAGA R 2 1 2 1 101000 r 74 goat snp9861-scaffold1352-727880 6 96996890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393847 Affx-122965153 AX-123264202 6 93698947 CATTTTTTTCACTCACTTCAATTTAAAAACAAATA[A/G]CAATCTCTTTTTGTCCTAGCACATGCTATGGTATA R 2 1 2 1 303000 r 74 goat snp9860-scaffold1352-697838 6 97026363 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427600 Affx-122939367 AX-123297943 6 93738088 CTGGCCGAATCAGAGCTTGCCATCTTGTATCAACT[C/T]TGGAAATCCCAAGGTTCTCTAAGTAGGATGACGTT Y 2 1 2 1 101000 r 74 goat snp9859-scaffold1352-658697 6 97063867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381908 Affx-122974149 AX-123252266 6 93778498 GTTTAACCTTCCATCTCTTAAAGGAGGAAATGACT[A/C]TTTTGGGCTTCCCTGGTAGCTGAGATGGTAAAGAA M 2 1 2 1 201000 f 74 goat snp9858-scaffold1352-618287 6 97104282 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413585 Affx-122950578 AX-123283934 6 93820402 ACTAAAACTGAAAAAAAAAAAATGACTTAGGTGGT[A/G]CCCTTCCTAGTGACAAGTCTGAGTATTTAATGCTA R 2 1 2 1 101000 r 74 goat snp9857-scaffold1352-576383 6 97144011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452890 Affx-122920220 AX-123323223 6 93858116 TACATATGTGGCGGGCATTGACAAAATGTGGGTGC[A/G]TCTTTGCCATCTCAGCTCCAGGACTTAAACAGCCT R 2 1 2 1 101000 r 74 goat snp9856-scaffold1352-538669 6 97189243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802302 Affx-122972191 AX-385289206 6 93909892 AGAAGTGCTGGTTTTAAGGAGCTCAGATTCACGCC[A/G]TTCATTCAGTTTACTGCATAGTAATCACTTACTTG R 2 1 2 1 101000 f 74 goat snp9855-scaffold1352-486893 6 97241865 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38393752 Affx-122965217 AX-123264107 6 93950010 AATCATTTTTGATTGATTTCTTTCACTCTGCATCC[A/G]TCTCCTTTACAAACAAACTGGAAACTCTGACAAGA R 2 1 2 1 101000 r 74 goat snp9854-scaffold1352-446775 6 97282038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396341 Affx-122963061 AX-123266696 6 93988222 TAATTTTTGAAAGTGAGGTGGACATTGAATGGACA[C/T]GTGATGGGAACGGGAAATGTCCAAGAGAAGGTACC Y 2 1 2 1 201000 f 74 goat snp9853-scaffold1352-408563 6 97320058 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772591 Affx-122928626 AX-385259740 6 94038060 TGGTGAGAAAGGGTTAATTTGGCAACAAAGCCACG[A/C]TGAGGTTATATTCATCTCAGAACCGAGTTGCTGGA M 2 1 2 1 101000 f 74 goat snp9852-scaffold1352-358725 6 97370118 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435718 Affx-122933302 AX-123306057 6 94071400 TCCCTACCATTCTGTTACTTATGTGGTCCACATTC[A/G]TGAATAAATATTAGAGCTTTACTTGCCTGGAATTA R 2 1 2 1 101000 f 74 goat snp9851-scaffold1352-325385 6 97404136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447423 Affx-122924389 AX-123317759 6 94114856 AATTCCACAGTTTTAAAAATTCATTTTCTAGATAT[A/G]CATAGTTATCAGAATATGTTCTTTGCATGATTTCT R 2 1 2 1 101000 r 74 goat snp9850-scaffold1352-281929 6 97447254 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434394 Affx-122934690 AX-123304735 6 94163806 AGTGAACTCCCCATTTTATTTCCAGAGACTTCACC[A/G]TCTTTCTCTGTTCCCACTTTGGCTTTTATACATTT R 2 1 2 1 201000 r 74 goat snp9849-scaffold1352-232979 6 97496389 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378505 Affx-122976649 AX-123248864 6 94202912 TAGCATCGTCATTATTATTTTTAATTTAGAAAAGT[C/T]ATTGTGTAAAGTAACACTCCTCATGGTTTAAAGTC Y 2 1 2 1 101000 r 74 goat snp9848-scaffold1352-193873 6 97536858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453983 Affx-122919449 AX-123324316 6 94269622 TTATTTTTTAAGGTTTTAAATGTCAGTCAATTTCT[A/G]AGGCCACCCCTTCCGACCTGTTATTCCATGGGTTA R 2 1 2 1 201000 f 74 goat snp9847-scaffold1352-127163 6 97604470 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378527 Affx-122976629 AX-123248886 6 94303804 CTTTCAGGACCACGTGGCCTCTGGTTCTTTCTATA[C/T]GTCTGCTCATTTTTTCTCTCTCTCTTCCTTCACAC Y 2 1 2 1 201000 f 74 goat snp9846-scaffold1352-92981 6 97638837 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438182 Affx-122931832 AX-123308520 6 94337697 ATCACCAAAACAATTACCAGCCGTATTAAAGGGGA[C/T]ACTGCAGAAAACAGGTGTGTATCAGAGTTCAAGAA Y 2 1 2 1 101000 r 74 goat snp9845-scaffold1352-59088 6 97672694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425082 Affx-122941247 AX-123295428 6 94373747 TCGACAGAAAAAAGAAATATAAGCAGCTAGTAACC[A/G]TCTTGGATCGTAGGCTTTACATCAGGCAATGCCCT R 2 1 2 1 101000 r 74 goat snp9844-scaffold1352-23038 6 97704927 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396871 Affx-122963242 AX-123267226 6 94409070 CTGCAGGGGAAGCATGGAGTTCTAAATACTGGACT[A/G]CCAGGAAATTCCCTTTTCTCCCCCATTATAATAAG R 2 1 2 1 103000 r 74 goat snp913-scaffold1025-12186 6 97740256 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273288 Affx-1111833524 AX-519546932 6 94412502 AAAGGAATGATATTCCACTGATCAAGAATGGTGAG[A/G]CTTGTGGTCCCTCAATTCAGCCATGTAAACGTGCC R 2 1 2 1 101000 r 74 goat 6_94412502_AF-PAKI 6 94412502 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426421 Affx-122940829 AX-123296767 6 94439813 AGAGTCCAGGGAAATCCTCAGGATGAACGAGGTCC[A/G]CGAATGAAGAAAGACAGAGAAAGCGATAAGGAAAG R 2 1 2 1 101000 r 74 goat snp914-scaffold1025-42929 6 97771372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403888 Affx-122957496 AX-123274240 6 94469753 AAGACCAGAAACAAGATGAGATCATTGGATCTGAC[A/G]GTTCAGAAATCATTGATGACGCTGGCATGAATGGT R 2 1 2 1 201000 r 74 goat snp915-scaffold1025-72869 6 97801339 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774200 Affx-122951869 AX-385261337 6 94513109 ACTAGTGAAAGGCATTTGATGAGAAATACATGAGT[G/T]AAGCAACTGCTATAAAGACACTTTAAGGTCAATTT K 2 1 2 1 101000 f 74 goat snp916-scaffold1025-116225 6 97844840 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397284 Affx-122962335 AX-123267639 6 94592948 TGTTTGAATGACATGTTGTAGCTATAGCGATTAAA[C/T]CACATGTCCGCGTTCTAGTGTTAAAGCATAGTTAC Y 2 1 2 1 101000 f 74 goat snp918-scaffold1025-196064 6 97923699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419027 Affx-122946035 AX-123289375 6 94643585 AAGTGAGGAAGTGAAAGCTGAGGGCTGATAAGAGA[C/T]GGCAGCCTTCCATCAATGAACTGTCCATCAAGTCT Y 2 1 2 1 201000 r 74 goat snp919-scaffold1025-246701 6 97975207 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396246 Affx-122963329 AX-123266601 6 94678132 TAAAATTCATAAACCATAACTATAGTTCAGCTTGC[A/G]TATTACCCAGAGATCATATTACTTTCCCCTGGTCC R 2 1 2 1 101000 r 74 goat snp920-scaffold1025-281248 6 98009447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402040 Affx-122958733 AX-123272393 6 94723323 CTGTCAGACACCAGATCCCACTGTGGACAGAGATG[C/T]GAGGCTGAAACAGAAGGGGACAGAAAAGCTGGGTA Y 2 1 2 1 201000 f 74 goat snp921-scaffold1025-326439 6 98054724 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388570 Affx-122969170 AX-123258928 6 94790824 AAGTTTTACCAGCTGAGCTGCTGGGATCACTATGT[A/G]GCCCTGGATTCACAAACTCGTTATCAAACCCTCTG R 2 1 2 1 201000 r 74 goat snp922-scaffold1025-393940 6 98122325 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417435 Affx-122947209 AX-123287783 6 94819532 CTCAAACTGTACAGAAAAGTCTCCCTGCCCCTCAA[C/T]ACACACTATTTGAGACACAGACTCTATCTAGTTGA Y 2 1 2 1 201000 r 74 goat snp923-scaffold1025-422648 6 98150451 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772879 Affx-122967692 AX-385260024 6 94927840 CCTTCTTCCACCCTTTCCTATTGTCCACTCCCTAA[C/T]AGCTTCAATCCAATTAAACTTAAGACAATGCTGAG Y 2 1 2 1 101000 f 74 goat snp925-scaffold1025-530956 6 98258349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419736 Affx-122945892 AX-123290084 6 94957295 TCTTGCTAAGTGGCCAAAAAAGTGGAAGAGAGAAC[G/T]CAAAACAAAACAAAAATATAAGGAGAGAAATTACA K 2 1 2 1 101000 f 74 goat snp926-scaffold1025-560411 6 98287229 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417438 Affx-122947207 AX-123287786 6 94998169 GATGGTTTCCATCTCTCTCTCTAGTTCTTCCACTT[A/G]GGATCCCTTCTCCGAACTCTGCCACTCCCTACCCC R 2 1 2 1 102000 f 74 goat snp927-scaffold1025-601285 6 98328030 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780792 Affx-122930658 AX-385267881 6 95109542 CCCAGTTATACCAATTGAACACTTTAAAAAGGGAC[C/T]TACCAGGTCATCTGTGATTGGAGTTAAATCAGGAC Y 2 1 2 1 101000 r 74 goat snp930-scaffold1025-712658 6 98436619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779895 Affx-122950588 AX-385266994 6 95169513 TTTTTATTGCTAAAGTGCTAAAAATCATGTAATTC[C/T]TGTGACTCTAGATGAGGATTACAACAGGAAGAAAG Y 2 1 2 1 101000 r 74 goat snp931-scaffold1025-772629 6 98497277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453960 Affx-122919465 AX-123324293 6 95302469 CAAGGATGGGTGATTCTCCCAAATAAGATGTGATC[A/G]TTATTGCTCTCATCAGCTTCTAGCAACTGCTGGAC R 2 1 2 1 101000 r 74 goat snp934-scaffold1025-905585 6 98631918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791959 Affx-122935620 AX-385278948 6 95343924 GCTTCAAGGTGACTCACTGTGGAGCCAAGCTGTTG[C/T]ATTAGTCAGCATTCTCTTACACGTAGCCTTAGAAT Y 2 1 2 1 101000 f 74 goat snp935-scaffold1025-947040 6 98673636 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771354 Affx-122935337 AX-385258512 6 95375413 AGTTATGATTACATTAATGATCACTTGAACAACAT[A/G]TATCAAGCATTTCATGCCAGGATTTACATTACTGT R 2 1 2 1 101000 r 74 goat snp936-scaffold1025-978529 6 98704551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797177 Affx-122969536 AX-385284117 6 95429832 TACTCTTTTTATTGCCGGATACCCTCTCTGATAGC[A/G]ACTAAACGGCACTAAACGACCTACTAACTTTTTTT R 2 1 2 1 101000 r 74 goat snp937-scaffold1025-1032948 6 98757845 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401696 Affx-122959548 AX-123272049 6 95501133 TAATGCTTTCACTGGATCAGGGATGGGCTTCCAAA[C/T]GCCCAGAGCCTCATTCACTGGGCCTCCCTTTGCCT Y 2 1 2 1 102000 f 74 goat snp939-scaffold1025-1104249 6 98829880 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420907 Affx-122944604 AX-123291254 6 95603714 GTGATGAGGCAGGCAGCCTCATACAGTGTTAGCCC[A/G]TCTTCTCTCTCTGGGCCACCTGCAGCTCCAGAGAT R 2 1 2 1 101000 f 74 goat snp941-scaffold1025-1206830 6 98932429 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388775 Affx-122968934 AX-123259133 6 95634077 CACAGTGCCTATCTTATAATAAGCACTCAATAAGT[A/G]TTAGCTGACATTATTATGAATCCAAAAAAGGTACT R 2 1 2 1 201000 r 74 goat snp942-scaffold1025-1237193 6 98961621 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379590 Affx-122976030 AX-123249948 6 95663380 TTAAAGAGGAAGTTTTGATTAGGTTTGTGAAGAAC[A/G]TGCTTTCTGCATATGTCACCCTTTCACCTCTTGCT R 2 1 2 1 101000 r 74 goat snp943-scaffold1025-1266496 6 98990988 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789512 Affx-122978475 AX-385276521 6 95694032 AATCATCCCAATCCATTCCCATGGTAACAAATCAC[A/C]TTTAAGACTAATGTTGCACTATGTGATTCTGGTAG M 2 1 2 1 202000 f 74 goat snp944-scaffold1025-1297148 6 99021532 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450288 Affx-122922162 AX-123320623 6 95725920 GAGATGGAAGTTGGAGTTTAGGGCTTATAAGATAT[C/T]GTGGCTCTGGTGAATACCCCAGGCTTTCATTTGAG Y 2 1 2 1 101000 f 74 goat snp945-scaffold1025-1329036 6 99053758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782281 Affx-122978470 AX-385269359 6 95770631 TCAAAGAATAAATTAAGATGAGACATATTAACAAA[A/C]GAAAATCAAACAAAAATTTGGTGAGATCTATACAT M 2 1 2 1 103000 r 74 goat snp946-scaffold1025-1373747 6 99099108 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420717 Affx-122944778 AX-123291064 6 95805495 TAACTTTACAGAACTCTCTCTTTCTGCTTTATTGT[C/T]TGCTTATTTTCATGTAGCATTAAAAAGCATGAGAG Y 2 1 2 1 201000 r 74 goat snp947-scaffold1025-1408611 6 99134404 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431692 Affx-122936778 AX-123302033 6 95840225 AAATCCAAAACAGTTGCATATTTTAAGGAAGAAAA[C/T]GATGATTATTAATATTTTCCCCAACAAATAGGAAA Y 2 1 2 1 103000 f 74 goat snp948-scaffold1025-1443341 6 99169858 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441032 Affx-122928940 AX-123311369 6 95891648 CAGCCATCTGGGCATTTCCCTTCAGTCATTACCAG[C/T]ACTCAAAAGGCCTTTGGTTCAGAACTGGACTCTGC Y 2 1 2 1 101000 f 74 goat snp949-scaffold1025-1494764 6 99221084 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446991 Affx-122924640 AX-123317327 6 95934828 GTATAAATGGAATCATACAATTGGTGACTTTTCCT[A/G]TGTAACTATTTTAACTTCTTTTTGAGCTTCAGTTT R 2 1 2 1 101000 r 74 goat snp950-scaffold1025-1537944 6 99265658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386019 Affx-122971496 AX-123256377 6 95976714 CAGTTGGGAGCTCAACAGAAAGGACTGGCTGGATG[C/T]GGAAGAACTGTAAGTTGGATCACCCAACATCCAAC Y 2 1 2 1 101000 r 74 goat snp951-scaffold1025-1579830 6 99307290 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801100 Affx-122946485 AX-385288014 6 96027196 ACCCTTTAACATCTGTTCACGATGGAGACTCGCAG[A/C]ACATTTTCTATGAAATGAAGCCATTCTAAAAACAT M 2 1 2 1 101000 f 74 goat snp952-scaffold1025-1630312 6 99358113 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408399 Affx-122954481 AX-123278750 6 96067380 AACAAAACTTTCCTGTTTATCTCCCCTATGCACTA[C/T]ATACACATATGAAATATTTATTTGGATGTTATATC Y 2 1 2 1 101000 f 74 goat snp953-scaffold1025-1670496 6 99398397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424163 Affx-122942533 AX-123294509 6 96105553 TGTGGGCTGGTCACTTACCTGCACTGAAGCTCAGC[A/G]TCCTCATCTGTAAAATAAGCAGAAACATGGTGCTC R 2 1 2 1 201000 f 74 goat snp954-scaffold1025-1708669 6 99436540 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416725 Affx-122947547 AX-123287073 6 96144838 CCTTTTTTCAATATTAAGAAGGATAAGCCATGCAC[A/G]TTATTTCAAGTGTACAGTCCTCTGGCATTAAGGGA R 2 1 2 1 101000 f 74 goat snp955-scaffold1025-1747954 6 99476254 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802333 Affx-122976987 AX-385289237 6 96178085 GGAATATCAGTCAGGGTCTCAGCAGGAAATAGAAG[A/C]TGTTTTTATAAACTGAAGAGAGTTTAAGAGAAGGG M 2 1 2 1 101000 f 74 goat snp956-scaffold1025-1781201 6 99509885 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445456 Affx-122925344 AX-123315793 6 96215626 TATCTCTGTGCATAAAGCCTTTGTTCAGCCATAAA[C/T]TGCAAAAATCTAAGTTGTTGTTATTATGCAGTATC Y 2 1 2 1 101000 r 74 goat snp957-scaffold1025-1818742 6 99547912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409369 Affx-122954162 AX-123279720 6 96274663 ACCACTTCCAGTTTGTTCATTTTCTAGCATAGCAG[C/T]AGGATGAGTTGTTTTAATATTTCAAAGGTCCTTGT Y 2 1 2 1 101000 f 74 goat snp958-scaffold1025-1877779 6 99605076 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425866 Affx-122940651 AX-123296212 6 96310768 CCATGCAAGGAAGATGGAATTTTTATAGAAGCTGT[A/C]GACATTTAAAAGCACATAGTCACGTGGAGTGATAA M 2 1 2 1 101000 f 74 goat snp959-scaffold1025-1913884 6 99641465 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419293 Affx-122946238 AX-123289641 6 96344638 AGGCAACCAAACTGAGGGTCTAAGAAAGTGATATC[A/G]CAAACAAAGGGAGACAATGACTAAGGAGGCAATGG R 2 1 2 1 201000 f 74 goat snp960-scaffold1025-1947754 6 99675698 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793246 Affx-122958901 AX-385280224 6 96377547 CTCTTCAAATACTTTTGTACACATAATCTCAAGTA[C/T]GTCATCCATCCATCAGTACGAGGCTAGATATCTAC Y 2 1 2 1 101000 r 74 goat snp961-scaffold1025-1980663 6 99708724 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423685 Affx-122942321 AX-123294031 6 96429633 TAACAACAGGCTCAGGCCAAGGATGGAACGAAAAC[A/G]CCTCACCCAGCCCCATGGAAGAGTTAACACACATG R 2 1 2 1 101000 f 74 goat snp962-scaffold1025-2032749 6 99761404 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405940 Affx-122955560 AX-123276292 6 96482462 TGCACTGGCAGGCCGATTCTCAGCCACTGGACCAC[A/C]GCGAAAATCCTCTCTGCTTTTGTTTTTGTGTTTCA M 2 1 2 1 101000 r 74 goat snp963-scaffold1025-2085578 6 99813876 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391279 Affx-122967353 AX-123261636 6 96519478 TGCTCTTAGCGAAGAGGGCATAGCTGGACACTATA[C/T]GGAGACAACAGGAAAGGCTTTGAAAGAGGAGATTA Y 2 1 2 1 101000 f 74 goat snp964-scaffold1025-2122594 6 99851245 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385874 Affx-122971603 AX-123256232 6 96575411 TAAGCGTCAATTTCTAGTGAATTACCAGGCTGAAT[G/T]ACTTGTATAATGCAGCCAGGTGTAATTAAGCAAGT K 2 1 2 1 101000 f 74 goat snp965-scaffold1025-2178527 6 99907267 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418741 Affx-122946217 AX-123289089 6 96607853 CCTGTCACCAGGGCCTAAGGATGAAAAATTGGGAA[C/T]GCCAAAGCCGCTGTCCTTCGTATGATACTCCGAGA Y 2 1 2 1 101000 f 74 goat snp966-scaffold1025-2210969 6 99939712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771501 Affx-122942289 AX-385258659 6 96645465 TTTCAAACTATGGAGGACAACCTACTGGTGGGTCA[C/T]GAAATCGGTTCAGTGGATTGTGGTCAGCATTTTGA Y 2 1 2 1 101000 f 74 goat snp967-scaffold1025-2248581 6 99977370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448476 Affx-122923624 AX-123318812 6 96686954 AATGAAATAAAACAACAACAAAACTAGTACCAATT[G/T]TGAGTCGACAGAAAAAGAAAGGTCAAGAAGACAGA K 2 1 2 1 101000 r 74 goat snp968-scaffold1025-2290070 6 100018914 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278413 Affx-1111836411 AX-519551898 6 96697678 GCAAACAATGAGGGAAAGGCAAACTCCAGAGCTTG[A/G]ACTGACAGGCCCAGGGTGTTTGAAGGCTGCAGGAG R 2 1 2 1 102000 f 74 goat Random2.2K-727 6 96697678 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320787949 Affx-122939756 AX-385274970 6 96716125 ATCCTACCTAGTTTATATTTCAAAGGTCTTTTCCA[C/T]GAGTTCTCCATTTCATTCTAAGGGAATGAATTCCA Y 2 1 2 1 101000 r 74 goat snp969-scaffold1025-2319241 6 100048079 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779955 Affx-122943702 AX-385267054 6 96851584 TTGGATATTGTACGAGAAATAGCAGGTTAACAACT[C/T]AGCAAAGCGTACAGACAGGTACCCCTTGAATTCTA Y 2 1 2 1 101000 r 74 goat snp971-scaffold1025-2454700 6 100183383 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390309 Affx-122967715 AX-123260666 6 96912199 TCACCTAAACGTGAGTTGTTTTTCTAATTGGGCTG[C/T]GGATTTCTTGGGGGTCGAAGAGTAGACATTTATGG Y 2 1 2 1 101000 f 74 goat snp972-scaffold1025-2515315 6 100244918 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778509 Affx-122923659 AX-385265623 6 96953090 GTTTTGAACATCAATAATTTCCCTTCATAGAGAGA[C/T]ATTTTATGATGTTATTCAATTTAATGAGATCTGCA Y 2 1 2 1 101000 f 74 goat snp973-scaffold1025-2556206 6 100284206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453850 Affx-122919537 AX-123324183 6 96982070 TTAGAGAACAAAATTTTCCTTAAGAACTGTCAGGA[G/T]CTGGCTTTTAGCAGACTAACTGGGGCAACCACAGC K 2 1 2 1 201000 f 74 goat snp974-scaffold1025-2585186 6 100313004 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795115 Affx-122922615 AX-385282073 6 97021068 TAAAGACTATATGGGAACTTTTCTGCTAATCCCAA[C/T]ATATGAATCATCTCTGGGTCTGATTGTGTTTTTTA Y 2 1 2 1 101000 f 74 goat snp975-scaffold1025-2624184 6 100351778 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391456 Affx-122966735 AX-123261813 6 97056129 ACACAATTCTGTTTGAACTTCTTTTATTTAAAAAA[C/T]AGCCTCAATTCTCTTGGATAAGTTAGATATGTGGT Y 2 1 2 1 103000 r 74 goat snp976-scaffold1025-2659245 6 100384143 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762489 Affx-986697019 AX-385250610 6 97058118 CCTGTAAGAATTCACACTGAATGGCTTCTTGACAT[A/C]AAAAATGGTGTTTCTAGATCTTTGTAAGTAACTAC M 2 1 2 1 600010 f 74 goat 6_97058118 6 97058118 Ancestral_priority_1043 ancestry 0.71 recommended IMAGE 10K 10K ancestral 320764770 Affx-986697021 AX-385252383 6 97058119 CTGTAAGAATTCACACTGAATGGCTTCTTGACATC[A/G]AAAATGGTGTTTCTAGATCTTTGTAAGTAACTACA R 2 1 2 1 600010 r 74 goat 6_97058119 6 97058119 Ancestral_priority_1043 ancestry 0.75 neutral IMAGE 10K 10K ancestral 320762493 Affx-986697023 AX-385250614 6 97058141 GCTTCTTGACATCAAAAATGGTGTTTCTAGATCTT[C/T]GTAAGTAACTACAGTTTTTCCAGGTACCTGACAGA Y 2 1 2 1 600010 f 74 goat 6_97058141 6 97058141 Ancestral_priority_1043 ancestry 0.658 neutral IMAGE 10K 10K ancestral 320764780 Affx-986697027 AX-385252394 6 97058156 AAATGGTGTTTCTAGATCTTTGTAAGTAACTACAG[C/T]TTTTCCAGGTACCTGACAGACACTGGGGTTGTGAT Y 2 1 2 1 600010 r 74 goat 6_97058156 6 97058156 Ancestral_priority_1043 ancestry 0.528 neutral IMAGE 10K 10K ancestral 320762499 Affx-986697029 AX-385250619 6 97058217 GGGTTGTGATCATATTCGGGGTGCAGAAAAAAGAA[G/T]AAGATAAACTGTAGGGTGTTCTGTATGGCAGAACT K 2 1 2 1 600010 f 74 goat 6_97058217 6 97058217 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 320769729 Affx-122920214 AX-385256899 6 97145813 AAAAAATGTAATAGCTGCAAATCTCAATAAAGTGA[C/T]GAACATTAAACAAGGTGTGCTTGTATTATAGTCCT Y 2 1 2 1 101000 r 74 goat snp978-scaffold1025-2748929 6 100474517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380369 Affx-122975345 AX-123250727 6 97194004 AGCCTCTTGACTGATGTGGTGGGGCTCCTTACCCA[C/T]GTAAGTGTTATTTTCCCTGTGTGCACTAGATTGTA Y 2 1 2 1 101000 r 74 goat snp979-scaffold1025-2797120 6 100522887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793250 Affx-122963922 AX-385280228 6 97227426 TCTGAGGGTCTCAAGCAAGAAAATTGCTTAAAGAT[C/T]AAGAAAATTATGCTTATTTGGGCATCTACAATGTA Y 2 1 2 1 101000 f 74 goat snp980-scaffold1025-2830542 6 100556772 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398203 Affx-122962227 AX-123268558 6 97279271 TTTGCATGCACCTGGCATAAAGTTCAATTTCAACC[A/G]CAGGCAATGGGTATACATCCAGGGTTTTAAGCTGG R 2 1 2 1 101000 r 74 goat snp981-scaffold1025-2882387 6 100609135 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414701 Affx-122949278 AX-123285050 6 97308631 GGATTTCCAGAATTGTTATAACTGGATTATCATTG[C/T]ATAGCAAAGTAACTGAGGAAGCAGTTATTTAAATT Y 2 1 2 1 101000 f 74 goat snp982-scaffold1025-2911747 6 100638524 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273246 Affx-1111833525 AX-519546899 6 97344063 GCTTGGAGATGGTGTGGGCAATGCTCTTCCCATCA[A/C]GGCAGAGTCAGTGGGTGCCTGCCCTTCAGGAATGT M 2 1 2 1 101000 f 74 goat 6_97344063_AF-PAKI 6 97344063 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38421027 Affx-122944541 AX-123291374 6 97344742 TATTTTTAGGGGTGATTTTTCATCCCAACTCTCAA[G/T]ATTGAGTTGGAAAGTTTTTCAGTGTAATTAGTTTC K 2 1 2 1 101000 f 74 goat snp983-scaffold1025-2947858 6 100674671 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397592 Affx-122961993 AX-123267947 6 97396726 AGTAATTTCAAAGCTAGTCTTTCTCAAGATAGGAG[C/T]GTTTATCCCAGAAACTGTTGGAGGGCATGTCACTC Y 2 1 2 1 101000 f 74 goat snp984-scaffold1025-2999842 6 100727119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380746 Affx-122975131 AX-123251104 6 97443273 GTGCTGATGTTTAACTTTTAGGATTATTACACATC[A/G]TTTGTACATTTATTTTGTAACTTATTTCTGAGGCG R 2 1 2 1 201000 f 74 goat snp985-scaffold1025-3046389 6 100773606 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387772 Affx-122969716 AX-123258130 6 97479817 TCTGTTTGTTTGTTTGTTTTCTCATAGCAATGGAA[C/T]AGATCCCTATTTTTTTGAACAACAGTGGGGAGTTT Y 2 1 2 1 101000 r 74 goat snp986-scaffold1025-3082933 6 100810429 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278583 Affx-1111836412 AX-519552062 6 97488308 ATTACTGGATTACATTGTTTTACAAACAAAGACTT[A/G]CAAAATTCTAGGAGCAGAGAGTGTGTTGTAGTAAA R 2 1 2 1 101000 r 74 goat Random2.2K-729 6 97488308 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415530 Affx-122948669 AX-123285879 6 97568213 ACCTGTGTCTCCTGCATTGGCAGACATTCTTTACC[A/G]CTGATACACCAGAGAAGCCCATGTAAGCACTAGCT R 2 1 2 1 303000 r 74 goat snp987-scaffold1025-3171329 6 100899078 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425974 Affx-122941162 AX-123296320 6 97604781 GAAGTAAATACAGATTTGGAATTTTATTACTAAAT[C/T]GAAACCAATTAATACTGAGAGCTAAAATGTACCAC Y 2 1 2 1 101000 r 74 goat snp988-scaffold1025-3207897 6 100936057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432503 Affx-122935579 AX-123302844 6 97610419 ACTGTACCATCGATAAGGTATAAAAATATATATAC[A/G]TAATGAACTGGTCAACTTCACTAAGATATTCAGGC R 2 1 2 1 101000 r 74 goat snp8746-scaffold1313-240208 6 100941940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771048 Affx-122919911 AX-385258208 6 97640124 CCCAGATGAACAATGATCATGAGCATCACAAGAAA[C/T]AAGGTGAAGTCTCAGCTTGACAATATATATGAATT Y 2 1 2 1 101000 f 74 goat snp8745-scaffold1313-210503 6 100971740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376033 Affx-122978944 AX-123246392 6 97690788 AACACCCTGAAGTTGGACTTCTCCTCAAGAAACTT[C/T]CACCCACTGAGTTTAAAGGCTCGTAGCATGTAAGC Y 2 1 2 1 101000 r 74 goat snp8744-scaffold1313-159839 6 101022226 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417540 Affx-122946927 AX-123287888 6 97748659 GACGTAGGGGGTAGGGCAGTTGTATGCTGCAACAC[C/T]TAATGACCTCCAGCTAGGACAAAATTTCATTCTTT Y 2 1 2 1 201000 r 74 goat snp8743-scaffold1313-101968 6 101080210 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385455 Affx-122971306 AX-123255813 6 97779140 TCCCTCTCCAGGTCTCAATTTCCTTACCTGTCTAA[C/T]GACACTCCAATCAGACAATGGATGCTGAGATGTCA Y 2 1 2 1 101000 r 74 goat snp8742-scaffold1313-71487 6 101110540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774994 Affx-122962472 AX-385262126 6 97812225 TACTGCCTGGCAAGCTTTACATTTATTTTACTAAG[C/T]ACTATCCATACATAATGCAATATTATTATATATCT Y 2 1 2 1 101000 f 74 goat snp8741-scaffold1313-38402 6 101143576 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429072 Affx-122938287 AX-123299414 6 97843846 TTTCAATTGCTGTGTAAACTCTGGGAGATTGAATG[C/T]GCATTACCTTAACCAGATACTGAGTGTTTTCTCTT Y 2 1 2 1 201000 r 74 goat snp8740-scaffold1313-6781 6 101175737 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441192 Affx-122929537 AX-123311529 6 97883679 GCACACACAGGGAGGCCACCAGGACATCATGGCTG[A/C]GAACAAGAGTCCCAGGAGGGGGAAAGAGCCACATG M 2 1 2 1 201000 f 74 goat snp31697-scaffold352-347477 6 101215199 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793672 Affx-122975027 AX-385280644 6 97918420 TATGCCTTCTAAGATGTATTTAAGAATGGCTCATA[C/T]GCATATAAAATGATGCACAGAATCAGTGTCATCAA Y 2 1 2 1 101000 r 74 goat snp31696-scaffold352-312736 6 101250006 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769306 Affx-122937650 AX-385256477 6 97979673 TTGAGAGGATCATTCAGTAAAGCCAGAGATGGATA[C/T]AGTTGAGAAGGCATATAGTATAGTGCAATAGAAAA Y 2 1 2 1 101000 f 74 goat snp31695-scaffold352-251483 6 101311551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773755 Affx-122927038 AX-385260895 6 98022117 TAATTGACTATTAGATTTGGCTATCAGTCATAGCT[A/G]TAACCAAAAGAGTTAATGCCCTTCTTAAAAAAATC R 2 1 2 1 101000 r 74 goat snp31694-scaffold352-209039 6 101354265 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381034 Affx-122974643 AX-123251392 6 98073350 TTGGATACATACTGTTCTGTAAGTAATAGTTAAGG[C/T]AGTAATTACCTGGTAAGCTTTTATAAATTCTGAAA Y 2 1 2 1 101000 f 74 goat snp31693-scaffold352-157806 6 101405174 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403996 Affx-122957201 AX-123274348 6 98104481 AAGAATACATAAATAAATCTCTTTTCTATTTTGGT[G/T]CTTTATGAGTGTTGGGTGTCTTGGGTTCCTAAATT K 2 1 2 1 101000 r 74 goat snp31692-scaffold352-126675 6 101436404 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788806 Affx-122975224 AX-385275821 6 98203668 AAGAAAAAATACGGTTTCATGCTCTTTACTAACCC[A/G]TGTGCCCAATAAAGAAGTTTCAAAATATCTTTACA R 2 1 2 1 101000 r 74 goat snp31690-scaffold352-27488 6 101536585 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438568 Affx-122931165 AX-123308906 6 98260962 ATCCCCAGAAAACTGGCTTTCAACCTTAATATTTG[C/T]GAAGTCTTAAAAATTAAAAAATAACAGTTTACTTC Y 2 1 2 1 101000 f 74 goat snp9293-scaffold1338-444199 6 101592607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377510 Affx-122977483 AX-123247869 6 98295991 ATAATTTGACTCCAAGATCCCAGTTCCAGTGTCGG[C/T]CTTTTCCTCATGGCTCAGATGGTAAAGAATCTGCC Y 2 1 2 1 102000 f 74 goat snp9292-scaffold1338-409170 6 101627469 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398904 Affx-122961017 AX-123269259 6 98346882 CTGCTAGTTGTCAGACCCCGGAAGATCTCACAGAA[C/T]GCTGATGCATGTGTTAAAATGGTTGCAGGAAGGCC Y 2 1 2 1 101000 r 74 goat snp9291-scaffold1338-358279 6 101678738 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784406 Affx-122946839 AX-385271455 6 98384529 CTGTTTAATATAGGGCATACAGCCACAGTAGTATT[A/G]TTAATAAACATGTAGATGTTTCTTGTTAAGGACTA R 2 1 2 1 201000 r 74 goat snp9290-scaffold1338-320632 6 101716228 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778269 Affx-122952306 AX-385265384 6 98493166 AAAGTTGAACTAGAGCATATTGCATAGATATACCA[C/T]TGCAATGGACTTTCTAATAATCTGTCGTTGGGATT Y 2 1 2 1 101000 r 74 goat snp9288-scaffold1338-211995 6 101825349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404763 Affx-122957217 AX-123275115 6 98523138 AGGTGAGTGTGGTACATGGCTACCAGATTCAGCAA[A/G]TAAAAACACAGGATGCCCTGCATTTTACCTGACGT R 2 1 2 1 101000 f 74 goat snp9287-scaffold1338-182023 6 101855285 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278418 Affx-1111836414 AX-519551903 6 98540183 AACTGAACTGAAACAAGTTGGTTTTCAAGCAATCG[A/G]GTTTGTGGAGGTTGGACAAGATGGTGATTTAGTAA R 2 1 2 1 101000 f 74 goat Random2.2K-731 6 98540183 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786776 Affx-122961620 AX-385273807 6 98557102 CTTAAATGCAATCCTTGAAAGGTACTGATAATAAT[A/G]CATAATAACTTATAGATTACTTCTGAGACTTATTT R 2 1 2 1 101000 f 74 goat snp9286-scaffold1338-148059 6 101890074 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799756 Affx-122975336 AX-385286683 6 98587446 AATTATACATATATAATTTAAGCGCTTTACTTTTA[C/T]GAAAAAAATCTGTCATTATACGTTCATTAGCAAAT Y 2 1 2 1 101000 r 74 goat snp9285-scaffold1338-117715 6 101920346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399249 Affx-122960574 AX-123269604 6 98648947 GGAGGACACCAGTTTGCCATCTTTTCAGACACTTG[G/T]CTTCCGGAATAAAGTTGCTATTTCTCCTCTCCTGA K 2 1 2 1 101000 f 74 goat snp9283-scaffold1338-56214 6 101981643 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791920 Affx-122956057 AX-385278910 6 98692861 TAGCATTAAAATTACGAAATCAACAAGTAACAACC[A/G]AGCATACAAACTTCAATTTTATAACATGGCCACTT R 2 1 2 1 101000 r 74 goat snp9282-scaffold1338-12300 6 102025381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440211 Affx-122930691 AX-123310548 6 98705925 CCATTTGCTGCCCCCTTCTGCAGGTAGTAGTTTGG[A/C]TATGTGAAGTCTGAGAGAAGTGTTTTTACATTTGA M 2 1 2 1 101000 r 74 goat snp2775-scaffold1080-665 6 102038298 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781615 Affx-122941058 AX-385268699 6 98739775 ACATTAGTCTTAGATCCCTGATGTGATGAATGCTC[A/G]TCTTTACGGCATCTTTTAAGGCATATGGATCACTG R 2 1 2 1 101000 f 74 goat snp2776-scaffold1080-34515 6 102072349 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384847 Affx-122971959 AX-123255205 6 98775438 TGCCGTGTTTCTCTGCTAAGAATTCAGGGAAAAGA[C/T]AAGACTCGGGTACACGTCCTGACTCTCCCAGTGAC Y 2 1 2 1 101000 f 74 goat snp2777-scaffold1080-70178 6 102107644 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389816 Affx-122968193 AX-123260173 6 98815960 AATGACATGAGAAGAACAGCCTTCTGGATGTCTGT[C/T]CATTTCTTTGCTCTCTACTTAAAGGTCACAGGACA Y 2 1 2 1 101000 r 74 goat snp2778-scaffold1080-110700 6 102148311 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448169 Affx-122924262 AX-123318505 6 98868783 CTTAGTCCAATGCACACAGAAACTGAAGACCCTAG[C/T]AAGTTTGTTGAAGGGTTTCATGTCCTAAGGCTGGT Y 2 1 2 1 201000 r 74 goat snp2779-scaffold1080-163523 6 102202032 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429894 Affx-122938121 AX-123300235 6 98913221 AAACTTTTTGCCTGGCTATGTGGTATAAATCTCTC[A/G]CCTGTATTCCAGGAAAACTGTAAATAAAGATCTAT R 2 1 2 1 103000 f 74 goat snp2780-scaffold1080-207961 6 102246995 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450158 Affx-122922736 AX-123320493 6 99039745 CGTGGTTGATTGCAGCAGCGTTTTGAATTAGTTCA[C/T]GGGGGAAAAATATACAGAAAGGGAGATAGGTAGGT Y 2 1 2 1 101000 f 74 goat snp2782-scaffold1080-334485 6 102373063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794423 Affx-122928902 AX-385281386 6 99080875 ATAAACTGCTAAGTGTGTACTTTAGACACTTGTTC[A/G]TATTTTAGTTGAAGAAAAACTTCCACAAGTTAGCC R 2 1 2 1 201000 r 74 goat snp2783-scaffold1080-375615 6 102413903 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400405 Affx-122959994 AX-123270760 6 99111260 TACGATAAATATCTCGAGAGTGACTCTAAAAGCAT[A/G]TACAATTACCCAGGAATTGTAAAAAAACAAATTGG R 2 1 2 1 101000 f 74 goat snp2784-scaffold1080-406000 6 102444191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440738 Affx-122929878 AX-123311075 6 99149286 CAGAGAGCATATGTTGAACTTTGTACCACAACAGC[A/G]TCAGTTGCTTTGATTCTGCCATGTGCAGACATAAC R 2 1 2 1 101000 f 74 goat snp2785-scaffold1080-444026 6 102482193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427789 Affx-122939771 AX-123298132 6 99233101 AACTCACAAGAATCAACTAAATTATTCACAGACAA[C/T]GAATTCTCTTGTACAGCCTTTAAAAAAAGTTTCAT Y 2 1 2 1 101000 f 74 goat snp2786-scaffold1080-527841 6 102567515 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422002 Affx-122943781 AX-123292349 6 99279871 TTCTAGATCGTACGTCTCTTTCGGTTCACTTTCCA[C/T]TGTGTGAAGAACCTCCTCTAGTAGCTTTCCAAGAA Y 2 1 2 1 101000 f 74 goat snp2787-scaffold1080-574611 6 102614137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395059 Affx-122964193 AX-123265414 6 99327030 ATCATCTCGGGTTTACTGGCCTGTTGTGGGGCAAG[C/T]AGAGCCAGCTTAGACTTGGTCACAGTACTGTTAGA Y 2 1 2 1 101000 r 74 goat snp2788-scaffold1080-621770 6 102661464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776411 Affx-122971500 AX-385263538 6 99368122 GTAATTAAATATTCATTTGGATGAACTTTTTAAAC[A/G]TCTGGCCCCATAACATCACTATAATAATCGCTATG R 2 1 2 1 101000 r 74 goat snp2789-scaffold1080-662862 6 102698879 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779489 Affx-122969935 AX-385266592 6 99418738 TGGTAACTTGTTACAGCATCCTGGAGAAACAAATA[C/T]ATCTGCACTTACAAATTATTAGATATACTGTGTGA Y 2 1 2 1 101000 f 74 goat snp2790-scaffold1080-713478 6 102748730 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801060 Affx-122950601 AX-385287974 6 99450940 CTTTTGATAAATATGATGGTAGAGTTGTAAAATGT[A/G]CTGACTACAAGCTAGGCACTGTATACTAAATGTTT R 2 1 2 1 101000 r 74 goat snp2791-scaffold1080-745680 6 102781195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378033 Affx-122977575 AX-123248392 6 99485471 ATAAGCATTGGATTTATATGGATTTTTATTAGGAT[A/G]TTAAGATATTGACAATAACACACACCAGTAACAAA R 2 1 2 1 101000 r 74 goat snp2792-scaffold1080-780211 6 102815687 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784051 Affx-122957176 AX-385271104 6 99520378 ACAGTTTGTAAGCAGCAATGAAGAATTGGCATGGG[C/T]ATTAAATATCTTGAGTGAAATATTCTTTAGAAGTA Y 2 1 2 1 101000 f 74 goat snp2793-scaffold1080-815118 6 102850454 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420775 Affx-122944705 AX-123291122 6 99576412 TTACTATGATTATATTAGCAATTCACTGACTTCTT[G/T]TTGCATGAAGGGATAAATAAATAAAGGACAAAAAC K 2 1 2 1 101000 f 74 goat snp2794-scaffold1080-871152 6 102906365 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440989 Affx-122928973 AX-123311326 6 99609624 TGGACATCAAGTAGCTGAAAGCAGTAATAGTACAG[A/G]TCAGGAGGCGGAAATCAATGGGAATTCCTGTAGAA R 2 1 2 1 101000 f 74 goat snp2795-scaffold1080-904364 6 102939561 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415433 Affx-122948718 AX-123285782 6 99672176 TCTGTGAACCTTGGTCTTCAGGAGCTGATCCAAGC[A/G]AGCAATGAGGCTTTGGCAATAGTCACTGGGAAGGT R 2 1 2 1 201000 r 74 goat snp2796-scaffold1080-966916 6 103003834 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392167 Affx-122966309 AX-123262524 6 99722725 GCTTAAGCCTGGAGCAGGGTGACATACAACTCCTG[C/T]AGCCTAACTCAGAGCCTCAGGCTTCTGACCTGTGC Y 2 1 2 1 101000 f 74 goat snp2797-scaffold1080-1017465 NW_017189523.1 83776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779425 Affx-122941407 AX-385266528 6 99760803 ACACTATTCAACCCAAAACAGGTAGTGCTAAAATT[A/G]TCCTAGATGGAGAAATTAAGGCCAAAAATGTAAGG R 2 1 2 1 101000 r 74 goat snp2798-scaffold1080-1055543 NW_017189523.1 45688 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390509 Affx-122967248 AX-123260866 6 99789653 TCCTATGCTGCAGTAACAAAGAACCCAAATTCTCA[C/T]GGTCCAAACACAACACAGGGTTATTTTGCCCTTAC Y 2 1 2 1 101000 f 74 goat snp2799-scaffold1080-1084393 NW_017189523.1 19225 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791330 Affx-122960968 AX-385278323 6 99831538 TTATCTTGAAAGGCCTAGGAATAAGACACTCCAAA[C/T]GGTTTCTGGTACAATGAATTCAAGATCATCCCTGG Y 2 1 2 1 101000 r 74 goat snp2800-scaffold1080-1126278 6 103085595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411896 Affx-122951187 AX-123282246 6 99889357 TCAGCTTAGAAAAGAAAATTAAAATGGGGTGTGTA[A/G]GTTAGAAAAAGGCAGTGATGTGGTCAGAAATTTAA R 2 1 2 1 101000 r 74 goat snp2801-scaffold1080-1184097 6 103144243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445905 Affx-122925942 AX-123316242 6 99921445 TCCATTCTTCTCATGATGGGTTCCTCGCCTGGCAC[C/T]GGACAACACATTGCAGTTTGTAGAGCCTTGCAGCA Y 2 1 2 1 101000 r 74 goat snp25682-scaffold2643-1656 6 103178690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393750 Affx-122965218 AX-123264105 6 99976735 GGCCTTCAGCTCATCGCTGCCCCAGGGCCTTTGCA[C/T]ATGATATGACTTCTGCCTGGAGTCCTCCTCCCTGG Y 2 1 2 1 101000 r 74 goat snp25683-scaffold2643-56946 6 103233689 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444304 Affx-122926751 AX-123314641 6 100044623 TTATTTGTCCAGAGTCACACAGAATTCTTACCCCC[A/G]TACAATATACTAATTACAGAAAACTTGGAGGATTA R 2 1 2 1 201000 r 74 goat snp25684-scaffold2643-124834 6 103301267 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431215 Affx-122937155 AX-123301556 6 100085511 TAAAACCACACTCCCCCAGTACTTACATCAACTGC[C/T]GAGAAGTCAAGGTCCTTGCCCTCAAATTCATGTCC Y 2 1 2 1 201000 r 74 goat snp25685-scaffold2643-165722 6 103341166 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439157 Affx-122931071 AX-123309494 6 100161365 ACGGGCCTGGCCTGGGTCTCGTTATCTTGCCCTGT[G/T]TCGGCTCCGTCCTCATTAGAGGCACTGCTTTCTGC K 2 1 2 1 201000 f 74 goat snp25687-scaffold2643-241576 6 103417295 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272327 Affx-1111833486 AX-519546062 6 100201228 AGCCCGTGCTCAGAGATTTCATGAAAATAATCACA[A/G]CCAGGTGGCAGGAGAAGCAGTTACGCAAGGGACCA R 2 1 2 1 101000 f 74 goat 6_100201228_AF-PAKI 6 100201228 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38383772 Affx-122973209 AX-123254130 6 100221994 AGCATCCATGGCCCCTCTGTTACTGTTAGTGTCAG[C/T]GGCCCCCTCTGTCTCTCCCAGGGACAGGCCCAGCC Y 2 1 2 1 103000 f 74 goat snp25688-scaffold2643-302205 6 103477997 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409508 Affx-122953633 AX-123279859 6 100266992 TGGGGTTCAGAAGTTAGGTCATCCTGACAGCGTGT[A/G]AGTAATGAGGGTTAAAAAGGCCTAAAAGTAAATGC R 2 1 2 1 101000 r 74 goat snp25689-scaffold2643-347203 6 103522407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425723 Affx-122940760 AX-123296069 6 100299154 CCTACAGCCTAAAAAAAAAATCCTAGGGCCTCATC[A/G]TGGTAGAAGGGTGTATTAAATCGTTTCTATGGCTG R 2 1 2 1 101000 r 74 goat snp25690-scaffold2643-379365 6 103554400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454090 Affx-122919370 AX-123324423 6 100409110 AGAGTACATTTCTGTGGTTGATAAGCGACCCAGTC[A/G]ATGGTACTTTTTATCCCAGCAGGCATGGACTAAGA R 2 1 2 1 101000 r 74 goat snp25693-scaffold2643-489321 6 103663955 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439107 Affx-122931108 AX-123309444 6 100448754 CCCTTTCACGTGTGGCTTTTTAAAAAATTAATGGC[A/G]CAGCCGGGATTAATTTAAAGCGGGTTTTTGGTGCC R 2 1 2 1 101000 r 74 goat snp25694-scaffold2643-528965 6 103703455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404801 Affx-122956662 AX-123275153 6 100478595 CTTTCTCAGTTTCCTCATCTGTACAGCATGATCAC[C/T]GCTGGCCCTGTCAACCTCAAACAATTGTTATGTGG Y 2 1 2 1 201000 r 74 goat snp25695-scaffold2643-558806 6 103733282 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802362 Affx-122969767 AX-385289266 6 100525126 TTCCCACCAAGTTCTCCGGGGCCAAGAAAAAGAGA[C/T]GGTGAGCTTGTCCCTCACTCGTAGGTCAAAAAAAC Y 2 1 2 1 101000 r 74 goat snp25696-scaffold2643-605337 6 103779833 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447671 Affx-122923955 AX-123318007 6 100576471 TAAATCAGATCTTAGAAGGGAAAGGAGAACCCTAT[A/G]TATGGAGCCCTTCAAACCCCCACATAGAGTGTGGG R 2 1 2 1 101000 r 74 goat snp25697-scaffold2643-656682 6 103831565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425098 Affx-122941235 AX-123295444 6 100617084 AGTGGCCTTAAGATTTGAGACCAGTGAGTCTTTGT[C/T]CCTTAGCCCGAAGGACTGGACTGGGGTCTGGAGGT Y 2 1 2 1 101000 f 74 goat snp25698-scaffold2643-697295 6 103872003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381624 Affx-122974772 AX-123251982 6 100672269 AGGGGGCTTCCAGAAAATAAATGGGATGACAGACC[A/G]TGTCTAGTATTGCCTGGAGTTCAGTCAAGTGTCTT R 2 1 2 1 201000 r 74 goat snp25699-scaffold2643-752480 6 103927848 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387145 Affx-122970643 AX-123257503 6 100709651 CCCATTGGTGGGGGAGGGATTCCACCTGCTGGTTA[C/T]GGGCATAGCCAGACACATGACACCTGATCCTGAGA Y 2 1 2 1 101000 r 74 goat snp25700-scaffold2643-789862 6 103964963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273532 Affx-1111833674 AX-519547147 6 100755325 ACAGGGATAAAGAAAGAGTTCCTCAAAGCAAAAGT[A/G]TTCTGCAGGTACTGCTTCAACTTTCTGTGCTAAAG R 2 1 2 1 101000 f 74 goat GoatD01.001140 6 100755325 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447127 Affx-122924463 AX-123317463 6 100773013 TGAGTTGAGCAAAAATGAAAATACAACTTGAAAAA[C/T]GTATGGATGCAGCACAAACAGTATGTAAGGGAAAA Y 2 1 2 1 101000 r 74 goat snp25701-scaffold2643-853224 6 104025861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782652 Affx-122943965 AX-385269725 6 100799919 ACTTGGGGAGTTAGTTTCGATTGCTTAGTGATCGC[A/G]TTCCTTTACTTAGGTTTTTAAGGTTAGAGAAGACA R 2 1 2 1 101000 f 74 goat snp26884-scaffold2836-1687 6 104052587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453185 Affx-122920459 AX-123323518 6 100851774 CATTCCAGATGAGGAGGTAGAGACATGAAGGGGTG[C/T]ATTTGGGTGAATGAAAGTGAAAATGTTAGTTGCTC Y 2 1 2 1 101000 f 74 goat snp26885-scaffold2836-53542 6 104104780 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762468 Affx-986696998 AX-385250594 6 100868099 CTATTTGTCCTCTTTGTAAACATTTTCAACATCTT[C/T]ATTGAGATATAATTCATCTAAGGTGTACTGTTTAG Y 2 1 2 1 600010 f 74 goat 6_100868099 6 100868099 Ancestral_priority_1043 ancestry 0.644 recommended IMAGE 10K 10K ancestral 320764738 Affx-986697001 AX-385252354 6 100868101 ATTTGTCCTCTTTGTAAACATTTTCAACATCTTCA[A/T]TGAGATATAATTCATCTAAGGTGTACTGTTTAGTG W 4 1 2 1 600010 r 74 goat 6_100868101 6 100868101 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 38431501 Affx-122936242 AX-123301842 6 100921543 TCAATTGGCTATGTTACACTACAAAATAAAAAGTT[C/T]AGTAAAAGAAATCAAAAGGTGCATAATCCTATTAA Y 2 1 2 1 101000 r 74 goat snp26886-scaffold2836-123311 6 104174904 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278588 Affx-1111836415 AX-519552067 6 100928424 ATATGAACATCAACTAATTTTTTCTGATTTTCAAT[A/C]AATGCAGATTTCTTGTGATATTATTATTTTCATGG M 2 1 2 1 101000 r 74 goat Random2.2K-732 6 100928424 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419358 Affx-122945635 AX-123289706 6 100952843 AAGAGAACAATAATTTAGGCAATAACTCTGGTTAC[C/T]GCTTTTTCTCACTGCGGATCCTTTGTCACCTGGGC Y 2 1 2 1 201000 f 74 goat snp26887-scaffold2836-154611 6 104206641 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393754 Affx-122965215 AX-123264109 6 101008970 GTTCCAAGATGTTCATGTCAATAGGGAACTCATAC[A/G]TTACAAGGTATATTGTAACTTGGAGACACAATATG R 2 1 2 1 101000 f 74 goat snp37608-scaffold4601-7753 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453067 Affx-122920059 AX-123323400 6 101017473 TCCCCTTCAGCGTCCACCCACCAGAGGTTGTCACT[A/G]TCTTGACCTAGAACAGCATGAATTCGCTTTGCCTG R 2 1 2 1 101000 r 74 goat snp48638-scaffold690-4047171 6 104242178 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420377 Affx-122944943 AX-123290724 6 101046702 TCCAATGCCTGGTTATTGAGGTGGGACAGGAGGGA[A/C]GATCCATTTAAAAATTCATTGATCACCTCATGGTG M 2 1 2 1 101000 r 74 goat snp48637-scaffold690-4017942 6 104271646 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437148 Affx-122932144 AX-123307486 6 101088510 TAGCAACCACGGAAGCTAGTATCCTATTTTGTTTA[C/T]GCAAGATCATGTTGCTGTTGTTCAGTTGCTCAGTC Y 2 1 2 1 201000 f 74 goat snp48636-scaffold690-3976134 6 104313510 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396230 Affx-122963342 AX-123266585 6 101133528 CAGCTTGAGGTGGTCTTCATAATGTGATACCTGTA[C/T]GACCACTGCTTATATCAAGAAATTCAAAATGGGAA Y 2 1 2 1 101000 r 74 goat snp48635-scaffold690-3931116 6 104358496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778163 Affx-122935617 AX-385265278 6 101179466 ATCCACATGTGGCTCACAGCTACCCTATAGGACAG[C/T]ACACTTTTTCCTCCTTGCCATTATTTGCTGTTATG Y 2 1 2 1 101000 f 74 goat snp48634-scaffold690-3885178 6 104404490 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413355 Affx-122950151 AX-123283704 6 101212746 CGATTCCAGTATTCAATGTCGATCCAGTTGCTAAT[A/G]TAAAGAATCTGTAAGACTTCCCTGTTGGTCCAGTG R 2 1 2 1 201000 f 74 goat snp48633-scaffold690-3851898 6 104438042 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389119 Affx-122968560 AX-123259477 6 101269923 ATTATTGTGTGTTCATTCCTAGTATCAGGCTAGCC[A/G]TTCCAGGCTCCTCCTTATACACCCAGCACCATGAA R 2 1 2 1 201000 f 74 goat snp48632-scaffold690-3794721 6 104495474 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416216 Affx-122948229 AX-123286565 6 101306511 TAGGGAAGGAGGGTAAGGAGCAAACTCTAGCTGGA[C/T]GGTAGCTTGCATTACTCTAGCCTGAGACTCTTTGT Y 2 1 2 1 101000 r 74 goat snp48631-scaffold690-3758133 6 104531980 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377620 Affx-122977885 AX-123247979 6 101335969 TGTTATTTTACCCCACACCCCCCAACATCTTCCCC[C/T]ACAAAGATTCCTGTTTTGTAATCCTTCAGCTTCTA Y 2 1 2 1 201000 r 74 goat snp48630-scaffold690-3728675 6 104561434 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385313 Affx-122971674 AX-123255671 6 101369505 AGAGACTTCCTGATAGAAACCGAAGGACCCAGAGA[C/T]AGCAGAGGGGTGAAGAGATCGAGGTTCCCAGATCT Y 2 1 2 1 201000 f 74 goat snp48629-scaffold690-3695139 6 104593721 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412641 Affx-122950795 AX-123282990 6 101402801 ACGCTCAGACATTCTCCAACTGGACAAGTTATAAG[C/T]ATCACAGATCACAAAAGAGTTCTACTTGTTTGATA Y 2 1 2 1 101000 f 74 goat snp48628-scaffold690-3661843 6 104627336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799863 Affx-122941140 AX-385286789 6 101461595 ACTTTTGAATTAAGCAGTCTACAGCAATTTAGTGC[A/G]CACTGGCTTTGAAGTGCCAACATCAGTCAGGCCAG R 2 1 2 1 101000 r 74 goat snp48627-scaffold690-3603049 6 104685697 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427158 Affx-122939627 AX-123297501 6 101515155 CTAAGCAAAAGGAAGCTAAATGTGCTTATACTAAC[A/G]TCTGACAAGGTAGACTTTAGGATGAGAAGCATTAT R 2 1 2 1 101000 f 74 goat snp48626-scaffold690-3549489 6 104739577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420996 Affx-122944561 AX-123291343 6 101550835 CTTTTGTGCCCTCTGAGCCCCAAAATGAAAACATG[A/C]TTTTGTTGATTTGAATTTTCTCTTTTCAAGTAACA M 2 1 2 1 103000 f 74 goat snp48625-scaffold690-3513809 6 104775254 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416259 Affx-122947962 AX-123286608 6 101583505 ATCCGGAACCTGCTCAAGTGGCAGAATATTAGTGC[A/G]GTCATCAGCCTGGGGTCCCACATGAGCTCTGCTTG R 2 1 2 1 101000 f 74 goat snp48624-scaffold690-3481139 6 104807887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800448 Affx-122954785 AX-385287369 6 101624121 TAGCGAATGGCATGCAATAGGTGTTTAAGAAATGT[C/T]AGCATATTAAGATGACTCCCCTAATATTGAGCATT Y 2 1 2 1 101000 f 74 goat snp48623-scaffold690-3440523 6 104848845 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447516 Affx-122924066 AX-123317852 6 101653868 CAGCTCATTCATACACAAGCGTATTTATGCTACAA[C/T]ATTTATTCAACATCCCCTAATAAAACTTTTCTTTG Y 2 1 2 1 101000 f 74 goat snp48622-scaffold690-3410776 6 104878675 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402420 Affx-122958638 AX-123272773 6 101693550 TGACAGATCCTTCTCAATCTAGCACTTATACAAGC[A/G]TTTACAGAATTTTCCTCCATTTCCTAAGTGGCTTG R 2 1 2 1 101000 f 74 goat snp48621-scaffold690-3371094 6 104918551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425840 Affx-122940671 AX-123296186 6 101740963 GCATAGGGTCAGTCAGTACTTGCAGACCGAGTAAA[C/T]GTCTAAATACAAAAACAGTATTTACCACTAAAGAA Y 2 1 2 1 101000 f 74 goat snp48620-scaffold690-3323681 6 104966276 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409668 Affx-122953509 AX-123280019 6 101772206 ACAGGAACCTGGTAACAGACTGCTGACTGGTGGTG[C/T]AGGAACATTTTAACCTAGAGAAAGTTTTCATCATG Y 2 1 2 1 201000 r 74 goat snp48619-scaffold690-3292438 6 104997835 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441737 Affx-122929133 AX-123312074 6 101848664 TTCCTCTCAGGAGGGTCAGAGGGTCAGATGAACTC[A/G]TCTTAAATTAGGGGTGGCATGAGCTAAGTTTTGTA R 2 1 2 1 102000 r 74 goat snp48618-scaffold690-3215980 6 105072961 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441394 Affx-122928846 AX-123311731 6 101899240 AGCCGACACGTCAGGCACTACGTTAGGCACTGGGG[A/G]GACTGGGGGTGCTGTGTGTATAAGTCCCAGGTAGG R 2 1 2 1 101000 r 74 goat snp48617-scaffold690-3165404 6 105126097 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446203 Affx-122925718 AX-123316539 6 101928598 CCTTGTTAACAGGAAGCGAATTCCTCATCAAATAC[A/G]GTCTTCTGTTGATTGTCTCCTTGTGAAAAGGTCAG R 2 1 2 1 101000 f 74 goat snp48616-scaffold690-3136046 6 105155598 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406828 Affx-122955677 AX-123277179 6 101972747 GGTATGGTTGCACAACCCTATGAATATACCAAGCC[A/G]CCAAACTGTACAATTTAAATCAGTGTGTTGTGTGG R 2 1 2 1 101000 f 74 goat snp48615-scaffold690-3091897 6 105200118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390412 Affx-122967651 AX-123260769 6 102031783 TGGAACTAAACACCTCCCCTCTGCAGTGCAGGTGG[A/C]AGAGAGGAAAAACTAAAAGACTGGAATTCATTGGG M 2 1 2 1 103000 r 74 goat snp48614-scaffold690-3032861 6 105259694 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394029 Affx-122965002 AX-123264384 6 102153111 ATCTGCACTCCCTCCTAGTTTATCTTCTAGGAGAG[C/T]TGAAGATGCAGACTAGTTCATTGGAAGCAGTCCTA Y 2 1 2 1 101000 r 74 goat snp48612-scaffold690-2911533 6 105381841 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453490 Affx-122919829 AX-123323823 6 102187731 CCCTCTTCAATATTTTATGAGCCACAGAGCTCCAC[A/G]TCGGAAGCAGTGGAATGGAGACTTTTCAGTCCCAA R 2 1 2 1 101000 f 74 goat snp48611-scaffold690-2876913 6 105416710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408548 Affx-122953683 AX-123278899 6 102236776 CTGGGGGGCTTAAAAGAAGAGTTCTAGGGGCCAGG[A/G]GTCCAAAATCAAGGTATCTGCAGACTTGGTCCCTT R 2 1 2 1 201000 f 74 goat snp48610-scaffold690-2827868 6 105465502 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388386 Affx-122969306 AX-123258744 6 102278141 GCCTCCCTGCATGACTGATACGCAGAATGAATATT[A/G]GACTGAATGATTCATGCACTCGGTAGATACCCAAC R 2 1 2 1 101000 r 74 goat snp48609-scaffold690-2786503 6 105506640 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776959 Affx-122921644 AX-385264083 6 102309689 GGCATAAAAGAAAATGGCCTGTCGCTAATGATTTT[C/T]ATTCGAATTATTCAGACAAATGAAAACGCTATGGT Y 2 1 2 1 101000 f 74 goat snp48608-scaffold690-2754955 6 105537591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384116 Affx-122972827 AX-123254474 6 102351335 TAACCCATGCCTGTCAGTGTTTACTGCGCTGCCTC[C/T]AGGCCTTCGGATCCTTTGTTAACGGGACGGGAGGC Y 2 1 2 1 101000 f 74 goat snp48607-scaffold690-2713309 6 105579813 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779487 Affx-122936227 AX-385266590 6 102398428 GTTGTTTTTTTCAGGAACTTGCCCAGATCGCTTGA[A/G]ACCACTGACTATTCAATGGGACCTGCCTGAGTGTG R 2 1 2 1 101000 f 74 goat snp48606-scaffold690-2666216 6 105626466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275366 Affx-1111834857 AX-519548940 6 102409835 GACTGCTTCTTTCTTGTTCGCTTCGCAGCTCAAGC[A/G]CTGGAGACAGAAGTAGGTAAACGCATGCTTGCTCT R 2 1 2 1 201000 f 74 goat GoatD01.056729 6 102409835 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38436529 Affx-122932935 AX-123306867 6 102443735 GGGTCAGTCATAACTTTTTGCAAAACAAATTAATC[A/G]TCTTGTAGGCCCCATCACTTTCCTTTCCCCCTTGA R 2 1 2 1 201000 f 74 goat snp48605-scaffold690-2620909 6 105671357 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406589 Affx-122956262 AX-123276941 6 102483316 AAATGTTCAAGGACTCTGGCCACAACCTCGCTGTG[C/T]TCAATCTGCACTTCCAATGTACACTTTCCAGCAGG Y 2 1 2 1 101000 r 74 goat snp48604-scaffold690-2581328 6 105710818 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418342 Affx-122946596 AX-123288690 6 102521591 TATCATCTCCTGCATTGGCAGGCAGATTCTTTACC[A/G]CTGGGGACCCTCTTCTTTATTTATCCTAGGCCTTA R 2 1 2 1 101000 r 74 goat snp48603-scaffold690-2543053 6 105749187 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423045 Affx-122942966 AX-123293391 6 102552284 CATTGTCTTGTATTCTTTAGCGCTTTAGTCCTCAT[A/G]CAGCTCTGTGGAGGAAGCTGACTAAGTCTGTAATT R 2 1 2 1 101000 f 74 goat snp48602-scaffold690-2512360 6 105780499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802419 Affx-122923559 AX-385289323 6 102594396 GACACTTCTCACCTAGGTAGCCTGGTCATTGTTTC[A/G]TCTTCAGATCAGTGGATCCAGTGCTTCTATCATTT R 2 1 2 1 101000 r 74 goat snp48601-scaffold690-2470248 6 105823076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378636 Affx-122977107 AX-123248995 6 102636828 TACCCTATTTTAAAGGTGATAAAACTAAAGCAAAA[C/T]AAGGTAAGCCTGAGATTTTAAAATGAAATTCTTAT Y 2 1 2 1 201000 f 74 goat snp48600-scaffold690-2427816 6 105865707 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410809 Affx-122952648 AX-123281159 6 102668410 GTGACACAAGATACAAAGAGCAGGGAGCTGCATCA[C/T]TTAGGCCAACCAGAGGCTTCTGAGAAGCCTTCTGC Y 2 1 2 1 101000 f 74 goat snp48599-scaffold690-2396234 6 105896865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420506 Affx-122944849 AX-123290853 6 102701287 CTTTGGAGCTGGAGTAAGAGGCCTCTGGGCTCAGC[A/G]CTCTCAACTAGGTAAATGAGATGGAAAGAAGAAGA R 2 1 2 1 101000 r 74 goat snp48598-scaffold690-2363357 6 105929769 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272328 Affx-1111833487 AX-519546063 6 102703096 CTCCGTCCATGGGATTTTCCAGGCAAAAGTACTGG[A/G]GTGGGGTGCCATTGCCTTCTCCGAATGTAGCCATA R 2 1 2 1 303000 f 74 goat 6_102703096_AF-PAKI 6 102703096 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38421870 Affx-122944278 AX-123292217 6 102781603 AAAGATAGCAGGCCTTCAAAGTGTAAGAAATATTT[A/C]TGATGAAAAACAAAAGTCCTTTAAATTGGGGTATT M 2 1 2 1 101000 r 74 goat snp48596-scaffold690-2283041 6 106010154 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793735 Affx-122974115 AX-385280707 6 102840879 GGGTAGACGCAAAGTCAAATGCTTGGTCTAAGGAC[A/C]CAGGGTCTCACCTACCATAAAGCAAGTAATTGACT M 2 1 2 1 201000 f 74 goat snp48595-scaffold690-2223765 6 106069097 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278590 Affx-1111836416 AX-519552069 6 102883861 GATAAATTAAAAGTCATTATTCCCGTACTTGCATT[A/G]CATTACCAACTGCCTCCATCAGACATTACATGAAA R 2 1 2 1 101000 r 74 goat Random2.2K-734 6 102883861 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421659 Affx-122944447 AX-123292006 6 102892446 CAGAAATCACTTCCATACCCCAGAAGTCATTTCTG[C/T]ACCCCCAGAAGGCTGTGGAAGGCAATGGACAAAGC Y 2 1 2 1 102000 r 74 goat snp48594-scaffold690-2172198 6 106120592 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399966 Affx-122960831 AX-123270321 6 102928229 TTGACCTAGATAATTGAGTGAGAATCTGAAATTAA[C/T]GGGAGAGGGGATCTATCATGAGGCAGAAACAATAG Y 2 1 2 1 201000 f 74 goat snp48593-scaffold690-2136415 6 106157001 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784550 Affx-122938353 AX-385271599 6 102974349 AAAGCCCTTGAATCAGATTTCTGAAGAGCCAAAAT[A/G]TTTTCCTGTACTTCCTTAAACGAAAGGAAAAATTC R 2 1 2 1 101000 f 74 goat snp48592-scaffold690-2090295 6 106203503 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442796 Affx-122927723 AX-123313133 6 103017766 TAGTCTGAAACCATCTATTATTTGATTATTTGTTC[A/G]TGTCCTTGCCCCACCCTCAACTAATCCATCATCTT R 2 1 2 1 101000 r 74 goat snp48591-scaffold690-2046878 6 106246954 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393010 Affx-122966182 AX-123263367 6 103066388 CATGTCGTAGTGACTAAACAACAATGCAAAATCAG[C/T]GAGTTTAGCAATAAAAATTTATCTGGGCTTTAGCT Y 2 1 2 1 101000 f 74 goat snp48590-scaffold690-1998256 6 106295249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780430 Affx-122921294 AX-385267522 6 103107038 ATATAAAGCATGATAAGTGATGGGAAAAACAAGTT[C/T]TCTGAGTCCTATACCTACTGAGGGTTGCTGAAGCC Y 2 1 2 1 201000 f 74 goat snp48589-scaffold690-1957606 6 106335906 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384296 Affx-122972289 AX-123254654 6 103137750 GCTGACATTCTAGTGTCTAAAATAGTGTCCCGTAT[A/G]TAAAAGGAACTCAGTAAACACATGCTGAGTAAATG R 2 1 2 1 101000 f 74 goat snp48588-scaffold690-1926894 6 106366612 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800195 Affx-122970802 AX-385287118 6 103188775 CTCTATTCACACAGCAAAGTGTGTGATAATAAGAT[A/C]CAGGTTTCAAAAGTAACTAGGAGAAGTTTTACTTG M 2 1 2 1 101000 r 74 goat snp48587-scaffold690-1875869 6 106417480 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768227 Affx-122927908 AX-385255409 6 103226788 TCTTGGTCAAGACTGAATCCTGCTGCTGTGGGTAT[A/G]TTACAGGAATCTTACTTTGTCTCAACTTCCATAGT R 2 1 2 1 102000 f 74 goat snp48586-scaffold690-1837856 6 106456012 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765021 Affx-122974837 AX-385252592 6 103255472 TGAAAACTAAATGAGAGAATGTTTAAAAATTCCCA[A/G]CACTATTTCTGACACACGTGAATCATGCAATAAAT R 2 1 2 1 101000 f 74 goat snp48585-scaffold690-1809172 6 106486451 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380049 Affx-122975572 AX-123250407 6 103294155 TCCAGATACTCCTCATTTGCTGCTGAGAGATAGGA[C/T]GCATCACCTAGACACGGAAGCACCCTCTATGATTT Y 2 1 2 1 101000 f 74 goat snp48584-scaffold690-1770489 6 106525496 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422062 Affx-122943603 AX-123292409 6 103344149 ATCAGAAGAATAGACGATGGATTCAGACTGTTAGA[C/T]GGACCAGTGATTTCATAATATATCATTCTGTTTGA Y 2 1 2 1 101000 f 74 goat snp48583-scaffold690-1720495 6 106575810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780321 Affx-122933691 AX-385267416 6 103399444 TACACTGGAAAGAAAAGACCTTTATTTTTGTATCA[G/T]CTCTGCTTGTCAGTTTGATGTGACCATGGGCAAGT K 2 1 2 1 101000 r 74 goat snp48582-scaffold690-1665200 6 106631905 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781153 Affx-122976950 AX-385268238 6 103437612 TTTCATACTTAAGAAAGCAAACCAGGGGCTAAAAG[C/T]AGATGAGGAATTAAAAATCAAGGTGGCAGATGAGA Y 2 1 2 1 101000 r 74 goat snp48581-scaffold690-1627032 6 106665727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387135 Affx-122970650 AX-123257493 6 103482245 TGGAGAGAGTGGGGATTATTCCTATACTACTGACT[C/T]TCTCTCCAGCACAATTTCTAATTTATCATATTATG Y 2 1 2 1 101000 f 74 goat snp48580-scaffold690-1582399 6 106710174 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38432687 Affx-122936038 AX-123303028 6 103530176 TGTCATTGGATTTCAACCTTATAAACACCCATGAC[A/G]TTGTTACTATGTCCCATTTAAAGAATTAAGAGAAT R 2 1 2 1 101000 f 74 goat snp48579-scaffold690-1534468 6 106759462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405730 Affx-122956519 AX-123276082 6 103574194 TCCAACACCATGAGAGTAGGGATTTTGCATCTTCC[A/G]TTCCTTCCTGAACCCTCAGAGCCAGCAGAGCGTCT R 2 1 2 1 101000 f 74 goat snp48578-scaffold690-1490450 6 106781738 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437546 Affx-122931902 AX-123307884 6 103610874 TTTCTCAGCCCTAACCTTAGTGCAGTTATCACGTA[C/T]GTTGCCTCCTCTCTCTCATCTGCCCCCCAAAACAC Y 2 1 2 1 101000 f 74 goat snp48577-scaffold690-1453770 6 106818314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278593 Affx-1111836417 AX-519552071 6 103640826 GACTTGGAGGACATCCATCCCAAGGAGCTGTGGGT[A/G]GAAAAAGGTCTCAGGGGTGAATTGGGGAAAGCCTA R 2 1 2 1 202000 r 74 goat Random2.2K-736 6 103640826 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425015 Affx-122941885 AX-123295361 6 103646801 TGAACCACCAGGGAAGCCTTATTTCACAATTATCT[A/G]CCACCTTTAAGTGCCCGTTTTAGCCACCTTCTGTG R 2 1 2 1 201000 r 74 goat snp48576-scaffold690-1417843 6 106854209 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385970 Affx-122971531 AX-123256328 6 103701600 CTAGACTGTAAGGAAGAGGAGCAGACTCATTTCCA[C/T]GTATCCCCCTTGAGCAATTTGGTGGCTGGTGGTAT Y 2 1 2 1 201000 r 74 goat snp48575-scaffold690-1363044 6 106910041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408455 Affx-122954440 AX-123278806 6 103776669 TGAACTTGACCACTTTCCAACAGCTCCACCATTAC[A/G]CCATCAGCTGAAGCTCTCACTGGACACAGCAACGT R 2 1 2 1 101000 f 74 goat snp48574-scaffold690-1287975 6 106985761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774841 Affx-122972758 AX-385261975 6 103810683 AACATTGCCAGGAAAATGTCTTAATCCATGGAAGG[C/T]GAGATTTAGGGACGAATGTCCCAGTGCCATCACAG Y 2 1 2 1 101000 f 74 goat snp48573-scaffold690-1253961 6 107020050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382593 Affx-122973720 AX-123252951 6 103841088 AATGAACATTTGTTGAATGCGCTGGACAGACCAAA[A/G]GTCTAGTTAATTGATGGAGCAAATGAGACCATTCT R 2 1 2 1 101000 f 74 goat snp48572-scaffold690-1223556 6 107050142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446738 Affx-122925342 AX-123317074 6 103870631 ATGCATTGACTGGTCTTTAGTCCTACCTAGAAACT[A/G]TAATTCTGAGAAGTCTGTTTCTATTGCTCACGATG R 2 1 2 1 101000 f 74 goat snp48571-scaffold690-1194013 6 107080847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797414 Affx-122943863 AX-385284353 6 103932759 AAAAATTTCAAACTTGAAAAAGGCTATATAATATT[A/G]TTCTACCAGTAAGACTTCATAGATAACTACTATGA R 2 1 2 1 202000 f 74 goat snp48570-scaffold690-1131885 6 107143729 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441047 Affx-122928929 AX-123311384 6 103973544 GCCTTGAGACAAAGGAACATGGATTCTGGCATCGT[G/T]TCTGACACCTTCCTACCAAGAGGGTAAAATAAGTC K 2 1 2 1 101000 r 74 goat snp48569-scaffold690-1091100 6 107183678 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404861 Affx-122956615 AX-123275213 6 104024885 TCTATATTAATTTCTGTGGTACAATGATTATATCA[C/T]ATTTTTAGATTTATCATATAAAATATTTAGTATTA Y 2 1 2 1 103000 f 74 goat snp48568-scaffold690-1039759 6 107234920 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451069 Affx-122921422 AX-123321403 6 104056957 ATCATTAACCTCATTTTATTCATTAGGACTCTGAG[A/G]CAGAGAGTGGTTAATTAATCACTCCAAAGTCCCAT R 2 1 2 1 101000 f 74 goat snp48567-scaffold690-1007687 6 107266984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427475 Affx-122940017 AX-123297818 6 104086795 TCCATATGCTCTCTAATTCACTTATATTTTTATTT[A/G]CTTTTTTTCAAGACTACTTTATTAGGATATAGAGA R 2 1 2 1 101000 r 74 goat snp48566-scaffold690-977849 6 107296634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417341 Affx-122947732 AX-123287689 6 104134157 TGTCTGAGGGGCCCTTGCCGAGCTCCCTGCAACAG[C/T]AGTGTCATAAAAGGCACATCTGTAGACTTAGGAAA Y 2 1 2 1 101000 r 74 goat snp48565-scaffold690-930487 6 107344449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275279 Affx-1111834811 AX-519548855 6 104153760 TTTGTTCTTCTCTGCTACACCCTTGCAGCATCCTC[A/G]CACTGCAGGGAGACTGGACCAAGGCCCTCGCCCTA R 2 1 2 1 202000 f 74 goat GoatD01.054430 6 104153760 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434673 Affx-122933968 AX-123305014 6 104180504 TATAAACACTGATTCAAAAACTCTAGTAGTCTTGC[A/G]CTATTTTTTCTTTATTATTTCACAATTATTATTCC R 2 1 2 1 101000 f 74 goat snp48564-scaffold690-884140 6 107391888 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783064 Affx-122947650 AX-385270131 6 104225398 ATTGAGAACACTGCAGTGTTAAGAGTGGCCATCAA[C/T]AGCAAATATTCCTATAGAGAGTTTCCCACTCACCA Y 2 1 2 1 101000 r 74 goat snp48563-scaffold690-839246 6 107436950 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445608 Affx-122925110 AX-123315945 6 104293150 TCCTTTGATGTGCACCTCATTATCTAGGGCCAGTA[G/T]CCTGTTCCTTCCTATCTTCTGCCCCCTCAGGATGC K 2 1 2 1 101000 f 74 goat snp48562-scaffold690-771494 6 107503161 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428238 Affx-122939427 AX-123298581 6 104342124 ATTACTTTTTAATATGTATATACACAAAGAACAGA[C/T]ATGTAACTATCTCTTTAGTTTTGGTCTCAGCACAA Y 2 1 2 1 101000 r 74 goat snp48561-scaffold690-722520 6 107552045 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432979 Affx-122935268 AX-123303320 6 104402846 GACATTCCCGGGGTCACTCTTGTGGCAGCACTCAC[A/G]TAGGAGCTTGAATTCCAGTGACTGCTTCAGGGTGG R 2 1 2 1 101000 r 74 goat snp48560-scaffold690-661798 6 107614358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411561 Affx-122951637 AX-123281911 6 104448968 ATTAAATTTTAGTTTAGAGTTAAGTTGTCCAGTAA[C/T]AGACATTTGCCTGTTTTCTATTTCAGGAATTCCCG Y 2 1 2 1 201000 f 74 goat snp48559-scaffold690-615676 6 107660476 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775338 Affx-122935281 AX-385262469 6 104504109 TGAATCACTGAAGGACTGAATGGACCATTTAAGAG[C/T]AAATCTTGCCAAACTCCAGTGCCTTGTTTCGATAG Y 2 1 2 1 101000 r 74 goat snp48558-scaffold690-560535 6 107715087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278595 Affx-1111836418 AX-519552074 6 104523250 TGGATTAAGTGAGATGGGTTGCATATACAGTACGC[A/G]TAGAAGAGTGTCTGTCCTACCCTAAGCTCTCTACC R 2 1 2 1 101000 r 74 goat Random2.2K-737 6 104523250 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398076 Affx-122961732 AX-123268431 6 104541817 AGACAGCTGACAGACAAATAATACAGTTGAGCCTA[C/T]ATGAGACCTCATCTTTGTTGGGTCCAATGTGTGTT Y 2 1 2 1 101000 f 74 goat snp48557-scaffold690-522827 6 107752270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278428 Affx-1111836419 AX-519551913 6 104546106 TCTGCCAGAATCTGGGCTCCGTTTCCGTGTGTTTA[A/G]CAATGAAGATCCCTTTCTTTGCTCCTGGTGTCCCT R 2 1 2 1 201000 f 74 goat Random2.2K-738 6 104546106 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416055 Affx-122948347 AX-123286404 6 104601372 AAAATTATCTAAAAGACTGACCCTATGTCTGAAGA[C/T]GGGGAACTTCTGAAGGGCCATATCAATGTTTGAGT Y 2 1 2 1 201000 f 74 goat snp48556-scaffold690-463272 6 107810588 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791887 Affx-122935526 AX-385278877 6 104631767 CATCTCATCAAGTTGAGATGCAGATCTGATATTCT[A/G]CCAGATCAGTAGGGAGCTCCAGACAAAATTGCCAG R 2 1 2 1 101000 r 74 goat snp48555-scaffold690-432877 6 107841440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444469 Affx-122926538 AX-123314806 6 104681989 GGAGACAGACAAAGAAAATACATAGATATATGGGC[A/G]TGGATAAGCCCGAATGCAGCTTTATTTACAAAGCA R 2 1 2 1 101000 r 74 goat snp48554-scaffold690-382655 6 107893685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435404 Affx-122933558 AX-123305744 6 104734673 GACCAGGGAAGTCCCAAGACAGGTCTCACCTACTA[C/T]AAGTCGCTTCATTTATAAGTGGTATTGCATGGAAG Y 2 1 2 1 101000 r 74 goat snp48553-scaffold690-329971 6 107946915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789459 Affx-122949433 AX-385276469 6 104806588 TTTAAAGACTAATTGTCATATAATGAATGTGTATG[C/T]GTATGCACACAAATACACGCACACATACCCCTGCA Y 2 1 2 1 102000 r 74 goat snp48552-scaffold690-258056 6 108020076 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445967 Affx-122925893 AX-123316304 6 104844112 TGACCCTATACTAGAAAGACTTTGGCCTTAGCACA[G/T]AGCAGGATGCTTTGGAAGCCCCAGTCACACACGCG K 2 1 2 1 101000 f 74 goat snp48551-scaffold690-220532 6 108057657 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388584 Affx-122969161 AX-123258942 6 104875528 ACTGTTTAACACATCCCTAATATAAACCAATGCCA[G/T]AACAGTGAACATTAGCACATTTCTACCCATGTTAA K 2 1 2 1 101000 f 74 goat snp48550-scaffold690-189116 6 108090550 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378165 Affx-122976964 AX-123248524 6 104924291 AGGGTTTCTGGCCTCACAGAATCTACAGTTTATGG[C/T]GGAGAGAGACATAGAAAAAACATAAGCTATATGGA Y 2 1 2 1 101000 f 74 goat snp48549-scaffold690-140353 6 108139280 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430035 Affx-122937575 AX-123300376 6 104957870 AAGGGGTCCTTGAGTTAAGAGACAGGGAAGCCTGG[C/T]ATGCTGTAGTCCATAGACTCGCAAAGAGTAAGACA Y 2 1 2 1 103000 r 74 goat snp48548-scaffold690-106774 6 108172833 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782197 Affx-122940058 AX-385269275 6 105001524 AATAAGGCACTGATGGAATTATTAGGGATAACAAA[C/T]GGACAAGGTTTTATTGCTAATAATGAAGGTCCTGA Y 2 1 2 1 101000 f 74 goat snp48547-scaffold690-63120 6 108216012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388331 Affx-122969360 AX-123258689 6 105030608 TACTCACCACCTTCATCTAACAAATGCTATCATTC[C/T]ATCATATTATTTCAGCCTTTAAAAAATATACAGAT Y 2 1 2 1 101000 f 74 goat snp48546-scaffold690-34036 6 108245012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385211 Affx-122971710 AX-123255569 6 105077529 AAATGCATTATGACTCTTGTCAATGGCCCAAATTA[C/T]ATTTTCAGTTCAGTGCAGTCACTGAGGCATATCCA Y 2 1 2 1 201000 f 74 goat snp4376-scaffold1139-12786 6 108294194 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766629 Affx-122926247 AX-385253980 6 105106989 CTTGATTGTATGACACTGAATAATTTCACTCTATC[A/G]TTTACTTCACCGATCTTCAAAAATCTTATTTTTAT R 2 1 2 1 101000 f 74 goat snp4377-scaffold1139-42246 6 108323330 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775927 Affx-122935647 AX-385263058 6 105151959 AGAACTGATATTTTTAACAGAGTATTTATTCCATT[A/C]TTTCTGCTTATTAAGAAGTTAGTTTTCATATACCT M 2 1 2 1 101000 f 74 goat snp4378-scaffold1139-87216 6 108368547 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274281 Affx-1111834159 AX-519547878 6 105173487 CAGCCTCAGTCCAAAACTATCCTGTTCTAATCATC[A/G]CTTTGGACAGAGATGTCTCTGCAGAAGCTAGAATG R 2 1 2 1 201000 f 74 goat GoatD01.022462 6 105173487 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38395063 Affx-122964190 AX-123265418 6 105189071 TCTGTGTTGACTGGGGCTTTAGCTAGGATGGTTCA[A/G]ATGGCTTGGGACTTGCCTGGGAAATCTGAGTTCTC R 2 1 2 1 303000 f 74 goat snp4379-scaffold1139-124328 6 108405188 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447750 Affx-122924580 AX-123318086 6 105284222 AATTATTCTCTTAAGACAACCCACAGCAAGGTTGA[C/T]GGAAGCCTGGGGCTGTCATGAGCGATCACATGAAA Y 2 1 2 1 201000 f 74 goat snp4381-scaffold1139-219479 6 108500560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408685 Affx-122953445 AX-123279036 6 105344328 TTCCCCGCTCATACCTCCCACCTTTCTAAAATTGC[A/G]CTCTCCCCATGGCCATCGATTCCACCGGGAATGCC R 2 1 2 1 103000 f 74 goat snp4382-scaffold1139-279585 6 108560682 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784434 Affx-122965392 AX-385271483 6 105382931 AGTGATTTGTCCAAATCACATAGCCAGTTATTCTT[A/G]TAGCTGGAATTTGAACTCAGATTTCTTTGATTATT R 2 1 2 1 303000 r 74 goat snp4383-scaffold1139-318188 6 108599248 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272237 Affx-1111833489 AX-185187933 6 105400668 GTCCGACTCTGTGCGACCCCATAGACGGCAGCCCA[A/C]CAGGCTCCCCTGTCCCTGGGATTCTCCAGGCAAGA M 2 1 2 1 303000 r 74 goat 6_105400668_AF-PAKI 6 105400668 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781260 Affx-122958544 AX-385268345 6 105436619 AGCTTATTTTTTTATGGCACTCATAGTTATCTGAT[A/G]CATTATTATTATACTTAGGTCTATGTTTATTAATG R 2 1 2 1 101000 f 74 goat snp4384-scaffold1139-371876 6 108653699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376083 Affx-122978907 AX-123246442 6 105475528 CCCATAATAATAATAGAAATAAAATCCACAATGTA[C/T]GTAATGTGCTTGAAGTATCTGCAAACCACTTCCCC Y 2 1 2 1 101000 r 74 goat snp4385-scaffold1139-410785 6 108692607 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433450 Affx-122935063 AX-123303791 6 105571648 TTTTTGCTCTGGTGAATGATATGAAGATAACAGGA[C/T]GGCCTGGAAGAAAGAGGAACTGAGGGCAAGGAGAA Y 2 1 2 1 201000 f 74 goat snp4387-scaffold1139-506905 6 108788010 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404944 Affx-122956426 AX-123275296 6 105613611 TGGTGGATGAATCAAAAGGAGGAAGACCCTGGGGT[A/G]CACTTTGAAAAGCACAGCCTGAAGCTGCCCTCACG R 2 1 2 1 101000 f 74 goat snp4388-scaffold1139-548868 6 108829907 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424578 Affx-122942218 AX-123294924 6 105705178 GTTCAACTGTTCTTTCTTTTTTTTTTTTTTAACAC[A/G]TGCACACGGAGTTCTGTGGCAAGAAAGACAGTAGA R 2 1 2 1 101000 r 74 goat snp4390-scaffold1139-640435 6 108922321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764747 Affx-986697007 AX-385252362 6 105705589 TCTGCCACACACCTACCCATTTCTGAGGAAAGCCA[A/C]ACCTCCTGGGTTTTCCTTTCAGAAGAAAAGGGACA M 2 1 2 1 600010 r 74 goat 6_105705589 6 105705589 Ancestral_priority_1043 ancestry 0.598 neutral IMAGE 10K 10K ancestral 320764750 Affx-986697009 AX-385252366 6 105705612 TGAGGAAAGCCAAACCTCCTGGGTTTTCCTTTCAG[A/T]AGAAAAGGGACACATTAGTCTCCACGAGCAAGGCT W 4 1 2 1 600010 r 74 goat 6_105705612 6 105705612 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320764754 Affx-986697011 AX-385252368 6 105708448 CTTGAGCTTCTCAAAACCTTCATTCAAACTTGAAT[A/T]TGGGTGAACGATGCTCATCTGTGGAGGGAAGTGTT W 4 1 2 1 600010 r 74 goat 6_105708448 6 105708448 Ancestral_priority_1043 ancestry 0.492 neutral IMAGE 10K 10K ancestral 38400033 Affx-122960784 AX-123270388 6 105748992 ACATAATTTCAAGACTTAAAATCATTTATTCAACT[A/G]TCTCCCACCTGAGAGGTTTATATTCCAATATTGAG R 2 1 2 1 101000 r 74 goat snp4391-scaffold1139-684249 6 108966512 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776958 Affx-122944650 AX-385264082 6 105785940 AATTTAAAAGAGGTAGGTATATCTATGTGTACAAA[C/T]GTGGAAAGCTCCTTAGATAACATTACAAGGTGAAA Y 2 1 2 1 201000 r 74 goat snp4392-scaffold1139-721197 6 109003824 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440387 Affx-122929629 AX-123310724 6 105843233 GCCTGGAAAACCTTACCTTTAGCCCTGTGAGCTCC[G/T]AACATCTTTTGGCTCTAAAAATCTGACCAGGGCAC K 2 1 2 1 101000 r 74 goat snp4393-scaffold1139-778490 6 109061607 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419349 Affx-122945642 AX-123289697 6 105877105 TCAGCAATTAACATCAACATCAAGTGGCAAAAGCT[A/G]TATCAAAGTAGTTTAAGGGTATTTGTAGGTCCAAC R 2 1 2 1 101000 r 74 goat snp4394-scaffold1139-812362 6 109095718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449548 Affx-122923248 AX-123319883 6 105913244 AGTGAGGAGGGTTCAGAAGGGCCGAGACCCTGTTA[C/T]GAAACCTCTCTAAGCCTCAGCGGCCTCATATGCTC Y 2 1 2 1 303000 f 74 goat snp4395-scaffold1139-848501 6 109131996 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765590 Affx-122942469 AX-385253069 6 105941839 GTTTAAACCTATAATTCTCTATTAACTGTATATTA[C/T]GAGGTATATTACTATGAATTTTAATGTGAACTGGC Y 2 1 2 1 201000 f 74 goat snp4396-scaffold1139-877096 6 109157234 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411852 Affx-122951221 AX-123282202 6 105979872 CTCAAGGTGCGAAGAGGATGCAAAAACAACATAAA[G/T]GGAAAGCCCAGGAAATGGGCCCAGACCCAGCTGGG K 2 1 2 1 101000 f 74 goat snp4397-scaffold1139-915129 6 109195358 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38438994 Affx-122930373 AX-123309331 6 106029098 CTGAGACAGGTTAAATGACTTGCCCACAGTCAGCA[A/G]TCTCTGAAGAGCCTCCTTATCTTCCTGCTCCACAT R 2 1 2 1 201000 r 74 goat snp4398-scaffold1139-964355 6 109244442 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435302 Affx-122934025 AX-123305642 6 106066465 AATCTACTGCCCTTTAGGGACAGACTCCCGAACAC[A/C]CCAATCAGTGCCCTGCACTCTTCCAGCCTCTTGGG M 2 1 2 1 101000 f 74 goat snp4399-scaffold1139-1001722 6 109283218 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278430 Affx-1111836420 AX-519551915 6 106128421 TTGTTTTCATTCCTGGTAACTTCCTATCAAACTGC[A/G]CAGGCCCCCCTCTCTTAGAACTGTCTCAAATATCT R 2 1 2 1 101000 f 74 goat Random2.2K-739 6 106128421 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38453446 Affx-122919863 AX-123323779 6 106151351 ATGCTCCAACCAAACTGAGCTACCAGCTGTCTTCC[A/G]CATCTCCTGATTTCCTTCTTTTGTAATTTGCTGCT R 2 1 2 1 201000 f 74 goat snp4401-scaffold1139-1086608 6 109367865 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397293 Affx-122962328 AX-123267648 6 106202907 TTTGTGGCAGATTTGTGATGTTCAATAGTAAGAAA[C/T]GGGCTTCCGTGGTGGCTCAGACGGTAAAGAATCTG Y 2 1 2 1 101000 f 74 goat snp4402-scaffold1139-1138164 6 109419324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380728 Affx-122975142 AX-123251086 6 106240879 ATACAACAAAGACTATGAGCTTAAGGGATAAACAA[C/T]GAATGTATTTTAAAGGCAAATAAATGTTATAAGGG Y 2 1 2 1 101000 f 74 goat snp4403-scaffold1139-1176136 6 109456269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797213 Affx-122977809 AX-385284152 6 106270978 ATGATATGTGAAACTGTGATAATAATGGTTCTGAC[C/T]TCTGGCTTATGCAAGGATTAAGAGAGTTGATACTT Y 2 1 2 1 101000 r 74 goat snp4404-scaffold1139-1206235 6 109486697 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791670 Affx-122937291 AX-385278661 6 106312647 TGAAAGATATTATCCCAGTGTGAATTCTTCATATA[C/T]GGAACAACCTCAGATTGTGGATTTAGAGTAACAAT Y 2 1 2 1 101000 r 74 goat snp4405-scaffold1139-1247904 6 109528830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395431 Affx-122963937 AX-123265786 6 106352919 TGCACTAGCTCAATGGCCTGAGAAGAGGTTACTTT[C/T]ATTTTGTGTGATGGAGGAAAATAGGATATGTCTCA Y 2 1 2 1 101000 f 74 goat snp4406-scaffold1139-1288176 6 109569665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777867 Affx-122953227 AX-385264984 6 106392132 GATCATCAGCTTTAACAGGAGCCCAAACTGATCAA[C/T]GTTTCGGTACCACTGACCCAGTAGCTGATAATACA Y 2 1 2 1 101000 r 74 goat snp4407-scaffold1139-1327389 6 109608340 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452110 Affx-122920838 AX-123322443 6 106426116 AGGAGACCTTGATTTCATGCATTTGGACAGAGCAG[C/T]AGCTCTGGTTATCTGTGTTGTGCTCATGGAGTCGC Y 2 1 2 1 101000 f 74 goat snp4408-scaffold1139-1361373 6 109642257 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391810 Affx-122967026 AX-123262167 6 106481850 ACCGTGCACAGGTCACAGTAGGGCTCGTGTTCTTA[C/T]GAGAATCTAATGTCTCTGCTGACCTGACGGGAAGC Y 2 1 2 1 101000 f 74 goat snp4409-scaffold1139-1417107 6 109700548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452102 Affx-122920846 AX-123322435 6 106526428 TCTGCATTATATATAGGATTATTGGAAGCATTACT[A/G]CTTCTTTACAAAATTTTTTGTTTGTGTATTTCAGA R 2 1 2 1 103000 f 74 goat snp4410-scaffold1139-1461685 6 109745122 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400682 Affx-122959946 AX-123271037 6 106555164 TTCAAATATAGAAAACAATTTTGTAAACTCCCTGC[C/T]GTTTCTGTTTTGCTTGGGCTCTGCAGAGGCTCAAA Y 2 1 2 1 201000 f 74 goat snp4411-scaffold1139-1490421 6 109773851 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394141 Affx-122965319 AX-123264496 6 106588034 CACATAATTCAAAACAAAGCTATAGGGAAGTCAGG[C/T]GTTTCTCCTCTACAATGTCAAGATTTATTAGGAAT Y 2 1 2 1 101000 f 74 goat snp4412-scaffold1139-1523291 6 109806743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278432 Affx-1111836421 AX-519551917 6 106606246 AGTACATTCTTGGCAGAGCTCTGCCTAGAACCCAA[C/G]AGGGGCTGATGGTTCCAAGCACATTAATTGCATTT S 4 1 2 1 202000 f 74 goat Random2.2K-740 6 106606246 C G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382856 Affx-122973530 AX-123253214 6 106621580 TCTGATTTAGTCTTATCAACCTTGGAACATGTTCC[A/G]TGGTCAGCACAAATGGCCAGGCTTTGGAACGACTG R 2 1 2 1 102000 r 74 goat snp4413-scaffold1139-1556837 6 109839838 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782530 Affx-122968086 AX-385269605 6 106654587 TCATGTTCTTAGTCTACATGTTAACATGTTGGAGA[C/T]GCTGGATTCAGTTTTTAAACACCTGCTATAGCATC Y 2 1 2 1 201000 r 74 goat snp4414-scaffold1139-1589844 6 109872807 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784188 Affx-122935135 AX-385271239 6 106689326 ATGACATTCATATTACTTTGGTAGAGCAAGTGTTG[C/T]GTTTTCTGTGCTGTCCTCTTCATGGCTGAACTCAC Y 2 1 2 1 201000 f 74 goat snp4415-scaffold1139-1624583 6 109907902 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437298 Affx-122931980 AX-123307636 6 106734402 TGAACAACTTCCATAGGGAAATAACATAATCAAGC[A/G]TCTGTTTTGGAAATAGTATTCTGATTACACTGCAT R 2 1 2 1 101000 f 74 goat snp4416-scaffold1139-1669659 6 109953548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434308 Affx-122934755 AX-123304649 6 106783020 AGCATTGGGGAACTATTCCACTGGTCCAGATAAGA[C/T]ACAATGATGGCTCAGAATAGGGTAAGAATGTAGTA Y 2 1 2 1 101000 f 74 goat snp4417-scaffold1139-1718277 6 109999715 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784296 Affx-122930718 AX-385271347 6 106825474 CAGGTACCAGAAATGTATAAAAGGACTATTTATAA[C/T]ACCACTTAATATTTTGTTATTGACACAAAGGAAGA Y 2 1 2 1 101000 r 74 goat snp4418-scaffold1139-1760731 6 110042226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393417 Affx-122965879 AX-123263773 6 106860475 GGTCCTGGGTGGTGCATCTCTATGTCAGCTGAAGC[A/G]CCTACTCCATGAGAGTCTGATGGAAACAGATGGAA R 2 1 2 1 101000 f 74 goat snp4419-scaffold1139-1795732 6 110077035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411547 Affx-122951649 AX-123281897 6 106898468 AATCTTAGTCTTGAGTGTTAAGAACAATCTGGATG[A/G]TTGCAAACAAGAGCAAGAGAACAATGGTAAGACTT R 2 1 2 1 101000 f 74 goat snp4420-scaffold1139-1833725 6 110115172 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794346 Affx-122945961 AX-385281310 6 106928162 TTCAGCCTGAGACAAATTCATAAACATGTTATTTT[A/C]TAATCTGCTTGGTGGGTCATTAAAGAATGAGGCTG M 2 1 2 1 101000 r 74 goat snp4421-scaffold1139-1863419 6 110144401 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399047 Affx-122960912 AX-123269402 6 106958322 TTCCCTTTAACACTTTTCTGATTAAAAGCTTTCCC[G/T]CCAAGCTTCTGAAACCAACTGTTTCCAAGATCATT K 2 1 2 1 101000 r 74 goat snp4422-scaffold1139-1893579 6 110174649 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430271 Affx-122937297 AX-123300612 6 106987657 GTCCAGAGTCTACCTACTTTCATCTTCTGGCTATA[C/T]GAGACCTATGAAAATGGGTACCATATATCTCACCT Y 2 1 2 1 101000 r 74 goat snp4423-scaffold1139-1922914 6 110203969 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443280 Affx-122927478 AX-123313617 6 107004855 AGCGTCGTTAGATTGTTGTGCTAAAGGTAAGGTTT[A/G]CATGTGACACTGTATATAAATTTCCTAGTGTGATT R 2 1 2 1 101000 f 74 goat snp8115-scaffold1296-951242 6 110220732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382790 Affx-122973577 AX-123253148 6 107049253 TCTATTTTGGGGGAAAGGGGTGATGAGCTGGGGAC[C/T]GGGCTCTTAATCTAGCCTCAAGCGCTACAGCTGTG Y 2 1 2 1 201000 r 74 goat snp8114-scaffold1296-906844 6 110264941 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405609 Affx-122956610 AX-123275961 6 107082036 CAGATCTGAATTTGAATCCCCTCTTCAACTAGCAG[G/T]TCTGAAGCTTTGGGCAAATTACTGGAGTTTGTTGA K 2 1 2 1 103000 f 74 goat snp8113-scaffold1296-874061 6 110297805 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780869 Affx-122921473 AX-385267957 6 107121598 TCTTCCTGTCTCCTCTCTTACTTTTCCTCTGTGCT[A/G]CTTCTAATTGTTGACTAAGCTTGTTGTTCAGAGTG R 2 1 2 1 101000 f 74 goat snp8112-scaffold1296-834499 6 110338290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790636 Affx-122949191 AX-385277638 6 107174494 GCAATCCTTAGGACTTTTGGACTTGGGGAGTTTGA[G/T]ACTTGAATCAGTCATTTTCTATTGATTGAAGCTGT K 2 1 2 1 101000 f 74 goat snp8111-scaffold1296-781603 6 110392085 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435175 Affx-122933653 AX-123305515 6 107252140 TTTACTCTTTCAAAGTCATTTTGTCACTGTTCATC[A/G]CCCATTACCACAACTGACTTTTACTGTCAGGAACT R 2 1 2 1 101000 r 74 goat snp8110-scaffold1296-703957 6 110470931 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444713 Affx-122926420 AX-123315050 6 107317932 CAATAGCCAAAGTTCATAGAAGTTGTACACTGTCC[A/G]TGGGTACCCAGTCCATCCCAGCAGTGGGAGAGGCT R 2 1 2 1 101000 f 74 goat snp8108-scaffold1296-638165 6 110536839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398670 Affx-122961880 AX-123269025 6 107396881 TGCAGGGAAGGAGAGACAAGACAAAGTATGCATTT[A/G]TTTTAGAAACAGCAGAGAGCAGGGAAGTAGGAAGA R 2 1 2 1 102000 r 74 goat snp8107-scaffold1296-559216 6 110615922 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418097 Affx-122947138 AX-123288445 6 107507640 AGGCTCTAGCTTTTGGGGGCCAGAAGGAGCTGGCT[A/G]TGTACAGGATGCTGGAGAGTCAAGGCTACTCTGGA R 2 1 2 1 101000 f 74 goat snp8105-scaffold1296-448457 6 110727512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387738 Affx-122969742 AX-123258096 6 107539639 CAGACTGAGAAATGCATGTGGGACTTTGAGCTCCC[A/G]TCTAATCCTTTGGCCGTGGACAGGTCACTTTACCT R 2 1 2 1 101000 r 74 goat snp8104-scaffold1296-416458 6 110759803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411090 Affx-122951926 AX-123281440 6 107579794 TCAAATCAAGGGGTAACAAGTCTAAACTAGGACCA[C/T]ATGGGTGGTGAGGGGATGGAATGGAACCAAAGGAC Y 2 1 2 1 101000 f 74 goat snp8103-scaffold1296-376303 6 110799782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449094 Affx-122923595 AX-123319429 6 107621029 ACAGACAAATGCCAATCACTAAGATTAGAGATTCA[A/G]AGATAACTAAGTCAGGGGTCTGTCATGAATAAGGT R 2 1 2 1 201000 f 74 goat snp8102-scaffold1296-335068 6 110840573 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385848 Affx-122971000 AX-123256206 6 107655325 TGGATACAGCAGCAACAGCACAGTCAGCATTGTTA[G/T]TGATCATAGGGCTGTTCTCCAGCTCTGGATGACCT K 2 1 2 1 201000 r 74 goat snp8101-scaffold1296-300772 6 110874949 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427536 Affx-122939507 AX-123297879 6 107692736 CAGGGTGAGCAGAAGCGCACAGCTTACAGGGGAAG[A/C]GCACAGAGAATGAGCCTGGGGCGCTGGGCAGACAG M 2 1 2 1 101000 f 74 goat snp8100-scaffold1296-263361 6 110913416 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438497 Affx-122931220 AX-123308835 6 107743192 AGAAGGAAAGAAAATAGTTTACAAAAATAAACAGC[A/G]CTTGTGGGGAAACTCTCTGTCACCACGTATTATGT R 2 1 2 1 101000 f 74 goat snp8099-scaffold1296-212905 6 110963666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784885 Affx-122975321 AX-385271932 6 107782061 AAGTAACCAAAGACATCTCTCCAAGAATAATTTCT[A/G]CATGAAAAATCATACTGCTTTTGATCAAAGACCTA R 2 1 2 1 101000 r 74 goat snp8098-scaffold1296-174036 6 111002469 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417260 Affx-122947264 AX-123287608 6 107833625 TGGTTTGGTACTTCAAAAAACAAAATGAAACTAAT[G/T]TAGCATATTTTTCTGAGTTAAAGTCTTGGTATCAT K 2 1 2 1 102000 r 74 goat snp8097-scaffold1296-122472 6 111053959 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275346 Affx-1111834742 AX-519548921 6 107852633 TTAAACAAATGGGTAAATTCCTTTTATCCTCAAGT[A/G]TATTTGGATCTTGTCTGCTAGACTGCAGTGGGAAA R 2 1 2 1 201000 r 74 goat GoatD01.051143 6 107852633 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386155 Affx-122971394 AX-123256513 6 107892440 GAAAAAGACATGGTCGTATGGATGAAAGTAAAATG[C/T]AACACACTCAATATTGTTACTGAGGAACTATACCA Y 2 1 2 1 101000 f 74 goat snp8096-scaffold1296-63657 6 111112916 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379397 Affx-122976131 AX-123249755 6 107922768 CCACAACAATAATGTCTTTCGGAATCCTTGGATCC[A/G]TTCCATCTGTTGCAATACATCATTGTTTTTCCCCT R 2 1 2 1 101000 r 74 goat snp8095-scaffold1296-33329 6 111142905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377723 Affx-122977392 AX-123248082 6 107952550 AGCATCTCTCTGTAAGTATCTCAAACTCCCCTTAA[C/T]ACAAATCACGGGTAGTGTGGCATCCAGAGAAGCAA Y 2 1 2 1 201000 r 74 goat snp8094-scaffold1296-3547 6 111173230 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272331 Affx-1111833490 AX-519546065 6 107986988 CCACAGCAAGTCATTTTCCAATCTTTCTAGTTAGA[A/G]TAACTTGCTGTCCCTTCTGTAGTCACAGAGCAATT R 2 1 2 1 101000 f 74 goat 6_107986988_AF-PAKI 6 107986988 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320797234 Affx-122958423 AX-385284173 6 108030960 ACAGCAGGACAGGCTGAAAGCTGAAGTGCTCCCAC[A/G]TCACTCCTGATTCATAACCAGAAATTGAGACAAGG R 2 1 2 1 102000 f 74 goat snp6947-scaffold1255-69991 6 111257699 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791495 Affx-122946355 AX-385278486 6 108060000 CCTCTTCATGAGGCAATGAAACTTAATTTTCCCAT[A/G]TGTTAACTACACAGGATGTTTTCAAACTTTCTGAT R 2 1 2 1 101000 f 74 goat snp6948-scaffold1255-99031 6 111287859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395311 Affx-122964058 AX-123265666 6 108093725 AAACTCATTTGGAAATCCTTCAGGGAGCCCAGTAG[A/G]TTTGTTGAAAACAGCATACATTTTGAAGTCGGACG R 2 1 2 1 201000 r 74 goat snp6949-scaffold1255-132756 6 111320639 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440542 Affx-122929325 AX-123310879 6 108126710 GACCAGAACAGGGGCAGCAAAACAGAGCAAGGAGT[A/C]GGAGCTATTAGAAATTAGAGATGAGACCAGAGAGA M 2 1 2 1 101000 r 74 goat snp6950-scaffold1255-165741 6 111353653 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785022 Affx-122945114 AX-385272069 6 108176232 TTGGCTCATCCTGAGATCCATCTCCATTGCTATGA[C/T]CATCACCTCATTGAATCATGACTTGCTCAAACAGG Y 2 1 2 1 101000 f 74 goat snp6951-scaffold1255-215263 6 111403063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417764 Affx-122947403 AX-123288112 6 108206352 ACGGGCGCTATGGCCAAGAAAAAGAGAGAGACAAA[C/T]AGATTGGAGTTGGAAAGACAAATAGATTTCTAGCT Y 2 1 2 1 201000 r 74 goat snp6952-scaffold1255-245383 6 111429008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422747 Affx-122943245 AX-123293093 6 108237574 TTTTTGCAGATTTATTTATCGGCTGCTGCAGCCCA[C/T]GGACTCTCGAGGTGTGGCTCGTGGGCTCATCACAA Y 2 1 2 1 101000 f 74 goat snp6953-scaffold1255-276605 6 111460300 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429933 Affx-122938091 AX-123300274 6 108268179 GTAACTATGTTTCTAAAAGTTTTGCAAATAATATG[C/T]AAACTTTGAGGGAAAATATGATTCAGAATATGAAG Y 2 1 2 1 303000 f 74 goat snp6954-scaffold1255-307210 6 111490725 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797563 Affx-122960384 AX-385284502 6 108297837 AGCTAAAATCTGCAAAATTTCAGATGTTTCCCAAT[A/G]CATAATCATTGAAAAGGTCATAATCAAATGTTCAA R 2 1 2 1 101000 f 74 goat snp6955-scaffold1255-336868 6 111519460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423535 Affx-122942439 AX-123293881 6 108375129 CCACACTGTTATGACCCCAGGTAAGGTGGTGGGCC[A/G]CTCTTCATCTAAGGAAGTTACTGTTAGTGGACAGC R 2 1 2 1 101000 r 74 goat snp28932-scaffold3114-9539 6 111596981 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403068 Affx-122958520 AX-123273421 6 108440735 AGTGCTCGCGCTGGTGCCTTGGCATGTTCGAACAG[C/T]GATTTGAACATGAAGTAGGCACGGATTACCGTGGT Y 2 1 2 1 101000 r 74 goat snp11988-scaffold1440-817770 6 111661862 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422357 Affx-122943436 AX-123292703 6 108509968 TTTTCAGAGAAGACAAAGACCAGCCAGATTCCCCC[A/G]ATATATGTTTAGATAAGGTTTACAGGATCTCTTTT R 2 1 2 1 201000 r 74 goat snp11987-scaffold1440-748537 6 111731768 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800453 Affx-122952403 AX-385287374 6 108563347 TCCGTTAAGCAAACTTGTTCCCTCTAGCTGTGAAG[C/T]ATTCTTGTGGCCCAAAGTGAGTCAATCCCAACTTT Y 2 1 2 1 101000 r 74 goat snp11986-scaffold1440-695158 6 111785161 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777218 Affx-122933449 AX-385264341 6 108649440 GGTCCAGTCACTGAACCATGGCCCATGGCCTCTAA[C/T]GAGTCCAAACCATATAGATATCATTCAAGTTTGGT Y 2 1 2 1 101000 f 74 goat snp11984-scaffold1440-609065 6 111871771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440955 Affx-122928999 AX-123311292 6 108682146 ACTGGCAAAGAAGTCTCCTCTCCCTCACGTCTCAA[C/T]ATCCCATGGATTCTACACAATCTGTGAGGCCATCA Y 2 1 2 1 101000 r 74 goat snp11983-scaffold1440-576359 6 111904181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433574 Affx-122934971 AX-123303915 6 108714830 TTCAGTCGCTGTCATGTTTGACTCTTTGTGACCCC[A/G]TGGACTGCAGCTTCCCACCCCAAGGAAGTCAGGCT R 2 1 2 1 103000 f 74 goat snp11982-scaffold1440-543675 6 111929464 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448493 Affx-122923467 AX-123318829 6 108748139 TCAACCACTGGGCCACCAGGGAACTCCTGGAACTT[C/T]TATTCTAAATAAGACCAAGATAAGTGCCATATGTA Y 2 1 2 1 101000 r 74 goat snp11981-scaffold1440-510366 6 111963122 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421032 Affx-122944536 AX-123291379 6 108825731 CCAGAGTGATTACAACTTCACACTTTCAGTGCAAA[C/T]GGTACAGGCTCAATCCCTGGTCAGAGAACTAGACT Y 2 1 2 1 101000 f 74 goat snp11979-scaffold1440-432774 6 112041070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443601 Affx-122927313 AX-123313938 6 108855574 TGCCTAATTAAAAGCACTAATGCACAGTATGGTAG[C/T]ATGATTTCCTTTTCCAATGAGGTAGAAAATCACTA Y 2 1 2 1 101000 f 74 goat snp11978-scaffold1440-402931 6 112069202 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430756 Affx-122937496 AX-123301097 6 108888931 CCCTTACCTGTGTTGAGCATCAAATGATGGACTTG[A/C]GTGCAGAAAGTAGAACATGCCTGCCTCTGTGCGCT M 2 1 2 1 101000 f 74 goat snp11977-scaffold1440-369574 6 112102568 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788741 Affx-122946558 AX-385275757 6 108928743 CAGATACTTCCATTTATCTTTTAGGGGATAATGAG[A/C]AGAAGTCTAGACTGCAAGAACTTGCTTAAGAATCA M 2 1 2 1 101000 r 74 goat snp11976-scaffold1440-329762 6 112141861 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451262 Affx-122921930 AX-123321595 6 108959206 TGTAACAGTTATTATAGCTACAGAGTAAAATGCTC[A/G]TCTGTGCTTTTTTAAGAAAATGGAATAAAAGGAAA R 2 1 2 1 101000 f 74 goat snp11975-scaffold1440-299299 6 112173392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404456 Affx-122956742 AX-123274808 6 109007223 GCTGATTTGGATTATCTGTCCATTTACTCTATCTA[G/T]CAATGTGGATAATTGAGAACTGACTCTGGTTTAAT K 2 1 2 1 101000 f 74 goat snp11974-scaffold1440-251282 6 112221282 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396885 Affx-122963231 AX-123267240 6 109051593 CTCATCAGCTGCTTTGCTGACAGTCGGGTGATGTG[C/T]GCACGCTTGCTGATGTGCGGGCTAGTGACAGCTGA Y 2 1 2 1 101000 f 74 goat snp11973-scaffold1440-206912 6 112264887 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787032 Affx-122930458 AX-385274060 6 109087772 TTCTGGACTTGAGAACTGTGGAAGAACAAGTTTCC[A/G]CTGTCTTAAGCTACCAGCGTGTGGACATTGGTTAC R 2 1 2 1 202000 r 74 goat snp11972-scaffold1440-170733 6 112296759 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796501 Affx-122948679 AX-385283450 6 109150145 TGGACCAACCATGGCATGTCACATGGACAGGGTTA[C/T]ACCCCAGATGCTGATAAATCTGGGCTTTTCCCTGA Y 2 1 2 1 101000 r 74 goat snp11971-scaffold1440-108360 6 112359265 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778301 Affx-122963996 AX-385265416 6 109184185 TTCATAATGAAATAAGCAGTAATTGCTATTAATAA[C/T]AGTCCTGTAAGGGACAGTAGTATCTCCATTTTAGA Y 2 1 2 1 201000 f 74 goat snp11970-scaffold1440-74320 6 112393301 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401882 Affx-122958852 AX-123272235 6 109227668 TCAACAGAGCCATAGAGAACTCCTGATCTTTAATG[C/T]ATTTAATGTAGCTATCAAGATGTGACCCGCTTTCT Y 2 1 2 1 101000 r 74 goat snp11969-scaffold1440-30837 6 112436822 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414956 Affx-122949076 AX-123285305 6 109296963 ATAAGGGTGGGGCTCCCGTAATGGGATTAGTGTCC[A/G]TATAGGAAAAGAAGGGAGGAGAGACAGAATCCTCT R 2 1 2 1 103000 f 74 goat snp16074-scaffold1692-38359 6 112507634 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376173 Affx-122978834 AX-123246532 6 109440131 GGCACACCTTGGTATTTTAAGATCACTTACTAAAT[A/G]TATGATTCAAATACTCCATGCTTCTTGCCCTGGCT R 2 1 2 1 101000 f 74 goat snp16077-scaffold1692-181527 6 112651995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393516 Affx-122965803 AX-123263872 6 109477575 TAGGGTCACCTAGAAAGCTTTTAAAAACTACCCAC[A/G]TCTGGGACTTCTCTGGTGGTCCAATGGTTAAGACC R 2 1 2 1 101000 f 74 goat snp16078-scaffold1692-218971 6 112689477 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448531 Affx-122923440 AX-123318867 6 109508284 ACAGCCTTCAGAGCAGTTCTGGAAGCTCAGAGAAA[C/T]GACCAGCAGCCTCTGAAGGGGCCCTGCTCAGCTAG Y 2 1 2 1 101000 f 74 goat snp16079-scaffold1692-249680 6 112720697 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382807 Affx-122973565 AX-123253165 6 109543757 GGAAAGCAACATAGATGATTAAAGTAAATCTGACC[A/G]CTTTCACTGAGAAATCTTTTTTTTAAATTTTTTTC R 2 1 2 1 101000 f 74 goat snp16080-scaffold1692-285153 6 112755828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452165 Affx-122921650 AX-123322498 6 109574269 AGACGGCTTGTCACCATGGCTGTATTTCATCCAAT[A/G]GGAAGGGAGAAAAGGGGATGGAAAGGCATCTTTCT R 2 1 2 1 102000 f 74 goat snp16081-scaffold1692-315665 6 112787413 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396519 Affx-122962960 AX-123266874 6 109619430 CAGCTAATTAAGAGTCGTCATCTCTGCAGCTCGGC[A/G]TGGGCTTCTGACTTTCTTTACCTGTAAACTTAGTT R 2 1 2 1 101000 f 74 goat snp16082-scaffold1692-360826 6 112832134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405193 Affx-122956919 AX-123275545 6 109658048 GATTTCTGCCTCTACAGGAAAAAGCACACGCCAAG[C/T]GACCAGCAGAATCCATGAGACAGTGTTCCAGGCTC Y 2 1 2 1 201000 r 74 goat snp16083-scaffold1692-399444 6 112870846 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799590 Affx-122926972 AX-385286520 6 109706111 TGTGGAGAATTCCTATCTGTTAGGCTTGTGTATAA[C/T]GACAAAGGTGATTCTCACCCAAAATATGTTTGTTA Y 2 1 2 1 101000 f 74 goat snp16084-scaffold1692-447507 6 112918873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801032 Affx-122937629 AX-385287946 6 109744288 CCAAATAAATATATTGTACAGACATTATACAAACA[C/T]GCACCACTTTGGCCAAAACTTAATTACAAGCAGAA Y 2 1 2 1 101000 r 74 goat snp16085-scaffold1692-485684 6 112955297 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770582 Affx-122936760 AX-385257746 6 109778960 GCAGACACCGCTGCACATCTGTAAGATGTTTATAG[C/T]GTTATTTAAGATACTCAGTTCTGCTAAGTAGAAAT Y 2 1 2 1 101000 f 74 goat snp16086-scaffold1692-520356 6 112990107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397381 Affx-122962273 AX-123267736 6 109818704 AAGGCAGATGAATTCGAGGCTATGAACACTACAGC[C/T]GTGATACAGGCACAACATTCAGAAACAAGTCAGGC Y 2 1 2 1 101000 f 74 goat snp16087-scaffold1692-560100 6 113029913 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392949 Affx-122965693 AX-123263306 6 109852107 ATCTAAACTTTGAAAGAAGAGGAGACTTTTTCCAG[C/T]GGTAAAGGAAGCAAGGTTGAAGGATTCCAGGTCAA Y 2 1 2 1 101000 f 74 goat snp16088-scaffold1692-593503 6 113063405 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424460 Affx-122941776 AX-123294806 6 109883131 CCTTGTAACCCTGAAGATGAGGCACCATCACAAAT[A/G]TGACTGTACACAGTCACTGCGGTGTTATTTCTGCC R 2 1 2 1 101000 f 74 goat snp16089-scaffold1692-624527 6 113103536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452094 Affx-122920853 AX-123322427 6 109953970 GGATCTGGGAGTCACTGGACATGCTCTCATCCTGC[A/G]GCACATCTGGTGGAGGACAGAGCAGAAAGAGAATC R 2 1 2 1 201000 f 74 goat snp23630-scaffold2388-62059 6 113307084 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398477 Affx-122961580 AX-123268832 6 110058292 TGGGGAGAGTCTAGAGAAATGCAAGAGATACATCA[A/G]TGTTAACAGTAACTGTTTCTGGGAGATGGAATTAA R 2 1 2 1 101000 f 74 goat snp23632-scaffold2388-166381 6 113408179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444700 Affx-122926430 AX-123315037 6 110097742 GATGGCATTTGGGCCCCCAACTTTAAACCTGGTTC[C/T]GCAAGCCCATACTGAGCACAGACTGTGCCAGCCAA Y 2 1 2 1 201000 r 74 goat snp23633-scaffold2388-205831 6 113447672 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405861 Affx-122955853 AX-123276213 6 110246178 GGGCCACCACTGTTCGGACTTCTGTCACCATAGAC[A/G]TGTTCCGCTCATTTTGAACTTTAGGTGTATGGCGT R 2 1 2 1 101000 r 74 goat snp31682-scaffold3510-2471 6 113595989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410069 Affx-122953216 AX-123280419 6 110315998 GGACCAGAGTCTTTAGCTTCGACGTTATCTGCTTA[G/T]GCCACCGAGTTAGATTCTTAGGATTCCAGGCTCAC K 2 1 2 1 101000 f 74 goat snp31684-scaffold3510-72291 6 113662634 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389847 Affx-122968162 AX-123260204 6 110396800 TTAGAGCTCTCCACTTAACAAATACTGAAAGCTCC[A/G]CTCTGTCCTAGGCCCTGATCCGGGCACTGGTGCTT R 2 1 2 1 101000 f 74 goat snp17700-scaffold1835-179311 6 113745536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395373 Affx-122963979 AX-123265728 6 110429585 GGGAGGAGAGAAGCTTTCAGTTCTAACGCCCTCAC[A/G]CCAGGAGTGAGCTGAGAATAGCAGAACAGGACATG R 2 1 2 1 101000 r 74 goat snp17699-scaffold1835-146526 6 113777113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430984 Affx-122936694 AX-123301325 6 110471654 CGACTTCCTGGCAGAAGGAATCTCAGCCCTGCCCA[C/T]ATTTCACTCCCCATGGGGAACTCTGTAGCTCAGGG Y 2 1 2 1 201000 r 74 goat snp17698-scaffold1835-104457 6 113819857 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405218 Affx-122956899 AX-123275570 6 110502512 AGATGAGGTGGAAAGCCTTTGTAAACCTTTGGATC[A/G]GGTCCAGGGTAGATTCTCCCCGGGGGTGGCCAAGG R 2 1 2 1 101000 f 74 goat snp17697-scaffold1835-73599 6 113850554 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416116 Affx-122948304 AX-123286465 6 110531528 TCCAGGTCTATGAGAACTGGTTGGCATGAAACGAA[C/T]GTGCCCAGCACAGGTCTGTGAGAATGGGAGGAAGG Y 2 1 2 1 101000 f 74 goat snp17696-scaffold1835-44583 6 113879530 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425534 Affx-122941455 AX-123295880 6 110569016 TGGTGAGTGGATGGATGAGTGGACAGATGGATGGA[C/T]GGTAGGCTGGGTGGACGGGGGAAAGTGGATGGGAG Y 2 1 2 1 103000 f 74 goat snp17695-scaffold1835-7095 6 113916509 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272332 Affx-1111833491 AX-186966361 6 110592768 AAGACTCTTGAGGGTCCCTTGGACTGCAAGGAGAT[A/C]TAACCAGTCCATCCTAAAGGAGATCAGTCCAGTCC M 2 1 2 1 103000 f 74 goat 6_110592768_AF-PAKI 6 110592768 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38422490 Affx-122943312 AX-123292836 6 110602800 TGTTATTTATGGTGTCACGAAGCAGGAGATGACAG[C/T]AGTGCCCTACTGTTGGACTGTCTTGAAGTAAGCTG Y 2 1 2 1 101000 f 74 goat snp23729-scaffold2398-26590 6 113949728 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437459 Affx-122932387 AX-123307797 6 110638581 AAAGACTATGACCAGATATGAGGGTTCATCAGAGG[C/T]GAGGTGCCCTGCAGTGGCCCTGCAGCCCGAGCTCA Y 2 1 2 1 101000 f 74 goat snp23730-scaffold2398-62371 6 113984656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788125 Affx-122943672 AX-385275145 6 110676063 ACATGTAAACACATGTGTACTTGCAACCGTCATCC[A/G]TTCACCATATGTCTTCATCAGACAATGAGTTCACT R 2 1 2 1 101000 f 74 goat snp23731-scaffold2398-99853 6 114020201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447437 Affx-122924379 AX-123317773 6 110719434 CTGGTGGGTTCAAGCCCTTCCCCTGTATGGTCTGA[C/T]GCTATCTACAGGTAGACAGTGTTGGAACTGAGCTG Y 2 1 2 1 201000 r 74 goat snp16468-scaffold1734-501206 6 114064855 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381435 Affx-122974348 AX-123251793 6 110771088 AATAGTGTCACCAAAACTGCTCCCAGGATTGCCAG[C/T]GGGATCAGTGCCCCACTCCATGCCCAGCACCCCAG Y 2 1 2 1 101000 f 74 goat snp16467-scaffold1734-449552 6 114116677 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781386 Affx-122942605 AX-385268471 6 110814419 GCCACAGAAGGGTTCACCTGAAAGGGCTAATTGTA[C/T]GTTATGTGAATTGCGTCTCAATTTTAAAAAATATT Y 2 1 2 1 101000 f 74 goat snp16466-scaffold1734-406221 6 114160070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425525 Affx-122941461 AX-123295871 6 110848916 CTAAAGGGGCTGACGCTGAGGCTCTGGAGTGAGTA[G/T]GATGTAATTGTTCTGTTTGGCTGTCTGAGGATGTT K 2 1 2 1 101000 r 74 goat snp16465-scaffold1734-371724 6 114194423 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399905 Affx-122960201 AX-123270260 6 110882587 AACAAGGCACGGTTTCCTGAGTTGAAAGTTTTGCC[A/G]TCATTTACAAGGGGCTCTCATGTATCATTTGGGAA R 2 1 2 1 101000 r 74 goat snp16464-scaffold1734-338053 6 114228059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413260 Affx-122950225 AX-123283609 6 110930970 TGTAAATTATGTTCATTCACCTTTCTTCACAAATA[C/T]GGTGTGAAAGGTTGGATCATCTCTCCCCCATCCAC Y 2 1 2 1 101000 f 74 goat snp16463-scaffold1734-289670 6 114275573 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797223 Affx-122930725 AX-385284162 6 110961310 CATCATCAATTTTACGATGCTCTTAAAAATGACTA[C/T]CTTTTCAGCGACCAGTTAGCCAGAAATCAGAGCAG Y 2 1 2 1 101000 r 74 goat snp16462-scaffold1734-259330 6 114296686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442039 Affx-122928399 AX-123312376 6 111013516 ATAAAATATAATTTAAATATAAAATAAAATTCTAC[A/G]TGCAAATGAGAGACTCATTGTGAGCAGCTGGCTCA R 2 1 2 1 103000 r 74 goat snp16461-scaffold1734-207124 6 114349047 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423109 Affx-122942916 AX-123293455 6 111044781 CTCTGTCTCTCCCTGCATCTGTGCTTTAACAGGCC[A/G]TCACCTCTGCCCGCGTCTGTAACCCCTGAGGCAGA R 2 1 2 1 201000 r 74 goat snp16460-scaffold1734-175859 6 114380279 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781767 Affx-122944620 AX-385268849 6 111078594 CTCACATCTCGCTTGTGAATTTGCCTCGAAAGGGT[A/G]TAGCGTTACATGGCTGTGTTTGTGCTTGTAGAGTA R 2 1 2 1 101000 r 74 goat snp16459-scaffold1734-142046 6 114414154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420410 Affx-122944919 AX-123290757 6 111136161 TGTGTCCTCGGGGTGGGTTGCCTCCCATCACATCT[A/G]CATGGAAGGCGCATTCTACAGCTAGGTCCCCTGGG R 2 1 2 1 201000 r 74 goat snp16458-scaffold1734-84479 6 114468243 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381023 Affx-122974652 AX-123251381 6 111180335 TGGGAGGGCCCGGGTCGGGCAATGAAAGTGAAATC[A/G]CATTCTAAACTGTCGTGATGCGGGATTGTTATTGC R 2 1 2 1 101000 r 74 goat snp16457-scaffold1734-40305 6 114512168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394161 Affx-122964938 AX-123264516 6 111218990 CTTCCGCGGACAGATCTGTGAGTGGTCTTCCGTCG[C/T]GTTTGTCCCACTCGCCCGGTGACGACCCTGTGATC Y 2 1 2 1 101000 f 74 goat snp16456-scaffold1734-1650 6 114549341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411631 Affx-122951581 AX-123281981 6 111237824 AGTGCTGTTCCTGAAGCCGTTTTCTGTAGTTACAG[A/C]CTCTGCTCCAGACAGAAATGGGAGCTTTGTCAAGG M 2 1 2 1 201000 f 74 goat snp38111-scaffold4753-105874 6 114567302 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453610 Affx-122920132 AX-123323943 6 111266875 GATGTTGTCACTCAGACTATTAATTCTCACCCCTG[C/T]GGGGCGCCGTTCTGTGCTCTGAGTCACCAAACGCA Y 2 1 2 1 101000 f 74 goat snp38110-scaffold4753-76823 6 114594989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384858 Affx-122971950 AX-123255216 6 111378869 TTTTCTCAGTGAAGAAGAAAGGTCTTTCTTTAGCC[A/G]TGAAGGACGCTTTTCTGAGGAGGAGGCCAGGCAGC R 2 1 2 1 101000 f 74 goat snp18927-scaffold1907-35072 6 114701418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436745 Affx-122932292 AX-123307083 6 111420199 GGCTCCCGGCGTTCCTGGGCTTGTGGCCCATCATG[C/T]GCTCCAGTCTCCATCTCCATCGTCACGTGGACATT Y 2 1 2 1 201000 f 74 goat snp18928-scaffold1907-76402 6 114737082 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437419 Affx-122932415 AX-123307757 6 111487234 TGAGACTGTTCAAAATTACTTTATTTTCTAAAAAC[A/G]ACTTTATTTTCATTTCTGAATAGATAATACAAGAG R 2 1 2 1 103000 f 74 goat snp18929-scaffold1907-143437 6 114800424 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379085 Affx-122976319 AX-123249444 6 111540304 AGAGGCTTTACAAGTGGGAACCAGCACTATCATGA[C/T]GATTTCCTGCACTGCAAGACATACACTTGCTCGCA Y 2 1 2 1 101000 r 74 goat snp18930-scaffold1907-196507 6 114855956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764762 Affx-986697016 AX-385252375 6 111555289 CCTTAGTACCGCCTCATACGTCCCACTCCAGTCCC[A/G]TCCGCACAGACCTGCCAATGGAAGGACCCTCGACT R 2 1 2 1 600010 r 74 goat 6_111555289 6 111555289 Ancestral_priority_1043 ancestry 0.446 neutral IMAGE 10K 10K ancestral 38400389 Affx-122960007 AX-123270744 6 111581297 TTTAGAAGTAATAAGGCCTCTCAAAGTATACAAAA[C/T]CAGAAGAACTTAGAGAAAACTGGAAGGAACTAACA Y 2 1 2 1 201000 f 74 goat snp18931-scaffold1907-237500 6 114896829 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762488 Affx-986697018 AX-385250609 6 111590903 ACGCCTCAAGCCCTGAAGCTCGGAAGCCGCCTCAG[G/T]CCTGAGCTCTCAGCACCACCCGCTCAGCGTGCTCA K 2 1 2 1 600010 f 74 goat 6_111590903 6 111590903 Ancestral_priority_1043 ancestry 0.482 neutral IMAGE 10K 10K ancestral 38403281 Affx-122957856 AX-123273634 6 111648664 GCTAAGCAAAATCCTAATTGGTGTCTTGACTTTCA[C/T]TATCAAGTAAAAAACTGAGACACAATTGCCTTGTC Y 2 1 2 1 101000 f 74 goat snp18932-scaffold1907-304867 6 114943099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390907 Affx-122967096 AX-123261264 6 111782844 ACTTTCACTCCCATCTCCCATTATTCGGTGTTTGC[C/T]GTTTTCAAAGAACTTTCACATCCAAGATTTCATTT Y 2 1 2 1 101000 f 74 goat snp18934-scaffold1907-439047 6 115075158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398691 Affx-122961862 AX-123269046 6 111796313 GCTGACGCACTCTTTTATACTCTAAGCCCCATCCC[A/G]AAATGACATCAGCTGCAAGCCCTCCGTAGCCTGAG R 2 1 2 1 201000 r 74 goat snp24779-scaffold2535-231601 6 115087407 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452818 Affx-122920746 AX-123323151 6 111864571 GCCACTGACATGGGCTGTGAGTGAGAAATTGATGC[A/G]TTTTGGATGGAGGGATGCTTGTTATCAGGCAAAGC R 2 1 2 1 101000 r 74 goat snp24778-scaffold2535-163343 6 115153661 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439413 Affx-122930242 AX-123309750 6 111946411 GTTCATGGGGTCGCAAAGAGTCGGGCATGACTGAG[C/T]GACTGAACTGAAGTGGAACCAGGGTTCATGCCCTC Y 2 1 2 1 103000 r 74 goat snp24777-scaffold2535-81503 6 115230601 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443193 Affx-122927596 AX-123313530 6 112002932 TAAAGAAAAGAAGAAGAAGATGACCTCTTCTTCCA[C/T]TAAACACGGCTGCACCTACTGTGACCTCTGGAGCG Y 2 1 2 1 201000 r 74 goat snp24776-scaffold2535-24982 NW_017216320.1 7631 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278603 Affx-1111836422 AX-519552082 6 112034217 GACTCATGGAGCACGTGGTCACAAGTCAAGGGCAC[A/G]TGACCCACAGTTGGACAAGCACTGACTAGAGCGTC R 2 1 2 1 101000 r 74 goat Random2.2K-744 6 112034217 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417011 Affx-122947977 AX-123287359 6 112035963 CACATTGACAAGTAATCAGTCCCTGGTGGCTCAGA[C/T]GGTAAACAATCCGCCTGCAATGCAGAAGAACCAGG Y 2 1 2 1 103000 f 74 goat snp27710-scaffold2951-473946 6 115318731 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791463 Affx-122966768 AX-385278454 6 112068334 ATAACGAGGCTCTTCTCTTATTACTGTGCAATTCC[A/G]TTAGAGATCGAAATCAAAAGATCTTTGAAATAACC R 2 1 2 1 101000 f 74 goat snp27709-scaffold2951-441575 6 115351393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381310 Affx-122974445 AX-123251668 6 112104044 CTTTTTCCGTTTGAGCCTGCATTTCTGTCTTTCTT[A/G]TTGGATGCCTTCTCGATGTTGGTGATCCAGGGTCA R 2 1 2 1 201000 r 74 goat snp27708-scaffold2951-405865 6 115384409 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430003 Affx-122938035 AX-123300344 6 112133690 GAAAATCAGCCGTATTTGTCTGATCGGAGAGACCA[C/T]GGCAGATTCACCAGGGACTGGGCTGCTTTAATTCC Y 2 1 2 1 101000 f 74 goat snp27707-scaffold2951-376219 6 115413517 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376583 Affx-122979071 AX-123246942 6 112193973 CTTTCTCTTCAGCAGGAAGTCTCAGGGTCTGTCAA[A/G]GGCTGCTGGCCAAACAGCCTTTCAGATCAGGAGCA R 2 1 2 1 101000 f 74 goat snp27706-scaffold2951-315936 6 115473655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404531 Affx-122957401 AX-123274883 6 112242129 ACGACCTTAAACAGACGTTCACCCCTCAGTCTCCC[A/G]GAGGGACTGCAGGGTCAGGCTCGGTTCTGGGGAGG R 2 1 2 1 201000 r 74 goat snp27705-scaffold2951-267780 6 115521563 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391206 Affx-122967412 AX-123261563 6 112373202 TCATCTGCGTACCTGAGGTTGCTGATATTTCTTGC[A/G]TCTGGGCTGCGGCTTCTGCTTCATCCAGCTGATGT R 2 1 2 1 101000 f 74 goat snp27703-scaffold2951-136707 6 115648298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443659 Affx-122927195 AX-123313996 6 112406194 TTGTCAGGGAAGCGAACGGCAGTCCGTGAGGTCCA[C/T]ACTGCAGAGTGTCCGACATGGAAAGACCCGTGGCC Y 2 1 2 1 201000 r 74 goat snp27702-scaffold2951-103715 6 115615131 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379097 Affx-122976763 AX-123249456 6 112447547 AATGTAAACTTTATATAGCATCAGAATCAGAAAGG[C/T]GTAACACTAATACATCTGAGCGAGTAACATGGACC Y 2 1 2 1 101000 r 74 goat snp27701-scaffold2951-62362 6 115573662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380375 Affx-122975341 AX-123250733 6 112482304 TTTGTGCCCGCTTTCTTTTCGTCTCAGGGTTTCCG[C/T]GGTTCCTGATAAGGACGCACTCATTTTTGTTGTGG Y 2 1 2 1 101000 r 74 goat snp27700-scaffold2951-27605 NW_017218119.1 8072 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439753 Affx-122930527 AX-123310090 6 112531139 CACCTGGGCCTGACTTTGCACCGTGACTTGTGTGA[A/G]TGTTGGTGAGAAACAGCTCTGCGCAGTTTCAGGCT R 2 1 2 1 101000 r 74 goat snp16120-scaffold1698-458655 6 116929335 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788722 Affx-122956786 AX-385275738 6 112604012 TGAAATTATGCAGTTTTTATGTTACAGGGTGGTGG[C/T]TAAGCACCACCTGTGGAAATAACGTTTACGTGTTT Y 2 1 2 1 101000 f 74 goat snp16119-scaffold1698-385782 6 116866391 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447387 Affx-122924417 AX-123317723 6 112652804 AATAACTTATAACCGTGACCCATTCCAGACTTAGC[A/G]TAGTTCTTCTCGGTGGAGGTAGGAGTCAGAGAAGT R 2 1 2 1 101000 f 74 goat snp16118-scaffold1698-336990 6 116827997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425030 Affx-122941873 AX-123295376 6 112692374 GCTATTTCTGTAAAATGTGCATTTTTGAGACAAGC[A/G]TTGGAATTTAATGGCTATGTCTGCTGGGAGTTCTG R 2 1 2 1 201000 f 74 goat snp16117-scaffold1698-297420 6 116787989 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793352 Affx-122968873 AX-385280330 6 112723527 ATGGTTCATTTTTAAAGGTACAGTAAATATATTTT[C/T]AGAAGTTAACAGGATTTTCTTGTATAAGTTACTTA Y 2 1 2 1 202000 f 74 goat snp16116-scaffold1698-266267 6 116756704 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790237 Affx-122924048 AX-385277241 6 112827501 ATTCAGGCTTGGTTTATTTTTGGCAAGAAGACTTC[A/G]TAGGTTAGTAGCAGATAAGGATTAGTAGTCTTTTT R 2 1 2 1 101000 f 74 goat snp16114-scaffold1698-162293 6 116652595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379420 Affx-122976112 AX-123249778 6 112873642 GTTGGGGCGCACCCTGGCCAGAGGAGTAGATGGCC[C/T]GTACTGACCCCTGTTAGCCATCTGGAAAAAGGGTC Y 2 1 2 1 101000 r 74 goat snp16113-scaffold1698-116152 6 116608885 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426099 Affx-122940642 AX-123296445 6 112912092 AAAGAAAGCGACGCAGAGCCCGGAAATCGACCCCC[A/G]CCTGGCGGACGGGTTGAGAAGGGCGCTAGGACCTT R 2 1 2 1 201000 r 74 goat snp16112-scaffold1698-77702 6 116572235 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449928 Affx-122922916 AX-123320263 6 112943808 GAATAAACTGGAAGAAAGTGAAACAAAGGAGATAA[C/T]ACATAAGAGAAATAGTGGAACAGGAACCAGAGATC Y 2 1 2 1 101000 r 74 goat snp16111-scaffold1698-45986 6 116541002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450482 Affx-122922932 AX-123320816 6 112984266 TCCCCCAGGTTCTTACTTGTGGTCGAGTCTTCCTC[C/T]TCAGACCTGGCCACCCTCGCGGCGTCCGAGTCTGC Y 2 1 2 1 101000 f 74 goat snp16110-scaffold1698-5528 6 116501794 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446572 Affx-122924832 AX-123316908 6 113090803 CTGGAATCAATCCAAGAACACAAATAGGGTAGTTG[C/T]GGAAAACTTAGTGAAACCCAGATAGTCTGTAGTTA Y 2 1 2 1 101000 f 74 goat snp31937-scaffold3576-100910 6 116407319 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272333 Affx-1111833492 AX-519546066 6 113107191 CTACCAGATGCAGCGCAGGCCCTACAGGAACTACA[A/G]GAGCAACACCATCGCTCGGGTACGTCCTGAGCTGT R 2 1 2 1 102000 f 74 goat 6_113107191_AF-PAKI 6 113107191 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38452511 Affx-122920971 AX-123322844 6 113162795 TCAGTCTCCTCCAAGCTCTGGGATGCCCAAGACAC[A/G]ACTATGACTCTAGTATCACCAGAGTGCTGGCTCAC R 2 1 2 1 101000 r 74 goat snp43773-scaffold588-1729470 6 116345452 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448851 Affx-122923289 AX-123319187 6 113193210 CGAGGCCTTGGTGATCTGCAGGAACCTCTGACATC[A/G]ATGTAGGCGGAATCATGGGTGGCCTCTGAATCACA R 2 1 2 1 101000 r 74 goat snp43772-scaffold588-1699055 6 116373942 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764769 Affx-986697020 AX-385252382 6 113263394 GGCAGAAAGGCCAGGTAACGCTACCCTCAGGGCGT[C/G]CTCACCAGGCAGATGAGAGTGGATGCCCTGGGGAT S 4 1 2 1 600010 r 74 goat 6_113263394 6 113263394 Ancestral_priority_1043 ancestry 0.49 neutral IMAGE 10K 10K ancestral 38441014 Affx-122928951 AX-123311351 6 113300715 TAATTCTCCCTTCTGTCAGCTACTTCCTGGAGGGG[A/G]TAGAAGCCTTATGGTGTGAAAGTGGGGCTAATTTT R 2 1 2 1 102000 f 74 goat snp12813-scaffold1495-99146 6 116117057 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405548 Affx-122955967 AX-123275900 6 113345217 GTTAGTCCAGCTGTCACTTACTTAGCACGAGCTTA[A/G]TTTGGGGGGACTCGGTGGGGGATCGGACTCGTAAC R 2 1 2 1 101000 f 74 goat snp12814-scaffold1495-143648 6 116072762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789730 Affx-122932659 AX-385276738 6 113377581 CAAGTGTTTCTCCAGTCCCATAGACTTCAGGAAGC[G/T]GATATCAGCCTTTCAACTATCACTTGAAAAATATC K 2 1 2 1 101000 f 74 goat snp12815-scaffold1495-176012 6 116039961 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438798 Affx-122930804 AX-123309135 6 113409526 TTCTCCTGGGGGACTCACAGGCCCCTTCCCTACCC[A/G]CTGCAAGGGGCACCTGCAGAATGCCCAGGCTGGTC R 2 1 2 1 303000 r 74 goat snp12816-scaffold1495-207957 6 116007013 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397059 Affx-122962733 AX-123267414 6 113459182 CAGGGACTTTCCACTCTAAGCGCAATCAACATAAA[C/T]GTGGTTTTGATCTGGCTTTCACTCGGCAGCAGCAT Y 2 1 2 1 101000 f 74 goat snp12817-scaffold1495-257613 6 115958780 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408894 Affx-122953974 AX-123279245 6 113498207 GTGGTCTTCATGGAAGTCCATGCAAAACCTAGGAA[C/T]GTTCCAGGCAGAGTGCTTCAGGTCCAGGATGGGGG Y 2 1 2 1 101000 f 74 goat snp11461-scaffold14176-10263 6 115929420 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391454 Affx-122966737 AX-123261811 6 113563723 AGGCTCCCCAGCACGCTGCAAGGGGGCAGCACACA[G/T]TAGGACCTCACCACACCGCTCTTGGACAGAAGGTT K 2 1 2 1 101000 r 74 goat snp27406-scaffold2914-70136 6 115867377 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448193 Affx-122924242 AX-123318529 6 113605312 GCTGTAGTCCTGGACGTCCCCCTTTAGCAGCTCCA[A/G]CTCCTCCTTCTCCTTTGTCAGGGACTTCTTCTGCT R 2 1 2 1 101000 r 74 goat snp27405-scaffold2914-28547 6 115831560 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278605 Affx-1111836423 AX-519552084 6 113615673 TAAACTGTTTTGGAATGCACTGCACTGGTTCATTC[A/G]TTGAAAATGAAAGGTTTCTAGGTCTCACTGGAAAG R 2 1 2 1 101000 r 74 goat Random2.2K-745 6 113615673 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432792 Affx-122935416 AX-123303133 6 113637732 TGCTTCAGACAGAAGAGACGTTAGGGCCGTGTGAC[C/T]GCTGTTCTTAGGCCGGAGGGCTGCCTGACTGTACA Y 2 1 2 1 101000 f 74 goat snp29346-scaffold3166-62970 6 117131301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432871 Affx-122935351 AX-123303212 6 113672597 CGCTTTGCGATGCTCCGTAGCCCTGCACCAGGCGG[C/T]GTGAGCCAGCGCGTGCCCCTGAGCCAGTGCTGCGG Y 2 1 2 1 101000 f 74 goat snp29345-scaffold3166-28105 6 117121073 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783692 Affx-122930408 AX-385270750 6 113735935 CACCAAAATGTGAAAGTATGTTTTATAAGGTTGAC[A/G]CCTCCTCATCTTTGGCTAAAAACACACCTTAACTT R 2 1 2 1 101000 r 74 goat snp38583-scaffold4894-81000 6 117210693 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380638 Affx-122975229 AX-123250996 6 113807848 CAAAAAGGAGGTGCACTTTCCAATCACGCTGAGAT[C/T]AACTTTCCAAATCCTTAGAGGAAAAAACGATAATC Y 2 1 2 1 101000 f 74 goat snp38582-scaffold4894-9087 6 117144237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412250 Affx-122950902 AX-123282599 6 113836628 TCCATGGGCTGAAACCCTGATGGCTCACGCCCCCA[A/G]TCCAGCGCTCCTCTGCCCTGGGGATGCTGCCCTGT R 2 1 2 1 103000 r 74 goat snp56632-scaffold8959-19594 NW_017189684.1 10786 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430769 Affx-122937487 AX-123301110 6 113873325 AGGTGTGCATAAGGGGGCTGGTTTCCTGGGGGTCA[A/G]AAGGCATGGAGTAGGGGGACCGACTCCCTGGAGGT R 2 1 2 1 102000 f 74 goat snp56633-scaffold8959-56291 6 117234337 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380057 Affx-122975567 AX-123250415 6 113883161 CTCGGGGTCGGGCCTTGTTGCTCTGCAGATGGGGC[A/G]CTGACCTCTGCTGTGGCCAGGTGGTCCAGAGCCCC R 2 1 2 1 103000 f 74 goat snp1272-scaffold1033-245117 6 117255452 G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386285 Affx-122970935 AX-123256643 6 113928208 CGGTCCAGCATGGGCTCCTCGTTCGCCAGCACCGT[A/G]CGCTGGACTGCGGGGTTGAGACGCCACCGTTAGCC R 2 1 2 1 101000 f 74 goat snp1271-scaffold1033-200070 6 117277230 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439432 Affx-122930193 AX-123309769 6 114047623 TTTGTGTCTTTATATTTCAGGTGCGTTTCTTACAG[G/T]TGTGATAAAGTTGGGTCTTGATTTTCTACCAAATC K 2 1 2 1 101000 r 74 goat snp1269-scaffold1033-80655 6 117376330 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413147 Affx-122950357 AX-123283496 6 114114152 TGTTGCCTGCTCCCAGTTAGTGTGATAGTAGGTAG[C/T]GGTTAGGGCAGTGGAGGCCCAGAGCCCATGAACGT Y 2 1 2 1 101000 f 74 goat snp1268-scaffold1033-14126 6 117434575 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430743 Affx-122937504 AX-123301084 6 114174001 TATGAGAGGTCAGACGCCCCCTCCCACCATATAGA[C/T]AAAAAATGAGAACAGTTACATATCCATCTCAGAAC Y 2 1 2 1 103000 r 74 goat snp8925-scaffold1321-38657 6 117491214 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377146 Affx-122978225 AX-123247505 6 114221133 TTCGTCTGAATGGATTCACGCAGTGCCTGTCCCTC[A/G]CCTGCCTCCCTCTGCCTGTCCCACCTCTGTCTGGG R 2 1 2 1 101000 f 74 goat snp8926-scaffold1321-85789 6 117528233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392913 Affx-122965718 AX-123263270 6 114263833 TCAGCTCCATTCCTGATAAAACTTTCTTCTAAAAC[A/G]TGTCAGATTGTGCTGTCCTTCCCAGGAACTTTCAA R 2 1 2 1 101000 r 74 goat snp8927-scaffold1321-128489 6 117571285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454294 Affx-122919266 AX-123324627 6 114319123 GCTCAGCTGTGAGCGCACAAGGCTGTGCTGAGACA[C/T]GTGAGCCTCCCAGCAAGTCCCCGAAGATGAGAGTG Y 2 1 2 1 201000 r 74 goat snp8928-scaffold1321-183779 6 117627235 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272334 Affx-1111833493 AX-431558663 6 115650573 AGGATTAACTGGTTTGATCTCCTTGCTGTCCAAGG[A/G]ACTCTCAAGGATCTTCTCCAACATAATTCGAAAGC R 2 1 2 1 303000 f 74 goat 6_115650573_AF-PAKI 6 115650573 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468275168 Affx-1111834634 AX-519548747 6 116266182 TGGGGACCTCGGGTTCTGCTTCCCTGGCAGCCAGA[A/G]TTCGGGCCATTCCTGCCACGGGCACCGTGCCCTTC R 2 1 2 1 102000 r 74 goat GoatD01.044110 6 116266182 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278607 Affx-1111836424 AX-519552086 6 117535649 AAAAAAAGATCATTTTAAGCCTAAAGCAAGCAGAA[A/G]GAAATGACTAATAAGTAACAAATATTAAAAACCAC R 2 1 2 1 101000 r 74 goat Random2.2K-749 6 117535649 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320790186 Affx-122922739 AX-385277190 7 19596 TTGAATACAATCAGAAAATTCAAGGATGATGCTCA[A/G]AACAAAGATGGTACTCAGAACATGATTTAGACACT R 2 1 2 1 101000 r 74 goat snp2565-scaffold1075-600374 7 108322088 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273301 Affx-1111833531 AX-519546945 7 20666 CGAAAAAAAGAAATAAAATAATGAAAGGACCTACC[A/G]TTCAATCTGTTGCTTTCCAGATATAAAGAGAAAAC R 2 1 2 1 201000 r 74 goat 7_20666_AF-PAKI 7 20666 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38375514 Affx-122979121 AX-123245873 7 64914 ATCGAGGATGAAAAAATTGCAGATGGCCACTTAAG[A/G]AAGAAACAAAACTTAAATTGGTCACAGTCATCAGA R 2 1 2 1 201000 f 74 goat snp2564-scaffold1075-555056 7 108274700 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413845 Affx-122949873 AX-123284194 7 164091 TCCTGTCTGTGTGGCCATGGTCCCAAGGACCTTGA[C/T]GGTCCCCTCTCAGGGGGCAGTCCCCAGACAGCTCT Y 2 1 2 1 303000 r 74 goat snp2562-scaffold1075-455879 7 108175941 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423131 Affx-122942901 AX-123293477 7 205057 CCCACTCATCCCCTCTGACCACTTCTCACTTTTTG[C/T]ACAACTGGAGCTCTTACTGCCTTTCCTGCCCCAGG Y 2 1 2 1 102000 r 74 goat snp2561-scaffold1075-414913 7 108134786 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417722 Affx-122947439 AX-123288070 7 235391 GCCAACAAAAGTGCACATAACGTATCCTCATGCAC[A/G]TATCACACAGACAAGCACTTTTGTCAACGTCAGTA R 2 1 2 1 101000 r 74 goat snp2560-scaffold1075-384579 7 108104319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422458 Affx-122943339 AX-123292804 7 265919 ATGTGTAAAACATTTTTCCAGGTGCTGTACTAGGC[A/G]TATGTAAGATATATAGATGGGGGAAAAAAAAGGTC R 2 1 2 1 101000 f 74 goat snp2559-scaffold1075-354051 7 108072676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422586 Affx-122943744 AX-123292932 7 311743 GAACCTTAACTCTGTGAAGACTCCCTGGTCTTCCC[G/T]AGCACTCTCCTCAGGGCTTCTGGTCCTATCAGCAA K 2 1 2 1 202000 r 74 goat snp2558-scaffold1075-308227 7 108026576 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429996 Affx-122938041 AX-123300337 7 342984 TCCGTGACCCAGTCTGCACTGCAAGGAGGAGCCTT[A/G]CAGAAGGCAAGAAACCTGGGTCACATCCTACCCTG R 2 1 2 1 102000 r 74 goat snp2557-scaffold1075-276986 7 107995112 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415469 Affx-122949160 AX-123285818 7 395229 TGGTGACAATTCAGTAAGCCTTGCATAAAAGGCAC[A/G]TGCTTCAGGCTTGCCCTCCAGCCAAGCTAGAGTCT R 2 1 2 1 101000 f 74 goat snp2556-scaffold1075-224741 7 107942625 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785712 Affx-122939643 AX-385272753 7 451339 CCTCTTTGTGCCTCATGGTGAATGGCTATCTTGTA[C/T]GGTTTCTGTGAGACAAAGCATTTTAAGTGCCTAGA Y 2 1 2 1 101000 r 74 goat snp2555-scaffold1075-168631 7 107886639 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394026 Affx-122965005 AX-123264381 7 503066 AGCTGGACTTAGAACTCGATTCTCCTGAATCACAG[C/T]GTTCCTATGCCTTATATCATATATCTACTTTATCA Y 2 1 2 1 101000 f 74 goat snp2554-scaffold1075-116904 7 107834923 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441163 Affx-122929559 AX-123311500 7 535861 ATATTTAAATTTACATCAGTCAAAACTATGTTTCA[C/T]TACTGCTAAGGGCTTTCTTTCTGAAAATTCGGAAT Y 2 1 2 1 101000 r 74 goat snp2553-scaffold1075-84109 7 107802996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278611 Affx-1111836426 AX-519552090 7 550696 TCAGATTAGAGGAAGATGTAGCTTTAATATGCTTT[C/G]ACCTCAGTAGAGCATTTTAGAAATTTCCCCTGCTC S 4 1 2 1 101000 r 74 goat Random2.2K-750 7 550696 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779719 Affx-122920627 AX-385266819 7 565145 CCCTTGTGCTCAGCCTGAGGATGGAGTAGGGAACT[A/G]CTCTAGCATGCGCCAAAGGCTATTTGTAGAAGACC R 2 1 2 1 202000 f 74 goat snp2552-scaffold1075-54825 7 107773803 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403058 Affx-122958527 AX-123273411 7 595952 TCGTTGTTGTCTTTTCTGGGAAGAATGAAGTCATC[C/T]GTGTTATAATAAAACAAAGAAACATACTGTTTTTC Y 2 1 2 1 101000 f 74 goat snp2551-scaffold1075-24018 7 107742699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392999 Affx-122965656 AX-123263356 7 622912 TCTGTTGTATCTGACAAGTGATCAGATGGAAATGC[G/T]AACCTATTTAAGGGGACAGATATTAACAGTGCTTG K 2 1 2 1 201000 f 74 goat snp4723-scaffold1154-240097 7 107678357 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427050 Affx-122939817 AX-123297395 7 657975 TAGAAGGCGCTCAGATTTGGTCTCCTGACTGAAGG[C/T]GCTCACCTGTGAGAAGGAAGAAGGAGTGAGGACTT Y 2 1 2 1 101000 f 74 goat snp4722-scaffold1154-205034 7 107643836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770605 Affx-122953044 AX-385257769 7 694651 GTATCCTGAATGAAGAATGATCCCATAAATGTAAA[A/G]TGGATGCATAACTCCCTCACACACGTTTTTTCAGT R 2 1 2 1 101000 r 74 goat snp4721-scaffold1154-168358 7 107606457 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381489 Affx-122974878 AX-123251847 7 735144 GAGAGCCCCAATTCCTTATGAAAAGGAGAAAAACA[C/T]TGTCATTTATAACACAAAAGTTGGTACTTGCTGGC Y 2 1 2 1 201000 r 74 goat snp4720-scaffold1154-127865 7 107565751 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405517 Affx-122955993 AX-123275869 7 771646 CACAAGCCCCTTCGCCATGACAAGGCTGTGATCCA[C/T]GAAGGGGCCCATTTGTCTAGAGTTTACTGTTTATT Y 2 1 2 1 303000 r 74 goat snp4719-scaffold1154-91363 7 107528186 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453159 Affx-122920478 AX-123323492 7 815192 ACTCTCTGCTAGAACTTGAAATAATGTGAAAAGGG[C/T]GAAAGCACAGTAATAAAACAGTAACACTGGCATTG Y 2 1 2 1 201000 f 74 goat snp4718-scaffold1154-47817 7 107484364 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778096 Affx-122920736 AX-173924733 7 845105 AGACCTCTTAAGAGAGTCCCAAGTAAGAGATGGGA[C/T]GCTTGATCTCTGATTGCTGAGTCTCAGCGCTCAGA Y 2 1 2 1 102000 r 74 goat snp4717-scaffold1154-17904 7 107453803 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774106 Affx-122926930 AX-385261244 7 877998 TGTATGTGCTATTATCAATCTAGATTTGTGAAAAC[A/G]CTAGAAGAGTCCATATGAAAATCCACCTGTCTGGC R 2 1 2 1 101000 r 74 goat snp19383-scaffold196-14890 7 107420885 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782474 Affx-122972874 AX-385269551 7 981965 CTAAAAGCCTCTTCTTGTTCCACAGTCCAAAGTAA[C/T]GGTTCTGTATCTGGGCATTTAGTGGCTTCATATAG Y 2 1 2 1 101000 r 74 goat snp19386-scaffold196-118857 NW_017192263.1 16212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800891 Affx-122935708 AX-385287806 7 1041681 ATACGGGAGTCATGAGGACACTTGGCATCCCCAGG[C/T]GTCACTGTCAGTCAGACCTCGTATCCAAGTGACCT Y 2 1 2 1 102000 f 74 goat snp19387-scaffold196-178573 7 107267597 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400438 Affx-122959964 AX-123270793 7 1117133 ATAACGAGAAATCAAAGATTGAATTACGAAGTATA[C/T]GAACAGAAACAGGTATGCCAGCAGGAAAAGCTAGT Y 2 1 2 1 201000 f 74 goat snp19388-scaffold196-254025 7 107193425 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403660 Affx-122957515 AX-123274012 7 1148060 GCATAGGGCAAGTTATGGGTGTATATGTTTGTGAA[C/T]GTGTACAGCTTCTATACCCACTGCAGGCATGCCAA Y 2 1 2 1 201000 r 74 goat snp19389-scaffold196-284952 7 107162748 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800438 Affx-122956638 AX-385287359 7 1200430 TAGACTTAAAAGTTGAGAAGCTTAGGTATTTAAAT[A/G]GGTTGTGAGTATATGCAGATGTTTTCTTCCTGGAG R 2 1 2 1 101000 r 74 goat snp19390-scaffold196-337322 7 107110289 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278444 Affx-1111836427 AX-519551929 7 1217432 TAACATAGTACTGAAATCCCTAGTGATAGCAAGTA[A/G]TAGAAATAATTTAATAGTTTTGCAAATGATGTGAT R 2 1 2 1 101000 f 74 goat Random2.2K-751 7 1217432 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380536 Affx-122975675 AX-123250894 7 1249622 CTCTTTGCCGCCGTCTAGATCCTGCACGTCTTTAA[C/T]GTAGAGAGAAAAATCGATCACTCCAACCTGATTGA Y 2 1 2 1 101000 r 74 goat snp19391-scaffold196-386514 7 107060768 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407078 Affx-122954907 AX-123277429 7 1305632 TTCTTCTCAGTCTGTTGGCTAGAACTAGTCACATG[C/T]GGTCTTCTGGTTGCTGGGAAGGAGTGGGAGGAGAT Y 2 1 2 1 101000 f 74 goat snp19392-scaffold196-442524 7 107003510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384314 Affx-122972275 AX-123254672 7 1350291 ATTAATTATAAACTGTGAAACTATACAGCTCTCAC[A/C]ACATAACATCTAGAAAAATCTCAAAGGCCTAGTTC M 2 1 2 1 101000 f 74 goat snp19393-scaffold196-487183 7 106958687 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379955 Affx-122975640 AX-123250313 7 1388185 GTAGATTTGCCCTGAGCTGCTAGCCTTGGCTTCAC[A/G]GTCCTCTTTCTTCCTATTTCCCTTTCATCTGGGGC R 2 1 2 1 101000 f 74 goat snp19394-scaffold196-525077 7 106921229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395710 Affx-122963720 AX-123266065 7 1416912 TTTTCAAGGTAGCTTTCTTTCTTGTCCCTCTTTAC[A/G]TCCCTATCCTTGTTTTTCTTTCTTTTTTGTCTCCC R 2 1 2 1 101000 f 74 goat snp19395-scaffold196-553804 7 106892402 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425392 Affx-122941556 AX-123295738 7 1462967 TGTCTGATATGAGTATTGATATCCTTACTTTCTTG[A/C]TATTTCTATTTGCATTTTCCATCCATTCACTTTAA M 2 1 2 1 201000 f 74 goat snp19396-scaffold196-599859 7 106846903 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432438 Affx-122935815 AX-123302779 7 1498319 TCACAGGGTTAAACACTCCACCCTGGGTGCACCCC[A/G]CTGCCATACTGCTTCTGAGCGCATGTCACATGGAG R 2 1 2 1 101000 r 74 goat snp19397-scaffold196-635211 7 106811270 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403826 Affx-122957953 AX-123274178 7 1537347 TTACTAACTCACCCTTCCTCCTGACTTTGGGGTGC[A/G]TATTTCGTATCTCTGAAGTTCATGAAGGTGATCTG R 2 1 2 1 101000 r 74 goat snp19398-scaffold196-674239 7 106772037 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443439 Affx-122927358 AX-123313776 7 1574920 GACTCTGTGGGGACAAAGTAACATGACGGCCGTTG[C/T]GCCCCCTTTTTGGGAGCGCAGGGGGATGAGGGGCC Y 2 1 2 1 101000 f 74 goat snp19399-scaffold196-711812 7 106734513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376624 Affx-122979037 AX-123246983 7 1614195 AGCTACTTACATTCTTGGCAAACTCACCAGTAGGA[C/T]GAACAGGGCCTGTCCTTGTCCTGGGACCTTGGACT Y 2 1 2 1 101000 f 74 goat snp19400-scaffold196-751087 7 106695496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413889 Affx-122949842 AX-123284238 7 1655014 CCCTGTGAGGCTGTGTCACAGATTGAATTTACAGC[A/G]TTCAGCACTTGCTCTGATTTCTCATTTCTGCCCTT R 2 1 2 1 101000 r 74 goat snp19401-scaffold196-791906 7 106654198 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449516 Affx-122922612 AX-123319851 7 1687626 CCTGGCGCAGGTCTGGGAAGGCCAGAGCTGACCAG[C/T]GAGGTGCAGCCATCGTTTCTTCATCTATGATGCCT Y 2 1 2 1 101000 r 74 goat snp19402-scaffold196-824518 7 106624333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451660 Affx-122921594 AX-123321993 7 1723537 CAGCAGCCGGGGGCTGCCCACCCATTATGCCATCG[A/G]AGCACTTGGGCAGGAGGGTCTTCTCACCCAGTTCT R 2 1 2 1 101000 r 74 goat snp19403-scaffold196-860429 7 106583314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411668 Affx-122951556 AX-123282018 7 1814701 CAAAGAGCAGCAGGAAGGGCATCAAAACAGACAGG[C/T]ACACTTTTAATTCTACAGAGATTTGTCCTTTCCCA Y 2 1 2 1 101000 r 74 goat snp19405-scaffold196-951593 7 106494659 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447045 Affx-122924526 AX-123317381 7 1848980 AGAAGTTATGAGAAGTGTCTGGAAATACTAAAATT[C/T]AAAATATGGAAAAGATGAGAATGTTAACATTGGAA Y 2 1 2 1 101000 f 74 goat snp19406-scaffold196-985872 7 106460237 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445098 Affx-122926199 AX-123315435 7 1885917 AGATGGTTTCTCTTGTTGGATTTTATGTCTCACTG[A/C]TTTTCACCCTCCATATCCTTCAGTGCTTCTTTGTT M 2 1 2 1 202000 r 74 goat snp19407-scaffold196-1022809 7 106422527 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391225 Affx-122967399 AX-123261582 7 1966454 ACAAGCTGTCAGTGGTAGGAAAGATGGTAACAGGT[A/C]GGTTTTGAGTTACAAGAAGTCCTTACCCAGTGAAA M 2 1 2 1 101000 f 74 goat snp19409-scaffold196-1103346 7 106343223 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395329 Affx-122922435 AX-123265684 7 2043010 CTGCTGCCCCAGGAAAAATTCCTGGGTCAGTGAGG[A/G]GCAGACAAGGCAGATAGAGGGTGATGCTAAGACAG R 2 1 2 1 101000 r 74 goat snp19411-scaffold196-1179902 7 106265859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428281 Affx-122939394 AX-123298624 7 2079958 GTCCTACAGGGATTGTCATGGAAGCCTCATTACAC[A/G]GGCACGGTTGATTGAATCATTGGATGTCAGTGATT R 2 1 2 1 101000 f 74 goat snp19412-scaffold196-1216850 7 106228892 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400933 Affx-122959716 AX-123271286 7 2111676 TCCTATGGCTAAGTGAATACAACTTATTACTTTCA[C/T]GTCTTCATGATAATGTTGCTAATTTTCTCCTGCAA Y 2 1 2 1 101000 f 74 goat snp19413-scaffold196-1248568 7 106197624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768644 Affx-122956867 AX-385255823 7 2148716 AAAGCAGAAATGATACAGGCCATATTTTCTGGTCA[C/T]TGTAAAATGACATTGCTGACTGTTGGTGAAAGGAT Y 2 1 2 1 101000 f 74 goat snp58165-scaffold941-229990 7 106160944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427331 Affx-122940125 AX-123297674 7 2199528 TCACAGGTGCCCAGAAACTGCTCCCCAGAGAGCAT[A/G]TGCCCCTAAGGGGTGAAGTGTGTGTGTGAAAATGC R 2 1 2 1 303000 f 74 goat snp58164-scaffold941-179178 7 106110283 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447133 Affx-122924458 AX-123317469 7 2296987 GAGGTATGCAAAATATTTGAAAAATTGTTATTCCA[C/T]GCTTATGGAGATGGTCCTAGAGAGAGAAGAATGAG Y 2 1 2 1 101000 r 74 goat snp58162-scaffold941-81719 7 106015314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376459 Affx-122978051 AX-123246818 7 2359777 CTGAGATCCTCTCTGTATTTACTTAAGTTTGATGG[A/C]GTATACACAGTTATTACAATTGGTGATATAAGCTG M 2 1 2 1 101000 f 74 goat snp58161-scaffold941-18929 7 105956464 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274800 Affx-1111834427 AX-515961991 7 2396254 AGAGG[A/G]GTGAGCTAGAAGGCCATCTGGAGGCCTCAAGGTCA R 2 1 2 1 102000 r 74 goat GoatD01.035377 7 2396254 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38423497 Affx-122942563 AX-123293843 7 2415670 TGCTAAGCCTTGGCTCTGGCCATTGAAGATCCAAC[A/G]GTGACCACATGGAGGCCCTGGAGTAGCTTCGTGGT R 2 1 2 1 101000 f 74 goat snp24183-scaffold2463-10708 7 105903754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777973 Affx-122971929 AX-385265089 7 2431310 CAAAAATGTGCCAGGAACAAAACCTCACTTCAAAG[C/T]GCAGGACCATCGATTGCACTGACAATGGGAAGGTT Y 2 1 2 1 101000 f 74 goat snp12675-scaffold1488-4833 7 105871510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380563 Affx-122975280 AX-123250921 7 2497711 TTCTAGCCCTAAGGGAAGGTAGAGGGAGTGTGAGC[A/G]GGAAAGGGGTCCAGGACATACAAACCATGGAGCAG R 2 1 2 1 201000 r 74 goat snp12676-scaffold1488-71234 7 105828175 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448876 Affx-122923268 AX-123319211 7 2530584 AAACCCTAGTGGCTTAAAATAACAGTCCTCATATA[C/T]GCAATCTCCTTGGGGGTTAGGACCTAGGAGCATCT Y 2 1 2 1 101000 f 74 goat snp12677-scaffold1488-104107 7 105795691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429568 Affx-122937813 AX-123299910 7 2561660 GGGTGTCTCTGACACTCCCTTCCCTTGGAGGGACA[C/T]GGAAAGGGCTAATATGGAGGGTGTCACCTACCCCC Y 2 1 2 1 101000 r 74 goat snp12678-scaffold1488-135183 7 105764673 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418753 Affx-122946207 AX-123289101 7 2593169 ACTGCAGTAGTTAATCCTGTCCCCGTGAAACTGTG[C/T]AACTGTTTTTCAGAAAAGGGGAAGCAGGAGGAATC Y 2 1 2 1 202000 r 74 goat snp12679-scaffold1488-166692 7 105733773 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436755 Affx-122932285 AX-123307093 7 2625416 CTTGATCCCAAAACCACTTGAGGCATGGGGCAACT[A/C]TCCTCAGGATGTGAGTCAGAACTGAGGCCCAGAGG M 2 1 2 1 101000 f 74 goat snp12680-scaffold1488-198939 7 105701840 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378476 Affx-122976670 AX-123248835 7 2723209 GCTTACGTGATGCCTTTTCCATCCATACGGGTCCT[C/T]TCTGCTATGAGTTCTCTCGGAGTCAGATATTCCAT Y 2 1 2 1 101000 r 74 goat snp12682-scaffold1488-296732 7 105608819 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273265 Affx-1111833534 AX-519546915 7 2734229 AGGATAGACTGACGTGGAATCTGTTACGATGTATT[A/G]CAGCTGATGGTGTTAAGAATAAATGTGGATCAAAA R 2 1 2 1 101000 f 74 goat 7_2734229_AF-PAKI 7 2734229 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38453288 Affx-122920378 AX-123323621 7 2766487 TGAGGGCACATCCTTCTACTCCACCATCTTGCTGG[G/T]AGTATGGAGCTCCCTAAAACCATTTTTAACATTGG K 2 1 2 1 201000 r 74 goat snp12683-scaffold1488-340010 7 105564223 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405813 Affx-122955892 AX-123276165 7 2818236 TAAAACAGCTTTCCCTCCGATATTCTTTCCTTCCT[A/C]GTCAGATCTAGACACACTGTTTCTTTTTGAAAATT M 2 1 2 1 201000 r 74 goat snp12684-scaffold1488-391759 7 105509430 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417350 Affx-122947724 AX-123287698 7 2885782 TCAACCATTGCTGTGTCTGCCCTCAATGACAAGCA[C/T]ATGAATTAGCTAATGTAAGTCAGAGAAACCAGGCT Y 2 1 2 1 101000 f 74 goat snp12685-scaffold1488-459305 7 105437902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414737 Affx-122949726 AX-123285086 7 2925761 GAAGGCAACGGGGTCTGCGCTGAGCAGGCCACGCC[A/G]GAGAGGCAGGCTCAGGACTGAACGCGATTCTGGAG R 2 1 2 1 101000 r 74 goat snp12686-scaffold1488-499284 7 105398029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403502 Affx-122957636 AX-123273855 7 2988452 ACACTGAGATTATGCACAAATCCCCCAAAGAACTA[C/T]TGAGTCTGGCACTGCAGCATCCAAGGAACCATGCT Y 2 1 2 1 101000 f 74 goat snp12687-scaffold1488-561975 7 105335477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784220 Affx-122940526 AX-385271271 7 3067764 AATTTTTTTCCCTTAAATGCATATTATGGGATACT[A/G]TGGTAAGTGGTATAATAAGGGGAATAGATTGTTTG R 2 1 2 1 201000 f 74 goat snp12688-scaffold1488-641287 7 105254447 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414994 Affx-122949045 AX-123285343 7 3100768 GTAATGTGTTAATCAAAATCTGTATTTCAGAACAC[A/G]CTCTCATAGTCTGTCTCTCCATGGCCTGCATTAAT R 2 1 2 1 201000 f 74 goat snp12689-scaffold1488-674291 7 105220342 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776507 Affx-122931815 AX-385263634 7 3136353 AAATCAATGGAGAACTACAAAGAACCCATCCAGGC[A/G]ATACTACTAATGACCTACTAATGACTCTTCGGGAA R 2 1 2 1 101000 f 74 goat snp12690-scaffold1488-709876 7 105182048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438004 Affx-122931578 AX-123308342 7 3170397 AAATGAATGCTCCCCTTCTGTCAAGGATGTGCAAA[C/T]ACATTACATGTATCTCATTTAATCCTAACACCTTT Y 2 1 2 1 103000 f 74 goat snp12691-scaffold1488-743920 7 105147871 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450589 Affx-122922025 AX-123320923 7 3200842 CAGAGGGAAAGGCCCCAGCACTGCCTTACGACCAA[C/T]GTCATCCAGAAAAGTTTTCAGTCCAAAAGTGAAGT Y 2 1 2 1 101000 r 74 goat snp12692-scaffold1488-774365 7 105116655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410621 Affx-122952096 AX-123280971 7 3237770 GGCCCCAGCGTCCCGGGAGATGAGGGCTGTTCCCC[C/T]GTTCCACCCCATCTTAGGGGAAAGTTGAGACTGGC Y 2 1 2 1 101000 r 74 goat snp12693-scaffold1488-811293 7 105079660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791676 Affx-122921557 AX-385278667 7 3272099 TTGGCATGCACCGTCTTAGTTGAAATTCAGCCCTC[A/G]TCAGCTGGAGACTTCCTGTGTAAGGGATAACCAGT R 2 1 2 1 101000 r 74 goat snp12694-scaffold1488-845622 7 105044835 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429540 Affx-122937832 AX-123299882 7 3334072 TTAATCAGGCGGTTGAGTCATGTAGTGGAATAGTA[G/T]ACAACCATTAAAAAGCTGAAGACGTTTTTCTCCAC K 2 1 2 1 101000 f 74 goat snp12696-scaffold1488-907595 7 104981541 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426132 Affx-122940619 AX-123296478 7 3386489 CAGCCTGCAAAAGCTTTGCTGAGAAGCAACGCTGG[A/G]GCACTTTAGAAAGCTGCAGGCTCGGCATCCTCGAC R 2 1 2 1 102000 r 74 goat snp12697-scaffold1488-960012 7 104929356 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431801 Affx-122936119 AX-123302142 7 3420304 AAAAATGGATCCCAATGGCCAGCCCCCACCAGATA[C/T]AGCAGAGAACAAGGACGAACCTTAGGAAGCAACTG Y 2 1 2 1 201000 r 74 goat snp12698-scaffold1488-993827 7 104895355 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394265 Affx-122964721 AX-123264620 7 3533097 CACGTTAAAAAAAAGTCTTAAAAAAAATAAAGCAT[A/G]CCCTTTGTAAAATTGAAAGAGAGAGAAAGTAATGA R 2 1 2 1 101000 f 74 goat snp12700-scaffold1488-1106620 7 104783934 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275023 Affx-1111834640 AX-519548605 7 3581936 AGAAGGGAGGTCAAACGAAAATGCCTGCAGGTTGA[A/G]AGTACCAAAGAACAGCCAGCCAGTTTCCCTCCCAG R 2 1 2 1 201000 f 74 goat GoatD01.044192 7 3581936 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320786738 Affx-122932506 AX-385273769 7 3603410 TAAGCTCACTTGACCAAAAAAATAGCTCAATATGA[C/T]AGGACCTAAAAACTAAAGGGCTGGAATTTGCAGGC Y 2 1 2 1 101000 r 74 goat snp12701-scaffold1488-1176933 7 104712755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413689 Affx-122950095 AX-123284038 7 3638010 TGGTGAATATTTCCTGGAGTGCTGTTGGAAACAAC[G/T]TTTTTATTAGACATGCATCAATGTGGCGGCAACAT K 2 1 2 1 102000 f 74 goat snp12702-scaffold1488-1211533 7 104679094 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450912 Affx-122922190 AX-123321246 7 3678926 TCACCATCTGCCTTTAGGTGGCGCCCAACAGTGCC[C/T]TCTGGATTCCGAAGTCCCCATGTCAAGTTTCAAAA Y 2 1 2 1 101000 r 74 goat snp12703-scaffold1488-1252449 7 104648946 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441340 Affx-122929424 AX-123311677 7 3715480 CCATGGGACACAAAGGCAAATCAAAGCACTCCCAG[C/T]GGCCAGAGCAGGAACACCCCGAGCAACACGAGCAG Y 2 1 2 1 101000 f 74 goat snp12704-scaffold1488-1289003 7 104612861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401087 Affx-122959627 AX-123271440 7 3766955 TCACACCTCAGCCTAGTTAATTAAGTCAGGATGCC[C/T]CAGGACTGCAGTGTGCAGCAGAATCTAGGTGCTGC Y 2 1 2 1 101000 f 74 goat snp12705-scaffold1488-1340478 7 104561294 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432365 Affx-122935868 AX-123302706 7 3808398 GACACATGTTGGGACTTCGCTAGTGGTGGAGCAGA[G/T]AAGAACCCACTTGCCAGTGCAGGGAACATGGGTTT K 2 1 2 1 101000 f 74 goat snp12706-scaffold1488-1381921 7 104520257 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399464 Affx-122961200 AX-123269819 7 3853454 TCCATAAAGTTGCAAAGAGTCGGACAGGACTAAAG[C/T]GAGTTAGCACAGAAGGGCTAATAGAAGGCGATTTT Y 2 1 2 1 101000 r 74 goat snp12707-scaffold1488-1426977 7 104475448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407490 Affx-122954756 AX-123277841 7 3891867 TGGATTATAAGAAACTTCTTCTGGCTCCCAGGAGA[C/T]GAATCCTGGGTAAGAAGGGGAGCCGGGCCCAGAGG Y 2 1 2 1 101000 f 74 goat snp12708-scaffold1488-1465390 7 104437319 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453127 Affx-122920010 AX-123323460 7 3968014 TAAAATTTATTTCAGACCATGCCAAAGTCCTGACA[A/G]GCCTCCACCACAGCTCAGGCTGGATTCCAGGTAGA R 2 1 2 1 101000 f 74 goat snp12710-scaffold1488-1541537 7 104360761 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603189 Affx-1002479442 AX-413837375 7 4002714 GGCCTGAGAAAATCTGTATTGGCATTTATGTTAGT[C/T]ATTTTGCAGGTGAAAGGTATTCTGATTTACATTTC Y 2 1 2 1 101000 f 74 goat 7_4002714_RH-map 7 4002714 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38389983 Affx-122968060 AX-123260340 7 4007720 TTGAGTCTCTGAGGGGAGGCTGGCCTAGAGACCCC[A/G]AACTTAGGCAGTGGTGATGGGGACTGCCATTGACT R 2 1 2 1 102000 r 74 goat snp12711-scaffold1488-1581243 7 104321849 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415269 Affx-122948842 AX-123285618 7 4046979 TAGCCAGGCGGGGGGTTAGGGGAGCACAGTGAAAA[C/T]GGAAGAGACCCCTGGAGCATACAGCCTGGGATGCG Y 2 1 2 1 103000 f 74 goat snp25492-scaffold2621-416911 7 104291183 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603276 Affx-1002479443 AX-413837456 7 4056409 AATTAAATAAGCAGGGTGACAATATACAGTCTTGA[C/T]GTATTCCTTACCAATTTGGAATCAGCCTATTGTTC Y 2 1 2 1 101000 r 74 goat 7_4056409_RH-map 7 4056409 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38429794 Affx-122938203 AX-123300135 7 4085344 GTTGACTGTGCTTTTGGTGTGATAGCCAAGAAGTC[A/G]TTGCCAAATCTAACGTTATGAGACTTTTCCTCTGC R 2 1 2 1 101000 r 74 goat snp25491-scaffold2621-378546 7 104253434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395991 Affx-122963504 AX-123266346 7 4145509 CTTCACACACAAATGATTGAGTACCCACTGTGTAC[A/G]GACCCTCTGCTAGAGATAGATCAGTTGCGTCTGGT R 2 1 2 1 201000 r 74 goat snp25490-scaffold2621-318381 7 104193334 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771285 Affx-122935943 AX-385258443 7 4192615 GGTGTTAGGTAAATGCTGATAAATAAATGCTGGAG[G/T]AAAGACCTGTACCTCAGCAACTCTAAGGCTGAGGA K 2 1 2 1 101000 f 74 goat snp25489-scaffold2621-271275 7 104150954 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603278 Affx-1002479444 AX-413837458 7 4222118 GACTAAGTATGAATAGAATGCTAGATTCCTAATTT[A/C]TATTCACCAAATACTTTGATAAGTTTCATTTATTC M 2 1 2 1 201000 r 74 goat 7_4222118_RH-map 7 4222118 C A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38405825 Affx-122955883 AX-123276177 7 4224218 ATATGGGTTCTCCTAGTTTCTCTCTTCCAGGACTT[C/T]TCTCAACACTGAGCACACTAATGAAGACTATGAAT Y 2 1 2 1 101000 r 74 goat snp25488-scaffold2621-239672 7 104116063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430672 Affx-122936931 AX-123301013 7 4265512 GGACCACCCTTGCAGGACCAAATGATGGGGAAATC[A/G]CAGCTCCCTTCAGGGAAGCAGTGCTGTGTCGGGCT R 2 1 2 1 101000 f 74 goat snp25487-scaffold2621-198378 7 104075829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603196 Affx-1002479445 AX-413837381 7 4321559 ATATGTGAAACATTTTATAAGCATATAGTTACATA[A/T]AAATACTGTTGTCCCTTGAACAACATGGGTTTGAA W 4 1 2 1 202000 f 74 goat 7_4321559_RH-map 7 4321559 A T 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38449106 Affx-122923585 AX-123319441 7 4361720 TGTGCAAAACCATGATTTGCGGGAAATCCAACACG[G/T]CAATGTGCCCCAGATGGTTGGAGGGCCTCTCTGAG K 2 1 2 1 101000 f 74 goat snp25485-scaffold2621-102170 7 103992457 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413273 Affx-122950214 AX-123283622 7 4395878 CTGATGCTTGGAACTACGATTAAGAAATGTCATAG[C/T]GGAACTTCCCTAGTGATACCGTGGATAAGAATCTG Y 2 1 2 1 101000 f 74 goat snp25484-scaffold2621-68012 7 103958251 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410228 Affx-122952553 AX-123280578 7 4426483 CTGTACCAGAGTCACGGCCGCTCAGCCTTTGTTCA[C/T]GTGCCCCCTCTGGGCAAGCCGTACAATGCAGACCA Y 2 1 2 1 101000 f 74 goat snp25483-scaffold2621-37407 7 103929268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784709 Affx-122921214 AX-385271757 7 4455825 ACTTCATGATGTTTGACGCCTGTGTACCTCTGTGG[C/T]GCCTGAGCCCAGTTGAAATCTAGAACATTCTCAGC Y 2 1 2 1 101000 r 74 goat snp25482-scaffold2621-8065 7 103900144 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385565 Affx-122971218 AX-123255923 7 4470037 TTTTCTAGACTTCAGTGCTAACCTGGGAGGCGGAT[A/G]TGTGGCCTGGGGTTGGGGAGAGTTCAGAGGCTGTG R 2 1 2 1 101000 f 74 goat snp44962-scaffold6120-6048 7 103877735 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603198 Affx-1002479446 AX-413837383 7 4488613 TCCCACATGAAATATATTTCATAGCAGTTTTTTTA[C/T]AATCAACAAAATGAAAAAGACATGTGTTAAACATA Y 2 1 2 1 101000 f 74 goat 7_4488613_RH-map 7 4488613 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38431770 Affx-122936716 AX-123302111 7 4526767 CTATCTCTTCAAGCACATTTTTTACTTTCACTTTC[A/G]TTTTTCTCTTTCTTTTCTTTTGAATATGTTTGTCT R 2 1 2 1 303000 r 74 goat snp40026-scaffold510-2843752 7 103820194 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603200 Affx-1002479447 AX-413837385 7 4539528 ATGTAACTTGATACAGCCACTGTGCAGGACAGTGT[G/T]GAGATTCCTTAAAAATCTAGGAATAAAGCTACCAG K 2 1 2 1 303000 f 74 goat 7_4539528_RH-map 7 4539528 G T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38445797 Affx-122926044 AX-123316134 7 4565365 ACCCTTCCCAGATCCCCAACCCCCAGAGAAGAATT[A/C]TCCCTCTTGAACAAATGCAAACATTTTCTCAAAAT M 2 1 2 1 202000 r 74 goat snp40025-scaffold510-2805154 7 103782945 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603202 Affx-1002479448 AX-413837387 7 4591935 GTGTAACATTGTAATAGGCAGGTGATTTAATTTGT[A/G]TTATTTAAAAAATGTAATTATTAAATATTCATGAC R 2 1 2 1 101000 f 74 goat 7_4591935_RH-map 7 4591935 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38429141 Affx-122937995 AX-123299483 7 4604088 GTATGTGGTTAGAATGCTTAAAATATACTTGCTTC[A/G]CAACTTTCTCATGTAGCAATACAACACTCTAACTA R 2 1 2 1 101000 r 74 goat snp40024-scaffold510-2766431 7 103743420 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409196 Affx-122953178 AX-123279547 7 4643072 GCAGGGACATGGCTTGGAAGGGTTCATCCGTGATC[C/T]TGGTCCTTACTCGCCCCGAGCATAGGGTTCTAGGA Y 2 1 2 1 101000 f 74 goat snp40023-scaffold510-2727447 7 103704042 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603204 Affx-1002479449 AX-413837389 7 4643574 TGTACCTTTGCCCAAATGTATGGCTACTTCACGCA[A/G]AACCCTATTTCTAACCTGAATTGTCTGGGTGTCTT R 2 1 2 1 101000 f 74 goat 7_4643574_RH-map 7 4643574 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603206 Affx-1002479450 AX-188570479 7 4664639 TGGAATGTGAAGTCAAGTGGGCCTTAGGAAGCATC[A/G]CTATGAAGAAAGCTAGTGGAGGTGATGGAATTCCA R 2 1 2 1 303000 f 74 goat 7_4664639_RH-map 7 4664639 G A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320801616 Affx-122927496 AX-385288524 7 4680516 TTTTCCCTAATTTCTCCTGCCACCTTGTTTCTAAC[A/G]CCCATCACCTAATTGCTAACACTCACCACCTTACT R 2 1 2 1 101000 f 74 goat snp40022-scaffold510-2690003 7 103666849 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427083 Affx-122939795 AX-123297426 7 4724483 GCAGGTGGGAGGGAGGCCAGAGGCAGGAGGATCCT[A/G]CCTGTCTGTGGAGTCTGGGCGGTTGTTGCTTTTCT R 2 1 2 1 101000 r 74 goat snp40021-scaffold510-2646036 7 103623130 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603291 Affx-1002479451 AX-413837471 7 4729190 GTGGGCCTCATCCAGTCCGCTGAGGCCTGAACAGA[A/G]CACAAAGGCTGATATGCCTTTGAGTGTGGGGGAAT R 2 1 2 1 202000 r 74 goat 7_4729190_RH-map 7 4729190 G A 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38429957 Affx-122938073 AX-123300298 7 4761793 CACCCAAAGGTCCCTCTGTAATCAACCCATCATTT[A/G]TAAAAGAGCTCACTCGAGGGCCTTTGCTGTCTGGT R 2 1 2 1 101000 r 74 goat snp40020-scaffold510-2608726 7 103585941 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436999 Affx-122933138 AX-123307337 7 4801805 TAAGAAAAGAATCTAGAGTTTTCAAGGGTCAGATT[C/T]CTAGAATTGGGGGATTTTAGGGGTAAAAACCTTTT Y 2 1 2 1 201000 f 74 goat snp40019-scaffold510-2568714 7 103546180 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418207 Affx-122947058 AX-123288555 7 4830799 GTCTTGTTTTCTTTACACACCCTGCAGAACTCAAG[A/G]GGGTGCAGCCAAGCTGTGAGTGCGCTGGGAGGGGT R 2 1 2 1 101000 f 74 goat snp40018-scaffold510-2539720 7 103517635 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603210 Affx-1002479452 AX-413837394 7 4833970 AATTCTAGAAACTATAGGGAAGGAGAGCAGGCAAG[C/T]AACGATTCTCTAGTTCACTTTGCTTTCTCTTCATT Y 2 1 2 1 101000 f 74 goat 7_4833970_RH-map 7 4833970 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38425411 Affx-122941542 AX-123295757 7 4880812 CCCTAGATGTGGGGTTTCATGGTGCTGTGTGGCAT[C/T]AGGAGTTTACCAGACTGGACTCCTGTGGGTCTCAG Y 2 1 2 1 101000 f 74 goat snp40017-scaffold510-2489707 7 103468743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603660 Affx-1002479453 AX-413837798 7 4917489 CAGAGCTGCCAAGCAGACGACCCACAAATAGCAAA[A/C]CAATTATACTGAACAATGCAATCTGATATCACAGT M 2 1 2 1 101000 r 74 goat 7_4917489_RH-map 7 4917489 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320790468 Affx-122955129 AX-385277471 7 4941609 AGAGGCTGAACTGAGATTTGATGGAGGTGAGGATG[A/G]AGCCATGTGGACTCCAGGAATGGAATTCTCAGCAG R 2 1 2 1 101000 r 74 goat snp40016-scaffold510-2428910 7 103407682 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603295 Affx-1002479454 AX-413837475 7 4954369 TCAGCATAATGTAAGCTCTTTACCACCTGTTTTGG[A/G]TTTTGCTGATTTTCTGGGTACATGGAAACCTACTC R 2 1 2 1 101000 r 74 goat 7_4954369_RH-map 7 4954369 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38420799 Affx-122944687 AX-123291146 7 4996496 TCACTTTGCCTTCCCAGCAGCATCTGCCTTTGCCC[A/G]TGTACCAAATGTTATTAAGGATAGAGGTGGTAGCA R 2 1 2 1 101000 r 74 goat snp40015-scaffold510-2374023 7 103353268 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448545 Affx-122923432 AX-123318881 7 5042197 GACCTGGGTTCAAACCCTGGCTCTGCCTCCTGCCA[C/T]GTGTGTGACCTTGGCAAGTCAACCCTCCTCTCAGA Y 2 1 2 1 101000 r 74 goat snp40014-scaffold510-2328322 7 103307821 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795038 Affx-122939264 AX-385281997 7 5132537 TTGCTCCAAATCTTAACTTAGATTCAAGTTTCCCA[A/G]CTGACAGTAGAGGTTTTACTGGTTTCCCCCTGCCT R 2 1 2 1 101000 r 74 goat snp40012-scaffold510-2237982 7 103218154 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426436 Affx-122940816 AX-123296782 7 5171479 GTGTTTGGTGCATCTCTTCCTTTTCGGCATTTTTC[C/T]GAGGACTAGGAAGTTTGAGCGAATCATCTCACACC Y 2 1 2 1 101000 r 74 goat snp40011-scaffold510-2199040 7 103178942 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435181 Affx-122933649 AX-123305521 7 5202152 TTGTCATAATACCAGTGTTCTAGTGTCCTCACAAT[A/C]TTGTAAGGAAGGAATGCTTACTAATCCCATTGGAT M 2 1 2 1 101000 f 74 goat snp40010-scaffold510-2168367 7 103148278 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780438 Affx-122976398 AX-385267529 7 5238471 GGAAGATTTAACACTGAGTCTCCAGAATCAGCAAC[A/G]TATTTTTCAAGATTGTAACAAAATATAAGATGTCA R 2 1 2 1 202000 r 74 goat snp40009-scaffold510-2132048 7 103111562 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420765 Affx-122944713 AX-123291112 7 5267661 CATCCTTTAGAGCCACTTTAAAATAAAAAGAGGGC[A/G]TATGGGGATTGAATTAGAGCAACAAGCTGCCTTTG R 2 1 2 1 103000 r 74 goat snp40008-scaffold510-2102858 7 103082087 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413746 Affx-122950051 AX-123284095 7 5322614 GGAGGCTGCTCGAAACAACTGAGGTCGACCTAGCT[A/C]GGGCGGCCGCACTTCTTTGTGACTAGCTGTGCGGC M 2 1 2 1 101000 f 74 goat snp40007-scaffold510-2047905 7 103029797 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273328 Affx-1111833545 AX-519546969 7 5343861 AAATACAAAGTTTTCTCAAAATCCAATTAGGAAAA[A/G]AAGGTTAGTAATGTACCGTAAAATTGGAAGGAATT R 2 1 2 1 101000 r 74 goat 7_5343861_AF-PAKI 7 5343861 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437901 Affx-122931660 AX-123308239 7 5386668 ACGCGAGAGCACCAAGCAAAGGAGGGAGGGTGTGT[A/G]TGTATGTCGAAGGCAGGCTTCAAATGCCTGTCAAA R 2 1 2 1 201000 r 74 goat snp40006-scaffold510-1983851 7 102965994 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396460 Affx-122962972 AX-123266815 7 5416007 TTTAATGGCCCCATGTGGGTGGCTCATAGCATCTT[A/G]AGCTGATTAAGGCCTAAGAGCTCTGGTCTCCCTTC R 2 1 2 1 201000 r 74 goat snp40005-scaffold510-1954512 7 102936661 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403026 Affx-122958554 AX-123273379 7 5453766 CCCAGTCCAGAGTGAGGGACAGATGGTGAACCCCA[C/T]ATTCCCAGCCTCTGGGAGCAGTGGGAACTGGCAGC Y 2 1 2 1 202000 f 74 goat snp40004-scaffold510-1916753 7 102898707 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443014 Affx-122928172 AX-123313351 7 5508582 ACAGGAAGGAGCCCCAGACAACCTGCTCCTACAAA[C/T]ACCTTTTACCTTCATCTGTGCTTCTCAATCCCCAG Y 2 1 2 1 101000 r 74 goat snp40003-scaffold510-1861937 7 102843517 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426552 Affx-122940180 AX-123296898 7 5545484 GACATCCCCCGAAGCTGTGGTCATCACAGCACCGC[A/G]ACAGGCAGGTATCAACAGCCCAGAGGCAGACCCAC R 2 1 2 1 101000 r 74 goat snp40002-scaffold510-1825035 7 102806626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799519 Affx-122924166 AX-385286449 7 5585772 AATGAATAGCTGTTCTTTGAAGAGTTTTCAGTTTC[A/G]TTCTTAACACGACACAGAGTTTTACATTCCATCCG R 2 1 2 1 101000 f 74 goat snp40001-scaffold510-1784747 7 102766349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376239 Affx-122978784 AX-123246598 7 5626727 TTGAAAAACACCATGCTGAGAGGAGGAAGCCAGAC[A/G]CAAAACAGACAGACGGTGTATGATTCTATTTATGC R 2 1 2 1 201000 r 74 goat snp40000-scaffold510-1743792 7 102725137 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383233 Affx-122972759 AX-123253591 7 5682737 AGAACAAAGAAGGTGGGAAGGAAGACAGTGAGAGA[C/T]GGAGGAACGTAAGAGGGGTACAAAGGGGGAGACGG Y 2 1 2 1 101000 f 74 goat snp39999-scaffold510-1687782 7 102668694 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439182 Affx-122931051 AX-123309519 7 5715219 CTTGCCCTAAGGACTTGATTCATGGCAATGGAAGA[C/T]GTCCAGTGCTGTGTTATTTATCTATGAAGATGTTC Y 2 1 2 1 101000 f 74 goat snp39998-scaffold510-1655300 7 102638042 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433590 Affx-122934961 AX-123303931 7 5745404 GATGTTACCATTGGGAAAGTTGGGTGAAAGGGTGC[A/G]TGAGACCTCTGCTCTGTTGCTATGCTGCTGCTGTT R 2 1 2 1 201000 f 74 goat snp39997-scaffold510-1625115 7 102607758 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786502 Affx-122947578 AX-385273536 7 5774581 GTTTGCCTCTGTTTTGTTTGAAGGCAGCACGATTT[A/G]TCCACCCAGCCCACCCTTCGTGTGGTGTCTCTGCA R 2 1 2 1 303000 r 74 goat snp39996-scaffold510-1595938 7 102578259 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408552 Affx-122953681 AX-123278903 7 5813705 TTCATTGCCCCCTCCAGACACGGCTATCTCATCCG[C/T]GAGCGTTTCCAGTGCCCTTCGTCAAGACTCTCACA Y 2 1 2 1 101000 r 74 goat snp39995-scaffold510-1556814 7 102540300 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428827 Affx-122938375 AX-123299169 7 5844733 GGGATTTCTTAGTCAAATCGTATGCACATTTTTCA[C/T]GTTTTCTATCTTTTTCTTAGCTTCTTATACTAAAA Y 2 1 2 1 101000 f 74 goat snp39994-scaffold510-1525786 7 102510173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444806 Affx-122926334 AX-123315143 7 5881940 ACATGCATATCCTTTCAAGATTAACTAGGAGTCTG[C/T]TTTATCTCTGTGTTACAAGAAGGGGAACACTTTCC Y 2 1 2 1 102000 r 74 goat snp39993-scaffold510-1488579 7 102472791 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451475 Affx-122921138 AX-123321808 7 5939457 GGCCCCCAGGGTCTATCTCCCCCCTGATGCTTGGC[A/G]TTCTCTCCCCAAAGGTACTTGATTTTCTTCTGCCC R 2 1 2 1 101000 r 74 goat snp39992-scaffold510-1431062 7 102404233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397799 Affx-122962497 AX-123268154 7 5972982 AAGTCCTGGGGCAACCTTAGTGGCACCGTGTGGCC[A/G]AGCACAGTCCATTGTGATGGGGAAGGAATCTGGAC R 2 1 2 1 103000 r 74 goat snp39991-scaffold510-1397537 7 102370856 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450155 Affx-122922738 AX-123320490 7 6020372 TCTGATGAACTTTACACGTTCCCCAAACGGGTGCC[A/G]TTCTGTGACTCAAACTGCCTCTACCACAAGTCAGT R 2 1 2 1 101000 r 74 goat snp39990-scaffold510-1350147 7 102323428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438065 Affx-122931533 AX-123308403 7 6073589 GGTTTCTGAGGCTCAGGCTGAGGGGAGAGTGAGAC[A/G]GCTGTGTCTTCAGACGGTGGGAGTTTTTATCCAGG R 2 1 2 1 101000 r 74 goat snp39989-scaffold510-1296930 7 102270440 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414021 Affx-122949801 AX-123284370 7 6125886 TTTAAAAGGTGGGCAGTGTTTCAGTCCCACCCCTG[C/T]GCTTCCAGGGAGTGAGTCTTTAGCTTCTGAGACTG Y 2 1 2 1 101000 r 74 goat snp39988-scaffold510-1244633 7 102218371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396956 Affx-122963173 AX-123267311 7 6162669 CTTTCTAGAAGCAGTAACACAGCTCTGTGGCCTTA[C/T]CATCCTGTCTTTAAAGGAACACTGTAAGTGGTGAG Y 2 1 2 1 101000 f 74 goat snp39987-scaffold510-1207850 7 102181429 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383274 Affx-122972728 AX-123253632 7 6196793 TGTCTCCTGCACACTGGTGGCCTCACCGCTGTTTC[C/T]TCTTCTCCAAAATGGAACTGATGAGTAAGAGCCCT Y 2 1 2 1 101000 r 74 goat snp39986-scaffold510-1173726 7 102147421 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395983 Affx-122963510 AX-123266338 7 6237778 CAAATAGATCTCTGAGTCTCCAACGTGTACAGGGG[A/C]CTTGAGGCCAAACGAGACGACAGGGTCCAGAGATG M 2 1 2 1 101000 f 74 goat snp39985-scaffold510-1132741 7 102105906 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375403 Affx-122979205 AX-123245762 7 6285794 TATGAATTCAGTCATCACTGAAAAGTCGTACCTCT[A/G]CAACCAGGTGTTGCGATATCCCTGATGCCGAATGT R 2 1 2 1 101000 f 74 goat snp39984-scaffold510-1084725 7 102063117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389076 Affx-122968594 AX-123259434 7 6322008 TTATAAAGAGATCCCAGAGGGCTCCCTTGCGCTTT[A/C]TGCCATGTAAAAACCCAGTGAAAAGGCAACAGTTA M 2 1 2 1 101000 r 74 goat snp39983-scaffold510-1048511 7 102027467 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381330 Affx-122974429 AX-123251688 7 6358818 TCTGTCCTTCCACGACCAGCTTCTTCCACTCAGTG[C/T]AACAGCCTCCCGGTTCATTCCACCTGCAGCAGGTG Y 2 1 2 1 201000 r 74 goat snp39982-scaffold510-1011701 7 101990608 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448025 Affx-122923719 AX-123318361 7 6388866 TTCTGAAAATCTGGTTCTACGGGTCTAATTAGCAG[C/T]CGTATTGCTGACACTCATCTCCACGCCTGCCCTGG Y 2 1 2 1 101000 f 74 goat snp39981-scaffold510-981653 7 101960803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433758 Affx-122934495 AX-123304099 7 6460819 GAATCTTTCTTAACACAGTGCCCCCCAGGCAGCTG[C/T]TCTCAGTCCATTAGGGTTTAGCCAGAATGCACTTT Y 2 1 2 1 101000 r 74 goat snp39980-scaffold510-909700 7 101898530 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776847 Affx-122956900 AX-385263971 7 6505315 ACTATGGGCAGATTGTGTAATTCACAGAAGTGGCC[A/G]TTTCTGTGTGATGGTCAGTGGGTTCCTTGTGTGGT R 2 1 2 1 101000 f 74 goat snp39979-scaffold510-865204 7 101854121 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422709 Affx-122943646 AX-123293055 7 6541230 TTCAGGATGGCTGAAACTGGGGCTAATCTCACCCT[A/G]GTCTCTGAGTTCCTGCTCCTGGGCCTCTCAGAGGA R 2 1 2 1 101000 f 74 goat snp39978-scaffold510-829289 7 101817987 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784276 Affx-122925846 AX-385271327 7 6604970 TGTGACTGTCCCAGGAGTTTGTTGCATCTTCATGG[C/T]ATTTATCTTGCAATATCCTGAATGACGTATGCACT Y 2 1 2 1 101000 f 74 goat snp39977-scaffold510-765549 7 101746363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411863 Affx-122951213 AX-123282213 7 6658775 ACAATAGCCATGAGGTGGAAGCACCCCAAATGTTC[A/G]TCCTTGGATGAATGGTAAGCAAAACGTGGTCTATC R 2 1 2 1 201000 r 74 goat snp39976-scaffold510-711744 7 101692807 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416506 Affx-122947780 AX-123286854 7 6688694 CGTTTTCTAATTTGGGGAACTGAATAGTTATACGG[C/T]GAAATTCCATCACCCTTCCCTCTCTTCCTACCTTC Y 2 1 2 1 101000 f 74 goat snp39975-scaffold510-681825 7 101662766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383057 Affx-122973285 AX-123253415 7 6732080 TATAAGCAGACAGGGAGCATCAGATGGGTGTGGGG[A/G]CACTGATGCAGGTGGATTGTCTTGAATGGGCAAGC R 2 1 2 1 201000 r 74 goat snp39974-scaffold510-638439 7 101618442 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394915 Affx-122964317 AX-123265270 7 6767625 TTGACCCCCTTTTTCTCTCTTTTTCCTTCTGGGAA[C/T]GTCTATAGCCTGTAAAAGGAATGTTGGTATGCTTG Y 2 1 2 1 201000 r 74 goat snp39973-scaffold510-602894 7 101582635 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439925 Affx-122930010 AX-123310262 7 6809788 CAGACAACACAAAGGTGAGAGCCACATGTGGAGAA[C/T]GCTTTCCATCTGCCCTGGGCAGAAGGCACCTTCCA Y 2 1 2 1 101000 f 74 goat snp39972-scaffold510-560731 7 101540701 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438657 Affx-122930893 AX-123308994 7 6868888 AGCATCTAAGCTACTACCCTATATTGCATATGATT[A/G]TTATGTCCCTTGAATTTCATGACCCTGGCTTATTG R 2 1 2 1 101000 r 74 goat snp39971-scaffold510-501631 7 101480470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440343 Affx-122929665 AX-123310680 7 6912911 GTTGGCATGATCAGGGTGGCAGGCTCCTTGCATTG[C/T]AGCCCTCACCTGTAAGGTCCTCATCTACAGGGAAA Y 2 1 2 1 101000 r 74 goat snp39970-scaffold510-457608 7 101434796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404981 Affx-122956403 AX-123275333 7 6942553 GCTTGGAACCAGGTTGGACACACAGCAGAACTTAG[C/T]GTTGGTCAGTGGAATCCAAGTGATGGCCAGAACCA Y 2 1 2 1 101000 r 74 goat snp39969-scaffold510-427966 7 101404986 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774882 Affx-122949772 AX-385262015 7 6972097 CATACAGAATCCTGGATCAGAGCAGCCCATTTATT[A/G]CTCATGGCAAAAACAGTAACCAGAGTAGAACTGTA R 2 1 2 1 101000 r 74 goat snp39968-scaffold510-398422 7 101375323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407780 Affx-122954961 AX-123278131 7 7002675 TGATTCATGAGGTCGCAGAGTTGGACACGACTGAG[C/T]GACTAAACTGAACTGAGAACCCTAAACGAATGAGA Y 2 1 2 1 103000 r 74 goat snp39967-scaffold510-367844 7 101344715 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436288 Affx-122932527 AX-123306627 7 7064302 CCAGGGAGCCGATGTCCTGCCACGGCCAGCACAAG[C/T]GAGGAGTCGCACCTGCACAGGGAGAGAACGGAGCG Y 2 1 2 1 303000 f 74 goat snp39966-scaffold510-306217 7 101280287 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390077 Affx-122968034 AX-123260434 7 7099454 CCATTTTATCATCCTGGGTCAGTGTCAGGTCCACA[C/T]GCCCTTGCAGACAGGAGTTTACTCACCCGCTGTAT Y 2 1 2 1 101000 f 74 goat snp39965-scaffold510-271065 7 101243842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380136 Affx-122975987 AX-123250494 7 7153615 TCCTTCCCTCTGGCAGCCTAGAAGAGTGTGAATTG[G/T]GTCCTATTTGTTCCTCTCCAGATTCAGAGTTCAGA K 2 1 2 1 101000 r 74 goat snp22603-scaffold224-33971 7 101185252 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403989 Affx-122957207 AX-123274341 7 7184278 TTTCAAGTTACTATTAATAGAAGAAAACAGCCTGA[C/T]ATTTTTAGAAGAATTTCTGAGCAAAGCACAACACT Y 2 1 2 1 101000 r 74 goat snp22604-scaffold224-64634 7 101154667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431547 Affx-122936207 AX-123301888 7 7230291 TAAACAACGCCTGCGAATGCATGTGTATGTGTGCA[C/T]GTGTTTGTATATGCGATGAAAAAGTCCAGAAGAAT Y 2 1 2 1 201000 r 74 goat snp22605-scaffold224-110647 7 101108729 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399630 Affx-122961076 AX-123269985 7 7261702 AGAAGTGAGACTGGAAGAGTTCAGAGGAAAGAGCT[A/G]TGGTCTGTGTGGGGAATCAAGGGAGGTTTCCAGGA R 2 1 2 1 202000 r 74 goat snp22606-scaffold224-142058 7 101077400 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430359 Affx-122937793 AX-123300700 7 7311165 AAATAAATAAAACCTTCTCTCAGAGACCCGTACAC[A/G]AGTTTATCAGGGTCTTCACTCTTATTATCGTTACT R 2 1 2 1 101000 r 74 goat snp22607-scaffold224-191521 7 101027845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278446 Affx-1111836428 AX-519551931 7 7316400 GAGAAATGGCACTGTGTCAGGCTGAAACTAAAAGC[A/G]TGAGACAGAGAATGAAGGCAAAGGATGAGAGCTGG R 2 1 2 1 101000 f 74 goat Random2.2K-754 7 7316400 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421467 Affx-122943929 AX-123291814 7 7402318 ACCCACCGCTCAGAGTTGAGGCCGTGCCCTCCTGC[C/T]GCCTGTTGGCAGGTGACGTGTGCAGTGCTGGGGCA Y 2 1 2 1 201000 r 74 goat snp22608-scaffold224-282674 7 100936748 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379297 Affx-122976206 AX-123249656 7 7547311 CTGGGGGCTGGGGTGGGGGGAATCTTGTGGGTGAC[G/T]CTAAGGACTGAGTCAGCTACTTAAGCTTAGCCCCA K 2 1 2 1 101000 r 74 goat snp22611-scaffold224-427667 7 100792887 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385456 Affx-122971305 AX-123255814 7 7667603 AGTGACTAGTTCTAGTTTATCTGTCTCCTTGTTCA[G/T]ACTGGGGCTGCATGAGGTAACACTTGTCTGTCTTA K 2 1 2 1 201000 f 74 goat snp22613-scaffold224-547959 7 100671811 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410461 Affx-122952216 AX-123280811 7 7698784 TTCAGGGCCAGTGTCCTCCCACTGTGGTCTCTGTG[C/T]TGCCTGCTTCAGGACCACCTGGAGAGCCTGTTAAG Y 2 1 2 1 103000 f 74 goat snp22614-scaffold224-579140 7 100640708 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386504 Affx-122970753 AX-123256862 7 7758943 CCTCTGGGCTCCCACAGCTCTGCCAGTCTACACTT[A/G]CGTTCCAGCTTTTGATTCTTATTCTAGTGACTGAA R 2 1 2 1 101000 r 74 goat snp22615-scaffold224-639299 7 100591581 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434454 Affx-122934647 AX-123304795 7 7796749 TGGAAACTTTCAAAGGGGAAAAAACTCATTAAAAA[G/T]CAATATAAGCAAAATTGAATTAAATCTGTCAAATA K 2 1 2 1 303000 r 74 goat snp22616-scaffold224-677105 7 100558698 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411948 Affx-122951145 AX-123282298 7 7878339 CAAAAAGCTGGAGCATTACAAAAATTACTCTTGTA[C/T]GTAATGGGAGCTGAAATTTATTTAGGACTTGCCAC Y 2 1 2 1 101000 r 74 goat snp22618-scaffold224-758695 7 100477563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393529 Affx-122965427 AX-123263885 7 7976080 TGCATTTCTAATGGCTGTGTAGGGTTATGAAGCTG[C/T]AGATTCTGCTCTTGAGGGTCACTCTTTGAGTAACA Y 2 1 2 1 101000 f 74 goat snp22620-scaffold224-856436 7 100376975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273752 Affx-1111833819 AX-519547363 7 7996958 TCACCCTCTCTATCCACGTCTCTGCCTGCAGACTT[A/G]AGGCAACAGAGGACCATTGCTTTTTT R 2 1 2 1 102000 f 74 goat GoatD01.005893 7 7996958 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38440553 Affx-122929316 AX-123310890 7 8006436 AGACAACAGGAAGGTGTCTCCTGTTGATCCTTTAG[C/T]CAGATATAGGATTCCAAAACCACAGCTGTGTCTCA Y 2 1 2 1 201000 r 74 goat snp22621-scaffold224-886792 7 100346549 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435179 Affx-122933650 AX-123305519 7 8048850 AAGCGTAAAGACCTGTCACATTGCCTGGAGTTTGA[A/G]CTTTTAAACCAGTAGCAAAAGCAATGTTGTTAATT R 2 1 2 1 101000 f 74 goat snp22622-scaffold224-929206 7 100303196 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426104 Affx-122940638 AX-123296450 7 8085665 CTAATTTAGTGCAGTACATGGTGTGTACCGAGCTT[C/T]CATGGTGGCTCAGGTGGTAAAGAATCTGCCTGCAG Y 2 1 2 1 103000 f 74 goat snp15572-scaffold1647-534096 7 99117466 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464488362 Affx-1110511173 AX-515960676 7 8094475 AAAATGGAGGGGGGTAATAATATACACCACAATTA[A/G]TAGGTCAACTGCAATTTTTAAAATGCACAAAATTG R 2 1 2 1 201000 f 74 goat 7_8094475_AF-PAKI 7 8094475 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791718 Affx-122948298 AX-385278709 7 8143104 TTCTTTAATTGAGACGTAACTTATATAAAAGTCCG[C/T]AAGTCTCAGTGTTCACCTCAGTGAATTTTATGTGT Y 2 1 2 1 101000 r 74 goat snp15571-scaffold1647-476657 7 96459974 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796587 Affx-122933382 AX-385283533 7 8184879 TATATGTAATCTAGATCACAAAATGGAGGGTTTCC[C/T]CCTTCCACTCCTGGCCAATAGATGGTAATTATAAC Y 2 1 2 1 101000 r 74 goat snp15570-scaffold1647-434882 7 96502184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419588 Affx-122945387 AX-123289936 7 8215010 CCAAAGAAGTTCTCCTGACCTTATTAGCACTTTAG[C/T]GAGTAGATGAGGAGAGAGGCCCTCTCTTCACTCTC Y 2 1 2 1 101000 f 74 goat snp15569-scaffold1647-404751 7 96532513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379404 Affx-122976125 AX-123249762 7 8247303 CTCCTGCATTGCAGCTCCTCTTCTTTTTAGAGTTA[G/T]ATCTCTTTCCTTTCTGAGATTCATCAAGGACACAT K 2 1 2 1 201000 r 74 goat snp15568-scaffold1647-372458 7 96565059 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416884 Affx-122948079 AX-123287232 7 8290463 CAGCCTGCTCACGCTGGGCACCGTAATGGTGGGAG[C/T]ATCCATGCCTCCATCTTGAGGGTCTCTCAGTCTGA Y 2 1 2 1 101000 r 74 goat snp15567-scaffold1647-329298 7 96608644 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418652 Affx-122946330 AX-123289000 7 8330946 TGTACTTAACAGGGAAGGAACCTGAGGCCCAGAGA[A/C]GTCAGTTAAGTTGCTCAAGGTCATAGAACCAGCAA M 2 1 2 1 201000 r 74 goat snp15566-scaffold1647-288815 7 96649115 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769767 Affx-122933780 AX-385256937 7 8362484 AGATTCTACCATGCCACTCCCTCATATTTTATTCA[C/T]AGCATTTATCAACCTCTTCCAAGTGTTTTCTTTAT Y 2 1 2 1 101000 f 74 goat snp15565-scaffold1647-257277 7 96680311 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781860 Affx-122940531 AX-385268942 7 8397245 TTCCTGTGTATCTCAGTGTCTGAATACCTGAGGGC[A/G]TCTCAACCCAACTGTCGTCCTGAATTTGAGACAGG R 2 1 2 1 101000 f 74 goat snp15564-scaffold1647-222516 7 96715280 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424858 Affx-122941342 AX-123295204 7 8436689 AACCAAACAGAATGAATGCTGGAGGTGTCCTGCTA[C/T]GCGAGGCATTTATTCTTGTTAATTAAATGTGATTA Y 2 1 2 1 201000 r 74 goat snp15563-scaffold1647-183072 7 96754736 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426255 Affx-122940332 AX-123296601 7 8509377 TCTCAAGTCTGTTAGCAAAGGGCCAGGAAGAATCC[A/G]TGTGGGGAAACAGCCCCACACAGACCCTGGCCCAG R 2 1 2 1 101000 f 74 goat snp15561-scaffold1647-110384 7 96826816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395834 Affx-122964027 AX-123266189 7 8556968 ACTGGCCCTGGAGAGTAAGTGGTCCAGTCTCAGAG[C/T]AAAAGAAAGCTCTTAAAGTTTCTTTTCTACCCCTC Y 2 1 2 1 202000 r 74 goat snp15560-scaffold1647-62793 7 96874657 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433701 Affx-122934536 AX-123304042 7 8587310 GAGCAAAAACTCGGTATGGATTTCCGCAGCCGAGC[A/G]ACTATACTGCAGCTGGTGGACTTGAAGTAGGACGA R 2 1 2 1 101000 f 74 goat snp15559-scaffold1647-32451 7 96904129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389358 Affx-122968465 AX-123259716 7 8617316 GCCAGGCCTCAGAGGGGGACCTGCTTCTCTATGGG[C/T]ATAATGTTCAGCTTCCAGGATTGGGAAGGGGCAGG Y 2 1 2 1 101000 r 74 goat snp15558-scaffold1647-2445 7 96934197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446824 Affx-122925279 AX-123317160 7 8694649 TGAGTCCCCTTATCAGAATCCAAGTCCTCCCCCTC[A/G]CTATGGGAGAATGCCAGTTTGGGCCACTGAACCGC R 2 1 2 1 201000 r 74 goat snp36377-scaffold437-74789 7 97007886 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416303 Affx-122947929 AX-123286652 7 8735725 CATCTTAGTAACTGAACAACAACAAAAACAACTAT[G/T]CAGTCAGCTAATACATACTGTGTGCCAGCCCCTGC K 2 1 2 1 101000 r 74 goat snp36378-scaffold437-115865 7 97048774 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403992 Affx-122957204 AX-123274344 7 8786564 CCACTCCAGTATGCTTGCCTGGAGAATCCCATGCA[C/T]ACCTGAGTTGTTTGCGTTTTGAGAAGTTTCATGAC Y 2 1 2 1 101000 r 74 goat snp36379-scaffold437-166704 7 97099681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278447 Affx-1111836429 AX-519551932 7 8795111 GAAGGCCTACAACGGAGGCAAATTCAACATGCTGC[A/G]TGGTTGCTAGGGGGATCGAGCAAGGGGCTAGTGGA R 2 1 2 1 101000 f 74 goat Random2.2K-755 7 8795111 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320770692 Affx-122948912 AX-385257856 7 8821306 TGATGTGAAATTGCTAGCTTTGTGGGATGGAGGGC[A/G]ACAGAGAGTTTTTGCTCTGTTTAATGACTCTGCAG R 2 1 2 1 101000 f 74 goat snp36380-scaffold437-201446 7 97134845 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278620 Affx-1111836430 AX-519552099 7 8835808 TTTGACATTGATTCTTTTGGTAGTAGAGAGGTAAA[A/G]TAAACTTAGGATTCTACATGAAAGCGAAATCTGAT R 2 1 2 1 101000 r 74 goat Random2.2K-756 7 8835808 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391093 Affx-122966825 AX-123261450 7 8853120 TGTGCAAAGAAACCTGCTTCACATCATCAAATAGA[C/T]GGGAGGAGACAGAGTCTTACAGATGTCACGTGATT Y 2 1 2 1 101000 f 74 goat snp36381-scaffold437-233260 7 97166371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388785 Affx-122968926 AX-123259143 7 8895212 CAAAAGCCCAAGTCCTCCCCACAGCCCTGCACACT[A/C]TATCTTTCTTGTCCCCTCCCTGCCTCACCTCCTCT M 2 1 2 1 201000 r 74 goat snp36382-scaffold437-275352 7 97208706 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439737 Affx-122930540 AX-123310074 7 8955865 AGGGCCCTTATGGATGAATTTTAGGCACCTGGCCA[C/T]AGTCAGGAAGTGTGGGGAAGCTGAGAAATATCTGT Y 2 1 2 1 102000 r 74 goat snp36383-scaffold437-336005 7 97269673 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382227 Affx-122973968 AX-123252585 7 8995749 GAACTCTGCCTCTAGTGGGTTTGACAGTAAAGTTC[C/T]GTGGTGCAGGGTGTGGGTTGGGGAGGAGTGAATAA Y 2 1 2 1 101000 f 74 goat snp36384-scaffold437-375889 7 97309857 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770011 Affx-122946743 AX-385257178 7 9088760 GTGAGCAAGAACAATGTAGGGAGGCTCAGTCTTCA[A/G]ATATTTTTTCAGGACTGGAAACCCAGACGACTCAC R 2 1 2 1 201000 r 74 goat snp36386-scaffold437-468900 7 97404023 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413815 Affx-122949895 AX-123284164 7 9121848 CCCCTCCCAGGGATCATATCACTCTGTTCATTACC[A/G]TTAGGTATTTTCTCTTCCATTATTAGACTGCCAGC R 2 1 2 1 101000 r 74 goat snp36387-scaffold437-501988 7 97436729 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392659 Affx-122966437 AX-123263016 7 9173836 TCTCATACTATTATTGTAATGGCTCTATAAGTTTC[G/T]TTTCCTTAGAACCTACCTAACAATTCTGCTATTTG K 2 1 2 1 101000 r 74 goat snp36388-scaffold437-553976 7 97488676 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410708 Affx-122952726 AX-123281058 7 9203040 AGGCAACCTGTAAAGGCTTACCCACAGGCACAGAA[C/T]GGAGAATTTATGTAAAGATGTATCACCTTGTCTAG Y 2 1 2 1 101000 f 74 goat snp36389-scaffold437-583180 7 97518222 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799351 Affx-122963847 AX-385286281 7 9259315 TGTGTGAGTTGGGCTCTTTTGGTAGAGGCTTTCAG[A/G]TTTGAGTGGTCTGTTATGAGGGCCAGCCCTAGTGC R 2 1 2 1 101000 f 74 goat snp36390-scaffold437-639455 7 97574499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445461 Affx-122925219 AX-123315798 7 9300871 CCAACCTCAGGGGGTTGTAAAATATATAGAGCATC[A/G]TTATAACAGTGAGGAGGAGGAGACTATGTTACCAG R 2 1 2 1 101000 f 74 goat snp36391-scaffold437-681011 7 97616042 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395890 Affx-122963619 AX-123266245 7 9331929 AGACAAAAGTCTCCACCCTCGTCGGGGAGACAGAC[A/G]TGACCAGTAAACGCTGATAAATAATAAACTGCTCA R 2 1 2 1 101000 r 74 goat snp36392-scaffold437-712069 7 97647083 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403434 Affx-122957740 AX-123273787 7 9368872 TTTTACAGAGCTGGGAAAGGGAAGGCTAGGATTCA[A/G]ACCCAGACTTGGCAAGTTCCAGAGCCTGAGTTCTT R 2 1 2 1 101000 f 74 goat snp36393-scaffold437-749012 7 97683946 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411532 Affx-122951660 AX-123281882 7 9440969 CAAGTAAAGAGAGCAGGAGGTGCCCCCAAATCGAG[C/T]GAAAGAATCAGGGGTGAGGCTGAGACTCGGAACAG Y 2 1 2 1 201000 f 74 goat snp36395-scaffold437-821109 7 97755919 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403672 Affx-122957506 AX-123274024 7 9492895 ATCAGCCCTCTACCTCCGGAGGCGTAGGGGCTTCG[A/G]GCAATAACCCGCAGGAAGGCGCAGTGACTCAGGCC R 2 1 2 1 102000 f 74 goat snp36396-scaffold437-873035 7 97808091 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430446 Affx-122937729 AX-123300787 7 9562781 CTTTGTCGTGGTGGCACTCTGCTTTGGAGAGAGCC[C/T]GTGGGACTTCCTCCCACACCCTGGGGAAGGGCAGC Y 2 1 2 1 101000 f 74 goat snp36397-scaffold437-942921 7 97878054 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389948 Affx-122968085 AX-123260305 7 9636804 ATTCCCCAGCCTGGGCACACTTGGCACACAGCTGG[C/T]AAGGCTCAGGTCGGCAGAGGGGACAATTAGGACCC Y 2 1 2 1 201000 f 74 goat snp36398-scaffold437-1016944 7 97949501 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386361 Affx-122970856 AX-123256719 7 9682106 GCAGCATCTTCTTCCTCCTCCTCTTCCTTCTCATC[G/T]TCATCCTCCTCATCCTCATCCTTGTCCTCGTCATC K 2 1 2 1 103000 r 74 goat snp36399-scaffold437-1062246 7 97992918 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764797 Affx-986697037 AX-385252405 7 9728133 TGGAGCTGGGAGATCAATGAATGCGTTGTTTACTA[A/T]TTTTATTAGTGGGTGAGTTTTTCGGATGTTGGTCA W 4 1 2 1 600010 r 74 goat 7_9728133 7 9728133 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320762509 Affx-986697039 AX-385250626 7 9728287 TACATTGTATTTATTTTAAGTGTTATTTTTGTGAT[A/G]GGTTTTGTGGGGTTTTCTTCAAAACCTTCACCTAT R 2 1 2 1 600010 f 74 goat 7_9728287 7 9728287 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 38440909 Affx-122929216 AX-123311246 7 9729962 CCCCACCCTTTCGCCTCGCCTTCCAGAGCCAAACA[C/T]GCCTGTTAGTCCTTATCCTAAATCAAGGAGATATC Y 2 1 2 1 101000 r 74 goat snp36400-scaffold437-1110102 7 98040330 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414255 Affx-122949620 AX-123284604 7 9777784 ATTGGTGCGATCATGGAAGTGAGGGCTGGTCTATA[C/T]CCTAGAGCATCTCACAACTTGGAATATTCGGATGC Y 2 1 2 1 101000 f 74 goat snp36401-scaffold437-1157924 7 98086659 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377169 Affx-122978210 AX-123247528 7 9825665 GGGTGTAGCCTTTAGCCCCGTTCTGGTCACCCACC[A/G]CCCCTTCTATTAGACACAGCCCGCAGTCAGAGGAT R 2 1 2 1 101000 r 74 goat snp36402-scaffold437-1205805 7 98133949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391511 Affx-122966668 AX-123261868 7 9867368 CAACGAAGTTTCAGCTTCTCAACCTTTTCCCCCTG[C/T]CCAGGGCTGCAGACCCTGACTGGCCTCGATCTGCA Y 2 1 2 1 201000 r 74 goat snp36403-scaffold437-1247508 7 98175840 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407908 Affx-122954389 AX-123278259 7 9916386 CTGCAGCCCACATAGAGACCAGTGTTTGGATGCTT[A/C]GGCCCCTGATTGTCAGATGTGCCTCCAGAAGGTAT M 2 1 2 1 101000 f 74 goat snp36404-scaffold437-1296526 7 98224644 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418539 Affx-122946407 AX-123288887 7 9946879 TAAATTTAAATCTAAAATAACCAAACTCACAAACA[A/G]TGTAAAGCTGCTTCATTTAAGTATGCAGGTGATGT R 2 1 2 1 101000 r 74 goat snp36405-scaffold437-1327019 7 98255427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425249 Affx-122940992 AX-123295595 7 9982011 ACTCAGAACTCCGACTGTCACAAACTTTCTCAATG[C/T]AGACAAATTACATTCTCGGCACAGCTACACTGTGA Y 2 1 2 1 101000 r 74 goat snp36406-scaffold437-1362151 7 98290793 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443633 Affx-122927290 AX-123313970 7 10068020 AACGGTACGATTCCAAGTATATGAGTGCCTTCAAG[C/T]ACTTCCCCTTGAAGGCGCCACGGGGGCCTTAGCCT Y 2 1 2 1 103000 f 74 goat snp36408-scaffold437-1448160 7 98379218 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443825 Affx-122927065 AX-123314162 7 10104102 GGCTTCGGGGAAGGGGATGCAGAACAGGGAGGAAG[A/G]GAGATGGGGTGATGGCTGCCCAGGAGTCAAGGAGA R 2 1 2 1 101000 f 74 goat snp36409-scaffold437-1484242 7 98416415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446557 Affx-122924844 AX-123316893 7 10152989 AAAATATCTCAGTGGATCAGTGGAATCAGTGGAAA[C/T]GGGAAGACCTAGAATCATGTCTGGAGGGCAAAGGT Y 2 1 2 1 101000 f 74 goat snp36410-scaffold437-1533129 7 98465370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446392 Affx-122925580 AX-123316728 7 10191342 CTCAGGGACCAGCAGGAATCTTCTGGGGATCCAGT[A/G]CCTGGGAAAGTGTTGATTTTCTGAGACTGAATGTT R 2 1 2 1 101000 r 74 goat snp36411-scaffold437-1571482 7 98505186 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376847 Affx-122977905 AX-123247206 7 10220115 CTGTGCCAGGGTGATCCTCTGTAGGTACGTGATCC[A/G]CAGTGGCCCGCATGCGCCTGCCTCATCCAGGGGCT R 2 1 2 1 101000 f 74 goat snp36412-scaffold437-1600255 7 98533846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386057 Affx-122971466 AX-123256415 7 10261617 GCACCAGATTTCAACTTGGTTCAGCTCAGTTCTGA[C/T]ACTATCTCTGCAGAGGTAGCATCAGGTTACCTGGG Y 2 1 2 1 201000 r 74 goat snp24505-scaffold2480-37460 7 98574280 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423357 Affx-122943150 AX-123293703 7 10293357 TGGGGGCAAAAGGGGGCCAATGAGGGGCTGCTGGC[A/G]TGACTCAGGGAAGCATAATTTGATTCATAGTGATG R 2 1 2 1 101000 r 74 goat snp24506-scaffold2480-69200 7 98606198 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427904 Affx-122939681 AX-123298247 7 10329359 GGGTCAACAAATGATGGAAGTTGATATCAGAATGA[C/T]GAACAAGACAAATCTCTCCCAGAGCTCTGATTTTT Y 2 1 2 1 101000 f 74 goat snp24507-scaffold2480-105202 7 98643074 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433033 Affx-122935769 AX-123303374 7 10392722 ATAATTGTTGCCATCACTCCCCCAGATGGTCTCCA[C/T]GTCTCTTCATTGGTCTCCCTAATTCCAGTCCAGCC Y 2 1 2 1 201000 r 74 goat snp52408-scaffold780-1254936 7 98862720 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429452 Affx-122938493 AX-123299794 7 10454373 CACAATCCAGTGAGTGCCAAGTGCAGTGGGAGACA[C/T]GAATGCAGGAGGGATTGAGTTGAGTCGGGGGGGAG Y 2 1 2 1 201000 r 74 goat snp52407-scaffold780-1193285 7 98924279 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406192 Affx-122956143 AX-123276544 7 10513687 TTGGAAACATCTGTTTGATTTCTGGTTTCCATATT[A/G]TTGATGAATCTGAAGGAAAAATGGAGTGAAAATAA R 2 1 2 1 101000 f 74 goat snp52406-scaffold780-1133971 7 98983676 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435960 Affx-122933527 AX-123306299 7 10552134 CATTTAGAGAGGGAGCTGTGTCCTCTCTAATTGAG[C/T]AGAAATCAAAGGTTTGTTGAACTCAGACACTGAAT Y 2 1 2 1 101000 r 74 goat snp52405-scaffold780-1095524 7 99023056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437812 Affx-122932116 AX-123308150 7 10582935 CTCCAAGGAAGGATGTAGCAGCCTCAGTGGTTTAC[A/G]CTGTGGTCACCCCCATGCTAAACCCCTTCATCTAT R 2 1 2 1 201000 f 74 goat snp52404-scaffold780-1064723 7 99055983 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273250 Affx-1111833527 AX-519546902 7 10600022 TTAGAGTAAATGTTTGACTGGTAGGGCTGAAATGT[A/G]ACTTCCAGTTCTTTGATATCCCGCTTGTTAATTCA R 2 1 2 1 101000 f 74 goat 7_10600022_AF-PAKI 7 10600022 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38407670 Affx-122954597 AX-123278021 7 10621827 AAGAGTTTTAAAAAATGTGGTTTTGGTTCACTTGT[A/G]TGTGTGTAGTGGATAAAGTGGGATGATTGTGAATA R 2 1 2 1 101000 r 74 goat snp52403-scaffold780-1025831 NW_017189632.1 15427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395795 Affx-122963655 AX-123266150 7 10653866 TAGATCAATGATTGAGTTCTGGGTCTTTCACCCTC[G/T]ATTAATGAAATGTCTGTAAATCTCCCCACCTCTCT K 2 1 2 1 101000 f 74 goat snp52402-scaffold780-993792 7 94010427 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452429 Affx-122920581 AX-123322762 7 10706079 TAATTTTAATGAATCTTCACTTGGGGTCACAAGAA[G/T]CAGACATGATTTAGCAACTAAACCACCGCCAAACC K 2 1 2 1 303000 f 74 goat snp52401-scaffold780-941579 7 94067051 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789807 Affx-122959073 AX-385276814 7 10747951 GCAAGAGATGTAAGTGGATAGATGAGGGAGCCCTG[C/T]ACTGAGGATTAAGTGGGCTATAATTTTATTGTCAA Y 2 1 2 1 101000 f 74 goat snp52400-scaffold780-899707 7 94109059 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800198 Affx-122936427 AX-385287121 7 10805142 GTCTTAGGTCCTCTTCTTTCTAGCCACACTCACTC[A/G]TGATTGATATGGAACCAATAACACAATCCTAAGCA R 2 1 2 1 102000 f 74 goat snp52399-scaffold780-842516 7 94167054 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396129 Affx-122963403 AX-123266484 7 10988091 CAGAGGTGGCCAAACCTGCTCCTGTGGGAGGAAGC[C/T]TCCCTCCCTGTCTCCCCATCTCTAATTAATGGCCT Y 2 1 2 1 101000 r 74 goat snp52395-scaffold780-659567 7 94350712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388147 Affx-122969463 AX-123258505 7 11032593 TGGGTGCCTGGGAACATGTGGTTTGGAGGTCTTCC[A/G]CTCAGTTGGGATTTACAAGTAGGAGTTTTCTCTTG R 2 1 2 1 101000 r 74 goat snp52394-scaffold780-615065 7 94393288 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449514 Affx-122922613 AX-123319849 7 11078259 CACTGTCACACACAGAAGTACCACATCCTGGCAGA[C/T]GCTAGATACACAGATGGACACGCAACCCCACACAC Y 2 1 2 1 101000 r 74 goat snp52393-scaffold780-569399 7 94439034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392631 Affx-122966458 AX-123262988 7 11108368 CTCGAGTTCCATACTTTTGGCATCTTGTTCTGGCA[C/T]AGTTACCTTGCGTTTGTGTGTGCTAAGTCTCTTCA Y 2 1 2 1 101000 f 74 goat snp52392-scaffold780-539290 7 94469295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382843 Affx-122973539 AX-123253201 7 11161278 AGCAGCAGCGTCCTGGATTTTAGCTCATCTGCCCA[C/T]GTGCCTAACCACTGGACAGCACTTTCCCTGCCTCT Y 2 1 2 1 101000 f 74 goat snp52391-scaffold780-486380 7 94521926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381964 Affx-122974106 AX-123252322 7 11210950 AACATGGTGGCCATGAGCTTCACATGCATGCCATG[A/C]GGGCCAAAGCTGTTGAGCACCAGGAGGGGCGGGTG M 2 1 2 1 101000 f 74 goat snp52390-scaffold780-436708 7 94571118 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396104 Affx-122963419 AX-123266459 7 11248048 TTGTTCCTAACTCTTACTTCCCTGAGTTCTAATGA[A/G]GTTAAACTTACATATTTTAAAATTCACCAAAAACT R 2 1 2 1 101000 f 74 goat snp52389-scaffold780-399610 7 94608030 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447184 Affx-122925003 AX-123317520 7 11290911 CGGCGGCATTTTGGGTGTTACTTTTAAAAGTGCAT[A/G]CTCTATCTAAAGTGAAAAAAAGAAAAAAGAAAAAC R 2 1 2 1 101000 f 74 goat snp52388-scaffold780-356747 7 94651324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425192 Affx-122941039 AX-123295538 7 11322477 TCCCACTCCCTCCATGCCAGCCCCACTGCCCCCTC[G/T]ACCTACTTAGCTCCTACCTATCACACAGCTGAGGT K 2 1 2 1 101000 r 74 goat snp52387-scaffold780-325181 7 94682718 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390648 Affx-122967143 AX-123261005 7 11359628 TTCAGTGAGGACTAATAGAATGTCAAATAGTGATC[A/G]TGCTACAGAGAAAAATAAAGTGGAACTTCCTGGTG R 2 1 2 1 201000 f 74 goat snp52386-scaffold780-288030 7 94719906 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414844 Affx-122949187 AX-123285193 7 11413741 GTGGCGATACAAGTAGGAGGTAGGAAGTCAGGAAA[C/T]ACCTGGAGTAACAGGCAAATTTGGCCTTGGAATAT Y 2 1 2 1 201000 f 74 goat snp52385-scaffold780-233917 7 94773358 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445959 Affx-122925900 AX-123316296 7 11514736 ATCTACCATGCTTTTGTGGCTCCCCGATAACAAAT[A/G]CTGGCTATTTTTTTCCTCTGATTATGAAATAACTT R 2 1 2 1 201000 r 74 goat snp52383-scaffold780-132922 7 94874347 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413173 Affx-122950340 AX-123283522 7 11553563 AGGATTCCTATTTACTGATAAGGAAACTGAGGCTC[A/G]AATGAATCCATCTGCTGATCACTAGAGGCAGAATT R 2 1 2 1 101000 r 74 goat snp52382-scaffold780-94095 7 94913469 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444232 Affx-122927232 AX-123314569 7 11582875 TGGGTCTCATCTGTATTAGCAAAGCTGGTCATTGG[C/T]ATGGAGACCCCTCCCCTGGCTTGAGTCTGCTGGGA Y 2 1 2 1 101000 f 74 goat snp52381-scaffold780-64783 7 94942349 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434554 Affx-122934134 AX-123304895 7 11625619 GTACCATTTGACAGAGGAGGCAAACAGAGGTCACA[C/T]GCTCAGACCGCATAGCTGATGAGGGAAGGAGCTCT Y 2 1 2 1 201000 r 74 goat snp52380-scaffold780-22039 7 94984417 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449434 Affx-122922678 AX-123319769 7 11689087 TTTCACAGGCACCTTATCAGCAAAATTGAACAGTT[A/C]TATAAACATAGTTGGCGATTTGATCTCTGGTTCCT M 2 1 2 1 101000 f 74 goat snp19195-scaffold1931-41330 7 95048654 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395407 Affx-122963954 AX-123265762 7 11735494 CCAGTGAGGGTGTCCACAACCTGTCCCATTGTCCC[A/G]TTGCCATCTGAACTCAGCCTCCTTACCTGTACGAT R 2 1 2 1 101000 r 74 goat snp19196-scaffold1931-87737 7 95095503 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399811 Affx-122960276 AX-123270166 7 11768363 CGGCCTCCCTCCTGCCTGCTTATCCCGCGTGCCCC[A/G]CCTCCTCTCTTTTCCTGTTCTATGCTTTCCATCTT R 2 1 2 1 101000 r 74 goat snp19197-scaffold1931-120606 7 95128429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791655 Affx-122939116 AX-385278646 7 11873897 AAAGGTTCACCCAGCTTCCCGCAACTGATAACATT[G/T]CATACTGTCCTTATTGTTCCATTGCTAACTGGAGT K 2 1 2 1 201000 r 74 goat snp19199-scaffold1931-226140 7 95233498 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392248 Affx-122967566 AX-123262605 7 11973151 CTAAATGTTGTCCTGCTGCCAAGAGCTTTTGGGAA[C/T]GAAGCAACTTATACTCTAGTTTAAAAAAAAATTTT Y 2 1 2 1 101000 f 74 goat snp19201-scaffold1931-325394 7 95332783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423901 Affx-122942284 AX-123294247 7 12007804 GAGCAAGGCTGGAAGGCTCGCAGCCCTGGTGCGTA[G/T]CGGGTGGGGGTGAGGTACTCTCCAGGGGATTTCTG K 2 1 2 1 201000 f 74 goat snp19202-scaffold1931-360047 7 95367504 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425475 Affx-122941496 AX-123295821 7 12049404 ACTGGGGAGCATTTTAAAATAAAAGGGATCGGGCC[C/T]CTTTTCCAAGTGTTTTATTTTTTCTTCCAGCTTTA Y 2 1 2 1 201000 r 74 goat snp19203-scaffold1931-401647 7 95409137 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401357 Affx-122959247 AX-123271710 7 12207159 ACAGCCTGCGTATGTATGTGCGTTAGTTGATCAGT[C/T]GTGTCCGACTCTTTGGGATCCCACGGACTGTGGCT Y 2 1 2 1 103000 f 74 goat snp19206-scaffold1931-559402 7 95567946 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438072 Affx-122931529 AX-123308410 7 12242012 GCCCAGAGCAGCCCCCAGTTTCCAGAATTCTATTC[C/T]GGATCGGGAATGCAGTGGGTCAGCTGTAACAGTGG Y 2 1 2 1 201000 r 74 goat snp19207-scaffold1931-594255 7 95600491 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278624 Affx-1111836432 AX-519552102 7 12284593 ACATTAGACCTTCTGAATCGAATGAAATGGTTCTA[A/T]AAGATGGCTGAATGTACTCTAACATTTAATTTGTA W 4 1 2 1 101000 r 74 goat Random2.2K-761 7 12284593 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381259 Affx-122974487 AX-123251617 7 12314961 TCTGAGGAGTGGGGACATGGTCTGTGTTTTTCACC[A/G]TATGGCAACCAATACCTAAAGCCATGCCAGGCACA R 2 1 2 1 101000 r 74 goat snp19208-scaffold1931-667204 7 95670649 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440717 Affx-122929894 AX-123311054 7 12403781 ACACTTAGAGGTGCCAGAACACATGGAAAGGATTC[A/G]GGAGTTCCACACCCCTCCCACGCCTTGCTCTGTAT R 2 1 2 1 101000 f 74 goat snp23249-scaffold2321-637241 7 95757426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794364 Affx-122926831 AX-385281328 7 12453735 GAGGACTACCATACACTGGTAAATAAACTAAGCAT[A/G]TTACAGCTCATTGTGGACTTATAATCTAATATTGT R 2 1 2 1 101000 f 74 goat snp23248-scaffold2321-587287 7 95807407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410661 Affx-122952764 AX-123281011 7 12516044 GATGTGTCCCCCTTGCTCCCCTCTGTGACTTCCAC[C/T]TACTTCTCATGGCCAGCAGAGCATGGGTTTTGGGG Y 2 1 2 1 101000 r 74 goat snp23247-scaffold2321-524978 7 95870624 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442895 Affx-122927648 AX-123313232 7 12609984 TTGCGTTCTGGAATCTTCTCCTCTTCCCCTTCCTC[A/G]TCCACCTCCCCCTGGTGGGGATGTAGCTGTGTTAA R 2 1 2 1 103000 f 74 goat snp23245-scaffold2321-431038 7 95965426 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405532 Affx-122955982 AX-123275884 7 12654744 GATGAACACATTGTTTAATTACCATGAGAAAACAC[G/T]TTCACCAGGTTGCTATTCTTGAAAGGAGCTGATAC K 2 1 2 1 201000 f 74 goat snp23244-scaffold2321-386278 7 96010310 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430785 Affx-122937476 AX-123301126 7 12699429 CTGTAGCTTGCTGTCACTCTTGACCTTCCAATGAC[A/G]TAGGCAGAACAGAATAATTCCTATTGCTGTTTGTA R 2 1 2 1 201000 r 74 goat snp23243-scaffold2321-341593 7 96054851 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403997 Affx-122957200 AX-123274349 7 12789506 CCGAGTTTCTGGCTGGTCATCTTATGAAACAGGCC[A/G]CGTAAATTCTGTCCTCTGTCCTCTGTCTGCCGGCT R 2 1 2 1 201000 f 74 goat snp23241-scaffold2321-251516 7 96144539 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376207 Affx-122978810 AX-123246566 7 12839648 CGACATTTTTTTTAACATGAGGTTTTCTACTTGAA[C/T]GCTGCTGAACGCAACACTTCGAGAACCACCTCGAA Y 2 1 2 1 101000 f 74 goat snp23240-scaffold2321-201374 7 96194598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428822 Affx-122938380 AX-123299164 7 12935219 CAGCAACAGAGACAGGTGGGAGAAAGAGACAGAGA[C/T]GAGTGGCCAAAGATATGGAAGGAAAGAGAATCCAG Y 2 1 2 1 101000 r 74 goat snp23238-scaffold2321-105803 7 96287405 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438032 Affx-122931558 AX-123308370 7 13032718 AGTTAGTTTCCCCCACCCAGGGGATTTGGTAACTG[C/T]GAACCAGCTCCAAGCATATGACACAGTATTATCTG Y 2 1 2 1 101000 r 74 goat snp23237-scaffold2321-8304 NW_017189666.1 6645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419107 Affx-122945773 AX-123289455 7 13051998 GTGAGCTGAGCTTGGGGTCTGAGGAGGATGGATGA[A/G]CATGTGAACACAGGGCTCCAGCCCTCCATGAGTTG R 2 1 2 1 201000 f 74 goat snp514-scaffold1013-1040227 7 93896860 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376359 Affx-122978323 AX-123246718 7 13084506 AGGGTTGTTGAGAGGATGTGAGAAGGTGGAGTGTG[C/T]AAATGCATCTATGCTGCTGCTGCTGCTGCCAAGTC Y 2 1 2 1 101000 f 74 goat snp513-scaffold1013-1007719 7 93864466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273255 Affx-1111833529 AX-519546906 7 13104625 ACATCCATCACGCAAGGGCTCTAGAAATATGAATG[A/G]CAGTTCTTTCACTTTTCCATATGGTAGAGACATTT R 2 1 2 1 101000 f 74 goat 7_13104625_AF-PAKI 7 13104625 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781853 Affx-122966881 AX-385268935 7 13117051 ATCCCCCTATTGGAAAATAACTTTGCAATGACCCA[C/T]CCACTTTTTTTCAGGTACAACTTCCTTGACCCTGC Y 2 1 2 1 101000 f 74 goat snp512-scaffold1013-975174 7 93832098 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420115 Affx-122945084 AX-123290463 7 13172444 ACCCCCTGAGTCCTGTCCGTCTGATCACAGGCACT[A/C]TGTTCCAGGTTGAGCAAGAACCTCTCACTGAGATG M 2 1 2 1 101000 r 74 goat snp511-scaffold1013-919781 7 93776704 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412275 Affx-122950885 AX-123282624 7 13211587 TACATTCTTTCTAGTCCAAATCCTATTCCTCTGGA[A/G]GCAGAAAAGGCTTTCTCTCCGGTTTGCTCGATAAC R 2 1 2 1 201000 f 74 goat snp510-scaffold1013-880638 7 93739114 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453248 Affx-122920411 AX-123323581 7 13306120 ATAATCTGGAGAGCTTAGCGGAGAGTCTGAGATGC[A/G]CCTATGATCACTGAGAGTGTGCTGGGATTGATTAG R 2 1 2 1 201000 r 74 goat snp509-scaffold1013-786105 7 93643989 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408423 Affx-122954463 AX-123278774 7 13351088 CTAATATGTGCAGATACTACATACCCACACAGTTG[C/T]GCATTCACACACTTATATATACTCACACACAGGAA Y 2 1 2 1 101000 f 74 goat snp508-scaffold1013-741137 7 93599611 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437827 Affx-122932104 AX-123308165 7 13412217 TCTGTGAAGCAAGTGCATTGAAAATCCCCATTTTG[C/T]TGCAGCAAGGGGGAACCCTTCCAGGTCCCAAAAGA Y 2 1 2 1 101000 f 74 goat snp507-scaffold1013-680008 7 93538452 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404347 Affx-122956826 AX-123274699 7 13445528 AGCAATACCCACCTCGCAGCCCAGCTTCATAAGGC[A/G]CACAAAGTGCTTAGCCTGGTGACTACGGACCCTTA R 2 1 2 1 101000 r 74 goat snp506-scaffold1013-646697 7 93507251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403248 Affx-122957882 AX-123273601 7 13487007 GGTTCTAGGTGGTATCTTTTTGCCATGTCCTCACA[C/T]GGGGGAAGGAGTCAGGGGTCTGAAGGGTCTCTTAT Y 2 1 2 1 101000 f 74 goat snp505-scaffold1013-605218 7 93465818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404710 Affx-122957257 AX-123275062 7 13548707 TGGCCAAGAAAGATCCTTCAGTAGGCTGGAGGAGG[A/G]GGTGTGACAACCCCACTCAGATCTGACAACCCCAG R 2 1 2 1 101000 r 74 goat snp504-scaffold1013-543518 7 93403689 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275503 Affx-1111834843 AX-519549075 7 13574411 GTCCTGATGACTGAAGAAAATGTCTAGGCTTACAT[A/G]AGAGACGTGAAAACCATTGGCAGATAAGTAGGTGT R 2 1 2 1 101000 r 74 goat GoatD01.056206 7 13574411 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38399902 Affx-122960204 AX-123270257 7 13588780 ACAAAATAGATCTAAGTGTTCCTAACTGCCTAAAA[C/T]ATTCTCTATTTAAACAGTCTCAGACTGAGGTTCTT Y 2 1 2 1 101000 f 74 goat snp503-scaffold1013-503445 7 93363803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476230 Affx-1251763736 AX-586011654 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 4 1 4 1 20000 f 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 539476484 Affx-1251763736 AX-586011883 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 4 1 4 1 20000 r 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 562165447 Affx-1251763736 AX-606940858 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 8 1 4 1 20100 f 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 562165501 Affx-1251763736 AX-606940912 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 8 1 4 1 20100 f 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 562165709 Affx-1251763736 AX-606941118 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 8 1 4 1 20100 r 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 562165971 Affx-1251763736 AX-606941380 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 8 1 4 1 20100 f 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 562166047 Affx-1251763736 AX-606941456 7 13621055 GCAGGGTCAGAATTATAACCCAGCCCTAGGTGTCT[-/TCCAAATCCTTACTCTTTTTTTTTTTTTTAATTTTTTTATGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCC]CCAAATCCTTACTCTTTTGAGCACACTCAGCTGCC - 8 1 4 1 20100 r 74 goat SV_166 7 13621055 - deletion junction SV-TF-chip 320803174 Affx-122968779 AX-385290036 7 13657749 AATAAAAACAGTGTAGAATCACATTCAAAATAGAT[A/G]TTGTTAGTGATAGAAACTTGGGCTGCTCTGGTGGC R 2 1 2 1 101000 r 74 goat snp502-scaffold1013-434476 7 93294681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390072 Affx-122968404 AX-123260429 7 13762230 GGGAACGATTTTGAGGAATTTAATGCATTCACCAC[A/C]ACCTCTATCTCAGTCCAAAACATTTTCATCACCTC M 2 1 2 1 201000 f 74 goat snp500-scaffold1013-329995 7 93190250 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424671 Affx-122942147 AX-123295017 7 13809868 CATTTTAAGTTTTTCAGACATCTTTATTTGGGACC[A/G]TTTTGATGCTGGGTATAGAATTTTGTCTTGACATG R 2 1 2 1 101000 f 74 goat snp499-scaffold1013-282357 7 93142056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385383 Affx-122971623 AX-123255741 7 13847191 CACCACAAAATATCATTCCAATTATAAATATTCAT[A/G]TTAGAGGAAAACACCATGGAATGAACTCATGTTCA R 2 1 2 1 101000 f 74 goat snp498-scaffold1013-245034 7 93106618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795070 Affx-122949989 AX-385282029 7 13917706 TTTTATACAATGAAAATAACATTTGATGGATACAG[C/T]GACTCCCTTTGACTCTCCAACCCTAGATTCTATTT Y 2 1 2 1 201000 f 74 goat snp497-scaffold1013-174519 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795945 Affx-122955319 AX-385282897 7 13978739 TAGGAATCTATCCAGGGGATATTGCAATCAGTGTA[A/G]TTTATAAATACAGGGACATAGGATATATAAATTTA R 2 1 2 1 101000 f 74 goat snp496-scaffold1013-113486 7 93051758 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421383 Affx-122944036 AX-123291730 7 14012766 GTTAGAGTGTGTTATTCCCCATATTTCATTTGACT[A/G]TTACTTTTCTTTCTCAGAGGATGCCAATAATGAGA R 2 1 2 1 101000 r 74 goat snp495-scaffold1013-79459 7 93017205 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389475 Affx-122968328 AX-123259833 7 14058559 TCTTTTCCCAGCACCTATTAATATTTGAAACCATA[C/T]TGATTTTTTGTTGTTGTTGTTTTACTTATCGTGTA Y 2 1 2 1 102000 f 74 goat snp494-scaffold1013-33666 7 92962595 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783608 Affx-122958395 AX-385270667 7 14089168 CTGATTTTTATGGAGATATGTGATGTCATCTCTGA[C/T]GTTTCTGGTGTATTTGTAGCAGTTAGCTATTGCTG Y 2 1 2 1 201000 f 74 goat snp493-scaffold1013-3057 7 92931457 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381359 Affx-122974407 AX-123251717 7 14093792 ATGAGGATTATATTTCCTCCCCTTGAATCTGAGCA[C/T]GCATGTGACTGTGGTGGTGGTGACACTAGGTCATA Y 2 1 2 1 303000 r 74 goat snp4921-scaffold1166-1468 7 92918718 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407338 Affx-122955292 AX-123277689 7 14122726 CAACTCGGAGTTTCCTATTGCTTTCCTCTAGCTCT[A/G]CCTCTCATAACTCAAATCCATCCCAAACCAGAGTA R 2 1 2 1 101000 r 74 goat snp4922-scaffold1166-30402 7 92889387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398458 Affx-122961593 AX-123268813 7 14178357 ACACAGAGATTAAACCCAGGTCTCCTGCACTGCAC[A/G]TGGATTTTTTTTACCATGTGAGCTAGGTAAACCAA R 2 1 2 1 303000 f 74 goat snp4923-scaffold1166-86033 7 92832827 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416223 Affx-122948224 AX-123286572 7 14207548 AGCTCCTGTCACATCTGCTTAGTGGACTTCTGCTC[A/G]TCCTTCAAGGCTCATCTCCAATAGCTCTTCTTCCA R 2 1 2 1 101000 f 74 goat snp4924-scaffold1166-115224 7 92803503 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790082 Affx-122953455 AX-385277088 7 14276898 TTGTAGTTTCAGGTTTTAAGGGTCTAGAGACTTCG[C/T]GTGGGTGTATGTGGCTGAGGGAGTGGATCTGGGTC Y 2 1 2 1 202000 r 74 goat snp4925-scaffold1166-184574 7 92735452 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389483 Affx-122968321 AX-123259841 7 14308922 TCATGCATAGAGGTCCTAGACACTCTCATCCAACC[A/G]CCCCCAAACCATTTTGCTACTCCACTACAAAACCC R 2 1 2 1 101000 r 74 goat snp2708-scaffold1079-3652 7 92644109 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274453 Affx-1111834206 AX-519548043 7 14324360 TTTAGGGGAGAAAAATGAGGCTGCAGCTACCTGAA[A/G]GCTGGTTACCATGAAGTGTTGCTCACTTCTGAATC R 2 1 2 1 201000 r 74 goat GoatD01.025369 7 14324360 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38409726 Affx-122953029 AX-123280077 7 14341084 CTGGTTTGATCTTGTTGATTGGCTCTGACCAAAAG[A/G]ACACAATGGAAGTGACATAGTGCCTATCCCAGTTC R 2 1 2 1 101000 f 74 goat snp2709-scaffold1079-35814 7 92612874 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411555 Affx-122951642 AX-123281905 7 14383974 GATGTGGCTGGGGTTTCATTGCTCTAACTAACTCA[A/G]CCATTATCAGTTTTCAAATTCTGTTGACTGTAAAG R 2 1 2 1 101000 f 74 goat snp2710-scaffold1079-78704 7 92569832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392011 Affx-122966488 AX-123262368 7 14422892 TCACGAGAATAACAAAAATCCCATGCCTAAGGCAC[A/G]GGGCAGTTTGAAGCCTCAAGATAACTCACATTGTC R 2 1 2 1 101000 r 74 goat snp2711-scaffold1079-117622 7 92530701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389652 Affx-122968729 AX-123260010 7 14464313 TAAGCCCACCCACCCTGAAAATGCAATGCTCTCTG[C/T]TCTCTTCTCTGCAGGGACACTCCGATCCTACCAGC Y 2 1 2 1 101000 r 74 goat snp2712-scaffold1079-159043 7 92491142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404482 Affx-122956723 AX-123274834 7 14532193 GGTGGAAAACCTCCCCACCCAGTTCTACAGGCCCT[G/T]GGCTGCCAAGTCAGAATGCCTGAGATGTCCGGCTA K 2 1 2 1 101000 r 74 goat snp2713-scaffold1079-226923 7 92423447 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278626 Affx-1111836433 AX-519552105 7 14647547 TGTTTTGGTTCAGATTCTAGTTCCACCATCTTTAC[A/G]GTGCAATGTAACATGCGCATCTTTTCTAAGTGCTA R 2 1 2 1 101000 r 74 goat Random2.2K-764 7 14647547 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412599 Affx-122951290 AX-123282948 7 14652710 CCTGTTCTACCAAGCTGAATGCTTTCTTTTTCATC[A/G]TCTTGTGCACTTTATTCTGTTCTGGCTCATTGCTG R 2 1 2 1 101000 f 74 goat snp2715-scaffold1079-347440 7 92303457 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771611 Affx-122945766 AX-385258769 7 14733257 CACACATACGAATAGCTCCTTCCATAAACCCATTC[A/G]CATAATTTATGCTGTTCCATACTCTTTTTTCCAAT R 2 1 2 1 101000 f 74 goat snp2716-scaffold1079-427987 7 92222272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394708 Affx-122964343 AX-123265063 7 14789228 GTCTCTGCTGGAGAAGGAGGGATGGCTTGGCTCCC[A/G]TCACGAAAACAGCAACAGAAGCCCAATTCTGACCA R 2 1 2 1 202000 f 74 goat snp2717-scaffold1079-483958 7 92165686 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382759 Affx-122973589 AX-123253117 7 14848028 GAATGGAAAGGGCCAGGGTGGCCAGTCTCTCAGGG[A/C]TTTGCCTTTTGGTCTCTTTTTAGTGTGTTTGGCTA M 2 1 2 1 101000 r 74 goat snp2718-scaffold1079-542758 7 92106887 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782915 Affx-122976536 AX-385269985 7 14886211 CAAGCCTCAGTAGACGGAATACTAGTAATTGCCGT[C/T]GATTCAGCCTTTACACAAAGGACGGGCGCTTCTCA Y 2 1 2 1 201000 r 74 goat snp2719-scaffold1079-580941 7 92068680 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439706 Affx-122930563 AX-123310043 7 14960350 CTCACTAACGATGCCTACAATTCCACCAGTGTGCC[A/C]ACCCCAAAGATGTGTGTCTAGAGTTAATTCATGGG M 2 1 2 1 101000 r 74 goat snp2720-scaffold1079-655080 NW_017189930.1 20183 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393358 Affx-122965924 AX-123263714 7 15016023 AAAGTTTAAAAAGTTGCCCCAAGTCCCATCATACG[A/G]ACCAGGGGTCAGCAAGTTTCTTCTGTAAAGGACCA R 2 1 2 1 102000 r 74 goat snp2721-scaffold1079-710753 7 91950772 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428638 Affx-122938668 AX-123298980 7 15057327 TGGTCCAGGTCATCATCCAGCTCACCTGAGCCACT[A/G]CAGCAATCTTCTTACCTGCTGAAAACCCTGCCTGT R 2 1 2 1 101000 r 74 goat snp2722-scaffold1079-752057 7 91909338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385252 Affx-122972086 AX-123255610 7 15090789 TGAAAATTCTTGTTAGTCACATAAAGCAAGCACTC[A/G]CCAGACATTTGACTTATTTTTAATATTATCACCAC R 2 1 2 1 101000 f 74 goat snp2723-scaffold1079-785519 7 91876658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278628 Affx-1111836434 AX-519552107 7 15118359 GTGAGCTACTTCATAGACAGAGAATAATATCTGAC[A/C]TTTACTGAGTGCTAATTGAGCACTTTAAGCTAAGT M 2 1 2 1 101000 r 74 goat Random2.2K-765 7 15118359 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443852 Affx-122927524 AX-123314189 7 15136184 TGCTATGGTTGTGCTCTTAAATTGTTAAGTGTTAT[C/T]GTCAGCTAAATAGAATTGATTTTTAAGAATCTGAC Y 2 1 2 1 101000 f 74 goat snp2724-scaffold1079-830914 7 91831328 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406820 Affx-122955683 AX-123277171 7 15178022 AGTCAAAGCCTAGCAGCTGAATGATGCACAAATGC[C/T]CACACAAGCAATGTTCAATATACAGTAAGCATTCA Y 2 1 2 1 101000 f 74 goat snp2725-scaffold1079-872752 7 91789243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396700 Affx-122962823 AX-123267055 7 15221110 CCTTGTGTTGCCTTACTTTCCCTGCTACCACAGCC[C/T]GTGAGTCTGTAGGTCTTGCCTCTTCTCCCCGCAAA Y 2 1 2 1 101000 f 74 goat snp2726-scaffold1079-915840 7 91747232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428884 Affx-122938935 AX-123299226 7 15273779 TCCCTAGTAATTCAGTCATTAAGACTTTGTGCTTG[C/T]GATGCAGAGGGACTCAAGTTCAATTCCTGGTTGGA Y 2 1 2 1 101000 f 74 goat snp2727-scaffold1079-968509 7 91716567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415829 Affx-122948881 AX-123286178 7 15316037 TTTCCATCTATATCTCCTCTGACTCAAAACCCCTC[A/G]CTGGTTTCTTAAGGTCCCCAGGATATACAAAACCC R 2 1 2 1 201000 r 74 goat snp2728-scaffold1079-1010767 7 91674193 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386157 Affx-122971392 AX-123256515 7 15358012 GGACAATTGGGTTGTTTCCGCCTTTTGGCTTACCG[C/T]GAATCATACTGCTTTGAATACACACGTACGGGTTT Y 2 1 2 1 101000 r 74 goat snp2729-scaffold1079-1052742 7 91631947 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414032 Affx-122949792 AX-123284381 7 15387445 AGGTTGGGCCCTGCCTTCCGGACGACCCCTGAAAC[A/C]CGGAGCCTGAACTTGAGCTGCAGCTGCAGTTTGCA M 2 1 2 1 101000 r 74 goat snp2730-scaffold1079-1082175 7 91602336 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406112 Affx-122956209 AX-123276464 7 15422080 GTCATAAATCTGACAATTACCAGCCTCAGGCAGAA[C/T]GGAGCTGAGATTGTTCCCATTAATAGATGAGGAAA Y 2 1 2 1 101000 f 74 goat snp2731-scaffold1079-1116810 7 91567868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377969 Affx-122977622 AX-123248328 7 15470575 CACAGAGGCTAAGAGTCCCACGTAGGAAGAGGAGT[A/G]CTCTGAGAAGCAGGGGGACATGGGGAGTTACAAGA R 2 1 2 1 101000 f 74 goat snp2732-scaffold1079-1165305 7 91520721 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381899 Affx-122974156 AX-123252257 7 15499689 TGTTCAGCTCCAGGCGAAAAGATTTGGTTGCGTGT[C/T]ATTTATCAGCCACCACCCACCCCTTGTTAACTTCC Y 2 1 2 1 101000 f 74 goat snp2733-scaffold1079-1194419 7 91492027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797053 Affx-122976806 AX-385283993 7 15529555 AAAACTGTCAAGCTGTACTCTGAAGGTTGGAGCAT[C/T]GCTTTGTAGTTAAGTTCTAACTTGATTTGTAAGAG Y 2 1 2 1 101000 f 74 goat snp2734-scaffold1079-1224285 7 91463507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422740 Affx-122943250 AX-123293086 7 15600048 ATTATTATCAAGAACAATGAAAATAAATAAGCAAA[C/T]GCCTTGTGAGTTAAAAATTAAATGAGTGTGTCAGG Y 2 1 2 1 102000 r 74 goat snp2735-scaffold1079-1294778 7 91392163 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393890 Affx-122965118 AX-123264245 7 15633834 GGCATGCCTGCCTCTGTTCAGACGTTCCCAGGGAC[A/G]TGAAAATCCACAACCATGAGCACCTTTCCCCCAAA R 2 1 2 1 101000 r 74 goat snp2736-scaffold1079-1328564 7 91361123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464493079 Affx-1110513525 AX-515965360 7 15657036 AACCAAATATCCAGATTTTAAGCAGTACGTTCAGA[C/T]AAATCTTTATGGAAAAGTGAGTCTTAAAGACCCTA Y 2 1 2 1 101000 f 74 goat 7_15657036_AF-PAKI 7 15657036 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433560 Affx-122934982 AX-123303901 7 15670011 GTGAGGGTTTCAACTGGCCCCAGCGGGACTTCTCC[A/G]CTTTTCCTTGGAACAGTTTCCTGCTGGTGATGCGG R 2 1 2 1 101000 r 74 goat snp2737-scaffold1079-1364741 7 91325083 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424300 Affx-122941972 AX-123294646 7 15710024 TACAACAACCATGCCAGGTACCAGGAAAGCAGCAG[C/T]AAAGAAAACAGGAAAGGTCCCTGGCATCCCTGGGG Y 2 1 2 1 201000 r 74 goat snp2738-scaffold1079-1404754 7 91285677 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440810 Affx-122929825 AX-123311147 7 15748410 CAGTGGGGTTCTCATGTCTTGTCACTGCCTGGCAC[A/G]CTGTGGGTGTCAAGGTCATGTTCAAACAAGTGAGC R 2 1 2 1 101000 r 74 goat snp2739-scaffold1079-1443140 7 91247199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419964 Affx-122945199 AX-123290312 7 15793303 TTTTTCATCATGACTGTATTTGTCACGATGAGCTG[C/T]GATCAGTCTCTTTGACTATTGTAATTTTGGGGATG Y 2 1 2 1 101000 r 74 goat snp2740-scaffold1079-1488033 7 91201927 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406680 Affx-122955784 AX-123277032 7 15823253 GGTGCATCTGAGGGACATGGCCAACAGCATATATC[A/G]CCATATGTTCTTGGGGTGGATGCCCCCTATATTGT R 2 1 2 1 101000 f 74 goat snp2741-scaffold1079-1517983 7 91173821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391586 Affx-122966609 AX-123261943 7 15884863 TTGAAAGCCAATTCCTCCTACAAGGGAATATGTAC[A/G]TGTGTCCACAGAAGCACTAATCCCAGAGGATGAGG R 2 1 2 1 101000 f 74 goat snp2742-scaffold1079-1579593 7 91112137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412942 Affx-122951465 AX-123283291 7 15916719 CTGAGAGACGAGACTGGAGACCCTGCCCGAGCTGA[C/T]GGCACTCCTGGTACTTGAGTTTCTAATGGCACAAT Y 2 1 2 1 101000 r 74 goat snp2743-scaffold1079-1611449 7 91080155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391478 Affx-122966716 AX-123261835 7 15948105 CCACCAGGGAAGCCCAGTTGTAAAACGGGTACCAG[C/T]AGCCAATCTATGGTTGCTGTGGATAAATGAAAGCA Y 2 1 2 1 202000 f 74 goat snp2744-scaffold1079-1642835 7 91048671 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383195 Affx-122972790 AX-123253553 7 15992536 AGCGCACCACTCCATCGTGGATTAAAAAAATGAAT[C/T]AACAAAAGGCCTCTCAGAGAGTAGGACGTTGACCA Y 2 1 2 1 101000 f 74 goat snp2745-scaffold1079-1687266 7 90999531 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394700 Affx-122964349 AX-123265055 7 16043582 ATCTAGACCTGTCTGAGAACAATCTCCACTCCCTG[A/C]CCCCTGGGCTCCTGGAGAATTTCCCCGACCTGCTC M 2 1 2 1 101000 f 74 goat snp2746-scaffold1079-1738312 7 90949468 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405868 Affx-122955848 AX-123276220 7 16080988 TCCTCCAAAAACAGACCACCCCTAACAGAGGGCCA[C/T]GGCTGACCATGGAGAGATGCGCAAGGAATTTTCCC Y 2 1 2 1 102000 r 74 goat snp2747-scaffold1079-1775718 7 90911962 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764731 Affx-122920857 AX-385252348 7 16141807 CTTAGGCCAAATCTCAAGAAGATAAAGTTATAGCC[A/G]TTCAGTAAGGTTTATCCAAATGTATGGTAAAGCAG R 2 1 2 1 101000 f 74 goat snp32989-scaffold3846-61867 7 90851828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384165 Affx-122972426 AX-123254523 7 16192526 CAAAGATTAGCCTTGGGAATTCACTGAAGAACTGT[A/G]TAACTCTTCCTCTCCTGAACTGTCTGGTAATGTTG R 2 1 2 1 101000 r 74 goat snp32988-scaffold3846-11148 7 90801069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404465 Affx-122956734 AX-123274817 7 16291240 GGATATGGATATGTATGGATATAGATATGGATATG[A/C]GGATATGGACCAGTATGGGCAAAGGTTTGGAGGCT M 2 1 2 1 101000 f 74 goat snp55237-scaffold85-2363783 7 90700993 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408533 Affx-122953693 AX-123278884 7 16437203 CTCTGTTTTGAGAAATTGAGAGTTGCCCTAGAGAT[A/G]CAGGGGTCCGAACCCTGCCAGCCCAAGGTGGCATC R 2 1 2 1 101000 f 74 goat snp55235-scaffold85-2217820 7 90555022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425643 Affx-122940889 AX-123295989 7 16490418 CTGCAGACCTACTGGGAGGCCCATGCTCCTTGTAG[C/T]ACTCAGCACTAACTTGCACCACCGCCCCCCCAATC Y 2 1 2 1 202000 f 74 goat snp55234-scaffold85-2164605 7 90502756 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425957 Affx-122941175 AX-123296303 7 16539778 GGAGGGCAGATCTGATTCAAGAAAAGACTGAAATC[G/T]AGAGTTTTTGTGTCTCATCTCTGATTTGACAGCGA K 2 1 2 1 101000 f 74 goat snp55233-scaffold85-2115245 7 90454437 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414774 Affx-122949241 AX-123285123 7 16571640 TTCATCCAGGTCAATGGTCTTGGTCCTTACTTCCA[C/T]AGCCACATAGAAGAACACCAATTACACTCAATGTG Y 2 1 2 1 101000 f 74 goat snp55232-scaffold85-2083383 7 90422629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389127 Affx-122968556 AX-123259485 7 16604814 TCCGCTGCTTAAAGCCCTCCAGTCTCCCCATTGCC[C/T]TGAGGAGGCAGTCACACCTCCGCACACGGCCTTCC Y 2 1 2 1 201000 r 74 goat snp55231-scaffold85-2050209 7 90389722 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383673 Affx-122972505 AX-123254031 7 16673383 GGCAGCTCATGAGATAGTGTTGCTTATTAATGTTA[A/C]ACAGAGGAGAAAGGTCATTATTATTCTCACTACAA M 2 1 2 1 101000 f 74 goat snp55230-scaffold85-1981640 7 90322724 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393787 Affx-122965190 AX-123264142 7 16702787 GGGGTCCTGCAGACCTGGGGACTGTCTCACCTTGA[A/G]TCAGCCAACTCCCAGATCACAAACAACATGTCCAT R 2 1 2 1 101000 r 74 goat snp55229-scaffold85-1952236 7 90294761 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382136 Affx-122974052 AX-123252494 7 16764414 CAGGGACATAGACCCTGAGTCTGTTTCACACTTCC[C/T]ATATGTGGGAATAAAAACTGCAACCCCAGGGCCCC Y 2 1 2 1 101000 f 74 goat snp55228-scaffold85-1890609 7 90233482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413225 Affx-122950250 AX-123283574 7 16806084 CACTTGGCCCCAACCCTGAGCTCAAGTCCTTGGGA[A/G]CACCCCTCCCAGCCCCCCCAGCTCACCCGGAACAC R 2 1 2 1 303000 r 74 goat snp55227-scaffold85-1848939 7 90191819 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376634 Affx-122979029 AX-123246993 7 16878963 ACTGAACTTCCTGAGTTTTATCCAGCAGCCCTGCT[C/T]AGGGGCCCAATCACTCGCCCAGGGTCACCTAGCAG Y 2 1 2 1 101000 f 74 goat snp55226-scaffold85-1776060 7 90119800 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433468 Affx-122935051 AX-123303809 7 16915150 TATGTGTAAGCACTGTTTAAGCACCAATTGCATGC[C/T]AGGCTCCATGAAGAGAGGCCACAGGAGGACCAGGG Y 2 1 2 1 201000 f 74 goat snp55225-scaffold85-1739873 7 90084856 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278630 Affx-1111836435 AX-519552109 7 16923739 TGTTCATTTACATCTAGGTATTCAAAGACATGGCA[A/C]TATGTTTATCCCTGGGCTTCAAATTGTGAGCCAGA M 2 1 2 1 101000 r 74 goat Random2.2K-767 7 16923739 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432031 Affx-122935911 AX-123302372 7 16974423 ATGTGAGGCTAATGCTGGGATCCCAGCTTCAGGGA[C/T]GGAAAGCAAGGGTGGGATTGTTCCTGAGATGGGAG Y 2 1 2 1 201000 f 74 goat snp55224-scaffold85-1680600 7 90025440 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414108 Affx-122949737 AX-123284457 7 17028582 GAGCTAGATCCTGGGGACAGAGGGGCTTGGCTTAC[A/G]TTTTTTCTTAAAATTTGAAAAATACTGCACATTTA R 2 1 2 1 202000 r 74 goat snp55223-scaffold85-1626441 7 89971016 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405625 Affx-122956599 AX-123275977 7 17102206 TGCCTGAGTAATGGTCGCATCCCCGGGTAAATGAC[A/G]CAGGGTTTGTTATCAGCGACCCATATTTCTTAGAA R 2 1 2 1 101000 r 74 goat snp55222-scaffold85-1552817 7 89898201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405622 Affx-122956601 AX-123275974 7 17184388 ATATCCTGTGTGGGGAGACTGATGTTCTCTTGACT[A/G]AAGTGCCAGGTGCCCTAGGGAACCACCTTTCCTCC R 2 1 2 1 101000 f 74 goat snp55220-scaffold85-1470635 7 89824932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413494 Affx-122950645 AX-123283843 7 17255866 CTGCCTGGGATGGAGGAGCCAAGTAGGGCACATAG[A/G]TGTGGGGGGAACACTTGGGCTGAGGGCCAGATGAC R 2 1 2 1 201000 f 74 goat snp55219-scaffold85-1399157 7 89753336 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762517 Affx-986697047 AX-385250632 7 17257039 AGGAATTAATTAGGTAGATGTTTCTGACCCATTCT[C/G]ATAACTGTAATATTTGAATTTTCATTGAGTGCACT S 4 1 2 1 600010 f 74 goat 7_17257039 7 17257039 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 320803636 Affx-986696152 AX-385290415 7 17257094 TTTCATTGAGTGCACTGGTATTTATTCTTGATGCT[A/G]AAATGGTTTTGCCACTGCTTTTAGCTCAAATGAAG R 2 1 2 1 600010 r 74 goat 7_17257094 7 17257094 Ancestral_priority_1043 ancestry 0.75 recommended IMAGE 10K 10K ancestral 320762519 Affx-986697049 AX-385250634 7 17257189 TCAAAACTGCCAGAAGCATTTAATGTCCCTTAACT[A/C]ATCTTTTTTTCTCTTGCCTTCCCTCCCTCCACCAA M 2 1 2 1 600010 f 74 goat 7_17257189 7 17257189 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320762521 Affx-986697051 AX-385250635 7 17257263 GTCTGTAGTATATTTACTTTATATCTGTCGTATAT[C/T]CATTCATTATTTCAGAGGAATAATGCAGTTCAATA Y 2 1 2 1 600010 f 74 goat 7_17257263 7 17257263 Ancestral_priority_1043 ancestry 0.68 recommended IMAGE 10K 10K ancestral 320764826 Affx-986697053 AX-385252430 7 17257265 CTGTAGTATATTTACTTTATATCTGTCGTATATTC[A/G]TTCATTATTTCAGAGGAATAATGCAGTTCAATAAT R 2 1 2 1 600010 r 74 goat 7_17257265 7 17257265 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 38382668 Affx-122973660 AX-123253026 7 17304333 TGTGTCACTTACTAAGCTACTGTCTCTCCTTCAGA[C/T]CCATGCTATGAGTTACCTGTTGCTGCTGTAACAAA Y 2 1 2 1 101000 f 74 goat snp55218-scaffold85-1350690 7 89704514 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394812 Affx-122964804 AX-123265167 7 17349263 AATGACCGTCATTAGGGTTAAAGTTGCCAGAAATG[C/T]TCTCCCAATTCATTTTTATCCTACTTAAAACGCAC Y 2 1 2 1 101000 f 74 goat snp55217-scaffold85-1305760 7 89659342 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401346 Affx-122959257 AX-123271699 7 17381410 GTCACTCTACCCTCCTGGGTGAAGGTGCTGAGAAC[A/C]AATAGGAGGCTTGCCAGCACATCTGGCTGTCCTCA M 2 1 2 1 101000 r 74 goat snp55216-scaffold85-1273613 7 89627079 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434236 Affx-122934834 AX-123304577 7 17410952 GACATGTGGGATGCTAGTGGTGGTACCAGAATGGC[A/G]GGTATGGGTACTGGCTCATCCTACACCCATTTCAC R 2 1 2 1 201000 r 74 goat snp55215-scaffold85-1244071 7 89597572 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785374 Affx-122928904 AX-385272419 7 17470374 ACTTATGACTGCTTTAAGGGCCCTCCAGGATAATC[G/T]CTTCATCTCAGAAGGCTTAATTGAATCACACCTGC K 2 1 2 1 101000 r 74 goat snp55214-scaffold85-1184649 7 89538233 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464499404 Affx-1110514094 AX-515971627 7 17640028 ACAAAGCTGCAGTTTTGTTCTTTCCTTCTAAATGA[A/G]TAAATACTTTTCTCAGGTTTAAAGAAGGAAGAGTA R 2 1 2 1 101000 r 74 goat GoatD01.060175 7 17640028 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407286 Affx-122955331 AX-123277637 7 17642717 CGGAACAGGGGTGGGGGTAGGTAATGAGATCCACC[A/G]CTGCAAAGCCATAAAGGTGACTCATCCCTCCTAGA R 2 1 2 1 101000 r 74 goat snp55211-scaffold85-1012306 7 89367303 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411427 Affx-122951832 AX-123281777 7 17679986 CTCACTAAGCACCCTGGCATGGATGCTGTCAGTGT[A/C]ATCTTGAAGTTCCTGAACCTGCTTTGTGGTTGTAA M 2 1 2 1 101000 r 74 goat snp55210-scaffold85-975037 7 89329920 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421852 Affx-122944289 AX-123292199 7 17716371 TTACCCAGAGCAGGGTTCCCAATGCCAGATGCTCC[C/T]GAATTTTCCATGACTTGGCATTTCTGAGAAAAATG Y 2 1 2 1 101000 r 74 goat snp55209-scaffold85-938652 7 89293291 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383105 Affx-122973274 AX-123253463 7 17751071 TTTAAATATAGCAGTGAGAACATTAACAGCAGAAG[C/T]AGAGGTGTTTCTGGCTGTGAGTCAGATGGCTGGTG Y 2 1 2 1 101000 f 74 goat snp55208-scaffold85-903952 7 89258650 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400699 Affx-122959936 AX-123271054 7 17970340 AATGAATGTCTACCCATAACTGAATCGTGTATCTG[C/T]ACAACTGAAACAAACACACCAGAAATCAACAATAT Y 2 1 2 1 101000 f 74 goat snp55205-scaffold85-684683 7 89043742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393693 Affx-122965256 AX-123264048 7 18027048 GACCCCAGAAAATGTAACAAGGACAGGTCTCCCCC[A/G]AGATTCCTGGGGCCTGCAGGCAGATAACCAGCCAC R 2 1 2 1 101000 r 74 goat snp55204-scaffold85-627975 7 88987749 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386906 Affx-122970033 AX-123257264 7 18062527 GTTTCTCAATCAGAAAGTCTGGTTTTTCCTTCAGG[C/T]AGAAGATTAAAAACACAAATATTTGTGACAACATT Y 2 1 2 1 101000 f 74 goat snp55203-scaffold85-592496 7 88952209 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278632 Affx-1111836436 AX-519552111 7 18201824 CCTTCCATTCTCATCTACCCACACTTCCCCACTCT[A/G]TCTTGGTAGAGTAAACTGGTTCACATCCTTTAGAA R 2 1 2 1 201000 r 74 goat Random2.2K-768 7 18201824 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433537 Affx-122935000 AX-123303878 7 18203718 TGTTAGATTTTGACAGGCTACTTTTGTTTTTACAG[A/C]TATTTCTTTTCTTTTTCGTATTTCAAAACTACTAG M 2 1 2 1 101000 f 74 goat snp55200-scaffold85-451305 7 88810263 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380533 Affx-122975678 AX-123250891 7 18234280 AAGTTCATACAGTTAGTAGGAGACAGAGTTAATTT[A/G]CTGGTATATATCTTATGATATGTAAGACATCTGAC R 2 1 2 1 101000 f 74 goat snp55199-scaffold85-420743 7 88779673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273256 Affx-1111833530 AX-519546907 7 18240107 GAAACATTAAACTGTATGGAGAAAAACAAAAGTAA[A/C]ATGAGCAAAGAAATAGAATCGACAAGAAGAATATA M 2 1 2 1 101000 f 74 goat 7_18240107_AF-PAKI 7 18240107 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320784300 Affx-122928092 AX-385271351 7 18328598 CCTAAAATATTTACTTTGCTTCTGAAGTTTAATTA[C/T]ACTGAATATAAAGACTCCACCATTGGCTGGCCCTC Y 2 1 2 1 101000 r 74 goat snp55198-scaffold85-326425 7 88684270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414150 Affx-122949694 AX-123284499 7 18397702 ACCCTCATCTGCCCGCCCCTCTGGTCTCCCACACC[A/G]CACACACCTGAGTTTGTGCTCAGCCAGGCACAAAC R 2 1 2 1 101000 r 74 goat snp55197-scaffold85-257321 7 88614936 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444799 Affx-122926339 AX-123315136 7 18446344 TGGAAGCTCTGTGAGAGCAGGGACTTGTCTTTTGC[A/G]TTCATGCCGTTGTTCCCAGGTCCTAGAGCAGCATC R 2 1 2 1 201000 r 74 goat snp55196-scaffold85-208679 7 88566427 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405096 Affx-122956987 AX-123275448 7 18480801 AGGGAGGCAGGCTACATCTCAGAGTCCTTATTGCT[A/G]GAGTCAACAAGCCTTGGCAACCAGCTGGGTTGCTC R 2 1 2 1 101000 f 74 goat snp55195-scaffold85-174222 7 88531454 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444153 Affx-122926790 AX-123314490 7 18556482 AGGTTTTAGAAGTCTCTCCATCTGGAGGAGGTTGA[A/G]CAGGGAGGGAGGTGCCTCTCTTCCTGTCCTGCTGG R 2 1 2 1 202000 r 74 goat snp55193-scaffold85-98541 7 88455754 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412516 Affx-122951357 AX-123282865 7 18590142 ACTGGTCTGTGATGGATCCAGAACTTGGGACCTAG[C/T]ATGTGGGACTGTCTGTCTCTCCGTGGCGGCTTTGC Y 2 1 2 1 101000 f 74 goat snp55192-scaffold85-64881 7 88422191 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398280 Affx-122962168 AX-123268635 7 18643964 AGAAAGATCACTGTGCATACATCATAGAGGGTTGA[C/T]GAAGGAGGGGTCAGAGCAGGAACAAGGAGGCCAGT Y 2 1 2 1 101000 f 74 goat snp55191-scaffold85-11059 7 88369781 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388327 Affx-122969364 AX-123258685 7 18659829 GCAGACTGTTTACTGCTGAGCTATCTGGGAAGCCC[A/G]TCTAAAATACATTAAACACAAATACTAATCCTGAG R 2 1 2 1 201000 r 74 goat snp29284-scaffold316-4707 7 88353797 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476231 Affx-1251763737 AX-586011655 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 4 1 4 1 20000 f 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 539476485 Affx-1251763737 AX-586011884 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 4 1 4 1 20000 r 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562165104 Affx-1251763737 AX-606940516 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 r 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562165418 Affx-1251763737 AX-606940829 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 r 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562165599 Affx-1251763737 AX-606941010 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 f 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562165785 Affx-1251763737 AX-606941194 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 f 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562166113 Affx-1251763737 AX-606941521 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 f 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 562166231 Affx-1251763737 AX-606941639 7 18660348 TTAGTCAAAGAAGTTTGAAATAATAGTCTGGACAA[-/AGATGCTCTATTTTATTTTTTTTTTATTTTTATTTTTTTTGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCC]GATGCTCTATTTTAAAAACAGAAGTACAAAGGAAG - 8 1 4 1 20100 r 74 goat SV_181 7 18660348 - deletion junction SV-TF-chip 38434936 Affx-122933866 AX-123305276 7 18693174 TCTGTGAGCTTTTCCTCATGTTTCTGAATCTCTTT[A/C]TGAGCTTGTGAGAGTACTTGAGAGTGTGTTCCTTG M 2 1 2 1 101000 r 74 goat snp29285-scaffold316-38052 7 88320099 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400178 Affx-122960674 AX-123270533 7 18738047 TTTCCTTCATCTTTTGGTTGTGTGGATAACTCTTT[A/G]TTTCTTATTAAAATTTGAAAAACAACCTTTCTGGG R 2 1 2 1 103000 f 74 goat snp29286-scaffold316-82925 7 88275396 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406767 Affx-122955721 AX-123277118 7 18816632 AAGGCCCTGGCCTGTGTGTACAAGGCACAGGGAGG[C/T]ATGTACATGTGTGCTTGGCTGCACATGTCTGCTCA Y 2 1 2 1 102000 f 74 goat snp29287-scaffold316-161510 7 88196269 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428496 Affx-122938773 AX-123298839 7 18859436 ACTCCGCAGCCTCTGATCTCTCTGCACGGAGTCTG[C/T]GTTGTCTGCCCACTTCCTGCAGTGACTGGCTACTG Y 2 1 2 1 101000 f 74 goat snp29288-scaffold316-204314 7 88153480 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402579 Affx-122958439 AX-123272932 7 18948318 TAGTGACAGAGTGGGCAGCTCAGCTCTGGGCTCCA[C/T]GTTCTGTTCCCAAGCCTAAACCCAGACTTTTGGGG Y 2 1 2 1 101000 r 74 goat snp29290-scaffold316-293196 7 88064278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403708 Affx-122958037 AX-123274060 7 18978510 GAAAGTATTTGAGCATACTTAACCATGATTTAACC[A/G]TTTTCTTGACATTTATATGGCTTATTAGTTTTTAT R 2 1 2 1 101000 f 74 goat snp29291-scaffold316-323388 7 88034036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420081 Affx-122945110 AX-123290429 7 19011106 TTTAAGAGTGATGCTCTCCTTTCATCTGTTATCCC[A/G]CACTCCACCAGTTTCTGTTAGTGTTGACCTCTGTT R 2 1 2 1 201000 r 74 goat snp29292-scaffold316-355984 7 88000331 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382089 Affx-122974904 AX-123252447 7 19053395 TGCATGACAATTCCTAGGGTAGAATAATCCCTGTT[A/G]TTCAGATGAACATATTAAAAGATTATATAGCTAAT R 2 1 2 1 101000 f 74 goat snp29293-scaffold316-398273 7 87956771 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801368 Affx-122957403 AX-385288279 7 19102522 GGAAATTGTTTAAAAAGTTTCATTGTTAAGCTTAA[A/C]GCTTGTACAAACTTATTTTATAGACAACTTGTATT M 2 1 2 1 201000 f 74 goat snp29294-scaffold316-447400 7 87907525 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788849 Affx-122926886 AX-385275864 7 19144804 GAAAGACAGTGCTTTCTAGGGGAAGATACTCTTTA[G/T]ATTTTCTCCACCAGGATACTTTTCAGTGGAAGTAA K 2 1 2 1 101000 r 74 goat snp29295-scaffold316-489682 7 87864773 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375568 Affx-122978748 AX-123245927 7 19199815 ATGCTTTTTTGTAGTCCCAGTTTAAATGTCACTTC[A/G]TTCATCTGCCTAGATTAACTTAAGTTCTTTCTTGG R 2 1 2 1 201000 r 74 goat snp29296-scaffold316-544693 7 87809023 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394307 Affx-122964689 AX-123264662 7 19261607 CCTGAAGTTGGTGTGCCTGCAGGCAGTTTGGCCCC[C/T]GTATCCTATCAGCTGTTTTAGTGCCTGAGTCTCCC Y 2 1 2 1 201000 r 74 goat snp29297-scaffold316-606485 7 87746885 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406455 Affx-122955184 AX-123276807 7 19302359 TGGGTGCGCAAGTTGCAAATGTCTTCTTCCATTGT[A/G]TGGCTTGCTTTTTTTATTCCATTAACGGCGTCTTT R 2 1 2 1 101000 f 74 goat snp29298-scaffold316-647237 7 87706042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798807 Affx-122923971 AX-385285738 7 19333733 CCAAAAAGATGTCATCTCACGGATTTTAAAACTCT[A/G]CAGGATGAACATAAACTCTAACAGGATAAATACAA R 2 1 2 1 101000 r 74 goat snp29299-scaffold316-678611 7 87674586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793434 Affx-122923087 AX-385280411 7 19473547 AAGGCCTACACTCATGATTTTTAACAGGAGAATTT[A/G]AACAAAGAATTGAAAAAGTGAGACGTCAAGAGGCC R 2 1 2 1 101000 r 74 goat snp29301-scaffold316-818425 7 87533099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420639 Affx-122945220 AX-123290986 7 19504658 TGTGTAGGGTAACTTGGAAGAACTGGGGGAAGAAA[C/T]CCTGCCATGTTTCACCTCTATAAACCCAGTATTTA Y 2 1 2 1 101000 f 74 goat snp29302-scaffold316-849536 7 87501398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793780 Affx-122947611 AX-385280752 7 19584929 CTCAGTGGTGAACACTGCAGACGTTCCAATTAATG[C/T]AATGTTTTGTGAAACATCAGAGGCATTAAATTAAT Y 2 1 2 1 201000 r 74 goat snp29303-scaffold316-929807 7 87420316 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416614 Affx-122947628 AX-123286962 7 19615271 CTAAGGGACTGGAGCTGAAGAATACCACAGGAATC[A/G]TAGCTGGAGGTTCCCACACATGGAATCCCCAAGAA R 2 1 2 1 201000 f 74 goat snp29304-scaffold316-960149 7 87389932 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404232 Affx-122957647 AX-123274584 7 19670982 TTTTAGGAACACAGAGATACACTCTGTCTCTAAAA[C/T]GAAACTGTATTGTTATTTCTTAGCTACTGAAATAA Y 2 1 2 1 202000 f 74 goat snp29305-scaffold316-1015860 7 87333993 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412712 Affx-122950743 AX-123283061 7 19718859 CCCTGCTCTGTCAAGTCCATGTTAATTTGATCCTT[A/G]CCCTCACATTTGTTAATATGTGGCTGTCACTGTAA R 2 1 2 1 101000 f 74 goat snp29306-scaffold316-1063737 7 87286544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429039 Affx-122938311 AX-123299381 7 19754441 ATTATACACTCAAGAAAGTACAATTTACACACAGC[A/G]TTGTGCAAATTATACGTGGTATGTTCACCCTCTAG R 2 1 2 1 101000 r 74 goat snp29307-scaffold316-1099319 7 87250516 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780498 Affx-122968157 AX-385267589 7 19784426 TGACAGTGAAGGGAACATTGAGTGGGTGAAAGAAT[A/G]CAATAAAAACATGGCAAAAGTTGAGAATTTTTTAA R 2 1 2 1 201000 r 74 goat snp29308-scaffold316-1129304 7 87219544 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378766 Affx-122977011 AX-123249125 7 19828734 TAAGCAAATGATCTCCATAACTGGAACTTCAAAAA[C/T]AGAACAAAGAGAATGACCGTATTAAAAAACCTGAA Y 2 1 2 1 101000 f 74 goat snp29309-scaffold316-1173612 7 87174978 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376036 Affx-122978942 AX-123246395 7 19895403 ACTCAAAGACTGTTATTAAATAAAATGCATCTGGG[A/G]AAAGCTAGGAAAAAGGTGATAGAATCTCTAGAAGG R 2 1 2 1 101000 r 74 goat snp29310-scaffold316-1240281 7 87108423 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417002 Affx-122947984 AX-123287350 7 19930419 CCTGCCAGGATGCAATGACAAAATAGGGATTATTC[G/T]CAGATGGAAAAGAATCTGCCTACAATGCAGGAGAC K 2 1 2 1 101000 f 74 goat snp29311-scaffold316-1275297 7 87072459 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443758 Affx-122927117 AX-123314095 7 19973203 TACTGTCTAATACCGCTTAGTACAACTCACTTAAT[A/G]TAAGACTTGTGGTTTCACTGATCTTTTAAGAAATA R 2 1 2 1 101000 f 74 goat snp29312-scaffold316-1318081 7 87029996 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774080 Affx-122958627 AX-385261218 7 20020121 AGGAATGTCAGACAAGGACATAAAGTGATACAGGC[A/C]TTCCGTACTAAATAATAGAGAACATCCTGCAATTG M 2 1 2 1 101000 f 74 goat snp29313-scaffold316-1364999 7 86982771 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404175 Affx-122957690 AX-123274527 7 20065201 CTCCAGGGAAAGAGGAAGATGTCTCCTCTAAGTGA[C/T]GTTTCAACACACAGTGGTAAATAAAATAACGCTGT Y 2 1 2 1 101000 f 74 goat snp29314-scaffold316-1410079 7 86936870 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767535 Affx-122921316 AX-385254791 7 20094048 TTACTACCGTGTTACCTTATACATCTAGGTTAATG[C/T]AAATGATGTTCTTAATTATCCTGCCCTACCTTCTG Y 2 1 2 1 101000 f 74 goat snp29315-scaffold316-1438926 7 86907999 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409110 Affx-122953315 AX-123279461 7 20150375 AATTTCCACAAATCTCATTAAGGCTACAGTAGTGA[C/T]GGGCCTTTAAAACACTGTCACTTTTTCTAGGAAGT Y 2 1 2 1 101000 f 74 goat snp29316-scaffold316-1495253 7 86851263 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437612 Affx-122931852 AX-123307950 7 20180565 TTATCAATTAAAGAAATATTTTATTGAGACCTGGG[A/G]CAGGTATTGGGGACATAAAAATTAGAGGAAATCTT R 2 1 2 1 103000 r 74 goat snp29317-scaffold316-1525443 7 86820971 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420092 Affx-122945101 AX-123290440 7 20209196 AGTAAAAAGTTAAATACTCTAAAAGAAATAGCTAT[A/G]TGGTCACTAAAAATAAAAGAAACATTTCCCTAGAT R 2 1 2 1 303000 f 74 goat snp29318-scaffold316-1554074 7 86792156 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414675 Affx-122949299 AX-123285024 7 20289969 CCACTGGGATACAAAAAGTCTGCACACATACACAC[A/G]CATACACATATGTGCATACCTACAAGTTATGGAGT R 2 1 2 1 102000 f 74 goat snp29320-scaffold316-1634847 7 86710593 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434004 Affx-122934237 AX-123304345 7 20379667 TGAGATCCCTGAGCCAGTGCATGAATTCAGTTCCA[C/T]GCTTTTCCAGAGCCTAAGCGCCCGGCACTGAGCAA Y 2 1 2 1 101000 f 74 goat snp29322-scaffold316-1724545 7 86620504 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408885 Affx-122953981 AX-123279236 7 20469000 GAGCATGATGCTTACAGATAACTTCAAATATATCA[C/T]GAACACATTTAAATATACAAGCATCTATGTGACTT Y 2 1 2 1 101000 f 74 goat snp29325-scaffold316-1813878 7 86530950 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436249 Affx-122932555 AX-123306588 7 20525776 ACATGGCTTGTATTTTTCTGTTTGTTTTTTATTAG[C/T]ATTAGATACAGGCTAAGAGCTACTATGAATTCTTC Y 2 1 2 1 201000 r 74 goat snp29326-scaffold316-1870654 7 86474575 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765679 Affx-122973482 AX-385253143 7 20583084 TTTTATGCACAGTCCTAACTCGACAACTTAACCCA[G/T]ATTTCCACTGTTTGGAAAATGTTCCTCCTTGTTTT K 2 1 2 1 101000 f 74 goat snp29327-scaffold316-1927962 7 86417341 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420394 Affx-122944930 AX-123290741 7 20620797 AATACATTATAAAGAATTGGGGGTTTGAAAGCAGA[C/T]AAACTTGACTCAGCAATTTTTTAGTGATCTGGCTT Y 2 1 2 1 101000 f 74 goat snp29328-scaffold316-1965675 7 86379760 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410517 Affx-122952175 AX-123280867 7 20696549 GTCTGTATATTTTAACTCTTTTCGGTGTTTTCTTG[G/T]CATTGCACCACTGAGAGCTGTGCTGAGGAGCAGGC K 2 1 2 1 201000 f 74 goat snp29330-scaffold316-2041427 7 86303527 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389824 Affx-122968187 AX-123260181 7 20737623 AAGTCAGTTTCTGTCAGATTTCCTTACCATCTTCA[C/T]GCAAAACAGAGTCAACATTTTCCCATTTGTATTCG Y 2 1 2 1 202000 r 74 goat snp29331-scaffold316-2082501 7 86261716 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380184 Affx-122975509 AX-123250542 7 20787152 TTAAAGGAGAATGATGAGTTACAAACTTAAATAAG[C/T]GTATAATTTTTCATCATTAGAGAATGACTTTCATA Y 2 1 2 1 101000 f 74 goat snp29332-scaffold316-2132030 7 86213764 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406295 Affx-122956071 AX-123276647 7 20845615 TCTCAATAGGTAGGTTAAGATCAGCATATAGAAAG[C/T]GTTGAACATCAGAGTGAGTACATGAAAGTGAAAGT Y 2 1 2 1 101000 r 74 goat snp29333-scaffold316-2190493 7 86155917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273261 Affx-1111833532 AX-519546911 7 20863367 GGCCTTCTTTTATTTCCTGGAGAAATAAATAAGTT[A/G]TAAAAAAGGTAAGGCTTTCAAGCTGTAATAATAAA R 2 1 2 1 101000 f 74 goat 7_20863367_AF-PAKI 7 20863367 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38424819 Affx-122941372 AX-123295165 7 20876860 GTTATCCCATAGTACACAATATCAAGCTTAGAACT[A/G]TACCATCGTGTATGGTACAACCATACATATTTTAA R 2 1 2 1 101000 f 74 goat snp29334-scaffold316-2221738 7 86124692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794021 Affx-122923796 AX-385280990 7 20935279 CATCATTCAGTTGATTCCTTTATTGCTTTAACAAA[C/T]ACTTATTGAACACTCTTTTAGGAGACAGAGGTACC Y 2 1 2 1 101000 r 74 goat snp29335-scaffold316-2280157 7 86065982 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446363 Affx-122925598 AX-123316699 7 20976522 AAGAAAGGGTACACTGTGAGAGAGAAGTCACTTCC[A/G]TATGAAAATTAAAGAATAAATGGTGATGAAATAAA R 2 1 2 1 103000 f 74 goat snp29336-scaffold316-2321400 7 86024585 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402199 Affx-122959168 AX-123272552 7 21006349 TGATTCTAAGAAAATGTGAGAATAATTAAATTACT[A/G]TACCTTTTACCTGATATAATCCTGAAACACTGTGT R 2 1 2 1 101000 r 74 goat snp29337-scaffold316-2351227 7 85993922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425222 Affx-122941015 AX-123295568 7 21037235 TAACAAATAAGTATTCTTTTATCGTATTAAAGCTA[C/T]GCCTAGTCATTTCTTCCCTTTCTATTTCAGGATAT Y 2 1 2 1 303000 f 74 goat snp29338-scaffold316-2382113 7 85962683 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415414 Affx-122948731 AX-123285763 7 21072124 ATTTGCTCTAAGAAAGTGATACTAAATTAGGGTTC[A/G]TTTTTTTATTTATTTGTTTTTGGCTGTGCTGGGTC R 2 1 2 1 303000 f 74 goat snp29339-scaffold316-2417002 7 85927913 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422366 Affx-122943429 AX-123292712 7 21109041 AAGTGGAAGTTCAAGAACTTTCCAGAGCAGAAGGC[A/G]TTTGTGTCCCAGGTGATTGCTCCTCAAAACCCTCC R 2 1 2 1 201000 r 74 goat snp29340-scaffold316-2453919 7 85891153 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786982 Affx-122928924 AX-385274010 7 21151757 GAATCATATTCACAACCAAATCTCAGAAAAACTTT[A/G]CCATAGTGGTCTGCAAGTTATCTATAGTTGTAATT R 2 1 2 1 101000 r 74 goat snp29341-scaffold316-2496635 7 85846558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433050 Affx-122935757 AX-123303391 7 21181931 TCACCTACGGACCCAAAGCTTCCTGTCACTTTTCT[A/G]CCAGATACCTGGGGGCAGTCTGAGTCTAACTTAGC R 2 1 2 1 101000 f 74 goat snp29342-scaffold316-2526809 7 85816479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782362 Affx-122922898 AX-385269438 7 21213523 GTACTCTCTAATAAGCCATCTGAGAATCTCATGTG[C/T]GTATTAAATTATATACCACACATACTGTAAAATCG Y 2 1 2 1 101000 f 74 goat snp29343-scaffold316-2558401 7 85783881 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411310 Affx-122952286 AX-123281660 7 21247665 CAGTTAAACAGAGGAGGAGAAAACACATAGCTGAA[C/T]GAAAGATGGGTCAACTCTATATGTTGGTGCTGCTC Y 2 1 2 1 101000 f 74 goat snp29344-scaffold316-2592543 7 85749755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386426 Affx-122970807 AX-123256784 7 21285995 AAATGATATACTTCATTTATTTTAGAAGTTTCAAG[C/T]AGAAAAATGTTCTTAGTTCCTGAGCACATGAAAGA Y 2 1 2 1 101000 r 74 goat snp1218-scaffold1031-37241 7 85721173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449765 Affx-122922445 AX-123320100 7 21346333 GCTGAGATATGTATTTCAAGTAGGTATTGTAATGA[C/T]ACTCTATACTTCCTTTCCATAGAAATTCTCTCATT Y 2 1 2 1 101000 f 74 goat snp1219-scaffold1031-97579 7 85661515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801735 Affx-122960622 AX-385288643 7 21383942 TGGGAGATTCCTTTCTTTGTGACAGTACAGGAAAA[C/T]TTCACAAGAGTGTGCACTTTTGAAAATATGATCAG Y 2 1 2 1 202000 r 74 goat snp1220-scaffold1031-135188 7 85623652 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785018 Affx-122959297 AX-385272065 7 21425896 TAATTCTCAGCATTTCTGTCTTCTCAGCCACTAAT[C/T]GTTTTACTGTCTTGTTAGGATAGTGATCTTTTCAA Y 2 1 2 1 101000 f 74 goat snp1221-scaffold1031-177142 7 85581755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774777 Affx-122967732 AX-385261911 7 21567638 TGAGAATTTGTTTGGTCAAAAAGATAGAACTGCTT[A/G]TAATACAAACAATGGAACATTGCTTGGAATTATTT R 2 1 2 1 201000 r 74 goat snp1223-scaffold1031-318884 7 85438479 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439807 Affx-122930485 AX-123310144 7 21599258 GCTCAGGGTCAAAGTCTATATCCTGAACAAAGAGG[C/T]AGATGTGATCCAAAGCAAAAGAAACGTCACATTCT Y 2 1 2 1 101000 f 74 goat snp1224-scaffold1031-350504 7 85407538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436983 Affx-122933150 AX-123307321 7 21631203 AAAGCCCTGGATTTTTCAGCTTGAGTGATAAGGAG[A/C]CTACTCTTGGATATACAGAGGGAAATTAGGATGGA M 2 1 2 1 101000 f 74 goat snp1225-scaffold1031-382449 7 85375826 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792131 Affx-122943866 AX-385279116 7 21660427 TAAATAATTTACAAAAATTGATTACACTTGAATAC[A/G]TAGAAACAGTAGGTGTTATTATAATTGGGCTCTGA R 2 1 2 1 101000 r 74 goat snp1226-scaffold1031-411673 7 85346585 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378289 Affx-122976864 AX-123248648 7 21693961 CACACCTTACAATATATCTGAAGAAAATGACTGCC[C/T]ATCTCAGAGTAGAACTGCTAGGTCAAGTGTGTGTT Y 2 1 2 1 201000 r 74 goat snp1227-scaffold1031-445207 7 85312880 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402957 Affx-122958165 AX-123273310 7 21730961 ATGTGTGTTTGAGGAATTTACCAAAAAGGTAAGGA[A/G]AGCCAGGAAGATGTGTAAAAGGTAAACCTGCAAGT R 2 1 2 1 201000 f 74 goat snp1228-scaffold1031-482207 7 85275951 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770598 Affx-122964500 AX-385257762 7 21769882 TCTTTACAGATTTTGATCTACCATTGGACATTTCA[G/T]ATCTACTGTTTAAATGCAAGATATTTAATACCACA K 2 1 2 1 101000 r 74 goat snp1229-scaffold1031-521128 7 85236624 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436457 Affx-122932988 AX-123306795 7 21835594 AGGCAATACGGTAAAGCAGAAGGAGCAAAGACCTC[A/G]TGGTACTTTGGCTTCAATTCCAGTCAAGATTATCA R 2 1 2 1 101000 r 74 goat snp1230-scaffold1031-586840 7 85170802 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794986 Affx-122927740 AX-385281946 7 21877769 ATTTCATCCTTAGGTTATATCTTACTGAAGATGTA[C/T]AGTTCAAACACTGTGTTTAAATGTAACTTTAAATA Y 2 1 2 1 101000 f 74 goat snp1231-scaffold1031-629015 7 85127912 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400008 Affx-122960802 AX-123270363 7 21923095 TATATTATATACCAAAAAAAGATAACATGAAAAAT[A/G]TGAGTATATTTAAAGGTACTGGAGGAAGATGTTTC R 2 1 2 1 101000 r 74 goat snp1232-scaffold1031-674341 7 85082457 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440665 Affx-122929932 AX-123311002 7 21954458 ACCTTCAATACCTGGTATATATAAGTAAGTCTTTC[A/G]TTTTTTTCCCCTTTCCAAAAGGCAGTATTGGGATT R 2 1 2 1 103000 r 74 goat snp1233-scaffold1031-705704 7 85050785 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441348 Affx-122928879 AX-123311685 7 21988297 TGTTTGCTTGAGCTTTACAGAAGTTTCAGTGTGCA[A/G]TATTGCCATGGAGTATTCTCAAGAAAACATAATGT R 2 1 2 1 101000 f 74 goat snp1234-scaffold1031-739543 7 85016897 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380713 Affx-122975152 AX-123251071 7 22056110 GAAATTGGTGCCCACAACTGTGACATGCATGCCTC[A/G]TGTCTGAACGTCCCAGGAAGCTTCAAATGTAGCTG R 2 1 2 1 201000 r 74 goat snp1235-scaffold1031-807356 7 84954574 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769149 Affx-122958447 AX-385256325 7 22110942 ATTCAAGAGATGTTTCCTTTGGTTTTCTGCCAGTC[A/G]TCCAACTGGTACACATCTGATTATTTTAAAGGAAG R 2 1 2 1 202000 f 74 goat snp1236-scaffold1031-862188 7 84899729 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377532 Affx-122977467 AX-123247891 7 22144303 TGTAGAGTTGTGCTCACTAAGATCCTATTGGTAGA[C/T]GTTGACTAATATTGTCATGTAGTTTTCCAAGACAG Y 2 1 2 1 101000 f 74 goat snp1237-scaffold1031-895549 7 84866240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779469 Affx-122978593 AX-385266572 7 22190668 AGCAAAGCAAAACAAGGGGCTTTTGCTTGAAGTTT[C/T]CTTTTGAAGAAACAGGTTCCTATAAAAATAAGTTG Y 2 1 2 1 101000 f 74 goat snp1238-scaffold1031-941914 7 84819536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394674 Affx-122964366 AX-123265029 7 22223501 CTCCATCAGCTAGCTGGCAGTGCTAGTTCTACTCC[A/G]TGGAAATAGAGGACTGAGGCAATGGTTCTCTAACT R 2 1 2 1 101000 r 74 goat snp1239-scaffold1031-974747 7 84786485 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278636 Affx-1111836438 AX-519552115 7 22250487 AGGGTTTACATAGAAGATTCCCTCAGGGAGTCTCT[A/C]ATAACCCACTGTACAAATTTAAATGCATATGTGCC M 2 1 2 1 101000 r 74 goat Random2.2K-770 7 22250487 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779577 Affx-122966878 AX-385266680 7 22266343 TAAACATATGTGTAAGTTTTGATAAAAGTTACAAA[G/T]CAAATATCTGTATAAATCACAGTCTAGGTCACATA K 2 1 2 1 101000 r 74 goat snp1240-scaffold1031-1017589 7 84743523 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797576 Affx-122972407 AX-385284515 7 22357432 TCAGAAGTGACCTGAGGTAAAACTGAAACTGCTAG[A/C]GAGTATCTCATCTTTGTTGAGGTTTTTCTTTATAA M 2 1 2 1 101000 f 74 goat snp1242-scaffold1031-1108678 7 84651695 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444254 Affx-122927216 AX-123314591 7 22388818 CGGACACGACTGAAGCGACTTAGCAGCAGCAGCAA[C/T]AGCAGCAGCAATGATACTGTGCAAGTTTCCAAAGC Y 2 1 2 1 103000 r 74 goat snp1243-scaffold1031-1140064 7 84619931 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402578 Affx-122958440 AX-123272931 7 22452314 AAGAACAGAGATAGAGAATGTCTACCAGATATTTT[A/G]TCAGGTGCTGAAGAGAGGGAAAATGAATAGATAAA R 2 1 2 1 101000 f 74 goat snp1245-scaffold1031-1203560 7 84555318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380403 Affx-122975320 AX-123250761 7 22503903 TGTTTCCCAAATTTCTTTTCTCCCTACAAGCAACT[A/G]CTATTTTGAATTTTTGAGTGATTCTTTCAGGTTAA R 2 1 2 1 201000 r 74 goat snp1246-scaffold1031-1255149 7 84503823 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419671 Affx-122945942 AX-123290019 7 22549945 AGCTAGATGTTTTGAATATCATCATTAAATAGATC[A/G]TCGCTCCCATCTCTCTCTTCCACTCCATGGAAGAA R 2 1 2 1 201000 f 74 goat snp1247-scaffold1031-1301191 7 84458127 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772100 Affx-122954117 AX-385259255 7 22578694 TTCCATTTTATACAATTAATCTGCTAAACACTGAA[C/T]GGAAGTATCTGAGTGTTATATGTTACATAAAGGGA Y 2 1 2 1 101000 r 74 goat snp1248-scaffold1031-1329940 7 84429319 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403968 Affx-122957437 AX-123274320 7 22620492 CAATCTACCAGATGCTCCTCAGCCAGTGAATTATT[A/G]TTTGTCCCAATAAGCCTTTATTATTATTTTATGAA R 2 1 2 1 101000 f 74 goat snp1249-scaffold1031-1371738 7 84387859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452332 Affx-122920657 AX-123322665 7 22657858 TGAAAAGTGAGGGGGTTGAAACAGATGATAGCAGT[A/G]TTTCTTTCCAGCTTTGCAAACTCCAGAGAATCCAG R 2 1 2 1 101000 f 74 goat snp1250-scaffold1031-1409104 7 84350492 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793973 Affx-122923174 AX-385280942 7 22731467 GGTCCTGGACATGTAGCAAAACTTAAGCAAATATG[C/T]GCTATAATGATTTAAGAGGGAAAACTTTTTACAGT Y 2 1 2 1 101000 f 74 goat snp1251-scaffold1031-1482713 7 84276534 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274011 Affx-1111833984 AX-519547616 7 22765442 AGATTTGTGAACTAAAGGTCTGCAGATTGAATGCT[A/G]TACTTGTTTGCTATAGGAAATAGACAACTGCAACA R 2 1 2 1 201000 f 74 goat GoatD01.012797 7 22765442 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278466 Affx-1111836439 AX-519551949 7 22853476 ATCTGGGATTATTGGAATGGTAGCTTTCTCCCTCC[A/G]CTTGTGCTTCAGATTTATACCTCTCCAAGGTAAGG R 2 1 2 1 101000 f 74 goat Random2.2K-771 7 22853476 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382140 Affx-122974049 AX-123252498 7 22864179 TCAGGCCGGCCAGTTTCATCAATGAGGGGTCTTTG[C/T]ATCATCTACCTGAGACTCTCAGCCTGGGTATCAGT Y 2 1 2 1 101000 f 74 goat snp36505-scaffold44-17777 7 84142027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435663 Affx-122933341 AX-123306002 7 22912307 GGAGTTTCCAGGCAAGAGTACTGGAGTGGGGTGCC[A/G]TTGCCTTCTCCAAAGAAACCCTATGATGCCACAAA R 2 1 2 1 103000 r 74 goat snp36506-scaffold44-65905 7 84097003 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401629 Affx-122959596 AX-123271982 7 22950451 AACAGATATTACTTAAAAAGTTTCTAATAAAAACA[C/T]AGATTTTTAAAAAACTACTCAAAGATGAAAAAGAC Y 2 1 2 1 303000 f 74 goat snp36507-scaffold44-104049 7 84058969 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380800 Affx-122975092 AX-123251158 7 23001802 CAAATATGCCTTCCCACAGCATGCTTTGCACCCCC[A/G]TGACATCTCTCTGTCTGCCCTACTTCATTGCGCTG R 2 1 2 1 101000 r 74 goat snp36508-scaffold44-155400 7 84007453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768681 Affx-122921441 AX-385255859 7 23042254 GAAGGCAGGCTTTGCCCATTCTGATACAAAAACCA[C/T]AGTAAACAATCAGGTTGAATAAAATCATCACAATG Y 2 1 2 1 101000 f 74 goat snp36509-scaffold44-195852 7 83971314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774676 Affx-122945736 AX-385261810 7 23075229 AATTTTCTAATGCATTTAACAGTATTTGAATCTCA[C/T]AAGATTCTCAGCTTCTAAACTAACATCTGAATCTA Y 2 1 2 1 101000 r 74 goat snp36510-scaffold44-228827 7 83938345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408081 Affx-122954726 AX-123278432 7 23138263 TGTTTCCCAACTACCTAGCATAGTACCATATTACC[A/G]GCAAATACTTTGTGAGGGCCTGCTATGCCCCAGCC R 2 1 2 1 101000 f 74 goat snp36511-scaffold44-291861 7 83875376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775766 Affx-122945345 AX-385262897 7 23166834 TATATAAAACACCATATCAGTGTCTCTCCTTCAAG[C/T]AGACACATAAATTTAAAACTCTGGGAAACACATGG Y 2 1 2 1 101000 r 74 goat snp36512-scaffold44-320432 7 83846861 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405149 Affx-122956952 AX-123275501 7 23208970 TTATGATAATTATATGTACTTCTGAACATTTATAC[A/G]CCTAATTAGAAGATTGAAAGTTTTAAGGCAAGTAA R 2 1 2 1 101000 r 74 goat snp36513-scaffold44-362568 7 83804722 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768624 Affx-122938263 AX-385255804 7 23255568 TTCTCTTTAAATGGGCCTAGCATTTTAGACTGCTA[C/T]AGCTAACTACTTCCAAGGCTTTCTTTGGAGCCTTT Y 2 1 2 1 101000 r 74 goat snp36514-scaffold44-409166 7 83757463 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383319 Affx-122972694 AX-123253677 7 23290308 CTGTACAGGAAGTCTGTTGGTTAGGGAAATTAGTA[C/T]TATGCATAGTTATTGTTTTTTAAATAAGGTTAATT Y 2 1 2 1 101000 f 74 goat snp36515-scaffold44-443906 7 83722712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391078 Affx-122966836 AX-123261435 7 23348687 CAAGTAAATATTGCACACTTGTGTGTGTCTGAAGG[A/C]TGAATTTCTGGAATAGGTATTTCTGTTTCATGAAT M 2 1 2 1 201000 r 74 goat snp36516-scaffold44-502285 7 83664157 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442213 Affx-122928783 AX-123312550 7 23392442 TTCCCCTCTTGAGGGTTCTAAAATGTTATTCACTC[A/G]TCCTTTTTTTCTAAATACAATAAAATTATTTTTTA R 2 1 2 1 101000 f 74 goat snp36517-scaffold44-546040 7 83620854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376979 Affx-122977748 AX-123247338 7 23421525 AACAATGTCAAGATTAAAATGAAACAGCCAGGAAA[C/T]GGTGGAAATCTGCAGGAAAGGCTTCCTAGGATCTG Y 2 1 2 1 101000 r 74 goat snp36518-scaffold44-575123 7 83591980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273304 Affx-1111833533 AX-519546948 7 23430743 GGACGGTTGCTGCCAGAGATCAGCTTCCCAGAAGT[A/G]ACATATGGCACACTTGAGAAGGTGTGCCCGTTGTA R 2 1 2 1 102000 r 74 goat 7_23430743_AF-PAKI 7 23430743 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425811 Affx-122940693 AX-123296157 7 23466807 TAGGCAATGCCCAGCAAAGCTAAATCGCCAGTGAA[C/T]GGTTATTGAAGGAATGAATGAATAAATGACTTAAC Y 2 1 2 1 101000 f 74 goat snp36519-scaffold44-620405 7 83546555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400601 Affx-122960391 AX-123270956 7 23502136 CAGACACAATGACTGAGAGGTGAGGGTGCTTTACA[C/T]ACCAGCTAGCTCAGGTCTATCCTTGCAGGTGTAAC Y 2 1 2 1 101000 f 74 goat snp36520-scaffold44-655734 7 83511376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447582 Affx-122924019 AX-123317918 7 23535096 CAATACCCAACTGGGAGTGGAGCAATATACAACAG[C/T]GGATAATCTAAATCCCCTTGTGTCAGAAAGCATTT Y 2 1 2 1 101000 f 74 goat snp36521-scaffold44-688694 7 83477829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400017 Affx-122960797 AX-123270372 7 23574719 ATCCTCAGTGTTCTTCGTTTTTAATTGTTACGTTT[A/C]TCCCAGGTTGTATTTCATGTATTCAATAAATATTT M 2 1 2 1 101000 f 74 goat snp36522-scaffold44-728317 7 83437621 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801716 Affx-122948879 AX-385288624 7 23628697 ACGTGTACAAAGAATCTTACTGGCAGCCAGAAAGC[A/G]AGGAGAATTAAATTCTCTATTGAAATGTCTGAGAA R 2 1 2 1 101000 f 74 goat snp36523-scaffold44-782295 7 83379163 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781230 Affx-122925945 AX-385268315 7 23665155 GGAAACTGGTTAGCCTGTAAATTTCCAGATGCTAG[C/T]GGCACTGTAAACAGATCTGCTGTGTATTTTCTGCA Y 2 1 2 1 101000 f 74 goat snp36524-scaffold44-818753 7 83342754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395290 Affx-122964074 AX-123265645 7 23738266 CTTGGTCCTGAGTGAGGAATAGATTAGCAAGAAGA[C/T]GTGCGCTGGGGTAGCCAGGAAGGAAGGGAAAAGTA Y 2 1 2 1 101000 f 74 goat snp36525-scaffold44-891864 7 83270065 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377063 Affx-122978290 AX-123247422 7 23816162 TTGGACATGACTGAGCATACAAGTTCACATGTAGC[A/G]CTTATATATGGCAGGCAGATTTCTAAGCACCTAAA R 2 1 2 1 101000 f 74 goat snp36527-scaffold44-969760 7 83192061 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796219 Affx-122974981 AX-385283169 7 23862238 GGAGGGGCCCTGTATGAATCCATTTACGTAAAATT[C/T]GAAAACAGGCTAAGTTCATGTATAATTTGACCAGA Y 2 1 2 1 201000 r 74 goat snp36528-scaffold44-1015836 7 83146068 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438773 Affx-122931383 AX-123309110 7 23890782 AAACTGCTGAGCTCTTCTGTTAACAATGCTTTATA[C/T]GAGAATTTGGGAAAAGGTCCTCATTTTTCCCTTTT Y 2 1 2 1 101000 f 74 goat snp36529-scaffold44-1044380 7 83117252 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789198 Affx-122970389 AX-385276210 7 23928994 TGTTATTAGGATCAGTGTTATGTGATCTTCCAAAA[C/T]GAATAGCTCTGATTACTGTGCATGTCCTATGTCTT Y 2 1 2 1 101000 r 74 goat snp36530-scaffold44-1082592 7 83077358 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445950 Affx-122925906 AX-123316287 7 23958101 TTGAGTTTAGCTAACTCAATAAGGCAACAAAAGCT[A/G]CTGACATTCAAAACCTGAAGAAGGCAGAGGAGGAC R 2 1 2 1 101000 f 74 goat snp36531-scaffold44-1111699 7 83048159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778939 Affx-122977955 AX-385266046 7 23994033 CAAGCAGAAGTACATGTTGACTCTCAGGAAATAAG[C/T]TGTTATCTAAATTCAACTATTTGGACCAGATACAA Y 2 1 2 1 201000 r 74 goat snp36532-scaffold44-1147631 7 83012086 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411579 Affx-122951623 AX-123281929 7 24022742 AGTCTGAACCACCAGGGCTGGCCCCTAGATAGCTG[C/T]ATTTTAAACAAGTTTGTCAAGTGATTGCGATGTAC Y 2 1 2 1 101000 r 74 goat snp36533-scaffold44-1176340 7 82983221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795061 Affx-122946198 AX-385282020 7 24076279 ACACCTTTCAAGTCTCCAGAACTTTTAGTTAGCTT[A/G]AATTGTCTTTGGATATCACAGAGCTAGTTGCCAGG R 2 1 2 1 101000 f 74 goat snp36534-scaffold44-1229877 7 82929419 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274704 Affx-1111834450 AX-519548290 7 24077404 TCGCTTTTTTCTTCCTGGTTCCCTGTCACTCCAGT[A/C]GCACTCCACCCTGGCAGCAGCAATTCGTTTCTGTT M 2 1 2 1 201000 f 74 goat GoatD01.036487 7 24077404 C A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320793087 Affx-122921700 AX-385280065 7 24115534 ATTGCGATGGGCCAGTGGATGAGATATAGTGGTAA[C/T]AGAAGGAGTTGTCCTTTTCTAGAGCTTTTACAGTT Y 2 1 2 1 101000 f 74 goat snp36535-scaffold44-1269132 7 82889887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416397 Affx-122947858 AX-123286746 7 24155186 AGTAGAGACACAAAAGTATACACACTATATCAAGC[A/G]TGATAGTTTAACTCTGTTCTCACTTTATTCATGTG R 2 1 2 1 101000 f 74 goat snp36536-scaffold44-1308784 7 82848918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452570 Affx-122920515 AX-123322903 7 24200420 GAAGGCTACACTCTAATACACAGTGGATATAGGGA[C/T]GGGATTGAGGATAAAAGAAATGCATTCCAAAAAAT Y 2 1 2 1 201000 r 74 goat snp36537-scaffold44-1354018 7 82803172 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398844 Affx-122961064 AX-123269199 7 24242398 TGATCTTTTTCTTCCAGGATGTTGTAATGATTAAC[A/G]TGGTCATCTCTACAGGATTTGAGTTTCAGTAGAAA R 2 1 2 1 101000 f 74 goat snp36538-scaffold44-1395996 7 82760502 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787918 Affx-122954364 AX-385274940 7 24298328 GACAACTTATGTTAAGTATGTTTGACTGAACTGCC[A/G]TTTGAAAGACTTCTATATATTTCAAATAGTGGAAT R 2 1 2 1 202000 r 74 goat snp36539-scaffold44-1451926 7 82704934 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419862 Affx-122945370 AX-123290210 7 24331167 TACTGTTTGACTCTTGCCCTCAAATCTTTAGTGTC[C/T]TATAGTCTTATATATTAAAGACTGTAATAATTTAT Y 2 1 2 1 101000 f 74 goat snp36540-scaffold44-1484765 7 82671785 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389495 Affx-122968312 AX-123259853 7 24342888 CTGCTTCTTTGGGCTATTTTTTAAATGACTAGATA[C/T]ATAAAATTTTGAGTTTGGTTCTAGCAGGCTTCTGA Y 2 1 2 1 103000 r 74 goat snp50484-scaffold724-910315 NW_017196265.1 16457 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775042 Affx-122943593 AX-385262174 7 24373800 CAGAGAAACAGAAGTTTTTAATAAGCGATGACCAA[C/T]ATTCTATTGCAAGTTGTGCCAGGAATTTTGTATTG Y 2 1 2 1 101000 f 74 goat snp50483-scaffold724-879403 7 82615208 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419074 Affx-122945800 AX-123289422 7 24403133 CATAACACAAGTGCTATTCATGGGTCCCACACTCC[A/G]CAGCTGTAAAACGAGATGTGTAGGAGCAGCCCCTA R 2 1 2 1 101000 f 74 goat snp50482-scaffold724-850070 7 82585912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401544 Affx-122958908 AX-123271897 7 24451268 GGTCACAAAGAGTCCGACACAACTGAGCGACTTTC[A/G]CTTTCACCCATTGGTCAGCCAATATGTTTATGCAA R 2 1 2 1 101000 r 74 goat snp50481-scaffold724-801935 7 82539014 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377701 Affx-122977409 AX-123248060 7 24504551 GCTTTAATGAGGGAAAAAAGTCAGGGTATTGACAA[C/T]GAGGAATAAGATGGAAATGACTACTGGTTAGATGA Y 2 1 2 1 201000 f 74 goat snp50480-scaffold724-748652 7 82485241 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414382 Affx-122949997 AX-123284731 7 24551032 GATATCTTGTCATGCAAGAAAAGTAAATATCCCAA[C/T]GTTAAAGTTATTTTTTTGTTAACTTATTATTGATT Y 2 1 2 1 101000 f 74 goat snp50479-scaffold724-702171 7 82438580 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432204 Affx-122936383 AX-123302545 7 24595884 ATATGTTTCCTTGTTCAGAAAATGAGGATATCAAA[A/C]TTCACCTTAGAGCAGATATTAAAATAAAGTAATAT M 2 1 2 1 201000 r 74 goat snp50478-scaffold724-657319 7 82393442 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401924 Affx-122958821 AX-123272277 7 24634939 ATAAAAAGTTGTCTAACAACCAATTGTTGGTAAAG[C/T]AGGCTAGACTGAAGTCAGGAGACAGCTCTTAGCCT Y 2 1 2 1 101000 f 74 goat snp50477-scaffold724-618264 7 82352355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382873 Affx-122973515 AX-123253231 7 24668667 GAAGCTTCAATAAAAGCCCCATCTCTAAGCTATTG[C/T]TCCAGGACTGATGAGCCAGTGTTTGCCCTGTCCAG Y 2 1 2 1 201000 f 74 goat snp50476-scaffold724-584536 7 82317994 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414230 Affx-122949638 AX-123284579 7 24749370 ATCCCTGACCCACCTCCTTGCCATCACAGGCAACC[A/G]CTCTTCTGAGTTTTATTCCTATAGATTAGTTTTCC R 2 1 2 1 201000 r 74 goat snp50474-scaffold724-503833 7 82237350 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384326 Affx-122972264 AX-123254684 7 24805807 TGTTAACTGGTCAGGAGAGTCACTGTCACAAAAAG[C/T]ACTTGGCAAAAATCTTGAAAAATTTGAATACTATT Y 2 1 2 1 101000 f 74 goat snp50473-scaffold724-447396 7 82182575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376680 Affx-122978996 AX-123247039 7 24851364 TCCCTCGGCTTCCCTTAAAGATAATTGGTAGTTGA[C/T]GCAGGAAGAGCAAAGAATGTGATAAATCTATAATA Y 2 1 2 1 101000 f 74 goat snp50472-scaffold724-401839 7 82137124 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799569 Affx-122977732 AX-385286499 7 24927572 AGTGAGACTAAGGAAATTTTCAGAGTGTGAATAGC[A/G]TGAAAAGAATGTAGTTGAGAATTCACTCCTGCATG R 2 1 2 1 101000 f 74 goat snp50470-scaffold724-325631 7 82060667 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800548 Affx-122964764 AX-385287467 7 24973149 GTAGCTTCAGGTAAGCTGGTTTAGTTGTTTAACAC[A/G]TTTGTGCTCAGTTATTGGTTCTTGGGGATATGGTG R 2 1 2 1 202000 r 74 goat snp50469-scaffold724-280054 7 82014640 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427041 Affx-122939824 AX-123297386 7 25002159 TTCAAGCCTCACATCAGTTGGTGGGAGTGTAGATT[C/T]AATGACATTTATTTTGGAAAACATGTTCTGCTAAA Y 2 1 2 1 101000 f 74 goat snp50468-scaffold724-251044 7 81984325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781812 Affx-122956938 AX-385268894 7 25101359 ACTTTAGGAAAATCCCATGTTCATCCTATTTTACC[A/G]TTGCAGAAGTCTGTGGGATAACCTTAATATTAAAA R 2 1 2 1 101000 f 74 goat snp50466-scaffold724-151844 7 81884915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273600 Affx-1111833693 AX-519547214 7 25138280 ATTTTATGCTGCCACGTGGCCTGCAGAAGACTTGA[A/G]CTGACACTAACCCCTCTTGCCAGTGTCAACCCTAG R 2 1 2 1 101000 r 74 goat GoatD01.001728 7 25138280 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38450792 Affx-122921819 AX-123321126 7 25139385 GCTCTTCTTGCCAAGTCCTGCTACGTTCTGTGCTG[C/T]ATCATTGCCAGAAAGTTTTCTTCCTCCCCTTAGGT Y 2 1 2 1 101000 r 74 goat snp50465-scaffold724-113818 7 81846883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429681 Affx-122937645 AX-123300022 7 25172890 CTATCATCTGTCTTTTCTCATTTTGTTCAAATCTA[C/T]GTTTCTAATGCATGTGATTCTCCTTAGAATCAGAT Y 2 1 2 1 101000 r 74 goat snp50464-scaffold724-80313 7 81812994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413120 Affx-122950379 AX-123283469 7 25212695 TAAAGTTTAAATCAGTATCTTTATGCATAGGGCTA[C/T]ATGAGGGTTATAGATTACTAGATGAAACTAAATGT Y 2 1 2 1 201000 r 74 goat snp50463-scaffold724-40508 7 81772446 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766895 Affx-122939032 AX-385254213 7 25242540 GCACTGGAGCCAAAAGCAACAAGCAGAATCTAATC[A/G]TGAGGAATTGCATAAGTAAGTGGTTCTCTTCAGCC R 2 1 2 1 101000 f 74 goat snp50462-scaffold724-10663 7 81741491 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772134 Affx-122962659 AX-385259289 7 25303837 GCCTCGTGCTAGGTTCGGGCAAAGCCATCAGTATA[C/T]GTTAGTTTCCAAGTTTAAAGGAAGGAGTTTCCCAA Y 2 1 2 1 101000 r 74 goat snp52632-scaffold786-1309169 7 81680273 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451359 Affx-122921250 AX-123321692 7 25360919 TGCTTGAACATACGGAGACTATTTCAAGAAAGACA[G/T]ACAAAACTGTTCCAAGTAGTTGACTCTGGGGAGTA K 2 1 2 1 101000 r 74 goat snp52631-scaffold786-1252087 7 81623183 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401456 Affx-122958975 AX-123271809 7 25395571 TGACGCTATTCAAACTTAAACAGGTATCAAGACCA[A/G]ATCATTTCGTTCTGTGAATTTATTCAACATTCAAC R 2 1 2 1 201000 r 74 goat snp52630-scaffold786-1217435 7 81588962 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435061 Affx-122933738 AX-123305401 7 25437693 TTGTTAAGACCCTTCTTTTTGCCAGAATTCTTCCC[A/C]GCCTTCGCTCCAATAACAGAACCTGGGCCGTTGCT M 2 1 2 1 101000 f 74 goat snp52629-scaffold786-1175313 7 81546833 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453793 Affx-122919579 AX-123324126 7 25497964 AGGAAAGATATAACTTGAACCCCATATCTGGCACC[G/T]CTCCCACTTCACCTCAAATGTTGTTTGTGCCTCTA K 2 1 2 1 201000 r 74 goat snp52628-scaffold786-1115042 7 81486343 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414299 Affx-122949589 AX-123284648 7 25546614 CATTAAAATAGCACTGATGTTGGAAAAAACAGTAA[G/T]ATTTGTCTGATGCCATACATACCAAGCAATGATTC K 2 1 2 1 101000 r 74 goat snp52627-scaffold786-1066392 7 81438161 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786892 Affx-122927900 AX-385273921 7 25625508 TCATTCTGAAATTTAAAAACCAACAAAGGCATACC[A/G]CTGCAGTTAGACAAAAAATCTAATGTTCTCACGGT R 2 1 2 1 101000 f 74 goat snp52625-scaffold786-987498 7 81359142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448516 Affx-122923451 AX-123318852 7 25674658 CCCACCACTTTATGCTCTCATTCTAATGGCTATTT[A/G]TTTTCTTCTGGTTAATTTCCCTTTCCTTTTCATAG R 2 1 2 1 101000 r 74 goat snp52624-scaffold786-938348 7 81309760 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408634 Affx-122953484 AX-123278985 7 25705672 AAACACAACTACTATCCAGAAGATCCTCTCTTCCC[C/T]CTATCTGTTCGTATTTTCGGTTACAATAGCCACAT Y 2 1 2 1 201000 r 74 goat snp52623-scaffold786-907334 7 81278831 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798875 Affx-122967564 AX-385285805 7 25744593 ACCCTGGCTGATACCAATAAAGGTTGGGCAATGGA[C/T]GTCAAAGAGAGTCTTATTGAAAGAGAAAGAAAATG Y 2 1 2 1 101000 f 74 goat snp52622-scaffold786-868413 7 81240097 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391925 Affx-122966936 AX-123262282 7 25798007 CCCAATTGTAAATGACTGGGGAATTTCAGTACCTA[C/T]GAGCTCAGCTTTATCTTTCTTTTCAGTATAAAGAT Y 2 1 2 1 101000 f 74 goat snp52621-scaffold786-814999 7 81186029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783972 Affx-122939778 AX-385271026 7 25832473 GGACAGACTTGGAATTTTATCAAAACATATTCCAC[A/G]TTCAACCCATTGTGGACTCTCAGCTTATTGCAAGT R 2 1 2 1 101000 r 74 goat snp52620-scaffold786-780533 7 81151173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399845 Affx-122960250 AX-123270200 7 25870071 TTTAACCAGAGTGATCGTGACAAAATGTGTAAGTC[G/T]CTTCTTAGAAGCTGCTCAGTGGATGTTCAATACGA K 2 1 2 1 201000 f 74 goat snp52619-scaffold786-742935 7 81113251 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381692 Affx-122974721 AX-123252050 7 25899986 GTATAGCCACACACTCAACGCTTTCACATGCGCTC[A/G]TTGACTCTCTTCACAATACAGTGATGTGGGGCTCG R 2 1 2 1 101000 r 74 goat snp52618-scaffold786-713020 7 81083633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781288 Affx-122944606 AX-385268373 7 25983257 AAATTCTTTTTCTTTTAGTACACTATAAAACATGA[A/G]GCAGAAGCACAATGACTTAATGAGTTTCTGTCTCT R 2 1 2 1 101000 r 74 goat snp52616-scaffold786-629749 7 80999001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464498600 Affx-1110516330 AX-515970828 7 26001149 TGTTGAATTCAACTGTGCTCTCACTGACTTTATGT[C/T]GACTAGACAGGTTAGTTTCTGACAGACAGATATTG Y 2 1 2 1 101000 f 74 goat 7_26001149_AF-PAKI 7 26001149 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401406 Affx-122959209 AX-123271759 7 26012099 ATCTTTGCACTTGTCCTTCTCTTTGTTTGGAAATG[C/T]ATTACCTTAAACCCTCTCATAGCTTTTCTTTCTCA Y 2 1 2 1 101000 f 74 goat snp52615-scaffold786-600907 7 80969711 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418357 Affx-122946585 AX-123288705 7 26056006 AAGCACCACAGTGGCTGCGAAGATTAAAGGGCAAA[C/T]GGAGTGCAACTCACCAGGTGACCTGAGCCATGCGA Y 2 1 2 1 101000 f 74 goat snp52614-scaffold786-557000 7 80925789 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405048 Affx-122956352 AX-123275400 7 26098137 GTGAACCGCCACAGAGCAGTCATCTCATTCCTTTC[C/T]GCAGTCAACTGCCCAGGGAACTCATGGAACAGACT Y 2 1 2 1 101000 f 74 goat snp52613-scaffold786-514869 7 80883685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802408 Affx-122928506 AX-385289312 7 26135571 ACCTTCACTGATCTATGGAGAGTGATTTTACAATT[A/G]TGTTTTTTGGTATTCACTGTTAACAGAAAGACCCC R 2 1 2 1 101000 r 74 goat snp52612-scaffold786-477435 7 80846515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388730 Affx-122968967 AX-123259088 7 26170671 TGAAACCCTGTCTTAGTCACTGGCAGTGTTTTCCC[A/G]TGGACACAGCACTGCAGTCTTTAGGGAAGTGGGGA R 2 1 2 1 201000 r 74 goat snp52611-scaffold786-442335 7 80810413 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423668 Affx-122942335 AX-123294014 7 26227934 AATATCTCAGAGCATTTCAGAGGCTAATGTGCTCC[A/G]TGAGATACCATGAACACATGTACCGTAAGGGGCTC R 2 1 2 1 101000 f 74 goat snp52610-scaffold786-385072 7 80751585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402196 Affx-122959171 AX-123272549 7 26282682 GCTAAGATCCCATTGTTTCCAGAAGCAGCTTCCTC[A/G]TGGAGCTCAATTCAGGGATGAAGAAGCTAGGAGGG R 2 1 2 1 101000 r 74 goat snp52609-scaffold786-330324 7 80696992 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383335 Affx-122972683 AX-123253693 7 26319244 AATGGCAAAAGCCCATTGATTAAGGTAAGGAATGA[C/T]AAAAGCTTGGATGATAAGGCCAGAGAAGAGGAGAG Y 2 1 2 1 101000 f 74 goat snp52608-scaffold786-293762 7 80660521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382974 Affx-122973353 AX-123253332 7 26353181 GAGGCATCAGCTGTCTCTTTTTTGCTTACCTTGCT[A/G]CACTTTCACTTTTAATACTCCGGTCACTCTTTCAA R 2 1 2 1 101000 r 74 goat snp52607-scaffold786-259825 7 80625938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426588 Affx-122939987 AX-123296934 7 26387084 AGAGAGATACCAGTCCTCAGGCAGCCCACAGAAAA[G/T]ATAGAATGCTGGATGTATGTTCCAACTCTCTCTCC K 2 1 2 1 101000 r 74 goat snp52606-scaffold786-225922 7 80591513 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793637 Affx-122966781 AX-385280610 7 26418342 TTACAAGGATAGTAAATTAAACCGAAAGTCCAGTT[A/C]GGAAATGACAGGTTGTTTACTTGTAAGAGGTTTTT M 2 1 2 1 101000 r 74 goat snp52605-scaffold786-194664 7 80560320 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391185 Affx-122967427 AX-123261542 7 26559403 GGGGAATCTTGGAAAATGATTTTCTTTTTAACTGA[C/T]GATTTAGTGTGCTCATTGGCCAAGAGGTCGTTAAC Y 2 1 2 1 101000 r 74 goat snp52601-scaffold786-53603 7 80420370 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446989 Affx-122924641 AX-123317325 7 26601706 ATAGGATTTATTGACCACACCAGGACAGTCTGGAG[C/T]GGGAAAGGAGATGACATGCTAATGAAAAGTATCCT Y 2 1 2 1 201000 r 74 goat snp52600-scaffold786-11300 7 80377740 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781832 Affx-122932170 AX-385268914 7 26628682 GTTCTAAAACCAAGTTGTTACTAGTGGTTCAAGAC[A/G]CTGGCATTTTCTGTTAAAGCTGACTCAGAGACAAA R 2 1 2 1 101000 r 74 goat snp56907-scaffold902-15577 7 80351081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450712 Affx-122921884 AX-123321046 7 26712206 TCTCTTCCCCTCAATGGCTCAGCACAACAGTAGCT[A/G]TTATTTCCTGCCCTTTTCAGGATCAAATGCAGTTG R 2 1 2 1 201000 r 74 goat snp56908-scaffold902-99101 7 80267867 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794665 Affx-122943604 AX-385281626 7 26758554 GGTTTTGGCAAAAAACAATGCCAGTAACTAGTAAC[A/G]TTTTGAAAAACTTTGCCTGAGACTCCGGGTCTAAA R 2 1 2 1 201000 r 74 goat snp56909-scaffold902-145449 7 80221744 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446498 Affx-122925044 AX-123316834 7 26798697 CTATTCATGGGTTGACAGAATTAGTATTGTTAAAA[C/T]GGTAATACTATCCAAATCAATCTTCAGGTTTAATC Y 2 1 2 1 303000 f 74 goat snp56910-scaffold902-185592 7 80182034 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767471 Affx-122930041 AX-385254737 7 26843268 ATAGTCCCCTAAATTATAGCTAAATCACTGATAAC[G/T]CTTTGTATACACCATGAACTTCCATTCAGTTGGGT K 2 1 2 1 201000 f 74 goat snp56911-scaffold902-230163 7 80136724 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779844 Affx-122929514 AX-385266943 7 26871900 AAATAAATGTGGTGACCACACAGCCTGGGAATAAT[A/G]CTCTGTTTTTGGCAGGATGACAGTCCTCCTGTTGG R 2 1 2 1 201000 r 74 goat snp56912-scaffold902-258795 7 80108020 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396549 Affx-122962938 AX-123266904 7 26906731 CTTAATGCAGTGTCTTGAGGCATCGTGTTCCTGGT[C/T]GAGAAAGAAAACTATGGACGTGTTCATATATACTG Y 2 1 2 1 101000 r 74 goat snp56913-scaffold902-293626 7 80073300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399153 Affx-122960648 AX-123269508 7 26969064 CTGGCTGAAGAGACAGATATTTGGCCCCGGAGAGA[G/T]CAGAAAGGAAGAGTTCATTTAAAGAAAAAATTTCA K 2 1 2 1 101000 f 74 goat snp56914-scaffold902-355959 7 80010488 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421507 Affx-122943898 AX-123291854 7 27008311 TCTGTGTGTTAGGGCTGCTCAGTATCCTTCAGACC[A/G]CAGAACTCTTCAATGAGAACACTTTGGGAAACTGC R 2 1 2 1 101000 r 74 goat snp56915-scaffold902-395206 7 79971354 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390413 Affx-122967650 AX-123260770 7 27049556 ATTTGTTCCAGAGGAATAAATAAGGAGCGTGAGTG[C/T]ATTAAATGCAAACGGGGGACACGGTGGTGTTTTTC Y 2 1 2 1 101000 f 74 goat snp56916-scaffold902-436451 7 79930153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777872 Affx-122920209 AX-385264988 7 27080700 CTTACTTATAAAGTAACACTTGGGATGGAAAAATT[G/T]TTTAATGATATATTGGCTGACTGAAACAAATTACC K 2 1 2 1 101000 f 74 goat snp56917-scaffold902-467595 7 79898860 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798651 Affx-122971358 AX-385285583 7 27160287 AAAATAGAAGCGATACAATCATAGCTTTAAAATAA[C/T]TGCTCATTACTTTGCTGCATGTGTTTGAAGGATTT Y 2 1 2 1 101000 r 74 goat snp56919-scaffold902-547182 7 79817948 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448421 Affx-122923666 AX-123318757 7 27190988 CTACATATTTTTCACAGAAAAAGGCAAAACAAAAT[A/G]CAACTGCTGATAATCATCATTCCTGGAATGCCATA R 2 1 2 1 101000 r 74 goat snp56920-scaffold902-577883 7 79787284 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417803 Affx-122947371 AX-123288151 7 27231201 GAAGCAATGCATTCCACTCACAACTGGGATTCCAC[A/G]TTACAGAGATCAGCTCTGGGTTCTGTCAAAACTGT R 2 1 2 1 101000 f 74 goat snp56921-scaffold902-618096 7 79747578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429537 Affx-122937834 AX-123299879 7 27286941 GAAATTGCTGAAAGTGATGGCATCCCTGGTACCCC[A/G]TGCAACACAGGGTGTACTGTGGGCCTTCAAGAACC R 2 1 2 1 102000 f 74 goat snp56922-scaffold902-673836 7 79691267 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392899 Affx-122965729 AX-123263256 7 27325112 ACCATCATTTTTGCTTCAGTTTCACGTTTTTTGAG[C/T]AAAGTAATTTGGGCATCTTCCCATTTCTGCCAGCA Y 2 1 2 1 101000 r 74 goat snp56923-scaffold902-712007 7 79653040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414525 Affx-122949518 AX-123284874 7 27376463 TATACCTTGTCATAAATCTCTTTCTAGTGTTTCCC[A/G]TGCAGTTGTCTTTAAATACCTGGTCAGAAAATGTC R 2 1 2 1 101000 r 74 goat snp56924-scaffold902-763358 7 79601396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451533 Affx-122921094 AX-123321866 7 27425741 GTGGCCACCCACGAGTGCAGGATTTTCCTTCCTTT[C/T]TGGTCTTACTGTCACTCCCCTAGAACTAATGGTTA Y 2 1 2 1 101000 r 74 goat snp56925-scaffold902-812636 7 79551979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379832 Affx-122975818 AX-123250190 7 27456545 TCTTATTTTCTAATTCATGGTAAGAAGCTGGAATT[A/G]CATACTTTCTCTCAGAGAAGAACTCTACAAGAAGG R 2 1 2 1 202000 f 74 goat snp56926-scaffold902-843440 7 79520395 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379255 Affx-122976256 AX-123249614 7 27487257 ATATTTTCCCACCAGACAGCATTTAGATTCTCCTT[A/G]TTCAAGGAACTCATGTGAACATGCATTTAACAAAT R 2 1 2 1 101000 r 74 goat snp56927-scaffold902-874152 7 79489728 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411054 Affx-122951952 AX-123281404 7 27534450 TTGGTTGAGGTAAAGAACATTGAGAAAGCTTTTGC[A/G]CATCATCCATGCATCCATCCATTCACTCTTTCATC R 2 1 2 1 101000 f 74 goat snp56928-scaffold902-921345 7 79442837 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400946 Affx-122959705 AX-123271299 7 27576087 ATTAATTACAAATAGAAAAAGTATATAACTTTTGG[C/T]GAAAAAGAAGTGACCATTTTGATGTGACTTAATGG Y 2 1 2 1 101000 r 74 goat snp56929-scaffold902-962982 7 79400980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770127 Affx-122967870 AX-385257294 7 27608432 AAGTAACCACTGTTGCTCATTTATTTATGACCATT[A/G]CTATTTTTTGATTTTAATGTGCCCACAAATATTTA R 2 1 2 1 101000 f 74 goat snp56930-scaffold902-995327 7 79369738 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427326 Affx-122940129 AX-123297669 7 27659176 CTTTATTCTTAGAAAAAGTCAAATAAGCCAAATGA[C/T]AAACCATGAATTGGGTCTAGAGTATGGATCTGAAA Y 2 1 2 1 101000 r 74 goat snp56931-scaffold902-1046071 7 79318483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411357 Affx-122952253 AX-123281707 7 27759665 TAATACCACAGAACTGCCTTATCAAAATGAAAAGC[A/G]TCCCCTAAACATGTGATTCACTTTTTTTTTTTTTT R 2 1 2 1 101000 f 74 goat snp56934-scaffold902-1146560 7 79221325 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769504 Affx-122927332 AX-385256674 7 27953823 AGAGATAGGAAAACGGATCAACAGAACACTAATCT[A/G]TTTGATATGTGAAAACTTAAGCAAAGAAAAAAAAG R 2 1 2 1 101000 f 74 goat snp56938-scaffold902-1340718 7 79026257 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450788 Affx-122921822 AX-123321122 7 27993254 CAACCACAACAGAAAACTACGTTCCCCAGGAGAGG[A/C]TTTCTGCTGAAAGCGCAACGCAGTGGCAAATGTCT M 2 1 2 1 201000 r 74 goat snp56939-scaffold902-1380149 7 78986494 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419930 Affx-122945319 AX-123290278 7 28028176 GCTCACATGTGCTAAGTGGGCAACCAGAAACCAGT[A/G]CAAGCTTAAAGACAATGGTGTTGTCCTTCTCCTGC R 2 1 2 1 201000 f 74 goat snp56940-scaffold902-1415071 7 78951515 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389504 Affx-122968304 AX-123259862 7 28080645 GCCCAGAATAGTGGTCAAACTATTCACTGCCATTA[C/T]GTGACCTATGGGGGACAGAGTTCCCACAAACAGTA Y 2 1 2 1 101000 f 74 goat snp56941-scaffold902-1467540 7 78898667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422280 Affx-122943492 AX-123292626 7 28154356 CAGAACTTCATTATGGATTGTGTGGGTTATAATAA[C/T]GTAACTGAGTTTCCTGCCTCCACAACCAGTAATTC Y 2 1 2 1 201000 f 74 goat snp56943-scaffold902-1541251 7 78824138 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782005 Affx-122971940 AX-385269084 7 28208298 ATGTAATGTACCATACTCTCAACAATGTAATTGTA[G/T]AATTTATTCCTCCTGCTAAGAGAATCAGTAAGCTT K 2 1 2 1 202000 f 74 goat snp56944-scaffold902-1595193 7 78770049 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775120 Affx-122965982 AX-385262252 7 28245317 GTTTTGATCTTTTACCTTTAGATGTACACACCATG[C/T]GGAATTGATTTTGGTCAACAGAGAAAAATAGGGGT Y 2 1 2 1 101000 f 74 goat snp56945-scaffold902-1632212 7 78732275 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406158 Affx-122956172 AX-123276510 7 28275898 AGTTTTAATAGAGAAAAATCTTAGAATACTTGAGT[C/T]ATCAGATATCATAGGATAGTGTAAACTTTCTGAAA Y 2 1 2 1 101000 r 74 goat snp56946-scaffold902-1662793 7 78701751 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393002 Affx-122965653 AX-123263359 7 28341368 CTGCGTCTGGCCACTTGACCGCCCTTCATCTGGGT[A/G]TGAGTGTCTCCCACCACAGAAGTTTAAAGACCCTT R 2 1 2 1 202000 f 74 goat snp56948-scaffold902-1728263 7 78635594 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435465 Affx-122933457 AX-123305805 7 28494728 ACATCTTGCTGACTTTTTACATTCCATTGATATAA[C/T]GTTGGGGCGTAAAATCAGGAATATTTCAGATCGAA Y 2 1 2 1 201000 f 74 goat snp56951-scaffold902-1881623 7 78483123 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383120 Affx-122973263 AX-123253478 7 28526733 AAGGCTGTCTACTTGATTTACTATTGCATTTGTTT[A/G]TTTATCTTCCAGTCACTCTGCTAGACATTTTCTGA R 2 1 2 1 101000 r 74 goat snp56952-scaffold902-1913628 7 78450343 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440888 Affx-122929230 AX-123311225 7 28567281 TGCACACTGATCTCATGAAAGGAGTGAAAGATTAA[C/T]GACAAATGAATCAAATGAATTAATGACAAATGAAT Y 2 1 2 1 101000 f 74 goat snp56953-scaffold902-1954176 7 78409136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273267 Affx-1111833535 AX-499506897 7 28645612 CCCAGGTCTCCCACATTGTAGGCAAACGCTTTACC[A/G]TCTGAGCTACCAGGAAAGCCCTGAATCATTTTAAG R 2 1 2 1 303000 f 74 goat 7_28645612_AF-PAKI 7 28645612 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320802044 Affx-122967681 AX-385288948 7 28649867 TTTTAAGAAGCTGGGTTTTCCTATGGCGAAAATTC[A/G]TTTCTCCAGAATACTGATCAAAACCCCCAAATACA R 2 1 2 1 101000 r 74 goat snp56955-scaffold902-2036762 7 78326691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415881 Affx-122948484 AX-123286230 7 28692563 CTCTGGTAGTGTAGAAACCTAAAGGAGACAGTCCC[A/G]TGGACTGCAGAATGCCCAACTTCCCTGTCTTCCAC R 2 1 2 1 101000 f 74 goat snp56956-scaffold902-2079458 7 78281281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791145 Affx-122976575 AX-385278140 7 28728065 TCAAAGCAATTACTGTTTCTTGTACTGCTTCTTAA[A/C]TTGAATGCTAAAAATGTTTTTCCACTCTTAAGGTT M 2 1 2 1 101000 r 74 goat snp56957-scaffold902-2114960 7 78245848 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780613 Affx-122927196 AX-385267703 7 28758970 TCTGTAAAGCTTCACTCTTGACAGTAAATCAGAAA[C/T]GTACCTTAAGTATTTATGGTCCCCTTGGCACCAAT Y 2 1 2 1 101000 r 74 goat snp56958-scaffold902-2145865 7 78214772 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777194 Affx-122950865 AX-385264317 7 28788805 AATATCCAGAGTAAAGTACTCTGTCCTCAGTTTGT[A/G]TGATATCATGGACAAAGTGTCTCATTTGGTTTAAT R 2 1 2 1 101000 f 74 goat snp56959-scaffold902-2175700 7 78184974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418622 Affx-122947151 AX-123288970 7 28827997 ACATGTAGTCCTTTATTTGCCACCCCGAATCTGAC[A/G]CTATTCAGCATCACAATATAGTGCTGATATCTGAT R 2 1 2 1 201000 r 74 goat snp56960-scaffold902-2214892 7 78144994 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453392 Affx-122919920 AX-123323725 7 28857214 CAATGGTATGGTGCAGTCACTGAATGGTCGTTATG[C/T]AAAGCCTGTTAAACAAGTTATTTAAATCTTCTTCT Y 2 1 2 1 101000 f 74 goat snp56961-scaffold902-2244109 7 78115977 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410965 Affx-122952023 AX-123281315 7 28923157 GTTGAAAGAAATTTTCCAGTGAAAACAGTGTGATC[C/T]ATGGGTTAGAGGCCTCATTCTCATTCACTCTTCAG Y 2 1 2 1 101000 r 74 goat snp56963-scaffold902-2310052 7 78048948 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399349 Affx-122961354 AX-123269704 7 28957336 AACTTAGGCTGGTGTTTTTCCTTTGGAAAGGTTTG[C/T]GATTTAAATTAGCTTTTACCAATAAGAGAATAATA Y 2 1 2 1 201000 r 74 goat snp56964-scaffold902-2344231 7 78014662 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791112 Affx-122945316 AX-385278107 7 28999071 TTCTAAATAGGGTACAGAGACTAACAGCTGAAAGG[C/T]GCTTAACTTCTCAGAACATATCTGCGTTTTGACAG Y 2 1 2 1 101000 r 74 goat snp56965-scaffold902-2385966 7 77973011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429521 Affx-122937846 AX-123299863 7 29036757 TCCCAATTTTAGCTAAGAATCACTGTAAAATCCTA[G/T]AGTCTCTCACACATCAATATTTACTCTGTGAAAAT K 2 1 2 1 101000 r 74 goat snp56966-scaffold902-2423652 7 77935935 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785337 Affx-122936254 AX-385272382 7 29069955 TATGAGGACTATCAATACCTGTCTCTGAGATAACT[A/G]CAGGAATATCTTAAAGAATTTAGAGGTATTGAGAT R 2 1 2 1 101000 f 74 goat snp56967-scaffold902-2456850 7 77903551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408880 Affx-122953984 AX-123279231 7 29145851 CTGTGCTAAAGAACTGATGGCAAAAAAAGGAAGCC[A/G]CAAAATTCTTGAACTAAAACTAGACAAAATCAATG R 2 1 2 1 101000 f 74 goat snp56969-scaffold902-2532746 7 77825853 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785860 Affx-122952882 AX-385272897 7 29250629 CCGTTTCCTCTAGAATATATCAAATTCCTTCTTTG[A/C]CCATAAAATTCTTCTGTTGTGTCTTAGATCATTCC M 2 1 2 1 101000 f 74 goat snp56971-scaffold902-2637524 7 77719794 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378070 Affx-122977177 AX-123248429 7 29312139 GTGCAGATCAGAGAGACACTGGCAGGTAAGCACTC[A/G]TAGGACTAGTACCTCCCTCACATTTGACAGAGGGG R 2 1 2 1 201000 r 74 goat snp56972-scaffold902-2699034 7 77656805 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452151 Affx-122921662 AX-123322484 7 29378297 TTTAGTGACTAGTTAAGGGACAGTTATCAGGTTAT[A/G]TTTAAGGCTTATTTTCTGACTTTGATAAATCTGTC R 2 1 2 1 201000 r 74 goat snp56973-scaffold902-2765192 7 77587693 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774347 Affx-122978076 AX-385261483 7 29411071 AGCAAATTATTAGAAATCTCAAAGACACAGAGTAA[C/T]GGTTTTAAGTGTATTTTTAATCCCTTAAATCCATC Y 2 1 2 1 101000 r 74 goat snp56974-scaffold902-2797966 7 77553825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774696 Affx-122933450 AX-385261830 7 29457232 CCAACCACACTGGTATTCTTAGTAAATGCTATAGC[C/T]TGCATCCTCAAACACAAAAAAATAATCACCTAGAA Y 2 1 2 1 101000 r 74 goat snp56975-scaffold902-2844127 7 77507546 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426139 Affx-122940614 AX-123296485 7 29488734 TTACATATCCATCCACAACTAGGTATTCAGCCTTA[C/T]ATTCATCCCAGGAATTAAGCCAGCACCGCTGATAC Y 2 1 2 1 201000 r 74 goat snp56976-scaffold902-2875629 7 77475916 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434218 Affx-122934848 AX-123304559 7 29552796 TGAATAGTCCCTTTTCTTTTTGAGCAAATCTGAAT[A/G]TATGTTTTAGAGAAGTTTCAGGTTTTCCAGTCCAT R 2 1 2 1 101000 f 74 goat snp59880-scaffold995-2759707 7 77403347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449412 Affx-122922694 AX-123319747 7 29581607 AATAAATCTCATTGTCAAATATTCTGTTACCTGAG[C/T]AAGCCCTCATGTCCCAGCCTCTCCCCACCTGGATC Y 2 1 2 1 201000 f 74 goat snp59879-scaffold995-2730896 7 77373959 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439475 Affx-122930163 AX-123309812 7 29621439 TGTGTATGTGAAACTAAAATGAAAAAATAGAATGA[C/T]GATCATAATACAATTATATTTTCAATTTTATTCAA Y 2 1 2 1 101000 f 74 goat snp59878-scaffold995-2691064 7 77334295 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425406 Affx-122941546 AX-123295752 7 29652892 ATGCTTGCTTTTGACCATTCTTCCCAGATGTATGG[G/T]ACAGATGGATGAATTTCATCTTGCAGGGGGTTGGT K 2 1 2 1 101000 f 74 goat snp59877-scaffold995-2659611 7 77303374 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772788 Affx-122935283 AX-385259933 7 29687684 ATCTTTTTCCATAGAAAAGCTGTTAATCTGTGTAG[G/T]GTGGCAACTGGCCAAGTTTTTAGAACACCTCTTTG K 2 1 2 1 101000 r 74 goat snp59876-scaffold995-2624819 7 77268586 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399134 Affx-122960662 AX-123269489 7 29775684 CTCAAACTAACAGCTTAACAACGCTCATGAGTACA[A/G]TACTTGCACTATATATTTGCCTATTTTTCTGAAAG R 2 1 2 1 101000 f 74 goat snp59875-scaffold995-2536819 7 77178132 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278641 Affx-1111836440 AX-519552120 7 29784609 GTCACATTCTGCCTCCTTTCCGCCTACTTATTGCT[A/G]TGGAGAGAGACAGAACTTAGCCGCTCAACAGAGTT R 2 1 2 1 102000 r 74 goat Random2.2K-777 7 29784609 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794880 Affx-122924572 AX-385281840 7 29804508 CTTAACAACTTCTGTTTGATTAAATTGTGGTTAAT[C/T]AGCTCTGAGTATTTTGTGGGCATGTTTAGATTTCC Y 2 1 2 1 101000 r 74 goat snp59874-scaffold995-2507995 7 77148449 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780894 Affx-122959793 AX-385267981 7 29834199 TTTTAAAACTCTGCCATGACTATGTACCTGGATTA[C/T]ATTATTTTATAGATAGCTGGGAGTTATTTTAGCCT Y 2 1 2 1 101000 f 74 goat snp59873-scaffold995-2478304 7 77118408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381663 Affx-122974744 AX-123252021 7 29878092 TAATGTGTAACTACCATATATCTAGAAAAAGACAA[C/T]GGAAACTTTTCCTACCAAAGGCCGCTAAGTGATCA Y 2 1 2 1 201000 f 74 goat snp59872-scaffold995-2434411 7 77074656 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376051 Affx-122978931 AX-123246410 7 29963833 AATGAATAAAAGAAATGAGAATCCAGGAAGCTACA[C/T]GCCCTGCATCAGTTCAGTTCAATTCAGTTGCTCAG Y 2 1 2 1 201000 f 74 goat snp59870-scaffold995-2348670 7 76980132 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384241 Affx-122972364 AX-123254599 7 30016042 CTCCTTCATTCTTAGGTTTAAATTTGCTGTGGATG[A/C]TAAACTAAGACCATTCATTCATTCATTATTAACTC M 2 1 2 1 101000 f 74 goat snp59869-scaffold995-2296461 7 76927017 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453971 Affx-122919457 AX-123324304 7 30098464 TGACCTTGGGACAAATGCATGGTTCTTGGAGCTCT[A/G]TCTTAGTGAATTCTATTGTAGCATAAAGATGATGA R 2 1 2 1 201000 r 74 goat snp59868-scaffold995-2214039 7 76843313 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415315 Affx-122948808 AX-123285664 7 30128867 TGCATAAACCTTAAGTTCTTAGAAGTGAAATTGCT[A/G]TTTGAAAGTTGAAAATTTTTATTTGTTTCCTTCCA R 2 1 2 1 103000 f 74 goat snp59867-scaffold995-2183636 7 76812535 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377360 Affx-122977651 AX-123247719 7 30185365 TTGTGGTAAGTAATGGTAGTAGTGATACTGCTATA[C/T]GATGAAGATAATATGAGCTAGATGCTGCCACAGTG Y 2 1 2 1 201000 f 74 goat snp59866-scaffold995-2127138 7 76757958 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427754 Affx-122939248 AX-123298097 7 30265456 TTTATACTTTTGATTCTTTTTAAATTGCTCATACC[A/G]TAATGTTACTTGAAAGGAGTAGAATTTAGAACACA R 2 1 2 1 101000 r 74 goat snp59865-scaffold995-2047047 7 76677203 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375954 Affx-122978447 AX-123246313 7 30306286 TATTTGAGGACTTGTATTTAAATATTTTAGTGTTA[C/T]AGAATATACAGTGGGTCTTGAAAGTCTTGTCATCC Y 2 1 2 1 101000 r 74 goat snp59864-scaffold995-2006217 7 76635824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398909 Affx-122961013 AX-123269264 7 30338105 TCATAATCAGATAGTTTTTCTAATGAAATCTTTCA[C/T]AGTTGTGTGTACAGTTACTGGTATGTAGAATCCTC Y 2 1 2 1 101000 r 74 goat snp59863-scaffold995-1974398 7 76604165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444465 Affx-122926540 AX-123314802 7 30392306 TTGATTTTCAACAGCATATTTTTTAAAGTAAAAAT[A/G]CCATGTTTATGAAACTCATTTACAGCCTACATGCT R 2 1 2 1 101000 r 74 goat snp59862-scaffold995-1920197 7 76549450 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382341 Affx-122973883 AX-123252699 7 30542945 GCCCAAAGGTTCCATGGTAAGAATAGGTATTGTGC[A/G]TGCCCAGGATGGACTGGTTTAGCCTGTAGGCCTTG R 2 1 2 1 101000 f 74 goat snp59859-scaffold995-1769558 7 76391448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403009 Affx-122958565 AX-123273362 7 30573904 AGCAACTGAGGCACAGGTGGCAGCCTTGATTTGCT[A/G]CTGGCATCTGAGTGTGTGTGTGCTCTCGTAGGACT R 2 1 2 1 303000 f 74 goat snp59858-scaffold995-1738599 7 76358830 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408013 Affx-122954309 AX-123278364 7 30611720 GGCTCAGATGGCGTCCCCTCCAGCCCTCCATCCCC[A/G]CTCCAGAATCTATCAAGTAACTTCTGCTGCCAGCA R 2 1 2 1 101000 r 74 goat snp59857-scaffold995-1700783 7 76320655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777852 Affx-122926781 AX-385264969 7 30668891 TGTTAGTGAACAATAGAAATTGAACAGAGTAGAAC[A/G]GGAGAAATTGCACAGATTTCTTTTGTCAGGTCAGA R 2 1 2 1 101000 r 74 goat snp59856-scaffold995-1643612 7 76262764 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273641 Affx-1111833717 AX-519547255 7 30695349 CGTGCCCCAGTGCCTCCCTGAGCTCACCATACCTC[A/G]AGTGAGCTGTCCCCTCAACAGCCTTCTGCAGGTTC R 2 1 2 1 202000 r 74 goat GoatD01.002314 7 30695349 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278469 Affx-1111836441 AX-519551952 7 30720207 AGCCTGCCTTCCAGGGCTGCTCTGAAAACAAAAAT[C/G]AGCTAACAAGGGAGTATTTTGGAAAAGGTTAAGGG S 4 1 2 1 101000 f 74 goat Random2.2K-779 7 30720207 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278472 Affx-1111836443 AX-519551956 7 30724499 TATTCGGATATGGGCTGAAGATTAGATTATCTTCT[A/G]TCAATGTTAATTTTGTTGTTATTGTTGTTGTTTGG R 2 1 2 1 101000 f 74 goat Random2.2K-780 7 30724499 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401449 Affx-122958981 AX-123271802 7 30732978 TTTTATTTTATTGACTTATTTTGTTACCCTCTCCC[A/G]TTTTCTCTGTGATATTTCAAAGCAAATCTCAGGCA R 2 1 2 1 101000 r 74 goat snp59855-scaffold995-1579525 7 76198961 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398705 Affx-122961852 AX-123269060 7 30795564 TATACATGGTTAATATAGAAATCAGATGTAGGTAA[A/C]ATGTACCTACTCTTTTTCTTTAATGCCGAAAAGGG M 2 1 2 1 101000 r 74 goat snp59854-scaffold995-1516939 7 76132878 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781981 Affx-122965035 AX-385269061 7 30838551 TCTGTTTTCAAGAGTGAGGCAGGAAAGAGTAAGGT[A/C]GTCCCTGCTATGGCTTGGATTAGAACTTGATAAAA M 2 1 2 1 101000 f 74 goat snp59853-scaffold995-1473952 7 76089778 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417939 Affx-122946712 AX-123288287 7 30872532 ACCTGGAACTGTTCCTCCTTCTCTCTCCTAACCTC[A/C]CTTTCTTTGGCTAATTCTTCGACCTTCAGATCTTA M 2 1 2 1 201000 r 74 goat snp59852-scaffold995-1439971 7 76055097 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409900 Affx-122952895 AX-123280251 7 30904605 CTTCAATATTAAAAGGGGTTAAATACATTGAAAGG[A/C]TATTATATAAGGTAAAAAATGGTTGACAGTACTCA M 2 1 2 1 101000 f 74 goat snp59851-scaffold995-1407898 7 76022845 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407721 Affx-122955005 AX-123278072 7 30941708 CATGTCTGTGTGTCCCAGTCTCTTCTTCTTGTAAG[C/T]ACAGCAGTCAGATTGCATTAGGGCCACCCGAGAAG Y 2 1 2 1 101000 f 74 goat snp59850-scaffold995-1370795 7 75985758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423334 Affx-122943169 AX-123293680 7 30971104 TCAAAAAATAATATCTCCATTAATACTGTCATTGG[A/G]ACTTTAGTGATAAATGAGTCAAATGGCTCCTTACG R 2 1 2 1 101000 f 74 goat snp59849-scaffold995-1341399 7 75955969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376294 Affx-122978374 AX-123246653 7 31005794 TACCTCCCCCTGAATGTCAAAACACAGAATTTTCT[A/G]TCTTCCCCTAATTCCAGCCTAAACCCACTCTTTCC R 2 1 2 1 101000 r 74 goat snp59848-scaffold995-1306709 7 75920817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427633 Affx-122939341 AX-123297976 7 31037195 TTAAGGCTTTTTATAAAAGATTTAAACATCATCCT[A/G]TGCTTAGTGATTGTTACGTAGCCAAGTTTGTATTG R 2 1 2 1 101000 r 74 goat snp59847-scaffold995-1275308 7 75888842 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795830 Affx-122932593 AX-385282783 7 31153065 CTTATAAATCTTTAATAACACCTTCACTGACATAA[C/T]CTCACCCTGTTCAAGCAAAGCATAACTATTGAAAG Y 2 1 2 1 101000 r 74 goat snp59845-scaffold995-1159438 7 75771708 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451172 Affx-122921345 AX-123321506 7 31192114 ACCGTGAAAACTCGTAAGATCATCTGTGGGAAGTG[C/T]ATGGGATTAAACAAGAGAATATAGAAAAGAGACCT Y 2 1 2 1 101000 f 74 goat snp59844-scaffold995-1120389 7 75731614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792169 Affx-122944124 AX-385279154 7 31246454 GACAGGAAATTAGACTTATATAAATTTAACTCTGC[A/G]TAACAGTATGACCTCAAACAAGACTTATACTCTGA R 2 1 2 1 101000 r 74 goat snp59843-scaffold995-1066049 7 75678116 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273269 Affx-1111833536 AX-519546917 7 31252448 GGCTGAAAGAAGCCTTGTTTCCAGAGTTCCACCTG[A/G]AGGGAAGGAACCTAGGCCTCAGCATTACTGATTTC R 2 1 2 1 201000 f 74 goat 7_31252448_AF-PAKI 7 31252448 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320787622 Affx-122959779 AX-385274645 7 31292916 AACATTATACAAAAACAGTCTACAGAAAACAGATT[A/C]GAGATTCACCAAGCTGACCTACCTGTGATGGTCAC M 2 1 2 1 101000 r 74 goat snp59842-scaffold995-1019587 7 75631115 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428917 Affx-122938911 AX-123299259 7 31332418 TGCAATGGACCAAATGTTCATGTCCCCTCAAACTT[A/C]ATGTGTTGAAATTCTAACCAATGTTATGGTATTAG M 2 1 2 1 201000 f 74 goat snp59841-scaffold995-980085 7 75591473 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421588 Affx-122944498 AX-123291935 7 31382640 CTTGAATACAATTGTCAATTATCAGGGTCTCTTTG[C/T]AGACTAGACAAGTAACAATGAATGTAAGGTCTAAA Y 2 1 2 1 101000 f 74 goat snp59840-scaffold995-929863 7 75540090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390149 Affx-122967985 AX-123260506 7 31415496 CTTTCCAGGCACTGCTTGTCAGCACTCTCCTTAAA[C/T]GCCCTTTTGTCTTCTCTAGCCTAATTCTAAAAGCC Y 2 1 2 1 101000 f 74 goat snp59839-scaffold995-897007 7 75506989 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391383 Affx-122967272 AX-123261740 7 31489379 CCACTTGTTCAACTATAAAGGTTACAAAACTAAAC[A/G]CTCACTATGCCAGCTCCCTCTGTAGCTAGAGAAAG R 2 1 2 1 101000 f 74 goat snp59838-scaffold995-823124 7 75431931 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785061 Affx-122920710 AX-385272108 7 31534666 ATCTCACAAAGGCCTTGTGTGGAAATCAGATGAGA[C/T]AGGTGAGGATCCAACACAGAAGTTGCTAAGAAAAT Y 2 1 2 1 101000 r 74 goat snp59837-scaffold995-777837 7 75386921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789883 Affx-122924564 AX-385276890 7 31566664 CTTAAAATGGTCCAAAGGCTCCTAGGCTTTAAATA[G/T]ATGATTGATTTAAGATACAGTGAGAGAATCAAAAT K 2 1 2 1 101000 f 74 goat snp59836-scaffold995-745839 7 75354713 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398787 Affx-122961423 AX-123269142 7 31613771 TGTGAGTTGCTGCCTTCTTAGCTCAAATTGCATTT[A/G]ATCTCAGGAAGGGCTCTTCAGAGGAAAAGCATATA R 2 1 2 1 101000 f 74 goat snp59835-scaffold995-698732 7 75308214 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780917 Affx-122935492 AX-385268004 7 31657055 GTGCTAAAAGCAGGCTTGCTGCTTGTTGATGACAA[C/T]GTTTCTTTTGTGATATGTTTCCTTTCTTATTCAGA Y 2 1 2 1 101000 f 74 goat snp59834-scaffold995-655448 7 75265252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770167 Affx-122948223 AX-385257334 7 31716395 CACTGTTAGTTCATGCACTTGGTAACCACTTTAAC[A/G]TATGTTGGCCAAACTCAAGCCACTCCAGCTTTCTG R 2 1 2 1 101000 r 74 goat snp59833-scaffold995-596108 7 75205642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776825 Affx-122961553 AX-385263949 7 31774797 GAGAAAGCGAATTCTTCGAAAGTCATCCTCCAAAC[A/G]TGATCTCCATCTTAGGTAGTCCCCTGTGTCCTCCA R 2 1 2 1 101000 f 74 goat snp59832-scaffold995-537706 7 75146491 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391230 Affx-122967394 AX-123261587 7 31845797 GTCTGATGGACGGAAAGTGTGAGATAGTGAGAGCA[C/T]GCGTGGGAGGGTGGGGGGACTGTGGGGGACTGGTC Y 2 1 2 1 101000 f 74 goat snp59831-scaffold995-466706 7 75075126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390831 Affx-122967840 AX-123261188 7 31898006 ATGTAGTATTCAGTTCACGTGATTCATGAATTCAT[A/G]CTAAGCCTCTCAGTTTCTCCTTAAGGCCTCAGCGA R 2 1 2 1 101000 r 74 goat snp59830-scaffold995-414497 7 75022478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413859 Affx-122949862 AX-123284208 7 31969000 CATTATGCAACTCTCAATGATAAGAAATTTTCTTC[A/G]TGAGCAGAACGCCTCATGTCATTTGACTCAATTTC R 2 1 2 1 101000 r 74 goat snp59829-scaffold995-343503 7 74952611 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792187 Affx-122947786 AX-385279172 7 32010688 TCTGCTATTACATGTTTAATAAATAGTGGTTCCCT[A/G]CAATAGTAATTTGAAAGCCAAAAAATACTGCAAGA R 2 1 2 1 101000 f 74 goat snp59828-scaffold995-301815 7 74910187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799767 Affx-122924051 AX-385286694 7 32054049 TTGCCAACCACTCAATACATTAAACAAGATAGTGC[A/G]TGGATAGAGATAAAACAGGTGATAAAGATTCCAAT R 2 1 2 1 101000 f 74 goat snp59827-scaffold995-258454 7 74866993 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448086 Affx-122924327 AX-123318422 7 32096832 CCTCAGGCTGGAGCTCAGGAAGCTACCGAACTCAA[A/G]GGCTCAGCCCCAGAGGACCCACGACATGGTAAGGA R 2 1 2 1 101000 f 74 goat snp59826-scaffold995-215671 7 74823907 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770193 Affx-122970729 AX-385257360 7 32165418 CTGACCTGAGATTATCTATTTTATGATCTTGAAAA[C/T]GTATATGAGCAATCTTCAAAGGAGGTTGTCTTTTG Y 2 1 2 1 201000 f 74 goat snp59825-scaffold995-147085 7 74754986 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38436788 Affx-122932258 AX-123307126 7 32208730 GTTAATTTTAGTGATACTGCCCATAGAGCTGAGGT[A/C]TATTAAGGCCAGCCAATTACATTAGCTTGCTAATT M 2 1 2 1 101000 f 74 goat snp59824-scaffold995-103773 7 74711456 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791683 Affx-122972104 AX-385278674 7 32244753 GTTTTTTCCAACATGATTTCCAACTTCTCTTCAAA[C/T]GTTAAGTATAATGGCAGAATAACATTGTTATAGGT Y 2 1 2 1 101000 f 74 goat snp59823-scaffold995-67750 7 74675493 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800600 Affx-122953992 AX-385287519 7 32301275 AATTTATTATATTCCCTGGGGCTTGACATCTTATT[A/G]TGATTCATTTTCCATGTAAATGGACTTTAAAAAGA R 2 1 2 1 101000 f 74 goat snp59822-scaffold995-11228 7 74619931 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274064 Affx-1111834017 AX-519547668 7 32302837 CCCTATACTGCTGCAACTGGTTGACCTTCAACTCC[A/G]TGAAGGGAATTCAGGATGAGGCACTCTGTGCTGCA R 2 1 2 1 201000 f 74 goat GoatD01.014109 7 32302837 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434576 Affx-122934116 AX-123304917 7 32337542 TTTCTGTCTCTCTGTACACTTAGTTAAATGCTCTC[A/G]TGGGCTTTTCTTCTCTTTATTTATCACTGGAAGCT R 2 1 2 1 101000 f 74 goat snp8842-scaffold1317-953886 7 74577020 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422408 Affx-122943378 AX-123292754 7 32367413 TAGACACTGCTCCCCCTGGGCCTCTAGAGTACTTC[A/G]TTTACTCATTCAACAAAATTTTGGGAGCATCTATT R 2 1 2 1 101000 r 74 goat snp8841-scaffold1317-924015 7 74546819 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776856 Affx-122922379 AX-385263980 7 32402393 TTAAGCTTAATAGATGTCCTCACGTGTCACCACCC[A/G]TGCATATGTACTTGTAAGCATACATATACACACAC R 2 1 2 1 201000 r 74 goat snp8840-scaffold1317-889035 7 74510498 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378483 Affx-122976666 AX-123248842 7 32433807 GAATGTGAACTGAAAGAGAGACACAAAGAGACGAC[A/G]AGAGAGCAGAGGCCTGGCTGTGTATGATTTCATGT R 2 1 2 1 201000 r 74 goat snp8839-scaffold1317-857621 7 74479085 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802632 Affx-122927745 AX-385289533 7 32463717 TTTAAATCATTTATCAGCTCAGTAATTGCATAAAA[C/T]GTGAAATGCTCTAACACTTTGTGGTTCTATGTAAC Y 2 1 2 1 101000 r 74 goat snp8838-scaffold1317-827711 7 74449176 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439283 Affx-122930976 AX-123309620 7 32509737 CACACAAGTAATCAAAATTTAAATCCAGATTTTTC[C/T]GAAAGAGGGAAAGCATGATATTAAATCAGAATTTT Y 2 1 2 1 201000 f 74 goat snp8837-scaffold1317-781691 7 74403155 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769841 Affx-122931154 AX-385257011 7 32548906 AAAAATGATTGGAAAAACTTAAATATGCCCAAATT[A/G]TGGCTACTAATTGAGATATTCCTTCAGGTATCTCC R 2 1 2 1 101000 r 74 goat snp8836-scaffold1317-742522 7 74363725 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786363 Affx-122932658 AX-385273397 7 32585452 ATCACACTGAATAGGTTAAAAAGCGTCACCCAGCA[C/T]ATCCACCAACAACACATTATGGACATTATTGCCAT Y 2 1 2 1 101000 f 74 goat snp8835-scaffold1317-705976 7 74326102 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791786 Affx-122945708 AX-385278776 7 32613960 TATTATATGTTTGATAGAATCCATTCCTTTTTGCC[A/G]CATATTCTGCAGCCATTCTTTACAGTGAACCTCGC R 2 1 2 1 101000 f 74 goat snp8834-scaffold1317-677468 7 74297017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434365 Affx-122934711 AX-123304706 7 32657269 TGGCAAGTCAGGATTCCATGGGTAGCTTCAAGGTT[A/G]CAGTTAAAAAACCTCCTCCATTCACTGTCTCTAAT R 2 1 2 1 101000 r 74 goat snp8833-scaffold1317-634159 7 74251917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778501 Affx-122941439 AX-385265615 7 32694953 CCCTGAGTGAAATTGTTGCATGATACTGAAACTCT[A/G]TTTTTAGTTTATTGAGGAATCCCCACACTGTTTTC R 2 1 2 1 303000 r 74 goat snp8832-scaffold1317-596475 7 74214524 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793945 Affx-122963475 AX-385280914 7 32742289 AGCTTATGTCCTAATAGAAGAGACATCTATCATTC[A/G]TATCTAATTCACTTAAATTCTAAGGGAGAATCCTA R 2 1 2 1 101000 f 74 goat snp8831-scaffold1317-549139 7 74166895 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793630 Affx-122960078 AX-385280604 7 32795078 TCAACCATAATATTATAATTCTCTTAGATATTTTC[A/G]TGGCAACCATAGCACAGGATAGCCTACCCTCTGTA R 2 1 2 1 101000 r 74 goat snp8830-scaffold1317-496350 7 74114434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442849 Affx-122927684 AX-123313186 7 32854041 TGGGAATGACTGCTAATGTATCAGTTAGATGCCTT[A/G]TCTTCCATTCTCTTTGTACTAAATAGTATCGAACA R 2 1 2 1 101000 f 74 goat snp8829-scaffold1317-437387 7 74054934 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425740 Affx-122940748 AX-123296086 7 32889111 CACTGACTTCCATTTTTCCAATATTTAAAAATGTT[A/G]CCTTTAAAACTAACACTTATTTCTGAGACTAGTCA R 2 1 2 1 101000 r 74 goat snp8828-scaffold1317-402317 7 74019888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772961 Affx-122971914 AX-385260105 7 32970531 ATTTAAAAAGATACATATCACCAAGTCTCATATGA[C/T]AGAGAATCTGATTTAATTTGTCTAGGATGGGGTCC Y 2 1 2 1 101000 r 74 goat snp8826-scaffold1317-320897 7 73938212 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439520 Affx-122930126 AX-123309857 7 33008909 GGCACCTGACTTTGTAGTGAGGGACTTGCCAGCTT[A/G]CAAATTCATTCTTCTCTGAAGTTATGCTACTTTAC R 2 1 2 1 101000 f 74 goat snp8825-scaffold1317-282519 7 73900870 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786378 Affx-122948760 AX-385273412 7 33038639 GGTGCTTGAGCTCGGAGTCCACAAATGACTTTTCA[C/T]GTTCTAAAAAGAAATTACTGGCAGTGTCCAAACAA Y 2 1 2 1 101000 f 74 goat snp8824-scaffold1317-252789 7 73871148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772430 Affx-122963602 AX-385259582 7 33072824 TATACTTCATCATGCTTAAATGACTGAGGACAGCC[A/G]CCTTTTGTCCTTCCCTGGGACATAAATTCCACTCT R 2 1 2 1 101000 f 74 goat snp8823-scaffold1317-218604 7 73837418 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418285 Affx-122946999 AX-123288633 7 33102014 AAGAATTAAATGAGTTAAGCTACCGGGAAAGTTCT[G/T]TATAACCTGTAATGCTTTATTACATATTCACCCCT K 2 1 2 1 101000 f 74 goat snp8822-scaffold1317-189414 7 73808687 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784027 Affx-122940652 AX-385271080 7 33136510 TGAGTCTAAAAGACCTGAAGCGAGGAGTAAGGTTG[A/G]ATTATTTCAGGAAGAAAAAGGCCAGTATGAATGAG R 2 1 2 1 201000 r 74 goat snp8821-scaffold1317-154918 7 73774138 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446187 Affx-122925731 AX-123316523 7 33186811 AAGCTGTTAAAATACTGAAAAAGTAAAAATTTCTT[A/G]TGCACAAAAATTCTCATTTCTATGAGCTAGATCTT R 2 1 2 1 101000 r 74 goat snp8820-scaffold1317-104617 7 73723780 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431589 Affx-122936176 AX-123301930 7 33218942 ATGACATCTCATAGGGACTCTCTAATCCCTTCCTT[C/T]TAAATAACTTTTTGTGAATTTGGGGTTTTGACCTA Y 2 1 2 1 202000 r 74 goat snp8819-scaffold1317-72486 7 73691517 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802272 Affx-122943155 AX-385289176 7 33276321 CAGAACATCTGTTTTAGCTTGCGATTCAATATTTG[C/T]ATGCTTGCTTATTGCCTGTGACCCCCATTAGATTG Y 2 1 2 1 101000 r 74 goat snp8818-scaffold1317-15107 7 73633921 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440112 Affx-122929706 AX-123310449 7 33304204 GAGAGCTGGGAACACCACACTGCAGGAGCCAGGAA[C/T]GAGAGAAGCCTGGCCTCCTTCCGGAGCTTGCTGCA Y 2 1 2 1 101000 f 74 goat snp33081-scaffold386-12677 7 73605832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379648 Affx-122975945 AX-123250006 7 33333240 CCTCTGGTTTGTAATTTTTAAAGGACTATAAGCCA[A/G]CCTTTATCCTGACACAGAGGCATCTTGAACTCTTA R 2 1 2 1 101000 r 74 goat snp33082-scaffold386-41713 7 73576052 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389082 Affx-122968590 AX-123259440 7 33363973 CTGTGTGGATAAGGTTTTCTCTCCCTTCTGTCTGG[C/T]GCAGGGAGGACAATGCACAAACCGAACCATTGCTT Y 2 1 2 1 201000 r 74 goat snp33083-scaffold386-72446 7 73545040 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791562 Affx-122939713 AX-385278553 7 33401484 AGAACAGTGAGGCTGGCTTAACACCATTTAAAATC[A/G]TGGAAGAACACTCATGGAAAAAGTTACACTTGCCG R 2 1 2 1 101000 f 74 goat snp33084-scaffold386-109957 7 73507326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418502 Affx-122946434 AX-123288850 7 33447581 AAGGTCAACTCAGCTGTTCACAAATCACTAGTGCT[A/G]CATATTTGTCCTTGACTTCATATTTTCCTTTTTGT R 2 1 2 1 101000 f 74 goat snp33085-scaffold386-156054 7 73461190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411034 Affx-122951967 AX-123281384 7 33495107 TGTGGTTGGTTTGAACCTTTTTCAACATTCTGTAC[A/G]TTGCTTGTCTCTTTAATTAATCTTGACCTTGAATT R 2 1 2 1 101000 f 74 goat snp33086-scaffold386-203580 7 73413020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407508 Affx-122954741 AX-123277859 7 33589260 GCTCCCTTCTTTTTCCAGCTTAAAGAGACATACAG[A/G]GCAGAAAACAGATTGTCCATGGTAAGTAAAATTCA R 2 1 2 1 101000 f 74 goat snp33088-scaffold386-297733 7 73318930 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393194 Affx-122965510 AX-123263551 7 33624308 GGTTCGACACACATTACTGAAGGGCTAGGGACCAT[C/T]TGACTGCGTTTTGCAACCCTGGCCCAGAGGTCTAC Y 2 1 2 1 101000 f 74 goat snp33089-scaffold386-332781 7 73285086 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400998 Affx-122959694 AX-123271351 7 33653847 CCTCTGCACAGTCTGCATGAACAGTCAGGGATTCC[A/G]ATGGCCAAAAGGTTACTAAGTAGGTGTGACACAGG R 2 1 2 1 101000 f 74 goat snp33090-scaffold386-362320 7 73255657 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802904 Affx-122959780 AX-385289801 7 33688374 ATCAAGTGAAAGGAAAGGGCAAGGACATGTATTTT[A/G]TCAAAATGAGCATAATTTAGCAAGTTAATGTGGAT R 2 1 2 1 201000 r 74 goat snp33091-scaffold386-396847 7 73221243 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441712 Affx-122929151 AX-123312049 7 33729741 CATATCACTGGCACTTTCTACAGCTGTTTCATGCC[A/G]AACTAAGACCTCTGTGCTGGTAAAGCTGAGCCCCA R 2 1 2 1 201000 r 74 goat snp33092-scaffold386-438214 7 73179984 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273271 Affx-1111833537 AX-519546919 7 33759264 TGTTCCATGGTATTAGGCCACAGGTAAAAGTTATG[A/G]ATAAGTAACTATCAATAATCATTTCTCAAGGGTAT R 2 1 2 1 101000 f 74 goat 7_33759264_AF-PAKI 7 33759264 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789620 Affx-122975964 AX-385276629 7 33787812 ACAGGAGGACTAGAGATTTCAGGCTGCAGATTTCC[G/T]CAATCACAGGATGACAGGCAAAAACAGGTACAGAA K 2 1 2 1 101000 f 74 goat snp33093-scaffold386-496285 7 73122843 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787985 Affx-122968225 AX-385275006 7 33825395 TTAATACATTGTCCCCTCAACAAACTCTTTAAGAA[C/T]CCATTAACAGCCTGGATTGTTCAGAAGGGTGATTC Y 2 1 2 1 202000 f 74 goat snp33094-scaffold386-533868 7 73085374 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392753 Affx-122966006 AX-123263110 7 33859881 CTCTGGCCAGCAGCAAAATGGTCAGAGCAAGAATC[C/T]TTTTCTGCAAGAAACTGAACAGGGTAGTATAAAGG Y 2 1 2 1 201000 r 74 goat snp33095-scaffold386-568354 7 73050633 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278474 Affx-1111836444 AX-519551957 7 33869749 AAATACCTTAACGTGTTCCTCCTCTTCCTTGCCTC[A/C]TGTAATTAGAGCATATTTTAAAATTAAGGAAGAGA M 2 1 2 1 103000 f 74 goat Random2.2K-781 7 33869749 G T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38400623 Affx-122960375 AX-123270978 7 33909315 TAAAAGTTCTGGGGAAATAAGGATGGAGATGGGGC[A/G]TGTAGGATAAAAAGGAAAGGGGGATGGGGCTGGCC R 2 1 2 1 101000 f 74 goat snp33096-scaffold386-617788 7 73001821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418087 Affx-122946600 AX-123288435 7 33962188 TGAAATAGGTGTCAGGAGATACAAAAAGATGAGAG[C/T]AGATTCAAGACAAAATTTGAAGAAAGAAGCAATAA Y 2 1 2 1 101000 f 74 goat snp33097-scaffold386-670661 7 72949179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769494 Affx-122942601 AX-385256664 7 34007238 GAACAAAAGAGTAAAAATGCCACACCTTCCTAGAA[C/T]GCACTTCCTTGTTGGAGTCATTATGAATCATTAGG Y 2 1 2 1 201000 r 74 goat snp33098-scaffold386-715711 7 72903849 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447881 Affx-122923825 AX-123318217 7 34039809 AATCCCACAGGGAGTTCAAGTAGACTATAACGTAA[C/T]ACTAGTAATTAAGGAAGTGGCATTCTTCCTCTATA Y 2 1 2 1 101000 f 74 goat snp33099-scaffold386-748282 7 72871376 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440345 Affx-122929663 AX-123310682 7 34076296 ATATACGACCTTACCCAGCATTAAGCCCCTGTCAG[C/T]ATTTATAAGTGGCAGGATTAAAGAGATAAAATCCA Y 2 1 2 1 202000 r 74 goat snp33100-scaffold386-784769 7 72834876 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386027 Affx-122971488 AX-123256385 7 34104967 ACTCTCTAGGAAATCCAGAGGACCTTTCCTAACCA[C/T]GCCAACTTTGCTTTCATATTCCCCTTAATACATAA Y 2 1 2 1 201000 r 74 goat snp33101-scaffold386-813440 7 72804089 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476232 Affx-1251763738 AX-586011656 7 34128266 CTCATTTACTTACTTTTCCAGAATCATTATTTGTT[-/TAATTTAATTTAATTTTATTTATTAATTTTTTTTTTTTAAAAACATTTTAAATCTCAAAAAAAAAAGGCAAAATAAAAAA]AATTTTATTTTTTAATTGAAAGATAATTGCTTTAA - 8 1 4 1 20000 f 74 goat SV_219 7 34128266 - deletion junction SV-TF-chip 560378500 Affx-1251763738 AX-605230915 7 34128266 CTCATTTACTTACTTTTCCAGAATCATTATTTGTT[-/TAATTTAATTTAATTTTATTTATTAATTTTTTTTTTTTAAAAACATTTTAAATCTCAAAAAAAAAAGGCAAAATAAAAAA]AATTTTATTTTTTAATTGAAAGATAATTGCTTTAA - 8 1 4 1 20000 r 74 goat SV_219 7 34128266 - deletion junction SV-TF-chip 562165098 Affx-1251763738 AX-606940510 7 34128266 CTCATTTACTTACTTTTCCAGAATCATTATTTGTT[-/TAATTTAATTTAATTTTATTTATTAATTTTTTTTTTTTAAAAACATTTTAAATCTCAAAAAAAAAAGGCAAAATAAAAAA]AATTTTATTTTTTAATTGAAAGATAATTGCTTTAA - 8 1 4 1 20100 f 74 goat SV_219 7 34128266 - deletion junction SV-TF-chip 562165891 Affx-1251763738 AX-606941300 7 34128266 CTCATTTACTTACTTTTCCAGAATCATTATTTGTT[-/TAATTTAATTTAATTTTATTTATTAATTTTTTTTTTTTAAAAACATTTTAAATCTCAAAAAAAAAAGGCAAAATAAAAAA]AATTTTATTTTTTAATTGAAAGATAATTGCTTTAA - 8 1 4 1 20100 r 74 goat SV_219 7 34128266 - deletion junction SV-TF-chip 562166128 Affx-1251763738 AX-606941536 7 34128266 CTCATTTACTTACTTTTCCAGAATCATTATTTGTT[-/TAATTTAATTTAATTTTATTTATTAATTTTTTTTTTTTAAAAACATTTTAAATCTCAAAAAAAAAAGGCAAAATAAAAAA]AATTTTATTTTTTAATTGAAAGATAATTGCTTTAA - 8 1 4 1 20100 r 74 goat SV_219 7 34128266 - deletion junction SV-TF-chip 38452721 Affx-122920290 AX-123323054 7 34152044 TCTTTCCTCTTTGTTTCCACTCAATCTCAAGAAAT[A/C]GGCACTAGCCAAGCAGATCAGACCCCAAATGGTCC M 2 1 2 1 101000 f 74 goat snp33102-scaffold386-860517 7 72757000 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441693 Affx-122929167 AX-123312030 7 34186905 AACACTATGCTTCCATTTCTTCCTCTCAGTTTTTG[C/T]GCAGTTGTTATTCTACATCTTATTTCTGTGTATGG Y 2 1 2 1 103000 f 74 goat snp33103-scaffold386-895378 7 72722273 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771076 Affx-122959875 AX-385258236 7 34224281 ATAATAAACATAGTGGTATAAACGAAGGAAATTTA[A/G]GGAATAATAGTATTGATGAAGGTGGGAGGGATAAA R 2 1 2 1 101000 r 74 goat snp33104-scaffold386-932754 7 72684183 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393661 Affx-122965281 AX-123264016 7 34256850 TGAAGTTAAGACAAGAAATTTTTTGTTTGTTTTAA[C/T]ATACATGATAACCATTTGAGTGAATTCTGAATAGT Y 2 1 2 1 103000 r 74 goat snp33105-scaffold386-965323 7 72651680 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376400 Affx-122978093 AX-123246759 7 34287976 CATCAAACAGCTACTGCAGCATCTCCTGAGGACTC[A/G]CTTCTCCCACCTCCAGAGAAGAGAGGAGAGAAGGC R 2 1 2 1 202000 r 74 goat snp33106-scaffold386-996449 7 72620090 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410138 Affx-122952805 AX-123280488 7 34343047 AGACAGAGAGCAGACTTGAGGCTCAGCGCCTTTCA[C/T]GGACACATCTCATCAGAAGTCGACACTTTTGCTTT Y 2 1 2 1 201000 r 74 goat snp33107-scaffold386-1051520 7 72564980 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399287 Affx-122960543 AX-123269642 7 34375434 TGCCAAAGAAACCGAACCCACTTCGCCTGAAGACA[C/T]GGGGTCCATATTTTTCAAAGACATGGGCTCCACCT Y 2 1 2 1 101000 f 74 goat snp33108-scaffold386-1083907 7 72532436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427793 Affx-122939767 AX-123298136 7 34414583 ACAGGCCTGGCAGCACCACCTGGAGCCTAGAGATG[C/T]GGGTTGAACGGATATTAACTGTCACCCATGGCTCT Y 2 1 2 1 101000 r 74 goat snp33109-scaffold386-1123056 7 72493234 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399488 Affx-122961179 AX-123269843 7 34456968 AGAAGTGAACTCCACTGTGAACCTCAACCCAGCCC[A/G]CAGTCGCTGGTGCTCCTAGACCTGATGCCCATCAC R 2 1 2 1 201000 f 74 goat snp33110-scaffold386-1165441 7 72450724 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447193 Affx-122924997 AX-123317529 7 34513382 GTGGGACTTGGGAAGGGGCGGGGTGGAGGGAGGGC[G/T]AGGATCTGCAGTGACAGAGCTGCACAAATACCAGG K 2 1 2 1 101000 r 74 goat snp33111-scaffold386-1221855 7 72394605 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448618 Affx-122923378 AX-123318954 7 34550029 GGTAACATGTCTTCCGGCTTGAAGTGTTTGCCAAG[C/T]TCATGTTCAGGAGCCGCCAGGAACAGGAGGGCTGC Y 2 1 2 1 101000 f 74 goat snp33112-scaffold386-1258502 7 72357643 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451232 Affx-122921954 AX-123321566 7 34585799 TAACTGAAAGGCCAGGGGTAGCTCTGGCTTCAGGC[A/G]TGGTTGGATCCAGGGAAAACGTGTGACCAGGATTC R 2 1 2 1 201000 r 74 goat snp33113-scaffold386-1294272 7 72321966 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414170 Affx-122949679 AX-123284519 7 34636152 AGCAGGGCTCATGGTTTCCCCTCAGCATCTGCATT[A/C]GCTGACTAAGTACCTGACTGAGCATACCCCGCCCC M 2 1 2 1 201000 r 74 goat snp33114-scaffold386-1344625 7 72271678 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404733 Affx-122957241 AX-123275085 7 34666781 CTTAAATTTTCTTTTTAACTATACTTGAATTCAAA[C/T]AGATTGTTATAAAACAAAACACTACACACAGTTGT Y 2 1 2 1 101000 r 74 goat snp33115-scaffold386-1375254 7 72241537 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400358 Affx-122960032 AX-123270713 7 34715611 TTTTTCCAAGATTGTTCATCTCTGTTACATCATTA[C/T]GTTAACAGAAAATGCTCCAGGACTTTGGAGACAAA Y 2 1 2 1 201000 r 74 goat snp33116-scaffold386-1424084 7 72192738 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407594 Affx-122954654 AX-123277945 7 34766743 AATACCACCTATGACCAATGCCTTCAACATTATTA[A/G]GAGACAAATCATACCGCAGAATTCAAATAACCAGT R 2 1 2 1 101000 r 74 goat snp33117-scaffold386-1475216 7 72140639 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425511 Affx-122941470 AX-123295857 7 34800413 AGCCTGGCCAAAAATAAACACCCAAAACTTGTTGA[C/T]TGAATTGAATTGGGAAATGGGGAGATCAGAAAAGC Y 2 1 2 1 201000 f 74 goat snp33118-scaffold386-1508886 7 72106966 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796569 Affx-122949186 AX-385283515 7 34855446 GAAAGCCCAAAAGGATAGATACGTATGAAAAAATT[A/G]CAGTGACTGACACATGATAGAAGCTATGTGAATGA R 2 1 2 1 201000 r 74 goat snp33119-scaffold386-1563919 7 72051288 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393053 Affx-122965621 AX-123263410 7 34896868 AATGTAGAAGCCTTCAGAGGACATGTTTCTGCTGC[A/G]GAGACACTCCAAGCAGCGATGGTATCTGCATTCCT R 2 1 2 1 101000 r 74 goat snp33120-scaffold386-1605341 7 72009894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435563 Affx-122933379 AX-123305903 7 34913707 AAAATAACTACAAAAACAAATTTTTTAAATCTGCA[A/G]CTGCCAAACTAAGAAATCAAGGAGTAGTACTAAAG R 2 1 2 1 101000 r 74 goat snp27549-scaffold2948-216447 7 71991795 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403804 Affx-122957967 AX-123274156 7 34966737 CAAGTAGCCCAACGGTAAATAATTCATCTACTGAG[C/T]AGCAGTCATGGGTTTGATCCCTGGGTCGGGAAGAT Y 2 1 2 1 101000 f 74 goat snp27548-scaffold2948-163417 7 71938715 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784330 Affx-122946711 AX-385271381 7 35017975 ACAATCTTAGTGTTACTATTAAGTAGAAATTTTAA[C/T]ACATGCTTGCTGATGTGATATAATAGGAAGTATAC Y 2 1 2 1 101000 r 74 goat snp27547-scaffold2948-112179 7 71887465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388054 Affx-122969534 AX-123258412 7 35055085 AGTTCTCTAGCTACTTGTGGAAGCTATGGGTTCCT[C/T]CTCAGAAAGGCTTCCTGGGGAACCAGCTTAGAGGC Y 2 1 2 1 101000 f 74 goat snp27546-scaffold2948-75069 7 71850364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273611 Affx-1111833700 AX-519547224 7 35081217 CTTCACTGCTGAGAACAGGGCAGGAGTG[A/G]CAGTGGGGACTCTGACTCCGTTCCTCTAGCTGCAA R 2 1 2 1 102000 r 74 goat GoatD01.001901 7 35081217 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38375847 Affx-122978526 AX-123246206 7 35112508 GAAGTTCATCAGAGCACTGGGTGCCAAAGTCCAGG[C/T]CTTTGAGGACCGTAAGTGTGCTCCCCTTTCCCGTC Y 2 1 2 1 201000 r 74 goat snp27545-scaffold2948-17646 7 71793591 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424428 Affx-122941801 AX-123294774 7 35157754 GAGGCTCCCTAAGGGTCAGAGGGAAGGGCTGATGG[G/T]CGGGTGTGCCATAGAGATGCGGACAGAGTAAGAGA K 2 1 2 1 101000 r 74 goat snp1811-scaffold105-1450869 7 71748671 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425415 Affx-122941539 AX-123295761 7 35214385 ATGGCAAGGCCTACATGGTTGGAAACTGGCCAACC[A/G]TCAAGAAGAATGAAGTCAATAGCTTTATGAATGAA R 2 1 2 1 101000 r 74 goat snp1810-scaffold105-1394238 7 71696659 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383873 Affx-122973134 AX-123254231 7 35244572 TGGGGTGTTAAGAGCGCTGCCTCCTGAGCTATTTT[A/G]TGGGTCTCTTTGGACTCCCCGCCCCCCATCCTCAG R 2 1 2 1 101000 f 74 goat snp1809-scaffold105-1364051 7 71666162 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446033 Affx-122925849 AX-123316370 7 35274588 TAAGTTCAGTTCAGTTGTGTCCAACTCTTTGTCAC[C/T]CCATAGACTACAGCATGTCAGGGAAGGACAGGGAA Y 2 1 2 1 303000 r 74 goat snp1808-scaffold105-1334035 7 71635780 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407386 Affx-122955259 AX-123277737 7 35319094 TGTCTCACACTTCCCAGGATAGTCCCGCTTACCCA[A/G]TGCTCAGCGAGATATTGCCTCCTCTGGGAAGCACC R 2 1 2 1 201000 r 74 goat snp1807-scaffold105-1289529 7 71592091 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772783 Affx-122937449 AX-385259928 7 35350320 TTCTCACAGCCTATAACATAGGTTCTACTGCTCTT[A/G]CCCAGTTATTTAATGATCAGGAGCCATTACTGGTT R 2 1 2 1 101000 f 74 goat snp1806-scaffold105-1258303 7 71560817 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420556 Affx-122945284 AX-123290903 7 35396650 CAGCACCAAGGCCTCTGCTTGGCCTGATCCCAGTT[C/T]CTTTAGTCCCCAAAAGAACAACCACATAAAGAACC Y 2 1 2 1 102000 r 74 goat snp1805-scaffold105-1211973 7 71513509 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387633 Affx-122969857 AX-123257991 7 35439923 CCTTGAGAGCTAAAACGGAGGGGTGCCATCCCATA[A/G]TAGGTGATGTCAACCTACCCATAGGCCTCTTCACT R 2 1 2 1 101000 f 74 goat snp1804-scaffold105-1168700 7 71469597 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416447 Affx-122947824 AX-123286796 7 35504800 GTCCCAAGGCTACCTGTCTAGTGCCCTAGTTCCGA[C/T]GAGGGGCCAGTGTGTGACTGGGGTCACAGGGGGAC Y 2 1 2 1 101000 f 74 goat snp1802-scaffold105-1103823 7 71404946 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278476 Affx-1111836445 AX-519551959 7 35523627 CCTCCAGGAATCAGGATCTGATATACCTTTATTGT[A/G]TTACATGGTACATTTTGGTCACTCAGGAGTTCAAT R 2 1 2 1 101000 f 74 goat Random2.2K-783 7 35523627 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429513 Affx-122937852 AX-123299855 7 35564393 TGGCTACAGCATGCAGAGGGGCCCAGCCTGGCTTC[A/G]TGTCACAGATCTCCTGTGTAGCTTCTAAGACTACT R 2 1 2 1 101000 r 74 goat snp1801-scaffold105-1044230 7 71346599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394071 Affx-122964970 AX-123264426 7 35643467 TGAAAGAGGAGACCAAGGAGACTATCTTGGGACGC[A/G]TGTTGAACTTGTCATTTGAGAAAAAGGCATTAAAA R 2 1 2 1 201000 r 74 goat snp1799-scaffold105-965156 7 71268245 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790905 Affx-122955480 AX-385277902 7 35683446 TGCCAAAGTGTTTAGTGAACAGAGGAAGGAGGTAG[A/G]TGGAGAGGATAGAGCCTGTTATCACTGAGTTTAAG R 2 1 2 1 101000 r 74 goat snp1798-scaffold105-925177 7 71227864 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449697 Affx-122922546 AX-123320032 7 35719076 CTTCCCACCAGCCAAGTCCCCTTGCCTTAGGGCCC[A/G]CCATCTCATCTATTGAGGGAACAATTTTTGCCTTG R 2 1 2 1 101000 r 74 goat snp1797-scaffold105-889547 7 71192032 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414941 Affx-122949090 AX-123285290 7 35763380 GTCCTTGAGCCATCCCCCCTGGAGTGACCCCCATC[C/T]GAGGACTGATTAGTCAGGTTACTGCAACCCTTGGC Y 2 1 2 1 102000 r 74 goat snp1796-scaffold105-845243 7 71147654 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410735 Affx-122952706 AX-123281085 7 35798740 AGCTCCCTGGACTCAGGGTCTTCAGCCCCCCACTG[A/C]TGGCACAAACCACATCACTCACCCTGCAAGGCAAG M 2 1 2 1 201000 r 74 goat snp1795-scaffold105-809883 7 71111905 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278653 Affx-1111836446 AX-519552132 7 35887342 TCTTTTGGTAAAAAAAAAAAAAAAACAAAGAAAAA[A/G]AAGGTCATTCCAGCCCTCATTATTTTCAAAGAAAG R 2 1 2 1 101000 r 74 goat Random2.2K-784 7 35887342 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437117 Affx-122932169 AX-123307455 7 35948200 CTTGATAATAATTTAGAAAGAAATGACATCTTCAC[A/G]ATACCAAGGTCTTCAATTTATGAACATGATGTATT R 2 1 2 1 101000 r 74 goat snp1792-scaffold105-660423 7 70963497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412624 Affx-122951271 AX-123282973 7 35990831 GGCTGTTCCTTCTAGCCATTCTGCTCACAGATGTC[A/G]CTGGATGGGAAGTGTACACAGCCTGGACAGTGACC R 2 1 2 1 101000 f 74 goat snp1791-scaffold105-617792 7 70920986 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386975 Affx-122969963 AX-123257333 7 36030590 AATGTCTTCCTGTAACATAGAGTTGACGTTGTTTA[A/G]TCGCTAAATCATGTCTGCACTCTTCTGACTGCAGC R 2 1 2 1 101000 f 74 goat snp1790-scaffold105-578033 7 70881307 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390629 Affx-122967158 AX-123260986 7 36075076 ATGTCAAATAGTCTAGTAGATTTAGAGTTCCATCC[A/G]TCATAATATACACTGAGCATTAAATGTGAAGACTC R 2 1 2 1 101000 f 74 goat snp1789-scaffold105-533547 7 70836818 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801701 Affx-122950405 AX-385288609 7 36135770 ATGGTATTATATGCAAATTTGGGGCGTCAGAAAAC[C/T]GAGCTTTTGAATCCTGGATCTATCACATGCTAATT Y 2 1 2 1 101000 r 74 goat snp1788-scaffold105-472853 7 70775969 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423488 Affx-122942569 AX-123293834 7 36164400 ATCTTATGCCTAGAAAATGGCCAGTACTCACCATA[C/T]GTTCCTCAAATGCATAAAATATTTCTCATTACAAC Y 2 1 2 1 101000 f 74 goat snp1787-scaffold105-444223 7 70747372 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434317 Affx-122934748 AX-123304658 7 36215722 GAATTTGTATCAGTCAGAGATACAAACATAAGGCC[A/G]TCATTTTACTGTGCACCTATTTGCAGATTAGAGGC R 2 1 2 1 101000 r 74 goat snp1786-scaffold105-392901 7 70695197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443023 Affx-122928165 AX-123313360 7 36248938 TTTATTGTCCAGAGATAGACTTCCATCCCCAATCC[A/G]TACCCTGCCAGTTCTACGTCCAATTACATGGTACA R 2 1 2 1 201000 r 74 goat snp1785-scaffold105-359685 7 70662097 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788281 Affx-122940561 AX-385275299 7 36281318 AAGGCTTTGTGCTTTTTTGCTGCACTAGCATCATA[C/T]ATCCCGTTAGCCTTTTCCAGGACGAATAACCTGTA Y 2 1 2 1 101000 f 74 goat snp1784-scaffold105-327305 7 70629848 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451269 Affx-122921318 AX-123321602 7 36328153 ACAAAACTTACTAAAGGTCTCACAGCTGGGAGGAG[C/T]ATGGGAAAGATTCTGAAGTGAGTTCAGTCCTTATG Y 2 1 2 1 101000 r 74 goat snp1783-scaffold105-280470 7 70582639 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431914 Affx-122935998 AX-123302255 7 36357290 CACCTGGGAAGCGAATTGTGAATCACTATATTGTA[C/T]ACCTGTGACACACAGTGTTGTACATGAGCTATAGT Y 2 1 2 1 303000 r 74 goat snp1782-scaffold105-251333 7 70553482 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439663 Affx-122930596 AX-123310000 7 36396710 AAGCCTCAAGAAGTGCATACAGGCCTGTGTTCAAA[A/G]AGATGAGCTCTGGACTCCTGGGGAGCTGCAAGTGA R 2 1 2 1 101000 f 74 goat snp1781-scaffold105-211913 7 70513324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425963 Affx-122941170 AX-123296309 7 36444779 TTGTGAACAACAGACTGCTACAGTGTATTTCAATC[G/T]AACTACTTTTTCTTGGATTTTCAATGCGAGAATCT K 2 1 2 1 101000 f 74 goat snp1780-scaffold105-163844 7 70466077 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393545 Affx-122965415 AX-123263901 7 36506050 CAGGCTGAAATCTACTGCCTCCTGTGCTTGGGGGA[G/T]GCCTGAGGGCAAGTATGACAAGACACCAAAGAGAG K 2 1 2 1 101000 r 74 goat snp1779-scaffold105-102573 7 70404573 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381888 Affx-122974165 AX-123252246 7 36550186 CCCAGAACTCAGAGAGCTCATTAATGTGTTGATAG[C/T]GGGAGAATTCTGTGCCTCTGCCTGGCTGCCTTCTG Y 2 1 2 1 101000 f 74 goat snp1778-scaffold105-58437 7 70363553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787332 Affx-122954457 AX-385274357 7 36595975 TTCACCTTTAGGAGACATTTATGAAGGGTATATCC[A/G]TCTACCTTACCTCATTATAAAGACAAACCAAGAAG R 2 1 2 1 101000 f 74 goat snp1777-scaffold105-12648 7 70317203 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773024 Affx-122925100 AX-385260168 7 36641470 TCTGTGCCCTGCACGTTTCCATGCTGGAGTTAATT[A/G]CTTCTGTAAAATTATAAGTGCTGCCTTGAGTTTCA R 2 1 2 1 201000 r 74 goat snp46306-scaffold639-32748 7 70260634 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400686 Affx-122959943 AX-123271041 7 36701898 GGTCTCTCTTGCAGAGCGATGAATGGTTTTACCGG[C/T]GGCAGCTGGGTGGCAGGGCAATACAGGCATCCAGT Y 2 1 2 1 101000 f 74 goat snp46307-scaffold639-93176 7 70200722 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448496 Affx-122923464 AX-123318832 7 36734835 ACTCTTGTGGTTTCTGTTGGAGATAACCTCACTGA[G/T]CTTTCTTACCTCCATCCATCAGGAAAGAGCGGCGA K 2 1 2 1 101000 f 74 goat snp46308-scaffold639-126113 7 70168742 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273273 Affx-1111833538 AX-501547691 7 36757037 CCATTTTTTCCCCATCTATTTGCCATAAAGTGATG[A/C]GATTGGATGCCATGATCTTCGGTTTTTGAATGTTG M 2 1 2 1 303000 f 74 goat 7_36757037_AF-PAKI 7 36757037 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38407761 Affx-122954975 AX-123278112 7 36793315 CTTTCCTTCCTAATTCATTTTCACTCTTTCATATC[G/T]CTTGTCCCTCATATTGTCTTGTTAACCCAGTGTTG K 2 1 2 1 101000 r 74 goat snp46309-scaffold639-184593 7 70112192 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453804 Affx-122919570 AX-123324137 7 36866190 CTTTGTACTTCTAACAATGGAAATTAACAAGACTC[A/G]AATTACCAATAATGCCAAATAAAGCTGAGCCTCAA R 2 1 2 1 101000 f 74 goat snp46311-scaffold639-257468 7 70024243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415617 Affx-122948597 AX-123285966 7 36941231 CTCACCGGGGGTAGCTGGAAGGTAGTCACCTGCTG[C/T]GCGTCCCTCAAACTCGCTTCCTGAAGAATGGAAGT Y 2 1 2 1 101000 r 74 goat snp46312-scaffold639-332509 7 69949108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391775 Affx-122967460 AX-123262132 7 36990679 CTACTCTCCCCACAGGCTTAGGAAGGGTGGTTAGC[A/G]TATCACGTTAACTGTGTGGAGGTCAATGGAAGGGC R 2 1 2 1 101000 r 74 goat snp46313-scaffold639-381957 7 69900466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385937 Affx-122971558 AX-123256295 7 37022345 ACTGAGCAGCAGCAGCAGTCTTCCTGCTAATTTTA[C/T]AGCTTCTGCTTCTCTGGGTTCACCTTGACTTCTCT Y 2 1 2 1 303000 r 74 goat snp46314-scaffold639-413623 7 69869058 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795005 Affx-122953899 AX-385281964 7 37074703 ATGTTCACTTGAAGAGGGTGTCTACTCAGGATAGA[C/T]GCCTTGAGACACCAGGTTAGACACTGAGTCATTTT Y 2 1 2 1 202000 r 74 goat snp46315-scaffold639-465981 7 69817227 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773141 Affx-122943384 AX-385260284 7 37119860 AGCTATTGTCCATAAATTTGAGGGGGCAATTTATC[A/G]GTTAGTAAAGAGGAAATGAGCTCAGTGTTAGCAGA R 2 1 2 1 101000 r 74 goat snp46316-scaffold639-511138 7 69771836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385486 Affx-122971279 AX-123255844 7 37153406 TAGACTTATATATCAGCCTAAAATCTTGATTTGCT[A/G]TTCAGTCGCTCAGTTGTGTCCTACTTTCTCCATCC R 2 1 2 1 303000 f 74 goat snp46317-scaffold639-544684 7 69738244 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424807 Affx-122941381 AX-123295153 7 37196206 AATCTCATGTTAACACATGCAAACACACACCCACA[C/T]GCAAACACCAACAGGATGTAAGGAAATTTTGGAGG Y 2 1 2 1 101000 r 74 goat snp46318-scaffold639-587484 7 69694602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378632 Affx-122977111 AX-123248991 7 37200712 ACTACAAGGATAGTACCCTTAAACTCTGAAAATCC[A/C]TGAAATTCTTGCTAATGATCTGCAGAAAGAAGGCT M 2 1 2 1 101000 f 74 goat snp12655-scaffold1485-1806 7 69690086 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418949 Affx-122946493 AX-123289297 7 37229958 TTCTAGGTGGGGAGATGAACAAATGCTCTTTAAAA[C/T]GTAGAAGAGAGAAGCAGAAGTGATGCAGCACAGTG Y 2 1 2 1 201000 f 74 goat snp12656-scaffold1485-31052 7 69663006 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444591 Affx-122926957 AX-123314928 7 37301840 AGAGACTGAGCACTTCTTCAGATACTTCTGCCTTG[C/T]AGGGGGAGAAAGGGAAAACTTTAAGATTTCTTCCA Y 2 1 2 1 201000 f 74 goat snp12658-scaffold1485-102934 7 69589641 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406668 Affx-122955793 AX-123277020 7 37337822 AAGGTTCGCTGTGTCCAACTAACTGCTGGGACCTG[A/G]ACAGCAGGATTTCTCAATTCCCTCCTTCATACAGT R 2 1 2 1 101000 r 74 goat snp12659-scaffold1485-138916 7 69552482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791363 Affx-122959541 AX-385278355 7 37407437 ATTAACAAGTACGTATTGTCATACCACTCCCAATA[C/T]ATTTGCAAACCCTGACATGCTTCTAATAAGCAAAT Y 2 1 2 1 101000 f 74 goat snp41012-scaffold529-569775 7 69481718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387699 Affx-122969811 AX-123258057 7 37457799 ACAAGTCATCTTTGCTGCTTCAAACCTATGTGTGC[A/G]TGCTTAGTTGCACAGTCTCCCAGTCATGTCGGACT R 2 1 2 1 101000 f 74 goat snp41011-scaffold529-519413 7 69431256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390849 Affx-122967827 AX-123261206 7 37518945 TTCACGTACCTGTGAAGGGGAATTTATTCAGCATT[A/G]CCCTCCCCCACCCTATATAACAGGTTGGTATTTTA R 2 1 2 1 101000 f 74 goat snp41009-scaffold529-458267 7 69368708 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451021 Affx-122921457 AX-123321355 7 37559772 ACTACAAAAACAATCTTGAAGAACTACAAAAACAA[C/T]GAGAAGAATGGCAATATGAACACATTAATACTTAT Y 2 1 2 1 101000 r 74 goat snp41008-scaffold529-417440 7 69326888 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278480 Affx-1111836447 AX-519551963 7 37568915 ATTACTAGGTTTAGTGTAAGCTGCCTTGTACATGG[A/G]CTTCCCTGATAGCTCAGTTGGTAAAGAATCCACCT R 2 1 2 1 201000 f 74 goat Random2.2K-785 7 37568915 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394880 Affx-122964751 AX-123265235 7 37599153 ACAATGCTTGTTTTCTTTTTTCTTTTAAATTTTGA[C/T]ATGTCAGTTTTGGTACATAATTGAAACAAGTTGTT Y 2 1 2 1 103000 r 74 goat snp41007-scaffold529-378059 7 69286459 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447519 Affx-122924064 AX-123317855 7 37634108 TGGTAGCAGAAGACTAAAGCAAAAAGTTTCAAGCA[C/T]GAGAAGAATTTAATGAGATATCCTTAAGATGGCAG Y 2 1 2 1 101000 f 74 goat snp41006-scaffold529-343104 7 69251214 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395339 Affx-122964037 AX-123265694 7 37671851 ATCCAACTGATTACAGTGGAGGAGGGATTGACTTA[C/T]AAGGAGACAGAAGCAATTGTGTATATGCAAATAAT Y 2 1 2 1 101000 f 74 goat snp41005-scaffold529-305361 7 69215216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793382 Affx-122972097 AX-385280360 7 37703238 ACAGGAATCATGGATAAAGGGATGGTTCTGAATAT[A/G]TTAATCTAGAAGGAAATGGAGGTTAAATGATGAGA R 2 1 2 1 101000 r 74 goat snp41004-scaffold529-273974 7 69183804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443093 Affx-122928109 AX-123313430 7 37734557 CTGTAGAAGTGCTATTACTCAGTGTTGGGTCTGCT[A/G]CACTAATTTTCTGTTTTTCCTCTTTTATGTCTTAT R 2 1 2 1 101000 f 74 goat snp41003-scaffold529-242655 7 69151065 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427220 Affx-122939578 AX-123297563 7 37783654 TACCGCAGGGGATGACATATAGCCGCATAGCGGTC[A/G]TAGGCCATGGCCGCTAAGAGAAAGCACTCGCCCCC R 2 1 2 1 201000 r 74 goat snp41002-scaffold529-193558 7 69097365 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802211 Affx-122922681 AX-385289115 7 37841803 TGAAACTCTAAATATAAGCCAAACTGATTTTCTCC[A/C]CCAAAAGTTTACAGCTATTCTCTATCATGGCTGTG M 2 1 2 1 101000 r 74 goat snp41001-scaffold529-135409 7 69038833 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404774 Affx-122956684 AX-123275126 7 37871169 TGTCCATCAAGATATCAAGTACTAATCTCCTGTGA[C/T]GATGGTCTTACATTACAAAGTTCTTGCAGATGTCG Y 2 1 2 1 101000 r 74 goat snp41000-scaffold529-106043 7 69008934 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788957 Affx-122964341 AX-385275970 7 37953260 TGACCTGTATCCCAGAAGTAGGAAACAACATTACT[A/G]ATAAACATCACTAATCAATCATTTCTCCTTTCATG R 2 1 2 1 202000 r 74 goat snp40999-scaffold529-23952 7 68925875 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433934 Affx-122934292 AX-123304275 7 38031145 CGGACACGACTGAGTCACTTCACTTTCACTTTCAT[A/G]CAGGTACTTCTAAATTTGGATTAGAAATAGTAAGG R 2 1 2 1 201000 r 74 goat snp23404-scaffold2347-53834 7 68836236 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431825 Affx-122936100 AX-123302166 7 38086082 TGGACCACAGCAGTAGCATCTTGAGGGGCAACCCT[A/G]CTCATACAGTTCTTGATATTCACACCAAATCTCCT R 2 1 2 1 101000 r 74 goat snp23405-scaffold2347-108771 7 68781119 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426594 Affx-122939983 AX-123296940 7 38116548 GATGGAAAAATAGAAAAATCACTGAAGATTGTTGT[A/G]TATGGAGGAGGGAAGATCTCTATCCACAATGTTCA R 2 1 2 1 103000 r 74 goat snp26646-scaffold2786-168676 7 68748249 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796567 Affx-122978550 AX-385283513 7 38162384 AGGGAGTAAACTTTCCCAATAAATACTTACAAAAG[C/T]GTACAAATAATCATTACAAAAAATCATATCATGGA Y 2 1 2 1 101000 f 74 goat snp26645-scaffold2786-122840 7 68702930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451956 Affx-122920955 AX-123322289 7 38239495 GTCTGGCCTCATAACCTATGGGCTTTGTGGGCACA[C/T]GCATGCAGGAGCTGGGCTGGGCCACTGGGTCAGGG Y 2 1 2 1 101000 f 74 goat snp26643-scaffold2786-45729 7 68624210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376425 Affx-122978073 AX-123246784 7 38318646 ATTAAGCCATGCTTTGGGAAAGTCAGTGGGTGACA[C/T]AGTGCATGGGAAGACTTCATGTGCTGGTGGTTTTT Y 2 1 2 1 102000 f 74 goat snp2500-scaffold1070-33323 7 68419778 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382006 Affx-122974072 AX-123252364 7 38375713 ACTTACATGTTAGAACAAGGCTTATGATTGTATAT[A/G]TGAGCTGGCATTATCAAAAGTTATCCTTTCCCTGA R 2 1 2 1 101000 r 74 goat snp2501-scaffold1070-90390 7 68350555 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439634 Affx-122930618 AX-123309971 7 38425538 GGCCTTGCTACGCCCTGCTGTTGATTTAATCCTCA[A/G]CACAGCTCGCGTTATAAAGCCATAGGAGACTAGAA R 2 1 2 1 101000 r 74 goat snp2502-scaffold1070-140215 7 68300400 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421668 Affx-122944430 AX-123292015 7 38482864 AAACTGTAAGTGGTTCAACAAGGCTGGAAATGAAG[C/T]GTACAGTGATGACAAATGGAGAGATTCCAAGTGAA Y 2 1 2 1 101000 f 74 goat snp2503-scaffold1070-197541 7 68241680 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427960 Affx-122939197 AX-123298303 7 38513035 AAGAGTTATTGCTGAAGGCTTTTCTCTGTAAAACT[A/G]GAACAGGCAGCTTCTTCAAATACTCAAACATTAAC R 2 1 2 1 101000 f 74 goat snp2504-scaffold1070-227712 7 68211595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772728 Affx-122919325 AX-385259874 7 38573151 TTTAATATATGGATTTTGAAAGAAGAAATCAGCCC[A/G]TTAAACTCTAACCTCTGCTCCGCCAAATCCATGTC R 2 1 2 1 202000 f 74 goat snp2506-scaffold1070-287828 7 68157161 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774422 Affx-122932038 AX-385261558 7 38618264 CATGAAATTTACTAGTTTCCTGATTAAACTAAGAT[A/G]CAAGATCAGTATATTGGGTTTTAAGGCTGTAGCTT R 2 1 2 1 101000 r 74 goat snp2507-scaffold1070-332941 7 68111902 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393813 Affx-122965576 AX-123264168 7 38656362 TTTCTCTCTTGGCTGACTGCAAATGCTGACAGGTA[C/T]GGTGGCACAGATATCGGGTTACAGGGAATGCAGAA Y 2 1 2 1 101000 f 74 goat snp15159-scaffold1620-31620 7 68047577 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797861 Affx-122956056 AX-385284799 7 38689360 CCAGAAAAATACACTGACATTTTGAACATCATTAA[C/T]GATTGATTGAAGATAATCAATTCAATACTGCTGTA Y 2 1 2 1 101000 f 74 goat snp15160-scaffold1620-64618 7 68013500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789742 Affx-122929008 AX-385276750 7 38756344 GGGCTGGTTTCTATTTCTGGTTTTCATAGGCTGTG[C/T]GATTTTGGCCAAAGTCCTTCCCCCGTTTGTACCCT Y 2 1 2 1 102000 f 74 goat snp15161-scaffold1620-131602 7 67946854 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386114 Affx-122971424 AX-123256472 7 38785571 CCCTGATCACTTCCTCCCCAACTCGTGGGGCAGGT[A/G]TCCATGGCAAGAGGGGTAAACTGAGAAGTTCTGAG R 2 1 2 1 103000 r 74 goat snp15162-scaffold1620-160829 7 67916911 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399831 Affx-122960260 AX-123270186 7 38837535 GGGCCTGAGCAGAGGCTGCTGGCTAAGAGTCTCTG[A/C]GGAGCTGCAGGGGAAACAATGGCCAAGTACATAGT M 2 1 2 1 101000 r 74 goat snp15163-scaffold1620-212793 7 67864086 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429032 Affx-122938318 AX-123299374 7 38894612 CTCCAATTAAAAAGCAAATAAAAAAGAAAATGCCC[A/G]TGCGATAAAACTACAAACACACGTTGTATTAATGT R 2 1 2 1 103000 r 74 goat snp15164-scaffold1620-269870 7 67806823 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430019 Affx-122938021 AX-123300360 7 38972420 GACGAGAGTGAGGAGATCATTGTGTGCCGCTGGCA[C/T]GATAGCAGTGTGGTCAACATCTGCTCCAATGCTGT Y 2 1 2 1 201000 r 74 goat snp15165-scaffold1620-347678 7 67733892 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451332 Affx-122921272 AX-123321665 7 39016563 GTCCATGAGGTCACAAAGAGTCAGACGCCACTGAG[C/T]GACTGAATGACCACAACATACATACATATACGAAA Y 2 1 2 1 103000 r 74 goat snp15166-scaffold1620-391821 7 67690305 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441366 Affx-122928866 AX-123311703 7 39064356 AACAATCACTAATCTTTTCTCCCTCTCTATTGTCG[C/T]CATTGTGTTCAGTTGCTAAGTCCTTTCTGTCTCTT Y 2 1 2 1 201000 f 74 goat snp15167-scaffold1620-439614 7 67642242 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390594 Affx-122967186 AX-123260951 7 39150839 TGGGGATCTTCATCCCCTGATAGTCACTACCTGCC[A/C]CCCTAACCTTGGTAGAGGGCAAATAACCAGTAGCT M 2 1 2 1 101000 r 74 goat snp15169-scaffold1620-526097 7 67555305 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452317 Affx-122920668 AX-123322650 7 39223275 TGTATAAGGAAGGGACTGATGACACGCACCAGCCT[A/G]TCTCGGGGGCAGCAGTGCTTGGTGGTGGCCAGCAC R 2 1 2 1 101000 f 74 goat snp15170-scaffold1620-598533 7 67481815 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430685 Affx-122936922 AX-123301026 7 39252535 AGTGGGTCTGCAGGTTAGTGGGAGTCAGGGGAACA[C/T]GAATCTTGCAGAACCAGCTCCAAGTGGACTGGCTG Y 2 1 2 1 201000 r 74 goat snp15171-scaffold1620-627793 7 67452978 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379043 Affx-122976350 AX-123249402 7 39308203 TCCCCACAGAGCATCCTCCTGGGTGCTCATGTCTG[C/T]GAAAAGCCCTTTCCAGTCACTGCTTCAACCTAATC Y 2 1 2 1 102000 r 74 goat snp15172-scaffold1620-683461 7 67397423 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273275 Affx-1111833539 AX-519546921 7 39337277 TGACACTAGTACATTTGTACCCTCGGCTCTCAGCT[A/G]CAATAAAGTATATGTTAACATGCACAGCTTAGCAC R 2 1 2 1 101000 f 74 goat 7_39337277_AF-PAKI 7 39337277 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418871 Affx-122946119 AX-123289219 7 39378327 CCTAAAACTCTGGGACAAAGGGTTCCCTTTTCTCC[A/G]CACCCTCTCCAGCATTTGTAATTCATAGACGTTTT R 2 1 2 1 103000 f 74 goat snp15173-scaffold1620-753585 7 67374472 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414748 Affx-122949256 AX-123285097 7 39439466 GTTTTCCACTCCTGATGGGGATATCACATTTCCTT[A/G]TAAAACTGAAGCAAGAAAATATGAATAACTCATGA R 2 1 2 1 101000 f 74 goat snp15174-scaffold1620-814724 7 67226350 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 468278482 Affx-1111836448 AX-519551965 7 39500910 CAGTGTCCAAGAAAAATAGCAGTGATTCACTGTAG[C/G]GGTCATCATAAAGGGAATGCAGAACTAATAAAAGG S 4 1 2 1 101000 f 74 goat Random2.2K-786 7 39500910 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392012 Affx-122966487 AX-123262369 7 39507171 GAAAGCTGGAGAGATCTGGAAAATATGCTTAACAA[G/T]CTTGATTGTCCTTATAAAACTCTGCCCAAGGGAGG K 2 1 2 1 101000 r 74 goat snp15175-scaffold1620-882429 7 67159327 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392538 Affx-122966101 AX-123262895 7 39538407 CCGGCTCCATTTTATTTATTTATTTAATTCAAGTG[A/C]TATATATATTTTTCATTTTTTGGCCTTGCTGCTGG M 2 1 2 1 303000 r 74 goat snp15176-scaffold1620-913665 7 67128074 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428134 Affx-122939060 AX-123298477 7 39668489 AGGTGGGTAGGAATGTAAGTTCTTCTTTAGCACCT[G/T]CTGTATACCAAGCCCACCCACTGTTACCTGTTCTG K 2 1 2 1 201000 r 74 goat snp15178-scaffold1620-1043747 7 66999643 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379088 Affx-122976316 AX-123249447 7 39719322 AGGCAGCATGTATTGAGTGCCAAGTGTGTGCCTGG[C/T]TTAGTTCCCTTGGCGTCCTCAACTCTACCCCCAAG Y 2 1 2 1 201000 r 74 goat snp15179-scaffold1620-1094580 7 66948522 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449965 Affx-122922888 AX-123320300 7 39760432 TCAGATCTGTGGATGGAACCTGCACTTGACCAGCC[A/G]TCCTGGCCCCTCTGGTTTCCCACTTCTGCCCCCGC R 2 1 2 1 101000 f 74 goat snp15180-scaffold1620-1135690 7 66908045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422123 Affx-122943555 AX-123292470 7 39818870 GACTCAACCTCCACTACATCCACCTCAGAAAAGCA[C/T]GAGATCTGTATTGGTAATTCTGCCTGAAATGGGGG Y 2 1 2 1 201000 r 74 goat snp15181-scaffold1620-1194128 7 66849525 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766388 Affx-122955579 AX-385253767 7 39990404 AACTTATTGTCATCACAGAGGAAGGGTTAGGGAAA[A/G]GATCAATTGGGAGTTTAAGATTAACAGATGCAGAC R 2 1 2 1 101000 f 74 goat snp1266-scaffold1032-575759 7 66681931 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428380 Affx-122938960 AX-123298723 7 40038557 GGGGAGGGAGGTCAGGTCACTGTCCACAGGTGGGC[C/T]CACTGGGGGAACTTGGGAAGAGGGGCTCCAGAAGA Y 2 1 2 1 201000 f 74 goat snp1265-scaffold1032-527606 7 66636281 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399443 Affx-122961215 AX-123269798 7 40070732 TTGTTGCTGCTGTGCTGGGGGGCTCAGCTGGGGAC[A/G]TTTCTGTCACCTGGAACGTGTTGGATGGGGCCACC R 2 1 2 1 101000 r 74 goat snp1264-scaffold1032-495431 7 66605800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418250 Affx-122947028 AX-123288598 7 40099629 GCCTGGTCCCAAGAAAACATGCCTAAAGGGACGTT[A/G]TAATGGTTTTCCCTCTTGTCCTGCCTACCAGGAAG R 2 1 2 1 101000 r 74 goat snp1263-scaffold1032-466534 7 66577037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449538 Affx-122922596 AX-123319873 7 40160055 TCCATTGTTAATTTAGTAGACGCCTTTGTAGCAAC[C/T]GCTGACTATTCAGCTGGGAACAAGCCCTAGGTCTC Y 2 1 2 1 101000 f 74 goat snp1262-scaffold1032-406108 7 66521220 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442158 Affx-122928315 AX-123312495 7 40282754 CATCTGCCTGTGATTATGTAAGCCCCTGTCCCAGC[A/G]GATTCTCCTGTTGGCCTTGAAGGAGTGAGCTGCCC R 2 1 2 1 201000 r 74 goat snp1260-scaffold1032-283409 7 66386689 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424924 Affx-122941292 AX-123295270 7 40318195 CTCCCACCTGGAAGTGCCTGGGGCTTGGGGGCCGA[C/T]GCGACAGAAGTGATTTGGAGATGGGATAAGCAGAA Y 2 1 2 1 101000 r 74 goat snp1259-scaffold1032-247968 7 66351155 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407312 Affx-122955312 AX-123277663 7 40348332 AGAGTGGAGCATCATGGTGAATTTGAGTGCTGAAG[C/T]GCCAAGGTGGTTCCTGCCTGGGTATGAGCACACTT Y 2 1 2 1 101000 f 74 goat snp1258-scaffold1032-217831 7 66320718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787312 Affx-122960159 AX-385274337 7 40380640 ATTATCAGTCATTAATTTATCAATTATGGCTTCTG[C/T]ATTTCAAATTATGCTCAGAGATAGCTTCCCTACTC Y 2 1 2 1 101000 r 74 goat snp1257-scaffold1032-185523 7 66288186 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425473 Affx-122941497 AX-123295819 7 40461523 GGAGAATTTGCTGCCAATGAACTCACACCATGGGC[A/G]TTTTATAGGAAGCTCTTCAGGATCTCAGAGAGAAC R 2 1 2 1 101000 r 74 goat snp1256-scaffold1032-104640 7 66207278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410739 Affx-122952702 AX-123281089 7 40495876 TATGGCTTTCCTGGGTGTCCAAGGGCCATGACCCA[C/T]AGGCAGAAGTCCCTTCTCCATGGGGGAGACCAGGC Y 2 1 2 1 101000 f 74 goat snp1255-scaffold1032-70287 7 66172784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386460 Affx-122970779 AX-123256818 7 40611254 CAGGGTGTTGAGTGCTGTGATGGGGAAGCTAGGAC[A/G]CTAGAGGGATCCCAAAGGGCCAGGAAACCTCTAAG R 2 1 2 1 101000 f 74 goat snp36186-scaffold432-182904 7 66054823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419422 Affx-122945516 AX-123289770 7 40650491 AAAATGTCTATTTGGAAATGCTGCCTTTCAGATCA[A/G]TGCCATAATTATCCATATTGTTGGGTTTGTTGTTG R 2 1 2 1 101000 r 74 goat snp36185-scaffold432-143667 7 66014995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798843 Affx-122953968 AX-385285773 7 40694096 AGGATAAATTCCTAAAGGTTATACCACCTTTAATT[A/C]ATTGTATTTTCTCAATCTACTTGACAGCTGGCTTT M 2 1 2 1 101000 r 74 goat snp36184-scaffold432-100062 7 65971354 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788162 Affx-122935162 AX-385275181 7 40751012 TTTGAGACTGCAAATTGTCCCCACAGTCACCTACT[A/G]CTTTTAGTATAGATAACAATAGTTATTACTGTGAT R 2 1 2 1 102000 f 74 goat snp36183-scaffold432-43146 7 65914221 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406812 Affx-122955689 AX-123277163 7 40845905 ATTCCGTGCTTCACGCTGGCTGCCCAGGGCAGTGG[C/T]GAACAAGGCAAGATCCATTCTTCAGTTGGAAAATA Y 2 1 2 1 101000 r 74 goat snp57590-scaffold921-555334 7 65818918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779463 Affx-122978340 AX-385266566 7 40905350 GACTGAAAGCTCTGCAGGGCCACAGATGAAACCTT[A/G]CCTGAAGGTATCCTTCACCACAATAACTGTGGGCT R 2 1 2 1 101000 f 74 goat snp57589-scaffold921-495889 7 65758394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438480 Affx-122931229 AX-123308818 7 40962322 TAAAACAAGAAAGGACACTCTAGTTGACTACAAAA[C/T]GTGAAGAATCAATCCATGAAAGGCAAAAAAATAGA Y 2 1 2 1 201000 f 74 goat snp57588-scaffold921-438917 7 65699939 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390802 Affx-122967864 AX-123261159 7 40992815 GGATGAACTTCAGACTAGGATAAAATACTAGCAAA[C/T]GATCTAGCCAGTAGAGGACTACTAACTTTGTTCTT Y 2 1 2 1 101000 r 74 goat snp57587-scaffold921-408424 7 65670051 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447835 Affx-122923906 AX-123318171 7 41024691 TCCATTTTTGCTTTGCTTTAAAATTGTAATATCTT[C/T]CTGAGTGGAAGACTTCTTTCAAAATATCCCTATTT Y 2 1 2 1 201000 f 74 goat snp57586-scaffold921-376548 7 65637848 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420292 Affx-122945035 AX-123290640 7 41055448 AACAGCTCAGATTAGAAACATGTCATCCCCAGAAG[C/T]GAGTAACTATTAACTTTTCATAAGCAACTCAGGTA Y 2 1 2 1 201000 r 74 goat snp57585-scaffold921-345791 7 65607106 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433047 Affx-122935759 AX-123303388 7 41111295 CCAAAATCACTTCCACACAGCAGCTAGGAAGGCCC[A/G]CCAGCTTGTCAGGATTTTCCCAGCCACTGTGGGCC R 2 1 2 1 201000 r 74 goat snp57584-scaffold921-289944 7 65551208 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436319 Affx-122933258 AX-123306658 7 41145066 TAGGAGCAGGGGGTTTGTCTTAGGACCTCCATGCC[C/T]AGCAGCAGCCAGGCACAGTGAGGGCCTCAGTAAAG Y 2 1 2 1 101000 f 74 goat snp57583-scaffold921-256173 7 65522513 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796208 Affx-122933171 AX-385283159 7 41183668 TCTAGAACCCTGCTCCCTCAACTATTGTGGATAAA[C/T]GTGTAGCAGAGGCTGCTACCGCCTGTGACTGGTAT Y 2 1 2 1 202000 r 74 goat snp57582-scaffold921-217571 7 65485012 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765073 Affx-122969979 AX-385252638 7 41216284 TGGAAAATTGTTTCTCAGTGAACTGGATGGCACAG[A/G]CCATTTTAATGACTTGAGCAGTTTTACTGGCATTT R 2 1 2 1 101000 f 74 goat snp57581-scaffold921-184955 7 65452187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792453 Affx-122935506 AX-385279434 7 41256206 GAACTCTTCACAGCATGCTATTTCCTTGTCTCTAA[C/T]GTGTTGAATCAAAATATCTCCCTATCCCCCATCTC Y 2 1 2 1 101000 f 74 goat snp57580-scaffold921-145033 7 65412158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417771 Affx-122947397 AX-123288119 7 41303831 AATTGGATATATAACCTGCTGGATCAGTATTTGCT[A/G]TCATACGTTTCTCTCAAAGCTTCTGTTTCCATGTA R 2 1 2 1 101000 f 74 goat snp57579-scaffold921-97408 7 65364517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430055 Affx-122937558 AX-123300396 7 41348311 ACGACAAAGCACACAGAAAATATTTTTAAACCGCC[A/G]CCTGGACCTTAAACACTATTACTGTTTGTATAATA R 2 1 2 1 101000 r 74 goat snp57578-scaffold921-52928 7 65320823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410816 Affx-122952642 AX-123281166 7 41383947 TGAAGTACCCGCAGGGTTAGGGTGATGGGACCCTG[C/T]AGGCTGCCACTGCCAGAGAGAACCAGAGACCTCCA Y 2 1 2 1 101000 r 74 goat snp57577-scaffold921-17292 7 65285643 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423520 Affx-122942452 AX-123293866 7 41407031 CTCTAAGGAGAAAAGCATTGATGGTGATTATGAGA[C/T]ACCACAGGGAAAAGAAAGAATGGGACTATGTGCCA Y 2 1 2 1 101000 f 74 goat snp30557-scaffold339-5693 7 65264980 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393297 Affx-122965435 AX-123263653 7 41460890 CGTACGGAGGTAAAGCTCACCCCACTAGGCACCCA[C/T]GTCAAGTAGCTGGAGGCCTCTACAGAACCCCAAAC Y 2 1 2 1 101000 r 74 goat snp30558-scaffold339-59552 7 65210992 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394057 Affx-122964981 AX-123264412 7 41498233 GACCCACAGTAGTGTTTCTGAGGATCAGATGAGAC[A/C]ATTTGCTACATTTACACCAGGGCTTGTCGTCAATG M 2 1 2 1 101000 r 74 goat snp30559-scaffold339-96895 7 65173321 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393245 Affx-122965472 AX-123263602 7 41555001 ATGACTAGAAGGAGATTTAGCTTGACCCTCGTAGA[C/T]GCTGAAATAGAGATGGCTACTTCCTGGGGGAGCTC Y 2 1 2 1 101000 f 74 goat snp30560-scaffold339-153663 7 65116268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439469 Affx-122930167 AX-123309806 7 41604143 CCCCAACTCAGTCACTATTCCTGGTTTATCCGTCA[C/T]ATTCCTCTCCAGTCTTCTCCTCTCTTACTCTGTGT Y 2 1 2 1 101000 f 74 goat snp30561-scaffold339-202805 7 65066952 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790313 Affx-122952234 AX-385277316 7 41669994 AGATATCATTTCAGACAACTTAGAACAGACCCTTT[A/G]CAATCTGACTAACAGCAAAATAGAAAGGGATTTAG R 2 1 2 1 101000 r 74 goat snp30563-scaffold339-268656 7 65000691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380471 Affx-122975725 AX-123250829 7 41722586 TGAGGGGCTAAGAGTCCTGCCTACTTCATGGACAA[C/T]GAGAATTTCCCATCATGCAAGGCAACTAACCAGCA Y 2 1 2 1 101000 r 74 goat snp30564-scaffold339-321248 7 64948126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803064 Affx-986696153 AX-385289936 7 41808925 GAGGTCTCAGGTCACACCCAATGGCCTGGTTGGCA[A/G]CAGGATGCAGTGACCAGAGGGTCTGGAGATTGGGT R 2 1 2 1 600010 f 74 goat 7_41808925 7 41808925 Ancestral_priority_1043 ancestry 0.51 neutral IMAGE 10K 10K ancestral 38398956 Affx-122960979 AX-123269311 7 41813640 AAAAACATAGATAAAAAATTATATACTCCTTGTTC[A/G]TGATACTTAATTTCCAAAGCACCAAGGCAAAATAA R 2 1 2 1 101000 r 74 goat snp30566-scaffold339-412302 7 64858750 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402591 Affx-122958431 AX-123272944 7 41850513 ACAACTAACGTGCCCCATCCTCACAATGGCCTAAG[G/T]AATGCTGAACTCAAGCTGAGGAGACCAACCAAGCG K 2 1 2 1 101000 r 74 goat snp30567-scaffold339-449175 7 64821749 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425437 Affx-122941524 AX-123295783 7 41894698 AGATTCTCACCATGGAAGGCCCAGTGTCTGGCTCC[A/G]CTCTGCCTCCTACCTACCAACCATCCCTCCTGAGG R 2 1 2 1 101000 f 74 goat snp30568-scaffold339-493360 7 64777052 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375621 Affx-122978709 AX-123245980 7 41924815 AGGCCAGGCCAGCATTTCCCACCCTGGTGTGCTGT[A/G]GGTCTGTCCCAGGTACAGGACTCAGCAACCAAAGT R 2 1 2 1 101000 r 74 goat snp30569-scaffold339-523477 7 64747096 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273319 Affx-1111833540 AX-519546962 7 41939872 ATTTTTATGGAGCTGAATTTCTTCTTCTTGAAAAT[A/C]TGACCTTTTCTCTGAGTTCATTTCTTCGGAGAATT M 2 1 2 1 101000 r 74 goat 7_41939872_AF-PAKI 7 41939872 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38402530 Affx-122958476 AX-123272883 7 41987800 GTGGGGGTGGGGAAAAAATTATATCAAAGAGAGCA[A/G]TACAGTTAGCTACTGGGGTGGGTCTCTGAGAAGAG R 2 1 2 1 101000 f 74 goat snp30570-scaffold339-586462 7 64684306 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789458 Affx-122934163 AX-385276468 7 42024975 ATTATTCTACGGTCAGGAAAACTAATCATGGAAAT[A/G]TCTGAGAGAAGCTCTGCTATCACAAGGAGACAGGC R 2 1 2 1 101000 r 74 goat snp30571-scaffold339-623637 7 64646148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438683 Affx-122930873 AX-123309020 7 42054890 TTACCTCGCTCTTTCATCTCATCCCACACCCTTCT[G/T]CAGTTTCAAGGAAGAGCAAGGATAGTAGAATGATG K 2 1 2 1 201000 r 74 goat snp30572-scaffold339-653552 7 64616057 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764843 Affx-986697063 AX-385252442 7 42067949 ACTGAAGAGATTTAAAATGCACACGTTTGTTTTTT[C/T]AATTCAGGGTCCAGAGTTTATACTTCATATTTCTG Y 2 1 2 1 600010 r 74 goat 7_42067949 7 42067949 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 320799909 Affx-122930504 AX-385286835 7 42087284 CCTTTAATAAACTCTAGTTCTTTACAGTTACCAAA[G/T]AAATAACTTTCTTCCTTTGATAAGTCTTTAGGTGT K 2 1 2 1 201000 r 74 goat snp30573-scaffold339-685946 7 64583706 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784863 Affx-122923936 AX-385271910 7 42118227 TCAGAATGTGAAAGATACTAAAAAGAATTTGTAGC[G/T]TAAAGTTTAGCTGTAAAACTACAAACAAATGTTCA K 2 1 2 1 201000 f 74 goat snp30574-scaffold339-716889 7 64552483 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383044 Affx-122973295 AX-123253402 7 42147405 CAAAACCTCCCTTCTCTTTGTTCAGGCTCCCACTT[C/T]GTGGCTGGTGCTCTGTAGAAGACCTCCCCGCCTAA Y 2 1 2 1 202000 r 74 goat snp30575-scaffold339-746067 NW_017218696.1 6891 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412332 Affx-122950843 AX-123282681 7 42183188 AAAGTGAGATTGTTCAAGGTCACAAATCTGGGAGA[A/C]GAGGTTGGAGCTGGGACTGGGGCCCACGTCAAACC M 2 1 2 1 101000 f 74 goat snp30576-scaffold339-781850 7 64487148 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410199 Affx-122952576 AX-123280549 7 42226561 TTATGAATTTGTTTATTATTGGATTTATTTCTCCT[A/G]TAAGCAAATGTGTTCACAACATTCCATCAGGGAAT R 2 1 2 1 101000 r 74 goat snp30577-scaffold339-825223 7 64443394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410768 Affx-122952683 AX-123281118 7 42258884 GGCCTGCGATGGGGACCACAGTCAGCTCCCCATCT[A/G]CTGGACCTTCCTCTATCCATAGTATCACTGGGCAT R 2 1 2 1 101000 r 74 goat snp30578-scaffold339-857546 7 64410714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449930 Affx-122922914 AX-123320265 7 42320404 TTCAGCTACCCTACAGGTCAGCATCAGATGGGACA[C/T]AATGTGGCATAATAGTTAAAAATAAAAGAATTAGA Y 2 1 2 1 101000 f 74 goat snp30579-scaffold339-919066 7 64349105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764790 Affx-986697033 AX-385252399 7 42340958 TTATTCTCCCACAGTTCTGGAGGCTACTAGCTGAA[A/G]AGAGGGACTTGGTGGTGTCGATTCTCCCTGAGCGC R 2 1 2 1 600010 r 74 goat 7_42340958 7 42340958 Ancestral_priority_1043 ancestry 0.576 neutral IMAGE 10K 10K ancestral 320762506 Affx-986697036 AX-385250623 7 42340991 AAGAGAGGGACTTGGTGGTGTCGATTCTCCCTGAG[C/T]GCACCTCCTTTCCTTTCTCCTCTCCAGGCTTCCGG Y 2 1 2 1 600010 f 74 goat 7_42340991 7 42340991 Ancestral_priority_1043 ancestry 0.504 neutral IMAGE 10K 10K ancestral 320762508 Affx-986697038 AX-385250625 7 42341208 TCAGATTAGATTCCACCTACTGTGTGATCTCATTT[C/T]AGCTTGACTATATCCACAAAGACTATTTACAAATA Y 2 1 2 1 600010 f 74 goat 7_42341208 7 42341208 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 320764803 Affx-986697040 AX-385252411 7 42341210 AGATTAGATTCCACCTACTGTGTGATCTCATTTCA[A/G]CTTGACTATATCCACAAAGACTATTTACAAATAAA R 2 1 2 1 600010 r 74 goat 7_42341210 7 42341210 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 38421332 Affx-122944075 AX-123291679 7 42349344 TGAAATTTTTTTTTGGTTACAACAGAAGGAAGACC[A/G]CCCTGAGGTGTCCCCAGGTAGAGCACCTTGATTAT R 2 1 2 1 201000 f 74 goat snp30580-scaffold339-948006 7 64321193 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397570 Affx-122962010 AX-123267925 7 42463453 TAAGTACCCCCAGAATTATCAAACTCTATTTAAAG[C/T]AGGCCTGTTTTCATTAAAGTGTCCTTTAATGTAAA Y 2 1 2 1 102000 f 74 goat snp30582-scaffold339-1062115 7 64206626 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791131 Affx-122976175 AX-385278126 7 42492114 TAGGGTATCCCTTTGAGCAGACTTCAGAAGTGTGA[A/G]TGAAATATGGCTAAGCATATTACTCTTGTTTTCAA R 2 1 2 1 101000 f 74 goat snp30583-scaffold339-1090776 7 64178465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430802 Affx-122937462 AX-123301143 7 42540403 GTGGGACATCGTCGCTAGGTGGACACAGCAGGAGA[C/T]TGTGGACTGGGAGTGATGGAGGGAAGCAGAAAGGT Y 2 1 2 1 201000 f 74 goat snp30584-scaffold339-1139065 7 64132033 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786881 Affx-122967193 AX-385273910 7 42583219 ATATGGTCTTTACAAAAGTCACTAAACAGACAACT[A/G]CTATCCATGGAAAGCAACAAACCCAACAATAAGGA R 2 1 2 1 101000 r 74 goat snp30585-scaffold339-1181881 7 64089207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443167 Affx-122927613 AX-123313504 7 42618419 CCAGGGGAGTGACTCAGTTCCTTTGCCTCAATGAC[C/T]GGGCTTTACGGGGGGTGCACACAAGGGCTCACCCC Y 2 1 2 1 101000 f 74 goat snp30586-scaffold339-1217081 7 64053674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768363 Affx-122970762 AX-385255543 7 42663391 AAAGCCAGTGATGAAAGGGATGTTGTCACAGGAGC[C/T]TCCTTAACTCTGCTCTAAATCTGCAGAAACAGTGA Y 2 1 2 1 101000 f 74 goat snp30587-scaffold339-1262053 7 64009119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433850 Affx-122934439 AX-123304191 7 42704866 GTTCCCTGGTGTCATCCTTACCTCTTGGGACCTCT[A/C]TTAGACACTACCAATGCTGATGGGGCTCCAAGTGT M 2 1 2 1 101000 r 74 goat snp30588-scaffold339-1303528 7 63967924 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417401 Affx-122947684 AX-123287749 7 42772761 AGTGGAAGACTGCAAAACAGTAAAAACCAAGGTAG[A/G]TACAGAGATCTGGGGCATTTAGGATGAAAGGCTGA R 2 1 2 1 101000 f 74 goat snp30590-scaffold339-1371423 7 63911342 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445533 Affx-122925167 AX-123315870 7 42825615 AGAAATGAGCAAGTGGAGGTGCTGCCTGCTGTGAA[C/T]GGATGGTGGATGGATAGGTAATGCCAAGGTGAGCC Y 2 1 2 1 201000 r 74 goat snp30591-scaffold339-1424277 7 63858466 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453112 Affx-122920022 AX-123323445 7 42875443 AAACCCTTGGAAACCTCTACCATGAAGCCCTCCTT[A/G]AACACCCCAGACCCTGTCTGCCCCCGAATCTCTGT R 2 1 2 1 201000 f 74 goat snp30592-scaffold339-1474105 7 63808662 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769421 Affx-122962177 AX-385256592 7 42921517 ACAGTTTCTTTATTTCAAGCCTAGGAAACAAGGGT[A/G]AAATCAGTGTCAGTGTAGTTGGTACTGCTAAGAAA R 2 1 2 1 101000 f 74 goat snp30593-scaffold339-1520179 7 63762376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389466 Affx-122968335 AX-123259824 7 42982884 TTACAAAAGCTCAAATTAAGCCAATATTCCCTGCT[C/T]CCTCCACCGAAAATAAAAACTCACATTGTGTGAAG Y 2 1 2 1 101000 f 74 goat snp30594-scaffold339-1581546 7 63700874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794537 Affx-122925254 AX-385281500 7 43023991 GACTTCATGATCTGCTTCACATGATCAGGTACAGT[G/T]ATCAAGAGCAGATGTCAATAAAAACAGACTAAACT K 2 1 2 1 101000 f 74 goat snp30595-scaffold339-1622653 7 63659893 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793539 Affx-122978597 AX-385280515 7 43053740 TTGAAACTGCATTCTGTTGGCACAGCTGTAGGAAA[C/T]AGGCTCTCATACATTCCTGGTAGATATACAAACTA Y 2 1 2 1 101000 f 74 goat snp30596-scaffold339-1652402 7 63629698 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436134 Affx-122932642 AX-123306473 7 43096064 AGCCATGGCCAGAGCTGGTGAAGCTCAGGCCCACT[A/G]TTTCTAGCCTCAACTTCATCCCTAACACACTCTGT R 2 1 2 1 101000 r 74 goat snp30597-scaffold339-1694726 7 63586597 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452596 Affx-122920496 AX-123322929 7 43135875 TGGGTATTTTCTCATTCAGCCTATGTGCAGGAGTC[A/G]CTCAGCTAGTCTCTGGTTTTCTCTCAGAGGAAATT R 2 1 2 1 101000 f 74 goat snp30598-scaffold339-1734537 7 63549163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403364 Affx-122957795 AX-123273717 7 43183149 ACAGACTAAAGAGCAGTTAGTGCCTCTGTTCACCA[C/T]GTGTAGAAATGCTTGAGACTCACCAAAGAATTGTC Y 2 1 2 1 101000 f 74 goat snp30599-scaffold339-1781811 7 63501830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439920 Affx-122930013 AX-123310257 7 43211900 GCTCTTTATGCACCGAGATGGGAAAGTCCCCAAGA[C/T]GTATTGAGAGAGAAAAAGCAAATAATAGCAAAAAC Y 2 1 2 1 101000 f 74 goat snp30600-scaffold339-1810562 7 63472938 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432029 Affx-122935913 AX-123302370 7 43256417 TACATGGAAATCCCTTTGGATGGGGTAGAAAGCGT[A/G]TGCCCAAATAGTCTTCCTTGGCTTGAAATGGGGGT R 2 1 2 1 101000 f 74 goat snp30601-scaffold339-1855079 7 63428514 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770981 Affx-122960024 AX-385258144 7 43285084 GGGCACATTCTTAGATCCTAATTAGAGGAAGGAGT[A/G]TGAGCTGGTCTTGGCCCTTTATCTGTGGATATTTG R 2 1 2 1 101000 f 74 goat snp30602-scaffold339-1883746 7 63399237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414475 Affx-122949556 AX-123284824 7 43325032 TGGACAAGCCTTGCTTGCTGGACCAAGCACGTCCA[C/T]GCAACTAAATGTTAGACTTTTGACTAAGAAGCTAC Y 2 1 2 1 101000 r 74 goat snp30603-scaffold339-1923694 7 63358471 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773644 Affx-122957753 AX-385260784 7 43365946 TTACATTGTCTTCTTTTGAAAATAAACCTTAATGC[G/T]AGCTAAGATCAAATTAGAAGCTCAAACCAAATAAG K 2 1 2 1 101000 f 74 goat snp30604-scaffold339-1964608 7 63317449 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444274 Affx-122926773 AX-123314611 7 43397174 AATCAGGAACATGGCGTGGATTTGCATCACCGTGT[C/T]ATTTACAAGGACGTGGCCTTGGACCTCGGGCGAGT Y 2 1 2 1 101000 f 74 goat snp30605-scaffold339-1995836 7 63286266 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435329 Affx-122933613 AX-123305669 7 43428667 GTGAGGTGGCATCTGAACCAGCATCTAAGGTCAGG[C/T]GATTGGAAAAGATACCCCAGGCACAGAGAACAGAA Y 2 1 2 1 101000 r 74 goat snp30606-scaffold339-2027329 7 63254882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419004 Affx-122946052 AX-123289352 7 43468074 CATGCTGTAGCTTTTTATTAAAGCACCTACATCCA[C/T]AGCCTTCCTGGCTTTTTGCCCTCCCTTACAAAAGG Y 2 1 2 1 101000 f 74 goat snp30607-scaffold339-2066736 7 63214660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378368 Affx-122976819 AX-123248727 7 43501911 TTCCTTCTCCTCACATGATTTAGATTTATTTTATC[A/G]TTCCTCTTCAAGCTCCTTGAGTCACACGTTTGCTT R 2 1 2 1 101000 r 74 goat snp30608-scaffold339-2100573 7 63180871 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451237 Affx-122921950 AX-26973902 7 43537473 GGAGAAAGTTTGAGTTTGAGCTGAACCAGTCAGCT[A/G]CTTCATATTTTAACTCCACTCATCCTGATCTCATT R 2 1 2 1 101000 r 74 goat snp30609-scaffold339-2136135 7 63145183 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773175 Affx-122947615 AX-385260318 7 43572845 AGGATTCTGCTTGAATTTTCAGTAACAGGCTCAGC[A/G]TTCAAAGCAATAGCTGTTTGCAGCTTGATGCATTT R 2 1 2 1 101000 f 74 goat snp30610-scaffold339-2171507 7 63109731 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386564 Affx-122970708 AX-123256922 7 43610401 TGGCTCTGCGACTCTGCGGTCTTGGCCCTGTCCCA[C/T]CCTTTCTGAGGTTCCCTGCCTCCTCTGTAAAAACG Y 2 1 2 1 201000 r 74 goat snp30611-scaffold339-2209063 7 63071985 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446974 Affx-122924654 AX-123317310 7 43643477 AGAAGGGAGAGGGGGAGTAAGGCTCAGAAGCAGGG[C/T]GAGCAAGAAGGCCTGCAGGACTGAGTGAAGAGCAC Y 2 1 2 1 201000 r 74 goat snp30612-scaffold339-2242139 7 63039120 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797394 Affx-122927445 AX-385284333 7 43678346 GCCAGTAGCTTCAAAAAGTCACCAAATATAACTTA[C/T]AGCAAGTATGTATTTTTCGTATTGAAGTACAGCTG Y 2 1 2 1 101000 f 74 goat snp30613-scaffold339-2277008 7 63004189 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440541 Affx-122929326 AX-123310878 7 43719968 TTATTAGATGGTTCCATGTGTGCGACACTGTAATT[A/G]TAATTCATTTTTGGAAGTCAGTTGTTAAAGTGCCT R 2 1 2 1 101000 f 74 goat snp30614-scaffold339-2318630 7 62962575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764989 Affx-122941116 AX-385252566 7 43835361 ACAAGTTTGTGTACATAGAGTATGGAAACTTTCCA[C/T]GACTATCATAGAAAACAGAAGCTTCTAATTTTGCC Y 2 1 2 1 201000 f 74 goat snp30616-scaffold339-2434023 7 62846346 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768530 Affx-122968783 AX-385255710 7 43868342 CCCCAACACAGACACTTTATAGTCACTTTCAATAC[A/G]CATATAATAAAAAGTATGGAATGAATTCCCCCCAA R 2 1 2 1 101000 f 74 goat snp30617-scaffold339-2467004 7 62817242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420835 Affx-122944660 AX-123291182 7 43908452 CACCTATTTTTCAGAATGGGAATGAGGCCCAAAGA[A/G]CTCCAAGGACTTATCCAAGACCGTGTGGCCATTAA R 2 1 2 1 201000 f 74 goat snp30618-scaffold339-2507114 7 62777524 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788383 Affx-122975174 AX-385275401 7 43944081 TTCTGCCTGATTCTCTTCAACAACGACAACCACTC[A/G]CTTTTAAGACCTGCAGCTTTCACAGCTTAAAAATA R 2 1 2 1 101000 f 74 goat snp30619-scaffold339-2542743 7 62740904 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419406 Affx-122945598 AX-123289754 7 43973961 GTGGTATCTTCTGGGAATTTATTTTAATGAAAAGA[G/T]AAAGAACTCTTACATTTTTCACTGAGTGTAGTGCT K 2 1 2 1 103000 r 74 goat snp30620-scaffold339-2572623 7 62710971 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376373 Affx-122978112 AX-123246732 7 44003345 ATCTGAATAAATGACCCCATTTGATTTCAGAGAGC[A/G]TAGTCATCCCCACACTCCAGCCAGACTCTAAGCAA R 2 1 2 1 201000 r 74 goat snp30621-scaffold339-2602007 7 62681609 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797125 Affx-122959695 AX-385284065 7 44093369 AACTTTCTGTTGGGCAGAAGGTCAGGATAGAGACG[C/T]AAATGGATGGTATAAAATCTGGATCATCAAGAATT Y 2 1 2 1 101000 f 74 goat snp30623-scaffold339-2692031 7 62591857 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789372 Affx-122929474 AX-385276382 7 44128360 TGACTCTTACTGCATGTCTACTATATGTGCAGCAT[A/G]TGGTGAACCTCATCATTACTAAATGGAATTTGGAC R 2 1 2 1 101000 f 74 goat snp30624-scaffold339-2727022 7 62556371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402177 Affx-122959185 AX-123272530 7 44166647 AAGAGAGAAGATGAAAATTACCTCTAGATGTCTCC[A/G]AAGAAGGGAATGAATAAGTAAGAATATCGTCAACA R 2 1 2 1 201000 f 74 goat snp30625-scaffold339-2765309 7 62518224 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416960 Affx-122948017 AX-123287308 7 44200211 CACTAAAGGAGGGGAGCACACACTTGAGGTTCTAG[A/C]TTTCTGCTCTCTCTTGTTTGTGCTGTAGACTGGCT M 2 1 2 1 101000 r 74 goat snp30626-scaffold339-2798873 7 62484347 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411793 Affx-122951265 AX-123282143 7 44238984 TTATTTTGTATCTTCTTTACAGTCCATAAGATAAA[C/T]GAGTTGTAGTTTGTTAAATCCATTCCAGTTTTTCT Y 2 1 2 1 101000 r 74 goat snp30627-scaffold339-2837646 7 62444945 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776603 Affx-122950597 AX-385263730 7 44274698 ATGTTTTTAAAAGAAGTTTGGAGAGAGTGTACTGG[C/T]GTTAATAGAAGTAATAATATCTTCATCATTAATAA Y 2 1 2 1 101000 f 74 goat snp30628-scaffold339-2873360 7 62409118 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409255 Affx-122953135 AX-123279606 7 44333360 TATACCAAGAAGACAGCAAGAGACTGAGAGTGAGC[A/G]TGAGATCACATCAGCGCACAAAACGCAGTGAGTGG R 2 1 2 1 201000 r 74 goat snp30629-scaffold339-2932022 7 62349621 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423577 Affx-122942404 AX-123293923 7 44411134 CATTCAGTGGCTTCCTTGAGCATGTGCAGAGGTTC[G/T]AAGTTGACCCTGTACACCATACACCTAGAATAGTC K 2 1 2 1 101000 r 74 goat snp30631-scaffold339-3009796 7 62272878 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273280 Affx-1111833541 AX-185475491 7 44471863 AAGAATACTGGAGTGGGTTGCCATTTCCTTCTCCA[A/G]GGGATCTTCCAGGGATTGAACTCAGGTCTCCTGCA R 2 1 2 1 303000 f 74 goat 7_44471863_AF-PAKI 7 44471863 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38405989 Affx-122955518 AX-123276341 7 44472226 AAGAAAGAAGCTGAATCAGTTTCCTCCAGGCTGTC[A/G]CAGCAGAGCAGCATGAGGCAACCAACCTGAAGCGT R 2 1 2 1 101000 f 74 goat snp30632-scaffold339-3070888 7 62212181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769817 Affx-122961408 AX-385256987 7 44504379 TTGTCCCATTTCACATGTGAGACTTCTTGCCCAAG[G/T]ATCATACCTAGTGGATTGTGGCAGTAGGAACCACC K 2 1 2 1 101000 f 74 goat snp30633-scaffold339-3103041 7 62181355 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434248 Affx-122934825 AX-123304589 7 44545185 CTGTCAGTTCTCTTTTTAAAAAGCAAGGAAAGCAA[C/T]GCAGGCTCTTTTTGGGCAAACAAATGAGGTGTCTG Y 2 1 2 1 101000 r 74 goat snp30634-scaffold339-3143847 7 62140002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382211 Affx-122973996 AX-123252569 7 44580924 TAGACTTAGGGCAGAAATGAGTATAGCTACTTAAC[A/G]TGATAAGATGGTATCCAGCCTCAAGGCACTTTTTT R 2 1 2 1 101000 f 74 goat snp30635-scaffold339-3179586 7 62103599 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411687 Affx-122951997 AX-123282037 7 44628435 CCTCCCTTGTCACGTGAATGACTCAGCCAAGCCTC[A/G]CTGGTGAAAGCAGCTCTTTTGCCATTTCCTGCTTG R 2 1 2 1 201000 f 74 goat snp30636-scaffold339-3227097 7 62055367 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380632 Affx-122975233 AX-123250990 7 44674625 GCATCTCTGAGGGGTGGTCCCTGGGCACCTGTCTC[A/G]TGTTGACTGCATTTCTTTGTCATCACAAACAGACT R 2 1 2 1 101000 r 74 goat snp30637-scaffold339-3273287 7 62009154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422307 Affx-122943474 AX-123292653 7 44708413 CACCTCACCATCCCTAAGACATGGTGTCCCCCTCA[C/T]GGGTCCCCCTCATATCCTGGCTACCCATCAGCGAG Y 2 1 2 1 303000 r 74 goat snp30638-scaffold339-3307075 7 61975484 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450107 Affx-122922777 AX-123320442 7 44752856 AGTGCCACCACTATCCAATTTCCATGATGTAAGAA[C/T]AAGATCCAATAGCTGTCACAGTCTGGGTAACATCT Y 2 1 2 1 101000 r 74 goat snp30639-scaffold339-3351518 7 61930777 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783366 Affx-122976421 AX-385270430 7 44785019 AGCAGACTATCTTATTAAATAATATAGTGTATGTG[C/T]GGCACGCCTGGCACAAGGCAGATACTCAAATTTCA Y 2 1 2 1 102000 r 74 goat snp30640-scaffold339-3383681 7 61898907 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451450 Affx-122921156 AX-123321783 7 44814083 GAGTGAATGAGGGAGTGAGCCAACTAGTGAATGTC[A/G]CTGGTCTCCATGCTGCATCCTTAGCCGTCAAAGAC R 2 1 2 1 101000 f 74 goat snp30641-scaffold339-3412745 7 61869256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433233 Affx-122935252 AX-123303574 7 44865363 TCACTTTCAGAAGCATAAACCACACGTCTGCTCCA[C/T]ACCCACTGTGTGTGTGCAGGTTTGCTGGGGGCTGG Y 2 1 2 1 101000 f 74 goat snp30642-scaffold339-3464025 7 61817466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377731 Affx-122977385 AX-123248090 7 44894653 AAAAGTTCTTGCAATTGTCTTCAGACAGACAGTAG[C/T]GAAGAGAGACAGCAAATTGCTCTCCACAATTACTC Y 2 1 2 1 101000 f 74 goat snp30643-scaffold339-3493315 7 61788113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425203 Affx-122941029 AX-123295549 7 44943240 TTGCATGTTACATGGAAAACAGATCTGGGACCCCA[C/T]CTCTGCCCTGCCAGGCCTCCCACCAGGCTTTGCTT Y 2 1 2 1 101000 f 74 goat snp30644-scaffold339-3541902 7 61738779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452723 Affx-122920288 AX-123323056 7 44991718 CCAGTCTAGGTCAGCTCTGCCCAATAGATATATAA[C/T]GTGAACACACACATACGCCATGGAGTAACACAAAT Y 2 1 2 1 101000 f 74 goat snp30645-scaffold339-3590380 7 61690249 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400394 Affx-122960002 AX-123270749 7 45044058 GAGAGGCAGAAACAATGCAGGGTCTTCACAGGTCA[A/G]AGCCACTGCCCACAGCGTTGCAGTCTGAGAAAAGT R 2 1 2 1 202000 f 74 goat snp30646-scaffold339-3642720 7 61638434 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404872 Affx-122956481 AX-123275224 7 45078418 ATTCAAATCATGACAGCTGAACACTGGAGGCCAAA[C/T]AGAGCTGTGAATATAAAATCCAAATTCCATCCAAA Y 2 1 2 1 101000 f 74 goat snp30647-scaffold339-3677080 7 61603939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383608 Affx-122972559 AX-123253966 7 45128025 ATCAAGCGTCCTGCCTGCTCCCTTCCCCAAGTGTC[A/G]CACAAGTGAAACCTCTGTAACTCAGGCTCTGCATT R 2 1 2 1 101000 r 74 goat snp30648-scaffold339-3726687 7 61554432 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421823 Affx-122944313 AX-123292170 7 45169393 GCAAAGAAATCCCCTGCTAGCTTACCTCAGCCCCA[G/T]TAACTCACACTCTGCACATGGGCTATTCAAAGAAG K 2 1 2 1 101000 r 74 goat snp30649-scaffold339-3768055 7 61512642 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446846 Affx-122925263 AX-123317182 7 45210691 CCATTCTGGGTAAGAAAAAAGGGGACTAGGCAAAT[A/G]TGAGAGGCTGAGAACTACCTAAAGATGTTGTTAAA R 2 1 2 1 101000 f 74 goat snp30650-scaffold339-3809353 7 61471870 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432271 Affx-122936334 AX-123302612 7 45241490 GACCGCACCCCTCTTCCTACCTCACCACACACATC[A/G]TTCCTGACTGAGCAGGACCCAGCACCAACCTTCCC R 2 1 2 1 101000 r 74 goat snp30651-scaffold339-3840152 7 61441295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439815 Affx-122930478 AX-123310152 7 45275431 CGATATGGGCTTTAATGGTTCAGGACAAGTATCCC[A/G]TCAGGTTGAATGTGTAGGCCACAGGCTCCTTGAGG R 2 1 2 1 101000 f 74 goat snp30652-scaffold339-3874093 7 61407025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773343 Affx-122938912 AX-385260485 7 45324051 TCCCTGCATCACCCATTCCACTCTAGTTTTTTCAG[A/G]CAGTCACCTAAACACCTTAAAACTTGATATAATCT R 2 1 2 1 101000 r 74 goat snp30653-scaffold339-3922713 7 61358387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773014 Affx-122933024 AX-385260158 7 45365817 AAAGACCTCTATTTCTGCCTTCACTGAATACCAAT[C/T]CAGATATTTGTAAAGGCAGATACATGACAACAAAG Y 2 1 2 1 101000 f 74 goat snp30654-scaffold339-3964479 7 61316595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376395 Affx-122978095 AX-123246754 7 45438722 TGAAAGCAGGAAAGGGCTTTCATCAAACTCTGATA[G/T]CACCCTCTCCCTTCACCCAAACACAAACACCCCAG K 2 1 2 1 101000 f 74 goat snp30655-scaffold339-4037384 7 61243380 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780805 Affx-122979093 AX-385267894 7 45478865 TCCCAACTGACATGGAAGAGACCTAGCAAAGTTAT[A/G]TTTGAAACTGGAAGAGATTGAGTGATTTCCCCTGA R 2 1 2 1 201000 r 74 goat snp30656-scaffold339-4077527 7 61202161 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389798 Affx-122968208 AX-123260155 7 45513718 GGAGGAAAGGACAAAGGAAATCTAAACCAAAATGA[C/T]GAGGAGTCATAATCTACTAATACTTGCTCAAAGAG Y 2 1 2 1 101000 f 74 goat snp30657-scaffold339-4112380 7 61167502 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781129 Affx-122953461 AX-385268214 7 45551987 ATTTTTGTCTCAAGAATGAACAATTTAAGATTCAA[A/G]CAATATATAACAACAGCCAACATCCTAGACATGAT R 2 1 2 1 101000 r 74 goat snp30658-scaffold339-4150649 7 61128997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376971 Affx-122977755 AX-123247330 7 45584641 ATGGTTTAGTAACCCTGCAGTCTCTCCACATGGTC[C/T]CTGGTTGGGATAATTCAAACACAGCCTAAGAACAT Y 2 1 2 1 101000 r 74 goat snp30659-scaffold339-4183303 7 61096191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401309 Affx-122959850 AX-123271662 7 45634200 AACATAGAATTAAGAATATCATGTAAGCAGAAAAG[C/T]ACAAACAAAAAATACCAGGGGCAAAAAGGTGAACT Y 2 1 2 1 201000 f 74 goat snp30660-scaffold339-4232862 7 61045906 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446061 Affx-122925827 AX-123316398 7 45710418 GGGACTGTTGCAGAGGTGTCTGCTCCTGGGTCCTA[C/T]ACCACTTTACAGTCATCAGGGAGGAGGCAAGAATG Y 2 1 2 1 202000 f 74 goat snp30661-scaffold339-4309080 7 60969383 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792526 Affx-122920124 AX-385279507 7 45790240 AGAAGTGTTACATGTGATCAGTAATGGTGCTTTCA[C/T]AAACTCATTTGAATGGTTAAAGTAGTAGAGATAAA Y 2 1 2 1 101000 f 74 goat snp30662-scaffold339-4388902 7 60889144 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440336 Affx-122929671 AX-123310673 7 45830609 AATTATCTTATTTGTTAAATGTTTTTTAAAAAATT[A/G]AAATCATGATCATCAGCTTTAGTAATGTGGACCCC R 2 1 2 1 103000 r 74 goat snp30663-scaffold339-4429271 7 60848376 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432866 Affx-122935355 AX-123303207 7 45947673 ACCTAGCTGTCAGGCACCAGAGAGCCTCAACCTCT[A/G]GTTTTCTAAGCTATGCCCAGGAGAGCACTGTGTTA R 2 1 2 1 101000 r 74 goat snp30665-scaffold339-4546335 7 60730551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395349 Affx-122964029 AX-123265704 7 45987364 CCATCGGGGAGGGTGCTCATGATGAAGGTAAGATT[C/T]CTAGAACTCAGTGCTTCAGGAGGGTGAGGTTTAGC Y 2 1 2 1 201000 f 74 goat snp30666-scaffold339-4586026 7 60690528 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786874 Affx-122932639 AX-385273903 7 46075314 ACATTTCAGGAATTGCAAAAGCTCGTGTGGTGGAG[C/T]AAGGTTAGTAATTTATGTGAGAGAGAATTTGTAGC Y 2 1 2 1 101000 f 74 goat snp30667-scaffold339-4673976 7 60603762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389548 Affx-122968271 AX-123259906 7 46120679 TTGTCCCTGTTTCCAAAGTTTCTCAGTATTAAGCT[A/G]TTTATCCTCCTTCATCTGGGGCTTGCTACAAGTAA R 2 1 2 1 201000 f 74 goat snp30668-scaffold339-4719341 7 60558288 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392624 Affx-122966464 AX-123262981 7 46162953 GGATCACAGGGCTATATAATGCTGACTTTTCCCAG[A/G]CAAGGAAAACCTGTATATTTCAAGCCACCAATAAG R 2 1 2 1 101000 r 74 goat snp30669-scaffold339-4761615 7 60515459 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775477 Affx-122933387 AX-385262608 7 46197514 CAAATAGATGGGACAATAATCTAGTGTTCCACAGA[A/G]TTTAAACTGAATTTAGTTTTGACTTAGAGAGATAA R 2 1 2 1 101000 f 74 goat snp30670-scaffold339-4796176 7 60480907 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400892 Affx-122959747 AX-123271245 7 46239582 TTTGGATGGTGACATGTACTATGAAGAAAATACAG[C/T]GGGGTGATGGGATAGAGAGTGACTATCCAGTTACC Y 2 1 2 1 201000 f 74 goat snp30671-scaffold339-4838244 7 60438727 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404689 Affx-122957273 AX-123275041 7 46289492 ATTGGCAGTGCCCTCTTGTAGTACCCATAATGTTT[A/G]TAAACTCAAAATCTTATATGTAAGAGTTACTGGGC R 2 1 2 1 101000 f 74 goat snp30672-scaffold339-4888154 7 60388717 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437223 Affx-122932033 AX-123307561 7 46325600 CACTTTGTGTTTTCTGGCAGAATTCCTCTACTGCT[A/G]TGTGCTTAGTATCCTAGTCTGTTTTCACCTTTGAC R 2 1 2 1 201000 r 74 goat snp30673-scaffold339-4924262 7 60353648 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275595 Affx-1111834897 AX-519549165 7 46343275 GAATATGCCCCC[A/C]AAAATTACATAACTGCAGTGAATGGAAAATTTACT M 2 1 2 1 101000 r 74 goat GoatD01.057755 7 46343275 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38429397 Affx-122938534 AX-123299739 7 46364246 TATGACAGTCGAACTTTTTCCTGTTAATAGAGTAG[A/C]TTACCTTTCGAGTTTTGGAAAGCATGAAGAGAAGT M 2 1 2 1 101000 r 74 goat snp30674-scaffold339-4962908 7 60315082 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794453 Affx-122940106 AX-385281415 7 46398001 TTGCACTTCCTGGTAGCATGGAGGAAAGGAAGAAA[C/T]ACAATTGGTTGTCTAGTTTTTGTCTTTAGGATGGA Y 2 1 2 1 101000 f 74 goat snp30675-scaffold339-4996663 7 60281051 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431844 Affx-122936085 AX-123302185 7 46473029 GTTATGTGCCTTGCTCTGCGCTAGGAGCTTCGTTT[A/G]TACTACATGTACATTATTTCATTTAATCCTCACAG R 2 1 2 1 101000 f 74 goat snp30677-scaffold339-5071691 7 60205718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409550 Affx-122953600 AX-123279901 7 46539792 TCATGGTGTGTAGGAGCCTGCTGTTGGCTTCCAAA[C/T]GCTCTGGCACCACACCATGCTGTCACTGTAACTGC Y 2 1 2 1 101000 f 74 goat snp30678-scaffold339-5138454 7 60137051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405092 Affx-122956990 AX-123275444 7 46568712 AAGATTTTTTTTAAAAAGGTATATTCAAGTAGAAC[A/G]GGAAAACCTTTCTCTGCAGAGGCTCCATGAAAAGG R 2 1 2 1 101000 r 74 goat snp30679-scaffold339-5167374 7 60107712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792890 Affx-122926366 AX-385279868 7 46601672 TTTCCCCAATCCCAAACCCATAGAGAGTTTAAATT[A/G]TATTCAAGCAGTCATACATCTTTTACTAAAAGCTA R 2 1 2 1 101000 f 74 goat snp30680-scaffold339-5200334 7 60074437 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451649 Affx-122921602 AX-123321982 7 46631559 GGTTATGTCTTCATGTTAGAAATCCTCAGAATAGA[C/T]TCTGCAGGAGGCGGGCAGGACATTTCTCCCACATC Y 2 1 2 1 101000 f 74 goat snp30681-scaffold339-5230221 7 60044265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772592 Affx-122939185 AX-385259741 7 46660320 AAACCATTCACTTACTACCTGTAGCTTCACATCCA[C/T]GCCAAAATCATTTCAACCCCAGGTAAGCACTCAAC Y 2 1 2 1 101000 r 74 goat snp30682-scaffold339-5258982 7 60015530 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395601 Affx-122963821 AX-123265956 7 46717263 TCCAAAGACAGGATGCTCATTTGCATGAGGAGTTG[C/T]GTGTCATTTGCATTATATTTGCAAGTAATTTGCAT Y 2 1 2 1 101000 f 74 goat snp30683-scaffold339-5315925 7 59958966 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788905 Affx-122968833 AX-385275920 7 46751363 CCCCCAAACTCAATTGGGAGCCTACCTTATCACCT[A/G]CTATAACCCAGAGTCTAGTACTAACGGGCTCTCCA R 2 1 2 1 101000 f 74 goat snp30684-scaffold339-5350025 7 59924160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387778 Affx-122969710 AX-123258136 7 46802222 CATGTCTAAGTGTTAACAATAAACTTGGAAATAAC[A/G]TGGAATAACAAGAATTAGTTGTATCAGCCTTTCAA R 2 1 2 1 101000 f 74 goat snp30685-scaffold339-5400884 7 59873520 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391666 Affx-122966550 AX-123262023 7 46858725 GGTTGCTAACCTGAGGACACAGATGCCTTCAAATT[A/G]TGCTGCCCTTTGTAATGAGATGGGTTTTTATCCCA R 2 1 2 1 101000 f 74 goat snp30686-scaffold339-5457387 7 59816634 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395712 Affx-122963719 AX-123266067 7 46892283 GGGAAATTGTGTTCAAGACCTAGGCTGGGAGGCCT[A/G]CAGTAACTCTTCATCTGCTAAACCACTTCACCTAG R 2 1 2 1 101000 r 74 goat snp30687-scaffold339-5490945 7 59782914 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424902 Affx-122941309 AX-123295248 7 46932949 CAGACTGGGTGAGAGCCTTGCCTCCTGTTCCATGT[A/G]AGACCAAATATCCTCTATCTGGCCTTGTGCAATAT R 2 1 2 1 101000 r 74 goat snp30688-scaffold339-5531611 7 59742381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394814 Affx-122964802 AX-123265169 7 46968566 TTACCACTGGCTTAATTGCCCAGTAATGTTGACCC[A/G]TGAAATTGGTAGAATCTTGAAATCTTAGATGGTGT R 2 1 2 1 101000 f 74 goat snp30689-scaffold339-5567228 7 59706702 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273322 Affx-1111833542 AX-519546964 7 46979286 ATGGAAAGCCAAGTCCTTTATCAAGCTTTCCTAAC[A/G]TGGTGTGTTTAAACCTCCAACTGCTGTCTCCTCTG R 2 1 2 1 101000 r 74 goat 7_46979286_AF-PAKI 7 46979286 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789835 Affx-122944194 AX-385276842 7 47001249 TCAGTTGGGGACAGGAAAGAGCAGTATTTGCATCA[A/G]GTATCATAAGTAGATGATTTTGTCTCTGTTTTGTA R 2 1 2 1 101000 f 74 goat snp30690-scaffold339-5599911 7 59674064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414785 Affx-122949232 AX-123285134 7 47050728 CCTTGGACCAGAGCGGCCCAGGGCTCATCTGGTCT[C/T]CCCCACCTCTGCCTCCACTTCCCTCTCCCAGGGGC Y 2 1 2 1 201000 f 74 goat snp30691-scaffold339-5649390 7 59624681 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419908 Affx-122945336 AX-123290256 7 47102793 TGTCCCTCACGGATCCAGCCCAGGGCTTTGCGGCT[C/T]GGAGCATATTTTTTCAGTTGAAGTTGAGGTAGATT Y 2 1 2 1 101000 r 74 goat snp30692-scaffold339-5701455 7 59583402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421536 Affx-122943874 AX-123291883 7 47151277 TGAGCCCACCTTGGCTTCAAGGCCCATCTAAACCT[C/T]GATGATTCTCACTGCATGATTCTTCAAGCTCCAAA Y 2 1 2 1 101000 r 74 goat snp10063-scaffold1356-3527945 7 59534189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422634 Affx-122943705 AX-123292980 7 47188598 GCCAAAAGATATATACCAGAAAGGGAAAAGAGAGA[C/T]GGAAGAGAAGGGAAGGGAATGGGAGGGGAGAGGGA Y 2 1 2 1 101000 f 74 goat snp10062-scaffold1356-3490624 7 59498016 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419155 Affx-122945741 AX-123289503 7 47233875 AGCTTTCTGGAGGCTGCTGCATGGATGAGATATCC[C/T]ACCCAGGACCCTGGCAAAAACCCTTTGGTAGGAAT Y 2 1 2 1 101000 f 74 goat snp10061-scaffold1356-3445347 7 59452588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278485 Affx-1111836450 AX-519551968 7 47284069 GGAATTTTCCATAAATCGAAACATAAAACAAAAAG[A/G]ATGATAGCGGTGGGAGATACCATAGGGAAGATGGT R 2 1 2 1 201000 f 74 goat Random2.2K-790 7 47284069 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786001 Affx-122959884 AX-385273037 7 47289853 ACTTAGAGGATAGAATAAAACAAGGTTTGTGGGAA[C/T]GTGTTTCAAGCTGTAAGAGTACAGGAAAAAACGTG Y 2 1 2 1 101000 f 74 goat snp10060-scaffold1356-3389369 7 59399281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384949 Affx-122971919 AX-123255307 7 47347235 CCCGCGGGGAGCTCCGCCTGAATCCTGCTGCCTCT[A/G]TTCCGGGCTCTCGTTTCTAGATCAGTCACACCACA R 2 1 2 1 101000 r 74 goat snp10059-scaffold1356-3331987 7 59341462 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778206 Affx-122959015 AX-385265321 7 47378770 GATGTTGACCAGCAGTTTCAGTGTAGTAATGGAGG[C/T]GAGGGCTTTATTTGAGTGGCTTTAACAGAAAATGA Y 2 1 2 1 103000 f 74 goat snp10058-scaffold1356-3300452 7 59309818 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395539 Affx-122963857 AX-123265894 7 47422061 CCTATTATATTCCCTGCTGTTTCGTGTCTCAATCA[A/G]TGGTGCCACCATCTGTCCAGTTGTTCAAACCCAAA R 2 1 2 1 101000 f 74 goat snp10057-scaffold1356-3257161 7 59266303 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797669 Affx-122949153 AX-385284608 7 47463413 ATTTCTAACCTTGTCACATAGATCGTTAGTAACTG[A/G]CCCCAACAGACCTAAATAATATAGGATTCTTCTGT R 2 1 2 1 101000 r 74 goat snp10056-scaffold1356-3215809 7 59224481 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377397 Affx-122977567 AX-123247756 7 47546736 TATAGTGTTATTTTGAAGATTAACTAAGATAATGT[A/G]TATGAAACCTAGACATGGAGCTTGGCACCTAGTAA R 2 1 2 1 101000 r 74 goat snp10055-scaffold1356-3132486 7 59140750 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406803 Affx-122955693 AX-123277154 7 47590963 GAAAGCCCAGTGGGCCGCGGTCCTGGACCCCCTCC[A/G]TCAGGGAGAGGGGAGGTCTCCAGTGCTGAGAGAAA R 2 1 2 1 303000 f 74 goat snp10054-scaffold1356-3088259 7 59095600 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453334 Affx-122919966 AX-123323667 7 47628621 GAAAAGCATTAATTTCGAGAAAGAGAGGAAAACAA[C/T]GTTCCTAAGAAAAGTCTATAGAGATAATGTCACAA Y 2 1 2 1 201000 r 74 goat snp10053-scaffold1356-3050601 7 59057682 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274369 Affx-1111834215 AX-519547964 7 47630192 CCATCCCTGCTCCCTTCTCTGCAGCTCACTTTAAG[A/G]ACTCTAGCTCTGCAAGGCACCCCTGCAGCTGCTGA R 2 1 2 1 202000 f 74 goat GoatD01.025888 7 47630192 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320787207 Affx-122958816 AX-385274233 7 47657429 TTGTCTGTGATAACAGACCCTCCTGGTAAGAACCT[A/G]CCTAGATACAGTGTTGTTTTTGTGACTCTGTTAGA R 2 1 2 1 202000 r 74 goat snp10052-scaffold1356-3021793 7 59028681 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422449 Affx-122943345 AX-123292795 7 47720691 ACCTGCGCTCAAGGTAATGATCCATCATTTGCCCC[A/G]TGGTACCATCACCGCCTTTCCTGGATCTAGGAAGT R 2 1 2 1 101000 f 74 goat snp10051-scaffold1356-2958531 7 58965437 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405340 Affx-122956332 AX-123275692 7 47785416 GGTGGCTCTAAGACTAAAGACAAAAGAAACAGCAC[A/G]TAAGCACTGTACTATTGTTAATCAAGTTGTTCCCC R 2 1 2 1 201000 r 74 goat snp10049-scaffold1356-2893806 7 58900531 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414368 Affx-122950007 AX-123284717 7 47848864 TTTGAAATGGTATTTATTGGTTATTTTTGGCCGAG[C/T]AATTGAGTAACAAATTTGTAAGGACACTGATAGTA Y 2 1 2 1 201000 r 74 goat snp10047-scaffold1356-2830358 7 58836517 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418178 Affx-122947078 AX-123288526 7 47955231 GGACCTGAAGAGGAGTGGGGAGAGGCATGTAAACA[C/T]AGCCCTTCTCCTGCCTGCCTCCCTCCAGTGTCCAG Y 2 1 2 1 101000 f 74 goat snp10045-scaffold1356-2723991 7 58734520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792821 Affx-122927045 AX-385279799 7 47985489 TTAACCCATCTAGGTGTTATTGCAGACAGAGCCCA[A/G]TTTCAGCCTCCTAGATGCCATGCACAAAGCTGGCT R 2 1 2 1 101000 f 74 goat snp10044-scaffold1356-2693733 7 58704557 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278487 Affx-1111836451 AX-519551970 7 48022999 GGTTCTTTAGAGTCTGCTATGACAAAACATGTGCT[A/G]CTGCTGCTGAGTCGCTTCAGCCGTGTCCGACTCTG R 2 1 2 1 101000 f 74 goat Random2.2K-791 7 48022999 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777778 Affx-122941684 AX-385264896 7 48098952 AGAAAATTATGTAAGTCTACCACACTGTTGAGATA[C/T]AACAGGTGAAACTGAAGCAATCTTTTAAAAGTTTG Y 2 1 2 1 202000 r 74 goat snp10042-scaffold1356-2580270 7 58590392 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784953 Affx-122963834 AX-385272000 7 48144996 ATAACAGGTTATCAAAATGATTACTTTGTTACTTT[A/C]TGTAATGGTGTCAGTATATGAAAGACTACTTCTTT M 2 1 2 1 201000 f 74 goat snp10041-scaffold1356-2534226 7 58543875 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413135 Affx-122950367 AX-123283484 7 48193142 AATGAATCTAACTCTATGTAGTTTGTGGCTTAACT[A/G]CACAGAGATGAACTATTCCAAGATACTTTAAAACA R 2 1 2 1 101000 f 74 goat snp10040-scaffold1356-2486080 7 58495693 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780061 Affx-122970579 AX-385267159 7 48244887 TTGCCACCAGGATGGGTCTCCAAAGCCATATTAAC[G/T]TTATATGACACTGCTTTAGTGACTGGGCAAGATAA K 2 1 2 1 101000 f 74 goat snp10039-scaffold1356-2434335 7 58443357 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770730 Affx-122927586 AX-385257894 7 48297075 AGAGCTATCTGAAAGGTAAAGGTGTTATTTTTATT[A/G]CCAATATCTCTCTGCTATTGCCATGGGATTTAAAA R 2 1 2 1 201000 f 74 goat snp10038-scaffold1356-2382147 7 58390416 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427174 Affx-122939614 AX-123297517 7 48336713 CTCAGAAAAGCCATCTACCAGGAGAATGTTAAGTG[A/G]GACAGTAGTAGAAAGAGCTGGTTGGCCATGATCCT R 2 1 2 1 101000 f 74 goat snp10037-scaffold1356-2342509 7 58350655 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425580 Affx-122941421 AX-123295926 7 48380166 TTTTTATTTTGAGCTGTAATTGAAATATAACACTA[C/T]GTTAGTTTCAGGTGTGACATAATTTGCTATTTGTG Y 2 1 2 1 303000 f 74 goat snp10036-scaffold1356-2299056 7 58306588 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793737 Affx-122963335 AX-385280709 7 48421335 ATAAGGAAGAGGAGTTCTGAAAGTGATGTGGGCCA[C/T]GTTGACTTAAGTAGAATTTATGTCACTAAAACAGC Y 2 1 2 1 101000 f 74 goat snp10035-scaffold1356-2257887 7 58264049 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439178 Affx-122931054 AX-123309515 7 48476886 TACGTCTTCTTAGGTAAAGGAAGTAATGTAGGTGT[A/G]TAAGATAATGAGATTCAGTCTATGAAATGTACTAG R 2 1 2 1 101000 f 74 goat snp10034-scaffold1356-2202336 7 58209365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791880 Affx-122964196 AX-385278870 7 48545017 ATCAATATGGCAGTCTAACATTATGCTCTGCAGAA[C/T]GTTCTATGTTGAGGTTTTTGTGGAGTACTTTACAA Y 2 1 2 1 101000 f 74 goat snp10033-scaffold1356-2134205 7 58140262 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406669 Affx-122955792 AX-123277021 7 48788700 GCAATATATTTTTATGCTGTATTTTCAAAGAAGAA[G/T]AACAAAGTCCTTGTGAAGGAGAGACTATATTTGCT K 2 1 2 1 201000 f 74 goat snp10029-scaffold1356-1890522 7 57899979 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410568 Affx-122952136 AX-123280918 7 48829165 TTAGTTCAGAGAAGAAAATGTGGGAACTTTTCAAA[G/T]AGAACCTTACTGGAAAATTAAGGGGCAGAGGAATT K 2 1 2 1 202000 r 74 goat snp10028-scaffold1356-1850057 7 57859435 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791007 Affx-122960636 AX-385278004 7 48872935 GTCATTCACAGGCTCACCCATGAGGAAGAGTAGAT[A/G]TTCTGCTTCTCACATCACAACATGGGAGGAGAAGA R 2 1 2 1 101000 r 74 goat snp10027-scaffold1356-1806287 7 57815478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404677 Affx-122957282 AX-123275029 7 48916893 CACCAGCTTTTCCAGTTCAGTGGGAATTGGGAAAA[A/G]GCCTAGGACCAGCCCTGTTTCCCTCATCAGATGCA R 2 1 2 1 201000 f 74 goat snp10026-scaffold1356-1762329 7 57771357 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422282 Affx-122943490 AX-123292628 7 48961695 AAGGACTTTCAAAACTGTCCCATCCTGACCAATCA[C/T]CTCCCATCAGAGAAGAAAGGCTGGTCAAACATGTC Y 2 1 2 1 101000 f 74 goat snp10025-scaffold1356-1717527 7 57726606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427636 Affx-122939339 AX-123297979 7 48999543 AAGTCTTTGGAACTCAAATCTGGAGTCTTTCCCAT[A/C]GCACCATACAAAATTTTCATGGCCATGCAGCATAT M 2 1 2 1 201000 r 74 goat snp10024-scaffold1356-1679679 7 57689053 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397008 Affx-122963135 AX-123267363 7 49046900 CCCAAGTCAGGAGGGAAGACAGATGGTTAGAAGCC[G/T]CCTGGAAGGGTTCCCGCCCTCACCCCCCTGGCCCC K 2 1 2 1 101000 f 74 goat snp10023-scaffold1356-1632322 7 57641811 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436021 Affx-122932739 AX-123306360 7 49080578 CCCCCTTCCTCTATCTTCCCTGTCATCTTTGCCAA[C/T]ATCATCTTCAGCATTATCATATTAGCATCAGCACC Y 2 1 2 1 201000 r 74 goat snp10022-scaffold1356-1598644 7 57608123 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393785 Affx-122965191 AX-123264140 7 49112508 TTCCTGGGATGATCATTAACCCATGGCAGGCAGAC[A/G]GAGCTGTTGGCTGGGAGCAGCCTGTCACTGTTGCT R 2 1 2 1 101000 f 74 goat snp10021-scaffold1356-1566714 7 57576184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433930 Affx-122934296 AX-123304271 7 49174567 AACAATACAAATACTAAAATAAAAAAAATATTAGC[C/T]TGAATGCTGCCTAAAATCCTCTTGTGAACCACCGG Y 2 1 2 1 101000 r 74 goat snp10019-scaffold1356-1504655 7 57514319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768886 Affx-122962016 AX-385256063 7 49203282 TGTACTCATGATTTTATGTAAATGTTCACTTCATT[A/G]TAACCTTATACTTTAGATACTATTTGTTATTCCTG R 2 1 2 1 101000 f 74 goat snp10018-scaffold1356-1475940 7 57485600 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391886 Affx-122966967 AX-123262243 7 49278113 TCTGTCATATGCATGGATTGATAGTTTTCTAAATC[A/G]TAGCCACTCATCTCCACCTTCATACTTTTTGTCAC R 2 1 2 1 101000 r 74 goat snp10017-scaffold1356-1401109 7 57411042 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397444 Affx-122962112 AX-123267799 7 49307117 GCACTGCCCTACTTCAGGAATGGCTATCCCATTGT[A/G]TTCTATGCAGTTGACACCCCCAGCCTTCATTTGGG R 2 1 2 1 101000 r 74 goat snp10016-scaffold1356-1372105 7 57382032 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273891 Affx-1111833916 AX-519547499 7 49322125 AGTCCTGATGTGGATTCTGCTTGACCTAGAACCCC[A/G]AGGACACACACTCTGAGGGGATTTGGGGATTTTTC R 2 1 2 1 202000 f 74 goat GoatD01.010368 7 49322125 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38389608 Affx-122968762 AX-123259966 7 49379770 CCAGCCACGGGCTCCTGCGGAGAGGAGGGCGGCGG[C/T]GGAAGATGGAGGCCAGTGAGAGGCATTTTTTACAT Y 2 1 2 1 101000 r 74 goat snp10015-scaffold1356-1299452 7 57309189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396722 Affx-122962805 AX-123267077 7 49412879 TGTCTCTAACAGTCCTCAGATACCTAGGTATTCCC[A/G]TTTCCCCAGTGCAGTGACCCCTCTGAAGGAAGGAT R 2 1 2 1 101000 f 74 goat snp10014-scaffold1356-1266343 7 57276052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416425 Affx-122947838 AX-123286774 7 49467500 CCACACACCAGCCTTAAGCCATCAGCCAGCACCAA[C/T]GTGCCAGGCATGTGAGTCAGCCATGTTGGATCCTC Y 2 1 2 1 101000 f 74 goat snp10013-scaffold1356-1211722 7 57221045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401470 Affx-122958964 AX-123271823 7 49536943 AGATAATTTTTCGCCACCCTGTATATTTAAACATG[A/C]TTTTTCCTTTATTCTTTCTTCACAATTTGATACGT M 2 1 2 1 101000 f 74 goat snp10011-scaffold1356-1142279 7 57151955 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789553 Affx-122972512 AX-385276562 7 49612336 CAGAGATTTGGGAGGGTCTAGCCTTCCAAACAGAA[G/T]ATGTGTGAGGGACACAGCATTCCATGAAGTAGGAA K 2 1 2 1 101000 r 74 goat snp10009-scaffold1356-1066886 7 57076146 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273324 Affx-1111833543 AX-519546966 7 49614240 TGGAGCCCAGCAGACCTCTGTTTGCATTCTCACCC[A/G]TAGCACTTTCTAGCTATGTGATCTCGAGCTGGTGG R 2 1 2 1 101000 r 74 goat 7_49614240_AF-PAKI 7 49614240 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38432530 Affx-122935556 AX-123302871 7 49662476 GGTCCGATTCCAAAGCCCTCACTCTTTTTATACCA[A/C]GCAACATCTCAAGTGTGTGCCTGTGTGCTCAGTTG M 2 1 2 1 101000 f 74 goat snp10008-scaffold1356-1016746 7 57025288 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376498 Affx-122978024 AX-123246857 7 49699807 TTAAAAGACAGGGCACTATCCACATCAATGGAAAG[A/G]ATCAGATTTCCCATCTCAAGTCAAAGGAAAAGATC R 2 1 2 1 101000 f 74 goat snp10007-scaffold1356-979415 7 56987741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787586 Affx-122932568 AX-385274610 7 49728439 CTCCAAGATTTCTGTCATCAGTAGAGTCTCTTCCA[C/T]GCTTTTGCTGTCTTAGAATTGTTTAAAACAGTACT Y 2 1 2 1 101000 f 74 goat snp10006-scaffold1356-950783 7 56958861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452550 Affx-122920529 AX-123322883 7 49772203 GGCTTTCTACAAATATTTATGAAGGCCAAAATACA[C/T]ACCAGGCCTAGTGCGTACAATGGTGCACAATGAGG Y 2 1 2 1 101000 f 74 goat snp10005-scaffold1356-907019 7 56914574 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424507 Affx-122941739 AX-123294853 7 49825946 TTCTGTTCCAGGGCCTTGGAAACTAATGTAGGAGA[C/T]GGTCAAGCAAACATAGTCAAATTATATTCATTCAC Y 2 1 2 1 101000 f 74 goat snp10004-scaffold1356-853276 7 56859680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390855 Affx-122967824 AX-123261212 7 49871102 CTTTACAGACTTTTAACTTACTTTTTCATTTAGCA[A/G]CATATCATGGGTGTCCTCCACTCAAGACTGTTCTG R 2 1 2 1 101000 r 74 goat snp10003-scaffold1356-808120 7 56814737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414125 Affx-122949711 AX-123284474 7 49912226 GTTTGTATTTGCATCACGGAGACCATCTTAACTGT[A/C]GCTAATCAGTGAGCCACACATTTCTTCACACTCTC M 2 1 2 1 101000 r 74 goat snp10002-scaffold1356-766996 7 56773751 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384964 Affx-122971908 AX-123255322 7 49975708 GTTCAGTGCACTTGCGTAGACAATTCTGCTATTGG[C/T]GACTCTTGCTCTGAGTCTTGACATTCTGGGAGATA Y 2 1 2 1 101000 f 74 goat snp10001-scaffold1356-703514 7 56710164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792200 Affx-122924773 AX-385279185 7 50027003 CCTTACACAGGAACTACACTAAGATTCAACCAAGC[A/G]CTGCTTTTGCCAACACACCCACAGAAAGTAAATGT R 2 1 2 1 101000 r 74 goat snp10000-scaffold1356-652219 7 56658752 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444829 Affx-122926315 AX-123315166 7 50056860 TGTAATGACACTTTTCACAAAGTGCTTCACCACGT[A/G]TCATGGCACTTAGTCCCCATTACAGCAGAAGGGGA R 2 1 2 1 101000 f 74 goat snp9999-scaffold1356-622362 7 56628811 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430661 Affx-122936940 AX-123301002 7 50089720 AAAAATAAGTGAACTCTAATTAAAATAAAGTCAGA[C/T]GGCCAGAAGGGCAAGCTCTCATGCCGTACAAAGCT Y 2 1 2 1 101000 r 74 goat snp9998-scaffold1356-589502 7 56595929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422050 Affx-122943611 AX-123292397 7 50127642 TGCTGCATCTGGTGGGTCTTAAAATATAATGGAAG[C/T]AGAGGTTCTCTGGGGAAATTAATTCATTTTCCCAT Y 2 1 2 1 201000 f 74 goat snp9997-scaffold1356-551580 7 56558034 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452058 Affx-122920879 AX-123322391 7 50177811 CCTTACACAGGACCCAGCCCTTATTCTCAAACCAG[C/T]GTTTCTTTCCTCCACGAAACTGATGTTGCCATCTC Y 2 1 2 1 101000 f 74 goat snp9996-scaffold1356-501411 7 56507403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278489 Affx-1111836452 AX-519551972 7 50204812 AGATATCGAGGTGATGTATTGTTAAGCCAAGGAAT[A/G]ACAGAATGCCAGAAAACCACCAGAATTTAGGAGAC R 2 1 2 1 201000 f 74 goat Random2.2K-794 7 50204812 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38387644 Affx-122969851 AX-123258002 7 50213129 AGGGCTAAGCTCACTTGGTCCCCTCCCCAGAGTGG[C/T]GGACAGAAGAGATTAGGACGTGCTTTACTTCTGAT Y 2 1 2 1 101000 r 74 goat snp9995-scaffold1356-466093 7 56471967 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450508 Affx-122922506 AX-123320842 7 50262755 AGGTTAACATCTAATTAAAATGTTATAGTATATCT[A/G]TACATATGTGACCCAAAAAAACCCACTACACTTTA R 2 1 2 1 101000 r 74 goat snp9994-scaffold1356-416467 7 56422390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386882 Affx-122970053 AX-123257240 7 50293914 TAGGCTGAGTAAGGCTTGAGTTCTGACGTCACCTG[C/T]ATTTCCATTAATTTAAAGTGCTAAAGTGCTAATGC Y 2 1 2 1 201000 r 74 goat snp9993-scaffold1356-385308 7 56389736 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404583 Affx-122957361 AX-123274935 7 50331245 TGGGAATTTGATGCCAGGCAGTCTGCAGTCCAGAG[C/T]TACTGCTACTAAATGCTCTCTGGTACAATGCAATG Y 2 1 2 1 101000 r 74 goat snp9992-scaffold1356-347977 7 56352023 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445869 Affx-122925990 AX-123316206 7 50385448 CGGCTCACACTGTGCAGGTAGGCTACGCCGGCAAA[C/T]GCTCAACTGGTGGTGCCATATAACCATATGGACAC Y 2 1 2 1 101000 r 74 goat snp9991-scaffold1356-293774 7 56297441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419438 Affx-122945505 AX-123289786 7 50420026 ACATTACAGGCAGATACTTTACTGCTGAGCCACTC[A/G]CTGGGGAAGCCCCAAAACAAACTAAAAGTTGAGCA R 2 1 2 1 201000 r 74 goat snp9990-scaffold1356-259196 7 56262899 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436092 Affx-122932681 AX-123306431 7 50467555 CAATGATATGGGTTGCCTCTAGGGAGGGAAACAGG[C/T]GGAACAGAAAATTTTCACCTTCCAACTTCCTCCAA Y 2 1 2 1 101000 f 74 goat snp9989-scaffold1356-211667 7 56215358 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804620 Affx-122976150 AX-385291146 7 50512975 GTTTGAATGTGTCCTTCATATACTGTGGTATCACA[A/G]TTCATCATGAAACACTTAATTCCATATAATTCTGT R 2 1 2 1 201000 r 74 goat snp9988-scaffold1356-166247 7 56169484 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399652 Affx-122960520 AX-123270007 7 50549642 TCTCTTGGCATCTTCAGAATGTTTGGCACAGCTGT[A/G]AACACACACTAAGCAAGGACTAAGACATTTTAGCT R 2 1 2 1 101000 r 74 goat snp9987-scaffold1356-129580 7 56134378 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390642 Affx-122967147 AX-123260999 7 50599960 CCCCAGGCAGGTATGAGACCGAGGCAAGTTATTAA[C/T]GATTTAGAATGTGGGAAAGTTAAGCAATATAAATC Y 2 1 2 1 101000 f 74 goat snp9986-scaffold1356-79262 7 56083993 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387291 Affx-122970530 AX-123257649 7 50633876 TTAAACAAGAACAAAAGTGTTTCCTAAAGACAGGA[C/T]ACTGTTTTAAAGCGGCATCTAATAGCTATGGTAGC Y 2 1 2 1 101000 r 74 goat snp9985-scaffold1356-45346 7 56050271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799435 Affx-122933671 AX-385286365 7 50678375 ACTAAGTATACAATTTTGTAGCGTTAATCACATTC[A/G]CCATTACCACTACCTACCTCTTAGTATCACGTTGC R 2 1 2 1 101000 r 74 goat snp9984-scaffold1356-847 7 56005795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398851 Affx-122961059 AX-123269206 7 50697091 GGATGTAGAGCTTATTATCCAAGTGGAGTAAGTCA[G/T]ATAGAGAAAGATAAATATTACATGGTAACACTGAA K 2 1 2 1 101000 f 74 goat snp57908-scaffold938-17770 7 55986922 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771083 Affx-122971980 AX-385258243 7 50733730 TCACTTCTGAATATATGACTGAGGCAGCTATGATA[C/T]GTTCAGTGCACAAAGAGTGTTGCCACCACTACAAA Y 2 1 2 1 101000 r 74 goat snp57909-scaffold938-54409 7 55950527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420006 Affx-122945166 AX-123290354 7 50814881 GCATGGAAGCGAAAAAACTTAATCAGCAGATGCAG[C/T]ATAGCCAAGAGAGCAGCTTATCAGACATCTTCTGC Y 2 1 2 1 201000 f 74 goat snp57911-scaffold938-135560 7 55869386 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378525 Affx-122976631 AX-123248884 7 50864591 TTGAATGGATTGAGCCACATAAAGCATTCAGAAAG[C/T]ATCTAGCTGACAAAAAAATACTCAAGTGGTAAGTG Y 2 1 2 1 101000 f 74 goat snp57912-scaffold938-185270 7 55819424 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445072 Affx-122926218 AX-123315409 7 50896808 TTTAAGTCAGCACATTTCTAATTCCATTTACCTCC[A/G]CTTGCTGTCTGCCCAGGGGTCAGGAGATGGGATCC R 2 1 2 1 101000 f 74 goat snp57913-scaffold938-217487 7 55787220 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412576 Affx-122951309 AX-123282925 7 50925458 GGGGACAGGGGCAATCTTCATTTTTCTGATCCCAC[A/G]TGCCCAGCATGGATGGGTTTTACTCATAAGACATG R 2 1 2 1 101000 r 74 goat snp57914-scaffold938-246137 7 55758571 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439004 Affx-122930363 AX-123309341 7 50973862 GCTTCCGACAGCCAGCATGCTGAAAATGGCCCAGA[C/T]ACATCTGTACTGCATGTGTCTTCCGTGCACAGGAC Y 2 1 2 1 202000 f 74 goat snp57915-scaffold938-294541 7 55709965 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428716 Affx-122938462 AX-123299058 7 51059425 GGTTCCTTATTTACCTGGATCCTAAAGCCATGGCA[A/G]GTGTGACCACAGTTCTGAAGAGTCTTGTAGAGCTG R 2 1 2 1 101000 f 74 goat snp57917-scaffold938-380104 7 55625508 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798951 Affx-122928878 AX-385285881 7 51134428 TGAAGAATAACTTGAACATCATCTTCAAGCTGAGG[C/T]GGCTCTGTCTCTGACTCAAATATAATAGAAGTCTG Y 2 1 2 1 101000 f 74 goat snp57919-scaffold938-455107 7 55549381 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422642 Affx-122943700 AX-123292988 7 51163578 TACACAGAGCATGAAGATTAACCCTGTCTCCCAGT[A/G]AGAGACCATCACTGAGATGAGCAAGATGCAACTAC R 2 1 2 1 101000 f 74 goat snp57920-scaffold938-484257 7 55520259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408993 Affx-122953896 AX-123279344 7 51205039 TTCTATCTTGAATTTCACACTTCATGATATAACTG[C/T]GCTTGTTTTAACTTAAAAAAAATGTACTGGAATTT Y 2 1 2 1 101000 f 74 goat snp57921-scaffold938-525718 7 55478676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769769 Affx-122974478 AX-385256939 7 51261590 AGGTTCTGGAGAAGAGGCAATCTCTCTTTCATGCC[C/T]TGACTTTGTTCTGCCCTCTTTGACTCTGTTCTACT Y 2 1 2 1 101000 f 74 goat snp57922-scaffold938-582269 7 55421280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403018 Affx-122958559 AX-123273371 7 51306984 ACAACCCTTCTCCACCACACCCCAAATTCTATTCA[C/T]GTTAGAATCTGTTTTATTTTTTCCTCTAAGCCAGG Y 2 1 2 1 103000 f 74 goat snp57923-scaffold938-627663 7 55375184 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381491 Affx-122974876 AX-123251849 7 51336895 ACCATCATGTCAAGTTTATACTGAGATACACCATC[A/G]CAAGTATGATTCAATCTAGGAAATGTAAGTGTAAT R 2 1 2 1 101000 f 74 goat snp57924-scaffold938-657574 7 55345089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769965 Affx-122959832 AX-284860865 7 51367710 TCTGTGATGTATGTTATGGCACATTTGGCGCAAGA[C/T]GCTTAAACAAAGACAGGGCTTTGTGGGTTTTTGTA Y 2 1 2 1 101000 r 74 goat snp57925-scaffold938-688389 7 55315475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796968 Affx-122974491 AX-385283909 7 51443471 TTAATTGGCAGTAACATTTATATAAGCACCTGGAA[C/T]GAAACTTCTTTACAAGCACTGAAGCAACGCTTACC Y 2 1 2 1 101000 r 74 goat snp57926-scaffold938-764150 7 55244313 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375868 Affx-122978510 AX-123246227 7 51485295 GAGTACGTCTTCTACCGTAAGTACAGAGTGTTCTT[A/G]TTGTTTTTCATGTGTATGGATTTGTTTAATAGATA R 2 1 2 1 101000 f 74 goat snp57927-scaffold938-805974 7 55202279 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773438 Affx-122977941 AX-385260580 7 51516129 GTTGGTGTGGCTCTGGTTTCCCATCCTGTTCAAGA[C/T]GGTCATGATGCTTATTTAGATCCTACGCCACGAGG Y 2 1 2 1 101000 f 74 goat snp57928-scaffold938-836808 7 55171295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769134 Affx-122931642 AX-385256309 7 51557831 AGGATATAGAATGGTTTTATCACTCCAGAAAATTA[C/T]GTGCTGCCCTCTTTGTAGTCAAATCCTACTTCCAC Y 2 1 2 1 101000 r 74 goat snp57929-scaffold938-878510 7 55129620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440368 Affx-122929645 AX-123310705 7 51600634 GCAGTTGGTCCCTCTGCCTTTGTTACTTCTTGGAA[C/T]GTATGCCCTCATCTTTCCCTTCTCTTTTCCTCTAA Y 2 1 2 1 101000 r 74 goat snp57930-scaffold938-921313 7 55086955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438086 Affx-122931518 AX-123308424 7 51629304 AGAAGTTATGATACTATTACTAATCTTTATTATGC[A/G]CTTAGTGTGTATATCATGCTGCTGAAGATTTTGAA R 2 1 2 1 101000 r 74 goat snp57931-scaffold938-949983 7 55058392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379376 Affx-122976146 AX-123249735 7 51678305 AGTAAGGGATTATTACTGTGGTTTTTAATCTCTAC[A/G]CATTGTAGGCAGTCACAGTAAATAACGGTGTTCCT R 2 1 2 1 101000 r 74 goat snp57932-scaffold938-998984 7 55008162 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411905 Affx-122951180 AX-123282255 7 51707235 GTTGGAACACAGCTATATCCATTTGTTTTCTGTAT[A/G]GTCTATGGTTGCTTTGCACCAGCATGATACAGGTT R 2 1 2 1 101000 r 74 goat snp57933-scaffold938-1027914 7 54979206 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405200 Affx-122956913 AX-123275552 7 51755301 CTGGAATAGTCACATACCTATGTCTTCTAAATTCA[C/T]AGTGATACTTATAATTCAGATTAAAAACTTCAGGA Y 2 1 2 1 101000 f 74 goat snp57934-scaffold938-1075980 7 54931115 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278492 Affx-1111836453 AX-519551975 7 51762697 AGGTGGACGGGTGTTTTTGAGCCTTTTAGATTATC[A/G]TGTATAGTTCCTATACTTCTTTCAAATTTCTAAAT R 2 1 2 1 101000 f 74 goat Random2.2K-796 7 51762697 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433966 Affx-122934265 AX-123304307 7 51833004 CTCATTAGTGGAGGAGGGGTGTTAGCTCACTGTTA[C/T]GTACAGCTGCTCTTCATTTTGGTGGTTTGGCTAGA Y 2 1 2 1 101000 f 74 goat snp23251-scaffold2322-63892 7 54851696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435640 Affx-122933766 AX-123305980 7 51911426 TATTAGTTACCATGGTTTCCAATACTTCAGAAACT[A/G]TCCAAGAAAGGAGTGGAATTTTTCTCACCATGCGG R 2 1 2 1 201000 f 74 goat snp23252-scaffold2322-142314 7 54772804 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278672 Affx-1111836454 AX-519552150 7 51937621 AGTATTTGATGAAAACTTCTAGATCATTAATATAG[A/C]TTAGAAGCTGACAGGTCTGTGTTAGTTCCTTTCCT M 2 1 2 1 101000 r 74 goat Random2.2K-797 7 51937621 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38423756 Affx-122942848 AX-123294102 7 51949344 ACTTGGTGACTGAACAACTACAACATCAGGGATTT[A/C]TAAAGTGGGAGCAGAGGTTAGAACAGAACAAGCAA M 2 1 2 1 201000 r 74 goat snp23253-scaffold2322-180232 7 54734578 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782517 Affx-122942682 AX-385269593 7 51990288 AAAACACTAGAGCTGTTTGGTTACCCTGAATTCTT[A/G]TAGCCATCATAAGGCAGGATAAACAATTGTTTCCA R 2 1 2 1 101000 f 74 goat snp22703-scaffold226-22195 NW_017190801.1 1139 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799382 Affx-122973579 AX-385286312 7 52030444 CTACAGACTACAAAGCACTTAGTGTGTTAGATGTT[A/G]AAAGTCTTCGGGCATGACTTTGGAAAGTGTGAAAT R 2 1 2 1 101000 f 74 goat snp22704-scaffold226-62351 7 54650902 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774825 Affx-122965209 AX-385261959 7 52072650 AACTGGGTGGGGTTTCTGTGGTGAGTGGGTATTAG[A/G]AACTTTTCTATTGGCTATGGTTAAGTTGTTTTTAC R 2 1 2 1 101000 f 74 goat snp22705-scaffold226-104557 7 54609220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769681 Affx-122924397 AX-385256851 7 52118596 CTTTCTGACTCTGAGAGCTCATAAGGTGAAGGTGA[C/T]GAGTGATTGGGAAACTTAGTACATTTAGAGTGAGT Y 2 1 2 1 101000 f 74 goat snp22706-scaffold226-150503 7 54562252 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801903 Affx-122966810 AX-385288808 7 52174501 TAATCTCATCTGATGATGGAAGCTAAGGAGGGTCT[A/G]TTGTCCTTTGTCCTGAGTTGTGATTGTCTTACTGG R 2 1 2 1 101000 f 74 goat snp22707-scaffold226-206408 7 54504319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377862 Affx-122977274 AX-123248221 7 52222039 GTCCCTGATGTTGCTCGTTCTGACACACTGTCTAT[C/T]GTGTGTGGGTTCCTTTTACCCTTACCCACTAGTAG Y 2 1 2 1 101000 f 74 goat snp22708-scaffold226-253946 7 54456122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793995 Affx-122919252 AX-385280964 7 52277240 TAAAACATTTGAACACTCATCCTAAAGTTCTGTCA[C/T]ATTTGAAGATGACATTAAGAATGCTGATTAGTCCA Y 2 1 2 1 101000 r 74 goat snp22709-scaffold226-309147 7 54400337 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784788 Affx-122960336 AX-385271835 7 52310748 ATAGATATTGAAACCTAGCCATGTTTCAGTATGAT[A/G]TCATTTTATTAATCACAAAACTCTATTATATGGAT R 2 1 2 1 101000 f 74 goat snp22710-scaffold226-342655 7 54366080 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389415 Affx-122968371 AX-123259773 7 52355008 GAGGCAGTAGGTGAGGGAGAGATGGGAGTTAGTTA[C/T]AGGCCATGTGTGTTTGCTAACTGGTCTTACCAGAA Y 2 1 2 1 101000 r 74 goat snp22711-scaffold226-386915 7 54321506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273287 Affx-1111833544 AX-519546931 7 52400126 ATTAGAGTTTTCTCTGTTATATGCCCATGAGTGGG[A/G]TTACTGGATCATATGGCAACTCTATTTTTTAGTTT R 2 1 2 1 103000 f 74 goat 7_52400126_AF-PAKI 7 52400126 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320766644 Affx-122928388 AX-385253994 7 52420125 CAAACTACTGAGATCTTAGCCAGCAGACGTTCCAC[A/G]TAACTCCTTCTATTTTCCTAATAACCACTCAGCTC R 2 1 2 1 101000 f 74 goat snp22712-scaffold226-452032 7 54255551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416845 Affx-122948106 AX-123287193 7 52457950 CTTTATGTTGGAAGAGAAAACAATGAGATACTGCA[C/T]GCCCTGAAAGAAGCAGATTAATTTATAATTAATAA Y 2 1 2 1 201000 r 74 goat snp22713-scaffold226-489857 7 54216797 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446070 Affx-122925820 AX-123316407 7 52488320 AGACTTTATTATTCATACCACTCAGAATGGACACT[A/G]TACAATCCCTTCTCTTGATTGTAGGCTGGACCTGG R 2 1 2 1 101000 f 74 goat snp22714-scaffold226-520227 7 54186495 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398859 Affx-122961053 AX-123269214 7 52533943 TGATTGGAAAAGTTTATGGACTGTTTTCATTCTTA[C/T]ATCCAGGGTGGATCTATCACAGCTAAATTATTGGA Y 2 1 2 1 101000 f 74 goat snp22715-scaffold226-565850 7 54140685 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779087 Affx-122950875 AX-385266192 7 52581800 AATGTAATGAAAATACTTGAAGCAGAGCAGACAGT[A/G]GTATCTTCAAGAGTTGTGTATTTTAAGCTGTGGTG R 2 1 2 1 101000 f 74 goat snp22716-scaffold226-613707 7 54092505 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778448 Affx-122968920 AX-385265562 7 52603879 TTGATCATTAAGAATATTAGGGAGAAAATCATAGT[A/G]TAGTAAATTAGGTAATCTCTTTGGAAGGCTTAAGA R 2 1 2 1 101000 r 74 goat snp7259-scaffold1269-8145 7 54070718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420177 Affx-122945569 AX-123290525 7 52634373 AAATGCAAAGTTGGAGTTTGCAGGCTGATATCACC[A/G]TGGAGTGTGGGTCACATATTCCTTTCTTAGATGGA R 2 1 2 1 101000 r 74 goat snp7260-scaffold1269-38639 7 54039626 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417712 Affx-122947447 AX-123288060 7 52704606 AGTCAATACTTCTCACTTTGCAGTGTTTCTTAAAC[A/G]TGTTTGAAGGCGGAACCCTTTTTCAGTGAGCCAGT R 2 1 2 1 101000 r 74 goat snp7261-scaffold1269-108872 7 53968681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437461 Affx-122932385 AX-123307799 7 52757462 TAGAACTTGACCATGGGCTTGGGTTTTGGCCCCTC[A/G]CCCTTGTACGCTATACTAGATTCTGTGAAGGTAGG R 2 1 2 1 101000 r 74 goat snp7262-scaffold1269-161728 7 53915845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782858 Affx-122939472 AX-385269927 7 52817723 TTTATAGCCTGACACAAATAACCAACTCTAACGTC[A/G]TAAAAGGACAAAGGGTCAATTCCATATATTTATAC R 2 1 2 1 101000 f 74 goat snp7263-scaffold1269-221989 7 53856548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273546 Affx-1111833665 AX-519547161 7 52921805 CTGCAGAACAA[A/G]AATAAGGCTTCTTTCACATAGGAGGCCTACAGATT R 2 1 2 1 101000 r 74 goat GoatD01.001029 7 52921805 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38379799 Affx-122975826 AX-123250157 7 52922004 ATGCATCATTCTATGATATGTTTTTCTCATCATCT[A/G]TGTATGTAAAATCTATCTATAGACAGAGACACGTG R 2 1 2 1 101000 r 74 goat snp7265-scaffold1269-326270 7 53750002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278675 Affx-1111836455 AX-519552153 7 52959560 GGCAGAAGTCAGCAGGTCAGTTTGAAGGCAAGGGT[A/G]GATGTTGGTCTAGACATGATGACCTTGGAAGTAGA R 2 1 2 1 101000 r 74 goat Random2.2K-798 7 52959560 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38404108 Affx-122957117 AX-123274460 7 52976151 AACCCCAATGAAGATGGAAAGAGACCCTGCTGTTG[C/T]AAGTTAATAAACTGTCTTATGTCTCAAGTCAGTCT Y 2 1 2 1 201000 r 74 goat snp7266-scaffold1269-380417 7 53695617 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412022 Affx-122951739 AX-123282372 7 53024686 AAATGACAGTGCAGGAAGCAGCCTAATGAACATTT[C/T]ATAGTATTCTCTAAATAACCCGTGGATGATGCTGT Y 2 1 2 1 101000 r 74 goat snp7267-scaffold1269-428952 7 53646748 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386767 Affx-122970120 AX-123257125 7 53064843 CTAACAATTTCACTACAATGACCTTAATAACCTAA[C/T]ATTATTTGCAGATCAGTAACTATTTCACCCCTAGA Y 2 1 2 1 101000 f 74 goat snp7268-scaffold1269-469109 7 53606354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772177 Affx-122926524 AX-385259332 7 53103055 AAGTTGAAAAAATTCCTAGGACCATGAAAATTATT[A/G]CTAATTTCTAAGAAATTCTCTACTTTTTAAGACTG R 2 1 2 1 101000 r 74 goat snp7269-scaffold1269-507321 7 53566693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416263 Affx-122947959 AX-123286612 7 53141597 TACAACATGTGAAATAAATGCAGTGGATGATCAGC[A/G]TGACAAACTGTGTCATTAGATAACACGTGCCAACT R 2 1 2 1 101000 f 74 goat snp7270-scaffold1269-545863 7 53527417 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378078 Affx-122977171 AX-123248437 7 53189112 ACACCTGCAGTAGGCATGTAAAGGTGCATGAGAAA[C/T]GGACTTTCCTAGGCAAGAAAATAGGATATAGCAAT Y 2 1 2 1 201000 f 74 goat snp7271-scaffold1269-593378 7 53478759 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435633 Affx-122933772 AX-123305973 7 53218891 TCCCCAACCCTGCAGCAGCTGTGTGCCTGTGAGCA[G/T]CCATGTGTGTATGTACGTGTATATAAGAGGTTGAC K 2 1 2 1 101000 r 74 goat snp7272-scaffold1269-623157 7 53448677 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396934 Affx-122963191 AX-123267289 7 53250483 CTAAGATCCTGACTGAGCTGGACTGAGAGCAGAGC[G/T]CCCATCAACCAAGAGGAAGAAATGAAAGCACTGAC K 2 1 2 1 101000 r 74 goat snp7273-scaffold1269-654749 7 53416669 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431377 Affx-122936560 AX-123301718 7 53295942 AGAAGGAGTTGGACTGGAAGAGCTGACATGGTGGA[A/G]GCTAAGCCTTTCTCTGTCTTTGCTAATGACATCTT R 2 1 2 1 101000 r 74 goat snp7274-scaffold1269-700208 7 53371531 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451112 Affx-122921389 AX-123321446 7 53332382 ATTGCTGCCTCAAGACAGAGAAACTCCATAGAAAA[C/T]GCCTGCTGCCCCACCCTACTCACCTCCAGCAACCA Y 2 1 2 1 101000 f 74 goat snp7275-scaffold1269-736648 7 53335081 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435529 Affx-122933404 AX-123305869 7 53379353 TGTAAAATTGCTACTGGCACTTAAAGATACATTAG[C/T]AGGGTCAAAACTGGGATCAAAAAGAGTCCAATAGG Y 2 1 2 1 201000 f 74 goat snp7276-scaffold1269-783619 7 53287737 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275157 Affx-1111834626 AX-519548736 7 53390586 ATGAGGAACAGGAAGTCCTTCCCTTACAGGCACAG[A/G]CATAACATGTCAGATAGTGAGAGAGATGAAGGTCC R 2 1 2 1 201000 r 74 goat GoatD01.043847 7 53390586 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320762516 Affx-986697046 AX-385250631 7 53412443 CAATTATATATTTAGAATGGCTGATCCTTTTAAAC[A/G]CTTCAAAACCTTAATTTATAAACATATAAAACAAA R 2 1 2 1 600010 f 74 goat 7_53412443 7 53412443 Ancestral_priority_1043 ancestry 0.728 recommended IMAGE 10K 10K ancestral 38403340 Affx-122957812 AX-123273693 7 53423260 CTTACCCAAGAACTTGTTCATTCATTGAATTCATC[C/T]ATGTACCAGGCTGTCTATGCAGATACAGTGAAGAG Y 2 1 2 1 101000 r 74 goat snp7277-scaffold1269-827526 7 53244018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425803 Affx-122940697 AX-123296149 7 53498400 GATTCGAAGACTGAAAACTCAGACATGCACAGTGA[C/T]GAGATGAACAGGAACAAGCTCAAGGTGTCAAGGAA Y 2 1 2 1 101000 f 74 goat snp7278-scaffold1269-902666 7 53169086 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416788 Affx-122948152 AX-123287136 7 53548324 AATCCAGTCCCACTCCTGACCAACTATGTGGCCTA[A/G]GTCGAACTAATCATTTAACTTCTCTGGACCTCACT R 2 1 2 1 201000 f 74 goat snp7279-scaffold1269-952590 7 53119312 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774473 Affx-122924426 AX-385261609 7 53593162 TTAATATTACTAAAATGATACAAGTTGACTTATAC[A/G]GCTTTTGATGTCAGACAGTGGGAAGAATAAAAAGT R 2 1 2 1 101000 r 74 goat snp7280-scaffold1269-997428 7 53074436 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382519 Affx-122973802 AX-123252877 7 53639374 AGCTTATTTTTACATAAGATTCATTCATATTGTGC[A/G]TGCCGTTTTGACTTTTTTAAACAGCTTGTTGATAT R 2 1 2 1 101000 r 74 goat snp7281-scaffold1269-1043640 7 53028112 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766553 Affx-122922810 AX-385253912 7 53674330 CCAAATAGTTGGGCGTTTAGATCCATGGCCAGCTC[G/T]GCTGAGGTGACATTAGATAATATAAAGCAGAATTT K 2 1 2 1 101000 f 74 goat snp7282-scaffold1269-1078596 7 52993163 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423633 Affx-122942364 AX-123293979 7 53712926 TTTCTCATCATTATCATCACCAGCATCATGAAAAG[G/T]AGTAACCATGAGAGAGTTGTCATGATATGGGGGTT K 2 1 2 1 101000 r 74 goat snp7283-scaffold1269-1117192 7 52954592 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379181 Affx-122976312 AX-123249540 7 53742969 GTTTAAAAAGTTGAATCAGAAGGGCCACATGACCA[C/T]GTTTAGTTGTGTTTTTTTGGAAGTAAATTATATCA Y 2 1 2 1 101000 f 74 goat snp7284-scaffold1269-1147235 7 52925614 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452378 Affx-122920622 AX-123322711 7 53800522 TTCCAAATCCTTTGTGAGAAGAAAAATAAGGACAA[C/T]GTATATGTCAGTGCAAGAATGCCAGTTGTTCTTTC Y 2 1 2 1 101000 r 74 goat snp7285-scaffold1269-1204788 7 52867730 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448339 Affx-122924133 AX-123318675 7 53842386 TCCTGAGCACTGGAATGTAAATTTCATGTTTATAA[C/T]GGAGAGAATTATTGTAGCTACTAGGTAGACTGTGA Y 2 1 2 1 101000 r 74 goat snp7286-scaffold1269-1246652 7 52825768 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412220 Affx-122950923 AX-123282570 7 53912503 AAGAGAATAGTGGTAAAAATAGAGCGGAACTCTCT[G/T]TAGTTGAACATATGACTTTCAAAATGGAGCTGTTA K 2 1 2 1 101000 r 74 goat snp7288-scaffold1269-1316769 7 52755743 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438841 Affx-122930772 AX-123309178 7 53954520 TCACCTAAGACATGATTCTCAGCAACTCCGAACAG[C/T]AGGGGCTTTTGGGGAAACAGAATCCCGTAGGACTC Y 2 1 2 1 101000 f 74 goat snp7289-scaffold1269-1358786 7 52712402 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790127 Affx-122948717 AX-385277133 7 53987567 GGGGCTGCTGTGTCTTTGAGGGTCGTGTTAAAACA[C/T]ACCATCCTCATCCACACATGGCCATAATGGAAGAA Y 2 1 2 1 101000 r 74 goat snp7290-scaffold1269-1391833 7 52679377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434776 Affx-122933888 AX-123305117 7 54042511 ATGTCGACTGACAGTGAATACCACTTTGATTTTCC[G/T]CCCCTGATTTGGCCCTATCTGTGAGTTTACTCTCA K 2 1 2 1 101000 f 74 goat snp7291-scaffold1269-1446777 7 52625857 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390443 Affx-122967626 AX-123260800 7 54072506 AGGTTTGTGGGAATCCACCAGGTGAAAGTGGGGGA[C/T]GAGGAGGAGAGGGAGCGGTGCTTCAGTTGGGGAGA Y 2 1 2 1 101000 f 74 goat snp7292-scaffold1269-1476772 7 52595873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774910 Affx-122959954 AX-385262043 7 54129629 TCATGAGACAAAACAGTTTAATCACCCTCCTCCTA[A/G]AAAGTTCCTTCATATTGCCTCTCTACAGTGAACAA R 2 1 2 1 101000 f 74 goat snp7293-scaffold1269-1533895 7 52539113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414742 Affx-122949722 AX-123285091 7 54159069 CTACTTATTCCTCTCTGTGTCTCCAGGGAATAAAC[G/T]CAGTATATGCTGGGTAGCTGAGGCTGAATACATAT K 2 1 2 1 201000 r 74 goat snp7294-scaffold1269-1563335 7 52509646 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793625 Affx-122972207 AX-385280599 7 54190311 AGGTCTTTTAAAACTTTGGTGAATAAAAAATATTG[G/T]AAGTGTCTCTTTACTAATATTAGTAAAAAACAAAA K 2 1 2 1 101000 f 74 goat snp7295-scaffold1269-1594577 7 52478312 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770269 Affx-122958859 AX-385257435 7 54221754 TATTCCACTTCTTAAATGAATGAGGAAATCCATCA[A/G]TTCTTCCATATGTTATTTTGGCTTGAATCCCCCAA R 2 1 2 1 101000 f 74 goat snp7296-scaffold1269-1626020 7 52447103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376921 Affx-122977791 AX-123247280 7 54293803 ATTAGAAAAGATAAATAGTAAAAATAAAAGTTCCA[C/T]TAGCCCAAGATAACCATCATTGGTATTTTGATAAT Y 2 1 2 1 101000 r 74 goat snp7297-scaffold1269-1698069 7 52374211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423336 Affx-122943167 AX-123293682 7 54323301 CAGAGAATGGAACTGTGTGGTCACGTGATGAGTGG[C/T]GTGATTTCTGAAGACTAACCTAACCCCATGGCCTT Y 2 1 2 1 201000 r 74 goat snp7298-scaffold1269-1727567 7 52345118 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770957 Affx-122945607 AX-385258120 7 54393980 AACCCAAATTTATTCTCTCAATGAGATCTTTAAGC[A/G]TAGTTTTCCCCCACTACCTTTAAAGGCAACATTGA R 2 1 2 1 101000 r 74 goat snp7299-scaffold1269-1798246 7 52274491 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413403 Affx-122950714 AX-123283752 7 54423585 GTAGCAAGGTTTGCTCAAAGAGAGCTCTGGTGACT[A/G]TATAGAAGGGTGATTTCAGGACTAGAATAAAGATG R 2 1 2 1 101000 r 74 goat snp7300-scaffold1269-1827851 7 52244963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441971 Affx-122928559 AX-123312308 7 54469469 CCCTAGTCCAAGGCTCTTCCTGTGAGGATAAGAAA[C/T]GAGCATGGGTTTTCAGAACAGGCTGCTCACCAGCT Y 2 1 2 1 101000 f 74 goat snp7301-scaffold1269-1873735 7 52199348 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393624 Affx-122965311 AX-123263979 7 54499458 AACTTGTTCACAATCAGACCAATTTTGCTTCCAGC[A/G]GATTGGAGCCCAGTACAAAGTACAGTTGTGTAGGA R 2 1 2 1 101000 f 74 goat snp7302-scaffold1269-1903724 7 52168490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379709 Affx-122975893 AX-123250067 7 54528567 ATCATTAGGGAGAGAACTACCGAGGGAAACGCAGC[C/T]CTGAGGGGCCTGAGCTAGTCAACCTCTTGCAGCTG Y 2 1 2 1 101000 f 74 goat snp7303-scaffold1269-1932833 7 52139654 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779727 Affx-122939645 AX-385266827 7 54563041 ACATCTCCAGTTTTATGTTGTAGAAACTAAGGCAT[A/G]GACTAGTAAGTCAACAATGACAGTGACAAACACAG R 2 1 2 1 101000 r 74 goat snp7304-scaffold1269-1967307 7 52104847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788600 Affx-122930568 AX-385275617 7 54591645 GGATCCTCAGCATCACCAAGCAGCTTGTTAGAAAT[A/G]CAAATGCTTCAGTTCCATTCTAGACCTACTGTATC R 2 1 2 1 101000 f 74 goat snp7305-scaffold1269-1995911 7 52075348 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434750 Affx-122933908 AX-123305091 7 54629382 AGCTATGTGATTTCAAAAATCACAAATGCAGGACC[A/G]CAAGCAAAGAAGCACCCAGGCATTTCATCCAGCAC R 2 1 2 1 101000 f 74 goat snp7306-scaffold1269-2033648 7 52036830 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382891 Affx-122973414 AX-123253249 7 54662582 TAGAACCTTCTGGCACCTTCAGGCAGAGGTAACCA[A/G]TGCTCTCCAGGGGCTCCCACTGGACACCTATCAAT R 2 1 2 1 101000 f 74 goat snp7307-scaffold1269-2066848 7 52002833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445128 Affx-122926178 AX-123315465 7 54699445 ATCATTTGTAATTTTTAGTTTTCAGTGGGCCAGAC[A/G]TTATACTTCTGACATTATACCTCATTTTCAAAACC R 2 1 2 1 101000 r 74 goat snp7308-scaffold1269-2103711 7 51966177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451922 Affx-122921020 AX-123322255 7 54736047 AGAACTTTTAAAAGTAATAGCTGATATTTGTCCTG[C/T]ATTTCCCATGCTTTGCTAGATGGAGACACCAGAAC Y 2 1 2 1 101000 r 74 goat snp7309-scaffold1269-2140313 7 51929302 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388507 Affx-122969215 AX-123258865 7 54768012 GAGAGAAGTCCAGACACCTGTATTTTGCAAAATGA[C/T]GCCAGAGCATCTGATCATGACAAATAGCAACAACT Y 2 1 2 1 101000 f 74 goat snp7310-scaffold1269-2172278 7 51897840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278498 Affx-1111836456 AX-519551981 7 54782077 AGAAGAGTTAATCACAGAGTATGAAGAAGCTGAGC[A/G]CCGAAGAATTGTTGCGTTTGAACTGTGGTGTTGGA R 2 1 2 1 101000 f 74 goat Random2.2K-801 7 54782077 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430514 Affx-122937216 AX-123300855 7 54813568 AGTGTTACAAAAAATCAACAAATTAAAAACATAGT[A/G]CCTGAAACATAAGTGCTTGAAAATACATTTTCCTA R 2 1 2 1 201000 r 74 goat snp7311-scaffold1269-2217834 7 51852421 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385284 Affx-122972064 AX-123255642 7 54864443 GTTTATCTGACCAGTCTAGTTTGGGGGCAACTGGC[A/G]CCTTTGTACCCTTATCAATGGCAGCCTTATCCAGA R 2 1 2 1 101000 r 74 goat snp7312-scaffold1269-2268709 7 51801127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436668 Affx-122932467 AX-123307006 7 54906783 CAAGAGGTCTTTTCCACCAGCCCCGTTCAGCTCTG[C/T]AGCTCCAGGCTGTTTGCTGCCTCGCACCTCTCCTA Y 2 1 2 1 201000 r 74 goat snp7313-scaffold1269-2311049 7 51763288 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273291 Affx-1111833546 AX-519546935 7 54932683 TTACATCTGCTACCACTTGTTTCTTAGTGTGAAGA[A/G]TTTTCTTTAGTTTTTTCTGGTAAGGAAGATCTATT R 2 1 2 1 101000 f 74 goat 7_54932683_AF-PAKI 7 54932683 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320771898 Affx-122919488 AX-385259054 7 54937351 TAAGTACTCTTTCCCAAGTTCCAGAATACTTGATG[A/G]TACAGAAATCAAGCTTGCTTGTTGGTTTTTTTTTT R 2 1 2 1 101000 f 74 goat snp7314-scaffold1269-2341617 7 51732527 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802179 Affx-122928510 AX-385289083 7 54981392 TAAGCAATGTATCCTGCATCTAGTGTCTTTGCTGT[A/G]TCTATGCTTCCCATCTCTACCTGCTGCTGCTGCTG R 2 1 2 1 101000 f 74 goat snp7315-scaffold1269-2385658 7 51688409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444103 Affx-122926826 AX-123314440 7 55018612 CTTGTCCTACTTCAGTGATGACCCATGAGCCCTAC[A/G]TCATCTCTGTCCTCCTGAAGATACATGCCACGGAT R 2 1 2 1 101000 f 74 goat snp7316-scaffold1269-2422878 7 51652105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434299 Affx-122934761 AX-123304640 7 55055605 TCCCCTGGCTCCTCAATCCAAAATGACACCTCTCC[A/G]TTCTGCTTTCCCACAGGGTTTTCCTGTAGGATGTC R 2 1 2 1 201000 f 74 goat snp7317-scaffold1269-2459871 7 51615185 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378108 Affx-122977146 AX-123248467 7 55085954 TGGAGATTGTAGTCAGATGCTTGACTAGAGCTAAC[A/G]CTTGCAGGAAGTGTGCAAGGAGCATGCTGCTGGCT R 2 1 2 1 101000 f 74 goat snp7318-scaffold1269-2490220 7 51584869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428108 Affx-122939080 AX-123298451 7 55126166 GAAGTGGAAGGTCTATTTTTGTAGGGGTAGAGGGA[A/G]AGGAAGGGGAAAGAAAGAGAGAGAAAGCTCAGGGG R 2 1 2 1 101000 f 74 goat snp7319-scaffold1269-2530432 7 51544431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404487 Affx-122956719 AX-123274839 7 55159266 TCTCTGGTGTAACTATTAACAGCACTCTAAAAGTA[G/T]CCAGGTCTGGACAAGGAATTATACACACTTTCCCC K 2 1 2 1 101000 f 74 goat snp7320-scaffold1269-2563532 7 51514889 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450265 Affx-122922181 AX-123320600 7 55215182 ACTTTACTCATCTCAGGCGTCTTTAGTATCCTGAG[A/C]TGCCTTAAAGCTGTGATACAGTAAAACATCAAGCA M 2 1 2 1 101000 r 74 goat snp7321-scaffold1269-2619448 7 51458376 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432425 Affx-122935827 AX-123302766 7 55245370 GGTGGTGGGTAAGTTTCCTCCAATCCTCCATCCAT[A/C]GATTGTGTGTTAGGAGTGTTCACTGTTTTGAGCAT M 2 1 2 1 101000 r 74 goat snp7322-scaffold1269-2649636 7 51428144 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427664 Affx-122939318 AX-123298007 7 55279123 GTTAATAGTACCTGATAAGGAGTCAACTATCTGTT[A/C]ATAGTTGGAAGACAGTCCTTTAAGTGATGCTTTTT M 2 1 2 1 101000 r 74 goat snp7323-scaffold1269-2683389 7 51394192 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787618 Affx-122927083 AX-385274641 7 55348071 GAGAAGGCATATTCGTAATGTGTAGGTACTAGGTT[A/G]TACATTCATCACTTTCCTAATCTTTATTCAATTCC R 2 1 2 1 201000 r 74 goat snp7325-scaffold1269-2752337 7 51325562 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407715 Affx-122955010 AX-123278066 7 55377533 AATCTCACGTCATGCTACTTATATATAAAGGGAGA[A/G]CTTAGATGTGAACTCAGTTCTATCTGATGAAAAAC R 2 1 2 1 101000 f 74 goat snp7326-scaffold1269-2781799 7 51295764 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437129 Affx-122932158 AX-123307467 7 55407423 CCAACCCCTCTAGGTATCTATTTCTTTGGTATACA[C/T]GTGTCCAAGGAGGCTGATGTAGACTTGACAATTCT Y 2 1 2 1 201000 f 74 goat snp7327-scaffold1269-2811689 7 51265869 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798305 Affx-122959966 AX-385285240 7 55446595 ATTAGTTTGCATTTTCTTGAGTTTTACATAAGATC[A/G]TGCAGTATGTAGTCTAGTTTCTTACCCTCGGAATG R 2 1 2 1 101000 r 74 goat snp7328-scaffold1269-2850861 7 51226679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436370 Affx-122933055 AX-123306709 7 55483399 ACATTCCTGAGTTAGGAAAGAGTTCGTGGTATCTT[A/G]TAAACACCAAGGAAGGTAGCGCAGTCAAAGCCAGG R 2 1 2 1 101000 f 74 goat snp7329-scaffold1269-2887665 7 51191300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765081 Affx-122931844 AX-385252645 7 55515786 AAATGACATTCTTTAAATCTAAGGAAATCCTATAC[A/G]ATGAATCATACTTCATGCATTTCACATTATGATTT R 2 1 2 1 101000 f 74 goat snp7330-scaffold1269-2920052 7 51158552 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427233 Affx-122939569 AX-123297576 7 55545584 CTTCCATCCTTCCTCATAGCTGGGATACTTCAGAG[A/C]CACAATCATCTTTCGGTTCTTTGTTACACCCTCTG M 2 1 2 1 101000 r 74 goat snp7331-scaffold1269-2949850 7 51128745 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428871 Affx-122938342 AX-123299213 7 55579635 GAAGGCAAAATGAAAGGGGTTCTTCGGGGAAATAG[C/T]AAAGATTTCAGTGTAATCAAGGGCTTTAGGGTGAT Y 2 1 2 1 101000 f 74 goat snp7332-scaffold1269-2983901 7 51094975 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788954 Affx-122930931 AX-385275967 7 55629229 CTCTGGCCTTCAGAATCACAGTCTTAGAACCAGGT[A/G]GTTCGGCTGCTGTTCTCTTGTATTAAGTGATGGAT R 2 1 2 1 101000 f 74 goat snp7333-scaffold1269-3033495 7 51044774 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782947 Affx-122929054 AX-385270017 7 55662649 GTTTTTTAAAGCATTCATTTGAGGTGATATTGGAA[C/T]AAACAAATTGAATGATTTCCTAGCTACGAATAGGG Y 2 1 2 1 101000 r 74 goat snp7334-scaffold1269-3066915 7 51011156 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405761 Affx-122956498 AX-123276113 7 55719183 TCCCTATCAATAACAGGGCTAAGCATGTAGAATGA[C/T]ATTGATAAATATTAAATCTATAAATAGTACACATG Y 2 1 2 1 101000 f 74 goat snp7335-scaffold1269-3123449 7 50954292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425543 Affx-122941448 AX-123295889 7 55755316 CATCTGTAGGAAAATTTTGTGGGAATCTCTACAGC[A/G]TCTCTACTGTGACACACTAAACTTGGAGTATCAGT R 2 1 2 1 101000 r 74 goat snp7336-scaffold1269-3159582 7 50917807 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415870 Affx-122948493 AX-123286219 7 55793699 TGTCAAATGAAAAAATAAACTCAAAATGCTTTAAA[G/T]ACTAAATCTAGGACATGGAACCATAAAGTTCTTAC K 2 1 2 1 101000 r 74 goat snp7337-scaffold1269-3197965 7 -1 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441122 Affx-122929591 AX-123311459 7 55866132 ATTTTATTTTCATGTGATGAGCATTTTTAAGATCC[A/G]TTCTTTTAGTAACTTTCAAATATGCAATACAGCAT R 2 1 2 1 103000 f 74 goat snp7338-scaffold1269-3270398 7 50804369 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403220 Affx-122957903 AX-123273573 7 55939007 GTAGGGTCCATCTGGGTAGCTCTCTGGAGCTGGGG[C/T]GATAAAGTTTCAGCTCTCTTGGGTCCCTCAAAGTA Y 2 1 2 1 101000 r 74 goat snp7339-scaffold1269-3343273 7 50730191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435651 Affx-122933348 AX-123305991 7 55990733 GAAATTACTTAACTTCCTTGTGACTTCATTCCCTC[A/G]TCTGTAAAACAAAGAAAATGGTAGTTACTGTCTGT R 2 1 2 1 101000 f 74 goat snp7340-scaffold1269-3394999 7 50677764 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774567 Affx-122942693 AX-385261701 7 56062085 AATATCCAGGAAGGATATATTGTCAGCTTGAAAAA[C/T]AGACTGTTGAACCTGTACACAGCAAACAGTGTCTT Y 2 1 2 1 101000 r 74 goat snp7342-scaffold1269-3466351 7 50606119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392132 Affx-122966335 AX-123262489 7 56099169 AATTGTCACCCGATTGTCTGAGCACTACTTACTGA[C/T]GCCCATCCTCACCGCGGTTTTGAAACACTGTCTCA Y 2 1 2 1 101000 f 74 goat snp7343-scaffold1269-3503435 7 50568772 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396020 Affx-122963481 AX-123266375 7 56128052 TTCTTCCATAATCTAAGGACCAGTCCCCACCCCTG[C/T]AGGAGGCTCTACCTCCTGGCCGTGTGTTAGTCAGG Y 2 1 2 1 303000 r 74 goat snp7344-scaffold1269-3532318 7 50539885 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401909 Affx-122958830 AX-123272262 7 56199613 CAGAGACACCGGGAGAGAACTAGACTAGATGATAA[C/T]GGTCAAACCCTGCAGAGCCATGTCTGAAGCCTGAC Y 2 1 2 1 101000 f 74 goat snp7345-scaffold1269-3603879 7 50467974 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794327 Affx-122937018 AX-385281291 7 56229595 CCACAAAAAAGACTAGAAAGAATGAGTAGTTATCT[C/T]TCTCCTCTGTCCCAAGAAGAAAACTAAAATTTGTG Y 2 1 2 1 102000 r 74 goat snp7346-scaffold1269-3633861 7 50437542 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442657 Affx-122927906 AX-123312994 7 56262909 GTACATAATGATGTTTAAAAACCAGCTTTTGAAGC[A/G]TTGTAAATTTTATTATAATTTGTGTATGTGATGCT R 2 1 2 1 101000 f 74 goat snp7347-scaffold1269-3667175 7 50404159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772921 Affx-122923962 AX-385260065 7 56302265 CAAGAGAAAGAGGGAGTCAAATAAACCTTTCTACC[A/G]TGTGAGGTATAAATGAAGGTCTCAGTATTATCTCA R 2 1 2 1 101000 f 74 goat snp7348-scaffold1269-3706531 7 50364324 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794821 Affx-122967165 AX-385281781 7 56357674 TGAATATTTTAAGCATATGTGAGTATATATTGTCC[A/G]CTTTTGATTATTCTTAACCAAGATCAGCTATTGCA R 2 1 2 1 101000 r 74 goat snp7349-scaffold1269-3761940 7 50307253 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422911 Affx-122943049 AX-123293257 7 56394159 AGTTATCTATGACATATGGGATTGTAGCTCCCTGA[C/T]CAGGGATCAAACTCATACACCTTGCATTGGAAAGC Y 2 1 2 1 201000 f 74 goat snp7350-scaffold1269-3798425 7 50270529 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785466 Affx-122965213 AX-385272511 7 56451499 ATGTGCTAGGCAATAGAATAAGTGCAGGAAAAAAT[A/G]AAATAAAAGAATAGCATCTATGTGCCCAACATCTT R 2 1 2 1 201000 r 74 goat snp7351-scaffold1269-3855765 7 50213120 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406655 Affx-122955808 AX-123277007 7 56490411 TGACCTGCCTTGGTGGCCCTCTGCATGTGCTGGCC[A/G]TTTTCAGCTAGGATTCTAGGTCAGTGGAGATGAAC R 2 1 2 1 101000 r 74 goat snp7352-scaffold1269-3894677 7 50174159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395510 Affx-122963880 AX-123265865 7 56533303 CCTGCTCTCAGAGAACAGAAGGGAGATCCAGGCAG[A/G]CTTGCTTTATTTATCAAACATGGTCTCTTTCAGGG R 2 1 2 1 101000 r 74 goat snp7353-scaffold1269-3937569 7 50131199 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278500 Affx-1111836457 AX-519551983 7 56568796 CCTCGGATAGTGACCTGCTTTTTCTCTGAAATCCC[A/G]TGTTGCTTGTAGGCAGACAGCCAAGTGGACCTGGT R 2 1 2 1 101000 f 74 goat Random2.2K-802 7 56568796 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451132 Affx-122921375 AX-123321466 7 56576338 TCTGAGCCAGAGTCCAGCTTCCAGGACTCTGTCAT[C/T]TGCCCACACACACACCATACAACCTTGAGTTTACT Y 2 1 2 1 303000 f 74 goat snp7354-scaffold1269-3980604 7 50088060 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439334 Affx-122930298 AX-123309671 7 56621565 ACAGTGACCGTTTCATTTTGCATTCCCTGCAGCAA[C/T]GTAGTCACCTTCATTCATAAATAAGTTGAATGTCA Y 2 1 2 1 201000 r 74 goat snp7355-scaffold1269-4025831 7 50042937 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381071 Affx-122974614 AX-123251429 7 56669844 CTTGGCAGCAAAGAAGTTGACCCCCTTGGCCAAAG[C/T]AGCCACAGTGGAGCTTGTGGAGGTGAAGGCCAGGT Y 2 1 2 1 202000 r 74 goat snp7356-scaffold1269-4074110 7 49994678 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800207 Affx-122939241 AX-385287130 7 56704689 TGCCAGATCTCTTCAAGATAGTATTGAAAGATAAG[A/G]CGGCAGTGCTAGAAGCTTTTAGGTCAACAAACCTT R 2 1 2 1 101000 r 74 goat snp7357-scaffold1269-4108955 7 49959380 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278502 Affx-1111836458 AX-519551985 7 56823034 TCACCAGGCGGACACACCTCCTAACTGGCAGAATA[A/C]TTGTACTGAAAAATGCCCATTTTCTTTATTTTTTT M 2 1 2 1 101000 f 74 goat Random2.2K-803 7 56823034 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384078 Affx-122972858 AX-123254436 7 56898816 GTTTCCCATAAATGCACATAATTTCAACCCAGACT[A/C]GTGTCCTTCTGTCGTTTCTCATGTGAGTGGAAATG M 2 1 2 1 101000 r 74 goat snp7361-scaffold1269-4303082 7 49765225 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447398 Affx-122924410 AX-123317734 7 56927773 ATTCATCATTTCCTTTGCTTTTACCCTTTCTGCAG[G/T]CAGACCCCCAATCCTGTTAACTGTTAATGAAAAAT K 2 1 2 1 101000 r 74 goat snp7362-scaffold1269-4332039 7 49736321 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450769 Affx-122921837 AX-123321103 7 56967626 CACAGCTCATGGACAGGATAGAGGGAATCAAGGTG[C/T]CAAGGAAAGCAGATGTGTCTGCATGCCAGGACCCC Y 2 1 2 1 101000 f 74 goat snp7363-scaffold1269-4371892 7 49696660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798289 Affx-122950985 AX-385285225 7 57030513 AGCAAGGAAGAGCCTTAAAAAGTCTTGAGAAGGGT[C/T]TGTTCCCTTCATTTAACTCACATCTACTGAGCACC Y 2 1 2 1 101000 f 74 goat snp7365-scaffold1269-4434779 7 49633847 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407553 Affx-122954683 AX-123277904 7 57158893 CTTGTTATATTTGAAACTGAGGAAGGCCCTGTGGA[G/T]CTTCCAGGCACAGAGGACCTTTTGTCCCCTGTTTT K 2 1 2 1 101000 f 74 goat snp7367-scaffold1269-4563159 7 49505592 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433882 Affx-122934414 AX-123304223 7 57188882 AGAGCTGGGGGTGGGGAAAGGAAGAAAAAGCCAAG[C/T]AAGCACATTGTCTGAATCCTGGGAGATGAATTAAA Y 2 1 2 1 201000 r 74 goat snp7368-scaffold1269-4593148 7 49475467 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395253 Affx-122964098 AX-123265608 7 57218883 TGTGGCCAGGCACCAGGAGGGACAATACTCCTGGA[A/C]CCCCACAGAGGGATGCTTTCTTAAAGGAAGGTGGG M 2 1 2 1 201000 r 74 goat snp7369-scaffold1269-4623149 7 49445383 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443284 Affx-122927476 AX-123313621 7 57271000 ATTTTGCTTTGTTTTGTTTTGAGAACCTACTCTGC[A/G]CCAGGCTCTGCATTAGACACTGACAATGCGATGAT R 2 1 2 1 101000 r 74 goat snp7370-scaffold1269-4675266 7 49392898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421116 Affx-122944208 AX-123291463 7 57315916 TCAGGAGAGCACATCTTTAGTGCTGAAGGTGATGA[C/T]ACCAGTGACCGTGGTGATGATGACGAGTGTGAGAA Y 2 1 2 1 101000 f 74 goat snp7371-scaffold1269-4720182 7 49347395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397924 Affx-122961934 AX-123268279 7 57372032 CAGCTGTAAATTGGGTGAGAGAAGCTGCAGGGCCC[A/G]TGTTCCTGCTGGAGATCTTTTCTAACCACATCAGA R 2 1 2 1 101000 r 74 goat snp7372-scaffold1269-4776298 7 49291451 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396011 Affx-122963486 AX-123266366 7 57405436 CAATATAATAATAATAATAGCGATAACAATAACAA[C/T]AATAATAACATACCATGTGCCAAGTCAGTGTGCCA Y 2 1 2 1 201000 f 74 goat snp7373-scaffold1269-4809702 7 49259023 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431750 Affx-122936732 AX-123302091 7 57450425 ATAAGGGGAACACCAGGGCATCTTTTCCCAAAGCC[A/G]TGTCTCCCTGAACTAGCAAAATTGGGGACATTTGA R 2 1 2 1 202000 f 74 goat snp7374-scaffold1269-4854691 7 49213982 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385562 Affx-122971221 AX-123255920 7 57504752 TGATGGCCACAAATGACCTCAAGAGATAGATACTC[G/T]ATTATCCCCATTTTACAAATAAGTAATCTGAGGTT K 2 1 2 1 101000 f 74 goat snp7375-scaffold1269-4909018 7 49159025 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378464 Affx-122976681 AX-123248823 7 57541824 TGCTCTCTCACAGTTACTGTACATTGTTGATGATT[A/G]CAAAGATGAACAAGATGTCTTCCCCCAGGAGCTGA R 2 1 2 1 201000 f 74 goat snp7376-scaffold1269-4946090 7 49122003 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382279 Affx-122973927 AX-123252637 7 57621235 GCTTAGTAGCCTTGTGGCCTCTGCCGCATCTCTTC[A/G]TTGCCCTAGCCTCTGTTGTTTTGTTTACAGAGGGC R 2 1 2 1 101000 r 74 goat snp7378-scaffold1269-5025501 7 49043285 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426166 Affx-122940594 AX-123296512 7 57631623 CCCCCTGCTGTGACAGAGAAGTGCACCGTGATGGC[A/G]TCCTTACTCTAGTGTTCCCAGAAAAACAATCCAGT R 2 1 2 1 101000 r 74 goat snp24790-scaffold254-3407 7 49032707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273293 Affx-1111833547 AX-519546937 7 57711033 CCAGTGGGCAAACAGGGGAGGGGAAGGTGGAATCA[A/G]GGGAGCCTCCTGCCTGGAGCGGAAGGGGTTGAGGC R 2 1 2 1 103000 f 74 goat 7_57711033_AF-PAKI 7 57711033 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446775 Affx-122925314 AX-123317111 7 57792066 AGGCACCAGGGACTAGCAAGAGGTACAGTCATACC[A/G]CCCCTGAGGCAAGGAGGCAGTGTTATCAGAATCAG R 2 1 2 1 101000 f 74 goat snp24794-scaffold254-163850 7 48871545 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401966 Affx-122958791 AX-123272319 7 57826701 TCCAGGAAAATGCCGTATGGCTTCCAGTCATTCAA[A/C]CATAAGCTCCAGTTTGAAAGAAAAGAAGTTAAGAT M 2 1 2 1 101000 f 74 goat snp24795-scaffold254-198485 7 48837006 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444816 Affx-122926325 AX-123315153 7 57867590 TCTACGATGATGGAAATACTGTCCATCATGACAGA[C/T]GCTAGCCTCCTATGGCTATAGGGTATTTGAAATGT Y 2 1 2 1 101000 f 74 goat snp24796-scaffold254-239374 7 48796594 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418520 Affx-122946422 AX-123288868 7 57969223 TGGCAACAAGGGGAAACTAGAAAGATGGTCCCTCT[C/T]GGCTCCAGCCAGTTGTGACCTGATGGACATGTGTG Y 2 1 2 1 201000 f 74 goat snp24798-scaffold254-341007 7 48694955 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449081 Affx-122923606 AX-123319416 7 57997743 CGAAACCTGCAGCTAGAAAAGCTGAGAAGCCACCA[A/G]TTTATGTGGTAGAACAGGTTCAGAAATTGAGAACT R 2 1 2 1 201000 r 74 goat snp24799-scaffold254-369527 7 48666716 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424554 Affx-122942236 AX-123294900 7 58050462 TGTTACCGAGAACACAGGCCCTGACACAGGGAAGA[C/T]GCCTGCAGGACCTCATGTGGATGAAAACGGTTTTC Y 2 1 2 1 101000 r 74 goat snp24800-scaffold254-422246 7 48613923 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437585 Affx-122931871 AX-123307923 7 58080759 TCAGTTCTCTCAGATACCCTCCCTCCTCCCACTGT[C/T]GCACTCCCTGCATCGTGGGTGCCTGTTTTCTTGGC Y 2 1 2 1 201000 r 74 goat snp24801-scaffold254-452543 7 48583949 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793916 Affx-122939353 AX-385280885 7 58110696 TATCAGAGGTAGTTGGGGTGATATACACAAGACAG[A/C]GTAAACATCCTGTATATATACAAGAAACATCTATA M 2 1 2 1 101000 f 74 goat snp24802-scaffold254-482480 7 48553951 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413168 Affx-122950344 AX-123283517 7 58172538 CATTTCCATGATCTTGGTTTTGGTTCCTAAAAATG[A/G]CACTAAAGGCATAAGATACAATGAAATTTAGATAC R 2 1 2 1 101000 r 74 goat snp24803-scaffold254-544322 7 48491844 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407547 Affx-122954686 AX-123277898 7 58213775 AGAAAGCCTACAAACCATAATGAAGAATCCTTGTC[A/G]CAACGAGGACCCAGAGCAACCCAAATAAAATAAAA R 2 1 2 1 101000 f 74 goat snp24804-scaffold254-585559 7 48450497 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449300 Affx-122923010 AX-123319635 7 58270461 TTTCTTCCCCTCATGGAGCCGAACAAACTGCCATC[A/G]GGAGTCAGAAAAAATGGGTTCCAGCCTCAGATCTG R 2 1 2 1 201000 r 74 goat snp24805-scaffold254-642245 7 48393481 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778787 Affx-122929572 AX-385265896 7 58395386 ATGATAGAATTGACTGGAAGGATTATTATTATCTT[A/G]TAAACAAACTTTCAGTTGCTTAAGAAAAACAGTCC R 2 1 2 1 201000 f 74 goat snp24807-scaffold254-767170 7 48267619 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401777 Affx-122959488 AX-123272130 7 58457376 GGCAGAAAATTATGAACAATGGAGACAAATTAGAG[A/G]AAGCATGCAGAGATGCACAGATGTGCCAATGGCCC R 2 1 2 1 201000 f 74 goat snp24808-scaffold254-829160 7 48205415 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788044 Affx-122961918 AX-385275065 7 58500383 GGAAGGAATTACTCCCACAACTTCTATTAAACATT[G/T]TGTTGGAGGGTCTAGTTAGCACAATAAGGCAAAAA K 2 1 2 1 201000 r 74 goat snp24809-scaffold254-872167 7 48162170 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380181 Affx-122975511 AX-123250539 7 58568620 GAGGCACTATATCCACACCACGTCCCAACATGATA[G/T]CCCCATTGCATGGCCTCACCCAATTCCTCCTGGGA K 2 1 2 1 101000 f 74 goat snp24810-scaffold254-940404 7 48093803 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422135 Affx-122943547 AX-123292482 7 58598608 GCCAAACTGGGAAGCTGAGTCTGACACTGAGAACC[A/G]AGTGACTCAGGCCACTGGGAACCTCTTGCTCTTCC R 2 1 2 1 101000 f 74 goat snp24811-scaffold254-970392 7 48064264 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394152 Affx-122964945 AX-123264507 7 58637602 TCCATAAAATGGACTGAGCAAAAACACTGGGAAAT[A/G]CCAAAACCAAACAAATGTATGTTCGATAGACACTG R 2 1 2 1 201000 f 74 goat snp24812-scaffold254-1009386 7 48025204 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422155 Affx-122943534 AX-123292502 7 58690565 GGAGACTGTCAGCTGAACGAATGCTGCTCACTAGG[C/T]GTCTCAGCTCTTGCCCATCTCCTGCCCACCTGAGC Y 2 1 2 1 101000 f 74 goat snp24813-scaffold254-1062349 7 47972346 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432768 Affx-122935435 AX-123303109 7 58721217 AGGATCAGAGCCTCCTGGGAATCCAGACTCAAGGC[A/G]GAGCCCTTCCCCTTCCTTCGTGCATACGCCAGATT R 2 1 2 1 101000 r 74 goat snp24814-scaffold254-1093001 7 47941686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429958 Affx-122938072 AX-123300299 7 58771708 AGCCCTTTTCCACAATGATGATGTTCCCCTGCTGA[A/G]AGTCACCTTATGCCACCTACAGAGGTTTTAACTGT R 2 1 2 1 201000 r 74 goat snp24815-scaffold254-1143492 7 47891177 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446526 Affx-122925022 AX-123316862 7 58806086 AGGCTATAATAAATGACTTATATTAAAAGGCTGTA[C/T]GGTGGTAAAATGGTCCCAGCAGGCTTGAGGGAAGA Y 2 1 2 1 201000 f 74 goat snp24816-scaffold254-1177870 7 47856121 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786594 Affx-122958784 AX-385273626 7 58837135 ACTTCCTAGGGATAATTTTGGAATTACTTGGACCT[A/G]CAGCTTAGAGGATGTAAGACTAGTTCAATAAAGTT R 2 1 2 1 101000 f 74 goat snp24817-scaffold254-1208919 7 47824997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423979 Affx-122942125 AX-123294325 7 58870675 TGACTGCTCCATGACAGTTCCCAAGACCTTTCTTA[C/T]AAATTCTCCTTTTGTTCCCCAGTTACTTTAGGTTG Y 2 1 2 1 201000 r 74 goat snp24818-scaffold254-1242459 7 47790750 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439109 Affx-122931106 AX-123309446 7 58912070 TATCTGTAAAATGAGCAGTTTGGAGTGACCTCCAA[C/T]GGCTCTTTTAGCAACAGACCCTCATATTCTGGGAG Y 2 1 2 1 101000 r 74 goat snp24819-scaffold254-1283854 7 47749155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412752 Affx-122950521 AX-123283101 7 58943013 TCAGAATGGGAGCTGATTTCACACCCCAGGTCACA[C/T]GCAGCCTGCTCCTGAGCAGGGATGGGTAATGCTGT Y 2 1 2 1 101000 f 74 goat snp24820-scaffold254-1314797 7 47718207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407465 Affx-122954777 AX-123277816 7 58986529 TTCCCCTTGGTGATTCGGAATGAGAAGGGGGGACC[A/G]TTCTCTGGGGAGTCTGGGTCACTCAGAATCAGTTG R 2 1 2 1 201000 f 74 goat snp24821-scaffold254-1358313 7 47674842 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422429 Affx-122943361 AX-123292775 7 59037161 TTCTGCCAAAGCCATTCATTTATGCATTCATTCAG[C/T]ACTTATTTATTGAGGGCCTACCCCATGAAGGCATT Y 2 1 2 1 101000 r 74 goat snp24822-scaffold254-1408945 7 47624290 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278504 Affx-1111836459 AX-519551987 7 59057650 AGCTTTTCTATACCTCAAGGTAGGACAGAGAGGAA[A/G]AGCATTAATTTAGAGAAAGAGAGGAAAACAACGTT R 2 1 2 1 101000 f 74 goat Random2.2K-804 7 59057650 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415583 Affx-122948626 AX-123285932 7 59073550 AAGCCCTTTGACAAGGATCTGCAGGTTCAAACCAC[C/T]GGTTAGAGCAGAGAGCTGGTGCTGGAGAATGTCCT Y 2 1 2 1 101000 f 74 goat snp24823-scaffold254-1445334 7 47588108 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447232 Affx-122924967 AX-123317568 7 59131195 GAGGAGGCGTGGCTTTAGATCACGAGGTCCTTGTC[A/G]ATGTCCTCTGCAAGGCAAGAAGGAGCAGAATTAGA R 2 1 2 1 101000 f 74 goat snp24824-scaffold254-1502979 7 47529737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419695 Affx-122945923 AX-123290043 7 59187102 TGCAGACTATTCCCGAAAGACGCTTATGAAATTGG[C/T]GATGATCAGTGTCCCCAAGGAAGAGAACCACAGAT Y 2 1 2 1 101000 f 74 goat snp24825-scaffold254-1558886 7 47474064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387563 Affx-122970282 AX-123257921 7 59225637 GAAAGAAAATCCCAGCCTCTCAGGGGTTTCTGAGG[A/C]GGTCCTGACTCCTTTCTCTACCTGTGGCTGCTGTA M 2 1 2 1 101000 f 74 goat snp24826-scaffold254-1597421 7 47434577 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798994 Affx-122932058 AX-385285924 7 59260800 TTAAGGCTGTAATACAACAACCTTACAGATAAGTA[C/T]GTTACGTACTGTTGTTCCCATTTAATAAACTAGGG Y 2 1 2 1 101000 r 74 goat snp24827-scaffold254-1632584 7 47408842 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278506 Affx-1111836460 AX-519551989 7 59292782 GGGAAAGGGTATGTGTGTAAGGTCCTCTAGATGGT[A/G]AGCTTCTTGAGTACAATATGGAACTGTAGCAAAGG R 2 1 2 1 101000 f 74 goat Random2.2K-805 7 59292782 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320771619 Affx-122962627 AX-385258777 7 59295753 CATGGATGGAATAGAATGTGGTGTTCAGACTGAAG[A/G]TGATCGGAGAATTTTCACCTAATGGTAAAAGTAAG R 2 1 2 1 101000 f 74 goat snp24828-scaffold254-1667537 7 47373988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380673 Affx-122975183 AX-123251031 7 59337127 CATGGAATTCATACCGGTTATTTACCATCTGCATA[C/T]AGTTCAGTGGGTTTGCTGCCACAATCTGGGAAAGC Y 2 1 2 1 101000 f 74 goat snp24829-scaffold254-1708911 7 47332770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423785 Affx-122942826 AX-123294131 7 59385315 TTTCCCTGACCATCTTCCCTATGGTATCTCCCACC[A/G]CTATCATTCTTTTTGTTTTATGTTTCGATTTATGG R 2 1 2 1 101000 f 74 goat snp24830-scaffold254-1757099 7 47284077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784742 Affx-122962397 AX-385271790 7 59428016 GATTACATGATAAAAGCTTAAAGTATGGTCCCATA[C/T]AGAAGACTGAAAATCCTTTAGGTTGGAAACCTTTG Y 2 1 2 1 101000 r 74 goat snp24831-scaffold254-1799800 7 47240993 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436338 Affx-122933077 AX-123306677 7 59456630 AGGTGGAGACGACAGAATATACGCTTTCATTTTTT[A/G]CTTAAAATTTTTTTCTTGGACTATAGTTGATTTAA R 2 1 2 1 103000 f 74 goat snp24832-scaffold254-1828414 7 47212310 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427471 Affx-122940020 AX-123297814 7 59510072 CCTCTGCCTATTCATTAATGACATGCTCATGAAGA[C/T]GCCAGTTTCCATCGACGGAGACCAGAGAGCAAACA Y 2 1 2 1 101000 f 74 goat snp24833-scaffold254-1881856 7 47158313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441953 Affx-122928571 AX-123312290 7 59574277 AGTCGTGACAAGGGACTGTGGTGAGTGGAAAACAG[G/T]CATCATTTTACGTCAGTGCGGAGCGCTGGCAAACG K 2 1 2 1 201000 f 74 goat snp24834-scaffold254-1946061 7 47093453 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765650 Affx-122950386 AX-385253117 7 59612161 TTACTAATCCTTCAGGTTTTTTAACCTCAGATATC[A/G]TTTGGTTCTGAAAGCCTTTCTTTCAGAAAGACCTA R 2 1 2 1 201000 f 74 goat snp24835-scaffold254-1983945 7 47056581 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789785 Affx-122947010 AX-385276793 7 59656314 GTAGAAGTTTTGAATTTTGATGCTGCTCAACTCAT[C/T]AGTTTTTCTTGCTTTAGGTGTTGTGTATAAGAAAT Y 2 1 2 1 101000 f 74 goat snp24836-scaffold254-2028098 7 47012452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448972 Affx-122923122 AX-123319307 7 59700563 TACCTTAGATTTCAATCTTCTATGAAACCTTTTTT[C/T]ACGTCCTAAGGTGTTCAATTTTTATTATGAGCCAT Y 2 1 2 1 101000 f 74 goat snp24837-scaffold254-2072347 7 46968264 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448628 Affx-122923370 AX-123318964 7 59732099 TCTAAATTCAGCTAGAAATGGCTGGCCATGTGATG[C/T]GTTTGGTACCACACAAAGGATAGTTCCCTGTGAGT Y 2 1 2 1 201000 r 74 goat snp24838-scaffold254-2103883 7 46937145 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393882 Affx-122965125 AX-123264237 7 59779713 TTCCTCACGTTTTTTCTAGTAACATTCAGAATAGA[C/T]GTATTATTCCCAATTGACAGATGGGGACACTGAGA Y 2 1 2 1 201000 f 74 goat snp24839-scaffold254-2151497 7 46889555 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432303 Affx-122936310 AX-123302644 7 59826502 GCAGGTGCTTAAAAATATGGACTGAATAGACAAAC[G/T]AAAGTAAACTAACAGTCCGTATCACCCAGGATTAA K 2 1 2 1 101000 f 74 goat snp24840-scaffold254-2198286 7 46842934 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449867 Affx-122922363 AX-123320202 7 59867370 GAATTATTCTCCTTTTAAACAGTTTCAGAATTTTT[A/G]CTATTTTATTTTTTACTATAATAACAAATTACTAT R 2 1 2 1 103000 f 74 goat snp24841-scaffold254-2239154 7 46802013 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437455 Affx-122932390 AX-123307793 7 59961357 CTGCGTGTCAGGCACTATTGCAGGCAGTAGGGATA[C/T]AGCAGTAAAAAGAAAAACTGGTGGTTGGTACATTA Y 2 1 2 1 102000 r 74 goat snp24843-scaffold254-2333141 7 46706146 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278507 Affx-1111836461 AX-519551991 7 59967624 TAATTGTGTAATTATAGAGAAATGTGTCTGTGGCA[A/G]TGTGCATTATCAATATGTAACAGAGTTCATATATG R 2 1 2 1 101000 f 74 goat Random2.2K-806 7 59967624 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380626 Affx-122975237 AX-123250984 7 59999982 TATCATTCTTTTCTCTGACATTGAGAAACTTAACT[A/C]TAATTATCCAAAATATATTATTTCCTTGGTCCTAG M 2 1 2 1 101000 f 74 goat snp24844-scaffold254-2371766 7 46665341 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762528 Affx-986697058 AX-185397685 7 60010920 AAGAGTTGACTCATTGGAAAAGACTCTGATGCTGG[A/G]AGGGATTGGGGGCAGGAGGAGAAGGGGACGACAGA R 2 1 2 1 103000 f 74 goat 2_76098518_AF-PAKI 2 76098518 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438584 Affx-122931155 AX-123308922 7 60055738 TGGAAGAGCACAGTTAGAGGTTTGAGGAGTTTGGA[A/G]CCTGTGTTTATAGGCCAAAGATCGAGGCAACAGTG R 2 1 2 1 101000 f 74 goat snp24845-scaffold254-2427522 7 46609072 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796750 Affx-122923371 AX-385283693 7 60119040 GTTCAAAAGCAGTCCATCTGAAGAATTAAAAATAT[A/G]TATATTATGTGCTGAGTACTTACCATGGTAAATGA R 2 1 2 1 201000 f 74 goat snp24846-scaffold254-2490824 7 46545588 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404686 Affx-122957276 AX-123275038 7 60150228 CCTTATTCAGAGTCAGCTGAGGTAGGAAGAGAAAA[C/T]GCACTGCCTGCTCCCCTGGTACAAATGAGGTACAC Y 2 1 2 1 101000 f 74 goat snp24847-scaffold254-2522012 7 46514762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419171 Affx-122945729 AX-123289519 7 60187788 CTTCCACTCCACTGCATCCCACAGGTAAATGCAGA[C/T]GTCACACTGATGGAGTTACAGGTAGCATTCCCGAT Y 2 1 2 1 201000 r 74 goat snp24848-scaffold254-2559572 7 46476124 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433037 Affx-122935766 AX-123303378 7 60257128 TTAGCACGAAGGTTAAGCTTTTAAGCTGCTCCATC[A/G]TAACCCAAAGTGGAATCCTTTCTTTCATTACCTCA R 2 1 2 1 101000 f 74 goat snp24850-scaffold254-2628912 7 46407040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784947 Affx-122967934 AX-385271994 7 60291314 CAAAAGAAATCAGAGCTAAGAGGTAGGAACATACA[A/G]ATTTACTGACGATATCCTTTTAGCAGCTAGCAGTT R 2 1 2 1 101000 f 74 goat snp24851-scaffold254-2663098 7 46372071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773500 Affx-122925751 AX-385260641 7 60369047 TACATGAATGGAAATTTCCAGCCAACCATTTTCAG[C/T]TCAACCATGGATGCATTCAACAAATAAAATAGCTA Y 2 1 2 1 102000 f 74 goat snp24852-scaffold254-2740831 7 46293298 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378205 Affx-122976932 AX-123248564 7 60402993 GCACAGAAATGGGATTTGGGCAGCGATGTTGCTTC[A/G]TGTTCAAGATGAGGTTGTTGTTCAGTTGCTCAGTC R 2 1 2 1 201000 f 74 goat snp24853-scaffold254-2774777 7 46258585 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792476 Affx-122962344 AX-385279457 7 60447759 AGCTCCACAATCCTGTCTTCTTATTAAACCACCAC[A/G]TGGAATTATATTGTTAAGTAATGACAATTAAAGTC R 2 1 2 1 101000 f 74 goat snp24854-scaffold254-2819543 7 46214002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765873 Affx-122974406 AX-385253313 7 60482113 GAGTATGGGACTCAGGAGTTAGTGGTGGAACAATC[A/G]CTTTTAGGATTAAGATCCAAATTTTAGGGCTCCTC R 2 1 2 1 101000 f 74 goat snp24855-scaffold254-2853897 7 46179088 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786889 Affx-122955698 AX-385273918 7 60513159 GCTGCTCGACTATTTGCACCTAGTATTTTTATTCA[A/G]TTAGTCCTGGGATGTTTTAAATGCCGCTCACCCAT R 2 1 2 1 101000 r 74 goat snp24856-scaffold254-2884943 7 46148290 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786935 Affx-122921571 AX-385273964 7 60572035 GCATTTCTAGCCAATGGTGCTCACTAAAACTTTTC[A/G]TATTTTTACAAATACTTATTTAGTGCCTACTATGT R 2 1 2 1 303000 r 74 goat snp24857-scaffold254-2943819 NW_017212694.1 18564 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450561 Affx-122922466 AX-123320895 7 60600634 GTGTGTTTGTCTCTGAGTGTCTGTCTGTCCCTCTC[A/G]CCTATGATCATAAGCACCAGGAGATGCTATGTTAC R 2 1 2 1 101000 r 74 goat snp24858-scaffold254-2972418 7 46061874 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796188 Affx-122949378 AX-385283139 7 60632489 AAACACTACAGAGATGACACTCTTTCAATAGTGAA[C/T]AGTCTTTCTTGACCAGTTTAAATTCTCTTTCATTA Y 2 1 2 1 101000 f 74 goat snp24859-scaffold254-3004273 7 46029832 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273951 Affx-1111833915 AX-515997015 7 60634861 ACTG[A/G]ACAGTAGAGAATGCATTAGAAGAGTTAATTCTGCT R 2 1 2 1 101000 r 74 goat GoatD01.010240 7 60634861 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38417894 Affx-122946748 AX-123288242 7 60664482 TATTGCATCTCTTGGGAAAACTATTTTAAAAAAGG[A/G]AAAGATTCCACAAAATTAACTCATGACTCATAGAT R 2 1 2 1 201000 r 74 goat snp24860-scaffold254-3036266 7 45998052 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781269 Affx-122974655 AX-385268354 7 60714977 AGTTGCTGCATATAGAACAAAGTAGTGATTAAAAG[C/T]GTTTCTCTGGTCTCAGGCCAGCTACTTTACTAGAG Y 2 1 2 1 101000 r 74 goat snp24861-scaffold254-3086761 7 45947409 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790744 Affx-122960905 AX-385277745 7 60755511 AAATTGTGGGTTTATTATAGATATTATTGATGAAC[A/G]TTGTTTTCCTATCCTAGTTCTCTGTTTCTACAGAA R 2 1 2 1 101000 f 74 goat snp24862-scaffold254-3127295 7 45905660 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787990 Affx-122921881 AX-385275011 7 60797287 ATATGAGAAGTAAATGCTGCTTTCAAGGAGCCATG[A/C]GCTTTGCACACTGTACCACATTAAATTATCATGGG M 2 1 2 1 101000 f 74 goat snp24863-scaffold254-3169071 7 45863645 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438868 Affx-122930751 AX-123309205 7 60833246 ACTCTGCTCACTTACATTGCTCTTATAAGAAAGTA[C/T]GGAGGACACAAAAGAAAACAAATGTATGATCACTG Y 2 1 2 1 101000 f 74 goat snp24864-scaffold254-3205030 7 45827620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385080 Affx-122971807 AX-123255438 7 60884278 CACAGGAATTTGTAATTTATGAAGCTCCCTCAGTC[A/G]TTTGGGCTTAGACAGTTTCTGAAACGCTGATATGC R 2 1 2 1 101000 f 74 goat snp24865-scaffold254-3256062 7 45768197 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415354 Affx-122948779 AX-123285703 7 60933302 GGACCTGAGAATGTAAAACTTTATGTATGAGAGAA[G/T]CATACCTTTTTGAAATACAAACACTTCTTAAGAGT K 2 1 2 1 101000 f 74 goat snp24866-scaffold254-3305086 7 45718396 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789803 Affx-122978568 AX-385276810 7 60977905 TTTTAATAATGTAAGTTTATACTCCTGTCACACCT[A/G]TTATTCAAGGTTATCAAATCACTCTGCCCACCTTA R 2 1 2 1 101000 f 74 goat snp24867-scaffold254-3349689 7 45673143 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411902 Affx-122951182 AX-123282252 7 61006812 TATTACCTTCCCAGATCTAGATGATCTTGGGTTTG[A/C]GTCTGATATTCTGATGCTATGATACAAGCTAAACC M 2 1 2 1 201000 r 74 goat snp24868-scaffold254-3378596 7 45644375 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412387 Affx-122950802 AX-123282736 7 61063821 TAAGAGTCTGGACTGCCTGGTGGTGGAGAGCCATC[A/G]TTTGAGCATGACTAGTGGATATCTGGCTCTTTTTC R 2 1 2 1 101000 r 74 goat snp24869-scaffold254-3435605 7 45587575 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789258 Affx-122964768 AX-385276269 7 61122006 TTAATCCATATGCAGGTCCTCTTATCCTCAGTCCA[A/G]TAATGCAGCAAGATCCAGAAACTAAATATTCCCTG R 2 1 2 1 101000 f 74 goat snp24870-scaffold254-3493790 7 45529076 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391221 Affx-122967402 AX-123261578 7 61151897 CCAATCTCTGGGAACACAAACATGAATAAAAGGAA[C/T]GAGGCACTTGGCTTCATGGACCTCAGCTCTAATGG Y 2 1 2 1 101000 f 74 goat snp24871-scaffold254-3523681 7 45501061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415272 Affx-122948840 AX-123285621 7 61199910 ATGCTAATTATGGAGGCATTTCAGAATAATGACCT[C/T]ATAAAGTTCAAGCTGCTGTCTCTGTGTGCAGACTT Y 2 1 2 1 101000 f 74 goat snp24872-scaffold254-3571694 7 45452683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422021 Affx-122943631 AX-123292368 7 61270721 GACAAAAAAAGCTTTGTACCTTTTCCCCAGAAAAA[C/T]GCACACATATATTTCTGCATGACCATGAGTCGGGG Y 2 1 2 1 101000 r 74 goat snp24873-scaffold254-3642505 7 45380951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764838 Affx-986697060 AX-385252438 7 61274476 TGGGGACCATGCTAGTGATAAAGGCACATGAAACG[A/G]CTGTTTTTACGTAAAGTGGGTACTTGGTAGATTTG R 2 1 2 1 600010 r 74 goat 7_61274476 7 61274476 Ancestral_priority_1043 ancestry 0.694 neutral IMAGE 10K 10K ancestral 320762532 Affx-986697062 AX-385250639 7 61274499 GCACATGAAACGGCTGTTTTTACGTAAAGTGGGTA[A/C]TTGGTAGATTTGTGGATGTTGAGGCTGGTTATTAT M 2 1 2 1 600010 f 74 goat 7_61274499 7 61274499 Ancestral_priority_1043 ancestry 0.646 neutral IMAGE 10K 10K ancestral 320764845 Affx-986697064 AX-385252444 7 61274505 GAAACGGCTGTTTTTACGTAAAGTGGGTACTTGGT[A/G]GATTTGTGGATGTTGAGGCTGGTTATTATGATGGG R 2 1 2 1 600010 r 74 goat 7_61274505 7 61274505 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 320762538 Affx-986697068 AX-385250645 7 61274832 TAGGGGGCCTAGGATAATTTTTGGGTTTAGGGATA[A/G]AAGTAGTAGCGGTAGTATGTGAAGTGATGAGTGTG R 2 1 2 1 600010 f 74 goat 7_61274832 7 61274832 Ancestral_priority_1043 ancestry 0.668 recommended IMAGE 10K 10K ancestral 320803069 Affx-986696155 AX-385289940 7 61274866 AGAAGTAGTAGCGGTAGTATGTGAAGTGATGAGTG[C/T]GTTTTCTCGTATGAAAGAGGGTGAGATGTTGTTGA Y 2 1 2 1 600010 f 74 goat 7_61274866 7 61274866 Ancestral_priority_1043 ancestry 0.684 recommended IMAGE 10K 10K ancestral 320762504 Affx-986697034 AX-385250621 7 61274969 ATTAGTATGTAGAGGGAGTATAGGGCAGTGATCAC[C/T]ATGTTAGGTCCTATTAGAATAATTGTGATGTTAGA Y 2 1 2 1 600010 f 74 goat 7_61274969 7 61274969 Ancestral_priority_1043 ancestry 0.574 neutral IMAGE 10K 10K ancestral 320764857 Affx-986697071 AX-385252455 7 61274976 TGTAGAGGGAGTATAGGGCAGTGATCACCATGTTA[A/G]GTCCTATTAGAATAATTGTGATGTTAGATCATGAA R 2 1 2 1 600010 r 74 goat 7_61274976 7 61274976 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 320762543 Affx-986697073 AX-385250650 7 61275035 TTAGATCATGAAAAAGTTGATATAACTACGAATAG[C/T]TCTCCGATTAGGTTGATTGTTGGGGGTAGGGCCAG Y 2 1 2 1 600010 f 74 goat 7_61275035 7 61275035 Ancestral_priority_1043 ancestry 0.738 recommended IMAGE 10K 10K ancestral 320762545 Affx-986697075 AX-385250652 7 61275761 TAGAGGCCGGCGTTTAGACGTTCTGTTTGGTTTCC[C/T]CATCGAGTGATGATGATGAGTGTAGGGACTAGTGT Y 2 1 2 1 600010 f 74 goat 7_61275761 7 61275761 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 320762547 Affx-986697077 AX-385250654 7 61275848 TAAAAGAAAATTAGTTCTGTAGCGGTAAATGTTAT[A/G]ATTAGGAATAGTTGTAATAGGACTAGTATTGAGAT R 2 1 2 1 600010 f 74 goat 7_61275848 7 61275848 Ancestral_priority_1043 ancestry 0.698 recommended IMAGE 10K 10K ancestral 320764870 Affx-986697079 AX-385252467 7 61276796 TTCATATGGGCTTGTTTTTTCTGAGTAAACGTTTA[A/G]TTGGGGGAGTCAGAATGCGATAGTTACGAGCAATG R 2 1 2 1 600010 r 74 goat 7_61276796 7 61276796 Ancestral_priority_1043 ancestry 0.416 neutral IMAGE 10K 10K ancestral 320764872 Affx-986697081 AX-385252469 7 61276885 TCAGGAGAGTAATTATAAGGTTTATTGTTCTTTTT[C/T]GGACTAGACCGAAACTAACTGATTGGAAGTCAGTC Y 2 1 2 1 600010 r 74 goat 7_61276885 7 61276885 Ancestral_priority_1043 ancestry 0.564 neutral IMAGE 10K 10K ancestral 320762553 Affx-986697083 AX-385250659 7 61277083 AAGTGAAATTTTAGTTGGCGGAAGAAGCAGACAAT[C/T]AAAAAGGTAGATCCGATGATGACATGAAGGCCATG Y 2 1 2 1 600010 f 74 goat 7_61277083 7 61277083 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 320762555 Affx-986697085 AX-385250660 7 61277109 GCAGACAATCAAAAAGGTAGATCCGATGATGACAT[A/G]AAGGCCATGGAATCCTGTGGCTACAAAGAAAGTTG R 2 1 2 1 600010 f 74 goat 7_61277109 7 61277109 Ancestral_priority_1043 ancestry 0.74 recommended IMAGE 10K 10K ancestral 320762557 Affx-986697087 AX-385250661 7 61277566 GTACTTTCTCGAATTACATCTCATCATCATTGGTA[C/T]ATTGTAAGTATATTTGTTGTTAGACCTAGGGTTAG Y 2 1 2 1 600010 f 74 goat 7_61277566 7 61277566 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 320803073 Affx-986696157 AX-385289944 7 61277649 GTTGAAGTGAAATCATATGATGAGGCCAGATGTTA[A/T]TAGGAGGGCGGATAGTGCTCCTGTGAGGGGTCAGG W 4 1 2 1 600010 f 74 goat 7_61277649 7 61277649 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 320764889 Affx-986697091 AX-385252484 7 61289884 TTGGAAATAATAAATCCTGCAAAAAGACTTCCGAT[C/T]AGTAAGCGTTTGATTGAGTTAATTAGGAACGGGTT Y 2 1 2 1 600010 r 74 goat 7_61289884 7 61289884 Ancestral_priority_1043 ancestry 0.714 recommended IMAGE 10K 10K ancestral 320762563 Affx-986697093 AX-385250665 7 61289959 TCATTAATGTTGATGAGAGTTGGGAATCGGGGCTG[C/T]CCTAGGAGTGCGAAGAAGATAATTCGAGTACTGTA Y 2 1 2 1 600010 f 74 goat 7_61289959 7 61289959 Ancestral_priority_1043 ancestry 0.59 neutral IMAGE 10K 10K ancestral 38437871 Affx-122932067 AX-123308209 7 61322992 TTATCCTTCCAAAGCAATACAGTAGAAAGAACTCT[C/T]AGCCTGAGGTAGGGGATTTGCCTTCTAAACCAAGT Y 2 1 2 1 101000 f 74 goat snp24874-scaffold254-3694776 7 45328333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408623 Affx-122953492 AX-123278974 7 61365799 ACATTTAATTCAGGGCATGGAAATTCCCACCCTTC[A/G]TGGCTCTCCCTCAGTGTCTTCAAACCTCGCTCATC R 2 1 2 1 101000 f 74 goat snp24875-scaffold254-3737583 7 45285533 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413558 Affx-122950598 AX-123283907 7 61413426 TACTTTGTGTGGTATGACCAGAGTTCTGGGATAGA[A/C]GTCAAGGGACTTGGCCTCTGTCGCTCTCTTAGTCA M 2 1 2 1 101000 f 74 goat snp24876-scaffold254-3785210 7 45237944 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784636 Affx-122967960 AX-385271684 7 61465005 ACCATCTCAGGAAAGCCTTCAAACATACAGACCAT[A/G]CAGTTCTCACAGGTCTATTATTCCTTTCCACATTA R 2 1 2 1 101000 f 74 goat snp24877-scaffold254-3836789 7 45185446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765435 Affx-122953640 AX-385252937 7 61497550 TGGCCTAATTAATGATTAAGACCATCAGGATGACC[A/G]TCAGTAAACTAGCACATTAGACTGCATTTCTTGCC R 2 1 2 1 101000 f 74 goat snp24878-scaffold254-3869334 7 45152938 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273334 Affx-1111833548 AX-519546974 7 61527126 AATGGAGGGGCACAGGGATAGCTAAAGAAAGAGGC[A/G]GAAAGCGCCAAGAAGGACGTTTTCTGAAGCCTGGA R 2 1 2 1 101000 r 74 goat 7_61527126_AF-PAKI 7 61527126 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38444743 Affx-122926398 AX-123315080 7 61532567 CCCTGGGAAGAACTTAGGACTCTGACTGGGAATTT[A/G]CACAACCATCAGAGCTTCTCAGGTGGCACAATGGT R 2 1 2 1 101000 f 74 goat snp24879-scaffold254-3904351 7 45119085 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795587 Affx-122938540 AX-385282542 7 61578661 TCAGGAAATTGAGCATCCCTGAATTTTGGTATCAA[C/T]AGGGGTCCCTGGAAGCAGGATACTTCTAAGGCTGT Y 2 1 2 1 202000 r 74 goat snp24880-scaffold254-3950445 7 45072944 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421702 Affx-122944403 AX-123292049 7 61634224 TTTTTCTATATTTCTTCTATGGTTTTTTCATGTAT[A/G]TTTACACATATATGTATGTACATTTTCTGTCCCCT R 2 1 2 1 201000 f 74 goat snp24881-scaffold254-4006008 7 45017035 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426502 Affx-122940215 AX-123296848 7 61665250 ACATTCACTATTATCCCATTGGCCAAAACCAGTCA[C/T]ATGGCTGAACCCAGAGTCAGAACGGGAGGGCAGGT Y 2 1 2 1 101000 f 74 goat snp24882-scaffold254-4037034 7 44985627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790348 Affx-122948404 AX-385277351 7 61709018 TCTTCTCCAAAAGCTGAGCCACGGCAGAATCTGTA[C/T]AGTGTACAAACCTTAAGATTGTCCCTAATTATCCT Y 2 1 2 1 101000 f 74 goat snp24883-scaffold254-4080802 7 44940884 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384458 Affx-122973090 AX-123254816 7 61765314 TGGTTGGCAGGCCCTGGTTTGTTGACCCCTGTTCT[A/G]TTCTCTTTGTAGTGGAGGAAATGCCTTCAATTGCT R 2 1 2 1 101000 r 74 goat snp24884-scaffold254-4137098 7 44884607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452916 Affx-122920199 AX-123323249 7 61816741 TAAACATAAACGTTTTCTAAGCCATGTTGCTCCAC[A/G]CTTCCAGAAGTTAGGGTATATGTCAGTAGGTATCA R 2 1 2 1 101000 r 74 goat snp24885-scaffold254-4188525 7 44833171 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383992 Affx-122972922 AX-123254350 7 61852858 GTAAATCCTAGGTTTTTCCAACTCTGGAGTCAGAA[C/T]GCTCTGAGTCATCAACTAGACTTCCTGCCCCATTG Y 2 1 2 1 101000 f 74 goat snp24886-scaffold254-4224642 7 44799266 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792824 Affx-122973066 AX-385279802 7 61882728 CCAACTGTTTGACCTCTCTGCCTTGTTTCCTCCTC[A/G]TTGTAATGGGAATAGTGATATTCCCATCATTCCCA R 2 1 2 1 303000 f 74 goat snp24887-scaffold254-4254512 7 44769204 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784708 Affx-122973007 AX-385271756 7 61931485 TCCTTCTCTGTTAACCACTCCTCCACACAACTGCT[A/G]CCTTTCCTCCTCTAAGAGCACAATGGTTATAAGCA R 2 1 2 1 101000 f 74 goat snp24888-scaffold254-4303269 7 44720415 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782254 Affx-122975815 AX-385269332 7 61964570 TACCTTGCTTTGGCTTCTGTAGAGTGCACATCACC[A/G]TCTGAAAGCCCCTGTATTAGGTACCTACTGCCACA R 2 1 2 1 101000 r 74 goat snp24889-scaffold254-4336354 7 44687166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417545 Affx-122946924 AX-123287893 7 62018981 ATTCAGCCGAGGTGGCTAATGAGACTTCCTGAGAG[C/T]GCACGGCCACCAGCAAGACTGGACTCTGATAAGGG Y 2 1 2 1 201000 r 74 goat snp24890-scaffold254-4390765 7 44632957 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396874 Affx-122963239 AX-123267229 7 62086332 CAGAGAGATGACCCAGAGTTGGAGAGTGGACCTCG[C/T]AGCAGCTGGATTAAGGAATCTTCTCCCTCTAGACT Y 2 1 2 1 101000 r 74 goat snp24891-scaffold254-4458116 7 44566007 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399697 Affx-122960485 AX-123270052 7 62118002 ATTTTATTTCATGGTTACTTGTTTGTAACATCTGT[A/C]TCCTGGTAAATGTCAGCCCTACGAGGACAGGAACC M 2 1 2 1 101000 f 74 goat snp24892-scaffold254-4489786 7 44534439 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398025 Affx-122961775 AX-123268380 7 62168779 CAGGAAATCCCCCAGGGATGTTCATTTTAAATTTT[A/G]CCCACAACAGGTTTTAAGAAAACAGAAGTATCTAT R 2 1 2 1 201000 r 74 goat snp35149-scaffold420-2129319 7 44485620 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464520166 Affx-1110527362 AX-515992242 7 62191545 GACATCTGGTGCCACCTGTTTCTCCAGTGACAAAA[C/T]GGAACTTTACCTCACCTTGTGCTCCCATCAATGAC Y 2 1 2 1 101000 f 74 goat GoatD01.004074 7 62191545 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320774887 Affx-122967363 AX-385262021 7 62210766 GTGCTATAAGTCAGTAAAACATTAATTAAGTAGTT[A/G]CAGGAAAACACATTCATTAGACAGACAGGGCCAAG R 2 1 2 1 101000 r 74 goat snp35148-scaffold420-2087332 7 44444995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407387 Affx-122955258 AX-123277738 7 62241140 TGCTCCAGGAAAAGCAAAGAGTCACGTCGTTGGAG[A/G]GGGAAAGTGGTGAAGATGGAGTCAGAGCTCAGGTC R 2 1 2 1 201000 f 74 goat snp35147-scaffold420-2056958 7 44418797 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801825 Affx-122935380 AX-385288732 7 62288275 TGACCTCTCCCAGAAAGAATAAGAACATTTACCTA[C/T]GGTACTCGTCCTGATCACCTCTAAATAGGGCACAG Y 2 1 2 1 101000 f 74 goat snp35146-scaffold420-2009823 7 44371387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796031 Affx-122955034 AX-385282983 7 62366380 TTCACACCTGCCACTTTCTCCAGAGGGAGGTGTTT[A/G]TAAAACTTACTTTATACTATGTTATCCAAGTACAA R 2 1 2 1 102000 f 74 goat snp35144-scaffold420-1931718 7 44293623 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391959 Affx-122966531 AX-123262316 7 62433321 CCTATTTCCTCACCCAAGTTTGCCCTCCCTATATG[C/T]AAAATTTATTGAGATAATCAATCATAGAATTTCCC Y 2 1 2 1 103000 f 74 goat snp35143-scaffold420-1864777 7 44228349 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400140 Affx-122960704 AX-123270495 7 62480136 TTATGTCCTGTGGCATGAATAATGTTGAAAAGTTC[A/G]CAAAGTTTTCTGGAATCTTTTAGGAGATAGCATAC R 2 1 2 1 101000 r 74 goat snp35142-scaffold420-1817962 7 44180686 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428423 Affx-122938829 AX-123298766 7 62533022 AGTTTCCCAACCTGCAAATTGAAAGAATTATCTAG[A/G]GTAGGAATCAGCAAACTACAGCCCATGGTCTAAAT R 2 1 2 1 201000 f 74 goat snp35141-scaffold420-1765076 7 44127860 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423501 Affx-122942560 AX-123293847 7 62569245 GCAGCCAAGGGTCAGGAGTGATCAGAAGCCAAGTC[C/T]GTGGGCCAGTGCTTTTAGGGGAATGGAGCTCAGGT Y 2 1 2 1 101000 f 74 goat snp35140-scaffold420-1728853 7 44091110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411400 Affx-122951851 AX-123281750 7 62627302 CCCAGTGTCCAAGGCCTTTTTAGCCTTCCTCTCCA[G/T]TCACCCAGAGTCCAAAATGCATTTCTCTTGTCTCC K 2 1 2 1 102000 r 74 goat snp35139-scaffold420-1670796 7 44035154 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399490 Affx-122961178 AX-123269845 7 62668519 AACAAACTGTCTGCAGATGCTTTCCAGGCAGCAGC[A/G]CAGGGAAGGGGGTGCAGGCAGAACCCAGTGGACTC R 2 1 2 1 101000 f 74 goat snp35138-scaffold420-1629579 7 43994039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390651 Affx-122967140 AX-123261008 7 62722619 CCAAATGATTAGGAGAAAACATGTTTTATCATCCA[C/T]AGGTCTGCAGTTTAAGAGTAATTCCAGCAAACCTC Y 2 1 2 1 101000 r 74 goat snp35137-scaffold420-1575479 7 43940527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388449 Affx-122969256 AX-123258807 7 62753868 CCCTTGATTACTGTTAATATTTCCACTTTTCAAGA[C/T]AGGAAACAGAGGCAAAGAGGACTTCAGTGGCAGAG Y 2 1 2 1 101000 f 74 goat snp35136-scaffold420-1544230 7 43909130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399594 Affx-122961102 AX-123269949 7 62793184 CAATAAAAACTGGTATGTCTTTCCTGCCCCACTTC[A/G]CATAAATTCAGGGTTATCTTCCAAAACCCAAAGTC R 2 1 2 1 201000 r 74 goat snp35135-scaffold420-1504914 7 43869653 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778991 Affx-122976115 AX-385266098 7 62824842 GGCTTGCCTAGGGTCACTGAGCAAGGACGTGGTGG[A/C]GCTGAGAGCTGCATACAAGCTACTCAACTAGTCCT M 2 1 2 1 303000 f 74 goat snp35134-scaffold420-1473256 7 43837644 T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772259 Affx-122967176 AX-385259414 7 62855208 ATGCAAACCATAAAAAAGAACTGATCAATTGATAA[C/T]GCTATAATTTAGAAGTTTGGCACCATAAAAGACAA Y 2 1 2 1 101000 f 74 goat snp35133-scaffold420-1442890 7 43805948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424728 Affx-122941670 AX-123295074 7 62890845 GCTTCACAAAGGAAATTATTATAAAATGGTCAGCT[C/T]ATTATGAGATCATACCTGTGCCTTCCATTCTGAAG Y 2 1 2 1 101000 r 74 goat snp35132-scaffold420-1407253 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406638 Affx-122955821 AX-123276990 7 62938003 TTAGGCTATGGGGTCACATACATTAAGGCTAATTA[C/T]GTTCTTCTACTTATCAGCAATGACATTGTCAAGTT Y 2 1 2 1 101000 r 74 goat snp35131-scaffold420-1360095 7 43730888 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431004 Affx-122936680 AX-123301345 7 62986933 TCATATCATGTGACCAATCACATGTCAGGGCCAAA[C/T]AGCGTGTGAAGCCCTGGAATGACAGCCCAGGTCTG Y 2 1 2 1 101000 f 74 goat snp35130-scaffold420-1311165 7 43681911 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432255 Affx-122936346 AX-123302596 7 63018642 ACTCTTGCAGCATTGACCAGCACTTCTGAAGTGTG[C/T]ACAAAGCCTTCATTCACTGTAAAGATGGTCATGCC Y 2 1 2 1 101000 f 74 goat snp35129-scaffold420-1279456 7 43649181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430691 Affx-122936918 AX-123301032 7 63049572 ACCAAGAAGGCCTCCACAACTTTCTCATCTGTCTG[C/T]TACCCAAGATCTGAGGAAAGCCTAGAACTAGTAAA Y 2 1 2 1 201000 r 74 goat snp35128-scaffold420-1248526 7 43618223 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420933 Affx-122944995 AX-123291280 7 63140307 TGAGGAAAAGAAAGGGAGTAATATTGCACTGAATT[A/G]CAATTAGCAAAGAAGTGTCTGACTTAATTTTCCAT R 2 1 2 1 101000 f 74 goat snp35126-scaffold420-1157791 7 43527085 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797691 Affx-122963517 AX-385284630 7 63172030 AAGAAAGTTTGATTTAGGTTTAGAAACCAGTACAA[A/G]AAATGCAAGTGCGGATGTAGAAGGCCATGTGCCAA R 2 1 2 1 101000 r 74 goat snp35125-scaffold420-1126068 7 43495007 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391735 Affx-122967489 AX-123262092 7 63201243 GAAGATCATCCTTCTACTTTTTACCCCAGAGGTTA[C/T]AAATCCAAATACTTGCAGAAACCAGTCAGGAACAG Y 2 1 2 1 101000 r 74 goat snp35124-scaffold420-1096855 7 43465707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430546 Affx-122937024 AX-123300887 7 63269454 GATCAGCAACTTTGTTCACTTACTCTAAGAATCAG[C/T]GATACTAAGACCCTTGTTGAAAAAGACTGGCGATA Y 2 1 2 1 101000 f 74 goat snp35122-scaffold420-1028644 7 43396439 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433765 Affx-122934489 AX-123304106 7 63317530 TGCTCAAAAATACTGAAAATGGTGTTGTATTAGTC[A/G]TGCATTAATTCATTCACACACCCATTCATCCATTC R 2 1 2 1 101000 r 74 goat snp35121-scaffold420-980568 7 43348234 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388611 Affx-122969142 AX-123258969 7 63362468 AACATTGGATTGAAAGGTCTCCAAAGATTCTTTTC[A/G]CTATAGAGGTCTTCAAATCTCTATTTTCTTAATCT R 2 1 2 1 101000 f 74 goat snp35120-scaffold420-935630 7 43302926 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777156 Affx-122945676 AX-385264279 7 63395815 TTGTTTTCAGGGTGGGTCTGTGTATGCATCTCTGT[A/C]TGTTTCACACTTGCTAAGAACTCAGTTTGTACAAC M 2 1 2 1 101000 f 74 goat snp35119-scaffold420-902283 7 43269792 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387992 Affx-122969582 AX-123258350 7 63446436 AGCAAGCATAATTCTAAAAATATTAGCTATTGAAT[A/G]TTAGAAGCACAGTAGAGAAGGACTCTAAAGCAAGT R 2 1 2 1 101000 r 74 goat snp35118-scaffold420-851662 7 43219825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770576 Affx-122978372 AX-385257740 7 63545972 AAAGCCTTTCTTCATACTAAGGTGCTAAAGCTGAA[A/G]TATATTAAAGCACCTCCCTTTCTAGAAAACTAGGT R 2 1 2 1 101000 f 74 goat snp35116-scaffold420-752126 7 43120299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409330 Affx-122953080 AX-123279681 7 63617442 TACTGGTCCAGGAATGTTCCAGATGTTCCATGTAT[A/C]TTAATTCCCTTCCCTCCTTCAATAGTGGATATATA M 2 1 2 1 101000 f 74 goat snp35114-scaffold420-680656 7 43047607 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795663 Affx-122930805 AX-385282618 7 63654081 CAGGGGAGTAGACCTGAAGACTAGAAAGAGCCTCA[G/T]AAACTAAAGCCTTGGCCTTTTTAAATGTAACAGGA K 2 1 2 1 201000 f 74 goat snp35113-scaffold420-644017 7 43010221 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377958 Affx-122977202 AX-123248317 7 63684357 TGACATAAACCAAGAAAAAATAATCAGGCTTCTTG[G/T]ATGCACAAAAAACTGTAACTCAACGAGGTTTCCTG K 2 1 2 1 101000 r 74 goat snp35112-scaffold420-613741 7 42979757 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386913 Affx-122970012 AX-123257271 7 63716845 GAAAGATTTAAAAAAACAGCATTCTTTCAAATTTC[A/G]TAACTTCCAAACATCCCTGGCTCAGGATGAGAACA R 2 1 2 1 201000 f 74 goat snp35111-scaffold420-581253 7 42947834 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430190 Affx-122937353 AX-123300531 7 63782549 CAGTTCCTATCATAGCTCAGAGACACTACAGATGA[C/T]GGGCTCAGCCTACACCCGGCTGTGTTATTGTCTGC Y 2 1 2 1 101000 f 74 goat snp35109-scaffold420-515549 7 42881699 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278689 Affx-1111836462 AX-519552167 7 63797825 TGAAATTTTGTGATACAGTTCTTTAGTGTAGATAT[A/G]TTTTTATTCATCGTGCAGGGCACTTTGTGAGCATT R 2 1 2 1 101000 r 74 goat Random2.2K-809 7 63797825 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38405668 Affx-122956566 AX-123276020 7 63811871 AATTCTGATTTGATCTCCCTACCTGCCATTGCCTC[G/T]GTCTTTGCTCAACATTTCAATTGTTGGAGGGGGAA K 2 1 2 1 201000 r 74 goat snp35108-scaffold420-486227 7 42852442 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424481 Affx-122941760 AX-123294827 7 63857575 AGGGATATTGGCATTGAATAGCCAAGCTACAGGCA[G/T]AGGACTTCCACAAGGGTGAGACCTTTGAACCACCT K 2 1 2 1 101000 f 74 goat snp35107-scaffold420-440523 7 42806929 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413872 Affx-122949854 AX-123284221 7 63886665 TGCAGTCTGTATCAGAGAAGAAAAACCTGACTTCA[C/T]ATTGCTAGTGTTTAGTCCTGCCGGCCCTACACCCT Y 2 1 2 1 101000 r 74 goat snp35106-scaffold420-411433 7 42777887 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403292 Affx-122957848 AX-123273645 7 63956189 GCTTATTTACCTAATTTCCTTTACTTAATTTCTTT[A/G]TTCACTCATCCATTCATTTAGTTTGCCAACATATG R 2 1 2 1 303000 f 74 goat snp35104-scaffold420-341909 7 42708518 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397578 Affx-122962004 AX-123267933 7 63987305 ACTACTGTATCTATTAATATTATTCTAATCTTCTC[A/G]CCAACATTATGGAATCCATTCTAAAATTGTGTTCA R 2 1 2 1 101000 r 74 goat snp35103-scaffold420-310793 7 42677571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378835 Affx-122976540 AX-123249194 7 64016240 GGAGAAAAGTAGATGGATCAAGGCACATCTTTCAG[A/G]TAGAGGCCAAGAGACTTTCTGATGGGTTTTATCGT R 2 1 2 1 201000 f 74 goat snp35102-scaffold420-281858 7 42649189 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783567 Affx-122958291 AX-385270629 7 64054189 TCCTCTTAATTAAGTGACACTATGTCTGTTAACAA[C/T]AGAAATTATTATGCAGTAAAACATGTAGCTCTGTA Y 2 1 2 1 101000 f 74 goat snp35101-scaffold420-243909 7 42611477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391887 Affx-122966966 AX-123262244 7 64088050 TTACCTTTCAGATGCCAGTATTTTCAAATGTACCT[A/G]CCTGTCCTTAATATTCACAAAATTCTGTTGAGGAG R 2 1 2 1 101000 f 74 goat snp35100-scaffold420-210048 7 42577537 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38385499 Affx-122971269 AX-123255857 7 64150640 ATTAAAACTCTAGTATTGATACTAATAGGAACAAA[C/T]GAGAATAATGATTAGATGTTGGAATATAGGAGGAA Y 2 1 2 1 101000 r 74 goat snp35099-scaffold420-147458 7 42515787 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272364 Affx-1111833769 AX-519546093 7 64161745 GTGTACATGAGTGAGGAGGTGCCTTCCCCTGACCC[A/G]GTGGGCCAGGACCTGTCTGCAGAAGAGACGGAGGC R 2 1 2 1 202000 r 74 goat GoatD01.004022 7 64161745 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38379400 Affx-122976128 AX-123249758 7 64190616 TTCTTCTATTCCTTATCTTAGTTTTTCTAGCTCAG[A/G]CATGAGACCACTGATCAGAATGACCCAGAGGGAAA R 2 1 2 1 201000 f 74 goat snp35098-scaffold420-107482 7 42475620 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450470 Affx-122922941 AX-123320804 7 64247675 CACCACTTCTTAATATTCTGAGAGATGTGATACTG[C/T]ATATAAAGATTAGAAAGCATTTCATTGTTATAAAT Y 2 1 2 1 101000 f 74 goat snp35097-scaffold420-50423 7 42416043 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781856 Affx-122936994 AX-385268938 7 64294925 TTATTTTAAGGTCTTCGCTTATTCCAATATCTGAG[C/T]CATTCCTCAGTCTGCTCCCATCGACAGTTTTTTTC Y 2 1 2 1 101000 r 74 goat snp35096-scaffold420-3173 7 42368839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384934 Affx-122972327 AX-123255292 7 64301578 GGAGGTGCCCCATTTCTCTCTGCCACACCTTCCTG[A/C]ACACCTGTCCTCAAAGGGGGCTCCCCACCTTCTTT M 2 1 2 1 103000 r 74 goat snp29839-scaffold323-3662766 7 42351319 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790035 Affx-122964414 AX-385277041 7 64367960 TTTGGCATAAATAGTGATGATACATCTCTATTTTT[A/G]CCTCTGTGTCTGGCCAGCTGTCCCACCACCATTTA R 2 1 2 1 103000 r 74 goat snp29838-scaffold323-3596384 7 42285218 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388315 Affx-122969373 AX-123258673 7 64433084 CTTGCTCCAGAACATTCAAAACAGAAAATTATGCC[A/G]CACTGAGAAATTGGCACTCATAGAACTTTCCAAAC R 2 1 2 1 201000 r 74 goat snp29836-scaffold323-3531260 7 42218827 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412534 Affx-122951342 AX-123282883 7 64469717 TTAAGAACTGAAGAAAGGCCCATGGGCAAGGGAAC[A/G]TGAGAAGAATAGAGTGGAGGCATGGGGTTGAAAAG R 2 1 2 1 101000 f 74 goat snp29835-scaffold323-3494627 7 42182054 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273336 Affx-1111833549 AX-519546977 7 64535111 TCTCAGAGGAACAATTTGATACTACTGGGGAAACT[A/G]ATAGCAACATCAAGTCAGAAAATAGTTCTTCCGCA R 2 1 2 1 101000 r 74 goat 7_64535111_AF-PAKI 7 64535111 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392016 Affx-122966483 AX-123262373 7 64577002 ATGGATATGGACAGCATTTTTTTATGCCTGTTAAA[C/T]AGCAGAACTGCCACCATGTAAGTGACTGTTGTATT Y 2 1 2 1 202000 f 74 goat snp29833-scaffold323-3387342 7 42074692 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798985 Affx-122964759 AX-385285915 7 64672320 TTGTGCTGGTCAATGTGCACATCTCCCTGGAAAGA[C/T]GTGTGGATGGATAGTTAGGAACACAAATAAGGTCA Y 2 1 2 1 201000 f 74 goat snp29831-scaffold323-3292024 7 41979565 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780133 Affx-122963095 AX-385267230 7 64712817 AAGACTCATAGAAAGTTTCACCCATATAAAACAGG[C/T]AATATAAGGTCCTGTCAAATAGATGTATTATTTGG Y 2 1 2 1 101000 f 74 goat snp29830-scaffold323-3251527 7 41939968 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452954 Affx-122920170 AX-123323287 7 64789847 CAAGTCATGAAAGGGGAACAAAGAAACAAACAAAA[A/G]CTGTGTGCGTTAGAGTCAATACATCCCTTTGCTGA R 2 1 2 1 101000 r 74 goat snp29829-scaffold323-3174497 7 41862430 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785071 Affx-122929283 AX-385272118 7 64830472 TTAGGATGCAGATATGTTGGGAGGGTACCCTTAGA[A/C]GTGACAGAAGTGAATGCTATTTATTTGGTCAATAT M 2 1 2 1 201000 r 74 goat snp29828-scaffold323-3133872 7 41941519 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800849 Affx-122954073 AX-385287764 7 64885849 AAAGTTTCATTTTTTCTCTTGGCTGTTCTTGCAAA[C/T]ACCATCTCAGCCTCTTACCCCTATCCTGGATGGGT Y 2 1 2 1 102000 r 74 goat snp29827-scaffold323-3078495 7 41764891 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447195 Affx-122924995 AX-123317531 7 64950135 TAACCCAAAGAGCTCATTCATGTAAACCTTTCAGA[C/T]GCCCTAAGATCATCAATTAGGGAGACTAATATCTT Y 2 1 2 1 101000 f 74 goat snp29825-scaffold323-3014209 7 41699831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774403 Affx-122942644 AX-385261539 7 64980711 GTGTCTCCACTTTCTAGGCCTCTGATTCTGTACCT[A/G]TAAAATGAAGGACCTAAACTAGTTTACACATAAAA R 2 1 2 1 101000 f 74 goat snp29824-scaffold323-2983633 7 41668670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433905 Affx-122934396 AX-123304246 7 65054018 AGCCCCAAGAGGAGGTGGTTCAAGGACAGGGGCCC[G/T]CTTCATCATGACACAGCAAACTCTTCTCAAGAGAT K 2 1 2 1 101000 r 74 goat snp29823-scaffold323-2910326 7 41595006 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451524 Affx-122921102 AX-123321857 7 65092856 CACAGGCTCAACTCTGGGGTTATGGCTGATGAGAA[C/T]AGTGGTCAAGAAAGCTGAGAACGAGTTGAACCTGA Y 2 1 2 1 101000 r 74 goat snp29822-scaffold323-2871488 7 41556107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378577 Affx-122976594 AX-123248936 7 65138526 CGTAACTGAGAGACTGAGCACAGCACAGCACCCAA[C/T]GGTGAACTGCTGGCTTGCAGGATGGGTGGTTTAAT Y 2 1 2 1 103000 r 74 goat snp29821-scaffold323-2825818 7 41510916 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278511 Affx-1111836463 AX-519551994 7 65140843 AGTGGAGTGACCTAACAGAGGTTACACAGTAGCTG[A/G]GATCGCAGAGCAGTGAAAAGAAAAGGCTTTCTGGA R 2 1 2 1 201000 f 74 goat Random2.2K-810 7 65140843 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403387 Affx-122957777 AX-123273740 7 65182604 TTTGAAAGCTTCACTGGAGAAGAGAAGTTAGAAAA[A/C]CATGGATATTCCACAGGCTGCAATACCAAGACAGG M 2 1 2 1 201000 r 74 goat snp29820-scaffold323-2781740 7 41466475 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378706 Affx-122977057 AX-123249065 7 65273419 ACCCATCATTCAGATTCAGTAAAAATCAAGATGCC[A/G]TGATTAATATAATCACCCATTTTGTTGGGTATTCA R 2 1 2 1 101000 f 74 goat snp29818-scaffold323-2690925 7 41375385 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803075 Affx-986696158 AX-385289946 7 65305401 CTCTTAGGTCCACAAGGTACTGCTTGTTGGTGGCA[A/T]GAAGTTCCTGGGACCGTGGCTCAGGAGTGTCACAA W 4 1 2 1 600010 f 74 goat 7_65305401 7 65305401 Ancestral_priority_1043 ancestry 0.446 neutral IMAGE 10K 10K ancestral 320772730 Affx-122929687 AX-385259876 7 65335219 GATTTCAGAGTGAGCACTTTTACAGACTAGGGGAA[C/T]GGGTACTCTGAGCAGCCATAATAATTTCAGTAATA Y 2 1 2 1 101000 f 74 goat snp29817-scaffold323-2629125 7 41315091 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778338 Affx-122940036 AX-385265453 7 65387187 ACATCAAAGTCCTTGGTTTGCCAGACTAGTAAATA[C/T]TCCATGTCAGACCTTTTAAGCAAATCAGGGTGAGT Y 2 1 2 1 101000 r 74 goat snp29816-scaffold323-2577157 7 41268915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780643 Affx-122963786 AX-385267733 7 65416066 CTGTGTTGAGGGGCAAAGTGGTCTTTGTGGGGTTG[A/C]TGCATAGCTTTCACCACTGTGGTAAAAGAGTCACT M 2 1 2 1 101000 r 74 goat snp29815-scaffold323-2548278 7 41240121 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438770 Affx-122930807 AX-123309107 7 65454685 TGTGATGGTAATATGAATGGGGCAGAACTTGAGGA[A/G]ACATTGGCATATGAAATAACTGCAGATCTCTTTTC R 2 1 2 1 101000 f 74 goat snp29814-scaffold323-2509659 7 41201887 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273502 Affx-1111833637 AX-516000231 7 65469142 CTCCTGGTGTGGCCTACTGCAGAAAACCCCACAG[A/C]GGCAGGCAAACCTGCTTCCTTGCACTTCTGAACAT M 2 1 2 1 102000 r 74 goat GoatD01.000107 7 65469142 A C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38380255 Affx-122975451 AX-123250613 7 65506054 TCCCTGTGGTTTTACACAGGTAGCATTTGGTATAC[A/G]TATTTTAGGATGTGTACATACATATGTGTAGTTAC R 2 1 2 1 303000 f 74 goat snp29813-scaffold323-2458290 7 41150615 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788406 Affx-122920904 AX-385275424 7 65536122 TTCCCTAGCTTCATGACTAGCAGCAATCAATTTCA[C/T]GTCTCCTTTGTGAATCAGTCCTCAATAGAAATTCT Y 2 1 2 1 101000 f 74 goat snp29812-scaffold323-2428222 7 41120631 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424893 Affx-122941316 AX-123295239 7 65595278 TTGTTCCTTACAACATAGGGGGCAGGCAGGTGGGA[C/T]ACATGTCCCCTTTTAGACTGGGGACCTGAGCTTCT Y 2 1 2 1 102000 f 74 goat snp29811-scaffold323-2369066 7 41061294 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773310 Affx-122972250 AX-385260453 7 65628060 GCCTCTGCCATGCCACAGAAATATTAGAACCAGCA[C/T]GAAAGATTATGGATGCTTTCCAATAACTTCCTCTA Y 2 1 2 1 101000 f 74 goat snp29810-scaffold323-2336284 7 41028128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393993 Affx-122965031 AX-123264348 7 65661416 CACTGTTAATATTTTTTAACTAATTTAAATAGCTC[C/T]ATGCTGCTGTCCTAGAGTAAAACCAAATGTGTACA Y 2 1 2 1 101000 r 74 goat snp29809-scaffold323-2302928 7 40994657 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393115 Affx-122965578 AX-123263472 7 65690498 TAATTCCTAAATTATTACTCTGATCCAGCCCTTCC[A/G]TCATGCTGTATTTTTGTTCTTCAAATGTAAATGGA R 2 1 2 1 101000 r 74 goat snp29808-scaffold323-2273846 7 40965440 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791103 Affx-122928219 AX-385278098 7 65759954 AAGGAATTGTGTTAGCCAAGCATGGAAGTATAGTG[C/T]GTGCTCAAAGGATGACAAATGGCTCACTGGAGATG Y 2 1 2 1 101000 r 74 goat snp29806-scaffold323-2204390 7 40896000 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798340 Affx-122952134 AX-385285275 7 65837360 GTAACTAGCTATGTAACCTATTATGTCTTACTCTC[A/G]TTTATAAAATGGGAATGCCAATACTTACTTTGTTC R 2 1 2 1 102000 f 74 goat snp29805-scaffold323-2126984 7 40825409 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389446 Affx-122968348 AX-123259804 7 65907360 ACAGGTAGGTGGTCTGGTTCAGGGGCAGGAGGGGA[G/T]CTCAGAGGCAAAGGATGGGCACAAAGGGGGATGTT K 2 1 2 1 303000 f 74 goat snp29803-scaffold323-2056984 7 40754895 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388301 Affx-122969385 AX-123258659 7 65938381 GCCATTCATCATGCATATTGATCACCAAGGTAGTA[C/T]GGTATGAATCAGAGAGCAGCAATCATTAAATCAAA Y 2 1 2 1 101000 f 74 goat snp29802-scaffold323-2025963 7 40723957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785693 Affx-122930573 AX-385272734 7 65973506 CTGTTGAGATGAATCATGAGCTTAGCCTAGCTAAT[C/T]GGAGAGAATTAAACTGCTGAAGAAGTAGCAGTGAG Y 2 1 2 1 101000 r 74 goat snp29801-scaffold323-1990838 7 40688552 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780035 Affx-122967287 AX-385267134 7 66076884 ATATTTTTCAGAGTTATCACAGGCTTAAAATCATA[C/T]GAAGTCCTGGGCCCATACCTATAACACCTCACCAA Y 2 1 2 1 101000 r 74 goat snp29799-scaffold323-1887460 7 40585125 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786508 Affx-122921256 AX-385273542 7 66181579 ACCCCCAGTGGCTTAATTTGGCTTTACACATGTTT[A/G]TTCAAATCTCACTTCAACAAAATTCACCTTTGCAA R 2 1 2 1 101000 f 74 goat snp29797-scaffold323-1782765 7 40480246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421893 Affx-122944261 AX-123292240 7 66227410 CTGTACAGTAGTTTTGAATACATATTTTTGAATAT[A/G]TAAATGAGGAAATGGGTAATTATTAGTGTTTATCA R 2 1 2 1 101000 r 74 goat snp29796-scaffold323-1736934 7 40434080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404342 Affx-122956996 AX-123274694 7 66273421 TGAGAATTCACCAATACAAAGGGCACACAGAAAAG[C/T]GGAATGAAGATTCAAAGTTGAATGAAACATGGTAC Y 2 1 2 1 101000 r 74 goat snp29795-scaffold323-1690923 7 40388022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417972 Affx-122946689 AX-123288320 7 66314871 GATGGGGGAAATACCACCCCTGGCACTTAGAGCTG[C/T]GTGATGCTGGGCATGTAACCTGACCTCTGGGAGCA Y 2 1 2 1 102000 r 74 goat snp29794-scaffold323-1649473 7 40346716 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375801 Affx-122978567 AX-123246160 7 66408280 GACTCTGAGCTCTCATGTTGGAATGGCACCCAAAG[C/T]GCTGTTCCCTTGATGCTGGGGAACACAACTCTCTT Y 2 1 2 1 101000 f 74 goat snp29792-scaffold323-1556064 7 40252996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780520 Affx-122934044 AX-385267611 7 66455323 ACACTTATTTACAGGCGTAAGAGGTTGATTTTCTT[C/T]CTGCTGTTTCCAAATAATATTAGTTATCTTGCCTG Y 2 1 2 1 101000 f 74 goat snp29791-scaffold323-1509021 7 40206275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766845 Affx-122938231 AX-385254167 7 66490652 CACTTATATGCGATGTTTGGACTCTGTGTGTTTAG[C/T]AGCCCAACTTACAACAATAGAAAATCTTCGCAGCC Y 2 1 2 1 101000 f 74 goat snp29790-scaffold323-1473692 7 40170933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389385 Affx-122968392 AX-123259743 7 66535487 TGGGTGACTTTGGCCATGCCACTTGATCTCTTTGA[G/T]CCTCAGTAGATCAATCCATCAAATGAGAGCAACTA K 2 1 2 1 101000 r 74 goat snp29789-scaffold323-1428857 7 40126215 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768838 Affx-122930110 AX-385256015 7 66566514 CCTTATAGAGATGTTGGGTGAGGGTTAAATCTTTT[C/T]TATTATGAAAGAGAACAGAAACATCATTTACTTGA Y 2 1 2 1 201000 r 74 goat snp29788-scaffold323-1397830 7 40095186 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452490 Affx-122920986 AX-123322823 7 66595612 GCCAAGGTTGTGCTTCCTTCCTTGGGCAGGGTACC[C/T]ACTCTTTCTGAGCACTGGTTTATTCACCTGTCCAA Y 2 1 2 1 101000 r 74 goat snp29787-scaffold323-1368732 7 40066085 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381626 Affx-122974770 AX-123251984 7 66634074 ACTGGGATGTGTATATTAACCTGTCTGTGGGGGGA[C/T]GATGCTGAGAGCAACAGGCCTATAATTTAGGTAAT Y 2 1 2 1 101000 f 74 goat snp29786-scaffold323-1330270 7 40027625 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797101 Affx-122950442 AX-385284041 7 66762744 ATAACACTCAGGAATATTTCTTATTGAGGGCGATA[C/T]GACAGTTGGACGCAGTGATTGTTATCAGGGTGTGT Y 2 1 2 1 101000 r 74 goat snp29784-scaffold323-1201600 7 39899049 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776581 Affx-122951911 AX-385263708 7 66794054 TATGACTCAATCAGATGCATGTTAGCTCTCTTACT[A/G]TACCCTCCTTGTGTCTTACTCTCCTTTAAATGTTT R 2 1 2 1 101000 f 74 goat snp29783-scaffold323-1170290 7 39867618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795671 Affx-122930025 AX-385282626 7 66848470 GTGAGAGGAATCTTGTATGTGTTTCTTAAACCACT[C/T]CATGTAGAAGGTGTTAAGAGGTTTAATGTTGGAAT Y 2 1 2 1 101000 f 74 goat snp29782-scaffold323-1115874 7 39813260 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405895 Affx-122955592 AX-123276247 7 66960369 AGCTTTCATGAAAATATTTTCCTTATTTCAATACA[C/T]ACTCCTCAAAGGTAGATGGAAAAAATCAACATACA Y 2 1 2 1 101000 r 74 goat snp29780-scaffold323-1003975 7 39701833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438203 Affx-122931459 AX-123308541 7 66997261 CACTCAGTGCCTTGCCACATTTTTGTCTTGGCATC[A/G]TTTAACTTTCATGCCTTATCAGGTCTCCCCAGAGT R 2 1 2 1 201000 r 74 goat snp29779-scaffold323-967083 7 39665187 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413032 Affx-122950994 AX-123283381 7 67032126 GGGAAGGGTTAAGAACAGTGTGGAGAGAAGTTGGC[G/T]CTAATGTGTGAAGTACACACACTGGGAAGAATTGA K 2 1 2 1 303000 r 74 goat snp29778-scaffold323-932218 7 39630111 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773049 Affx-122925536 AX-385260193 7 67075668 CCCTTCATTAACCTTGCTTGAATTAAGGAAATGCT[A/G]TTTCCTCAAGGGATCAAGTAAGGTTTACTGAGGAA R 2 1 2 1 201000 r 74 goat snp29777-scaffold323-888676 7 39586855 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789663 Affx-122965750 AX-385276672 7 67135249 AAAAGCAGTATCATCAGAGAAAGTATATATCACTC[C/T]CAAGGTGACACTTTGAAGGAGAAGAATTCACTGGG Y 2 1 2 1 101000 r 74 goat snp29776-scaffold323-829095 7 39529340 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397676 Affx-122962589 AX-123268031 7 67177953 ATCGCTTGGCAGCAGGAACAACATAAGGATGATCA[C/T]AAGGTTCTTAGTATGCAGCCATAGTTCTAAATGCT Y 2 1 2 1 101000 r 74 goat snp29775-scaffold323-786391 7 39486619 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405010 Affx-122956381 AX-123275362 7 67206516 TTAATCTCCACATAAGAAGTTCACCAAATGGAGAA[C/T]GCCACTGATCCTCTCTGCCTGAGCCAATTAGATAT Y 2 1 2 1 201000 f 74 goat snp29774-scaffold323-757828 7 39458044 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376162 Affx-122978844 AX-123246521 7 67306059 AACATGGTATGCTAAAGACAGGAAGCGGGTCAGGG[C/T]TGCTGGAGAATAAAATGCCCAGCAATGAGGGTAGG Y 2 1 2 1 201000 r 74 goat snp29772-scaffold323-658285 7 39356185 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434198 Affx-122934863 AX-123304539 7 67341239 GGATGAAGGAAGAAGAGAACAGGGACAGAAAAGTA[C/T]GATAAAAGCCCTGAGGTCATGGTTGGGTTGGGAAA Y 2 1 2 1 101000 f 74 goat snp29771-scaffold323-623105 7 39323222 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442330 Affx-122928052 AX-123312667 7 67377900 TTTTCCAAGGTAAGAAATGCCTCATTTCTTGGTGG[C/T]GGACACAGGTGAGGAAACTCTTAAACATGCCTCCT Y 2 1 2 1 202000 r 74 goat snp29770-scaffold323-586444 7 39286451 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376342 Affx-122978337 AX-123246701 7 67458963 CAGAACTCTTCAGGCTGGATTTAAAAGGGAGACTT[A/C]TACAGGTGTGGATCTTTGAATTCTAAATCCCCAAG M 2 1 2 1 101000 r 74 goat snp29768-scaffold323-505381 7 39204461 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417976 Affx-122946685 AX-123288324 7 67491317 GGGTCAGCAAAAGGAAATGAAAGTGTCACAGTTTA[C/T]GGGCATTTTAGAAATTGTTAGCCCAGGGATAATAG Y 2 1 2 1 101000 f 74 goat snp29767-scaffold323-473027 7 39172361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399983 Affx-122960819 AX-123270338 7 67606954 CCAGTGATTCCATTTCTCGGAATTTATCCTGAGTA[C/T]GTGGGCACAGACACAGAGACAAGAGTCCTCATTGC Y 2 1 2 1 101000 f 74 goat snp29765-scaffold323-357390 7 39055127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451981 Affx-122920936 AX-123322314 7 67645199 ATTTACTATCCCATTGACTGTGTAATGAGTGTGAT[A/G]TTTTCCCCACATCTCCACAACTTTGTGGTGTGGTC R 2 1 2 1 101000 r 74 goat snp29764-scaffold323-319145 7 39016499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405441 Affx-122956051 AX-123275793 7 67682084 GCTAGAGGCGAAGGCTGGGAGACTGGGGATGAAGG[A/C]AGGCACTACTGAGCCGAAAGGAAGAAGCACTCCAT M 2 1 2 1 101000 r 74 goat snp29763-scaffold323-282260 7 38979863 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765136 Affx-122934613 AX-385252692 7 67827391 CTATATTCGTTACTGTCATTCTGGATAGGGGGTTC[C/T]TTCTGAAGATCCTAACTTCGTAAGACATGCGTCTG Y 2 1 2 1 101000 f 74 goat snp29760-scaffold323-136953 7 38834685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394749 Affx-122964854 AX-123265104 7 67883046 AGCCCATGCCTCTAAAGCCAGCTTCCCAGAGGCCC[G/T]CCTCTCAGGGCAGAAGAACATCCTCTATTTTATGT K 2 1 2 1 101000 r 74 goat snp29759-scaffold323-81298 7 38779102 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384086 Affx-122972851 AX-123254444 7 67928183 AAGTGTGTATATAGAGAAAGAAAAGGTGAGTAACA[A/G]CTAATGAGTCTGGGCGAAGGCTATTTGGAGCTCTC R 2 1 2 1 101000 r 74 goat snp29758-scaffold323-36161 7 38734601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409906 Affx-122952891 AX-123280257 7 67960735 CCTAAGGTTTTGGAGAGAAAAGTGACTACAATCTA[C/T]GTGCAGAAAGGCTGTAAATGGTTTTACCTGAGCCT Y 2 1 2 1 101000 r 74 goat snp29757-scaffold323-3609 7 38702257 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429486 Affx-122937875 AX-123299828 7 67976068 GACCACTGAACAGCTGGGGAAGTCCCTTCATGGTG[A/C]GGTCTTTAAGTGGCATCGCTATCAACAGGGATCTT M 2 1 2 1 101000 r 74 goat snp41452-scaffold54-11625 7 38687294 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273998 Affx-1111833974 AX-519547604 7 67985880 TCCATTCTTGTCTGTATTCTGCAGACCTAAGTGAC[A/G]CTT R 2 1 2 1 101000 f 74 goat GoatD01.012461 7 67985880 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320780812 Affx-122926204 AX-385267901 7 68007612 ACTATTATAACTATAGTTTACTGCTAAGCTAAGCA[C/T]GATACTATAATTATACTTCCTTTGTTATATACATT Y 2 1 2 1 201000 r 74 goat snp41453-scaffold54-43169 7 38655666 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376010 Affx-122978408 AX-123246369 7 68056206 GAAAAGCCAGTGAACTGTTAAAAGTCAATGTACTC[A/G]TGTCAGGGGTTTTAAACAGGCTGTTTTCACCCATC R 2 1 2 1 101000 f 74 goat snp41454-scaffold54-91763 7 38606788 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384070 Affx-122972864 AX-123254428 7 68194794 TGATTTTATTGGCCTGAGTGCTGCCCAGGCATGAA[C/T]ATTTTTAAAAAGGTCTTCAGGTGATTTTAATGTGC Y 2 1 2 1 101000 f 74 goat snp41457-scaffold54-230351 7 38468667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428251 Affx-122939417 AX-123298594 7 68223723 TCAACTGGGGTTTTGCATTTTTAACAAGCTTTCTT[C/T]ATTAGTCATTATCTAGTCAGAGAAATAGCAATGTC Y 2 1 2 1 201000 r 74 goat snp41458-scaffold54-259280 7 38440423 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476234 Affx-1251763740 AX-586011658 7 68252186 ATGAAAACATGCTCAACATTGCTCATTATTAAAGC[-/AGTGCTAGAGGAACTGTAAAGATGGCGGAGGAATAGGACGTTTAAAATTAAAAATAAATAAAATAAAAAAAATAAAGCAG]TGCTAATCAAAACTGGAATGAGATCACCTCACATC - 8 1 4 1 20000 f 74 goat SV_313 7 68252186 - deletion junction SV-TF-chip 539476487 Affx-1251763740 AX-586011885 7 68252186 ATGAAAACATGCTCAACATTGCTCATTATTAAAGC[-/AGTGCTAGAGGAACTGTAAAGATGGCGGAGGAATAGGACGTTTAAAATTAAAAATAAATAAAATAAAAAAAATAAAGCAG]TGCTAATCAAAACTGGAATGAGATCACCTCACATC - 8 1 4 1 20000 r 74 goat SV_313 7 68252186 - deletion junction SV-TF-chip 562165045 Affx-1251763740 AX-606940458 7 68252186 ATGAAAACATGCTCAACATTGCTCATTATTAAAGC[-/AGTGCTAGAGGAACTGTAAAGATGGCGGAGGAATAGGACGTTTAAAATTAAAAATAAATAAAATAAAAAAAATAAAGCAG]TGCTAATCAAAACTGGAATGAGATCACCTCACATC - 8 1 4 1 20100 f 74 goat SV_313 7 68252186 - deletion junction SV-TF-chip 562165585 Affx-1251763740 AX-606940996 7 68252186 ATGAAAACATGCTCAACATTGCTCATTATTAAAGC[-/AGTGCTAGAGGAACTGTAAAGATGGCGGAGGAATAGGACGTTTAAAATTAAAAATAAATAAAATAAAAAAAATAAAGCAG]TGCTAATCAAAACTGGAATGAGATCACCTCACATC - 8 1 4 1 20100 r 74 goat SV_313 7 68252186 - deletion junction SV-TF-chip 562165682 Affx-1251763740 AX-606941091 7 68252186 ATGAAAACATGCTCAACATTGCTCATTATTAAAGC[-/AGTGCTAGAGGAACTGTAAAGATGGCGGAGGAATAGGACGTTTAAAATTAAAAATAAATAAAATAAAAAAAATAAAGCAG]TGCTAATCAAAACTGGAATGAGATCACCTCACATC - 8 1 4 1 20100 f 74 goat SV_313 7 68252186 - deletion junction SV-TF-chip 562166152 Affx-1251763740 AX-606941560 7 68252186 ATGAAAACATGCTCAACATTGCTCATTATTAAAGC[-/AGTGCTAGAGGAACTGTAAAGATGGCGGAGGAATAGGACGTTTAAAATTAAAAATAAATAAAATAAAAAAAATAAAGCAG]TGCTAATCAAAACTGGAATGAGATCACCTCACATC - 8 1 4 1 20100 r 74 goat SV_313 7 68252186 - deletion junction SV-TF-chip 562166252 Affx-1251763740 AX-606941660 7 68252186 ATGAAAACATGCTCAACATTGCTCATTATTAAAGC[-/AGTGCTAGAGGAACTGTAAAGATGGCGGAGGAATAGGACGTTTAAAATTAAAAATAAATAAAATAAAAAAAATAAAGCAG]TGCTAATCAAAACTGGAATGAGATCACCTCACATC - 8 1 4 1 20100 r 74 goat SV_313 7 68252186 - deletion junction SV-TF-chip 320781801 Affx-122939911 AX-385268883 7 68253960 CTCTGTGTGAGCTTTCAGATCATGCTGACTTTGGC[A/G]CTGCTCTTGCCGCACCTTAGCTGTTGGTATGCCTG R 2 1 2 1 101000 f 74 goat snp41459-scaffold54-289517 7 38409990 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453229 Affx-122920425 AX-123323562 7 68297740 TAGGGGATAAAGAAACAGACGAGGCTCTGGTAGAA[C/T]GCATCCGCCATGGAGATCCAGAAAGTCAGCAGGTT Y 2 1 2 1 101000 f 74 goat snp41460-scaffold54-333297 7 38365514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436441 Affx-122933000 AX-123306779 7 68329491 TAGAGAGTAGTAGGAACTGTGACCAACCCCGGAAC[A/G]CAGAAGAATGTATTCCTTAGCAGGAATCTGCTGCT R 2 1 2 1 101000 r 74 goat snp41461-scaffold54-365048 7 38333916 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441226 Affx-122929513 AX-123311563 7 68361519 GTAGTTAAGACAGATGATTCACATGCTGGTGAAAA[C/T]ACACAAGCAAACAAGGTCATTACAGTTGGTGATAA Y 2 1 2 1 101000 f 74 goat snp41462-scaffold54-397076 7 38301791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278693 Affx-1111836464 AX-519552171 7 68389467 GCAGTTGTTTCTTTCCTCTAATTCTTTACTCCCCT[A/G]TAGCACTAGCAGAGTAGAGAGTAGATGTCCCTTGT R 2 1 2 1 101000 r 74 goat Random2.2K-813 7 68389467 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376502 Affx-122978021 AX-123246861 7 68397216 TTTAAAGGAGAAGGGGACCATATATTCATATTAAC[A/G]TCATATTCTTTATAAACTTCACTTCCCAGAATACC R 2 1 2 1 101000 r 74 goat snp41463-scaffold54-432773 7 38265710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388681 Affx-122969003 AX-123259039 7 68458023 ATGTCAGAGAGACTAACAACATGATCTAGGGTGGA[C/T]GCTTTGGGTCATGTAGTGTCAGCTCAGTGTCCAGA Y 2 1 2 1 101000 f 74 goat snp41464-scaffold54-493580 7 38203967 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395999 Affx-122963496 AX-123266354 7 68502307 GCCACTTAGCAAGGAGTGGAACGGTAAAAAGAAGC[A/G]CTGAAACCACCTCATTCTCATGTTCAATAGCGTTT R 2 1 2 1 101000 f 74 goat snp41465-scaffold54-537864 7 38159730 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773650 Affx-122948513 AX-385260790 7 68548520 GAAAAGAGATAGTTTAAACTGTTAATTCCATTTTC[A/G]TTAGTGGTTAAGATCTTTCATTGTATATTAGGATT R 2 1 2 1 101000 f 74 goat snp41466-scaffold54-584077 7 38114130 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434927 Affx-122934308 AX-123305267 7 68589464 CAGATTCCTCATGACTTGAGTTTTTATTTTACCAA[C/T]GTGGCTCATCCACTCTCAATATTATTCTCAAGCAT Y 2 1 2 1 101000 r 74 goat snp41467-scaffold54-625021 7 38073018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411244 Affx-122952336 AX-123281594 7 68622822 GCAAAACTCCTAGGCATCTAGGATAGTACCTGGAA[C/T]GCAGCAGTTGCTCAAATATTTGTTTAATGTATTGA Y 2 1 2 1 101000 f 74 goat snp41468-scaffold54-658379 7 38039176 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433029 Affx-122935773 AX-123303370 7 68677696 GCTCCTTCAATAACCTTTCCCACTTTGGAAAAATC[A/G]TATCCATCCTTCCAATTTCTCAGATTGAAAACTGG R 2 1 2 1 101000 r 74 goat snp41469-scaffold54-713253 7 37985584 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765202 Affx-122962075 AX-385252742 7 68707850 TGATCTTGTGCTAAGCCCTTCTTAGGGATCATCTC[A/G]TTTAATCATAACAACAACTGTATAATGTAAAATCT R 2 1 2 1 101000 f 74 goat snp41470-scaffold54-743407 7 37956159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408987 Affx-122953902 AX-123279338 7 68744476 GTAAAAGAAGAACATTTCTCTGACTTTATCCTCAT[A/G]CCTCTCTGATAGGAGATGTTTTGTTTGTGATGTAT R 2 1 2 1 101000 r 74 goat snp41471-scaffold54-780033 7 37919235 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769963 Affx-122970684 AX-385257132 7 68780333 TCAATCACATGGCTTCAGGCCAGGATGTAGTAAAC[A/G]TTCAACAAAGGGCCTTGGTATCATTTAATATCTAA R 2 1 2 1 101000 f 74 goat snp41472-scaffold54-815890 7 37883169 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798642 Affx-122921849 AX-385285574 7 68824383 GACACTTCTGTGGGCTTAATAAACACTGATATTTT[A/G]CTAGCCCATGCCCATTTTCTGCCACGTTCTCCCTT R 2 1 2 1 101000 f 74 goat snp41473-scaffold54-859940 7 37838830 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278515 Affx-1111836465 AX-519551998 7 68835875 CCTACTTCCTTAGTCTTCTAATATGAAAAGACGGT[A/G]TTGGGGATTTTCTATGGTGTTTATCCATTAGCACT R 2 1 2 1 101000 f 74 goat Random2.2K-814 7 68835875 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320767669 Affx-122939839 AX-385254909 7 68865794 CTAGAAAAAGTTCATTACATTGGTCCTTGGGCACT[A/G]TAATATCGCCATTCTTTATTTTCCAATTACTTTCT R 2 1 2 1 101000 f 74 goat snp41474-scaffold54-901351 7 37798852 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775861 Affx-122940111 AX-385262992 7 68901902 GAAAGGAGATTTAATTGTACACCTCACTGATGCTA[C/T]GAGAGACCATCAGAGGTATTTTAGAGGTCTTCTAA Y 2 1 2 1 101000 r 74 goat snp41475-scaffold54-937459 7 37762552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772609 Affx-122968604 AX-385259757 7 68937530 AATAAATGACTGCATAGATGAGTAAAAGGCAATAA[A/G]ACTGTAGGAATAAAACTATATTTGGCTTGTGTCAA R 2 1 2 1 101000 r 74 goat snp41476-scaffold54-973087 7 37726772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402248 Affx-122959135 AX-123272601 7 68992401 AGAGGGTAGGCACTCAGTGTGGGAGCCCCTCTTAG[C/T]ATTACTGCGGATCTCTCACCGCTGAGATAGCGAAC Y 2 1 2 1 101000 r 74 goat snp41477-scaffold54-1027958 7 37669744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430578 Affx-122937001 AX-123300919 7 69047083 TATACACCACGTAACTGGTAATTCACAATTTCCAA[C/T]ACATTTTAAAATAATACCATAGAGGACATTTGGTT Y 2 1 2 1 201000 f 74 goat snp41478-scaffold54-1082640 7 37615117 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436737 Affx-122932298 AX-123307075 7 69080315 CTGATTACGAATCTCATTCTCTCAAACATTATCAC[A/G]TTATCACTTAGCCTTGGTACTCTGAGAAGAAAAGA R 2 1 2 1 101000 f 74 goat snp41479-scaffold54-1115872 7 37581510 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451602 Affx-122921638 AX-123321935 7 69115019 TGTTTCTTAGCCATGGCATGGTCAGAAACTTTCTC[A/G]GAAGTACATTTTCAGAATGACCTTGATGTTAAAAG R 2 1 2 1 101000 f 74 goat snp41480-scaffold54-1150576 7 37546080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442890 Affx-122927651 AX-123313227 7 69187547 AAAGTAACAGAGAAATAAAGCCTCTTCTTTGTCTT[A/G]AGATGTCTATGACTTTTGCAATAAAATAAACTAAA R 2 1 2 1 101000 f 74 goat snp41482-scaffold54-1223104 7 37473692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770933 Affx-122970815 AX-385258096 7 69217916 TCCTACTGGAGGTGTCATTTATATTGAGACTTATC[A/G]CATATAGCTTCCTACCTATCTAAACAATATAAGTT R 2 1 2 1 101000 f 74 goat snp41483-scaffold54-1253473 7 37442366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391571 Affx-122966618 AX-123261928 7 69263913 AAGGGAGGGGATTCATTATAACTCACATGCAAAAA[C/T]AGGTCAACAGCAAAATTATTTACAGTTCCAGCATA Y 2 1 2 1 101000 f 74 goat snp41484-scaffold54-1299470 7 37396090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793668 Affx-122972240 AX-385280641 7 69317805 CTCACCTCCTTCTTCAGGCAATTAAGATCACTCTT[A/G]TCTCTAGAGTGAGCCTTAGGTCCAATGTAAGAATG R 2 1 2 1 101000 f 74 goat snp41485-scaffold54-1353362 7 37341865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762573 Affx-986697103 AX-385250671 7 69347227 TGCAACTGGTATTTCTATATTGTACCACAGACTGA[A/T]TGAGCAGGCACAACATCTTTCTGAGCTGTTGCAGA W 4 1 2 1 600010 f 74 goat 7_69347227 7 69347227 Ancestral_priority_1043 ancestry 0.714 recommended IMAGE 10K 10K ancestral 320783179 Affx-122950824 AX-385270246 7 69366930 CTGGAAGCACCAAGGACATACTGTTTTATGAAATG[C/T]GGACAACTAGAAATTCTTATGGAGTGAGCCTTGTA Y 2 1 2 1 101000 r 74 goat snp41486-scaffold54-1402487 7 37292943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775902 Affx-122923068 AX-385263033 7 69403829 GTAGATTAGAAGATGAAAACTGTGTCACTTATAAA[C/T]GACAATTTTGCACAGTCAATTAAACAAAAGCACTG Y 2 1 2 1 102000 r 74 goat snp41487-scaffold54-1439386 7 37256211 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404828 Affx-122956639 AX-123275180 7 69438060 TATTTTTATCTCCAATGTTCCAGACGTGATTCTAA[C/T]GAGCAACTATGTTTAAAAACAACTGGAAAGTATTT Y 2 1 2 1 101000 f 74 goat snp41488-scaffold54-1473617 7 37221874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448881 Affx-122923265 AX-123319216 7 69492332 GGCACAAGTGGTCAAGTGATTTTCTGAAGTTTCCA[G/T]AGGGAGTCAGTAGGGATTTGTGTAGAACTGAACTT K 2 1 2 1 101000 f 74 goat snp41489-scaffold54-1527889 7 37167355 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772981 Affx-122955999 AX-385260125 7 69523066 TTCCACCTGGCCTGAACAATGTAACCTGTTTTAAT[A/G]TTAAGCCTTTATAGACACCTTAGATTAATACAGGA R 2 1 2 1 101000 f 74 goat snp41490-scaffold54-1558623 7 37135733 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389930 Affx-122968099 AX-123260287 7 69554022 AGCAAGTGTCTTTTCTAATTCAGAAATTCAAATGT[A/G]TTATGGTACTTGCTTGCTTTCAAACTTTCTGCCAT R 2 1 2 1 101000 r 74 goat snp57743-scaffold93-1315337 7 37104066 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782293 Affx-122957302 AX-385269371 7 69687414 ATCACTGGATAGCAGCTTTTTGAGACAAACATTGC[G/T]CAAAACTTGGGTATGGATCCCAATTGTCTTATTTG K 2 1 2 1 201000 r 74 goat snp57741-scaffold93-1181945 7 36970910 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783731 Affx-122959935 AX-385270787 7 69741551 CATTCATTTAGTTATTTGTCACCTTGGAAAAGACC[G/T]ACCTGATTGGTTATAACTGAGAATGAGGTTTTCTT K 2 1 2 1 101000 f 74 goat snp57740-scaffold93-1127808 7 36916637 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402407 Affx-122959010 AX-123272760 7 69772851 TCTATGGGGTCGCACAGAGTCGGACACAACTGAAG[C/T]GACTTAGCAGCAGCAGTCCTCATTAGCAGTAAGAA Y 2 1 2 1 303000 f 74 goat snp57739-scaffold93-1096508 7 36884764 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428470 Affx-122938794 AX-123298813 7 69804872 AACATTACCACCAAATTTCATTTTCTGAAGGCTTC[A/G]CAGCACAAGCTTGGGTTGATGCTGAATGGAACACA R 2 1 2 1 201000 r 74 goat snp57738-scaffold93-1064487 7 36852817 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415629 Affx-122948587 AX-123285978 7 69838167 AATTCTCAAGGTTCCCAGGGGGGAGGAAGGAGGAA[G/T]AGGGTTAGCTTCACAGAACCCATCCAACTCCCCCG K 2 1 2 1 103000 r 74 goat snp57737-scaffold93-1031192 7 36819472 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788424 Affx-122926392 AX-385275441 7 69873424 ACAGTGCAAATAAAAATAGTGCAGTGACTAAGAGC[A/G]TGAGTCTGAAAGCAAACCGCCTGAATTCATGTCCC R 2 1 2 1 101000 f 74 goat snp57736-scaffold93-995935 7 36783956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448846 Affx-122923291 AX-123319182 7 69915319 TGATCGCCAAGAGAAAGAATAAAGCTGAGGAATGA[C/T]AAGGCTAAATATCAAGATATTTATAAATTAGAGTA Y 2 1 2 1 101000 f 74 goat snp57735-scaffold93-954040 7 36742044 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413006 Affx-122951012 AX-123283355 7 69948145 GAGTAATCACAGAGGGACCTGCCGTGGACCAGGCA[A/C]TGTACTGGGAGTGAGGGAGACATTGATTGATACCC M 2 1 2 1 101000 r 74 goat snp57734-scaffold93-921214 7 36709918 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273338 Affx-1111833550 AX-519546978 7 70083946 CATATGTTGGAAGTTTATCTCAACTGTAAGAACCG[A/G]ACAACTGACTGATAGCTACTAGCAACATACTTCTG R 2 1 2 1 101000 r 74 goat 7_70083946_AF-PAKI 7 70083946 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38408420 Affx-122954466 AX-123278771 7 70106166 TCTTCATTTATTTGCAAGAGCAAAATATCTAGTCT[A/G]TTAGATCCTAATGTTTTGTCTTGTTTTGGTGGATC R 2 1 2 1 303000 f 74 goat snp57730-scaffold93-763193 7 36550271 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803077 Affx-986696159 AX-385289948 7 70129101 CCAAGGGTGAAAGGGAAGTTTCTTATACCTAACAC[A/G]GCATTCAGAAGGGACTGAATGATTTCACAGGCAGA R 2 1 2 1 600010 f 74 goat 7_70129101 7 70129101 Ancestral_priority_1043 ancestry 0.692 recommended IMAGE 10K 10K ancestral 38446432 Affx-122925977 AX-123316768 7 70155147 TCAAAACACATATTTCTACCAGCCCTCTTAAAATG[C/T]ATTTTATTGTGTGGCCCTTAGGTAATATGATATGA Y 2 1 2 1 101000 r 74 goat snp57729-scaffold93-714212 7 36501176 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414157 Affx-122949688 AX-123284506 7 70183743 ATCAATGCCCTCTAGCCAAAGACCTCCTGGAACAT[A/G]CCTGTAGCTGAACAAATTGGACCTATTATTCATTT R 2 1 2 1 201000 r 74 goat snp57728-scaffold93-685616 7 36472968 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767703 Affx-122919610 AX-385254940 7 70241349 ATCGTTCCCTTGGCCATCTGAAATGTCACTTTTAT[A/G]CTAATTTACATCTTATACTTACTTGAATCTAAATT R 2 1 2 1 101000 f 74 goat snp57727-scaffold93-628010 7 36414414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278517 Affx-1111836466 AX-519552000 7 70266408 AGGACTAAATTTACCTCAAAGTAATAAATTTCCAA[A/G]AGTGAGGGAAAAAAAAAAAAAAAAACACCTCAGGA R 2 1 2 1 101000 f 74 goat Random2.2K-816 7 70266408 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431165 Affx-122937194 AX-123301506 7 70305148 TTCCAAATACATAGTCACAACCTGAAAATGCTTTA[C/T]AGTAGACTGGATTCGATAGAAGTAAATGTTCTTCA Y 2 1 2 1 101000 r 74 goat snp57725-scaffold93-564211 7 36349850 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395130 Affx-122964138 AX-123265485 7 70333768 TGCATTTATAAGACTAATATCATTGAAATAAATAT[A/G]TGGATAAAATTCATGCCTCCTTTGCAAACTATTCT R 2 1 2 1 101000 r 74 goat snp57724-scaffold93-535591 7 36320939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784834 Affx-122949082 AX-385271881 7 70366708 GTAACTTGCAAAATTTAACATTTTCATACACAAAC[A/G]CACACACTTAAGACATCATATAAGAGTTCAAATTC R 2 1 2 1 201000 f 74 goat snp57723-scaffold93-502651 7 36288538 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774576 Affx-122944950 AX-385261710 7 70397926 ACTGAGAATGAGATTCACGTTGGCTATGGGAAGTA[C/T]GTATGGATATATCTTGCCATTTACCAGCTTCATAA Y 2 1 2 1 201000 r 74 goat snp57722-scaffold93-471433 7 36257418 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385839 Affx-122971006 AX-123256197 7 70545136 GGCCATTGACTGCTGTTTTTAGAGTGCCATTTCCC[A/G]TGGGCAAAACACAAAAAGAAAATTGTGCTTACAAA R 2 1 2 1 101000 f 74 goat snp57719-scaffold93-324223 7 36119738 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785454 Affx-122931532 AX-385272499 7 70592657 TAATATTGAATGAAAAAATACTGTTTAGCTAGCAT[A/G]TATTCGACATTTGCTGTATTTCAGGTGCTTTTCTG R 2 1 2 1 101000 r 74 goat snp57718-scaffold93-276702 7 36071173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787905 Affx-122930625 AX-385274927 7 70627615 CACTGAATATGGATTAAAGTTTTAGATCTTTCAGT[C/T]TTCTGTGTCCTGGTCTGTATCTACTTCTCAGGCAC Y 2 1 2 1 101000 r 74 goat snp57717-scaffold93-241744 7 36036330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783572 Affx-122962238 AX-385270634 7 70658566 GGAAGTGGGAATTAAGGTCACTATTTAAAATGATC[A/G]TCTGGCCCAACATGGCTTACATACACATTAATGTG R 2 1 2 1 101000 r 74 goat snp57716-scaffold93-210793 7 35997456 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449636 Affx-122922594 AX-123319971 7 70802329 ACTGTATCCCACGTGCTTTGTTAGTTTGGGTTATC[A/G]CTCATAACTTTCTTACTCCTATTGTTGCTATTCCT R 2 1 2 1 201000 r 74 goat snp57713-scaffold93-67030 7 35852438 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405747 Affx-122956507 AX-123276099 7 70948048 TTCACTCAGCTATTGCAGGGAGAAGCACAGCGGCC[A/G]TAGACAAAGTGTCCATGGTTGGCTTTGCTAACCGA R 2 1 2 1 101000 r 74 goat snp22328-scaffold2204-799526 7 35698383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274150 Affx-1111834072 AX-519547752 7 71041782 GGTGCAGCTGGGAATGGATGGAACTACAGGCTTTG[A/G]GGGTGTGAGGAGGGGCTCCTGGGCTTTCCCAGGCA R 2 1 2 1 201000 f 74 goat GoatD01.017144 7 71041782 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38404461 Affx-122956738 AX-123274813 7 71052597 AGGAGTCATAAATCTCACTGCCTGTCAGAATCCCC[A/G]CAATTCACAGAGGGTTATTTCAACATCATTATGCA R 2 1 2 1 201000 r 74 goat snp22326-scaffold2204-694977 7 35591650 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392493 Affx-122966135 AX-123262850 7 71134048 ATGGGTTATTGGGCAGAGACTCTTACAAGTCTGAA[G/T]CAAAGTCCTAGAATGACAGCCCACTGTGTACAGCC K 2 1 2 1 101000 f 74 goat snp22324-scaffold2204-613526 7 35511181 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417067 Affx-122947510 AX-123287415 7 71181062 CTTACTGTTCCCGGCACAGTGCCTGACGTATCATA[A/G]GACCTCAGTGTGCTTGTTACTCAAAGCATTGCTCA R 2 1 2 1 101000 r 74 goat snp22323-scaffold2204-566512 7 35465909 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445203 Affx-122925520 AX-123315540 7 71219485 GCATAAGATATTCCAGGCTTATTATGCTTTCCCTA[C/T]CCTTGGCCAAGAATCAGCCATTTTTCTGGAGTCCT Y 2 1 2 1 201000 f 74 goat snp22322-scaffold2204-528089 7 35426920 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450647 Affx-122921979 AX-123320981 7 71260264 TTAAAGTAGTGGCAAGAACAAGCCAAGATATTTTA[A/G]CCTAGCATAAGAGGTTCGGACTAGAAAAGGTATCC R 2 1 2 1 101000 r 74 goat snp22321-scaffold2204-487310 7 35385960 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418544 Affx-122946404 AX-123288892 7 71345305 AAGGATCCAGAGAATGACAAGCTTATTAGGAACTC[A/G]CAGTGGGTGATAGCTATTGGGAAAGCTATTAGGAA R 2 1 2 1 101000 r 74 goat snp22319-scaffold2204-402269 7 35301052 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394904 Affx-122964327 AX-123265259 7 71398055 AGCGATCAGACAGAGATGTCTACACAGACAGGGAA[C/T]GGTGACATATTAGTGGTAGAATACATTCCATATAT Y 2 1 2 1 101000 f 74 goat snp22318-scaffold2204-349519 7 35248108 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779467 Affx-122941089 AX-385266570 7 71463134 TTAACTGCCTGTTCATCAGCTTCCCAGAATCTAAG[C/T]ACTTATCTGGTGCCTTCCGCTTTGGCAAGGGAAAG Y 2 1 2 1 101000 f 74 goat snp22316-scaffold2204-284440 7 35183275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427979 Affx-122939182 AX-123298322 7 71495847 TTTACAAGAATATGGCTCTGCTAGAGTTCTGAGAT[G/T]TTCTGTGTGCCTTAAAAGAGACAGAAGAACATGAG K 2 1 2 1 101000 f 74 goat snp22315-scaffold2204-251727 7 35150726 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441783 Affx-122929095 AX-123312120 7 71525169 TTTTAAACTTCCCACAACCACAAACTAAAAGACAC[A/G]TTTTAGGAATTTCAGGGCTGACAGTATATTACAGA R 2 1 2 1 201000 r 74 goat snp22314-scaffold2204-222405 7 35121656 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382977 Affx-122973350 AX-123253335 7 71554457 AGTGACTCATAGCTAGTGACTATGATGTCAGACAT[A/G]TTTATAATAGTCTCCTAGTCTCAGAAATTTCTATT R 2 1 2 1 201000 r 74 goat snp22313-scaffold2204-193117 7 35092362 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796652 Affx-122946517 AX-385283598 7 71584990 TTGGATCTTTCATGCCATGGAAAGCATAGGATTCT[A/C]GGTTTAAGGGCAGCAAGTAGTGAGAATTTCCACTG M 2 1 2 1 101000 r 74 goat snp22312-scaffold2204-162584 7 35061812 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399187 Affx-122960624 AX-123269542 7 71616396 GAAAGGAAATGAACATCTTTTCATTTACAAAACTT[A/C]TCTGAGCTTACTATGATGTTAAAGCTTGGGTTTCA M 2 1 2 1 101000 r 74 goat snp22311-scaffold2204-131178 7 35030199 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381171 Affx-122975209 AX-123251529 7 71662527 ATTCCTTTACACATTTCAGTCACCCATTAAGAATG[A/C]TGAAAGCCCTTGGAAAATATCCTTTGAATCATAGC M 2 1 2 1 101000 f 74 goat snp22310-scaffold2204-85047 7 34983658 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429143 Affx-122937993 AX-123299485 7 71692108 AAGGCTGACTCGCATTATGGTATGGCAGAAGCCAA[C/T]GCAACACTGTAAAGCAAGTTTCCTCCCGTTAAAAA Y 2 1 2 1 101000 f 74 goat snp22309-scaffold2204-55466 7 34954076 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774734 Affx-122945251 AX-385261868 7 71776420 ATTTGTAGACCAACCTAGCACATTCTGCTTGCCAT[A/G]TTTGTGTCAACACCCCATGACCTTGCTTAGTTGGG R 2 1 2 1 101000 f 74 goat snp18522-scaffold1870-28747 7 34870890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428264 Affx-122939408 AX-123298607 7 71805882 GTTTATAGAGAATTTCTGTGACTGCCCAACAAATA[C/T]GCAGGCTCTCTCCACCCCATGATGACCTTCCATTC Y 2 1 2 1 101000 f 74 goat snp18523-scaffold1870-58209 7 34841788 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426957 Affx-122940409 AX-123297302 7 71862558 TTCAGTTATTTTCTTTTCCTTCCTTCCTTTTGTCA[C/T]GTACTGAGTATGACCTCTCCTGTTAGTTTTTTTAG Y 2 1 2 1 201000 r 74 goat snp18524-scaffold1870-114885 7 34788038 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803342 Affx-122949359 AX-385290178 7 71896335 GAGCAAAGATATGCATTATAGCAAATTATAATGAT[A/G]CAATGAAATATAGCACACAAGAGCACACTTGACAG R 2 1 2 1 101000 r 74 goat snp18525-scaffold1870-148662 7 34755883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451479 Affx-122921135 AX-123321812 7 71925317 TAAAAAGTTCTCAGTCAAAATAGGAGAAGCAATGC[A/G]TCAATAAAACTAGGATAGAGTTTGGGATAGGGAGA R 2 1 2 1 101000 r 74 goat snp18526-scaffold1870-177644 7 34727139 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800174 Affx-122919665 AX-385287097 7 71966616 AAAAATGATAAACTTTCTGAAGCCTACAGGCTATG[A/C]TGAGAGAGCTGGTACTATACTTTTACACATACAGA M 2 1 2 1 101000 f 74 goat snp18527-scaffold1870-218943 7 34684510 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396659 Affx-122962852 AX-123267014 7 71998856 AGTCAGGGGTTCCTCTGCAGGCTTAGATTAAGAGA[C/T]AGTTAGGAATGGGCATGTAATCAACAGGAGATGTG Y 2 1 2 1 101000 r 74 goat snp18528-scaffold1870-251183 7 34651854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762539 Affx-986697069 AX-385250646 7 72028240 CCCGCCTCCCTTACGTTGCTAGTTTTCTTGTAGTA[A/G]TCAATGTGGTGGATGCCACGGGCCAGCCCGAAGTC R 2 1 2 1 600010 f 74 goat 7_72028240 7 72028240 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 320764865 Affx-986697076 AX-385252463 7 72028282 TGGTGGATGCCACGGGCCAGCCCGAAGTCTGCAAT[C/T]TTCATCACGTTGTCCTCGGTCACCAGCACATTGCG Y 2 1 2 1 600010 r 74 goat 7_72028282 7 72028282 Ancestral_priority_1043 ancestry 0.68 recommended IMAGE 10K 10K ancestral 38444967 Affx-122926672 AX-123315304 7 72073599 TCTGCAGATACCTTATGTTAATACAGTGTCATGTG[C/T]AATCAAGCTTGAATTTGGGTGCCTCTAGTCAGGGA Y 2 1 2 1 101000 f 74 goat snp18530-scaffold1870-325926 7 34577273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448361 Affx-122924114 AX-123318697 7 72112032 AGAAACTGCTACTGGATAAAAAGCTTCTGAAAGTC[A/G]TCATTACTCCTATTCTCTTCCCAAAGCAATAAAAA R 2 1 2 1 201000 r 74 goat snp18531-scaffold1870-364359 7 34537936 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426614 Affx-122939965 AX-123296960 7 72141628 GAGAAAGAAGTTATTTGTGTTTATTAGCAATATCT[A/G]TAACCCCAAATTCAGTGGTAACTGTTGCATGGTCA R 2 1 2 1 101000 r 74 goat snp18532-scaffold1870-393955 7 34508282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795312 Affx-122950281 AX-385282270 7 72239218 GTCATCTGAATGATTTGATTAGGCCCTATTTTACA[A/G]TTTTTTAAAAAACTTCTCAACGTTAAACTTTTTTT R 2 1 2 1 303000 r 74 goat snp18534-scaffold1870-491545 7 34410577 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769541 Affx-122978011 AX-385256712 7 72275019 TAAAATAAGTCAGGAACGTGGATGACTGATGAAAT[A/G]CCTACATATTTTACCGTGTGCTGTGCTTGCCTACA R 2 1 2 1 101000 f 74 goat snp18535-scaffold1870-527346 7 34374897 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429366 Affx-122938559 AX-123299708 7 72316878 GATGAGATGAACCTTGGGACACTTCACACCTCTAA[C/T]AAGATTTGATTTACATCTTCAAGAGTTTTGCAAGT Y 2 1 2 1 101000 f 74 goat snp18536-scaffold1870-569205 7 34332835 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790143 Affx-122970757 AX-385277148 7 72345670 ATAAAGGGAAGAAATAGAATGTGAAGAGATGAGTA[A/C]TATCTGTCTTGTAGAGGAATTCATGACTCAGATAC M 2 1 2 1 101000 f 74 goat snp18537-scaffold1870-597997 7 34304049 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427861 Affx-122939715 AX-123298204 7 72398309 AGGTGATTCATATGCCTGTTAAAGTTTGAGAAGCA[C/T]AGAAATATTTGCACCATCCAAGGGCAAAACATTGC Y 2 1 2 1 201000 r 74 goat snp18538-scaffold1870-650636 7 34251328 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407838 Affx-122954532 AX-123278189 7 72450247 TGTTGGTTAACAATGTTGTCCCATAGAAGAAGATA[C/T]AACACAATGAGAAATACTTGAAAACTTTGTATGCT Y 2 1 2 1 101000 f 74 goat snp18539-scaffold1870-702574 7 34198919 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779511 Affx-122925956 AX-385266614 7 72483175 ATTTATTTCACTGTGTTCACATACTAGAATCTGCC[A/G]TTTCAAATAATCAGTACAACTTTAGTAATAAAGGG R 2 1 2 1 101000 f 74 goat snp18540-scaffold1870-735502 7 34166172 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414007 Affx-122950271 AX-123284356 7 72557974 CATTCTGGCTCAAATGGGGCATGTTATAAAGCACT[C/T]TGTTTTTCTATTTAAAGCATTTACTTCAGGTATTT Y 2 1 2 1 101000 f 74 goat snp18541-scaffold1870-810301 7 34087260 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779653 Affx-122977076 AX-385266755 7 72614602 ATTTATCAAGTAACCACAATGTGTCCAAATATTTA[C/T]GCATAGCAATTTGGAAGAATTCATATATTTCTTAC Y 2 1 2 1 201000 f 74 goat snp10399-scaffold1372-50004 7 34028462 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781979 Affx-122966709 AX-385269059 7 72679314 ATGTCTATCATAGTAGTTGTCCTCCCACAAAGATG[G/T]TAAAAATAGCACAATGGGAATAAGTCTGTAGATCA K 2 1 2 1 101000 f 74 goat snp10401-scaffold1372-114716 7 33963199 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273302 Affx-1111833551 AX-319137024 7 72729669 GACTCTTTGCGACCCCGTGGACTGTAGCCTACCAG[A/G]CTCCTCTGTCCATGGGATTTTCCAGGCAATAGTAC R 2 1 2 1 303000 f 74 goat 7_72729669_AF-PAKI 7 72729669 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320793805 Affx-122944573 AX-385280776 7 72761079 ACTTTTCATTTCAATACATTGTATGATGTTTTAAC[A/G]TGTAAAAACCCAGCTGACTCGATTAGTATGTTAAT R 2 1 2 1 101000 r 74 goat snp10403-scaffold1372-196481 7 33880424 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784383 Affx-122979217 AX-385271433 7 72803911 TCCTAGCCTCTTATGATAATTTCTAGTAACTTTCT[A/G]CCTTGTTTCAAAACCAATGTTATATATGGTAGGGA R 2 1 2 1 101000 f 74 goat snp10404-scaffold1372-239313 7 33837188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396587 Affx-122962908 AX-123266942 7 72844763 GACAGGAAGTTTCCCCTGTACATGAGAGGAAATCA[C/T]GTACAAAAGTAATAGAGAGTATACAGATTCATGTC Y 2 1 2 1 201000 r 74 goat snp10405-scaffold1372-280165 7 33796227 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786287 Affx-122975593 AX-385273322 7 72905702 AAAAGTTCCCTTCCATGTGCTTCACAAACTCTCTC[C/T]TTTCTTTGAACTTCAACATTCCTTGTCCTCTCCTA Y 2 1 2 1 101000 f 74 goat snp10406-scaffold1372-341104 7 33735136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421586 Affx-122944500 AX-123291933 7 72939160 AAATAAGCAATTGTTAACTGTATCATCAAATGACT[A/G]TTACCTATTCTGTTTAATTATACCAATGAGAATTC R 2 1 2 1 101000 f 74 goat snp10407-scaffold1372-374562 7 33700674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383989 Affx-122972924 AX-123254347 7 73040087 GATTCTCAACATTAAGAAACAAGAAAACTATCACT[C/T]AGTGCGCTAGTCCTCCAACTAACAGGAAATATATA Y 2 1 2 1 101000 r 74 goat snp10409-scaffold1372-475489 7 33599025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790812 Affx-122956809 AX-385277812 7 73070153 AGGTGATTCATATTTATTGAAGATAACCAATTTCT[A/C]TCTATATTCACTTTTCTTAAATCTGCCACCCAGCA M 2 1 2 1 101000 r 74 goat snp10410-scaffold1372-505555 7 33568867 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402621 Affx-122958404 AX-123272974 7 73107300 TTAGCTCTAGCGCTATAAGCCAGAAATCTCATGGT[A/G]TCTTTTTCACATTTTCTCAGCCTGTTTCCTGAGAA R 2 1 2 1 101000 f 74 goat snp10411-scaffold1372-542702 7 33531287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404878 Affx-122956477 AX-123275230 7 73141100 GCTATCTTTGCCTGTAAAGTAACCGTGTCAAATGT[A/G]CTCACTTCCAAATCCATTAGATACAAGCCAGTAAT R 2 1 2 1 101000 r 74 goat snp49975-scaffold716-5230 7 33494168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278519 Affx-1111836467 AX-519552001 7 73156549 GCCCTCATTTGGTGACTTAGAGTTCTCACTTCTCA[A/C]CAGGCAAAGCAGCTGAGAAGAAAGTGCCTCGCATT M 2 1 2 1 101000 f 74 goat Random2.2K-817 7 73156549 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800483 Affx-122948230 AX-385287403 7 73189684 TTTTCAAAAAGATGAATTTTGCCTGCAAAGCATGG[A/C]TACAACAAGCTGAGTCATCATCTCTAATTTTTCAT M 2 1 2 1 101000 f 74 goat snp49976-scaffold716-53814 7 33449367 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773458 Affx-122937750 AX-385260600 7 73257620 GATTTCAATATTATAATGCATTGTTCAATAGGCCC[A/G]GTGCATATTGTACAGGGAATCTGATCATCCCTTTC R 2 1 2 1 101000 r 74 goat snp49978-scaffold716-121750 7 33380939 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38402593 Affx-122958429 AX-123272946 7 73303172 GGTCTGATGACAATCTCATTTTCATCTTTTGTGTT[A/C]TCTGTTCAAATAGCCCTCCAGAGAACCTCAACCAT M 2 1 2 1 101000 r 74 goat snp49979-scaffold716-167302 7 33337789 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783319 Affx-122947742 AX-385270384 7 73332167 ATAGCACCACTTACATTATCTTTGAAGTACATTTG[A/C]TCACCACTTGTAGATTCTTCTTGAGAACAGAGATG M 2 1 2 1 101000 r 74 goat snp49980-scaffold716-196297 7 33308593 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320782782 Affx-122954331 AX-385269854 7 73381972 ATACAGTTTTCTACATGGTAATTTATGTTATAACT[A/G]TAACTGTGTAAATTAAGCCGCCTCAAAAACATTTT R 2 1 2 1 101000 r 74 goat snp49981-scaffold716-246102 7 33258388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790277 Affx-122960572 AX-385277281 7 73412545 TGTATGTATGCTCTAGAACTGCTCTTCTCAGAAGA[A/G]TTACAAAACAACACAGAGCTTGATCGCAAGAGCTC R 2 1 2 1 202000 f 74 goat snp49982-scaffold716-276675 7 33228124 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394757 Affx-122964847 AX-123265112 7 73477721 CCAACTTTTTATTAATAAATTGTTATAAACCTTCT[A/G]TATGTCCAACATTATGAAATAAACTACAAAATGTG R 2 1 2 1 101000 r 74 goat snp49983-scaffold716-341851 7 33163893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390246 Affx-122967763 AX-123260603 7 73532783 AAATGTATTCCTCTCAGAATTTATTTCATAGAATT[A/C]TTTTCCAAACTTTTGCTGATCTAGTAGAACTGTAT M 2 1 2 1 101000 r 74 goat snp49984-scaffold716-396913 7 33108526 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445788 Affx-122926051 AX-123316125 7 73563407 TGTGCCATATCATTTCAATGCTCAGGACCTAAGTC[A/G]CCAGGGTATGCAAATTGAAGGTTCTGTTCCTAAAG R 2 1 2 1 101000 f 74 goat snp49985-scaffold716-427537 7 33077895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437706 Affx-122931753 AX-123308044 7 73599546 GTGCTTCATGAAACTGAGGGTTGGAAAGTGGAGCC[A/G]TACCTGGCTGAGCTGTTGCCGTAACTGTTTCCATC R 2 1 2 1 101000 f 74 goat snp49986-scaffold716-463676 7 33042253 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412370 Affx-122950815 AX-123282719 7 73631655 TATGAACTATCACTAGGCAGTCAGCTTTTCTCTTC[A/G]TGGGAAAATGCAATATAAATCTAGATGGGGGGGGA R 2 1 2 1 101000 f 74 goat snp49987-scaffold716-495785 7 33010401 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798275 Affx-122974653 AX-385285210 7 73676030 TTTTCAACAGTTTCCAACAACTGCATGCATCCTGC[A/G]TCATAGTGTGATCCTCATAGAATCTGGTTAAATAG R 2 1 2 1 101000 f 74 goat snp49988-scaffold716-540160 7 32966073 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383549 Affx-122972612 AX-123253907 7 73715526 AAACTTCTTAACTGAGCATCCCATCAGTTCAGTTC[A/G]GTCGCTCAGTCGTGTCCGACTCTTTGCAACCCCAT R 2 1 2 1 103000 f 74 goat snp49989-scaffold716-579656 7 32926860 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444852 Affx-122926296 AX-123315189 7 73766360 ATACATAGAAACAGATGTAATATTTTATGATTCAT[A/G]TCCTTGCTTAGAGCCAGGGAGTAGATGGTTGGTGA R 2 1 2 1 101000 r 74 goat snp49990-scaffold716-630490 7 32875452 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413365 Affx-122950142 AX-123283714 7 73795247 ACCATTCATCATTGAAGAATCTAAAAAAATAATAA[G/T]AAGAAGAAAAATGGGATCATAAAAGCCCTTACAAA K 2 1 2 1 303000 f 74 goat snp49991-scaffold716-659377 7 32846789 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440094 Affx-122929717 AX-123310431 7 73824876 AAAGAAGCCATTATCTTGACCAAATTGCAATTCCA[G/T]ATGGTGTGTGTTGAGTGAGTGCTACCTCTGAGAGG K 2 1 2 1 201000 f 74 goat snp49992-scaffold716-689006 7 32816834 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439609 Affx-122931147 AX-123309946 7 73863186 TTCTCAACAGCGGTACACAAAGCATCAATTCTGTT[A/G]TGCATTTAAGGTAATAATTACAACGCACAGTAAAT R 2 1 2 1 101000 r 74 goat snp49993-scaffold716-727316 7 32778518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770620 Affx-122936108 AX-385257784 7 73916776 TTTTTTTAAGAAATGTATAGTGAAGTTAAGTTTTA[C/T]GTAGACACAATTAACTGAGGCTTGCGTATAACAAA Y 2 1 2 1 101000 r 74 goat snp49994-scaffold716-780906 7 32724023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409899 Affx-122952896 AX-123280250 7 73958233 GAAAGAACAGCAAGCATGAAGCCTGAATCCTTTAC[A/G]CTAGATTACAAGAAAAGACTAGTAACACCCATACT R 2 1 2 1 101000 f 74 goat snp49995-scaffold716-822363 7 32682602 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789418 Affx-122972693 AX-385276428 7 74030019 ACACAACTAAGTTAATAATCTAAATCCACACTAAA[C/T]AGCCAATTTTTCTCTAAAAGCTTGAGTTTCTGCTT Y 2 1 2 1 101000 r 74 goat snp49996-scaffold716-894149 7 32611475 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376354 Affx-122978328 AX-123246713 7 74088603 TTCTTCTTTGTTTGGAGATCAGGTCATATGATTGG[C/T]AAATATTATCACCTTGAATATTTTCATAATACCTG Y 2 1 2 1 101000 f 74 goat snp49997-scaffold716-952733 7 32552343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423676 Affx-122942329 AX-123294022 7 74128884 TTTTATTCCATCAAAAACTAGTTATCAGCAAACAC[G/T]AAAAGTTATGTTTTATTCAGCTGTTCCCAGGTATT K 2 1 2 1 201000 f 74 goat snp49998-scaffold716-993014 7 32510623 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776002 Affx-122943224 AX-385263132 7 74166345 TTCTTTCTATAGCCTCAGGTAATTTCCTCTCATGC[A/G]TTTACTTTACTGATCAGCACTCAGCTGAAAACTTA R 2 1 2 1 101000 f 74 goat snp49999-scaffold716-1030475 7 32472889 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394859 Affx-122964767 AX-123265214 7 74197892 TAAAGTTATTTATTATTAATTTAATGAAAGATACA[C/T]GATATTTCTCTTGTTTTTTTCCTTTAATACCTGTC Y 2 1 2 1 101000 r 74 goat snp50000-scaffold716-1062022 7 32441006 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786149 Affx-122956188 AX-385273185 7 74227345 TGAGACTACAGATGCTTTGGGGTGGGAAGGTGCTA[C/T]GTATGTGTCCATTTGGTGCCAGACAAAATACTGCA Y 2 1 2 1 101000 f 74 goat snp50001-scaffold716-1091475 7 32411579 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38403044 Affx-122958539 AX-123273397 7 74262697 GCTCTATTATGAAGAAAAAACCTCAGGAACAGAGA[A/G]ACCAAGAGGCTGGCTGCATATTGAACAGCTGGGAA R 2 1 2 1 101000 f 74 goat snp50002-scaffold716-1126827 7 32375536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379426 Affx-122976108 AX-123249784 7 74292644 ATATAAGGATAGAATAAATTCCAAAAATAAACCAG[C/T]TCACCATGAACCTCATATCTCTAAGGTGAAAAACC Y 2 1 2 1 101000 r 74 goat snp50003-scaffold716-1156774 7 32338011 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419012 Affx-122946047 AX-123289360 7 74328780 CCCAAATAAAACTTAATTCACAACTCTCACGTTGT[A/G]CATCTTTTTAAGTCAACAATATCAGAAACTCTGCT R 2 1 2 1 103000 r 74 goat snp50004-scaffold716-1192910 7 32301581 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381925 Affx-122974136 AX-123252283 7 74380925 TCTGAATCTTTCTTTACTTTCTTTCTATGACTTCT[A/G]CTCCTTCTCTTTCACCTAATCTTAGTTTTCTTTAT R 2 1 2 1 101000 r 74 goat snp50005-scaffold716-1245055 7 32249608 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786010 Affx-122927961 AX-385273046 7 74438604 CACAAGAGATGAAGTTCATGTCAGTGAAAACAGGT[A/G]TGAGTAAAGGTGATCACCTCTACTCTCAACAGCAT R 2 1 2 1 201000 f 74 goat snp50006-scaffold716-1302734 7 32191388 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798685 Affx-122931749 AX-385285617 7 74511304 GTCACATACTTGCTTCAGTGGCAAGGTCAGATGCC[A/G]TTCTCAATTCTAATTCACTATTTCTTGTTTTAAAA R 2 1 2 1 101000 f 74 goat snp50007-scaffold716-1375434 7 32117227 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790318 Affx-122938491 AX-385277321 7 74541338 ACAAGTTTGGAGCAAACTGGGTAATGATAATATTT[C/T]CAAATGTAGACTCTCAAATAAAATCCTAGCAAAAT Y 2 1 2 1 101000 f 74 goat snp50008-scaffold716-1405468 7 32088893 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452850 Affx-122920721 AX-123323183 7 74573003 GTGTGTCAGCATAATATAAAATAAGAACATGAGTC[C/T]GTCTTCAGGTTAAATGGAAAGAAAACCACCCATAT Y 2 1 2 1 101000 f 74 goat snp50009-scaffold716-1437133 7 32056964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430809 Affx-122937458 AX-123301150 7 74647012 GGAAAAAATCAATATGGCTCTTGAAAGGAAACAAG[C/T]AGAGGCGTGGAGTGGTCCAAACACTAGACAATGGT Y 2 1 2 1 201000 f 74 goat snp50010-scaffold716-1511142 7 31982967 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788042 Affx-122967302 AX-385275063 7 74682093 TTGAACAAATGCAAATGGAGTATTCCATTCCAATT[A/G]CTTTGGTTTATAGTTGCCTAAGATTATATTTAGTT R 2 1 2 1 201000 r 74 goat snp50011-scaffold716-1546223 7 31947469 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278700 Affx-1111836468 AX-519552178 7 74699902 ATTTATGATCTATATATTTACATTTTTTATTCTTT[A/G]ATTACTTATAGCTCTTTCATGCTTCAGTTATGTCT R 2 1 2 1 101000 r 74 goat Random2.2K-820 7 74699902 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403776 Affx-122957988 AX-123274128 7 74735387 AAGCAACGCTGTTTATTTCTCATGGGCCTGTCCTT[C/T]GGCTCACTCACCGGGAAAATCCTCATCTCTTCAGA Y 2 1 2 1 201000 r 74 goat snp50012-scaffold716-1599517 7 31894881 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420740 Affx-122944761 AX-123291087 7 74785492 CAATTAGCAAACTGCCACCATCTGGGCTTCCTTGT[A/C]TTCCCTGGGGACATGTGGAAAAGTCATGATATGTA M 2 1 2 1 201000 f 74 goat snp50013-scaffold716-1649622 7 31844739 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798895 Affx-122940367 AX-385285825 7 74854648 GCATCTCTCCACTGTGGCTTGGCTTCCAACACAAT[A/G]CTTCAGATTTAGGGCAACCTGATAGCATATCAGAA R 2 1 2 1 101000 f 74 goat snp50014-scaffold716-1718778 7 31774728 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378372 Affx-122976816 AX-123248731 7 74893033 TCCACTCTGCCATGTAATTTTTTTTTACTTCCTTC[A/G]TGCATTTATTAAGTTCCTTCTGCTTACCTGACACA R 2 1 2 1 201000 r 74 goat snp50015-scaffold716-1757163 7 31735795 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778268 Affx-122924738 AX-385265383 7 74928126 AGAAAGGTAGCATCAAGCACCCATTTAAATAGAAG[C/T]TGTTATTGTTCTTATGGGTAGTATGTAATATACCA Y 2 1 2 1 101000 f 74 goat snp50016-scaffold716-1792256 7 31700594 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404949 Affx-122956423 AX-123275301 7 74966906 AACCTGTTATTTCTCCAAGGATGTTTGTTGATGGC[C/T]GGGAACTGTTCAAAGATTTTAGGGAAGGAAAAAGA Y 2 1 2 1 101000 f 74 goat snp50017-scaffold716-1831036 7 31661584 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778888 Affx-122935609 AX-385265996 7 75038103 CTTTGTGTTGGTGATTTTCTGTTTTAAGTGAAAGT[A/G]TTTTCATATTTCTTGGTTTGTGGACCATGTTATAT R 2 1 2 1 102000 f 74 goat snp50018-scaffold716-1902233 7 31590304 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278703 Affx-1111836469 AX-519552181 7 75070857 AAATAAAATATTCATTAAGTGTTCATATTATATTT[C/G]TATGAGCCATGACATTACCTACTGGGGAAAATAAT S 4 1 2 1 102000 r 74 goat Random2.2K-821 7 75070857 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429260 Affx-122937896 AX-123299602 7 75079107 CTTACCTTTGGGTGGGACAATTAAAGGGTTCTCTG[C/T]GAACAATCAGTATGTTGTACAATTCTGATTTGGAG Y 2 1 2 1 101000 f 74 goat snp50019-scaffold716-1943237 7 31549275 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429962 Affx-122938068 AX-123300303 7 75134098 ACTTTTAACTCATCAGTAGTGAGTTTTCAAATTCT[A/G]TTGAGACAGGTAGATTAGTTAGATCATGTAATTTC R 2 1 2 1 101000 f 74 goat snp50020-scaffold716-1998228 7 31494388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776940 Affx-122962474 AX-385264064 7 75194178 ATTCTATTTACCCAACTTTTCTTTGTGAGTAAATA[G/T]AGCACTTTACCCTTTCTGAAGTCTCCCTTGAACCA K 2 1 2 1 101000 r 74 goat snp50021-scaffold716-2058308 7 31433910 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273343 Affx-1111833552 AX-519546981 7 75274397 CTCTTCTGAGTCACTTGCATTTTATTTCTCTTTTT[A/G]ATGAATTTCTCTAAGTACACAACAGGCTGAATTGG R 2 1 2 1 101000 r 74 goat 7_75274397_AF-PAKI 7 75274397 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406439 Affx-122955195 AX-123276791 7 75274678 AAATATTTTCTTTACTCTTCTTGATGGAGAATGGG[C/T]GGAAGCTAAAGCTCTCTCCCTGCTCCCTTTTGGAC Y 2 1 2 1 201000 f 74 goat snp50022-scaffold716-2138808 7 31353321 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376589 Affx-122979067 AX-123246948 7 75324205 CGTCTCTTATGTTACATGCCAGGACCCTCAAAGGC[A/G]TTGCCATTGCAAAACTAACCAGAACTTTCCTGTGT R 2 1 2 1 101000 r 74 goat snp50023-scaffold716-2188335 7 31303605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386953 Affx-122969980 AX-123257311 7 75386957 ACAAACAACCATTTTTGATCCTTAAAGCCCTAAAA[C/T]GTTAGAATGTGTCAGTTACACACTCTGAACTATGT Y 2 1 2 1 101000 f 74 goat snp50024-scaffold716-2251087 7 31241134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451239 Affx-122921948 AX-123321572 7 75425376 AAATCCCCGTTCTTGTATTGATCCTGCAGTAAAGA[C/T]GATGGGGATTAGATCATTTGCACTTAGATTCTCCA Y 2 1 2 1 101000 f 74 goat snp50025-scaffold716-2289506 7 31203819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445235 Affx-122925494 AX-123315572 7 75455024 GCTGCTCCAAATGGTGACGTGTGCTTCTCAGGGCT[A/G]TTGTGAAGGTGTTGGGAGATCTTGCCCGTGAAGCA R 2 1 2 1 101000 f 74 goat snp50026-scaffold716-2319154 7 31174291 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786887 Affx-122948607 AX-385273916 7 75535811 TTCAGTAAATAAGACCCAGCAATTGAGTCAGATTC[A/G]CTGGCCTGGAGTTCATTGGGTATAATGACACTTAA R 2 1 2 1 101000 r 74 goat snp50028-scaffold716-2399941 7 31093479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396359 Affx-122963046 AX-123266714 7 75584281 TGCACTTGATACATTCATAACATGACAGTGTAAAG[C/T]ACAGGGTCATTCTAATGGGACTTGAACTTGAAGTC Y 2 1 2 1 101000 f 74 goat snp50029-scaffold716-2448411 7 31044750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414789 Affx-122949230 AX-123285138 7 75618323 TTTCTTGCTAGCTGACATGATTAATTTCCCATAAT[A/C]TGACATGCAATGTACTAGTTACCAGATGAACCACA M 2 1 2 1 101000 f 74 goat snp50030-scaffold716-2482453 7 31010691 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421939 Affx-122943826 AX-123292286 7 75652953 GAAGATTTTTTTCTTTTAATCTTTAGTGTCATCAA[C/T]GAATAAACATTCAGACTACCTTAATTATAATTCAG Y 2 1 2 1 201000 r 74 goat snp50031-scaffold716-2517083 7 30976540 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391047 Affx-122966859 AX-123261404 7 75755904 TTTAAACTCTGGTTCCGTGTCCTCCTTCAGAAAGA[G/T]AAAAGCTAAGAGTCCATGTTATTGACTGTCATATG K 2 1 2 1 101000 f 74 goat snp50033-scaffold716-2620034 7 30873659 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430188 Affx-122937354 AX-123300529 7 75799441 GGAATTCAGGGATTGTTCTGGGCTCTTGATGTAGC[A/G]CTCCCCCTGCGAAAGGACCACTGGCAGCATTTAGT R 2 1 2 1 101000 f 74 goat snp50034-scaffold716-2663571 7 30830158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397312 Affx-122962315 AX-123267667 7 75858904 GCTAATAAAAAGCAAGCGTGCTAAATGCAGTGTGG[C/T]GTCCTGGTTTGGATCCTGGGACAGGAAAACCTGGC Y 2 1 2 1 101000 f 74 goat snp50035-scaffold716-2723034 7 30779561 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422115 Affx-122943562 AX-123292462 7 75895268 ACCTCTGCCCCCAGAGCCAGTGCCCTTGGCAGGAT[A/G]TTGGCAGACAGAAGCCAGTCTGTTCCTCGCTTGGC R 2 1 2 1 101000 r 74 goat snp50036-scaffold716-2759398 7 30743175 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440165 Affx-122930727 AX-123310502 7 75926187 CCAAAGACCTCGCGGTGGCTTGTCAGGCCTCCCTC[A/G]TCCCCATCTGTCATCACTTTCCAGGCTCCCTAACC R 2 1 2 1 101000 r 74 goat snp50037-scaffold716-2790317 7 30712255 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413879 Affx-122949848 AX-123284228 7 75959397 CTGTCCACTTACCTATTTTTCTCCTTTGTTGCCTG[C/T]GCTTTTAGTGTCATATTACAAACACGTTTAAGGGC Y 2 1 2 1 201000 r 74 goat snp50038-scaffold716-2823527 7 30678749 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404100 Affx-122957123 AX-123274452 7 75990171 TAGGCATCCAAAACCTGTTATTAAGAGCACAAAAT[A/G]TAAACTTCTTATTAGAAGATTTGAATTTTTTCCAA R 2 1 2 1 101000 f 74 goat snp50039-scaffold716-2854301 7 30648010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439382 Affx-122930265 AX-123309719 7 76023359 GCAAGTAAACTACAAATCACTCCTTATGAGTGAGT[A/G]CTGTCCTTTCCTTCTCTGGTGCTCCAGTCAGGCTG R 2 1 2 1 303000 f 74 goat snp50040-scaffold716-2887489 7 30614953 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769323 Affx-122959066 AX-385256494 7 76053402 GGCCCACATGATCCCTGGGCTGCATCCTGGTAAAT[A/G]CAACTCTTCAGGTTTTCCTGAGATCACTGAAGCAC R 2 1 2 1 101000 r 74 goat snp50041-scaffold716-2917532 7 30584922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444150 Affx-122926792 AX-123314487 7 76117277 GTCAAAAACTCAAAAATAAGCCTAGCTGTGTCACT[A/G]TCTTATTGCAGATGAAAATATGCTTCTCTTTTGAT R 2 1 2 1 101000 r 74 goat snp50042-scaffold716-2981407 7 30520460 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275356 Affx-1111834747 AX-519548931 7 76143024 TGGCTAGCCCTCCTGGAGATTTG[A/G]TCAGCTGTCACGGAGTTGCAGCTGGTTTGAGACTG R 2 1 2 1 102000 r 74 goat GoatD01.051287 7 76143024 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38376865 Affx-122977833 AX-123247224 7 76189850 TCTCAGATACCACCTGTCTTTCCTGGAACAAGCAC[G/T]GATGTTCCTTTAGACCACCTGTCTTTCACACCTGT K 2 1 2 1 201000 r 74 goat snp50043-scaffold716-3053980 7 30447966 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412570 Affx-122951315 AX-123282919 7 76218948 GCTTGGCTCCTTGGAGCATAACCCAGGGGTTGGAT[A/G]TAGAGATTCTTTGCAATTCCTTGGTTCATCTCCTG R 2 1 2 1 101000 r 74 goat snp50044-scaffold716-3083078 7 30418858 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449663 Affx-122922573 AX-123319998 7 76263155 CTTTCTTGCCCCAACTTGTCACCTTCTTCCTTCCC[A/G]CCACTGCTTCATTCACTCCCCCCTCCTCTCCATCA R 2 1 2 1 103000 f 74 goat snp50045-scaffold716-3127285 7 30374812 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384448 Affx-122973097 AX-123254806 7 76316515 TTAGATGGTAGGGGAAAGGAAACAAAATTAAGTCC[A/G]TTTTCATTTATTTTTTTCCATTTCAGCTAAAATAT R 2 1 2 1 101000 f 74 goat snp50046-scaffold716-3180645 7 30321385 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422638 Affx-122943703 AX-123292984 7 76349544 AGCATCAAGCCCGTCATAAGTGAGACTCCCCTTCC[C/T]GTTGACCTCTACCGCTATGATGAGATTTCCGGCAA Y 2 1 2 1 101000 r 74 goat snp50047-scaffold716-3213674 7 30288468 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419919 Affx-122945327 AX-123290267 7 76397153 GAGGAAGTGAGTCCTTTTGACAGAGATTGAGCATA[C/T]GGCCTGCAAAGTCAAAATATGTATTGTCTGGTTCT Y 2 1 2 1 101000 f 74 goat snp50048-scaffold716-3261283 7 30240646 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449725 Affx-122922524 AX-123320060 7 76438614 AAAACCTAATCTGCTCTTTAGGGTGTTTGGGGAGA[C/T]GGGTGGCTGCAGAGCAGAGCATTTATAATTAACGA Y 2 1 2 1 101000 f 74 goat snp50049-scaffold716-3302744 7 30199024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390852 Affx-122967825 AX-123261209 7 76510205 TGAACCCTTTTGAAAATTGTAAAGCACTATAGAAT[C/T]GAAAGACTTTCATTCAGTAAAATAAAATAAGGGGG Y 2 1 2 1 103000 f 74 goat snp50050-scaffold716-3374335 7 30127700 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442978 Affx-122928199 AX-123313315 7 76542094 CTGAGAACCCAGCTCCAAACCCAGTTTCTCCATCT[A/G]TGACATAGAGATTTAAGAAATAGCCATTGTACATG R 2 1 2 1 101000 r 74 goat snp50051-scaffold716-3406224 7 30095596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403727 Affx-122958024 AX-123274079 7 76614769 AAGATACCTGGTGAAAGGGGTCCATCAAGGAGTTA[C/T]AGCTTGGGGACTGTGCTTCCTCCAGCCACGCAAAA Y 2 1 2 1 101000 f 74 goat snp50052-scaffold716-3478899 7 30023406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393525 Affx-122965795 AX-123263881 7 76665281 CAGTGAGACAGAAGATACAATAAATGAGATAATTC[A/G]AAGTCCTACTTCTCAGGTTCCACCTGTGGAAAAAC R 2 1 2 1 202000 f 74 goat snp50053-scaffold716-3529411 7 29972170 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793476 Affx-122962514 AX-385280453 7 76699451 CAGAAGGAGTATGTGCTAAGTGCAGAGAATACCAC[A/G]AGAAAGAGTAGGTTTGGCCATGTAGGAACAAAGAT R 2 1 2 1 101000 f 74 goat snp50054-scaffold716-3563581 7 29937730 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436041 Affx-122932723 AX-123306380 7 76765612 CTCTACGGAGCTGGAGTCCTAGGTTTGGATTGTCC[A/G]TTGCCCACATCCATTTGTTTGCGGAAATCAGAGGT R 2 1 2 1 201000 r 74 goat snp50055-scaffold716-3629742 7 29871014 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418583 Affx-122946371 AX-123288931 7 76806366 AGGCTCTGGTTTCAATTCTTGCCACCAGGGGACTT[C/T]CCCACTTTGGACTGTCTTGATAGATATATTCTACC Y 2 1 2 1 101000 r 74 goat snp50056-scaffold716-3670496 7 29830132 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273796 Affx-1111833821 AX-519547407 7 76844697 TAAGCAGT[A/G]TCCAGTCAAGTCTGCAGGGGACAAATCAGTTAAGA R 2 1 2 1 102000 r 74 goat GoatD01.005959 7 76844697 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38378211 Affx-122976927 AX-123248570 7 76863775 AACTCACATTTGTTGTCATGGCAGATATATGTGGT[A/G]TTAGCTTGCCTGTATTTAATTTTCTTTTTTTCATA R 2 1 2 1 101000 f 74 goat snp50057-scaffold716-3727905 7 29772292 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407777 Affx-122954963 AX-123278128 7 76900299 TTAAATTTAAGTTCAGTTTTGACGTGTTTCAGTTC[A/G]TCCAAATGATACTAACCTAGACTACAAATTTACCC R 2 1 2 1 101000 r 74 goat snp50058-scaffold716-3764429 7 29735349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383798 Affx-122973191 AX-123254156 7 76989621 GGACAGAGGCCCACCCATTTGCTGTAATTTAGAAA[C/T]GTCTAGAATGTTATTTCAAAATATCAAGACTTCAT Y 2 1 2 1 201000 r 74 goat snp50059-scaffold716-3853751 7 29644964 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780085 Affx-122960149 AX-385267183 7 77023402 GGGTTGTAGAAAGAAATCCTGATGAAACACAGAGT[A/G]TTTTCTTCTTAGTAAATAAAAACCCCCTGAAATAC R 2 1 2 1 303000 r 74 goat snp50060-scaffold716-3887532 7 29610894 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430649 Affx-122936948 AX-123300990 7 77080160 TGTTTTTCTTGTGTATAATTTGAAGTCAGAGAACT[A/G]TAAGAAAATTAATATTTCCTGAAATCCCATTCCTC R 2 1 2 1 303000 r 74 goat snp50061-scaffold716-3944290 7 29553511 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413332 Affx-122950171 AX-123283681 7 77119366 AAAAAGGTTTTTTGGAGGTTTCGTATGAATTTAGA[A/G]ATTCTAGATTAGTTCAGGAGAGGCTGGGATAGAAT R 2 1 2 1 101000 f 74 goat snp50062-scaffold716-3983496 7 29514432 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780461 Affx-122928317 AX-385267552 7 77178111 GATGATTGGACTTGGGCATTCTTCAAGCCAAGCTC[C/T]ACATTAATTCTGGCTCCATTAAACAATCTAGGTGA Y 2 1 2 1 101000 f 74 goat snp50063-scaffold716-4042241 7 29455866 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433104 Affx-122935713 AX-123303445 7 77238727 CCCCAGTATGTGTATATGTCTGCCTGTCAAGTCCT[A/G]TGCTGAGAATAAACAGCCCTTTTTTTCTGACCCAG R 2 1 2 1 101000 r 74 goat snp50064-scaffold716-4102857 7 29393876 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397506 Affx-122962061 AX-123267861 7 77292146 ACACACATCCCATGCATGCTTAGTGATGCATAGGT[A/G]TTGTTGTTCAGTTGCTGAGTTGTGCCCAGCTCTTC R 2 1 2 1 103000 f 74 goat snp50065-scaffold716-4156276 7 29340662 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415989 Affx-122948402 AX-123286338 7 77329309 GGCCACGCTGTTTCCTGGGCAATAATAGTCCCTAA[A/G]CCTGTCCCAGCTCTTCCACTTAGAGACTATAGAAG R 2 1 2 1 101000 f 74 goat snp50066-scaffold716-4193439 7 29303503 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384390 Affx-122972214 AX-123254748 7 77363305 AGACTCGGTATTATCACGTGACACTAAACGAATAT[A/G]TTTTGCTTATCAATCTTCCGGAAGGAGTTGTAATG R 2 1 2 1 101000 r 74 goat snp50067-scaffold716-4227435 7 29273573 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411383 Affx-122952231 AX-123281733 7 77393202 CTAAAGTATAAATAATTGAAAAGCTGTGGGTTCAG[C/T]GTACAGATATGTGATCAAATATTTTCTGCTTAGAA Y 2 1 2 1 201000 r 74 goat snp50068-scaffold716-4257332 7 29243309 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396630 Affx-122962873 AX-123266985 7 77422620 GCTCAACAGATCCCAAGAGAATTTTCTTCTTGATG[C/T]GAGACAGAATCTAGAATATTAAATAAGATTTCTCA Y 2 1 2 1 201000 r 74 goat snp50069-scaffold716-4286750 7 29213977 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378851 Affx-122976527 AX-123249210 7 77448659 TAGTACCGACAATTAGTCCTTGTAATTAAGGTATA[C/T]GTAGAATTATTTTAAAAAATGTAACTTCATAAATA Y 2 1 2 1 103000 f 74 goat snp50838-scaffold735-1903594 7 29188642 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798748 Affx-122960564 AX-385285679 7 77482819 GTTTCAGATTCAACCAACTCTGGAGACAACATGTA[C/T]ACTTTAATGAATGCAGTACCTCCAGGACCTAACAG Y 2 1 2 1 201000 f 74 goat snp50837-scaffold735-1869434 7 29154418 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399233 Affx-122960587 AX-123269588 7 77533491 AGCTAAGGGCTCCTTTGAGGAATCTGTTCTTTGCA[A/G]GTTATCAACAGAGTGAGTACTGACAGGTCTATCAA R 2 1 2 1 201000 r 74 goat snp50836-scaffold735-1818762 7 29103760 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387522 Affx-122970314 AX-123257880 7 77584624 AAAGAGAGTTTAGGCAATTGAAACTACATATTTGA[C/T]ATAACTATTTTTATATTAAAAGCTAGAGAAGGTAA Y 2 1 2 1 101000 f 74 goat snp50835-scaffold735-1767629 7 29052931 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777289 Affx-122921873 AX-385264411 7 77650317 TCCCTGTTGCTGGATGTGTCCAATGTGAACTCTCT[A/G]TCCTAGAACAACTAATACAATGTGTTGGTGTTAAT R 2 1 2 1 101000 f 74 goat snp50834-scaffold735-1701936 7 28986569 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791326 Affx-122929049 AX-385278319 7 77679501 TCCTATTTTAATTATTAAGTTCTTTCTGAACGTAC[A/G]TGTATAAACTCCCATTGAAAAGATGTTGGAAGAGT R 2 1 2 1 101000 r 74 goat snp50833-scaffold735-1672752 7 28957612 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768812 Affx-122927883 AX-385255989 7 77762755 GGGGAATTTAGAATGTTCTCCCTTCCATAGAGATC[A/G]CAACTGTTACATTAATGTTGGGACATAGGGTTGAG R 2 1 2 1 101000 r 74 goat snp50831-scaffold735-1589498 7 28874200 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273306 Affx-1111833553 AX-519546950 7 77778817 TTCTGCCCATTTTTAAATTGTGTGTGTGTATCTAT[A/G]TATATACACATGTATATATGGATGAAAGTAAAAGT R 2 1 2 1 103000 f 74 goat 7_77778817_AF-PAKI 7 77778817 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38410657 Affx-122952767 AX-123281007 7 77818044 ATTTATACTTTTAGTTTTGTCCTCAGTAAATGTCC[A/G]CCTGGTTCTAACACTGACTGATATTTTAATGCTAT R 2 1 2 1 101000 r 74 goat snp50830-scaffold735-1534209 7 28818900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777503 Affx-122934651 AX-385264622 7 77868504 ATTTGAATCAGTTTGATTTGTGTTTGTCAAAAGTA[A/G]CTTCCAGTGCCAGAGAAACACCTCAGTTCTTTAGG R 2 1 2 1 101000 r 74 goat snp50829-scaffold735-1483749 7 28768782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795101 Affx-122977535 AX-385282060 7 77907401 TGAATTTATCAAGAATATCGATTTCAAAGCTGGTA[C/T]GTTATGAATTTTTAGAAATTGTTTGGTTGCTGAGT Y 2 1 2 1 101000 r 74 goat snp50828-scaffold735-1444852 7 28729797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406074 Affx-122956240 AX-123276426 7 77971575 ATAGAGTACCCACTGGCCACACGTGGCTACTGAGC[A/G]CTGGTCATGCAGCTAGTCTGAACTGAGATGTCTGT R 2 1 2 1 101000 r 74 goat snp50827-scaffold735-1380678 7 28688829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442844 Affx-122927689 AX-123313181 7 78016213 CCTCCATTCAAAGAGGGTTTTTGGTTTTTTTGTTG[C/T]TTATAAGTCAAGTTTCCTTGAAAACAACTTGGTGG Y 2 1 2 1 303000 r 74 goat snp50826-scaffold735-1336040 7 28643758 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782856 Affx-122953799 AX-385269926 7 78049136 GTTTTTCTTACTAGATTTTCTTATGAGAATATCAA[C/T]ACCAACTTTCACTCAATGGTCACTAGAGCATAACG Y 2 1 2 1 101000 r 74 goat snp50825-scaffold735-1303117 7 28610419 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802606 Affx-122973641 AX-385289508 7 78157600 TAAGTTAAGGAGAGGACAGTTACCCAGAAGCAGAG[C/T]AGTTTGACAGTGCCAGGTCAGACTAAGAGTAGATG Y 2 1 2 1 101000 f 74 goat snp50823-scaffold735-1194653 7 28511380 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779355 Affx-122962282 AX-385266459 7 78215818 AGGTGTTAGAAACTATATATTTGAAAGGAGATGAC[A/G]CAGGTTGAGTTTTGTATACAACCCTTTCTCTTACT R 2 1 2 1 201000 f 74 goat snp50822-scaffold735-1136435 7 28452500 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435166 Affx-122933660 AX-123305506 7 78246335 CTGCTTGAGCAGGAGTATGTGAACGAGGGGGAGTC[A/G]TAGGAAGTTGCACATCAGAGCAATCAAGAGGCTAG R 2 1 2 1 101000 r 74 goat snp50821-scaffold735-1105918 7 28421449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428641 Affx-122938666 AX-123298983 7 78283873 CTTGGTTTAAGACCTTAGCAAGTTAAAATGAAAAA[C/T]GAAACAGCAACCCCAAACCAAACTTTCCATGGTTC Y 2 1 2 1 201000 f 74 goat snp50820-scaffold735-1068380 7 28383840 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800078 Affx-122932497 AX-385287001 7 78318070 GCTGTGCTATGAGTAGCAAAGATCTAATTTCTATT[C/T]GATCAATCAAAACAAAATATGAGCTACATATGTAA Y 2 1 2 1 201000 r 74 goat snp50819-scaffold735-1034183 7 28349952 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413621 Affx-122950554 AX-123283970 7 78352580 CAAAGGGACCATGGGACCATTTACACAGATCCCAG[C/T]AGGTATAGGGAAGATCCCCTGGAGAAGGGAAAGGC Y 2 1 2 1 101000 f 74 goat snp50818-scaffold735-999673 7 28314843 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377105 Affx-122978258 AX-123247464 7 78381646 TTCATCTGTAGCTCCAGGAGGCTGGGGACACAGCC[A/G]TTGGCTTATTGCTGCACAGATAACCCACCCTGTGC R 2 1 2 1 101000 r 74 goat snp50817-scaffold735-970607 7 28285920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438424 Affx-122931272 AX-123308762 7 78447335 AATTTAAAACCTGCCCAGCACAAGGTCCCTTTTCC[A/G]GTCAGCGTGAGGAACAGCCGGTGGCTGCCCTCGGG R 2 1 2 1 101000 f 74 goat snp50816-scaffold735-904918 7 28219743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383641 Affx-122972532 AX-123253999 7 78494262 GCCTGCCCAGGAAAGAAGTATCCTTTCCAGAACTA[C/T]AGCTCCCATAAAGGAAATGGGATCGTTTCTATGTT Y 2 1 2 1 101000 f 74 goat snp50815-scaffold735-857991 7 28172348 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441974 Affx-122928446 AX-123312311 7 78530526 AATATTGCATGACCTACTAACCCGACATAGTTCAC[G/T]CTCAACATCAAATCACACTACATTCCTTTCAAGGA K 2 1 2 1 101000 f 74 goat snp50814-scaffold735-821727 7 28136104 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769184 Affx-122947814 AX-385256359 7 78567896 GTTACCTATTAGAGAAAACTTTTTCAGGATTACTC[A/G]TTATGAGTAATTTTAATAGGGTACAAATAGGAAAT R 2 1 2 1 101000 f 74 goat snp50813-scaffold735-784357 7 28097812 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451670 Affx-122921587 AX-123322003 7 78603639 GACTCTTGTAGAATTCTAATTTTCTAGAAGAGTGT[A/C]AACAGAAAAATTAACATCACCTGAGACTAAATGGG M 2 1 2 1 201000 r 74 goat snp50812-scaffold735-748614 7 28061953 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396178 Affx-122963771 AX-123266533 7 78648416 GCCGTTCCACTCATCTTGCCGCTTTATGTTGTCCA[C/T]GCATTCCCAGGCCCACACACCCCTGAAGCCCATTC Y 2 1 2 1 101000 f 74 goat snp50811-scaffold735-703837 7 28017147 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438471 Affx-122931235 AX-123308809 7 78680936 CCTTTGAAGTGTTCTGAGATTAAGAGAAGCTCCAA[C/T]ACCCAGATGGAAGTGCCATTTGCTTTGCGTTTTCC Y 2 1 2 1 101000 f 74 goat snp50810-scaffold735-671317 7 27985166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390547 Affx-122967219 AX-123260904 7 78721018 ACCCAGGAAGACACAAGTGCTGGTATATGCTCCAC[C/T]CTTAAGCTAACTGCCTTCTAGAAGCCTTTTCTTAT Y 2 1 2 1 101000 f 74 goat snp50809-scaffold735-631235 7 27945076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794100 Affx-122925709 AX-385281067 7 78759404 AACTGTATTATTACAAGAGAGCTTTTGTGTATACG[C/T]GGCATCTAATAATGCATTCACCCTACTAAGCCAAG Y 2 1 2 1 101000 r 74 goat snp50808-scaffold735-592849 7 27906981 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778342 Affx-122944526 AX-385265457 7 78797749 CACATTATCAAATCCTTTGCTCCACTGAAATCATA[G/T]AGGTTTTCTTTAGGAATGGAGGCCAATAGTGTGCT K 2 1 2 1 101000 r 74 goat snp50807-scaffold735-554504 7 27868153 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413901 Affx-122949833 AX-123284250 7 78852072 CCAAAAGATGATTATTATGTTCATACAATGGGATG[C/T]AATATAGCAGCTAAAAATAAAAGAGCAATGGTAAC Y 2 1 2 1 101000 f 74 goat snp50806-scaffold735-500181 7 27813856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790111 Affx-122925872 AX-385277117 7 78896564 TAAATTAAAGCCTTTAGATGAAGAGTTTTTCTTAT[A/G]CTCGATTTTATAGACTCCAAACTCTCAAAACAGAA R 2 1 2 1 101000 r 74 goat snp50805-scaffold735-455689 7 27769555 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278705 Affx-1111836470 AX-519552182 7 78930779 AGCAATTAAAGCTAGACCCAGAGTTTTACTCTCCC[A/C]TAGAAGGAGTAGTAGATAGGTATTCCCTAGACCAA M 2 1 2 1 101000 r 74 goat Random2.2K-825 7 78930779 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407409 Affx-122955241 AX-123277760 7 78960177 TGTATATTGAAGTCAGTTTTTGGCATGAAAAGATG[C/T]ATGTAATACATTAAGTGATGAAATCACGTTACAAA Y 2 1 2 1 101000 f 74 goat snp50803-scaffold735-392076 7 27706123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782320 Affx-122964456 AX-385269397 7 79007641 TTAAGAGGAGTGCTTAGGTAGGCTAGGCAGTGGTA[G/T]ACTAACGTCTGTGATTTTGAAACACTCTTGACCAG K 2 1 2 1 101000 f 74 goat snp50802-scaffold735-344612 7 27658629 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424722 Affx-122941675 AX-123295068 7 79042240 CAAGAATACTTCAGTTCTAATGGCAGAGTTCATAT[A/G]AGAATGACACACAGAAATGAAGAGATAAGACAGTT R 2 1 2 1 101000 f 74 goat snp50801-scaffold735-310013 7 27623209 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785896 Affx-122977272 AX-385272933 7 79148763 GTCACCTATGATTCTTCCTTAAAAATCAAGTACAT[A/G]TTCATGCTCAGAGCCATTTGATCCTAAAATTAACA R 2 1 2 1 101000 r 74 goat snp50799-scaffold735-203490 7 27515980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395014 Affx-122964225 AX-123265369 7 79195271 ACCATCACCATGCATTCAAAAAGTTTACAACTGAG[C/T]AGGGCAGAAAGACACAACTATTTTTGCAACAAAGC Y 2 1 2 1 101000 f 74 goat snp50798-scaffold735-156982 7 27468198 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790087 Affx-122964603 AX-385277093 7 79228637 AGTATCTTTAAATATAAATTGAGGGGGTTGGACCG[C/T]ATCTTCAAGGTTCTCTACAAGTTATATATTTCACG Y 2 1 2 1 101000 f 74 goat snp50797-scaffold735-123616 7 27434936 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447642 Affx-122923975 AX-123317978 7 79292803 ATGGCTCAAATATTATTCTAATCTATGAGTTTAAA[C/T]GTTTCAGGATCACTTAAGAGAGAAACAGACCTGAG Y 2 1 2 1 201000 f 74 goat snp50796-scaffold735-59450 7 27370779 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448343 Affx-122924130 AX-123318679 7 79345827 GGATATACTTTTCAAAATATATGTATATACATATG[C/T]GCATTTTAAAAAATAATACTAGCTGGTATTTAGTG Y 2 1 2 1 103000 r 74 goat snp50795-scaffold735-6426 7 27318013 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448952 Affx-122923138 AX-123319287 7 79389620 TACAAATTAAGTTAATATTAATAACCTCTAAAAAT[A/G]AAACCAGAAATTATTTAAGAAGACAACTAAGAAAT R 2 1 2 1 303000 f 74 goat snp4761-scaffold1158-832343 7 27273310 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770729 Affx-122963756 AX-385257893 7 79433043 AACGACAGCAGCGAACAATTACAGGCCAGTTCAAG[C/T]CTCCCCACATACTGTGCATTTTCTCATTGGAGCAA Y 2 1 2 1 101000 r 74 goat snp4760-scaffold1158-788920 7 27229811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421043 Affx-122944527 AX-123291390 7 79485573 AATGGAATCCGGCAGACGGGCTCCTTCCATCACAT[C/T]GGGTGCCTCTGTTAAACTCTGAGCCGTAAGGTAGG Y 2 1 2 1 101000 r 74 goat snp4759-scaffold1158-736390 7 27176990 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786364 Affx-122931270 AX-385273398 7 79542436 TTCAACCATTGGCACGGTTCTACAGAACAAAGATA[C/T]GATCTTGGAACCGGTGAAGTCTGCTCTGTGATGAT Y 2 1 2 1 101000 r 74 goat snp4758-scaffold1158-679527 7 27120098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433972 Affx-122934261 AX-123304313 7 79576356 CAGGAAGAACCAAGCTTAATGACATTTTTATCACC[A/G]CACATCCACACTCTTTGGAAACTTTAATTGAAATG R 2 1 2 1 101000 r 74 goat snp4757-scaffold1158-645607 7 27086384 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800850 Affx-122923154 AX-385287765 7 79627943 CACATATAACACAAGTCAAAGGTTTAAGAGCATAG[C/T]AGGTTCAAGTAAAAGAGCCTAAATTTAAAAAGGTA Y 2 1 2 1 101000 r 74 goat snp4756-scaffold1158-594020 7 27034676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453568 Affx-122919768 AX-123323901 7 79684027 AGACCAAGGATTCAACCTTGAAAACACTACAGGGA[C/T]GACAGAAGAGAAAACTCCAGCAAAACACAGCAGTG Y 2 1 2 1 101000 f 74 goat snp4755-scaffold1158-537936 7 26978691 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444624 Affx-122926937 AX-123314961 7 79714628 CTTTTTCTTTTTTTTTGGCATCTTTTTTCCTTTTT[A/G]CTATGTTTTCTGAGAGAATTTTTCAGCCTTTCTAA R 2 1 2 1 101000 r 74 goat snp4754-scaffold1158-507335 7 26948181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440626 Affx-122929960 AX-123310963 7 79744364 AAAATAGATAAAAATGTGTTAAAATCTACTCAAAT[A/G]TGGTTTAGTTTGCTATCTTTGATGTTTCTTTTCAG R 2 1 2 1 101000 r 74 goat snp4753-scaffold1158-477599 7 26918414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278526 Affx-1111836471 AX-519552009 7 79754464 CTCTCTACAGCTTGCTCTTATGTTTAACAAGATTA[A/C]CATCTCATTTTATGTTAATAAATCTTCTATGACAT M 2 1 2 1 101000 f 74 goat Random2.2K-826 7 79754464 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427236 Affx-122939566 AX-123297579 7 79777570 GCCGTGTTTTGTGATGTGAAATGTTTCATGCCTCA[C/T]GGCACAGAAGTTAAGAGAGATCAGTCAGTAATCAA Y 2 1 2 1 101000 f 74 goat snp4752-scaffold1158-444393 7 26884100 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766055 Affx-122944175 AX-385253473 7 79832582 CTGTCTGATCTTAGAATCATGGCTCCTGTAAACTC[A/G]TCCTGTTCCTTCTGATCTCTTTCCCTTCCTTCTAT R 2 1 2 1 101000 f 74 goat snp4751-scaffold1158-389381 7 26829137 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386462 Affx-122970778 AX-123256820 7 79866604 AGAGGGAAGTGACAGTGCTGTAGTTGGCTGCCATG[A/G]CAGATTCTCCATCTCCAGTTCCTGTGGACTCATAA R 2 1 2 1 201000 f 74 goat snp4750-scaffold1158-355359 7 26796851 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380662 Affx-122975193 AX-123251020 7 79961697 AAAAACACAAATGCCTTTGATAAGATTATATTCAG[C/T]AATGTAGTTATCAAAAATATATATTCAACAGCTCT Y 2 1 2 1 201000 f 74 goat snp4748-scaffold1158-260266 7 26701684 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417147 Affx-122947352 AX-123287495 7 80012873 AAATAAATGATATCTCCTGATATCATTTCCCTTCC[A/G]TTTTATCTCCTCTACATCATGGCAACTGTAGATCT R 2 1 2 1 101000 r 74 goat snp4747-scaffold1158-209090 7 26649959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780187 Affx-122973739 AX-385267285 7 80072818 CTGTTTCCAGTCACTATTAATTGATATTTTCTCTA[C/T]GTCCATGACAAGGCATTTCTTCCATTATTATTTGA Y 2 1 2 1 101000 r 74 goat snp4746-scaffold1158-149145 7 26590112 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398287 Affx-122962162 AX-123268642 7 80106617 TAGCTTTAAGTATAATAAAACATGAGCACTTTCCT[A/G]CAGGGATTTGTATAAAAGATGCTCTTAGCCCCCTC R 2 1 2 1 101000 r 74 goat snp4745-scaffold1158-115346 7 26556259 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380462 Affx-122975732 AX-123250820 7 80152602 TCTTCCTTTGTAAAATAGAAATAACTGGGCCCTTT[A/G]CCTACCTTTAGGTCCAAGTTAATGATGCCCAGACA R 2 1 2 1 201000 r 74 goat snp4744-scaffold1158-69361 7 26510089 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791505 Affx-122949924 AX-385278496 7 80183350 GAAAACTTGGCTACTTAAATACAGAGACATATTCA[A/G]TCAACAAAGGTACTCTGAGTACATCATTCCCAGAC R 2 1 2 1 101000 r 74 goat snp4743-scaffold1158-38613 7 26479247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408295 Affx-122953782 AX-123278646 7 80218077 TGTGTATATAATTGTTTTAAATGGGTAGAATTTCT[A/G]TGTTTTGAAAGTGTACTTAAAACACCCAAGGATAA R 2 1 2 1 101000 f 74 goat snp4742-scaffold1158-3886 7 26444197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792021 Affx-122960984 AX-385279009 7 80251983 ATGCATAAACCATCAGATAGTTACATATCAATGAG[G/T]CAAATTAGCTGTTCTGTCCACCCGATTCCCAGGTT K 2 1 2 1 101000 r 74 goat snp59697-scaffold989-1036483 7 26413138 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431419 Affx-122936525 AX-123301760 7 80300536 AGATTGGCAAATCTAAAATTTGTCCTGTCTTAATT[A/G]CTATCTTTTGTAGTTCTTGGTGTTGGGTTCCTTTT R 2 1 2 1 101000 r 74 goat snp59696-scaffold989-987930 7 26364568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792557 Affx-122956888 AX-385279538 7 80334620 CTATCTCAAATGCCCAGTTCCTGTGATTTCATACC[C/T]ATTCATTAAGGCTTCTGTAAGTCAGTTCAAATATT Y 2 1 2 1 101000 f 74 goat snp59695-scaffold989-953846 7 26330091 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273308 Affx-1111833554 AX-519546951 7 80337144 ATGGCAATTCTTTCATGTTGGTAAGAGTTCAGTTC[A/G]GTTCAGTTGCTCAGTCATGTCCGACTCTTTGCGAC R 2 1 2 1 101000 f 74 goat 7_80337144_AF-PAKI 7 80337144 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38385863 Affx-122971612 AX-123256221 7 80368448 CTTGTCCATAAAGAATTCTTTTTTCTCAAATTTAC[A/G]TGTTTCAGATATTTGTCAACCATGATGTTCCTTCT R 2 1 2 1 101000 r 74 goat snp59694-scaffold989-920018 7 26296364 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791843 Affx-122935983 AX-385278833 7 80411347 CAGCTGGTACATATCTGAATCTCCTCAGTTATCCC[A/G]TTTGAGGCCACTGTACACCAGCTGATGAACGTGTA R 2 1 2 1 101000 f 74 goat snp59693-scaffold989-877119 7 26253297 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781737 Affx-122954445 AX-385268819 7 80444512 ATCTGTTTTTAGCTCTCTGGAACCTGGCAGTAGAA[C/T]AGAATAAACACACTCAATACATTGTTATGAATGAA Y 2 1 2 1 101000 f 74 goat snp59692-scaffold989-843954 7 26219675 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385209 Affx-122971712 AX-123255567 7 80479983 AGTCAACAATTCAACTAGTCCACTCTCCTAGCATT[A/G]TCTCAGTAATGTATTTTGTTTCTTTTGGTTGACAT R 2 1 2 1 101000 f 74 goat snp59691-scaffold989-808483 7 26183197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771243 Affx-122953800 AX-385258401 7 80541864 TACTTTCAAATTTTGAATAAGGGTGTCCTTAAGAA[C/T]GAAGAGGACATAACCAAGTAATGTGTAGTAATGTG Y 2 1 2 1 201000 r 74 goat snp59690-scaffold989-746602 7 26121190 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789931 Affx-122967385 AX-385276937 7 80573579 GCAAAATTAAAGGAAGTAGCATAACCAGTGTGAAT[C/T]AGAAGAGTTAATGACCCAGCCCCTAGCTATCCTAA Y 2 1 2 1 101000 r 74 goat snp59689-scaffold989-714887 7 26089305 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792612 Affx-122960691 AX-385279593 7 80605685 AAAGGACAATCTCAACAAGCTCAAAATAACCAGAT[A/G]CTATATAGTATACCTGATAAAATGCCAGTGTTCTT R 2 1 2 1 201000 r 74 goat snp59688-scaffold989-682781 7 26057189 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427422 Affx-122940057 AX-123297765 7 80637381 AAATTTTATAAAGATCAACCTTGTGGAAGAAGAGG[C/T]GGTGGATTATAAGTGAAAATGAATGATGTCAAGTA Y 2 1 2 1 101000 f 74 goat snp59687-scaffold989-651085 7 26025300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417165 Affx-122947337 AX-123287513 7 80672047 CTTTTAAATGACTTGGAAGTATCAGCATGTTCAAA[C/T]AATATTTAAATGGTTTAAATTATTTTAATTCCCCA Y 2 1 2 1 103000 f 74 goat snp59686-scaffold989-616419 7 25990514 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413860 Affx-122949861 AX-123284209 7 80705300 AAAAAGGAGGGAACATGGTAGTTTCAGGAACATGG[C/T]AGTTTAAAATGGTTTGAGCAGGGGCTGCATTTGGA Y 2 1 2 1 101000 f 74 goat snp59685-scaffold989-583166 7 25957201 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409893 Affx-122952900 AX-123280244 7 80749038 GTAAAATGAAAGTCATTATTATTATGAAACATCCT[A/G]TTTTGACATTTTTTAAAGCATAGCGTGTTAATGGT R 2 1 2 1 103000 f 74 goat snp59684-scaffold989-539428 7 25912267 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453410 Affx-122919893 AX-123323743 7 80797022 AGCCTAGGGTAGAGTAAAATACAGAATATAAATAT[A/G]ATCTATTATTATTTCACATCTGAGTTCTTCCAGCA R 2 1 2 1 103000 r 74 goat snp59683-scaffold989-491444 7 25863562 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425653 Affx-122940882 AX-123295999 7 80833307 TTTCAAAGAGGCAAGTTATTTGCATTTTGGCCAAG[A/G]TATTCTCATAAGAGAAAAGACAGAAAATAACTAAC R 2 1 2 1 101000 f 74 goat snp59682-scaffold989-455159 7 25827398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793390 Affx-122919703 AX-385280368 7 80863043 AAAATGCAATATAGCAAACTTTGATACAACCCTTT[A/G]TAAAAGATGTGAGTGGTAATTTCTTTCTAGGGAAT R 2 1 2 1 101000 r 74 goat snp59681-scaffold989-425423 7 25797483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784246 Affx-122972180 AX-385271297 7 80901772 TTAAGACCACTCAAACCCTGACATTAAAAACCACT[A/C]ACCATAGATTAGCATTACCAAACATCCTTTTACCC M 2 1 2 1 101000 f 74 goat snp59680-scaffold989-386694 7 25758305 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793642 Affx-122975742 AX-385280615 7 80945126 GAACAAGAAAAATAATAGAACCTAGAGAAAGAGAA[C/T]GGGAAAACTTCTGCACATAAGTAAGTTCATCACTG Y 2 1 2 1 201000 f 74 goat snp59679-scaffold989-343340 7 25714340 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783538 Affx-122960516 AX-385270601 7 80997210 TAACTACAAGAAGAAAGTAGACTTGGTACTTGATT[A/C]TTTTAGCTAACCCAAGCCCCAACCGACGAATTAGG M 2 1 2 1 202000 f 74 goat snp59678-scaffold989-291256 7 25661367 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377838 Affx-122977293 AX-123248197 7 81029406 AACTTTTGGTGTCTTTTGTGTTTCTATTCTTTATA[A/G]CATTGCTTTCATTTCACAGGCACTTTTTTGAGAAT R 2 1 2 1 303000 r 74 goat snp59677-scaffold989-259060 7 25628557 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388145 Affx-122969465 AX-123258503 7 81080465 ACACAGCTTGCGAAAGAGACTGTCTTTTTTTCTAT[C/T]GTATATTCTGTCCTTCGTCAAAGATTAGTTGCCCC Y 2 1 2 1 101000 r 74 goat snp59676-scaffold989-208001 7 25572925 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791087 Affx-122950000 AX-385278082 7 81136814 AACCTTTGTTAATCAGGTTGGATAAATATTTCTTG[C/T]AATTGGGTATGTCAGTGGAAACAATCAATAAACCA Y 2 1 2 1 101000 f 74 goat snp59675-scaffold989-151652 7 25516955 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789168 Affx-122935817 AX-385276180 7 81183447 TAACTATTAAAAGCTAGTGCATTTGTCCCTTTGTG[A/C]CTTGAGATCTTCATGGAATTGAAGAATCTTCACAG M 2 1 2 1 201000 f 74 goat snp59674-scaffold989-105019 7 25469593 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386321 Affx-122970887 AX-123256679 7 81235124 TGGGTTCCACAGGAGTCCATCTGAGCAGAGTAGCC[A/G]CCTTCTTCAAGACCATGCCCTTCCTAAGCAATCTG R 2 1 2 1 101000 r 74 goat snp59673-scaffold989-53342 7 25419326 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402253 Affx-122959130 AX-123272606 7 81280182 CAGCTTAGGATCTTTGATAAACAATGCAATTGAGC[A/G]TGCTATCCATATAGTTTACCTTCACATGGCATCTA R 2 1 2 1 101000 r 74 goat snp59672-scaffold989-8284 7 25372439 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428465 Affx-122938796 AX-123298808 7 81315974 TCTCCAGTGAACAAACAGGAAAAGGGAGAGCCTTA[C/T]AAGACAGAAAAATCTAGATAATAGAAAATAATCAC Y 2 1 2 1 101000 f 74 goat snp59727-scaffold990-471989 7 25332724 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452105 Affx-122920843 AX-123322438 7 81356503 TTTCTCTGGTTTTTATTTGCTATCCCTCACTATTT[A/G]TATTATCCAATATGTAATTCACCCTATGTCTTCCT R 2 1 2 1 101000 r 74 goat snp59726-scaffold990-431460 7 25292194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802638 Affx-122976963 AX-385289539 7 81387233 TAAGATTCATAATTATTTGTAAGGATTTATTGAGC[A/G]TCTATTATGTACTGGTCAGCATTCAGATGTTGCTG R 2 1 2 1 101000 r 74 goat snp59725-scaffold990-400730 7 25261124 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787663 Affx-122970561 AX-385274686 7 81425431 CCTCAGCTACTGGGCATAATCAAAACAACAGTGGA[G/T]AATATCAGATTATTAACCTCTGCTGTACTATGAGC K 2 1 2 1 101000 f 74 goat snp59724-scaffold990-362532 7 25222918 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776112 Affx-122927030 AX-385263242 7 81490779 AGATTTGGTAGTCCGGTCAATCCAATTCTTTGTGC[A/G]CTCTTCCATCACTCCACTTGCAAAACTAATAACCT R 2 1 2 1 101000 f 74 goat snp59723-scaffold990-297184 7 25156585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774471 Affx-122945579 AX-385261607 7 81522167 CTTTAGGTACAAATTATATCCTATGTCTTGAATTA[C/T]AATGCTAGAATATTGACCATATTTTGACTCTGTGT Y 2 1 2 1 101000 r 74 goat snp59722-scaffold990-265796 7 25124810 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791855 Affx-122930199 AX-385278845 7 81562264 ATCAAAAATTATCAGCCCAATGATGTGTGAAACTT[A/G]CCTTCAGTCTTTCATATATAGGCAACCTGAGATTA R 2 1 2 1 101000 r 74 goat snp59721-scaffold990-225699 7 25084080 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417953 Affx-122946703 AX-123288301 7 81594017 GGTTGGCAAGTCTCCAGATATAATACAAGACCAGA[A/C]GCTGCCAATGAATTAAGCTGTGTTGGCACTACCTT M 2 1 2 1 101000 r 74 goat snp59720-scaffold990-193946 7 25053353 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428795 Affx-122938403 AX-123299137 7 81638816 GATTTTATGATATAAATAAAAATGAACATAAATTT[A/C]TGAAAAACTAAATTATGCTACCACCACCATCCATA M 2 1 2 1 103000 r 74 goat snp59719-scaffold990-149147 7 25006860 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396806 Affx-122963291 AX-123267161 7 81677237 GAATTGGACACGACTGAGTGACTGAACTGAACTGA[A/G]CTGAATATGGAATCAGTTGCCAGAGAAGAAATGCA R 2 1 2 1 303000 r 74 goat snp59718-scaffold990-110726 7 24966477 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789184 Affx-122933030 AX-385276196 7 81718743 ACACCTGACTTTTCTTATTTCCTGCCCATTAATGC[C/T]TACCAAAATATATCCATTACTGTGTGTTTTTGCTC Y 2 1 2 1 101000 f 74 goat snp59717-scaffold990-69220 7 24924407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464532364 Affx-1110533621 AX-516004348 7 81742965 ACTTTTCACCTGCATAGATGCGAAAACTTCTCACC[C/T]TGTCTCCTCTTCCAGACTCTTCTTTCTCCAGTCTG Y 2 1 2 1 201000 f 74 goat GoatD01.045412 7 81742965 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407672 Affx-122954595 AX-123278023 7 81757213 GCTTATTGGTTTGGTTTGTGGACAGATGTTACTGG[A/G]TAAGAAATATAGTTAGAATTTAAAGGTTCTGACTT R 2 1 2 1 101000 f 74 goat snp59716-scaffold990-30750 7 24885209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770549 Affx-122936791 AX-385257713 7 81810589 TCAGAAAAATTGGGTACTTCTATTTCTCATAATCT[A/G]TGCATAGATTTCCCCAGCAGTATATGCTCCCAGAG R 2 1 2 1 101000 r 74 goat snp28483-scaffold3037-29580 7 24820285 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786901 Affx-122971688 AX-385273930 7 81919546 TACATATATTTGTTTATAGATATGAGGTTATAGAT[A/G]TATTTGTAGATTATCTGATGGTTCTCAACTTTTTG R 2 1 2 1 101000 r 74 goat snp56888-scaffold901-79278 7 24711930 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444428 Affx-122926566 AX-123314765 7 81966984 TCTATGCTTAAAGAAAAGTTGGTTTATATCCCACT[A/G]TGCAATTTACTATATGCCCATCAACAATATGGATT R 2 1 2 1 101000 r 74 goat snp56889-scaffold901-126716 7 24663184 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417037 Affx-122947532 AX-123287385 7 82007440 AGATTGCAGGGTGGAGGTGCCATCTGTCCATAGAG[C/T]ACATGGCTAGAACCTGAGTTTTCCCAATAAAAGGA Y 2 1 2 1 201000 r 74 goat snp56890-scaffold901-167172 7 24622734 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448453 Affx-122923642 AX-123318789 7 82045121 TGATTACTTCTGATATTTTTAAGATAAGTGTACTC[G/T]ATTTTGATGGTTACTTTTCTCAGTGTAGTGACCTT K 2 1 2 1 101000 r 74 goat snp56891-scaffold901-204853 7 24585607 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383819 Affx-122973175 AX-123254177 7 82159989 GCAGAGTGCCCACAGTAGTTAACTCACCACACATA[A/C]AGACCCATGAGGCACACATAGAGGTGACTCCCAGA M 2 1 2 1 101000 r 74 goat snp56893-scaffold901-319721 7 24474562 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774308 Affx-122959160 AX-385261443 7 82219945 TCTTACAACAAATTAACAAATTCACCAGCTGACTT[A/G]TAGGTATTTAGAAGATATTCAATGAGTTTCCTGTA R 2 1 2 1 101000 f 74 goat snp56894-scaffold901-379677 7 24412817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278528 Affx-1111836472 AX-519552011 7 82242100 CTGCTCAAGGTGTTCTTAAACCTATAAGAATGATT[A/G]ATCATATTTAAGAAAAAGGGGAGGCTTTTAAGTAG R 2 1 2 1 101000 f 74 goat Random2.2K-828 7 82242100 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38453486 Affx-122919833 AX-123323819 7 82358581 CAATTATTGTAGAACTCCACCAGGTTATGAACTAC[G/T]GCCACTTGCTCCTTCCTCTATCATCTGAGTGCTAA K 2 1 2 1 101000 r 74 goat snp56897-scaffold901-518313 7 24274119 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790256 Affx-122974198 AX-385277260 7 82396670 CAGCTCTATTTGCATATGTACATAGGATGTCAGTA[G/T]TCCATCAAAGCAGAACTCTAGTATCCTGCCCAAGG K 2 1 2 1 101000 r 74 goat snp56898-scaffold901-556402 7 24236234 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424083 Affx-122942043 AX-123294429 7 82436891 TTGGCCCGCTGTCTATGTGGTTGCTATTACCCTAG[C/T]ATGGTGCCAATTATCTAAGTTGTGTCCCTGTATTT Y 2 1 2 1 101000 r 74 goat snp56899-scaffold901-596623 7 24196419 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411818 Affx-122951247 AX-123282168 7 82477389 GTCTTAAGAGTTTAACTGATGACCTGCTTAAATTT[A/G]TTGCTCATTTAGCCAAAGAAATCTGAGTCCATTCA R 2 1 2 1 101000 r 74 goat snp56900-scaffold901-637121 7 24156172 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766914 Affx-122958356 AX-385254229 7 82515762 CATGGTTGGGAAAAGATCTGGACATCATCAGCTAT[A/G]CAGTGAATGTAACTCTTTAACATATAACAATTCAT R 2 1 2 1 101000 f 74 goat snp56901-scaffold901-675494 7 24117675 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432746 Affx-122935449 AX-123303087 7 82551050 ATTTTAACATAGATAATATTTCCATAGTTTAAATC[A/G]TAGTTCAAATGCTTTGGGAGGGGAAAGAACTCCAG R 2 1 2 1 201000 f 74 goat snp56902-scaffold901-710782 7 24082243 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430115 Affx-122937513 AX-123300456 7 82673095 ACTGAGTGAGAAATAGAGTCTCTGTGTTTATCTGT[A/C]TACCTATCTATCAATTCCAGTTACATTTGTTTAAT M 2 1 2 1 201000 r 74 goat snp56905-scaffold901-832827 7 23961463 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779086 Affx-122923025 AX-385266191 7 82712878 ACTGTGATTTGATTTTATGGAAATTCTCCTACCTA[C/T]AACTATTCTCTGTTTCTGCCCCTGATCCCTGGTCT Y 2 1 2 1 101000 r 74 goat snp56906-scaffold901-872610 7 23921959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430940 Affx-122936835 AX-123301281 7 82738006 TCCCACATCTACTGTGATTTCCCCTTTTCTGCTTT[G/T]AATTTAGCAAATTCTAAATTTAATTATTTGGCATA K 2 1 2 1 303000 r 74 goat snp5722-scaffold12-1553051 7 23897017 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450831 Affx-122921788 AX-123321165 7 82795432 GTATTTGCACACACTCTTACTGGTCCTGACCCTGC[G/T]ACTGAAATGGAGGTTTCTCTGGGAAACCTTCCTTT K 2 1 2 1 101000 r 74 goat snp5721-scaffold12-1495625 7 23840082 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273310 Affx-1111833555 AX-519546953 7 82927686 TTCCAACAACACAAGAGAGGGCTCTACACATGGGT[A/G]TCACCAGATGGTCAGTACCAAAATCAGATTGATTA R 2 1 2 1 202000 f 74 goat 7_82927686_AF-PAKI 7 82927686 A G 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320782695 Affx-122942273 AX-385269767 7 82938651 GGGCATAGATGACTAATGACTTCACTATACCATGG[A/C]GGGAACATTTGTGTAAAATCATATTACCACATAAT M 2 1 2 1 101000 r 74 goat snp5718-scaffold12-1352406 7 23696453 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770381 Affx-122919908 AX-385257547 7 82978120 TGAGATAACAGAACAAAGTAGGAGCTCAATGAACT[A/G]TATCTATTACAATGAATAAAATTCTGGTTGAAAGG R 2 1 2 1 101000 f 74 goat snp5717-scaffold12-1312937 7 23656763 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437520 Affx-122931920 AX-123307858 7 83118887 TTGGGAAGAATTAACAGTAATTTTTTTAAAAAGCC[A/G]CAGGAATTACCTTTATGTTGATGACATACCCCTAG R 2 1 2 1 101000 r 74 goat snp5714-scaffold12-1172170 7 23514900 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399366 Affx-122961342 AX-123269721 7 83148674 CAAGTCCCTGTACTCAAGACCCAGCCTCATTTCCT[A/G]TTCCCTTCTCCACACCATATTGTTAACTCCATGAT R 2 1 2 1 201000 r 74 goat snp5713-scaffold12-1142383 7 23484929 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451038 Affx-122921445 AX-123321372 7 83307478 TGAAGTATGATATCATTATATATTTTAAAATAATT[A/C]TTCCCTAAAGGAATCACCCTTTCATTACTATGGGA M 2 1 2 1 103000 r 74 goat snp5709-scaffold12-983579 7 23323796 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443946 Affx-122927018 AX-123314283 7 83379519 AACCTCCAACATTGATATTTTTAGTGAGAATTGAG[C/T]GTTTTAATTTGAGTGCTTCCAAATAATCTATTTTG Y 2 1 2 1 101000 f 74 goat snp5707-scaffold12-911538 7 23250506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278712 Affx-1111836474 AX-519552190 7 83387976 CTATAACTTTTTATTAATGAAAAATTTCAAATGTG[A/C]AGAATAGATGAAAAAATAACAGCATGTATACCAAT M 2 1 2 1 101000 r 74 goat Random2.2K-830 7 83387976 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320775546 Affx-122956800 AX-385262677 7 83412536 ACTCTTCTCAATGGTAAGCGTACTCTGCATTATAA[C/T]ACATAGTGAATTTTCTCAAGGACTTTTCTGTATTT Y 2 1 2 1 101000 r 74 goat snp5706-scaffold12-878521 7 23216562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420436 Affx-122944901 AX-123290783 7 83446382 AGTCACCTTACTGAGCCCACAGTCTGATGAAAGTC[C/T]TTCTCTAGTTCAAAGTTTCTCCTCTTGTTGGAGAT Y 2 1 2 1 201000 r 74 goat snp5705-scaffold12-844675 7 23182439 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379685 Affx-122975914 AX-123250043 7 83494847 AAGACCTGAGAAAAATATCCTTATTTTTCTTTAAC[A/G]CTGATGAGTCATTTAAGAAAAACAGCATGTGTGGT R 2 1 2 1 103000 r 74 goat snp5704-scaffold12-796210 7 23133772 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416404 Affx-122947853 AX-123286753 7 83541266 GATCAGGACCTGAACCCATGTGCTGGGACTCGAAC[G/T]CATGTGACCAGGACTTAGTTTGGACTGTATGTGGC K 2 1 2 1 101000 r 74 goat snp5703-scaffold12-749791 7 23087288 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789507 Affx-122931107 AX-385276516 7 83597520 CCATAAGTAAAATGTCTGAGGCCAGTAAATTAGTC[A/G]TAAGAATTTTTAATGAACATTGTGAGGGATTACTT R 2 1 2 1 201000 r 74 goat snp5702-scaffold12-693537 7 23030787 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397183 Affx-122962412 AX-123267538 7 83673944 AATCAGGGACTACCATAGAAACTTGCTATGCTGTT[A/G]CAAAGTTCTCCCAGGGACCCAGCATCTCTTTTAGT R 2 1 2 1 101000 f 74 goat snp5700-scaffold12-617113 7 22953902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382678 Affx-122973653 AX-123253036 7 83707045 GCCCCTTTATTCTCTCCACCTTCTTCAGTGTGATT[A/G]TGGGATAGATTTGTTATACCCTTAGACCAGGTTCT R 2 1 2 1 101000 r 74 goat snp5699-scaffold12-584012 7 22920602 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422671 Affx-122943676 AX-123293017 7 83774644 CATTGTCAACATTGCTGAGGTGTAATCCAGATCTC[A/G]TCTCTTGCAAAGCTGCGGGTGCAGTGGTGAATTTT R 2 1 2 1 101000 f 74 goat snp5698-scaffold12-516413 7 22852313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387133 Affx-122970651 AX-123257491 7 83809765 AGTTCAAAATCTGGTCAGGCAACAAAGATTCTGCA[G/T]GCTGCATGATGGAGCAGGAAAAAAAAAATGATGTA K 2 1 2 1 303000 f 74 goat snp5697-scaffold12-481292 7 22815083 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383314 Affx-122972698 AX-123253672 7 83844292 CTCTGTCATTTTCCTTTATTTTAATTTTGAAAGTG[C/T]TTCTGTGTTTTTCCTCTCCTCCCTTTTTTCCTGCA Y 2 1 2 1 101000 r 74 goat snp5696-scaffold12-446765 7 22780606 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401012 Affx-122959684 AX-123271365 7 84005467 GCTGAACCTCACCAACAGAGGGCCTCTGATACCCC[A/G]TAGGTGATTTTGATCACGTTCTCCATTGTGGGGAC R 2 1 2 1 101000 r 74 goat snp5692-scaffold12-285590 7 22618342 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423157 Affx-122942749 AX-123293503 7 84035351 CAGCCCCACAGTTGCAAACTGGGCTCTATCCCACT[A/G]CAAATGAAAAGAACAAACAAACAACACTTCCTTGG R 2 1 2 1 201000 f 74 goat snp5691-scaffold12-255706 7 22588484 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452311 Affx-122920673 AX-123322644 7 84109555 TCTTGCTTAAAATATATAGATATTTAAGGCCAGAT[A/G]TAAGATTCTCCACATGATTTATATTGACCGTTGCC R 2 1 2 1 101000 r 74 goat snp5690-scaffold12-181502 7 22514095 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798382 Affx-122952190 AX-385285316 7 84164209 AAAGAGAATCAGTATTTATAGAATACTATATTCCA[A/G]ATGTTATATTGGGCACTTTGTTGGTTAGTCTCCAT R 2 1 2 1 101000 r 74 goat snp5689-scaffold12-126848 7 22459488 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382782 Affx-122973584 AX-123253140 7 84194224 GGACTCAAGAAGGTAAGAGACCAAAACATTTACCA[C/T]TGATGTAGTCCAGGCAGGAAATGATAAAAGACTGA Y 2 1 2 1 101000 f 74 goat snp5688-scaffold12-96833 7 22429407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401247 Affx-122959301 AX-123271600 7 84226773 GTGCAAGCATGGGATTGTAGAAGGAGTCCCACTGG[A/C]AGCTCCAGAGCTGGGGTTGCTCTTTAGAATTGGCC M 2 1 2 1 101000 f 74 goat snp5687-scaffold12-64284 7 22396793 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768946 Affx-122924299 AX-385256121 7 84260332 ATAGAGTTAGAAGTTAAATGTAAACCTTGTGGATA[C/T]AGAGGGCTGACTGTACCTGTTCGTCATTTGTATGT Y 2 1 2 1 101000 r 74 goat snp5686-scaffold12-30725 7 22362763 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438126 Affx-122931487 AX-123308464 7 84314513 GGAATGCAGAAAATAAACATTTTGCTACTCTCCCC[A/G]GTGGCTTATTTTTAAAATGTGAAGTTAGAATAGTG R 2 1 2 1 201000 r 74 goat snp55300-scaffold853-23357 7 22308216 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783850 Affx-122949868 AX-385270906 7 84356262 CAAATTATGAGGGAACATGGGATAAGAACTGAAAA[C/T]GTAACGTGTAACTCGGTAATTTCAAACATCAAGGT Y 2 1 2 1 101000 r 74 goat snp55301-scaffold853-65106 7 22266404 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792145 Affx-122945603 AX-385279129 7 84413506 GCACGGGTTCTTATGTTTTATCCCATGGCCACACA[G/T]AGTCACTTAGTCACTAGCCCAGACTAGATGAGCAG K 2 1 2 1 101000 r 74 goat snp55302-scaffold853-122350 7 22209042 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464534332 Affx-1110534631 AX-516006301 7 84434308 TCAGAGGCCTGAGCTTGGTCTCCATGCATTCAAAC[A/G]TGGCTTCCATCCTCAGGGTCCAAGAGGCACCTGCA R 2 1 2 1 202000 f 74 goat GoatD01.021010 7 84434308 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770798 Affx-122967703 AX-385257962 7 84442142 ACCTTAATTCACTCCCTCGAGGCACATGAAGAATT[A/C]TATACAGGCGAAGAGCCAAATGGATACATTATTTA M 2 1 2 1 101000 f 74 goat snp55303-scaffold853-150986 7 22180429 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379806 Affx-122976235 AX-123250164 7 84476536 TCAGTTTTTTCATCTATAAAATGGGGATAATAACA[G/T]TGCCTGTATCGTTTGGTTTTGAGGAAAAAATGAGT K 2 1 2 1 103000 r 74 goat snp55304-scaffold853-185380 7 22146332 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377726 Affx-122977389 AX-123248085 7 84648649 GTGGCTAATTAACTTTCTGTAAGTATCAGGGTACA[G/T]ATGCTTCCAAGTTTTATGCTGTATGGTACATTAAA K 2 1 2 1 101000 f 74 goat snp55309-scaffold853-357493 7 21973909 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427757 Affx-122939245 AX-123298100 7 84769426 TCATTAATGTTCCAGGATCTAATACAGAGTAACTC[A/G]TTGCATCTGCTGACCATATTTCCTCAGTCTCCTCT R 2 1 2 1 101000 r 74 goat snp55312-scaffold853-478270 7 21853127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452004 Affx-122920919 AX-123322337 7 84840013 TATTTGCATGTAGCTTGGACATTTTTCTAAGAATC[A/G]TTCCTGTACAGTGTTTTGTAGAAGCTACTGAATTA R 2 1 2 1 101000 f 74 goat snp55313-scaffold853-548857 7 21782317 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782526 Affx-122976875 AX-385269601 7 84883019 ACAGGTAGGCGTAATTATAGTTTAATCAGATTCTT[A/C]AGTGTCTCTAGAGACCACTTTTGGCACACCGTTTA M 2 1 2 1 101000 r 74 goat snp55314-scaffold853-591863 7 21738946 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379279 Affx-122976220 AX-123249638 7 84946455 TTCTACTAATTATTTCTTCAATTCTGGTTCATTGG[C/T]AGAATAACTACTTAGTTTTGTTTCTAGCATTTACT Y 2 1 2 1 101000 r 74 goat snp55315-scaffold853-655299 7 21676105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783443 Affx-122949422 AX-385270506 7 85111982 GCTGGCATCAGCAGCAAAGCAAAGTAAAGATGGGC[A/G]TTTTTTGGATAACACAGGTAGAGATGGTGATTTTT R 2 1 2 1 102000 f 74 goat snp55318-scaffold853-820826 7 21512489 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385022 Affx-122971864 AX-123255380 7 85436503 AGGAAGAAGATTCGCTGATCGCAATATTGTGCTTA[C/T]GCGGTGGCTTGCTTATGATGCTTGACACATCCTTA Y 2 1 2 1 101000 f 74 goat snp55325-scaffold853-1145347 7 21186422 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787515 Affx-122951355 AX-385274540 7 85491292 AATTCTAATTATTGGAACTAAGGTGTGTACAGGTG[C/T]GCCCAGCTTGGAAATGTACTTTTTGCTAATCAGAA Y 2 1 2 1 101000 r 74 goat snp55326-scaffold853-1200136 7 21131442 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389512 Affx-122968297 AX-123259870 7 85564277 AAATTAAAATAAAAACAAAAATGAATTGTTACTGG[A/G]AGCACCCTAAGTGTTGCCCTATAAGTAATGTGTGA R 2 1 2 1 101000 r 74 goat snp55328-scaffold853-1273121 7 21058114 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273351 Affx-1111833556 AX-519546986 7 85609463 TCTGAGCACAGAGAAGGCCATGTGAACATGAAGGC[A/G]GAGATCAGCGTGGTTCGTCTACAAGTGAAGCCATG R 2 1 2 1 201000 r 74 goat 7_85609463_AF-PAKI 7 85609463 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38432404 Affx-122935842 AX-123302745 7 85633067 TCTTCTAAACTTTGTAGAAAAGATCACCATCCCCA[A/G]TATCCATTGGGGATATCCACTGGCATTATCCAATC R 2 1 2 1 202000 r 74 goat snp55330-scaffold853-1341911 7 20993979 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778344 Affx-122972384 AX-385265459 7 85706142 GATTACGTTGTTATGTTACCCTCTGGCAAGGGCTG[C/T]GGAAAGTGAAACCTCATAACCCCTTGACAAATTTT Y 2 1 2 1 102000 f 74 goat snp55332-scaffold853-1414986 7 20920549 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386290 Affx-122970932 AX-123256648 7 85762477 GCCACTTCACATATTATTCTGACTCTTCTTTCCAC[A/G]TGGTAAACCAACCCTGAATATTCATTGGAAGGACC R 2 1 2 1 201000 f 74 goat snp55333-scaffold853-1471321 7 20865070 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393877 Affx-122965129 AX-123264232 7 85801778 GGGCTACAGTCCCTGGGGTCGCAAAGAGTCAGACA[C/T]GACTGAGTGGCTTCACTTCGCTATCATGTCCTTGA Y 2 1 2 1 303000 f 74 goat snp55334-scaffold853-1510622 7 20824963 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422201 Affx-122943500 AX-123292547 7 85882815 ACATAATACTTGGGTGTTCAATGTTGGGAAGAAGA[C/T]GGTTAGCAAAGAAAAATCACCCTGAAGTACCAGAC Y 2 1 2 1 101000 f 74 goat snp20161-scaffold2-6491395 7 20742456 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381398 Affx-122974376 AX-123251756 7 85926658 GATGAGAAAATAAATTTATACATGATATATAGAAA[C/T]GCGAAATGTAATCTCTGGGTGGCAGCACAAATTCA Y 2 1 2 1 202000 f 74 goat snp20160-scaffold2-6447552 7 20698589 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427244 Affx-122939560 AX-123297587 7 85972992 TCTATTTGCCTATTATGGGAATTACAAGTAGCTTT[A/G]TTTAAATATCATTAGGGCCTAATTTAGATAGATGA R 2 1 2 1 201000 r 74 goat snp20159-scaffold2-6401218 7 20651716 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770122 Affx-122933471 AX-385257289 7 86031382 AATTAAAAAAATTGTATCATAATGATGAATATGCC[A/G]TCCTTGTCTTAATCACAAAATATGTTGATTTCCAG R 2 1 2 1 101000 r 74 goat snp20158-scaffold2-6342828 7 20592148 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784884 Affx-122938589 AX-385271931 7 86064596 CCAATTTTGGAGGAAAGAGAAGAATTTTGCAGGAA[C/T]ATTATGATTTGTTAAACTAAAAGAACCATTATTTC Y 2 1 2 1 101000 f 74 goat snp20157-scaffold2-6309614 7 20558965 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425029 Affx-122941874 AX-123295375 7 86116387 CTTCCATGCATATTCTCATAGAATCTAGTTTTCAC[C/T]TTCTCTGGGGACTTAGCTCATTTGCTTTATATTGC Y 2 1 2 1 101000 f 74 goat snp20156-scaffold2-6257823 7 20507926 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791930 Affx-122953586 AX-385278920 7 86262466 GCTTCTGAATTCTTTGTGAAACAACCACAAGATTC[A/G]TAAAAGATGTTAAGTAAGAACTGCACGAGCAAAGG R 2 1 2 1 101000 f 74 goat snp20153-scaffold2-6111744 7 20361414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400189 Affx-122960190 AX-123270544 7 86307336 TACTCGGGTGGCTGTCCTATGTAGAATGGGTCTTA[C/T]AGGCGAAACTGTGGAATAAGGATTTCTCCTTTGTT Y 2 1 2 1 101000 r 74 goat snp20152-scaffold2-6066874 7 20316408 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780042 Affx-122951704 AX-385267141 7 86395334 CAACAATGCAAAACCATTTTCACTGCACGCACAAG[C/T]AAACTTCCTCTAAGAACTATCTAAATGTAAACATG Y 2 1 2 1 101000 f 74 goat snp20150-scaffold2-5978876 7 20228934 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772800 Affx-122969960 AX-385259945 7 86428415 CCCACTGAGAATGTTGAAAATAACCAGTTCTGCCC[A/G]CTACAGTTAAGAAATTAAGGCCAGAGTTTACGTGG R 2 1 2 1 101000 f 74 goat snp20149-scaffold2-5945795 7 20195406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418855 Affx-122946131 AX-123289203 7 86519430 CCTCAGTGGTAACCCACTGAGAAGGTACACTTCTG[A/C]AGTCTATAATGCACATAATTTGCCTGGAGCTCAAA M 2 1 2 1 600000 f 74 goat snp20147-scaffold2-5854780 7 86519430 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785927 Affx-122946131 AX-385272964 7 86519430 CCTCAGTGGTAACCCACTGAGAAGGTACACTTCTG[A/C]AGTCTATAATGCACATAATTTGCCTGGAGCTCAAA M 2 1 2 1 101000 r 74 goat snp20147-scaffold2-5854780 7 20104575 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386087 Affx-122971445 AX-123256445 7 86574457 CCATGTGAACGGCCTCGTGAGGATGATGAAGTAAA[C/T]GGTCCTTTGTTCCAGACTTTTAAACAATTTTTTAC Y 2 1 2 1 101000 f 74 goat snp20146-scaffold2-5799753 7 20049555 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437794 Affx-122931687 AX-123308132 7 86627300 GGAGAGCAGATTACCTAAAATTGTGGTTAGACTGA[C/T]TAAGGCAAACAGGTGACTTGAGTTGGACAGTCAGT Y 2 1 2 1 101000 f 74 goat snp20145-scaffold2-5746910 7 19997237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796415 Affx-122946531 AX-385283365 7 86692546 TTCCCCTCAAACTCTTTTAACAAGGGGTGGTATGT[A/C]TCTTGCTTACTTTAATTCTTGTTGGTTTGATATTT M 2 1 2 1 101000 f 74 goat snp20143-scaffold2-5681664 7 19932109 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441387 Affx-122928851 AX-123311724 7 86726348 AGTGACAGGCGACCAAAGAAAAGGGCTGATGATGA[C/T]GAAAAGGGAAAATTGACTTGGAGCCCATAAAAGTA Y 2 1 2 1 101000 f 74 goat snp20142-scaffold2-5647862 7 19898225 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802361 Affx-122950105 AX-385289265 7 86762421 TTGTACCATTTTCCAACTTTTTAGTAAATCTTTTG[A/C]GCTCCAAGTTTGTCCAATATTTTACAATGCTTGAC M 2 1 2 1 101000 r 74 goat snp20141-scaffold2-5611789 7 19861664 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379077 Affx-122976324 AX-123249436 7 86811767 AAGAAATTTATGGTGAAAGGACAAAGTGGACTAGC[A/G]TTTATGGAATTATTTTATCATGTGTTCCCATTATA R 2 1 2 1 201000 r 74 goat snp20140-scaffold2-5562443 7 19812432 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389894 Affx-122968125 AX-123260251 7 86866335 AGGTAGTAACTCAAGCAAAGGAAGCACTCTGGCTG[A/G]ATGAGTGATTGGTCAGCAAGGCCTGAATCATGGGA R 2 1 2 1 101000 f 74 goat snp20139-scaffold2-5507875 7 19757502 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771630 Affx-122943777 AX-385258788 7 86967625 CCAGATGCTGATCCCTGGGGATCTATACACAAAAC[A/G]TTTCTTTCGTTCTGTCACTCAGTGTCCACTGAGGC R 2 1 2 1 101000 f 74 goat snp20137-scaffold2-5406585 7 19655815 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778841 Affx-122971696 AX-385265949 7 87010353 GTCCCATGTAGTCTCGTGTAAATACTTGCGTGAGA[C/T]AAGTATTATCACTCCACTTTACAGGGGAGGAAACT Y 2 1 2 1 202000 r 74 goat snp20136-scaffold2-5363857 7 19612502 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766832 Affx-122926494 AX-385254155 7 87065433 GGGAAAAAAAAAGACTAGGTATGCCGCATTTTGGG[C/T]GAAACTGGCTTATAATAGGTTTGAGCCACCAAAGT Y 2 1 2 1 101000 f 74 goat snp20135-scaffold2-5308777 7 19556525 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379054 Affx-122976341 AX-123249413 7 87099258 CGGTCATTTTCAGTTTCATTGATACTGCGTGATCA[C/T]GGAGGGAAAACCCTGGTATTTTCCCCCCTCAATAT Y 2 1 2 1 202000 f 74 goat snp20134-scaffold2-5274952 7 19521985 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778364 Affx-122940639 AX-385265479 7 87129803 CTATTCTACTGGGGAAAATGGATCCTAGTTTATAC[C/T]CAAAAGCTAATGGTTGTTGGTTGGATGAGTTCAAG Y 2 1 2 1 101000 r 74 goat snp20133-scaffold2-5244407 7 19490246 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448060 Affx-122923691 AX-123318396 7 87178558 GAAGTTCCTTGTTGCTCTTGTTTAGTTGCGGTCAT[A/G]TTTGACTCTACCATCCCAAGGACTGCAGCACACCA R 2 1 2 1 101000 f 74 goat snp20132-scaffold2-5195652 7 19440010 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441786 Affx-122929092 AX-123312123 7 87219999 GCAAAAAAATAGAAGAAAGTAAAATGCAAATAAGA[A/C]GGTATCATTCCATTGTTTAAATACTGATGGGACCC M 2 1 2 1 101000 r 74 goat snp20131-scaffold2-5154211 7 19398458 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419165 Affx-122945734 AX-123289513 7 87249467 TATGCTTCAAGGAGTTGCTAAAACTACCATACCTC[A/G]CCACAGCTAAACAATCTGCCTAGAACAGTGACACA R 2 1 2 1 101000 f 74 goat snp20130-scaffold2-5124743 7 19369123 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426212 Affx-122940364 AX-123296558 7 87326472 AAAGATGTAATAATGAGATGTAATAACAGGGAAAA[C/T]GGCTAAACACAAATATTGCATAATAAAAAATATAG Y 2 1 2 1 101000 f 74 goat snp20128-scaffold2-5047738 7 19291533 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429640 Affx-122937681 AX-123299981 7 87366809 AGCATCTGGTCAGGATCGGGGCTGCCAGAACATCA[C/T]ATATCAATCACATATAAAAGAATGCACTAGTCCAC Y 2 1 2 1 101000 r 74 goat snp20127-scaffold2-5007401 7 19251536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385363 Affx-122971640 AX-123255721 7 87401186 GGACAGGCCACTGATGAGACTTTCAAGTGCATGTT[A/G]TGAGATGTAAAAGCTCACAGAAGGTGGGCAAAGAG R 2 1 2 1 101000 r 74 goat snp20126-scaffold2-4973024 7 19217179 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781052 Affx-122979085 AX-385268139 7 87430318 CAGACCTCATGTCCAGGTAATGCTAGAATGCCAGC[A/G]TTTTATCCTGATAAAAGCGCAAGCATAATTCCATA R 2 1 2 1 102000 f 74 goat snp20125-scaffold2-4943892 7 19188396 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403403 Affx-122957766 AX-123273756 7 87478578 TTAGATAGTATTATAAGTAAGCATAAAAATAAGTC[A/G]CTAATTCTGGAGTGATACTTCAAATACTGCAAATA R 2 1 2 1 101000 r 74 goat snp20124-scaffold2-4895632 7 19140428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782819 Affx-122976424 AX-385269892 7 87507639 CTTAAAAAAGATAGTGTCCTCGATTATTTCAAAAA[C/T]AAGGGTTAGAATAATTATTCTATGCAGGCAATAGG Y 2 1 2 1 101000 r 74 goat snp20123-scaffold2-4866571 7 19110928 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423132 Affx-122942900 AX-123293478 7 87564238 AGCAAAAATCTGAGAGCAAACCAAATGTGTGACTA[C/T]AGGAAAAAAGTTAAAAAATTACTTTGTATGATGAA Y 2 1 2 1 101000 f 74 goat snp20122-scaffold2-4809972 7 19054107 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767667 Affx-122969986 AX-385254907 7 87605098 CATAGGGTGAGAGGCTTTTTAACTTGTTTTCTCAC[A/G]CTCTTTGGTCAAATACAGACGTTACATCTTTATTC R 2 1 2 1 202000 f 74 goat snp20121-scaffold2-4769112 7 19013354 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799350 Affx-122932214 AX-385286280 7 87647263 ATAATTAAATCCCATAATGTCTTATAGACCCTGAT[A/G]CTACCAGTGAACAGGCCATGTGTTTTATCATGATT R 2 1 2 1 102000 r 74 goat snp20120-scaffold2-4726947 7 18971231 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395956 Affx-122963568 AX-123266311 7 87710437 AGAGTGATTATTTCTGGATTCTGCCATATGTATTT[A/C]TAAATATTTTAAATTTTCCTAATTTTATTGGAATA M 2 1 2 1 103000 f 74 goat snp20119-scaffold2-4663773 7 18908148 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790175 Affx-122962815 AX-385277179 7 87751097 TGGACTCTCACAAAGAATAGCAGTCAGGTGAGATC[A/G]TCTTAGATAGTCCTTTCAAGACAGGTATTTTGTGA R 2 1 2 1 101000 f 74 goat snp20118-scaffold2-4623113 7 18868086 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381037 Affx-122974640 AX-123251395 7 87779777 AAAAACAATGAGAAAAGAAGGAGGAAGAGAAGAAG[A/G]GAGGAATGAACTGTTAAAATCTAGAATTTCCAATG R 2 1 2 1 101000 r 74 goat snp20117-scaffold2-4594433 7 18839304 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428925 Affx-122938904 AX-123299267 7 87854067 TATCAAAGTATGAGTGAACTCAAGTTGCTACTGCT[A/G]CTGCTCCTAAGTCACTTCAGTCATGTCGGAACCCA R 2 1 2 1 101000 f 74 goat snp20116-scaffold2-4520143 7 18764710 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424505 Affx-122941741 AX-123294851 7 87942043 CACCAGATAAGTGAATAAGAAAATTCATGGATTAC[A/G]CTCTTCCATTCACATGCTGTTATGTCAACCAGCAT R 2 1 2 1 101000 r 74 goat snp20115-scaffold2-4432167 7 18676187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407978 Affx-122954333 AX-123278329 7 87976676 TAGATGAGATGAATTAAATAACTTGCCTAGATCAC[A/G]TAGATTTGGAAAAAATGGCAGGCTTGGAATAAAAT R 2 1 2 1 101000 r 74 goat snp20114-scaffold2-4397534 7 18634960 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778059 Affx-122925204 AX-385265175 7 88030164 ACTTTTTTTTTAGGTGGCAATAGAATTGTTATGAA[C/T]GTTTCATAGCACTGATCCTTGCTGATACATTAGGG Y 2 1 2 1 101000 r 74 goat snp20113-scaffold2-4344046 7 18581302 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793977 Affx-122953512 AX-385280946 7 88068579 TTGTGTCATTTCATTTTCAGTGCCTGACTTCTTCC[C/T]GATGACTGCTCAGACTTTAGCATTGCAGAACCCAT Y 2 1 2 1 101000 f 74 goat snp20112-scaffold2-4305631 7 18542812 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769137 Affx-122949391 AX-385256312 7 88101721 TGCTTAGTGTCCCGTGGCCCCTTTACAATTTCTTA[C/T]ATAATGGTTTTGCCAATTCCTAAAGATAATTTTTA Y 2 1 2 1 102000 f 74 goat snp20111-scaffold2-4272489 7 18509554 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388313 Affx-122969375 AX-123258671 7 88142476 CCAATACTTAAATATATTTTGTGAAATATATTTAT[A/G]CTGACTTTAGATTCATCTACAATGTATGTCACAGT R 2 1 2 1 101000 r 74 goat snp20110-scaffold2-4231734 7 18468808 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440302 Affx-122930217 AX-123310639 7 88221155 GATCAGTTTATCTCTTCAGAGCAGAAAATTATGGC[A/G]TGTACTGAGCTTTCTGTGCAACTGCTGGGTTGCTT R 2 1 2 1 101000 f 74 goat snp20108-scaffold2-4153055 7 18388338 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320797789 Affx-122948028 AX-385284728 7 88258368 AAAAACCAGCACCCAGTAACGTAAACAGGGAAAAC[G/T]CAATATGAAGGGTTAACTAGCAAAAAACAAACAAA K 2 1 2 1 101000 f 74 goat snp20107-scaffold2-4115842 7 18351187 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448562 Affx-122923419 AX-123318898 7 88294007 GTAGAGCCATTTTTCCTTCCAAAAACTGAGATACC[A/G]CCAAACTAAAGAGAAGACATAGGTAAATACTAGCC R 2 1 2 1 101000 f 74 goat snp20106-scaffold2-4080203 7 18315586 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770074 Affx-122952643 AX-385257241 7 88333507 GGAGCCTCTTTTCTTCTTATACTTATCTATTACCT[A/C]GTCAAAGTGACTAAGTTCACTTGCTGAATGACTTG M 2 1 2 1 201000 r 74 goat snp20105-scaffold2-4040703 7 18274100 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432551 Affx-122935542 AX-123302892 7 88366652 CTCATCTGCCCAGGAACCCCAAGTTTCTGTATACA[C/T]AAGTTGGGCTGGTTTTAGATTTTAACAGAGGTTAT Y 2 1 2 1 101000 r 74 goat snp20104-scaffold2-4007558 7 18240261 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449113 Affx-122923580 AX-123319448 7 88414528 GCAACCATATTTTAAAATGACCCTTTGAGTTTTAG[C/T]ATGAAATTATATAAACCATTAAATAATGGTCACCA Y 2 1 2 1 101000 f 74 goat snp20103-scaffold2-3959682 7 18192007 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273314 Affx-1111833557 AX-519546957 7 88419770 TACAGAGAGCTCTAATCCTCCACAGACTAATTCCA[A/G]TTCATCACAGGATGAAAAGTGAAGTAAAGGCCCAG R 2 1 2 1 101000 f 74 goat 7_88419770_AF-PAKI 7 88419770 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320800872 Affx-122931848 AX-385287787 7 88459693 AGTTATTCAATACCAGGGTCCCAGTGAAAAAAATC[A/G]TCACTAAGTTACAGTTCTGATGTTTGAAGCTGATG R 2 1 2 1 101000 f 74 goat snp20102-scaffold2-3914517 7 18146950 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464536844 Affx-1110535911 AX-516008791 7 88461755 GATGCCTGACTTGGGGCTTCTCCAAGCCCTGAGTA[C/T]GGTGCTGCTGTGATCTGCACAGGCCACTTCTTGTG Y 2 1 2 1 202000 f 74 goat GoatD01.038282 7 88461755 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320784002 Affx-122967182 AX-385271056 7 88535646 AGTAAATCAACAGTGCCTTTCTGATAGTCTCCCAG[C/T]ACATTTATAATCAGTTCCATTTAGTGATAAGTGAT Y 2 1 2 1 101000 f 74 goat snp20101-scaffold2-3838564 7 18071098 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795183 Affx-122935724 AX-385282141 7 88564647 AATAAAGGCATTTTCTTTCCAGATAGGCATGTAAG[C/T]GTAGTTGAGATCCTGTTATAAATTATGTCTTACTT Y 2 1 2 1 101000 f 74 goat snp20100-scaffold2-3809563 7 18041854 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278535 Affx-1111836475 AX-519552017 7 88594020 ATTTTTACTGTTCACATTTGGTGTGCATCTTTCTA[C/G]ACATTTTTCTATGCACATATACACAAATTTAAAAT S 4 1 2 1 101000 f 74 goat Random2.2K-834 7 88594020 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418994 Affx-122946058 AX-123289342 7 88594482 TAGTTTGTGCAAAGTGAGTCAGAAACCAATCAACA[C/T]TCATGATTTCCACTTTTACAGAAATTTGTAATATA Y 2 1 2 1 101000 f 74 goat snp20099-scaffold2-3779728 7 18012019 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783966 Affx-122961221 AX-385271020 7 88626674 AGGGAAAAGTTAGAAAAAATATGGTAAAAGAATAA[C/T]GACAGAATATGATGAAAATTAAGGCTAGTGGTTTC Y 2 1 2 1 201000 f 74 goat snp20098-scaffold2-3747536 7 17979874 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422094 Affx-122943579 AX-123292441 7 88656168 TTGGAGGAATAAGATGGTTTAAAGTGACAAAATGG[A/G]CCTCAGCGTACTGGGGATAAAATGGAAACGAGAGG R 2 1 2 1 201000 f 74 goat snp20097-scaffold2-3718042 7 17950335 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770100 Affx-122944290 AX-385257267 7 88701775 TGAAGACATAGAAGAAAAGGGAGGTAAGTTTTAAT[A/G]GAGAAGTAGAAGGTGGTGATTCATAGTGTGCATGT R 2 1 2 1 101000 r 74 goat snp20096-scaffold2-3672435 7 17904773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444370 Affx-122926610 AX-123314707 7 88840970 CAACTCATCGCTGACTGGGATTCTTTTTGAAACCA[C/T]GTGATGGATCAACATAAACATCTGACCGGTATGTT Y 2 1 2 1 101000 f 74 goat snp20093-scaffold2-3533240 7 17765943 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385914 Affx-122971573 AX-123256272 7 88886472 TTCATCTCCTTGTTCAAGTCTCCACTCTCCCATTT[A/C]CCTGCCAGCATAAGGCGTGTGCTTTTGTTTTGCAA M 2 1 2 1 201000 r 74 goat snp20092-scaffold2-3487738 7 17720201 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414890 Affx-122949128 AX-123285239 7 88929412 GTGTGCCATATGGTACCTGGCTAACCTCACCACTA[C/T]GTCTATCCCTGTGGAGGATGGAGCCCTTCATTCTG Y 2 1 2 1 101000 f 74 goat snp20091-scaffold2-3444798 7 17676766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399857 Affx-122960240 AX-123270212 7 88967958 CTAAATACTAAAACCTTGTAAGAGATGAGGAATGG[C/T]GAAAGAGGGAAAATTAGTGTATAAGATACGAAAGA Y 2 1 2 1 101000 f 74 goat snp20090-scaffold2-3406252 7 17638184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427167 Affx-122939619 AX-123297510 7 89006410 CTTCTACTTGTGTCTTCCTGTTGCTTTCTTTTACT[C/T]GTCTCATTAAAACTGTATCTAGTGTTAGCATGTCA Y 2 1 2 1 201000 r 74 goat snp20089-scaffold2-3367800 7 17599769 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443341 Affx-122927433 AX-123313678 7 89044199 GTATCATAAATCTGTTAAAACTAATGTCTGTTTGC[A/G]TTATAGAGGAAACACTAAGGTCTTCAAAGCTAATT R 2 1 2 1 101000 r 74 goat snp20088-scaffold2-3330011 7 17562122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452988 Affx-122920120 AX-123323321 7 89082953 ATTATATTTAGGTCCTTTGATGTCTGCATTGATTC[G/T]CCTCTGTTCTTAATGACTTCACTTTATTTATTAAG K 2 1 2 1 101000 f 74 goat snp20087-scaffold2-3291257 7 17522942 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381631 Affx-122974767 AX-123251989 7 89185793 AAATATATAGTGCAATTACTTTAAATAGCAGAGTC[A/G]TGAATGAAAGTAGTGTGGATCTTTCCAGCATTGTA R 2 1 2 1 101000 r 74 goat snp20085-scaffold2-3188417 7 17420097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381892 Affx-122974162 AX-123252250 7 89234771 ATAATAGTTTCCCCGTGGGTCATTTTGCTGTGTTT[A/G]CTGATTCCTGCTTGCCACTGTGTGGAGGGCTTCCT R 2 1 2 1 202000 r 74 goat snp20084-scaffold2-3139439 7 17370994 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410053 Affx-122953230 AX-123280403 7 89267003 GAACAGTTTACCAGAGATAGATTTCCTCTTGATCA[C/T]GCTCATTTGATCTTATACTAAGTCGTCAGCTCTTG Y 2 1 2 1 101000 r 74 goat snp20083-scaffold2-3107207 7 17338856 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390066 Affx-122968410 AX-123260423 7 89317076 TTAGGGTCAGGGTCCTCAGGGCCTGTGAAATTATC[A/G]CAAGCTGAGCTAAAGTTTTTCTCCATCACAGGAAG R 2 1 2 1 101000 r 74 goat snp20082-scaffold2-3057134 7 17288499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275013 Affx-1111834542 AX-519548595 7 89319642 CCCAGGTGCTGTCTGCCGAGGCCCCACTCTGGGGG[A/G]CATCACCAGAGACCCCTGCAGACCCCAGCTGGAGC R 2 1 2 1 202000 r 74 goat GoatD01.040940 7 89319642 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38412062 Affx-122951708 AX-123282412 7 89347409 AAATTATTGGATGAATAAATGGACTGAATGACTTT[A/C]TTTTGAGATTTGGCTTTACTTAGACAATGGCCATG M 2 1 2 1 101000 r 74 goat snp20081-scaffold2-3026801 7 17258148 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450739 Affx-122921863 AX-123321073 7 89445040 CTAATTCAGGCAGTTAAAGTTACTGTTTTTACTTT[A/G]CCTACCTTAAATGTCCTCTTTTGTTTCTGTTCTTG R 2 1 2 1 101000 r 74 goat snp20079-scaffold2-2929170 7 17160365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382145 Affx-122974046 AX-123252503 7 89475326 TCATTTTGGGTTCTACACTCATCTAAGTAATTGCC[A/G]TTTTATATGAGACTTGCTTCCTTTGATCAATGCAT R 2 1 2 1 201000 r 74 goat snp20078-scaffold2-2898884 7 17130559 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389712 Affx-122968681 AX-123260070 7 89526719 TTCTTCATGGAATGAGTACTACCATAACATGTAAC[A/G]CATTTAGGGAAATAGAATAAGTCATGCCAGTTACC R 2 1 2 1 101000 f 74 goat snp20077-scaffold2-2847491 7 17078815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387618 Affx-122969869 AX-123257976 7 89570957 TACCAAACTGATCACTGGAACAGTTACTCAGTGAT[C/T]TGTGACTGTTTTTATTTTACACCTCTCAAGGTCTT Y 2 1 2 1 101000 r 74 goat snp20076-scaffold2-2803253 7 17033481 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395701 Affx-122963728 AX-123266056 7 89608603 CAGTGAAATTTGGATCATTGCTTCAGGTGAAATCA[C/T]AGCTGGTTGATAGTCCCGAGGCTCTTTCCCACAAT Y 2 1 2 1 101000 f 74 goat snp20075-scaffold2-2765607 7 16997015 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778881 Affx-122960749 AX-385265989 7 89673177 TTTTTGGAAACAAGAATTCCTTTCACATTCTAAGA[C/T]AAGCTCTCTGCCCCTCAAAACTTGCAACATATCCA Y 2 1 2 1 101000 r 74 goat snp20074-scaffold2-2701033 7 16930950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382397 Affx-122973839 AX-123252755 7 89706196 GTGGCTGATACAATGAGGTACAGAGGTGAGTGAGA[C/T]GTGACCCTGCTGCAAAGACCCTACAGCCCAAAGGA Y 2 1 2 1 101000 f 74 goat snp20073-scaffold2-2668014 7 16897904 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801022 Affx-122934492 AX-385287936 7 89734943 AATGCGGCAAATAGATAAACACCACAGAATTTATG[C/T]GCATGGTATCTTGAAAATGGAAAAGAATTCAAGCA Y 2 1 2 1 101000 r 74 goat snp20072-scaffold2-2639267 7 16869188 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388335 Affx-122969358 AX-123258693 7 89788757 TGTATTGATCGATACCAGTTCTTATGGTTTTCCTT[A/G]CTAAATAATACTTTTTCATAAAATTATCAGTAAGA R 2 1 2 1 201000 r 74 goat snp20071-scaffold2-2585453 7 16815626 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419772 Affx-122945866 AX-123290120 7 89833045 GCATCATTTCTTGACTCCTTGGTGAATCCCTTGAC[A/G]TACAAATATACTCCTCCCTGCTCCCCATGTGCGGT R 2 1 2 1 101000 f 74 goat snp20070-scaffold2-2541165 7 16771636 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407979 Affx-122954332 AX-123278330 7 89896924 TTATTCATAGTTTGTTGCACACTGCAGGATTTTTC[A/G]TCTGCATGTATCAGAATTAATATACAGGTTTGTAT R 2 1 2 1 101000 f 74 goat snp20069-scaffold2-2477286 7 16707877 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780295 Affx-122978699 AX-385267390 7 89943204 GGATACACGATGGCCATAAAGATATGATCCCTAAC[A/G]TCTCCTTTTTCCTTGTGGAGGCATAACGCCCACAA R 2 1 2 1 101000 r 74 goat snp20068-scaffold2-2431006 7 16661500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429767 Affx-122938251 AX-123300108 7 90023348 ATTATGAAATAGCCAAAATGTGCTAAGGCCTGTGG[G/T]GTGAAATCTGGTTCCCTTTCACTTGTTCTGGGCTT K 2 1 2 1 101000 f 74 goat snp20066-scaffold2-2350862 7 16581107 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450039 Affx-122922831 AX-123320374 7 90064132 CCTATGCTAGTTAAACCCATCTAACCATCTACTTA[A/G]GACTTCCCTGGTGGCTCAACTTACAAAGTACTGAA R 2 1 2 1 303000 f 74 goat snp20065-scaffold2-2310078 7 16539957 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384982 Affx-122971893 AX-123255340 7 90113621 ACAAATTTATTTGTTAAATATCAGGGTTTCGGATC[A/G]TCTGTCTTGTTCATTGAATCCTTAGCATCTGACAC R 2 1 2 1 101000 r 74 goat snp20064-scaffold2-2260589 7 16490820 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770556 Affx-122977114 AX-385257720 7 90176082 TTATGTCTAAATGAATCCTGAGTTAAGATATAATA[C/T]TGCAAAATTATCTGTTTGGTCAGACCAAGTGAATG Y 2 1 2 1 101000 r 74 goat snp20063-scaffold2-2198128 7 16428594 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422687 Affx-122943663 AX-123293033 7 90217405 CTTAGAACAGAAACAGAAGATAGAAAAAGAGTCAC[A/G]GTAACGTATACACAATACTATATTTAAAATAGATA R 2 1 2 1 101000 f 74 goat snp20062-scaffold2-2156805 7 16387334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437717 Affx-122931744 AX-123308055 7 90249992 ATCCCTGAGTGGGGAAGAACCCCTGAAACAGGAAA[C/T]GGCAACCCACTCCCATATTATAATTGCTATATAAT Y 2 1 2 1 103000 f 74 goat snp20061-scaffold2-2124218 7 16354675 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401832 Affx-122959443 AX-123272185 7 90289618 CTTTAGGTGTGAAATATGAAACCCAGCTATGGACA[C/T]GTGTCTCTCTCTGCTCTTTCTTCCCATGATGTATT Y 2 1 2 1 201000 f 74 goat snp20060-scaffold2-2084592 7 16315045 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435951 Affx-122933534 AX-123306290 7 90322987 AATATTCAGTAATTCATAATCTCTTTCTCAGAGAT[A/G]CTTTTCTAATTCTGAAGCCTTCTGAGTATTGATCA R 2 1 2 1 101000 r 74 goat snp20059-scaffold2-2051223 7 16281674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787311 Affx-122938182 AX-385274336 7 90352263 CACTTTGTAGCAGACCAGTCCAAAATAAAATATTA[C/T]ATCACACAACGTATATGTCCAACAAATACTGAATT Y 2 1 2 1 101000 f 74 goat snp20058-scaffold2-2021947 7 16251516 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781676 Affx-122974637 AX-385268759 7 90406277 AAATTATGTAATTAGAGCCCGAGAAGTTAAAATAT[A/G]CTTGGAGTTTCAGATGTCTAGTTCGCTTTCTGATT R 2 1 2 1 101000 r 74 goat snp20057-scaffold2-1967933 7 16197150 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795099 Affx-122940955 AX-385282058 7 90449038 TTAGTTTATTTCTAATCAACTATGCTGTATAGCTG[C/T]AAGCTGAAAGGTGCCTGTAATTTGCCAGTTATTTA Y 2 1 2 1 101000 r 74 goat snp20056-scaffold2-1925172 7 16154465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447304 Affx-122924915 AX-123317640 7 90492567 TTGAAGGAATGTTCTTAGGTTTGATCATCCCTCTA[C/T]AGACTGAATGCTCCCAGCACCTTTGGTAGGAGAGC Y 2 1 2 1 101000 f 74 goat snp20055-scaffold2-1881643 7 16109193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771485 Affx-122934735 AX-385258643 7 90564513 GAAAAGGGAAACTTGCTTTAAGATGATACCACCTG[C/T]ACCCTTAAAGAAATGATGTCACTCTGTCAGCCAGC Y 2 1 2 1 101000 r 74 goat snp20053-scaffold2-1809697 7 16037036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380152 Affx-122975974 AX-123250510 7 90616210 TGCAAAGAGACAGAAATGACTGAAGTGATGTAGCA[C/T]GCACACATGCCTGAGAAGTCTAGTTTAAGAAAACA Y 2 1 2 1 201000 r 74 goat snp20052-scaffold2-1758000 7 15985704 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388039 Affx-122969546 AX-123258397 7 90647040 AAGCAGAAATTACCACTAATCAATAGTGACTCTCC[A/G]CACTCAGGTGTTTTCCTTTTATTCACATCATCTTT R 2 1 2 1 101000 f 74 goat snp20051-scaffold2-1727170 7 15955811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773666 Affx-122969547 AX-385260806 7 90680012 ATAAAATGAAAGGTTGTTATTGAAATCCAGTGAAA[G/T]GACAACACTCTGACAGATGTTTTGTGAATCATAAA K 2 1 2 1 101000 r 74 goat snp20050-scaffold2-1694198 7 15922591 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377424 Affx-122977549 AX-123247783 7 90715586 CTCTCACTGTTGTTGTTCAGTGATGAGCTGCTTCT[C/T]CCGTGGAACTGGAAATATCTTGAGTACACAGCTGA Y 2 1 2 1 102000 r 74 goat snp20049-scaffold2-1658624 7 15887002 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389710 Affx-122968683 AX-123260068 7 90757341 TTTGTAACAAGTGTTACCGCCGAGGGTTTCCATTG[A/C]GTGTTGCAATCAGGATACACCTATTCTTGAGAACC M 2 1 2 1 101000 f 74 goat snp20048-scaffold2-1616869 7 15845188 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779847 Affx-122952334 AX-385266946 7 90844247 TCTAACTTCTGACCAAAGGTAAAGTAGCTTATTTT[A/G]TAATATGTAATTTTAAAGTATTGCTGTTATCATTC R 2 1 2 1 303000 r 74 goat snp20046-scaffold2-1529963 7 15759346 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416095 Affx-122948319 AX-123286444 7 90879006 TTCATCTAACAACCAAAATTGTTACTGCTGAGTAG[A/G]AAAGGGAGACCTGGTGTCAAGTGGTGGCTGAGTCT R 2 1 2 1 201000 f 74 goat snp20045-scaffold2-1495204 7 15724108 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779652 Affx-122942229 AX-385266754 7 90913484 AGGTGGTTCACATAGTAATTCAATCTGAACTGAAA[C/T]GGATCTTAACATGGTTAGCTGATGAAAACCACAGA Y 2 1 2 1 201000 r 74 goat snp20044-scaffold2-1460726 7 15689345 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273355 Affx-1111833558 AX-519546990 7 90954455 AGGGGGCCCCTCCCTTCCTCTGTGTTAGAGTCTCA[A/G]TTGGGCATCTCATCAAGGGCAGCCTGTTCTGCCCA R 2 1 2 1 102000 r 74 goat 7_90954455_AF-PAKI 7 90954455 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398402 Affx-122961638 AX-123268757 7 90995222 TGACTTCTGACAGTTTAGCTTGCTTCTTACATTAA[C/T]GTCTTTCTTTCTCTTTGCCATGTGTGTGCCAAACT Y 2 1 2 1 101000 f 74 goat snp20042-scaffold2-1378988 7 15608049 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431456 Affx-122936494 AX-123301797 7 91034327 TGAGAAAGTAAAGAATGGTTTCTGTTCTGTTAACC[A/G]TCAGATTTCTAAGCACTATCAGGCTTATTCCTGCA R 2 1 2 1 101000 r 74 goat snp20041-scaffold2-1339883 7 15568804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402101 Affx-122958691 AX-123272454 7 91064391 CACTGAATATCCCTGAAATGAGAGGTAGAGTAAAG[C/T]ATTTAATATTCCCAATGCCTAACCTGCCACCCAGG Y 2 1 2 1 101000 f 74 goat snp20040-scaffold2-1309819 7 15538575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428765 Affx-122938425 AX-123299107 7 91106486 GCCCGTGTTTGCTCAGGGCAAACATTCCGGAGCAC[A/G]CCCTCTCATGGGTTCTGCCTCTGCCTCCCAGTCCA R 2 1 2 1 101000 f 74 goat snp20039-scaffold2-1267724 7 15497213 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786644 Affx-122945424 AX-385273676 7 91135860 TGATTGTAAATTCTCTAGAAAGCATCTTTTCCTAC[A/G]AGCATTTTCATAAATGCATATTAAAGTCACACCGG R 2 1 2 1 101000 r 74 goat snp20038-scaffold2-1238350 7 15467679 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403428 Affx-122957744 AX-123273781 7 91181787 CGTTTAAATATACAAAGCTGCAGAAAGCTAACCTG[A/G]AGTGTTTTACTTTTCACTTATTGCTGACTTATTGC R 2 1 2 1 101000 f 74 goat snp20037-scaffold2-1192423 7 15423856 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377922 Affx-122977227 AX-123248281 7 91236334 TTTTCTGAAGGAAATGGAGGAGGAAGGGGAGCAAG[C/T]GTCCACTGAGCACTAGTATTAAACACCCAGAATCG Y 2 1 2 1 201000 r 74 goat snp20036-scaffold2-1137876 7 15368534 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417164 Affx-122947338 AX-123287512 7 91265130 ACTTGTTGCCAGCATTTCACCCTGTGGAGCACCCT[A/G]ATTCTTCAAGCTTTTTATTCCCATGACTTGACACA R 2 1 2 1 101000 r 74 goat snp20035-scaffold2-1109080 7 15339760 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391243 Affx-122967383 AX-123261600 7 91363411 TTGACACCGAATGTTAATTCAGGGAAAAGGTATTA[C/T]ATTACCATATGAAAGATAAAGAAAGCATAAGTTAA Y 2 1 2 1 101000 f 74 goat snp20034-scaffold2-1010799 7 15240868 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451752 Affx-122921525 AX-123322085 7 91408906 TCTGGCCTCCTAGCCAGTTCTTGAGCTTACTATGC[A/G]CACCTCAGGGCATCCGTTCTTGCTGGTTTTTTTCT R 2 1 2 1 201000 r 74 goat snp20033-scaffold2-965304 7 15195310 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413656 Affx-122950120 AX-123284005 7 91455756 AAAAACTATTTCAGATGGACCTGTTTCAATTCATC[A/G]GATGTGGAGTAGTCTCCAGGTCAGCTTCACAGGCA R 2 1 2 1 101000 f 74 goat snp20032-scaffold2-918454 7 15148501 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769283 Affx-122944826 AX-385256455 7 91485272 TCTTATAACTTGTCTAACATTTATATGAGATCAAC[A/G]TTCAAAGGGCTTATTGTTGATATTAAGAAATACAA R 2 1 2 1 201000 r 74 goat snp20031-scaffold2-888938 7 15119480 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388654 Affx-122969109 AX-123259012 7 91524538 TGCGTATTTTAAAGGGTCTCACAAATACACAAAGC[A/G]GAAAATCTGTCTTATTTTTAAAAACTTACACTCTT R 2 1 2 1 101000 f 74 goat snp20030-scaffold2-849672 7 15080461 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777818 Affx-122968384 AX-385264936 7 91598482 TCCTTAGCCCTCAACTCACAACAATTCAGAGAGAT[A/G]CACTGGAAGTGCCATCCAAGTACATAACTTCGGGC R 2 1 2 1 101000 f 74 goat snp20029-scaffold2-775728 7 15006553 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418903 Affx-122946097 AX-123289251 7 91630255 GGCTTTAGAACCAAAGAGACCAAAGTTTGAATGCT[G/T]ATTTGATCATTTATCAGTCTTAAGATATGGGCCAT K 2 1 2 1 101000 f 74 goat snp20028-scaffold2-743955 7 14975653 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405709 Affx-122956535 AX-123276061 7 91660212 CAATTCTTTTTCTTCCTGAAAAGGAAGTTCTATCC[A/G]TTTGTGCAGTTCAGTCTCTTATTAGAAAGTTCTAT R 2 1 2 1 101000 f 74 goat snp20027-scaffold2-713998 7 14945958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410694 Affx-122952737 AX-123281044 7 91694459 GGAAGATCTCTCTCTCTGATTTTTCTGGGCTGAGC[C/T]ATCCTCCAGGGAGGTCTGACTATCCCTAAAGAGAA Y 2 1 2 1 202000 f 74 goat snp20026-scaffold2-679751 7 14911425 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417903 Affx-122946741 AX-123288251 7 91727735 AGGGAATGAAATTTTCATTTAAATAATTCAAGGAG[G/T]TGCCAAAATCATTGTGAAGTTTCAGAACCCTGGGC K 2 1 2 1 101000 r 74 goat snp20025-scaffold2-646475 7 14879104 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769447 Affx-122968530 AX-385256617 7 91756918 CATAAATGATGTATGAAAAAGATGAGCTATCTCTA[C/T]AACATCCTTCTAGAATATGAACTTACTAGAGGTTT Y 2 1 2 1 101000 r 74 goat snp20024-scaffold2-617292 7 14850185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379534 Affx-122976066 AX-123249892 7 91790958 AAAGGCATCACAGGCAAAGGCGTTGTTATCACTGT[A/C]CTGGATGATGGCTTGGAGTGGAACCACACAGACAT M 2 1 2 1 101000 f 74 goat snp20023-scaffold2-583252 7 14815667 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421096 Affx-122944223 AX-123291443 7 91936326 GAAACAAACTAGAGAGAGAACTGCATCCTTGAAAA[C/T]GTTATAGTTGCTCCCTGTGTGGAGGCAGGGTATGG Y 2 1 2 1 101000 f 74 goat snp20021-scaffold2-437884 7 14669546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450260 Affx-122922185 AX-123320595 7 91965985 ATTTGGTCTTTATCAGATTATTCAGTGATCCTTCC[A/G]TTGTCATCGTCAAGGATTTACTGCTGAAAAAACTT R 2 1 2 1 101000 r 74 goat snp20020-scaffold2-408225 7 14640054 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377367 Affx-122977645 AX-123247726 7 92013304 CTTATGCTTCAAACATTGTGCTGTTTGCCAAACTA[C/T]GACGGCCTCAGAACTGATGTTCACTTTGGGGTTTA Y 2 1 2 1 101000 f 74 goat snp20019-scaffold2-360906 7 14593328 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382537 Affx-122973789 AX-123252895 7 92063001 TTTCATACTATCTCCAGGTGACTCATAGGCATGCT[C/T]AAACTTGAGAAATACTGCATAATCTCATGTAATGT Y 2 1 2 1 101000 f 74 goat snp20018-scaffold2-311209 7 14543357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774209 Affx-122933088 AX-385261346 7 92103052 AACACAGACACTGACAATAAGGTCCATAAGCTTTA[C/T]GCTATAACAAGTTGACTCCCCTACTTTCAAAAAGT Y 2 1 2 1 101000 f 74 goat snp20017-scaffold2-271158 7 14503579 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439064 Affx-122930318 AX-123309401 7 92139636 AAAAACTATTTCCAGTTATATTCTATTTCAGGATA[C/T]AGTGGACGTCGTATTACACCGTAGTTCTCCCCAGT Y 2 1 2 1 101000 r 74 goat snp20016-scaffold2-234574 7 14466831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773096 Affx-122938716 AX-385260239 7 92168538 TATTGCTTTCCAGGGAATTACTCTACAGCTTTTGC[A/C]GTGTCCATTTCATTGCTAATAGCATAAAGAGAACA M 2 1 2 1 101000 f 74 goat snp20015-scaffold2-205672 7 14437181 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410900 Affx-122952069 AX-123281250 7 92205597 GGAACCAACATTTCCAAAAGCTAGCAACGGGGCAC[C/T]GTTTCCTTGGAATAAAATGCGGCTTCCAGAGCACA Y 2 1 2 1 101000 r 74 goat snp20014-scaffold2-168613 7 14401961 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408814 Affx-122954035 AX-123279165 7 92243650 CTGAGGTAAGGGGTAAGGCTGTATGGCTGTAAATT[G/T]CCCACTTAGAGCTGCTTTCCTGCATCTCATAGGTT K 2 1 2 1 201000 f 74 goat snp20013-scaffold2-130560 7 14363243 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785555 Affx-122966008 AX-385272599 7 92276084 TCCCAACACTGTACTTAACAAGACCCTCTCTTTCT[C/T]AGATGACAGTCAAGCACATTGCTTGAGGTCTCATC Y 2 1 2 1 101000 f 74 goat snp20012-scaffold2-98126 7 14330305 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375420 Affx-122979193 AX-123245779 7 92337966 GTCAAATACTGAACCCCCGGGGCTAAGCTAGTGCA[A/G]CATCTTGGGTTAGCAAGGTGCCAGAGGAAATAGAC R 2 1 2 1 201000 r 74 goat snp20011-scaffold2-36244 7 14268206 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780971 Affx-122965353 AX-385268058 7 92367206 CACAGTTCAACTCATTGTAACAGCATCTTTCTAAT[A/G]GAAATAAGACAAGGGTGAAGACAAATTTGTCTTCG R 2 1 2 1 101000 r 74 goat snp20010-scaffold2-7004 7 14239096 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426048 Affx-122941105 AX-123296394 7 92447244 TCTCCTGCCAGTTAGAATATATTTCTGCCTTCCTC[A/G]CTGACTTCAGCTTTTGCATCATGGTGCTTTCCTGT R 2 1 2 1 101000 f 74 goat snp8084-scaffold1294-72935 7 14158383 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388407 Affx-122969290 AX-123258765 7 92534850 CTGGGTGAGGAGCTCCTTACTGTGCTTGCATTTCT[A/G]TGGAGAAATAAAAAGGGTTCAAAACATATTGCCAA R 2 1 2 1 101000 r 74 goat snp8086-scaffold1294-160541 7 14070220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421627 Affx-122944468 AX-123291974 7 92576393 TATTTCTGAATATATGTGCTTCAAAATGTAGGGCT[G/T]TGCTATTTTGCAGGAAATCAGGAGAGTCACAGTTT K 2 1 2 1 101000 r 74 goat snp8087-scaffold1294-202084 7 14028725 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385350 Affx-122971649 AX-123255708 7 92605665 TTACCGTCTGAGCCACCAGGGAAGATTGTTCACTA[C/T]GGATGCTTTAAAATCTGAGGGTTACATCTTGTCTG Y 2 1 2 1 101000 r 74 goat snp8088-scaffold1294-231356 7 13999444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802284 Affx-122923401 AX-385289188 7 92653729 AGTCATATATGCAGATGAATTCTGAATAATAAGGA[A/C]TGCTAATCATGAAATGCAGGATTTAATAAAGATTT M 2 1 2 1 101000 f 74 goat snp8089-scaffold1294-279420 NW_017211897.1 22839 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803660 Affx-986696164 AX-385290437 7 92674370 AGCGACTTCACATCACTTTGCCTGTGCCACACACA[C/T]AATATTCTGTTTTATTCCCTATGGAGACTCTTCTT Y 2 1 2 1 600010 r 74 goat 7_92674370 7 92674370 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 38413396 Affx-122950720 AX-123283745 7 92693786 AGATTTGCCTGAGAGTGTTGCTTAAATTACATAAT[A/G]CTATCGTTTAACTGCTCCTACAAAAAGTGTCATTG R 2 1 2 1 101000 r 74 goat snp8090-scaffold1294-319477 7 13915062 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409257 Affx-122953133 AX-123279608 7 92736661 ATTACATTCGCTTTGTACATTTGTTTTTCTCTTAC[A/G]ATAGATGTAGCAACACTAGTTCCAGAGAAGGGACA R 2 1 2 1 102000 r 74 goat snp8091-scaffold1294-362352 7 13872212 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446117 Affx-122925786 AX-123316454 7 92766654 ACAGCATTCTTGGCCCTTCAAAATAGGGTTCAGTG[C/T]GCCTTTTAAATTATGTTTTCACACTCATTTTTACT Y 2 1 2 1 101000 f 74 goat snp8092-scaffold1294-392345 7 13841881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777477 Affx-122940362 AX-385264597 7 92804247 CTGAATTGAGAAGGAACTTTAGGGAGAACCAGGAG[C/T]AGGAAAAGGAATGGTGGGATTAAAGGTCCAAAAAA Y 2 1 2 1 101000 f 74 goat snp8093-scaffold1294-429938 7 13803943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424311 Affx-122941963 AX-123294657 7 92833698 AGACATTAGGTTAAAGAGACTTGGCAGCTAGAATA[G/T]GTTGACATCCTGATAGCCTTCAAATCTGAAAAGGT K 2 1 2 1 101000 f 74 goat snp50291-scaffold718-1388086 7 13765526 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388354 Affx-122969343 AX-123258712 7 92896427 TGGTGTACATAAACTGATCACAGAATTAATGTTAA[C/T]GTATACACACATATGCACACAACCAATAGCATTAG Y 2 1 2 1 103000 f 74 goat snp50290-scaffold718-1325357 7 13702588 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794635 Affx-122957411 AX-385281596 7 92937104 ATTTTCAATCTTCAAGAGAATCTTTTTAGGTACAG[C/T]GATAGAGAACAAGCACAAAATATGAAGAATGGACA Y 2 1 2 1 102000 r 74 goat snp50289-scaffold718-1284680 7 13661890 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418591 Affx-122946365 AX-123288939 7 92970394 CCACGGACCCTGGTTTACTTCACAGAATTCAGAAA[C/T]TAGCTAAAGAGACAGTCTCATCAGGAGCTCAATAA Y 2 1 2 1 101000 f 74 goat snp50288-scaffold718-1251390 7 13629507 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476236 Affx-1251763742 AX-586011659 7 92979805 CTCCAGAGCTGCTGCACTTAGGCACAGAGTTACCT[-/ACACTCATGTGCCGCGGCCAGCACAAACAAGAGTCGCACCAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CACTCATGAACACCTCAGCACCATCTCCCAGCCTA - 4 1 4 1 20000 f 74 goat SV_350 7 92979805 - deletion junction SV-TF-chip 539476489 Affx-1251763742 AX-586011886 7 92979805 CTCCAGAGCTGCTGCACTTAGGCACAGAGTTACCT[-/ACACTCATGTGCCGCGGCCAGCACAAACAAGAGTCGCACCAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CACTCATGAACACCTCAGCACCATCTCCCAGCCTA - 4 1 4 1 20000 r 74 goat SV_350 7 92979805 - deletion junction SV-TF-chip 562165047 Affx-1251763742 AX-606940459 7 92979805 CTCCAGAGCTGCTGCACTTAGGCACAGAGTTACCT[-/ACACTCATGTGCCGCGGCCAGCACAAACAAGAGTCGCACCAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CACTCATGAACACCTCAGCACCATCTCCCAGCCTA - 8 1 4 1 20100 f 74 goat SV_350 7 92979805 - deletion junction SV-TF-chip 562165216 Affx-1251763742 AX-606940628 7 92979805 CTCCAGAGCTGCTGCACTTAGGCACAGAGTTACCT[-/ACACTCATGTGCCGCGGCCAGCACAAACAAGAGTCGCACCAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CACTCATGAACACCTCAGCACCATCTCCCAGCCTA - 8 1 4 1 20100 f 74 goat SV_350 7 92979805 - deletion junction SV-TF-chip 562165401 Affx-1251763742 AX-606940812 7 92979805 CTCCAGAGCTGCTGCACTTAGGCACAGAGTTACCT[-/ACACTCATGTGCCGCGGCCAGCACAAACAAGAGTCGCACCAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CACTCATGAACACCTCAGCACCATCTCCCAGCCTA - 8 1 4 1 20100 f 74 goat SV_350 7 92979805 - deletion junction SV-TF-chip 562165702 Affx-1251763742 AX-606941111 7 92979805 CTCCAGAGCTGCTGCACTTAGGCACAGAGTTACCT[-/ACACTCATGTGCCGCGGCCAGCACAAACAAGAGTCGCACCAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CACTCATGAACACCTCAGCACCATCTCCCAGCCTA - 8 1 4 1 20100 r 74 goat SV_350 7 92979805 - deletion junction SV-TF-chip 562165933 Affx-1251763742 AX-606941342 7 92979805 CTCCAGAGCTGCTGCACTTAGGCACAGAGTTACCT[-/ACACTCATGTGCCGCGGCCAGCACAAACAAGAGTCGCACCAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CACTCATGAACACCTCAGCACCATCTCCCAGCCTA - 8 1 4 1 20100 r 74 goat SV_350 7 92979805 - deletion junction SV-TF-chip 38425827 Affx-122940681 AX-123296173 7 93000739 ACACACTGGGACCGTGGGTATGAATGCCTTCACAA[C/T]ATTATTTCCTTTCAATATCTTCTTTCAGAATTTAA Y 2 1 2 1 101000 f 74 goat snp50287-scaffold718-1221045 7 13591175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417911 Affx-122946733 AX-123288259 7 93038686 GCTTAAATTCATCAGAGATTACTAGGCAACCAAAG[C/T]AAAGTAATAAAAGGGATAGAAAACATGTTTTTGTT Y 2 1 2 1 101000 f 74 goat snp50286-scaffold718-1183098 7 13553163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424169 Affx-122942529 AX-123294515 7 93074799 CAATCTGTTAAGCGAACATTGTGCATATCTGGAAA[G/T]GTTGTGTTCCATATGGAAGGACACAGTTAAGTCAC K 2 1 2 1 101000 f 74 goat snp50285-scaffold718-1146985 7 13516435 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464545824 Affx-1110537378 AX-516017703 7 93095274 ACTGTATGCAGCTGCAGCCATCTGTCCACCTTTGC[C/T]GTCCTCATGGCCTCAGTTGAGCTGAAGGTATGTGT Y 2 1 2 1 102000 r 74 goat GoatD01.018605 7 93095274 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320764949 Affx-986697125 AX-385252530 7 93111477 GTATGTTGTCAGTCTCTTCCTTTTGTTGCTGAGTA[C/T]CATTTCACACTATTGTATATCACAATGTGTTTATC Y 2 1 2 1 600010 r 74 goat 7_93111477 7 93111477 Ancestral_priority_1043 ancestry 0.752 recommended IMAGE 10K 10K ancestral 38390769 Affx-122967891 AX-123261126 7 93141298 CTAGAAGACATTAAATCGTTTTGAGCTGGATAGTA[C/T]ATAAATAGACCTAAATAAAGTTCACATCATTCCTA Y 2 1 2 1 101000 f 74 goat snp50284-scaffold718-1080486 7 13452081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376330 Affx-122978347 AX-123246689 7 93182377 GCAAGGTGTATGATTGGCATTCTGAATATTATTTA[C/T]ACCCCAATTCTGATTTTAATATTCCTTTAGATAAA Y 2 1 2 1 101000 f 74 goat snp50283-scaffold718-1039407 7 13410719 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778984 Affx-122929656 AX-385266091 7 93255950 ATTCTTCTGTTCACTCTGTTTATTCTGATCTACTT[A/G]CCAACTTAAGTTTTCAGGCCAGCAAAAGCTTAGAG R 2 1 2 1 101000 r 74 goat snp50281-scaffold718-965834 7 13336762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781113 Affx-122971156 AX-385268198 7 93304471 TAAGGAGCTCTGATTAACAATGCTTGCTTTCATTA[C/T]GGAAGAAATACTCATCTCCTGTGTTTGGGATCATC Y 2 1 2 1 201000 f 74 goat snp50280-scaffold718-917313 7 13288126 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406739 Affx-122955743 AX-123277090 7 93354767 AGACAGTTTGGAGTTCAAAACAGAGCTAAATGTTC[A/G]TTTTCAAGACCCTAACAACTCTTCATATTATCAAA R 2 1 2 1 201000 r 74 goat snp50279-scaffold718-867017 7 13235631 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413203 Affx-122950318 AX-123283552 7 93409675 TCTAAAGCGCTCTGCACGGCATTGGAGGAAGACAT[A/C]TAGAGGAAAGGGGTTCTGTGGTGATGACCCAGGGC M 2 1 2 1 101000 f 74 goat snp50278-scaffold718-812109 7 13183736 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790324 Affx-122950439 AX-385277327 7 93442268 AAAAACTGATTAAGTACTTAATCTTAAATACTTAC[A/G]CGTGGTCTGCAGCCAGGAGCATCTGCATCACCTAA R 2 1 2 1 102000 r 74 goat snp50277-scaffold718-779516 7 13151805 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416393 Affx-122947860 AX-123286742 7 93480413 TTAGAACAGAGGCTGCCCGTGAGACTGGCCTGAGG[C/T]GTGTACACCTGATATTTCTTACCTGAACCACCTGA Y 2 1 2 1 102000 f 74 goat snp50276-scaffold718-741371 7 13112408 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394774 Affx-122964833 AX-123265129 7 93513634 ATACAAAGCACAATAGCTACAACAATTACCATACC[A/G]AAGAACACGCATAGCAAAATCTTCAAACGATATGG R 2 1 2 1 101000 f 74 goat snp50275-scaffold718-708150 7 13078883 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273318 Affx-1111833559 AX-519546961 7 93550657 CCATGGGTACCAATGTGTAAAGACATGTATCCACC[A/G]TCACAGTATCATACAGAATAGTTCTGCTACCTTAA R 2 1 2 1 202000 f 74 goat 7_93550657_AF-PAKI 7 93550657 A G 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38385063 Affx-122971822 AX-123255421 7 93577015 ATTACCTCACCAGATGCATGGTGATAAATTTCCAC[C/T]TGAGACAAGAAAAACAATGCCATAACAAGATATTG Y 2 1 2 1 101000 f 74 goat snp50274-scaffold718-644769 7 13014999 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448201 Affx-122924236 AX-123318537 7 93607903 CCCTTCTTTCAAGGACTGTGTTCCCTCCAGTATAC[A/G]CCCTCTGTTATCTTTCTTTCAGCACATTTAAACTT R 2 1 2 1 101000 r 74 goat snp50273-scaffold718-613881 7 12984018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436702 Affx-122932325 AX-123307040 7 93683135 ACATGGGAATGTGGTGTGGGCCTTGAGAAGATTAT[G/T]CATAAGTGGCATTGAGGAAATATTTTCAGTGAATC K 2 1 2 1 101000 f 74 goat snp50271-scaffold718-538649 7 12907468 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416812 Affx-122948132 AX-123287160 7 93712754 GGAGGTGTGTTCGAGAATTACTGAGTAGAGTAGCT[A/G]GCAACTTTAGATGGGGTAATTTCGGATCAAATCAG R 2 1 2 1 201000 f 74 goat snp50270-scaffold718-509030 7 12877806 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793331 Affx-122929786 AX-385280309 7 93758707 AGGATAACTATTACAAGGATATTCTGCAAAAGATC[G/T]CTGTCTGGATGCCTGGATTTAAAACCTCAGTCCAC K 2 1 2 1 101000 r 74 goat snp50269-scaffold718-463077 7 12831809 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449945 Affx-122922903 AX-123320280 7 93796115 GCAGATGTTTTAAATCATCTCTCTTGGATGCTGTT[A/G]CCCCTTCCTTTTGTTCAAGTCTCAGCTAAAGGGAC R 2 1 2 1 101000 r 74 goat snp50268-scaffold718-425669 7 12793238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278537 Affx-1111836476 AX-519552019 7 93849810 ATATACTTTCTGGAGTGATTAAAATAAAAGCAAAA[A/G]TTAAAAAATGAGACCTAATTAAACTTAATAGCTTT R 2 1 2 1 303000 f 74 goat Random2.2K-839 7 93849810 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380491 Affx-122975710 AX-123250849 7 93861373 ACTTCCCTATGAGGCCAAGTTTTTCCTGTTGCAAG[C/T]TCTTTGTACTTACTGAGTGTCCACCTTGAAATCTC Y 2 1 2 1 201000 r 74 goat snp50267-scaffold718-360411 7 12728107 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396071 Affx-122963441 AX-123266426 7 93905224 CATCGCCTGTGGAGTTCTCTTCATCTCTCTTCATT[C/T]ATTACTTTCCAAGCTCAAAAGATATGATCCTGAGA Y 2 1 2 1 201000 r 74 goat snp50266-scaffold718-316560 7 12684011 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766184 Affx-122922244 AX-385253585 7 93950127 CTCCCTTACGTACTTAGTATCTTCTAGTGCCTTTC[C/T]GGAACAAAAGCCCATTTAGGTTCTGCCTGATAACT Y 2 1 2 1 101000 f 74 goat snp50265-scaffold718-271657 7 12639302 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803090 Affx-986696165 AX-385289960 7 93962811 ATGACACATGGGATGCAATGCTTCTATGTCAGACT[C/T]CCACATGCTGCATCACAGTCACACCCATCACACAC Y 2 1 2 1 600010 f 74 goat 7_93962811 7 93962811 Ancestral_priority_1043 ancestry 0.68 recommended IMAGE 10K 10K ancestral 38425881 Affx-122941637 AX-123296227 7 93994842 GACTATGTATGTACTCCCCAGTCAGAATTCGCTCC[A/G]TTTAGTATTCTACCCAGCGGCACGAACAGTGCGTC R 2 1 2 1 201000 r 74 goat snp50264-scaffold718-226942 7 12594119 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790008 Affx-122968111 AX-385277014 7 94039060 CTCCCATAAATTTTTAGCAGACTGCCACACACTTA[C/T]GTGTGGATTAAATTTCACAGTGATTTGTATATCAA Y 2 1 2 1 201000 r 74 goat snp50263-scaffold718-182724 7 12549605 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434569 Affx-122934123 AX-123304910 7 94099058 TCCCCTTCAGTGTGGTTATGTCATAAATTTGTAAT[A/G]AAGTTAGAGTTATCAGTTTACATTTCATTCTCAAT R 2 1 2 1 101000 f 74 goat snp50262-scaffold718-122726 7 12489568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389777 Affx-122968228 AX-123260134 7 94141922 TTCCTTATCTCTGGGAAAACAGAAACAGCTTGAAC[A/G]CCAAACTTAGAATTTAATCGTCAAGATGCTTTAAA R 2 1 2 1 201000 r 74 goat snp50261-scaffold718-79862 7 12446669 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769577 Affx-122954295 AX-385256747 7 94185040 AACAAAATCCCTATAAGATTTTGGAATCTGTCCAG[A/G]AAAATGTTAAGGGATAAAAAATGAAAGTTAAACAC R 2 1 2 1 201000 r 74 goat snp50260-scaffold718-36744 7 12403110 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449329 Affx-122922988 AX-123319664 7 94221708 TGATTGTCACTGTGAAGAATTTGAGGAATTTCTTA[C/T]GGGAGGCAGAAACATTGTTTTTCTCCCAAACTGGT Y 2 1 2 1 201000 f 74 goat snp50259-scaffold718-76 7 12365479 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444560 Affx-122926979 AX-123314897 7 94265019 TTAGTCCAACTGGCTGTTTTACTCTTTTTTGTACC[G/T]ACACAGTCCAGAGGATGATTCTGATTCACTGATGG K 2 1 2 1 101000 f 74 goat snp36591-scaffold441-43136 7 12321437 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442182 Affx-122928803 AX-123312519 7 94390871 CAGAGGTACATGGTCCAGTGAAAGGAGAGCCTTAA[G/T]CACAAAGCAGAGACTATGGACTGTGACATGGCTTT K 2 1 2 1 201000 f 74 goat snp36594-scaffold441-168988 7 12194285 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779413 Affx-122949878 AX-385266516 7 94445332 AAATGCATTAGACTTTTTCAGGCAGTCAAGGCATC[A/G]TCATTTCATTCTACCAAATTATACTCTATAATATG R 2 1 2 1 201000 r 74 goat snp36595-scaffold441-223449 7 12139885 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442791 Affx-122927725 AX-123313128 7 94477385 AAAGTAGAACCCAAGAATCTATAAATAAAAAGTAG[C/T]AGTTTTTGAGGGGAAAAACCTAAAACAGATACATC Y 2 1 2 1 303000 f 74 goat snp36596-scaffold441-255502 7 12107840 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408666 Affx-122953462 AX-123279017 7 94514590 GCTGCTTATCATACTGTACTTGATAATATCTTTGC[A/G]TTCAGAATCAACCTCATGAATCTATCTATCTTCTT R 2 1 2 1 101000 f 74 goat snp36597-scaffold441-292707 7 12069523 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791939 Affx-122953705 AX-385278929 7 94544326 TTTCTGTTTGACTTCTTCCTCCTGGGACACATTTT[A/G]CTGATGGCTTGAAAGAGACTGTAGACTCTAATCAG R 2 1 2 1 101000 f 74 goat snp36598-scaffold441-322443 7 12039276 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792539 Affx-122970135 AX-385279520 7 94585782 CCAAGGGACTCTGCCAAAAACCCAGATATATCTCT[A/G]ACTTGTTTAAACACTGCAGTGATGCCCTATTTCCT R 2 1 2 1 101000 f 74 goat snp36599-scaffold441-363899 7 11997580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773149 Affx-122937674 AX-385260292 7 94671348 TCTAGGAGTATATATTCAGACCAATGATTTTGCTT[A/G]TGCTCCAATAGTATTGTTACAAAAAGTATGTACAT R 2 1 2 1 101000 f 74 goat snp36601-scaffold441-449465 7 11912668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784634 Affx-122972607 AX-385271682 7 94722746 TTATTTGTTGGTATATATTCATGATCTATCTCAGT[A/C]TTTGGACATTGTAAATCCTTACTAAATATTTATTG M 2 1 2 1 101000 f 74 goat snp36602-scaffold441-500863 7 11862223 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442265 Affx-122928273 AX-123312602 7 94753235 ATCCCATTCCTCTTCTTTGCTTCTTAGTTTTCAGT[A/G]CTTATCATGCTAGGGTAATACCATATTTTTTTTTT R 2 1 2 1 201000 r 74 goat snp36603-scaffold441-531352 7 11831867 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422178 Affx-122943519 AX-123292524 7 94791151 TGCTAATCTGAAACCATTGTGACTTTTGGGAAATA[C/T]ATAAAACATTCCTCTCCCCTTCACCACTCTCTCCC Y 2 1 2 1 201000 f 74 goat snp36604-scaffold441-569268 7 11794931 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771730 Affx-122940785 AX-385258887 7 94837871 ACTTTTCTTTAGGAAAATTAAGCAAATAGAATTCT[A/G]CAAGGACAATACCACTCTTCTTATTAAGGAAATGA R 2 1 2 1 101000 r 74 goat snp36605-scaffold441-615988 7 11747589 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422572 Affx-122943755 AX-123292918 7 94873318 GGGGATTATTTTATGTATTTAAATACCTAAAGTTA[C/T]AGACTAGTTTTGTCTTCATTTTACACATGTGGGGT Y 2 1 2 1 103000 r 74 goat snp36606-scaffold441-651435 7 11711967 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400310 Affx-122960066 AX-123270665 7 94920288 ATTGCATCTTATCTCCTGATCCACATACTACACTG[A/G]AAATTGCTTTCCAGGTTTTACTAATTTTATTGATA R 2 1 2 1 101000 f 74 goat snp36607-scaffold441-698405 7 11664307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773524 Affx-122978012 AX-385260665 7 94963206 TGTTTATATGAAAGAACCTATAAAATTCAGGACAC[A/G]CAGATTAGGCTGGTGAATTTTCCTCCACAGTCACA R 2 1 2 1 101000 r 74 goat snp36608-scaffold441-741323 7 11614970 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393219 Affx-122965491 AX-123263576 7 95073160 CCTTTCACTCCTGCCAATGTTATGTCCTTTGTTGC[A/C]TGAGTAATTAAAATTTGAACTCTTTGCATCCATGA M 2 1 2 1 101000 f 74 goat snp36610-scaffold441-851277 7 11504740 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444441 Affx-122926556 AX-123314778 7 95104862 AGACCCACCAAATCAGAAGTCTAGAAAGTTGTGCC[A/G]TGCACAGTCGTGCACAACTCTTCCCTGGGGTGGGT R 2 1 2 1 101000 f 74 goat snp36611-scaffold441-882979 7 11472828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408058 Affx-122954272 AX-123278409 7 95135734 ACATACATAATGAATTGCAAGAGAAGTACTACCTA[C/T]GGATGGAGCATCTCTGGAACCAAATGCCCCAACAG Y 2 1 2 1 201000 f 74 goat snp36612-scaffold441-913851 7 11441635 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449342 Affx-122922978 AX-123319677 7 95180254 ACGGTTTAAAACATAAGTCTACCCTTCAACATATG[A/C]TGTGCAATTTTGCAATATTTGAGATTAATAGAAAT M 2 1 2 1 101000 r 74 goat snp36613-scaffold441-958371 7 11396399 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440501 Affx-122929358 AX-123310838 7 95217648 GTTATTCAAGGTTCAGCTGTATAATGATCACCTCA[C/T]ATTCAAATGACAAGTAAAACTTTAATTTCAGACAG Y 2 1 2 1 101000 f 74 goat snp36614-scaffold441-995765 7 11358921 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389855 Affx-122968156 AX-123260212 7 95265607 TGAGCCCTTTAAATCTGAATACAGAGGTTGCTGCT[A/G]CTGCTGCTGCTAAGTCGCTTCAGTCCTGTCCGACT R 2 1 2 1 103000 f 74 goat snp36615-scaffold441-1043724 7 11310445 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785800 Affx-122946936 AX-385272839 7 95295269 CAGTAAATATAGAAAGTAATGAAGTAGCAAAACCT[A/G]CACAGAACTGTGATACTTTCCTATTCCATTCAACT R 2 1 2 1 101000 r 74 goat snp36616-scaffold441-1073386 7 11281060 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394956 Affx-122964283 AX-123265311 7 95326338 AGCATTCTGTGCTCTAAATATTGGCCCTAGAGAAT[C/T]GCAACATGTATCTAATAAATAGCTTCATTGAACCC Y 2 1 2 1 101000 r 74 goat snp36617-scaffold441-1104455 7 11249626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775615 Affx-122944754 AX-385262746 7 95373095 TTTACCCTTCCATGTATCTTGCTTCTATAAGTTGA[G/T]CTGATTAGGATAGTGAAATTGTGATGATAAGAGTA K 2 1 2 1 101000 f 74 goat snp36618-scaffold441-1151212 7 11204226 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381130 Affx-122974570 AX-123251488 7 95404424 ATAAACATTTGAGAACCTCACTCAATCAAATGCTG[A/C]TACATCAGGAAAGAAAAGCTGTAAAGGATAACCAC M 2 1 2 1 101000 f 74 goat snp36619-scaffold441-1182541 7 11172806 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379829 Affx-122975820 AX-123250187 7 95435483 GGCCTTTTCCTTAATTTGGGGAGGTGGTCAATAGT[A/G]CAAAGAAAAATAGCCTGTTTGAGGAGATAGCATCA R 2 1 2 1 101000 f 74 goat snp36620-scaffold441-1213600 7 11140822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445396 Affx-122925392 AX-123315733 7 95465094 TGTGTGTATGTTTATTCTGTTTTGCCTTTTAATCA[A/G]TAAGCTTGATTTCTCAACTCGTACTATTTAATGTT R 2 1 2 1 101000 r 74 goat snp36621-scaffold441-1243211 7 11111150 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443410 Affx-122927381 AX-123313747 7 95544671 TTCAGACTCAGAAGTTTCAGTCCAGCCTGGTGACG[C/T]AACCTTGGGATTCATCAGTGAATATGTAGTAATAA Y 2 1 2 1 201000 r 74 goat snp36623-scaffold441-1322788 7 11031388 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278541 Affx-1111836478 AX-519552023 7 95554272 GCTCCTTGCTGAGCCTGGCAGGGACGTTGGAAACC[A/G]CGACCTCATCTTGGACCATGCGAGTGAGAGCTGAT R 2 1 2 1 202000 f 74 goat Random2.2K-842 7 95554272 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778676 Affx-122947161 AX-385265787 7 95640993 AATTATTACCTGTCTCTATAAAGCAGATGTTTAGA[A/G]TAAATAATGCAAATATAAGCCTGCTTGCTTCTAAT R 2 1 2 1 101000 r 74 goat snp36625-scaffold441-1419110 7 10934389 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785313 Affx-122938988 AX-385272358 7 95685266 GATAAAACCAAAGGAAGCAAAACAGAGACTATATG[A/C]GTAACTATAATTTTACTGAAAGACAAAGCTTAATT M 2 1 2 1 101000 f 74 goat snp36626-scaffold441-1463383 7 10889549 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800670 Affx-122937677 AX-385287588 7 95709825 ATGAACACATTGATGAATCATACTAAAGCATAAAA[C/T]CTACTTTAAAAGTTCTCTTCCATAAGCTCTGATTG Y 2 1 2 1 101000 r 74 goat snp4675-scaffold1152-6076 7 10860752 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400105 Affx-122960730 AX-123270460 7 95739668 ATGAATATTGGAGGTGCCTGTGATATCCTAGAGGA[C/T]GTAATAAATTGGATGAATTCATCTCTTCATTAAAA Y 2 1 2 1 201000 r 74 goat snp4676-scaffold1152-35919 7 10830573 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777662 Affx-122938537 AX-385264781 7 95788706 TCTGGGACGGTCCCTCTGACATAGATACACAGACA[C/T]GCAGAAATAGGGTAAAATGGCAATATATACTCATG Y 2 1 2 1 101000 f 74 goat snp4677-scaffold1152-84957 7 10781596 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777452 Affx-122929094 AX-385264572 7 95818822 TGTGGAATGAATAAGGTAATGAAGAGAGGCATGTT[C/T]AATAAAGACACTGTAAGAAAACAGAATTCCCTGGC Y 2 1 2 1 101000 r 74 goat snp4678-scaffold1152-115073 7 10751459 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410270 Affx-122952521 AX-123280620 7 95849055 GCCGGATTCTCTGGCTCAGAGACTGAGTCAGCTGT[A/G]TTCAAAATAAAGACAGAGATCATGCACATCAATTT R 2 1 2 1 201000 r 74 goat snp4679-scaffold1152-145306 7 10720833 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786142 Affx-122976865 AX-385273178 7 95885925 CTTTTATTCGTTTGCAATTTTTGTCCCTATTTAGC[G/T]AACTCAAATCAATATATATCTAACTTTAACTTTCT K 2 1 2 1 101000 f 74 goat snp4680-scaffold1152-182176 7 10683691 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392073 Affx-122966381 AX-123262430 7 95927414 AAGGGGAAAAAAAAAAAAGCTCTTTGATCAAATTC[A/G]TTTGGGGAAATTCTGGGATACATAAAATCCAATAG R 2 1 2 1 303000 r 74 goat snp4681-scaffold1152-223665 7 10642502 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449225 Affx-122923493 AX-123319560 7 95968547 CTACTCAATGCATTTATGAGATGAACATCAATGCA[C/T]GGAACAGTGGATGTCTGGGATGCTTTTGCTGTGGC Y 2 1 2 1 201000 f 74 goat snp4682-scaffold1152-264798 7 10601100 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379718 Affx-122975887 AX-123250076 7 96011151 ATTTCTCTAATATATGCAAGATCCTTGAATCAACA[C/T]GTATTCTGGAGGGCTGGATGTGGCTCAATGATTAA Y 2 1 2 1 201000 f 74 goat snp4683-scaffold1152-307402 7 10565922 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423134 Affx-122942767 AX-123293480 7 96054404 CATCTCATCCCTTCTCTTAGGAAGCTAGATCATCA[C/T]AAAGTAAAACATTTTTATCTTCTACTTTGGTTTCC Y 2 1 2 1 103000 f 74 goat snp4684-scaffold1152-350655 7 10521909 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453183 Affx-122920460 AX-123323516 7 96101612 GCTCAGTAACCCTTGACTCCCTGGGAGAGTACTGC[A/G]TCTGGCAGACACAAAAGGCACAAGTTCCTGTTCTC R 2 1 2 1 201000 f 74 goat snp4685-scaffold1152-397863 7 10474601 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438861 Affx-122930757 AX-123309198 7 96155335 AACAAATATTTCTAAAAGACCACAACACCAAAAGT[A/C]GATTGCAGGTTCTGAGCGAAGCTGTGCTTGGCAAG M 2 1 2 1 201000 f 74 goat snp4686-scaffold1152-451586 7 10420376 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394072 Affx-122964969 AX-123264427 7 96202066 AATGAACTGGACATGTATGTCAAGGTAGAGGGGAA[C/T]AGTGATAGGTCAGGATTTGGGGAAAGTAGTATCCG Y 2 1 2 1 201000 f 74 goat snp4687-scaffold1152-498317 7 10373702 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273359 Affx-1111833560 AX-519546993 7 96228029 TCCCACACTTAGAAAAGCACTAAAATCATTAACTG[A/C]AGTATTTGCTCTTTGTAACCAGAAACAACTTTCCA M 2 1 2 1 101000 r 74 goat 7_96228029_AF-PAKI 7 96228029 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437685 Affx-122931768 AX-123308023 7 96257271 TAGCCCAATACATTTTTACAAAGGAAACATGCCTC[C/T]GTAACTGCCAACAAAAGCAAGATTCCCATTGCACA Y 2 1 2 1 101000 r 74 goat snp4688-scaffold1152-553522 7 10317564 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394916 Affx-122964316 AX-123265271 7 96291436 TTTTAAGGATGTGTGTGTCTGTGTATACATAAATC[A/G]TGTGAAAATATGTCCCCTGAAATCATAGTAGACCT R 2 1 2 1 101000 r 74 goat snp4689-scaffold1152-587687 7 10282841 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764924 Affx-122926183 AX-385252510 7 96361899 CCAAAGTTCAAGGAAAACTTGAGTTTCCAAGAGAT[G/T]AAAAAATATGCATAGTGTCCACATGCATGGTACGT K 2 1 2 1 201000 f 74 goat snp4690-scaffold1152-658150 7 10211718 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400808 Affx-122959812 AX-123271163 7 96396644 AAGGGAGCCTTCACCAGAGATGTCTATAGTATGAA[C/T]ATGGGACAACAGACTGGTTCCAAATTGGGAAAGAG Y 2 1 2 1 101000 f 74 goat snp4691-scaffold1152-692895 7 10177119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777113 Affx-122970792 AX-385264236 7 96432806 TTTCATCACCCTCCTTACCATCATAATTCATGTCT[A/G]CTGATTTTCCCTATATCTGTTTCATTAAACTCTTC R 2 1 2 1 101000 f 74 goat snp4692-scaffold1152-729057 7 10141026 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38401715 Affx-122959533 AX-123272068 7 96511726 TTCCTCTTCTATTTCTTTTTATTTTGTTAACTTTA[A/G]CAGACTCCTACATTCACAAAGTCCTGATGTATATG R 2 1 2 1 101000 r 74 goat snp4694-scaffold1152-807977 7 10059633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769753 Affx-122972265 AX-385256923 7 96560096 CATTTTCATTCTATTTAATAATCTTTCTATTATTA[C/T]AGGTAGCACATTCAGTAAGCATCTAGAGAAATGAA Y 2 1 2 1 202000 f 74 goat snp4695-scaffold1152-856347 7 10011205 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795169 Affx-122974067 AX-385282127 7 96613376 TTTGACTCTCTGGTTGGTTCTAAGTTGGAAGAGAA[G/T]ACAAAAATTAGGGAAATTGTTATTAACCAAGTTCT K 2 1 2 1 101000 f 74 goat snp4696-scaffold1152-909627 7 9958010 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430112 Affx-122937515 AX-123300453 7 96685743 TGAAAGAAAGAGTTAAAAAAAAACACCAAGAGAAT[A/G]TGTAAATACATAGAAACTAAAATGAGTAAGCTTGC R 2 1 2 1 101000 r 74 goat snp4697-scaffold1152-981994 7 9885323 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274289 Affx-1111834114 AX-519547886 7 96710381 CCTGCCCCTCTCTCAGGGACCCTGGAGGTGCGTGT[A/G]GTGGGCTGCAGAGACCTTCCAGAGACCATCCCTTG R 2 1 2 1 102000 r 74 goat GoatD01.019059 7 96710381 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382218 Affx-122973989 AX-123252576 7 96753078 TAGAGTTTTAGATGTAGCACTCCTACCCTGAATCT[A/G]CATTTCTTAGAGTATTTTTCTTCATAAAAATTTAA R 2 1 2 1 101000 f 74 goat snp4698-scaffold1152-1049329 7 9818606 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450733 Affx-122921866 AX-123321067 7 96801913 CTTCCTAGTAAAGGCATTCTTAGTCCTGCATTACA[C/T]GAAAGCATTGTAAAATATTTCAAAATAATGTAAAA Y 2 1 2 1 101000 f 74 goat snp4699-scaffold1152-1098164 7 9767826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792691 Affx-122928049 AX-385279671 7 96834764 TTTTTATATTAGCCATTCAGATGAGTAAAATAGTC[C/T]AGGGTGTTTTTATACAAAAAATGAGAAAAATAACT Y 2 1 2 1 101000 r 74 goat snp4700-scaffold1152-1131015 7 9734585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396177 Affx-122963772 AX-123266532 7 96889765 ACAGTCTATACTTCAGACTCAGACTGAATTATGCC[A/G]CCGGCTTTCCTGGTTCTCCAGATTCAGAACATGGG R 2 1 2 1 201000 r 74 goat snp4701-scaffold1152-1186016 7 9677962 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407432 Affx-122954803 AX-123277783 7 96970542 TTTGAATAGGTTCCAGCCTGGGAAGCAAAATAAAG[C/T]CTTGGAGTTTGGAGTGAATCCCTGCTCCATAACAG Y 2 1 2 1 101000 f 74 goat snp4703-scaffold1152-1266793 7 9593703 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769427 Affx-122950908 AX-124373867 7 97009060 TAAAATAACCATTCTTGTCCAGTTGGTATAGCATT[A/C]TTGTTGCTTTTAGGGAAAGCACTGTTGAGTCTCCT M 2 1 2 1 101000 r 74 goat snp4704-scaffold1152-1305311 7 9555266 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436126 Affx-122932649 AX-123306465 7 97041115 TTTCTTTAACTCAAAATACATGTTGTTACCAGTAA[C/T]GATATTAAGCCTACAAACGATAGCTTCTCACACTG Y 2 1 2 1 101000 r 74 goat snp4705-scaffold1152-1337366 7 9523804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411987 Affx-122951769 AX-123282337 7 97070664 ATTTTCCTGGAAAGAAAACTTTTTAAAAATGACTC[A/G]TGTCATAAAATAGTTAATGCATTTCTATGTTTAAT R 2 1 2 1 201000 r 74 goat snp4706-scaffold1152-1366915 7 9494025 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794239 Affx-122934844 AX-385281205 7 97089193 GGTATTTCATCATTGTTTGGATAAAGAACTGAAAC[A/G]TTTTCTTAACCTTCTATATAAGACATTTTAGCACA R 2 1 2 1 201000 f 74 goat snp9294-scaffold134-17288 7 9474837 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426762 Affx-122940563 AX-123297108 7 97135151 CCAGATCCCTTGTCACTCTGAGGTTACAGTAACCA[C/T]GGTTATGTTAAAGCCTAAGAGAGAATGAGACACCT Y 2 1 2 1 101000 r 74 goat snp9295-scaffold134-63246 7 9428394 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377476 Affx-122977506 AX-123247835 7 97171019 TCTCAAGACGTCTTAGAGGAAACAGGAATATGCAC[G/T]AAGGAAAACCGACAAATCAAAGACAGAGGAACGCA K 2 1 2 1 101000 f 74 goat snp9296-scaffold134-99114 7 9392297 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442694 Affx-122927879 AX-123313031 7 97211379 TTACTTCCACATTCATTAATATCCCAGAGAATACA[C/T]GTGCTGTCTATTGTGCTGCCAAATATAATAGGTCC Y 2 1 2 1 101000 r 74 goat snp9297-scaffold134-139474 7 9351136 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424933 Affx-122941285 AX-123295279 7 97258497 TATCCATGAATTGCCCCTGGCACTAACACTACTGG[C/T]ACTATATGAGTTTATTGTGGAATATCAATGGAGAA Y 2 1 2 1 201000 r 74 goat snp9298-scaffold134-186592 7 9303667 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435152 Affx-122933669 AX-123305492 7 97342427 TAATAGATCCAACAATTTCCAGTGCTTCCACAGCG[C/T]TCAGTATCCCGAAAGATGCAAGAAGTTTCTTTTAT Y 2 1 2 1 201000 r 74 goat snp9300-scaffold134-270522 7 9219166 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802152 Affx-122928294 AX-385289056 7 97400197 GGTGAAATGGATCCTATTTTCCATTATCTAGAAAA[C/T]GAGTAGGTTAATTAAGACCTCAAAAGTTCCATTCA Y 2 1 2 1 201000 f 74 goat snp9301-scaffold134-328292 7 9160805 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396910 Affx-122963211 AX-123267265 7 97439614 TTCTCCATACTTCTTACTGATTTGATGTTTTGGTC[A/G]CAGGTTAGTTGAGAGAGTGAAAATGAAGTGGAAAG R 2 1 2 1 201000 f 74 goat snp9302-scaffold134-367709 7 9121115 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435513 Affx-122933414 AX-123305853 7 97474376 ATCTCCCAGAAGAAAGGGCAAAGGACTGAGCAAAT[C/T]TCCTGGTGAACTGCCCTGGGTCTGCCAGCACATAC Y 2 1 2 1 101000 f 74 goat snp9303-scaffold134-402471 7 9086291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787355 Affx-122941645 AX-385274380 7 97510242 AAAGAAGATGCACAAGTCGAGAGTAACTTAGAGTC[A/G]TTTTAAAGATTAAAGGAACGTTTCTATTCTCTGAG R 2 1 2 1 101000 f 74 goat snp9304-scaffold134-438337 7 9050115 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378537 Affx-122976621 AX-123248896 7 97614462 TTTGGCAAGGAAACCTCTCTTTTGTATATGAATAA[C/T]AGGGACTCTTGGCTACGTGGGAAGGACATTCAGCT Y 2 1 2 1 101000 f 74 goat snp9306-scaffold134-542557 7 8946616 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380432 Affx-122975300 AX-123250790 7 97672373 AGTCCATAGGGTTGTAAAGAGTCGAACACGACTGA[A/G]GCGATTTTGCACGCATGCACACATCACTTATTCAA R 2 1 2 1 103000 r 74 goat snp9307-scaffold134-600468 7 8888673 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414296 Affx-122949591 AX-123284645 7 97711002 AGCACAAGGCATCCCGTCCCAGAATCAAGCCCCGG[C/T]GGGAAGGCCTGCAAGGACAGTTCTTGTTCTGTTGC Y 2 1 2 1 101000 r 74 goat snp9308-scaffold134-639097 7 8850595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411586 Affx-122951618 AX-123281936 7 97740195 ACTTTGTGATCAACACTTCTTTCAGCTGAACACAT[C/T]GGCACCATCTGCCTTCAGTTGACTTAGTGACTGGT Y 2 1 2 1 101000 f 74 goat snp9309-scaffold134-668290 7 8821915 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411638 Affx-122951576 AX-123281988 7 97780576 ATCTCATTTCATGTGAGGAAGCCCTTCTCCAGATT[A/C]TGAGGTGGTTTTCCCTCTCAAGGTTTCCTTGCCGA M 2 1 2 1 101000 f 74 goat snp9310-scaffold134-708671 7 8781068 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427682 Affx-122939306 AX-123298025 7 97829288 TTAAAGGCAGACACAGTAGATGCAAGAAAGAAGAT[A/G]CCTTGGTAGCCTGGGCAAATGCAAGTGTAGTGTGG R 2 1 2 1 101000 f 74 goat snp9311-scaffold134-757383 7 8731947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768996 Affx-122928511 AX-385256171 7 97858023 TCTAAAGCATAGCACTAGCTGAAAAGTACTGTTGA[C/T]GAAAATTGCTTAATAGCATGTAGAAATATCCACAG Y 2 1 2 1 101000 f 74 goat snp9312-scaffold134-786118 7 8703257 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784025 Affx-122978972 AX-385271078 7 97915049 AAAACCCATACTTTTTTATTGGATGAACTATGATG[A/C]GACTTGACTGAGTATTACAAGTTCAGTCTTAATGC M 2 1 2 1 101000 r 74 goat snp9313-scaffold134-843144 7 8645536 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790001 Affx-122971642 AX-385277007 7 97984029 CACAGTATTCTCCCAATAGCACTTCCATTGCCAGT[A/G]TCTTTCTTTGGTGCCTTTCCTGTTCAGCATTCTCA R 2 1 2 1 101000 f 74 goat snp9314-scaffold134-912124 7 8576363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798836 Affx-122970490 AX-385285766 7 98028823 GTTTTTGTTTTGGTTAAATCTTTCTCCTTCTAAGA[C/T]AGAATATTTGTGATGATGCTACCATACAATCTGAA Y 2 1 2 1 101000 f 74 goat snp9315-scaffold134-956918 7 8531067 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429328 Affx-122938587 AX-123299670 7 98094750 GTTCGCAATATTTAGTGATTAGAATCAACAGGATT[C/T]GGTGTTTGGACATTGTGACTCTTTTACTGTAATAT Y 2 1 2 1 101000 f 74 goat snp9316-scaffold134-1022845 7 8464331 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383018 Affx-122973316 AX-123253376 7 98157414 TAGTAATAAATTGCCTAAAGCATAGTTGGTATTCA[A/G]TGAATACTTTTTAAAAGTGAATCAATGTCCAGTCT R 2 1 2 1 303000 f 74 goat snp9317-scaffold134-1085509 7 8401010 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778469 Affx-122954605 AX-385265583 7 98186106 ATTTGTTTGTTCAGCATACTATCTGATGAGGCTTC[A/G]TATGGTTCTCTAAAGTTTATTAGATGAGAAGTCTT R 2 1 2 1 101000 f 74 goat snp9318-scaffold134-1114201 7 8372476 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410719 Affx-122952717 AX-123281069 7 98218845 GAATATAAAGGGGAAATGGGTTCTTTCATTGTCTC[A/G]GTATCTTTCCTTCTGAAACAGTGGGAAATCAGGTA R 2 1 2 1 101000 f 74 goat snp9319-scaffold134-1146940 7 8339676 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403185 Affx-122958073 AX-123273538 7 98273640 CTTGAAGGGGTGTTCCCACGTGGGAGCATCCTCAT[A/G]CAGACAGTGTGGTCCAGTGCCTTTGCTGGGAGAGC R 2 1 2 1 101000 f 74 goat snp9320-scaffold134-1201735 7 8284932 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391552 Affx-122966633 AX-123261909 7 98302496 TTTGGTCCACTATAAGCTGAGGGTCTTTAACTTTC[A/G]CCAACAATATTCCAAAGCTTCCTGGCCCATCCCAC R 2 1 2 1 101000 f 74 goat snp9321-scaffold134-1230591 7 8256810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439719 Affx-122930553 AX-123310056 7 98348655 AATTGGAATTCATTTGTTTATGCTTTTACTGTATG[A/G]ATATTGAATGGTTAAGGTATGCTGGACATTGTGCT R 2 1 2 1 101000 r 74 goat snp9322-scaffold134-1276750 7 8210337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801375 Affx-122963525 AX-385288286 7 98396524 TTAGAAAAATAGAGAAACACATTATACAAGTCGAT[G/T]AAGACCTTGGTCTCTATGGTATGTACAGCTCAGAG K 2 1 2 1 101000 r 74 goat snp9323-scaffold134-1324619 7 8162479 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413401 Affx-122950715 AX-123283750 7 98442637 TGTCATTGTCTTTTCAGAGACTGTGTGGTCACATC[A/G]TCAAGTAATTTATCCCCCCAAATAGCATTTCCTTG R 2 1 2 1 101000 f 74 goat snp9324-scaffold134-1370732 7 8115445 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452256 Affx-122920771 AX-123322589 7 98497618 AGCAAAAGAAGCTTCTTTAATTCAATGACAAATGG[C/T]AAACAAATTAATACATAAGGAAAGAACATTCTTAA Y 2 1 2 1 101000 f 74 goat snp9325-scaffold134-1425713 7 8058754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396983 Affx-122963155 AX-123267338 7 98549733 ATATCTACTTGAACTTGGAAACATTCTTCCTTATC[A/G]TTAGAAGTGTAGTAATAATAGTAGTTTGAAAGTTG R 2 1 2 1 201000 r 74 goat snp9326-scaffold134-1477828 7 8006096 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802657 Affx-122925261 AX-385289556 7 98597506 TTGCACATAGAAAAAGCAACATCTCAAAGAAAATT[A/G]TTCTATTATCTAAATCACTATGGAATATTATTATT R 2 1 2 1 102000 f 74 goat snp9327-scaffold134-1525601 7 7958280 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389380 Affx-122968396 AX-123259738 7 98649198 AAGTATACTTAAAAATTTGCTCATTTACTCCTTGC[A/G]TGACATTATTATTCCTCAGGAAACAAAAGTTGCTG R 2 1 2 1 101000 r 74 goat snp9328-scaffold134-1577293 7 7906412 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794768 Affx-122942587 AX-385281728 7 98683945 TCTCTTTTTTTAGTGAGGTTAGGTCTCCTAACAAA[C/T]GCTCTACGAGCTAAAAAGTGAGACTCCAAATGGTG Y 2 1 2 1 101000 r 74 goat snp9329-scaffold134-1612040 7 7871357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390901 Affx-122967100 AX-123261258 7 98746877 TTGTGCTCAGGAGGCATGTAACTATGAAGCAGGTC[A/G]CGTCAGGAGTCACATCGTTGACTATGATCATCTGT R 2 1 2 1 101000 r 74 goat snp9330-scaffold134-1674972 7 7807269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273361 Affx-1111833561 AX-519546995 7 98755630 TGAATTGAACCTTAGATGTAAGCCTACTGTGAGAC[A/C]TAGTGGCTGATCTTTTATACCCCAGTTCAGGAGTT M 2 1 2 1 101000 r 74 goat 7_98755630_AF-PAKI 7 98755630 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438745 Affx-122930826 AX-123309082 7 98786911 CTGAGTAGCTAGTTTCTTTCCATTTCTCTACTTTA[C/T]CTTCTGCAAAGTCACTTCTGAATCCAGACCTGTCT Y 2 1 2 1 201000 r 74 goat snp9331-scaffold134-1715006 7 7767750 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409530 Affx-122953616 AX-123279881 7 98816380 TCATGCTTCATTCATCATGAATGGGCTTTCCTTGA[C/T]GCAGGGATGTTTTTTCTTAAATTTTAATTCAGAGA Y 2 1 2 1 101000 f 74 goat snp9332-scaffold134-1744475 7 7737943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776083 Affx-122923151 AX-385263213 7 98852545 TTATATGTATTATTAATAATGAACATATTGAAAGA[G/T]TTAAAGTTTTTTCTGTTTCTCGCATTTTACTGAAT K 2 1 2 1 201000 f 74 goat snp9333-scaffold134-1780640 7 7701755 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765560 Affx-122953126 AX-385253040 7 98882259 TTGGAAAAAGGCTTGCATGGTTATTTAAGTTCATC[C/T]ATTCATTTCAACAGGATTAAAATAGATGACGCAGT Y 2 1 2 1 101000 f 74 goat snp9334-scaffold134-1810354 7 7671958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400679 Affx-122960335 AX-123271034 7 98913462 CTTGATTCCAATTAGGAGAGATGTATTAGAGTCCA[C/T]AGTCCTGTGAAGAAAAAATATTGTTTTATAAATAC Y 2 1 2 1 101000 f 74 goat snp9335-scaffold134-1841557 7 7639010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764961 Affx-986697133 AX-385252540 7 98967797 CTATTACCTGCTCAAGTTTAAAAAAAAGATGCCTA[C/T]GGAAGACAGAATAATTATGGGAGGAAAATAGACAT Y 2 1 2 1 600010 r 74 goat 7_98967797 7 98967797 Ancestral_priority_1043 ancestry 0.612 recommended IMAGE 10K 10K ancestral 38414231 Affx-122949637 AX-123284580 7 98997025 GGAAAGCAAAGCAAACAAAACGAAATCGAAAAAGG[C/T]GAAAGCCTAAAACCATTAGCAGTTTCAACACAAAC Y 2 1 2 1 101000 f 74 goat snp9337-scaffold134-1925120 7 7554400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446181 Affx-122925736 AX-123316517 7 99031876 ACTCACAACTGTGTGCCAACAAATTCTGTTACCTA[C/T]GCCACACTCACTTGTGGCACTTTGTTATGGCAGCT Y 2 1 2 1 101000 f 74 goat snp9338-scaffold134-1959971 7 7519334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382827 Affx-122973549 AX-123253185 7 99124039 TTGGCCACTAGAAATCCCTGGTCACCTTAATCCAA[C/T]AAAAGACTGAGGTGAATTGAAGCTGGATTTTTATT Y 2 1 2 1 101000 f 74 goat snp9340-scaffold134-2052134 7 7427406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775303 Affx-122968143 AX-385262434 7 99149523 GGAAAGAGACCAGGAAAAATCAGACTTCATACATC[A/G]GTGATTATGAATTAGGTCTTTTAAGTAAAACAAGG R 2 1 2 1 101000 f 74 goat snp4375-scaffold1137-1488878 7 7402023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801682 Affx-122947679 AX-385288590 7 99185113 TGTACACAGAAAAATACAAGAATAGCAACATGTAC[A/G]TCGATTATTTGATCTTATCCACTGTCCTCTTGGAT R 2 1 2 1 101000 r 74 goat snp4374-scaffold1137-1453288 7 7366104 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422304 Affx-122943476 AX-123292650 7 99215313 TTTGTTCTAATCATTTAAAAATGCCTTTAGAGAAT[A/G]CACCATTAAACACAGCAAAATATTTTCTGTAACTG R 2 1 2 1 103000 r 74 goat snp4373-scaffold1137-1423088 7 7334284 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764965 Affx-986697135 AX-385252544 7 99236900 AGGTACAGAATTTTCACAGGTGTTGGGGGATGTGG[C/T]ATAGCACAAGGGACTCCTTTTCTTGGTAGTAACCT Y 2 1 2 1 600010 r 74 goat 7_99236900 7 99236900 Ancestral_priority_1043 ancestry 0.64 recommended IMAGE 10K 10K ancestral 38388612 Affx-122969141 AX-123258970 7 99252243 TACCAAGTTCTGTATTATTTCTACCAAAAACAAGG[A/C]TGGAAATTCTGGATTCTTGGCTATATTGCCCATAA M 2 1 2 1 101000 r 74 goat snp4372-scaffold1137-1386158 7 7297335 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278544 Affx-1111836479 AX-519552025 7 99276220 GAGTGAACTCTGACTCAGTAAAATGCATTACCAAA[A/G]TCAGACAGGAGCCCAGTGTGGACCACAGGCTGCAG R 2 1 2 1 101000 f 74 goat Random2.2K-845 7 99276220 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776398 Affx-122932644 AX-385263525 7 99282912 CTGGAATTTAAACAGACATGGCATATATGGCCAAT[C/T]ATTGTCACAGCCATGTATAATAAATTGTCTTATGC Y 2 1 2 1 201000 r 74 goat snp4371-scaffold1137-1355489 7 7266587 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771118 Affx-122977355 AX-385258278 7 99319993 GGAGGAGAAAAAGACTAATGAGAAAGATGCGTAGC[A/G]TCAAAACTAATAGAAGAAAAAATCGACTAAAATAT R 2 1 2 1 101000 f 74 goat snp4370-scaffold1137-1318408 7 7230524 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441680 Affx-122929177 AX-123312017 7 99350420 AAGCTTTCATCCAAAGTCTCTTTCTGATCTAAATG[C/T]CTCCAATGAGGAGCTGTGGTAAATGTTTGACTTCT Y 2 1 2 1 101000 f 74 goat snp4369-scaffold1137-1287981 7 7200175 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799092 Affx-122922008 AX-385286022 7 99387363 ACTAAAAAAATCAACAGTTCTCACTTGATTTCATG[C/T]GCTAAAAAAACCACTTCAAAATAAAAAGAGGCTTT Y 2 1 2 1 201000 r 74 goat snp4368-scaffold1137-1251038 7 7163127 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407750 Affx-122954982 AX-123278101 7 99423347 TGGCCAGTATTGTTTTGCACATAAAAAACAGTAAG[C/T]AAGCCAGCAACATGAATTTGTGTATGCAAAAAAAA Y 2 1 2 1 201000 f 74 goat snp4367-scaffold1137-1215054 7 7127040 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798736 Affx-122945778 AX-385285667 7 99463133 TTTACAGAGGGTAACATCCATTAACTCCAGTCCTT[C/T]ATTAGTGATGGAGGTGGAACTACTGCATATCAAAA Y 2 1 2 1 101000 r 74 goat snp4366-scaffold1137-1175268 7 7087384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388526 Affx-122969202 AX-123258884 7 99524840 GAAGCAGGATACAACTGTTGAAGGGGAGTATTTAG[C/T]TGGAAAATGACAGTACTCTGTATGTTAAAAGCAGT Y 2 1 2 1 101000 f 74 goat snp4365-scaffold1137-1113561 7 7025212 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395750 Affx-122963689 AX-123266105 7 99559045 TACTCTTCAACAGGAAAAACATTAAGCATAAAAGG[C/T]GGGGAGGTGGGGACAGACACCTCTACGCTCACAGC Y 2 1 2 1 101000 f 74 goat snp4364-scaffold1137-1079356 7 6991189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788505 Affx-122976630 AX-385275522 7 99594378 GTACGGAAACAGGTTCATCTTAAAAAGAATATACA[G/T]GCAAAAAGTAGGGTGAGTAGCACAGTAAAGTTCAT K 2 1 2 1 201000 f 74 goat snp4363-scaffold1137-1044023 7 6956207 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422539 Affx-122943270 AX-123292885 7 99640656 TTAATGCTCATCTACAATGTATCAGAGACTGGACT[C/T]ATCTTTCCTCCTCCTCCCTTTTCTCCTCCACCTTT Y 2 1 2 1 201000 f 74 goat snp4362-scaffold1137-997745 7 6910321 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788035 Affx-122955587 AX-385275056 7 99706649 ACATTTTCACTATAAGAACCCCTTCTCATATATCA[A/G]TCTACACATTTTTACCCCAGAGTTTATTTTCTCTC R 2 1 2 1 101000 f 74 goat snp4361-scaffold1137-931752 7 6851301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407438 Affx-122954798 AX-123277789 7 99752123 GTCATCTAATCGCTTGATTTTAAGACAGGGAAGTT[A/G]TCCAGATTACCTAGATTATATGAATGTTTCAATAG R 2 1 2 1 101000 f 74 goat snp4360-scaffold1137-886278 7 6805860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383780 Affx-122973203 AX-123254138 7 99792145 TGCTATCTCTATTATATCACAAAGCCACTCAGAAA[C/T]AATACAGGTGAGTTTTCTAATATTGCATATGGAAC Y 2 1 2 1 101000 f 74 goat snp4359-scaffold1137-846256 7 6765501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781878 Affx-122925017 AX-385268959 7 99841379 AAAATTTTAAAACCCACACAAGTTATACAGGGACA[A/C]GTCACATGTATGTAGCCCTCCAAGACTACATTAGA M 2 1 2 1 101000 r 74 goat snp4358-scaffold1137-797022 7 6716040 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380460 Affx-122975734 AX-123250818 7 99901059 GATTGGTTCTTAAAGTTATTGAAATCTACCCCATT[A/C]TCAACTGTCACTCTATAATCAAAATACTGCATCTG M 2 1 2 1 101000 r 74 goat snp4357-scaffold1137-737342 7 6656600 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772220 Affx-122931386 AX-385259375 7 99944234 GCCCATTTATTCCAGGAGTTCTATTAAAGAAATAA[A/G]CATGTTTTCATGATTTAGAGTGTAGAATTCCAGGG R 2 1 2 1 201000 f 74 goat snp4356-scaffold1137-694167 7 6613340 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779275 Affx-122978775 AX-385266379 7 99977265 TTGCAGCAGTCAGACATCAGATTCTACCCAAATAT[A/G]CTAACAGTGTGTAGTGAATGGTCAAAATAGCAAAT R 2 1 2 1 101000 f 74 goat snp4355-scaffold1137-661136 7 6580300 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434275 Affx-122934780 AX-123304616 7 100012590 TTTGAATTTTGAGCCAATGGGATTTCCTTAGGAGA[C/T]ATATGTAAAGTCAGCAAAACCAGGTTTCTACTGTT Y 2 1 2 1 101000 f 74 goat snp4354-scaffold1137-625811 7 6544936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421649 Affx-122944452 AX-123291996 7 100060446 TGCAAACAGGTGCGTGCGGGCACAGGACCAAATCA[C/T]CCCTCAAACACAAGTGACCAGTCTGCTTCTGTATA Y 2 1 2 1 201000 f 74 goat snp4353-scaffold1137-577955 7 6496752 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798440 Affx-122929701 AX-385285373 7 100102173 AGATGTCTTGATATGTATTTGAACTCACTGCACTT[A/G]TATGAATTAGATGCTTTTCTACCATAAATTGCAAA R 2 1 2 1 101000 f 74 goat snp4352-scaffold1137-536228 7 6453930 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774213 Affx-122923718 AX-385261350 7 100163431 AATTTGAGCACAGTCTTGCCTTTTGATGCAAGAGA[C/T]TGGGCTCTCTTCACAATGTGATAAAGACTCATTTG Y 2 1 2 1 201000 r 74 goat snp4350-scaffold1137-474970 7 6392543 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395597 Affx-122963825 AX-123265952 7 100196560 CTATCTATATTCTTTTAGCCTTTTCGTATTGTCCA[C/T]GGGGTTCTCAAGACAAGAATACTGAAGTGGTTTGC Y 2 1 2 1 303000 f 74 goat snp4349-scaffold1137-441841 7 6360303 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764968 Affx-986697137 AX-385252547 7 100214459 GTCAACAGACGCAAACCATTATACGTGGAGTGGGT[A/G]AACAGTGAAGTCCCACTACACCGAATATCCGATGA R 2 1 2 1 600010 r 74 goat 7_100214459 7 100214459 Ancestral_priority_1043 ancestry 0.622 recommended IMAGE 10K 10K ancestral 38447213 Affx-122924983 AX-123317549 7 100241600 CAAGCTCCTGCACTATGTGCTCAGTCTGGTTCATC[A/G]CTCCATTTTTCCATCTTCAGAGCCAACAGCAACAC R 2 1 2 1 102000 r 74 goat snp4348-scaffold1137-396801 7 6323939 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443092 Affx-122928110 AX-123313429 7 100274814 ATGGTCCTCAAAATAAAAAGCAAAGCAAAACAGGA[A/G]AAGACTGAAAATGTATAAAACAAACTTATGGTTGC R 2 1 2 1 201000 r 74 goat snp4347-scaffold1137-363587 7 6290819 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773465 Affx-122926100 AX-385260607 7 100329328 TCATCTTTCCTGTTAGAATATTTTTACAGTAAAAA[C/T]GTATGTGTTCCTCCTGAGTTAAAAAATGTTAAATG Y 2 1 2 1 201000 f 74 goat snp4346-scaffold1137-309073 7 6235119 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376663 Affx-122979008 AX-123247022 7 100359659 GTTTCTAGACACAAACATCACAGAGTATAGTCAAA[C/T]ACAACTCTTTTCCTGTCATCTTAAGTAGGAGAGAG Y 2 1 2 1 101000 r 74 goat snp4345-scaffold1137-278742 7 6204778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428888 Affx-122938932 AX-123299230 7 100438873 GACTGCTCTGGATTATAGCTGTTCTCGTGGATTGC[C/T]GTGAAGAGAAGCAGTGAGAGATTCAGAGTGCAGAC Y 2 1 2 1 101000 f 74 goat snp4343-scaffold1137-199528 7 6126097 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796231 Affx-122973174 AX-385283181 7 100476028 CCCCTGTCTAGTTTGAAGTAATAGTAGACGTCACT[A/G]TACTAAATACTAGCATAAAATATTTCCTCTCCTTA R 2 1 2 1 101000 f 74 goat snp4342-scaffold1137-162373 7 6088586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780981 Affx-122964857 AX-385268067 7 100535593 TTATAACATAGTTCATAAATTTAAGATCATGTTAA[C/T]ATCCTGGTTATGTGCAGAGCACTTAAATATGAAAG Y 2 1 2 1 201000 f 74 goat snp4341-scaffold1137-102808 7 6029372 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779676 Affx-122926569 AX-385266776 7 100572431 TGCTTTATAATTACTGGATGGTTTTGTTATGCTAG[C/T]GGTGCCAAAATCTGCTTCCAACCCAGTGAACCAGA Y 2 1 2 1 101000 r 74 goat snp4340-scaffold1137-65970 7 5989136 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419666 Affx-122945946 AX-123290014 7 100645998 ACATACAGCTAACCATTTCAAATTGTACAATTCAG[A/C]GGCATACAGTATATTCGCAACATTGTCTATTTTAA M 2 1 2 1 101000 r 74 goat snp47707-scaffold671-7498 7 5915464 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445639 Affx-122925085 AX-123315976 7 100675288 CATTTTCCCACCTGCTTATAGAATAGATTACCTCT[A/C]AGATCATTGCTAAATTTTATTATTCCTTAATTTTA M 2 1 2 1 202000 r 74 goat snp47708-scaffold671-36788 7 5886277 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794738 Affx-122954645 AX-385281698 7 100705709 GATGTTTCCTTTTCATATCAAAGTTTTCCATATAT[A/G]CACATGAAATAAACTACAGAAGAATTGATATAACT R 2 1 2 1 101000 r 74 goat snp47709-scaffold671-67209 7 5855756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423112 Affx-122942914 AX-123293458 7 100765905 GACTATGAATACCCCAATTACTGACAGATTACTGC[A/G]CATCAGTTCTGAGCTAATTCATATACCTGAGAACC R 2 1 2 1 201000 r 74 goat snp47710-scaffold671-127405 7 5795437 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768593 Affx-122937450 AX-385255773 7 100808236 ACCCCAGGTTTCTACCACACAAGTAGCTAAGTCTA[C/T]AGCAAATATCTTTAGCTTGACTTTAGATTGATATA Y 2 1 2 1 101000 f 74 goat snp47711-scaffold671-169736 7 5753308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420140 Affx-122946001 AX-123290488 7 100840999 AAAGAAGGAAGAGAATATCACAAACACAGAGGTCC[C/T]CCCTGAGGAGAAAGAAGTTTGAGCCTCACATTGGG Y 2 1 2 1 101000 f 74 goat snp47712-scaffold671-202499 7 5720598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445737 Affx-122926091 AX-123316074 7 100880957 CTACTACCAATACGATCACCTTCTAAGCTTTTGAA[A/G]TGTATTATTATTGTGGCCACACAGTTCTCAAGAAG R 2 1 2 1 101000 f 74 goat snp47713-scaffold671-242457 7 5680371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430738 Affx-122937506 AX-123301079 7 100914928 CTACTGGAATATGTTTGGTAGTTTCATTATTTCTC[A/G]TCTGTAAAAATATTGATAGTTTACTCAGAAATTAT R 2 1 2 1 101000 f 74 goat snp47714-scaffold671-276428 7 5646342 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396378 Affx-122963030 AX-123266733 7 100972325 AGCCAGAATAGAAATTGTTTTATTTCTATTTTACT[C/T]CAGATAACAACTAAGAGTATAAAGAAAAGCCATTT Y 2 1 2 1 103000 r 74 goat snp47715-scaffold671-333825 7 5588183 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381439 Affx-122974346 AX-123251797 7 101015337 ATCAATACCCATGGCTTGCACACTAAGTATGGATT[C/T]TGTGCTTCACAACTCTAAGCAGACAAACTGAATAT Y 2 1 2 1 101000 f 74 goat snp47716-scaffold671-376837 7 5545191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800001 Affx-122938815 AX-385286924 7 101053085 AAAAGGAGTGTCTCACTTTGACAAAGAATTAAGCA[C/T]GTAGGAGTAAAGCAAGAAATCAAGGTGTGACTCCC Y 2 1 2 1 101000 r 74 goat snp47717-scaffold671-414585 7 5507584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400498 Affx-122961283 AX-123270853 7 101086827 AAGAAAAATCTACTCCTTCTGGGGCAATGAGTTTG[A/G]AAGAAGAAAATCATATCTGCATCTCAGGAAATAGA R 2 1 2 1 101000 f 74 goat snp47718-scaffold671-448327 7 5473770 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773937 Affx-122945804 AX-385261076 7 101131867 CTTAGCACACGTTGCTTTGGGTAAATTAGACCGGG[C/T]GAAAAACTAGAATGGAGAGCATTATAGTTTAGGAA Y 2 1 2 1 101000 f 74 goat snp47719-scaffold671-493367 7 5428199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406852 Affx-122955659 AX-123277203 7 101171935 GGTTTCATTACTCACAGTAATAGCAGAAGTCAGAG[C/T]ATCAGCACTTTCTTGTGCTTTTTCTCAAGCCCAAA Y 2 1 2 1 201000 f 74 goat snp47720-scaffold671-533435 7 5387601 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417024 Affx-122947969 AX-123287372 7 101222816 GTTCTTGTTATTTTAAGAATCCCCTCCTCACCAAA[C/T]GCCTAATTTATTCTCATTAATACTTCAGATTTCAG Y 2 1 2 1 101000 r 74 goat snp47721-scaffold671-584316 7 5336296 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792665 Affx-122967869 AX-385279645 7 101258568 ACTGGGAGAACCTTCATGTTAATATAGTTACTTAT[A/G]GTATTATTCTATGAACACATAAAGCCTATGTGTGC R 2 1 2 1 101000 r 74 goat snp47722-scaffold671-620068 7 5299757 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432952 Affx-122935288 AX-123303293 7 101290610 GAGAGAAACTTTCTGAAAACTGAAGGACAGGGCGT[A/G]CTTATGCAATACTGTTGTTGCTGTTAGCCTACATT R 2 1 2 1 102000 f 74 goat snp47723-scaffold671-652110 7 5267720 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273248 Affx-1111833526 AX-314340645 7 101336465 GGAAGCTTGTGTTGGTGTTCTGGTGGGTGGAGCTG[A/G]ATTGCTTCTCTCTGGAGTGCAATGAAGTGTCCAGT R 2 1 2 1 103000 f 74 goat 7_101336465_AF-PAKI 7 101336465 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445406 Affx-122925383 AX-123315743 7 101356478 TTCAAGGAATATAAAACTGTAGAACATGAAGATAT[C/T]AGGGAGAAAAAAAATTTACTATCTTAGATTCTATG Y 2 1 2 1 201000 f 74 goat snp47724-scaffold671-717978 7 5200583 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785903 Affx-122950870 AX-385272940 7 101388530 ATTCCTAGTTTCTCTGTAGTTTATGAGCTGACCAA[C/T]ACAGTTGCATCCCTTTCTCTAATGGAGACAACAGT Y 2 1 2 1 101000 r 74 goat snp47725-scaffold671-750030 7 5168165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779082 Affx-122954068 AX-385266187 7 101432462 TTAGAAGTTAATAGGTCTTCTTTAAATACTGATTT[A/C]TAATTCAAAACATAAAAATCAGGCCTACACTGCCT M 2 1 2 1 101000 r 74 goat snp47726-scaffold671-793962 7 5124130 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417327 Affx-122947743 AX-123287675 7 101467397 GGTGGCTTTTGTCACAATCAGAATAAAATCCAAGC[A/G]TCTCCACAACCACAGAACATCTGGTTCTTGCTTGT R 2 1 2 1 101000 r 74 goat snp47727-scaffold671-828897 7 5089173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790749 Affx-122973293 AX-385277750 7 101539896 TACTGAAAACCTTATAGTAGAAGCATGCCAAGAAG[C/T]ATGAAATGTTTCTAAGTCTGTTTCCTCCTTTGTGT Y 2 1 2 1 101000 r 74 goat snp47729-scaffold671-901396 7 5016755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407496 Affx-122954752 AX-123277847 7 101579459 TCCATAATGTAGTCCTTGAAGTGTGAAAATGAAAA[C/T]TCTTCTCGTTCCTGTATTTCCTGGTACTTTCTTTA Y 2 1 2 1 101000 r 74 goat snp47730-scaffold671-940959 7 4978707 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438411 Affx-122931283 AX-123308749 7 101665876 GAATGGTCTAATTTATTCATGAGGCCCTTTGTTCT[A/G]CAAGGGACACCACTATATTCAAAGTCTTTTGGAAG R 2 1 2 1 101000 r 74 goat snp47731-scaffold671-1027376 7 4893058 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382594 Affx-122973719 AX-123252952 7 101707202 AGTTACCTAAGCCACACCCTTGACTTCAGATTAAT[A/G]TTCTCTTTTATCACACTCTCTCTGAGCATGAGCGC R 2 1 2 1 101000 r 74 goat snp47732-scaffold671-1068702 7 4850589 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770740 Affx-122958648 AX-385257904 7 101748926 TGGTCTCTGCATGCGGTGGGCAGGGCTGAGAGTTC[A/G]CCTGTTCTGTCTACAGACCAGTCTTGGTGCGGGGT R 2 1 2 1 202000 f 74 goat snp47733-scaffold671-1110426 7 4807911 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476240 Affx-1251763746 AX-586011663 7 101759586 ACCTAGCCACAACACCACCAGGGAACCGTAGGACA[-/TAGAAGCAATCTAGAGGGGGGAGAGGGAAAGATGGCGGAGATAAATAAAAAATAAATAAAAATAATAATAAAAAAAAAAA]AGAAGCAATCTAGATGTCCACTGACAGATGGATGG - 8 1 4 1 20000 f 74 goat SV_363 7 101759586 - deletion junction SV-TF-chip 539476493 Affx-1251763746 AX-586011889 7 101759586 ACCTAGCCACAACACCACCAGGGAACCGTAGGACA[-/TAGAAGCAATCTAGAGGGGGGAGAGGGAAAGATGGCGGAGATAAATAAAAAATAAATAAAAATAATAATAAAAAAAAAAA]AGAAGCAATCTAGATGTCCACTGACAGATGGATGG - 4 1 4 1 20000 r 74 goat SV_363 7 101759586 - deletion junction SV-TF-chip 562165219 Affx-1251763746 AX-606940631 7 101759586 ACCTAGCCACAACACCACCAGGGAACCGTAGGACA[-/TAGAAGCAATCTAGAGGGGGGAGAGGGAAAGATGGCGGAGATAAATAAAAAATAAATAAAAATAATAATAAAAAAAAAAA]AGAAGCAATCTAGATGTCCACTGACAGATGGATGG - 8 1 4 1 20100 f 74 goat SV_363 7 101759586 - deletion junction SV-TF-chip 562165291 Affx-1251763746 AX-606940702 7 101759586 ACCTAGCCACAACACCACCAGGGAACCGTAGGACA[-/TAGAAGCAATCTAGAGGGGGGAGAGGGAAAGATGGCGGAGATAAATAAAAAATAAATAAAAATAATAATAAAAAAAAAAA]AGAAGCAATCTAGATGTCCACTGACAGATGGATGG - 8 1 4 1 20100 r 74 goat SV_363 7 101759586 - deletion junction SV-TF-chip 562165343 Affx-1251763746 AX-606940754 7 101759586 ACCTAGCCACAACACCACCAGGGAACCGTAGGACA[-/TAGAAGCAATCTAGAGGGGGGAGAGGGAAAGATGGCGGAGATAAATAAAAAATAAATAAAAATAATAATAAAAAAAAAAA]AGAAGCAATCTAGATGTCCACTGACAGATGGATGG - 8 1 4 1 20100 f 74 goat SV_363 7 101759586 - deletion junction SV-TF-chip 562165556 Affx-1251763746 AX-606940967 7 101759586 ACCTAGCCACAACACCACCAGGGAACCGTAGGACA[-/TAGAAGCAATCTAGAGGGGGGAGAGGGAAAGATGGCGGAGATAAATAAAAAATAAATAAAAATAATAATAAAAAAAAAAA]AGAAGCAATCTAGATGTCCACTGACAGATGGATGG - 8 1 4 1 20100 f 74 goat SV_363 7 101759586 - deletion junction SV-TF-chip 562166106 Affx-1251763746 AX-606941514 7 101759586 ACCTAGCCACAACACCACCAGGGAACCGTAGGACA[-/TAGAAGCAATCTAGAGGGGGGAGAGGGAAAGATGGCGGAGATAAATAAAAAATAAATAAAAATAATAATAAAAAAAAAAA]AGAAGCAATCTAGATGTCCACTGACAGATGGATGG - 8 1 4 1 20100 f 74 goat SV_363 7 101759586 - deletion junction SV-TF-chip 562166182 Affx-1251763746 AX-606941590 7 101759586 ACCTAGCCACAACACCACCAGGGAACCGTAGGACA[-/TAGAAGCAATCTAGAGGGGGGAGAGGGAAAGATGGCGGAGATAAATAAAAAATAAATAAAAATAATAATAAAAAAAAAAA]AGAAGCAATCTAGATGTCCACTGACAGATGGATGG - 8 1 4 1 20100 f 74 goat SV_363 7 101759586 - deletion junction SV-TF-chip 468278724 Affx-1111836480 AX-519552201 7 101790053 TATAAGTTCCACAATACAACAACAAAAAGCTAGAT[A/G]AACTAAAAAGTCATCATTTATTTAAAGCTTTTCAA R 2 1 2 1 202000 r 74 goat Random2.2K-848 7 101790053 A G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797249 Affx-122943392 AX-385284188 7 101795846 GTTAATGCTTCCTGCACCTTAAATTGGAAATTATT[A/G]CCGAGAATAACATCTGGAACCCAGTTTCAACTCCT R 2 1 2 1 101000 r 74 goat snp47734-scaffold671-1157346 7 4761002 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390871 Affx-122967811 AX-123261228 7 101855908 AGGATAAAGGGTCATTTTTCTCTCTGATACAAGAT[A/G]GTTGAGAAGTTCTCCACAAATTTTCCAAGAGACCA R 2 1 2 1 101000 r 74 goat snp47735-scaffold671-1217408 7 4705586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397485 Affx-122962078 AX-123267840 7 101947048 TTATTTATAAGAATAGAGAGTTAAAAGGAAGAAAT[A/G]CTGTTCTTAGTCACTCATTATACTTAAACACATAG R 2 1 2 1 201000 f 74 goat snp47737-scaffold671-1308548 7 4613979 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437933 Affx-122931634 AX-123308271 7 101998510 AGTAATTAGTAATCTTTTCTTTTTCCCAATATTTA[A/G]TCATCTGCAGTGATACATGAGGATTTTGTAACTGT R 2 1 2 1 102000 r 74 goat snp47738-scaffold671-1360010 7 4562627 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776844 Affx-122978145 AX-385263968 7 102046982 CACTTAATTGGGGCCATTTAAATCATAAAGCACAA[C/T]ATGGTTCCAGGCAAGTTAATTATATAGACAGCTGA Y 2 1 2 1 101000 r 74 goat snp47739-scaffold671-1408482 7 4513826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801119 Affx-122930383 AX-385288032 7 102105340 GTAATTAGCAAAAATTTGCTGATAGTAGCATATTT[A/G]TATGTGAAACTTAAGCAGAATTTCTAGGAGTAAAT R 2 1 2 1 101000 r 74 goat snp47740-scaffold671-1466840 7 4454324 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779706 Affx-122919823 AX-385266806 7 102149837 TTCTGGTACTTTCATTCATTTGATAAGTGGAATGT[A/G]TTTGGTATGTTCTAATGAGTCTCAGACATTCTAAC R 2 1 2 1 101000 f 74 goat snp47741-scaffold671-1511337 7 4409360 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796659 Affx-122955786 AX-385283605 7 102197460 AGACATTGCATGAAACCATGGAAGCCAAACACATC[A/G]TTGCCTGCCAATATGCTCCTTAAGGGAGATGTGAG R 2 1 2 1 101000 f 74 goat snp47742-scaffold671-1558960 7 4361578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443608 Affx-122927308 AX-123313945 7 102250706 GGATGTAGGGAGGAGGCTACCTGCTGTACTGTACT[A/C]CCCATGGCTGGCCTCACCTCTGTCCTCCTCGTGTG M 2 1 2 1 101000 f 74 goat snp47743-scaffold671-1612206 7 4308193 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376117 Affx-122978877 AX-123246476 7 102253662 TGTACATACAACCCTACATAGTATGTGTCTAATAC[A/G]TGAAAAATAGTACAAATGCAATACTGCCTTTTACA R 2 1 2 1 101000 f 74 goat snp21566-scaffold210-2963078 7 4300493 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389055 Affx-122968610 AX-123259413 7 102302341 ACATATACAACAAACCTCTCCTCTGAAGAAATACA[C/T]GTTACTACTGAGCAATTCCTGCCCCTCAGATGAAG Y 2 1 2 1 101000 f 74 goat snp21565-scaffold210-2914399 7 4251206 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406861 Affx-122922823 AX-123277212 7 102347431 TCGCCTTCCTCCCGCGTTTTGCATTCCCCCAGAAC[C/T]GTGAATGGACAGGTCCGTCTCTGGTTTGGCATCAC Y 2 1 2 1 201000 r 74 goat snp21564-scaffold210-2869309 7 4206773 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772171 Affx-122976721 AX-385259326 7 102387148 TGCACGCTCATCCGTCCCACGTGTTTACATGTGTT[A/G]TCTCATCCATATCTTATCTCCGCTATGTGTTCGGT R 2 1 2 1 201000 f 74 goat snp21563-scaffold210-2829592 7 4167845 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774446 Affx-122932101 AX-385261582 7 102423568 CTCGATTTCCTGCGGTTGTCTAAAGAAAACGAGAA[A/G]CCTCCAGAAGCATTACCTTTGTTCTCTTAAGAAAT R 2 1 2 1 101000 r 74 goat snp21562-scaffold210-2793172 7 4130568 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773974 Affx-122919876 AX-385261112 7 102452816 CCCAGGCTTTTCCCTTCCTATGGTTTGAAAACGTG[C/T]TCCTGTATTGCAGTAGTTATCCCTAAAAATGGCCA Y 2 1 2 1 101000 f 74 goat snp21561-scaffold210-2763924 7 4101481 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278726 Affx-1111836481 AX-519552203 7 102454064 GTGGAGGGATGGTTCTCAACCAGGAGCAGGAGGTG[A/C]GGACTCTACCACACAGGGTGTACTTGGCCAGGTAG M 2 1 2 1 102000 r 74 goat Random2.2K-849 7 102454064 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380333 Affx-122975373 AX-123250691 7 102524987 GGGGAGCCCTGGTTTAGACCGCGGACTCTAAAGCC[A/G]CTAGCCTGAGCTTGAACCCAGGTCTGCCTCCTGTG R 2 1 2 1 101000 f 74 goat snp21559-scaffold210-2691753 7 4029345 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419118 Affx-122945767 AX-123289466 7 102584643 TCAGGGTCAAGCTTAAGTCAAGATGTGAGCAAATC[A/G]TTTTATGTTGACTTCTGTGAAATGATTACAACCTT R 2 1 2 1 102000 f 74 goat snp21558-scaffold210-2632097 7 3970797 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388777 Affx-122968932 AX-123259135 7 102621306 TGTGGACATCTGCTTTGCAGGCTAACCCAGGTCTG[C/T]GGGCTGAAATATGTGCCTGGAAACATGGGGTGATT Y 2 1 2 1 101000 f 74 goat snp21557-scaffold210-2595434 7 3934394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400035 Affx-122960783 AX-123270390 7 102652035 TTGACCCTTGCAGGGCCCCCGCAGCTGCTGTCTTG[C/T]GCCAGCCCTTCCTGCTGAAAGATGGAGGTGCCATG Y 2 1 2 1 101000 r 74 goat snp21556-scaffold210-2564705 7 3903286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429879 Affx-122938133 AX-123300220 7 102711210 TCTCTCAGATGTAGAGGATTTGATCAGGAAATTAG[C/T]AATTGATTCTTATTTCTGATCAACAAGAAGGAAAA Y 2 1 2 1 101000 f 74 goat snp21555-scaffold210-2505530 7 3844130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434634 Affx-122933998 AX-123304975 7 102765804 CATAGAGCTTCACATCATTGCTGGGAGGGCTAAGC[A/G]TTGTCTGTAGACTCCGACTGAGGGAGTGTATTGGA R 2 1 2 1 101000 r 74 goat snp21554-scaffold210-2450936 7 3789090 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415218 Affx-122948972 AX-123285567 7 102814125 CATCCTTTTTACATTTTTTCAGTATATTGTCAGAT[A/G]CTCTTCAAGTAAATAGAACTCATTTAGACTTTCTC R 2 1 2 1 101000 r 74 goat snp21553-scaffold210-2402615 7 3740479 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778548 Affx-122964497 AX-385265660 7 102846776 AGAGAGCCAGCAATGATATAGATGGTGCCATTTCC[A/G]TTCAAAGTTGTAATAATCTTGGGAGCGTTACAGTT R 2 1 2 1 101000 f 74 goat snp21552-scaffold210-2369964 7 3707797 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790896 Affx-122938481 AX-385277893 7 102896453 TGTGATCTCCTACAAATTAGTCATCTTTTGAGACT[A/G]TTCCTTATTCATTGCACTGTAGTCGCACTTCATTG R 2 1 2 1 101000 r 74 goat snp21551-scaffold210-2320287 7 3658171 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438493 Affx-122931223 AX-123308831 7 102937129 ATAGATTGAATAAGATGGGGCTGATAGACATCTCC[A/G]CTTCACCAACTGGTGACTGAGTATCTTAGCCTATT R 2 1 2 1 101000 f 74 goat snp21550-scaffold210-2279611 7 3617510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423085 Affx-122942932 AX-123293431 7 102972828 TGTGTGTTCCCCCACAAAATGATCGGAACTCATAA[C/T]GACCCCAGTGATGAAACGAGTAGTCCAGTTGATGG Y 2 1 2 1 201000 r 74 goat snp21549-scaffold210-2243912 7 3581422 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399337 Affx-122961363 AX-123269692 7 103033114 TTCTGAATGAATATATGGAACTTTATTCCCACTGG[C/T]TGCACTTTTCTCACTCCCTAGCCTGGAACTCCTTC Y 2 1 2 1 101000 f 74 goat snp21548-scaffold210-2183626 7 3521905 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762550 Affx-986697080 AX-385250656 7 103037675 GCTTCTTTCAGCACAGCCCGACCACTACCCAGATT[C/T]TGCTGGCTCAGCCATTTGCAGGGTTTGCGGTCAGC Y 2 1 2 1 600010 f 74 goat 7_103037675 7 103037675 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 320764874 Affx-986697082 AX-385252471 7 103037678 TCTTTCAGCACAGCCCGACCACTACCCAGATTCTG[C/T]TGGCTCAGCCATTTGCAGGGTTTGCGGTCAGCTGG Y 2 1 2 1 600010 r 74 goat 7_103037678 7 103037678 Ancestral_priority_1043 ancestry 0.544 neutral IMAGE 10K 10K ancestral 38397659 Affx-122962601 AX-123268014 7 103071356 AGAGTAATGTGCTAGCCCATAACTTAGAACTGGCT[A/G]TATTTTGATTTTTTAACAAGAACTGACATATATTT R 2 1 2 1 101000 f 74 goat snp21547-scaffold210-2145384 7 3483064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438546 Affx-122931183 AX-123308884 7 103135682 TATATAGAGTAAAGCCAAGGGAAAACTTGCCAGAC[A/G]TGCCAGCAGACAGAGACAATGGGAAAGAAGCAAAG R 2 1 2 1 102000 r 74 goat snp21546-scaffold210-2081058 7 3418799 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774041 Affx-122957022 AX-385261179 7 103184978 TAAAGGGTGTTTATTGTTTCTGAGTAATAGTCACT[A/G]TGTGAGGTGTATCAAAATCTGAAGAAAATTGATGA R 2 1 2 1 101000 f 74 goat snp21545-scaffold210-2031762 7 3369616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437902 Affx-122931659 AX-123308240 7 103230593 ATAGTGGATTTTATCAGGGCAATAAAGGGTGGCTG[C/T]AGAAGGATTTCTTTTAAAGGGTCGTTTGATTCAAC Y 2 1 2 1 101000 f 74 goat snp21544-scaffold210-1986147 7 3324332 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445281 Affx-122925460 AX-123315618 7 103268188 GCCAAAGGTGAAGAATTAATAAGTGGTGGGAATCA[C/T]AGAGTCCACAGATCCCTGAGTTTCATCTGATTTTT Y 2 1 2 1 101000 f 74 goat snp21543-scaffold210-1948552 7 3286205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423949 Affx-122942245 AX-123294295 7 103301788 AGTTTCCACTTTTAGAGAGTTTCAGTCTAAATGGC[G/T]ATCTCAAATGTGTGCATATATGTGTGCTTATACAT K 2 1 2 1 101000 f 74 goat snp21542-scaffold210-1914952 7 3252687 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453757 Affx-122919604 AX-123324090 7 103370969 TCTCCCACCTGCCCCAGAAGGGGTTACACCTTGAA[C/T]GGTCCATTCAGTGCCTCTAGTTTGCGGATCCTGGT Y 2 1 2 1 101000 r 74 goat snp21541-scaffold210-1845771 7 3183294 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797453 Affx-122950840 AX-385284392 7 103401489 ATCCTGTTTAAAGAAACTTTGGATATCATGGAGCT[G/T]ATTGTAAAACATATTTTGGAAGGTACTAGTACTTG K 2 1 2 1 101000 f 74 goat snp21540-scaffold210-1815251 7 3151883 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389698 Affx-122968692 AX-123260056 7 103433105 GAGGCTGGCACATTCATCAGACACCTCCCGGGCCC[A/G]TTGGTTAGAAAGACCTTCAGAGGCATTCAGGTATC R 2 1 2 1 101000 r 74 goat snp21539-scaffold210-1783635 7 3120412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788930 Affx-122952937 AX-385275944 7 103478194 CCAGTTTGTTTTGGTCTCTTTAGAAGAAGCAGAAA[C/T]GTAGAATCGTCCAGTATAGCCTCTGATAGTCTCTT Y 2 1 2 1 101000 f 74 goat snp21538-scaffold210-1738546 7 3075724 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771146 Affx-122947933 AX-385258306 7 103519154 TTGCTTTTTTACAAGTTGAAGCTGAATTCTAGTGT[A/G]AGTATAGAATTGAGTTAGTCCTTGAAGGCCACCCT R 2 1 2 1 101000 r 74 goat snp21537-scaffold210-1697586 7 3034804 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377032 Affx-122977710 AX-123247391 7 103551407 TTGTAGACATTACTATACTCCACTTCTGAATTCTT[C/T]AGTGTGTATCTCCTAAGAACAAGGACATGAATCAC Y 2 1 2 1 201000 f 74 goat snp21536-scaffold210-1665333 7 3004927 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440819 Affx-122929281 AX-123311156 7 103613271 TAGGTTTTAAAAGGTGGTATTTGATACGGGTAAGT[G/T]CCCAGTCACTCAGTCGTGTCTGGCTCTTCGCAGCC K 2 1 2 1 101000 f 74 goat snp21535-scaffold210-1603469 7 2942560 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422102 Affx-122943573 AX-123292449 7 103671416 TCCGTTTCTGTACCTATTAATTGCATAGTAATTCT[A/G]TCTTCACTGATTCTTATGATAATTGAGATAGAGTA R 2 1 2 1 101000 f 74 goat snp21534-scaffold210-1545324 7 2882810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796301 Affx-122944423 AX-385283250 7 103700389 AAACGCCTCGCTTAAGGGAGTTAGTGAAAGTACCC[A/G]TTTGTTACTAATGCATCAGCCTCATAACTCAAGTC R 2 1 2 1 101000 f 74 goat snp21533-scaffold210-1516351 7 2853757 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791171 Affx-122937578 AX-385278166 7 103733730 CCCCTAGTCTGCACAGGAAAAAGACCCCATTAATC[A/G]TTCCAGACTTCAACCTGAACAGGAGGGTTCATGTC R 2 1 2 1 202000 f 74 goat snp21532-scaffold210-1483010 7 2819088 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784704 Affx-122940777 AX-385271752 7 103787092 AGACCATCAGAAGGCTGTAAGAAAGGCGAATAGCA[C/T]GGTGCGCACGTCCTGGGATCCTCAAAGGAAGCGAG Y 2 1 2 1 202000 r 74 goat snp21531-scaffold210-1429648 7 2765155 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445199 Affx-122925523 AX-123315536 7 103865631 TAAATGAAAATACCTGTCTCCTCTCTATACAACCG[A/G]AAGACGTCATCTGCTTTAGAAACTTGGATCTTGAG R 2 1 2 1 101000 r 74 goat snp21530-scaffold210-1351109 7 2685111 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464553650 Affx-1110541338 AX-516025468 7 103876748 TCTGAACTATCAGGGAAGCCACCAGGACAAACGGA[C/T]AAAGTGTCATATATCTACACAATGGAATAGCACCT Y 2 1 2 1 101000 r 74 goat 7_103876748_AF-PAKI 7 103876748 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320766744 Affx-122931993 AX-385254080 7 103908635 TTGCTCTTTCTTCCCTGCTTCTTTAGTTCCTTTAC[G/T]CAACTTCTTTTTATGAGTAATCGTTTTTTCTCATT K 2 1 2 1 101000 f 74 goat snp21529-scaffold210-1308105 7 2642686 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438947 Affx-122930406 AX-123309284 7 103940315 CAGCACACTCTGTCATCCTGCACAACTCTTGGAAG[C/T]GTTCCCTGGACTCTCAAGGTAAGAGGCCCTTCTTA Y 2 1 2 1 201000 f 74 goat snp21528-scaffold210-1276425 7 2611125 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391817 Affx-122967021 AX-123262174 7 103975960 TTCGCTCTCTAAGTCTGCTGCTTCTCTTCCCCCTC[A/G]TGATCCCACTGCACTTCTCAAGCAGCCTGGCATGT R 2 1 2 1 201000 r 74 goat snp21527-scaffold210-1240780 7 2574702 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766113 Affx-122934766 AX-385253524 7 104042315 AGCAGCCTTTGATATAAAGATAAGAATGGACAGGA[C/T]GATCAGGTGTATAAAGAGGTTGGTTCCTGGAATAC Y 2 1 2 1 101000 f 74 goat snp21526-scaffold210-1174425 7 2511261 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439629 Affx-122930622 AX-123309966 7 104077562 ATACTGCAGGCCTGTATGCCCGATTCACCTCGGGC[A/G]CTGCTGTGTGCAGTGTGGGCGTCATAATCCCCGTA R 2 1 2 1 103000 r 74 goat snp21525-scaffold210-1139178 7 2476536 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382201 Affx-122974003 AX-123252559 7 104108435 TTTCATTCCTGACCGTGTGGAAGACTGCCTTCTTC[A/G]CCTCCTCACAGCTAGGTGGGCCACGGCAAACAAAT R 2 1 2 1 102000 f 74 goat snp21524-scaffold210-1108305 7 2445441 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423065 Affx-122942949 AX-123293411 7 104207586 CACAAAGGCCAAGGCACCCTGGCTATCTTGTTTCA[G/T]AGCAAGATTTAAGACGGAGAAATGAGAGGCCGAGA K 2 1 2 1 101000 f 74 goat snp21522-scaffold210-1009154 7 2346270 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376235 Affx-122978787 AX-123246594 7 104268981 ACCAAATGGCTCTGCGCCTGCTGTAACTTGGGCAA[A/G]CAAGTTATGATAAAGCTGTCCACTGCTTGAAGAAC R 2 1 2 1 101000 r 74 goat snp21521-scaffold210-947759 7 2285290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436378 Affx-122933048 AX-123306717 7 104305212 AGTCTCTACCTAAAATGGTAGGAGAAGTGAAATCA[C/T]GTTTAGAATCAAACCCCATTCCTGCCAGAGATGCT Y 2 1 2 1 303000 f 74 goat snp21520-scaffold210-911528 7 2247168 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423466 Affx-122942583 AX-123293812 7 104351930 CATTTTGCTTTAACCGTGGGCATTTCAGCGATCAT[C/T]TTGGTTAAGTCAGGTATGAGTGAATCAGAGCCACC Y 2 1 2 1 101000 f 74 goat snp21519-scaffold210-864810 7 2204156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393712 Affx-122965243 AX-123264067 7 104400623 CCTGGAGTTCACTGTTGGCAAAAGTGGACTTTGAA[C/T]GGACCATGATAGACCCAGGATTGGGAGAGAATTGG Y 2 1 2 1 101000 f 74 goat snp21518-scaffold210-816117 7 2155496 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377859 Affx-122977276 AX-123248218 7 104432039 GAGGTTCCTGAGGGGTTTCCAGGGTTTGGACTGTG[A/G]CCGAGTGGACAGAGGGTCTCCACACCCTGACCTCA R 2 1 2 1 101000 f 74 goat snp21517-scaffold210-784701 7 2123476 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769725 Affx-122949779 AX-385256895 7 104481986 TGATGACATGGCTAGCCTTCCCATCGGCTAAATAA[G/T]ACACGAACATAACTCAGAGATGAAGATACACCAGA K 2 1 2 1 201000 r 74 goat snp21516-scaffold210-734754 7 2073224 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392942 Affx-122922562 AX-123263299 7 104514056 GTCATGGCTCATAATGAATCAGAATCCAGTGCAGT[A/C]TGCTATCTTTGCTAATAATAATAAAGGCCAAACTG M 2 1 2 1 101000 f 74 goat snp21515-scaffold210-702684 7 2042818 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432982 Affx-122935266 AX-123303323 7 104543214 GTAAGGAAGATAGCGTTTGCTCTTGAATAGTTTCC[A/G]TTTGAATCCTAGCATCTCAATCTAACTGGATGGCA R 2 1 2 1 101000 f 74 goat snp21514-scaffold210-673526 7 2013592 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451365 Affx-122921246 AX-123321698 7 104601941 AGAAAACATTAAATATTCCCCAAAGGGTTTTGGAT[A/G]TAAGCTGTAATTGAACCTCCCAATAAGCTTTTACT R 2 1 2 1 101000 r 74 goat snp21513-scaffold210-614799 7 1954858 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441509 Affx-122928725 AX-123311846 7 104672350 TCAGTGGGACTAGAGATGTGCAGAGATAGCGCCAC[A/G]TTGACATTGTGTTTGCTGTGCAAGTAATAAATTGT R 2 1 2 1 101000 r 74 goat snp21511-scaffold210-544390 7 1891528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387450 Affx-122970375 AX-123257808 7 104742963 GCCGTCAACCCCACCTACGGGTGGGAGATAAAATG[C/T]ACTGTGTGAGAATCACCTCTTATCCGGGACATCTT Y 2 1 2 1 101000 r 74 goat snp21510-scaffold210-473777 7 1820810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765415 Affx-122919749 AX-385252921 7 104773254 CCTCAATGCCAGTATGTGTTGGCATCACTGCCCTT[A/G]AGAGGTAAGAAGCCTCCCACAAAGTAAGATTGGAG R 2 1 2 1 101000 f 74 goat snp21509-scaffold210-443486 7 1790523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449510 Affx-122922617 AX-123319845 7 104806171 CAAATGGGAAAAAGAAGGGTTTGAGCAGGAGAGTC[A/G]CAACATCATTGCTAACACTTGCTGAGTGCCTACTA R 2 1 2 1 101000 f 74 goat snp21508-scaffold210-410569 7 1757243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430137 Affx-122937395 AX-123300478 7 104835576 AAAAACCAGAACACACACAAAACAAAGGCAGCCGC[A/G]TTCCTCGTACCCTCCCTAACTCCTGTGGAGCTGAA R 2 1 2 1 201000 r 74 goat snp21507-scaffold210-381164 7 1727858 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417965 Affx-122946693 AX-123288313 7 104923526 ATCTAAAGGGAAGGCTCCTATAGACCCTCTGTCTC[A/G]CTGACCCTGTTCGTGATGCCAACTGTCTTGCCGTC R 2 1 2 1 101000 f 74 goat snp21505-scaffold210-293214 7 1640056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441872 Affx-122929027 AX-123312209 7 104953737 GTGCCACTTCTGACCCTGCTCTGTCTGCAGCTTCC[A/G]TCTCAGCAGGACACCCACAAAGCTCCCTGCACACC R 2 1 2 1 201000 f 74 goat snp21504-scaffold210-263003 7 1610078 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444004 Affx-122926903 AX-123314341 7 104990147 GTTAACGCAAGTGCACAAAGTGACCCAGCGGGGCC[A/G]CTGGACAGCCCTGGGCAATGACACGGCCATTTAGT R 2 1 2 1 101000 r 74 goat snp21503-scaffold210-226593 7 1576790 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446821 Affx-122925281 AX-123317157 7 105051869 CTAAACAGTGGGGGCAGACAAGAGTGTAGGATCAG[C/T]GGGGGCAAGGAACTAGACATCCACTTCCAATTCTA Y 2 1 2 1 201000 r 74 goat snp21502-scaffold210-164871 7 1518191 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765953 Affx-122948892 AX-385253379 7 105090032 CACAGTGAGGTACTCTTTAGGCCTGTTCAGATGCT[A/G]TCATCAAAAAGTCAGAAGTTGGCAAGTGATGGATG R 2 1 2 1 101000 f 74 goat snp21501-scaffold210-126708 7 1482690 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416654 Affx-122947601 AX-123287002 7 105121313 GCCTGCATCAGGCAGTGAAACCCACTTGGAAAGAG[A/G]TAACACAAGCATGTGAATTGCGTGAGTCCATTACA R 2 1 2 1 101000 r 74 goat snp21500-scaffold210-95427 7 1451655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436672 Affx-122932464 AX-123307010 7 105157446 GTACATATTTGAATCCCACATTCTTCCTCAGGTGG[A/C]GGCTCTTTTGAAAAATGAGTAGCACGTTGTTCTCG M 2 1 2 1 101000 f 74 goat snp21499-scaffold210-59294 7 1414902 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421463 Affx-122943931 AX-123291810 7 105203117 ATGTAACCTGCCAGCGTGACTCACGCTCTGGAGAT[A/G]CTGGTTGCATTCTAGGGCATGCCAGAGTTGGAGAG R 2 1 2 1 102000 f 74 goat snp21498-scaffold210-13623 7 1368818 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381401 Affx-122974374 AX-123251759 7 105218786 AGAGAAGACTTTTTTTGGCATCAGGAATAGCAAAC[A/G]GGCAACATAGAGAGAGGTTTGGGAGGAAGCTAGAA R 2 1 2 1 101000 f 74 goat snp13790-scaffold1539-710641 7 1353954 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794095 Affx-122968885 AX-385281062 7 105262263 CTTTGCAAAGTAGATATTAATGTTATACTCATTTA[C/T]AGATGAGAAAATCAATTTAGTAATCTGTCCATGGC Y 2 1 2 1 101000 r 74 goat snp13789-scaffold1539-667164 7 1310349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406796 Affx-122955699 AX-123277147 7 105312020 GTATTTGGGAAACCATTCTCTTTTTTTCCTGGTCA[C/T]GGGCATTTGGATTTTCTTTTGCAAAATTATCTTTG Y 2 1 2 1 101000 f 74 goat snp13788-scaffold1539-617407 7 1260336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780649 Affx-122958778 AX-385267739 7 105344771 CACTTATAAAATACTAGCCTTATTCTGTCTCCTGA[A/G]TTAGTACCGATTTTTGTGAGTGTGTGATAGGAATC R 2 1 2 1 201000 f 74 goat snp13787-scaffold1539-584656 7 1227456 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782846 Affx-122949697 AX-385269917 7 105375944 TCAAGAAATGCTACATGTCAAAGGTTACCAAAGGC[A/G]CTAATAAAATATATGTTTTGCATGATATCTCCCTT R 2 1 2 1 101000 r 74 goat snp13786-scaffold1539-553483 7 1196030 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379126 Affx-122976742 AX-123249485 7 105452563 GAAGGGCAGTGATACCATCAACTGTATATATGTAT[A/G]TCTTTGACAGAAATGGATTTCTAACCTCTAAAGAA R 2 1 2 1 101000 f 74 goat snp13785-scaffold1539-476864 7 1119412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442122 Affx-122928341 AX-123312459 7 105491983 AATCAACAGGTGAACAGCTTACTTTTAAAGTCATC[A/G]TTGGCATTTGAAAACTGAGTTTTGAGAACACAGTT R 2 1 2 1 101000 f 74 goat snp13784-scaffold1539-437444 7 1079984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447251 Affx-122924953 AX-123317587 7 105544296 ACCCAGTGTCCCCACTTCAGTTGAGTATTTTACCC[A/G]TTCAGTACCCATCTGTCTCAACTTCTGGGGAGCAA R 2 1 2 1 101000 f 74 goat snp13783-scaffold1539-385131 7 1025715 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792807 Affx-122924895 AX-385279785 7 105601345 GTTAAAGCAGAGCTTACACTATGTTTTGCTAATTT[A/G]TTTTCTCAGAGCCACGCTGGATAACTACTTCTTTG R 2 1 2 1 201000 f 74 goat snp13782-scaffold1539-328082 7 967688 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447957 Affx-122923772 AX-123318293 7 105635660 AAAGTATGAGAGGAGCAACTTTCAGCTGATGAAAC[A/G]TTTTTGTTTGCAATATTGTGCAAAGCTGTGTTAAA R 2 1 2 1 202000 f 74 goat snp13781-scaffold1539-293767 7 932615 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767651 Affx-122968231 AX-385254892 7 105673477 AGTTGATGGAAGCTCTGCCAGTTAGGTACTGGGCT[A/G]TACATAATACAACAGTTTATCTGGTTTAATAAGAT R 2 1 2 1 101000 f 74 goat snp13780-scaffold1539-255950 7 895002 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784181 Affx-122954934 AX-385271232 7 105740282 CTCTATTGCTAGTAGTAGTAGTTATGATTTTAGTG[C/T]GGTTTTGCCTGAAAGATAAATGGCACTATGGCATC Y 2 1 2 1 101000 r 74 goat snp13778-scaffold1539-189145 7 827494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442423 Affx-122927978 AX-123312760 7 105771051 CAGCAGCTTTTTAAGGTGTTACTAGCCTTTTTGAA[G/T]AAATTGAGTCTCAGAAAGTTTAACTTCTCCAAGAA K 2 1 2 1 101000 f 74 goat snp13777-scaffold1539-158376 7 796377 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769768 Affx-122924254 AX-385256938 7 105805496 AATAATCTAGTTCTGAAATACTATATATGCCAAAG[A/C]GATTGCATGACATAAATGAGATAATTATCCATAAC M 2 1 2 1 101000 r 74 goat snp13776-scaffold1539-123931 7 760726 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274345 Affx-1111834147 AX-519547940 7 105832152 AGTTCGCTTGGGCGCTGCAGCCGCCGCCATATGCC[A/G]TGCAGCAGGGAGCAGGGCCCTGCTGAGACTTGCCT R 2 1 2 1 303000 r 74 goat GoatD01.021548 7 105832152 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38376108 Affx-122978886 AX-123246467 7 105853308 TGGAGAAAAATACTTGAATTATAGAGCTGTGTTAA[C/T]GTTACAAGCTGGATACAGAGGACCAAATGTATTTC Y 2 1 2 1 101000 f 74 goat snp13775-scaffold1539-76119 7 712000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436564 Affx-122932907 AX-123306902 7 105895579 CCTGGGTCTCATGCATTGTAGGCAGATGCTTTACC[A/G]TCTCAGCCCCCAGGGAACTCTTAAATCATTACCTG R 2 1 2 1 201000 r 74 goat snp13774-scaffold1539-33848 7 668310 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787505 Affx-122934271 AX-385274530 7 105941659 ATTTAAACAAAAACTGTGGTATGTATTGTAGAACA[C/T]TGTAACTGCATGGGATATGTAAACCCATGGGGTAT Y 2 1 2 1 101000 r 74 goat snp7076-scaffold1261-466776 7 620083 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439938 Affx-122930000 AX-123310275 7 105973777 CTTTGCTTTTGCTACCTTTTCTCTTTCTGCTTTTA[C/T]GATTTTCCTAGACCAGCTTTTGCTCTCTGGTCCAG Y 2 1 2 1 101000 r 74 goat snp7075-scaffold1261-434658 7 586901 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764884 Affx-986697088 AX-385252479 7 105973968 CGAAAGTGCACTTGGAGGCCAAGGGCTGCACCCGG[A/C]AGCTGGTGGTGCAGCAGGCGGGCAAGGCGGACGCC M 2 1 2 1 600010 r 74 goat 7_105973968 7 105973968 Ancestral_priority_1043 ancestry 0.4 neutral IMAGE 10K 10K ancestral 468278553 Affx-1111836483 AX-519552035 7 105986778 TTCTGAGAATCTCTGTGGTGGGGAGGATTATTGCA[A/G]TTTTTTTGAGAGACAGTCAAGAAGTTCCTAATAGT R 2 1 2 1 102000 f 74 goat Random2.2K-850 7 105986778 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781408 Affx-122929750 AX-385268493 7 106005606 CAGGTTTTTCATATGGCTGCCTGGTACTGAATATC[C/T]AACTAAAGCTCATTCCAGAACCCTATGGCTTCAAT Y 2 1 2 1 101000 f 74 goat snp7074-scaffold1261-402829 7 555703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399492 Affx-122961177 AX-123269847 7 106048364 TTGGAAAGAAACGCTGCAAGGTTTCGAGGAGGTGG[C/T]ACCGCTGAACTCTGTCATGGTGGCAGAAAACAGAT Y 2 1 2 1 201000 r 74 goat snp7073-scaffold1261-360071 7 512583 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411479 Affx-122951795 AX-123281829 7 106087175 CCCATGAAAACATAGTCTATACACTTCTATAAGGC[A/G]TTTGATATTACAATGGCAATGTCTATGCTTTTACG R 2 1 2 1 101000 r 74 goat snp7072-scaffold1261-321260 7 473593 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385135 Affx-122971767 AX-123255493 7 106121693 CCTGAGCCAAATGTGTGGCTCTTCTCCAGTAAGGA[C/T]GGCTCTGCAGAGTGCAGTGTTTCTACTTTGACTTT Y 2 1 2 1 101000 f 74 goat snp7071-scaffold1261-286742 7 438955 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452467 Affx-122921006 AX-123322800 7 106152126 CCCACTCTGAAAATCAGCCAATCACTAAACTCCAC[A/G]CTAAACATCATCCAATTCTTAAAAAAATACCGCTT R 2 1 2 1 101000 f 74 goat snp7070-scaffold1261-256309 7 408107 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404427 Affx-122956764 AX-123274779 7 106193195 GTTAGCAGCTACGAATTTCACATGCAGCACTGGGC[A/G]TGTGTCAAACCTTATCTTTCAATTTATGAATCTCC R 2 1 2 1 101000 f 74 goat snp7069-scaffold1261-215240 7 366480 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774503 Affx-122963750 AX-385261638 7 106224183 TCCTTCTTGGATCACCTCAAGCTCATACAAAGTCA[C/T]GCAGTGTCTACTCCATGACTCTACATTGTATATAA Y 2 1 2 1 101000 r 74 goat snp7068-scaffold1261-184252 7 335088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794945 Affx-122929835 AX-385281905 7 106276835 GCGTTACTGTAAGACTGACTGATTATACCCACACA[A/G]TGTTAGCATGACATAGGTTATGCATTTATGGTGTG R 2 1 2 1 101000 f 74 goat snp7067-scaffold1261-131600 7 282687 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800452 Affx-122942513 AX-385287373 7 106308648 ACCCAAATATAGAAAGCTTGATCATTTTTCATAGT[A/G]CTATTATTTAGCAAGCCATTTAGTATCAGATAAAT R 2 1 2 1 101000 f 74 goat snp7066-scaffold1261-99787 7 250789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390380 Affx-122967665 AX-123260737 7 106343734 AAAGAGTCGGACACGACTGAGTGACTAAGCACACA[C/T]GCAGACTCAAGTACACACACAACCATAATCATCAC Y 2 1 2 1 103000 r 74 goat snp7065-scaffold1261-64701 7 215688 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278555 Affx-1111836484 AX-519552037 7 106379781 CTCTAAAAAAATAAAATGGGTAAAACACAGTATTA[A/G]AACCAATAGCAGAACTGTGTGAACAATCACATTAA R 2 1 2 1 201000 f 74 goat Random2.2K-851 7 106379781 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273253 Affx-1111833528 AX-519546905 7 106387985 GGATTGGCAGAGATAAATCTATGAAAAGGTAACTT[A/G]ATAAAAAGTTAATTGGTGGGTAGAAGCATGGATGA R 2 1 2 1 101000 f 74 goat 7_106387985_AF-PAKI 7 106387985 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320771152 Affx-122923231 AX-385258312 7 106402434 CAAGGCCAGTTCTATAATATTCCCAGCACTCAAAA[C/T]GCTGGGATCCTAAATAAGCTTTTGAAAATAACTGG Y 2 1 2 1 202000 r 74 goat snp7064-scaffold1261-6001 7 154732 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426388 Affx-122940852 AX-123296734 7 106426750 CTGGGTGTCGGGGTAGAGGGAGCTGAGTGGTTGAA[G/T]GAGATCGAGACAATCCATCCACTGCGCTGGAGGCA K 2 1 2 1 101000 f 74 goat snp23716-scaffold2395-18216 7 128023 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391115 Affx-122966806 AX-123261472 7 106468705 ATACACTTTCCAAGACTAAATAGTAAGAGAATGCT[A/G]CTGAGTTGCTGCAGTCGTGTCCGACTCTGTGCGAC R 2 1 2 1 101000 f 74 goat snp23717-scaffold2395-60171 7 83812 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395007 Affx-122964231 AX-123265362 7 106502640 AAAATACTGGCCAACATTTATTATTTATTACATGA[G/T]CAATCTTTTTGGCCACTTTAAACTGTATTCTTTCA K 2 1 2 1 101000 r 74 goat snp23718-scaffold2395-94106 7 49729 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464556715 Affx-1110542895 AX-516028506 7 107708613 ACCCCATCAAGGCTGGGCCTGCCTTCTGGTGGACA[G/T]CAGAAGTCTCTCCTTGTCAGCACTGTGGAGTGCTT K 2 1 2 1 202000 r 74 goat GoatD01.023776 7 107708613 T G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38445080 Affx-122926211 AX-123315417 7 GGGCCCTATTTTGTTCTAGTACGTAGCTGGAAAAA[C/T]GGAGCAGATGGGAGACAGGATGGTAACAAAATGTA Y 2 1 2 1 201000 f 74 goat snp35515-scaffold428-491297 NW_017189517.1 21135315 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431881 Affx-122936058 AX-123302222 8 8807 CTCAAGAAGTACCCCAAGATCCATGTCAGCACTGG[A/C]GAGGAATCCTCAGGTTCCGGCCCCGACTCCACACA M 2 1 2 1 103000 f 74 goat snp54527-scaffold832-448148 8 17587 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440308 Affx-122930214 AX-123310645 8 38347 CTCTTGGCATGGGTGCTGTTCTTACCGTGGGTGTC[G/T]TTAGTGCCGCTGATGTCTTGGGTGTCATGTGTGCC K 2 1 2 1 102000 r 74 goat snp54526-scaffold832-418608 8 47188 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772832 Affx-122968576 AX-385259977 8 77703 ACTATTACTTCCTAGTTCATTTTGCTCTCTTTCAG[A/G]GTAAGATGTCATTCCTCAGACACCTTCCTTTGCCA R 2 1 2 1 101000 r 74 goat snp54525-scaffold832-379252 8 87218 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786731 Affx-122970541 AX-385273762 8 240268 TTATTAACAACTCTCTTCCCATCAGATGTAATAGA[C/T]GCCAGAAAGCAATATAATGATATACAAAAAGTGCT Y 2 1 2 1 101000 f 74 goat snp54523-scaffold832-216687 8 251428 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395505 Affx-122963883 AX-123265860 8 301198 CCTGATACTGAGTGACTCCTGAAGCAGCCACTCAC[A/G]AACGGTCATGGGATAAATGCACACAGTTCAGAGGA R 2 1 2 1 101000 r 74 goat snp54522-scaffold832-155757 8 312356 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781165 Affx-122964669 AX-385268250 8 337688 GAGAAATACACATAGCAATAACAATAAATAACTGT[A/G]CTTTCAGTTGAATCAAGTTTATCTTTAATGGCAAA R 2 1 2 1 101000 f 74 goat snp54521-scaffold832-119267 8 349353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273352 Affx-1111833576 AX-519546987 8 361732 ATCTTTGACAAAGGAGACAAGAATATACAATTAAG[A/G]AAAGACAGCCTCTTCAATAAGTGGTGATGAGAAAA R 2 1 2 1 303000 f 74 goat 8_361732_AF-PAKI 8 361732 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781440 Affx-122968308 AX-385268525 8 380246 ATGGAGTCACAGTAAAGGTGGAAGCCATTCATTAC[G/T]ACAAGATTTCTTTATAGACATTAGCTGTGCTTCTG K 2 1 2 1 101000 r 74 goat snp54520-scaffold832-76709 8 392231 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427403 Affx-122940072 AX-123297746 8 441516 CCCAGTAGAGGTTATTGAAAAGTAATGACATGGTC[A/G]TAGTCAATAGAATGGGGTTTATATAAAGCTGATGA R 2 1 2 1 101000 f 74 goat snp54519-scaffold832-15439 8 453992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404721 Affx-122957248 AX-123275073 8 485191 GGTGGGGAGGTTGGTTTATAAATAGGCTTCCTCAA[C/T]GTTTCTCATTGGAAAGGTTATGTCTTCAAGAAAGG Y 2 1 2 1 101000 r 74 goat snp55249-scaffold851-28137 8 499129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778540 Affx-122972909 AX-385265652 8 567144 ATTTTTCTTTCACTGTGCAAGCAGTTTATAAGCAA[C/T]ACCTGATTCAGACAACCAGATCCCATCAAGTGGCA Y 2 1 2 1 101000 r 74 goat snp55251-scaffold851-110090 8 582548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799884 Affx-122959927 AX-385286810 8 621338 CAATTTGGTGAAGGGAGTTTCATATTATCTCTGCA[C/T]GATAATTTGATTTTGTTACCTTGTTTGAATTTTTG Y 2 1 2 1 101000 f 74 goat snp55252-scaffold851-164284 8 636654 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402838 Affx-122958257 AX-123273191 8 655181 ATGCATTTGTGGGTAACTGAACAAGCTTCAGTCAA[C/T]ATGAGCAAGAGAAGGTCCATGCAAGGGCACAGCGG Y 2 1 2 1 101000 f 74 goat snp55253-scaffold851-198127 8 671266 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436605 Affx-122932514 AX-123306943 8 722681 AGAGGGGAGTGGGTGACCTGTGTGCATGGCCCTCT[A/C]GACAGCTGAGTGGACACAGGTGGGCAGGGGAATGT M 2 1 2 1 201000 f 74 goat snp55254-scaffold851-265627 8 738879 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401538 Affx-122958912 AX-123271891 8 757086 TCTTATTAAGTGAATCTGAAAAGGGTATTTTATTT[A/G]TTAGAGTCCTGAAAAGTGTCATTGTTAGAAGGAAA R 2 1 2 1 201000 f 74 goat snp55255-scaffold851-300032 8 773403 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278733 Affx-1111836485 AX-519552210 8 828072 GTGCTGCCCTGGTGTGACGCCTGGACCCTGAGGAG[A/G]TCCGTTTCCGGGTGTAAGCCCTGTGTCACTGTCTC R 2 1 2 1 102000 r 74 goat Random2.2K-854 8 828072 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786795 Affx-122955500 AX-385273825 8 840909 ATTTTTGTAAAAAAGCTATGTAGCTATAAATGTCA[A/G]TAGTTACACCAACAGTATTTGCTCTCACAGTCACA R 2 1 2 1 101000 r 74 goat snp55257-scaffold851-383855 8 856979 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412781 Affx-122950500 AX-123283130 8 880671 CAAATTTGTGAGGAAACTTTGAGTCCCTCTCTGGG[C/T]GACATGCTACATCATTCTCACTTCTGCTCTGCTCT Y 2 1 2 1 101000 f 74 goat snp55258-scaffold851-423617 8 898087 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383922 Affx-122972975 AX-123254280 8 933114 CGACTGGTGTCTCTCCATACTTGCCAAATGTTCCC[A/G]AATGTGACATTTTGCTGACTTGCTGGGTCTGGGAT R 2 1 2 1 101000 f 74 goat snp55259-scaffold851-476060 8 953786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408394 Affx-122954486 AX-123278745 8 963534 GATTGTGCAGCTTGACAGACCAAATTTTAAAATAC[A/G]TAACTTTTCTTCCAATTAGAATTAAAACAAGTTAA R 2 1 2 1 103000 f 74 goat snp55260-scaffold851-506480 8 984256 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444007 Affx-122926901 AX-123314344 8 1000217 GGCTCAAGGAGGCTGCTGTATATACCCAGCGACCT[A/G]CTAGAACTGAACGTTTGTGCTTTTCCATTGAACAA R 2 1 2 1 101000 r 74 goat snp55261-scaffold851-543163 8 1021609 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449359 Affx-122922733 AX-123319694 8 1043044 TTTCTGAACACGGAGAATACCAATGGGTTTCTGTC[A/G]TCTGGGAAAAAAATCTGACACTTCATTAGCAGTTA R 2 1 2 1 101000 f 74 goat snp55262-scaffold851-585990 8 1065541 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409637 Affx-122953531 AX-123279988 8 1086666 TCCTCCCTGATGTGGCTGGTACCCATCTTCTCCCC[A/G]CTCCACACCTGGTGTCCCAGGTCCAAAATTCTCTG R 2 1 2 1 101000 r 74 goat snp55263-scaffold851-629612 8 1109122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771346 Affx-122922145 AX-385258504 8 1119826 AATGCCAACAATGCAAGAAAAATTACAAAATCCAG[C/T]TTCAGATACTTCTTTCTAAATGTAGCTAATCTCTC Y 2 1 2 1 101000 f 74 goat snp55264-scaffold851-662772 8 1142380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376116 Affx-122978878 AX-123246475 8 1190183 GTGATTGTCCTCCTTTTACTGAAATCAGATTGCTC[A/G]CTGATTTTCTGTCCTTCGGTCCTCTCAACCTACAC R 2 1 2 1 201000 r 74 goat snp55265-scaffold851-733129 8 1211992 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376054 Affx-122978929 AX-123246413 8 1237632 ACAAAAAGGGGTGATTTGTTTTCATGAGAGCACTT[C/T]TGACTCCACGGGACTTTGCAGAGATAACAACACGT Y 2 1 2 1 101000 f 74 goat snp55266-scaffold851-780578 8 1260893 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383469 Affx-122973446 AX-123253827 8 1276495 GACATTACATTTGGTACTATTTAGAAGAAATTTTA[C/T]GTATGTGTCTAAAAATTTAATTCCACCTCCTTGAT Y 2 1 2 1 101000 r 74 goat snp55267-scaffold851-819441 8 1297423 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376769 Affx-122977965 AX-123247128 8 1310770 AATCAAGGCAGTGTAATAATAATGAAAACAGATAA[C/T]GGAACAGACCAGAGAGCCCAGAAACAGACCCACAC Y 2 1 2 1 201000 f 74 goat snp55268-scaffold851-853716 8 1331703 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452162 Affx-122921652 AX-123322495 8 1349120 TCCATTTTAAATATATTCTGATTTACTTAAAGCAC[A/G]CAGATAAAGTTATTACAACCATACGCTGGTTCAAA R 2 1 2 1 101000 r 74 goat snp55269-scaffold851-892066 8 1370271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785324 Affx-122948672 AX-385272369 8 1394152 AAAAGAAGATTCAATATCAGAAAGATTTTAATTCT[C/T]AACCTTTAAATTTAATGCTTCTCTAATATAAACAT Y 2 1 2 1 201000 f 74 goat snp55270-scaffold851-937098 8 1415576 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434668 Affx-122933973 AX-123305009 8 1476853 AATCACCTAGGTACCTGAGAGATTGATTAGTAGGT[A/C]GTTCCTGCTGGCTTATGTGGCAGCCCTGGGATTTG M 2 1 2 1 201000 f 74 goat snp55272-scaffold851-1019799 8 1497041 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415852 Affx-122948863 AX-123286201 8 1519496 GTTCCAGGTGTGAGCTTAGCCAAGTCTGAGTCGGG[C/T]AATGGTTTTGTTAAATTGGATGAAGCTGCTTTTAT Y 2 1 2 1 201000 r 74 goat snp55273-scaffold851-1062442 8 1539899 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777343 Affx-122932240 AX-385264465 8 1559592 CAGAGTGTTGTGTTTGACAGGGTTGGGGCTTTTTG[C/T]ACCAGATGTTAAACTCCTAAGGGTGGGAACGTCTC Y 2 1 2 1 202000 f 74 goat snp55274-scaffold851-1102538 8 1580042 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390999 Affx-122966899 AX-123261356 8 1612107 GCAGGAGCTCCTCACACACTTGCTAAGTAAGAGAA[C/T]GCATCCTCCACGCCTGCAGCTGACTCTCATGGAGC Y 2 1 2 1 101000 f 74 goat snp55275-scaffold851-1155053 8 1633668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770333 Affx-122969118 AX-385257499 8 1647972 CTGTCACAAAGACTGAATTTATAAGGGGGAACAGA[C/T]AATAAATAAGATTAAATAAGAATATCAGAATATTA Y 2 1 2 1 303000 r 74 goat snp55276-scaffold851-1190918 8 1670055 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779335 Affx-122955205 AX-385266439 8 1701978 AGCAACAGGAACTCAGACACCAAGAAACAAATCTG[C/T]ACACTTATTTCTATTGGAAAATATGATGCTAAAGC Y 2 1 2 1 101000 f 74 goat snp55277-scaffold851-1244924 8 1723796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400509 Affx-122961274 AX-123270864 8 1735026 ACGTCCCTTTGCACGCTGGGAAAACGTTCCACAAA[C/T]GGACTTTGTTCAGCTTGTCAGACTTTGCACATGGC Y 2 1 2 1 101000 f 74 goat snp55278-scaffold851-1277972 8 1756534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384393 Affx-122972212 AX-123254751 8 1775615 GTCACTCAGATTTTGAAGAGTGGATGTGTGCGGCC[A/G]GGCTGTGGAGTGGACGGTAATGAGTGTCTGGCTGG R 2 1 2 1 202000 r 74 goat snp55279-scaffold851-1318561 8 1794326 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430965 Affx-122936818 AX-123301306 8 1811175 GGAAGACTTTTTAAGTTTAAAAGCAATTGAAGAAA[G/T]CACAAGAGAAAAATCAATTTATAGAAAAATTCTGC K 2 1 2 1 102000 f 74 goat snp55280-scaffold851-1354121 8 1829591 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442622 Affx-122928467 AX-123312959 8 1861714 GAGAGCAGGGAGCTATGGCCCTGGAGTCAGAAAAT[A/G]CTTGGCATGTTTTAGGGACAGAAGTTTCTAGAAGG R 2 1 2 1 101000 r 74 goat snp55281-scaffold851-1404660 8 1880672 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775111 Affx-122931776 AX-385262243 8 1906902 CTCGGCCCTGTAATGTAGTAACAGTAATTGCTGCT[A/C]TTTTTCCAGTGCTCGTACTGTGCCAGGCATTGTGC M 2 1 2 1 101000 f 74 goat snp55282-scaffold851-1449848 8 1927576 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398528 Affx-122961536 AX-123268883 8 1937320 GTGCTGGCTCTCTCCCTGCTCTTCATGTGATAAGC[A/C]GCTTGGCACAGCTCTCTCCCTGGCTGCTTTGCTGG M 2 1 2 1 101000 f 74 goat snp55283-scaffold851-1480266 8 1957904 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390244 Affx-122967764 AX-123260601 8 1973902 CATTTCTTTTCCATTTCCTCTGAATTCTCACTTGC[A/G]TTCCACAGTCTGCTCTCCCCACATGCTACCCCATT R 2 1 2 1 101000 f 74 goat snp55284-scaffold851-1516848 8 1994886 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387056 Affx-122969902 AX-123257414 8 2038519 AGAATTTTAAAGAAAATTAATTCAATAAAATAAAA[G/T]CTCAAAGGCAAAACAATAAGACAGAAAAAGGAATG K 2 1 2 1 303000 f 74 goat snp32987-scaffold384-519164 8 2068686 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429738 Affx-122937598 AX-123300079 8 2067233 CTGTCCTCAGATGATCAAACTCATCCTTACCTGTA[C/T]GACCTCTCCATTTCTGATTTCAGCAGCCAACAAAA Y 2 1 2 1 101000 f 74 goat snp32986-scaffold384-490450 8 2097398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434835 Affx-122934790 AX-123305176 8 2100688 GGTCAGTAAATGATCCAGAAACCTTACAGGACCAT[A/G]CTAAACAGCGCCAGCAGAGAAGAGTTTAATGAAGA R 2 1 2 1 101000 f 74 goat snp32985-scaffold384-456995 8 2131040 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424632 Affx-122942177 AX-123294978 8 2129884 GAACAGTTATGTCAACATTTTCTTCTTTAATAATC[G/T]CTCTAGTTCTAATAACCTCATTTACAGGATGTGTT K 2 1 2 1 101000 r 74 goat snp32984-scaffold384-427799 8 2160784 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424434 Affx-122941796 AX-123294780 8 2174087 GAAAGTTGATCGGTTGGAAACAGCCAGTGATATAG[A/C]TGGGAGATGGGGTGGAGTGTGGGGATGGGAGACGG M 2 1 2 1 101000 f 74 goat snp32983-scaffold384-383596 8 2203819 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441499 Affx-122928731 AX-123311836 8 2294122 TGATGAGCTTGATTTTGCCCCTAAATGGAACAGTT[A/G]CTCTGAAGCTTGAAAACAAAAGCAACAAACTCTGA R 2 1 2 1 101000 f 74 goat snp32981-scaffold384-263561 8 2326694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398771 Affx-122961435 AX-123269126 8 2344080 TGCCAGAGTAGTGTTGTTAGATGTGACTGAACTTT[C/T]CAAGGAAGCAGAGGGATACTGAGGGGTTTAGAAAG Y 2 1 2 1 201000 f 74 goat snp32980-scaffold384-213603 8 2377491 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786247 Affx-122931289 AX-385273282 8 2381423 ATAAGCGTTTTTTCAACCTTTGCAAGATAACCTTG[C/T]ATTTAAGATCAATAAGCAAATCTACAATTTCCTTT Y 2 1 2 1 201000 r 74 goat snp32979-scaffold384-176260 8 2413313 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799674 Affx-122941443 AX-385286602 8 2413526 AACTTCTCACATCTTTGTTACAGGAGGGAACTTTG[C/T]AACTTGGAGCAAAGTCTCCACTGAAATTAGGCTTT Y 2 1 2 1 101000 r 74 goat snp32978-scaffold384-144157 8 2445652 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788481 Affx-122957287 AX-385275498 8 2443069 TTTCTGCTGCTCTTATTAGACACATATATTTCTAG[A/C]GAGAGCCAAAATAAGCATATACCCAAGCTTAGCAG M 2 1 2 1 101000 r 74 goat snp32977-scaffold384-114614 8 2475585 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785397 Affx-122928719 AX-385272442 8 2476816 CAGTGTAGCTGGCTTCCCTTTGTTTCATAAGGTAT[A/G]CGCCATGGGAGTCAAGGTATTTGGAATTCCACTCA R 2 1 2 1 101000 f 74 goat snp32976-scaffold384-80867 8 2509169 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421271 Affx-122944745 AX-123291618 8 2544326 TAGAAGGCAGCAGGTATTACTCTAGATGCTGGAAA[C/T]ACAACCATGAACCAAAGAGAAAAAAGCTTGGCACC Y 2 1 2 1 101000 f 74 goat snp32975-scaffold384-13357 8 2576589 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768516 Affx-122957461 AX-385255696 8 2581668 TTCTTTCCATAGCATGCGGTGTACATTTCTCCACT[A/G]TCTAATGAAATGGGACCCATTTTCCAGGGCATGTG R 2 1 2 1 202000 r 74 goat snp10154-scaffold1363-23886 8 2619614 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444581 Affx-122926963 AX-123314918 8 2633605 AACTCTCTTGAGTTCCTCCAGCACATACTGATTCA[C/T]ACTGTACATTGTTAACTTTTTAAAAAATTAACAAT Y 2 1 2 1 101000 f 74 goat snp10155-scaffold1363-75823 8 2672068 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395205 Affx-122964498 AX-123265560 8 2679890 GGGGCTTCAATATTTGCATTCTGGGGGATATAATT[A/C]AGTCCATAGCATCAGCCAACACTACTGCGAGTGTA M 2 1 2 1 101000 f 74 goat snp10156-scaffold1363-122108 8 2718704 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425270 Affx-122940975 AX-123295616 8 2729006 GCACTTGAGGGACAGTATTCTCAGACTTCTCTGTC[A/G]TTTTTGTTTTTGCTTTTTTTTATATGGACCATTTT R 2 1 2 1 101000 f 74 goat snp10157-scaffold1363-171224 8 2768166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274974 Affx-1111834521 AX-519548556 8 2734006 GCTGGACTG[A/C]CAGAGATGAGACTGTGATAGAGATGTGAAGAGGGG M 2 1 2 1 101000 r 74 goat GoatD01.039490 8 2734006 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437710 Affx-122931750 AX-123308048 8 2765604 GTGTTAGTTGCTTTTATGAATACCATTCTAGATGA[C/T]GATTTGTGTGCTGTGTGCTCAGTCGTGTCTAACTC Y 2 1 2 1 201000 f 74 goat snp10158-scaffold1363-207822 8 2805153 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424464 Affx-122941772 AX-123294810 8 2839070 AGCTTTGACTATATGGACCTTTGTCAGCAAAATGA[C/T]GTGCATAGCACAAAAGAGCAGTACTGTCCTCTCCT Y 2 1 2 1 201000 r 74 goat snp33361-scaffold391-4071722 8 2881728 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420849 Affx-122944648 AX-123291196 8 2886334 ATACCAGTGAATTTGAGCTTTATAGTGTCTGAGTT[A/G]TAGTTGTGTTCCTTTCTTTAGGTTTAAATAAAGCA R 2 1 2 1 101000 f 74 goat snp33360-scaffold391-4024458 8 2929249 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273385 Affx-1111833573 AX-519547017 8 2920675 ATGAAGCCATTGGAAGGAGAAGAAAACTATGTAAA[A/C]TTTAACTATGTATGCTACAGAAGAAATGTTGTATA M 2 1 2 1 201000 r 74 goat 8_2920675_AF-PAKI 8 2920675 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38382968 Affx-122973357 AX-123253326 8 2935579 CATTTGAGTCAATAACATTCTCTTTTGCTTTTATC[A/G]TTCTGGTATAATTGAAGGCGGAATTCCACTAATGT R 2 1 2 1 101000 r 74 goat snp33359-scaffold391-3975213 8 2978942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376188 Affx-122978824 AX-123246547 8 2971193 GTATATACAGCATGGAAGCTGTGTATGTATGTAGG[C/T]AACTAACCATGTATCACTCTGTCAGGAGGCTCTCC Y 2 1 2 1 101000 r 74 goat snp33358-scaffold391-3939599 8 3015711 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395796 Affx-122963654 AX-123266151 8 3042144 CCTGGTTTGTGAATATAACTACGTTGTAAAACAAG[C/T]GTTAACAATTGACAGCTTTTCAGTTGTTATAGTGT Y 2 1 2 1 101000 f 74 goat snp33356-scaffold391-3868648 8 3086583 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786878 Affx-122949582 AX-385273907 8 3071875 GTTTTGAACTTTCTTCAAAATGCAGAACATGCACA[C/T]ACAATATGTCAAAGACAGTGTTAGAAAAATCCAAG Y 2 1 2 1 101000 f 74 goat snp33355-scaffold391-3838917 8 3116893 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783713 Affx-122954164 AX-385270770 8 3113571 ATCTCTTTATATTCTAAAATTAACTTCAGAAGCTG[A/C]GTCTCCATTATCACTATGACTTTATGATTATTTTC M 2 1 2 1 101000 f 74 goat snp33354-scaffold391-3797221 8 3158455 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802511 Affx-122956963 AX-385289415 8 3142505 AGATTAACATACTTTCTGTTTTAAAGTTTAGAAAG[G/T]CAAAATAAGCTACATGTAGTAACAGTGGAAAGAAA K 2 1 2 1 201000 f 74 goat snp33353-scaffold391-3768287 8 3187412 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436993 Affx-122933142 AX-123307331 8 3178169 GCTCTGTGTGCAGCACTCTGAGAATCACACCTGGG[C/T]GTTAAGTTTTGCCTTTAAAGGTGGAATACTAGAGA Y 2 1 2 1 101000 r 74 goat snp33352-scaffold391-3732623 8 3223536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394443 Affx-122964592 AX-123264798 8 3257356 GAGAGATTTTTTCCTGGTTTTAAGCTTTCTTTCTG[C/T]GTCTGTTTCTGCCTTTCTTTTTCCCTTTCAATCAA Y 2 1 2 1 103000 f 74 goat snp33350-scaffold391-3653436 8 3303546 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783687 Affx-122952318 AX-385270745 8 3287103 TACACAATGTTAAATCAATGTGTACTCAGTGGTCA[A/G]GATTTGATAAAATGAGTAGGTATTACTGTTTCATC R 2 1 2 1 101000 f 74 goat snp33349-scaffold391-3623689 8 3333561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385572 Affx-122971843 AX-123255930 8 3347328 GATTTGGGTTCTAACTCAGGGTCCCTCTCTCCTAG[G/T]GCAGCACATCTATTTTACATACCCCTGTGATTACC K 2 1 2 1 201000 r 74 goat snp33348-scaffold391-3563464 8 3394007 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446358 Affx-122925602 AX-123316694 8 3397509 AAATTTAACCATGGCAACAATAAACATCTCACCAT[A/G]CTATGTTTTAAATATCAAAAACAGTCAAGTATTTG R 2 1 2 1 103000 f 74 goat snp33347-scaffold391-3513283 8 3447760 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278735 Affx-1111836486 AX-519552212 8 3448812 TCTTGGTGAAGGATGTGTTGATATCCTTGACTTCA[A/G]TTGAAGTCATTGATTCTTTCTCTGTGCAGTGGGGC R 2 1 2 1 101000 r 74 goat Random2.2K-856 8 3448812 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408449 Affx-122954444 AX-123278800 8 3449472 ATTTATGTACTTAACTAAAACTTTCATAATGTGTT[A/G]TTAGCAAACAGAAATGTTACACTAAAGCTGCAGGC R 2 1 2 1 101000 r 74 goat snp33346-scaffold391-3461320 8 3499965 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788063 Affx-122927962 AX-385275083 8 3485510 AGATTCAAAGACCATTGGATTATATTATTTTGGAA[C/T]ATGAGGGATGCAGTGAGATTTTTAGAACTAGTTAT Y 2 1 2 1 101000 r 74 goat snp33345-scaffold391-3425282 8 3536099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406960 Affx-122955058 AX-123277311 8 3527610 ATGATTCCATGTGCTTTGTTAAAATCAAGAAAATT[A/G]TACAACACAAATGTTTTAATGTACAATAAAAAACA R 2 1 2 1 101000 f 74 goat snp33344-scaffold391-3383182 8 3578753 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450056 Affx-122922817 AX-123320391 8 3566463 TCAATCGCTTACTCATTTGCAATGTATTGCTGGCT[A/C]TCTGGGGCATTAATTGTACTATTTTTGACTCTTTA M 2 1 2 1 101000 f 74 goat snp33343-scaffold391-3344329 8 3616900 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438225 Affx-122931442 AX-123308563 8 3617364 GGTCTTCTGCAAAGCAGGCAGAATCTTTGCCATCT[A/G]AACCACCAGGTAAGCCCCATTGTATTCAAAGTCTG R 2 1 2 1 303000 f 74 goat snp33342-scaffold391-3293428 8 3668320 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770571 Affx-122922167 AX-385257735 8 3665139 TATTAAAGGAAATAGGTTGGCTGTTTAGCTAAGCC[A/G]CCAGAGATTCCTAATGCATAGGGTCTTCCCTGAGG R 2 1 2 1 101000 r 74 goat snp33341-scaffold391-3245653 8 3709756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381746 Affx-122974321 AX-123252104 8 3699796 TATAGAAAACTATTTGAGCAAACTCTAGGAGATGA[C/T]GAAGGACAGTGAAGCCTGGCATTCTGCAGTCCATC Y 2 1 2 1 303000 f 74 goat snp33340-scaffold391-3210996 8 3744760 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794180 Affx-122927193 AX-385281146 8 3731776 GCAAGGGTCCTGCACTTCCAACTTTCTATCTGGGA[C/T]GCTTTATCTGGACTTTTGACGCATTATCCTGTCTC Y 2 1 2 1 101000 f 74 goat snp33339-scaffold391-3179016 8 3777748 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401032 Affx-122959668 AX-123271385 8 3760916 CCCAGGGATAGAACCCAGGTCTCCTGCATTGCAGG[C/T]AGATTCTTTGCCATCTTACCCACACCACTGGGATT Y 2 1 2 1 303000 f 74 goat snp33338-scaffold391-3149876 8 3806287 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780278 Affx-122921302 AX-385267373 8 3791393 CTTTTGACTATGAAACTAAGTTTTGAAGGTGCAGC[G/T]CCTTCTTGTTCACCCACTTGCAAGCCTTAAAAGCA K 2 1 2 1 101000 f 74 goat snp33337-scaffold391-3119399 8 3828600 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423730 Affx-122942868 AX-123294076 8 3836881 CTGGAACACAATTTAATGACACAAAAACAACAACC[A/G]TCCATAGACACATTTTATGTAACATTCAACCTATG R 2 1 2 1 101000 f 74 goat snp33336-scaffold391-3073911 8 3874337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278561 Affx-1111836487 AX-519552041 8 3856520 TTTTCTATATTCCTCTAACTCTACTGACGGAAACA[A/G]TAACTCTATAAAGTATTTCTGTAGTTAACTGAAAT R 2 1 2 1 101000 f 74 goat Random2.2K-858 8 3856520 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320774530 Affx-122943718 AX-385261664 8 3875080 AGACGAAACAGTGGGGAATTATTTTGTGAGCAGAA[C/T]AGAAAATGTGATTGGAAGGATGTGGTGAGTGAGTG Y 2 1 2 1 101000 f 74 goat snp33335-scaffold391-3035712 8 3913726 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382438 Affx-122974233 AX-123252796 8 3905416 CTATTTTTACTTTGTGGTAAAATATCCTGCTGGTG[A/G]TTTGTGACAGTGTTTGCAGGATGATGAATTTGTCC R 2 1 2 1 101000 r 74 goat snp33334-scaffold391-3005376 8 3944176 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431618 Affx-122936153 AX-123301959 8 3949732 TTATTTAAAGTCATCCAGACAAAAGTATCTTTATC[A/G]TACTGAAGTACCCTCTGTGAACTAGTTCTAGGTTG R 2 1 2 1 101000 r 74 goat snp33333-scaffold391-2961060 8 3989369 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782788 Affx-122941685 AX-385269860 8 3986852 GTGAAGTTCTAAAAATCCTGTTGGTATGGGACATT[A/G]CATTTTTCCATTTTAGAATATGGAAAAGTAGTCAC R 2 1 2 1 201000 r 74 goat snp33332-scaffold391-2923940 8 4026022 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433277 Affx-122935218 AX-123303618 8 4018949 CATAGCAACAGCAATGGTTCAATATTATTCGCTCA[C/T]ACACACACCTAGAGCCTTGTGCTTAATTATAATTT Y 2 1 2 1 101000 f 74 goat snp33331-scaffold391-2891843 8 4058100 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408639 Affx-122953480 AX-123278990 8 4069897 CAGTTTTTACAGCAGAACATTAGGGAAGAGGAAGA[C/T]GAGGATGCAGTTGTTATATCTTCATGGGAGCTTGC Y 2 1 2 1 101000 f 74 goat snp33330-scaffold391-2840895 8 4108791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439274 Affx-122930983 AX-123309611 8 4110878 AAACACCACATTCTTTACCCTCATTAAACAGGCTG[C/T]ACTCATTCTATCAGATCTGTTGTTTTTAATGCAAT Y 2 1 2 1 101000 r 74 goat snp33329-scaffold391-2799914 8 4151532 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779439 Affx-122933478 AX-385266542 8 4149313 TTATAAATTAATGTCTTTTTTAGACACTTGGCACA[C/T]ACTCCACTTGTGCGTGGACTGCAGAATAGGGCGAT Y 2 1 2 1 101000 r 74 goat snp33328-scaffold391-2761479 8 4189568 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405944 Affx-122955556 AX-123276296 8 4183704 CACACAAAGATTGAGGAAACACCTTCCAGGGAGCA[C/T]TGAAGATTGGAAGTGGTGGTCTGAAGCATGTCTGG Y 2 1 2 1 101000 f 74 goat snp33327-scaffold391-2727088 8 4327903 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435782 Affx-122932864 AX-123306121 8 4213023 GTTTCACTAATAAGTCCTTACTGCAAGATGCTACA[C/T]ATAACCACCTTCTCTTTCACTCTTCTGTTGAAATC Y 2 1 2 1 101000 f 74 goat snp33326-scaffold391-2697769 8 4355398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447065 Affx-122924510 AX-123317401 8 4253812 AGGAAGATTCATGCTATATCAATCATTCATTAGGC[G/T]ATTACAACCTGATATTATCATAACACCGTTAATCA K 2 1 2 1 101000 r 74 goat snp33325-scaffold391-2656980 8 4397066 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385630 Affx-122971178 AX-123255988 8 4295892 CTAAAACTCAAATGACCTCTTGTTCATTTCCTATT[A/G]TAAATGCAATTCTTTTTTTCCTCTCTGAAATTTGA R 2 1 2 1 101000 f 74 goat snp33324-scaffold391-2614900 8 4439248 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439880 Affx-122930042 AX-123310217 8 4354190 TATCTAAACCTTTGATCTGACATGAAAATGTAGGA[C/T]AGTAAGACTTCTGACTAGGAAATGCAATTTGTTTT Y 2 1 2 1 101000 f 74 goat snp33323-scaffold391-2556602 8 4498186 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453340 Affx-122919960 AX-123323673 8 4394899 TCTTCAACACACTGTATTATTGTTCAGAAATAGCT[G/T]ATGGCCCTAACATCAGTAAGATTAGATTTCTTGTC K 2 1 2 1 101000 f 74 goat snp33322-scaffold391-2515893 8 4539360 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447259 Affx-122924948 AX-123317595 8 4433793 CAGTTATTCAAAACTGAATAACACTTTGACAGAAA[C/T]AGAGTCACAGAGAGGGGGTAGGAAACAAACACATG Y 2 1 2 1 201000 f 74 goat snp33321-scaffold391-2476999 8 4579573 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393083 Affx-122965601 AX-123263440 8 4483563 AGCCACGATTCACACCTACAACCATGCCCAAAGCA[C/T]GTACTTAACCACCCCTCTCATGACAGAGAAGGGAA Y 2 1 2 1 201000 r 74 goat snp33320-scaffold391-2427229 8 4629583 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379708 Affx-122975894 AX-123250066 8 4532101 GCTTGAAGAATTTTTCTATCTTCATGATTTTTTTT[A/C]TCATTTACTTCAACTTACTTCACTGTCATGACTTT M 2 1 2 1 201000 r 74 goat snp33319-scaffold391-2378691 8 4678113 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396245 Affx-122963330 AX-123266600 8 4563201 ATGGATCTGTTTTGTCCACTAGAACGGACTGGAGC[A/G]ACAAAAGCATTCAAGTTCCGAGACCAGATAAAATG R 2 1 2 1 101000 f 74 goat snp33318-scaffold391-2347591 8 4709523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427946 Affx-122939207 AX-123298289 8 4598401 GGTGACCAAGAACCCCTCCTAATTGCTCCTCCTTT[A/G]TGTATGCATATAAGTTTTTAAGTTGATTGCTGGTG R 2 1 2 1 201000 r 74 goat snp33317-scaffold391-2312391 8 4745355 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783420 Affx-122937196 AX-385270483 8 4644512 GAGGATACATCAGCTATTTTGAATACAAAATCAGT[C/T]TAGCAGACAGAAAAAGTGATGAGGGCTTGTCTACC Y 2 1 2 1 101000 r 74 goat snp33316-scaffold391-2266280 8 4791126 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379105 Affx-122976757 AX-123249464 8 4679321 TTCAGATGTACAGTCAGCAAGACTTGCTGATAAAG[C/T]AGTTTTAAGCAGAGCTCTGGAACTGTCTTCCCTGC Y 2 1 2 1 101000 f 74 goat snp33315-scaffold391-2231471 8 4826089 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443354 Affx-122927422 AX-123313691 8 4719730 ACACTGAAGTAGAGAGGCTGATCTTTCCCTTCCAC[A/G]TGTGCTCAGTTGCTAAGTTGTGTCTGACTCTGTGT R 2 1 2 1 101000 f 74 goat snp33314-scaffold391-2191062 8 4866822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435137 Affx-122933680 AX-123305477 8 4762923 CAATATTACCTTTTAGAAGCATCACATGGAGGGGA[C/T]GTGGAGACTAGATGCCAGGAAGGCTATACTGTGGA Y 2 1 2 1 101000 f 74 goat snp33313-scaffold391-2147869 8 4910497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788173 Affx-122926141 AX-385275192 8 4802436 AATTTCTTAACACTGGCAAATTGTCCAAAAGAAAA[C/T]GATTTGCTTTAACAGGGATTATTGCTGGTTTGGGC Y 2 1 2 1 101000 r 74 goat snp33312-scaffold391-2108356 8 4950462 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408224 Affx-122953840 AX-123278575 8 4847470 ATAGTCTCTGGGTCTTGCTCACAACGTCGTGTTTG[C/T]GATAGTCTAGTTAGCGTGCTTTCTGACTTGGAGCA Y 2 1 2 1 101000 r 74 goat snp33311-scaffold391-2063322 8 4995450 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447819 Affx-122923916 AX-123318155 8 4897767 AACCAGATCAGCATCTCATGGTAGAGAAAAATGAC[A/G]TATTCACAAAAGCAGAATCTAGAAACATAAAGGCA R 2 1 2 1 101000 f 74 goat snp33310-scaffold391-2013025 8 5045719 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431757 Affx-122936727 AX-123302098 8 4945381 TTCCTTGTGGTGCTATGAATATTTAAGTGGCAAAC[G/T]CGTTCTAGCATGTTGCCTCTTATTGGCATAAATCT K 2 1 2 1 101000 r 74 goat snp33309-scaffold391-1965411 8 5091926 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278739 Affx-1111836488 AX-519552215 8 4964844 AGTACAATATACCATAAGTCAGTAATTCCATTTTT[A/G]CCTAACAACCCCTCTACTGCTACCATAAGGCTGGG R 2 1 2 1 101000 r 74 goat Random2.2K-859 8 4964844 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386765 Affx-122970121 AX-123257123 8 4990300 CCTGAACAGAGTAAGACATCTACCTTGTGCTTTTG[C/T]AGAACTTGTGGCCCAGAAAAGATGCTGACCCTTGA Y 2 1 2 1 101000 f 74 goat snp33308-scaffold391-1920492 8 5137211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380297 Affx-122975401 AX-123250655 8 5026289 TACAGTCCAGGGGGTTGCAAAGAATTGCACAAGAC[C/T]GAGTGACTTTCACTTCACTAATGAAGTGCTATTGG Y 2 1 2 1 303000 f 74 goat snp33307-scaffold391-1884503 8 5174553 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389532 Affx-122968282 AX-123259890 8 5113748 ATATCTAGATAATAGAATTTTCATAAAGTGCAACT[C/T]TAAAGATACTTTTCAAGGACATGGAGATTGTCCCA Y 2 1 2 1 101000 r 74 goat snp33305-scaffold391-1797044 8 5261913 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783413 Affx-122924047 AX-385270476 8 5149102 TGTGTATACTCTCTGTAGATGGAAAGATTACAGGA[C/T]AGGAAGAGGGATTTATTTCTCCCCTAGGAAAGTGA Y 2 1 2 1 101000 r 74 goat snp33304-scaffold391-1761690 8 5296902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434173 Affx-122934885 AX-123304514 8 5238043 CCCTGGACATAGAGCAGAACCGAACAACAAAACTA[C/T]GCAGAACAAAATAAAAGAGGTCTTAGAGACAGCCT Y 2 1 2 1 201000 f 74 goat snp33302-scaffold391-1672749 8 5386309 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404908 Affx-122956452 AX-123275260 8 5267629 GCTATACAGAAATCAAAGAAAAAGTTCCTGCCCTC[A/G]TGTGGTTAACTTCTGTAAGGGGAGACTAGCTGTGA R 2 1 2 1 201000 r 74 goat snp33301-scaffold391-1643163 8 5415927 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397690 Affx-122962577 AX-123268045 8 5332718 TCATTAGCACACAGAGTATCATGTGCATAGTCACT[A/G]TGTATCATATAATATCTTTATTTTATGGTTTATTT R 2 1 2 1 201000 r 74 goat snp33299-scaffold391-1578074 8 5480572 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771729 Affx-122949568 AX-385258886 8 5402085 TCAAGGGACTGAACCAGAATTAAACTGTAGACCTC[A/G]TTTCATAAAACTAGCACTACTGAAACTCTGAGCAC R 2 1 2 1 101000 f 74 goat snp33298-scaffold391-1508707 8 5548496 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273367 Affx-1111833583 AX-519547000 8 5424450 TCCTAAAGGAGATCAGTTCTGAATATTCATTGGAA[A/G]GACTGAGGCTGAAACTGAAGCTCCAATACTTTGGC R 2 1 2 1 103000 f 74 goat 8_5424450_AF-PAKI 8 5424450 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392439 Affx-122966178 AX-123262796 8 5450496 TCGTGAGTGTGATCTCGCGTTCAGGTCAGTATTTA[C/T]ATGAATCATTAAAAGGTGAAAGAACCGTTCTTCTG Y 2 1 2 1 101000 f 74 goat snp33297-scaffold391-1460296 8 5597495 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438488 Affx-122931602 AX-123308826 8 5507035 CTTTGCTGCTTTTTACTTCTTTGGAAGAAGTTATT[A/G]TGAAAATCTGTTTCTGTACATTTACTTGATCTTCT R 2 1 2 1 303000 r 74 goat snp33296-scaffold391-1403757 8 5653614 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385309 Affx-122971677 AX-123255667 8 5538193 ACCGCATTGCAGGGACTGGACAGGGACCATCGCGG[C/T]GACAGCGAGCGGGCCTTAAGGCCAGGGTCGCAGGG Y 2 1 2 1 201000 r 74 goat snp33295-scaffold391-1372599 8 5684829 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385753 Affx-122971074 AX-123256111 8 5574622 AAATACTTAACATTTTTAAGATGGCAATTATTAAG[C/T]GATCTACAGAGACAGTACAATCTTCATCAAAAGTC Y 2 1 2 1 101000 r 74 goat snp33294-scaffold391-1336170 8 5720539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407824 Affx-122954543 AX-123278175 8 5623858 TGGCCACTGTACTGACTCCTGAGGGGATGTAGGAG[A/C]GATTCAGGAGATGTCTGAGATACATGGGAATGGGT M 2 1 2 1 101000 r 74 goat snp33293-scaffold391-1286934 8 5769531 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769417 Affx-122953264 AX-385256588 8 5671785 CTTCAGAACAGTGTTTTTCATACTGCAGGTTGCTA[G/T]CCATTAGTAACTCGTGAAATTAGTAATGTGCAATT K 2 1 2 1 101000 f 74 goat snp33292-scaffold391-1239007 8 5817591 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423398 Affx-122943120 AX-123293744 8 5739041 AATGCTGTCATGCAACCCCAGGTTCAGACTTTAGT[A/G]AAGCAAGTAAGGATTTGGTTTCCTGGCTATGTCTA R 2 1 2 1 101000 r 74 goat snp33291-scaffold391-1171751 8 5884725 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278565 Affx-1111836489 AX-519552045 8 5768473 GTTTTCCTTCATTATCTTTATGACAATTCTCCTAC[A/C]TTTCCACTTTTTTATTTCTTAAGATGCATCCTTTA M 2 1 2 1 101000 f 74 goat Random2.2K-860 8 5768473 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776413 Affx-122947740 AX-385263540 8 5772903 TTATCTAACAATACACCATATGCATTGTTGCAGAA[C/T]GAACCCACGCTGCTCAATTGAGTGAGAAGAAGCAT Y 2 1 2 1 101000 r 74 goat snp33290-scaffold391-1137889 8 5918066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402771 Affx-122958311 AX-123273124 8 5816975 CCATTGATCTACTCCATTTCTATATCTAAATACCA[C/T]GAAGACAATCCCAGGGCCATGATATCTGGCATCAG Y 2 1 2 1 201000 f 74 goat snp33289-scaffold391-1093817 8 5962547 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391852 Affx-122966993 AX-123262209 8 5893110 ACATGTGCCTTCAGTAACTTTCCGAATCCCACCTC[A/G]CAGGTACCTCTGTGGCTTGGTAAACTGCTTCTATG R 2 1 2 1 201000 r 74 goat snp33287-scaffold391-1017682 8 6038631 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768361 Affx-122946827 AX-385255541 8 5927802 AACTCAGCACCTGTTAGATTTTGTTTCTCCACTCT[A/G]CCTGAATGGCATTATCCATACTTTTATTGGATGAT R 2 1 2 1 101000 f 74 goat snp33286-scaffold391-982990 8 6073679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413210 Affx-122950261 AX-123283559 8 5997682 GGGCAGGGTAGGATGAACTCAAGAGTCTGAACTGA[A/G]CTTATTAAGAGAAAAAAAAAATCAGAATGTGGTGA R 2 1 2 1 103000 f 74 goat snp33285-scaffold391-913110 8 6144247 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790463 Affx-122946679 AX-385277466 8 6045665 AGATGACTTTGGGGCTTTAAAAAAGTCAGACGAAT[A/C]TTCTAAATTGTTGAACTCTTTGGGTACATGTATCT M 2 1 2 1 101000 f 74 goat snp33284-scaffold391-865127 8 6192269 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801090 Affx-122921987 AX-385288004 8 6146204 ATTTTATGTGCTGTCCCTGTCTAAATATGAGGGAA[C/T]ATTTTAGAAGCTCAGATTAGTTTTTGACTCCCATA Y 2 1 2 1 101000 f 74 goat snp33282-scaffold391-764588 8 6293250 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417876 Affx-122946761 AX-123288224 8 6194981 AGTTATCTCACTCTGATCATGGTAAGGTGGTTGTC[A/G]TGGGTCCTAGGGGTGCTTCTTGCTGGCTGTTGAAA R 2 1 2 1 101000 f 74 goat snp33281-scaffold391-715811 8 6342816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412595 Affx-122951293 AX-123282944 8 6225911 CATTTGACATCACGAAACCACGGGGGTTTCCAGTC[A/C]GGGGGAACCATGGTGTCATAAGGGAATCAGACATA M 2 1 2 1 201000 f 74 goat snp33280-scaffold391-684881 NW_017189594.1 39026 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423844 Affx-122942780 AX-123294190 8 6258237 GCTCCAGATTGTGTTTTCTTTTTCGCGGAGGCTTA[A/G]TGGCACCCCCTTTACTGGTGCTCTTTCTAATATAA R 2 1 2 1 101000 r 74 goat snp33279-scaffold391-652555 NW_017199998.1 4236 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436075 Affx-122932695 AX-123306414 8 6298309 TTTTTTTTTTTTTTTTTTTTAATGAGAAAAGCCAT[A/G]TTGTTGTACATGCACAAACCACTTTCTAATGGTCT R 2 1 2 1 101000 r 74 goat snp33278-scaffold391-612483 8 6405193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791238 Affx-122925974 AX-385278232 8 6362638 GAATGTATACATTAGCAAATGTGTTTGGCTACTCC[A/G]CAGCATGAATGTGACTCTAAGATGTTAGTGTTTTT R 2 1 2 1 101000 f 74 goat snp33276-scaffold391-548154 8 6469915 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445405 Affx-122925384 AX-123315742 8 6419479 CATTTGGGAAGACATATCCCCCTAAAATAATCTCT[A/G]TCAATGACTATTTTGGCTACTTTTTAAAGGGTACA R 2 1 2 1 201000 r 74 goat snp33275-scaffold391-491313 8 6526681 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441016 Affx-122928950 AX-123311353 8 6459322 ACCTCTATTTTTTAAGGTTTAGAGTGATGCTGATT[A/C]TTGTCCTGCATCAGAATGATCATATTAGATGCATC M 2 1 2 1 101000 f 74 goat snp33274-scaffold391-451470 8 6566780 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376154 Affx-122978849 AX-123246513 8 6522539 CTGTCTGCTTGCCACCAAAAGGATGAATGACAGAT[C/T]AGGTAGTGAAATACAAGATGCTTGGGGAGGATGGG Y 2 1 2 1 201000 f 74 goat snp33273-scaffold391-388253 8 6627073 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398423 Affx-122961623 AX-123268778 8 6567563 TCTTATCAGTTGAGTATCTCTACAGAGGAATGCCC[C/T]TTGTGTGTTACTTTCTTAAATATATGCATTATCCC Y 2 1 2 1 101000 f 74 goat snp33272-scaffold391-343229 8 6671852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385270 Affx-122972074 AX-123255628 8 6612392 GAGGTTCTCTCATCTCAGAAAGAATATTAAAATGT[A/G]CTGTTTTGTGTCTTATCCACTCATTATGAGCCTCT R 2 1 2 1 101000 r 74 goat snp33271-scaffold391-298400 8 6716914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793433 Affx-122948048 AX-385280410 8 6642192 CTACAGAGGGGCAAATTCTCCAGGATTCCAAGTCA[C/T]AGATCCTAGCAGTTTCTGAATTTGGTTTTCTGTTG Y 2 1 2 1 101000 f 74 goat snp33270-scaffold391-268600 8 6747070 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388235 Affx-122969795 AX-123258593 8 6690323 AAAATAGAGCAATACTTGATCAAAAAAAGCAAGCA[C/T]ATACTAACTAGGCATTAAGATAAAACTCTATAGTC Y 2 1 2 1 101000 r 74 goat snp33269-scaffold391-220469 8 6796249 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796124 Affx-122964017 AX-385283075 8 6729163 ATCAAAAAGCATTAGTAGCACAAGTTCAGTGCATT[A/G]TTCAGAATAAAGTCATATTTTAGGGCTCCTATCAA R 2 1 2 1 101000 r 74 goat snp33268-scaffold391-181629 8 6834497 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425170 Affx-122941056 AX-123295516 8 6760127 TAGTTTACAACTAGTGGCAGACAACAAGTAATAAA[C/T]GATGAGTTGCACTGAAACTGTGAGCTCCTTGAGGA Y 2 1 2 1 101000 f 74 goat snp33267-scaffold391-150665 8 6866384 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440688 Affx-122929915 AX-123311025 8 6832856 AGGTATATTTTGCTAACTCTTGATCCTTGAGAAAC[A/G]TGCATCTATTTCCTCTCTAGGTAAAATGATATTTA R 2 1 2 1 101000 f 74 goat snp33266-scaffold391-77936 8 6937586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768750 Affx-122934497 AX-385255927 8 6900363 AGGATTATGTAATAAAACTTAATCCATTCTGACCA[C/T]GTCAACAGTTGAAGCAAGCTTCACTGCTCTTACTT Y 2 1 2 1 101000 r 74 goat snp33264-scaffold391-10429 8 7005861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779104 Affx-122941915 AX-385266209 8 6929004 TTTCCCTCTATAAAAGCTATAGGAGCTGTATTTTA[C/T]AGCTGAACATTCACATTTTCTTATGCTTGAATCAC Y 2 1 2 1 101000 r 74 goat snp25305-scaffold2605-262579 8 7034681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779787 Affx-122962920 AX-385266887 8 6965300 GTAGAAAGTAATAAAGCCTACTGAACAGCAAAATT[A/G]TTCTATGATGTGCTATTTTCTTATCATCTCCAGTC R 2 1 2 1 101000 r 74 goat snp25304-scaffold2605-226283 8 7070688 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391587 Affx-122966608 AX-123261944 8 7002403 CAGATTCTAGGACTTGAATTGTGTTCCCTCGGACT[A/G]CAAAATGGGGGAGGCTTATAAAGGCAAAAAAGTTG R 2 1 2 1 102000 f 74 goat snp25303-scaffold2605-189180 8 7105566 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796192 Affx-122974546 AX-385283143 8 7067886 TACAGACCTTATTCCCATCCCATGTATTCCCTGCA[C/T]GTGGTATAAGTGTTTCGTGTTTTTTATTCACTTTA Y 2 1 2 1 101000 f 74 goat snp25302-scaffold2605-123697 8 7170111 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275040 Affx-1111834557 AX-519548622 8 7102192 AGTGACAAAAACTTTGCAAGCTGCGTGGCCTGA[A/G]GGATTTTAGTTCTGGACCATGGATTCTACTTGTGC R 2 1 2 1 101000 r 74 goat GoatD01.041444 8 7102192 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38389195 Affx-122969074 AX-123259553 8 7153536 TCCAAAACCTCTGCTATGAGAAGCCCCCTTGAAAG[C/T]AGAAGTTGCTCACCACTAGAGCAAGAAGAATCAAT Y 2 1 2 1 201000 r 74 goat snp25300-scaffold2605-38047 8 7258145 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413721 Affx-122950070 AX-123284070 8 7241301 TCACTCATGACCCTTTGTAACTTGGCTCTACCTCC[A/G]TCTCCAGCCTCATCTGTAACCACATCCCACCTTTC R 2 1 2 1 201000 f 74 goat snp13909-scaffold1543-49619 8 7351588 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448837 Affx-122923298 AX-123319173 8 7270896 GTGACCTCCGCAGTAGTCCTGAGGACTTTGCTAGG[C/T]GGCTTTTGAGTTATAGTCCCAGCGGTGAGAAGCTG Y 2 1 2 1 101000 f 74 goat snp13910-scaffold1543-79214 8 7381458 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779799 Affx-122932165 AX-385266899 8 7308481 AAGCTTTCAGGCTCACAAAAGCCCTAAAGGAAGAA[C/T]GTATCTGTGCTGTCAGCCTCCCAGGAAAGGGACCT Y 2 1 2 1 202000 r 74 goat snp13911-scaffold1543-116799 8 7419386 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410183 Affx-122952587 AX-123280533 8 7339833 AAGCAGGCAGCTTTCTGGATCTGGAGTAGGACAGA[C/T]CTGAGAAGAGACAGTGGGGCAGCCCTTTGGAGAAA Y 2 1 2 1 101000 f 74 goat snp13912-scaffold1543-148151 8 7448560 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320762568 Affx-986697098 AX-385250669 8 7352091 TGCTCCATGCTCACAGTGATCATGGCCCTTCTGTA[C/T]TTTCCCCACGTGGGTCTGTAACTCACTTCTTACAG Y 2 1 2 1 600010 f 74 goat 8_7352091 8 7352091 Ancestral_priority_1043 ancestry 0.64 recommended IMAGE 10K 10K ancestral 38411679 Affx-122952003 AX-123282029 8 7396244 TCTTCTCTCATCGCTCGTCGTCTTTCTTCCATGAG[C/T]TGTGTTGTGTTTGTTTAAATATATATTGGAAAATC Y 2 1 2 1 101000 r 74 goat snp13913-scaffold1543-204562 8 7505268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386081 Affx-122971449 AX-123256439 8 7431757 TTTCTCTAATTGGGAACAGCTGGGTGGCTCAGGCG[C/T]CAAGCATCTGCCTGTCAATGCAGAAGACACAGGAA Y 2 1 2 1 101000 f 74 goat snp13914-scaffold1543-240075 8 7540204 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787030 Affx-122963445 AX-385274058 8 7487510 ATGCAGTGACATTGGAGACTAAAATGTAAACTACA[A/G]CACACCCTCCAGCATGACTATTTCCATTCCTGTTG R 2 1 2 1 202000 r 74 goat snp13915-scaffold1543-295828 8 7595521 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408706 Affx-122953433 AX-123279057 8 7530954 GAGCAGCTGGCAATCTGAGCCATCAGAACCACACA[C/T]ACCTTTCCCTCCCTTGATTCCAGAATGCAGGGGCC Y 2 1 2 1 201000 r 74 goat snp13916-scaffold1543-339272 8 7634445 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391725 Affx-122967498 AX-123262082 8 7571564 ATGGAGAGGGTCCCTCTCCCACTGACAAAGCTAAG[C/T]GGAGCCACCGCTAGGGTTCCAGGCACCTGGGGGAG Y 2 1 2 1 201000 r 74 goat snp13917-scaffold1543-379882 8 7675032 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395075 Affx-122964181 AX-123265430 8 7601844 GAGCGATGGACCGGGGAAAAGACGTGCAAACTGCA[C/T]GGCAGACAAATGTCTATTTATAACGTGCACAGAGC Y 2 1 2 1 201000 f 74 goat snp13918-scaffold1543-410162 8 7705281 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439167 Affx-122931063 AX-123309504 8 7632836 CTCAGAGACGCAGAGAACAATGGAGTTGATGGGGA[C/T]GGACCGTAGCATCTAGGGTGGTGAGGTGCTGTCCT Y 2 1 2 1 101000 f 74 goat snp13919-scaffold1543-441154 8 7736082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408543 Affx-122953686 AX-123278894 8 7663105 AGCCCTCATGAGGCTCAGAGTCCAGTGGAGGAGAC[C/T]GTGGAGAAAGTTCCCGGTAGAAGTGCTGTGGTCTA Y 2 1 2 1 201000 r 74 goat snp13920-scaffold1543-471423 8 7765900 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433031 Affx-122935771 AX-123303372 8 7721368 GGCCAAGGAAAGATGCGCCAGACTCCAGAGTCCAC[A/G]TTTTGTCCACACACCTTGGATCTTGAGCAGGAAAG R 2 1 2 1 101000 r 74 goat snp13921-scaffold1543-529686 8 7823787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376397 Affx-122978094 AX-123246756 8 7743114 AGACGTCGTCCCATCACAAGAACTGTGTGCTCCAC[G/T]TGAAAAAATGAGACACACGGTCCTGGGGGGCAGAC K 2 1 2 1 101000 f 74 goat snp14911-scaffold16-2932535 8 7844837 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379287 Affx-122976213 AX-123249646 8 7787400 GCTTTGTGTGCAGAGTAACTGCCTTTGGCTTAACT[A/G]TTAAAGGGAGGCAGAAAGGCTCAAACCTGTAACTA R 2 1 2 1 101000 f 74 goat snp14910-scaffold16-2888249 8 7889333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769741 Affx-122922285 AX-385256911 8 7840071 TTGGTAACATCTTTGTGGTTCTAAAATGAAAATCA[C/T]AGCTATAACCACCTACAGACATAATGTTTAAAAAC Y 2 1 2 1 101000 r 74 goat snp14909-scaffold16-2835578 8 7940940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418219 Affx-122947051 AX-123288567 8 7884023 CAGGCTGGGAACCAGGGGCGCTGTGGGAGTCAGGC[C/T]CCCTCTCTCTTGGGAGAGACAACACTTCCTTATAT Y 2 1 2 1 101000 r 74 goat snp14908-scaffold16-2791626 8 7985069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278743 Affx-1111836490 AX-191762991 8 7910877 CAAGGCAGAAGGAAGCGCGTCAGTAAAATACAGAC[A/G]TGAGAGAATGCAGGACACGGATGAACCAAAATGAA R 2 1 2 1 101000 r 74 goat Random2.2K-862 8 7910877 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273386 Affx-1111833593 AX-519547018 8 7928713 ATGTCCTGGCTGTTATAAACAGTGCTGCAATGAAC[A/G]CTGGGGTACAAGATGCTCAACATCACTCATTATCA R 2 1 2 1 303000 f 74 goat 8_7928713_AF-PAKI 8 7928713 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320801563 Affx-122969671 AX-385288472 8 7929924 GTTCTCAAGGAACCCTTCTGCACAATGTGCAGTAA[C/T]ACCCTCCTGACCTGGAAGAGTCGAACCTGAAGCCT Y 2 1 2 1 202000 r 74 goat snp14907-scaffold16-2745725 8 8031804 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406774 Affx-122955717 AX-123277125 8 7976525 TGATGAATTAAATATTGATTAATTAAATATTAATA[G/T]CAAATATAGAAATGGAAATGATCGCTCTATTTTTG K 2 1 2 1 103000 r 74 goat snp14906-scaffold16-2699124 8 8078262 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407174 Affx-122954831 AX-123277525 8 8014077 AGCACTGAGCAAGCTGTTGCTCACTGAAGGAGTTC[A/G]CCGAGCTCTTAAGTATCTGTGCTTTAGGTTCAGCC R 2 1 2 1 101000 f 74 goat snp14905-scaffold16-2661572 8 8115895 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782019 Affx-122946819 AX-385269098 8 8063268 CATACTCTGGAGACAGCTGTCTTGTGAAGATTCGC[G/T]GTTTCTATGGACCGTGTATTTTCCCAGGCAGTTTA K 2 1 2 1 101000 f 74 goat snp14904-scaffold16-2612381 8 8163692 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389016 Affx-122968639 AX-123259374 8 8108030 ACATGTGAGTGCATAGATAATGAGTATGCGCCTGT[A/G]TGTCTTAGCTTAATTTTTTGTATATTCTAAACTTT R 2 1 2 1 101000 f 74 goat snp14903-scaffold16-2567619 8 8207219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444466 Affx-122926539 AX-123314803 8 8137242 AGTGTACCTGTGGTCCGTTTTTGGTAACTTTTGCC[A/G]GTGGTGGTGTTCTCTAGGAGAACCTCTCTCCCCAT R 2 1 2 1 101000 f 74 goat snp14902-scaffold16-2538407 8 8236515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447720 Affx-122924603 AX-123318056 8 8171265 ATTGACTAACACAAACTAAATTATTAAACATAATA[A/G]TAAATGAATAGCTGTGAACTTACCTCTCAAGAACC R 2 1 2 1 101000 r 74 goat snp14901-scaffold16-2504384 8 8270555 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426219 Affx-122940359 AX-123296565 8 8242575 CTAAATACAATTAATTAAACTTAAAAATCAAACAC[A/G]TGAACCAGAACCTCTGACTTCCTCTTAATGGTGCA R 2 1 2 1 101000 r 74 goat snp14899-scaffold16-2433074 8 8340061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416832 Affx-122948117 AX-123287180 8 8334622 ACGTTTTCTCCAACCACTGGGCCTTTGTACACGCC[A/G]TTTCTCCTGTCTGCTTCCTCCTTTTCCACCTTTCT R 2 1 2 1 101000 r 74 goat snp14897-scaffold16-2341027 8 8431342 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437668 Affx-122931782 AX-123308006 8 8378908 TGTCTGTTACTCCATTATCATCAGGAAAGTTGATG[C/T]AGCGGAGAGAGAAGGAGAGAGTGAAGGGGAGAGAG Y 2 1 2 1 201000 f 74 goat snp14896-scaffold16-2296741 8 8475291 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407935 Affx-122954367 AX-123278286 8 8409307 TTCTTCTCCCAAGCATTCATATCTCCAGAGTCACC[A/G]AATATAGTCAAGACTAGAAAAAAAGCACTTCAAAG R 2 1 2 1 201000 r 74 goat snp14895-scaffold16-2266342 8 8506441 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768473 Affx-122940059 AX-385255653 8 8445993 CTGGTGGTGAAACAAAGGAGAACCTCATCTCCTAG[C/T]GGTTAATCACAAGCAACAGCTCCCAGCATACAGGC Y 2 1 2 1 101000 f 74 goat snp14894-scaffold16-2229656 8 8542173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422659 Affx-122943685 AX-123293005 8 8486968 CTGAAATGAGAAGAACTGAAACTCATGCAGCAAAC[G/T]TTGAGGATTTTCAGACTATGGCATTATAGTTTTAA K 2 1 2 1 101000 r 74 goat snp14893-scaffold16-2188681 8 8583690 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385798 Affx-122971039 AX-123256156 8 8515546 TGAAATAAACAACACTGTTAATTGCAGCCATGCAG[A/G]GGCAGCTCCTTAGTCCAGTGTAACTTTCTGCATCC R 2 1 2 1 101000 r 74 goat snp14892-scaffold16-2160103 8 8612633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798719 Affx-122945334 AX-385285650 8 8549119 CTGAAAGAAGATGGTGTGCTTCAGTGGGGGAAGAT[A/G]CAACATTTCAGTAACTTCTCACGTTCCTGTGTTTG R 2 1 2 1 101000 r 74 goat snp14891-scaffold16-2126530 8 8644974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414620 Affx-122949342 AX-123284969 8 8583944 GCTGCAGCATCCCCTCCGTCCCTTTCTTTCCTTAC[A/G]CTTTTTCTGGGGAAGGACTCAGGCATTTTAAATCT R 2 1 2 1 201000 r 74 goat snp14890-scaffold16-2091705 8 8679867 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413953 Affx-122950310 AX-123284302 8 8615732 CCATTCCGATTAGGGCAGGCTGGAGAATCTCACAG[A/G]AGAGGACTCGAGTGAAACCTCAATTTCACCTTGAG R 2 1 2 1 201000 r 74 goat snp14889-scaffold16-2059917 8 8712088 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801573 Affx-122978549 AX-385288482 8 8658069 GGTACTTCACCACTGTATTAATAGTAATGACGGAA[C/T]GAGTTTCTGTGTTTGTGTATGCCTTTTCTTTTCTC Y 2 1 2 1 101000 r 74 goat snp14888-scaffold16-2017580 8 8755752 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768854 Affx-122946070 AX-385256031 8 8734978 TAGCTTTTGAATGGGATTATAGCCCTTTGATATAC[A/G]TTTTAATACCTCTGACAGGGGCTCTGGGGTCCTAA R 2 1 2 1 102000 r 74 goat snp14887-scaffold16-1940671 8 8834293 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398219 Affx-122962215 AX-123268574 8 8795903 TCCATCATTTCTGCAGGATGCTTTTGTTCACACAG[A/C]CCAGCTGTAATGAAGGGTCGGAGGGACCACAGGAG M 2 1 2 1 101000 f 74 goat snp14886-scaffold16-1879746 8 8893905 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438361 Affx-122931322 AX-123308699 8 8839128 CACTGGCCAGTTTACCATTGAGCCACCAGGGAAGC[A/G]CTGAACGTTTATTTTTAAAAGCGAATAAAAGCCTG R 2 1 2 1 101000 r 74 goat snp14885-scaffold16-1836521 8 8937684 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785471 Affx-122955217 AX-385272516 8 8879714 TGATCAGTTATTACGTGTTTGGCTCCAGCAGTGCT[A/G]TAGATACGTTTATTAATCACGGTCTGTTGTGCACA R 2 1 2 1 101000 f 74 goat snp14884-scaffold16-1795935 8 8978401 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438367 Affx-122931317 AX-123308705 8 8924548 CCACCAAAAGATAGAGAAAGCAGAAGAAGATATAA[C/T]GTGAAACAGCATAAAACAGTACTTATTTATCTTGC Y 2 1 2 1 101000 f 74 goat snp14883-scaffold16-1751101 8 9023240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444155 Affx-122926789 AX-123314492 8 8958336 TAATTGTTCTTTGGCCTGGCTTCTGGGGCAAAATA[C/T]GGTATTCGTCCATCAAGTTCTGAGTCACCATTGAT Y 2 1 2 1 101000 r 74 goat snp14882-scaffold16-1717313 8 9057435 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453279 Affx-122920386 AX-123323612 8 8996084 CAGCCTCCCTTTGTGGAGGGACACACTTAGCCCGA[G/T]ATGACCAGAAAAACAAATACTGTGTTCATATCTTT K 2 1 2 1 201000 f 74 goat snp14881-scaffold16-1679565 8 9095272 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771464 Affx-122920432 AX-385258622 8 9090329 TACCTCATTTTCTTTAGCTGTAAAATGGGATGCTC[A/G]TGCCTATCTCTTAGCATACCCTGGTTTTTAATGTG R 2 1 2 1 101000 f 74 goat snp14879-scaffold16-1585320 8 9189407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278745 Affx-1111836491 AX-519552220 8 9102610 ACTTACACACTATGGTTTAAGTTTTGTTGACCCGT[A/G]TTCCTACAGAAGGATCTGTCGGGAGTTCTGAACTC R 2 1 2 1 101000 r 74 goat Random2.2K-864 8 9102610 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38445039 Affx-122926618 AX-123315376 8 9131798 AAATCCTGGTGGTCAACCTCAGAAGTCAGTGACCA[C/T]GGAAGGTGGGTAAGCTATGCCACGTCCAATTGACA Y 2 1 2 1 101000 r 74 goat snp14878-scaffold16-1543851 8 9232011 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422345 Affx-122943447 AX-123292691 8 9199787 CTCATGTGTGGAAGAACCTTCCAGGCTCTCCCACC[A/G]TCCATACCAACCATCATGCTATTCTTTGTATCTGA R 2 1 2 1 201000 r 74 goat snp14877-scaffold16-1475862 8 9300380 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424352 Affx-122941930 AX-123294698 8 9237630 TCTTGAGGAAAATGTAACTACATCACTACACATAG[C/T]ACATGGTGAATTAATAAAGTCAGTACTTGAGTCAA Y 2 1 2 1 101000 f 74 goat snp14876-scaffold16-1438019 8 9338447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789265 Affx-122970559 AX-385276276 8 9285165 TGGGCTGCAGGGGTGTAGGGTTTTGTGACAGCTAC[A/G]TAAAACTAGAATATGTGTTTAATTGGCCCCAAACA R 2 1 2 1 101000 r 74 goat snp14875-scaffold16-1390484 8 9386078 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445946 Affx-122925909 AX-123316283 8 9343420 CCTATAATCGATTTATATATATAACCTAATTATCT[A/G]TCAGTCCGTCTTGATGGGGATCATTCTCAACTGCA R 2 1 2 1 101000 r 74 goat snp14874-scaffold16-1332229 8 9444893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410529 Affx-122952166 AX-123280879 8 9395358 AGTTCTATACTGAAATGGTGTCCGTTAAGCTATGA[C/T]AGTTGAATCACAGTATCTCTTAAGACCATCCCATT Y 2 1 2 1 101000 f 74 goat snp14873-scaffold16-1280291 8 9496904 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799316 Affx-122942184 AX-385286246 8 9484606 CATCCAGTAAAATCTTATTAGCTGTTGATGCTTTA[C/T]AAGTAAGGTGGTTGTGTCATTTTTGCACAGATGAT Y 2 1 2 1 101000 r 74 goat snp14872-scaffold16-1191043 8 9586280 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404510 Affx-122956701 AX-123274862 8 9538684 TAAAATTATGATATTATCTTTTATATTCCAGGACT[A/G]CTAAATAAGTAACAGCAAACGATCCTCTGTCCTTT R 2 1 2 1 101000 r 74 goat snp14871-scaffold16-1136965 8 9640536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798844 Affx-122940379 AX-385285774 8 9571137 CCATGATTTATCTTTTATTGACGAAACCTGGTCTG[C/T]GTTTCAACCATTTAGGTGCCAAGCTCTTTGGCTTC Y 2 1 2 1 101000 f 74 goat snp14870-scaffold16-1104512 8 9673107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421150 Affx-122944184 AX-123291497 8 9604531 ATCAATTAAAAAATAAAAAGACTAGGTAAAGTGAA[C/T]GAACAATTTTACAAATATTTTTCTATTGCTAGTTT Y 2 1 2 1 101000 f 74 goat snp14869-scaffold16-1071118 8 9706910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789294 Affx-122969160 AX-385276305 8 9681456 TAAGTATTTATACCAAGGACATAAGCTATGTTTAG[C/T]ATCTTATACTAAAAAACATAACTTAGTTGCTCAGT Y 2 1 2 1 201000 f 74 goat snp14867-scaffold16-994193 8 9801810 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435484 Affx-122933440 AX-123305824 8 9735248 AGAACTCCCAGCCTGTTTTCCAGAGTAGCTACACC[A/G]TTTTATATTGCACCAGCAGCGAATGGGGATTCCGA R 2 1 2 1 103000 f 74 goat snp14866-scaffold16-940401 8 9856146 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392842 Affx-122965769 AX-123263199 8 9783185 GGTTCAAAGAGTGGATGGTGGTAGAGGAAGTGGAC[A/G]CAGAGTAGCGATTATTCTTCTAAGGATTTTAGCTG R 2 1 2 1 101000 r 74 goat snp14865-scaffold16-892464 8 9904284 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441021 Affx-122928946 AX-123311358 8 9828286 GTTTGTCACCTTGCTTCTAGCACATGGTAACCTAG[A/G]TGTGTAAAAGCTGAGGAGAGTCAGAGTGCTCTGAA R 2 1 2 1 101000 f 74 goat snp14864-scaffold16-847363 8 9950874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433700 Affx-122934537 AX-123304041 8 9877885 ACTGACCCCTCCTCAGTTTTGAAAATTAAGTTTAT[A/G]AATATCTTCCATCTCTCCCTTAGCCCTGCCTCAGA R 2 1 2 1 103000 r 74 goat snp14863-scaffold16-797764 8 10000739 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397144 Affx-122962443 AX-123267499 8 9907151 TTAGGTTACACATTGTTTTTACTCTGTTATAAATA[A/G]TGCTGCAATGAATATTGTACATCTGTGTGAGCTTC R 2 1 2 1 303000 f 74 goat snp14862-scaffold16-768498 8 10029812 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400673 Affx-122960339 AX-123271028 8 9945995 TTAGCTCTGTGTCAGGCCCAAACCTAGGAACTTCC[A/C]TGTTCACCCATCTGTCACTTTTGTTTTGAATTTTG M 2 1 2 1 102000 f 74 goat snp14861-scaffold16-729654 8 10069653 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764912 Affx-986697104 AX-385252501 8 9964675 CTAACTCACTGAAACAGCGAGGACTCAGGATCCCT[A/G]CTCACACCAAGTACATCTAATTTTTCAGGAGTTTT R 2 1 2 1 600010 r 74 goat 8_9964675 8 9964675 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 320769560 Affx-122923672 AX-385256730 8 9995339 ATTGAGACTGTGTTTCCTTTGAGGAAGTGTGAAAG[C/T]AACTTAGATATGGATATACAGATACATAGATTTAT Y 2 1 2 1 101000 f 74 goat snp14860-scaffold16-680310 8 10119204 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378823 Affx-122976548 AX-123249182 8 10037880 TCCTGCTGGACAGCTGAATGAAGACAGAATCAAGG[C/T]ATGGCGGTACACCGACCACATATCCAGCTGGGTAG Y 2 1 2 1 101000 f 74 goat snp14859-scaffold16-637769 8 10162547 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762576 Affx-986697106 AX-385250674 8 10060842 GGGAGCTTAGGTCAATGAAGGAGGAATATGCCATC[C/T]AGGAATTTAAAAAAAAAAATGAGCAAGGAGTAAAA Y 2 1 2 1 600010 f 74 goat 8_10060842 8 10060842 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 38395144 Affx-122964125 AX-123265499 8 10088172 GGAAACAGAAATCATGGAAGAGCTCTGACATAGGG[A/C]CCTCTGTGTAGACTGGACTGTCATCCTACCGGGAT M 2 1 2 1 101000 f 74 goat snp14858-scaffold16-587477 8 10212885 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409991 Affx-122953276 AX-123280341 8 10133468 AGATCAATTTGGCACCAATCTGGGACTTTCCAGAT[A/G]CTCCTCCATGCTGTGTCTGAATACAGCAATGTCAT R 2 1 2 1 201000 r 74 goat snp14857-scaffold16-542181 8 10258059 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389302 Affx-122968508 AX-123259660 8 10163696 TGGAGCATGTTTTGCTTTGTGCTAATTCTAAATGC[A/G]TTTTTCAAGCTTCAACGGTTACTCTGTGCGACAGA R 2 1 2 1 101000 r 74 goat snp14856-scaffold16-511953 8 10288134 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785347 Affx-122927192 AX-385272392 8 10206908 TTTTTACTATTATGAGTAAGAGTACTGTGTACATT[C/T]TGTGCAAGTCAGAGACCATTTTTCACTAAAGAGAC Y 2 1 2 1 101000 r 74 goat snp14855-scaffold16-468741 8 10330831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408817 Affx-122954032 AX-123279168 8 10236242 TGCCCACAGAGTTCTGAGGTGCTTTGCTACATGGC[A/G]GTAGATAACTGATCCAGGGTGACAGAACAAGGAGG R 2 1 2 1 101000 r 74 goat snp14854-scaffold16-439407 8 10360387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274311 Affx-1111834180 AX-519547907 8 10238478 TCCTCCCGCTTGAACTGGTCGGAGTCCACGGAGTC[A/G]CTGCAAGGGAGAGAGAGGTGGTGACGACCAGGGAT R 2 1 2 1 103000 f 74 goat GoatD01.023798 8 10238478 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38446555 Affx-122924846 AX-123316891 8 10266499 TCAAAACAATAGACAATAAAAATACATTAAGAAGA[C/T]GATTTCTTATAGTTTGAGACTTAGAGACGCTCAGA Y 2 1 2 1 101000 r 74 goat snp14853-scaffold16-409150 8 10390849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278570 Affx-1111836492 AX-519552050 8 10279845 TAAAAAAAAAAACTGAATGGCTCTAAAGCTTGTAG[C/G]CACCTGGCTTGGGCCCCTTGATTGCAAGAGGATGG S 4 1 2 1 201000 f 74 goat Random2.2K-865 8 10279845 G C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441103 Affx-122928888 AX-123311440 8 10320788 GTAGTCTTGGTCGAATGGACTGCCTCATAAGAAAC[A/G]TCAGCTAGGCATGATCCCTTCAGCCTCAGCATGAA R 2 1 2 1 101000 f 74 goat snp14852-scaffold16-354861 8 10445475 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789489 Affx-122952513 AX-191732760 8 10350559 TATGAGAACAATCAGCTTATGAAATAATATGCAGG[C/T]AGGAAATAATAGTTAATTGCTGCTAAATACCCAAG Y 2 1 2 1 101000 f 74 goat snp14851-scaffold16-325090 8 10474548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387420 Affx-122970400 AX-123257778 8 10385204 TCCAAGTTCCTCTGTTTCTTTTTGTTTGGTCTACC[G/T]TTCCTGTTTGAGACTTCCCCCCAAGTATCTGGTAA K 2 1 2 1 303000 r 74 goat snp14850-scaffold16-290445 8 10509377 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401710 Affx-122959537 AX-123272063 8 10414365 TTTCTCACTGCAGCTGTTCTCTTGTTGCAGACCTT[A/G]TGCATTAAGTGAGTTTGAATCATAAATATCTTAGA R 2 1 2 1 201000 r 74 goat snp14849-scaffold16-261284 8 10538726 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446773 Affx-122925316 AX-123317109 8 10451354 AGAAAAACAACTTACCAGATGTCACTTTGCATGCT[A/G]CAGCTCCAAGATTCCACAAAGACAGTGGCAACGTC R 2 1 2 1 101000 r 74 goat snp14848-scaffold16-224295 8 10575623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273329 Affx-1111833564 AX-185665844 8 10491963 CAGCCTTCTTTATGGTCCAACTCTCACATCCATAC[A/G]TGACTACTGGAAAAACCATAGCTTTGACTACATAG R 2 1 2 1 303000 f 74 goat 8_10491963_AF-PAKI 8 10491963 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789974 Affx-122969431 AX-385276980 8 10499191 GTGAATTTTATGTCTTCACCTGTCTGAGCTATGAT[A/G]CCCAGATAGTTGGTCAAACACTATTCTGGATGTTT R 2 1 2 1 303000 r 74 goat snp14847-scaffold16-176458 8 10623540 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438686 Affx-122930870 AX-123309023 8 10531751 ATCGCGTCCTGCAACAGGAGAGGAGAGAGCAGATA[C/T]GGGGGTGGGGGAGAGTAAAAGCTGTAGTTGGAGAT Y 2 1 2 1 201000 f 74 goat snp14846-scaffold16-143898 8 10656277 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406391 Affx-122955398 AX-123276743 8 10575370 CTCCAAGCCCCTGGGCAGGGGCAGATGAGGCATAA[C/T]GCCTAGAATCATTGCAAAAAATTCCCAGAGTTTAT Y 2 1 2 1 101000 r 74 goat snp14845-scaffold16-100279 8 10699732 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450096 Affx-122922784 AX-123320431 8 10621095 ACTTGAAGGGTTGCTCTGGATCAGAGGACACCCTC[A/G]ATTCTTTCTGATGATCCTGGTCTCAGGGGCCCTGA R 2 1 2 1 201000 f 74 goat snp14844-scaffold16-54554 8 10745672 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377030 Affx-122977712 AX-123247389 8 10660717 TGGAACACAGAAATGCCCAGCATGACCTCCTCCTC[A/G]TGTCAAAAGCAGACTCTGATCTCCCCATCACTAGG R 2 1 2 1 101000 r 74 goat snp14843-scaffold16-14932 8 10785268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779126 Affx-122974977 AX-385266231 8 10702188 AAAACACATTATGTAATGCAGTGATGTCAAGAATT[A/G]CATGTTGAGTTCAAATAAAGTTGATTCATGAAATG R 2 1 2 1 201000 r 74 goat snp15960-scaffold168-26440 8 10827888 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409741 Affx-122953018 AX-123280092 8 10735802 GAAGGTCATTAGACCTGTTCATCAAGGAATCTAAG[A/G]GTTGGCGCTACTGGCACAGGCTCTTTTAGATGGGG R 2 1 2 1 101000 f 74 goat snp15961-scaffold168-60054 8 10862222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801813 Affx-122922938 AX-385288721 8 10766693 CAGGTGATAGATGCGTCTCAGGTCTTTATTTGTAA[C/T]GTTGTTGGATATCTTTATTTTCGTTATTTGTTACT Y 2 1 2 1 101000 f 74 goat snp15962-scaffold168-90945 8 10893129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380449 Affx-122975743 AX-123250807 8 10799040 AACCTTTTGTGAAATCTTCTCAGTGACTCTGATGA[C/T]CACACAGGTTAGAAACCATGCACTTGAGGCTACAC Y 2 1 2 1 101000 f 74 goat snp15963-scaffold168-123292 8 10925770 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409334 Affx-122953077 AX-123279685 8 10841829 TAGATCCGTTTCCCAAAGTTTACACACAGAACAAC[A/G]TATTGATTCACAGTGGTTGTAGCAAACCTTTATGA R 2 1 2 1 101000 r 74 goat snp15964-scaffold168-166081 8 10965386 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423201 Affx-122942716 AX-123293547 8 10879294 TGGGGGACTGCACAGGTGATCCAACCATAAAGCCA[A/G]TCCTACCTGCTTGGGCCTGTTTCCCCAACCACACC R 2 1 2 1 101000 f 74 goat snp15965-scaffold168-203546 8 11002435 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439739 Affx-122930538 AX-123310076 8 10924126 TGTAACAACCTCTCTTTCAAACCTCAGGCCAATCT[A/G]TTTTTTCCCTGTTTAAGAATCTAAGTTTCACAAGC R 2 1 2 1 201000 r 74 goat snp15966-scaffold168-248378 8 11047638 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777157 Affx-122956813 AX-385264280 8 10957130 GTCTGTCATGTCAAAGAGGAATAAGACCAATTCTG[C/T]GGTATGCCACTGTCCTGGAGTGGAAAATTATCCAG Y 2 1 2 1 101000 r 74 goat snp15967-scaffold168-281382 8 11081243 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770257 Affx-122945932 AX-385257423 8 11037038 TTGCAGAGTTGGACTTGAAATACACAAAAGAGGTA[C/T]GCCCCAAATTTTTGTCCTCAGTTCCCCTTTTGGGA Y 2 1 2 1 101000 r 74 goat snp33881-scaffold3990-54919 8 11165255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429856 Affx-122938151 AX-123300197 8 11068530 GTGTGTTCTGTGCAAATCCCTGACACACAAGATTG[C/T]GAGCGCATAGAATCTCTGATGTCTGAATCTACCAA Y 2 1 2 1 101000 f 74 goat snp33882-scaffold3990-86411 8 11197126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796034 Affx-122941067 AX-385282986 8 11117812 TGGTGTTTTTCTTGGCTATACCTGTTAACTTCAAA[C/T]GATGCTAGGATACCAGGTGACGTTTTGTCCAATTC Y 2 1 2 1 101000 r 74 goat snp33883-scaffold3990-135693 8 11246682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392327 Affx-122966694 AX-123262684 8 11184288 AGAAACGGATGGGGGTGGGAAAGAGACTACAATTA[C/T]TGAGCACTTAGAACACAGAGGTCCTGTTGGTCTTC Y 2 1 2 1 201000 r 74 goat snp17210-scaffold1796-522264 8 11314441 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392354 Affx-122966253 AX-123262711 8 11214996 AGTACATGAGTAAAAGCAAAGACACTGTGTCGGTA[C/T]GTCTTATAGATCTGGGGGAGAAAAAAAATACATGA Y 2 1 2 1 101000 f 74 goat snp17209-scaffold1796-491556 8 11344492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424931 Affx-122941286 AX-123295277 8 11337112 CCTTTGTATAGTTCAGGGAAAGCTGACAATCGGAG[C/T]GCTACCTTCTGCCTCTGTCCCTCAATTAAACAGTG Y 2 1 2 1 101000 f 74 goat snp17207-scaffold1796-369440 8 11465590 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398992 Affx-122960951 AX-123269347 8 11380083 ATTCCTGGTGACAGGCCCAAGAGCAAAAGAGTAGG[A/G]TGACGCGAGAACTTTTTCCTTCACAGTTTTGGCCA R 2 1 2 1 101000 r 74 goat snp17206-scaffold1796-326469 8 11508856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397964 Affx-122961902 AX-123268319 8 11416470 TTTCTAAAAGCACAGGTGAGCAACACAGCACAGAG[C/T]AGCTTCTCCCAGTTCTTACCAAAAATGCAAATACG Y 2 1 2 1 201000 r 74 goat snp17205-scaffold1796-290082 8 11545336 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422079 Affx-122943592 AX-123292426 8 11472406 ATAACAAATGTTTGATCAAATATCTGATGATTTTC[A/G]TAGGATAAATCTTTACAATTCTCAAGGAAACCATT R 2 1 2 1 101000 r 74 goat snp17204-scaffold1796-234146 8 11601497 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416351 Affx-122947889 AX-123286700 8 11520659 AGGCATCAAACCTGGGTTTCTTGCATTGCAGGCAG[A/G]TTCTTTACCCTCTGAGACACAAGAACTGTTCTGTA R 2 1 2 1 303000 r 74 goat snp17203-scaffold1796-185893 8 11651013 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782355 Affx-122946830 AX-385269431 8 11557397 ATACAACTAAGTCATATTTTCCAAACACCTATTAG[C/T]AATGAGTTGGTGTTTTGATCTCTAATTCCTTTGTC Y 2 1 2 1 101000 r 74 goat snp17202-scaffold1796-149155 NW_017212252.1 11325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433440 Affx-122935071 AX-123303781 8 11615229 GTTGAAAACAAACTCACAAGTATGTTGTTCTGTTA[C/T]GTTTCTATCCCCCCAGAAACCTCGTATTGATTTTG Y 2 1 2 1 101000 r 74 goat snp17201-scaffold1796-91323 8 11773510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794471 Affx-122968971 AX-385281434 8 11651928 TCCTTTTAGCCCATGTCTAGTCAAGTAATAAGATA[A/G]TAAATTAAAAATTCTTCTAGGAAATTCCCTGTATT R 2 1 2 1 201000 r 74 goat snp17200-scaffold1796-54624 8 11810664 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790422 Affx-122932518 AX-385277425 8 11691244 ACATTTCATCTATGGAAAAAGCTACACGACTTAGT[A/G]TTGCTTTATCAAGTAATCAAACACAGGCTTTTAAA R 2 1 2 1 101000 r 74 goat snp17199-scaffold1796-15308 8 11842877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390114 Affx-122968011 AX-123260471 8 11718243 AGAAACTAGACATGTCAAAATGCTTGCCCAAGCTC[A/G]TTTAGCTGGATAGCAGCAATAGTGAGTTTTTTTCA R 2 1 2 1 102000 r 74 goat snp22776-scaffold2272-11592 8 11878751 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786654 Affx-122924975 AX-385273686 8 11756531 TATGGTTTCAATTCAGTGAAAACATAAAATTTCTC[A/G]TTAATTTCCTCAATTATATGCAAACAGTTGAGTAG R 2 1 2 1 201000 f 74 goat snp22777-scaffold2272-49880 8 11916774 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441866 Affx-122929030 AX-123312203 8 11789135 AAAGTTAGAAAAAATGATGAGGTTCAGAGTGGGGA[C/T]GAAGCAGCAGAGAGAGGAGGCAGTGTACGTGCAAA Y 2 1 2 1 201000 f 74 goat snp22778-scaffold2272-82484 8 11949855 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787408 Affx-122930830 AX-385274433 8 11831485 ATGTACCTTATATTGTGCTTGCCTAATATGTGATT[A/G]TTTCATATAAAGGTTCCATGGGCATTAGAAAATAA R 2 1 2 1 201000 r 74 goat snp22779-scaffold2272-124834 8 11991865 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801470 Affx-122936882 AX-385288379 8 11881557 GCATTGTATTTAAACATAACTATTATTTCTTCTGC[A/G]TTTTCCTCTCCTTGGTATTAGAATAAAGGTGTCAT R 2 1 2 1 201000 f 74 goat snp27137-scaffold2898-214323 8 4315006 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766649 Affx-122933543 AX-385253998 8 11916067 TTACAGTAGCCTTAGCTCTGAAAAGATCCTTACCT[A/G]TAACAATTAAACAAATCAATGTTATCACCACAAGG R 2 1 2 1 101000 f 74 goat snp27136-scaffold2898-179813 8 4279888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793926 Affx-122974581 AX-385280895 8 11944940 GAACCTTTACTCTAGGAATGCCTTGCAAACCTCCC[A/G]CCATTGCCGCCTAATTGGTTTCTCATTAGGATTAC R 2 1 2 1 101000 f 74 goat snp27135-scaffold2898-150940 8 12081259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406272 Affx-122956089 AX-123276624 8 11981796 ATGAGAGTACCTGAAAGAAAATAAAAGGATCAGAA[C/T]ACCTCCTGAAGTTACGGAGGAGCTGGGCCCATCGT Y 2 1 2 1 103000 r 74 goat snp27134-scaffold2898-114084 8 12118217 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397849 Affx-122962461 AX-123268204 8 12027380 TGAATGATAAAAATACATTTAGTAAATGAGTGAAC[A/G]AGAGCTTACATTGAGATTTTCCTGCCAAAAACATT R 2 1 2 1 101000 r 74 goat snp27133-scaffold2898-68500 8 12164260 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786580 Affx-122956259 AX-385273612 8 12080100 ATTCCTGAAAAGGGTGGCTCATGCTTTCTTTAACA[C/T]AGAGCTTTCCATGACTCAGTAAAGCCTAGGTGAGT Y 2 1 2 1 101000 r 74 goat snp27132-scaffold2898-15780 8 12216924 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787111 Affx-122942751 AX-385274137 8 12101597 TCCATACCTAAGAGAGTGGTACTTTTGATTGTTTT[A/C]TGTGTTTTGTATTCACTTTCTCACAAGTCATATTT M 2 1 2 1 101000 f 74 goat snp55239-scaffold850-5618 8 12237007 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787568 Affx-122937045 AX-385274592 8 12131343 ACTTGGCCCAAGAGTCAAAACCATATTTAAAAGAA[C/T]GCTTATGCAGAGGAGCTCGACTCCTATCTTGTCCC Y 2 1 2 1 201000 f 74 goat snp55240-scaffold850-35364 8 12266586 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410491 Affx-122952195 AX-123280841 8 12161025 TTTTATATAACTTGCTTATATGAGTGCCAGTCCCG[A/G]AGCCTTTTTCATGACATAAGCAGGACATTAGGTGA R 2 1 2 1 101000 r 74 goat snp55241-scaffold850-65046 8 12296621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417187 Affx-122947320 AX-123287535 8 12190497 GAAAATGAAAAATGATGCTAGCAGCTCATGGCTAG[A/C]AGCTGATAGCATAGTGGTAGTGTTTCGAACTAAAC M 2 1 2 1 101000 r 74 goat snp55242-scaffold850-94518 8 12327457 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384419 Affx-122972190 AX-123254777 8 12237950 ATTGTATTAGTATAATGTATTACATTAATTGATTT[C/T]GAAGTGTTAACCTTTTTGGCAATTCAGCATAGTCA Y 2 1 2 1 103000 r 74 goat snp55243-scaffold850-141971 8 12376650 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419222 Affx-122945687 AX-123289570 8 12281325 TACTAACATGAAGGTCATGAGAATAGCTATCTTTT[A/C]TACAAAGAAAACTATATGGGATGGAGGCGGGGATT M 2 1 2 1 202000 f 74 goat snp55244-scaffold850-185346 8 12419959 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433889 Affx-122934407 AX-123304230 8 12314521 GCGAATTATTGAGCCCATCTGTGTGCCAGGCGCAC[A/G]TCCAAGCTCTGGCTGTCGGAGAAAACACATGTGTG R 2 1 2 1 201000 r 74 goat snp55245-scaffold850-218542 8 12453349 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404447 Affx-122956749 AX-123274799 8 12344002 AGCAAATACTATAATAATATGGTTCTATACAGTCC[A/G]TGGTTAGTTAAATCTAAGGACTCGGAATTGAGGAT R 2 1 2 1 101000 r 74 goat snp55246-scaffold850-248023 8 12482104 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397665 Affx-122962596 AX-123268020 8 12432118 CTCCAGAGTTGTAAAACTAAGCAGTGATTCATTTT[A/G]TTTATTGTACACTGGAAATCAGTGGGAAGGTGAAT R 2 1 2 1 102000 f 74 goat snp55248-scaffold850-336139 8 12570287 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449895 Affx-122922340 AX-123320230 8 12540892 AGTGCATCTATGGTACATAATGTAGGCTGATGACA[C/T]GTTACACTTACTATGATAATATTCACTAAAGAAAA Y 2 1 2 1 101000 f 74 goat snp30022-scaffold328-86015 8 12682877 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389247 Affx-122969036 AX-123259605 8 12590331 GATGACGGGAAGATCTACTTAGAATTTGGCTAGGT[A/C]TTTTAAGAGAGGCTTTTTATCTTTTGGCTAAAGTG M 2 1 2 1 201000 r 74 goat snp30023-scaffold328-135454 8 12733010 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801585 Affx-122945459 AX-385288494 8 12626183 GATTAGGTCATACTTCATTAATTCCTTGAGTTAAG[C/T]GCTAGGCAATTTGAAACTTGTTTTGTGGTCTTAAT Y 2 1 2 1 101000 r 74 goat snp30024-scaffold328-171306 8 12768899 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430860 Affx-122937421 AX-123301201 8 12685569 GCTGCTTTCAGTATGGAGTTTATTTTCTTCTGTGA[C/T]GATGAACCATCTCTTTCTCTAACATACCTGGCAAC Y 2 1 2 1 101000 r 74 goat snp30025-scaffold328-230692 8 12828589 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786954 Affx-122976740 AX-385273983 8 12734864 AAACATATGTAATACATTTACAATAATTGTTGTAG[A/C]GCTCCTGTCTACTAATCAAACATCTGCTTCAGTTC M 2 1 2 1 101000 r 74 goat snp30026-scaffold328-279987 8 12878568 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451880 Affx-122921054 AX-123322213 8 12779385 AGACGATGGAATGTGATAGTTAACAGCATTTTGAA[A/G]CCCACTAGTTTCTCATGAAATGCATGCTCAAATAG R 2 1 2 1 101000 f 74 goat snp30027-scaffold328-324508 8 12924058 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412482 Affx-122951385 AX-123282831 8 12863980 ACAATATGGGTACTGTGAACTAGGGGATGTTATGT[A/G]TAAGACCAGTCAGGTGATAAGGAGCTTGGCCCTTT R 2 1 2 1 101000 f 74 goat snp30029-scaffold328-409103 8 13012880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799329 Affx-122960443 AX-385286259 8 12892892 TGTGGACTTGGTATATTTGTTTAAAGATAATGATT[A/C]TAGGTGGAAATGTTTAATTGCATATTTAAAAGGAA M 2 1 2 1 101000 f 74 goat snp30030-scaffold328-438015 8 13041664 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431924 Affx-122935990 AX-123302265 8 12927316 ATTGTTTGTCCAGTTGCAATTCCCATCTATCTTTT[C/T]CAATGAAGTGACATAGTTTTCATCATTGCTATGAT Y 2 1 2 1 102000 f 74 goat snp30031-scaffold328-472439 8 13076726 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386915 Affx-122970011 AX-123257273 8 12977681 ATTTTCTTTAAGATTGACTGGTTTTGTCTCCGCCC[A/G]TAGAGGTTGTTTATGATGACAAAATGGAGATCCTC R 2 1 2 1 101000 r 74 goat snp30032-scaffold328-522804 8 13127621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445493 Affx-122925196 AX-123315830 8 13016915 AAGAAATGGAGGGGCACACAAGCTGTTGATATTTC[A/G]CCACCAAAAAACTGAACCTGAGAACAGAAATAGAA R 2 1 2 1 101000 r 74 goat snp30033-scaffold328-562038 8 13166519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273333 Affx-1111833566 AX-519546973 8 13028501 ATGACTGAGTGATATTTTCTCAATGGATGAAGAGA[A/G]TGCTTTCTCATAGACAAAAAATGTCTTCAGATTAA R 2 1 2 1 101000 f 74 goat 8_13028501_AF-PAKI 8 13028501 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38384196 Affx-122972401 AX-123254554 8 13114502 AAAATGGGAATTTCTGCACATTCCTTGGTTTCTCC[A/G]TTTTTCTCATTTCCCATATCTATGTCTATTTTTTT R 2 1 2 1 202000 r 74 goat snp30035-scaffold328-659625 8 13262033 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278749 Affx-1111836493 AX-519552224 8 13151633 AGCATAGAAAAATTTAATATACATGCAAATAATGG[A/G]TTTTTATAAATCAATTACTATCTAATTTTCACAGA R 2 1 2 1 202000 r 74 goat Random2.2K-866 8 13151633 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380882 Affx-122975048 AX-123251240 8 13179247 CTTGTCTTCCTTCAAAAGGCTATTGATATTTCCCC[G/T]CTAAGTCATTAGACATTATTTAATTCTTGCCCAAC K 2 1 2 1 201000 r 74 goat snp32584-scaffold3732-47064 8 13645232 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775962 Affx-122972402 AX-385263093 8 13205792 TCCATTCAATACCAGGTGATTCGTCTAAGCCAATC[A/G]TTATTTTCCATGTTTCAAAGATTAATCTCAGTCAC R 2 1 2 1 201000 r 74 goat snp48117-scaffold681-21179 8 13672078 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776651 Affx-122947896 AX-385263778 8 13235641 CCTGATTATCTTCAACTTTTTTCAAGTCAGACATT[A/G]CCTATTGTCCCCAAATTTAGTAAAATCTCTCTTTG R 2 1 2 1 101000 r 74 goat snp48118-scaffold681-51028 8 13701144 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797163 Affx-122921743 AX-385284103 8 13270330 GAGAGGAAGAGGAGAGAGATTGATTGAAATGTAAA[C/T]GTTAGCTTTTCTTATGCATCTCTCAGTCCTTTGCA Y 2 1 2 1 101000 f 74 goat snp48119-scaffold681-85717 8 13737055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409611 Affx-122953548 AX-123279962 8 13309370 CCAGAGGAGAGAGCTGAGAAATCTGGCTTAATATA[C/T]GAAGGTTTTTGAATGAAATTATAATGTGACCTTCT Y 2 1 2 1 101000 f 74 goat snp48120-scaffold681-124757 8 13775887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394973 Affx-122964268 AX-123265328 8 13342466 TAGCTTAATCTATGAAGGAAGAAGAGAAATTAAAT[C/T]GAAATGAATTTACTTACCAATATTCTAGATGAATG Y 2 1 2 1 103000 f 74 goat snp48121-scaffold681-157853 8 13808525 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392155 Affx-122966316 AX-123262512 8 13407700 TGCTAGACATCACTAATTTTCTCTGAAGAATATTA[C/T]ACAAAGCAAGCAACAAATTTGGATTAAAAAGGCTA Y 2 1 2 1 201000 f 74 goat snp48122-scaffold681-223087 8 13874208 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784917 Affx-122944092 AX-385271964 8 13438631 TGTTTCCTTTTGTTCTCTGGAAGCACTCGTTCTTT[C/T]ACACTTTAAGTGTATTATAAACACAGGTGTGCTTC Y 2 1 2 1 201000 r 74 goat snp48123-scaffold681-254018 8 13902534 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441979 Affx-122928443 AX-123312316 8 13469597 TATAATTCAAATATTCTTACTTTTCTCCTAATTTG[C/T]AGAGTCCAATTAAATAGAAATAACAATAATTTAGA Y 2 1 2 1 201000 f 74 goat snp48124-scaffold681-284984 8 13933123 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411519 Affx-122951671 AX-123281869 8 13506885 CCACTGTCTAATTATTATAATCATTTATAAATACC[A/G]AATCTCTCAACTCAGATATTTAACAATATCCCTAT R 2 1 2 1 101000 r 74 goat snp48125-scaffold681-322272 8 13971089 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430780 Affx-122937479 AX-123301121 8 13552989 AACCTTTGGCAAGCATTATTCTCATAATTGAAGAG[C/T]AGGATCCTAAAGTGGAGGAGAAAAGCCATGATTTT Y 2 1 2 1 101000 f 74 goat snp48126-scaffold681-368376 8 14017824 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785920 Affx-122953117 AX-385272957 8 13588897 TCCATAGGTTTTGCCACCTGGTCCCATTCACAGAG[C/T]CTATTGAAAATGGAAAGTGGCTTCATTTTCCATCT Y 2 1 2 1 202000 f 74 goat snp48127-scaffold681-404284 8 14054243 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416280 Affx-122947946 AX-123286629 8 13683136 AGTTTTATGTTATTTTGTGAAATACAAAAGGTAAA[C/T]GTTTGAGAGTGATGTCTTCCCACCCCCCAACAGTA Y 2 1 2 1 303000 f 74 goat snp48129-scaffold681-498523 8 14149725 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278574 Affx-1111836494 AX-519552054 8 13720138 GCTTTCATAATCATATTGAAAACATAAGCACTTCA[A/G]TGTAAAAGGAAAGAAAGACCTAACTACCACAGCAA R 2 1 2 1 201000 f 74 goat Random2.2K-867 8 13720138 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320765993 Affx-122940251 AX-385253417 8 13739140 ACTACTTCAGCTTAGTATTTGAACATGACAAGAAC[A/G]TGACTTTCGTCACAGGATTTACACTTGCCGTTACT R 2 1 2 1 101000 f 74 goat snp48130-scaffold681-554527 8 14206877 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278576 Affx-1111836495 AX-519552056 8 13776307 CCATCTCTCCTTCGTTTCACGCTTCATTATGACAC[A/G]TGTCAATTGAAGGTACTTATTTTCCATTTGTTTTA R 2 1 2 1 101000 f 74 goat Random2.2K-868 8 13776307 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38405815 Affx-122955891 AX-123276167 8 13794194 ATCCAGGATGTTCCCTACCCTAACTTCCAGGACTG[A/G]TCCTCACTGTGGTGCACTCAGGGAAAAGAGTGTGT R 2 1 2 1 102000 r 74 goat snp48131-scaffold681-609581 8 14263397 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767819 Affx-122972005 AX-385255042 8 13843577 TAGATAAAGCATAATGAAGTAGATAAAGCATAATT[A/C]TTTTCATGGTGAGGGCACTGTAATTCTGAATATGG M 2 1 2 1 202000 f 74 goat snp48132-scaffold681-658964 8 14314114 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432098 Affx-122936478 AX-123302439 8 13907710 ATAGTGACATAATATAAACAGGAAAATAAAACACA[C/T]GCACATTAAAACTGCATCACCAAATATCAGATGAA Y 2 1 2 1 101000 r 74 goat snp48133-scaffold681-723097 8 14380776 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798656 Affx-122942242 AX-385285588 8 13956993 AGACTGTATGGAGAGTTCCTAGATTCACCAGGAGT[C/T]CTTGGCCTGAATAACTACCTGCCCATCTCCACCTA Y 2 1 2 1 101000 r 74 goat snp48134-scaffold681-772380 8 14431015 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417116 Affx-122947469 AX-123287464 8 13991315 ACATACACCTATTCTTCAACAGGAAAGGGTAGCAC[A/G]AGCTCTATCACTCGCTTCTAGGCTCTCATATAGGA R 2 1 2 1 101000 f 74 goat snp48135-scaffold681-806702 8 14465172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397459 Affx-122962100 AX-123267814 8 14021385 ATGCTACAAATGTCAAGATGATTTTAAATTATTTC[A/G]TGTTGGGACCATATTATATAATCTCAACTCAGTGT R 2 1 2 1 101000 r 74 goat snp48136-scaffold681-836772 8 14495722 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278756 Affx-1111836496 AX-519552231 8 14035513 GGCTAGAGCTGATATCAATCAGTGCACTTGTGGCT[A/G]TAGAAATCGTCGCAGAGCTTGAGTCAAGTTACTCT R 2 1 2 1 101000 r 74 goat Random2.2K-871 8 14035513 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441435 Affx-122928815 AX-123311772 8 14114079 TCTCCTTGCATTTTCCAACTTTTAGCGCCCACCTG[C/T]ATTCCTAAGCTTGTGATCTCTTCCTCCATCTCCAA Y 2 1 2 1 101000 r 74 goat snp48138-scaffold681-929466 8 14597863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770121 Affx-122960347 AX-385257288 8 14165688 ATAGCCACCAATTTCTTGGTTGGGTGAAAACTCAC[A/G]TTTCTGGGAATTAAGAATTCTTTTGCATTTATCTC R 2 1 2 1 101000 f 74 goat snp48139-scaffold681-981075 8 14650993 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773613 Affx-122937921 AX-385260753 8 14196771 CCATTTCATTCATATGAACTATAAATATGAGGTCA[C/T]AATTAATATTCCCAGTCATTTCTATCTTACATCTT Y 2 1 2 1 101000 f 74 goat snp48140-scaffold681-1012158 8 14682468 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434928 Affx-122934307 AX-123305268 8 14230100 AATATTTGTGAACATACTACCCAGAATGAAGGTGA[A/G]ATTCTTTTTTGTCAATTTTCCTGGGGTACAATTTA R 2 1 2 1 101000 f 74 goat snp48141-scaffold681-1045487 8 14716088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426153 Affx-122940604 AX-123296499 8 14284979 TTCTTAGAACTCTTCTACCATGGAACTTACATTTT[A/G]CTTACATTCTATTTACTTTTTTTTTTTAGATATAC R 2 1 2 1 103000 f 74 goat snp48142-scaffold681-1100366 8 14771122 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429062 Affx-122938295 AX-123299404 8 14333247 ACTATGGTATTCGCAACATAGAGAAATTAGGCAGT[G/T]AAGCAGCCCCCGAATGTTTTGTGATCTTAGCATTT K 2 1 2 1 201000 r 74 goat snp48143-scaffold681-1148634 8 14819369 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779070 Affx-122929491 AX-385266175 8 14366081 AAACTTTAAGGTAAAGCTAGAAAAAGTGATTAATG[C/T]AGTCACAAGCTCTTCTTTTTTATACTGAGTGGGAA Y 2 1 2 1 101000 r 74 goat snp48144-scaffold681-1181468 8 14854164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397418 Affx-122962246 AX-123267773 8 14398533 GGAACTGTAAGCAGATCATGGTGCCTGTAGTGTGA[C/T]GGAGAGGTAGCCACGAGTCATGCCATGCATGCCTT Y 2 1 2 1 201000 f 74 goat snp48145-scaffold681-1213920 8 14886406 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799696 Affx-122934468 AX-385286624 8 14429690 GTTTCTTTTAAAGCTGCAGGTGTTATTAACAAATA[C/T]AAGCACACTTCACTGTTTGATAGATTAATCTCTGA Y 2 1 2 1 101000 r 74 goat snp48146-scaffold681-1245077 8 14917443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406072 Affx-122956241 AX-123276424 8 14482874 CATAAATTGTAAGGATTCTGTTTCGAATCCCCAGT[C/T]GATGGTACATCTGGGGTTGTGTTTTTAAGGCATGT Y 2 1 2 1 202000 r 74 goat snp48147-scaffold681-1298261 NW_017195854.1 13402 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394219 Affx-122964895 AX-123264574 8 14524242 ATCCCCTAAAGAAATGGTATATTTCTCCCTTTGCC[A/G]CAAACACTGAAAAATAGAGTTTGAAATATAAATCC R 2 1 2 1 103000 f 74 goat snp48148-scaffold681-1339629 8 15010999 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785278 Affx-122920097 AX-385272323 8 14553095 GAAGACTCATATATGAACAGATCAAATGGAGACAC[A/G]TTTTAGCTTAATTGTAATTTACTTCACAGATTTTT R 2 1 2 1 101000 f 74 goat snp48149-scaffold681-1368482 8 15040599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448612 Affx-122923384 AX-123318948 8 14590676 TCATTCTCTAGTAGAGAAGATAAGTATAAAAAACT[A/C]TTTTAATTATAATAATATGAAATTTAAGTAGCAGA M 2 1 2 1 103000 f 74 goat snp48150-scaffold681-1406063 8 15078386 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451899 Affx-122921037 AX-123322232 8 14649501 TTTGAAATTTTCAGGCACTTCTTATTTATAAAGCC[A/G]TCTTTGCTTTCTGAAATCCTTTTATATTCTGTTTT R 2 1 2 1 101000 f 74 goat snp48151-scaffold681-1464888 8 15137039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437263 Affx-122932005 AX-123307601 8 14681302 TTATGTTTGATTCTTTAGAAGTGGGTTGTGAATAT[A/G]TCTCATAAAGTTGGGGGGCTTAAAATAAATTATTG R 2 1 2 1 201000 f 74 goat snp48152-scaffold681-1496689 8 15168842 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777154 Affx-122927934 AX-385264277 8 14714424 TTCCAGAAGAGGGTCAGGATTGCAGAAGTATGTTT[A/G]TTTCTGTTCAAAGATGATAGTTCCCAACTAATGGT R 2 1 2 1 201000 r 74 goat snp48153-scaffold681-1529811 8 15202321 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409523 Affx-122953622 AX-123279874 8 14756049 TACCAGGAGAAAAAACGATGTTGATATACCAGACA[C/T]AATGACCTGCTTTTTGTTACCTCTCGATATACTAA Y 2 1 2 1 101000 f 74 goat snp48154-scaffold681-1571436 8 15243706 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442320 Affx-122928234 AX-123312657 8 14819214 AGACTGAAGATCTGCAATAGGAGAATACCCCCAGA[A/G]GCAGAAGCAGTACCTGGAAAGAATCAATAGCTCCT R 2 1 2 1 101000 f 74 goat snp48155-scaffold681-1634601 8 15306986 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800181 Affx-122938335 AX-385287104 8 14843709 ATTGTGTTGAACAGAAATATGAGGTTCAATATCAA[A/G]TAACTAAGGAATGATAGAACTAGGGTGTGACTCCA R 2 1 2 1 101000 r 74 goat snp44177-scaffold600-8721 8 15332031 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422647 Affx-122943696 AX-123292993 8 14882636 AGTAACATTTCATATACGTGGAGATTTTGGTCTAA[C/T]GAAGGAGACAGATATTAACCAACTCATGCAAATAT Y 2 1 2 1 201000 f 74 goat snp44178-scaffold600-47648 8 15371625 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451973 Affx-122920943 AX-123322306 8 14934205 ACAAATGGATTCCACCTCTTGATGACAGTAGCTGT[A/C]AAATAACAATGCAAAGAGTGTGGATACAGGGAGGA M 2 1 2 1 201000 r 74 goat snp44179-scaffold600-99217 8 15423201 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442503 Affx-122928557 AX-123312840 8 14963089 TGGTTCTCCCCAATGGTAATATCTTTTCTAACTGT[A/G]ACATATTATCAAAACCTACAATACTCTAGAAAGTG R 2 1 2 1 201000 r 74 goat snp44180-scaffold600-128101 8 15452133 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766715 Affx-122971740 AX-385254057 8 15018955 GTATTTCTGCAATATATTTGGGAATGAATGTTGGC[A/G]AAGTCTTGAGAAATTTAAATCCTGAATAATTAGAA R 2 1 2 1 101000 f 74 goat snp44181-scaffold600-183967 8 15508322 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799069 Affx-122934594 AX-385285999 8 15048148 TCTTCTCAAGTAGTAGACCCTAGTTGCCTTGTCTG[C/T]CCCAGAAGCCAGTCCTCTAACTCAAAGCTGACTTA Y 2 1 2 1 101000 r 74 goat snp44182-scaffold600-213160 8 15538179 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428352 Affx-122938983 AX-123298695 8 15097584 GAAACCACAGGAATGAATGAAACTGTTTGGGAAGA[C/T]GGTGTGGCAGGAAAGCAGTCAAAGGTGGAATTTTG Y 2 1 2 1 201000 f 74 goat snp44183-scaffold600-262596 8 15587229 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388470 Affx-122969241 AX-123258828 8 15132411 CAAACCAACTTTATGACAAAATACTAAAGGAACTC[A/G]TCTAGGCAGAAAAGGCCACAAATAGACGCATGAAA R 2 1 2 1 101000 f 74 goat snp44184-scaffold600-297423 8 15622322 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438906 Affx-122930437 AX-123309243 8 15172534 TTTCACACTTCCATTTGAAATTTGTGTCTCTTTTC[A/G]CTTTGAAGTTATACTTGTCTCCTAAACCACACTCC R 2 1 2 1 101000 r 74 goat snp44185-scaffold600-337546 8 15663774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379578 Affx-122976038 AX-123249936 8 15204157 CATCTCCAAGTTTTCTTTAAAGTCTACACTTTTCT[A/G]TAACTGTAATTACCTTTACTCCATAGTCATCAGGA R 2 1 2 1 101000 r 74 goat snp44186-scaffold600-369169 8 15695143 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398315 Affx-122962141 AX-123268670 8 15282919 GATAATTCAATCTTTCCTCACTTGTTTGGGATGTT[A/G]CTTTTACCATATATATTATATATAGTTTATATTTA R 2 1 2 1 103000 f 74 goat snp44188-scaffold600-447931 8 15774000 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420929 Affx-122944999 AX-123291276 8 15312804 TTGGATTGCTGTGTGTGACAAAGAAGAAGAAACCC[G/T]CTAAGCCCTCCCTGGGCCTATGATGCAATGATTTG K 2 1 2 1 201000 r 74 goat snp44189-scaffold600-477816 8 15804803 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376421 Affx-122978077 AX-123246780 8 15358006 AGGTAAGATTTGATGGAGTCATCTGATCATTTATC[A/G]TTTGTTTAGGCATTTCTAAGGGCTTTAGAGTGCTG R 2 1 2 1 101000 r 74 goat snp44190-scaffold600-523018 8 15850146 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794996 Affx-122956336 AX-385281955 8 15454524 ACAAAAGGTTCAAGCTCTCAGCAGTAGAAGAAACC[A/G]TTTGACTGGACATCAGGCCAAGTAGAAACATTTAA R 2 1 2 1 101000 f 74 goat snp44192-scaffold600-619536 8 15945639 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416060 Affx-122948342 AX-123286409 8 15520087 CAGACTTCAACTCAGTCTTTTCATTGAGTCAAAAC[A/G]CAAAAACTGAAAGTGTTTGTGTTTTTATTACATGT R 2 1 2 1 103000 f 74 goat snp44193-scaffold600-685099 8 16011232 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273335 Affx-1111833567 AX-519546975 8 15536206 AAAGCTTTCATAGATATTGCCAGTTTATGTGTAGA[A/G]ATATTTTTCCAGTTTAAATTCCAAATTATTTTATG R 2 1 2 1 101000 f 74 goat 8_15536206_AF-PAKI 8 15536206 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320803112 Affx-122960162 AX-385289983 8 15552519 CAAAGATAAGTCTTTTTGTTTACTGAGACTTTGTC[A/G]TAATGTTTCAAATGCCATTTTAAAACCATTGCTAT R 2 1 2 1 101000 r 74 goat snp44194-scaffold600-717531 8 16043990 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433851 Affx-122934438 AX-123304192 8 15585008 CTTAAAAACACTTAAAGGCAAAAGAACAAACAAGT[A/G]TTTCACAGAAGAGAAAATAGAACATTCCAATAAAT R 2 1 2 1 103000 f 74 goat snp44195-scaffold600-750020 8 16077049 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776515 Affx-122952142 AX-385263642 8 15614408 AACTACTTCAGCATCTATGTCTGAATACCTAGAAC[G/T]CTCCTCTACATAACCACAATAGCATTAGTATACCT K 2 1 2 1 101000 f 74 goat snp44196-scaffold600-779420 8 16107149 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376748 Affx-122978538 AX-123247107 8 15659502 CTCAAAGCACTAAGTGGCACTTGTATCAAGAGACT[A/G]TTATGCAATTATAATTAAAAACCATTCGTCACTGG R 2 1 2 1 101000 f 74 goat snp44197-scaffold600-824514 8 16152431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789239 Affx-122966656 AX-385276249 8 15715902 TCACCTTACTGATGGCTGCAGTTTCAACTTGTGAG[C/T]AAATCAAATGCATTACATGCTGTTTCAATTACCTA Y 2 1 2 1 101000 f 74 goat snp44198-scaffold600-880914 8 16209536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278580 Affx-1111836497 AX-519552059 8 15724443 TTCATTTTATTGATTGCATTATATTTCATTTCCCC[A/G]GAGAAGGAAATGGCAACCCACTCCAGTATTCGTGG R 2 1 2 1 202000 f 74 goat Random2.2K-873 8 15724443 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784979 Affx-122958582 AX-385272026 8 15748614 GGATGATGTATGAGGCAGTGCCTCTAATAGTGATC[A/G]TTACAGTTTGGATTTGAAACCAGTAAGTACACAGA R 2 1 2 1 101000 f 74 goat snp44199-scaffold600-913626 8 16242073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440993 Affx-122928969 AX-123311330 8 15779841 CTCTTACCAGCCAACTGTCAGCTCTCAAGTGTCGC[A/G]TCAAATTTAGAAGACGAGATGTATGTATTAGCCCA R 2 1 2 1 201000 r 74 goat snp44200-scaffold600-944853 8 16273654 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777370 Affx-122952952 AX-385264492 8 15809098 GATACAAAAGAGTACATACGATTCAACATGGTTGC[A/G]TATATGGAAAATACACTTTTTCCTGGAAAACTATT R 2 1 2 1 101000 f 74 goat snp44201-scaffold600-974110 8 16302730 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439181 Affx-122931052 AX-123309518 8 15844140 AAACACTCAGTTGGAGTAGTTGGCATGGCAAACAA[C/T]AGTCCAGGGGCCAAATCCAGCCTTTTCCTGCTTCT Y 2 1 2 1 101000 f 74 goat snp44202-scaffold600-1009152 8 16337825 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428870 Affx-122938343 AX-123299212 8 15928987 GCTTCCTAATTTTAAATGTCTAGGAGGATTTTTTT[A/G]TAAACAATTATTATAATTATGGGTAGGAAAGATCT R 2 1 2 1 303000 r 74 goat snp44204-scaffold600-1093999 8 16424739 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422250 Affx-122944004 AX-123292596 8 15970731 TTTTAACTGCCTTGCTTCTGCCAGGGAATGCTTCC[C/T]TCCTTAGCATCACGGCTCTGAGCTTCCCCTGCAGG Y 2 1 2 1 201000 f 74 goat snp44205-scaffold600-1135743 8 16464097 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395993 Affx-122963502 AX-123266348 8 16001432 GCAAGAGCTAATCTTGGAATGTAATTCCCTGTCTG[C/T]CTAGTTTCAAACCTTGGGTTCTCAAGAGCACAAAT Y 2 1 2 1 201000 r 74 goat snp44206-scaffold600-1166444 8 16494310 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416591 Affx-122947648 AX-123286939 8 16041885 AAGTCACTGGTAGTCAGCTGGGCTGGGGAAGACCA[C/T]AGGCATTTTGTCTGAATCACCTGGGGCAAACTTCA Y 2 1 2 1 101000 r 74 goat snp44207-scaffold600-1206897 8 16534846 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385223 Affx-122971700 AX-123255581 8 16070640 AGTCTTTAGATATGCTTAATTTACTGTCCTTGCCT[A/G]CAAGCACAGAAAAGAGTGTAAAGAGCAGAAAAAAG R 2 1 2 1 201000 f 74 goat snp44208-scaffold600-1235652 8 16559067 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275219 Affx-1111834662 AX-519548798 8 16078394 AAGTTTCT[A/G]TGTACCAGTCTGGTCTATAAATTGAAAGCCCTCTC R 2 1 2 1 101000 r 74 goat GoatD01.044881 8 16078394 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38400172 Affx-122960678 AX-123270527 8 16125322 TGCATATATCAAAGACTCTTTCTCTATCAAAGACC[A/G]TATGAGGTAGATCAAAAGAGAACTTGACTTCAAAA R 2 1 2 1 101000 f 74 goat snp44209-scaffold600-1290334 8 16613834 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386802 Affx-122970909 AX-123257160 8 16154166 AGGGTGAGAAAACCGAACGGTTACAGAGCAGTGAA[C/T]GCTGTATCAGAAAGCAACAGGGGAAAAGGCAAGAA Y 2 1 2 1 201000 f 74 goat snp44210-scaffold600-1319178 8 16642432 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404351 Affx-122956822 AX-123274703 8 16188714 TGTGGAGCATGGACATTGAAGAAATCTGATCTAGT[A/G]CTGAGAAAATCATTCCTGAGCTCAGAATTGGCTCA R 2 1 2 1 101000 f 74 goat snp44211-scaffold600-1353726 8 16677005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399000 Affx-122960946 AX-123269355 8 16223140 GCATGCTCCTCATTCCTCATGTGCTGATGATGTTG[A/G]CAATATTCACGACAAGAAAGGAAAGATGATTGACA R 2 1 2 1 101000 f 74 goat snp44212-scaffold600-1388152 8 16711928 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392470 Affx-122966152 AX-123262827 8 16260119 ATATTTTTGCAGAGCCTATGCGTGCGTGCTAAGTC[A/G]CTTCAGTCATGTCCAACTCTTTGTGACCCTGTGAA R 2 1 2 1 103000 f 74 goat snp44213-scaffold600-1425131 8 16748954 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380472 Affx-122975724 AX-123250830 8 16301695 TCACCCTACAGTAGCTGGCTCCTGTCTGGCTTTTG[G/T]GCTGGCTGAAGTGAGGAGGCCTAATGCCTGTGTGG K 2 1 2 1 101000 f 74 goat snp44214-scaffold600-1466707 8 16790603 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384131 Affx-122972816 AX-123254489 8 16350719 AAGTTAGGGAGCAGGCAGGGCAGAGCCGTGTTCAG[C/T]TTTGCCCAGTTTGCCTAAAAGCCCTGGACTCCTTT Y 2 1 2 1 101000 r 74 goat snp44215-scaffold600-1515731 8 16839806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386238 Affx-122970970 AX-123256596 8 16390293 GTTTCTTTCTGCCATGTTTCTGCCACTCACAGCCA[C/T]ACTCCTCTGCACCCAGAGCCCACTGTGTTGCTTTT Y 2 1 2 1 101000 f 74 goat snp44216-scaffold600-1555305 8 16879013 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424264 Affx-122941998 AX-123294610 8 16430198 TCACTGCCCCAAACAGGGTCTGCACTCTTTCACTG[C/T]GGGGACGAGACTGGTCTCTAGCCTAAGGCTGGCTA Y 2 1 2 1 201000 f 74 goat snp44217-scaffold600-1595210 8 16918705 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783237 Affx-122925939 AX-385270303 8 16502222 AACTATACAAAGTAACTATACAGAGTTTTGGACCT[C/T]ACATCAGATCACTTGCATGGTAAAGTCTTAATGGT Y 2 1 2 1 101000 r 74 goat snp44219-scaffold600-1667234 8 16991773 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384354 Affx-122972243 AX-123254712 8 16532061 ACTGCAGACTGAAGGGTACACAGGGATGGCGATCC[A/G]CACGTGGATATAATTCATATATATATGGGGGATAC R 2 1 2 1 101000 f 74 goat snp44220-scaffold600-1697073 8 17021493 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792648 Affx-122967278 AX-385279628 8 16573903 TATGCTCCCAGAGAAAGTCCTCAGGAGGAAAGAAA[C/T]ACAGTAATTCTGTCAGCTCCAATGAGATCCTGGCT Y 2 1 2 1 201000 f 74 goat snp44221-scaffold600-1738915 8 17063083 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769762 Affx-122972889 AX-385256932 8 16641915 GTCTCTTATGGATGCTTCTCATGGTCTAACTGGCT[A/G]TCTCAATTGTGCCACAGCTGGACTTCTACAGCTTC R 2 1 2 1 101000 f 74 goat snp44223-scaffold600-1806927 8 17130888 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417958 Affx-122946699 AX-123288306 8 16708298 TTATAACTTGGCAGTAAAACCACCAATGATGGTGT[C/T]ATAAAATGAGTAAACAACAAAGGTGAAACTCACTG Y 2 1 2 1 101000 f 74 goat snp44224-scaffold600-1873310 8 17197205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776813 Affx-122955378 AX-385263937 8 16754774 GAGAGCACTTCCTGTATCTTTGGACTGTTATTTCT[A/G]TATTTATGTAGCAAATCAAGTCCCAGAAGGAATGT R 2 1 2 1 202000 f 74 goat snp44225-scaffold600-1919786 8 17243696 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409306 Affx-122953097 AX-123279657 8 16787495 AGATAATTCTGAAGAAAAGACGATTGTAGCTTCCT[C/T]AACAGTTATCACTGTATTATGGTTATCTTGTGAAA Y 2 1 2 1 101000 f 74 goat snp44226-scaffold600-1952507 8 17276241 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453560 Affx-122919774 AX-123323893 8 16830990 GTTTTTTATTCTCTGAATTTCTATCCACATTTAAT[A/G]AATACTTTTTGGGTCTTTGTCTCCCTCATATTATA R 2 1 2 1 101000 r 74 goat snp44227-scaffold600-1996002 8 17319641 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399347 Affx-122961356 AX-123269702 8 16872273 CTTGAGTGATTGATGGTATCTGGTATAATGGGTCC[C/T]TTGCAGTAAGCCTTGGCCCACTTTTTGATGTTCCT Y 2 1 2 1 201000 f 74 goat snp15735-scaffold1653-17613 8 17363386 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438941 Affx-122930411 AX-123309278 8 16905680 TGTGGTCAGGGTTGCCGGGCAATCTCGAGAGTCTG[A/C]CAGGTAGGAGAGCTAAGTCCTCGTAAAGCTTTCTT M 2 1 2 1 101000 r 74 goat snp15736-scaffold1653-51020 8 17397096 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379715 Affx-122975889 AX-123250073 8 16950321 ATATGAAACACAGAAAGGGAATCAGGAAAAAGTGA[C/T]GAAATTCAAACCAGAAATATTCAAGTACCAGGTAT Y 2 1 2 1 101000 f 74 goat snp15737-scaffold1653-95661 8 17441959 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376737 Affx-122978951 AX-123247096 8 16980780 GGATGAATCTAAACTGAAAAAGACTGATTATTTCT[A/G]CTCACTAGTGGGAAGAATAACAGCCAAAGTGATCA R 2 1 2 1 201000 f 74 goat snp15738-scaffold1653-126120 8 17472817 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447447 Affx-122924372 AX-123317783 8 17029445 TAAAAATAGTTTCAGACAAGCGGAAATGTACAAGT[A/G]TGTCTGCAGGTGGTTTAATATGGGGAATCATTATT R 2 1 2 1 101000 f 74 goat snp15739-scaffold1653-174785 8 17521604 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380643 Affx-122975225 AX-123251001 8 17058568 CATTCACTACTATTTGGTTTCCTGTGCCGGAGGAA[A/C]TTTCCCATGGTATATAAAGAGAAGCCCAGAATCTC M 2 1 2 1 102000 r 74 goat snp15740-scaffold1653-203908 8 17551032 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796196 Affx-122949371 AX-385283147 8 17094795 TAGCATACCTCTGATTTTTTGGATGCACAAATAGT[A/G]TAAAGTTCAAAATAGTACAGAGTTAAAAACTGTGA R 2 1 2 1 101000 f 74 goat snp15741-scaffold1653-240135 8 17587629 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384054 Affx-122972877 AX-123254412 8 17179919 TTAGTTCAGCTCTTGTCTAGTTTATTTCATTTCTT[C/T]CATTTGCCTTCATTCCCATGGAGAAGAGGGTGTGG Y 2 1 2 1 101000 r 74 goat snp21858-scaffold2142-217611 8 17676496 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426024 Affx-122941124 AX-123296370 8 17211817 GACTGATTTGAGAGACATTGAAAATAATGTTCATG[C/T]ACCCTCCAAATACCAGATCTCTCAGTTGATTTCAG Y 2 1 2 1 101000 r 74 goat snp21857-scaffold2142-185713 8 17708386 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385337 Affx-122971657 AX-123255695 8 17257753 AAATGGTGGAAATTTCAAAGGAGGAGAAAACCCTC[A/G]TGATCAGACTCAAGAAATATTTTAAACCACCAGAA R 2 1 2 1 101000 f 74 goat snp21856-scaffold2142-139777 8 17754916 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320790570 Affx-122964405 AX-385277573 8 17289788 GCTTTCTACCATGCCAAGCTCTGTAATTCTGTTTG[G/T]CATTGGTGCACAGTGAGTCAAAATTTTGCCAACAA K 2 1 2 1 101000 f 74 goat snp21855-scaffold2142-107742 8 17786620 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430248 Affx-122937310 AX-123300589 8 17321120 GGCCCCATTAACTGAAACATTCATAAGGACATCAA[C/T]AAGAATGAAAATGCCTAAGGTAATACTCTGGAGAG Y 2 1 2 1 201000 r 74 goat snp21854-scaffold2142-76410 8 17817253 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772153 Affx-122952675 AX-385259308 8 17356970 TCCTCTTCCAAAGTAGGTGGCAGGTACTCCTCTAC[A/G]TCATTTTTAGGTCTGATCATGCAGCTTTCTTTGGC R 2 1 2 1 201000 f 74 goat snp21853-scaffold2142-40560 8 17853491 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438774 Affx-122931382 AX-123309111 8 17385832 AAAGAAAAAATAAAATATTCTGTTTATAAGAACAT[A/G]CAATCTTGTATCAGTCTGACCAGAGGATTATCACA R 2 1 2 1 101000 r 74 goat snp21852-scaffold2142-11698 8 17882197 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795385 Affx-122924533 AX-385282341 8 17397780 GTATTCATGAAGAAAAACACACTTGATTCTGTAAT[A/G]ATCATTGCCTCCAAGGGGCTCCATACTCAGTCTTG R 2 1 2 1 101000 r 74 goat snp24601-scaffold25-1726943 8 17894074 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775107 Affx-122966777 AX-385262239 8 17476578 ATGAGTGGCAACAGTTAGAAGGTCTACAGGATTTA[C/T]GGATTATGTGAATGGTCAAATGGTGTAGTTCTCAA Y 2 1 2 1 101000 f 74 goat snp24599-scaffold25-1648145 8 17982054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802583 Affx-122967964 AX-385289485 8 17527536 ATATTCTGTATCTCTTGAACAGATTTGCATTGGAT[A/G]CTAAACTATAACCACTTCGAGAATAGGGATTCAAA R 2 1 2 1 101000 f 74 goat snp24598-scaffold25-1597187 8 18033182 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773858 Affx-122950083 AX-385260998 8 17566595 AGCATTTTAGACCCCCAAATCTCCCTCAGCAAACA[C/T]AGACTAACATATATTTAGTAGTTTTAACTTTCCTA Y 2 1 2 1 102000 f 74 goat snp24597-scaffold25-1558128 8 18074391 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769515 Affx-122954231 AX-385256685 8 17617322 CAAAATCTTACCACTGCACAATATTCTCAAAGAGT[A/G]CATATTGCTGCTCAAGGAAAGCGAGTATTTCAGGT R 2 1 2 1 101000 r 74 goat snp24596-scaffold25-1507401 8 18121761 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404632 Affx-122957321 AX-123274984 8 17675763 AAGAAATTTTTAACAGTAAAGGAAACACTGGTGAC[A/G]ATGAGGCAGATAGATGCACACACAGGTTGAATAAA R 2 1 2 1 201000 f 74 goat snp24595-scaffold25-1448960 8 18179403 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399043 Affx-122960915 AX-123269398 8 17749358 GTAGAGGATTATAAATTTAGCATTGAAAAATGTAC[G/T]ACAAAGTCATAAATAGAAGCCAGAAGCACCAGTAC K 2 1 2 1 101000 r 74 goat snp24593-scaffold25-1375365 8 18253634 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274693 Affx-1111834445 AX-519548279 8 17793489 GCAATTATCTGATTAACTGCTAATGTTACACCAAG[A/G]AACCTCTTCAAGACTGCACTTTTTTTTTTTT R 2 1 2 1 101000 f 74 goat GoatD01.036269 8 17793489 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38413531 Affx-122950617 AX-123283880 8 17802441 AAAGTAAAAAGGCAGCTTCAAATCCAATTGCAAAC[A/G]TTAATCTCTGATGCTACATTGTATTTTTCTATATA R 2 1 2 1 101000 f 74 goat snp24592-scaffold25-1322282 8 18306036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430558 Affx-122937016 AX-123300899 8 17858741 ATGTTACTGTCGTATTCTGCCCCGATGGGGAAGGC[A/G]CCCCAGTTCCATAAGGGGAGAAGGAAAGAACAAAA R 2 1 2 1 202000 f 74 goat snp24591-scaffold25-1265982 8 18362585 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444882 Affx-122926270 AX-123315219 8 17901259 AGGGTATTTCCCCAGGCCCTTCCTTTTTACACTGG[C/T]CATGTACTCTCTGGCACAGAAAAACAGTCACACTC Y 2 1 2 1 201000 r 74 goat snp24590-scaffold25-1223464 8 18406281 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771733 Affx-122937895 AX-385258890 8 17934327 TCTTTCTTTCAACTATCTCACAAACTTAAACATAG[C/T]GGCATTTAGGGTAACAATTTTCATACTGGAGCAAT Y 2 1 2 1 101000 r 74 goat snp24589-scaffold25-1190396 8 18440236 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406001 Affx-122955509 AX-123276353 8 17966064 GTAGAGCTAATGAACCAGAAAATTTCTTAAAAACA[C/T]GGGAAAAGACAAGAAACAGTGTACTGTGTGAATAG Y 2 1 2 1 101000 f 74 goat snp24588-scaffold25-1158659 8 18472125 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770617 Affx-122938183 AX-385257781 8 17999765 ACAATGTTAAAAACATGCTTTCTACAGCCTTAGGT[A/G]TGAAATTATTAGATAGTGGGTCTATCTAGACTTAT R 2 1 2 1 101000 f 74 goat snp24587-scaffold25-1124958 8 18505833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380415 Affx-122975311 AX-123250773 8 18050225 AATGTGTAGTTTTAATACTTTAGCTGAGATGAGGG[A/C]AACTCCTACCATATTTCAAAGAAAGAAAACATGTC M 2 1 2 1 101000 f 74 goat snp24586-scaffold25-1074498 8 18556391 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273337 Affx-1111833568 AX-519546976 8 18052126 GCATTATTCATTATATATTGACTCTTTTTTAATTT[A/C]TTCTAGGTCCTTGTTAAACCTTTCTTGCATCTTCT M 2 1 2 1 303000 f 74 goat 8_18052126_AF-PAKI 8 18052126 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450405 Affx-122922068 AX-123320740 8 18079221 AATATAGCAGAGGCAAAGGAAGGAATGACTCTGCT[G/T]AAGAATTGGGGGAATGAAAACAAGTGAAGCAAAAT K 2 1 2 1 102000 r 74 goat snp24585-scaffold25-1045502 8 18585488 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796372 Affx-122975289 AX-385283322 8 18148549 CAAAGGAGCAATATCTTATCTCCCTACTTTATCAA[C/T]AGACATATCAATTTGGGGAAAAATGATATTGTCAG Y 2 1 2 1 202000 r 74 goat snp24584-scaffold25-976174 8 18655976 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777451 Affx-122929252 AX-385264571 8 18190835 TGCTTTGCATGCATATCTATTCTCCTTCTTATTCC[C/T]GAATCAAAGAAAATCTTATTAGACTTGAATTTTTA Y 2 1 2 1 101000 f 74 goat snp24583-scaffold25-933888 8 18698182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423874 Affx-122942307 AX-123294220 8 18220804 CCTGACTTTTGTAGACCTAATGCTTTTACCCCTGT[C/T]CTTTTTTTGGCTAAAGTTCACAACTATAGGTTATT Y 2 1 2 1 201000 r 74 goat snp24582-scaffold25-903919 8 18728135 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798085 Affx-122970555 AX-385285020 8 18251938 AAAATAGACGGCAAGTCCAGTGACAGTTTAAATTA[C/T]ACATCAGTGCTAGATACTTATGCTAACATCTTCAT Y 2 1 2 1 101000 f 74 goat snp24581-scaffold25-872785 8 18759801 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397528 Affx-122962044 AX-123267883 8 18289480 GCATTATGCTTTATTCAAAGAAATGGTTGTCTCCA[C/T]GAAGAAATCAGACATGTAGATAGTAATCACAACTC Y 2 1 2 1 101000 f 74 goat snp24580-scaffold25-835243 8 18797742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409608 Affx-122953551 AX-123279959 8 18333793 CCTCACTCCTGGGCCAATGTATCAGCTTATTAAAG[A/G]GCCACTGAATAGGGACTCATGCCCTCTGCTATTTA R 2 1 2 1 101000 f 74 goat snp24579-scaffold25-790930 8 18841786 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769488 Affx-122959045 AX-385256658 8 18426279 TCCTTACAAGTCAATCTATGTTTTCTCCTCTTTCT[A/G]TTTTCAATAGAAAGTAAGAGTGTTAAAAGTTACTG R 2 1 2 1 102000 f 74 goat snp24577-scaffold25-698444 8 18934213 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443587 Affx-122927325 AX-123313924 8 18469829 CTGTTTCAGAGGTAGTGTCTTTACATCTGTTACAG[C/T]GCTTGAGATTGATCTGTGCTTTTTGTCTTGTCTTT Y 2 1 2 1 101000 f 74 goat snp24576-scaffold25-654894 8 18978776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786991 Affx-122919867 AX-385274019 8 18504418 CAGAAAAATCCCACACCATGTTATTAGTTCAAAGA[A/G]CTAGCTAGTGGCAAGAAAGTTTCCGATCTTAATAT R 2 1 2 1 201000 r 74 goat snp24575-scaffold25-620305 8 19013543 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38404823 Affx-122956643 AX-123275175 8 18556179 AGTTGAACTCTTAGTTTTCATGTAGATTCAGAGAA[G/T]AATATTCCCTAACTCTGTCTTTCATTCTTCTTTTT K 2 1 2 1 101000 f 74 goat snp24574-scaffold25-568544 8 19065654 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424811 Affx-122941378 AX-123295157 8 18592582 TGTCCTTTGCTTTTTTGTTAATTTTGATTGAGTTC[A/G]TTTCTTCTTAGAACTTTTTTTTAATGTATAATTTA R 2 1 2 1 303000 r 74 goat snp24573-scaffold25-532141 8 19101919 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425686 Affx-122940858 AX-123296032 8 18634196 GAAGGTATATCCCAGGTTAAGTGTTTTTATCACAA[G/T]AAAATGCTTTTTAAAAATTTAAAAAGAAGATAGCA K 2 1 2 1 103000 f 74 goat snp24572-scaffold25-490527 8 19144700 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784101 Affx-122958750 AX-385271153 8 18693708 GTGGCTTTTTATGTATTAAATATGGCGATGTCTAA[C/T]ATCTTTCAAAAAATTGGATAGTATGGTAAGACTTA Y 2 1 2 1 101000 r 74 goat snp24571-scaffold25-431015 8 19203567 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394764 Affx-122964841 AX-123265119 8 18751698 AGACTCTGAAGGTGCAAATAAGTTACATGAAAAGA[C/T]GGCCCAAATACCTGTGGTCGCTAATCTTGCTACAC Y 2 1 2 1 101000 r 74 goat snp24570-scaffold25-373025 8 19261904 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405768 Affx-122956493 AX-123276120 8 18785693 GAGAGCCTTAGGCTTAAACTTAAAATTCTCACTAT[A/C]GAGGTAAAATTTCCACCCTTTTATGGGAAACATAA M 2 1 2 1 101000 r 74 goat snp24569-scaffold25-339030 8 19296658 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377293 Affx-122978115 AX-123247652 8 18824507 AATAACCTTCTTACATCCTCTCCACACTGGGTTCT[A/G]AAGCTAGCCATATCTCCAAAGGGAATGATTAAATT R 2 1 2 1 201000 r 74 goat snp24568-scaffold25-300216 8 19335443 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405170 Affx-122956936 AX-123275522 8 18857809 TGGAACCCTCATGAATGGGATTAGTGTACTTAGAC[A/C]AGACTCAAGAGAGATTTTCTCTCTCTGCCATGTGG M 2 1 2 1 101000 f 74 goat snp24567-scaffold25-266914 8 19368814 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394619 Affx-122964410 AX-123264974 8 18908325 GGAGGAAACCACAATATCCTTAAGTAGGTAATGTG[C/T]AAATAAACTGTAGTATATCCAGGCAGTAGAGTACT Y 2 1 2 1 101000 f 74 goat snp24566-scaffold25-216398 8 19419757 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789190 Affx-122936865 AX-385276202 8 18951679 TTAGTATGCCCCAGTACTGTGAATAGATACAGTCT[A/G]TATTTGTCTGGTTCCGAGTTCTATGAAGGGCCTCC R 2 1 2 1 101000 f 74 goat snp24565-scaffold25-173044 8 19463548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790907 Affx-122941327 AX-385277904 8 19012247 AGTTAAAAATTGCATTATATTGCAGGTTTTTAAAA[C/T]GTGAAATGTGTATCTGGAAAGCTGACAACAAATCT Y 2 1 2 1 102000 r 74 goat snp24564-scaffold25-112476 8 19522821 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423967 Affx-122942134 AX-123294313 8 19060749 GAAGCACCACCAAAAGACACAGTAGTCGCATCAAA[C/T]AGGTAAACTCTGAAGGAGGCATGAGGGATAAGCAA Y 2 1 2 1 101000 r 74 goat snp24563-scaffold25-63974 8 19571702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278760 Affx-1111836498 AX-519552233 8 19088372 AAAAACTAAGATAGAGGGCATGGGCCTGTAATCAT[A/G]GTTACTTATGAGGAAACTCAAGCAAGTAATTGTGC R 2 1 2 1 101000 r 74 goat Random2.2K-875 8 19088372 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417659 Affx-122946838 AX-123288007 8 19116617 CTACTGGTTTTTTATTAGAAAAACCAGGGCTCTCC[A/G]TTGCCTAAAAAAATACCCTAATTATCTGTGTAACT R 2 1 2 1 103000 f 74 goat snp24562-scaffold25-8106 8 19628069 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390499 Affx-122967256 AX-123260856 8 19130536 AATGGCATTGTCTCAGGAGTACCTTCTATTACCCC[A/G]CCCTACAGGTTTTTCCTTAGCTACTGCTGTCCACG R 2 1 2 1 201000 r 74 goat snp1273-scaffold1034-5714 8 19656739 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801603 Affx-122957331 AX-385288512 8 19179274 TAAATTCTTTCCCAACTGCTAAATCTACCACACAC[A/G]CATACATATATCTGCTTCAAAATTGTGAGAGAGAC R 2 1 2 1 101000 f 74 goat snp1274-scaffold1034-54452 8 19705971 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383597 Affx-122972566 AX-123253955 8 19207970 TTCTCGCAGCAACACAAATGTTGTGCTGCATGTAC[A/G]TTGACCACCTCAAGCCCATGGAGCACGCATGTAAT R 2 1 2 1 101000 f 74 goat snp1275-scaffold1034-83148 8 19734654 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384500 Affx-122973056 AX-123254858 8 19240523 ACAAAGGCCTATTAAAATTCTGAAGGATGGAGCCT[A/G]CCCATCACAAATACCAAGGTGGTGGGTGAGCAAGA R 2 1 2 1 101000 f 74 goat snp1276-scaffold1034-115701 8 19770356 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413981 Affx-122950290 AX-123284330 8 19324204 GTGGGGGTGGTGAAAGGGAAATGCTTCTGTCTTTA[C/T]GGTTTTGTTTTTCTACCAGATGATTAGAAAGCGAA Y 2 1 2 1 201000 r 74 goat snp1278-scaffold1034-199382 8 19855553 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419726 Affx-122945900 AX-123290074 8 19363212 AACAAGATGAGAGGGTTTAATCTCCAAGTAGTCCA[C/T]AGTACTCTTAGAAACACAGAATTTCAGGCAGTAAG Y 2 1 2 1 101000 f 74 goat snp1279-scaffold1034-238390 8 19894632 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382088 Affx-122974905 AX-123252446 8 19392592 CTGTGAATTCTTGCCATGCAAAACTCACAGGATCT[A/G]CTAAAGGAGATGTGAGAGGTAGGGTAGAGAACAAA R 2 1 2 1 101000 r 74 goat snp1280-scaffold1034-267770 8 19924009 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453481 Affx-122919838 AX-123323814 8 19470453 TCATCTCTGCATAGAACACCTCCACATCCATTTTA[C/T]CCTCAGAGAAGGCTGGAGCAGTGAAGTTAAACTAC Y 2 1 2 1 202000 r 74 goat snp1282-scaffold1034-345631 8 20001865 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424360 Affx-122941851 AX-123294706 8 19506285 AATCATTTTCAGTTCTTTTTAAAAATCTTCTTACA[C/T]GGTTAATTACCACTTGGCCATGGCATTGCTCTTCC Y 2 1 2 1 101000 r 74 goat snp1283-scaffold1034-381463 8 20037814 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428183 Affx-122939023 AX-123298526 8 19560799 GACTCACAATGACCAGAGCTGCTGTGGAGAGAGTA[C/T]AGCCTTCCCAGGGGCAGGGAAGGAACTTAGGCTCC Y 2 1 2 1 101000 f 74 goat snp1284-scaffold1034-435977 8 20093874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433923 Affx-122934301 AX-123304264 8 19615344 TCCAAGATACTGTAATACTCAAGATATGGAAGCTA[A/G]TCAGCTATTCAGCTGCAAAGTAGAAGAATATTGGT R 2 1 2 1 101000 r 74 goat snp1285-scaffold1034-490522 8 20149313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376107 Affx-122978887 AX-123246466 8 19657145 GGCATAGCCAACACTGGGACCCAGTTACTAAACTC[A/G]TTTTACACAACTTGCCTTTTTACAAAATGTTCCAT R 2 1 2 1 201000 r 74 goat snp1286-scaffold1034-532323 8 20191891 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381274 Affx-122974475 AX-123251632 8 19736994 GTCAATATGAGTATCTCATCTAGATTGTAATTTAC[A/G]TTATGTGGCAGCGTCTACTTCTTCATACCTGTTCA R 2 1 2 1 101000 r 74 goat snp1288-scaffold1034-612172 8 20272644 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779675 Affx-122974064 AX-385266775 8 19775397 AATGGGCAAAAAACATAGACATTGCACAGAAAAGA[A/G]AAACAAATAGTCCTTAGATTATGAAAGGATTTTAC R 2 1 2 1 101000 f 74 goat snp1289-scaffold1034-650575 8 20311563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786389 Affx-122977714 AX-385273423 8 19804487 CTTAAGCGATTTCACTTTCCTTTTGTATTGCTTTC[A/G]CATTTACAGTGGAGGAGGAAAGTACTATTAATCTC R 2 1 2 1 102000 f 74 goat snp1290-scaffold1034-679665 8 20340602 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402292 Affx-122959101 AX-123272645 8 19849275 GGAAACTTCCTTAGCATGGGATTCTCCAACTTACC[A/G]GAGATTCTCAAACTTTTTTCCTTTGGACCTCTTTT R 2 1 2 1 201000 r 74 goat snp1291-scaffold1034-724453 8 20385156 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432082 Affx-122935875 AX-123302423 8 19892385 AAACTGCACTCCATAGTTGACTACTTAAGAACCAT[A/G]CTGTAGATCATTAACATATTAAAATTATGTTAAAA R 2 1 2 1 101000 f 74 goat snp1292-scaffold1034-767563 8 20428310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452021 Affx-122920907 AX-123322354 8 19979743 TTCCTATTAAATCTTTATTTTTCTGATTTAAGAGA[C/T]GAGAGAGCATTTGTTCTTTTGGAGGTAAGCTACTC Y 2 1 2 1 101000 r 74 goat snp1294-scaffold1034-854921 8 20515844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442476 Affx-122927935 AX-123312813 8 20040912 AAGCAGAGCAATCCAGTTTCACCCCATACATAGGC[A/G]TCTGGGGCACCCAGCAGTGGTAGTGGTGGTGCTGC R 2 1 2 1 101000 f 74 goat snp29180-scaffold314-39651 8 20578932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802877 Affx-122964924 AX-385289775 8 20079991 GTCCCTGACCTGGCTCAGTTCTGAATTTACCTCAA[G/T]AAAGGCTTTTATTACCCCATTCAGGCTAATGTACT K 2 1 2 1 201000 f 74 goat snp29181-scaffold314-78730 8 20617665 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771676 Affx-122937254 AX-385258834 8 20116164 CAACGTCCCTGTTTTTGGGAGTTTCCTTCATTCTC[A/G]TGAGGAGAGTCGCTAACAGTGAGTTACTGCCACTT R 2 1 2 1 101000 f 74 goat snp29182-scaffold314-114903 8 20653676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380622 Affx-122975239 AX-123250980 8 20148959 GGTGAGCTGGAGTTTTCCAGGTAGAAACCAATGAA[G/T]AATCTCACACAGAACCAAGAGCCTGCGCCCAAGGC K 2 1 2 1 101000 f 74 goat snp29183-scaffold314-147698 8 20686488 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802642 Affx-122930913 AX-385289543 8 20200664 CATACTTTTATTGGCATGTAGATACGTGTGATCTA[C/T]GTTGATGACCGTGGTATGAAATAAAGGTCAAATAT Y 2 1 2 1 101000 r 74 goat snp29184-scaffold314-199403 8 20738389 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793689 Affx-122923717 AX-385280661 8 20232738 CTGAATCCACCAAATTTTTCTAAATTAGCAACACT[A/G]TCTCTTTTAAACTTTGCCCTTTTACCCACACATAT R 2 1 2 1 101000 f 74 goat snp29185-scaffold314-231477 8 20770599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418742 Affx-122946216 AX-123289090 8 20264253 CCACAGGCAAATGTCAACAGGTTGGAAAGCATGCC[A/G]CCTCTCCCGAAGACAAATGAAGAGCGCTTGTTCTG R 2 1 2 1 201000 f 74 goat snp29186-scaffold314-262992 8 20801897 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416347 Affx-122947891 AX-123286696 8 20301900 GGCCATTATGCTAGCATCCATACATGACACACAAA[G/T]AAACAGAAAATTATACTGTGCTCACGGGTTGGAAA K 2 1 2 1 303000 r 74 goat snp29187-scaffold314-300639 8 20839397 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413574 Affx-122950586 AX-123283923 8 20344642 TGACTTGATTAGTTGCCAATTATTACACAAATTAT[A/G]CTCCACCCAAACACACTGCCGTCACAGACAGGAAA R 2 1 2 1 201000 f 74 goat snp29188-scaffold314-343381 8 20882265 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383154 Affx-122973237 AX-123253512 8 20374336 TCACTGTAACCTCCTCTCTCCCAACAATCAAAAAT[A/G]TCAGGAAAAATCTAGAGCAGAATCCTCAACTTTAA R 2 1 2 1 101000 f 74 goat snp29189-scaffold314-373075 8 20911878 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425546 Affx-122941445 AX-123295892 8 20417952 ATTCTTAAATTTTGCTCAGCATGAGATCTAGAAAT[A/G]TCAGCTATTATTTTTTAATTGCTCTGTCATCTCAT R 2 1 2 1 101000 f 74 goat snp29190-scaffold314-416691 8 20956708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411089 Affx-122951927 AX-123281439 8 20470791 TCATTATTAAAATTGGCTCATATAGGCCATCCTCA[C/T]CCTCAATTTATTGTGGAGAAAAATAAAATATTTTT Y 2 1 2 1 101000 f 74 goat snp29191-scaffold314-469530 8 21010556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388750 Affx-122968952 AX-123259108 8 20546954 GAGACCCTTCTTAAAAAAAAGAAAAGCATAGTTCT[A/G]TTGCTTCCTTTTCTAATATTCAGACTTGACAGATG R 2 1 2 1 101000 r 74 goat snp29193-scaffold314-545693 8 21086959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396410 Affx-122963008 AX-123266765 8 20591194 CTGCAGTGCAGGAGACCAGGGTTCGATCCCTGGGT[C/T]GGGAAGATTCTTTATGATTTGCCTCTGAAGAAGAG Y 2 1 2 1 103000 r 74 goat snp29194-scaffold314-589933 8 21130076 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454298 Affx-122919262 AX-123324631 8 20645352 GGAAATTCTGTAGTGTGGATAGCTGGAATGAGGAG[C/T]GGAAAAAGGAATGTGGGCCTGAGCCACAGCCATTG Y 2 1 2 1 101000 f 74 goat snp29195-scaffold314-644091 8 21183755 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273376 Affx-1111833569 AX-519547008 8 20671941 AAGGTTGAGACATACTCAAGTTCAGTCACACAGTA[A/G]ATTAGTAATGGAATCATATCCAGCCTTTGCACATT R 2 1 2 1 201000 r 74 goat 8_20671941_AF-PAKI 8 20671941 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320772415 Affx-122927514 AX-385259567 8 20683297 AAGTGCAACCATTTAATTTTCAGTTTCAAGTGAAG[C/T]GCCAAAGTGATTTATGTCGTAGACTAACTTGAAGT Y 2 1 2 1 201000 f 74 goat snp29196-scaffold314-682036 8 21220165 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435578 Affx-122933368 AX-123305918 8 20745830 CAAGCAAATTATTTTGGTTTATCAGGAATAACAAT[A/G]GTAATGTAAATTTTCTCTCTTTATTAGCTTTACAT R 2 1 2 1 101000 f 74 goat snp29197-scaffold314-744569 8 21283931 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435200 Affx-122933637 AX-123305540 8 20778828 TTGATTGAGAGGTATAACTGCTCTATTGGGCCTCA[C/T]AACTTGGCAGCTGGTTTCTTCAATTACACTTTTTA Y 2 1 2 1 101000 f 74 goat snp29198-scaffold314-777567 8 21316401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450335 Affx-122922123 AX-123320670 8 20809516 TCCTGAGCTAATTCCTAGGAAGCAAACTACACTGT[A/G]CCAACTACTTTTTATCTGTGAAATATTTATTGATG R 2 1 2 1 101000 f 74 goat snp29199-scaffold314-808255 8 21347370 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404810 Affx-122956653 AX-123275162 8 20847893 TTAGCAACTTAGGCTTTAGAATGCACTTGGAAATT[A/G]TTAGGGCATGCTTATTTTATTATGTTCTTTCTTTT R 2 1 2 1 101000 f 74 goat snp29200-scaffold314-846632 8 21388282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777658 Affx-122961336 AX-385264777 8 20920402 TTATAACTCAACATTCTATATTATTTGAGGATAAT[A/G]TATAGATTATTCTCAGTACATTCCAAAATCTATTT R 2 1 2 1 202000 f 74 goat snp29201-scaffold314-919141 8 21462415 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401605 Affx-122959621 AX-123271958 8 20977766 TGGGTTAGATAACTACAAGGGGACGCATAAGAAGG[C/T]AGGAGAAAAACAAGACAATTGAGCCATAACATTTT Y 2 1 2 1 101000 f 74 goat snp29202-scaffold314-976505 8 21519259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448867 Affx-122923276 AX-123319202 8 21014533 AGAAAAGAATAAATGTATGCAGCAGATGAACATAC[C/T]AAAAGGCTGAAATCAATAAGATAATTCTTTACAAA Y 2 1 2 1 201000 f 74 goat snp29203-scaffold314-1013272 8 21555954 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423494 Affx-122942565 AX-123293840 8 21045137 AAAATGAGGTGATAAATACATTCTAAACAAATGAG[C/T]AGACAAAACTTCAGAAAAAATGAAAACTAAATGAA Y 2 1 2 1 101000 f 74 goat snp29204-scaffold314-1043876 8 21586482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399041 Affx-122960917 AX-123269396 8 21080380 TGATTTCCCTTGCCCAAGCCTCCAGGACCAACTCT[A/G]CAGATGCTCTAAGCACAATATAATTGGGATATTCT R 2 1 2 1 101000 r 74 goat snp29205-scaffold314-1079119 8 21622401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273498 Affx-1111833635 AX-519547114 8 21086275 CAGAAAAAGATAAT[A/G]CCTCCAAATCCCTTTGTGAATATTCTTCATCAATT R 2 1 2 1 101000 r 74 goat GoatD01.000042 8 21086275 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38442034 Affx-122928402 AX-123312371 8 21129243 TATATGCATCATACCACTAATATCCCATTGCCTGG[A/G]ATTCAGTCAAATACTCACACCTAGCTATAAGGAAA R 2 1 2 1 201000 r 74 goat snp29206-scaffold314-1127982 8 21671143 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791282 Affx-122942269 AX-385278276 8 21270960 AGAAGGAATGTTGATAAGCTTTGAAGAAGAGGTAG[C/T]GCTCAAGAAGGATCTCAAAATTTGCAGTCCTGTAT Y 2 1 2 1 101000 r 74 goat snp29209-scaffold314-1269699 8 21811787 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383542 Affx-122972618 AX-123253900 8 21388419 CCAACCCTCCCCTCATACACCTTCAGGGACATGTC[G/T]TCTTCTCTGTCTCCCTCAAGGATAACTGAGATGAT K 2 1 2 1 101000 r 74 goat snp29211-scaffold314-1387158 8 21929256 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769562 Affx-122926002 AX-385256732 8 21435882 TCCAACTCTACATTTGCAAGTTTTGTGATCTTGGG[C/T]AAGTTACATCCCCTTATTGAGATTCCATCTTCTTA Y 2 1 2 1 101000 f 74 goat snp29212-scaffold314-1434621 8 21977406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449082 Affx-122923605 AX-123319417 8 21477969 AGTAAATTCTCAATGTAGTTAGAATGTTAGCCAAA[C/T]GGTTTTCTGTTTGACTGAGCCCCAGCCCTTCTCTG Y 2 1 2 1 101000 f 74 goat snp29213-scaffold314-1476708 8 22019588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773564 Affx-122926554 AX-385260704 8 21522125 GTGGCAAAAGTGGGCCATGAACCAACAATGTCAGC[A/G]TCTTGGTTGAATGCTCCCTCTAAACCAGTTATGTA R 2 1 2 1 101000 f 74 goat snp29214-scaffold314-1520864 8 22064513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438485 Affx-122931226 AX-123308823 8 21560314 CTGTTTCACAGAGAAGACAAAGGCAAATAGGCAGA[A/G]AAGCAGGCACGTGGTTAGCGTCCACGTGACACAAG R 2 1 2 1 101000 f 74 goat snp29215-scaffold314-1559053 8 22103244 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775516 Affx-122931094 AX-385262647 8 21594140 ATCTCCAGGCCTAAAATAATGGGAATCTGCTCATA[C/T]GCTACTGTCTGGAATTTCTATAAAACTTTTCTCAG Y 2 1 2 1 101000 f 74 goat snp29216-scaffold314-1592879 8 22136796 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447394 Affx-122924413 AX-123317730 8 21623712 CCAGAGCTCCCCCAGTGGTTTCTGAGGGCAACTGG[A/C]GCGGATACCTCCCCACCTCTGCGCACTGGGATTTG M 2 1 2 1 101000 r 74 goat snp29217-scaffold314-1622451 8 22166523 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443364 Affx-122927415 AX-123313701 8 21705038 AGATATACATTACTAAAGGACTGAGAAACAGACTA[C/T]AGTGGGGAGTAATTCTGAGGGAAAAATGATCTTTC Y 2 1 2 1 101000 f 74 goat snp29218-scaffold314-1703777 8 22249506 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792425 Affx-122960467 AX-385279406 8 21735860 GACGAATTACTAGAAACCTAATGAAGTCACCTGAG[C/T]AATTTTTTTTCAATGAATAGCTTTAAATCTATTGT Y 2 1 2 1 202000 r 74 goat snp29219-scaffold314-1734599 8 22280346 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392828 Affx-122965780 AX-123263185 8 21764421 TTATGCTAGAATCCTCTCATCAGTTTCCTGTCCAC[A/G]TTTTTGTTTTGTTTTGTTTTGTTTTTAAATGAGTG R 2 1 2 1 101000 f 74 goat snp29220-scaffold314-1763160 8 22308911 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428187 Affx-122939020 AX-123298530 8 21809526 AATACTCCTTAAGTAGTATATTGACTGACAGACAT[A/G]TTATAATGTAATTGGTTAATTTATCAACTTGGGTA R 2 1 2 1 101000 f 74 goat snp29221-scaffold314-1808265 8 22354231 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767405 Affx-122955252 AX-385254678 8 21875642 AATATTAAAGGATTTAGAGACAAATACATCCTTTA[C/T]AGCTAATTTTACCTTACTTTTTCCATGGAAGGTAA Y 2 1 2 1 201000 f 74 goat snp29223-scaffold314-1874381 8 22421361 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382631 Affx-122973690 AX-123252989 8 21935521 GGCTCCAACTAATTCTGTTCCTCTCTGTGTGTACA[G/T]ACTGTCCCTCCCACCAAGAGTCAGAGTTTGTGTTT K 2 1 2 1 101000 r 74 goat snp29224-scaffold314-1934260 8 22480961 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse538 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38427708 Affx-122939285 AX-123298051 8 21995538 CTGTTGGATTAAGATAGTTTTTGTTTGGGTTGATA[A/C]TATTTGAGATGAATTATCCTTTCTTTGGCTCTTTT M 2 1 2 1 101000 r 74 goat snp29225-scaffold314-1994277 8 22540776 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse539 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38382183 Affx-122974018 AX-123252541 8 22044101 GATTAGATGAGGCCCATCCACAATATGAAGGACAG[G/T]CAGTCTCACTCAGAGTCCATTGATTTACGTGTAAG K 2 1 2 1 201000 r 74 goat snp29226-scaffold314-2042840 8 22589340 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse540 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320789005 Affx-122938155 AX-385276018 8 22075692 AGCTGCCTGTACATATTTCTAGCTTTCTTTTATAC[A/G]TATAAGCAAAGGCATTATTTTAGATACAAGGCAAT R 2 1 2 1 101000 f 74 goat snp29227-scaffold314-2074431 8 22619260 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse541 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38395514 Affx-122963876 AX-123265869 8 22133514 CTCCCGTCCATTAAAACATCCATGCCTCTTCTTGA[C/T]GGCACATTCTTTCTTTGGTCTTGAAGCTGGGCAAA Y 2 1 2 1 303000 f 74 goat snp29228-scaffold314-2132253 8 22651131 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse542 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38445255 Affx-122925478 AX-123315592 8 22172553 CCCTATGGACTGTAGCCCGCCAGACTCTTGTGTCT[A/G]TGGGATTTTCCAGGTGAGACTACTACCCAGGTGGT R 2 1 2 1 303000 f 74 goat snp29229-scaffold314-2171292 8 22668553 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse543 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320776314 Affx-122940330 AX-385263442 8 22228923 CTGCTCATCTAGACCGTGATGCCTGCGCACACTGC[A/G]TGCACTGAGCCCTCACTTAATTTCCTAGTTCATTT R 2 1 2 1 202000 f 74 goat snp11616-scaffold1428-15423 8 22824078 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse544 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38445415 Affx-122925376 AX-123315752 8 22324402 GAAGGATCTAGAAAGACAAACCTTACAGTGGACAG[C/T]GGCCTCAGGGTCCCCCTTGCTAGTGGACAGCCACC Y 2 1 2 1 101000 f 74 goat snp11618-scaffold1428-110902 8 22934016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse545 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320800102 Affx-122964266 AX-385287025 8 22377162 GAGATTTCTCTAGACTTAAGACCACCTCCCTTACT[A/G]CCCCACAAAGCCATTTAGCATTTGCAGGGGCTTAA R 2 1 2 1 102000 r 74 goat snp11619-scaffold1428-163662 8 22987453 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse546 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320786916 Affx-122923155 AX-385273945 8 22417990 CCTGGCTGTCAGGGTAACTGGAGGAATATTTCAGC[C/T]CTTGTGTTTGCCCTTAATTCCTCTATTATCTATGG Y 2 1 2 1 101000 f 74 goat snp51941-scaffold764-33021 8 23216101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse547 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38452070 Affx-122920871 AX-123322403 8 22457384 TACTAACAAATGAAAGACAAACTCTATATTCCCCA[A/G]TCATCTATTTAATCCTTTTAAAAGGCAATGTGTCC R 2 1 2 1 201000 r 74 goat snp51942-scaffold764-72415 8 23255940 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse548 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38376513 Affx-122978014 AX-123246872 8 22504770 CCAACTGGCACTGAGGCCAAGGAGGAGAGGGGCAG[C/T]GTGATCTGCCCATGCAACCACTGCGGCTGCAAAGA Y 2 1 2 1 101000 r 74 goat snp51943-scaffold764-119801 8 23303895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse549 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320771155 Affx-122969778 AX-385258315 8 22551320 AATACAACATAGGCTTAACACCTGGCCTGAATCCT[A/G]TAATAACCCACAATGGCCAATATTAAGACTTTGGA R 2 1 2 1 101000 f 74 goat snp51944-scaffold764-166351 8 23343826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse550 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38377194 Affx-122978191 AX-123247553 8 22582865 TTGTGTGCTGTTTGCTTTGCTTTCCTGCTAACCCT[A/G]CTTTCCCATCTATAATCCCATTCTACATGAGGTTA R 2 1 2 1 201000 r 74 goat snp51945-scaffold764-197896 8 23375283 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse551 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320764937 Affx-986697118 AX-385252518 8 22627278 TCCAATCCAAAAACTGTAGGGTATTCCTGAGGTGG[C/T]CATCTGCTACTATATGGTGCCCAAGAATTGCTGGG Y 2 1 2 1 600010 r 74 goat 8_22627278 8 22627278 Ancestral_priority_1043 ancestry 0.732 recommended IMAGE 10K 10K ancestral 320764941 Affx-986697120 AX-385252522 8 22628346 ACCTACGGCTCCCATGTGAGAACATTCTTTTCCTT[C/T]ACTTCTCTTTGCAGTCTTTAGTATAATTGAAATAA Y 2 1 2 1 600010 r 74 goat 8_22628346 8 22628346 Ancestral_priority_1043 ancestry 0.69 recommended IMAGE 10K 10K ancestral 320762592 Affx-986697122 AX-385250684 8 22628536 ACTCAACGTATGTGTATAATATGAATGGAACGAAT[A/G]AGTAAACAAATGTAAACACCCATTCCTTAATAATA R 2 1 2 1 600010 f 74 goat 8_22628536 8 22628536 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320764947 Affx-986697124 AX-385252528 8 22628612 AATGGAGGTTTGGATTTAATTTTTGAGTAAAGAAA[C/G]TCATTTTCTTTCATAAGAATTAATAAATAGAACAA S 4 1 2 1 600010 r 74 goat 8_22628612 8 22628612 Ancestral_priority_1043 ancestry 0.698 recommended IMAGE 10K 10K ancestral 320790436 Affx-122976962 AX-385277439 8 22639816 TCCTTTTAGTCATGTCATTATTTCTAGCTCAGTGG[C/T]GTTTATTCAGATGAGCACAATTTGCAACCACTGAG Y 2 1 2 1 101000 f 74 goat snp51946-scaffold764-254847 8 23431856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse552 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38425920 Affx-122941610 AX-123296266 8 22676333 ACGTGCCCAAGAATTCCTCAGATGTTTGCTACCAC[A/G]TTATCTGTAATGGCAGCAATAACAACAACAACAAA R 2 1 2 1 101000 f 74 goat snp51947-scaffold764-291364 8 23468406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse553 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38394221 Affx-122964894 AX-123264576 8 22706306 TTTTTACATGAGGATGCTCTTGGAGAAAATTCATA[C/T]CATAGGCCAAAAAGTAAAATCAACTCTTTTTTTTT Y 2 1 2 1 101000 f 74 goat snp51948-scaffold764-321337 8 23498504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse554 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320777274 Affx-122942183 AX-385264396 8 22753945 AATGCCAACATCCTCATCTGAGCAACTTAGAATCA[C/T]AATAATAAACTCAATCTTGTGTTGTTTTAAAGAAT Y 2 1 2 1 101000 f 74 goat snp51949-scaffold764-368976 8 23546204 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse555 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320797690 Affx-122978975 AX-385284629 8 22807290 TATAAGGTTTATAGTTGCTTTTATTACTTTATAGA[C/T]AGATGATATTCCCTTTCAATCTTAATAACTCCAAA Y 2 1 2 1 101000 f 74 goat snp51950-scaffold764-422321 8 23598756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse556 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38437653 Affx-122931795 AX-123307991 8 22895484 TCAGAGGCATTGAAAGGGTTTGCGTGCGTGAAGGA[A/G]AAGGAGGGCTAAACCTCATTTGCATGGTTCAAAGT R 2 1 2 1 101000 f 74 goat snp51951-scaffold764-510515 8 23687279 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse557 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38379701 Affx-122975901 AX-123250059 8 22934892 TAACTTGAAGAAGTATTTGCTTTCTTGTCTGTAGA[C/T]GCTGCTATTTCTTACATGATTCTTTGCACTCTGAC Y 2 1 2 1 101000 r 74 goat snp51952-scaffold764-549923 8 23725476 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse558 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38384856 Affx-122971952 AX-123255214 8 22974011 TTTATTTACAGTTTTAAACAAGTCACTTAAGCCTT[A/C]GTCATATCTTGTTTGTGGTGAAGTTGTATAGTGGT M 2 1 2 1 101000 r 74 goat snp51953-scaffold764-589042 8 23764611 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436982 Affx-122933151 AX-123307320 8 23019861 TGATGGACCTTCTGCAATATGGTATTCTGAAAAAT[A/G]TTTTGCCCGAGGTTTAACTTTAAAAGTGATAGTCT R 2 1 2 1 101000 f 74 goat snp51954-scaffold764-634892 8 23810468 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405522 Affx-122955989 AX-123275874 8 23048393 TTTAAGATGCACTTTATCTGATCTGACTCTTGACA[C/T]GGTAAAGAGCCTGCCTGCTCTGTGGGAGACCTGGG Y 2 1 2 1 101000 f 74 goat snp51955-scaffold764-663424 8 23839160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390757 Affx-122967900 AX-123261114 8 23098758 TCCCAAAGTAGATCTTACCAGTGGTTTTCCTTCAC[C/T]GTGTTTACCTGCTGCTCAAGCTGTCACTAATTGTG Y 2 1 2 1 101000 f 74 goat snp51956-scaffold764-713789 8 23889350 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797839 Affx-122944499 AX-385284779 8 23164900 ATTTGGGAGTAGATTTTTCTGCTGTTGATAAAAAC[A/G]TTCTTAATGAAGACTTTTGGATTAAAGTTGGATTG R 2 1 2 1 101000 f 74 goat snp51957-scaffold764-779931 8 23955349 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452291 Affx-122920689 AX-123322624 8 23196071 GGGGTTGAGCTCAGAGAGGCTGAGCAGCCCACCCA[G/T]CTGTACTTCCCCTCTGTCCCTCGAAGGCCAGCAGT K 2 1 2 1 101000 r 74 goat snp51958-scaffold764-811102 8 23987081 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398962 Affx-122960974 AX-123269317 8 23224937 GAACCCTGCCCTGGAAACTTAGCCTAGGATAAATA[G/T]CAGTGGGATCTGTCTTTCTCCTGTTGTTCACCTGG K 2 1 2 1 101000 f 74 goat snp51959-scaffold764-839968 8 24016541 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601277 Affx-1002480121 AX-413835710 8 23255181 CATAGGGAGATAACCATAGAAAATCAATTCTAGAG[C/G]ACAAAAATTTCCCAGGGAAATTAGACAGGAAGTTT S 4 1 2 1 201000 f 74 goat QTLAlpine8.0 8 23255181 G C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601418 Affx-1002480122 AX-413835838 8 23265704 GTTATTAAAGTGTGCAGGATACTGTCCATTAAAAA[A/G]CTGAAGCTCCATATCATGTAAAAGCGTTAAAGACA R 2 1 2 1 101000 r 74 goat QTLAlpine8.1 8 23265704 G A 1 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601307 Affx-1002480123 AX-413835737 8 23270477 CAGTTCAAAAGCATCAATTCCTCAGCATTCAGCTT[C/T]TCTTCACAGTCCAACTCTCACATCCATACATGACC Y 2 1 2 1 303000 f 74 goat QTLAlpine8.3 8 23270477 T C 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601308 Affx-1002480124 AX-413835738 8 23273348 TCTAGTTACCATCTGTTAAAATACAAATTTATTAC[A/G]AATATTATTGACTATATTCCCCTTGTTGGACATTT R 2 1 2 1 103000 f 74 goat QTLAlpine8.4 8 23273348 A G 1 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601423 Affx-1002480125 AX-413835842 8 23279660 AATCAAGCAGCTCTGCTGGAAAAAGAGGGGCTACA[A/G]AGTTGAAGCATATGCAAAGACATGACTGTAATAGC R 2 1 2 1 201000 r 74 goat QTLAlpine8.5 8 23279660 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601310 Affx-1002480126 AX-413835740 8 23286566 ACATCTAGGAATGGCATGGGTTAATAACAAAAGAG[A/T]AGCTCGTTAGAAGTGTCATTAGCTGAGCCAAATAA W 4 1 2 1 201000 f 74 goat QTLAlpine8.6 8 23286566 A T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320788243 Affx-122939779 AX-385275262 8 23293556 CAAACACCTCAGAAAATTCAGGTGCAGGTGGTCCA[C/T]GTGCATGTTTTGTAAACCACTGTTCAACATCCCTC Y 2 1 2 1 101000 f 74 goat snp51961-scaffold764-908587 8 24085048 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405968 Affx-122955536 AX-123276320 8 23352740 TGAGGGGGAAAATTAATATAAAGCATTTAGAGGGT[A/G]CTCAGTAGATACTGCTTTTTTTAAAGCTAAAAGCT R 2 1 2 1 101000 r 74 goat snp51962-scaffold764-967771 8 24144754 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273340 Affx-1111833570 AX-519546980 8 23387762 TCTCCACATACATTTTAAATCAGCTTGGAGAAACT[A/G]TTTTTAAAACCTGCTGTAATTTTAGTTACAAATGC R 2 1 2 1 101000 f 74 goat 8_23387762_AF-PAKI 8 23387762 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38430989 Affx-122936691 AX-123301330 8 23392930 GAATGCCAAATTATAGCTTCAAAGTGATTTGTCAA[C/T]GAAACTATTAATTTTCCTAAATGAATAATAAATTA Y 2 1 2 1 101000 f 74 goat snp51963-scaffold764-1007961 8 24185409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440447 Affx-122929402 AX-123310784 8 23447826 TCTGACGGTAGGGTGTCTACCACATCAACACAAAA[C/T]GACTGTGGACTTGGGTTGACCTGTGGATACAAGGC Y 2 1 2 1 101000 f 74 goat snp51964-scaffold764-1062857 8 24240487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790885 Affx-122922956 AX-385277882 8 23477973 TGGGACGTAATAAGCAACCTGCTCTGTAAGTGTCA[A/G]CTGTCGAAATCATCATCACGGCCACTTGGAAATTC R 2 1 2 1 101000 f 74 goat snp51965-scaffold764-1093004 8 24270756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402423 Affx-122958635 AX-123272776 8 23532990 CATGACAAAAAGTACACACAGCCTCTCAAAATTCC[A/G]TTTTCTCGGTGCCTATATACACCATGAACGAGTAT R 2 1 2 1 201000 r 74 goat snp51966-scaffold764-1148021 8 24320835 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410478 Affx-122952205 AX-123280828 8 23601537 GTTTCCTGGACTAACAGGAAAGGCTAGACAACGTT[A/G]CTGTGTTCAGATATATTGTTGTTGAGTCGATATAT R 2 1 2 1 101000 r 74 goat snp51967-scaffold764-1216568 8 24389358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438044 Affx-122931549 AX-123308382 8 23644133 ATTTAATCTCAGCTTGTCACATCTCCGTCCAGTCA[C/T]GGCTGGGCCTTATGTTGGCCAGCATCTGAGTTTTC Y 2 1 2 1 101000 f 74 goat snp51968-scaffold764-1259164 8 24432920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386638 Affx-122970218 AX-123256996 8 23693035 AACCCAGACTGGTTCCTATCTTTCTCTGCTCTGCC[G/T]CTCACCTTCTGGACCCTTTCTCTTCTGCCATTAGT K 2 1 2 1 101000 f 74 goat snp51969-scaffold764-1308066 8 24482600 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405252 Affx-122956877 AX-123275604 8 23723543 TACTTCAGATGATGGCCAAGCCCTTTAGATCTCTT[A/G]TTTATTTCATTAATAAATTGTTATTTTCCCAAAAG R 2 1 2 1 202000 r 74 goat snp51970-scaffold764-1338574 8 24513890 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388542 Affx-122969191 AX-123258900 8 23765050 AGGGATTGTCCTAGGGAATATTCAAATGCTATCTC[A/G]TGATTAAAGTTTCAGAAAAAAATGAAAGGGTTGAT R 2 1 2 1 101000 f 74 goat snp51971-scaffold764-1380081 8 24555691 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440020 Affx-122929773 AX-123310357 8 23799619 TCATCTCCTCTTCCCTTGGCTGCCAGCCTCGGACA[C/T]GCACAATTAACTGCCCTCTGGCGTCCTAAACAAAT Y 2 1 2 1 101000 r 74 goat snp51972-scaffold764-1414650 8 24590301 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426932 Affx-122940431 AX-123297277 8 23891086 ATGAAACGCTCATTACACCTAGGGTCCTGAAACAG[C/T]GACTTGTGACCAGAGGAAAAGAATGGAGACTCTAA Y 2 1 2 1 201000 f 74 goat snp51974-scaffold764-1506117 8 24681254 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396213 Affx-122963355 AX-123266568 8 23965576 ATAATCAGATACTTTCAAACCGTACCACCTCGCTG[C/T]GTCCGAAGGTTTAGGACCCAGACACAGAACAGCAG Y 2 1 2 1 101000 f 74 goat snp51976-scaffold764-1580607 8 24755676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794660 Affx-122962083 AX-385281621 8 24053187 TTTCAAATAAGGTAACAAATATGCTTTGCAAGTTA[A/G]TCATAAGGTTACTTGGGCATTTTCAGTAGTACATA R 2 1 2 1 101000 f 74 goat snp51978-scaffold764-1668218 8 24842890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786722 Affx-122947785 AX-385273753 8 24083765 AATGATGATGTCATGAACAAGTATTATAATTATTA[C/T]AATTCTGTATACCCTAAGTTCAAAAAAACAGTACT Y 2 1 2 1 101000 f 74 goat snp51979-scaffold764-1698796 8 24873513 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789874 Affx-122961043 AX-385276881 8 24113932 TCATCTAGTTTAATATAAATACAGATTGTGACATA[G/T]AGGTAGAGTTACAGACATAGGTATATAATAGGTTA K 2 1 2 1 101000 f 74 goat snp51980-scaffold764-1728963 8 24903518 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793956 Affx-122937932 AX-385280925 8 24148631 GATAAATGAGTTGTATTATGCACAAAAAATTTTAA[A/G]TCATTCTATTTCACCATGCTGCCTGCAAACTAATC R 2 1 2 1 101000 r 74 goat snp51981-scaffold764-1763662 8 24938136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392165 Affx-122966310 AX-123262522 8 24210720 GTGCATAATGCCAACCAGAAGATTCAGGATGCTCA[C/T]GATAAGCTCTATCTGTCCTGGCTGGAGTGGAAGAG Y 2 1 2 1 101000 f 74 goat snp51982-scaffold764-1825751 8 25000518 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386050 Affx-122971471 AX-123256408 8 24244229 ATTTCTCTTTATGTTAGGTTCTTTTACATTTGAGG[C/T]ATAGTTGGAGGACAAAGTAGTCTTCTTCTAATATT Y 2 1 2 1 101000 r 74 goat snp51983-scaffold764-1859260 8 25032736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427505 Affx-122939996 AX-123297848 8 24286544 AAGGAAAACAATACCTTGTTCTGGGTTTTTCTTTT[A/C]TTTTTTTAAAAATAGATTTACCTTAAGTTTTCTAA M 2 1 2 1 303000 r 74 goat snp51984-scaffold764-1901575 8 25075361 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445179 Affx-122925537 AX-123315516 8 24316337 TCTCAGTGCGGTGATTACAGGGGAGCTGTCTGTGT[A/C]TGTCCCCACTTCCATTCCTCCGGCTGAGTCACTGG M 2 1 2 1 101000 f 74 goat snp51985-scaffold764-1931368 8 25105228 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382096 Affx-122974897 AX-123252454 8 24400825 CTGCTGTACTTCTTCCCCCTTTCAGACATCACCAG[C/T]GGTTTCATGGAGGAGGGTCTGGGGGCTCAGAGAGA Y 2 1 2 1 103000 f 74 goat snp51987-scaffold764-2015856 8 25190305 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448744 Affx-122923325 AX-123319080 8 24433729 TTAATGGGTACAGAGTTTAGCTTGGGATGATGAAA[C/T]GGTTTTGAGGATGCACAGTGGTGATAGTTGAACAA Y 2 1 2 1 201000 f 74 goat snp51988-scaffold764-2048760 8 25222848 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792709 Affx-122966739 AX-385279689 8 24496008 AGCCAAGGCTCTGCTACCTTAGCCCTGTTTCAAAT[A/C]GCCTGAGAATATCTATGCAGCTCTTTCTTCTCCCC M 2 1 2 1 101000 r 74 goat snp51989-scaffold764-2111039 8 25285942 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441561 Affx-122928690 AX-123311898 8 24541599 TGGCCGTGAGTTTCTGGAACCAGGGAGGTAGGTAG[C/T]GAAACATTAGGCATCTCCACCCTGAGAGGTACTCG Y 2 1 2 1 101000 r 74 goat snp51990-scaffold764-2156630 8 25331679 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405312 Affx-122956836 AX-123275664 8 24592707 AACCCCACAGGTGAGACTGCAAGGACTCCACTTGC[C/T]AATTTCCCATCTGTGAAGAAATCAGAGGAAGAGAA Y 2 1 2 1 101000 r 74 goat snp51991-scaffold764-2207738 8 25382747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415636 Affx-122948581 AX-123285985 8 24638279 CAGCTTCAAGTCTTCCCTCAGCTAGACTTTAATAT[C/T]AATTTTACCATTTAAGAGATCAACAATAAAGCTGT Y 2 1 2 1 101000 f 74 goat snp51992-scaffold764-2253310 8 25428390 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450749 Affx-122921854 AX-123321083 8 24693287 TGTGATTTCTGCTTAGGAGCCCTGCCTATTGTTTC[A/G]CCTTTAATAAAAACAATTTGGGGGATGCTGAATTA R 2 1 2 1 102000 f 74 goat snp51993-scaffold764-2308318 8 25483324 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778463 Affx-122945665 AX-385265577 8 24728794 ATTCTTACTGTACCCTTTAAAATTAACTAACTTTA[C/T]GTCTATTTTACAAAAACAAAGCTGGACTCAGAAAG Y 2 1 2 1 101000 r 74 goat snp51994-scaffold764-2343825 8 25518918 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396098 Affx-122963423 AX-123266453 8 24760881 GGCTGCACAGATACTGTGTTGCTCAATAAAAGACT[A/G]TTGCCTGGATGGATGAATCAAGAAATTAACCATCC R 2 1 2 1 101000 f 74 goat snp51995-scaffold764-2375912 8 25551025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397236 Affx-122962371 AX-123267591 8 24818628 ACACTGTGTTCCTTCATCCTTTAGAGCCTCTGTAC[C/T]GGCTGTTCCTCCTCTCTGATTCACTCTTCCCCTGA Y 2 1 2 1 101000 f 74 goat snp51996-scaffold764-2433659 8 25609286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403928 Affx-122957469 AX-123274280 8 24859211 CCAAGCGGGAGTAAAAACCCATATGCTCAGCCAGC[A/G]TGGCATTGGAAAAAGGAAACGCATGCCTGGGGGAA R 2 1 2 1 201000 f 74 goat snp51997-scaffold764-2474242 8 25650269 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402028 Affx-122958742 AX-123272381 8 24909363 GGAAAAGCAAACATACAGTCAAGGATTATACCCTG[C/T]AGGACAAACAACCAGCTAACTATAATTTCAGAAAA Y 2 1 2 1 101000 f 74 goat snp51998-scaffold764-2524394 8 25700181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421908 Affx-122944248 AX-123292255 8 24939773 TTCATGTCTTCTATTCCTATTGCCTATTAATCTTC[C/T]ATCCTTCTACTAGAGCCCCACTGGCCTCCTTGTTT Y 2 1 2 1 201000 f 74 goat snp51999-scaffold764-2554804 8 25730849 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402943 Affx-122958176 AX-123273296 8 24997926 AGACAATACTTCATTGCTCCAGGGGTCTTTAAAAT[A/G]TACACACCTCATTTGGACATTAGCCTCTAAAATCT R 2 1 2 1 101000 r 74 goat snp52000-scaffold764-2612957 8 25789108 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791673 Affx-122950058 AX-385278664 8 25033884 ATTGTGTCAGGGGAAATGAGTTCTCATTTAAAATA[A/C]AAAGACTATTCATCATAGCAACAAAGTGTCTGACC M 2 1 2 1 101000 f 74 goat snp52001-scaffold764-2648915 8 25824536 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396267 Affx-122963312 AX-123266622 8 25065222 AGGCTTTCAGCCAAACCTTGGCTGTACAGGAGAAA[C/T]ATCCAGAGAGGCTTTTAAGAAATACAGATGTCTGC Y 2 1 2 1 101000 f 74 goat snp52002-scaffold764-2680253 8 25856056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421506 Affx-122943899 AX-123291853 8 25112661 ATGAAGCTCCTCCAGAGCTGCAGATGAGGCTCTTG[C/T]GGCAAATCTCCCCATGCATCTCCCAGTCCTGCTCC Y 2 1 2 1 101000 r 74 goat snp52003-scaffold764-2727692 8 25904031 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400318 Affx-122960059 AX-123270673 8 25141999 GCAGTATGAGTAAGTTGGCCCCAGGACAGATGGAG[A/C]AGGAGGAGAGAAACCTGGAAAGACACGTTAAAACT M 2 1 2 1 202000 f 74 goat snp52004-scaffold764-2757030 8 25933538 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274706 Affx-1111834451 AX-519548292 8 25172484 TATGGTGCCTGCCTTGTTGAGGGTAACAGACAAAG[A/G]AAAAGGCAGACCCCTGCTCTCTTAGAGCCTGCAGT R 2 1 2 1 201000 f 74 goat GoatD01.036502 8 25172484 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320783552 Affx-122920832 AX-385270614 8 25233986 AATAAATATTCCTGAGCACATAAGTCTATGAAGAA[C/T]AGTACACTAAAAGCTGCAAATAACTCAAAGATCCT Y 2 1 2 1 101000 r 74 goat snp52006-scaffold764-2849017 8 26025865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436434 Affx-122933004 AX-123306772 8 25265483 GGTGCTGGACTTCGGTGGTGAGCAAATCAGGCTCA[G/T]CTGGTCCCTGCCAGTGTGAGGTCCACACTCCAGTT K 2 1 2 1 201000 f 74 goat snp52007-scaffold764-2880514 8 26058187 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783650 Affx-122964010 AX-385270709 8 25299343 GCAGCATGGAAGCTTCTTATTGAAACAATCAATCC[C/T]GTATTGAAGAATGTCAGTCTCCAGAATGGCCAAAA Y 2 1 2 1 101000 f 74 goat snp52008-scaffold764-2914374 8 26092154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436733 Affx-122932302 AX-123307071 8 25368507 AAAACTCTAACAACTCTTCCAAGATAAAGATGCTA[C/T]GAACATGATGTGTTTATTCCCTGTTCCTAAAGTGG Y 2 1 2 1 201000 f 74 goat snp52009-scaffold764-2983538 8 26162251 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278761 Affx-1111836499 AX-519552234 8 25402021 AGACCTCTTCAAGTAGAATGCATGTTTTACTCTTC[A/G]ATGTTTTGTTATCTCAGCGTGAGTTAAAGGATTAT R 2 1 2 1 201000 r 74 goat Random2.2K-879 8 25402021 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382176 Affx-122974022 AX-123252534 8 25408869 GCCTCTACTGCCTTGGCCTCCCTGCTATTCCTCTG[A/C]GAGCAATTCCCACTGATCCAACATGATCCTCCAGC M 2 1 2 1 101000 r 74 goat snp52010-scaffold764-3023900 8 26203000 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772461 Affx-122974520 AX-385259612 8 25437893 TCATTAACTGTGTCTCAGTAGATGGGATTATTAGC[A/G]TATATTATATTCTCTTTGCTTTGTGTTCTGATTTT R 2 1 2 1 201000 r 74 goat snp52011-scaffold764-3052924 8 26231697 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425164 Affx-122941062 AX-123295510 8 25468403 AGACTGCCATCGCTGTGGGGAAGCCCAAATTTGCT[A/G]CATGAAGATGCCATGTGGGAAGGAGAGAGAAACTT R 2 1 2 1 101000 r 74 goat snp52012-scaffold764-3083434 8 26262376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791126 Affx-122931356 AX-385278121 8 25519855 GAACTAGAGTTAGATGAATTAACATGCAAATCGAC[A/G]TATTTAAGATTATTTCTGCTTCCTTCTAAGGGAAA R 2 1 2 1 201000 r 74 goat snp52013-scaffold764-3134886 8 26314247 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445485 Affx-122925201 AX-123315822 8 25561716 CTCCGTGATTCTCCCTCCAAGACCAGTCGGGTTCC[A/G]TGAAAAAGGGCCATTGTTCTCACATGCCCACTGAG R 2 1 2 1 101000 r 74 goat snp52014-scaffold764-3176747 8 26356400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802357 Affx-122961660 AX-385289261 8 25607998 CACAGCAAGTGCTAAACTAAGCCTTGCGTGGTGTT[C/T]AGAGCTTCACAGGGCAGTAGGCACAGGCTTTCTCT Y 2 1 2 1 202000 r 74 goat snp52015-scaffold764-3223029 8 26402715 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414635 Affx-122949332 AX-123284984 8 25638322 ACACTAATTGCAAAGCAGGAAAGTACCTCAAAAAA[C/T]GTATCTTTTTGTTTGGCCTTCTTTTGTTTCCCCGT Y 2 1 2 1 101000 r 74 goat snp52016-scaffold764-3253353 8 26431579 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376733 Affx-122978955 AX-123247092 8 25671381 AAGATATTTACAGAGCCTTTAGGTATTTACCACCC[A/G]CCTTGATTGGTGACAGGGGAGGCATGTTGACCATA R 2 1 2 1 101000 f 74 goat snp45335-scaffold619-1653933 8 26453161 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426822 Affx-122940517 AX-123297167 8 25725019 CATTATCAGAGGGAAATGATTATTGTATGATACTA[C/T]TGTCCCTTGGAACTTTCAAAAGGAAAATGTTAGTG Y 2 1 2 1 201000 f 74 goat snp45334-scaffold619-1600295 8 26507259 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430233 Affx-122937320 AX-123300574 8 25756369 TAATGAGTGAGATACCCTGCTAGATGCTAAGGATA[C/T]AGAAGAGGATATACTCTCTCTGCCTCTCAGAAACT Y 2 1 2 1 101000 f 74 goat snp45333-scaffold619-1568945 8 26537097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407364 Affx-122955272 AX-123277715 8 25854719 ACAGCAAGATGCATCATACTTGGGCTTCTCAAGGC[A/G]CTGTTTTGCTGGCCCAAGATTTCCAGGCCACTAAC R 2 1 2 1 201000 f 74 goat snp45331-scaffold619-1470595 8 26634829 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784515 Affx-122926525 AX-385271564 8 25890049 TTCTTTCAGGGTTACAAAAGCAGCATATATGCTAT[C/T]CGTAAATTATCAGGCAGGACTTCCTTGATGTAACT Y 2 1 2 1 101000 r 74 goat snp45330-scaffold619-1435265 8 26670077 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394305 Affx-122964691 AX-123264660 8 25932795 GGAAGGCCTTTTTTATGATCGATTTTTACCATTTT[A/G]TCTCATTTTCATGGTAGAATCACCAAAAACTGTCT R 2 1 2 1 101000 r 74 goat snp45329-scaffold619-1392519 8 26714117 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437100 Affx-122932180 AX-123307438 8 26002265 TTCACTTCTACTCAGTCCATACCTTGAGCTCCACC[A/G]TGAATACAGAAATAAAATATTCCTGAATTATGAAA R 2 1 2 1 101000 f 74 goat snp45328-scaffold619-1323049 8 26785674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389653 Affx-122968728 AX-123260011 8 26052611 AGATGGCAGAATAGGAAGCACCAGATCTTTTCCTA[C/T]AGAGACACCATTTCAACAATACTCAGACCAGATCC Y 2 1 2 1 101000 r 74 goat snp45327-scaffold619-1272703 8 26836526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382504 Affx-122973813 AX-123252862 8 26120317 AAGTGTTAAATATCTCATATAATTTATTAACTAGT[A/G]TACTGAAAGTGAAAAATAAAATAGTGGTATGGTTA R 2 1 2 1 101000 r 74 goat snp45326-scaffold619-1204997 8 26906241 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273342 Affx-1111833571 AX-185962840 8 26157693 AGAATCCCAGGGACGGCGGAGCCTGGTGGGCTGCC[A/G]TCTATGGGGTCGCACTGAGTCGGACACGACTGAAG R 2 1 2 1 303000 f 74 goat 8_26157693_AF-PAKI 8 26157693 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445305 Affx-122925441 AX-123315642 8 26161259 CACTCTAACATTTTTCCCAGCAGGAAGGAAGAGGA[C/T]GCTGAAGGTATATATAGAGAAGTGAGAGCCTTGAA Y 2 1 2 1 201000 r 74 goat snp45325-scaffold619-1164055 8 26947758 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783741 Affx-122949972 AX-385270797 8 26238173 GATAAAAGTGAAGTGCAAGTAACCATATGCTCCTA[C/T]ATTAAATTACAGGTTCTATGAGCATGGAGACCATT Y 2 1 2 1 101000 f 74 goat snp45324-scaffold619-1087141 8 27026459 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781321 Affx-122949717 AX-385268406 8 26267972 TCTTTAGTTAGTAGTTTGTGCAGTGTCCAACAGCT[A/G]TCAATCAATGCTGTTTTCACCTTATTTAAAATATC R 2 1 2 1 101000 f 74 goat snp45323-scaffold619-1057342 8 27056825 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407243 Affx-122955364 AX-123277594 8 26298640 GCTGGTTTGACTTACACAAATCAATAAATGTAACA[C/T]ACTACAGAAACACAATGAAGTATAAAAATTATATG Y 2 1 2 1 303000 r 74 goat snp45322-scaffold619-1026674 8 27087346 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802470 Affx-122938276 AX-385289374 8 26353981 AGCATCCATTTTTCTCTCACCTTAAGAATTAGTAC[A/G]TCTTAAATTTGTCCTGATTCTCCTCCAAATTGTGA R 2 1 2 1 101000 r 74 goat snp45321-scaffold619-971333 8 27142938 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770419 Affx-122938022 AX-385257585 8 26394597 GATAATTCTTATTCCAGAAATTTATTCTAAGGAAC[G/T]AATCATAGATGTACATAATGATCTGTGTTCAAAGA K 2 1 2 1 201000 f 74 goat snp45320-scaffold619-930717 8 27184440 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423075 Affx-122942941 AX-123293421 8 26435292 TGTATTTAAAAGTAATAATATGGATGAAATACTCT[A/G]AGACAAGTTTTGTACTTGGATTTTTGTATTCCACT R 2 1 2 1 101000 r 74 goat snp45319-scaffold619-890022 8 27225663 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400872 Affx-122959765 AX-123271226 8 26513028 AACCCCAGAGACAGGGCTGGGTGGAGAAGGCACCC[A/G]GATAGCAACTCTGACCTCAGTCTAGGAACAGGGAA R 2 1 2 1 101000 r 74 goat snp45318-scaffold619-812286 8 27303416 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443070 Affx-122928127 AX-123313407 8 26543477 GGAAAACATAATATTGTGATGGTGCTCTGAACACG[C/T]GCAGCCAAATCTGATGGGAACAAAACACTTAGGGT Y 2 1 2 1 201000 r 74 goat snp45317-scaffold619-781837 8 27333711 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449247 Affx-122923475 AX-123319582 8 26574202 TATCCATACATATACCTAAAACTACAAAAACACTG[C/T]ATCAGGTGTTACTGCAGTATGAAAATGCATGTTAA Y 2 1 2 1 101000 r 74 goat snp45316-scaffold619-751112 8 27360582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405365 Affx-122956315 AX-123275717 8 26623306 AAACCCAACCTTCAGTTTATGGGATGTGCATTTTA[C/T]AAGATCATTTGAAGTGACATACATCAAACAGTCTG Y 2 1 2 1 101000 f 74 goat snp45315-scaffold619-702008 8 27409969 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413444 Affx-122950684 AX-123283793 8 26663547 CACAAAGAATCGGACACAACTCTGTGACTGAGCAC[A/G]TAGACACACAGCACTCTCTCTCAGATTAATAAAAT R 2 1 2 1 201000 r 74 goat snp45314-scaffold619-661767 8 27449689 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448996 Affx-122923105 AX-123319331 8 26702268 AGTCAATATGCTTTAAAAAATCAAGAATTTTTAAA[C/T]GAAAACTATGGATTCCCAGCGTTTGGGGACAGGGC Y 2 1 2 1 103000 r 74 goat snp45313-scaffold619-623046 8 27488754 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476242 Affx-1251763748 AX-586011664 8 26734889 TGAGAGAAACTGGGTAAAATACACATTAGTTCTTT[-/TCTGTATTATTTCTTTTTTTTTTTTAATTTTAATTTTTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCC]CTGTATTATTTCTTACAACTGCATGTGAATCTACA - 4 1 4 1 20000 f 74 goat SV_199 8 26734889 - deletion junction SV-TF-chip 539476495 Affx-1251763748 AX-586011891 8 26734889 TGAGAGAAACTGGGTAAAATACACATTAGTTCTTT[-/TCTGTATTATTTCTTTTTTTTTTTTAATTTTAATTTTTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCC]CTGTATTATTTCTTACAACTGCATGTGAATCTACA - 4 1 4 1 20000 r 74 goat SV_199 8 26734889 - deletion junction SV-TF-chip 562165246 Affx-1251763748 AX-606940658 8 26734889 TGAGAGAAACTGGGTAAAATACACATTAGTTCTTT[-/TCTGTATTATTTCTTTTTTTTTTTTAATTTTAATTTTTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCC]CTGTATTATTTCTTACAACTGCATGTGAATCTACA - 8 1 4 1 20100 f 74 goat SV_199 8 26734889 - deletion junction SV-TF-chip 562165371 Affx-1251763748 AX-606940782 8 26734889 TGAGAGAAACTGGGTAAAATACACATTAGTTCTTT[-/TCTGTATTATTTCTTTTTTTTTTTTAATTTTAATTTTTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCC]CTGTATTATTTCTTACAACTGCATGTGAATCTACA - 8 1 4 1 20100 f 74 goat SV_199 8 26734889 - deletion junction SV-TF-chip 562165448 Affx-1251763748 AX-606940859 8 26734889 TGAGAGAAACTGGGTAAAATACACATTAGTTCTTT[-/TCTGTATTATTTCTTTTTTTTTTTTAATTTTAATTTTTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCC]CTGTATTATTTCTTACAACTGCATGTGAATCTACA - 8 1 4 1 20100 f 74 goat SV_199 8 26734889 - deletion junction SV-TF-chip 562165672 Affx-1251763748 AX-606941081 8 26734889 TGAGAGAAACTGGGTAAAATACACATTAGTTCTTT[-/TCTGTATTATTTCTTTTTTTTTTTTAATTTTAATTTTTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCC]CTGTATTATTTCTTACAACTGCATGTGAATCTACA - 8 1 4 1 20100 f 74 goat SV_199 8 26734889 - deletion junction SV-TF-chip 562166471 Affx-1251763748 AX-606941879 8 26734889 TGAGAGAAACTGGGTAAAATACACATTAGTTCTTT[-/TCTGTATTATTTCTTTTTTTTTTTTAATTTTAATTTTTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCC]CTGTATTATTTCTTACAACTGCATGTGAATCTACA - 8 1 4 1 20100 r 74 goat SV_199 8 26734889 - deletion junction SV-TF-chip 562166548 Affx-1251763748 AX-606941956 8 26734889 TGAGAGAAACTGGGTAAAATACACATTAGTTCTTT[-/TCTGTATTATTTCTTTTTTTTTTTTAATTTTAATTTTTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCC]CTGTATTATTTCTTACAACTGCATGTGAATCTACA - 8 1 4 1 20100 r 74 goat SV_199 8 26734889 - deletion junction SV-TF-chip 562166582 Affx-1251763748 AX-606941990 8 26734889 TGAGAGAAACTGGGTAAAATACACATTAGTTCTTT[-/TCTGTATTATTTCTTTTTTTTTTTTAATTTTAATTTTTTTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCC]CTGTATTATTTCTTACAACTGCATGTGAATCTACA - 8 1 4 1 20100 f 74 goat SV_199 8 26734889 - deletion junction SV-TF-chip 38390726 Affx-122967923 AX-123261083 8 26747916 AAATAGCTTATAGACAACTGGGAGTAGATTTCCAG[C/T]GCCCATCAGTTTCTCCTTTGTTTCAAGCCAGGAGT Y 2 1 2 1 101000 f 74 goat snp45312-scaffold619-577398 8 27534517 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421734 Affx-122944380 AX-123292081 8 26803289 TGAGTCCCAGGCCTAAGTCACGCAAAGTTCCTCTC[A/G]TGGAGCATCACGCGCAGGTCTTTGCATCCGTCTGT R 2 1 2 1 101000 f 74 goat snp45311-scaffold619-522025 8 27591988 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434252 Affx-122934821 AX-123304593 8 26844990 CCACGCCCAGCTTATTCTTAGGACTACTGTCTACT[C/T]GCAAGTTTCCAAAAACCCCATCGTGGGGTCAGCGG Y 2 1 2 1 101000 f 74 goat snp45310-scaffold619-480324 8 27633844 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775655 Affx-122947351 AX-385262786 8 26898643 CACAGGTAGAACAGACAAGGCAGAAGTATATCCCT[A/C]GATACGCTATGAGACCATCAGAGAGTAAGAGTATT M 2 1 2 1 101000 f 74 goat snp45309-scaffold619-426671 8 27686225 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388521 Affx-122969206 AX-123258879 8 26930561 GGCTTCAGCTTCAGGTCTCTCATCTGACCAGGCCA[C/T]TGGTGTTTCAGTGAGCTGTAGAAAGTTCTAGGTGG Y 2 1 2 1 101000 r 74 goat snp45308-scaffold619-394753 8 27718121 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777777 Affx-122930197 AX-385264895 8 26978210 TCAACTGTGCAGTCTGAGGAGAAAAATTCAGACAA[C/T]ATGACCTGGTTCAATCACCTTCTACCTCCTACCAG Y 2 1 2 1 101000 f 74 goat snp45307-scaffold619-347104 8 27765809 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403920 Affx-122957475 AX-123274272 8 27041663 AAAGCAGCAAGGTTGCTTTTATGTCTGTAGGAAGG[C/T]GAATGAGCTCACATTTTGATCAAGAGATCTTTGCA Y 2 1 2 1 101000 r 74 goat snp45306-scaffold619-283651 8 27829463 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409503 Affx-122953636 AX-123279854 8 27118981 GTTTCTTTCCCCCAAATATCTACATTGATTTTGTC[A/G]TACATTCATCTTATGTTGTATTTTAAAGACCCAAC R 2 1 2 1 101000 r 74 goat snp45305-scaffold619-206333 8 27907697 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426761 Affx-122940564 AX-123297107 8 27153381 AACAGGAGAAATGTTTCTTTGAAGTTTTTCAAAGA[C/T]GTTGCTTTTACTTAGAATGTTCTTCCCTTTTCTTT Y 2 1 2 1 101000 r 74 goat snp45304-scaffold619-171933 8 27941916 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398368 Affx-122961664 AX-123268723 8 27192933 TACATCTTTATTCCTCCCTCCTCCTTACCATTCTA[C/T]TGAGCATACACATGTCATCTTCCTTCAAGTCAAAG Y 2 1 2 1 201000 r 74 goat snp45303-scaffold619-132381 8 27981123 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450714 Affx-122921882 AX-123321048 8 27235195 TACAGAAGACCCAGAATCAATATGGCAGCCCCATT[A/G]TACCTCCAAGGCATGCCCTAATTTCCTTCTATCTT R 2 1 2 1 201000 r 74 goat snp45302-scaffold619-90119 8 28023477 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421107 Affx-122944215 AX-123291454 8 27296572 AGATCTCAGATTAAGGCAAATTCCCTTGTCTCCCC[A/G]TGTTGATGGCTCCCTTGTCAATGCCTGCCTTTGAC R 2 1 2 1 201000 r 74 goat snp45301-scaffold619-28742 8 28084796 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403885 Affx-122957499 AX-123274237 8 27401137 CAAAACCAGGCTTTTTCTATGATTTCCCACACTCC[A/G]TCTTTCTAACATTTCTACAGGGAAGCAGGTGATAA R 2 1 2 1 101000 f 74 goat snp59349-scaffold978-75724 8 28190536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382559 Affx-122973771 AX-123252917 8 27439371 TATAATGTTATTGTCTGCCTTTTTAACTGTAAAAT[A/G]TAAACATTCTTCCATGTTATTTTCTCCTGCTCAGA R 2 1 2 1 201000 f 74 goat snp59350-scaffold978-113958 8 28228923 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448166 Affx-122924264 AX-123318502 8 27468108 GCTGTGTCCAAGATGCATGGTCAGAACTTCCTTCC[A/G]TGGTCATGTGGATTCCTAGAAAGGGACGGCCTCTT R 2 1 2 1 101000 f 74 goat snp59351-scaffold978-142695 8 28257654 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400708 Affx-122959928 AX-123271063 8 27506465 CTATTAATAAGTAACCTCACCTGTAAAAGACAGTC[A/G]AAGCAGAAAATTTGGGGACAGTATGAGACAATATG R 2 1 2 1 101000 f 74 goat snp59352-scaffold978-181052 8 28296853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419942 Affx-122945217 AX-123290290 8 27551506 ACCACACAATTTGGCATTTGTGACGGAACTCTGGG[C/T]AAACTATTGCTATGTCCCAGATACTGTGCAAATAT Y 2 1 2 1 101000 f 74 goat snp59353-scaffold978-226093 8 28342477 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423714 Affx-122942880 AX-123294060 8 27611526 ATTATACAACCTCAAATAAGCTATTTTTTAAACCA[C/T]GATTCTGACAATTTCAAGTTTAACTAGGGAGAGGA Y 2 1 2 1 101000 r 74 goat snp59354-scaffold978-286113 8 28403342 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446309 Affx-122925642 AX-123316645 8 27683765 GATGGCAAGATTCCCACAGAGAACACTGAGCGAGA[G/T]CCCACAGAGAGATGAGAGTGACGGAGGCGAGAGCG K 2 1 2 1 101000 f 74 goat snp59356-scaffold978-358352 8 28478132 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787267 Affx-122932004 AX-385274292 8 27726031 TAACAGAAGCCAGATATAATGGGTACTTATTTATG[C/T]ACCCAAGTAGTGTTCTTTATCCAAGAACATTTAAA Y 2 1 2 1 201000 r 74 goat snp59357-scaffold978-400618 8 28521173 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436680 Affx-122932459 AX-123307018 8 27768276 GCCATGAGCATGATACAGTAGGACAAGCTTGGTTT[A/G]TAAACCTCAGTGAACTGGGAGGTAAGGGAAGTAAG R 2 1 2 1 201000 f 74 goat snp59358-scaffold978-442863 8 28563191 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771279 Affx-122974489 AX-385258437 8 27812696 TATCAAAAGACTCCATAGAGTAGCTAAGAAAAATC[G/T]CAGTGTAAAACAAGCCTAAAACAGTTTTATATTTA K 2 1 2 1 101000 f 74 goat snp59359-scaffold978-487283 8 28608448 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278765 Affx-1111836501 AX-519552238 8 27836290 TTCTCTTTGCTCCAGTCTCTCCTTACCTCAGTCTC[A/G]GATTTTGATGATGTTTAATGTCATTTGCCTCCAAT R 2 1 2 1 201000 r 74 goat Random2.2K-881 8 27836290 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432743 Affx-122935452 AX-123303084 8 27848986 ACTGCTCTGTATTCCAGGAACTACACGTGCCATGA[C/T]GACTTGACCATGGCTTCTCAAGCATCTGAGTCAAT Y 2 1 2 1 101000 f 74 goat snp59360-scaffold978-523573 8 28645300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799465 Affx-122975736 AX-385286395 8 27895291 TTTGTGACATTTAGGAATTGAGACTTAAAAGCACC[A/G]TTTTCAGAAAAAAGATCTTTTAGCTTATAGTAGGA R 2 1 2 1 101000 f 74 goat snp59361-scaffold978-569878 8 28691658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390792 Affx-122967874 AX-123261149 8 27952218 CACTGGTCTCTAGTGCTGTCACTCAGTCACCCCCA[C/T]AAATTAAAATCCTATGAGTACAACAAACACTTGGT Y 2 1 2 1 201000 r 74 goat snp59362-scaffold978-626805 8 28748902 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402496 Affx-122958579 AX-123272849 8 28009941 TAGAGCCAGAGAGAAAGAACTAGAGAGGATGTACA[C/T]GACTGTGAGTCAGACACATCTCTATACATGGACGT Y 2 1 2 1 201000 f 74 goat snp59363-scaffold978-684528 8 28807336 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429704 Affx-122937625 AX-123300045 8 28049699 GCAAGAATGTATTAGCCTGTTTTTAAAAGTGGTGA[C/T]ACTGAAATATAATATATAGGGGCATAAAATCTACC Y 2 1 2 1 101000 f 74 goat snp59364-scaffold978-724286 8 28847202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438671 Affx-122930881 AX-123309008 8 28081928 TCATACAGTTAACTATTTCATTTTTTAAAAAACAC[A/G]CTTCTCTATATGTTAGTAGAAACTAAAGCAATGCT R 2 1 2 1 101000 r 74 goat snp59365-scaffold978-756515 8 28878917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795054 Affx-122957999 AX-385282013 8 28119051 AATATAGATGTGAAATACACTTTACTGATGATTTT[A/G]CATCTGGGCTTGCCCTTCCTTGAGAAATCCTTGGC R 2 1 2 1 102000 r 74 goat snp59366-scaffold978-793638 8 28916563 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780443 Affx-122949189 AX-385267534 8 28166436 AAAATCAGAAAGATTGGCTTTGGTGAGGAGAGAAA[A/G]TTAAGAAGAAAGTTGCAGGCAGTTGTGATGGACTT R 2 1 2 1 101000 r 74 goat snp59367-scaffold978-841023 8 28964321 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785001 Affx-122935886 AX-385272049 8 28225660 TCTTTCCAGGAGACGACTCTCCATATTAGCCATAT[C/T]GGAGCCAATGGCAATCACTATTTTCTTCCTATTGT Y 2 1 2 1 101000 f 74 goat snp59368-scaffold978-900247 8 29024137 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801732 Affx-122922319 AX-385288640 8 28264253 TGGGCTTATTAAGTCCTTCCTCATGAGGTATTATC[A/G]TTTTATATACAGTAAGCATGAAAGGAGCATTTGCA R 2 1 2 1 201000 r 74 goat snp59369-scaffold978-938840 8 29068050 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427175 Affx-122939613 AX-123297518 8 28302449 AATTAAAAGTGCAGTGCCCTAGAAAGGATGAATTC[C/T]CTCCTGGGCTCTGCTCAGGACCTACTTTTTATAGT Y 2 1 2 1 201000 f 74 goat snp21995-scaffold2164-18028 8 29118048 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798100 Affx-122929957 AX-385285035 8 28357064 TGTTTCTATTGCAGCATCAAATTAAGTCCCTCTGG[C/T]GAAAAGTCAGTTAGTTTATAAGAGTCCTTATGGAA Y 2 1 2 1 101000 f 74 goat snp21996-scaffold2164-72643 8 29172499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427704 Affx-122939288 AX-123298047 8 28416822 CCGCTAGGTTAAGTGAAACCATGAGAGACTCTTGA[G/T]GCCATACTGACCTGAAGTTCCAGAAACCTAAACAC K 2 1 2 1 101000 r 74 goat snp21997-scaffold2164-132401 8 29232215 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441646 Affx-122929200 AX-123311983 8 28450459 ATTGAATATATTACTTAACCTCTTGCTACCTCTTT[A/G]TCAACCTCTTTGTAAATGAGGGTAATAACGGTATC R 2 1 2 1 201000 f 74 goat snp21998-scaffold2164-166038 8 29265707 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798447 Affx-122928869 AX-385285380 8 28496559 TTCATTGTTAAGTCTCTTTTCATGCCAGTTTATTA[C/T]GACAGCTACCTATGTGGACTCCCAACTTCTAGCTT Y 2 1 2 1 101000 r 74 goat snp21999-scaffold2164-212138 8 29311942 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380022 Affx-122975592 AX-123250380 8 28535945 GCCCATGTATAATTAGAAAATTGCTCCTAAGAACC[A/G]GGCAATCAAATTTCCTTTGAACTCTTATTTTGAAT R 2 1 2 1 101000 f 74 goat snp22000-scaffold2164-251524 8 29351738 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415043 Affx-122949492 AX-123285392 8 28569367 AATGCCAGTTTACTCTATGATCTCAATCCATAATG[A/G]AAATTGAAGTTAAATTATTTGAAGCTTATGGTGAA R 2 1 2 1 101000 f 74 goat snp22001-scaffold2164-284946 8 29385153 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787278 Affx-122977183 AX-385274303 8 28618430 AGTGTTCTTGTTTTAAAATGTGAACAACTGGTTAC[A/G]TTTGAAAAATGTGTGCATGTAGTGAAAAGATAGAT R 2 1 2 1 101000 f 74 goat snp22002-scaffold2164-334009 8 29434117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380900 Affx-122975034 AX-123251258 8 28669962 TTTAAATTCTCCAGAACCACTTTCCCTGAATAAGA[A/G]AAATTTCCCAAGCTGTTTCTCCTTCGCGATGTACC R 2 1 2 1 101000 f 74 goat snp22003-scaffold2164-385541 8 29487008 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273345 Affx-1111833572 AX-519546982 8 28678107 TGGTTGGGAGTTTGCCTTGCAATGCGCGGCTTGCC[A/G]GTTCAATCCCTGGTCTGGGAAAATCCCATATGCTG R 2 1 2 1 202000 f 74 goat 8_28678107_AF-PAKI 8 28678107 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320794142 Affx-122932406 AX-385281108 8 28716166 GCAAACATTTTGTCAGGAAGTATAAACCCCAAGCC[A/G]TCATATCATCAGGAAACCCCCTTTGAAAATTAATG R 2 1 2 1 102000 f 74 goat snp22004-scaffold2164-431745 8 29533279 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387176 Affx-122970621 AX-123257534 8 28776621 CAAAATAGCAATTCTTACCATTGTCTTATGCAGAG[C/T]GTTCTAGTTATTTCTAGCCTAGTCCCCATTCTCAG Y 2 1 2 1 101000 f 74 goat snp22005-scaffold2164-492200 8 29593316 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402323 Affx-122959077 AX-123272676 8 28815008 ATTGATCATCACCAACAACAAACTCTTTTCATTAT[A/G]TTTAATTGCTGTAGACTAAATGTTTCCCTGTAAAT R 2 1 2 1 101000 r 74 goat snp22006-scaffold2164-530587 8 29632182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424248 Affx-122942467 AX-123294594 8 28884533 CAGGGCCCAGCCCGAACTGTCCTTGCCACAGGTTC[A/C]TGTGAGAGACAAGCCCCTGTCGGCAACTTCCGAAA M 2 1 2 1 101000 r 74 goat snp22007-scaffold2164-600112 8 29701435 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443529 Affx-122927777 AX-123313866 8 28916836 AGGGTGAGAAAAGGGATGCGGCAGAATGTGCAACA[C/T]AAAGTGATGTTTTGGGCTTTTTTCTTTTTTTAAAT Y 2 1 2 1 101000 f 74 goat snp22008-scaffold2164-632415 8 29733880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772243 Affx-122949911 AX-385259398 8 28968064 TTTCATGATTGTTAGAGAGCTCTCTATAAGAAGCA[C/T]GTCATGGTATTCCTGGACAGACTTCCATTTGCAGA Y 2 1 2 1 101000 r 74 goat snp22009-scaffold2164-683643 8 29783702 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778778 Affx-122965659 AX-385265888 8 29039622 AGAGCTTGGTATTGTGTATAAGATTATTATTTGCT[G/T]AATTTAAATGGTAGTCAGGCAGTGTTAAGTTTTGC K 2 1 2 1 101000 r 74 goat snp22011-scaffold2164-755201 8 29855422 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787816 Affx-122960214 AX-385274839 8 29077306 TGAGGACAGAACTCAAGAGCAGAAGAGGGGTGGAT[A/G]GGAAATGTGTTTTGTTAGCAGATTAATTTTAGGAG R 2 1 2 1 101000 f 74 goat snp22012-scaffold2164-792885 8 29893820 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476243 Affx-1251763749 AX-586011665 8 29085993 ATAATAAGATACCATCAGTATCTTACAATTAAAAA[-/CCAATCTGTTTAGAGAGGGAAAGATGGCGGAGGAATAGGAACAAAAATAGAGGCTTCAAACTAACTGTAAAAAAAAAAAA]CAATCTGTTTAAAAAGTCAAATGGAGATATAAATA - 4 1 4 1 20000 f 74 goat SV_206 8 29085993 - deletion junction SV-TF-chip 560378501 Affx-1251763749 AX-605230916 8 29085993 ATAATAAGATACCATCAGTATCTTACAATTAAAAA[-/CCAATCTGTTTAGAGAGGGAAAGATGGCGGAGGAATAGGAACAAAAATAGAGGCTTCAAACTAACTGTAAAAAAAAAAAA]CAATCTGTTTAAAAAGTCAAATGGAGATATAAATA - 8 1 4 1 20000 r 74 goat SV_206 8 29085993 - deletion junction SV-TF-chip 562166255 Affx-1251763749 AX-606941663 8 29085993 ATAATAAGATACCATCAGTATCTTACAATTAAAAA[-/CCAATCTGTTTAGAGAGGGAAAGATGGCGGAGGAATAGGAACAAAAATAGAGGCTTCAAACTAACTGTAAAAAAAAAAAA]CAATCTGTTTAAAAAGTCAAATGGAGATATAAATA - 8 1 4 1 20100 f 74 goat SV_206 8 29085993 - deletion junction SV-TF-chip 562166378 Affx-1251763749 AX-606941786 8 29085993 ATAATAAGATACCATCAGTATCTTACAATTAAAAA[-/CCAATCTGTTTAGAGAGGGAAAGATGGCGGAGGAATAGGAACAAAAATAGAGGCTTCAAACTAACTGTAAAAAAAAAAAA]CAATCTGTTTAAAAAGTCAAATGGAGATATAAATA - 8 1 4 1 20100 f 74 goat SV_206 8 29085993 - deletion junction SV-TF-chip 562166446 Affx-1251763749 AX-606941854 8 29085993 ATAATAAGATACCATCAGTATCTTACAATTAAAAA[-/CCAATCTGTTTAGAGAGGGAAAGATGGCGGAGGAATAGGAACAAAAATAGAGGCTTCAAACTAACTGTAAAAAAAAAAAA]CAATCTGTTTAAAAAGTCAAATGGAGATATAAATA - 8 1 4 1 20100 r 74 goat SV_206 8 29085993 - deletion junction SV-TF-chip 38392472 Affx-122966151 AX-123262829 8 29106292 ACTGCAGTATTTGAACTTTTTATGTTTATTTTTAA[C/T]TTGTAAAGGAACGTGCCTGAGTGACTTACTACCAC Y 2 1 2 1 101000 r 74 goat snp22013-scaffold2164-821871 8 29923063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381029 Affx-122974648 AX-123251387 8 29145526 TTAAAGAATCATTGACTTGTAATTTATATGCAGGC[A/G]TTTAGATAAATATTCTGCTTTATTGCTTCCTTTGC R 2 1 2 1 101000 r 74 goat snp22014-scaffold2164-861105 8 29962877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434626 Affx-122934004 AX-123304967 8 29183786 TCTTCCCCACCCCCAATAGGGTGACCACAGAAGTA[A/G]ACGAGCCCAGGGCTACACGGGATCCATGCCTGTCA R 2 1 2 1 201000 r 74 goat snp22015-scaffold2164-899365 8 30001038 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429684 Affx-122937642 AX-123300025 8 29220753 GAATTCTTTACTAAATTTTTTGCTTTACTAGCTCT[A/G]TAACTTGGGTGAATGACACTTTACCCTGCCTTCCA R 2 1 2 1 101000 r 74 goat snp22016-scaffold2164-936332 8 30037642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387471 Affx-122970357 AX-123257829 8 29236774 CAGTCCTCTCCAATCCTCTGCCTCTTAAACCTGTG[G/T]TTCTCAGCCTAGGCTGCAAGCCAGGATCCCCTGGG K 2 1 2 1 202000 r 74 goat snp3869-scaffold1121-2055731 8 30054180 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793300 Affx-122965949 AX-385280278 8 29289312 TCTAAAGGAAACCCAATATTCATGCCTCGTGACAT[A/G]TAACCCAGACTCTTTATTGATTTTTGACTTAGAAT R 2 1 2 1 101000 f 74 goat snp3868-scaffold1121-2003193 8 30107980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777740 Affx-122975648 AX-385264858 8 29360691 ACAAGGCAGAGTTTTCCATTATAGCACCTGTTTCC[A/G]TACAAGTTTTGTACTCTGTCACTTTTTATACTTTC R 2 1 2 1 101000 f 74 goat snp3867-scaffold1121-1931814 8 30180303 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795389 Affx-122939299 AX-385282345 8 29393575 TGTTCAGTTTTATAGCAGTGTTGAAAAGATGTCCT[A/G]TCTTGACGACACTGCTTTCCTTTTTCTCTAAAGAT R 2 1 2 1 101000 r 74 goat snp3866-scaffold1121-1898930 8 30213321 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427238 Affx-122939565 AX-123297581 8 29459622 AATGGGCAGTAGGCATGCCTGCCCTCTAGGCATGG[C/T]CTGGAAGGAACGTCATGTTTATTATACTGAACTGT Y 2 1 2 1 101000 r 74 goat snp3865-scaffold1121-1832883 8 30280536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425765 Affx-122940728 AX-123296111 8 29498984 AGGTGTCCTATGGAGGGAGCAAAGAAATAAAAGAA[A/G]TGATGTCAGAAGACCAGAGATATGTCAGGCAGATT R 2 1 2 1 303000 r 74 goat snp3864-scaffold1121-1793521 8 30320249 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432220 Affx-122936371 AX-123302561 8 29548409 CTCAAGGAAAGTAGATCCTTGGGAAAATTTAACAC[A/C]TTTCATTAATAATAACAAAGTTATAAGTGTAGTCT M 2 1 2 1 101000 f 74 goat snp3863-scaffold1121-1744096 8 30370111 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771480 Affx-122976182 AX-385258638 8 29581601 TCCTCCCTGGAAGTCCTTCTAGAACTGGAACCAAG[C/T]GACTGTTAAATATCATAGAAACTCGGGAGTTACTC Y 2 1 2 1 101000 f 74 goat snp3862-scaffold1121-1710904 8 30403632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424195 Affx-122942511 AX-123294541 8 29614043 GATACTACTCAGCTCCTTACTTTAACTTTCTCATT[C/T]AATAAATGTCCCTAGGAAATATACTTCCTCCAAGA Y 2 1 2 1 101000 f 74 goat snp3861-scaffold1121-1678462 8 30436117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768741 Affx-122975632 AX-385255919 8 29657171 TAGATAACTTGACTGGCTCATGCTCTGATCAATAC[A/G]TGGCCCAATCTATTGTGACTCAGTAACAAATGGCC R 2 1 2 1 101000 r 74 goat snp3860-scaffold1121-1635334 8 30479072 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376181 Affx-122978829 AX-123246540 8 29697553 CCATAGAGATTAGAAAGTTAGGAGAATAACCTGTA[C/T]ATTTCTAGTTTATAGATAGTAATTTAATTAGGGAA Y 2 1 2 1 102000 f 74 goat snp3859-scaffold1121-1594952 8 30519413 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401711 Affx-122959536 AX-123272064 8 29733047 TGCTTTCATCACACTGATGACATAAGGAAAAACTC[A/G]CCTCTTAACACGGAATAGATGACCATTTCTATAAT R 2 1 2 1 101000 f 74 goat snp3858-scaffold1121-1559458 8 30554862 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434382 Affx-122934698 AX-123304723 8 29770824 GGATTCAAAGTACACACAAGGGAGGTGGATAGGAA[C/T]GGGGCTGGTAGCAATCCCAAGAAGCCCTGATATAA Y 2 1 2 1 101000 f 74 goat snp3857-scaffold1121-1521681 NW_017204143.1 280 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789698 Affx-122941612 AX-385276706 8 29801360 TGGTGTAAGAAGGTAGGCTCCAGTTTTTGCTAGAA[A/G]TGTCTCTGTTAAAAATGGCTGACATGTAAATAATT R 2 1 2 1 101000 f 74 goat snp3856-scaffold1121-1491145 8 30625478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414608 Affx-122949351 AX-123284957 8 29842055 GGCTTTGCCGCTTGTCCCTTGTTAGAGTTGGACAA[C/T]AGGCAGTAGGAAAGGGGAAGTGCCAGTAAGAAAGG Y 2 1 2 1 201000 f 74 goat snp3855-scaffold1121-1450450 8 30666110 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391136 Affx-122966792 AX-123261493 8 29891540 TGAGGTTCGGTGGAGACACAGAACTTCATGCTCCT[A/G]TGTCAGAGGTCACTTTCCAGGAAAGACTGCACTGC R 2 1 2 1 201000 r 74 goat snp3854-scaffold1121-1400965 8 30715623 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446514 Affx-122925031 AX-123316850 8 29921728 TCATTTCTGAATGTCTCTATTGAAGTGAAGGCCAA[C/T]ATAGCTAAAGTTTCAGTTTGTTTCTTGGCAGTCGA Y 2 1 2 1 101000 f 74 goat snp3853-scaffold1121-1370777 8 30745731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429840 Affx-122938164 AX-123300181 8 29980906 ATTGATGTCTCTCAAGTGCATAGGATGGTGCTGGA[C/T]GTGTAGGAGACCTTCAAAGAGTATTTATAGAATGA Y 2 1 2 1 201000 r 74 goat snp3852-scaffold1121-1311599 8 30805172 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419146 Affx-122945748 AX-123289494 8 30034682 CACCATGGGGACGACTCTAGTGTGTCTGTGATTAG[A/C]GTGAACTCAGCAACCTGAGGGCCAGAGGCATGCCA M 2 1 2 1 202000 r 74 goat snp3851-scaffold1121-1257823 8 30859339 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398023 Affx-122961776 AX-123268378 8 30120045 TCTAAATATCAAAACACATTGCCCTAGTACAATGA[C/T]AGTGGATTAAAAAAAAATTAACCAAATTATTATAG Y 2 1 2 1 101000 f 74 goat snp3849-scaffold1121-1172460 8 30944776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440021 Affx-122929772 AX-123310358 8 30164820 AACAAAGCCTATTAGCTTCTAGGAAACAGAGTGAG[C/T]AGATAACTTGTGAAAGAAATTATGAACCCCAAATT Y 2 1 2 1 101000 f 74 goat snp3848-scaffold1121-1127685 8 30989809 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401069 Affx-122959641 AX-123271422 8 30212683 TTTATTCATTGTAGAATAAATAGTTAATAAATATG[C/T]AAAAAGGCACCTCTCTGATGGTCAACTTTAAATCT Y 2 1 2 1 303000 f 74 goat snp3847-scaffold1121-1079822 8 31037713 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764967 Affx-986697136 AX-385252546 8 30235377 AGGAGCCTGCAGTCAGTCTGGGCTTCCAGGTCATC[C/T]TGGGTTTAAGCCTCACTTACTGTCACTCTCCCTTC Y 2 1 2 1 600010 r 74 goat 8_30235377 8 30235377 Ancestral_priority_1043 ancestry 0.618 recommended IMAGE 10K 10K ancestral 320792433 Affx-122977451 AX-385279414 8 30264832 TGTCATTAAGATTAATACTAACTGAAAACCAATTG[C/T]ACAGCACACAGACATATTTTCAGCAAAGCATCCCT Y 2 1 2 1 101000 r 74 goat snp3846-scaffold1121-1027673 8 31093531 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392637 Affx-122966455 AX-123262994 8 30307773 GCTATTGTATTTCCTCTCTTCCCAGGCCCACCTGA[A/G]TGGCTCTGAGTGGGTCCTTCATCTTCTCTCAGCAG R 2 1 2 1 201000 r 74 goat snp3845-scaffold1121-984732 8 31136831 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437817 Affx-122932113 AX-123308155 8 30350155 CTTGCTCCTTCTCTTCTTCCCACTCTTGTTTGAAA[C/T]GGGTATAGGCAGAAGACAGGATATTAATCCCACAA Y 2 1 2 1 101000 f 74 goat snp3844-scaffold1121-942350 8 31179455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765684 Affx-122927171 AX-385253147 8 30441964 TCCTCCAAGACATCATTTCAAAAGAAAGAGGCATG[C/T]GTTTCATTAACTTAGTTGCATTAATAACTGTCATA Y 2 1 2 1 101000 f 74 goat snp3842-scaffold1121-850541 8 31271743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780418 Affx-122955528 AX-385267510 8 30490996 TGCCTCGTATCTGTATCGTGCTCTCTCTGCCCTAA[C/T]AGTATTTTTTGTCACCATCTTACCTTATTCAGTAT Y 2 1 2 1 101000 f 74 goat snp3841-scaffold1121-801509 8 31320475 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392918 Affx-122965713 AX-123263275 8 30546702 CCTGGTCAAACCAAACCAGACCCAGTGCTAGGATC[A/G]TATGACATCTACCTGTATTTATGAGCGCTAGTTAA R 2 1 2 1 201000 r 74 goat snp3840-scaffold1121-745803 8 31375972 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405617 Affx-122956605 AX-123275969 8 30579775 AACATAGTTTGTTTAGTAATTAAGTTAGAAACAAC[A/G]TTATTGCATCTGAAAGGCATGTAACAAACTTCCTT R 2 1 2 1 101000 r 74 goat snp3839-scaffold1121-712730 8 31410949 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775573 Affx-122957883 AX-385262704 8 30619637 CTAATTCAGATTTATGCCATGTTAAAATTCAATAA[A/G]CATCTATTTCGACACTCCATAGAGAAAGCAATATT R 2 1 2 1 101000 r 74 goat snp3838-scaffold1121-672868 8 31450657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778250 Affx-122925641 AX-385265365 8 30669689 GCTTCCCTATATTAAACAATCTTCAGGCTATGTAT[A/G]CAAGATATTCAAAATGTGTTAGCAAAAGAGAATGT R 2 1 2 1 101000 f 74 goat snp3837-scaffold1121-622816 8 31501340 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798142 Affx-122926294 AX-385285077 8 30700702 TGCTTGAAAGTATGGTCATAATTTTTAACAGTCAC[A/G]TGAAAATTCTGCTAACAGGTCACTGACAAATCACA R 2 1 2 1 201000 f 74 goat snp3836-scaffold1121-591803 8 31532282 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768583 Affx-122958590 AX-385255763 8 30732465 TAATCCTAAATAAATGAGAATCATGATAATAATAG[C/T]ACATATTCTTAGTTTACATAACTGGAATCTTCTTA Y 2 1 2 1 101000 r 74 goat snp3835-scaffold1121-560040 8 31564946 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432711 Affx-122936020 AX-123303052 8 30778194 CAACCCTTCATTCTGCAAGGATTTAGTGAGTATCT[A/G]TGTGATGATCACTAGGATAAGCATGAAGGAAAGCA R 2 1 2 1 101000 f 74 goat snp3834-scaffold1121-514311 8 31610862 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774087 Affx-122929700 AX-385261225 8 30811603 GATATTTACAGAAACAATTAATTCAATATATGGAG[C/T]GAAATCCAAATGAGTCCCATGGTGTCATGACATAT Y 2 1 2 1 101000 r 74 goat snp3833-scaffold1121-480902 8 31645318 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803009 Affx-122957336 AX-385289888 8 30843250 CATTTGGTAATATACAGTTTTGAGTTAGATGTATA[C/T]GAAATTGCTAACAGTGATTTGAACTGAATGAAACA Y 2 1 2 1 101000 r 74 goat snp3832-scaffold1121-449255 8 31675878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387600 Affx-122970252 AX-123257958 8 30940131 TACCTCCCCCTTTGAAGATCTCTCTTTGGTGATTG[C/T]ATTAGTTTGCCAGGGTTGTCAAATAAAAGTACCAC Y 2 1 2 1 201000 r 74 goat snp3830-scaffold1121-352374 8 31773341 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773563 Affx-122950003 AX-385260703 8 30980083 TATATTCCAGACATGGTAACAAGCGTTTTACATAA[A/G]TCATCTCATTTAACCTAGCTTCGACCCACTGGAGT R 2 1 2 1 101000 r 74 goat snp3829-scaffold1121-312422 8 31812995 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772959 Affx-122941621 AX-385260103 8 31013828 AGAGCAGTTTTGTCCAGTAGGATTTTCTGTGAAGA[C/T]GAAAATTTTTAAATGCTGTGCTGTGGAATATAGTA Y 2 1 2 1 201000 r 74 goat snp3828-scaffold1121-278677 8 31846735 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442519 Affx-122928547 AX-123312856 8 31118575 TCATCAGTTTTCCAGTCTGAAAAGTGGCAATAATT[A/G]CAGTGTTTATCTCACTAGGTTGCTGTCAACAAACA R 2 1 2 1 101000 r 74 goat snp3825-scaffold1121-173930 8 31952537 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802676 Affx-122978606 AX-385289575 8 31153937 CATGCTTTCTAGAATGTTTACAATTCAAGATTTAG[G/T]CAATGTGAAATCCTTGAAGGAGTTCTATCTAGCCA K 2 1 2 1 101000 r 74 goat snp3824-scaffold1121-138568 8 31987752 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802091 Affx-122940869 AX-385288995 8 31196667 TTGTTTCTCTTTGTATGCTGTATGGCAAAAGTTTT[G/T]AAAGCTAATCATTTTTATGTACCATTACAGCTAGA K 2 1 2 1 101000 f 74 goat snp3823-scaffold1121-95838 8 32030731 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783516 Affx-122941589 AX-385270579 8 31226479 TACCTGATTTCAGTTCTAAGTTAGCAACTTATTAC[G/T]TCCCCCTGGTAAGTTACTTAATTCCTCTGGATCTT K 2 1 2 1 102000 r 74 goat snp3822-scaffold1121-66026 8 32061168 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273348 Affx-1111833574 AX-505078940 8 31255799 ACTTTCACTTTTCACTTTCATGCATTGGAGGAGGA[A/C]ATGGCAACCCACTCCTGTGTTCTTGCCTGGAGAAT M 2 1 2 1 103000 f 74 goat 8_31255799_AF-PAKI 8 31255799 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320766777 Affx-122942143 AX-385254110 8 31259674 TATTTTACTAGATTGCATGTCAGAGGTATGGTAAT[A/C]TCATGTGATAAAGTATTTATCTGCTCTGAATATTT M 2 1 2 1 101000 f 74 goat snp3821-scaffold1121-32831 8 32094729 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278767 Affx-1111836502 AX-519552240 8 31260420 ATATAAAATAACATATAATATCATCTGAAATATGT[A/G]TTTGCCTTGAGAGAAAATTATATTTCCTTACCTGA R 2 1 2 1 101000 r 74 goat Random2.2K-885 8 31260420 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392317 Affx-122966701 AX-123262674 8 31325028 AAAGAGGAAGGACACACTGAATGCTGATGTAACCT[A/G]CCAATAAAACAATAACATCTTAATTTTAATAACGT R 2 1 2 1 101000 f 74 goat snp56351-scaffold882-507422 8 32304395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393012 Affx-122966181 AX-123263369 8 31358765 ATGGTAAAATTAAATTTCCTATTTACAGGAATACC[A/G]TGGTATCCATAGATAAGCATCTTAGTCAAAAGTTT R 2 1 2 1 101000 r 74 goat snp56350-scaffold882-473685 8 32338883 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785786 Affx-122928610 AX-385272826 8 31423355 CCCCATATTCAAAGCTTAAACAGCAAGACATTTCC[A/G]TTGACTGTCTTCTTAACATAACCTCCCCAAAGGAG R 2 1 2 1 101000 f 74 goat snp56349-scaffold882-409095 8 32404868 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778678 Affx-122968484 AX-385265789 8 31490787 TGAATTACTCATGATAATATGGAAGCCATTTAATA[C/T]AGCCAATGAACTTCTACCTTCAAGGGCAGAGACTG Y 2 1 2 1 101000 r 74 goat snp56348-scaffold882-341663 8 32473018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275835 Affx-1111835034 AX-519549399 8 31503131 GGTGCCTCTTGTCTGATTCGTGCCAGAAGCAACAT[A/G]GATGAAGCCAATCAGCCTCTCCTTACTGATCAGTA R 2 1 2 1 101000 r 74 goat ilmnseq_rs643165967 8 31503131 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276342 Affx-1111835289 AX-519549875 8 31503179 ACCATAGCAGTAGTGGCTGCATTATTACTGGTCGC[A/G]GTCATTTTTGCAGGTGCCTCTTGTCTGATTCGTGC R 2 1 2 1 201000 r 74 goat ilmnseq_rs672503072 8 31503179 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468276053 Affx-1111835141 AX-519549606 8 31503180 CACGAATCAGACAAGAGGCACCTGCAAAAATGACC[A/G]CGACCAGTAATAATGCAGCCACTACTGCTATGGTG R 2 1 2 1 101000 r 74 goat ilmnseq_rs656070666 8 31503180 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276276 Affx-1111835255 AX-519549820 8 31503220 ATTTTCAAACAGGTCGGAGTTTTAGTATTCCTGAG[A/G]TTGTCACCATAGCAGTAGTGGCTGCATTATTACTG R 2 1 2 1 101000 r 74 goat ilmnseq_rs668369082 8 31503220 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275716 Affx-1111835049 AX-519549284 8 31504120 AAATGTTTGTTACTGCTCCAGACAACCTGGGCTAT[A/G]CTTACGAAGTTCAATGGCCAGGTGAGTACTGAAAA R 2 1 2 1 101000 f 74 goat ilmnseq_rs645085610 8 31504120 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275870 Affx-1111835125 AX-519549431 8 31507209 ACAGTCTCACCAGCATTGTATCGCCTCAGCCATTC[A/G]TCAAATACTGCGTCAGTGAATGTATGTAGGAGGAC R 2 1 2 1 102000 f 74 goat ilmnseq_rs654916551 8 31507209 A G 1 neutral Goat_IGGC_65K_v2 Illumina 468276175 Affx-1111835278 AX-519549725 8 31507215 ATTTTTGTCCTCCTACATACATTCACTGACGCAGT[A/G]TTTGATGAATGGCTGAGGCGATACAATGCTGGTGA R 2 1 2 1 201000 f 74 goat ilmnseq_rs671078291 8 31507215 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275890 Affx-1111835061 AX-519549449 8 31507272 AGGAGGACAAAAATAGGATCATTGGGAGATAAATG[A/C]GTTTGTCCCCCTGTTCCATTCAGGAATAGATGAGC M 2 1 2 1 101000 r 74 goat ilmnseq_rs646224512 8 31507272 A C 1 recommended Goat_IGGC_65K_v2 Illumina 468276128 Affx-1111835182 AX-519549678 8 31510435 CAATGGTGCAACGTCTTCCTGAACCACAGGATATC[A/G]CTCAGTGCTTGGAAGTTGGTTCATTTGACACACCT R 2 1 2 1 101000 r 74 goat ilmnseq_rs661182511 8 31510435 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276126 Affx-1111835253 AX-519549676 8 31510436 CCAATGGTGCAACGTCTTCCTGAACCACAGGATAT[A/C]GCTCAGTGCTTGGAAGTTGGTTCATTTGACACACC M 2 1 2 1 201000 f 74 goat ilmnseq_rs668199098 8 31510436 G T 2 recommended Goat_IGGC_65K_v2 Illumina 468275726 Affx-1111834977 AX-519549293 8 31510513 TGTTCATATACCCCATCTTTTTCCCAGGCACTGAG[A/G]GTGGGCCAATTAAGAGAAACCCAGCTGGAAATGTG R 2 1 2 1 201000 r 74 goat ilmnseq_rs636253132 8 31510513 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468276239 Affx-1111835237 AX-519549788 8 31516928 TTTGGTGAAGTGGATTTCTCTCACGAGGGACCAGC[A/G]TTTCTCACATGGCACAGGTACCACCTGCTGCAGCT R 2 1 2 1 101000 r 74 goat ilmnseq_rs666934292 8 31516928 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468276021 Affx-1111835205 AX-519549575 8 31517102 TCTGGCCCCAATATTTCTTCTGACCTCCTGGTGGC[A/G]ATGACAAACTGAGGGTGAGTGGTGTGCTTTGCCAT R 2 1 2 1 202000 f 74 goat ilmnseq_rs663468593 8 31517102 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468276190 Affx-1111835212 AX-519549740 8 31517108 CCCAATATTTCTTCTGACCTCCTGGTGGCGATGAC[A/G]AACTGAGGGTGAGTGGTGTGCTTTGCCATATCCAG R 2 1 2 1 202000 r 74 goat ilmnseq_rs663889201 8 31517108 A G 2 neutral Goat_IGGC_65K_v2 Illumina 468275919 Affx-1111835075 AX-519549477 8 31518903 CTGCTTTTTTTCCAGCAGGCCTGGGCTCAGTTCCC[A/G]AGAGAGTGTGCTACCATTGAGGCTTTGAGGAATGG R 2 1 2 1 101000 r 74 goat ilmnseq_rs647807562 8 31518903 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275573 Affx-1111834978 AX-519549143 8 31518955 CCTGCTGGAAAAAAAGCAGGACCAGGAACATGTAA[A/C]CCAGAGAGAGGAGTGTAGGAGATTTCATTCTGCCT M 2 1 2 1 201000 f 74 goat ilmnseq_rs636312441 8 31518955 A C 2 recommended Goat_IGGC_65K_v2 Illumina 320776385 Affx-122940666 AX-385263512 8 31520358 GGTTCAGCAACTTTGGAGAGAGTTTAGGCCATTGT[A/G]TTGTGTTAGAAGCAAGGATCTATTTAAAATACGAT R 2 1 2 1 101000 f 74 goat snp56347-scaffold882-312092 8 32501172 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445709 Affx-122926112 AX-123316046 8 31551354 GCAGGGACACTCTCCTGTCCCACAGCCTGTTATTG[A/G]TGAGGCCTCTCTTGATGAGGCTAAGTGCAGAGTAG R 2 1 2 1 101000 r 74 goat snp56346-scaffold882-281096 8 32532103 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780064 Affx-122932879 AX-385267162 8 31580409 CAACTGAGCATATGTGCATCCTAACTATACTTTTT[A/C]TATACTGTATGACCTGGTATAAATAATTTCATCTG M 2 1 2 1 102000 f 74 goat snp56345-scaffold882-252041 8 32560904 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410233 Affx-122952550 AX-123280583 8 31618679 AAGTCTTTCATATTTTATTCTTAAATAATGTAGAA[G/T]CAGGGACAATGTGGGAAAGTTCAAGGACATTCTAT K 2 1 2 1 103000 r 74 goat snp56344-scaffold882-213771 8 32599755 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421864 Affx-122944281 AX-123292211 8 31651799 AAATAAATCATATATATATTTGTTTATGTTTATAT[A/G]CACTTATGTATATATAAACAAATTCATCACATACT R 2 1 2 1 303000 f 74 goat snp56343-scaffold882-180651 8 32632785 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443343 Affx-122927432 AX-123313680 8 31691582 AAGTAAATATATAATATATACAAGTGAAACATCTT[A/G]TATTTTCCCAGTCCCCCCACAGATCCCTTGATTTC R 2 1 2 1 103000 r 74 goat snp56342-scaffold882-140868 8 32672660 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429310 Affx-122938601 AX-123299652 8 31850295 TGTTATTAAATATCTTTACTATTTAAAAGTAAAGA[C/T]ATTTTCTGGACTCTTTCTGGACTTCTTTGATAAAG Y 2 1 2 1 103000 r 74 goat snp46319-scaffold64-17500 8 32861259 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435836 Affx-122932822 AX-123306175 8 31885112 TGAGACAATGTCTGCAATGCCCTTAGCATCATCAA[C/T]ATTTGACTATTCTTTTTTTCCAGTGTCATATATTT Y 2 1 2 1 101000 f 74 goat snp46320-scaffold64-52317 8 32895500 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768942 Affx-122970739 AX-385256117 8 31944535 GAAAATGAAAGTTGATCTCTTAAATGCCCTTCAGT[A/G]TTTATTGGACATACAAACATGTATGAAATCACTTT R 2 1 2 1 101000 f 74 goat snp46321-scaffold64-111740 8 32956257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435318 Affx-122934015 AX-123305658 8 32019118 TACTGCTTAGTGCACATGTTTTACAGATGGGTATG[C/T]ATCTTTTCAGAAAGGCATTTTATGAAAATCTAATC Y 2 1 2 1 201000 r 74 goat snp46323-scaffold64-186323 8 33031693 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780285 Affx-122941892 AX-385267380 8 32124278 AAATGACAATGTTTGGAGATAGAGCCTTTGGGAGG[C/T]AATTAAGTCATGAGGTTATAGCCCTCATGGTAGAG Y 2 1 2 1 103000 f 74 goat snp46325-scaffold64-291483 8 33133609 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274347 Affx-1111834199 AX-519547942 8 32162067 GGCTAAATATCTAAGACAAAAGGCCAGTTCACCTA[A/G]T R 2 1 2 1 101000 f 74 goat GoatD01.025142 8 32162067 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427692 Affx-122939296 AX-123298035 8 32176980 TTACCTTTGTTTTTGATAGATATTTTTCCTAGGCA[C/T]CAATTTCTAGGATAGCATTATGTTTCATACATTAA Y 2 1 2 1 101000 r 74 goat snp46326-scaffold64-344185 8 33188226 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409080 Affx-122953338 AX-123279431 8 32244005 GGAGAAATAGGTCTGCAGCACACTCCTTGCCAAAC[A/G]CTGGGAGTATAGGTTTCCCATTTTAAATTTGCAAA R 2 1 2 1 101000 r 74 goat snp46327-scaffold64-411210 8 33256175 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780088 Affx-122968103 AX-385267186 8 32288758 GAAGCTTCTAGTTCAACTGATGTTAACATCTATGC[A/G]TTTCATCACTGTACCTGAATGCCGCATCCTGGATC R 2 1 2 1 101000 f 74 goat snp46328-scaffold64-455963 8 33301881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402459 Affx-122958608 AX-123272812 8 32327150 AGCACTGTTGAAATAAATTTCTCCAGGATGGATAT[A/G]CTCCTGCCTGGGACACCGCATAAGGAAACTGAAAT R 2 1 2 1 201000 f 74 goat snp46329-scaffold64-494355 8 33340352 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793524 Affx-122933405 AX-385280501 8 32380269 AGTATAGACAGTATGTAAACCTGAGTCCTTAATCT[A/G]CTTATTGTCCATCAAAGCATGTGATGATAGATGCT R 2 1 2 1 201000 r 74 goat snp46330-scaffold64-547474 8 33394817 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777957 Affx-122949618 AX-385265073 8 32433193 TTCCCAAAGCAAATTATTTGAAAGCTAACAGGTTA[C/T]GACTAGTTCTCTTAGATCAATTATTACCAAAATAT Y 2 1 2 1 101000 r 74 goat snp46331-scaffold64-600398 8 33448361 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436932 Affx-122933188 AX-123307270 8 32509514 TTTAATATGCTTAGCTTTTAAAGCTAAATATTTCC[A/G]TTTAAGCCTTGTTTTAGCTTCACCACAAGGGGCTT R 2 1 2 1 101000 r 74 goat snp46332-scaffold64-676719 8 33526182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778035 Affx-122939840 AX-385265151 8 32552496 AAAAAGCCACCTTCATATAACTCATATTGCATACT[A/G]TTTATTTTATTACCGTTTCAAATAAGTTATCTATT R 2 1 2 1 101000 f 74 goat snp46333-scaffold64-719701 8 33569458 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383848 Affx-122973152 AX-123254206 8 32628653 GCTTATACAGTGGAATTCAGGACATCAAAACTTCT[A/G]TTTCTGTATTTTCTGTCTGGTCTCTGCTGAAGACA R 2 1 2 1 101000 f 74 goat snp46335-scaffold64-795858 8 33646005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386719 Affx-122970157 AX-123257077 8 32696925 ATGCCACAGTTTGAGTTCCACTGAGAAGCAGACTC[G/T]GAGGCAAATTTCAGTATTCAAGATGTTCCCTACAG K 2 1 2 1 101000 r 74 goat snp46336-scaffold64-864130 8 33712824 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410331 Affx-122952472 AX-123280681 8 32731805 GAAACTACACACTCCCCCAACAATATGACCCTGGG[C/T]AATGAAGAGTTTAACAGATGAGAAATCTCATGTTG Y 2 1 2 1 201000 r 74 goat snp46337-scaffold64-899010 8 33748078 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447202 Affx-122924990 AX-123317538 8 32763501 GTTGGTTGAATAGGGAAAAAATGGGGAGGATCTAG[A/C]ACAGGGGTTGTCAGCCCGGGGACCACAGACCAGTG M 2 1 2 1 101000 f 74 goat snp46338-scaffold64-930706 8 33779847 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383490 Affx-122973431 AX-123253848 8 32800197 GAGTAGACTAAATGGCCACTTGATTCCAAATTGAC[C/T]GTATTGAGTCTTCCTATTAGCTAAGGCCATGTGGT Y 2 1 2 1 101000 f 74 goat snp46339-scaffold64-967402 8 33816602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404940 Affx-122956430 AX-123275292 8 32838342 ATTATATGTAAAATTTATAGCTTAATGATAACCCA[G/T]AGTAAGTGCTAATATCTTAGCTATTGTGAAAGGCT K 2 1 2 1 201000 f 74 goat snp46340-scaffold64-1005547 8 33854745 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800080 Affx-122968447 AX-385287003 8 32867650 AACAGCAGTTGCATGATATTTATGAGATGAATGTC[A/G]CAAAGGATTGTTCTAGTTATAGATGTGTGGAATGC R 2 1 2 1 101000 f 74 goat snp46341-scaffold64-1034855 8 33886050 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411040 Affx-122951963 AX-123281390 8 32934896 CCCCATGAAGGTGGTACACTTATTATTTTTAATTT[A/G]CAGATGAGGGAACTAAAGTACACAGAAGCTAAGGA R 2 1 2 1 102000 r 74 goat snp46342-scaffold64-1102101 8 33953302 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770932 Affx-122943989 AX-385258095 8 32975308 GCTCATCAGTATCTTCTAAGACTTGAACATAAATG[C/T]GGTAAGAAGATCAGATGAAAAGGCCTTTTGGGTAA Y 2 1 2 1 101000 r 74 goat snp46343-scaffold64-1142513 8 33994370 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768842 Affx-122945731 AX-385256019 8 33018578 TAAAGTGTTGTCACTTACTAACTATCAATAGATTT[A/C]AAAGAAGATTGGTTGAATCATGAAATAGGGCATGT M 2 1 2 1 201000 f 74 goat snp46344-scaffold64-1185783 8 34037816 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428408 Affx-122938941 AX-123298751 8 33056836 TCTTGCTGGTTCCTGGTAACTCTCCATTTGTCTCC[A/G]TTAATTTTCTTTGTAATTGTGCAACGTGAAGAAAC R 2 1 2 1 201000 r 74 goat snp46345-scaffold64-1224041 8 34077792 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412870 Affx-122950436 AX-123283219 8 33119140 TTTTCCACACCTTATTATCTACTTCTCCTTTGTAA[A/G]AGAGATAGCAGAAAGAGAGGGTATCAATAGAACAC R 2 1 2 1 201000 f 74 goat snp46346-scaffold64-1286345 8 34139837 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390194 Affx-122967799 AX-123260551 8 33159571 TGAGGTTGGAACGTCATCTCACAATTACTGTTCTC[A/G]CATTCAGGTCACCCAGCTCTCCTCAACTCTAAGGA R 2 1 2 1 201000 f 74 goat snp46347-scaffold64-1326776 8 34180926 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384429 Affx-122972182 AX-123254787 8 33206301 GGTATTCTCTGCATCCTGTTACACCCATCTTGACA[C/T]AAAATAGCACTTTGAACACTCATTAGTTTCAAGGA Y 2 1 2 1 101000 r 74 goat snp46348-scaffold64-1373506 8 34228108 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802869 Affx-122920686 AX-385289767 8 33235672 TGAGGGTTCCAGCTATGACTGAATTTGACATGCCT[A/G]CTTAGCACCTTGTAATCACTCCATGGCTTCAACAC R 2 1 2 1 101000 f 74 goat snp46349-scaffold64-1402877 8 34256478 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771093 Affx-122921944 AX-385258253 8 33280273 GGATTAGTCTCAATTCTGAGATACCTGTTCTCAGG[C/T]GTAAAAACTAGCTATCATTACCTATAATCATCAGA Y 2 1 2 1 101000 f 74 goat snp46350-scaffold64-1447478 8 34301235 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394039 Affx-122964993 AX-123264394 8 33331854 CACAAACTATGAAGACATTGTTTTCCTTCTTAAAA[C/T]GTAAATCAATATTTAAAATTATGTTTTAAATGAAT Y 2 1 2 1 103000 f 74 goat snp46351-scaffold64-1499059 8 34353806 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773632 Affx-122947706 AX-385260772 8 33389388 AGATGAACCTGCCTGATCATTTATAGAAAAATCAT[A/C]TTGAGAGAAAGATTGGAATTGAAATATTTTCTTGC M 2 1 2 1 101000 f 74 goat snp46352-scaffold64-1556593 8 34412099 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278769 Affx-1111836503 AX-519552242 8 33424456 AGGAGATTATCCATATAATGATATAGAATATAATT[A/G]GGGTATTTTTGATGGAGGGATTGTAAAGAGCGAGC R 2 1 2 1 103000 r 74 goat Random2.2K-886 8 33424456 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441541 Affx-122928705 AX-123311878 8 33427514 AGGTTTAGATTCTTACCTTCTTGGAATTTTAAGTG[C/T]AGACTTATCCCTAAAGTATCATTTTATTTTTATGA Y 2 1 2 1 101000 f 74 goat snp46353-scaffold64-1594719 8 34450827 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400969 Affx-122960107 AX-123271322 8 33458650 CCATGTCTATTTTGTTTCAGTTAAACATATTAGTA[G/T]CCAGAGTTTCTTAAAAATGTGTTATTTTTATCTCC K 2 1 2 1 303000 f 74 goat snp46354-scaffold64-1625855 8 34482022 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387647 Affx-122969849 AX-123258005 8 33487615 TAGTGCCCTGCCCCTTTCCCTCCTATTACATTACC[A/G]TTTGTAGAATTGTGAATTGTTTGTATTTAAAATGG R 2 1 2 1 201000 r 74 goat snp46355-scaffold64-1654820 8 34510135 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386502 Affx-122970754 AX-123256860 8 33518526 ATTAAAAAAGACAAGCTATAAAAAGTATCTAAAAG[C/T]ATGAGCAGATATGAGTGCTGGGTAAGTAAAAATTG Y 2 1 2 1 101000 r 74 goat snp46356-scaffold64-1685731 8 34541056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779728 Affx-122932272 AX-385266828 8 33575098 AGTTTTATCATCTATATACTGGGGTAAAAATAGTA[C/T]CTCTCTCTTTCGAACATAAGTAGGAAGACTAATTA Y 2 1 2 1 101000 f 74 goat snp46357-scaffold64-1742303 8 34598647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800182 Affx-122933862 AX-385287105 8 33632653 TACACAGAATTTATTTCTAATAAGTTTTTACTCTG[C/T]ACAGAAGGCTAAGATCTTAAATATGAAATGTATGC Y 2 1 2 1 101000 f 74 goat snp46358-scaffold64-1799858 8 34656965 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411453 Affx-122951813 AX-123281803 8 33676007 CAGATAACAAACAGGACTTTCTTTTTTTATAGAGG[A/G]CATTGTTTTAATGGCTCTAGCTTTAATGGAGAATT R 2 1 2 1 101000 r 74 goat snp46359-scaffold64-1843212 8 34700297 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420631 Affx-122945226 AX-123290978 8 33706713 CACTGTTTTTTAAATAGGACTTTTATTAAAATCTC[C/T]TCAAATTGTCCTAATTTTAAAGTGCCATCTGTTTT Y 2 1 2 1 101000 r 74 goat snp46360-scaffold64-1873918 8 34731195 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273924 Affx-1111833933 AX-519547530 8 33721284 ATTTCCAATAAATCCCATCCTGTGAAGTGAGGCTG[A/G]TGTAGGAAGCACATTTTGAGATCT R 2 1 2 1 101000 f 74 goat GoatD01.010915 8 33721284 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38446633 Affx-122924788 AX-123316969 8 33738484 ATAACAGAAATAAGAGGAATTGAAAGCTTAAAACC[A/G]TTAGCATATTAATCACATGGGGAAAACATTCAGAT R 2 1 2 1 101000 f 74 goat snp46361-scaffold64-1905689 8 34762898 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414297 Affx-122949590 AX-123284646 8 33776183 GAAGCAAGGGCTGAATAGAAGAGAGAAAATAAAAT[A/G]CCTCTTCCTGCCTTTGTTTTCCTAGTTGTGGAAGT R 2 1 2 1 201000 f 74 goat snp46362-scaffold64-1943388 8 34800293 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273350 Affx-1111833575 AX-284995833 8 33809410 TTTTCCAGGCAAGAGTACTGGAGTGGGATGCCATT[A/G]CCTTCTCCGTTCCCATACATAGAAAAGTACAAAAA R 2 1 2 1 103000 f 74 goat 8_33809410_AF-PAKI 8 33809410 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320778904 Affx-122969513 AX-385266011 8 33823098 AAGGTCATTCTTCCTTTTTGAATAAAGCAATTAGG[C/T]ACCATTTTAACCAAAATGCTTTTTAAGCTGAAAGA Y 2 1 2 1 101000 f 74 goat snp46363-scaffold64-1990303 8 34846886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431778 Affx-122936709 AX-123302119 8 33871014 ATATAGTTGAAGTATTTTCTTTAAGGTATCTCATA[C/T]GTGCTAACATATTTGCCCCCAAACATACCTGAGGA Y 2 1 2 1 101000 r 74 goat snp46364-scaffold64-2038219 8 34894937 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405284 Affx-122956854 AX-123275636 8 33911347 CAAATTGTAAGAGCTCTCAAAATTGTCTCATGCTT[A/G]CCCAGAATTGTATGATTATGGACAGAAACCAAGTC R 2 1 2 1 101000 r 74 goat snp46365-scaffold64-2078552 8 34934753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437532 Affx-122931910 AX-123307870 8 33945119 ATGGGTCAACTCTGAAGGCAGTAAACATTTTCCCC[A/G]TCTTTTGTTTGGTTGGTTGGTTTTGCCTGAATCCT R 2 1 2 1 103000 f 74 goat snp46366-scaffold64-2112324 8 34965105 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801454 Affx-122956125 AX-385288363 8 33997194 TTTGCTTTTGGAAGCATTGTGCTCTGATTTTACAC[A/G]TTGCTAGCTGCTTTGGGTTAATATAAGTTTATTAT R 2 1 2 1 101000 f 74 goat snp46367-scaffold64-2164399 8 35016727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773856 Affx-122933600 AX-385260996 8 34032467 GAGGCTTTAATGTACATAATTAAATAACTCATTAC[A/G]TTCAGTCTGTATGGTGGTATCAGTCATGTGCTCTG R 2 1 2 1 201000 f 74 goat snp46368-scaffold64-2199672 8 35052059 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404764 Affx-122957216 AX-123275116 8 34147390 TTCAACAGATAGGAACTGGGGAAAGAACATGGAGA[C/T]AGTGCAGAAGCAAAGAAAGGAAATGATTGATTGGT Y 2 1 2 1 101000 f 74 goat snp46370-scaffold64-2314595 8 35167196 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414206 Affx-122949652 AX-123284555 8 34189556 TATTTTCCCACACTCCAAAAAGCCACACCAGTATT[A/G]TAAAGCAATTTTTCTTCAATTAAAAGGTAAATTAA R 2 1 2 1 101000 f 74 goat snp46371-scaffold64-2356761 8 35209349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766897 Affx-122948353 AX-385254215 8 34228095 ATTGTCAATTGTATTCAGCTTGTTTTGTGAAAGAC[A/G]TCAGTAAAATAAGTAACAGTACCTTTTAGAAAGAT R 2 1 2 1 101000 f 74 goat snp52644-scaffold788-10912 8 35251914 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801634 Affx-122964162 AX-385288542 8 34257033 ATATATCACAGCTGTGTCAGGATGGAATATCTGAT[A/G]CAAGTTGGCATCATGTGAGATACATGTTAAGCCCC R 2 1 2 1 101000 f 74 goat snp52645-scaffold788-39850 8 35280671 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415890 Affx-122948477 AX-123286239 8 34295747 ACTGAGCGACTGAGTGCAGCAGAGCACAGTACACT[A/G]TGAAGAGGGTGAAATATCCCCATGGGGACAAATGT R 2 1 2 1 201000 f 74 goat snp52646-scaffold788-78564 8 35319779 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430936 Affx-122936838 AX-123301277 8 34325392 ATTCACATTAAGATTAAAGGGTGATAACACAAATC[A/G]CAACATGTAAATGAAGAAATAAGGAGACACAGAAA R 2 1 2 1 101000 f 74 goat snp52647-scaffold788-108209 8 35351543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802340 Affx-122921885 AX-385289244 8 34397204 TGGACTAGGGAAATTATACATTTCACTTTAGCTAA[C/T]AGATTGGGAAGCCTCTACAGAAAATAAAACACATT Y 2 1 2 1 101000 r 74 goat snp52648-scaffold788-180021 8 35424397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781686 Affx-122938977 AX-385268768 8 34440375 TCTCTCTCCTGTATGTAACAGAGTAGAGAAATAAG[C/T]CTGTCACCAAAACTAGAAAACCAGGCATTTTAACT Y 2 1 2 1 101000 r 74 goat snp52649-scaffold788-223192 8 35467363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803131 Affx-122974095 AX-385289997 8 34476532 AGTCCTCCAGTCCTCCTGTACTTGAAGAGTTGGGT[A/G]TATTGATTTTTTTTAAGCCTGGGAAACCATATGTC R 2 1 2 1 102000 r 74 goat snp52650-scaffold788-259349 8 35503620 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387661 Affx-122969840 AX-123258019 8 34557779 TATCCATCTTTCTCTCCATGAATGCCCAGTGCCCA[C/T]CACAGTGGTCAGACTTTTTCACTATGGGGCCAGAT Y 2 1 2 1 201000 f 74 goat snp52652-scaffold788-340596 8 35584324 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399431 Affx-122961225 AX-123269786 8 34635998 GTAAGCAAGTTGTTAACCAAAACTCCTAAAAGAAG[A/C]GAGATATTAAGTTTCTCAACAACACAGGATGCTTC M 2 1 2 1 101000 r 74 goat snp52653-scaffold788-418815 8 35663270 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435085 Affx-122933721 AX-123305425 8 34672650 ACTGAGGTCACCTAGGTAGAAAAGAGAAGCAACTG[A/G]AATTGGGACTAAGAACTCTGCCCACAGTTTGTGTA R 2 1 2 1 201000 r 74 goat snp52654-scaffold788-455467 8 35700549 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790859 Affx-122952328 AX-385277857 8 34785282 ATGGATTTACTCAGAATTATTGACATAAAACCATA[C/T]AGAGCTGGTACTTGTGCCCAGGTCACAACTCTAAT Y 2 1 2 1 101000 r 74 goat snp27999-scaffold300-200 8 35814671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442199 Affx-122928793 AX-123312536 8 34850397 ATGTAGCAGCCCATAAAACCCCAAACTCTAGCAAA[C/T]GAAGAATGGCATTTGAACAATGTTGCTTTGAAATT Y 2 1 2 1 201000 r 74 goat snp28000-scaffold300-65315 8 35879599 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454242 Affx-122919660 AX-123324575 8 34884147 CCTATATAAGAAAAAAAGAAAATAATGTTTAAAAT[A/C]TTGTGAACATAACTTGAATTTGATTTCTTGTTTAA M 2 1 2 1 103000 r 74 goat snp28001-scaffold300-99065 8 35913468 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278594 Affx-1111836504 AX-519552073 8 34900179 GAGTCATCTTGGTTTGTGGATTTGTAAGCCAGGGA[A/G]CCTATTTTCCTTTATATTGGTGATATAGACTAGAA R 2 1 2 1 101000 f 74 goat Random2.2K-887 8 34900179 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418943 Affx-122946498 AX-123289291 8 34950772 TTTTAAAATTTAAAATTATCTTTTAAAGACAGTCT[A/G]CTATTCCTCCTCTTGTTCTCCCTCTTCTCTTTCTC R 2 1 2 1 101000 r 74 goat snp28002-scaffold300-165690 8 35979929 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377428 Affx-122977545 AX-123247787 8 34989551 ATGGGGCAAAGCCTCCCTACAAATTGCATTAGACT[A/G]TGACATGAATGAAATACAAATTTTACTGTGCCAAG R 2 1 2 1 101000 f 74 goat snp28003-scaffold300-204469 8 36018658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399051 Affx-122960908 AX-123269406 8 35019840 GAATTATGCCTCCATCCATTATTGTTAGAAGTTGT[A/G]CAGTTAATTTTCCCCTCATTAGGCTGAAGTGTTCA R 2 1 2 1 101000 r 74 goat snp28004-scaffold300-234758 8 36048969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416770 Affx-122948175 AX-123287118 8 35055182 ATTAAAAGGTGCTTTCCTAATTTTTTCATCCCAGT[A/G]TATTTGTGTGTGTATTATATCTGTATTGACTGAAA R 2 1 2 1 101000 f 74 goat snp28005-scaffold300-270100 8 36091329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414592 Affx-122949363 AX-123284941 8 35096233 TTAATGAGTGCTAGCACAAAGTCTGTTGTTCCAGG[A/G]TTAAATCTAGTAAAACAAACAAAATTTCCACTTAA R 2 1 2 1 303000 r 74 goat snp28006-scaffold300-311151 8 36132596 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778249 Affx-122930428 AX-385265364 8 35134904 AAAATTTTCTAAAGATTCTTGCCTTGTTGGGAACA[A/G]TGTGACAAGACTCGATTGTGAATGTGAACTATTAA R 2 1 2 1 101000 r 74 goat snp28007-scaffold300-349822 8 36171427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423435 Affx-122942604 AX-123293781 8 35173659 CTTGCTTGGGAAAAGATAAGTTTTTATTATGCTAG[C/T]GTTGATGATGTAAAAAATTTTTTAAAAAAGAAGAA Y 2 1 2 1 101000 f 74 goat snp28008-scaffold300-388577 8 36210154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765417 Affx-122957571 AX-385252923 8 35202181 TAGTTTGTATTAGAATGGGCATTAAGAAAGTTTAT[A/C]TTTTAACTCTCATGTAAATTCTACTTTATATGAAT M 2 1 2 1 101000 f 74 goat snp28009-scaffold300-417099 8 36238874 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801882 Affx-122949365 AX-385288789 8 35252422 TGTAGGTTGATGAATAAAAGTGAGTCTGACATTAA[C/T]ACACACACAAATGCTTTGCTTGCCCATGTACTCGC Y 2 1 2 1 101000 r 74 goat snp28010-scaffold300-467340 8 36288962 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382324 Affx-122973897 AX-123252682 8 35313995 GGCATCTGAATGCTTCAACTCCACTTAGCTCACAG[C/T]GTACTCGGAAAGGAGTACATTCTGCAGGGAAGATA Y 2 1 2 1 101000 f 74 goat snp28011-scaffold300-528913 8 36350476 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389479 Affx-122968324 AX-123259837 8 35349456 GATCCTGTGAGAAAGGAGAAGTTTCTGAAAGAAGA[C/T]AACAAAAATGGGATGGGACTGGAAAAGGAGAAAAT Y 2 1 2 1 101000 f 74 goat snp28012-scaffold300-564374 8 36385911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392363 Affx-122966246 AX-123262720 8 35381165 CTTCTTTGAATCGGTTTCCACCAACTGGAAAACAA[C/T]CCATGAGTCCATGAGTAATAGAGTTTAAAAAAATG Y 2 1 2 1 201000 r 74 goat snp28013-scaffold300-596083 8 36417587 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476245 Affx-1251763751 AX-586011667 8 35384337 CAAAATTTCCTATGATTTGGTAATTATTTATAGCA[-/AATACTTTTTTTTTTTTAATTTTATTTTTTTTTGAATTTTTGTGAGGGAGAAAGTGGTCTTGCCGTCCTATTCCTCCGCC]ATACTTTTAAGACTGTAATGCTTACCAGTGTGCCT - 8 1 4 1 20000 f 74 goat SV_220 8 35384337 - deletion junction SV-TF-chip 539476497 Affx-1251763751 AX-586011893 8 35384337 CAAAATTTCCTATGATTTGGTAATTATTTATAGCA[-/AATACTTTTTTTTTTTTAATTTTATTTTTTTTTGAATTTTTGTGAGGGAGAAAGTGGTCTTGCCGTCCTATTCCTCCGCC]ATACTTTTAAGACTGTAATGCTTACCAGTGTGCCT - 4 1 4 1 20000 r 74 goat SV_220 8 35384337 - deletion junction SV-TF-chip 562165125 Affx-1251763751 AX-606940537 8 35384337 CAAAATTTCCTATGATTTGGTAATTATTTATAGCA[-/AATACTTTTTTTTTTTTAATTTTATTTTTTTTTGAATTTTTGTGAGGGAGAAAGTGGTCTTGCCGTCCTATTCCTCCGCC]ATACTTTTAAGACTGTAATGCTTACCAGTGTGCCT - 8 1 4 1 20100 r 74 goat SV_220 8 35384337 - deletion junction SV-TF-chip 562165332 Affx-1251763751 AX-606940743 8 35384337 CAAAATTTCCTATGATTTGGTAATTATTTATAGCA[-/AATACTTTTTTTTTTTTAATTTTATTTTTTTTTGAATTTTTGTGAGGGAGAAAGTGGTCTTGCCGTCCTATTCCTCCGCC]ATACTTTTAAGACTGTAATGCTTACCAGTGTGCCT - 8 1 4 1 20100 f 74 goat SV_220 8 35384337 - deletion junction SV-TF-chip 562165394 Affx-1251763751 AX-606940805 8 35384337 CAAAATTTCCTATGATTTGGTAATTATTTATAGCA[-/AATACTTTTTTTTTTTTAATTTTATTTTTTTTTGAATTTTTGTGAGGGAGAAAGTGGTCTTGCCGTCCTATTCCTCCGCC]ATACTTTTAAGACTGTAATGCTTACCAGTGTGCCT - 8 1 4 1 20100 r 74 goat SV_220 8 35384337 - deletion junction SV-TF-chip 562166293 Affx-1251763751 AX-606941701 8 35384337 CAAAATTTCCTATGATTTGGTAATTATTTATAGCA[-/AATACTTTTTTTTTTTTAATTTTATTTTTTTTTGAATTTTTGTGAGGGAGAAAGTGGTCTTGCCGTCCTATTCCTCCGCC]ATACTTTTAAGACTGTAATGCTTACCAGTGTGCCT - 8 1 4 1 20100 r 74 goat SV_220 8 35384337 - deletion junction SV-TF-chip 562166364 Affx-1251763751 AX-606941772 8 35384337 CAAAATTTCCTATGATTTGGTAATTATTTATAGCA[-/AATACTTTTTTTTTTTTAATTTTATTTTTTTTTGAATTTTTGTGAGGGAGAAAGTGGTCTTGCCGTCCTATTCCTCCGCC]ATACTTTTAAGACTGTAATGCTTACCAGTGTGCCT - 8 1 4 1 20100 r 74 goat SV_220 8 35384337 - deletion junction SV-TF-chip 562166511 Affx-1251763751 AX-606941919 8 35384337 CAAAATTTCCTATGATTTGGTAATTATTTATAGCA[-/AATACTTTTTTTTTTTTAATTTTATTTTTTTTTGAATTTTTGTGAGGGAGAAAGTGGTCTTGCCGTCCTATTCCTCCGCC]ATACTTTTAAGACTGTAATGCTTACCAGTGTGCCT - 8 1 4 1 20100 r 74 goat SV_220 8 35384337 - deletion junction SV-TF-chip 38383281 Affx-122972723 AX-123253639 8 35425779 GTGATACTGTATGAGGGCCCTCCTAAAAGACCCTA[C/T]GACCAAATATGGTTACATTCTGAAGTACTGAGGGC Y 2 1 2 1 101000 f 74 goat snp28014-scaffold300-640697 8 36462081 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453631 Affx-122919746 AX-123323964 8 35471091 CCCTAATGGTAAGAGCAATCCACTGTTTCTTATAA[C/T]GAGTCGGATAGGAAAGCAGTTCCCTAGATGATGGA Y 2 1 2 1 201000 f 74 goat snp28015-scaffold300-686009 8 36507473 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421755 Affx-122944364 AX-123292102 8 35528648 TGTGAATAACACAAAGATTTCTATTTATGTGTTCC[A/G]TTTTAACTCTGCATTTTTACTTTTCCAAATTCCTT R 2 1 2 1 101000 r 74 goat snp28016-scaffold300-743566 8 36565895 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398553 Affx-122961521 AX-123268908 8 35564551 TTTTTCCACTTTTTGGTATTTGTGACTAGATTGAA[C/T]ATACCTGTATTACAGTAGAATCTACAAGAGGCTTC Y 2 1 2 1 101000 r 74 goat snp28017-scaffold300-779469 8 36601889 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278596 Affx-1111836505 AX-519552075 8 35568476 GTCATACCTCCATGAAATTCTCTTCTGGTGATTCT[A/G]GGATGGGAATCTGTACTTCATACATACTTTCCCAC R 2 1 2 1 101000 f 74 goat Random2.2K-888 8 35568476 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320774789 Affx-122943982 AX-385261923 8 35622193 TAATGTGGTATTTGCTTTCATATTCCTAAATGTCA[C/T]GATGATACTATAGCATCTTGATTCAAGTTTAGGTA Y 2 1 2 1 201000 f 74 goat snp28018-scaffold300-837111 8 36660751 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417442 Affx-122947205 AX-123287790 8 35651426 CTGAGTGGAAGTATTATGTCTTCTGGCAGAGTAAA[C/T]AGAACAAGCACTTACTTCCCTCTTGTTTCTAAGAA Y 2 1 2 1 201000 f 74 goat snp28019-scaffold300-866344 8 36690617 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382389 Affx-122973844 AX-123252747 8 35690790 CTGCAAGACACTGTAAGACATTAGGGAACCAGTGA[C/T]GATATTCAGTAAAGACAATTCCCTCCTTTTTCTGT Y 2 1 2 1 101000 f 74 goat snp28020-scaffold300-905708 8 36730154 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389025 Affx-122968633 AX-123259383 8 35752645 TCATACTTTCTAATACTTTCTGATAACCAGGCTCT[C/T]TTCTTGTTCCAGAGTGTGCATTCTTTTTCCTCTTA Y 2 1 2 1 101000 f 74 goat snp28021-scaffold300-967563 8 36792443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441926 Affx-122928592 AX-123312263 8 35793760 TCCAAAAAGGCAGACACAGCTGGCTCTTTTGGGGC[A/G]CTTAAAGTCTAGCTAGAAAAAGAGACACTGAGCAC R 2 1 2 1 201000 r 74 goat snp28022-scaffold300-1008678 8 36834293 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797179 Affx-122941208 AX-385284119 8 35830056 TAAGCCCTAGACATAGAACCATATGCAAAGTAGGT[A/G]TTCAAAGAATGCCAGTTCCTTCTGCTCATATACTG R 2 1 2 1 102000 r 74 goat snp28023-scaffold300-1044974 8 36870955 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779551 Affx-122934511 AX-385266654 8 35892172 GCAATGAATACAAGGCATACAACTTCCTTGAATAC[A/C]AGGAAGTTTGAATACAAGGAATCAGAAGTGTTTTG M 2 1 2 1 101000 f 74 goat snp28024-scaffold300-1107090 8 36933680 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395399 Affx-122963959 AX-123265754 8 35929992 TTTTAGGTAACTGAATTTGATATAAAATGGGTTAG[C/T]ATAATTTGTTTCAAGTGAAATACCAAGTTTGACTA Y 2 1 2 1 101000 r 74 goat snp28025-scaffold300-1144910 8 36971610 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787804 Affx-122949783 AX-385274827 8 35960326 TTTATTTGGCTGCTGGCTCTGAGCTGCTATTTGAA[A/G]AGAGCAGTACCATATGCAGCACATGCATATTCAAT R 2 1 2 1 101000 f 74 goat snp28026-scaffold300-1175244 8 37002137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385049 Affx-122971832 AX-123255407 8 36013311 TTGGGAGAGAACTTTAGATTATTACTGACTGGGCA[C/T]TAAAGGAAACATGACTCTTGAGGACTGCAGATGTC Y 2 1 2 1 101000 f 74 goat snp28027-scaffold300-1228229 8 37056904 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385413 Affx-122971336 AX-123255771 8 36042761 CACTTAAGTTGGCAATTCATTTGCAACTACAGCCT[C/T]ACCTACCCTAGTTAACATGCCTAGTTACTCAACTG Y 2 1 2 1 101000 r 74 goat snp28028-scaffold300-1257679 8 37086349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398905 Affx-122961016 AX-123269260 8 36079333 GCTCAAATGGAACACAAGAGACCTGGGTTCAAATC[G/T]AATTTCTGTCACTAATTGGATGATAGTCCCTTGAT K 2 1 2 1 201000 r 74 goat snp28029-scaffold300-1294251 8 37123744 T G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320775050 Affx-122924673 AX-385262182 8 36130787 CCAAATAATCACTTTCATGAATGTTTAATTAGAGG[C/T]ATATAAGTGTTCTGGATGAAGAGGACCAGTGATAT Y 2 1 2 1 101000 r 74 goat snp28030-scaffold300-1345705 8 37174178 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785907 Affx-122942696 AX-385272944 8 36161367 CTACTTCTGCTCTTACTTTTATCTACCAGAAGTTA[C/T]GGTAAGAGTTCTTCACTTAGTATGTCATTCAGTTG Y 2 1 2 1 101000 r 74 goat snp28031-scaffold300-1376285 8 37204592 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417462 Affx-122947188 AX-123287810 8 36257817 TGGCATAGCACCCAATGATGGTAGTTATGTGTGCT[A/G]CTAATCCTTAATAAAGCTAGAGATGTGAGAAAATA R 2 1 2 1 201000 r 74 goat snp28033-scaffold300-1472735 8 37301669 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795323 Affx-122959761 AX-385282281 8 36357028 TTTGCAGGTAAAAACCACCACAAATTAATTAGCAC[A/G]TCTTCATTTGCTTGAGGATGATTAATAATACTCAG R 2 1 2 1 101000 f 74 goat snp28035-scaffold300-1571946 8 37401457 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391310 Affx-122967329 AX-123261667 8 36398333 GCAGAATGGTGCACTTTAAGAAGGGGGTTAGAATG[C/T]AGCTTATGTGATGCATATTTTCCCACAATTTTTTA Y 2 1 2 1 101000 f 74 goat snp28036-scaffold300-1613251 8 37442399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464579824 Affx-1110554578 AX-516051354 8 36411272 TAAGGTATGGCAGTTACCAATAAAGAGGTAAAAAC[A/G]GTCATAAGGATACAAATAGAGATAAACAAGGACAA R 2 1 2 1 101000 r 74 goat 8_36411272_AF-PAKI 8 36411272 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791167 Affx-122920257 AX-385278162 8 36429536 GTACTTCTTCTTTCTTACACAGAACCAGGCTAAGG[C/T]GATAAGACTGTCTAACCAACAGGTCAGAGCTGATG Y 2 1 2 1 101000 f 74 goat snp28037-scaffold300-1644454 8 37474270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403126 Affx-122958115 AX-123273479 8 36460984 AGATGAGTAGAAGCAGGGAGGTGGAGGTCAGTCTC[C/T]GGGGAAGTTCTCTCGGACCAAGTCCCCTCCCCCTT Y 2 1 2 1 101000 f 74 goat snp28038-scaffold300-1675902 8 37505390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419248 Affx-122946270 AX-123289596 8 36514405 CCTGGAAAGCCTATGTATACCAATATGAATTAGAG[G/T]TGTTGATGGTCTTCAACACATCAAGGTCCCAGAAG K 2 1 2 1 101000 f 74 goat snp28039-scaffold300-1729323 8 37559433 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395593 Affx-122963828 AX-123265948 8 36572883 CAATTCAGTAAACCAGCTTATCACTCTTCCCGTGA[C/T]ATGACTTCCTTCAATCTCTGGTCCATCATCAATTA Y 2 1 2 1 101000 f 74 goat snp28040-scaffold300-1787801 8 37618064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386362 Affx-122970855 AX-123256720 8 36635373 AAAGATGTCTCAGGGAGTTTCTGTTGAAGGCAAAG[A/G]GAGGAAACCCCTGGATACTCTCTGCTCTAAGCTGG R 2 1 2 1 101000 f 74 goat snp28042-scaffold300-1850291 8 37680743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401910 Affx-122958829 AX-123272263 8 36678453 CTGTCAAGAAAATTGATATCCTCCAACGTGCTGTT[C/T]TGTTTGGTTAAAGTAAAATAATTATTACCACTCTG Y 2 1 2 1 101000 f 74 goat snp28043-scaffold300-1893371 8 37724340 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399957 Affx-122960838 AX-123270312 8 36723871 GAGTCTTTTGAAAGAATCACTACAATTGCCAAATG[A/G]AGATCTGACTAGTAGGGGTGACTAGAGTGGACATT R 2 1 2 1 101000 f 74 goat snp28044-scaffold300-1938789 8 37769753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389003 Affx-122968648 AX-123259361 8 36755189 ACATAAATTTTTCACATTATCTATTCCTTTGTACA[C/T]AGTACAATGCTAATGCCCAGAGGATTCACTGAACT Y 2 1 2 1 101000 r 74 goat snp28045-scaffold300-1970107 8 37801093 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795234 Affx-122927748 AX-385282192 8 36812601 AATCACCTCAGTAAGTGTACTTTTGTTTTTGTAAA[C/T]GTACTTTTTCCAGTTATTTCTTAGGAGTGTAAGAA Y 2 1 2 1 101000 r 74 goat snp28046-scaffold300-2027519 8 37858610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788601 Affx-122946025 AX-385275618 8 36860805 AAGCATACTGGGGAATATCCTTAGAGTCATTTATA[G/T]TGCTCTTTTCCTACAGTAGCTATCTTAGAAAATGG K 2 1 2 1 101000 r 74 goat snp28047-scaffold300-2075723 8 37907064 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446337 Affx-122925619 AX-123316673 8 36920134 TGAAATGTCTTATTATAAAGGGAATGCTTCTAACC[A/G]TTCCTCTTCAGAATGTTTACTATGTATAGGTACCC R 2 1 2 1 101000 f 74 goat snp28048-scaffold300-2135052 8 37965858 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783039 Affx-122973870 AX-385270107 8 36979121 GTTTGGAGGGTCCTTTTAAGGCAGTGATTTCCAAA[C/T]GAAGTTGTTTGGGCCTTCTAGGCCTTCTAACAGCT Y 2 1 2 1 101000 r 74 goat snp28049-scaffold300-2194039 8 38023421 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378994 Affx-122976387 AX-123249353 8 37034094 GTGATTTTAACAAATGGTTAATGGAGGGCAGTGAG[C/T]AAAGGGTGCAGTGTTGTGCAATGCAGCTGCAGGTG Y 2 1 2 1 101000 f 74 goat snp28050-scaffold300-2249012 8 38078995 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409602 Affx-122953557 AX-123279953 8 37080405 CTGTGATTAGTTTTATCATAATGTCAGTTTCTTAG[A/C]TAACATTTCACTTGGGTCATTTTTTTATTCCTAAC M 2 1 2 1 101000 r 74 goat snp28051-scaffold300-2295323 8 38125349 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785606 Affx-122929013 AX-385272650 8 37118490 GGAGGGGAAGGATTCAGAAGCAGAAGAGGAAAGAT[C/T]GTCATTAGCTCAGTGACAAGCCAGGTGCAAGACTG Y 2 1 2 1 201000 f 74 goat snp28052-scaffold300-2333408 8 38163542 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441272 Affx-122929477 AX-123311609 8 37154094 TATAGTCATCCCTGGGATCCATCTCTTTATCAGGT[G/T]TGTTATGAGTCCAGGTACTATTTTGGCACTGGATA K 2 1 2 1 101000 f 74 goat snp28053-scaffold300-2369012 8 38199485 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416286 Affx-122947942 AX-123286635 8 37206152 ACAGGGGAGGGACAGAAAAAGAATGGAATACCTAT[A/G]CAGACTTGGTCTCTGCTCTCGTTGGAAATTTTACA R 2 1 2 1 101000 f 74 goat snp28054-scaffold300-2421070 8 38251840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418107 Affx-122947133 AX-123288455 8 37239104 AGCTAGAACAACTTCTGCTGCCAAGCAAGGAGAAA[C/T]TGAGCATTTTGTTATAAACCACTGGATTCAGAGCA Y 2 1 2 1 201000 r 74 goat snp28055-scaffold300-2454022 8 38284709 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386083 Affx-122971448 AX-123256441 8 37270787 GCATGGAAGTATTTTCATATTTTACAGTAGGTATT[A/G]TTATAATGGTACACATAACTAATTGTCAACCCTGA R 2 1 2 1 201000 r 74 goat snp28056-scaffold300-2485705 8 38316743 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800110 Affx-122948144 AX-385287033 8 37308908 TTTCATCTTGAAGGTATAGCTACTCTCTGATTTTA[C/T]CTGCCCTTCAACTTATTTCAGACACGTTGAGTTTG Y 2 1 2 1 101000 r 74 goat snp28057-scaffold300-2523826 8 38355313 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799929 Affx-122974150 AX-385286855 8 37361625 AATGATTTAATTCCTTCATAGAGCAGAACTTTTTA[C/T]AGTGACTCAGTACATTGCCTGAAGTTTGTTGAAAA Y 2 1 2 1 101000 r 74 goat snp28058-scaffold300-2576543 8 38406924 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409119 Affx-122953310 AX-123279470 8 37399631 GGGACCATACTGCCAGTTCTGCCCCGACTAGACCC[C/T]TGGTCCTCTGGCAGAGATGTCTGCCCCAGGAAGAT Y 2 1 2 1 201000 r 74 goat snp28059-scaffold300-2614549 8 38445431 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413462 Affx-122950669 AX-123283811 8 37430577 AAATTAAGAAAAAAGTTAGGAAAGTAAATCTTAGA[C/T]GCCTGAAGGAGGAGCCTTTTGGGGCTATGACTCAG Y 2 1 2 1 101000 f 74 goat snp28060-scaffold300-2645495 8 38476967 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414110 Affx-122949735 AX-123284459 8 37479280 GACTTTTTCTGCTTGGCTTGTTGCTATTGACTTCT[A/G]TAAATTTTGATTAAAAATTAAGTAGTAGGTAGCTA R 2 1 2 1 103000 f 74 goat snp28061-scaffold300-2694198 8 38525878 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797464 Affx-122968720 AX-385284403 8 37519371 CAGTTTTTCTATGTAGAGAAGATTTTGAAGTGTGT[A/C]GTTTCTTCAGTAAATACAGGTTTATTCAGATTTTC M 2 1 2 1 101000 r 74 goat snp28062-scaffold300-2734289 8 38565649 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790015 Affx-122978509 AX-385277021 8 37558596 TCTTGAGATCAGCACTGGGTAGAAAAGAACATACT[A/G]TTTTAAATCCATTTAGGTTATATTGACCAAAGAAG R 2 1 2 1 101000 f 74 goat snp28063-scaffold300-2773514 8 38605094 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381204 Affx-122974530 AX-123251562 8 37608349 CTATTGGTTGCTTGAGGAGATGGGTTCTGTGCTAG[C/T]GGTTAAAAGTTGGAAGGAAAATGCCTCAAAAGAAA Y 2 1 2 1 201000 r 74 goat snp28064-scaffold300-2823267 8 38654979 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413115 Affx-122950382 AX-123283464 8 37648594 AATTTCACTGATTTCCTCTTTCCTTCTGGAACTTC[C/T]GCCTGTACCAGTTGATGGCTTTATGGCCTCAAAAG Y 2 1 2 1 101000 r 74 goat snp28065-scaffold300-2863512 8 38695225 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416567 Affx-122947666 AX-123286915 8 37738075 GAAAGAAACCAAGAGCCAAGACCACATAACAACAC[C/T]GGAAGGAAAACAAGGACCTCACAAAACAGGCAAAT Y 2 1 2 1 101000 f 74 goat snp28067-scaffold300-2952993 8 38785131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770669 Affx-122978402 AX-385257833 8 37767881 GGATATCTGATCTCTAAATTCAAATTAATTGAAGA[C/T]AATTTTCCTATTAAAAAGTAAACCTCTTGATGGTA Y 2 1 2 1 101000 r 74 goat snp28068-scaffold300-2982799 8 38814946 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786894 Affx-122919910 AX-385273923 8 37818972 AGTTAACCATCATAATAACTCAATTTTTAAGTAAG[C/T]AGTTAATTCACAATCAATGGATTCATGTATGAGGC Y 2 1 2 1 101000 f 74 goat snp28069-scaffold300-3033890 8 38866229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416676 Affx-122947584 AX-123287024 8 37849796 CTTGTGTATTGCTGGTGGGAATGGTGCAGCCACTG[C/T]GAAAAAACAGTATGAAAACAAAACTCCAGCAATTT Y 2 1 2 1 101000 f 74 goat snp28070-scaffold300-3064714 8 38897578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773561 Affx-122952591 AX-385260701 8 37890818 TATTTCATGGCAAATTTGTTATCAAACCCTGTAAA[G/T]TATTTCTTCCTAATAGTTTTCAACTTCATTCCCAC K 2 1 2 1 201000 r 74 goat snp28071-scaffold300-3105736 8 38938760 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772042 Affx-122945262 AX-385259197 8 37933280 AGTATACAGAAAGAGGTATACAGAGGTATTTAGAA[A/C]GCTGGCCTCTTATATTTTAATCTTAACCCAAACTA M 2 1 2 1 101000 r 74 goat snp28072-scaffold300-3148198 8 38982592 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436127 Affx-122932648 AX-123306466 8 37975508 TACAGAATGGGTTTGGGCAGTGCTTCTGTATAAAA[C/T]GTTAATTAAGCTTGCATTTTTTTGGCCACATTGAG Y 2 1 2 1 101000 f 74 goat snp28073-scaffold300-3190426 8 39025376 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427763 Affx-122939239 AX-123298106 8 38007977 AATATCAGAAAAGCTTTATTCCAAGGTTTATGACC[A/G]ACCTTCATAAATTGTTCTTAGCAGCAGTTTAGGTT R 2 1 2 1 101000 r 74 goat snp28074-scaffold300-3222895 8 39057925 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387304 Affx-122970519 AX-123257662 8 38090797 CAGAATCTGCTTTTAACACATCCTGATGATTCATA[C/T]GCATGTTAGAGCTTGAGAAGCACTGCCCTGGGTGA Y 2 1 2 1 201000 f 74 goat snp28075-scaffold300-3305715 8 39141210 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772802 Affx-122955907 AX-385259947 8 38121025 GAGAAAACTGTGCCTTTTAGAGACATAGTATTGGG[C/T]ATTTAAAGTAGTTGGTTATTGAAACCAGTAGACTC Y 2 1 2 1 101000 f 74 goat snp28076-scaffold300-3335943 8 39170505 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383078 Affx-122973740 AX-123253436 8 38154895 GGACACAACTGATTAACTAAGCACAGCAGCACATA[C/T]ATTATCCACTAATTATTTTATAACCTCCTGTTCCC Y 2 1 2 1 201000 r 74 goat snp28077-scaffold300-3369813 8 39205350 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425035 Affx-122941869 AX-123295381 8 38197294 ATATAAAATTAAAAGAATCCTGAAAGAAAACATAT[A/G]CAGTATTAAAGTGATTACCTCTGAGTAGCTGCATT R 2 1 2 1 101000 r 74 goat snp28078-scaffold300-3412212 8 39247938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800930 Affx-122946271 AX-385287845 8 38238440 TGTTTTTTCTTTATAGATGTTGGAATCTTTAAGAC[A/G]ACTTCAGTGAGTTCCTGAAATCATTCCCTATGGCC R 2 1 2 1 102000 r 74 goat snp28079-scaffold300-3453358 8 39289171 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781457 Affx-122943292 AX-385268542 8 38268317 AATAGTCAATCTTAATGATTGATTAAGTCATAAAG[C/T]GATTTAATCAATCAAAACTATTAAACAATTTTAAT Y 2 1 2 1 201000 r 74 goat snp28080-scaffold300-3483235 8 39319223 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762611 Affx-986697141 AX-385250701 8 38291552 ATAGCAGAGAAAAACAACTACCTGAGGGGAACAGT[A/T]AACAGAACAACTATCACTGTTGGTACAAGACTGAG W 4 1 2 1 600010 f 74 goat 8_38291552 8 38291552 Ancestral_priority_1043 ancestry 0.672 recommended IMAGE 10K 10K ancestral 320762613 Affx-986697143 AX-385250703 8 38291574 TGAGGGGAACAGTAAACAGAACAACTATCACTGTT[C/G]GTACAAGACTGAGACAATCAGAGTAGAAAGAACTC S 4 1 2 1 600010 f 74 goat 8_38291574 8 38291574 Ancestral_priority_1043 ancestry 0.628 neutral IMAGE 10K 10K ancestral 320764983 Affx-986697145 AX-385252561 8 38291575 GAGGGGAACAGTAAACAGAACAACTATCACTGTTG[A/G]TACAAGACTGAGACAATCAGAGTAGAAAGAACTCA R 2 1 2 1 600010 r 74 goat 8_38291575 8 38291575 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 320803096 Affx-986696168 AX-385289967 8 38291774 ATAACTGACTCAAATATCTTCATTGCTTGTCAGAA[A/C]AAAGTTCATCATTTTTTATATAGAGATGTGTAAGC M 2 1 2 1 600010 f 74 goat 8_38291774 8 38291774 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 320762617 Affx-986697147 AX-385250707 8 38291815 TCATCATTTTTTATATAGAGATGTGTAAGCAGACA[C/T]ACAACAAAACAATATTCACAATATTCAGGATACAA Y 2 1 2 1 600010 f 74 goat 8_38291815 8 38291815 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 320764990 Affx-986697149 AX-385252567 8 38292154 ATGAATAGCTCAGTACTCTAACTGTGGTACTGGTT[A/G]TAGTTGAACTGATGTATGCATATGTCCAAACTCAT R 2 1 2 1 600010 r 74 goat 8_38292154 8 38292154 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 320801795 Affx-122929783 AX-385288703 8 38303620 TCCAGAGTAGCTACATCATACAGGTTTCAAAAACA[A/G]ATAACACTTCCTTTTACCCTTTCCAATTCTCTTAA R 2 1 2 1 101000 f 74 goat snp28081-scaffold300-3518538 8 39354527 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394426 Affx-122964596 AX-123264781 8 38346826 AAGGGAGAGGATAAATCCCAGTAAAGACCATATAA[A/G]CTTTGCCTAAATCACTGCCTGCCCTCTGAATTACA R 2 1 2 1 101000 f 74 goat snp28082-scaffold300-3561744 8 39398170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785881 Affx-122946136 AX-385272918 8 38380604 TGGCTAATTTAGTTATAGTACATCCAGGGAATGTC[A/G]TGCAGCCCTTAAAAGAATAACACAGATCTATCTGT R 2 1 2 1 101000 r 74 goat snp28083-scaffold300-3595522 8 39432012 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393980 Affx-122965040 AX-123264335 8 38418109 TACAGACCATCTATACACGTACAGTTCCTTGTTCA[A/G]TCAGCTGAGAGAATCTAGAAACAATGACATCCCAG R 2 1 2 1 101000 f 74 goat snp28084-scaffold300-3633027 8 39469495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397786 Affx-122962505 AX-123268141 8 38454821 GTAAGGTGCTCCCCTGCTTGTGTAAATGAACAGGA[G/T]CTTCCCAAAGTAATCACCTGGGAAGGTGAGATCTT K 2 1 2 1 102000 f 74 goat snp28085-scaffold300-3669739 8 39506176 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443438 Affx-122927359 AX-123313775 8 38504356 GAAAAGCCCTGGTCCCAGTACAGGCTCTAGTTTGC[C/T]GTGTGGCCTCAAACAAGAATATCTCAACTTCTAAA Y 2 1 2 1 101000 r 74 goat snp28086-scaffold300-3719274 8 39555790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421543 Affx-122943868 AX-123291890 8 38565567 TTTTTTTGCCACACAGCGTATTTGATCTTAGTTCT[A/C]GGACCAGGAACTGAACCCGGGCACTTGGTAGTGAA M 2 1 2 1 201000 f 74 goat snp28087-scaffold300-3780485 8 39618083 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788816 Affx-122934507 AX-385275831 8 38618209 AGCATCATGCCCGAAATCTGAAAAATGCTAATCTT[A/C]CAACAGTAAGATAATAAGATACCAAGAAAGCAAAG M 2 1 2 1 201000 r 74 goat snp28088-scaffold300-3833127 8 39670877 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384473 Affx-122973078 AX-123254831 8 38660983 AAAAGTTGTACTTTCTGTAACACATGCTCCCTCTC[C/T]GCACCTGGTCTATTGAATTTTCCCCACTTTCAGAA Y 2 1 2 1 101000 r 74 goat snp28089-scaffold300-3875901 8 39713942 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791834 Affx-122949788 AX-385278824 8 38698228 TCTAAGTGCATGAAATAGGGAAGTTGACCTCCTCT[A/G]TAGGAAGGAACTTTTCCTGAGAAATCAATAACTGA R 2 1 2 1 101000 f 74 goat snp28090-scaffold300-3913146 8 39751214 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428500 Affx-122938771 AX-123298843 8 38738827 TCAGAGTTGCAGAAAAGATATCAGCCCAGCTATGT[C/T]CTTTGTGTTGGCCTCCCTCAGGAGCCTAATGAAAT Y 2 1 2 1 101000 r 74 goat snp28091-scaffold300-3953745 8 39791831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795376 Affx-122925158 AX-385282332 8 38777834 ATTTAGTGCATATGACCAGGAAGCCACTGCATTAC[A/G]TAGTTTTTACTCATTAAACCTGATTGTGAACGGCA R 2 1 2 1 101000 f 74 goat snp28092-scaffold300-3992752 8 39831131 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387391 Affx-122970421 AX-123257749 8 38821852 TCCTGAACCGGGCTGAATTAGATGAGAGCTCCAAA[A/G]GAGCTTTAGTGGCCAGTATCAGTTAGGGAAAGCTT R 2 1 2 1 101000 f 74 goat snp28093-scaffold300-4036770 8 39875313 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792138 Affx-122931061 AX-385279123 8 38911185 AATAAGATTTTAATAAACTCTCATGTCTGAGTGTA[A/G]GAGCATACAGCACACTCTCTAGCTTCGTGACCGTT R 2 1 2 1 101000 r 74 goat snp28095-scaffold300-4126103 8 39965634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430404 Affx-122937759 AX-123300745 8 38953883 CTCCCCAAGATTGCTAAAGGAAAGAAAGACTTAGA[C/T]GATTTCCCTGAGAGCTGGCAGCAGTGAGTAAGACC Y 2 1 2 1 201000 r 74 goat snp28096-scaffold300-4168801 8 40008273 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388690 Affx-122968996 AX-123259048 8 39047072 TTTATTTATTTCGATCCTTCTTCCTCTGTGTATTT[A/C]TCTCTTTATTCATTCATTTAGGAAAAAAGGCTGAG M 2 1 2 1 103000 f 74 goat snp28098-scaffold300-4261990 8 40101478 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419741 Affx-122945888 AX-123290089 8 39091817 TGCGCTCTGTATTGCTGCTTCCTCATTGTGCAGGC[A/G]CAATTAGAAAAAGAATGCTTATGTCATGGCATTGC R 2 1 2 1 102000 f 74 goat snp28099-scaffold300-4306735 8 40146159 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273354 Affx-1111833577 AX-519546989 8 39107175 TAATGGAGAAAGAAATTCATACTCCTTTAGAAAGC[A/G]TCTCTTTAAAAGGAAATACATCTGAGTACACCCTG R 2 1 2 1 101000 f 74 goat 8_39107175_AF-PAKI 8 39107175 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320778034 Affx-122950776 AX-385265150 8 39163622 ATTATGCTCAAATTTAAATCAAGTCATATTTAGGT[A/G]TATTTTAAGAAAAATAAGGAACAGCTCTTAACAAT R 2 1 2 1 201000 r 74 goat snp28101-scaffold300-4378540 8 40217924 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413188 Affx-122950329 AX-123283537 8 39236912 ATGCTTTTGTGCTCCCTGTTGTACATGTGTGTTCA[C/T]AGTTGCTAATTATGGAAAAACAAAAATAAATAAAA Y 2 1 2 1 101000 f 74 goat snp28102-scaffold300-4451830 8 40291989 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434507 Affx-122934609 AX-123304848 8 39279879 AAGTTCAGAAATCTCAAGGCAGAGGAGTTGCATTG[G/T]TTTTTCAGCATTAGGGACTCTCACTGTCACTTCGC K 2 1 2 1 201000 r 74 goat snp28103-scaffold300-4494797 8 40334990 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802409 Affx-122961543 AX-385289313 8 39313081 GTAGAAGATGGTATTCTACAGAAGAACATACATTT[A/G]CCTTCTGGCTTCAAACATCCATGTACCAGAAATTA R 2 1 2 1 101000 r 74 goat snp28104-scaffold300-4527999 8 40368239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434635 Affx-122933997 AX-123304976 8 39349284 TTGTTCCTCACGCACTCACAGTCTAGTGCCTTCTC[C/T]TCACTGCCGCCTCAATAGCAACTTTTACGATCTTC Y 2 1 2 1 101000 r 74 goat snp28105-scaffold300-4564202 8 40404419 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392045 Affx-122966399 AX-123262402 8 39413033 ATGGCATACAGAATGCTTAAAACATGCCTAATGCA[C/T]AGTAAATGTTCAGCATCTGCAGTTATTATTGTGAC Y 2 1 2 1 101000 f 74 goat snp28107-scaffold300-4627951 8 40468155 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393107 Affx-122965582 AX-123263464 8 39444663 AATAACACTTTTCCTCTCATTTCTCATGTGACATT[A/C]TCATTACTCTCTCTTCTGAATGTTTTTCTCTCATC M 2 1 2 1 101000 r 74 goat snp28108-scaffold300-4659581 8 40497092 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391422 Affx-122966761 AX-123261779 8 39495879 CTTCATGTTAGGTATGTTTTACCATAATAAAAAGC[A/G]TAATATAAACAGAGCACCTAATAGGGTACCTGACA R 2 1 2 1 101000 r 74 goat snp28109-scaffold300-4710797 8 40548849 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376825 Affx-122977922 AX-123247184 8 39529006 CCCTCATCAGGTCACTTCATGGAAAGTAGAAAATT[C/T]CTTGGAATAACAATGCCTTGTTGTGTCCTTAGCAA Y 2 1 2 1 201000 r 74 goat snp28110-scaffold300-4743924 8 40581953 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424440 Affx-122941792 AX-123294786 8 39579731 GTTAAGCTGTGCCTAGTCATGGAAACCCACAACAT[A/G]CTGGCATCTTTACAACAGCTAGAAATCTCTATTAT R 2 1 2 1 101000 f 74 goat snp28111-scaffold300-4794649 8 40632238 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424843 Affx-122941354 AX-123295189 8 39713688 AATTATCTCCCCACTTTTCTACCTTATTTTGTAAG[C/T]ACCTCATGGTTTCAGACCCCAAAGGTTATAACAGA Y 2 1 2 1 101000 r 74 goat snp28114-scaffold300-4928606 8 40766952 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417481 Affx-122947173 AX-123287829 8 39787590 TAGTATGGTCATATCTTTCTAGCTTACTCTTTGTG[G/T]TAGGATGTGAAGAGGGTTTTGCTGGAGAGGGTGGC K 2 1 2 1 101000 f 74 goat snp28115-scaffold300-5002508 8 40841185 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424005 Affx-122942103 AX-123294351 8 39839081 TCCAGAAGGTGAAGCAGTGATAAGAAAGCAGTCTA[C/T]GCTCTCAACTAGTAAATGTCCTGCGATTAAATGAC Y 2 1 2 1 101000 r 74 goat snp28116-scaffold300-5053999 8 40893241 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392420 Affx-122966199 AX-123262777 8 39868662 AAATCATGTTTCTGAAATACATTTCTCCTTTTGAA[G/T]CGCTTCATGTTTATAAAACTCCTTGCCTCTCAATG K 2 1 2 1 101000 r 74 goat snp28117-scaffold300-5083580 8 40922760 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389749 Affx-122968248 AX-123260106 8 39959176 TAGACATACTTAATTGCCGTATACACTGGGTGCAC[A/G]TATGAGTTTGCACCTGTGGGATCTCACCATGGAAT R 2 1 2 1 101000 r 74 goat snp28119-scaffold300-5174094 8 41015117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764593 Affx-122942507 AX-385252241 8 40007110 CCTCTCTTTCTATACATTAGAAGATGGAGTGAGGT[A/G]TTAAACTTTATATCCCTGTTCAGCATATTCTTAAG R 2 1 2 1 101000 f 74 goat snp28120-scaffold300-5222028 8 41063047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442588 Affx-122928492 AX-123312925 8 40050438 GTTTTCTGTTTAATTGATAGCATTATAGTAGTATT[G/T]CTTTCTAATTTTTTTGTGTGTAAATGGATAGTTTT K 2 1 2 1 303000 f 74 goat snp28121-scaffold300-5265356 8 41106344 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422890 Affx-122943066 AX-123293236 8 40105183 CGGCTAGTAAGGTAGTAATGAACTCTTTTGGAGTG[A/C]TTTCAGGAGCGGTAACAAGTACTGATTCACTGTCT M 2 1 2 1 101000 r 74 goat snp28122-scaffold300-5320101 8 41161594 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409903 Affx-122952893 AX-123280254 8 40165708 TATGAAAGTAAGAATTATGCTTAATTTGTTTTATT[A/G]GAACTACTATTTAAGAGGCCTTATTGATTTTTATT R 2 1 2 1 101000 r 74 goat snp28123-scaffold300-5380626 8 41222963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393535 Affx-122965423 AX-123263891 8 40204784 TGACCTTGCTCCCTTCTTTCCTTTCTGCTTGGGAA[A/G]CTCTTACTTTTCTTCCAGCGTTCCCACCCAGTGTA R 2 1 2 1 103000 r 74 goat snp28124-scaffold300-5419702 8 41263005 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437995 Affx-122931584 AX-123308333 8 40294096 TGAAAGAAGAATCTGCATGGTGTGCCACAGCAGGT[A/G]CTACAGGATCAGGATTCAGGATCCTGACTTTAGTC R 2 1 2 1 101000 r 74 goat snp28125-scaffold300-5509014 8 41353029 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426361 Affx-122940254 AX-123296707 8 40326363 TAGATAGTAATCCCATGGGCTCTTCTGCTCTTGAC[A/G]TTTGATGACTTGAAATTTGGAATTTTTCCTCCCAA R 2 1 2 1 201000 r 74 goat snp28126-scaffold300-5541281 8 41385411 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444077 Affx-122926845 AX-123314414 8 40362038 CCATAGTTGTCTTGATGCAGTGTTTCTTCTGGTCC[A/G]TTTCTGTGGGCCCTGTTCTCATGCAAGCCAGTAAT R 2 1 2 1 201000 r 74 goat snp28127-scaffold300-5576956 8 41421325 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434566 Affx-122934126 AX-123304907 8 40395152 AAATACAATCACTTTTAATGACTCTAAACATTGAT[A/G]TTATTTCCCAATCTTTGAACAGTCTTAAAGATTTG R 2 1 2 1 101000 f 74 goat snp28128-scaffold300-5610070 8 41454384 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392981 Affx-122965667 AX-123263338 8 40435620 GGACCAGCAGGAGTTAGCCAGCATCCACTGTCAGG[G/T]GAGAGGCCCACCGAGGGACTGGGGTGTGAGGGGAC K 2 1 2 1 101000 f 74 goat snp28129-scaffold300-5650538 8 41495148 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278600 Affx-1111836507 AX-519552079 8 40461474 GGAAAATGCACAAAAGCCCAGGCTAACAAAGTAAA[A/T]GAAAAAAAAAATGTCCTTATTGAATAATAATCCTT W 4 1 2 1 101000 f 74 goat Random2.2K-890 8 40461474 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449660 Affx-122922575 AX-123319995 8 40465007 GCAGCCAACTTGCTTGGAACAAAATGGAGTAAGAG[A/C]TTCTCTAGTGAGTTGTTTTCAAAGTGTGAGAAATT M 2 1 2 1 101000 f 74 goat snp28130-scaffold300-5679925 8 41524439 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786464 Affx-122943124 AX-385273498 8 40540607 CATCAGCTCTCTATCCAGGTGTGTGAACAGCTTCC[A/G]TATGTCACTAACCCTGTTACTCACACCTCTTTGTG R 2 1 2 1 101000 f 74 goat snp28131-scaffold300-5755525 8 41600127 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786762 Affx-122941706 AX-385273793 8 40596743 GGGAACAAACACAATTGGGATTCTTAAAAAGGACA[A/G]TGTTGACTCTCAACTTGATTACCCTGTTTTCATCC R 2 1 2 1 101000 f 74 goat snp28132-scaffold300-5811661 8 41656565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780617 Affx-122948831 AX-385267707 8 40630921 AGAAAGATGCCAGAGGGTCTCGGTTATTGTAATTC[A/G]CCCTGTGATACTCTTCAGAAGTTGTGAAAGAGAGA R 2 1 2 1 101000 r 74 goat snp28133-scaffold300-5845839 8 41691201 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438123 Affx-122931489 AX-123308461 8 40675422 TCATGCTGAATCCCAAGGGACTACCCAGAACATTA[C/T]GATCATTCATACAATAATCTTTGTACAGTTGGAGG Y 2 1 2 1 101000 r 74 goat snp28134-scaffold300-5890340 8 41735681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791264 Affx-122955857 AX-385278258 8 40716966 AATAATTAAAAACCTGACCAGCTCAAATCTACAGT[G/T]GTGTGTCTTCCTGAAATATCCTTTCTAAAAGTGTA K 2 1 2 1 101000 r 74 goat snp28135-scaffold300-5931884 8 41777808 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426253 Affx-122940334 AX-123296599 8 40768160 TACATTTATTACTGATCTTTTCATCTGAACCCACC[A/G]CAGCACCTTCTTTGAATCTGTTATAAGCCAGTTTT R 2 1 2 1 101000 f 74 goat snp28136-scaffold300-5983078 8 41829328 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420234 Affx-122945525 AX-123290582 8 40798147 AACAAAGCAAACTTGGTGCCTATATCTTTCCTGAA[A/G]CTGACATCATAAATAGAATTCAGATATTGTGACCC R 2 1 2 1 201000 r 74 goat snp28137-scaffold300-6013065 8 41859287 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771613 Affx-122973899 AX-385258771 8 40845992 CTGATGCCAACGAACTTTGGAAAATTACATTCAGC[A/G]TCTGGATACATCACTTCATTTACCAATAAAACATA R 2 1 2 1 101000 f 74 goat snp28138-scaffold300-6060910 8 41907719 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769555 Affx-122937414 AX-385256725 8 40883974 CTGTAAGTTAAGATGCAGTGTCTCCCTCCACTATC[A/G]CTGAAGTCCTATTTTCTAGGCTATTTTATAAAATC R 2 1 2 1 101000 f 74 goat snp28139-scaffold300-6098892 8 41945805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398741 Affx-122961823 AX-123269096 8 40939197 TGAATTTCATCTCCTTGAAATTTTAATTTTTTAAA[C/T]AGGAACAATAATACTTTATGCCTGAAGGAATGAAC Y 2 1 2 1 103000 r 74 goat snp28140-scaffold300-6154115 8 42003196 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396078 Affx-122963436 AX-123266433 8 40976460 AACCATAATATCAAAGCAGCTCCAAAGAACTAACA[C/T]GGTGGTCAAGTAAGACATGGAGCCTCGACCCCTGT Y 2 1 2 1 201000 f 74 goat snp28141-scaffold300-6191378 8 42040702 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420854 Affx-122944645 AX-123291201 8 41057005 TTGAGTGCAGAAACACTCTTGCATTTGGTGCAGAT[A/G]TTGTAAATATAAGAAGAGATGGCGTGTGCGCTCAA R 2 1 2 1 101000 f 74 goat snp28143-scaffold300-6271923 8 42121296 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440928 Affx-122929020 AX-123311265 8 41109573 GGGCCCTCGAGTTGCCACATGCCAAGCAGCCTGAG[C/T]GTGAAATCTGGGGTTCTCCTGGTGTGTTGATCCTC Y 2 1 2 1 101000 r 74 goat snp28144-scaffold300-6324491 8 42173389 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445851 Affx-122926004 AX-123316188 8 41203734 GTGATTTATTTAATATCTATCTTTTACCAAACCCC[A/G]TACTCCCACAGACTTGCACTGATGCGCATTTTCAA R 2 1 2 1 101000 r 74 goat snp28146-scaffold300-6418652 8 42267887 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784651 Affx-122954954 AX-385271699 8 41246440 ATGTACTAAGTGTATAGATCTTAGCTTAGTGCAGT[C/T]ATAACATCCCTTCCACACTGTGCTTTTCTGCATTA Y 2 1 2 1 101000 r 74 goat snp28147-scaffold300-6461358 8 42310403 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426557 Affx-122940175 AX-123296903 8 41303685 GAAATAAAGAATCTACTCATTCCACCTAAGAAAAC[A/G]TAGCAAAGATTAAGATTCAAGAGAGCATTTTTCTC R 2 1 2 1 101000 f 74 goat snp28148-scaffold300-6518603 8 42367212 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796605 Affx-122930537 AX-385283551 8 41337450 AGTTTCATCCAGCAAACTATTCATGCTGGCTGAAA[C/T]GTGGTCTAGCTTCAAACAGGAGCAAGTAAGACCAT Y 2 1 2 1 101000 r 74 goat snp28149-scaffold300-6552368 8 42401015 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377796 Affx-122977323 AX-123248155 8 41367556 CCTCCTCAGCTGTAAACATTTCTTGAGCATTGCTT[C/T]GCTGGAGGAAAAAGAAAAATCACAACCATATAGAA Y 2 1 2 1 101000 r 74 goat snp28150-scaffold300-6582474 8 42431302 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425520 Affx-122941463 AX-123295866 8 41424167 GTCCCAGATTTCATGGGCACAATTGTGCAGTCCAC[A/G]CGGTCAGAGTTTCTGCTCCTGAGTCCTCCTTAGAG R 2 1 2 1 101000 f 74 goat snp28151-scaffold300-6639085 8 42488476 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802246 Affx-122959790 AX-385289150 8 41502547 TCTACCCTGAGTCATTCAGGTAAAATAACTACAAT[A/G]TGCATATACATGGGAAAAGACTTTTCTTGTCCTCC R 2 1 2 1 101000 r 74 goat snp28153-scaffold300-6717465 8 42568207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803348 Affx-122953075 AX-385290184 8 41582417 AAGCATATTGAATTTGAGCTCTTCTACAGAAATCT[A/G]CTAGGAGACCAGGTTTTTCACTAGCTCTCAGTTGA R 2 1 2 1 101000 r 74 goat snp28155-scaffold300-6797335 8 42647519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273356 Affx-1111833578 AX-519546991 8 41610126 ACGCCAGACCTCCCTGTCTATCACCAACTCCCGGC[A/G]TCCACCCAAACCCATGTCCATTGAGTCGGTGATGC R 2 1 2 1 303000 f 74 goat 8_41610126_AF-PAKI 8 41610126 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38421330 Affx-122944077 AX-123291677 8 41619803 CAAGGACTAGCTTGAAGCAGATCACCGAGCCTGCC[A/C]TGGAATGAATCTGCATCCAATTGCTCTTGTGAAAA M 2 1 2 1 201000 r 74 goat snp28156-scaffold300-6834721 8 42685419 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377847 Affx-122977285 AX-123248206 8 41691691 CAGGGCAGCAACCCACATCCAAAAACTGACTGATG[C/T]GCTTGTTAAGAGCCCAGCTTTCGGTCAATTGGCTC Y 2 1 2 1 101000 r 74 goat snp28157-scaffold300-6906609 8 42758402 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440992 Affx-122928970 AX-123311329 8 41726530 GTGCAAGGCTTTCTTCTATAGTCTTGTTTACAATG[G/T]CAATTTCTGTCAGAGAAGGTATTTTTGCTGAATGG K 2 1 2 1 101000 f 74 goat snp28158-scaffold300-6941448 8 42793073 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795626 Affx-122972642 AX-385282581 8 41757067 ATAAAATAAGACTCCTCCTTGTGCTCAATTTAGAC[C/T]ATGTGTCTCCAGTAGAGTTCATGATTTCTGCTCTA Y 2 1 2 1 101000 r 74 goat snp28159-scaffold300-6971985 8 42823544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770911 Affx-122939804 AX-385258074 8 41790408 TTTTGCATGTGTGCTACTAATGTTGAAACCTTTTC[A/G]TATGCATATTGACCTCTGAATTTACACTTCTAAGA R 2 1 2 1 101000 f 74 goat snp28160-scaffold300-7005326 8 42864490 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803670 Affx-986696169 AX-385290445 8 41879496 ATGACTGTATGAACTTAAGATGTTTGTATTCTTTA[C/T]GTGATGCCGTGCAGATCGTTTTTATATAGAAGGAT Y 2 1 2 1 600010 r 74 goat 8_41879496 8 41879496 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 38376358 Affx-122978324 AX-123246717 8 41903653 ATGAGCTTCTTCGGCCCTCTACTCCTCACCCCCAC[A/C]CCCTTCCTTGTTATTTGCCGCATTTTACACGTGTA M 2 1 2 1 101000 r 74 goat snp28162-scaffold300-7118571 8 42977839 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429850 Affx-122938157 AX-123300191 8 41950464 ACAGCAGGCCATGTGGCCCCATCACTCAGTGTGTC[G/T]CATCCTTTCACAGAAAGAGGTCATTAATTGGTTTC K 2 1 2 1 101000 r 74 goat snp28163-scaffold300-7165382 8 43024639 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416005 Affx-122948388 AX-123286354 8 42021914 GAGTAACAAAATTTAAGTTCCATAAACATTCTGTT[A/G]CTAAGACGGCAGTGAGAATTTAATGAATTCCCTGA R 2 1 2 1 201000 f 74 goat snp28164-scaffold300-7236832 8 43096568 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377519 Affx-122977478 AX-123247878 8 42054317 ATTTGATTGCAAAAATGTTATTAGCACTTTAGGAC[A/G]CTATCAGCATTTTCCAATCTTGATAAAGTGACTCC R 2 1 2 1 101000 f 74 goat snp28165-scaffold300-7269235 8 43129095 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412531 Affx-122951345 AX-123282880 8 42097858 CCCACTTTACATGGGTGGAAACTGAGGCATAGAGA[C/T]AAAACTAACTGACTAAATCACACAGCTGTAAGTAG Y 2 1 2 1 201000 r 74 goat snp28166-scaffold300-7312776 8 43172715 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787627 Affx-122946908 AX-385274650 8 42221896 ATTTCTTATTAAAAACTTTTATGGGTCCTCTCTCA[A/G]AGAAGAGGGTCTCGCCTACTTAACTTGTTCTAGAA R 2 1 2 1 101000 f 74 goat snp28169-scaffold300-7436814 8 43297246 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410356 Affx-122952998 AX-123280706 8 42300185 CTGATATAGCTTGGAAAGAGTGAAAATTCTAAAAA[C/T]TATCTTAGAAAAAAATAATCATAATACAAATATTT Y 2 1 2 1 102000 f 74 goat snp28170-scaffold300-7515103 8 43375469 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422171 Affx-122943525 AX-123292517 8 42369719 ACCACTGACCTAACTCCCCAAAGAACAGGGAAGGA[G/T]CCACATCATATTTGTGGTCAAAGCCCTTTGATAGT K 2 1 2 1 201000 r 74 goat snp28171-scaffold300-7584637 8 43444874 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452705 Affx-122920301 AX-123323038 8 42413873 CAGGCCACAGGCCCAAGTGACCCACAGGCTCAAGT[C/T]TGCAGCCCAGGGTCTAGACGTTAAACCGCCAATTC Y 2 1 2 1 101000 r 74 goat snp28172-scaffold300-7628791 8 43488761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274644 Affx-1111834340 AX-519548230 8 42423155 C[A/G]CTGCTTGGTCCTGCAGTAGTAATCACTGTATTTAT R 2 1 2 1 101000 r 74 goat GoatD01.030584 8 42423155 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38414568 Affx-122949383 AX-123284917 8 42467626 TACCATTTAAAATGTTTTTTAAGTGTACAGTTCGG[C/T]GGCATTAAGTACCTTCACAGTGCTGTTTAACTATC Y 2 1 2 1 103000 r 74 goat snp28173-scaffold300-7682544 8 43542552 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416965 Affx-122948013 AX-123287313 8 42525116 TTCCTACAACTGTACATAACGGAGCAGAGACTCAA[C/T]AGCAAGTGTGCCCTACACAGAGGGAGACGGCCAGA Y 2 1 2 1 101000 f 74 goat snp28174-scaffold300-7740034 8 43599922 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402779 Affx-122958305 AX-123273132 8 42562602 AGCTATTGAACACAGGAGCGAAGTGGTGAGATTTG[C/T]ATCTTAGCAGGACTGCTCTGGCTAGATGCTGGAGT Y 2 1 2 1 101000 r 74 goat snp28175-scaffold300-7777520 8 43637584 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781080 Affx-122976910 AX-385268166 8 42603764 GCTTCTATTTTTAAACCAAACATGACAACAAACAC[A/G]TCCACACTTGACAATTTTACAATGCCTTCACATGC R 2 1 2 1 101000 r 74 goat snp28176-scaffold300-7818682 8 43679019 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415021 Affx-122949025 AX-123285370 8 42655753 TTTTAACACCTACGAGTGCTCAGTCGCTCAGTCAC[A/G]TCTGACTCTTTGCTACAATAGGCAAGAATACTGGA R 2 1 2 1 303000 r 74 goat snp28177-scaffold300-7870671 8 43731234 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427717 Affx-122939278 AX-123298060 8 42719454 AAACTATCCAAGATTCTTGCCTCAAGAGACTGCCC[A/G]TCATGCAAAGGTAAACATGTAGGAATGAGCAAGCT R 2 1 2 1 201000 r 74 goat snp28178-scaffold300-7934372 8 43794951 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390604 Affx-122967178 AX-123260961 8 42762703 GTCATCTTATCTCATTTAGTCCTCACGCACCTTAA[C/T]AGACAGGTAAGAACTAAGGCTTACAAAGTTCATCA Y 2 1 2 1 201000 r 74 goat snp28179-scaffold300-7977621 8 43838304 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780717 Affx-122973826 AX-385267807 8 42802222 CTGCCATGTGCAAGCACACATTTCCTAAAAGATTT[G/T]CTATGTCTCATTCGAGAGAAAGGAGACTTGGTTCA K 2 1 2 1 101000 f 74 goat snp28180-scaffold300-8017140 8 43877769 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388523 Affx-122969204 AX-123258881 8 42831553 GGAAATGAGACTCAAAGAAGTTGAATGACTTATTT[A/C]TGGTCACTAAAGGATTAACTACAGAGAGTTATTAG M 2 1 2 1 101000 r 74 goat snp28181-scaffold300-8046471 8 43906852 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476246 Affx-1251763752 AX-586011668 8 42844731 TGCTCCATTGTTATTCCTTGCTCTAGGTGACACTG[-/ACTAATATTTTTTTTTAATTTTTTTATTTTTATTTATTTTTGGTCTTCCCGTCCTATTCCTCTGCCATCTTTCCCTCTCC]CTAATATTTTGTCTTTAAATGTTTTTTAACAAAGC - 4 1 4 1 20000 f 74 goat SV_248 8 42844731 - deletion junction SV-TF-chip 539476498 Affx-1251763752 AX-586011894 8 42844731 TGCTCCATTGTTATTCCTTGCTCTAGGTGACACTG[-/ACTAATATTTTTTTTTAATTTTTTTATTTTTATTTATTTTTGGTCTTCCCGTCCTATTCCTCTGCCATCTTTCCCTCTCC]CTAATATTTTGTCTTTAAATGTTTTTTAACAAAGC - 8 1 4 1 20000 r 74 goat SV_248 8 42844731 - deletion junction SV-TF-chip 562165163 Affx-1251763752 AX-606940575 8 42844731 TGCTCCATTGTTATTCCTTGCTCTAGGTGACACTG[-/ACTAATATTTTTTTTTAATTTTTTTATTTTTATTTATTTTTGGTCTTCCCGTCCTATTCCTCTGCCATCTTTCCCTCTCC]CTAATATTTTGTCTTTAAATGTTTTTTAACAAAGC - 8 1 4 1 20100 r 74 goat SV_248 8 42844731 - deletion junction SV-TF-chip 562165360 Affx-1251763752 AX-606940771 8 42844731 TGCTCCATTGTTATTCCTTGCTCTAGGTGACACTG[-/ACTAATATTTTTTTTTAATTTTTTTATTTTTATTTATTTTTGGTCTTCCCGTCCTATTCCTCTGCCATCTTTCCCTCTCC]CTAATATTTTGTCTTTAAATGTTTTTTAACAAAGC - 8 1 4 1 20100 r 74 goat SV_248 8 42844731 - deletion junction SV-TF-chip 562165537 Affx-1251763752 AX-606940948 8 42844731 TGCTCCATTGTTATTCCTTGCTCTAGGTGACACTG[-/ACTAATATTTTTTTTTAATTTTTTTATTTTTATTTATTTTTGGTCTTCCCGTCCTATTCCTCTGCCATCTTTCCCTCTCC]CTAATATTTTGTCTTTAAATGTTTTTTAACAAAGC - 8 1 4 1 20100 f 74 goat SV_248 8 42844731 - deletion junction SV-TF-chip 562165642 Affx-1251763752 AX-606941052 8 42844731 TGCTCCATTGTTATTCCTTGCTCTAGGTGACACTG[-/ACTAATATTTTTTTTTAATTTTTTTATTTTTATTTATTTTTGGTCTTCCCGTCCTATTCCTCTGCCATCTTTCCCTCTCC]CTAATATTTTGTCTTTAAATGTTTTTTAACAAAGC - 8 1 4 1 20100 f 74 goat SV_248 8 42844731 - deletion junction SV-TF-chip 562165926 Affx-1251763752 AX-606941335 8 42844731 TGCTCCATTGTTATTCCTTGCTCTAGGTGACACTG[-/ACTAATATTTTTTTTTAATTTTTTTATTTTTATTTATTTTTGGTCTTCCCGTCCTATTCCTCTGCCATCTTTCCCTCTCC]CTAATATTTTGTCTTTAAATGTTTTTTAACAAAGC - 8 1 4 1 20100 f 74 goat SV_248 8 42844731 - deletion junction SV-TF-chip 38420104 Affx-122945091 AX-123290452 8 42864702 GGTGTCCGTGTGGCTTATACACTCCTCTCTGCTTG[C/T]TCTCGGTCATCTCCACGGCCACCACACCCACCAGC Y 2 1 2 1 101000 f 74 goat snp28182-scaffold300-8079620 8 43939747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413591 Affx-122950573 AX-123283940 8 42895502 AACGACATGAATTAATCCATATAATAGAATCAATG[C/T]AACCATCAAAATAGTGCTTTATGACAGTATCTAAT Y 2 1 2 1 201000 f 74 goat snp28183-scaffold300-8110420 8 43970949 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795871 Affx-122942392 AX-385282823 8 42924660 GATATAGTGTATAAACTCTTTACTTTTAAATCATA[A/G]ATATAACTCTTTATCTTTAAATCTGGGGGAAATAT R 2 1 2 1 102000 r 74 goat snp28184-scaffold300-8139578 8 44000152 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442869 Affx-122927668 AX-123313206 8 42970185 GGCAGGAAGCTGTCATCTAATGAAGTTAATCCCTT[C/T]GTTTACAGGACAACTGTAAAATTCAGGGCTGTAAG Y 2 1 2 1 101000 f 74 goat snp28185-scaffold300-8185103 8 44046942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777295 Affx-122924152 AX-385264417 8 43067638 ATTTTGTGTTTGGCAAATGCTTATAATAGTAAAAA[C/T]AGTAAAACTTACGATAGTATAGCAATTGTGAAACT Y 2 1 2 1 202000 f 74 goat snp28187-scaffold300-8282556 8 44145274 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773139 Affx-122962744 AX-385260282 8 43123306 TCCTTATGGGTTTGTGTCATTAAAAAACTTTCTTC[A/G]GTGGTTTTAGGAGGAAGTTGAGACAAAGAGGTGTG R 2 1 2 1 101000 r 74 goat snp28188-scaffold300-8338224 8 44200435 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802170 Affx-122978335 AX-385289074 8 43152972 TCCCAAATCTTCCTCCCAGAATTGTGGAAATAGGA[A/G]ATCTATTATATAAGCAATAGCAAGTTTTAGGGAGC R 2 1 2 1 101000 f 74 goat snp28189-scaffold300-8367890 8 44230286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393209 Affx-122965499 AX-123263566 8 43198258 TTTGTCAATTTATTCGTTGCAGAGGATAATAAATA[C/T]ACCGAGTGATAAGGAGAAAAGGAATGATGTATAAT Y 2 1 2 1 303000 f 74 goat snp28190-scaffold300-8413176 8 44276029 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419814 Affx-122945834 AX-123290162 8 43256733 CCTGTGTTAAACTCTGCTCAAACTACTCCATGTGC[A/G]TGTATCATCTATTCCTGTTGGGACTGTAACTGATA R 2 1 2 1 101000 r 74 goat snp28191-scaffold300-8471651 8 44334976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449118 Affx-122923577 AX-123319453 8 43286015 TTGATGCCTTTGTTTGACTGTTTAATTTATCTGTC[A/G]CTGTTATGGCATTATAGTTCACTTGCCTTGAAGTT R 2 1 2 1 101000 r 74 goat snp28192-scaffold300-8500933 8 44364793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428357 Affx-122938979 AX-123298700 8 43325981 ACTCAGCTTGAAAAGGGAGCATGAATGAATTTGCC[G/T]TGGTCACACAAGTACAGAGGGTCACTGGCCGTAAC K 2 1 2 1 101000 f 74 goat snp28193-scaffold300-8540899 8 44405166 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425761 Affx-122940731 AX-123296107 8 43378807 CTATGCATCTGGTGATTCTGCATCCCTGGTCCTGC[A/G]TGATAACAATCCAAGAGCTGCAACTCAGTTGCCTG R 2 1 2 1 201000 r 74 goat snp28194-scaffold300-8593725 8 44458135 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445621 Affx-122925099 AX-123315958 8 43414283 GGCAAAGGTATTGTCATCAGCAGAATAGACTAAAC[C/T]AAACTTTCAGTCACCGGTCAGTGTATCCAACTCTG Y 2 1 2 1 101000 r 74 goat snp28195-scaffold300-8629201 8 44492877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404519 Affx-122956695 AX-123274871 8 43501613 AGACTTGCTGGGCTGATCATCCCAACACCCCTGCC[A/G]TGTCTGGCTCTGATTCTTGCCCTATCTCTTCACAC R 2 1 2 1 101000 r 74 goat snp28197-scaffold300-8716531 8 44580448 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278602 Affx-1111836508 AX-519552081 8 43509499 ACACTCCAGTGACTTCCCATGGCACTCACCATAAA[A/G]TCCCAGCCCCTGCAGCCTCCAAGGGCCAGCGAGTT R 2 1 2 1 101000 f 74 goat Random2.2K-894 8 43509499 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38411814 Affx-122951249 AX-123282164 8 43544378 AAGTTTCTAGACAGAGAGGACAATGTGATGGAAGA[C/T]GACTCTTCAGGAGTCATGAGGGATGCAACTTCCTA Y 2 1 2 1 101000 f 74 goat snp28198-scaffold300-8759296 8 44623471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414339 Affx-122950029 AX-123284688 8 43623418 GGGCCCATGTTTGCAGAGAAGTAGCCATTGCCTCT[A/G]TTTTCCTCGATGCATTTTTCTTTCTGAATTCTGCA R 2 1 2 1 101000 f 74 goat snp28200-scaffold300-8838336 8 44702982 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406185 Affx-122956149 AX-123276537 8 43655032 CTAGACAGTTTTCACTTAAAAGCAAGGTTATTTTG[C/T]AGCATAGATATACCCTAGTAGGGTGTGAAGATGAA Y 2 1 2 1 101000 r 74 goat snp28201-scaffold300-8869950 8 44734504 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419010 Affx-122946048 AX-123289358 8 43693524 GTATGTATAAACTTAAAATAAATGTGTATAAAGCA[C/T]GGCACTGTGACCCAACCTCACTTGCTCTTCAAGCC Y 2 1 2 1 101000 r 74 goat snp28202-scaffold300-8908442 8 44773074 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437986 Affx-122931590 AX-123308324 8 43790524 TGGTTGACTGTATCACGTGTGTGTACTAGCTGAGC[A/G]AAAAGACTGAAAGAAAGAAACCATTTTCCTTGACT R 2 1 2 1 101000 f 74 goat snp28204-scaffold300-9005442 8 44870980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409439 Affx-122954093 AX-123279790 8 43889498 GGCTGAGACCAGTCAGCTTGTCGACAGGGACCTTC[A/G]GCTCTGAACACCCTATAATCCTTCTGTGCTGAACG R 2 1 2 1 101000 r 74 goat snp28206-scaffold300-9104416 8 44970753 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391366 Affx-122967283 AX-123261723 8 43963040 AGGATATCAGAGAAAGTGTTTAGACCATCAGACAT[A/C]TTGGAATGTAAGTCCCAAGAGAGCAGGGATTTATA M 2 1 2 1 101000 f 74 goat snp28207-scaffold300-9177958 8 45041810 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801459 Affx-122962244 AX-385288368 8 44023543 AACTACAAAACATGCAAAACTCAGAATCACATAGG[C/T]AGCAAGTAGCAAAGTCAAAACTAGAAACAAGGCTC Y 2 1 2 1 101000 r 74 goat snp28208-scaffold300-9238461 8 45102350 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399573 Affx-122961119 AX-123269928 8 44086596 TCCTGTTTTGTGCCTCACGCCCAATGCTGACAGCA[C/T]GTGCTAGTCTACTAAAACATTTGGCAATAGTGTCT Y 2 1 2 1 101000 r 74 goat snp28209-scaffold300-9301514 8 45165154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777470 Affx-122967648 AX-385264590 8 44138861 TGAATATTCTGGATATCAGATGAAGTTAAGAATTT[A/G]TTACTTCTGTTTTTAAGGTGAAAATGATACTGTGA R 2 1 2 1 201000 r 74 goat snp28210-scaffold300-9353779 8 45217263 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432946 Affx-122935293 AX-123303287 8 44181728 AAGAGAATGGAATAAAACATGTTGGTCTTTGTCAG[C/T]AGAGGAAGCAGCCAAGTTGGAATGTCATGCAGTTC Y 2 1 2 1 101000 f 74 goat snp28211-scaffold300-9396646 8 45260021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773707 Affx-122971256 AX-385260847 8 44212700 ATTACTGATGCAGTATTTTAACATATTAGACAGCA[A/G]GATAGGAGAAAAGGAGGCTTTGGATGAATCTTGTG R 2 1 2 1 101000 r 74 goat snp28212-scaffold300-9427618 8 45291313 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386302 Affx-122970924 AX-123256660 8 44242310 CTGGCCATCTCTGAACTTTTTAAGAGGACTTTTCC[A/G]TGACAAATATCTCCCTGTGGCAAAAAGCAAAAGAA R 2 1 2 1 101000 r 74 goat snp28213-scaffold300-9457228 8 45320636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377783 Affx-122977330 AX-123248142 8 44276628 TTGTTTATGTGTAGGTGGCCAGGCCTTATCTTTAC[A/G]ATGGGTTTGGGACTTGGAGCAGTGGTAGTCAGGTG R 2 1 2 1 101000 f 74 goat snp28214-scaffold300-9491546 8 45355227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444124 Affx-122926811 AX-123314461 8 44323073 CCCAAGCTGAGAACAACTTCCCTAGGGTCTGATCA[G/T]AGATGCTGCTGGAATGATATCAGGGTGGCCGAGCA K 2 1 2 1 101000 r 74 goat snp28215-scaffold300-9537991 8 45401731 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384188 Affx-122972408 AX-123254546 8 44352342 AAAGGGAACTCCGATTTCAAAAATGCTTTACGTTA[A/C]TTTTACTTTCTATTTACTCAAGTGAGAAGACAGGC M 2 1 2 1 101000 r 74 goat snp28216-scaffold300-9567260 8 45430884 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386432 Affx-122970801 AX-123256790 8 44393965 GAATGCTTATTAACCAACCTTTGATTAAGCTTCTC[A/G]CCTTCTTCCAGGTACCTGAACTTTTGCCAGTTTAC R 2 1 2 1 201000 f 74 goat snp28217-scaffold300-9608883 8 45472344 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420707 Affx-122944786 AX-123291054 8 44445968 ACAATTTTCATCAAGATCCAACTTGAAGACCTACA[C/T]TGTATTTTCTGAAATAAAAAAAATTCTTAAGCACA Y 2 1 2 1 102000 f 74 goat snp28218-scaffold300-9660886 8 45524247 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385803 Affx-122971036 AX-123256161 8 44497364 CAGGGCTGTCTGTTACCCTGTTTGTTTAACTCACA[C/T]GCTGAGCACATCACGAGAAATACTGATGCACTGGT Y 2 1 2 1 303000 r 74 goat snp28219-scaffold300-9712282 8 45575107 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797732 Affx-122931205 AX-385284671 8 44544716 GATGTGTTCTCAAATGCAAAGGTGCTGAGGGTTTA[C/T]AAGGAAACCTAATATGAACTACAAGATTGGGTAAG Y 2 1 2 1 101000 f 74 goat snp28220-scaffold300-9759634 8 45622894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788891 Affx-122960851 AX-385275906 8 44576318 ACATACATGTATATATCTAGACAATCATAAATTCA[C/T]ATGACCTGAATATATCTAAATGATAGCATATCACC Y 2 1 2 1 101000 r 74 goat snp28221-scaffold300-9791236 8 45654589 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278604 Affx-1111836509 AX-519552083 8 44602268 TGTACAAGTGGCCTCTCAAGAGTGGGCAATGATCT[A/G]CTTCTTAACCGGGATATACGTACATGGATCTTTAC R 2 1 2 1 101000 f 74 goat Random2.2K-896 8 44602268 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776217 Affx-122958739 AX-385263345 8 44640302 TCTTATTTTATACACTCAAACTTTTTGAGTGTCAA[C/T]GGTATGCCATTCAGGTAGCTGCTGGTGATAACAGT Y 2 1 2 1 101000 r 74 goat snp28222-scaffold300-9855220 8 45719098 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427430 Affx-122940052 AX-123297773 8 44679690 GCACTGCAGGCCACAGAAAAGCGCTTAGTAGTTGT[A/G]TGTATTCAAATTTGTGGAATCTAATCCAGAACACT R 2 1 2 1 101000 r 74 goat snp28223-scaffold300-9894608 8 45759453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278606 Affx-1111836510 AX-519552085 8 44711369 GACAATTGTACTTCCAGCACAGTGACCTTAGACAA[A/G]TTTGTCAGCTTCTCTGGGCTTGCTTTACTCATTTA R 2 1 2 1 101000 f 74 goat Random2.2K-897 8 44711369 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791962 Affx-122930407 AX-385278951 8 44721376 GTTTTGTATGGGACAAATATTGAATCCTCAGCATA[C/T]ATTTTTATTCCTAGGATCCTCTAGACATTACCCAT Y 2 1 2 1 101000 r 74 goat snp28224-scaffold300-9936294 8 45801941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416454 Affx-122947819 AX-123286803 8 44768431 GCTCAAGGAGGCACAATGAATATTTGTTGAATAAA[C/T]GAGTGAATAAATGAATAGGTGTAGTTCAGCCTGTA Y 2 1 2 1 103000 f 74 goat snp26650-scaffold2793-11235 8 45898227 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430261 Affx-122937302 AX-123300602 8 44809581 GGACAATGATAATGGTGATCCCAGCAACTTACTGT[C/T]AGTATAGGAGATATTTGGGGTTTATTTTCTTTTTA Y 2 1 2 1 101000 f 74 goat snp26651-scaffold2793-52385 8 45939668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785878 Affx-122977803 AX-385272915 8 44821855 ATTGTCCTCATGTCTTCTGACTACTGAAGAGGAGA[A/C]TATTAGATGGGCCACTTTGAACCATTTCCCTAAAT M 2 1 2 1 101000 f 74 goat snp47153-scaffold66-11765 8 45952943 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778046 Affx-122919722 AX-385265162 8 44861317 AATCATATTTGCATATGTTATTGGCTAAGGAATTA[A/G]CTTCCATTGTTGAGGAAGCAAAGATTTTTGTTTGT R 2 1 2 1 101000 r 74 goat snp47154-scaffold66-51227 8 45993349 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780636 Affx-122938763 AX-385267726 8 44938705 TTAAGGCCATCAGAAAGGAGTAAATAATGCTCTGC[A/G]CATCTATTTTGTTTACAGCTACATCTCCAGGATCT R 2 1 2 1 101000 f 74 goat snp47156-scaffold66-128615 8 46071301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379975 Affx-122975628 AX-123250333 8 45005809 TCTAGGCCACCATCATTTCTTACCTAGATTGCTCC[A/G]TATCTTTCTATCTGGTTTTTCTGCTTCCACCTTGC R 2 1 2 1 101000 r 74 goat snp47157-scaffold66-195719 8 46138885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427335 Affx-122940123 AX-123297678 8 45034719 TCCTGAGTTGGCTCCGATCACAGTCTGTCCTCTCA[C/T]GGTAGCAAGAGGCTGCTGCAGTGGCAGCTTCATGG Y 2 1 2 1 101000 f 74 goat snp47158-scaffold66-224629 8 46169054 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772202 Affx-122920510 AX-385259357 8 45121557 ATGTATTGTTCCTAAGAAGTAGCAGATATGAGAGG[C/T]AGACAGAGACCCTATTAGGTAGACCCCTGAAGAAA Y 2 1 2 1 101000 f 74 goat snp47160-scaffold66-311467 8 46256270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408038 Affx-122954287 AX-123278389 8 45169704 CTCAAATCAGAACTACAGTGGAAGGGATTATCAGT[C/T]ACAAGAAGTTTAGTTGATATGGGGGAACCCTGAGC Y 2 1 2 1 201000 f 74 goat snp47161-scaffold66-359614 8 46304441 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408941 Affx-122953936 AX-123279292 8 45278710 CGGCCGTCTAGTACATGTTAGGTGCAGTGACAAAA[C/T]GATCTCATTTGAGATTTCATTCTCATGTCTTGCCA Y 2 1 2 1 101000 f 74 goat snp47163-scaffold66-468620 8 46411473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789340 Affx-122935345 AX-385276350 8 45319458 TGTATATATTTAATAGGCACCAACTGGGATTAGAG[A/G]CCAAACCCTTTTAGTCATCTTGCACAGTCATTAAG R 2 1 2 1 101000 r 74 goat snp47164-scaffold66-509368 8 46452449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386136 Affx-122971408 AX-123256494 8 45358744 TCACCCATCTCTCACCCTCCCCCAGGCCAGGCTCA[C/T]ACACAATGCGAGAAAAGCCCCAAGGTAGGAGAGTG Y 2 1 2 1 101000 r 74 goat snp47165-scaffold66-548654 8 46491936 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394181 Affx-122964922 AX-123264536 8 45413103 GCACAGGGCAGAGTTGGCAGGGGTTTCTGCTCCGG[C/T]CTCATCCAGTCCCACCACTAGGCTCACACAGCTCT Y 2 1 2 1 101000 r 74 goat snp47166-scaffold66-603013 8 46546586 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451582 Affx-122921685 AX-123321915 8 45450145 AGGGCACTCAGTGGCATGGAAAGTATAAGCACACA[C/T]AGCAGCACCACTGGTTACACTGGGAATGTGCAAAA Y 2 1 2 1 101000 f 74 goat snp47167-scaffold66-640055 8 46583358 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427443 Affx-122940042 AX-123297786 8 45561162 CTCCACCATGCTGCCTCACATGACACCGAGTGCAA[C/T]GCAAGTGTGCTTGTACACCTCTTGGTGAACACCTC Y 2 1 2 1 102000 r 74 goat snp47170-scaffold66-751072 8 46692367 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407718 Affx-122955008 AX-123278069 8 45610670 AGGATGCAGTGGAGAAATGGTCTCAAGGGGAAAAA[C/T]GGGAGAATAAAGGGCTAAGGATTTTGCATCAAATA Y 2 1 2 1 101000 f 74 goat snp47171-scaffold66-800580 8 46741091 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410237 Affx-122952547 AX-123280587 8 45649334 CCAGATAACTGGCAGAGGCACATGCAAATTATTTG[C/T]GAAGGAATGCATCATCAATCCAGGTCTCAAGTAAT Y 2 1 2 1 101000 r 74 goat snp47172-scaffold66-839244 8 46779814 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434704 Affx-122933944 AX-123305045 8 45687234 GAGCTGCCATTCCTAGCATACAGTAGGCACTTAAA[C/T]GATTATGGGTGCATTTTACTAAATTACCTAACTTC Y 2 1 2 1 201000 r 74 goat snp47173-scaffold66-877144 8 46816916 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769431 Affx-122936608 AX-385256601 8 45716021 TCTTTGAAGGTGTTGAAGTTTTGCTAATTTTAAGA[C/T]ATTTTAAAAGAAGACTTAGAGGAGAGTTTTAAATT Y 2 1 2 1 101000 r 74 goat snp47174-scaffold66-905931 8 46845710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433364 Affx-122935130 AX-123303705 8 45799892 TTATGCTTTCAATAATTATTATTTCCAATATTAAA[G/T]ATTAAATAATTGAGGCCTCAATGACATTTTAAGTG K 2 1 2 1 303000 f 74 goat snp47175-scaffold66-989802 8 46929954 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781212 Affx-122944635 AX-385268297 8 45835713 ATTTTCTAACAATAAGAAATCTAACTCTCTTTGAA[C/T]GGTATTCATCAGGGTTTCCTAAAAGGATTTACTAA Y 2 1 2 1 101000 r 74 goat snp47176-scaffold66-1025623 8 46966168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401131 Affx-122959387 AX-123271484 8 45896970 CATGCCACTTTGTAAAGGAATGATGAGGCTATCTA[C/T]GTACCCCTATAAAAAGCTAAGATGTCTTGTGAAAG Y 2 1 2 1 101000 f 74 goat snp47177-scaffold66-1086880 8 47027509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450926 Affx-122921776 AX-123321260 8 45937076 AAAATTTAAAGTGGGCCTATGTTTTTCCTTTCTGG[C/T]GACTGCCATGGCTTTATCAAGCAAGTTAAGTTAAA Y 2 1 2 1 101000 f 74 goat snp47178-scaffold66-1126986 8 47068390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450927 Affx-122921776 AX-123321261 8 45937076 AAAATTTAAAGTGGGCCTATGTTTTTCCTTTCTGG[C/T]GACTGCCATGGCTTTATCAAGCAAGTTAAGTTAAA Y 2 1 2 1 600000 r 74 goat snp47178-scaffold66-1126986 8 45937076 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449842 Affx-122922384 AX-123320177 8 45970017 CTCTCCCCTGCCCCCCACTGTTCCTCACTGTTAAG[G/T]ACCCCACAAAAAATGACAGCACCATTCCAAAAACA K 2 1 2 1 101000 r 74 goat snp47179-scaffold66-1159927 8 47101319 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413979 Affx-122950291 AX-123284328 8 46039723 TAGAAATCAGAGTCCAAGGACACTAAGAGATGCTG[A/C]TGATGAAGGTGATGCAGCCATCAGATGAGGGCCAC M 2 1 2 1 101000 f 74 goat snp47180-scaffold66-1229633 8 47169861 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427388 Affx-122940082 AX-123297731 8 46082186 TTTCTTCAGCTAAGCATACTGTTTGGAATTGAAGC[A/G]AGTTTCTGAAACAAAGTGGCTGGGGAGGAGATATG R 2 1 2 1 201000 f 74 goat snp47181-scaffold66-1272096 8 47212205 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275122 Affx-1111834609 AX-519548701 8 46097602 A[A/G]ACAGGACTGAATCTAGGAGATGCATTTGAGCTGTT R 2 1 2 1 101000 r 74 goat GoatD01.042977 8 46097602 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320782540 Affx-122971689 AX-385269615 8 46177987 CCTTTTTTTTAATTAAAAAGGTGATACATTCTAAA[C/T]GTCAAGATTGGATAGTTATTAAATATATTTCAACA Y 2 1 2 1 102000 r 74 goat snp47183-scaffold66-1367897 8 47306492 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278785 Affx-1111836511 AX-519552258 8 46201592 CGGTGCAATCTTTACACCTGTTGGAGAGCGCAACA[A/G]ACACGAGCGCTATGTTTTAAGGGAAGAGCTGGCAT R 2 1 2 1 101000 r 74 goat Random2.2K-898 8 46201592 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320787302 Affx-122945274 AX-385274327 8 46211073 ACTAACTACAAGAAAATCTCAATGATTGTCACCAT[C/T]TTTCCTGGCATGGAGTAATTTGTTTCTGAAAAAAA Y 2 1 2 1 101000 r 74 goat snp47184-scaffold66-1400983 8 47339550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451435 Affx-122921168 AX-123321768 8 46254823 TGGCAGAATGGAAGGACACGCACTCATCTTCTCTT[A/G]CAACAACACCAAAATCTACTACTACTTGTAGTAGC R 2 1 2 1 201000 r 74 goat snp47185-scaffold66-1444733 8 47383420 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392295 Affx-122967528 AX-123262652 8 46287601 TAAATAAAACACAGTCCTTATCCTAAAGGAGATCC[G/T]AAACCAAAGTCCTAAATTATACTCTAGGTCCACTG K 2 1 2 1 201000 r 74 goat snp47186-scaffold66-1477511 8 47416106 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777832 Affx-122971061 AX-385264949 8 46322476 TGTTTCCATGTACTCTCCTCCCAATTTCTATCAAC[A/G]GTTATATCTTGTGTAAAAAAGCACAGTATCTAAGT R 2 1 2 1 101000 f 74 goat snp47187-scaffold66-1512386 8 47449558 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393228 Affx-122965485 AX-123263585 8 46363289 CCCCAACTAGTACTGAGATATTAATAAGAACAAAA[C/T]GGTAAGCTGAATATTACACCAACATATAAAACTGA Y 2 1 2 1 101000 f 74 goat snp47188-scaffold66-1553199 8 47491106 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448277 Affx-122924181 AX-123318613 8 46418343 GTTTCCTGACCCAGGTCCTATTTATAGCAGAAGTC[G/T]CCACTGTTCACAGTGCCTTGTGGGATCAGGAGGGA K 2 1 2 1 101000 f 74 goat snp47189-scaffold66-1608253 8 47546440 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379691 Affx-122975909 AX-123250049 8 46448569 AATTTATTCCCCATGCACATTTTGAGGATAATGAC[A/G]TTTCTTCTCCAGATGCTATTCCAGGTGATTTTCTA R 2 1 2 1 102000 r 74 goat snp47190-scaffold66-1638479 8 47576681 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781754 Affx-122942220 AX-385268836 8 46493806 ATTCTTGCCTGAAGCACGTAAGGCTGGAGAATGCT[A/G]TAGTGGCCTGCCAACTTTCTCCCCACCATACCAAC R 2 1 2 1 101000 f 74 goat snp47191-scaffold66-1683716 8 47622732 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432175 Affx-122936406 AX-123302516 8 46528914 CTTAAAATTTTTAATATGCTTCAGTTTATCTTATA[A/G]CAGTGCTGATGTCAGAAGAGGGGACTAAAAGAAGC R 2 1 2 1 202000 f 74 goat snp47192-scaffold66-1718824 8 47657298 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388204 Affx-122969420 AX-123258562 8 46569579 CCCCAGAAGTATCGAAGCGTCTGCAGAATGCTGCA[C/T]GTAATCCACACGACTTCTCTGTTTTCTGTTTCTCT Y 2 1 2 1 201000 r 74 goat snp47193-scaffold66-1759489 8 47697879 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411284 Affx-122952305 AX-123281634 8 46620648 AGCTGTTCTCTTGTCTTCTCCTCCCTCTCAAGTCT[G/T]TAGACCATCCCCCTTCACTCTTGTGGAGAGACTCC K 2 1 2 1 201000 r 74 goat snp47194-scaffold66-1810558 8 47748932 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788167 Affx-122962005 AX-385275186 8 46652009 AGCTATATACCCAAAAACTTGTGCTAGAATGTACA[C/T]ATGTTATATTGGCTATCTGCAAATATCCCAGAGAA Y 2 1 2 1 102000 r 74 goat snp47195-scaffold66-1841919 8 47780184 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775605 Affx-122970367 AX-385262736 8 46703042 ATGCTATTTTCAGAACAAAGAACCAAGTGGTCCCA[G/T]ATTACAAACCCACTTGGGATCACTAGGACCATGGG K 2 1 2 1 101000 f 74 goat snp47196-scaffold66-1892952 8 47830007 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793032 Affx-122969581 AX-385280010 8 46738116 AGATCAACAGCATTTCCATGTGAAAAGAGTAAAGT[A/G]TATTTGGCATTGGGTGAGCAACGCACAAACATGCA R 2 1 2 1 101000 f 74 goat snp47197-scaffold66-1928026 8 47864740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409186 Affx-122953185 AX-123279537 8 46771241 CAGGGCAATCTTTCTCAATAATGGCTTTGTAGTTG[C/T]AACAAATGGGGGGCACTACTGAATAGATGCCAGGG Y 2 1 2 1 101000 f 74 goat snp47198-scaffold66-1961151 8 47897385 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273360 Affx-1111833580 AX-519546994 8 46775363 TAAACGATAAGTGGAAACATCTCTTCTTAGAAAAT[A/G]TATTTCATATCTTCTATAAAAATGGTCACTTGAGA R 2 1 2 1 101000 f 74 goat 8_46775363_AF-PAKI 8 46775363 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320777605 Affx-122975702 AX-385264724 8 46844387 TCAAAAGATAATAAGTAATAAGCCTAAGGTTCATA[C/T]CAAGTCTATGTGACTCCAAAGCCTACATTATTTCA Y 2 1 2 1 101000 r 74 goat snp47200-scaffold66-2034297 8 47971217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380288 Affx-122975410 AX-123250646 8 46895818 GGGACAAGATCCAGCTCAAATCATTGTTTTATTGA[G/T]GTGATGTAATCCAGGTAAATCCCTTAGTAAAGCAT K 2 1 2 1 101000 f 74 goat snp47201-scaffold66-2085728 8 48022931 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432647 Affx-122935471 AX-123302988 8 46937596 CTGCTTTCTTCAATCCCATCTGCTGCTGCTGTCAG[A/G]GTCCTTCAGAAACACAGATAGATATCTTTATAACA R 2 1 2 1 201000 r 74 goat snp47202-scaffold66-2127506 8 48065314 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415615 Affx-122948599 AX-123285964 8 46953500 AACTAAGACATTTTCTCCAGCAGTCCTAATCAGCA[C/T]GGAGGCAAATATTTGGATTAATCCAGGTTAGAAAT Y 2 1 2 1 101000 r 74 goat snp53430-scaffold81-11233 8 48088528 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431425 Affx-122936520 AX-123301766 8 46984095 GCATGCTGGTCTCAGGACAGTGAGCTTGTTTTCCA[C/T]ACTCTACCTCCACAGCCATGGGCATCCTCCCGCTT Y 2 1 2 1 101000 f 74 goat snp53431-scaffold81-41828 8 48120076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452659 Affx-122920332 AX-123322992 8 47017751 CAGTGTAGAGTGGTATCAGGGCACTGCAGGCAGAG[A/G]GATCGTGAGCACAGCAGATGTATTGTATGTGGCAA R 2 1 2 1 201000 r 74 goat snp53432-scaffold81-75484 8 48154661 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38430586 Affx-122936995 AX-123300927 8 47064512 CATACAGCTGTATCTCAGTGACCAAATCGGATGAA[A/G]AGAAATGAATTGTGATTTAAACAAGCAGAATGAAG R 2 1 2 1 101000 f 74 goat snp53433-scaffold81-122245 8 48201709 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452671 Affx-122920323 AX-123323004 8 47145491 AGCCAAGGTAATGAGCATTTTCTTTCTTTCTCACA[C/T]GATGCACAACCATGCCAATCTATGTCCGTGGCTGA Y 2 1 2 1 201000 r 74 goat snp53435-scaffold81-203224 8 48289421 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401977 Affx-122958779 AX-123272330 8 47182036 GGAAAACTCTAAAAAGAGTTTTGGAAATAAACTTG[A/C]TCTACTTCTCTATTTTGTCTTGAACTCACCAGGGT M 2 1 2 1 101000 r 74 goat snp53436-scaffold81-239769 8 48324324 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773130 Affx-122973307 AX-385260273 8 47249216 AGCAGCAGTAAAAAGGTCAGTAGTTGGCAGTTGTA[C/T]ATTATGATGGATTTGTCACTATAGATTTGTGCAAA Y 2 1 2 1 101000 f 74 goat snp53438-scaffold81-306949 8 48391656 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274921 Affx-1111834577 AX-519548503 8 47272085 ATCTGTTTTGAGCTAGAGAGAGGTGTAGAGAGATG[A/G]CAGAGGTGACATTAGAAGGTCTTTCCTGTGTCGCT R 2 1 2 1 101000 f 74 goat GoatD01.042119 8 47272085 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320782154 Affx-122945382 AX-385269232 8 47296150 TGAATCATTTACTTCCAGAAAATAGTACAGTTACC[A/G]TAGACTCAGTTTAGTCCTAGTAATTAAATTCAGTT R 2 1 2 1 101000 f 74 goat snp53439-scaffold81-353883 8 48438562 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424973 Affx-122941917 AX-123295319 8 47331510 CCTTTGAATTCAAATTGTGTTTGAAGTTCTTCTCA[A/G]CTTTAAAGGGAGTCAACAACGTTGTAGAGCTACAA R 2 1 2 1 101000 f 74 goat snp53440-scaffold81-389243 8 48474636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381143 Affx-122974561 AX-123251501 8 47362510 CATGCTCCTGGTGGGAACTTGCGTTCATTTGTGGT[A/G]TTTCTGTTAAAGGACTGGCAACGGAAGAAAGACCA R 2 1 2 1 101000 f 74 goat snp53441-scaffold81-420243 8 48506055 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410394 Affx-122952430 AX-123280744 8 47395519 TAAGTCATAAGCATAGTTTCAATTCAGGCTCTACA[A/G]TGTCCAGGGCCATGTAAAGTCAAAACTACAAACAT R 2 1 2 1 101000 f 74 goat snp53442-scaffold81-453252 8 48534534 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387929 Affx-122970437 AX-123258287 8 47452946 ACAAACCTCAGAATGTTCCTCTTGCTTTTAACGTT[C/T]GACGTGCCTGACAGATTACCCTTTCAAAACAGGAT Y 2 1 2 1 101000 r 74 goat snp53443-scaffold81-510679 8 48591967 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445064 Affx-122926224 AX-123315401 8 47500460 CCATATAGTAAATATTTTTGGCTTTACAGATTATA[C/T]AATACAATATTCTTCAACTCTGTTCTCTTAGTGAT Y 2 1 2 1 103000 r 74 goat snp53444-scaffold81-558193 8 48634127 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413968 Affx-122950298 AX-123284317 8 47552668 CTTATTGCAGAACAGAATTTATTTTGGTTGAAGTT[A/G]TTTTGAATTGAACTGACAGGCTTATGATTGACATG R 2 1 2 1 101000 r 74 goat snp53445-scaffold81-610401 8 48686069 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415778 Affx-122948917 AX-123286127 8 47596863 ATTACACTTTGAGCTCCCCTGGGTGGGGATTATTA[C/T]GGCAGGGATTCATTTTTGCCTATCATTTTGGAGTG Y 2 1 2 1 202000 f 74 goat snp53446-scaffold81-654596 8 48730566 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766670 Affx-122976173 AX-385254016 8 47627363 CTTTTGACTGTTTTAATTAACTGTATATTTTCTTA[G/T]TTTTTATATGTGCCATTTGCCATTCTTTTCCTTAT K 2 1 2 1 303000 f 74 goat snp53447-scaffold81-685096 8 48760512 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800606 Affx-122935550 AX-385287525 8 47746332 AATTTTAAATGAAAGGTGACATACACAGTGGATCT[A/G]TAATATATATTTTAACTCAGACACCTCCTCTTTAC R 2 1 2 1 201000 r 74 goat snp53450-scaffold81-804065 8 48884596 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278787 Affx-1111836512 AX-519552260 8 47777979 TTGGGATCAGAAGACCTGGGTCCAATACTTCATAG[A/G]ACCTGCATAGTTTGTAAGTCACATAATCTCTCTAG R 2 1 2 1 201000 r 74 goat Random2.2K-899 8 47777979 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320798285 Affx-122970706 AX-385285220 8 47793567 AATCTCTCTTCCATCTCTCTATTTGATTAACTACT[A/G]CTTCAGGTCTTGGTATTACTAGGTCTGTATTCCCC R 2 1 2 1 101000 r 74 goat snp53451-scaffold81-851300 8 48931987 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391220 Affx-122967403 AX-123261577 8 47835105 GTGGAATGATTCTATATTGAAGGAACCTGTAACAA[C/T]ATGGCAACTACAGGCAATATGTTTTCTTCTGTTAT Y 2 1 2 1 101000 f 74 goat snp53452-scaffold81-892838 8 48973700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777021 Affx-122977766 AX-385264144 8 47888124 TAAGCAGAAGGCTTTCTTATAAAGTGACGAAGATG[C/T]AGGGTGTGTCCGTATTAGATGTGCCCTTGGAACAG Y 2 1 2 1 101000 f 74 goat snp53453-scaffold81-945857 8 49028911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378036 Affx-122977573 AX-123248395 8 47921628 TGGCCAAACTCAACGGGTTAGGAGGAAAGAGAACC[A/G]TTGAGCTAGCCCCTATGTGTTAATTTCCCAGAACA R 2 1 2 1 101000 r 74 goat snp53454-scaffold81-979361 8 49062951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773926 Affx-122959624 AX-385261065 8 47964119 AAAATAAATGGAACTAATGAGTCATCTTCTAGAAA[C/T]AGCAAGACTGGTGACTCATTCCTCCAGACTTGTAG Y 2 1 2 1 102000 r 74 goat snp53455-scaffold81-1021852 8 49105821 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785078 Affx-122938285 AX-385272125 8 48024566 ATGGGATGTAGAAGTGGAGAAGAAACCACTAGTTA[C/T]GGACAGTAGCTAATCTAATAGCTGAATTTTGTTCT Y 2 1 2 1 101000 f 74 goat snp53456-scaffold81-1082299 8 49166169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452346 Affx-122920646 AX-123322679 8 48131845 GCTGTTGGCCATTACAGCGACATCTATGATATCAA[A/C]AATAAACCTGGAAATGGAAACTGTGATGAAGCCAG M 2 1 2 1 202000 r 74 goat snp44524-scaffold606-34356 8 49293971 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779708 Affx-122922883 AX-385266808 8 48166915 TTTCCCTTATAGTAAAGACTTGTTATGAGTCATAA[A/G]TCTTCTCCAGAGGGTGTGGTTATCATCTGATAATC R 2 1 2 1 101000 r 74 goat snp44525-scaffold606-69426 8 49329036 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405878 Affx-122955605 AX-123276230 8 48225031 GCAGCAAGGACACTGGTGGCATTTCCAACACTGAG[A/C]GGAGGGAGAGGACTGCTGCATGAGTGCTCAGTCGC M 2 1 2 1 201000 f 74 goat snp44526-scaffold606-127542 8 49388077 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414982 Affx-122949055 AX-123285331 8 48265737 TAGCATATGGGCACCTACCGTATAACCTGTATAGG[A/G]CTTGTTAAAACTGATTTTGGATACCATCCCCAAAT R 2 1 2 1 101000 f 74 goat snp44527-scaffold606-168248 8 49429802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794113 Affx-122922670 AX-385281079 8 48315104 CTTCACCAACTGAAAAGCCACTCATTGATTACAAT[A/G]CAATTAATTCTCTAACGGTAGTCACATATATTTAT R 2 1 2 1 101000 f 74 goat snp44528-scaffold606-217615 8 49479666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796382 Affx-122934545 AX-385283332 8 48400458 AAAATAGTACTACATATTGAATATCAGTATACATA[C/T]GTAATTTCAAAAATGAACTATGTTAACAGGTTTCA Y 2 1 2 1 101000 r 74 goat snp44530-scaffold606-302969 8 49565650 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777029 Affx-122947323 AX-385264152 8 48444641 AGTATATTTTGTAAAAGATATAACCATTATATTAT[A/G]CAATTATTCCCAGGACAGACAAAGAAATGTTATTA R 2 1 2 1 202000 f 74 goat snp44531-scaffold606-347152 8 49631371 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441051 Affx-122928925 AX-123311388 8 48481076 TCCCTCCTTTCCTCACCATTTCTTCAATTTATACA[C/T]AAAGAACTTCATGGTGTATATACTAACAAAATTAT Y 2 1 2 1 101000 f 74 goat snp44532-scaffold606-383587 8 49668831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440748 Affx-122929871 AX-123311085 8 48514009 GTCAAGTAAATATTTTGAATAGATAATAAGAGTTC[A/G]CCAGAGAAATAACAGGACTCATTAAAGAGATGGCA R 2 1 2 1 101000 r 74 goat snp44533-scaffold606-416520 8 49702412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773231 Affx-122963896 AX-385260374 8 48568100 ACTCCTGGTGTCAAAAATAAAGTGGTGTCTCTAAC[A/G]TGAAAATCTACCATACCTTTATTAGGAATTATAAG R 2 1 2 1 101000 f 74 goat snp44534-scaffold606-470611 8 49756746 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278614 Affx-1111836514 AX-519552093 8 48604910 AGAAGTTGAAACCAAGCTGCATTAATGCTTCTTGC[A/G]AGGTCACTATATGGCAAAACTATAATTATTCTTTT R 2 1 2 1 101000 f 74 goat Random2.2K-900 8 48604910 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320790353 Affx-122963371 AX-385277356 8 48614317 GCTCTAGAAGCAGGCAACCTCTATCTTCTCCTGAG[C/T]ACTACTATCAACTCGGGAAGCAGTGCTTCAGGTTT Y 2 1 2 1 101000 f 74 goat snp44535-scaffold606-516828 8 49802727 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383867 Affx-122973138 AX-123254225 8 48650692 CCAAATCCAGATTTATGTCCTTTTCCTGTACTTCA[A/G]ATTCTTCTTCTTAGTTGTCTTCTTCTCCCTTTGAA R 2 1 2 1 101000 r 74 goat snp44536-scaffold606-553203 8 49839526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386387 Affx-122970838 AX-123256745 8 48679272 GTATGGGGGTGTAATCTGCCAAACAGGAAGCATGA[C/T]TGAGAGGTATCAAAGGCAAGGAATGCAAGGCCAAG Y 2 1 2 1 201000 r 74 goat snp44537-scaffold606-581783 8 49868627 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448346 Affx-122924128 AX-123318682 8 48709979 CCAAGAACTTGCATCCACAATCCTAGAGTGGTCTT[A/C]GAGTGCCATTTTCTGCTTGATTTTCACAAGTAACA M 2 1 2 1 101000 f 74 goat snp44538-scaffold606-612490 8 49899243 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383723 Affx-122972465 AX-123254081 8 48765557 TCTATGGGGCTGACCCCAATGTGGCTAACTGGGGG[C/T]GGAATCACTAACTAGATCAATCATTCACTCTGTTC Y 2 1 2 1 101000 r 74 goat snp44539-scaffold606-668068 8 49955561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429795 Affx-122938202 AX-123300136 8 48794899 CTGCTGAAGCTCTGCACGTAGTAATTTTTTTCCCC[A/G]CCAAATATAAGTGAAAAGAACCATCTTTCAGAATA R 2 1 2 1 101000 f 74 goat snp44540-scaffold606-697410 8 49985432 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436990 Affx-122933144 AX-123307328 8 48844147 CTTCTGAGAGACTGAAGAAAAACATTCCACCTGTA[C/T]GACCAATCTCATTTCTTAATTCTCACTGAAATAAA Y 2 1 2 1 201000 r 74 goat snp44541-scaffold606-746658 8 50034400 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768906 Affx-122953048 AX-385256083 8 48876307 GCAGGAAATTAAGGAAAGTAAGGAATCTTTTGATA[A/G]TACTATAATTCTACAGCCCAAGGAAGAAACCAATA R 2 1 2 1 201000 r 74 goat snp44542-scaffold606-778818 8 50066571 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408900 Affx-122953970 AX-123279251 8 48932083 TCAAGCAGGTCCTTTTTTTCCTACCTCTTCCTGTT[A/G]TTGATATGAAGATGATACCTTCATTAGATATATAT R 2 1 2 1 201000 r 74 goat snp44543-scaffold606-834594 8 50121873 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791021 Affx-122969394 AX-385278017 8 49021605 GAAATTTAACTGAAATGGATATAACCAAGATATAG[C/T]GTAGTAATTGAAATTGCCATTTTCCTGAACTGGTT Y 2 1 2 1 101000 r 74 goat snp44545-scaffold606-924116 8 50210872 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400163 Affx-122960686 AX-123270518 8 49057484 ACATGTATGGGCATCTATGGGATGCTTCACACAAG[C/T]GCAAATTTATTTTGTGAACTGAACTTGACCATATG Y 2 1 2 1 101000 f 74 goat snp44546-scaffold606-959995 8 50247872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775000 Affx-122958884 AX-385262132 8 49112058 CTGAAGCAGTCATCTTCCTACAATTACTCCACTCC[A/G]TCTCAATCAGTCCATGCCAACCCACATCTTTCCTT R 2 1 2 1 101000 f 74 goat snp44547-scaffold606-1014569 8 50299220 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398256 Affx-122962186 AX-123268611 8 49149191 CTGCGGACTGTCGCTGATATTTGCTGACTGTTCCC[A/G]CAGCCCCATGTGCTTCCATATGTTGCTTCCATTGT R 2 1 2 1 201000 f 74 goat snp44548-scaffold606-1051702 8 50337931 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407051 Affx-122954929 AX-123277402 8 49196690 TCAGGTTTTTCTACCAGTTGACTGAGATTGTAAAC[A/G]TACCACTAGGGAATTAAAATATACTCGCTTTGAGT R 2 1 2 1 101000 f 74 goat snp44549-scaffold606-1099201 8 50385433 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785770 Affx-122925653 AX-385272810 8 49229088 CAGGCAACTAGGCCACATTTTAATAGAATGAGCCT[A/G]TAGTACATTATTTACACTCATCCTCATATTGAATC R 2 1 2 1 101000 f 74 goat snp44550-scaffold606-1131599 8 50418033 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765030 Affx-986697171 AX-385252601 8 49260448 TTGGATTACAGTTAGTTAGATAAATGGATTTTGTT[A/G]AGAATGACACAGCCATAAAAAACTGGTTAGTCAAC R 2 1 2 1 600010 r 74 goat 8_49260448 8 49260448 Ancestral_priority_1043 ancestry 0.524 neutral IMAGE 10K 10K ancestral 320779893 Affx-122936231 AX-385266992 8 49263445 AGGAAGAGATGGAATTTGAGCATGGGCATAGAGCA[C/T]GGGTTTAAATAAGAAGTTTTTATCTCCCTTGGAAG Y 2 1 2 1 101000 f 74 goat snp44551-scaffold606-1165956 8 50452684 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387259 Affx-122970556 AX-123257617 8 49294506 ATGGGGAAGCACAGAAAAGATTTTATTTACAAAGG[C/T]GATTGTCACTGGTTTAAAAGAAAAATAGGACTGAT Y 2 1 2 1 101000 f 74 goat snp44552-scaffold606-1197017 8 50483528 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430902 Affx-122936864 AX-123301243 8 49323428 TGAATCTGTCTCCTCTCTGTCCTGAGAGAACAGGC[A/G]TGGAGAAGACAAGATTGTCACCTATCAGAATCTAC R 2 1 2 1 201000 r 74 goat snp44553-scaffold606-1225939 8 50512588 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768061 Affx-122946051 AX-385255268 8 49375100 ACACAAAACAGAGAGGAGATACTTGGCCATGCTTC[A/G]TTTTCTGAGTTTTTCACAAGATTGGCCAAGCTCTC R 2 1 2 1 101000 f 74 goat snp44554-scaffold606-1277611 8 50563701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386122 Affx-122971418 AX-123256480 8 49421809 GCCTTCTTTCTTTTTGAACATCTTTTTCCAACGTC[A/G]GTTCCCTTCATCTGGGGCCAGGGAGGACACTGATT R 2 1 2 1 101000 f 74 goat snp44555-scaffold606-1324320 8 50610927 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778061 Affx-122952121 AX-385265177 8 49515028 ATAGAGAATGGCTGAAATCACTTTTGACTATACCA[C/T]ATTGGCATATACAATAAGTGGTATTTCAGGCAGGC Y 2 1 2 1 101000 f 74 goat snp44557-scaffold606-1417539 8 50704739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401602 Affx-122958865 AX-123271955 8 49581216 TCCTTGACCCAGTTCCCTCAAAATTTTAATGTGAG[C/T]AGTTAACTGATTCAGGAGCCCCGCTAAGGCATGTA Y 2 1 2 1 101000 f 74 goat snp44559-scaffold606-1483727 8 50770714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423007 Affx-122942979 AX-123293353 8 49621506 GGCAGCTATTCTATAACCTCAAAGAGAAAGCCCAT[A/C]TAAGAACAAAATAAGAGAAAGAGATAAGACGGACA M 2 1 2 1 101000 f 74 goat snp44560-scaffold606-1524017 8 50811775 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412001 Affx-122951756 AX-123282351 8 49658842 ATTATTAACTCTGCCTAATCAAAGTACTTCATGGG[C/T]TCAGTCAAATCCATATTTTCATATTCATGAATTTG Y 2 1 2 1 101000 f 74 goat snp44561-scaffold606-1561353 8 50849664 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273401 Affx-1111833581 AX-519547030 8 49712942 GCATAAACAGTTATAAAGTACAATTTTGATATTTT[A/C]CTTTTAAATTATGAAGTTCATGCAACGCTTAATTG M 2 1 2 1 101000 r 74 goat 8_49712942_AF-PAKI 8 49712942 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38421902 Affx-122944253 AX-123292249 8 49727206 GTGATGCTCGAAAAGGTAAAAAACACTTCTGGACA[C/T]GAAAGCATAACAATCTTTGGCATAGTTGGAGAATA Y 2 1 2 1 201000 r 74 goat snp44563-scaffold606-1629717 8 50918225 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396573 Affx-122962919 AX-123266928 8 49807447 GGTAGGTATGATTCTTTTCGATTGAGATAAATAGT[A/G]CAGTAAAACACACAGATAATAATTATATAATTTGA R 2 1 2 1 101000 f 74 goat snp44565-scaffold606-1709958 8 50998207 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791100 Affx-122933807 AX-385278095 8 49854210 CATTTGATGCTCAATATGTTTAGTCAACGAGCAAG[C/T]AAAAGGCTTTAGTTTTTATCAGTTCTGATATTGGC Y 2 1 2 1 101000 r 74 goat snp44566-scaffold606-1756721 8 51045946 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443579 Affx-122927333 AX-123313916 8 49883410 ATTTACTTGTCAATTAATTTGTTCATTCATTTATT[A/G]CCTCATTTATTCACAAGCATTTAGTATTTACCATG R 2 1 2 1 101000 r 74 goat snp44567-scaffold606-1785921 8 51075675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786837 Affx-122930850 AX-385273866 8 49955213 ATTTTCAGAGGGGTTGGTTATCTCCACAAATTACC[A/G]TCATGGTTGGTGAATTCATTTACAGTAAAAAAAAA R 2 1 2 1 101000 f 74 goat snp44568-scaffold606-1857724 8 51148796 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396794 Affx-122962753 AX-123267149 8 49985808 TTGCTGGGACTAATTTTTAGATTTCTCAGCTCTTT[A/G]TTTGATGTTCTTCCCTTCTACACAGTGCTTTCAGC R 2 1 2 1 101000 r 74 goat snp44569-scaffold606-1888319 8 51179935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379537 Affx-122976063 AX-123249895 8 50043207 CCCAACATGGAGTCTTTGCATTTCCAGCATCAGTA[C/T]GTCTTAAGGCCATTCATTTCTCCCTGTTATCTTCA Y 2 1 2 1 201000 f 74 goat snp44570-scaffold606-1945718 8 51237684 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403542 Affx-122957604 AX-123273895 8 50071836 CTGCTCTATTTAAGGATATATTCCCTTGAATCAAA[G/T]CTTGGATGGGACTTCTCAGAGATTTAAGTTTCTAT K 2 1 2 1 201000 f 74 goat snp44571-scaffold606-1974347 8 51267223 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431516 Affx-122936232 AX-123301857 8 50112108 ATACAACATAGAAACCCCTAATCCTCTTATTTAAA[G/T]CAAAAAAGAAATGAAACTTAAGCAGTGACTTTGAA K 2 1 2 1 303000 f 74 goat snp44572-scaffold606-2014619 8 51308554 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790178 Affx-122931700 AX-385277182 8 50144537 GGGCATGATCACTTTTAAGCAATTTTCTGGAATAC[C/T]ATGTTTTCACTTTGAAACAGGATTGTAATACACAT Y 2 1 2 1 101000 r 74 goat snp44573-scaffold606-2047048 8 51341771 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442774 Affx-122927737 AX-123313111 8 50183657 AGCCTCACTGCCCATATTTTCTGCTTTAGCCTGTT[G/T]CTATATGTAACTGCTATTTAATGTTTGATATAAAT K 2 1 2 1 201000 r 74 goat snp44574-scaffold606-2086168 8 51381236 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787396 Affx-122944549 AX-385274421 8 50212875 TAATCCTCTCTTATTAAGATACCCATATTTCCTTA[C/T]GGTAGGTACTCTTCTTTGCTAACAAATCCTCAATT Y 2 1 2 1 101000 r 74 goat snp44575-scaffold606-2115386 8 51409191 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416897 Affx-122948068 AX-123287245 8 50263106 TTACCTTTTAAGCTGGAACACATATTTGCATGATG[C/T]AAAGATATTATGCGACTCTGATTTTATCTTTCTAA Y 2 1 2 1 101000 f 74 goat snp44576-scaffold606-2165617 8 51459602 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797167 Affx-122954734 AX-385284107 8 50309645 AAGAAGTTACTTCGACATTGCTTGATTCTTTAAAG[C/T]GAATGATCATTTGGGGAGCTTTATAGTGGATGCCT Y 2 1 2 1 102000 r 74 goat snp44577-scaffold606-2212156 8 51506148 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445839 Affx-122926014 AX-123316176 8 50367550 GCACAGTTCCAGGATAGGAACCCAGGTGATCTGGC[C/T]CCAGAGTTCACGCTTCTAACCAAGACCCTGTAGCT Y 2 1 2 1 201000 r 74 goat snp44578-scaffold606-2270061 8 51564296 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412539 Affx-122951338 AX-123282888 8 50396918 TTTTCTGAATGATTCTTGTATCTTTTTAGTCTGAG[A/G]CCTGATTCTCTCCTCTGCCCGTTGTTTCCTGTCAT R 2 1 2 1 101000 r 74 goat snp44579-scaffold606-2299429 8 51593842 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426381 Affx-122940238 AX-123296727 8 50437303 CACACAGGGAGGAAGGAGATGGCGGAGGAATAGGA[C/T]GGGGAGACCACTTTCTCCCTCACAGATTCATCAAA Y 2 1 2 1 303000 f 74 goat snp44580-scaffold606-2339814 8 51635042 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434267 Affx-122934786 AX-123304608 8 50471166 GCTGACAGGGGAAACTGCTTGCTGCCTTATGTCTT[A/G]CTGTTTGGAAAGTAAGAGAAGGGGGTCTTTCAGTG R 2 1 2 1 201000 f 74 goat snp44581-scaffold606-2373677 8 51669743 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791592 Affx-122919656 AX-385278583 8 50510060 TGTCCAGTACTTTCGATCAAGTGTGAACTTTGCCA[A/G]TCAGCCTCCTCCTTCTAAAAACAAGATCAGAGACA R 2 1 2 1 101000 r 74 goat snp44582-scaffold606-2412571 8 51708696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769902 Affx-122963492 AX-385257071 8 50548913 TCTGGAGTACCTTACTGAGAAATACTGTTACCATG[C/T]GTTTAAAGTACAACAAACTATGAACCTTTTTTTCA Y 2 1 2 1 101000 f 74 goat snp44583-scaffold606-2451424 8 51748007 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418612 Affx-122946350 AX-123288960 8 50595110 GTCCCTAGAAACATGTCTGTACTGAGCAAATGGCA[C/T]GATTGGGCACCCTATAGAACTATCTATAAGAAATT Y 2 1 2 1 101000 f 74 goat snp44584-scaffold606-2497621 8 51792463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798942 Affx-122966513 AX-385285872 8 50630911 GATCAAGTGGATTTAGACCTGAGGAAAACCAAAGG[A/G]AAATTAATACATACATATCCCATGGAAACCTCCAG R 2 1 2 1 101000 r 74 goat snp44585-scaffold606-2533422 8 51816913 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432864 Affx-122935356 AX-123303205 8 50661987 AATAGTTGTGTTCAGCTCTGGTACACATCAACTCT[A/G]CTCTGAAACCAGTCTGGTTAATGAATACTGGCTCT R 2 1 2 1 101000 f 74 goat snp44586-scaffold606-2564498 NW_017194931.1 2523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395193 Affx-122964508 AX-123265548 8 50711175 TGGGATGCCTGGGTTCCAGTTTTCATTCCATAGGC[A/G]ATTCGTTTCATGCCTTTGGCCAAGTTACATAACCT R 2 1 2 1 101000 r 74 goat snp44587-scaffold606-2613686 8 51897515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776781 Affx-122963905 AX-385263905 8 50739923 AAGTCAGTGCTCTTGTGTCTTTTCCTATACAGGCG[C/T]TCTTTCCATCGTGAGACTACCGTACATCACCTAGT Y 2 1 2 1 101000 f 74 goat snp44588-scaffold606-2642434 8 51926576 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378910 Affx-122976454 AX-123249269 8 50799887 TTGGTAGAAAATCCACTATATTTTAAGCTTTTTAA[C/T]GGTCTAGTCCAGTGATTTGTCCACAGTATATAGTA Y 2 1 2 1 101000 r 74 goat snp44590-scaffold606-2702398 8 51986634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403084 Affx-122958506 AX-123273437 8 50831674 CTGTACCAATTTACATTCCCACCAACTGGGTAAGA[C/T]GGTTCCTTTTAGGAGAGAGGCCTTTAGAATGGCCA Y 2 1 2 1 201000 r 74 goat snp44591-scaffold606-2734185 8 52018614 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420701 Affx-122944790 AX-123291048 8 50872537 AACTGAAGGATGCTTTGGCATCTAGTCGCTGGACA[C/T]GCCCTCCTCCCTGTGCAGTCAGGGATCGCAGCTGC Y 2 1 2 1 101000 f 74 goat snp44592-scaffold606-2775048 8 52059739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418845 Affx-122946139 AX-123289193 8 50921760 ACTGGAGTGTCAGGATTGTGGGCAAAAGTGGAAAA[C/T]GAAGAACCATGATTTGTGATGAGTCCCTTTTCAGG Y 2 1 2 1 101000 f 74 goat snp44593-scaffold606-2824271 8 52109253 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377606 Affx-122977895 AX-123247965 8 50976226 GCTGTTGGGTCCAATCTTTGGCCAAGGATGGGTAC[A/G]TGACTAATGCTCCCCATGTTCTAAGATGATCAGTC R 2 1 2 1 101000 r 74 goat snp44594-scaffold606-2878737 8 52163608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435963 Affx-122933524 AX-123306302 8 51011994 ACCAGATTGCAAGCTCCTTGAGAGCACGGGTTGCC[C/T]TTCTTATCTGCATATACTCTGTACAACATGAAAAG Y 2 1 2 1 101000 r 74 goat snp44595-scaffold606-2914505 8 52199571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385193 Affx-122971724 AX-123255551 8 51062380 AAACTTGACCATAGGCAGAATATTACATTGCATCT[A/C]TGTGTTGGTGACATCAGAGCACATTCTGAGGATTG M 2 1 2 1 101000 f 74 goat snp44596-scaffold606-2964891 8 52249941 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447719 Affx-122924604 AX-123318055 8 51148747 CAGGCAAGAGACTGGAATGGGCTGCTGTGCCCTCT[A/G]CCATCTTCTCTTTTAAACATAGCCATTCAAGGGAT R 2 1 2 1 101000 r 74 goat snp44598-scaffold606-3051258 8 52336505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426485 Affx-122940229 AX-123296831 8 51242820 TTGTTGTTTTTTTAAATTCAGGATCCAAAGATCAC[A/G]TTGTATTTGATCATCATGTTTCCTCAGTATCCTTG R 2 1 2 1 101000 f 74 goat snp44600-scaffold606-3145331 8 52430708 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446418 Affx-122925561 AX-123316754 8 51296496 ATCAACCTGTACATCTGTGCTATCCTAATATGACA[C/T]GTGAGACCTTCTTTTATCATAATCAGTCTTCTTAA Y 2 1 2 1 101000 f 74 goat snp44601-scaffold606-3199007 8 52484212 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767226 Affx-122923550 AX-385254507 8 51327033 AAAATGATTGATGTTCCCATTCCCTCCCTATATTT[G/T]TGTCTTGAAAACAGCTTCTTAATTTAATAAATCTG K 2 1 2 1 101000 f 74 goat snp44602-scaffold606-3229544 8 52514771 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417391 Affx-122947693 AX-123287739 8 51359611 TTTAATCCCTCCCACTCCCCTTCCCTCTCTTATTG[C/T]GACTCCTTTCCACCTCAATCCAGGTCTACCAAACA Y 2 1 2 1 201000 r 74 goat snp44603-scaffold606-3262122 8 52552890 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378633 Affx-122977110 AX-123248992 8 51407801 CAACAGGAGCAAAATTCAGCTTTGCGAAAGGCAGA[C/T]ATAATGCTAGTTGTAGACAAATCTGGGGGGAAAAT Y 2 1 2 1 201000 f 74 goat snp44604-scaffold606-3310312 8 52600738 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278616 Affx-1111836515 AX-519552095 8 51425914 TACAAGCTAGGAGCAATTTTCACTAGGAGTCTGGA[C/G]AGCAGCATTAAAAACAAATTGTTACAAGTACCATA S 4 1 2 1 101000 f 74 goat Random2.2K-903 8 51425914 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447331 Affx-122924891 AX-123317667 8 51460183 GATAAGAATATGTGAGGAGGGCTTCCCTGTGGTCC[A/G]GTGGTTAGGAATCCACTTGCCAATGCAGGGGACAC R 2 1 2 1 103000 f 74 goat snp44605-scaffold606-3362694 8 52653348 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425075 Affx-122941252 AX-123295421 8 51497941 CTTAACAAGCATTGCTTTGTCTAGAGCCAGGCAAG[C/T]TTCTTTCTTTTTTGTTTTAAATGAGACTAGTCACT Y 2 1 2 1 101000 f 74 goat snp44606-scaffold606-3400452 8 52691747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395766 Affx-122963676 AX-123266121 8 51533626 TGGTCATCCACTTAAAAAGGATGCTACCTGAAAGG[C/T]GTGAACAAAATCACCTTTAAACTTTCTAGTCAAGC Y 2 1 2 1 101000 f 74 goat snp44607-scaffold606-3436137 8 52727403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772407 Affx-122950174 AX-385259559 8 51573395 AAACTGCAGCCGGCATACAGTAGTTGGGTATTTAA[G/T]AAAGATTTATTAAAATACCTGTCTGGTGACACAGA K 2 1 2 1 101000 r 74 goat snp44608-scaffold606-3475906 8 52767480 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422369 Affx-122943426 AX-123292715 8 51621369 GGCCTCATGGCCACTCCAACGGCTATGTGGATAGC[A/G]CTCCTGCTATATAGGCAGGAAGAGTTACAGACCTC R 2 1 2 1 202000 f 74 goat snp44609-scaffold606-3523880 8 52814639 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376028 Affx-122978395 AX-123246387 8 51651761 TGACTGTGGGACTAGGTGGCTAGACAGGAATGAAG[C/T]TACTAATCATTAAGGTGAATAATCACAAGAGACCC Y 2 1 2 1 101000 r 74 goat snp44610-scaffold606-3554272 8 52845457 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393000 Affx-122965655 AX-123263357 8 51692420 ATGCTCTCTATCAAAAGTACAAATCTGAAAGAAGT[A/G]CTGATGGAGTGAAGAGGTAGGGAACACTGGTCAGA R 2 1 2 1 201000 f 74 goat snp44611-scaffold606-3594931 8 52885370 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406270 Affx-122956090 AX-123276622 8 51721059 ATAGAAGTGATGCCTTAGGAGAAGAAGCCTTGGCC[A/G]CCAAAGCCGCTGGTTCCCTTTAAAGTCCATTCACC R 2 1 2 1 101000 r 74 goat snp44612-scaffold606-3623570 8 52914273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424634 Affx-122942175 AX-123294980 8 51795642 AATTATAATAATAACCAAATGTGCCAAGTGGCTTC[A/G]GTCATGTCCAACTCTTTGCGACCCCCCATACTGCA R 2 1 2 1 103000 f 74 goat snp44613-scaffold606-3698153 8 52989503 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420744 Affx-122944729 AX-123291091 8 51827874 AGTACTTCGTAGACACATCTGCGATTCGCCTCCCA[A/G]CTTTGCTAAACCATCTAGTGTTTAATATTTCATTC R 2 1 2 1 201000 r 74 goat snp44614-scaffold606-3730385 8 53021909 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405638 Affx-122956589 AX-123275990 8 51880395 CTAGATAATATTTTCACATTCTCTGTATTATGTAT[A/G]TTGTTAGAACAGAAGTGATATCAGTTATATTTCAT R 2 1 2 1 101000 r 74 goat snp44615-scaffold606-3782906 8 53076475 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375942 Affx-122978455 AX-123246301 8 51993622 TGCTAGGCATTTACAGAAGCTGCCACTGGATCTTC[A/C]GCTACCTTCATAAGGGATCTGGCACCTTTTATGAT M 2 1 2 1 101000 r 74 goat snp44618-scaffold606-3896133 8 53191839 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802120 Affx-122948313 AX-385289024 8 52036632 TACGTTGGTGGAAATCATATACTCAAATTATAGAC[A/G]TTGGAAGCAAGACAGCTAACCTTTTGAAGATGAGG R 2 1 2 1 101000 r 74 goat snp44619-scaffold606-3939143 8 53235154 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785161 Affx-122974712 AX-385272207 8 52141730 GTTTATGATAGCAAGGCGACCTTGGACTTGCTCTA[C/T]ACAACTGGACCCAAGGCAATCAGGAGTGATGTCCG Y 2 1 2 1 101000 r 74 goat snp44621-scaffold606-4044241 8 53340674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442831 Affx-122927699 AX-123313168 8 52184889 CTTCCCACCCCTCTGAAGGAACTGTCTTCCACTTC[A/G]TCCCCTCAAGAGTTAGTCCTGCCCTATATAAACTC R 2 1 2 1 101000 r 74 goat snp44622-scaffold606-4087400 8 53379386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791474 Affx-122947629 AX-385278465 8 52217315 TCTATGGAGTGCAACTTTGAGTCATGTCTCTATGT[A/G]TATTAGTTTGATAGAGCTCATATAGACTTGCTTTA R 2 1 2 1 101000 f 74 goat snp44623-scaffold606-4119826 8 53412223 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431238 Affx-122937137 AX-123301579 8 52248148 ATAGGAAAAGCCACTGATTCCAAACTCAAGTGCCC[A/G]CAACAGTCAGGAAGGGATCACAAGATCATAAGAGA R 2 1 2 1 201000 r 74 goat snp44624-scaffold606-4150659 8 53443063 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423032 Affx-122943407 AX-123293378 8 52277164 AGTCCTTGCCAACCCAGACACTAGCTACCATAAAA[C/T]GTGCTGTGCCATATTCACAGAACGCTAATGTAGAA Y 2 1 2 1 201000 r 74 goat snp44625-scaffold606-4179675 8 53471719 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273365 Affx-1111833582 AX-519546999 8 52353381 TTAAGCCACAGCAGAAAGCCATTTTCCTTAATCCC[A/G]GGCAGCGGGGTTGGAACTGCCTGGGTTCCTAGTAG R 2 1 2 1 102000 f 74 goat 8_52353381_AF-PAKI 8 52353381 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795563 Affx-122928464 AX-385282518 8 52368356 AGCACCCTCCAGGACACTCTAGGAAGACTTTCTGA[G/T]AGTCAGCAATGGCAATATGGAAAATTAGATTAAAT K 2 1 2 1 101000 f 74 goat snp44626-scaffold606-4270867 8 53562473 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430144 Affx-122937389 AX-123300485 8 52404749 AAACAGGTAAATATAACTGTTCTGCATGGTATCCT[C/T]ATGATTTCAAAGAGACACTATATTCCCTTTGGCCC Y 2 1 2 1 101000 r 74 goat snp44627-scaffold606-4307260 8 53600204 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438347 Affx-122931332 AX-123308685 8 52434759 GAACCACACTTTGCAAAACAGTGACTGAACAAACA[C/T]CGAGACTCCCAATAGCCAAGTGGGGACTGGTTTTA Y 2 1 2 1 201000 r 74 goat snp44628-scaffold606-4337270 8 53630251 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278617 Affx-1111836516 AX-519552097 8 52500701 ATAGATCATAGAAAAGCCTTGTTAAGGTGCTTTGG[A/G]ACGTCAAGGGGCTGTTCCCTTCTACTGTGTCTCCT R 2 1 2 1 201000 f 74 goat Random2.2K-905 8 52500701 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 539476248 Affx-1251763754 AX-586011669 8 52529689 TTCACATTATCAGGCTTCCCTGGTGGCTCAGATGG[-/TAAAGAATCTGCCTACAGGGGGAGTGAAATCTGCCGCCGTAAAATTTAAAAAAAAATAAAAAATTATAAAAAAAAAAAAA]AAAGAATCTGCCTACAATGCAGGAGACCCAGGTTT - 8 1 4 1 20000 f 74 goat SV_273 8 52529689 - deletion junction SV-TF-chip 539476500 Affx-1251763754 AX-427316868 8 52529689 TTCACATTATCAGGCTTCCCTGGTGGCTCAGATGG[-/TAAAGAATCTGCCTACAGGGGGAGTGAAATCTGCCGCCGTAAAATTTAAAAAAAAATAAAAAATTATAAAAAAAAAAAAA]AAAGAATCTGCCTACAATGCAGGAGACCCAGGTTT - 4 1 4 1 20000 r 74 goat SV_273 8 52529689 - deletion junction SV-TF-chip 562165380 Affx-1251763754 AX-606940791 8 52529689 TTCACATTATCAGGCTTCCCTGGTGGCTCAGATGG[-/TAAAGAATCTGCCTACAGGGGGAGTGAAATCTGCCGCCGTAAAATTTAAAAAAAAATAAAAAATTATAAAAAAAAAAAAA]AAAGAATCTGCCTACAATGCAGGAGACCCAGGTTT - 8 1 4 1 20100 r 74 goat SV_273 8 52529689 - deletion junction SV-TF-chip 562165751 Affx-1251763754 AX-606941160 8 52529689 TTCACATTATCAGGCTTCCCTGGTGGCTCAGATGG[-/TAAAGAATCTGCCTACAGGGGGAGTGAAATCTGCCGCCGTAAAATTTAAAAAAAAATAAAAAATTATAAAAAAAAAAAAA]AAAGAATCTGCCTACAATGCAGGAGACCCAGGTTT - 8 1 4 1 20100 r 74 goat SV_273 8 52529689 - deletion junction SV-TF-chip 562166462 Affx-1251763754 AX-606941870 8 52529689 TTCACATTATCAGGCTTCCCTGGTGGCTCAGATGG[-/TAAAGAATCTGCCTACAGGGGGAGTGAAATCTGCCGCCGTAAAATTTAAAAAAAAATAAAAAATTATAAAAAAAAAAAAA]AAAGAATCTGCCTACAATGCAGGAGACCCAGGTTT - 8 1 4 1 20100 f 74 goat SV_273 8 52529689 - deletion junction SV-TF-chip 320798000 Affx-122938892 AX-385284936 8 52540719 GTACCATCTTGTGACTATATCAAACACCATTAAAA[C/T]GGACAGTTTAAAATGATGAACTTATGGTATGTAAA Y 2 1 2 1 201000 r 74 goat snp44630-scaffold606-4443230 8 53735143 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774143 Affx-122942959 AX-385261281 8 52585310 GAGGTTTTAGCAGCCCTGAAACCAACCTGGCTTAC[G/T]TACTAGCCACATCACCAGTTCAATCCTATGGATTT K 2 1 2 1 101000 f 74 goat snp44631-scaffold606-4487821 8 53779543 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784895 Affx-122950397 AX-385271942 8 52631589 AGGTGCTCAATATCTGTTCATTTGACCAGCATTCC[A/G]TATGCAACTGTTCTTTCTTATGGTACATCTGGTTA R 2 1 2 1 101000 f 74 goat snp44632-scaffold606-4534100 8 53825777 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410263 Affx-122952526 AX-123280613 8 52679273 AGCAGATAGTAGACATCACCTTATCCTGATTTACA[C/T]GAGAATAGAAAAGCTGGTGACCTGGAGCCAGCTTA Y 2 1 2 1 101000 f 74 goat snp44633-scaffold606-4581784 8 53874026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802063 Affx-122948978 AX-385288967 8 52718949 AATAATCCTAGAGAAAGATGATGATAGAGTCAACT[A/G]GAACAGGTGATAGAAGAAGTGATGTTGAGAAGTTA R 2 1 2 1 101000 r 74 goat snp44634-scaffold606-4621460 8 53914320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769398 Affx-122976677 AX-385256569 8 52763175 AGTGATAAGCAGGAGCATGTCAAGGAATATTACAT[A/G]TTCTGTTTTAGGAACTTTGAAAGTGCTTAGTGCCT R 2 1 2 1 101000 r 74 goat snp44635-scaffold606-4665686 8 53956889 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402739 Affx-122958334 AX-123273092 8 52802064 AACTTTCCCACACAGGATTATTGCATGTTAGTTGC[A/G]CAGCTTGTGTTTTGCACAGAAGGATGAAATCTGAA R 2 1 2 1 101000 r 74 goat snp44636-scaffold606-4704575 8 53995141 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378449 Affx-122976694 AX-123248808 8 52835871 GTCACAGAGAGTTGGATATGACTGAAGCGACTGAA[C/T]GCTTTCAACGGTAGGCCTTGTTCATCACTGAATTT Y 2 1 2 1 101000 r 74 goat snp44637-scaffold606-4738382 8 54028959 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430612 Affx-122936974 AX-123300953 8 52895653 CCCTCTCTTTTTTCTAAAAACTCTTAACAAATACT[A/G]TCTTTGCTGCTACTCTTTCTGCTTAGATCTCATAT R 2 1 2 1 101000 r 74 goat snp44638-scaffold606-4798164 8 54089317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375938 Affx-122978459 AX-123246297 8 52952410 AAAGTCAGGAACTCCTTTTCTGAGTTTTCAGGCTT[A/G]CTGTACTCAGATGGTTCCAGAAGCCAGGATTTAAT R 2 1 2 1 101000 r 74 goat snp44639-scaffold606-4854921 8 54145753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766062 Affx-122938000 AX-385253478 8 52993665 GAATGTATGTGTATCTCCCTTTTGAATGGCTAATC[A/G]TATGCCACTCACTACTGCATTCATTATGGGGATGG R 2 1 2 1 101000 f 74 goat snp44640-scaffold606-4896176 8 54186993 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437133 Affx-122932155 AX-123307471 8 53024914 TAATGAGCTGAGACCACCAGCCCTGGGAGGCTTCT[A/G]TAGACTGTGGATAAATGTCCACAAGGGGTGACGAC R 2 1 2 1 101000 f 74 goat snp44641-scaffold606-4927425 8 54219295 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377184 Affx-122978199 AX-123247543 8 53075962 AGCTGCTCAGATTAGGACAACTGAATGCTGATAAA[C/T]GAGATGCAAGGAACTGGGAGAGGGTACATCAGAGG Y 2 1 2 1 101000 f 74 goat snp44642-scaffold606-4978473 8 54270063 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447312 Affx-122924908 AX-123317648 8 53114515 ATCAAAATTCCAAGTCTGGATGAAATTTAGGAAAA[C/T]GTGGAATGATAAACTTTGTACTTAAGCATAAAACA Y 2 1 2 1 101000 f 74 goat snp44643-scaffold606-5017026 8 54309350 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393622 Affx-122965354 AX-123263977 8 53156993 GTGCTGGGTTTGCACCTTCTGGTGAACTCATTTTA[C/T]AGAATCAGATAGAGGAAAACTCTACCATTTCTAAT Y 2 1 2 1 101000 f 74 goat snp44644-scaffold606-5059504 8 54351897 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435553 Affx-122933385 AX-123305893 8 53242343 CGTGCTGTTAAAATCCAAATAGATGCATATGTAAC[A/G]TGTTAGTGAGTGGGATTTTTTTTTCTGTTACTCCA R 2 1 2 1 201000 f 74 goat snp44646-scaffold606-5144854 8 54436581 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429226 Affx-122937924 AX-123299568 8 53297465 ATTGTTGCCAAAGATGTGTAACCTGAATTGAATGA[C/T]GACTTTAGACCTAAACTCTAGAGCACAGGACACAT Y 2 1 2 1 101000 f 74 goat snp44647-scaffold606-5199976 8 54470370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767099 Affx-122921620 AX-385254386 8 53326165 TGATACATAGATGCTCTTTCCTTTAGTGAAAAAGT[A/G]TCTGGTTTTATAGTATAGAACCACTATACTTTCTC R 2 1 2 1 101000 f 74 goat snp44648-scaffold606-5228676 8 54499252 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779189 Affx-122930925 AX-385266293 8 53369091 TAATAGCAGAAGAGAGCAGGAACAAGGAAGTTCTA[C/T]AAGACAGAAAAGCAAGTTGGTTATTATAAGTTTAG Y 2 1 2 1 101000 f 74 goat snp44649-scaffold606-5271602 8 54542182 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464589142 Affx-1110559257 AX-516060598 8 53402118 GTATATTCTCAGTTGGTACCCTATGATACTATGCA[A/G]TGGATTAATTTTCTTAGGCATGATCACTGTATTAT R 2 1 2 1 101000 r 74 goat Random2.2K-906 8 53402118 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436190 Affx-122932602 AX-123306529 8 53447709 GCCTCTTTCAAGAAGATAAATTGGAAATAATGAGA[C/T]GAGAAAAGAACATGACACATTTACAAAATTTCATG Y 2 1 2 1 101000 f 74 goat snp44651-scaffold606-5350220 8 54620980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422396 Affx-122943388 AX-123292742 8 53496774 GAAAATATGACAACCTAACGATTTCTTATGAATGA[C/T]ATCTGGGAGAATGAAGAATGAAACCAATTACAATT Y 2 1 2 1 101000 f 74 goat snp44652-scaffold606-5399285 8 54670699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773586 Affx-122929797 AX-385260726 8 53544784 TTTTAATGAAAATATTAAGTGTACTCTAAGAACAG[C/T]GGATAGGTGACATTTTGATTGAAACATGCAAGGAA Y 2 1 2 1 101000 r 74 goat snp44653-scaffold606-5447295 8 54718020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380007 Affx-122975604 AX-123250365 8 53576814 TTATGCTTCTCATTCAACAAATATTCTGTTATTTC[G/T]ACAGTGCATTTTTAAAATTCCTTTTTAAAACAAAA K 2 1 2 1 101000 f 74 goat snp44654-scaffold606-5479325 24 54398098 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393965 Affx-122965051 AX-123264320 8 53627184 AGATTTATTTAAAAGTTTGAATTCAATGAAAATTT[A/G]TGTAAAACTAATGCAAAATGCATTATGTTTGATGT R 2 1 2 1 101000 r 74 goat snp44655-scaffold606-5529695 8 54801705 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413603 Affx-122950566 AX-123283952 8 53630706 CCAGCTTAGAGAGTCTCTCTCCAAAGAAATCATCT[C/T]ACCAGTCTGTTCTCTTTAATTTTTTTTCTGATCCT Y 2 1 2 1 101000 f 74 goat snp49889-scaffold713-2191 8 54805184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434614 Affx-122934088 AX-123304955 8 53673698 AAAGGGGCAATCTTCCTTCCTCATGCAAGGGAACA[C/T]AGAGAAAGAACAGTAGACATAGAGGGTAGCTACAA Y 2 1 2 1 201000 f 74 goat snp49890-scaffold713-45183 8 54848996 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767944 Affx-122964748 AX-385255160 8 53703216 GCAATTTAAAGGTCTACACAAACTTCCCTGGACTG[A/G]TAGATTCTTTTTTAACCTCAGTAATAAGAATAAGA R 2 1 2 1 101000 f 74 goat snp49891-scaffold713-74701 8 54879151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400043 Affx-122960777 AX-123270398 8 53737288 AACTCTGCTGTTAGCAGGAGTTGGCTAATACAGGG[A/C]GCCCAGGGAATAAGCAAGCTTTTGCCTTCATTTTA M 2 1 2 1 101000 f 74 goat snp49892-scaffold713-108773 8 54913131 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385945 Affx-122971552 AX-123256303 8 53806023 AGAGCCCAGCTGATATGCCCATGGTCCCAGGGAAC[A/G]TATGCTGCAAGGCGTAACCCCCTGTGTCCATCAGC R 2 1 2 1 201000 r 74 goat snp49894-scaffold713-177508 8 54981714 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424206 Affx-122942501 AX-123294552 8 53874425 TGCTAAATCGTTTGCTGCATTCCAAGCTCTTTTCA[C/T]TTAGAAAGGCATGTTAGGGTTAAGAATGACAAAGA Y 2 1 2 1 101000 f 74 goat snp49896-scaffold713-245910 8 55050458 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789990 Affx-122944685 AX-385276996 8 53905040 CCATTTAAACTTCTAGGCTTACCTCCAGCAGAGGC[G/T]ATGTGCACTAATGTAAGTCAGCAAGCTTACCCTTT K 2 1 2 1 101000 f 74 goat snp49897-scaffold713-276525 8 55081064 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446607 Affx-122924807 AX-123316943 8 53946536 CAAGTTAAGTACGTATTTCAAAACAAATTTCTCTT[A/G]TTTGTTTTGAAAATTTTACTCTATTTAACATCATA R 2 1 2 1 303000 r 74 goat snp49898-scaffold713-318021 8 55123190 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800261 Affx-122953901 AX-385287184 8 53958200 AAGTTACAAGGAAGTGTCTGGGCCCCAAGCTACCT[A/G]TGTTACACAAGTAGTGTCCTTGAACTCTGCATTGG R 2 1 2 1 202000 f 74 goat snp7785-scaffold128-860393 8 55135156 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379841 Affx-122975811 AX-123250199 8 53999859 CATTACCACTCACCCTTTGTTCTTTCCTCCCATCC[A/G]TCTTTTCCTCCTTCTACTACGGAGGCTTGTATGAA R 2 1 2 1 202000 r 74 goat snp7784-scaffold128-818734 8 55177392 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801437 Affx-122933039 AX-385288346 8 54035656 CTGCTTATATTTCTATCACAGATTTCATTCGCTCT[A/G]AGAAATACATATCACTTTCCTCAAGAAAAGCAGGA R 2 1 2 1 101000 r 74 goat snp7783-scaffold128-782937 8 55213429 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792892 Affx-122950644 AX-385279870 8 54064325 GGAAACATTTGTAAATCTTGTAAATCACAATTATT[A/G]TAATATCTGTGTTATGTGCCTTTTACCTATTGCAT R 2 1 2 1 201000 f 74 goat snp7782-scaffold128-754268 8 55242185 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399878 Affx-122960224 AX-123270233 8 54098633 CCTCTCCCACAAAATTTGAACATTAGAAAAAGCTC[A/G]TGAGTTAGTTGAACACATACACACATAGAGAGACT R 2 1 2 1 201000 f 74 goat snp7781-scaffold128-719960 8 55276473 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403365 Affx-122957794 AX-123273718 8 54139459 AGATCATGTGATCAGACGATGAGTAAGTGAGATAA[C/T]GGTAGTACATGCATTTTTATTCATATAGTCAAATA Y 2 1 2 1 101000 f 74 goat snp7780-scaffold128-679134 8 55318142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454291 Affx-122919268 AX-123324624 8 54173557 ACTGACATTCAGAGAGAAGCAAGAGGAAAGAAAGA[C/T]GATAGAGTTTAGAGCACCCCAGTTCCTGGTACAGT Y 2 1 2 1 201000 r 74 goat snp7779-scaffold128-645036 8 55352630 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453672 Affx-122919713 AX-123324005 8 54229034 GGCGTGCAGACCACACTCCGAGTAGCAAGGTTCCC[A/G]AGAATGGAGGAGCAATGAGGGCAGAGATAGATCTG R 2 1 2 1 101000 r 74 goat snp7778-scaffold128-589559 8 55408373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414417 Affx-122949971 AX-123284766 8 54266419 ATTTATTCACATGGATCAGAAGAGAGGAGAAATCA[A/G]CCTATAAGTACAATCTTTCTAATTTTTAATTAATA R 2 1 2 1 201000 r 74 goat snp7777-scaffold128-552174 8 55445762 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414727 Affx-122949262 AX-123285076 8 54296690 GCCCTGGGCCAAAATGGGGAGCAAACACAAAGACA[C/T]GGCTTAGCAGAACCATTCAAATACATTTCAGTACA Y 2 1 2 1 101000 r 74 goat snp7776-scaffold128-521903 8 55476116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415555 Affx-122948648 AX-123285904 8 54336276 CCGGGGCTGGTCAGCTCCCCATTCATCCCCGCGTG[C/T]GGCACAATCCCAAACGGGGTTGGGTATGGACAAGG Y 2 1 2 1 103000 r 74 goat snp7775-scaffold128-482317 8 55515852 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391748 Affx-122967480 AX-123262105 8 54376583 GGGTAAAATGAGTTATTGAAAACAAATATCAACCA[C/T]CTATGAGTGAAGTCACTCAGTCGTGTTCAACTCTT Y 2 1 2 1 201000 f 74 goat snp7774-scaffold128-442010 8 55555359 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425785 Affx-122940712 AX-123296131 8 54406324 CCTCGTTCTTCAGCACTCCAGCAGGATGCACTGGG[C/T]GGTTCACTTAACCTCCCTGAGCTTCAGCTTCTCCA Y 2 1 2 1 201000 f 74 goat snp7773-scaffold128-412269 8 55584458 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792286 Affx-122973323 AX-385279268 8 54440443 TTATCTGGAATTTTCCTGAGACCACAGTGACCTTC[A/G]TTCTAGTATTGTACTCTCCAGTGTGGGAGCCACCA R 2 1 2 1 101000 f 74 goat snp7772-scaffold128-378150 8 55618583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780293 Affx-122954767 AX-385267387 8 54486108 AAATGAATTAGCAGTGTTTGTCAATTACAAATTAA[A/G]GAATCTGTATTCAGAAAATCCAAATAGCTCAAAAA R 2 1 2 1 101000 r 74 goat snp7771-scaffold128-332485 8 55664077 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385353 Affx-122971647 AX-123255711 8 54519425 GACAAGCAGTTGAAAGACGAACGGCAGTGAGGTGA[C/T]GGTTCCAGGCTCTGCCATTTGCTAGCTCAGTGGCC Y 2 1 2 1 101000 f 74 goat snp7770-scaffold128-299168 8 55697420 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442751 Affx-122927757 AX-123313088 8 54553086 CTATGGGAAAAAGCTCCTCTAAGGAATTCAGTTCA[C/T]GACAGGACCATGAAGCATTCAGGGACACAACTGTC Y 2 1 2 1 101000 f 74 goat snp7769-scaffold128-265507 8 55730923 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408741 Affx-122953406 AX-123279092 8 54583549 TATCACTCTTAATGTATTTTGGCTGCAAGTTGCAG[C/T]ATTCAAAATTCAAAAATTTCAATCCTGAGGAATCG Y 2 1 2 1 103000 r 74 goat snp7768-scaffold128-235044 8 55761768 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802184 Affx-122969284 AX-385289088 8 54636576 CAGGAATTACCTGATCAGCACTAATTAGGTCATCC[A/G]TCTGATAAACCACTGTGATCCCCTAAAGGAAAGAA R 2 1 2 1 101000 r 74 goat snp7767-scaffold128-182017 8 55815077 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425032 Affx-122941872 AX-123295378 8 54679021 CAGAGATTCTTAGCTGGTCTGGAATCAGGCCCAGG[C/T]GACCGTATTTTTGTAACAAACCTAGATATCTATGC Y 2 1 2 1 201000 r 74 goat snp7766-scaffold128-139572 8 55857485 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382568 Affx-122973765 AX-123252926 8 54711729 TAAAACTACCTTTGTTTAAACAAACAATTCGCGTC[A/G]TGTGGCCCATACATTTAAACTGTTTTTCCATAGCA R 2 1 2 1 101000 r 74 goat snp7765-scaffold128-106864 8 55890304 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779393 Affx-122932342 AX-385266496 8 54744036 CTCTGTGAAACCATATTAAAATTTGTATCACTGCC[G/T]CCCTTAGTGTCTATGTTATTATCATAGTGATGTCC K 2 1 2 1 101000 f 74 goat snp7764-scaffold128-74557 8 55922899 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419162 Affx-122945737 AX-123289510 8 54804493 CCATCCCTCTGCTCTGAACACCTCTGCCCTGATGC[A/G]CTGCCTCTATTCTCTGCTCCAAAAGGGTTTCTAAG R 2 1 2 1 101000 r 74 goat snp7763-scaffold128-14100 8 55984335 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390969 Affx-122967047 AX-123261326 8 54820119 AGTGCTTATCCTCCTCGGAGGTCCAGAAAGCCTAC[G/T]AGTCTGTGGATAAAGGTGGGTAAGGAAAGAGAGAC K 2 1 2 1 101000 r 74 goat snp12176-scaffold1454-1427 8 56000511 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421432 Affx-122943956 AX-123291779 8 54863911 GAGAAAATTATTTTGGTATCAGGTTTCAGTGCTTC[A/G]TTTTTGTGATTTATCAGCTTTGGCTGAAGAAGACT R 2 1 2 1 101000 f 74 goat snp12177-scaffold1454-45219 8 56044219 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380341 Affx-122975367 AX-123250699 8 54920306 ATAGACATGATATTTCCATAGAGAAGCCAGATGAA[G/T]AAGAGAAAGAGAGCTTTTGAATTAACCAGAGCAGT K 2 1 2 1 201000 f 74 goat snp12178-scaffold1454-101614 8 56101229 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427494 Affx-122940003 AX-123297837 8 54960332 ACGGATGGCCCATTTACCTTGGGTCCTATTACCTG[A/C]TGCAGCATGTCTGACTTTTAGTGAATAATTACAAG M 2 1 2 1 101000 r 74 goat snp12179-scaffold1454-141640 8 56140684 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378962 Affx-122976414 AX-123249321 8 54990156 CATGTGGAGTTTCAGTTCTGAATTTTTGTCACTAT[A/G]CTATTTTATCTTATATTTTAGTTGTTGCTAATTTA R 2 1 2 1 102000 f 74 goat snp12180-scaffold1454-171464 8 56170912 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772462 Affx-122930443 AX-385259613 8 55023411 GGGAACACTTCTTCAAAGTGCCTTTGAGCTGAAAT[A/G]TAAGGAATGGAAAGGTACTGGTCATGCAGAGGAAA R 2 1 2 1 101000 f 74 goat snp12181-scaffold1454-204719 8 56204413 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799469 Affx-122959745 AX-385286399 8 55069097 TTGTTGAAGTGATATTAAAAGGGATATTTAAAAGA[A/G]TTTCCACCAAGTTTTAGTTGAGATTTTAGTGGTGA R 2 1 2 1 201000 f 74 goat snp12182-scaffold1454-250405 8 56251053 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273369 Affx-1111833584 AX-519547002 8 55088642 AAGGTCTGTCTAGTCAAAGCTACGGTTTTTCCAGT[A/G]GTCATATATGGATGTGAGAGCTGGACTATAAAGAA R 2 1 2 1 103000 f 74 goat 8_55088642_AF-PAKI 8 55088642 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38430544 Affx-122937026 AX-123300885 8 55103209 ACTGCTGAGGACATAATGATGTAATTGGCTTCAGA[G/T]CTCTCCAGAGCACCCTTCAGGGAGAGTATGAAAGA K 2 1 2 1 101000 f 74 goat snp12183-scaffold1454-284517 8 56286108 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273949 Affx-1111833914 AX-519547555 8 55132872 GATGAGGCAGAAATGTCA[A/G]TTAGGGCTCAGATACTCTGCAGAGTAGGAATTTCA R 2 1 2 1 101000 r 74 goat GoatD01.010185 8 55132872 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38410885 Affx-122952079 AX-123281235 8 55257845 AGAGCAGCAGGCTCTACACAGACAAATGGCAAGGA[A/G]CACGCATTCAGAGAAGTAAGGAGTCGTTTTTGTAA R 2 1 2 1 101000 r 74 goat snp12187-scaffold1454-439153 8 56441014 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385624 Affx-122971183 AX-123255982 8 55296208 ATGTGCAAGGGTCAGATCCAAGTTTTAATAAATAG[C/T]ACTGAATGCTTTAGAAATATATATTAAAAACAATG Y 2 1 2 1 101000 f 74 goat snp12188-scaffold1454-477516 8 56477133 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382417 Affx-122974249 AX-123252775 8 55351345 CCATCTGTAGCAATCACTGGAACATATTTTCTATA[C/T]ATTGAGCATTTGACTCACCCAAAGAGAGCTGAAAC Y 2 1 2 1 101000 f 74 goat snp12189-scaffold1454-532653 8 56532772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803422 Affx-122968697 AX-385290253 8 55386239 TGCTCTTACATTTTAAGACCATTGGCAAATTCAAG[C/T]TCTTTAGCTGCACTTAGGGACTCACACAAACAGAA Y 2 1 2 1 101000 r 74 goat snp12190-scaffold1454-567547 8 56567696 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405077 Affx-122957409 AX-123275429 8 55456261 GAACATTCTTTCCAGTAGAGAGTTCAATCAATACC[A/G]ACATTCAATAAATTTTTACTGACTACCTAAATGGA R 2 1 2 1 101000 f 74 goat snp12191-scaffold1454-637569 8 56637460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415160 Affx-122949402 AX-123285509 8 55493106 ACAAACACTTTGACTTCACTACTAAGCTTCTAACT[A/G]TACCCCAGGCTATGTGACTCCTTTTGCTACTATGA R 2 1 2 1 101000 f 74 goat snp12192-scaffold1454-674414 NW_017205177.1 3519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379986 Affx-122975618 AX-123250344 8 55536110 TAAAGCCTATATCAGCACAATGGTTGGCATTAAAA[C/T]AATCAGACACAGATCTAACCCCAAAGCATTGATGA Y 2 1 2 1 201000 f 74 goat snp12193-scaffold1454-717418 8 56724585 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394979 Affx-122964264 AX-123265334 8 55624948 TTCCAGTTAAACTAAATCCTTTCCTAACACTGGTG[C/T]GAGGAAAGGGAATTATACACTCCTTGGGGCATAAA Y 2 1 2 1 102000 r 74 goat snp12195-scaffold1454-806256 8 56814152 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786919 Affx-122968736 AX-385273948 8 55723003 CACACTAAATACCCAATAAATGTAGATTGAATAAA[C/T]GAACAAATGCATGAACAATCTAAGATTAGCTAACA Y 2 1 2 1 102000 r 74 goat snp12197-scaffold1454-904311 8 56914213 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391881 Affx-122966971 AX-123262238 8 55778580 TTCACTGATAGAAAGACTCAGTATGGTTAAGATGG[C/T]AGTACTCCTCAATTAATTTTATTGTCAATTGATTT Y 2 1 2 1 101000 f 74 goat snp12198-scaffold1454-959888 8 56970148 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386781 Affx-122970108 AX-123257139 8 55837076 ATTACTGAGCCTTCTGAAGGCTCTATTTAAAGCCT[C/T]ATATAACATGAGATTTTTCAAGGGAGGTTATTCGG Y 2 1 2 1 101000 r 74 goat snp12199-scaffold1454-1018384 8 57030768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787107 Affx-122926049 AX-385274133 8 55874397 AGGGCACAGTCTACATCTAGAGTTTGCTGCAGATA[C/T]AATATATTCTAACTAAGACTTCTGGCAGTATCTTT Y 2 1 2 1 202000 r 74 goat snp12200-scaffold1454-1055705 8 57068847 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785238 Affx-122931172 AX-385272283 8 55904850 GGAAGCATACCATAGTGGAAAAAAATAGGTCTTTA[C/T]ATAACTAAGTATGGTGCCCTATCCTCAGAGCCCGA Y 2 1 2 1 101000 f 74 goat snp12201-scaffold1454-1086158 8 57096607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432231 Affx-122936362 AX-123302572 8 55933868 CTGTGTGTTCAACATGTTCCAGAGTTCCAGAAGTT[C/T]CTGAATATACAGACTGAAATATGAATGCTGTGCCT Y 2 1 2 1 101000 f 74 goat snp12202-scaffold1454-1115176 8 57125619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382139 Affx-122974050 AX-123252497 8 55972392 TCCCCAGCACTGAGAAAGATCAAAACTGTCAAAAG[A/G]TTTGGGAGCTGCACACATACACATACACAGAAAGG R 2 1 2 1 101000 f 74 goat snp12203-scaffold1454-1153700 8 57163830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375443 Affx-122979174 AX-123245802 8 56008999 AAGTGTATTATTTTCTTACAAGATGGACTTCTTTG[A/C]GGATAAATAAAATAAGAATGTCAAGGGTGCTTAAC M 2 1 2 1 201000 f 74 goat snp12204-scaffold1454-1190307 8 57200548 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801793 Affx-122921564 AX-385288701 8 56063152 ATATAATCCTGACATATCTATTAGAATGCCTCTCT[C/T]ATCAAAATTTAAACTTCCACATTATAGAACTGAAG Y 2 1 2 1 101000 f 74 goat snp12205-scaffold1454-1244460 8 57255107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378243 Affx-122976902 AX-123248602 8 56100386 CGAAGAACTGGCCAACGGATTTGGTGAGGAGGGTA[G/T]CAGTGACCTCGTCAAAAGCAGTTTCTGTGGCATGG K 2 1 2 1 101000 f 74 goat snp12206-scaffold1454-1281694 8 57292388 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798707 Affx-122934493 AX-310768763 8 56137856 ATGTCTCAACTCATTAATTGTTACCTAATCACTTA[C/T]GAATCGAGGCATGAAAGACTGCTCCAGTAAGGAAA Y 2 1 2 1 101000 r 74 goat snp12207-scaffold1454-1319164 8 57329432 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278619 Affx-1111836517 AX-519552098 8 56171831 GCTTAAGTTGTGTTGTTATTGTGTCTGGGCCATTA[A/G]TTCTGCTTTCTGTGGTGTAGATTATTCAATTTGTT R 2 1 2 1 101000 f 74 goat Random2.2K-909 8 56171831 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320783266 Affx-122942708 AX-385270331 8 56215865 CATGGAAACTGCATAAATAGGCAACTCATTGGCTG[A/C]GTAGATACACCAGCGGCTTAGTACTAGGCTTCTAA M 2 1 2 1 101000 f 74 goat snp12208-scaffold1454-1397173 8 57407526 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393017 Affx-122965648 AX-123263374 8 56249950 CTTTCTTTTTCTTCCTGTTCTGATTAGCAAAGATC[G/T]AATTTTTCCATAGGGGATCTCACTGGGTTCTGCCC K 2 1 2 1 201000 f 74 goat snp12209-scaffold1454-1431258 8 57441565 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786179 Affx-122957523 AX-385273215 8 56278974 AATGCATCTGTGAAACTAGAAGTCATGTTAAAAGC[A/G]CTAGTTAATGGTTTTTGAGCATTTATTGTGTATTG R 2 1 2 1 101000 r 74 goat snp12210-scaffold1454-1460282 8 57470624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381469 Affx-122974974 AX-123251827 8 56316006 AGTTCCTAACCCAGGGACAATATTTAGAAAGCAGC[A/G]TTAGGCTCAGGCAGCCCACTCAATTACTTTGGCCA R 2 1 2 1 201000 r 74 goat snp12211-scaffold1454-1497314 8 57509754 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450790 Affx-122921820 AX-123321124 8 56348540 TTATCTTGCTAATTTTATGGGCCAGTCAAATGGGA[C/T]CTATACCTATCCTGGGAATGCAGTGATAAAGGCCA Y 2 1 2 1 101000 r 74 goat snp12212-scaffold1454-1529848 8 57542288 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390917 Affx-122967089 AX-123261274 8 56382740 TAGCTCATTGGAACTCAATAGTTGATTTAATTGAT[A/C]GTTAGTCACCTGGGGAGAAACAAATGGATTTGAAG M 2 1 2 1 201000 f 74 goat snp12213-scaffold1454-1564048 8 57576724 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440702 Affx-122929905 AX-123311039 8 56416473 GGAGGGACTGCTGAGAAGGCTGGGGACAGAGTAAA[C/T]GATGACTCAGTCACAGGAGCTGTGGAAGCCAAAGG Y 2 1 2 1 103000 r 74 goat snp13773-scaffold1538-76227 8 57616940 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433320 Affx-122935181 AX-123303661 8 56453893 TTTTCTGATAAGGTGATATTAATATTTGAGCAAGA[C/T]GTCTAAAAAAACTGAAGAATTTAAGCCAAGAAAAT Y 2 1 2 1 101000 f 74 goat snp13772-scaffold1538-38807 8 57652664 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774132 Affx-122950085 AX-385261270 8 56483521 GTAGAAAATCTGCAAAGAGGGGCTACTTCCTCCTC[A/G]CCTTGATATGCAGCCTCAGTCTAGTTTTCATTTAA R 2 1 2 1 101000 f 74 goat snp13771-scaffold1538-9179 8 57683383 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417859 Affx-122946773 AX-123288207 8 56511756 ACATATGAATAATTCTTATTTAAAAACTCTTTGTC[A/G]CAAAGAGTAACAAATTAAGCAAGTAGTCTAAATGT R 2 1 2 1 103000 r 74 goat snp34573-scaffold409-18957 8 57715537 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429257 Affx-122937898 AX-123299599 8 56596157 TTATTGTTTGTTGTGGTGTGCCACTGCCTGACCTG[A/C]TGTAAATGCCAAGTTCACAGCCCCTTCTTTGAATT M 2 1 2 1 201000 r 74 goat snp34575-scaffold409-103358 8 57799980 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800796 Affx-122954470 AX-385287712 8 56632807 TCTATGATTCATGGAATAAGTGATTTCTATTTGAT[A/G]TGATTGGTATCAGTGTTAAATTTGTGCTAAAAAAT R 2 1 2 1 101000 r 74 goat snp34576-scaffold409-140008 8 57836814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379878 Affx-122975783 AX-123250236 8 56690904 TCAAGGAGATGATTAATTTGTTTGTCTGTCACTTA[A/G]TTATTTGTTTGTCTTTCACTCTCATTATAGAAAGT R 2 1 2 1 201000 r 74 goat snp34577-scaffold409-198105 8 57895936 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427997 Affx-122939168 AX-123298340 8 56720496 TTTTTACCTCATTGGTAAGAGGTAGAACCAGAATA[C/T]GAATCATGCAACTGACTCTAGGCTCCATATTTGTA Y 2 1 2 1 101000 f 74 goat snp34578-scaffold409-227697 8 57926063 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406024 Affx-122955493 AX-123276376 8 56751326 TGCCCTTTAAAAAGTCTTCATAAAATTCTTCCTTA[C/T]ATTCTTCTACACAATTGTCATAATGGGTTCCCTGA Y 2 1 2 1 101000 r 74 goat snp34579-scaffold409-258527 8 57957202 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774665 Affx-122935600 AX-385261799 8 56785183 ATAAATGCAAGGTAAATAACCATTAAATCTTATTT[A/G]TTTACATTGAAAAACTGTTATAGTCTGCAGTGAAG R 2 1 2 1 202000 f 74 goat snp34580-scaffold409-292384 8 57990759 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776466 Affx-122926488 AX-385263593 8 56833413 ATTACAGGGATTGAATGAGGTTCTGTAGGCTGAGG[C/T]ACTAAGTATTGGATGGACTGACCTATGTTGAGCTT Y 2 1 2 1 101000 f 74 goat snp34581-scaffold409-340614 8 58039235 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774797 Affx-122948494 AX-385261931 8 56863134 AAATGAGTTTTCCCTCACTTCCTATCAGAACTTTA[G/T]CTGATGTTCAATTAGTTACCAAACTCAACTCGTTT K 2 1 2 1 101000 f 74 goat snp34582-scaffold409-370335 8 58069848 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419662 Affx-122945949 AX-123290010 8 56923004 ATGAGATTAATGATCCTTATAAAATGGCCCACCCT[A/G]TGCTTCCAGGCTCCTAGCATTTTATATGTGTGAGT R 2 1 2 1 101000 f 74 goat snp34583-scaffold409-430205 8 58129470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784571 Affx-122936037 AX-385271619 8 56965340 GTGGTAAGATCTAACACTAGAGTTAATGCATTGAG[A/G]GTGGAATAGGTGTAGCAGTTCTCCAGAATTGCTTT R 2 1 2 1 101000 r 74 goat snp34584-scaffold409-472541 8 58172154 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380032 Affx-122975586 AX-123250390 8 56996173 GAAAACCAAAACCAGCATCGAAATTGGTTAAGCTT[A/G]TATATTATTCTTCAGAAATACAGAGATTTATGCAG R 2 1 2 1 101000 r 74 goat snp34585-scaffold409-503374 8 58203210 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275072 Affx-1111834581 AX-519548653 8 57024749 TCCAGGCAAGAGTACTGGAGTGGCCCATCCTAGCC[A/G]TCTTCAAACTACCTGCAGTCCCTGGGTCTGTGTTA R 2 1 2 1 202000 r 74 goat GoatD01.042199 8 57024749 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38380416 Affx-122975310 AX-123250774 8 57029632 CCTCAACATGAGGAAGCAAGGCTCACCTGACCTTT[C/T]CTCTTAACTTGGGCTACTGAATTGCTTTCCAGAAC Y 2 1 2 1 101000 r 74 goat snp34586-scaffold409-536833 8 58237026 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451354 Affx-122921253 AX-123321687 8 57068159 TTAGCTTACTATTTATTTGCTTTTCCAGTAGCATT[A/C]TTTTAAAAATGAACTCAATTTTTTAGTCAGAAGGT M 2 1 2 1 103000 f 74 goat snp34587-scaffold409-575360 8 58276139 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390440 Affx-122967629 AX-123260797 8 57130554 GGACACATTTTATTTTTGTCTGTTCAGCACCCCTC[A/G]TGTTAAGAGAATCTGTCTCTTCCTTCAGCCGTTAC R 2 1 2 1 201000 r 74 goat snp34588-scaffold409-637755 8 58339527 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452173 Affx-122921237 AX-123322506 8 57178229 ACTTATTTCCCCTCTGCCTTTGATTCCATATCCAC[A/G]CATTGAACAAAATTCTATTTGCTTTCAAGATCAAG R 2 1 2 1 201000 r 74 goat snp34589-scaffold409-685430 8 58387807 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802630 Affx-122964996 AX-385289531 8 57209158 TTCTGTTTTAGACTGTTCTCAAATGTTTGATTAAC[A/G]TTGAATATTTAGTCAAACATAAGAATAAGGCAATA R 2 1 2 1 101000 r 74 goat snp34590-scaffold409-716359 8 58419389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426468 Affx-122940793 AX-123296814 8 57245030 GACAGATTATGGATGCGGAGTACAGTAATAGCCTT[A/G]GTAGAATTTCCGTTCTGGTTTCTGTCTTGTCAGGA R 2 1 2 1 101000 f 74 goat snp34591-scaffold409-752231 8 58456081 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423607 Affx-122942382 AX-123293953 8 57273677 CCCCAAATGCTTTAGATAGTGAAGGAGGTGCCTCT[A/G]GGCTTTCTCAGGGTTGATACTTGGGAGGGGGTAAG R 2 1 2 1 101000 f 74 goat snp34592-scaffold409-780878 8 58485238 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776188 Affx-122920449 AX-385263316 8 57335344 CATCAGATATTGGAAGTGAAATGACAGAATGGAGC[A/G]TGCACTCTGTGGCAAGAATTGAGATTTAGAGGCAA R 2 1 2 1 101000 f 74 goat snp34593-scaffold409-842545 8 58547450 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788308 Affx-122956367 AX-385275326 8 57366045 ACAGACCTGAGTAAAGGATCTGAAAGTAAGAGGCT[C/T]ATTTGGGTGATGATTACAGGAAGCCTTCATAAAGG Y 2 1 2 1 101000 f 74 goat snp34594-scaffold409-873246 8 58578236 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779417 Affx-122933237 AX-385266520 8 57421542 AAACATTAAGTACTTATTCAAGGAAGCTAGTCAGT[A/G]GCAGAATCAGGATCAAAATAGATGTGGCTGATTCC R 2 1 2 1 101000 r 74 goat snp34595-scaffold409-928743 8 58633621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419100 Affx-122945779 AX-123289448 8 57450753 AAACTGCAGTCAAGTAAGTTAAGGAAGAGCTTCAC[A/G]TTTTACCCTCTGTAGATATTCCCAGTGTGATTTTA R 2 1 2 1 201000 r 74 goat snp34596-scaffold409-957954 8 58663423 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377529 Affx-122977470 AX-123247888 8 57484244 GGCGTTTGGGGGGGAAAAAAATCATGCAGTCTCTA[A/C]TTTTAAAATATTAGGTATGTGTACTATTCCACTCA M 2 1 2 1 303000 r 74 goat snp34597-scaffold409-991445 8 58697759 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795608 Affx-122925406 AX-385282563 8 57515759 TAAAAAGCAAATATGACCTCACCAGATTGACCTTC[C/T]TGTTTTGTTTCCCATAGTGACATTACCATACTTCC Y 2 1 2 1 101000 r 74 goat snp34598-scaffold409-1022960 8 58729453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417751 Affx-122947414 AX-123288099 8 57548641 CAGTCTTCCTGTCATTCAGATCAAGATGCATGATA[C/T]AGCTTCAAATTAAGTTTAATTTCTCAATTTTTAAG Y 2 1 2 1 101000 f 74 goat snp34599-scaffold409-1055842 8 58762330 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320778158 Affx-122931638 AX-385265273 8 57611436 TAGCTATAGATCAGATTTTCTCAAACTCAAATTAT[A/G]TAAATACCCTTTTAAAAGTAAACTATTCTTATCTG R 2 1 2 1 101000 r 74 goat snp34600-scaffold409-1118637 8 58825145 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762612 Affx-986697142 AX-385250702 8 57625801 TTCTCAGAGGACAGAGATAAAGTTTACCTCATCAC[A/T]GCTGCACATATGTAGTAGAGCTCAGAAACTTTTGG W 4 1 2 1 600010 f 74 goat 8_57625801 8 57625801 Ancestral_priority_1043 ancestry 0.426 neutral IMAGE 10K 10K ancestral 38434649 Affx-122933986 AX-123304990 8 57639980 AAGGCAGATATCATACTTGTTAAGCTCACAGAAAA[C/T]AGTCGTAGGGCTTAGGACACAAGTCTACCAAATGA Y 2 1 2 1 201000 f 74 goat snp34601-scaffold409-1147181 8 58854674 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786799 Affx-122925922 AX-385273828 8 57670742 GCAATTCTCTGAAAATCTTCTTTTCATGATATCTA[C/T]AAAGCCTCTTAAAGAGACTGCAGGAAATATTGAGT Y 2 1 2 1 101000 r 74 goat snp34602-scaffold409-1177943 8 58885856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273409 Affx-1111833585 AX-519547037 8 57703246 TTCTGAAATATCAGACTTTCAAAAACAGATCCTTA[A/C]TGAGTTAAAGTTTAAATTCAAGAATAAGGAGCATA M 2 1 2 1 101000 r 74 goat 8_57703246_AF-PAKI 8 57703246 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320799087 Affx-122937276 AX-385286017 8 57714212 CATAGGCAATATCATCTTTATGGAGACTATGAAAT[A/G]CTGAATAATTTTCTCCTAAAATCAAGAGCAAGGAA R 2 1 2 1 101000 r 74 goat snp24508-scaffold2485-18839 8 59016422 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439929 Affx-122930007 AX-123310266 8 57750093 CCCCAATGACTCAGATCAGAGAGGATGTCAGGTCT[A/G]CTCACGTCAGTGACTAAGGAGCCCAATAACATTCC R 2 1 2 1 101000 r 74 goat snp24509-scaffold2485-54720 8 59052142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398191 Affx-122962643 AX-123268546 8 57832225 ACTGGGGGGTGTGAGACCCTGTATCAAGGTGAAGA[G/T]CCTGAGGAGCAACACTTCCCTAAAGATAAGAGGGG K 2 1 2 1 101000 r 74 goat snp24510-scaffold2485-136852 8 59138903 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801678 Affx-122967451 AX-385288586 8 57893529 TTTTTCTATAATGTTGTTAGGATTAAGTGCCTACT[A/G]TAGCTCCTGTTTTACAGATAGGCATTGAAACGAAG R 2 1 2 1 101000 r 74 goat snp24511-scaffold2485-198156 8 59200348 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411522 Affx-122951669 AX-123281872 8 57924476 GCTACTCAATAGGACAGGACATACTATATCAGTTA[C/T]GAACAAGCTTATATTTGAAGTTCTTACAGGACAGG Y 2 1 2 1 101000 f 74 goat snp24512-scaffold2485-229103 8 59231281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439000 Affx-122930367 AX-123309337 8 58016229 TCACACCTTCCTTTTTATCCTTTTCATATCTTTGC[G/T]TATCCTATATCCTCTGCCTTGAATGTCTTTTCTTC K 2 1 2 1 201000 r 74 goat snp24514-scaffold2485-320856 8 59323995 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417936 Affx-122946714 AX-123288284 8 58060889 AAGGGAGAGCATGACTGGGGAACCTGAGGAAAACC[A/G]TGTCTACCGAGTCCACCACTCAGTCCCCAGAGCAT R 2 1 2 1 201000 f 74 goat snp24515-scaffold2485-365516 8 59368666 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784894 Affx-122928037 AX-385271941 8 58099066 GCAAGATGATCTACCTAAAGCATGTAGGAATGTAT[C/T]CAGCACACAGTAAAGTTTGTCAAATTGTAGGTATT Y 2 1 2 1 101000 r 74 goat snp24516-scaffold2485-403693 8 59407536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421790 Affx-122944337 AX-123292137 8 58169604 GTTACTTTGAACAGTTCACACCTTGTGACAAAGGG[A/C]GTAGGTTTGAAGACCTCTGAGTAGACTTAGAAGTT M 2 1 2 1 101000 f 74 goat snp24517-scaffold2485-474231 8 59478851 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440961 Affx-122928993 AX-123311298 8 58259117 AACTTTGAATACCGCATTAAGGAATTTGGATTATC[C/T]TGTAGGCAGTGGGGAGCCACTAACAACTTTTTAGT Y 2 1 2 1 201000 f 74 goat snp24518-scaffold2485-563744 8 59569195 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416021 Affx-122948375 AX-123286370 8 58290047 AGGCCGAGGTGGCACAACTCTATATCCTTATTACC[C/T]CTCCTCCCAGAAGCAAACGGGTATGCTCTTACCCT Y 2 1 2 1 201000 f 74 goat snp54383-scaffold830-3326 8 59599880 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438141 Affx-122931475 AX-123308479 8 58355830 CCATCAAGCTGTGGCGTTTTATTTGGCTGCAACCT[A/C]TTGTGCCTGTTTGTGGTGTTTCTGTTACCTGCTGT M 2 1 2 1 101000 r 74 goat snp54384-scaffold830-69109 8 59665844 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379913 Affx-122975755 AX-123250271 8 58389538 GCACATTTCTCCATCTAGGGATGACAGGGAGACTC[A/G]GACTCAGCCACAGGAGAAACAGGGAAGAGAGAGCT R 2 1 2 1 201000 f 74 goat snp54385-scaffold830-102817 8 59699146 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399790 Affx-122960292 AX-123270145 8 58420864 AGAACAGGAGGGTACATTCTGGGAGTGAGGGGAGA[C/T]GGAGGGAAGACGAACAGTGGGAAGGCAGCTCTTCT Y 2 1 2 1 201000 r 74 goat snp54386-scaffold830-134143 8 59729106 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393739 Affx-122965225 AX-123264094 8 58467653 CAGTATAAGAGAAGGGACAGTCAAGAACATGCCAA[C/T]GGGAAAATCAAGGTGGTGAGGTGGGGAGAGAGGGT Y 2 1 2 1 101000 f 74 goat snp54387-scaffold830-180932 8 59776035 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792382 Affx-122927099 AX-385279363 8 58507456 AGACACAGATAAATAAGACGTATATTAGTGAGATA[C/T]GGAAGGCATTTTAAGAGGACAAAGGAAAGGTTTAT Y 2 1 2 1 101000 r 74 goat snp54388-scaffold830-220735 8 59815831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401835 Affx-122959441 AX-123272188 8 58547620 CAATGTCCCAGAAGTGCCTGCATCTGGATTCCCGC[A/G]TCTCTCCTCCTCACTATGATGGCAGAGGTCCTGAG R 2 1 2 1 201000 r 74 goat snp54389-scaffold830-260899 8 59855182 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449708 Affx-122922537 AX-123320043 8 58587814 CTTTTCATGGAAACTTCTTTAATTACCCCCTTTGT[A/G]TATGCTCTGAAATCAATCCTTGCTCTGACCCTTAT R 2 1 2 1 101000 r 74 goat snp54390-scaffold830-301093 8 59895990 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453723 Affx-122919628 AX-123324056 8 58655314 GTGATATCACTGAAATTGTTTCATTTCCTCCCTTC[C/T]CAAGCCCCAGTCCCTTCAAAAAATCAAGAAGCTGG Y 2 1 2 1 101000 f 74 goat snp54392-scaffold830-368593 8 59962718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439748 Affx-122930531 AX-123310085 8 58703243 CTTCCTCTAGATACCAAAGAGAAATCTGGAGTTAC[A/G]TAAAGGAATGAAGAGCATCAGAAATGCTTGACATA R 2 1 2 1 101000 f 74 goat snp54393-scaffold830-416522 8 60011580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413019 Affx-122951003 AX-123283368 8 58773822 TAAGGTCCTTTTGGAATTCCATAAGTCAAAAAGAA[C/T]GGGGCCAGTGATTGTATAGTTTTAGTTAAATGGAA Y 2 1 2 1 201000 f 74 goat snp54394-scaffold830-487101 8 60082649 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421149 Affx-122944185 AX-123291496 8 58816691 GAAGATGTTTTATTTCATCCTGTGAACAAGATTCA[C/T]GAGCAATCACACATGTGTCAGAGCAAGTTACTGGT Y 2 1 2 1 101000 f 74 goat snp54395-scaffold830-529970 8 60125954 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395435 Affx-122963934 AX-123265790 8 58857720 CCCTCCCTTCTCTGAAAGGGCAGAGTGGTGCTGTG[A/G]ATAGAGTCTTGGAGTGAAAGACTGGGTTCCAGGCC R 2 1 2 1 101000 r 74 goat snp54396-scaffold830-570999 8 60167268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783331 Affx-122948671 AX-385270396 8 58895782 TCTGAATGATGGAAATTATCTCCTGAATTCTTTTC[A/G]TATGGTACCATTCATGCAGCATAATTCTGACTAGG R 2 1 2 1 201000 f 74 goat snp54397-scaffold830-609061 8 60205416 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449425 Affx-122922686 AX-123319760 8 58965598 GGCTAGGTTGAGTTGGTTTGGAACACATGCATGTA[C/T]GCTCCTAACACACACTAACTACTTAATAAGCAAAT Y 2 1 2 1 101000 f 74 goat snp54398-scaffold830-678877 8 60274912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762622 Affx-986697152 AX-385250711 8 58985946 AATGGGCCCTCTACAAAATTTTTTATACACTGGAA[A/G]CTACCAGACTATGAACTCTTAAAAAATTACTGTAA R 2 1 2 1 600010 f 74 goat 8_58985946 8 58985946 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 320800223 Affx-122928734 AX-385287146 8 59081508 TTGGGTTTTTAATTACACAGGATCAGGAAAAATTA[C/T]ATAACTATTCCATCAAACAATTCTATTTTGAAAGG Y 2 1 2 1 101000 f 74 goat snp54400-scaffold830-794787 8 60391464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445381 Affx-122925403 AX-123315718 8 59123005 GAAAGGACTCTAATGAACTACAGCTGAATTCTGCC[A/G]TCCAGAAACTTCTTCAATCCTTTCCCTTCCATTTC R 2 1 2 1 101000 r 74 goat snp54401-scaffold830-836284 8 60432814 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453553 Affx-122919779 AX-123323886 8 59160945 AGTGGAAGCAGAAATATTTCATTTTATGTCACCAG[C/T]TTTCTGTTAGCGTCAGGACCTGACTTTCCTTCTTT Y 2 1 2 1 101000 r 74 goat snp54402-scaffold830-874224 8 60470733 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392408 Affx-122966208 AX-123262765 8 59196204 AATAATTCAGATTTACTTGGATATTTAAGGTAGAG[A/G]TGTTGTTCTGTAACTGTATGCATGTTCTATCATTT R 2 1 2 1 101000 r 74 goat snp54403-scaffold830-909483 8 60505882 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787451 Affx-122974809 AX-385274476 8 59254259 TCTTCTTTTTTGCATTTCATACATGCAAAGGTAAG[C/T]AGTGTGGCCACTTGTTGCCCAGGGAAAACTTCTAT Y 2 1 2 1 201000 r 74 goat snp54404-scaffold830-967538 8 60563797 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784882 Affx-122963435 AX-385271929 8 59291459 AACAAACCTCCAAATATAAAGTGGCTCAAACACAG[C/T]AGACATTTATATCTCATGCCTGTAAAATACCAGAC Y 2 1 2 1 101000 f 74 goat snp54405-scaffold830-1004738 8 60601351 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442342 Affx-122928041 AX-123312679 8 59389414 TATGGCCAGAGTGATCCTGATCATAGCACCCAACA[C/T]GGGCATTGTCAGCCTTGCAAATATATTACATATTA Y 2 1 2 1 201000 r 74 goat snp54407-scaffold830-1102693 8 60699605 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391498 Affx-122966678 AX-123261855 8 59426780 CCTGCTGCTACCTCCCACGACTCCCTAGGGCTGGG[A/G]CTGGACCACTGGGTCCTCACGTTTTCCTTCCCTGA R 2 1 2 1 201000 r 74 goat snp54408-scaffold830-1140059 8 60736826 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776328 Affx-122951560 AX-385263456 8 59470334 CATCTTGTTTAATCTGTGCAGCCCAAATGACACAA[G/T]AACTATTATTACCCCATAATATGAGAAAACCGAGG K 2 1 2 1 101000 f 74 goat snp54409-scaffold830-1183613 8 60779948 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781762 Affx-122959864 AX-385268844 8 59502220 TAAGGCACATGTGGAAATGGTAACAACAATTACAA[C/T]AATAATAACAATCATCACTCCTCAAGTACACATTC Y 2 1 2 1 101000 f 74 goat snp54410-scaffold830-1215499 8 60811862 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765142 Affx-122950293 AX-385252697 8 59533590 TAGGTGTGTTTGGCCTGGAGAGTACATTTATTTTC[A/G]TTTGAATTAGTTGTCAATTAGTTGTAAGTTGGGAG R 2 1 2 1 101000 f 74 goat snp54411-scaffold830-1246869 8 60840954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432058 Affx-122935893 AX-123302399 8 59564133 GTGCCCAATCCTGTCAAGAGCCCCAGCATGATGTC[A/G]CTTGAACCCCAGATCCTGTTCAGAGAGGAGACAGA R 2 1 2 1 101000 r 74 goat snp54412-scaffold830-1277412 8 60870789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379295 Affx-122976207 AX-123249654 8 59607978 AATATTGCCTCCTGACAGGCAGAGATTTATATGCC[A/G]TTATAGATTTTCAAAACAGTGCTTAAACTCTCTTT R 2 1 2 1 201000 r 74 goat snp54413-scaffold830-1321257 8 60914439 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401064 Affx-122959644 AX-123271417 8 59660855 TTTTCATATGAGTATGGATATATTGAGAACATGCT[A/G]TAAAAATTGGACCAGTGGTACTTTATTGGTATTTA R 2 1 2 1 101000 r 74 goat snp54414-scaffold830-1374134 8 60968108 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789469 Affx-122931484 AX-385276479 8 59691228 GGATATTTTGTTTGGAACATCCCTGCTTATGGACT[A/G]TCTAGTTATTTCTTTGGTGCATACTTTGAGAATTT R 2 1 2 1 101000 f 74 goat snp54415-scaffold830-1404507 8 60998971 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412892 Affx-122950421 AX-123283241 8 59734992 CCAGAGTGGCCTGTTAGGACCTGGGGCATTTGGAG[C/T]TTCTGGGCTAGTGTTCTAACTGAAAATGCCCTCTT Y 2 1 2 1 101000 r 74 goat snp54416-scaffold830-1448271 8 61042494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452985 Affx-122920122 AX-123323318 8 59785411 GCTCTAGCTAGGACTTCCAGTACAGTCAATTCTCC[A/G]TATCCATGGGTTTTACATCCAGGGATACTAAGGGC R 2 1 2 1 201000 r 74 goat snp54417-scaffold830-1498690 8 61092878 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789681 Affx-122958196 AX-385276689 8 59824453 ATGCAGGTTAGTCTAAAACAAATACAGCTCATAGA[A/G]TTATTCAGACAAAATATAGTAGTTAATAGGTTTAC R 2 1 2 1 101000 f 74 goat snp54418-scaffold830-1537732 8 61132635 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439309 Affx-122930958 AX-123309646 8 59863421 GACTTGGACAGGGGGTGAATTAGTCTTCCCAGGCA[G/T]GGGAGCCACTCAAGGGAGGTCCTGAGATTTCCTAA K 2 1 2 1 201000 r 74 goat snp54419-scaffold830-1576700 8 61172144 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795573 Affx-122925657 AX-385282528 8 59895103 GCACAACCCACAGTCATATATACTCAGATTTAAAC[A/G]TCATCTCATCCACTTATTAGTTGTGAATGCTTGGG R 2 1 2 1 101000 f 74 goat snp54420-scaffold830-1608382 8 61203819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392257 Affx-122967559 AX-123262614 8 59931155 GAGTGAATGCTCATAACTGATATTAATGATTACTG[C/T]GAGTCATCAGAAAAGCAAACCATTAGAGGCATACA Y 2 1 2 1 101000 f 74 goat snp54421-scaffold830-1644434 8 61240195 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771603 Affx-122960969 AX-385258761 8 59975261 ATTTGACTCTGGGAAAAGAATCCCTAGTGTGTTTG[C/T]GGGTGTCATCATGAATACATTTAGATTCTGATGGT Y 2 1 2 1 101000 r 74 goat snp54422-scaffold830-1688540 8 61285304 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436247 Affx-122932557 AX-123306586 8 60036907 TATAAATGTATTGGTTTGCTGCTGCTGCTCTAATA[A/G]ATTATTCAAACTTAAAACCACACAAATTACCTTAC R 2 1 2 1 201000 r 74 goat snp54423-scaffold830-1750186 8 61347109 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427597 Affx-122939458 AX-123297940 8 60071490 AACAGTATACCCAATGTCCAATGAGAGCTGGAGCC[A/G]TGGAGGTGCTGTGGTCTAGGAAAGAAAAGCAAGAG R 2 1 2 1 201000 f 74 goat snp54424-scaffold830-1784769 8 61381714 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777882 Affx-122972959 AX-385264997 8 60124986 TGACACTGGCGATTTAGAGGATGAATATCTGTTTC[A/G]CATGGTGCAGTGATGTCCTGAGATAGTAATGAGTG R 2 1 2 1 101000 r 74 goat snp54425-scaffold830-1838265 8 61435502 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413451 Affx-122950678 AX-123283800 8 60186427 TCTATTTGGTCATAAGTTGCAGAAGGAATTCCTAA[G/T]CACATAGGGAGTGGGCATAAGTTATTTGATTCTGT K 2 1 2 1 101000 f 74 goat snp54426-scaffold830-1899706 8 61493844 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273373 Affx-1111833586 AX-519547006 8 60225508 GCCCATCTGTTAGCAGGCCAGTGCCACTTCAGGGT[A/G]GATTAAAGACTTAAACGTAAGACCTGAAGCCATAA R 2 1 2 1 202000 f 74 goat 8_60225508_AF-PAKI 8 60225508 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38430185 Affx-122937356 AX-123300526 8 60226874 TGAACAGTGAATTCCTGTTTGTCCTTCCTGATTCC[A/G]TTCACAGGCATCTTGGCTGCTCCCTTCCCCTTCCA R 2 1 2 1 101000 f 74 goat snp54427-scaffold830-1940153 8 61534300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412142 Affx-122951091 AX-123282492 8 60260123 GATGTAAGCAGGATTGACCCTGGGCTCTGTCGCTT[G/T]TAAGGTTGAATTCAGATTTCGGCTCCTCTCAGTAA K 2 1 2 1 101000 r 74 goat snp54428-scaffold830-1973402 8 61568243 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439013 Affx-122930356 AX-123309350 8 60291019 ATTCCTCTGTTGATAGACACATGGGTTATTTTCAT[A/G]CCACAGCAATTGTAAATAATTTTCCTGTGCACATT R 2 1 2 1 201000 f 74 goat snp54429-scaffold830-2004298 8 61600495 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398201 Affx-122962635 AX-123268556 8 60328285 TGCTTTTTTATCTGGAAGAAAATATTTTAAAATCC[A/G]ATTCCTTTGACAAGCAAAGTTTTGTCTGTTAGGTA R 2 1 2 1 103000 r 74 goat snp54430-scaffold830-2041564 8 61637714 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445879 Affx-122925964 AX-123316216 8 60396659 TTCCAGAATAAACTAATGCACATCCACAGGGGATG[C/T]GGGGGGAGCACAGAGGGGCCCCAGCCCAAACTGGG Y 2 1 2 1 101000 f 74 goat snp54431-scaffold830-2109938 8 61705669 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388029 Affx-122969555 AX-123258387 8 60473311 GGATACTTAGGTGATTTCCGCTCTTTCATTTTTCC[A/G]AATGCTGTAGGATACTGGTAGCTAAATCACTGTGA R 2 1 2 1 201000 r 74 goat snp54432-scaffold830-2186590 8 61780538 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452950 Affx-122920172 AX-123323283 8 60510935 CGACCATACCTAACACACTGTGAGTGCTGACCATA[C/T]GGGCTTGGGTCTCAGCATTTTACATGGACATAAGT Y 2 1 2 1 101000 f 74 goat snp54433-scaffold830-2224214 8 61818266 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777941 Affx-122929627 AX-385265057 8 60557265 TGCAGGGAGCTTCTCTCTATCAGACAGGTTTTAGT[A/G]TCACCAGTGGAAAGAGGCTAATTTTTTCCAGCAGC R 2 1 2 1 101000 r 74 goat snp54434-scaffold830-2270544 8 61864637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448874 Affx-122923270 AX-123319209 8 60590800 GGACTTTTCAAAACTAGAAGTAACCAGAAAGCCAC[A/G]TGATCTGTTCAAATGTCAATATGGGGCAGAAAGAA R 2 1 2 1 101000 f 74 goat snp54435-scaffold830-2304079 8 61898237 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409909 Affx-122952888 AX-123280260 8 60619965 TCCTAAAAGCAGTTGATTAGACAGAAGAAAAATGA[C/T]GCAAGATGGAATTTTGAATCCACAGAGAGTAATGA Y 2 1 2 1 201000 f 74 goat snp54436-scaffold830-2333244 8 61927772 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778428 Affx-122971139 AX-385265542 8 60662206 ACAAGTCAAAAATCAATTGCTCAATTATGCATTTA[C/T]GATGAAATCTCAGATATGCCAAATTCTCATATATA Y 2 1 2 1 101000 r 74 goat snp54437-scaffold830-2375485 8 61970363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427229 Affx-122939572 AX-123297572 8 60713148 AGTCCTCTGTTCTGGCTTTGCATGGCGCAGGCCAC[A/G]CATGGCTCTCCACTTTCTACATTCATCTGCACCAA R 2 1 2 1 101000 r 74 goat snp54438-scaffold830-2426427 8 62021338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416321 Affx-122947915 AX-123286670 8 60742158 AGCATTTAACCAGACAACAGCTGTCGTGTGAATTG[A/C]GTGACCCAGTCGTCCTTGAGAAATGTTTGTCTTCT M 2 1 2 1 101000 f 74 goat snp54439-scaffold830-2455437 8 62050336 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395052 Affx-122964197 AX-123265407 8 60795401 TCAGTTCTGACTTTATTCAAAGAAGGGGTTCCACT[A/G]TTTTAAAGTTTGAAAACCACTGATCTAGTTTCATT R 2 1 2 1 102000 f 74 goat snp54440-scaffold830-2508680 8 62103372 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393069 Affx-122965610 AX-123263426 8 60843754 TTGACCAGCACTGCTTCCGTGGAGTGATGGTGGCA[G/T]AAGCCAGGTTAGGGGGTCGAAGAGCAAGTGAGAGG K 2 1 2 1 101000 f 74 goat snp54441-scaffold830-2557033 8 62152312 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448609 Affx-122923386 AX-123318945 8 60890803 AAGACTGGAGAAATCAGTGGGCCTGGGGAGAGGAG[C/T]GGGAGATGAGTCCAGGAGAGGCTTGCCGGCCATAG Y 2 1 2 1 303000 r 74 goat snp54442-scaffold830-2604082 8 62199510 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399387 Affx-122961325 AX-123269742 8 60923549 GAGGAGAGGATTTCATCTGGACTGGGGAAGTAGTG[A/C]TTCCCAAGGCTTGATGGAGGAGGAGGAGCCAGCCG M 2 1 2 1 101000 f 74 goat snp54443-scaffold830-2636828 8 62232378 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447716 Affx-122924605 AX-123318052 8 60959829 TAGTACGGAGATGCAGAATCCTAAGCAATACATGG[A/G]TCCATCCCTGTGTCTGTGGAATAAATAAGAATGTC R 2 1 2 1 101000 f 74 goat snp54444-scaffold830-2673108 8 62268365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777913 Affx-122965508 AX-385265029 8 61057717 TCTCTGTAGCCCAGTTATGCCTGGATATGGCAAGC[A/G]TCCATACCAATGTATATATTTGGTATGTGAGCATA R 2 1 2 1 101000 f 74 goat snp54446-scaffold830-2770996 8 62363167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413439 Affx-122950687 AX-123283788 8 61119882 TGGTCCCCTACACAGGGGAGAAGCGAGGTACTGGA[C/T]GATGTTGTGCTTTTGAGTACGTCACCCCTCCATGC Y 2 1 2 1 101000 r 74 goat snp54447-scaffold830-2833161 8 62425642 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443115 Affx-122928093 AX-123313452 8 61149051 AGGCCATGGCATCCCCAGTGTAGGGAACCACATGA[A/G]CAAAGAGAAGGAGAGAGGACAGCTGTAGAGTCAGT R 2 1 2 1 201000 f 74 goat snp54448-scaffold830-2862330 8 62454903 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792799 Affx-122968584 AX-385279778 8 61247086 ATGAGTGCAGACTCGCAGTCATAACATCTTGGCTC[C/T]AGTCCCAACTTTCCAGAAACTATGTAACTAGTCAC Y 2 1 2 1 101000 r 74 goat snp54449-scaffold830-2960365 8 62552089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434265 Affx-122934787 AX-123304606 8 61291395 GGAGCTGGAGTGTTTACACCTCTGTATCCCTGGTT[A/G]CCCCTGGTTATGGGGGAGGCGGGGTGGTGGGCAAT R 2 1 2 1 102000 f 74 goat snp54450-scaffold830-3004674 8 62595581 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413551 Affx-122950603 AX-123283900 8 61325350 CAACTCTCTGGGGGGCTTTCCCAACATTACTGTTA[A/C]ATAGAAGCTTTCATCCCCATTGAAAGAGGAAAAAC M 2 1 2 1 101000 r 74 goat snp54451-scaffold830-3038629 8 62629966 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439648 Affx-122930606 AX-123309985 8 61356417 TGAGGAAGAAGGGACAGGAGACAAGTCTGTGGGGA[C/T]GGCTGCTGTGAAGACAGCAGGGAAATAGGCCATAA Y 2 1 2 1 101000 f 74 goat snp54452-scaffold830-3069696 8 62660830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423188 Affx-122942725 AX-123293534 8 61396337 TCCCAGAGGCCTCCATACCTGAACCTAGGGCAGAA[A/G]ATGCTGTTCGGTATCTGAACCTTCCCTTAGGCCCC R 2 1 2 1 101000 r 74 goat snp54453-scaffold830-3109616 8 62701559 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417666 Affx-122946833 AX-123288014 8 61441670 CCAAAAAGGACCCCATGACTTAATTATCAAAACCA[C/T]GCAAGTCAAATTTCAGTACAGTGAGTTTCAATGTG Y 2 1 2 1 101000 r 74 goat snp54454-scaffold830-3154949 8 62747035 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381507 Affx-122974865 AX-123251865 8 61471579 CTTTCAGTCTAGTTTGTTTCGAATTCCCTCCTCTG[A/G]CCTCCTCCACCAATATTGCTTTCTACTTCTTAATG R 2 1 2 1 101000 f 74 goat snp54455-scaffold830-3184858 8 62776984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433335 Affx-122935153 AX-123303676 8 61513879 AGAAAGAAACAAAAAGATGTAATGGGCCTGTGTGC[A/G]TCTTGAGAGCAAGGCTTCTGAAGAGGAAGTAGAGT R 2 1 2 1 101000 f 74 goat snp54456-scaffold830-3227158 8 62819099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426993 Affx-122940382 AX-123297338 8 61555500 ACCTTGGCTAGCTTACCTGCCCTCCATACACCTCC[A/G]TTTCCATGTGTTTAAAATGTGATACTGAACTGGAT R 2 1 2 1 101000 r 74 goat snp54457-scaffold830-3268779 8 62863001 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410181 Affx-122952588 AX-123280531 8 61584017 GTCATGAGGCAAGTTGGAAGCTGAGCTGGGACTAG[A/G]GCCCCTCTGATCCTCAGAGGCCCACATCAGGTATT R 2 1 2 1 101000 f 74 goat snp54458-scaffold830-3297296 8 62891735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405036 Affx-122956362 AX-123275388 8 61680491 GCTCCTGTCACCACCCTCCAGGGAGGAGGTTGCAG[A/C]CTGTGGCAGGCATCACACCTATAATAAAGTCCTCA M 2 1 2 1 101000 r 74 goat snp54460-scaffold830-3393770 8 62989411 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398441 Affx-122961612 AX-123268796 8 61730053 AAGACTGTGCACGCTCAGGAGTCACAACGGGTCAC[A/G]GATGCACACACTCACCTCCGACTGTCCGATACTTT R 2 1 2 1 101000 r 74 goat snp54461-scaffold830-3443332 8 63037531 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379952 Affx-122975643 AX-123250310 8 61758942 ACTGCTGTCCCCTCCCCACACCTAGGGCCCGACTC[A/G]CCTGGGGCTGTCCCTTGAGCTAGCCCTGGTTATTC R 2 1 2 1 101000 r 74 goat snp54462-scaffold830-3472221 8 63066432 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418190 Affx-122947070 AX-123288538 8 61801049 ATTTACTTTAATAGAAGGTTAAACAATAAAGGAGT[C/T]GGGATTCTCAGCAAGTGGAGGTAGCTGGGAGGTAA Y 2 1 2 1 201000 f 74 goat snp54463-scaffold830-3514328 8 63108639 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427318 Affx-122940136 AX-123297661 8 61833138 AAAGGAGCCTGAGCGATAACCGGTGGGAACAGAGG[C/T]GATGGGTTCTGAGTCAAGTCCGCATGGCAACTAGA Y 2 1 2 1 201000 r 74 goat snp54464-scaffold830-3546417 8 63140151 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446007 Affx-122925867 AX-123316344 8 61869257 ATTGTCAGTTTATACCAGAAAAGGCCCCGTAGAGA[C/T]GGTCACACATGCCGTCTCAATCTGCAGCAGGAGAC Y 2 1 2 1 102000 f 74 goat snp54465-scaffold830-3582536 8 63174138 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412761 Affx-122950514 AX-123283110 8 61906442 TTGACCTATTTGAATTTCTGGTCAGAATGACTATA[G/T]TTGATTTTCACTATTAGTTTATGTTTTCTAGTTTT K 2 1 2 1 101000 f 74 goat snp54466-scaffold830-3619721 8 63211738 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278621 Affx-1111836518 AX-519552100 8 61938114 TGTCTGTTTTCATGTCAAAAAAGTGAGAAAAACCT[A/G]CCTTGGTGAAGGTGAAATACTGACGGTATGCATCA R 2 1 2 1 101000 f 74 goat Random2.2K-915 8 61938114 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432600 Affx-122935504 AX-123302941 8 61962298 GGTTAAACCAGTGAAGAGCGTGTGGCAATCAATTC[A/G]TTATGTCTGCAATTAGCACAGGATGGGGGAAATAA R 2 1 2 1 201000 f 74 goat snp54467-scaffold830-3675577 8 63268197 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412485 Affx-122951382 AX-123282834 8 61999887 TGGGCCAAGTTCTAACCATGGCGAGATTCCCACCC[G/T]ATACAGAGTAAGGCAAAGTTGCTCGTGGCCTGCAC K 2 1 2 1 201000 f 74 goat snp54468-scaffold830-3713166 8 63305588 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798528 Affx-122923028 AX-385285461 8 62066362 ACACACTTTGTAGAATAATTCAGCTTTTATCAATT[A/G]TTCTACATTTTGTATATATGAAATTATTGTACTTA R 2 1 2 1 303000 r 74 goat snp54469-scaffold830-3779641 8 63372124 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388929 Affx-122968830 AX-123259287 8 62138934 CCCACCCCCAGCTGCTGTGAGGCCTCATGACTGCT[A/G]CTGCCGAGTCACAGCAGGGTCTCCCTGACAGTGTT R 2 1 2 1 103000 r 74 goat snp54470-scaffold830-3852213 8 63444540 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385772 Affx-122971058 AX-123256130 8 62182708 GTTTGTCTGAAGACCTTTTCTTCCAATTTTTACCT[C/T]TCAGCCTTAAATGCTCACATGCTGCAGCCTGGCCT Y 2 1 2 1 101000 f 74 goat snp54471-scaffold830-3895987 8 63488196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799660 Affx-122935343 AX-385286588 8 62243711 TTCTTGGAGATCTCCTTAGCTACAGAACTAGGTTC[C/T]CTTAGCTATCTAATCAGTTTCATCTCAAAAATTCT Y 2 1 2 1 101000 f 74 goat snp54472-scaffold830-3956990 8 63549020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423777 Affx-122942832 AX-123294123 8 62280515 GCTAAAATTTCCCCAGCAACAACCACATGTCTGGC[A/G]TTATGTGAGGCTTTGGGATGCAGCAATTAATCACA R 2 1 2 1 201000 r 74 goat snp54473-scaffold830-3993794 8 63585659 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38443019 Affx-122928168 AX-123313356 8 62328607 TGGAGGGGCTCATAATCTAGTAGTAGAGGCCGAGG[G/T]GCAGCAGCTGGCTTGAATGCTATGGAGCTTGTCCT K 2 1 2 1 101000 r 74 goat snp54474-scaffold830-4041886 8 63633747 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389707 Affx-122968685 AX-123260065 8 62363355 TCAGCGTTTGCCACATTGAGTCACTAAGCTTAGCC[C/T]ACCCTTTCCTGACTGTCTTGTGTTTCCTGCACGCT Y 2 1 2 1 101000 f 74 goat snp54475-scaffold830-4076634 8 63668465 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783442 Affx-122932167 AX-385270505 8 62391977 CAAAAATACCAAATGTAGATAAGAATGTGGTGAAA[C/T]AGAAAAATCTCTTTGTTGGAAGTATAAATTGTACA Y 2 1 2 1 101000 r 74 goat snp54476-scaffold830-4105256 8 63696971 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447864 Affx-122923884 AX-123318200 8 62425092 TCTTTTTTTTCCATGTAATAAGTGAACATAAAAAC[A/G]TCTTTTCCAGGCGCTTTCTTCTGTTTGACTTTTTC R 2 1 2 1 101000 r 74 goat snp54477-scaffold830-4138371 8 63729890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803086 Affx-122940294 AX-385289957 8 62479990 GCTTTGTAAGTCCAGGTTTATCAGACCTCATACCT[C/T]ATCAAACACTTGCCAGCATGCAGTCCTCAAAGGCC Y 2 1 2 1 101000 r 74 goat snp54478-scaffold830-4193269 8 63784797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446126 Affx-122925778 AX-123316463 8 62514961 AAATGTCTATCTGGTCATCACAACTCATAGTTAAC[C/T]ATTATTAAAACAGCCTTTGCTGATTGTATTGCAGA Y 2 1 2 1 101000 r 74 goat snp54479-scaffold830-4228240 8 63819734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381830 Affx-122974261 AX-123252188 8 62553070 CAGTGTTGCTCTTTTATCGGTTTTGGGTCTGGGGT[A/G]TTTCTTCTGTTTTGTTTTTCTAAGATTTTGAACAG R 2 1 2 1 103000 f 74 goat snp54480-scaffold830-4266349 8 63857911 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408989 Affx-122953900 AX-123279340 8 62582265 ACTTGCTTGCTCTTGAGATTACTGTGGTCAAATAG[A/G]TTGGGTACACTGGAAATAAAAGTAAACCACCTTCA R 2 1 2 1 101000 f 74 goat snp54481-scaffold830-4295544 8 63886924 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784113 Affx-122977277 AX-385271165 8 62640344 GTTTGAATAATATCTGATGTGTTCTGTTATTTAAC[A/G]ATTTTAAGGCGATACCTCTGCACCCTATATGGCCA R 2 1 2 1 101000 r 74 goat snp54482-scaffold830-4353623 8 63945025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391741 Affx-122967485 AX-123262098 8 62673978 TCTGCTCTAGAAGCACTCCTCGAGCCCTTCCATTG[C/T]GTGTTATCCACTCATCTGCCTGTTGGCCGCTGCCA Y 2 1 2 1 101000 f 74 goat snp54483-scaffold830-4387257 8 63978365 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395452 Affx-122963921 AX-123265807 8 62703559 TACACTTCGCATTTCAGTTGAAATCTTAACCCCAA[C/T]GTGATGGTAGCTGGAGAGGTTCTGCTGTCATGAAT Y 2 1 2 1 201000 r 74 goat snp54484-scaffold830-4416838 8 64007615 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434511 Affx-122934606 AX-123304852 8 62756581 TGCTCACAATGCATCTCTTTGGAAGCCTGCCCTCT[A/G]AGGGTTGCCATGGTGACTATTTTGGTACTGCATGC R 2 1 2 1 101000 r 74 goat snp54485-scaffold830-4469860 8 64060523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273375 Affx-1111833587 AX-519547007 8 62762888 CTATACATACTATGCATTTTGGGAAGCTTTAGTAA[A/G]AGGTGAAGAAAAATGAACCCTATGTAGAGTCAATT R 2 1 2 1 101000 f 74 goat 8_62762888_AF-PAKI 8 62762888 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320780146 Affx-122928870 AX-385267243 8 62793505 GCTAATCGTGAAGGAAATCCAAATCAGAGACCAGT[C/T]TGAAAATGGCCAGAGCTATCCTGTAGCTGCGCATT Y 2 1 2 1 101000 f 74 goat snp54486-scaffold830-4506784 8 64097180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382455 Affx-122974220 AX-123252813 8 62828040 TGTGCCCTGATGGTGGGCACATCCCTGCCAAGCCT[A/G]AGACAAGTGCCTGCCTCCTACACTGTGCTCCCAGC R 2 1 2 1 201000 r 74 goat snp54487-scaffold830-4541319 8 64132116 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388822 Affx-122968897 AX-123259180 8 62884676 CTTCCTTGTTTTGAGCTGAAATTTGCTCTAATTTT[A/C]GCCTCAAAGACCTAATTCCATCTTCTGGGATAATA M 2 1 2 1 101000 r 74 goat snp54488-scaffold830-4597955 8 64189478 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398818 Affx-122961399 AX-123269173 8 62921130 TGTTTGTTGTTTTCATTTTTAAGACAAAAAGGATC[A/G]TCTCTGAGAGTATGATTGCAGTAGGACTTTTGATT R 2 1 2 1 103000 r 74 goat snp54489-scaffold830-4634409 8 64226751 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273735 Affx-1111833779 AX-519547347 8 62983764 CAGGAGGCACTGCAGTGGGAAGCCAGCGAGGCCTC[A/G]GCCGACAGCATCGTGCTCAGCCCCAGCACCGTCAG R 2 1 2 1 303000 r 74 goat GoatD01.004568 8 62983764 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320794974 Affx-122950147 AX-385281934 8 62994911 GGAAACCAGGTCCCACATGATAATGGCAAATACCT[A/G]TCTAGTATTTATCATGTATTGAATGCTATTCTAAA R 2 1 2 1 101000 f 74 goat snp54491-scaffold830-4708190 8 64300536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418524 Affx-122946419 AX-123288872 8 63024260 CCTTCAGCTCTGCAGAAACTATGAAACTGAGTCAC[A/G]TAAAGAAATCTATTGGCTTTTCTGGCTCTAGGAAG R 2 1 2 1 201000 r 74 goat snp54492-scaffold830-4737539 8 64328445 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401080 Affx-122959633 AX-123271433 8 63056145 AGCAGGGGAAGAGCATTTCAGGCAGTGGCCCTGAC[A/G]TGAGGAAGTACTTGGACATATTCTAGGATCAGAAT R 2 1 2 1 101000 r 74 goat snp54493-scaffold830-4769424 8 64360567 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377827 Affx-122977301 AX-123248186 8 63098787 GCTCTGGTGACCAAAAGTGAGTGAGCTGCTGGAAT[A/G]CATAGGACATCTCCTACAGAAGGCAGCTTATCCAA R 2 1 2 1 101000 f 74 goat snp54494-scaffold830-4812066 8 64404093 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393997 Affx-122965028 AX-123264352 8 63131254 GCCTTCTTGGTTAAGGTTATCTGATATTATCAACT[G/T]AAATGCTGGAGAGCATCTGTCAAATGCAGCGAATT K 2 1 2 1 201000 f 74 goat snp54495-scaffold830-4844533 8 64437081 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778359 Affx-122933918 AX-385265474 8 63167757 TTGTTTTACTATTATCAATATTGCTGTGTGCCTGG[C/T]AATTTCCTAAGTACTTTATGGGCAATGTTTTCATT Y 2 1 2 1 101000 f 74 goat snp54496-scaffold830-4881036 8 64473950 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422075 Affx-122943595 AX-123292422 8 63204200 ATCCAAAAGGCTCCAGAAGAGATGGCAGGTGCTGG[C/T]GGATTCCCTGCTGCTTTCTGTGAAGAACCCTGGTC Y 2 1 2 1 201000 r 74 goat snp54497-scaffold830-4917479 8 64510966 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428326 Affx-122939004 AX-123298669 8 63251797 GGCTCAGCGTCTATGGGACTGCCCGTCAGGAAAGG[A/C]TGTTCTGACATGAGAAGTAGCAGTGAGATGACTTC M 2 1 2 1 101000 r 74 goat snp54498-scaffold830-4965076 8 64558777 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272418 Affx-1111834497 AX-516060645 8 63277602 GGTCCCTGATGCTGACTGCAGGGATGTCCAGAGGA[A/G]CTGAGAACGCTACTGCAACTGCA R 2 1 2 1 102000 f 74 goat GoatD01.038319 8 63277602 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38399502 Affx-122961170 AX-123269857 8 63282979 TTTTCAATGTCATATCTTTTATTTATTTTGTTAAG[C/T]GTCCTGTATCCTAACTTGTGTTATCTCTGAATCTA Y 2 1 2 1 101000 r 74 goat snp54499-scaffold830-4996258 8 64590020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392356 Affx-122966252 AX-123262713 8 63312550 AACACTTCAAAGAGAGAAACATTATTTAAAGTAAT[A/C]GTTTTTAATGTTTGTGGAGTGATAGAGTGTTTTGA M 2 1 2 1 101000 r 74 goat snp54500-scaffold830-5025829 8 64619750 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426981 Affx-122940390 AX-123297326 8 63432666 GTAAAGGCTTCCTAGAAGTAGTAGTAGATGGTATG[C/T]ATTACAAAATATCAACATTATTTTCCCTTCTAAAT Y 2 1 2 1 101000 f 74 goat snp54503-scaffold830-5145945 8 64738883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435723 Affx-122933298 AX-123306062 8 63472625 TTGGAGGAAGACGGAGTGGGGGTTAGATTCCTTTG[C/T]AAGATGGGATGGTGCTGAGCCGGTGAGGCAGTTAA Y 2 1 2 1 101000 f 74 goat snp54504-scaffold830-5185904 8 64779601 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384839 Affx-122971966 AX-123255197 8 63531167 TATAAAAGTAGATCCCCACTCTTTACCTCAGGATC[A/G]TGTCATGTGGCCTTAAGAGATGATACTAAATTCTT R 2 1 2 1 201000 r 74 goat snp54505-scaffold830-5244446 8 64838135 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378541 Affx-122976618 AX-123248900 8 63583210 TTCTATATGCTCCCGCAGCTTTCCTGTGCATCCCT[A/G]TTGTAAAGATCCTCAGCTTGCACTGTCCGTGGATT R 2 1 2 1 101000 r 74 goat snp54506-scaffold830-5296489 8 64890120 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377625 Affx-122977881 AX-123247984 8 63736091 GTGAGGGTTGTAACAGGCATGGGGCAGGGCCATTC[C/T]AGCTGTCACTGGGATCAGAGGCCCCTTCTGGAGCT Y 2 1 2 1 201000 r 74 goat snp54508-scaffold830-5449370 8 65043665 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411075 Affx-122951936 AX-123281425 8 63765152 TTTATAGGTGAGCAAACAGGTCCCAAAGAGGGTAA[A/G]TGGCTACCCTAAAATGTGGCAGCACAGCCTGAGCC R 2 1 2 1 101000 f 74 goat snp54509-scaffold830-5478431 8 65073152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789059 Affx-122919274 AX-385276072 8 63786060 GTCCTGGACTTTGATTTACTGGGAAGGTGTTGTTT[A/G]CTATTTCAGTTACACTCTATGACTAGGGACCAGTC R 2 1 2 1 101000 f 74 goat snp58903-scaffold964-959237 8 65160469 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767920 Affx-122933432 AX-385255137 8 63821088 AATAAAAGTGAATATTCACTGGCAAAGAGGAGGAG[C/T]GCCTGGAACTGTCACGCACTAACAGTAGAAGTAAA Y 2 1 2 1 202000 f 74 goat snp58902-scaffold964-924209 8 65194823 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423528 Affx-122942445 AX-123293874 8 63876645 CTCAAGCTCACATGGAGACCCAGGCCCAACCCCAA[C/T]GTTTTACTCCAATGCCACCTCCTCAGGCTCACATG Y 2 1 2 1 101000 r 74 goat snp58901-scaffold964-868652 8 65250661 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394183 Affx-122964921 AX-123264538 8 63907242 GAGAAACAAGAGCCACTCCCTGCTATAGCAGCAGT[A/G]CTGATTATGGGGTGTTGGGGAAAGAAAGAGAGGTT R 2 1 2 1 202000 r 74 goat snp58900-scaffold964-838055 8 65281907 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785578 Affx-122952931 AX-385272622 8 63973108 CTGACTCTTTGTGGTGTTGAAGTCTAAGCATTTTG[A/G]CAAATACATTCAGTCATATACTTAACATCAAAATT R 2 1 2 1 101000 f 74 goat snp58899-scaffold964-772189 8 65349336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429305 Affx-122938605 AX-123299647 8 64028236 GGCTTTACCACATAAGAGAAGCAGAGTGACAAGCA[C/T]GGGTGCATTTAAGATCCTTACTTCAGTGATGAAGA Y 2 1 2 1 201000 r 74 goat snp58898-scaffold964-717061 8 65404212 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770202 Affx-122955880 AX-385257369 8 64106495 CCAGTTCTTTCAAATCAGCACTACCATCATGCCGG[G/T]TCTCTTATTAATGAGTTCATTAAATCTGTGACATA K 2 1 2 1 101000 f 74 goat snp58897-scaffold964-638802 8 65482456 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410382 Affx-122952437 AX-123280732 8 64150018 TGCATTCAACAGAAAGACATGAAGAGAAAGTGCCA[G/T]AAGTAAAGGGAGGGGAAAGTGAAAGTCCTGTGTAA K 2 1 2 1 101000 f 74 goat snp58896-scaffold964-595279 8 65526303 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781218 Affx-122959124 AX-385268303 8 64178829 ATAGCAAACATTAGTCTTGATCAGAGGTTTATTAG[C/T]AGATGTTTAACATCGGGCTGAGTGGTAGCATTTGT Y 2 1 2 1 101000 r 74 goat snp58895-scaffold964-566468 8 65557769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448615 Affx-122923381 AX-123318951 8 64218773 ATCAGCCCTCAGCAAGCAATGTAAAATAGCATTAA[G/T]AAGAAGAAAATGGTGATTAAAAGAAAAGTATTACT K 2 1 2 1 101000 f 74 goat snp58894-scaffold964-526524 8 65595708 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431816 Affx-122936107 AX-123302157 8 64254986 TCACTGCAACAATCAATGTAGTTTTTTAAGTAAAA[G/T]AAACACAAGGTTTTAAAACAGGCAAGTACATGTTC K 2 1 2 1 202000 f 74 goat snp58893-scaffold964-490311 8 65631144 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438698 Affx-122930863 AX-123309035 8 64292189 TAGGCGGATGGCTGAGCACAGAGCACAGTGCACAG[C/T]GCCCAAAGACAGCCCAGGCGTGGGTGTCTGCTTTG Y 2 1 2 1 103000 r 74 goat snp58892-scaffold964-453108 8 65667995 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427360 Affx-122940103 AX-123297703 8 64326654 CTGTGTCTCTCATCACAACCTGAGTAACCGGCAGG[C/T]GCTTCTTATGGGAAAGGACTACTGTGTCGCTGGTC Y 2 1 2 1 101000 r 74 goat snp58891-scaffold964-418643 8 65702534 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411072 Affx-122951939 AX-123281422 8 64367239 AGATAATGTGAAGAACGCATCTGATGGCTTCCATA[A/C]CCTTCCTATCAGCAACTCCAGTGTAAATGTGTTTT M 2 1 2 1 101000 f 74 goat snp58890-scaffold964-378058 8 65743105 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428584 Affx-122938707 AX-123298926 8 64402270 AGGTTTCACCTCTTTGGAAATACTGCTTCTGAAAA[C/T]CAAGACTATTTACCTAGCCTATCTTACTGTTCACA Y 2 1 2 1 101000 r 74 goat snp58889-scaffold964-343027 8 65778155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778097 Affx-122956659 AX-385265212 8 64432927 TGACTCTATTCCATAACTGTCTCCAGGTACAGGAA[C/T]ATAAATTTAAGGCAACATGTGTTGGTAAGTTGGTA Y 2 1 2 1 101000 f 74 goat snp58888-scaffold964-312370 8 65809131 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376860 Affx-122977836 AX-123247219 8 64465517 ATTGCATGCCCACAAAGAAAGTGAGAAGTAATATG[C/T]AGACTTAGAAATTTGCTTTTGGAACACATGCTACC Y 2 1 2 1 101000 f 74 goat snp58887-scaffold964-279780 8 65841700 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420991 Affx-122944565 AX-123291338 8 64494421 TTATTCATTCTTGACTGATGAAATGGCAAGCAACA[G/T]ATTTTAGTCTGCAAAGGGGAAAAAGAAAACAGGCA K 2 1 2 1 201000 f 74 goat snp58886-scaffold964-250876 8 65871035 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421579 Affx-122944506 AX-123291926 8 64541680 AGGAAGGGCTTTTAGGTCCAATGAGCTGCACCTTT[A/G]CCCTCTTGATCTCATTTTTACTTAAAATTTGTTGG R 2 1 2 1 101000 f 74 goat snp58885-scaffold964-203617 8 65918472 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387476 Affx-122970354 AX-123257834 8 64574159 TGAAGAACAGGGAAGCCTGGTCTTGTGGCAGTCCA[C/T]GGTGTTGCAGAGACTTAGCAAGTGAAGAATAACAA Y 2 1 2 1 101000 r 74 goat snp58884-scaffold964-171138 8 65950034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780632 Affx-122976648 AX-385267722 8 64637074 GTTTTACATGGAGCTAAACAGAGTCTTAAAAAAAA[A/G]TTGGTGCTTGTTATTACCTTACATGTTGGTAGCAC R 2 1 2 1 303000 f 74 goat snp58882-scaffold964-108223 8 66013561 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793707 Affx-122927574 AX-385280679 8 64675923 GAAAATGTTGCTTGGAGAGAGGAATTAGTTTGGCC[A/G]TGTTATAACAACTAATGCTTAACAAACAGACCATT R 2 1 2 1 101000 f 74 goat snp58881-scaffold964-69374 8 66052144 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397761 Affx-122962523 AX-123268116 8 64705508 AACTGAATGTACTCCAATTGTATTGAAATGGAATC[A/G]TCTTTCTGAAGCACAGTGGGCTCAGTGGCCAGAAT R 2 1 2 1 201000 f 74 goat snp58880-scaffold964-39789 8 66082070 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441547 Affx-122928700 AX-123311884 8 64737981 AGAGAAGAAGGAAGAGAAAAGCAGGGTCACCCAAG[C/T]GGTCACTCATCTAGGTCACCCAGGGCTTTCTACAA Y 2 1 2 1 201000 r 74 goat snp58879-scaffold964-7316 8 66114895 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429909 Affx-122938111 AX-123300250 8 64761041 GAAATAAACTATGGGATTCCACCAAGAAATGTAAG[C/T]GATGAATATGTCACTTCATAGTTTTGTGTTCATGA Y 2 1 2 1 101000 f 74 goat snp19561-scaffold1972-15645 8 66145575 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798679 Affx-122976638 AX-385285611 8 64793858 TCCAAAACTCCCATCTAACTGACTTTTAATAAGGG[C/T]GTTTTGATGAAATTCTTGTTTGATTTAATGTGCTT Y 2 1 2 1 101000 f 74 goat snp19562-scaffold1972-48462 8 66179331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798509 Affx-122975390 AX-385285442 8 64829974 TAGAACTGAGATTTAGGGAATTTTTATGCACAAGG[C/T]AAATGGTGGACTCTGAATCCTGCATCTCATTTCTA Y 2 1 2 1 101000 r 74 goat snp19563-scaffold1972-84578 8 66215248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379618 Affx-122923163 AX-123249976 8 64882514 CCACCTGAGGAAGTGAAGGGAGACAGGGAGGTGCT[G/T]AGGGGTGAAAACTCTGATGGCTCCATGAAATCCAG K 2 1 2 1 101000 r 74 goat snp19564-scaffold1972-137118 8 66268282 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405264 Affx-122956868 AX-123275616 8 64915462 GTCTACTGATGTAAACCCCAAGGAAATCCATGAGA[G/T]ACTCACAGATTCTTTTTTTTTTCCTTGTTGATAAA K 2 1 2 1 101000 f 74 goat snp19565-scaffold1972-170066 8 66301277 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767761 Affx-122955192 AX-385254988 8 64945360 AGCCTTTCAAAATTTAAATCAGAAGATCAGAAAAC[A/G]TGTTATTATAATATGCCTTGATTCCATAGTTTTGT R 2 1 2 1 101000 f 74 goat snp19566-scaffold1972-199964 8 66331544 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799181 Affx-122959120 AX-385286111 8 64991613 ATAAATATGTATAAACCAGATACATAAAAGGGTTG[C/T]AATTCTTTTTAAGAAGGGAGAATCCTTCTTTATGC Y 2 1 2 1 201000 f 74 goat snp19567-scaffold1972-246217 8 66378222 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783554 Affx-122961567 AX-385270616 8 65033285 TGAATTATGTTAATAGTTAAATACAGGGCCTCATC[A/G]TGGAGTCCCCTACAAAGAGTAGTGAAAATGGAAAT R 2 1 2 1 201000 f 74 goat snp19568-scaffold1972-287889 8 66420322 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771592 Affx-122956224 AX-385258750 8 65080112 CAAACTAAACACAAAAGCTTTCCTGTTAAAGACTT[A/G]GTCAGTGTGGACACAGCCAATGCCTCCACTCTACT R 2 1 2 1 101000 r 74 goat snp19569-scaffold1972-334716 8 66468677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398443 Affx-122961611 AX-123268798 8 65137620 ATAAAAATGAAAACCAGGCTGCTGCTGGTTTCCAT[A/G]CAACCCACTCATCCTTTCTCAGGTCTGTACTTTGG R 2 1 2 1 202000 r 74 goat snp12967-scaffold1499-3389913 8 66526708 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762626 Affx-986697156 AX-385250713 8 65158874 TATCTTGAGACTAATGAAAATGGAAATGCATTACT[C/T]TAAACTATATGGGAAGCAGCAAAATCAGTTTGAAA Y 2 1 2 1 600010 f 74 goat 8_65158874 8 65158874 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 320803671 Affx-986696170 AX-385290446 8 65158889 GAAAATGGAAATGCATTACTTTAAACTATATGGGA[A/T]GCAGCAAAATCAGTTTGAAAAGTTCATAGTGATAA W 4 1 2 1 600010 r 74 goat 8_65158889 8 65158889 Ancestral_priority_1043 ancestry 0.572 neutral IMAGE 10K 10K ancestral 320765007 Affx-986697158 AX-385252581 8 65158949 CATAGTGATAAAAACTTCCTCAAAAAACAAGAAAA[C/T]TCTCAAATAAATAACCTCCCTTCTAAAGTAGTTAT Y 2 1 2 1 600010 r 74 goat 8_65158949 8 65158949 Ancestral_priority_1043 ancestry 0.584 neutral IMAGE 10K 10K ancestral 38387547 Affx-122970295 AX-123257905 8 65180318 TATAGTACTACATTTGAGTTTTCTGAGGTTTGTTA[C/T]ATTTTCTGGAAGGAGGAGGCTTGTAAGAGAAAATC Y 2 1 2 1 101000 f 74 goat snp12966-scaffold1499-3347215 8 66569681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431645 Affx-122936132 AX-123301986 8 65231960 AGGAAAATCCACTTTCCACCATCTAAAGCACTGGG[C/T]GTCTTTTGTAAAAGTTACTTCATTCTTCATAGAAT Y 2 1 2 1 201000 r 74 goat snp12965-scaffold1499-3295573 8 66621364 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772252 Affx-122960307 AX-385259407 8 65289742 AAGAGTTCCTTCTTTTTGTCACTATGTAATATTGC[A/G]TAGCATGGATGTACTTCAGTTTATTTAACCATTTC R 2 1 2 1 101000 r 74 goat snp12964-scaffold1499-3237791 8 66679640 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378214 Affx-122976924 AX-123248573 8 65427585 CTGGAGGGAATCTGATGGGCTAGCCTGTTGACAGC[A/G]TCCTCTGGAATTAAGTTCTGTGCATCTTTTCCTTT R 2 1 2 1 201000 r 74 goat snp12961-scaffold1499-3099948 8 66818723 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782137 Affx-122931886 AX-385269215 8 65496659 GCTACAACTTGCCTAATTAGGAAAGCTCTGCTACT[A/G]CTCTGCTCAAAAGTTGTATTTTCTCTTTTATAAAT R 2 1 2 1 201000 r 74 goat snp12960-scaffold1499-3030874 8 66886037 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420397 Affx-122944927 AX-123290744 8 65543913 AAGGAGAACAATGCAAATTAGCCAATATTTAATGA[C/T]GGAAAATAAATGAAAAAGGTTAAGAATCCCTAATT Y 2 1 2 1 201000 f 74 goat snp12959-scaffold1499-2983620 8 66933720 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375902 Affx-122978485 AX-123246261 8 65581310 CCAGAGAGGGTGATGACTGACGGAAGCTCCCTTCC[A/G]CCTCTTTTCCTACAACTTTTCTTGCCCCCCATTCC R 2 1 2 1 101000 r 74 goat snp12958-scaffold1499-2946223 8 66970891 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273377 Affx-1111833588 AX-519547009 8 65609856 GTTATCAAAGGAAGTGTTAAGTATGATTTAGCCAA[A/C]TACGTTTAAAAACATGTCAAGATCAAACAGCTGTT M 2 1 2 1 101000 f 74 goat 8_65609856_AF-PAKI 8 65609856 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38386945 Affx-122969987 AX-123257303 8 65642567 CCTGGGAAATCTTTAGACGATTTACATGGTGGGTC[A/G]CTGAGCTGGCTTTTGAATAGATGTTTGTGCTGCTG R 2 1 2 1 101000 f 74 goat snp12957-scaffold1499-2884966 8 67031469 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384846 Affx-122971960 AX-123255204 8 65687737 TTTGCTGATGGTGTAAAAGAGCAAAAGAAATGAGA[C/T]GTTCTGAGGAAGACGTCACACAATGATGGGAAAAT Y 2 1 2 1 101000 r 74 goat snp12956-scaffold1499-2839796 8 67076718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453763 Affx-122919600 AX-123324096 8 65725762 ATTTTACCATAAAGCAGGATGTAGACACAGAAGAT[A/G]CAGTTTGGAGGCTGGCTTGAACACCTGGTTATACC R 2 1 2 1 101000 f 74 goat snp12955-scaffold1499-2801771 8 67115339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780478 Affx-122932189 AX-385267569 8 65797238 GTTACTTGCCTTTGTGTGTTAATTTCAATTCAAAT[A/G]TTGCCTAGACTTCCCCCAAATGAAAGCTACTTGTG R 2 1 2 1 101000 r 74 goat snp12954-scaffold1499-2730295 8 67185964 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392258 Affx-122967558 AX-123262615 8 65861746 CCTCCACACACATCTTTTTTTCATGCTAATAATTG[C/T]GAAGTCAAAGCATATTTGCATGCCACTGGGACAAG Y 2 1 2 1 101000 f 74 goat snp12953-scaffold1499-2665787 8 67250679 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387498 Affx-122970335 AX-123257856 8 65894398 TTTGCAGTTTCGATCTTGGATTATTTTCTTGATCT[A/G]TTAAAGCTTCAGCTTTCACAACTGTAAGACCAGTT R 2 1 2 1 101000 r 74 goat snp12952-scaffold1499-2633135 8 67284196 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406331 Affx-122955448 AX-123276683 8 65942540 CCTAGATGTGGACCCACCTTAGTGTCTCAGGAGTG[C/T]GCCTGAGTGTCATGTCATCAGCATCAGGATGAAGA Y 2 1 2 1 101000 f 74 goat snp12951-scaffold1499-2584993 8 67332738 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433787 Affx-122934472 AX-123304128 8 65990652 AGGCTCCCGGGATCTTGGGCTTAGCTGCTGTACCA[C/T]GTGTGTAATCTTAGCTGCCCAACCAAGGACTAAAC Y 2 1 2 1 201000 f 74 goat snp12950-scaffold1499-2536881 8 67380747 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396291 Affx-122963096 AX-123266646 8 66049013 ACTTGGGCCTTAAATGGACAATGAGGGTGCAGACT[G/T]TGGGCTACACTTGCAGGAGCAGAATGGAGTTTCAG K 2 1 2 1 201000 f 74 goat snp12949-scaffold1499-2478520 8 67439356 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440285 Affx-122930229 AX-123310622 8 66078111 AGAAAAAGTGATGCTCCCCTGAATCTATGCAACCT[G/T]GCAGAGTGGTAGGAACAGGGGTCAGGGACAGACCT K 2 1 2 1 103000 f 74 goat snp12948-scaffold1499-2449422 8 67468501 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278623 Affx-1111836519 AX-519552103 8 66110587 TGTGTCTTCCACTGTGATGTTCTCCAAGAGTGAGA[A/G]GATGGCTTTCAGGGCTGACACTAAAACCAGCCCTA R 2 1 2 1 101000 f 74 goat Random2.2K-917 8 66110587 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438112 Affx-122931498 AX-123308450 8 66113241 AACACAGCAGTGCAGGAACAATCAACAAGGCCAAA[C/T]ACCGTCTCCTGACCTTTACATCAGTAGTAGGTAGC Y 2 1 2 1 101000 r 74 goat snp12947-scaffold1499-2414292 8 67503568 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392613 Affx-122966045 AX-123262970 8 66144842 TCACCTAGTAGAGAAGTAAGAGAAAGAAAAGCAGT[A/C]GTTTTAAAGGCAAGAATTTCCTGGGGCACCATTGT M 2 1 2 1 201000 r 74 goat snp12946-scaffold1499-2382691 8 67535218 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441228 Affx-122929511 AX-123311565 8 66196299 CAGGGCTGGCTTGATATTGTCAAGGAAGGTGTCAA[C/T]GAGAAGATGGACAAACAAGCTGAGCTTTAAGGATG Y 2 1 2 1 201000 f 74 goat snp12945-scaffold1499-2331234 8 67586596 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414622 Affx-122949341 AX-123284971 8 66226030 GCTTATAAACAATAGAAATTTACTCCTCATAGTTA[C/T]AGAGGCTGAAAGTCCCAAGAAACTGAGAGATTCAG Y 2 1 2 1 102000 r 74 goat snp12944-scaffold1499-2301503 8 67616703 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436646 Affx-122932484 AX-123306984 8 66272150 GAGTCCAGAATGACTGAGGCCCCAAAAGGAAAACT[A/G]TCACTTAAAAAAAATTCCATAGAAGTCTAGTTGAT R 2 1 2 1 101000 f 74 goat snp12943-scaffold1499-2255383 8 67662963 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798752 Affx-122938866 AX-385285683 8 66330375 AACTTATTTATAAGATCCTAGTGAATCTTTCCTCA[C/T]CTTAGATGAGATGAGGAATGTCAAAAGAATTCATT Y 2 1 2 1 101000 f 74 goat snp12942-scaffold1499-2197158 8 67722298 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797355 Affx-122936548 AX-385284294 8 66359275 AATATCTTTGGAAGAACAAAGATACTCCTGTTTCC[A/G]TATGAACCCTAATCCCTAGGGACATAGCTGACTCC R 2 1 2 1 101000 f 74 goat snp12941-scaffold1499-2168258 8 67751200 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421275 Affx-122944741 AX-123291622 8 66450712 GGATAAGGAAAGTGAGCCCAGAGAGGCACAGACAA[C/T]GGCTCAAGGTGGCCCAACAAAGAAGTGAGACCTGA Y 2 1 2 1 101000 f 74 goat snp12939-scaffold1499-2076821 8 67842292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433012 Affx-122935787 AX-123303353 8 66486614 TTGCCTCCTTCTTTCAATGCCTTTGCTCAATCACC[A/G]CTACCATTGAGCCAGGCCAGCAAAGGTTCATGGAG R 2 1 2 1 101000 f 74 goat snp12938-scaffold1499-2040919 8 67878814 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396581 Affx-122962913 AX-123266936 8 66600508 CTGTTTCCAGCCGGGCCCCAGAGACTCCATTGGGC[A/G]GGACAGGGCCCTTCCATGTAAATCATTGCACCTGG R 2 1 2 1 101000 r 74 goat snp12936-scaffold1499-1927025 8 67993420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395862 Affx-122964007 AX-123266217 8 66630367 AGGTAGGTTCTTTACCACTTAGTTACCTGGGATAC[C/T]TATGAGGGGAGGCAGCTAAATAAAATATCTAAATC Y 2 1 2 1 102000 f 74 goat snp12935-scaffold1499-1897166 8 68023421 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419877 Affx-122945357 AX-123290225 8 66663161 TCTCTGTGGTCATCTGGGAGTTTGGATGGGACTGC[A/G]TGATGGAGAATGAGCTCACTCATGTATCAGGCAGG R 2 1 2 1 201000 r 74 goat snp12934-scaffold1499-1864372 8 68056756 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765193 Affx-122956478 AX-385252738 8 66721563 GAGGTTGTACTAAGGGACTCTTTCTTGACATCTTG[C/T]AAAGTTATATTTCTGGATCTACCAGGCTGTGGGTC Y 2 1 2 1 101000 f 74 goat snp12933-scaffold1499-1805970 8 68115674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404213 Affx-122957663 AX-123274565 8 66781090 TCTGTTGCTTTCCTTTAGTCTACCTCTCTCTCCTT[A/G]TTGGGATGATGCTCACTTGGACAACCCAGGGCCAG R 2 1 2 1 201000 r 74 goat snp12932-scaffold1499-1746443 8 68163141 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417892 Affx-122946750 AX-123288240 8 66821198 AGTATGAAGTTGCAAGGTACTGAAATGGAGGAGAC[A/G]TGCAGAAGGGTTGGGGAGCAAGATTCTGGAGCTTC R 2 1 2 1 101000 f 74 goat snp12931-scaffold1499-1706335 8 68203190 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377106 Affx-122978257 AX-123247465 8 66859283 TCTATTTCTCCTTTGATTTTAGAACATACTTCTGA[C/T]ATAAAAATGCAGCTCCTCAGGGCAATTTAATTTTT Y 2 1 2 1 101000 r 74 goat snp12930-scaffold1499-1668250 8 68241161 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792063 Affx-122924688 AX-385279050 8 66889351 CCTTCTTCCTCTCTGGTTTCCTACCAACAGAGGCC[A/G]ACTCCTGTTTGTGTTCATCGCTGTCTTAAAGTTTC R 2 1 2 1 202000 f 74 goat snp12929-scaffold1499-1638182 8 68271744 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784263 Affx-122945500 AX-385271314 8 66926319 TTGGAAACACTGAAAGACAAAGGTATCCAGTTTGC[C/T]CCAATTTAGTGGGCTATGGACCAGTTCTGGCTGAT Y 2 1 2 1 101000 f 74 goat snp12928-scaffold1499-1601214 8 68308549 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275266 Affx-1111834691 AX-516068846 8 66932983 TTTGTCTCTGCAGTATGC[A/G]TGCTATGCTATTGGTAAGGATGTGCAAGCCATGAA R 2 1 2 1 101000 r 74 goat GoatD01.046076 8 66932983 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38378151 Affx-122976974 AX-123248510 8 66981637 TCTGGTGCCCAGAGACCTGCATGGGAAGGTGCCTT[A/G]CTTATGTTTCCTGGGCATCTTGCAGATGCCAAGCA R 2 1 2 1 101000 r 74 goat snp12927-scaffold1499-1545896 8 68364607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380076 Affx-122975552 AX-123250434 8 67043790 TTTGTAAGAATGTTTATGGGCAGGGTAGAATTGGG[C/T]GTTTCTAAAGGCATGATGAGAGTGATGAAAGTCAT Y 2 1 2 1 101000 f 74 goat snp12925-scaffold1499-1483743 8 68426778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410810 Affx-122952647 AX-123281160 8 67135137 ATGCTCAATAAATGATAGCTGGTAATAGAGTGCCT[C/T]TGAGTGTTTTCTGCTCAGAAAAACAGAGAAAACTT Y 2 1 2 1 101000 f 74 goat snp12923-scaffold1499-1392396 8 68571542 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419109 Affx-122945772 AX-123289457 8 67170996 CCCATGAGAAAAATCTCTGCATCACTCCTTTATTT[A/G]CTGACTCCTGGGGGGTCAAGCTCAGCCAGCCTGCC R 2 1 2 1 101000 f 74 goat snp12922-scaffold1499-1356537 8 68608008 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383918 Affx-122972978 AX-123254276 8 67226424 AGGACCCAGAGCTTGAGATGCAGGAAAAATGCATT[A/C]TTTTAACATCATTTATCCAGGGTTGGCTGTGTGGT M 2 1 2 1 101000 r 74 goat snp12921-scaffold1499-1301109 8 68663935 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418976 Affx-122946072 AX-123289324 8 67259824 CTTCACTGGATGACCCCCTCTCTCTGGATGACCTT[A/G]TCTGTCACTGTGGCATCAATTTCTCATTTTCACAT R 2 1 2 1 101000 r 74 goat snp12920-scaffold1499-1267709 8 68697272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427877 Affx-122939702 AX-123298220 8 67327707 CCCTGAGGGGCACAGTCAGTGCCAGTTGAGAAGCA[C/T]GACTCTAGACTGTGAAATGAAAGACTCTCTAGTGA Y 2 1 2 1 101000 r 74 goat snp12918-scaffold1499-1199826 8 68764833 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38381024 Affx-122974651 AX-123251382 8 67359020 GAGTCCCTGCTTTCATGGCGTTTACGATTTGGTTG[A/C]GGGTATCCGACATTCCCAGGTGGAGCTAGTTGTAA M 2 1 2 1 101000 f 74 goat snp12917-scaffold1499-1168513 8 68796086 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379245 Affx-122976264 AX-123249604 8 67399568 AAGTGATTGACCCACAGCAGGCATCCAACAGAGAC[C/T]TGTTTCTTGCTTTTCTCATAAGAGGCATTCTCGAA Y 2 1 2 1 101000 r 74 goat snp12916-scaffold1499-1127965 8 68836903 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782719 Affx-122928905 AX-385269791 8 67439818 TATTAAAATTTAGTTAGCTGCCTTTCCTGCCAAAA[G/T]CCCTTAGCCTGAGGCCTGTTTTTCCTTTGTAAAGA K 2 1 2 1 102000 r 74 goat snp12915-scaffold1499-1087715 8 68876879 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395005 Affx-122964233 AX-123265360 8 67477506 TCTAGCCATTTGTACTCCTGAAGCCTGCCCGAGAC[A/G]GTATCAGAATTTGACACTTCAGCAGGCTGGCTCCA R 2 1 2 1 101000 r 74 goat snp12914-scaffold1499-1050027 8 68913596 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786285 Affx-122936054 AX-385273320 8 67528652 GTGGAGGAGAGTCTAGGTGACCTTTATCTAAAAAT[A/C]ATCACTTATAGCCCTCTTCATTTTATGCTTTAGAA M 2 1 2 1 101000 f 74 goat snp12913-scaffold1499-998881 8 68964568 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414164 Affx-122949682 AX-123284513 8 67574238 GGACCAGGCAATGCCACCTGCTCCTGCTTGTCTGG[C/T]CAAGTTCCTCCCTGCCCCACCCTTTCTCCCCTCCT Y 2 1 2 1 101000 f 74 goat snp12912-scaffold1499-953295 8 69010119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771571 Affx-122961443 AX-385258729 8 67631747 AAGGATGAAAACAACCTATGTGTGTTGTTGACCTC[A/G]CGAGTTTGTTAAGAAGATCAAACAATGTTTTGGAT R 2 1 2 1 101000 f 74 goat snp12911-scaffold1499-895786 8 69067819 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274191 Affx-1111834096 AX-519547792 8 67641840 TTCTATCCATTTTCCTAAGAGTTGGAGGGACATCA[A/G]AAGCTTTCAGGAGGTGATCTGGCTGCAGGTGATAG R 2 1 2 1 101000 f 74 goat GoatD01.018129 8 67641840 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382484 Affx-122973828 AX-123252842 8 67661301 GGCCCTCTTCCTCAAGGAGGCTCAGTGGGCCACCC[C/T]CAGTCCAGCCCTGTCCTTTGGGCCTTTGTTTCTCC Y 2 1 2 1 101000 r 74 goat snp12910-scaffold1499-866232 8 69097301 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431883 Affx-122936057 AX-123302224 8 67694744 CAAGTCCAACCAATAGGGCTAAGGACAAGCTCAGT[G/T]GTTCGTCGCCTCTCCATCCCCCTCTGCTGGACAAA K 2 1 2 1 101000 f 74 goat snp12909-scaffold1499-832789 8 69129962 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416011 Affx-122948383 AX-123286360 8 67752953 CGGGGATCACCTGTGGAGTGGGACGCCTGGAAGCC[C/T]TTCCTCTGCACGGAGTTGTCAGAGTAGAAGCGCAG Y 2 1 2 1 101000 r 74 goat snp12908-scaffold1499-774580 8 69188343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451840 Affx-122921460 AX-123322173 8 67834015 GGCATACTTCTAACTTAAGTCTGTACCTCAGCTGT[C/T]CCTCTAACAAGAATGCCCTTAGCCTGTATGTTCAC Y 2 1 2 1 101000 f 74 goat snp12907-scaffold1499-693518 8 69270111 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429008 Affx-122938842 AX-123299350 8 67945588 ATTCCAAGGATACAGAACATAATGCATTCAAACAC[A/G]CCAAAGAACATGTCATGCCCTTAAGGAAAGAAATC R 2 1 2 1 201000 f 74 goat snp12905-scaffold1499-581945 8 69381793 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423692 Affx-122942897 AX-123294038 8 67991848 AACAGAAACCCTAAATTGTTCCCAAACTCAGAAAA[A/C]ACACTATGACTTAGAAGTCAGAAAAAGTGAACCGA M 2 1 2 1 201000 f 74 goat snp12904-scaffold1499-535685 8 69428231 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380604 Affx-122975251 AX-123250962 8 68047290 AATTAAAGTGATGTCTCATTGCAGTTAGTGTCTAA[C/T]GATGTAGAACATCTTTTTACATGCTTATTGGTCAC Y 2 1 2 1 101000 f 74 goat snp12903-scaffold1499-480243 8 69483791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398234 Affx-122962205 AX-123268589 8 68087681 CTGTCTGAGGCATGCTCCCACCTCTCCAAGCCCTA[C/T]TCACCCACATTCCACCTCCCCTGAGCTCTCAATGC Y 2 1 2 1 201000 f 74 goat snp12902-scaffold1499-439852 8 69521596 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273417 Affx-1111833589 AX-519547044 8 68153403 AGATAAAAGGAAACTAAAAGGAAAGAGAAAAAAGA[A/G]AATAGACCCTTCTTGCTTCTTCTCTTTGTCTTTCT R 2 1 2 1 101000 r 74 goat 8_68153403_AF-PAKI 8 68153403 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38443247 Affx-122927552 AX-123313584 8 68161200 GCTTCCCTTTCCCTGGTAATGACACAGCCAGAGCT[A/G]ATTTGTTTACAGAAGCCACGTGAATGAGCCAGCCG R 2 1 2 1 101000 r 74 goat snp12901-scaffold1499-366333 8 69594909 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421687 Affx-122944415 AX-123292034 8 68190478 CTTGGAACCTCAAAATACTAGTGACTTTGGTGATG[A/C]GATCCATCCACTCATCTCAAAGAAGGAATCAAGGC M 2 1 2 1 101000 f 74 goat snp12900-scaffold1499-337055 8 69623759 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769245 Affx-122934171 AX-385256418 8 68221344 TCAGCCCTCAGAGTGATGGGATGGGCCAGAGGCAA[C/T]GTCAGTTCTTTACACCAGTGGTTGTAAAGAATTTC Y 2 1 2 1 202000 f 74 goat snp12899-scaffold1499-306189 8 69654548 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382789 Affx-122973578 AX-123253147 8 68320716 GCTAATTAAATGTTTGTTGAATAAATTGAATATGA[C/T]AGCTTAAATACTGGCATACAGGACTCTGTGTATTA Y 2 1 2 1 101000 r 74 goat snp12897-scaffold1499-206817 8 69753575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395608 Affx-122963815 AX-123265963 8 68355073 GACTTCCATTCATCAGGAGCCAGCTCAGAGGTGCC[A/G]TTCTCTGTGAGGCTTTATTCAGTCACCCCACGGCA R 2 1 2 1 101000 r 74 goat snp12896-scaffold1499-172460 8 69787939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275222 Affx-1111834776 AX-519548801 8 68423636 CTCCTTTCCTTGCCTGTTGTCTCTGGGAACAATGA[A/G]TCTAA R 2 1 2 1 101000 f 74 goat GoatD01.052423 8 68423636 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38435702 Affx-122933314 AX-123306041 8 68426173 TCTCTTGGGTCCGGGATGAGTTAGATGCTATTCCA[A/G]GCCCCCCAGTGCTTCAAGAGACATTCTGCCCAAGA R 2 1 2 1 201000 f 74 goat snp12894-scaffold1499-101360 8 69858822 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762632 Affx-986697162 AX-385250717 8 68451321 TCCTGGCTTTGCAGGGTAGGGACAAACTAGAATAT[C/T]CAAAAGCCTTTCCAGGAGGCTGGGAGCAAATGAAG Y 2 1 2 1 600010 f 74 goat 8_68451321 8 68451321 Ancestral_priority_1043 ancestry 0.724 recommended IMAGE 10K 10K ancestral 38412523 Affx-122951351 AX-123282872 8 68455281 AGTTGGATCCTGGAAGTAGGAGTTCAACCAGAAAG[A/C]CAGCTCAGCTAAAAATGATTTCTTCAAAGATCTAG M 2 1 2 1 101000 f 74 goat snp12893-scaffold1499-72252 8 69887944 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453320 Affx-122919976 AX-123323653 8 68488210 AATTTGATGATTAAATGAATTCTTATTTCTCTTCA[C/T]GCTGGTAAGATAAACACACAATTTTTTCAGTCCAC Y 2 1 2 1 101000 r 74 goat snp12892-scaffold1499-39323 8 69920907 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441848 Affx-122929044 AX-123312185 8 68549947 TGAATAGTATTTACCTGTGGTGGTTTTAAGGCAGA[G/T]GCACAAATTCTTTGATCTTTTTCTTTCAAGATATG K 2 1 2 1 303000 f 74 goat snp1009-scaffold1026-942284 8 70121641 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421128 Affx-122944200 AX-123291475 8 68598960 GCACTGCTGTGTTATGGGAGACTTTCCCAGTCTTT[A/C]TTTCCTCTTCCTTCCTTCCTGCTCTAGGCTGGATT M 2 1 2 1 101000 f 74 goat snp1008-scaffold1026-893271 8 70171104 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452157 Affx-122921656 AX-123322490 8 68650214 AATGACCTGCCTCTACTCTGTTTATTCTATTCACA[C/T]GTATAAGTAATGCTGCCAACCGTCTTCTGATCCAG Y 2 1 2 1 101000 r 74 goat snp1007-scaffold1026-842017 8 70222701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422346 Affx-122943446 AX-123292692 8 68690059 CCCGAGAGAGTCTTCGAATCATAGATGGCATTGCT[A/G]CAGAAGAGCTCAGAGGTCATCTGGTCCAAGAGATG R 2 1 2 1 101000 f 74 goat snp1006-scaffold1026-802172 8 70262701 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770679 Affx-122974344 AX-385257843 8 68720107 GGCTTACCCAACCCAGTTTCATACTTTTCATCACC[A/G]CTGTTTATATAACTTCATATGAAGTAAGTAGCCAC R 2 1 2 1 102000 f 74 goat snp1005-scaffold1026-772124 8 70292707 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425976 Affx-122941160 AX-123296322 8 68759140 AGTAAGGCAGGAAACACACCTATGAATACACCTCT[A/G]TTGTATATATTAGGGCTTCCCAAGTGGCACTAGTG R 2 1 2 1 101000 f 74 goat snp1004-scaffold1026-733091 8 70331750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770583 Affx-122976799 AX-385257747 8 68812494 TAGATTTAAACACCCTTTTGAGAATTTGAACAGAA[C/T]TTGTATCCTACTATTGTGCAAAAACTATATGAATC Y 2 1 2 1 201000 r 74 goat snp1003-scaffold1026-679737 8 70384961 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446488 Affx-122925051 AX-123316824 8 68919936 CTAGGGATTCATATTCCCAGTCTATAGACAAGGAA[A/C]CCGAGCTTAGAGAGGTCAAGTAAGATGGCCCAGGT M 2 1 2 1 102000 f 74 goat snp1001-scaffold1026-572295 8 70489946 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387032 Affx-122969921 AX-123257390 8 68958341 GAAGCCATGATATTTATGATAGGCTTTTAAGAAAC[A/G]ACACTGGCCCACCACGGTAACATACACCATGCATC R 2 1 2 1 101000 f 74 goat snp1000-scaffold1026-533890 8 70528476 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773874 Affx-122952991 AX-385261013 8 68995633 AATTTTCTTTGCACTCTTCACCTGTGCAAACAGAT[C/T]GTCCTTCTAAACTTGGAGAGCCTTTCAACTTTAAT Y 2 1 2 1 101000 f 74 goat snp999-scaffold1026-496598 8 70565957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445243 Affx-122925487 AX-123315580 8 69041442 AAAACCTAAAACTTTCAGACGGTAACACAGGAGTG[C/T]ATCTTTAGACTTAGGAATAAGCAAGGAGTTCTTAG Y 2 1 2 1 101000 r 74 goat snp998-scaffold1026-450789 8 70611713 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395044 Affx-122964204 AX-123265399 8 69113675 TACAGAGCTAGGAGTGTTCTTTTCTTGGTGGCCAC[A/G]TCAGCAGAAGCCTGACCTAAAATGTGCATGAACCT R 2 1 2 1 101000 r 74 goat snp997-scaffold1026-378556 8 70684382 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380590 Affx-122975260 AX-123250948 8 69156131 ATCTAAACATCACTGTGCTTTGGAGAAATTACACT[A/G]CAGAAGCCAAACAGATAAATAAACTCTGATCTTAG R 2 1 2 1 101000 f 74 goat snp996-scaffold1026-336100 8 70727183 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278625 Affx-1111836520 AX-519552104 8 69253560 GACAAAGCTATTTCCTCTTCATAGCTTCATAGCTG[A/G]AACAGAATATTGGCTTAGGATGAATCAGACCTCAA R 2 1 2 1 101000 f 74 goat Random2.2K-920 8 69253560 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450465 Affx-122922944 AX-123320799 8 69289952 TTGAATATGGCCAAAGAAAGAGTCAGAGAACTTGA[A/C]GACAGGTCAGATAGAAACTTTTCAAATTTTTTCTC M 2 1 2 1 103000 f 74 goat snp994-scaffold1026-202279 8 70861727 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765592 Affx-122921840 AX-385253071 8 69335611 GGAGAGAGGGTTCTGCTCATTTCTCACTGTCAGTC[A/G]TTTCCTTTGGCTTCTGTTGGGTCTCACTAATTGTA R 2 1 2 1 202000 f 74 goat snp993-scaffold1026-156620 8 70907910 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449213 Affx-122923502 AX-123319548 8 69364930 GATTCTTTAAGAATTCTATTACTCCAAATTCCTTC[A/G]TTCCTTCTCCCTCCTTCCCTTTATGTTCTTTCTCT R 2 1 2 1 201000 f 74 goat snp992-scaffold1026-127301 8 70937412 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454185 Affx-122919304 AX-123324518 8 69407918 TGGTTGTATCTTCTCTGCCCACCCACTCATCCCCA[C/T]CAATCATTGTTCTCTTCTCTTTGGTTTTCCAAACT Y 2 1 2 1 201000 r 74 goat snp991-scaffold1026-84313 8 70980345 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403183 Affx-122958075 AX-123273536 8 69444685 TGACAAAAACTTGTTGGAAAGAAAAGAAACTGTTT[A/G]GAGAAGATTGGCATGACAGAGAACAGATGGGGTCA R 2 1 2 1 101000 r 74 goat snp990-scaffold1026-47546 8 71016790 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422893 Affx-122943063 AX-123293239 8 69501741 AGATGTCATTTCAGGATAAAATGCTCCAGGGTAAG[C/T]GATGGGATTGAGAAATTTTCCCTGACTGTGACCAT Y 2 1 2 1 101000 f 74 goat snp32554-scaffold372-9411 8 71080400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423422 Affx-122942615 AX-123293768 8 69551773 GTGGCAGTATCTTAGAGCAAGTTATTGGGTATACA[G/T]AAATAGAGTCATGTGCTCAGTCATGTTCAGTTCTT K 2 1 2 1 201000 f 74 goat snp32555-scaffold372-59443 8 71131637 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775640 Affx-122948435 AX-385262771 8 69611026 TAGGCTATAGCAAAAGGCTTTCTAATTAAGAGACA[C/T]GCCTTTGATTCTGACAACACAGGGCAAAACTCCAG Y 2 1 2 1 201000 r 74 goat snp32556-scaffold372-118696 8 71191521 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409592 Affx-122953566 AX-123279943 8 69660259 GATTTTAATGTAGTCACTCTTTACTGCAGCCTTCA[G/T]GAGTAGATGCAATAGGCATTACTCTGTCAAGTTTA K 2 1 2 1 101000 f 74 goat snp32557-scaffold372-167929 8 71241090 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766819 Affx-122921012 AX-385254143 8 69707936 TTCAATCAACAATGATTTTAGTGCTCTTCTAGATA[C/T]GGGAAAATGCAAGAAATTAGGCTTATAATATCGTC Y 2 1 2 1 303000 f 74 goat snp32558-scaffold372-215606 8 71292728 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390748 Affx-122967906 AX-123261105 8 69750123 GGTAGTGTTTGGGATAGGTGTTTTTTGTTTGTTTT[C/T]GGTTTTGTTTTGTTTTGATGTTGGAGGGAGAGGAA Y 2 1 2 1 103000 f 74 goat snp32559-scaffold372-257793 8 71334930 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385010 Affx-122971874 AX-123255368 8 69802696 TCCTAAGAAACTACACATTTTACACAAAAGAGAGA[C/T]ACAGAATAACCAAACAGAGAAGCATGGCAAAGAGG Y 2 1 2 1 201000 f 74 goat snp32560-scaffold372-310366 8 71387717 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799916 Affx-122936118 AX-385286842 8 69850983 TTTTAGTAGAATATTTGTTCAGTTCTGATAAACTC[A/G]TATTTATCATCTGTAAATTAAGTGCAGCAATAATG R 2 1 2 1 101000 f 74 goat snp32561-scaffold372-358653 8 71436556 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762634 Affx-986697164 AX-385250719 8 69957383 AAAACGCAAGTGGAAATGCCTTTCCCTAGTGTGGA[C/T]CGTCGGCTCCACTCCCTGGGCAGCTGACTCTCTTT Y 2 1 2 1 600010 f 74 goat 8_69957383 8 69957383 Ancestral_priority_1043 ancestry 0.542 neutral IMAGE 10K 10K ancestral 320765022 Affx-986697166 AX-385252593 8 69957546 GCAGGGGTGGGAGTCCCTCTGCCCCTCCTCCTGCA[C/T]CTTCCTCACCCAGCCCTACTGCCGTTCTGCCCCAG Y 2 1 2 1 600010 r 74 goat 8_69957546 8 69957546 Ancestral_priority_1043 ancestry 0.42 neutral IMAGE 10K 10K ancestral 38375518 Affx-122979118 AX-123245877 8 69967581 TAGAAACACTCTGTACAATGTTACTGGAACAGATC[A/G]TTCTGAGCAGGTCATTCTTCAGATAAAACTCAAAG R 2 1 2 1 101000 r 74 goat snp32564-scaffold372-475251 8 71552572 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387856 Affx-122969644 AX-123258214 8 69996639 CTTCACATTCTGAGCTACTGAGGGGTTAGGACTTG[G/T]ATTCATGCCTCTGGAGGAATGGTAAAATTCAACCC K 2 1 2 1 101000 f 74 goat snp32565-scaffold372-504309 8 71581647 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423702 Affx-122942889 AX-123294048 8 70031010 CAACCTAGAAGAGGGCCTTCACCCGGCCATGCTGA[C/T]ACCCTGATCTTGGACTTCCAGCCTCCAGTACCACT Y 2 1 2 1 201000 f 74 goat snp32566-scaffold372-538680 8 71616463 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445393 Affx-122925394 AX-123315730 8 70066555 AATTTTTCCTTCCTGCTACTTTAGAATTTCTTCTT[A/G]TCGCAAACTCCAGAAAGTGAACAGCTGAGTTTTAT R 2 1 2 1 201000 f 74 goat snp32567-scaffold372-574225 8 71652288 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777756 Affx-122924097 AX-385264874 8 70105283 TTTCACAGCTGCATGGTATCACTAATGCATGATTT[A/G]TCTAAATACCCCCTACTAATGAATTTATATAATTA R 2 1 2 1 101000 f 74 goat snp32568-scaffold372-612953 8 71691645 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765026 Affx-986697168 AX-385252597 8 70133081 GTGGTGGTAGGGAGTGCTGCTGCAGGCTCAGGAGA[C/T]CCCACAGGCACAAGGCAGCTCTGAGAGGTGGGAGG Y 2 1 2 1 600010 r 74 goat 8_70133081 8 70133081 Ancestral_priority_1043 ancestry 0.444 neutral IMAGE 10K 10K ancestral 38382798 Affx-122973572 AX-123253156 8 70144771 CAGCACTTGAAATTGTGGCTAATTTAAACAGAGAT[A/G]TACTATAAGTGTAAAATACACACTGGGTTTTGAAA R 2 1 2 1 103000 f 74 goat snp32569-scaffold372-652441 8 71731498 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779008 Affx-122924620 AX-385266115 8 70190118 AATAGTTAATGTCTCCTAGAGGAGGGTATATTGCT[C/T]AAGTTCAAGAATATGCATTATGACTGCATTTTTTA Y 2 1 2 1 101000 f 74 goat snp32570-scaffold372-697788 8 71776941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776139 Affx-122946206 AX-385263269 8 70252952 AAGTTCGTGACTTCTACATCCCTAAGTGAACATAA[C/T]GGGTCTCAATGAATAACTTACTAGTTATTTTTCCT Y 2 1 2 1 101000 f 74 goat snp32571-scaffold372-760622 8 71840165 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387168 Affx-122970627 AX-123257526 8 70285953 AAGGAAATTCTCAGAGAAAGAACCATGTAAAGGCC[A/C]CAAAAGAGCAAAGGATGTTTTCCTTTGTCAAAAAT M 2 1 2 1 102000 f 74 goat snp32572-scaffold372-793623 8 71873514 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771953 Affx-122939971 AX-385259109 8 70333591 AACATTTAGCACCTTCTTTCTGACTTTTATCCACC[A/G]CATTCATGCAAGCAGTCTTCGGTCACATAATGCAC R 2 1 2 1 101000 r 74 goat snp32573-scaffold372-841261 8 71920161 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797661 Affx-122923812 AX-385284600 8 70386933 ATTCTCAAACCAACCATTTCCATTTGGCTAAGGTT[A/G]CTTTTTCACATATAATTTGCTTCTGTCTGAAATTG R 2 1 2 1 101000 r 74 goat snp32574-scaffold372-894603 8 71973707 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788680 Affx-122940538 AX-385275696 8 70429015 TAATTACCTAAGTATCAGTTTCCTTGCTGTGAGCC[A/G]CAGATGACAGAATAGAGATAATAAAGTCCCCAGGA R 2 1 2 1 101000 f 74 goat snp32575-scaffold372-936685 8 72015558 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801390 Affx-122924127 AX-385288300 8 70470849 TCATCAATCACAGAGGGTTGGATTTATCACTCTCT[A/G]TGCTAGTCACTAACTCAAGTCTTGGCATGAAGAGA R 2 1 2 1 101000 f 74 goat snp32576-scaffold372-978519 8 72058188 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392896 Affx-122965731 AX-123263253 8 70514595 TTCTAATCTTAATCTTAGGGGTGTCTCGAATGGCT[A/G]TGTTAACGATATTGTTCTCTGCATCAGTTCCTGCC R 2 1 2 1 201000 r 74 goat snp32577-scaffold372-1022265 8 72101880 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786834 Affx-122921076 AX-385273863 8 70553058 TCAAAAGTCATTTTTCTTGCAGACAGATTTGTCTA[C/T]GAAGATTTGTCTATGTATGCAAACTTGGCCTGGCA Y 2 1 2 1 101000 r 74 goat snp32578-scaffold372-1060728 8 72140080 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437761 Affx-122931712 AX-123308099 8 70588886 ACTCGCTATTGATGTCCAATGTTAGAATTAATCTA[C/T]AGTCAAAGCATCGGCTTCCCTAGTGGGTGGCTCAG Y 2 1 2 1 201000 f 74 goat snp32579-scaffold372-1096556 8 72175274 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404690 Affx-122957272 AX-123275042 8 70631648 ATCAGATGGGAGTGGTTTGTTATTTATGACGCGTG[G/T]ATACAAGGGAGTACCATACAGTCCTTAGAATCAAA K 2 1 2 1 101000 f 74 goat snp32580-scaffold372-1139318 8 72218060 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438422 Affx-122931274 AX-123308760 8 70650997 CTCAGTCTGGCTGTCTACTGTAGCCACTTGGACTA[A/G]CTTGCCTTATGCCAGGTTCTGTTCTGTGTTTTTTT R 2 1 2 1 101000 f 74 goat snp50292-scaffold719-7258 8 72236990 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788804 Affx-122971977 AX-385275819 8 70691974 GAATCAAGGCCAAAAACTGAGAATCCATTTATTCT[C/T]TCTGAAGATTGGGGTAGGAATGAGGTAGGAAGCGA Y 2 1 2 1 102000 r 74 goat snp50293-scaffold719-48235 8 72278952 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389081 Affx-122968591 AX-123259439 8 70727744 CCATCATCCTTTCTAAGTGCTTGGAACTATTCATC[A/G]TCACAGCAGTCCTAGTCCTATAAAGTAGATGTAAT R 2 1 2 1 101000 r 74 goat snp50294-scaffold719-84005 8 72314993 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444866 Affx-122926285 AX-123315203 8 70768623 ACATCCCACGTGATTGGGGAGAATGAGCCACTCAC[A/G]TCAATCTTGAATAAAGTGATAGCAACCAAAGAAGT R 2 1 2 1 201000 r 74 goat snp50295-scaffold719-124884 8 72356188 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417272 Affx-122947254 AX-123287620 8 70822831 TCTGTGAGCTGCCCTTCTTATGCCATCACTGTTCA[C/T]AGTTCACTGAGAGCACCTGGGGCTGAACGTTGAGT Y 2 1 2 1 101000 f 74 goat snp50296-scaffold719-179092 8 72409506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440923 Affx-122929023 AX-123311260 8 70873832 TTTCCACAGAAAACGGGCTGACCTCTTTTATAACC[A/G]TATCCTATAGTTTTCGGACCTCTTGGATCTCATGT R 2 1 2 1 101000 f 74 goat snp50297-scaffold719-230093 8 72460777 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447455 Affx-122924365 AX-123317791 8 70912449 CATTCATTCATATTTTATAGCTTTGATGGCAGTGC[A/G]TTTGGATTTCACACCTATTTCAAAGCTGGCCCTGT R 2 1 2 1 101000 r 74 goat snp50298-scaffold719-268710 8 72500050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273419 Affx-1111833590 AX-519547045 8 70914683 TATTCTCCCAGATGTGAAGCTGCAGTGGTTTGTCT[A/C]ATTTGCTCCTTCCTGCCTTGATCCATTCCTTAACC M 2 1 2 1 201000 r 74 goat 8_70914683_AF-PAKI 8 70914683 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38443589 Affx-122927323 AX-123313926 8 70973649 ATTGTATGTGTCCCTGGAAACCAGGATTACTGATA[C/T]GCAAGAAAGCAGACACAGATAAAAGAAAATGTTAA Y 2 1 2 1 101000 f 74 goat snp50299-scaffold719-329910 8 72561093 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444092 Affx-122926835 AX-123314429 8 71005219 TACTTTTGCTTGTTAGTGTAATTCCTTAAGTTGCT[A/G]TAAGCTCCAAATCAGTGGAAATATGTTAGTCTAAA R 2 1 2 1 101000 r 74 goat snp50300-scaffold719-361480 8 72592875 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770722 Affx-122950189 AX-385257886 8 71057859 AGCCCTTTTCTGGATGATATGAAGAAAGACATTAA[C/T]GATTTAAGAACATCCGATCTTTGGCATTCCATGTA Y 2 1 2 1 101000 f 74 goat snp29931-scaffold326-17958 8 72645550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409486 Affx-122954054 AX-123279837 8 71170684 TGCAACAATTCAGGTCTAGGGCCAACTTCTATTAG[C/T]AAAATGTCCTTGCTCTTAAAAAGCCAAGTTACAAT Y 2 1 2 1 101000 f 74 goat snp29933-scaffold326-130783 8 72759773 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771108 Affx-122960284 AX-385258268 8 71218402 ATACTTTTATTCCCTACACAGTGGTTTTATGCTCT[A/G]TACAAATTTTTGTAATTCTGTTGGTTTTACTTGCA R 2 1 2 1 101000 f 74 goat snp29934-scaffold326-178501 8 72807684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383979 Affx-122972933 AX-123254337 8 71251334 ATGTTCCAAGCCCACCATATGACATATAATAAATG[C/T]TGAATAAATTATTATAAAATGAAACAATAAAACAG Y 2 1 2 1 103000 f 74 goat snp29935-scaffold326-211433 8 72840978 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379317 Affx-122976191 AX-123249676 8 71288783 CTGCTCAGATAATGTCAGTTGGTCACTTTTCCTTG[A/G]AAACAGGGGACACATGACTTATGATTCAAACCGAG R 2 1 2 1 101000 f 74 goat snp29936-scaffold326-248882 8 72891254 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399008 Affx-122960940 AX-123269363 8 71320521 GGAAATAAAAAATAAAAGAGAGAATGAGTGAAGGA[A/G]CCATGCTTCAGATATTATCACAGAGACATTCAACA R 2 1 2 1 101000 r 74 goat snp29937-scaffold326-280620 8 72922898 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448728 Affx-122923838 AX-123319064 8 71377899 AAAATCTCGAGTATTTTAACAAACAGATGGAGAGT[A/G]TTCCTTCCAAAAGGACTTCTCAGTCTCATCAATGT R 2 1 2 1 101000 r 74 goat snp29938-scaffold326-337998 8 72980248 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408314 Affx-122953768 AX-123278665 8 71423708 CAGTCATGTGCCTGGGCCCAACTGACAGATCTCTG[C/T]ACATTTAACCTCAGCCTCAAAATGTTAGTCCTGGA Y 2 1 2 1 201000 r 74 goat snp29939-scaffold326-383807 8 73025963 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406121 Affx-122956203 AX-123276473 8 71456150 TCACCTTGGTTTAACCAAGACCTAGAGAAATGACT[C/T]GCTACTGAAGGTCAAGACTTTCTTCTCCTTGACAC Y 2 1 2 1 101000 f 74 goat snp29940-scaffold326-416249 8 73058393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796057 Affx-122934880 AX-385283009 8 71492992 CCTCAACATCAAGTCGCATTTATGAAGCACAAATA[G/T]ATTTTGTATTGCGTGCCAAGCCCTGGGAAAGATGG K 2 1 2 1 101000 f 74 goat snp29941-scaffold326-453091 8 73095209 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428989 Affx-122938854 AX-123299331 8 71526175 CACGATTTCGTAGACTCTTCACAGCACTGGGCTCC[A/G]CTACCCTGGCGATGAGGAGTCTGCAGAGATGGCAC R 2 1 2 1 101000 f 74 goat snp29942-scaffold326-486274 8 73128419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795702 Affx-122978779 AX-385282655 8 71554996 ATTTAAATATACCTACAACTAAACTTATATTCAAA[C/T]TCATCTTCTAAGATTTTGGTCCTTATTGTTGAAAG Y 2 1 2 1 101000 r 74 goat snp10602-scaffold1376-3046065 8 73156732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442593 Affx-122928488 AX-123312930 8 71585475 TGTGTATTTTCAGAATACTCAGCACCCAGACCCAG[C/T]GCCTGGCAGCGTAGCAAGCCTTCTTGTGATTGACT Y 2 1 2 1 202000 r 74 goat snp10601-scaffold1376-3015586 8 73187572 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443210 Affx-122927581 AX-123313547 8 71619428 TGACCAAGGAACCTTGTTGGAGCACAGAATCACAG[C/T]GGATAAGTGAGCACTGAAGGGAGCTCTGTCTAGGG Y 2 1 2 1 101000 f 74 goat snp10600-scaffold1376-2981633 8 73221859 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395132 Affx-122964136 AX-123265487 8 71672929 GTTGGTCATTTGAGTAATTTTCAGTTCTTATTATT[A/G]CACATGGTCTATTTTTAATCGTGTAGAGATTCCTA R 2 1 2 1 101000 r 74 goat snp10599-scaffold1376-2928132 8 73276006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404424 Affx-122956767 AX-123274776 8 71706543 GCTGCTTTGGTTTGACGTTGTAGAGTCATCCCCAC[G/T]CTTCTTTGTCGCGGGAGTGAATTCCTCTGCAGAAA K 2 1 2 1 101000 f 74 goat snp10598-scaffold1376-2894518 8 73309098 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798791 Affx-122952436 AX-385285722 8 71736657 TATCTGAATTTTTAACAATCCTATGCTCACAAGTC[A/G]AATTTGAACAAATTAACAAATTATGAGAATTGTCA R 2 1 2 1 202000 r 74 goat snp10597-scaffold1376-2864404 8 73335157 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410249 Affx-122952537 AX-123280599 8 71766028 AAGAACAACGTAAAGTGCTAGCGGCCTACATAATA[A/G]GCCTTTCCTCAGCCTCTGACTCAGTGAACCAGAAC R 2 1 2 1 101000 f 74 goat snp10596-scaffold1376-2835033 8 73364651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799383 Affx-122933359 AX-385286313 8 71811266 TACTAAGAGTGAAATAGTAAATTTCTTTCCTCTAA[C/T]AGAATTCACATTTGAATAAGATGTTCAGTTCAAAT Y 2 1 2 1 201000 r 74 goat snp10595-scaffold1376-2789795 8 73410096 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796842 Affx-122927263 AX-385283785 8 71849351 GTAAGTGATGCTTCCTAAAACAAGAAGCCTGTATT[G/T]ATACCACAAATTGGAACTCATTCCAAAGCCTCTTA K 2 1 2 1 101000 f 74 goat snp10594-scaffold1376-2751710 8 73448168 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414395 Affx-122949988 AX-123284744 8 71878607 TGGAGAAGTCCCAGGAGGCAATGCATGTATAAAGA[C/T]ATTGTCTAAATAAAGTTGGGGGCTTCCCTGGTGGT Y 2 1 2 1 101000 f 74 goat snp10593-scaffold1376-2722454 8 73477423 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389387 Affx-122968390 AX-123259745 8 71908515 GCAGACAGGTACACAGACAGGATGCCAACATACAA[A/C]TCAACCAGAGTGGGCCGGCCACATCCCCCGGGATT M 2 1 2 1 101000 f 74 goat snp10592-scaffold1376-2692546 8 73507404 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444318 Affx-122926740 AX-123314655 8 71939450 CATCTCCCCTTGCAAACACCTTTGCTCCCTCCTGG[C/T]AAATGCTAACTCACTCTGCCCCACCAGCCACTGTG Y 2 1 2 1 101000 r 74 goat snp10591-scaffold1376-2661611 8 73538324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448190 Affx-122924243 AX-123318526 8 71971121 AAACTTCCTGTCTTTCCCAGGGGCACCAAACTGTG[A/C]TTCCCCCACCTACCCCCACCACTTCCCAATATCAC M 2 1 2 1 201000 f 74 goat snp10590-scaffold1376-2629940 8 73569945 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411168 Affx-122951866 AX-123281518 8 72006536 TGTTGTCCTGGCATAACAATTGTTGCTGTTCTGTC[A/G]CTCAGTCATGTCCTCAGTCATGTCCGACTCTTTGT R 2 1 2 1 101000 f 74 goat snp10589-scaffold1376-2594525 8 73606016 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397179 Affx-122962416 AX-123267534 8 72035821 AGAATGGCAGAACAAGGATATTAAGCCCTCGGTGC[A/G]TGCAAAACATTCCAAGTGATTTCCGCTTTTGCTTT R 2 1 2 1 201000 r 74 goat snp10588-scaffold1376-2565240 8 73635164 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386536 Affx-122970728 AX-123256894 8 72065188 CAAAGGCACATCCTGGGGATATGAGTGGGTAGCAC[A/G]AGTTTTATACAGACTAGGACAGCATCTTACAATGG R 2 1 2 1 101000 r 74 goat snp10587-scaffold1376-2535873 8 73664501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408108 Affx-122954259 AX-123278459 8 72095628 GGTTCAATCCCTGGTCAGAGAACTAAGGTCCCACA[C/T]ACTGCATCGTGCAGCAACCCCCCACCCAGAAAAAA Y 2 1 2 1 103000 r 74 goat snp10586-scaffold1376-2505433 8 73694748 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800689 Affx-122946661 AX-385287607 8 72127541 GAGTGTTCAAAAGCACAGATGCCCTCATCCTCTCA[C/T]ACCACTCATTCTAGTATTATCCTCCTATCTGATTC Y 2 1 2 1 101000 f 74 goat snp10585-scaffold1376-2473520 8 73726599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278805 Affx-1111836521 AX-519552278 8 72145644 ATACTAAAAGCTTTAACCACAAAAGAAAAAGAAGC[A/G]ATAAATTGGACTTTATTGTAGTTAAAATCTTCTAT R 2 1 2 1 202000 r 74 goat Random2.2K-921 8 72145644 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413145 Affx-122950359 AX-123283494 8 72182365 ATTATTAATCCTTATTGTGATGATTAATACTTTTT[A/G]TTATCCTTATCAAGCTTCAAACCATGCCAGCTTTG R 2 1 2 1 101000 r 74 goat snp10584-scaffold1376-2418696 8 73781956 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421025 Affx-122944543 AX-123291372 8 72227526 GCCTCCAAAACTGAGGTAACAGATTGGAGAATCTA[C/T]AGGCTGTCTATGTGAATTGGGTGGCCTGTGCAGCT Y 2 1 2 1 101000 f 74 goat snp10583-scaffold1376-2373535 8 73826184 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409851 Affx-122952929 AX-123280202 8 72288707 TTTGACAGTCTGAAAACAGAAAAAGTCCTTCTGGA[C/T]GTAGTGATGTCTGTGGACAAAGGAACAATGACTAG Y 2 1 2 1 201000 r 74 goat snp10581-scaffold1376-2312354 8 73887105 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381941 Affx-122974124 AX-123252299 8 72324912 GCGAAGAGGGCTCTCTATTGGGCAAGAGTGTATCT[A/G]ATAGAGAAAAAGAAAAAAAGTGTTTCTTTAAAAAG R 2 1 2 1 101000 f 74 goat snp10580-scaffold1376-2276149 8 73923849 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449325 Affx-122922991 AX-123319660 8 72364605 CTTCACTAGATCTCAGTTGTATACCCCTGGTTTGT[A/G]TAGGAGCTAAAATAATATTTTGATGTAGTTTGACT R 2 1 2 1 101000 f 74 goat snp10579-scaffold1376-2236456 8 73964077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273849 Affx-1111833855 AX-519547459 8 72376045 TGGTCCTTCTGCCCC[A/G]CTCAGACATTTATTCTTGTCTTTTCAGCCAGAGAT R 2 1 2 1 102000 r 74 goat GoatD01.007762 8 72376045 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386703 Affx-122970168 AX-123257061 8 72415408 CTTTAAAAAGGCAACATGGAAAGAAACTGTGGTCC[A/G]TCCAGGCAACGGAAGATTATTCAAAGCCAAAGAGA R 2 1 2 1 101000 r 74 goat snp10578-scaffold1376-2185653 8 74014558 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454029 Affx-122919415 AX-123324362 8 72448391 GTGTCTTATCTTTACTTTCTTTACTTTCCTTAAAG[A/G]TTTTTAATGGTTCTTTATTCCCCAGACCAGAGAAT R 2 1 2 1 303000 f 74 goat snp10577-scaffold1376-2152670 8 74047879 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423051 Affx-122942961 AX-123293397 8 72519056 TAATTTAGTAATTCTTAACCATATAAAATTACACA[A/G]GCAGTATATGCTAATTTATGTGTTTAGCTTTTCAT R 2 1 2 1 101000 r 74 goat snp10576-scaffold1376-2082005 8 74118547 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446808 Affx-122925290 AX-123317144 8 72562145 GGCCACGTGCTTTGTCAGATATCCAGTGACTGCCG[C/T]GGGGTTACTGCTTGGAGGTTCCTCCTTCTTCATTT Y 2 1 2 1 201000 f 74 goat snp10575-scaffold1376-2038916 8 74162125 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452625 Affx-122920359 AX-123322958 8 72592894 TGATTTGTGTGTTGGAGACTACTTTGGCAACCACA[C/T]GAGGAACTCCACCAAAAATAACAACCATAGCAGAC Y 2 1 2 1 101000 f 74 goat snp10574-scaffold1376-2008167 8 74193578 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375612 Affx-122978714 AX-123245971 8 72633168 CTCCCGGTGAACCTCAGCAGCCCCACTGGAAAGGA[A/G]TGAGTTCTCTTAACAAGAACTGCAAGACAGTGTTG R 2 1 2 1 102000 r 74 goat snp10573-scaffold1376-1967893 8 74231928 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416855 Affx-122948097 AX-123287203 8 72707941 TTCAGGTAAGGAAGAGTATGAAGTGTACTGTCTGG[A/G]GGGCTGCCTGGTACTGAGCAGGCTTTTACCAGAAG R 2 1 2 1 101000 f 74 goat snp10571-scaffold1376-1893120 8 74306734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428051 Affx-122939127 AX-123298394 8 72746520 TCTGGCCACTCTGATGAACAAGACACACAGGCCGC[A/G]TGGGACTGCTTGGAGTAACAGTCAGAAGACCTGAT R 2 1 2 1 101000 r 74 goat snp10570-scaffold1376-1854541 8 74345201 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386265 Affx-122970949 AX-123256623 8 72794174 ACAAGCACTGTGCTAAGCACTTTTCAATCTTCATA[A/G]CAGCCTAGGAGATGGACAGTGTTATTTGTCTCATT R 2 1 2 1 101000 r 74 goat snp10569-scaffold1376-1806887 8 74393542 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423038 Affx-122942973 AX-123293384 8 72838221 TACTGGTTCCTGGAAGTAGAGCTGATAATTGAAGG[A/C]GGGGTTGGCCTTGATGATCTCCATGGAGGACACTT M 2 1 2 1 101000 f 74 goat snp10568-scaffold1376-1762840 8 74438126 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382978 Affx-122973349 AX-123253336 8 72908958 TCACATGACTTAGTGACTAAACCTAAACCAATAGA[A/G]GTGATTACAACCAGCATGATGTAGTGTGCTTAGAA R 2 1 2 1 101000 r 74 goat snp10567-scaffold1376-1692103 8 74508923 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799100 Affx-122974012 AX-385286030 8 72995797 CCTGTTCTTTCAAGATGTTACTCCCAACAGTTACT[A/G]TAGTCCTATTCCAGTCAAATGTTGCAACCAAGCTT R 2 1 2 1 101000 r 74 goat snp10565-scaffold1376-1605264 8 74595707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385771 Affx-122971059 AX-123256129 8 73028181 AGGAAACCATGAGGATAAAGGAAGGAGTTTAGATT[G/T]CCAGGACAGAATTTAAGTTAGAGTTGTTAAAGAAC K 2 1 2 1 101000 r 74 goat snp10564-scaffold1376-1572880 8 74628423 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406941 Affx-122955072 AX-123277292 8 73060888 TTTCCTAAAACTGGCCTGTGGCACTCAGGGTCAAA[C/T]AGACTGTCCATTCTCCAGCATGAATGTGCCTTTTA Y 2 1 2 1 201000 f 74 goat snp10563-scaffold1376-1540173 8 74660350 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451129 Affx-122921377 AX-123321463 8 73104957 TTCGGTGACATCCACAGGGTTCCACCTGTCCCTTA[A/G]CTTGGTGAGGGACCGTGGCTGTGATTGCAAAAGCC R 2 1 2 1 101000 f 74 goat snp10562-scaffold1376-1496104 8 74705628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377310 Affx-122977687 AX-123247669 8 73194248 GGTCATCTGGGTCCGCTCCCCTTTTCCACTCAGGC[C/T]TTCCTTCAGCAGCCCTACAAAGAAGTCATTCATCC Y 2 1 2 1 101000 r 74 goat snp10560-scaffold1376-1406813 8 74795117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414333 Affx-122950034 AX-123284682 8 73264665 CTGAACTCTATTACAAAAACCAAGGAATCAGATTC[G/T]TTCTTAAAAGTAGGGATATCCTACCTTGCATAGGT K 2 1 2 1 101000 r 74 goat snp10558-scaffold1376-1336396 8 74864035 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427100 Affx-122939782 AX-123297443 8 73295347 TTAAATGTTCTACCAGTTTTTTCCAGGAGAAAGCA[C/T]GGGATAGTCAAGTGTAAACAGGTAGATGAAATCCA Y 2 1 2 1 201000 r 74 goat snp10557-scaffold1376-1305714 8 74894814 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415918 Affx-122948456 AX-123286267 8 73355317 ACAGAGGGTTCAGACAGAAAGGGTCCAAGGGAGAC[A/C]AGGTGCTCAGGGAAGAATGAGAGGGGAGATGGTGA M 2 1 2 1 101000 f 74 goat snp10556-scaffold1376-1245744 8 74954797 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383302 Affx-122972707 AX-123253660 8 73407238 GAGGCTGTCAGAGAAGAAGAAAGAGCGGATTGATG[A/C]TTTCCTACGGGAGGTCAACCAGCGGATCATGAGGG M 2 1 2 1 201000 r 74 goat snp10555-scaffold1376-1193823 8 75006989 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389550 Affx-122968270 AX-123259908 8 73441679 CTGAAGGTTCAATGGTTAACATTCCACGGTTTCAC[C/T]GCAGGGGATGGGTTCAATTCTGGTCGAGATTCTGC Y 2 1 2 1 101000 f 74 goat snp10554-scaffold1376-1159382 8 75041515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430531 Affx-122937203 AX-123300872 8 73482173 TATCACACTCCTTAGCTCCCCTTGTCTCCTTTTTA[A/C]TTTGATGTGCTCTCATATAACTTTTCCCAGATTCT M 2 1 2 1 201000 r 74 goat snp10553-scaffold1376-1118888 8 75082888 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413292 Affx-122950201 AX-123283641 8 73511525 TCTTTCTTTAGGCCATTCTGTGTGGTTTGCAGGAT[A/C]TTAGTTCCCTGACCAGGGACTGAACCCTGCTAAGG M 2 1 2 1 103000 f 74 goat snp10552-scaffold1376-1089536 8 75112273 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273421 Affx-1111833591 AX-519547047 8 73514309 CCCTCTTTGAGATAAATCTAACCTAGATTAGACAA[A/C]CAAAGACTTGTAGACGTGGAGGAATTTATAACGCT M 2 1 2 1 101000 r 74 goat 8_73514309_AF-PAKI 8 73514309 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38431794 Affx-122936124 AX-123302135 8 73546351 GAACATTCAACATAAACCAAATTGTATAAATAATC[A/G]AGGTAAAGAAAGTCCCTTTTATCAGTTAGAGCATT R 2 1 2 1 101000 r 74 goat snp10551-scaffold1376-1054710 8 75147130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409040 Affx-122953858 AX-123279391 8 73577467 ATGAACCCAGGTCTGTCTTCTGAGGTATTAGATGA[A/G]AACAGGTATTTGTACCAGGTCATGATAAAGGGAAA R 2 1 2 1 101000 f 74 goat snp10550-scaffold1376-1023594 8 75178681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780048 Affx-122958237 AX-385267146 8 73616304 TTGTTTGCTATTAGAGTGCAGTAACATGCCTGTAG[C/T]TTAAGCATTCCAGTTGACAGAGAACATATTAAGAA Y 2 1 2 1 101000 f 74 goat snp10549-scaffold1376-984757 8 75217496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383161 Affx-122973232 AX-123253519 8 73649291 CAGCCAGCATTTCCCCATGTTTTGGCACATTCTTC[A/G]TAAATGTTATTTATAAAAGCTTCGTTGTGTGGGAT R 2 1 2 1 101000 f 74 goat snp10548-scaffold1376-951770 8 75250816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786045 Affx-122944502 AX-385273081 8 73720457 ATAGATTTACTCAAGATTCTGAAAGCAAGTTATTG[C/T]AGCATTACTCTCATCACAGTCTCTTCCCTGTACCT Y 2 1 2 1 101000 r 74 goat snp10546-scaffold1376-880604 8 75321900 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445816 Affx-122926030 AX-123316153 8 73764143 CCCAGCTTGGGAAAATATATATAACCTGTGTGTAC[A/G]GTTCAGGTTGTGCTTTTAAAATCCTTTTAAAACCC R 2 1 2 1 101000 r 74 goat snp10545-scaffold1376-836918 8 75365691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802269 Affx-122976682 AX-385289173 8 73797443 CATTTTTTTCTAAATCTCTGTTGAAAGCAGGAGAA[G/T]CTAAGCATCTAGATGCAGGAAATTAGTGTTTTCAT K 2 1 2 1 101000 f 74 goat snp10544-scaffold1376-803618 8 75399168 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439065 Affx-122930317 AX-123309402 8 73842425 TGTGGTTTTAGCAACCATCAGTGAGCATTACTTTT[A/G]TCCCATTGCTTTATTAGGGATTCCAAAATGGTGAT R 2 1 2 1 101000 f 74 goat snp10543-scaffold1376-758636 8 75443989 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401508 Affx-122958934 AX-123271861 8 73952391 GTAAAACTAAGTGTGATTTTTTTTATTTTAGCATA[C/T]ATCACTTTATAATAGAAAAATCTATTAAACTCGCC Y 2 1 2 1 101000 f 74 goat snp10541-scaffold1376-648670 8 75555563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436918 Affx-122933201 AX-123307256 8 73988634 TTATGTAAGTATGGAACTTTTTCCTTGTTATATCT[A/G]TTAACATCTTACAGAACCGTTGTGTTTTGTGGAAT R 2 1 2 1 101000 r 74 goat snp10540-scaffold1376-612427 8 75591723 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444827 Affx-122926317 AX-123315164 8 74020716 GACAAAGACAGCACTAAAAGCACCCTAAATCCAGA[C/T]GGATGGGAAACCATCCTAACCAGTACATTTTGAAC Y 2 1 2 1 101000 f 74 goat snp10539-scaffold1376-580345 8 75623762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403174 Affx-122958080 AX-123273527 8 74063715 CTCCTAGCACCCAAATGGACAGGACTGGGATCTAG[G/T]GTTTGGGATTTTTAATTTGGACCCTTGGGCTCTGG K 2 1 2 1 101000 r 74 goat snp10538-scaffold1376-537346 8 75666788 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426428 Affx-122940823 AX-123296774 8 74107662 TTGTGCCGTCGGGTGGGTGTCCTTCTCTTGTGGCT[A/G]TTCCTGCCTGCCCCAATATTAGTGAGCCATGCTGG R 2 1 2 1 101000 r 74 goat snp10537-scaffold1376-493399 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422820 Affx-122943193 AX-123293166 8 74159226 ATGGTAGAGACGTGTAGCCCAGAGGAAGAGAGGCT[A/G]TACGATGAGTGGATTAATTAACTGTGGCATATCTG R 2 1 2 1 201000 r 74 goat snp10536-scaffold1376-441835 8 75810429 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782624 Affx-122933814 AX-385269697 8 74216412 GACTTAACATTTTAAGGGTATCATCTAATGTAAGA[C/T]CATTTTTGTCTATACAACCAAAAAGATGCACTGAT Y 2 1 2 1 201000 f 74 goat snp10535-scaffold1376-384649 8 75867697 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785987 Affx-122934330 AX-385273023 8 74284519 CCATTGAGAAACTGAAGACAACTTTACAGCACAAG[G/T]ATCTGGCCTTCTTGTCAGGACTGCCTGCTCCTTAT K 2 1 2 1 102000 f 74 goat snp10534-scaffold1376-316542 8 75936721 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412791 Affx-122950494 AX-123283140 8 74354349 GTATACATGTTACTGTGTTGTCTTTATTTATTTTC[C/T]CCCCAGTGTCTATATTTGTCTTACAGTATGTATAT Y 2 1 2 1 101000 r 74 goat snp10533-scaffold1376-246712 8 76003633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442015 Affx-122928414 AX-123312352 8 74404275 CTAGCACACAGTGGATACCTGACCACAGACCACCC[A/G]TTATAACTTCATGTTTTGTTCATTATAACATCTTC R 2 1 2 1 201000 r 74 goat snp10532-scaffold1376-196786 8 76053707 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799155 Affx-122959498 AX-385286085 8 74436847 TTTGGATGGTGTTTGTAGTGTTTAAAGATAAACAT[A/G]TTTGTCACTCATGTGACCAATCATGTCCGGTGTTC R 2 1 2 1 101000 r 74 goat snp10531-scaffold1376-164214 8 76086143 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415585 Affx-122948625 AX-123285934 8 74469352 GGGTGGCAATATAATAGGCAAACAACAGCAAGTCT[A/G]CTCTTCAGAATAGCAAAATTATAAAATATTCACTC R 2 1 2 1 101000 f 74 goat snp10530-scaffold1376-131709 8 76118406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405971 Affx-122955533 AX-123276323 8 74509031 GAATAAAACCAGGGAAAGGAGGAGATAATGAACTC[A/G]CAAAGGGAGGAGGATGGGAGTCCACTGGATGAGGC R 2 1 2 1 101000 f 74 goat snp10529-scaffold1376-92030 8 76156896 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439190 Affx-122931047 AX-123309527 8 74557439 AATGACCCCATAACTAGATAGTAAGTGGGACAAAC[A/G]CTCTCGTACCTTCCTTCATGCCACTGAATCCATGA R 2 1 2 1 201000 r 74 goat snp10528-scaffold1376-43622 8 76205533 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783138 Affx-122949203 AX-385270205 8 74594746 ACAGTTGGAAGTCTGCATGCTACTTAAAGTGGATA[G/T]AAAACATTTTATGGACTGATAGCACATGCGGAATA K 2 1 2 1 101000 f 74 goat snp10527-scaffold1376-6315 8 76243631 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397677 Affx-122962588 AX-123268032 8 74609866 ACCAGGTAGTCAGTCATTTGTATAATTCAATTTCC[C/T]CCTTTGTAAAATGAGACATTATCTGTCCTATCCAT Y 2 1 2 1 101000 f 74 goat snp15573-scaffold1648-8706 8 76258916 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386408 Affx-122970821 AX-123256766 8 74641787 GCTCCTGCCCTTCTAAGTCCCATGCAGAGGCCACT[A/G]CCTCAGAACAGCCTCTTGGTGGAAGGCCTCACAGC R 2 1 2 1 201000 f 74 goat snp15574-scaffold1648-40627 8 76290569 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427279 Affx-122939535 AX-123297622 8 74677689 TGGGTACTTCTCCTTTCAGAAAAACTTGTGAGATA[C/T]AATGGCCTTGAACTGCCAAACACAGCAAATAAGTA Y 2 1 2 1 101000 r 74 goat snp15575-scaffold1648-76529 8 76326488 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778936 Affx-122920106 AX-385266043 8 74743441 ATGGCTTTTTATAGTGAAAGGTGGCTTTTTCTCTA[C/T]AATAAGATACTGTCTGAGAAGCTTCAGCAAACTCT Y 2 1 2 1 101000 r 74 goat snp15577-scaffold1648-142281 8 76393166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427458 Affx-122940029 AX-123297801 8 74773985 TGTTATACTACCAAATGTCTGTTGTAAGACCTGAC[A/G]CAAATATTTGATTCTTCCTGAAATGATGGAATTGA R 2 1 2 1 101000 f 74 goat snp15578-scaffold1648-172825 8 76423475 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420129 Affx-122946009 AX-123290477 8 74807473 GGGCAAAATGCATCTCATCAGCCTTCTCTCTACTC[C/T]TCTTCAGAACAGCAGGGTTTCCATGTGGCAGCCTG Y 2 1 2 1 101000 f 74 goat snp15579-scaffold1648-206313 8 76456884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409534 Affx-122953613 AX-123279885 8 74838054 GAGTATACCCAACTTCAGTAACCACATGAATCAAA[C/T]GAACGTAATGTGTACCTATTTCAGATCCTATGTGA Y 2 1 2 1 101000 f 74 goat snp15580-scaffold1648-236894 8 76487534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396218 Affx-122963352 AX-123266573 8 74867429 CCGAAGGAGTACCCAGCACCAGAAGAGAAGGCCAC[A/G]TACCACGTTGCCTGGCAAAGTTGGAGTTTAGTTGA R 2 1 2 1 101000 r 74 goat snp15581-scaffold1648-266269 8 76516955 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777103 Affx-122948867 AX-385264226 8 74922454 CAGAGGCATCAAGCATTCCTATGCACTCTTGTGCC[A/C]TTCTCTTATGAGAATATGTCCCAAAGAAACACTGC M 2 1 2 1 102000 f 74 goat snp15582-scaffold1648-321294 8 76571721 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423213 Affx-122942707 AX-123293559 8 74951593 TGAGTTAAATTTAGATGGTAGTTACACTTGCTCTG[C/T]GACCTTGAGAAAATCTTCATCTAATTTCTTTCCAC Y 2 1 2 1 101000 f 74 goat snp15583-scaffold1648-350433 8 76598822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449479 Affx-122922641 AX-123319814 8 74986372 CATTCTTGATCATGCTTGTACTTGGACAAATAAAT[G/T]AAACTTGGCTATCCTTGGCACCCTCTGGAGACTGG K 2 1 2 1 201000 f 74 goat snp15584-scaffold1648-385212 8 76633668 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405027 Affx-122956369 AX-123275379 8 75091120 CAACACAACATTTTCCCTGCAAATTGAAATTCTTA[C/T]CTCTCATTTTTACTTCATTGTTTTACCCATCCGTT Y 2 1 2 1 101000 f 74 goat snp57819-scaffold932-69105 8 76716480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401271 Affx-122959283 AX-123271624 8 75120769 GCTTTGTGAGACCTGGGGTAGCAGCTTTCAGAACC[A/G]AAGGTATACCACTAGCTCCCTGAAGTCCACTCTTT R 2 1 2 1 101000 r 74 goat snp57820-scaffold932-98754 8 76745896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438264 Affx-122931413 AX-123308602 8 75242723 ATGAGTGATAACTAGTTTACCCAAACTGAGAAATT[G/T]AGTACCTAAGCTTTTGGGAGGGGTTTGAGCCAGCC K 2 1 2 1 201000 f 74 goat snp57823-scaffold932-220708 8 76867333 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774453 Affx-122948135 AX-385261589 8 75272799 CAAATCTAGAAAACATCCAACTAATAGTGCCTGAA[G/T]AATATATGGATTAAATTCTTTGGATTTTAAAACTA K 2 1 2 1 201000 r 74 goat snp57824-scaffold932-250784 8 76897351 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275523 Affx-1111834950 AX-519549095 8 75352080 TGGTTCACTAATTGTAACAGATGTACCACACTAAG[A/G]CAGTATGTTAATAGTAGGGGAAACTGCAGTGGAGC R 2 1 2 1 201000 f 74 goat GoatD01.059677 8 75352080 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402456 Affx-122958611 AX-123272809 8 75365055 AATATTGCTTATTTTTACATAAAACTGGAAACAAT[A/G]AGATATAAACTTTAATTTAAAAATAAAACTATATA R 2 1 2 1 303000 r 74 goat snp57826-scaffold932-343040 8 76989885 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792432 Affx-122947467 AX-385279413 8 75469388 TTATACCTGGAGTGGATAAATTGGGTCCAATCATA[C/T]GTATCAAGTATCATTAGGATGCCGTGTTGAGAAGA Y 2 1 2 1 101000 f 74 goat snp57828-scaffold932-447373 8 77094121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398516 Affx-122961547 AX-123268871 8 75512078 GACTCTGTGCTGAAAGCCACCATTCTATAAACTTT[A/G]TCCACAAACAGAAACACAAACACAAAGCTTTTTTG R 2 1 2 1 101000 f 74 goat snp57829-scaffold932-490063 8 77137181 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38390278 Affx-122967738 AX-123260635 8 75549505 ATGTGAAGGTGTGTTGACACATTGAATTAAAAGTA[C/T]AGAAATTCATTTTCCTAAATACCATAGGAATTTAT Y 2 1 2 1 101000 f 74 goat snp57830-scaffold932-527490 8 77174913 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418101 Affx-122947136 AX-123288449 8 75619848 ACCACCAACTGTGGGGATGTGAGCAGCTGGGCAAG[C/T]CCCGGATGCCCAGGCAGCTTCAGGAATCCTCAGAA Y 2 1 2 1 303000 f 74 goat snp57832-scaffold932-597833 8 77249441 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417901 Affx-122946742 AX-123288249 8 75700630 CCAAGCACTCTCATTTACTCCTTTACCAAATACTT[A/C]CTGTGCGCCTACTATGCCAGAGACCCTGTATTAGT M 2 1 2 1 101000 f 74 goat snp57834-scaffold932-678615 8 77329466 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278807 Affx-1111836522 AX-519552280 8 75708610 CAACCCCTCGTGTGACCCCCGACTTCACTCAGTGG[A/G]GGAGTCCGTGAGGCCCAGACCCTTGGCCCAGATCA R 2 1 2 1 202000 r 74 goat Random2.2K-926 8 75708610 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320762644 Affx-986697174 AX-385250728 8 75718207 ATGTTGCCTAGTAGATCACAGCCTTATTGTAAAAG[A/G]TAATAAACTCAGGAACAGCAGATGGAGGGGGATAC R 2 1 2 1 600010 f 74 goat 8_75718207 8 75718207 Ancestral_priority_1043 ancestry 0.534 neutral IMAGE 10K 10K ancestral 320762610 Affx-986697140 AX-385250700 8 75718326 GCCTCACTTTCCCCAAATCTGCATGTGTTCCTCAA[C/G]CCAGAAGCTGTCCAGACCCTGTTTGGGGGTTTTTA S 4 1 2 1 600010 f 74 goat 8_75718326 8 75718326 Ancestral_priority_1043 ancestry 0.458 neutral IMAGE 10K 10K ancestral 38448256 Affx-122924196 AX-123318592 8 75734448 TGGAGACTGAGTACAGCCTTGGCAAACAGCAGAGA[C/T]AGGGCAATGGGTGCCCCAGGCAGAATTGCTTTGCC Y 2 1 2 1 101000 f 74 goat snp57835-scaffold932-712433 8 77363836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765040 Affx-986697177 AX-385252609 8 75757138 AAGACTGTGAAGTCTATGCATGGTTAAAGCTCGAA[A/G]TGCTTCACATCAAAGTTCAAGTAACTGTTCCTTTA R 2 1 2 1 600010 r 74 goat 8_75757138 8 75757138 Ancestral_priority_1043 ancestry 0.738 recommended IMAGE 10K 10K ancestral 38446872 Affx-122925240 AX-123317208 8 75774785 TGTTCTTAATACTGGGGATACAGCAGTGGACAAAA[C/T]GGGGAGAAACACTCTATCTCTATGGAGCTTATATT Y 2 1 2 1 103000 f 74 goat snp57836-scaffold932-752770 8 77404834 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385791 Affx-122971044 AX-123256149 8 75807445 AATAAAACTATTTACAAAGACAAGTCTCAAGTCAC[A/G]TTTGGCCAGTGGGCTTGTGTTTGCTGACCCCTGAC R 2 1 2 1 201000 f 74 goat snp57837-scaffold932-785430 8 77437771 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435509 Affx-122933418 AX-123305849 8 75856248 GTCAGTACAAGAAAAACTCTTTTCCAGTCTAAGTA[C/T]GTTATTTCTCTCTTTTAAAAGGAAATTCCATCCTG Y 2 1 2 1 102000 f 74 goat snp57838-scaffold932-834233 8 77486749 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422708 Affx-122943647 AX-123293054 8 75895899 GCCTCAATTAAATGGGGGAGGAGACCAGGGAGTAA[A/G]TGCCCCAGCTGTCCATTGCTGAGGTAGGCAACTCT R 2 1 2 1 101000 f 74 goat snp57839-scaffold932-873884 8 77526983 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392233 Affx-122967578 AX-123262590 8 75939196 CCTTCACTGACTGACTTATTTTTTCCTCACAGCAG[A/G]TCTAGCTAAGGAAGGGTGAGTCCTCCAAACTTTGA R 2 1 2 1 101000 r 74 goat snp57840-scaffold932-917181 8 77571173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801325 Affx-122922169 AX-385288237 8 75979744 GTTCTTAGTCTTATTTGAAATATCACATCCACCAA[G/T]AAGCTGTGCGTCTCATCCATCCTGAAGTAGGTTTT K 2 1 2 1 101000 r 74 goat snp57841-scaffold932-957729 8 77612074 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419461 Affx-122945486 AX-123289809 8 76014536 GTAAACAGTACCCATCTGCTGAAGAGCCATTCCAG[G/T]TTGGAGAGTCCACCAGGCCCAACCACATAGGTGGG K 2 1 2 1 101000 f 74 goat snp57842-scaffold932-992521 8 77646982 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383011 Affx-122973322 AX-123253369 8 76060148 GAGTCCAAAGGATACTGGTGGTCAGTGGGTGATAA[C/T]GTCTTTGGAATTGTAAGATTACTGGGGATGGCTCT Y 2 1 2 1 101000 f 74 goat snp57843-scaffold932-1038133 8 77693094 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380771 Affx-122975113 AX-123251129 8 76159293 TTGTCTGATGTTCAAGTACTATCTTCTGAAGAGTC[C/T]GTTGAGTACCTCCAGGTGCTACACTCACTAGTACC Y 2 1 2 1 101000 f 74 goat snp43699-scaffold585-2967031 8 77793741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452969 Affx-122920158 AX-123323302 8 76191763 TCCCACACTCTTAATTCTGGTCTTTACACAATCTT[A/C]TTTTACAGGTACGGGAAAGGCTCAGTTGGGTGGTT M 2 1 2 1 101000 r 74 goat snp43698-scaffold585-2934561 8 77826082 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273384 Affx-1111833592 AX-519547016 8 76199969 GATTAAAAATCATGGGTTTTGGGGTGGGACTATAA[A/C]TGACACAGAAGATTATTTTAAAAGAGGTTTCTGGC M 2 1 2 1 101000 f 74 goat 8_76199969_AF-PAKI 8 76199969 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38441810 Affx-122929073 AX-123312147 8 76232572 CAAGTGTTGGCTACAGACACAGAGCTGGAACAAAA[C/T]GTTAACGTGGTGCCAAAGACAGAAATCAAACCAGG Y 2 1 2 1 101000 f 74 goat snp43697-scaffold585-2893752 8 77867352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781833 Affx-122977529 AX-385268915 8 76269176 TTAATCCTAAGGGGAAAAACCCAAAGATATGAACA[A/G]TGGTTTAGGCACAAAGATGTCTATGACAGTGTGTT R 2 1 2 1 101000 f 74 goat snp43696-scaffold585-2857148 8 77904196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433554 Affx-122934987 AX-123303895 8 76317776 CTTTCTGATCCAGCCTGTTTCTCATATTGACCCTA[C/T]AAGTCACTGGGGTTTAGGATGCTTGCCCTAAGCTA Y 2 1 2 1 101000 f 74 goat snp43695-scaffold585-2808548 8 77944130 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428674 Affx-122938643 AX-123299016 8 76348130 CACTGTGTCTCACAGGCAAAATGGAGCAATGAGAT[A/G]TCTGGTTTGCTTGAGATGTCCCCAGACTCAGTTGT R 2 1 2 1 101000 f 74 goat snp43694-scaffold585-2778194 8 77974501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414422 Affx-122949967 AX-123284771 8 76391882 GAGTTTTAGTCCTTGGTCTGACATTAAGTGATCTC[A/G]TTCAAGCTATGTGACTTTGGAAGGATCATTTATCT R 2 1 2 1 101000 f 74 goat snp43693-scaffold585-2734442 8 78017950 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430848 Affx-122937429 AX-123301189 8 76471716 TCTCCGGTCCCAGAGACAAAGTGACCTGCCAGAGA[C/T]CACACAGGTTAGAAGGCAGAGTCTACACCAGAACC Y 2 1 2 1 201000 r 74 goat snp43691-scaffold585-2654608 8 78097663 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794428 Affx-122937390 AX-385281391 8 76523794 AGAGTGCCTCCTACTGTATTCGCTGGTAATGCTAT[A/G]CCTAATACTCAGATACTTTCACCCCAGTAAATTGC R 2 1 2 1 101000 f 74 goat snp43690-scaffold585-2602530 8 78149592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273948 Affx-1111833945 AX-519547554 8 76524597 TCCCTGCACTTGAATAAAAATGTGAAGGAGGTAAG[A/C]AATCAGGCCCTGTGGATGGATATCTGCAGGGAGAG M 2 1 2 1 101000 f 74 goat GoatD01.011195 8 76524597 T G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38452860 Affx-122920714 AX-123323193 8 76570070 TTTATAGAAAGACCTGGCTGTGAATCCCATAACAC[C/T]GGAATCCCAGGAATGAAAAAGCAGCTCAGAAGGGG Y 2 1 2 1 101000 f 74 goat snp43689-scaffold585-2556254 8 78195952 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785550 Affx-122954921 AX-385272594 8 76606150 GAAATGATAATCCATCTAAGCAACCTGGAATTCTA[C/T]GCTCAAACAGTCAGCAACTGTTTGAGGTCAGAGAT Y 2 1 2 1 101000 r 74 goat snp43688-scaffold585-2520174 8 78232006 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801848 Affx-122963942 AX-385288755 8 76640237 TTATAAGAAGGTGGTGAAGTACGAACCTCACTTAT[A/G]CAGATGATGGGCATTTCAATGATACGGAGATGGTG R 2 1 2 1 101000 r 74 goat snp43687-scaffold585-2486087 8 78265882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376632 Affx-122979031 AX-123246991 8 76681840 GAATGAAATGTGAACCCCAAGCTTCCTAACTCTAT[A/C]GCTCGATTTCTCTTTACCAGATCATTTTGCTTTAA M 2 1 2 1 201000 r 74 goat snp43686-scaffold585-2444484 8 78305996 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407700 Affx-122954573 AX-123278051 8 76710664 GGTCTAGTGCAGGGATTGTTTGGAATAGAACTGTC[A/G]GTGGCTTCTTCTATAACCTTCTGTAACTGTGCAAC R 2 1 2 1 101000 f 74 goat snp43685-scaffold585-2415660 8 78335071 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434660 Affx-122933979 AX-123305001 8 76750347 AAATTCCATTGGAGAGATCCTACGTTTGTCTAACA[G/T]ACTGGTCAAATACAGAGGTCTACTTGTTAGCGAAA K 2 1 2 1 101000 f 74 goat snp43684-scaffold585-2375977 8 78374813 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414850 Affx-122949183 AX-123285199 8 76787174 AAATGAATTTCATTACACTTCCATCAGACAGCCCC[A/G]TGGGAACTCAGAATAAAAACTAAACTTAGAGAATG R 2 1 2 1 201000 r 74 goat snp43683-scaffold585-2339150 8 78412056 G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426803 Affx-122940533 AX-123297149 8 76830607 CTAAATGAGTCACATTCAGAGAAATCATTCAAATT[A/G]TCTGTGGGCACAGATACTTTTCTTTCATCTGTGGC R 2 1 2 1 101000 f 74 goat snp43682-scaffold585-2295717 8 78456053 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424037 Affx-122942079 AX-123294383 8 76870799 CCGCCCTGCTCCCTAGCTCCTTCGTAGACATGAGT[G/T]TGCTTTTAGCACAATTTGTATCTTGGGCTTGTGTG K 2 1 2 1 101000 r 74 goat snp43681-scaffold585-2255525 8 78496104 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411489 Affx-122951786 AX-123281839 8 76915389 TATTATGACACCAGCTCCACTCTGGTGGGTGGTAA[C/T]GTCTCAACTGTCCTCGAAGGGAAAATTGATCTTCT Y 2 1 2 1 201000 r 74 goat snp43680-scaffold585-2210935 8 78541827 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415042 Affx-122949493 AX-123285391 8 76947834 CCTCCATCTAGAGTCAATGATTTACATTTTGCTAT[A/G]CATGATTTCTCTATCTCTATGAGTGTGTGTTCAAA R 2 1 2 1 101000 f 74 goat snp43679-scaffold585-2178490 8 78574466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796355 Affx-122936025 AX-385283305 8 77002820 TTAGTTCTGTTTGAGATCTGGATGCATTTATTCCT[A/G]TTTATCATAGGGAGGTTTTAAATGATTGTATACTT R 2 1 2 1 102000 f 74 goat snp43678-scaffold585-2123504 8 78629171 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424785 Affx-122941397 AX-123295131 8 77060919 TCAGAGACCTAAAGAGTGGTTGGGTCACTTAATCA[C/T]ACCACCTACCAAGACCTGCAGAAGTGATAGGTGAA Y 2 1 2 1 101000 f 74 goat snp43677-scaffold585-2065405 8 78687545 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786222 Affx-122967966 AX-385273257 8 77140124 AGATCCCATTAGTACCTTTAATGTGTCAAACTACT[A/G]TAATTTGCAGCTGTATGTTTTGAATATTGCTAGAG R 2 1 2 1 101000 r 74 goat snp43676-scaffold585-1986200 8 78766822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410743 Affx-122952700 AX-123281093 8 77176647 GGGCAGCCCTTAACCAAAAGAGGAGAGAAGTTAGT[A/C]GATAAAGGCCTCAGACTCCAGCCTTTTTAGCGAAC M 2 1 2 1 101000 r 74 goat snp43675-scaffold585-1949677 8 78803487 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395353 Affx-122963993 AX-123265708 8 77264459 TTATTTTCAAACCTCAAATATACAATAATACTCTC[A/G]TCTTTGGGGCAACAGAATTTGTATTTCCAATTTGA R 2 1 2 1 201000 f 74 goat snp43673-scaffold585-1861865 8 78892374 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798506 Affx-122974299 AX-385285439 8 77297464 GTAAAGGGTGCAAAACACTTACTTGGCAGTATGAG[G/T]GTAGTGTCATTTAATGTCTTGTACTGATGGTCATT K 2 1 2 1 101000 f 74 goat snp43672-scaffold585-1828860 8 78926184 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391039 Affx-122966865 AX-123261396 8 77349709 GAGCCCAACAAGTTGCTTTCCAAGTGATTATGATG[C/T]ATGCTAAATTTAAGAATTATTGTTTTAGTTGTTTT Y 2 1 2 1 101000 f 74 goat snp43671-scaffold585-1776615 8 78977388 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792831 Affx-122947725 AX-385279809 8 77388991 TAGCATACAAAAACTCTGTACTTACGCATATCAGA[G/T]TACTTTTGTGGTCAAAACAATAAACATTTAAAAAG K 2 1 2 1 201000 r 74 goat snp43670-scaffold585-1737333 8 79015507 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430943 Affx-122936833 AX-123301284 8 77438168 CATTTCCCAGCTCATAGACTTGAAAAACAGGGAGA[C/T]AGTAACTCTTGGGAAAATTCCTACTCACCTCCACA Y 2 1 2 1 101000 f 74 goat snp43669-scaffold585-1688156 8 79064691 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765044 Affx-986697179 AX-385252613 8 77461264 ACTGATCCATAAAAAGGAGAATAAGTATGCAGTGG[C/T]ACCAGCTCATATTGTCACTTCTAGATATTTGTAAT Y 2 1 2 1 600010 r 74 goat 8_77461264 8 77461264 Ancestral_priority_1043 ancestry 0.698 recommended IMAGE 10K 10K ancestral 320777883 Affx-122971334 AX-385264999 8 77473635 AAACGAGAACATGGAGCATTATTCTGTGATTCTAC[A/G]TGAGCAATGATTTTTTGCACAAGAGATCAAAAAAA R 2 1 2 1 101000 f 74 goat snp43668-scaffold585-1652689 8 79100481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411649 Affx-122951570 AX-123281999 8 77503677 AATATCACCACACAGGGAAGATGCCAGAGTCACCC[A/G]CTAGAAACAGATCAGCCCAGCTGCTTGTTTGCTTG R 2 1 2 1 101000 r 74 goat snp43667-scaffold585-1622647 8 79131097 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416722 Affx-122947550 AX-123287070 8 77554132 ACTGATGACTGGAAATTCAGAGGCAAGAAGTCTAG[A/G]CTGCTGGCGTCTTGTGATGGTGCACTGTTTTCCTA R 2 1 2 1 201000 r 74 goat snp43666-scaffold585-1572192 8 79183944 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783205 Affx-122970533 AX-385270272 8 77616825 CAAAGGTAGGTTTGAGTTCTTTAAATGAATAAATA[C/T]ATTCTACATATGCTTAAGCAGTACACTTTGATTTT Y 2 1 2 1 103000 f 74 goat snp43665-scaffold585-1509499 8 79246344 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427764 Affx-122939238 AX-123298107 8 77657081 AACATCATGGTAAAGTAGCTTTTATTTTTAGTTCC[C/T]GGAATGTGTGTTTCTTGCAACTATAATGAGATCCT Y 2 1 2 1 201000 r 74 goat snp43664-scaffold585-1469243 8 79286875 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776913 Affx-122953623 AX-385264037 8 77685605 TAATGTGAATATGTAACTTCATGATTTTGATCAAA[A/G]GCAGAGGGGCAATTACAGATAAGCATCGCTAGGAG R 2 1 2 1 102000 r 74 goat snp43663-scaffold585-1440719 8 79315524 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405317 Affx-122956832 AX-123275669 8 77720372 GGAAAATAAAGTTGAACAGAATGGAAAGTAAAATG[C/T]ATTCTTGATTCTGTGTGATAGGCCCATTTTATCTC Y 2 1 2 1 101000 r 74 goat snp43662-scaffold585-1405952 8 79350162 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445890 Affx-122925955 AX-123316227 8 77834371 CAATGGATTGAAACATACCAATTATGTTAAAAACC[A/G]AGAAATTCAACATGACACTAAAAATACTAAACAGT R 2 1 2 1 101000 f 74 goat snp43660-scaffold585-1291953 8 79465516 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273654 Affx-1111833753 AX-519547267 8 77875952 TGCAGACACCAAGCTGGCACTTTTCTACTTCTCCA[A/G]TAACAAATGCGATA R 2 1 2 1 102000 f 74 goat GoatD01.003558 8 77875952 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38438912 Affx-122930432 AX-123309249 8 77902949 CACAATATTGCAAATGCAGGTGGTTTCAGGTATAA[C/T]AAAAAAGACATTGCCAGAACACTCAGCAATCCAAG Y 2 1 2 1 201000 f 74 goat snp43659-scaffold585-1223375 8 79534871 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801696 Affx-122971924 AX-385288604 8 77975123 TAACTTTGTATAATCAATTTACCCCCCTAAAAATA[C/T]GTGAATAGAAGAACCTCTTTAAATATTGCTTCCTT Y 2 1 2 1 202000 f 74 goat snp43658-scaffold585-1151201 8 79605635 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420400 Affx-122944925 AX-123290747 8 78004506 AGAATCAGATGCCCTGAGGCAGCCGCCTCAGCCCC[C/T]AGTCTCTTGGGCCCTTCTCTCATGCTGTCCTCACA Y 2 1 2 1 101000 r 74 goat snp43657-scaffold585-1121818 8 79635087 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443504 Affx-122927798 AX-123313841 8 78034318 AAGAAGATGAAGAACATTCTTTAAACTTCATCACA[C/T]GCTTCTTTGGAATCTATTATTATCATTATGTGTTT Y 2 1 2 1 201000 r 74 goat snp43656-scaffold585-1092006 8 79664899 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397703 Affx-122962566 AX-123268058 8 78064952 GGAAGGTATAGAGATTGGTTATGCTAAAGCTTTTG[C/T]ACAAGATCAGATAACACAGATTAAGTTGATATATA Y 2 1 2 1 201000 r 74 goat snp43655-scaffold585-1061372 8 79695545 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425762 Affx-122940730 AX-123296108 8 78104056 AGATACATAAAGGAACTCCTCAAACTGATCCTATG[C/T]GTAAATCTCCCTGCTTCCCTCTGGTATATGGTGTT Y 2 1 2 1 201000 f 74 goat snp43654-scaffold585-1022268 8 79734470 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774081 Affx-122935408 AX-385261219 8 78140259 ACATATTGAATTAGAAAGCAAAATTGATGATCATG[C/T]GGTGTTTCTTGCAAAACATTACAAAAGAGAAGAAA Y 2 1 2 1 101000 r 74 goat snp43653-scaffold585-986065 8 79770929 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273527 Affx-1111833672 AX-519547142 8 78141775 GGGCTAGAGAGGTGGAGTGATTACAACAAAAGTCT[A/G]TCACTCCGTGTGTTCTGCAGGCCAACTGGAGCAGG R 2 1 2 1 201000 f 74 goat GoatD01.001096 8 78141775 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38453940 Affx-122919484 AX-123324273 8 78172120 AACCCCAGACACCAGGAGATACTGGAGAAGGGTCT[A/G]TATTCAGGCTGCTCCTTGGGTTACACCCACGGCAT R 2 1 2 1 101000 r 74 goat snp43652-scaffold585-954204 8 79802573 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435240 Affx-122934078 AX-123305580 8 78215683 ATTGACTCAATAAATACTCGGCTCCCTTCTAGGCA[C/T]AGGAGAAAAAAGCAGTGATTGAACTGTCCCTGCCT Y 2 1 2 1 201000 f 74 goat snp43651-scaffold585-910641 8 79846376 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406866 Affx-122955651 AX-123277217 8 78247667 GGCAAATGCTGACATGCCAAGGTTGACTGCAAAGC[A/G]TGTATTCCCAAGGCAGTCAAATGAGGAGACCTAAG R 2 1 2 1 101000 r 74 goat snp43650-scaffold585-878657 8 79879578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789519 Affx-122966648 AX-385276528 8 78290971 CATCTCATTTTGCCCTGTTTTTGGCCAATTGTATG[C/T]ATGCATTTCAGTGGTCCTCAAAACTTTTATCATGA Y 2 1 2 1 101000 f 74 goat snp43649-scaffold585-835353 8 79922396 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781203 Affx-122949121 AX-385268288 8 78350833 TAAAAAAATGTATCTTGTTCTTGAAGCTTAAACCA[C/T]GGCGATGTGTTCATTGATGAAGAAACTTCTAGTGA Y 2 1 2 1 101000 r 74 goat snp43648-scaffold585-775491 8 79982415 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38422558 Affx-122943766 AX-123292904 8 78390674 AAGATGTTAATTTGGTCTGTGAGCCTTTTCCTTAC[A/G]TGATCACTAGAATAACTGCCTGGTAATCTATATGA R 2 1 2 1 101000 f 74 goat snp43647-scaffold585-735650 8 80023463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797494 Affx-122933586 AX-385284433 8 78503514 TTTTTTTTATATTTCCAGTTTGGACTTTATAGATT[A/G]TCTTTAAATGGAACATATATGTGTCTCCATAAACA R 2 1 2 1 101000 r 74 goat snp43645-scaffold585-622810 8 80137092 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426745 Affx-122939865 AX-123297091 8 78540171 TTTTCTTAAAATGAAAAAAATATTTTATTTGTTTA[C/T]GGTTGTTAAAGTAATCCCAAAGTGTTAAAGAATTC Y 2 1 2 1 101000 r 74 goat snp43644-scaffold585-586153 8 80174115 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432261 Affx-122936343 AX-123302602 8 78610800 TTAAAAAAAAAAAAACAGATTGAGAAGAACCAAAT[A/G]CAGTTTTTGAAGCAGAAACATTCATATGTCATTAT R 2 1 2 1 101000 r 74 goat snp43642-scaffold585-515524 8 80244359 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399803 Affx-122960281 AX-123270158 8 78643334 TGCTCAGCATTTCTGGATTTCACCACCGTGACAAG[C/T]GTCAGGGAGCCCTTTCTTCCAGACTGTTGGCCCGA Y 2 1 2 1 201000 f 74 goat snp43641-scaffold585-482990 8 80277178 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398647 Affx-122961898 AX-123269002 8 78675566 TTCCCTTCTAGAATCCCAACTGGGGTGAAGAGGCC[A/G]CTGGGGCAGGTCTACTTCTTTCCAGTCCTTTCATG R 2 1 2 1 201000 f 74 goat snp43640-scaffold585-450758 8 80309341 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438695 Affx-122930865 AX-123309032 8 78724931 TGGACATGACTGAGCGACTAACACTTTCACTTTTC[A/C]TGGGTTGTATGTGTGCTTTGCTGCCCTGGTGGGAT M 2 1 2 1 201000 r 74 goat snp43639-scaffold585-401393 8 80358854 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415090 Affx-122949454 AX-123285439 8 78761198 AGAGCTCACTGTTTAATGCAGGAGAATTTCAGACA[A/G]CTGCCAACAATTTGGCAAAATCTAAAATCCAAGAG R 2 1 2 1 101000 r 74 goat snp43638-scaffold585-365126 8 80395904 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464598897 Affx-1110567252 AX-516070282 8 78770356 TGTGTCTAAAAAGCAAACCTGTCTGTCTATGTTTG[C/T]CATAGCTTTTCTTACAAGCATCTTTTAATTTCACA Y 2 1 2 1 202000 f 74 goat 8_78770356_AF-PAKI 8 78770356 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448205 Affx-122924234 AX-123318541 8 78809197 TCACCTGGATTCTCACTGGCCACACTCCTTCCAAG[C/T]GTTTCCTGAAGTAAGACCAAGTTCTGCTGCTTTGA Y 2 1 2 1 101000 r 74 goat snp43637-scaffold585-317127 8 80444212 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394066 Affx-122964974 AX-123264421 8 78872132 GAAAATTTTTTGCATAAAAAGCAATTTTTAAGAGA[C/T]GAGCACTGAGAAAGATTCATCCAAATGCCTGTTAA Y 2 1 2 1 101000 r 74 goat snp43636-scaffold585-254192 8 80506506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797775 Affx-122919285 AX-385284714 8 78923377 AAAGATTAACACTATTGAGTGCTAAGAGCACAACA[C/T]GGTACATTCAATAAAATTCTGGAATTAATAATATG Y 2 1 2 1 101000 f 74 goat snp43635-scaffold585-202947 8 80557704 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426748 Affx-122939863 AX-123297094 8 78962160 AAGAAGAGGAAGATTCTAGTCTTGTACAAAAGACA[C/T]ATTTGGAAATAAGCTGGGGTCCCAATAAGGTCCCC Y 2 1 2 1 101000 f 74 goat snp43634-scaffold585-164164 8 80597126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447872 Affx-122923879 AX-123318208 8 79044417 GTGACAAAGCTCCACCCCTACCCCAAATGTTTCAC[A/G]TCTAATCCAAAATGCAGGGGGGAAAATGCATAAAG R 2 1 2 1 103000 f 74 goat snp43632-scaffold585-81907 8 80679730 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451935 Affx-122921011 AX-123322268 8 79074305 TCATGCCCTCCTCCAGGAGATATATGGCTGACCAT[A/G]TATATTCCAATTATGTATTCCAGAGCTGGGGAAAT R 2 1 2 1 201000 r 74 goat snp43631-scaffold585-52019 8 80709703 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396061 Affx-122963448 AX-123266416 8 79120592 GCTTATGAATGTGAAGACAAACATTCTTGGCAATG[A/C]TTTGGGTCTTTTGCAAAGTAGCCACGTTGTCTTGT M 2 1 2 1 101000 r 74 goat snp43630-scaffold585-5732 8 80756536 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765047 Affx-986697181 AX-385252616 8 79122163 ATTAAAATTTAAAGGAACAACAACAAAGTTATATA[A/G]AGCAATGAGAATCCTCATAGTCTGCTGGTAGAACA R 2 1 2 1 600010 r 74 goat 8_79122163 8 79122163 Ancestral_priority_1043 ancestry 0.66 recommended IMAGE 10K 10K ancestral 38420423 Affx-122944910 AX-123290770 8 79156981 ATGTGAGCATGGCAGACTCTGACTTTCTTCATTAG[C/T]AATCAATATCTTTCTTTCATAGCTAAGATTTACCT Y 2 1 2 1 201000 r 74 goat snp51334-scaffold750-1385368 8 80792773 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781523 Affx-122925609 AX-385268608 8 79192908 TCTAACGCAGCTATTTATTTATATGGGGTGGTTTA[A/G]AGGATGGGCCATTTCCATAGTGTTTCCTTTTCAAT R 2 1 2 1 101000 f 74 goat snp51333-scaffold750-1349441 8 80829594 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425613 Affx-122940911 AX-123295959 8 79226348 CATGTGCCCACCATTGGAGCTAACAGTGAGGGGGA[C/T]GGTATCTTAAGGAAGATTAAAGTTCACTTGTCAGC Y 2 1 2 1 101000 r 74 goat snp51332-scaffold750-1316001 8 80863922 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401581 Affx-122958879 AX-123271934 8 79283169 GTCAGTGTATACCTCCAGATGGCTCAGTGCCTGTC[A/G]CTTCTGGCTTGTGCCATCCAGCCCGTTGGCACAAG R 2 1 2 1 202000 f 74 goat snp51331-scaffold750-1259180 8 80920732 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437547 Affx-122931901 AX-123307885 8 79326778 ATTGGTGAAAGAGGTGACATTCTCAAGTTAGGTCA[C/T]TTCCATGGCCATGGCAGGCTTTGGAGATAGGCAGC Y 2 1 2 1 101000 f 74 goat snp51330-scaffold750-1215571 8 80964262 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387232 Affx-122970577 AX-123257590 8 79382526 GTATTGGTCCCAAGCTAGCAAAATGAATCTAGAGC[A/G]ACTTACAGAAATCAGGCAGACCAGAGTCTTTCACC R 2 1 2 1 101000 f 74 goat snp51329-scaffold750-1159823 8 81019985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410910 Affx-122952062 AX-123281260 8 79414734 GGCAATGAAGGATCAGGTCAAAGCTCCCAAGAGAG[C/T]AGGTATCCTCAACAGGTAAGACTCAGGGCCTGGAG Y 2 1 2 1 101000 r 74 goat snp51328-scaffold750-1127615 8 81052263 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392467 Affx-122966154 AX-123262824 8 79527786 CTGTCACTACTGATTCCAACATACCTTTTCATTCT[A/C]TTTCATGGCTCACAATATAATCACCGACCAAAACA M 2 1 2 1 101000 f 74 goat snp51326-scaffold750-1014563 8 81165565 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772847 Affx-122941981 AX-385259992 8 79585346 TAATGCAATCCTTACACAATAACTGCTTTTATAAC[A/G]TTTTAAACTACTTTTCTTAAGCAATATGCAAATGG R 2 1 2 1 103000 r 74 goat snp51325-scaffold750-957003 8 81223756 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278631 Affx-1111836523 AX-519552110 8 79605564 AGTTTCAGTAATATTAAATGTGTCTCCTGCATTCC[A/G]TGCTCTGCAGGCCAATTCTTTACTGCTGAGCCATC R 2 1 2 1 303000 f 74 goat Random2.2K-927 8 79605564 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38426082 Affx-122941080 AX-123296428 8 79618015 TACTCCCTTAATATCATCAACACAATATTGAATTC[A/G]CTGTTTCCTTACATTGACTGAAATAATCAGATATA R 2 1 2 1 101000 r 74 goat snp51324-scaffold750-924334 8 81254480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799946 Affx-122954040 AX-385286872 8 79653268 TATACTTCAATGAAAAAAAATTGATCAGTAAAAGA[C/T]GGAAGGAGACAATCCCAAATAGAATGCAGTATAGT Y 2 1 2 1 202000 f 74 goat snp51323-scaffold750-889081 8 81290099 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383882 Affx-122973128 AX-123254240 8 79682456 GGAATTTTAAGACATTAACAACCATACCAAAATTG[G/T]TTTCATCTCCTGAAGGTCAAACAGGTTAATACCTG K 2 1 2 1 101000 r 74 goat snp51322-scaffold750-859893 8 81319526 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379617 Affx-122976008 AX-123249975 8 79722539 CAAGATGTTCTGACTGTTCCTCAACCTCAGTCACA[C/T]GGCTGACTCTGGGCACTGACCGCTCCTAGGGGACG Y 2 1 2 1 101000 f 74 goat snp51321-scaffold750-819810 8 81360350 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400004 Affx-122960804 AX-123270359 8 79752251 CTACTAAATGATACATCAGAGCTGAGCATGGTACC[A/G]TGGGGGAACTTTCTAACACCCCACCACTCCCATCC R 2 1 2 1 201000 f 74 goat snp51320-scaffold750-790098 8 81390119 G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408179 Affx-122954200 AX-123278530 8 79807392 CTGGTTAACACAAGGCTTCTGCTAGTGCCAGGAAC[A/G]TCTACCTGGATGCCAGGAACAGGCTAAGACTTGGC R 2 1 2 1 101000 f 74 goat snp51319-scaffold750-734957 8 81446208 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415913 Affx-122948459 AX-123286262 8 79837227 GGATGATAATTGACCCGGAAGTCTGTATAATGCAG[G/T]AAGTGTTCTCCACATGCAGGTGCCCATCACATCGT K 2 1 2 1 101000 f 74 goat snp51318-scaffold750-705122 8 81476090 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434834 Affx-122934791 AX-123305175 8 79876150 GAAAATGGTGAAATGACAGTAGTAAGTGCTTCTCC[A/G]TTAGTACAGTAAGTCCCCTACTTGTGAATGAGTTC R 2 1 2 1 101000 f 74 goat snp51317-scaffold750-666199 8 81514684 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415397 Affx-122948746 AX-123285746 8 79907464 ATTAATTGTATTTTTATATTGCTTAGTACCAGATT[A/G]CATTGTGTGGATTTGCTTTCTTGTTAGGAGATGTA R 2 1 2 1 101000 r 74 goat snp51316-scaffold750-634885 8 81546064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798138 Affx-122955725 AX-385285073 8 79978300 CTGAACCGATACTTTTTGAGAACTTACTGTTTGCC[C/T]GGCACTATTAAAGAGCCCAAGGATACCATCATAGA Y 2 1 2 1 101000 f 74 goat snp51315-scaffold750-564049 8 81614695 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439867 Affx-122930052 AX-123310204 8 80021549 AACTAGGTTCTGAGGAGATGTGCCAGGGAGGACAC[A/G]TTTGACTGTAAGAAAACCCAATAAAAGGTGGCTTA R 2 1 2 1 201000 r 74 goat snp51314-scaffold750-520800 8 81658042 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391080 Affx-122966834 AX-123261437 8 80139548 TATTAATGTAAGAAGATGTCTCTCATATATGTATT[A/G]TGCATAGTAAAGTTTCTAGAATGTTCTTCCAATAC R 2 1 2 1 201000 f 74 goat snp51312-scaffold750-402801 8 81776967 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800944 Affx-122948989 AX-385287860 8 80174528 TCGTTATTAGTCTCATTTTTGGAAGAAGAGAACTT[C/T]ATGTGTCCACAGGGCTTTTCCTTCCTTCTCAGCTG Y 2 1 2 1 101000 r 74 goat snp51311-scaffold750-367821 8 81811636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396040 Affx-122963463 AX-123266395 8 80211491 TCACTTCAAACCCAGATCAAGCTGTATCTAACACT[A/C]TGCCTGAAATGTTCAGTTCTGGAAAGGCTTCTTAT M 2 1 2 1 101000 f 74 goat snp51310-scaffold750-330858 8 81850297 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426419 Affx-122940830 AX-123296765 8 80240808 GTGTTTTTCCTGCTCTGAATGGAATTTCTGGTTGT[A/G]TTGAAGAACCCATGGCTTAGCACCTAATGTGTCAC R 2 1 2 1 201000 r 74 goat snp51309-scaffold750-301541 8 81879514 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452343 Affx-122920648 AX-123322676 8 80273778 CCCTCTCTACTCTCTCCCTCCCACCTGTCCGTCTT[C/T]CCACCTATTCATAAACTGCCCGAATCCAATCCTAG Y 2 1 2 1 101000 r 74 goat snp51308-scaffold750-268571 8 81912306 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440111 Affx-122929707 AX-123310448 8 80308346 AACATCAAAGCGACACGTGTCTATCAATAGATGAA[C/T]GGATAAACAAAATGTGGAATAGTCATACAACAGAA Y 2 1 2 1 303000 r 74 goat snp51307-scaffold750-234003 8 81947525 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785674 Affx-122922683 AX-385272715 8 80358698 ATTCCAACCCTTACCCAGAATAAGTAGTCTCTATG[C/T]ATATCTATTCTCATTATCAGATCCTATGTGTGCTT Y 2 1 2 1 101000 f 74 goat snp51306-scaffold750-183651 8 81998120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446784 Affx-122925308 AX-123317120 8 80412211 GAAGATGACCGGCTGACCCATCACAGCCATTTTCC[A/C]TTCAGTGTGGACTTCTAGCCTCTGAAGCTTATTCC M 2 1 2 1 101000 f 74 goat snp51305-scaffold750-130138 8 82051652 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428664 Affx-122938650 AX-123299006 8 80441639 GAGTTCAGGGGTCCATTCCCCCAAATAGTTTTCCT[A/G]CTTACTCAGTAACATCTGAAATTTCTTATAAGACG R 2 1 2 1 201000 r 74 goat snp51304-scaffold750-100710 8 82081092 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784024 Affx-122978545 AX-385271077 8 80480868 AGGGCTTCTCAGTTTAATTTCAAATCTAAGACAGT[A/C]TTAACACCAAAATCTAATAAAGGCAAAAGAATACT M 2 1 2 1 101000 f 74 goat snp51303-scaffold750-61481 8 82120589 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383735 Affx-122972454 AX-123254093 8 80511032 AGAGTTACGGGGCTTTGCCTGCTTTTTGCTGTCTG[C/T]GTTGGCAATGCAAAAGGCCAACAAGGAAAGGTATG Y 2 1 2 1 102000 f 74 goat snp51302-scaffold750-31317 8 82152235 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448220 Affx-122924224 AX-123318556 8 80541054 GGAAGAATTACCTGGTGGGAGGAGAGCAGCAGTTG[A/G]GAGCACTGAATTAGGAATGGAAATGTTTTTAAGAA R 2 1 2 1 201000 r 74 goat snp51301-scaffold750-1295 8 82182169 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419883 Affx-122945353 AX-123290231 8 80544806 GGACAAAACACATCGCAATTCTTTGGAAATGGAGA[A/C]TTTTTCTCACATCAATGAAAAAATTCATGGGCATT M 2 1 2 1 101000 f 74 goat snp39054-scaffold497-2358 8 82187846 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413183 Affx-122950332 AX-123283532 8 80575673 AGCGCCTTTCTTCAAGGAGCTCACGGTGATTTATG[C/T]GTCGTTAATTCAGAGGCAAGCACCTTGTTCAGCTG Y 2 1 2 1 101000 f 74 goat snp39055-scaffold497-33225 8 82218685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802732 Affx-122930436 AX-385289630 8 80649795 ATCCTGCAGAATAGTCTGCTTCCACGCCTAACATG[C/T]ACTTGCCCTTCTTGGACATTATTTAAAGTCGGTCA Y 2 1 2 1 101000 f 74 goat snp39056-scaffold497-107347 8 82294688 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780663 Affx-122933080 AX-385267753 8 80726818 ATAAATATATTAGGACATTTTTGTGGCTTAACATA[C/T]GATGTTTTCTAGAGAATGTCCCATGTGAATTTAAG Y 2 1 2 1 101000 r 74 goat snp39058-scaffold497-184370 8 82372960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390758 Affx-122967899 AX-123261115 8 80764905 AAACAATCTTCAAACCATCTGACAGTTGCACTCAT[C/T]TCCCATGCTATGCTAGTAAGGTCCTAATTAAACTC Y 2 1 2 1 101000 r 74 goat snp39059-scaffold497-222457 8 82411425 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394984 Affx-122964260 AX-123265339 8 80802390 CTGCCAGGGAAATTAAAATAAAATTTCCTCCCTAC[A/G]GAGATTCTGCCTGCTCAAGCTAAAGCTGTGTATAT R 2 1 2 1 101000 r 74 goat snp39060-scaffold497-259942 8 82448736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403511 Affx-122957630 AX-123273864 8 80837617 AGCTTTCTTAAGTAACCCATGGAGCTTCCCTGGTA[A/G]CGCGGCTGGTAAAGAACCCACCTGCAATGCGGGAG R 2 1 2 1 103000 f 74 goat snp39061-scaffold497-295169 8 82484740 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399779 Affx-122960298 AX-123270134 8 80879799 GAGTTTGCTCTTAGTTTGGGGGTCACAGGGGGACA[C/T]GGGAACCCACCAGAAAGGTGAAAGATAAAGAGGAA Y 2 1 2 1 102000 f 74 goat snp39062-scaffold497-337351 8 82527570 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420726 Affx-122944771 AX-123291073 8 81009788 GCATTGGTGCGTGAGGTTGTTCTCTACAATAAGTC[A/G]CCTGAGAAATAAAAGTTTCCTATATATCTTTTGAG R 2 1 2 1 101000 f 74 goat snp39064-scaffold497-467340 8 82657601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768744 Affx-122944316 AX-385255922 8 81048350 CTTCAAACATAATTCCAGTTGTAACCTGGGTTTTA[C/T]GACCTCTCTGCTTTGGGAAGGTGATTATCACAGTC Y 2 1 2 1 101000 r 74 goat snp39065-scaffold497-505902 8 82696683 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404123 Affx-122957103 AX-123274475 8 81093908 ACTGGCTGATTCTTCTAGAAGAAAAACAAAGTTGA[C/T]AAACCATTAGCCAGATCCATCAAGAAAAAAAGGAG Y 2 1 2 1 303000 f 74 goat snp39066-scaffold497-551460 8 82742704 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401771 Affx-122959493 AX-123272124 8 81133996 TCATGGGTCTGAGTTAAGCTTGTTGAACTTACAAC[A/G]CCCTCAGCCACAAAGTCTGTACTATGGACTTCTTT R 2 1 2 1 101000 f 74 goat snp39067-scaffold497-591548 8 82781334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442619 Affx-122928469 AX-123312956 8 81163860 GCAGAAGTGCAGGAAAATGCATTTAGAGAATCTCA[C/T]GCATTTCGTCAGGTAGACCAGGCAAACCAACAACC Y 2 1 2 1 101000 r 74 goat snp39068-scaffold497-621412 8 82811276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406211 Affx-122956128 AX-123276563 8 81278321 CCCACACTGCAGGCGGATTCCTTACCACTAGTGCC[A/G]CCTGGGAACCCTGGTACATCATCACACCTAGCTAA R 2 1 2 1 101000 r 74 goat snp39070-scaffold497-735873 8 82925380 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803007 Affx-122976061 AX-385289886 8 81317389 GAGTCAAAGTCAAAACAAGTTTGACATATTAACAA[A/G]CATTAGTCACAAAAGGATGTGAAAATCATAAGATT R 2 1 2 1 201000 r 74 goat snp39071-scaffold497-774941 8 82965079 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464600568 Affx-1110568109 AX-516071936 8 81325484 AATATACTAATATCTATTTTCTATCAAGTCTGTTC[C/T]CTAGACCTTTATGGAATAGGATTGTATTTTACAGG Y 2 1 2 1 101000 f 74 goat 8_81325484_AF-PAKI 8 81325484 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38434988 Affx-122933828 AX-123305328 8 81350665 AAGCTGGGGTGACACTCTTCCCATTTTACTGAAGA[A/C]ACTGGGGAACAGTCACAAACTTGTTACACAGTTGA M 2 1 2 1 202000 f 74 goat snp39072-scaffold497-808217 8 82998376 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375464 Affx-122979157 AX-123245823 8 81458724 ACAAAGATGATAAATCAAATTGGATGTTGAATAAA[C/T]AAACAGTATTAGGTAGCCACCTGAAAAAGTAAATA Y 2 1 2 1 201000 f 74 goat snp39074-scaffold497-916276 8 83106938 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453015 Affx-122920101 AX-123323348 8 81491738 TTCCAGCTGCTCAGCCTGGGGTCTATCTATCTCCT[A/G]CTTCACCTGATCTTGGACTTCTCATGTTCTGAAAT R 2 1 2 1 303000 f 74 goat snp39075-scaffold497-949290 8 83139810 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444130 Affx-122926806 AX-123314467 8 81538823 ACTTCCCACTAAAGATATTAAGACTCTAGAAAAAT[A/G]AAAGATGACAATTGTTCATTAAATAAAAGCAACTT R 2 1 2 1 101000 f 74 goat snp39076-scaffold497-996375 8 83188241 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409074 Affx-122953342 AX-123279425 8 81575622 CAACATATCTGGAGACTTTTGAGTCTTGAATATGA[C/T]GAGTTCTTTCCCCAAGTTTGGGAAGTTTTCAGATA Y 2 1 2 1 101000 f 74 goat snp39077-scaffold497-1033174 8 83222889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425010 Affx-122941889 AX-123295356 8 81607604 TTATAAGAATTTAATTTAAATTGATGTCAACTTGA[C/T]GTCAATCATATGAAAGCTGTATAGTTCTATCCTCT Y 2 1 2 1 101000 r 74 goat snp39078-scaffold497-1065156 8 83254950 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413982 Affx-122950289 AX-123284331 8 81655119 GTCTTCATGAGGCCCTAATTCATAGGTGAGAGTCA[C/T]AAAACCTACACAACACAATTTTCTCATCTAAAATA Y 2 1 2 1 101000 f 74 goat snp39079-scaffold497-1112671 8 83302025 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799073 Affx-122936113 AX-385286003 8 81706537 TCTTCTTTACCACTATCCAAATTTACACAAATTCC[A/G]TTCACTTTCCACAGAGTCACGCAACCATCACTGGA R 2 1 2 1 101000 r 74 goat snp32300-scaffold366-3920045 8 83354360 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448210 Affx-122924230 AX-123318546 8 81765834 AAAGCCTCCTTTGGTTTCTTTCTTTGTCTTCATAT[A/G]CATACTTCACATTCCCTGACCACTTAGTGTGGCAA R 2 1 2 1 201000 r 74 goat snp32299-scaffold366-3860748 8 83413650 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436212 Affx-122932584 AX-123306551 8 81801309 AACTATAGAGACCAAAACATGACTAATTTGCCTTA[C/T]GCTTTGATTTAAAACAAACACCTTTAAACATACAG Y 2 1 2 1 101000 f 74 goat snp32298-scaffold366-3825273 8 83449297 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396570 Affx-122962922 AX-123266925 8 81867835 CTCTGTGAAATCTACTCAGATCTTTGCATTAAAGC[A/G]TCTCTGAGCGAAGCCCTGCAAGATGCTGGCTAGTC R 2 1 2 1 101000 f 74 goat snp32297-scaffold366-3758747 8 83516141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437912 Affx-122931651 AX-123308250 8 81919840 TTATATTTAGGGCACAGTGGTTAATAGGGAATAGA[G/T]AAAGCAGAGAGATTAAGATTTATAGATGAAGGATA K 2 1 2 1 101000 f 74 goat snp32296-scaffold366-3706742 8 83564855 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783144 Affx-122964194 AX-385270211 8 81999485 CTCAGCCTGGAAGCTTGGTAAGATTTTCTGCAAAG[C/T]GGAACCTTAAAGAATAAGGAGTCATTTACCAGTCA Y 2 1 2 1 101000 f 74 goat snp32294-scaffold366-3627097 8 83644565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771026 Affx-122965881 AX-385258188 8 82030049 TTTAAGCATTTAGACAAGTAGTGTAGTAGCTTCCT[A/G]TTGGGGTTCTTCCTACCTCTATTCTCCATTCACCT R 2 1 2 1 101000 r 74 goat snp32293-scaffold366-3596533 8 83675077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443163 Affx-122927615 AX-123313500 8 82069592 TTGAAGATGGAGAGCTTAAAGAATCTGCCTGCAGT[A/G]TGGGAGACCTGGGTTCCATCCTTGGGTTGGGAAGA R 2 1 2 1 103000 f 74 goat snp32292-scaffold366-3556990 8 83714961 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401332 Affx-122959269 AX-123271685 8 82123790 ATGTAGAAGTAAATGATGTCTATAATATGAAGAGA[C/T]AGGCATGTAAAGGGACCTATTTAGTACAAAATTTC Y 2 1 2 1 101000 f 74 goat snp32291-scaffold366-3502792 8 83769598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440601 Affx-122929981 AX-123310938 8 82171564 ATTCCTGTGTATCTAGAAATTAACTCAAAAAAAAA[C/T]AGTGGAAAGAAAAAAGCTAGGAGGGTAATTAGGAA Y 2 1 2 1 303000 f 74 goat snp32290-scaffold366-3455018 8 83818063 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424342 Affx-122941939 AX-123294688 8 82208956 ACACTGAAGAATTTGATGCTGAAGGACATGGAAGA[C/T]GAAGGTGATAGTGATGCTGACAACTCTCTCTTTCC Y 2 1 2 1 101000 f 74 goat snp32289-scaffold366-3417626 8 83855538 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431572 Affx-122936188 AX-123301913 8 82251905 AAATGGCTGTGAGACTCCTTCCAGCAATAACACAG[C/T]GTTCCTGTTGCTTTCCCCCTGGTTTTAGCTACTTG Y 2 1 2 1 101000 r 74 goat snp32288-scaffold366-3374677 8 83898512 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437306 Affx-122931972 AX-123307644 8 82308879 GGTCAAGATGACCTTGTAACTGGCTGCCAGCCACT[C/T]GGTTTTCTGATGCTTTTGAACTAAACATTCCTAAG Y 2 1 2 1 201000 f 74 goat snp32287-scaffold366-3317703 8 83956193 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423829 Affx-122942792 AX-123294175 8 82357632 GTGACAGTTTTAAATGATGAACAGGTTAGAAGAGA[A/G]AGCAGTTTTCCTTGAAGCAGACACAACACAACACT R 2 1 2 1 101000 f 74 goat snp32286-scaffold366-3268950 8 84004943 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444328 Affx-122926732 AX-123314665 8 82413595 GTAACACTGTGTGGTTCCCTTTAGATGAAATATCC[C/T]GAGTAGACAAAGCCACAGAGATAGAAAGTACACTG Y 2 1 2 1 101000 f 74 goat snp32285-scaffold366-3212987 8 84060958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278633 Affx-1111836524 AX-519552112 8 82437772 GAAGAAGCTACAGGGATTGTACCTATAGTTAACCA[A/G]TGTGGTGAGTCAGGTTAGAGTTTTAATTAGCACTG R 2 1 2 1 101000 f 74 goat Random2.2K-929 8 82437772 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795131 Affx-122940047 AX-385282089 8 82448817 GAAAGAAAGCATTGAGACAAAACTGACTCCAGTTT[C/T]GAAAATTTGAACTGGGCAAAAAGAATGTACCAGAG Y 2 1 2 1 201000 f 74 goat snp32284-scaffold366-3177765 8 84096636 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454195 Affx-122919295 AX-123324528 8 82491409 AAAGCAGACCAGGATGTTGCCTGGAAGGAGGGGTA[C/T]GTGTGGTGTGGGGGTTACGATGGAACACAAGGAAG Y 2 1 2 1 101000 f 74 goat snp32283-scaffold366-3135173 8 84139614 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275505 Affx-1111834844 AX-519549077 8 82521723 CAGTGGTCATTTGGGCAGATCTTACAAATGTATTT[A/G]GAGGTTTGGGCACATCATATGAATCCAGGTGCCCC R 2 1 2 1 201000 r 74 goat GoatD01.056241 8 82521723 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38413772 Affx-122949928 AX-123284121 8 82620832 TATTTAGGGAGTGGAAGGCAAACATGTGGGGCAAG[C/T]AAAGCCCTGGCCTGGGGAACAGTCCCTCAGCAGGC Y 2 1 2 1 101000 f 74 goat snp32281-scaffold366-3005750 8 84269878 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427296 Affx-122940154 AX-123297639 8 82676680 TATTTTCATCTGCTGTTGCTTCATTTTATTTCTGA[C/T]AGTTTTTTAACATGTTTTACCATTTTCCCTAAACT Y 2 1 2 1 101000 r 74 goat snp32280-scaffold366-2949902 8 84324885 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790383 Affx-122924450 AX-385277386 8 82709587 ACAGACAAAAATGACTCATCTAGAAGGTGGCGTTA[C/T]GGCTTTTTCCTTTAGTCCGGTGTTTTTAATTTTTC Y 2 1 2 1 101000 f 74 goat snp32279-scaffold366-2916995 8 84357409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426624 Affx-122939958 AX-123296970 8 82745948 ACATTACCAACAACACCGCACTGTCTTGATCACTA[C/T]GATTTTATAATAATTCTTGAAATCAGCTAGTGTTA Y 2 1 2 1 101000 f 74 goat snp32278-scaffold366-2880634 8 84393100 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412177 Affx-122951065 AX-123282527 8 82785599 AAAAAAAAAAAGAGGCATGAGATGAGAGCAGTGGG[C/T]GGCCCAGGTAAACTGATACCCATTTTGTCCCGGCA Y 2 1 2 1 101000 r 74 goat snp32277-scaffold366-2840983 8 84432825 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386222 Affx-122970982 AX-123256580 8 82879392 CATAAGAAACAGCATGAAATTCCTTGCAGCATCAA[C/T]GTACACCATGATGTTTCTCTGCCCTACAAGTCTAG Y 2 1 2 1 101000 r 74 goat snp32276-scaffold366-2747190 8 84526728 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387058 Affx-122969901 AX-123257416 8 82918323 GTATAGAGAGGCCAAAATAGAACCTGAAGAGCTAT[A/G]CAGGAGAACACCACTTGTAGGAGGTCTAAGGAGAG R 2 1 2 1 101000 f 74 goat snp32275-scaffold366-2708259 8 84565537 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382536 Affx-122973790 AX-123252894 8 82951800 ATAGAAGTCTAATTTAAAACGCTTTCTGAGGGTGG[C/T]AGTAGGGAAATCACAGCCCGAAGAGAGTCAAGTAG Y 2 1 2 1 101000 r 74 goat snp32274-scaffold366-2674782 8 84599047 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788316 Affx-122925343 AX-385275334 8 82993354 AAAGCTGAAGCTGACTGTAAAGCAGAGAACACACA[C/T]TACTGTGCATTGTGTGATGCACAGTAACAGGAGGA Y 2 1 2 1 101000 f 74 goat snp32273-scaffold366-2633228 8 84640606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391239 Affx-122967387 AX-123261596 8 83032661 TGTTCTGGTGAATTTTTAATAGATATTCCAGATAA[A/C]TGACATGTTGTCTTTAAAAATCAGAAGCAGGTTCT M 2 1 2 1 201000 f 74 goat snp32272-scaffold366-2593921 8 84679964 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801697 Affx-122945553 AX-385288605 8 83080899 AGTCCTCACCACTGCTCAGACAATGAGCTATAAGG[C/T]TGAAGAGCTTTCTGTGGACAGTTGAGGCTGCACTG Y 2 1 2 1 201000 r 74 goat snp32271-scaffold366-2545683 8 84728457 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393375 Affx-122965912 AX-123263731 8 83125919 GGCAGGCATGGACCTCAAACCAGGGCCTGGATATG[C/T]AGGGAGACCACACACAGGACCCTGGGAAAGTTCAG Y 2 1 2 1 201000 f 74 goat snp32270-scaffold366-2500663 8 84774112 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400420 Affx-122959979 AX-123270775 8 83190573 TCCCAAACCCCGTTCCCACTGCCAACTAAGATCTG[C/T]ATGCAGAGAGATCTGTACTCACCATTTCATTCCAT Y 2 1 2 1 101000 r 74 goat snp32269-scaffold366-2436009 8 84839409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418929 Affx-122946511 AX-123289277 8 83241110 CTGCGAAGACCCTGGGGCAAGGCCAGCCTGGGAAG[G/T]TTCCAAGAACATTGAAAAAAAATGGCTCAGCTAGA K 2 1 2 1 101000 r 74 goat snp32268-scaffold366-2385472 8 84892766 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398061 Affx-122961746 AX-123268416 8 83272368 ATAATCAAGTCACCAAACAAATAACAAAACAAAAA[C/T]AAAACCCTCAGAGAGGAAGGGCAGGCAAAAGTTGC Y 2 1 2 1 103000 r 74 goat snp32267-scaffold366-2354214 8 84924424 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381517 Affx-122974857 AX-123251875 8 83320463 CTCTGCAGTTGTTTCGAGGAGTCGATGGAGCCTTG[A/G]ACACAAAAGCCCCCGTTGTTTTGTTCTCATGCACT R 2 1 2 1 201000 f 74 goat snp32266-scaffold366-2306119 8 84973040 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417817 Affx-122946806 AX-123288165 8 83351026 ATCCTCAACCTCGAGTAGATTCTTGTGAAGGTTTC[A/G]CTGAGAGCAGTGGAGGCAGTCTGGCTTGGTGACTG R 2 1 2 1 101000 f 74 goat snp32265-scaffold366-2275556 8 85003746 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390679 Affx-122967957 AX-123261036 8 83380275 TGTGGTCCCAGGTGACCAAGAGTTACCCACACAGA[C/T]GTGCTTGCCATAATACCTCAGTTGTGTGATTTTGG Y 2 1 2 1 101000 r 74 goat snp32264-scaffold366-2246307 8 85032981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417983 Affx-122946680 AX-123288331 8 83429646 CAAAGTGCTACTCCCTAAATATAACCAGAGGCAGC[G/T]CAGAGAAAACAAAAACTTGTGCTATAGCGCCACCT K 2 1 2 1 201000 f 74 goat snp32263-scaffold366-2196936 8 85082604 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400339 Affx-122960045 AX-123270694 8 83530659 ACAGGAAAGCCTCAAATCCTTTTAAATTTGTCGAT[A/G]CTTGTTTTGTGGTCTATCTTGGTGAGCTGTGTGAA R 2 1 2 1 101000 r 74 goat snp32261-scaffold366-2095923 8 85184244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803103 Affx-986696172 AX-385289974 8 83541565 GGTTAAGTGTGTCACAAGTGCATGAATCAAAAGGT[A/G]ATGTATTCGTTCCAGGAAGGAATAGAATGTTACTT R 2 1 2 1 600010 f 74 goat 8_83541565 8 83541565 Ancestral_priority_1043 ancestry 0.59 neutral IMAGE 10K 10K ancestral 320765054 Affx-986697185 AX-385252622 8 83541574 TGTCACAAGTGCATGAATCAAAAGGTGATGTATTC[A/G]TTCCAGGAAGGAATAGAATGTTACTTTGAACAGTC R 2 1 2 1 600010 r 74 goat 8_83541574 8 83541574 Ancestral_priority_1043 ancestry 0.652 recommended IMAGE 10K 10K ancestral 320762657 Affx-986697187 AX-385250740 8 83541677 AAAATAATAAAACATTTACCTGAAATGTACAGCCT[C/T]CTGGAAAGTTGTGTTCTATCTATGAAAACATTTCC Y 2 1 2 1 600010 f 74 goat 8_83541677 8 83541677 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 38453443 Affx-122919865 AX-123323776 8 83626229 AGGGTGTGCCAATACTTATCAGTGTCCCCAAAGAT[A/G]TGGGAAACCTTCTTATGCCTATTTAGGCTTCTAGA R 2 1 2 1 201000 r 74 goat snp32260-scaffold366-2000353 8 85280478 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798968 Affx-122933495 AX-385285898 8 83700229 TAGAAACTGTTGAGTGACTGGCTGGATTTAAGACA[C/T]ATTGGACAGGAGATATTGCAGATCACATAGTAGGA Y 2 1 2 1 101000 f 74 goat snp32259-scaffold366-1926353 8 85353614 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413284 Affx-122950207 AX-123283633 8 83729240 ACGCAATCAGATTAGGGCCCGCCCCAATGATTTCA[G/T]CTTAACTTAATCCTCTGCATAGATCCTAATTGGAA K 2 1 2 1 201000 r 74 goat snp32258-scaffold366-1897342 8 85382925 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393213 Affx-122965496 AX-123263570 8 83770093 TTTGTTATAATTTTGTTATACATATTGCTATTTTA[C/T]GACAATAATTTCAGGTCAGAAAGACATGATACAGA Y 2 1 2 1 102000 r 74 goat snp32257-scaffold366-1856489 8 85424435 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278812 Affx-1111836525 AX-519552284 8 83800696 ATTGAAAATATTTTTCTCAATTTTAAGTTGTCTTC[A/G]GCTTCATTTATGATGATTTTTGCCATGCAAATGTT R 2 1 2 1 101000 r 74 goat Random2.2K-931 8 83800696 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320772773 Affx-122951876 AX-385259918 8 83817888 GTTGCAATGCAGAATGTCAGGTCCTTTTTGGCTCC[A/G]TTTCTTCTCAAATTTTGGCCGTCATCTCCTTCAGT R 2 1 2 1 101000 f 74 goat snp32256-scaffold366-1808694 8 85472670 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273427 Affx-1111833594 AX-519547053 8 83828377 GGGAAAGGAGTACGTCAAGGCTGTATATTGTCACC[A/G]TGCTTACTTAACTTATATGCAGAGTACATTATGAG R 2 1 2 1 303000 r 74 goat 8_83828377_AF-PAKI 8 83828377 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38405916 Affx-122955576 AX-123276268 8 83913057 CTACGCATATTCATCACAGGAATGTGTATGATCAT[A/G]TAGTGCTGCTCCTAGGCTATCACCTAAACAAAGAC R 2 1 2 1 101000 r 74 goat snp32254-scaffold366-1713525 8 85569311 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418339 Affx-122946955 AX-123288687 8 83943754 GTATTCACTCAACGTTTATTGTGTCAATGAGAGTC[C/T]GGTTGCACTGATGCAGGGGGCAGGGGGGACAAAGA Y 2 1 2 1 101000 f 74 goat snp32253-scaffold366-1682828 8 85600636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375670 Affx-122978673 AX-123246029 8 84001144 AAGTGGGAAACTGCTTTTGCACACCCCAAATGTGC[C/T]TGGCATTGTGCGGGGGAATCCAACCAATAATCAGG Y 2 1 2 1 101000 r 74 goat snp32252-scaffold366-1625438 8 85658593 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385427 Affx-122971326 AX-123255785 8 84043501 AGTTTACTGTTTTTATTCTTTCAGTTAAGGTCATA[C/T]GATCTTCGCATTATTAAATGGACTTCATCTAATTG Y 2 1 2 1 101000 r 74 goat snp32251-scaffold366-1583081 8 85700851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432504 Affx-122935578 AX-123302845 8 84102230 ATGCAAGTAGTATGTGAATACACTGCCCACCCCAA[A/G]TCACACTCGTAAATATAGCTGAAGTCCACTCACCC R 2 1 2 1 201000 r 74 goat snp32250-scaffold366-1524352 8 85760203 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785742 Affx-122961552 AX-385272782 8 84146261 CCATGCATTTACTTTGTTTCCACATGGCTATTTTG[C/T]AACTACAAGCGAGGCTACAGTAAACATCCTTACAC Y 2 1 2 1 101000 f 74 goat snp32249-scaffold366-1480321 8 85804093 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383562 Affx-122972603 AX-123253920 8 84185965 TTCAGCACCACAACATAACATGTCACAGATAGCAG[C/T]GGGCAGCCTGGTGAGTAAGGCACCAACTCCTGCCT Y 2 1 2 1 101000 f 74 goat snp32248-scaffold366-1440617 8 85844770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411947 Affx-122951146 AX-123282297 8 84220920 TTTGGAAATCTCCTTCATTCCTGATGCCACCAGGC[A/G]CTAATAGCACAGATAAAGAGGAAACCTTTATAGCA R 2 1 2 1 201000 r 74 goat snp32247-scaffold366-1405662 8 85879920 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801111 Affx-122979052 AX-385288025 8 84262907 CTTGTAGTTCCTAGGGGTTTTAGTTGTACTAACAA[C/T]GAGGAGTAAGAAAATGTACATCTACTCCATTTCAC Y 2 1 2 1 102000 r 74 goat snp32246-scaffold366-1363675 8 85922163 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389083 Affx-122968589 AX-123259441 8 84297080 AAGCTGTGTCATGCTTGTCGAATATGCTGATCACT[A/G]TCTTGAGGACTTCCATACATGGGCCATGTGGTGAG R 2 1 2 1 101000 f 74 goat snp32245-scaffold366-1329502 8 85956506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405148 Affx-122956953 AX-123275500 8 84330708 AATAATTAATTGACAGTGAAAGCACTTTTCACTAA[C/T]GAAGACATTTGAAAAACTGAAAATGACAACCAAAG Y 2 1 2 1 103000 r 74 goat snp32244-scaffold366-1295874 8 85990337 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802421 Affx-122969655 AX-385289325 8 84374108 TTCCTAGAAATATGGGAGGATTTTCTGAGTAGACA[A/G]ATTGGCTGAAGCTCACTGTGCAGTGAGGACACTGA R 2 1 2 1 101000 r 74 goat snp32243-scaffold366-1252474 8 86033924 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437734 Affx-122931732 AX-123308072 8 84410709 TGCATCAGAAGGCTGAGGGGTGTGTAGGAAAGTCC[G/T]ATGTGGCCTCAAACTAAGCGTGAGGTTTCTCCAGG K 2 1 2 1 201000 r 74 goat snp32242-scaffold366-1215873 8 86083370 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377956 Affx-122977203 AX-123248315 8 84449158 TGAGACTTTTATCACACAAATGTTGGTGCACTGGA[C/T]GGTGTTCCATGGATCTCTGAGGCCCTGCATTTTTT Y 2 1 2 1 101000 f 74 goat snp32241-scaffold366-1177424 8 86121620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771500 Affx-122934688 AX-385258658 8 84491446 ATACAGGAAGGATATCCATTTACTAACCTTAGACT[G/T]CCTGCCAAATAGGAAGGAAATTGCTGGAGCCTTTC K 2 1 2 1 202000 r 74 goat snp32240-scaffold366-1135136 8 86163951 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390678 Affx-122967958 AX-123261035 8 84548290 CTACCAAATAAGACTCAGCCGAAGTCACATAATAT[A/G]TGAGGGGCAAACTGAGACCAGATTTGGAGATTTAG R 2 1 2 1 201000 f 74 goat snp32239-scaffold366-1078292 8 86220953 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379349 Affx-122976164 AX-123249708 8 84651359 ACAAAACAAGCACAAAAAATTTAACAAATTTCCTA[C/T]GGACCTACAACAATAACCAGACTTCAACAGAAATA Y 2 1 2 1 101000 r 74 goat snp32237-scaffold366-975223 8 86325741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790430 Affx-122955959 AX-385277433 8 84680129 TTTGAATAAGGACTCTGTTACAAGCAAACAAGATC[A/G]CATTAGTCTCTTTACCCAAAATGTTTGTTGCCTTT R 2 1 2 1 101000 f 74 goat snp32236-scaffold366-946453 8 86354603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780277 Affx-122929426 AX-385267372 8 84721359 GAAGCAACATTTTATTTCAGCTGCCTTTCACACAA[C/T]GTCCAGTAACTAATTAATTGGCTTTAAACACTAGG Y 2 1 2 1 101000 r 74 goat snp32235-scaffold366-905223 8 86395787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397811 Affx-122962489 AX-123268166 8 84783987 ATGTAGGAGAGGCGGTGAGGAGTTTGAACTTTTCT[C/T]AGTTGCCAAACTGCTCTTCACTTTCTGTAAACTGC Y 2 1 2 1 201000 f 74 goat snp32234-scaffold366-842595 8 86458285 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421770 Affx-122944353 AX-123292117 8 84836726 TCTAGACCGGGTAAGAAAAAGATCTGAGGCTTCTG[C/T]GTATGTCTCTCTGAACACTTGTTCTCAGACACCCT Y 2 1 2 1 101000 r 74 goat snp32233-scaffold366-789856 8 86509208 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428967 Affx-122938873 AX-123299309 8 84887498 GTGTTTGAGGCAGCACAGACTTGGTCCTAAGTCAC[A/C]GACTGACACCAGGCAAGCACAGTCTGGGGTTCTGG M 2 1 2 1 101000 f 74 goat snp32232-scaffold366-739084 8 86559860 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406435 Affx-122955198 AX-123276787 8 84924135 GCTGATCCAAATGAACTCTTTCCCTGCTCCAGGCC[A/G]CCGGGAAATCCAGCTGCCCCAGAACCCTGGGCCCT R 2 1 2 1 101000 f 74 goat snp32231-scaffold366-702447 8 86597415 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400350 Affx-122960037 AX-123270705 8 84973391 CTTAGTTTCTTTATCTATAAAATGAGAGTGAGTGA[A/G]ATTGTCTTGAGATCAAATAAATGAATTCACGTAAA R 2 1 2 1 101000 r 74 goat snp32230-scaffold366-653191 8 86647387 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778078 Affx-122965840 AX-385265194 8 85021951 TTATCTATCTGCTTTCCTATGAAAAACCACATGAC[A/G]CAGCTACCGGAGTGAGCACAGAATATTACAGACTG R 2 1 2 1 101000 r 74 goat snp32229-scaffold366-604631 8 86695802 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391088 Affx-122966829 AX-123261445 8 85066880 CCCACTCCCACTGGAATCCCCATTATCAATATAGA[C/T]GTGTCTCTGTTTATAAATGACTGGACCTGGAGATT Y 2 1 2 1 101000 r 74 goat snp32228-scaffold366-559702 8 86740443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786614 Affx-122923497 AX-385273646 8 85108751 GACAGGTGAACATTCTGTGTGTGCCAGTAGATAAG[C/T]AACTGTGTAAAATTCAGCTTACTGTCTGTTTCTTT Y 2 1 2 1 101000 f 74 goat snp32227-scaffold366-517831 8 86781505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377004 Affx-122977728 AX-123247363 8 85149745 GGCAAGAGGAGGAAGGGGCTTGGGCCAAATCAAGT[A/C]GGCTTTGAAGGTCAGGGGAGGAGGGTTTGGGATGT M 2 1 2 1 101000 f 74 goat snp32226-scaffold366-476837 8 86822529 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400159 Affx-122960689 AX-123270514 8 85182353 ATTTTTGATATTATGTACAAAGCTGCAGAGAATGT[A/G]CTTTTTCTTTCATTCGCTCCCTCTCTTTTACCCTT R 2 1 2 1 101000 r 74 goat snp32225-scaffold366-444229 8 86854895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411521 Affx-122951670 AX-123281871 8 85233527 TACTGAACTATCCAAATGTTCATTCATTAACTTTG[C/T]ATTTATTCATTTGTAAGTATTTACTAGCACCACTT Y 2 1 2 1 101000 r 74 goat snp32224-scaffold366-393055 8 86906035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450933 Affx-122921771 AX-123321267 8 85289022 TTTCATAGAATAGAAGGAAGAGAAGGTTCTTTCTG[C/T]GGTGACCCCTAGGGTCAGGTGGCATGGAGAATATG Y 2 1 2 1 101000 f 74 goat snp32223-scaffold366-337560 8 86962741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430758 Affx-122937494 AX-123301099 8 85326494 TTTATGGGAAGACACTTAATGCACTAAGGAGAGAA[C/T]TACACGCAATCTTCCTTTCCTGAATTTGCCCATGA Y 2 1 2 1 101000 f 74 goat snp32222-scaffold366-300088 8 87000345 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775917 Affx-122949088 AX-385263048 8 85382513 GATTTTCACTTGCCATAGAAAATTCCTAACTACTA[G/T]AGCTTGAGTTTGCTTTCACCTTTGCAGCCATGTGC K 2 1 2 1 101000 r 74 goat snp32221-scaffold366-244069 8 87056634 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445722 Affx-122926102 AX-123316059 8 85439563 CATCTACTAAAGTCTCTGTATCAGAGTGTGAAACT[C/T]GTGTAAGAATATACAAGCTTCTTCTTCCATTCCAT Y 2 1 2 1 101000 f 74 goat snp32220-scaffold366-187019 8 87111028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378278 Affx-122976873 AX-123248637 8 85476558 CATGCTTGTTTTCTTTCTATGCCTCACATGAATCA[C/T]GCTAATAACTCAAGGGGCTTCATTAGTAATCTATT Y 2 1 2 1 101000 f 74 goat snp32219-scaffold366-150024 8 87148187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802238 Affx-122965695 AX-385289142 8 85546517 GGGTTCTGAGTGTATGAGCAGCATAATCAGATTTA[C/T]AGCTTTAAATGTCACTTCTGGGGTTCTATAAACAA Y 2 1 2 1 201000 r 74 goat snp32217-scaffold366-80065 8 87218533 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444165 Affx-122922950 AX-123314502 8 85598945 AGACATGGCTGATTCCAAGACTAGGGCAGGAAATG[C/T]ACAAGTTAAGCCTGAAACATTTTTTCATATCAGAA Y 2 1 2 1 101000 f 74 goat snp32216-scaffold366-27637 8 87270623 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788018 Affx-122937830 AX-385275039 8 85649609 AGATAGATCACTTTATATCTTGCTAAGACATACTG[C/T]AAAGTAGAATTAGTAAGTTGCAGAACAATTTATCT Y 2 1 2 1 101000 f 74 goat snp19318-scaffold1950-232200 8 87322025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278637 Affx-1111836526 AX-519552116 8 85680837 CTTAGGAAAAATATAATGTTTGTCATCCTCCCATG[A/G]GCTGTCTTCAATGCTTTCAATATGAATTTTAGAAA R 2 1 2 1 101000 f 74 goat Random2.2K-932 8 85680837 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383928 Affx-122972971 AX-123254286 8 85705296 GCTCTATTTAAACTTATGCACACACACATGCATGT[A/G]TGATTTTCATACATATTCCACAGGCTGGGAAGTTC R 2 1 2 1 103000 r 74 goat snp19317-scaffold1950-176513 8 87377705 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425541 Affx-122941450 AX-123295887 8 85746827 CTTCTCATTTCCATGTGGTCTCTATAGTCCCCATC[A/G]TAGATGATCAATGCTAACAAACACTGATCTTGAGA R 2 1 2 1 201000 r 74 goat snp19316-scaffold1950-134982 8 87419228 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802788 Affx-122933681 AX-385289687 8 85783274 CTTGACAAATAGGTTTATTTTAGTACATTAGGAAG[C/T]AGAATTGTTCAAAAGTATCATCTGCTTTCCACTCC Y 2 1 2 1 101000 r 74 goat snp19315-scaffold1950-98535 8 87455713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773355 Affx-122958142 AX-385260497 8 85851565 TAATGGTGGTGATATTTCAAAGGTTAGATAAATAG[G/T]GTATATTGATGGGAATTACCTTTTACTGTGCATCC K 2 1 2 1 101000 r 74 goat snp19314-scaffold1950-30244 8 87524484 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408278 Affx-122953798 AX-123278629 8 85917129 GCTTTTTGGATTAAAGCCACAAGTTCATTACTCTG[C/T]ATGCATGGCAGAACCCTCATTTGTGAAAATGTGTG Y 2 1 2 1 101000 f 74 goat snp12214-scaffold1455-35221 8 87579933 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440455 Affx-122929394 AX-123310792 8 85948294 AGTAGGAATATTTTAAACTGAACAATGATAAAAAT[A/G]CATGACAAAGCTTTTGGGACACAGCTAAAGCTGAA R 2 1 2 1 101000 r 74 goat snp12215-scaffold1455-66386 8 87611612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776462 Affx-122934435 AX-385263589 8 85982655 AAATATACTATAAAGACATATTCGTAACCAGCATA[C/T]AGTGCCTTCAAGAGACTTCTGCCGTTGAGCACTTA Y 2 1 2 1 101000 r 74 goat snp12216-scaffold1455-100747 8 87645641 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403114 Affx-122958125 AX-123273467 8 86011462 GTTGTTACTTTGGGCGATATTCTGATGAGGTGCAT[A/G]TATTTTGCATGCCGGACAGACATTAATTTGGAGTG R 2 1 2 1 101000 r 74 goat snp12217-scaffold1455-129554 8 87674544 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417776 Affx-122947393 AX-123288124 8 86060362 ATGGAGTGCAGAGATGCTCACAGGGAGGAGGGCAC[A/G]TGGCCCCACACCCAGCCTGACTTCTTTCTGCATTT R 2 1 2 1 201000 f 74 goat snp12218-scaffold1455-178454 8 87723644 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417661 Affx-122946837 AX-123288009 8 86119415 CCTACATTTCCTGCATTACAGGTAAATTCTTTACC[A/G]CTGAGCCATGGGGAAGCCCCTAAGCATGTTGACAT R 2 1 2 1 303000 f 74 goat snp12219-scaffold1455-237507 8 87782705 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379109 Affx-122976754 AX-123249468 8 86149446 TATTACAGTCTTACAAGCACCACAATGCCGAATTC[A/G]TTTGACTAGGCAGGTTGTGACTAGGTAGTCACACA R 2 1 2 1 101000 r 74 goat snp12220-scaffold1455-267538 8 87812767 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409435 Affx-122954097 AX-123279786 8 86189925 ATGGCATACTCACCATACTAGATTGTCCATGAGTC[C/T]ACCTCCCCAGCTAACCTGTGACCTTCCTGGGCAAG Y 2 1 2 1 101000 f 74 goat snp12221-scaffold1455-308017 8 87853217 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433145 Affx-122935680 AX-123303486 8 86267719 TTTTAAAATGTCAAGAGTAATGAATGACCTGAAAA[C/T]GCAGAGAAAGTAAAACAGTATAATGCATAGCATTT Y 2 1 2 1 201000 f 74 goat snp12223-scaffold1455-385811 8 87930949 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445120 Affx-122926184 AX-123315457 8 86305882 TCCACCATCTTCTAGTTTCTTAGACACATAGAGCT[C/T]GGTCCCACCTCAGGGTCTTCACCCATGCAGCTCCC Y 2 1 2 1 101000 f 74 goat snp12224-scaffold1455-423974 8 87969074 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770019 Affx-122968824 AX-385257186 8 86365535 CTTTGCTTTCAGTTACAGAACACATTCAAAAAGAA[C/T]AGTCAGAATTTGAGTTCTATCTCATTCTGACTCTC Y 2 1 2 1 101000 f 74 goat snp12226-scaffold1455-483627 8 88043942 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394404 Affx-122964614 AX-123264759 8 86402437 GATTTACATGTACACTATTTTCCCCCCAGGTATTC[G/T]CAATACTCACCCTTTGGGCCAGTCTTCAAGTGGAA K 2 1 2 1 101000 r 74 goat snp12227-scaffold1455-520529 8 88081105 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393362 Affx-122965921 AX-123263718 8 86436687 ACAGGCCTCTCAGGCCTGGTCGTCATTCATCCCAT[A/G]CGGTTGCAGCCCCCAACATGCTGGAGCAAGCTTTG R 2 1 2 1 201000 f 74 goat snp12228-scaffold1455-554779 8 88115312 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377801 Affx-122977319 AX-123248160 8 86493807 TTTCTCCAGTGAATCAGGCTGTACCACCATCCACT[A/G]TTTTTTGGAGGGTGGGTCCATTTTGGCTATAAACT R 2 1 2 1 102000 f 74 goat snp12229-scaffold1455-611899 8 88172242 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427378 Affx-122940090 AX-123297721 8 86564862 AGGGGAAGGGCAACTACAAGGAACTGTTCATCATG[A/G]CCTTGGACACCATGATGACCCTGGACACCCACACC R 2 1 2 1 101000 f 74 goat snp12230-scaffold1455-682954 8 88243331 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464603684 Affx-1110569679 AX-516075027 8 86588883 AAAGCTTCTCAGGGGTGACGTTATTGCAGGTGATA[C/T]TGTTATCTTTCCACTTATGAGAAAGTATTAGCATT Y 2 1 2 1 101000 f 74 goat 8_86588883_AF-PAKI 8 86588883 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401864 Affx-122959419 AX-123272217 8 86601124 CACTGGAGGCACGCAGGAGGGGCCAGTAGCTAAAT[A/G]CCTAGGCACCTACCTCTCCACAGACAGGCAACTCG R 2 1 2 1 101000 f 74 goat snp12231-scaffold1455-719216 8 88279751 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433182 Affx-122935651 AX-123303523 8 86657440 TTAGCAATTCTTTGGTGCCAGTAGGTCTGATGGCT[A/G]TGTGTTCATGATCATTATAAGTTAATTTCTTTCAT R 2 1 2 1 201000 r 74 goat snp12232-scaffold1455-775532 8 88336511 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393335 Affx-122965941 AX-123263691 8 86687610 TGTGTTCTTTTTCAGTGCTTTTAGTACTCTTGAAA[G/T]ATGTCACGGTAAAATTTAGATGCTCGAATACGGAG K 2 1 2 1 101000 r 74 goat snp12233-scaffold1455-805702 8 88365978 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444449 Affx-122926551 AX-123314786 8 86734247 ATAATCCTGAATGCTAGACATCTGAGATCAGGGTG[C/T]CAGAACAGTAGGTCGGGTTATTGTTCAGTTGCTAA Y 2 1 2 1 101000 r 74 goat snp42366-scaffold56-18607 8 88412423 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384443 Affx-122973101 AX-123254801 8 86764639 CTCAGGACTTGGAACACATCTGTTTCAGCTTATGT[A/G]TTTCCGCTGGGTTCAGCATCTTAGCCCCACAGTGG R 2 1 2 1 202000 r 74 goat snp42367-scaffold56-48999 8 88442633 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444219 Affx-122927243 AX-123314556 8 86807179 GAATCTAGCTTCAGGCTCTTACAGAAAGTTCTTCC[A/G]TGAGCTGTGGGGTACAAGGAAGGCAAAGAAAGTGA R 2 1 2 1 201000 f 74 goat snp42368-scaffold56-91539 8 88485028 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443256 Affx-122927544 AX-123313593 8 86851663 ACCGAGGTTGCTTATTTCCTTCTCCTTTCTTAACG[C/T]GAGTTTAATTAAGCCACTGGCATTTCTGTTTGCAT Y 2 1 2 1 201000 r 74 goat snp42369-scaffold56-136023 8 88532184 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790179 Affx-122960936 AX-385277183 8 86913460 ACTCAGAATAACACATGCAAGAATGCTCAGAGAAC[C/T]GTAAACACCATGCTAATCTAAGTTACTCTGGTGAA Y 2 1 2 1 101000 f 74 goat snp42370-scaffold56-197820 8 88593859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406620 Affx-122955833 AX-123276972 8 86950206 TCGTAGCACTGACGGGTTGGAAATAATTTTCCTTT[A/G]ACAATTCTCTGTGAGTACTGTTTATTTTCAGAGTA R 2 1 2 1 201000 r 74 goat snp42371-scaffold56-234566 8 88630796 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427610 Affx-122939360 AX-123297953 8 86983646 ACCTAACCTCCAACCCATTAATCATTAACTCTTTG[C/T]TCCCCTCCTCCTAGGCCCTGGTGGCCACCATTCTA Y 2 1 2 1 101000 f 74 goat snp42372-scaffold56-268006 8 88664166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377573 Affx-122977438 AX-123247932 8 87033219 ATAAGGTGCTAATGGCATAGCGAGAGATTGGTGGT[A/G]GCTGGAGTTATCAAGAAAGGCTTCACAGAAGGTGT R 2 1 2 1 101000 f 74 goat snp42373-scaffold56-317579 8 88714477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447168 Affx-122924430 AX-123317504 8 87084594 CCTAAGCAACCTATCTCTGACTCTCTGTTCTGTTT[A/C]TGTCTCTCCATTCTCATCTCTGTTACCATAGTTGG M 2 1 2 1 201000 r 74 goat snp42374-scaffold56-368954 8 88766280 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796303 Affx-122920777 AX-385283253 8 87118414 AGAAAGTAAGGATTAGCATCTGGGGCTGGCTATTG[A/G]AGCCAGTAATTGTACTCTCAGATGACTCTGGAGGT R 2 1 2 1 101000 f 74 goat snp42375-scaffold56-402774 8 88800059 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434324 Affx-122934743 AX-123304665 8 87171416 CCTCAACAGTCTTGCTTCAGTTGGGAAGTCCCATG[A/C]TGACACAAGCCTGATTCTGTTTTATAAGGAAAGTG M 2 1 2 1 101000 r 74 goat snp42376-scaffold56-455776 8 88853276 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437791 Affx-122931690 AX-123308129 8 87219975 ACAAGAACACACACTTCCAGAGCCCCCAGGTCCGC[A/G]TTCCAGGCGGTATAAGCTTAATTATCCCAGGAAAA R 2 1 2 1 102000 r 74 goat snp42377-scaffold56-504335 8 88902308 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416635 Affx-122947616 AX-123286983 8 87261811 AGTCCTGCAGGGGCTTCTGATGCGAGGAACCACGG[C/T]AATGCAGAAATAATAAGTTCACACCAGTGCAGATC Y 2 1 2 1 101000 r 74 goat snp42378-scaffold56-546171 8 88941722 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405755 Affx-122956502 AX-123276107 8 87299926 GTCTAAAAATATCTCCCATCTCTATTTATTTGCCT[A/G]CTTATTTATTTTTGTCTGGAGAAAACATGCCATTT R 2 1 2 1 303000 f 74 goat snp42379-scaffold56-584286 8 88979889 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420496 Affx-122944856 AX-123290843 8 87352175 GTGAACATTCATTTGCAGCTCCTGGTCTGTGTCAC[A/G]CTCTGTGAAAGTGAGTAAGGGCAACACATGGCCCC R 2 1 2 1 101000 f 74 goat snp42380-scaffold56-636535 8 89032354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417234 Affx-122947285 AX-123287582 8 87394978 TGGTACTCTCATTTCTTCTTAATCCTCCTCCCTCT[A/G]TGCTCCTTTAATTTATTTCTGATCAGCCTGGCTCT R 2 1 2 1 201000 r 74 goat snp42381-scaffold56-679338 8 89075328 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425529 Affx-122941458 AX-123295875 8 87450747 GCACCAGGGACAGTAAGTTGTTTCTGAGAATGGTT[A/G]CAAACGAATGGAAGACAAAGCAAGCAGATCCCATA R 2 1 2 1 101000 f 74 goat snp42382-scaffold56-735107 8 89132122 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446018 Affx-122925860 AX-123316355 8 87492497 TGAATCTCTAACTACAAGATCGAGTAGCAGAACAC[C/T]GTACCAGAAGGAAACTCATTGATCATCATCTTGAA Y 2 1 2 1 101000 f 74 goat snp42383-scaffold56-776857 8 89174183 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440001 Affx-122929789 AX-123310338 8 87586649 CTGAAACTTCTGACACGGAACCTTCAGGATTCACT[A/G]CACACAAATATTCTTTACAGGCTCCAAGGTCCTGT R 2 1 2 1 101000 f 74 goat snp42385-scaffold56-871009 8 89269042 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765790 Affx-122929823 AX-385253245 8 87634860 ACTTCACCGAGACCTATCACTTTATAGAAAGGGCC[A/G]TAGACTATCAGCACACTTAGCACCACTTCCCATCC R 2 1 2 1 101000 f 74 goat snp42386-scaffold56-919220 8 89316476 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393378 Affx-122965910 AX-123263734 8 87680184 GGACCCATTGAATCCCACTACCTTTTTAGTACTGC[G/T]CAGGTATTCTGATGAGTTCTCCTGATATTGCATCC K 2 1 2 1 101000 f 74 goat snp42387-scaffold56-964544 8 89361907 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412305 Affx-122950861 AX-123282654 8 87724933 CTTATGCCAGTCATCCTGACACACTAGTAGCAGTG[C/T]GCCTTTTAATTTCCACATGTATCTTGGTCTGGACC Y 2 1 2 1 101000 f 74 goat snp42388-scaffold56-1009293 8 89407219 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436946 Affx-122933179 AX-123307284 8 87765352 AATATCCTAGGAGCCCTATACACTGAAGGCTTCCC[A/G]TTTCAGTTTTGAGATGGCACCAGACTAAGGGCATA R 2 1 2 1 101000 r 74 goat snp42389-scaffold56-1049712 8 89447776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399258 Affx-122960567 AX-123269613 8 87826682 GTTCTCATCTCTCAAAGCATGTTATTAATAAATTC[A/G]AAATAATATCAAGGCAAATCAGTGCATAAATGCTT R 2 1 2 1 101000 r 74 goat snp42391-scaffold56-1111042 8 89509644 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383803 Affx-122973188 AX-123254161 8 87870941 GTCCTGCCTTTTATTTACTAACTAGGCCAGTTAAC[C/T]GACATTTCTCACCACTGTAGTACGATGCTGACCCT Y 2 1 2 1 101000 r 74 goat snp42392-scaffold56-1155301 8 89554105 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416838 Affx-122948111 AX-123287186 8 87900284 ATGTTGCAACTGACCCTACTTTGGAGATGTTAAAG[G/T]GCTGGTACCTCCTAGGAAGGTTCTGTGGGTGGAAC K 2 1 2 1 101000 f 74 goat snp42393-scaffold56-1184644 8 89583479 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397149 Affx-122962439 AX-123267504 8 87933288 TGTATTTTCCAAAATCGGCCACAGCAATAACTTCT[A/G]CCCACCAGCTCTTCAGGAGGCCACGGTGTCAAGAC R 2 1 2 1 101000 f 74 goat snp42394-scaffold56-1217648 8 89615044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382173 Affx-122974024 AX-123252531 8 87994832 ACTAGTGCTTCCTACTTACCTGCTTGGGGTTTACT[A/G]TGTACTATTTTCATGGGAACTATCACAGGATCACA R 2 1 2 1 101000 r 74 goat snp42395-scaffold56-1279192 8 89676547 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430487 Affx-122937239 AX-123300828 8 88080564 GTATCTTTCTTCAAGCCCTTCAATGCTATATCAGT[A/G]TTGCCTCCCCAAATACTAAGTGTATTTTTATCCCT R 2 1 2 1 101000 f 74 goat snp42397-scaffold56-1364924 8 89761270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427697 Affx-122939292 AX-123298040 8 88119144 AGTCCATATGTATTACAGGGACTCAGCCACACAAT[A/G]TATCACTAGAGTTTAATTTCCTTTAATTGTAGGGT R 2 1 2 1 101000 f 74 goat snp42398-scaffold56-1403504 8 89800840 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407519 Affx-122954707 AX-123277870 8 88159478 TGCTGGTTTCCCTGGTAACTGACAAGCCAGCCTGA[C/T]GTCAGTTACCTCTGTAATTGGTCTTCCTCCTATAT Y 2 1 2 1 101000 r 74 goat snp42399-scaffold56-1443838 8 89841458 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424702 Affx-122941691 AX-123295048 8 88208415 GAATCAAGTATTGTCTGAGTTCCAAGTGGAATTAA[C/T]TGAAACTTGACTTATGTCTCTCTAACAGGATGAAA Y 2 1 2 1 101000 r 74 goat snp42400-scaffold56-1492775 8 89891888 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428792 Affx-122938405 AX-123299134 8 88246331 GCTACATTGACAAGCTGTGTTCCCAGGAAGACTTC[A/G]TCACCAAGGTGGGCTGGGCATGGAGCCTGGGGTCT R 2 1 2 1 101000 f 74 goat snp42401-scaffold56-1530691 8 89930372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376986 Affx-122977743 AX-123247345 8 88288458 CTCTTCTCCCAGCTTGTGACTGCATCTTCCTTGAG[C/T]GTTGTGGAAGGTCGGGGCTCGACTCAGGCTGACTT Y 2 1 2 1 101000 f 74 goat snp42402-scaffold56-1572818 8 89973519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450591 Affx-122922023 AX-123320925 8 88326408 GTCTGGTCTCCAACTTCATCCTTTGTGTCATTTGC[A/G]TCCTCAGTCTTCAGGCTTCAACCACAGCTGCCTTT R 2 1 2 1 101000 f 74 goat snp42403-scaffold56-1610768 8 90009447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451222 Affx-122921961 AX-123321556 8 88356382 TTCCTAGTTCATCTCACTTGCTGAGACTGAAGTCA[A/G]CATTAACTGGACAGATCTGCTGTTTCAGTTTTCAA R 2 1 2 1 202000 r 74 goat snp42404-scaffold56-1640742 8 90039704 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425507 Affx-122941473 AX-123295853 8 88390826 GAGGGCAGTAGGCATCCTGGTAATGGCAGCCAGCA[A/G]CATGACTGTGCACAGAGTGAAACTGTTTCATTGTG R 2 1 2 1 102000 r 74 goat snp42405-scaffold56-1675186 8 90075694 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798855 Affx-122964625 AX-385285785 8 88428702 TGGGAAATATTTTTGCTAAGTATGAACCTCCTGTG[A/G]GAGTGTGATTCAGACTTGATTTTGTAGCAGTTCAG R 2 1 2 1 101000 r 74 goat snp42406-scaffold56-1713062 8 90113633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449608 Affx-122923206 AX-123319943 8 88461921 CTAAGGTATTGCCTGGATACCTGGCTGAGGCAGCA[C/T]GTGATGCCATCCAGTGACAGAACACAAGAAAAGAT Y 2 1 2 1 101000 r 74 goat snp42407-scaffold56-1746281 8 90147393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378557 Affx-122976608 AX-123248916 8 88472537 CAGCTCTGCCCTCCTAACATGTTATTTACCTGGCT[C/T]GGTGCTGGTTCAGAGTAAAATGGAGATGTAACAAA Y 2 1 2 1 201000 f 74 goat snp34726-scaffold412-7685 8 90157695 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407874 Affx-122954504 AX-123278225 8 88515814 CGGTGACTTTTTCCTCCTCTTCTCTGCTTATGGCA[A/G]TCCAATTCCTACTGAGAAGCCAAATGTGTTATTTG R 2 1 2 1 201000 r 74 goat snp34727-scaffold412-50962 NW_017193128.1 15901 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798436 Affx-122950053 AX-385285370 8 88545680 AGAGGGTTAAAGAATGAACGGGTTCAAGGAGCAAA[C/T]GATTCTTTTAAGAGTAGAACATTTTGGTATATATC Y 2 1 2 1 101000 f 74 goat snp34728-scaffold412-80828 8 90233393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417306 Affx-122948163 AX-123287654 8 88580921 ACACTAAAGGCCTCTAGTTACTGTGTGATGACAGA[C/T]GCTCTCTTTCCCCTACTGACCAGTCCAAGGTATTG Y 2 1 2 1 101000 f 74 goat snp34729-scaffold412-116069 8 90269468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415285 Affx-122948832 AX-123285634 8 88637255 CAGTTTTGTGGGCTTGTGACTCTAGTGGCAATAGT[A/G]TATTTTTGAAGAAGGCTTTCCTTAGGAATTCTCCA R 2 1 2 1 201000 f 74 goat snp34730-scaffold412-172403 8 90328208 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771615 Affx-122976599 AX-385258773 8 88697043 GAATAAGAAGTAAAGATTTGGGAAGCTGGAGGCGA[A/G]ACAAGTACGATTCAGTCCATTGAGCTAAATTCTAG R 2 1 2 1 101000 f 74 goat snp34731-scaffold412-232191 8 90387692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428534 Affx-122938743 AX-123298876 8 88729052 AGTTACAAAGCCTGCCCCTTGCCTCATTTTCAGAC[A/G]ACTTTGATGGGCCGTCCTCTCTCCAGAGTTCCCTG R 2 1 2 1 201000 r 74 goat snp34732-scaffold412-264200 8 90420409 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776267 Affx-122973546 AX-385263395 8 88760337 GAAATGAACTATAGTAATAAATTGGGCATGCTATC[A/G]TTCCTCATCATGCTTTTAGCATCCATTAACCAATT R 2 1 2 1 101000 f 74 goat snp34733-scaffold412-295485 8 90451640 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435500 Affx-122933426 AX-123305840 8 88813816 GATTTTCCAAATTATTTTTGTTATAACTTCAATGA[A/C]TTCTATTTATGTAGTTCATAGATTGTGCAAAGTAC M 2 1 2 1 101000 r 74 goat snp34734-scaffold412-348964 8 90505419 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797617 Affx-122946273 AX-385284556 8 88842416 TTCCAGAAGCCAGTGGAAAGTTTCTTAGACAAAAT[G/T]ATTTTTAACTATGAAATAAGAGAATGTGAACAGTT K 2 1 2 1 201000 r 74 goat snp34735-scaffold412-377564 8 90535205 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788013 Affx-122963386 AX-385275034 8 88892073 TTTGGGAATCACTTTGAATGTTTATGAACAGCTGC[A/G]TATTTGTCCTTTGGGTCCATGTAATTGCATGGGTC R 2 1 2 1 101000 r 74 goat snp34736-scaffold412-427221 8 90583456 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385777 Affx-122971055 AX-123256135 8 88946711 CTTTAAAATCCGCTCTTACTGTCCCCTCCAGCCCC[A/G]TCGTTCTCTCCACTTGCCTATTGCTTGCTATGCTC R 2 1 2 1 101000 r 74 goat snp34737-scaffold412-481859 8 90637694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426507 Affx-122940212 AX-123296853 8 88976478 ACAGAGTACTGACACCAGAGACTAACAGAAACTCA[A/G]TATTTATTGACTAAATGAATGGATAAAAGAAGCAA R 2 1 2 1 103000 f 74 goat snp34738-scaffold412-511626 8 90667543 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383719 Affx-122972469 AX-123254077 8 89008733 TAAAACCCAAACCTTGTTACTAAGACTGCCATGTA[C/T]CCCTTTCTCTATTCCCGTTTAGGTTCACTGTGTCG Y 2 1 2 1 101000 f 74 goat snp34739-scaffold412-543881 8 90699926 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791684 Affx-122939553 AX-385278675 8 89045329 AAGGAATCATATCTTTAAAAGGAACTAATAGAAAA[C/T]AGACTAAACCTATGTATCTGATCTCTGGGGCAGTG Y 2 1 2 1 102000 r 74 goat snp34740-scaffold412-580477 8 90736506 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416649 Affx-122947605 AX-123286997 8 89075630 ATACATTAGGATTTTAGTGTGGATATTAGTATAGT[A/G]TGGATAGGCCATACTATAAAGGAAGTAAGAATAAA R 2 1 2 1 101000 r 74 goat snp34741-scaffold412-610778 8 90766810 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442821 Affx-122927707 AX-123313158 8 89109370 AAGGGGGACTACTGCAATTTGTGATCCCTTGGAGA[C/T]GAGGGACTGTATCTTTCTTGCTTTGTATCAGTAGC Y 2 1 2 1 201000 r 74 goat snp34742-scaffold412-644518 8 90800695 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273390 Affx-1111833595 AX-519547020 8 89121146 GGGTTGTGTCCAAAAGATACAGGATTGAGACTGGA[A/G]AAGTTTCTACTAGTTACATCTTGGGAAATTTGAGC R 2 1 2 1 101000 f 74 goat 8_89121146_AF-PAKI 8 89121146 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38393960 Affx-122965056 AX-123264315 8 89141186 TTCTCTCTCCTCCCTCAGGACCAGTAGTAGTTGAC[G/T]AAGAGACACCCAGGCCATGTTTTGGGGGATTCTGC K 2 1 2 1 101000 r 74 goat snp34743-scaffold412-676334 8 90830658 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278639 Affx-1111836527 AX-519552118 8 89174581 CCAAAGAGAAAGCAGTCGATGAGAAATAATAAAAG[A/G]AAATGTATTTGATTTTTGAGCAAGAATATTCTTCT R 2 1 2 1 101000 f 74 goat Random2.2K-933 8 89174581 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384028 Affx-122972894 AX-123254386 8 89189794 ATGCTCAGTAAATCTTTAATCCAATTTTCTGTTGA[C/T]GGACAGAGCTGCTCTTTCATTAGGCCTCTGCTCTT Y 2 1 2 1 101000 r 74 goat snp34744-scaffold412-724942 8 90879821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394283 Affx-122964708 AX-123264638 8 89221664 ATGAACATCTTCCAGGGAGATCTCCTGCCAACTGG[C/T]AGGAACAGATGAACCAAAAACTTCTTTGACATGAG Y 2 1 2 1 201000 r 74 goat snp34745-scaffold412-756812 8 90911938 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403034 Affx-122958548 AX-123273387 8 89254021 ACAGCTGCAGGAACGGTACGGTGGAGAGCTGTAAC[C/T]GTGGCCATTGCCACCTGCTCTGGAGTATACTTCTT Y 2 1 2 1 101000 f 74 goat snp34746-scaffold412-789169 8 90944496 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426705 Affx-122939894 AX-123297051 8 89297328 GGGATTAGCTAGCTTAAATGTTCTGTCATTGGACA[C/T]AAACTTTCCACAAGGAGATCTAATTTTAATGCAAC Y 2 1 2 1 101000 f 74 goat snp34747-scaffold412-832476 8 90987912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389818 Affx-122968192 AX-123260175 8 89336571 TCAGTTACACACACACACACATATATAAATGTCAC[A/G]TTTCTATAAATTTATTCCATTCTCCAACCAATGCT R 2 1 2 1 201000 r 74 goat snp34748-scaffold412-871719 8 91027795 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409729 Affx-122953027 AX-123280080 8 89395262 TCTCCGGAGCCAAGGACATGAATACCAGGTCGGTC[A/G]TCCTTTGGGGACCCCTATACTTCCACCTTCTAGCC R 2 1 2 1 103000 r 74 goat snp34749-scaffold412-930410 8 91087017 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400063 Affx-122960765 AX-123270418 8 89443663 ACAGGGGAAATGGCTTACTCATATCAACTATTAGA[C/T]AGGGTTTGGGGGAGAATCAGAGGGACCAATGCCTG Y 2 1 2 1 101000 f 74 goat snp34750-scaffold412-978811 8 91135877 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799085 Affx-122979056 AX-385286015 8 89489430 TCTTGAGGATATTTTGCGATCCACATCATGACCAG[C/T]AATTAACAGTTAAACCAAACACTGTTAATGTCAGT Y 2 1 2 1 101000 f 74 goat snp34751-scaffold412-1024578 8 91181582 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401685 Affx-122959556 AX-123272038 8 89563328 TACTTTTCTGCTTCTGCATTTTCCACATCGTTTAG[C/T]GTAAAAGAGAAAAAAGATAAAATCACTCAAAGAAT Y 2 1 2 1 101000 f 74 goat snp34753-scaffold412-1098476 8 91255152 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431677 Affx-122936790 AX-123302018 8 89592511 TGGCTTTGTGAAACTTTGAAAAGACACACACATCT[C/T]AAAGTTCACTATTTACAATAGCCAAGACATGAAAG Y 2 1 2 1 103000 f 74 goat snp34754-scaffold412-1127659 8 91284328 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391750 Affx-122967479 AX-123262107 8 89628167 GAGAGACACATATATCAACAAATAATCATTAGGCT[A/G]TGCAACAGATCTAGAAAAGAAGAGTGTTCAAGGTA R 2 1 2 1 101000 f 74 goat snp34755-scaffold412-1163315 8 91320049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390921 Affx-122967086 AX-123261278 8 89660512 ACCTCCTTTTCCTTGTTTAAAGATTTTTCTCAGCC[A/G]TAGCCTGTTCTCTCCCAGTGTTTTTCTGCCTCTAG R 2 1 2 1 101000 r 74 goat snp34756-scaffold412-1195660 8 91350490 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392151 Affx-122966319 AX-123262508 8 89690910 CTCAGTCACAGGAGTACCAGTGTTCCTTCAGATGT[C/T]CCTCAGGAACAGAGTTTACAAACCACCTATAGTGA Y 2 1 2 1 101000 f 74 goat snp34757-scaffold412-1226058 8 91382380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426346 Affx-122940264 AX-123296692 8 89720048 CACCAAAGGAGTGAGGATAGAAAAGAGGCCAGGGA[C/T]GGAATCTCAGGCCACTTTAACAAGATCAGAGATCA Y 2 1 2 1 101000 f 74 goat snp34758-scaffold412-1255196 8 91411747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448992 Affx-122923107 AX-123319327 8 89754876 CTGGATACCCAGCATCTAGTATAATACTCAACTTG[C/T]GGTAAGTGGTTTAATACACATTTGCTGAACAAATA Y 2 1 2 1 101000 f 74 goat snp34759-scaffold412-1290024 8 91447031 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407565 Affx-122954675 AX-123277916 8 89786411 TGGGCACTTTTAACATTTAAAAGCAACCAGTAATT[A/G]TCACATTTCTGCCCTTACTTCAATTGGGTACATAT R 2 1 2 1 101000 r 74 goat snp34760-scaffold412-1321559 8 91478567 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440566 Affx-122929307 AX-123310903 8 89815942 TTAAAATCAATAATTTATTTTGAAAGAAGACATTA[C/T]GATGACTTTATTTTCTAAGTCAGAATGTTTCTGGA Y 2 1 2 1 103000 r 74 goat snp34761-scaffold412-1351090 8 91508030 G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398306 Affx-122962147 AX-123268661 8 89890385 CAGGTCACTGGACATTTCTCCCAAGGCAGCTGTGG[C/T]GAGAGGGGATATATCACATAACCTACTCTGGACTT Y 2 1 2 1 101000 r 74 goat snp34763-scaffold412-1425533 8 91583191 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385188 Affx-122971727 AX-123255546 8 89919151 GTCATCCTTTCCCAGGCCCCTTAGGTAGGGAAAAA[G/T]ACTTTTCTTGAAGGTTTTTGTTTGTTTGTACCTAG K 2 1 2 1 103000 f 74 goat snp34764-scaffold412-1454299 8 91611966 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476250 Affx-1251763756 AX-586011671 8 89943082 TCACTAGTTTTTAAGCAGGTTGTTATATATAAGAA[-/TATATATGTTATGCTCCGAGCCCGTATCTCCGAACCGACCCATGACTCATGTCCTAGAGACTGTCGTTTGGTCCCTAACA]ATATAATGCCCTGATTAAAAAAAAAAAAAAAAAAA - 8 1 4 1 20000 f 74 goat SV_348 8 89943082 - deletion junction SV-TF-chip 539476502 Affx-1251763756 AX-586011896 8 89943082 TCACTAGTTTTTAAGCAGGTTGTTATATATAAGAA[-/TATATATGTTATGCTCCGAGCCCGTATCTCCGAACCGACCCATGACTCATGTCCTAGAGACTGTCGTTTGGTCCCTAACA]ATATAATGCCCTGATTAAAAAAAAAAAAAAAAAAA - 4 1 4 1 20000 r 74 goat SV_348 8 89943082 - deletion junction SV-TF-chip 562165333 Affx-1251763756 AX-606940744 8 89943082 TCACTAGTTTTTAAGCAGGTTGTTATATATAAGAA[-/TATATATGTTATGCTCCGAGCCCGTATCTCCGAACCGACCCATGACTCATGTCCTAGAGACTGTCGTTTGGTCCCTAACA]ATATAATGCCCTGATTAAAAAAAAAAAAAAAAAAA - 8 1 4 1 20100 f 74 goat SV_348 8 89943082 - deletion junction SV-TF-chip 562165548 Affx-1251763756 AX-606940959 8 89943082 TCACTAGTTTTTAAGCAGGTTGTTATATATAAGAA[-/TATATATGTTATGCTCCGAGCCCGTATCTCCGAACCGACCCATGACTCATGTCCTAGAGACTGTCGTTTGGTCCCTAACA]ATATAATGCCCTGATTAAAAAAAAAAAAAAAAAAA - 8 1 4 1 20100 f 74 goat SV_348 8 89943082 - deletion junction SV-TF-chip 562165763 Affx-1251763756 AX-606941172 8 89943082 TCACTAGTTTTTAAGCAGGTTGTTATATATAAGAA[-/TATATATGTTATGCTCCGAGCCCGTATCTCCGAACCGACCCATGACTCATGTCCTAGAGACTGTCGTTTGGTCCCTAACA]ATATAATGCCCTGATTAAAAAAAAAAAAAAAAAAA - 8 1 4 1 20100 r 74 goat SV_348 8 89943082 - deletion junction SV-TF-chip 320797318 Affx-122977998 AX-385284257 8 89952072 ACGTAACTAGTGAGTCAGGAAAACTGGATAAAATG[A/G]CTGCAATTTGCAATGAGAGTATAACTAAATTAATT R 2 1 2 1 101000 f 74 goat snp34765-scaffold412-1487220 8 91645490 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406912 Affx-122955618 AX-123277263 8 89981503 CCTCTACTGGTACTGTTCTCTCTCAAGCCACCGTC[A/G]TCTTTCGTCTGAATGATGTAACAGCCTCCTATTTG R 2 1 2 1 101000 r 74 goat snp34766-scaffold412-1516651 8 91674807 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791130 Affx-122961666 AX-385278125 8 90013365 AAACAAAACTGTACTTATTCTACCTACCTGTGTCT[A/G]CCTCTAGAGCAGAGCTCTTGTACCCTCTGTAGCTG R 2 1 2 1 102000 r 74 goat snp34767-scaffold412-1548513 8 91707173 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446103 Affx-122925798 AX-123316440 8 90052578 ATGAGACTGAGCCTGAGTCTAAGGCAGTGGTGGAA[C/T]GGGAGAATGATGAGAGATTCAGCACAATCACCTTC Y 2 1 2 1 101000 r 74 goat snp34768-scaffold412-1587726 8 91747856 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446379 Affx-122925588 AX-123316715 8 90098317 CAAAAATAACAGACATATAAACACATGTTGTAATC[A/G]CCTAATGTATTCGTACTATTGTTTTTAAAGAAACA R 2 1 2 1 101000 r 74 goat snp34769-scaffold412-1633465 8 91793520 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430951 Affx-122936829 AX-123301292 8 90127793 ATTGTATTTGAAAATGTTTTAGTTTTTCTGTTGAA[C/T]GACTACAAAGACATGTTACTTACAGTGACTTTTAA Y 2 1 2 1 101000 r 74 goat snp34770-scaffold412-1662941 8 91823115 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401730 Affx-122959521 AX-123272083 8 90161228 GTCAAGCATTCCCCATTATAGACTTAAGTCTGCAC[A/G]TAGATTTAAGTATCCCCTTGCTGTAGGCTAACCAG R 2 1 2 1 201000 r 74 goat snp34771-scaffold412-1696376 8 91856990 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798383 Affx-122960164 AX-385285317 8 90279229 TTCATAGCCTGTAGCAAAATCCTGGTTTAAATGTG[C/T]CATTCAATTTTTACCACACATAATAAAATAAAATA Y 2 1 2 1 101000 f 74 goat snp32856-scaffold38-4250952 8 91982918 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394558 Affx-122964457 AX-123264913 8 90328129 TTCTGCCTAATACAAGCTATTCAGAACTGAAAATG[G/T]ACATGCTTATTCTGTTCAGTGGAAATAGCTCAAAG K 2 1 2 1 101000 f 74 goat snp32855-scaffold38-4202052 NW_017189864.1 1771 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791068 Affx-122961234 AX-385278063 8 90360748 TTGACTTAGAGTTAGATTTTCACCTTTATTTAATT[A/G]CTAATATATACTTTCTATTTTAAAGTAGTCATTCA R 2 1 2 1 202000 r 74 goat snp32854-scaffold38-4169433 8 92063595 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383538 Affx-122972621 AX-123253896 8 90393367 TATCTTTAAAGGCAAATAGGAGATATCCAGTGTAT[A/G]TAGGTATGCTTGTGTCAGCTGGTATATTTCTTCCT R 2 1 2 1 101000 r 74 goat snp32853-scaffold38-4136814 8 92097207 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406441 Affx-122955194 AX-123276793 8 90450902 GATCTCTTAACAAATATGTATGCATTCCCTACCTC[C/T]GGATTCCTCTACCCTATCTGCTGTTTATTCATGAT Y 2 1 2 1 101000 r 74 goat snp32852-scaffold38-4079279 8 92155670 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791053 Affx-122968775 AX-385278048 8 90517672 GCTGCCGCATTTGTTATGAGATGGCTTTGAAAGCA[C/T]GCAAACATGACATTGAACTTCCAGCTCTATTCTAG Y 2 1 2 1 101000 f 74 goat snp32851-scaffold38-4012509 8 92222661 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801087 Affx-122945902 AX-385288001 8 90590028 ATTCAATGTTTTCTGGTAGCACTGAACAGGTCACT[G/T]TGTCTCTGACTTGAGTATTTAAACATGTATACATT K 2 1 2 1 101000 f 74 goat snp32850-scaffold38-3940153 8 92295734 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412226 Affx-122950919 AX-123282576 8 90629469 CACTGTCTACTCAGTACCATAATATGATAGTTATA[G/T]AGACAACATGGATAAGAATATCCTCATTTAATACT K 2 1 2 1 101000 f 74 goat snp32849-scaffold38-3900712 8 92334754 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278818 Affx-1111836528 AX-519552289 8 90639413 CCCATGGTAAGCACTTGATAAATAATTGCATAATG[A/G]AAATCAGTCATCATTCCCACAACTATCACAGCTGC R 2 1 2 1 101000 r 74 goat Random2.2K-935 8 90639413 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448226 Affx-122924220 AX-123318562 8 90667911 ATGTTTATATCTGTGTTTATTTAATCCCACATCAG[C/T]ATCCATAAAATTTGTCACTTCTTCCACTTTTCCCC Y 2 1 2 1 101000 r 74 goat snp32848-scaffold38-3862270 8 92373202 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387969 Affx-122969601 AX-123258327 8 90739837 CTGGCTTTACAATCCTCAAGGGATTAAAAGACAGG[A/C]GAAGAAGAATCATCCTACACTGATGCTACCAACAC M 2 1 2 1 101000 f 74 goat snp32846-scaffold38-3790344 8 92445414 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410011 Affx-122953261 AX-123280361 8 90835376 GTGAGATTTTTGAGAGACAGGGGTCTCAAAGAGTA[A/G]TAAGTGTGTGTGTGAATTTCAAATAACAGAAGCAA R 2 1 2 1 103000 f 74 goat snp32844-scaffold38-3694805 8 92542235 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419043 Affx-122946024 AX-123289391 8 90871893 TTCTATGCCAGAGTTCTGTGGTTTCTAAGATCTTT[A/C]ATGATTCAGAAAAGCAAGTTTGCTTTAGCCCTTTT M 2 1 2 1 101000 f 74 goat snp32843-scaffold38-3658288 8 92579066 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410646 Affx-122952775 AX-123280996 8 90912786 GCACCCTAAACATAATAAATTGCATTTTGGTAGTG[C/T]AATTCTTTTAAATAAATATTTTCTCATTTTTAATT Y 2 1 2 1 103000 f 74 goat snp32842-scaffold38-3617395 8 92620189 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795346 Affx-122919757 AX-385282302 8 90990128 GTACACACAGCACAGTCTTAAGGGTTACAAGTAGA[A/G]AGAGTGCAGCAGGACCTGAGAATTTTATTAAGGTC R 2 1 2 1 101000 r 74 goat snp32841-scaffold38-3540053 8 92698740 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396708 Affx-122962817 AX-123267063 8 91038589 TTATCTTGATACAACCTTGATACTTGAAACTTTTT[C/T]TTCCGTGACTTAAATAAGAAACCAATCTCCTACTT Y 2 1 2 1 101000 r 74 goat snp32840-scaffold38-3491592 8 92748226 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762667 Affx-986697197 AX-385250747 8 91059611 TGTTTTAGGTGCTGAATACTCAGTATGTAGTAGGG[A/G]ATACGTAGCCCAGGATTTTTTTATTTGTGCAAAGA R 2 1 2 1 600010 f 74 goat 8_91059611 8 91059611 Ancestral_priority_1043 ancestry 0.648 recommended IMAGE 10K 10K ancestral 38400482 Affx-122961294 AX-123270837 8 91076807 ACAAGTTTGTGTAGAACCATTTTTCACCCCCTCTG[A/C]TTATCAAATATAACTATAAAATCCTAGAAATGACA M 2 1 2 1 201000 r 74 goat snp32839-scaffold38-3453374 8 92786063 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444983 Affx-122926659 AX-123315320 8 91106362 CTTGTGACCATTTGTGACTCCATGGAATATGCCAG[A/G]CTTCCCTGTCCTTCACTATCTATCAGAGCTTGCTC R 2 1 2 1 303000 f 74 goat snp32838-scaffold38-3423819 8 92815931 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790148 Affx-122938985 AX-385277153 8 91177394 AACAACCACTCAAATGTGTTGGAACATCAAGATAA[C/T]GCTTTCTAATTAAGGGAATTTTAACTTATTGGGCT Y 2 1 2 1 201000 r 74 goat snp32837-scaffold38-3352787 8 92887914 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799757 Affx-122945506 AX-385286684 8 91209682 TTTCAGGGCCATTTGGGTGTACTGCATGATTCTTA[C/T]ATTTGTTATTAATTTCAGTAGTTATCAGGATGTGG Y 2 1 2 1 101000 f 74 goat snp32836-scaffold38-3320499 8 92920500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788306 Affx-122965970 AX-385275324 8 91265535 TTCCACAAGACTTTCAAAGAAAGATCTACACTAAT[A/G]TCTGTGGTTATCATAAATGATAAGAATTGACTTTC R 2 1 2 1 201000 f 74 goat snp32835-scaffold38-3264646 8 92971093 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274010 Affx-1111833949 AX-519547615 8 91334753 CCCAGAAGATTCCTATTTAATGTTGAACTGTAGAG[A/G]TTTGATCTGCAGAGTGCAGACTAATTAACTTTAAG R 2 1 2 1 201000 r 74 goat GoatD01.011270 8 91334753 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437750 Affx-122931720 AX-123308088 8 91342697 AAAACAACGGTAAGATAAATTTTTTCCTGGTTGCC[A/G]CAAGTATCACTGCTTAAGTATTTCAGTCTCATTTT R 2 1 2 1 101000 r 74 goat snp32834-scaffold38-3187484 8 93059994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404705 Affx-122957260 AX-123275057 8 91381127 TATGATTACCCTCATGCACTATAGCCCTTCAATTC[A/G]TCTAGAGTTTAACATTTAATTTTATCTTGTATAGC R 2 1 2 1 101000 f 74 goat snp32833-scaffold38-3149054 8 93098508 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779507 Affx-122943541 AX-385266610 8 91411861 GAATCTACAACAGGGTCTAGCATTGCATAGGAATG[C/T]AACTTAGATTCAAGCGAATTAATGAAATATATGTC Y 2 1 2 1 101000 f 74 goat snp32832-scaffold38-3118320 8 93129855 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404103 Affx-122957121 AX-123274455 8 91452597 GTATGGTTTATTTAAAAGTAACTGTATTTTCTCAA[G/T]CCCTTTGCATCATATGAATTTTAAGTTTCCTTCAA K 2 1 2 1 101000 f 74 goat snp32831-scaffold38-3077584 8 93178442 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432604 Affx-122935502 AX-123302945 8 91488071 CTTCTCTCCAACAGCTTGCCCTCTCTGGGCCCCAT[A/G]CTCACTGTCCCTCCTCTTCTTTGTTCTCATTATCC R 2 1 2 1 101000 r 74 goat snp32830-scaffold38-3042110 8 93213843 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391100 Affx-122966819 AX-123261457 8 91529955 CAGCCAACCATCTGTATGACCTTTATTTTACCTAG[A/G]GAGCCTCTCTGCGACTCTGTGCTCAACCTCACTAT R 2 1 2 1 101000 f 74 goat snp32829-scaffold38-3000226 8 93255976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785973 Affx-122957829 AX-385273009 8 91596562 AACTCATGTAGGTCTGTTCCTTAAAACGAAGAACC[A/G]CATGTAAACTGAGGATGGAGGTGGGTACCAGTCTT R 2 1 2 1 201000 r 74 goat snp32828-scaffold38-2933619 8 93322484 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432555 Affx-122935540 AX-123302896 8 91631461 ACACTGACTTAATTTGCCTGTGCAAAGGATTTTTT[A/C]TTCATTTGATCTTTTTCAAACACACCACCCCAGCC M 2 1 2 1 201000 r 74 goat snp32827-scaffold38-2898720 8 93357766 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273430 Affx-1111833596 AX-519547056 8 91635604 GTGTTTATTTTATACAGCTATTAGCAAACTGTGTT[A/G]CCACAAATCTTCATATAATTCTTTATAAGCAAGAC R 2 1 2 1 101000 r 74 goat 8_91635604_AF-PAKI 8 91635604 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320787038 Affx-122922420 AX-385274066 8 91701276 CGTTGCAATAACTTTAACCCAGATATCATTCTCCC[A/G]TCTATTACAAACAAAGCACCTCACGAGTGTTTAAC R 2 1 2 1 101000 r 74 goat snp32826-scaffold38-2828905 8 93429233 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801188 Affx-122972329 AX-385288101 8 91740491 GAATTTAACATTACATTAATAAATGTGAAGGAGGG[C/T]AGTAGCAGAGCTTTCAATTTTTAATCATATATTTT Y 2 1 2 1 101000 f 74 goat snp32825-scaffold38-2789690 8 93468166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434446 Affx-122934653 AX-123304787 8 91845373 CAATTACTTTGCACCTACCTCTGTGAAATTCTGCC[A/G]TAAGGACCTCTAAATTAGTATTTCTTTCTCAAAGT R 2 1 2 1 201000 r 74 goat snp32823-scaffold38-2684808 8 93576530 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414469 Affx-122949562 AX-123284818 8 91876738 AATGATCATTGGATTGACCACATGAAAGGTAACTG[A/G]TGAACTTGACCAAAGAAAATGACAAATGTTTAGTC R 2 1 2 1 101000 f 74 goat snp32822-scaffold38-2653443 8 93607886 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441067 Affx-122928913 AX-123311404 8 91909764 AGAATCTAATGTAGAGCTCAGAAAGCTTAAAGTGT[A/G]CATATGATTTAGTCATTAGAAGTGCTGATTCATGG R 2 1 2 1 101000 f 74 goat snp32821-scaffold38-2620417 8 93640986 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452245 Affx-122920781 AX-123322578 8 92036556 TGAAGGCCTATCCTGCAAAAGGAAAATAGGGAAGA[A/G]AACATGTTATGTATAGAGATGGTAGCAAAAATTCT R 2 1 2 1 101000 f 74 goat snp32819-scaffold38-2493625 8 93765686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798622 Affx-122922146 AX-385285554 8 92076283 GGATTAAATGAGGTATAATAAGGTGTTTATCTCAG[C/T]GCTTGCCACAAAATAGGTTCTCTTTGAAGCCAAAG Y 2 1 2 1 101000 r 74 goat snp32818-scaffold38-2453898 8 93803351 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787758 Affx-122947407 AX-385274781 8 92108060 CAAATTTTAAGTAGAATTGCCTAATAAACATATGA[A/C]TAGGTCACATATTAATAATTAAAAGTGGCATGAAT M 2 1 2 1 101000 r 74 goat snp32817-scaffold38-2422121 8 93839151 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425125 Affx-122941217 AX-123295471 8 92141092 AGAGATTTCACCCTGGGGTATCTCAAGTGGCCCAC[A/G]TATCTTCTCACAGAAGCTGACAGAATTGATTTTGG R 2 1 2 1 201000 r 74 goat snp32816-scaffold38-2389089 8 93872153 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278642 Affx-1111836529 AX-519552121 8 92174917 TAAGAAGTACAGAAAATTACACATAGAGAAGGAGG[A/G]AAGGAATTTGACCAATATACCTGATCTTCAATCTT R 2 1 2 1 101000 f 74 goat Random2.2K-936 8 92174917 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38423672 Affx-122942332 AX-123294018 8 92194453 TGCCTCAACAGAACTACCTCTTCCTAGGAGTGGAG[C/T]AAAGAACCAAAGCAATAGTTTCCAAGTTAATTTAT Y 2 1 2 1 101000 f 74 goat snp32815-scaffold38-2335728 8 93926228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404387 Affx-122956796 AX-123274739 8 92274828 TGTTTATTGTTTATTACCTGTGCTCAGTGCCTGGC[A/G]CATGGTAGGTGATTAATGAATATTTATTGAACGTA R 2 1 2 1 103000 f 74 goat snp32814-scaffold38-2255353 8 94006792 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375835 Affx-122978543 AX-123246194 8 92332922 CCCAATAAGGTGATCAGGTACATCAGCAAGCACAG[A/C]ACGAATATGATGATCTCACCTTTGGGGTAGTGGGA M 2 1 2 1 101000 f 74 goat snp32813-scaffold38-2197259 8 94065144 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409585 Affx-122953572 AX-123279936 8 92366186 ATATTTTCAAGGGTCAGAGCTGTCACTTCCATCTT[A/G]CATTTGGATTGTTCATTTTAAACAGGGCTGAGATA R 2 1 2 1 201000 r 74 goat snp32812-scaffold38-2163995 8 94098715 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793998 Affx-122966218 AX-385280967 8 92418501 GTAACCTGTTTTGATGTAGCCATGTATTCAAGTTT[A/G]CTTGGCAAATACACTATCATTATGTTAAATACACT R 2 1 2 1 101000 f 74 goat snp32811-scaffold38-2111680 8 94155548 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378802 Affx-122976985 AX-123249161 8 92476758 ATCTACCTGAATTCATACCTTAAACTGCCCATTCT[G/T]TACTTCTTCCCCTCTTCCTCCTCTCTCTCCTGCTT K 2 1 2 1 303000 f 74 goat snp32810-scaffold38-2053423 8 94219858 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783709 Affx-122944562 AX-385270766 8 92515747 AATATACCATATACATTTAGTTCTTCAAATACTGT[A/G]TATAGTTTGTATATTATGAACTTATATGTTGCTTT R 2 1 2 1 101000 f 74 goat snp32809-scaffold38-2014434 8 94259534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424653 Affx-122942160 AX-123294999 8 92566452 GATACAAGAACACTCATCACTATATATCATTCCTT[A/G]TTTCATTCCAGTATCTTACCATCTTCTTTGTATCC R 2 1 2 1 101000 r 74 goat snp32808-scaffold38-1963729 8 94309459 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762677 Affx-986697207 AX-385250756 8 92667550 GGTAGAAGTCGTGTTTTGAGATTTTTAGCTGGAAA[A/G]TAATAAAGAGAGCTAGAAATATTGATAGAATCGTT R 2 1 2 1 600010 f 74 goat 8_92667550 8 92667550 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38395442 Affx-122963929 AX-123265797 8 92753749 AATTTTGTTCCTCTTTGTGTACGCAATGGAGCTGA[C/T]GTTCAGAGAGGCTAAGTTATCTGCCTAAGGAAACA Y 2 1 2 1 101000 f 74 goat snp32804-scaffold38-1776432 8 94496852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403547 Affx-122957599 AX-123273900 8 92801747 AAGTGAGTGCGTGGTATATACATTCATATAATAGA[C/T]GATAAATTTGATATTAAAAAATTCCTTGGTGATAA Y 2 1 2 1 101000 f 74 goat snp32803-scaffold38-1728434 8 94545300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426160 Affx-122940597 AX-123296506 8 92835123 AAATTTGCAAAATTCAGCAAAATCAGCAAAAATTT[A/G]CAAAAATCAGCAAAATTCTGAAAGATGGAAAGTTG R 2 1 2 1 201000 f 74 goat snp32802-scaffold38-1695058 8 94578667 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442189 Affx-122928799 AX-123312526 8 92868381 CAGTCATAAGCACAGCATCATCAGAAGGCAAATTA[A/G]TTGTACCCAGTGTGTAGAGACTGTGGGCCTGAGGA R 2 1 2 1 101000 f 74 goat snp32801-scaffold38-1661800 8 94611485 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767548 Affx-122927652 AX-385254802 8 92923160 AAGAAGACTAATTTCAATTCCCAATCCCAATGTTA[C/T]TAGGTCTGTTATGTGCTATTACACATTTATATACA Y 2 1 2 1 101000 f 74 goat snp32800-scaffold38-1607021 8 94666358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776214 Affx-122960465 AX-385263342 8 92976303 TTCCTCTCCAGGAAATAGGTAATATTAGACTATGT[C/T]AAGCAATAACATTAGGCAATATTATTTTGTAGATT Y 2 1 2 1 201000 r 74 goat snp32799-scaffold38-1553878 8 94720106 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437890 Affx-122931668 AX-123308228 8 93028940 CAAACTGTAGATAAATATGGATGCCTGCCCTCCCA[A/G]AAGAGGAGGGTAAGTGTTCTCCTGGGTGCTGATGA R 2 1 2 1 101000 f 74 goat snp32798-scaffold38-1501241 8 94773604 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773911 Affx-122953998 AX-385261050 8 93071905 ACAAACACAAGCCATTTAATGTTTAAGCAGAAGAA[A/G]ATTCTGGATCATCAGCTGACCAGATTCCAGGCTCA R 2 1 2 1 101000 r 74 goat snp32797-scaffold38-1458276 8 94816975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408150 Affx-122954224 AX-123278501 8 93109281 TTATCATTAGAGTTTGCAGACAAGCTCCTTTAAGA[C/T]GTTTTAGCCACTGCTCCCACTAAAATATAAGCACT Y 2 1 2 1 101000 f 74 goat snp32796-scaffold38-1420900 8 94854731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476251 Affx-1251763757 AX-586011672 8 93141114 TTATTGTTCTTTATGATTTCTTTCCTTCTACAAAC[-/TTTGGATGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCACGTCCTATTCCTCTGCCATCTTAGGACTGCCCCTCT]GGATGTTCTTTGTTCTTCTTTCTCTAGTTACTTTA - 4 1 4 1 20000 f 74 goat SV_351 8 93141114 - deletion junction SV-TF-chip 539476503 Affx-1251763757 AX-586011897 8 93141114 TTATTGTTCTTTATGATTTCTTTCCTTCTACAAAC[-/TTTGGATGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCACGTCCTATTCCTCTGCCATCTTAGGACTGCCCCTCT]GGATGTTCTTTGTTCTTCTTTCTCTAGTTACTTTA - 4 1 4 1 20000 r 74 goat SV_351 8 93141114 - deletion junction SV-TF-chip 562165235 Affx-1251763757 AX-606940647 8 93141114 TTATTGTTCTTTATGATTTCTTTCCTTCTACAAAC[-/TTTGGATGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCACGTCCTATTCCTCTGCCATCTTAGGACTGCCCCTCT]GGATGTTCTTTGTTCTTCTTTCTCTAGTTACTTTA - 8 1 4 1 20100 r 74 goat SV_351 8 93141114 - deletion junction SV-TF-chip 562165536 Affx-1251763757 AX-606940947 8 93141114 TTATTGTTCTTTATGATTTCTTTCCTTCTACAAAC[-/TTTGGATGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCACGTCCTATTCCTCTGCCATCTTAGGACTGCCCCTCT]GGATGTTCTTTGTTCTTCTTTCTCTAGTTACTTTA - 8 1 4 1 20100 f 74 goat SV_351 8 93141114 - deletion junction SV-TF-chip 562165984 Affx-1251763757 AX-606941393 8 93141114 TTATTGTTCTTTATGATTTCTTTCCTTCTACAAAC[-/TTTGGATGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCACGTCCTATTCCTCTGCCATCTTAGGACTGCCCCTCT]GGATGTTCTTTGTTCTTCTTTCTCTAGTTACTTTA - 8 1 4 1 20100 r 74 goat SV_351 8 93141114 - deletion junction SV-TF-chip 562166024 Affx-1251763757 AX-606941433 8 93141114 TTATTGTTCTTTATGATTTCTTTCCTTCTACAAAC[-/TTTGGATGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCACGTCCTATTCCTCTGCCATCTTAGGACTGCCCCTCT]GGATGTTCTTTGTTCTTCTTTCTCTAGTTACTTTA - 8 1 4 1 20100 f 74 goat SV_351 8 93141114 - deletion junction SV-TF-chip 562166225 Affx-1251763757 AX-606941633 8 93141114 TTATTGTTCTTTATGATTTCTTTCCTTCTACAAAC[-/TTTGGATGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCACGTCCTATTCCTCTGCCATCTTAGGACTGCCCCTCT]GGATGTTCTTTGTTCTTCTTTCTCTAGTTACTTTA - 8 1 4 1 20100 r 74 goat SV_351 8 93141114 - deletion junction SV-TF-chip 562166491 Affx-1251763757 AX-606941899 8 93141114 TTATTGTTCTTTATGATTTCTTTCCTTCTACAAAC[-/TTTGGATGTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCACGTCCTATTCCTCTGCCATCTTAGGACTGCCCCTCT]GGATGTTCTTTGTTCTTCTTTCTCTAGTTACTTTA - 8 1 4 1 20100 r 74 goat SV_351 8 93141114 - deletion junction SV-TF-chip 38449879 Affx-122922354 AX-123320214 8 93163386 AGCCACGGTATGTCTGTGCAGCTACGGTCCTCCAG[A/C]GGCTTCCATTCTCGCTTGGAGCTCTAATTGAAAAC M 2 1 2 1 101000 r 74 goat snp32795-scaffold38-1366795 8 94908332 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451651 Affx-122921601 AX-123321984 8 93194371 GTCCAACCTATGCAGCTGACAGCCGTGGTGTCCCG[C/T]GTACCCACTGCCTTCCCAATCCTAAAGAGGCCATG Y 2 1 2 1 101000 r 74 goat snp32794-scaffold38-1335810 8 94939546 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402615 Affx-122958410 AX-123272968 8 93245143 ACGGGAATGTATTTTGCTAATGAAATGTGAAATCT[A/G]CTTCTTCGCATTAATCATAGAACTCCAATAAAGCA R 2 1 2 1 101000 r 74 goat snp32793-scaffold38-1285038 8 94989905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769893 Affx-122927565 AX-385257062 8 93282405 TTTAAAACTATGTACCTTTCTTGTTGTCCTCTTTA[C/T]AAGACTGACAGAAAACTTGGAGTTAATCTTATGGG Y 2 1 2 1 101000 r 74 goat snp32792-scaffold38-1247776 8 95027078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390423 Affx-122967642 AX-123260780 8 93315288 TAAAGGGAGTCTGCTCACTCCGCTCCTAGAGCTCA[C/T]TAGCCCATGGAACTAATTAACAGGCAAGGTTTCAT Y 2 1 2 1 101000 r 74 goat snp32791-scaffold38-1214893 8 95060398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398707 Affx-122961851 AX-123269062 8 93355024 CATTCCCTTCCTCCTTGTCTGACAACTGAGTTATG[C/T]GTGGCAAGATTGTGATGAAGTGGTTGGTGAGTTAT Y 2 1 2 1 101000 r 74 goat snp32790-scaffold38-1175157 8 95100356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405165 Affx-122956940 AX-123275517 8 93383562 ATTCATTCAATACACAGGCAGCCACACCACCCCTG[A/C]GTAGAAAGTCCACCCACGTGACTGTGATGCTTTTA M 2 1 2 1 201000 r 74 goat snp32789-scaffold38-1146619 8 95129357 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379658 Affx-122975936 AX-123250016 8 93433449 AATCATCTTTATATCCCTAGGGTCAGGAGAGTTCC[C/T]GGGAAGCCGGCTTTTAATAAATGTTTATTGAACTG Y 2 1 2 1 101000 f 74 goat snp32788-scaffold38-1096732 8 95180068 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782183 Affx-122934632 AX-385269261 8 93465940 CAGTGGGTGAGGGTTTACTGGAGTGTGCGAACTCA[C/T]TACAAGTGTGTTTCCTAGATACAGCTCTGGTCCCA Y 2 1 2 1 101000 r 74 goat snp32787-scaffold38-1064241 8 95212733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391505 Affx-122966672 AX-123261862 8 93494675 TCACCATGCTGACTCTAGTACTTGCAAAAAGGCTG[C/T]TGACAGCTAGTGACTTCTGAACCAGTGCTGCCTGG Y 2 1 2 1 101000 f 74 goat snp32786-scaffold38-1035506 8 95241486 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450521 Affx-122922497 AX-123320855 8 93532805 ATTTCAGACTCTACAAGTAATCTGAAACTTGTTTC[A/G]TTTCAAAACTAAAAATATGTCAGATCCCCCACTCT R 2 1 2 1 103000 r 74 goat snp32785-scaffold38-997376 8 95280317 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448678 Affx-122923877 AX-123319014 8 93568256 ATCATCTGTACGAATTCTTCATAGTTGACTTCTCC[A/G]TCTCCATCGATGTCAGCTTCTCTGATCATCTCCTC R 2 1 2 1 101000 f 74 goat snp32784-scaffold38-961925 8 95316464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451843 Affx-122921082 AX-123322176 8 93600222 AAGCTCCTCAAAACTTACAAAGCAAAACATGGGCT[A/G]GGTAACTTATTAAAAATTATGCCCCTGATTTTCTT R 2 1 2 1 201000 r 74 goat snp32783-scaffold38-929959 8 95348225 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441911 Affx-122928604 AX-123312248 8 93636763 AGGGAAGCCCCATGAACTCTTAAGATGGCTTGATA[G/T]AGACACTGCTTTAGAGGTATACACCATATGTGTGA K 2 1 2 1 101000 r 74 goat snp32782-scaffold38-893418 8 95383182 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398115 Affx-122961705 AX-123268470 8 93665680 TGGGAATCATTAGACAATGAGATGTTAGACACAGC[A/G]TCCAGCGAGTACCTAGCACAGAATAGGAATTCCAT R 2 1 2 1 101000 f 74 goat snp32781-scaffold38-864501 8 95412737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452519 Affx-122920552 AX-123322852 8 93738279 CCCACAAACTCATTTCTCATCTTTATGGAAAGCAA[A/G]CCCAATGAGAGCTTTGAACAAGTTTTGGTCAGTGG R 2 1 2 1 101000 r 74 goat snp32780-scaffold38-791902 8 95483348 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768770 Affx-122960145 AX-385255947 8 93789689 TGGGTAAACCAGGTTTCCTAGTTTCCCATGGAACT[A/G]TAAGAAAATTTCTAGAATACATATATAAATACACA R 2 1 2 1 201000 r 74 goat snp32779-scaffold38-740492 8 95534242 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476252 Affx-1251763758 AX-586011673 8 93812972 AGAATTTCATATGATAGTTCTAATTTTAATTTTTT[-/TTTCAATGCTATTCTCTCCTTTTTTTTTAATTTTTATTTTCTCCGCCATCTTTCCCTCTCTCCCTAATTTTAATTTTTTG]AGGACTCTCCATACTGTTTTCCATAGTGACTGCAC - 8 1 4 1 20000 f 74 goat SV_352 8 93812972 - deletion junction SV-TF-chip 539476504 Affx-1251763758 AX-586011898 8 93812972 AGAATTTCATATGATAGTTCTAATTTTAATTTTTT[-/TTTCAATGCTATTCTCTCCTTTTTTTTTAATTTTTATTTTCTCCGCCATCTTTCCCTCTCTCCCTAATTTTAATTTTTTG]AGGACTCTCCATACTGTTTTCCATAGTGACTGCAC - 4 1 4 1 20000 r 74 goat SV_352 8 93812972 - deletion junction SV-TF-chip 560378489 Affx-1251763758 AX-605230904 8 93812972 AGAATTTCATATGATAGTTCTAATTTTAATTTTTT[-/TTTCAATGCTATTCTCTCCTTTTTTTTTAATTTTTATTTTCTCCGCCATCTTTCCCTCTCTCCCTAATTTTAATTTTTTG]AGGACTCTCCATACTGTTTTCCATAGTGACTGCAC - 8 1 4 1 20000 f 74 goat SV_352 8 93812972 - deletion junction SV-TF-chip 562165519 Affx-1251763758 AX-606940930 8 93812972 AGAATTTCATATGATAGTTCTAATTTTAATTTTTT[-/TTTCAATGCTATTCTCTCCTTTTTTTTTAATTTTTATTTTCTCCGCCATCTTTCCCTCTCTCCCTAATTTTAATTTTTTG]AGGACTCTCCATACTGTTTTCCATAGTGACTGCAC - 8 1 4 1 20100 f 74 goat SV_352 8 93812972 - deletion junction SV-TF-chip 562165898 Affx-1251763758 AX-606941307 8 93812972 AGAATTTCATATGATAGTTCTAATTTTAATTTTTT[-/TTTCAATGCTATTCTCTCCTTTTTTTTTAATTTTTATTTTCTCCGCCATCTTTCCCTCTCTCCCTAATTTTAATTTTTTG]AGGACTCTCCATACTGTTTTCCATAGTGACTGCAC - 8 1 4 1 20100 f 74 goat SV_352 8 93812972 - deletion junction SV-TF-chip 562166109 Affx-1251763758 AX-606941517 8 93812972 AGAATTTCATATGATAGTTCTAATTTTAATTTTTT[-/TTTCAATGCTATTCTCTCCTTTTTTTTTAATTTTTATTTTCTCCGCCATCTTTCCCTCTCTCCCTAATTTTAATTTTTTG]AGGACTCTCCATACTGTTTTCCATAGTGACTGCAC - 8 1 4 1 20100 r 74 goat SV_352 8 93812972 - deletion junction SV-TF-chip 562166555 Affx-1251763758 AX-606941963 8 93812972 AGAATTTCATATGATAGTTCTAATTTTAATTTTTT[-/TTTCAATGCTATTCTCTCCTTTTTTTTTAATTTTTATTTTCTCCGCCATCTTTCCCTCTCTCCCTAATTTTAATTTTTTG]AGGACTCTCCATACTGTTTTCCATAGTGACTGCAC - 8 1 4 1 20100 r 74 goat SV_352 8 93812972 - deletion junction SV-TF-chip 38438972 Affx-122930387 AX-123309309 8 93822243 CAAAACAGGATTAATTGAATCACTATGACCGGGTT[C/T]CTCCTGCAACTCTGCGGAAGACAAAAGACACGTAC Y 2 1 2 1 101000 r 74 goat snp32778-scaffold38-707938 8 95565216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419509 Affx-122945451 AX-123289857 8 93856351 CCCTTATTACTCAGACCTTTCTCCATTCTACTTGC[A/G]CTCACTGAAATATTCTTTCCTAGCTCTTTCATTTA R 2 1 2 1 101000 f 74 goat snp32777-scaffold38-673830 8 95598947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414709 Affx-122949273 AX-123285058 8 93898542 TCTTCAAATAGACAAAACCAAAGAAATCTAGAATG[C/T]ATAAAATCTCTCAAAATATAAAGACAAAATCACAG Y 2 1 2 1 101000 f 74 goat snp32776-scaffold38-631639 8 95641234 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793053 Affx-122976026 AX-385280031 8 93956657 ATATTAATTGCATTGTATAATCACATGATCAAAGC[A/G]CTGTAATCTACACATAAGCACTTTGCAACTTAATT R 2 1 2 1 101000 r 74 goat snp32775-scaffold38-573524 8 95699686 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433852 Affx-122934437 AX-123304193 8 94027145 CATATAGACTTTTCAGTCAAAAGTGCTGGGGTTTG[C/T]GGGTGCTATCAGAGAAAATGCCAAATATCTTCACA Y 2 1 2 1 101000 f 74 goat snp32774-scaffold38-503036 8 95770587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773227 Affx-122974635 AX-385260370 8 94102658 ATCCCCAAAGAGACTGGAATCAGAATTCAGATTCA[G/T]ATTCAGATTTCTGGGCACCTACTACAACATGCCTG K 2 1 2 1 101000 f 74 goat snp32773-scaffold38-427523 8 95846550 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381991 Affx-122974085 AX-123252349 8 94140762 CGGTAAACATAAGGATAAGGGAATTTGAAAGCACA[C/T]TGTGGACATTTTGCATTGTCTATTCTTGGAATTTG Y 2 1 2 1 101000 f 74 goat snp32772-scaffold38-389419 8 95884908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431920 Affx-122935994 AX-123302261 8 94200353 GAGAGATCTGGGCCCCAGGATTCTAGTGGGCAGAA[G/T]ATGAGTAAAACAAGAGCCTGGGACTTCACTGTATC K 2 1 2 1 201000 r 74 goat snp32771-scaffold38-329828 8 95944376 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402133 Affx-122958668 AX-123272486 8 94252496 CTTCTTCACTTTTCTTTACAGCACTAGTAACTACC[G/T]AAAGTTAAGTTACTTATTTACTTATCGTCAGCCTC K 2 1 2 1 101000 f 74 goat snp32770-scaffold38-277685 NW_017212951.1 5192 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446038 Affx-122925845 AX-123316375 8 94311383 ACTTGTAAAACAAAGCAAATTGCAACCCAATATGA[G/T]TCCCAAAATTTTATTTGAAATTTTATTACTGTATG K 2 1 2 1 101000 f 74 goat snp32769-scaffold38-218798 8 96056838 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452249 Affx-122920778 AX-123322582 8 94370750 GTCATTTTCACTTAACATGGCTGCAAGATCCAGTA[C/T]ATTTATTTTCCTGAAAGGCTGAGTGAATGAATAAG Y 2 1 2 1 101000 f 74 goat snp32768-scaffold38-159431 8 96116529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796736 Affx-122959501 AX-385283680 8 94405753 TAACTAGAACTATTGTAGACAAGAGAATCCTAGAG[C/T]CCCTCACTTCTCCAATAAATCAATCCCAACATTCA Y 2 1 2 1 101000 r 74 goat snp32767-scaffold38-124428 8 96151177 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273394 Affx-1111833597 AX-519547024 8 94435525 TACAGACTGACAGGGTTTCCCTCTGGTTCCTTTAA[A/G]ACCTATGACTCGTGGCAACATCAGGGCTTTAGATT R 2 1 2 1 101000 f 74 goat 8_94435525_AF-PAKI 8 94435525 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38407404 Affx-122955246 AX-123277755 8 94454691 CATGACAAGTATTGTAACAGGTACTGGGGATTCAC[A/G]AGCTAGCCAACTGTATTAGTCAGAGTTCTCTAGAG R 2 1 2 1 201000 f 74 goat snp32766-scaffold38-75490 8 96200269 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390272 Affx-122967743 AX-123260629 8 94490564 CTTCTATGAGCACTCACTATGTTCCAGGCACTGTG[C/T]GAGGTGCTAGGGACCCAAAGGCGAGCAGTATACAG Y 2 1 2 1 201000 r 74 goat snp32765-scaffold38-39617 8 96236857 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797758 Affx-122948086 AX-385284697 8 94525781 GTTTTATTTGCATGATGGTTGTTGAGCACACACTG[C/T]GTGCTAGAGATGGTCCTAGGTCCCTGCTTCCATGA Y 2 1 2 1 202000 r 74 goat snp32764-scaffold38-4400 8 96271710 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788415 Affx-122972061 AX-385275433 8 94531281 GATTGCCAAGGGGAGAGATTCTACAAGTTGCCTTC[A/G]TAACTCAGTCCACTGTTTAGCAAACCCTCTCATCT R 2 1 2 1 101000 f 74 goat snp38281-scaffold4816-178390 8 96277071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770429 Affx-122955646 AX-385257595 8 94585706 TATTACACAAATCATGGTAACCATGCTCAATGGAT[A/G]CTTTATCAGCCATTAACCTTGCATGGTTTATGCCC R 2 1 2 1 201000 f 74 goat snp38280-scaffold4816-123965 8 96332061 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448549 Affx-122923429 AX-123318885 8 94632773 GTCATCCCACCATCCAACAAAGAAAACCAAATACA[C/T]CAAACTTAATAAGAATGCGACCTGTAAATATAGAT Y 2 1 2 1 201000 r 74 goat snp38279-scaffold4816-76898 8 96379094 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384626 Affx-122972165 AX-123254984 8 94689951 GCTAAGTACCCCAGGCATCCAGCTCCTTGGCCTGC[A/G]TTACAAAGCCAGTGCTTCTCCTTAAGGAATTCTTA R 2 1 2 1 101000 r 74 goat snp38278-scaffold4816-19720 8 96433458 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424089 Affx-122942039 AX-123294435 8 94735131 TAAGTTGCAGTATTTAAAAGTGTTTTTCTCTTTCT[A/G]TAGAAGAAAGGATGATGAATGTAAACACTCTGGGT R 2 1 2 1 101000 r 74 goat snp21701-scaffold2122-25361 8 96478765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423744 Affx-122942856 AX-123294090 8 94764522 ATGCTTTCTCCACGACTTCTTGCATTTTTATTTCT[C/T]CAAGTTTCATATCATAGAAGTACCGGTGTGAAAAT Y 2 1 2 1 201000 r 74 goat snp21702-scaffold2122-54752 8 96507916 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382027 Affx-122974954 AX-123252385 8 94806965 TAAATAGGAAATGAATAGGTGCTAAACTGTGAGGC[A/G]CCAAGACAGCGCCACAGGAGGGAGAGGTGTGATAG R 2 1 2 1 101000 f 74 goat snp21703-scaffold2122-97195 8 96549392 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415581 Affx-122948628 AX-123285930 8 94870686 GCTCTTCCCTCTGGCAGGGAGACTATCCCCTCTAC[A/G]TTTATCCTTTAAGTCTCCCTTGAGAGGCACTTCCC R 2 1 2 1 201000 r 74 goat snp21704-scaffold2122-160916 8 96590489 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769154 Affx-122922006 AX-385256329 8 94900624 AATCATATTTGCTTGTAATTTTTGTTATGTATTCA[C/T]GTAGAATTACATTTACATCAATGGGATTAAACTAG Y 2 1 2 1 201000 f 74 goat snp21705-scaffold2122-190854 8 96620494 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431983 Affx-122935947 AX-123302324 8 94944796 TCTTTCCACCTCCACCACTATCACCATGACACACA[C/T]GGGCATCCTCACTCTCTTGGAAAATTACAAGAGCT Y 2 1 2 1 201000 r 74 goat snp21706-scaffold2122-235026 8 96665144 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391963 Affx-122966528 AX-123262320 8 94980320 CCTGAGAGGATTTCACTTCCTGGTCCTGGAAAAGC[G/T]AAGTGCTGCCTTCTATTCCTCCTCAGCATTCGAGA K 2 1 2 1 101000 r 74 goat snp21707-scaffold2122-270550 8 96700668 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428482 Affx-122938785 AX-123298825 8 94998288 CAAAATAAGCCTAAAGAGTTGCGCATGATTAGAGT[A/C]CATCAAGACAGTTCATAACACCTTGGGGGGGAGAC M 2 1 2 1 101000 f 74 goat snp15968-scaffold1680-4437 8 96719047 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439810 Affx-122930482 AX-123310147 8 95057808 AACTACGTGGACACATCATTATCACCTGAAGTACA[C/T]GGTATAAATCAGGGTGCACTCTGTTGTACACTCTA Y 2 1 2 1 101000 r 74 goat snp15969-scaffold1680-63957 8 96779227 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392638 Affx-122966454 AX-123262995 8 95091817 GCAGTGTTGTCTGTGTCTTGAATGAAGTGGAAAGT[A/G]GTCATCTGTGTGGAGGGGGCAAGTGTTGGGAATCA R 2 1 2 1 101000 f 74 goat snp15970-scaffold1680-97966 8 96813325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381822 Affx-122974267 AX-123252180 8 95128641 TCAAGTTATTTTTCACAAAAATTAAAAATAATATG[C/T]AGTAGGTTTATTTTAAATGAATTAACTTGGGGGGA Y 2 1 2 1 303000 f 74 goat snp15971-scaffold1680-134790 8 96849881 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418310 Affx-122946978 AX-123288658 8 95270237 TGAGAGGGGAAGCCAGGAGACTTGCTGGCTCTCAG[A/C]GGTTTTTATCTCGTTCAGTTCCTACAGCCACCCTT M 2 1 2 1 101000 r 74 goat snp59196-scaffold972-117983 8 96990666 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400250 Affx-122960142 AX-123270605 8 95304133 ACACATACCAACCACAGCTTCTAAAGAATCTAATC[A/G]TGCCACACAGTTTGCAAGATCTTAATCGCTGACCA R 2 1 2 1 101000 f 74 goat snp59197-scaffold972-151879 8 97024675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433464 Affx-122935054 AX-123303805 8 95352813 GCATGGTTCATAGCAAGCTCCTTTGCCATGGCAAG[A/G]CAGTGATCCATGAAGCGGGGGATTAAACCAGGACT R 2 1 2 1 102000 r 74 goat snp59198-scaffold972-200559 8 97073475 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781173 Affx-122941369 AX-385268258 8 95384635 TGATTTCATGAATACAAAACTGCACGCACAGCTGC[A/G]TACTTCCCCATGAACATATATGGGTATAAACTCAG R 2 1 2 1 101000 f 74 goat snp59199-scaffold972-232381 8 97105195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400381 Affx-122960013 AX-123270736 8 95414875 TTTGTTTAAAGGGCAGAAGTGTGTGTTGGGGAAGA[C/T]GTCATAAGCATGCAGCTAAAATAATATCCCTCCCA Y 2 1 2 1 201000 r 74 goat snp59200-scaffold972-262621 8 97135773 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401122 Affx-122959393 AX-123271475 8 95443929 TTTTCTCCCAGAGAACACCTGGGGTGTTCTATGCC[A/G]TCTTATCTCAGGCAGTGAGTACTGAGACACCAGCT R 2 1 2 1 101000 r 74 goat snp59201-scaffold972-291675 8 97164845 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412136 Affx-122951095 AX-123282486 8 95501541 CCACGGTCACACACAGAGCAGGCTGTGGCACTGAC[G/T]GTGGACCCCTTTTCTTTCTGATACCAGGGTCCAAG K 2 1 2 1 103000 r 74 goat snp20358-scaffold2018-57880 8 97222618 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416457 Affx-122947818 AX-123286806 8 95534443 CAGCATCCCCTTCCGGACCACAGGGTAGGTCATGT[A/G]ACTCCAGAGTAGCCAATCATAATGCCCTGGGCCTC R 2 1 2 1 101000 r 74 goat snp20357-scaffold2018-24978 8 97255523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434157 Affx-122934899 AX-123304498 8 95588518 GATACCTGAGATGTGCAAAGTCGTCAAAATCCAAC[C/T]GTTCCAGAGAGTCCCTGGCCAGTGCTCTTCCACTG Y 2 1 2 1 101000 f 74 goat snp34222-scaffold401-2749621 8 97309002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775216 Affx-122952196 AX-385262347 8 95678114 ATTCATTCAGATCACCAAAATATGAGGCCAAAAGT[A/G]CTTATATCACAGTGGTAAAACAACCACACCTGACA R 2 1 2 1 101000 f 74 goat snp34220-scaffold401-2660025 8 97399293 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424512 Affx-122941735 AX-123294858 8 95822612 CAAGGGGACTGTCAGGGATAGATTTGTCTGTAATA[C/T]GTAGAATGGGTTTCAGGAAGGTAAAAGCAGAGGCA Y 2 1 2 1 101000 f 74 goat snp34217-scaffold401-2515527 8 97543762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400422 Affx-122959977 AX-123270777 8 95852588 TTGCCAGTTGGGTGCAAGGATAGGCTTAGTCAATC[A/G]TGGCCTGCCTGAAAGCTGGAACTGGGAGTGGACTG R 2 1 2 1 101000 f 74 goat snp34216-scaffold401-2485551 8 97573754 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421444 Affx-122943946 AX-123291791 8 95885733 GGGGTCCTTACAAAGCAGATGTAGTGTTTCCCCTT[A/G]TCCTGGCTTTACTTTGAAAGAATCAAGCACTTTAT R 2 1 2 1 101000 r 74 goat snp34215-scaffold401-2452406 8 97607087 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432571 Affx-122935528 AX-123302912 8 95964866 AAGAGAGATTTTGAGTTTCAGTCCTGGGGACTTGT[A/G]CTATTTTACCTAAAAATGAGATAGTATTCTGGGGC R 2 1 2 1 201000 r 74 goat snp34213-scaffold401-2373273 NW_017213455.1 3760 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408684 Affx-122953446 AX-123279035 8 96057714 GAAAGGATAGATAGTAGGTCTTGTGTGGGGAGGAC[A/G]TATCTATCATGTGTGCTGTCTCTCTAGTAAGTCAG R 2 1 2 1 101000 r 74 goat snp34211-scaffold401-2280425 8 97779729 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379329 Affx-122976180 AX-123249688 8 96108738 GTCATATATATTTATATCTACAGTGTCTCCTTGCA[C/T]ACTTCCAGCTAATTCTCTTATGGAGAGTCTGGCAC Y 2 1 2 1 101000 r 74 goat snp34210-scaffold401-2229401 8 97827912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780420 Affx-122960344 AX-385267512 8 96160160 TTGCTTTAGGTAAGTTTACATCTTTTGTAAGAAGG[C/T]TGTTGATAAGTCTCGAATAACAGTCCCTCTGGTAT Y 2 1 2 1 101000 f 74 goat snp34209-scaffold401-2177979 8 97879404 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415104 Affx-122949444 AX-123285453 8 96193285 AGTGGAAATGCTAAATGTGGAAGGCTGACAGAACA[A/C]GACTTGTTTTATCTGACACAAATGAGGGGGAAATG M 2 1 2 1 201000 f 74 goat snp34208-scaffold401-2144854 8 97912747 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415410 Affx-122948734 AX-123285759 8 96253927 TGAACTGAACTGAACCTCAAGGGAAGTGGAGTGGT[G/T]GTTTCCATAGGCAGGGCATCATGGGTATGACTGCT K 2 1 2 1 201000 r 74 goat snp34207-scaffold401-2084212 8 97973474 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382647 Affx-122973679 AX-123253005 8 96347262 AGTCTGCCCTGCAGCATCTTCAACAAGCAGTCCCC[C/T]TGCATCTGTCCGCACAGCGCTAGGGACTGGAGCTC Y 2 1 2 1 201000 r 74 goat snp34206-scaffold401-1990877 8 98066611 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438581 Affx-122931157 AX-123308919 8 96385920 GTTCCATATAAATTTTAGGGTTATTTGTTCTAGTT[C/T]TCACAGGGCTGATCTAAGCTCAGAAGAATGTCCTC Y 2 1 2 1 103000 r 74 goat snp34205-scaffold401-1952219 8 98106168 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394783 Affx-122964826 AX-123265138 8 96462283 TTTTCCAATAGTGAATTTTCCATTTTCATAATGCC[A/G]CTCTTTATATGTAAAATGTCTGGCATTTACAAAGT R 2 1 2 1 101000 f 74 goat snp34203-scaffold401-1875856 8 98183501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278822 Affx-1111836530 AX-519552293 8 96479822 TTTCAACTTAATGCATTGTTTAGAATAGCAATTAC[A/G]TGTCATTTCCCATTATCTTACACACAGAAGCAGCA R 2 1 2 1 101000 r 74 goat Random2.2K-941 8 96479822 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421515 Affx-122943891 AX-123291862 8 96565211 ACTATTACTGAATACATGGAATATTACATGGAATA[G/T]TACTGAAGACATGTAATTGAAGGAGAAGTAGGTTG K 2 1 2 1 101000 r 74 goat snp34201-scaffold401-1772928 8 98286921 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787595 Affx-122967543 AX-385274619 8 96650090 AAATTTCTAAACCTTGGCTGACCACACTGAAATTA[A/G]TTAAGTATTAAGCTGCTATTAATGGTGACAATATG R 2 1 2 1 201000 r 74 goat snp34199-scaffold401-1688049 8 98372345 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448555 Affx-122923425 AX-123318891 8 96691429 AAGTCTCTTGTGTACCCCTCCCTGACTGTGCATCC[A/G]TGTCCCAGCCCTTTTGCTTCCAGGGTAGCTATTAT R 2 1 2 1 101000 r 74 goat snp34198-scaffold401-1646710 8 98413749 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375605 Affx-122978719 AX-123245964 8 96744470 ACACAAATCGTGGTGGAAGGTGATTTTTCTCTTCT[A/G]TCTGCTGTACCACTTTAGATTTTAGAGAATGAGTG R 2 1 2 1 201000 r 74 goat snp34197-scaffold401-1593669 8 98466606 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385395 Affx-122971347 AX-123255753 8 96780457 ACTCCAGGCTCAGATACAGCCGCTAGGCAACACTC[A/G]TAGGGGCCCTTGGTTTACTTCCTCAGCAAGCAAGG R 2 1 2 1 201000 f 74 goat snp34196-scaffold401-1557682 8 98503144 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451275 Affx-122921313 AX-123321608 8 96813033 TGACCGATTTGAAATTAAATCATGGTTTCTCTTCT[C/T]CAAGTAGTCCTCACTCCCAAACTCCTTTTTCCTGT Y 2 1 2 1 101000 r 74 goat snp34195-scaffold401-1525106 8 98535679 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442572 Affx-122928505 AX-123312909 8 96877018 CCCAGTGTACCCCATTGCCTGGAAGGGTGACTGGC[A/G]TTTGATGAGCAGTTGATAAACATTTGTTGAATGAG R 2 1 2 1 101000 r 74 goat snp34193-scaffold401-1461121 8 98599699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415531 Affx-122948668 AX-123285880 8 96926556 GGAAGAGAACATCTGAGCATATACTATGCCCCAGG[C/T]GTAGCAATTATCTGATATCATTTAACCTGTTTGAT Y 2 1 2 1 201000 r 74 goat snp34192-scaffold401-1411583 8 98649772 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424838 Affx-122941357 AX-123295184 8 96981294 CTATCCCCACCTAAGAATGAGTGAATTGCTGTGCT[A/G]TTCCAAAGCTCAGCCAGTTCTGAGTGTTCTTTTAC R 2 1 2 1 201000 r 74 goat snp34191-scaffold401-1356845 8 98705630 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438132 Affx-122931482 AX-123308470 8 97014427 GGTAAGGGAGTCCACAGCTAGCAAGGTGGAAGAGC[C/T]GGAATTTGAGCCAGTCTTTATGAATCTGAGCTGCC Y 2 1 2 1 101000 r 74 goat snp34190-scaffold401-1323712 8 98738732 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441303 Affx-122929453 AX-123311640 8 97174928 ATACCTCCCCTCTTGAATGGTGGCTGTATTTAAGG[C/T]ACTTGAAGCCCTGTAACACTCTGCAGTCCTAACTC Y 2 1 2 1 201000 r 74 goat snp34186-scaffold401-1163211 8 98900098 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416702 Affx-122947565 AX-123287050 8 97228638 TGGGTATTTGTTCATCTAGAGCTGCTCATGTGTGT[A/G]TATGTGAGGTGGGGGTGTAATTACATAATTTACCG R 2 1 2 1 101000 f 74 goat snp34185-scaffold401-1109501 8 98954239 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273396 Affx-1111833598 AX-519547025 8 97236607 TCCAACAAGTCAGTTCTTCGTATGAGGTGGCCAAA[A/G]TATTGGAGCTTCAGTTTCAGCATCAGTCCTTCCAA R 2 1 2 1 103000 f 74 goat 8_97236607_AF-PAKI 8 97236607 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433273 Affx-122935222 AX-123303614 8 97278094 TCATTTATGTGTTTATTTAATCATTCATGCAGGCA[A/G]TACTTGAATACCTACTAGCTGTTAGGGTCTGGGAA R 2 1 2 1 101000 r 74 goat snp34184-scaffold401-1060045 8 99004043 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797866 Affx-122968857 AX-385284804 8 97308770 TAGATATGTTCCTATGGCTTTGTACAAGGCATTAA[A/C]TGCAATTAATCAACTGAGACCTTGGACCAAAAGGA M 2 1 2 1 101000 r 74 goat snp34183-scaffold401-1029369 8 99030950 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397461 Affx-122962099 AX-123267816 8 97459942 TTAAAAAAGTCATGCTATAATATTTTCAAAGTATA[C/T]AGCACACTGATTCAGTTAGATAATACATGAGAGAC Y 2 1 2 1 101000 r 74 goat snp34179-scaffold401-878197 8 99182961 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379497 Affx-122976466 AX-123249855 8 97493550 TTCTGACATGTTGAGGTTTAGGTGTCTAGGTGATA[C/T]CCAAATGGAGATGTCTAGGAGAAGGTTGGCCAAAT Y 2 1 2 1 201000 f 74 goat snp34178-scaffold401-844589 8 99216647 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770472 Affx-122927054 AX-385257638 8 97590188 TGAAGGCAGAAGGCACAGATATTAATTAATTTTTA[C/T]ATTGTTTTATGAGCCTGTGTTGTTTTCAATTCAAG Y 2 1 2 1 101000 f 74 goat snp34176-scaffold401-747951 8 99313701 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799220 Affx-122963795 AX-385286150 8 97664827 TAACAGTTATCTCAGTGATGTTGTTATCAACAAAA[C/T]GGTTCAATCTAGGGTCCCATGTGGGATTAATTCTC Y 2 1 2 1 201000 r 74 goat snp34174-scaffold401-673312 8 99387745 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776655 Affx-122944824 AX-385263782 8 97696671 AAGCCTTGGCATAAGAACATATCCCAGACAGATAA[C/T]GTCAATCAGCGGTTAACAACTCAGAGATAATCCCT Y 2 1 2 1 101000 r 74 goat snp34173-scaffold401-641468 8 99419522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384573 Affx-122972999 AX-123254931 8 97751203 GAGATTTAATTTCCCTGAAATGTTCTGCAAGTTTC[A/G]TTGAACTAGACTTGACCCTGCATCGAGGTTTTTGA R 2 1 2 1 101000 r 74 goat snp34172-scaffold401-586936 8 99473614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439257 Affx-122930997 AX-123309594 8 97861228 CAAGGCTGCTCATGGAGCACCTGGCAACAGTGAAA[G/T]AAAAACAGTAGCAGGTGTTTGGACTTAGTTCGTGC K 2 1 2 1 101000 f 74 goat snp34170-scaffold401-476911 8 99584928 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437688 Affx-122931766 AX-123308026 8 97946339 AAGACTTCATTCAAGGAAATACTCTGAAATGTAAA[C/T]GATCAATCCTATTTTCTGACAACCAGCCTTGCCTT Y 2 1 2 1 201000 f 74 goat snp34168-scaffold401-391800 8 99670313 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274017 Affx-1111833953 AX-519547621 8 97960345 GGGACTGCACTGCAGATCCTATTTGG[A/G]ATTTTAAATCTCAGCTCCTTTACAACTATGGCCTC R 2 1 2 1 101000 r 74 goat GoatD01.011490 8 97960345 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38451745 Affx-122921529 AX-123322078 8 98008475 CCTGTCCTTAGTAAACTTTTTAAATGCCTTAAATG[A/C]AGTCTAACGTGCAACCAGCACTGAGTGACACTGCC M 2 1 2 1 101000 f 74 goat snp34166-scaffold401-329664 8 99732382 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407069 Affx-122954914 AX-123277420 8 98037083 TTGGAACTATTTCATTTGCACTTTCTTTGGGGAGC[A/G]TAGTAAATACTGTTAGATTTATAAATTTAACTATG R 2 1 2 1 101000 f 74 goat snp34165-scaffold401-301056 8 99761647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449611 Affx-122923204 AX-123319946 8 98094436 GTGATTTCCAGTCTATCATAATTGTTAAAACAGGA[C/T]GAAATGTATCATTAGACTGTAGGTGTGAAACACTA Y 2 1 2 1 101000 r 74 goat snp34164-scaffold401-243703 8 99819314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774740 Affx-122944358 AX-385261874 8 98154286 AATTTCTTTTTCATTACCCTTTGTCTATATTCTCA[A/G]TTGCCTTGCTAATGTAGACTTACAAGATGCATTAT R 2 1 2 1 101000 r 74 goat snp34163-scaffold401-183853 8 99879532 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395490 Affx-122963894 AX-123265845 8 98200202 TCTTGAGGACAGTAAGATGTTGGGGAAGGAAAAGG[C/T]GAAAAAGAATTACCCTGAGGGGTGAATTGATGATT Y 2 1 2 1 201000 f 74 goat snp34162-scaffold401-137937 8 99924777 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278824 Affx-1111836531 AX-519552295 8 98203526 TACCACATTTAGCCAAAGTAACCAATTTTTGTTTT[C/G]TTTAGACACAGGGAAAACTTACCTGCTGAACTACA S 4 1 2 1 101000 r 74 goat Random2.2K-942 8 98203526 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38387861 Affx-122969641 AX-123258219 8 98299571 AAAATATGACTCCACATTTCTTACAAATAAGCTGA[C/T]GTAGCAACAAATACATCTACAAAACACATCCATCA Y 2 1 2 1 101000 r 74 goat snp34160-scaffold401-38568 8 100023909 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438135 Affx-122931480 AX-123308473 8 98331697 TTCCAGAAAACCTAGAACAGATGAAAGACAATCAG[C/T]TGGAAAGAAAAAGAAGTGCATACTTGACAATTTAC Y 2 1 2 1 101000 f 74 goat snp34159-scaffold401-6442 8 100056188 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431013 Affx-122936674 AX-123301354 8 98347073 ATATCAGTGGCAATGTAAAACGAGGATTGCTGAGC[G/T]TCAGCATCACGCTCTCAGGCATTGCTCTTGCTTTA K 2 1 2 1 101000 f 74 goat snp31799-scaffold356-8835 8 100070733 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450322 Affx-122922133 AX-123320657 8 98383348 AATCCAGGAAATTATGTTTTCACAGGAAAAAACAA[A/G]ACAAAACAAACAGCAACAAAACATGGTTAATTTGT R 2 1 2 1 103000 f 74 goat snp31800-scaffold356-45110 8 100107368 A G 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38451167 Affx-122921350 AX-123321501 8 98450185 TTTTGAATGCCTAGTCTCCTGACTTGTCCAGACAT[A/C]TAGGGTCTCTTTCCTCATTTATACTCAATAGATCA M 2 1 2 1 101000 f 74 goat snp31801-scaffold356-111947 8 100173349 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389155 Affx-122968536 AX-123259513 8 98481301 ATTTACCATTGACAGTCTCATTGCAGGATGTCCTT[C/T]GCAAAGTAGGGAGGAAACTGGTCAAAATGAAGGCG Y 2 1 2 1 101000 r 74 goat snp31802-scaffold356-143063 8 100204872 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420296 Affx-122945032 AX-123290644 8 98534295 CCCAGGATGAGTGAAGTCATTTTAGACAAAGAAAA[C/T]AAGAAAACACTGGAAATATTAATATCAGGAAAATA Y 2 1 2 1 102000 f 74 goat snp31803-scaffold356-196057 8 100257810 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435276 Affx-122934048 AX-123305616 8 98563980 TAAGATGAAAACTGTAAGAAATTACAGCTGCAACA[C/T]GGCACTTATTGTGATGTAACTTGTAATTAGTAGGT Y 2 1 2 1 101000 r 74 goat snp31804-scaffold356-225742 8 100286739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801062 Affx-122955551 AX-385287976 8 98669920 AAATTAAGTAATACATGTATAAGTAACAGAATTCC[A/G]CCTTTATGTGAATTTTTAATCACTTAATATATTTG R 2 1 2 1 201000 r 74 goat snp31806-scaffold356-331682 8 100395904 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395729 Affx-122963706 AX-123266084 8 98702415 AACCAAGGTGCCATTCAGCAAGAGATAGTGCAAAA[C/T]GACAATGAGCACACCAAAGGAGAAATCATTGGCAG Y 2 1 2 1 101000 f 74 goat snp31807-scaffold356-364177 8 100428694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384786 Affx-122972007 AX-123255144 8 98734532 TAATAATAAAAATAAATTACTCAATCCTTGGTACA[G/T]CATGTTTTCTTTAGGCTGACAGTCACCACAGAAAT K 2 1 2 1 101000 r 74 goat snp31808-scaffold356-396294 8 100460886 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395928 Affx-122963590 AX-123266283 8 98769695 ACTGGATCAAGGAGTCTACAATCCGATTTGACAAA[C/T]GCCTTTTTTTCAGCAGACAGATAACCTAAAATCAA Y 2 1 2 1 101000 f 74 goat snp31809-scaffold356-431457 8 100496368 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388483 Affx-122969232 AX-123258841 8 98800245 GCCTAGGTTCCATCCTGAGTCCTCTTCTGACATAA[C/T]GGTCATTTATAACCCGCTTCAGTGACTCATGTCAA Y 2 1 2 1 101000 r 74 goat snp31810-scaffold356-462007 8 100526850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402030 Affx-122958740 AX-123272383 8 98840634 CATGGAAAAGTCTGAACAAACTTTGGCCAACCCAA[C/T]AAATCATACTTGGAAAAACTAAGACAACTTAGGAA Y 2 1 2 1 201000 r 74 goat snp31811-scaffold356-502396 8 100567597 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439851 Affx-122930453 AX-123310188 8 98877823 GTTTTCCTAATCCAGCTCTTCTTTCACCTCTTATC[A/G]AAATACCTCATTTGGATAGCCACAATCCTACTATC R 2 1 2 1 201000 r 74 goat snp31812-scaffold356-539585 8 100604709 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431384 Affx-122936554 AX-123301725 8 98939696 TTCCACTGCAGTGACCCACTCCTATGGGCACACTG[G/T]AGACCTGGTCACCACTTACAACTCTCCTACTGTTT K 2 1 2 1 101000 r 74 goat snp31813-scaffold356-601458 8 100666911 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390938 Affx-122967071 AX-123261295 8 99003225 CGGAGCTGGCACTCCCTGTGCTTTCTCTTATATCT[A/G]TTTACTCAGCATTCATTTCATGCTTTACATAGATT R 2 1 2 1 201000 r 74 goat snp31814-scaffold356-664987 8 100730611 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431625 Affx-122936148 AX-123301966 8 99053857 GCTTGGGCATAAGGTTCTAGAAAAACACTGAGAAC[A/G]CCAGGTGTTTGACTTTTGCCTCTGACACCCCCATG R 2 1 2 1 201000 f 74 goat snp31815-scaffold356-715619 8 100781679 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448241 Affx-122924207 AX-123318577 8 99084370 TCTGGCTAGAAGGAGGCTGAACTGAGAAGGAACAG[A/G]GCCAGCCTGCCTGTGATGGGCCAGATGAAAAAGGA R 2 1 2 1 101000 f 74 goat snp31816-scaffold356-746132 8 100808304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797089 Affx-122971024 AX-385284029 8 99161253 TGGGAGAGGTTTTAAAATTCCCTATACCTGGGATG[C/T]ACACCAGACCAATTAGATAATAATACATCTGAGTA Y 2 1 2 1 101000 r 74 goat snp31818-scaffold356-823015 8 100886348 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768907 Affx-122940425 AX-385256084 8 99190229 TGTTAAGCTTCGTTGTTGGAGTCACATGCTGTGCT[G/T]TTGAGGCTATAGCAATAATGTTTAATGTTTTTGAG K 2 1 2 1 101000 f 74 goat snp31819-scaffold356-851991 8 100915247 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464612031 Affx-1110573899 AX-516083306 8 99251068 GGAATGAATCAGGCACATAAAGTGATATTTCCAGT[G/T]TAAGGAAAGACTCCCAAATCTGTTTTCCAATTCTG K 2 1 2 1 101000 f 74 goat Random2.2K-944 8 99251068 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409103 Affx-122953319 AX-123279454 8 99251171 TTAATTTCTAAGCATTCACCAGGGTTGCCTCATGC[A/G]TGCTCAGGAACTGGCCCCACATTGCATTCCATGTG R 2 1 2 1 101000 f 74 goat snp31820-scaffold356-912933 8 100975758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772429 Affx-122944933 AX-385259581 8 99291816 GGAACAAAGGAGAAAATTCCCAGTGTCAAATAAAT[C/T]GCTTCAACTGATTTGCACAGCAGAGCTATAAAAAC Y 2 1 2 1 101000 r 74 goat snp31821-scaffold356-953578 8 101016918 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453977 Affx-122919453 AX-123324310 8 99322005 ATTTCCTTCCAATGAAGTTTCACTTAAGCAGACAG[A/G]GCGATTGTTTGTTTATGAGCAAGTTTGAAGTGATG R 2 1 2 1 201000 r 74 goat snp31822-scaffold356-983767 8 101047097 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389113 Affx-122968565 AX-123259471 8 99369617 ACATGGGCAGAGGTCACGCCCAGTTTGAAGAGAGG[C/T]CTCAAAGTAAAGGGACTTCAAAGCTAGGTCTGAAA Y 2 1 2 1 101000 r 74 goat snp31823-scaffold356-1031379 8 101095390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416141 Affx-122948287 AX-123286490 8 99402740 ATAGCATCTGTTTCCTCTCGTGGACCAGACGTCTG[A/G]GGACTGACGCAGGACGGTGGATCAGGGAATGAACT R 2 1 2 1 102000 r 74 goat snp31824-scaffold356-1064502 8 101128414 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772167 Affx-122952497 AX-385259322 8 99451367 TCACAGGAAGCGGAAACTTGGCTGTAGAGTTGACA[G/T]AACACATCCACATTTACTACCTCATGGAATTTTCA K 2 1 2 1 101000 f 74 goat snp31825-scaffold356-1113129 8 101177341 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397527 Affx-122962045 AX-123267882 8 99518906 CCCACATCCCTGTACGAATTTGATGACAAAACCAG[C/T]GGCAACTACTATGCCAAAATATTAATAAAATATAA Y 2 1 2 1 201000 r 74 goat snp31826-scaffold356-1180668 8 101244317 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453746 Affx-122919612 AX-123324079 8 99560480 CAAAAGTCAGACATGACTTAGGGACTAAACGACAA[C/T]GAAGAGAAGCCTAGCCCAACAAAGTATAACTTTCG Y 2 1 2 1 202000 r 74 goat snp31827-scaffold356-1222242 8 101286125 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449165 Affx-122923541 AX-123319500 8 99626666 TAGTATCCTTCGTTTTCCACTGACTAATTGTTGCT[C/T]AGAGTTGAGGGAATTTTGCTTTTGAACAATCCAGA Y 2 1 2 1 101000 f 74 goat snp31828-scaffold356-1288428 8 101351827 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765907 Affx-122964279 AX-385253339 8 99668391 TTCTTCTCATGAAACAACATCACTGACCTACTGTA[A/G]AGAAAAAATAGTAGCTCTTAAAACATTAGGATTCC R 2 1 2 1 101000 f 74 goat snp31829-scaffold356-1330153 8 101390847 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774374 Affx-122967120 AX-385261510 8 99730910 TCCAGCAGACCTCACATTTGCCAGAACTAGAAAAC[A/C]TATCCACTGCTAAACAAGACATTGAATAAATGGCT M 2 1 2 1 101000 f 74 goat snp31830-scaffold356-1392672 8 101453295 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320772806 Affx-122933075 AX-385259951 8 99766247 AGAGTCAGAAAGTTAGTATCTGTACATCTCCTTCA[C/T]ATCACTTACAGCATTTGAAGTTAAATTACTGATAA Y 2 1 2 1 101000 f 74 goat snp31831-scaffold356-1428009 8 101488763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273436 Affx-1111833599 AX-519547061 8 99782668 CTGAAAGCCTTGGAAAAATTAGAAAATTGTGCCTG[A/C]TTCACAGTTAGAAATCTTTAATAATATTGCCTATG M 2 1 2 1 201000 r 74 goat 8_99782668_AF-PAKI 8 99782668 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38447658 Affx-122923963 AX-123317994 8 99828942 TACAAATTCTTGGCTTTGGTGAGCCCCACAGTTGA[C/T]GGGGATTCAGTTTAGGAACTAGCCACAGTTTGTGC Y 2 1 2 1 102000 f 74 goat snp31832-scaffold356-1490704 8 101552163 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391482 Affx-122966714 AX-123261839 8 99858967 TTGTTTATCTGATACCTCCCTTTAAAGGCACCTCA[A/G]AGTAACATGGCATAAACCAAACTTTTTCTCAGTGG R 2 1 2 1 101000 r 74 goat snp31833-scaffold356-1520729 8 101582318 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394247 Affx-122964871 AX-123264602 8 99916852 AAAATTTAATCCTTAAATACAGTCATGAAGGAACC[A/G]TGTATGCTGTTTTATTTTCACGAATTTCTTTTCCC R 2 1 2 1 101000 f 74 goat snp31834-scaffold356-1578614 8 101640131 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397775 Affx-122962515 AX-123268130 8 99945477 AAAAGATAGCAACAAAACTGTGTCCTGATGTTTTC[A/G]TTGTCCTGGATCTTTTTTTAATGTAGAGAGACTGT R 2 1 2 1 202000 r 74 goat snp31835-scaffold356-1607239 8 101668881 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411196 Affx-122952370 AX-123281546 8 99986745 TATACAGTCATTCTCTGTAGTCATCTTATACATTG[C/T]AGTTTCACATGCCGATCCCAATCTCCCAGTCACCT Y 2 1 2 1 201000 f 74 goat snp31836-scaffold356-1648507 8 101710605 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377234 Affx-122978159 AX-123247593 8 100047343 ATAATGATTTAGAATTCTCTGAACTATTTGTCTCT[A/G]TCCATTCACAAAAGTGAGTATTTTGCTAGTGGCCA R 2 1 2 1 101000 r 74 goat snp31837-scaffold356-1709105 8 101771506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433110 Affx-122935707 AX-123303451 8 100097008 TCTTAGGATACAGTGAAGGTTTGTAAACTCTAGTG[C/T]GAATGAATGCTCCACATGAAGTGCTTTAACTTTGC Y 2 1 2 1 101000 f 74 goat snp31838-scaffold356-1758770 8 101821389 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436760 Affx-122932281 AX-123307098 8 100146375 CAACTTGTTTATGAGTCCTGATCCTCCCTACCCCT[A/C]CAGTCTCATTTCACTTGACCCTCCTCCTTGTCTAC M 2 1 2 1 201000 r 74 goat snp31839-scaffold356-1808137 8 101869009 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397094 Affx-122962707 AX-123267449 8 100203277 CATTTTGATGCCATGAGGACAGATTTAAGATCTCT[A/G]AGCCTCAGATTCCTCATCATGGGGATAATTACACC R 2 1 2 1 101000 f 74 goat snp31840-scaffold356-1865039 8 101926444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438075 Affx-122931526 AX-123308413 8 100236305 CAAAAATAGCTGAAATTCCTGCCCTTACTGAGCTT[A/C]TACAATGGTTTATTTCTTTTTAATCTTCATATTCT M 2 1 2 1 101000 f 74 goat snp31841-scaffold356-1898067 8 101959082 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783586 Affx-122934320 AX-385270646 8 100281469 TGCTATCAATCCCCATCATTGACACCAACAGAACC[A/G]TCACACAGCCTTTACAGAAACCTTAACCACTGCCA R 2 1 2 1 102000 f 74 goat snp31842-scaffold356-1943231 8 102004261 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391053 Affx-122966855 AX-123261410 8 100330465 AAAGGTTAATGACTCATTATTTTCCAAGTTGTTCA[C/T]ACCACTGTTAGGACAACAAATGAAAAAGGAATAAA Y 2 1 2 1 201000 f 74 goat snp31843-scaffold356-1992227 8 102053645 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412233 Affx-122950915 AX-123282583 8 100381633 CTCACCCATAGTGATCTGGTGGGGAAACATGATTC[A/G]TTCAAATACTGAGTAAGCCACAGGGCGTATCGACT R 2 1 2 1 201000 r 74 goat snp31844-scaffold356-2043395 8 102106393 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768779 Affx-122974038 AX-385255956 8 100411459 AAGAGATGTAGGGAGAGAGGTAAACAGGAACTCTG[C/T]GTTCTAAATTCAGGTTCATTTAACACTGACTTGGC Y 2 1 2 1 101000 f 74 goat snp31845-scaffold356-2073221 8 102136203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442239 Affx-122928293 AX-123312576 8 100446868 CCATATTAGGACAACACGTGTCCCTTACCTGAAAG[G/T]TTTAATCTGTTAACATGAGTACGGAGTGAAGTGGT K 2 1 2 1 201000 r 74 goat snp31846-scaffold356-2108630 8 102171652 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441922 Affx-122928595 AX-123312259 8 100478486 CTGGGTCAGTGATGGAAATGGGTTAACTTTAGCCA[A/G]GATTGATGGCAGGCAAGGGAAAGTCTTGCCCAGCT R 2 1 2 1 101000 f 74 goat snp31847-scaffold356-2140248 8 102203070 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382972 Affx-122973354 AX-123253330 8 100528037 TTTTTTTTTTTTTTTTTTTGCATAGACCATTTGAT[C/T]GTGTGAAACCACCCTCAGAAGAAAGCAGGATCAAG Y 2 1 2 1 101000 r 74 goat snp31848-scaffold356-2189799 8 102252844 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770133 Affx-122964982 AX-385257300 8 100562686 AGAAATTCTAGGAGATGAGTTTCTTACGGGAACGA[C/T]GAGCCTACCTAGTTCTAGGAAGAATAGTCTATAAC Y 2 1 2 1 101000 f 74 goat snp31849-scaffold356-2224448 8 102288559 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395845 Affx-122964018 AX-123266200 8 100591219 AATGTATCAGTGTGTAAGTGAGGGTGGGGTTTCCT[A/G]TGTAGCTCAGTCAGTAAAGAATCTGCCTGCAATGC R 2 1 2 1 101000 f 74 goat snp31850-scaffold356-2252981 8 102317157 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376901 Affx-122977806 AX-123247260 8 100648504 CATCCAGGAGAATAGTATGTTGGCCCATTTTGTTC[A/G]TTGCTGAATTCCTAGCCCCAGCCCTCTGCCTGGCA R 2 1 2 1 101000 f 74 goat snp31851-scaffold356-2310266 8 102374793 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438395 Affx-122931295 AX-123308733 8 100690379 CTCAGATCTCCACGAGCTCGAGCTTCTTTCTGTAT[A/G]TTTATTGGCCGTTTTGTCATCTCTGAATCTCCAGT R 2 1 2 1 101000 r 74 goat snp31852-scaffold356-2352141 8 102416654 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414626 Affx-122949338 AX-123284975 8 100750108 AGAACAGTTGCGAGGTGGGTGTACCACTCCCTGCC[G/T]CGTGACCTTGGGCAACAGCTTCCCGCCAAGGCCTT K 2 1 2 1 101000 f 74 goat snp31853-scaffold356-2411870 8 102476120 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451075 Affx-122921417 AX-123321409 8 100782307 TGGCTCAATTTCCCCTTTGGAGCAACCAGGGACTG[C/T]ACCAGGTATTGCCAGGCCCCATCCTGCTATCCAGA Y 2 1 2 1 101000 f 74 goat snp31854-scaffold356-2444069 8 102505838 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434547 Affx-122934140 AX-123304888 8 100887507 ACCTGCTGCTACCGCTGATACCCACAAGAGGGCGC[A/C]AGGGTCACCAGGAAGGCAAAAATCAAGCCTAATAT M 2 1 2 1 101000 r 74 goat snp31856-scaffold356-2549269 8 102610321 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390080 Affx-122968033 AX-123260437 8 100931637 TCTACTGATAAACTGGAGAATGTGTCTTTATCTCC[A/G]TACCTCTGATCAAAGAACTTGCTAAAAATCTTCCC R 2 1 2 1 101000 r 74 goat snp31857-scaffold356-2593399 8 102654474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429463 Affx-122938484 AX-123299805 8 100983923 TTGGTAGCTTTCTCACTGCTTCCTCTCAGCTTTCA[C/T]GAGTGGCTGAGGGCATGGAGAAGAGGCCTCCGCAG Y 2 1 2 1 102000 f 74 goat snp31858-scaffold356-2645685 8 102707115 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377691 Affx-122977416 AX-123248050 8 101018487 GGAAGGGCCTTGTGGCATAAAGGCAACTCAGCTAG[C/T]ACAAGAGGTAAATTCTGTTTTAGATGCTTTCTAAA Y 2 1 2 1 101000 f 74 goat snp31859-scaffold356-2680249 8 102741824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384776 Affx-122972014 AX-123255134 8 101058210 TGAGCTATCATTGTAAATGTCCTGATGTCGCTGAA[C/T]GGAAAGCGGAATACTCTAGGCTTGTTAGCTCTGCT Y 2 1 2 1 101000 f 74 goat snp31860-scaffold356-2719972 8 102781864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403138 Affx-122958106 AX-123273491 8 101095868 TATAAATACAATTTAAAAATTACATTGTAATGAAC[A/G]TCTTATATTAAATATTCTGATGTTTTAAAGCCATC R 2 1 2 1 201000 r 74 goat snp31861-scaffold356-2757630 8 102819424 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441656 Affx-122929194 AX-123311993 8 101128944 CACAGTGCCTGGCATATGGGAGGAGTCACAGTGAC[A/G]GTTTGTAGTAGTCCTAATAGGATTTAGCGGTGGGT R 2 1 2 1 101000 r 74 goat snp31862-scaffold356-2790706 8 102852229 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408904 Affx-122953966 AX-123279255 8 101193546 TTACTGTCGAGTGACCCAGCAATCAGTGTGAGAAG[C/T]GAGTTCTGCGTTAAACGTCCAGAGAACATTAACAT Y 2 1 2 1 101000 r 74 goat snp31863-scaffold356-2855308 8 102917531 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414412 Affx-122949974 AX-123284761 8 101277769 TGTGAGTGCCGCAAGGTTTCTGAAGGCTGTTCCTG[G/T]GACTGCCTCGTCCAGATAACGGGCACAAGGTCGCA K 2 1 2 1 201000 f 74 goat snp31865-scaffold356-2939531 8 103001596 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387729 Affx-122969748 AX-123258087 8 101312497 ACTTCCGTGGGGAAAAAGAGGGCATAACTATGGAA[C/T]GTTACCTGGGCTACTTTCCACAGTGGTGGGTACAA Y 2 1 2 1 101000 f 74 goat snp31866-scaffold356-2974259 8 103036499 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404122 Affx-122957104 AX-123274474 8 101353752 AGTATAATCTGACTAGTGTCTCTCTACTGTCCATC[A/G]CATCTCCAAGTATTCATCTGATGACCAGAAGTCTG R 2 1 2 1 101000 r 74 goat snp31867-scaffold356-3015514 8 103077903 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401785 Affx-122959481 AX-123272138 8 101401469 CTTGTTCGGAGGAGGCCGAGTGCTCCCTTGACTGC[A/G]TGTGCAGCTCCAGAGGCTCGTGCAGAGTCTAGTTG R 2 1 2 1 101000 r 74 goat snp31868-scaffold356-3063231 8 103123404 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376200 Affx-122978815 AX-123246559 8 101433032 GGTTATCATGAATTCCATTGTTAGCACCTAACCAG[C/T]GTGTGATGGCATTTTAGAATTTACCGGAGGCTAAG Y 2 1 2 1 101000 f 74 goat snp31869-scaffold356-3094794 8 103154984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401573 Affx-122958886 AX-123271926 8 101483873 TCATTTAGGGCCTCTTCCTCATTTGGGTTTCTCTC[A/C]GGGCTCTCAGGGGGTGGGTAAAGGTGATCAGCCTC M 2 1 2 1 101000 f 74 goat snp31870-scaffold356-3145635 8 103205553 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447401 Affx-122924407 AX-123317737 8 101520080 TAACCACAGCTGTGGAAACGGTAAACCCACTAGAT[C/T]AGGCCAATTTTGTGCAGCAGGAGATGGGCCTCATC Y 2 1 2 1 101000 f 74 goat snp31871-scaffold356-3181842 8 103241548 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416444 Affx-122947825 AX-123286793 8 101618760 TTGGTGATACAAGGACAGGGGGCACCCTTGAGAAG[A/G]GGAGAGCTGCTCCTTCCCACCTTGATCAGAGGCAC R 2 1 2 1 201000 r 74 goat snp31872-scaffold356-3280522 8 103339911 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418554 Affx-122946395 AX-123288902 8 101673127 AGGACTTCCTTGGTCCCAGGGGCAACGAAAGGGTG[C/T]AATGCAAACAGCACCCCGAATTAACCTTAAAAATC Y 2 1 2 1 101000 r 74 goat snp31873-scaffold356-3334889 8 103394181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391147 Affx-122966784 AX-123261504 8 101739760 TACATGCTCTTAAAACACAGCTGCCTCCCATACTG[A/C]GGGGAAGCACAAGCAGCCCTGTGCAAAAGTCCACA M 2 1 2 1 101000 f 74 goat snp31874-scaffold356-3401522 8 103460881 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417184 Affx-122947322 AX-123287532 8 101771653 CAGCCACCCAAGTGACTGTATCAGCTTCTGCTCCC[A/G]CAAATCGTGGGAACGCTGACTTCTCACATGCTCTT R 2 1 2 1 101000 r 74 goat snp31875-scaffold356-3433415 8 103492424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446115 Affx-122925788 AX-123316452 8 101808289 TATTTTTTTATTTTTAAAAATTACCTCTTTAATCT[A/G]TTAATCCAAATCAGCTCACCTTGGTTTTTTTGGCC R 2 1 2 1 101000 r 74 goat snp31876-scaffold356-3470051 8 103529363 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386652 Affx-122970206 AX-123257010 8 101849624 TGATTGAACTTAGAGGTTTTGCTTTGGATGGAATA[A/G]CCTAAGTTTCTGTGTCTGTATTAATTTTTTTTTTT R 2 1 2 1 101000 f 74 goat snp31877-scaffold356-3511386 8 103570546 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407731 Affx-122954997 AX-123278082 8 101902496 AATTAGAAGCTATATGGTTAATTTAGGAAATGACT[A/G]CAAACTAATATGAGCAATATGATCCCATTTTTGTT R 2 1 2 1 101000 f 74 goat snp31878-scaffold356-3564258 8 103623556 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767296 Affx-122924838 AX-385254577 8 101953262 TGGACTCAATAAATTGGCAACTCAGGGGAGCATTC[A/G]TCTTTGACTAGATTTATAATTATATGACTCTCTGA R 2 1 2 1 101000 f 74 goat snp31879-scaffold356-3615024 8 103672544 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382718 Affx-122973620 AX-123253076 8 101997274 AACTTCATATGGCACGCCAGCAAAGGCTATGGACA[C/T]GGACAGACCTGGATGTGGATCTCAGCACTTGTTAG Y 2 1 2 1 201000 f 74 goat snp31880-scaffold356-3659036 8 103716275 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765037 Affx-986697175 AX-385252607 8 102011475 CACATCCCCACCTCTACCAAGCCCAGCCCAGAAAC[C/T]TACCTGCTCTGTGGTAAAGGCCTGCTCTGCAGGAG Y 2 1 2 1 600010 r 74 goat 8_102011475 8 102011475 Ancestral_priority_1043 ancestry 0.57 neutral IMAGE 10K 10K ancestral 320803683 Affx-986696176 AX-385290456 8 102051950 ATATTGACTGTATTAATATTTCAGCGACAGGATGA[C/T]GGAGCATTCTTCAGTTCCCTTCTTTGGGTTTAGTT Y 2 1 2 1 600010 r 74 goat 8_102051950 8 102051950 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 38375855 Affx-122978520 AX-123246214 8 102089628 CTGTCTCTTTTGTTTTTCAGACTCTGAGTATCTCA[C/T]GGGTATCCTCAACAATGTTTCTGTGTATGGAGGGA Y 2 1 2 1 101000 f 74 goat snp31881-scaffold356-3751390 8 103808974 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448491 Affx-122923468 AX-123318827 8 102134972 TTGACATGAAGAAAGATCTCTAGTTGCTTAAAAGC[A/G]CATAGATGTCAACAGACAGACCTAGAATTTGAAGT R 2 1 2 1 101000 f 74 goat snp31882-scaffold356-3796734 8 103854948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777280 Affx-122931547 AX-385264402 8 102168678 GTTTGCAGGCAGCACACTCTGGCTGAAATTTAATT[A/G]TGTTGGAAATTCAATTAAAAGGTAACTTAATAAAA R 2 1 2 1 101000 f 74 goat snp31883-scaffold356-3830440 8 103889116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278826 Affx-1111836532 AX-519552297 8 102194013 GTTTAAGTATCCTTATGATTAACTGCACTCTAAGA[A/T]GGATACAGGCCAAGGAAAGAGAGTTAAAATATCCA W 4 1 2 1 101000 r 74 goat Random2.2K-945 8 102194013 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38393789 Affx-122965188 AX-123264144 8 102202071 AGCTATCGTTTCCTCCTAATCCGTTTCTCTTCCAC[A/G]TTTCGCTGTGGGTTAGGACAGACGACAGGGGGTCC R 2 1 2 1 101000 f 74 goat snp31884-scaffold356-3863833 8 103922004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380321 Affx-122975382 AX-123250679 8 102237339 TACTGCTCATGGCAGTGTTCTGAGGTCAGAGTATT[A/G]TCTCTAATTCAAAGGTGAGAAAAGAAGGCTCAGAG R 2 1 2 1 101000 f 74 goat snp31885-scaffold356-3899101 8 103956896 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402350 Affx-122959056 AX-123272703 8 102283352 CAAACTTTGATCCTGGGGGCAACCTCTGAAAGCAA[A/G]GACATTTCCTGAAGTCTGCATCCTGAGATGGTTTC R 2 1 2 1 101000 f 74 goat snp31886-scaffold356-3945114 8 104002974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391125 Affx-122966799 AX-123261482 8 102354435 AAAAATTAATTAAAAGAATACTGTAGGAAATGGCC[A/G]TAGGGGACATCTGAAGTGAACAGTATCCTTTTTCA R 2 1 2 1 201000 f 74 goat snp31888-scaffold356-4016197 8 104073755 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273325 Affx-1111833562 AX-186152373 8 102372409 CTGGAGAAGGGAAAGGCTACCCACTCCAGTATTCT[A/G]GCCTGGAGAGTTCCATGGGCTGTACAGTCCATGGG R 2 1 2 1 103000 f 74 goat 8_102372409_AF-PAKI 8 102372409 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320790396 Affx-122941207 AX-385277399 8 102445340 AGGACATGAAGGTATTAGAAGATGTTTATTTTGAT[A/G]GACTTGGAATATGGAAATGGAATCGTTTTCAAAAG R 2 1 2 1 101000 f 74 goat snp31890-scaffold356-4107102 8 104164610 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792961 Affx-122959673 AX-385279939 8 102520071 AGATTTTGACCCACACTAGCAGGTGTTCAGGAAAT[A/G]TTTCTTGTCCTGATCAAAAATCACAAACCACACAG R 2 1 2 1 101000 f 74 goat snp31892-scaffold356-4181833 8 104239375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775372 Affx-122974058 AX-385262503 8 102561651 CAAAATGGGCTTTGATGTAATTCCATTAAGATTCT[A/G]TGATAAAGATGACATCATACAACAGTTAATGGTGA R 2 1 2 1 101000 f 74 goat snp31893-scaffold356-4223413 8 104281506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451989 Affx-122920930 AX-123322322 8 102616159 TAGACAACTGTGCATAAGTCATTTAACAAGTCCTG[A/C]TTCTATCTTTTCAGTAAATGTTTTTACTTCAGAAT M 2 1 2 1 101000 f 74 goat snp31894-scaffold356-4277921 8 104336085 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394929 Affx-122964306 AX-123265284 8 102660416 CAAGCCGTCACTTTTAGTTATAAAACTGGGCACAG[C/T]CATTCGTGTGCCAAGCGTTTTCAGTCACTTTCCAT Y 2 1 2 1 101000 r 74 goat snp31895-scaffold356-4322178 8 104380872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401263 Affx-122959289 AX-123271616 8 102689643 TCCAGTACTCTCCAAAGCCTCGCTGGGCACACGCT[A/G]AGTGTTTGGAGGTGAATCAGATGGAGACCCGCTCC R 2 1 2 1 101000 r 74 goat snp31896-scaffold356-4351405 8 104410242 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787018 Affx-122932366 AX-385274046 8 102751687 AAGTAAAAGCAACAGACTGCAAGAAATAAACATAA[C/T]AGATTCCCAAGACATCAAAATGTAAGTGACAGAAC Y 2 1 2 1 101000 r 74 goat snp31897-scaffold356-4413449 8 104471363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415345 Affx-122948786 AX-123285694 8 102783778 GTTACTAATGATATTTTTAAATGATGCAGAGAGTC[A/G]TACGTGATCACTGTCTTGCAAACGATCACTCTCTT R 2 1 2 1 101000 r 74 goat snp31898-scaffold356-4445540 8 104503380 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404596 Affx-122957350 AX-123274948 8 102817299 GTTGACTGCCTCTCTTTTTGTGGGATAACACCATC[A/G]CCACTCTCATGATTACTTCCTCATCACCTCCATTG R 2 1 2 1 101000 f 74 goat snp31899-scaffold356-4479061 8 104536925 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391458 Affx-122966733 AX-123261815 8 102864051 ATGAACAGTAAGTCTCTGATGAAAAGACAGAGTCT[G/T]TTACAGAACCCACTTTTTTGTCTTAGGATCCACTA K 2 1 2 1 101000 r 74 goat snp31900-scaffold356-4525813 8 104584704 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438595 Affx-122930943 AX-123308932 8 102916456 TAAGTTCTACAAGCAATTTATTACCTAATTGCTTC[A/G]TAGATATGTATGAGAGAGAGAGAGGCAGATAGATA R 2 1 2 1 201000 f 74 goat snp31901-scaffold356-4578218 8 104638095 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388534 Affx-122969197 AX-123258892 8 102957754 GAAAACTCTAAGTGGAAAGGTTCTTGTCCACAAAG[A/C]TATGCTTTAGAGACCTTGTCAGTAAGAGCTTTTGT M 2 1 2 1 101000 f 74 goat snp31902-scaffold356-4619516 8 104679707 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378074 Affx-122977174 AX-123248433 8 103014791 CATAAGAAGGGTTCTTATTCTGATTTATTCATTCT[A/G]TTACTGAGTTAATGGTTGATCTCTCATTATCCCTG R 2 1 2 1 101000 r 74 goat snp31903-scaffold356-4676553 8 104737389 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397121 Affx-122962684 AX-123267476 8 103070905 ATAAATGCCTCAAGGGCAGGGGTTGTACCTACTTC[A/G]CTTGTCACATTTAAGATCCTGGAACCAGCATTCAG R 2 1 2 1 201000 r 74 goat snp31904-scaffold356-4732667 8 104791638 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426517 Affx-122940206 AX-123296863 8 103115286 ATACATCCTGGATCCAGCTACTCCTCACCATCTCC[A/G]TGGCCACAGTCTGATGCAAGCCTCCATCAACTCTT R 2 1 2 1 201000 r 74 goat snp31905-scaffold356-4777048 8 104836595 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781191 Affx-122962907 AX-385268276 8 103154476 ATCATATCTGTAACGTGGAGGAGGTTGCTTAACCT[A/G]TTTAAGCATCACTTTCCTCCTCTACGTAGTCGTCA R 2 1 2 1 202000 f 74 goat snp31906-scaffold356-4816238 8 104875734 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383135 Affx-122973252 AX-123253493 8 103183745 CACTTGAAGTTCACACTGAAGTCATGGATGAGCAC[C/T]CGGGAGCTGTTTTGGGGAAAATGAACATGCAGAGA Y 2 1 2 1 201000 f 74 goat snp31907-scaffold356-4845507 8 104905233 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782585 Affx-122938419 AX-385269659 8 103213482 CCATCTTTAAAGCTCCGCTACACCCACTGGATGCG[G/T]ATTCCCAACCCCATGCTGCTTAAACCTGGCTATAG K 2 1 2 1 101000 f 74 goat snp31908-scaffold356-4875244 8 104935660 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793418 Affx-122930869 AX-385280395 8 103259654 TGCCTATTGCTAAGTACCAGAATCCTTCTTGAAGC[A/G]CAATTATAATGAGAATGAAGGCTGACTATGTAACT R 2 1 2 1 101000 f 74 goat snp31909-scaffold356-4921416 8 104981639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445630 Affx-122925091 AX-123315967 8 103299255 TTGACTCTTGCAATTAGATGGGGTGGGAGGAAGCT[A/G]CCCTATTCAGAGGGATTCATTGTATAAAGGACATT R 2 1 2 1 201000 r 74 goat snp31910-scaffold356-4961017 8 105020940 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397926 Affx-122961932 AX-123268281 8 103335273 TACCCAATGAGTGACTGATAAATAGTTCTTAAACT[A/G]GTAAGAGAAGACCACGTACAATTTTATCTGGGATG R 2 1 2 1 101000 f 74 goat snp31911-scaffold356-4997035 8 105056891 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386190 Affx-122971367 AX-123256548 8 103400041 TTTCTGCGTGCCAGGTATTATTCTAAGCCCTTTAC[A/G]CTTCCTTTATTAATGTCCCAAATCCTCAGACCAAC R 2 1 2 1 201000 r 74 goat snp31912-scaffold356-5061803 8 105121181 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794912 Affx-122938736 AX-385281872 8 103465418 AATAAACTTTGAGAGTAAGAAGGGCTGTCATCTTC[A/G]CTAATTGGATTTTTCTATGGGATGATACATGCTAA R 2 1 2 1 101000 f 74 goat snp31913-scaffold356-5127180 8 105186315 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375916 Affx-122978474 AX-123246275 8 103496368 AGAGGAACTGGGAAGGTGTACCTGGCAAGATGATC[A/G]CTTTTGGACAGCTACCTCCAGATTTCTCCTTGTGT R 2 1 2 1 201000 r 74 goat snp31914-scaffold356-5158130 8 105217288 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428562 Affx-122938722 AX-123298904 8 103549212 CGACTCTAGAAGAGGTGCTCTCTGGCTAGGCATGC[C/T]GCTCCCAGCAATCTTGTGAAGTCATCTGACTTGCA Y 2 1 2 1 201000 f 74 goat snp31915-scaffold356-5210974 8 105269910 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388345 Affx-122969350 AX-123258703 8 103585156 AAGGAGCCCTGTGCTTCAGGAGGACAGAGTGGTCT[A/C]TCCTGTGCTTTTGCGCACCCAGCATATAAGTGTGT M 2 1 2 1 101000 r 74 goat snp31916-scaffold356-5246918 8 105305606 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381722 Affx-122974696 AX-123252080 8 103666024 TGGACCTCCTGTCAGCTGCCACCTACAGGGAATGC[C/T]AACTGTCTGTAAGAGTCTCACTTTCTCCTACCAAA Y 2 1 2 1 101000 r 74 goat snp31918-scaffold356-5327786 8 105386202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420359 Affx-122944957 AX-123290706 8 103713352 AGACATTTAATCAATGATTAATACACATCTACACC[A/G]TGCATCATTGGAATGGGGAGCTTTCACAGGTGGTT R 2 1 2 1 201000 f 74 goat snp31919-scaffold356-5375114 8 105433587 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770137 Affx-122958293 AX-385257304 8 103755062 TCCTTCATTAATCCATCCACCCAGTTTTTCATACA[G/T]CTATATATTCGTCTATTAATTCATCTCTGAACTCA K 2 1 2 1 101000 f 74 goat snp31920-scaffold356-5416824 8 105475500 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389822 Affx-122968188 AX-123260179 8 103787128 CCCTCTCACTTGGAAGGAATACTTTTCAGATAAAA[C/T]GAAATAATGGATTCAAAGGCCCTTCAGTTCATCTT Y 2 1 2 1 101000 f 74 goat snp31921-scaffold356-5448890 8 105507582 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787124 Affx-122945614 AX-385274150 8 103820983 CCACTGTGCCTTTGCTCATGGCTTCCCTCAGCCTA[C/T]AATATCTTTCCTCCATTCTACCCTTAAACAAAGCA Y 2 1 2 1 102000 f 74 goat snp31922-scaffold356-5482745 8 105541723 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385653 Affx-122971160 AX-123256011 8 103912339 ACCTCTTTTGATTATCAAAACATTTACAAGACCAA[C/T]TTCTCTGCCCTCATTCCCTCCCTAAACCTCCCCTG Y 2 1 2 1 201000 f 74 goat snp31924-scaffold356-5574101 8 105633376 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435766 Affx-122932877 AX-123306105 8 103942574 GTACATCAAGGATGAATATTTTAGGCAAAGAAACC[A/G]GAACAGCATCCTCAGTTCAGTCGCTCAGTTGTGTC R 2 1 2 1 101000 f 74 goat snp31925-scaffold356-5604336 8 105663369 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443909 Affx-122927051 AX-123314246 8 103962921 GATGGAGATGGGAGTTGAGGCTCAGAGAGAGGCGG[C/T]ACCTGCCCCAGGTAGTGAAACACAAGAATGGAGAA Y 2 1 2 1 201000 r 74 goat snp28893-scaffold311-5098 8 105684169 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388746 Affx-122968954 AX-123259104 8 103998726 GACAATGTACATTTATTTCCTGTGGTTTTCAGATC[G/T]TAGCTGCTGGCTTCCACCTAAATTGAGATTTCCTA K 2 1 2 1 101000 r 74 goat snp28894-scaffold311-40903 8 105719907 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789769 Affx-122929896 AX-385276777 8 104035612 GAGAAATAAAATGTTTAATGTCATAAAAGGGTGCA[C/T]AGGCTTTATGAGAATGCCACACATTATAATCGTGA Y 2 1 2 1 101000 r 74 goat snp28895-scaffold311-77789 8 105756744 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769063 Affx-122954094 AX-385256238 8 104072193 GGGATCTCTGTAGCTCCATGCCTAATACAATGACA[C/T]GTAATAGAGGGTGACACATACTGAATCAGTCCTGA Y 2 1 2 1 101000 f 74 goat snp28896-scaffold311-114370 8 105794076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799137 Affx-122957144 AX-385286067 8 104114428 GGAGTGGTGGGTAGAGAAGGCAACCTCATACTGAA[C/T]GGAGCTTTTTCTCACATGTCACCAGGTTAGAGGTT Y 2 1 2 1 101000 r 74 goat snp28897-scaffold311-156605 8 105836491 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438249 Affx-122931425 AX-123308587 8 104158431 CCCCAGCTTCCTCCCCAGACAGTGAGTGGCTAAGA[C/T]GGGATCTGAACACTAGAGCATGCGCTGCTAAGGAC Y 2 1 2 1 201000 r 74 goat snp28898-scaffold311-200608 8 105880550 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429875 Affx-122938136 AX-123300216 8 104187143 GGCTCACCAGTGAAGAGGAGGGAACCCTGAGATTC[A/G]TAACTGCCAGGTAGTGCTGGAATTTCTCTATTTAG R 2 1 2 1 101000 r 74 goat snp28899-scaffold311-229320 8 105909100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422484 Affx-122943317 AX-123292830 8 104242864 TCACAACTTAGGGGGTGAGCCCAATATTAACTAGG[C/T]AAGAATATTACAAATAGAAAAGCATGCAATCAAAG Y 2 1 2 1 101000 f 74 goat snp28900-scaffold311-285041 8 105965786 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391589 Affx-122966607 AX-123261946 8 104304380 GAAAGGCAAGTAGATTTCTAGATTGGTTTAATCTA[C/T]GAGTCACGAGAGGCCACGCATGTCTGTACAAAGAC Y 2 1 2 1 201000 f 74 goat snp28902-scaffold311-346557 8 106026122 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381083 Affx-122974603 AX-123251441 8 104343016 AACCTCAACCAAGTTACAGGCAATGACCGGGCAGA[A/C]GGAAATGGATGTGTGAGCCCTGAGGTCAAATGAGC M 2 1 2 1 101000 f 74 goat snp28903-scaffold311-385193 8 106064578 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378660 Affx-122977090 AX-123249019 8 104372472 GGTCAAATGAGGGTCAGATTATCCAGGCTGGGGTT[C/T]GCCTGGCTGCAAAACAACAGGTTGAGTTTGGGTCT Y 2 1 2 1 101000 f 74 goat snp28904-scaffold311-414649 8 106094301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441424 Affx-122928823 AX-123311761 8 104427271 ACATGATTCATGAGACTCATGAAATACTCTGCTCC[A/G]TGAGCTCCTCCAGGGCAGGGGTGCTTCTAAAGCCC R 2 1 2 1 101000 f 74 goat snp28905-scaffold311-469448 8 106147664 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382549 Affx-122973779 AX-123252907 8 104473595 CCGACTCCACTTTCCTAGCTCAGCCTGAATTGTCC[A/G]TATCACCAAAGGTTTCCCTAATAAATTACCCAGCC R 2 1 2 1 101000 r 74 goat snp28906-scaffold311-515772 8 106193876 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433854 Affx-122934436 AX-123304195 8 104503428 TACAAAGCCATTAATTTCAGCTTTTCAAATCCATC[A/G]TTAATGTGAGTCTACATACATCACAGACTTACCAT R 2 1 2 1 101000 r 74 goat snp28907-scaffold311-545605 8 106223285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406285 Affx-122956079 AX-123276637 8 104532377 ACGCAAAACCCATGCTGAAGAAAAACAAGTCCTCG[A/C]GTGCCCCTGGCTCATGACACTGGGGACACGGACTT M 2 1 2 1 101000 f 74 goat snp28908-scaffold311-574554 8 106252079 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376862 Affx-122977835 AX-123247221 8 104562581 AAAGACACATGGAAAAGAGAGAAGGTGTGGCCATG[C/T]GGGGAGAGATAGTAGGCTGGCAGGAAGAGAGGTTG Y 2 1 2 1 201000 f 74 goat snp28909-scaffold311-604758 8 106282437 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773280 Affx-122976222 AX-385260423 8 104607287 GAATTACAAAGACGGTAGATGAAAAGATCACAAGA[C/T]GACTTAATCTGGACCACAGTAACTCAAAAACGTTT Y 2 1 2 1 101000 r 74 goat snp28910-scaffold311-649464 8 106327466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391620 Affx-122966584 AX-123261977 8 104637220 TTACTTGGCAAGCATCTTTAAGTCCTCAGTCCCCC[C/T]CTTAATGAGACCACCAATAGAGATTATATTCAGAG Y 2 1 2 1 201000 r 74 goat snp28911-scaffold311-679397 8 106357743 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768887 Affx-122964302 AX-385256064 8 104667711 TCGTGAAAAGTAACTTCTATAAATAATAAGAGAAC[A/G]CACCTAGCACCAAGAACTCTGTACTCAGTAAGTGT R 2 1 2 1 101000 r 74 goat snp28912-scaffold311-709888 8 106387989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436936 Affx-122933186 AX-123307274 8 104706757 CAGAAGGAGGCAAGAAGAGGGAGGGACGCAGGAGA[C/T]GTGAAAAGAGAAGCAAGAGGTTGGAGTGTTCCTAG Y 2 1 2 1 101000 r 74 goat snp28913-scaffold311-748934 8 106426643 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434311 Affx-122934753 AX-123304652 8 104735832 AATAGCACCTGTCTTATGCTGATGTTTTAGACAGT[A/G]AGTTAGTGTACCTAGTGTTTAGAACTTTGCTTGAC R 2 1 2 1 101000 r 74 goat snp28914-scaffold311-778009 8 106455927 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410595 Affx-122952115 AX-123280945 8 104793675 AGAAACTTGCTAGTTACCACAGAGCTTGTGACAGA[G/T]CACAGTCGAAACAGTGGACTTGCTGAGTCCAAAAT K 2 1 2 1 101000 f 74 goat snp28915-scaffold311-835852 8 106513580 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405995 Affx-122955515 AX-123276347 8 104831890 GGGAATGAGGATTGAGGACAGAAGTGGCAGTTGCC[A/G]TGGAAATGCAGGAGTTTTTGCAGAGCCCAGTTTTG R 2 1 2 1 201000 r 74 goat snp28916-scaffold311-874067 8 106552146 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273364 Affx-1111833563 AX-519546998 8 104893959 GGAGAGAGAAAGAGTAAGTGGGGGCTTCTGTAGGA[A/G]CTTACCTAGAACAAATCAGGCCTGTGAGAGGCACG R 2 1 2 1 101000 r 74 goat 8_104893959_AF-PAKI 8 104893959 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320798249 Affx-122970299 AX-385285184 8 104920763 CTGGATCCAGGTGAATGATCCTGAGCAGGAGAAAC[A/G]TTAGTTCAGATCAGGTGTTCAGAAATTTTTAGGTG R 2 1 2 1 101000 f 74 goat snp28918-scaffold311-962940 8 106638013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403417 Affx-122957755 AX-123273770 8 104954661 AGAATTCCATGGACAGACGAGCCTGCTACACCATG[C/T]GCTTACATTGGAGCTGGCACTCAGTTTTGTCTAAT Y 2 1 2 1 101000 r 74 goat snp28919-scaffold311-996838 8 106671927 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387704 Affx-122969808 AX-123258062 8 104999629 AGAGTCCAGACATTGAGGACATGGGGGAATTCGTG[C/T]AACGTGTAAGAAGACAAACTTGTCATCCCAAGTCC Y 2 1 2 1 201000 r 74 goat snp28920-scaffold311-1041806 8 106717470 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273885 Affx-1111833911 AX-519547493 8 105047164 TTTATTCCCTTGGCTCGTCTTCTGGTGCCATGTCA[A/G]CAGGCACAAGGTTCCTGGAGTCTACTCTGCAGCAA R 2 1 2 1 202000 f 74 goat GoatD01.010144 8 105047164 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320784191 Affx-122927926 AX-385271242 8 105055044 CATTTATCAAATGTATATTGAGGATCTGTTCTGTA[C/T]GGGATGTGTTACAGGCAACATCTCACTCATTAATA Y 2 1 2 1 101000 r 74 goat snp28921-scaffold311-1097221 8 106772854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449462 Affx-122922655 AX-123319797 8 105112956 TCTTCCTGCTCCGTGTCATGGGTATATATGACAGC[A/G]CATTCATTTACTAAACACTGATGCTCTATTATATG R 2 1 2 1 101000 f 74 goat snp28922-scaffold311-1155133 8 106831501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776091 Affx-122969321 AX-385263221 8 105129203 AAAATTTCTGTGTGATTTGTGTCTCTGGATTGAAC[C/T]TGATCATTATGATAGGAGACAAAAGATAAGAACCT Y 2 1 2 1 101000 f 74 goat snp2061-scaffold1063-5476 8 106847111 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437428 Affx-122932409 AX-123307766 8 105158402 CCAGATAAAGAAAAAGTAAAATATCCATGTGTTTA[C/T]AGCTTTATGGTCTTCTAGGTTGCCTTTCTGCTGAG Y 2 1 2 1 101000 r 74 goat snp2062-scaffold1063-34675 8 106876093 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390434 Affx-122967634 AX-123260791 8 105195019 ACTCAAGGTCATTTTCCCATTAAAATAGCCTCCCT[A/G]CTTTGAATGTAAACTCTCTTCCTCTGCGATACACC R 2 1 2 1 101000 r 74 goat snp2063-scaffold1063-71292 8 106912544 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451907 Affx-122921031 AX-123322240 8 105223799 TTCCATGCAACCCTAACAGTCATAATTTCTAGGGA[C/T]GAGGATGTCTTTGGTGGTGGTGGTGTGTGTTTTCT Y 2 1 2 1 201000 f 74 goat snp2064-scaffold1063-100072 8 106941667 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381720 Affx-122974698 AX-123252078 8 105273780 CACCATTCAGACCAACTGGCTACAGGTTCAGGAGT[G/T]TCCACCATATGCTCAGGTTCAATCATTCTCTGGAA K 2 1 2 1 101000 r 74 goat snp2065-scaffold1063-150053 8 106992018 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411529 Affx-122951663 AX-123281879 8 105365003 CCTTGGACAGCCCTCAGACTTAAGTGATAAACTGA[C/T]GTCTTAGTGATGTTTGCTGTTTTTATTATATAGCT Y 2 1 2 1 101000 f 74 goat snp2067-scaffold1063-241276 8 107083179 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773070 Affx-122932842 AX-385260213 8 105411270 GAGTTTCAAAGCACAGCTCCTTGGCCACAGGTACA[C/T]AAATTCAGATAACAAATGACACTGGAGTTTTTCCC Y 2 1 2 1 102000 f 74 goat snp2068-scaffold1063-287543 8 107130543 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376944 Affx-122977772 AX-123247303 8 105444063 AGTCCATGGGGTTGCAAGGGACAGACACGTGGTAG[C/T]GACTAAACCACCACCAGAGCAAAGATTATTAACAA Y 2 1 2 1 303000 f 74 goat snp2069-scaffold1063-320336 8 107163244 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799006 Affx-122957964 AX-385285936 8 105475493 TAGATGGAGCTCAAACATCATATGCATATAAATTA[C/T]AAAGACAAACCTGGGTTTTCTCATTTGCTTCTTCT Y 2 1 2 1 102000 r 74 goat snp2070-scaffold1063-351766 8 107195479 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382352 Affx-122973875 AX-123252710 8 105505625 AAATTACCCCAAAACATAAAGGTTCAAAGCAACAG[C/T]CGACCTTTAGTATTTATTAGAGTTTGCATCCATGA Y 2 1 2 1 201000 r 74 goat snp2071-scaffold1063-381898 8 107222561 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802555 Affx-122948701 AX-385289458 8 105550052 CAAGATATTGTGCTCTTGGAAAGAGTCTAATTTAT[A/G]CATTATTTAACCCAGAGGACATAGAATATTGCCAA R 2 1 2 1 202000 r 74 goat snp2072-scaffold1063-426325 8 107267741 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407224 Affx-122955380 AX-123277575 8 105602256 AAAGAGTCTGATACAACTGAGCAACTTTCACACCC[A/G]CACAACTGGAATGAACACAGTTTTCAAAATTTATT R 2 1 2 1 201000 r 74 goat snp2073-scaffold1063-478529 8 107320163 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780050 Affx-122946970 AX-385267148 8 105667667 TATGAGTGAGCCAAAAATTAGCTTTGCTCTTGGTA[C/T]ATAGTCATCTAATGATAGGAGAATTTTGAAAAAAA Y 2 1 2 1 101000 f 74 goat snp2074-scaffold1063-543940 8 107381420 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791447 Affx-122933622 AX-385278438 8 105720942 GTCACAGCCAGTCTAGTTCTATCCAATTAAACCAA[C/T]GGCATTAAATAAGCATTATGCACGTGGACCCACAC Y 2 1 2 1 101000 r 74 goat snp2075-scaffold1063-597215 8 107435311 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422604 Affx-122943730 AX-123292950 8 105763498 AATCGAATCAAAATAAGATTTTAGAAAGAATACTT[A/G]TGCATTCTTTACACCTTCTGAACACTCTACTAAGT R 2 1 2 1 101000 r 74 goat snp2076-scaffold1063-639771 8 107478626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416445 Affx-122948419 AX-123286794 8 105802859 GCGATGGTGGAATGTCTTTGTGTGTTTTATACATG[C/T]GATGTGAATCATTTTCGAAACCATAATTACAATGC Y 2 1 2 1 101000 r 74 goat snp2077-scaffold1063-679132 8 107517455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382074 Affx-122974915 AX-123252432 8 105840674 TGCGCAGGGCCCATTCATGTGCCATGTCTCCAAGC[A/G]TGCTGATTAAACCGTATGCTCATTGATCTCGGGGG R 2 1 2 1 101000 r 74 goat snp2078-scaffold1063-716947 8 107555231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798879 Affx-122943151 AX-385285809 8 105881333 GATAACTTTGTGTATGATAATCATTTAATTAGACA[G/T]TCCAATGAAATGAATCCTGATTGTTTTCATGAAGC K 2 1 2 1 101000 r 74 goat snp2079-scaffold1063-757606 8 107596108 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449527 Affx-122922604 AX-123319862 8 105911235 TCTCAATAAGTTAATTTTCTTCCTTTTGTCTCCAT[C/T]ATTTTTCTTTTCTCTCACCCGTTGCAAGTAAACGT Y 2 1 2 1 101000 r 74 goat snp2080-scaffold1063-787508 8 107625613 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405006 Affx-122956385 AX-123275358 8 105946579 GAATTCTTCTTTTTACAGATGAAAGAAATAGAGGC[A/G]CCAGTTTGTTGGTTAAGGTCAGACAGCAAATAAAT R 2 1 2 1 101000 r 74 goat snp2081-scaffold1063-822852 8 107661965 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429985 Affx-122938049 AX-123300326 8 105980970 CTCTTTTCTTTTTCTTCAGATCAACTGTTCCTAAG[C/T]GCATCCCTCAACTAAGTAACCATGGCAACATTTTG Y 2 1 2 1 101000 f 74 goat snp2082-scaffold1063-857243 8 107696362 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776656 Affx-122942411 AX-385263783 8 106064064 GGTGACAAAATCTGTTGAGTTGAGAACACCTCGCC[A/G]CTTATGATAGTTAAGATAGCTTGCCTTGCCTTGGG R 2 1 2 1 101000 f 74 goat snp2084-scaffold1063-940337 8 107780304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793822 Affx-122947419 AX-385280793 8 106101607 CGCTAAGGATGCGAGTGAAGTCTAATTAAATTCTC[A/G]TTTTCTCGTTGCCATCAAACACAGGACAATTTTTG R 2 1 2 1 101000 f 74 goat snp2085-scaffold1063-977880 8 107817804 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437431 Affx-122932407 AX-123307769 8 106132667 CTCTGGGTAATTTAAAATGAAAAGAAGCCTTATTC[G/T]AAGCACGAGACAGAGATTCATAGAACTTTGAGGCA K 2 1 2 1 103000 r 74 goat snp2086-scaffold1063-1008940 8 107849404 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384469 Affx-122973081 AX-123254827 8 106164358 CCCATCTCAGAGTTTCCATACTTGCTTTTTCTTCC[A/G]CCTAGGACATCCTTCCTCTGCCTTCTCTGAGTGGC R 2 1 2 1 101000 f 74 goat snp2087-scaffold1063-1040631 8 107881244 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790544 Affx-122951489 AX-385277547 8 106193506 CTTGACTGGAACCGCTAGAACCAGGACTCAAATCA[C/T]ACTTTAATGCGAGTGACTTTTATATCTCTCAAAAC Y 2 1 2 1 101000 f 74 goat snp2088-scaffold1063-1069779 8 107910501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278650 Affx-1111836533 AX-519552129 8 106212636 CCGCAGGGCTTAAAACAACAGAAAACTGATGCTTT[A/T]ACAGTTTTGGAGACCAGAAGTCCAAAATCGAGGTG W 4 1 2 1 303000 f 74 goat Random2.2K-946 8 106212636 A T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320772073 Affx-122961458 AX-385259228 8 106226168 TATACATGATAAGGAATACAGTCTTCCTAAAAATA[A/G]TTTGGAAAAGTCACTAAATAATGGATTGCTGTAGC R 2 1 2 1 101000 r 74 goat snp2089-scaffold1063-1102441 8 107942465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396554 Affx-122962934 AX-123266909 8 106301029 TGAAAAATATGAAATTGTTAACTCTTCCCCTTGAC[A/G]TAAAGAATGAAAATGACATTTTATCTTAGTTTACA R 2 1 2 1 303000 f 74 goat snp2090-scaffold1063-1177302 8 108017467 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440041 Affx-122929757 AX-123310378 8 106333762 AAATTACCATGTCCCACAAGGATCTCATTCAAATA[C/T]GAAGGAAAAATCTAAAGATTTATAGACAAGCAGAT Y 2 1 2 1 303000 r 74 goat snp2091-scaffold1063-1210035 8 108049993 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422584 Affx-122943745 AX-123292930 8 106421200 GGGAAAAGAGACCCCCATCTGCTCAGTTTGAGAAG[C/T]AGAATATTTTGGGAAAAGGAGCAGGAAAAAGATTT Y 2 1 2 1 201000 r 74 goat snp2093-scaffold1063-1297473 8 108136609 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376027 Affx-122978396 AX-123246386 8 106453768 AGGCCGATCATGGCTGTGATCCATTTATCTGATTA[C/T]GACTCAAGGCTAAAGGGGCTGAGGTTTCTGTGCTG Y 2 1 2 1 101000 f 74 goat snp2094-scaffold1063-1330041 8 108169506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434155 Affx-122934900 AX-123304496 8 106489904 CCAGGCCAATCCAGCAGGATTCTCCTGGATGTCAC[A/C]CACCAAGGCTGTGCAGGGCATGGGGCTCCAGTAAT M 2 1 2 1 101000 f 74 goat snp21879-scaffold2147-351570 8 108205765 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382834 Affx-122973545 AX-123253192 8 106520430 CAAAAGTTTATTTAAAAATTCAAAGTCCGGTTTTA[C/T]AAAGTTAATAAAGCTGTTGTACAGTTTATCTCCGA Y 2 1 2 1 103000 r 74 goat snp21878-scaffold2147-321044 8 108236516 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278830 Affx-1111836534 AX-519552301 8 106529824 ACTTACCACATGTGATTGTTGCAAGGATTAAATGA[A/G]TTACTAAGAGCGCAATATTTAGAAGGGTTACTGCA R 2 1 2 1 101000 r 74 goat Random2.2K-947 8 106529824 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424711 Affx-122941683 AX-123295057 8 106584007 TTGGTTAAAGAGCCATCTCACTTATCAGAAGGAAA[G/T]CAGAACCGCAAAATGAATCAAAAAAGAATACGTCC K 2 1 2 1 201000 f 74 goat snp21876-scaffold2147-257467 8 108299137 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440802 Affx-122929830 AX-123311139 8 106634519 CTCTTACGAGCAGACTCTGAAGATGACCTGCAAGT[A/G]TGCCGTGGTCTGGCCCTGCCGGCCTCTTGCTCCGT R 2 1 2 1 101000 f 74 goat snp21875-scaffold2147-206955 8 108349906 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417852 Affx-122946778 AX-123288200 8 106704445 TGCCCAAGCCAAAAGCTGTTTACTCTTCCCTGATC[C/T]GCCTTGTTCGCTCATCTCTCTCATCTTGTCTGATA Y 2 1 2 1 201000 r 74 goat snp21873-scaffold2147-137029 8 108419815 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275675 Affx-1111834946 AX-519549245 8 106725461 CCGTATCACGGCCTCTAAGGAGCAAGAACTACGGA[A/G]TTTGCCAAGGAACCTCACTTGGCTAAATCTTACTC R 2 1 2 1 201000 r 74 goat GoatD01.059588 8 106725461 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38400162 Affx-122960687 AX-123270517 8 106733739 CATCTTTTTCCTGCTGTTCTTCTTCCTGTTGAAAT[A/G]TACCTTCCCTATGTAATGCTTCCCTGGTGGCTCAG R 2 1 2 1 101000 r 74 goat snp21872-scaffold2147-107735 8 108449273 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440270 Affx-122930645 AX-123310607 8 106771679 GCATGGTAGGTCTTCAGTGTGGATCATATTCACCT[A/G]GAACATTTATTAAAAATGCAATTTGTTTTGAGAAA R 2 1 2 1 101000 f 74 goat snp21871-scaffold2147-69795 8 108487817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430287 Affx-122937285 AX-123300628 8 106809192 GGTGGGGGTGGGGGGAGAGGAAAGGTAGAAGAGAA[C/T]GGAAGCAGCAGCAAGCAATAAGAGAAATAGGAGAT Y 2 1 2 1 101000 r 74 goat snp21870-scaffold2147-32282 8 108525168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792027 Affx-122978480 AX-385279015 8 106838606 TTTCACTATAACACCTCTGTCCAATAGAAAGATAA[C/T]GTGAGCCAGAAATGCTAGCCATGTTTGTAATTTTA Y 2 1 2 1 101000 r 74 goat snp21869-scaffold2147-2868 8 108554391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420787 Affx-122944696 AX-123291134 8 106845995 TTTACTGCCCATAAGGCCTTGGGCAAATTACTCAC[C/T]TACCATGAGTCTCCCTTTCACAATGAGAGCAGCAG Y 2 1 2 1 201000 r 74 goat snp16427-scaffold1732-4422 8 108561547 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425741 Affx-122940747 AX-123296087 8 106880548 CACTCATTAAAATGCATTCACCTCTCTGACCCTTC[A/G]CCCAGTTCTGCTGTGTTTCACACTCTCCATGAGTC R 2 1 2 1 101000 f 74 goat snp16428-scaffold1732-38975 8 108596307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408738 Affx-122953407 AX-123279089 8 106916506 CCCATCCTCTGCCTGCTTGGTCCACCCTGCTGCGT[C/T]TCACCTTTCCATCCCCACCTGCCTCAAGGTGTATC Y 2 1 2 1 201000 f 74 goat snp16429-scaffold1732-74933 8 108632838 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404488 Affx-122956718 AX-123274840 8 106945568 AGGAGAGAAGCTTGCATATTCTGTAAGCGCCTTCA[G/T]AGACACTGCTCATAAACCTACAAAAATAGGTCCAC K 2 1 2 1 101000 r 74 goat snp16430-scaffold1732-103995 8 108661860 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411352 Affx-122952257 AX-123281702 8 106980331 TCCCTGAGCCCATTACCCACATCCCTGTTATCTAG[C/T]ATCCAGGCTCTGCTGGAATATTTCCAGGAGTGTGA Y 2 1 2 1 202000 r 74 goat snp16431-scaffold1732-138758 8 108696661 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412618 Affx-122951275 AX-123282967 8 107051052 CGTGTCGACAAGGACTATAATGTGCTATGAACGTA[G/T]CATTTATTTCTGTATTTTACAAAGCCACAGGTGTT K 2 1 2 1 101000 f 74 goat snp16433-scaffold1732-209479 8 108768921 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401368 Affx-122959239 AX-123271721 8 107079629 AACAGGACTGGTTCTGGAGTGCCCATGTCTGCACT[A/G]TGCTTTCTGTGTGTTTATTACTTCTCTGAACACCA R 2 1 2 1 101000 r 74 goat snp16434-scaffold1732-238056 8 108796647 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418657 Affx-122946325 AX-123289005 8 107124999 TGCTCCATAAACTGTTAAATAAATTGACTTGTCAA[A/G]TAGAGCAAATAGCCCCATGTGATTAAGGTAGCCTA R 2 1 2 1 101000 r 74 goat snp16435-scaffold1732-283426 8 108842126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451044 Affx-122921440 AX-123321378 8 107160601 GTTCCGCCTTATTTCCCAAGATCTCAGGAGACGCC[G/T]CCTCTGTAAATCCTTCCCTGGTCACCCCATGGAGA K 2 1 2 1 101000 f 74 goat snp16436-scaffold1732-319028 8 108876917 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442705 Affx-122927870 AX-123313042 8 107211732 ACTTCCCGTCATACTGCACCTGCCTAAATCCTACA[C/T]GTCCTTAGACACAACACCAGGAGTCTCGAAAAACA Y 2 1 2 1 101000 r 74 goat snp16437-scaffold1732-370159 8 108927684 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405354 Affx-122956321 AX-123275706 8 107241678 AGTGTTACCCCAATTGTTCCATCTGGGGTTAGCAT[C/T]CTCTAAGGTCCCAGGCTGGCCTAAATTTCTATGAA Y 2 1 2 1 102000 f 74 goat snp16438-scaffold1732-400105 8 108958035 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770623 Affx-122957992 AX-385257787 8 107277940 TTACCCACAGGGTCTGTGAATCTGTACCTTTCACT[A/G]TCCATCTGATTACCACCAACCAGGTAATTCTGATG R 2 1 2 1 101000 f 74 goat snp16439-scaffold1732-436367 8 108994345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387916 Affx-122970449 AX-123258274 8 107314529 AAGTGTTGGCTATCATTAGTAGAGATAAAGACATG[C/T]ACCTTACAAAAATAATAATAATCCAAAGTAGGAAA Y 2 1 2 1 101000 f 74 goat snp16440-scaffold1732-472956 8 109030988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442426 Affx-122927976 AX-123312763 8 107347223 TTGCACCTATTTCTGCTTCTTTTCTTCTAAGAAGA[C/T]GGTAGTACTGCTCTTCCTCACCTACTGGACTCTGG Y 2 1 2 1 101000 r 74 goat snp16441-scaffold1732-505650 8 109062911 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397911 Affx-122961942 AX-123268266 8 107379515 TCCCTTCTCAGCTTCAAAGTCTATATAGATACCAT[A/G]TCTCCAAGCAGTTGTTGGGATTTTCTGCACCTGGG R 2 1 2 1 101000 f 74 goat snp16442-scaffold1732-537942 8 109095388 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403347 Affx-122957808 AX-123273700 8 107437296 TCTCTTGGCTGGCTTGTAGGGCACCCCTAGGAAAG[C/T]GACAGGGACTGTGGTATAAGTTGCCATATTGTGAA Y 2 1 2 1 101000 r 74 goat snp16443-scaffold1732-595723 8 109152421 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396228 Affx-122963344 AX-123266583 8 107469576 GAGGTATGTGTCTTGGGAAGGCATCCTTGGTATCT[A/G]CAACAAAGCCTGGACCAAGGAAATCCCCATGCATA R 2 1 2 1 101000 f 74 goat snp16444-scaffold1732-628003 8 109184210 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377420 Affx-122977551 AX-123247779 8 107503098 AGGGTAGGTACCTTCCTGCATCCCCCACCTCCCCG[A/G]TCAAGAGGCAGCTCTGGGCTGAGCAGTCCTTGGGT R 2 1 2 1 101000 r 74 goat snp16445-scaffold1732-661525 8 109218090 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392124 Affx-122966342 AX-123262481 8 107534026 AAGAGGCTCACACAACTCACCCCGGGCACGGTCCA[A/C]GGCAAGAACTAACTCTCATCCTCGGCCGAGTCTCC M 2 1 2 1 101000 r 74 goat snp16446-scaffold1732-692453 8 109249092 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418060 Affx-122946620 AX-123288408 8 107574085 ACTTTTGTTCTATTGGTCCTCAAGGCATTGGAGGA[C/T]GCCCACCCTCGCTGGAGAGGACCATCTGATTTACT Y 2 1 2 1 102000 r 74 goat snp16447-scaffold1732-732512 8 109289931 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379651 Affx-122975942 AX-123250009 8 107621115 TCCGACAGTGTTGCTAAGATAATGCAATTAACCAA[C/T]GCTGATGAGTGAGTGCTGTCAATCAGGCCAGTATT Y 2 1 2 1 101000 f 74 goat snp16448-scaffold1732-779542 8 109336760 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418797 Affx-122946176 AX-123289145 8 107659080 GTTTCTTGAATGAATGGCTGAGCTGCTGAGTAAAC[C/T]GCAAGCTTCTCTGGGGATGGGAGGGCTTAAGGGGC Y 2 1 2 1 101000 f 74 goat snp16449-scaffold1732-817507 8 109374645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408771 Affx-122953384 AX-123279122 8 107698578 GCTTCAGCATCACTTAGAACTTGGAAATAAAGCAA[A/G]GCTCTCAGGTCCTGGCCCAAACTCACTGAATGTGA R 2 1 2 1 101000 f 74 goat snp58830-scaffold962-16356 8 109425251 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386084 Affx-122971447 AX-123256442 8 107730371 AAAGGTGGAGAAAGACAGATGGGGGCTCGTTCATT[C/T]CAGCCATCCTTTCTCCTCCACACCCAAGGCTGGGG Y 2 1 2 1 101000 f 74 goat snp58831-scaffold962-48149 8 109457167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274146 Affx-1111834069 AX-519547748 8 107753040 TCTGAAAGTTCCCCATAAAGTATCTGAAAGCAAAC[A/G]CCTA R 2 1 2 1 102000 f 74 goat GoatD01.016784 8 107753040 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38439665 Affx-122930594 AX-123310002 8 107772141 CTTGTTAGTTTTACATTTTAAAAAGGGGCCTCCAC[G/T]CTGAGTCATGAGAATTAGCTAGGCGCATACCAGAG K 2 1 2 1 201000 r 74 goat snp58832-scaffold962-89919 8 109499048 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802779 Affx-122953074 AX-385289678 8 107810735 GTCCTCAAAATAAAGTGACCCTCGCAGAGAGAACC[A/G]TGGTGAAATGGAAGCCAAAAATCATAGCTTGCCCA R 2 1 2 1 101000 r 74 goat snp58833-scaffold962-128513 8 109536654 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399967 Affx-122960830 AX-123270322 8 107842747 GGAGAAGAACGCACATTCGTATTTGTATTAACACT[A/G]TAAGGACAGAGAAGAAAACTAACAGAGGTGGGAGG R 2 1 2 1 101000 f 74 goat snp58834-scaffold962-160525 8 109568939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417434 Affx-122947210 AX-123287782 8 107871484 GTAAGCATAGAGCATGGAGACGATGCCCACAGAAC[A/G]CTGCCTCTCAGACACGAGGTCTGTACAAAGGAAAA R 2 1 2 1 101000 r 74 goat snp58835-scaffold962-189262 8 109597587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438810 Affx-122930795 AX-123309147 8 107910041 ACCTTTTTATAAGCATCCTTGAAAAAGAGTTTTTA[A/G]AGAACAATAACAACAACAAAGAAAACCTATGCTGA R 2 1 2 1 102000 f 74 goat snp58836-scaffold962-227819 8 109635009 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405595 Affx-122955930 AX-123275947 8 107943366 AATTGCATCTGTGACTCACATTATATTCATACTGG[A/C]CATCCCTGGATTAGCCTCTACAGAAGAATTTCTAA M 2 1 2 1 101000 r 74 goat snp58837-scaffold962-261144 8 109666404 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386331 Affx-122970879 AX-123256689 8 107973947 TGCGGCTCCCTTGTTCCCGATGTTTCACACTCACA[C/T]GCAACGTGGCAACAGCGCCACGCTCGCAGCTCTTC Y 2 1 2 1 101000 f 74 goat snp58838-scaffold962-291725 8 109696602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447493 Affx-122924085 AX-123317829 8 108020047 TGTAACCATCTTTACACTGGACACATTCAGGTGCC[A/G]ATTCACCCAGCTCTAAAACAGCAAGAACACCAACA R 2 1 2 1 101000 r 74 goat snp58839-scaffold962-337825 8 109743438 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383536 Affx-122972623 AX-123253894 8 108050983 TTTATTTCATGAGTAAAATTTTGTCTTCTGCCCTG[C/T]GGCATATTCCCATAATTAAAAATGCAAAGTAGTAA Y 2 1 2 1 101000 f 74 goat snp58840-scaffold962-368761 8 109774175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386943 Affx-122969989 AX-123257301 8 108101371 TCCCTTAGCTTGCTATAATTATAATACAGGGGATT[A/G]CCGACAGGTGCAGGACACACACAGTTTTCCCAGTC R 2 1 2 1 201000 f 74 goat snp58841-scaffold962-419149 8 109824995 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278654 Affx-1111836535 AX-519552133 8 108147499 AGATCAAAGGGTAATTCAAGTCGACATGCAAATCC[A/C]TCAGTTTATCTTTTTCTTTCTACGTAGTTAAAATT M 2 1 2 1 101000 f 74 goat Random2.2K-950 8 108147499 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431908 Affx-122936001 AX-123302249 8 108216230 CATGTGCACTCGTTCAGGCACACTGTATCGTGTTC[A/G]CCAGGGCCCTGCACAGGGATCAGACCATCAGAGCA R 2 1 2 1 101000 f 74 goat snp58843-scaffold962-534008 8 109940492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443475 Affx-122927819 AX-123313812 8 108246131 AGGAAGGAAAGCAGCAACCATTCATGTAACCTGTG[C/T]GGTGCCAGATGCTTTTATCATCTCACTGGATGTTA Y 2 1 2 1 201000 f 74 goat snp58844-scaffold962-563909 8 109970035 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385681 Affx-122971134 AX-123256039 8 108295902 CTGCAGCGTACAGACCTCCTTTCTCACACCTAGAT[A/C]CTTACCTTGAAGGAGCAGCCAACACCTGCAAAGGG M 2 1 2 1 101000 f 74 goat snp58845-scaffold962-613680 8 110018625 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453011 Affx-122920105 AX-123323344 8 108330423 AATAGTAATTCTCGTACTCCATGAGATTCTGGAAA[C/T]ATTAAATGGGAATAAATATGAGAACTCTTCCATAA Y 2 1 2 1 101000 f 74 goat snp58846-scaffold962-648201 8 110053093 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434474 Affx-122934633 AX-123304815 8 108360593 AAATGTAAGCAACACATCTTCTGTGCCTGCAGCAT[C/T]GCTAGCCTGCACACAAGCTGAAAATTGATGCCTGA Y 2 1 2 1 101000 f 74 goat snp58847-scaffold962-678371 8 110083315 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411525 Affx-122951667 AX-123281875 8 108394886 TGGACTGTGATGTGAAGGTATGTTTTCTGTGAAAC[A/G]CACCTTTTAAATTCCTTTCTTTGCTTTATACATTT R 2 1 2 1 101000 f 74 goat snp58848-scaffold962-712664 8 110118695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795567 Affx-122940792 AX-385282522 8 108424278 ACCTCCGGCGAGTTACTGCCTCTGTCTGGATTTAT[A/G]CTTACATTTGATATAGGTTTGATTAGATACTCTCC R 2 1 2 1 101000 f 74 goat snp58849-scaffold962-742056 8 110147702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392694 Affx-122966411 AX-123263051 8 108461434 AATTAGCATGCCATTGCCTTAATCATGATAAGCTA[C/T]GTTATCAAGTAACTACAGAAAGGCTACTGATTTTC Y 2 1 2 1 101000 f 74 goat snp58850-scaffold962-779212 8 110184864 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424531 Affx-122941723 AX-123294877 8 108538565 AGAGGAAGGTAGTGTCCACAGGTACTTCCTGTGGC[A/G]TCACCACGACACAGATCATAACGCCTGTTCGTGTC R 2 1 2 1 201000 r 74 goat snp58852-scaffold962-856343 8 110262163 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421056 Affx-122944517 AX-123291403 8 108578580 TGAAGTCCAGCATCAGTGCTCCGTTTAAGTCATGG[A/C]CTGGTGACATACCTATCAGGAGGACAGTCAGGGGG M 2 1 2 1 201000 r 74 goat snp58853-scaffold962-896358 8 110302363 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780353 Affx-122955080 AX-385267448 8 108634739 TCTCTTTAGGAACGGGCACATGTTGTCTGTGCAAC[A/C]TGTGTTTTCTATCATTACTATTCTTGAGTAGATGA M 2 1 2 1 101000 f 74 goat snp58854-scaffold962-952517 8 110358293 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421683 Affx-122944417 AX-123292030 8 108690383 CGCATGTGAGAACAGTGGGGTTTTATCATCCTCCA[G/T]ATGCCTAGGGAGAGGGAAGAGCTCTCTGAATTTAG K 2 1 2 1 101000 f 74 goat snp58855-scaffold962-1008161 8 110415062 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411554 Affx-122951643 AX-123281904 8 108727560 ATCATGTACCGATGGAGAAGTCATTGCAAAATGCC[A/G]TGAAATGCCCAAGTGCCAATGGGGCGTCTCCTGGA R 2 1 2 1 101000 f 74 goat snp7086-scaffold1263-32712 8 110452358 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772955 Affx-122946265 AX-385260099 8 108758413 TGGATTGAATATGACCCACGTCTGGAAAGACTGAT[A/G]TTCTTTATTAAATTTAGACTGACCCTGAAATATAT R 2 1 2 1 201000 r 74 goat snp7087-scaffold1263-63565 8 110483490 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381334 Affx-122974427 AX-123251692 8 108812835 CCTCATCTGTTGACACGCCTTACAAGCATGCACTA[C/T]GTTCCTTACAGTTGTCTGGTGCCGGGGAAATCACA Y 2 1 2 1 303000 r 74 goat snp7088-scaffold1263-117987 8 110539287 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412207 Affx-122950934 AX-123282557 8 108866970 ACAAGGATGAAGAGGTGCCGTAGACTCAGGCTAGG[C/T]GGTACGAAACAAACGTTGAATTAACTCACCCTGTT Y 2 1 2 1 101000 r 74 goat snp7089-scaffold1263-172122 8 110593830 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788247 Affx-122952141 AX-385275266 8 108910434 CTTAAAACACAGAGCTCCACACATCTGCCTGCTGT[A/G]GTTCTTAAATACACTAAGCCCGAAGCCCCAGGGCC R 2 1 2 1 101000 f 74 goat snp7090-scaffold1263-215586 8 110638547 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410606 Affx-122952108 AX-123280956 8 108945552 AGTGACTGCCAAGTGGGCGGGGACTGGTTGCAACA[A/G]GAGCCCACTGCCTTCATCCTGCCTCCTCTCGAGTC R 2 1 2 1 103000 r 74 goat snp7091-scaffold1263-250704 8 110673321 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796463 Affx-122972668 AX-385283413 8 108987271 TTTACTATTGACTGGAACATATCAATGGACTTTCT[A/G]CTCTCCTTGTATGTAAAATACTCAGAGTCTAGAAG R 2 1 2 1 101000 r 74 goat snp7092-scaffold1263-292423 8 110715112 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412415 Affx-122951433 AX-123282764 8 109022432 GAACACTATTTTTTTGATCAGAACATGTTTAATGG[A/G]CGGAGCTATGGAGCTGGTTGGATGTGCAACCAGCT R 2 1 2 1 101000 f 74 goat snp7093-scaffold1263-327584 8 110750894 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428271 Affx-122939403 AX-123298614 8 109075772 GTAGTACGTGGTTCCGTAACAGTTGAGATAAGTTA[C/T]AGCTCTGTGCCTCTCAATGTCCCCGCCTGGCCACC Y 2 1 2 1 101000 f 74 goat snp7094-scaffold1263-380924 8 110804867 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439200 Affx-122931039 AX-123309537 8 109149033 TCTCTTGCAAAGCTGAAGTTCCGTGTGGGTTGGCA[C/T]GAGGTATTTTCATGTTTTCTCCTCTCCTGATGTGC Y 2 1 2 1 201000 f 74 goat snp7095-scaffold1263-454185 8 110877675 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385519 Affx-122971254 AX-123255877 8 109219549 TTTTTATGATGCGATCACTGCAAATCCACATGTAG[C/T]GGTGACAGACGGCACCGCAGGATCCTGGGGACTCT Y 2 1 2 1 103000 f 74 goat snp7097-scaffold1263-524701 8 110937856 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430610 Affx-122936975 AX-123300951 8 109253130 AATGCCGTGTGGTTTTACAGTGATAAGAGAATAGA[C/T]TCTGTATGATTTCAGTACCTCTGGGTGAGTGAGTG Y 2 1 2 1 101000 f 74 goat snp7098-scaffold1263-558282 8 110970967 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397701 Affx-122962567 AX-123268056 8 109272886 CATGGGAGGAGTCTTCTAACACAGCTGCTAGATCT[C/T]AGCTGGTAGTGAGACTAGTCGGACAACCCAGACAG Y 2 1 2 1 101000 r 74 goat snp42569-scaffold565-11040 8 110987863 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802036 Affx-122923540 AX-385288940 8 109309279 GGAACACCTCCTGGTGCTATACGCAAAGTTGTCCA[A/G]TATTTTGAGTCCTTGCGTGAAAAACACAAGGGAGT R 2 1 2 1 101000 f 74 goat snp42570-scaffold565-47433 8 111024214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431407 Affx-122936535 AX-123301748 8 109392388 GAGGGGAGAGGTGAGAGAGTGAGTGGAGCAGGCGA[C/T]GGAGCTGAGCAGGCACAGGCTTCCAGTTACGAAAT Y 2 1 2 1 201000 f 74 goat snp42572-scaffold565-130542 8 111107240 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408575 Affx-122953665 AX-123278926 8 109448970 TTCATGATTCGCAAATATTCTCCCATCCCCTGAGG[C/T]GCCTTTCTACTCTGTTAATAGTGTATCTGGACGCA Y 2 1 2 1 201000 r 74 goat snp42573-scaffold565-187124 8 111160158 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382835 Affx-122973544 AX-123253193 8 109523424 GATTAAAAGCGACCTTGGCCAAGGGGGAGGGATGC[G/T]GAGTGTAGGTGGGTCCTGGGGTTTCAGGAGGGCCT K 2 1 2 1 101000 f 74 goat snp42574-scaffold565-261578 8 111235029 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431161 Affx-122936564 AX-123301502 8 109560873 ACTCATGGTGCAGCTAGATCACAGCGATCAAATGA[C/T]GGAAGAAAAGCCATGACCCACCCAGGCAGTGTATT Y 2 1 2 1 101000 f 74 goat snp42575-scaffold565-299027 8 111274163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418914 Affx-122946089 AX-123289262 8 109598106 CACTGTGTTTCTAGTTTGAATGTCCATGATAACCC[A/G]TAAGGTGCAGCTCTGTTATCTGTGCTTACTAACCC R 2 1 2 1 101000 f 74 goat snp42576-scaffold565-336260 8 111311415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387776 Affx-122969712 AX-123258134 8 109666946 AGCACTCTAACAACAGTAATCTTAGCTCAGACTAA[C/T]AAATGCACAGCACTGAATGCTGTACTTAAGGATTT Y 2 1 2 1 201000 f 74 goat snp42578-scaffold565-405100 8 111379946 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796581 Affx-122966693 AX-385283527 8 109697948 ACGTTATGAAGTCACCTTTAAGAAAAAGTAATCTC[A/G]CAGTATGCGATTTAAGGTTTTGTCTCTATACGTGG R 2 1 2 1 101000 r 74 goat snp42579-scaffold565-436102 8 111410040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784613 Affx-122969604 AX-385271661 8 109704955 TGTTTCAGTGAGCAGAAAGTGGAGCGGCATCGTGT[A/G]TCACGCACCAGCTTGTAGGGAATAAGCCCAACGTC R 2 1 2 1 102000 f 74 goat snp20626-scaffold2031-3678 8 111416924 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422414 Affx-122943372 AX-123292760 8 109777301 ACTAAAATTTCCATTTGATTTTTAAAATACTTCCC[A/G]CTTACCTCCTGAGAGCTAACATTGTGTTCAGCTGC R 2 1 2 1 101000 r 74 goat snp20628-scaffold2031-76024 8 111489744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394159 Affx-122964939 AX-123264514 8 109807662 TTCCTGGAGTGTGTGTTACTGTGTTAATGTGATTC[A/G]ATGCGTTCAGTCCTACACACCACCCTAGGCCTTTT R 2 1 2 1 101000 f 74 goat snp20629-scaffold2031-106385 8 111519141 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434420 Affx-122934672 AX-123304761 8 109838686 TCTCATCTTCAGAGGTCATGTCTGCTCTGATTCTT[A/G]CACAGCCTGTGAAGTTAGGCACTGAAAATTATTCT R 2 1 2 1 101000 f 74 goat snp20630-scaffold2031-137409 8 111549934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452410 Affx-122920596 AX-123322743 8 109873943 TTTGTTTTCAATATTTAACTCCTCAATCCACTTTG[A/C]GTTTACTTTGTAGAAGATATAAGAATCCAACTTTG M 2 1 2 1 101000 f 74 goat snp20631-scaffold2031-172666 8 111585127 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418531 Affx-122946414 AX-123288879 8 109914071 AAATCTGATTTAACTTTGAAAAGTGAAGACATTTG[A/G]GCCAGGTGCCCATCAGCACTGAACTGTATGGTCAC R 2 1 2 1 101000 r 74 goat snp20632-scaffold2031-212794 8 111613648 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273866 Affx-1111833864 AX-519547475 8 109940983 CGCTTGCATAAGGTCACACAGCCATCCTGCTGCAG[A/G]GCCGGGTTGGAATCCGGGTCTTTTTGTTCTCCTTC R 2 1 2 1 202000 r 74 goat GoatD01.008114 8 109940983 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38408355 Affx-122953741 AX-123278706 8 109955111 TGTCCCTTGGCTAAAAAAAGAAAAACGCAAGACAA[A/G]CAGCCCCAAGAGCCTGCTCCCAAGCGGAAACCGTT R 2 1 2 1 201000 r 74 goat snp20633-scaffold2031-253834 8 111654593 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445407 Affx-122925382 AX-123315744 8 109999350 CCACCTGTGTGCACCAGCGCCTCAACTCAGCACGC[A/G]TGAACATTCTTGAGGATTCTGGTCACCTGTGTGGG R 2 1 2 1 101000 r 74 goat snp20634-scaffold2031-298073 8 111698500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464626641 Affx-1110578188 AX-516097789 8 110053131 TAAATGGGAATAAATATGAGAACTCTTCCATAAGA[C/T]CTAAAGTGCTGCAGAATATCACTTAGAAATGAGCC Y 2 1 2 1 101000 r 74 goat 8_110053131_AF-PAKI 8 110053131 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387281 Affx-122970539 AX-123257639 8 110173914 TTCCACACTTACCTCTGCTTATTCACAAGGCTTCT[A/C]GGCTGAAAGCAAACTTCTCCACAATGAGTTTCAGC M 2 1 2 1 101000 f 74 goat snp17070-scaffold178-633241 8 111861143 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451432 Affx-122921171 AX-123321765 8 110209569 TAGTAGTTACTCCCAGAAATTTTACACCATTCAAC[A/G]TCCCCATGAATTAAAATAGGTTGTCTCTGAGCTGT R 2 1 2 1 101000 f 74 goat snp17069-scaffold178-597586 8 111896729 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378681 Affx-122977074 AX-123249040 8 110240229 CCTTCTTTTCAAGCAGCCACTGAGACGTGAGAGTG[C/T]TTTCCTGCTGAAGGTCCCAGCGTCTTGGAGGTGGG Y 2 1 2 1 101000 f 74 goat snp17068-scaffold178-566926 8 111929603 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431104 Affx-122936609 AX-123301445 8 110283725 GTTATTTACCCACAGACCAACCCACCTGCTCTCGA[C/T]GGCCGCCTTGTATGGATCAGACTCTTCTGGGCATT Y 2 1 2 1 201000 r 74 goat snp17067-scaffold178-523430 8 111974106 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382113 Affx-122974885 AX-123252471 8 110338672 TGACTTCAGCTGAAGGCAGACACCCTGCCCCTGTG[C/T]GGTGAGTGGTAAGTGCATTTAAGCGCTGACTAAAA Y 2 1 2 1 101000 r 74 goat snp17066-scaffold178-468483 8 112022395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772630 Affx-122974771 AX-385259778 8 110399612 ATTTATTTTTTCCTCAAATGAGGCTAGTTGAACAT[A/G]AGAAAAGGACAAGCATGTGCATTCAGGGCCCCAGG R 2 1 2 1 201000 r 74 goat snp17065-scaffold178-407543 8 112091195 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401165 Affx-122959361 AX-123271518 8 110444364 CAAGCCTTCTTAGACCAGAGCTCTGAAAGCAACCA[C/T]GTCTTTTTCCAGTTTCTGATAAATTCAATTAGGAC Y 2 1 2 1 101000 f 74 goat snp17064-scaffold178-362791 8 112136368 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278655 Affx-1111836536 AX-519552134 8 110486436 TAGTCTTTCTTTAAAGCCAGTGCGTCCACTCTGTA[A/G]TGAAATAATGCGTGGGTTACAAAGACATGCGTGAT R 2 1 2 1 101000 f 74 goat Random2.2K-951 8 110486436 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444432 Affx-122926563 AX-123314769 8 110491841 GGCATAATGCAATATATTTTTCCATTCTCCTATAA[C/T]GGTCCCTGACATTTCCAGTGTTTCTCTTTTACAAA Y 2 1 2 1 101000 r 74 goat snp17063-scaffold178-315314 8 112182940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443281 Affx-122927477 AX-123313618 8 110528589 GGATGATAGACCCAGGAACAGAATGGACAGGGAAG[C/T]CCACGGCAGCGGGACGCTCAGCTAAGGGCAGTGGA Y 2 1 2 1 101000 f 74 goat snp17062-scaffold178-278566 8 112219657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376552 Affx-122977983 AX-123246911 8 110570883 AAAGTGGTAATCCATCTTTCAGGATTTAAATGTCT[A/G]TTAAAAGCTATGCTTGCATCTCTAGCTTCTGGCTT R 2 1 2 1 103000 r 74 goat snp17061-scaffold178-236272 8 112261823 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412793 Affx-122950493 AX-123283142 8 110632866 CACAGAAAGACAAATAGCATATGGTATCACTTACG[C/T]GTGGAATCTGAAACAAAGGGCTCAGTGGTCCTCCC Y 2 1 2 1 201000 r 74 goat snp17060-scaffold178-174289 8 112325708 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447349 Affx-122924878 AX-123317685 8 110667348 GCCAAGAGTCACTCCTTGGAAAAGTACTCCTTTCC[A/G]TAGTATATTTGCTTAACGAAATGGAGAATCTTCTC R 2 1 2 1 101000 r 74 goat snp17059-scaffold178-139807 8 112359893 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424591 Affx-122942208 AX-123294937 8 110707378 TTGCTCCATGCCATCATCAGAGAGAGCCGGGCCTG[C/T]GAGGGCTGATACTGCGAGCCATCATCAGAGAGAGC Y 2 1 2 1 201000 r 74 goat snp17058-scaffold178-99777 8 112400572 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798729 Affx-122937127 AX-385285660 8 110755950 CAAACATGTCGCATGTTTATAAGTATGGATGGCAG[C/T]GTGGAAACTGTAATTGAGTACTAGTGCTTAAATCA Y 2 1 2 1 101000 f 74 goat snp17057-scaffold178-51205 8 112449716 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796701 Affx-122953711 AX-385283646 8 110800231 TTTTAGTCAAAACTTGGAAGCACAGTTTTGGGAAC[G/T]ATTAGCTAGATGCCAGGTTAAAGAGGAAGTTCCTT K 2 1 2 1 101000 f 74 goat snp17056-scaffold178-6924 8 112493744 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441689 Affx-122929171 AX-123312026 8 110830411 TATTTAAAAAGTGATCCTTTTCCTTTAACTCAGGC[G/T]TACATGTAAATATTTGCTGTTTTCTTTCATGTTAG K 2 1 2 1 101000 f 74 goat snp16242-scaffold1709-23157 8 112527820 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275158 Affx-1111834734 AX-519548737 8 110863639 TGGACCCAAGTGGGCTGTCTGGCTGTCCGCTGCCC[A/C]CCCCCCCAGCCCCGGGTCTGCAGCAGCTGCCTGGC M 2 1 2 1 102000 f 74 goat GoatD01.050475 8 110863639 A C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320798564 Affx-122926771 AX-385285497 8 110864528 TAGGCCATAATATCTACCTTAATGCCAAAGCATAA[C/T]GGGCCACACTTTATCATCTCTCTTGTATCTGGCTC Y 2 1 2 1 101000 r 74 goat snp16243-scaffold1709-57274 8 112562053 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770081 Affx-122954577 AX-385257248 8 110894399 GCAAAGCAGGCATCAGGCAAAGTTCAGAGCAAATC[A/G]AATGGAAGTTAGTAGGGAAAGATTTGCATATAGTG R 2 1 2 1 101000 f 74 goat snp16244-scaffold1709-87145 8 112591777 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419319 Affx-122945661 AX-123289667 8 110976021 CACACACTCAGAAATTGTTAAGGTAAATAAAGATG[C/T]GCAGAGGCATGGTGGACCATGGCGGATGTATTCCC Y 2 1 2 1 101000 f 74 goat snp16245-scaffold1709-168767 NW_017189611.1 2655 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800668 Affx-122952921 AX-385287586 8 111015725 CTGTTAAACTGATACAGTCTGTGTTGTTAAATACC[A/G]CTTACCTCATCCTGAAAGCAGCAGTGATCAAGCAA R 2 1 2 1 101000 r 74 goat snp16246-scaffold1709-208471 NW_017189611.1 43859 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278837 Affx-1111836537 AX-519552308 8 111710216 TGGGGCTGCACGCTGGTCGTCGGCATACATGTGGC[A/G]GCTAACGCTCCTGAACTAGAAGAGTGAGGCACCAG R 2 1 2 1 101000 r 74 goat Random2.2K-953 8 111710216 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 539476253 Affx-1251763759 AX-586011674 8 112060360 TAATACTCAGCAGCTGATTTTCAAGATACTGTCAG[-/TAAACACTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]AAACACCATAAAATTGTATTAAATATTCATATAAT - 8 1 4 1 20000 f 74 goat SV_371 8 112060360 - deletion junction SV-TF-chip 539476505 Affx-1251763759 AX-586011899 8 112060360 TAATACTCAGCAGCTGATTTTCAAGATACTGTCAG[-/TAAACACTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]AAACACCATAAAATTGTATTAAATATTCATATAAT - 4 1 4 1 20000 r 74 goat SV_371 8 112060360 - deletion junction SV-TF-chip 562165099 Affx-1251763759 AX-606940511 8 112060360 TAATACTCAGCAGCTGATTTTCAAGATACTGTCAG[-/TAAACACTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]AAACACCATAAAATTGTATTAAATATTCATATAAT - 8 1 4 1 20100 f 74 goat SV_371 8 112060360 - deletion junction SV-TF-chip 562165224 Affx-1251763759 AX-606940636 8 112060360 TAATACTCAGCAGCTGATTTTCAAGATACTGTCAG[-/TAAACACTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]AAACACCATAAAATTGTATTAAATATTCATATAAT - 8 1 4 1 20100 f 74 goat SV_371 8 112060360 - deletion junction SV-TF-chip 562165822 Affx-1251763759 AX-606941231 8 112060360 TAATACTCAGCAGCTGATTTTCAAGATACTGTCAG[-/TAAACACTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]AAACACCATAAAATTGTATTAAATATTCATATAAT - 8 1 4 1 20100 r 74 goat SV_371 8 112060360 - deletion junction SV-TF-chip 562166499 Affx-1251763759 AX-606941907 8 112060360 TAATACTCAGCAGCTGATTTTCAAGATACTGTCAG[-/TAAACACTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]AAACACCATAAAATTGTATTAAATATTCATATAAT - 8 1 4 1 20100 r 74 goat SV_371 8 112060360 - deletion junction SV-TF-chip 562166527 Affx-1251763759 AX-606941935 8 112060360 TAATACTCAGCAGCTGATTTTCAAGATACTGTCAG[-/TAAACACTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]AAACACCATAAAATTGTATTAAATATTCATATAAT - 8 1 4 1 20100 f 74 goat SV_371 8 112060360 - deletion junction SV-TF-chip 468273331 Affx-1111833565 AX-519546971 8 112622718 TCAGTTGTGTCCGACTCTTTGCACCTGATGACTGT[A/G]GCCTGCCGGGCTCCTCTGTGCATGGGATTCTCCAG R 2 1 2 1 103000 f 74 goat 8_112622718_AF-PAKI 8 112622718 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38397386 Affx-122962269 AX-123267741 8 CTGCCGGAATCCTTACCGAAAGCCTGTGTTTATTC[A/G]TCAGAGGGAGGAAGAATGGATTGATAATTTTCTTA R 2 1 2 1 101000 f 74 goat snp19060-scaffold1917-20193 4 24516134 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762668 Affx-986697198 AX-385250748 9 53945 TTCACCCATCTCTTGCAGTTCCCTGAGAACAGGTG[C/T]TTCCCTCCTGGGTTAGATGGACTCCTAGGTATTTC Y 2 1 2 1 600010 f 74 goat 9_53945 9 53945 Ancestral_priority_1043 ancestry 0.554 neutral IMAGE 10K 10K ancestral 320803685 Affx-986696177 AX-385290459 9 53950 CCATCTCTTGCAGTTCCCTGAGAACAGGTGCTTCC[C/T]TCCTGGGTTAGATGGACTCCTAGGTATTTCCTTTC Y 2 1 2 1 600010 r 74 goat 9_53950 9 53950 Ancestral_priority_1043 ancestry 0.606 recommended IMAGE 10K 10K ancestral 38421681 Affx-122944418 AX-123292028 9 54124 AACCCTTTGTTATGCTCGTCCCAGCTTCCTACTTC[A/G]TCATGAGTGGAGCAAATACATTCTCAGTATTTGCT R 2 1 2 1 103000 f 74 goat snp15124-scaffold1614-514416 9 20691 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783116 Affx-122978727 AX-385270183 9 135861 CAATAATACACATACGGTACAAAACTCAGAGTATG[A/G]AAATGTTACCCTCTCTCTGTACTCAGGAAGCATTC R 2 1 2 1 201000 f 74 goat snp15123-scaffold1614-432679 9 105598 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796741 Affx-122962724 AX-385283685 9 165578 TGCGGGAAACGTCTTCCTGCAATGTTCCTCCAGCA[A/G]TTTCTACTGAAAAAAGTTACCATAGTGCGCACTTT R 2 1 2 1 101000 f 74 goat snp15122-scaffold1614-402962 9 135237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273445 Affx-1111833604 AX-519547069 9 190627 ATTTCGTTGTATAACTTCTGTACATTTTTTTTACT[A/G]TGTACCTATTTCAACATGTTTGCAAATAAAATGAT R 2 1 2 1 101000 r 74 goat 9_190627_AF-PAKI 9 190627 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320784539 Affx-122931181 AX-385271588 9 218266 GCCCTTATTGCTAAACTAAAAAGGTCTCATCCAGT[C/T]TCACCTTAGATTTATGCCTAAAATGTAGTTAGAAT Y 2 1 2 1 101000 f 74 goat snp15121-scaffold1614-350274 9 187461 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437032 Affx-122933114 AX-123307370 9 260597 GGAACCCACAGGCCCTGGGACTGGCCCAAAGCTGG[A/G]CAAGCAAGAGCCTTTTGCCAAGAAACAGCTCAGGA R 2 1 2 1 101000 r 74 goat snp15120-scaffold1614-307943 9 229715 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393229 Affx-122965484 AX-123263586 9 305603 AATAATTAAAGCATGAAGTTGTTTTTAAATTTAAA[C/T]GTTTAACTATCATCACCTCTGTAAAAACATTACAT Y 2 1 2 1 103000 r 74 goat snp15119-scaffold1614-262937 9 275929 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426348 Affx-122940263 AX-123296694 9 374394 TCAACAGCACTGTGGTTTCACACACTAGTTAAAAA[A/C]ACAAATTTGAACCTTAATCTTCTAATCTGCCTGAG M 2 1 2 1 101000 f 74 goat snp15118-scaffold1614-194146 9 345100 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768664 Affx-122919880 AX-385255842 9 426341 AAACAGGGAAGAAACCAGTCATAATTTGAATATGA[C/T]GATGTAACATAAAACTCATTAAGACTCTCCTAATA Y 2 1 2 1 201000 r 74 goat snp15117-scaffold1614-142199 9 396935 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390172 Affx-122967970 AX-123260529 9 479875 TTCAATTGCTTGTTGCCAATAACCACCAATTCAAA[C/T]GGTGATCCCACCTAGAAAAAAAATTTTAATTAATA Y 2 1 2 1 102000 f 74 goat snp15116-scaffold1614-88665 9 450460 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442318 Affx-122928235 AX-123312655 9 530048 CCTTAGGAGGACCTGCAGGTTCAGTATCACATCAG[C/T]GACATCCAGCCCACCAAGAGTCCAAGGTCAATCAG Y 2 1 2 1 101000 f 74 goat snp15115-scaffold1614-38492 9 500731 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401895 Affx-122958842 AX-123272248 9 564278 ATCACAAACTGATCCTTGCTTACTGCGCTTTTCCA[A/G]GTCGCCTCCTATAACTGCCCCCATCCTCAACATCC R 2 1 2 1 101000 f 74 goat snp15114-scaffold1614-4262 9 535408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379488 Affx-122976473 AX-123249846 9 579338 TTCTGTAATATGCAAGTCATTGTCCATTAGCATAC[C/T]GACCATTATACAGTTTTCAAATGAGTTCAATTTTT Y 2 1 2 1 101000 f 74 goat snp6772-scaffold1246-9473 9 550847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375657 Affx-122978683 AX-123246016 9 612195 CTGCTGTCTATCCATTCTAATTTGTGATTGTAGAC[A/G]TAGGAATACTCTTCATCTCCTTCTCTCCTCATTTA R 2 1 2 1 201000 f 74 goat snp6773-scaffold1246-42330 9 583745 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769973 Affx-122970217 AX-180660644 9 656308 TTTAGAAAGTCTGACTCACTTGCATATGCTCTGAA[A/C]GTATTATGTGCAGGAGGTCAGTCACCACAGAGCTT M 2 1 2 1 101000 f 74 goat snp6774-scaffold1246-86443 9 629262 C A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799141 Affx-122957629 AX-385286071 9 698823 TTCCAGAGATTTTAAAAGCGATTGCAAAACATTCC[A/G]TGAAATATACCGGCCAGATATTTTTCCACTACCAC R 2 1 2 1 101000 r 74 goat snp6775-scaffold1246-128958 9 673125 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443706 Affx-122927157 AX-123314043 9 739404 ATGACGCTGGCTGTGGTTGGTATTCAGCATACAGA[C/T]CTAAAAGAGAGATCTCAAACTATCACACACAAAAA Y 2 1 2 1 101000 f 74 goat snp6776-scaffold1246-169539 9 715278 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787520 Affx-122933943 AX-385274544 9 780464 ACAGGGCTCCATCAGCTGGGATAATCCAGAAGACA[C/T]GAACAAACCTCACTAGGAATCACCAGTGCCTGGGG Y 2 1 2 1 101000 f 74 goat snp17475-scaffold1807-205584 9 757148 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451787 Affx-122921500 AX-123322120 9 820352 AGTTAGAAATTCCCAACAAAGACTTAGAAAATCCA[C/T]GAAAAACCCAAACAGAGACTAACAGTACAATAACT Y 2 1 2 1 101000 f 74 goat snp17474-scaffold1807-165696 9 797447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434340 Affx-122934729 AX-123304681 9 853644 AAGTTGATAAATTTTTTGTTCATTTGTTTATATCT[C/T]GCCTTGCTCCAAAAAGGATTCATGGCCACTTATCA Y 2 1 2 1 103000 r 74 goat snp17473-scaffold1807-132404 9 830336 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771362 Affx-122950448 AX-385258520 9 886389 AGGCTTCCATGAAAAATCATGGTAATCCCATGAGT[C/T]ATATTGCCCAGCAGATTACCTAAAAAGATTGCCAC Y 2 1 2 1 101000 f 74 goat snp17472-scaffold1807-99659 9 863011 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425016 Affx-122941884 AX-123295362 9 917838 AATGACCCCACAATGAAATAGCAACATTCTTGGTC[C/T]TCTGAATCCCATGAATTTTAGTTTCTCATTCCCAG Y 2 1 2 1 201000 r 74 goat snp17471-scaffold1807-68210 9 895198 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782567 Affx-122963739 AX-385269641 9 954107 AAAATAATCTAGTCCTGCCAGACTCTAAAATTCTC[A/G]TTATTCTCATTATTAATTACCATACACACATAATA R 2 1 2 1 101000 f 74 goat snp17470-scaffold1807-31941 9 932183 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393372 Affx-122965915 AX-123263728 9 1055373 AATCATTTCCCCAAACCAGGCACTTTTCTGCATAG[G/T]CATTCATGTTTCTTTGTTCAGTTCTACAGAATATA K 2 1 2 1 201000 r 74 goat snp39619-scaffold504-1697389 9 1032617 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383581 Affx-122972588 AX-123253939 9 1084814 CTACAGTCCATAGGATGGCAAAGAGTTGGACTGAG[A/C]ACCAACAGGATCTCCTTTAACACTAAACCTTGTCA M 2 1 2 1 101000 r 74 goat snp39618-scaffold504-1667948 9 1062000 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419599 Affx-122945996 AX-123289947 9 1198981 AGAGACCATCTGGAATTTGTGATCATTAATTTAAC[A/G]CGAGGACATTAAGAAGAGGCTTCCCCCCCTACCCC R 2 1 2 1 101000 f 74 goat snp39616-scaffold504-1553781 9 1177105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383613 Affx-122972555 AX-123253971 9 1244955 ACAAATCTAAGTTTAGAGCTCAAATACAATCTTTA[C/T]AGTTCAAATTTTTGTAAAAGTTTTTGTAACACCAA Y 2 1 2 1 101000 f 74 goat snp39615-scaffold504-1507807 9 1222977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781267 Affx-122961035 AX-385268352 9 1276779 CCTTCATGTCTACTCAAGATGGGAAGCAGATCAAA[C/T]TTTGAAATTCAAAAAGGTGGATAGGGACATGGAAC Y 2 1 2 1 202000 r 74 goat snp39614-scaffold504-1475983 9 1255588 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414772 Affx-122949242 AX-123285121 9 1333988 ATTAAAAAGTCAACCCTTGCCCACCTGGGTCCTAC[G/T]CATCTCCGTGCCTGCTCTGTCTTCCTCCAGATCAC K 2 1 2 1 101000 f 74 goat snp39613-scaffold504-1418774 9 1313416 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418382 Affx-122946564 AX-123288730 9 1385667 ATTCATATGGGGACATTTTCCATAATTGAATGAAG[C/T]ATATCTGCATTTCCAATGCTTCTTATTAAACATAT Y 2 1 2 1 101000 f 74 goat snp39612-scaffold504-1367095 9 1365385 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774063 Affx-122951051 AX-385261201 9 1434148 CTCAACAGACCACATAGCAGAATAGAACTCAAAGG[C/T]AGAATTAATGAAGATATAGGAAATTTATTATAAGG Y 2 1 2 1 101000 f 74 goat snp39611-scaffold504-1318614 9 1412632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784618 Affx-122940473 AX-385271666 9 1492158 ACATACTTGATAGTAACTTTGAATTCTTCTGTAGG[A/C]CATAAGGCTGCCATTGAGGTGGAAGATGGTAACTT M 2 1 2 1 101000 r 74 goat snp39610-scaffold504-1260604 9 1468180 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780447 Affx-122925640 AX-385267538 9 1528842 AGGGCCATACAATCTGAAAAGAGCCCTGAATTCCC[A/G]GTTTCTCACTTAGGAGCTAAGGATTTGAACCCCAT R 2 1 2 1 101000 r 74 goat snp39609-scaffold504-1223920 9 1502682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410840 Affx-122952622 AX-123281190 9 1568803 TTGTTTTTCACTTAAGGAAACACAGAATACCAGAT[A/G]CAAATATTTTGGAAGTAAAGTGTGCCCGTGAACAA R 2 1 2 1 101000 f 74 goat snp39608-scaffold504-1183959 9 1542457 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801668 Affx-122942838 AX-385288576 9 1600822 CTTCCAAGGAAAGGTCTTCTGAGTCCTATCCAAGG[A/G]TAGGATGGCTAACTACCCAAGCAGAAGTTTGGCAT R 2 1 2 1 101000 f 74 goat snp39607-scaffold504-1151940 9 1575153 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780366 Affx-122945894 AX-385267461 9 1658219 AGGTAAGCAAGCATGCTGGATTAATACTCTTTGTT[A/G]CACAAAACTCTTACAGACATGACAGAAAGTGGCAA R 2 1 2 1 101000 r 74 goat snp39606-scaffold504-1094543 9 1632491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778311 Affx-122965165 AX-385265426 9 1697466 GTGTCTTACGGTTTTCAGTGTTATTCTGAGCTTCA[C/T]TGAGATGTTCTGCTGCTACTTCACCTTTCACATGT Y 2 1 2 1 101000 f 74 goat snp39605-scaffold504-1055296 9 1672047 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394603 Affx-122964422 AX-123264958 9 1741615 ATTTACAAAGATTTAATTGAATTCAGCATCTTCAG[C/T]GTACACAGAGTTTTAGAAGTTCTTTAATGAGTATG Y 2 1 2 1 101000 f 74 goat snp39604-scaffold504-1011147 9 1717152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400864 Affx-122959771 AX-123271218 9 1777987 GTCATAGGAATAGAAAAGACCTTCTCATGCTTTTA[A/C]AGACAGAGGTCCAGGCTATAGAATTTAATACCACT M 2 1 2 1 101000 f 74 goat snp39603-scaffold504-974775 9 1753963 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789193 Affx-122954403 AX-385276204 9 1850443 TTTAGTTCACAACAAAGGAGCATTTCTTAGAAAGT[A/G]TGAAAGTGAGATCATTTGGAACACAGCTCTAACAG R 2 1 2 1 101000 r 74 goat snp39601-scaffold504-902319 9 1825997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793463 Affx-122956772 AX-385280440 9 1888647 ATTTTGCTAATTTGTTAGAAAATAGACCTTGCTGT[C/T]TTTCATCATGTCCATTCATAAGTCATTTGAGACCG Y 2 1 2 1 101000 f 74 goat snp39600-scaffold504-864115 9 1864861 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445338 Affx-122926394 AX-123315675 9 1927488 GCTGGCCATCAGTCTGCTGGGTTCTGTTAACTGGG[C/T]GACATTGCTAAGACTTTTTTTCCACTTCATTCAGC Y 2 1 2 1 101000 r 74 goat snp39599-scaffold504-825274 9 1903664 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784138 Affx-122977525 AX-385271190 9 1959931 AATTCCTTTATTTTAAAGAGTTAATTATAAAGCAG[A/G]AAAACAATTGAAATCCTTGAAGCATTTCAAAGTAT R 2 1 2 1 201000 f 74 goat snp39598-scaffold504-792831 9 1936120 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431877 Affx-122936060 AX-123302218 9 2006936 TAGGTGTATAAAATGTATTATCAAGTGGAGCCTTC[A/G]TCTGGCTACACTTCTTTCTGCACAGGAGCTCCAAC R 2 1 2 1 201000 f 74 goat snp39597-scaffold504-745826 9 1983574 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794499 Affx-122974513 AX-385281462 9 2117715 TGTGTACAGTACTTTTCACGTTGAACTCACAGATG[A/C]TTTTACTTACAGGGGCGTATTACCGGTAAAAGGTA M 2 1 2 1 102000 f 74 goat snp39595-scaffold504-635047 9 2109748 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450002 Affx-122922859 AX-123320337 9 2180748 TATGAAAATAGATTTACCCAAGAGACAGACGAATC[A/G]TATCTTAATAAAAGGCTTTGCCACAGGATATGTTT R 2 1 2 1 101000 r 74 goat snp39594-scaffold504-572014 9 2173003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421084 Affx-122944232 AX-123291431 9 2240408 CACCTGCTCCCCTCCTCAGGCTCATCTCTCGTTGC[A/G]TCTCCTGTCTGTGGTTCTGCCCTAAAGACTTGTCT R 2 1 2 1 101000 r 74 goat snp39592-scaffold504-512354 9 2231909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798493 Affx-122934096 AX-385285426 9 2270344 GTGGAAAGAATGTGGTCTTAGAAGAACAAGGTATT[A/G]CATAAGTAGAAATTGAAGAAAAAAGTCTGCTGAAA R 2 1 2 1 201000 r 74 goat snp39591-scaffold504-482418 9 2261751 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414109 Affx-122949736 AX-123284458 9 2311259 AAGCTTCTCAATTGGCTCTGTGCTTTAAGAATAAT[A/G]GATGTAGTTTTTCTCTTTGTCCTATGAAGGCTTTG R 2 1 2 1 101000 f 74 goat snp39590-scaffold504-441503 9 2302584 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412696 Affx-122950756 AX-123283045 9 2357673 AGCAAATAAAAATATCTGAAGGCATTCTTCATTTT[A/G]GAGTTCTGGGTAGAAGTGACCACTCTTGGAGACTT R 2 1 2 1 101000 r 74 goat snp39589-scaffold504-395089 9 2351835 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775572 Affx-122958716 AX-385262703 9 2394396 ATTTAGGGGTGATGTAAATTAAGATTTACTTGCTC[A/G]TTAAATCATTTGGTCATTCACACATTATTTAATCC R 2 1 2 1 101000 f 74 goat snp39588-scaffold504-358366 9 2388136 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398079 Affx-122961729 AX-123268434 9 2447192 TTTGCCTAAGCCTACATAAATAAATATACTCACTT[C/T]ATCCTCACAATTTTAGGCCGATCATGTATTTTGCT Y 2 1 2 1 101000 r 74 goat snp39587-scaffold504-305570 9 2441332 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405474 Affx-122956025 AX-123275826 9 2476473 AATTAAGAAGAGGGGAAATACACACAAATTAACCT[A/C]AAAAACAAAAAGAAACTCATAGAATACCTTTTTAG M 2 1 2 1 101000 f 74 goat snp39586-scaffold504-276289 9 2469901 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425343 Affx-122941591 AX-123295689 9 2555145 ATGCTTTCTCTTCTGTTAATCCTGTCATTGTCGTC[A/G]TCGTCATCATCATCATCACTGGACAAAATGACTAT R 2 1 2 1 101000 f 74 goat snp39585-scaffold504-197617 9 2548353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788568 Affx-122954847 AX-385275585 9 2584252 ATATTAGTAGTTATGGGTAAGCTCTTCAACTTGGC[A/G]CACTTTTCCTTCATGTTTGGTTATATTCATAAGAT R 2 1 2 1 101000 f 74 goat snp39584-scaffold504-168510 9 2577379 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454295 Affx-122919265 AX-123324628 9 2620118 GAAACTGTGATAAAAGGTGGAACATATTAGTATTT[A/G]TCAGGAGTCGACTGGTAATAGGGCTGTGACTCAGG R 2 1 2 1 101000 f 74 goat snp39583-scaffold504-132644 9 2613307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432908 Affx-122935321 AX-123303249 9 2650311 CACGTGCTAACATGTTTGGAACTAAGATCTATTTA[C/T]AATCAATGGTGTGTCATGATTTAATTGGCAGTGTT Y 2 1 2 1 101000 f 74 goat snp39582-scaffold504-102451 9 2642865 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273452 Affx-1111833607 AX-519547076 9 2696066 TGCACACTTTGTTTGTTTGAAGTGATAGGTGGCAT[A/G]TTCACACGCCTTGTGTTATTACCTTGGGGTAGGAC R 2 1 2 1 101000 r 74 goat 9_2696066_AF-PAKI 9 2696066 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320803052 Affx-122939902 AX-385289925 9 2706442 ACAAACCTTGTTAATATATTAAATCTCTGGAGTAA[C/T]AGAATGCCTTATCACCAAAACTCGTATGACTGCAG Y 2 1 2 1 101000 r 74 goat snp39581-scaffold504-46320 9 2698825 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398152 Affx-122961678 AX-123268507 9 2738327 GAGATCCTACCCAGAATCACCCTGGTGGAAGCTGA[C/T]TTCTCCTGGGCTCAAGAGTGAGTAGAAGGCAGGAA Y 2 1 2 1 101000 f 74 goat snp39580-scaffold504-14435 9 2731376 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798980 Affx-122956984 AX-385285910 9 2770645 AAGAAATTAAATGGTCCTGTCTGTCCTGTTGAGAA[C/T]GTCGATGTGATCATCCTTTGAAAGCTGTGTTACTG Y 2 1 2 1 101000 f 74 goat snp32021-scaffold36-17784 9 2763851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450267 Affx-122922180 AX-123320602 9 2806448 CTACAAAAGTACGTGAAGAAACAAAATAAATATGC[A/G]ATTTTGGGGGGTGTTTCATAATCAGAGTTATATGC R 2 1 2 1 103000 r 74 goat snp32022-scaffold36-53587 9 2799560 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438121 Affx-122931491 AX-123308459 9 2839750 GTGTAGATGAGCAATGAATTGCAGCAATGCCCCTC[C/T]AACATTTGTTTCTCTAGCCTCGGGTGGGAGCTGGG Y 2 1 2 1 201000 r 74 goat snp32023-scaffold36-86889 9 2833936 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398213 Affx-122962220 AX-123268568 9 2893140 CACTACTCTCTCATTTTCTCTGCTCCATCCCCTCA[C/T]GTGGGACTTTATTTGTAGGCCAGCTTCCACCAAAT Y 2 1 2 1 101000 r 74 goat snp32024-scaffold36-140279 9 2887502 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388436 Affx-122969266 AX-123258794 9 2967374 AGTGATTCTCGACTTTATCCCTCATTTCTATTCTC[A/G]CTGCAGCTGCCCTAGAATAGCATCTATTAGCTCTC R 2 1 2 1 101000 f 74 goat snp32025-scaffold36-214513 9 2962816 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797407 Affx-122950954 AX-385284346 9 3000526 TGGGAAATTTCCAGTTCATTATTAGTTTTCTAGGT[A/G]TAGATGGTATAGGAAGAGGTTCTGTTAAGGAAAAT R 2 1 2 1 101000 r 74 goat snp32026-scaffold36-247665 9 2996519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775490 Affx-122958401 AX-385262621 9 3035268 ATCATATTGGTAACTTTGACAGATTGTCAGGAATT[A/G]TGAACTTTGAATTTCTCTCTGGGCTAGGATTTCTC R 2 1 2 1 101000 r 74 goat snp32027-scaffold36-282407 9 3031442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792480 Affx-122921608 AX-385279461 9 3089646 ACCTGCTCCCATATTTCTGACCTTTAGAAACTCTG[C/T]GCTTAGTATGTTAAGTTGATATCTTATAGGGTAAT Y 2 1 2 1 101000 f 74 goat snp32028-scaffold36-336785 9 3086314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776358 Affx-122940392 AX-385263485 9 3118287 CTGCATTTCAAAGGCTCAATGCCATATGTGGGTAA[C/T]GGCTACCCCATTAGACAGTGAAGCTCTAGAACTTC Y 2 1 2 1 101000 r 74 goat snp32029-scaffold36-365426 9 3115401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394447 Affx-122964589 AX-123264802 9 3183496 AAGGTATATTTCTGAATATAATGCATAATGGGCTA[G/T]AGGACACATTTTGAAAGATGGATTTCGGGGACTTC K 2 1 2 1 201000 f 74 goat snp32031-scaffold36-430635 9 3176598 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278659 Affx-1111836538 AX-519552137 9 3196746 AGGGTTAAGAAGGTAACCCATGATTTCTTTGCCAG[A/G]ATATCCTTACTGGGGAGCCTTAGGAGGCAGAGGGC R 2 1 2 1 101000 f 74 goat Random2.2K-957 9 3196746 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793569 Affx-122934433 AX-385280544 9 3217844 GTTCTCATTCTGTTACACTAAGGAAAAATAGTTGC[G/T]ATTCCAACAGAGATGAGCATCAGAGCTTCATAAAA K 2 1 2 1 101000 r 74 goat snp32032-scaffold36-464983 9 3211275 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404205 Affx-122957669 AX-123274557 9 3257621 CACTTTAAGAGCGCTGGGAACAATCAACTGCAAAT[A/G]CTTTAATCTGGGAAAGGACTCGCCTTGTTCCCTAA R 2 1 2 1 101000 f 74 goat snp32033-scaffold36-504760 9 3250773 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476254 Affx-1251763761 AX-586011675 9 3289806 ATATCAAAATGTTATCAAAATGGGTGAAGACATCT[-/TCAAACATTAGTTTTTTTTTTTTTTTTAAAATCTTTAATTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCCTATACTTC]CAAACATTAGTTTTTATCATGACCAAAGCTTGCAA - 4 1 4 1 20000 f 74 goat SV_127 9 3289806 - deletion junction SV-TF-chip 539476507 Affx-1251763761 AX-586011901 9 3289806 ATATCAAAATGTTATCAAAATGGGTGAAGACATCT[-/TCAAACATTAGTTTTTTTTTTTTTTTTAAAATCTTTAATTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCCTATACTTC]CAAACATTAGTTTTTATCATGACCAAAGCTTGCAA - 4 1 4 1 20000 r 74 goat SV_127 9 3289806 - deletion junction SV-TF-chip 562165062 Affx-1251763761 AX-606940474 9 3289806 ATATCAAAATGTTATCAAAATGGGTGAAGACATCT[-/TCAAACATTAGTTTTTTTTTTTTTTTTAAAATCTTTAATTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCCTATACTTC]CAAACATTAGTTTTTATCATGACCAAAGCTTGCAA - 8 1 4 1 20100 r 74 goat SV_127 9 3289806 - deletion junction SV-TF-chip 562165257 Affx-1251763761 AX-606940669 9 3289806 ATATCAAAATGTTATCAAAATGGGTGAAGACATCT[-/TCAAACATTAGTTTTTTTTTTTTTTTTAAAATCTTTAATTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCCTATACTTC]CAAACATTAGTTTTTATCATGACCAAAGCTTGCAA - 8 1 4 1 20100 f 74 goat SV_127 9 3289806 - deletion junction SV-TF-chip 562165313 Affx-1251763761 AX-606940724 9 3289806 ATATCAAAATGTTATCAAAATGGGTGAAGACATCT[-/TCAAACATTAGTTTTTTTTTTTTTTTTAAAATCTTTAATTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCCTATACTTC]CAAACATTAGTTTTTATCATGACCAAAGCTTGCAA - 8 1 4 1 20100 f 74 goat SV_127 9 3289806 - deletion junction SV-TF-chip 562165654 Affx-1251763761 AX-606941063 9 3289806 ATATCAAAATGTTATCAAAATGGGTGAAGACATCT[-/TCAAACATTAGTTTTTTTTTTTTTTTTAAAATCTTTAATTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCCTATACTTC]CAAACATTAGTTTTTATCATGACCAAAGCTTGCAA - 8 1 4 1 20100 r 74 goat SV_127 9 3289806 - deletion junction SV-TF-chip 562165793 Affx-1251763761 AX-606941202 9 3289806 ATATCAAAATGTTATCAAAATGGGTGAAGACATCT[-/TCAAACATTAGTTTTTTTTTTTTTTTTAAAATCTTTAATTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCCTATACTTC]CAAACATTAGTTTTTATCATGACCAAAGCTTGCAA - 8 1 4 1 20100 r 74 goat SV_127 9 3289806 - deletion junction SV-TF-chip 562165983 Affx-1251763761 AX-606941392 9 3289806 ATATCAAAATGTTATCAAAATGGGTGAAGACATCT[-/TCAAACATTAGTTTTTTTTTTTTTTTTAAAATCTTTAATTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCCTATACTTC]CAAACATTAGTTTTTATCATGACCAAAGCTTGCAA - 8 1 4 1 20100 f 74 goat SV_127 9 3289806 - deletion junction SV-TF-chip 38376982 Affx-122977746 AX-123247341 9 3298549 ATAACTATTTCTAGCTCTCTAGACAAATATGCATC[A/G]CAGAATTTTAGAGTTACATAATGAAAACTTCTAGA R 2 1 2 1 101000 f 74 goat snp32034-scaffold36-545688 9 3287082 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421745 Affx-122944372 AX-123292092 9 3328701 TTTCTACTCTAAAGACTCATGCGTGTGTGCAAGTC[A/G]CTTCAGTCGTGTCTGACTCTTTGTGACTCTATGGA R 2 1 2 1 103000 f 74 goat snp32035-scaffold36-575840 9 3325311 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770447 Affx-122923860 AX-385257613 9 3358257 GAACTTGACGATTTTACTCTCAATTTGACTATTTC[A/G]TTAGCAAAAGCTGATGAATGACCTTGCAAGATGAT R 2 1 2 1 101000 r 74 goat snp32036-scaffold36-605396 9 3355444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790554 Affx-122947864 AX-385277557 9 3388072 AATCTCTTCTTGAGAGAGATCTTCCAATCTCTTTC[A/G]TGGAAATCAGCCAGTAATTTATTGATGCAGTTTCC R 2 1 2 1 102000 f 74 goat snp32037-scaffold36-635211 NW_017219062.1 5877 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452462 Affx-122920558 AX-123322795 9 3436991 GAATTCTTTACCACTGAGCCATCAAGGAAGTCTCT[A/G]TCCTTCCATAGTTGGGTATATGATAATCCATAGTT R 2 1 2 1 201000 r 74 goat snp32038-scaffold36-684130 9 3429502 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377183 Affx-122978200 AX-123247542 9 3483770 CATGGACTGTATTGGAGACTAAGTTAATCAAGTAC[A/G]TTTCATAATTATAGATTGCTTTCCACCAATTAGGT R 2 1 2 1 101000 f 74 goat snp32039-scaffold36-730909 9 3475918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391830 Affx-122967010 AX-123262187 9 3512497 TTCATTAAGTCACAGTGGCTAATTACAATAGCTCT[A/G]AGAAATGGACAGAAAAGTTGCTAATATTCATAATT R 2 1 2 1 101000 f 74 goat snp32040-scaffold36-759636 9 3505078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450803 Affx-122921810 AX-123321137 9 3566655 GTACATTCTCATGAAATTGGTTAGAGGGCTATAAT[A/G]TTCACAGAAAGAGGTTGAAATCACTCCACCTATAG R 2 1 2 1 101000 f 74 goat snp32041-scaffold36-813794 9 3562174 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417718 Affx-122947442 AX-123288066 9 3603167 GCCTTTCACGGTTCAGCTATTCCTGACTATCTCTT[A/C]TCTCTCACTCTTGCAAAGCCATCCTATCCATTTTA M 2 1 2 1 201000 r 74 goat snp32042-scaffold36-850306 9 3599524 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442494 Affx-122927921 AX-123312831 9 3633708 TGAGAAGGATTGAGAGAGGAATAAGATGATTTCTA[C/T]GTTTTATTTTCTTAGTACACCAAAGTAGATCCAGT Y 2 1 2 1 101000 r 74 goat snp32043-scaffold36-880847 9 3628487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448754 Affx-122923317 AX-123319090 9 3675030 CATTTATCTACCTGGGTGTTCTCTAGATAGAATTG[C/T]TGTGACTGTGTTAGAAGAATGAGCAGTTTTAGGTA Y 2 1 2 1 101000 r 74 goat snp32044-scaffold36-922169 9 3669608 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787159 Affx-122922935 AX-385274185 9 3734054 AGCAGGATATGGAGTTCAGAAATTTCTCAACATTG[A/C]TGATTAAAAATCAAGCTCTACAAAACAGACTTAAT M 2 1 2 1 101000 f 74 goat snp32045-scaffold36-981193 9 3723715 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382072 Affx-122974916 AX-123252430 9 3764235 ATTTTCAGCTGAAGACAGAAGCCACTGAATTTGGG[C/T]ATACCACACAAATAAACATGTATTATTGCTTTGTT Y 2 1 2 1 101000 f 74 goat snp32046-scaffold36-1011374 9 3754050 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377134 Affx-122978234 AX-123247493 9 3822159 GTGGACATTGGTAGGGTCTATTCTGGGAAGGCCAT[A/G]GGATCCTGCTCAGTTACAGGAACCAGTAAAAAGTA R 2 1 2 1 101000 f 74 goat snp27466-scaffold2929-1551 9 3822313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779672 Affx-122958987 AX-385266773 9 3852474 AGGAAGTAGTATAAAAATGTCTAAAGATATTGAGC[A/G]CAAAATTACAATTTGTCTTAAAATTTTGTCAAGGT R 2 1 2 1 201000 r 74 goat snp27467-scaffold2929-31866 9 3853176 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772143 Affx-122946968 AX-385259298 9 3901444 GTTTTTAATCTTTATCCAAAGATTCTTTGGATCTA[C/T]ACAGAGAAATCTTCAAAGGACATCATGACAGATAT Y 2 1 2 1 102000 r 74 goat snp27468-scaffold2929-80836 9 3903656 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392598 Affx-122966054 AX-123262955 9 3936838 GTCTCTGCTATTAGCAATAGGATGGAACCATGAGA[C/T]GGTGAAAAAGGAGAATAAAATTTAGAGCCACAGAA Y 2 1 2 1 101000 f 74 goat snp27469-scaffold2929-116230 9 3939523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378154 Affx-122976971 AX-123248513 9 3974235 TACTTGTCACAGATACTTGAGAATATCACCTATGC[A/G]TAAGGAGAGGAGAGTCAACTGGAAAAATGATGATG R 2 1 2 1 101000 r 74 goat snp27470-scaffold2929-153627 9 3977460 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780781 Affx-122968221 AX-385267870 9 4012943 GTTCCTTTTTTACCCTATGACTGTGGTATGTGATG[C/T]GAACACTGGCATGATAGAGGTAAGGTGAGCTATCA Y 2 1 2 1 101000 r 74 goat snp27471-scaffold2929-192335 9 4015629 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424192 Affx-122942514 AX-123294538 9 4031585 CACAGCTCAAACCTACTCTAAAAATCTCAAGCCAA[A/G]CTGGGCCCTTCTTCATCTGAAAGTTGATACTTGAC R 2 1 2 1 101000 f 74 goat snp40496-scaffold518-733376 9 4034244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425841 Affx-122940670 AX-123296187 9 4126716 ATCATATTAGTGAATGGAAGCATAGGAGACCTAGA[C/T]AGGTTTTTATTTTAGGGTAGTCCTTCACCCACTGA Y 2 1 2 1 101000 f 74 goat snp40494-scaffold518-638245 9 4129491 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434321 Affx-122934745 AX-123304662 9 4165282 TCTAGTCTTCATGAGAAAACAATTACTGATCAGCT[A/G]CCCAATCTCAGGCTCTGTGTCAATACTTGAGTATG R 2 1 2 1 101000 f 74 goat snp40493-scaffold518-599679 9 4169554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376282 Affx-122978383 AX-123246641 9 4241405 GCTATGCATCTTTGAGTACTTTCCTGTATGAAACA[C/T]GACATTAAAGAAAATTATACCTTTCTAAACAGAAA Y 2 1 2 1 101000 f 74 goat snp40492-scaffold518-523556 9 4243967 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428241 Affx-122939425 AX-123298584 9 4273093 GGGCCTGGCGCTGGGCTTCACACTTTGCAGGAACT[A/G]CTTAAGTGATCAGTAAGTGAATGTGTGAGGAATGA R 2 1 2 1 202000 r 74 goat snp40491-scaffold518-491868 9 4276356 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381198 Affx-122974535 AX-123251556 9 4326527 AGTGAGATTTGCAAAGTTTAAAATCAAGAAGACGA[C/T]GAGAGTCTTCTGACTGCTGGTTGGCTTCTCTAAAG Y 2 1 2 1 101000 r 74 goat snp40490-scaffold518-438434 9 4329520 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380484 Affx-122975715 AX-123250842 9 4357519 TGAGAGAGATAAAAGCAAATTCTTGGTGGGCACTC[G/T]GACCCTAAATATTCCTCTAAAGTTTTGAGGTACTT K 2 1 2 1 101000 r 74 goat snp40489-scaffold518-407442 9 4360928 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389007 Affx-122968644 AX-123259365 9 4433789 AAGTCAGAGATAATAGAAGTGATGAGTGGGAAGAC[A/G]TTAGGGGCAAATGTTGAGAGATTAAATATGAAATA R 2 1 2 1 101000 f 74 goat snp40487-scaffold518-331172 9 4438139 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415375 Affx-122948762 AX-123285724 9 4469169 CCTTTCTTTGGTTTCTTAGAGCTTCTCCTTCAACT[A/G]CTACTTCCTGTCCAAGAGACAGTTTCCCGTTTCAA R 2 1 2 1 201000 f 74 goat snp40486-scaffold518-295792 9 4474291 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790634 Affx-122952856 AX-385277636 9 4553883 AGTAAGTCGGACTCCAAATGCAGTTCTGGTGTAAG[C/T]AGAAAATCAATTATTCAATTCTGTCCCCAAATGTT Y 2 1 2 1 101000 f 74 goat snp40484-scaffold518-211078 9 4558956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408912 Affx-122953960 AX-123279263 9 4592726 TGCCAAAACAATGACAGAAGGTAACAGCTAGACTC[A/C]CACAGAATGTTCCAAGACTCCTAACAGAATCAGAC M 2 1 2 1 101000 f 74 goat snp40483-scaffold518-172235 9 4597450 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437203 Affx-122932048 AX-123307541 9 4630820 ACTGTGAGTCCCTGCTTTGCATCTTCAAAAGACAG[C/T]AGCCAGAGAAGGCACGGAGACTTGTTTTTAGCAAT Y 2 1 2 1 101000 f 74 goat snp40482-scaffold518-134141 9 4636010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783381 Affx-122973177 AX-385270445 9 4675059 AGTTATCAGCCTTAAATATGGGTGGACAATGAATC[A/G]CTTCCTACTTCCTGAAGCATGTAACATTATACTTC R 2 1 2 1 101000 f 74 goat snp40481-scaffold518-89902 9 4682150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454026 Affx-122919417 AX-123324359 9 4707326 ATCTCCTAAAAAGATCGAGCCTCCATGCGGCAAAT[A/G]CTCAAGCTAATTTTCATCTCCATTGTCAGTTGAGC R 2 1 2 1 101000 f 74 goat snp40480-scaffold518-57635 9 4714602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385824 Affx-122971020 AX-123256182 9 4764721 AGAAAAGCTACTGGTATTACTCAAGTACTGTACCA[C/T]GGTCAACTGTTGGGAGCATTTCCAGCTCATTGTGA Y 2 1 2 1 101000 r 74 goat snp40479-scaffold518-240 9 4773594 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426146 Affx-122940608 AX-123296492 9 4779052 GAGTCAACAAGCGCTGCCTAAACTTTTGGGGGGAA[C/T]ATGCCACTGAGGTGCTTTAAATTATTTTCTATGTC Y 2 1 2 1 101000 f 74 goat snp15591-scaffold1649-288777 9 4792377 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433654 Affx-122934571 AX-123303995 9 4824900 GAGAGGAGACAGGAGGAGAAGAGGGAAAGAAATGA[C/T]GGAGCAGACAGAAGGAGAAGTATCATGAAACCCCT Y 2 1 2 1 101000 r 74 goat snp15590-scaffold1649-242929 9 4838224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426435 Affx-122940817 AX-123296781 9 4916090 ACTTGCATCTGGTACTTTACACTCTGCCTTCCCTA[C/T]TGTTGAAATTGATAAGCTGGCTGTTCCTAGACCAG Y 2 1 2 1 101000 r 74 goat snp15589-scaffold1649-151739 9 4931445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412455 Affx-122951405 AX-123282804 9 4949779 CCCAGCTTTTAGGGTTAGGTACTATTTGGGGGTAA[C/T]ACAGATTGTGTTGTTTCATATCCTATTCTAGTAAG Y 2 1 2 1 101000 f 74 goat snp15588-scaffold1649-118050 9 4965190 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386818 Affx-122970102 AX-123257176 9 4996843 CCATGAAATCAGCCATACATAGCACAGCCACAGAT[A/G]ACCTAAATGGCTTTTCATTTCATTTAGTGCCAACA R 2 1 2 1 101000 f 74 goat snp15587-scaffold1649-70986 9 5012716 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416980 Affx-122948002 AX-123287328 9 5026501 ATCACTTAGTGTCAAAATGTGTTAGTAAGACAATG[C/T]GGCTATATCATATAAGAATGTAAGAAAATAATTTA Y 2 1 2 1 101000 f 74 goat snp15586-scaffold1649-41328 9 5042775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800613 Affx-122956658 AX-385287532 9 5056716 CCTTGAATGTTCTCTGCCAAAAATTTCCTAATAGC[G/T]ATACTCTGCTTAGTTATCAATGGGCAGCACTGAAA K 2 1 2 1 101000 f 74 goat snp15585-scaffold1649-11113 9 5073669 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453844 Affx-122919541 AX-123324177 9 5099106 TGTCTTATTTATCCACACTCTCCAAACACAAGCAC[A/G]TTTTTTCAACTCTATATTGATTTTTTTTAGTTCTG R 2 1 2 1 102000 f 74 goat snp8883-scaffold1318-1609989 9 5115400 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391161 Affx-122967445 AX-123261518 9 5182282 GGCCCTTCCTTCCTGACTTTTGTCAGAGCAAGAGA[A/G]CTCTTTTAACTTGAAAAATGGGGATGAATTTCTGT R 2 1 2 1 202000 r 74 goat snp8881-scaffold1318-1526813 9 5199183 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378135 Affx-122977125 AX-123248494 9 5213972 GCCTTTCTCTTCTTGTTCTTGCCTAATTGCTCTGG[A/C]TGGTGCTTCCAGTACTATGCTGGATAAAAGCAGCA M 2 1 2 1 201000 r 74 goat snp8880-scaffold1318-1495123 9 5230992 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452446 Affx-122920569 AX-123322779 9 5242964 ATGACCACAGGTCAGTGTCAAACAGTTTAGGCTCT[A/G]TTACACCAGGAACACATTTCATGCTATATGTATAT R 2 1 2 1 101000 f 74 goat snp8879-scaffold1318-1466131 9 5260129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772865 Affx-122938238 AX-385260010 9 5285552 AGAATATTGTGTAATATTTGTCTTCTACACATACT[A/G]TGTTTATAAATCAACTTGAAGACAAACAAAAGTTG R 2 1 2 1 101000 f 74 goat snp8878-scaffold1318-1423543 9 5302921 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417841 Affx-122946786 AX-123288189 9 5319668 ACACCTTGACATTGACCCTGGTCCCTCCTTTTGGC[A/G]CCTAGTGATGCCCCACCATGCTGGCATCATGTAGA R 2 1 2 1 101000 f 74 goat snp8877-scaffold1318-1389427 9 5333778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380219 Affx-122975482 AX-123250577 9 5358322 GTTTGGTTTCTGGAGATTTTTAGCCTTTGGTGATA[C/T]GATATTAGCTTGGTTTTTCATGGTGCTTATCAGTT Y 2 1 2 1 101000 r 74 goat snp8876-scaffold1318-1350773 9 5373257 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416731 Affx-122947543 AX-123287079 9 5387755 ACAGGAGTTCATGTAAATCATTCTCTAATTCTAGG[C/T]ATGTGGTAATCTAATACCTTGGTGGCTCATTTACA Y 2 1 2 1 101000 f 74 goat snp8875-scaffold1318-1321340 9 5403681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437636 Affx-122931806 AX-123307974 9 5425886 CAGTCCTGAGATGAGGAGACTGACACTTAGGTTTC[A/G]TGGACTGGGGAAGCCAACAGAGACGTGGTGGTCCT R 2 1 2 1 101000 f 74 goat snp8874-scaffold1318-1283209 9 5441287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394906 Affx-122964325 AX-123265261 9 5461836 CTTGACAGACATATTATTGCAGATCATCTCATATG[C/T]GATAATTTTAAAGACATACAGTAGTGATATTCAGA Y 2 1 2 1 101000 r 74 goat snp8873-scaffold1318-1247259 9 5478865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464632576 Affx-1110581185 AX-516103683 9 5491828 CCAGAAATCTCTTTAGGTTGGAGTTAGTATCATTT[A/G]TTAACATTTCACACCCTGCCCAACACGTTTAGAAT R 2 1 2 1 101000 r 74 goat 9_5491828_AF-PAKI 9 5491828 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38444772 Affx-122926355 AX-123315109 9 5513823 GTATAAAACATAGCAGGAGAGTAAGCTAGAGATTG[C/T]GTGAGAAGGAAAAAAGAAAGCTTATATCATTTTAG Y 2 1 2 1 101000 f 74 goat snp8872-scaffold1318-1195272 9 5530771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790811 Affx-122943540 AX-385277811 9 5558416 TATTATTGGGAATAATAGAGATAATATTTCACAGA[C/T]ATTATCTGTGAAAACTGTGGGAATTTTTAGAAATT Y 2 1 2 1 201000 f 74 goat snp8871-scaffold1318-1150679 9 5598328 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408334 Affx-122953754 AX-123278685 9 5590784 GCTAATACCTTTTCGAATTAGTCTTTTTGGATGAG[C/T]GTTTTTCATGTGGCTCAGGGCTTTGCATCTGCCTC Y 2 1 2 1 101000 f 74 goat snp8870-scaffold1318-1118311 9 5630782 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798692 Affx-122960153 AX-385285624 9 5620731 TGCATACAGTCAGCAGCACAATTTATTCTGAAGAA[C/T]GCTGACAAAAAGTCCCTCTAGTCTGAAGTGAAGTG Y 2 1 2 1 101000 r 74 goat snp8869-scaffold1318-1088364 9 5661265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765093 Affx-986697206 AX-385252657 9 5632647 CTGTGGCGCCATGAGAAGTGCTCTGGAATCGGAGT[A/G]CACAGGGCAATCATTCAAAAAGCTGTGGACTGGCT R 2 1 2 1 600010 r 74 goat 9_5632647 9 5632647 Ancestral_priority_1043 ancestry 0.568 neutral IMAGE 10K 10K ancestral 38415306 Affx-122948815 AX-123285655 9 5664517 TATTCAGTTAAAATCAGATGCTACTTTGACAATTC[A/G]TTTTTAAAAGGCATAAACTGAATTGCTGTGCTGTT R 2 1 2 1 102000 r 74 goat snp8868-scaffold1318-1044578 9 5706994 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389750 Affx-122968247 AX-123260107 9 5695988 TATCTGGAAAATATTTTTTATATCTCCACCCTTAA[C/T]AGTTAAAATTTAATTTTGTACTGTTGATCCATTCT Y 2 1 2 1 103000 f 74 goat snp8867-scaffold1318-1013107 9 5738775 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441942 Affx-122928578 AX-123312279 9 5736385 CTTTTTCCTAAGGAAACTTTACACAAGCTCAATAC[A/G]TAAAACAATAAAGTGCAGGTACTGAAGTACTTTAT R 2 1 2 1 101000 f 74 goat snp8866-scaffold1318-972710 9 5780090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448730 Affx-122923836 AX-123319066 9 5770418 GAATGCTTTAAAAGCAACATCTTCCAACTGATAAA[A/G]TGTTCATTCCAAATGCACCATCTAATTGTAGCTTT R 2 1 2 1 101000 f 74 goat snp8865-scaffold1318-938677 9 5815264 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431352 Affx-122937048 AX-123301693 9 5822706 AATGGCACAAGTTCTTCAGATGTGAGAGCTCGCCA[C/T]ATCCATAAATTTCTGTTTTCATTTTGACTTGTTTT Y 2 1 2 1 101000 f 74 goat snp8864-scaffold1318-886389 9 5867884 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444049 Affx-122926865 AX-123314386 9 5913393 AACTTTCAGGGCTTAATACAGCATCTAGAATAAGG[C/T]AGATGCTCTACAAATGCTTCATTTATAAAGAACCA Y 2 1 2 1 101000 f 74 goat snp8862-scaffold1318-795702 9 5958840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449386 Affx-122922713 AX-123319721 9 5948714 GAGATCTGAGAGGTTCACATTTACTGATGTGAAGA[C/T]GATGAACTCATTGAGGAGAAGAAATAGAGTGGCCA Y 2 1 2 1 201000 r 74 goat snp8861-scaffold1318-760381 9 5994791 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409797 Affx-122952968 AX-123280148 9 5981393 TCCTTCTTATATGTTCTATCATAATAATTTAATTC[A/G]TTTTATTGCATTTATTTGTTGAATGTATCTTCTCT R 2 1 2 1 102000 f 74 goat snp8860-scaffold1318-727702 9 6027571 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446075 Affx-122925817 AX-123316412 9 6026267 AGGAGGCCAGTAACAGTCTTTTCTTACAAGGACAA[C/T]GATGGAACGTGAGTTTTGGTGAATGGAAGTGATTT Y 2 1 2 1 201000 r 74 goat snp8859-scaffold1318-682828 9 6072800 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405816 Affx-122955890 AX-123276168 9 6056602 CTTCTATGTTGCTTTTGCAGGACATTAAAGACTCC[A/G]TATCTTTCATAGTAGCCCTCACTATAATTTTGTCC R 2 1 2 1 101000 r 74 goat snp8858-scaffold1318-652493 9 6103333 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443879 Affx-122927502 AX-123314216 9 6096173 TATCAGGTGTTTGGGAAGCAGGTAGCTTGGCTACA[C/T]CCAGACTTGATGGAGAGGACTGAATAGCTCCGGGA Y 2 1 2 1 101000 f 74 goat snp8857-scaffold1318-612922 9 6143105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435684 Affx-122933327 AX-123306023 9 6133036 CAGACACGACTGAAGTGACTTAGCAGTAGCAGCAG[C/T]AGCTCGAAAGCACGTGTGCTATGAAACCTGGGCAC Y 2 1 2 1 101000 r 74 goat snp8856-scaffold1318-576059 9 6180720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410187 Affx-122952585 AX-123280537 9 6229184 AAATCTGGGGACAAAGATGCCAAGCAAAATGACAT[A/G]CTTAAAAGGATCTCACTGGGGTCCTTTATGTATGA R 2 1 2 1 101000 f 74 goat snp8854-scaffold1318-479911 9 6277028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428001 Affx-122939165 AX-123298344 9 6265918 ACAGCAGGGATCAGAAAGAGTAGAATTATCAGGAA[C/T]ATGTTCCGTATTTGTTGCGCCTTTATTCTCCAGAG Y 2 1 2 1 101000 r 74 goat snp8853-scaffold1318-443177 9 6313782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402561 Affx-122958452 AX-123272914 9 6308994 AATCTCAGTCATCACTCAGAAATAAATGATAGTAA[A/G]TCATTTCTGAATGATAGTGTACATAGTACCGTCAT R 2 1 2 1 101000 f 74 goat snp8852-scaffold1318-400101 9 6357252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438210 Affx-122931453 AX-123308548 9 6337793 AATAGTTGTGATAGCAGTCATACTTGTTTTGCATA[C/T]GATTTTTGATAGAAATACTTCTATTGGTTTCCCTT Y 2 1 2 1 101000 r 74 goat snp8851-scaffold1318-371302 9 6385713 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446870 Affx-122925242 AX-123317206 9 6398831 GAGGTAACTCATTAGTTTTTTAAAATAGCATATGA[C/T]GTCATGAATTTAAACACGTTCTGTGTGTTTTAATC Y 2 1 2 1 101000 r 74 goat snp8850-scaffold1318-310264 9 6447529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398679 Affx-122961872 AX-123269034 9 6430035 TAGAAAATCTCTGCCGGATGTTGCATGAAAGGATA[C/T]GCTCTTCTGGCACATTGGCAGAAAAAGTATTAAAA Y 2 1 2 1 101000 f 74 goat snp8849-scaffold1318-279060 9 6478346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392688 Affx-122966415 AX-123263045 9 6470910 CGTTGCTCATCTGTGGCTGGTGTTTCTAATACATC[A/C]TGTTATGGGCTATGTGTGAGGGGGTGGCTGGGTCA M 2 1 2 1 101000 f 74 goat snp8848-scaffold1318-238185 9 6519817 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800338 Affx-122946914 AX-385287261 9 6503536 TCAGTAGTTACGAATCTCACCAGTATGTAGTGTCC[C/T]ACAATTTGCTACATTTTGCCTTTGTTCCTCACTTA Y 2 1 2 1 101000 r 74 goat snp8847-scaffold1318-205559 9 6551800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784122 Affx-122929347 AX-385271174 9 6541928 AGGGCAGGGAACTTATGCTATGTCTCTTTGACTTT[A/G]AAGTACCTTGCACGTTGCCTCGGCAAATGATGAAG R 2 1 2 1 101000 f 74 goat snp8846-scaffold1318-167167 9 6588773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406168 Affx-122956163 AX-123276520 9 6592997 GATGGCACTCTGTATTTTGTCTAATTTTGAAAAGG[C/T]GTAATCTGATTTTTTAGCAGCACATTTCCTTTGCT Y 2 1 2 1 101000 r 74 goat snp8845-scaffold1318-116098 9 6639878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424062 Affx-122942058 AX-123294408 9 6653398 TCTCGTCTTAAATATTTACTTATCTGCTGAGATAC[A/G]TGACTGATGACACGTACAGGATGCATTCCCATGGC R 2 1 2 1 101000 r 74 goat snp8844-scaffold1318-55697 9 6699672 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775199 Affx-122925444 AX-385262330 9 6707990 GCAGTAGCCTCAAGTCACAGTAAAGTGACAGAAAT[G/T]ATTTCCACCAAGAACTTAGCAAACTTTCTCCTCTT K 2 1 2 1 101000 r 74 goat snp8843-scaffold1318-1105 9 6754355 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798292 Affx-122930351 AX-385285227 9 6750129 TGATATACAGTGGTTTGTTCCTTTTCATTGGTCAG[C/T]AGAATTTCACTGAATGGGTATTCCATCATATAATT Y 2 1 2 1 102000 f 74 goat snp13502-scaffold1521-187579 9 6789196 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383896 Affx-122973117 AX-123254254 9 6796658 AAACAGGTTGTGTATTTAGAATACCTCCAAATTAG[A/G]TTGACGGTATTTTCTTTTCGATTTGCTAAAACGGA R 2 1 2 1 101000 f 74 goat snp13501-scaffold1521-141050 9 6835963 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415291 Affx-122948827 AX-123285640 9 6854402 TGTCAAGAGGTAGCATGTTTGTGTCAGAATTTAGA[C/T]GTTACACAGAAAGCTTTGCTTATCACTTTAAGGTA Y 2 1 2 1 101000 f 74 goat snp13500-scaffold1521-83306 9 6894166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426371 Affx-122940247 AX-123296717 9 6926250 TGACCTCATTTAAATCTCGCAACACACGTATGCTT[A/C]GGTACCATTATTCAACTGATTTTACCATAAGATAC M 2 1 2 1 101000 f 74 goat snp13498-scaffold1521-11458 9 6965816 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437225 Affx-122932032 AX-123307563 9 6965099 GTGTAAGAAACTTAACTGCAGCTGTCCCTTGTTAA[C/T]GCCAAAGCTTGTCTTTTGAACCCTCGCGTTCCCAG Y 2 1 2 1 101000 r 74 goat snp26060-scaffold2707-92496 9 7008732 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433340 Affx-122935150 AX-123303681 9 7005518 TGAATCCCTAGAACGTGCAGCACCGAGACGGAACT[A/G]TAATACATACTATGGACTTTGGGTGATTATTAGTG R 2 1 2 1 101000 f 74 goat snp26059-scaffold2707-52077 9 7049263 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408202 Affx-122954186 AX-123278553 9 7055187 TCCACAGGAGGGAAAAAAAAAATCTCTTACATCGA[C/T]AGCTCCAGGCCTATATTTCCACCTCCCTCCCATCC Y 2 1 2 1 201000 r 74 goat snp26058-scaffold2707-2408 9 7100116 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795677 Affx-122939567 AX-385282632 9 7072386 ATGAATGGAATAAAAATTTCCCATAACTGTAGTTT[C/T]AATATAAATACAATCTGCATTATTTAATCAGAGGC Y 2 1 2 1 201000 r 74 goat snp50453-scaffold723-14692 9 7117485 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766103 Affx-122956075 AX-385253517 9 7103797 TCTAGCCCTGTGACTCACAGATACTTTAAAAAGGG[A/C]TGATAGAGTTAGTGAATGTTATTTATTTTCTAGTT M 2 1 2 1 101000 f 74 goat snp50454-scaffold723-46103 9 7148706 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795482 Affx-122954916 AX-385282437 9 7254399 TAATTTCAAAGGAATGGCCTTTTGACACTTTTTTC[A/G]TGTTGAATACTGGCTCTGAATCACTGCAGCTTTTT R 2 1 2 1 101000 r 74 goat snp50457-scaffold723-196705 9 7289127 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389419 Affx-122968368 AX-123259777 9 7288662 AAGCAGTCGAAAATGAAAGCTGTAAACAGAAATCA[C/T]GTAGTTTATAATTGTTTTGATTTGAAGAAAATCTA Y 2 1 2 1 101000 f 74 goat snp50458-scaffold723-230968 9 7323401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442787 Affx-122927728 AX-123313124 9 7343438 TAATGTCTGTGAGCACACCCGGCGCCAACAGTCTC[A/G]CTCAGGTCTGGTTGGAGGACTTCCTCACTTTTATG R 2 1 2 1 101000 r 74 goat snp50459-scaffold723-285744 9 7378675 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430223 Affx-122937328 AX-123300564 9 7417201 GACTGGGTGGAGTGGAAGGGGAAAATCGCCTCTGA[C/T]AGAAAGAGTTGCAGAAAAAAAAAATTCTTCCTGGG Y 2 1 2 1 101000 f 74 goat snp50460-scaffold723-359507 9 7452896 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437157 Affx-122932137 AX-123307495 9 7470912 CACGTCGTCATCCTCACTAAACAAATGGCGAGCCC[A/G]TCATAAGGTTGGTATCAAACCTGTGTGGCCACCCA R 2 1 2 1 201000 f 74 goat snp50461-scaffold723-413218 9 7506856 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797718 Affx-122958994 AX-385284657 9 7493113 GAGTTCCTTCGGTGGAGATGTTTGCAAAGATGTTC[A/G]CTAGACTTTCCCATGAGCAGCCTGTTTTCCCAGCT R 2 1 2 1 101000 f 74 goat snp23264-scaffold2326-7633 9 7528918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380289 Affx-122975409 AX-123250647 9 7547250 GGGCTCTAGAATGGATTGTCTTTCAGAGCAGCAAA[C/T]GGAGAGTCAGACCCAAGCACCCTCTTGTCACCCTG Y 2 1 2 1 101000 f 74 goat snp23265-scaffold2326-61770 9 7583337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382785 Affx-122973581 AX-123253143 9 7589466 CTAGAATTTTAACATAGAGTATATTGATAGTTCTT[C/T]ACTTACAGCTCAACTTGTTTCTGCACAATAGATTC Y 2 1 2 1 101000 r 74 goat snp23266-scaffold2326-103986 9 7626300 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421803 Affx-122944326 AX-123292150 9 7619806 TCTAGTCTATTCATATCATGATTTAATTGTTTCCC[A/G]CTGACAATTCTTCACATATCATGTGATTTTCCTCA R 2 1 2 1 101000 r 74 goat snp23267-scaffold2326-134326 9 7658934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432162 Affx-122936416 AX-123302503 9 7654847 TTCACTCTCTGCTTGTTTTTTCATGGTTGCAAGAT[A/G]CCTGCCCCTACAGGACCCACAGAAAGGCAAGGGAA R 2 1 2 1 101000 f 74 goat snp23268-scaffold2326-169367 9 7694045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394641 Affx-122964392 AX-123264996 9 7703826 TTTCCATTTACTTAGCTTGGGGAAATCTCTCACAT[A/C]ACCTGAAAAATGTCCTCTGGTATATGAATGAAGAC M 2 1 2 1 101000 f 74 goat snp23269-scaffold2326-218346 NW_017190638.1 3810 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770230 Affx-122969304 AX-385257396 9 7735206 TCACTTTGCTAGTGCCATAGCCTATGTCTTCTTTC[A/G]TAATCCATACCAGATTCATTATTTCTGAAGATTAT R 2 1 2 1 101000 f 74 goat snp23270-scaffold2326-249726 9 7774971 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785214 Affx-122975867 AX-385272260 9 7784863 CTAATGGGAAAAGGAAACTGGAGTCTCTGAATCCA[C/T]GTGCAGGTTGGGTACTCCCTTTTTATATTCTTAGA Y 2 1 2 1 101000 f 74 goat snp16053-scaffold169-990821 9 7824790 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799148 Affx-122939492 AX-385286078 9 7829131 TATCAGTGAAGAACCTATGGAGTTGGTTATTTTTC[A/G]TCAAAAATAAATGATTATTTGGGATATAATGGGTC R 2 1 2 1 303000 r 74 goat snp16052-scaffold169-946553 9 7869145 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413325 Affx-122950177 AX-123283674 9 7922985 GTAGATGCTAGATTCTAGAAATGCACTGAACCAAA[C/T]ACAGTACTAGAGACAAAAAGAAAACCATTTTCCAA Y 2 1 2 1 101000 f 74 goat snp16050-scaffold169-852699 9 7964025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765303 Affx-122958563 AX-385252829 9 8021856 ATGGGAAAAAATCCACTTAAATATAACAAACCATC[A/G]TCATTGTTAAAAAAACTTCTACATCAGAAGCTCAC R 2 1 2 1 101000 f 74 goat snp16048-scaffold169-753828 9 8063794 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273487 Affx-1111833625 AX-519547103 9 8050703 CTGACTTTGAATCTTTCCAGTCTCTTCTTAAAAAG[A/C]GATAAGACAGCTAGGACAGAAAAAAGTAGTCTGCC M 2 1 2 1 101000 r 74 goat 9_8050703_AF-PAKI 9 8050703 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320803054 Affx-122942986 AX-385289927 9 8078816 ATTTGTTTCATCACAGATTAATGATGTACCAGCAT[A/G]CCCACTGAGGGAGACAGCTATAAAAAGTGGCTTTG R 2 1 2 1 101000 r 74 goat snp16047-scaffold169-696868 9 8123061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394638 Affx-122964395 AX-123264993 9 8130381 GAGTTTTAAATGTTTTTGACTTAATTTCACAGATG[C/T]TATTTCATTTGCTCATATCAGAACTATGGCTTAAG Y 2 1 2 1 101000 f 74 goat snp16046-scaffold169-645303 9 8174827 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449076 Affx-122923609 AX-123319411 9 8170424 ATAGTTTCTGCTGCTGGAATGAAAAGCAATGTTTT[A/G]CAAAAATATATACTCTTTTTCCTATTACTATTACA R 2 1 2 1 102000 f 74 goat snp16045-scaffold169-605260 9 8216941 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398942 Affx-122960989 AX-123269297 9 8199523 ATTTGATAATAATCCTTTATACAGAATTTCTACTC[A/G]TCTCTTCTCATCTCAAACATCCTTCTTTTCTGAGG R 2 1 2 1 101000 r 74 goat snp16044-scaffold169-576161 9 8247128 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788803 Affx-122945360 AX-385275818 9 8231544 AAGTTGAAGTCATCTTCATGGATGCGGAGCAAGCA[C/T]GCACACAGTCTTGAAATGGTGTTCCAGATGCAATC Y 2 1 2 1 101000 f 74 goat snp16043-scaffold169-544140 9 8279320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381438 Affx-122974347 AX-123251796 9 8274703 CAGAGTTTGAAAAAGCAAAACCAGAGAGGTCACTG[C/T]GGTACCCCTTACTCTAGCTTATGGATATCATGCTG Y 2 1 2 1 201000 r 74 goat snp16042-scaffold169-500981 9 8322412 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407027 Affx-122954947 AX-123277378 9 8348696 CAAAATGAATAGAAAATAACCCTTTTAAATTAGTG[A/C]CAAAAAGTGACAACCCAAAAAAGATTCTATCAGGA M 2 1 2 1 201000 f 74 goat snp16040-scaffold169-426988 9 8396268 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443113 Affx-122928095 AX-123313450 9 8415877 ATGAAATTTTTGCTTTTTTTAAATTCCAAAAACTC[A/G]TATGCCATATATAGAGAGCTATCAGTACAGCTGCA R 2 1 2 1 101000 r 74 goat snp16039-scaffold169-359807 9 8464951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410892 Affx-122952074 AX-123281242 9 8446654 TCGCCTTGTGTGACATCAGCTCCGCATCTGCAGAG[C/T]GGCGGAGAAAGGGAGAGAAGGCAGGAAATGTGGTT Y 2 1 2 1 202000 f 74 goat snp16038-scaffold169-329030 9 8494787 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431603 Affx-122936165 AX-123301944 9 8503803 ACAGCTTGGAGAATTTCAGGAACTGAAAGGAGGTC[A/G]TTTTGATTGGAGTAGAGAGAGAGTAAGTGGGCCAC R 2 1 2 1 102000 f 74 goat snp16037-scaffold169-271881 9 8552391 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444793 Affx-122926342 AX-123315130 9 8537921 GAGACCAGGCTTGCAAATTGCCCAAGCCATGTTGC[A/G]TGCGTGCATGCGTGCGTACTCAGTCACGTCGGACT R 2 1 2 1 103000 f 74 goat snp16036-scaffold169-237763 9 8586451 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428471 Affx-122938793 AX-123298814 9 8596722 CTTCAGTGCTGTATGTTGTTGAAACGTATAAAGAA[C/T]AAAACTAAGTTAACAGTCTTTTAAAGTTGAAGATT Y 2 1 2 1 101000 f 74 goat snp16035-scaffold169-178962 9 8645326 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394839 Affx-122964783 AX-123265194 9 8629896 AACTAATCCTCACAGTAACTGTCTGAGAAAAGAGA[C/T]AACTGATAAGTTTTACTAATATGGTCAATAATACT Y 2 1 2 1 101000 r 74 goat snp16034-scaffold169-145788 9 8679096 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406358 Affx-122955426 AX-123276710 9 8727081 TGACTTCAACTACTCAAGTGGCATGATTTCCTTAT[A/G]CTTGCCTTAGAATTTTTTGATCTTTCCTTCAGTTA R 2 1 2 1 101000 f 74 goat snp16032-scaffold169-48603 9 8775540 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801048 Affx-122927353 AX-385287962 9 8769402 CAACTCTTGACTGGCTCAGTCAGCTCCATTAGAAT[A/C]TAGATAATGAGTACTGACATTTTGAATCTGGTTAT M 2 1 2 1 101000 f 74 goat snp16031-scaffold169-6282 9 8817786 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384897 Affx-122971922 AX-123255255 9 8792700 TCCAGTTTGAGAAGCAACAGGGCAGGCATCCCAAG[C/T]AGCAACTTGTCAAGTTCCCAGTGGAAGTTAATTTC Y 2 1 2 1 101000 r 74 goat snp21065-scaffold2061-608263 9 8843564 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391486 Affx-122966711 AX-123261843 9 8837334 CCCATATGACAGGATATTTTGGTTTCCTATCTAGG[C/T]ACACATCCCATGCTGCCAAACCCAAGTGGCATCTT Y 2 1 2 1 201000 f 74 goat snp21064-scaffold2061-563629 9 8887631 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431838 Affx-122936090 AX-123302179 9 8904878 GTTAGGCCTTTCATGCTTGCAGCTTCTGCTTTAGA[C/T]CTGCACTTACTTTCTCTGCACATTTTCTTTGCTTT Y 2 1 2 1 101000 f 74 goat snp21063-scaffold2061-496085 9 8956114 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419388 Affx-122945612 AX-123289736 9 8961366 AATAGCCTGTGCCAATGTGCTCAAGTTTAAAGTGC[A/G]TGCATGCTATGTTGCTTTAGTTGTGTCTGACTCTT R 2 1 2 1 101000 f 74 goat snp21062-scaffold2061-439597 9 9012510 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430027 Affx-122937580 AX-123300368 9 9013249 TCCACCAGTAGTCTACTGCTTGGCCCACAGATGCC[A/G]CTCAAATGCTTGTTGAATGAAAGAGTAAATTAAAT R 2 1 2 1 101000 f 74 goat snp21061-scaffold2061-387714 9 9064750 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778507 Affx-122948446 AX-385265621 9 9050144 CTGCTAAAATGACTCCTTGGTATTGGGTTCTCTCG[C/T]TGTAACATGCGTATTTTCTTTTTGTCATAGGTGAT Y 2 1 2 1 101000 f 74 goat snp21060-scaffold2061-350819 9 9101663 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377831 Affx-122977297 AX-123248190 9 9108295 TCTTACAGCCTGCTCTTGTTGTTGTTCAGTTTCTA[C/T]GGACTGGGAGAAGGCAATGGCACCCCACTCCAGTA Y 2 1 2 1 103000 f 74 goat snp21059-scaffold2061-292668 9 9159872 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434495 Affx-122934617 AX-123304836 9 9161440 GTGACTTAATTGCTAGTGCTGAGAAGAAAGACCCA[C/T]GTGTCAGTGGAACACTTCATCCAGCCTGATTTGTG Y 2 1 2 1 101000 f 74 goat snp21058-scaffold2061-239523 9 9213038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448566 Affx-122923416 AX-123318902 9 9195566 CTTATAGATAATATACCAATACATGTGTCCATTAC[A/G]TCTTTATCCTGTTGAATTATTATTAATAATGTATC R 2 1 2 1 101000 f 74 goat snp21057-scaffold2061-205397 9 9247901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395614 Affx-122963810 AX-123265969 9 9289815 CATATCTAAAATAGGATGCTGGAAAACGATGTGTC[A/G]CACTGTTTTCAGCTACTACGTTGTATCCAGTTTGC R 2 1 2 1 101000 r 74 goat snp21055-scaffold2061-111148 9 9341160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769067 Affx-122932355 AX-385256242 9 9327181 TTTGTTCATTGACAATCCTTGTGAAATCAGATGTC[A/G]TTACTGTCTAGAACACAATGAAGTTAGAATTGGTA R 2 1 2 1 101000 f 74 goat snp21054-scaffold2061-73782 9 9384617 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476255 Affx-1251763762 AX-586011676 9 9353059 ATACATTATAAATCAATAATAGTCCAATATAAAAT[-/AAAAACTTTATTATTTTTTTTAAATTTTTTTATTTTTTAACAACATAATAAAAGCTACATATGACAAACCCACAGCAAAC]AAAACTTTATTTTTAATGGGCAAAAGATCTTAGAC - 4 1 4 1 20000 f 74 goat SV_151 9 9353059 - deletion junction SV-TF-chip 539476508 Affx-1251763762 AX-586011902 9 9353059 ATACATTATAAATCAATAATAGTCCAATATAAAAT[-/AAAAACTTTATTATTTTTTTTAAATTTTTTTATTTTTTAACAACATAATAAAAGCTACATATGACAAACCCACAGCAAAC]AAAACTTTATTTTTAATGGGCAAAAGATCTTAGAC - 4 1 4 1 20000 r 74 goat SV_151 9 9353059 - deletion junction SV-TF-chip 562165451 Affx-1251763762 AX-606940862 9 9353059 ATACATTATAAATCAATAATAGTCCAATATAAAAT[-/AAAAACTTTATTATTTTTTTTAAATTTTTTTATTTTTTAACAACATAATAAAAGCTACATATGACAAACCCACAGCAAAC]AAAACTTTATTTTTAATGGGCAAAAGATCTTAGAC - 8 1 4 1 20100 r 74 goat SV_151 9 9353059 - deletion junction SV-TF-chip 562166114 Affx-1251763762 AX-606941522 9 9353059 ATACATTATAAATCAATAATAGTCCAATATAAAAT[-/AAAAACTTTATTATTTTTTTTAAATTTTTTTATTTTTTAACAACATAATAAAAGCTACATATGACAAACCCACAGCAAAC]AAAACTTTATTTTTAATGGGCAAAAGATCTTAGAC - 8 1 4 1 20100 r 74 goat SV_151 9 9353059 - deletion junction SV-TF-chip 562166546 Affx-1251763762 AX-606941954 9 9353059 ATACATTATAAATCAATAATAGTCCAATATAAAAT[-/AAAAACTTTATTATTTTTTTTAAATTTTTTTATTTTTTAACAACATAATAAAAGCTACATATGACAAACCCACAGCAAAC]AAAACTTTATTTTTAATGGGCAAAAGATCTTAGAC - 8 1 4 1 20100 f 74 goat SV_151 9 9353059 - deletion junction SV-TF-chip 38417021 Affx-122947970 AX-123287369 9 9366214 CCGATATTATGGGCTCCACTGGGAAAGCCATCCAA[G/T]CCTGCTTTAGACATCAGTCTCTGCTGGAAGAGACC K 2 1 2 1 101000 f 74 goat snp21053-scaffold2061-34749 9 9423467 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771130 Affx-122962808 AX-385258290 9 9396261 AAATTTTTATGACTCACAGCTCACCTTAGGGTTCC[G/T]AGTTGGCTGCTTCTCCACACCTACTTCCCTCTCAC K 2 1 2 1 101000 f 74 goat snp21052-scaffold2061-4702 9 9454139 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787427 Affx-122975426 AX-385274452 9 9406080 CTGCAATTCTATCTCATGCTTTGAAAGTTAGCCTG[C/T]GTGTCAAACAATTGTAAATACTTTGCTTATCACGG Y 2 1 2 1 101000 f 74 goat snp13757-scaffold1536-5018 9 9463868 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453838 Affx-122919545 AX-123324171 9 9441990 TTTGCAGCTCATTTCTTTACGCTCCTGCTCTGTTA[C/T]GCCTCTATCTACCTGGTTACCGCTTTAAGTGCCCA Y 2 1 2 1 201000 r 74 goat snp13758-scaffold1536-40928 9 9499895 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782089 Affx-122955597 AX-385269167 9 9473453 TGAAGCTTTCATGAATAGATGAGAAATATTTGATC[A/G]TCTCTAAAGAAAATGCATCATCTTCTTATCAAACC R 2 1 2 1 101000 r 74 goat snp13759-scaffold1536-72391 9 9531649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378616 Affx-122976566 AX-123248975 9 9509186 TCTCCAGAAGACAGTCACATGAGCAATATAATCTG[C/T]GTTTTCAGGAAGATGAGGCATGAAGCTGGTGAACA Y 2 1 2 1 101000 r 74 goat snp13760-scaffold1536-108124 9 9567396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801136 Affx-122938451 AX-385288051 9 9568396 AAATAAGACAAAATTTGTCTATAATGATAGATACT[A/G]TGGATATAGCATAGGGGAAAGAACATGAACTCTGG R 2 1 2 1 102000 r 74 goat snp13761-scaffold1536-167334 9 9627042 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278841 Affx-1111836539 AX-519552312 9 9593299 GAAAACCATCAAACAAAAGATAAACCTGTTAAAAG[A/G]TCATTTTCTTCCATACATTACGACAGCAGTGATCC R 2 1 2 1 101000 r 74 goat Random2.2K-959 9 9593299 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421074 Affx-122944239 AX-123291421 9 9599263 TTTTTCTATTAAGTAAGTATTTCTTGCTAAAAATG[A/C]GTAGGTCTTTTAGGTCAGTGATTTCGATATGTTTG M 2 1 2 1 101000 r 74 goat snp13762-scaffold1536-198201 9 9658013 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410058 Affx-122953225 AX-123280408 9 9627917 AAGAGTCAGACACGACTGGGTGACTAAACAACAAC[C/T]GTCTGCAAACTTAAAATTGCTTTAACTATAATCTC Y 2 1 2 1 201000 r 74 goat snp13763-scaffold1536-226855 9 9686479 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419367 Affx-122945628 AX-123289715 9 9659059 TTAGTCTTAAGCTAGAAATGTTTTAACAAATGGCA[C/T]TGTTTTGAGAGAATAATGAAATGATTTTTTAAAGA Y 2 1 2 1 101000 f 74 goat snp13764-scaffold1536-257997 9 9717735 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768817 Affx-122930100 AX-385255994 9 9701873 GCATATACTGAGGGATGAGGCAGACATGTGAATAT[A/C]TGTTAGTGATCACAGTCCTGGTCTGTTTGATGTAA M 2 1 2 1 101000 r 74 goat snp13765-scaffold1536-300811 9 9761064 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771758 Affx-122923561 AX-385258915 9 9720322 AATTGCGATATCTTAACTTTCATTGGAAGTTTATC[A/G]GATGCCAAGGACTTGATATTAACTCACGTGGATCC R 2 1 2 1 101000 r 74 goat snp21594-scaffold2110-99167 9 9781857 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38386561 Affx-122970709 AX-123256919 9 9749612 GACAGTATTTAGGAAGCAAAGGAAAATTCATTTCA[A/G]TTGGGCAAGTACCTGCCAAGTACATCTTGTGTGGT R 2 1 2 1 201000 f 74 goat snp21593-scaffold2110-69877 9 9811156 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394420 Affx-122964602 AX-123264775 9 9796768 GTCCCTTGCCTTTTAGATTAAAGTTATTAAAACAT[A/G]CCTGGTGGACAGAGGGAAAGCAGATTATGGGAAAA R 2 1 2 1 201000 f 74 goat snp21592-scaffold2110-22721 9 9855372 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419979 Affx-122945185 AX-123290327 9 9830754 CCATTAGTTGAGAATGAAGAGGGAAGGAAATGTTT[A/G]AGGCCTAAGGAGAGAAAAGGGAGTAACTGGAAGAG R 2 1 2 1 101000 f 74 goat snp58923-scaffold965-815143 9 9888890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448128 Affx-122924297 AX-123318464 9 9868455 CAAGTCTCATGTAATTCTACCTTCAGCATTTAATA[C/T]GATTTTTTAAAGGTAATAGCTATTTTTCTGGAATT Y 2 1 2 1 101000 f 74 goat snp58922-scaffold965-777442 9 9926585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788895 Affx-122965911 AX-385275910 9 9898389 TCTATGAAGTTATCAAATGAACGTCGCCTAGAATC[A/G]CTTTACCCTTCTTGCTAGTGATTCCCCAGAAGTTA R 2 1 2 1 101000 r 74 goat snp58921-scaffold965-747508 9 9954614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391815 Affx-122967022 AX-123262172 9 9965894 ACTAAAGGGAGACTTACAGGATGTAGCAATTCCAA[C/T]GACAAAAGAAAGAAAGGAAAGAAAAAGCTTTGTTA Y 2 1 2 1 101000 f 74 goat snp58920-scaffold965-680003 9 10021429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413064 Affx-122950969 AX-123283413 9 10001780 AAAGAATTTGGACCACCGGCTAAGTCCATCCAGTG[C/T]CTGTTTGTATAAATAAAGTTTTATTGGAACACAGC Y 2 1 2 1 101000 f 74 goat snp58919-scaffold965-644117 9 10056773 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377924 Affx-122977225 AX-123248283 9 10037193 ACCCTACATAGGTAGGTGGAGGGAGGCTTTTGGCT[A/G]AATAAGCTTCTCTCCTCATCAGTGGGGAGGAGGAA R 2 1 2 1 102000 f 74 goat snp58918-scaffold965-608704 9 10092217 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439431 Affx-122930194 AX-123309768 9 10133697 CTGCTTTAAGTAGTATTGCACTGTGTGTGTTGTAC[A/G]TTTGTTTTGTGATTATGTATAGTTTTTATGAGGTA R 2 1 2 1 201000 r 74 goat snp58916-scaffold965-512200 9 10188136 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790304 Affx-122972437 AX-385277307 9 10173787 AACATAATCACATTTATTTAGAATATAATCCAATA[G/T]CAAATAGCAAATTTCAGCACTGCGAAAGTGCAGGT K 2 1 2 1 201000 f 74 goat snp58915-scaffold965-472110 9 10228217 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392126 Affx-122966340 AX-123262483 9 10202766 TAAAAGTTGGTGAACAATATGCCAGCAATTAACTT[C/T]ACAATTCAACTTTAAACTAGATTGGTTTCCATACA Y 2 1 2 1 303000 r 74 goat snp58914-scaffold965-443131 9 10256970 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440493 Affx-122929364 AX-123310830 9 10258131 GTAACAGCATAAGAACTGTGACATTATAATGCCAA[C/T]GATTAAAGGTGGCCATTTGAACTGAACCTGTCCAT Y 2 1 2 1 101000 f 74 goat snp58913-scaffold965-387766 9 10311962 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423637 Affx-122942360 AX-123293983 9 10302339 GTAAGCTTAGTTATTAGCGGAATTGGTTTTGCATA[C/T]AGACAAATACTAAAGTTCATCTTGTGCTTTGCATA Y 2 1 2 1 101000 f 74 goat snp58912-scaffold965-343558 9 10356051 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375832 Affx-122978546 AX-123246191 9 10335006 CAATGCCCTTGCCCCACAGAATGATGCAAACTGGC[A/G]CAGGGAAGACCCAAGTGCACAATCTGTGGGACACT R 2 1 2 1 101000 r 74 goat snp58911-scaffold965-310891 9 10388557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386784 Affx-122970105 AX-123257142 9 10368816 TTCTGAGACTCTTACTCTCATGCTGCTTTCACTTC[C/T]TCATGTAGAAGGCCGCCTCTTGGCTTGGCAATATA Y 2 1 2 1 101000 f 74 goat snp58910-scaffold965-277081 9 10422166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446938 Affx-122924680 AX-123317274 9 10413694 TTATCATCACTGAATATTTTATTTGAGATGACCCT[A/G]CCTTTACCCTGGGGCTTCCCTGGTAGGTCAGACAG R 2 1 2 1 303000 f 74 goat snp58909-scaffold965-232203 9 10465968 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438531 Affx-122931195 AX-123308869 9 10470386 AAAATCTAGCTGAGTAAAGAAGGACTTTCAATCAG[A/C]GTAGACTGCTAGTTTAGAGGAAAAAAATAAAAGTA M 2 1 2 1 101000 f 74 goat snp58908-scaffold965-175511 9 10522450 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770436 Affx-122974892 AX-385257602 9 10499903 AATACAGTTGCAAACAGGTATATCTTTTGATCTTA[C/T]ACTTTTTAATAAATCTTAATGACACGATACTTTCT Y 2 1 2 1 101000 f 74 goat snp58907-scaffold965-145994 9 10551942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397975 Affx-122961812 AX-123268330 9 10556385 ACACCTTTTCCAGTGCCCCATCTTGAAACTTCTGA[C/T]GTTTGCAGTGTTAAAATGTTTCACAGATACATACA Y 2 1 2 1 201000 r 74 goat snp58906-scaffold965-89512 9 10609594 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415335 Affx-122948794 AX-123285684 9 10589344 TAGAGACTCTTGAGTTCTGCAAAATAGTGGATATG[C/T]GGTCTAGGCCTCAGGAAAGAGATCTGTGCTTGGAC Y 2 1 2 1 101000 f 74 goat snp58905-scaffold965-56553 9 10643104 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273399 Affx-1111833600 AX-519547027 9 10608629 ACTAGGAGGTTTTAAAGAGATGTACACTTATTTTG[A/G]TGGTGGTTTAGTCATTAAGTCATTTTCGACTCTTG R 2 1 2 1 201000 f 74 goat 9_10608629_AF-PAKI 9 10608629 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38427654 Affx-122939326 AX-123297997 9 10626290 TCTAAGGCCAACCCCTCTGCCTGTACCTAGATCTC[A/G]CCTCCTCCCTTCTCTCCAAACTTGCTTCATGAATG R 2 1 2 1 101000 r 74 goat snp58904-scaffold965-19607 9 10680135 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278664 Affx-1111836541 AX-519552142 9 10665473 AAGCTTCTTATCTACCAGAAGAGCCATTGACTCCC[A/G]GGGACTGAATGCTGGAGGAGCTGGTTGTCCATACT R 2 1 2 1 101000 f 74 goat Random2.2K-962 9 10665473 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320775470 Affx-122953667 AX-385262601 9 10665668 TACAGATCACTAAAACCCTTTAAACACAATGGCCT[A/G]AACTAACGCACTTATTTGTCAGGAAGATCCCCTGG R 2 1 2 1 101000 r 74 goat snp21962-scaffold2158-251148 9 10738749 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425675 Affx-122940866 AX-123296021 9 10723872 TTAGTGACTGAACAATAACAAACCTTCTCTTAGAC[C/T]GTTGGCCCCAGTTCTTAGTGCTTTCATGTTGCCCT Y 2 1 2 1 201000 r 74 goat snp21961-scaffold2158-192944 9 10797818 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389283 Affx-122968523 AX-123259641 9 10777403 AGCCTTCACTCAGATTGGTAGAAAATAATAGCAAC[A/G]TTTTTGAGATCCCTAGAGAATAGCATCGGCTTAGA R 2 1 2 1 201000 r 74 goat snp21960-scaffold2158-139413 9 10851747 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771652 Affx-122950491 AX-385258810 9 10821943 CATCTTTCTCTGATGCATAAATGTTGGGTCTGAGA[C/T]ACCCAATCATTTTTTACCTTGTTTACACACTGAGG Y 2 1 2 1 202000 f 74 goat snp21959-scaffold2158-94873 9 10896623 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431875 Affx-122936061 AX-123302216 9 10857163 TTTTACCCATGAAATGGAAGCTTTAGGGTTTTCTT[A/G]TAATGCCAACATTCATTCTTTCTTATCAGCAACAT R 2 1 2 1 201000 f 74 goat snp21958-scaffold2158-59653 9 10931522 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392762 Affx-122965998 AX-123263119 9 10899261 AATGTGAGGGCTAGAATTAAGGAACACTGTTGGAG[C/T]GCGAAAGAAGAGAAGGATTTAGAAAAGAGAATCAA Y 2 1 2 1 101000 f 74 goat snp21957-scaffold2158-17555 9 10973542 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416669 Affx-122947589 AX-123287017 9 10940608 GTCCTGCTTGGTCTAAAGCTTCTTCATGAAGTGGA[C/T]AGCGCGACAGGTAAAGGCTTATAAACAATACCTTT Y 2 1 2 1 101000 f 74 goat snp32014-scaffold359-2115545 9 11024709 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392197 Affx-122966287 AX-123262554 9 10974007 GACAGCCCTGTGGCTCCCAGTTTCTCTACTGTAGC[A/G]CAAAGCCACCCTCAGGTATTAGCTAAAAATCACGT R 2 1 2 1 201000 r 74 goat snp32013-scaffold359-2082146 9 11058321 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425451 Affx-122941515 AX-123295797 9 11044280 TTCTCCCTTTTAGATGAAAAGCATATTATATGAGC[A/G]ACATCACTTGATATCTAGGGTCCTTTTCTCTTACC R 2 1 2 1 101000 f 74 goat snp32012-scaffold359-2011873 9 11128786 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787134 Affx-122928352 AX-385274160 9 11091339 ACATTGGAAATCTGGACCGTATTTCTACCACACTT[A/G]TTTAATTAACCCAGAGGCTTAAAGAGAAGTGTGGT R 2 1 2 1 101000 f 74 goat snp32011-scaffold359-1964814 9 11177591 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768653 Affx-122937473 AX-385255831 9 11143136 TGCAAATTTTACTTAAGATAACTTAATATGGGCAG[C/T]GAGAAGGACAATTATAGAGTTCCCAGAGAACATAA Y 2 1 2 1 101000 r 74 goat snp32010-scaffold359-1913017 9 11229595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403345 Affx-122957809 AX-123273698 9 11240764 GGCCACCTGAAGCTGTTTGCCTGTAGACTTGGAGC[A/G]AAAAAGCCAAGGCACCTGAGAGCTTATGTACCTCC R 2 1 2 1 101000 f 74 goat snp32008-scaffold359-1815389 9 11327382 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375754 Affx-122978605 AX-123246113 9 11300216 TTCTCACATAATAATAAAAATGAAAGACAAGTAAC[A/G]TGATTAAATTTTGGGCAACTTAGTTTTTAGGTACC R 2 1 2 1 101000 r 74 goat snp32007-scaffold359-1755937 9 11386812 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387585 Affx-122970264 AX-123257943 9 11358009 TGGTAAGTCTGACATTCTTTTATGATTCAGAATGA[C/T]GTCAGTATATTTCAGTACTCCTGTAATCTTAAACC Y 2 1 2 1 101000 r 74 goat snp32006-scaffold359-1698144 9 11443836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768183 Affx-122949068 AX-385255375 9 11393587 AGTCACAATGGCTTTAATACTCAAAATATTCCTCT[A/G]TCATTTAAAGGCACACCTTAAACTGCAAAAGGAAT R 2 1 2 1 101000 f 74 goat snp32005-scaffold359-1662566 9 11479078 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777461 Affx-122947702 AX-385264581 9 11430766 ACTCAGGCTTTGTCAGAAAGTTTACAGACACACAC[A/G]TTGATAGAGGTAGAGTGAAAATTTAAATTTTCTCA R 2 1 2 1 101000 f 74 goat snp32004-scaffold359-1625387 9 11516411 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453659 Affx-122919720 AX-123323992 9 11463217 ATACAGTCCTCAAAGGTTTCCTCACTGACATTTTG[C/T]ACCAATGTGCTCCTTGTGTGTGTTATGTTTCTCTC Y 2 1 2 1 201000 f 74 goat snp32003-scaffold359-1592936 9 11549168 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423330 Affx-122943172 AX-123293676 9 11495683 TCTATGCTTTCCACCATTTGGCTATTCCTTTGCCC[G/T]ATTATTCAGTCCACAAATATTGATTGAATGCCCAA K 2 1 2 1 101000 f 74 goat snp32002-scaffold359-1560470 9 11582750 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429247 Affx-122937906 AX-123299589 9 11525781 ACATAACAGCAACTAAAAAGGATTATGTAACATGA[A/C]CAAGCTGGATCTACCCTAGGGATGCAAGGCTGGTT M 2 1 2 1 201000 f 74 goat snp32001-scaffold359-1530372 9 11612188 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789614 Affx-122977382 AX-385276623 9 11558507 ACTACCAGATTTATCAGCACATGCATTCAGGGGAT[A/G]CAAATAAAGGTGTTTAATACATAGCTAAGTTCCAT R 2 1 2 1 101000 f 74 goat snp32000-scaffold359-1497646 9 11644748 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440134 Affx-122929690 AX-123310471 9 11609026 CTGCTTCTGGCAACCATCAATCTGTTCTCTGTATC[C/T]GTGAGCTTATATTTCTATTTGTAAAACCCGCTCAA Y 2 1 2 1 201000 r 74 goat snp31999-scaffold359-1447127 9 11695226 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416253 Affx-122948203 AX-123286602 9 11651769 AATTCGCACAAGACTTTTTGTCTGAAGGGAGAGTT[C/T]AAGAAAACAACAGGGCAGAGTGGACGAACTCTAAG Y 2 1 2 1 201000 f 74 goat snp31998-scaffold359-1404384 9 11738223 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427864 Affx-122939712 AX-123298207 9 11707277 CCTATTTTCCACCACTCTTTCTTCTCCACATTTAA[C/T]GGAGGAAATGAAAATGCTTCCAGGGTCAATCTCAA Y 2 1 2 1 102000 f 74 goat snp31997-scaffold359-1348876 9 11794219 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446174 Affx-122925741 AX-123316510 9 11753790 TAGTTCTCAGCTCAGAGTCCCAGTGCCCTGCTTTC[A/G]CAACTTTCACTCTCACAAGTGAATTTTGCTTTTCA R 2 1 2 1 102000 f 74 goat snp31996-scaffold359-1302363 9 11840473 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416284 Affx-122947943 AX-123286633 9 11786117 CGCAGCTCAGCAAGGACTGAGGGCACACATCTTCT[A/G]TAACAGCTTTTGGGGCTGCAGATGTTGCTGTCCCA R 2 1 2 1 201000 f 74 goat snp31995-scaffold359-1270036 9 11872765 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451245 Affx-122921945 AX-123321578 9 11824437 ATTTAAAAAATGGTGATTGATAAGAGAGCAATAAC[A/G]TTATCTATATAACCACTGATCGGTAAACAATCACA R 2 1 2 1 101000 r 74 goat snp31994-scaffold359-1231716 9 11911350 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778652 Affx-122927428 AX-385265763 9 11869691 CTTTACTTTCTTCTTACTAGAATTCATCCTATAGT[A/G]CAGTAAGGTCTACAAAATTTAAAGTTTTAGCCTTT R 2 1 2 1 201000 r 74 goat snp31993-scaffold359-1186462 9 11956957 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764761 Affx-122937117 AX-385252374 9 11928076 AAATTTCTGATTCATCCTGCAGGTCATGGGATTTA[A/C]CCACATCAATAATTGCATCACTCATTTTCTTATAA M 2 1 2 1 101000 f 74 goat snp31992-scaffold359-1128077 9 12016568 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782429 Affx-122932803 AX-385269505 9 11988673 GGGGTGGGTGTAAAGCTACAGATTTCATAAACCTA[C/T]GGAAATTTTCAGTATAGTGGCTGATGAAGGATAAG Y 2 1 2 1 303000 r 74 goat snp31991-scaffold359-1067480 9 12077596 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765772 Affx-122923682 AX-385253228 9 12045995 TCCTACCATCATCTCCTTCCACACTTTTCTATCCT[A/G]TAATTCATGGTCCTCAATAGATTTTATTTTTCTAC R 2 1 2 1 101000 f 74 goat snp31990-scaffold359-1010158 9 12135349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396895 Affx-122963223 AX-123267250 9 12081614 CTATCTGAGAGTTTTAAAGCTAACAGCATTACTGT[A/G]TGGACAGACGCAAAGAAGTGAATTAGTCAGTGTCA R 2 1 2 1 101000 r 74 goat snp31989-scaffold359-974539 9 12171293 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412463 Affx-122951399 AX-123282812 9 12121971 ATGGGGTCGAGCATGACTTAGCGACTGAATAGTAA[C/T]AGCCCAATCTAGTTCTTTTGAGGCCTACGTTTGAG Y 2 1 2 1 101000 r 74 goat snp31988-scaffold359-934182 9 12212465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401807 Affx-122959464 AX-123272160 9 12185267 TTGTATTTAATAAATATGATTGGATTAAGTTCTTT[A/G]CTTATATATGCCTCTCAAGGACATCGGTCACCCTA R 2 1 2 1 101000 r 74 goat snp31987-scaffold359-870886 9 12275894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419992 Affx-122945176 AX-123290340 9 12224059 CCAGTCTGCTGTTCCATGTTCGGTTTTAAGTGTTC[A/G]TTCTTGGCTTGCACAGCAACAGGTCACCTGTGTGA R 2 1 2 1 201000 r 74 goat snp31986-scaffold359-832094 9 12314742 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393260 Affx-122965460 AX-123263617 9 12253599 GCTTTCACGAGTTGGCCGAGGTGTCAGGGTGTCGC[A/G]TTGACCAAAATAAGCCACCTCATGAAAAGTAGGAA R 2 1 2 1 101000 r 74 goat snp31985-scaffold359-802554 9 12344294 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447504 Affx-122924076 AX-123317840 9 12323489 CCTTTTTGTATTCCACTTCGTGATGCTGGGGCTGC[A/G]AATCTACAAATGACAAATTCTTAACCATCTGGCTC R 2 1 2 1 101000 f 74 goat snp31984-scaffold359-732664 9 12414609 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785843 Affx-122939016 AX-385272880 9 12357124 TTAAAACTGTTGCAATGTTATATGGGACTATTTTA[C/T]ATATTTATGTTTCAATGGTGATATAGTCTCAAAGG Y 2 1 2 1 101000 r 74 goat snp31983-scaffold359-699029 9 12448382 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801410 Affx-122960563 AX-385288320 9 12405554 CCTGCCCAGGGTAACCCAGGTTTAGGCCTATTCAC[C/T]GCTAACTTCCTTATGACTAATTCTTTAAATACAGA Y 2 1 2 1 101000 f 74 goat snp31982-scaffold359-650599 9 12497174 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421828 Affx-122944309 AX-123292175 9 12458139 GGTACTCATTTTATAATTTGCAATTAATTATGTAT[A/G]TGTGAAATTGTGAATTTATGAGCCATATATTTGGG R 2 1 2 1 101000 r 74 goat snp31981-scaffold359-598014 9 12549232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794457 Affx-122947723 AX-385281420 9 12516947 CAAGAATGTCTCAGTATGATCACGTTTACCATTTA[C/T]GCCATTTGCAACCATATGCTATTAACAAAATGGTC Y 2 1 2 1 101000 f 74 goat snp31980-scaffold359-539206 9 12608634 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273964 Affx-1111833922 AX-519547569 9 12537066 TCCATTAATTGTCCTTATGTTGTTATCGTTCAGTC[A/G]CCAAATCGTATCTGACTCCTCGAGACCCCACAGAC R 2 1 2 1 202000 r 74 goat GoatD01.010511 9 12537066 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38441608 Affx-122928654 AX-123311945 9 12562897 TCATTTTGTCAGTGTGCCTAATTCTGTGTACTGTG[C/T]ATGTGCTAGCAGTATAAACACCTTTAGAAGCTCTC Y 2 1 2 1 101000 r 74 goat snp31979-scaffold359-493256 9 12653205 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278666 Affx-1111836542 AX-519552144 9 12587452 AGGCCGGGGCCTAGTTTCGTGCTGGGGAGGCAGCT[A/G]GCTCTGATACTGGATTAAGTCAGCGTAAGGCCGGG R 2 1 2 1 303000 f 74 goat Random2.2K-963 9 12587452 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416137 Affx-122948289 AX-123286486 9 12613257 GGGGGAAGCATGGGAGGTTCTCTGAAACATCCAGC[A/G]TGAACCCACCCCAAGGCTCCTCGGAAAGTGTGGCA R 2 1 2 1 201000 f 74 goat snp31978-scaffold359-442896 9 12703660 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415801 Affx-122948901 AX-123286150 9 12642537 TGATTTAATTGAAGAATACTGCTTTTCAAGCTGTA[C/T]GTTACCAACCTATTGGGCATTGTGAAATCAGTTTA Y 2 1 2 1 101000 r 74 goat snp31977-scaffold359-413616 9 12732976 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418743 Affx-122946215 AX-123289091 9 12691113 GCTCCTCTTTTCTGCTGCATTCAATCTCTTGGTGT[A/G]CATCTCCATTCATGAGGGTTTCATTCTCACTTCAA R 2 1 2 1 101000 r 74 goat snp31976-scaffold359-365040 9 12781487 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433914 Affx-122934388 AX-123304255 9 12755373 TTTAGAAATGCTATCAAGTGCTTGGGATGGACAGG[C/T]GTAGAGAACTGACACAGGAGTCCAGCTGCTAGTTT Y 2 1 2 1 101000 f 74 goat snp31975-scaffold359-300780 9 12846038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391758 Affx-122967473 AX-123262115 9 12795958 CCTGGAGCCTGTAAACATGCTGATTTCAAGTTACT[A/G]AAAAGGAATTTGTAAAACATTAAAATCACCTAAAA R 2 1 2 1 101000 f 74 goat snp31974-scaffold359-260195 9 12886633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451084 Affx-122921411 AX-123321418 9 12840115 CCCTCTGGTCTCAGAGAATGTGCTCTCTCTCCCAC[A/G]TGCCAAAACTCCACCTAGTCTTGACTCAGTTCTCA R 2 1 2 1 101000 r 74 goat snp31973-scaffold359-216038 9 12926939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391698 Affx-122967579 AX-123262055 9 12874717 AGTGGCCTTGAAGATCATGTAATCTTGATCATCTC[A/G]TATAGCTGCAAAGGGCAAACTGTGCATTTATTTCC R 2 1 2 1 201000 r 74 goat snp31972-scaffold359-181436 9 12961402 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393201 Affx-122965505 AX-123263558 9 12926194 GTCTTTGTCCAAGGCCCAGGACGTTTAGAAAATAG[C/T]GCTGTTTATTATCTTACAGTCAAATCTACGCTTGT Y 2 1 2 1 101000 f 74 goat snp31971-scaffold359-129959 9 13012878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386244 Affx-122970966 AX-123256602 9 12955837 TTTCCATTTGTTTTTCTTCATTTTTCAAATTTGCT[A/G]CAAGAATCATAGATGCTTTTTTAATCAGAAAGAAA R 2 1 2 1 101000 r 74 goat snp31970-scaffold359-100316 9 13042461 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376079 Affx-122978910 AX-123246438 9 12991411 ACTGTACACTGCACCTTTGCTTGTCTTATTTTTTC[C/T]ACTATAACTGGCCATCCATGTATCTGCCCAGCTCA Y 2 1 2 1 201000 r 74 goat snp31969-scaffold359-64742 9 13077884 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796949 Affx-122940236 AX-385283891 9 13020535 AAGCCATGATACTTGCTTTGTTGGCTTCTTGATTG[C/T]GTGAAATAATACTAAATTTTACAGTCTATGAGAAA Y 2 1 2 1 101000 f 74 goat snp31968-scaffold359-35618 9 13107223 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379823 Affx-122975824 AX-123250181 9 13053688 CCTCCTGATGGACTGACCCTTTTATCATTATGAAA[C/T]GTTCCTTATATCTTTCTCAATACTTATTTTTTTCT Y 2 1 2 1 303000 r 74 goat snp31967-scaffold359-2465 9 13141373 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439173 Affx-122931059 AX-123309510 9 13078502 GAGGACTGCTCCCAGGTGACTGAGAAGCCTGCAGA[C/T]GCCAGGACAACCTCAGGCCAGCATGGGACATCCTA Y 2 1 2 1 101000 r 74 goat snp43730-scaffold588-22250 9 13165114 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401159 Affx-122959367 AX-123271512 9 13115692 GAATAAATAAAAACAATTTTTTTTAAAAAGAAAGG[C/T]ATTATCATTTCCATCTACATGCTTCTTGTACTCAC Y 2 1 2 1 101000 r 74 goat snp43731-scaffold588-59440 9 13202091 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793205 Affx-122924936 AX-385280183 9 13146993 CTCTGGTCTCTACTTTGAGAGTTGGAGATGAATCA[C/T]GGCTTAAGCATTAGTCACCTCATATCTTTCCAGGC Y 2 1 2 1 201000 r 74 goat snp43732-scaffold588-90741 9 13233484 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389764 Affx-122968239 AX-123260121 9 13185492 TCCCCTTCTCCTGCCCTTTCCTCCTACAATGTAAA[C/T]GCTCCTTAGCAAAGTGTTGAGGGGCTAGTGGGTGA Y 2 1 2 1 303000 r 74 goat snp43733-scaffold588-129240 9 13264679 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448517 Affx-122923450 AX-123318853 9 13216357 TGAAGGCCGGTGAGGACTTGTGATGTCCCACAGTT[A/G]TCCACTTCTTCCTTTGCTCAGAACTCTCTCTCTCC R 2 1 2 1 101000 r 74 goat snp43734-scaffold588-160105 9 13295290 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433294 Affx-122935203 AX-123303635 9 13285941 GAGAGTATTCCTGGACTGAAAAAGTGCCACACAAA[C/T]ACATCCTATATGAAACACACCCCTCTGAATCTATA Y 2 1 2 1 101000 r 74 goat snp43735-scaffold588-229689 9 13363496 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442771 Affx-122927739 AX-123313108 9 13317638 CTGACTCTCAATTTGTAAACACTGTCAACTTAAAG[C/T]GATGGTGTCGAGGGAAAACTGAGGAGCAGAGCAGC Y 2 1 2 1 101000 f 74 goat snp43736-scaffold588-261386 9 13395631 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273440 Affx-1111833601 AX-519547065 9 13347660 TTAAAGCCACTGGAGGCAATAAGAGGTCTGTATTG[A/G]AACACTTTACACTTCATCGCTAAGCAATTACCAGG R 2 1 2 1 101000 r 74 goat 9_13347660_AF-PAKI 9 13347660 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320790703 Affx-122944389 AX-385277704 9 13370701 AACCAACACTAGGTAATAGTCAGAGATGACCGATA[C/T]GGAGATAACAGTAACTGAGACAGGAAGCTAGGAAG Y 2 1 2 1 101000 r 74 goat snp43737-scaffold588-314449 9 13448610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392071 Affx-122966382 AX-123262428 9 13465166 CTCAAGTAGGCAGAAATGGCTGAAACCTTCAGGCT[A/G]CTGCTTAAAGGATCTGAATGGTACTAATGTGGAAG R 2 1 2 1 201000 r 74 goat snp43739-scaffold588-408914 9 13543114 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395881 Affx-122963626 AX-123266236 9 13497442 GGGTTCCTGGCACCCTATTTCAGGAGTGGAGACGA[C/T]GTGGAAAAAATCTGACCTTACCTTGGAGAGATTCC Y 2 1 2 1 101000 r 74 goat snp43740-scaffold588-441190 9 13575856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396787 Affx-122962758 AX-123267142 9 13536883 TCACACACTTCCCTTTGCTCTTCAGGAATACAACC[A/G]TCATGCCCAAACTGGGAAGGCCAAACTAGCCCATG R 2 1 2 1 101000 f 74 goat snp43741-scaffold588-480631 9 13615721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416752 Affx-122948190 AX-123287100 9 13569159 GCTTTTATTGGCAAATGAATAAGCATCATGCCTAG[C/T]ACTTAGCGCTCAAAAATTAGCTAGTTTCTATTTCC Y 2 1 2 1 101000 f 74 goat snp43742-scaffold588-512907 9 13647775 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423880 Affx-122942301 AX-123294226 9 13620128 CTAATAGGAGAAAAACACTAAACAGCTACATTGTC[A/G]ATGGAAAAATCATGCTGGACTGTGGTCTCCAGGCC R 2 1 2 1 101000 r 74 goat snp43743-scaffold588-563876 9 13700768 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394677 Affx-122964364 AX-123265032 9 13665257 AAAGTGGTTAGATTAAACTTTGGCTCCCGGCTACA[C/T]GTTTCCAGCACCAAAAATAACCATATGGCATTGAG Y 2 1 2 1 101000 f 74 goat snp43744-scaffold588-609005 9 13746129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393547 Affx-122965413 AX-123263903 9 13696315 TCCCTGTTAAAAGTGGCAGTGATTAGGAAAAAGCA[C/T]ACAGCCACCTTCTACCCACAGGTTCCAACTGCGTG Y 2 1 2 1 101000 f 74 goat snp43745-scaffold588-640063 9 13777586 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382442 Affx-122974229 AX-123252800 9 13731599 TCTGTTTTTAACAGGAATAGAATATTATAATTGCT[A/C]ACAGGGAACAAGTTGAGAATATTTGCAAACCTGAG M 2 1 2 1 201000 f 74 goat snp43746-scaffold588-675347 9 13812226 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788650 Affx-122960208 AX-385275665 9 13770886 GCATAAAGTCTTGTCTCTTTTAGGTCTATTCTTTG[C/T]AGAAGAAATACTGGTATAGTGGAGAGTGTATATAT Y 2 1 2 1 101000 f 74 goat snp43747-scaffold588-714634 9 13851388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447180 Affx-122924420 AX-123317516 9 13802244 GGCTCACTGAGACTTTCAGCCCACATTCGGTTAGC[C/T]CAGCAAGCCACATGTCTGAGACCAAGTCAGGATGT Y 2 1 2 1 101000 f 74 goat snp43748-scaffold588-745992 9 13882168 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438170 Affx-122931839 AX-123308508 9 13831096 TTGCTTGTACTGATGTGTGTAGAGAAAGTGTGGGA[C/T]GCAGGGAGTGAGGAAAGACAATGGAAAGCAATTAA Y 2 1 2 1 101000 f 74 goat snp43749-scaffold588-774844 9 13909226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432795 Affx-122935414 AX-123303136 9 13873820 ATGAGAACAAAGGAATGAGGGGAAAAGTGAAGAAA[C/T]GAAAAGCGGGAGTGCTTTGAAAAACAGAGAAAAAA Y 2 1 2 1 101000 f 74 goat snp43750-scaffold588-817568 9 13952783 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443380 Affx-122927404 AX-123313717 9 13905673 GTATTTCTTCTTCTTATCATTTCTATAATGCAGCA[A/G]TAACTCTGACATCTCTATAGGTTAAAGTTGTCATC R 2 1 2 1 101000 r 74 goat snp43751-scaffold588-849421 9 13984756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435823 Affx-122932831 AX-123306162 9 13941545 CTACTGGGTCTGAGCTACGGGATCGCCCAGATCTA[C/T]ATCAGCCTGCTCAAATTTATCTTGACAGTGCCTTT Y 2 1 2 1 201000 r 74 goat snp43752-scaffold588-885293 9 14020992 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320797322 Affx-122972233 AX-385284261 9 14008521 GAAATTTCTACTTGACAATCCTGGGCCAAAGTAAT[C/T]CTGAGACAAAAGAACTAGTCTTGTCTACTCTCCTT Y 2 1 2 1 101000 f 74 goat snp43754-scaffold588-952269 9 14087795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423315 Affx-122943186 AX-123293661 9 14091709 TCTCTGACCATGAAATATATGTATTTTAGGGACCT[A/G]TTACTTAATAAAATCAGGTATTTTTCCTCACTTCT R 2 1 2 1 201000 r 74 goat snp43756-scaffold588-1035457 9 14171331 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444659 Affx-122926460 AX-123314996 9 14143970 CAGAATTTTTTTTCCAAAAATTATTTGATGACTTA[C/T]GAACAGGAATTATTTAGACTGTTAAAATGTAATTA Y 2 1 2 1 201000 r 74 goat snp43757-scaffold588-1087718 9 14223972 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764935 Affx-122946505 AX-385252516 9 14178321 CTTGCACAAAGTCATGGAGACCACAGAGAAATCCA[G/T]ATATTTAGATCCAGAGTCCACTTTTCCAACCACAG K 2 1 2 1 101000 f 74 goat snp43758-scaffold588-1122069 9 14257904 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801457 Affx-122962202 AX-385288366 9 14207732 GCTGTTGATTATATAACAGGCTTATTAAAGATCAA[C/T]AGCAAGATTAGAGCAAAGTGGTAGCCAGGTATTTG Y 2 1 2 1 102000 r 74 goat snp43759-scaffold588-1151480 9 14287161 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439997 Affx-122929792 AX-123310334 9 14237042 ACTTAATTTGTTACTTTTTGGCTATTTCATCTTTC[A/C]TGGTACTCAAACCCAGTAAATTGGTACTTCAAAAA M 2 1 2 1 101000 r 74 goat snp43760-scaffold588-1180790 9 14317759 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403793 Affx-122957975 AX-123274145 9 14277594 TAGCTATCACCTCAGTAGGTATCAAGATGTCACTA[G/T]CAGGTGAAATTCAAAGACCTGGAAAGTGAGGACCA K 2 1 2 1 101000 f 74 goat snp43761-scaffold588-1221342 9 14357870 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773973 Affx-122938105 AX-174710767 9 14359941 TAATTCACTTATAAAATGCATGGAGAAAATTGATA[C/T]GGCAGATCCTGGTGTGAGTCTCCTTTTAACAAATT Y 2 1 2 1 101000 r 74 goat snp43763-scaffold588-1303689 9 14439965 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432846 Affx-122935370 AX-123303187 9 14409830 AACCTGCTATTGGATATCATATACATGTTGGCCAG[C/T]GCCCCAGATGCTAAATTTAAGACACTAATCATTGT Y 2 1 2 1 201000 f 74 goat snp43764-scaffold588-1353578 9 14489047 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404133 Affx-122957097 AX-123274485 9 14455002 GTCAGCAGAGAGAATCCTCTGCTGTTGAACTTGAA[C/T]GGCAAGAGTCTGGTTACAGAAACATACTGGTTATA Y 2 1 2 1 101000 f 74 goat snp43765-scaffold588-1398750 9 14534276 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793621 Affx-122947851 AX-385280595 9 14490151 AGATAAAATTAATTTTCATGTGTAGGAGAAAAACT[A/G]TTTCAGAAGTATATGCACAAACTAAAAATATGATG R 2 1 2 1 201000 f 74 goat snp43766-scaffold588-1433899 9 14569416 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775664 Affx-122933112 AX-385262795 9 14559344 CACATGAGGAATAGATATTAGACATATTAGACATA[C/T]GAGGAATAAGGAGGTTTGGTTTGTTGTGTTGACTA Y 2 1 2 1 101000 r 74 goat snp43767-scaffold588-1503092 9 14639384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793176 Affx-122938250 AX-385280154 9 14608432 AAGAGCTAAAGATACATATACAAGGATACAGCATA[A/G]CCTGCTTTAGAATTAATGCCCTTTGTTAGAGCTTT R 2 1 2 1 101000 r 74 goat snp43768-scaffold588-1552180 9 14688456 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451469 Affx-122921141 AX-123321802 9 14641136 CTGCAGAGGGAGATGGATGCATCATTTTATCCACA[C/T]GGATCTTTCTCCAGTTTGCGTCTGTGGGCACAGAG Y 2 1 2 1 101000 f 74 goat snp43769-scaffold588-1584884 9 14721327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411506 Affx-122951682 AX-123281856 9 14691468 AGCTGGGTCATGACGGAGACATACCTGGTTCCCCC[A/C]CAGACGCACATCCCTCAGTCTCACCAAGACCTCGG M 2 1 2 1 101000 r 74 goat snp43770-scaffold588-1635216 9 14771519 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397123 Affx-122962682 AX-123267478 9 14724319 AGATGTAATTGGTAAGATTCACTTGGACTTGACCA[C/T]GAGGCTGGAAAGAGAAGGTCATGTATAGCATGAGA Y 2 1 2 1 101000 f 74 goat snp43771-scaffold588-1668067 9 14804618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442070 Affx-122928379 AX-123312407 9 14759064 GTGTGCTGCAATAGATGTAAACCATCACTCCTTTC[G/T]AGCAATCAGACACTTCCAATGGAGGTGGCTGGATC K 2 1 2 1 101000 f 74 goat snp53226-scaffold802-11917 9 14843663 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274954 Affx-1111834599 AX-519548536 9 14820358 CAAGTCTGGGGGTGCCGGCTCCACTACAGAACATA[A/G]CAAA R 2 1 2 1 102000 f 74 goat GoatD01.042755 9 14820358 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38408137 Affx-122954236 AX-123278488 9 14824938 CAACCAGATGATAGGAAATATTTTTGTTTTATAGC[A/G]TTTTACAAGGTGTGTTGATTCCTTCTTCCCATTGA R 2 1 2 1 101000 r 74 goat snp53227-scaffold802-77791 9 14909472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778728 Affx-122961261 AX-385265839 9 14870817 CAGAAGGGTTTTTGTCCTGTGTATGGAATCCTTCC[C/T]TTACTGTTAGTTGAACCACATTTTACTGCTCTGTA Y 2 1 2 1 101000 f 74 goat snp53228-scaffold802-123670 9 14951168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394049 Affx-122964987 AX-123264404 9 14931016 ATTTCTTACTAAATGCAATGTTGAAACACTGTTCC[A/G]ATAATACTGTTGTCTACTTTGATCAGAGTAGAGTC R 2 1 2 1 101000 f 74 goat snp53229-scaffold802-183869 9 15011769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436019 Affx-122932741 AX-123306358 9 14994161 CACCACAGAGCAAGCAAGGCTGGAGGGGTGCTTGG[C/T]TCAGGCTGGGCATGAGCTGTGGTGGTCACCGGACA Y 2 1 2 1 103000 r 74 goat snp53231-scaffold802-247014 9 15074881 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404480 Affx-122956724 AX-123274832 9 15079531 AGGTGAATTTAGTGCCTGATAAACAGATTTGTGAG[A/C]GACTGATGCTTAAAGGGATGAGGTATAACTGAAAA M 2 1 2 1 101000 f 74 goat snp53233-scaffold802-332384 9 15159558 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789976 Affx-122968955 AX-385276982 9 15121728 AAACCTGAGGACAAAGTACAGCTGAAAGTGTTTCT[G/T]TAAAAATATAACTTAATTCTTCTTCAGATTGCTTG K 2 1 2 1 201000 r 74 goat snp53234-scaffold802-374581 9 15201864 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388167 Affx-122969446 AX-123258525 9 15160640 TTATTATTCTACATTGAGGTTTAAACTAGGAACTG[C/T]GTTACAATGCTAAGTGGAAATTACTGATTTTACAA Y 2 1 2 1 101000 f 74 goat snp53235-scaffold802-413493 9 15240841 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381929 Affx-122974133 AX-123252287 9 15194662 CACCTTACTGATAGCTTATTGACTCCACTGTGTGT[A/G]TGTTAGTATTTTGATCTTGGTTTCAAACACATGTT R 2 1 2 1 201000 r 74 goat snp53236-scaffold802-447515 9 15274771 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781027 Affx-122953191 AX-385268114 9 15224365 TATTGAAAAGTTGGCGCATTGTAATCAACATAAGC[A/G]TGTTCTTTTTTTAGCTTACCCATTTATGTCTCAGT R 2 1 2 1 201000 r 74 goat snp53237-scaffold802-477218 9 15303972 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402095 Affx-122958695 AX-123272448 9 15254930 GAACCTGCCCGTCAAGGAACTCTAGACTTTTTGCC[A/G]CAGAGGGCTATGGTTTCTTTTGTGTAGAGCAGTGA R 2 1 2 1 101000 f 74 goat snp53238-scaffold802-507783 9 15334732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435160 Affx-122933664 AX-123305500 9 15317829 TCTAGAGCAGAGAACACACTACTTCCTCGCACAGC[A/G]TCTTACACAGGCTCCTTGTCCCCCAGTTCTTCTTA R 2 1 2 1 201000 r 74 goat snp53239-scaffold802-570682 9 15397916 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407081 Affx-122954905 AX-123277432 9 15361365 TGCCTAGGTCCACACACATCTTTGAATGGCATAGA[C/T]AGAGCCTGACCTCAAAATATCATCAATCAAAGCTT Y 2 1 2 1 101000 f 74 goat snp53240-scaffold802-614218 9 15441562 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388855 Affx-122968874 AX-123259213 9 15391968 AGGATAAAGAAATTTAGTTTCGTCCGTGTTAAATG[C/T]GGTATTCCATTAAATATCCAAATGAAATGTTTAGA Y 2 1 2 1 101000 f 74 goat snp53241-scaffold802-644821 9 15471882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403930 Affx-122957468 AX-123274282 9 15431520 GCCTTCAGAGAAGAGTGGCATGCTCAGTCATGCTG[C/T]GGGAACACCTATCTAGCAGGGCTGTGTAGTTTGTT Y 2 1 2 1 101000 r 74 goat snp53242-scaffold802-684373 9 15511431 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434599 Affx-122934100 AX-123304940 9 15491981 TAAAAAGCTTCCTGTAATTCTATGCCATTTCCCCC[A/G]CAAAAACTGTTTAATTCTACAATGTTATTTCCAGG R 2 1 2 1 201000 r 74 goat snp53244-scaffold802-744834 9 15571766 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406043 Affx-122955478 AX-123276395 9 15610627 TCAGCTCAATGTACTTGCCTGGAGACACATCTTTA[C/T]GGTCTGGGATAAAATTCATTGCCTGTTTCTATTTA Y 2 1 2 1 201000 r 74 goat snp53247-scaffold802-863480 9 15690670 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405181 Affx-122956927 AX-123275533 9 15673844 GGACAATGGCAAATACAATGCCTTGCAGGTATAAG[C/T]AATGCTGTTTGTCAAATGCAGAGTAGTAGCTAATG Y 2 1 2 1 101000 f 74 goat snp53248-scaffold802-926697 9 15754057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453856 Affx-122919533 AX-123324189 9 15707498 TGTGGGGATAGGCCAAAGTGAATGAAGGAGGGCAA[C/T]GATTTGAAACAATTGCAAGGTTTTATGTTTAGGGA Y 2 1 2 1 201000 r 74 goat snp53249-scaffold802-960351 9 15787594 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397379 Affx-122962275 AX-123267734 9 15775150 GTGGCATCATAGTTATGGAAGCTTATTTTATCACA[C/T]GATTTATGGGGTGCTTTTTTCTATTTAAAAAGGAA Y 2 1 2 1 101000 f 74 goat snp53251-scaffold802-1028003 9 15855893 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405105 Affx-122956982 AX-123275457 9 15811129 ATCTTGGAAAGCAGACATCTGCTTCCACTGAGGGT[A/C]TTAAGCTGCTAGAAGACGGAAAGCCTGGAGTTGGC M 2 1 2 1 201000 r 74 goat snp53252-scaffold802-1063982 9 15892003 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380477 Affx-122975721 AX-123250835 9 15843349 GGTTAAAAGTGAAACAATAACATTAAAATACATGA[C/T]TCTGGATTATATGAAAGTATACTTGCCTTTATGGT Y 2 1 2 1 201000 r 74 goat snp53253-scaffold802-1096202 9 15924791 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273404 Affx-1111833602 AX-507461781 9 15878755 GTACATGTAACCATTCTTACATTCTTCCCATTCTC[A/G]GTATATTTTCTTTCTGATTGGGTTCTAAACATTTA R 2 1 2 1 101000 f 74 goat 9_15878755_AF-PAKI 9 15878755 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394046 Affx-122964989 AX-123264401 9 15881041 GTATACCGTCTGTGCTTTGGCTTGGCTATGTTCTA[C/T]CTTCTTCTCTCTCTCTTAATGATCAAAGTGAAGAG Y 2 1 2 1 101000 f 74 goat snp53254-scaffold802-1133894 9 15961924 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381406 Affx-122974370 AX-123251764 9 15966865 GTTGAGCCTTGAAGAAATGGGATGAACAAAGGTTC[A/C]GAGGAAGAAATTCCTTCTTTCCCCTTACTTTTCCC M 2 1 2 1 101000 f 74 goat snp53255-scaffold802-1219718 9 16048221 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801380 Affx-122937330 AX-385288291 9 16024682 TTTTAAAAACTGTTATCAAGATTCTAAAATTTCCA[C/T]GCTTGGCAAATTTTTATATTCCATGGTGAAAGCTA Y 2 1 2 1 201000 r 74 goat snp53256-scaffold802-1277535 9 16105540 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774336 Affx-122932003 AX-385261472 9 16069296 TGGTATAATTGATCCCAATCATCTTCAATTTTTTT[A/G]TGCAGAAGTTATTCTAGCATTGGCTTCTTAAGAAC R 2 1 2 1 201000 f 74 goat snp53257-scaffold802-1322149 9 16151825 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793308 Affx-122926546 AX-385280286 9 16108862 AGCATACCTCTCTAGCCATAAATGTCTGAAAATCT[A/G]CTGTTTGCACTTCTATCTATAATGCTCAATGTTGA R 2 1 2 1 101000 f 74 goat snp53258-scaffold802-1361715 9 16191153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278850 Affx-1111836543 AX-519552321 9 16167210 TGGACAATCATCTGGCAAAGTAAAGCTGAAAATAA[A/G]TGTTGGTGTTTAAGAACTTCAAAAAATATCATCCC R 2 1 2 1 101000 r 74 goat Random2.2K-966 9 16167210 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785649 Affx-122971885 AX-385272691 9 16175239 TCTAAGTGAAGGTCTTAGAGGACCAAACAGAGGTT[A/G]CTTTGACAAAGCAATTCTAAAATTGAATATTAGAA R 2 1 2 1 201000 r 74 goat snp53260-scaffold802-1428092 9 16257928 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389046 Affx-122968617 AX-123259404 9 16240102 TAGTTAAAAATTACAGTGTTTTTCATGATGCCAAG[A/C]GTAAATTAGTAAATTCTATGCTAAAGGCATAAAAG M 2 1 2 1 201000 r 74 goat snp53262-scaffold802-1492955 9 16324351 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407981 Affx-122954330 AX-123278332 9 16274933 TAAGGACTTGTTCCCTCTTGGGTGTGCCACTAGTT[A/G]TATAGTTAAGTGTTAGGATTATTAAAAACTATGTC R 2 1 2 1 201000 r 74 goat snp53263-scaffold802-1527786 9 16359708 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786465 Affx-122972389 AX-385273499 9 16304710 ATTTGTAGGTCCTAAAATAGACTCTGATATTTCAC[A/G]TATCTCTACAATAAAGCTAATGCAGTTCTAAGTAT R 2 1 2 1 101000 f 74 goat snp53264-scaffold802-1557563 9 16389372 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447453 Affx-122924367 AX-123317789 9 16372175 TTACAAAAATATCATAATGAAATAAACTTAACAAT[A/G]TATCTTTTACTAAATGTCAGATATCTATCATGCGC R 2 1 2 1 101000 r 74 goat snp53265-scaffold802-1625028 9 16457547 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448597 Affx-122923394 AX-123318933 9 16409219 TCTTCACTTTTCCTATATTTGCGCATATTTCCTAT[A/G]TTTGTTTTCCAAGTTTCATCTGGTTGTTGTTCAGT R 2 1 2 1 201000 f 74 goat snp53266-scaffold802-1662072 9 16495475 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441562 Affx-122928689 AX-123311899 9 16479391 CAGAATAATGAACAACCCACACTCAAAGGATGCAT[A/G]CTAGATTCTGGGACAATGTTTTTGGTCACACAATT R 2 1 2 1 101000 r 74 goat snp53267-scaffold802-1732244 9 16568750 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380290 Affx-122975408 AX-123250648 9 16519527 AGGAGTTAGGGGTGCCAACTTCGAAAGTTCACATA[C/T]AACTTATAGTAGGCCTTCTGTATCCTTGGCTCCTC Y 2 1 2 1 101000 f 74 goat snp53268-scaffold802-1772380 9 16608869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421730 Affx-122944383 AX-123292077 9 16573701 GGTAGAAGACAAAAAATGGAAATTTAAAGGGTCTG[C/T]GTCTGGCATGGTAACAGGGAAACAAGGAGGTTATC Y 2 1 2 1 101000 r 74 goat snp53269-scaffold802-1826554 9 16663485 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389864 Affx-122968150 AX-123260221 9 16646117 GAGAAGGAAAGGATTCTTCAAGAAATGTGTTTTAA[C/T]GGTGGAACGATCTTTAGGGTTTTTAACCAACCAAG Y 2 1 2 1 101000 r 74 goat snp53271-scaffold802-1898970 9 16737065 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449015 Affx-122923091 AX-123319350 9 16701993 CTCAAATGAGAAGCATCTGAATGAGCAGCTAATGC[A/G]TGAAGCAAGAACTGAAAGCAAAAAGAAGATGGATC R 2 1 2 1 101000 f 74 goat snp53272-scaffold802-1954846 9 16792820 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789054 Affx-122957017 AX-385276067 9 16746848 ATTGGGGTGGAAGGGATCCCTCCCACTATTATATC[A/C]TCCTCTGAATTTTGTGTCTGTCCTTTGAAGCAAAG M 2 1 2 1 101000 r 74 goat snp53273-scaffold802-1999701 9 16837750 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416207 Affx-122948238 AX-123286556 9 16816845 AAAGATTTATTCAAAATAAAATTTAAAGATGGGGT[A/C]GGAGAGTTCGATTGATGCTAATTTTTCGGCCTGAA M 2 1 2 1 101000 r 74 goat snp53275-scaffold802-2069698 9 16907186 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386174 Affx-122971378 AX-123256532 9 16848990 GAAATGGATGATAAAGAAGCTAATAATATTGTATC[A/G]TATTAAACTTCCTGAGTCTGATAATGATATGGAGA R 2 1 2 1 101000 r 74 goat snp53276-scaffold802-2101843 9 16939334 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390095 Affx-122968023 AX-123260452 9 16903699 GAAACAACACAGTTATCTTTAAGGCATCATGCTTC[A/G]TAGGAATTATAAATTTTATATGTATTAAAAAGTAA R 2 1 2 1 101000 f 74 goat snp53277-scaffold802-2156552 9 16994587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452755 Affx-122920265 AX-123323088 9 16938458 ATGTGTACTGGTAATAACACAATAAAGGAGTAATT[A/G]TTTCACTGCATATTGTTCAACCCTAAATGTATATA R 2 1 2 1 101000 r 74 goat snp53278-scaffold802-2191311 9 17029696 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430354 Affx-122937797 AX-123300695 9 16995951 ATATAGAATGAAACATTTTTAATAGCTCTACAATA[C/T]ATTTTTGTATGATTTTACCATAATTTATTCAAATT Y 2 1 2 1 101000 f 74 goat snp53279-scaffold802-2248804 9 17086165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798973 Affx-122942586 AX-385285903 9 17120633 AGAACTATGATCTTAGAAACATTCTTAATGAAATA[A/G]AGTATAACACAACAATGGTCATACAAGCAGAAGGA R 2 1 2 1 101000 r 74 goat snp18910-scaffold1905-32338 9 17215586 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414266 Affx-122949611 AX-123284615 9 17167814 AGCTTATTTTGCAGTGCAGTACTCAACTCATCACA[C/T]ATTTACTGTTGGGTCATTTTCAGAAATATGTATCC Y 2 1 2 1 101000 f 74 goat snp18911-scaffold1905-79519 9 17262773 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400825 Affx-122959798 AX-123271180 9 17244450 ACAAAAAGTTGAATAACCATCTCCTTAGCCTTAGC[A/G]TGGACAAAGTGGGAGTTTTTTTTGTTTGCTTATTT R 2 1 2 1 101000 f 74 goat snp18912-scaffold1905-156155 9 17336848 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777971 Affx-122972846 AX-385265087 9 17317259 AGTGGAACGAGACTCTGGTAAAGTCCTTTTCTTCA[G/T]AGAATGGCACTTTGATATAGAGGATATTTTGTACC K 2 1 2 1 101000 f 74 goat snp25769-scaffold2651-4061 9 17409952 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400931 Affx-122959718 AX-123271284 9 17358644 ATCATATGAATGAGGGAATAGCCTAGAGACTTTCT[A/G]CTGGGTAAATTGTTTTCTAAGATATTTATATCATG R 2 1 2 1 101000 f 74 goat snp25770-scaffold2651-45446 9 17452668 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387072 Affx-122969889 AX-123257430 9 17412909 CAAACTCTGAATAGATGACACGTGAGCTAATAACA[A/G]AAATAAACTTTAGGGAGACTGGAAAAAGAGAATGT R 2 1 2 1 101000 f 74 goat snp25771-scaffold2651-99711 9 17506449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776777 Affx-122940477 AX-385263901 9 17442338 ACTGCATTCCTATACTTTGACTTAGCTTGCAAAGA[G/T]CTTGATAACATGGTACTATATTTGACTGTTGCAAC K 2 1 2 1 201000 f 74 goat snp25772-scaffold2651-129140 9 17535663 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786341 Affx-122959660 AX-385273375 9 17519705 CCAAATTTGAGCATTCTGCTATATGTCTCTGATAA[C/T]ATTGCTTCTCCCATGCTAAAAATGCCCAAAGTAAC Y 2 1 2 1 101000 r 74 goat snp19363-scaffold1955-598583 9 17613295 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406057 Affx-122956252 AX-123276409 9 17560032 AATGCAAATCAATTACATACACACATAAATTAGGA[A/G]TCACATCATTAGAGCTCTTAAAAATTTAGGGACTG R 2 1 2 1 101000 r 74 goat snp19362-scaffold1955-558256 9 17653652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398145 Affx-122961684 AX-123268500 9 17601783 ATATCTGCACTGACAAGTGAAGCTGGAAGGGCTCC[A/G]CAGCACCCACGGGGGCAGTATTGGTTCACTCATTA R 2 1 2 1 101000 f 74 goat snp19361-scaffold1955-516505 9 17695407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278853 Affx-1111836544 AX-519552323 9 17602361 TCTGTCATCTGAGCTGGAAGCAATCAGAAGCCAGC[A/C]ATGAAGGATTAAAGTGAAATACTTTAGGTGTATAC M 2 1 2 1 201000 r 74 goat Random2.2K-967 9 17602361 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278671 Affx-1111836545 AX-519552149 9 17621360 CCTAAAGTGATAAACTAATCAAATGTTGAAATTCA[A/G]GAAATGCTGCACAATGAAGCATACTATTCTTAATG R 2 1 2 1 101000 f 74 goat Random2.2K-968 9 17621360 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437853 Affx-122932082 AX-123308191 9 17632966 CACCGAAATACTGTCCCAGTTTGTCTGTGCAAACA[A/C]TATGATATATGGTGGACACCTGTTTTCCTCTGGGT M 2 1 2 1 201000 r 74 goat snp19360-scaffold1955-485322 9 17727051 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451260 Affx-122921932 AX-123321593 9 17664774 AACTGAACTTATTTTTTTCCTATATGTCCCCTGTC[A/G]TTTTCTATATAAACTTTAATCATTTCTGTCTATAT R 2 1 2 1 201000 r 74 goat snp19359-scaffold1955-453514 9 17758940 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388516 Affx-122969209 AX-123258874 9 17702160 CAGGGCTTGTATGTGAGGGTTGTCTGCTGTTTCTG[C/T]GATGAACTGGAGGGAAGGGCAATAGCCAATAAGTG Y 2 1 2 1 201000 f 74 goat snp19358-scaffold1955-416128 9 17796935 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769556 Affx-122941326 AX-385256726 9 17746993 TGTGCCACTATTGTTCATAACTAAAGCATTCATAG[C/T]ACCAGTGCCTTGGATTATTACTGTTTCATGTTTTT Y 2 1 2 1 201000 r 74 goat snp19357-scaffold1955-371295 9 17842176 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784234 Affx-122935095 AX-385271285 9 17802247 CTCATTTATCTTTCATTTCTAGAAATGCAAACACT[A/G]CAAGCATTGTACAGAGTTGATCATTCACTCATTTA R 2 1 2 1 101000 f 74 goat snp19356-scaffold1955-316041 9 17898831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799175 Affx-122937736 AX-385286105 9 17868580 ACACTCTATTATACTAATTTATAGGGAGAAGGACT[A/G]CTTGGTGGGTTTAACCATGAGATTCAAGGTTATGA R 2 1 2 1 101000 r 74 goat snp19355-scaffold1955-249708 9 17962439 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430851 Affx-122937426 AX-123301192 9 17914010 ATATATATATCAGCTTCAACTGATTTACAGTGTTG[A/C]TCAAACCTTTTGTCTTTTAATTTATGTTTTCTCTG M 2 1 2 1 101000 f 74 goat snp19354-scaffold1955-204278 9 18005427 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437624 Affx-122931814 AX-123307962 9 17963156 AAAATAAAGTCTGACACTGTTTCCACTGTTTCCCC[A/G]TCTATGTCCTATGAAGTGAATGTTTTAAAATTTGG R 2 1 2 1 303000 r 74 goat snp19353-scaffold1955-155132 9 18055508 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789631 Affx-122967945 AX-385276640 9 18045647 TTATCTTGTATTGAAATTACATTAATATTTTCAAG[C/T]TCTTGCTTCATTTTCTCACAGAATCCATTATGGCC Y 2 1 2 1 201000 f 74 goat snp19351-scaffold1955-72641 9 18140922 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278673 Affx-1111836546 AX-519552151 9 18069682 GAAATTTATAAAACAATATTTTCCCTCCTTTGACT[A/G]TTTATTCATTTGTTTTTAACTGTGAAAATATTGTT R 2 1 2 1 102000 f 74 goat Random2.2K-969 9 18069682 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786170 Affx-122967609 AX-385273206 9 18117222 TGAGTTGAACTTGGTGTAGAGTAATTTACTGGGAA[C/T]GCATGTTGCCATCATTTGGGATTAAATAAGGGAGA Y 2 1 2 1 101000 r 74 goat snp19349-scaffold1955-1066 9 18210321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775923 Affx-122952200 AX-385263054 9 18138178 CACAACACTGGAGCCAGTGTTCATTACAACTTCTC[G/T]CAGTGCCATTCACTTCCTTTAAAGGTCAAAGAAAC K 2 1 2 1 101000 f 74 goat snp433-scaffold1011-19791 9 18239904 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792088 Affx-122922138 AX-385279075 9 18169521 GACTAAGTTCTGTGATTCTGGTATTAAATATGACT[A/G]TTATTAAATTATCAAATATTGGTTTGTGAGACTTC R 2 1 2 1 303000 r 74 goat snp434-scaffold1011-51134 9 18271748 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453791 Affx-122919580 AX-123324124 9 18226450 ATGCTGCTCTGTTGTTCTTCAACTGTTGCCAAAAT[A/G]TACTGGAAAGGGGAACAAAATTGAGTGTTTTTAGC R 2 1 2 1 101000 f 74 goat snp435-scaffold1011-108063 9 18325570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427939 Affx-122939211 AX-123298282 9 18277903 GTTTTCTGGGGGCTGTGATGCTTTTGCTGGATTTT[A/G]TGGAATGAGCAGAAATGAAAGAGAGGAAGTGGGGA R 2 1 2 1 101000 f 74 goat snp436-scaffold1011-159516 9 18377539 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38389470 Affx-122968333 AX-123259828 9 18327796 CATATTCCCAAACTCTGCTCTGTTTTCTTCTAATA[G/T]CTGTGACTGAAAGAAATGATCTTGAGTTCCTGTTC K 2 1 2 1 101000 r 74 goat snp437-scaffold1011-209409 9 18427111 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413049 Affx-122950981 AX-123283398 9 18373915 ATTATTTCCTCTCTTCTGCTGTTTTAGCCCTTCCC[A/G]TTTTCAGTTTGGAGCACTGACTGGTGACTTATCTT R 2 1 2 1 201000 r 74 goat snp438-scaffold1011-255528 9 18473407 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273444 Affx-1111833603 AX-519547068 9 18387479 TAAGTGAATGCTCTGAAGGGTCAGAACCCCAGTCT[A/G]AGAGACTCCATAAATCAGTGCTCTTGGTTGGGGGT R 2 1 2 1 201000 r 74 goat 9_18387479_AF-PAKI 9 18387479 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38375864 Affx-122978513 AX-123246223 9 18422381 AACGAAGTTGAAACAGAAATGCCAGCTGAGAAGGT[A/G]TTTAATCTTCAAGGTGTGAGGTATTACATTCTAGC R 2 1 2 1 201000 r 74 goat snp439-scaffold1011-303994 9 18522963 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376602 Affx-122979057 AX-123246961 9 18456552 CTAGGTTTAAACTTCAGGTGGACAATCTACATAAC[A/G]CCAGAAGAATTCCAAGATTACTGTTCAGGGTGGAT R 2 1 2 1 101000 f 74 goat snp440-scaffold1011-338165 9 18557151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785946 Affx-122940083 AX-385272983 9 18523390 AGACTCTTAAGTGCTCTGAGTTTCACAGATTTAAA[C/T]ATTTTCTGAAAAAGCCAAGGAATGAATCATGGAAT Y 2 1 2 1 101000 r 74 goat snp441-scaffold1011-405003 9 18624626 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399040 Affx-122960918 AX-123269395 9 18572549 ACTATCACACCTATCCCCCATGTGTCTGAAATTCC[A/G]TTATTAGTAGTTCAGTCCTTTGAATCTGGTAGGAT R 2 1 2 1 201000 r 74 goat snp442-scaffold1011-454162 9 18674503 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446405 Affx-122925572 AX-123316741 9 18609971 GAAATATTTACATTTTAACAAGACAAGAAAAGCAC[A/G]TTCTTTGTTCAGCTACTCCACATTAATTAAGTATA R 2 1 2 1 101000 r 74 goat snp443-scaffold1011-491584 9 18711562 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404574 Affx-122957367 AX-123274926 9 18646401 ACAGTGACAAGGATGAGAAAAGACTCATGGATAAG[C/T]GGCATGAGTATCACAGGGAAGGAAAGAACTTCAGG Y 2 1 2 1 101000 f 74 goat snp444-scaffold1011-528014 9 18748096 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393432 Affx-122965866 AX-123263788 9 18676389 CAGTAAGCCTCCCCAAAGGTAATCATTTCTTTGAC[A/G]TCAGTTACATTCTTGAACTTTATATAAAGGCACTT R 2 1 2 1 101000 f 74 goat snp445-scaffold1011-558002 9 18778582 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774794 Affx-122949747 AX-385261928 9 18717506 ACGGTTGAGTTTACTAGGGAAACACTATAATGTCA[C/T]GCAGTACCAAGTGCCTATTTAAGGGATTTAATATT Y 2 1 2 1 101000 r 74 goat snp446-scaffold1011-599119 9 18819840 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448614 Affx-122923382 AX-123318950 9 18782676 CCCCACCCCATGAAAACTTCATAAATAAATAAACT[A/C]TGGGACTTCCATGAAATTTATAATACATACATAGT M 2 1 2 1 201000 r 74 goat snp447-scaffold1011-664289 9 18885367 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411317 Affx-122952282 AX-123281667 9 18835852 GAAAGTCAAAGTGAAGGAGCAGTTTTCCAGCCCAC[A/G]TAGTTTTGTGGGTAGGCTTTAAATGTCCAGCTTCC R 2 1 2 1 101000 r 74 goat snp448-scaffold1011-717465 9 18938607 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425066 Affx-122941258 AX-123295412 9 18868082 ATAAAGATTTTTTTCCCTGAAATCTGATAAACGTC[A/G]TATCAAAGGAAGCATAAGCTATTTGGGTTTTCATT R 2 1 2 1 101000 r 74 goat snp449-scaffold1011-749695 9 18966777 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770033 Affx-122925976 AX-385257200 9 18902404 AAAAGCCTAAACTCAGAAGGTGCAGGTCTATATGC[A/G]TATCTTTATCAGCTCACCTTACATATGTTTAAAAT R 2 1 2 1 101000 f 74 goat snp450-scaffold1011-784017 9 19001124 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438855 Affx-122930762 AX-123309192 9 18954516 GAATAATTAAAATAGCACTTAATTTTGTTTCTGCA[C/T]ATGTTTGGTATACATTGTGTGATACACATATAAGT Y 2 1 2 1 101000 r 74 goat snp451-scaffold1011-836129 9 19053809 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375494 Affx-122979134 AX-123245853 9 19011214 TTTCAGCACTCTCTTTAGGGTTGGGTGAAGCTTTC[C/T]CTGAGTCTATACTGCAGCCTGACTTCTCCCTTCTC Y 2 1 2 1 101000 f 74 goat snp452-scaffold1011-892827 9 19110777 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410731 Affx-122952709 AX-123281081 9 19047746 TGGTTCAGTCTCTGCTTTCAGAGAAACTCAAATGA[C/T]GCAGACTGATAAGTCAGTTAGCTGCTGATCACGAT Y 2 1 2 1 201000 r 74 goat snp453-scaffold1011-929359 9 19154997 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409149 Affx-122953215 AX-123279500 9 19079570 TTTACAGAAAAATACCTGAGTCTTAGAGATGTTTA[A/G]AGTAACTTTCTCTCGCAGTTGTACATGCAAGTGAT R 2 1 2 1 101000 r 74 goat snp454-scaffold1011-961183 9 19187129 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442731 Affx-122927851 AX-123313068 9 19116623 CACCACATGGCAATTGAGGCTGTCCACAGCAATGC[A/G]CTTAAGGATAAGAAAAAACTGCAGCTGGTGAGTAA R 2 1 2 1 101000 f 74 goat snp455-scaffold1011-998236 9 19252661 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476257 Affx-1251763764 AX-586011678 9 19137241 GTGAACATCGACATTCTAGGAATCAGAGGACTAAA[-/ATGGACTGGAATGGGTGAATTTAACTCAGATGACCATTATCTACTGCGGGCAGGAATCCCTTAGAAGAAATGGAGTAGCC]ATCATGGTCAACAAAAGTGTCCGAAATGCAGTACT - 8 1 4 1 20000 f 74 goat SV_183 9 19137241 - deletion junction SV-TF-chip 539476510 Affx-1251763764 AX-586011904 9 19137241 GTGAACATCGACATTCTAGGAATCAGAGGACTAAA[-/ATGGACTGGAATGGGTGAATTTAACTCAGATGACCATTATCTACTGCGGGCAGGAATCCCTTAGAAGAAATGGAGTAGCC]ATCATGGTCAACAAAAGTGTCCGAAATGCAGTACT - 4 1 4 1 20000 r 74 goat SV_183 9 19137241 - deletion junction SV-TF-chip 562166344 Affx-1251763764 AX-606941752 9 19137241 GTGAACATCGACATTCTAGGAATCAGAGGACTAAA[-/ATGGACTGGAATGGGTGAATTTAACTCAGATGACCATTATCTACTGCGGGCAGGAATCCCTTAGAAGAAATGGAGTAGCC]ATCATGGTCAACAAAAGTGTCCGAAATGCAGTACT - 8 1 4 1 20100 r 74 goat SV_183 9 19137241 - deletion junction SV-TF-chip 562166483 Affx-1251763764 AX-606941891 9 19137241 GTGAACATCGACATTCTAGGAATCAGAGGACTAAA[-/ATGGACTGGAATGGGTGAATTTAACTCAGATGACCATTATCTACTGCGGGCAGGAATCCCTTAGAAGAAATGGAGTAGCC]ATCATGGTCAACAAAAGTGTCCGAAATGCAGTACT - 8 1 4 1 20100 r 74 goat SV_183 9 19137241 - deletion junction SV-TF-chip 562166489 Affx-1251763764 AX-606941897 9 19137241 GTGAACATCGACATTCTAGGAATCAGAGGACTAAA[-/ATGGACTGGAATGGGTGAATTTAACTCAGATGACCATTATCTACTGCGGGCAGGAATCCCTTAGAAGAAATGGAGTAGCC]ATCATGGTCAACAAAAGTGTCCGAAATGCAGTACT - 8 1 4 1 20100 f 74 goat SV_183 9 19137241 - deletion junction SV-TF-chip 38435021 Affx-122933803 AX-123305361 9 19146910 CCCTGAACTTTTACACTAAACCAGATTATTATTCA[A/G]TCTTTACGTTTTCAGTGATCATCTCATATTTATTT R 2 1 2 1 101000 f 74 goat snp456-scaffold1011-1028523 9 19290550 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418027 Affx-122946645 AX-123288375 9 19187937 TACCTTGACTCTTGGATAGTAGAAAGAGGTTGTAA[G/T]CAGGCAAGGTACAGGAAGGAAATTCCAGTTCAGTT K 2 1 2 1 201000 f 74 goat snp457-scaffold1011-1069550 9 19331660 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448329 Affx-122924141 AX-123318665 9 19221474 CTTTTATGATGATCACAGTGTGAGGAAATGGTGAG[A/C]TAAGAATTAGGCACAAGTAATACAGGTATAATAGT M 2 1 2 1 101000 f 74 goat snp458-scaffold1011-1103087 9 19366014 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799497 Affx-122964902 AX-385286427 9 19262812 TGGGCTAGACACTGAGTAGTACAGAGATGAATACA[A/G]CACCATCCTTGAGGTGTTCACTGTTTTGTTGGGAA R 2 1 2 1 101000 r 74 goat snp459-scaffold1011-1144425 9 19407686 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476258 Affx-1251763765 AX-586011679 9 19277579 TGTGAGAGGTGAACTACAAAGAAAGCTGAGCACCA[-/AAGAATTGATGCTTTTTTTTTTTTTTTTTTTTTTTTTAACTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]AGAATTGATGCTTTTGAACAGTGGTGTTGGAGAAG - 4 1 4 1 20000 f 74 goat SV_186 9 19277579 - deletion junction SV-TF-chip 539476511 Affx-1251763765 AX-311121716 9 19277579 TGTGAGAGGTGAACTACAAAGAAAGCTGAGCACCA[-/AAGAATTGATGCTTTTTTTTTTTTTTTTTTTTTTTTTAACTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]AGAATTGATGCTTTTGAACAGTGGTGTTGGAGAAG - 4 1 4 1 20000 r 74 goat SV_186 9 19277579 - deletion junction SV-TF-chip 562165496 Affx-1251763765 AX-606940907 9 19277579 TGTGAGAGGTGAACTACAAAGAAAGCTGAGCACCA[-/AAGAATTGATGCTTTTTTTTTTTTTTTTTTTTTTTTTAACTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]AGAATTGATGCTTTTGAACAGTGGTGTTGGAGAAG - 8 1 4 1 20100 r 74 goat SV_186 9 19277579 - deletion junction SV-TF-chip 562165975 Affx-1251763765 AX-606941384 9 19277579 TGTGAGAGGTGAACTACAAAGAAAGCTGAGCACCA[-/AAGAATTGATGCTTTTTTTTTTTTTTTTTTTTTTTTTAACTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]AGAATTGATGCTTTTGAACAGTGGTGTTGGAGAAG - 8 1 4 1 20100 r 74 goat SV_186 9 19277579 - deletion junction SV-TF-chip 562166215 Affx-1251763765 AX-606941623 9 19277579 TGTGAGAGGTGAACTACAAAGAAAGCTGAGCACCA[-/AAGAATTGATGCTTTTTTTTTTTTTTTTTTTTTTTTTAACTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]AGAATTGATGCTTTTGAACAGTGGTGTTGGAGAAG - 8 1 4 1 20100 f 74 goat SV_186 9 19277579 - deletion junction SV-TF-chip 38415064 Affx-122949475 AX-123285413 9 19293158 AATGTGGAAGGTAAGGCCGGTGCGTACTCCTCAGC[A/G]TTGAGAATTACGTTTTCCGTGTCTGCTTTCCATAT R 2 1 2 1 201000 r 74 goat snp460-scaffold1011-1174771 9 19438394 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779625 Affx-122942509 AX-385266727 9 19349294 TTTTTTACTTAAGAACTGTTGATGATGAGGCCCTT[A/G]CTAAACTTTAGACTCAGGTAGATGAAAAGCATTGT R 2 1 2 1 201000 r 74 goat snp461-scaffold1011-1230907 9 19494346 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762689 Affx-986697219 AX-385250764 9 19373422 CTTCCAGTTTTTCTGTGTTATCTTCCCAATTAATG[C/T]GGAATCTTGTGACTCTGGGATTGGATGCCAAAATA Y 2 1 2 1 600010 f 74 goat 9_19373422 9 19373422 Ancestral_priority_1043 ancestry 0.716 recommended IMAGE 10K 10K ancestral 320762691 Affx-986697221 AX-385250766 9 19374784 GGTTTTACTGGCGGATTTTCCCTTAATTCTGTCTC[A/G]GTATATTCATTATTTACATAATAACCAACTCTAAT R 2 1 2 1 600010 f 74 goat 9_19374784 9 19374784 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 320803695 Affx-986696182 AX-385290465 9 19374806 TTAATTCTGTCTCGGTATATTCATTATTTACATAA[C/T]AACCAACTCTAATAAACTCTTGACCTCGATAGGTG Y 2 1 2 1 600010 r 74 goat 9_19374806 9 19374806 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 320792530 Affx-122962892 AX-385279511 9 19384918 CTTTAAAATTCAGCTGTAGGGAAACAATTAGGACC[A/G]TAGCTCATAATTACTTATTATGCGAGATTATGAAA R 2 1 2 1 101000 f 74 goat snp462-scaffold1011-1266531 9 19529989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399044 Affx-122960914 AX-123269399 9 19434896 CGTTTATTTGGATGGTTTTTAGCTGTTGAGTTGTA[G/T]AAGTTCTTTGTATGTTTTGTGTTATTAACTTCTTA K 2 1 2 1 103000 f 74 goat snp463-scaffold1011-1316509 9 19580290 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431860 Affx-122936072 AX-123302201 9 19471378 GTGTAGTGTGTGGGACAGGATAGGTAACACTAGAC[C/T]GAGAAACAGGAGACTGGGATTCTATTTTGAGATCT Y 2 1 2 1 101000 f 74 goat snp464-scaffold1011-1352991 9 19617594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787297 Affx-122935479 AX-385274322 9 19504595 TTGTGTTACAATTGTAATGAGATCATGTTTCATGC[A/G]TAGATCATTCCTTTGTTGGCATTTTTAAAAAACAT R 2 1 2 1 101000 f 74 goat snp465-scaffold1011-1386208 9 19650626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445558 Affx-122925149 AX-123315895 9 19545245 TTTCTTCATAGTGTGAAGACTTCTGTGGATCACCT[A/G]CTATCTAGAGCTTAGGGTTGTCTGACCCATAATAC R 2 1 2 1 201000 r 74 goat snp466-scaffold1011-1426858 9 19686946 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274006 Affx-1111833981 AX-519547611 9 19547394 TGTAATATGACCCATTCATCAGAGTTACACATTTG[A/G]TGATATTTGAATCTGCAGAGATTC R 2 1 2 1 101000 f 74 goat GoatD01.012654 9 19547394 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38435280 Affx-122934045 AX-123305620 9 19597652 AAGAACTTGATGACTCAGGGTGGAGACTTCTCAAA[G/T]CAGAATGGGACAGGTGGAGAAAGCATTTGTGGTGA K 2 1 2 1 201000 f 74 goat snp467-scaffold1011-1479265 9 19735745 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445845 Affx-122926008 AX-123316182 9 19628213 TTATTATTCACAAAGTGATCTCTATTATCCTAGGT[A/G]ATCCTTATACTAGTTCAGGAAGTATCGTTCTTTCC R 2 1 2 1 101000 r 74 goat snp468-scaffold1011-1509826 9 19766449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801851 Affx-122959742 AX-385288758 9 19684273 ACAACCAATGAAATCCCACAATCAAGATAATTTCC[A/G]TGCTGGTATATTTCAAAAAGGGTTTCACACAAAAG R 2 1 2 1 101000 f 74 goat snp469-scaffold1011-1565886 9 19822360 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765122 Affx-986697223 AX-385252682 9 19689604 TATTTAAATAGTGAGATAATATAATAAATATTGTT[C/T]TGTGCTGTACACTTTTTATCTAATAATATATACTG Y 2 1 2 1 600010 r 74 goat 9_19689604 9 19689604 Ancestral_priority_1043 ancestry 0.73 recommended IMAGE 10K 10K ancestral 38394415 Affx-122964606 AX-123264770 9 19736026 TTAGTGACTGAACAACAACATAGTATTCTAGAGTG[C/T]TGAAAGACTACTAATGAAATTTAGGAAAATGAAGC Y 2 1 2 1 201000 r 74 goat snp470-scaffold1011-1617639 9 19871604 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380943 Affx-122975005 AX-123251301 9 19768730 GGATGGATCGATGGTTGTGCATAACATGGGTTGAA[C/T]AAAACACTTGAGGACAAGGGGAACGTTGCTAAAGA Y 2 1 2 1 101000 f 74 goat snp471-scaffold1011-1650343 9 19904234 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438957 Affx-122930399 AX-123309294 9 19803838 CACGACTTCACTCACTTCACTCACTCAGCTAGGAG[C/T]AACGAAGTTTGCAGTTATTTCTCCTCTAATGTCTC Y 2 1 2 1 101000 r 74 goat snp472-scaffold1011-1685451 9 19939129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443501 Affx-122927799 AX-123313838 9 19918131 GATAAACTCCAGGCCTTATTTGTTCCTATTGTTTT[A/C]TAAAACAGTTCCCCAAATTCTTCAAATTTCAGCAA M 2 1 2 1 102000 f 74 goat snp474-scaffold1011-1799744 9 20053640 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799740 Affx-122973608 AX-385286667 9 19979736 AACAAAGACGTGTAGAATTTGCCCATCTACAAAGT[A/G]CTTTGGACTCTGGATAAAGGAATCACACCTACAAA R 2 1 2 1 101000 r 74 goat snp475-scaffold1011-1861349 9 20114584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393726 Affx-122965232 AX-123264081 9 20042776 AAAACCTAAAAATGTGCTTGGCACAGAGTAGGCAC[A/G]CAAATAAACACCTGTTAAGTGGATGAATGAACCAG R 2 1 2 1 201000 r 74 goat snp477-scaffold1011-1924389 9 20178164 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396638 Affx-122962869 AX-123266993 9 20095029 ACTATTGCAAAATTTTCATTCCATTCTTCACTTAC[A/G]TCTTCTGAGCCTCACTTAAGACACACACACTTCTG R 2 1 2 1 101000 r 74 goat snp478-scaffold1011-1976642 9 20230485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409408 Affx-122954134 AX-123279759 9 20183642 GAATTTGCCAATAACTGGTGGCTCAGAGGGTAAAG[C/T]GTCTGCCTGCAATGTGGGAGATCTGGGTTCAATCC Y 2 1 2 1 103000 f 74 goat snp480-scaffold1011-2065255 9 20319086 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278861 Affx-1111836548 AX-519552331 9 20187315 TATACAAGGAAATCATTTTTCATTTCAAAGTGAGT[A/G]TAGTCGGAGGAGAGAAATACATAAGGGTCAAGAGC R 2 1 2 1 101000 r 74 goat Random2.2K-971 9 20187315 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380193 Affx-122975501 AX-123250551 9 20196534 AAGCACAGAACAGACACTGAACAAATAAAGGTCTG[C/T]GGAAAGACCATGACAGGTCAGAGACCTTCTTCCTT Y 2 1 2 1 101000 r 74 goat snp13747-scaffold1533-8473 9 20332533 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407953 Affx-122954353 AX-123278304 9 20232037 GGTCCCTGGAGAAAATTGAATGTAACTAAAGCGTG[A/C]TCTTTTCAGGAAGCCTGGTATAGGAACATCTGCAG M 2 1 2 1 101000 f 74 goat snp13748-scaffold1533-43976 9 20368354 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419920 Affx-122945326 AX-123290268 9 20262354 TGGGCTTCCCTGGTGGCTCAAATGCTAAAGAATCT[A/G]CCTGTTGAAATCCATACTAACCTCACAGCTAATTA R 2 1 2 1 201000 r 74 goat snp13749-scaffold1533-74293 9 20398627 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436518 Affx-122932943 AX-123306856 9 20366390 TTTAGATTTTCATGGAACAATTGAAAGGAAAGGCT[A/G]CAAAATCATAAATACTTTACATGTATAGATAAGAG R 2 1 2 1 101000 f 74 goat snp13751-scaffold1533-178329 9 20500984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272480 Affx-1111836549 AX-519546202 9 20431047 CTCCTTTTCTATTTGAATTTATTCCCAGAGAAAGA[A/G]TGTGCCTGTTGGTTTCTTATTCACCCACTGCATGT R 2 1 2 1 101000 r 74 goat Random2.2K-972 9 20431047 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320798041 Affx-122934826 AX-385284977 9 20456346 AGCCATGAGAGCTGAGAAACACTGTTCATATTAGT[A/G]CATGAGACTTTATGAGGAGCAAAATCAAGTTGTTT R 2 1 2 1 101000 f 74 goat snp50839-scaffold736-10061 9 20593398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448871 Affx-122923273 AX-123319206 9 20490175 CATCCCCTTGACTTCGTCTGTAATCACCCTGCTGT[C/T]CTGATCTCGTCCTTTGGGATACATCGTCTCAGGAT Y 2 1 2 1 201000 r 74 goat snp50840-scaffold736-43890 9 20627018 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432592 Affx-122935511 AX-123302933 9 20552676 TTGCTCACCCCTAGTGTGTTTACATAATGAAGCTA[C/T]GAAAGCCATAGGTATTGCGGGTCTGCAGTGCAGGT Y 2 1 2 1 201000 r 74 goat snp50841-scaffold736-106391 9 20689518 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449381 Affx-122922716 AX-123319716 9 20602294 TTTGTTTCTGGGCATATGAGGGAGTAGCGAAAAAG[C/T]AAGGCACTGTATTATTTTTGTAATGGATGTGGTAA Y 2 1 2 1 101000 f 74 goat snp50842-scaffold736-156009 9 20737557 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788052 Affx-122961577 AX-385275073 9 20688877 GACAAACAGAGAGTGCCTTTAGCAAGATGAGCCAT[C/T]GCTTTATTTTTAAAGCTCGCTTATGTCAACGCTTT Y 2 1 2 1 101000 f 74 goat snp50844-scaffold736-242592 9 20824606 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441805 Affx-122929078 AX-123312142 9 20720160 TAAATAATTCTTAATATGCATTTTCTTTGTTCTTC[C/T]TGTTCTTAATTTTATCAATAAAATCTGTAATTCAG Y 2 1 2 1 201000 r 74 goat snp50845-scaffold736-273875 9 20855427 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781287 Affx-122926335 AX-385268372 9 20767724 ACTGATTCCATTGAGAGAGATCATTGTGTCTTCTT[A/G]TCAGCTGTCTAATCTTTAGTTTAGAGGAAGCAAAT R 2 1 2 1 101000 f 74 goat snp50846-scaffold736-321439 9 20902779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436984 Affx-122933149 AX-123307322 9 20825316 TTTTGGAGGTCTTGAAAGACAGTCAGAACAGCTTT[A/G]CCTTGCTGCTGGTAAATGTGCGTGTACGAGCCCAG R 2 1 2 1 101000 f 74 goat snp50847-scaffold736-379031 9 20960666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443021 Affx-122928166 AX-123313358 9 20854004 GAGGACTGGTTCTGTAGTTTTTATCACCTCCTCAG[C/T]GTTTCATGGCTCCCCAAACAGTTAAGAATTACTAT Y 2 1 2 1 101000 f 74 goat snp50848-scaffold736-407719 9 20989344 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441818 Affx-122929068 AX-123312155 9 20886638 TTGAAAATACTCTAGTATCAACATCAGTAGGGTAA[C/T]AAAAAGTGATCTTTAGACTTTTTCAACTTTGGGCT Y 2 1 2 1 101000 f 74 goat snp50849-scaffold736-440353 9 21022314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273447 Affx-1111833605 AX-519547071 9 20919715 CTCACCTTTAAGTTTAAGTATAGTTTATCAATAAA[A/G]ATAACAAGAGTAATTTTGTAATTCTCTTTGGCTAA R 2 1 2 1 101000 r 74 goat 9_20919715_AF-PAKI 9 20919715 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38419765 Affx-122945871 AX-123290113 9 20981378 AAAGAAAAAAAAAGGGGGGGGCAGAGCTCCTATTC[A/G]ACTCCACTAGATCTTTAGTATGTGGCAACAATGCC R 2 1 2 1 101000 r 74 goat snp50851-scaffold736-535093 9 21119029 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388998 Affx-122968652 AX-123259356 9 21011369 ACCAACCGCACATGCCCTGCTTCTTGATCTTCTCT[A/G]TTCTCAAGTCTTGTTTCTTAGAGAGGCTGTCACTT R 2 1 2 1 201000 r 74 goat snp50852-scaffold736-565084 9 21149613 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414930 Affx-122949099 AX-123285279 9 21044368 TGTGATAAACTCTTTATAACTTAGCACTCAGATAA[C/T]GCACATAAACATCTAACGAACCATTTAAAATTAGA Y 2 1 2 1 101000 f 74 goat snp50853-scaffold736-598083 9 21182656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399073 Affx-122960889 AX-123269428 9 21089800 AGGAAGGGAACACATTTGCATTTTAAGATGATAAC[A/G]TGGGTTGAAGAATAGAGAATAAATGGAGATGGACT R 2 1 2 1 101000 r 74 goat snp50854-scaffold736-643515 9 21228686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428903 Affx-122938923 AX-123299245 9 21131898 TTAATATTCATGGAGAATAAATTGAAACAAATTCA[A/C]TGCAGGGTAATTTCCAGTTCTAATTAAACTTACAA M 2 1 2 1 101000 r 74 goat snp50855-scaffold736-685613 9 21294055 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419957 Affx-122945205 AX-123290305 9 21226557 CTACTTCCCAATATTAGCAGTCTTCAAAATGTGTT[C/T]TGAAGTTTATTTTTGCTTTTCTGTGCTTATGAGTT Y 2 1 2 1 103000 f 74 goat snp50857-scaffold736-780272 9 21389516 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380186 Affx-122975507 AX-123250544 9 21272946 AAAGTGGAAAACATTAGAGGGATGTAACGAAGGAG[A/C]GTCTTGATGGAAACAATGCCCACCAGTGTTGGGAT M 2 1 2 1 101000 f 74 goat snp50858-scaffold736-826661 9 21435441 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803452 Affx-122975507 AX-180660641 9 21272946 AAAGTGGAAAACATTAGAGGGATGTAACGAAGGAG[A/C]GTCTTGATGGAAACAATGCCCACCAGTGTTGGGAT M 2 1 2 1 600000 r 74 goat snp50858-scaffold736-826661 9 21272946 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375776 Affx-122978588 AX-123246135 9 21337983 ACATGGCAACGTGGCTAGAGGAAACAACACACAAA[C/T]GCTACCCAGAGCTCTGGCGTGTAGATTGCATTATG Y 2 1 2 1 201000 f 74 goat snp4040-scaffold1127-24466 9 21537186 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377896 Affx-122977246 AX-123248255 9 21367004 TTGCGTTAAAGTGATAGCTGTCAGTTTCTAGGAAA[C/T]ACCAAGGGTGGAGGAACTCACTACACAGCACCTTG Y 2 1 2 1 101000 f 74 goat snp4041-scaffold1127-53487 9 21566067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779876 Affx-122951812 AX-385266975 9 21407384 CCACTACAATGATGACCTTCCCTCTACAAGAGGGT[A/C]TTGATCTCCTCAAAGGCCTACCACAAACATATTCT M 2 1 2 1 101000 f 74 goat snp4042-scaffold1127-93867 9 21606151 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384983 Affx-122971892 AX-123255341 9 21443954 ACAGAACTACTTGCTAAGAGCATTTAAGAGTCAAG[C/T]ATTCTGAGAATGCTTCAAAGTTCTAACCTCTAAAT Y 2 1 2 1 101000 f 74 goat snp4043-scaffold1127-130437 9 21642675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440461 Affx-122929389 AX-123310798 9 21506243 TGCATGGCCTTCCACTGCTTCTGTGCCAAGCACAT[A/G]ATACTGTAGATACCCACTGCCTTCTTTTGCATGCT R 2 1 2 1 101000 r 74 goat snp4044-scaffold1127-192726 9 21704962 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784029 Affx-122943890 AX-385271082 9 21551049 GTTTAGAAGTTTTGTTATCAATTAGAGGACTCTTA[C/T]GGAAAGCAACACACTACTCTCCCTCCTTATTTACT Y 2 1 2 1 101000 r 74 goat snp4045-scaffold1127-237532 9 21749626 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392501 Affx-122966129 AX-123262858 9 21589050 CCAAATATTTTATTGCCAACTTGGGAAAGGAATAC[A/G]TCAAGGCTGTATATTGTCACCCTCCTTATTTAACT R 2 1 2 1 303000 f 74 goat snp4046-scaffold1127-275533 9 21787476 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793264 Affx-122948428 AX-385280242 9 21620285 TTACAATTACTTTTGTGCAGATTATTGTAACTGCC[C/T]GACCCCTTCCTCCATTTGTAAGCTATGTATGAGGT Y 2 1 2 1 101000 r 74 goat snp4047-scaffold1127-306768 9 21818739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272390 Affx-1111833899 AX-519546119 9 21633676 AGGCTGCAGAGGTCCAGGCACAAGGGGAAGCTGGA[A/G]AATCTTGATTAACTGGCAAGAGCTGCTTTGTTTTA R 2 1 2 1 201000 r 74 goat GoatD01.009863 9 21633676 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320791932 Affx-122973749 AX-385278922 9 21651239 CTCTTTTAATTGGAGAATGCCTGTTGGACATATGG[C/T]AATATTCTTTTCACCCTTTGGGTTACGATTTTGTG Y 2 1 2 1 101000 f 74 goat snp4048-scaffold1127-337722 9 21850026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400291 Affx-122960080 AX-123270646 9 21690022 CAAAAATACTATGAGTAATTCTGTGTTGTCATCAT[A/G]TAAAATTATCCTGCGCATTTCAAATATGTTTCTCC R 2 1 2 1 101000 r 74 goat snp4049-scaffold1127-376505 9 21888626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425482 Affx-122941490 AX-123295828 9 21721127 GGTTATATGCTGTGCAAGTAACTTTTCTAGGTCTG[C/T]GGCTTATTTTTAAATTTTATTTCATGGCAATCTTG Y 2 1 2 1 101000 f 74 goat snp4050-scaffold1127-407610 9 21919566 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413046 Affx-122950983 AX-123283395 9 21756592 AAAATGGGAGAAGCCTGTCAAAAAACTTTAGCACT[A/G]TGGGTAACTGATGCCTGGTATTTCTTATTGAAACT R 2 1 2 1 101000 f 74 goat snp4051-scaffold1127-443075 9 21954520 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453330 Affx-122919969 AX-123323663 9 21786366 TTAGATGAGATGGACATTTAAATGAATAGACCGAA[C/T]AAAGCTGGTTGCCCTCCCTAACATGGATGGGACTC Y 2 1 2 1 201000 f 74 goat snp4052-scaffold1127-472849 9 21984723 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422884 Affx-122943071 AX-123293230 9 21804538 GGAGGGATGGAAGGCAAGAAGATCCTTAGGGAAGG[C/T]GGTTTGAAGGAAGGAAAGGTGAAGTAGTGAGAAGA Y 2 1 2 1 201000 f 74 goat snp38317-scaffold4845-17713 9 22002893 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778989 Affx-122953414 AX-385266096 9 21837737 AGCTACCTTCTGATTTAACTTTGAATGAGAAGGGA[G/T]GCTGTGAGGAAAGTAGAATTAAGACATAATCTCTA K 2 1 2 1 101000 f 74 goat snp38318-scaffold4845-50912 9 22036200 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435587 Affx-122933361 AX-123305927 9 21866932 GAAATAGTAAAATATTGAGGTGATTATGTTTGATA[C/T]GGGGAGCTGCAGGTTATTCTCTCTACATCTCTGCA Y 2 1 2 1 201000 f 74 goat snp3870-scaffold1122-21685 9 22065221 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785923 Affx-122937088 AX-385272960 9 21911493 GTACAGTAACTATTTTATGTTTCTTGCCAGTAAAA[C/T]GTTGAATTATTGTGAAGAGAGTGGGTATCCTGATT Y 2 1 2 1 102000 r 74 goat snp3871-scaffold1122-66246 9 22110973 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787964 Affx-122946815 AX-385274985 9 21951698 GTTCACTGCAGTACCCAGAGGCCAAGTTAGTGCTT[A/G]TCAGAGTAGACCCTTGGTACATATATGTTAAATAT R 2 1 2 1 101000 f 74 goat snp3872-scaffold1122-106451 9 22151564 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427643 Affx-122939334 AX-123297986 9 22001603 GCTGGAGCAGGTTCTTGGTGAGGTAGAGGTGTCAC[A/G]CTGCAGAGGATTTAAGACTGAAGGGAAGTGAGGAA R 2 1 2 1 101000 f 74 goat snp3873-scaffold1122-156356 9 22201487 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418445 Affx-122946478 AX-123288793 9 22033981 CCTTTTGCTTTCTTGGTCTTAACATGGAGCCTGCC[A/G]TTTCTTCAGGGGTGACTTGTTCATTTTATTTATCT R 2 1 2 1 101000 f 74 goat snp3874-scaffold1122-188734 9 22231688 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419794 Affx-122945849 AX-123290142 9 22066353 ATGCAGTCTTTCATTTTTTACCAAGCACTTGCTAT[A/G]CATGGGGTCCTAAGAGTCCCAGAGCTACAGCTGTG R 2 1 2 1 101000 f 74 goat snp3875-scaffold1122-221106 9 22263801 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405902 Affx-122955586 AX-123276254 9 22107657 TTATTCTCTATTATGCTGTTTGCTTCTAACAGTTT[A/G]CATGTTTAAAGACACTTCCATCAATAATTTCAGTT R 2 1 2 1 101000 r 74 goat snp3876-scaffold1122-262410 9 22304603 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425086 Affx-122941244 AX-123295432 9 22142334 TCTCATTTTTTAATGATCACCTTGGACAGATTTAG[A/G]TGTCTCTTCCTCAGTAAATTCAATATTGTCATATC R 2 1 2 1 101000 f 74 goat snp3877-scaffold1122-297087 9 22339365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783522 Affx-122960582 AX-385270585 9 22177140 TCACTGATACATAAAAATTGTCAAGTTTGGCCAAG[C/T]AAATGCTACCAGGGCTTTTTCCTGTTAGGGAAGTT Y 2 1 2 1 101000 r 74 goat snp3878-scaffold1122-331893 9 22374786 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387010 Affx-122969937 AX-123257368 9 22230912 ACAGGTGATCTATGGCTGACATTCGGAGCGATATG[A/G]CCGAGTAAGGTTGCAGACCTCTGGTAGCTGTTTTC R 2 1 2 1 101000 f 74 goat snp3879-scaffold1122-385665 9 22428517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428394 Affx-122938952 AX-123298737 9 22268424 AAAACTAGATGCCCTTGGACACAGTAATGGCTTTT[A/G]TCTCTTTTTCAACTCTTCTTAATATTTTTCTTTTC R 2 1 2 1 103000 f 74 goat snp3880-scaffold1122-423177 9 22466615 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420782 Affx-122944701 AX-123291129 9 22302542 GCACAGAACACAGGTGTCCTAGCTGCTGTTCTTGC[A/G]TCACAGCCTTCTATTCCTTGGTCTGTTGGGAAAGA R 2 1 2 1 101000 r 74 goat snp3881-scaffold1122-457295 9 22500655 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442225 Affx-122928305 AX-123312562 9 22342206 AATGAGACACTGCATACCATTTTGTTTGAAGGTGA[C/T]ATCTCAGGATAAAAAAAGAAAAGAAATTTTAAGAT Y 2 1 2 1 101000 f 74 goat snp3882-scaffold1122-496959 9 22540412 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412013 Affx-122951747 AX-123282363 9 22404763 GTTGAAAGTGGTTTTCTGAGTTTTATTTAGAAACT[A/G]CAAATCTTATGATATATAGGAAAGTGGAGATTGGA R 2 1 2 1 101000 r 74 goat snp3884-scaffold1122-559516 9 22604024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430959 Affx-122936823 AX-123301300 9 22442627 GACAGTGAAAAGAGCTATCTCTACCTGAGGCGGAA[C/T]ACCACAGGAGCTTTAGGGAGGGGAGGGAGAGAAGT Y 2 1 2 1 101000 f 74 goat snp3885-scaffold1122-597380 9 22640300 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453968 Affx-122919459 AX-123324301 9 22472523 TTGTTTTCCTAGAATGAACCCTGCTCAATTACGGC[C/T]AATTGGTCTTTGAAAATATTTCTGAATTTTAATTG Y 2 1 2 1 101000 f 74 goat snp3886-scaffold1122-627276 9 22670528 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428084 Affx-122939100 AX-123298427 9 22515657 TTTCTTAATCTCTTTTGTATTTCATACATTTTTTA[G/T]TCTCAAATCTATTTTGAAAAACTTCTTCAGCTATA K 2 1 2 1 303000 f 74 goat snp3887-scaffold1122-670410 9 22714367 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765128 Affx-986697227 AX-385252686 9 22525498 GAAGGATAATGTGTGAGATATCGCTCTGAGGAGTG[G/T]TTTTGATGGACAGCTGCTGACCAGTGCTGTGAGAA K 2 1 2 1 600010 r 74 goat 9_22525498 9 22525498 Ancestral_priority_1043 ancestry 0.652 recommended IMAGE 10K 10K ancestral 320762699 Affx-986697229 AX-385250771 9 22525568 ACTGTTTTATCCACCTACTGGTCCAATGGGCTCTG[C/T]CTGAATGTCTGCATTGTCTCCCTCCGACCCACCAT Y 2 1 2 1 600010 f 74 goat 9_22525568 9 22525568 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 320765134 Affx-986697231 AX-385252690 9 22525633 CACCATTGAATCCATCCCTAGGGGCTTGTCCCAGA[C/T]CACTGGGTACTGGGCATCCTTAGGTTTTTCAGTCT Y 2 1 2 1 600010 r 74 goat 9_22525633 9 22525633 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 539476259 Affx-1251763766 AX-586011680 9 22583677 TTATAGATCCAATATTTTATGACATTGTGGCTTGG[-/ACTGCCTATGAGCTTTGTTTTTTTTTTTTTTAATTAATTTGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCT]CTGCCTATGAGCTTTGTGAGTTGTTGCACTTACTC - 4 1 4 1 20000 f 74 goat SV_194 9 22583677 - deletion junction SV-TF-chip 539476512 Affx-1251763766 AX-586011905 9 22583677 TTATAGATCCAATATTTTATGACATTGTGGCTTGG[-/ACTGCCTATGAGCTTTGTTTTTTTTTTTTTTAATTAATTTGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCT]CTGCCTATGAGCTTTGTGAGTTGTTGCACTTACTC - 4 1 4 1 20000 r 74 goat SV_194 9 22583677 - deletion junction SV-TF-chip 562165268 Affx-1251763766 AX-606940680 9 22583677 TTATAGATCCAATATTTTATGACATTGTGGCTTGG[-/ACTGCCTATGAGCTTTGTTTTTTTTTTTTTTAATTAATTTGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCT]CTGCCTATGAGCTTTGTGAGTTGTTGCACTTACTC - 8 1 4 1 20100 f 74 goat SV_194 9 22583677 - deletion junction SV-TF-chip 562165425 Affx-1251763766 AX-606940836 9 22583677 TTATAGATCCAATATTTTATGACATTGTGGCTTGG[-/ACTGCCTATGAGCTTTGTTTTTTTTTTTTTTAATTAATTTGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCT]CTGCCTATGAGCTTTGTGAGTTGTTGCACTTACTC - 8 1 4 1 20100 r 74 goat SV_194 9 22583677 - deletion junction SV-TF-chip 562165528 Affx-1251763766 AX-606940939 9 22583677 TTATAGATCCAATATTTTATGACATTGTGGCTTGG[-/ACTGCCTATGAGCTTTGTTTTTTTTTTTTTTAATTAATTTGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCT]CTGCCTATGAGCTTTGTGAGTTGTTGCACTTACTC - 8 1 4 1 20100 f 74 goat SV_194 9 22583677 - deletion junction SV-TF-chip 562166243 Affx-1251763766 AX-606941651 9 22583677 TTATAGATCCAATATTTTATGACATTGTGGCTTGG[-/ACTGCCTATGAGCTTTGTTTTTTTTTTTTTTAATTAATTTGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCT]CTGCCTATGAGCTTTGTGAGTTGTTGCACTTACTC - 8 1 4 1 20100 r 74 goat SV_194 9 22583677 - deletion junction SV-TF-chip 562166263 Affx-1251763766 AX-606941672 9 22583677 TTATAGATCCAATATTTTATGACATTGTGGCTTGG[-/ACTGCCTATGAGCTTTGTTTTTTTTTTTTTTAATTAATTTGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCT]CTGCCTATGAGCTTTGTGAGTTGTTGCACTTACTC - 8 1 4 1 20100 f 74 goat SV_194 9 22583677 - deletion junction SV-TF-chip 562166480 Affx-1251763766 AX-606941888 9 22583677 TTATAGATCCAATATTTTATGACATTGTGGCTTGG[-/ACTGCCTATGAGCTTTGTTTTTTTTTTTTTTAATTAATTTGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCT]CTGCCTATGAGCTTTGTGAGTTGTTGCACTTACTC - 8 1 4 1 20100 r 74 goat SV_194 9 22583677 - deletion junction SV-TF-chip 38435379 Affx-122933576 AX-123305719 9 22587339 GTAAATTATAAGCACTATATATACCGCATAAGAGC[A/G]TTTCAGATCCTTTTCTTGGATGCCAGTTCTTCAAA R 2 1 2 1 101000 f 74 goat snp3888-scaffold1122-742092 9 22787339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441752 Affx-122929122 AX-123312089 9 22652293 AAATCAGTAAAGGATCATAGTGTCTGGGTTCTCTA[C/T]GAGGCTCCATCTCTTCCTCAGGCAAGTGACAACAT Y 2 1 2 1 101000 f 74 goat snp3889-scaffold1122-807046 9 22852681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427375 Affx-122940092 AX-123297718 9 22708701 TTAAGGTTCAAACTCTGTTCATTTTTGACATACCA[C/T]ATTAACATGAGATAAAATATTAATTAATTTACATT Y 2 1 2 1 101000 f 74 goat snp3890-scaffold1122-863454 9 22912123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395977 Affx-122963514 AX-123266332 9 22753364 TCAGCTACAATGGGAGAAACATTCTGCAGAAAGAA[C/T]GTGAATCTGCCCTTGCTCTGGCGCTCAAGTACAAA Y 2 1 2 1 201000 f 74 goat snp3891-scaffold1122-908117 9 22955785 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787678 Affx-122938814 AX-385274701 9 22829411 AGGCATTTGAGTTATGAATGTGCTCCTCAAAGAAG[C/T]ACAAGTTAATAACTGCTAATGTAAAATTAACGAGA Y 2 1 2 1 101000 f 74 goat snp3893-scaffold1122-984164 9 23032950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423499 Affx-122942562 AX-123293845 9 22873218 ATTCATGAAGAAGTTTCTAGAAGTTTTTTAAGAGC[A/G]CAGTATCAGTTATACTATGTCAGGGTAGACATACA R 2 1 2 1 101000 r 74 goat snp3894-scaffold1122-1027971 9 23077830 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424501 Affx-122941744 AX-123294847 9 22915069 GGTCACAATGAACAGCTCGTTTCCTTTTTTTAAAG[G/T]CCCTGTTAACGACCAAGTCAAAATCTTTCTTCAGT K 2 1 2 1 101000 r 74 goat snp3895-scaffold1122-1069822 9 23117311 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413136 Affx-122950366 AX-123283485 9 22969680 TAAAATCTTAAAAGTTGATTCTCCCAGAAACTGTG[C/T]AATGATTAACAGAAAGAAAATAGCATTATAATATT Y 2 1 2 1 101000 f 74 goat snp3896-scaffold1122-1124433 9 23171716 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792607 Affx-122954244 AX-385279588 9 23023987 AAGTTATCTAAGAATCTCCTAAGTATTAAAAATTG[C/T]GGAAGATTATAATTTCAATACAATTGTTGTTTAGT Y 2 1 2 1 101000 r 74 goat snp3897-scaffold1122-1178740 9 23225856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424759 Affx-122941644 AX-123295105 9 23062728 AGCCAAAAGAATAAGACATTTCAAGAAGATAAATA[C/T]GATTATTTGTATAAATCTTAGAAGAAATCCCTAAA Y 2 1 2 1 103000 f 74 goat snp3898-scaffold1122-1217481 9 23264673 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800392 Affx-122928043 AX-385287314 9 23131907 TTTTAAAATCTCTCTCCTATTTTCTGCGAGCTTAC[A/G]CTCCATGAATTGTATAGTCAGTGGAAGAAAGGGCA R 2 1 2 1 101000 r 74 goat snp3899-scaffold1122-1286660 9 23333982 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442079 Affx-122928372 AX-123312416 9 23186014 TACACAAACCACTAAATGTTTGGCAAAGTATAAGT[A/G]CATTTGAATTAATCAGCTAAATTACAACTTGATTA R 2 1 2 1 101000 f 74 goat snp3900-scaffold1122-1340767 9 23388130 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784951 Affx-122961973 AX-385271998 9 23232415 AACAAGCATTTGTTTCTCATTTTTAAGTAGTTTAC[A/G]TTCGTGTTCTTTGAAACATTTGAGACTTAATTATT R 2 1 2 1 201000 f 74 goat snp3901-scaffold1122-1387168 9 23434356 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432358 Affx-122936270 AX-123302699 9 23267478 CTTATTTACCATAGTGTTCCTATTACTTGCCCTAG[C/T]GTCCGCTACATAACAGTTTCTCAGTAAGTATTTGT Y 2 1 2 1 101000 f 74 goat snp3902-scaffold1122-1422231 9 23470189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781870 Affx-122958840 AX-385268952 9 23309420 ACCTTAGCAACACTTTTATTAAATGTTGATGAGCA[A/G]TACACTGTTGCTCTTAGCTTCTATGCTGACAGCAC R 2 1 2 1 101000 r 74 goat snp3903-scaffold1122-1464173 9 23508989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795214 Affx-122976290 AX-385282172 9 23350823 TCAAACTTGGTGAGTTGGAAGTTCAGACTGAGCTA[C/T]GTATAAAATGCTTTTCAGCATTTTTCAGGAGTAAA Y 2 1 2 1 201000 r 74 goat snp3904-scaffold1122-1505576 9 23550560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437577 Affx-122931876 AX-123307915 9 23379761 TTGGTAACTTGAGATTTATCACTCTAAAACCACTT[A/G]TATCACATTTTTAATAAATTCTTTCCTCTGCTTCA R 2 1 2 1 101000 f 74 goat snp3905-scaffold1122-1534514 9 23579716 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422814 Affx-122943197 AX-123293160 9 23413548 CTTCCTTTATAGTTAAAAAGAACAACCAGGGAAAC[A/G]CAGCTTAGCTCTCACCCACAAACTCTCAGCACTGC R 2 1 2 1 101000 r 74 goat snp3906-scaffold1122-1568301 9 23613808 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387677 Affx-122969826 AX-123258035 9 23450141 CTGAGGAGTGCACAGCTTCCATGTCGCATTATTAA[A/G]CTATCATTGTTTTCTTCCAGGTCTGTGCATCTAAT R 2 1 2 1 101000 f 74 goat snp3907-scaffold1122-1604894 9 23650394 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383654 Affx-122972523 AX-123254012 9 23497508 CAATGGGGTCTCTTGGGAAAAGCAAGAGACAGCCT[C/T]ATTGCCCTACAGAGAGGAGGACATCAACTCCAAAT Y 2 1 2 1 101000 r 74 goat snp3908-scaffold1122-1652261 9 23697846 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405590 Affx-122955935 AX-123275942 9 23528912 CCCTGCTCTCCCTCATTGCAGGCAGACGCTTTACC[A/G]TCCCTGTAAACATTATCTTCATTGCTGGCTGGATT R 2 1 2 1 101000 r 74 goat snp3909-scaffold1122-1683665 9 23727148 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449049 Affx-122923064 AX-123319384 9 23557852 AAAGCTGTCATCAAACCTTCTTTGATGTGAAAAAT[A/G]GAATAATTTTACTACATATAAGGCTCAACATCTTC R 2 1 2 1 101000 r 74 goat snp3910-scaffold1122-1712605 9 23756197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774612 Affx-122964890 AX-385261746 9 23588802 GAGATTTCTTTTAGCATGCCACTCAAAATTAGTCC[G/T]AAAATATTATGTTAAGGTAAGTTTTAAGTCTGTGG K 2 1 2 1 201000 r 74 goat snp3911-scaffold1122-1743555 9 23787554 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273412 Affx-1111833606 AX-519547039 9 23591333 CCACTTCACACCTGTCAGTATAGTTATTACCAAAA[A/C]AGACAACAAATAATAAGTGTTGGTGAGGATGTTGA M 2 1 2 1 101000 f 74 goat 9_23591333_AF-PAKI 9 23591333 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395337 Affx-122964038 AX-123265692 9 23648381 GGTCCTTTGGCATTGCAATGCAACTGCTGAGTGAC[A/G]TACATGAATGAAGTTTGGAAGGATTGTGGTCTACT R 2 1 2 1 101000 f 74 goat snp3912-scaffold1122-1803134 9 23845603 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779186 Affx-122935941 AX-385266290 9 23679741 CGGTTAGTTCAAGCCAATAACTCTTTGTTCAAGTA[C/T]TGCTTTGAAAGTCACCAAGTTGCAGATCCTTACAA Y 2 1 2 1 101000 r 74 goat snp3913-scaffold1122-1834494 9 23877069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777321 Affx-122950127 AX-385264443 9 23736649 GTGCTGCTTTCCATACAGTAGTTTTTAAATATTCT[A/G]TTCTGTTCCATCAGTACATATGTATCATTTCAATT R 2 1 2 1 101000 f 74 goat snp3914-scaffold1122-1891402 9 23934111 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775585 Affx-122925733 AX-385262716 9 23797843 AGCATGAGCTGTGATACATTCTTCAAAATGCAACC[A/G]TTTCTCCATCTAAGGAGATGCACAAGAAAAGCAGA R 2 1 2 1 101000 f 74 goat snp3915-scaffold1122-1952596 9 23996428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450873 Affx-122922219 AX-123321207 9 23828851 CCATAGCTGTGTTTATTGTTGTTCTAGCTAATACA[C/T]ACTAAAACACAGACTGAAAGATAGGGAACCCTAAA Y 2 1 2 1 101000 f 74 goat snp3916-scaffold1122-1983604 9 24028197 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802995 Affx-122960606 AX-385289877 9 23858193 TCTGTTCGAGGATATTTCCAACACAGAATTTTGTA[C/T]GACATTTGGAAATATTCTGCACGTTGAAAGAGAAT Y 2 1 2 1 101000 r 74 goat snp3917-scaffold1122-2012946 9 24057673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435036 Affx-122933756 AX-123305376 9 23907935 CACGGACATCCCACAAGGGTTCTTATAAGAAATGG[C/T]AGGAGGTCAGAGTGAATAGTAGGAAAAGAAGGTTG Y 2 1 2 1 101000 r 74 goat snp3918-scaffold1122-2062688 9 24107512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428680 Affx-122938638 AX-123299022 9 23942276 ATATTGCTTGGAAGCCAGGTAAGTGGTAAATCTAC[A/G]TTATGCAAGAATATTTTGCAGGTGGTACCTGGGGT R 2 1 2 1 201000 r 74 goat snp3919-scaffold1122-2097029 9 24141843 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408906 Affx-122953964 AX-123279257 9 23991859 AAAGAAGTAAAATAATGAGTTCTGCATGTTGAATG[C/T]AACAAAATAGCAGCCATTATGCATTTTTCCAAAAT Y 2 1 2 1 101000 f 74 goat snp3920-scaffold1122-2146612 9 24191265 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380023 Affx-122975591 AX-123250381 9 24054290 ATGCAGAATTTCTTTGTTAACTGGAGAAAGGCAAA[C/T]GGTCCAGTGCCAAGGCAAAGCAGTAAAGCATAGAA Y 2 1 2 1 201000 f 74 goat snp3921-scaffold1122-2209043 9 24254545 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391432 Affx-122966753 AX-123261789 9 24085295 GTGGAAAGAAAGTCTGGAAAGGTACTCTGGGTCAG[A/C]TCATGATGGATTTTGAATTCCAGTCCCAAACATTG M 2 1 2 1 101000 f 74 goat snp3922-scaffold1122-2240048 9 24284388 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412068 Affx-122951703 AX-123282418 9 24139800 AAATTGTTTATCCTTTGCTTTGTATCCAAGAAAAC[A/G]TTGGATCCTTAAGGGTAAAGTGTGTATTCAATGTA R 2 1 2 1 101000 r 74 goat snp3923-scaffold1122-2294553 9 24338994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791458 Affx-122964263 AX-385278449 9 24170403 AATGTATATCTCACAGTTGACAGATCACACTGATT[A/G]TTGTGAATTTTACTGAGCACACTCAGAGGGCAAAC R 2 1 2 1 102000 r 74 goat snp3924-scaffold1122-2325156 9 24369634 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436030 Affx-122932732 AX-123306369 9 24209726 TATGAACATATACTTTAATTGATAGGTATAAAAAT[A/G]CAAGGGACTTTTTAATAATGAAAAATATCAGCTGT R 2 1 2 1 303000 f 74 goat snp3925-scaffold1122-2364479 9 24408040 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396323 Affx-122963074 AX-123266678 9 24256114 CCAAAGGAACTTGCATTTGATTGTAAATACATGAG[C/T]GAACGTTTGACAAGACAAATGAAGCTCAACCCAGG Y 2 1 2 1 101000 f 74 goat snp3926-scaffold1122-2410867 9 24454975 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394427 Affx-122964595 AX-123264782 9 24326933 GTTTCATTAGGTTCATTATTTACTTTGTCTGATAC[A/G]TGTTGTGGCTTACTTGAATAAGTTTTCTACTCAAG R 2 1 2 1 101000 r 74 goat snp3927-scaffold1122-2481686 9 24524925 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418589 Affx-122946366 AX-123288937 9 24384328 GAAGAAAGGCAGGCTCACAAAAGTAATATTCTTAA[C/T]AATTGAGAAAGAGGAAGATATAAAAAGACGGTTTT Y 2 1 2 1 101000 f 74 goat snp3928-scaffold1122-2539081 9 24583044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406785 Affx-122955708 AX-123277136 9 24450181 CCCAATGGCAGGCATGGTAATAAATCACTGAGTCA[A/G]GAACATGATTTCTTCAAATATTTCCAAGTGGAATT R 2 1 2 1 101000 f 74 goat snp3929-scaffold1122-2604934 9 24646720 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784149 Affx-122965897 AX-385271201 9 24494444 AGGAAGTTTGTCTGTCTCTGGTGGTATCACAGTAT[A/G]TAGTGTGTACTTGTTATTTATAGCTAACCAGCAGG R 2 1 2 1 101000 f 74 goat snp3930-scaffold1122-2649197 9 24691701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391645 Affx-122966566 AX-123262002 9 24555771 TGTATACTGTCTTCCTTTCTTTTGCTTTTTCATGT[A/G]AAGGTCGTCTCTCTGACCTTTCAGAATCACTAATT R 2 1 2 1 303000 r 74 goat snp3932-scaffold1122-2710524 9 24754036 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429083 Affx-122938277 AX-123299425 9 24585189 TCTTATGAAAATGATGTCTGACCTTTTGGGGGACT[A/G]CTTTCATTATGTTGTTGTAACAGATTTTTGAGGGC R 2 1 2 1 201000 r 74 goat snp3933-scaffold1122-2739942 9 24782939 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794793 Affx-122947919 AX-385281753 9 24615230 TATTAGTTTTATGTTGATCCAATATGTGGTAACAG[C/T]AAAGCCTACAATTCCTTTAGAGCTCTACCCAAATC Y 2 1 2 1 101000 r 74 goat snp3934-scaffold1122-2769983 9 24815373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779762 Affx-122977902 AX-385266862 9 24650033 TGCACTCATCTGAGTCGCTGTTTTCCACTGCTGAT[C/T]GGTAGACCAGTAATCAGATGCCTTATGCTGGAACC Y 2 1 2 1 101000 f 74 goat snp3935-scaffold1122-2804786 9 24849991 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772355 Affx-122959195 AX-385259508 9 24690482 ACTCATCTAGTTCAGTTACCATGATATTGTCAATG[C/T]AGTAGATTGGTGTAATATTGTACACAATGCTCATT Y 2 1 2 1 101000 r 74 goat snp3936-scaffold1122-2845235 9 24890776 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799430 Affx-122972522 AX-385286360 9 24747600 GCTATATAAAATGATGCTGTTATTGTTTGCCTGTC[A/G]CTAAGTAATAATTTTAGAGAGAGCTAAAGTCAAGA R 2 1 2 1 101000 f 74 goat snp3937-scaffold1122-2902353 9 24947997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434761 Affx-122933899 AX-123305102 9 24787136 GCAAAACCTTAGTCATCTGAGTTTGCAACTTGAAG[A/G]TATTCCAACTGTTCTTTCTAAATTAGTAAATTTAT R 2 1 2 1 202000 r 74 goat snp3938-scaffold1122-2941889 9 24987721 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785279 Affx-122948174 AX-385272324 9 24822549 TATTTAAATTCAGAACACTTACAGAAGTGCTTTCA[C/T]AGCTCCAAAGTTATTCCTGTGGATGAAACACCTAA Y 2 1 2 1 101000 r 74 goat snp3939-scaffold1122-2977302 9 25023408 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408203 Affx-122953856 AX-123278554 9 24856019 GGAACTAATGGTCCATTGTGAGGATCTATTATATG[C/T]GATCCATCATAGACCTCTTAAGTGAGAATACAAAT Y 2 1 2 1 101000 f 74 goat snp3940-scaffold1122-3010772 9 25057156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430053 Affx-122937560 AX-123300394 9 24895461 TTACTTCCTATTCAGATGTCTGGGTTTGGCTGCAG[C/T]GGGTCTGCCAAGCTGTGGTTTGGGTGCAGGAGTGT Y 2 1 2 1 102000 r 74 goat snp3941-scaffold1122-3050214 9 25096304 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783881 Affx-122965235 AX-385270937 9 24925988 CAGAGGGGAAGGCCAGTAAACCTGCATGACATCAC[A/G]TTGAGGAAGAAACAAAAGTGACTCATGTATCAGAG R 2 1 2 1 101000 r 74 goat snp3942-scaffold1122-3080741 9 25127266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278678 Affx-1111836550 AX-519552156 9 24943429 CTTTCCACTAGTATTATGTGTTAATTTTGGATGTA[A/G]AGCAAAATGATTCAGTTGAACACATATTTTTTCCT R 2 1 2 1 101000 f 74 goat Random2.2K-974 9 24943429 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397235 Affx-122962372 AX-123267590 9 24956449 TGTCTTAGATTTTACATTCTCACCAAAGACTTCAT[A/G]ACCTTTTAAGCCCTTCCAGTACAACCCCACAGCAC R 2 1 2 1 101000 r 74 goat snp3943-scaffold1122-3111202 9 25157666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443005 Affx-122928178 AX-123313342 9 24996333 TTACATTAAGATGACTCTGAGCACTCAGAGCCAGA[C/T]AGGGGCATAAAGCTGATGTGTTCCTTATAAACTCT Y 2 1 2 1 101000 f 74 goat snp3944-scaffold1122-3151086 9 25195901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387991 Affx-122969583 AX-123258349 9 25144013 AAGTTCGCTGAGAAAGCTTGGCTTGGCTGCAAGGC[A/G]TGAGCAACAATTCCCTCCCGTTGAGAACTGAGCTG R 2 1 2 1 101000 r 74 goat snp40802-scaffold524-101136 9 25350422 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432185 Affx-122936399 AX-123302526 9 25176424 AGAGTTTTCCTATGGAGAGTGTAAAAGTCAATAAG[C/T]GCTGTCAGATTTCTGATCTTAAAGTGAGCTATCAG Y 2 1 2 1 101000 f 74 goat snp40803-scaffold524-133547 9 25382814 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438155 Affx-122931463 AX-123308493 9 25286956 ATGCCACTTGAAATACATATTTCACAGCTATTGCA[G/T]AAAAATGTTTATCTTTTAACAAGAGAAACACATAA K 2 1 2 1 103000 f 74 goat snp40805-scaffold524-244079 9 25494182 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476260 Affx-1251763767 AX-586011681 9 25319634 TTTTATGGTTCCCTAAAGGTTTTTCTTAGTAAGAT[-/TAGAAAAAACACATTACCGGATATGAGTATTGCCACTCCTATTAAAGATTTTAAAATTTAAAAAATAAAAAAGAAAAAAA]AGAAAAAACACATTACCATCTCATCTCCATCTAGA - 8 1 4 1 20000 f 74 goat SV_198 9 25319634 - deletion junction SV-TF-chip 539476513 Affx-1251763767 AX-586011906 9 25319634 TTTTATGGTTCCCTAAAGGTTTTTCTTAGTAAGAT[-/TAGAAAAAACACATTACCGGATATGAGTATTGCCACTCCTATTAAAGATTTTAAAATTTAAAAAATAAAAAAGAAAAAAA]AGAAAAAACACATTACCATCTCATCTCCATCTAGA - 8 1 4 1 20000 r 74 goat SV_198 9 25319634 - deletion junction SV-TF-chip 562165707 Affx-1251763767 AX-606941116 9 25319634 TTTTATGGTTCCCTAAAGGTTTTTCTTAGTAAGAT[-/TAGAAAAAACACATTACCGGATATGAGTATTGCCACTCCTATTAAAGATTTTAAAATTTAAAAAATAAAAAAGAAAAAAA]AGAAAAAACACATTACCATCTCATCTCCATCTAGA - 8 1 4 1 20100 r 74 goat SV_198 9 25319634 - deletion junction SV-TF-chip 562165733 Affx-1251763767 AX-606941142 9 25319634 TTTTATGGTTCCCTAAAGGTTTTTCTTAGTAAGAT[-/TAGAAAAAACACATTACCGGATATGAGTATTGCCACTCCTATTAAAGATTTTAAAATTTAAAAAATAAAAAAGAAAAAAA]AGAAAAAACACATTACCATCTCATCTCCATCTAGA - 8 1 4 1 20100 f 74 goat SV_198 9 25319634 - deletion junction SV-TF-chip 562166023 Affx-1251763767 AX-606941432 9 25319634 TTTTATGGTTCCCTAAAGGTTTTTCTTAGTAAGAT[-/TAGAAAAAACACATTACCGGATATGAGTATTGCCACTCCTATTAAAGATTTTAAAATTTAAAAAATAAAAAAGAAAAAAA]AGAAAAAACACATTACCATCTCATCTCCATCTAGA - 8 1 4 1 20100 r 74 goat SV_198 9 25319634 - deletion junction SV-TF-chip 562166088 Affx-1251763767 AX-606941497 9 25319634 TTTTATGGTTCCCTAAAGGTTTTTCTTAGTAAGAT[-/TAGAAAAAACACATTACCGGATATGAGTATTGCCACTCCTATTAAAGATTTTAAAATTTAAAAAATAAAAAAGAAAAAAA]AGAAAAAACACATTACCATCTCATCTCCATCTAGA - 8 1 4 1 20100 f 74 goat SV_198 9 25319634 - deletion junction SV-TF-chip 562166180 Affx-1251763767 AX-606941588 9 25319634 TTTTATGGTTCCCTAAAGGTTTTTCTTAGTAAGAT[-/TAGAAAAAACACATTACCGGATATGAGTATTGCCACTCCTATTAAAGATTTTAAAATTTAAAAAATAAAAAAGAAAAAAA]AGAAAAAACACATTACCATCTCATCTCCATCTAGA - 8 1 4 1 20100 f 74 goat SV_198 9 25319634 - deletion junction SV-TF-chip 562166310 Affx-1251763767 AX-606941718 9 25319634 TTTTATGGTTCCCTAAAGGTTTTTCTTAGTAAGAT[-/TAGAAAAAACACATTACCGGATATGAGTATTGCCACTCCTATTAAAGATTTTAAAATTTAAAAAATAAAAAAGAAAAAAA]AGAAAAAACACATTACCATCTCATCTCCATCTAGA - 8 1 4 1 20100 f 74 goat SV_198 9 25319634 - deletion junction SV-TF-chip 38389031 Affx-122968629 AX-123259389 9 25335171 ACCCTAGCTTTATGATGCCAATCCTAAGAAGAAAT[A/G]TCTTTGAATTGGATAAACCCCTGAGGAATGTTGAA R 2 1 2 1 101000 f 74 goat snp40806-scaffold524-292294 9 25542353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772292 Affx-122975442 AX-385259447 9 25376259 TAGTCCTTGGAAATTATGAAAAGTTGATTATAGTC[A/G]TGCGCTCCATCCTAAACCAGGAGCTGTCATCTATG R 2 1 2 1 101000 r 74 goat snp40807-scaffold524-333382 9 25583776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413178 Affx-122950336 AX-123283527 9 25419658 ACCTTCCCAAGTTGAGTGTGTCATGCCATAAAACT[A/G]AAGGTTTAGTTTATAAAGCAAAATTGGTTTTCTTT R 2 1 2 1 101000 f 74 goat snp40808-scaffold524-376781 9 25627346 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275336 Affx-1111834736 AX-519548911 9 25467522 AAGACTGCAGTGGCCCTCCTTGAGGCAGTTGTCTT[A/G]AAGAAGATGCTGAGGACTGCAGGGTTTTAAGCAGA R 2 1 2 1 202000 r 74 goat GoatD01.050637 9 25467522 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38445758 Affx-122926077 AX-123316095 9 25472212 TTCAGCCTGATGGGAGATGGATAAGGGGGATGGAG[A/G]CTAAGAATGGCCCCTTTGTTGCCTTTTGTGTTTGC R 2 1 2 1 101000 r 74 goat snp40809-scaffold524-429335 9 25680983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411656 Affx-122951565 AX-123282006 9 25536541 TAAATAACAAAATTTCCAAGCTGGAGGGAGCCCTG[C/T]GCCATAGTACACACAGTCTGGAGATGCAGGGCTAA Y 2 1 2 1 201000 r 74 goat snp40810-scaffold524-493664 9 25744891 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392704 Affx-122966404 AX-123263061 9 25573595 TGTACTTAGACGCAAAGAAAGATAGACGCAAAGTC[A/G]CATGTGAGCCATCCTCAGTACCTGGGCCATTCTTC R 2 1 2 1 201000 f 74 goat snp40811-scaffold524-530718 9 25781801 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448036 Affx-122923710 AX-123318372 9 25628918 CAGTGAACCTGGACGGTGAACGGAAGAGAGCCAGC[A/G]CTTCTGGTTGTGCTGCTGCAGTGTCTTCCTTGACT R 2 1 2 1 101000 r 74 goat snp40812-scaffold524-586041 9 25835913 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278865 Affx-1111836551 AX-519552334 9 25639539 ACTGGTTTTTCAAAAGTGAGGCTGATGACAAAAGA[A/G]AAATGCTTGAGTAAAGAAAGTAACTGACGCTGGGA R 2 1 2 1 101000 r 74 goat Random2.2K-975 9 25639539 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419269 Affx-122946253 AX-123289617 9 25662004 TCGGCACACACTCATTCATCAACAGTTTGAGTGCC[A/G]ACTCTCTGCCAAACCCTCTGCCAGGTGCTAGGGAA R 2 1 2 1 201000 f 74 goat snp40813-scaffold524-619127 9 25869065 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412368 Affx-122950817 AX-123282717 9 25705751 TTCTGTTTGCAAGAGACTCTGTAGATGTAGCAATT[A/G]CAGTTTGTTAGGATATAGCCACTTGATGAATGCAG R 2 1 2 1 101000 r 74 goat snp40814-scaffold524-662874 9 25912775 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392621 Affx-122966040 AX-123262978 9 25741563 TGCTTTCCACCACCCGCCTTCCGGCGCCTCCCTGC[A/G]CTCCTCTGCCCATGAGGTGGGTGGCTCAGCTGTTT R 2 1 2 1 103000 r 74 goat snp40815-scaffold524-698686 9 25948676 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389448 Affx-122968347 AX-123259806 9 25782240 GCTGGGAACAGCAAATGCTGTGGTAAGGCTGGGCA[C/T]GAGGGAGAAAAAAGAAATGGGCGATAAGGCCGAGT Y 2 1 2 1 201000 f 74 goat snp40816-scaffold524-739363 9 25989680 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780721 Affx-122956834 AX-385267811 9 25832687 CAGAATGTGTCTGCTGAACAAAGGCTGGAGGTAGG[G/T]CTTAGAGTGTAGATAAAAGGATGTGTGCAAAGCGA K 2 1 2 1 101000 f 74 goat snp40817-scaffold524-789810 9 26040020 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411575 Affx-122951627 AX-123281925 9 25887374 CAGCACCACACTCGTTGTGGCATAGGTCTCCTGAC[A/G]TTGTCCCCTTTTTCCTACAAATCCATCCAATTAGA R 2 1 2 1 101000 r 74 goat snp40818-scaffold524-844497 9 26094636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428158 Affx-122939044 AX-123298501 9 25947116 CTTCTTGCTCTGCTATTTGTCTTCTTCCAGGGACA[C/T]AACACCTTCATTAAATCCCATCCGTCCTTGCCTCA Y 2 1 2 1 201000 r 74 goat snp40819-scaffold524-904239 9 26154166 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441058 Affx-122928919 AX-123311395 9 26007149 TCCCATCTCAGGACCCTTGTCGTGAGAGCTGTTCC[A/G]CAGCCATCCTCAGCTTGGCTTGTCTGTTCCATCAG R 2 1 2 1 201000 f 74 goat snp40820-scaffold524-964272 9 26214045 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767106 Affx-122960169 AX-385254393 9 26064044 GGAGGTGTCTGTGCCAGAGGTCATTGCAAAGGTGA[C/T]AGTAGGAACTATTGCTCCCTTTTTTTGCCTTTTTG Y 2 1 2 1 101000 f 74 goat snp40821-scaffold524-1021167 9 26270942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278682 Affx-1111836552 AX-519552160 9 26090325 ATTGCCTAGCCCAAAAGGACCTTCATTCACTGATC[A/G]GGGCCTGGGAGGTTGGGATGAGCCCTCCTGACCTA R 2 1 2 1 101000 f 74 goat Random2.2K-976 9 26090325 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397062 Affx-122962731 AX-123267417 9 26153564 TGAAGGAAATGAAAAAGGAAACAGCACAGCTCTCA[A/G]TAATTTATTCCCTTCATCATTAAGTGAAAATTGTG R 2 1 2 1 201000 r 74 goat snp40822-scaffold524-1110687 9 26360406 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767578 Affx-122937881 AX-385254830 9 26207616 GAGGCTCACAGACTTCCTAAAGCCCATTATCTATG[A/G]GCTGACAAAGGATAGGACTGCCTTTGAATCCTAAA R 2 1 2 1 101000 f 74 goat snp40823-scaffold524-1164739 9 26414494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779150 Affx-122963399 AX-385266254 9 26257117 GTCAAAAGGAAGACAGGAGACAATAATAAGAATCA[A/G]TAGTCACAGTGCAAGAACCTAAGGGATCCTCCTTG R 2 1 2 1 101000 r 74 goat snp40824-scaffold524-1214240 9 26464368 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464640261 Affx-1110588108 AX-516111306 9 26285549 AAGCCCATAGGGAAATCTGTAACAATAAATCAATA[G/T]AATTTATGAAGGGGGAAAAATAAAGGGGGCTGAAC K 2 1 2 1 201000 f 74 goat 9_26285549_AF-PAKI 9 26285549 G T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418815 Affx-122946162 AX-123289163 9 26286109 ACTAAGCAACCAGTGGAACTAAGCAAGGATAGTCA[C/T]TGACTCTTCAGCAGGTTTTTGAAGGATGCAGGGAA Y 2 1 2 1 101000 f 74 goat snp40825-scaffold524-1243232 9 26493229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404723 Affx-122957246 AX-123275075 9 26330890 TTGTAAACAAAGTTTCTGAAAGGAAATCTAGAAGA[C/T]AGCTCACAGATTTTGAAAACATGAAGAAACCAAGT Y 2 1 2 1 303000 f 74 goat snp40826-scaffold524-1288013 9 26538199 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435931 Affx-122932751 AX-123306270 9 26359662 CTATTGGGGAAAACGAAATCTTTTTTTCAAGCGTT[A/G]AGTAGAAAAGTCAGTTTCTCAGCCATCAACCAATC R 2 1 2 1 101000 f 74 goat snp40827-scaffold524-1316785 9 26567090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781678 Affx-122938629 AX-385268761 9 26411537 ATAATTATAGTCATAAAGCATTTATGAGATTGTAA[A/G]ATTAAGTTTTGACTTCTCTCCAGCTCATTCTGGAA R 2 1 2 1 101000 r 74 goat snp40828-scaffold524-1368660 9 26619028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768341 Affx-122923351 AX-385255521 9 26440286 GTGGTCTGAGCAGACTAGAGAACAATGGGTCTCTG[C/T]TCTCCCACTTTTTATTACTGTATACTCATATCAGG Y 2 1 2 1 101000 f 74 goat snp40829-scaffold524-1397409 9 26647896 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772494 Affx-122950027 AX-385259645 9 26481447 CTCTGCGCTGCAACAAAGCCTTTACCTACATTCTC[G/T]CAAATAATTCTCACATTCTATGAAGAATGACTATT K 2 1 2 1 101000 f 74 goat snp40830-scaffold524-1438570 9 26689135 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432730 Affx-122935463 AX-123303071 9 26534051 CTAAACATTCATGCAGTTTTACCTAGTTAGTATAA[C/T]GAACACATTTCCTTTAGCATTTTAATGTAATTGCA Y 2 1 2 1 101000 f 74 goat snp40831-scaffold524-1491174 9 26742456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778240 Affx-122954125 AX-385265355 9 26599848 AAGTAGCAGTGTGCTTTAAGTGGGATTTCCAGGTG[A/G]TTCAGTGGATGTCAGTATGGATGAATTAAGAATTT R 2 1 2 1 101000 f 74 goat snp40832-scaffold524-1556971 9 26809251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779485 Affx-122970225 AX-385266588 9 26641907 TTCATCTTTTGGGTTCTAGCTATACCTGTCTTCTG[A/C]TGATTTCTTGAGTATAATGTGGATTTTACTCTTCA M 2 1 2 1 101000 f 74 goat snp40833-scaffold524-1599030 9 26851297 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416795 Affx-122948147 AX-123287143 9 26714619 AAACTTCTTTTTGTGTGAGCTTAAGAGTAGAGTTG[C/T]AGTTTTAGTCAACGAGTAGGTTTTTCAAATGCTTC Y 2 1 2 1 101000 f 74 goat snp40834-scaffold524-1671742 9 26923765 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399439 Affx-122961218 AX-123269794 9 26806044 GAAAAATGTGGCAGCAGCAATATGCTGTGGCAAAA[C/T]AGGCTCAGCGCCCCACCTTTACTTTCGTTGCTCTC Y 2 1 2 1 101000 f 74 goat snp40836-scaffold524-1763167 9 27011859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797817 Affx-122976909 AX-385284756 9 26844309 ACCTTTTGAATTTTGATCTACGTATACCCAGGCAC[A/G]CACACACTAAACAGTCTTAAAATATTGGAGGGGGG R 2 1 2 1 101000 r 74 goat snp40837-scaffold524-1801432 9 27050099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799238 Affx-122928751 AX-385286168 9 26880029 TATATGCATTTTCAGGAATACCATTTTTGGCTAGT[A/G]GTGGCAACTATGGCTGGAAAATTTTTCATAGGGGC R 2 1 2 1 201000 f 74 goat snp40838-scaffold524-1837152 9 27086131 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801791 Affx-122957791 AX-385288699 9 26916830 CATTTAGTGGAAGACAAAGGACGATTTCTGCTAGT[A/G]TTAATGGCAACCTCTACTTCCCTTCAGCTGGCAGA R 2 1 2 1 101000 f 74 goat snp40839-scaffold524-1873953 9 27122699 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278870 Affx-1111836553 AX-519552339 9 26920074 TATATCCCTAGAATCTCCAAAAGCCTAAGCAAAAT[A/C]AAAGTTCCAATTATAAACTCAAGGGTATTACAGCT M 2 1 2 1 101000 r 74 goat Random2.2K-977 9 26920074 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779685 Affx-122960632 AX-385266785 9 26969359 AGTAACAGGTGCCTGCTTCATTACCATGAGACTCA[C/T]GCTACGGCATATTATCTACCAGCGTTGATAAGCTT Y 2 1 2 1 101000 f 74 goat snp40840-scaffold524-1926482 9 27176411 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278686 Affx-1111836554 AX-519552164 9 27014418 GATAATATCCTTCAATTATTCTAGGAGACTGACTC[A/G]ATAGAGAACATCTAGAGGGAATTGAAGCCTCTACA R 2 1 2 1 101000 f 74 goat Random2.2K-978 9 27014418 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418044 Affx-122946631 AX-123288392 9 27050589 GTTTTAGTGTTTTTTTTAATTATGGAGATGACATA[C/T]GTTCATTGTAGAAAATCTAGATTACAGAGAGTACA Y 2 1 2 1 101000 r 74 goat snp40841-scaffold524-2007712 9 27258578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375578 Affx-122978741 AX-123245937 9 27089174 TTTAGTACACCATGGGGGTAAACCCAAACTGCCTG[C/T]CAGCAATAACCACTTGTCAAATGTAAAGTCCGTAG Y 2 1 2 1 201000 r 74 goat snp40842-scaffold524-2046297 9 27296806 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424321 Affx-122941955 AX-123294667 9 27120309 TGTAGCCCCACATCTCATGTTGTTAACCTGGACTG[C/T]ATTGGTCATTAAAAAAAAATTGCTAGTTAACACAC Y 2 1 2 1 101000 f 74 goat snp40843-scaffold524-2077432 9 27328032 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762703 Affx-986697233 AX-385250773 9 27170723 GGTCCAGTCCTTTCGTGCCCAGCTGGAGGCATGGC[A/G]TCTCCAAGGGGAGGCTCCTCAGGGTGCACCCAAGT R 2 1 2 1 600010 f 74 goat 9_27170723 9 27170723 Ancestral_priority_1043 ancestry 0.43 neutral IMAGE 10K 10K ancestral 320762709 Affx-986697239 AX-385250777 9 27170909 TATTCTGGGAGCCCTTCCTGTACCAGAGCGGAACC[C/T]GGGTGAGGCCTTTGATGTGCACCATCTCACTTAAT Y 2 1 2 1 600010 f 74 goat 9_27170909 9 27170909 Ancestral_priority_1043 ancestry 0.452 neutral IMAGE 10K 10K ancestral 320803701 Affx-986696185 AX-385290469 9 27171563 CAAGGGTTGATTTTGTTCCCCTGGGGACATTTGGC[C/T]GTGCCCAGAGACACTTTTGATTGTCACGTCTGGGA Y 2 1 2 1 600010 r 74 goat 9_27171563 9 27171563 Ancestral_priority_1043 ancestry 0.566 neutral IMAGE 10K 10K ancestral 320762711 Affx-986697241 AX-385250778 9 27171685 TATATGTTTATTGTAAATTTTACTGATATAGAGCA[A/T]GTTTAGTGTGCAACTTACGAATAAAAAATATGTCA W 4 1 2 1 600010 f 74 goat 9_27171685 9 27171685 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 320765156 Affx-986697243 AX-385252708 9 27171704 TTACTGATATAGAGCAAGTTTAGTGTGCAACTTAC[A/G]AATAAAAAATATGTCATGCTTCTATTGTGAAAAAA R 2 1 2 1 600010 r 74 goat 9_27171704 9 27171704 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 38414834 Affx-122949194 AX-123285183 9 27184969 TCAGTTTTACAGTATTAACCCATTTCTCACATAAC[A/G]TAAAGGTAAAGAATTTTCATGTCTGATACAGACAG R 2 1 2 1 101000 f 74 goat snp40844-scaffold524-2142092 9 27392792 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418951 Affx-122946491 AX-123289299 9 27269954 GGGACTCGAAACCATGGGCTGGCACTTGAATACAC[C/T]GTCTTTTAACTGAAATTGACCATTTGGTCTCAGGA Y 2 1 2 1 101000 r 74 goat snp40846-scaffold524-2227077 9 27478163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377749 Affx-122977373 AX-123248108 9 27301888 CTTCCCATGGTTTCCCTGGTCCCTGGAGCCCTCTG[A/G]CTGGAGTTACTGTGCCTGAAGCATATCCTGCCCTG R 2 1 2 1 101000 r 74 goat snp40847-scaffold524-2259011 9 27507083 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432702 Affx-122936027 AX-123303043 9 27366163 TAGCACTTTCTTAGTTAATTGACATTTTCTTCAAT[C/T]CTGTATTGCTTATAGTTCCATCAGATCTGTGGAAG Y 2 1 2 1 101000 r 74 goat snp10111-scaffold1358-1774980 9 27572432 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791271 Affx-122955076 AX-385278265 9 27405382 ACTCTGCCTTATTCTCTTTAATTATGGCTAATTAA[C/T]TGAATGTTTATCTTCATGAAAGACTCATGAGGTAC Y 2 1 2 1 101000 r 74 goat snp10110-scaffold1358-1735761 9 27612254 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769591 Affx-122943942 AX-385256761 9 27490477 ACGCATCCAAGTATAAGATACAGATATTTTAGTAC[A/G]TGGTCACATCATAAGGAAACAAGTAAGAGCATATT R 2 1 2 1 101000 r 74 goat snp10108-scaffold1358-1650666 9 27698328 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412527 Affx-122951348 AX-123282876 9 27547096 CTCAGACAGAGGACTTAATAGATTTTCTGTGTATT[A/G]CTTTAACATTGTGTGGGCGATGACTGTTATTTTAT R 2 1 2 1 101000 r 74 goat snp10107-scaffold1358-1594047 9 27755124 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789172 Affx-122968947 AX-385276184 9 27581882 CTTGCTAGTTATTGAGTACACCTTGCATTCTAGAA[A/G]TTAATTCTTACAATGTCCCTATTGAGTACAGACCA R 2 1 2 1 201000 f 74 goat snp10106-scaffold1358-1559261 9 27790497 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781373 Affx-122924210 AX-385268458 9 27611692 TAAACATTTATTACTTTTGTGGACATGCACTTTAT[C/T]TATTCTAATTCAACCATGCTTAGAATGTTTGAAGA Y 2 1 2 1 101000 f 74 goat snp10105-scaffold1358-1529451 9 27820262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790370 Affx-122965372 AX-385277373 9 27662230 CCTGTATTCTTAATAGTCACAGCGCCCTCTCTTAA[C/T]GTACTGAGACTATAAAGCAGATCTCTCTATTTTTT Y 2 1 2 1 101000 f 74 goat snp10104-scaffold1358-1478913 9 27870987 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387608 Affx-122970247 AX-123257966 9 27730905 AGTTCTCTGCTTGGGATGAGTGCCCAGCCTAATAA[C/T]GGTGTTACCCTTTATGTAAAGAGTTAGTTTGGCTG Y 2 1 2 1 101000 f 74 goat snp10103-scaffold1358-1410238 9 27939706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785797 Affx-122975512 AX-385272837 9 27760733 TACATACAGACACAGCTCTGACTCATATACTTAGC[A/G]TCATAGAGCTAGATTTTGATGGACTTTGAGAGATA R 2 1 2 1 101000 f 74 goat snp10102-scaffold1358-1380410 9 27969960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400158 Affx-122960690 AX-123270513 9 27789793 ATCACACTATTATAGACAATGCTGGCTTACTAAGA[C/T]GCTGAGGCTCAAAAGTATTTTTAAAATTAGGAGAA Y 2 1 2 1 101000 f 74 goat snp10101-scaffold1358-1351350 9 27999512 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375711 Affx-122978641 AX-123246070 9 27836117 TCCAAAGCACGTCCGTAATGTTTTATGTAACTCAC[A/G]TAGTTTTACCATCCAAGTATGCCTCCCTAGGCACT R 2 1 2 1 101000 r 74 goat snp10100-scaffold1358-1305026 9 28046036 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379384 Affx-122976140 AX-123249743 9 27883446 TTATCTGTGGAAAAGACAAATCTGTGTAGCGGTGT[G/T]ACCCTCATTTACTGTGCTTTTCCTGGTAACCTCTC K 2 1 2 1 201000 f 74 goat snp10099-scaffold1358-1257697 9 28093198 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403525 Affx-122957619 AX-123273878 9 27915767 TGGGGAAAGAAAATGCTAGAATTTCTAAATAGATT[A/G]AGTCCGTACATAAGAAATCCATGTTACACTCTATA R 2 1 2 1 101000 r 74 goat snp10098-scaffold1358-1225376 9 28124637 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782037 Affx-122939556 AX-385269115 9 27952181 GACATCATATAGAACTGTTGTGGCTTTAATATTTT[A/G]CTCAGTGGAGTAGAAGAAATATTCAGGAAAAAAAC R 2 1 2 1 101000 r 74 goat snp10097-scaffold1358-1188962 9 28160976 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386899 Affx-122970039 AX-123257257 9 28002482 CATAGCCACATGTGATTAGAACCTACTGTATTGAA[G/T]AATTCAGCTCTGGATATTAGAAAACATTTTCTTAT K 2 1 2 1 201000 r 74 goat snp10096-scaffold1358-1138661 9 28211271 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274606 Affx-1111834394 AX-519548194 9 28016091 GCACAGGGGCCCGGTCTGCAGGCAAAGGCCTGGGA[A/G]GGGCAGGGAGGTGTTTCAGGGGAAGGGCCGACCTT R 2 1 2 1 303000 f 74 goat GoatD01.033219 9 28016091 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320777065 Affx-122978920 AX-385264188 9 28084539 AGTTCCAAAAGTAGCCAAGCTATTCTGAAGAAGAA[G/T]AAGATGAGGTCTTTCCCTATGATGTATTGATACTA K 2 1 2 1 101000 f 74 goat snp10095-scaffold1358-1056604 9 28293755 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278876 Affx-1111836556 AX-519552345 9 28102669 TCCCACAGTGTGATGTGAGGGCAAAGGTAGGGAGC[A/G]ACGAGGGCCAAACTGTAAACTATGATTGGGGCCTA R 2 1 2 1 102000 r 74 goat Random2.2K-980 9 28102669 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38400067 Affx-122960761 AX-123270422 9 28154676 AAATGAAGGTATAAATTGACAGGAAAACTTCATAG[C/T]AGAGATTCTTGATTCCTTTTGCAGAATGAATGAGT Y 2 1 2 1 101000 f 74 goat snp10094-scaffold1358-986467 9 28364996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792498 Affx-122934972 AX-385279479 9 28244870 CCACAGAATGACTGATGAATGTAATATATTCACTG[C/T]GTAAATCTGTTTATGTACTGAATGTATTGTTATTA Y 2 1 2 1 101000 f 74 goat snp10093-scaffold1358-896273 9 28455413 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386628 Affx-122970226 AX-123256986 9 28285273 CAGCTGGGTGGCAGCAATTGAAATGGATATATAAG[C/T]GAGAGTATACTTAAATTTCAATTTTTTTACAGCGA Y 2 1 2 1 101000 f 74 goat snp10092-scaffold1358-855870 9 28495873 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779034 Affx-122962783 AX-385266141 9 28322031 CAGGCTAGTTTTATTTGCCTTTATAAATGATTAAA[A/G]TGACATCAACTCTTTAGTGGGAATGGTTTATACAT R 2 1 2 1 201000 f 74 goat snp10091-scaffold1358-819112 9 28531158 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435776 Affx-122932868 AX-123306115 9 28367751 CTGCTGTTGGTCAGCCACCAAATTTTCATCTGAAG[C/T]GCAAAATACTTGTTATCTGGGGACTGCCTGAATTT Y 2 1 2 1 101000 f 74 goat snp10090-scaffold1358-773392 9 28577280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781935 Affx-122958623 AX-385269016 9 28431915 ACAGAATGCATTGGCCAAATAATACATTTTTAAGC[A/G]TAAAAACTGTAAGTAACCTGTGCACACAGGAAAAA R 2 1 2 1 202000 f 74 goat snp10089-scaffold1358-709228 9 28641101 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400722 Affx-122959916 AX-123271077 9 28470401 TTCCAATCAAATGCCCAGATTTTGGTGAAAATTGA[C/T]GAGCTATTTTTAAAATTTATAAGGAAAGGCAGAAG Y 2 1 2 1 201000 f 74 goat snp10088-scaffold1358-670742 9 28680287 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386168 Affx-122971383 AX-123256526 9 28503942 GGTCCTTGGTTTAGAGTTTGTAACAAAACAGGAAG[C/T]TCCACCTCTGACCCAGCCCCAATTCCTTTCACCCC Y 2 1 2 1 101000 f 74 goat snp10087-scaffold1358-637201 9 28713791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433726 Affx-122934520 AX-123304067 9 28544666 GGATCCGAGAGCACCTGCTGGAGTGAACAGACATC[A/G]TTCACTCACATCCCACATTTGCAGCCACCCCACTT R 2 1 2 1 201000 r 74 goat snp10086-scaffold1358-596477 9 28755346 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376626 Affx-122979035 AX-123246985 9 28585944 GAAAACTATTCTTTTCTTAAAGAAACAACAACAGT[A/G]GCACAAGTGTTTGCTGTGCGCACCGGCCCAGGAAC R 2 1 2 1 101000 f 74 goat snp10085-scaffold1358-555199 9 28797003 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453636 Affx-122919741 AX-123323969 9 28630664 AGGTCTGGACTCTTTAGGAAAAGTGAATGGTAATT[A/G]CTCTCAACTTTAAAGTTATTCCAATTTGACAGCAG R 2 1 2 1 101000 r 74 goat snp10084-scaffold1358-510479 9 28842941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420678 Affx-122944807 AX-123291025 9 28697594 TTGGGTCCCCAGTTCTGTCTTATGGGGTCACGATA[C/T]AGGACCAGCCTCTTGGCGTGGATGTGGAGCCTTGA Y 2 1 2 1 201000 r 74 goat snp10082-scaffold1358-443549 9 28909923 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278692 Affx-1111836557 AX-519552170 9 28705812 ATTTTCCTGGTATTTTCCCTTTCATCCAAAAAATA[A/C]AAGTGCCCACTTTCCTGGCTTCAATGGATATCTCA M 2 1 2 1 201000 f 74 goat Random2.2K-982 9 28705812 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450235 Affx-122922265 AX-123320570 9 28751657 TAAAGAGTGAGCTTAATTATATATAACTGCATACC[G/T]AAAATGAGGCTTTACATTTTTTTTTAACATATACT K 2 1 2 1 101000 f 74 goat snp10081-scaffold1358-389486 9 28964837 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429157 Affx-122937983 AX-123299499 9 28790326 CAAAGTGGAGGTGATTCCAAATGAATCCCTGTGAA[C/T]GATGTTGGCAAAGCCATCTAAACATACATGTGCTT Y 2 1 2 1 101000 f 74 goat snp10080-scaffold1358-350817 9 29003864 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783043 Affx-122938036 AX-385270111 9 28822149 TATTATTCATTATTGTATTTCCAGTAACCAAGGAT[A/G]TGCCCAGCATTTAGTATTCAATGATAATTGTTAAG R 2 1 2 1 101000 f 74 goat snp10079-scaffold1358-318994 9 29035945 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433556 Affx-122934985 AX-123303897 9 28859671 TGGAAACATTGTGGTATATCTGTTACAAGAATGAA[C/T]AAGACAAGGATGTCAGTTATCACTTTTTAACATTG Y 2 1 2 1 101000 f 74 goat snp10078-scaffold1358-281472 9 29073334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798451 Affx-122935309 AX-385285384 9 28889407 TTCCTAGCTTTCACTCAGAGATAACTTCCATTTCT[A/G]TCTTTCAACCCACCACCAGCAGGAATAGGATGAGG R 2 1 2 1 101000 r 74 goat snp10077-scaffold1358-251736 9 29103189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792385 Affx-122935797 AX-385279366 9 28934004 GCATCTAAGAAAGGAAATAGGAGGTGCTTAGAGAC[A/G]TGAGAATGGAAGAACTAGCTTGGTAATATTTGTAG R 2 1 2 1 101000 f 74 goat snp10076-scaffold1358-207139 9 29148328 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379478 Affx-122976479 AX-123249836 9 28967653 TTAAAAGATATGCTGTGTTATAATAAAACATTAAA[C/T]AGGGAAGCCCACAGCTGCTGATCCCTGTTCTATAG Y 2 1 2 1 201000 f 74 goat snp10075-scaffold1358-173490 9 29182034 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411458 Affx-122951810 AX-123281808 9 29023433 TCAAGGCTGTTTATCCATGTATTAGTCAATTTTTA[C/T]TTCAATAATGCTGAATTGCTTCCAACAACAAACGT Y 2 1 2 1 101000 r 74 goat snp10074-scaffold1358-117710 9 29236869 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273416 Affx-1111833608 AX-519547043 9 29036860 ATATAAGTGATATCATATGATATCGGTCTTTCTCT[A/G]TCTGACTTCCTTCACTCAGTATGACAATCTCTGGG R 2 1 2 1 303000 f 74 goat 9_29036860_AF-PAKI 9 29036860 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789854 Affx-122954279 AX-385276861 9 29178182 ACAACAGGTAGAAAGAGAATGAACACAGAAACAGC[A/G]ATTACAGGCACTGTGTCACTGCAAGGGACTGAACA R 2 1 2 1 101000 f 74 goat snp59112-scaffold969-3751805 9 29392400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447591 Affx-122924013 AX-123317927 9 29214795 GCACAGACTACCTGCTGCTCAGCTAGGACTGCGTC[A/G]TCAGCCTGAAGGAAATTAGGTTTCCTTTAGGAGTT R 2 1 2 1 101000 r 74 goat snp59111-scaffold969-3715192 9 29429614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439339 Affx-122930294 AX-123309676 9 29271422 TAATCCTAACTTTCAAACTCTACGAGGAAGGTACC[A/G]TTATTATTTTCTTTTTTGCAGATAGGGAATCTGCA R 2 1 2 1 303000 f 74 goat snp59110-scaffold969-3658565 9 29486141 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392540 Affx-122966099 AX-123262897 9 29300697 GATTATGTGGAATGTGACAGAATGCCAACTTATGA[C/T]CAAGATAGGCAAAAATAAAATATTTAAAGCTATGA Y 2 1 2 1 101000 f 74 goat snp59109-scaffold969-3629290 9 29515535 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375771 Affx-122978592 AX-123246130 9 29351012 CTTCTCCAAGACACATTACAGGGAGGATTCAGAGG[A/C]TCACATCCTCTATAGGTGAACTAAGCAATAGCACC M 2 1 2 1 201000 r 74 goat snp59108-scaffold969-3578975 9 29566528 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278694 Affx-1111836558 AX-519552172 9 29351110 AACTTATCTTCCTTCATCTACCAATACATGGTGGT[A/G]GAACAGGATAAGTATAAATTTACAAAGAGGAAGGA R 2 1 2 1 101000 f 74 goat Random2.2K-983 9 29351110 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38454216 Affx-122919682 AX-123324549 9 29414683 ATTTGTAGTTCAACAAGGAAGAAGATTTGATTTCT[A/G]GATGCTGGGTATGCAGAGGTACTGTGCGTGTCTGT R 2 1 2 1 201000 f 74 goat snp59107-scaffold969-3515304 9 29630608 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795006 Affx-122940201 AX-385281965 9 29476518 CTTGTACCTGTACCTGGCTGCAATTGCTGAAGAAA[G/T]GTTCAGTGGTATTTTCTTGTACATTAGCCAACAAG K 2 1 2 1 101000 f 74 goat snp59106-scaffold969-3453469 9 29692988 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378609 Affx-122976571 AX-123248968 9 29527624 CAGCAGAACCTTCTGGAGAATCTAGGGTGGAGCAG[A/G]CATCTGACTGCTCCACCTGCTTGTTAGTGATGTCT R 2 1 2 1 201000 r 74 goat snp59105-scaffold969-3402363 9 29744339 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449024 Affx-122923083 AX-123319359 9 29566250 GTAGAGCATCAGAGCTTCGAGTGGTCACCCTGAAG[G/T]CACACTGCCTAGGTTTGAATCTTGATTCTACCACT K 2 1 2 1 101000 f 74 goat snp59104-scaffold969-3363737 9 29782967 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278696 Affx-1111836559 AX-519552174 9 29606088 TTCCTCTCTCACTCCTTTGGAGGATAGCTTTGTCC[A/G]CGTCGCTGCCCATAGCTTTCCCTGGGGACACATTG R 2 1 2 1 101000 f 74 goat Random2.2K-984 9 29606088 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421470 Affx-122943927 AX-123291817 9 29620486 ACACAAAGTTGAGTAAATAAATGAATCCTTTATCT[A/G]CAATGAAGGTTTCCCCTCTGGGGAGATTTGTCAAG R 2 1 2 1 103000 r 74 goat snp59103-scaffold969-3309501 9 29837279 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378655 Affx-122977094 AX-123249014 9 29652977 CCAGTGCTGCAGGACTAAGTATGGAATTAACCTTC[A/G]TGCACAGAATTTCCTCTTTTTAAAATGTTATGTTT R 2 1 2 1 101000 f 74 goat snp59102-scaffold969-3277010 9 29869801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404761 Affx-122957219 AX-123275113 9 29704424 CCAGATAGGCCAATTAATCTATGAAGTGGCCAGCT[A/G]TAGCTAGAGAATCTTGAATGGTAAACTGGAGGACA R 2 1 2 1 201000 r 74 goat snp59101-scaffold969-3225563 9 29922147 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426487 Affx-122940228 AX-123296833 9 29753867 TTGTACTTCTATTTAGTAACCCAATTGGAAGAAAA[C/T]AAGACCAGGCAAAGATCTGAATAACCTAGCAGACT Y 2 1 2 1 201000 f 74 goat snp59100-scaffold969-3176120 9 29980214 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776363 Affx-122958351 AX-385263491 9 29786519 TGGGTGTCAAATCTAATACACATGAGGGAGACTGG[C/T]TAAAAAGGTTTCTAATAATACTTGTGACTGTGACC Y 2 1 2 1 101000 f 74 goat snp59099-scaffold969-3143468 9 30012097 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417073 Affx-122947505 AX-123287421 9 29821216 GCAGCATGTCAAATAGGAGTTGACAATTACAGTCT[C/T]TATCAATACATATTATGCCAGACGGTAATGAGCCA Y 2 1 2 1 101000 r 74 goat snp59098-scaffold969-3108771 9 30046177 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412475 Affx-122951390 AX-123282824 9 29861233 GGAACTGGTGATAAGCATTCTGTGCAGACAACTTG[C/T]GCCCTTCTAAATAAATGTGATTCAGGAGTACTGTC Y 2 1 2 1 101000 f 74 goat snp59097-scaffold969-3068754 9 30086197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389307 Affx-122968504 AX-123259665 9 29923176 GCACAGCTTGCTGCTGGGAAGGGAATTTTAATGTG[C/T]ACCCTATGCAAATGTGTTTTATAATAAAACAAAAT Y 2 1 2 1 101000 f 74 goat snp59096-scaffold969-3006811 9 30148050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476261 Affx-1251763768 AX-586011682 9 29968835 AGCTTCAGCATCAGTCCTTCCAATGAATAGCCAGG[-/ACTGATCTCCTTTATTTATTTATTTATTTATTTATTTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTACC]CTGATCTCCTTTAGAATGGACTGGATGGGTCTCCT - 4 1 4 1 20000 f 74 goat SV_207 9 29968835 - deletion junction SV-TF-chip 539476514 Affx-1251763768 AX-586011907 9 29968835 AGCTTCAGCATCAGTCCTTCCAATGAATAGCCAGG[-/ACTGATCTCCTTTATTTATTTATTTATTTATTTATTTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTACC]CTGATCTCCTTTAGAATGGACTGGATGGGTCTCCT - 8 1 4 1 20000 r 74 goat SV_207 9 29968835 - deletion junction SV-TF-chip 562165301 Affx-1251763768 AX-606940712 9 29968835 AGCTTCAGCATCAGTCCTTCCAATGAATAGCCAGG[-/ACTGATCTCCTTTATTTATTTATTTATTTATTTATTTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTACC]CTGATCTCCTTTAGAATGGACTGGATGGGTCTCCT - 8 1 4 1 20100 r 74 goat SV_207 9 29968835 - deletion junction SV-TF-chip 562165364 Affx-1251763768 AX-606940775 9 29968835 AGCTTCAGCATCAGTCCTTCCAATGAATAGCCAGG[-/ACTGATCTCCTTTATTTATTTATTTATTTATTTATTTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTACC]CTGATCTCCTTTAGAATGGACTGGATGGGTCTCCT - 8 1 4 1 20100 r 74 goat SV_207 9 29968835 - deletion junction SV-TF-chip 562165846 Affx-1251763768 AX-606941255 9 29968835 AGCTTCAGCATCAGTCCTTCCAATGAATAGCCAGG[-/ACTGATCTCCTTTATTTATTTATTTATTTATTTATTTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTACC]CTGATCTCCTTTAGAATGGACTGGATGGGTCTCCT - 8 1 4 1 20100 f 74 goat SV_207 9 29968835 - deletion junction SV-TF-chip 562166193 Affx-1251763768 AX-606941601 9 29968835 AGCTTCAGCATCAGTCCTTCCAATGAATAGCCAGG[-/ACTGATCTCCTTTATTTATTTATTTATTTATTTATTTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTACC]CTGATCTCCTTTAGAATGGACTGGATGGGTCTCCT - 8 1 4 1 20100 f 74 goat SV_207 9 29968835 - deletion junction SV-TF-chip 320795760 Affx-122945520 AX-385282713 9 29977872 GGTTCATATGATGGTCCTGAATGCTGTCTGGAAGA[G/T]ACCACTTTAAATTCAAACTCCACCCAGGAAGGGAA K 2 1 2 1 101000 f 74 goat snp59095-scaffold969-2952115 9 30204039 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415784 Affx-122948913 AX-123286133 9 30006751 TTTAAATGGTGCTTTTATAAAAGTAACCCTGGAAA[G/T]ATACATAAGATACCATAAGTGTGAGTGGAGAAGGG K 2 1 2 1 101000 r 74 goat snp59094-scaffold969-2923236 9 30232772 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450342 Affx-122922117 AX-123320677 9 30051338 CAACTATGAAGGGGATCAGAGTATCTCACTTTAAC[A/G]TAAGGATTATTTTGAATTGAAGGCAACTAAGAAAC R 2 1 2 1 101000 f 74 goat snp59093-scaffold969-2878649 9 30277334 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394543 Affx-122964467 AX-123264898 9 30138403 GTGAGAGAGAATTCACTCTGTCTGCTTGTCTTTGT[A/G]CTGGACCATCAGTCTCCTGACTTCAGACTCAGACT R 2 1 2 1 101000 f 74 goat snp59092-scaffold969-2791584 9 30364777 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435292 Affx-122934035 AX-123305632 9 30171285 GCTCAGAGCTGGTCAGTGGGGATGGGTGGAAGTGA[C/T]GTAAACCACTTCCAGGTCTGAATATTAACAATATA Y 2 1 2 1 101000 r 74 goat snp59091-scaffold969-2758702 9 30398000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405270 Affx-122956864 AX-123275622 9 30207984 CTCTGCCTCTATCAGCATGTGGCCTTCTTACTGTA[C/T]GTCTGTCTCAAACCTCCCTGTGACTTTCTCTAACA Y 2 1 2 1 101000 r 74 goat snp59090-scaffold969-2722003 9 30434763 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765159 Affx-986697245 AX-385252710 9 30247718 AGCCATACAGGTGGGCTTCAGGGGCTTTTTTTTTT[C/T]TTTTTTTACATGAAGCAATAGAATTATAAAATGCC Y 2 1 2 1 600010 r 74 goat 9_30247718 9 30247718 Ancestral_priority_1043 ancestry 0.59 neutral IMAGE 10K 10K ancestral 320794756 Affx-122940845 AX-385281716 9 30249905 ATGCTGCTCATAGCACTTCAATCTCCAGGACAATA[C/T]ATCTGTATCAATATGCTTTGGTAACTGTCCCCAGA Y 2 1 2 1 101000 f 74 goat snp59089-scaffold969-2680082 9 30476440 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409521 Affx-122953624 AX-123279872 9 30297767 TGGGAATCACCCTTCATCTACCCAAACCATGTGTG[C/T]AGGAGAATGCCTCGGGGGAGTGCCTTGGCCAGGAG Y 2 1 2 1 101000 f 74 goat snp59088-scaffold969-2632220 9 30524193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384628 Affx-122972163 AX-123254986 9 30358484 CTTACTCATAACCAGAAGTTTGTGCCTTTAGACCA[C/T]CTTCATCCTATTCCCCCTTCCCCTACCTCCTACTT Y 2 1 2 1 103000 f 74 goat snp59087-scaffold969-2571503 9 30584977 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446580 Affx-122924826 AX-123316916 9 30395801 CAAATTTCCTCAGGAAGAGAGCTTGTGAGGCACTG[C/T]ACTTCCCAATCCATGGAATGTTTTCCCTTGAATAA Y 2 1 2 1 101000 r 74 goat snp59086-scaffold969-2534186 9 30622516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419962 Affx-122945201 AX-123290310 9 30425223 AGCAGGGCAGAGCCCGGGCTGACAAAGTCTCCAGA[C/T]GGCACGCTCTTGGCTCAGGGCGCTCTCAGTATGCC Y 2 1 2 1 101000 r 74 goat snp59085-scaffold969-2504764 9 30650988 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384218 Affx-122972382 AX-123254576 9 30471671 GCTGTGGGACATCCCAGGGAGGCAGGGTAGAGAAG[C/T]GCCCTAGGCTGGAAGCACAGTGTTTGCAAAGCCCT Y 2 1 2 1 101000 r 74 goat snp59084-scaffold969-2458316 9 30697270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427722 Affx-122939274 AX-123298065 9 30528264 CGAGGTTATCTGCCATCAGACTGCTCACCTTGAGG[C/T]TTCTGCAGGTCTGGAATTCTCTTCCCACTGGACAG Y 2 1 2 1 101000 f 74 goat snp59083-scaffold969-2401723 9 30753890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419036 Affx-122946029 AX-123289384 9 30557992 GTGTTTCTACCACCATCACTTTTGACAGCTTTTTC[A/G]TCACCCAATTAATCTTATAATTGTCAAGGGGGAGT R 2 1 2 1 101000 f 74 goat snp59082-scaffold969-2371995 9 30783681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795965 Affx-122944429 AX-385282917 9 30600042 TTGTGATTCCAAACATTGAAGGAAAAGTAAGTTAC[A/G]TTCAGCATACTCAGGGTGAAGAAGCACATATTTCA R 2 1 2 1 101000 r 74 goat snp59081-scaffold969-2329945 9 30825773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407955 Affx-122954351 AX-123278306 9 30634779 TTGAGTATATAATTTTATCTGTATTAAGACATTTC[A/G]CTTTCAGCAGGAGACTCATAAACACAGAATACACT R 2 1 2 1 101000 r 74 goat snp59080-scaffold969-2295208 9 30860414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407613 Affx-122954640 AX-123277964 9 30711644 CAGATGCGATGAGTGTGAAGAAGTAAAGGATGTCA[C/T]AGGCGCAAACAGCAAAGAAATTTGCAGGAAAGCTC Y 2 1 2 1 201000 f 74 goat snp59078-scaffold969-2218343 9 30935909 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443097 Affx-122928107 AX-123313434 9 30758242 CTAAAAGAGAGGTGCTATTTAAAAAAAGCCAATTA[C/T]TGGGATTGGCTCTTGGAATATAGACGTTGTAACTC Y 2 1 2 1 101000 r 74 goat snp59077-scaffold969-2171745 9 30982804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432557 Affx-122935539 AX-123302898 9 30832524 TCAGAGAACCCTCCCTGTTTCGCGCTTTCACAGAG[C/T]GAAGCTGTTCTAAGTCTTGGGGTCACACCCAGCTC Y 2 1 2 1 202000 r 74 goat snp59075-scaffold969-2097463 9 31056954 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425165 Affx-122941061 AX-123295511 9 30873075 TGTGCATGGTGCTGCATTTTGAGTTTTCAGAGGCA[C/T]GGGACAGCGCAATCTCTGTTGTAAATCCCTAGGAT Y 2 1 2 1 101000 f 74 goat snp59074-scaffold969-2056912 9 31097519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401684 Affx-122959557 AX-123272037 9 30922727 AGTATTGCTCCAATGCAGAGGGGAAGCAGAGAGAA[A/G]GAACAGTTCCCTCTTCTGTCCCACAAAGTTAGTCC R 2 1 2 1 201000 r 74 goat snp59073-scaffold969-2007260 9 31147008 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444170 Affx-122927279 AX-123314507 9 30970126 ACAATGGTCCCTGATGGACGGCTGGGACTGTGAGG[A/G]CCAGTAGGAGGGCAAGGCTGGAGACTGGACCAACG R 2 1 2 1 102000 f 74 goat snp59072-scaffold969-1959861 9 31194089 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397037 Affx-122963110 AX-123267392 9 31003719 TAACTTCTAAAAAACCAAGTAGTGATCATATGAAA[A/G]CTTATGTGGATTTCTTTTCCATTTGGGGTGGGGAG R 2 1 2 1 201000 f 74 goat snp59071-scaffold969-1926268 9 31227718 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407563 Affx-122954677 AX-123277914 9 31068564 TGAGCCATATCCCCCAGCTCTCCTAGAGCCACAGA[C/T]GCACCTAGGGATACCCAGTGCCTGGGCTCACTGGG Y 2 1 2 1 101000 r 74 goat snp59070-scaffold969-1861423 9 31293208 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798828 Affx-122932509 AX-385285758 9 31115495 GGACTAGAGATGCTTAACAAACTCTGAACCAGCCA[A/G]CTCCTACAATAGGCTCATAAGGGAGGTATACTAAG R 2 1 2 1 101000 f 74 goat snp59069-scaffold969-1814492 9 31340313 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448739 Affx-122923329 AX-123319075 9 31168881 GAGCCTCCCATCAGAGTGTAATTGAGCTCTAATTG[C/T]TCCATATGATCACCAGCACTTGGGATTGTAAGGTG Y 2 1 2 1 101000 r 74 goat snp59068-scaffold969-1761106 9 31393871 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380694 Affx-122975168 AX-123251052 9 31198570 CTCCATGATGGCACTGTGGTGTCCCACCCAGCAGT[C/T]TCCCTGTGGGCCAAGTGTTGGGATAAATGGATTCA Y 2 1 2 1 101000 r 74 goat snp59067-scaffold969-1731417 9 31423298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778176 Affx-122919922 AX-385265292 9 31311574 AAAGGAAATATGAGGAAAGAAGTTGAAATATCAGC[A/G]TTTATAAAATTGAAATCCCAAGAGGAACAAAAAGA R 2 1 2 1 101000 f 74 goat snp59064-scaffold969-1618413 9 31537081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802180 Affx-122977817 AX-385289084 9 31347468 CCAATATAGATTCTTTTGATTCATGACCTACATTT[G/T]GAGGCTGAGAGCCTTCTGAGTATCCTATGACAATA K 2 1 2 1 101000 r 74 goat snp59063-scaffold969-1582519 9 31573370 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801366 Affx-122945675 AX-385288277 9 31437939 AAAAGATAACACCTTCCCTCCTGTGGACTTTGACA[A/G]ATTCAAGTTCTGAGTCTACTGAAACCATGTATTCT R 2 1 2 1 101000 f 74 goat snp59061-scaffold969-1492048 9 31664655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453096 Affx-122920036 AX-123323429 9 31468162 TTTTTACTTAAAATAACTGAAATCCCTAACTGGTG[C/T]AAAGGCACCATGAATATAAGGATACACTTGGATCC Y 2 1 2 1 101000 r 74 goat snp59060-scaffold969-1461825 9 31695327 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273456 Affx-1111833609 AX-186491575 9 31540225 ATGGAGGAGGCTGGTGGGCTGCCGTCTATGGGGTC[A/G]CACAGAGTTGGACACGACTGAAGTGACTTAGCAGC R 2 1 2 1 103000 r 74 goat 9_31540225_AF-PAKI 9 31540225 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320794480 Affx-122938371 AX-385281443 9 31562255 ACTCCAAGGGTGTGATTTGACTATCGTTTACAAGA[C/T]GACTCAAGCAAAAAGCACACACTAGAGAGGACACA Y 2 1 2 1 101000 r 74 goat snp59058-scaffold969-1367732 9 31789979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405941 Affx-122955559 AX-123276293 9 31605690 GAATGACATGGTTGTGCACTGCACTGGCCCACTTA[C/T]ATGTGAATGTTTTTCAGGAAACCTATTGGAAAAAA Y 2 1 2 1 101000 f 74 goat snp59057-scaffold969-1324297 9 31834933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400430 Affx-122959970 AX-123270785 9 31637855 GGTCTCAAACCTCGCCATTACCAGGGAGCTCATTC[A/G]CAGGTGGAACACTAACCTGAGCTGGCTCTGTTCTT R 2 1 2 1 101000 f 74 goat snp59056-scaffold969-1292132 9 31867023 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381500 Affx-122974870 AX-123251858 9 31692549 AAGCAGCACGCACTCTTACCTAAGACGTCTTTCTC[A/G]TGCTCAGGAACCAGCACTTTCCACCTGGACTCCTC R 2 1 2 1 101000 f 74 goat snp59055-scaffold969-1237438 9 31922291 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791276 Affx-122925912 AX-385278270 9 31743260 AAAATCAGGTGAATCAAGGGCTCCAGACTTAGCAT[A/G]TTGGTTTGGGATGTAAATCAAACATATGGTATGTT R 2 1 2 1 101000 f 74 goat snp59054-scaffold969-1186727 9 31972855 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440444 Affx-122929404 AX-123310781 9 31802109 CAAGGGCCAACTTTGTAAGCAGGCCTTTCAGAAGA[C/T]AGCATCAGATCTGCTACATGAACTTTACTCCACAG Y 2 1 2 1 101000 r 74 goat snp59053-scaffold969-1127878 9 32031826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442308 Affx-122928243 AX-123312645 9 31842007 TAAATCAGAGCCTGCTTATCAGTTCACCTCTGGTC[A/G]CAGTGCAGTCTTAGACAAGGCCTCTGAGGAACCCA R 2 1 2 1 101000 f 74 goat snp59052-scaffold969-1087980 9 32071870 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441375 Affx-122928860 AX-123311712 9 31899157 CAGAGGAACTAGTCCTCTCTGCCTTTTCCATCCTC[A/G]CTCTATCTAGGTTAACAGATGTTCTAACATCTTCT R 2 1 2 1 101000 r 74 goat snp59051-scaffold969-1030830 9 32129770 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430380 Affx-122937777 AX-123300721 9 31929382 TACATTAATGTGAAAGAACTCCACACCTCTTAAGA[C/T]GATAGAAAAATATGCATGCCTAAATTTACAGACAG Y 2 1 2 1 101000 r 74 goat snp59050-scaffold969-1000605 9 32160087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386684 Affx-122970182 AX-123257042 9 31964258 AATCACCAGTATGGGGTGAGGTAGGAGAGTGAGAG[G/T]CCTTATGAGGAAGGTCTGAGACAAAGGGGACATGG K 2 1 2 1 101000 r 74 goat snp59049-scaffold969-965729 9 32195845 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448901 Affx-122923181 AX-123319236 9 32005570 GTCCATGGGGTTACAAAGAGTTGGATACAACTGAG[C/T]GACTGACACACACAGTGATGATAAAAAGATGTAGG Y 2 1 2 1 103000 r 74 goat snp59048-scaffold969-924417 9 32237539 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376436 Affx-122978066 AX-123246795 9 32050654 CATTGAGAGGAGGAAAAGGAATATAGCAAGACAGT[G/T]GAGCATCAGTATTTTTATAATTCTGAAATAATTTT K 2 1 2 1 101000 f 74 goat snp59047-scaffold969-879333 9 32283141 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451349 Affx-122921258 AX-123321682 9 32113717 ACATTGGTTGCTTTATTTAAATGGCTTTTCCCCCC[G/T]AAATGAGATTATTTAGACAGGCTTGTGTGTAAGGC K 2 1 2 1 102000 r 74 goat snp59046-scaffold969-816270 9 32345788 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429981 Affx-122938051 AX-123300322 9 32154893 TTCATCTTGTATCCCTAGGGCTGGTCTGGGCACAC[A/G]CCTAATAAGTGTATGTTTTTATTCTAAGTGGTATT R 2 1 2 1 101000 f 74 goat snp59045-scaffold969-775094 9 32386822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390909 Affx-122967095 AX-123261266 9 32229929 CACATTATAAACCAGTAAATAAACACTATAAAATA[C/T]AAAGTGCTATGAAGGAAATGATCATGATGCTGTGA Y 2 1 2 1 201000 f 74 goat snp59043-scaffold969-700058 9 32461998 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428042 Affx-122939133 AX-123298385 9 32266728 CAAAATATCTCAACACATATATGTACATATGCCTA[C/T]AAAACCAAAGGACACATTTCTGTATGTAAACTTTC Y 2 1 2 1 101000 r 74 goat snp59042-scaffold969-663259 9 32498741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435373 Affx-122933580 AX-123305713 9 32361843 GGCTCAAAATTGGTGGGTCTCACCTTGTACATAGT[A/G]CTGCTTTCAGGGTCTGCCAGATACTGCAGCTCCAC R 2 1 2 1 101000 f 74 goat snp59040-scaffold969-568144 9 32593641 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410240 Affx-122952545 AX-123280590 9 32409207 CAAAATAAGTCCAGCTTATTGCTGCCCCGAGTGCC[C/T]CACATGTATTCCCTCTGCCTGAAGCATCCCTCCTG Y 2 1 2 1 101000 f 74 goat snp59039-scaffold969-520780 9 32640951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391326 Affx-122967317 AX-123261683 9 32459895 CCATGCATTAGGAACACAGAGTCTTAAACACAGAA[C/T]GCTAGGAAAGTCCCAACAATTACCCTTCTAATAAT Y 2 1 2 1 201000 r 74 goat snp59038-scaffold969-470092 9 32691591 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771065 Affx-122925985 AX-385258225 9 32488451 CTAGAGCACATGCCACTGTAAGATTTCACAACACT[C/T]AGGAGAGAAGCTGATTTCAAGATAGCATTTAGCTA Y 2 1 2 1 101000 f 74 goat snp59037-scaffold969-441536 9 32720778 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783753 Affx-122920571 AX-385270809 9 32553232 TAATGCAGTCTCCCAACTCCTTGCCTTTCAATTCA[C/T]AGCACCCATAATCTGAAAGAGTCCCATCAACTCCT Y 2 1 2 1 101000 f 74 goat snp59036-scaffold969-376755 9 32784793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390146 Affx-122922563 AX-123260503 9 32591561 GCTTTGGTGCATCCAAGAATCCCTGCCTGCCCTTC[A/G]TCACTGCCTGCCTTAGAGATTTGGACTTGCCCAGC R 2 1 2 1 101000 r 74 goat snp59035-scaffold969-338426 9 32824268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788176 Affx-122954939 AX-385275195 9 32624500 CTACAAACATTATTGTCTCTCTATAGTGGGCACAA[C/T]GAAATCAGAGATGGTTATGAGATTGGATTTATAGA Y 2 1 2 1 201000 f 74 goat snp59034-scaffold969-305487 9 32857766 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278884 Affx-1111836560 AX-519552352 9 32694167 CTTCCTGGTACTCCATTTTTTTCTTGACTTTGTTA[A/T]AGTCTCATAGTTTTCTGGGCTCTGCTCATCTTTGT W 4 1 2 1 101000 r 74 goat Random2.2K-985 9 32694167 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408920 Affx-122953954 AX-123279271 9 32757487 AAAAACCAAGGCAGGGTGGAGCCCTTCTACCACAA[C/T]AATGGTAGAAGATTTGTAACATCAACAGCAAGGTT Y 2 1 2 1 201000 r 74 goat snp59031-scaffold969-172500 9 32991460 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385618 Affx-122971188 AX-123255976 9 32795892 ACCTAAATAGATAGGCACAAATCATAATAACTCAA[C/T]ACTCTAAAGATACCTTTCAAATTAGTTTTTAGGTT Y 2 1 2 1 101000 f 74 goat snp59030-scaffold969-134095 9 33030033 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410623 Affx-122952094 AX-123280973 9 32824559 TCAATCTTCCTTGCCAGCTTCCTTTCCTTCCCCTT[A/G]CCTCAAATCTTCCACTGAAGTAATGTGTCATTTAT R 2 1 2 1 201000 r 74 goat snp59029-scaffold969-105428 9 33058591 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408750 Affx-122953400 AX-123279101 9 32857481 GCATAGATTTTATGTTGATATTTTTTAATGGGCTG[A/C]TATTTATATTTTCTTAAAAGTTAAGTCTATATCAG M 2 1 2 1 201000 r 74 goat snp59028-scaffold969-72506 9 33091353 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773975 Affx-122932238 AX-385261113 9 32917561 AAATAGGTAATAAACTTGGGATGGATGTGAATAAA[C/T]ATAGTCATACTGTTTATGAGAGCATTAACTACTCT Y 2 1 2 1 101000 r 74 goat snp59027-scaffold969-12426 9 33152432 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385436 Affx-122971319 AX-123255794 9 32959592 TATACTCTAGGCAGTGTTCTTTCTCTGAGTAATGC[A/G]TTAGGGAAAGACAAAGCTTTCCTCATTTTTCTCCT R 2 1 2 1 101000 f 74 goat snp32138-scaffold363-1508669 9 33216713 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449464 Affx-122922653 AX-123319799 9 33006099 ACTGAAGGCCTTTTTCAGCTCTGACACTCTCTATT[A/G]CTATAGTTCTTCTACATGGAGGGCCTCTGTGAAAT R 2 1 2 1 101000 f 74 goat snp32137-scaffold363-1462162 9 33262845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793021 Affx-122970554 AX-385279999 9 33048256 AAGAACAAATGAAGATCCAATGATGGTCCATCTGG[A/G]TAGGATGCTAGTGAAACTTGGAAATCTTTAGTCAA R 2 1 2 1 101000 f 74 goat snp32136-scaffold363-1420005 9 33305163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789338 Affx-122934386 AX-385276348 9 33107955 GACAAGTCTCCTCAATGTGTCTTTATAGGGATTTT[A/G]CTTCCAGGATTAAATTTGAATCCCAAACAGAGCAT R 2 1 2 1 201000 r 74 goat snp32135-scaffold363-1360306 9 33365066 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406492 Affx-122955157 AX-123276844 9 33163901 AAAGTAGGATGCTTCCATTAAGGTCCCTGCAATCT[A/G]CATTTCCTAATACAGGTTTACAGAAATGGTTTTGA R 2 1 2 1 101000 f 74 goat snp32134-scaffold363-1304360 9 33420963 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278701 Affx-1111836561 AX-519552179 9 33189809 GGTCACTGGTCTTCACTGGAATCACCCAGGAGCTT[A/T]AGAAACCCTGCTGCTCAGTCCCACTCTCAGAGGTG W 4 1 2 1 102000 f 74 goat Random2.2K-986 9 33189809 T A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776206 Affx-122954666 AX-385263334 9 33255900 TGCTTTTCCTTCCTTCCACCAGTCAGGGGAAATAT[A/C]TTCCTATACTGCACATAGATCCAATATTAAGCTAA M 2 1 2 1 101000 f 74 goat snp32133-scaffold363-1212361 9 33513047 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427344 Affx-122940116 AX-123297687 9 33296736 AATCGAATACCACAGGCAGAAATGACTAATTTGTA[C/T]GACTCTCCCAGCACTGGGTTCCATCTGCTTACCCT Y 2 1 2 1 201000 f 74 goat snp32132-scaffold363-1171525 9 33555071 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774562 Affx-122925723 AX-385261696 9 33338629 TCTGAAAGAGTTCCTTTGAAACTTACTGACATCTA[C/T]GTGATGTACTGCTAACACTTGATACCTGGCATCTC Y 2 1 2 1 101000 r 74 goat snp32131-scaffold363-1129632 9 33595266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776213 Affx-122924833 AX-385263341 9 33402827 CCCATGATGTACATTTTGGGACCTGCATTTTAATG[C/T]ATTTGATGGGAGTTCTCTCATATAATTGGCGCTCT Y 2 1 2 1 201000 r 74 goat snp32130-scaffold363-1065434 9 33662132 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376668 Affx-122979003 AX-123247027 9 33443727 AATATGAGGACACTCTTGATTAGCAATGGCAAAAA[G/T]CCCCTCAGACAAAAGGACCAATTGAAATTGCCAAA K 2 1 2 1 101000 f 74 goat snp32129-scaffold363-1024534 9 33703116 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799135 Affx-122952326 AX-385286065 9 33473557 GGTGGAATTTAACAAGCATTCTAAATATCCCAATT[A/G]TGAAATATATCATGTTTTGATATGTGAATTTTTCC R 2 1 2 1 202000 r 74 goat snp32128-scaffold363-994704 9 33733022 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392116 Affx-122966348 AX-123262473 9 33525501 TCCAGTTAATTAATTGTAGATGCTAAATCCCTCAG[C/T]AGAACACATTAAACCAAAGTCATGTGGGTGAAAAT Y 2 1 2 1 101000 f 74 goat snp32127-scaffold363-942760 9 33782237 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388897 Affx-122968854 AX-123259255 9 33566736 CCAAATTTCCACCTCAGTCTCACCAGATATACTTG[C/T]GCCCCTGTTGTTTCTCCCCTCACACTTACACCCCA Y 2 1 2 1 201000 r 74 goat snp32126-scaffold363-901525 9 33824400 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791538 Affx-122956657 AX-385278529 9 33595914 ATAGAACAAAAAAGCAGTAAACCTAACCATTAAAA[C/T]ACAAAGTATGAAAATCATCAGCAAACTCTTATGGA Y 2 1 2 1 101000 r 74 goat snp32125-scaffold363-872347 9 33853668 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783336 Affx-122974523 AX-385270400 9 33646507 TTTAAAGCAAAAATTGGAGTAAGACTAGTGTTTAG[C/T]AGTTCAATAAAATGAGCCACTCTTTGAATTTCTGA Y 2 1 2 1 101000 r 74 goat snp32124-scaffold363-821754 9 33905511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779811 Affx-122968062 AX-385266911 9 33677299 TTGTTTGTTTGATTGTTTTTAACAAATATTCAGGT[A/G]TCAGTCTCCTATTGAATACTGAATAGTCACAAGTT R 2 1 2 1 201000 f 74 goat snp32123-scaffold363-790962 9 33936408 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412956 Affx-122951048 AX-123283305 9 33705886 CTAGAAAAGTGGAAGTAGAGTTCATCAAATCAGGT[A/G]CAGTAATTATTCAGCTTTTTAAAATATCAGTACTT R 2 1 2 1 101000 f 74 goat snp32122-scaffold363-762375 9 33965361 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440772 Affx-122929853 AX-123311109 9 33741538 CGACCCCAATCGTCAGGCAAGGTAGAGCGGGTGAA[C/T]GGCATCATCAAGACACATCTGGCCAAGCTAGCCTC Y 2 1 2 1 103000 r 74 goat snp32121-scaffold363-726723 9 34002533 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441199 Affx-122929532 AX-123311536 9 33771095 ATAACTGAAAATTATATAATGTTTAAGGCAATTAT[A/G]CTGCAATATAAAAAATAGAAAATATTGAGATTGCC R 2 1 2 1 303000 f 74 goat snp32120-scaffold363-697166 9 34032083 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799001 Affx-122924884 AX-385285931 9 33818240 AATTGGTTAGAGTAAGAACACTACTGTAACTGTAA[C/T]ATCTTCAGTTCTCAGAACTCTGAAATTCAATTATA Y 2 1 2 1 101000 r 74 goat snp32119-scaffold363-650021 9 34080312 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794461 Affx-122947359 AX-385281424 9 33949919 ATTTTAAAGTACCAGATATTCCTTGGACTTTCACT[A/G]CTTGTGTACACTGTTTCTTCACCCATACTGTGTCT R 2 1 2 1 101000 f 74 goat snp32117-scaffold363-518342 9 34213084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430609 Affx-122936976 AX-123300950 9 34008563 GTCAAGTTTGTGGTAATTTGTTACAGCAGCAATAG[A/G]AAGCTAATGAAGGGCTATCAACATATGTTGTTGAA R 2 1 2 1 201000 r 74 goat snp32116-scaffold363-459698 9 34273170 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424692 Affx-122941700 AX-123295038 9 34045572 GTCCCATAGCTAAAGACTCAGTCTCACAGACTGCA[A/G]CCCAAGCCCCATTGACCCTCCCATAGCAAACCCAG R 2 1 2 1 101000 f 74 goat snp32115-scaffold363-422689 9 34308020 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426754 Affx-122939858 AX-123297100 9 34074191 TCTGAGATGCTGTCTTGCAAAGAAGAGTGACCTGA[C/T]AGCTAAGAATTCCCTAGAGCCTTAACGATTATCTT Y 2 1 2 1 101000 r 74 goat snp32114-scaffold363-394070 9 34336172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776344 Affx-122925136 AX-385263472 9 34113391 AAGAGTAGGGATAGCACACTTATGAGGAGGAGATA[C/T]GTTACAGTTCCATGCATGGTAGGAACTTTGTACCT Y 2 1 2 1 101000 f 74 goat snp32113-scaffold363-354870 9 34375352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273458 Affx-1111833610 AX-519547079 9 34140888 TTTTCAAACTAAAGCAAAGTTTAAAGAGCAATACA[A/G]TGATTACAACTGGGCCGAGCTTTAGCTTTATTTAC R 2 1 2 1 101000 r 74 goat 9_34140888_AF-PAKI 9 34140888 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38414526 Affx-122949517 AX-123284875 9 34144063 GTTAAAAATGAAAAAAAAATATGATTCTTACCATA[C/T]GCCATTAAATTGGCCATGCTAGTGTATTCACATCT Y 2 1 2 1 101000 r 74 goat snp32112-scaffold363-324198 9 34405638 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394358 Affx-122964650 AX-123264713 9 34174696 AAGTTTCATGATTTATCCCTTTTTTAATTAAAAAG[C/T]ATGCAAAATGTAGCTCGAAGTCAATGTAGGAAGTC Y 2 1 2 1 101000 r 74 goat snp32111-scaffold363-293565 9 34436536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770136 Affx-122965431 AX-385257303 9 34206369 TTTTAAAATAAAATGTCGTTTCAACTAATCCTGGC[A/G]TATGCACCAACAGTGTTAAGTTCTAATGCCCTGAA R 2 1 2 1 101000 r 74 goat snp32110-scaffold363-261892 9 34468692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380956 Affx-122974996 AX-123251314 9 34263835 ATTTCAGGCCCCCAAACCTTGTTTTTCTCCAAATG[C/T]GCTATGCACAGTATTGATTTTATAGATGTGGCAGT Y 2 1 2 1 201000 r 74 goat snp32109-scaffold363-204426 9 34524856 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386740 Affx-122970140 AX-123257098 9 34306762 TAGAAATCCTCCCCTATTACTCATCCTGCAAAAAC[A/G]TTTTGTAAACAAACGATGCTACATATTTTTAACTT R 2 1 2 1 201000 r 74 goat snp32108-scaffold363-161499 9 34568758 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407335 Affx-122955295 AX-123277686 9 34350880 TTTACTTACTAAAGTATTTTTTCAGTTCCAAGATA[C/T]AATTCTGGATTTCAACATGCATTTTATTGTCATAT Y 2 1 2 1 101000 r 74 goat snp32107-scaffold363-117381 9 34613488 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385428 Affx-122971325 AX-123255786 9 34404732 AGAGTATAATTGAACCTCTATGAACAAAATCTCTA[C/T]ATCTCATCTCTAACTCAGTTACAATTACATTACCT Y 2 1 2 1 101000 f 74 goat snp32106-scaffold363-63529 9 34668391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376981 Affx-122977747 AX-123247340 9 34444181 AAAAACTATGTTGTTTTATTCAAATATGATAAAAA[C/T]GGTAGCTGACTTTGAAATTGTTCCTAACTCCTGCT Y 2 1 2 1 101000 r 74 goat snp32105-scaffold363-24080 9 34707540 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425110 Affx-122941227 AX-123295456 9 34490598 GCTACAAGGAAACATACAGATAACATACAGAGGTG[A/C]AGGTTTAGCTTTCATTTTTTATAAAACAAATCTGT M 2 1 2 1 101000 f 74 goat snp44056-scaffold596-1028511 9 34751465 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320781667 Affx-122955428 AX-385268751 9 34536641 TGGTACAGAGAATAACCATTTAAATATGTGATAAT[A/G]CTATGTCTTTACTGAGAAACTTGCTTCCCACTGTC R 2 1 2 1 101000 r 74 goat snp44055-scaffold596-982468 9 34796993 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383521 Affx-122972633 AX-123253879 9 34585635 TGACCATTAATTAGAAATTTCTTCAATTATCTTTC[A/G]TACTCTTATAACTATAAATGGTCAACCATTATATA R 2 1 2 1 201000 r 74 goat snp44054-scaffold596-933474 9 34845891 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771642 Affx-122961769 AX-385258800 9 34625480 ATGATTGCTTTTGAATTCATAATACTAAATAAAGT[A/G]TTACCAGTCTATAACCTCAGATCATCATTTCTAAC R 2 1 2 1 101000 r 74 goat snp44053-scaffold596-893629 9 34883902 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771301 Affx-122934011 AX-385258459 9 34682201 ACATCATTAACAGCTATAGTAGAGTGAAAGCCTAA[C/T]TCCCAGGCATAGATGCTGACGTGCCAAGATCACTG Y 2 1 2 1 101000 r 74 goat snp44052-scaffold596-836908 9 34941150 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428943 Affx-122938890 AX-123299285 9 34716419 AGCCTTCTATTTTTGTATAGTTAAAAAAAAATATG[A/G]CACCGTTCCTTAAAGCTTACTTATCTAACTGTTAC R 2 1 2 1 101000 r 74 goat snp44051-scaffold596-802690 9 34976413 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796802 Affx-122952548 AX-385283745 9 34765442 GATGGTACAGAAAGAAAATATAACCGCAAAAAATA[A/G]CCTAATATTTGTGGCACAATAAAAGAAACTTCACT R 2 1 2 1 101000 f 74 goat snp44050-scaffold596-753667 9 35026106 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406465 Affx-122955179 AX-123276817 9 34837300 ATTTTGAGAGAAGTTCTTGTCAGTACTTTTGGCAA[A/C]ATCAGTCCCTTATTTGGTGTGTGTGTATGGCAGAT M 2 1 2 1 201000 r 74 goat snp44048-scaffold596-681809 9 35098160 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426443 Affx-122940811 AX-123296789 9 34867935 CTGTTAAACTTTTTCTTGGATTGCATATCTGAGCA[G/T]CCTCAGGGTATGTCACTGTTCTGCTCTACAACACT K 2 1 2 1 101000 f 74 goat snp44047-scaffold596-651174 9 35129285 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390559 Affx-122967212 AX-123260916 9 34948687 ACTACTGAGCTAACATTTTTCTAATTTTCTTTGAT[C/T]TCATAACTTTAAAACTGGTGGTGTGAAAACTGGGT Y 2 1 2 1 103000 r 74 goat snp44046-scaffold596-570422 9 35210079 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399838 Affx-122960254 AX-123270193 9 34977759 AAAACTATTATAGAGAATATGGTCACCTCAATGGC[A/G]TAAATAATTATTTCCAAAAATATAATGTAAGTTTT R 2 1 2 1 101000 f 74 goat snp44045-scaffold596-541350 9 35239711 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442349 Affx-122928035 AX-123312686 9 35087731 CCTAGTTATTTTATTTTTTAAGAAATAATTCAGGC[A/G]TTTATTCTTGGTCAGGAAAACATTATTTCATAATT R 2 1 2 1 303000 r 74 goat snp44043-scaffold596-431378 9 35349143 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440900 Affx-122929222 AX-123311237 9 35120000 TAACAATATACTATTCTTGAATTATTTCATGTGTG[C/T]ACTATTTCTCCAAACATCACTGACCACTCCTTTGA Y 2 1 2 1 101000 r 74 goat snp44042-scaffold596-399109 9 35381404 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411241 Affx-122952338 AX-123281591 9 35158131 TAAGCCTCAACTCTTCAGAATCTTTTACCCACACC[A/G]TTAGATTGTTAAAGAAAATTAAATCATATCTGAAA R 2 1 2 1 101000 f 74 goat snp44041-scaffold596-360978 9 35419551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425536 Affx-122941454 AX-123295882 9 35189828 TTTCTGTTAGACGTGCCCTACCTAACAAACTACAA[C/T]GAGACTCTTACAGCTTTTGTTCTAGGGCAGTGATT Y 2 1 2 1 201000 f 74 goat snp44040-scaffold596-329281 9 35451430 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776442 Affx-122979151 AX-385263569 9 35226746 GAACTGCCTTGTTTTACTTATGCTGTTTTTATCTT[A/G]CTTGACTTTGGCACCTGGTTGAGGTTCTAGTCACC R 2 1 2 1 101000 r 74 goat snp44039-scaffold596-292363 9 35488313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388574 Affx-122969169 AX-123258932 9 35283054 AACTCGAGATTTTTGAACTGCCCGTACTCTCATAA[C/T]ACTTTCCATACTCTCATAAGTTTTCTACCTGCAGT Y 2 1 2 1 101000 f 74 goat snp44038-scaffold596-236055 9 35545376 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376714 Affx-122978969 AX-123247073 9 35314356 CATTTACCTAAAAGAGGAAAACAAGGAAAAAAATG[C/T]GGGAAAAGGTATAATAAGTCTGACTTTTAACACAT Y 2 1 2 1 101000 r 74 goat snp44037-scaffold596-204753 9 35575980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401060 Affx-122959647 AX-123271413 9 35360366 GTAATGTGTAATTATAATATGACACCAGATGCATG[C/T]GGATAACGCAGTAAAATCCGACGGATGTATTGGTA Y 2 1 2 1 101000 r 74 goat snp44036-scaffold596-158743 9 35622317 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785404 Affx-122926330 AX-385272449 9 35393001 AGTTTGTTCTAATCCTCTTCTGTAGAACATATGTA[C/T]GTTTTAAACTTGATGGGAACAAAGACAGTTCAAGG Y 2 1 2 1 201000 r 74 goat snp44035-scaffold596-126108 9 35654821 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399964 Affx-122960833 AX-123270319 9 35442211 TAAATCTTAAATCTCACAACTTGCCTGCCGACAGT[A/G]CTGTTAGGCCATTCATGCATCCATGTACGGTACTG R 2 1 2 1 101000 r 74 goat snp44034-scaffold596-76898 9 35704259 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389264 Affx-122969022 AX-123259622 9 35471918 ATCTTTAATCCTGTGATATCTTCTCTAGATTACCT[A/G]TCTTGGCCTGGAGAAAATGACATTTCGATGTCACC R 2 1 2 1 201000 f 74 goat snp44033-scaffold596-47191 9 35733871 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404105 Affx-122957120 AX-123274457 9 35506620 CACTTTTCTTTCTATCAGCAAAAGGAAGGAGAGAG[C/T]TGCAGAAAGTATTCAGTAGTCATCTGTTAATATAT Y 2 1 2 1 101000 r 74 goat snp44032-scaffold596-12489 9 35768514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426312 Affx-122940288 AX-123296658 9 35530899 TGCTGTAACAATTTCAAAACCATAGTTAAAATATC[A/G]CTTCCTCTGTGAAGCCTTTCTTAAATTCCCTCCAG R 2 1 2 1 201000 f 74 goat snp59779-scaffold992-2444696 9 35789425 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391647 Affx-122966565 AX-123262004 9 35574767 CCAGACACACCATACTCATAATTCTCCCCACTTTC[A/G]CAGAGCCTCCTTCTGGGGCTTCTTACCTATAATTG R 2 1 2 1 101000 r 74 goat snp59778-scaffold992-2400828 9 35833596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762684 Affx-986697214 AX-385250760 9 35621652 TCATATATTATCATAAGGAAATTAAACTATAATAT[A/C]GTGTTAAGAGCAGGAAAAATGTTCATTATCAAATA M 2 1 2 1 600010 f 74 goat 9_35621652 9 35621652 Ancestral_priority_1043 ancestry 0.56 neutral IMAGE 10K 10K ancestral 320765110 Affx-986697216 AX-385252671 9 35621653 CATATATTATCATAAGGAAATTAAACTATAATATA[G/T]TGTTAAGAGCAGGAAAAATGTTCATTATCAAATAG K 2 1 2 1 600010 r 74 goat 9_35621653 9 35621653 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 320762688 Affx-986697218 AX-385250763 9 35621696 AGCAGGAAAAATGTTCATTATCAAATAGGTCATTA[C/T]ATATTTAAATAAATTATTGGCTTTTTAAACTATCA Y 2 1 2 1 600010 f 74 goat 9_35621696 9 35621696 Ancestral_priority_1043 ancestry 0.708 recommended IMAGE 10K 10K ancestral 320765117 Affx-986697220 AX-385252677 9 35621716 TCAAATAGGTCATTACATATTTAAATAAATTATTG[A/G]CTTTTTAAACTATCATTATGTGGCTAATTAAGCAA R 2 1 2 1 600010 r 74 goat 9_35621716 9 35621716 Ancestral_priority_1043 ancestry 0.756 recommended IMAGE 10K 10K ancestral 320762692 Affx-986697222 AX-385250767 9 35621950 ACTTAAAATCTGTGTCCTGTATCAATTATACATTG[C/T]CTTGCCTTGTTCTTTATTTCTGCCATAACTTTGTG Y 2 1 2 1 600010 f 74 goat 9_35621950 9 35621950 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 320792859 Affx-122924422 AX-385279837 9 35639191 ACTGATCTGGAAGCAGATTGAGACAGTTATCTTAA[C/T]ATATTAAAAGTTGGTACAACAGATTGCAAAATAAG Y 2 1 2 1 101000 f 74 goat snp59777-scaffold992-2336404 9 35875793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381995 Affx-122974082 AX-123252353 9 35670624 CCTTTGTTCTCAACACTGATTTCACAAACACATCC[A/G]CTGAATTCACATCAGACTTGCCTGGCAAGCTTAAA R 2 1 2 1 101000 f 74 goat snp59776-scaffold992-2304971 9 35907371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442931 Affx-122927620 AX-123313268 9 35722018 TTCACAAACACAGAAAATTGAGAACAGATTATATG[C/T]AAAGGTCAGCAGCATCCATGGAGAATTGAGAGGAA Y 2 1 2 1 201000 f 74 goat snp59775-scaffold992-2253577 9 35958997 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422205 Affx-122944446 AX-123292551 9 35781574 TTGCCTAATTTTTTATATCTTAGATTTATTAACCA[C/T]GGGTGGCTAAGTATGAAATATAATGCAAAAGAAAA Y 2 1 2 1 101000 r 74 goat snp59774-scaffold992-2194021 9 36018721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789795 Affx-122920815 AX-385276802 9 35846663 AGGATCTTTTTAATTAATGAAATTTACAGTAAATA[C/T]GTATTAATAGATTTCATCTGCTATAGTCTATCTGA Y 2 1 2 1 202000 f 74 goat snp59773-scaffold992-2128932 9 36084052 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405395 Affx-122956295 AX-123275747 9 35895795 AAAATACAGGGCTCTCAATTAGAGGACGTTCAGAG[C/T]AGCCCTCAATGGAAAATCAGGGAGACTCTAATCTT Y 2 1 2 1 101000 r 74 goat snp59772-scaffold992-2079800 9 36133189 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790822 Affx-122970448 AX-385277822 9 35934501 AAGAACTCGGAAGGCCATTAATTTTAGCTCTGACC[A/G]TGCAGCTATGCTATGTATTAATCTTCTCTGTCATT R 2 1 2 1 101000 f 74 goat snp59771-scaffold992-2041094 9 36172562 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411186 Affx-122952378 AX-123281536 9 35972584 GTTAGCCAACATTTCTAAAGGAAAATTTAGGTAGG[C/T]AAACAAATGGAGATGGTAGAAAACTGTCTCATTTT Y 2 1 2 1 101000 f 74 goat snp59770-scaffold992-2003011 9 36211935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773431 Affx-122942950 AX-385260573 9 36002904 GTCCCCTCATTAATGCTTTGATGTATCTTTTGAGG[C/T]AATGGGTGGAATGGCTGTTGAATTTCACATTTGAC Y 2 1 2 1 101000 r 74 goat snp59769-scaffold992-1972691 9 36243289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427965 Affx-122939193 AX-123298308 9 36050144 TGAAGGAATTTATGTCTGTTAGAAAATAAGATGCA[A/G]ATTCTATAACAGTAAAATAATGGCATGTCTGAATT R 2 1 2 1 201000 r 74 goat snp59768-scaffold992-1925451 9 36289864 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447967 Affx-122923764 AX-123318303 9 36107853 AAGACAAAATGGGAATCTAATTTACAAAGGTCCCC[A/C]AGGGTTATTCTACTCAAATAACAATTTCTTAGAGG M 2 1 2 1 201000 r 74 goat snp59767-scaffold992-1867742 9 36347766 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799018 Affx-122966220 AX-385285948 9 36156170 TTAAATAAATGCTTACAGCAATTTCTAAATGTAAT[C/T]GCCATACTTATTTATGCCTATAAACTGACAACTAA Y 2 1 2 1 101000 r 74 goat snp59766-scaffold992-1819425 9 36396426 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278702 Affx-1111836562 AX-519552180 9 36195902 GTCCCTCATTTTTGTTCCAGATTTCATCAGAATGG[A/C]CTTTGACTGTCCATATTTCTATGAACATTCTGTTC M 2 1 2 1 101000 f 74 goat Random2.2K-987 9 36195902 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401198 Affx-122959337 AX-123271551 9 36247396 GTGATATTAAGCAGTTCTTTAAAACTCAGTGAAGG[C/T]AGTCTGTCAGTAAATTGCACTGTAAAGTGTACAGA Y 2 1 2 1 101000 r 74 goat snp59765-scaffold992-1728199 9 36488547 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434912 Affx-122934321 AX-123305252 9 36292003 GTTGTAGAAGCTGGGTGTAGTCTGCATGGAAAAAG[A/C]TATGGTAGTCTACAGAGTATTTAGCCCTGGTGGTT M 2 1 2 1 101000 f 74 goat snp59764-scaffold992-1683592 9 36533590 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786546 Affx-122966803 AX-385273579 9 36327214 AATTCTGTGTAACATAATACAAATAGGACATTTTA[A/G]TCTGGAATGATACAAACTGGGTGGGAACAATGATC R 2 1 2 1 101000 r 74 goat snp59763-scaffold992-1648381 9 36568879 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275104 Affx-1111834600 AX-519548683 9 36359999 TAAAG[A/G]AGTATGTTCAACCATGCTTTTAACTACATTGAAGG R 2 1 2 1 101000 r 74 goat GoatD01.042762 9 36359999 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38392550 Affx-122966090 AX-123262907 9 36389403 GGCATAGAACAGAAAAGCTTCCAGATAAGAGAAAA[C/T]GAAGGACAAGCAAGAGAAAGTATAATCAGCAAGGA Y 2 1 2 1 201000 f 74 goat snp59762-scaffold992-1586192 9 36630898 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420702 Affx-122944789 AX-123291049 9 36429955 CCATTTGGTTATTAGTTTAGTCAGTTCAGTCATGT[A/C]TGACTCTGTGCGACCCCATGGACTGCAGCATGTCA M 2 1 2 1 303000 f 74 goat snp59761-scaffold992-1545640 9 36671765 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409266 Affx-122953125 AX-123279617 9 36461376 GGCTATACTGCATGAAGAATAGGCTGACTTCTGGA[C/T]ACACAAGTCCAACTAGTGGGAGTAACTCTTTTTCT Y 2 1 2 1 201000 f 74 goat snp59760-scaffold992-1514219 9 36702966 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427725 Affx-122939272 AX-123298068 9 36497891 GACTTTATCTAGGGAAATATTAATGTCTAGGGAAA[C/T]ACTAACGTTTTTCTTCTTCCATGTACGTGAATGAG Y 2 1 2 1 101000 r 74 goat snp59759-scaffold992-1477704 9 36739943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412569 Affx-122951316 AX-123282918 9 36564435 TTATGATAAAGCAATTTTTGGTAGTGTTGAAACAC[A/G]TGATCCCTACGCCTGTTCCTGTTCCTGTCGCACTT R 2 1 2 1 201000 f 74 goat snp59758-scaffold992-1411160 9 36806836 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395029 Affx-122964213 AX-123265384 9 36611290 CCTCATGTCAATTCTTTGGGACTGAGAAAGTGTGT[A/G]CTATTACCCCAATTACATGTGAGGTATTCTTTGCT R 2 1 2 1 101000 r 74 goat snp59757-scaffold992-1364305 9 36853935 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778897 Affx-122976232 AX-385266005 9 36663114 GCATTTATATTGCCAAAGTATAACCATACTTTAAG[C/T]AACAGTATTAGAAAACAAGTTCTGATTTCCTGATT Y 2 1 2 1 201000 r 74 goat snp59756-scaffold992-1312481 9 36905848 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464646006 Affx-1110591019 AX-516116991 9 36677607 AGAAGAGGACCTGCAGAGAAGTGTTAGCATTTGTC[C/T]ACTACGAAGCTTGAAGCCGTTGAAGAAACTTAAGC Y 2 1 2 1 101000 f 74 goat 9_36677607_AF-PAKI 9 36677607 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38420175 Affx-122945570 AX-123290523 9 36724690 CTGAATGAAGCCACTGGTGGCTAGAATTCGCTTAT[C/T]GCCCTTTTAGTGTGAAAACAGAATCCAGCTAGAGA Y 2 1 2 1 101000 f 74 goat snp59755-scaffold992-1250905 9 36967744 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438276 Affx-122931404 AX-123308614 9 36761694 GGTGTATTCTTTCAATTGAAACATGCCTTTTTCAA[C/T]TGGACTTAAGGGGAATTAGACCTAAGGTTTACTAA Y 2 1 2 1 201000 f 74 goat snp59754-scaffold992-1213901 9 37004856 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438198 Affx-122931822 AX-123308536 9 36815138 TTGTCAAGTTTTCTCGGCTCTCTTTCTGGCTGGCG[A/G]CCTGAATGGCTTTCTGATGTCTGTCTAAATTAACC R 2 1 2 1 101000 r 74 goat snp59753-scaffold992-1160457 9 37058159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278704 Affx-1111836563 AX-519552183 9 36885714 ATTTATTTCTTACTGATTTTTATGAATTAAAAAAA[A/T]TTTTTGAGGTATATCTGTTTCTCTTTTGCTTGGTT W 4 1 2 1 303000 f 74 goat Random2.2K-988 9 36885714 T A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415340 Affx-122948790 AX-123285689 9 36920100 GTGGCAAGAAACTGCATCTCTTCCCTCCAGACTGC[A/G]TGGTTGCTTTAACACTGCTCTCAGTTACACACTAT R 2 1 2 1 101000 r 74 goat snp59751-scaffold992-1055495 9 37161673 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400262 Affx-122960133 AX-123270617 9 36956181 CTAAACTTACCAGGCTTTATTCCACACACTGTGAG[A/C]TTTGGAGGCATCAGCTGAATTAACCAGATATACCT M 2 1 2 1 101000 r 74 goat snp59750-scaffold992-1019414 9 37197307 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795948 Affx-122958810 AX-385282900 9 37002751 ATTTTTTTTATCTCTATGATTGCCAAAGTAAACTT[C/T]AAGACCAAGGGAGTGATAAAGTTGTTTCCCAAGTG Y 2 1 2 1 102000 r 74 goat snp59749-scaffold992-972844 9 37251316 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789310 Affx-122937583 AX-385276320 9 37038649 CTAATTTGTTCTCATTTACTTCCAGGCCTGATCAT[A/G]TTTTTCGAGCTTCTTTTACTTGGCGTGTCTCCTGG R 2 1 2 1 101000 r 74 goat snp59748-scaffold992-936946 9 37287702 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418173 Affx-122947082 AX-123288521 9 37080097 CCACAGCCAAACCAGCATTCTCACCTGGCTGTTCC[A/G]TGTGCAACCTGACGGATACATCCTGTTTGTTCTCA R 2 1 2 1 101000 r 74 goat snp59747-scaffold992-895498 9 37330366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439127 Affx-122931091 AX-123309464 9 37127285 GATGAAGGAATGAATTCACTGAGCACCTGCTCTGA[G/T]CTGGCTGCTGCCTTTTCATCCTAGGTCCCTGAGTA K 2 1 2 1 201000 r 74 goat snp59746-scaffold992-848310 9 37378430 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453038 Affx-122920082 AX-123323371 9 37212952 GATACGACTACCTATTATGACTACTCTACATGAAT[A/G]TTCATTAACTTAAAAAACACCAAACAACCAAAAAA R 2 1 2 1 101000 f 74 goat snp59744-scaffold992-762643 9 37463872 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790911 Affx-122977694 AX-385277908 9 37248637 TTTTTTTTCTCTTAAACATACCAAGATCTTGAGGT[A/G]TTTCTACAGAGGGATATTATTGGATATAACAACCT R 2 1 2 1 101000 r 74 goat snp59743-scaffold992-726958 9 37499598 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442908 Affx-122927637 AX-123313245 9 37294741 ATACTCTCCACAAGGAAGCAGAACTCTAAAAGTCC[A/G]TTTATAAACTATATGAAATTACTACTTGATAAACC R 2 1 2 1 102000 f 74 goat snp59742-scaffold992-680854 9 37545410 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407297 Affx-122955322 AX-123277648 9 37356918 CTGAAGCTAAGCTACTGACACATATGCTACCTAAA[A/G]ATGTACTCAATTGAAGGGTCAGGAGTCTGGTATTA R 2 1 2 1 201000 f 74 goat snp59741-scaffold992-618677 9 37607694 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320785897 Affx-122942595 AX-385272934 9 37406245 TTCTTCAAGATAAAGTCAATCCCAGGAGCTGTGTG[C/T]GGTCTTTCATGTACTCGTCATGACCTACAACATCT Y 2 1 2 1 101000 f 74 goat snp59740-scaffold992-569350 9 37656919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438006 Affx-122931577 AX-123308344 9 37450160 CAAGGAGGAAGAGGAAAAGAATAAAGGATAAAGGA[C/T]AGGTTCAGAGAAACAGAAAATAAAAGCCGAGATTC Y 2 1 2 1 201000 f 74 goat snp59739-scaffold992-525435 9 37700936 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780367 Affx-122928651 AX-385267462 9 37524160 GCACAGTCTGCCTTGTCAAATCTTAAACTTTGGAT[A/C]TTTCTTTGCAATTTGATTTGTCTTTTACCTGAGAA M 2 1 2 1 101000 f 74 goat snp59738-scaffold992-451435 9 37774272 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378377 Affx-122976812 AX-123248736 9 37563772 CCGAATCACCACAGGAAGGGAGGGGGAAGCTGCAG[C/T]GTTTCTCTCGCAATTCCCATCTCTCAAGTTTGAAG Y 2 1 2 1 101000 r 74 goat snp59737-scaffold992-411823 9 37813554 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397431 Affx-122962235 AX-123267786 9 37613246 ATTGTCTTAATCTTCTAAACATGTGGCAATTTTGC[A/G]TAGCAATATGAAAAAAATACAGATATAGATAGCAG R 2 1 2 1 103000 f 74 goat snp59736-scaffold992-362349 9 37863007 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389266 Affx-122969020 AX-123259624 9 37655748 ATAAGTTAGTGACCCAAAAAAGTTCCAACCTAAAT[A/G]TGAAATCTAGCTATATCTGGTTTTTCTGCTTGGTG R 2 1 2 1 101000 r 74 goat snp59735-scaffold992-319847 9 37905375 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428554 Affx-122938728 AX-123298896 9 37687261 GGGCCCTGGGATGATTAATACATATTTGAGAAGTC[A/G]TTCCTGAAGTATGTGAACGTCCTGGCAGCAGAAGT R 2 1 2 1 101000 f 74 goat snp59734-scaffold992-288334 9 37937137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377877 Affx-122977262 AX-123248236 9 37735570 GTCGGTCCCAGCCAGGCCATGATTCCATCCTTCCT[A/G]CCTGTCTCAGTGTGGCTTTTTCTTTTTATCTTTAG R 2 1 2 1 101000 r 74 goat snp59733-scaffold992-240025 9 37985500 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400938 Affx-122959712 AX-123271291 9 37767430 ATGCTAACAATAAGATTACCTAGAATGACGTGAGA[C/T]GGTCAATTATTTGGTTCATTCAGCCCCCTTAACTA Y 2 1 2 1 101000 f 74 goat snp59732-scaffold992-208165 9 38017240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408791 Affx-122953368 AX-123279142 9 37809060 TATACCCAATTAGCATGAGAAGAGTGTAAACACTA[C/T]GATTTTCGTCCAGACATCTTTAAGTAACAGGCAAT Y 2 1 2 1 101000 r 74 goat snp59731-scaffold992-166535 9 38059339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274871 Affx-1111834465 AX-519548455 9 37813434 CCATCTGAAAGACCTGCAGGCTGTTCCTGGGTACA[A/G]TGGAATTTATTCTGGAGAGTATCCTCCTGTCACAG R 2 1 2 1 201000 r 74 goat GoatD01.036935 9 37813434 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320796840 Affx-122947883 AX-385283783 9 37857180 TTCCAGTAAACATATCACTGACAATAACAGCAGGA[A/G]CTTTTACAGTTAACAAAACCCTTACAATCACCCCA R 2 1 2 1 101000 f 74 goat snp59730-scaffold992-118415 9 38107900 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398930 Affx-122960998 AX-123269285 9 37907172 TTCATAGCATAAGGATGGATTGCTACTGTTCAGCA[C/T]ATAGATGATAGCTTATCTTCCAGGCTTATTCTCGT Y 2 1 2 1 101000 f 74 goat snp59729-scaffold992-68423 9 38157832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774988 Affx-122930846 AX-385262120 9 37960364 GTTCCAGTCTACGGACATAGTCTTCTGGGGACTTC[A/G]GAAAACTTTCACTGCCTCTCAATAAAGAGACACAT R 2 1 2 1 101000 f 74 goat snp59728-scaffold992-15231 9 38211339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416047 Affx-122948354 AX-123286396 9 37993426 CAGCACCAGCAATGGACTTGGCTGTCAAGCTGACC[A/G]TGTCTGTCTTTATATCCTATCCATCTCTAAAACCT R 2 1 2 1 101000 r 74 goat snp4763-scaffold1159-17732 9 38244451 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775023 Affx-122933963 AX-385262155 9 38036429 AAACAAGTAAAGCCACCATGGGAGACATTACCAGT[A/G]CCCACCAATATCTTGTTCTCATCCAGAAGCAAGAG R 2 1 2 1 101000 f 74 goat snp4764-scaffold1159-60735 9 38287774 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770330 Affx-122972956 AX-385257496 9 38076828 AATACCCATAGTGATACTGAGGGGATCTTCAGACT[A/G]TAAATATGTGTGGTGAACTCACTCTACAGGCACAC R 2 1 2 1 101000 f 74 goat snp4765-scaffold1159-101134 9 38327729 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389866 Affx-122968148 AX-123260223 9 38114473 GCTAAATGAACCTAGGTGATTGTGAAGACTAGCTA[C/T]TTGAGTTTTGAAATGAAATAAACTCCAAAGAATAA Y 2 1 2 1 101000 f 74 goat snp4766-scaffold1159-138779 9 38365373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376630 Affx-122979032 AX-123246989 9 38147566 ATAAATAAATATATGTATATATATATTTATCACCA[C/T]GCACACAAATATACACACATGTGTGTGGTGATATT Y 2 1 2 1 303000 f 74 goat snp4767-scaffold1159-171872 9 38398812 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388302 Affx-122969384 AX-123258660 9 38199417 ACCCGTAGACCCAAATGGAGCTTTTCATTTCCTGG[A/C]GTGGAGTTGTTTCTCTCATTTGATCTCACTTCAAA M 2 1 2 1 101000 f 74 goat snp4768-scaffold1159-223723 9 38452428 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391271 Affx-122967359 AX-123261628 9 38233747 ATAAAAACAAGATTAAAAAGCCCCCATATGCTCTA[C/T]ACTGTAGCAGGAGTGACTTTTTACACACCCAAATC Y 2 1 2 1 101000 r 74 goat snp4769-scaffold1159-258053 9 38487171 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392194 Affx-122966289 AX-123262551 9 38263690 CAGGGTGAACCAGCATCCGTTTGAAGACAGACAGT[A/G]CACTTGTGGGATGAAGCTGAAAGGTGGGCGGAAGC R 2 1 2 1 201000 f 74 goat snp4770-scaffold1159-287996 9 38517135 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786915 Affx-122967397 AX-385273944 9 38353349 TCTCTAACTTTAATAAGTGCGAAAAAACAAAGTGC[A/G]TGTGCATTATATTTAACCAAACCATAACTCCCACA R 2 1 2 1 101000 r 74 goat snp4772-scaffold1159-377655 9 38606675 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801279 Affx-122945118 AX-385288191 9 38421138 AGGTAAAAGCATAGCTATGTTTGGCAAGGCCCAGA[C/T]CTTCATTATAACGAAAGCTTAGGGTTTCAGTTTTG Y 2 1 2 1 101000 f 74 goat snp4774-scaffold1159-445444 9 38674794 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424228 Affx-122942483 AX-123294574 9 38449835 ACTTTCTGGTGTGATACTTAACTGCTGTCTGTAAA[G/T]AAACATCCTCTGAGAAAAGGGCTCTAAAAGAGTTT K 2 1 2 1 101000 f 74 goat snp4775-scaffold1159-474141 9 38704024 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379622 Affx-122975965 AX-123249980 9 38484679 GTGGGAGATCTGGCCTAACAAATAAACAAAAATAA[C/T]GCCACCAGGTGAAATAATGCATTATTAGAAATTTA Y 2 1 2 1 303000 r 74 goat snp4776-scaffold1159-508985 9 38739009 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439884 Affx-122930038 AX-123310221 9 38522259 AACTTTTCTGGTCTTTTCTCATGCTCTGACCCCAA[C/T]ATACACATCCAGTGACTAAATCATAAAGTCTTTTA Y 2 1 2 1 201000 r 74 goat snp4777-scaffold1159-546565 9 38776428 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788778 Affx-122938497 AX-385275793 9 38553211 CCCTATTGGTGTTATACTATTTCATCTTACACCCA[A/G]TAATGTGTGAGTGCCTGCTTCTCCATAGCCTCATT R 2 1 2 1 101000 r 74 goat snp4778-scaffold1159-577517 9 38800193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386996 Affx-122969947 AX-123257354 9 38604655 TGGCATTGGATTAGCCAATGCCAATTGAATGCCAT[C/T]GAATAAACACATCAATGAACACATACATGCACACA Y 2 1 2 1 101000 f 74 goat snp4779-scaffold1159-628961 9 38852477 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780562 Affx-122927136 AX-385267653 9 38720596 GCTGCTGGTCTTTTAAGAGTTGAGATGCGGGTAGC[C/T]GCAATAAGTGATTTTCCATGAAACAATCTCTTGGT Y 2 1 2 1 101000 f 74 goat snp4781-scaffold1159-744902 9 38968749 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387544 Affx-122970297 AX-123257902 9 38822502 TTAATTACACACGACCTAGACAATGTTACACCTGG[A/C]AACCAGTGGGGCATGCACACCTGCTCTTCTTGTAT M 2 1 2 1 101000 f 74 goat snp4783-scaffold1159-846808 9 39071363 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784329 Affx-122973665 AX-385271380 9 38868168 GGGGCCCAAGAACGTGCATTTCGAACAAGTTCTCA[C/T]ATGATGCTTCCACTGGTTCAGAAAGAGTGCTTTCA Y 2 1 2 1 303000 f 74 goat snp4784-scaffold1159-892474 9 39117239 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394993 Affx-122964242 AX-123265348 9 38900386 TTCAACTGCATAACAAGTACAAGGCTGTTTGTAAG[C/T]ATGAAGTCTTCTAATTATGCAACAAAAATGCTTTT Y 2 1 2 1 101000 f 74 goat snp4785-scaffold1159-924692 9 39149909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402290 Affx-122959102 AX-123272643 9 38965925 CACTGCTTTCTCACCCTTATGAGAAACTATGAGAG[C/T]AAAGACACACCAAATGTAATTAGAATTTTCATATA Y 2 1 2 1 101000 f 74 goat snp4786-scaffold1159-990231 9 39215390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429972 Affx-122938060 AX-123300313 9 38996980 TCTCTTTGCAGCACATCACATTTCAGATTTAAACC[A/G]CTTCAGACACATCACTGCCCCAAGCTCACACATTT R 2 1 2 1 201000 f 74 goat snp4787-scaffold1159-1021286 9 39245903 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412426 Affx-122951425 AX-123282775 9 39039137 CTGCCAGAGGTGTCACGGGTGCCCTTGTTGTCTCC[A/G]TTTGTGCCTCTGGGCTCATAGGTACCTTGCTGCTA R 2 1 2 1 101000 r 74 goat snp4788-scaffold1159-1063443 9 39288214 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405424 Affx-122956273 AX-123275776 9 39073924 CTAGAAAGAGGGAAAACTAACATTTCAAAGGGCAG[C/T]ACTGCTTACAATTCAGTTCTCTGATAGGTGAAATG Y 2 1 2 1 101000 f 74 goat snp4789-scaffold1159-1098230 9 39324614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802765 Affx-122931697 AX-385289664 9 39107117 ATTTATATTATAAGAATTCTGCTTAGTTTCTGTGG[C/T]AAGGACTGGTTTGTAGGGAGGCAATCTCACTGGTA Y 2 1 2 1 101000 r 74 goat snp4790-scaffold1159-1131423 9 39358384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390437 Affx-122967631 AX-123260794 9 39170270 ACTCTGTAGAAGTTTGCACTCTGTAGAAGTTTGTA[C/T]AGCAGAAGACAGTGTTAGATGTTCTCAGAAAATAG Y 2 1 2 1 101000 f 74 goat snp4791-scaffold1159-1194576 9 39421446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388378 Affx-122969324 AX-123258736 9 39201786 ACCCAGACCAAGAAAAACTCAAGCATCTTTGTCCC[C/T]TTTGGGGATAATATAGCCAGCTCCTCACCACTGGT Y 2 1 2 1 101000 f 74 goat snp4792-scaffold1159-1226092 9 39446330 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437089 Affx-122932190 AX-123307427 9 39310634 CCAGAATATGCTTATAGATTTTTACTTAGAAACCC[A/G]TTAGAAATATTTGAAGAAAAGACTAAATTACTCCC R 2 1 2 1 303000 f 74 goat snp4794-scaffold1159-1334940 9 39555783 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398769 Affx-122961437 AX-123269124 9 39344131 ATCGTCCCCACAAGCATTCAACTACCTATTGTACA[C/T]AAGAGAATAGACTGGCACTGTGAAAATTTTCTTCT Y 2 1 2 1 101000 r 74 goat snp4795-scaffold1159-1368437 9 39589606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389827 Affx-122968185 AX-123260184 9 39402999 CTTGTTGTATGTGAACTGATTCTTGTATGATCTTG[A/G]GAGGCCAGGAAGTACATTCTCTCTTGACTTAAGAT R 2 1 2 1 101000 r 74 goat snp4796-scaffold1159-1427305 9 39649086 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794535 Affx-122937607 AX-385281498 9 39434481 CAAATCTGCTGTAATAGCATGAAAGTTACCACAGA[C/T]AATATACAAATGAATGAGCATTGTGTTCCAATAAA Y 2 1 2 1 101000 f 74 goat snp4797-scaffold1159-1458787 9 39680525 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773295 Affx-122938054 AX-385260438 9 39505086 TTTTTAAAGCAATAGTTAGGTGAACTTATTCTGAC[A/G]CAGGTACAAATTTTGTTATCTGTTACCTTGGTTTG R 2 1 2 1 101000 r 74 goat snp4798-scaffold1159-1529392 9 39751567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439901 Affx-122930027 AX-123310238 9 39543786 ATCGAAATGTAAAAACTCTTTGATGCTGTGATGTT[A/C]GAATTTGAAATGTAGGAAGTGACAGGTTGATGGTA M 2 1 2 1 101000 r 74 goat snp4799-scaffold1159-1568092 9 39790028 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801079 Affx-122957601 AX-385287993 9 39582630 GAATATTTACCCATCCCAGAAGATCCTAAAAAAGC[G/T]CTTGTTCGGTTCTTTGAGGTACTGTTTTATTCATT K 2 1 2 1 101000 f 74 goat snp4800-scaffold1159-1606936 9 39828929 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416762 Affx-122948182 AX-123287110 9 39683725 CAAATATTCTTTTTAAAGTCTCTTTGTATAGAGAT[A/G]CTGGGTTTCTTCTGATTAGAAGTCAGTCCAGTTCA R 2 1 2 1 101000 r 74 goat snp4802-scaffold1159-1708031 9 39929440 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436595 Affx-122932521 AX-123306933 9 39729495 TTTGGAAATGCATATAGATATTTTTAGTTGTCCCA[A/G]GAAGGGGGACACTATTGGCCTTTATTGGACAGTAG R 2 1 2 1 201000 f 74 goat snp4803-scaffold1159-1753801 9 39975227 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379032 Affx-122976358 AX-123249391 9 39771834 TTATGTGAAACCTTAAACAGTGAAATCATTAGAGG[C/T]AACCAGGAACACCTGAGTCTTGTCAAGGACCTGAG Y 2 1 2 1 201000 f 74 goat snp4804-scaffold1159-1796140 9 40017974 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425214 Affx-122941021 AX-123295560 9 39811804 ACTTACTGCCACTTTTTTGCTAGGGGAATAAAAGA[C/T]GAAGGATTTCACTACTAATGTCCCTTCCTGCTCTG Y 2 1 2 1 101000 f 74 goat snp4805-scaffold1159-1836110 9 40058274 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450751 Affx-122921853 AX-123321085 9 39867923 GAGTTTATACAAGGAGACTGGCAGAAGGAAAAGCT[A/G]CTGGGAGAGGAGCTGGGTGTGTAGACTTCTCAGCC R 2 1 2 1 101000 f 74 goat snp4806-scaffold1159-1892229 9 40114453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418237 Affx-122947037 AX-123288585 9 39918103 AGAAAAGTCTTAAGTCTCTGATGATAACTCAGGGG[G/T]GTTGACTTGAGAGAAATTTCTATGAAGTAGAAGGC K 2 1 2 1 101000 f 74 goat snp4807-scaffold1159-1942409 9 40164976 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432937 Affx-122935299 AX-123303278 9 39975505 AACCTGGGAACAGACGGGAAAAAATAAAAAAGCCT[A/G]CTTCCCTTATCCAAAGGATGAGGAAAAGAATGGTT R 2 1 2 1 201000 r 74 goat snp4808-scaffold1159-1999811 9 40222964 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444022 Affx-122926888 AX-123314359 9 40023540 TGAACAAAAAAGGCAGCCAGATCAGTACAGTGTTG[C/T]GTGGAAATGAAGAAAACTTATATTTAGTAACATAG Y 2 1 2 1 101000 f 74 goat snp4809-scaffold1159-2047846 9 40271603 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443836 Affx-122927535 AX-123314173 9 40056868 ATAAGGTCGCAAAGAGTCGGACATGACTGAAGTGA[C/T]TTAGCAAGTATGCACGCACATACAGTGACCAAATG Y 2 1 2 1 103000 r 74 goat snp4810-scaffold1159-2081174 9 40304930 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464653767 Affx-1110591914 AX-516124670 9 40066229 CATACCATTTCATCTCATTTTCCAGGGAGGAAAAG[A/G]TAACTCAACAAAACAATTCCAGTTCTAAAATGGTC R 2 1 2 1 201000 r 74 goat 9_40066229_AF-PAKI 9 40066229 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38385987 Affx-122971519 AX-123256345 9 40088921 GTCACTTTCTGCTGCTCAACACAGCCCCCAATTGT[C/T]GAATCACTCTCCCTAAGGTTACAAAGGTTACAGGT Y 2 1 2 1 101000 r 74 goat snp4811-scaffold1159-2113227 9 40336929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407556 Affx-122954682 AX-123277907 9 40119658 TACTTCTTGTCTGCTGCACGAGGAGGTGGAGTGTT[A/G]CTCCAGGACCTTGCTCCAGAAAGGTAAGCTCCCCC R 2 1 2 1 201000 r 74 goat snp4812-scaffold1159-2143964 9 40367780 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422692 Affx-122943660 AX-123293038 9 40148426 AATTAGAGCTTGGAAGGATTTCAAATTTAGATCAG[A/G]AGTATGGAAAACATGTAGTGGCTTTATGATTAGGG R 2 1 2 1 101000 r 74 goat snp4813-scaffold1159-2172732 9 40396412 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798063 Affx-122965616 AX-385284999 9 40187096 TTCATCATTTATACTCTTGTCATTCTAGAAAAAAC[A/C]CTTTAGCTGTGTAACTTTGGTCAAATAACTTCTTT M 2 1 2 1 101000 r 74 goat snp4814-scaffold1159-2211402 9 40435053 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406421 Affx-122955208 AX-123276773 9 40225867 GAAAGGACAATGACACACACATGCACACATGTGTG[C/T]GCACTAAGTGACTCTTCTAAGTTATCAGATTTAGT Y 2 1 2 1 101000 r 74 goat snp4815-scaffold1159-2250173 9 40474936 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420855 Affx-122944644 AX-123291202 9 40256360 CTTGGTTTGTGCCTCCAGGTGTGTCCAGAACCCAG[A/C]TCCCATCTTCTCTTCCCCACTGTTCCCCCATCTTA M 2 1 2 1 101000 f 74 goat snp4816-scaffold1159-2280666 9 40505401 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787025 Affx-122930141 AX-385274053 9 40309661 CATTATGTGTAAAGGACTCAAAGTCTTTTCAACTA[C/T]ACTAGTATGTGGTTGTGGCACCATCCTTAGATTCA Y 2 1 2 1 201000 r 74 goat snp4817-scaffold1159-2333967 9 40558700 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770614 Affx-122939291 AX-385257778 9 40324189 ATTAGAGGGTAAACAATGGGTCAGTAAGAAAATAT[C/T]CAACTCCTCAAGGTGTGTATTTTTCATAAGTTGTT Y 2 1 2 1 101000 r 74 goat snp35415-scaffold427-8355 9 40573170 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435773 Affx-122932871 AX-123306112 9 40398379 AAGGGGTGCCTGCATCTTGTAGGGGAATATGGGCA[G/T]CCCACAACTGAGGAGGCTACTGCTCCTATTCATTC K 2 1 2 1 201000 f 74 goat snp35417-scaffold427-82545 9 40648721 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272362 Affx-1111833768 AX-519546092 9 40408899 GGTGAGGGCATGGCTCTGGAGGCTGTTCTTGGGGA[A/G]TGTTAAGGCTAAGCAGAGTCACCTACGCTTGCCTG R 2 1 2 1 101000 r 74 goat GoatD01.004012 9 40408899 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443468 Affx-122927824 AX-123313805 9 40442364 CTTTACCTGATTAAAATACATGAATTAAGTTTCAA[C/T]ATGGGCCATGCACGTTTCACCTCCCTGAAGGGAAT Y 2 1 2 1 201000 f 74 goat snp35418-scaffold427-126530 9 40693189 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426157 Affx-122940600 AX-123296503 9 40478383 CTCTATGACAGCCATCAAATGCTCACATAGAAGAT[C/T]ATGAAAAATTCTGAGAATGGATTCCTATGGTTCTG Y 2 1 2 1 101000 f 74 goat snp35419-scaffold427-162549 9 40732375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436694 Affx-122932331 AX-123307032 9 40532627 CTGGTTTTCTTCCTTACATTTTCTTTTTAATGATT[A/G]TGTGAAATACTAGTGCTGGATGGAAAATACTGAAA R 2 1 2 1 101000 r 74 goat snp35420-scaffold427-216793 9 40792413 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789496 Affx-122971897 AX-385276505 9 40578261 TAAGCAAGAGTGCAGAGGGACAATGTGGTACAAAC[C/T]AGATTGAAAGATGCATGGTATGCAAATGCCCTAGC Y 2 1 2 1 101000 r 74 goat snp35421-scaffold427-262427 9 40838211 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779147 Affx-122922865 AX-385266251 9 40630910 ACTTGGAATAGTAGCTACAGTCAGGTTTTCATACC[A/G]CTATACTAACTTCACTGAAGCTGTTAAAATAATCT R 2 1 2 1 101000 f 74 goat snp35422-scaffold427-315076 9 40891698 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788544 Affx-122942372 AX-385275561 9 40752630 TCAGTGCATTTTTATGCATTGTAACAGATATCAAA[C/T]GAGAGTTAAGCATAGGATGAACTAGATTGAGTTTT Y 2 1 2 1 101000 r 74 goat snp35424-scaffold427-436796 9 41015041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445112 Affx-122926190 AX-123315449 9 40788600 TTTCTTTTTTAAAGTGTCAGTGTGCCAGACACTTA[C/T]TGGAAATAGGAAATGAATCAGACAGAGTCAACCCT Y 2 1 2 1 101000 r 74 goat snp35425-scaffold427-472766 9 41051101 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774360 Affx-122960546 AX-385261496 9 40838835 TTATCAAATGAGATTGGTCCCTGGCCTTTTAAAAT[A/G]CTCATATGACAGGTAGAACATATAAGATGATACAT R 2 1 2 1 101000 f 74 goat snp35426-scaffold427-523001 9 41101060 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775667 Affx-122920613 AX-385262798 9 40876054 GATTTTAAGACAATCTTCACTCAATAAATTCTTCA[C/T]GTAATTGCTCACCTTTGCCTATTTTTTTGTGTAAG Y 2 1 2 1 101000 r 74 goat snp35427-scaffold427-560220 9 41138847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395103 Affx-122964161 AX-123265458 9 40928920 CCATTTTCTATCTCAATCATTTTCTAGTTCTTATG[A/G]TGCCACTTTTAGATTCTCCAAATTCACGTTACCTC R 2 1 2 1 101000 r 74 goat snp35428-scaffold427-613086 9 41191788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413118 Affx-122950380 AX-123283467 9 41011767 GTCCACCCCTGATTTTCCATCTGCTATTGGATGTT[A/G]CATGGGTATCAAAGAAGGAAAGACAATAAAGATAT R 2 1 2 1 101000 f 74 goat snp35430-scaffold427-695933 9 41274154 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429771 Affx-122938248 AX-123300112 9 41073960 TCTTAAGCATGCATAAGCTTCCACTTGAACTGTAG[C/T]AACCCAATCTAAAGTCTTTAGTTCTTCTTAAGCAT Y 2 1 2 1 101000 f 74 goat snp35431-scaffold427-758126 9 41336263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443335 Affx-122927438 AX-123313672 9 41111097 AATCCTGCAAGATTTGAAACCTCTGCTTTTATTAT[A/G]CTCACTAAAATTCCACTGGCCATGGAAACTCACAT R 2 1 2 1 101000 r 74 goat snp35432-scaffold427-795263 9 41373482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383503 Affx-122972647 AX-123253861 9 41176618 CTCCAGCCATTTTGGGCTGATTCTGATTCTGCAAA[C/T]ATGCCAGGGTCCTGGCACCGGCTCTTCTTTCTATT Y 2 1 2 1 101000 f 74 goat snp35433-scaffold427-860784 9 41438846 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400819 Affx-122959803 AX-123271174 9 41218520 AGACACTCAGGCTGGGACCCACATGGAGTCCTTTG[C/T]GTCCTCCAGGATCTTGCCTGCGGAGGGCCTTGGAC Y 2 1 2 1 101000 f 74 goat snp35434-scaffold427-902686 9 41481667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765935 Affx-122939503 AX-385253361 9 41264923 AGTCTGCATATGGATAATATGGGTGATTAAAAAAC[A/G]TTATATAGAATGGTGGTCAAGAAATATAAATTTAG R 2 1 2 1 101000 f 74 goat snp35435-scaffold427-949089 9 41528091 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440576 Affx-122929299 AX-123310913 9 41296996 AACTCAGTGGACAAAGCAGAGAGGTAACAGACAGG[C/T]ACCCAATCTTTCTGTGAAAGAGGACTATTGTCCTA Y 2 1 2 1 101000 f 74 goat snp35436-scaffold427-981162 9 41560213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775577 Affx-122951228 AX-385262708 9 41365474 GTGAGCATACAGAGAGATAGATATGGAAAGGCAAT[A/G]GATATGGAAAGATATAGAGTTTTGAACATGTTGCT R 2 1 2 1 101000 f 74 goat snp35437-scaffold427-1049640 9 41628189 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388270 Affx-122969769 AX-123258628 9 41403164 GAGGCTCTCAACAAATTGGGCGATGCCAAATCTCA[C/T]TGGTGACATTGAACTTTCTTCCTTAGTCTATTTAT Y 2 1 2 1 101000 f 74 goat snp35438-scaffold427-1087330 9 41666112 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775094 Affx-122959264 AX-385262226 9 41463767 ATTTTAAAATATTGTCAGTCATGTTGATTGAAATA[C/T]GCTTTGAGAGAAACAATGATATCACTATGCTCTTA Y 2 1 2 1 101000 r 74 goat snp35439-scaffold427-1147933 NW_017195677.1 10225 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776879 Affx-122927078 AX-385264003 9 41542475 TCCTCAGTAAGACTACAGGAAAAGATTGCTTGGCT[A/G]TTTTGTTGGCATTCTAGTCAATGTTTGTTTCTTTA R 2 1 2 1 101000 f 74 goat snp35441-scaffold427-1226641 9 41800974 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795129 Affx-122943528 AX-385282087 9 41579151 ATGGCTCTAATAAGGTACTTTTGTAACTACATACC[A/G]CATGACAACTCAGGGCTACCCTTTTCACTAAATTT R 2 1 2 1 101000 r 74 goat snp35442-scaffold427-1263317 9 41838335 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777972 Affx-122975199 AX-385265088 9 41629368 AACTTCTCTATTTCAGTTTACTAACGAACTTCTGT[G/T]TCACTTTCCTTTGAGATCTGATCTTTTTGTTGCAC K 2 1 2 1 101000 r 74 goat snp35443-scaffold427-1313534 9 41888533 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421303 Affx-122944097 AX-123291650 9 41682863 CTAGCCTGATGTTGGATTATCTGCATTGTACAACC[A/G]TTGCCTGCTTTCACTGTGATTATCTCTGGGTTATG R 2 1 2 1 101000 f 74 goat snp35444-scaffold427-1367029 9 41943022 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405958 Affx-122955544 AX-123276310 9 41749150 AATGTCTAGAAATTGTACTTCTAAAAACTTCATAG[C/T]AACTACTCTCTAAATATATTTACTTAAACTTTGCT Y 2 1 2 1 101000 f 74 goat snp35445-scaffold427-1433316 9 42009529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400029 Affx-122960787 AX-123270384 9 41790414 GAGAGATAGACTGAGGTCCTAATGTAAATAACCTA[C/T]AATGCTCATTGAAATTAAGTAGACATTAAAATATG Y 2 1 2 1 101000 f 74 goat snp35446-scaffold427-1474580 9 42051397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443631 Affx-122927292 AX-123313968 9 41831429 GTGGAGTTTGGGGACAGAGTTAAGCTCAAGGTAAA[G/T]CTGCTTCAACAAAAGCCAAATTTAGAGGATTTCTT K 2 1 2 1 101000 f 74 goat snp35447-scaffold427-1515595 9 42092439 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776218 Affx-122958558 AX-385263346 9 41864176 GTCAGAACTAACAGTATGTGTTCAAAGAAAGCAGT[A/G]TTTTAGAGTATTCAGCTTTTCTGCACACAAACCTG R 2 1 2 1 201000 f 74 goat snp35448-scaffold427-1548342 9 42125471 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793249 Affx-122936661 AX-385280227 9 41930977 TGGTCAATATAGTTGTTCATATTGCAGCTGAAAAT[A/G]CAAATGATGTCAAACTCAATAATTGACAGTAATTC R 2 1 2 1 201000 r 74 goat snp35449-scaffold427-1615143 9 42192925 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441210 Affx-122929526 AX-123311547 9 41961991 AATGAGGTCAAAAGATAATGAGAATCAGCATCTCA[C/T]AGGCCTAAATGTCCTTACATGACTTGGTATTTAGT Y 2 1 2 1 201000 r 74 goat snp35450-scaffold427-1646157 9 42224716 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452854 Affx-122920718 AX-123323187 9 42006129 TAAATCATGTTGGGATGTTTTATTTTGACCTATCT[A/G]TTAAAGTCAATTCATCTAAAGCAGCTTGATGCCAT R 2 1 2 1 101000 r 74 goat snp35451-scaffold427-1690295 9 42269123 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387062 Affx-122969897 AX-123257420 9 42054390 TAAATAACTCCCTCTACTGTTGAGTATGTTGGAAA[C/T]GTATGCATACCTTGCTGAGTGTGGAAATCATTACC Y 2 1 2 1 101000 f 74 goat snp35452-scaffold427-1738556 9 42317104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775524 Affx-122942911 AX-385262655 9 42117529 TAATTTCCTCTATATCAGCAAGGACTAGAATACTA[C/T]AGCCTATCTCTAGGTGAGAAATTCCATACAGGACA Y 2 1 2 1 101000 r 74 goat snp35453-scaffold427-1801695 9 42381530 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433303 Affx-122935195 AX-123303644 9 42200443 GAACAAGTCAGGTTTTAACTCAGAAATCCTGGTGT[C/T]TTACTCTGTAAGTTTTAGCACTGACCTTTCCACTT Y 2 1 2 1 600000 r 74 goat snp35455-scaffold427-1884609 9 42200443 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795532 Affx-122935195 AX-385282487 9 42200443 GAACAAGTCAGGTTTTAACTCAGAAATCCTGGTGT[C/T]TTACTCTGTAAGTTTTAGCACTGACCTTTCCACTT Y 2 1 2 1 101000 f 74 goat snp35455-scaffold427-1884609 9 42464404 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394516 Affx-122964539 AX-123264871 9 42297850 GCAGAGTTAGATCCCAAGACAGTTGGATTTAAGAA[C/T]GTAGAGATGGACTGAACACAAGTCAGATATAAGCT Y 2 1 2 1 101000 f 74 goat snp35457-scaffold427-1982016 9 42562872 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789982 Affx-122978306 AX-385276988 9 42342864 AAAGCAAAGAGAAGTCAAAATATTGCAAGAAAAGT[C/T]GAATTGCTTGATAAGTACTTTAGATTGAGGTCTGC Y 2 1 2 1 201000 f 74 goat snp35458-scaffold427-2027030 9 42608624 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774629 Affx-122968725 AX-385261763 9 42372506 TTATGAAACTAATGACCTAAGAATGCCTTTAAATC[A/G]GAGAGCATCAGGTACAGCAAAAAGACCTTCAAAAT R 2 1 2 1 101000 r 74 goat snp35459-scaffold427-2056672 9 42638640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444697 Affx-122926432 AX-123315034 9 42438086 TGGAGTTCACACAATTAAAAGTTATCGCATAGACA[A/G]CATTTCTTCTGCCAGGGTCTTTAAGATACAATTTC R 2 1 2 1 101000 r 74 goat snp35460-scaffold427-2122252 9 42704426 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435671 Affx-122933335 AX-123306010 9 42469568 CAGGAAAACTAAGGAGTCAAAAATTAAGAGAAAAC[A/G]TATTTATAAAATTAAATTTCATGAGTGAATATGTT R 2 1 2 1 103000 f 74 goat snp35461-scaffold427-2153734 9 42735944 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437281 Affx-122931991 AX-123307619 9 42499293 TTGAAGGTCTAGGCAAAGAAGTTACCACAGAAGGA[C/T]GCTTTGGAGTTTTGATCCAGCTTCACTTAGTTTGA Y 2 1 2 1 101000 f 74 goat snp35462-scaffold427-2183459 9 42765767 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783414 Affx-122969080 AX-385270477 9 42548398 ATTGCTGTGACCTGAGAATAAAGTGGTGGAGAGAA[C/T]ACATTTCCTAATATTCTCAGATTGCGTTAAACACG Y 2 1 2 1 101000 f 74 goat snp35463-scaffold427-2232564 9 42815379 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273422 Affx-1111833611 AX-519547048 9 42580210 TGTTTGTGACTGAAGTCAATTGAGGAAAGGGGTGA[A/G]GGAGGTTGAAGAGTAAAAACAATAGTGAAAGTGAA R 2 1 2 1 101000 f 74 goat 9_42580210_AF-PAKI 9 42580210 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320771293 Affx-122939562 AX-385258451 9 42594380 CTACAATCACAAACACAGAATCATAGAATGTTGGG[C/T]ATAAAATTATGTGACAAAAATAAGCCATCATTTTT Y 2 1 2 1 101000 f 74 goat snp35464-scaffold427-2278546 9 42861450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418569 Affx-122946383 AX-123288917 9 42648993 TGCAAGGAGTAAAAATGTGTCAAATTTTAATTATT[C/T]ATTGAGACTATTAAGAAACAGGCAAAAGTAATGGT Y 2 1 2 1 101000 f 74 goat snp35465-scaffold427-2333159 9 42917226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784684 Affx-122936436 AX-385271733 9 42690967 AAACCTAATATAAACTATATCTTTGGATGATAATG[A/C]TTTGTCAATGTAGGGTTCATCAGTTATAACAAATC M 2 1 2 1 201000 f 74 goat snp35466-scaffold427-2375133 9 42959344 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778222 Affx-122943449 AX-385265337 9 42730430 TGTCACAATAACCCATATTATAAATAGATAATGTA[C/T]GAAGATGTGCAGGCTTCTCTTAGTTATAGTTGTAG Y 2 1 2 1 102000 r 74 goat snp35467-scaffold427-2414596 9 42999156 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395114 Affx-122964152 AX-123265469 9 42792815 AAATTTATTTGATTATCAGGTCTAAGTTTTCCTCT[A/G]CTTAGTCCATTCAGCTCAACAATTAAACTAGGATT R 2 1 2 1 101000 r 74 goat snp35468-scaffold427-2476981 9 43062446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384914 Affx-122972340 AX-123255272 9 42828202 CCTCTCCCCCTTTACCATTTCTACTGTACTTATTA[C/T]ACTGTAGTTTAATTTTCTTTTTATTTCTTTTTTCC Y 2 1 2 1 103000 f 74 goat snp35469-scaffold427-2512368 NW_017189702.1 2405 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387700 Affx-122969810 AX-123258058 9 42867262 CTTGCACCTTAGTCTCCATTAGAATCTGCCTCCCA[C/T]GGATCCGACCTGAAAAAATATCAAAGTTATTTATA Y 2 1 2 1 101000 f 74 goat snp35470-scaffold427-2551428 9 43137690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422091 Affx-122943582 AX-123292438 9 42907633 GAATATGTTATGAAAAGCAGCATATAGAGATGACA[C/T]AGTTCAAGGAAAAGTCATTCTACCCAATGCCTTGG Y 2 1 2 1 101000 r 74 goat snp35471-scaffold427-2591799 9 43178065 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382195 Affx-122974006 AX-123252553 9 42986335 TGGGCTCCCATGTGTCTCCTAGATTCTGTTTATTT[A/G]TTTATTTATTTTTCTTTGTGTTCCTCAGACTGGAT R 2 1 2 1 103000 f 74 goat snp35473-scaffold427-2670501 9 43256916 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782748 Affx-122964438 AX-385269820 9 43019042 TCCAGTGGACAATAGCTATAGAAAACTTTATTGAA[C/T]AAATTATGACCACCAGTGTCCCTAAGGACAATTCA Y 2 1 2 1 201000 f 74 goat snp35474-scaffold427-2703208 9 43290247 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388124 Affx-122969482 AX-123258482 9 43084391 GAAGCCCTAATTCACCTAAGGAGGGGGAAATTGGA[C/T]AAACAAGTGAGACTCAGTAATAGATAACAGCTGAG Y 2 1 2 1 101000 r 74 goat snp35475-scaffold427-2768557 9 43355941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446501 Affx-122925042 AX-123316837 9 43125367 ATTTCTGTCATAGTACTTATAACAAAAAATGTTTT[A/G]TTTGTTAAGAAGTGGGATAAACAGCTTAATAAGTG R 2 1 2 1 101000 r 74 goat snp35476-scaffold427-2809533 9 43397181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399554 Affx-122961132 AX-123269909 9 43206730 GAATAGTGTATAATTTTCAAAACTTAGATGTGTAT[A/G]CTGAGATTTCCCCACTAGGACTTGTCATAAACTCT R 2 1 2 1 101000 r 74 goat snp35478-scaffold427-2890896 9 43478580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784500 Affx-122932224 AX-385271549 9 43289657 AGTGTGTATCTTGTAGCTCTTTAGGCACTGTACTG[A/C]TGAACCAGCATCTGCAACTACTTCCAGAATTCTTG M 2 1 2 1 101000 f 74 goat snp35480-scaffold427-2973823 9 43562654 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405383 Affx-122956301 AX-123275735 9 43326880 TTAGAATAAGGTTATACTCATAATTTTTAACTATT[C/T]ACATGTAACAACTAATATAAAAATATTGACTTTTA Y 2 1 2 1 101000 f 74 goat snp35481-scaffold427-3011046 9 43600243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384134 Affx-122972814 AX-123254492 9 43401992 TGTATGCAGTCACCGTGTTGATCCCAGGTCAATAA[G/T]CAGTTCTTTACCTTGTGGCCAAACATGCCTAAGAA K 2 1 2 1 101000 f 74 goat snp35483-scaffold427-3086158 9 43675223 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385414 Affx-122971335 AX-123255772 9 43447362 AGAAGGGAGTCAGTGTGTGGACAGCCCCCTCAGCA[G/T]ACTCTGGGAGCACTCAGCCCAGTTTCTGCCTGGGG K 2 1 2 1 103000 f 74 goat snp35484-scaffold427-3131528 9 43721198 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275467 Affx-1111834915 AX-519549039 9 43472663 GTTGGGAAGACAAATGTGTAACCATGATACAAGAG[A/C]AAAATAAAGCCTGAAGACTGGATACGCACCCTCAC M 2 1 2 1 101000 f 74 goat GoatD01.058699 9 43472663 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38405444 Affx-122956049 AX-123275796 9 43483561 CCCTTTTGGCCTTCCCTATCTGGAAACCTCCCTGA[G/T]TAGGAATGGTCACACATCCAGGGTGTTTCCTACTG K 2 1 2 1 201000 r 74 goat snp35485-scaffold427-3167727 9 43757811 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392590 Affx-122966060 AX-123262947 9 43533865 TATTCCATTGCCAAATCGAGCTGGCCAGATATCTG[A/G]CTGGTCATGCTGAATAATAAGGTTTGGGAACCGAT R 2 1 2 1 101000 r 74 goat snp35486-scaffold427-3218031 9 43808466 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425085 Affx-122941245 AX-123295431 9 43592343 GACATCTCTGGAAATGGAGGTCTAAACTGGCAAAG[C/T]AAAACTATGATACATGGGAACTTTATTCTTATCTC Y 2 1 2 1 101000 f 74 goat snp35487-scaffold427-3276509 9 43867947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420015 Affx-122945160 AX-123290363 9 43669114 TAACATGTACTCTGCTAGGCACCAGAGATTAAAAA[C/T]GATCTCTGCTCTACAGAAATTCACAGTGTAGTAAA Y 2 1 2 1 202000 r 74 goat snp35489-scaffold427-3353280 9 43945381 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783531 Affx-122961849 AX-385270593 9 43717290 AAATAAACAGCTCTATAAAACATTACTCTTTTATA[G/T]CTCATTTTGCAAAGAAAGATTCCCCATTATGAATA K 2 1 2 1 101000 r 74 goat snp35490-scaffold427-3401456 9 43992361 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797160 Affx-122919856 AX-385284100 9 43767806 AATAGGCTATAATTCTTTCAGTTACTACAAATAAC[G/T]AATATAATGTTTGGGTAGCTGGCCTCCCCTAATTT K 2 1 2 1 101000 r 74 goat snp35491-scaffold427-3451972 9 44043241 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798125 Affx-122971127 AX-385285060 9 43821523 TTGATATAATAAGAATTCACTGCACTGCTTTAAAG[C/T]ATCCCCTTACCAAACACCTTTAGCATGATTTAGTT Y 2 1 2 1 202000 f 74 goat snp35492-scaffold427-3505689 9 44097378 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803258 Affx-122951063 AX-385290109 9 43850708 AAATGGTCAGGTTTTGCTACTCAAGGTGATCTATA[C/T]GCTGGATCTAAAATTGCAGCCATCAGCAATATTTC Y 2 1 2 1 101000 r 74 goat snp35493-scaffold427-3534874 9 44127148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439599 Affx-122930062 AX-123309936 9 43901747 TTCACCTTTGAGAAAAGAAACTGGTGATAGTTCTC[A/G]GGTATGTACATCTCACTCCAAGAGACCATTTATAA R 2 1 2 1 101000 r 74 goat snp35494-scaffold427-3585913 9 44178544 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400289 Affx-122960082 AX-123270644 9 43940117 TTAGTCATGGGTTTATTTTTTTCAATTTCCAATGA[C/T]AAGTAAAGGTTGGTTGCTTACAGTTCTCAAATTAG Y 2 1 2 1 101000 r 74 goat snp35495-scaffold427-3624283 9 44217154 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434186 Affx-122934875 AX-123304527 9 44000801 TATTAAGCTGAGGTAACCATAGGAGGAAGTGTAGG[A/C]TGCATTCAAAAGCAAACCAAGACCTAAAAGTGCAA M 2 1 2 1 101000 f 74 goat snp35496-scaffold427-3684967 9 44278124 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395801 Affx-122963650 AX-123266156 9 44038849 ATCTTTCCAAAATGTTCCTAAAATTTCTTTAGGCT[A/G]CTCTCTCTGCTCGAAACCAACAGTATCCACACCAC R 2 1 2 1 101000 r 74 goat snp35497-scaffold427-3723015 9 44316265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773541 Affx-122927970 AX-385260682 9 44069245 CATGATAATAGTATCAGAGACAAAAATTTGGCTTT[A/G]CAGATCACCAATTTAGCAGATAGCAAAGAATGTAT R 2 1 2 1 201000 f 74 goat snp35498-scaffold427-3753411 9 44346975 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406967 Affx-122955054 AX-123277318 9 44117255 AGAACACAAGCTGTGTTACTAACTAACTTAATCTC[A/G]TTTTTCAGGTCTCAGCTTAAATGTTACTTCCTGTA R 2 1 2 1 103000 f 74 goat snp35499-scaffold427-3801421 9 44394956 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399374 Affx-122961335 AX-123269729 9 44163164 ATTCCAGAAGGCCTTAAAAATTAATAACAGTATAT[A/C]TATAGCGTTTCCCTCTGTGTTTGATTGACTATTTT M 2 1 2 1 101000 r 74 goat snp35500-scaffold427-3847330 9 44440938 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384693 Affx-122972118 AX-123255051 9 44169661 CTTATTACAAACTCACCATTTAAGATGTTAATTTC[A/G]TTCATAGGTAAAAGTGTAATAAATCCTGTCTTGAT R 2 1 2 1 101000 r 74 goat snp28687-scaffold31-274 9 44635759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787947 Affx-122956373 AX-385274968 9 44225916 ATAAATAGAGACCTACATGAACCTTCTCATGTTCA[G/T]ATAACAATAAAGAATTTGGCCTTTGTTGTTAAAAG K 2 1 2 1 102000 f 74 goat snp28688-scaffold31-56529 9 44692369 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432854 Affx-122935363 AX-123303195 9 44262730 GCATTTTCTGCATTCACTGGTGCTCCAACAGAACA[A/G]TGCCTGCCCTCGCACCCCCTACTCTTTATTCCTGT R 2 1 2 1 102000 f 74 goat snp28689-scaffold31-93343 9 44727048 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395188 Affx-122964511 AX-123265543 9 44295123 TTCACTTATTGATTAATTAGCTGATTGACAGATTC[A/G]TTGCTTTCCTGTCTCTCTCACAAAATGTATAGCTC R 2 1 2 1 201000 f 74 goat snp28690-scaffold31-125736 9 44759437 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388493 Affx-122969226 AX-123258851 9 44351648 CTTAAATCAGTGCATTTAAATTTTCATACACTGAT[A/G]CATCTCATCAATGGAGGGAAACTTGTAGCTACTAT R 2 1 2 1 101000 r 74 goat snp28691-scaffold31-182261 9 44815969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424889 Affx-122941319 AX-123295235 9 44393036 GATCGTGATTTCTCAGGAAGGGGAGACTAGAGTTG[C/T]CAAGTAGAGGAAACACTACCCTGATTATTCTCCTG Y 2 1 2 1 101000 f 74 goat snp28692-scaffold31-223649 9 44857448 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380570 Affx-122975274 AX-123250928 9 44433386 TGGTACTATAAGCAGAATGAAGGAATAGAGACAAA[C/T]GGTCCATGGAAATTTAGAAGAATTGCTAAAATTAA Y 2 1 2 1 103000 f 74 goat snp28693-scaffold31-263999 9 44898996 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424809 Affx-122941379 AX-123295155 9 44466619 ATAAGCTGGTAAAGTGAAATTGCCTTTAGTTTGTT[A/G]CTTTCTTTTTCATGTGCCCTTATCCACATCCTCAA R 2 1 2 1 101000 r 74 goat snp28694-scaffold31-297232 9 44931940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780292 Affx-122946503 AX-385267388 9 44498194 ATATATCATGGATTGAACTTGGAGGCAAAATGATC[A/G]TATAGGATATGATGGTGTTTCTTCTTAATGAGTAT R 2 1 2 1 101000 f 74 goat snp28695-scaffold31-328807 9 44963727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387257 Affx-122970557 AX-123257615 9 44568596 TGGTGTACAGCAAAGTGAGAAAAGAGGGATAAGGT[A/C]GAGGGCAGAGGATGAAGGAGGCCTGTCTGTGTTAC M 2 1 2 1 101000 f 74 goat snp28696-scaffold31-399209 9 45035151 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399270 Affx-122960556 AX-123269625 9 44623922 TTAAAATGTTTCACATTAGGATGAGTTTGAAATAT[A/G]CTTTTATGATTAAAACTATGTGGCATATTAATATA R 2 1 2 1 101000 f 74 goat snp28697-scaffold31-454535 9 45093341 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779023 Affx-122954393 AX-385266130 9 44653498 TTTATAGCAGAAACCATTGGACAGGACATGCTTTA[A/G]CAGCAATCTATGTTTTAGAATACTTTCTTAGTCAA R 2 1 2 1 201000 r 74 goat snp28698-scaffold31-484111 9 45123901 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801868 Affx-122944140 AX-385288775 9 44768058 AGTTCTTGTGACCCATTACCCTTTACCATTTTACA[G/T]CTTTATGTTATGAAATATAAAATGTGTTTCTTGCT K 2 1 2 1 201000 r 74 goat snp28700-scaffold31-598671 9 45240925 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397024 Affx-122963120 AX-123267379 9 44816684 TATTTTTACGTGTAGAATTCTCTTTAATTTATCCC[A/G]TTAGCTACTTGCATTACTCACATGACCCTCTACAG R 2 1 2 1 101000 r 74 goat snp28701-scaffold31-647297 9 45290763 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436899 Affx-122933216 AX-123307237 9 44846246 ATAGTGGCAATGGGGAAAAATATTCAACTCATTGC[A/G]TAAGCCATTACTTTATCTGTGTGATTGACCGCACT R 2 1 2 1 101000 r 74 goat snp28702-scaffold31-676859 9 45320858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785060 Affx-122922213 AX-385272107 9 44950317 CAACTGAAACTTTAAGTGATATTTTCTTTAATTCT[C/T]TGGTCACTTTTAAGTATAACAGTTGTATCTAGAAT Y 2 1 2 1 201000 f 74 goat snp28704-scaffold31-780930 9 45425300 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770449 Affx-122930921 AX-385257615 9 44956629 AAGTTCTCATGTTACCTCATGGAAAAATACTTGGA[A/G]GAATTGCATACTTATGTATTTTCCTTTTATTAAGA R 2 1 2 1 201000 r 74 goat snp295-scaffold1008-4058 9 45429593 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391178 Affx-122967432 AX-123261535 9 44991852 CCTCAATAGTTTCTTTAATTCACGTATTTGATTAG[C/T]ATCTTGGTGGGTAGAGAGGGAGAGGTACATCCGTA Y 2 1 2 1 201000 f 74 goat snp296-scaffold1008-39281 9 45465347 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433094 Affx-122935721 AX-123303435 9 45045048 GTCATGTCGCCCAGGATGACTTGTGATTCCACAAG[G/T]TATTTGTGCTAAGGCATAGGTCCTCTCTCGGTGTT K 2 1 2 1 101000 r 74 goat snp297-scaffold1008-92477 9 45519387 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446594 Affx-122924815 AX-123316930 9 45075071 AGTTACACCAGGAGGAGACACTGAAGAGATAAACA[C/T]GGCATCAGGAGAGACTGACAGCAGATAATAGGAAG Y 2 1 2 1 101000 f 74 goat snp298-scaffold1008-122500 9 45550014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273424 Affx-1111833612 AX-519547050 9 45106521 ATGAAATTAAAAGACTCTTACTCTTTGGAAGGAAA[A/G]TTATGACCAACCTAGATAGCATATTCAAAAGCAGA R 2 1 2 1 103000 f 74 goat 9_45106521_AF-PAKI 9 45106521 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320773955 Affx-122963262 AX-385261094 9 45115278 CATGATTTTCATGAAGACAAAAAATGTTATTTTGT[A/G]TAGGAGAAATAACATACACCTATATTAATAAGACT R 2 1 2 1 202000 f 74 goat snp299-scaffold1008-162707 9 45592381 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414967 Affx-122949067 AX-123285316 9 45179446 CTCAGTGTCGTTCTCAAAATAGGCATGAATAGGAT[A/G]GCTTCTTCAAATACTAAGCATAAACTGCAACAGAA R 2 1 2 1 101000 f 74 goat snp300-scaffold1008-226875 9 45657912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431765 Affx-122936719 AX-123302106 9 45208015 AGGCCTAGTCAAGTGAGGCATCTCTCTCTTAAGGA[C/T]GCATTTAATCTGAGTCCTTCTGATGAGTTCTTAAA Y 2 1 2 1 101000 f 74 goat snp301-scaffold1008-255444 9 45686485 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441502 Affx-122928729 AX-123311839 9 45249709 GCAGCTGCGGAAAGCAGGCTCTAGAATGTTCTCTA[A/G]TTATAATCTCTGTCTCCTAGTATTCATGTTCTTAT R 2 1 2 1 101000 f 74 goat snp302-scaffold1008-297138 9 45728722 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423006 Affx-122942980 AX-123293352 9 45289753 AGATCTTGAATAATATTTTTACTTGAAATGACTAA[C/T]TGGACAAGTCTGTTTCCTTTATCAAGACAGTGTCC Y 2 1 2 1 101000 r 74 goat snp303-scaffold1008-337182 9 45768968 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774123 Affx-122937480 AX-385261261 9 45347275 ATTCACTCCAAGGAGTAGTCAATACCTAAACAGGT[A/G]CCATTTTTGTTGATCACACATACTTGAATATCATC R 2 1 2 1 101000 f 74 goat snp304-scaffold1008-394704 9 45826307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439621 Affx-122930629 AX-123309958 9 45393440 TCATCTCCTTCCCTCTTCTCTTCCTCTCTTGGATT[A/G]CCAAATTTTGGTAAATTGCATCAATTATTGCTATC R 2 1 2 1 202000 r 74 goat snp305-scaffold1008-440869 9 45874080 C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452213 Affx-122920808 AX-123322546 9 45436157 GTCTTTGGGGCCACAAAGAATCAGACACAGTTTAG[C/T]AACTGAACAGCAACAAAAACAATGACTCTCCATAG Y 2 1 2 1 103000 r 74 goat snp306-scaffold1008-483586 9 45916882 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429546 Affx-122937827 AX-123299888 9 45493989 GAAGTTTGTAGATAATATAATCTACAGTACATACA[A/G]CTTCAAAGAATCAATATAATGACATGACAGGTAAA R 2 1 2 1 103000 f 74 goat snp307-scaffold1008-541418 9 45976607 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776591 Affx-122926493 AX-385263718 9 45543965 ATTGTTGAAGTTTGTATCAATCCACAGGGGAGGAA[A/C]GATTGGAAGTTAAAACCTGAACCACACTCTTACAA M 2 1 2 1 101000 f 74 goat snp308-scaffold1008-591394 9 46026696 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391007 Affx-122966892 AX-123261364 9 45576229 TTAATATGTATTATTTGCATGTAGTAAGTAATATA[C/T]TTTTACTAGAATTTATACTCTTCAGCCATCACTAG Y 2 1 2 1 101000 r 74 goat snp309-scaffold1008-623658 9 46058915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792246 Affx-122939259 AX-385279230 9 45609761 AAGTTTTCCCTTAGGTGTCAATTATTTTAAATCCA[G/T]ATTTCACTTATTTCTATAAGAATGTGGTGGTTATT K 2 1 2 1 101000 r 74 goat snp310-scaffold1008-657190 9 46092439 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769613 Affx-122942256 AX-385256783 9 45641876 CAGTAACTTCTTATTCCATTTTGTCTTTCATATCA[A/G]CTATTAAGTTTAGTTGTAGATACTTAGTGAACAGG R 2 1 2 1 201000 f 74 goat snp311-scaffold1008-689305 9 46125193 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391380 Affx-122967274 AX-123261737 9 45686107 TCTCAAGAGATCTTGATTTAATGTCTCATACATTT[A/C]TCAATATTTAATTTTTTCTTTGGTTCTGAACATAT M 2 1 2 1 103000 f 74 goat snp312-scaffold1008-733536 9 46169330 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433529 Affx-122935006 AX-123303870 9 45747539 ATTATTTCCATTTTTGCTACTGAAAGAAAGCTAAG[C/T]ACTGGGAGGCTAAATGACATTCCAAAAGTCATACA Y 2 1 2 1 101000 r 74 goat snp313-scaffold1008-794968 9 46230949 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442959 Affx-122928215 AX-123313296 9 45783085 TGACTTGAAACTATGAAAATATATATTTTTAAATG[C/T]ATTTTATCAGGACCCAGTGATGTCAGTGGACAAGC Y 2 1 2 1 101000 r 74 goat snp314-scaffold1008-830514 9 46266576 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402168 Affx-122959192 AX-123272521 9 45816359 AGAGTTGAAATAACTGGAATTCAGTCACAAAGAAG[C/T]GAATGACAGAGCTGGGATTCCAGCCTAATTCCATG Y 2 1 2 1 303000 f 74 goat snp315-scaffold1008-863788 9 46300471 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430720 Affx-122936898 AX-123301061 9 45845119 TGTCCAAAATGCCTGAAAGGAATCTGACTATTCAG[C/T]ATTTTTAAATTAAATGGACAAATTAGCTTAATTCC Y 2 1 2 1 202000 r 74 goat snp316-scaffold1008-892548 9 46329140 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421404 Affx-122943978 AX-123291751 9 45892900 ATGAAGTGACACAAGGAGGAAGCTGAGAACTGCTG[C/T]GGTACCTGGCCAGGATTGGGGTGGGATGGCTATAA Y 2 1 2 1 101000 f 74 goat snp317-scaffold1008-940329 9 46376713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440721 Affx-122929892 AX-123311058 9 45965856 TGACTGGTGTTTGCAGGGTGGGATACTGAAGAGGA[A/G]AAAGTTGCACACAAAGAGAACTCCAAAGATTGCAG R 2 1 2 1 101000 r 74 goat snp319-scaffold1008-1013285 9 46450505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415238 Affx-122948955 AX-123285587 9 46015658 TAGTGGCATTCTTTATTTTTTATTTGAATAGTACC[A/G]TGGATGGGATTGTACTTTCCAGGACTTAAATTATA R 2 1 2 1 101000 r 74 goat snp320-scaffold1008-1063087 9 46500078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787643 Affx-122928765 AX-385274666 9 46076261 GACAAAACTGGCAAATTTACTACATTAAACTGAAA[C/T]GTCTCATCAGAAGACATCACAAAGAAATGAATTAG Y 2 1 2 1 101000 r 74 goat snp321-scaffold1008-1123690 9 46559336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404269 Affx-122957050 AX-123274621 9 46120594 TAGGGAAGATGCAAATTTCTTTTGTCCGGCAGTTA[A/G]ACTTGGGGCAGATATCCTTGATCCAATTAGGAAGT R 2 1 2 1 101000 f 74 goat snp322-scaffold1008-1168023 9 46603948 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399219 Affx-122960598 AX-123269574 9 46169262 CAGATCTGAAACAAGTGAAGAGGAACTGGGATTGG[C/T]AGGCAGCCCTTCTCTGTTAAAAGTCAGACCTGACT Y 2 1 2 1 201000 r 74 goat snp323-scaffold1008-1216691 9 46653050 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416380 Affx-122947869 AX-123286729 9 46208641 CATAAAAATGCCCACCTAACGTTTGGAGGTTAACA[C/T]GACACAATGACACTGGCCACAGTTACTCTTACATA Y 2 1 2 1 101000 f 74 goat snp324-scaffold1008-1256070 9 46692678 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789664 Affx-122943106 AX-385276673 9 46252595 TATCTCATCTAATAGACTGAGTCTCATCCATTAGG[C/T]AAATATAATGTGGAAACATTGTCTTGTTTCTCTAA Y 2 1 2 1 201000 f 74 goat snp325-scaffold1008-1300024 9 46736989 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791692 Affx-122975915 AX-385278683 9 46317562 ACTTGCTGCAAAGTTCAGAGTTGATCAGAAAAGTT[A/G]CTAAACATCCAATGGATCCTTGGACTTGCTTGTGT R 2 1 2 1 101000 f 74 goat snp326-scaffold1008-1364991 9 46802441 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380040 Affx-122975580 AX-123250398 9 46369724 ATATAGATGAAGTTGATTCGGCAATACTGGAACAT[A/G]CGGGAATTAGAAAACTAAGTAGACTATGGGAGCAA R 2 1 2 1 101000 f 74 goat snp327-scaffold1008-1417153 9 46855014 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784737 Affx-122956250 AX-385271785 9 46405902 GAGCAAGGGCAGAAGCTATATTAGTAATGCGTATT[A/C]GGAAGTTATTCAACATAGAACTGATATCTGAAGTC M 2 1 2 1 101000 f 74 goat snp328-scaffold1008-1453331 9 46892045 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432722 Affx-122935469 AX-123303063 9 46460012 AAGCACCACACACATTTGTAACAACAGCATATAAA[C/T]AGAACTGGAAACAACAACACAAGCTCAACTTTAAG Y 2 1 2 1 201000 f 74 goat snp329-scaffold1008-1507441 9 46946134 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398279 Affx-122962169 AX-123268634 9 46510765 AAAAGTAAAATCTTTTGGTAACCTTACCAGTAGTC[A/G]TGAAGTCCTGAACGTTATACTAACAAGTATTGTTT R 2 1 2 1 101000 r 74 goat snp330-scaffold1008-1558194 9 46996901 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778144 Affx-122926217 AX-385265259 9 46548074 CTAACTCATGTATTTTGGGGGGATGGAAATAGCTA[A/G]CAGACATGGAAGTATCTAAAAGGTCCTAGTCTGAA R 2 1 2 1 101000 r 74 goat snp331-scaffold1008-1595503 9 47034853 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437396 Affx-122932431 AX-123307734 9 46601410 GTGCACTATCTGAACATCTGCCTCCAAAAACCCAT[A/G]TCAGCATTTTTAGCAGTTCCTCCAAAAGTTGCTGT R 2 1 2 1 101000 r 74 goat snp332-scaffold1008-1648839 9 47088187 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395613 Affx-122963811 AX-123265968 9 46640532 CATGGTCTGTGCATTGCACTCTCCTGCTCAAATGC[C/T]CTCAGTGACCCCTATCAAGACTTTATTATTTATGC Y 2 1 2 1 101000 r 74 goat snp333-scaffold1008-1687961 9 47126719 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399973 Affx-122960827 AX-123270328 9 46671492 TCCCAGGATCTCCACCCTGTCCCGTATCCAGTATC[A/G]TCTAATCCTAACGGGACTGGTGACCGCCACGGTCC R 2 1 2 1 201000 r 74 goat snp334-scaffold1008-1718921 9 47157802 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415792 Affx-122948906 AX-123286141 9 46700507 TGGTGACATCTAAGGACCTCCTGGGGAAGCAGGAC[A/G]CTGAGCTCCAGCCGCAGAGTAGAACCTGTTCCTGG R 2 1 2 1 101000 f 74 goat snp335-scaffold1008-1747936 9 47186963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379896 Affx-122975768 AX-123250254 9 46732254 TGAGTCAGGGGGCAAGTGAAGTGCAGAATCACTCA[C/T]GGTCCCAGACACCCTCCATTAGACAACCTGATTAT Y 2 1 2 1 201000 f 74 goat snp336-scaffold1008-1779683 9 47218481 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398826 Affx-122961392 AX-123269181 9 46778564 ACCTGACGTGTGGTTCCAGGCCCAGCAGCATCAGC[A/G]TCATCCAGAGCACGTTAGAATGCAGAATCTCAGGC R 2 1 2 1 101000 r 74 goat snp337-scaffold1008-1825993 9 47264855 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396782 Affx-122962761 AX-123267137 9 46809707 AAAGTCTCTTTTAAACTGTATCCATGTTCTTGTTA[C/T]AGTAGTAGTGTGCAGGTTGACAATTTATATTTGGT Y 2 1 2 1 101000 r 74 goat snp338-scaffold1008-1857136 9 47295993 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278706 Affx-1111836564 AX-519552184 9 46810190 CATAGACAGTGATTATGACATTTCCCAAGTTCTAT[A/G]CAGCAACCATACCTTTATTATTATTTTTTGTCACT R 2 1 2 1 101000 f 74 goat Random2.2K-992 9 46810190 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398890 Affx-122961029 AX-123269245 9 46857562 ACCTACCTGGAAGGGGTACACTTCTGGCCCTCAGA[C/T]AGCCAGCGCAGATACCTTAGTGCTGGCAGAAAACA Y 2 1 2 1 101000 r 74 goat snp339-scaffold1008-1904991 9 47344242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426977 Affx-122940394 AX-123297322 9 46897906 TGACTGCTGTAAATCCAGCCCTTCACACTCATTCA[C/T]TCATCAGCCAAGATTTCTGGAGCTCCACCAATCCT Y 2 1 2 1 101000 f 74 goat snp340-scaffold1008-1945335 9 47384645 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423207 Affx-122942712 AX-123293553 9 46930428 AGCCTGTCATGGAGGCTCTGTATCATCAGTGCCCC[A/G]TTGACCATGAGACCCAAGTCAGTACATAAATGTTT R 2 1 2 1 101000 r 74 goat snp341-scaffold1008-1977857 9 47417176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444497 Affx-122926515 AX-123314834 9 46983561 CAGGACTGACATATTTTTAAGATAAGCATGTTACT[A/G]TGTTAGCTTTGGGACAAGCCAGTTACCTCTCTGCT R 2 1 2 1 101000 r 74 goat snp342-scaffold1008-2030990 9 47470111 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388393 Affx-122969301 AX-123258751 9 47066354 TCATTGTGCCATCGACTCCTCAAATATGTTGACAG[C/T]CTCTCTCACTGACATTGGCACCTCTTCCGAGCTCA Y 2 1 2 1 101000 f 74 goat snp343-scaffold1008-2113783 9 47552830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429665 Affx-122937659 AX-123300006 9 47105084 AAAATACTGGAACACCCCCAACCAAGTATTGTAGG[C/T]GCCTGAACTCACATCCTTAAAGGTATATTCTGAAA Y 2 1 2 1 201000 r 74 goat snp344-scaffold1008-2152513 9 47591864 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405116 Affx-122956974 AX-123275468 9 47141083 TGTCTCTTGCTCGATCTCTGGCTCTCTCTCTTCCC[G/T]CTTCCCTCTCTCTTTCTCATCCTCTCTCATCCACT K 2 1 2 1 303000 f 74 goat snp345-scaffold1008-2188512 9 47627837 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797378 Affx-122973148 AX-385284317 9 47172434 TTCTGACCAGTATTGGGTGAGCAAGTTGGACTGAT[A/G]TCAGGAACAAGTTGACCATGTTGGCCTGAAGTAAA R 2 1 2 1 202000 r 74 goat snp346-scaffold1008-2219863 9 47659591 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772045 Affx-122936556 AX-385259200 9 47226108 CTTACGACTCTTAGTCTTATCCTTGGAAAGAGATC[A/G]TTCTCCATATTCTCGAATTTTCTCTAGGGAAGAAT R 2 1 2 1 101000 f 74 goat snp347-scaffold1008-2273537 9 47713166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407412 Affx-122955239 AX-123277763 9 47271261 TGACTCTGTCCTGGAAAGACTCAACAGGTACACGC[G/T]TGTAAGAGGTTTGCCCTGTGTTTGATGCTTTTGCT K 2 1 2 1 101000 r 74 goat snp348-scaffold1008-2318690 9 47758534 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427932 Affx-122939217 AX-123298275 9 47314245 ACGAGTGCATTTCACACATACTGCTAGTGCAGCTG[A/C]CATTTTTAAACCAGCTTGAAATGTAGCTGTGGTCC M 2 1 2 1 101000 r 74 goat snp349-scaffold1008-2361674 9 47801583 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429077 Affx-122938282 AX-123299419 9 47349617 AAGATTTGGCTTCGAAGAACCAAGCCTAGTAAACG[G/T]CAGTATCAAATCTGTCTGGCTATTGATGACTCTTC K 2 1 2 1 101000 f 74 goat snp350-scaffold1008-2397046 9 47837362 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770733 Affx-122943829 AX-385257897 9 47398887 GCAACCACTGAGGTCTAAAACTTGGTTCTGAAATA[C/T]GTGTTTTCTCCTACATGGTGAAAAAGAGTGAGCAC Y 2 1 2 1 101000 r 74 goat snp351-scaffold1008-2446316 9 47886631 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384492 Affx-122973062 AX-123254850 9 47432421 TTCTTGCTAAACCATCCCCGATGCTGTGGTTGTTG[A/C]TTCTGTGGTGTATGAAGCATTTATTGAAGAGACAG M 2 1 2 1 201000 r 74 goat snp352-scaffold1008-2479850 9 47920174 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453202 Affx-122920448 AX-123323535 9 47493142 AGCTGGTAAAGACAGGCCTGCTGAACAAGGAACCC[A/G]GGCCACAGCTCACACTTCCACGTCCGGGAGCAAAC R 2 1 2 1 101000 f 74 goat snp353-scaffold1008-2540571 9 47980718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434389 Affx-122934694 AX-123304730 9 47590338 TCCAGGAAGTTAATCGATGTTGAGGTTTACTATTA[C/T]AGGTAGTATCTATAATCATAAGGAATCCTCTAAAA Y 2 1 2 1 101000 f 74 goat snp355-scaffold1008-2637767 9 48077907 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396309 Affx-122963084 AX-123266664 9 47647225 AAGAACATCCCCATGTCTCAGCCTATGCTGAGATA[A/G]ATTGTGTGCTAGGAACAATCTCCCCTGCTTTCCCT R 2 1 2 1 202000 r 74 goat snp356-scaffold1008-2694654 9 48135819 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417293 Affx-122947238 AX-123287641 9 47698554 AGAATTCATTGCTCATAGTATTTTCAGGCAAAAAG[C/T]GATTTATTTCTTTACTTAGAGAAGCGGCTGAAAAA Y 2 1 2 1 101000 f 74 goat snp357-scaffold1008-2745983 9 48187149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430614 Affx-122936973 AX-123300955 9 47735962 GTACACGGGAGGACACACACACGCTGCTGTTGGGA[C/T]GAGGAGCTGGAAGGGCAGTTCATTGTTTCTGTGAG Y 2 1 2 1 101000 r 74 goat snp358-scaffold1008-2783391 9 48224438 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438709 Affx-122930854 AX-123309046 9 47779129 TTTCTTAAAATCGCTAAATAAACTTTAAGACTTAA[A/G]GATCAACTCATCTATATTCTTAATGGTCACTCTCC R 2 1 2 1 101000 r 74 goat snp359-scaffold1008-2826558 9 48267271 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426503 Affx-122940214 AX-123296849 9 47816552 AATCTAAGAGCTCCATGAGGCAGTAGGATGTAGTC[A/G]TTAGGAAGCCAGACTGGTTAGTGTCAGATTGTGGG R 2 1 2 1 101000 f 74 goat snp360-scaffold1008-2863981 9 48304963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273464 Affx-1111833613 AX-519547083 9 47855509 CTTACTCTCATCAGTAAGTGCCCAGCTCTGCTTTA[A/G]GACATACAGTGAGATGTATTGTCCTGAACTATCAG R 2 1 2 1 101000 r 74 goat 9_47855509_AF-PAKI 9 47855509 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449091 Affx-122923598 AX-123319426 9 47864414 TGTTAACAAAATAACAGGGTAAAACCCACAGAACC[A/G]CAGAAAGGAGTATACAAATTGAAACTGGGTGGTGT R 2 1 2 1 201000 f 74 goat snp361-scaffold1008-2911843 9 48352961 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800639 Affx-122960311 AX-385287558 9 47918884 ACCCAGAACATTTTCGTTAATGAAAATTATTACCT[A/G]TCTTTATGTTATTTAGGAAGATTCTTACCTCTGAA R 2 1 2 1 101000 r 74 goat snp362-scaffold1008-2966313 9 48407483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433359 Affx-122935133 AX-123303700 9 47953034 TGGAACCTACCTTGAAGGAAAACAAGGTAGATGAC[A/G]TTTTAAATAACTATAAAATATGATTCAGAACTAGG R 2 1 2 1 103000 f 74 goat snp363-scaffold1008-3000463 9 48441860 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395312 Affx-122964057 AX-123265667 9 47993216 TTTATGTGAACTGTTAAGGAGGTTTAACATTTTTC[A/G]CTTATTACTGTATTTAGTATGGTACAGAGATAGGG R 2 1 2 1 101000 r 74 goat snp364-scaffold1008-3040645 9 48482947 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408836 Affx-122954019 AX-123279187 9 48069116 CTTACCTGGTTATCCAGAAAAGTCCTGTTAGTTTT[A/G]CTTCTCAGCTGTTGCTTAAGTCTGTTGACTTTGTT R 2 1 2 1 101000 r 74 goat snp366-scaffold1008-3116545 9 48560116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427034 Affx-122939828 AX-123297379 9 48104865 TGAGCCTGTATTATAACTTTCCGGACGTTTAAAGT[A/C]ATGCATTGTTACCAACAAGTCATATAGAAATTGCA M 2 1 2 1 101000 f 74 goat snp367-scaffold1008-3152294 9 48595987 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785137 Affx-122942783 AX-385272183 9 48152776 ACTAGTATTCAAGTAGTATTAACTTTCAGTATTTA[C/T]AGGTGGTGTTACCATACCTTGAATATTGGCATTGC Y 2 1 2 1 101000 r 74 goat snp368-scaffold1008-3200205 9 48643939 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416713 Affx-122947557 AX-123287061 9 48183865 GAAAGACTGTATGTGGTTACTTGTAACACTAACAA[C/T]GGGGACAGAGCCAGACAGATAGGGCAACAGGGGGT Y 2 1 2 1 103000 f 74 goat snp47013-scaffold657-799799 9 48674890 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378136 Affx-122977124 AX-123248495 9 48246289 CAAGGAAATCAGATGGGGAATCTGGCTCCAGCCTT[A/G]TGCCTTCCTGCTCTTAGATTTCAGTTCCATCTTCA R 2 1 2 1 201000 r 74 goat snp47012-scaffold657-737375 9 48735531 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449354 Affx-122922969 AX-123319689 9 48288603 GAGAAGAAGCTGAGAAAAAGAGGAGAGGAGACAGA[C/T]AAGAGGAAAGCAGAAAGAGCCAGAGATAAGAGGGA Y 2 1 2 1 101000 f 74 goat snp47011-scaffold657-695061 9 48778585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448737 Affx-122923831 AX-123319073 9 48334899 ATATTGTATCATCATTTAGCTCATAATATTCTCTC[A/G]TTTTCATTTAATTTCTTCTTAGGTCCATGGATTGT R 2 1 2 1 202000 f 74 goat snp47010-scaffold657-648765 9 48825707 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768241 Affx-122959902 AX-385255422 9 48368037 TTATAATAATTTAGGATAGATAATGTTACCTAGAG[C/T]TCCTTGGAAAGCTGCTTTAGTGTATATGAAAGACT Y 2 1 2 1 101000 r 74 goat snp47009-scaffold657-615627 9 48858995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799825 Affx-122935509 AX-385286751 9 48398004 TTATTGTATTTTATTCAAATTCATACAGCATTATG[A/G]TCTCTCTGGTGATTACTCTCTAGTTAGAGGTGAAG R 2 1 2 1 101000 r 74 goat snp47008-scaffold657-585660 9 48889240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790336 Affx-122920396 AX-385277339 9 48450300 GTCAGACGTGAAGAAACATTATGATCCTCTGATAA[C/T]TGTGAACATTAATGCTATCAGCCTGCGTGGTACAC Y 2 1 2 1 101000 r 74 goat snp47007-scaffold657-533364 9 48941597 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418679 Affx-122946309 AX-123289027 9 48495128 TCAGAGACATGAAGCCAGCTTACAACAGTACCAAC[A/G]TGACACAGACCTTTTCTATGCTCCCACCACTCATC R 2 1 2 1 101000 f 74 goat snp47006-scaffold657-488536 9 48986406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394621 Affx-122964408 AX-123264976 9 48529202 AGTAATTTAATCATTTTTATGTTATTTCTCAATAA[A/G]AGTAAGAAAAATGCAAGAGGACTTTGGTATTTAAT R 2 1 2 1 202000 f 74 goat snp47005-scaffold657-454462 9 49020611 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423620 Affx-122942373 AX-123293966 9 48584827 AGGGACAGAGAAGAGTGCTATAATCTGTGAGAGCC[A/G]TTAATGGCCCTGGCACATCCTCAAATCTCGCTTTT R 2 1 2 1 101000 f 74 goat snp47004-scaffold657-398837 9 49077272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781232 Affx-122952246 AX-385268317 9 48635458 TATAACATCATCTAAGTTTGCAGTGTCAATATAAA[A/G]TAAATGTAAGGAAAACTACGCTTAAGCACATCACA R 2 1 2 1 201000 r 74 goat snp47003-scaffold657-348206 9 49128178 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441155 Affx-122929564 AX-123311492 9 48667031 ATATTGGATCCCCTCAGCTGGGCACTTTGGCTCTT[A/G]TGTCTCTCAATCTCTGTCAGTCACATTACCTGCTT R 2 1 2 1 201000 r 74 goat snp47002-scaffold657-316633 9 49160062 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387128 Affx-122970655 AX-123257486 9 48726929 AGATAAATAGGAGTGAGAGTATAGCTTTAGACTCA[C/T]AAATTGCATAGCATATCTGAGACACTTTCTGCAGT Y 2 1 2 1 101000 f 74 goat snp47001-scaffold657-256735 9 49218685 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439635 Affx-122930617 AX-123309972 9 48769172 CCATCACCACTCCTATCTCAATGTGCCTCACCTCA[C/T]GACTTTCTTCAGTTTTAAAAAGCCATAGAGACTTC Y 2 1 2 1 101000 f 74 goat snp47000-scaffold657-214492 9 49261140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791403 Affx-122930786 AX-385278395 9 48808775 TTTAACTTCATCAGAAGTCAGAGGATATGGAGAAG[G/T]TATTTCTTCTTAAAAGGTTTATCTTCCAACTCCAA K 2 1 2 1 201000 r 74 goat snp46999-scaffold657-174889 9 49302012 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441489 Affx-122928740 AX-123311826 9 48838728 CTCTCCTCTGGAGGCTTTGAGAGACTGTTGGTAAT[A/G]TATTTATTAAATTCTGCTTCTGAATGTGAGTAGAG R 2 1 2 1 101000 f 74 goat snp46998-scaffold657-144936 9 49331879 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412211 Affx-122950931 AX-123282561 9 48902753 TATTTTCTTTATCCTCTGTATTCATCATTCCACCT[A/G]TGAAACATACCAGCTCCTTAATTCCTTTCTCCATT R 2 1 2 1 101000 r 74 goat snp46997-scaffold657-80911 9 49395990 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786535 Affx-122958325 AX-385273568 9 48946985 TTTTCAAGGCCTCTATGCTTTGAGCACAGTGTAGG[C/T]AGGACATGTAAGTAAGATTTAGGAACTGATATAAT Y 2 1 2 1 101000 f 74 goat snp46996-scaffold657-36679 9 49439972 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418973 Affx-122946074 AX-123289321 9 49008755 CAGAGGTATTTCTTATAGTTATAGAAATATAGTCT[A/G]CGTATTAAGTGAGGCCTCATTACCTTAGTGCAAGA R 2 1 2 1 101000 r 74 goat snp5475-scaffold1191-1880931 9 49504888 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401017 Affx-122959680 AX-123271370 9 49061456 AATCATGAAGTTTACAATATCAATATCCATTAAAT[C/T]TGTGGCTTAAAAATCAGGGGGGAAAGTCTGATTAT Y 2 1 2 1 201000 f 74 goat snp5474-scaffold1191-1828230 9 49557800 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778384 Affx-122948757 AX-385265499 9 49122258 CATATCAGCTTCACTACCAGTGATCATTCAGGCAC[A/G]TCCCATGATGTGTTCCTGAAGCCAGTAAAATGTTA R 2 1 2 1 201000 f 74 goat snp5473-scaffold1191-1767428 9 49618933 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407678 Affx-122954590 AX-123278029 9 49197973 CCTTACTCCAGCCATGTGGGTTCTTTGCTGAAACC[C/T]TGCTCAGGCAGCCCATCTGATCCTCCCTCCTCAGT Y 2 1 2 1 101000 f 74 goat snp5471-scaffold1191-1691713 9 49693610 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429673 Affx-122937653 AX-123300014 9 49246682 TAGGTGTATTTTTTCAAAATTTTAACCATTCATTG[C/T]GTTGTTTTGGAATCAGGAACCTATATAATCGCTGA Y 2 1 2 1 101000 r 74 goat snp5470-scaffold1191-1643004 9 49742935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422522 Affx-122943284 AX-123292868 9 49281915 TTTGTGCTTATTTTAGATTTGTTGAAAAATGGTCA[C/T]AGAAGAAAGTATGAGAAACTTATAATTTAAAAAGT Y 2 1 2 1 101000 f 74 goat snp5469-scaffold1191-1607771 9 49778504 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278893 Affx-1111836565 AX-519552361 9 49453423 GATTCTATGGCCAGTGCACCCAACTGGCCCCAAGC[A/G]GCTTTGACTTTATGGCAAAAATGGAGGCGTCAGGT R 2 1 2 1 101000 r 74 goat Random2.2K-994 9 49453423 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38393493 Affx-122965820 AX-123263849 9 49466961 CTTTTCAGTCTTTATTGTGTTCGTTTCTTTTTCTC[A/G]TTGCTCTGATGAGGCCTACAGCATTGAGTAGAAGC R 2 1 2 1 101000 r 74 goat snp5465-scaffold1191-1422725 9 49963574 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405136 Affx-122956961 AX-123275488 9 49536719 ACAAATCAGATCTTATAAAGAGGGCAGTTTCTGGG[A/G]CCAAGTTACTCAAGGTATGAATTTGTGAATTAAAT R 2 1 2 1 101000 f 74 goat snp5464-scaffold1191-1352967 9 50033394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443929 Affx-122927033 AX-123314266 9 49581331 TCCAGGGTAGATTTGGCTGCCCTGAATGGCCATGG[A/G]GATGTCCAGTTCCTCTCTCATTACTCATTCCATCC R 2 1 2 1 101000 r 74 goat snp5463-scaffold1191-1308355 9 50078224 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450042 Affx-122922829 AX-123320377 9 49624663 GACAGAGACTGTACTTTATTTTTCAGATGAATCCT[A/G]TCACCTGAGAGCACTTTCTGCTGTTTTCCAAGAAT R 2 1 2 1 101000 r 74 goat snp5462-scaffold1191-1265023 9 50121794 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401269 Affx-122959284 AX-123271622 9 49667085 GACTCAAAATGATGGTCCTCAAGACATTTGCTGCC[A/G]TTTGGAAGGACAGTGACTATTTTTTTAATTCTAGG R 2 1 2 1 101000 f 74 goat snp5461-scaffold1191-1222601 9 50163737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803454 Affx-122969096 AX-385290281 9 49708074 AAGGGTCTTATTGCATATCTCATTAGATAGCTAGG[C/T]ACATAGTCTTTGGAAGATGTGAGCATTAAGATGAG Y 2 1 2 1 101000 r 74 goat snp5460-scaffold1191-1181612 9 50201026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377642 Affx-122977867 AX-123248001 9 49738123 GCTGGGGAAACCCTGCTCCCACACCAGACGCAGCA[A/G]CCCCTGAGTTGGACACTCTGCCTCTGACCTCGTGA R 2 1 2 1 201000 f 74 goat snp5459-scaffold1191-1151563 9 50231174 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377591 Affx-122978313 AX-123247950 9 49769220 AGCTACATAGCAATGCCGACATTTCAAGGAGTCAG[C/T]AAGGACCAATAGAAAAACAGCACAAGTTCAACTGA Y 2 1 2 1 101000 f 74 goat snp5458-scaffold1191-1120466 9 50262318 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419763 Affx-122945873 AX-123290111 9 49874044 CCTGCATCACTGGCAGATTCTTTATCGTCTGAGCC[A/G]CCAGGGAAGGCCAACCTCATCCTTGATTTAATCTT R 2 1 2 1 103000 r 74 goat snp5456-scaffold1191-1015642 9 50358648 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430666 Affx-122936936 AX-123301007 9 49947275 CTAAACATTTGTTTTTATATTTTCTCTTTTAAAAC[C/T]AGAAGACAAACTACACTAACTTTGAGATAGAACAT Y 2 1 2 1 103000 r 74 goat snp5455-scaffold1191-942411 9 50435368 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409537 Affx-122953610 AX-123279888 9 50000090 TGAACTTAGTATTCCTGCGGCAGAGAAAGCTAACG[C/T]TACAACAATTTGTCCACTGCATCCATGCTATAGGG Y 2 1 2 1 101000 f 74 goat snp5454-scaffold1191-889596 9 50459093 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401968 Affx-122958790 AX-123272321 9 50044511 TAATTTTCAAAGATTTTGTTTTCAGATTCCTTCAG[C/T]ATTTTATTCAAATTTTTCCCTCAATAATGACACCA Y 2 1 2 1 101000 r 74 goat snp5453-scaffold1191-845175 9 50503138 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775853 Affx-122968142 AX-385262984 9 50074324 TGGAGTGGATGGACATATGAAAACAGATATGATAC[A/G]TGAAAATCTTTGTATAATGTACAAATACACACTAG R 2 1 2 1 101000 f 74 goat snp5452-scaffold1191-815362 9 50533268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437140 Affx-122932150 AX-123307478 9 50110470 TTTATTTAAATGTCATCTCATAAAGGCAGGCCACA[C/T]GGATAACCTTTTCTGGAGTGATTCTATTCTAATGT Y 2 1 2 1 101000 r 74 goat snp5451-scaffold1191-779216 9 50569817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397816 Affx-122962486 AX-123268171 9 50152533 TGTCATCATCTGGAGTCGCCTCAGTCCCTCCCTTT[A/C]ACCAGGTCTGTTTCTTCACCAGCAAAATGAAGAGG M 2 1 2 1 201000 f 74 goat snp5450-scaffold1191-737153 9 50612425 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275167 Affx-1111834740 AX-519548746 9 50197186 TCAGGTCACTTCAGTTTGGGTTTTTCATCACTTCC[A/G]ACTGCAGTTT R 2 1 2 1 101000 f 74 goat GoatD01.050960 9 50197186 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38387765 Affx-122969722 AX-123258123 9 50197825 CCATGCATCTGGATTTCTCTAAAACAGGCAACAAA[C/T]ACTAGCAAGAGAGAGGTGGCTTGTCTTGTTGGTAC Y 2 1 2 1 201000 f 74 goat snp5449-scaffold1191-691861 9 50658419 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452491 Affx-122920985 AX-123322824 9 50244617 CTCAGATCTCTTGTCTGAGAAATGAAATGGATGAG[C/T]GAACAAGGTTTTCCAATATCTGGGCTGCAGCCAGG Y 2 1 2 1 201000 r 74 goat "GoatD01.019782;snp5448-scaffold1191-645069" 9 50705468 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320803136 Affx-986696188 AX-385290000 9 50327082 TTCCAAGGAGCAAGTTTATTTTACTTTCATGCCTG[C/T]AGTCACCATCTGCAGTGATTTTGGAGCCCAAGAAA Y 2 1 2 1 600010 f 74 goat 9_50327082 9 50327082 Ancestral_priority_1043 ancestry 0.474 neutral IMAGE 10K 10K ancestral 38433101 Affx-122935716 AX-123303442 9 50379139 ATGGACTCCTTTTGCATTAAATTTTTTTCTGATAT[A/G]TTTAACAACTCTAGGATTTTGCCTCATCAACCAGT R 2 1 2 1 101000 r 74 goat snp5445-scaffold1191-510547 9 50837280 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452465 Affx-122921008 AX-123322798 9 50414983 CAATAGGATACACATGCACACACACACACATATAA[A/G]TGCAGAGAGAGATTTGTTTTAAGGGATTGACCTAC R 2 1 2 1 101000 r 74 goat snp5444-scaffold1191-474703 9 50873288 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418287 Affx-122946997 AX-123288635 9 50450697 GGGATAAGTGGGAAAATTACTCTTTTCAGTTCTGC[A/G]CTAGGATGATCAAAATGCAACACCATCTGAAACTG R 2 1 2 1 101000 r 74 goat snp5443-scaffold1191-438989 9 50909293 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386956 Affx-122969977 AX-123257314 9 50486376 CCTGAAAAGGATGGTAAATTTGGTGGGGAAAGAGA[C/T]GCTATTTGTCTTTCCTACATCTTCCCTGTCACATA Y 2 1 2 1 201000 r 74 goat snp5442-scaffold1191-403310 9 50945160 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273429 Affx-1111833614 AX-519547055 9 50515099 TTTGGGCCTTAAAGGCTGGCAAGAAATAAATAAGG[A/G]GACGAGAAAAGACAGGGAATCTTAGGTGAGGAAAC R 2 1 2 1 201000 f 74 goat 9_50515099_AF-PAKI 9 50515099 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396120 Affx-122963408 AX-123266475 9 50527654 CTATTCTTGATTTTTAAAGTTTTCTTGCCAATGTA[C/T]AATCTCAAAAGGTTTTTCCTGATTATATTTTCTGA Y 2 1 2 1 103000 r 74 goat snp5441-scaffold1191-362032 9 50986647 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770865 Affx-122959656 AX-385258029 9 50581975 ATGGTGAATTCTGAGTATTCTGAAATGGTCTTCCC[A/G]TTGTTAACTCTTTTGAAGAGAACTGAGTCAACTAA R 2 1 2 1 101000 f 74 goat snp5440-scaffold1191-307711 9 51041299 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278711 Affx-1111836566 AX-519552189 9 50598628 TAAAACCTTCACTTTAAAAGACTGCTTTTCCCTCA[A/C]ACCAAATGGAGTCACTCTTCATAAATTTCTTAAAA M 2 1 2 1 201000 f 74 goat Random2.2K-995 9 50598628 A C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786923 Affx-122957206 AX-385273952 9 50645938 TTTTTTAAAACACAAGTTGTATCTCATAGAAGAAT[A/G]TAAGCTTGCAAAATAGTGGGTTGGCCAAAAAGTTC R 2 1 2 1 102000 r 74 goat snp5439-scaffold1191-243748 9 51105019 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769176 Affx-122968139 AX-385256351 9 50698501 CTACAGGTTAATTTTAAGAGATATACCAAATAGCT[A/G]ATATAAAGGCAGCTATAATGTTTCTTTTTTTTTTT R 2 1 2 1 201000 r 74 goat snp5438-scaffold1191-191185 9 51157459 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386634 Affx-122970221 AX-123256992 9 50743693 CTCTACCCTGGCACAGGAGAACCACTCTCAGCTCA[C/T]GTCCCAGAGGAGAGCTGGGGGAGAGCTGGGTTCAG Y 2 1 2 1 101000 f 74 goat snp5437-scaffold1191-145993 9 51203207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413030 Affx-122950995 AX-123283379 9 50788418 CCTCCTATTTCCAGGCTTTTCCTGACTTAGTGGCC[A/G]TGCTTGTGCCCATGGGGTTGTGGCAGAGAGAAGCA R 2 1 2 1 101000 f 74 goat snp5436-scaffold1191-101268 9 51248363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439329 Affx-122930302 AX-123309666 9 50907482 CTGGGGGTGTGCGATGCAGGGCAGATGGCTTCAGC[A/G]TTTCTGGATCTCAGTCTCCTTACTATTAAGAGTAG R 2 1 2 1 101000 r 74 goat snp29438-scaffold318-2862885 9 51373013 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781514 Affx-122965880 AX-385268599 9 50945050 TATAATGAAATAGTGGTGTGATGGTGAATCACACA[G/T]ATGTATATTTTACTTGGAACAAATGCAGTTCACCT K 2 1 2 1 201000 r 74 goat snp29437-scaffold318-2825317 9 51411622 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786365 Affx-122933869 AX-385273399 9 50982469 CGAATGTATAAATTTCTGGGAGAAAGATAAGGAGA[C/T]GAGTTAAATAGCAACTGTCTCTAGTCTGAGGACTT Y 2 1 2 1 202000 f 74 goat snp29436-scaffold318-2787898 9 51444917 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423151 Affx-122942755 AX-123293497 9 51023895 GTGTCTGCCCTCATGTCAATTACACAGGCAGATCC[C/T]GATTTTTCAAGCTGACTGCACTAAGGCCTAAGGAT Y 2 1 2 1 101000 r 74 goat snp29435-scaffold318-2746472 9 51486948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801619 Affx-122963226 AX-385288527 9 51058930 TATAAATTTTTAACCTTGAAACTCACACATTTGAA[C/T]GAAACCTACTAAGTTAGAAGTCCTTGTTTGTTAGT Y 2 1 2 1 101000 r 74 goat snp29434-scaffold318-2711437 9 51522009 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772263 Affx-122968997 AX-385259418 9 51124500 GTTTCAGAAAGAAGAATCCAATGTGGCTGAGCAAG[A/G]GGGTAAAGAATATGAGATAGAGTTGAAGAGGTAAG R 2 1 2 1 101000 f 74 goat snp29433-scaffold318-2645867 9 51587892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433142 Affx-122935682 AX-123303483 9 51181192 GCCTAATAATGAGTATGCATAGCGGCGCCCCAGCG[A/C]GACCAGATGCGTGTGTAAAATAAATAAATAAAGTC M 2 1 2 1 101000 r 74 goat snp29432-scaffold318-2589175 9 51644257 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425918 Affx-122941611 AX-123296264 9 51270766 ATTAGCACATTCAATCTTCCCAGCAATCCTGGACC[A/G]TAGACACTATATTATTCCTATTTTGTAGATGGGAA R 2 1 2 1 101000 f 74 goat snp29431-scaffold318-2499601 9 51734444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395397 Affx-122963961 AX-123265752 9 51339640 ACCTTTTTTGTGTGGGGGGAGAGAGTAAATTCCAC[A/G]TAACGGCTAACAAGTGGAGGTCAAAGTGAGCATCT R 2 1 2 1 101000 r 74 goat snp29430-scaffold318-2430727 9 51803423 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400951 Affx-122959701 AX-123271304 9 51378773 ATGGGTAGTCTGAGGATCAGGTTTACTGTGTTCAT[A/G]CTCATGCACTCATGGGCTTTCTGCTGCAACCCTCC R 2 1 2 1 101000 f 74 goat snp29429-scaffold318-2391594 9 51842509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393073 Affx-122965608 AX-123263430 9 51439411 CAACTGTGCACACTCTAGTCAACCAGGAGAGGAAT[A/G]TCATGATCTTAGAAAAGTTCATTTCCTTCAGGCAG R 2 1 2 1 101000 f 74 goat snp29428-scaffold318-2330956 9 51903324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788213 Affx-122951101 AX-385275232 9 51513969 CACCAATAATTTTAAAGGAATTAGATTAATTCAGC[A/G]TATTACAGACATGCTTCATTTGTTGCACTTTACTT R 2 1 2 1 201000 f 74 goat snp29427-scaffold318-2256398 9 51979403 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397204 Affx-122962395 AX-123267559 9 51623547 TGGTCCCCATAGCAATAGAAGTCTCTGAAGACCCA[C/T]GCTTGGTGAAGATGACCTTGGTCCTGGCATGGGTG Y 2 1 2 1 101000 f 74 goat snp29425-scaffold318-2146820 9 52090016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382655 Affx-122973673 AX-123253013 9 51659622 CACCTACCCATCTCTTGCACAAATTATAATGCAGA[A/C]AAAAATGAACTTCTAAAGCATTTGATGCTTCCATT M 2 1 2 1 101000 f 74 goat snp29424-scaffold318-2110745 9 52124527 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789195 Affx-122945531 AX-385276207 9 51688973 GAAGGGAGTCCAAGGATGACTGACCACTTCATAGA[A/G]CTAGAAGGTAGTTAGCCACAGTATGAATTAGTCTC R 2 1 2 1 101000 f 74 goat snp29423-scaffold318-2081394 9 52154220 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448134 Affx-122924291 AX-123318470 9 51727599 ATCACAACTTCAGTGACAGTCTCATGAGAACTGAA[C/T]GTCTCTTGTTAAGTCATTGAGTCATAATGGACAAT Y 2 1 2 1 101000 r 74 goat snp29422-scaffold318-2042768 9 52193219 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386103 Affx-122971432 AX-123256461 9 51774790 AATATTCTTCCAGAGGCATAGTTTGGATTGTGCTA[C/T]ATTTACCATTTTCCATCTTATTTGTTTTACTTAAT Y 2 1 2 1 101000 f 74 goat snp29421-scaffold318-1995577 9 52240829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401094 Affx-122959417 AX-123271447 9 51811637 AGAGGCATTAGATTCCTGCTTATTGTGTAACGTCA[G/T]GGTCTCTACAGCTCATAGACTGTCAAAGTATTATC K 2 1 2 1 101000 r 74 goat snp29420-scaffold318-1958730 9 52277732 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379412 Affx-122976118 AX-123249770 9 51846561 GCAGTTTTTGTTTATTAAGCTTCATTAGTGATTCC[A/G]TTTTCCTCATCAGTTTGAATACAGAGTAACGGGGG R 2 1 2 1 201000 r 74 goat snp29419-scaffold318-1923806 9 52313829 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800950 Affx-122926368 AX-385287865 9 51904621 AATGAAAAATATAAGAAAACTATCTGTTAAACACC[A/G]TGATTATAAAAGTATATTAGTTGTAAGCAAATAAT R 2 1 2 1 101000 f 74 goat snp29418-scaffold318-1865746 9 52371391 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790929 Affx-122976706 AX-385277926 9 51937205 AAGCTGTAAGTTGTGAAATGAAAAAATAAGTTTCC[A/G]TATGTGTAAAAACAATATCTCACTGAGTCTTACAA R 2 1 2 1 101000 f 74 goat snp29417-scaffold318-1833162 9 52403812 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784219 Affx-122939520 AX-385271270 9 51968940 AAAGCTAAATCAGATATAAGCTACTGAATTTCATA[C/T]TCAAGAATCCCAGATTTATCACTGAAAATGTTTCT Y 2 1 2 1 201000 r 74 goat snp29416-scaffold318-1801427 9 52435830 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399727 Affx-122960458 AX-123270082 9 52044293 TTATGGCAGTATTGTGGGCTGGGCGCTATGCTAAG[C/T]ACTTTACAAATGTTGACTCAGTTGATCTTTTTTAT Y 2 1 2 1 201000 r 74 goat snp29414-scaffold318-1726074 9 52512224 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417691 Affx-122947462 AX-123288039 9 52133314 CTCCCAAAACAGCAGATATTAAAAAACAAACTTCT[A/G]ATTCTTTTCTATTTGAGTTGAGAACACTTCTGCCT R 2 1 2 1 101000 r 74 goat snp29412-scaffold318-1637053 9 52600475 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377866 Affx-122977271 AX-123248225 9 52165328 CCTGTACCAAGGTACAAGTACATGTAATTAAACCA[C/T]GATAAGAAGACATGTTGGAAGCTGTGACAAGAAGC Y 2 1 2 1 101000 f 74 goat snp29411-scaffold318-1605039 9 52632410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432150 Affx-122936424 AX-123302491 9 52227288 TTTTCATGTTGCAGAACAGGGATATGATGTTTTCT[A/G]TATAAACTTATATGTTAATTTTTAAATATACCTTT R 2 1 2 1 103000 f 74 goat snp29410-scaffold318-1543079 9 52695016 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769844 Affx-122957177 AX-385257014 9 52264147 GATCAATTTCTTGACCCTGCTCAGACTGAGACACC[A/G]TATGTATAGAAGGTTGAGGTAAAACAGAGGGAATT R 2 1 2 1 101000 f 74 goat snp29409-scaffold318-1506220 9 52732446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800072 Affx-122934879 AX-385286995 9 52313745 CCTCAAACAAAATTTTATCGACATAAAATGTTGAT[C/T]ATAGAAGTGCCAATTCCACTGTAAAGGTAAAAAGA Y 2 1 2 1 101000 r 74 goat snp29408-scaffold318-1456622 9 52782216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770070 Affx-122950001 AX-385257237 9 52343373 ATATAAGCATATAGATGACAATTACAATGGAAAAG[C/T]AAAATACAGCAAAGTTATTAAAGTTGCAATTACAA Y 2 1 2 1 101000 r 74 goat snp29407-scaffold318-1426994 9 52812069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768434 Affx-122936895 AX-385255614 9 52399498 AGATAAAGACATTAACTTAATGAAGGAACATCACT[A/G]CACATCCTATAGACAGTAAAAAGATAATAAAGAAA R 2 1 2 1 201000 r 74 goat snp29406-scaffold318-1370869 9 52869563 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791467 Affx-122955623 AX-385278458 9 52445206 AGCATCTAAGTGAGGAATGAGGTCCTTTTAAGACC[A/G]TATGACTGTAGTATAAGAAATACTGGCCGACTCTC R 2 1 2 1 101000 f 74 goat snp29405-scaffold318-1325161 9 52916325 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400327 Affx-122960053 AX-123270682 9 52478698 CAAGAATCCCGATTTATACAAGAATTTCCACATCA[G/T]TTCAAAATTCACCTAATATTACCTTAAATATTTTG K 2 1 2 1 101000 f 74 goat snp29404-scaffold318-1291669 9 52950671 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425498 Affx-122941480 AX-123295844 9 52514289 AGAAATTGTTCGTATAGTGGGTTGGTTAGGAATTA[C/T]ATTGGTGAAGGATTCTTCATTTGTTGTGTCAATAA Y 2 1 2 1 103000 r 74 goat snp29403-scaffold318-1256078 9 52986539 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451149 Affx-122921363 AX-123321483 9 52559989 GGATAATGTTGATAAAAATGTGGGTTATTTTAAAG[C/T]AAATATTATGCTTAGTTTTATAATATAAAAGATGT Y 2 1 2 1 103000 f 74 goat snp29402-scaffold318-1210378 9 53032371 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415161 Affx-122949401 AX-123285510 9 52603592 CCTTCAACTGTGCATGGAATTGCACCAACTACCTA[C/T]GTACCTGCTTAAAAATATAAAACAGATTAAAGTCT Y 2 1 2 1 101000 f 74 goat snp29401-scaffold318-1166775 9 53076584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413606 Affx-122950564 AX-123283955 9 52664411 AATTAGTAAAACAAAGAGAGATGCTGTGTTTACTC[C/T]CTATACTCAGGAATGATAGCAGCCTCAGGCTTCAA Y 2 1 2 1 101000 r 74 goat snp29400-scaffold318-1105956 9 53138117 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38446169 Affx-122925745 AX-123316505 9 52716650 TGAATTGGACCTCCAATGCATGCATGTGTTGCTCA[A/G]TTACTTCAGCCATGTTTGACTCTTTGTGACCCTAT R 2 1 2 1 303000 r 74 goat snp29399-scaffold318-1053717 9 53192047 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278713 Affx-1111836567 AX-519552191 9 52717852 CTCAGAGAATAGAAACACTCCCAAGGAGAGGAAGA[A/G]AGAGGGAAATGGCCAGTCCATGGAACAGTCAAATC R 2 1 2 1 201000 f 74 goat Random2.2K-998 9 52717852 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784239 Affx-122960328 AX-385271290 9 52751813 TAATGATCTGAACTAAAGTGGTAGTAGTGGAGAAT[A/G]TAGAGCAAGAACAAGGTTATTATTGCTGCCTATAG R 2 1 2 1 101000 r 74 goat snp29398-scaffold318-1018554 9 53227252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444909 Affx-122926250 AX-123315246 9 52787543 CAATGGATAATGACTTCTAAGTTTAGTCAAGTCAC[A/G]CATGGTTCTTAAAAACCACCACTGAACTATACAGT R 2 1 2 1 101000 f 74 goat snp29397-scaffold318-982824 9 53263734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429986 Affx-122938048 AX-123300327 9 52816817 GTGAAATAGCAGTTTATTTCCAGCTTATACCCATA[C/T]ACTGAGTCAACCAATTCATGAATTTAACTTGGCCT Y 2 1 2 1 101000 f 74 goat snp29396-scaffold318-953550 9 53293881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404796 Affx-122956666 AX-123275148 9 52868428 CCACCAAACACATTCAAGGTGGGAGTGTTATTCCT[C/T]CCATATACCTTGTTTCCTTTCTTGGAGCCAGTGCC Y 2 1 2 1 101000 r 74 goat snp29395-scaffold318-901939 9 53346107 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762719 Affx-986697249 AX-385250783 9 52921021 CAAAGCAAAAAAATTGCAAGGACGTTCTCTAAAAG[C/T]TAATTACTACCAATTTCTGCCTATAACTCTTAAAA Y 2 1 2 1 600010 f 74 goat 9_52921021 9 52921021 Ancestral_priority_1043 ancestry 0.69 recommended IMAGE 10K 10K ancestral 320787466 Affx-122966396 AX-385274491 9 52923735 ACAAACATTAAATAACTAGTTTCAAAATCATGTCT[A/C]TTTCAGTTTCATCTTTCTCCTTACTACTATTTCTT M 2 1 2 1 101000 r 74 goat snp29394-scaffold318-846632 9 53401351 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376347 Affx-122978333 AX-123246706 9 52976298 TACAGAAACACTTGCTGTTGAGAAGTGACTCAAAA[G/T]AAGCACTCTCTGTCGACCCATGTCTTAATTTTTCT K 2 1 2 1 101000 f 74 goat snp29393-scaffold318-794069 9 53453770 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794959 Affx-122948448 AX-385281919 9 53039246 AGCACGCACAACACCCTAAATTATTCTTCCGTGAT[A/G]TTCTGTAGATGTTTAAACAAGTTGCTCGGAGTCCT R 2 1 2 1 101000 f 74 goat snp29392-scaffold318-731121 9 53517356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764708 Affx-122932017 AX-385252328 9 53099575 AACACCTACTATTAGTATGTGCAGAACAAATATTT[A/G]TACAAGACAGTGGTCTGAAATATACTCACATTGTT R 2 1 2 1 201000 f 74 goat snp29391-scaffold318-670792 9 53577641 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396561 Affx-122962929 AX-123266916 9 53132901 GTTGTGTATCCTAAGAAATACATGTAGTCAAATAC[A/G]TCTGATTTAATCTAAGAAAAAGGGGAACAAAATTA R 2 1 2 1 201000 f 74 goat snp29390-scaffold318-637466 9 53611426 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273468 Affx-1111833615 AX-519547086 9 53204128 GTTATCATGACTCTCCTAAGGACTTACAGCAATTA[A/G]GGGTTATTCATTTTCCTCAGGCTCCTTCTACTGCT R 2 1 2 1 101000 r 74 goat 9_53204128_AF-PAKI 9 53204128 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320788563 Affx-122956289 AX-385275580 9 53234033 AAAATAATAACAGACTGCAACAAAAGTGAGGGCAC[A/G]TCTGTCAGCCTTACCAAAATCATGGGATCTCTGGA R 2 1 2 1 101000 r 74 goat snp29388-scaffold318-536334 9 53712703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415241 Affx-122948953 AX-123285590 9 53271520 CCGTAAAAGGAAAGCCAGTATGTGGTAGAAATGAT[A/G]TGACTATTCATTACTGTATTTAAATGAAAATGTGG R 2 1 2 1 101000 f 74 goat snp29387-scaffold318-498847 9 53751463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801143 Affx-122934898 AX-385288057 9 53315902 CTGTCAAAAAACTTGTTGAATGTTAGCGGGTTTAC[A/G]TGTATTATCACTAATCCTCATATAATTGTACTGTA R 2 1 2 1 101000 f 74 goat snp29386-scaffold318-454465 9 53795743 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434018 Affx-122934224 AX-123304359 9 53415307 GCTAACAGCTGCTGAAATTTGTCAGATTTAAAGGG[C/T]GAGAATCCATGGCACCCATCTTTCCTGCCTTGTGG Y 2 1 2 1 201000 f 74 goat snp29384-scaffold318-355060 9 53894972 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424781 Affx-122941400 AX-123295127 9 53475704 GAGAGTTTGGGGTTCAAATCTTGGCTCAGCTCTTT[A/G]CTGCAATATGATCATTAGAAAGACAATTAACCTCC R 2 1 2 1 201000 r 74 goat snp29383-scaffold318-294663 9 53955792 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379575 Affx-122976040 AX-123249933 9 53535289 TATAGGGACAGAGCAGCATAAATCATCCTAACCTA[C/T]GGACTATGAGGCTTCTCCCAAGGAGGAAAAGATCC Y 2 1 2 1 101000 f 74 goat snp29382-scaffold318-235078 9 54016097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785598 Affx-122930241 AX-385272642 9 53581376 CTTAGATTAATTCTGCATGGATTACCTCACTGTCG[C/T]AATGTTTCTGCTGGCCTTCTCCTATCACCTGCTGT Y 2 1 2 1 101000 f 74 goat snp29381-scaffold318-188991 9 54062504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389977 Affx-122968064 AX-123260334 9 53610944 GCAGGTTCTATTACTTTAGTTCTTCCTACTCAAAG[A/G]TCATGATGTTTGTGGAAACACAAACTCCTCAAGAC R 2 1 2 1 101000 f 74 goat snp29380-scaffold318-159423 9 54092064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779058 Affx-122950907 AX-385266163 9 53643477 TTAACTTCCAATCAATATATCCTATTAAATTATAA[A/G]CTATATCCGGAGTGATTTCTTAAAATCCACAGTTT R 2 1 2 1 202000 f 74 goat snp29379-scaffold318-126890 9 54125416 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424820 Affx-122941371 AX-123295166 9 53728020 GAATTAATTTAATTTGAAAACCAAAATGTCACAGA[C/T]GTATAGGATTTATCTCTATTTTCAACATATCCTCC Y 2 1 2 1 101000 r 74 goat snp29377-scaffold318-42347 9 54210980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432461 Affx-122935799 AX-123302802 9 53760210 ATAGCATTTTTATTCATTTATGTTACAAAAGGGTA[C/T]TGTATTTTTGTAACATAAAGTGAAAACTGAGAATT Y 2 1 2 1 103000 r 74 goat snp29376-scaffold318-10157 9 54244198 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428713 Affx-122938465 AX-123299055 9 53772093 AATCCACATAGAAGAATAAATAAAATTTTGAGAAA[C/T]AGAGGTGCTATGTAAGAAAAAAATTAAGGAACTAC Y 2 1 2 1 101000 r 74 goat snp34569-scaffold408-935478 9 54256011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785431 Affx-122973895 AX-385272476 9 53825527 ATAAATCATTTTTACCAAACTAGTAGGCCAATATG[C/T]AGTGAACAAGCCAACAAGTTACAAATGTAACAAAA Y 2 1 2 1 101000 r 74 goat snp34568-scaffold408-882044 9 54310360 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775809 Affx-122924687 AX-385262940 9 53862967 AACTAGAGAGATTTGCATAAGGCCTGGTCTTTCAT[A/G]CTAAATAATTCACATTAACAAATATGCAGTCCATG R 2 1 2 1 101000 f 74 goat snp34567-scaffold408-844604 9 54348220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376176 Affx-122978832 AX-123246535 9 53902690 TCTACAACATCTTGTTTCATTTATGGCTGTACTTT[A/G]CTCACCATATGCTATTTACTTTAAAAATTGTTTCT R 2 1 2 1 101000 f 74 goat snp34566-scaffold408-804881 9 54388752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800843 Affx-122954889 AX-385287758 9 53944914 GCAAAAATAAGCAAACCCAAGATGCATAAATAACA[C/T]GCATGATAAAAAGCTGTATTTTTGTGCATCATTTC Y 2 1 2 1 101000 r 74 goat snp34565-scaffold408-762657 9 54431406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430111 Affx-122937516 AX-123300452 9 54014677 GCAACTATTACACTCTACTGTGGATTACTGCAAAA[C/T]AACGGCAGCTGTTCTCAAAGCATTATAAGAGGTAT Y 2 1 2 1 101000 f 74 goat snp34563-scaffold408-692894 9 54501330 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441494 Affx-122928736 AX-123311831 9 54043455 GCCTTAATCAGGGATAGGCTAAGGGTGCCTGGTAT[A/C]CTGGGCTCGCCTCCCCTCAGGACCATGAAGACACT M 2 1 2 1 101000 f 74 goat snp34562-scaffold408-664116 9 54530208 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410128 Affx-122952813 AX-123280478 9 54074031 CATGCATATTAAAGTTTATCAGAATGTGATGTGGT[A/G]TGAGTGTCTGCCTGTGTGTGTGTATGTACTGAGTC R 2 1 2 1 201000 f 74 goat snp34561-scaffold408-633540 9 54560811 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386299 Affx-122970926 AX-123256657 9 54146056 GGAAAGACTATATACTTATGATTCCAACTACATAA[C/T]ACCCTGAAAGAGAAAACTACGGAGACAATAAAGAA Y 2 1 2 1 101000 r 74 goat snp34560-scaffold408-561515 9 54631365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441248 Affx-122929496 AX-123311585 9 54188065 TAAAAAGTTCCACCCCAGCATTGTAAATAGACACT[C/T]ATAAAACAAAGCTGATGATTTGTATTGTGCCGTAT Y 2 1 2 1 202000 r 74 goat snp34559-scaffold408-519506 9 54673705 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438040 Affx-122931552 AX-123308378 9 54250041 TTCACTGGTCAGCTCCGACTTCTTACCTTACATTC[A/G]TCACACCGACGCCCCTGCACGTTAGGTTTGCATTC R 2 1 2 1 101000 f 74 goat snp34558-scaffold408-457530 9 54735326 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411958 Affx-122951139 AX-123282308 9 54298123 TTCTTGTACAGATCAGTTCATCAGAGGTAGATTAG[C/T]GAAAGGAGGATGAAAATAATATATTTCACACACCA Y 2 1 2 1 201000 f 74 goat snp34557-scaffold408-409448 9 54783171 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447513 Affx-122924069 AX-123317849 9 54344329 TACATGATATTCTCAAGGGTCATCTTCAGATACTA[C/T]TGGTTCTGTATATCCAAGGGTCAGTGAAGTGCTAG Y 2 1 2 1 101000 r 74 goat snp34556-scaffold408-363242 9 54831023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782269 Affx-122975541 AX-385269347 9 54379211 CAGACACTTAATTATTTTTACACAGCTTATGGGGA[C/T]GGAATAACAAGAACAAGTGGACATGCCGTATGCAT Y 2 1 2 1 101000 r 74 goat snp34555-scaffold408-328360 9 54865695 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784836 Affx-122978074 AX-385271883 9 54414444 CTGTTACCTTCCAGAAAGTTTTGCCTCTATCCTTA[G/T]AGTCTTATAACTGGGTTAATAAAGAGCAAAATTTT K 2 1 2 1 101000 f 74 goat snp34554-scaffold408-293127 9 54900891 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765277 Affx-122968376 AX-385252808 9 54453461 GTAGATGCTTATCAAACACCTGTTGAATGAATAAA[C/T]GGATTTTGGAGTAATAACTATGCCACTATTCAAAT Y 2 1 2 1 103000 f 74 goat snp34553-scaffold408-254110 9 54940406 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778069 Affx-122937668 AX-385265185 9 54502825 CCAGTTTTTCACTGAAAGAACACTTTACAATGTCT[C/T]TTGCCTATTTTCAAGTTCTGAATAATTTTTCTGAC Y 2 1 2 1 101000 f 74 goat snp34552-scaffold408-204746 9 54989721 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789035 Affx-122960486 AX-385276048 9 54546263 TAAAGCACTTAATTTTGCCACTGTTTAAACCTAAT[A/G]TTCTGGAGACTTTACTCTTTGAAGAGTGTAAGCCT R 2 1 2 1 101000 r 74 goat snp34551-scaffold408-161308 9 55033030 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792339 Affx-122930962 AX-385279321 9 54621648 TCTTTGAAGGTCATTTGGAGCTATCCATAAAATTA[C/T]GCTTTGCAGGCTAAGTGAAGCAGCTTTCTTTTTCC Y 2 1 2 1 101000 r 74 goat snp34549-scaffold408-85923 9 55108694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780396 Affx-122978790 AX-385267490 9 54651503 AGTGGATGGAGATTGAATGGTAAGACAGTGGAGAA[G/T]AAATAATAAGTGTATTATGTAGTTATCTGGAATAT K 2 1 2 1 201000 r 74 goat snp34548-scaffold408-56068 9 55138509 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375382 Affx-122979220 AX-123245741 9 54683081 ACACCAGGGCACAAGCTGTCTCCCTGTTACAGGAA[A/G]CATTCTCAGATCAGTAACAACAGGGCTTATTAGGA R 2 1 2 1 201000 r 74 goat snp34547-scaffold408-24490 9 55169746 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376778 Affx-122977959 AX-123247137 9 54709449 AAGTTTATGTATAGTAATGTAGATAAGGCTAGTAT[A/G]CTAAACATCCATAATGTAAAAGGCATGATGAATAC R 2 1 2 1 101000 r 74 goat snp45521-scaffold620-3607455 9 55196251 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416732 Affx-122947542 AX-123287080 9 54754940 CAGACATGCAGGATAGAATGAGAAGGTTCAACATA[C/T]GTGTAACTGGTACACCATGAGAAGACACTAATGAG Y 2 1 2 1 101000 f 74 goat snp45520-scaffold620-3561964 9 55241475 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422105 Affx-122943570 AX-123292452 9 54837725 CCCCAGTCTCATCTCTAAGCATTAACTCTTGAGTT[A/G]CCACTAAATTTGATTCATATCTTGTCTAGAGTCCC R 2 1 2 1 101000 r 74 goat snp45518-scaffold620-3479179 9 55324754 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276461 Affx-1111835352 AX-519549973 9 54858153 CTGGTCCCTGGAAGCTAAATCTTCAGAGATCAAGA[A/C]TCTGACACCTTTTGCCATAGGTTATCAGAAGCGAT M 2 1 2 1 202000 r 74 goat Random2.2K-1001 9 54858153 T G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38379321 Affx-122976187 AX-123249680 9 54883656 GAGCAGTAATGGGTCAGTTTTGTCTGTCACCAACA[G/T]ACAGAGTCAACCATTGTGCTTTTTCCTTCAGTCTT K 2 1 2 1 101000 f 74 goat snp45517-scaffold620-3433248 9 55371203 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422100 Affx-122943575 AX-123292447 9 55019205 AATCATCTTTCTACTTTCCTTTTAATGTAGGAGAT[A/C]TCCTGAATCATAATTATCCATATTGTCTAGGAGTC M 2 1 2 1 101000 r 74 goat snp45514-scaffold620-3297699 9 55506869 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437507 Affx-122932346 AX-123307845 9 55060001 GGCTCCCAAAGTAATTCTGCAAACGGTCTATAAAA[C/T]TTATCACAGATAACTTGTAAGCAAAAGTGCATCTT Y 2 1 2 1 101000 f 74 goat snp45513-scaffold620-3256903 9 55547411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766071 Affx-122940774 AX-385253487 9 55089915 GTTTGCCTCAACTGGGGTTGCTCCCTCAAATCTTG[C/T]CTTTTCAGTAAAATCTATATACTCTCTCTTTAGCC Y 2 1 2 1 101000 f 74 goat snp45512-scaffold620-3226989 9 55576851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381982 Affx-122974094 AX-123252340 9 55124709 ATAGACACTGAGTGTTTAGTGCAGTAGACTCTGGT[G/T]CAGATAGACTGGGAATCAGTCCTAGCCATTAACTT K 2 1 2 1 201000 f 74 goat snp45511-scaffold620-3192195 9 55612759 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377631 Affx-122977875 AX-123247990 9 55175556 AGCATTTCCTCTCAACTACACTTCAGCACACACAG[C/T]GCCCTGAAGAAAGTGAGGGATTTGAACTCTGTGAA Y 2 1 2 1 101000 f 74 goat snp45510-scaffold620-3141348 9 55664001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781946 Affx-122963550 AX-385269027 9 55208275 ATTTTAGTAGGGTGCAAGGCACTTAACTGAAGAGC[G/T]ATGTTTACTAGAAGAAAGTAAAGAGCAACACTGTG K 2 1 2 1 101000 f 74 goat snp45509-scaffold620-3108629 9 55697261 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801241 Affx-122942048 AX-385288154 9 55242986 CTCTGAATTGAAAGCAAGAACTCGGCATATCTACT[A/G]CATCTTTATTCTGAAAGTCATTAATGTTTGACCGC R 2 1 2 1 101000 f 74 goat snp45508-scaffold620-3073918 9 55731948 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276308 Affx-1111835353 AX-519549841 9 55259815 GGTATGATGTCTATAAAGAACAATGGGTTTCCCTG[A/G]TGGCTCAGATGGTAGAGTCTGCCTACAGTGTAGGA R 2 1 2 1 101000 f 74 goat Random2.2K-1002 9 55259815 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381384 Affx-122974386 AX-123251742 9 55271700 CTATGCTAGGAACAGCTTTTTTTTTTTAAAGCTTT[A/G]CATAAGAACTTCCTGGCTGACTCATTAAGCTGTTT R 2 1 2 1 101000 r 74 goat snp45507-scaffold620-3045204 9 55759114 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440519 Affx-122929345 AX-123310856 9 55302805 AGAGTCTTGATAACTGTCACATTCCAAAGTGAACT[A/G]AATACCTGGATAGAAGACAATATTCCATTAGAATT R 2 1 2 1 101000 f 74 goat snp45506-scaffold620-3014099 9 55790263 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417457 Affx-122947192 AX-123287805 9 55368497 ATGATGCAAACAGGTTTCTAGGAGGGCAGTGCATC[A/G]TTCTGTGGCACCATTGACATCCTTTGGCCAAAGAA R 2 1 2 1 101000 r 74 goat snp45505-scaffold620-2948407 9 55856180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396319 Affx-122963076 AX-123266674 9 55423545 ATGCTGGGCAGAGTTAATGTCCCATCTACCATGCC[A/G]TACATGATGGGGACAAATGCTGCTTCCAGACTTCA R 2 1 2 1 201000 f 74 goat snp45504-scaffold620-2893359 9 55911228 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446212 Affx-122925712 AX-123316548 9 55473455 CTAGAGCCAGGCCAACCCTAGGCAGTGCTCACCAA[A/G]CAGCTAACCCACACTGGCAGAGTGCCACCCAAGTG R 2 1 2 1 101000 f 74 goat snp45503-scaffold620-2843449 9 55960726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798191 Affx-122938517 AX-385285126 9 55506051 TAACAGTGTTTGGACAATGTTCTTGTTTATGTCAG[C/T]GTTCAGATATCATTTGGAGGTAGTCTTGACTGTGT Y 2 1 2 1 101000 f 74 goat snp45502-scaffold620-2810853 9 55993733 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412686 Affx-122950764 AX-123283035 9 55547569 GTAAAATCCCTAATGATATGTGTGGCAAAAAGACA[C/T]GATTTTAAAAAAGAATCAGACAGGACTGAGTGACT Y 2 1 2 1 202000 f 74 goat snp45501-scaffold620-2769335 9 56035599 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411528 Affx-122951664 AX-123281878 9 55602107 GAGACAGATTTTAATCCCTGTGACATCCCTTACCT[A/C]TTACTCTATTCCCAGGTGAATCCCTATGTTACCAA M 2 1 2 1 101000 r 74 goat snp45500-scaffold620-2714797 9 56090631 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399301 Affx-122960534 AX-123269656 9 55641261 CAAATGTTAAAAATCATGACTTAGGCTTCTGATGG[A/G]TTAAAAATATATTCTGAGTAATGTTCAGCCCTGAA R 2 1 2 1 201000 f 74 goat snp45499-scaffold620-2675643 9 56129779 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779174 Affx-122962150 AX-385266278 9 55679727 TCAACGGTAATTCTTTTCATAAAGTGCTTTGGAAA[C/T]GACGTTTTTCAACTGTCTATTAATTATTTAAGCAC Y 2 1 2 1 101000 f 74 goat snp45498-scaffold620-2637177 9 56168082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273470 Affx-1111833616 AX-519547088 9 55710515 TTTTAAAGATCTAACCCTGCTAAATCCAGCATACT[A/G]CCTTGGCTTTTGAATGCCTCATGCTCAGATCTAGA R 2 1 2 1 101000 r 74 goat 9_55710515_AF-PAKI 9 55710515 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38410550 Affx-122952149 AX-123280900 9 55737298 AGAGGCAATCATAATTTTTTGAAAGGGAAAGATGG[C/T]AGAAAATGTAAGTGACCCATAAAATCACTCTGCTC Y 2 1 2 1 101000 r 74 goat snp45497-scaffold620-2579606 9 56226220 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790924 Affx-122940537 AX-385277921 9 55780958 CTACCATCCTTTGAAATATGCCAGCTGAAGGAATG[C/T]TGTAATGAGAACTAGATGTCAGCACTTAAGAGTTA Y 2 1 2 1 101000 f 74 goat snp45496-scaffold620-2535946 9 56269800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397848 Affx-122962462 AX-123268203 9 55824629 GACTCTCGTGATATTGCCACTGAAGTCATTTACAT[A/G]CTTGATGTGTTAAAACAGCAGGGCTCTTTCCTCTA R 2 1 2 1 101000 f 74 goat snp45495-scaffold620-2492275 9 56313068 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429198 Affx-122937947 AX-123299540 9 55857275 ACATTTAACTTTTTGTTTAGAGAGTCCCAACTGCC[A/G]TCCCTTTATTCTTTTGCTTCCCTCCTGTACCGGCT R 2 1 2 1 101000 f 74 goat snp45494-scaffold620-2459629 9 56345787 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423326 Affx-122943176 AX-123293672 9 55892487 ATGACTTTTTCTAGTGGTGTGAGAAATGTAAAAAT[A/G]TAACAGTAGCAAAGAGGTTCTTTAATTACCCATTT R 2 1 2 1 201000 f 74 goat snp45493-scaffold620-2424417 9 56381078 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770446 Affx-122947572 AX-385257612 9 55921275 TCCATTGAACACATTTTCCTTATATTATTTTTGAT[A/G]TTGGTGACCAACCATATTGTCTTTGAAATTCTCTC R 2 1 2 1 201000 f 74 goat snp45492-scaffold620-2395629 9 56410111 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776676 Affx-122935339 AX-385263802 9 55986208 ATTCTATGTTTGGGAGGCAAGATGGTAGAAATAGA[C/T]GCAAAAGACAGTGGGTCTACCAGTGTGACTGGATC Y 2 1 2 1 101000 r 74 goat snp45490-scaffold620-2330696 9 56475892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783424 Affx-122934137 AX-385270487 9 56016189 TGGAGAAACACATTCTCATATACATGCAATTAGGA[C/T]ATTTTTATGCATTCTAATTCATTTTCCAAATCTAT Y 2 1 2 1 201000 r 74 goat snp45489-scaffold620-2300715 9 56506169 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796891 Affx-122943135 AX-385283833 9 56062448 TGGGGAAACGGTGTCATTCATTCCCTTTGAACAGA[C/T]AAAAGATTAGTGATAACTTAGCAGAAAAATTAAGA Y 2 1 2 1 102000 f 74 goat snp45488-scaffold620-2254456 9 56552320 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392788 Affx-122965980 AX-123263145 9 56115423 CATATGTAATAGGGATTGGAATACAAAAGCATATA[C/T]GCCAAGAGTGAGAACTGGCACCTAAACCCTCCTTC Y 2 1 2 1 101000 r 74 goat snp45487-scaffold620-2201481 9 56605145 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787582 Affx-122968716 AX-385274606 9 56148201 AAAAGTACCACTTAGCTTTCATTTCCCATCCTTCA[C/T]ATGTGTTTCCTCTGTGATAGGCAGTAGGGTGGAAG Y 2 1 2 1 101000 f 74 goat snp45486-scaffold620-2168703 9 56637894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799517 Affx-122954503 AX-385286447 9 56185065 TAGAAACATATGTCATAAAATATTGTCTCTGTGAA[C/T]ATAGTGTGAGTTTTCTTAAAAGGAGGTTTCCTTTT Y 2 1 2 1 101000 f 74 goat snp45485-scaffold620-2131839 9 56674616 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382248 Affx-122973952 AX-123252606 9 56229626 AGGAGATTGCGTGGGTGCAGGGATGGCTTCACTGG[A/G]AGGTTAAGGAAACTTACACGGCAGCATCCCTCACT R 2 1 2 1 201000 r 74 goat snp45484-scaffold620-2087278 9 56720930 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436507 Affx-122932951 AX-123306845 9 56266890 CATGTTCAGCCTGCAAACCCTATCTGATAAGAATC[G/T]AAAAATTTTAGTGAAATTGTGCCTTTCTTTTACAG K 2 1 2 1 101000 f 74 goat snp45483-scaffold620-2050014 9 56759155 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439033 Affx-122930342 AX-123309370 9 56298529 TGGTCTTGCAGCTCTGCAGAAGCCTCACAAGCCTA[C/T]TGACACGCAGGCCATCAAAAGGGGTGTCGTGCAGA Y 2 1 2 1 101000 f 74 goat snp45482-scaffold620-2018375 9 56791817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390254 Affx-122967756 AX-123260611 9 56336631 AAATAAGTGAAAGGTGGAGCATTTGGAAGCCACAG[A/G]TAATTTTCAGTGAAATCGCAACCTAAATTAGCATA R 2 1 2 1 101000 f 74 goat snp45481-scaffold620-1980273 9 56829986 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802341 Affx-122934488 AX-385289245 9 56376670 TGGATTAAAACAGTAATAATCCTTTTATTATTAAC[A/G]TTCACAATTACAGTGCTTGCTTGGACAAGGAGTAG R 2 1 2 1 101000 r 74 goat snp45480-scaffold620-1940234 9 56869936 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422150 Affx-122943537 AX-123292497 9 56413147 CAAGAATAGCACTTGCTATTTTCTCATGCCTAAAA[C/T]GTTCTTTGCCAAAATATCCTTGTTTCTTCCCCACT Y 2 1 2 1 202000 r 74 goat snp45479-scaffold620-1903757 9 56906425 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768304 Affx-122932704 AX-385255484 9 56461312 CGATCCACCAAAAGATTGACTTTGTCAATTCTGAC[A/G]TGTTTGGCAAAATGTAGGCGTTTTGGCAAATCAGG R 2 1 2 1 201000 r 74 goat snp45478-scaffold620-1855592 9 56956033 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437197 Affx-122932053 AX-123307535 9 56514799 ACCCTAGGATGATAGAATAAAGCTTTTCTTCCCCT[A/G]TAGCCCTCATGGAATGCATGGAAATGTTTTCCCCC R 2 1 2 1 102000 f 74 goat snp45477-scaffold620-1802105 9 57009734 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439717 Affx-122930555 AX-123310054 9 56566605 CACACCACATCTTGCTACTCTAGGCCCTTTGTACA[C/T]GCTGCCGCTGTCCCTCAGAATCCTTTGCTGTTTGC Y 2 1 2 1 102000 r 74 goat snp45476-scaffold620-1750299 9 57061349 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436072 Affx-122932697 AX-123306411 9 56628562 ACGATCCTGCCAGGTCTTTCCCTAGAAAACCCAGA[C/T]GGAAGCTAAAAATCCTCTTATACCTATAACCACAT Y 2 1 2 1 101000 f 74 goat snp45475-scaffold620-1688342 9 57123391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438801 Affx-122930801 AX-123309138 9 56680806 TGATGTCCTTCAAAGTCTGATCTGTAGGTTGGAAA[C/T]GTGGTAGCCTCACTTTTAACGAACAAATGACCTTT Y 2 1 2 1 101000 f 74 goat snp45474-scaffold620-1636098 9 57176153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445750 Affx-122926082 AX-123316087 9 56736654 ATGAATAAATGTGGTCAGCTTACTAACAGCTTATG[C/T]GCTTGCTAGGTATGGTACCGTTTCACTCCTCTAAC Y 2 1 2 1 101000 r 74 goat snp45473-scaffold620-1580250 9 57232046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772935 Affx-122951873 AX-385260079 9 56788072 CAGTTATGTCCATGAACATAACAACAGACTGGACC[A/G]TGAACGCCTACTGGGTGAAGAGACATCTTAGCATC R 2 1 2 1 101000 f 74 goat snp45472-scaffold620-1528832 9 57284056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425233 Affx-122941005 AX-123295579 9 56821777 GGTAGAGGCTCCCGAGATGCGATGTGATACCAAGA[G/T]CAAAGCTGTCCGTGGCATTAGTACTAGAAAAACTA K 2 1 2 1 101000 r 74 goat snp45471-scaffold620-1495127 9 57318073 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387225 Affx-122970582 AX-123257583 9 56851677 CAGTCTAGTCCTGCATCTAGAACACAAAGTGTACA[C/T]ATCCAACTATACAACTGCTCTTGGATATCCCACGG Y 2 1 2 1 101000 r 74 goat snp45470-scaffold620-1465227 9 57347927 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431267 Affx-122937112 AX-123301608 9 56960711 CAGTTACCTAATGTTCGAGTTGAAGTTTGAATGTG[A/G]TGTGATTTAGTCTCCAAGTCATGTTCGACTCTTGC R 2 1 2 1 101000 f 74 goat snp45468-scaffold620-1356193 9 57457972 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433791 Affx-122934469 AX-123304132 9 57001139 ACATCAAAGCAAGATTCCACAGGCTTCAGCTTGAC[A/G]TCTTTGGAAGAGCATCCAGGTGTTTCAACATTTTC R 2 1 2 1 101000 f 74 goat snp45467-scaffold620-1315765 9 57498373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407781 Affx-122954960 AX-123278132 9 57067294 CTCCCCCTTACAGTAGTGATAGACAAATAAGCATT[A/G]CAGCCTTGTTTGTCTCCAAAAGTTTTAAGTACAGA R 2 1 2 1 101000 f 74 goat snp45466-scaffold620-1249610 9 57564607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772021 Affx-122965861 AX-385259177 9 57121574 AACGACACTATCAGTTTGATGATGACAGGCACTTT[A/G]TCTTGTAGTCTATACTGTACAGGCACGTGTTTTCA R 2 1 2 1 101000 f 74 goat snp45465-scaffold620-1195330 9 57618259 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380525 Affx-122975685 AX-123250883 9 57158170 AGGTGTGCTCCTCTACTCTCCCTTTCACCCACCCC[A/G]CTCCATGTATGTTCACATGTGTGTTTCTGTTTGCC R 2 1 2 1 101000 r 74 goat snp45464-scaffold620-1158734 9 57654776 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788761 Affx-122921722 AX-385275775 9 57190495 TAAACCTGAGTGATTTTATATGTTAATTTAGCACT[A/G]TTGCCAGCTACAAATTTCAAGTAGTATATATGTAA R 2 1 2 1 101000 f 74 goat snp45463-scaffold620-1126409 9 57687211 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413201 Affx-122950320 AX-123283550 9 57225192 TAATTGAATGCCTTTTCTCTGCCAGGAATTATTTT[A/G]TATGTTGGAGAAAGAAAGATAGATAGTATGTGGAC R 2 1 2 1 101000 r 74 goat snp45462-scaffold620-1091712 9 57721887 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384653 Affx-122972146 AX-123255011 9 57254785 CCAATAAAATGACCATTTCACACTTCCATGTTTCC[A/G]TCTTCTGCCACATAATCGAGAAATCGTTTATTTAA R 2 1 2 1 101000 f 74 goat snp45461-scaffold620-1062119 9 57751731 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424004 Affx-122942104 AX-123294350 9 57287135 CTGCTTGTTTAACTTATATGAAGAATACATCCTGC[G/T]AAATGCTAGGCTGGGTAAAGACTGGAGCTGGAAAT K 2 1 2 1 101000 r 74 goat snp45460-scaffold620-1029769 9 57785195 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419830 Affx-122945820 AX-123290178 9 57352961 GAAGGGGAATGTTGCCCAGTCTGCCCCTTGCTGTT[G/T]AGTCACTAAGTCTTGTCTTTTCTTTTGTGACCCCG K 2 1 2 1 303000 f 74 goat snp45459-scaffold620-963943 9 57851188 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450227 Affx-122922272 AX-123320562 9 57384545 AACATTTATTAGCCATCTACTATGTGCCAAGTGCT[G/T]CTCTGAGTGCTTGTGGTTCCAAGATGAATAAAACA K 2 1 2 1 101000 r 74 goat snp45458-scaffold620-932359 9 57882751 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774016 Affx-122947802 AX-385261154 9 57440256 CTAGTTTTGGAACTATGAATAATATTTTCTAGGTA[C/T]ACTGTTAATCAGAAATAAACTTGGGTGTTGCTTCT Y 2 1 2 1 101000 f 74 goat snp45457-scaffold620-876648 9 57938931 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394551 Affx-122964462 AX-123264906 9 57475623 TTATTTGACCCTCACACAGCCCTGTAAGAAGGGGT[C/T]ATTTGTCATGTAAGATCTGTTCACATCTATGTCTG Y 2 1 2 1 201000 r 74 goat snp45456-scaffold620-841281 9 57974298 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781394 Affx-122957265 AX-385268479 9 57506470 CAACAACTAGAGGAAAATGTTGCCAGCATTAGGCC[A/G]CATGTGCTGAACATCATGTAAGTATAGGTCAATGT R 2 1 2 1 101000 f 74 goat snp45455-scaffold620-810434 9 58007699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782414 Affx-122928281 AX-385269490 9 57536907 GACAAGGATGTGCATTACGTACCACTGCCATCTGG[G/T]AGTAAGGAAGTTGCAAAATTTAATTACATGCATGC K 2 1 2 1 101000 f 74 goat snp45454-scaffold620-779997 9 58037907 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799852 Affx-122925177 AX-385286778 9 57567651 AGCACCACCACCACCTGTAGCAAATTTAGGAGCCA[C/T]GATAGGGTAGTCTATAAACAATCATAGGAACCATT Y 2 1 2 1 101000 f 74 goat snp45453-scaffold620-749253 9 58068763 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797640 Affx-122964683 AX-385284579 9 57610801 GTAAATCATCTTAGTGACGTAGACTATCTTAGTGA[C/T]GGTACTTTAATTTGATGGTTCACAACTACTAAGTG Y 2 1 2 1 101000 f 74 goat snp45452-scaffold620-706103 9 58112105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782214 Affx-122966545 AX-385269292 9 57656145 AGTTAGGCTTGTTTTTATCTGGAAGTCTTCCTTAT[A/G]CCCTTGTTGGCACAGGTTGTGTTATCTTGGATATT R 2 1 2 1 201000 r 74 goat snp45451-scaffold620-660759 9 58157369 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434008 Affx-122934234 AX-123304349 9 57691869 GGTGACGATGGTGACAATGACAATGACAATGATGA[C/T]GTTACTGAGATCTCTCATTCATTAAAGGAGGAGAG Y 2 1 2 1 201000 r 74 goat snp45450-scaffold620-625035 9 58193065 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412293 Affx-122950872 AX-123282642 9 57737851 GCCACGTTTCTCAGCCTTGGCCAAGGAATAAAACA[C/T]TGGTTCACCTCAAAGGCTACCATTAAATTTACCTC Y 2 1 2 1 101000 r 74 goat snp45449-scaffold620-579053 9 58228631 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454309 Affx-122919253 AX-123324642 9 57776632 GTTGCTTTTGCAAAGGTTTCATAGTAATAGTAAAT[C/T]TAGGGGGAAAGTGTTTACCAAAAGACCTTGTTCCA Y 2 1 2 1 201000 f 74 goat snp45448-scaffold620-540272 9 58268170 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444459 Affx-122926544 AX-123314796 9 57816898 TGTCAAGTTTTCATTCAATCAGCTTTGTCTATACC[A/G]TTGCTAACTGCTTAATATGGCCACTCCCATTAAGC R 2 1 2 1 101000 f 74 goat snp45447-scaffold620-500006 9 58307506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786690 Affx-122952249 AX-385273722 9 57846265 CACATGACCTTGCAAGGGCTCAATGTTATTGGACC[A/G]CTCCTTTATTGTAATGCTAATTTCCCTCTACTTTC R 2 1 2 1 101000 f 74 goat snp45446-scaffold620-470639 9 58336587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801631 Affx-122920644 AX-385288539 9 57892648 ATAATACCATTTACTGTTTATCCAGAACTCATTGT[A/G]TACCAAACAACATGGCAAGTGTCTTATATACAGTT R 2 1 2 1 101000 r 74 goat snp45445-scaffold620-424256 9 58383883 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393776 Affx-122965197 AX-123264131 9 57953316 GTTTTTAGGACAGAAAGATAAGAGACGAGAAATAG[C/T]AAAAATAGGTTAAAAAGTATGTAAGCTAGAGTAAG Y 2 1 2 1 101000 f 74 goat snp45444-scaffold620-363588 9 58452986 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769820 Affx-122940758 AX-385256990 9 58011263 GGCTGCCTAAGTACTAGGAAATATAAAGGGAAGGA[C/T]ATAGGGTTAGAGAAAGGAGTTACATGTTGATTCTA Y 2 1 2 1 101000 f 74 goat snp45443-scaffold620-305641 9 58511083 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406578 Affx-122956270 AX-123276930 9 58050013 CCCTCCAAATTTCATTAATGGGTCTCTGAAGCTAG[A/G]TCAGGCACTGGCTCGTTCCAGCTGCTCAGGAAGCA R 2 1 2 1 101000 f 74 goat snp45442-scaffold620-266891 9 58549665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769954 Affx-122939137 AX-385257123 9 58086327 GAAAGTCTTCTACCACTGTTGACTTACAATTTAAA[C/T]AGAAACCTTGTAGAGCTTTTACTATTATTGATACA Y 2 1 2 1 202000 f 74 goat snp45441-scaffold620-230577 9 58584491 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428418 Affx-122938834 AX-123298761 9 58116214 GAAGGCAAATTATATTAGTGGGTTGGGAAGAAAAA[C/T]AGTGCTTTACTAGCATCTGGGAGAATTAATTCATT Y 2 1 2 1 101000 f 74 goat snp45440-scaffold620-200690 9 58614562 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768649 Affx-122923622 AX-385255827 9 58167425 GATATTTCAAGCTGTGACATATGGAACTTCACTAA[C/T]GGTATTAAACTTGTTGATTAAGCTATGAATGATTG Y 2 1 2 1 101000 f 74 goat snp45439-scaffold620-149479 9 58667107 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786599 Affx-122943967 AX-385273631 9 58198137 TTAAAGTGGATACAGCTCTACTCACCAGGATCTCT[A/G]TAAAATACTCCCCACATTTTACAGCAGCAGCATGC R 2 1 2 1 202000 r 74 goat snp45438-scaffold620-118767 9 58697817 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273435 Affx-1111833617 AX-519547060 9 58221150 TCACATACAGAAAGCTCTATATGAGCAATTGTTTA[A/G]AAACAACAAAAAAACTCAGTGTTTCATGGGGATTT R 2 1 2 1 101000 f 74 goat 9_58221150_AF-PAKI 9 58221150 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38384836 Affx-122971969 AX-123255194 9 58253302 AGCACAGTGTTTAAGGGCAGTGTTATGGATATTGG[C/T]AGCAGAGGAGAGAAGGGTTAACTTTGCTGGGTTTT Y 2 1 2 1 101000 f 74 goat snp45437-scaffold620-63602 9 58753125 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397259 Affx-122962354 AX-123267614 9 58288809 GAACTATGACAGCCAGCAGCAATCCTATTTACAAA[C/T]GTATTTTGAACTCTCACAGACTAGACTTTTTTGAG Y 2 1 2 1 101000 f 74 goat snp45436-scaffold620-28095 9 58788757 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405619 Affx-122956603 AX-123275971 9 58460274 GGTATTTGCCCTACTTTTCATCCTTACTGCCTACC[A/G]AACCAGAGGTGCTCTGGAAAAACTCCTAGGATCGT R 2 1 2 1 201000 f 74 goat snp3577-scaffold1110-1010972 9 58960266 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440138 Affx-122929688 AX-123310475 9 58503785 AGCTCATCTACAAGAATATGGTTTCTTTCTTTCGC[A/G]TGTACAATCTAGACAAAATGGGACAAACCCCATCT R 2 1 2 1 201000 r 74 goat snp3576-scaffold1110-967461 9 59004319 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405470 Affx-122956029 AX-123275822 9 58547070 GGCACCCACGTTACCTTGGTTTCTGGGCTGAACAA[C/T]TGGGGTGAATTATGATGTCTTTTTCTGAGCTAGAA Y 2 1 2 1 201000 f 74 goat snp3575-scaffold1110-924176 9 59047836 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406542 Affx-122955118 AX-123276894 9 58605318 TGTGATTTGGGTTTGTGACAGGACTGAGATGGCGA[C/T]ACAGCACAAGTTTTTGCTTTGGTCTGCTTGTTTTG Y 2 1 2 1 101000 f 74 goat snp3574-scaffold1110-865928 9 59106271 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410879 Affx-122952598 AX-123281229 9 58647481 CAACCACAATGACAACAATAAGAACAACAGACCTC[A/G]GACTTTGTCTTGGTTTCCTTTTCTGAGGAATCATT R 2 1 2 1 101000 r 74 goat snp3573-scaffold1110-823765 9 59148906 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399230 Affx-122960589 AX-123269585 9 58701014 CAACGGACCCTTTTAGCATCTTTGCACGATTTCTC[A/G]TCCCCTGGGTGAGGGCTCCACAAAGATGGGGAATC R 2 1 2 1 101000 f 74 goat snp3572-scaffold1110-770232 9 59202647 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389758 Affx-122968242 AX-123260115 9 58730881 AATCTTACAGAATGTGTATCTTTTCAAAACAATGA[C/T]AGGAATATTTCTAAAAACAAACAAAAATGAGCCCT Y 2 1 2 1 101000 f 74 goat snp3571-scaffold1110-740365 9 59232526 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272439 Affx-1111834262 AX-519546165 9 58764614 ACTGGGTACCAAGTCCCACTCTCTGGAAAAAAGCA[A/C]TTCTGGCCATCTTAAACCAACACATTTCAGATAAG M 2 1 2 1 101000 r 74 goat GoatD01.028077 9 58764614 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443060 Affx-122928135 AX-123313397 9 58768148 GACAAATAAAGAAGGATCAGGGATAAGATCAATGG[C/T]CTTAAGGGGGTCACTCAAGGTTTAGGAGGAGTTTT Y 2 1 2 1 101000 f 74 goat snp3570-scaffold1110-703098 9 59269731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434494 Affx-122934618 AX-123304835 9 58802250 ATTTAAATTGAATGGAATTGGGGCTCCCAAATTCA[G/T]CTTTTTCTCATGAAGAGCCTTCCCAAGTGGATGAG K 2 1 2 1 101000 r 74 goat snp3569-scaffold1110-668996 9 59304246 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419066 Affx-122945806 AX-123289414 9 58840652 GATAGTAAGAATTGTTTCCAGTGTTTCAGCAAGGG[C/T]GAATGAGGTTGATGACAGGTGTGGTCATTGCTAAG Y 2 1 2 1 101000 r 74 goat snp3568-scaffold1110-630594 9 59342507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441575 Affx-122928680 AX-123311912 9 58878591 TGTCCAGTCATCCAGCCGTCATGGACTTTACTCTA[C/T]GTGGCATCAAGAAATTGCAGGCTGCTAATGTCAGT Y 2 1 2 1 101000 f 74 goat snp3567-scaffold1110-592655 9 59380373 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379353 Affx-122976161 AX-123249712 9 58920305 CAGGACTGAAGGGTTTGCCAGCATTTGAGCCTTTC[A/C]GTGCTACAAGCAGCATAGTCCTGGCTGAACCAGGA M 2 1 2 1 101000 f 74 goat snp3566-scaffold1110-550941 9 59422067 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431271 Affx-122937108 AX-123301612 9 58966259 AGCAAAGTAGTGTTAAGATGTATAAAGGAATAAAT[A/G]TAGTTACGGCCCAAAAATAATCAAACAATTCCTGT R 2 1 2 1 101000 f 74 goat snp3565-scaffold1110-504987 9 59468044 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437241 Affx-122932021 AX-123307579 9 59018228 GATTCTTAGCCATTAGACCACCAGAGAAGACCCAG[C/T]GTGACGAATCTTTGATGTAAACACTCCTATCCTGA Y 2 1 2 1 101000 r 74 goat snp3564-scaffold1110-453018 9 59520112 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792008 Affx-122939186 AX-385278996 9 59047008 AGGTAATTACTGTCCTTAAAACCCAAACCAACCTC[A/G]TCCTAGCCTGCTCTCACTCTCATGAAAGTTATTAA R 2 1 2 1 101000 f 74 goat snp3563-scaffold1110-424238 9 59548815 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376831 Affx-122977917 AX-123247190 9 59125437 GCCTCCCCTAGACGCTTAGTAAAAGTAGAACCATA[C/T]GATATCTGTCCATTAATTTCTGGCTTATTTCACTT Y 2 1 2 1 101000 f 74 goat snp3561-scaffold1110-345809 9 59626575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394579 Affx-122964440 AX-123264934 9 59175431 ATAGAAATGAACAAAGGGCATGAACAAAAAGTTCA[C/T]AAAAAAATAAATTCAAATGTCTCTGAAAGTTATGA Y 2 1 2 1 103000 f 74 goat snp3560-scaffold1110-295815 9 59676573 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380123 Affx-122975998 AX-123250481 9 59261812 CTTAGAGCTAGGCAAAGAAACAAAGAAATGAATGA[C/T]GCTTAATTGGGGTTCTTGAGGAACTCACAATGTAC Y 2 1 2 1 102000 r 74 goat snp3558-scaffold1110-209434 NW_017193950.1 9515 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792332 Affx-122940819 AX-385279314 9 59301374 GAACTGTTTTCTAGTGAGACTCCTTCCCTTTGTCA[C/T]GTAAAAGTAAACTCCAGTTGCAGTGCCCGAGTAGG Y 2 1 2 1 101000 r 74 goat snp3557-scaffold1110-169872 9 59803199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787879 Affx-122929320 AX-385274901 9 59365070 TAAAATATCACCATGGAAGTGAAGTGAGTCACTAG[C/T]ATTTTGTACCTAAGGGATGTATAGTTAAGTAATAT Y 2 1 2 1 101000 f 74 goat snp3556-scaffold1110-106176 9 59866496 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797417 Affx-122959473 AX-385284356 9 59402575 TCACAATAATAATGCAACTATTGTCATTTTCATGC[A/G]TTTCCTCCACTTTTCACATGTGTATACATAGGTTA R 2 1 2 1 101000 r 74 goat snp3555-scaffold1110-68671 9 59904173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426320 Affx-122940282 AX-123296666 9 59461721 TAAGAAATTCATTCAGTGAAGAAAGATTTATGGAG[C/T]ACTTTTATGAGTCAGATGCTGTGGTCAGCGCTGTG Y 2 1 2 1 101000 r 74 goat snp3554-scaffold1110-9525 9 59963073 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418369 Affx-122946575 AX-123288717 9 59478646 TAACACCATAATTTAATCATTTGCTCTCTAGTTTG[A/C]GACAAACCAGTTCCATCCTGCAACAAAAAATGGGA M 2 1 2 1 101000 r 74 goat snp43511-scaffold579-6340779 9 59981447 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398259 Affx-122962184 AX-123268614 9 59516256 TAACAAAGTTCACATCCCCAGGTCCTAGGATGCTA[C/T]ATATCCTTCACTGAAGCAGTTCAGTTCAGTTCAGT Y 2 1 2 1 103000 f 74 goat snp43510-scaffold579-6303169 9 60019929 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413214 Affx-122950258 AX-123283563 9 59563873 CCCATTTTTCTCAAGAGGAAACCGAGGCCTAGAGC[A/G]TTTGAATCCCTCAGCTGGTAAGGACCTGAGATCGG R 2 1 2 1 101000 r 74 goat snp43509-scaffold579-6255552 9 60067798 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404713 Affx-122957254 AX-123275065 9 59595830 TCATTCAATTGTGATGGAGTGATCCTTTTATTTAC[A/G]TTATGTTTATATGAATTGTTGTTGAGGGGGTGGTG R 2 1 2 1 201000 f 74 goat snp43508-scaffold579-6223595 9 60099796 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788960 Affx-122934106 AX-385275973 9 59632367 TACTGTTCCTTGATCACTAAGACTTTGGCAGCTCA[C/T]TTGCAGTTTTCTCTTATGCCCTGAGCTCTTCCTGA Y 2 1 2 1 101000 f 74 goat snp43507-scaffold579-6187058 9 60136514 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431600 Affx-122936167 AX-123301941 9 59672480 GGGCAGGGTTTTTATAGAGAAGACATGAAGCAAAA[C/T]GAGGAAATTATTTGATTGGCTTACTGCTTAAAACA Y 2 1 2 1 101000 f 74 goat snp43506-scaffold579-6146945 9 60176512 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769269 Affx-122933619 AX-385256442 9 59747702 GCTCCTTTAGGATTGGATTCCTAGGATTTAATATG[A/G]TTTTTTGTGCATTCTCACATAGCTAGAGTGCCCAT R 2 1 2 1 101000 r 74 goat snp43504-scaffold579-6071723 9 60252782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770349 Affx-122929298 AX-385257515 9 59782924 TAAAGGATTCCTTACAGAAAGTAATATTTAACTGC[A/G]TATAGGTAACTCTAGACTTTTGATGCATAGCTAAG R 2 1 2 1 101000 f 74 goat snp43503-scaffold579-6036501 9 60287512 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789324 Affx-122947083 AX-385276334 9 59821774 TGTTTAGAGTTTTGAAGTTTACAGAGTGCTCTGAT[A/G]TATTTTATTTGGTACTAACACTGGCCCTGAAAAGT R 2 1 2 1 101000 f 74 goat snp43502-scaffold579-5997651 9 60326316 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792764 Affx-122949536 AX-385279743 9 59869861 CTGTATGGGGCTACTGGAGATATTTTGCTTTCATA[C/T]ATCTGCAAGCAAGTGCAGAGAGTCAGAAGCATCTG Y 2 1 2 1 101000 f 74 goat snp43501-scaffold579-5949564 9 60374419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435435 Affx-122933481 AX-123305775 9 59955958 GGTTTTTCAAAAGAAAGAAGAATCAAATATAGTGA[C/T]TACTGTAACATAACAGAGAAAGAGGGTTCTCATAG Y 2 1 2 1 103000 r 74 goat snp43500-scaffold579-5863467 9 60461621 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405956 Affx-122955546 AX-123276308 9 59994141 ACATCTCTAGAAGCATAAAATTTCTTTATTATCTT[C/T]CTAGGGTATATTAATGTCTGGAAAATCAGGAAAAA Y 2 1 2 1 101000 r 74 goat snp43499-scaffold579-5825284 9 60499806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431776 Affx-122936710 AX-123302117 9 60036423 CTGTCTGAATGCCCAAAGAGTAAAGTGTTCTGCAC[A/G]TATTTGGCAAGGCTTTATGGAGAACATCCTCTGCT R 2 1 2 1 101000 f 74 goat snp43498-scaffold579-5783002 9 60542564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800802 Affx-122939896 AX-385287718 9 60066191 TAAGTACTGTATTTCATGTTACATGAGTTCATTGA[C/T]AGTTTCACGATGGTAAAAATGTTTATGCAGTGACA Y 2 1 2 1 101000 r 74 goat snp43497-scaffold579-5753234 9 60572281 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408747 Affx-122953402 AX-123279098 9 60103561 ACAACATGCATTTGAATAGAAATCTGATTAATGCC[A/G]TGACAGACAGTTTAAGACAACACTGAAATTATGAG R 2 1 2 1 101000 f 74 goat snp43496-scaffold579-5715864 9 60609036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427457 Affx-122940030 AX-123297800 9 60183256 AGCTAAATCTTCTTCAAAGATCACAAATCCGACAT[C/T]CTTCACCGTAAGCTATCACTAGTAGCAACCTCTCC Y 2 1 2 1 201000 r 74 goat snp43494-scaffold579-5636169 9 60688671 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782177 Affx-122978984 AX-385269255 9 60217935 TGTCAGGAAAGCACATGGCATTACACCTATCAGGT[A/G]CTCATCACTGAGCTTGAATGGGACCCTACTCTGAA R 2 1 2 1 201000 r 74 goat snp43493-scaffold579-5601490 9 60723427 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410021 Affx-122953255 AX-123280371 9 60265747 TCCCCAGTGATTCCCTCTGCCCACTCTCCAGGATA[C/T]GCCTCATTCTCCATGTCTCATCCATTTAACTGTAA Y 2 1 2 1 101000 r 74 goat snp43492-scaffold579-5553678 9 60771997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780532 Affx-122932367 AX-385267623 9 60295239 TGACCCTATCATTTCATATGTCACTCTCAATACAT[A/G]CTTTTTCTATATCTATGGACACTGTATTCTACTAA R 2 1 2 1 101000 r 74 goat snp43491-scaffold579-5524186 9 60801682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790413 Affx-122947076 AX-385277416 9 60333387 AATACTAAAAAGCACATATGATTCCATGTAAGTAA[C/T]AAAATCATGTTTCCAGCATTCTGCTGAACAATTGG Y 2 1 2 1 101000 r 74 goat snp43490-scaffold579-5486038 9 60840442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447131 Affx-122924460 AX-123317467 9 60376994 AGCACTTACTATACGATGAACCTCACAGAAATATA[A/C]TCACGTACAGTAAAATAACAAACATGAAATGAAAT M 2 1 2 1 101000 f 74 goat snp43489-scaffold579-5442431 9 60884163 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402448 Affx-122958616 AX-123272801 9 60417045 TGGTCCAGCTCCCACCAACCCCCAGGACATCTTAG[C/T]GATGCCAACTGCTCTTCCCTTACCCCCACAAGTTT Y 2 1 2 1 101000 r 74 goat snp43488-scaffold579-5402380 9 60924886 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412031 Affx-122951731 AX-123282381 9 60445876 AAGGGCTTTGAAGTAAAGGAAAATAAGGGCACAGA[A/G]GGCCATCTGTGTGTGTGCGCATATGCACAAGTGTG R 2 1 2 1 101000 f 74 goat snp43487-scaffold579-5373549 9 60953907 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415563 Affx-122948643 AX-123285912 9 60476870 TCTTCCTCCAGAAGTCTGGAAGCTGCTGTGATTAA[C/T]TGCCCTTGGCATGTTGGAAATGTCAGAGAATAGTA Y 2 1 2 1 201000 r 74 goat snp43486-scaffold579-5342555 9 60984809 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453372 Affx-122919935 AX-123323705 9 60523487 CTAAGAGACTTTCAAAACAAGGAGGCTTGCAGTAG[C/T]ACAAGTGGAAAGATTGGCTTGGATTGCTATCCTCT Y 2 1 2 1 101000 r 74 goat snp43485-scaffold579-5295938 9 61030572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788870 Affx-122934413 AX-385275885 9 60577323 TTATCTTTTTATCTGTGAGACCTCTTTGCTCTTAA[C/T]GAGCCAAGAAAGATCCTAAAATACAGTTAAGTACC Y 2 1 2 1 101000 r 74 goat snp43484-scaffold579-5242102 9 61084856 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395210 Affx-122964493 AX-123265565 9 60606238 ACACACCACAATCACAGACACCATGCCCATATACG[C/T]AGTATTTGAGTCTAATAGTAACCGTACAGAGAATT Y 2 1 2 1 201000 r 74 goat snp43483-scaffold579-5213187 9 61114529 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429878 Affx-122938134 AX-123300219 9 60648915 CACAGTTCAGTGTACTTCATCTTAACTATTTCTCA[G/T]GAAAACGTATGCATGCATTTATCTTTCCACAAATC K 2 1 2 1 101000 f 74 goat snp43482-scaffold579-5170510 9 61157196 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411297 Affx-122952294 AX-123281647 9 60692088 TTGAACTTCAAGTCTTGTGGGTACTGGTGTGCTGG[C/T]GATGGAATGGATCACTCCACAGAATTGCTACTGAT Y 2 1 2 1 101000 f 74 goat snp43481-scaffold579-5127337 9 61200400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410761 Affx-122952687 AX-123281111 9 60723172 GTGTTCAATGAATCTGGCAGACTTTGGTCCATTGT[C/T]GTCTGAGACAGGAGCTAGCCATCATGTAAAAGGTG Y 2 1 2 1 101000 r 74 goat snp43480-scaffold579-5096253 9 61231341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772938 Affx-122951558 AX-385260082 9 60758844 CACGGTTAATTCCATGTACTGGTTCCCATCTCTCA[A/G]TTGACTTGAGCAAAGTGAGACACAAGATTATGAGA R 2 1 2 1 101000 f 74 goat snp43479-scaffold579-5060581 9 61267002 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397980 Affx-122961808 AX-123268335 9 60789630 TACTATGAAGAAAATGACACAATAAATACCATTAC[A/G]TACCTCCAATTATACATTTGTAAAGTTTCTCTAGG R 2 1 2 1 101000 r 74 goat snp43478-scaffold579-5029795 9 61297537 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426990 Affx-122940384 AX-123297335 9 60834280 TCAGCCTTTGACTAGGTCTCTGTCTGGTCCTCCCC[A/G]CTAAGGACCTTGAGTTCCCTGCTTCACGGTCAGGC R 2 1 2 1 201000 r 74 goat snp43477-scaffold579-4985145 9 61342242 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274310 Affx-1111834179 AX-519547906 9 60857279 GTGCCTGCCCATGATGTTACATAATAAAACATGTC[A/G]CTGCAGCACCAATGGACACATGTCCCAGAAATTCC R 2 1 2 1 101000 f 74 goat GoatD01.023772 9 60857279 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320779248 Affx-122935798 AX-385266352 9 60866062 TTCTGATTTGGTATTGAAGAGGATTATTCTGCAGA[A/G]TAACTTGATAACGTTAAAAAGATGTGTACCTGACG R 2 1 2 1 201000 f 74 goat snp43476-scaffold579-4953363 9 61374496 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273437 Affx-1111833618 AX-519547062 9 60899899 ACTGGCACCCCTTCTTAGGCAGATGGTGACTGTCC[A/G]GAACCCCAGGAAGTCTTAGTTAGCAAAGAAGCTTG R 2 1 2 1 303000 f 74 goat 9_60899899_AF-PAKI 9 60899899 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378236 Affx-122976908 AX-123248595 9 60969605 ATGCCCTAATTATATTTGTTTGGAAAACAGCCTTA[A/G]TGGTTGCCTGTTAACCCCACTGTATTTTTAACAGG R 2 1 2 1 101000 r 74 goat snp43474-scaffold579-4849820 9 61479257 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446559 Affx-122924842 AX-123316895 9 61018639 ATAAGCGTTGGCCTTATTTATAGTGTTTATTGATA[C/T]ATCTTGATAGCACTATATACAACCTGGTTTCTGAG Y 2 1 2 1 101000 r 74 goat snp43473-scaffold579-4800786 9 61528653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785369 Affx-122942577 AX-385272414 9 61051150 TCGAGTGAATTTAGTGGGAACCGCATCCCAGGGTT[A/C]CTCCATATCCTTGGATTCAGCCAACCCCGGGCCAT M 2 1 2 1 202000 r 74 goat snp43472-scaffold579-4768275 9 61560947 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413481 Affx-122950656 AX-123283830 9 61079663 GTAGCCTTGGTTTTTAAAAAAAATTTCACCCCCAC[A/G]TAGTGTCAGAACTGCTGAAAAGCTGAAAAGTTGTA R 2 1 2 1 201000 r 74 goat snp43471-scaffold579-4739762 9 61589634 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794478 Affx-122940320 AX-385281441 9 61113302 AATAATTGTCACTGGTTCTTAAAGGTCTTACTAAC[A/G]CAGGGATTCTGAGAGATGTTGATGGTATTAGAATC R 2 1 2 1 101000 r 74 goat snp43470-scaffold579-4706123 9 61623309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388051 Affx-122969537 AX-123258409 9 61143561 CAGTCACCCGACAGTCCACTCTGTTAACAGACTCT[A/G]CATGGGGTCTGGAATAGAGAATCTGTACAGGGCCT R 2 1 2 1 201000 f 74 goat snp43469-scaffold579-4675864 9 61653594 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385506 Affx-122971264 AX-123255864 9 61174623 AATGTATTTTCATTGTATTAAATATTTCTAGATAC[A/G]TCTTCACATTTAAGCCTGCCCCTTTATGACAGACT R 2 1 2 1 101000 r 74 goat snp43468-scaffold579-4644802 9 61684744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433686 Affx-122934548 AX-123304027 9 61211303 CAAACAGCCATGCTGTTCCAGCCTCTGGACTTGGC[A/G]TGCAGATGCCCAACTCCACATGCTTTTTCTGCTTT R 2 1 2 1 101000 r 74 goat snp43467-scaffold579-4608122 9 61721415 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434808 Affx-122934809 AX-123305149 9 61263601 CATGTTGTAGCTTGTGTCCGAATCTTCATTCTAAA[C/T]GCTGAATAATATTCCATTTTATGTACATTGTCTTT Y 2 1 2 1 103000 f 74 goat snp43466-scaffold579-4555824 9 61773866 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381670 Affx-122974738 AX-123252028 9 61296964 CTTGAATAATAAGGTCCAGTTAAGACTCGCTGAAA[G/T]AAGCAATGATGACAAAGAAGAGGAAGTTGATTATA K 2 1 2 1 101000 f 74 goat snp43465-scaffold579-4522461 9 61807552 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438645 Affx-122930902 AX-123308982 9 61328792 GCAAGGGGCTATGAGTTCAGAAACTGCCTGATTCT[A/G]CTCCATCCCATTTTTATAGTTTCCTCTATTATTTT R 2 1 2 1 201000 r 74 goat snp43464-scaffold579-4490633 9 61839811 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400485 Affx-122961292 AX-123270840 9 61366988 CTTTCATTGTTTTTATATATTGGCTTTTATCTTTG[A/G]CTGGAGATGTTGACTTAAGGAACTCATCAAAATAT R 2 1 2 1 101000 r 74 goat snp43463-scaffold579-4452437 9 61878295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802198 Affx-122958490 AX-385289102 9 61404316 TACGTGGAATGTCAATGAGGAAGTCCAGGTCAACT[A/G]TAATTCCCATCATGACTAAGTGGCATAAAGACTCA R 2 1 2 1 101000 f 74 goat snp43462-scaffold579-4415109 9 61915711 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276310 Affx-1111835354 AX-519549843 9 61407352 CCACAGATCATGCCAGCTGGCTATTTAATCTAGCT[A/G]TTAAAGAGCAGAGAGGAAAGGCCACCTAAAGTGAG R 2 1 2 1 101000 f 74 goat Random2.2K-1006 9 61407352 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320783867 Affx-122919796 AX-385270923 9 61435819 AGCTTTCCTACTGGAAATAGTATCTATTTTCTGGT[A/C]CTTATTTAATCTGAACCCAGAAGTCATTCTTAAAA M 2 1 2 1 101000 f 74 goat snp43461-scaffold579-4383606 9 61947372 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452253 Affx-122920774 AX-123322586 9 61468024 CCCACAGTGGATCATTGAGGAAGCGAAGATCTGAA[C/T]GAAAAAGCCAGTGAGAAAATTAGGAACCTAATGGA Y 2 1 2 1 101000 f 74 goat snp43460-scaffold579-4351401 9 61979720 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429517 Affx-122937849 AX-123299859 9 61507388 AATCCAATACTCAGGTTTTAAATGAAAAAAGAATC[A/G]TATACGTGGAGCAGGAATTTATAGAACACTCGCTG R 2 1 2 1 101000 r 74 goat snp43459-scaffold579-4312037 9 62019292 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434875 Affx-122934354 AX-123305216 9 61544695 AACCATTGCTTGCAGCTCTTAGTTACAAGGCTACT[A/G]TCAGTCTTCCCAGGCTGTTGGTTTTAAGAGCTGTA R 2 1 2 1 101000 f 74 goat snp43458-scaffold579-4274730 9 62055583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793041 Affx-122936707 AX-385280019 9 61594974 CTTCTGTCTTCATCTTATTTGATTAGACAGCTTGA[G/T]ATCACACTCTCAACCTCATTTGCCTCAAAATCCCA K 2 1 2 1 101000 r 74 goat snp43457-scaffold579-4224451 9 62106448 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773463 Affx-122919254 AX-385260605 9 61650817 ACCCAGCAAGTCCTCAAAGGTGAGTAGTGGCCAAA[C/T]GAGGAATGTACGCATGTCTGTGGATAATAAAGACT Y 2 1 2 1 101000 f 74 goat snp43456-scaffold579-4168608 9 62162794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801908 Affx-122973361 AX-385288813 9 61687558 GTTGCTGCTTTACTCCTCTTTCTTGTATTTGCTGC[A/G]GTAGTTGTATGCTGCATCATTAAGAAGTTGTATCC R 2 1 2 1 101000 f 74 goat snp43455-scaffold579-4131867 9 62199424 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448461 Affx-122923635 AX-123318797 9 61728005 ATCCTTTCAGCACAGCGCATGCTTTCTTCTTCTTA[C/T]AATCCAGATAATAGAAACCAGACCAAGCTACTTGA Y 2 1 2 1 201000 r 74 goat snp43454-scaffold579-4091420 9 62239997 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412437 Affx-122951417 AX-123282786 9 61774619 TGTAATGGTTCACAAGCTATGACCAGCCTAGGTAG[C/T]GTACTAAAAAGCAGAGACATTACTTTATGAACAAA Y 2 1 2 1 101000 f 74 goat snp43453-scaffold579-4044806 9 62287074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392061 Affx-122966389 AX-123262418 9 61819899 AAGCTACTTGGTAGGAATTTTCATTTCTATGTCTA[C/T]AACCAAAACCTGGAGAAGTATTTTCAGAAGCCCTT Y 2 1 2 1 101000 r 74 goat snp43452-scaffold579-3999526 NW_017204013.1 22067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445684 Affx-122926129 AX-123316021 9 61867945 GGACTGACCCAAGCTTTTGCACTGGGTAATAAACA[C/T]TGAACTGGTCATGCCTGGAGATAGGCAACCCCCCC Y 2 1 2 1 101000 f 74 goat snp43451-scaffold579-3951480 9 62376967 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276312 Affx-1111835355 AX-519549845 9 61884661 ATTTTACAATGCAGGTGCGTGCGACTTCACAATGC[A/T]GGGCCCCAGGCTCCGCGGTCGGGGGCCACCGCAGG W 4 1 2 1 102000 f 74 goat Random2.2K-1007 9 61884661 A T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449308 Affx-122923004 AX-123319643 9 61908621 CCTCTGATGCAGGTCATAAATCCTCATGCAAGAAG[C/T]GTCCTCTCTGTACCCAGAAGAAAGGAGCGTTTTTA Y 2 1 2 1 201000 f 74 goat snp43450-scaffold579-3910804 9 62417991 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387837 Affx-122969660 AX-123258195 9 61954935 CCTAAATGTAGCTCTTTTTCCTTCTGTGACATTTC[C/T]CACATTTAATCCCTCCGAAGCACTATCCTGGGTAA Y 2 1 2 1 202000 r 74 goat snp43449-scaffold579-3864490 9 62465603 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771144 Affx-122928272 AX-385258304 9 61985430 CCCGAGATAAAAGAAAAACAGTACTTGAAACTTCA[G/T]TTGTCTGGGTAATTGCTTCAATTTTATTATATATC K 2 1 2 1 101000 f 74 goat snp43448-scaffold579-3833995 9 62498199 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783723 Affx-122959386 AX-385270779 9 62022635 AGTGATATCTAAGATTTATATTTTATATCCTTCCC[A/G]CAATTAGGTATCATCAGATCTTTTTTTATCTTTCG R 2 1 2 1 101000 f 74 goat snp43447-scaffold579-3796790 9 62535963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770891 Affx-122957398 AX-385258054 9 62054796 GAAAGCTCTCTACTCACCTTGGGTATTAGCTGGAC[A/G]TCAGAAAGGCCAGGTCTTTCCAGTCAGGCATTTCC R 2 1 2 1 101000 r 74 goat snp43446-scaffold579-3764629 9 62568115 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795103 Affx-122964630 AX-385282062 9 62115149 TGAAAACAAGACTATCATTTCAACTGAATCTCTCA[C/T]AGAGATTTTCTCACATTTGTTTTCTTAGCCCATCT Y 2 1 2 1 201000 r 74 goat snp43445-scaffold579-3704276 9 62628674 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453205 Affx-122920446 AX-123323538 9 62153395 GACAGTGTGCTTTCTGAACTGTGATATGACGTGAC[A/G]CAGAAAAATCTAAGGTACACAGGCAAAAAACAACA R 2 1 2 1 101000 f 74 goat snp43444-scaffold579-3666030 9 62667026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276468 Affx-1111835356 AX-519549980 9 62206344 TTCTCATCAAAACTCTTTATATTTCCAGTGCCTAT[A/G]GACACATGGCACAAAGATGTCATGAAAGTTTGCAA R 2 1 2 1 101000 r 74 goat Random2.2K-1008 9 62206344 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399277 Affx-122960551 AX-123269632 9 62220654 TGTGCTTTCTGTGCTCGGCCCGGACCCACTTGCCC[A/G]TCAGCCTGTCCTGACCGTCAGATTCCTGTTGCTGA R 2 1 2 1 101000 r 74 goat snp43443-scaffold579-3598771 9 62735123 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394661 Affx-122964376 AX-123265016 9 62253970 GAGTACTGGTGTGGGGTGCCATTTGCAGTAGCAGG[C/T]ATTTAATGCAGAGAACTGAGAAAGCTGCAGCTCTC Y 2 1 2 1 101000 r 74 goat snp43442-scaffold579-3565455 9 62768907 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780000 Affx-122974562 AX-385267099 9 62284316 TATTACTGAAATTTCTTAACTTAGATGAAATGGGT[A/G]TTTGAGAAGTACCCATACATCACTAGATCTTACGG R 2 1 2 1 201000 f 74 goat snp43441-scaffold579-3535109 9 62799089 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437024 Affx-122933120 AX-123307362 9 62337592 TTTCAGAAAGTACTACTTCAAAAAGTCAAAAATTG[C/T]ACAAAGAATTGAAAACAACAAAATAAAGCAGCACC Y 2 1 2 1 201000 f 74 goat snp43440-scaffold579-3481833 9 62852162 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404560 Affx-122957378 AX-123274912 9 62369789 GAATTAAGGTAGATAGATGAAAGTTAGAGGGAAGA[C/T]ACCTAAGTATATGTTAATGTTGTATCGAAGGAGAA Y 2 1 2 1 101000 f 74 goat snp43439-scaffold579-3449636 9 62884191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446387 Affx-122925583 AX-123316723 9 62401098 GGTTTCTAGCTTAAGGCTCTGGGTGAATGCCAGGG[C/T]CAGGAACTGGGCTGGGTTGATTGCAGTAGAAGCAG Y 2 1 2 1 201000 r 74 goat snp43438-scaffold579-3418327 9 62915539 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430058 Affx-122937556 AX-123300399 9 62433818 CATGGATGACTTGGTACAAAATAATTCTGAATACT[C/T]GAAACCTGCAAAGTTCCTTCTAAAGAGCTAAAATG Y 2 1 2 1 201000 f 74 goat snp43437-scaffold579-3385607 9 62948524 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273549 Affx-1111833684 AX-519547164 9 62467115 CACTGTTTAGAGCAACAGATATTTTCTTACCCCAG[A/G]GCATCCGTCAGACTTCGTTCTGCAGTGACCTTGAG R 2 1 2 1 202000 f 74 goat GoatD01.001395 9 62467115 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38453635 Affx-122919742 AX-123323968 9 62474701 GACCTGACGTTAAAGTTGACACCCATGTAGCTGAG[C/T]GTCTTGAAGCAGGGCCCCTCCAGTTCTGTCTGATG Y 2 1 2 1 101000 f 74 goat snp43436-scaffold579-3344724 9 62989677 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402049 Affx-122958729 AX-123272402 9 62521578 AAACAGGCAGAGCAGTGAGAATGCAGTTGGGGCAG[C/T]AAAGAGAAATGAACCAGAGTAGGAGCAGCAGGGAG Y 2 1 2 1 201000 r 74 goat snp43435-scaffold579-3297847 9 63036379 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797057 Affx-122963701 AX-385283997 9 62574562 TACTTTTCAATCATGGTGCTTCATCAAATAACTTA[A/C]GGCATGAAATTTAGTTTTATATATCTTAGCATTTC M 2 1 2 1 101000 r 74 goat snp43434-scaffold579-3244863 9 63089132 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382419 Affx-122974247 AX-123252777 9 62622827 GGCAGCACAAAAGGAAATTGTTCTGAGAATCCAAA[C/T]GTCAGATCCAGGTGGTGTGACTGGCAAAATCCAGG Y 2 1 2 1 101000 f 74 goat snp43433-scaffold579-3196598 9 63137387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792685 Affx-122952899 AX-385279665 9 62667662 CACGGCACACCTGTTTAAATGCCGTTTGGGTCACA[A/G]TGTTGACATTCGGCAGACAGAAGGGTCTGAGATTG R 2 1 2 1 101000 r 74 goat snp43432-scaffold579-3151763 9 63181987 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423961 Affx-122942139 AX-123294307 9 62699468 GTGATTCCTACACTTTCAAACTACATTTTGTAATC[A/C]ATAGAGTCTGGGGGAAGGCATCTTAACTTTTGCTT M 2 1 2 1 201000 f 74 goat snp43431-scaffold579-3119957 9 63213958 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383593 Affx-122972579 AX-123253951 9 62729912 ATATTCCCATGGAAGACAAAATTTAAAAATACTAA[C/T]GCTGAAAAAAGCTGTCGGTTTTAAATCCTTACTTC Y 2 1 2 1 101000 r 74 goat snp43430-scaffold579-3089513 9 63244413 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439985 Affx-122929801 AX-123310322 9 62760279 CACTAATAGAAAACAAAGAATTATCTTTTAAGTTA[C/T]ATTCTCCTAAAACTCAGTCGAGTACTGACATCTTA Y 2 1 2 1 101000 r 74 goat snp43429-scaffold579-3059146 9 63274798 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422474 Affx-122943325 AX-123292820 9 62818964 GGACCAGATGAAGCAAATAAATTCATCTCCAGCTG[A/C]TGGAACCAAAATACATGCTGATGTAAAGTGTGATT M 2 1 2 1 101000 r 74 goat snp43428-scaffold579-3000461 9 63332945 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446833 Affx-122925273 AX-123317169 9 62871217 TTTGGAGGACACACGGCGAGCTCCACCCTGTGCAA[A/G]ATTCTCAGATCATAACTAAGAACTAAGTCAGGGCT R 2 1 2 1 101000 r 74 goat snp43427-scaffold579-2948208 9 63385554 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438292 Affx-122931394 AX-123308630 9 62918320 CTGATGCCAACTTGTGTGTGAATCTTTATTTCCTC[A/G]TCTGAAAAATGGCAGTGCCGTGGAAGTGTAACACC R 2 1 2 1 101000 r 74 goat snp43426-scaffold579-2901105 9 63432617 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794563 Affx-122945685 AX-385281525 9 62962208 TCAAGATTTCAAACATGATTTTCAGTAGAGCATAG[C/T]TGAAGCAAAAAGTCTTCTAATAAGGCCATCTGCTC Y 2 1 2 1 101000 f 74 goat snp43425-scaffold579-2857217 9 63477252 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406858 Affx-122955655 AX-123277209 9 63009686 AGCAACCTGCTATGTGGACTTGGTATATGCTGCTA[C/T]GTTTTGACTTTTTTCTAATATTAATTTAGATCCTA Y 2 1 2 1 101000 f 74 goat snp43424-scaffold579-2809739 9 63524969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388343 Affx-122969351 AX-123258701 9 63044937 GTGTGCAGTATTATTATAGACACTGTTAAGAGCAG[A/C]GACAAGTCAGCAAACATGATTATTTTTCATTTACT M 2 1 2 1 102000 f 74 goat snp43423-scaffold579-2774488 9 63560270 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778057 Affx-122940142 AX-385265173 9 63079881 ATTTAATGAAGCATCTGTGCACAGAGTAAAATCCT[A/G]TCACAGATTGCAGAGACTCTGTTTCTGACTTTGGG R 2 1 2 1 101000 r 74 goat snp43422-scaffold579-2739544 9 63595282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435385 Affx-122933572 AX-123305725 9 63116691 TGCCATTTCTTTATCTCATTTGATCATTATCATTT[A/G]CTAGGAGCAGAATGCAGGATAACAGCCTCCCAACG R 2 1 2 1 101000 r 74 goat snp43421-scaffold579-2702734 9 63631840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395829 Affx-122963630 AX-123266184 9 63154412 TCCTGCAAAGTTTATTCCCTATCCTTCTAATCACT[A/G]CCTTTTATTTTCCTCTTTCACCTTTCACTTACCAC R 2 1 2 1 201000 f 74 goat snp43420-scaffold579-2665013 9 63669929 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785787 Affx-122945508 AX-385272827 9 63202253 CCTGACATACTTTAAAGAATGCCTCCTATAGGCTA[G/T]TTCATGAAGATGGTGCTATCCTATTCTGTGGGAAT K 2 1 2 1 202000 r 74 goat snp43419-scaffold579-2617172 9 63718794 T G 2 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38442195 Affx-122928795 AX-123312532 9 63296329 TTCCTGGAAAAAAGAAAATCCAGGCAGCCAGGATT[A/C]TGTGCCCTTCAGTAAGATGTTACAGTTACTCAGAG M 2 1 2 1 202000 f 74 goat snp43417-scaffold579-2523096 9 63812907 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376527 Affx-122978003 AX-123246886 9 63333112 GTCATCTGTAAGGTCAGCACTCTGCAGAGTAACTC[A/G]TAGCAGACGAAATAAAAACCCATACTGAACAGTCT R 2 1 2 1 101000 f 74 goat snp43416-scaffold579-2486313 9 63849844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421479 Affx-122943920 AX-123291826 9 63478566 GGTCAGCCAAATTATCATCATCCAAACCGAAAGAC[A/G]AAGAGTATTAGTCAAACTCTCACAGTCAGCTGTGT R 2 1 2 1 101000 f 74 goat snp43413-scaffold579-2340859 9 63993124 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273439 Affx-1111833619 AX-519547064 9 63502022 GATATAAAGTCCCACAAGGTCCCTCGTGTGTGCCT[A/G]CACACTGTCATGTCGGACTCTGCAGCCCCATGGAC R 2 1 2 1 102000 f 74 goat 9_63502022_AF-PAKI 9 63502022 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38379439 Affx-122976100 AX-123249797 9 63531719 AAAAAAAAAAAAAAAAAAAAAGGTGCCCATACTCT[A/G]CAGAGAGATCATGTATGGGAACGACCTGGTAGACC R 2 1 2 1 101000 r 74 goat snp43412-scaffold579-2287706 9 64047927 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786501 Affx-122965529 AX-385273535 9 63599463 ATGACCACACAATACTGCTTTATGTTCCTTCCTGC[C/T]AGTTTCATGAAATAGTCAAATTACTGTCAGAATCA Y 2 1 2 1 101000 f 74 goat snp43411-scaffold579-2219962 9 64117011 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273928 Affx-1111833935 AX-519547534 9 63644933 GGAACTCAGATCTGCATGGGTAGAGTACAAAGAGT[A/G]GTGAAGTTAGA R 2 1 2 1 101000 f 74 goat GoatD01.010950 9 63644933 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38448569 Affx-122923413 AX-123318905 9 63653337 ACATAAGACTTTCCTGCCAATCAAAGTTTCTGATC[A/G]TTAGGAAAAAAAATCTTTGTTATCATACCAAGTTG R 2 1 2 1 101000 f 74 goat snp43410-scaffold579-2166088 9 64171473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412724 Affx-122950733 AX-123283073 9 63706349 TTATAGCTCATGACAGTGGAAGAAATGGGCTGCAC[A/G]AGTACAAATCTTGAAAATAGTAAAAAGAAAAAACA R 2 1 2 1 101000 f 74 goat snp43409-scaffold579-2113076 9 64224458 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423992 Affx-122942114 AX-123294338 9 63737562 TCATTCACTCATTCGTGGCCAGTAAAGGGACTGAA[A/G]GAAGGCCAGTTTGACTGAAACAGGAGGAGATGAGA R 2 1 2 1 101000 f 74 goat snp43408-scaffold579-2081863 9 64256102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380262 Affx-122975429 AX-123250620 9 63800673 GTAAGCCAGCACTGGATTTAGGAGTTGAAAGTTTA[C/T]GGAGTCAGCAGGACCCCAAGGGACTGAAAGCTAAG Y 2 1 2 1 101000 f 74 goat snp43407-scaffold579-2018752 9 64319169 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771673 Affx-122938486 AX-385258831 9 63849664 TAGCTCAGAACTCTCATCTTAGTTCTAGAGTTTCA[C/T]GGCTAAAGAACTACTTGGTATTTGTACTTGGATAT Y 2 1 2 1 101000 r 74 goat snp43406-scaffold579-1969761 9 64368876 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387551 Affx-122970292 AX-123257909 9 63880896 CTGGTGGGAAAAGAGAACGTGACAAATATTATAAG[C/T]ATTACAAACAGGGTGTGGTGGGAAGCCAGGGAGAT Y 2 1 2 1 101000 f 74 goat snp43405-scaffold579-1938529 9 64399093 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395035 Affx-122964209 AX-123265390 9 63933356 CTTTACTACTTCCTTAGCTTCTCTGAGAAAGTCAA[C/T]GACACTCTCTGATATCAGCTATCTCACTCTTAAAA Y 2 1 2 1 101000 r 74 goat snp43404-scaffold579-1886069 9 64451674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384183 Affx-122972411 AX-123254541 9 63967757 GTGGATTATGGGAGAGTCAATCACTGCTCACAAAA[C/T]GGTGCATTTCTTTCCAGTCTTTTCTTATTTTGCAA Y 2 1 2 1 101000 f 74 goat snp43403-scaffold579-1851668 9 64486093 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773275 Affx-122958369 AX-385260418 9 63999144 CCCATACTTGGCTGTACACATCCAAGAGTGAGCTG[C/T]GAATCCTTGAGCTTGCCTTGGGCAAACATAGCTGT Y 2 1 2 1 101000 f 74 goat snp43402-scaffold579-1820281 9 64517386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435395 Affx-122933565 AX-123305735 9 64056600 AAATCATTGGCTGTGAATCAGAGTGTAGTTGCTTA[C/T]AACTTTATCACTTGAAGGATGAAGAAGCTGAGGCC Y 2 1 2 1 101000 r 74 goat snp43401-scaffold579-1762825 9 64576208 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416903 Affx-122948064 AX-123287251 9 64113283 TAGAGCCAAATTTCCTAATTTGCTGTATTTGAGAA[C/T]AGATCAAGATTCCATTTGTGCACACATAAAGAAGT Y 2 1 2 1 101000 r 74 goat snp43400-scaffold579-1706142 9 64633197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786049 Affx-122975696 AX-385273085 9 64157848 GAACGTAAAGTCTGGCTTGACTGATGAGTTACACT[A/G]TTTCTCCCAGACACAGTCTTGGCAATGTGATTCAT R 2 1 2 1 101000 r 74 goat snp43399-scaffold579-1661577 9 64677804 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381603 Affx-122974788 AX-123251961 9 64196339 TGATCCCCTTGCATTTATCCTGGGATATGAAAACC[A/G]CAGGAGTTTTATTAAAACAGAGTTTGCTCACAATA R 2 1 2 1 101000 f 74 goat snp43398-scaffold579-1623086 9 64716586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422236 Affx-122944015 AX-123292582 9 64229649 ATATGACATCTTCAAAGGTGGATTTAATTCGGGAC[A/G]TCACTGTTACTTTTATTGGCTGCATAATTCTGGGC R 2 1 2 1 600000 f 74 goat snp43397-scaffold579-1589776 9 64229649 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771407 Affx-122944015 AX-385258565 9 64229649 ATATGACATCTTCAAAGGTGGATTTAATTCGGGAC[A/G]TCACTGTTACTTTTATTGGCTGCATAATTCTGGGC R 2 1 2 1 101000 r 74 goat snp43397-scaffold579-1589776 9 64749675 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781278 Affx-122927594 AX-385268363 9 64307799 TTTCTCAATATCCCACCAATGGGTGCTGAGGAAAG[C/T]AAATTATCATCATCTTCCCATGCTTTCTAGCACTA Y 2 1 2 1 201000 r 74 goat snp43395-scaffold579-1511626 9 64828674 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406064 Affx-122956246 AX-123276416 9 64369112 ACTTCAGGTCACTTCACATCAATGGATAACAGAAC[A/G]GCTAAATGTCCTGGAGTGAGTGCTGCAGTGTGTGA R 2 1 2 1 101000 f 74 goat snp43394-scaffold579-1450313 9 64890811 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787888 Affx-122935490 AX-385274910 9 64401981 GTCATTTCATATTAGGTTTACTATGCAAAACACAG[C/T]GAAAACTTGACAGGCCCCATAAAAACGCATCCTAA Y 2 1 2 1 101000 r 74 goat snp43393-scaffold579-1417444 9 64924229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781034 Affx-122962492 AX-385268121 9 64440962 GGTCTCTGAAGTATCATCTCAAGGGCTTGTGTTTT[A/G]TTAGCCACAGAGTTTCCATAGAATGGAGGCAGTTT R 2 1 2 1 101000 f 74 goat snp43392-scaffold579-1378463 9 64963588 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798352 Affx-122955253 AX-385285287 9 64480618 TATTTGCCTTCACTGGAATTTCCTGGACAAGTTTC[A/G]TCATTTAGCTTCAGTGTCAACCTTTTGCTGAAAAC R 2 1 2 1 101000 f 74 goat snp43391-scaffold579-1338807 9 65003282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771543 Affx-122943817 AX-385258701 9 64509986 ATGCCCATAAGACATAGCAACAGAGTTATGTTGCA[C/T]AATGGTCTTCCTAAAACCAAGTGGCATAATTTGAT Y 2 1 2 1 201000 r 74 goat snp43390-scaffold579-1309439 9 65033768 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766192 Affx-122978184 AX-385253592 9 64547394 AGCTATAACAAGATGGATGAAGAAAGTTGGAATAC[A/G]TATTAAAAGAGCAGTTTGATGCCCACATGTTTAAA R 2 1 2 1 101000 f 74 goat snp43389-scaffold579-1272031 9 65071357 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429514 Affx-122937851 AX-123299856 9 64582779 ATACAGAAATTCAAACTGACTAAAACACTACCCAC[A/C]CTACTCCATGGAATTCAAAGGTGATGTTATCTCAA M 2 1 2 1 101000 f 74 goat snp43388-scaffold579-1236646 9 65106761 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430321 Affx-122938228 AX-123300662 9 64620141 CACAGCACTTAAATCCTAACTAATTTAATCACAAA[G/T]AAAGAAATAAAAAAGCATTCAGCTTGGAAAGAAAG K 2 1 2 1 101000 f 74 goat snp43387-scaffold579-1199284 9 65144156 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773829 Affx-122933233 AX-385260969 9 64658280 CCAGGAAGTACATTGAAAAGGATTTATCTTTTAAC[A/G]TGTTTTATACTTTGTACCAAGATCATGTTGGAACA R 2 1 2 1 201000 r 74 goat snp43386-scaffold579-1161145 9 65182766 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449191 Affx-122923519 AX-123319526 9 64730886 CCCTTTATATTACCTTGGAAATGATTTGTTTAGCA[C/T]TTTTATAAATACCCTTCTTTTTTTCTCTTCCCATC Y 2 1 2 1 202000 f 74 goat snp43385-scaffold579-1088539 9 65268444 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800265 Affx-122958133 AX-385287188 9 64789204 CTTAATAAAATATACAAAGGGTAAAAATTGATGCC[A/G]CATATCTGGTAAAAATTGGGCAAGTAGAAGCATAT R 2 1 2 1 101000 r 74 goat snp43384-scaffold579-1030221 9 65325576 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391291 Affx-122967344 AX-123261648 9 64828379 AAGATAATCTTTTGTTTCTGTTAGGAGACTGGAAA[C/T]GTTACTCGTCTTACTTTAATTTATAGTCAAGGCTT Y 2 1 2 1 201000 r 74 goat snp43383-scaffold579-991046 9 65365128 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408614 Affx-122953498 AX-123278965 9 64934168 ATTTGACAAAAGTAATGATTTCTTTGATATCTGTT[A/G]CAAGATTTTTGGTTTAGATTACATACCCTATTTTT R 2 1 2 1 101000 r 74 goat snp43380-scaffold579-885257 9 65472062 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441513 Affx-122928722 AX-123311850 9 64974517 CACCACTCTCTGAAAGAATCCACATGAAATAGCAA[C/T]GGGGAGATTTCTTTCTCTCCCATTTATCCTAATGT Y 2 1 2 1 202000 r 74 goat snp43379-scaffold579-844908 9 65510649 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380750 Affx-122975129 AX-123251108 9 65030684 GAATCCCAAGCCTTTCGCTGACTTTTAAAATTCAG[C/T]GCCCTGCATTCCATGGGCATATTTCAAGTTTTAAC Y 2 1 2 1 201000 r 74 goat snp43378-scaffold579-788741 9 65566152 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784686 Affx-122943237 AX-385271734 9 65065798 ACATGGGTTGTAGGCAGCTACATGATCTACTAGAA[C/T]AATGTATAATAGAACATTAAACTTTTGGTGGAATT Y 2 1 2 1 202000 r 74 goat snp43377-scaffold579-753627 9 65606222 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398171 Affx-122962657 AX-123268526 9 65110638 ACAAGGTGTTTTTTTCTTATTGGTTTTTAAGAACA[G/T]AGGAAGGAACAAAGACTAAGGCCATGTTACTTCCA K 2 1 2 1 201000 f 74 goat snp43376-scaffold579-708787 9 65651716 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796230 Affx-122932863 AX-385283180 9 65119223 TCCAATCACTTGGGTTATAATAGCGAACAAAAAAC[A/C]AACAAAGACCCTACTCTTATCAAACATAAATCCTG M 2 1 2 1 201000 r 74 goat snp50487-scaffold725-3231 9 65667728 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434551 Affx-122934136 AX-123304892 9 65158021 TATTTTCCCACTATGTGCTTTGGCAAAAGTCATTG[C/T]ATAAGTTTCCCATTGTTTTTGTAACAAAGTAACAC Y 2 1 2 1 101000 r 74 goat snp50488-scaffold725-42029 9 65707109 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801527 Affx-122975832 AX-385288436 9 65210060 CTTCTACGCTATCTTTATTCCTAAGGAGAAGAAGC[G/T]CAACAGTTTTTGTCATAACAGAAATCAATGACTAT K 2 1 2 1 101000 f 74 goat snp50489-scaffold725-94068 9 65757079 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793941 Affx-122939249 AX-385280910 9 65246147 TCTTAGGTCTCACCTCCAAAAAGCAACCTTCCTTT[A/G]TCTTTACAAAGTCCTTGATCCATTCTTCCTATTCC R 2 1 2 1 101000 f 74 goat snp50490-scaffold725-130155 9 65793556 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451980 Affx-122920937 AX-123322313 9 65279973 TCCATTTTCCCATCATATTCCTGAATCAAAATCTT[A/G]TCATTCCAAAACCCCATTTTACAGAATTTTTAAAA R 2 1 2 1 101000 f 74 goat snp50491-scaffold725-163981 9 65827728 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408588 Affx-122953655 AX-123278939 9 65352678 CCTGTGTGCCCAACACTATCTGAGTTAGGGCTTCA[C/T]GCAGCAGCTCACTCAGCAGATGAACATCACAGCAC Y 2 1 2 1 101000 f 74 goat snp50492-scaffold725-236686 9 65893084 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790326 Affx-122975925 AX-385277329 9 65404466 GAAATTTTATAGAGAGTAATATGAGCAAAAACAAA[G/T]GCATGAGTAAATCTGCTTCATAATAGTTTACCTCC K 2 1 2 1 101000 r 74 goat snp50493-scaffold725-288474 9 65936390 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794924 Affx-122970026 AX-385281884 9 65450960 ACTTAGTGGTAACCATGCTTTTCCAGTATAAACTG[C/T]ATAATATGCTCTGTAATGTACACAGATCTCAAACA Y 2 1 2 1 101000 f 74 goat snp50494-scaffold725-334968 9 65982803 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413287 Affx-122950204 AX-123283636 9 65493901 TCTTGTCTTTCCCATTAATCTCTAATGACACATAG[C/T]ATTGTTTGGCATTGAATAAAATATATTTATCTTCC Y 2 1 2 1 101000 f 74 goat snp50495-scaffold725-377909 9 66025851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438149 Affx-122931468 AX-123308487 9 65523185 AATTGATCCTCAAGAGAGTTTATTAAAATAAAGAG[C/T]ACTTTATGAGCAGAAAAGAAATATTCTGAAGTGGA Y 2 1 2 1 103000 r 74 goat snp50496-scaffold725-407193 9 66055298 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398802 Affx-122961411 AX-123269157 9 65587263 TAGTTTTCTTATATCAGTTTGCATAGGAGTCAACA[C/T]AAACTCAAATCACAGAATGAAGATCAATCGTATAA Y 2 1 2 1 101000 f 74 goat snp50497-scaffold725-471271 9 66122630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777567 Affx-122950246 AX-385264686 9 65637802 AGACAAACTTGAATACAGAGAAGACATTTTTGATG[A/G]ATCATGGATCGTGGATTTCTTCCATTGATCATGCC R 2 1 2 1 101000 r 74 goat snp50498-scaffold725-521810 9 66174168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476262 Affx-1251763769 AX-586011683 9 65656749 TAATGCATAATAAGACTAATAATAATATATAGATG[-/TTGAAATTAACTATTTTTTTTTGTTTTGTTTTTAAAAATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTCC]TGAAATTAACTATTTAAAATTTTATAAAAATCACA - 4 1 4 1 20000 f 74 goat SV_304 9 65656749 - deletion junction SV-TF-chip 539476515 Affx-1251763769 AX-586011908 9 65656749 TAATGCATAATAAGACTAATAATAATATATAGATG[-/TTGAAATTAACTATTTTTTTTTGTTTTGTTTTTAAAAATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTCC]TGAAATTAACTATTTAAAATTTTATAAAAATCACA - 8 1 4 1 20000 r 74 goat SV_304 9 65656749 - deletion junction SV-TF-chip 562165209 Affx-1251763769 AX-606940621 9 65656749 TAATGCATAATAAGACTAATAATAATATATAGATG[-/TTGAAATTAACTATTTTTTTTTGTTTTGTTTTTAAAAATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTCC]TGAAATTAACTATTTAAAATTTTATAAAAATCACA - 8 1 4 1 20100 r 74 goat SV_304 9 65656749 - deletion junction SV-TF-chip 562165732 Affx-1251763769 AX-606941141 9 65656749 TAATGCATAATAAGACTAATAATAATATATAGATG[-/TTGAAATTAACTATTTTTTTTTGTTTTGTTTTTAAAAATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTCC]TGAAATTAACTATTTAAAATTTTATAAAAATCACA - 8 1 4 1 20100 f 74 goat SV_304 9 65656749 - deletion junction SV-TF-chip 562166376 Affx-1251763769 AX-606941784 9 65656749 TAATGCATAATAAGACTAATAATAATATATAGATG[-/TTGAAATTAACTATTTTTTTTTGTTTTGTTTTTAAAAATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTCC]TGAAATTAACTATTTAAAATTTTATAAAAATCACA - 8 1 4 1 20100 r 74 goat SV_304 9 65656749 - deletion junction SV-TF-chip 38399495 Affx-122961175 AX-123269850 9 65701414 TTTCTAATACCCCAAAACATAAAATTCAATGAAAA[C/T]GCTTGCTTCAAACTTTCTAACAATACATCTAAAAG Y 2 1 2 1 101000 r 74 goat snp50500-scaffold725-585422 9 66238984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446794 Affx-122925302 AX-123317130 9 65761893 GACTTCACAGATGAGCAGTTTATTTTAGCTTAGAC[A/G]CAAACTACTTCAACTTTCTTTGGTAGATTCACAGG R 2 1 2 1 101000 r 74 goat snp50501-scaffold725-645901 9 66300683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439434 Affx-122930191 AX-123309771 9 65834939 AGATACTCTCTCTGAGGCCAACACTGAATCTATGT[C/T]AGAAGAAAGGTGACAGGGCAGCTGCTCCTGAGGAA Y 2 1 2 1 101000 f 74 goat snp50503-scaffold725-718947 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783557 Affx-122957591 AX-385270619 9 65879723 GGGATCTCCTAGAGGGCTATGTATAACTACTTTAT[A/G]CTATTAAAAGGAAGGAATGCTTCATTTGTGACTAA R 2 1 2 1 201000 r 74 goat snp50504-scaffold725-763731 9 66415367 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790397 Affx-122967539 AX-385277400 9 65914562 TTCTCCATTTTTCTTAACATGTTTATAGGAGTAAT[A/G]CTAAGATCTTTTCTGCTATTTCTAACATATGAACT R 2 1 2 1 101000 r 74 goat snp50505-scaffold725-798570 9 66448357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770970 Affx-122938571 AX-385258133 9 65958051 TGATTTCAAGGGATGACACTTTAAATGTTTGGCCC[A/G]TTATTACCACCTTATCAATTCATGACACAGCACAA R 2 1 2 1 101000 f 74 goat snp50506-scaffold725-842059 9 66492265 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395849 Affx-122964016 AX-123266204 9 65994657 TAGCTATTATTATGAAAAATATGAAAGTGAAAGTC[A/G]CTCAATAGCGTCCAGCTCATTGTGATCTCATGGTC R 2 1 2 1 101000 r 74 goat snp50507-scaffold725-878665 9 66529214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431454 Affx-122936496 AX-123301795 9 66049702 TAACTATGGCTTTCCTCATTCCCATCCACATCTCA[C/T]AGACTGGTTTAAAGCCAATGGATACCATGAGACTA Y 2 1 2 1 201000 r 74 goat snp50508-scaffold725-933710 9 66584485 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388248 Affx-122969786 AX-123258606 9 66080261 TGAGAAGGAGTCTAGACCAGGAAGCAGAATGTGGC[A/G]CTCTGGATATAGTCCAGTAGCATCAATTAGACAAC R 2 1 2 1 201000 r 74 goat snp50509-scaffold725-964269 9 66615044 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398598 Affx-122961490 AX-123268953 9 66114711 TGTGCTGACAGTGTAGGTCAGGGGATTATTAGGTC[A/G]ACTACATACCCCAGGCTCTTTGTTTTTGTTTTGTT R 2 1 2 1 101000 r 74 goat snp50510-scaffold725-998719 9 66649959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798892 Affx-122965853 AX-385285822 9 66154367 CTTGTCCATCAGAAATGTAGTAAAAGCAAAACGTG[C/T]AATTTTAAATTATCTACTAGCTACATTTTAAAAAG Y 2 1 2 1 201000 r 74 goat snp50511-scaffold725-1038375 9 66690120 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773134 Affx-122923707 AX-385260277 9 66216485 AAGTGCTGATGCGAGAATGACTTTTAAAAGTTTCC[A/G]TTTTTCCTACTGGTTAAGTGTAAATGCCTTTTGAG R 2 1 2 1 102000 f 74 goat snp50512-scaffold725-1100493 9 66753032 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273441 Affx-1111833620 AX-185321237 9 66261923 AGAATCCCAGGGATGGGGGAGCCTGGTGGGCTGCC[A/G]TCTATGGGGTCGCACAGAGTCGGACACAACTGAAG R 2 1 2 1 303000 f 74 goat 9_66261923_AF-PAKI 9 66261923 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38409715 Affx-122953038 AX-123280066 9 66272679 TGCCTCCTGTATTTTCATGGATTAACTGGTGGTAC[C/T]CAAGGGTGAGGGAACGTGTTTGCTAGTGTGAGTCC Y 2 1 2 1 101000 f 74 goat snp50513-scaffold725-1156687 9 66809894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401028 Affx-122959671 AX-123271381 9 66399393 AGTAGTGAGCTTCTTATTTTGGAAGGTTAAGTTGT[A/G]TTTATGTGTCTTTGCCAAGGCCTCTGCTATACCAT R 2 1 2 1 101000 f 74 goat snp50516-scaffold725-1283401 9 66936671 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450958 Affx-122921752 AX-123321292 9 66429854 GTAGGATAAGAACAAGAAGATTTCAGTTTAAGGTT[A/G]ACTCTAAATACTTTTTAATGGTTTTGGAAAGGAAA R 2 1 2 1 101000 r 74 goat snp50517-scaffold725-1313862 9 66967017 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414208 Affx-122949651 AX-123284557 9 66461656 TATTATGAACCCCTACTGACCAATTAATAGCATGC[A/G]CAATACAACTACTGAACAAATATAGATCAAAGAAA R 2 1 2 1 101000 r 74 goat snp50518-scaffold725-1345664 9 66999108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382085 Affx-122974906 AX-123252443 9 66501775 CAAGGGTAACCCAGGTGGTCACTGGTTGCCATCAC[A/G]CTTACTCTGTAAGGCCTCTCTGATTACTTGCTATG R 2 1 2 1 201000 f 74 goat snp50519-scaffold725-1385783 9 67039339 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435055 Affx-122933743 AX-123305395 9 66558928 GTTGGCAAAACTGGGTCCTTATGGTTCAGCATGGC[G/T]ATTATTGTCCAAAGCCAGGCCTGGCTGCGCCTATA K 2 1 2 1 101000 f 74 goat snp50520-scaffold725-1442936 9 67096417 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786757 Affx-122924696 AX-385273788 9 66590179 ACTATTGCTTATTATTCGTCTTGTAAACCACTACA[C/T]AAACTATGGAATCATGAGGTTGGTAGGAATGGCAG Y 2 1 2 1 101000 r 74 goat snp50521-scaffold725-1474187 9 67127481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387156 Affx-122970635 AX-123257514 9 66637357 ACAAAAATATATAAATGATTGTGCAACTGTGAAAG[A/G]CTACTTCTTATTTCCGTTGAGAAACTGATCCAGTC R 2 1 2 1 101000 r 74 goat snp19115-scaffold1923-24294 9 67174644 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399147 Affx-122960652 AX-123269502 9 66675758 ATAAATAACAAAACAAAAGAAGAAAAGTTTCTCCC[A/G]TAGTCACAGGGCTTTTTAGCTGGAGCTGGAACTGG R 2 1 2 1 101000 r 74 goat snp19116-scaffold1923-62695 9 67212514 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448512 Affx-122923454 AX-123318848 9 66705457 TACAGAAACTGGTCCCTCCAGTGTGCAAGACACTG[A/C]TCTAAAGAAATAGATTTCTGCTCAGGAGGCATCAA M 2 1 2 1 102000 r 74 goat snp19117-scaffold1923-92394 9 67242137 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427778 Affx-122939229 AX-123298121 9 66754007 TTGAGTGAATGGAGGAATAAATAAATGTGAATAAG[C/T]GAATGAAATAAAGAATGACTGTGAATATACCACAT Y 2 1 2 1 101000 r 74 goat snp19118-scaffold1923-140944 9 67290830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439362 Affx-122930279 AX-123309699 9 66821685 ACTTTACAGAAACATCTGTCGTGTGCATTTGAGAG[C/T]GCTTGACAATGGTTGTCTCATTACTTTTGGCCACA Y 2 1 2 1 101000 f 74 goat snp19120-scaffold1923-208622 9 67358486 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376755 Affx-122978532 AX-123247114 9 66854314 TTCCCATCCTACAGTTCATCTACTTAAGGATGAAT[A/G]CTCACACACACAAACACACAAAACACACACCACAT R 2 1 2 1 103000 f 74 goat snp19121-scaffold1923-241251 9 67391324 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449314 Affx-122923000 AX-123319649 9 66885718 CAGGGGGTGCCCCTGGACTTGTTTTCTTACTAAAC[A/G]TCCTCCTTTGCATCCTCTCATCTGCCCCAATTCAA R 2 1 2 1 101000 r 74 goat snp19122-scaffold1923-272655 9 67422926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791925 Affx-122951442 AX-385278915 9 66924878 CCTAAATCCTTATACTTTGGCAATTTCTGAAAATA[A/G]CAACTTGACCCACTCCCAGTCTATCTGCTGATCAG R 2 1 2 1 102000 r 74 goat snp19123-scaffold1923-311815 9 67462406 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411786 Affx-122951477 AX-123282136 9 66964746 TGTGTGTGTGATACTGACCATTTCTTAGTTTTCTG[C/T]GCAACCAGAGCGCCAAGAATGTTACCAGCATTGAA Y 2 1 2 1 101000 r 74 goat snp19124-scaffold1923-351683 9 67514860 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404789 Affx-122956672 AX-123275141 9 67008781 AACATGAGAAAACACAACCCAAAGCACATGGCTCA[G/T]CGGAACCAGAAGAGGAATTACACCTGGGGTCTTAG K 2 1 2 1 101000 f 74 goat snp19125-scaffold1923-395718 9 67559196 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430154 Affx-122937380 AX-123300495 9 67039704 AAAAGGGAATAGCCTTCTATCTAGACATGGTCTCT[A/G]TCAAATATAAGTTAGAAATTAATAGGAGTTTGTTA R 2 1 2 1 101000 f 74 goat snp19126-scaffold1923-426641 9 67590129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768867 Affx-122963960 AX-385256044 9 67069543 ATAGAAGCATCAACAGATAGTTATGGTGTGATTTG[A/C]TGTGTACCATGCTACAGGTGTTTTAAAACAAGGAA M 2 1 2 1 101000 r 74 goat snp19127-scaffold1923-456480 9 67620753 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772869 Affx-122939489 AX-385260014 9 67104674 GCTTATGTTCATTTCCTGAAAGTCTATACAAAATT[C/T]GTCACAGGTAGCCCTGCTTTAGTCCAGCAACTCAG Y 2 1 2 1 101000 r 74 goat snp19128-scaffold1923-491611 9 67655912 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397378 Affx-122962276 AX-123267733 9 67146104 TCCCTTCAGTTGAACAGGGGTCTTTTCTCCAAAGG[C/T]AGGGACTTTCATTACCTTTATTCTAACGTGATGGC Y 2 1 2 1 101000 r 74 goat snp19129-scaffold1923-533041 9 67696883 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320764672 Affx-122971311 AX-385252304 9 67195240 TGCATCAAGTCAACCTGGATGGCGCTGCTTTGTCC[A/G]TACCAAACTATATTGCTTTCTCACACCTGTTTAAG R 2 1 2 1 101000 f 74 goat snp19130-scaffold1923-582177 9 67746310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428096 Affx-122939091 AX-123298439 9 67231219 CCTGTACTGTTTTCCAGTAGTACGGCAATTATTAA[C/T]GTAAAAGAGAAAAGAGAAGTAAAGAGGGGGAAATT Y 2 1 2 1 101000 f 74 goat snp19131-scaffold1923-618156 9 67782314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780790 Affx-122958926 AX-385267879 9 67262516 CCAATCCATCATCAAGTTCTCTTAATTCTATTTCC[G/T]ATATCAGTGCCTTTCAAACTAATCTTACTATAAAT K 2 1 2 1 101000 f 74 goat snp19132-scaffold1923-649453 9 67813445 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378250 Affx-122976896 AX-123248609 9 67295989 CTAGCGGGGCCAAAAAAACCCCACCTACCTATCAA[C/T]ATTAAGACATGGTCCCCTCTTGTCTTTGCTCTGAA Y 2 1 2 1 101000 r 74 goat snp19133-scaffold1923-682926 9 67847063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794256 Affx-122961817 AX-385281221 9 67360015 AAAGTGACTTCTAACTTTGCCCTATCACTCTGTCC[A/G]TTAGCACAAAGACAAATCAAATGCCCTTCACCTAA R 2 1 2 1 101000 f 74 goat snp19134-scaffold1923-746952 9 67911741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448085 Affx-122924328 AX-123318421 9 67417348 GTATTTTTAGTGGGATATATACTCTTAGAACATAC[A/G]GAATTGAAAAAAACAAAAACCTTAAACTCTTTTCA R 2 1 2 1 101000 f 74 goat snp19135-scaffold1923-804285 9 67969044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778149 Affx-122925122 AX-385265264 9 67493847 AAATAAGTACACTTAAAGAATACAACTAAAGTAAC[A/G]CTGGAATTGATACATCAGTCCTTTTATTGGGGTTA R 2 1 2 1 101000 r 74 goat snp19136-scaffold1923-880784 9 68046008 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392028 Affx-122966474 AX-123262385 9 67539551 GGGCTACAAAGAGCTGGACATGACTGAGTGACTAG[C/T]ACACACGGACATTTACCTGTTTCCGCTTAGGCTGT Y 2 1 2 1 101000 r 74 goat snp19137-scaffold1923-926488 9 68091868 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405159 Affx-122956944 AX-123275511 9 67614329 TCCTGTATATCCTTGGAGAAGGCAAGATCTGGTCA[C/T]AGTGGTGGGTGTTTTGAGATAGGGGAAGGTTGTTA Y 2 1 2 1 303000 r 74 goat snp19139-scaffold1923-1001266 9 68167106 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778828 Affx-122975498 AX-318223453 9 67627612 AATCACTAGATGTATAATTGGCTCACAAAACAGTA[C/T]GGTATATACACCTATAAAGAAGACATAAAAATCTG Y 2 1 2 1 101000 f 74 goat snp11549-scaffold1423-6882 9 68179957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780018 Affx-122921380 AX-385267117 9 67656593 ATTGTTGATCCTTTAATTAAGCCTGTTTAATTTAA[A/G]TAGAGGAAAGGTTCCAACATACTTTCTTGTCCTAG R 2 1 2 1 101000 r 74 goat snp11550-scaffold1423-35863 9 68209352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783111 Affx-122973351 AX-385270178 9 67723264 CACTATTCGTAAATCCAAATGACATGATATTCAAC[A/G]TATGAATATTCTAGAAGAAGCTAAGAGATGCTTTC R 2 1 2 1 101000 f 74 goat snp11551-scaffold1423-102534 9 68276281 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782500 Affx-122959205 AX-385269576 9 67755998 TTTAGCATGCTCAGCAAGCAAATACAAATGTTGCA[A/G]TATTGAATACTGATATTATATTCACAGTAAAAACA R 2 1 2 1 101000 f 74 goat snp11552-scaffold1423-135268 9 68308963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427093 Affx-122939788 AX-123297436 9 67848050 CTTTCTCTCCCACCCACTATGCCAGAAAAGGGGAC[A/G]TAAGCGTCAAGGAGGCAGGAACCTGTCTACTTGGT R 2 1 2 1 201000 r 74 goat snp11554-scaffold1423-227320 9 68401154 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791861 Affx-122932883 AX-385278851 9 67882563 GACTAATTTGTTGATTCAAAGACACTGCAGTAATC[A/G]TAGGTCCTTGTGGCACCAAATGTCTACAGGGGTTT R 2 1 2 1 101000 f 74 goat snp11555-scaffold1423-261833 9 68434441 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452417 Affx-122920591 AX-123322750 9 67961984 TACTGTAAGAATATTCTCTCTTTAAAAATTTACCC[A/G]TTTAAAAAGAAATAAAATACTCCCACACGCCAATT R 2 1 2 1 201000 r 74 goat snp11556-scaffold1423-341254 9 68513834 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773557 Affx-122977135 AX-385260697 9 68004356 AGAGAGCACAGTGACTCTGCAGGACTGTAGCAGTC[A/G]GAGACAGACACGGATATCTCTGAGTACATGAGTAC R 2 1 2 1 202000 f 74 goat snp11557-scaffold1423-383626 9 68556447 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793827 Affx-122974147 AX-385280797 9 68062961 AGCAGTATAGGGAAGTAACTGAGATGAAGTCTGAC[A/G]TGGTAACCGTGCAGAAAGAGAAACATTTTAAAACA R 2 1 2 1 101000 r 74 goat snp11558-scaffold1423-442231 9 68614995 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421396 Affx-122943985 AX-123291743 9 68093884 AGAGTAAGATACCAAATAGATGCTCCAGTACAACC[A/G]TTAAAATCAGTAAATTAACATTGATAATTTACTAC R 2 1 2 1 101000 f 74 goat snp11559-scaffold1423-473154 9 68645494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409304 Affx-122953099 AX-123279655 9 68136707 CCCTCCTTCTCTGTTTCTGATTCATCAGTGGAGTG[C/T]GGAAATGTTTAATACTTTCTCCTTTGGAATAATTC Y 2 1 2 1 201000 r 74 goat snp11560-scaffold1423-515977 9 68688410 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772006 Affx-122925147 AX-385259162 9 68180651 AAAAGGAGAAGGGAAGAATGGATAATGCCATGTAT[A/G]CTTTTATAACAATGCCAAGTATACTGTTATAACAG R 2 1 2 1 101000 f 74 goat snp11561-scaffold1423-559921 9 68732411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381726 Affx-122974693 AX-123252084 9 68210345 TAGGAAAGTTCAGCGGTCAGTTTCATAGTCAGCTG[C/T]ATGCCAAGAAATAACGAAAACAGTGGATTACATAG Y 2 1 2 1 101000 r 74 goat snp11562-scaffold1423-589615 9 68761630 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405608 Affx-122956611 AX-123275960 9 68242616 AATAAAATATATGTAAAAATCGAGTCTTTTCTGTA[C/T]GTAGTCAGTTATCTGGAATAACACAAGTTTACAAG Y 2 1 2 1 101000 r 74 goat snp11563-scaffold1423-621886 9 68793878 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787736 Affx-122922990 AX-385274759 9 68276643 CAGGACCCTGTGCTCTCTAAATTGTAATTTTAGTC[A/G]CAATTCAGTATGGACTTTGAGAACCTGGGTTTGGA R 2 1 2 1 101000 f 74 goat snp11564-scaffold1423-655913 9 68828052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420277 Affx-122945046 AX-123290625 9 68313720 AAGTTCTTGGCTCATGGAAGGAGAGAATGATGACT[A/G]TGGACAGTGGGGATGTGGAAGCACCATTATCAGAG R 2 1 2 1 101000 f 74 goat snp11565-scaffold1423-692990 9 68865291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381429 Affx-122974353 AX-123251787 9 68343445 GTTTATTTGAGCGAATGACTTTTCCTTTGTAGATT[A/G]CTATTAAAAAGAATAGGTTGTCTGAAAGTCAGGAA R 2 1 2 1 101000 r 74 goat snp11566-scaffold1423-722715 9 68895047 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452104 Affx-122920844 AX-123322437 9 68377495 CCGTTATCATATCCGTGTCTGGTCACTACTGAAGC[A/G]TTTGAAGTTGGTGTGCCTTTCTCTGACTTGGAAAA R 2 1 2 1 101000 f 74 goat snp11567-scaffold1423-756765 9 68929123 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438064 Affx-122931534 AX-123308402 9 68462245 ATATATTGCAAAATTTCCCCTTGGCAAGACAAACT[A/G]TTTACATGCTTACTGGCAGCTTGAATTCTCCTTTC R 2 1 2 1 101000 r 74 goat snp11569-scaffold1423-841515 9 69014239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436232 Affx-122932570 AX-123306571 9 68528692 CAGATTAGGAGTTGAAAAGTTGGGTGCCCAGGACT[A/G]TAGTTTAAAATATTGAAAATACAGAAACCTTTGAG R 2 1 2 1 101000 f 74 goat snp11570-scaffold1423-907962 9 69080631 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415401 Affx-122948742 AX-123285750 9 68562535 CCTTCTAAAATTGAGATGCATTGTGGTTCAGGCCA[C/T]GCCAGCTTCTCTATATTCATTCCTCCCTGAACTCC Y 2 1 2 1 101000 f 74 goat snp11571-scaffold1423-941805 9 69114693 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800322 Affx-122938376 AX-385287245 9 68592762 GAAAATGCAGCCAAATCATGATAAATTTGTTCTTT[A/G]TATCAGAACACATAGCAGATCTGAAACGGTTTTAC R 2 1 2 1 101000 r 74 goat snp11572-scaffold1423-972032 9 69144791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274675 Affx-1111834435 AX-519548261 9 68633136 GCAGGAGAAGGAATGGCCTTGCCAGTTATTTCTCT[A/G]CTCAATTCGCCTGCAGTTGAACATTTTTGTACTGG R 2 1 2 1 101000 f 74 goat GoatD01.035747 9 68633136 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320796975 Affx-122972544 AX-385283916 9 68635272 TCTAGCATGCATGTGACACTTATACAGGTTACTTT[C/T]GTAATTAGCTGGAATTTTACTATCTGAGGAAATGG Y 2 1 2 1 101000 f 74 goat snp11573-scaffold1423-1014542 9 69188004 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422976 Affx-122943003 AX-123293322 9 68664799 CTGTGCTAATACATCACCCTCATTACATCTACTGA[G/T]ATCTACAAAATCTTTTGTTCTTTTTATTTCTTTGA K 2 1 2 1 101000 f 74 goat snp11574-scaffold1423-1044069 9 69217566 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787161 Affx-122933952 AX-385274187 9 68734601 ACCAATAAAATGGGACTTGGTTTGGTCTGATAAGC[A/G]TACTCTATTGAGACCTTTTACGCTAGGGAGAGTCT R 2 1 2 1 101000 f 74 goat snp11575-scaffold1423-1113871 9 69287655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424238 Affx-122942474 AX-123294584 9 68780491 TAAAATCTTTGACACACATTCATTTTACAACTATA[C/T]AAAAGTAAGAATTTCAGCTTTTTGACAATTACATT Y 2 1 2 1 101000 f 74 goat snp11576-scaffold1423-1159761 9 69334039 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449264 Affx-122923035 AX-123319599 9 68812365 TTTGTATCATAGTATCTCCATTTCCTCTTACTGAC[C/T]TATGCTACCAACAATTCTCTTTTTGCATTTTCATT Y 2 1 2 1 101000 f 74 goat snp11577-scaffold1423-1191635 9 69366088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802491 Affx-122924211 AX-385289395 9 68843756 AATAAGGATCAAGCTACAGTTGTTGACCTGATTTC[A/G]TCAGTGCATAGCTGAAGTTATGGAAGTTTATCAAA R 2 1 2 1 201000 f 74 goat snp11578-scaffold1423-1223026 9 69397281 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419838 Affx-122945813 AX-123290186 9 68906364 ACAGCACATGTTCACAAGGTATTGGAGAAAGACTA[C/T]GCCATTATAAGCAGAGAACTGTACATCTTCTAAAT Y 2 1 2 1 101000 f 74 goat snp11579-scaffold1423-1285634 9 69460153 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777491 Affx-122949316 AX-124357069 9 68978117 AGTCTGGCCCTCCCTCATAACAATAATAATTTATC[A/G]GTTCTGTCTTGTTAGTTCCCAAAGTGTTCTCACTC R 2 1 2 1 101000 f 74 goat snp11580-scaffold1423-1357387 9 69532561 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432049 Affx-122935898 AX-123302390 9 69019508 CAGAAAAAAGAAGAAATGTCCATCGCTTAGACTCT[A/G]CTGGAAATAAGCCCGACTTTCCCCAGTTGTGATTG R 2 1 2 1 101000 f 74 goat snp11581-scaffold1423-1398778 9 69574266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388688 Affx-122968998 AX-123259046 9 69059848 CTGACATTTCCTAGAAAACATGCTGCCCTCCCCCA[A/G]CCCAGGAGGCCTGGCCTTCTCTATGTCTGCAGACA R 2 1 2 1 202000 r 74 goat snp11582-scaffold1423-1439118 9 69614727 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452564 Affx-122920519 AX-123322897 9 69089564 GTGAACAGAAAATGAACTCAGAGGACCTGGGAAAA[A/G]AGTAGAGATCCAAAGTGGAAAAAGATTGGGTTAAA R 2 1 2 1 101000 f 74 goat snp11583-scaffold1423-1468834 9 69644366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798970 Affx-122964605 AX-385285900 9 69120705 TCTTTTAGTGATTGCTTTTAGCCTCATGTCTGATT[G/T]CTAAAGTTAAGATGAAGTTCACTATTTCTTTCTAT K 2 1 2 1 101000 f 74 goat snp11584-scaffold1423-1499975 9 69675760 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396467 Affx-122962967 AX-123266822 9 69164943 TATTAAGACAAAACAAAAACAATTAAACCAAAAAC[A/G]CAGATCTTAAAATCAGACTCTACCCTGTTGCCCCT R 2 1 2 1 101000 r 74 goat snp11585-scaffold1423-1544213 9 69720104 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405184 Affx-122956924 AX-123275536 9 69199372 CAAGGTCACTGAGACATGGATACAGGCTTCCCTTT[A/G]CTCCCTGTGCCAGACTGCAATAGTGATCAAGCAAA R 2 1 2 1 101000 f 74 goat snp11586-scaffold1423-1578642 NW_017217856.1 8908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790664 Affx-122921007 AX-385277666 9 69250765 TTATCTACCACTAGATTTGTTGACTTGTCTTTTAT[C/T]CCCCTCATAATTCCTGCACAACGGATCTATCATCA Y 2 1 2 1 101000 r 74 goat snp11587-scaffold1423-1630035 9 69807085 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396736 Affx-122962796 AX-123267091 9 69280813 TGACTAAAATAAAAATGATAGACAACACAAGAAGA[C/T]GTAGAAAAACTGAAAGCATCCAGTGGAACTGTCAA Y 2 1 2 1 101000 r 74 goat snp11588-scaffold1423-1660083 9 69838237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378867 Affx-122976515 AX-123249226 9 69335299 ACCAATAAAACAATGAGTCAGTCTCTGCCTGGATC[C/T]GTTAGCTTTTCTGATATTCACAACCTAATTTTCTC Y 2 1 2 1 101000 r 74 goat snp11589-scaffold1423-1714569 9 69892639 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407656 Affx-122954607 AX-123278007 9 69366548 GCATTGGCAAGTGGGTTCTTTACCACTAGCACCAC[A/G]TAGGAAGCCCATGGTTGGCTTAATTGGCTGCAGAT R 2 1 2 1 103000 r 74 goat snp11590-scaffold1423-1745818 9 69923744 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795800 Affx-122962614 AX-385282753 9 69396847 TTTCCTTCAAGAATTTACTATTACACTCAAGAACA[A/G]TGTATTAGATTTTGGGCACATTAGACCATTTATGA R 2 1 2 1 101000 f 74 goat snp11591-scaffold1423-1776117 9 69954031 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427079 Affx-122939797 AX-123297422 9 69429167 GTGGGCATCCAGATGTAGGCCAAGCCTTCCTCCTT[A/G]TACAGCCTAATCATAGTGTCTGGTGTCATGGGTTC R 2 1 2 1 101000 r 74 goat snp11592-scaffold1423-1808437 9 69986963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424087 Affx-122942040 AX-123294433 9 69509284 TCTCCATCAAATCCCTTCTTAGTGACCATGCAGAG[A/G]TAGCCTAGGTATTACACAGCCACCATGACCTCCTG R 2 1 2 1 101000 r 74 goat snp11593-scaffold1423-1888554 9 70068603 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440545 Affx-122929322 AX-123310882 9 69543579 GTAAAAGTCAGAAATATTTTTTCAACTTAAAACAT[A/C]ATTTTGGGCCCAGAAACACAGGCTGTTTGGTCAAA M 2 1 2 1 101000 r 74 goat snp11594-scaffold1423-1922849 9 70104268 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408428 Affx-122954460 AX-123278779 9 69573028 GAGAACACTTTACTTTTTGGCTTTAGTAATGACTT[A/G]CAAACACTCCCTCTTTTTAAAAACACTGGGGTAAA R 2 1 2 1 101000 f 74 goat snp11595-scaffold1423-1952298 9 70134050 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397015 Affx-122963129 AX-123267370 9 69614393 ATTTGTCCTAGAGGGTTTCCCTTAGTCTAGAATTT[A/G]CTGATGGCCCTCCAGCTTTGTAAAGATTTCCTGTA R 2 1 2 1 101000 f 74 goat snp11596-scaffold1423-1993663 9 70175429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273443 Affx-1111833621 AX-519547067 9 69622671 TGAAATATCTCACCACAGGTTTGCTTTCACCTACT[A/G]CTAATATGAGATCTTCAAATCTCTGTCCAGCTCAA R 2 1 2 1 101000 f 74 goat 9_69622671_AF-PAKI 9 69622671 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448207 Affx-122924232 AX-123318543 9 69674670 ATGCCTCTCCCACACCTTTTCCTTCGTAGCATCTA[C/T]GGATTCTCATGGTCAGGCTCAGCTCCACTGGCAGA Y 2 1 2 1 101000 f 74 goat snp11598-scaffold1423-2053940 9 70236103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407650 Affx-122954611 AX-123278001 9 69784868 ATTTCCATTAAGCATGGAAAACCACAGCAGTCATT[C/T]AAGGGTAGTATAAAGGGGCAAATGAACTCTGAATA Y 2 1 2 1 101000 f 74 goat snp8460-scaffold1304-2050544 9 70355759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797212 Affx-122975350 AX-385284151 9 69815705 TTTTCTGCAAAATTCTCTCAATGATGTACACTATG[A/G]GATGAGGTAAGAACCACATCATGAGCAAATGATGA R 2 1 2 1 201000 f 74 goat snp8459-scaffold1304-2019707 9 70388450 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275405 Affx-1111834781 AX-519548978 9 69895973 CAAAAGCTGCAGTGAGCACTCAGTGGCTTACAGCA[A/G]AAGTCACTTGTTTTGCTCACTTGAGGTGTATGGGT R 2 1 2 1 201000 r 74 goat GoatD01.052629 9 69895973 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38394075 Affx-122964967 AX-123264430 9 69899245 TAAAGGTAAACAGAATTCTTAGAGATTTGAAAAGA[C/T]GTCATACAAAAAATAATGAATCTACTAAATCAAAG Y 2 1 2 1 101000 f 74 goat snp8458-scaffold1304-1936167 9 70472878 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773226 Affx-122939632 AX-385260369 9 69953030 TTATAGCTAACATGTATTGGTTTAATAATAATGTA[A/G]GGAGATTCTGTTAAGTGTTTAAAATCTATTACCTC R 2 1 2 1 101000 r 74 goat snp8457-scaffold1304-1882382 9 70526734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782004 Affx-122929531 AX-385269083 9 69986301 TATTCTCATTTCAATGATAATGCTTCTGACCTTAA[C/T]ATTTTTCCTTTCATGAATGAAATACACTCTTGCAT Y 2 1 2 1 101000 r 74 goat snp8456-scaffold1304-1849111 9 70559694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413632 Affx-122950548 AX-123283981 9 70018970 ATATTTATAATTGAATTTTAGAAAGCATCCATTCC[A/G]TTTCCAATGATTTGCTTTGTAGAGCCCATTGGACA R 2 1 2 1 101000 r 74 goat snp8455-scaffold1304-1816442 9 70592308 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387231 Affx-122970578 AX-123257589 9 70050100 AGAATCAACAGATAGTATCAAAGGGTTATCATTTA[C/T]GTAACATTTCAAGTTAACTTATTTCACCTGTAGGT Y 2 1 2 1 101000 f 74 goat snp8454-scaffold1304-1785312 9 70623585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399509 Affx-122961165 AX-123269864 9 70093654 TAAAATCAAGGACAACCAAAACATGATAGAGAAAA[C/T]AGTCAAACTAAGATTAGTTGGTGAATATCCTTTGA Y 2 1 2 1 101000 f 74 goat snp8453-scaffold1304-1741758 9 70667197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407505 Affx-122954744 AX-123277856 9 70136645 AACTGGAATCACCAGATACACTCACAACTGCTCAC[A/G]TAGACGGGAGCAGCATAAAAATTCACAGGTGGATT R 2 1 2 1 101000 r 74 goat snp8452-scaffold1304-1698767 9 70709806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441639 Affx-122929207 AX-123311976 9 70190093 GTGCTTCATTATGACACTTGTCAATTGATGTCAAA[C/T]AGCTCTTTTCCAAGGGCACAGTTCTGGGTCAGACT Y 2 1 2 1 101000 f 74 goat snp8451-scaffold1304-1645319 9 70763152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377490 Affx-122977496 AX-123247849 9 70235242 AGCAACAAACTACTAAACATGTGAACTCCTGGGAT[A/G]CTCATTTAACCATAAAGGACTCAAGAAAGAAAAGA R 2 1 2 1 101000 r 74 goat snp8450-scaffold1304-1600170 9 70808636 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767061 Affx-122957349 AX-385254350 9 70333153 ACTGTGTTCCTTTCTTGTCAGTTTCTTTGCTGTAC[A/G]TGTGTAAGCAATTTTTATGTCTGCACTTCCATTTA R 2 1 2 1 101000 f 74 goat snp8448-scaffold1304-1502259 9 70907281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782575 Affx-122924799 AX-385269649 9 70363283 CACCTCCCTAGTAGCCAGTTCTGAAAGCCTTCTTG[C/T]AGCTGACTGAAATAAGCTGTAACATATCTATGCTT Y 2 1 2 1 101000 f 74 goat snp8447-scaffold1304-1472129 9 70937396 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394351 Affx-122964656 AX-123264706 9 70413470 AAGCAAATGGCTTTCTAGAAGAGGAAACAGCCAGA[A/G]CAAAGGCCCTGGGGTACGTATTCCAGGATGTGAAA R 2 1 2 1 103000 f 74 goat snp8446-scaffold1304-1421942 9 70987958 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444868 Affx-122926283 AX-123315205 9 70456583 GATAATTTACTATGATTGTCTGGGTAGGTAGACTC[A/G]TAGGGACATTTCATTTACTAATTTAAACATTTTAA R 2 1 2 1 101000 f 74 goat snp8445-scaffold1304-1378829 9 71031168 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389680 Affx-122968707 AX-123260038 9 70527250 ATTAGTATATTTTCTAAATCAAGAAAATACTCTTA[C/T]GCAGTCAGAGAGGCTCTGAAAAACTTTCTGTTTCT Y 2 1 2 1 201000 f 74 goat snp8443-scaffold1304-1308162 9 71102228 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427206 Affx-122939589 AX-123297549 9 70572106 ACTGATTTAACTTGTGTGCAGAAAAGTGAAAATAA[C/T]AAGACCACAGAAAGAAAATAAGGTTACTAAAATGA Y 2 1 2 1 201000 f 74 goat snp8442-scaffold1304-1263306 9 71147450 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783169 Affx-122944546 AX-385270236 9 70602936 ATAGCATTAATAATCCTTTCCCTAGTGTTCTGTGC[A/G]TAATAAATCTTAAAGTTCCTTATTGTTACCAAGTC R 2 1 2 1 101000 f 74 goat snp8441-scaffold1304-1232476 9 71178463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417505 Affx-122946954 AX-123287853 9 70654494 CGCCCAAGAACTCCTCATACCATCATATGTATGTG[C/T]GAGTTGTTCAGTCGTGTCTGACTCGTCACAATCCT Y 2 1 2 1 103000 f 74 goat snp8440-scaffold1304-1180918 9 71230093 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779381 Affx-122924071 AX-385266485 9 70687025 ATGAGATTCAGAACCTGATGCAGATTTATGCTAAC[G/T]CTCCAAATGATTGGGCTGATTGCTCTTTGATTGAC K 2 1 2 1 101000 f 74 goat snp8439-scaffold1304-1148387 9 71262738 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777838 Affx-122923821 AX-385264955 9 70750031 GATTAAACTCCAACAAAAGAGAGTTTAATGCAGGA[C/T]GTAATTTACTTGGGTAGGGAACAGAAAGGGTATTA Y 2 1 2 1 101000 r 74 goat snp8438-scaffold1304-1085381 9 71326108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770584 Affx-122960592 AX-385257748 9 70790219 TCTTGTGGCAGTTGTGTAGTTTACATTTAGGTCTC[A/G]CACCTTATTATGTACACAATTTTAATTTATCTTGG R 2 1 2 1 101000 f 74 goat snp8437-scaffold1304-1045193 9 71366514 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787866 Affx-122968815 AX-385274890 9 70824979 GGCCTGTAAGATTTTCACAGTGCTCTGTGAAAATT[A/G]CTTTTCAACTCCACACACTGCTGTATGGGTATAAA R 2 1 2 1 101000 f 74 goat snp8436-scaffold1304-1010433 9 71401588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402527 Affx-122958478 AX-123272880 9 70862517 CACCCACATAATTTCCTCCACCCTGATGAGATTCC[A/G]TAGGAGAGGCTTCAGAGAATATCAAGGCTAAGATA R 2 1 2 1 101000 f 74 goat snp8435-scaffold1304-972895 9 71439314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439690 Affx-122930576 AX-123310027 9 70918789 ATCACGTTGTCTCATGGTTCCATGGGAATCTACCA[C/T]GTCCAATATATATAACCTTGTCTGTACATTTACTT Y 2 1 2 1 101000 f 74 goat snp8434-scaffold1304-916623 9 71495545 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421662 Affx-122944434 AX-123292009 9 70960823 TACTATCTCAACAGTTTCATCTGAAAAGTGAAGAT[A/G]CTCGTAGTATCCTTATGGAGTTCTTATGATAATTA R 2 1 2 1 201000 r 74 goat snp8433-scaffold1304-874589 9 71537556 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448954 Affx-122923137 AX-123319289 9 70999592 AGATAATTTGGGAAAGAACCATTTAGACATACTGT[A/C]TTAGAAACTCACAAACTGAGATCTAGCCTGGTCAG M 2 1 2 1 101000 r 74 goat snp8432-scaffold1304-835820 9 71577149 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798804 Affx-122958330 AX-385285735 9 71035597 GATTAAATCCACAGGGAGAAGGGAGGTGAAAAATC[A/G]TACGGTAATCTAAAAATATGTTATAAAGGCATTAA R 2 1 2 1 101000 f 74 goat snp8431-scaffold1304-799815 9 71612927 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793792 Affx-122971703 AX-385280764 9 71095916 CCTGTTTACATCACAATGACCTCAAGAACCTAACC[A/G]TTCTCTATTTCATCTTCTTAATCAACATGAGTTCT R 2 1 2 1 201000 r 74 goat snp8430-scaffold1304-739496 9 71672760 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796665 Affx-122923778 AX-385283611 9 71133502 CTATCACACATTATTTTACTAGCTATTGGAACTAA[C/T]AATATCAATTTCTACCTCCCATGCTAGAATATAAA Y 2 1 2 1 101000 f 74 goat snp8429-scaffold1304-701910 9 71710720 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397272 Affx-122962343 AX-123267627 9 71182541 GGTACGCAGAGCTAGAAATCACACCACGTGTGTGA[C/T]GGGGTTCTCTTGATGCTGGTTCTGGTGGTCTTTTA Y 2 1 2 1 103000 r 74 goat snp8428-scaffold1304-652871 9 71760038 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797360 Affx-122940226 AX-385284299 9 71231879 GTAGAGTGCTAAAAAAAATACAGGTGTCAAATCAA[C/T]AGGTTCATCTCTAGTCTCATAAAGTTATGCTCTAA Y 2 1 2 1 101000 f 74 goat snp8427-scaffold1304-603533 9 71810877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423546 Affx-122942430 AX-123293892 9 71268749 TTTGGCATGTGTACAAGAATGCCACAAGCACTAAC[A/G]TAGTTTAGTGTCTCTGTCTTAATTGGCATTAATGT R 2 1 2 1 101000 f 74 goat snp8426-scaffold1304-566663 9 71847898 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388877 Affx-122968867 AX-123259235 9 71304622 TTTTTGCTGTCAAGGCCCTTTTCCATTCTTTCTGT[A/G]TCTTTATATTTATCTTTATATCACTTACATCTTTA R 2 1 2 1 103000 f 74 goat snp8425-scaffold1304-530790 9 71884124 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276318 Affx-1111835358 AX-519549851 9 71354902 GGAGCATGGGCTGTAGGGCATACCATGCAGCCTTC[A/G]GTAGTTGTGGCACACTGACTTGGAAGTTGTGGTTC R 2 1 2 1 202000 f 74 goat Random2.2K-1011 9 71354902 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382040 Affx-122974944 AX-123252398 9 71363179 CCAACTAACCAATAGGGCCAACCTCATTCACATTC[A/G]CCCTGAGCCCTGCACCCAGATAAGCAAGAGGGCAG R 2 1 2 1 101000 f 74 goat snp8424-scaffold1304-472233 9 71943009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414584 Affx-122949370 AX-123284933 9 71398304 CATACATAAACAAGCATTTAGTCTCCTTGTTAGAA[G/T]GATAAATTATCCACAAAACTTAAGAAAAAAAGGAA K 2 1 2 1 101000 f 74 goat snp8423-scaffold1304-437108 9 71977692 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432680 Affx-122936043 AX-123303021 9 71431408 ATACAGAATTAGCCCTGAATTTGGGGGGCAACTCC[A/G]TTGAGCCAGTACCCAACACTCAATGGAATCTTGAG R 2 1 2 1 101000 f 74 goat snp8422-scaffold1304-404004 9 72010650 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773889 Affx-122935880 AX-385261028 9 71463624 TCTATTTAGAAACTAAGTTTGGGAGAATAGTAAAC[A/G]CTCCCGTAATCTAACCATTTTTCATCATCAGTGTT R 2 1 2 1 101000 r 74 goat snp8421-scaffold1304-371788 9 72042742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276474 Affx-1111835359 AX-519549986 9 71472034 AGGAATATGCACTAAACACATCTATAATGAGCTAC[A/G]TTGCACCGCTTCATTCACGAATTCCCTGACAACAC R 2 1 2 1 101000 r 74 goat Random2.2K-1012 9 71472034 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450117 Affx-122922769 AX-123320452 9 71501466 TTCTCTCAAGCTGTAGCCGTGTGCAGCTAGCTGTC[A/G]TCCATTTATAGGAGAGGGAAGAGAGAACGTAGCTG R 2 1 2 1 102000 f 74 goat snp8420-scaffold1304-333946 9 72080597 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442219 Affx-122928778 AX-123312556 9 71566076 ACCTGGGTAAACTATAACCCTGTCTGGGTCTGGAG[C/T]AATGTGCATTGTCTTTTGAGCTTTATTTATTTTAT Y 2 1 2 1 201000 r 74 goat snp8419-scaffold1304-269336 9 72145944 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447577 Affx-122924023 AX-123317913 9 71612939 ACAACAGAAGTCTGGAAGAATAGAAGGGAGCAGAG[C/T]GTGCTTGTGCAAGTGTGTGGGGGCAAGGAGGGAGG Y 2 1 2 1 101000 f 74 goat snp8418-scaffold1304-222473 9 72193875 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438543 Affx-122931185 AX-123308881 9 71663191 GCAAAGGATTGTCAGGGCATCAAGAGTGCTTTGCC[A/G]TGAACTAGTAACAGGATATGGAAGGGAGTGCTGTG R 2 1 2 1 101000 f 74 goat snp8417-scaffold1304-172221 9 72243899 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392781 Affx-122965984 AX-123263138 9 71730026 CTCAACATGATCATCTACATAAAGCACCCCCATAA[G/T]CATATTAAGATTAAGGAAAATATGTATGAAACGTT K 2 1 2 1 102000 f 74 goat snp8415-scaffold1304-105386 9 72310588 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275583 Affx-1111834890 AX-519549153 9 71745262 CTTGGACTAATGGTACCTGCAGTCACATTATTGTT[A/G]AAGGAACACAGAGGTGACTACCTTTTCTAACTGCA R 2 1 2 1 101000 r 74 goat GoatD01.057593 9 71745262 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407793 Affx-122954950 AX-123278144 9 71798381 TTCATTGGAATTTCCTACTGATTTCCACTGTCTCT[A/G]TGGAGAATATCCTGGCTTTATTTTTCACACTGGTC R 2 1 2 1 101000 r 74 goat snp8414-scaffold1304-37031 9 72378859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389499 Affx-122968309 AX-123259857 9 71828259 GAGGGATGAATTGTCTGTTGCCTTAAACTGACTGG[C/T]ACAGAATTTTAGAACTTCTCACCCATGTTGGTGGG Y 2 1 2 1 101000 f 74 goat snp8413-scaffold1304-7153 9 72408601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445983 Affx-122925883 AX-123316320 9 71895327 TCTTATATGGGGATGTGCCTTGGATACCCTTAAGT[A/G]TCTAGATGCCCTTGCGTTTTTAAAAAAATATGACT R 2 1 2 1 101000 f 74 goat snp22940-scaffold2290-59816 9 72475167 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444802 Affx-122926336 AX-123315139 9 71924270 GCATGGCATCGATTCCAGAAACAGTGCTCCAAGCA[C/T]ACCAACACTCAGACCTGACTTCTCAGGAGGAGAAG Y 2 1 2 1 201000 f 74 goat snp22941-scaffold2290-88759 9 72503750 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406839 Affx-122955670 AX-123277190 9 71970568 CGCCACCATTCCATTCCTGACAGGTTGACTTCACA[C/T]TGAGAACATAGGCAGGTGTGATGCCCCGTTGGTGG Y 2 1 2 1 101000 f 74 goat snp22942-scaffold2290-135057 9 72549476 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418114 Affx-122947128 AX-123288462 9 72069328 CCAGGCTGCTATCTCTAGTTGGTATAAACAATAGC[A/G]TAAATGCAGTCTCTGGTACTCAAAAGTCTGATTCC R 2 1 2 1 101000 f 74 goat snp22944-scaffold2290-233817 9 72648614 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449346 Affx-122922975 AX-123319681 9 72106616 CGAAAAGGGACATCAGAGTCTAGCTATTTGCAGGC[G/T]CCCCCACCACCTCCTCATGTCAACCTTTGTTTTAG K 2 1 2 1 101000 f 74 goat snp22945-scaffold2290-271105 9 72681043 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385527 Affx-122971247 AX-123255885 9 72136586 GATCCGTCTTGTTCATTGCTCCATGGAGAATCCCA[C/T]GGACGGAGGAGCCTGGCGGGCTACAGTCCATGGGG Y 2 1 2 1 103000 f 74 goat snp22946-scaffold2290-301075 9 72711157 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397475 Affx-122962087 AX-123267830 9 72165542 GGGGTGACCCTTAGATTTTCATGGCCGACAGTGGA[C/T]AATATGAGATGAATTTTGTTTCATTTCATTTCGGT Y 2 1 2 1 103000 f 74 goat snp22947-scaffold2290-330031 9 72739665 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400925 Affx-122959724 AX-123271278 9 72204895 GCATCAGTGAAGGAGAAACGTCCTGCATTTACTCT[A/G]GTGGCTAAACCGGAAAGAATAAAAAGCAGGGAGAG R 2 1 2 1 201000 r 74 goat snp22948-scaffold2290-369384 9 72779268 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273446 Affx-1111833622 AX-519547070 9 72214728 ACTCAGGAGGACCTGAAATCCATTAATAGTTACAA[A/C]ATGGGGGAGGGAAGGATGGTAAGGGTCTGTTTTTT M 2 1 2 1 303000 f 74 goat 9_72214728_AF-PAKI 9 72214728 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38385036 Affx-122971851 AX-123255394 9 72292662 CCAAAGGGTCGTGTCATACTCAGTTTGGGCTGCTA[C/T]ACCACAATACCATAGGGCAGCTTGTAAACAACAGC Y 2 1 2 1 201000 r 74 goat snp22950-scaffold2290-457151 9 72866926 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410217 Affx-122952562 AX-123280567 9 72325360 GTTCGATCAATGTGCTTGGTGTGTGATAGGCCTAT[A/G]CTAAAGGCTTGTTTTGCCATGAGTCCTAATTGGAA R 2 1 2 1 101000 r 74 goat snp22951-scaffold2290-489849 9 72900576 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795549 Affx-122921824 AX-385282504 9 72457729 AGACCCCAATTAGAGAGGTCCAAGGGCCCTAAACT[A/G]TCACCTCATTTACACAGAGTGTGTTAAACCTTAGT R 2 1 2 1 101000 r 74 goat snp22954-scaffold2290-622218 9 73033529 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431937 Affx-122935980 AX-123302278 9 72487116 GAGGGTGCCCAGGGATAAAGTGAATATTTCAAGTT[A/G]TACTCTGGGATTTTCTTCTTTTTTAGTTATTAAAT R 2 1 2 1 101000 f 74 goat snp22955-scaffold2290-651605 9 73063631 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38392190 Affx-122966292 AX-123262547 9 72538571 TAGTGTGATCCCACGTCTTAAAACTTGTATGCATA[C/T]GTCTGTGTGTACACAGAGAGAAGCCTGGGAGAATA Y 2 1 2 1 201000 f 74 goat snp22956-scaffold2290-703060 9 73114747 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438847 Affx-122930768 AX-123309184 9 72698675 CAAATTCTGGTCAACCCCCCTGGCATTCCATAGCA[C/T]GATTCTAAAGGAATGTTAAAATGACATTTTCCTGT Y 2 1 2 1 201000 r 74 goat snp22959-scaffold2290-863164 9 73270021 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770674 Affx-122921922 AX-385257838 9 72752456 AGGAATCATTATAGACTGAAGATTCAGTAAGATAA[C/T]AAGAGAACAATCTGTCCTGTTTCAATCCCATTGAT Y 2 1 2 1 101000 r 74 goat snp22960-scaffold2290-916945 9 73323784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273640 Affx-1111833715 AX-519547253 9 72780595 TCAGCAAGGTCTCCAGCGGTCCCCCAAAGGGTTCT[A/G]GTTGCTCCGTGCAAGTTCAGATTAGTCTTTATTAC R 2 1 2 1 201000 r 74 goat GoatD01.002285 9 72780595 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38420718 Affx-122944777 AX-123291065 9 72783658 GGTTTGTGCGTGTACCACAGTGCCAGATAAGACAG[C/T]GCTTCCTATTATATTGGGTTGGCCAAAATGTTTGT Y 2 1 2 1 101000 f 74 goat snp22961-scaffold2290-948147 9 73354997 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396567 Affx-122962925 AX-123266922 9 72855988 TCAAATCGCATGGATTTTTCCCCATAAATCTTCCT[A/G]TCTGTACTGTCAGATGCTGACATGTGCGTCAGTGG R 2 1 2 1 201000 r 74 goat snp22963-scaffold2290-1020477 9 73427846 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399705 Affx-122960478 AX-123270060 9 72951564 AATTAATTTAAATACAAATAGCTACCGGTAGCTAG[C/T]GGCTACACAGTACTAGACTAAAAGGCTCTTGAGTG Y 2 1 2 1 101000 r 74 goat snp22965-scaffold2290-1116053 9 73523552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800582 Affx-122967350 AX-385287501 9 73123090 CCCTGGGACAATGGGAGAAATCTGAGTATGTGGTA[C/T]GTAATATGAGATTGTTGTTTTCAGTGTGACAATAC Y 2 1 2 1 101000 f 74 goat snp22969-scaffold2290-1287579 9 73695390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780067 Affx-122973345 AX-385267165 9 73167600 CGGTCAATAAGACAAATAAAAATGGGGCCTTACAG[C/T]AAAACAGTACCCACTTATCTGTGTTACAAAATGTA Y 2 1 2 1 101000 f 74 goat snp22970-scaffold2290-1332089 9 73740928 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401912 Affx-122958828 AX-123272265 9 73207137 TTTTCCTAGACAATACCAGGGAAGCCAGTAAAAAA[C/T]AAGTTGTTTGATATATTTTATAAACTACACTATAA Y 2 1 2 1 102000 f 74 goat snp22971-scaffold2290-1371626 9 73781210 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787291 Affx-122948610 AX-385274316 9 73242133 TTATTATTTTTTAATCTCAGAGTCAAAATATGAAA[G/T]ATCTTAGCTTTTAGTACTAAAACTTTTAATTTATG K 2 1 2 1 201000 f 74 goat snp22972-scaffold2290-1406622 9 73816312 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417899 Affx-122946744 AX-123288247 9 73276211 AATTTCTCTCTATATTAAGAGGTTTACTCTTGTGA[A/G]GCTGAGGGAGAAAAGAGCAGGGAAAGAAGAGAGGG R 2 1 2 1 101000 f 74 goat snp22973-scaffold2290-1440700 9 73850464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444648 Affx-122926469 AX-123314985 9 73328395 GGAATACACAGCTGTGAATTTGACCATTCTAGTGG[A/C]ACTTACAGTCAGGTAGAGGATCCAAAAAATCAAAA M 2 1 2 1 201000 r 74 goat snp22974-scaffold2290-1492884 9 73903334 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431723 Affx-122936754 AX-123302064 9 73365307 CCTTTTTCTATTTACTTTTCATCACAGATATGACC[C/T]AAAATTTCATAAAAGAAGCAAAATGAACTCAATTG Y 2 1 2 1 101000 f 74 goat snp22975-scaffold2290-1529796 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430798 Affx-122937465 AX-123301139 9 73398932 TAGATCGCTTCTTTTCTGCTCCTGCCCTTCTCAGC[A/G]TGGTTCTTTCTCTATGCTGGTTGTAGAGGGGATGT R 2 1 2 1 102000 r 74 goat snp45588-scaffold623-669903 NW_017189711.1 2861 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452523 Affx-122920549 AX-123322856 9 73446853 TGTTTTGCTCACCACTGTGCTGAGTGCTGGAAATA[C/T]ATTGCTGAGTGAGACAGACACAGTCCCTACCCATG Y 2 1 2 1 201000 r 74 goat snp45587-scaffold623-621982 9 74598659 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406108 Affx-122956213 AX-123276460 9 73481532 TATGCTTAAAAAATCCCTCCATATCCCCCATTCCT[A/C]TCAGGCTAAAGTACGAACAACCTCGCATTGCACAC M 2 1 2 1 201000 r 74 goat snp45586-scaffold623-587303 9 74633347 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435735 Affx-122933290 AX-123306074 9 73523944 AATGAGGAGCTTTTGAGATTTTCCTGAATGTGTGG[A/C]TTCCTTTCTGCAATTCTGGATGAAATATTAAACTA M 2 1 2 1 201000 r 74 goat snp45585-scaffold623-544891 9 74673861 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415137 Affx-122949420 AX-123285486 9 73601474 CAGAGTTCACAGCCCAGTGAAGAGGCGTAAGTAAA[C/T]AGGCAGTGATAAGATGCTGGGGTAGGTGGTGTGAA Y 2 1 2 1 201000 f 74 goat snp45583-scaffold623-467361 9 74750937 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768651 Affx-122938621 AX-385255829 9 73680324 AAACACCCAAGGTCTTGCACTTGGAAAAACCAGAG[A/C]TGAGACATGAACTGAGATGTGATCCCAGCTGGCAT M 2 1 2 1 101000 f 74 goat snp45581-scaffold623-388511 9 74829658 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400454 Affx-122959952 AX-123270809 9 73728744 TTTAATGACATCTTAACTGGTCTTCCTTAATCTAC[A/G]CTTACCCATCTTCAGTATCATTCTTCATGCTTCAG R 2 1 2 1 101000 f 74 goat snp45580-scaffold623-340091 9 74878071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375893 Affx-122978491 AX-123246252 9 73762842 GGAGGTGAGCAACCAGCTCACAAACTGGAGCAAAT[G/T]CCTGACACTGAACAAAAGAAAGTGTCATCGAATCT K 2 1 2 1 201000 f 74 goat snp45579-scaffold623-305993 9 74912117 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774390 Affx-122978442 AX-385261526 9 73798672 ATCACACTAATATTGGTGCTTATGAACACTTGCTA[C/T]ATTCTACATGCTTCCAGACATTTCCTCCATAGGAA Y 2 1 2 1 101000 r 74 goat snp45578-scaffold623-270163 9 74947785 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779741 Affx-122959382 AX-385266841 9 73851188 GACATGACCTTCCTTCTGGGAGAAGTTTTAGTTCC[A/G]CATTTTGTACTGGGTTTTCCTAAACACCCCAGGGA R 2 1 2 1 101000 f 74 goat snp45577-scaffold623-217647 9 75000446 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387124 Affx-122970659 AX-123257482 9 73899096 ACAGCCTTAGGCCAAAGCACTGGCAATGATTAACA[C/T]GCTGGGCGCTTCACAGATGGGGTGTCTGGGGGGAC Y 2 1 2 1 101000 f 74 goat snp45576-scaffold623-169739 9 75048516 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392957 Affx-122965688 AX-123263314 9 73934917 AACTAGAGTAATGTTTACACCCTTCAGACAAGAAC[A/G]TGACCACATAGTTGGGTTCAGAAAATGCTAGCAAG R 2 1 2 1 101000 r 74 goat snp45575-scaffold623-133918 9 75084374 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762739 Affx-986697269 AX-385250796 9 73958146 CACTGAAAACAGTGAATCATGGGAATAGGTTGAAA[C/T]GTCAATATTAATGTGAGTATGGGAGAAGTAGATTT Y 2 1 2 1 600010 f 74 goat 9_73958146 9 73958146 Ancestral_priority_1043 ancestry 0.634 recommended IMAGE 10K 10K ancestral 320803709 Affx-986696189 AX-385290471 9 73958152 AAACAGTGAATCATGGGAATAGGTTGAAACGTCAA[C/T]ATTAATGTGAGTATGGGAGAAGTAGATTTCTCCCT Y 2 1 2 1 600010 r 74 goat 9_73958152 9 73958152 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320762741 Affx-986697271 AX-385250797 9 73989924 TTATTGACTGACTACATGTTCAGTTACTGCTTGTT[C/T]TCTAGTGTTAATGAATATGTTATCTGTCCAGGATC Y 2 1 2 1 600010 f 74 goat 9_73989924 9 73989924 Ancestral_priority_1043 ancestry 0.546 neutral IMAGE 10K 10K ancestral 320765210 Affx-986697273 AX-385252749 9 73989926 ATTGACTGACTACATGTTCAGTTACTGCTTGTTCT[A/C]TAGTGTTAATGAATATGTTATCTGTCCAGGATCAT M 2 1 2 1 600010 r 74 goat 9_73989926 9 73989926 Ancestral_priority_1043 ancestry 0.692 recommended IMAGE 10K 10K ancestral 38390727 Affx-122967922 AX-123261084 9 74004552 AAGGATAGGAAGGGGTGCTTTGCAAAAATGTTCTT[A/G]TTCAAACAAGAGGTGAGGGGTTGAAAGAGGATCAA R 2 1 2 1 101000 f 74 goat snp45574-scaffold623-64283 9 75153568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803711 Affx-986696190 AX-385290473 9 74006719 ACGAAATCCTACTCAGCATTTCTAAAAAAAAAAAA[A/C]CAGAAACAATTTATTTCACCACTTTCTCCTGGTGC M 2 1 2 1 600010 r 74 goat 9_74006719 9 74006719 Ancestral_priority_1043 ancestry 0.494 neutral IMAGE 10K 10K ancestral 320803142 Affx-986696191 AX-385290006 9 74015383 GCAAGGCCCTAGCTCACTTCAAGTCTATGAAGGCT[A/G]AAGGAGGTGAGGAAGCTGCAGAAAAAAGAGCTGAA R 2 1 2 1 600010 f 74 goat 9_74015383 9 74015383 Ancestral_priority_1043 ancestry 0.626 recommended IMAGE 10K 10K ancestral 320762749 Affx-986697279 AX-385250805 9 74015441 AAAAAGAGCTGAAAGCCTGTAGAGGCTGGTTCATG[A/T]GTTTTAAGGAAAGAAGCCATCTTTGTAATATAAAG W 4 1 2 1 600010 f 74 goat 9_74015441 9 74015441 Ancestral_priority_1043 ancestry 0.544 neutral IMAGE 10K 10K ancestral 320762751 Affx-986697281 AX-385250807 9 74015516 GAGTGGAAGAGAGAGGGTTGATGCCGAAGCTGCAG[C/T]AATTTATCTAGAATATCTAATAAAATAATCTCTGA Y 2 1 2 1 600010 f 74 goat 9_74015516 9 74015516 Ancestral_priority_1043 ancestry 0.496 neutral IMAGE 10K 10K ancestral 320803715 Affx-986696192 AX-385290477 9 74015521 GAAGAGAGAGGGTTGATGCCGAAGCTGCAGTAATT[C/T]ATCTAGAATATCTAATAAAATAATCTCTGAAGATG Y 2 1 2 1 600010 r 74 goat 9_74015521 9 74015521 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 320762720 Affx-986697250 AX-385250784 9 74016154 GCAAAGTCAATTGAAAACTTTCTAAAGCGAATTCA[A/G]GATTACAAGTTCCACTCAAAACATTCGTGATTCAT R 2 1 2 1 600010 f 74 goat 9_74016154 9 74016154 Ancestral_priority_1043 ancestry 0.736 recommended IMAGE 10K 10K ancestral 320765172 Affx-986697252 AX-385252723 9 74016170 ACTTTCTAAAGCGAATTCAAGATTACAAGTTCCAC[C/T]CAAAACATTCGTGATTCATGAACAGAGGTTGAAAT Y 2 1 2 1 600010 r 74 goat 9_74016170 9 74016170 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 320765175 Affx-986697254 AX-385252726 9 74016323 AAGTAACTATAGATGTGGTGAAAATAGCAAGAGAG[C/T]TAGAATTAAAGTGGAGCCTAATGTAAAGATGGGAC Y 2 1 2 1 600010 r 74 goat 9_74016323 9 74016323 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320797779 Affx-122934360 AX-385284718 9 74088701 AATTGGGTTTTGACATCTCATAATTGACAACTGAC[A/G]TCTGTAAACCTGAAGATAGAAAATGTGATAGATAC R 2 1 2 1 101000 f 74 goat snp37014-scaffold448-4895195 9 75239216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419047 Affx-122946021 AX-123289395 9 74133963 ATTATTCCTACAGTGCCAAACAAAGCAAAGGAGGC[A/G]TTATCAGGTTCAATAAGTCTAAAAAGTGGCATAAA R 2 1 2 1 201000 r 74 goat snp37013-scaffold448-4849933 9 75285557 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449417 Affx-122922692 AX-123319752 9 74164752 GACCCCAAAAAGGAAATCATTGCCTCACCAGCCCC[A/G]CTGCCTATGTAGAGGCCAGGCCCCACCCGGAGGGC R 2 1 2 1 202000 r 74 goat snp37012-scaffold448-4819144 9 75316067 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779294 Affx-122951562 AX-385266398 9 74197112 TATGAACTGTTTAAGTAATAAGTGGAATATATAAC[A/G]CTCCTATAGGTTCTTCAATTGTAATTGTTACAATT R 2 1 2 1 201000 f 74 goat snp37011-scaffold448-4786784 9 75348261 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436511 Affx-122932948 AX-123306849 9 74230591 ATATTCCTTTGAAAGTATTCAATTTGGAATGAACA[C/T]AGCTACAAGTCATTTTCTTCCCCTTTACTATACTT Y 2 1 2 1 201000 f 74 goat snp37010-scaffold448-4753305 9 75381426 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439467 Affx-122930169 AX-123309804 9 74277091 GCAGAATCTGATATTCAACATGAAAATGCATGAGA[C/T]GGAGCAACTATAAATTGAGTGTTCTGCTTTTAAAC Y 2 1 2 1 101000 f 74 goat snp37009-scaffold448-4706805 9 75427626 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441896 Affx-122928616 AX-123312233 9 74312735 TTTGCTATTAATTTCTCTGTTTTGATCCCATCACT[C/T]AGGTCGAGGACCAGTGTTAGCACCTGTGATGTCTA Y 2 1 2 1 101000 r 74 goat snp37008-scaffold448-4671161 9 75463057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391017 Affx-122966883 AX-123261374 9 74342918 GTCTGGAAGGCACGTTCACCCGGTATCACCAGAAG[A/C]GGACTGGTGATCAAATGCAGACAGCAGACCCCGAG M 2 1 2 1 101000 r 74 goat snp37007-scaffold448-4640978 9 75494694 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375852 Affx-122978522 AX-123246211 9 74371462 ATGTATGTAAAATTACATATGTAGATCTGTATGCC[C/T]GTCTATGTATAGAATGTAAGTGGAGATTATCACTA Y 2 1 2 1 101000 r 74 goat snp37006-scaffold448-4612434 9 75523935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398839 Affx-122961384 AX-123269194 9 74430725 ACAAGCTCCCCAAGAATGAGACCACATTTTATACC[A/G]TTTTGTTTCCCCATGACTTATCATCATCCAAGAAA R 2 1 2 1 201000 r 74 goat snp37005-scaffold448-4553171 9 75582881 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449792 Affx-122922424 AX-123320127 9 74503406 CCATGCACGACAACAAAGGACCCAGTGTGATGAAA[C/T]GAAGATCCTGTGTGCTTCAATTAACCAAATAAATA Y 2 1 2 1 101000 f 74 goat snp37004-scaffold448-4480490 9 75655762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403544 Affx-122957602 AX-123273897 9 74550189 CTTTTTCTGGGATGGGAGAGCTACCTCTTCAAGCC[A/G]CTGGTCTTCTACCCTGGAACCTTCTATGCTAGTGG R 2 1 2 1 201000 r 74 goat snp37003-scaffold448-4433707 9 75702726 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391856 Affx-122966990 AX-123262213 9 74601042 TTTAATGTTCTGTGCAAAATCGTGGTAAATATGGT[A/G]CACTAGCACATGTCAATCAACCCAGACAGGCATCT R 2 1 2 1 101000 f 74 goat snp37002-scaffold448-4382854 9 75753910 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380185 Affx-122975508 AX-123250543 9 74657312 ATATGGATGCAGTACTTTGGGAGTCTTTGCTCCCA[C/T]GTGTTGAAGTTCTTGAAGGACCAATGTTAAATATT Y 2 1 2 1 101000 r 74 goat snp37001-scaffold448-4326584 9 75810387 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380548 Affx-122975291 AX-123250906 9 74763181 TTCTGGGTGAAGTAGGAAACAAGATTATTGGCTGA[C/T]AGTGAAGAAGGAGGACACAAGGTAAGAGCCTTGAG Y 2 1 2 1 201000 f 74 goat snp36999-scaffold448-4220715 9 75916474 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413664 Affx-122950114 AX-123284013 9 74796564 TGCCTACCACATAGGAGGTGCTTATTATATGACAT[C/T]TATCACCATTTTAAATAAAAATGTTATAAGCACAT Y 2 1 2 1 101000 f 74 goat snp36998-scaffold448-4187332 9 75949926 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439071 Affx-122930311 AX-123309408 9 74828125 TCCAAAACCTCCTAGCTAGAGCTGGATCAAATAAA[C/T]AGGCGTTATCTGGAGCAAGCAGACAGCCTGTCAGT Y 2 1 2 1 101000 f 74 goat snp36997-scaffold448-4155771 9 75981632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779434 Affx-122922042 AX-385266537 9 74887036 TTCTGGAAAATATTGTGAAGTTATACCTGTGTCTC[A/G]TATCATCGTTTGTGTATATGTAGGATGCTTACTCT R 2 1 2 1 101000 f 74 goat snp36996-scaffold448-4096860 9 76040666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275459 Affx-1111834814 AX-519549032 9 74887896 CCCTACTTTCTGCAGAAGTTCA[A/G]TCTTTTAGAAGGAAACTCATCTCCTACAATCAAGT R 2 1 2 1 101000 r 74 goat GoatD01.054562 9 74887896 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276323 Affx-1111835360 AX-519549856 9 74892310 CACCCCAGCTGACTTCTCGTCCTTGTTTCGCCTTC[C/G]CCACCATACTCCCGGTTTCTCCTGAGGGCATCTTA S 4 1 2 1 201000 f 74 goat Random2.2K-1016 9 74892310 G C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272342 Affx-1111833623 AX-519546073 9 74913084 ATGCTGGGAAAGATTGAGGGCAAGCGGAGAAGAGG[A/G]TGACAGAGGATGAGATGGTTGGGTGGCATCACTGA R 2 1 2 1 303000 f 74 goat 9_74913084_AF-PAKI 9 74913084 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413966 Affx-122950299 AX-123284315 9 74925634 GTCCCCAGAACTGGGGTACAGGGTGTGAATCAGAA[A/G]CACCATACACGAGCTTCAAAAGGCTGCCAGATCCA R 2 1 2 1 101000 f 74 goat snp36995-scaffold448-4058262 9 76079329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429600 Affx-122937712 AX-123299941 9 74968481 TTTGAAGACAGTGTCATCCAAATACAGCAGAACGC[A/G]TGGGACACTGACAGAGCCACAGACGACATCAGTCT R 2 1 2 1 101000 f 74 goat snp36994-scaffold448-4015415 9 76121475 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397153 Affx-122962436 AX-123267508 9 75000852 ACTGAGCGACTGAACACTTTGACTTTAGTGCAAAA[C/T]GCCTGTTCAGTTTGGAGGCAGAACTCTTTGGGAAT Y 2 1 2 1 202000 f 74 goat snp36993-scaffold448-3983044 9 76153945 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441606 Affx-122928655 AX-123311943 9 75084532 AGAAGGGTTAGGAATGAGACTCATGAAGGCAGCTG[C/T]GAGAGGACTGTCAGAACAGCGGGTAGTTTCTGAAG Y 2 1 2 1 201000 f 74 goat snp36991-scaffold448-3899364 9 76238370 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398272 Affx-122962175 AX-123268627 9 75142080 GATGTTTAGCAAATCCAGAATGCAGCTGTCTTTGT[A/G]CACCCCCAAAATAAATGGCTGACTGAACTCAGAAA R 2 1 2 1 101000 f 74 goat snp36990-scaffold448-3841816 9 76295959 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438309 Affx-122931361 AX-123308647 9 75189555 GGGATTGACATTCATCAGCAAAACACCTCAAAAGA[C/T]AAGCAGGTGCCAATTCTCCTCAAATGGGGATCAAC Y 2 1 2 1 201000 f 74 goat snp36989-scaffold448-3794341 9 76343686 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765187 Affx-986697260 AX-385252734 9 75259110 ACACGACTGAGCAACTTCACTTTCACTTTCACCCA[C/T]CTTTTAAATATTAAGTAGATTTCCCTTTGGGGTTT Y 2 1 2 1 600010 r 74 goat 9_75259110 9 75259110 Ancestral_priority_1043 ancestry 0.684 recommended IMAGE 10K 10K ancestral 38386389 Affx-122970837 AX-123256747 9 75260401 GAACACATGGATGTGGAGAGAAGGGATTGAATTTA[A/C]GCCTTCAAAGATGGAAAGATTTGGGGGCATCCCTG M 2 1 2 1 101000 r 74 goat snp36987-scaffold448-3723495 9 76414210 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382188 Affx-122974013 AX-123252546 9 75298748 GAAAAGTGAAGGTATCATGACTAGATTTTCCTTTG[C/T]AAACATTGATTTACAGAAAATGTAACAGAAGTGAT Y 2 1 2 1 101000 f 74 goat snp36986-scaffold448-3685148 9 76452280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377133 Affx-122978235 AX-123247492 9 75338681 AATAGCATCTATGATCCCTGAACCAACCAGTCTCC[A/G]TCAATCCATTCCATGTGTCCAAACCAAGAAAATGT R 2 1 2 1 201000 r 74 goat snp36985-scaffold448-3645215 9 76491655 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273553 Affx-1111833668 AX-519547167 9 75361091 CAGAACAAC[A/G]TGCAGACCCCGGCTGGGCATTCCAGGTGCTTCCGG R 2 1 2 1 102000 r 74 goat GoatD01.001049 9 75361091 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38430246 Affx-122937311 AX-123300587 9 75372836 TTTTAGAAAGTGTATTTTCTCAAGTGTTCAAAATT[A/G]TAGTTTACATTTCATACATGGTTGAATGGAAAAGA R 2 1 2 1 101000 f 74 goat snp36984-scaffold448-3611060 9 76525804 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380539 Affx-122975672 AX-123250897 9 75422228 GATTCAAAAAATAATCATTTTATATCACAGAAAAC[A/G]ACCACTGATGATTATGGCCAGAGCACTTTTAGTGG R 2 1 2 1 101000 r 74 goat snp36983-scaffold448-3561668 9 76575423 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276325 Affx-1111835361 AX-519549858 9 75477455 ACTCTTCCGCAATAAGAGGGGCAGAGAATCTCTAA[A/G]AAGAGACTTTCTTTATAGGGAAAATGCTTAAACAC R 2 1 2 1 101000 f 74 goat Random2.2K-1018 9 75477455 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434388 Affx-122934695 AX-123304729 9 75477820 TACAGAGATGAGGTTGAGGAAGTGGGAGCCAGAGC[A/G]CAGGAGATCCTGGACGAGAGCCACGTGAGCAGCCG R 2 1 2 1 201000 r 74 goat snp36982-scaffold448-3506076 9 76631091 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439036 Affx-122930340 AX-123309373 9 75506392 CTGAAGATGAGTTAGAATAGTTTGTAAAGCTAAAT[A/G]TTGGAGGTATTTTTAAAATGCCAGTTTAGAAAGCC R 2 1 2 1 101000 f 74 goat snp36981-scaffold448-3477504 9 76659608 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440785 Affx-122929843 AX-123311122 9 75575356 GTTGTGATAAACAGACTGTTTAGAGACTCTTTATC[A/G]TTATAGTATGGGCTAATAAAGGCAGAGTACAGATG R 2 1 2 1 101000 r 74 goat snp36979-scaffold448-3408540 9 76728330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380327 Affx-122975378 AX-123250685 9 75604439 GTGGAAACAAGTATGTAACTCTCCAGTTCTTTTTC[A/G]TTTTTAAGATGTGAGTGGTAGCTTGTATGCATTCA R 2 1 2 1 101000 r 74 goat snp36978-scaffold448-3379457 9 76757962 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377101 Affx-122978262 AX-123247460 9 75633917 ATAAATAACATAAACATTTTTATTTTAAAGAAAAA[G/T]ATTTTGTCCAGCTTCTAATTAGTCTGCTAATAGTC K 2 1 2 1 103000 r 74 goat snp36977-scaffold448-3349979 9 76787462 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437075 Affx-122932670 AX-123307413 9 75664081 TGATGTATCTGTTACCTTCTCTCCATCACACCCCC[A/G]TACATACCTAATTGAAATTCCTCGTGGTAAGAATG R 2 1 2 1 201000 r 74 goat snp36976-scaffold448-3319815 9 76818040 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449288 Affx-122923018 AX-123319623 9 75738059 TTCTCTCCCTTGCTTTCTCTTCTGCAGTCCCACGG[A/G]TTTTCACTTCTTCAAAATCACCATGTGCTTTGCTT R 2 1 2 1 101000 r 74 goat snp36974-scaffold448-3245837 9 76891886 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403443 Affx-122957734 AX-123273796 9 75806288 GCAGTTTTTAAACAAATGAGGGAAGCCTGACAATC[A/G]CTTCTATTTCTTTTTTTGGAAGGTGTATTCCAGGG R 2 1 2 1 101000 f 74 goat snp36973-scaffold448-3177608 9 76957569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422930 Affx-122943036 AX-123293276 9 75854733 AAACTGCTGAGATCACTCTAGGAACAGTGGGCTCA[A/G]TTGATCTATGTCAGGGTACAGTAAGAAACTAGGTG R 2 1 2 1 101000 r 74 goat snp36972-scaffold448-3129163 9 77006448 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398476 Affx-122961581 AX-123268831 9 75887251 AGTTTTCTATAAATAGAATTGCCTGTATGCTTCTA[C/T]GACTTGCTTTTCCCTCCTCACCATTCTATTTGTGA Y 2 1 2 1 101000 r 74 goat snp36971-scaffold448-3096645 9 77039202 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800755 Affx-122925164 AX-385287673 9 75916206 AAAGTGCTTAAAATAGTGCCTGGAAATAGTACACG[A/G]GATCATTATTATTCCTAGATGAAAAAGTTGAGTCT R 2 1 2 1 101000 f 74 goat snp36970-scaffold448-3067690 9 77068120 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769282 Affx-122923256 AX-385256454 9 75948762 AGAGTGTGGTAACAGATACAGAATGAATTCCATTA[C/T]GGTTCTGGTATCTAGTAATTCTGTATTTTATTTCC Y 2 1 2 1 101000 f 74 goat snp36969-scaffold448-3035134 9 77100227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770849 Affx-122968425 AX-385258013 9 76000067 AGATTTGCAAAAAGAAAGAGGTACATACATCTGTT[G/T]ACATCTAGTAAAATTCAGAAAGGCCCTGCCCAAAC K 2 1 2 1 101000 r 74 goat snp36968-scaffold448-2983829 9 77152077 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798835 Affx-122921760 AX-385285765 9 76077281 CCACCAGGTGCTGGAGATACCAAAAAAAGTGAGAC[C/T]CTTTAGGGTGTCAGAGTCCAGTTCTCATATAAACA Y 2 1 2 1 101000 r 74 goat snp36966-scaffold448-2906615 9 77230175 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774040 Affx-122953549 AX-385261178 9 76111988 GAGCCAATCTCAAAGTAGCTGTACAATAAATATTC[A/G]TTGAATAAACCAATGAAGCCATTTGATACATGCAA R 2 1 2 1 202000 r 74 goat snp36965-scaffold448-2871908 9 77264950 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444792 Affx-122926343 AX-123315129 9 76144860 CAGCATGACCTGAGATTTCCCGAATACATTAGAGG[G/T]GCCCTGTCACAGAGCTCTACTCACATTATTCCTAA K 2 1 2 1 101000 f 74 goat snp36964-scaffold448-2839036 9 77297834 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438278 Affx-122931402 AX-123308616 9 76203144 ATATTATTTGGTAGCTCTGAGTTTGGCCACCTGAT[A/G]CAAAGAGTTAACTCACTGGAAAAGACCCTGATGCT R 2 1 2 1 103000 f 74 goat snp36963-scaffold448-2780752 9 77356270 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801576 Affx-122944325 AX-385288485 9 76258686 GTTCTCTGTTCTTAATTGTTATAGGTTTCAGTGCT[A/G]CTGAAGAAATTACCATAGGGAAGTCTACTTATTTC R 2 1 2 1 101000 f 74 goat snp36962-scaffold448-2725210 9 77412316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377947 Affx-122977208 AX-123248306 9 76293934 CCAGAGTCAATGTTCTTTCCATTTTACTGCCCTCT[A/C]TCTGAATACATTTATAAATCAAAACAATGAATAAA M 2 1 2 1 101000 f 74 goat snp36961-scaffold448-2689962 9 77444698 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775013 Affx-122955115 AX-385262145 9 76393671 CAAACATCTGCTGGGCATGTCAAGTGACATAATCT[A/G]CCTACCCTCAAACTTACCATCAGAGAAACTTTTAA R 2 1 2 1 201000 r 74 goat snp36959-scaffold448-2590225 9 77535897 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413502 Affx-122950639 AX-123283851 9 76448992 ATCTTGTGGAAGAGAGATGAAGCACAAGATGAGAA[C/T]ACTGAAAGGCCCTTTCATATCAAGAGATTTCACAC Y 2 1 2 1 303000 r 74 goat snp36958-scaffold448-2534904 9 77591852 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794465 Affx-122925785 AX-385281428 9 76548421 TCATATGTAATTGCATCTCTTTGTGTGTAATTTTA[C/T]AGTTAGAAGGGAATGAAAAGCCTCACCATGCACTT Y 2 1 2 1 101000 r 74 goat snp36956-scaffold448-2435475 9 77692507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405484 Affx-122956017 AX-123275836 9 76610533 TTAGTTTTAGCTGATAGCAACGTGCGCTCAGTCTT[A/G]TCCAACCCTTTTGACTGCACAGACAGTAGCCTGCC R 2 1 2 1 101000 f 74 goat snp36955-scaffold448-2373363 9 77755506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403302 Affx-122957841 AX-123273655 9 76641045 ACCCCTAATGTATGGTCAGCATGCACTCATTGCAA[C/T]AGAGGTTATCACCTGAAAGAATCAAATTGAACCAG Y 2 1 2 1 101000 r 74 goat snp36954-scaffold448-2342851 9 77787297 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411994 Affx-122951762 AX-123282344 9 76699500 GTATTCTTCAGGATTGTTGACCTTTAAAAGCTAGT[A/G]ATGCAACATACTAGTAAAATGCCACCTGAGATATC R 2 1 2 1 101000 r 74 goat snp36953-scaffold448-2284396 9 77848397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780679 Affx-122971796 AX-385267769 9 76742680 AAATAGTTCATATGCAGATATTTGTCAAACCAGCA[C/T]ACAGTATCATCTCCTTTTCCTGCAATGCCAAATCC Y 2 1 2 1 101000 r 74 goat snp36952-scaffold448-2241216 9 77892003 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793599 Affx-122967565 AX-385280574 9 76792226 GTCTTATGGACTATTTTCATTCTAAATATCTACTG[C/T]AATTAGAAAGACTACTGGTAAGAAACTCTTGCCAA Y 2 1 2 1 101000 f 74 goat snp36951-scaffold448-2191670 9 77941900 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793403 Affx-122956086 AX-385280380 9 76838824 AGTAGTAGGTAGAAAGTTAAAACTTGTTTAGGTAC[A/G]TTTTTTATCATTCCAATGGATAATTGTAGATACCT R 2 1 2 1 101000 f 74 goat snp36950-scaffold448-2145072 9 77988656 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379742 Affx-122975869 AX-123250100 9 76889709 AGAGTATGCTGCTGCCCATCAGGATCCAGGGGTCT[A/G]TGAACTGCTAGCAGGAGTGTTGCCTTGGGAGTCCA R 2 1 2 1 101000 r 74 goat snp36949-scaffold448-2094187 9 78039641 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781110 Affx-122930473 AX-385268195 9 76995912 ATAATAGATTATCCATTCAGCATAGAATCCAGCAC[A/G]AGATGGGCACCAGTAAATCAAACTGAATACAGGAA R 2 1 2 1 101000 r 74 goat snp36947-scaffold448-1987984 9 78123282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409372 Affx-122954160 AX-123279723 9 77030303 TGATTGTTCAAAACCAAAACTAAAGAGGACACACC[A/G]TTTGAAAAATATAAAAATATTTATACTTCCATTGA R 2 1 2 1 101000 f 74 goat snp36946-scaffold448-1953593 9 78156184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765116 Affx-122926182 AX-385252676 9 77067318 AATGTCAGCAAGCAAAAAGACAAGGCTGCAAAAGA[C/T]GACTGAGTGACTCTTAGTCAGATGTCCCTGTTCAT Y 2 1 2 1 101000 f 74 goat snp36945-scaffold448-1916578 9 78193023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774365 Affx-122951455 AX-385261501 9 77167602 ACCATCTGTCGGATTATCCTCAAAGTGGAGAGACC[A/G]CAGAAAAGAAATGCGGTGAAATAAGTGGAAGAGTT R 2 1 2 1 101000 f 74 goat snp36943-scaffold448-1816294 9 78294710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781913 Affx-122942461 AX-385268994 9 77203043 GCATGTTGTATGGAAAAGTAGAAATCAAAACAGAA[C/T]TGAAGCTTCCATTGCATCCATAATCTTGAGTTTAC Y 2 1 2 1 303000 f 74 goat snp36942-scaffold448-1780853 9 78330410 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453342 Affx-122919958 AX-123323675 9 77235536 TTTCTAAGGACCAGAACTTGAGAAGACACATGTCA[C/T]GGGTGCTTATAAACATTATAAAACATAATTCGAGA Y 2 1 2 1 101000 f 74 goat snp36941-scaffold448-1748360 9 78363396 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384908 Affx-122972344 AX-123255266 9 77288757 GATGAACGCTGTTCACACAGCCACCAAGGGAGGAT[A/G]CACAGCCATCAGGGCAGGTGGTGCCCAGATAGGAT R 2 1 2 1 101000 f 74 goat snp36940-scaffold448-1695139 9 78417650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428808 Affx-122938393 AX-123299150 9 77328556 GCAAGGGAAGGGGAATACAATGGTGAGCCATCAGA[A/G]CTGTTATTATATTCTGAATTTTCATCATCCCTGTA R 2 1 2 1 101000 f 74 goat snp36939-scaffold448-1655340 9 78457732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413678 Affx-122950104 AX-123284027 9 77373914 TTGAGTGTCATATGATAGTTTTCTTTTTGTCTGCT[A/G]CAGTTAACATTTCTATTTGATGGAACCACATCCAT R 2 1 2 1 101000 r 74 goat snp36938-scaffold448-1609982 9 78503081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386991 Affx-122969950 AX-123257349 9 77414264 TTACTCACAGAGTACTTGGGACCCCTTGCCTTCTA[C/T]AGCATCCCTTCTGTCTCCCCAGCGCCAACATCCTG Y 2 1 2 1 101000 f 74 goat snp36937-scaffold448-1569632 9 78543502 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273448 Affx-1111833624 AX-519547072 9 77414366 AACAAGACTTGCCCTCAGGGGGAACTATTTTACTG[A/G]AGGCTTTGTTATTGGTGATTTCTCAGCTCTGAACT R 2 1 2 1 101000 f 74 goat 9_77414366_AF-PAKI 9 77414366 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38447335 Affx-122924889 AX-123317671 9 77444486 AAACTGAGAACTCAGCAGTAAATGCAGGGAAGCAC[A/G]TGACCCAAGCCGCAAGAGGCTCTATGCGGGACACA R 2 1 2 1 101000 f 74 goat snp36936-scaffold448-1539410 9 78571269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380014 Affx-122975599 AX-123250372 9 77491098 GGCATAAACCCTAGCACTCAGCATATCAGAAAAAT[A/G]CCAGAAAAACACCCCCAGGACATGTGGGGGTGGTA R 2 1 2 1 201000 f 74 goat snp36935-scaffold448-1492798 9 78617631 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400737 Affx-122959903 AX-123271092 9 77521282 TCGGAAAGGAAGAAACACAACTCCTGTTATCCATG[C/T]GGGGCGTGATTATTTACACAGCAGATAAAGGCTCT Y 2 1 2 1 101000 f 74 goat snp36934-scaffold448-1462614 9 78648285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389672 Affx-122968713 AX-123260030 9 77550356 TGATGGTGCCTCTTCTTACTGAGTTCAAAAGTTCT[A/G]CGTGAGATACCTGATGTTTACTAAGCTCCATCCCA R 2 1 2 1 101000 r 74 goat snp36933-scaffold448-1433540 9 78677364 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436645 Affx-122932485 AX-123306983 9 77612289 AATAGCTTGCCCTGCAAAAATCCAGAGTCTCATCC[A/G]TCAAAATCAAGGTACTCAGAGAGCACGAGCAGCAC R 2 1 2 1 201000 r 74 goat snp36932-scaffold448-1371607 9 78739289 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780260 Affx-122948613 AX-385267355 9 77656489 CCTTTCTGTATTCTTACAAGTGAACCTACTTGAAG[C/T]AGAAGACAGTATTTTTCAACAGAGTGTATGTGGAG Y 2 1 2 1 101000 r 74 goat snp36931-scaffold448-1327407 9 78783890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416791 Affx-122948150 AX-123287139 9 77698800 AAAGCAGGTTAAACATGCTTTCCCAACTCCCTCCT[A/G]TTCTCTTCAATTTCACATACCCAAATGCTCATTCA R 2 1 2 1 201000 r 74 goat snp36930-scaffold448-1285096 9 78826303 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396056 Affx-122963452 AX-123266411 9 77738571 ATACTATTTCCTGGAGTGCAAAACTCCTCAAACAC[A/G]TGTCACAAGGAAACCATGATAGGCGGCTAGGCCAG R 2 1 2 1 101000 f 74 goat snp36929-scaffold448-1245325 9 78865854 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476264 Affx-1251763771 AX-586011685 9 77761389 TATCACTAAACATCAGTAATACATAATTAAGTAGT[-/TTAAAAATTACTAGATTGGCCCCGGAGGGAAAGATGGCGGATAAAATGTGTTAACATTAAAAAAAAAATAAAAATAAAAA]TAAAAATTACTAGATTGAATTTTGTGGGAGAAATG - 8 1 4 1 20000 f 74 goat SV_326 9 77761389 - deletion junction SV-TF-chip 539476517 Affx-1251763771 AX-586011910 9 77761389 TATCACTAAACATCAGTAATACATAATTAAGTAGT[-/TTAAAAATTACTAGATTGGCCCCGGAGGGAAAGATGGCGGATAAAATGTGTTAACATTAAAAAAAAAATAAAAATAAAAA]TAAAAATTACTAGATTGAATTTTGTGGGAGAAATG - 8 1 4 1 20000 r 74 goat SV_326 9 77761389 - deletion junction SV-TF-chip 562165126 Affx-1251763771 AX-606940538 9 77761389 TATCACTAAACATCAGTAATACATAATTAAGTAGT[-/TTAAAAATTACTAGATTGGCCCCGGAGGGAAAGATGGCGGATAAAATGTGTTAACATTAAAAAAAAAATAAAAATAAAAA]TAAAAATTACTAGATTGAATTTTGTGGGAGAAATG - 8 1 4 1 20100 f 74 goat SV_326 9 77761389 - deletion junction SV-TF-chip 562165630 Affx-1251763771 AX-606941040 9 77761389 TATCACTAAACATCAGTAATACATAATTAAGTAGT[-/TTAAAAATTACTAGATTGGCCCCGGAGGGAAAGATGGCGGATAAAATGTGTTAACATTAAAAAAAAAATAAAAATAAAAA]TAAAAATTACTAGATTGAATTTTGTGGGAGAAATG - 8 1 4 1 20100 r 74 goat SV_326 9 77761389 - deletion junction SV-TF-chip 562165826 Affx-1251763771 AX-606941235 9 77761389 TATCACTAAACATCAGTAATACATAATTAAGTAGT[-/TTAAAAATTACTAGATTGGCCCCGGAGGGAAAGATGGCGGATAAAATGTGTTAACATTAAAAAAAAAATAAAAATAAAAA]TAAAAATTACTAGATTGAATTTTGTGGGAGAAATG - 8 1 4 1 20100 r 74 goat SV_326 9 77761389 - deletion junction SV-TF-chip 320773311 Affx-122924256 AX-385260454 9 77791290 TTGACCTTAAACTACGTAGAGAATGGATTTCCACC[A/G]TTATGTTAGAACCAGCAGCTTTCTCCTCGTAAGTG R 2 1 2 1 201000 r 74 goat snp36928-scaffold448-1192606 9 78918341 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426072 Affx-122941087 AX-123296418 9 77823828 TCTCCTTGACTTGCTCCCAACTTTCCCCCCATCCC[A/G]TCTCCCCATGCTCTTAGCAGCACCATCTTCATCAC R 2 1 2 1 101000 r 74 goat snp36927-scaffold448-1160068 9 78951305 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791315 Affx-122972736 AX-385278308 9 77864791 TTCCTGAGATGCTTTCCTTCCCTAAGTAAAATAAA[C/T]GTGGAGAATGAAACTTAACTTGAATTAGTAAAAAG Y 2 1 2 1 101000 f 74 goat snp36926-scaffold448-1119105 9 78992895 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397494 Affx-122962070 AX-123267849 9 77899641 ATTACTAAAGAAATATTCTGTCCTCAAACACACAA[C/T]GCAAAATGACACACGTAAAAGCAAATATAGCAAAA Y 2 1 2 1 101000 f 74 goat snp36925-scaffold448-1084255 9 79027553 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422948 Affx-122943022 AX-123293294 9 77931107 CTCCCTGGTACTCTCTGATCCCTTGAGTACTCTGA[A/G]CGGGGCACTGAGCAATCTCTCCTCCCACAATCAAC R 2 1 2 1 201000 f 74 goat snp36924-scaffold448-1052789 9 79059154 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417213 Affx-122947302 AX-123287561 9 77963577 GACCATCCTGACTGCTGCTGTAAAGCAATTCAGGG[A/C]TGTACTTTCAGAGCAGAGCCGAGCCGGGAAACCTG M 2 1 2 1 101000 f 74 goat snp36923-scaffold448-1020319 9 79092416 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381453 Affx-122974335 AX-123251811 9 78005461 ATGACATCCCCTAGGCATCTTAGATCAGCTTCCTA[C/T]CATAGTGTTACATCTCAGCCAGCTCTAACCGGTTG Y 2 1 2 1 201000 r 74 goat snp36922-scaffold448-978435 9 79134303 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442010 Affx-122928419 AX-123312347 9 78041965 TGACCACAGGCCTCTCTGGGCACTGGATCCTGTTC[C/T]GTGGTGTTTTTGAGAAGCTCTAAGGAAAGTCCTGG Y 2 1 2 1 101000 r 74 goat snp36921-scaffold448-941931 9 79170706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416470 Affx-122947808 AX-123286818 9 78071795 GGCTTGTAGACACTTGCAAGTTGCAGCTCGTAAAG[C/T]AGAATCAGACTGCGTAGCAGTAAATGAGAGCGTAA Y 2 1 2 1 101000 f 74 goat snp36920-scaffold448-912101 9 79200680 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440135 Affx-122929689 AX-123310472 9 78149923 ATTTAGCCACTCTCTCCAGAATGACTGTGAGTATG[C/T]GTATTTATCTCTATATTAACATTTTATTTACATAG Y 2 1 2 1 101000 f 74 goat snp36919-scaffold448-833973 9 79276952 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432676 Affx-122936046 AX-123303017 9 78212390 TATGTATCCGTGGCAATCACAAGGCACAAAATCAC[A/G]TTCAAATCTGAGAGCTTTATTATTATTATTTTTTT R 2 1 2 1 101000 f 74 goat snp36917-scaffold448-771506 9 79339181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389544 Affx-122968274 AX-123259902 9 78276541 TTCTAGTTTACTAAGGAACAGAACAAATCTCCCAG[A/C]TTCTTTCTTGTTTCTCTAGCCATAAAGCATGCTCA M 2 1 2 1 101000 r 74 goat snp36915-scaffold448-707355 9 79404022 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787316 Affx-122945713 AX-385274341 9 78321101 ACTCATTTAATATCACATTTGTTCCCAGAAATAAA[C/T]GATAAAGGAGGCATTGAGTATTAATATGTCAGAGT Y 2 1 2 1 101000 r 74 goat snp36914-scaffold448-662795 9 79448385 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380576 Affx-122975271 AX-123250934 9 78354355 TCCAGAAAGTCAGAGAAGGCATTTCTGGGAGAAGA[C/T]GACTGAAAGAAAAGTAGAATTTGGATAGGCTGGCT Y 2 1 2 1 201000 r 74 goat snp36913-scaffold448-629541 9 79482394 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410289 Affx-122952505 AX-123280639 9 78409063 AAAATTAATTAACAGAAAAAAGAATTCAAATATCT[A/G]CTCACAGAAAGCCAGTTAAATTCCACCATACACAC R 2 1 2 1 101000 r 74 goat snp36912-scaffold448-574833 9 79537239 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444844 Affx-122926301 AX-123315181 9 78525331 TCACAACTACACAACAGCTCAGCTCTGCCCTTGCA[G/T]CATGAAAGTGCCGTAGACAATATGCAAATGAATGA K 2 1 2 1 101000 r 74 goat snp36910-scaffold448-458565 9 79653724 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789207 Affx-122924711 AX-385276219 9 78561432 TTTATTTCCTTATTGTGCCAGAGATGCCACTGGCC[A/G]CATAATTGCAGTGATGGATAATTCTGGTATCTGAA R 2 1 2 1 101000 f 74 goat snp36909-scaffold448-422464 9 79690016 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779450 Affx-122928072 AX-385266553 9 78595394 GATTACTAGAACTGTTTAAATTGATTTATAGAGGA[C/T]ATTTAATGAGAATAGGAATTGAAATTACACTTGAC Y 2 1 2 1 101000 f 74 goat snp36908-scaffold448-388502 9 79724074 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782767 Affx-122967808 AX-385269839 9 78627919 AGCTGGAGGAGCACACGGGAAAGAACGGATGATTC[A/G]GAACAAGGAGGCTTATTGACTTTTGTATTGAAGCT R 2 1 2 1 101000 f 74 goat snp36907-scaffold448-355977 9 79757116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418614 Affx-122946348 AX-123288962 9 78659175 TTTTTTCCCCTTTATCTGCTGTGCTTTTGGTGTTA[C/T]ATCTAAGAAGACTTTGCCTAACCCAATATGACAAA Y 2 1 2 1 102000 f 74 goat snp36906-scaffold448-324721 9 79789485 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767507 Affx-122945011 AX-385254769 9 78689844 TCTAATATGTACACACATATGTTAGAGAAATATAG[C/T]AATACTCTACATATAGTGCTATAACCTGGTACTCT Y 2 1 2 1 201000 f 74 goat snp36905-scaffold448-294052 9 79820080 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393906 Affx-122965106 AX-123264261 9 78729268 GTAATGGGAACTATTTACTGAAACTGAAGATTTTG[C/T]TAGGTGAGGAAATGGTAGCTGCTGAGAATAGTTAC Y 2 1 2 1 101000 r 74 goat snp36904-scaffold448-254628 9 79859529 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775390 Affx-122963553 AX-385262521 9 78758697 AGATGCATAGAAGTGAACATAACTTGTGCTAATTT[A/G]CATTATTTGGTGAAGCCAAAATTTGAATCCAGTTC R 2 1 2 1 101000 r 74 goat snp36903-scaffold448-225199 9 79888992 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448967 Affx-122923127 AX-123319302 9 78796682 TACTTATTTTCTCTAAGACTAAATATCTAAGCCAT[A/G]CTGTAGCAAACAAAAACATAAACTGTTGAGAAGGC R 2 1 2 1 101000 f 74 goat snp36902-scaffold448-187214 9 79927365 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410537 Affx-122952159 AX-123280887 9 78832105 CTTCCATACCAAGTGCCTTATTCTTATTACTATTA[C/T]GGTTATTAGCTATTATTCATATTCCTCTCTTGAAG Y 2 1 2 1 101000 r 74 goat snp36901-scaffold448-151791 9 79963228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406770 Affx-122955719 AX-123277121 9 78864624 AAGGAATACCAAGGGGCACAGAGATGGGGCGTGTG[C/T]AGGTGATGGATATGTTCACTGCCTTGATTTTGGTG Y 2 1 2 1 201000 f 74 goat snp36900-scaffold448-119272 9 79995999 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386226 Affx-122970979 AX-123256584 9 78893689 TAATATTATAGCTCCCCTTGCTTTCTCTAAATCAA[C/T]GGTCCCTACGGACTTTCGGAGCTGTTCCACTAATT Y 2 1 2 1 101000 r 74 goat snp36899-scaffold448-90207 9 80025447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384814 Affx-122971986 AX-123255172 9 78961833 TTTTCTTTGGCTTTAGTACTGCAATGAATATTTGT[A/G]CATCTGTCTTTTTTGTTGCTTTTGATTTTTTTGGA R 2 1 2 1 101000 f 74 goat snp36898-scaffold448-22063 9 80093901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420733 Affx-122944766 AX-123291080 9 79010974 CCTAAATCAGTAAATAGGAAGAATTCTTTCAATAT[A/C]GGCTCAATGGACCAGGACCAACAGAGAGAGTGATG M 2 1 2 1 201000 f 74 goat snp36894-scaffold447-4394460 9 80143207 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453555 Affx-122919778 AX-123323888 9 79065036 ACGCTGGGATTCATGCTTGCCCCAGGTGAAAGGTC[A/G]CCTCTTCTTGCTTCAGGCCACCAATCAGGAAACTT R 2 1 2 1 101000 r 74 goat snp36893-scaffold447-4340398 9 80201276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425900 Affx-122941624 AX-123296246 9 79093674 TGTGTCTCTTTACTTTTCTTTCTCTAAAATGCATG[A/G]GGATGGGGAACTGTATATGCGTAGCTCTTGATAAC R 2 1 2 1 101000 r 74 goat snp36892-scaffold447-4311760 9 80230151 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433591 Affx-122934960 AX-123303932 9 79135689 GCTGACATGTGTGGGGAGACACAGAGACAAGTTTA[C/T]AAAAGACTGTAGTCCTGATCTGAGGCCATCAGTTA Y 2 1 2 1 101000 f 74 goat snp36891-scaffold447-4269745 9 80273688 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430994 Affx-122936687 AX-123301335 9 79191383 CAAGTATATATGAAATATGCTCTGTACTTCAATAG[C/T]AACTCTGTATTTATAATTTCACATTCTTTATTATT Y 2 1 2 1 101000 f 74 goat snp36890-scaffold447-4214051 9 80328990 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433205 Affx-122935632 AX-123303546 9 79222611 AGAAGGATTTTCAGAGATGTGGATCTTGGTGGTGG[A/C]TGCTGCAAGGCACATATAGAGAAGGGAATCACCAG M 2 1 2 1 201000 r 74 goat snp36889-scaffold447-4182823 9 80360426 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423235 Affx-122942689 AX-123293581 9 79273445 GTTGTAGTCATATGAGTTACAGCTCATGTCTGTTC[A/G]TTACTGCTTTTATTTGCTATGTTCTTTTTTTGTGC R 2 1 2 1 101000 f 74 goat snp36888-scaffold447-4131989 9 80411634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450249 Affx-122922255 AX-123320584 9 79322885 AAGAAGAAACAGGAGGCTGGTGACTTTCCAGGTCC[A/G]TCAAAGCCGTGATTGAATTCTGCGGGAGTCCTCGG R 2 1 2 1 101000 r 74 goat snp36887-scaffold447-4082549 9 80461056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446020 Affx-122925858 AX-123316357 9 79366190 TCAATGACATATTAAATACTACAGTTTATAAATAT[A/G]TTCCACAATACTTAATTGCAAGAAATGTGTGAGAA R 2 1 2 1 102000 r 74 goat snp36886-scaffold447-4039244 9 80503830 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411368 Affx-122952243 AX-123281718 9 79397702 GAGTCATTTTGTTCATCCACAAAAATTTGCTGGAC[A/G]TCTATTACCTGCCACCAATTTGTTGGTCCTTAATT R 2 1 2 1 101000 f 74 goat snp36885-scaffold447-4007732 9 80535489 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453001 Affx-122920111 AX-123323334 9 79446218 AATTGTGAGGTCATGAGGGCAGAGGGTCTAGTGCT[A/G]TGTGCAAGGACATCCCAGTGTGTGGCAGAGCCAGG R 2 1 2 1 201000 r 74 goat snp36884-scaffold447-3959216 9 80583919 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795586 Affx-122969903 AX-385282541 9 79499119 TGCTGACTTATAATTTGTTTCTTCACTTAACAATG[C/T]ACTGGGAACATCTTTCCGATAAATAAACTTCATTT Y 2 1 2 1 101000 f 74 goat snp36883-scaffold447-3906315 9 80637469 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780647 Affx-122960433 AX-385267737 9 79545862 TCTGACAACCAAACCAGAGCAGCAGGCAAAATACA[C/T]GAAGAGAATTAACATCGGATCGCAGATGACAAGAC Y 2 1 2 1 101000 f 74 goat snp36882-scaffold447-3859572 9 80684344 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396617 Affx-122962884 AX-123266972 9 79581534 AAATGACCACATTCATTTTTCCTAATGAATTCTTT[A/C]TTTTTACACCTCTTGCCTAAATTTCAAACCATAAT M 2 1 2 1 102000 r 74 goat snp36881-scaffold447-3823900 9 80719855 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784439 Affx-122976849 AX-385271488 9 79618779 AAAAGAGGGAATTTTTAAGCTATTATCATTAAAAG[A/C]GAGACCACGTTACCTTTGTCACTGTATTTTCAAAT M 2 1 2 1 101000 r 74 goat snp36880-scaffold447-3786655 9 80757478 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440750 Affx-122929869 AX-123311087 9 79655888 CAGTGTCACAAAGGTCTTCTCATGCATTTTTAATC[C/T]GCAGGAGAAAGTGAACAATCGTCCTTCAATCATCA Y 2 1 2 1 101000 r 74 goat snp36879-scaffold447-3749546 9 80794595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783968 Affx-122964862 AX-385271022 9 79686647 AACTTATCAACTTTCCTGTGAAGGCTTCAAAGTGC[A/G]CTTCTGTCTCTAACACAGCCACATGACACACAATC R 2 1 2 1 101000 f 74 goat snp36878-scaffold447-3718787 9 80825354 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768670 Affx-122922375 AX-385255848 9 79721987 GCAATACAATTCTGAAAGTAATCTGATGTTTCAAA[C/T]ATCTACAGATAATCATCTTCCAGAATACAAATACG Y 2 1 2 1 101000 r 74 goat snp36877-scaffold447-3683447 9 80861100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424414 Affx-122941810 AX-123294760 9 79753186 TGTATCACAGAAACTCTCGGTGGTCAAAGGGTCAA[C/T]GATTTTAAAGTAAAAGAGAACATCTTTCAAACACA Y 2 1 2 1 101000 f 74 goat snp36876-scaffold447-3652248 9 80892719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442469 Affx-122927940 AX-123312806 9 79800476 AAAACATGGAACATATCCTCACACCACTCAAACCT[A/G]CTAAGAATGCACAGAAATCTTTCCTGAAGAGCCAC R 2 1 2 1 101000 f 74 goat snp36875-scaffold447-3604958 9 80940063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402773 Affx-122958310 AX-123273126 9 79855383 GGCATGGGTTTTACCTCCCCATCTCTCCAACTGCT[C/T]GGGGGAGTCAATGACGGCTAGAACAAGGTCTCACA Y 2 1 2 1 201000 r 74 goat snp36874-scaffold447-3550051 9 80995601 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381228 Affx-122974508 AX-123251586 9 79940003 AATCCGGGAGAATGTGCATCAGAGCACAACCACCA[C/T]GCACACCCACACGCATGCGTGCACTCATGCTTAGA Y 2 1 2 1 101000 f 74 goat snp36872-scaffold447-3465431 9 81080286 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411440 Affx-122951822 AX-123281790 9 79974646 CAAAAATGATATTAAGAAAAACAAAAGCCCTAGGA[C/T]GTAAAGACTATACACTTTATCACTGATTAGGCTCA Y 2 1 2 1 201000 r 74 goat snp36871-scaffold447-3430788 9 81114949 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391191 Affx-122967422 AX-123261548 9 80006023 TCTTTAAAGTCAATTTGCTTCCCCAAAAATGCAAT[A/G]CGACATGGAAAAGAACATTAAAAAGAAAATCTGAA R 2 1 2 1 101000 f 74 goat snp36870-scaffold447-3399411 9 81146287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429855 Affx-122938152 AX-123300196 9 80064765 TGCCTGGGGCAGCCTTTTTGGATGCAAGAGGTGAT[A/G]AGGATAAAGCCAACTAACTGAAGATGCACTGGACG R 2 1 2 1 101000 r 74 goat snp36869-scaffold447-3340669 9 81200640 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410060 Affx-122953224 AX-123280410 9 80115579 CTGGGCCTCCCAGTGGTGAGAGGCACTCTGTGAGT[A/G]TGGAGAAGCAATTGGGTGACAGGGAGACCGAGTCA R 2 1 2 1 101000 r 74 goat snp36868-scaffold447-3289855 9 81251718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424278 Affx-122941989 AX-123294624 9 80156237 GACTCAGATATAACTGGTGTGTCAGTCTTACAGTA[C/T]CAACTCTTTCCTTTGGGGGCTGTTTAATTCCTTGG Y 2 1 2 1 101000 f 74 goat snp36867-scaffold447-3249197 9 81292005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453384 Affx-122919926 AX-123323717 9 80219638 ATATTCTGGTATAGCTAAAAACCCCAAAAGAATCC[A/G]CTAAGAAACTATGCTAACCACGAGAGAGTTCAGGA R 2 1 2 1 201000 r 74 goat snp36866-scaffold447-3185796 9 81355474 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423670 Affx-122942334 AX-123294016 9 80253000 CATTATAGCACTGACTTAGCCAGCACCACCAGGGG[C/T]ATCCAACTTTCTGACCCACTCACAAGAGTTCCCAG Y 2 1 2 1 101000 r 74 goat snp36865-scaffold447-3152434 9 81390060 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377941 Affx-122977213 AX-123248300 9 80282907 TGAAATTTAAAGGGCAGGAAGACAGCACCTGGACA[C/T]GGCCGTTCTAACCTGTACAAGTCACACATACCTGA Y 2 1 2 1 201000 r 74 goat snp36864-scaffold447-3122527 9 81419938 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405094 Affx-122956989 AX-123275446 9 80336923 GTGGGGAAGACTCCCACCGTGTAATTATCCAGCCC[A/G]TCAGAAGACAAGGTCAGAACAGACTGATAAAGTCA R 2 1 2 1 101000 r 74 goat snp36863-scaffold447-3068511 9 81473867 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413121 Affx-122950378 AX-123283470 9 80366564 TGTGCCCATGGAGAGAAAAATGCGGTCATCTCTCT[A/G]TCGTCACCGTGCGGAAGTCTGTCCAACGACGACAA R 2 1 2 1 101000 f 74 goat snp36862-scaffold447-3038870 9 81503853 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403465 Affx-122957716 AX-123273818 9 80397341 CCTTTAAATGACCTGAGGACTCCTAGGGGTCTGAG[C/T]AAACAGAGATGACCCCTTAGCCCCAGCTGTCAGTT Y 2 1 2 1 101000 f 74 goat snp36861-scaffold447-3008093 9 81534455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424623 Affx-122942185 AX-123294969 9 80427547 GTTAAGACACATCAAGAAAGCAATAATTCTTTCAA[C/T]GGAACTTAGCTGTTTTGAAAAAACAAAGGATGTGC Y 2 1 2 1 101000 f 74 goat snp36860-scaffold447-2977887 9 81564633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399822 Affx-122960266 AX-123270177 9 80478235 GCTCTGAAGCCATCTGTTTTCATTATCCCCAGAAA[C/T]TGTGTTTTCCAGTGAAGCTTCCAGACTGACCTAAC Y 2 1 2 1 102000 f 74 goat snp36859-scaffold447-2927199 9 81615442 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791945 Affx-122955204 AX-385278935 9 80518371 TATTACTAATGTTACTTGTTTTACTTCATTAATGC[A/G]AGTTAAGGAGGTTCCTATTTTCCATAAGTGTGCTT R 2 1 2 1 101000 r 74 goat snp36858-scaffold447-2887063 9 81655504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438242 Affx-122931429 AX-123308580 9 80573243 CTCTAAATCTCACCAAGGATTTGCTGATGAACCTG[C/T]AATTTGTTCATAAGGAAAAAAATATTTGTCGTTTA Y 2 1 2 1 101000 f 74 goat snp36857-scaffold447-2832191 9 81710815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405111 Affx-122956977 AX-123275463 9 80613722 ACAGGATGTGTGTGCATGCTAAGTCCCTTCAGTCG[C/T]GTCTGACTCTGTGACTCCCATGGAGACACCACCAG Y 2 1 2 1 303000 r 74 goat snp36856-scaffold447-2791712 9 81751587 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444031 Affx-122926882 AX-123314368 9 80647170 GCATGGAAAACCTCAGAATTCAGGATTCACGGGGT[A/G]TGATATTAGGTACAGAACCGCAAAGGCTTTTGGCT R 2 1 2 1 101000 r 74 goat snp36855-scaffold447-2758264 9 81785298 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418880 Affx-122946113 AX-123289228 9 80681738 TCAAACATCAGCCCCCAACCTGCACCCCCACCTCC[A/G]TCACGAACAAATCCTCTTCCTTGAGCAGTCTTTTT R 2 1 2 1 101000 r 74 goat snp36854-scaffold447-2723696 9 81819901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443323 Affx-122927447 AX-123313660 9 80739287 TACCTAAGCAGATGCACTGCCTCCCTGCAAGAATG[C/T]GCTCGCCTGTACCACCAGCCAGAGGGGAAAAGAGG Y 2 1 2 1 101000 f 74 goat snp36853-scaffold447-2666147 9 81877721 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274947 Affx-1111834594 AX-519548529 9 80770651 AGTGAGCAGAACGGAAATCGCTGCCCTCCAAGAGC[A/G]CCTGTCCT R 2 1 2 1 102000 f 74 goat GoatD01.042561 9 80770651 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38441729 Affx-122929139 AX-123312066 9 80771599 ACAACCCCCAAGAGAAAGGGACAGCAGGAAGACTC[A/G]CCAGTGGGACTGATGCTTTTCTCTAAAAGGCTTTC R 2 1 2 1 101000 r 74 goat snp36852-scaffold447-2633835 9 81910069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387533 Affx-122970306 AX-123257891 9 80806229 TATGACTCATTTTGCCCCTCTGTTCACGGGCCGAG[C/T]ACACTGGATGGTGGCTTTACGTGACGCCCAGCTGC Y 2 1 2 1 201000 r 74 goat snp36851-scaffold447-2599205 9 81944583 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777433 Affx-122950809 AX-385264554 9 80860869 GGAATTTGGATATGGAGTTAGACTGATTTTTAGAC[G/T]ATCTGGAAGATTTTTGTTAGTACTCTTAGGTGTTA K 2 1 2 1 101000 f 74 goat snp36850-scaffold447-2544565 9 81996327 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768634 Affx-122962180 AX-385255813 9 80893934 CCAAAGCATGGCCCTGCGGACTGATTTAAAAAATG[C/T]CAAAGACAATGTCTGGCTAGTAATAAATACTCAAG Y 2 1 2 1 101000 f 74 goat snp36849-scaffold447-2511500 9 82029219 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450697 Affx-122921894 AX-123321031 9 80940230 ATATTCTGGGCTTACTTTGATGTCGAGGAACTTTC[A/G]ATTCCTCATGGTGAGGACGCCTTTCTGAGACTTAA R 2 1 2 1 101000 r 74 goat snp36848-scaffold447-2465204 9 82075452 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396369 Affx-122963037 AX-123266724 9 81031879 TGAGGTAAGTTATTTTAAAGAAACAGTACTACTGC[C/T]ATCTAGAACGTAAGGAAAGAGCTCATGAACTTTGC Y 2 1 2 1 101000 r 74 goat snp36847-scaffold447-2373555 9 82165783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420484 Affx-122944867 AX-123290831 9 81076900 AAAGTCAAAGAAAACTTGGAGGATATAGCTCAGCA[C/T]ATCACCTAGAAAATTACATTAGGCAAAGAAAAGAA Y 2 1 2 1 101000 r 74 goat snp36846-scaffold447-2328534 9 82207848 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406792 Affx-122955702 AX-123277143 9 81112666 GCGATGTGCAGGGAGTGGGCCGTCACTAAGCCACA[A/G]AGCAGATGGAGTTCATGTTAGATTTTTCCCCCAAA R 2 1 2 1 101000 r 74 goat snp36845-scaffold447-2292768 9 82243732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390243 Affx-122967765 AX-123260600 9 81175431 CGGGCTGGAAGGCCTTTGCCCCACCGACCAGCAGG[A/G]TGATCTGGGGAGAACCACGTTCCCTTCCAGAGCCC R 2 1 2 1 103000 r 74 goat snp36844-scaffold447-2230003 9 82307242 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428698 Affx-122938626 AX-123299040 9 81220326 GCTTGAGCACAGCCCCCACTTTGACAGAGCTGCTC[A/G]CTCAGCCGTGTCCAACTCATTGTGACCCCACGGAC R 2 1 2 1 103000 f 74 goat snp36843-scaffold447-2185108 9 82351911 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399982 Affx-122960820 AX-123270337 9 81259335 GCAGCAAAGCTACAAGAGGAATATTATATTGCTAT[C/T]CTGAAAAGGAATATTATATATCAAACTGAATCACT Y 2 1 2 1 101000 f 74 goat snp36842-scaffold447-2146099 9 82391062 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376144 Affx-122978856 AX-123246503 9 81304217 CACAGGAAGAGCATTACCATAGGGAAGTCAGACAG[C/T]GGTGGTGGAACCAGATAGACGTCCCCCTGGGCCCT Y 2 1 2 1 101000 f 74 goat snp36841-scaffold447-2101217 9 82435715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390169 Affx-122967972 AX-123260526 9 81380993 ATTCATTATTTATGGGAGCCTGCATCCTGAGTAGT[A/G]TTTTAAAGGAAGGGAAAGATAGAGTTGCTGAAGAC R 2 1 2 1 101000 f 74 goat snp36839-scaffold447-2024441 9 82512368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389986 Affx-122968058 AX-123260343 9 81414831 CGTGCAGGTGTGGGGCCTGAAACTCATGTCCCACT[G/T]TCTCTGTAAAGCCATTTTTGTTTCCACATAAATCA K 2 1 2 1 101000 r 74 goat snp36838-scaffold447-1990603 9 82546460 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772133 Affx-122977394 AX-385259288 9 81461940 TTCACAGTAAGCGTAATGTGGTCTCAAAATCCTGA[C/T]GTGTAACTCATCGACTGAAAACTTCGTATCATGTT Y 2 1 2 1 101000 f 74 goat snp36837-scaffold447-1943494 9 82593482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276331 Affx-1111835363 AX-519549863 9 81465097 AGAGACGGAGTCCTTACATTAAGTGCTAAGAAAGC[A/G]TGTGTTGAGGAGTTTTTATCTGCTTGGCCAGAGGG R 2 1 2 1 101000 f 74 goat Random2.2K-1021 9 81465097 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381604 Affx-122974787 AX-123251962 9 81522487 CAGAAAAAAACAACATGTAACAGGCTGATGTGTAC[G/T]CTATGCTATAATTTATCTTTAAAAGAAGGAATTAA K 2 1 2 1 101000 f 74 goat snp36836-scaffold447-1882947 9 82654052 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402558 Affx-122958455 AX-123272911 9 81570068 TTTGGGGCAAGAGGAAGAAGCAAGAGAGTCTAGAC[A/G]TGTAATCTGATGTAGTCTTGAGATTCCTGGCCCAT R 2 1 2 1 101000 r 74 goat snp36835-scaffold447-1835366 9 82701410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413941 Affx-122950725 AX-123284290 9 81626778 GGAAAAGCAGCCCATAATTTTTCCTGAACGGAACC[A/G]CAACTGATCCTGTCCATTTCTGTTCAGAGTTTACG R 2 1 2 1 101000 r 74 goat snp36834-scaffold447-1778656 9 82758146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430338 Affx-122938214 AX-123300679 9 81662449 GCTCCTTGATAACATCCTATCTGGGTCCATAAAAA[C/T]AAATCACTTTTTTCTCTTAATTTCTAAATGAAAGC Y 2 1 2 1 101000 f 74 goat snp36833-scaffold447-1742985 9 82792729 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798184 Affx-122957901 AX-385285119 9 81694006 TTGTCTCAAGTGTTTAGTACAAATAGTCCAATTCA[C/T]TAACAGCACAGTACTGACTCATTGAATGAATTCCT Y 2 1 2 1 101000 r 74 goat snp36832-scaffold447-1711428 9 82824063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442603 Affx-122928480 AX-123312940 9 81726277 CAGCATTCACGTTCAGATTGAATGATGGTGTGCTA[C/T]GAACTCAGGGCACACGTGTGATTCCTGAAATGAAG Y 2 1 2 1 101000 r 74 goat snp36831-scaffold447-1679157 9 82855394 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389960 Affx-122968076 AX-123260317 9 81792522 AGGTTGAAGCATATCAAGGCACCAGTAATGGCACC[A/G]CCGAAGGTTCTCCGCAGAGGTGGCTCTCCAGCAAT R 2 1 2 1 101000 f 74 goat snp36830-scaffold447-1612912 9 82922656 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388597 Affx-122969153 AX-123258955 9 81832060 TAGCATCCTTGGTGTCTCAGATGAGGTGCTGGGGA[C/T]GGGAAGATGTGGGAGCTAGCCTGAGAGGCCCTCCC Y 2 1 2 1 201000 r 74 goat snp36829-scaffold447-1573374 9 82962450 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448431 Affx-122923657 AX-123318767 9 81873714 GCAAGCCCCTGTGGTTACTCCTTGCTGGACTTGCC[A/G]TTGAAGGTGGATAAACCCTAACTGCCCTTAGTCAC R 2 1 2 1 101000 r 74 goat snp36828-scaffold447-1531720 9 83004575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383814 Affx-122973179 AX-123254172 9 81921475 CTGCTGGGCACAAGGCTTGAGGCTTCATGAAGAAA[C/T]GCCTTTCTGTGTCATCTTTAAAAGACTTCGTTTGC Y 2 1 2 1 101000 r 74 goat snp36827-scaffold447-1483959 9 83052675 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774995 Affx-122972905 AX-385262127 9 81966867 GCAAGCATAAAAGCAGTGAGAAAGGTGTGGCCAAT[A/C]TGTTCTTTAAAAACATTGCAATAAAAGTAGTCAGT M 2 1 2 1 101000 f 74 goat snp36826-scaffold447-1438567 9 83098356 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381352 Affx-122974412 AX-123251710 9 82012973 AAAAACTGGGGTTCTTCTTGTGAAGGAGAGGCTAA[C/T]GGCCCCCAGGAGGTACCTCTAAATCTCTGTGGAAA Y 2 1 2 1 101000 f 74 goat snp36825-scaffold447-1392461 9 83145375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770445 Affx-122943415 AX-385257611 9 82046268 AGCCCATTGATCTGAAATAATCATGGTAATTGATG[A/G]TAAAATAGGACCCAAATCAAGGAGTCACAGAGTGA R 2 1 2 1 102000 r 74 goat snp36824-scaffold447-1359166 9 83178294 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441280 Affx-122929472 AX-123311617 9 82092212 TGAGCTCTTCCAATCCACGCCCTGGATGGTTCTCT[G/T]GAACCAAGCAGAGCCATTAGATACCAAAATCAACA K 2 1 2 1 101000 r 74 goat snp36823-scaffold447-1313222 9 83224674 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778795 Affx-122934235 AX-385265904 9 82126873 TTGTGTAATAATGAAACTTTGATACTGAGAAATTA[C/T]AGCTTCACTGCAAATCTCAGATTCGTGACTCTAAA Y 2 1 2 1 10000 f 74 goat "snp36822-scaffold447-1278561;SV_335" 9 83259300 A G SV_335 2 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398501 Affx-122961560 AX-123268856 9 82157390 AGTTTAGGGGTGTTTTAAAGAAACCCGGGTTAATC[A/G]TCGTCTTGTGACATTTCTCTCTCTCTTTTTGTTTT R 2 1 2 1 101000 f 74 goat snp36821-scaffold447-1248044 9 83290032 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440523 Affx-122929342 AX-123310860 9 82259011 TTAATGAAGTTCCTTTGTTTTCTGCCCAAGATAAC[A/G]TCACAGTATTTAGGCACCACCCACACTGCTCCTCC R 2 1 2 1 201000 r 74 goat snp36819-scaffold447-1146423 9 83392074 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448592 Affx-122923398 AX-123318928 9 82350376 TCCAGTGTCCAAAACTCTCTATTAAGACTAGATGG[C/T]AAACATTTTAGGCATTGTGGTCTCCGTCATAACTG Y 2 1 2 1 101000 f 74 goat snp36817-scaffold447-1055058 9 83484271 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770816 Affx-122922850 AX-385257980 9 82385435 TTCACTACATGAAGTATTTTATATGCAATGAAACT[C/T]GCTGTCTGTTCAAACCTCTGACAAAGTAGACACTG Y 2 1 2 1 101000 r 74 goat snp36816-scaffold447-1019999 9 83519316 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377461 Affx-122977517 AX-123247820 9 82466561 TGGGACCCTGACATGGGCTGCTCAGTCCACAAGAC[A/G]CAGGACTGGACCTGGGCCTTTCATGTTAGAACCGA R 2 1 2 1 101000 r 74 goat snp36815-scaffold447-938873 9 83597567 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383005 Affx-122973327 AX-123253363 9 82503488 GTCGTGACCACCCCACCAGTCCTGGCTTTTTATTA[G/T]CCTGCAATAGTGTCCTTTCTGACACAGCTCTTGAA K 2 1 2 1 101000 r 74 goat snp36814-scaffold447-901946 9 83634314 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433136 Affx-122935687 AX-123303477 9 82548888 CAACTGTACTGTGTTGGTAAAAGATGTGGATAGAC[C/T]GGCAGTGTCCTTAAAATCTTTTTGATGGGCAGTAT Y 2 1 2 1 101000 f 74 goat snp36813-scaffold447-856546 9 83680312 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431158 Affx-122936567 AX-123301499 9 82584191 CACCTCACATTGACAGAACTGTTGCTCTCTGATCC[A/G]CCAGGTAAGCCTGATTGCTGATGTCACTGTTACTG R 2 1 2 1 201000 r 74 goat snp36812-scaffold447-821243 9 83715632 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782349 Affx-122937885 AX-385269426 9 82627561 AGCGTAATTTTTCTAGGTCATCTACAATATCCTTC[A/G]GCTCTCTGAGTCATTTTAGGAAAGCTCAGTGACTC R 2 1 2 1 101000 r 74 goat snp36811-scaffold447-777873 9 83759495 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419105 Affx-122945775 AX-123289453 9 82668199 TACCAGGCTTCCAACGGGAGCCACTCAGAAAACAG[C/T]GTGCACCCGCTCGGCCTGTCTCTTCTGGTGCCCCC Y 2 1 2 1 102000 f 74 goat snp36810-scaffold447-737235 9 83800617 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419092 Affx-122945787 AX-123289440 9 82717083 ATGAGGGATTGGTTTCTGGGCAAGAAACAAACTTA[C/T]AGTTACCAAAGGGGAAAGGGTGGGAGGGATAAATT Y 2 1 2 1 103000 f 74 goat snp36809-scaffold447-688351 9 83849441 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419089 Affx-122945789 AX-123289437 9 82746596 TGGCACTGGGATGAATGTGTTCAAAGCTGCAACGT[A/G]GGGAATCATGAGAACAAATTCTACCTTGGGAATAA R 2 1 2 1 101000 f 74 goat snp36808-scaffold447-658838 9 83879455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413923 Affx-122949816 AX-123284272 9 82797926 GTTCATGATAAAGAAATGACACGGTAGAGTAAGAA[C/T]TAACATAACATTATAAATTAACTATATTTCTATAA Y 2 1 2 1 101000 f 74 goat snp36807-scaffold447-607508 9 83930721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435300 Affx-122934027 AX-123305640 9 82851034 TCTTTTCATCATCAGCGAAAGTCATTTTTAACAGC[A/G]CACTTTCAATTCTCTCTGTTCCTTTTACTTTTACC R 2 1 2 1 101000 f 74 goat snp36806-scaffold447-554400 9 83983886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797761 Affx-122938083 AX-385284700 9 82893135 ACCCAAAATCAATTTACTGACTAATATACCCAGAC[G/T]AATATAACTTTGTTAAAGTTAATTTAACAAAGAAA K 2 1 2 1 202000 r 74 goat snp36805-scaffold447-512299 9 84026426 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406748 Affx-122955736 AX-123277099 9 82930037 ATTTTGGAACGATTACAAAAGAAAAGTATTTCAAG[A/G]GTTACTGGAGTTTTTATGTGGATAGGTTCACACAC R 2 1 2 1 101000 r 74 goat snp36804-scaffold447-475397 9 84062386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420891 Affx-122944616 AX-123291238 9 82960991 TCAATCTTTTAAAAACATTTAATAGCAAAAAGAAA[G/T]AAAAGAATACCATCAACAACAGGTAATTTGGGCTA K 2 1 2 1 103000 r 74 goat snp36803-scaffold447-444443 9 84088103 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391494 Affx-122966680 AX-123261851 9 83003589 CTTACAGCTGCCCAGCATCTGGACTGGGACGACCA[A/G]CATCAGGGCTGAAGGCAGGGAGGTCACCTGCTGCT R 2 1 2 1 201000 f 74 goat snp36802-scaffold447-401845 9 84132982 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435491 Affx-122933435 AX-123305831 9 83038741 TAATTTTTTTTTTTAAAGATCTGTTCACACATAAT[A/C]TTTTATAGGAAGATACCCAGCTGGGTCATTATTTC M 2 1 2 1 102000 r 74 goat snp36801-scaffold447-366693 9 84168109 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393781 Affx-122965193 AX-123264136 9 83067824 CTTGGTGGACAGATGAGCTAATGAATGAATGAAGT[C/T]GTTAGTGGATGAATGAATGCTTGCCTGAATCCCAG Y 2 1 2 1 101000 f 74 goat snp36800-scaffold447-337610 9 84200090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273451 Affx-1111833626 AX-519547075 9 83084398 GTTTTAAAATTGTTAAAAGTTTCCCAGGAAATACA[A/G]AGCTTGCCTGGCCTGGGACTGTGAATTAGTGTTTG R 2 1 2 1 201000 f 74 goat 9_83084398_AF-PAKI 9 83084398 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320780234 Affx-122967644 AX-385267329 9 83108337 GGTTCTACGCTATTTTAGGAGCTTCACATACACTG[C/T]CTCATTTAAACATCACAATCACTCCATGAATTTGA Y 2 1 2 1 101000 f 74 goat snp36799-scaffold447-297097 9 84241495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386233 Affx-122970974 AX-123256591 9 83149475 TCCTGTATTATGAATTTTTTCAAGCCAAGTAACAC[C/T]GAAGAAGTGATTTAAAATTACTCATGGTATATATT Y 2 1 2 1 101000 f 74 goat snp36798-scaffold447-255959 9 84279453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452380 Affx-122920620 AX-123322713 9 83196475 GGGAATCTAGGATGAGTAGGATCCAAGTCCTCTTC[A/G]TTTGGGTTTCCCTGGTGGCTCATCAGTAAAGAATC R 2 1 2 1 101000 f 74 goat snp36797-scaffold447-208959 9 84326777 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274067 Affx-1111833987 AX-519547671 9 83208852 GGAATGGGGCAGAGGCTAGGAGGCAATGAGAGGAA[A/G]ATAAGACACCGCTAAATCTGCAGTTGGGCTCTTTC R 2 1 2 1 201000 r 74 goat GoatD01.012888 9 83208852 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402555 Affx-122958458 AX-123272908 9 83230360 CCTTGAGCAAAACAGCAAGTGGAGAGATTTATTTA[C/T]GAAATAGTGCAAAATGGTAACGTCCAAATTGCTTT Y 2 1 2 1 101000 f 74 goat snp36796-scaffold447-175074 9 84360485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447528 Affx-122924058 AX-123317864 9 83272139 ACCCTTTAGAGGAACACATTTAAAGATTTCAGATT[G/T]CTCCTAAAGCAAAACCAAATTATCTGAGTGTAAAA K 2 1 2 1 101000 f 74 goat snp36795-scaffold447-133295 9 84402719 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792868 Affx-122940181 AX-385279846 9 83321286 GACTCCAGGTGTGTCATTCTCAAACCAAGGTATCC[G/T]ACATGGAGGATAATACACAGAGTCATAGGATGAAT K 2 1 2 1 101000 f 74 goat snp36794-scaffold447-84148 9 84452008 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780327 Affx-122943584 AX-385267422 9 83352083 TGACAGATGTCCAGGGATGAAAAGAACATTATTAG[C/T]AATAAAACTGAGACTATAAACAGCAATGTGACAGG Y 2 1 2 1 201000 f 74 goat snp36793-scaffold447-53351 9 84482785 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798673 Affx-122940324 AX-385285605 9 83380742 TTCTTAAAGCTTCAAAATCTACAAATGTTCCTGCT[A/C]TCCTACTCAGATAAGCTGTGCTTACTGATAAAGTG M 2 1 2 1 101000 f 74 goat snp36792-scaffold447-24692 9 84511545 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451009 Affx-122921715 AX-123321343 9 83419941 AAGAACCTCCCCTATATCACATCCTCCTCTGGGTT[G/T]ATATTAGCATTATGTCTTCGGGAGAGTTGATTTAT K 2 1 2 1 201000 r 74 goat snp39169-scaffold5-14408 9 84550844 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382609 Affx-122973708 AX-123252967 9 83487389 TTCCTAATGTCAAGAGTCCAGGCTCCTTTATAGGC[A/G]CCCCCCAGAATCCTTATAAGCAGAAGAACCTGGAA R 2 1 2 1 101000 f 74 goat snp39170-scaffold5-81856 9 84618439 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375557 Affx-122979088 AX-123245916 9 83539979 AAAAAAAAAAAACCAGTGAGAGGTAATATTAGATA[C/T]GGGACAGAGAAGCAACGGGGCCAATTTCTACAATT Y 2 1 2 1 201000 f 74 goat snp39171-scaffold5-134446 9 84670580 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788912 Affx-122935906 AX-385275926 9 83584008 CTACATCATCTATAATCTGCTTATGTGTTTTAAAG[C/T]AGGAGCTTTTTCAAACAAAGGTCTACACATACATT Y 2 1 2 1 101000 r 74 goat snp39172-scaffold5-178475 9 84714292 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787965 Affx-122960901 AX-385274986 9 83638391 AATAATTGATTGAATAGTTTTAGTTTGTCATAGAT[A/G]TATCTTAGACTTGATGATAACCTCTTAAGGATTTC R 2 1 2 1 101000 r 74 goat snp39173-scaffold5-232858 9 84767558 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389625 Affx-122968749 AX-123259983 9 83679009 GTAATTAACATATCTACTATACACACTGAAAAATC[A/G]TTTCTACAAAATAGCCACAGTTGCAAATGCCTAAT R 2 1 2 1 101000 r 74 goat snp39174-scaffold5-273476 9 84808012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406200 Affx-122956136 AX-123276552 9 83708260 CAGTACCAACGCAAAGCTGATCGCGACCCCACACG[C/T]GCAGGTGTTTTCTATAATATGAGAGCATGATAGAA Y 2 1 2 1 101000 r 74 goat snp39175-scaffold5-302727 9 84837051 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799418 Affx-122979159 AX-385286348 9 83822243 ATGTAGAAAGTGTGAAAAAGTCTAGGGTCAGAGGA[C/T]CTATGAAGTGATTGATCTGCTCGAAGTCCTTGCTT Y 2 1 2 1 101000 f 74 goat snp39178-scaffold5-416710 9 84950549 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418244 Affx-122947032 AX-123288592 9 83860810 AGCGCCAATGTCTGATACAGGCACAGTTAACAACA[C/T]GAGCAGAGACAGGGACTACCTACTGCAGGGTGACA Y 2 1 2 1 101000 f 74 goat snp39179-scaffold5-455277 9 84988869 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38411237 Affx-122952341 AX-123281587 9 83893490 TGATGACTCTGCAGACTGTAGAGCAACTGGAACTT[G/T]CTGTTTGCTGCCAGTGTCCCTGGCAAACACTCTGG K 2 1 2 1 101000 f 74 goat snp39180-scaffold5-487957 9 85021523 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442802 Affx-122927718 AX-123313139 9 83943166 ACCACTTAGCTGCATTGATCTGCTCTAACCTGCCA[C/T]GCTCAGTTCAGCCCTTCCTTGAGTCCCTTAGGGAG Y 2 1 2 1 101000 f 74 goat snp39181-scaffold5-537633 9 85070784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438667 Affx-122930885 AX-123309004 9 83993290 GGAAAAAAAGCCCAACACAACCACCTCAGGCTCAA[C/T]AGGACGGCGACTCTTGCACTTAAATTCTTGGTTTA Y 2 1 2 1 101000 r 74 goat snp39182-scaffold5-587757 9 85120442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795019 Affx-122931329 AX-385281978 9 84046454 TTTTATGAGTCAATTCTCACTTAGTGAATTATCAC[A/G]CTGGTGATTTGGAGACATTATCTTAATTCCTAATG R 2 1 2 1 101000 f 74 goat snp39183-scaffold5-640921 9 85173618 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436219 Affx-122932579 AX-123306558 9 84082975 GGATCTAGTTCCCTCAGCCTATCCTGTTTCTGTAA[C/T]GAGAAAGCACAGCCAGCCCCATATTAATGGTCTGA Y 2 1 2 1 201000 f 74 goat snp39184-scaffold5-677442 9 85210122 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377185 Affx-122978198 AX-123247544 9 84114779 AGACTGAATTTCTAAACTGTTCAGATCTTAGTATT[A/G]TCTTCATATTTTATTATTTCTGCATAAAATGTCTT R 2 1 2 1 103000 f 74 goat snp39185-scaffold5-709246 9 85241842 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772639 Affx-122930206 AX-385259787 9 84147442 ATATAAAGAGTACAGTCATACAGCACTTAATACAG[C/T]GAATATTATTCCTAAGCTGCAATATATCTGCTGCA Y 2 1 2 1 101000 f 74 goat snp39186-scaffold5-741909 9 85274564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450114 Affx-122922771 AX-123320449 9 84184666 CAGAGTCGGACACAACTGAAGCGACTTGGCGGCGG[C/T]GGCAGCGTCTCCGTATTTTACACTACAACTTATCT Y 2 1 2 1 101000 r 74 goat snp39187-scaffold5-779133 9 85311835 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391774 Affx-122967461 AX-123262131 9 84225474 TGCCTTCTTCTGACAACTGCCTGAGATTCTGCTCT[A/G]TGATGATTATTTGGTTCACTGTTCGTTTTTCGACT R 2 1 2 1 201000 r 74 goat snp39188-scaffold5-819941 9 85352569 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780100 Affx-122967666 AX-385267197 9 84285629 TTCAACAGAGATTTGTTTGGTGTACATGGCATTAT[A/G]TTTACTTGATAGGTATATTTGTTCAGTATGGCAAA R 2 1 2 1 101000 f 74 goat snp39189-scaffold5-880096 9 85412771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787689 Affx-122925552 AX-385274712 9 84341838 GAATCAGTGTCAGAGCAAAGCTTCACTGCCTGTAC[A/G]TTGTTGACTGACATCTAGAAGGACTGACTGAAACC R 2 1 2 1 101000 f 74 goat snp39190-scaffold5-936305 9 85469293 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422278 Affx-122943493 AX-123292624 9 84402996 AGACAAAGAATGGGATAAGGAAAAAGGGGCAGAGA[C/T]ACAATAAAAATTATATAGTGAAAGGAACTGAAGGT Y 2 1 2 1 101000 f 74 goat snp39191-scaffold5-997463 9 85530938 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771703 Affx-122969429 AX-385258860 9 84437280 AGCTTAAAGAACAAACAATTAATTAGAAATTAGCC[A/G]TAGAGACCAAGTCTTCTGGTAGCAAATTAAGATAA R 2 1 2 1 101000 r 74 goat snp39192-scaffold5-1031747 9 85565356 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390252 Affx-122967758 AX-123260609 9 84472598 TGTGTATTAAAATAATTGTGACTTTTATTTTATTT[A/G]CTAAAAATACAGATATTCTGGGATTTGCCAGTTTA R 2 1 2 1 103000 r 74 goat snp39193-scaffold5-1067065 9 85601326 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792317 Affx-122950037 AX-385279299 9 84507922 TAAGACTTGTATAATCCGAAGAGAAAGGCTGCAGT[A/G]CTTTCTATATACGAATAACAATCTTGGTTCTTTCT R 2 1 2 1 101000 f 74 goat snp39194-scaffold5-1102389 9 85636824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389191 Affx-122969077 AX-123259549 9 84547979 GGGACATAGGAAACTAAAGGATGGAGGCATTAGGT[A/G]TGGGAAGTTGAGACAGTTAGGGTGGTCAGAGGGTA R 2 1 2 1 201000 f 74 goat "Random2.2K-1025;snp39195-scaffold5-1142446" 9 85678600 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380892 Affx-122975041 AX-123251250 9 84630894 CATTATTGCTCCAAACCTCCCTTTCTCCATACTCC[A/G]TCCTCTCTGAAGTCCCATGAGTCAAATGTGGGAGC R 2 1 2 1 201000 r 74 goat snp39197-scaffold5-1225361 9 85758334 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274228 Affx-1111834125 AX-519547826 9 84665445 TCACACCCAGCTCTCCATCAGCCCTGCTTGGCGCT[A/G]GGGCTGCAGTCCCCCCGAGCCTCAGTATGTGTGAC R 2 1 2 1 202000 f 74 goat GoatD01.020206 9 84665445 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38431439 Affx-122936507 AX-123301780 9 84668164 TCTTTTCTGCAGGTTGGCATGACCCATTGAGATCA[C/T]GGCCACCCCTTCACGTGGGGCCTGGCCTTGACTTT Y 2 1 2 1 103000 f 74 goat snp39198-scaffold5-1262631 9 85795217 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395241 Affx-122964472 AX-123265596 9 84708503 GGAGGAAAAAACCACACCTGGGAAGTTACAGGCCA[C/T]GAGCAGATCCAGGGGGAAAACCCCCGCCTTCTGTC Y 2 1 2 1 101000 f 74 goat snp39199-scaffold5-1302970 9 85835669 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793499 Affx-122976906 AX-385280476 9 84766919 TTTACTTCATCCCGGTTCTCAGTTAAAACACAGAG[C/T]GAGACTGGCCTTTGGAATGTCCTTCTGTCTACAAA Y 2 1 2 1 101000 r 74 goat snp39200-scaffold5-1361386 9 85894346 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779953 Affx-122972210 AX-385267052 9 84796315 TCACCATATGTGACTGAGTTTTTTCATAACTTAAG[C/T]ATTATGCGTATATAATGGAACTAAAGAAGAAAGTC Y 2 1 2 1 101000 r 74 goat snp39201-scaffold5-1390782 9 85924534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450995 Affx-122921724 AX-123321329 9 84830824 TTGGAATCTTGAAGAAGCCTTTTGAAAGTCTGTGC[A/G]TACCAATTAAAATAGGTATGCCACTCTGTTTAATG R 2 1 2 1 101000 f 74 goat snp39202-scaffold5-1425291 9 85959160 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402027 Affx-122958743 AX-123272380 9 84880560 GTGGGCACCAAAGTTGCCTCTGCGGTTTGGAACAT[A/C]TAGAGGCCCAGCCTCAGCCCTTCTAGCTCCTGGTG M 2 1 2 1 101000 f 74 goat snp39203-scaffold5-1475027 9 86009022 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395326 Affx-122964047 AX-123265681 9 84931077 TTTTTCCCACTTTATCCCGAAATGTTGGGGGGCGG[A/G]GAAAGGATGAGTAGAATCTTTGGTCAAATAAGATC R 2 1 2 1 201000 r 74 goat snp39204-scaffold5-1525544 9 86058930 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450789 Affx-122921821 AX-123321123 9 85144583 AAATCAGACTCATTTCTACCGAACCAGATCACTTG[C/T]GTAGTCCATCTCTGCTGGTTTTAGTGGCCTAAGCC Y 2 1 2 1 101000 f 74 goat snp39209-scaffold5-1739050 9 86273862 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391877 Affx-122966974 AX-123262234 9 85203916 GAGGATGAATAATGAGAATGTTACTCATGCCCCGA[G/T]AGCATGGCATTTGCGAATCTCATCATCGTTTTGCT K 2 1 2 1 101000 r 74 goat snp39210-scaffold5-1798383 9 86333729 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393871 Affx-122965135 AX-123264226 9 85261749 AGAACTGTCAGGTTGGGGTTCTAAGTCACTTTAGA[C/T]AACCGGAGACCCTTAAACTAATGACCACACCGAAT Y 2 1 2 1 101000 r 74 goat snp39211-scaffold5-1856216 9 86390256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381721 Affx-122974697 AX-123252079 9 85313386 TTAATAGGAGCTAGACTGGCCACAGGTTCAGAACG[C/T]GTTAAAGAGCAATTTAGACATGTATGCAGAAACAA Y 2 1 2 1 201000 r 74 goat snp39212-scaffold5-1907853 9 86441087 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407289 Affx-122955329 AX-123277640 9 85395394 AGGTGCTGGAGATTCAAGAGACTTGTAAAAGCAGA[C/T]GTGGCCCCTGGATCCACCTGCAAAGCCTTCCCCTT Y 2 1 2 1 101000 f 74 goat snp39214-scaffold5-1989861 9 86523137 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801967 Affx-122974214 AX-385288871 9 85446151 TGGATTTTTGAGACAAATAACAGAAATAACAGCCT[A/G]TAAGCCAAACTGACTTTGATTTATAAGAACTAGAC R 2 1 2 1 101000 f 74 goat snp39215-scaffold5-2040618 9 86573644 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385219 Affx-122971704 AX-123255577 9 85489020 TACTCCCTGTCCACCTGAAATTCGAACTTAGCTGG[C/T]ATCCTATTTCTATCTTCTAAATCCAGCCACCCTAA Y 2 1 2 1 201000 r 74 goat snp39216-scaffold5-2083487 9 86616390 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379626 Affx-122975961 AX-123249984 9 85540823 CTCAATAGCAGAAAGCTGTCAAGTGGTTGGATATG[C/T]GTGTTTCTATATAGAAATGCTTGGCTCATTAAGTT Y 2 1 2 1 101000 f 74 goat snp39217-scaffold5-2135290 9 86657015 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386338 Affx-122970873 AX-123256696 9 85582106 AGCTTACAGTCTAATGGGAAATGAGACATGTGAAA[A/G]TAAGTTTTAAAACAAAGATGTTTGAATTGCGACTG R 2 1 2 1 101000 f 74 goat snp39218-scaffold5-2176573 9 86698811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409470 Affx-122954066 AX-123279821 9 85624398 AATCAGTGTTAATTTCCCAAAGTGGATAACTGCTG[C/T]GGTGATGGAAGAGTTCCATCTTATCAATGTACACG Y 2 1 2 1 101000 r 74 goat snp39219-scaffold5-2218865 9 86740413 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803018 Affx-122963212 AX-385289895 9 85675811 TTTCCGTTTGGTGGTTTTTAGTACACCCATAAATT[A/G]ATAGATAAACTTGTTAAAAACTCAAGAAAAAATAA R 2 1 2 1 201000 r 74 goat snp39220-scaffold5-2270278 9 86791692 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436944 Affx-122933181 AX-123307282 9 85710601 TCCGGACAGAATGCCCCAGAGTCTGCTTGTTAGCA[C/T]GAGTCTATGCATCTGATGAGCACTGAGCTACCTTT Y 2 1 2 1 101000 r 74 goat snp39221-scaffold5-2305068 9 86826341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273490 Affx-1111833627 AX-519547107 9 85715472 TCTGAGTGGAACATTATTAATCCTGGTGATTCATG[A/G]TCTGCCCTGCCATTTTGCAGTCTTTTAGTACAAAA R 2 1 2 1 101000 r 74 goat 9_85715472_AF-PAKI 9 85715472 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38432916 Affx-122935315 AX-123303257 9 85751084 GGGTTAAAGTCAAGTCAGGGGTGTGGGAACACCAT[A/G]CTTTGTTAAGATCTCAGAGTTTTAAGAGGTGCTTG R 2 1 2 1 101000 r 74 goat snp39222-scaffold5-2345551 9 86866786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384829 Affx-122971975 AX-123255187 9 85782864 GGATAAAGAAATTCTGCTTAGTCATCACTGCCAAC[C/T]CTGTGTCATGTTCCCTCCTCCATCCACAGCTCCAT Y 2 1 2 1 101000 f 74 goat snp39223-scaffold5-2377331 9 86898421 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773264 Affx-122920947 AX-385260407 9 85825977 AGTCCTGGCAAAATATTATCCTCAGAAAGCAGTAA[G/T]AATAATCACACCTTTAGCTACTTCTATTGATTAGT K 2 1 2 1 101000 f 74 goat snp39224-scaffold5-2420444 9 86941581 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792376 Affx-122927854 AX-385279357 9 86005690 AGCATATCTTTAATTAGGACAAGCTGGTATAAATT[A/G]TCAAATGAAGAGACAGACTTAGAAAATTTAAAACC R 2 1 2 1 101000 r 74 goat snp39228-scaffold5-2600157 9 87122863 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793405 Affx-122958905 AX-385280382 9 86036046 GTGATTGTCACTTCACACACTGATTCAGTTTTCTC[A/G]TCCAAAATATAATTGCCAATAATCTTACATGTACA R 2 1 2 1 101000 f 74 goat snp39229-scaffold5-2630513 9 87153710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445375 Affx-122925407 AX-123315712 9 86076292 TTGCCACTCTGGTTCCTGGAAGGCACCTGGCTTTC[A/G]TCAGATTACCTTGGAAGCCCTGCTGGCACAGGTCA R 2 1 2 1 201000 r 74 goat snp39230-scaffold5-2670759 9 87194104 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276483 Affx-1111835364 AX-519549995 9 86079492 CGCATCATTTACAATTTCTCAGACTTAAAAGAATC[A/G]TGTCTGGTCACCCAGACCCATGATTATATATCAGG R 2 1 2 1 101000 r 74 goat Random2.2K-1027 9 86079492 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412308 Affx-122950859 AX-123282657 9 86113193 TATTTACTTTCCCAGTGGACACTATTATTATCCTC[A/G]TTTACCAGAGAGGCTTAAAGATGCAATGTGACAGT R 2 1 2 1 101000 r 74 goat snp39231-scaffold5-2707660 9 87231527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441780 Affx-122929098 AX-123312117 9 86144146 GTGATATGAGTAAGATATGTGGTGAAGGGAAATGA[C/T]ATGATCATAAAGGTATTTGAAAGAAGGAGGGATAA Y 2 1 2 1 101000 f 74 goat snp39232-scaffold5-2738613 9 87263222 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405634 Affx-122956592 AX-123275986 9 86210597 TGCAGCGTCTCTTCGTGGTGATGGAGGAGGCACGG[A/C]GATGCAACTGGTTGCAAAAACATCTTTAGCTTTTT M 2 1 2 1 101000 r 74 goat snp39233-scaffold5-2805064 9 87329842 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794232 Affx-122935702 AX-385281198 9 86250564 ACAGCATTTCAGAAAAGATCACTCATGGTATATAA[C/T]TGTGAACTAAGAGATGTTGAGTGAATAGTGTAGTC Y 2 1 2 1 101000 r 74 goat snp39234-scaffold5-2845031 9 87369624 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776927 Affx-122923126 AX-385264051 9 86279732 CAGATCTGACCACTAAGATTAGTTTTATTAGGCAG[C/T]ATTTCACTTCAAGGTACCCCTTTCTTCACTGTTTG Y 2 1 2 1 101000 f 74 goat snp39235-scaffold5-2874199 9 87404501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432686 Affx-122936039 AX-123303027 9 86310057 AGATTAAGTTCCCCAAGGTAGACACTGTGATAAAC[A/G]TTTAAGGGCAAATGCTTTGTCTTGGAAATAGTCCC R 2 1 2 1 201000 r 74 goat snp39236-scaffold5-2904524 9 87434662 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791461 Affx-122973392 AX-385278452 9 86358887 ACGGAGGAACAGAGAGGGGAGAACGCTTGAGAATT[A/G]TCGTGTGCACCCAACCATAAAAATTCCATCTAAAT R 2 1 2 1 101000 f 74 goat snp39237-scaffold5-2953354 9 87483807 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382436 Affx-122974235 AX-123252794 9 86414293 CTGTTTTCAGCACGAGTTTAAGGTAACTCATTTGA[C/T]AGCCTTTATAAGTGAACAAACTATTTGTCAAATAC Y 2 1 2 1 101000 f 74 goat snp39238-scaffold5-3008760 9 87538828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802805 Affx-122955756 AX-385289704 9 86466311 GACATTGCTACTCTTGCTAGTTATTTCAAGAGCAT[A/G]TTAGGGTATTTCAAAGATCCTCAAAATTAAATTAT R 2 1 2 1 101000 f 74 goat snp39239-scaffold5-3060778 9 87591285 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392556 Affx-122966085 AX-123262913 9 86524777 TTACTCTCGTATTTCTGCCACACATTTGCCTCGTG[C/T]ATTCACTTACACATTTTTTTTTCATTTAACAAATA Y 2 1 2 1 101000 f 74 goat snp39240-scaffold5-3119244 9 87650346 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778314 Affx-122963923 AX-385265429 9 86564281 TTCAACTTTCTTACTGTTTAAAGTAGTACTAATAG[C/T]GTACATCTTGTACACCATTGAGAGGTGAATAGGTT Y 2 1 2 1 201000 r 74 goat snp39241-scaffold5-3158748 9 87688760 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405385 Affx-122956300 AX-123275737 9 86606794 ATGTTTGACTTGTTTTTGATGACTGAACATTTACT[A/G]TGTTCTATAAATATCATTCTGAGCAAGAATTCTAC R 2 1 2 1 201000 r 74 goat snp39242-scaffold5-3201261 9 87731670 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419278 Affx-122946248 AX-123289626 9 86637923 GTCCAGAGCAGTCACTAAGAACATCTTAAAAGCAA[C/T]AGAATTACAAACACACAAAAGGAAAAAAAAAAGAA Y 2 1 2 1 101000 f 74 goat snp39243-scaffold5-3232390 9 87762398 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453995 Affx-122919441 AX-123324328 9 86691307 GTGTGTGGATCCACTTACGTGCAGATCTCTTTCAA[C/T]AGATACCACAGTAGCACTGTACATCCAGGACGGGT Y 2 1 2 1 101000 f 74 goat snp39244-scaffold5-3285774 9 87816700 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772516 Affx-122928531 AX-385259667 9 86727829 AAAAGATCACTCTTTTGGCTTTAATAATTTACCTT[A/G]TCCTGCCTTATGCAACAGAGCTTTTGCCCACAGCA R 2 1 2 1 101000 r 74 goat snp39245-scaffold5-3322296 9 87853302 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413035 Affx-122950991 AX-123283384 9 86776497 GTAAACCTCACATTAATAGTAGTATATAATGTTTT[G/T]AAAAAACTTTAAAATATATGGAAAGGAATGAAAAT K 2 1 2 1 103000 f 74 goat snp39246-scaffold5-3370964 9 87901693 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412186 Affx-122951058 AX-123282536 9 86821951 CATGCCTTTAAATCTTATTTTTATATATCATGGAA[C/T]GCAATTAGAAGCTAACAGAAAGAAGACTGCAAGCC Y 2 1 2 1 101000 r 74 goat snp39247-scaffold5-3416418 9 87947270 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442279 Affx-122928264 AX-123312616 9 86863619 GGATCATCAGGGCTGTCCCTCAAACCCTGGCTACT[A/C]TGGGGAAGTCATGCCTTCAGCAAGAGGCCCAAGTA M 2 1 2 1 101000 f 74 goat snp39248-scaffold5-3458086 9 88180925 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391720 Affx-122967502 AX-123262077 9 86895951 AGCTCTTGCCTCTCCCAGGCTGGAGGGGCTGCCTC[C/T]TCCTCCTTCTGACAAAAACCCTCCAGAGATGCTCT Y 2 1 2 1 101000 r 74 goat snp39249-scaffold5-3490418 9 88213486 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787535 Affx-122921244 AX-385274559 9 87007664 AACTTGTGTGATAGTGTGTAATCTGAAAATACAGC[A/G]GACTAGGTAGGTGAAAGTGTCAGTACATTCAGGTC R 2 1 2 1 101000 r 74 goat snp39251-scaffold5-3602131 9 88326123 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427882 Affx-122939699 AX-123298225 9 87045834 TTCTCTGCACAGCCTCCCCCAGGTGTCCCCAGGAC[A/G]TTCCTTCATAAGGCCAGAGCTTGGCAGATGTGACT R 2 1 2 1 201000 r 74 goat snp39252-scaffold5-3640301 9 88367046 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793814 Affx-122934943 AX-385280785 9 87084055 CGAGTCCTAAAGACTGTCATTTCTGATTTTCAAGC[C/T]TTCTGGAATCTTGGCCCAGGCGGATTTTTTCCAGA Y 2 1 2 1 101000 f 74 goat snp39253-scaffold5-3678522 9 88405576 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422781 Affx-122943219 AX-123293127 9 87115353 CGAGGTCTTCGGGAGGTCACTCCACCGGCTGAGTT[C/T]AGGATTCTGTGACAGAATCAACTGCAGCCACCTTC Y 2 1 2 1 202000 f 74 goat snp39254-scaffold5-3709820 9 88436705 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391954 Affx-122966535 AX-123262311 9 87145793 TACCCCTACCACGGCCGCATGTCTACCCTCAAGAA[C/T]GAAGCCCCGGGGGCAGCTGCGTGCCACCTAATCAG Y 2 1 2 1 201000 f 74 goat snp39255-scaffold5-3740260 9 88467136 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406115 Affx-122956207 AX-123276467 9 87179867 AATGTCACCTGGGCAGTGAGGATCCTTGTCCAAGA[A/C]AGTTAACCTGACTCTGATCATCAGGGGACGTCAGA M 2 1 2 1 202000 f 74 goat snp39256-scaffold5-3774334 9 88501245 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444980 Affx-122926662 AX-123315317 9 87210758 GCAGAACCCTCAGAACCTGCTCACAACTTTCAACT[A/G]AAAGTGAGCATCCAGAGCACACAGCCTTGGAATAA R 2 1 2 1 102000 r 74 goat snp39257-scaffold5-3805225 9 88532373 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792356 Affx-122951062 AX-385279338 9 87262845 CAAGCTGGTAAACTGTCCACAAGCAGCAGCACCTT[C/T]TCAAGGTCGTCCAAAGAGATGCCACAGAAAAGCCA Y 2 1 2 1 101000 r 74 goat snp39258-scaffold5-3857312 9 88583951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384728 Affx-122972051 AX-123255086 9 87318430 TCTTTACTGAAGTAACTTGTCTATTGTTGCTTTTG[A/C]GATGTCATCTGCATTTCTAATTTTTAATCTATTTC M 2 1 2 1 101000 f 74 goat snp39259-scaffold5-3912897 9 88639508 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394890 Affx-122964743 AX-123265245 9 87403158 ACGGGCAAGGCTGTGCGCCCATCACCAGAATCAGC[A/G]TCAGACCGTTTTCAACATCCCAAAGGAAGACCCTG R 2 1 2 1 101000 r 74 goat snp39261-scaffold5-3997625 9 88722926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408787 Affx-122953372 AX-123279138 9 87442804 CCGCCTGGCCTGCCCTCCTCCTCGGCGTCCGCGCC[A/G]CCTGTTTTTGGGCCCACCCTGCACAACACACTGAA R 2 1 2 1 102000 r 74 goat snp39262-scaffold5-4037271 9 88762651 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774399 Affx-122949575 AX-385261535 9 87494593 TCTATCCACAAGGAACTTTCCACTCTTACTAACAG[A/G]CTATCACCAGAACATAAGCCCCTAAAAATAGGTGT R 2 1 2 1 101000 f 74 goat snp39263-scaffold5-4089060 9 88814897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391997 Affx-122966499 AX-123262354 9 87554833 CAGAAATGCCAATCGTGGGGTCCAATCTTTGGGGA[C/T]GGAGTTAGAAGCCAGTTGCTGACAAAGCTTAATTC Y 2 1 2 1 101000 r 74 goat snp39264-scaffold5-4149300 9 88877601 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388891 Affx-122968858 AX-123259249 9 87597736 AAATCAATGAAAAACAAACAAAGCCACTGCTTGAG[A/C]GTAAGAACAACGCCAAGATTCCCACGAGCAAACTG M 2 1 2 1 201000 r 74 goat snp20241-scaffold2000-26770 9 88920510 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426281 Affx-122940312 AX-123296627 9 87642789 TATTAGATCTAATAATAGAAGGTTTGGATGCAAAG[C/T]AAAACACAAAACTCATCAGCATCCTTATAAACCAA Y 2 1 2 1 201000 f 74 goat snp20242-scaffold2000-71823 9 88963663 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274906 Affx-1111834487 AX-519548489 9 87688288 GTGAAGGTCCACCCTGTGCCTTTTGTAGACAGTGC[A/G]CCTTGGCTTGGGTCAGCGACTCAAAGACTTTCCCT R 2 1 2 1 202000 r 74 goat GoatD01.038163 9 87688288 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802102 Affx-122934006 AX-385289006 9 87719318 TAAGGAGTATTCTCAAACGTAGACCATTAACTAAC[A/G]TCCTATTTCCTGTGAATATGTTCCTACAAGTTGGA R 2 1 2 1 101000 r 74 goat snp20244-scaffold2000-148352 9 89039648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388163 Affx-122969450 AX-123258521 9 87767778 AAATTTTTGTCAAAAGGCACAATTTGACTTCAGCA[A/C]CAAGCGTGGAGCCCCATGTTCCAGACTGTTCTGTG M 2 1 2 1 101000 f 74 goat snp20245-scaffold2000-196812 9 89088139 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423511 Affx-122942459 AX-123293857 9 87804040 ACCAAAAAAATCACCTTGGATCCTAGAACTTAATG[A/G]AAATCCCTAAGAATTTTGGGATTTTTTTTTTCCTA R 2 1 2 1 103000 f 74 goat snp20246-scaffold2000-233074 9 89124392 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434258 Affx-122934817 AX-123304599 9 87870468 GTACGGAATTCTCTTTTATTGGAGAAAGTGGTAGT[C/T]AGAGGAGGCATTTGAATCCACAACTGAATTAGACT Y 2 1 2 1 101000 r 74 goat snp20248-scaffold2000-299502 9 89190734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406894 Affx-122955632 AX-123277245 9 87907529 GTCCAAGGGACTCTCAAGAGTCTTCTCCAACACCA[C/T]AGTTACCCATGAATAATTTTCTTGTCATGCAATCA Y 2 1 2 1 201000 r 74 goat snp20249-scaffold2000-336563 9 89227835 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382516 Affx-122973804 AX-123252874 9 87951787 AGTCCTGTATGCTCCAGGGACCTCTAATTCATTAA[C/T]GTTTAAAATCGTTATTATCACACCTAAAAATTTCT Y 2 1 2 1 201000 r 74 goat snp20250-scaffold2000-380821 9 89272699 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765222 Affx-986697280 AX-385252761 9 87965645 TCTCACCTCAGGACCTGTCGCAGGGGCTGCCATAT[A/G]GTTGGTTCAAATGACTGCATGACACGAGACAGACT R 2 1 2 1 600010 r 74 goat 9_87965645 9 87965645 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 320762752 Affx-986697282 AX-385250808 9 87967732 TCCCAGTCTCCCTGCCAAACTTGGAAATAGACATT[C/T]CAAGCTGAGTCCTCAAACTTTTTCTAAAGAGCAAT Y 2 1 2 1 600010 f 74 goat 9_87967732 9 87967732 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 320765165 Affx-986697248 AX-385252716 9 87974973 CCGAGCACAACATTTTCTGAAGCCAAAGCCTAATC[A/G]AGATCACAGCCCTAACTCTTCGTTTCTATGAAGGC R 2 1 2 1 600010 r 74 goat 9_87974973 9 87974973 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320788147 Affx-122960186 AX-385275167 9 87981955 AGTCTTCAGATTTGATGCTAAAGTTATTTTTTCCT[A/G]TGAATGTTAATTTTCAAACACTGGTGCCAGGCCAG R 2 1 2 1 101000 r 74 goat snp20251-scaffold2000-410989 NW_017209962.1 62 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770853 Affx-122956254 AX-385258017 9 88027412 TACTGTCATTCTGCTCACATGATAGCACTGAGGCA[C/T]GTGCCTTAATCTTTGGTTGGGTCTTCTCTTATTAA Y 2 1 2 1 101000 r 74 goat snp20252-scaffold2000-456446 9 89347920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419922 Affx-122945324 AX-123290270 9 88076937 CAGGGGCACAGTAGAAAGGCCATGCCCACATTTCA[C/T]GCCTGGTTCTGGCAAGGAGCCTACATGGGAGGCAC Y 2 1 2 1 101000 f 74 goat snp20253-scaffold2000-505971 9 89385371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390784 Affx-122967879 AX-123261141 9 88111611 CCTCAAGTCCACAGGAAACAGTGACAGTGAGCTCT[A/G]CCATACCGAGGGTCCAAGGCCTTCAAAGGTCCACT R 2 1 2 1 201000 r 74 goat snp20254-scaffold2000-540645 9 89417398 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786853 Affx-122936982 AX-385273882 9 88155805 TCAAAAGCAAATGCCTCTTTCTTACATGAGTGACC[A/G]TATTCAAAGGCCTGTCTTTGCAAATGTGAGCCAAC R 2 1 2 1 101000 r 74 goat snp20255-scaffold2000-584839 9 89461885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383746 Affx-122972446 AX-123254104 9 88180326 AGAAACAATGGGGCATAGAGGGGAATTTTAGCAAA[G/T]CCATCCTGAGGATGACCATGGATATAACCGAGTAT K 2 1 2 1 101000 f 74 goat snp31782-scaffold3555-11231 9 89486481 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433803 Affx-122934460 AX-123304144 9 88233386 CATTTTTTGCTAGCCTTTGGGTGGATAACTTTGCT[A/G]CAGAACATTAAAGTTAACCTTTTCTCTCAATAATT R 2 1 2 1 101000 f 74 goat snp31783-scaffold3555-64291 9 89539396 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780378 Affx-122938421 AX-385267472 9 88280964 TTCTTGTCGTTTCTAGTCTGGGTATCAGTGTTATG[C/T]TGACCTTATGAATCAAATTAGAAAATGTCACTCCT Y 2 1 2 1 101000 f 74 goat snp31784-scaffold3555-111869 9 89587582 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381382 Affx-122974388 AX-123251740 9 88323641 GGCTGAGTATGCCTGCATGACGCTGATCTGAAATC[A/G]TCTTGATAAGATTAATTCACATTCTTATCGTTCTT R 2 1 2 1 101000 f 74 goat snp31785-scaffold3555-154546 9 89630152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432314 Affx-122936304 AX-123302655 9 88362058 GGCATTAGCTCTGCTGCCCCACAAGTTTTATTGGC[A/G]AACAAACAACTGAGCCTCCACTTAAACAGCGACTG R 2 1 2 1 101000 r 74 goat snp31786-scaffold3555-192963 9 89662460 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440383 Affx-122929632 AX-123310720 9 88419915 TACATAACTGTTGACCATCTGTGATTGGTGGTTTC[A/G]GGCAGCATTGCTAACTGCTGATCTGGGGTGTTTGT R 2 1 2 1 101000 f 74 goat snp31787-scaffold3555-250820 9 89721015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387189 Affx-122970610 AX-123257547 9 88469142 GCAAGTTGACTTGGGTGGTAGCAGAGATAGGATGA[C/T]GAGTGCTCCCCGAGTGCTTCCTAGGTGGCAGACAC Y 2 1 2 1 101000 f 74 goat snp31788-scaffold3555-300047 9 89770242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775396 Affx-122956473 AX-385262527 9 88528889 GTTTTATATTATGTGATGTTAAAACAGTCAATGAT[C/T]TTGTGATCATGAGCAGATGTTCTGTTTGACAAGCC Y 2 1 2 1 101000 r 74 goat snp31789-scaffold3555-359794 9 89829038 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782855 Affx-122928507 AX-385269925 9 88576928 TTTGAAAAAGCCTAAAGGAAGTCGCGCCTCTGACC[A/G]TAAGTTTACGCGAGCTAACCCAAACTGCCAGCTTT R 2 1 2 1 101000 f 74 goat snp31790-scaffold3555-407833 9 89876139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778858 Affx-122925917 AX-385265966 9 88641224 CTGGCCTGTGTCTAGGGACCAAGTGACAGCGTTCA[C/T]GGACATACATCTCATTTCAGCTTGACGTGACTGAA Y 2 1 2 1 101000 r 74 goat snp33517-scaffold3935-25388 9 89919994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430057 Affx-122937557 AX-123300398 9 88713101 AGCATGTCCATCAGCAGATAGGGTTCCCTTTATCT[A/G]TAAGACCATCTCATAAAGAAGATTGGGACCTGTGA R 2 1 2 1 101000 r 74 goat snp33518-scaffold3935-97265 9 89987288 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436634 Affx-122932494 AX-123306972 9 88786750 GCCCCCGACGCACTGCCAAAGCTTCGGATTAAACA[C/T]GGGATTAAAAGTCAGATTCGGATTTTCTGTTTTCT Y 2 1 2 1 101000 r 74 goat snp33520-scaffold3935-170914 9 90061741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418839 Affx-122946144 AX-123289187 9 88833837 ACAGTGCCGACCCCCCACCCCCCGCCCACATTGGC[A/G]TTTATCAGCACAAATGTTGACCACTTTCTCTCTCT R 2 1 2 1 101000 r 74 goat snp33521-scaffold3935-218001 9 90109671 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412783 Affx-122950499 AX-123283132 9 88862689 CGTGCTCTTCAGACCTCAGATGCCCATCACATTGC[A/G]AACCAGCAGCTTGGAGACTGCAGGCCCTAGATTAC R 2 1 2 1 101000 f 74 goat snp33522-scaffold3935-246853 9 90138255 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428877 Affx-122938338 AX-123299219 9 88907083 CGCTTTCTATTCACCAAAAGTCTGAATCCCTCGAC[A/G]CTGCAGGTGCCACCCTAGGGGACATACAGGGAACA R 2 1 2 1 101000 f 74 goat snp8955-scaffold1324-11103 9 90182272 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447630 Affx-122923984 AX-123317966 9 88950812 TGGCTTTGCCAGGGACCTACTGTCCTGGCGGCATC[A/G]CTGACGCTATGCTGGAAGCTCCACGGCTCCATAGA R 2 1 2 1 102000 r 74 goat snp8956-scaffold1324-54832 9 90224944 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276335 Affx-1111835365 AX-519549868 9 88955989 GTAGCGAAGACTCCTGCTCCAGTGATGACAGAAAC[A/G]GCCATTCAGCAGACATCGCGTGACAGTGATCCGTT R 2 1 2 1 101000 f 74 goat Random2.2K-1029 9 88955989 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403506 Affx-122957634 AX-123273859 9 88981628 TGTCCTTTTTTGTCAATGCTGAGACTCTAACTAAA[C/T]GCTGAAATGGTCCTGGGTGATCATGAGAAAAAGTA Y 2 1 2 1 201000 f 74 goat snp8957-scaffold1324-85648 9 90255420 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420441 Affx-122944898 AX-123290788 9 89014128 TTTGCACCACGCTCATCGCCCTTGATCCTCAGTCC[A/G]TGCACACAGCTGAGATTCACGGTGTCCTTTGCACC R 2 1 2 1 101000 r 74 goat snp8958-scaffold1324-118148 9 90283999 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786986 Affx-122945196 AX-385274014 9 89057331 GTTCTCCTTTTTGCATGGATAAAATACTAGGTGAA[C/T]GTACAAATATGTTACTCAAGTATTTGAGAAATTTA Y 2 1 2 1 101000 f 74 goat snp8959-scaffold1324-161351 9 90328403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400411 Affx-122959988 AX-123270766 9 89113780 AGTCAACCCTGAGTTGTATATAAATACAGCAAGAT[C/T]ATGTTAAAAAGGAGAACTGAAGTAAACGTGTTTGG Y 2 1 2 1 101000 r 74 goat snp8960-scaffold1324-217800 9 90383985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396377 Affx-122963031 AX-123266732 9 89151109 TCCTGGAGGTGAAGACGCCAAAGCCCCAGAGCTCC[A/G]TGCTGTAATTTTCCGTCTACGTGACGTCCTGGAAA R 2 1 2 1 101000 r 74 goat snp8961-scaffold1324-255129 9 90420996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435497 Affx-122933429 AX-123305837 9 89207416 TATGCTTGTTTGAAATTAACATCATTATTCTGTTC[A/G]TTAACTCTTCAAGCTTCTAAAATTGCCAGACTGAC R 2 1 2 1 101000 r 74 goat snp8962-scaffold1324-311436 9 90477797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453346 Affx-122919956 AX-123323679 9 89264614 TCCCTTCTGGCTGCTGTAAAGAATACGTGACCACG[C/T]GAGCTTTGAGAGAAATCCACCAAATTCCGATCACG Y 2 1 2 1 101000 r 74 goat snp8963-scaffold1324-368634 9 90537774 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276337 Affx-1111835366 AX-519549870 9 89350841 TTTTTGCTTAGAAGCTTTGGAAAGAATAAGGCTGC[A/G]TCTAAAATACTGTGCTCGGGGTTAGAACTTTAAAG R 2 1 2 1 101000 f 74 goat Random2.2K-1031 9 89350841 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424546 Affx-122942240 AX-123294892 9 89362999 CGTCCCCTATGGGACCACAGGACACTTTGATGGGA[C/T]GACGGTACAGTCACCCTCCTGCAAGGCAGCCGATG Y 2 1 2 1 101000 f 74 goat snp8965-scaffold1324-467019 9 90633379 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410527 Affx-122952168 AX-123280877 9 89412216 TCTACTTGGAAGAAGAAAAGAATTTCAAATTTGGG[C/T]GGGCTCCTTAATTCTTGTCATTGGCAGAGACGGAG Y 2 1 2 1 101000 r 74 goat snp8966-scaffold1324-516236 9 90680424 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437502 Affx-122932351 AX-123307840 9 89466032 TCTTATGATTGACTGGCTCCAATAGGAACTTGCAA[C/T]GGGTACATGATCAGTTCCTGTTAACATAATTAACA Y 2 1 2 1 101000 r 74 goat snp8967-scaffold1324-570052 9 90734619 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453843 Affx-122919542 AX-123324176 9 89515939 TAAGACCACGGATGAAGCAACCTAAATGTCCACGG[A/G]CAGAGCAATGTGGCACATACATACGATGGAATAGT R 2 1 2 1 201000 r 74 goat snp8968-scaffold1324-619959 9 90783702 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434781 Affx-122933886 AX-123305122 9 89552126 GTGTGTGAGGATGTGTGTGTGTTTGCTCTCCTCTC[A/G]AGTCCTTTCTGCCCCCACTTTCTTGATCCCACTCA R 2 1 2 1 101000 r 74 goat snp8969-scaffold1324-656146 9 90820210 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390330 Affx-122967700 AX-123260687 9 89597481 AAATCAAATATTCAGAATTTTCTCCAAGCAGTTGA[C/T]GAAATGAAAACTGAAAACATACATTCCTCTCTAAT Y 2 1 2 1 101000 f 74 goat snp8970-scaffold1324-701501 9 90879613 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788951 Affx-122953440 AX-385275964 9 89629231 TAATACTACATATCCAATTTCCCAAAATTATTCAA[A/G]AAATTCTTTGGCAGGCTGGAATTCTATGAAAAAAA R 2 1 2 1 101000 r 74 goat snp8971-scaffold1324-733251 9 90911133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397408 Affx-122962253 AX-123267763 9 89692968 ATATCATGAATCCAAGAATACAGAGGTAGTGAGTA[C/T]GTTGGTCAGGCACATCAAAGCTGGACCGCCTGGAA Y 2 1 2 1 101000 f 74 goat snp8972-scaffold1324-796988 9 90976443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427661 Affx-122939320 AX-123298004 9 89769135 ATTTTAATATTTCCCCACCAAAGACTGAGGAAAAC[A/G]TTTTTAGACAGATTATTATAATGACATTTAAAAAA R 2 1 2 1 102000 f 74 goat snp8973-scaffold1324-873155 9 91054261 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420523 Affx-122944836 AX-123290870 9 89829059 TGAGGCGTGGCATGGTGGATAAGAAACGAGCTCTT[A/G]AGACGCCGAGCTTAGAATTTAACAGGAGGATGGAA R 2 1 2 1 201000 f 74 goat snp23862-scaffold2403-465023 9 91113467 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802677 Affx-122945068 AX-385289576 9 89928986 TTACAGCTGGTTTTTAAACTGAGCTGTTTTACTGG[C/T]AAACAAAATTCAGGTTTTCCAATGCGAAAGTTGTA Y 2 1 2 1 101000 f 74 goat snp23861-scaffold2403-365096 9 91212566 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274854 Affx-1111834534 AX-519548439 9 89996692 CCAGAAATCGCATTTTGAACACGTCTCCTGGCTTG[A/C]GCCCCTGCAGCCACTCGGAGGGCTCCAGAACTC M 2 1 2 1 101000 f 74 goat GoatD01.040341 9 89996692 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38398077 Affx-122961731 AX-123268432 9 90016543 TTTAAGTCTTAACAGAGCTAGGAAGATAGATATCA[G/T]ACAAAGTGTATTCTCAGACCACAACAGAATAAAAT K 2 1 2 1 101000 f 74 goat snp23860-scaffold2403-277539 9 91294564 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453310 Affx-122919982 AX-123323643 9 90082497 AACATTCAGTGGACAGAGAAACGAGCGAGATCTGC[C/T]CTCCTGCCGTCCTCTCTGGGCCTGGATGGCAGTTA Y 2 1 2 1 101000 f 74 goat snp23859-scaffold2403-211585 9 91351518 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406994 Affx-122955037 AX-123277345 9 90126068 ACCGCCAGAGGGAGCAGGAGGGCAGGCGGACGGGA[G/T]GCATGAGGCAAGAGCGACAGGGATGCCTTTATTTA K 2 1 2 1 101000 r 74 goat snp23858-scaffold2403-168014 9 91395459 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775257 Affx-122962510 AX-385262388 9 90188097 TGTGGTCTGCAAGTGTCTGCGTGTACTGCACACAT[A/C]TGTGCACGTGCTGTGCACGTGTCTGCATGTCCAGG M 2 1 2 1 303000 r 74 goat snp23857-scaffold2403-105985 9 91456500 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402580 Affx-122958438 AX-123272933 9 90267441 GTGAAGAAACCAGGAGTATGTTTCTGTAATCTCTA[C/T]ACTTGGTACAGTGTCTGACACACGATATGTTGATG Y 2 1 2 1 101000 f 74 goat snp23856-scaffold2403-26641 9 91536675 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426575 Affx-122940160 AX-123296921 10 18539 TATGTCAACTCAACAAGAAGCCTGACACTACTGTT[A/C]GAGCTCGAGAGGAAAGAGGATTTGCATGTCTCCAC M 2 1 2 1 103000 f 74 goat snp6870-scaffold1250-266880 10 101054232 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272579 Affx-1111832884 AX-519546294 10 26570 TTTATTTTTAGATATAGTTGGTATATAGAAAAACA[A/G]GTAGTAGACCTGGTATTAGCAACATTAGATCTTTG R 2 1 2 1 303000 f 74 goat 10_26570_AF-PAKI 10 26570 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38441027 Affx-122928943 AX-123311364 10 62970 ACCATCATTCCTGTCCCTGTCACCACATTTTGGGC[A/G]TGCCAGGAGAAAACACATTTGTGACTCCCGATGAG R 2 1 2 1 102000 r 74 goat snp6869-scaffold1250-222449 10 77762688 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449528 Affx-122922603 AX-123319863 10 108202 TGTCTCCCCGAGTATCGATTCACACAATGCTGGCA[C/T]GTGTAACAGCCCTTTGGGAAAGCCTGGAAGGAAAA Y 2 1 2 1 201000 f 74 goat snp6868-scaffold1250-177217 10 100963863 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419719 Affx-122945906 AX-123290067 10 215441 GAAGCTAACACGGTCCTTCCAAACAAAGGCTTGTA[C/T]ACACATGCTAGTTTTCTGCCTCTTTTTCCCCAAAG Y 2 1 2 1 101000 f 74 goat snp6866-scaffold1250-69978 10 100856819 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796296 Affx-122935269 AX-385283246 10 269103 GGATTTATCAGGGTCAGTTCACAAGCAAACACCAA[C/T]AGTTGCCCAATGGGACTAACTTAAATGGCATGCTT Y 2 1 2 1 101000 r 74 goat snp6865-scaffold1250-16316 10 100808683 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276339 Affx-1111835367 AX-519549872 10 294960 CTTTTCTCTAGGTGATGCTAAGTATCAGAGCTTAC[A/G]GCCCTCGCTTAAGATACAGTATTTTAAACCTGTAC R 2 1 2 1 101000 f 74 goat Random2.2K-1033 10 294960 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446171 Affx-122925743 AX-123316507 10 335523 AGGGTTTAATTCCCAAGGTGCTGTCTCTTGACTTC[A/G]TCAGGGGCTAGTAGTTGATGAATGGCTGTTAGCAT R 2 1 2 1 101000 f 74 goat snp10753-scaffold1382-387761 10 100741789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794901 Affx-122977872 AX-385281861 10 366402 GCACATAAAATGATGTCAGATAAGAATCAGTGGTA[C/T]GATGCATAAGGGCATGTGGAAGAGTATATGAGAAG Y 2 1 2 1 101000 r 74 goat snp10752-scaffold1382-356882 10 100710163 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394937 Affx-122964298 AX-123265292 10 404927 ATCCATGTGTAACACTGATTTTTGCTATAACCCAC[A/G]CTTCTATGTCACTGTCTTGAAAAAGGTGCATCTGA R 2 1 2 1 101000 f 74 goat snp10751-scaffold1382-318357 10 100670677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423813 Affx-122942804 AX-123294159 10 449645 AACCCACTTTAAAAAACAAAACAAAACAAAACTGT[A/G]TTCAAACATCTCCCTTCAGGGAATGGGCCATATGT R 2 1 2 1 101000 r 74 goat snp10750-scaffold1382-273639 10 100626177 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392210 Affx-122966278 AX-123262567 10 494550 ATTCCCTGCTCTATTCTGAGTCATGCCTTCAACAC[A/G]CAGGGTCTTTGTCAATTGGCTCTTCTTTGATTTTC R 2 1 2 1 101000 r 74 goat snp10749-scaffold1382-228734 10 100581436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379890 Affx-122975773 AX-123250248 10 536168 CAAATTTAATCTTCACAAAGTGACTATACTTTCCA[C/T]GTATGAAGCAGAGAACGGTGGGGAGTTGTCACTGC Y 2 1 2 1 101000 f 74 goat snp10748-scaffold1382-187116 10 100539890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393784 Affx-122965192 AX-123264139 10 592596 ATCAAAGACAGTCTCTGCCCTCAGAGTCTGAACTC[G/T]AGTTCTGGACATGAGACACACCTGTGGTTGTCTCA K 2 1 2 1 201000 r 74 goat snp10747-scaffold1382-130688 10 100486915 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427446 Affx-122940039 AX-123297789 10 634404 CGCTGAGATAACTGGGTAGAGATGAGCTGTGAACC[A/G]AGAAACAGCTTGAGGTTATTCTCAAAAGAGAACTT R 2 1 2 1 101000 f 74 goat snp10746-scaffold1382-88880 10 100445046 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453524 Affx-122919801 AX-123323857 10 662913 TCTTCTCTGAGAAAAGAACACTGCTGGCCTTGTCT[C/T]GGCTCTGGGCTGGGCTGCTCCTCTGACCTTGGGTG Y 2 1 2 1 102000 f 74 goat snp10745-scaffold1382-60371 10 100416426 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394510 Affx-122964543 AX-123264865 10 716131 TCTCAGCCCCTCTCTGGTAAGATGGAGCATCTGTC[G/T]AGCTCTGGTCCATGGGCTGTGAACAGAAGCATTCA K 2 1 2 1 201000 f 74 goat snp10744-scaffold1382-7153 10 100364905 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797520 Affx-122960331 AX-385284459 10 724985 GTTTAGAACTTAGACGTGTCTTTTGGATAAGGTAC[G/T]CAATTCAACTCACTGCAGTGGGTAAGAACAAAAGC K 2 1 2 1 101000 f 74 goat snp38015-scaffold473-1602 10 100356576 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390919 Affx-122967087 AX-123261276 10 830651 AGAGGCAGGAAGAAACAGTTGATACATAATATAAG[C/T]GTACACTATATTACATATACAAATGTATATGTATG Y 2 1 2 1 101000 f 74 goat snp38018-scaffold473-107268 10 100249514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415959 Affx-122948426 AX-123286308 10 871071 TAAGCCCCCGTTTTTCACTTTTGCACGTTTATATG[C/T]GTTTCTGCTCCTTGCCATAAGTTACACCAGACTTC Y 2 1 2 1 201000 r 74 goat snp38019-scaffold473-147688 10 100209094 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396184 Affx-122963374 AX-123266539 10 916008 ATGAAAGCCATAGAAAGCCCCAACAAAGAAGACGA[C/T]ACCCAGTGGCTGACCTACTGGGTAGTGTATGGTGT Y 2 1 2 1 101000 f 74 goat snp38020-scaffold473-192625 10 100162384 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396688 Affx-122962831 AX-123267043 10 945256 TAAGAGGCAAAAAAGAAAAATGTCTTTTATACTGC[A/G]TAAGAGCTGGATGCAAACTTCTGATGTATATTTAT R 2 1 2 1 201000 r 74 goat snp38021-scaffold473-221873 10 100132571 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390636 Affx-122967151 AX-123260993 10 1032480 TTACAGTCAGAAATTATGTCAGTGTATCACAACTG[C/T]GAGACAGGAAATAAATTTGCACAAGGATGTCTTTC Y 2 1 2 1 101000 f 74 goat snp38023-scaffold473-309097 10 100043978 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406938 Affx-122955074 AX-123277289 10 1075876 CAGGCAGACCACTCTCTTCTACTTGAAGCAGACGT[C/T]GTCTCCTGTCCTCCACGCCATGTTCTCCTGGTTTT Y 2 1 2 1 101000 f 74 goat snp38024-scaffold473-352493 10 100000306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438789 Affx-122931371 AX-123309126 10 1105224 GGAGAAGACATAAATCGTCAGTATCAGTAATGAAA[C/T]GGCTTATCATTATAATTTCTGCAGTCTTTAATAAG Y 2 1 2 1 101000 f 74 goat snp38025-scaffold473-381841 10 99970819 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395602 Affx-122963820 AX-123265957 10 1137828 TATGTCCCAATTTAAAAATCAAACCACCTTGGTGG[C/T]ATCTCAGGGGCTGAGCTTACTGTCACCTTTGGCTC Y 2 1 2 1 202000 f 74 goat snp38026-scaffold473-414445 10 99938551 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798648 Affx-122932856 AX-385285580 10 1171191 TGACAAGATGTCTATTGCAGCATAGCTTGTACCAA[C/T]GATTATTAATATAATAGAGAGCATCTAACTGTGTA Y 2 1 2 1 101000 f 74 goat snp38027-scaffold473-447808 10 99905049 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403575 Affx-122957578 AX-123273928 10 1202698 AGGAGGTCTCATGCTTTGCCCTAGTGGGCGAGTCC[G/T]CAAGAAGGAATCTCAGCGTGGCAGGCTAGTCCTGA K 2 1 2 1 201000 r 74 goat snp38028-scaffold473-479315 10 99872111 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414305 Affx-122949583 AX-123284654 10 1255175 ATGGGTTAGGATAAATCAAGAAATGTACTGGAAAA[C/T]AAGCCACATTAAACATAACTAGTCTTTCATTTAAA Y 2 1 2 1 101000 f 74 goat snp38029-scaffold473-531792 10 99819689 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782425 Affx-122945010 AX-385269501 10 1298003 TCAGACTGAGGAGGAGCACACCTTTGAGTTATTTC[A/C]CCTTTACCTTAAAAACGAGCGCTTTTACTCTAATG M 2 1 2 1 101000 f 74 goat snp38030-scaffold473-574620 10 99776756 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408751 Affx-122953399 AX-123279102 10 1328157 AAAGTCCCCATGCTGACAAGTGCAGTCCTAGGTGG[C/T]GAATTGGAGGAGGGGATGAAAGAGACAGAAGCAAG Y 2 1 2 1 303000 f 74 goat snp38031-scaffold473-604774 10 99746918 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773636 Affx-122932142 AX-385260776 10 1371454 AGGGAGTGGGGTCTACATTAACTTAGTTTATCACT[A/G]TCCCATCCAGGTTGTTTCTCTTTCCTGCATTTATT R 2 1 2 1 101000 r 74 goat snp38032-scaffold473-648071 10 99704003 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400801 Affx-122959818 AX-123271156 10 1416835 GCGCAGACAAGCCAAGATGCGGGGAGACCTCGTGA[A/G]ATTTCCTTTTCTGTTATTTGTGTTGGCACGCAACT R 2 1 2 1 101000 r 74 goat snp38033-scaffold473-693452 10 99661125 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438680 Affx-122930874 AX-123309017 10 1457937 AAAATTTTAATAGGTTAACCAGTTTTTCCTGTTAC[A/G]TTTAGCTTAAAGTCTCCTTCCTGTTTTCTTTCTTT R 2 1 2 1 201000 f 74 goat snp38034-scaffold473-734554 10 99620018 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399034 Affx-122961596 AX-123269389 10 1515513 TACAAGCCTGGCCCAAAGCTCAGCTCTAGCAGAAA[C/T]GCGTGGTCTTCAGTAGGTTACTTTTTCAATCTCCT Y 2 1 2 1 201000 r 74 goat snp26696-scaffold2803-4541 10 99562924 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781468 Affx-122948253 AX-385268553 10 1544408 CTATATATGTCTATGTACTTCCTTAAAGAAACCAA[C/T]ACTTGGTAATTCACAATACCTAAGTCATAATTTTT Y 2 1 2 1 201000 f 74 goat snp11072-scaffold1399-798540 10 99534042 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798064 Affx-122923785 AX-385285000 10 1582724 TACAGTCAAATAATCAAGTTCAATTAGAAAGTCAT[A/G]CCACAAACATTTGCTAAGTCTTTTTATGGTTTGTT R 2 1 2 1 101000 f 74 goat snp11071-scaffold1399-760224 10 99495398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379466 Affx-122976083 AX-123249824 10 1624966 TTGTGAGAAGCCCTGGAGAGAGCTGCCTCTGGAAT[A/G]TGCATGGGGCCTTTCACACCAAGCTGCAAGATTCC R 2 1 2 1 201000 r 74 goat snp11070-scaffold1399-717982 10 99453574 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38426881 Affx-122940472 AX-123297226 10 1680434 TCCACATTCTTCAAGGGTCAACTGTTGAACGAAAG[C/T]GTAGAGCATCTTAAATCAAGGCAGAAGGTGAACCA Y 2 1 2 1 101000 r 74 goat snp11069-scaffold1399-662514 10 99397706 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272454 Affx-1111834272 AX-519546179 10 1695291 GGGAGCCCGAGAGGCTCGGGTCTGCAGCTGTCGCC[A/G]AGCGGGATCCCTTTTCACACGGATCGTCTCAGCAC R 2 1 2 1 202000 r 74 goat GoatD01.028346 10 1695291 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320792690 Affx-122932778 AX-385279670 10 1762393 AGCATGCTTTCAACAAAATACATAAGAACTGACAA[C/T]GACTGTAACTTAAGAATGTTTATCACTTTCCTAAC Y 2 1 2 1 101000 f 74 goat snp11067-scaffold1399-580555 10 99314684 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385534 Affx-122971241 AX-123255892 10 1795928 AAGAAGAAAGGGAAAGAAATTGAGAGGGTCCATTA[A/G]AAACAAAGACCCTGCTTTCTGTAAGTCAGGGATAT R 2 1 2 1 201000 f 74 goat snp11066-scaffold1399-547020 10 99281369 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408188 Affx-122954195 AX-123278539 10 1832136 TGCGAGTACTTCCTTAGTCAATTACCCACTTCAGC[A/G]TCAGTCTCAAGGGAACCTGACCTAAGACACCAGCC R 2 1 2 1 101000 f 74 goat snp11065-scaffold1399-510812 10 99244808 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433948 Affx-122934281 AX-123304289 10 1864234 CTTTAAAGTCAGAGACACCTGGCTTAAAATGCTTA[C/T]GTGGAAAAGACGAACAAATAGAGTCATGAGGATTC Y 2 1 2 1 201000 r 74 goat snp11064-scaffold1399-478714 10 99212574 G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400942 Affx-122959709 AX-123271295 10 1897005 TTCGTTTTTTAACATAAATGGTATCATACCATTTG[C/T]TTCATTCTGCAGCTTGTTTTATCACTCAACAATAG Y 2 1 2 1 101000 r 74 goat snp11063-scaffold1399-445943 10 99178429 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428098 Affx-122939089 AX-123298441 10 1941041 TCCCTGACCCATAAGCCAGATTTCACAAAATCAAA[C/T]GTACAACTCATTTCATTTCTATAATGCCTGATATG Y 2 1 2 1 101000 f 74 goat snp11062-scaffold1399-401907 10 99134368 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440356 Affx-122929654 AX-123310693 10 1970620 GAGGACAAAAGTGAATATACCTAGTTGGTTTTGTT[A/C]TAAACAGGGACTGGAGACTCTGTCTTGACTGAATG M 2 1 2 1 101000 r 74 goat snp11061-scaffold1399-372328 10 99103915 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795737 Affx-122924145 AX-385282690 10 2002938 ACCAAGATGAATCAGACAAAATCAAGTTATTTTGT[A/G]TTAAGCGTAATTATTCAGATAATTATCTCAACCCT R 2 1 2 1 201000 f 74 goat snp11060-scaffold1399-340010 10 99071240 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428079 Affx-122939104 AX-123298422 10 2040425 TCAAATGTCCCTCATTCTCTATTTGTTTTAAAAGA[G/T]ACAATAGGACCTTGTTTCTGGGATTAAAGTTGTGC K 2 1 2 1 103000 r 74 goat snp11059-scaffold1399-302523 10 99033901 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428010 Affx-122939156 AX-123298353 10 2091826 TCAGAAAGGACAGCTCTTCATGGTCTTTTGCTCTT[C/T]GCTCCAGCTGTAAGGGAATCCCAGGTCAGGTCCAC Y 2 1 2 1 101000 f 74 goat snp11058-scaffold1399-251122 10 98982112 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412038 Affx-122951726 AX-123282388 10 2127744 ATGATTTAACAATGGAAGATAGATGAAGACGAACT[A/G]CTTGGGAGGGGGCTTTGAAGGTATGAGGCAGATGC R 2 1 2 1 201000 f 74 goat snp11057-scaffold1399-215204 10 98945989 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431579 Affx-122936183 AX-123301920 10 2165237 CATAGGGTAGAATACTGGGGAAGCCCATTTGCTTC[A/G]TGTTTTATTCAACTCAGTACACGTTCATCAGACCA R 2 1 2 1 101000 r 74 goat snp11056-scaffold1399-177711 10 98908736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412903 Affx-122950412 AX-123283252 10 2231907 AACAGTACGCACAAAGGCCCTATCGTGTGAAAGAG[C/T]ATGATGGTCTCAAGGAACTAAAAAGCCAAGCTATT Y 2 1 2 1 101000 f 74 goat snp11055-scaffold1399-111041 10 98840662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419574 Affx-122945398 AX-123289922 10 2267382 TGTAGAAACAAAGCATTTGTATAAACCTTTCCACC[C/T]ACAATTTCATTTAAGACAAACAAAGAATTCTGATA Y 2 1 2 1 101000 f 74 goat snp11054-scaffold1399-75566 10 98805090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435439 Affx-122933477 AX-123305779 10 2298200 TCCTCTAAGCATTTGGCAGCAATTTCACCCACAAA[C/T]GGCTTACAGTATCATTTAATTTCCCACTGGAACTT Y 2 1 2 1 101000 f 74 goat snp11053-scaffold1399-44748 10 98771925 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38419316 Affx-122945663 AX-123289664 10 2336587 GCTCCTTCTGAAAGTTTTTAACACCAAACTGATCA[C/T]AACGCAATGAACGAATCAAAACACGTCTCCTCACA Y 2 1 2 1 201000 f 74 goat snp11052-scaffold1399-6361 10 98732716 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774014 Affx-122957512 AX-385261152 10 2349024 TGCAAGAAGAAAGAGAGAGCTGAACAATCACCATG[C/T]ACATATTACATAGCATTCAGCTTCAAAGGGCTCTG Y 2 1 2 1 101000 f 74 goat snp44963-scaffold6122-7612 10 98720558 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390667 Affx-122967128 AX-123261024 10 2383564 TTACTCAACTTTTAAGAAGAAATGAAGTATCTTGA[C/T]GGCTTCAGTTTCTTTAAGGGTACATGGAATCCTAA Y 2 1 2 1 101000 r 74 goat snp21977-scaffold216-548520 10 98678820 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419372 Affx-122945624 AX-123289720 10 2425576 GTTTTAGTAGCAAACTCTTAATATTGCTGAGAAAA[C/T]GGAAACCATCTGCTGTTCTCACACCCAGCCAGAAA Y 2 1 2 1 101000 f 74 goat snp21976-scaffold216-506508 10 98636433 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387179 Affx-122970619 AX-123257537 10 2458539 ATAGTTGTATAATACTTCAAGAAAGAAAAGTGCAG[C/T]GGTGTCTCCAAATTTCCAAAGTAAAAAATGTTTGA Y 2 1 2 1 101000 f 74 goat snp21975-scaffold216-473545 10 98603490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388513 Affx-122969211 AX-123258871 10 2487878 CTAAGTACAAAGATAGGAGCAATCTCCCCTACAAG[C/T]AGGAGGCCACCCACCAAATCTCTAGGAGGGCTGAA Y 2 1 2 1 101000 f 74 goat snp21974-scaffold216-444206 10 98573952 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780248 Affx-122939834 AX-385267343 10 2536986 CAAAAAGAACTTTCTCTACTAACAAGCAGTGAAAG[C/T]ATGATTCTTGAACCTATCCTTGGGCCAATCAATGA Y 2 1 2 1 101000 r 74 goat snp21973-scaffold216-395098 10 98524245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271744 Affx-1111832882 AX-519545538 10 2563393 CTTAGCAACTGAACAACGACAACACTTGGTCCGTC[A/G]GGAAAAGAATGCTGAAATAAAACTGCTACATTAGA R 2 1 2 1 303000 r 74 goat 10_2563393_AF-PAKI 10 2563393 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426716 Affx-122939886 AX-123297062 10 2568737 ACCAGCCCTTCCCTGCCTGGCACTGAGAATAAGGT[C/T]GGAGCACGCCTGGGAAATCCTGGTGAGCAGCAAAA Y 2 1 2 1 201000 r 74 goat snp21972-scaffold216-363347 10 98494007 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412320 Affx-122950850 AX-123282669 10 2612821 GTGTGAAGAAGGTTGAAAGTTTATTTTTACCAGAT[A/G]TAAAACATATTAAAAGGAGGTAAAATATTATAATA R 2 1 2 1 103000 f 74 goat snp21971-scaffold216-319263 10 98449103 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390226 Affx-122967776 AX-123260583 10 2699743 ATATTAGAAGTGAAGCCTTTTTCTAAGATTTCACA[G/T]CATTAGAAAAAGAAAATACAAAAAACCCATATGAT K 2 1 2 1 103000 f 74 goat snp21969-scaffold216-232341 10 98356923 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411627 Affx-122951585 AX-123281977 10 2732288 CAGCATGTAATTTATCTAAAAACGCTTATATACCT[C/T]TTATTTTTAAGCACTATTTTAAATATTTGGAAAAT Y 2 1 2 1 101000 f 74 goat snp21968-scaffold216-199796 10 98324666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463063175 Affx-1109795036 AX-514550769 10 2792769 CACTTCAAACTTGGCATTGACTCCTCAAATAAACC[A/G]CTTAGTAGCAACAGTAACATTTGTTGACTTATCAA R 2 1 2 1 101000 f 74 goat Random2.2K-1034 10 2792769 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403445 Affx-122957732 AX-123273798 10 2812047 GCAGTTAAAGGATGCGTTAGTTTTTAATGCCTCAT[C/T]GTACAAGGACTCCTTACACTAATTTTTGGTTCATC Y 2 1 2 1 101000 r 74 goat snp21966-scaffold216-120037 10 98245295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780968 Affx-122974945 AX-385268055 10 2865100 CCTCACCTCACTTTCCAGTATGTTTCATCCCACAT[C/T]GCTGTTGATAAAACTCAGGTTTTACTACTTCAGTG Y 2 1 2 1 201000 f 74 goat snp21965-scaffold216-66984 10 98192641 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434734 Affx-122933920 AX-123305075 10 2919101 GGAGTTAGATGGAGAGGAAGGTGAGGTGGTAATAT[C/T]AAAATATGTTGCCATATTTTAATGTTGCACTCACT Y 2 1 2 1 101000 f 74 goat snp21964-scaffold216-12983 10 98132864 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453423 Affx-122919882 AX-123323756 10 2948326 GAATTTAGGGTTAGTCTTAGAGCTTTCCATAATAG[C/T]ACATACAGAAGTTATTACTATTTTTTTGGTTAATT Y 2 1 2 1 101000 f 74 goat snp9660-scaffold1346-16143 10 98095096 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801788 Affx-122926581 AX-385288696 10 2986716 ATCACAGTTTGTTCCACTGCAGCTACTGACATCAG[C/T]GTTCTGCTCGCTGATGTCTGATTTTAAAAAAGGAA Y 2 1 2 1 201000 r 74 goat snp9661-scaffold1346-54533 10 98056848 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434309 Affx-122934754 AX-123304650 10 3020809 TTCAGTCATTTCATGTTTATCTTGGCTAGGATTTT[A/G]CATTTCAGGGGTCATGCAGATTAAAAGTAGAAGAT R 2 1 2 1 201000 f 74 goat snp9662-scaffold1346-88626 10 98023015 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398346 Affx-122962119 AX-123268701 10 3108218 GATGTTTCTGGAAAATGTTCTCCACTAATGAGGAG[A/G]CATCCTATAGGAGGCATCTATTCCTGATATTACTT R 2 1 2 1 101000 r 74 goat snp9664-scaffold1346-176035 10 97936281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795855 Affx-122920803 AX-385282808 10 3145244 CTATACATAATATTGTACGTTTTTAACATTATACT[A/G]CTACAGTTGTGATATAGAAGCATGTTTTATATTTA R 2 1 2 1 101000 f 74 goat snp9665-scaffold1346-213061 10 97899185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417289 Affx-122947242 AX-123287637 10 3189475 CATGAAAACGATCTTGAAATGTATCAAACAATTGA[C/T]GAATAACACATTTTCAATTAAATAATCAGTGCTTA Y 2 1 2 1 101000 f 74 goat snp9666-scaffold1346-257292 10 97855122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785639 Affx-122946589 AX-385272681 10 3227376 GGCAAGATGCTGTGTCTTTCAGTTACTTCTTTAGT[A/G]CCATGCTTATTATTATTGCAGGACTGTCCATGACA R 2 1 2 1 101000 r 74 goat snp9667-scaffold1346-295193 10 97817196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445224 Affx-122925503 AX-123315561 10 3350060 GATTTAAAACGAGAGTTTACTGGAGGGCTACACAG[A/G]AATAAAGAAAAGCCCTCACCAGAAGCAGAAATAAG R 2 1 2 1 101000 f 74 goat snp9669-scaffold1346-417877 10 97699526 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388118 Affx-122969485 AX-123258476 10 3393267 AATAAAATGAAAAAAAAAAGTTGTTTTTTAAAGAC[A/G]CATTAGCCAGACTTTACTGAGTCACGCAGTCATAC R 2 1 2 1 101000 r 74 goat snp9670-scaffold1346-461084 10 97655116 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278862 Affx-1111836642 AX-185316164 10 3402309 AGCGTCTTTTAATTTCATGGCTGCAGTCACCATCT[A/G]CAGTGATTTTGGAGCCCAAAAAAATAAAGTCTGAC R 2 1 2 1 103000 f 74 goat Random2.2K_MT-27 10 3402309 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38385047 Affx-122971833 AX-123255405 10 3459901 TGAGGTGCCGGAACTTGTCTCCTGTTTCTTCAAGA[C/T]ACAGATAATGACAGAAGCAGAGCTCTGCTTGAGTA Y 2 1 2 1 201000 f 74 goat snp9671-scaffold1346-527718 10 97588807 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448679 Affx-122923876 AX-123319015 10 3495905 ATCTCCACCTGTGTCTTTCTTTAGTGAAACAGCAA[A/G]CTTTCAGCCACTGTCATGATCCAGATGAAGTCTGA R 2 1 2 1 201000 r 74 goat snp9672-scaffold1346-563722 10 97552326 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415664 Affx-122948558 AX-123286013 10 3523611 GCAGGTGGCCAGTCTCTTCTTCATTTGTGTGTGGG[A/G]ACTCAGATGGAAGACTCAGGTTGGACCAGGAAGTG R 2 1 2 1 101000 r 74 goat snp4986-scaffold1169-1214641 10 97522684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799041 Affx-122938078 AX-385285970 10 3552852 TTTGTTTGCTGGTGGTACTCAAACTAGCTCACATG[C/T]GAATCTAGAGGGCCTGGAAATATTCAAGATACCTT Y 2 1 2 1 101000 r 74 goat snp4985-scaffold1169-1185400 10 97493520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276491 Affx-1111835368 AX-519550003 10 3557976 GAACATCCTTCAGGACTAAGTAAATTCCTTTTGAT[A/G]AGTCCTCTTAAGACTTAGATACTTTGTTGGTTACG R 2 1 2 1 201000 r 74 goat Random2.2K-1035 10 3557976 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397018 Affx-122963126 AX-123267373 10 3606515 CTAAACCCTTGTTCATAGGAGTTCAATAAAAAGGG[A/C]TTGGAGGCATTTTCTAACAAAATTTCCATTATATA M 2 1 2 1 202000 r 74 goat snp4984-scaffold1169-1131737 10 97439599 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438923 Affx-122930425 AX-123309260 10 3646667 TTGAGCTGATACATAAGAGTTTTGGCTAACCTAAA[G/T]CCACCAGGCTGCAGAAGTCACATGGAGAGACCACA K 2 1 2 1 102000 f 74 goat snp4983-scaffold1169-1091585 10 97399826 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276343 Affx-1111835369 AX-519549876 10 3669306 CTGAAGGCGTAATGTTACATGAAGAAGTGACCCAA[A/G]TGCCCATGTTTCCTATTCCTGCGATAGCTCCTTCT R 2 1 2 1 101000 f 74 goat Random2.2K-1037 10 3669306 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320790247 Affx-122944113 AX-385277251 10 3681109 GCATGATATGTTTCAAGAATCTTTACAAGTTTTCT[A/G]TATGAGTCATTATGGAATGGCAAACCTATTGTTTT R 2 1 2 1 101000 r 74 goat snp4982-scaffold1169-1057143 10 97364313 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400669 Affx-122960343 AX-123271024 10 3730895 TATTCATAGGTAGGGTCACAGATGAGGAAACAGAG[G/T]TTGCTATTGCAGGAAACATTAAGTTGCTCAATGTC K 2 1 2 1 303000 r 74 goat snp4981-scaffold1169-1007357 10 97313417 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385550 Affx-122971230 AX-123255908 10 3768304 TACAAATAATCTGCTGAGAGCTGACATTGTCTTTC[A/G]AGGCAAATAAGTTGGTAAAGCTTATGAATAAAGAT R 2 1 2 1 201000 r 74 goat snp4980-scaffold1169-969948 10 97275165 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437474 Affx-122932374 AX-123307812 10 3812441 GATGTATAAAAGTAACCATTTTTATATAATTGTGT[A/G]CTTTCAAAAGGTCTTGACCCTGTGTAGTATTGTAT R 2 1 2 1 101000 r 74 goat snp4979-scaffold1169-925811 10 97229841 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276345 Affx-1111835370 AX-519549878 10 3846614 TGAATTTGCAGGGCTGTTTTAAATTCTAAGAAATA[A/G]GGGGATGGTCCTCAACTTTTTCATCAAAGGGATTC R 2 1 2 1 201000 f 74 goat Random2.2K-1038 10 3846614 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276496 Affx-1111835371 AX-519550008 10 3847767 AGTCACTGAGGACTTGGTTCAAATCCTCTCTCACC[A/G]CGGATGACTGAAATGGACGCCAAGAAAGGGCTCCT R 2 1 2 1 101000 r 74 goat Random2.2K-1039 10 3847767 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408523 Affx-122953701 AX-123278874 10 3864548 AGCCAGGTGATCTTTGCCCACGTCGTCTGTCCAGA[C/T]TCCTTACCCACCAGTGCCACCCTATCAAGCATCTC Y 2 1 2 1 101000 f 74 goat snp4978-scaffold1169-873704 10 97181322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399533 Affx-122961147 AX-123269888 10 3912224 CATCAGTGTATAGGAAAATCTCCAAAAGCATGCAT[A/C]GACAGCCTTTGTCGAGGGGAAAGTAGATGAGAACA M 2 1 2 1 201000 f 74 goat snp4977-scaffold1169-826028 10 97133385 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394564 Affx-122964452 AX-123264919 10 3964684 AGATGCTAGGAGAGAGGCGTGGAACAGATTAACCC[A/G]CTCTGAGTAGGGAGGAGCTGAGGAACCAGGATCAA R 2 1 2 1 101000 f 74 goat snp4976-scaffold1169-773568 10 97080476 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450252 Affx-122922253 AX-123320587 10 4007901 TCCACAGCTGTGTATGTTCTATTATTAGCATAATT[A/G]TTTTTAAGCTACCACTATTTATACTGTCCCTTTAG R 2 1 2 1 101000 r 74 goat snp4975-scaffold1169-730351 10 97036265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387236 Affx-122970575 AX-123257594 10 4042931 CAAGAGATATTTATTTTTATAAGTGTGGGTTAGCT[A/G]TGAGCTTCATGTTCTACAGTGGGAAGGAAGACCTC R 2 1 2 1 101000 r 74 goat snp4974-scaffold1169-695321 10 97000518 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603297 Affx-1002479455 AX-413837477 10 4064030 TGATTCAGCAGCTTACAAGAAAACCCATTTATTAT[C/T]GCACCATATCTGTGTGTCAGAAATCAGCACAGCAT Y 2 1 2 1 101000 r 74 goat 10_4064030_RH-map 10 4064030 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38383297 Affx-122972711 AX-123253655 10 4091414 CATGTAGAGTGCTGGCTACTCAGAGAGTTTTTCCT[A/G]GCCCAGGGATCAAGCCTAGAAATGAGCATTTCTTT R 2 1 2 1 201000 f 74 goat snp4973-scaffold1169-646838 10 96952871 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278936 Affx-1111836677 AX-192011485 10 4093728 GGAACTCCCCAGGTCATTAGGTGCCCAATATGCTA[C/G]TGGAGATCAGTGGAGAAATAACTCCAGAAAGAATG S 4 1 2 1 103000 f 74 goat Random2.2K_MT-61 10 4093728 G C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776041 Affx-122955212 AX-385263171 10 4133648 TCTATTATAAGAGCCAATAAATTCTTCTTTAGTAA[A/G]TTCAGGTTGGGTTTCTGTACCTGGGAACCAAATAT R 2 1 2 1 101000 r 74 goat snp4972-scaffold1169-604604 10 96910784 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603299 Affx-1002479456 AX-413837479 10 4142679 CTCTTGGTTGTAGCCTTCAGGGGAAATTGGATGGG[A/G]AAATGCATTTCAAATACTATATACTGTGTGTGTAT R 2 1 2 1 201000 r 74 goat 10_4142679_RH-map 10 4142679 A G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38450171 Affx-122922314 AX-123320506 10 4167517 TTGAGAACTCAACTTTAGAATGGAAAATGGAGGCT[A/G]AAAAGGAGACTGAGAAAACAGTTGTTAGGATCCTC R 2 1 2 1 101000 f 74 goat snp4971-scaffold1169-570735 10 96876880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276350 Affx-1111835373 AX-519549882 10 4186356 TTGCTGTATGAATGGACACGCTACCCACCATTACC[A/T]GCTGCTGCCTGCAGCACAGAGGAAATGCTGTGGAT W 4 1 2 1 102000 f 74 goat Random2.2K-1040 10 4186356 A T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452146 Affx-122921667 AX-123322479 10 4217729 GTGGCTGTGTCCTTTGCGCTCTCACAGTTGTATAC[A/G]TATCTTTCACTCTGGTCTGTTTATTGCCCCATTTC R 2 1 2 1 101000 r 74 goat snp4970-scaffold1169-520523 10 96826490 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603219 Affx-1002479457 AX-413837403 10 4259168 CCTTATGATCATACAATGGAAGTGAGAAGTAGATT[C/T]AAGGGACTGGATCTGATAGACAGAGTGTTCCAGAA Y 2 1 2 1 303000 f 74 goat 10_4259168_RH-map 10 4259168 C T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38445534 Affx-122925166 AX-123315871 10 4320309 TGAATCCTTGATCTCCTTGCTGACATGGGTTGTAC[A/G]TTGTCGATGTCATCTTCATATTATTAAGGGCTATA R 2 1 2 1 201000 r 74 goat snp4968-scaffold1169-417943 10 96721581 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603222 Affx-1002479458 AX-413837406 10 4387341 TGGAAAATTCTTAAAGAGATGGGAATATCAGAACA[C/T]CTTACCTGCCTCCTGAGAAACCTCTATGCAGGTCA Y 2 1 2 1 303000 f 74 goat 10_4387341_RH-map 10 4387341 C T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38387984 Affx-122969589 AX-123258342 10 4396137 ATCAGTACACGGGGCTGCAGACAAGTCTGGGTGAT[A/C]TTTTGGTAGTTATATCATTCTCAAGCCACGGGGTG M 2 1 2 1 101000 r 74 goat snp4966-scaffold1169-342115 10 96644964 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768448 Affx-122926482 AX-385255628 10 4450874 TAAGAGATCAGTAAATACAACCAAGAAAGTGATTC[A/G]TGGCTAGTGTTGCCTTTTTAAAACAGCAGTCTGAG R 2 1 2 1 101000 r 74 goat snp4965-scaffold1169-287378 10 96589949 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413272 Affx-122950215 AX-123283621 10 4498984 GCAGAGGTGTTGACACACTGGAAAACTGCTTTAGA[A/G]AAGAGTCGTGGTTTTGGTTTGTTCTATTGGGAAAC R 2 1 2 1 201000 r 74 goat snp4964-scaffold1169-239268 10 96542091 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603224 Affx-1002479459 AX-320754546 10 4536087 TTTCTGATTACAGTTTCAATTTCCATGCTTGTGAT[A/G]GGTCTGTTAAGATTTTCTATTTCTTCCTGGTTCAG R 2 1 2 1 103000 f 74 goat 10_4536087_RH-map 10 4536087 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38378051 Affx-122977190 AX-123248410 10 4585647 TTCTACCATCTTAAAATATTTTTTCAAGCTTGAAA[C/T]AGACCATAATAAGATGGTAGTGGAATGATATTTAC Y 2 1 2 1 103000 r 74 goat snp4963-scaffold1169-152605 10 96455257 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410585 Affx-122952123 AX-123280935 10 4620910 GGAAATCAATCGATCCATCAGCACTGAATGTACTT[A/C]TTGAGAGCAAGGAAATATTCAAAATATGAACCAAG M 2 1 2 1 101000 f 74 goat snp4962-scaffold1169-117342 10 96419783 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784698 Affx-122955995 AX-385271746 10 4660108 AGGTCAAATTTACGTTGAGGTCTAATGACTCTCCC[A/G]TTTTCCTCCCAACTTGCCTCCTATTTTCTTCCCCA R 2 1 2 1 101000 f 74 goat snp4961-scaffold1169-78144 10 96380247 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397250 Affx-122962361 AX-123267605 10 4696800 TGCAGATTGCTGTCCCCCAACCAAATGCTCACTTG[C/T]CTTTGCTTTTATTTCTGCTGGAAAGTTTGTCTTGC Y 2 1 2 1 103000 f 74 goat snp4960-scaffold1169-41452 10 96342798 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603604 Affx-1002479460 AX-413837754 10 4714666 GATGACAGATGAAACATTACAGAAATTCGGCGTAC[C/T]CCTGAGGACGCTCAACTACTCAAAAGATACACTTA Y 2 1 2 1 101000 f 74 goat 10_4714666_RH-map 10 4714666 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320788672 Affx-122946155 AX-385275688 10 4729817 TCAGCATCCAAGCATATGTAGTAATATGTTGCATA[C/T]GTTGTTTCTTAAAGATACGGCGATGTATTTCACAA Y 2 1 2 1 101000 f 74 goat snp4959-scaffold1169-8435 10 96309723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603226 Affx-1002479461 AX-185310632 10 4730976 TTCTGTTGTTTTCCTCTATTTCTTTGCACTGATCA[A/C]TGAGGAAGGCTTTCTTATCTCTCCTTGCTAGTCTT M 2 1 2 1 303000 f 74 goat 10_4730976_RH-map 10 4730976 A C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38377186 Affx-122978197 AX-123247545 10 4787162 GTACGAAAGAGCCTACAGCCCAAAGTCTGCCCACA[C/T]TCACTTCAGAGATCTTTCCAATCCCTGCCCCGCCA Y 2 1 2 1 101000 f 74 goat snp42253-scaffold555-153202 10 96243861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423915 Affx-122942274 AX-123294261 10 4820110 GCTCGGCTCCTTGTGTAGACACAATACCGTCCAAA[G/T]CAAGAGACAGCAGGAAAGGACGGTGTTCAAGACAG K 2 1 2 1 202000 r 74 goat snp42252-scaffold555-120254 10 96209419 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404558 Affx-122957380 AX-123274910 10 4852852 AAGGGACAAAACCTGCCCGGGCGAGTCTTCTTTCT[A/G]CGTTATGTAGTACAGACCCTGGAAGATGATTTCCA R 2 1 2 1 101000 r 74 goat snp42251-scaffold555-87512 10 96176327 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603309 Affx-1002479462 AX-413837487 10 4897553 GTATGCTATCTTTTAATACTTTTGGTAATTTTATG[A/T]GATAAATAATATTTCTTCTTTCACATATAAGGGAA W 4 1 2 1 101000 r 74 goat 10_4897553_RH-map 10 4897553 A T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38401842 Affx-122959434 AX-123272195 10 4903268 GTATCATTAAAGCATTGGAAATGGTTGAGATTGTG[C/T]AGGCAGAGTATGCAAAGGTCATGAGGAACTCGATG Y 2 1 2 1 201000 f 74 goat snp42250-scaffold555-37096 10 96124707 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776449 Affx-122930728 AX-385263576 10 4952157 CTGCAGGCACTGTGCCAAAGGCTTATACACAATGT[C/T]TCACTGAACTCTTATAACCACCTTTGGAATTATGA Y 2 1 2 1 101000 f 74 goat snp59669-scaffold987-1202231 10 96075542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439008 Affx-122930361 AX-123309345 10 4993416 AAAAATTAGATTATCAGCAGACTTCTGACAGTAAC[A/G]CTTTACACCAAAAGAAAATGGAGTAAAACGAAAAA R 2 1 2 1 101000 f 74 goat snp59668-scaffold987-1160972 10 96034586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445331 Affx-122925421 AX-123315668 10 5029781 GAAGAAACAGCTTCTCCTCAATTGTGGGGGAATGC[A/G]TTCAGTTAGCACCATAAATCTCTAGAAAAGCTCAT R 2 1 2 1 101000 r 74 goat snp59667-scaffold987-1124607 10 95998174 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443894 Affx-122927059 AX-123314231 10 5098888 CTTAGTACATATTTGCTCACTGAATGAAGCCCTCA[C/T]GCTCAGTGAGTCCCCCCTCCTCAAAGGGCTCAAAA Y 2 1 2 1 101000 f 74 goat snp59665-scaffold987-1055500 10 95929058 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433902 Affx-122934398 AX-123304243 10 5129271 CAGCAAGGCCACACATGTGAGACTCTCAGCATTCT[A/G]CTTGCTGGGAGTAAGCTCTCCACAACATTAGCTAA R 2 1 2 1 101000 r 74 goat snp59664-scaffold987-1025117 10 95899065 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396544 Affx-122962942 AX-123266899 10 5174052 AGGGAAAGTGGCGGAATACAAGGCCTGACTAACAG[C/T]GGCCAGACCACGTGAAACCTTTAAGGGCATGATAG Y 2 1 2 1 101000 r 74 goat snp59663-scaffold987-980336 10 95854547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271746 Affx-1111832893 AX-519545540 10 5225696 TGAAAAAATAGTATAATTGTTCTTCTGTGTCTGTG[A/G]TCTGAATTAAGAGGGACCCTAAAATCGACATCCAC R 2 1 2 1 101000 r 74 goat 10_5225696_AF-PAKI 10 5225696 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38430033 Affx-122937576 AX-123300374 10 5275466 TTATATTAGCTGTGATGGTAACAACGATGGTGATC[A/G]TGAAGACAGTGATCTTGGGGTTGTGACCCCAAGGG R 2 1 2 1 101000 f 74 goat snp59661-scaffold987-878922 10 95753467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445279 Affx-122925462 AX-123315616 10 5327006 CCAAGAAACAAAGACTGTAAGAGTCTTTATGAAAC[A/G]CCCAACTGGAGAAGGAAGGCTCAGATAGACTCAGC R 2 1 2 1 101000 f 74 goat snp59660-scaffold987-827382 10 95702107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405778 Affx-122955919 AX-123276130 10 5360190 CATGTGGTCAACCGAAAACTCTATCATCATAAAAA[C/T]GGAAAACAATAAGCAACCCCCAAATAAATACATCT Y 2 1 2 1 102000 f 74 goat snp59659-scaffold987-794198 10 95668146 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385901 Affx-122971582 AX-123256259 10 5395019 GTGGAGTCACATGATGTCTTGAATTTAATTTAAAA[C/T]AGTACAACCTTCTCCTCCCCTGGAAAAAAAAGATA Y 2 1 2 1 201000 f 74 goat snp59658-scaffold987-759369 10 95635388 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411717 Affx-122951529 AX-123282067 10 5428836 ACCCCTGGACCACCCCCAGGAAGCAGCATTCTCAC[A/G]TGCCTGCTGAGTCTCCATCCATCTCCTGGTGGATT R 2 1 2 1 101000 r 74 goat snp59657-scaffold987-725552 10 95601923 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399316 Affx-122961377 AX-123269671 10 5534925 GGGAGTCATGTTCCTCTGACCAAGAGGGACCGCCA[C/T]GCTCTAGGAGACATGCTGAGCTACCCAGCAGGCAC Y 2 1 2 1 101000 r 74 goat snp59655-scaffold987-619463 10 95496028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409302 Affx-122953100 AX-123279653 10 5585539 GAAAGAATTCTGCATCATCAGAGGTGAAAGGGCTG[C/T]AAAATCCCTTCATCCATTCTTCTCTTTCCAGAGGG Y 2 1 2 1 201000 f 74 goat snp59654-scaffold987-568849 10 95445610 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419124 Affx-122945762 AX-123289472 10 5642366 TGTATGTGGCCTAACTTTACTTCTGCGTTTCTATG[A/C]GGCCTCTGTGCTCCTCCCATCTAAAAAGCAAACAA M 2 1 2 1 101000 f 74 goat snp59653-scaffold987-512022 10 95390770 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398693 Affx-122961860 AX-123269048 10 5718784 CAGTACCAGAAGATTAACCAAGGGTTACAGTAGCC[A/G]AGAGGAAGAACTAAGAAACTCTGTTTCAGAGAGGA R 2 1 2 1 101000 f 74 goat snp59651-scaffold987-435604 10 95314942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802283 Affx-122965091 AX-385289187 10 5812010 TAAGGAACAAATAGTTGAGTAAGTTCCTAAGAAAA[G/T]AATTTATAAAATAGGAGTTTCAACTAGATTTTTAA K 2 1 2 1 202000 r 74 goat snp59649-scaffold987-342378 10 95221797 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405250 Affx-122956878 AX-123275602 10 5883028 TCTCTCGGACTGCAGCAGGAGAGTGGATAGAAGGG[A/G]GAAAGGATGAAAGTGGAGAATCTCAAAGCCTATTT R 2 1 2 1 201000 r 74 goat snp59647-scaffold987-271360 10 95152695 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428566 Affx-122938720 AX-123298908 10 5983630 CTCTTTCAGAAATGCTTCCAGGCCTTTACACAGCT[A/C]TTTCTTCTCTCTGGCATGCCCTTCCTTACTCTCGC M 2 1 2 1 101000 r 74 goat snp59645-scaffold987-170758 10 95052356 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426465 Affx-122940795 AX-123296811 10 6024181 TTTTTACTCCCCTACCAGTATTTCCCTTTATCTTC[C/T]AAGTTAATGACTTGTACCCAAATCCTTAACCCAGG Y 2 1 2 1 201000 r 74 goat snp59644-scaffold987-130207 10 95009902 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427018 Affx-122939841 AX-123297363 10 6066581 CTGGGACTGAGTGAGAGCTCAAAATGGGAATTGCT[A/G]TGACTTCTCAGATGCCTCGATTTTTGTTTTCCTAA R 2 1 2 1 101000 r 74 goat snp59643-scaffold987-87807 10 94963290 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450286 Affx-122922164 AX-123320621 10 6111876 GCTGTGGCTAAAAGTTTGGTGACATGGTTGGTAAC[A/G]TGGAAGGGACATGATTAGAAAGTTAGTGGCAAGTC R 2 1 2 1 101000 f 74 goat snp59642-scaffold987-42512 10 94917207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438213 Affx-122931451 AX-123308551 10 6143746 AGTAGGACCCAAGCCTGCTCAGCTTCCAGGACTGC[A/G]TTTCTTCCCTTTTCTTTAACATCGTGTGCTATAGA R 2 1 2 1 101000 r 74 goat snp59641-scaffold987-10642 10 94872304 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399172 Affx-122960634 AX-123269527 10 6169548 GAAATCCTCTTCTGTTAGTGGGGAATCCCCTGGAC[A/G]CCACCTCTGTCCTCAGAATATCCCAGGAAACCACC R 2 1 2 1 102000 f 74 goat snp47385-scaffold6668-15061 10 94848627 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791415 Affx-122928313 AX-385278407 10 6211297 CACTAGTTACAAAGCCCAAGTAGTAAAGTGAACGA[C/T]GCTATGGTATATTATGTGGAAAAATAACAATAAAT Y 2 1 2 1 101000 f 74 goat snp56339-scaffold8810-22057 10 94801865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773417 Affx-122930864 AX-385260559 10 6237416 TGCTGGGTTCAAATTGTTGCAACACACTGAGAAAG[C/T]GCTATTTGAAATGGGCCATTTGTAGGTGTGTTATT Y 2 1 2 1 101000 f 74 goat snp26833-scaffold282-537958 10 94760776 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377698 Affx-122977411 AX-123248057 10 6267367 CATTTGTGCAATCTGAATAAAATTTTACAATGTCT[A/G]ATATTTACTGTAGCCTCCTTTAGGGTCTGCCCAAT R 2 1 2 1 101000 r 74 goat snp26832-scaffold282-508007 10 94730787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388834 Affx-122968889 AX-123259192 10 6297986 TTCTCTCACCCCAGTTCTTCGCCTTATAAAAACCT[A/G]CAGCACACTGTGCCACAGTCTTCTTCCTAAAGGTC R 2 1 2 1 201000 r 74 goat snp26831-scaffold282-477388 10 94699558 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762767 Affx-986697297 AX-385250820 10 6348866 AGTCCATGAGGTCCCAAATCATGGGACATGACTGA[C/G]GAAACTGAAACTGCCCTGAAGGCATTCCCTGTCTA S 4 1 2 1 600010 f 74 goat 10_6348866 10 6348866 Ancestral_priority_1043 ancestry 0.71 recommended IMAGE 10K 10K ancestral 38422418 Affx-122943368 AX-123292764 10 6397666 CTTACTCAGGAGCAATCTCCTTGTATAAAACTGCC[A/G]TCATGCCTTTGAGTTTTGAAAAGTATTAGTCAAAA R 2 1 2 1 101000 f 74 goat snp26829-scaffold282-377708 10 94599728 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794911 Affx-122941486 AX-385281871 10 6441906 AAATAGTCAGTGAAATACTTTATCTATCTTTATTG[C/T]GGGAGGTGGTAAATAAAGTAATAAAGTGAAATGTG Y 2 1 2 1 101000 r 74 goat snp26828-scaffold282-333468 10 94555281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429825 Affx-122938178 AX-123300166 10 6503567 TTTCCTAATTCCCTTAAATATAGGTCATCTCTTCC[C/T]ACTTTGAACACCCAAACAGGTCCATATTATATGAC Y 2 1 2 1 101000 f 74 goat snp26827-scaffold282-271807 10 94492545 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792561 Affx-122961311 AX-385279542 10 6536066 ATTGCTATTGAGAAAATTTTAGTTGGGCTGAGCTG[A/G]TTCTCTTGTGAAATTGTGCTGGTTATCTTTAAACT R 2 1 2 1 101000 f 74 goat snp26826-scaffold282-239308 10 94459906 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417319 Affx-122947748 AX-123287667 10 6594086 ATATTTTCTCCGTTACCATTATTTTGTTATTAACT[A/G]TAGATTAGCTCTCTAGACTTACTTATCCCACAACT R 2 1 2 1 101000 r 74 goat snp26825-scaffold282-181288 10 94400962 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435268 Affx-122934054 AX-123305608 10 6628420 ATGAGCATGGTTTTTGGTAATTTTACCCTTGCTGT[A/G]CTCTTTATCTGAAATATCTTCAAAAAGTTATTTGA R 2 1 2 1 101000 f 74 goat snp26824-scaffold282-146954 10 94366748 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396729 Affx-122962800 AX-123267084 10 6672909 ATCTCTGTTATGCAAGGAAGTGGCCACGAAGCATG[C/T]GGAATCCTAGCTCCCCGACCAAGGATCGAAACTGC Y 2 1 2 1 101000 f 74 goat snp26823-scaffold282-102465 10 94322283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435855 Affx-122932807 AX-123306194 10 6713434 CCCTTCATGCCCAGCTTGTATGCCATACCAAGTAG[A/G]TCAGAAAGTCTAGGAGAAGAAGTCAGATATAAATA R 2 1 2 1 101000 r 74 goat snp26822-scaffold282-61940 10 94280914 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405546 Affx-122955969 AX-123275898 10 6752662 CCTTTTGTTTTCTTTGATGCTGAGTACTTTGTCAG[C/T]GATCCTGGCCTGGAATAAAACAGAGCACGTGATTA Y 2 1 2 1 101000 f 74 goat snp26821-scaffold282-22712 10 94241596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454246 Affx-122919657 AX-123324579 10 6777699 AATGTGTGCTCTGGATGATGGTTAGAGTATGAGGC[A/G]GAGAGCATCACTGACTCAATGGACCTGAATTTGAG R 2 1 2 1 201000 f 74 goat snp56397-scaffold886-2226 10 94204434 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802842 Affx-122932441 AX-385289741 10 6809713 CAGTAAACATTTCCCATTCATCCCTACCCTCTATC[A/G]TCTGGCTCTCATGCTATCCTTGCCATACATATCCA R 2 1 2 1 101000 f 74 goat snp56398-scaffold886-34240 10 94172057 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770404 Affx-122959786 AX-385257570 10 6838535 GGTCGCACTGTGCCTAAGGATTTATGTTCTTTCCA[C/T]TATTTCATACAACTATCCTGATAAATGGCCTGGTA Y 2 1 2 1 101000 f 74 goat snp56399-scaffold886-63062 10 94147031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410277 Affx-122952515 AX-123280627 10 6868819 CTGGGTCAGGCCTGTCCTGCCCCTCTCTGTGAGCC[A/G]CATGCTCTCTGGATACAAGTTTCAGCCTTCCCCAG R 2 1 2 1 101000 r 74 goat snp56400-scaffold886-93346 10 94116723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435865 Affx-122932799 AX-123306204 10 6906042 AAGGGAAGTTTATCAAGTATGCACAGCAGCATTTC[A/G]CTGTTAAATAGCAATGGTTAGCACTTTGCTGCCCA R 2 1 2 1 101000 r 74 goat snp56401-scaffold886-130569 10 94079141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409270 Affx-122953123 AX-123279621 10 6959557 AAGAAAAGAAAGAATAAAAAAATATAGCTTGTGAA[A/G]ATCACCATACTGAGAGTATTGCTAGTTTCCTTAAG R 2 1 2 1 101000 r 74 goat snp56402-scaffold886-184084 10 94030079 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418518 Affx-122946423 AX-123288866 10 6991922 GGGCCATAGGAATGGGCCAGTGGGAGAGAGAGATA[G/T]CAGGTGCTTGGGCCCAACCTAGTAATTTAGGGTTT K 2 1 2 1 201000 f 74 goat snp56403-scaffold886-216449 10 93996873 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776925 Affx-122973982 AX-385264049 10 7039542 GCAGAAATTATAGTGAAATGGCTCATTTGAAGAGC[A/G]CATTTGAAAGGCAGGTATAGTTTAATTGAGAATTA R 2 1 2 1 101000 f 74 goat snp56404-scaffold886-264069 10 93949238 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778066 Affx-122953786 AX-385265182 10 7079841 TAAAAATGTGTTAACTGGGAATGGTCCAGTGCTCA[A/G]CTAGCGTTAATTATTCTTTGCTACTGAGACTAGCA R 2 1 2 1 101000 r 74 goat snp56405-scaffold886-304368 10 93908372 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411155 Affx-122951878 AX-123281505 10 7112855 GAATGAAAGGGAGTGGAAAGAAGGAAAGGAGCTTC[A/G]TTCCCAGCACTTCAGGGAGCAACAAGTGCCTCATA R 2 1 2 1 101000 r 74 goat snp56406-scaffold886-337382 10 93875587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449565 Affx-122923237 AX-123319900 10 7142300 TTAAGTTAAAAGTGTGTGTATAAAGCAGTTCATCC[A/G]TTTTTGTTATGAATTGTGTGGTACACGGCTATGGG R 2 1 2 1 101000 r 74 goat snp56407-scaffold886-366827 10 93846050 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377942 Affx-122977212 AX-123248301 10 7173695 CCAGGAAGGCCCTGAAGAACTCGGTGAAGTGTTAT[C/T]GGATTAGGGAATTTGTTAACTGTGCACTTTGGTAT Y 2 1 2 1 101000 r 74 goat snp56408-scaffold886-398222 10 93814497 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38447029 Affx-122924538 AX-123317365 10 7205067 GACTGCTCATGCTAAACATAAATCATTTATAATAA[G/T]AAGAAGAATAATCTGCCAGTAAATAATAGCTTCAG K 2 1 2 1 201000 f 74 goat snp56409-scaffold886-429594 10 93782478 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402466 Affx-122958603 AX-123272819 10 7244512 GTCATGGGGAACGCAGTCAGGCTTGTATTTCTGGA[C/T]GTCACCTTTCTGCATTTGTGGCAGAGCAGTCTGTG Y 2 1 2 1 101000 f 74 goat snp56410-scaffold886-469039 10 93744424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428392 Affx-122938953 AX-123298735 10 7301946 AGCTAGTAGCAGAAGGGCCTCCTGTACTCGCTTAC[A/G]CCTCAGGTCAGGAGGAGAGTAGGATTGCCAGAACC R 2 1 2 1 102000 f 74 goat snp56411-scaffold886-526473 10 93687163 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787091 Affx-122963080 AX-385274118 10 7341352 ACTGGACAGCTTGGCTTCATCTCGTTTCCTCTGCT[A/G]TTGTTATACATTTATTGTACTGAATCTATGTCCTA R 2 1 2 1 101000 f 74 goat snp56412-scaffold886-565879 10 93648053 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446966 Affx-122924659 AX-123317302 10 7395804 TGGCATCAGCACTTGAATGTCAGGGGAGGGGTATC[A/G]CCCTCATCTCTGCTGCCTCTTGCCTGTCTTCCCAC R 2 1 2 1 101000 f 74 goat snp56413-scaffold886-620331 10 93593578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426466 Affx-122940794 AX-123296812 10 7453553 TCAGTTGACCGTGCCTGGGTATTTTTTCGTGAAAA[C/T]GGTGGTCCCCCTGTGGTGACACTTGTGTTTGATCT Y 2 1 2 1 201000 f 74 goat snp56414-scaffold886-678080 10 93535947 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382064 Affx-122974923 AX-123252422 10 7483893 CAAGCCATTGCCCTGGAGAAACTGTTTGCAAAAGA[C/T]AGGTCTGATAAAGGACTGCCATCCGAAGTATGCAA Y 2 1 2 1 201000 r 74 goat snp56415-scaffold886-708420 10 93506092 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437976 Affx-122931597 AX-123308314 10 7513739 CCCATCATTGTTCCAGGTTTCATAGTTAGATTGAG[A/G]CTCATTGTCCTCAGCATTGAGAAAGTAGCCCAAGG R 2 1 2 1 101000 f 74 goat snp56416-scaffold886-738266 10 93474382 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399085 Affx-122960880 AX-123269440 10 7545082 GTCCTGCCCCTCAGCTCCCAGTGTCCCCCTGCCTT[A/G]CCTTTCCAAATCCTCCCTTTCCAGCTGAATCCAGA R 2 1 2 1 101000 r 74 goat snp56417-scaffold886-769609 10 93443402 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407507 Affx-122954742 AX-123277858 10 7583888 ACTAGGATACAGAAGGATGAGCATATGGAGGACCA[A/G]CTTACATGGGGCAGAGGAGCCTGGTGGGCTACAGT R 2 1 2 1 101000 f 74 goat snp56418-scaffold886-808415 10 93404919 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389077 Affx-122968593 AX-123259435 10 7620539 ATATGTTTGACCACAGGCAAGATTTGAAAGGGCAC[A/G]GTAACTCAAGACTCCTTGCTTTTGGCCCGATGTCC R 2 1 2 1 101000 f 74 goat snp56419-scaffold886-845066 10 93368658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411305 Affx-122952289 AX-123281655 10 7659508 AACACGGTTAAAAGACAAAATCTACTGTACAAAAA[A/G]TTACTTTTCAATCCACGATTTATTACCTCTCTTTA R 2 1 2 1 101000 r 74 goat snp56420-scaffold886-884035 10 93329605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452485 Affx-122920989 AX-123322818 10 7691182 TGGAACATTTAGATAAATTGAGGAAGAGAAAAGAA[C/T]GCAGTGATGTGCTTTGGTTAGTGATTCGTCTCTAA Y 2 1 2 1 101000 r 74 goat snp56421-scaffold886-915709 10 93298133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382068 Affx-122974919 AX-123252426 10 7721280 TGTTACGTATCCATCATCCGATGCCTCAGCTCTTC[C/T]GCGGTTGCCAACCAGAACAAGAAGTCGCGGGCTTT Y 2 1 2 1 101000 f 74 goat snp56422-scaffold886-945807 10 93267543 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271752 Affx-1111832899 AX-519545546 10 7737096 TTTGGACTTCACAGGTGGCTCTGGTGGTAAAGAAC[A/C]TGCCTGTCAACACAGGGGATGTAACAGATGTGGGT M 2 1 2 1 303000 r 74 goat 10_7737096_AF-PAKI 10 7737096 G T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412322 Affx-122950849 AX-123282671 10 7764491 AGTGTTCTCCTCCCTGGAGCTGCAGAGTCTCCACC[A/G]CAAACTAGTCCAGCCCTTCTCTTCTCCACGTGATC R 2 1 2 1 202000 f 74 goat snp56423-scaffold886-989018 10 93223967 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377553 Affx-122977453 AX-123247912 10 7794557 GAATTTGAATCAGAAGCATGTGATTCTTTTCCTTC[C/T]GCAGTTACAGAAAAGGGTATTATTATGGTGGATAC Y 2 1 2 1 201000 r 74 goat snp56424-scaffold886-1019084 10 93193985 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388314 Affx-122969374 AX-123258672 10 7835255 ATTTAGATTTTGGCTCAAGCAAATGATGCACTTTA[C/T]GGAATGGGAAAGACTAGGGTAGGAGCAGCTTTGTG Y 2 1 2 1 201000 f 74 goat snp56425-scaffold886-1059782 10 93153540 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441722 Affx-122929144 AX-123312059 10 7873420 CTGAGCTCAGATCAGTTAAGGGGCAGAGAGCCTCC[A/G]CTCCTCACTGCTCTATAAAAGGGACCCAGCAAAGG R 2 1 2 1 201000 r 74 goat snp56426-scaffold886-1097947 10 93115181 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413883 Affx-122949846 AX-123284232 10 7905711 TTTGCTTTTTGATGGAAGTACTGGGTCATTTCTTC[A/G]TTTTTCATTTCATTATGCATAAGATCTGACTTGTG R 2 1 2 1 202000 r 74 goat snp49215-scaffold703-20511 10 93083366 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794566 Affx-122962255 AX-385281528 10 7959942 TTTCAGCTTTTGATGACAGTAATGATGGAACTCAG[C/T]ACACCCACATTCTTCAACCTCTGTGGTCTACAAAT Y 2 1 2 1 101000 r 74 goat snp49216-scaffold703-74742 10 93029129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454024 Affx-122919419 AX-123324357 10 8037739 CAGGACATGACTGATGACCTCTGGGTCATGGTAGC[C/T]TGTTTTCAAAGAACAGTTGTCTTTGGTTTCTTCTT Y 2 1 2 1 101000 r 74 goat snp49218-scaffold703-152539 10 92952900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788776 Affx-122977129 AX-385275791 10 8075663 AGTACCTATGTATGCAATAAATGGATGACTACTTT[A/G]CTGGTACCCTTTGTTTAACTGTTTATAAGTGGTCA R 2 1 2 1 101000 r 74 goat snp49219-scaffold703-190463 10 92914890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407217 Affx-122955386 AX-123277568 10 8130888 CTGAGTTGTTCAGCTTACAGCTTGCCAGTCACTCT[C/T]TTCCTGGTCTGTAGAATTTCACCCTACTCGTGCAT Y 2 1 2 1 101000 r 74 goat snp49220-scaffold703-245688 10 92860086 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276352 Affx-1111835374 AX-519549885 10 8141969 AAGAAGAAAAGTTAACTAGTGCTCTGTCCATTGTG[A/G]TCTACAGAGGAGCTTTATAAAATGTTTCTCAAATC R 2 1 2 1 101000 f 74 goat Random2.2K-1042 10 8141969 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320801981 Affx-122922326 AX-385288885 10 8173870 GAGGACTTATTTACTAGGATCATTCTGCCTGATGC[A/G]TTGAGACTAGTCTGAAAGAGACAAGTTAGAAGCTC R 2 1 2 1 101000 f 74 goat snp49221-scaffold703-288670 10 92816558 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476266 Affx-1251763773 AX-586011687 10 8193673 GATTTTCATTTTCACAGTGATTAATATGGCCATTT[-/TTAAAGATAAGGAGGGGAGAGGGAAAGATGGCGGAGGAATAAAAAAAATAAATTAATTAATTAATTAATTAAAAAAAAAA]TAAAGATAAGGAGAAGAGAGTTCTTCTCAGTATGC - 8 1 4 1 20000 f 74 goat SV_149 10 8193673 - deletion junction SV-TF-chip 539476519 Affx-1251763773 AX-586011912 10 8193673 GATTTTCATTTTCACAGTGATTAATATGGCCATTT[-/TTAAAGATAAGGAGGGGAGAGGGAAAGATGGCGGAGGAATAAAAAAAATAAATTAATTAATTAATTAATTAAAAAAAAAA]TAAAGATAAGGAGAAGAGAGTTCTTCTCAGTATGC - 8 1 4 1 20000 r 74 goat SV_149 10 8193673 - deletion junction SV-TF-chip 560378496 Affx-1251763773 AX-605230911 10 8193673 GATTTTCATTTTCACAGTGATTAATATGGCCATTT[-/TTAAAGATAAGGAGGGGAGAGGGAAAGATGGCGGAGGAATAAAAAAAATAAATTAATTAATTAATTAATTAAAAAAAAAA]TAAAGATAAGGAGAAGAGAGTTCTTCTCAGTATGC - 8 1 4 1 20000 r 74 goat SV_149 10 8193673 - deletion junction SV-TF-chip 562165186 Affx-1251763773 AX-606940598 10 8193673 GATTTTCATTTTCACAGTGATTAATATGGCCATTT[-/TTAAAGATAAGGAGGGGAGAGGGAAAGATGGCGGAGGAATAAAAAAAATAAATTAATTAATTAATTAATTAAAAAAAAAA]TAAAGATAAGGAGAAGAGAGTTCTTCTCAGTATGC - 8 1 4 1 20100 f 74 goat SV_149 10 8193673 - deletion junction SV-TF-chip 562165631 Affx-1251763773 AX-606941041 10 8193673 GATTTTCATTTTCACAGTGATTAATATGGCCATTT[-/TTAAAGATAAGGAGGGGAGAGGGAAAGATGGCGGAGGAATAAAAAAAATAAATTAATTAATTAATTAATTAAAAAAAAAA]TAAAGATAAGGAGAAGAGAGTTCTTCTCAGTATGC - 8 1 4 1 20100 r 74 goat SV_149 10 8193673 - deletion junction SV-TF-chip 562165685 Affx-1251763773 AX-606941094 10 8193673 GATTTTCATTTTCACAGTGATTAATATGGCCATTT[-/TTAAAGATAAGGAGGGGAGAGGGAAAGATGGCGGAGGAATAAAAAAAATAAATTAATTAATTAATTAATTAAAAAAAAAA]TAAAGATAAGGAGAAGAGAGTTCTTCTCAGTATGC - 8 1 4 1 20100 f 74 goat SV_149 10 8193673 - deletion junction SV-TF-chip 562165801 Affx-1251763773 AX-606941210 10 8193673 GATTTTCATTTTCACAGTGATTAATATGGCCATTT[-/TTAAAGATAAGGAGGGGAGAGGGAAAGATGGCGGAGGAATAAAAAAAATAAATTAATTAATTAATTAATTAAAAAAAAAA]TAAAGATAAGGAGAAGAGAGTTCTTCTCAGTATGC - 8 1 4 1 20100 r 74 goat SV_149 10 8193673 - deletion junction SV-TF-chip 562166081 Affx-1251763773 AX-606941490 10 8193673 GATTTTCATTTTCACAGTGATTAATATGGCCATTT[-/TTAAAGATAAGGAGGGGAGAGGGAAAGATGGCGGAGGAATAAAAAAAATAAATTAATTAATTAATTAATTAAAAAAAAAA]TAAAGATAAGGAGAAGAGAGTTCTTCTCAGTATGC - 8 1 4 1 20100 r 74 goat SV_149 10 8193673 - deletion junction SV-TF-chip 38429608 Affx-122937705 AX-123299949 10 8206195 AAGGACAAAGGCGGATTATAGAGAAAGCATACCAC[A/G]TAAAGATTTTCTTCAAAAAACAGAAACTAAATAAA R 2 1 2 1 101000 f 74 goat snp49222-scaffold703-320995 10 92783499 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452032 Affx-122920900 AX-123322365 10 8243399 TTGCATGGTGATGAGCAGTTGTTTTTCCCAGTGAC[G/T]GTAATATCTTGGGTGGTCAGCAGTTGTTGAGGAAA K 2 1 2 1 101000 r 74 goat snp49223-scaffold703-358199 10 92746465 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38408673 Affx-122953456 AX-123279024 10 8273456 CAGACTCCTTTGGACGGACGTTTGATTTTTCTTCC[A/G]TTTTCCCTGTGAAGAAGTCCCACAGTCGGTCAGTC R 2 1 2 1 101000 f 74 goat snp49224-scaffold703-388256 10 92716490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378890 Affx-122976498 AX-123249249 10 8326623 GAAGCTTTAAGCACAGTGAAATTTTTTCTGGGGTG[A/C]TTCATCTGTAAGTTTCTCTTTGTCCCTAGCAGTGA M 2 1 2 1 102000 f 74 goat snp49225-scaffold703-441423 10 92662899 A C 1 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38400875 Affx-122959762 AX-123271229 10 8359058 ACAGACCATGTGTATGGAGGACTCAATGGATGGCC[A/G]ATAACTGGATAAACAAGTGTTTAACTCTTCAAAGG R 2 1 2 1 101000 f 74 goat snp49226-scaffold703-473858 10 92630738 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782398 Affx-122972024 AX-385269474 10 8407731 GCTTGCCCTTTTACCAGTATTTAAATTCCATTCCT[A/G]TTGAAACAGCACTCAAGCAACCACGTGGAGAGATC R 2 1 2 1 101000 f 74 goat snp49227-scaffold703-522531 10 92582118 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391661 Affx-122966554 AX-123262018 10 8529820 ATCCTTCTCATTCTATACCCCTGGGTCATTAACAC[G/T]TCCTTCCTCAGGTCCCCCTTCCCTGTTTTAAAAAA K 2 1 2 1 101000 f 74 goat snp49229-scaffold703-644620 10 92461137 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413426 Affx-122950696 AX-123283775 10 8580324 CCACTACCCTCGGACTTCTAGTTGTGAGGGACTCT[C/T]GATCACCTTTGGGCTTCCCGGTGGCTCAGCAGTGA Y 2 1 2 1 101000 f 74 goat snp49230-scaffold703-695124 10 92410041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767312 Affx-122945594 AX-385254593 10 8624362 GCTGGCCAGGAAACTGTGAAATTAGGATTTGAAAT[G/T]ATGACTTCTAACTTTAAGTGCCAATGCTTTTTAAA K 2 1 2 1 101000 f 74 goat snp49231-scaffold703-739162 10 92365913 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463067863 Affx-1109797192 AX-514555416 10 8665142 ATTAAGTATCCATACTTATGTATATATCTATTAAA[C/T]TTTTAATTGATTTCCTTGTCAGTTGAATATACAGA Y 2 1 2 1 102000 r 74 goat Random2.2K-1043 10 8665142 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399025 Affx-122960926 AX-123269380 10 8680890 AATGTGCGACTTAAATGGCCACATGTCACAGGGTA[C/T]GGAGGTTGGAAGGCTGCATGTTTTAGATAACAAGA Y 2 1 2 1 101000 r 74 goat snp49232-scaffold703-795690 10 92310685 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443745 Affx-122927128 AX-123314082 10 8720839 ACCAACAGCTAGGGGTCTTTGAGCTGACAGTTTAT[A/G]TTTTGATAATGTTTTTATAATGATAATGCTACCTA R 2 1 2 1 201000 r 74 goat snp49233-scaffold703-835639 10 92270444 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403322 Affx-122957826 AX-123273675 10 8758507 CTGAAATAAGAGCCATATCAGCTTCTCCCAGGTGG[C/T]GGAGTTGAGTTCAGTTCCGTCATTCAGGCGTGTCT Y 2 1 2 1 101000 f 74 goat snp49234-scaffold703-873307 10 92232871 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424418 Affx-122941807 AX-123294764 10 8788407 GCATCATAAGAATAAATGAATTAATAAAAGATAGG[C/T]GCACATGTGAACTAGGAAGCCTATATGTCATAAAC Y 2 1 2 1 101000 r 74 goat snp49235-scaffold703-903207 10 92202131 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401673 Affx-122959566 AX-123272026 10 8845071 AATCCGGGAAGCAAAGAACTCTGAGAGGTGGGTAT[A/G]CACACATATCCAGACTGTGGGATCTTGGAATAGTC R 2 1 2 1 201000 r 74 goat snp49236-scaffold703-959871 10 92144792 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436459 Affx-122932986 AX-123306797 10 8906195 AACAGTCCAAGCAGGGGTTTTCAGCACTGACTGTG[C/T]GTGTAGCCTTAGTGCATCCTGACAGTGATCCTAAG Y 2 1 2 1 101000 r 74 goat snp49238-scaffold703-1020995 10 92084061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800316 Affx-122929436 AX-385287239 10 8936781 TGAAAATGGACAAGCCAACATATTACTGGCTATGG[A/C]AGGCATTTGCTGGGTGGAGGATGATGCATTGCTCT M 2 1 2 1 101000 r 74 goat snp49239-scaffold703-1051581 10 92053505 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380098 Affx-122975535 AX-123250456 10 9002577 TCATCTTCGCTGGTGAAGCTTTTAGCCGTCTTCCT[C/T]AAAACATCAGGGGCAATTTTAGGAACTCGTTCACA Y 2 1 2 1 101000 f 74 goat snp49241-scaffold703-1117377 10 91987189 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376854 Affx-122977900 AX-123247213 10 9060822 AAGCCATTTTCTATTAGAAAGTTAAATGCTACAAA[A/C]GGATTTCTTTAAAGTTAACCTGAAAGGAAAAGGAA M 2 1 2 1 101000 r 74 goat snp49242-scaffold703-1175622 10 91929210 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793438 Affx-122932139 AX-385280415 10 9098237 CTTCTTCCAAAACATTTTAGACAGGAAATTTTAAG[C/T]TAATAATAAAGGGTAGATGGGAGTGCTTGATTTGG Y 2 1 2 1 101000 r 74 goat snp49243-scaffold703-1213037 10 91891991 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416144 Affx-122948284 AX-123286493 10 9149084 GTTTGATTTAACACCTGTTAAATTCTTCAGTCCAC[A/G]TATCAAAGGTGTTGCAGAAAAAGTAAATACTATAA R 2 1 2 1 101000 f 74 goat snp49244-scaffold703-1263884 10 91841276 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803118 Affx-122942671 AX-385289987 10 9189196 TGTCTGAATATCTTTTTATCATTGTCCTTGAAGTA[C/T]GGTCATTGTATCACCTCTAACAGAATCACCTGGGG Y 2 1 2 1 101000 r 74 goat snp49245-scaffold703-1303996 10 91800773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777221 Affx-122947917 AX-385264344 10 9231331 GAATAAAATGAGTAAGAGAGGCTTAATCTTGAACA[A/G]TCTAGGTGGTGCCTGTATGTGACACTGATTTGTAC R 2 1 2 1 101000 r 74 goat snp49246-scaffold703-1346131 10 91758264 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276354 Affx-1111835375 AX-519549886 10 9270704 AATTTCTGTATTCTCACAGGAGCAGGCAGAGAAGG[A/C]AATGGCACCCCACTCCAGTACTCTTGCCTAGAAAA M 2 1 2 1 102000 f 74 goat Random2.2K-1045 10 9270704 G T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320801418 Affx-122958507 AX-385288327 10 9279082 TCAAACGTGTAAAAAACAGCAATGTTTTGAAAAAT[A/G]CTAAATGGAAATGGGGTAGACTATATGTGCTTTTA R 2 1 2 1 102000 r 74 goat snp49247-scaffold703-1393882 10 91710155 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411910 Affx-122951175 AX-123282260 10 9314394 GGGAGTTGTTTATAGAATCATAGAAATGATTTTCT[A/G]TAATACTTTCTTTTCAATAAAAATGTTCTGGGATG R 2 1 2 1 303000 f 74 goat snp49248-scaffold703-1429194 10 91674725 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797511 Affx-122975365 AX-385284450 10 9377106 CCCTGATAGTGAGCAGGACGACAGCAGACTTGCTT[A/G]TGTGCTGACAAGCAGACACTCTGAGTTAGGCCAAG R 2 1 2 1 101000 r 74 goat snp49250-scaffold703-1491906 10 91612776 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426426 Affx-122940825 AX-123296772 10 9429960 ACATAAAAATATTAACATGAGTTGTTTTATGAACT[G/T]GGAACTCTGCAAAGTGTCATCTTGGTTAGCCCCCG K 2 1 2 1 101000 r 74 goat snp49251-scaffold703-1544760 10 91561553 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434685 Affx-122933959 AX-123305026 10 9480112 CTCTAAAACAGCTACATTAAACACACATGCACGCA[C/T]GTGTCCTGATATGCAATCTGTACTCCTGCTGGGGC Y 2 1 2 1 201000 r 74 goat snp49252-scaffold703-1594912 10 91511296 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442106 Affx-122928353 AX-123312443 10 9512428 GGTGGTAGTGTTGGTGAAAGTTGCTTGGTCACGTC[C/T]GACTCTTTGTGACCCCATGGACTATAGAGTCCATT Y 2 1 2 1 103000 f 74 goat snp49253-scaffold703-1627228 10 91478963 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791949 Affx-122965717 AX-385278939 10 9554793 AAGTTGCAATAAGAGCCAAGCTCTATGCTTTTAAT[A/G]TTGTTGTACATTAGTCAGAACACAGAAATGTGAGT R 2 1 2 1 201000 r 74 goat snp49254-scaffold703-1669593 10 91434953 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799341 Affx-122943048 AX-385286271 10 9592926 CCAAAAGAATGAGTTGTGTTTCTTGGGCATTAACT[A/G]TTTGATACAATTATATAACGCAGTATGTCTTCCTT R 2 1 2 1 101000 f 74 goat snp49255-scaffold703-1707726 10 91398029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450353 Affx-122922108 AX-123320688 10 9685641 ATTTGAATCTCTCCACACATTACCCTTAAAAGACA[C/T]ACTGAAAAGGAAAGAAAGCAAAACTACCCAACACT Y 2 1 2 1 101000 f 74 goat snp49257-scaffold703-1800441 10 91304882 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276505 Affx-1111835376 AX-519550016 10 9711657 TGGAGTAGGTGTTGGTAGCTTCTGCTTTCTGGATT[A/G]TAACCTGCTATTTTGTGGGTAGATGAAGATGAGGA R 2 1 2 1 201000 r 74 goat Random2.2K-1046 10 9711657 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38426129 Affx-122940621 AX-123296475 10 9716752 ATTATTTGCAAGGCCTTAATTCAGTACCTCTCAGC[A/G]CCCATGACTGCTGGTTAGCATTGTGAGAAAAGACA R 2 1 2 1 101000 r 74 goat snp49258-scaffold703-1831552 10 91274107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435177 Affx-122933651 AX-123305517 10 9773806 AGGCGATGAAAACTAATTGCGTGTGTTAGTTGTTC[C/T]GTCCTGTCTGTTTCTTTGCCACCGCATAGCCTGCC Y 2 1 2 1 101000 f 74 goat snp49259-scaffold703-1888606 10 91216636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417458 Affx-122947191 AX-123287806 10 9824907 AAGTTGTGTGACCACCCTGAGCTTTAGTCTCCTCA[C/T]GTGCACACTTTATGGTGCTGGTGGAGAATTAATTG Y 2 1 2 1 101000 f 74 goat snp49260-scaffold703-1939707 10 91165171 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376428 Affx-122978071 AX-123246787 10 9857039 ACAGAAAGGGAGGATGGAATGAAAATATAGACATA[A/G]TGCAAATAATTTACAGTGTTCTTTATTTTACACAG R 2 1 2 1 101000 f 74 goat snp49261-scaffold703-1971839 10 91133339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796663 Affx-122936448 AX-385283609 10 9959681 CTTTATTTATATGACTCCCACAGAAATCATCTTTG[A/G]CTAATATATTACCAGAACAACACGTTACTGCATTA R 2 1 2 1 201000 f 74 goat snp49263-scaffold703-2074481 10 91040792 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415612 Affx-122948601 AX-123285961 10 10001696 GCACTCGTACCTCCTAGAATTGTCATCAAGCTGCC[A/G]GCAGAGTCTGTGACCACCGCAGGCTGGCCCTGGAG R 2 1 2 1 101000 f 74 goat snp49264-scaffold703-2116496 10 90998349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276358 Affx-1111835377 AX-519549889 10 10047137 TTATGTCACCCAAGCTTCTACTTCTTTCTTGTGGT[A/G]CAGATCGCTGAGCCCAGAGGCAGGAAAGAACTGCT R 2 1 2 1 102000 f 74 goat Random2.2K-1047 10 10047137 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320783665 Affx-122938572 AX-385270724 10 10055084 AGGTAGTTTTGTGTTACACAGAGCCTGAATACCTC[A/G]TTTTAAAACCATCTGAAAAGGTGACTGTGCTGAGT R 2 1 2 1 101000 f 74 goat snp49265-scaffold703-2169884 10 90944858 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378177 Affx-122976954 AX-123248536 10 10100978 ACTCTGTGAAGGTTGTCCTCATACCTGAAGATAGG[A/C]GGTGAAAGCAGAATCTCACTAGCAGCCCCCAATGG M 2 1 2 1 101000 f 74 goat snp49266-scaffold703-2215778 10 90898736 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442060 Affx-122928386 AX-123312397 10 10130683 CTAGAGATGTGGTTGATGTGAAGACCCAGACAGAG[C/T]AAACAGCTCCTATCCCAACAGTCCTCTGATTGGCT Y 2 1 2 1 101000 f 74 goat snp49267-scaffold703-2245483 10 90869025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419535 Affx-122945430 AX-123289883 10 10161621 GGCAGAGACACACAAAGGAGAGGGGTGGGGCACGG[A/C]CAAGGTGCGCTCAAAATGGATTTGCGCAGGAAAAA M 2 1 2 1 101000 r 74 goat snp49268-scaffold703-2276421 10 90838072 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377434 Affx-122977540 AX-123247793 10 10204657 TTGTCTTGATCATCTTACAGAGAATGACTTATAGT[C/T]ACCAAGATGAAAGTTAAAACAGTCGTAAAACTGAG Y 2 1 2 1 101000 f 74 goat snp49269-scaffold703-2319457 10 90794712 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777371 Affx-122926273 AX-385264493 10 10276674 ACTAGTTTTCCCTTTGGCACAATAGTCTTTACTTC[A/G]CTCAAGACCTCATACTATTTCTTTGTGAATTTCCC R 2 1 2 1 101000 r 74 goat snp49271-scaffold703-2391474 10 90722528 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389198 Affx-122969072 AX-123259556 10 10317862 TTAGAAATCTTCAAATCACAAGTATTTTAATAGTA[C/T]GTCCTCCTTTTGGATAAAACTTCGAGTTAGGAAAC Y 2 1 2 1 201000 f 74 goat snp49272-scaffold703-2432662 10 90682212 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463069233 Affx-1109797880 AX-514556778 10 10351609 GATGTATCTCTGTGCTCTTTTATCCACCCTCCCCC[A/G]GCCCAATCATCTTGAAATAAAAGCCAGCTGGGATT R 2 1 2 1 101000 r 74 goat 10_10351609_AF-PAKI 10 10351609 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320792099 Affx-122967889 AX-385279086 10 10357880 GAAGTGAGATAAGTGTAGGAAACTTGAGGAAAGGT[A/G]TAAACATTTTGGAATGCTGATGGTGAAAAATGGAA R 2 1 2 1 101000 f 74 goat snp49273-scaffold703-2472680 10 90642113 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376299 Affx-122978370 AX-123246658 10 10400541 TCTGGGACTGTAGAGTGCCAGCCGCTGGACCACCA[A/G]GAAGTCCCTGTTTGCTCATTTTCAACCCTCCCAGC R 2 1 2 1 103000 r 74 goat snp49274-scaffold703-2515341 10 90599564 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417820 Affx-122946804 AX-123288168 10 10466162 GTTAGGTAGAAAATTATTTCTAGCCTACATGCATT[A/G]CTTAGTTCCCTACAACTGCCTATTCCTTAAAATTT R 2 1 2 1 101000 r 74 goat snp49275-scaffold703-2580962 10 90533131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412206 Affx-122950935 AX-123282556 10 10494902 AGCAAAATTCAGATTTTGGAGGAGGGGGCTGCTCT[A/G]TTGTTCTTTCTTGTGGGTGCTAGACAGCATTCAAA R 2 1 2 1 101000 r 74 goat snp49276-scaffold703-2609702 10 90504638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425059 Affx-122941263 AX-123295405 10 10533993 CCACTGCAGTACCACCTCTCCGTAGGAAAGCCTGG[G/T]AAGGCAGATGCATAGATAAAACGAGGGTGGGAGAA K 2 1 2 1 101000 r 74 goat snp49277-scaffold703-2648793 10 90465258 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420372 Affx-122944946 AX-123290719 10 10627738 CTCACAGTTGCCATCCTGGAATGACGGCCCCCTCC[A/G]CAGACACACCAGGAGCATAAAGCCCATGAATAGAA R 2 1 2 1 101000 r 74 goat snp49279-scaffold703-2742538 10 90370426 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411989 Affx-122951767 AX-123282339 10 10659256 CTCCTCGGGGTCATTTTGCTAAATCCAGCAGTCAC[A/G]TGGTCCCTTTCCTACACAGGCTATCACTCTAGTCA R 2 1 2 1 101000 r 74 goat snp49280-scaffold703-2774056 10 90338791 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781586 Affx-122969999 AX-385268670 10 10707357 ATTTTGCTTGTCTTGTTAGTGGTTTGCACCACTAG[C/T]AGCTATTAAAACCCCAAGCATAGACAAACTGCTTG Y 2 1 2 1 201000 f 74 goat snp49281-scaffold703-2822157 10 90290725 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412272 Affx-122950888 AX-123282621 10 10802064 GAAAGACTCTTTAACCCCCACCCCTCACCTCCCGG[C/T]AACCAAAGAAAGACTAATTTAAACAATAGTGAGTG Y 2 1 2 1 201000 r 74 goat snp49283-scaffold703-2916864 10 90195477 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440800 Affx-122929832 AX-123311137 10 10838724 ACGATGTCATTCCCCAAACTCTGCTTTGGTAAAAA[C/T]ACACTGAAGGGAAATACTAGCCTGACCACTATCCC Y 2 1 2 1 101000 r 74 goat snp49284-scaffold703-2953524 10 90159044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391736 Affx-122967488 AX-123262093 10 10871396 ATCTGTACAATGAAATAATACTGCCTTCCACCTCA[C/T]GAAGCTGCTCTGAGAATTAAATCAGTGAATCCTTG Y 2 1 2 1 101000 f 74 goat snp49285-scaffold703-2986196 10 90126347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395002 Affx-122964235 AX-123265357 10 10899938 GGGGGCATGTAACACCAAGAAAATAGAAGAAAAAT[A/G]CTCAAGACATAAAAGTAGGTTCAGAATATTTTATA R 2 1 2 1 201000 r 74 goat snp49286-scaffold703-3014738 10 90098353 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436012 Affx-122932745 AX-123306351 10 10930494 TGTTTAGAATACACACAGACATGTGAGTGTGACCA[C/T]AGGGCTACATGGAACCCCCAGAGCCCATTCTCAGG Y 2 1 2 1 101000 f 74 goat snp49287-scaffold703-3045294 10 90066981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388424 Affx-122969276 AX-123258782 10 10959829 TAGGCACAGTCATTTCTGACCCATCCTTCAAAGTA[C/T]GAAATCCAAAATGGGGGCTCATGGCTTGAGTCACT Y 2 1 2 1 101000 f 74 goat snp49288-scaffold703-3074629 10 90037448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383734 Affx-122972455 AX-123254092 10 11011217 CTCATTCTTAATTGCATGGCTGAAGGAGGCTTCAC[A/C]GTGTCCTCTATAGTGGCCGTTACCAGTTTACATCC M 2 1 2 1 201000 r 74 goat snp49289-scaffold703-3126017 10 89985725 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384865 Affx-122971945 AX-123255223 10 11049018 CTCCATTCCTGTGTGCAAAATCAAAGCCTCTGAAG[C/T]GGTACACAGAAGTGCTCCCTGCACACTGTTAGAGC Y 2 1 2 1 101000 f 74 goat snp49290-scaffold703-3163818 10 89947235 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793979 Affx-122929673 AX-385280948 10 11080607 TTCCAATACACAACTGCTGTCAGTGGTTTCCTATC[A/G]CTATCAAGATCAAGTCCTAAAAAAGAAACAAAGAA R 2 1 2 1 101000 f 74 goat snp49291-scaffold703-3195407 10 89915645 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435267 Affx-122934055 AX-123305607 10 11111208 AACTTTTAAGTCGCTTGTGGATATAATATTTCATG[C/T]GGCTTACTTTTTTCTTTTACATTCTCAACATAGCA Y 2 1 2 1 303000 f 74 goat snp49292-scaffold703-3226008 10 89885434 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762771 Affx-986697301 AX-385250823 10 11133766 ATACATATCAATCATTACTGTAAATCACTGGATTA[A/G]ATGCTCCTATTAAAGATATGGAAAAGGTCAGCTTT R 2 1 2 1 600010 f 74 goat 10_11133766 10 11133766 Ancestral_priority_1043 ancestry 0.74 recommended IMAGE 10K 10K ancestral 320769231 Affx-122941901 AX-385256404 10 11149456 CTGGGAGAAAAAAACAGGCAAGTGAAAAAGAACAA[C/T]AATAGTCAAATACGCATTAGAAGAAAACTTTCTGT Y 2 1 2 1 101000 f 74 goat snp49293-scaffold703-3264256 10 89847259 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792553 Affx-122946713 AX-385279534 10 11229209 GTTGCCTACTACCCAGGATAGAGTCTTTTTGGTGC[A/G]TCTATGCTTTCTTTTGACAGAGTTGTTCCAGTCTG R 2 1 2 1 101000 f 74 goat snp49294-scaffold703-3344009 10 89767145 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433764 Affx-122934490 AX-123304105 10 11281156 CTTTGGTGATTTATTGTGGGAGATGTCTTTAAGGA[A/G]ACAAATGCAAGAATTTAGGTTCCCTGGTCAGGGAT R 2 1 2 1 201000 f 74 goat snp49295-scaffold703-3395956 10 89714960 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794678 Affx-122950748 AX-311040359 10 11323475 GATGCTTTATCACTGTCAGATAATGACAACTACAC[A/G]TCTTAGATATCAGTGAGACTAACCACTTTACAAAT R 2 1 2 1 101000 f 74 goat snp49296-scaffold703-3438275 10 89672920 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448077 Affx-122924335 AX-123318413 10 11360665 TAGAGCAGTTTTGGGATTACAGAAAATTGAACAGA[A/C]AATACAGAGAATTCTTCATTTCTTCTCTGTACTCA M 2 1 2 1 102000 r 74 goat snp49297-scaffold703-3475465 10 89635141 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435523 Affx-122933409 AX-123305863 10 11418797 ACTCTCATAAATGCCTATCTCCTTGCTCAGCAGTT[G/T]GGTGAGCAGTCCAAAAAGTTAAGAACCATTCAGTG K 2 1 2 1 201000 r 74 goat snp49298-scaffold703-3533597 10 89576510 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430356 Affx-122937796 AX-123300697 10 11448808 GATTCAGGGCAGCTAAACAAGCTAAGGGCCAGACA[A/G]CTTTCTAGGGGAGATGATACTTGAGCTGAATTTTG R 2 1 2 1 201000 f 74 goat snp49299-scaffold703-3563608 10 89544538 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420223 Affx-122945533 AX-123290571 10 11489208 TCAATGCATTTAAAAAATTGTGAGATTAATTCTAA[C/T]GCCAGAAGATAGAACATTGTGAATAAAACATTTGC Y 2 1 2 1 201000 f 74 goat snp49300-scaffold703-3604008 10 89504170 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446883 Affx-122925231 AX-123317219 10 11518691 GATGGAACAATAGCAAACAATTGGTCTTGTAAAAG[C/T]ATTTGCATATTTCTGCTTCTTCTCTTGGAGCCTTA Y 2 1 2 1 101000 f 74 goat snp49301-scaffold703-3633491 10 89474281 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791773 Affx-122968769 AX-385278764 10 11551873 CAATCACCTCGACCAAGAGTGTAGACATAACACAT[C/T]ACTTCTCTTTAGGGAAATGCCCTATAGTTCTTGCT Y 2 1 2 1 201000 r 74 goat snp49302-scaffold703-3666673 10 89441548 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386777 Affx-122970111 AX-123257135 10 11592268 CAATAGGCAAATACATTGCAGCAAATTCTAAACAT[C/T]GCTTCCAACAAAGGGAAGAATTCCATTGTTAATTT Y 2 1 2 1 101000 f 74 goat snp49303-scaffold703-3707068 10 89401963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795327 Affx-122966638 AX-385282285 10 11675822 ATTGCCACAAGTCTTGAATTTTATATCAAGCTCTG[C/T]AAATATTGGCTATCAACTTCTATTACAAATATACT Y 2 1 2 1 101000 f 74 goat snp49305-scaffold703-3790622 10 89317696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398393 Affx-122961643 AX-123268748 10 11723682 CTTTTAAGCTGTGTGGCTTGGCCAAGTCTTTTCAA[C/T]ATTTTGAGGCTCTGTTTTCCAATTTTAAAATAAGG Y 2 1 2 1 101000 f 74 goat snp49306-scaffold703-3838482 10 89269253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420527 Affx-122945307 AX-123290874 10 11758499 CATAGTTTCTAGGGATGGGAAGGTTTGGGGCAGAC[A/G]GGAGAAGGATGGGGGAGTAACACCGGGGAAGACAC R 2 1 2 1 103000 f 74 goat snp49307-scaffold703-3873299 10 89234334 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411430 Affx-122951830 AX-123281780 10 11808699 TTACCGCAGAACCTTCCCAACAATCTGAAACATGT[A/C]TCTAGTGATGTTCAATTCTCATGCTTAAAATCCTT M 2 1 2 1 101000 r 74 goat snp49308-scaffold703-3923499 10 89183762 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381875 Affx-122974175 AX-123252233 10 11838319 AAATGTTTTCAAGATAAAATGTTTATGACACTGAG[C/T]GAGGACTTATACCTTCTTGGGGGGAGGAGGCGGTT Y 2 1 2 1 101000 f 74 goat snp49309-scaffold703-3953119 10 89153478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378588 Affx-122976585 AX-123248947 10 11918312 CTCAGCACCTCAGCTACCCTGAGCTCCTACTCAGC[A/G]CATTTCTCAATTCAGAATCCCTGGCTAGGCCCTAG R 2 1 2 1 101000 r 74 goat snp49310-scaffold703-4033112 10 89073567 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428212 Affx-122939447 AX-123298555 10 11982120 TAGTAAGAGTTTATTATGCCTATAAAAGCAGTCCA[C/T]GAACCGGAAGGTTCGAAATTCAAAGACTGATGTGA Y 2 1 2 1 201000 f 74 goat snp49311-scaffold703-4096920 10 89011988 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442776 Affx-122927736 AX-123313113 10 12014693 TTTATTGGCCAGGCTCATTCCGGGGGATGGATGTG[A/G]CTCTCTGAGGTGCAGTTAAAGCACCTGCTGAACTC R 2 1 2 1 202000 r 74 goat snp49312-scaffold703-4129493 10 88979742 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397972 Affx-122961814 AX-123268327 10 12048010 AGACCTTAGAGGAGTGAGGGGGAGGAGAGAAGGAA[A/G]AGCAAGAGAAAGCAGATTTTCAAAAGCAGGCACTT R 2 1 2 1 101000 r 74 goat snp49313-scaffold703-4162810 10 88946446 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432127 Affx-122936443 AX-123302468 10 12120753 ATTTCTAAAAGCAAATACTTTTAGATGCCACATTT[G/T]CTTCAAGGAGCTTCTTAATCATTGCAAACATATTT K 2 1 2 1 101000 r 74 goat snp49314-scaffold703-4235553 10 88873723 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445403 Affx-122925386 AX-123315740 10 12151789 TCTACAGTTCAATGACACTACTACTCTATATTTTA[C/T]GGTAAATGTATATTCTGCATTTCCTTGCATAGACC Y 2 1 2 1 101000 f 74 goat snp49315-scaffold703-4266589 10 88842562 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423409 Affx-122942625 AX-123293755 10 12220446 CACTGCAATTCCTGCTTCGTGGTGGTGGTCTGGAA[C/T]ATCCTGCAATATCTCTGAGGCATGCCTGTATACGT Y 2 1 2 1 201000 f 74 goat snp49317-scaffold703-4335246 10 88774228 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411235 Affx-122952342 AX-123281585 10 12278805 GCATCCTCTGAAGCCTTGAGCAGAGGCCCTGTTCT[C/T]TCTCTCCATGGCCCATCTCCCCAGCTGTGAGTTTT Y 2 1 2 1 101000 f 74 goat snp49318-scaffold703-4393605 10 88715440 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276361 Affx-1111835378 AX-185411097 10 12311966 TACGGGGAGGGAGGTGGGAGGGGGGTTCAGGATGG[A/G]GAACACGTGTACACCCAAAAAAATAATAAATGGCA R 2 1 2 1 303000 f 74 goat Random2.2K-1050 10 12311966 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794663 Affx-122954477 AX-385281624 10 12320281 TCAAAGCCACAAATATCAACTCTACAATTGAAATA[C/T]AGCTGATAATCCTTTTGTAAACCAAGTTACACTAA Y 2 1 2 1 101000 r 74 goat snp49319-scaffold703-4435081 10 88674300 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772769 Affx-122941725 AX-385259914 10 12350607 TTTTTTCTTATAAAAAGGTTCAGCAAAAAATAAAG[C/T]AGGAAGGGCTGTTGTTCTTAAAATACTTTAAATGT Y 2 1 2 1 101000 r 74 goat snp49320-scaffold703-4465407 10 88643765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379712 Affx-122975891 AX-123250070 10 12384622 TGTGACGGCCAGCTCCTGAGTAATATGTGAGACCT[A/G]CTCCTTGAAGCCTTCCCTAATCCTGCTCCCCAGGA R 2 1 2 1 101000 f 74 goat snp49321-scaffold703-4499422 10 88614045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379807 Affx-122976234 AX-123250165 10 12437425 GTTCTGAAGATGTTACTTCCTAAGTTACAGGAAGA[A/G]CTGGAGAAACATAGTCAGCAAAGCAATGTGTGGGT R 2 1 2 1 303000 f 74 goat snp49322-scaffold703-4552225 10 88561177 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781219 Affx-122940535 AX-385268304 10 12467303 GAAAGACAAAAGGGAGAAGTAGCGTGTTTAGACCA[C/T]AATTTAGGTTCAATACCTATGCAAGGAGATTGGGA Y 2 1 2 1 101000 f 74 goat snp49323-scaffold703-4582103 10 88530920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784656 Affx-122964322 AX-385271704 10 12497482 GTCACAAGCATGTGTTTTAAAAGATCCTAAAACAG[A/G]TGCACCCAGTGTCCTATAGTGGGTGATAACTTCTA R 2 1 2 1 101000 r 74 goat snp49324-scaffold703-4612282 10 88500829 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446620 Affx-122924797 AX-123316956 10 12530686 TTTTCAGGGCTCTCTACACATCTATATTGATGGGT[A/G]CAGCTAGACTAAGAATCCATGTATTGTGACCTCTA R 2 1 2 1 201000 f 74 goat snp49325-scaffold703-4645486 10 88468639 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430362 Affx-122937791 AX-123300703 10 12577458 GCCACCGCAACAAATGAAGCGGTGAACCTGGGGGC[A/G]TTTGAGGAAAGAGGTGGGCCACCCCTGCATCCTAG R 2 1 2 1 102000 r 74 goat snp49326-scaffold703-4692258 10 88422066 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416348 Affx-122947890 AX-123286697 10 12636766 CTTGGCTTTATTGTCTTTCTTCCTTGTCAGCACTA[A/G]CAGGCTTCTGCCCAGCGTACGCTTTCAGTAAACGC R 2 1 2 1 101000 f 74 goat snp49327-scaffold703-4751566 10 88362583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387862 Affx-122969640 AX-123258220 10 12721305 AAATGAACACATTGTTCAGCCTTTTGAGTAGGCAC[A/G]CAATAAATGTTTGTTAAACGGATGACCCTATTTCT R 2 1 2 1 101000 f 74 goat snp49329-scaffold703-4836105 10 88277540 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433651 Affx-122934573 AX-123303992 10 12773637 GCTGGGTGCACCCAGCTGATGAGTAAACCAGGGCT[A/G]AAGTTTGAGCTCAAGTGAGCATTGTGTACCAATGC R 2 1 2 1 101000 r 74 goat snp49330-scaffold703-4888437 10 88225732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402554 Affx-122958459 AX-123272907 10 12813575 GATCTTGCTCTGACTGACCACTTAAATACAGTAGC[A/G]GGCCAGGACACCACAGAGGCGCCCAGGTCCCAGCC R 2 1 2 1 101000 f 74 goat snp49331-scaffold703-4928375 10 88185928 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775871 Affx-122969838 AX-385263002 10 12867868 TTAAACAAGTTCAACAAAGGGGCTAAACAAAACAA[G/T]CCCATCCATTTCCTGCAGGACCCATCAGAACCTTT K 2 1 2 1 201000 r 74 goat snp49332-scaffold703-4982668 10 88132129 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436885 Affx-122933229 AX-123307223 10 12909306 AAGCATTGACAAGTGTCCGTGGACATCTAAGAAAT[A/G]TACAAATACTATATACACACGTCAGTTCTTTGGAC R 2 1 2 1 101000 f 74 goat snp49333-scaffold703-5024106 10 88091201 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272621 Affx-1111832878 AX-519546332 10 12962405 TAGCTTAACCCTATGCGCTCTCAGAATCTAATTCA[A/G]ATATTGCCACTTTGGAACTCTCCACACCAATTCCT R 2 1 2 1 101000 r 74 goat 10_12962405_AF-PAKI 10 12962405 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38380994 Affx-122974672 AX-123251352 10 12965301 GATTTTCACTCAAAGCAAACAAAATGCACTGCACC[A/G]TCATCTCAAATTTGGAAGACAGCAAGTTAATAGAT R 2 1 2 1 101000 r 74 goat snp49334-scaffold703-5080101 10 88035412 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772824 Affx-122957670 AX-385259969 10 13007307 GAACAGACCTGTGATGTGAGCTCAACCACATTCCT[C/T]AGACAAACTCCTTTCTGAAGTATCTGTTTTGCATG Y 2 1 2 1 101000 r 74 goat snp49335-scaffold703-5122107 10 87992979 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382652 Affx-122973675 AX-123253010 10 13039053 CCGTAGCTTGTAGTTTTTGCCATGTCTCCTCGCTC[C/T]GTGGCTCCACTCTCTGAAAGCACAAACCAGAAGCT Y 2 1 2 1 101000 f 74 goat snp49336-scaffold703-5153853 10 87961096 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434283 Affx-122934772 AX-123304624 10 13073829 TAGCAGAGTAGGTATTTTGTTTTGTTGTTACTGTC[A/G]TCATTAGCCCCATTTTACAGCTGAGGAAACAGGCT R 2 1 2 1 101000 f 74 goat snp49337-scaffold703-5188629 10 87926611 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786290 Affx-122954027 AX-385273325 10 13102484 AGTTACTTTGGGGCCAGGACCCGTTTTTTGGGTTT[A/G]TCGTTTCTTGAAGTAGATAGAAACAGGATATAACA R 2 1 2 1 101000 f 74 goat snp49338-scaffold703-5217284 10 87898064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788077 Affx-122962912 AX-385275097 10 13145193 ATTTACAGCAGAAACGTACACAATATCACAACTTT[A/G]TAAAGCGCCTACACCCCAATAAAGGGAGAGAGAAA R 2 1 2 1 101000 r 74 goat snp49339-scaffold703-5259993 10 87855363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396968 Affx-122963167 AX-123267323 10 13230411 CTCCTGATGAGTTTCTCTCTCCTGCCTTCTCTCAG[C/T]CTTGGATCCCTACTCAACATTTCTCATCCCAAGAC Y 2 1 2 1 201000 r 74 goat snp49341-scaffold703-5345211 10 87769825 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395840 Affx-122964022 AX-123266195 10 13283555 TGGACAGACCTGTCCCTTAACAGGGACAACACCCC[A/G]TTGCTGGTGGCAGAGGCACAGGCCCAGGGAAAACT R 2 1 2 1 201000 r 74 goat snp49342-scaffold703-5398355 10 87717887 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451094 Affx-122921402 AX-123321428 10 13343844 GGGATGAAGGTCTTTCGTTTGTGACTCACCAGCTT[G/T]TGGGGAAGCACTTCTAGGGATTCACAGCCCACGAG K 2 1 2 1 101000 f 74 goat snp49343-scaffold703-5458644 10 87657966 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443768 Affx-122927109 AX-123314105 10 13411662 CGAGAAAGACCCAGGGGGGAGGCAGCTTTGGGTTC[A/G]CCCTGTGCACCCGCCTATCTCAGAACCCAGAGGAA R 2 1 2 1 101000 r 74 goat snp49344-scaffold703-5526462 10 87585899 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384082 Affx-122972855 AX-123254440 10 13451437 TGCTTGGCTAGGATGATGAAGACCTAGGTGAGTGA[C/T]GATAGGTTCCAAGAGGCCAAGTTATCTCCTGGGAG Y 2 1 2 1 101000 f 74 goat snp49345-scaffold703-5566237 10 87546119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794325 Affx-122930613 AX-385281289 10 13527114 AGAATAAGAAATATTCAAACAACTTCCTAAGCTAC[A/G]CTAACCAAAACAACTCTACTCTGGAACTTAGGGAC R 2 1 2 1 101000 r 74 goat snp49347-scaffold703-5641914 10 87470711 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392729 Affx-122966024 AX-123263086 10 13577472 TTTGCTAATTGTACCCCTCGGCCTCTGTCACAGGG[C/T]GGGGCAGAGCTGGGTCCGCAGTAGGACCTCAGTAA Y 2 1 2 1 303000 f 74 goat snp49348-scaffold703-5692272 10 87420840 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418017 Affx-122946653 AX-123288365 10 13630980 GCTGCTATGAATATGTTACCTCCGAGTCTGCACCT[A/G]AAGACCAGTGGCTTGTGTCCAGTATTTTATGCCAC R 2 1 2 1 101000 r 74 goat snp49349-scaffold703-5745780 10 87368191 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381017 Affx-122974657 AX-123251375 10 13675729 GGGATATCCTGTCCTAGGACACCGATCCATCCCTC[A/G]CCATGCAAGGGGAAATCTTACCCACAGAGGACCAG R 2 1 2 1 201000 r 74 goat snp49350-scaffold703-5790529 10 87323545 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401659 Affx-122959576 AX-123272012 10 13705703 TTTGGAGTTCAGAGCTTGACTCTGCTCTCCTGCTC[A/G]CTGTGTGACCTTGTGGAAGAATCTTAACCTTTCTG R 2 1 2 1 101000 r 74 goat snp49351-scaffold703-5820503 10 87293547 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385221 Affx-122971702 AX-123255579 10 13783917 CCAGCCTCCCCTTTCCTCCTTCTTACTGAGGTATC[A/C]TTTACATATACATAACATTCAACTTCTTCAAAGTA M 2 1 2 1 201000 r 74 goat snp49353-scaffold703-5898717 10 87215438 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440130 Affx-122929692 AX-123310467 10 13820509 ATTCAATGAAGAACATTTATTCTGTAGTCCCGGTA[C/T]GCATGCATTGAAAATAAGCTTGGTCCAATGAAAAA Y 2 1 2 1 101000 f 74 goat snp49354-scaffold703-5935309 10 87179021 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392346 Affx-122966259 AX-123262703 10 13860430 TGTTACGATTGATCTGTAAGTCTGTGTATTACCAG[A/C]TTGATCTAGTCTTATAAAGTTCCCCACAACCTTTC M 2 1 2 1 101000 r 74 goat snp49355-scaffold703-5975230 10 87139204 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435728 Affx-122933295 AX-123306067 10 13897413 CACTTCTGCCACAGTTTTACTGGCGACATTTAGTC[A/G]CAGAGGACACTGGGAAAATGTGGTCTTATAACTGG R 2 1 2 1 201000 f 74 goat snp49356-scaffold703-6012213 10 87102372 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770235 Affx-122951135 AX-385257401 10 13996552 CATCCTATGTATTCTACTACAACATGCTTTTACTT[A/G]TTCAATATTTCATCCATGAAATTCTGCATGTATAC R 2 1 2 1 101000 r 74 goat snp49358-scaffold703-6111352 10 87003275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385645 Affx-122971168 AX-123256003 10 14055859 CTCATTAGTTCACTGGCACAGTCGTGTCCTGAGAG[C/T]AAATGAAACCCTCTGTCTCCTTATGGCTCTCATCT Y 2 1 2 1 101000 r 74 goat snp49359-scaffold703-6170659 10 86945405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768533 Affx-122968217 AX-385255713 10 14087186 CTCTGTAATTCTCTGCTGTTTGCAGCATTAAATAG[A/C]GCCTTGATTTCTTGCCTGATGTGCTCACTGTGTAA M 2 1 2 1 101000 r 74 goat snp49360-scaffold703-6201986 10 86914194 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420610 Affx-122945242 AX-123290957 10 14129181 AGGTTCTCTGCCTCTGATCGAATCAGCAATTAGAT[A/G]CCCAAGAGTGACCAAAATAAATAAATAAATAAAAT R 2 1 2 1 101000 f 74 goat snp49361-scaffold703-6243981 10 86871754 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797595 Affx-122961160 AX-385284534 10 14186952 TGAGCTGTTCTACATAGGATAGTCAGAGAAGTAAC[A/G]TTGGACCTGAAGGAAGTGATGGAAAAAGTCGAGTG R 2 1 2 1 101000 r 74 goat snp49362-scaffold703-6301752 10 86814216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400639 Affx-122960367 AX-123270994 10 14217759 CTCAGCAGCAGAACCTTCGTTTAAAGGCCTTTGCC[A/G]TGGAAATGCAAATGTTATTATTAAAGTGACCCTTA R 2 1 2 1 101000 f 74 goat snp49363-scaffold703-6332559 10 86783339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446468 Affx-122925066 AX-123316804 10 14262778 GCCTCTCCCCACACTCTTCCACAAAAGATGATGCC[A/G]CATGCTGCTAAAATGTGCCATTTAAAAAGTCACAG R 2 1 2 1 101000 r 74 goat snp49364-scaffold703-6377578 10 86738995 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769888 Affx-122978664 AX-385257057 10 14316370 CTATTTGTACATCATTTTAGAGTCACATGCAGTTA[C/T]AAGAAATAATGTAAAGACATCCTGTGTATCCTTAA Y 2 1 2 1 101000 r 74 goat snp49365-scaffold703-6431170 10 86685671 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380417 Affx-122975309 AX-123250775 10 14360857 AGTCTAAAGATCAGAGAAGAGGGACTCAAAGCCTG[C/T]AGGAGCTGACGCCACTGGAAGGCTTGATCCACACC Y 2 1 2 1 101000 f 74 goat snp49366-scaffold703-6475657 10 86640780 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439691 Affx-122930575 AX-123310028 10 14405294 ACAGTCAGAATCCAGTGTTTGCTCCTACATCTCAC[A/G]CAGCCTCCTTGTTCTCGTGTGTTTGTGGGTGCACG R 2 1 2 1 201000 r 74 goat snp49367-scaffold703-6520094 10 86596145 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385556 Affx-122971226 AX-123255914 10 14467261 TATTCCTTTCTGCACTACTTTGTATTCTGGCTGCT[C/T]TTCAGAGTGTGCAGCCCATGGCCCAGTCTCTCAGA Y 2 1 2 1 101000 f 74 goat snp49368-scaffold703-6582061 10 86533448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802196 Affx-122968257 AX-385289100 10 14513669 GAAGCTTCAACAAACAATACTAAATATTCACCCTA[A/G]TTATATATGTTGCACTCTTGTTTGCCATTCTGGCT R 2 1 2 1 101000 f 74 goat snp49369-scaffold703-6628469 10 86486526 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440214 Affx-122930689 AX-123310551 10 14570479 TTAATAACCCCTCACTGATGAGGACTTGCCTGATG[G/T]TCCAGGGGTTAAGAATCCATCTGCCAGTGCAGGGG K 2 1 2 1 103000 f 74 goat snp49370-scaffold703-6685279 10 86434193 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423542 Affx-122942433 AX-123293888 10 14622770 TAATACCTTATATGGTACTTTGCAGTTCATAATGT[A/G]TCACATTATCTGATTTTATTTTTCCATCAGTTCTT R 2 1 2 1 201000 f 74 goat snp49371-scaffold703-6737570 10 86382822 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443512 Affx-122927790 AX-123313849 10 14653456 CAGACCTTGAGATTATGCAGAAGCTGCTCCAGTAG[C/T]AGCGATAGAGCCTCATCTTTCACTATATCTGATTA Y 2 1 2 1 101000 f 74 goat snp49372-scaffold703-6768256 10 86351808 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394609 Affx-122964418 AX-123264964 10 14682818 AAAAAACAAACTACTGTTTTCCTAATTTCCCTCCC[A/G]CTATACCCCCATTTTCTTTTCCTTAACTGCAAAAT R 2 1 2 1 102000 r 74 goat snp49373-scaffold703-6797618 10 86322441 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791665 Affx-122963261 AX-385278656 10 14745470 ACCTTTGTGTATAAAATTGTCATATTTTAAACCTT[A/G]CAGTGGTAACAAATTGACCTACTTTAATCCAGTTA R 2 1 2 1 101000 r 74 goat snp49374-scaffold703-6860270 10 86260024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413590 Affx-122950574 AX-123283939 10 14775697 AGCCAGGCGGGATGAACATATTAGGGTTCTGAATA[C/T]AATCATGATGGAAGTGGGGGGTGGGCTCTGGGGCC Y 2 1 2 1 101000 f 74 goat snp49375-scaffold703-6890497 10 86229637 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448125 Affx-122924300 AX-123318461 10 14827815 ATAATTGAAACTTTTTCTAGGCTCTGTCATATCAC[C/T]GTAGGGAAAATGGAAATTAATAGATTACATTGGAA Y 2 1 2 1 101000 f 74 goat snp49376-scaffold703-6942615 10 86179219 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388886 Affx-122968861 AX-123259244 10 14864580 GATGGACCAGGGAGAGGGTAGTCTGGGAAGAAGGA[C/T]GAGTCTGTGCAAGGGCCTGAGGCCTGAGGCAGCAT Y 2 1 2 1 201000 r 74 goat snp49377-scaffold703-6979380 10 86142185 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385861 Affx-122971614 AX-123256219 10 14930241 GTGTCCAGTAGCTGGATGTAACATCCTCAAGTTCC[A/C]ACAGGTTGAAAAGTGGATGAGCCCAGGTTTGTGTA M 2 1 2 1 101000 f 74 goat snp49379-scaffold703-7045041 10 86076498 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784845 Affx-122932573 AX-385271892 10 14986494 TTTGCAGTAAAGATATCAAAGGGAATAAGTATGGC[A/G]CCAGCACAAACAGACGTGCAGAATGGATAAGGAAA R 2 1 2 1 101000 r 74 goat snp49380-scaffold703-7101294 10 86019243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389441 Affx-122968352 AX-123259799 10 15019293 CGATGGCAGCTACACAGACCTGCATTTTCATGATT[A/G]CTGTGAAGGAGACTTGGAATTCACCAGCCTTGACC R 2 1 2 1 101000 f 74 goat snp3656-scaffold1118-26017 10 85984942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390044 Affx-122968428 AX-123260401 10 15064272 CATAGAATACTAGGATTTCTGCTGATGTCCTGCTG[C/T]TTCCAGAATTTCTGAGATGAATGTCCTTCCTTGTC Y 2 1 2 1 101000 r 74 goat snp3657-scaffold1118-70996 10 85939418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382001 Affx-122974076 AX-123252359 10 15077769 AGAAATCTCTTTGAAGAGTTGTAGGACTACCAAAG[C/T]AGCCATTATTTAAGGGGCCAGGATTTTGCAGGAAA Y 2 1 2 1 201000 f 74 goat snp47213-scaffold661-467290 10 85924553 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384324 Affx-122972266 AX-123254682 10 15134466 CCTGCCTACCACCCCCAGCTTGTAAGTGTGATCCC[A/G]CTTCCCAGACTCCCTTTAGGGTTCTTCTTCATATC R 2 1 2 1 101000 r 74 goat snp47212-scaffold661-410593 10 85867725 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431895 Affx-122936009 AX-123302236 10 15172654 CTCTCATGAACGATGGTGCTGTGGGTCTCCTGGTG[A/C]GTGTCAGCATCCACGTGCTGACGCCTGCACACAAG M 2 1 2 1 102000 r 74 goat snp47211-scaffold661-372405 10 85829460 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781643 Affx-122923157 AX-385268727 10 15204075 AAATCTGTTTCTGTAGCCATAAGAGAGAAACAACT[A/C]TGTTATTTGCCCAGTAAGTTATAATAAGAATTAAA M 2 1 2 1 101000 f 74 goat snp47210-scaffold661-340984 10 85798030 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404729 Affx-122957243 AX-123275081 10 15234184 GCCAGAACTACCCAGCTAAGGCTGGGTCTTTTGTT[A/G]TGCAGCAGTAGAAACTCATATGGACAGTTTCCATT R 2 1 2 1 101000 r 74 goat snp47209-scaffold661-310875 10 85766807 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446919 Affx-122924694 AX-123317255 10 15267060 TACCTGGGGGTAGGATCTGGGGCTCCATTCTCCCC[A/G]CCAGCAGCTTTGGGTTCTTCTTTTTCCTACTAGGA R 2 1 2 1 101000 r 74 goat snp47208-scaffold661-277999 10 85734235 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776311 Affx-122925443 AX-385263439 10 15437146 ACTAATGAAAAACACAAAGCCTTGACTTCAATTTA[C/T]GGGTTCTTGATTAATATTAATAACTAATACTTCAG Y 2 1 2 1 101000 r 74 goat snp47205-scaffold661-107913 10 85562937 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783190 Affx-122923356 AX-385270256 10 15466140 CCTACCCACTCTATTCCCTTAGCCCATTTGGAAAC[C/T]TCCAGAAATAACCCTTCTTTTAGAACCATTCGTGA Y 2 1 2 1 101000 r 74 goat snp47204-scaffold661-78919 10 85533249 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272572 Affx-1111832879 AX-519546287 10 15499690 TGTGTCCGACTCTGTGCGACCCCCATAGATGGCAG[A/C]CCTGACTTAAAAAAAAAAAATGACTTCTTGCAGCT M 2 1 2 1 303000 f 74 goat 10_15499690_AF-PAKI 10 15499690 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320794136 Affx-122957441 AX-385281102 10 15518907 TTATTAAAACAAAATTCTTAGTTATGTTCTATAAC[A/C]CAGGGGTGTGTTATAGTAGACTCACAGTGGCTCAT M 2 1 2 1 102000 r 74 goat snp47203-scaffold661-26152 10 85479531 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430538 Affx-122937197 AX-123300879 10 15574225 TGAAATGACCAGACTGTATTGCATTTCAAACTACT[A/G]TGGTGATCCATGTTTAGATGGTAAGAGCTGATGCG R 2 1 2 1 101000 f 74 goat snp16573-scaffold1748-28486 10 85372853 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407765 Affx-122954972 AX-123278116 10 15612288 CACAGGAGGTGGAGCCAAGGAGGAGCCAAGGTAAA[C/T]GTATAAAACCAGATGCAAAGGGACTTCCCAGGTGG Y 2 1 2 1 201000 f 74 goat snp16574-scaffold1748-66549 10 85334470 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773319 Affx-122963936 AX-385260461 10 15647089 GAATCACTTACCTGCAGTTGCAAGGGACTGGAAAA[C/T]GTCTAGAAGCCAGTAAAACAACTGACATTTGTGCA Y 2 1 2 1 101000 r 74 goat snp16575-scaffold1748-101350 10 85299594 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398059 Affx-122961747 AX-123268414 10 15696826 TTAAGAATAATGGCCCAGGGTGTGGGGAGTGGGGA[C/T]ATGGATTCTGCCACTCAGAATGACCTCTGGCCAGT Y 2 1 2 1 201000 r 74 goat snp16576-scaffold1748-151087 10 85250807 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435551 Affx-122933386 AX-123305891 10 15730468 TGTTGTAAAACAATTATTTGAAAGAAAAGCAAGTG[C/T]CTGATTCTCACCCCACCCCACCCCCCAACTCCCAA Y 2 1 2 1 101000 f 74 goat snp16577-scaffold1748-184729 10 85217034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802368 Affx-122969978 AX-385289272 10 15786317 CTTCATTGAGCTGAATTAATGAAAAGGTGTGGAAT[A/G]TTCATCACCTGCTTTCTGTCATTTCAAAGACTACT R 2 1 2 1 101000 r 74 goat snp16578-scaffold1748-240578 10 85160459 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398915 Affx-122961009 AX-123269270 10 15862771 GCTCACTAGAAATCTATCAAGAATTCTTGTCCCAC[A/G]TGATTGATGGGAATGTAAACTGGTACAGCCGCTAT R 2 1 2 1 101000 f 74 goat snp16580-scaffold1748-317032 10 85086507 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454000 Affx-122919437 AX-123324333 10 15951929 AGGACACGAGATTTTAGAAACCATGGGAAGGAAGC[A/G]GGAAGCAGCTTGACAGATCAAGGACCCGGGGTCAG R 2 1 2 1 101000 f 74 goat snp16582-scaffold1748-406190 10 84999210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386649 Affx-122970209 AX-123257007 10 15984696 GCCTGTTGAGGGTGTCCAGCAGTGGGAACTACTGT[A/G]GTATTACATATAGGGAAATGACATGATCAGATCTG R 2 1 2 1 101000 r 74 goat snp16583-scaffold1748-438957 10 84966119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435046 Affx-122933749 AX-123305386 10 16036755 ACAAAGTGCACATCAAAAGAAGTAAACTGTGACAT[A/C]GAAAGTATAAAAGGGGAGGAATAAACAGGGTTGGA M 2 1 2 1 201000 f 74 goat snp16584-scaffold1748-491016 10 84913797 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450518 Affx-122922498 AX-123320852 10 16078554 TCACATAGATACTTGAGCTGAGTTTTGAAGATGGA[C/T]GCTTGCAGGCTGATCCACTTTGCCAAATGGATCAG Y 2 1 2 1 202000 f 74 goat snp16585-scaffold1748-532815 10 -1 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435966 Affx-122933522 AX-123306305 10 16115060 ACCCCGAGGCAGTGGGTATGGAGTGTGCTGCAGAC[C/T]TACAGGAGGGTGTCAGAAGTGGTTCTCAAGAAGGT Y 2 1 2 1 101000 r 74 goat snp16586-scaffold1748-569321 10 84835580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801115 Affx-122949849 AX-385288029 10 16150354 TTCTGTGACTCTTCTTAGAAGTTGTGGACCAATAG[C/T]GACATGTGATTCCAGCCCTCTTATGTTGTTTGGAC Y 2 1 2 1 101000 r 74 goat snp16587-scaffold1748-604615 10 84800376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801993 Affx-122950560 AX-385288897 10 16193237 GGCCAAGACAAATGTAATTTTGGATTGTTAAGTCC[A/G]CATGACAAATGAGTGCCTATTAATTTTTATTTATC R 2 1 2 1 101000 f 74 goat snp16588-scaffold1748-647498 10 84757297 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447383 Affx-122924852 AX-123317719 10 16226391 CCTGTATTCTCTCTCTCCAGGGAGGCTGGATTTCA[C/T]GAAGGGCAAGAGCCAACTGGCTCTTTACCCTGTAA Y 2 1 2 1 102000 f 74 goat snp16589-scaffold1748-680652 10 84724199 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785804 Affx-122952151 AX-385272843 10 16279469 GAGATAGGAACCAACTGTGTGGGCTCTTGCATCCC[A/G]CGGAAAAGAGTTTAGACTTAAACTCTTAAGAAGTT R 2 1 2 1 102000 f 74 goat snp11548-scaffold1421-876266 10 84674163 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765281 Affx-986697312 AX-385252811 10 16322021 ATGATGCTGATGTGGTAGGCAAGCTTGTCCTGGTC[G/T]TTGATGTTGGGTACCAAGACGGGAGGGACCAAGAA K 2 1 2 1 600010 r 74 goat 10_16322021 10 16322021 Ancestral_priority_1043 ancestry 0.566 neutral IMAGE 10K 10K ancestral 38407734 Affx-122954995 AX-123278085 10 16369668 AAAATGGCAGAGGAGGCAAGGGAGCCAGGAAAAGA[C/T]AGGCCAAGATGCAGACTTGGTTACACCCTGAGAAG Y 2 1 2 1 201000 r 74 goat snp11546-scaffold1421-786067 10 84585827 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408622 Affx-122953493 AX-123278973 10 16403910 TAACAATCTGGAAACAAGATAAATATCCAGTAATA[C/T]GGGAGTTCTCAGGTAATGGGGGAGGACAGTTTAAG Y 2 1 2 1 201000 f 74 goat snp11545-scaffold1421-751825 10 84552399 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405659 Affx-122956572 AX-123276011 10 16453109 TGAGGCTGGAGATGGAAAACAGAGCAGAAGCAAAA[C/T]ATGCTAAGACTGGGAGTCTGGAGACCGGGGATTGG Y 2 1 2 1 101000 f 74 goat snp11544-scaffold1421-702626 10 84503461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449814 Affx-122922406 AX-123320149 10 16503809 ACACAGCAGAGAGGCACCTGGGAGCAAGCTCCTTG[A/G]AATGGGGGAAGGGTTCCACTGCCAACAAAAAATCC R 2 1 2 1 202000 f 74 goat snp11543-scaffold1421-651926 10 84452453 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407389 Affx-122955257 AX-123277740 10 16535843 ATCTGTCCAGAGCAGAGGCTCTGATTCTTAGCACC[A/G]TTTCTAGGCTCAGCGGAGGAGCCCAGCCACAGATA R 2 1 2 1 201000 f 74 goat snp11542-scaffold1421-619892 10 84420080 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409236 Affx-122953149 AX-123279587 10 16601383 ACCTTCTTCAGGGGCTGCAGGGAAGAGACTGAGGC[G/T]TCAGAAGCAGAACTGAGTTGAGGAAAGAGAGGTCT K 2 1 2 1 101000 r 74 goat snp11541-scaffold1421-554352 10 84357068 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415166 Affx-122949014 AX-123285515 10 16664334 AAGGGGTGTAGAAAGGGAGCCTTAGAATGAATGCA[C/T]CCTTTTCTCTCAGCCGGGGGCCGTGGTAGAGAAAA Y 2 1 2 1 101000 f 74 goat snp11540-scaffold1421-491401 10 84292680 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394218 Affx-122964896 AX-123264573 10 16706469 TAGACATCCACCTCTAGGATCTGTGACTTGGTGAA[C/T]ACCTGCTGTTACCAAGAGTCAGAGCTCAGAAATCT Y 2 1 2 1 101000 f 74 goat snp11539-scaffold1421-449266 10 84254230 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448173 Affx-122924258 AX-123318509 10 16741718 ATTAAATGCAGCTAATAACACAGAGCTATTTTGAG[C/T]GAGCAGAGCCCTCTACCTCCCCTCAGAGCTCTCAC Y 2 1 2 1 101000 f 74 goat snp11538-scaffold1421-414017 10 84219187 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410939 Affx-122952042 AX-123281289 10 16796511 CTCAGGATAACTGCCTGTCAAGTGGTTCTCATGTT[G/T]TGACAGTAGGCAATTATGATTTATTTCACAGGGAG K 2 1 2 1 101000 f 74 goat snp11537-scaffold1421-359224 10 84164271 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451155 Affx-122921359 AX-123321489 10 16828157 TTGGGTTCATGCCCAGGCAGGATCTTTAGTTGTTG[C/T]GGCCAAGAAGTCCTCTAGAAGCTCAAGTCTTACTT Y 2 1 2 1 101000 r 74 goat snp11536-scaffold1421-327578 10 84121630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383910 Affx-122973107 AX-123254268 10 16900092 ATTTCATGCTCTTCCCTGATTCTATGGACCCCCAA[C/T]GTTCGTATCCACTGGGTTTTTCACAGCCTCAGCCC Y 2 1 2 1 201000 r 74 goat snp11535-scaffold1421-255643 10 84050728 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440675 Affx-122929926 AX-123311012 10 16932843 AGCAACAGCACCCCACTCAGTACAGCCGTGGACCA[C/T]GAAGCTGGGCAGGAATGCTGTCTGCAGGTCATTAT Y 2 1 2 1 101000 r 74 goat snp11534-scaffold1421-222892 10 84017956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435259 Affx-122934061 AX-123305599 10 16995221 TATTTTTTGTTGAACTGCACAGGTGTCTCACTGAG[A/G]TGACTTCTCTTGTTGTGAAGCACAGGTTCTAGGTG R 2 1 2 1 201000 f 74 goat snp11533-scaffold1421-160514 10 83955585 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444163 Affx-122926782 AX-123314500 10 17044540 TAATGAAGCAAGTCAGTGTGATAGAGTGTCAAGAG[C/T]TCAGGCTTCGGAGTCAAACAAAACTGTTTTCCTTA Y 2 1 2 1 101000 f 74 goat snp11532-scaffold1421-111195 10 83906260 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386912 Affx-122970013 AX-123257270 10 17076800 CCACCCTTCTGCCCAGGGAACCTCTAAGAGCTCCA[A/G]TGTCTTTGCACATGAGGCCTGTAGGTGGCAGAGAC R 2 1 2 1 101000 r 74 goat snp11531-scaffold1421-78935 10 83873721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420875 Affx-122944629 AX-123291222 10 17122057 AACAGTGTTTTTAATTCTGAGTGTTGGTAACGGGA[C/T]ACTATTCTTTTCCCAAGAAAAGATACCAAGAGTAG Y 2 1 2 1 101000 f 74 goat snp11530-scaffold1421-33678 10 83828653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448111 Affx-122924310 AX-123318447 10 17153006 TGGAACCATGTTACTCACATACCTCGCCTTTAGGT[A/G]CGTACACTGTCCAAGGGTTCTTTATTCAGGAAATA R 2 1 2 1 101000 r 74 goat snp11529-scaffold1421-2729 10 83797427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431007 Affx-122936678 AX-123301348 10 17162030 TGAAGACGTGAGCTCTCACACGCTGTTGGTCGGAA[C/T]GAAAACCCCCACACTCTTTTAAAAGAGAGTAATTT Y 2 1 2 1 303000 f 74 goat snp39512-scaffold501-3186696 10 83787418 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382402 Affx-122973835 AX-123252760 10 17214234 GGCGAGAGATGTCCCCGTGAGTGCCAGTTTTGTGT[A/G]CTGAGGAAGCCCCTGCTGAGGATAAGTGTGGTCCT R 2 1 2 1 201000 f 74 goat snp39511-scaffold501-3134492 10 83734297 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770565 Affx-122978539 AX-385257729 10 17252238 GGTGGGGAGTTCTTTGGAGGGGAAATAGTAGAAAG[C/T]ATAGAAGCTCTGTGTTAGTGAGGGTGAACTTGCCT Y 2 1 2 1 101000 r 74 goat snp39510-scaffold501-3096488 10 83696484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423636 Affx-122942361 AX-123293982 10 17302869 TGGGGATAACACTATTCAGGGATTTGTAGACATCA[C/T]GAGCATAGCCTGGTGTGCTACAGTCCATGAGGTTG Y 2 1 2 1 101000 f 74 goat snp39509-scaffold501-3045857 10 83645743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425798 Affx-122940701 AX-123296144 10 17332120 GCCCTTGAGAGAGAGTAGATATTGGACTGAACCAG[C/T]GAGGATAAATGGCTGTTGATTTTAAAAATCTTTTT Y 2 1 2 1 101000 f 74 goat snp39508-scaffold501-3016606 10 83616326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403093 Affx-122958500 AX-123273446 10 17368398 TTTTCCACCAAGTTGTCCTCAAATTCTTCTCAACA[C/T]GGCCTTCCAGAAAGACACTACCAATCAATAAAATT Y 2 1 2 1 101000 f 74 goat snp39507-scaffold501-2980328 10 83579920 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443390 Affx-122927395 AX-123313727 10 17430096 TAGAGGTGACAGAGAGGAGGAATACAGAGCACCTC[A/G]CCCTAGACCTCTGGATCGGACTAGTCCATTCCGAA R 2 1 2 1 101000 r 74 goat snp39506-scaffold501-2918630 10 83517771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434827 Affx-122934797 AX-123305168 10 17481344 TTTGGTGACTCCGAAAAGAAATGTTGTTAATTCAT[A/G]TTAGGTATAAATCTGTAATTTAAAAAAAATCACTG R 2 1 2 1 101000 f 74 goat snp39505-scaffold501-2867382 10 83465784 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427545 Affx-122939499 AX-123297888 10 17593464 CTTTCACAAATTCATACTAATAATTAATATAATAA[C/T]ACCATAACTGGAAAAGGCAAATTTCTCAAAGTAAC Y 2 1 2 1 303000 f 74 goat snp39503-scaffold501-2755262 10 83360682 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399460 Affx-122961202 AX-123269815 10 17635742 TTCTGATTGGCACATGCCCAGGCTGATTAACCAGC[A/G]CCATGCTCTACTTGATGTTGAATAATTTAAATATC R 2 1 2 1 201000 r 74 goat snp39502-scaffold501-2712984 10 83318362 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400833 Affx-122959792 AX-123271188 10 17664432 TGAATAATAAGGAAATAAGGAAAGCATGATTTAAA[C/T]ACGACAATGCGACACAACAGAGCCCCTTGCGAACG Y 2 1 2 1 201000 f 74 goat snp39501-scaffold501-2684294 10 83289737 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784818 Affx-122973506 AX-385271865 10 17708984 TATAGAAAGAGCTTAATTCATTGAATTAATGAATA[C/T]GCCTTCATCATCTTGTGACTGGTGAAATTTCAAGA Y 2 1 2 1 303000 f 74 goat snp39500-scaffold501-2639742 10 83244446 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440633 Affx-122929954 AX-123310970 10 17746109 CTGCCGCCAGTGTCTCCCCATCGCCATCCACCCTA[C/T]GCACACTCCAGCTGACAAGAGAGATGTCCTCCCTA Y 2 1 2 1 101000 r 74 goat snp39499-scaffold501-2602617 10 83207400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429224 Affx-122937926 AX-123299566 10 17783010 TCTACATGAATGGATATTACTGTGATATTAACAAA[C/T]GTTACTGAACGAATGAATGAATGGTAAGCTCTTAA Y 2 1 2 1 101000 r 74 goat snp39498-scaffold501-2565716 10 83170443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377089 Affx-122978271 AX-123247448 10 17832140 CGATGACAAGTTATCTGCATAGTTCAGGCTGAAAA[C/T]AGCTGGGGTTGGAACCAGGATAATTCAGATATACA Y 2 1 2 1 101000 f 74 goat snp39497-scaffold501-2516586 10 83122876 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402956 Affx-122958166 AX-123273309 10 17870168 TAATCACCAAAAATAGGGCGCCATGTTGAAATTGT[A/G]CAAGGTAATGTGTGAGTATCATATGATTCCTGCTC R 2 1 2 1 101000 f 74 goat snp39496-scaffold501-2478558 10 83084566 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446602 Affx-122924809 AX-123316938 10 17920122 AATATTACTTGAGCAGTAGCAGGCACTGTTCTCAG[C/T]ACTTTATGCTCATTATTTCATTGAATCCTCACAGC Y 2 1 2 1 101000 f 74 goat snp39495-scaffold501-2428604 10 83034395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401014 Affx-122959682 AX-123271367 10 18002145 GAGAGATCCAGAAAGTGGAACAAACATTTGAGGGA[C/T]GAAGGATGAATTTGGAGCTTCTACCCCCGTGGGAC Y 2 1 2 1 101000 f 74 goat snp39493-scaffold501-2346581 10 82951577 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375914 Affx-122978476 AX-123246273 10 18031049 AGCACTTCATCAGAGCACATAAATCGCTTCCTAGG[C/T]CCCGAAAGAGAAACATATGCCCCAAATATGTCGAT Y 2 1 2 1 101000 r 74 goat snp39492-scaffold501-2317677 10 82923343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786841 Affx-122973308 AX-385273870 10 18066337 CAGTCATGACAGCAGCTTTTGCATTTGCTTGCTGG[A/G]TGAATCAGGACGAAATGGTGATGAAGAGATCTTAG R 2 1 2 1 101000 f 74 goat snp39491-scaffold501-2282389 10 82887765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427245 Affx-122939559 AX-123297588 10 18097642 GACAGAGGCTCTCTCTTTGATCTGATAAATATCGG[C/T]ACTCAGTCCCAGAAAGTAAATTAATAAACACTTGA Y 2 1 2 1 101000 f 74 goat snp39490-scaffold501-2251084 10 82856127 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380452 Affx-122975741 AX-123250810 10 18131683 ATCTTAAACTGACAGCACAAGTACCACCAATTTCA[C/T]AAGAAAAAAGTCAGCGCAATCCAGAGCCCCCAATT Y 2 1 2 1 201000 f 74 goat snp39489-scaffold501-2217043 10 82821882 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411642 Affx-122951574 AX-123281992 10 18163647 GATCCCATGGGTGGACAGAAGAGCCCTACTGAGCA[C/T]AACAGTTGGTATGAATATATGTTAATAAACAGTGT Y 2 1 2 1 201000 r 74 goat snp39488-scaffold501-2185079 10 82789982 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383750 Affx-122972443 AX-123254108 10 18208537 AATGCTGTTTTCAGAAGATGCTTGGCACACACAGA[C/T]GGCGGATTACAGATGGGAGAGACTAGAGGTTGAGA Y 2 1 2 1 101000 f 74 goat snp39487-scaffold501-2140189 10 82744663 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384985 Affx-122971890 AX-123255343 10 18238115 AGAATCGGACTGCAGTTCTGCTTAATGAGAGAAGC[A/G]TGCTCAGTTTCTCCTGGAGGGAAGAGGGGGCCTGT R 2 1 2 1 101000 f 74 goat snp39486-scaffold501-2110611 10 82715035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423806 Affx-122942809 AX-123294152 10 18269491 TCAGCTCTGATCCAGGGCTTTAGTTTTCTGGTTGC[A/G]CATTTGGAATATTCTTGGGACTTCCTGATTTCAAA R 2 1 2 1 201000 r 74 goat snp39485-scaffold501-2079235 10 82683728 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415422 Affx-122948725 AX-123285771 10 18301053 TGGACAGAGTCCCTCCAAATTGTTAAGAGAGATTG[A/C]GTCTGGGAAGCTGGGCAAGGTATGAGACTGGGAAT M 2 1 2 1 101000 f 74 goat snp39484-scaffold501-2047673 10 82652198 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790386 Affx-122954133 AX-385277389 10 18331592 ATAATAGAACTATTTTGGTGTAGTGACTCATTCCG[C/T]GGGTCGAGTTCAGAATACACATTTCCTATAAACAT Y 2 1 2 1 101000 r 74 goat snp39483-scaffold501-2017134 10 82621356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411144 Affx-122951886 AX-123281494 10 18400817 GAAGAGCTCCAAAGGAAAAAGATATTCAGGCGTGG[A/G]CTTGCCTCTGGCAAGTGTTCCTATCATTTCCTTAT R 2 1 2 1 101000 f 74 goat snp39482-scaffold501-1947909 10 82551531 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272574 Affx-1111832880 AX-519546289 10 18423382 CTTTCTCTTTTTTCAGCAAGAGCACCACTGTCAGG[A/G]GCCCTAAGAATCAGATATCTCTCAGCTGATGAGGA R 2 1 2 1 101000 f 74 goat 10_18423382_AF-PAKI 10 18423382 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449820 Affx-122922402 AX-123320155 10 18444294 TTACATTTATCTTTTTATTTTCTCCCTCATTGACA[A/G]TTGTTTTCCATAGAACCTTTTCTGTTTGTGCAAGA R 2 1 2 1 102000 r 74 goat snp39481-scaffold501-1904432 10 82507640 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443036 Affx-122928155 AX-123313373 10 18526301 TTTTTGTTGCCCCTGTTTTATTTTGGTTTATGTTT[A/G]TTTGGTCTGGAAGATCCACTGAAGTAGGAAATGGC R 2 1 2 1 103000 r 74 goat snp39479-scaffold501-1822425 10 82428539 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434804 Affx-122934812 AX-123305145 10 18590832 TTCAGCTTTCATGAGTAAAAGGCAGGTAATATGAG[A/G]ATAAATGTTTGTTTATTGGTGTTTTTGTGCTACAA R 2 1 2 1 201000 f 74 goat snp39477-scaffold501-1757894 10 82363782 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429559 Affx-122937818 AX-123299901 10 18624442 ACATGGGAAGCCCCAAATTATTTATAAATTTGAAC[A/C]ATATACCTCTCACATGAATCTTTTACCAACAGAGG M 2 1 2 1 201000 r 74 goat snp39476-scaffold501-1724284 10 82330106 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376170 Affx-122978837 AX-123246529 10 18690248 GGGCAACAGCTCCTGCTTCCCTTCCTTTGTGTACC[C/T]GATTCAGTTCCTGTAGAAAATGGATATCCAGAGAA Y 2 1 2 1 101000 r 74 goat snp39475-scaffold501-1658478 10 82265233 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401434 Affx-122958991 AX-123271787 10 18726874 CCTGGCTTCTGGTGGCCACAAAATTCTTATTTGTT[A/G]TCTGTTTTCTCCCTATTCTCCTCTCCCATTGGCCT R 2 1 2 1 101000 f 74 goat snp39474-scaffold501-1621852 10 82228503 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778194 Affx-122941552 AX-385265309 10 18773988 GAATTTTGATGCCAATGCAACAGAGTAGTATTACT[A/G]TTATTTTTAATCAATAGACATGAGGATTGTGGTTG R 2 1 2 1 201000 r 74 goat snp39473-scaffold501-1574738 10 82181488 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393587 Affx-122965383 AX-123263943 10 18831243 TGTTAGTCAATAAATATGTTAGGATGACTGGTTGA[C/T]GGTTATCCATTTGGAAAATTTTTTAATCTTTACCT Y 2 1 2 1 101000 r 74 goat snp39472-scaffold501-1517483 10 82123828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449234 Affx-122923484 AX-123319569 10 18860780 TCTCGCCCCAATTTTAAGTGGAAGACCTCAGGTGC[A/G]TCTCAACAGATGCAGGAATCAGTCTGTCAGCCATA R 2 1 2 1 102000 f 74 goat snp39471-scaffold501-1487946 10 82094419 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381558 Affx-122974825 AX-123251916 10 18905563 GAGACTTACAATGTTTTGTTTTAGACCTGAGAATA[C/T]ACAAAGAAAATTATTCAGTCAATTTTAAAGCAGTT Y 2 1 2 1 101000 f 74 goat snp39470-scaffold501-1443163 10 82049483 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376827 Affx-122977920 AX-123247186 10 18953676 ACAGCTACAATACAAAGGGACAGACACAAACATTA[C/T]CCATATAGCTGTAAGGTTTCTATGTCTCACTTGGA Y 2 1 2 1 101000 f 74 goat snp39469-scaffold501-1395050 10 82001609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431274 Affx-122937106 AX-123301615 10 19008569 CAGGTCTAAATTTGTTTTATATTGTTTATCATACT[A/G]CAAAAATAATTCACATGGATCTCTCTTATTATACT R 2 1 2 1 101000 r 74 goat snp39468-scaffold501-1340157 10 81946432 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398461 Affx-122961591 AX-123268816 10 19098341 TATCTGTTTTGTTGTGATTGTTTCAGGCAGGAGGG[C/T]AAGTCTGGCCCTTGTTGTCTCACCTTGGAAGCTGA Y 2 1 2 1 101000 r 74 goat snp39467-scaffold501-1250385 10 81856250 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274522 Affx-1111834345 AX-519548113 10 19120133 AGTTCTTCCCACCTCTTTCATTTCCACTCTCCAGC[A/G]CAGAGAGTCCTGCAGGCTCCCGAAGGCTGGCCCTG R 2 1 2 1 202000 f 74 goat GoatD01.030916 10 19120133 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38444895 Affx-122926260 AX-123315232 10 19132522 AAGTAAAGTACAGAAGAACAAATTCTTTTTATCCC[A/G]TTTGTATTTTTAAAAACATGTTTGTGCATGCACAG R 2 1 2 1 303000 f 74 goat snp39466-scaffold501-1216204 10 81822788 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398808 Affx-122961406 AX-123269163 10 19171381 CAAATCAGGTCCTGCTGATTTGAAGATTCCAGCTG[A/C]TGATGAAGATTCTAGAAAAGGGATCCAAACCCCAG M 2 1 2 1 101000 r 74 goat snp39465-scaffold501-1177345 10 81784072 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789332 Affx-122971190 AX-385276342 10 19205598 TCATCCTCTCTGGAGACTCTCCTCTAACTTTCTTA[C/T]GTTCTGCTCCAGTTGGAGCAGAATCATTGCTTTGC Y 2 1 2 1 102000 f 74 goat snp39464-scaffold501-1143128 10 81750547 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783066 Affx-122961686 AX-385270133 10 19242036 GTTCTAAAATACACATGGATGTAGTCATTAAGGGA[C/T]GAGGCACACCAGGCAAAATGCATAATTGTTTCTTG Y 2 1 2 1 101000 r 74 goat snp39463-scaffold501-1106690 10 81713892 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424987 Affx-122941906 AX-123295333 10 19293259 GGCTGACCTTGGACTTTCTCTGAAGCTATCGGGAA[A/C]GAGACCGTCTTTCTCCTGAGCTGGAAGTCAGTAGC M 2 1 2 1 101000 f 74 goat snp39462-scaffold501-1055467 10 81662462 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778165 Affx-122925707 AX-385265280 10 19327578 ATCTGAGTATCAGTGAGAATAGTCTAGGTTGTGTT[A/G]TGATAACAAATAATCTCCAAATCTTGACAGCCTGT R 2 1 2 1 101000 f 74 goat snp39461-scaffold501-1021148 10 81628205 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428343 Affx-122938991 AX-123298686 10 19358089 TCTTGGCAGACTGGAAATAACCCTAGTGTCAATCA[C/T]ATGGGATCGGATTAAACCAGGCCAACAGCACAGTA Y 2 1 2 1 101000 f 74 goat snp39460-scaffold501-990637 10 81597542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452350 Affx-122920642 AX-123322683 10 19387035 TGTTTAAGTTTGGACTATGTTTTTGTCTGCCAGGC[A/G]TCTTTCCTTTTGGACAAATTTCCCTCCTTCCAACT R 2 1 2 1 101000 r 74 goat snp39459-scaffold501-961691 10 81569302 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391583 Affx-122966611 AX-123261940 10 19441309 GAAAAATAGAGATTATACTTCAAAAATTACTTAAG[C/T]ATGCTGGCCTTGGCTAAAGCAACCAGCCCCTATGA Y 2 1 2 1 201000 f 74 goat snp39458-scaffold501-907417 10 81514691 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789200 Affx-122969148 AX-385276212 10 19515154 GAACCCCAATGTGCTCAATTCCTATCAATCAGAGT[A/G]GGAATGTGACTACTTCCCACTCTGAATCCCACAAA R 2 1 2 1 101000 r 74 goat snp39457-scaffold501-833572 10 81439523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418859 Affx-122946128 AX-123289207 10 19555343 GTCACTAAAAATTTTCAGTAGCTCACAAAATGTCT[A/G]TTTTTGAAAGCTTTTTTCAAAAAGAATCAAACAGA R 2 1 2 1 103000 f 74 goat snp39456-scaffold501-793383 10 81400373 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416001 Affx-122948392 AX-123286350 10 19609523 CTCAGGATTTCTACCCCAGTAACAATGAGCATGAA[C/T]AGTGCTCAAATACTGGTTTCCAAATATCATTTTCT Y 2 1 2 1 201000 r 74 goat snp39455-scaffold501-739203 10 81346413 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452921 Affx-122920195 AX-123323254 10 19651526 GATTTCCAGAATCCTGCCCGGCACTATCCTCCATG[A/G]CCAGCTAGCAGGGCAGCAGGAGGCCCAGCACTGCT R 2 1 2 1 101000 f 74 goat snp39454-scaffold501-697200 10 81304011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418897 Affx-122946101 AX-123289245 10 19682856 GAGGCGTCGCTCTTTCCCTTCTCTGACATCAGTGC[A/G]TGTCTCCAGGCCCCAGACCCCTGGGGGCGAACCTC R 2 1 2 1 101000 f 74 goat snp39453-scaffold501-665870 10 81272524 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393079 Affx-122965603 AX-123263436 10 19731771 CCCAGATGGGCAATGTGGGACAGCTCCTCTAGGAC[A/G]TGTCCCATGGGTGGCACCCAGCAGCACTGGGCTGG R 2 1 2 1 201000 f 74 goat snp39452-scaffold501-616955 10 81224811 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381242 Affx-122974500 AX-123251600 10 19763739 CTGGTGGCTTACTTACAAAGCCCATATACTGATCA[C/T]GGACTGCCTTAGGTAAAGAATGGGACCTTTGTTCA Y 2 1 2 1 101000 r 74 goat snp39451-scaffold501-584987 10 81193347 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441485 Affx-122928742 AX-123311822 10 19807678 GGCCTGGGATACATAGGTTTTAAATGGACATCATC[G/T]GTACCAGCTTCATTAAAATAAACAAAATATTTGTA K 2 1 2 1 101000 f 74 goat snp39450-scaffold501-541048 10 81149221 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402227 Affx-122959150 AX-123272580 10 19846324 TTTTAGAATGATTACTCAGAAAACAGTCCAGACAC[C/T]AAATAAGAGATGAGAAGTGATGAGTGGAAGGCTAC Y 2 1 2 1 102000 f 74 goat snp39449-scaffold501-502402 10 81110161 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400304 Affx-122960070 AX-123270659 10 19883224 GAGAACTCCACATTGAGTTTTTGCTAATTCTATGA[A/C]TCTTCTGTGAAACTGAGCTTTCTTGTTTACAATTA M 2 1 2 1 101000 f 74 goat snp39448-scaffold501-465502 10 81073230 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382740 Affx-122973605 AX-123253098 10 19921724 CTGGAAGCTGATGTTTCTTTGTTTTCTGTAATTAC[A/G]CACTAGCCTTTCTGCACATGTTTGGGGTGGTGGTG R 2 1 2 1 101000 r 74 goat snp39447-scaffold501-427002 10 81034826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771779 Affx-122924618 AX-385258936 10 20015214 CCATGTCTGCTTTATTTATTAGATCCTTTATCCTA[C/T]TGGATCCTTAGTTTTAGCTAAGGTTTGGCACATAA Y 2 1 2 1 101000 f 74 goat snp39445-scaffold501-333512 10 80940196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418063 Affx-122946618 AX-123288411 10 20063971 AACCTGAATGTCACAGCTGTCGACACAAAGCCTGG[C/T]ACCCAGTGGATTATGGGTTCAATAAATGTTTGTTG Y 2 1 2 1 201000 r 74 goat snp39444-scaffold501-284755 10 80891377 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440347 Affx-122929661 AX-123310684 10 20146103 GCTTTGTCTCCTTCGTGCGCATCTGGACATGCCTC[A/G]TGGTGCCTGCCCCCTCGGAGCCTCTTTAAGAAAGG R 2 1 2 1 101000 f 74 goat snp39442-scaffold501-202623 10 80809306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377823 Affx-122977304 AX-123248182 10 20197579 CATGAGCACATATACAGGGCTTACCGTGTATCTCC[A/G]CAGTGTGAATTTTATTCCAAAATGGGTTCTTTTGC R 2 1 2 1 101000 r 74 goat snp39441-scaffold501-151147 10 80759589 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410933 Affx-122952047 AX-123281283 10 20282561 GTACGTATCCTTCTGCAGCTGGCATCTGTCCCCAC[A/G]TTTGATTGTTTTTCCCAGGCTCGTGCCGTGTTAGT R 2 1 2 1 101000 r 74 goat snp39439-scaffold501-66165 10 80674539 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376604 Affx-122979055 AX-123246963 10 20313403 CTTCAGATAGGGTTTTGATGGGTTGAGGAAGTGAA[C/T]GAATATAATGGACAAAAATTCAGAGTCTGTGTTAT Y 2 1 2 1 101000 f 74 goat snp39438-scaffold501-35323 10 80643883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446293 Affx-122925654 AX-123316629 10 20345023 TCAAGTTGCCTAAGGTTGAGGAGGTCACGTGGTTG[A/G]CCCAAAGATGGGCTTTGGGCCCCAAGCAGCTGCTT R 2 1 2 1 101000 f 74 goat snp39437-scaffold501-3703 10 80611991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394346 Affx-122964659 AX-123264701 10 20377942 TGTGTCTGGAGTGTCAGGAGACCCTTCCTTCATGC[A/G]CGTGTCGCCCTCACTCTCCAGGTCCTTGCAATAGC R 2 1 2 1 101000 f 74 goat snp54017-scaffold8218-72392 10 80577908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377256 Affx-122978143 AX-123247615 10 20433382 GTCTCCTGGTGTCCTGTGACAGGCTCTTTCAATAT[A/C]ACAGGCGTCTCTGGGGTTGTATAACTCAGGGGGCA M 2 1 2 1 101000 f 74 goat snp54016-scaffold8218-16952 10 80522836 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428582 Affx-122938709 AX-123298924 10 20504368 GAGGCCATGATGTCAGCTATCTGTGGTCACAATCC[C/T]ATCCTCCTGCCACCCCTCCTCCCACTGCAAAATTA Y 2 1 2 1 101000 f 74 goat snp28471-scaffold3030-53935 10 80457465 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407028 Affx-122954946 AX-123277379 10 20545213 TTCTTAATCACATGGCAAAGAACTATGCTTGGCTC[A/G]ATGAACATCTTTTAAGAAAATAAGCATGTATAGAC R 2 1 2 1 101000 f 74 goat snp28472-scaffold3030-94780 10 80416494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788869 Affx-122935310 AX-385275884 10 20562130 ATGGTGGTGGCAGTTTTAGTGTTTGGCAAAGTTCT[A/G]TTTTTCTGGGTAATGACTTCAAGGTTCGATTTAGT R 2 1 2 1 101000 f 74 goat snp5134-scaffold1179-15262 10 80399555 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444418 Affx-122926574 AX-123314755 10 20607819 AGAGACTGGAAATGACCTCTAGAAAGAGTGGAGGT[A/G]TGGTCAGGTTGTGGGGCTGCAGAGGGGTAGTGCAG R 2 1 2 1 101000 f 74 goat snp5135-scaffold1179-60951 10 80353503 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376753 Affx-122978534 AX-123247112 10 20669131 CTATCCTGGTGGATAATACATCAGGGGAGGGCTGG[C/T]GGGCCACCATTTGTCTACAGAGTCTGAATCCAGGC Y 2 1 2 1 201000 r 74 goat snp5136-scaffold1179-122263 10 80291820 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439225 Affx-122931021 AX-123309562 10 20701087 GGTACGGTATATTTATTTATATAAGTGATATGTGC[A/G]CTAAGTCTCATTATTTCCTTCCTGTTTTCACTTGG R 2 1 2 1 101000 r 74 goat snp5137-scaffold1179-154219 10 80259353 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383062 Affx-122973751 AX-123253420 10 20880830 GTTTGGTCTCAGAGGGGTGACAACTTTCCCAAAGA[C/T]GCACAAAGTTTATGTATGTACAGATGCCAGCGCCC Y 2 1 2 1 101000 f 74 goat snp5141-scaffold1179-333962 10 80079939 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382770 Affx-122973975 AX-123253128 10 20948923 AGCCTCATGCTTCCTGCAGCTCCCAGCCACAGTGA[A/G]GTGTCTGATAGAGGCTAGCAGAGAAGCAGGTAGAT R 2 1 2 1 101000 r 74 goat snp617-scaffold1019-6970 10 80013175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399178 Affx-122960630 AX-123269533 10 20987555 CTCCAGCACTGAGGACAGGCCACACACTCAATAAG[C/T]CGACAATGGATAGAACTGTTGAGAATATTAAGTCA Y 2 1 2 1 101000 r 74 goat snp618-scaffold1019-45602 10 79974616 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392043 Affx-122966400 AX-123262400 10 21046851 CGGGTAAGAAGGGCCCAGAGATACCAACAGACTTG[A/C]GGTGGGCAGACCCAGCCCAGAGCATTTTGTCTGCA M 2 1 2 1 101000 f 74 goat snp619-scaffold1019-104898 10 79915495 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398677 Affx-122961874 AX-123269032 10 21090617 CCTAACAAGATAATGCGTGTGAACAGCCCAGCAAC[A/G]CAGAAAGTTACATGGATTACAATTCCAAGACAGAC R 2 1 2 1 101000 r 74 goat snp620-scaffold1019-148664 10 79870921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382355 Affx-122973872 AX-123252713 10 21130577 ACTGGCTGGGGAGTGATGGCAGGTAACAGTCAGAG[A/C]TCCTTCCTCCAGCGGCAGCCCTGGGGATGAAAATG M 2 1 2 1 201000 f 74 goat snp621-scaffold1019-188624 10 79831373 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272576 Affx-1111832881 AX-519546291 10 21146442 TTAACTTGACCTCTTCCACCATAGAACTTTCTCAA[A/G]TGCCTCAATTCTCAGTAACCATCCCTTTTGTTGTT R 2 1 2 1 101000 f 74 goat 10_21146442_AF-PAKI 10 21146442 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320784693 Affx-122932899 AX-385271741 10 21177390 GTCACATCAGCAGAGAACTTAAAAGGGTCATGAGA[G/T]TCACACCTCAAAAAAGCTTCTCCAGAGGTGAGCTA K 2 1 2 1 101000 r 74 goat snp622-scaffold1019-235437 10 79784447 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382711 Affx-122973625 AX-123253069 10 21210255 CAGACGGAATAGGAATATTTTCATCTTTCGCTTTT[A/G]TCTGCCTGGGTCTTTTATTTATTTATTTATTTTAA R 2 1 2 1 101000 f 74 goat snp623-scaffold1019-268302 10 79744577 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446407 Affx-122925570 AX-123316743 10 21250973 GGATAGAAATCAAACTTACATGCCCTCAAAACTAA[C/T]ACCACATTGTAAATCAACTATACTCCAATAAAAAT Y 2 1 2 1 101000 f 74 goat snp624-scaffold1019-309020 10 79703939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376270 Affx-122978757 AX-123246629 10 21287252 TCAAACAAACATCAGGGTGAAGGGAACAAACATCT[A/G]TCTCCTGATTTTTCCATAATTTTACTAAATCATCA R 2 1 2 1 101000 f 74 goat snp625-scaffold1019-345299 10 79667630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452246 Affx-122920780 AX-123322579 10 21341007 AGCTGGAAAAGGCTGGGTCGGGGTAAGGTGGTACA[A/G]TCACAGTGGACCTGCTGCCTCCACCCTTCATTCTT R 2 1 2 1 201000 f 74 goat snp626-scaffold1019-399054 10 79613717 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418624 Affx-122947149 AX-123288972 10 21409884 GCAGTAAGGTGTTAACGGTGGTGCCCTCTGAGAGG[C/T]GGGAAAGTGCTTTGCTGCTGTTGGCCTACGTTTTT Y 2 1 2 1 202000 f 74 goat snp627-scaffold1019-467931 10 79545411 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419354 Affx-122945638 AX-123289702 10 21453204 GTGACGGCACCGGTCTGCTCTGCTATTCACAACCC[A/G]ACAGGCCGCTCTTACACCATCGGCCTCTAGCCCTG R 2 1 2 1 101000 f 74 goat snp628-scaffold1019-511251 10 79502215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433641 Affx-122934580 AX-123303982 10 21488471 ACCTCTCTACAAATGGTACAAACAGTTTTCTATTC[A/G]TGACATTTGTTGTTGTTATCAGTTTTGATGTATTC R 2 1 2 1 101000 f 74 goat snp629-scaffold1019-546518 10 79467309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422829 Affx-122943114 AX-123293175 10 21523272 TTGAGATGGGAGCACAGAGTTCTAACGCCCTAACC[A/G]TGGATCTTGTGCCCTGCACAGGAGCAAGGATAGTA R 2 1 2 1 201000 r 74 goat snp630-scaffold1019-581319 10 79432273 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395874 Affx-122964000 AX-123266229 10 21556558 TGGGTCGTGCACAACACGTTGGGGAATTTTCAGTA[C/T]AGTGCGTACAGCAGGAATACGGAGACAGGCCACCT Y 2 1 2 1 101000 f 74 goat snp631-scaffold1019-614605 10 79399294 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800233 Affx-122968575 AX-385287156 10 21602919 GTCATCCACAGAGTCAAGATTCAGGACTGTGTTTA[C/T]GAAGAGAACTTGAATTAGTGTCTTAGTGTGTTTTC Y 2 1 2 1 101000 f 74 goat snp632-scaffold1019-660966 10 79352799 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388848 Affx-122968879 AX-123259206 10 21660208 GCCCAAGCTGTTGATGGAAATTTTGGCAAAGTCAC[A/G]TTGTAGAAAAGCATTTGGGAATGAGAGTTATAGTT R 2 1 2 1 201000 r 74 goat snp16259-scaffold1711-4791 10 79336718 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795612 Affx-122921962 AX-385282567 10 21691724 CAATTTAGTTAGGTTGAGGAACTCATCTGATTTAT[A/G]TTAGACTTAATATCTTCATCTGTGAGATGAGAAGG R 2 1 2 1 101000 r 74 goat snp16260-scaffold1711-36307 10 79305047 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406922 Affx-122955088 AX-123277273 10 21743609 TGTGGGGAGCTTCATCCTAGCGGGTAATGATTCTA[G/T]AAGTGATCTCAATAATAATGTGTTGCTTTGGTGTG K 2 1 2 1 101000 f 74 goat snp16261-scaffold1711-88192 10 79253213 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273562 Affx-1111833692 AX-519547177 10 21751992 CAAGAAAGGACACTCTTCAGGAGCCCCTAAGGAGT[A/G]GGAGGCATCTCAGGGGGGCTCAGGACCCACAGTTG R 2 1 2 1 102000 f 74 goat GoatD01.001706 10 21751992 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38388390 Affx-122969303 AX-123258748 10 21778782 CAGCAGTGAGGAACAGCGTGGGTGGCAGCCGTGCT[A/G]GACAGCTTGTCAGCATCTTGATCACCAGTATCTGG R 2 1 2 1 101000 r 74 goat snp16262-scaffold1711-123365 10 79219143 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777293 Affx-122945972 AX-385264415 10 21826525 AAAGGCAGAGAAGATTAACCAAAGAATGAGCTTAA[C/T]GGGTAACTCTGGACTGTTTGGAACATCAGACCTAC Y 2 1 2 1 101000 r 74 goat snp16263-scaffold1711-171108 10 79171673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375558 Affx-122979087 AX-123245917 10 21866426 CACGTTTGTTAAGTTGAGGAAAGCACATTTCCTCT[A/G]CATTTTACTCTGATCTCTGCTAATAGCTCTGAGAG R 2 1 2 1 101000 r 74 goat snp16264-scaffold1711-211009 10 79131540 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798128 Affx-122921773 AX-385285063 10 21898793 GTAGACACATATAGACACATGATATGCTTGGAAAA[C/T]GTTTGAAGATAAAAAAACAGTTCTAGTGATCATAA Y 2 1 2 1 201000 r 74 goat snp16265-scaffold1711-243376 10 79098780 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420627 Affx-122945230 AX-123290974 10 21932511 TGTGGAATTTTAAACCATTTAAATAAAATTTTCAT[A/G]TTATTTTCCATTAAAATCCACGGGCCTAGTTTGTA R 2 1 2 1 103000 r 74 goat snp16266-scaffold1711-277094 10 79064519 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418051 Affx-122946627 AX-123288399 10 21964725 CTGAATTCAGGGCCAGGATCCCATATGCTGCTTTG[C/T]GTGACTTGGAAAAGGCAACTTGCTGGGCAAATGCA Y 2 1 2 1 201000 r 74 goat snp16267-scaffold1711-309308 10 79032517 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381100 Affx-122974590 AX-123251458 10 21993775 AGGAAAGGCATGTATGTCAGCCTTCTCTGGCCTCC[A/G]TTTGTTAAACTATTTCTTCAAGAGAAAGTCATGAT R 2 1 2 1 201000 r 74 goat snp16268-scaffold1711-338358 10 79003133 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403761 Affx-122958000 AX-123274113 10 22052834 AAAGCCTTGCAACCATTTGCCAAGGTTATAGTGCA[C/T]TGGAGCAGGGAAATAATCAGAATTTGGGGGATATC Y 2 1 2 1 101000 f 74 goat snp16269-scaffold1711-397417 10 78944115 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404660 Affx-122957297 AX-123275012 10 22103521 TAGCCTGAAAAGGACAAAGTTGAATTCACTGTTTA[A/G]CAAAATGCAAACAAACAAAAATGGAGGAAGTGGAA R 2 1 2 1 201000 f 74 goat snp16270-scaffold1711-448104 10 78893357 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771034 Affx-122965239 AX-385258196 10 22139844 AAAATCTTACTCTAAAGAAAACAGTACAATATAGG[A/C]ACAGGATTAAGCCAGTAAGAGGAACATAGCCAAGT M 2 1 2 1 101000 r 74 goat snp16271-scaffold1711-484427 10 78857048 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428645 Affx-122938663 AX-123298987 10 22164106 TTATGAGGGAACAATGAATGCTGAGAACATTCATG[A/G]TTTTGCCCAAGCCGAATTCTCCTAAAACTTCTCAG R 2 1 2 1 101000 r 74 goat snp29454-scaffold319-13994 10 77389793 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276362 Affx-1111835379 AX-519549893 10 22181349 AACCATACCACCTTTCCTAAACCCTCATACACTGA[A/G]CACACTCCTCAAGTCCTTGCCCTTAGCCTTGGCCT R 2 1 2 1 101000 f 74 goat Random2.2K-1053 10 22181349 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320767653 Affx-122921306 AX-385254894 10 22206572 TCTAGCCAAAAAAGGTAAAACTAAGCCTATTTGCC[A/G]TTCCATTTCAATCATTAACTATTATGAACACCATT R 2 1 2 1 101000 f 74 goat snp29455-scaffold319-56460 10 77348336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773883 Affx-122934796 AX-385261022 10 22261660 TTTCTGGCCTGATACCCAAATCATACCTCATTCTA[C/T]GCTCCATTTAATGAGTCCAAACATTGGGAGCAGGG Y 2 1 2 1 101000 f 74 goat snp29456-scaffold319-111548 10 77292797 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431362 Affx-122937040 AX-123301703 10 22319431 TACGACAGTTATACCAACAAGTTTCCTCAAACAAT[C/T]CCCCGCCCATCCATCACCCCTATGTTCTACTTGTT Y 2 1 2 1 201000 f 74 goat snp29457-scaffold319-169319 10 77235042 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442406 Affx-122927992 AX-123312743 10 22353932 TCCTTTTATCCTTCCATTATAATTTTGTCCACTTT[G/T]CCTTTTATTTTGACTCACTGACATTGTCCCTTTTC K 2 1 2 1 101000 r 74 goat snp29458-scaffold319-203820 10 77200729 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387362 Affx-122970473 AX-123257720 10 22391863 AATAGAGGGGATTTCTCTTTTTAAAACCATTCTCA[C/T]GTGGAACATCTTCCTCTAGTTCTTTCTGACCCTTT Y 2 1 2 1 101000 r 74 goat snp29459-scaffold319-241751 10 77162584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420954 Affx-122944979 AX-123291301 10 22445005 TTCAACTGAAAAACATTTAAATACTTAATATTTTA[G/T]ATTAAATACTAAAATATTTTCCACATTAGGTGCTG K 2 1 2 1 303000 f 74 goat snp29460-scaffold319-294893 10 77109418 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410179 Affx-122952590 AX-123280529 10 22502997 GAGACCTTTACAGGCAGAAGGCAATGGGAACAAGG[A/G]AGTTATACCAGACAGAAGAGTGCTTAGTTATTGCA R 2 1 2 1 101000 r 74 goat snp29461-scaffold319-352885 10 77051379 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770374 Affx-122929084 AX-385257539 10 22533476 GGAGGGACCATTTTGTATTACTGTTTTGACAGTTA[G/T]GATACTTCTGGCGTGTAGAGTGAGATTGGTCCCTA K 2 1 2 1 101000 r 74 goat snp29462-scaffold319-383364 10 77019517 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443928 Affx-122927034 AX-123314265 10 22564568 CTTCTATTCATCCTTAGAATTTAGCTCAGGTGTCA[C/T]TCCAGGAATCCTCCCTACCTTTCCTAAGTAGACCA Y 2 1 2 1 201000 f 74 goat snp29463-scaffold319-414456 10 76988028 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774304 Affx-122931388 AX-385261440 10 22632227 CCTGAATTTTGTGGATTAAATCCAAGTTCCAATCC[A/G]TCTGTTAGAATTCTCCCCTCTCTCTCACTCTTGCA R 2 1 2 1 101000 r 74 goat snp29464-scaffold319-482115 10 76919396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437453 Affx-122932391 AX-123307791 10 22658065 TTTCTGTGTCTTGGCTATTGTAAGTAATACAGCGA[C/T]GAGCACAGACATTCACATATCTTTTCTTCAGGAAG Y 2 1 2 1 201000 r 74 goat snp23978-scaffold2437-207783 10 76892644 C T 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446372 Affx-122925593 AX-123316708 10 22692101 TGGCTGAGACTGAGGCACTCAGTGGGAGAAAAGTC[A/G]GAGACGAAGTCAGAAAGGCAGGTTTGCCAGATTGT R 2 1 2 1 101000 f 74 goat snp23977-scaffold2437-173747 10 76858691 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433636 Affx-122934584 AX-123303977 10 22752649 CATACTGAGATTCCAAAAATGAATATAAAGCACAA[G/T]ACGCAGAATCAATAATCAAAGATAGAAGAAATATT K 2 1 2 1 101000 r 74 goat snp23976-scaffold2437-113199 10 76797707 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428049 Affx-122939128 AX-123298392 10 22784559 AGAAAACCGAAGTTTCCCTCTCTTTCTCCATTTCC[A/G]TCTCTCCAAGATCGTGGTGCACATATCAGGCAAAT R 2 1 2 1 201000 r 74 goat snp23975-scaffold2437-81289 10 76766013 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784918 Affx-122960610 AX-385271965 10 22813869 TCTAAAACCCAAGGAAGATTCTTCAATAGCCTACC[A/G]TGTAGGTATTCCTAAGTATTGTTACCAAAAAGTGG R 2 1 2 1 101000 f 74 goat snp23974-scaffold2437-51979 10 76736689 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448510 Affx-122923455 AX-123318846 10 22855761 TTCAAACCCCGATCAAGTCCTTGATCTGCATTAAA[C/T]AGCACTTTGAGGTTAGCTAAAGACCCATAACATAT Y 2 1 2 1 101000 r 74 goat snp23973-scaffold2437-10087 10 76693939 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391153 Affx-122967450 AX-123261510 10 22879911 CTTTTCATTTCATGATTGGAATAATCATCCACAGC[A/G]AATGAATATACATCTATCCAAATAGGGGAAGTGGA R 2 1 2 1 101000 f 74 goat snp56132-scaffold876-13964 10 76669425 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386852 Affx-122970075 AX-123257210 10 22972219 ACATTTGAAGGCTTTTTTGCAGCTGAAATATCTCA[G/T]CTACTAGGATTTATGCTGTGTACCTACACAAATGT K 2 1 2 1 101000 r 74 goat snp56134-scaffold876-106272 10 76578552 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421848 Affx-122944293 AX-123292195 10 23016346 AAAAGTCTGAAAATGTTTTAACCCATAATCTGAAC[A/G]CCTGTTAGACATTTTCACCTCCTGAATTGTGAATA R 2 1 2 1 101000 r 74 goat snp56135-scaffold876-150399 10 76536383 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447700 Affx-122924615 AX-123318036 10 23067424 GATTCTATGGGTCTAGGGTAAAGCCCAGGTTTCTG[C/T]ATTTTTCATCAGTAGCCAAGGGACTCTGATGGGTT Y 2 1 2 1 101000 f 74 goat snp56136-scaffold876-201477 10 76485348 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394248 Affx-122964733 AX-123264603 10 23219782 TGGTCACATATGTGAAATATCTACTAAATGTCTAT[C/T]ATTTCTCTTTAGGCCATCACAAGCCAAGTCTCCAT Y 2 1 2 1 101000 r 74 goat snp56140-scaffold876-353835 10 76333720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405068 Affx-122957415 AX-123275420 10 23265135 ACCACGAGGGAAGTCTGCTAGCCTTAGTTTTGAAA[C/T]GGTGGTTGGAATGAGAAGAGAGGAAAAGGTTTCTG Y 2 1 2 1 101000 f 74 goat snp56141-scaffold876-399188 10 76288254 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779116 Affx-122929444 AX-385266221 10 23312232 TGTATCACAGATAGAATTTTGAAAAGTCTTGACCA[G/T]CTCAGAGCAGAAAACACTTACTTTGTCTGGGAAGC K 2 1 2 1 101000 r 74 goat snp56142-scaffold876-446285 10 76243347 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790345 Affx-122974622 AX-385277348 10 23373283 AAACGGCCGCCTTCCTGGCTTTCCATTGATTTAGA[C/T]ATTTCTCTGGGCCTCCACAGCCCAACCTTTGGCTT Y 2 1 2 1 101000 r 74 goat snp56143-scaffold876-507336 10 76182389 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767096 Affx-122965664 AX-385254384 10 23417895 AAATGCTTAAGTGATACACCAGATACATTGCTCAC[A/G]TTAAAAACAAAGTTGTTCTAAAATAGAGTTTTGAC R 2 1 2 1 101000 f 74 goat snp56144-scaffold876-551948 10 76137897 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792046 Affx-122922174 AX-385279034 10 23448818 CATTTCAATAAAATTGGCATAACAATAGAATCTTT[A/C]TATTACTTGGATTTTGTTTATCAAAGGATTAGGTT M 2 1 2 1 101000 f 74 goat snp56145-scaffold876-582871 10 76107448 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768273 Affx-122930083 AX-385255454 10 23483334 CATTACTTGTGATGTGCATGAGAGTAAGTGGGAAT[A/G]TTATATTTAATTGGGGCACTGTAGAAAATGAGTTA R 2 1 2 1 202000 r 74 goat snp56146-scaffold876-617387 10 76072344 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800253 Affx-122970733 AX-385287176 10 23528929 AGTTTCAGATAAATCTTTCAAATGTAAGTTTGACC[A/G]TATATTTTCTGTCACTCTTCATGATTATTACATTT R 2 1 2 1 101000 f 74 goat snp38282-scaffold482-20568 10 75922876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770392 Affx-122945144 AX-385257558 10 23677973 GTGCTTTATATGGAACACATATGTAATGTTCACAA[C/T]ACTTATGAGGTATATATTAATCTTATCCACCTTTT Y 2 1 2 1 101000 f 74 goat snp38285-scaffold482-169612 10 75774237 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463078832 Affx-1109802713 AX-514566307 10 23714487 GGGACACGACTGAACCAACTGAGCACATAGTACAC[A/G]ATGGCTAACTCACAAGGTTATTTTGCAGACTATCA R 2 1 2 1 101000 r 74 goat 10_23714487_AF-PAKI 10 23714487 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440583 Affx-122929294 AX-123310920 10 23732211 ACTGAATATGCCAACTGTGCAAACATGGGCAGGCA[G/T]AGCCTTCCAGGCAGATGGAACAGGTACGGCAAAAA K 2 1 2 1 101000 f 74 goat snp38286-scaffold482-223850 10 75719560 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762758 Affx-986697288 AX-385250813 10 23760513 AAATATTTTCTAAGACCTTTTCCTCCACTCCAAAT[G/T]CCTGTTCTCACTGACAGGGTTTTATGATTCTTGTG K 2 1 2 1 600010 f 74 goat 10_23760513 10 23760513 Ancestral_priority_1043 ancestry 0.708 recommended IMAGE 10K 10K ancestral 320762760 Affx-986697290 AX-385250814 10 23760537 CCACTCCAAATGCCTGTTCTCACTGACAGGGTTTT[A/G]TGATTCTTGTGCCTTTCCTCAAGCTACATCATTTA R 2 1 2 1 600010 f 74 goat 10_23760537 10 23760537 Ancestral_priority_1043 ancestry 0.624 neutral IMAGE 10K 10K ancestral 320765245 Affx-986697292 AX-385252782 10 23760551 TGTTCTCACTGACAGGGTTTTATGATTCTTGTGCC[C/T]TTCCTCAAGCTACATCATTTAGTATTTTTGTCATT Y 2 1 2 1 600010 r 74 goat 10_23760551 10 23760551 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 38418983 Affx-122946067 AX-123289331 10 23764043 AGAAAGATTTATGAGTCAATGACATTGAAGAAAAG[C/T]ATATTTTAATTTTAGCAGTTATTGCCAAGATATTG Y 2 1 2 1 101000 f 74 goat snp38287-scaffold482-255682 10 75686912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428120 Affx-122939071 AX-123298463 10 23795288 CAGGTGCGTTCCTAATGGTCTCCCAGTTCTCCTTT[A/G]TGGCAAACAGCGGCCCATAATAATAGCCAGGTTAG R 2 1 2 1 101000 r 74 goat snp38288-scaffold482-286927 10 75655396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422669 Affx-122943677 AX-123293015 10 23842505 GAAGTACTTGTCAACAAAACATTTAAGAGTGTTTT[A/G]GATGCATGTGTTTGGGAAGAGATGAAGAATCAGTT R 2 1 2 1 202000 f 74 goat snp38289-scaffold482-334144 10 75607808 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802363 Affx-122926408 AX-385289267 10 23876411 CAGTTTCTTATTGAATTAAACACACATTTATTCTA[C/T]GATTGAAAAGTTCCAGTTGATATGCACACACATCC Y 2 1 2 1 202000 f 74 goat snp38290-scaffold482-368050 10 75573914 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431084 Affx-122936623 AX-123301425 10 23958314 ATGAACAATATGACAATAAATAAAATGCATTCTTT[A/G]TCAGCAAACACCATGGAAAGGTACACACAAACCAT R 2 1 2 1 101000 r 74 goat snp38292-scaffold482-449953 10 75492300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423277 Affx-122942657 AX-123293623 10 23998861 TGTGTCTTTTTTTTCCTGACCTGCAAGTGATTGTC[A/G]TGTATATCCACAGAGGCAAAAAGATAAATATCTAT R 2 1 2 1 201000 r 74 goat snp38293-scaffold482-490500 10 75450011 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440359 Affx-122929652 AX-123310696 10 24041767 GAAAATATAATGCATTAATTTATTTCTTCAACTAA[C/T]GCAGCTAATGAGTGTAACTGATATTACTAATGAGT Y 2 1 2 1 101000 r 74 goat snp38294-scaffold482-533406 10 75406082 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384691 Affx-122972120 AX-123255049 10 24083613 CTCTTTCCACTTGTACTACCCACATCACAGTGGTC[A/G]TGTTATTCTTTGGGCCTGCATCTTAATCTATCTGT R 2 1 2 1 102000 r 74 goat snp38295-scaffold482-575252 10 75363238 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384206 Affx-122972392 AX-123254564 10 24144977 ATACTGTCCCATAAATATTTCTCAAAGGAGACAAT[A/G]TATTGTTTGTATTCCTGCAAGCTGACTGTATTTCA R 2 1 2 1 101000 r 74 goat snp35150-scaffold4201-29258 10 75299443 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440820 Affx-122929280 AX-123311157 10 24198052 CAAGAGCAGAGGGTGGAGTCACAAAAGTCACATAA[C/T]AAACAGTACTAAACCTCACAGGGAGATTAGGGTAA Y 2 1 2 1 101000 f 74 goat snp17707-scaffold184-22099 10 75241723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386517 Affx-122970743 AX-123256875 10 24287998 TTTCCCAATTTCACAGAACAATGCCAGCTGTTGGA[A/G]GACATTCACCCCTTTTCTTTCTTATTAGCTGGTCC R 2 1 2 1 101000 f 74 goat snp17709-scaffold184-112045 10 75151032 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803152 Affx-986696196 AX-385290015 10 24304762 AAAAGGAAGGGAGTAAGAGAAAAAGAAGGTAACAA[C/T]GGAATTATGAAACAGCAAGAAAACAATTTTTAAAA Y 2 1 2 1 600010 f 74 goat 10_24304762 10 24304762 Ancestral_priority_1043 ancestry 0.684 recommended IMAGE 10K 10K ancestral 320765248 Affx-986697294 AX-385252785 10 24304763 AAAGGAAGGGAGTAAGAGAAAAAGAAGGTAACAAT[A/G]GAATTATGAAACAGCAAGAAAACAATTTTTAAAAT R 2 1 2 1 600010 r 74 goat 10_24304763 10 24304763 Ancestral_priority_1043 ancestry 0.634 recommended IMAGE 10K 10K ancestral 320786600 Affx-122935843 AX-385273632 10 24326615 AGCAGGTTGACTGAGATTAACATAAATAAAGCTGA[A/G]GAATATGAAACATCAGATATAGGCAAGAATAATAA R 2 1 2 1 101000 f 74 goat snp17710-scaffold184-150662 10 75112036 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392687 Affx-122966416 AX-123263044 10 24371038 GATAACTCATAAAGAAATAAATTTAACAGGTCAAT[A/G]AATACATGTAAAAAGTACGAATTTTGGAAGTAAGT R 2 1 2 1 101000 r 74 goat snp17711-scaffold184-195085 10 75067990 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446964 Affx-122924661 AX-123317300 10 24421820 TGTTTTAAAAAAGAAATGTGACTGTCTTTATGTGG[C/T]AAAGTTATCTTTGAGGATATGATGAATGTGCATCA Y 2 1 2 1 201000 r 74 goat snp17712-scaffold184-245867 10 75017243 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417182 Affx-122947324 AX-123287530 10 24457853 TCATGAGTATTTAGAAACTTCTTTACCAATCTGAC[A/G]TTACAGTGACAGTCATGTTTCTGATTTTGTTTGTT R 2 1 2 1 101000 f 74 goat snp17713-scaffold184-281900 10 74980683 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424938 Affx-122941281 AX-123295284 10 24515154 TGAATTCTAGGGGCATAAGCCTGTTGTGACACTTC[A/G]CTTTTTTAAAAAATGTCTCCAGAGCCAAAGTTGCA R 2 1 2 1 102000 f 74 goat snp17714-scaffold184-339201 10 74922280 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801900 Affx-122924772 AX-385288806 10 24546716 CAGTTTGACTATCCTTGAATAATTAATCATTATAA[C/T]ATGCAGAATTATTAATATTCTTATGTTAGTTTCCT Y 2 1 2 1 101000 r 74 goat snp17715-scaffold184-370763 10 74890664 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425299 Affx-122940953 AX-123295645 10 24576905 CTAATTGTGACATGCTTCCTGAGTATTCCAAGCTG[C/T]TACAATTCTACCACTTTCAGGGGGCAAGGGACTAC Y 2 1 2 1 101000 f 74 goat snp17716-scaffold184-400952 10 74860568 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406538 Affx-122955122 AX-123276890 10 24612706 AGCTACAGTCCATGGGGTTGCAAAGAGCTGGACAC[A/G]ACTTAAACAACTGAGCACAACAACTCTGAGGAATT R 2 1 2 1 103000 r 74 goat snp17717-scaffold184-436753 10 74824812 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443520 Affx-122927785 AX-123313857 10 24681359 CCCGCAATGCTCTGAGCCCTAAACTCCCCTTTTCC[A/G]TGGTCCTCGTCTGTTGTTCTACACCCAAAGCTGGA R 2 1 2 1 201000 r 74 goat snp17718-scaffold184-505406 10 74756309 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450709 Affx-122921886 AX-123321043 10 24722454 GCCATTTCCTTCTCCAAGGAAGAAAATCTTTATTG[A/G]TATTGAAGAGCATCTTCAAACATTAACTCTGAGTA R 2 1 2 1 303000 r 74 goat snp17719-scaffold184-546501 10 74715016 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782124 Affx-122957786 AX-385269202 10 24753031 ACTAGGTATCCTCGAAAGGCATCTTAGGATTCTGC[A/G]TAATTCTAAAGAAGTCCTAGGATGGATCTGAGTTT R 2 1 2 1 201000 r 74 goat snp17720-scaffold184-577078 10 74684081 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433475 Affx-122935045 AX-123303816 10 24784280 TTAAACTCATCTCTGTCTAGAGCATTTCATGTCTA[C/T]GTGTCACTTATGTTTGCAAAGCATCTTGTCTCTTA Y 2 1 2 1 101000 f 74 goat snp17721-scaffold184-608327 10 74652826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778687 Affx-122970313 AX-385265799 10 24821907 AAAAATTAACCTTAAAAAACTATATACTTTGATCA[C/T]GATGATACTAATACGCTCCCTGTTGCTCTGTTGAG Y 2 1 2 1 101000 r 74 goat snp17722-scaffold184-645954 10 74614787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779683 Affx-122965947 AX-385266782 10 24854336 TGTGTAGCTATATTTTATATAGCTATGTATTCCTC[A/G]CAGTGAACATCAGTTGTAGTAACTGATTATTCTCT R 2 1 2 1 101000 f 74 goat snp17723-scaffold184-678383 10 74582293 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379260 Affx-122976253 AX-123249619 10 24885250 ACTGATCACCTCTCACTTTTACATCATTTTCCATA[A/G]TAAAGTAGGTCTGCTTGAAATTCACATGGGTCAGG R 2 1 2 1 101000 r 74 goat snp17724-scaffold184-709297 10 74551319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784829 Affx-122978825 AX-385271876 10 24926890 CAATATCTGCTGTATCCACCTTACAGATTGTTTTG[A/G]GGACTCCCAAATCAAATAATGTACCCAGGTCCTTT R 2 1 2 1 101000 r 74 goat snp17725-scaffold184-750937 10 74509386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453974 Affx-122919455 AX-123324307 10 25007702 TTCAGATCCAGTCAGTGGACATTTAGATTTCCTCT[A/G]TGCATGGACTAGTGTCTTAATCAACAGACACTTGT R 2 1 2 1 201000 r 74 goat snp17726-scaffold184-831749 10 74428147 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409397 Affx-122954141 AX-123279748 10 25037421 TTGATGTGAAATGATTCCAAAGTTTCAGCATTATG[G/T]ATGTTTGTTGAAGATTTTGTATAACTTCTATCAGT K 2 1 2 1 101000 f 74 goat snp17727-scaffold184-861468 10 74398692 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380827 Affx-122975073 AX-123251185 10 25073820 GTAACTGATTCAGCTATATAATCAGATTTTTTGTA[C/T]TTAAAATAAATAAAAATGTTTCTCCGTCTACTTTG Y 2 1 2 1 303000 f 74 goat snp17728-scaffold184-897867 10 74362387 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445418 Affx-122925374 AX-123315755 10 25083597 GGACTCCTAGAAGAGATGATGCCTAATCTGAAAGA[C/T]GGCAAAGCTTTGTCAAAATGAGAGAGTGAAAAAAT Y 2 1 2 1 101000 f 74 goat snp31078-scaffold343-3143441 10 74352966 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423316 Affx-122943185 AX-123293662 10 25134417 CTGTTCTCTTCTCTGCTTTAGGTGATCAACAAATA[C/T]GGAGATCTCTACGGAGCAGAACGCATTGCTGAACT Y 2 1 2 1 101000 f 74 goat snp31077-scaffold343-3092621 10 74301806 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429049 Affx-122938305 AX-123299391 10 25174118 CCAGCCAGATCCCAAAGCAGCCCTACCAACCTGGG[C/T]GGTCCCGTTTTCCTGCAGACCTTAGGATGCCTGTG Y 2 1 2 1 101000 r 74 goat snp31076-scaffold343-3052920 10 74262393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771582 Affx-122974325 AX-385258740 10 25213819 AACCTGAAGCTCGGCAAGTTTACCCATTCCAGAAC[A/G]CAGATCAAAGGTGTCTCTCAAAATATTAACTACAC R 2 1 2 1 101000 f 74 goat snp31075-scaffold343-3013219 10 74222021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422107 Affx-122943568 AX-123292454 10 25262021 TACAGACAGTAGGAAAAGCAATGGGCAATCATGAC[A/G]TTCTTATTAATCATTCCTGTGATGAGAATGACTGC R 2 1 2 1 201000 r 74 goat snp31074-scaffold343-2965017 10 74174452 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799414 Affx-122931598 AX-385286344 10 25302187 AGTTTATGGCTTTATTTCATTAGTGTATTATTTAC[A/G]TCTTTGTATTCTCATGACCCGTCTCTCCAAAGATC R 2 1 2 1 101000 f 74 goat snp31073-scaffold343-2924851 10 74135000 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794331 Affx-122940998 AX-385281295 10 25332748 CAGAAAAGAGCTTAGAGAGACAGTAACTGTAGGAG[C/T]GAACAGTTTTCTACAGCTCCTGCTTGAAAATCTCA Y 2 1 2 1 101000 f 74 goat snp31072-scaffold343-2894290 10 74104614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392102 Affx-122966360 AX-123262459 10 25391141 ATCAGACTTAGGATAATGTAGAAAGTCTTGGCAAC[A/G]TGGCATGTTCTTAAATGAAATCAGACTTGCCATGA R 2 1 2 1 101000 f 74 goat snp31071-scaffold343-2835897 10 74046572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386868 Affx-122970063 AX-123257226 10 25420824 GGGAGGGGTCAAAGTTAAGCATCAGCTGCAGTGTC[A/G]CTTTGTTCAAATGGAATCAAACTGTGGTCTCTGAG R 2 1 2 1 101000 r 74 goat snp31070-scaffold343-2806214 10 74016730 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395741 Affx-122963697 AX-123266096 10 25473326 TTTGACAGAATTTCTTTCTTCAAGAGCCAGATATT[A/G]TTTTCAGAAATTATATAATAATGAAAGATCTCCAA R 2 1 2 1 202000 r 74 goat snp31069-scaffold343-2753712 10 73963307 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388731 Affx-122968966 AX-123259089 10 25539926 TTTTGTCAAAGTGTGTAGGAGGTCAGTAACTTTGG[C/T]GCATGGATCTCTTTGCTCCAAAGACCGGGAGCCTG Y 2 1 2 1 101000 f 74 goat snp31068-scaffold343-2687112 10 73896152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779626 Affx-122930595 AX-385266728 10 25657425 TCTGTTCATGTATGGTGGTGATTTGAAGAGTCAGT[A/G]TTAAAGCTATCACTGGATTACTTCTAAAAAATATA R 2 1 2 1 101000 f 74 goat snp31066-scaffold343-2569613 10 73780140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787906 Affx-122954399 AX-385274928 10 25686237 TTACCTTCATTAACATCAGTGTCAACACCATCGTC[A/G]TATATAGTCTTTGATAAGAGAGTTTAAGAGCTCCA R 2 1 2 1 101000 f 74 goat snp31065-scaffold343-2540801 10 73751448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382884 Affx-122973419 AX-123253242 10 25724913 ATAAATTTCTGCCATCGGGCCTGAATATTGGGAGC[A/G]TTTATGGTTTTCACTATTTCCAATCATTTTTCATT R 2 1 2 1 101000 r 74 goat snp31064-scaffold343-2502125 10 73712698 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796393 Affx-122919963 AX-385283343 10 25794867 GCTCCTATATGCATCCTCTGAAAAATGAAAGATCC[G/T]AAGTAATGTCTCCCATGTGGGATACCTTGAAAAAT K 2 1 2 1 101000 f 74 goat snp31063-scaffold343-2432171 10 73642339 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441172 Affx-122929553 AX-123311509 10 25824166 GAGACCCAGCACAGCCATGAATAAATACATAAAAC[A/G]TTTTTTTAAAAAGAGGATGAGCTTGCTCTATGTCA R 2 1 2 1 303000 r 74 goat snp31062-scaffold343-2402872 10 73612704 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772066 Affx-122966329 AX-385259221 10 25876600 AATATATATGTAGTAACATAATAAGATGCAAATAA[C/T]AGAGGTCCAAAACCTACTGTCTTCACAAAAATATG Y 2 1 2 1 101000 r 74 goat snp31061-scaffold343-2350438 10 73559986 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790252 Affx-122930444 AX-385277256 10 25906782 GGCTATGCCGAGCCCAGGAGATGATTTCAGAAAGG[C/T]ATTATAGTGATGCTAGTGGTCCACTAGCAGTGTCT Y 2 1 2 1 201000 f 74 goat snp31060-scaffold343-2320256 10 73530095 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396746 Affx-122962788 AX-123267101 10 25935642 TAAGTTGCAAAACATTTAAATGGAGTATGACGGGA[C/T]AAGAGGAGAAATGAACACTATCCAGTGACTGTGAA Y 2 1 2 1 101000 r 74 goat snp31059-scaffold343-2291396 10 73501298 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803482 Affx-122941290 AX-385290305 10 25989292 AGAACTGCTCAACCATATAAACAACATTCTCCAAG[C/T]ATCAACAAGATTACTCGTTAGGAACACCCTTCCTT Y 2 1 2 1 101000 r 74 goat snp31058-scaffold343-2237746 10 73447941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435561 Affx-122933380 AX-123305901 10 26027979 ATCCCACTGGTGAATCAAATTTCCTTCCAGCAGGA[C/T]GACTTAGAATGTGGGGTCACAGCACCGCACAGGCT Y 2 1 2 1 201000 r 74 goat snp31057-scaffold343-2199059 10 73408952 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786707 Affx-122950111 AX-385273738 10 26074952 CCTGGAAGAGGCAATCGGATGCCACCTTTGGAATA[C/T]AGAGATTCTGGTTCTGCCTTTTGCAGAGAAACAAG Y 2 1 2 1 101000 r 74 goat snp31056-scaffold343-2152086 10 73361886 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431968 Affx-122935957 AX-123302309 10 26121833 GTATATGTGTGAATAACTCTAATTATGAAAAATAA[C/T]GTATTGAACGACTTAAGGGAAATAAAAGATAACTT Y 2 1 2 1 101000 r 74 goat snp31055-scaffold343-2105205 10 73314994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769261 Affx-122967757 AX-385256434 10 26154574 TGCTCATTCAACAATTATTGGCTGAGCAACAACCA[C/T]GTGGTAGCTACTGATCAACACAGTAGATAGAAACA Y 2 1 2 1 101000 r 74 goat snp31054-scaffold343-2072464 10 73282329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432209 Affx-122936379 AX-123302550 10 26194188 CATGTGAAATCATTTTAAATATCATTTACTACAGA[A/C]AGGATATCCAGAATTTACCACATATTGTTTTTTGG M 2 1 2 1 101000 r 74 goat snp31053-scaffold343-2032850 10 73244722 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275507 Affx-1111834845 AX-519549079 10 26206629 CTTCTACTGCAGTGGTCC[A/G]TGTGCATCAGACTTCCCCAGAGGGCCTGTTAAAAC R 2 1 2 1 102000 r 74 goat GoatD01.056242 10 26206629 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468272629 Affx-1111832883 AX-519546340 10 26219091 CATACGCACAGGCGGAGGCTGGAGCACTATTCCAT[A/G]CATTCGGTTTTTTCCTCAAGCATATCATTATCATA R 2 1 2 1 101000 r 74 goat 10_26219091_AF-PAKI 10 26219091 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38379812 Affx-122976230 AX-123250170 10 26274783 AAAGAGTGGGGTTAATTTCAGTACTTAAAAATGAG[C/T]AAATATTCCAGAAAAGGCAAAACCATGGAGACAAT Y 2 1 2 1 201000 f 74 goat snp31051-scaffold343-1952255 10 73164277 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276365 Affx-1111835380 AX-519549895 10 26303176 CCACCCACTTCCCTTCCTGGTGTCAAAACTTGCTT[A/G]TCAGGGCCAGCTCACCCTTCCTGACACACAGGAAG R 2 1 2 1 101000 f 74 goat Random2.2K-1055 10 26303176 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449953 Affx-122922896 AX-123320288 10 26304610 ATGTGGTTCAGGTGGAGCAGCTGGTGTTGGCACTT[A/G]CTCAAACAGAGATCCAGAAGCAGCCCAGGCCTCTG R 2 1 2 1 102000 f 74 goat snp31050-scaffold343-1922428 10 73134449 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383441 Affx-122973466 AX-123253799 10 26354893 CAGTAAAGCAAAGTGTGCTTTGAATGGAAGGGACT[A/G]TTAGTTCAGTCGCTCAGTCATGTCTGACTCTTTAC R 2 1 2 1 303000 f 74 goat snp31049-scaffold343-1872145 10 73083947 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383253 Affx-122972743 AX-123253611 10 26397973 CTCAGCACCTTCAGGGGAAGAGCTGATAGGGTAGA[C/T]GTGAGAGTGAGCCCTCCTCACTGACACATGTACAA Y 2 1 2 1 101000 f 74 goat snp31048-scaffold343-1829065 10 73040933 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375567 Affx-122978749 AX-123245926 10 26459341 CTACTGTAAGTAATGATAAGGTCTTTCCCCCTGGC[A/G]TAAGCAGCAGGGTCCTTAGAAAACCATCAGAAAAA R 2 1 2 1 201000 r 74 goat snp31046-scaffold343-1767697 10 72979723 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766815 Affx-122945232 AX-385254139 10 26493304 CACTTGGCAAACTTGGCCATAAAAATGCAGTAAGG[C/T]ATTTCATTCTTCTCATCAACCATAACTTGATCAAA Y 2 1 2 1 101000 f 74 goat snp31045-scaffold343-1733734 10 72946373 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385981 Affx-122971524 AX-123256339 10 26526103 AGTTTTCCTGTCATAACCATATGAAGAAGGCCCAC[C/T]CTGTGTAAAACCTTGTGATCAACTGTATGTGTGGC Y 2 1 2 1 101000 r 74 goat snp31044-scaffold343-1700935 10 72913528 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381930 Affx-122974132 AX-123252288 10 26557108 CTGGTGTGAGTTCCTTACCCTCTCACAATGGGTAA[C/T]AAACAATTCGCAAGTAAGTACCAGTCCTCCAATGA Y 2 1 2 1 101000 r 74 goat snp31043-scaffold343-1669930 10 72882437 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380645 Affx-122975223 AX-123251003 10 26586913 CCGCTCCAGGGACTGGGCTGCTGTTTTGGTCTGAG[C/T]AGCTCTGCAAAAGCTGGCACAGGCTGCAGGAAATC Y 2 1 2 1 101000 f 74 goat snp31042-scaffold343-1640125 10 72852840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430372 Affx-122937783 AX-123300713 10 26620596 ATACTGACCCCTTTACAGTTTATGTGGATATTTGT[A/G]CTCTTCTGAGGCCTTCTCTGGGCAGAGGGAAGTTT R 2 1 2 1 202000 r 74 goat snp31041-scaffold343-1606442 10 72819093 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444511 Affx-122926504 AX-123314848 10 26649375 TCTCACCTCATATTATCAACACACAAACTTGACAG[C/T]GTGAACCACAACATATTTCAAAGTAGCTCCTCTGT Y 2 1 2 1 101000 f 74 goat snp31040-scaffold343-1577663 10 72790675 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767743 Affx-122928044 AX-385254972 10 26693103 ACCCAGTGCAGGCAAAAACAAGTAGATGAATAAAT[A/G]AAGAGTGCTGAATTATTCCCATAAAAAAGTTCCCA R 2 1 2 1 101000 f 74 goat snp31039-scaffold343-1533935 10 72747506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406294 Affx-122956072 AX-123276646 10 26736536 TTCTAATCCCAGACTTCCCCAAGAATAGTAGTGGA[A/C]CAAGAATAGACAAAGTTAATTTACATTTTATTTTG M 2 1 2 1 201000 r 74 goat snp31038-scaffold343-1490502 10 72703886 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385695 Affx-122971122 AX-123256053 10 26784347 CTGGCCCCAACTCAACTTTCCACCTGCTAGCTTAC[A/G]TCTGAAACTCCTTTAGCTAAGGAAAGCCTTTCATT R 2 1 2 1 201000 r 74 goat snp31037-scaffold343-1442691 10 72656342 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412937 Affx-122951467 AX-123283286 10 26830441 TTGTATGATTATTAGATTTTGTTTGCCCATGTGAT[A/G]CTACTATACATTTTTTATCTTTTTGGCCCACGCCT R 2 1 2 1 201000 f 74 goat snp31036-scaffold343-1396597 10 72610280 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273751 Affx-1111833788 AX-519547362 10 26852464 GACACTGTGTGAAAACTTAGAAATTA[A/G]CATATTCTTCATCCGAACTGACTTATGCTTTTCGT R 2 1 2 1 101000 r 74 goat GoatD01.005097 10 26852464 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770542 Affx-122921415 AX-385257706 10 26876426 GATAGTTTCTACTCAATTGATATATACCAGATTTA[C/T]TCAGAAATCATACCAGCTTTGAGATTCCTGATCAA Y 2 1 2 1 101000 r 74 goat snp31035-scaffold343-1350612 10 72564303 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391637 Affx-122966571 AX-123261994 10 26922319 AACAATATTCAAAAAGCCAACAGGTTGGGCCATCC[G/T]CATGAGGAGGATGAGCAGTTCCGGGCAACCACTGA K 2 1 2 1 101000 f 74 goat snp31034-scaffold343-1304719 10 72517808 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276367 Affx-1111835381 AX-519549897 10 26955933 ATGCAAAGAAATAGTTGAGTACTAATGAGTTTTGA[A/G]TATTTGTTACCCGTTTTAATATAATTTATGTAATT R 2 1 2 1 101000 f 74 goat Random2.2K-1056 10 26955933 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38387014 Affx-122969933 AX-123257372 10 26972551 CTGAAAATAAAATTTGACAGAAAATGCACATTCCA[C/T]TTTTCCAGTACCTAACTAGACATGATTTGCTGAGA Y 2 1 2 1 101000 r 74 goat snp31033-scaffold343-1254487 10 72467583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377904 Affx-122977240 AX-123248263 10 27003257 CCATTTAAGTAAATGCTCACAGGAGTAAAGCTAAG[C/T]CTGTTTTCTTCTTAATTACAGACCCTTGGTTTTTT Y 2 1 2 1 101000 f 74 goat snp31032-scaffold343-1223781 10 72436845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408374 Affx-122953726 AX-123278725 10 27044091 TGGTAATCAGACTGAATGTTTCTACTGAAGATCAA[C/T]AACTCCATGCCCTGTAGCTACTACTACCCCTACGA Y 2 1 2 1 101000 f 74 goat snp31031-scaffold343-1182947 10 72396071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389209 Affx-122969063 AX-123259567 10 27108431 TATTTTAGCAATAAGCCTCTCTTCCCTCTTCCCTA[C/T]TGCGGGACTCCTTGTGGAAATGGCCTTCCATTTGA Y 2 1 2 1 201000 r 74 goat snp31030-scaffold343-1118607 10 72331797 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275450 Affx-1111834906 AX-519549023 10 27148353 CAAAGAACTGGAAATGACAGCAACTGAAGAACACA[A/G]CATCCCCCAAGGAAAAGGGGATTCTGTCAGCAGAC R 2 1 2 1 101000 f 74 goat GoatD01.058139 10 27148353 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447047 Affx-122924525 AX-123317383 10 27159182 TCATATCCTTTGCTTTATTTTTTAAATCTGTATAC[A/G]ATTTTCTTTCCTGAATAAATTATATGTCCTAAAGG R 2 1 2 1 103000 r 74 goat snp31029-scaffold343-1067856 10 72281204 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392709 Affx-122966038 AX-123263066 10 27190331 ACTCAGCCCTTGTGCCAAGGAAGCTTGGAAGAGTG[A/G]GGAAGATATTGCCACTTGCAGCAATATGCATCTAA R 2 1 2 1 201000 f 74 goat snp31028-scaffold343-1036707 10 72250016 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769514 Affx-122975740 AX-385256684 10 27300958 TTCTCAAAATGCAGTCTCAGGTACACTTCAACAAA[C/T]AGTTTAACCATATTATATACCATAAAGCACATCTG Y 2 1 2 1 101000 f 74 goat snp31026-scaffold343-926080 10 72138138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439745 Affx-122930533 AX-123310082 10 27340354 AATTTCATTACAGGATAGTTGTGAGAAGGGTCAGA[C/T]AAGATAATATATATGAAATTGCTTCATAAATTCAG Y 2 1 2 1 101000 f 74 goat snp31025-scaffold343-886684 10 72098456 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403768 Affx-122957994 AX-123274120 10 27388610 TCAGTTATTACAGTGTGTAAACTTATCACAGATCT[A/G]CAGTCTTCATCTATAGATTTCCCTTAAAGCCTGAA R 2 1 2 1 101000 r 74 goat snp31024-scaffold343-838428 10 72050280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798541 Affx-122974797 AX-385285474 10 27442620 TCCCTCCTCTCTTTATCACAGCCTGCTTACCTTCA[C/T]TCATGGTAACAATTAAATGCTGCTACAAGGAAACA Y 2 1 2 1 101000 f 74 goat snp31023-scaffold343-784418 10 71995326 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395805 Affx-122963648 AX-123266160 10 27486572 ACCTGGGTATCAACCATCTCTGTGCTGACCCATCC[A/G]TAACAGCAGAATGGAAGCAGGCAATAAACATTGCT R 2 1 2 1 201000 r 74 goat snp31022-scaffold343-740466 10 71950843 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390578 Affx-122967199 AX-123260935 10 27542507 ATACCTGACTGTCTGAGAGGGTCAGGCCCAAAGAC[A/G]TCAAAAGGATGGAGCTGAACTGCGTTTCTTTGTGT R 2 1 2 1 101000 r 74 goat snp31021-scaffold343-684531 10 71894035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791661 Affx-122946688 AX-385278652 10 27578273 TGTTGAGTCAAACTGCATATTTTACTTAAACAATT[A/G]CCAATCCAAACACAATAGGAAGTATTATCTGTTTA R 2 1 2 1 101000 r 74 goat snp31020-scaffold343-648765 10 71858355 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377530 Affx-122977469 AX-123247889 10 27628300 TAAATATGGATCAAGCATGAACTACAGGAGGGAAA[C/T]GAGAAATTATGGATTAGATGGGAGATTAAAAATTT Y 2 1 2 1 101000 f 74 goat snp31019-scaffold343-598738 10 71807795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429945 Affx-122938082 AX-123300286 10 27672995 TAAATACTGAGACAGGCCCTGGTGCCAGCCCAAAA[C/T]ACAACTAGTCAACTCACATTTCCCTTGGCCTTTTA Y 2 1 2 1 101000 r 74 goat snp31018-scaffold343-554043 10 71762246 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445026 Affx-122926627 AX-123315363 10 27734128 TGCAGGAAACATTATTCTCCATCCATGGAAGAAAA[G/T]AGTTAAGATCTTTCTGTTTTTAACTCCCAACTAGT K 2 1 2 1 303000 r 74 goat snp31017-scaffold343-492910 10 71700516 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792387 Affx-122943109 AX-385279368 10 27800376 TCCCATATACTCTGTATAGTAATAATTTGTATTCT[A/G]CCTTCATTGTGCTTATCTAGTGTTTAATACTTCAA R 2 1 2 1 101000 f 74 goat snp31016-scaffold343-426662 10 71633646 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779067 Affx-122927960 AX-385266172 10 27838698 CAGAGAAGCCTTTCTGGGTCGAGCTAGTCCTAGAT[G/T]CCTAAGGACACACAAAAGCAGTGAGTTGTGTGATA K 2 1 2 1 101000 r 74 goat snp31015-scaffold343-388340 10 71594961 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452816 Affx-122920747 AX-123323149 10 27886353 ACTAAATGGCAGCTTAAGTTTAATCATGTAAACTT[A/G]AAAGTGAGATGTGCTTCTGGTGTGCCAGAGATTTC R 2 1 2 1 202000 f 74 goat snp31014-scaffold343-340685 10 71545643 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395893 Affx-122963616 AX-123266248 10 27963210 AACTTTCACTTTCACTTTGGTTACAGGAAGTTTCA[C/T]AGACAAACCATATTAAAAATTATCCCTCCTTTATG Y 2 1 2 1 101000 f 74 goat snp31013-scaffold343-263828 10 71467559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785237 Affx-122923824 AX-385272282 10 28012204 ATTGAAGACAGAAGCTAGTTCAGATTTTAATCATA[G/T]AGTAGCAGTTTTATGATGGAGTTGGGCCAAACTTG K 2 1 2 1 101000 r 74 goat snp31012-scaffold343-214834 10 71417974 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785617 Affx-122970156 AX-385272660 10 28092608 TCTCATAGAGAAACTCTGAAGTGCTATGACATAGG[A/C]TTAATGAGCAAATCTTTTGAAGGCATACTTTGGCA M 2 1 2 1 101000 f 74 goat snp31011-scaffold343-134430 10 71337988 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398921 Affx-122961005 AX-123269276 10 28136169 AGATTGTGTTTTATAGAATTTGTTTTTACTAATGA[C/T]ATAGATTTCACCCTCATTCTGAAATTTTCATTAAA Y 2 1 2 1 101000 r 74 goat snp31010-scaffold343-90869 10 71294479 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444056 Affx-122926858 AX-123314393 10 28168451 TAGCCAGCATAGAAAGAAAGCTTTACAAAAAGCAC[A/G]CCATAAATTAATTTCACTTTTTGTTTTGTTTATGT R 2 1 2 1 101000 f 74 goat snp31009-scaffold343-58587 10 71262212 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443684 Affx-122927174 AX-123314021 10 28205100 GACTACCAAGGAAGCCCCAAGAGGAGATGTTTTAG[A/G]CTTAACAGCAAAGAACTCTTACCTTCTACTGGATA R 2 1 2 1 201000 r 74 goat snp31008-scaffold343-21938 10 71225510 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776578 Affx-122975455 AX-385263705 10 28258983 AAATTGGCAAGTATAAGGAAGCATTCTTTGGTTCC[C/T]CTACACTGCTAACATTGAGTCTTACTCATCTTAGT Y 2 1 2 1 101000 f 74 goat snp58393-scaffold947-4585767 10 71171384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784356 Affx-122940113 AX-385271407 10 28308968 GCAACTTGGACTAAATAAAAAGAACTTTCTAATAA[C/T]TGCCATGCACTTTCACCATATTCTGAATTTCGCTT Y 2 1 2 1 201000 f 74 goat snp58392-scaffold947-4535782 10 71121009 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404454 Affx-122956744 AX-123274806 10 28392338 TACCACTCAAAAGATGTTTTAAGGGAAAAATGCAT[A/G]CACATGTTCTGATGGCTGTGGTCCTACGAGTGTGA R 2 1 2 1 101000 r 74 goat snp58391-scaffold947-4452412 10 71036812 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377651 Affx-122977860 AX-123248010 10 28423831 TTTATTAAAACTGTATATATTATGTTTTATCTGTG[A/C]TTATGGCCCAGCTTTCTTCCACCTGTCCCCTAAAC M 2 1 2 1 101000 r 74 goat snp58390-scaffold947-4420919 10 71005181 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396148 Affx-122963389 AX-123266503 10 28466887 CTACCACGAGTCCGACTGCCACTCCCTGAGAGAGA[C/T]AAACAGCCTGACCTGTAGTAACACTGAGAAAAAAA Y 2 1 2 1 101000 r 74 goat snp58389-scaffold947-4377863 10 70962497 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393481 Affx-122965829 AX-123263837 10 28497480 TGAGAGAGAATTAAAAACATTCTGGAATATTGTAC[A/G]TGGTATATTCAGTAACACATGGTCATCACTGACGA R 2 1 2 1 101000 r 74 goat snp58388-scaffold947-4347270 10 70931746 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420163 Affx-122945580 AX-123290511 10 28540690 CAAGACAGATATTTCCAAGCTTATTTTACAGATGA[A/G]GACTCTCAGACTCTGAGAAGTTAACCATTTGTTCA R 2 1 2 1 103000 r 74 goat snp58387-scaffold947-4304060 10 70889864 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802158 Affx-122959134 AX-385289062 10 28626292 GTTAAATTTATACCCAGAAGCCCTGAATTGGAGTT[C/T]AACTATTTCTATAATTCCCTAGGCTTATGTTCATC Y 2 1 2 1 101000 f 74 goat snp58385-scaffold947-4218458 10 70804021 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782287 Affx-122947567 AX-385269365 10 28682906 TTACACCAGGTACCTGTAAATCAAGGAAAAAATAC[A/G]TTGTGCTACAAGCAGGACTTAGTGGAGGAATACTT R 2 1 2 1 101000 r 74 goat snp58384-scaffold947-4161844 10 70748871 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784514 Affx-122948591 AX-385271563 10 28714959 CTAAAGGAGAAAAACAAATCAACATAGCTCTGCAA[C/T]AAATATTCTAGAATGACCAAAAATGTCAATACATA Y 2 1 2 1 101000 f 74 goat snp58383-scaffold947-4129791 10 70716777 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272581 Affx-1111832885 AX-425508318 10 28726161 AGATGTGGGAGACCCAGGTTCGATCCCTGGGTTGG[A/G]AAGATCCTCTGAAGAAGGAAATGGCAACCCACTCC R 2 1 2 1 303000 f 74 goat 10_28726161_AF-PAKI 10 28726161 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426236 Affx-122940345 AX-123296582 10 28769331 CCGAGCTTACAAATGAGATTTCTATGCTCCTGACT[C/T]GGTGCTGTTGGGCATTGTTCATGTGCTGTATGGCT Y 2 1 2 1 101000 f 74 goat snp58382-scaffold947-4075419 10 70662397 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783565 Affx-122945095 AX-385270627 10 28822957 TGGGAAATGAATAAACACTTAAAGATTCTATGTAG[C/T]AGATAAATGCAGAATCTTTACAAGGCAATATGTTA Y 2 1 2 1 201000 r 74 goat snp58381-scaffold947-4021793 10 70608732 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436895 Affx-122933220 AX-123307233 10 28878941 AATGGTGCATTTCATTTATTAGATGGATCCTTCTA[C/T]GGTAGTGATATTATTAATAACTATATAATGTACAA Y 2 1 2 1 101000 f 74 goat snp58380-scaffold947-3965809 10 70552757 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276517 Affx-1111835382 AX-519550028 10 28909791 GAGTAATGATAATTCAACATAACTTGTATTTATAC[A/G]GTACCATTTACAAACATTTCTGATTGTAAAATTCA R 2 1 2 1 101000 r 74 goat Random2.2K-1057 10 28909791 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443054 Affx-122928139 AX-123313391 10 28917779 CAGCTCCTTTTCTAATGTCTGCAATCTTTTCCTGG[C/T]GGCCAGTCACTTAGTCCCCCTAAGCTGGACTCTCT Y 2 1 2 1 101000 f 74 goat snp58379-scaffold947-3926971 10 70513903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377436 Affx-122977538 AX-123247795 10 28950423 TAAAGAAATAAAAAAAAATACTTTTAGTTTGATTT[G/T]TGTAAGTCTATAATTAAATGGCTTCATTTTATGTA K 2 1 2 1 101000 r 74 goat snp58378-scaffold947-3894327 10 70481222 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426182 Affx-122940582 AX-123296528 10 28979406 CAAATTTCATTTTTTTCCAACGATACTGGAAGGTC[A/G]TTAGTGTACCAGCCTCCATACTGTTTTAGGTATGG R 2 1 2 1 101000 f 74 goat snp58377-scaffold947-3865344 10 70452276 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388134 Affx-122969475 AX-123258492 10 29014097 CAGCATTACCAGTGCAGAGCTATGCATCCCTGTGA[C/T]GAGGCCGTGTTTTCATTTTTGTTATTTGCAGAATT Y 2 1 2 1 201000 f 74 goat snp58376-scaffold947-3830653 10 70417665 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411765 Affx-122951493 AX-123282115 10 29060934 TTGGCCATTAATCACAAACCCAGTCAGCTCTCAGC[A/G]CCCACGCCACTGTGAAAGTTGGGTCATGAGCAGAG R 2 1 2 1 201000 f 74 goat snp58375-scaffold947-3783816 10 70370715 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383499 Affx-122972651 AX-123253857 10 29103681 ATGCCGTTACCTCCTCTACCTCCTTTGACACGTGC[A/G]TCTGTGCCCGTATACCCACCCTTTTCGGCACAGAA R 2 1 2 1 201000 r 74 goat snp58374-scaffold947-3741069 10 70328109 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383889 Affx-122973122 AX-123254247 10 29138365 TGAGGAGGGCAGATTGTCACAATCTGGGTATAGGA[C/T]GCTGAAGGTGGTTTGTGACTATCAGAAGTGTGAGA Y 2 1 2 1 101000 f 74 goat snp58373-scaffold947-3706385 10 70293405 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425266 Affx-122940979 AX-123295612 10 29183136 GTATTATTACCTATATTGAAGGCCCAGATAATTTA[C/T]AGAGAAATTGATATATTAAAATGGAGTAAAGATCA Y 2 1 2 1 101000 f 74 goat snp58372-scaffold947-3661614 10 70248230 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395414 Affx-122963949 AX-123265769 10 29211717 CCTGGGTCTCCCGCACTGTAGGCAGATTCTTTACC[A/G]TTGGAACCAACAAGGAAGCCTGAAGATGGGCCAGG R 2 1 2 1 303000 r 74 goat snp58371-scaffold947-3633033 10 70219640 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451509 Affx-122921112 AX-123321842 10 29243215 TAGGATTAGCTTTTTCATTTTCAAACTCACACAAA[C/T]ACATACAGACACACAGTGGAAAGGATTGATATCTT Y 2 1 2 1 201000 f 74 goat snp58370-scaffold947-3601535 10 70187818 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792485 Affx-122940008 AX-385279466 10 29280651 ACTTTGCACTGCAGAAATTATTTTTGTCCAAATAC[A/G]TTAGCTTGCTTTCAAATCTCTTAATTTCAGATTTT R 2 1 2 1 101000 f 74 goat snp58369-scaffold947-3564099 10 70150128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454187 Affx-122919303 AX-123324520 10 29330934 CACAGGTGGCCCCCATGTTGAATGCACAGCCACAG[C/T]GTCTGTTATTGAGAGCTGCAGTCAGACCTCACTTG Y 2 1 2 1 101000 r 74 goat snp58368-scaffold947-3513816 10 70099526 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410953 Affx-122952033 AX-123281303 10 29405205 TGAAGAGGAAAACCCATCCTCCAGAAGCTGGACCC[A/G]TTGCCTGTGTAGATCAGCATCTGACTGGAGAACAT R 2 1 2 1 101000 r 74 goat snp58366-scaffold947-3439545 10 70026727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796508 Affx-122920502 AX-385283457 10 29464705 TTAAATATTAAATCCATTTAAATGCAATAAGTTGT[A/G]TGGAGAATTTTCATCTTTATTTCAGAGTCATGCTA R 2 1 2 1 101000 r 74 goat snp58365-scaffold947-3380045 10 69967295 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428284 Affx-122939392 AX-123298627 10 29494051 TTTTCTATTAGAAGATGGGTATTTTCTGAGTTTCC[A/G]CAGGAGGAAAATATTAGATTTCAATGTGCCTCCAT R 2 1 2 1 101000 r 74 goat snp58364-scaffold947-3350699 10 69937521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449827 Affx-122922397 AX-123320162 10 29540194 TCTTGGCATGATTCTAAGAATTTAATTTAGAAAGC[A/G]TAGTTCTAGAAACAGTCATTGTCAGATGCAATGCA R 2 1 2 1 101000 r 74 goat snp58363-scaffold947-3304556 10 69891924 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787924 Affx-122933083 AX-385274946 10 29661786 CACATTGTCTCAGAAAAAATCCATTCAGTCTCTAA[A/G]CATTAACAAGCCTAGACCTCCCTCGGTAAGGATAG R 2 1 2 1 101000 r 74 goat snp58361-scaffold947-3182964 10 69769637 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424276 Affx-122941990 AX-123294622 10 29708736 TAACATGGCTTTAAAAATTCTGCTTATCTCACCCC[A/G]AAAGTTGTTTTATGTTTTTGAAAATAAACTACAGT R 2 1 2 1 101000 f 74 goat snp58360-scaffold947-3136014 10 69721851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802103 Affx-122936553 AX-385289007 10 29750142 CCTAGAAGGGAGAGATTTTTCTGAGAGATGCAGCA[C/T]GTATAACCTCTCTTGACATCAAGGACACAGACAAA Y 2 1 2 1 101000 f 74 goat snp58359-scaffold947-3094608 10 69679557 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442062 Affx-122928385 AX-123312399 10 29787268 CATTAGAGAACAAGGTTAGGCAGGCAGGGCTTGAG[A/G]CAGTTTTGGCAAGGGCAGTTCAGCAGTGATGGTTT R 2 1 2 1 201000 r 74 goat snp58358-scaffold947-3057482 10 69642549 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387191 Affx-122970608 AX-123257549 10 29868450 TGTATCCGAGTTCTGTATCTTATGCATATTTTCTT[A/G]CCTGCTTCATAATCCAGATGAACCCATTCTTATCT R 2 1 2 1 101000 r 74 goat snp58356-scaffold947-2976300 10 69561325 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419506 Affx-122945453 AX-123289854 10 29906516 TGGGTAGTAATGACTGTGTAGTTTTCCTTGCATAC[C/T]CAGCGGCCTTGTAGGCAGCTTCATAACTGTTTCAT Y 2 1 2 1 101000 f 74 goat snp58355-scaffold947-2938234 10 69523046 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779768 Affx-122934845 AX-385266868 10 29942401 GTCATTTCTCACTGACAAAGGCTCTGTAATCATCC[A/G]GCATAGTCTACAAATAAGCCCACTGGCATATTTGA R 2 1 2 1 101000 f 74 goat snp58354-scaffold947-2902349 10 69487142 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382351 Affx-122973876 AX-123252709 10 29983230 CTATTAGACTGGGAGAACCATTAGGCCCTGGTGGT[A/G]TCTGAGACAGGATGACATTTGTTGTTTGTGTTCTG R 2 1 2 1 101000 r 74 goat snp58353-scaffold947-2861520 10 69446965 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405023 Affx-122956371 AX-123275375 10 30031251 GTAATTCAGAGAGGGCTCCCAAGTTGGTTGTTCTT[A/G]TTACAGAAAGAAAAAAGCAGAACATTTTAAGTCTT R 2 1 2 1 101000 f 74 goat snp58352-scaffold947-2813499 10 69397957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407468 Affx-122954775 AX-123277819 10 30074243 CCATTTAGACAATTGTCAAGAGAGTTGATACAAAG[C/T]GTTTCTCGGTACTTTTCAAAACAAAACAAACAAGA Y 2 1 2 1 101000 f 74 goat snp58351-scaffold947-2770507 10 69354939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381189 Affx-122974541 AX-123251547 10 30127086 CCAGATGGCCTTTTTTTAATCTAGCTCTTTATGGA[C/T]GGCCCATAGGTTAGAAACACCAAATAGTATGCTGC Y 2 1 2 1 101000 r 74 goat snp58350-scaffold947-2717664 10 69301556 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415005 Affx-122949036 AX-123285354 10 30158255 TGTCCTTATAATGCCACTACATTCCTCACTCAAAG[A/C]GCCATTCTGCTGATGTGGTAAAAAAAAATATGCTC M 2 1 2 1 101000 f 74 goat snp58349-scaffold947-2686495 10 69270246 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771372 Affx-122949415 AX-385258530 10 30191647 AATAAAGAAAACAGAATAGCCTACATTGCTACTCC[C/T]CTGGTTCCTTGGTTGGACAAAGTTTATTGCTCTCG Y 2 1 2 1 101000 r 74 goat snp58348-scaffold947-2653103 10 69236972 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451571 Affx-122921692 AX-123321904 10 30226001 AACAGGGTAGTCCAAGGCATATCACAGGCTGACGC[A/G]TATATTGATCAAGGCTGGAGGGCTGGTTCAACAGG R 2 1 2 1 202000 f 74 goat snp58347-scaffold947-2618749 10 69202561 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792229 Affx-122971068 AX-385279213 10 30268043 TAATCTATATAAGGGGCCTATTAATGTACAAAGAT[A/G]TAAATTGTGACAATAACAACATAAAAGGTAGCGGA R 2 1 2 1 101000 r 74 goat snp58346-scaffold947-2576707 10 69160642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766237 Affx-122960778 AX-385253633 10 30318253 CATTACGTTTCTCTTTTCTTTAGGAGATACCCACG[C/T]GATTTATTCAATTTTTCTAAACACTCTGACCTACG Y 2 1 2 1 101000 f 74 goat snp58345-scaffold947-2526497 10 69109804 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386832 Affx-122970091 AX-123257190 10 30364060 AGGAGGCCCCATCCCTTTATCTTGGCCCCTCCCTG[C/T]TAGGGACTGAGCAATGCTAGACTCTCCCAACTGTC Y 2 1 2 1 101000 r 74 goat snp58344-scaffold947-2480690 10 69063772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777666 Affx-122971693 AX-385264785 10 30393347 ATGGTCCTGCTACAATGATAAGAAGTCTCCCTTTC[A/G]CTTTCAAAATTCTCCAGATTCTAAATTATACGGCT R 2 1 2 1 101000 f 74 goat snp58343-scaffold947-2451403 10 69033857 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423794 Affx-122942820 AX-123294140 10 30439826 TGTTCTCCCAGAGCTGATTTTTGCGTGTGTATTAG[C/T]GAGTGGAGAGGGTGGATGTTCAAGAGACAATAACA Y 2 1 2 1 101000 f 74 goat snp58342-scaffold947-2404924 10 68987160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801386 Affx-122961793 AX-385288297 10 30471798 AAGATGACACTCAAGTAGTTATTTAGAATACTATG[C/T]CTAATGTACCTATCAAGAAGTAAGCACTGCTATCT Y 2 1 2 1 101000 r 74 goat snp58341-scaffold947-2372952 10 68955283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418394 Affx-122946555 AX-123288742 10 30539114 CTAGATTCTATTCTATGCATATTTATGTTCTGCAA[G/T]CATATTAACTTTTTCTGGTAGGTTGGCTATAATTA K 2 1 2 1 101000 f 74 goat snp58339-scaffold947-2305636 10 68887807 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392743 Affx-122966013 AX-123263100 10 30581366 AGCAGGAAATGCAGGGCAAGTACCAGCTTCAAGGA[G/T]AACTTAATGTTCATTTTAACTTGTTTTCAACTGCA K 2 1 2 1 101000 f 74 goat snp58338-scaffold947-2263384 10 68845694 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442174 Affx-122928808 AX-123312511 10 30621649 TATGACAAAACTGAGGCAGGGAGCCAATGAATTAC[A/G]CTTTCCTACTATTAATACATCACAAGTTGGCTTGA R 2 1 2 1 101000 f 74 goat snp58337-scaffold947-2223101 10 68805546 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417373 Affx-122947707 AX-123287721 10 30655698 TTTCAGTGGTTCAGTATCTTTAGTTCCCCCCACCC[A/G]CCACCCTCTTACCATGGTGAGGATAGAACCACCGC R 2 1 2 1 202000 r 74 goat snp58336-scaffold947-2189052 10 68771616 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803725 Affx-986696197 AX-385290486 10 30675431 CCAAGTCCAAACACAACATGACTTGAAAGGGCTAT[A/G]TATCTGTTGCATCACACAATAAGCCAAATATTTCT R 2 1 2 1 600010 r 74 goat 10_30675431 10 30675431 Ancestral_priority_1043 ancestry 0.758 recommended IMAGE 10K 10K ancestral 320765255 Affx-986697298 AX-385252791 10 30675478 TCACACAATAAGCCAAATATTTCTTATAACTTCGA[C/T]AGTGATTTAAAGCAGTTCATAATTAAATATGAGCA Y 2 1 2 1 600010 r 74 goat 10_30675478 10 30675478 Ancestral_priority_1043 ancestry 0.708 recommended IMAGE 10K 10K ancestral 320762770 Affx-986697300 AX-385250822 10 30685549 CCTTTTCCATGGACACATTTGTAATCAAAGTCCCC[A/G]AGGGCCCTCGACACAGCCAGAGAGCCATTCACACG R 2 1 2 1 600010 f 74 goat 10_30685549 10 30685549 Ancestral_priority_1043 ancestry 0.516 neutral IMAGE 10K 10K ancestral 320762772 Affx-986697302 AX-385250824 10 30685807 TCAGCACCGTGTTTCTTCTCCGACATAACTCTCAT[A/G]TGTTCATCAATCTCCAGGAAACCTGTTCTGATTCC R 2 1 2 1 600010 f 74 goat 10_30685807 10 30685807 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38439150 Affx-122931075 AX-123309487 10 30692646 GAGCTCTCACTGTGAGCCTTAGGGCAATGAGGCAA[A/C]CTCTCTTTGCTTCTGTGTCTTGATCCATTAAAAGG M 2 1 2 1 201000 f 74 goat snp58335-scaffold947-2152104 10 68733974 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438246 Affx-122931427 AX-123308584 10 30723170 AGATACTTATCATTTTCTTGGTTCCAGTGGACCCT[A/C]TTCTATTGATCCATCCTTAAGTGTGTGATTTACTG M 2 1 2 1 101000 r 74 goat snp58334-scaffold947-2121580 10 68703798 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406078 Affx-122956237 AX-123276430 10 30819740 CCTATGCCACAGGGCCCACGCTGGTCTCATTCTGT[C/T]GACACTGATTTCTGAACGTCCAGCCACCTAGATTT Y 2 1 2 1 101000 r 74 goat snp58332-scaffold947-2025010 10 68607143 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415427 Affx-122948721 AX-123285776 10 30849310 ATTTGAGAAAAGAAATAAATAGTACCTTTGCAGGC[A/G]CATATTATGCCGCCTGAAGAGAAGTTGAAAAATGA R 2 1 2 1 201000 f 74 goat snp58331-scaffold947-1995440 10 68577669 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787142 Affx-122949923 AX-385274168 10 30901924 CAGTAGAATTACCCTTTGTTCATCTATCTTCAAAC[A/G]TCTTCTGACATGCCCTGAGGACATTTCATAGCTGA R 2 1 2 1 101000 r 74 goat snp58330-scaffold947-1942826 10 68525115 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438781 Affx-122931377 AX-123309118 10 30954826 TGTGTTCTTAGGTGGTAAATGTATCCAGAATTCTT[A/G]CCTGGAAATTCCATGGACAGAGGAGCCTGGAAGGC R 2 1 2 1 101000 f 74 goat snp58329-scaffold947-1889924 10 68471157 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276519 Affx-1111835383 AX-519550030 10 30979908 AATTGGTGTCATATCTTCAGTTCCAGCTCTTTTAT[A/G]GCACTATATGCATTTGCATTTACACTGGGTAAGCA R 2 1 2 1 101000 r 74 goat Random2.2K-1058 10 30979908 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769810 Affx-122929791 AX-385256980 10 31012355 CAGGACCTGAATTGAATGCCTATATTATACTTGTG[C/T]AAATCAAATGCATAATATTTTATGCAGTCTCAATC Y 2 1 2 1 101000 r 74 goat snp58328-scaffold947-1832395 10 68413740 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377145 Affx-122978226 AX-123247504 10 31050275 CTGAATAGGAAAGGCATTGAAGTGTTAACAAATCT[C/T]TAAGTATTGTTCTTTTTCTCACTAGAGTCCCATGA Y 2 1 2 1 101000 f 74 goat snp58327-scaffold947-1794475 10 68375054 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770114 Affx-122924026 AX-385257281 10 31089780 TTGCCAGACATTGTAACCTACATTTTCTCAGTTAA[C/T]GCTTTCAATAGCTCTATCCTTGCTTTAAAGAAGAT Y 2 1 2 1 101000 r 74 goat snp58326-scaffold947-1754970 10 68335892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435649 Affx-122933349 AX-123305989 10 31126664 AAGAAAGCTAGACAGACAGATAGACAGATAACATG[C/T]AGAAATAATATTTTGGATGCATTGGGTTAAATTGA Y 2 1 2 1 101000 f 74 goat snp58325-scaffold947-1718086 10 68298665 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449272 Affx-122923030 AX-123319607 10 31155957 TGTGCGAAACTTTCTCTGAACACACCATTCCCTCA[C/T]ATGTCCTGCAACTTTTGATTTCCTTATTTCCTCTC Y 2 1 2 1 101000 f 74 goat snp58324-scaffold947-1688793 10 68269006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787917 Affx-122931885 AX-385274939 10 31189625 GTGAGCCAATAAAAGCCTCCACAACCCACAAAGGT[C/T]GAAACATCTCTCCCATGCATAAAAATCCAAAGCCA Y 2 1 2 1 101000 f 74 goat snp58323-scaffold947-1655125 10 68235387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386741 Affx-122970139 AX-123257099 10 31224929 CGAACTCTCTGCTTTCTTTCTGCCTCTGGAGGTCA[C/T]AGGCTCCTGGATCCCAGCTCTGTAGATTTTGTATT Y 2 1 2 1 202000 f 74 goat snp58322-scaffold947-1619821 10 68199927 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786111 Affx-122952059 AX-385273147 10 31257144 TTTGTCAGGTATGGATCTATAATCATTGGAAAGAA[G/T]AAAAGATATTTTGTAGAAGAAGGCTCAGGGCTATC K 2 1 2 1 102000 r 74 goat snp58321-scaffold947-1587606 10 68167372 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272583 Affx-1111832886 AX-519546297 10 31271006 CTCAGTAGATCTCTGAACCTCACAGAAATTTGGCT[A/C]TTTGAGGATTGTTCATAAAAGGATTAGAATTCTTG M 2 1 2 1 101000 f 74 goat 10_31271006_AF-PAKI 10 31271006 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795111 Affx-122943156 AX-385282069 10 31316149 CCCTAAAAAATATAAGCCAACTTTACTTCATTTGA[C/T]AATACTGAGGCACTAACCAAAATTGATATTGACAA Y 2 1 2 1 101000 r 74 goat snp58320-scaffold947-1528601 10 68108470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425468 Affx-122941501 AX-123295814 10 31376263 CAATACCTAGTATAAGATCGATGCTGCTTAAATAG[C/T]ATAAATATGCTGAAAGTAGTTTGTGTAAATAGTGG Y 2 1 2 1 101000 f 74 goat snp58319-scaffold947-1468487 10 68048662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772158 Affx-122930525 AX-385259313 10 31419617 CAACTGAGCTATCAGGGATTTATGATTAATTAAAT[C/T]ACACAGCCTGATCAGGCTAACAGTTGGTAATTTTC Y 2 1 2 1 101000 r 74 goat snp58318-scaffold947-1425133 10 68005609 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424305 Affx-122941969 AX-123294651 10 31456656 AAGAACCAGAGATGGTTGGGCATTTTTCTGCTTTC[A/G]TTTTTATTTAGCAAATCCTGACAGGAAAGTGGCAC R 2 1 2 1 201000 r 74 goat snp58317-scaffold947-1388094 10 67968295 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398981 Affx-122960960 AX-123269336 10 31489809 ACCACCAGGGAAGTCCCTCAAAGGGAGATGTTGAG[C/T]ACGCAGAGGGCTATTCAGATTTGAAACTCTGCAGA Y 2 1 2 1 101000 r 74 goat snp58316-scaffold947-1354941 10 67934978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400571 Affx-122960414 AX-123270926 10 31563894 TTGATCTTTATTTAGACCTAGAAAATGGGGCTTGG[C/T]GGTGGAAGGGGGTCAAGTCTCTGAACTTTGGTGAG Y 2 1 2 1 101000 f 74 goat snp58314-scaffold947-1280856 10 67860184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395140 Affx-122964129 AX-123265495 10 31611605 AATGGTGACCCCCTTGGAGAGAGGAATGGGTTGAG[C/T]ATGCTGTTTCTTCCCCTAGACTCACCAATCAGATA Y 2 1 2 1 101000 r 74 goat snp58313-scaffold947-1233145 10 67812462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425347 Affx-122941588 AX-123295693 10 31698747 GAGTCCAAGTGTGGTTTTCGTGGAGCACTGGGCTG[C/T]AGTCCCATGCCCAGAACACGCAGTCCTTGGGAATA Y 2 1 2 1 201000 f 74 goat snp58312-scaffold947-1146003 10 67724319 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411484 Affx-122951790 AX-123281834 10 31747815 CTGTCCCTTACTCTGCCACATTCTTCTAGCTCCTC[C/T]AATTTAACAAGCAGTGAAGCTCACCAAATGGGTTT Y 2 1 2 1 101000 r 74 goat snp58311-scaffold947-1096935 10 67675153 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765216 Affx-122957111 AX-385252755 10 31781286 GTTGACCAGATGTTGGCACTGACTTGTGTACAGCC[A/G]TTGCACTTTTAAGATAAGGAACATTATAACAACAG R 2 1 2 1 101000 f 74 goat snp58310-scaffold947-1063464 10 67641504 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414988 Affx-122949050 AX-123285337 10 31818487 CTATGCCTCCCAGCGGGAGGCTGAGCTGCATGCCA[C/T]GCTGCTGTCCATGGTGATGGTCTTCATCTTATGCA Y 2 1 2 1 101000 r 74 goat snp58309-scaffold947-1026263 10 67603833 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375511 Affx-122979123 AX-123245870 10 31907638 TAAACAGAACAATTAATTAAATAGCCACTATCCTG[A/C]TTTGCATGAGGCTTAGGAGCATTCTGACTGTGAAT M 2 1 2 1 101000 f 74 goat snp58307-scaffold947-937112 10 67514111 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381545 Affx-122974835 AX-123251903 10 31943364 GGTTGCCATTTCCTTCTCCAGGCTAGTCCTGTTAG[C/T]GCGCTAACAGCAGTGGTGTGTGAGCGAACCTGCGG Y 2 1 2 1 201000 r 74 goat snp58306-scaffold947-901386 10 67477925 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790573 Affx-122963544 AX-385277576 10 31989033 AAGGCTTTTAATTATGGGTTTATCTTTCAAAGATA[C/T]ACATTAGAGAAATCACGTTACTTGCGGACCAAAAT Y 2 1 2 1 101000 r 74 goat snp58305-scaffold947-855717 10 67432133 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423302 Affx-122942637 AX-123293648 10 32089942 TGATATTTAGCTAGATGGGCCATTCTCCGCCATAC[A/G]TATTTCTGAACTCCTCTGGAGTCCCGTGGGTACAG R 2 1 2 1 101000 f 74 goat snp58303-scaffold947-754808 10 67331443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410881 Affx-122952596 AX-123281231 10 32144716 ATAAGGATAGGGATTTTTGTGTTTTTGTTACACCT[A/C]GTACTTTGTAGGCGGTTAATAAATATATCTCGCAT M 2 1 2 1 201000 r 74 goat snp58302-scaffold947-700034 10 67276519 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782558 Affx-122953890 AX-385269632 10 32175579 TCTTCTTGCTATTTGCATTCAATAAACAAAATTAG[C/T]ATGTCCCTTTTATCTAGAAAATGCTACCTATTTTC Y 2 1 2 1 101000 r 74 goat snp58301-scaffold947-669171 10 67245671 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421756 Affx-122944363 AX-123292103 10 32206709 CAGGCTGCACACATAGACATTTTGATTGAGCTGTG[C/T]GGTGTGGGACCACGTGGCCTGTTTAGTCATAAAAA Y 2 1 2 1 101000 f 74 goat snp58300-scaffold947-638041 10 67215173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453861 Affx-122919529 AX-123324194 10 32293339 CCAAGAAGTATGAAAAGAGAAACGATCAACTTACA[C/T]AGCCTGACGTAGAGTTCTTAGAATGTATTTTTGTT Y 2 1 2 1 101000 f 74 goat snp58298-scaffold947-551411 10 67128471 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397747 Affx-122962533 AX-123268102 10 32321871 TGTTAATTTCTGCAACACAGAAACTGTACAAAGTG[C/T]ACCCTCCCAACCTATGTCAAAGTCCATGACACTAA Y 2 1 2 1 201000 f 74 goat snp58297-scaffold947-522879 10 67100479 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800577 Affx-122938674 AX-385287496 10 32359869 CTCAGCTGGAGCAATGAAATCCTCTAGGATTCCAT[A/G]TAGTATCCCACGGTTCATCCAAGCAATTCAAAGAA R 2 1 2 1 101000 f 74 goat snp58296-scaffold947-484881 10 67062439 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442231 Affx-122928300 AX-123312568 10 32389320 TTGCTACTCTGTTCCCATAAATAGAACCAGCATTT[A/G]GGGTGGGTCCTGGTTGCCCTGAAAATACTCAACTT R 2 1 2 1 101000 f 74 goat snp58295-scaffold947-455430 10 67032897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389902 Affx-122968119 AX-123260259 10 32437737 AGGCCTGGCACAAGGAAGTAATTAATAAACTATGA[A/C]TGACCTTTGCACCTACAAAAGAATGATTTCATAAA M 2 1 2 1 101000 f 74 goat snp58294-scaffold947-407013 10 66984272 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384999 Affx-122971881 AX-123255357 10 32471313 TTTAACAAAGGCCATTTGATCATTTTGCTCTCTCT[A/C]TATATATACATAAACACATTTTTTGCTGAACCTTT M 2 1 2 1 103000 f 74 goat snp58293-scaffold947-373437 10 66950556 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447459 Affx-122924362 AX-123317795 10 32502121 TCCAGAGGGAACAGCGGAGCACTCATTGGCAGTGA[C/T]GGCGGCAGCAAGGAGGTATCTAGGGAGGGAAAAAG Y 2 1 2 1 201000 r 74 goat snp58292-scaffold947-342629 10 66919812 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463084698 Affx-1109805691 AX-514572124 10 32516727 TTTAAAATGCCATGAAAAGAAATATCACCAAAGAA[A/G]GAAAAAAACAGTTTTAAGGAGAGGTCTCACAAAGC R 2 1 2 1 101000 r 74 goat Random2.2K-1059 10 32516727 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38440436 Affx-122929411 AX-123310773 10 32540781 GTCCAGTACTTTCACCATAAGTGTCCTTGCAGAGA[C/T]ATCTCTCCTACAAACACTTTTGCTGCATAACTAAC Y 2 1 2 1 101000 f 74 goat snp58291-scaffold947-303969 10 66881104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437803 Affx-122931681 AX-123308141 10 32656826 AATGTTAACCCATTAGAGCAAAGCATCTAGGGCTC[A/G]TCCAGACCACTCCCCTCATGTGTGTGTGATAGAAG R 2 1 2 1 201000 f 74 goat snp58288-scaffold947-187924 10 66764471 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408307 Affx-122953773 AX-123278658 10 32704284 GTCCTGAGGGCAGTGTTGCAAATTGAGGCAAAAGA[C/T]ACCCTGTTCTCCCTTCCTCTTCCTCTCAACCAGTT Y 2 1 2 1 101000 f 74 goat snp58287-scaffold947-140466 10 66739256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443041 Affx-122928150 AX-123313378 10 32737353 TCGAGATTCTAGTATAGTAACAAAGTTTGCTCCAA[C/T]AACAAGAATAACATTTTGAGCACTTAACCCTACAC Y 2 1 2 1 201000 f 74 goat snp58286-scaffold947-107397 10 66706422 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444923 Affx-122926239 AX-123315260 10 32774711 GATTTACCTCTTGTTCCAAACCCACCATCTCACTC[A/G]CTGTGTCTCTACCATGTGACCTCTCTCTACTTTTC R 2 1 2 1 201000 r 74 goat snp58285-scaffold947-70039 10 66669083 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379789 Affx-122975833 AX-123250147 10 32824744 AAGGAGGAAGCTGGAAAGAGCTAGGATGGGTCTAT[C/T]GAGTGGGCATCAAAAGAATGCAGGCAAAAGACCTG Y 2 1 2 1 101000 r 74 goat snp58284-scaffold947-20006 10 66619056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385074 Affx-122971812 AX-123255432 10 32867175 CATAGAATTGGTTAAATAAATTTTGTACATCACTA[C/T]GTTGAACTAGGTGACCATCAAAAATCATATCTTTT Y 2 1 2 1 101000 r 74 goat snp16072-scaffold1690-806329 10 66577685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276521 Affx-1111835384 AX-519550032 10 32890562 ACTAAGACTGAAGTCCAGATGCCAGAACAGATAAA[A/T]AGTATGATATCAATGTTAAATGTACTCAAGTTGAT W 4 1 2 1 201000 r 74 goat Random2.2K-1060 10 32890562 A T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800385 Affx-122974609 AX-385287307 10 32907349 ATGTTACTCTTAGATGTCCACATGACCTGCTGTCT[A/C]TTGAATAAGAATGTGGAACAGGGAAATTTTCAGGT M 2 1 2 1 101000 f 74 goat snp16071-scaffold1690-766155 10 66537497 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401063 Affx-122959645 AX-123271416 10 32950081 GAAATTATTTAGATTTATTCATATTATTCACATTC[A/G]TTTGTCATTGATGTTCATCCCTTCTTGCATATTTG R 2 1 2 1 101000 r 74 goat snp16070-scaffold1690-723423 NW_017198550.1 4795 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762776 Affx-986697306 AX-385250826 10 32951663 CTACAATGGAAAAGCTTGATAATATAAAGCCCTGG[A/C]GAGGATATGGAATGACTGGAACTCTTATACACTAG M 2 1 2 1 600010 f 74 goat 10_32951663 10 32951663 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 320765272 Affx-986697308 AX-385252804 10 32951755 CAACTGCATCAGAAAAACAGTGGCATTCTATAACA[A/C]AGTTTAAGAAATACATATTCCTATGATTCAGAAAT M 2 1 2 1 600010 r 74 goat 10_32951755 10 32951755 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 38408540 Affx-122953688 AX-123278891 10 32980536 ATTACAGAGATGTTATTTATAGGATAAGGGCAAGG[C/T]AGTATCCATAAAGGCATAGCAGTGATTAGAGAATG Y 2 1 2 1 101000 r 74 goat snp16069-scaffold1690-692968 10 66466448 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787664 Affx-122936780 AX-385274687 10 33057293 CCCTAGAAATTTGCTAATTTGACTGCTATACAGCC[A/G]TCTATTATTTATTGCACTTAGGGAAAACGTAGAGA R 2 1 2 1 101000 f 74 goat snp16068-scaffold1690-616211 10 66389673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414103 Affx-122949739 AX-123284452 10 33088546 ATAACCTTAGGGACTGTCAGTGTGTAAGCGGCAAG[C/T]AGTGGTGGTAGAGGCAGCTGAAACCAGAAGGAGCA Y 2 1 2 1 101000 f 74 goat snp16067-scaffold1690-584958 10 66357742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779279 Affx-122932970 AX-385266383 10 33224102 GGTGATGCTAAAACAGGTGGCTTTATTTGAAAATG[A/G]AAGAAGTAATCCTATGTGGGAATATACAGCAGATT R 2 1 2 1 101000 f 74 goat snp16065-scaffold1690-449402 10 66222228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443973 Affx-122926998 AX-123314310 10 33260873 ACTCACCAAAAATAATACCAAAGCATATTTTCTTC[C/T]ATTAAAGTTAGGTATTCCCTCCCCCCGACAGAGAA Y 2 1 2 1 101000 r 74 goat snp16064-scaffold1690-412631 10 66185170 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437425 Affx-122932411 AX-123307763 10 33289466 CAGGGCAGGGGCCAAACTGGGGAGATTTCTCCGGG[G/T]TGGGAGGGTGATGGGAAAAAGGAGGTGGGGGAGAA K 2 1 2 1 201000 f 74 goat snp16063-scaffold1690-384038 10 66156736 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388700 Affx-122968989 AX-123259058 10 33331350 GCAGGAACAGCAGCGGTTGCTGGCTCAGCTTGGTA[C/T]GGGTACTGGCCTTTCCTGCCAAGATCGGGCGAGGA Y 2 1 2 1 201000 f 74 goat snp16062-scaffold1690-342154 10 66114635 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412830 Affx-122950464 AX-123283179 10 33383402 CACACTGATACCCTAGTCAGCCTGCGCTGGTCTGG[A/C]GTTTCCCTGCTGTCCTGTTGGCAGCAACTCCAGGG M 2 1 2 1 201000 r 74 goat snp16061-scaffold1690-290102 10 66062165 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798841 Affx-122930486 AX-385285771 10 33415595 CCTCACAAAGTGGTAAGCTCCCTTGTTATCAGATA[C/T]ATTTAGCAAAAAGTGATCAACTTTTGTGGCTTTTG Y 2 1 2 1 101000 r 74 goat snp16060-scaffold1690-257909 10 66029657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781531 Affx-122936349 AX-385268616 10 33454541 GTCTAATTTTACATTTCATCAGAGCTATTGACAAG[C/T]AATAATAAAATCATCTGATCTGAATTTTACATCTT Y 2 1 2 1 101000 r 74 goat snp16059-scaffold1690-218963 10 65990990 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377035 Affx-122977707 AX-123247394 10 33492363 CTCATCTTATTGGTATAAATCTATATCCTTTGTTC[C/T]TAAATTTGAATTTTTTCTGTTACTAGTGACCAGTT Y 2 1 2 1 101000 f 74 goat snp16058-scaffold1690-181141 10 65953214 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276523 Affx-1111835385 AX-519550034 10 33493788 GGCATACATCAAATTTGAGGGCTATAGAATTTAAT[A/C]AAAGGATGGATTATTAGTATATTGTTTTACCACAT M 2 1 2 1 101000 r 74 goat Random2.2K-1061 10 33493788 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382214 Affx-122973993 AX-123252572 10 33520866 AACTTACCTATAGTGTCTATTTTTACCAAAACTAG[A/G]AACAAGGTAGGGAGACATGCTCTGGATTGGTAGCT R 2 1 2 1 201000 f 74 goat snp16057-scaffold1690-152638 10 65924339 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417617 Affx-122946867 AX-123287965 10 33574217 AACATGGCAGGCCACAGTGATTCTTTTAAGAAAGA[C/T]GGGAGTTCGTGTCATTATGCTGCTCAAATGCCTCC Y 2 1 2 1 101000 r 74 goat snp16056-scaffold1690-99287 10 65870873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435311 Affx-122934019 AX-123305651 10 33625755 GCGGGCCAGAGGGCTGGCGCCCCCCATCCCCCAAC[C/T]TAGGACAGTCTGGCTCCTTGGGACCACTGCGCAGT Y 2 1 2 1 101000 r 74 goat snp16055-scaffold1690-47749 10 65820285 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437188 Affx-122932059 AX-123307526 10 33677392 CACTTTGCAGCTCTGCCCTTTCCTGATGCCCAGAG[C/T]AATGCCATGGACAGATTGCCTTGGAGATAAGCAAA Y 2 1 2 1 101000 r 74 goat snp33782-scaffold397-2433248 10 65768828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785502 Affx-122923487 AX-385272547 10 33719768 AAAACAGGAAAAAACTAGACTTTCAAGCATCAGAT[A/C]CTCACACATGTATTTCAATTCCTGCATATTCATGT M 2 1 2 1 101000 r 74 goat snp33781-scaffold397-2390872 10 65726463 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777323 Affx-122973783 AX-385264445 10 33761373 CAGGTGTTCAGAAAACTGCATCTATATTTGGATAC[A/G]TGCCATTTCTATTAAGTAGCGGCCTCTTTTTCTGG R 2 1 2 1 201000 f 74 goat snp33780-scaffold397-2349267 10 65684611 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272585 Affx-1111832887 AX-519546299 10 33784642 TGGTCAAAGACAAGGGTATTGAGATTCTTGCTGAA[A/G]AACAGGACAGAAATCCAGGGGCTTTTGAAGTCCTT R 2 1 2 1 201000 f 74 goat 10_33784642_AF-PAKI 10 33784642 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38397805 Affx-122962494 AX-123268160 10 33810928 CCCCCAGGTAGAGCAGAGCCTGGCATATGAGAGGA[A/G]GGTAATGAATTGTGTTCCCAACCTCCCCACCAGAG R 2 1 2 1 101000 r 74 goat snp33779-scaffold397-2299712 10 65634929 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429977 Affx-122938055 AX-123300318 10 33888144 TGCCCCTGAAGGGAAGGGTTCCCACAAATTCTACC[C/T]GCTTTGAGGTCTGCCATTCTCTGACAGCCACAGCC Y 2 1 2 1 101000 f 74 goat snp33777-scaffold397-2222496 10 65557967 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446282 Affx-122925663 AX-123316618 10 33916790 GAGGGCATATCCATTTATTGGGGCAGAGCAAACAC[A/G]AACCTGCGTGTGTGTGTTTTCCCAGTGGCTCTGGC R 2 1 2 1 101000 f 74 goat snp33776-scaffold397-2193850 10 65529268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775364 Affx-122933246 AX-385262495 10 33947729 GTTTATCTTTAAATTGCTGTGCTTCTGTCTGGGAA[C/T]CATGTTCGCCTTCCGTGTAGATCCTACCCACGTGA Y 2 1 2 1 101000 f 74 goat snp33775-scaffold397-2162911 10 65498086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433098 Affx-122935718 AX-123303439 10 33977614 ATTTTTATTTGTTTTCCAAAGAAACAGTGGAAAAA[C/T]AAGAATGATTAAAATGGTTACTTACAGCAGAAGGA Y 2 1 2 1 103000 r 74 goat snp33774-scaffold397-2133026 10 65468189 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775545 Affx-122939118 AX-385262676 10 34022806 TTAGAACTGTAGTCCTGTGAGCCGACAGATCAGGT[A/G]CTGGTTGGAAATGCCAAAAAACATTAGTCTTATTA R 2 1 2 1 101000 f 74 goat snp33773-scaffold397-2087834 10 65423087 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411146 Affx-122951885 AX-123281496 10 34052807 ATAGTTGCTTGCTTTAGGAAGAAGAGGGTAGTGAG[C/T]ACTTTTAAAGTTTGCCAGCTGAAAGGCTGCGTGTC Y 2 1 2 1 101000 f 74 goat snp33772-scaffold397-2057833 10 65393116 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394836 Affx-122964786 AX-123265191 10 34108272 TTCTTAGGGTCAATTGTGATCATACTATTCGCCAG[C/T]ATGAGTCTCAGGGAGTCTAAGGACTCCCCTCAGGG Y 2 1 2 1 101000 f 74 goat snp33771-scaffold397-2002368 10 65336877 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407398 Affx-122955250 AX-123277749 10 34160474 TTTGTTTTTCTCTTTTTGGTAGATTATACAGTGGA[C/T]AACTTTAGTGACTAGGAATGTGGATGATTTGGTGG Y 2 1 2 1 101000 r 74 goat snp33770-scaffold397-1950166 10 65283961 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781084 Affx-122921690 AX-385268170 10 34214648 AATACTCTTGAAGGTTATACTCCAGTTTTTATTAT[A/G]TTTCTAGTCGAAATATCATTGCTGATTTCTGCAGT R 2 1 2 1 201000 f 74 goat snp33769-scaffold397-1895992 10 65229809 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380365 Affx-122975348 AX-123250723 10 34281066 AGTCACAGAAAGCAACTCTAACTGACAAGAGTGGA[A/G]GGAAGCCTCTTGGAATCTAAGTTTCCAGATGCCAG R 2 1 2 1 101000 f 74 goat snp33768-scaffold397-1829574 10 65163204 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800212 Affx-122920864 AX-385287135 10 34328411 AAAGGCAATTATTACCAGTCACTGATGGATGCAGG[A/G]AAACTCAGGACATTTTTGATTGCTGTTGTTGCTGT R 2 1 2 1 101000 f 74 goat snp33767-scaffold397-1782229 10 65115525 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426395 Affx-122940848 AX-123296741 10 34371527 CAGTCTGCCAGCCTGTATAATGTAAAAATGCTAAT[A/G]AGCCTGGAATGAAGCAAAAATCAGAATATATAGCT R 2 1 2 1 101000 f 74 goat snp33766-scaffold397-1739113 10 65072176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773992 Affx-122950232 AX-385261130 10 34413175 TTTCTTAGGAAAAGTTCTCAGCTGTCAAAGAGGTC[A/G]CCAACCCAAGGAAGCTACCTAGGTAAGAGGCTCTG R 2 1 2 1 101000 f 74 goat snp33765-scaffold397-1697465 10 65023376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425277 Affx-122940970 AX-123295623 10 34453430 GATAAAGCTTGGGATTTGTAAGGTGTGTATTTCTT[A/G]CATAGGAAATGATATCTATCTCTGTCTTATTTTTC R 2 1 2 1 101000 f 74 goat snp33764-scaffold397-1657210 10 64983040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422298 Affx-122943480 AX-123292644 10 34569718 AAGATCCTGTATGCCATGTGGAGGCCCAAAAAAAA[A/C]CACAGAAAACAAATTGAGGGTAATAACTTCTCCAA M 2 1 2 1 202000 r 74 goat snp33761-scaffold397-1540922 10 64866327 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775965 Affx-122968609 AX-385263096 10 34624743 TACCATATTTATACCACAGTTGTGAAAAAAGGCTA[A/G]CATTTAATGAATACTCACTGTGTGCCACTGATTAA R 2 1 2 1 101000 r 74 goat snp33760-scaffold397-1485897 10 64811243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408396 Affx-122954484 AX-123278747 10 34701223 CAGCAAATAATTATTCAGTTTAAAATGTCAGTACT[A/G]CTGAGATTTGGAAATCCTGCTGTGAGTAAGTTAGT R 2 1 2 1 101000 r 74 goat snp33759-scaffold397-1409417 10 64733693 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421301 Affx-122944099 AX-123291648 10 34739282 ACATTTTTTTCTTTCACCTAAAGACCTGAGATCTC[G/T]CTCATGTTTTTATTTATGGATTTACAGTTAGTCAA K 2 1 2 1 101000 r 74 goat snp33758-scaffold397-1371358 10 64695309 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415686 Affx-122948541 AX-123286035 10 34792214 TGTACTTCTTATCTTTCTTATTAATATTAGTGAAT[A/G]TATTTTATCCTTTTCTTGCTGACCCACAATCCTTA R 2 1 2 1 101000 r 74 goat snp33757-scaffold397-1318426 10 64641053 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411758 Affx-122951499 AX-123282108 10 34829465 CTAATGTCAAAAGTAGAATCCCAAAAATGGAGCCC[A/G]CCCATGACTGTACTGTTGCCCTTCCAGGCAGTGGG R 2 1 2 1 101000 f 74 goat snp33756-scaffold397-1281175 10 64603796 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772189 Affx-122948775 AX-385259344 10 34886233 CTATCTCCTAACCTGCTCTAATGGTTCTTAAACTA[G/T]CTCCTCTATTTTTACCTTCCATTCACCTGAATGCC K 2 1 2 1 101000 r 74 goat snp33755-scaffold397-1224407 10 64547446 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448514 Affx-122923452 AX-123318850 10 34919361 GTCATCTTTTTCCTGGGTTCCATAGACCTCTTCCT[A/G]TCTTAAGGAAAGTTCTCTCTGGTCTGGGGTAGGTT R 2 1 2 1 201000 f 74 goat snp33754-scaffold397-1191279 10 64514314 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437646 Affx-122931800 AX-123307984 10 34948877 AAGTGATTAATTATTAAATCTCTAATTTTGTATCA[C/T]ATCTCCAGAAAGGTCTGAGTGTGGAAAAAACAAAT Y 2 1 2 1 101000 r 74 goat snp33753-scaffold397-1161763 10 64484882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395926 Affx-122963592 AX-123266281 10 34994257 TGCAAAGTGCTGGAAATTCAAAAAGAATAAAATGT[A/G]AGCCCTCCCTGAAGATAAATGAAAACACTTCCATG R 2 1 2 1 101000 r 74 goat snp33752-scaffold397-1116383 10 64438867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431404 Affx-122936538 AX-123301745 10 35024090 AAGTCCAGGGCCCTTCCTACTTTTTGTTCTCTCAT[C/T]CTAGCATTACTGTCCATCCTCAAGGGCAACTTAAT Y 2 1 2 1 201000 r 74 goat snp33751-scaffold397-1086550 10 64416170 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376172 Affx-122978835 AX-123246531 10 35076354 GAATAGAGGTCACATTCAATACAAACAAGGTGATA[C/T]GAAGTATATGTGTGTGACCTTCCTTTGCAATCAAA Y 2 1 2 1 201000 f 74 goat snp33750-scaffold397-1034286 10 64363706 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386753 Affx-122970130 AX-123257111 10 35163727 GAACAGGTCACATTATGATATTGGCATATCTCACT[A/G]CGATTTCATTTTAATGAGAAAATTGCATTGTGAGA R 2 1 2 1 101000 f 74 goat snp33748-scaffold397-946913 10 64275618 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386169 Affx-122971382 AX-123256527 10 35215607 AATGGTGATAATAATGTCACTGGCTACCATTCACT[A/G]TGCCATGACCACCTACTGCATCTCAGGGGCTATGA R 2 1 2 1 101000 f 74 goat snp33747-scaffold397-895033 10 64223255 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789916 Affx-122929715 AX-385276922 10 35245645 ATACAGTGAAATGTAGCAGACTTGGGGAGAAAATC[C/T]CAAAGGATTAAAATTATATGCATTTACAGTAAGAA Y 2 1 2 1 201000 r 74 goat snp33746-scaffold397-864995 10 64192962 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422631 Affx-122943707 AX-123292977 10 35288952 CAATTATAAGGACAAGAGCAATATAAGCAGAATCT[A/G]TGATCCCTTGCAAGCTCTTTGTGCCACTAAAATTC R 2 1 2 1 101000 r 74 goat snp33745-scaffold397-821688 10 64149537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780465 Affx-122921940 AX-385267556 10 35321417 TTGTAAAACTGTTTCTTGTCATTAGACATGTAGCT[A/G]TTTCCAGTAATTCTGTTCTCTCTCATGTTTCCTAG R 2 1 2 1 101000 r 74 goat snp33744-scaffold397-789223 10 64116906 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379585 Affx-122976034 AX-123249943 10 35358218 AATTCAAAGAACTAGAAAGAAAAGGCACCCAATAC[C/T]GGGAAGAAAAGCTTTTTGAACAGTTTTACGGAGAT Y 2 1 2 1 101000 r 74 goat snp33743-scaffold397-752422 10 64086395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443732 Affx-122927138 AX-123314069 10 35396522 CCCTTATTTACATATATATTATTTGTCAGAAAGAA[C/T]CACTCTAAGTGTTTACTTTTTTTTATCTAGCACAT Y 2 1 2 1 303000 f 74 goat snp33742-scaffold397-714118 10 64048275 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795036 Affx-122936906 AX-385281995 10 35443817 CATTATAACTGGACTGTTTTCTTGTACTTGAAGTA[C/T]AAAAGACCTGTTTGACATATCCTTCTGTTATTTAT Y 2 1 2 1 201000 r 74 goat snp33741-scaffold397-666823 10 64000894 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452035 Affx-122920897 AX-123322368 10 35493751 ATTATACTTTATACAAGTGAAAATTTCATTTTGTC[A/G]CAAATATTGTCTTTTTTTCATTCATAAAATATGTT R 2 1 2 1 103000 f 74 goat snp33740-scaffold397-616889 10 63954290 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786460 Affx-122949037 AX-385273494 10 35535710 AATGATCGTGTTTATAATATTCCCTGCTCAGTTGC[A/G]TAATACTTTTACCACACACAACAAAACTGAGGTTA R 2 1 2 1 101000 f 74 goat snp33739-scaffold397-574930 10 63912159 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397820 Affx-122962484 AX-123268175 10 35629811 GTGAAAGAAGGGGAAAGGAGGTTGGATGTCTAAGA[C/T]GAGAGCAGGGAATCAGGGGAGGGAGGGAGAACAGA Y 2 1 2 1 101000 f 74 goat snp33738-scaffold397-480829 10 63818187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377432 Affx-122977542 AX-123247791 10 35694902 GAGCAAAGGGTAAATGAAGACTTAATTGCTTGAAG[C/T]ATCTGAGATTAAACCTTGACTGACTTTAAAGTATG Y 2 1 2 1 101000 f 74 goat snp33737-scaffold397-415738 10 63750882 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394515 Affx-122964540 AX-123264870 10 35730288 CCATTAACTCTCATTGGACTATCACAATATCCTGC[G/T]AAGTAGCTTTACTAACTGTTCAAATGATCATTTCT K 2 1 2 1 101000 f 74 goat snp33736-scaffold397-380352 10 63714621 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792058 Affx-122964096 AX-385279046 10 35763280 TGTAAAATGAAAGTAATTCCAATCACACAGGTTTT[A/C]GTCTGCCCAAATTTTTAAGATGGGTGTACACTGGG M 2 1 2 1 102000 r 74 goat snp33735-scaffold397-347360 10 63680367 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454139 Affx-122919336 AX-123324472 10 35798940 AGTCTCAAAGAGTCAGACACAACTGAGTGACTGAA[C/T]AACAAAAGATATTCATTTTCACTGTTTCCTGTTCA Y 2 1 2 1 202000 r 74 goat snp33734-scaffold397-311700 10 63644092 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395997 Affx-122963498 AX-123266352 10 35832217 TATTCTATTATAAAAGTGGTGTTAGTATTAGTAAT[A/C]GATTTAGAGGATGTTTTTGAGGGGAAGGGGATTAC M 2 1 2 1 201000 f 74 goat snp33733-scaffold397-278423 10 63610694 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802323 Affx-122972360 AX-385289227 10 35861127 TCACCTAACATACAATCTTTTGCCTGAAAGAGAAA[C/T]GTATTGCATGTATCAAAGATACATCACACAAGTTG Y 2 1 2 1 101000 f 74 goat snp33732-scaffold397-249513 10 63581501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778598 Affx-122966059 AX-385265709 10 35911247 ATGACTAACACAAAATAGGATAGGATACACATACA[C/T]GTATTAATATTCATGTGCTATGGTTACAATAAAAG Y 2 1 2 1 101000 f 74 goat snp33731-scaffold397-199393 10 63531735 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407244 Affx-122955363 AX-123277595 10 35964274 CACACAAATATATATACATAAATGATGGATTGTGA[C/T]AATAATTTTTATGCCAGGTCATATATTCACCTCTA Y 2 1 2 1 303000 r 74 goat snp33730-scaffold397-146366 10 63478198 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431609 Affx-122936160 AX-123301950 10 36004963 CTCATGGTCAATGGCAGCACTCTTGGAGAGAGGTG[C/T]ATACATTTATGTCCCACTGTTGCAAGTTGAAGAGA Y 2 1 2 1 201000 r 74 goat snp33729-scaffold397-105677 10 63437218 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774651 Affx-122932096 AX-385261785 10 36047955 TACAGAGAATAGTTTGTTGTCATTATTTCCTGCTG[A/C]GATATGGAGGAAGGTTGATCTTTTCAAAAATATTT M 2 1 2 1 102000 f 74 goat snp33728-scaffold397-62685 10 63392402 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449635 Affx-122923185 AX-123319970 10 36078098 AAGGCATGGAATGAGCCATGCTTTAACCAGATTTC[A/G]CTTGAGGGGATTTAATAGGGAGAGGAACTCCAGTC R 2 1 2 1 201000 f 74 goat snp33727-scaffold397-32542 10 63362056 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800651 Affx-122946537 AX-385287570 10 36109471 CCATTCTTTCTCTAAATGGACTTTTCCAAGGAAAA[C/T]ATAAGTGTTTGATTTTGCCGCTGGTTTCTGTTGCT Y 2 1 2 1 101000 r 74 goat snp33726-scaffold397-1169 10 63330707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429007 Affx-122938843 AX-123299349 10 36131860 ATTCTAATTTTTTTTTTCAAACTGATCTTACATAA[G/T]TAAACCATTCAGTAAACTACTGTGCATCTACCATA K 2 1 2 1 101000 r 74 goat snp11193-scaffold1400-21121 10 63247426 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379714 Affx-122975890 AX-123250072 10 36163556 TATTTGAGAAAAGGGCCACAGTTTGTTTCTTTGTT[A/G]CTTAAGTTTTCTAACACTTCATGGATATTTTAATG R 2 1 2 1 201000 r 74 goat snp11194-scaffold1400-52817 10 63215096 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788209 Affx-122941052 AX-385275228 10 36245485 TCCCCCTAAGCTACCAATTCAGTTCAAGTTGTTCC[A/G]TACATTAAAAAATTACCACTGGATACTTTAGTAAA R 2 1 2 1 101000 f 74 goat snp11196-scaffold1400-134746 10 63132947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409156 Affx-122953209 AX-123279507 10 36282604 TAAAAGCTTTAAATGTATATTGCTAAATACAGTAA[A/G]TCAGTTTGGAAAGGTTATATGTTGCATGATTCCAA R 2 1 2 1 101000 r 74 goat snp11197-scaffold1400-171865 10 63095861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463086656 Affx-1109806905 AX-514574057 10 36286052 TCTATTTCAATCATATCTTAGTTTTGAATAGAGCC[A/C]GAATTATCTCTTGTGTTTTCCCCTGTCCCTGGCCT M 2 1 2 1 101000 f 74 goat 10_36286052_AF-PAKI 10 36286052 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395049 Affx-122964200 AX-123265404 10 36336452 CTTGGAGATAGCATGTAAGAAACAAAAACACAAGA[C/T]AAAAACATACAGCTAGGAAGTCAATGATATCTCTC Y 2 1 2 1 303000 r 74 goat snp11198-scaffold1400-225713 10 63042402 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771940 Affx-122931078 AX-385259096 10 36370435 AACTGTTAAAACAAACTTTATCTAGAACAAAATAA[C/T]AATGTAAAGGAGTATATTCTTTTAAGATATGCCTA Y 2 1 2 1 101000 r 74 goat snp11199-scaffold1400-259696 10 63008104 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395198 Affx-122964504 AX-123265553 10 36477726 TGGACCCAAGTCCCAGGCTCTACACACACTAAGCT[A/G]CCTGATGTCAGTCAGACATTTCTCAAATTGACTTG R 2 1 2 1 101000 r 74 goat snp11201-scaffold1400-366987 10 62900577 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401386 Affx-122959225 AX-123271739 10 36533065 ATAAGAACATCAGCTAGAAATTCTGAAAATTCTTA[C/T]AATCCTTCTATACTCTTGTGAAACCAGATAATATA Y 2 1 2 1 101000 r 74 goat snp11202-scaffold1400-422326 10 62844585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402759 Affx-122958320 AX-123273112 10 36583124 TCACCTTTCCTGGTGAATCTTTTTAAAAGGAACCA[C/T]GGTAGGATGATAGTCATCATCTCTTACTATTGCCA Y 2 1 2 1 101000 f 74 goat snp11203-scaffold1400-472385 10 62794195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276525 Affx-1111835386 AX-519550036 10 36612805 GAAGGCAAGAGGTTGGCTAACAGCCACTGGAGCAG[A/G]GAAATGCCTGCAAGTCTCTGTGAGAACAAGCCAGT R 2 1 2 1 101000 r 74 goat Random2.2K-1063 10 36612805 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403062 Affx-122958524 AX-123273415 10 36617912 TAGAAGTTTTACTATCAATGCTTACTTATGGTATC[C/T]ATTTTTAGAACAGGCTATCTCAGGGCCATTTTATC Y 2 1 2 1 101000 f 74 goat snp11204-scaffold1400-507173 10 62759336 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398314 Affx-122962142 AX-123268669 10 36691040 TTTGAGCAAATACCTGAAGGAAAGTAAGGGAGTGA[C/T]GCAAACATTTCAGAAGAAATAGCAAAGACAAGATC Y 2 1 2 1 101000 r 74 goat snp33169-scaffold388-1730681 10 62680184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397954 Affx-122961911 AX-123268309 10 36727070 GATGTTACATAAAGATGGATCAAAGATTTTTATTG[C/T]AACATTTTTATACTAGGAAAAATATAGAAACATCT Y 2 1 2 1 101000 f 74 goat snp33168-scaffold388-1694651 10 62643391 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400461 Affx-122961309 AX-123270816 10 36760917 TGGTTTAAATTTCTTTAAAAATTATCCAGATTGAA[C/T]AACACTGAACATGTCTTTAGACCACTTGTGTTTGG Y 2 1 2 1 103000 r 74 goat snp33167-scaffold388-1660804 10 62609491 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435547 Affx-122933390 AX-123305887 10 36793985 AGAGTGTAGGCAATGTAGAACGTTGAACATGGAAT[G/T]TAGAATGCTGAATAGCAAATGGTCTGTTTGGAGCT K 2 1 2 1 101000 f 74 goat snp33166-scaffold388-1627736 10 62575581 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422331 Affx-122943456 AX-123292677 10 36878056 CTATTAATGCACCATTATATAAGCAAATATTTTCT[A/G]TAGATGTCAATAAAATTTGATTTTACCCTTTCTGT R 2 1 2 1 101000 f 74 goat snp33165-scaffold388-1543665 10 62489495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775676 Affx-122977972 AX-385262807 10 36909696 AGTTGGTGGCCTTCCACGCTGTAATCCATGGACTT[A/G]AATGCCTTTAATCTTATGTCTCTACCATCCCCTCA R 2 1 2 1 101000 f 74 goat snp33164-scaffold388-1512025 10 62459162 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799036 Affx-122926960 AX-385285966 10 36958807 TGATAGAATAGCAAAATGGATATTTACATACACTG[C/T]CACTGAGAATGCAAATTTATGTATCCTCTTTGTAA Y 2 1 2 1 101000 r 74 goat snp33163-scaffold388-1462914 10 62410252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411784 Affx-122951478 AX-123282134 10 37004948 GATTAAAGGTCCCCAGAGAGAAGTAGTGTTTGCAT[A/G]TCAAAGGCCTGCTCTTGGCTGGGCCTTTTGCTGTC R 2 1 2 1 102000 f 74 goat snp33162-scaffold388-1416773 10 62370537 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386469 Affx-122970772 AX-123256827 10 37058915 AACTCAGAACATAGTAGGATGAGTTTATGTGAGTT[A/G]CTTCTTTTTAAAATATTTCTTCGAGTACAGTCATT R 2 1 2 1 201000 f 74 goat snp33161-scaffold388-1362806 10 62315774 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431141 Affx-122936579 AX-123301482 10 37089349 TCAGGGCTCTGTCATTCTGAGATTCCATCTCTGCC[A/G]TTGGAAGGCTGGAGTGGTGTTTCCTAGAGCTCTTT R 2 1 2 1 101000 r 74 goat snp33160-scaffold388-1332372 10 62285150 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421743 Affx-122944374 AX-123292090 10 37128833 GATGCCCCAGATAGAGGAAAACCCCTTTTCACCCC[G/T]CCCTTTTAACTAATCACTGGGTGTGGATTGCCCCT K 2 1 2 1 101000 r 74 goat snp33159-scaffold388-1292888 10 62245890 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766753 Affx-122954533 AX-385254089 10 37171446 GTTCTTAGGAAGGATTTTAGGGTCACACCATCAGC[A/G]TTTTCTCCAGAGTATTTTTGTGATAGTGAATTTCT R 2 1 2 1 101000 f 74 goat snp33158-scaffold388-1250275 10 62203595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450474 Affx-122922939 AX-123320808 10 37237778 ACCAACTCCCCGAGTTAGGAAGGTAGAAGGGAAAA[G/T]AATTTTTCCTCCTCTCTAGGATAATAGGTAAAGAT K 2 1 2 1 102000 f 74 goat snp33157-scaffold388-1183943 10 62137053 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439675 Affx-122930586 AX-123310012 10 37280616 GATCTTTATAAAAAGAGATAGTCCAACTGTTATAT[A/G]TAAAATACAGAAAATCTAAAATGAAAATATCAAAT R 2 1 2 1 103000 f 74 goat snp33156-scaffold388-1141105 10 62093624 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382508 Affx-122973810 AX-123252866 10 37318672 CACTACTTTCAGAATCAAATGACAGCACCTCCACT[A/G]TTACCAGTCTGGTCCATCTTTTACTTGGATTATCT R 2 1 2 1 201000 r 74 goat snp33155-scaffold388-1103049 10 62054497 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453814 Affx-122919562 AX-123324147 10 37360624 AGGAAATGAGATTTCCCACAGGAGAGAACTATGAA[G/T]AGATGAACTGACATTCTGCAGCTTTTTTCCCTGGA K 2 1 2 1 101000 r 74 goat snp33154-scaffold388-1061097 10 62012040 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380889 Affx-122975042 AX-123251247 10 37399646 GAATTGATACTTAAGACCTGGAGGATGAGAAAAAG[C/T]AAATATGCAAGAATAAAAAATATAATCTTTATGAA Y 2 1 2 1 102000 f 74 goat snp33153-scaffold388-1022075 10 61972949 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802702 Affx-122950268 AX-385289601 10 37536063 CCCAATGTTGAGAACCACTCTTACAGATTAAGTGC[A/G]TAGATTAGTTTACCAATTCACAAAATAACTTTTGA R 2 1 2 1 101000 f 74 goat snp33150-scaffold388-885658 10 61834970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419204 Affx-122945702 AX-123289552 10 37589211 TAGGAAAAAAAAAAAAAAAAGTCCTGGGAGGAAAC[G/T]ACACCTTTCCTTTGTGTCTTTGGGATGAAAATGTT K 2 1 2 1 103000 r 74 goat snp33149-scaffold388-832510 10 61772914 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276527 Affx-1111835387 AX-519550038 10 37640610 AACCTACCTCCTTCTCCATGGTTTGTGAATATGAA[A/G]GTTTCTACCATTACAAGGATCGTATTTCAGCACAA R 2 1 2 1 101000 r 74 goat Random2.2K-1064 10 37640610 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791747 Affx-122933867 AX-385278738 10 37669209 AGCACAGAGGGATAATTAAGGACAAAAGGTAATTA[C/T]ACACATTTATTTAGCACTCAGAAACAGGAAAATTA Y 2 1 2 1 101000 r 74 goat snp33147-scaffold388-752512 10 61692084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401532 Affx-122958917 AX-123271885 10 37698499 AAATCTCTTTAAGACTTGAACCTCTCTCCCTCACA[C/T]GTCCTACTTCAAGCCATATCATTCTAATGATACGT Y 2 1 2 1 101000 r 74 goat snp33146-scaffold388-723222 10 61665194 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415096 Affx-122949450 AX-123285445 10 37745419 ATCAAAGCATTTCCTCCTATCTTCATTAAACAGCA[G/T]AGCAATGTAGCTTTGAATGGAAAAATGTATCTTGA K 2 1 2 1 101000 f 74 goat snp33145-scaffold388-676302 10 61617436 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414030 Affx-122949793 AX-123284379 10 37783715 ATCAAGGTTGAAAAACTACTCATCATGGTGGGAGG[C/T]AGGATTGCTTCATGGAATCAGTCAGTGATTAGCTA Y 2 1 2 1 101000 f 74 goat snp33144-scaffold388-638006 10 61579192 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430975 Affx-122936701 AX-123301316 10 37823558 ACCTATAGAGAATCTAGCATAGGACTGACAGTCTA[G/T]ACAAGTTTATAAATATTGATGCTTGTACTAGGAGA K 2 1 2 1 101000 f 74 goat snp33143-scaffold388-598163 10 61539396 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795998 Affx-122950780 AX-385282950 10 37919303 TACTTGAAGACATACTGTAATGATACAAAATTAAA[G/T]AGCATCTCTAATCAGCATAAGCCTAGACATAAAAA K 2 1 2 1 201000 f 74 goat snp33141-scaffold388-502418 10 61443142 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425909 Affx-122941617 AX-123296255 10 37961541 CTGAATATCCAAGCACTGACTAGACCACATGCCAA[G/T]GTGGAAGGAAGAGAGAATCACCTGGGTAAGTTGAA K 2 1 2 1 101000 f 74 goat snp33140-scaffold388-460180 10 61401206 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446703 Affx-122924735 AX-123317039 10 38003183 TCCATGCTTAAATCCTTTCAATTGCTCTCATCTCC[A/G]TTTTGATACAGTTTAAATCTTTTCTTAAGAAAACA R 2 1 2 1 101000 r 74 goat snp33139-scaffold388-418538 10 61359453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781418 Affx-122972399 AX-385268503 10 38060227 TTTATGAATCATTTTCACCTGTGATGCTTTACCCA[C/T]AATCCAACCAACTTGGACTATTTTAAAGTATCACA Y 2 1 2 1 201000 f 74 goat snp33138-scaffold388-361494 10 61301587 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445787 Affx-122926052 AX-123316124 10 38104279 CTTTCTCCATTGCTAAGTACTAGCTGAGCTTAGTC[A/G]CTCAGTTGTATCAGACTTTGTGACCCCATGGACTG R 2 1 2 1 103000 f 74 goat snp33137-scaffold388-317442 10 61257367 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429994 Affx-122938042 AX-123300335 10 38159589 CAGCTGCCCTAGGTAGCACAAAGACTTATTGGGCT[A/G]TACTTCAAAGAAAGGGAGAGAGGTTACCTGATGCA R 2 1 2 1 201000 f 74 goat snp33136-scaffold388-262132 10 61201259 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439756 Affx-122930524 AX-123310093 10 38214119 CGTTGGTTTCTTTTAAAGAAAGATCAATCCTCAGC[A/G]CTACTCTTGTCTTCAATGAAATGTTTCCCACAATA R 2 1 2 1 201000 r 74 goat snp33135-scaffold388-207602 10 61145916 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425228 Affx-122941010 AX-123295574 10 38251239 CCTATGTGAAGGCAGAATTCTAAGATAGCCTGCAC[A/G]GTTCCTGCCCTCTAGAATTCATATTTTTTTTGCAG R 2 1 2 1 201000 r 74 goat snp33134-scaffold388-170482 10 61106778 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401537 Affx-122958913 AX-123271890 10 38283648 AAGGCTACTTTAAGATTTAATCATTAAATTATTCT[C/T]CTGGATTGTTTACAAGTCAATTCTCATAGGAGTAA Y 2 1 2 1 101000 r 74 goat snp33133-scaffold388-138073 10 61074713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385982 Affx-122971523 AX-123256340 10 38353876 CCTGTGACTTTGGCTTTTACACTGACTTTGTAATA[G/T]AACCCTGGAATAAGTTCCTGTTTTTCTATAACTCA K 2 1 2 1 101000 f 74 goat snp33132-scaffold388-67845 10 61006690 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407999 Affx-122954317 AX-123278350 10 38382457 TTCTCTTCTTTTCGGACTCTGCTCTGTGATGTGTT[G/T]TTGAGATCTTGGTTACGTGTGATGTGAGGGGTTGC K 2 1 2 1 101000 f 74 goat snp33131-scaffold388-39264 10 60978235 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793590 Affx-122975986 AX-385280565 10 38453550 ATAAATTTTATCAGAAATATTAAGGCATGAAAACA[C/T]GACTCCAAATAAGAGGGAAAACAATCAACAGAGAC Y 2 1 2 1 101000 r 74 goat snp31452-scaffold349-31730 10 60907485 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780432 Affx-122944663 AX-385267524 10 38493829 GGGGAGGGATTCAATTTTCCTGAGCACTTGTCAAG[C/T]GTATTTGGTAAGAGGTCAGCTCAGAAGGGAAGCAA Y 2 1 2 1 101000 r 74 goat snp31453-scaffold349-72009 10 60866879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773549 Affx-122930489 AX-385260690 10 38545620 TGAATTTTAGGCTCAAAAAATATTGGAGGCAGAGA[C/T]AGAAAAATATATGGATATCTTATCTCCAACTTTGC Y 2 1 2 1 101000 f 74 goat snp31454-scaffold349-123800 10 60815572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419401 Affx-122945602 AX-123289749 10 38592483 CAGAACAGTGATCCATACTACTGACCTAGATTACC[A/G]TAGATGGCGCCTTATGATTATCTGATTCCCTTGCT R 2 1 2 1 101000 f 74 goat snp31455-scaffold349-170663 10 60768132 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781619 Affx-122947882 AX-385268703 10 38638077 TCAAAACTAGTTTCTGTGCTTTGATCTCTAGACCA[C/T]AGCACCTCAGTTATATTCTCTTAAATGAATTTTTC Y 2 1 2 1 101000 f 74 goat snp31456-scaffold349-216257 10 60721729 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427370 Affx-122940096 AX-123297713 10 38702104 CTTCACAACAGTACAAGCAGTGGTGTGATGATGAA[C/T]GGGTTCTAAGAGGAGAGAACTCCAGCATTCTTTCC Y 2 1 2 1 101000 f 74 goat snp31457-scaffold349-280284 10 60658093 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792727 Affx-122922691 AX-385279707 10 38734850 TATCCTCCTCCTCCAATTCAAACGTCTTAAAAATG[C/T]AAAATACACAAATCTGAGCCATTATGACATATGCA Y 2 1 2 1 101000 r 74 goat snp31458-scaffold349-313030 10 60625342 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786266 Affx-122928650 AX-385273301 10 38772493 GCCTACCCAGATTAGCATTACTAACCTTGCAAATA[C/T]GCATACAAATAATGTTTATACAGTGTCAAATGCCA Y 2 1 2 1 101000 f 74 goat snp31459-scaffold349-350673 10 60587119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794904 Affx-122974350 AX-385281864 10 38806847 CCTCAGGGATTCACCACTTCTCATTTTTCAAGTTA[C/T]ACTGGCTTTCATAGGTGAAAAGATTCTCATACTCA Y 2 1 2 1 101000 f 74 goat snp31460-scaffold349-385027 10 60552725 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272640 Affx-1111832888 AX-519546351 10 38885660 GCATGTTCAGCACTTCATCCCCTTTTATGACTAGC[A/G]TTCCACTCTATGAATATATATCACAGTGTTTATCC R 2 1 2 1 201000 r 74 goat 10_38885660_AF-PAKI 10 38885660 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440936 Affx-122929014 AX-123311273 10 38891312 AAAGATCCCACCTGGAGTAGAGGATACACTGAGGC[A/G]TGTTTACTGGGTGAGGGAAAAGTATCAGAGTGAGG R 2 1 2 1 201000 r 74 goat snp31462-scaffold349-469492 10 60468747 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405663 Affx-122956570 AX-123276015 10 38934664 ATAAAGGCTGGTTGATTTAAGAGAGCAAGACATTA[C/T]GCGGAGACAGAACAAGACCTAGAGTATTTTAAAAA Y 2 1 2 1 101000 f 74 goat snp31463-scaffold349-512844 10 60425333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792544 Affx-122948527 AX-385279526 10 38995846 TCTCAAATTGCCACTTCATCCTTAACCACAATTCG[C/T]TTATCACAGTATGCAGATTAACTTTCTTGAGGAAT Y 2 1 2 1 201000 f 74 goat snp31464-scaffold349-574026 10 60363544 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768098 Affx-122946529 AX-385255300 10 39030393 TCTTATTCCTAGTTTTCTCATATATTTTCCACACT[A/G]CTGAAATTCATACAAACTTTAGTATTACAACTAGG R 2 1 2 1 101000 f 74 goat snp31465-scaffold349-608573 10 60328934 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395248 Affx-122964101 AX-123265603 10 39085220 CTGGATCTTAAGGCTTCATAGACAATGCCTCTGAT[C/T]ACTTGCATGGACAGCAATTCTGTAAACATCAGAGT Y 2 1 2 1 101000 f 74 goat snp31466-scaffold349-663400 10 60274093 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789325 Affx-122944827 AX-385276335 10 39134339 GGTAACTAAGGATTAAGAGGCAAGAAGAATGGTGA[A/G]GCCATCAGCAGTCTTCCTTTTATAACTGATGACAC R 2 1 2 1 101000 r 74 goat snp31467-scaffold349-712519 10 60224527 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768730 Affx-122959568 AX-385255908 10 39182529 AGCCATAACCATTGGTGATCATGGGGACCGGTAAT[G/T]AAGCCTGCAGGAAAAATTACAATCTAAGAATTTAA K 2 1 2 1 202000 r 74 goat snp31468-scaffold349-760709 10 60176503 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426534 Affx-122940193 AX-123296880 10 39229396 GCTTATAAATGTGTTTTCTGGAATGTAGTTAGAAG[C/T]AAATATATGATGTTAACACATATCCTATCAATTGT Y 2 1 2 1 101000 f 74 goat snp31469-scaffold349-807576 10 60129563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450285 Affx-122922165 AX-123320620 10 39261585 AGTCCTTGTTGCCCTAGGCGCTCACCCATGAGACT[A/G]AGAACTTTAATGCCAGAAAGAAGTTAGAAACTTAT R 2 1 2 1 101000 r 74 goat snp31470-scaffold349-839765 10 60097447 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390317 Affx-122967710 AX-123260674 10 39300185 CGATGAGAGGCAGCAGGGAAATCACTTGAGCCCAG[C/T]GCTGTCACCAGACTCGTCTGTTACTGGCACTTAAA Y 2 1 2 1 201000 r 74 goat snp31471-scaffold349-878365 10 60058995 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380490 Affx-122975711 AX-123250848 10 39333470 GAGTAGTTTATACACTGTAAGCAATTCTGCCTGCT[A/G]TTCCACTCAGTGAAGGGATATGAATCTGCTATTCC R 2 1 2 1 101000 r 74 goat snp31472-scaffold349-911650 10 60027099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399282 Affx-122960547 AX-123269637 10 39368924 TTTGGCTACTTTACAACTGCTGCTAGCACTAAGAG[C/T]AAAACACGCTTTTTCATCACTTTGAACAGAGGAGT Y 2 1 2 1 101000 f 74 goat snp31473-scaffold349-947104 10 59991766 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437751 Affx-122931719 AX-123308089 10 39418163 TCAGCTAATTAAAAATATACATTTCATCTTTCATG[A/G]CTAATATAACTTTAACAACAGTCTTCTCAGCTTTT R 2 1 2 1 101000 r 74 goat snp31474-scaffold349-996343 10 59943063 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410619 Affx-122952097 AX-123280969 10 39451654 GAAGTCTATGAATACTAGGTCATAAACCCCAGCAA[C/T]AGAAGTATCTCTGAATGACCATACAATTTTATAAA Y 2 1 2 1 201000 r 74 goat snp31475-scaffold349-1029834 10 59909341 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781299 Affx-122961877 AX-385268384 10 39487766 CAAAATGTGGCAAAGCCTAATTATATCATTTATTA[C/T]GATGATGATTATTATTTAAGATTCTAAGCATGTAA Y 2 1 2 1 201000 r 74 goat snp31476-scaffold349-1065946 10 59873204 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407716 Affx-122955009 AX-123278067 10 39552571 TTGGCGGCTTCTGCAATCCGAGAGACCCTCTCTGG[C/T]TTAGGGCTGATACCCTGGGGTGTTCTTGACTTTCT Y 2 1 2 1 202000 f 74 goat snp31477-scaffold349-1130751 10 59808001 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422928 Affx-122943037 AX-123293274 10 39609907 CAAATTAACCCTTTTATCCTGGGGCTAGAAGTCTG[C/T]AAACTGTGTTTTCCAGAATCCACTCCAGTTAGGGA Y 2 1 2 1 101000 f 74 goat snp31478-scaffold349-1188087 10 59749901 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420362 Affx-122944954 AX-123290709 10 39661792 ATGGACCAATTTAAATCAACACAAGATGGTCTCAG[C/T]AGGAAATCTCAAATTGCAGATGATAATCGTCAGAA Y 2 1 2 1 101000 r 74 goat snp31479-scaffold349-1239972 10 59697780 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450067 Affx-122922808 AX-123320402 10 39704724 CCTATATATGAGAAAGAGAGGAATAAAGGAGAACC[A/G]CCAAATTTATCTAAAAGGAAAAAATACTTCCACAC R 2 1 2 1 101000 f 74 goat snp31480-scaffold349-1282904 10 59654607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784229 Affx-122922126 AX-385271280 10 39735507 GGTTTTAAAATATTGACAATGGATATGCTATGAAA[C/T]AGTTTTCCAGAAATATTTTTCCTAGGGGACTCACA Y 2 1 2 1 103000 r 74 goat snp31481-scaffold349-1313687 10 59623810 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411309 Affx-122952287 AX-123281659 10 39777805 GTCCATGAGGTCTCATAGAGTTGGACACAAGTTAG[C/T]GACAGAACAGCAAATTCCACCATGCTCCTGTTTCA Y 2 1 2 1 101000 r 74 goat snp31482-scaffold349-1355985 10 59581151 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419369 Affx-122945626 AX-123289717 10 39812505 CTCTGCTGAAATTCAGGTTTTTAAAAATCATGGTA[C/T]CTTTGCTTAGATACCAAGTCTCTGGATATACCAAG Y 2 1 2 1 103000 r 74 goat snp31483-scaffold349-1390685 10 59546274 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417717 Affx-122947443 AX-123288065 10 39852081 TGATGTACCCATCTGATCTGTTCTGTAAGAAACCA[C/T]TGCAAATACAAGGACAAATCTGGAAGGTTGATGAT Y 2 1 2 1 101000 f 74 goat snp31484-scaffold349-1430261 10 59506475 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393444 Affx-122965857 AX-123263800 10 39908107 ATTTAACTATTTGAAAACTTAGGTAATATAAGATT[A/G]TGTCTGGTAGTGAGCTGGGATAATGCTAATTCAAA R 2 1 2 1 101000 r 74 goat snp31485-scaffold349-1486287 10 59452728 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407816 Affx-122954550 AX-123278167 10 39953358 GTGAATTACTACATTAAAAACAGTGAAACTGATCT[A/G]CACTGGATCATTTTGCCCCTTATCATGCTATGTTC R 2 1 2 1 101000 r 74 goat snp31486-scaffold349-1531538 10 59407510 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407527 Affx-122954701 AX-123277878 10 39990424 GGCCATTAGCATGCTGACATATGGGACACATATAA[C/T]ACATATTTGTCAAATTAGTGAGTAGATGAATATAC Y 2 1 2 1 101000 f 74 goat snp31487-scaffold349-1568604 10 59370438 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792272 Affx-122957522 AX-385279255 10 40024474 TTTAAAATATACACAGGGACACATGGCAGTCACAT[A/G]TCTTTATGGCTGAAATCATGTTCAAAGAAGAAGAA R 2 1 2 1 101000 f 74 goat snp31488-scaffold349-1602654 10 59336330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407528 Affx-122954700 AX-123277879 10 40054232 CAAACACCTGTTCCTTTTTCCCACCCAGGTACAAG[C/T]AGACTAAGCTAGGTGTTGGGGGAGGGCCCAGACAA Y 2 1 2 1 101000 f 74 goat snp31489-scaffold349-1632412 10 59306520 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389393 Affx-122968385 AX-123259751 10 40114026 TCTATCCAGAGCACAAAGTAGATGGCACTTTCTCC[A/G]TTTCAAAGTCTTAGATGTAAATATATATTGACATC R 2 1 2 1 201000 r 74 goat snp31490-scaffold349-1692206 10 59246977 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442352 Affx-122928033 AX-123312689 10 40144746 GGATCCTATTTGAGAAGCTCAGAGCAGGGCACTGG[C/T]AGGTTTCAGGTTAATACTGCCAACCTAGCCTCATT Y 2 1 2 1 201000 r 74 goat snp31491-scaffold349-1722926 10 59216251 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786657 Affx-122954135 AX-385273689 10 40175228 ACCATTCTCCCACATGGCTTATGGAAATATGCAAA[C/T]ATTTCCCCCATTCTCTTGATACTGTCTTCTGTAGC Y 2 1 2 1 101000 f 74 goat snp31492-scaffold349-1753408 10 59185617 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413599 Affx-122950568 AX-123283948 10 40228446 TGGTAAGTTGATGACTTTGTTTTCATAAAAGTAAA[C/T]AGAAGACCTAAGGGAGTGAAACTATAATATAATTC Y 2 1 2 1 303000 f 74 goat snp31493-scaffold349-1806626 10 59131988 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424968 Affx-122941921 AX-123295314 10 40271062 GTCAGGACTTCAACATATGAATTTGGGGGGAACAC[A/G]ATTCAGCTCATCTCTTTTCAAGTCATAAAGACTAT R 2 1 2 1 201000 r 74 goat snp31494-scaffold349-1849242 10 59089255 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402301 Affx-122959094 AX-123272654 10 40332723 TAAGAAAGAAATAGTACTTATTTTTCTTGGCTAAA[C/T]AATTTTGCATACAGTACTCCTTTAAAAAAAAAATA Y 2 1 2 1 101000 r 74 goat snp31495-scaffold349-1910903 10 59026929 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781206 Affx-122953025 AX-385268291 10 40371964 GAAGGGACAAACAAAGACTTTGCACAGAATGCTGT[A/C]AGACAGCGTTCTGTGGGTCCTTCACTGGCCACAGA M 2 1 2 1 202000 r 74 goat snp31496-scaffold349-1950144 10 58987727 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450615 Affx-122922005 AX-123320949 10 40412580 CTTTACCACTACACCACCTGGGAAGCTCCAGGTAG[C/T]GGTAGAGATGGTCAAATATTTATTACAGACAGTAG Y 2 1 2 1 101000 r 74 goat snp31497-scaffold349-1990760 10 58947754 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796222 Affx-122973669 AX-385283172 10 40470928 ACCCAAATAATAAGTGAGGGAAAATGTGTGTGTTT[A/G]TATATATATTTGGTTGGGCTACGTCTTAATTGCAG R 2 1 2 1 102000 f 74 goat snp31498-scaffold349-2049108 10 58891536 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406781 Affx-122955712 AX-123277132 10 40529037 CCCAACCTGCAACCCAAAGAAAATCATGGCTCAAC[A/G]TGTTCATATGTTTTATATCTTGTCAGATTTTTCTC R 2 1 2 1 101000 f 74 goat snp31499-scaffold349-2107217 10 58832635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386924 Affx-122970004 AX-123257282 10 40557924 TAATAAGATCACGAAGGCACCAGAATGGGATTAAC[A/G]CCAAAGGACTTCAATCTGATGGCCAATGGCCATAA R 2 1 2 1 101000 f 74 goat snp31500-scaffold349-2136104 10 58803527 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790618 Affx-122976723 AX-385277620 10 40606895 GCTGATTGAGGCCTGAGGTTTTGCATTTGTAACCA[A/G]CTCCAGGCCAAAGCATTGGTCTATGGATCACATTT R 2 1 2 1 101000 f 74 goat snp31501-scaffold349-2185075 10 58753923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765099 Affx-122944804 AX-385252661 10 40649640 CTTACATGACCCGAAAGGTTATGCTTTCCTGCTTG[C/T]TTTACAAAAAACTAATGAACTGGGCAGAGGAACAG Y 2 1 2 1 201000 f 74 goat snp31502-scaffold349-2227820 10 58712792 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776064 Affx-122928452 AX-385263194 10 40679336 TTCCTGTCCTTGTAGTGTTTACAGTCTAGTGGAGA[C/T]GTATTAAATATTCCCACAAGTGGTGAGTAATTATA Y 2 1 2 1 101000 f 74 goat snp31503-scaffold349-2257516 10 58682009 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398150 Affx-122961680 AX-123268505 10 40709979 TCCAGAGCACTTCTTAAGGGAACTTGGTTGCTTTA[C/T]AAGAAATTCATATTGCATAATATTTGTGAAATGTC Y 2 1 2 1 101000 f 74 goat snp31504-scaffold349-2288159 10 58651360 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276529 Affx-1111835388 AX-519550040 10 40736118 GTATCAAACTATATGAGGCAAAAACCACTAAATGT[C/G]CAAGGACAAATGGATTCTACTACCACAGTTGAAGA S 4 1 2 1 101000 r 74 goat Random2.2K-1066 10 40736118 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424283 Affx-122941985 AX-123294629 10 40743003 AAATCCTCTGGCTTGCCTAAATACAGACATATAGG[A/G]GAAATTGGATTTGGGGATTGAAGGTTGGAGAAGGT R 2 1 2 1 101000 f 74 goat snp31505-scaffold349-2321183 10 58618315 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777438 Affx-122954844 AX-385264559 10 40776474 TTTCTTTTCCTCTTCAAAGTCACTGTATACTTAAA[G/T]AAGTGATACAAGACAACATAAAATGTGTATCAAGT K 2 1 2 1 102000 r 74 goat snp31506-scaffold349-2354654 10 58584657 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792389 Affx-122958197 AX-385279370 10 40848574 TAGGTCAGATGTTTACCCATAGGCACCTCAAACTC[A/G]CAGTGTCCCAGGTCAGATTATCTGCTTCCACCTCA R 2 1 2 1 101000 f 74 goat snp31507-scaffold349-2426754 10 58511992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377137 Affx-122978233 AX-123247496 10 40893210 GACACTTTTGTTGAGCAGCGAGGAGGAGGGAGGCA[C/T]GTCAAAGAGGATAAAATAAGGAAGCCAGAGCCCAG Y 2 1 2 1 101000 r 74 goat snp31508-scaffold349-2471390 10 58466952 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439459 Affx-122930174 AX-123309796 10 40936190 TGTACTAGGCAGTGATTTCCTCCAGGATGAGTCTC[A/G]TGACAATTTTGAAATCTCCACCAACCAGCATTTTA R 2 1 2 1 101000 r 74 goat snp31509-scaffold349-2514370 10 58424276 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397047 Affx-122962742 AX-123267402 10 40981187 TCTGACTTACTCTAAATTTGCACATCAAGCACCTT[A/G]CGGACTTGGCGGAACACGCAACCCACTGAAACTGA R 2 1 2 1 101000 f 74 goat snp31510-scaffold349-2559367 10 58379223 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395118 Affx-122964148 AX-123265473 10 41017355 TTTTTGAGGAGCTTCTTCCTACTTCTTTGATAGCC[C/T]GCTACAACACATAGACATGGTCAGCTCTGCCTTCT Y 2 1 2 1 101000 f 74 goat snp31511-scaffold349-2595535 10 58344600 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441565 Affx-122928686 AX-123311902 10 41050964 CCTATTGGGTGTTTGAGTTTGCCAGCCTTTGCACC[A/G]TCACAGTAAACGGTATGAACCAAACCACCATTCAT R 2 1 2 1 101000 r 74 goat snp31512-scaffold349-2629144 10 58310658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396499 Affx-122963531 AX-123266854 10 41061930 CAAGTGGGGCTAATAACTCTAAGACTGCACACGTG[C/T]GTCTAACATTTGTGACAGCATTTTGAACATTGTGG Y 2 1 2 1 101000 r 74 goat snp28336-scaffold302-584060 10 58299920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380670 Affx-122975186 AX-123251028 10 41103678 TACAGACAAATCCAGCCTATATTTTCACTACTCTA[A/G]TGGAGAGGGGTGGAGGGAAGGGTGGGGGAAAAGGG R 2 1 2 1 101000 f 74 goat snp28335-scaffold302-542312 10 58258259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415389 Affx-122948751 AX-123285738 10 41153979 TAATATTTTAAGATTTTACAAATAAAAATATTTAA[C/T]AGTAATTCACTAAATTTAATGCCCCCAAAGACATC Y 2 1 2 1 103000 r 74 goat snp28334-scaffold302-492011 10 58207228 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762754 Affx-986697284 AX-385250810 10 41210570 AGCGACTTAACCTGCAAAATCAAGTCTGTAGACTT[A/G]CAACACAAAAGGACATACAAAACCAAGACATAACA R 2 1 2 1 600010 f 74 goat 10_41210570 10 41210570 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 320765295 Affx-986697320 AX-385252822 10 41210573 GACTTAACCTGCAAAATCAAGTCTGTAGACTTGCA[A/T]CACAAAAGGACATACAAAACCAAGACATAACACCA W 4 1 2 1 600010 r 74 goat 10_41210573 10 41210573 Ancestral_priority_1043 ancestry 0.562 neutral IMAGE 10K 10K ancestral 320765302 Affx-986697324 AX-385252828 10 41210926 GAGATGAGGTGTTGAGGCAAGGACTACAATTTTAT[C/T]AGAAAGAGGATGGCAGATGAATGTCTCAAAATAAT Y 2 1 2 1 600010 r 74 goat 10_41210926 10 41210926 Ancestral_priority_1043 ancestry 0.584 neutral IMAGE 10K 10K ancestral 320762797 Affx-986697326 AX-385250838 10 41211066 AAAAGGCGGTTACTCCTACAAATCTCTCCTGGAAT[A/G]GCTAGCCTCAGGAAAGACATGTGTTAATTTCTTCC R 2 1 2 1 600010 f 74 goat 10_41211066 10 41211066 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 38443703 Affx-122927159 AX-123314040 10 41226618 TGGAGTGTGGGCTTTTCACATAGGCAGCACTTCCC[C/T]GTTGGACAACGTCAGGCCAGCGACCGTTGGAGGAG Y 2 1 2 1 101000 f 74 goat snp28333-scaffold302-419372 10 58130477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416530 Affx-122947762 AX-123286878 10 41266137 CCTATTCACATGGCTTATTAACGAGTCAGGCTTGA[C/T]AAATTTGGGTTGTAAACAGAAAAGGCTAAAACAGA Y 2 1 2 1 101000 f 74 goat snp28332-scaffold302-379853 10 58090996 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408872 Affx-122953989 AX-123279223 10 41307072 TGGGATTAGTGCTTATTTACTCATCATTGCTAAAG[C/T]GAGACAAGAAGAGGAATGAACGTTTAGTTAAGAAG Y 2 1 2 1 101000 f 74 goat snp28331-scaffold302-338918 10 58049307 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404397 Affx-122956788 AX-123274749 10 41339680 CCCCACTGCTATACTAGAAGTTTGTGGACCTGAGA[C/T]ACATGGCTCTGTGTGTTTATGTGTGAGTTGTTTAG Y 2 1 2 1 201000 f 74 goat snp28330-scaffold302-306310 10 58016358 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398534 Affx-122961533 AX-123268889 10 41405540 ATGGTTGCCAGGGACTGAGTGGGGGAGGGTTGACT[A/G]CAAAGTCCAACACAAGGGAATTTTGGAGGCAATGA R 2 1 2 1 303000 f 74 goat snp28329-scaffold302-240450 10 57949694 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783061 Affx-122920348 AX-385270128 10 41446419 ATATGGGGCCATGTATCCTAATCCAGTGAGAAAAG[C/T]GTTACATTAGATTCAGTGGAAATATCTTTATAAAG Y 2 1 2 1 101000 f 74 goat snp28328-scaffold302-199571 10 57908429 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272588 Affx-1111832889 AX-519546302 10 41461044 ACCATGCATGAGAGAATGAAGGAGAATTACCACCA[A/G]CCTACCTATCTTCCATTCTGTTCTTCAACTGCTGG R 2 1 2 1 101000 f 74 goat 10_41461044_AF-PAKI 10 41461044 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276531 Affx-1111835389 AX-519550042 10 41461525 AGATCAATATTTTAATGTCAGACTTTATGTGAGCC[A/G]GAGTATGAAGCCTTTTGGAAGCATAAATTCTAATA R 2 1 2 1 101000 r 74 goat Random2.2K-1068 10 41461525 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320790204 Affx-122924471 AX-385277208 10 41497922 TCTCAAGTACAACCCATTCTGTTGAGTTTAACGAG[C/T]ATCTTTTTGTTTGTACTGTATCTATCTTTGCAAAT Y 2 1 2 1 101000 f 74 goat snp28327-scaffold302-148068 10 57856889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417534 Affx-122946931 AX-123287882 10 41528179 GAGGAAGGCCTGGCTCCATGCCAAGCGGTCTGTGG[A/G]CACCTGGGGCACAGTGCTTGATGTAACCCTGGAAG R 2 1 2 1 303000 f 74 goat snp28326-scaffold302-117811 10 57827121 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420221 Affx-122945535 AX-123290569 10 41564708 TTCTGTTATCTTCCAGCCATTAGTGCGGGGCCTGA[A/C]AAATAATTAGGGCAAATAAAATATTCGTGTTGAAA M 2 1 2 1 201000 r 74 goat snp28325-scaffold302-81282 10 57790403 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451156 Affx-122921358 AX-123321490 10 41625709 TGGAATAGGGAAAGAAGCTGAAACTGGGGAGGTCA[C/T]GCTGGTCCCTGGGCAGGCAGTAGACAGGGTTCGGC Y 2 1 2 1 101000 f 74 goat snp28324-scaffold302-20281 10 57730410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438107 Affx-122931501 AX-123308445 10 41646817 TCCTTTCTCTACCCGTTTCGCTTACCTCTCCCCGG[C/T]GCTCCCCACCCCTGCCGTGGTTCCTCGTTCTTTCC Y 2 1 2 1 101000 f 74 goat snp24634-scaffold251-728 10 57709170 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439458 Affx-122930175 AX-123309795 10 41676666 TTGTTGGGTGTGGAGTGGTAGGGAGAGTAAGTTTT[C/T]CTTTGATGTGCCTTCAAGGTCATCCCCACAGAGAG Y 2 1 2 1 101000 f 74 goat snp24635-scaffold251-30577 10 57679313 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404532 Affx-122957400 AX-123274884 10 41724776 GCTATCAAATGATTTTATACATTTTATGCAATTTA[C/T]AATTGATCCCCAAGACTCACATCTCAAGAGAAGCT Y 2 1 2 1 101000 r 74 goat snp24636-scaffold251-78687 10 57631292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436007 Affx-122933493 AX-123306346 10 41767901 TTTGCGTAACCATCTTAGTTTTCAGAAAAATTAGC[G/T]AATGGGTCCACTTCCATAGTATCTCAGAGGGAGAA K 2 1 2 1 101000 r 74 goat snp24637-scaffold251-121812 10 57588233 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450070 Affx-122922806 AX-123320405 10 41813057 TTTGACAAAAACATAGGGGATACTAGATTTAGCAA[C/T]GATTTCTTCACTAGGACACCAAAAGCACAGGCATC Y 2 1 2 1 201000 f 74 goat snp24638-scaffold251-166968 10 57542977 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791768 Affx-122944213 AX-385278759 10 41846674 AAAAAGAATGATTTAGATTCTAAATCAGAAAAGGA[C/T]AGAAAATGAAGAGTAGCTGAAAGAGGCTACCAAAG Y 2 1 2 1 101000 r 74 goat snp24639-scaffold251-200585 10 57509421 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789071 Affx-122926166 AX-385276084 10 41936123 TTTGATTACAACAAAGACTGACGCCAACTATTTCA[C/T]AGTCTAGCTTTCATGTTATCTTCTTATATTTCTAG Y 2 1 2 1 101000 f 74 goat snp24640-scaffold251-290034 10 57420786 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375757 Affx-122978602 AX-123246116 10 42005714 TTCCCCTAATAGCCATGGTCTATAGTGTACTGAGT[A/G]TGTTTTACCAGGTAAATTACTAGTCCAGATGGCTA R 2 1 2 1 101000 f 74 goat snp24641-scaffold251-359625 10 57351041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765530 Affx-122924666 AX-385253013 10 42041099 TGGAATTGAGCACAACATGCTATCTTTTCATGTGT[A/G]CTTTCTATAGATTGTTCTGAGTACACAAGATTAGA R 2 1 2 1 102000 f 74 goat snp24642-scaffold251-395010 10 57315170 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769430 Affx-122959826 AX-385256600 10 42076511 CTTATAGTCTACGGTCCAAGGACTTGAGGGAATAC[C/T]AACAGTCGTCATTGTGGGATGTTCTTATCCTTTTC Y 2 1 2 1 101000 f 74 goat snp24643-scaffold251-430422 10 57278721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429466 Affx-122938483 AX-123299808 10 42147633 CCAGCCCCTCCACCCACACTGACCCCTCTCATCTA[A/G]CATGTTCTCCTAGAGCAAAGGGCCTGGCAGGAAGA R 2 1 2 1 201000 r 74 goat snp24644-scaffold251-501544 10 57207894 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437579 Affx-122931875 AX-123307917 10 42198706 AGAGCCTAAAGGAGAGGGCCCCTTGGCTCTAAGTT[A/G]CTTGGTTGAGACATTTTTCCTCCCTGGCTGGGTGT R 2 1 2 1 101000 r 74 goat snp24645-scaffold251-552617 10 57157012 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797556 Affx-122957169 AX-385284495 10 42232048 AGCCATTTACTTTGGGGCCTAGAGTCAGACTGGTA[C/T]CAATGGACATATCTGTCCTAACCTCAGGATTTCTC Y 2 1 2 1 101000 f 74 goat snp24646-scaffold251-585959 10 57125499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452758 Affx-122920262 AX-123323091 10 42267788 TAAGACTCGCTGAATGTCTTAGGGCAGAGGGGTGC[A/G]CCAGAGATGGGAACAGAGGAGGGCCTTGTGTCCAG R 2 1 2 1 101000 f 74 goat snp24647-scaffold251-621699 10 57090975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425792 Affx-122940706 AX-123296138 10 42366251 AATTTCCCCAGGGTTGGTAGGGACCGGAAGCCTCC[A/G]TTACTGACTCCTTGATTAGAAATTATTTCATAGGT R 2 1 2 1 201000 r 74 goat snp24649-scaffold251-720162 10 56993369 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411937 Affx-122951153 AX-123282287 10 42411028 GGAGCAGATGGAGAACAGACTGGAAGATTCATTCT[A/G]AGGAGGAAATAAACCCGCACAGGCTTTCTCCTCCA R 2 1 2 1 101000 f 74 goat snp24650-scaffold251-764939 10 56948158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429606 Affx-122937707 AX-123299947 10 42497091 TAATACTTTCTGGTAACGTTCTCTAAATTTACACC[A/G]TTTTCAAATATGTGATGCCACTTGATGACCTAAAA R 2 1 2 1 101000 f 74 goat snp24651-scaffold251-851002 10 56861966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785068 Affx-122969656 AX-385272115 10 42541992 TACTTAAAGGGCTTCATGTAGGAGAGGAAATAAAC[A/G]TGTTCCCTGTTGTTCCAGAGGACACAGGTAGGACC R 2 1 2 1 101000 f 74 goat snp24652-scaffold251-895903 10 56817510 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409518 Affx-122953626 AX-123279869 10 42614259 AAGGAGAGAGCCTAAAATGACTTAAAATCAGCAAG[A/G]GAATTCAATTTTTGTTTCAAAAGAATGAAAGATTA R 2 1 2 1 101000 f 74 goat snp24653-scaffold251-968170 10 56743130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414504 Affx-122949533 AX-123284853 10 42665163 TCCAAAGAAAAAAAACAAGCAAATGAGAATCAGAC[A/G]TGTAATGGACTTATCATTTATAACTATGAATGGTG R 2 1 2 1 101000 r 74 goat snp24654-scaffold251-1019074 10 56692331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386850 Affx-122970077 AX-123257208 10 42710790 ATATATTTACCAACTCCTTTGATTCAGCTATGCTA[C/T]GAAGCATGCTGTAAAACAGATCCTAAACAGCACAT Y 2 1 2 1 201000 f 74 goat snp24655-scaffold251-1064701 10 56647061 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377123 Affx-122978243 AX-123247482 10 42743412 CAACCCCAAATTCTTGATGAAGATTCTTAAGAAAA[C/T]ATCACTGGCACTTACAAGAATTCCTTTTCTCTTCA Y 2 1 2 1 101000 f 74 goat snp24656-scaffold251-1097323 10 56614316 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378599 Affx-122976579 AX-123248958 10 42777999 GTATTAATATATCCATACAATGGAATATTACTCAG[C/T]GATAAAAAGGAACAGAGTCCTGAAATATGCTACTA Y 2 1 2 1 103000 r 74 goat snp24657-scaffold251-1131910 10 56579855 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385421 Affx-122971330 AX-123255779 10 42810981 CCCAAACCTCTGCAGCACTGTAACTGCTGTTAACT[A/G]CAGGCTCCCCAAAGGATCAAAACATTTAGGGGCCA R 2 1 2 1 101000 f 74 goat snp24658-scaffold251-1164892 10 56546932 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781356 Affx-122931742 AX-385268440 10 42851304 TGCTGTAGTGTAAATTCTGATCTGGTAAGTCTAGA[C/T]TGGGACTTGAAATTCTGTATTTGTAAGCTTGTAGG Y 2 1 2 1 101000 r 74 goat snp24659-scaffold251-1205215 10 56506652 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383360 Affx-122972665 AX-123253718 10 42906414 AACCTGAAAAACGTGTCTATTTCAGGTGATCCTTA[A/G]GCAATCTGTTAGAGAACCTCTGAGAAGATGATTCC R 2 1 2 1 101000 f 74 goat snp24660-scaffold251-1260325 10 56451417 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417986 Affx-122946678 AX-123288334 10 42941965 AAAAATCTTTATGGAGGGCCCTTGAAAGTGTAACA[A/G]TTTTTCTGGATTGAGTTTATATATGAAGACTCTGG R 2 1 2 1 201000 r 74 goat snp24661-scaffold251-1295876 10 56416755 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408043 Affx-122954284 AX-123278394 10 42978234 GGTTTTATATCATCTTCCCAGGAAGTTGGAAAACA[A/G]TTGGGTTTTAGTTAAAGAAATGGAACCTATGCTCA R 2 1 2 1 101000 f 74 goat snp24662-scaffold251-1332145 10 56380548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766279 Affx-122936340 AX-385253671 10 43026103 CTCAGACTCTTATTTGAAAAGGTCGAGCCCAATCA[C/T]TGTCAAAAATCAGCACACTGATAATAAAATGCAGC Y 2 1 2 1 101000 f 74 goat snp24663-scaffold251-1380014 10 56332422 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403326 Affx-122957823 AX-123273679 10 43079810 CTGAAGAACTCATTCCTTATATCATCACATTAACA[C/T]CCTGCACCCAAGGCCAAGGGCTGTCTTGGACACCT Y 2 1 2 1 101000 f 74 goat snp24664-scaffold251-1433721 10 56278645 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784468 Affx-122969789 AX-385271517 10 43117767 CAATCTGAGGCACAAATTCATTTATGTTAGAACCT[A/G]CAGGTTTTCTGCTTCTAATCTCTGATTTCAGGTTT R 2 1 2 1 101000 r 74 goat snp24665-scaffold251-1471678 10 56240478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768761 Affx-122938242 AX-385255938 10 43157040 AGCTAAAAACCGATTTCTCTGCATTCCTTACAGCT[A/G]AATGTGGCCTGACACTAAAATTCTGGCCAAAGAAA R 2 1 2 1 101000 f 74 goat snp24666-scaffold251-1510951 10 56200749 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795753 Affx-122927238 AX-385282706 10 43199273 TGGCCACCTGCCTTGCAGTCACTGAGATGACTGAA[C/T]GAACTGAGATGATACATACGTAGTCTTAGAACAGC Y 2 1 2 1 101000 r 74 goat snp24667-scaffold251-1553184 10 56157719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380165 Affx-122975524 AX-123250523 10 43272002 CGCTAGGCTGTATCACCTCTCCCAATACTTAAGGA[C/T]AGTAGACCCGCAACATACATTTATTGAGTGAACAA Y 2 1 2 1 101000 f 74 goat snp24669-scaffold251-1625913 10 56089166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778475 Affx-122936433 AX-385265589 10 43301291 TAAAGGACTTGTCCAAAAGTGTGACAATGGCAACA[G/T]AACTGGCTTGATCTTTCTCAATTCAAAGTCTCAAA K 2 1 2 1 101000 f 74 goat snp24670-scaffold251-1655202 10 56060025 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380588 Affx-122975261 AX-123250946 10 43333293 ATGGCCATGGGTAACTGTGGAAGGGACAATTCCCA[C/T]GGAATAGTGGGGACTGATCAAGTACTGTGAAGAGC Y 2 1 2 1 101000 f 74 goat snp24671-scaffold251-1687204 10 56028163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778690 Affx-122952399 AX-385265801 10 43367458 GGCAAGTTATTAATCCTTATTAAATAGCCAGCCAT[G/T]AATCTCAATTAACTTGACTGTTAATTGAGGGAAAA K 2 1 2 1 101000 f 74 goat snp24672-scaffold251-1721369 10 55993619 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441157 Affx-122929563 AX-123311494 10 43377625 ACTATATACTCCCATTTTTAAAAAAGACAGACACA[C/T]GAGAACAGGGCACAGTTGAAACTGAAATAAAAGGT Y 2 1 2 1 101000 r 74 goat snp57256-scaffold912-6642 10 55983259 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425724 Affx-122940759 AX-123296070 10 43431727 CACCTTCTGTTTCTGGCACTAGTCCAGCTTCCTGT[A/G]TGACTTGGGGCAAATTAATTATCTGATCTCTTTCT R 2 1 2 1 101000 f 74 goat snp57257-scaffold912-60744 10 55930210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801995 Affx-122952219 AX-385288899 10 43494483 ATATAGCCATCCACTGGGAACATGTGACAGTTTAC[A/G]TCTTTAAATAGACTAATGGACAGCAAGGAAACAGA R 2 1 2 1 101000 f 74 goat snp57259-scaffold912-123500 10 55867646 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378188 Affx-122976946 AX-123248547 10 43574915 GTATATGGCTCACAGGCCAGCCAACCTCACAGTCC[A/G]TCAACTCCCTGCTCACATGATTCAAAGGGTGCCCT R 2 1 2 1 201000 r 74 goat snp57261-scaffold912-203932 10 55787131 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383398 Affx-122973499 AX-123253756 10 43604159 CTCGGGGCTGGTGAGCTGTGTGGGCTAAACTCCTG[C/T]GACTTTTTCCCTCTGGGCATTGGTTTCCCACAGGT Y 2 1 2 1 101000 r 74 goat snp57262-scaffold912-233176 10 55758376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791641 Affx-122919728 AX-385278632 10 43634448 CCTGTCCTATATATACTCCCCAAAGTAAACAGAGG[C/T]ATTTTTGCAAGAATCATTACTATATTAATTTTGTA Y 2 1 2 1 102000 f 74 goat snp57263-scaffold912-263465 10 55728175 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386492 Affx-122971547 AX-123256850 10 43663195 CACCAATATAGAAGGAAATATGACAGAAGGATCTA[G/T]AAACACATCAAACTTGTTCTCTCACAATATATATG K 2 1 2 1 101000 f 74 goat snp57264-scaffold912-292212 10 55699119 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399598 Affx-122961099 AX-123269953 10 43714608 CGGGCCTGTGTGAACTTGTGATTCCAGAGTTAAAA[C/T]GCACACTGAGTCTCAGTTCACACAAAACTCACTTA Y 2 1 2 1 201000 f 74 goat snp57265-scaffold912-343625 10 55648302 G A 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429707 Affx-122937623 AX-123300048 10 43819847 AAAGAGATTGAAAGACACTGACAATCAAGGCTCAA[C/T]GCAAAATGGAAACAAATATCCTTAAAGTTATAGTA Y 2 1 2 1 101000 f 74 goat snp57267-scaffold912-448864 10 55543569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425665 Affx-122940875 AX-123296011 10 43858264 GGGCTACAACAACCATAACTTACAAATTAAGTGAC[A/G]TGCTAATTCCCTGGCCCAGCTCAAAGAAGTAGTCT R 2 1 2 1 101000 f 74 goat snp57268-scaffold912-487281 10 55508252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401097 Affx-122959415 AX-123271450 10 43939978 AAGGTGGAGACCCTGAGTTCTTCACCCTAGGAGGA[A/C]ACATTTCTCACCACTTCTGTCCCGCTATTTGAGGC M 2 1 2 1 101000 r 74 goat snp57270-scaffold912-568995 10 55426744 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785424 Affx-122961762 AX-385272469 10 43996273 ACTACAATGCAGGAGTGCTAATGGACTGGCACATA[C/T]GCCATTTGTCTCACCGTTTTGAATATATTTTTACT Y 2 1 2 1 101000 f 74 goat snp57271-scaffold912-625290 10 55370543 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444033 Affx-122926880 AX-123314370 10 44043018 TATTCACTTCCCTTGCACACCCAAGGCACTCAGTG[C/T]ATGTTTGTCATTGCTCACAAAGTGAGTGGGGATGA Y 2 1 2 1 201000 r 74 goat snp57272-scaffold912-672035 10 55323959 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272590 Affx-1111832890 AX-519546303 10 44085713 TCTCACCTAAGATGGGACCAAAGAGAATTGTGAAG[A/G]ATGGAGGAGGTAGGAAAAGAGATAGAGGATTGCGA R 2 1 2 1 201000 f 74 goat 10_44085713_AF-PAKI 10 44085713 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425673 Affx-122940867 AX-123296019 10 44112257 ATGTGCTCCATGTTCTTGGGGGAACCTGCTCTCTT[C/T]CACCCTCCCCTCCTGCTTTTTGATCCCTCTGTCTC Y 2 1 2 1 101000 f 74 goat snp57274-scaffold912-741274 10 55254386 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442137 Affx-122928329 AX-123312474 10 44157391 GTGTAGTTTAGACTATAAAATAATGGCTCAGAGAT[A/G]TTAGTCATGGGATATAAACTTTCAGTTATAAGGTG R 2 1 2 1 101000 f 74 goat snp57275-scaffold912-786408 10 55209010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385661 Affx-122971153 AX-123256019 10 44187150 TGGAAAAAAAAGGATGAGGTCCAGAGCATAGGTGA[C/T]GCAAAGTTTAAACTTGGATAGAGAGGAGTGAATGT Y 2 1 2 1 101000 f 74 goat snp57276-scaffold912-816167 10 55178504 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444439 Affx-122926558 AX-123314776 10 44216116 CCTCTTAAGAAAGTTTTAGGTTAAAGTATTAAAAG[C/T]GTCCAAGTAATTGCAGGATTGTGTGAACTAGTTTG Y 2 1 2 1 101000 r 74 goat snp57277-scaffold912-845133 10 55149307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424835 Affx-122941359 AX-123295181 10 44258672 GCATCTACCCCAGGTACACTATGAGAAACTAGCCC[A/C]AATTGTCTGTGAGAAGATTTAAGCATACAAGGATA M 2 1 2 1 201000 r 74 goat snp57278-scaffold912-887689 10 55105673 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789130 Affx-122952533 AX-385276143 10 44299007 AAACTATAGGGGTAAAAAGGTTTGGGTAGAATTGA[G/T]CTGATACAGTTGAGGGTAGATTGGGACATTTGCTT K 2 1 2 1 201000 f 74 goat snp57279-scaffold912-928024 10 55065311 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797856 Affx-122973028 AX-385284795 10 44328597 TGTGTATATTTTGTGCATTTCTTAGAGGCATAGAA[C/T]ACCATGTTCCTCCTTGGAGATTCTACTTTTACCAT Y 2 1 2 1 101000 r 74 goat snp57280-scaffold912-957614 10 55035076 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436470 Affx-122932979 AX-123306808 10 44373959 TGACTATGTAGCTGTGTATGCTAGGTAGTATACTC[G/T]ATCTGACTTTAAAATAAGATTCAGTAGTAATATAC K 2 1 2 1 101000 r 74 goat snp57281-scaffold912-1002976 10 54990438 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787812 Affx-122923837 AX-385274835 10 44406435 ACTAATTTTCGTTATACCATCTTTTGCTGAACAGT[A/G]TTTGAATTTTAGTACATACAAATCAATATTCCTTT R 2 1 2 1 101000 f 74 goat snp57282-scaffold912-1035452 10 54957956 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396536 Affx-122962947 AX-123266891 10 44503167 TCTTTACTGAGTAGCTCATGGGAGAGTCATTGGAC[G/T]CATGGAGCAGAGCATGGTGGGGTATAAGTGAGCCG K 2 1 2 1 101000 f 74 goat snp57284-scaffold912-1132184 10 54861467 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442659 Affx-122927905 AX-123312996 10 44577872 CTCTTCTCAATTGGTCTGGCCATGCCAGTGCTTAC[A/G]GCTTAGTGTCTCGTCTCAAAATAGCAGCAGTGTTA R 2 1 2 1 101000 r 74 goat snp57286-scaffold912-1206889 10 54786273 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774521 Affx-122927700 AX-385261655 10 44631034 CACAAATTTGTCTCACTGTGCTTTGAGTATGTTTA[C/T]AAATGGCCTCTACCACCTCCAGGGCTAGTAAGTCC Y 2 1 2 1 101000 f 74 goat snp57287-scaffold912-1260051 10 54732774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396436 Affx-122962987 AX-123266791 10 44683453 GAAAACCTAGAAACAGAGAGATTTCATTGCTGATG[C/T]AGTGCTGGCTCTCATGGCAGGTTGTCTGACCCTCT Y 2 1 2 1 101000 f 74 goat snp57288-scaffold912-1312470 10 54680257 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434678 Affx-122933965 AX-123305019 10 44722843 TTAGATTGGAAACAATGCCGCCTGTGGCTCTCTGT[A/G]CCCTCCCCTCTCATTATAGCCCATCCTTGGAACAC R 2 1 2 1 201000 f 74 goat snp57289-scaffold912-1351860 10 54640356 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423561 Affx-122942418 AX-123293907 10 44782958 AAAGCAGATGGGAAACTAAAACTAGGAAGAAAGGT[A/G]CAGTAGGTGCAAATTCAGACACCTAGGTAAATAGT R 2 1 2 1 101000 f 74 goat snp57291-scaffold912-1411975 10 54580613 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446004 Affx-122925869 AX-123316341 10 44842771 CAGAGACATAAAGGGTCTTACCCAAGATCACACAG[C/T]ACACCAGAGCCAAAAACCAGGTCTGGAACCTAAGA Y 2 1 2 1 103000 f 74 goat snp57292-scaffold912-1471788 10 54520236 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424629 Affx-122942179 AX-123294975 10 44926055 CTCCTCTGAACCCCCTCACCCAGCGGCCTGTGTTC[G/T]CTGCATTTTGTGGTATGTCCTGTCTTCCTTACACA K 2 1 2 1 101000 r 74 goat snp57294-scaffold912-1555072 10 54436567 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434583 Affx-122934112 AX-123304924 10 44963372 AGTTGGGAGCACGAGGGGCTTACTGAGTCTCCCTT[A/G]TACCATATTTTTCTCAAAACTGGAGATGGACCCCA R 2 1 2 1 101000 r 74 goat snp57295-scaffold912-1592389 10 54398294 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391590 Affx-122966606 AX-123261947 10 45001585 GAAGATCAGTTCTAATGGTCTCAAATATTTTTCAG[G/T]CTACAACTATTTCATCCTCGTTGTATGAAGTATTA K 2 1 2 1 201000 f 74 goat snp57296-scaffold912-1630602 10 54359819 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450378 Affx-122922090 AX-123320713 10 45032545 ACCCATTGATTGTATCACAACCTCAGGAAGAGTTA[C/T]CTTGCCTTAGAACTCTTGGGTGGCTTTCCTTCTGA Y 2 1 2 1 101000 f 74 goat snp57297-scaffold912-1661562 10 54328848 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385752 Affx-122971075 AX-123256110 10 45076645 CATTTTTTACATCGATTGCATTTTGTATGATCAAA[C/T]ATAATTTTATTTTATCTTTGTAAGCCTCTAGATCA Y 2 1 2 1 101000 f 74 goat snp57298-scaffold912-1705662 10 54284488 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427538 Affx-122939506 AX-123297881 10 45120363 TTTGGCTAACCCAGTAGAACAGACCTTTAAAGAAA[C/T]GTAGGGATTCACTTAACAGAGAAGGCAGAAAGGAC Y 2 1 2 1 101000 f 74 goat snp57299-scaffold912-1749380 10 54240281 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800040 Affx-122963505 AX-385286963 10 45154310 AGTAAGGAGTGGCATCCTCAGAATTATGCTTCCAG[C/T]GAAGTAAAATATACAGCTGCAGAGAGATTCATCTT Y 2 1 2 1 101000 f 74 goat snp57300-scaffold912-1783327 10 54206030 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430517 Affx-122937214 AX-123300858 10 45191357 ACATCTTTCTCTGGGTCTTCTGATGACCCGGGGCA[C/T]GCTGACATGGGGAAAAGTACATGTCCCTTTCACAG Y 2 1 2 1 101000 r 74 goat snp57301-scaffold912-1820374 10 54169374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399641 Affx-122961068 AX-123269996 10 45244442 TATAACCAATGTCCAGAGCAGGGTCTTGCTGTCAC[A/G]TTTAGTGTGTCTTAGTTGAATGAAATAATGAAAGA R 2 1 2 1 201000 r 74 goat snp57302-scaffold912-1873459 10 54116919 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770524 Affx-122947491 AX-385257689 10 45284605 GATGAACGAGTGACTGTATGAGAAATTTAGCCACT[A/G]TTAAGAGACCCTTGAAATCTTCGTACGCTACTTAG R 2 1 2 1 101000 f 74 goat snp57303-scaffold912-1913622 10 54076783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440296 Affx-122930221 AX-123310633 10 45331324 TGAATCTCTCTGAATTTAACTTTTGTTTTCATATC[A/G]CCAGGAAGTAGTCTCCAGAAATTGAAACTCCAGCT R 2 1 2 1 101000 r 74 goat snp57304-scaffold912-1960341 10 54030162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432682 Affx-122936042 AX-123303023 10 45369400 CTTCTTCTAAAAGCAATCTGGGGTAAGGATAAAGT[C/T]TTCCTCAGAGCTGGCTCTTTTCTCCTCCACCTCCT Y 2 1 2 1 201000 f 74 goat snp57305-scaffold912-1998417 10 53992142 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450717 Affx-122921879 AX-123321051 10 45405187 TGCATAATTTCAAAGCACCTCCCTACAAAGGACTG[A/G]TGAATTACAAAAGGAAAATGAGTAAATTTACAGAG R 2 1 2 1 101000 f 74 goat snp57306-scaffold912-2034204 10 53956241 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420811 Affx-122944679 AX-123291158 10 45493457 TGAAATGAGAATGTGTAATACCCTCTTCCCTCTGA[A/G]AAATCAGGGCTCCCAGCTTAATCCCATTCCCTCTT R 2 1 2 1 101000 r 74 goat snp57308-scaffold912-2122474 10 53867590 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427140 Affx-122939644 AX-123297483 10 45523068 GTGGATTGGCCTTTGCACTGAGCTGGACTGAACAA[A/G]CATTGGGAAGAAGATGGATGCAAGATGAGTCAGGC R 2 1 2 1 101000 r 74 goat snp57309-scaffold912-2152085 10 53838138 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410938 Affx-122952043 AX-123281288 10 45593325 CTTGTTTCCTTTAGAGATTCAGAACTCCCCTCCAC[A/G]ATGTTTTTGGACCAAGGTAAATCAGAAGTAAAGTC R 2 1 2 1 201000 r 74 goat snp57311-scaffold912-2222342 10 53767780 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773863 Affx-122955197 AX-385261003 10 45647692 TGAAGAACTGTTATGAAAATAGACCCAATTTCCCA[A/C]AATCAATGCCAGGTTTCCTGTGTTTAAACCCTCTG M 2 1 2 1 101000 r 74 goat snp57312-scaffold912-2276709 10 53713433 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412553 Affx-122951328 AX-123282902 10 45677016 AAATACTTCTTGATTTGTTATTTGAATTATAGATG[C/T]GTGGATGGTGTTAAAGACTGGCTTGCCTTGAGCCA Y 2 1 2 1 201000 f 74 goat snp57313-scaffold912-2306033 10 53684032 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416471 Affx-122947807 AX-123286819 10 45745063 ATATTTATTATTTGAAATTATACTGTGAGATTTGT[A/G]CTATATTATTTTGGAAACCAATATTAGAACTCAAA R 2 1 2 1 101000 r 74 goat snp57314-scaffold912-2374080 10 53616278 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442301 Affx-122928250 AX-123312638 10 45797731 GACAAGAAGGGGACAAAAAGGGGAGAAGAGATGCA[C/T]GCGCTAGCATCTGTCTCATACTCCCTGAAGACACA Y 2 1 2 1 201000 r 74 goat snp57315-scaffold912-2426748 10 53563556 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378106 Affx-122977148 AX-123248465 10 45838244 CAAGAGAGAAGAGTTCTGCCCAGATAGCCATTGGC[A/G]CCTAGAGTGTGCCAAGAAGGCTGAGCCTTCAACTG R 2 1 2 1 102000 r 74 goat snp57316-scaffold912-2467261 10 53523934 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412883 Affx-122950426 AX-123283232 10 45914527 TCCTCCAACCTCTCCACCCTTCAGTCCACCAGCGG[C/T]AGAACTACATGTTCTGTTTCCCCAAGTACAGTTTT Y 2 1 2 1 101000 r 74 goat snp57317-scaffold912-2543544 10 53447698 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788882 Affx-122964052 AX-385275897 10 45959053 GTGTCCATGGGAGATTCCAGAGATACCGAGAGACA[A/G]TTGTATCTTAGAAGATAATGTAGTGTGTATGGTTT R 2 1 2 1 101000 f 74 goat snp57318-scaffold912-2588070 10 53403332 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404345 Affx-122956827 AX-123274697 10 46013047 ACTTACAGGAAGCTGATGTCATTCATTGGAAACTG[C/T]AGCAAACCTGACCATTCCTTTGCCCGTGGGAGTAT Y 2 1 2 1 201000 f 74 goat snp57319-scaffold912-2642064 10 53349008 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450773 Affx-122921834 AX-123321107 10 46054293 TCTGTGGTATCACTTGTCAGAACTGTGGCTTCAGG[C/T]GACTGGCACTTAGATCAGAGACTGATTTTCCAGAT Y 2 1 2 1 101000 r 74 goat snp57320-scaffold912-2683310 10 53307757 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276386 Affx-1111835391 AX-519549914 10 46128633 GCTTCTTGGTGCATAATCTTCATTCAAATGGCCAA[A/G]AATAATTTAAAGAGTCTCTTCTATTTGGGAATCAT R 2 1 2 1 101000 f 74 goat Random2.2K-1074 10 46128633 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446465 Affx-122925067 AX-123316801 10 46138073 GTGACCTGCTCCCGTGCCCAAGTGGCTGAGGCAGC[A/G]TGCCCTGGGAGGGACCTAGTATGGGACTGGACTAT R 2 1 2 1 303000 f 74 goat snp57322-scaffold912-2767090 10 53223508 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411088 Affx-122951928 AX-123281438 10 46169759 GGACCTTGATTAGGGAGTTCTAGCTTCCAGAAGTG[C/T]GGGGAAAATAGGCTTTAAAAAGTCTGTTGTTTAAG Y 2 1 2 1 101000 f 74 goat snp57323-scaffold912-2798776 10 53192063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375860 Affx-122978516 AX-123246219 10 46199809 ATATAATGGACCTCCGGAACCACGTTCTGCACCTG[C/T]GGATTCAGTCCACAGTTGGTTGAATCCGAGAAGGC Y 2 1 2 1 101000 f 74 goat snp57324-scaffold912-2828826 10 53162170 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780397 Affx-122963102 AX-385267491 10 46231796 TCAGTGAATGTGTGCTGCACTTCACATGGCTTTCC[A/G]TCTATTAGACTTGTTTTGTTCTCTAGCTGATAAAT R 2 1 2 1 101000 f 74 goat snp57325-scaffold912-2860813 10 53130552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439746 Affx-122930532 AX-123310083 10 46289543 AATGACCATCTTCTATAGGCAGAGTGGAGCAGGAA[C/T]GAGGAAGTTATACTAGGGGAAAAGTGGCTTGTTTA Y 2 1 2 1 101000 f 74 goat snp57326-scaffold912-2918560 10 53072715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375892 Affx-122978492 AX-123246251 10 46334654 TGGGGTATTCATAACAATGATGAGGAATTCTCTTC[A/G]CTCAGTCCCACACACCTGCTACACCTGTGTCTTTG R 2 1 2 1 101000 f 74 goat snp57327-scaffold912-2963671 10 53027658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769454 Affx-122937825 AX-385256624 10 46372123 GTATTTCCAGGTACAACTTTCACCTAGGACAAGGG[C/T]AGTCATCACAAAAACTTCAGGATCCTCAAGAACCT Y 2 1 2 1 101000 r 74 goat snp57328-scaffold912-3001140 10 52990377 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409752 Affx-122953008 AX-123280103 10 46402125 GGTCAGAGGCATTTTCACTAGTTTGATGAAATGCT[A/G]TCGTAGGAAGAGAGTGTGAGCAGGTCTTGTGGAGC R 2 1 2 1 101000 f 74 goat snp57329-scaffold912-3031142 10 52960500 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447804 Affx-122923929 AX-123318140 10 46446049 CAGGGAGGTAAGAGGCTAGGAGATGTGTGTGATCT[A/G]CTGATGTTTATAATGATGTAGGTTTGTTTAAATCA R 2 1 2 1 101000 f 74 goat snp57330-scaffold912-3075066 10 52918388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410048 Affx-122953235 AX-123280398 10 46487622 TCTTTCTGGCACCTCTGAGCTGTCTTAGACAAGGT[A/G]CTCACTGGTCTGTACTGCTGAAATTTCCAGGGTAC R 2 1 2 1 201000 r 74 goat snp57331-scaffold912-3116639 10 52878400 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408054 Affx-122954275 AX-123278405 10 46526573 GAAAATTAAGCTCCTATTGAAACATAGTAATCAAG[C/T]CCCACTGGTGATGGTTCCAACCGCCTTGTCAGGAA Y 2 1 2 1 201000 f 74 goat snp57332-scaffold912-3155590 10 52842475 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393614 Affx-122965360 AX-123201889 10 46558724 TCTCAGCACAAAGATGGAATACCATCTTTGGAGGC[A/G]TTCCAAGCTCTCTGATATATTCAAACAGTCTGACC R 2 1 2 1 101000 r 74 goat snp57333-scaffold912-3187741 10 52810012 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780796 Affx-122956214 AX-385267885 10 46601319 ATTAGGAAAAGGATGATCAGAGAGGGACAGAGGAT[A/G]GAAAGAAATGTCCTTGATCCAACATCTCAGGAGAA R 2 1 2 1 101000 f 74 goat snp10188-scaffold1366-22556 10 52767491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447002 Affx-122924557 AX-123317338 10 46654085 TGCAGGAGTTGCTTAAAAGTGATGTTTTTGCTAGC[A/G]TCACTTACTCTGGGATGACTTCATCTTTTTATCAT R 2 1 2 1 101000 r 74 goat snp10189-scaffold1366-75322 10 52713083 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764599 Affx-122957736 AX-385252245 10 46710644 GGTCTCATCAACTGTACAGGCTTTGTATTATACCC[A/G]TTTCTTCTAATGATCCAAGATTCATGCTGCCAACA R 2 1 2 1 101000 f 74 goat snp10190-scaffold1366-131881 10 52656605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272646 Affx-1111832891 AX-519546356 10 46733631 AAAGTGGAATATTGGGTCTCATCCACCCCACACAC[A/C]CACTGCCTGAACACTCCCAATATCACCAGCTGCAG M 2 1 2 1 101000 r 74 goat 10_46733631_AF-PAKI 10 46733631 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38382800 Affx-122973571 AX-123253158 10 46752947 TTTCTCTGAGGAAAATCTGAAATAGAGAAAAACCT[A/G]TTTTTGTTTGTATCTGCATGTTTGTGGCTCCTGAC R 2 1 2 1 101000 r 74 goat snp10191-scaffold1366-174184 10 52613832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442504 Affx-122928556 AX-123312841 10 46810170 GCTTAGCAGAAGGCTGTTAACATAAATACTTGAGT[A/G]TCACAGTGCTATAATATAGAAAAATGTTTCTTTGT R 2 1 2 1 101000 f 74 goat snp10192-scaffold1366-231407 10 52556681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430659 Affx-122936941 AX-123301000 10 46846089 AGTAAATCCAGATTAAAAGAGATGAAAATCATCAT[A/G]TAAAAAGACCATAGATGTTATTTTGCATTTAAGAG R 2 1 2 1 101000 r 74 goat snp10193-scaffold1366-267326 10 52520908 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414193 Affx-122949661 AX-123284542 10 46887395 TCAAAATGCTTGAGTTAACTGGCACTCCCTTCCTC[A/G]TGCCCATGAATGCAACCATTTTCTGCCCAGAAATG R 2 1 2 1 101000 f 74 goat snp10194-scaffold1366-308632 10 52479446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449961 Affx-122922891 AX-123320296 10 46918765 TATTTCCCAAAGAATTAATTGCTCCCTTCACCAGC[A/G]TGCCCCAAGTGTTAAACTGAGCTTAATGCTAGCTC R 2 1 2 1 101000 r 74 goat snp10195-scaffold1366-340002 10 52447733 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417452 Affx-122947196 AX-123287800 10 46971411 TAACAAGACACTGATTTTGCCTTTATGAAGCTACC[A/G]TGAACAAGGGAATAAATATTAGAACAAAAAAACAT R 2 1 2 1 101000 f 74 goat snp10196-scaffold1366-392648 10 52393817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794308 Affx-122925933 AX-385281272 10 47017268 ACAAGTTTAAATAGCTATAGACCCAACTCAGCTTT[A/G]TTCACCTGTGATTGACTGTCTTTGACAGGGTGTCC R 2 1 2 1 101000 r 74 goat snp10197-scaffold1366-438505 10 52347678 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454106 Affx-122919359 AX-123324439 10 47072844 GTGCTCTTAGAAATCAGAGAAAATGTGTACAATTT[A/G]CTATTAAGCAAAAAGAAAGAGTATAAATAAATACA R 2 1 2 1 103000 f 74 goat snp10198-scaffold1366-494081 10 52291872 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453007 Affx-122920108 AX-123323340 10 47110320 TTTCCCTTGGATTCCCACTGCCTGGCACATGGTAT[A/G]CACCCAGTAAATACATATGGAATTCAATGCTATGT R 2 1 2 1 201000 r 74 goat snp10199-scaffold1366-531557 10 52254469 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426257 Affx-122940331 AX-123296603 10 47171191 ATTTTGAAGCTGACATGCCCCTGAGACATGGATTT[A/G]CCTGAGAATAATGAGTCACATCCGAATATACTTAG R 2 1 2 1 201000 r 74 goat snp10200-scaffold1366-592428 10 52192661 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418025 Affx-122946647 AX-123288373 10 47199978 TCATTCTGTTTTTAATGAATGTATTTTTTGTTGTT[A/G]TTGTTAAAAAGGAAAATACCAGCCACCAATGTCTT R 2 1 2 1 101000 r 74 goat snp10201-scaffold1366-621215 10 52163856 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782632 Affx-122972239 AX-385269705 10 47235129 GCAGCTTTAAAAAAAAGGTGTCAAAGTGGCATCCT[A/G]CAGATCAATGAATAATTCCAAAGGGAAAATGTACC R 2 1 2 1 101000 f 74 goat snp10202-scaffold1366-656366 10 52128480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789738 Affx-122964869 AX-385276746 10 47268020 AATTCAGATGGCTTGAGAAATTATGATCACATGAC[A/G]TAACTATTGTGGGATATGTATTCTTTCTACTTCTG R 2 1 2 1 101000 f 74 goat snp10203-scaffold1366-689257 10 52095698 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418610 Affx-122946351 AX-123288958 10 47284569 TTACTCAGACACATTGACCAGACTCTGAAATGAGC[A/G]ACTATTGCAAAAGCACTGCTGCTGACAGCGTCCTA R 2 1 2 1 101000 f 74 goat snp48105-scaffold68-4327516 10 52078863 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276388 Affx-1111835392 AX-519549916 10 47303581 GTATGGATCTCTCCCTTTTAAACAGATGTATTGAG[A/G]TATCACTTCAGTCGCTCAGTCATGTCTGACTCTTT R 2 1 2 1 201000 f 74 goat Random2.2K-1076 10 47303581 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418713 Affx-122946284 AX-123289061 10 47316791 CTGCAGGTGGACTCTGACTAGCAAATGGGTAGATG[C/T]GAGAACTGTGATCATGTACTGCCCTGACCATGTTT Y 2 1 2 1 101000 r 74 goat snp48104-scaffold68-4295294 10 52046758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389614 Affx-122968757 AX-123259972 10 47350872 TTTCAGGTTCTGCCAGGCTCCTCCTCACTTGGACA[G/T]AGAATCATCTGCTTCTAATCAACTCGTAAAATGGT K 2 1 2 1 101000 r 74 goat snp48103-scaffold68-4261213 10 52012666 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430303 Affx-122937273 AX-123300644 10 47387251 CTATAACGGCAAGTATTTATTTAAAACAAACAACC[A/G]TTTGTATACAAATGATAGTGAAAGTGTTAGTCGCT R 2 1 2 1 201000 r 74 goat snp48102-scaffold68-4224834 10 51976414 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777427 Affx-122969924 AX-385264548 10 47435965 GTACAACAACTCAACAGTGGTGGAAGTTGAAATTG[A/G]CACTTAAGTCAGTAACCTTTATTCTACCGTTAGGT R 2 1 2 1 201000 f 74 goat snp48101-scaffold68-4176120 10 51927590 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380614 Affx-122975244 AX-123250972 10 47464888 TAAGGTCTACCTGAAATTTCTTTCAGTTTCTACTA[C/T]AGAAACTTTAATTTTCATTAGAAAGCACTGATAAA Y 2 1 2 1 303000 r 74 goat snp48100-scaffold68-4147197 10 51898656 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787827 Affx-122933123 AX-385274850 10 47514819 CTACTGTGCATTGAGAGGTTAGAAAGGGCTGTTTT[C/T]TTTAGAGGTAATATTTGATTTGCAATCAGTGGTTA Y 2 1 2 1 101000 f 74 goat snp48099-scaffold68-4097266 10 51848635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767126 Affx-122947881 AX-385254413 10 47566317 CCCTTGCCTTGTACATAAACACTGTATTCAGTCTC[A/C]CTAATTTACAATAAACTGTCAAAATAACCCTAAAC M 2 1 2 1 101000 f 74 goat snp48098-scaffold68-4045768 10 51797080 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421287 Affx-122944733 AX-123291634 10 47640471 AAGTTATTCCTCTGTTAGTTGTTACTGTCTTCTTA[A/G]TTTGTTCCAAAGACAACACTGCCATTCTGCATTCC R 2 1 2 1 101000 r 74 goat snp48097-scaffold68-3971614 10 51722836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438857 Affx-122930761 AX-123309194 10 47676204 CTGATTGCCCACTGTGGAACACTGTTTTCCTGCCC[G/T]AACACATTGTTCTTCCAGATCTTTCCATTTCTGGT K 2 1 2 1 201000 r 74 goat snp48096-scaffold68-3935881 10 51687105 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454218 Affx-122919680 AX-123324551 10 47711865 ATGTTTAATAACAGAGTGAGTCCCTCCTTTGTCAC[A/G]CTTTTGTTTTCTTATAGAAAGAATATAGGTTTAAG R 2 1 2 1 101000 f 74 goat snp48095-scaffold68-3900220 10 51651896 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782580 Affx-122934953 AX-385269654 10 47745751 AAGTCTGGTCCCAGAGACTCGTCATTCAGGACATA[G/T]TCTCAAGGCCAAACTTGTGATCTCTCAACAAAGTT K 2 1 2 1 201000 r 74 goat snp48094-scaffold68-3866334 10 51617709 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765956 Affx-122963353 AX-385253382 10 47785084 CGCATGAAAAGGAAGAGATTATCGAAGGCCAATGG[C/T]ACAGATAAGTAATTTAGAAGTTCAGAGTAAGGTGT Y 2 1 2 1 101000 f 74 goat snp48093-scaffold68-3827001 10 51578278 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777449 Affx-122929031 AX-385264569 10 47851789 GGAAAACCCTATAAATACTAAGTTAAGGAAACTGT[A/G]TTAGCAATATCAACTGGTATTGGATGTAGGGTTGT R 2 1 2 1 101000 r 74 goat snp48092-scaffold68-3760296 10 51511370 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393497 Affx-122965817 AX-123263853 10 47908084 GCTAGTCATGCATTAATCCCCTGCTTAAGACCATC[A/G]TTTCAACTTCATGCTTTTCAGCCTCCCTCTCGGGT R 2 1 2 1 101000 r 74 goat snp48091-scaffold68-3704001 10 51454902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429037 Affx-122938313 AX-123299379 10 47961767 ACTCATCAGACAGCACAGACCTGCCATACAGAGGA[C/T]AGGCACTCTCTTGTTGGCTCAAAACCTTCTGCAGC Y 2 1 2 1 101000 r 74 goat snp48090-scaffold68-3650318 10 51401450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447913 Affx-122923803 AX-123318249 10 48002865 GGGCTCTGTGTCCCAGAGATGAAGCCAGAGTTTAC[C/T]GGACTCTCAGATGTTCAATGAATTTCCACCTTCCA Y 2 1 2 1 101000 r 74 goat snp48089-scaffold68-3609220 10 51359767 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274571 Affx-1111834300 AX-519548160 10 48003374 CCTCTGTTCTGAGTTTCAGAGC[A/G]AGGAGTTTGTGCATGAGCCCTTTAAGAGTGAAGTC R 2 1 2 1 102000 r 74 goat GoatD01.029505 10 48003374 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386128 Affx-122971414 AX-123256486 10 48041854 ATAACTGTTAACATGTTAGCATATTTATTCTCTCT[A/C]TATATGCATATTTATATGTGTGTGTGACACAGAAC M 2 1 2 1 201000 f 74 goat snp48088-scaffold68-3570231 10 51320437 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412947 Affx-122951462 AX-123283296 10 48091278 CATGGGTCTCAGCCCCTAAAATGCTATCTACCAAT[C/T]GTAATTAACAGTGCTGTCAACAAGGGTTTATTATT Y 2 1 2 1 201000 r 74 goat snp48087-scaffold68-3520807 10 51270985 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443791 Affx-122927093 AX-123314128 10 48120058 TTCCCCACGCTGCTGTGAACTGGTCCTTGTCTTTT[A/C]TGTCCCTCCCTTTGTCTAGCACCATGCTTGCATCC M 2 1 2 1 201000 r 74 goat snp48086-scaffold68-3492027 10 51242202 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276539 Affx-1111835393 AX-519550050 10 48158679 GCAGCTGCACTCAGGTGAGTGTATCAAAGTCACCT[A/G]ACGGCCTTATTAAACCATAGACCCTCCTTAGAACT R 2 1 2 1 101000 r 74 goat Random2.2K-1077 10 48158679 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443951 Affx-122927015 AX-123314288 10 48160488 ATCCTTCACAAATACACCCTCTTTAAACTGGGCTT[C/T]GGGGAAGAACAAGGCGGCCCTGAGTTTGAGGTTAT Y 2 1 2 1 101000 f 74 goat snp48085-scaffold68-3451597 10 51201646 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401353 Affx-122959250 AX-123271706 10 48232249 GCGTCAAAGCCCGTTGGAGTCACACCTCCGTGCTC[C/T]CACTGCACTCCTCTCTTGCCATCTCCCACTGTCTC Y 2 1 2 1 101000 f 74 goat snp48083-scaffold68-3379836 10 51129606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417800 Affx-122947374 AX-123288148 10 48271668 AGGACATCTGAAATGGCTCCTTCATCCACAGAGGT[A/G]ATGCCTTAGTTCTCCTCCATATGGCATACCATCCC R 2 1 2 1 201000 f 74 goat snp48082-scaffold68-3340417 10 51090326 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404585 Affx-122957360 AX-123274937 10 48300393 ACCCCCGGAACAAGCCCTCTGCCTGAACTTGCAAA[C/T]GGATAAGAATCAAAGAGGATGATTTCTTCAGTCAG Y 2 1 2 1 101000 r 74 goat snp48081-scaffold68-3311692 10 51061623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391074 Affx-122966839 AX-123261431 10 48330352 GAATTATACATTTCTACATCTATTGAGATAACCAC[A/G]TGGGTTTCTGTTCTTATCTGTTGATAAAGAAAATT R 2 1 2 1 303000 r 74 goat snp48080-scaffold68-3281733 10 51031284 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798746 Affx-122959921 AX-385285677 10 48381298 CTCCCTCAACTATCTAGATATTCTTTTGAAATGTT[A/G]AGTCAGTTCACATGGTTCCACTCAAGTAGTTTCAC R 2 1 2 1 101000 r 74 goat snp48079-scaffold68-3230787 10 50979504 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436192 Affx-122932601 AX-123306531 10 48506280 TTGTGCAATGCCCATTAATCTAGAATCCAAGCAAG[C/T]GAGAGGTGAGTTTGAAGAAAGCACTTCCCATTGTG Y 2 1 2 1 101000 f 74 goat snp48077-scaffold68-3105805 10 50854844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408583 Affx-122953660 AX-123278934 10 48548412 GCTCAAAGTTCCTAAGGGAGTTCATTTGTTTTTCC[A/G]TTAATTCATTTATTCCTTACTTCCTTGCTCTGTAC R 2 1 2 1 303000 r 74 goat snp48076-scaffold68-3063673 10 50812797 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439563 Affx-122930089 AX-123309900 10 48591523 CGGCATTAAGTGGATCCACTAGCAGAACTATCAGT[C/T]CTGCCACCCAGTCTCATCTCTTTCTAGCCCATCAC Y 2 1 2 1 101000 f 74 goat snp48075-scaffold68-3020562 10 50777613 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409841 Affx-122952936 AX-123280192 10 48632945 GGTATGGGGAACACCCAGGGGTGAGAAGAATGGCT[A/G]TGTCACGTCTCAGCCTGGCCTCCCACACCTTTGAA R 2 1 2 1 201000 f 74 goat snp48074-scaffold68-2979140 10 50736066 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770418 Affx-122935450 AX-385257584 10 48738029 ACTGGAAGTCTGCAATAATCTATACAATAACCTTA[C/T]AATGTACAAACAGTTATTCTCCCTGCCTTAGGGGG Y 2 1 2 1 101000 r 74 goat snp48072-scaffold68-2874056 10 50631087 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438356 Affx-122931325 AX-123308694 10 48799379 TGTGTTCACCCTTCTTTGCCTGTACTGCCCACCTC[C/T]TCCTCACTCACCTGAGGAATGCCTAGGCATCCTTC Y 2 1 2 1 202000 r 74 goat snp48071-scaffold68-2812706 10 50570013 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802292 Affx-122930960 AX-385289196 10 48843785 TCTGTGCAGCAGAAAGGGAGCACATGGATAACTTC[A/G]CACTTGAGTAGTGAACTGGTAATGTAGTTTTACTC R 2 1 2 1 101000 f 74 goat snp48070-scaffold68-2768300 10 50525540 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408062 Affx-122954269 AX-123278413 10 48873295 GTCATTTTGGATGGAAAAACCACTACAGATCTTCA[C/T]GGTGATGTGAAAAGTGTTATCGCTCAGTTGTGTCC Y 2 1 2 1 201000 f 74 goat snp48069-scaffold68-2738790 10 50496257 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780013 Affx-122976485 AX-385267112 10 48931840 CCTCATTATTCTTTCTGAGAAGGAGATGAATAACT[C/T]ATTTTAAAGTGGCTGGTGAGCTTCAGTTCTTATAA Y 2 1 2 1 101000 f 74 goat snp48068-scaffold68-2680245 10 50437649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413711 Affx-122950079 AX-123284060 10 48988347 CAGTAGTGTAGGTAGGTAACCTCTTCCCTCTTTTA[C/T]AAATGAGGAAACTAAGGCTCTAGGAGGCCAGGCCC Y 2 1 2 1 103000 f 74 goat snp48067-scaffold68-2623738 10 50380947 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387272 Affx-122970547 AX-123257630 10 49137161 TTTTCCTATTTGGAACCAGTCTGTTGGAATAGGAT[A/G]TAGGATGCTGCAAATGAACCTAACCATGATACAGA R 2 1 2 1 201000 r 74 goat snp48065-scaffold68-2474924 10 50231513 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436686 Affx-122932453 AX-123307024 10 49256201 AGTGATTTCATCCTGTATTGTTCAGTAGTAACCAG[C/T]AGCCATGACTGTTTAAATTAAAATTTTAAATTCAG Y 2 1 2 1 101000 f 74 goat snp48063-scaffold68-2355884 10 50111939 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787940 Affx-122931869 AX-385274962 10 49290315 AATTCTTGGAAGAAGTAACTCACTGGCTACATTTC[A/G]TTCACCTGTAAGTACCTATTGTTATCTTACAACTT R 2 1 2 1 101000 f 74 goat snp48062-scaffold68-2321770 10 50077818 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463093974 Affx-1109810600 AX-514581322 10 49317107 GAAAGCAAGTCTTGAAAATTTCTACACCCAAATTC[A/C]TAGCAGCATTATTCAAAAAAGTTAAAAGGTGAAAG M 2 1 2 1 101000 f 74 goat 10_49317107_AF-PAKI 10 49317107 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38444250 Affx-122927218 AX-123314587 10 49334953 CCAGTGGGAAAGGGTGCACAACATGTACAAAGTAA[C/T]GGAAAATTTTTAGCAGATAGAGGTAAAAACAGTCA Y 2 1 2 1 101000 f 74 goat snp48061-scaffold68-2277132 10 50033023 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404885 Affx-122956470 AX-123275237 10 49452327 ATGTCTGTGTGTTGTTTAGCTACCAAGCCTAATGA[A/G]GATTTAGGTTTCTCTATAACTTTTAAAATAATTTT R 2 1 2 1 101000 f 74 goat snp48059-scaffold68-2159758 10 49915019 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771862 Affx-122968808 AX-385259018 10 49486259 ACCAGAAATAAGTCTGTATTAAGTAAGCTTTGCTT[A/C]ATATGAGTTTGCTGAATTTGATTTTATTGAATGTG M 2 1 2 1 201000 r 74 goat snp48058-scaffold68-2125826 10 49880424 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406586 Affx-122956264 AX-123276938 10 49530523 TTGGCTTGGAAGACACTTCTTTCAAGAGAAAATAC[A/G]GATATCATAAAAAAATAAAAAAAATACTCATTTAT R 2 1 2 1 101000 f 74 goat snp48057-scaffold68-2081562 10 49836402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276541 Affx-1111835394 AX-519550052 10 49558203 ACTTCATTACAGTTACTCCCCCCATAAAACTTTAA[A/C]TTCATCAGATTAATTTATCCCTACACTTATGAATC M 2 1 2 1 201000 r 74 goat Random2.2K-1078 10 49558203 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778125 Affx-122944852 AX-385265240 10 49559805 AAAAATGGAAGCAAGAATTCAGTTTTATAGGGGAA[A/G]TAACCTTCCACACTTAGGAAACCGATTTTCTTCAG R 2 1 2 1 101000 f 74 goat snp48056-scaffold68-2052280 10 49807003 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418506 Affx-122946432 AX-123288854 10 49610540 ACCAAGGATACATCAGTGAATAAAACAAATACCTG[C/T]GCGTGGGAATCTTATTATAGTTCCTCCAGTGGGGA Y 2 1 2 1 101000 r 74 goat snp48055-scaffold68-2001545 10 49756473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272383 Affx-1111833858 AX-519546111 10 49643686 TGGTAAAGAATTTCTTCCACC[A/G]TCTGCCACTAAAATCCATGCTGGACACAAGTTATG R 2 1 2 1 101000 r 74 goat GoatD01.007920 10 49643686 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38395713 Affx-122963718 AX-123266068 10 49694214 ATCTTCCTGGGGTCTAATGTTTACCATCTATACGG[C/T]TGGAGACACTGATGTGGGCTGGGCTAGGTCAGGTA Y 2 1 2 1 201000 f 74 goat snp48054-scaffold68-1917871 10 49671178 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447975 Affx-122923757 AX-123318311 10 49724087 GTTAAAAGTCAGAAATCATGCCTCCCTAGTGCCAC[A/G]TGTAGCTGAGCACAAGCATGTGACCCAGATCACCC R 2 1 2 1 201000 r 74 goat snp48053-scaffold68-1887998 10 49640682 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434671 Affx-122933970 AX-123305012 10 49765993 TGATTTTTCCATGATAGAAACAGAAATAACAATAG[C/T]TCCCACTTTACATTATAAAGCCTTCCTGTATGTAA Y 2 1 2 1 101000 r 74 goat snp48052-scaffold68-1846092 10 49597989 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783838 Affx-122931845 AX-385270894 10 49834141 GGATGTTAATATTAATAGATACATGGTAAAGGGAA[C/T]GCCTTCTAGAACCCTTACTCCATTAGTGAAGGAAT Y 2 1 2 1 101000 r 74 goat snp48051-scaffold68-1777944 10 49528911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383205 Affx-122972782 AX-123253563 10 49904455 CCTGATTGAAGAGGTCCAACCGAAGCTCGAATAGT[A/G]ACCTGCAAAAATGAAGATAATATCTGCTTTAGAAA R 2 1 2 1 101000 f 74 goat snp48050-scaffold68-1707630 10 49457556 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765249 Affx-122929398 AX-385252786 10 49939874 GGTTAGTGAAGTCTCCAACTATGACTGCAAAATAG[G/T]CTATTTCTCCCTTCAACTCTATGAATTTTTCCTTC K 2 1 2 1 101000 f 74 goat snp48049-scaffold68-1672211 10 49422191 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774031 Affx-122930442 AX-385261169 10 49969304 GCCAAAAAGAAATAGATAATATGAACAGATCAACT[A/G]CCAGTAATAATACTGAATCTACCATAGAACAACTC R 2 1 2 1 101000 f 74 goat snp48048-scaffold68-1642781 10 49392171 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409161 Affx-122953205 AX-123279512 10 50012626 CTAGATATTTTTTTCCAAGTAAACAGTCTGTTTAC[A/G]TTTGTCATAATGACCTCAGATCTTTAAACTCTGGA R 2 1 2 1 101000 r 74 goat snp48047-scaffold68-1599459 10 49348485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425440 Affx-122941523 AX-123295786 10 50060186 CACCCTTAGCTTTGGGCCTTCCCTGGGTTCCTGCA[C/T]GTTAGAGGGTCTCTCCATACTGATCTCCTTCCCCA Y 2 1 2 1 101000 r 74 goat snp48046-scaffold68-1551899 10 49301207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407420 Affx-122955233 AX-123277771 10 50115031 GGATCTAGGAGAGAGGGAACTCTGCTATTAAAATG[C/T]CCTACAAAATAATAGAGAAATGAGGGCGAGGGAAC Y 2 1 2 1 201000 r 74 goat snp48045-scaffold68-1497054 10 49245891 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440078 Affx-122929730 AX-123310415 10 50144613 AAAGCAACTGATCTTCCTGTCTCCAGTCGTACTCC[A/G]CTCATGTCTGTCCTCAGCACTGCTACCTGAATCAT R 2 1 2 1 201000 r 74 goat snp48044-scaffold68-1467472 10 49215354 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772085 Affx-122971513 AX-385259240 10 50173790 GTTTCTTTTACTAGACATAATGTTGAGATTCATCC[A/G]TGTTTCAGGCTTTTTCCGTTGGTAAGTCTTGCCAT R 2 1 2 1 101000 r 74 goat snp48043-scaffold68-1438295 10 49186155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770962 Affx-122976389 AX-385258125 10 50290187 AAAATAAATGTGGCCAAGTTTCAGAGCTTGAGTAT[A/G]GGAAGTCTTTCTGTAGTGATGATTGGGTACTGTCA R 2 1 2 1 101000 r 74 goat snp48041-scaffold68-1321898 10 49067701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448093 Affx-122924323 AX-123318429 10 50326533 GGTTCTTTTCCACTGAGTCACCAGGGGAGCCCACC[A/G]AAGAGCATAGAGTACCTCTAAACCTAAAGCTACAG R 2 1 2 1 101000 r 74 goat snp48040-scaffold68-1285552 10 49031278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801477 Affx-122962105 AX-385288386 10 50376489 AAGGTATTAGTAGTCAACTGAGAAATCTCAAGAGT[A/G]TTAATAGGAGTTTCAAACACATCTGCTCCTTCTGA R 2 1 2 1 101000 r 74 goat snp48039-scaffold68-1235596 10 48980133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384730 Affx-122972049 AX-123255088 10 50406265 AGGAGAGCAGGAAGCCAGACGGCAGGAATTAAAAA[C/T]GTTAAGGCAGAGAAAAGATCTGAAGGAAAGATAGC Y 2 1 2 1 201000 f 74 goat snp48038-scaffold68-1205820 10 48949051 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771894 Affx-122952679 AX-385259050 10 50455815 TTATCTAATTACTTTGACTAAAATATCTAATTTAA[C/T]GGTAAAAAGTAGGAGTGACAGTAGACATCCTTGTT Y 2 1 2 1 202000 f 74 goat snp48037-scaffold68-1156270 10 48899459 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435013 Affx-122933810 AX-123305353 10 50535133 ATCTAGACTGCTCTTGTAAAAGCTGGTTATTCTTT[C/T]GTTTACTAGCAAACAATGTGATTAAATGGGGGAAC Y 2 1 2 1 101000 r 74 goat snp48036-scaffold68-1076952 10 48820655 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787932 Affx-122959021 AX-385274954 10 50571822 ATCAATTACACACTTTTATTGAACTGATCATGCCA[A/G]TTCAGCTATCCTAAGAAGCCTAAGCCTTAGTTATA R 2 1 2 1 101000 r 74 goat snp48035-scaffold68-1040263 10 48783621 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771283 Affx-122948386 AX-385258441 10 50632755 GACTATAATTAATAGCTTCCTAGCAGGAGGCTCTA[C/T]GTCAACTATCTTATCTTTGAAATCTATCTTTCCTA Y 2 1 2 1 101000 f 74 goat snp48034-scaffold68-979330 10 48722731 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442481 Affx-122927931 AX-123312818 10 50666869 CTGACCTTTTCCCCCTCTACCGGCTGGAAGCTACA[C/T]TCCCATCCTTAGCCTACAGAATATATCTCTTGGAA Y 2 1 2 1 101000 r 74 goat snp48033-scaffold68-945216 10 48688561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779103 Affx-122922564 AX-385266208 10 50699539 AAGAGCACCTCTATATTAACTGAAATGGTCCAATG[C/T]CTATGATACAGTACATAAAAAAGTTACCAAAAAGT Y 2 1 2 1 101000 f 74 goat snp48032-scaffold68-912546 10 48655401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428739 Affx-122938443 AX-123299081 10 50733374 GTCCAGGCGATTAAAGCTGAAAGAACAGAGAGAGG[A/C]TGGTTATGACGGACAGTGACAAAGTGACAAAGCAA M 2 1 2 1 101000 f 74 goat snp48031-scaffold68-878711 10 48621192 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433084 Affx-122935730 AX-123303425 10 50762788 CAGTTTGTGTTTCTGATTAGCCAGCACCATTGCAG[G/T]AGCAGGGGAGTAGAGACTCTGGAGAAGAGCAAGGG K 2 1 2 1 101000 f 74 goat snp48030-scaffold68-849297 10 48591823 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438174 Affx-122931836 AX-123308512 10 50797983 TCTACTTGAGACCACCTTTTTCTGCTTTACCTGGA[C/T]CAGTAAACACATACACAGTTGGTACCGTTGGGCTA Y 2 1 2 1 101000 f 74 goat snp48029-scaffold68-814102 10 48556369 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435071 Affx-122933730 AX-123305411 10 50886681 AATTTTTCATCTCTTTCATTCACTACTAAACACTG[A/G]ATAATACATAGCAGGTACTCAATAAATATTTGTTG R 2 1 2 1 101000 f 74 goat snp48027-scaffold68-725404 10 48466800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785240 Affx-122927548 AX-385272285 10 50979450 ACTTTGTATGCATCTGTGACATTTCTGTGTTATTA[C/T]GCCACTCTAAAATACATCCTCACCTCTCCAATGTC Y 2 1 2 1 201000 f 74 goat snp48026-scaffold68-632635 10 48373896 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433290 Affx-122935207 AX-123303631 10 51027674 TACTACCGCATCAACAGGGTTCCAGGATAATGACA[A/C]TGGATCACAGAAGAAAAGAGCTGTATGACAAAGGC M 2 1 2 1 101000 f 74 goat snp48025-scaffold68-584411 NW_017211556.1 9848 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389115 Affx-122968563 AX-123259473 10 51056768 TATGATTAGCTGTACTTTGTTTCTCTGGATGTCAC[C/T]AGTTAGTAAGTTTTCTTCCATCTCTCCTCATTTTT Y 2 1 2 1 101000 f 74 goat snp48024-scaffold68-555317 10 48285468 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414393 Affx-122949990 AX-123284742 10 51119775 TTATATGCTTTGTCTTCATAACTGACATGAGACCA[G/T]AGAAAAGGACTGCCCAATTATTCCCCATGAGCAAG K 2 1 2 1 101000 r 74 goat snp48023-scaffold68-492310 10 48222991 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781249 Affx-122975398 AX-385268334 10 51155214 CCATCTACCTTCTCAAAAACCTCTATTTAATTTGA[A/G]CCATCCTGATTCTCAATTTACACCTCCATTCTGCC R 2 1 2 1 201000 f 74 goat snp48022-scaffold68-456871 10 48187507 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772850 Affx-122973622 AX-385259995 10 51185517 CAGAAAAGAAAGGAAGAATGCAGTCAGTATTCATA[A/C]CCACTCTCTGGTAACTGAAAATGCACTTTTCAAAC M 2 1 2 1 101000 r 74 goat snp48021-scaffold68-426568 10 48156901 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778202 Affx-122925277 AX-385265317 10 51219804 ACACCTAAGTCTATAAATGGTCTTCATGGGTTTTG[C/T]TTTCTATTCATGGTAACAGCAATACATAACAGTCT Y 2 1 2 1 101000 f 74 goat snp48020-scaffold68-392281 10 48122208 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778190 Affx-122973879 AX-385265305 10 51248745 TTCACTGAAGATATACTTCAATTTTACACAAGACT[A/G]TAAATAGAAAAATACATTGACACACAAAAAAAGTT R 2 1 2 1 201000 r 74 goat snp48019-scaffold68-363340 10 48093271 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795552 Affx-122938096 AX-385282507 10 51279090 AGAGCAGATACTTGAGATGGATCTTGAAGCACAGG[C/T]AGGATCTGACAAGTGGAGCTCAGTGCTACAGAGCA Y 2 1 2 1 101000 f 74 goat snp48018-scaffold68-332995 10 48062578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442404 Affx-122927994 AX-123312741 10 51309592 CTTACACATTTCATGATCCTTCTGTCACTCATATC[A/G]TCCTTGGAAATGGTAAGAACTCAACAAGACTTCTT R 2 1 2 1 101000 f 74 goat snp48017-scaffold68-302493 10 48032310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418147 Affx-122947103 AX-123288495 10 51344728 CTGAGTTCAGAAATGATTCAACCAAACACTCAAAA[C/T]GGATTTTCATCACTGGGATATTTTTGTTTCCCATT Y 2 1 2 1 101000 f 74 goat snp48016-scaffold68-267357 10 47996477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403389 Affx-122957775 AX-123273742 10 51378390 ACACCCAACTTGTCCCAGACTTCTGCACAAACCCC[A/G]TTTTCTGCATATACCAATACCACTCTCAACATCAC R 2 1 2 1 101000 r 74 goat snp48015-scaffold68-233695 NW_017195302.1 6115 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785323 Affx-122948156 AX-385272368 10 51413273 GGAACTTTTAACCAGTCTCTCGAGTCACCTTAAAA[C/T]TTGGAAGCTAGCTAAACAAATGCCAACCTAGTACA Y 2 1 2 1 102000 r 74 goat snp48014-scaffold68-198812 10 47926859 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419164 Affx-122945735 AX-123289512 10 51483490 GAAGAAAAATTGCCAAGTTTGGCAGGGCAATCAGT[A/G]AGGAAGGCTCCAGAGCAAATTTCATTTCTCAGCAG R 2 1 2 1 101000 f 74 goat snp48013-scaffold68-128595 10 47855663 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782571 Affx-122955425 AX-385269645 10 51526613 GGAAGGGATAGAGTTGTTAATTTATATTTATGACA[C/T]GTTTCTACTTATATTCATTTCATCTAAAAAATCAC Y 2 1 2 1 101000 f 74 goat snp48012-scaffold68-85472 10 47813359 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414761 Affx-122949248 AX-123285110 10 51594821 GCATCTCAGTGTTTCTGCACTTTTCAGTAAGTTTT[A/G]TTTCATAATGAAAGAGAAAAAAGAAGGTTGAGTAC R 2 1 2 1 103000 f 74 goat snp48011-scaffold68-17264 10 47744446 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426877 Affx-122940476 AX-123297222 10 51636811 GGCCAGCTGGGTAAAAAGGTCATCCAATCTCAGAC[A/C]CAGCCTGCTGCCAAGGGATCAACTGTTCATTGAAA M 2 1 2 1 101000 f 74 goat snp25253-scaffold259-7948182 10 47701945 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423258 Affx-122942670 AX-123293604 10 51668495 AAATCCAGAAATGACGGTTTTGCCTTACTTCACAA[C/T]ATAGGTAACTCCATAGCATGCTAATGATTATGACC Y 2 1 2 1 101000 r 74 goat snp25252-scaffold259-7916498 10 47669868 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377265 Affx-122978135 AX-123247624 10 51700288 CAAGTTCCCTACCTCCAGTCTTCCATCCTCCTGGC[A/G]CAGGAAGGATCCCTTCCCATAGGAGCTGTATTTTC R 2 1 2 1 103000 r 74 goat snp25251-scaffold259-7884705 10 47637525 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799248 Affx-122925699 AX-385286178 10 51732101 ATCTGCTCCTTTTCTTCTGAAAGTCTGGGAAACAA[C/T]TATTTATTCCCAGGAATTAAGTTATTATTAATTTC Y 2 1 2 1 102000 f 74 goat snp25250-scaffold259-7852892 10 47605286 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776901 Affx-122919251 AX-385264025 10 51767957 TTGGGGATAATGCATCCTCACTATGGATGTCCCAA[G/T]TATTGACAGCCACTTATCTAGAGAAGGACAGGAGG K 2 1 2 1 101000 r 74 goat snp25249-scaffold259-7817036 10 47569654 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795315 Affx-122920350 AX-385282273 10 51812328 CAGAGACGCGCACACAACCTGAATGCATTTGCACT[A/G]CCTCTCATTGACTGTTATTTCAACAATAGTTAAAC R 2 1 2 1 101000 f 74 goat snp25248-scaffold259-7772665 10 47525194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421120 Affx-122944205 AX-123291467 10 51847736 CCACCAGCAAAAATGCCATTATGTAACATTCCCCA[G/T]GCAGATAGAGTCATATCATGATTGCTTATCTACAT K 2 1 2 1 201000 r 74 goat snp25247-scaffold259-7737257 10 47489812 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383546 Affx-122972615 AX-123253904 10 51884180 TACTCTTATCACCTAATTTCCTAACAACCCCTTGA[C/T]GTTTTTGTCATGACTCTTTTCTATGGATGAGACAA Y 2 1 2 1 201000 r 74 goat snp25246-scaffold259-7700813 10 47453214 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430799 Affx-122937464 AX-123301140 10 51940122 TCCCATATTCCAGATCTGTAACTATTTCTGTTGTC[A/G]ACAATGGCAATCTGCAAACCTTGGTAGCATTTGGA R 2 1 2 1 101000 r 74 goat snp25245-scaffold259-7644871 10 47397057 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398721 Affx-122961839 AX-123269076 10 52003078 GCTTGGGATTCTTTAAGCACACTTCTTAAATTGGG[A/G]TTTGTGGCTGGGCTTTAAACTGTATCCTGAAATTA R 2 1 2 1 101000 f 74 goat snp25244-scaffold259-7581915 10 47334379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271745 Affx-1111832892 AX-519545539 10 52037431 CACGCCTCACCTCTGCTGCAGCCATCACTGTCCAC[A/G]CCTCACCATTCTTGCTCAGTCTCCCTGGGAGTCTG R 2 1 2 1 102000 r 74 goat 10_52037431_AF-PAKI 10 52037431 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38451975 Affx-122920942 AX-123322308 10 52054804 TGCAGACCTGTTCTTTTCCACATGGACTTCTCCAT[A/G]GGGCTGCCTGGGTGTGCTCACAGCATAGTTGCTAA R 2 1 2 1 102000 r 74 goat snp25243-scaffold259-7530189 10 47282952 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386337 Affx-122970874 AX-123256695 10 52110343 CTCTTTCCTTGTCCTTTACATCTAAAAGAAAGTGC[A/G]TGGGAAATGTGTGAGATCAGTTGGAATGAATTAAA R 2 1 2 1 101000 f 74 goat snp25242-scaffold259-7474650 10 47226952 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774931 Affx-122930484 AX-385262064 10 52156434 CTTTTACTATGACCCAGTTTTGACAGGGGTAAGAG[C/T]AAAATTAAGAAAACAGGATGGAAAATTGCCACTAA Y 2 1 2 1 202000 r 74 goat snp25241-scaffold259-7428559 10 47180273 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451099 Affx-122921398 AX-123321433 10 52215374 GATCTCCTGATGCCTCTGTCTCATTTGTAATGCCT[G/T]TAGTCTAAAGACTCCTTTTTCATCAGGGGAACACT K 2 1 2 1 102000 f 74 goat snp25240-scaffold259-7369619 10 47120425 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381987 Affx-122974089 AX-123252345 10 52269739 CTTAGACCAGAGATAGAAGTGAATCTCAACATTCC[C/T]GCTAAGCCTGAATATAAATATTGGAGAATCATACC Y 2 1 2 1 101000 f 74 goat snp25239-scaffold259-7315254 10 47065914 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389253 Affx-122969031 AX-123259611 10 52309260 TCCATTCATTGGTTGTCCTTTAAGTGTGCCCCAAT[C/T]TGTTGCTTTTATGAAGAGATTACACCTTGCCAGCT Y 2 1 2 1 101000 r 74 goat snp25238-scaffold259-7275733 10 47025899 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429721 Affx-122937612 AX-123300062 10 52359630 TTAGGTGGAAAAGATCTGGTTTACTGTGGAGCCCT[G/T]AGAGGAAGATCCAGGAAATAAAATAACCCTGTATT K 2 1 2 1 101000 f 74 goat snp25237-scaffold259-7225363 10 46975523 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402730 Affx-122958341 AX-123273083 10 52397631 TTCTTATATTTAATTGCCTTTAAAATGTGTCCTCC[C/T]CTTTCATCTGTAAACATGGAAAGCATTTAGGAATT Y 2 1 2 1 101000 f 74 goat snp25236-scaffold259-7187362 10 46936955 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442089 Affx-122928365 AX-123312426 10 52435783 TAGTTTTGTAGGCTGGCCATCTGGGGCTTGAGTTA[C/T]AGAGAATTATTGTTGTCCTAGGGACTTGAAAGCCA Y 2 1 2 1 201000 r 74 goat snp25235-scaffold259-7149210 10 46900851 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426988 Affx-122940385 AX-123297333 10 52528193 TTCATGAACCAATGAAGCAGAAAGTGAAAGAGAGC[C/T]CTTGTTAGTGTTTTGTGAACCTCAGGGGTTCTTGT Y 2 1 2 1 201000 r 74 goat snp25233-scaffold259-7056800 10 46807947 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434887 Affx-122934343 AX-123305227 10 52571827 TTTCCTCTGTAACAGTCTTGTTTTCATCACAGACT[A/G]CTCAGATCAATGTCACTTCTCAAAGAGTTCTCTTC R 2 1 2 1 101000 r 74 goat snp25232-scaffold259-7013166 10 46763743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789388 Affx-122978584 AX-385276398 10 52611610 AGAAACACTGAACTCTGTAATTTAATGATCCATCA[A/C]AATCTATTTTGAATCTTACTTTGTGTTTTTCTTGA M 2 1 2 1 101000 f 74 goat snp25231-scaffold259-6973383 10 46724094 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402472 Affx-122958600 AX-123272825 10 52651928 AGAGGGACACACAATTTAAAGCTTACAAATGGCTG[A/C]TTTCTGGCATTTTTCATTTAACATTTTCAGGCTGC M 2 1 2 1 101000 f 74 goat snp25230-scaffold259-6933065 10 46683729 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439253 Affx-122931001 AX-123309590 10 52702345 ACAACAGTTTCTTTGGCCTGGAATGCTCTTCCTCA[G/T]AATTTCCTCCTGGCAAACTCCTGTAAAAATGGAGC K 2 1 2 1 201000 r 74 goat snp25229-scaffold259-6882648 10 46632841 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784498 Affx-122950348 AX-385271547 10 52732641 GAAGACCAACCAGATTCTCTAGTTCTTTAGCAATC[A/G]TAGTTACAGGACTTATACAGCTGAATTAATCTATC R 2 1 2 1 101000 f 74 goat snp25228-scaffold259-6852352 10 46602084 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435086 Affx-122933720 AX-123305426 10 52785781 CATTTTACAGACAAGAAGTGCAGAAAAAAAAAATT[A/C]AACCAACCAACCAACTAATAGACAAAAAAGGACTT M 2 1 2 1 303000 f 74 goat snp25227-scaffold259-6799212 10 46548951 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398600 Affx-122961488 AX-123268955 10 52878487 CCAGGTGTCTAATGGCTATCATTGTGGCATGGCTA[C/T]GATTGTCTAATACAATAATTATTTTGGGGGAAGTA Y 2 1 2 1 101000 f 74 goat snp25226-scaffold259-6706506 10 46455734 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404746 Affx-122957232 AX-123275098 10 52998255 ATGTCTGGAAGAAAAAAATAAAGAGACATCAAGAC[G/T]ATTTTCCTTACAATACATTCTTTGAGAAAGATTGC K 2 1 2 1 202000 r 74 goat snp25223-scaffold259-6586738 10 46334622 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765827 Affx-122933076 AX-385253274 10 53064023 GGATCAATTAACTGATTCAAGCCTTAGTTTCAGCC[A/G]CTGTAAATTATTTCCCCATAAGGCTTTCCACTGGA R 2 1 2 1 101000 f 74 goat snp25222-scaffold259-6520970 10 46268365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390660 Affx-122967133 AX-123261017 10 53110527 AGAGAGGAGAATTTCATTCATCAGAATAAAAGCTG[A/C]GTTGACCCTTCCTGTGCAGGTTCAAGCAGTTAAGC M 2 1 2 1 201000 f 74 goat snp25221-scaffold259-6474466 10 46220846 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376316 Affx-122978357 AX-123246675 10 53183633 GAATTTCTTGCTTTTGAAGGTTTCTCCCTGGCAAA[A/G]TCCTCTAGGCCACAATCCACCCATGAGCCAACGTT R 2 1 2 1 201000 f 74 goat snp25220-scaffold259-6401360 10 46148373 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404939 Affx-122956431 AX-123275291 10 53222541 CTTGTTAAGAAAAAAGTGGTGATCTATGCCACATT[A/C]GGTTCTCTGTGGGAGAACCTGAGGTGGGAACATAA M 2 1 2 1 101000 f 74 goat snp25219-scaffold259-6362452 10 46109584 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396654 Affx-122962857 AX-123267009 10 53277250 TATGGTTTAGCTTTCTTCCTCATTTCAGTTGGCTT[A/G]TGCTGCATCTTTAACAGCATCTTCAGAGAAATGGA R 2 1 2 1 201000 r 74 goat snp25218-scaffold259-6307743 10 46054517 T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774117 Affx-122942158 AX-385261255 10 53334703 CATGGGAGAAAAAGATGGAAGACAATTAAAAGGTT[A/G]CTGTGTTTTTGAGTCTGTATCACTAATAGAAATAC R 2 1 2 1 101000 f 74 goat snp25217-scaffold259-6250290 10 45996187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779232 Affx-122945069 AX-385266336 10 53368548 TTACTTCTATATCCATTCTCTGGACCTAAAGATGG[A/G]ATTACCTTCCCTGTTCTGTTCCTCTTGTCTCATCT R 2 1 2 1 101000 r 74 goat snp25216-scaffold259-6216445 10 45962341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416082 Affx-122948328 AX-123286431 10 53445388 TGAGCAACTAAAACTTGCTCACAACAAATTGTGGA[A/C]GATTCTTAAAGAATTGGGAATACCAGACCACCTTA M 2 1 2 1 103000 r 74 goat snp25215-scaffold259-6139605 10 45884369 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423353 Affx-122943154 AX-123293699 10 53578404 ATTTTTTTGGCATTAAAACTGCTAAGTCTGACTGA[C/T]GCCTTAACTGTTTAAACTTCCGGAACTTCAGTTTT Y 2 1 2 1 101000 f 74 goat snp25212-scaffold259-6006589 10 45750848 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418576 Affx-122946377 AX-123288924 10 53648611 GCCCCCTCCAACGCCCTTGCTTCCTGATACCCACA[A/G]GGAAGGGAAAGAGGCTGTGGCATTTCAGTATTGTT R 2 1 2 1 101000 r 74 goat snp25211-scaffold259-5936382 10 45680289 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430638 Affx-122936957 AX-123300979 10 53706466 TAACCGTGGGATGTGTTTGGGACATCAATTTAGTG[A/C]TGTAGTGGGAGCCTTGATGGGAAGATGGGAGTAGG M 2 1 2 1 101000 f 74 goat snp25210-scaffold259-5878527 10 45620233 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447482 Affx-122924093 AX-123317818 10 53776940 CTTTTAATAGCTGAACTATAATTGTGCCATATTTA[G/T]AAGGGGGAATTTAAAGATGGAATTTGGGGTGAGAT K 2 1 2 1 201000 f 74 goat snp25208-scaffold259-5808053 10 45552877 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796945 Affx-122953679 AX-385283887 10 53808966 GTTGAACAAGTTTGAAAATTAGGCTCACCTTTCTT[A/G]TCCTCGATCTCCTCTTCAGTCTGCTACTTATAATT R 2 1 2 1 101000 f 74 goat snp25207-scaffold259-5776027 10 45520406 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377407 Affx-122977561 AX-123247766 10 53864562 TTTTTTTGTGGGTGTGAAATACAGCATGCAATGTA[C/T]GGAAGTTTAAAGAAATCCTATGGCTAATTTTTTCA Y 2 1 2 1 101000 f 74 goat snp25206-scaffold259-5720431 10 45465119 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790928 Affx-122952499 AX-385277925 10 53906653 AACAGTTGCTCCTAAGCTATGAAATGCTGAGTGTT[A/G]CCAAGATGTCAACTACTCCATGTGAGTACTAAGGA R 2 1 2 1 101000 r 74 goat snp25205-scaffold259-5678340 10 45422971 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779140 Affx-122956225 AX-385266244 10 53946209 TGTTTAGACAAGCCACATCAGGGCAATATTTGCTT[A/G]TATTTTGTCCCCAGTGTCCAGCAATTCCTACATAG R 2 1 2 1 101000 f 74 goat snp25204-scaffold259-5638784 10 45383867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276395 Affx-1111835396 AX-519549922 10 53960063 CCCAGATTTCCTATGAGTCATGTGATGATTTTAGC[A/C]AAGCCGCCTCCATTTTTAATTCTTTTTAATCTATG M 2 1 2 1 201000 f 74 goat Random2.2K-1081 10 53960063 T G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399833 Affx-122960258 AX-123270188 10 53992048 TAATCCTCAAAAAAACACTATGAAGTAAGCATTAC[G/T]ATTATCCCATCCTAAAGATAGGAAAACTAGAATGG K 2 1 2 1 101000 r 74 goat snp25203-scaffold259-5592945 10 45338019 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785659 Affx-122947665 AX-385272700 10 54032148 ATAGTGGAATACTAAAAAAACAGTAAGATAGGTCT[A/G]CATGTACTGATGTGGAAAGATACTGCTGACTGGAA R 2 1 2 1 101000 r 74 goat snp25202-scaffold259-5552845 10 45298192 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431772 Affx-122936714 AX-123302113 10 54062632 TCTCTTTTTCTCTCATACCCCCATATAAGCAAGCC[A/G]TCTTATGTTCTACCTTAAAAATTTATCCAGAGCCT R 2 1 2 1 201000 r 74 goat snp25201-scaffold259-5522361 10 45267524 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449616 Affx-122923199 AX-123319951 10 54096541 GTGATTTTTTTCTTCTTTGAACTTAAGTATTCAAA[C/T]AGAAAAGAGATAATAAAGCTTCCTTACTTTGTCAG Y 2 1 2 1 201000 f 74 goat snp25200-scaffold259-5488452 10 45233617 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769677 Affx-122927540 AX-385256847 10 54151657 AAAGCACAGAATTTATATGCTAATCAATCATTATT[A/G]TGTTATTGAGTTTATTCATCAATTCTTAGGCACTG R 2 1 2 1 101000 r 74 goat snp25199-scaffold259-5433336 10 45178498 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403868 Affx-122957922 AX-123274220 10 54218435 ACAGGTCTCCAAAGACTGCTGCAACTTCTTTGCCT[A/G]GTCAGGGGCCCTCAGGAGATGTCCATGTTTTAGAT R 2 1 2 1 201000 f 74 goat snp25198-scaffold259-5366558 10 45111643 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413384 Affx-122950130 AX-123283733 10 54302494 ACTATTTTTTAAGTCATTGTATGAAAGATATTAAA[C/T]AATGAAAAGTTATGGCAAACATGTTGGCAGAGAAA Y 2 1 2 1 103000 r 74 goat snp25196-scaffold259-5282499 10 45027841 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276546 Affx-1111835397 AX-519550057 10 54303928 ATCTCTAGAATGTATGCTTATTTTCAACTCTACTT[A/T]TCCTGTTTTCATGTCTTCTTCTAACATGAGTTCAG W 4 1 2 1 101000 r 74 goat Random2.2K-1084 10 54303928 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407879 Affx-122954499 AX-123278230 10 54381421 GCAGAACTGACTGCTTGCTCAATTGAACTGTTTCA[C/T]AAAACAGCTGCTCTGGTTCTGCATGGCTGGAAGCA Y 2 1 2 1 101000 f 74 goat snp25194-scaffold259-5203572 10 44948526 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423348 Affx-122943159 AX-123293694 10 54420712 AATTCAGGAAAGTATATCCGAGATGAGGAGGGTGG[A/C]TTAGAAAATTCTGTGTAGGTGATTGTGGGGGCAAA M 2 1 2 1 101000 f 74 goat snp25193-scaffold259-5164281 10 44908966 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451517 Affx-122921106 AX-123321850 10 54449924 ACCTTGTCAGTTTTGTTCAATAATGTATCCCAAAT[A/G]CCTAGAGCAGTGTCAACCATATAGTAGGTACTAAA R 2 1 2 1 101000 f 74 goat snp25192-scaffold259-5135069 10 44879588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781540 Affx-122927473 AX-385268625 10 54480418 TTGGCCTGACTGATGTGATATTTCAGAAACAACCA[A/G]TTTTATAATGAGTTTGGTGCTATGAGGGAATCTAA R 2 1 2 1 101000 f 74 goat snp25191-scaffold259-5104575 10 44848725 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437521 Affx-122931919 AX-123307859 10 54522189 GGAAGAGAAGGAAGCAGGCTTAGCTGGAAGGAAAA[G/T]CAAGCTGCATATGAGGAAAGCCCAGTAGCCTGAAC K 2 1 2 1 101000 f 74 goat snp25190-scaffold259-5062804 10 44806612 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403260 Affx-122957873 AX-123273613 10 54565815 GCACTCAGTCCTCGCTGGTGCTGTTTCTCTCTCAT[G/T]CGGCGCTGCTGAGACTCCCTACGAATAGAAGCCCT K 2 1 2 1 101000 f 74 goat snp25189-scaffold259-5019178 10 44762712 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271747 Affx-1111832894 AX-519545541 10 54615313 GGTGGGCTCTGCTTCTGTTTGCCATGACTATGCAG[A/G]TTGTGTAAATTGCCTTTGCAATTCTCATCTATAAA R 2 1 2 1 201000 r 74 goat 10_54615313_AF-PAKI 10 54615313 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38377799 Affx-122977320 AX-123248158 10 54699512 AGGTAAATGTATACTGTTTTAATTAATCAATATCC[G/T]TCTGCTTTTAAAAGATAATAATGTATTCATTTGTG K 2 1 2 1 101000 f 74 goat snp25187-scaffold259-4885481 10 44629807 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441429 Affx-122928818 AX-123311766 10 54754924 AGCTGTTTGGCAGGAAAGATGATGCAAGTACTTCT[A/G]CCATTTGAGATGCCTGATTCAGTGAAGTGGAGATG R 2 1 2 1 201000 f 74 goat snp25186-scaffold259-4830069 10 44573491 C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797506 Affx-122977013 AX-385284445 10 54847065 TAGGCAACTTACTTCAATGAAGGTATAAGGAATAC[A/G]TCTATCATTTTAAATACTGCTAGTGAATTATCCCA R 2 1 2 1 101000 f 74 goat snp25184-scaffold259-4737928 10 44481587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443069 Affx-122928128 AX-123313406 10 54876896 TGCCTTCACCTCTATTTGTTTTCTCCTCACTAGAA[C/T]CCCACATTGTACCTGGAAAATAGATGCCCACATCT Y 2 1 2 1 101000 f 74 goat snp25183-scaffold259-4708097 10 44451694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772659 Affx-122975023 AX-385259806 10 54920349 TTCCAACACAATTCCACATGGCTTAAAGAGCTAGT[G/T]AAATAGACATGAACCCCTGAGGCAGAGTTACATGT K 2 1 2 1 101000 f 74 goat snp25182-scaffold259-4664644 10 44408001 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434711 Affx-122933938 AX-123305052 10 54998726 CCAGCTGAAATACAGAACAAGTGGAATGAGATACT[A/G]CCACCCACTAATAACATATTCTAACCACAGGACTT R 2 1 2 1 101000 f 74 goat snp25181-scaffold259-4586267 10 44330865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432235 Affx-122936360 AX-123302576 10 55039025 TCAATAAGAATGAATTAAATGTTTAGAAAATGTAT[A/C]AATCACTGTGTGAAATGGTTAATTTTCCAGAAAGC M 2 1 2 1 201000 f 74 goat snp25180-scaffold259-4545968 10 44290442 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409116 Affx-122953312 AX-123279467 10 55075332 AGAAGGTCATGCCCCCTGCTGAAAACAAGGTCCTT[A/G]TGGATTATCTATGTCTGACCCAGTTTTCAGTGTAT R 2 1 2 1 101000 r 74 goat snp25179-scaffold259-4509661 10 44254096 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420464 Affx-122944880 AX-123290811 10 55117866 AGGGAATTCTGTGATTCCTAGCTGTTGCTGCTCTC[A/G]CAACTTTTATGTATTTGGTTTTGGATTTTATTTTT R 2 1 2 1 101000 f 74 goat snp25178-scaffold259-4467127 10 44211188 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390623 Affx-122967162 AX-123260980 10 55150145 TGATTATACCTGACTCTGGCAGAGACTGGCTTCTT[A/G]TCTCAGGGGAGGAGTGCCTACCCACTGCCTTCAGA R 2 1 2 1 101000 f 74 goat snp25177-scaffold259-4434848 10 44179172 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781777 Affx-122963780 AX-385268859 10 55198213 ATCCAACAAGTAACCAAGAGAATTCCTGAGTCTCC[C/T]TAGTCTCTCCCATTTGATTAAGGTAGGTGTCCAAA Y 2 1 2 1 101000 f 74 goat snp25176-scaffold259-4386780 10 44131083 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397884 Affx-122961963 AX-123268239 10 55227366 AAACCCTACATCTGCAGACCTGACCGTGTCTTCAG[A/G]AAGAAAAGGCTGTGAGGAACCCTTTTGAGGTACTT R 2 1 2 1 101000 r 74 goat snp25175-scaffold259-4357627 10 44101224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783854 Affx-122937533 AX-385270910 10 55258664 TTTTTCAGCTGTTTTAGTTTGAAGTGGCTATTTCA[G/T]CAGAGATGGCACAATGCCTTGACATAGTTACTACA K 2 1 2 1 101000 r 74 goat snp25174-scaffold259-4326329 10 44069773 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422025 Affx-122943628 AX-123292372 10 55295287 GGCTGGTTTTATCTAACCAGAGTAAATCAGGAGAG[C/T]GAAGAAGGGAAGGTTGGTGAGGCGCTCAGGACATC Y 2 1 2 1 101000 f 74 goat snp25173-scaffold259-4289706 10 44033070 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772904 Affx-122925235 AX-385260049 10 55357130 TCACTTTGTTGAGATTTTTTTATTAAGACTGCTTA[G/T]AAGTTAGGGTACAGCATTGGCAAAAAAAATCAACC K 2 1 2 1 101000 f 74 goat snp25172-scaffold259-4227863 10 43971292 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767456 Affx-122938981 AX-385254725 10 55415913 TTTGCAGTTTGATGTATTCTCCCTGAAAGGACCAC[A/G]TCTTACAGAAACTGCTCCATTACATGGAGCCTATT R 2 1 2 1 101000 f 74 goat snp25171-scaffold259-4169080 10 43911228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762819 Affx-986697348 AX-385250852 10 55439733 CAGTGTTTTGCCGTCGTCCAGAAGCTGGTCGTCCT[C/T]GTACAGCCGCTGCTCATCCGGCGGCCGCTTGAGGA Y 2 1 2 1 600010 f 74 goat 10_55439733 10 55439733 Ancestral_priority_1043 ancestry 0.546 neutral IMAGE 10K 10K ancestral 320762821 Affx-986697350 AX-385250854 10 55439759 GGTCGTCCTTGTACAGCCGCTGCTCATCCGGCGGC[A/C]GCTTGAGGATACCCTAGACGATGCGCTTCAGCTCG M 2 1 2 1 600010 f 74 goat 10_55439759 10 55439759 Ancestral_priority_1043 ancestry 0.432 neutral IMAGE 10K 10K ancestral 320765291 Affx-986697318 AX-385252819 10 55439775 CCGCTGCTCATCCGGCGGCCGCTTGAGGATACCCT[A/C]GACGATGCGCTTCAGCTCGAACACGGTGTTCGACT M 2 1 2 1 600010 r 74 goat 10_55439775 10 55439775 Ancestral_priority_1043 ancestry 0.524 neutral IMAGE 10K 10K ancestral 38429886 Affx-122938127 AX-123300227 10 55454674 ACACAAATAGAAAAAAGACATACACATAAAAACAA[C/T]AGGTTAGTGGATTGTTATAAGGTTAACATCCTTCA Y 2 1 2 1 101000 r 74 goat snp25170-scaffold259-4130319 10 43872407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398100 Affx-122961714 AX-123268455 10 55529772 CATTTTTATGAATGAAATTGTGTGTTTGAAACAGC[A/G]CATCTCGACACAGATTGCAAACCCAGCCTGTTAGA R 2 1 2 1 201000 f 74 goat snp25169-scaffold259-4055221 10 43796984 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793770 Affx-122934310 AX-385280742 10 55561879 TCACTAATTACTAACTTGTGCTTTTGGGTATAATA[C/T]TTAAACACTCTGTTCCCCAGTTTCTTTTCTGTATA Y 2 1 2 1 101000 r 74 goat snp25168-scaffold259-4023114 10 43764520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274013 Affx-1111833950 AX-514585451 10 55563399 GTTTTCCT[A/G]CTAGGTCAGGTTCCTATCCCCTCTCAAGAACTTTC R 2 1 2 1 101000 r 74 goat GoatD01.011338 10 55563399 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38394967 Affx-122964273 AX-123265322 10 55612182 TAAGAGATAGAAGTAAAACAGTTTGAATTTTGCCT[A/G]CTATGGAGATGAGCAGTAGAAGAAGTATTGAGAAA R 2 1 2 1 101000 r 74 goat snp25167-scaffold259-3972811 10 43712951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792473 Affx-122969559 AX-385279454 10 55688377 AATTCCACTAGAAAGAGTCTAGTCCCTCATAGGAT[C/T]GCTGCTCCATCTAGGCTATTCTTCTCTCTCTGTGA Y 2 1 2 1 101000 f 74 goat snp25166-scaffold259-3896616 10 43658791 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791072 Affx-122935189 AX-385278067 10 55717945 TGCTATTATCTTTCAATAAATTTCCATTATTTAAC[A/G]TGACTTAAAACTTAGAAGAACATAACTTACCATTT R 2 1 2 1 201000 f 74 goat snp25165-scaffold259-3867048 10 43628904 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798646 Affx-122965917 AX-385285578 10 55750186 GCTGTGAAATGCTACCTTGTGAAAATGCTGCAATG[C/T]GTAAAAGAGTATGTAAAAATGTGCTGCACAATGTC Y 2 1 2 1 101000 f 74 goat snp25164-scaffold259-3834807 10 43596638 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429427 Affx-122938512 AX-123299769 10 55785539 CTAGGTCACCTGAGAAAGACCCTATGGTGGAAGGA[C/T]ACCTTCCTTTACATCTTGCCAGTTAGAGACATGCT Y 2 1 2 1 101000 r 74 goat snp25163-scaffold259-3799454 10 43561186 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782691 Affx-122937031 AX-385269763 10 55829267 CCTGTCTTCTGTCTCCAATTCTTTCCTCTGAAGCA[C/T]AGTTTGTATATTAGTAAACCATGCTTCACCCAAAT Y 2 1 2 1 102000 f 74 goat snp25162-scaffold259-3755726 10 43517425 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385391 Affx-122971351 AX-123255749 10 55900005 TAATTTTATTAACTTAGTACTTTTTAAAATGCTTA[C/T]ACTTTTTATATTTTAGCTACACCTGTGAAGTTTCT Y 2 1 2 1 101000 r 74 goat snp25160-scaffold259-3684988 10 43446590 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409332 Affx-122953079 AX-123279683 10 55996883 CTGTGTGCATGCAGTTTCTGGCTCTACTTTCTTCA[A/G]GTTCAGTTCAGTTGCTCAGTCGTGTCCAACTCTTT R 2 1 2 1 102000 f 74 goat snp25158-scaffold259-3588110 10 43349003 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769872 Affx-122948670 AX-385257041 10 56038286 CTTCTTTGCTTTCTCATTCAATTAGGGAAAAATAC[C/T]CTTTACCTTGTGCTTTGACTTCTCCAGAAATATAT Y 2 1 2 1 101000 r 74 goat snp25157-scaffold259-3546707 10 43307693 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393747 Affx-122965220 AX-123264102 10 56095542 TTAACGCATCCTGAAGATCCTTTCCTATTAGTTCA[C/T]AGACAGCTTCCTCATTTTCTGTAAAGCTGCTTAGC Y 2 1 2 1 101000 f 74 goat snp25156-scaffold259-3489451 10 43250317 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379280 Affx-122976219 AX-123249639 10 56140683 ATGAACTCATGGCAAGAGATATGGCTGTAACTCTG[A/C]GACTCTGTTACTTAGGTAATCAGAGATCACAATAC M 2 1 2 1 101000 f 74 goat snp25155-scaffold259-3444310 10 43204513 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391460 Affx-122966731 AX-123261817 10 56176514 TGATGGCTCATCGGCCCCCTCTGGCTTCATCTCAC[C/T]AATCTACAAACATGACCCATTCATATCTGTGATCA Y 2 1 2 1 101000 r 74 goat snp25154-scaffold259-3408479 10 43168312 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411669 Affx-122951555 AX-123282019 10 56235325 CAATTGACCCACTCTGGTTTTAAACTCTAGACTCA[G/T]CCACTGTGCAATGACTTCATGGCTGCCCCAACTAA K 2 1 2 1 101000 f 74 goat snp25153-scaffold259-3349668 10 43109007 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434469 Affx-122934636 AX-123304810 10 56266116 CTATGCCTAGGAGAGAATGTCATGATTGGTTGCCA[C/T]GGTGCCCAGAAGGTTCCTATATATTCTCTGGAGCA Y 2 1 2 1 101000 f 74 goat snp25152-scaffold259-3318877 10 43078246 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801924 Affx-122940424 AX-385288828 10 56303135 TGGTTCTATGCCTAATGATAACAGTCACACTATAA[C/T]AGTAATTTAGCAACTGGCCTATGGTTTGACATTCA Y 2 1 2 1 101000 r 74 goat snp25151-scaffold259-3281858 10 43041650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405202 Affx-122956911 AX-123275554 10 56366035 GGGGATTTATCATTTACCAAGGTAAGCTCATTCCT[A/G]CACAACTGGTATCACTAAATGTGTCTGGTTCCAAA R 2 1 2 1 101000 f 74 goat snp25150-scaffold259-3218958 10 42977975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388501 Affx-122969219 AX-123258859 10 56395747 GCAAAGATCCCAAAAGAATGCATGTATGGGGCAAG[C/T]GGGTGTGGAGATCCGGTGTCTGGCGCCTCACTGGT Y 2 1 2 1 101000 f 74 goat snp25149-scaffold259-3189246 10 42948087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782156 Affx-122975103 AX-385269234 10 56426800 GTACAGAATCAGCAACAGTACTTTTCAAAATGTCA[C/T]ACATATCAAATTACAAACAGATGCTACCTCTAAAG Y 2 1 2 1 101000 f 74 goat snp25148-scaffold259-3158193 10 42916394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772104 Affx-122965574 AX-385259259 10 56461893 AAGAAAAACCCTCCCATTTTAATAGAGGATTTGCA[A/G]TATACAAACACTCTGAAAGCAAGTTAATTCATTGT R 2 1 2 1 101000 f 74 goat snp25147-scaffold259-3123100 10 42880988 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446984 Affx-122924646 AX-123317320 10 56510177 ATCAACTCAATTCTAACATTAGGTTGCATGAGACT[A/G]CACAGTAGCCTGTGTATTCCAGAGGAAAACATTCC R 2 1 2 1 101000 f 74 goat snp25146-scaffold259-3074816 10 42832096 C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448116 Affx-122924306 AX-123318452 10 56551430 ACAGGGTATTTTTTAATATTAAATATAGGGCTTGG[C/T]AAAGAAAATGAACTCTCAATTGCTTTTTAAAGGAG Y 2 1 2 1 101000 r 74 goat snp25145-scaffold259-3033563 10 42789745 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798224 Affx-122957869 AX-385285159 10 56598263 CTGAACTGCTAAGCAATAAGCAAAGGATCCATGAA[C/T]ATCTTCAGAGGGAGATACAGAAATGAACCTGTCAG Y 2 1 2 1 101000 r 74 goat snp25144-scaffold259-2986730 10 42742535 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422467 Affx-122943332 AX-123292813 10 56715308 CCTTGCCATTTTTTTCTTCTTTCAGCCAAATATTG[A/G]GGCATTGGCTGCATTGCTCTTAAAATACACAAGTA R 2 1 2 1 101000 r 74 goat snp25141-scaffold259-2869685 10 42624441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404474 Affx-122956728 AX-123274826 10 56771896 CCTTCCTCTCTCCCTATCCCCTTTCCCCATAATGT[C/T]TCTGTTTCTAATCAGGAAGAACAAAGTTCATGGCT Y 2 1 2 1 201000 r 74 goat snp25140-scaffold259-2813097 10 42567616 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793240 Affx-122929380 AX-385280218 10 56826147 GTAGTACACAGTAAGTGAGAGCATGTTTTATATCT[A/G]TGACAGGATTTTCTAACATTTAGAGGCACAGACTA R 2 1 2 1 101000 r 74 goat snp25139-scaffold259-2758846 10 42512991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452476 Affx-122920997 AX-123322809 10 56856366 GAAGATTAAAAGTATTGCATGAATGAAGACGTTTA[A/G]TAAAGTAATTGGGGTTCTCCCAAATATGGGAGCTG R 2 1 2 1 201000 f 74 goat snp25138-scaffold259-2728627 10 42482826 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429477 Affx-122938476 AX-123299819 10 56972116 ACACTAACTATGGAAGATGAGCAGTATTTGAATAC[A/G]TTCTAGTGAAAAATTATGAACCACTCTAACTAGAA R 2 1 2 1 101000 f 74 goat snp25136-scaffold259-2612877 10 42365575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401512 Affx-122958931 AX-123271865 10 57016111 GAGAAGGAAAAGGAATACAGATTACAGATACATCA[C/T]GAAAAGAGAGACAAAAGGCAGAGAGGGATGCTCTG Y 2 1 2 1 101000 f 74 goat snp25135-scaffold259-2568882 10 42321410 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441253 Affx-122929493 AX-123311590 10 57055305 TGGAGAATGATTTTTAATTATTTTAATTATATTTC[A/G]TTGGCAAATTGTAAAAGGAGTTGGGGATGAATACC R 2 1 2 1 103000 r 74 goat snp25134-scaffold259-2529688 10 42282177 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405364 Affx-122956316 AX-123275716 10 57178129 CAAGAAAGTGTTTTCTTTCATAGAGTTTACATTTG[A/G]TTAAAGGGAGACAGAAAATAAAGGAAACGATAACG R 2 1 2 1 101000 r 74 goat snp25132-scaffold259-2406864 10 42158709 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775711 Affx-122953425 AX-385262842 10 57246549 TTTTTTTTTACTACATTTACTTAAGCTGAACACTG[G/T]ATGTTAAAAGGGCAGAAAAGCAGAGGACTCTTTGT K 2 1 2 1 101000 r 74 goat snp25130-scaffold259-2338444 10 42090030 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421860 Affx-122944284 AX-123292207 10 57277060 TCCTAACTTAAGACTTTCCTTTAGTTATCCGCTAA[C/T]ACAACACAACCAGACTAATAAATATGATATGTAAG Y 2 1 2 1 101000 f 74 goat snp25129-scaffold259-2307933 10 42059129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797102 Affx-122961453 AX-385284042 10 57326878 AAATGTTTTGAGAACATTTACTGAGTGTTCTAAGG[A/G]TATATCAGTGCACAACTTTTATGAAGTTGTAACAG R 2 1 2 1 102000 f 74 goat snp25128-scaffold259-2258115 10 42009437 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449017 Affx-122923089 AX-123319352 10 57397794 ACTGGATAGGAAAGAGACACTTAAATATACACAAA[C/T]AGTAGGGCTGAGAAGAGGGAAAATTGTTCATCAGT Y 2 1 2 1 201000 f 74 goat snp25127-scaffold259-2187199 10 41942710 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276398 Affx-1111835398 AX-519549925 10 57422565 GGCAACAAGTGCATGAATTTTAAAGAGTGATAATG[A/C]TGGCATATTCCTTTATGATAGTTTGGTTGCCTTTT M 2 1 2 1 101000 f 74 goat Random2.2K-1085 10 57422565 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38445321 Affx-122925429 AX-123315658 10 57432964 GAACAGGAACAGGTGACGAACAGATTATTTTCCAG[C/T]AGACCCTAACCAGCTGTCAGCAGTACAGACACTGC Y 2 1 2 1 101000 f 74 goat snp25126-scaffold259-2152029 10 41907669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440115 Affx-122929704 AX-123310452 10 57470281 GACCTGTCTCTCCACAAAGGAAAAACCAGAAGCGC[A/G]ACCCTCCTCTGGGACACTACGCTACCACTGAGGAT R 2 1 2 1 101000 f 74 goat snp25125-scaffold259-2114712 10 41870184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380957 Affx-122974995 AX-123251315 10 57510737 GCACTTCATACAAGGGAAATCAGACTACTTTTTTG[C/T]GTTTGTCTTTTTGTATTTTTCCTTAGCACAATATG Y 2 1 2 1 101000 f 74 goat snp25124-scaffold259-2074256 10 41830426 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271748 Affx-1111832895 AX-519545542 10 57531799 ATATTACATGAAGTAAATCAGACTGAGAACATCAA[A/G]TATCGTATTATTTCACACATATGAAGAACCTAATT R 2 1 2 1 201000 r 74 goat 10_57531799_AF-PAKI 10 57531799 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791313 Affx-122969116 AX-385278306 10 57549736 GGTTTTGAATCACATACAAACATACCCAATTCCCA[C/T]TGCTAGACCCATCTCCAAAAACTCAGATAAGCACC Y 2 1 2 1 101000 f 74 goat snp25123-scaffold259-2035257 10 41791180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780554 Affx-122967994 AX-385267645 10 57628206 CAGTCACCAACTGCTCAGTCTGGTTTTCCTTTAGG[C/T]TGAATTTGAATCTGATGGCTTCTAAAGTCTCTCTC Y 2 1 2 1 101000 f 74 goat snp25121-scaffold259-1956787 10 41716785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797968 Affx-122948232 AX-385284904 10 57660946 AAGTGTTTCCAAATGGCTCTTCTGGAAGTCCTACC[A/G]AGATGCTACGAGAAGAAACATGGTGAACACCGCAG R 2 1 2 1 101000 f 74 goat snp25120-scaffold259-1924047 10 41683823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430829 Affx-122937443 AX-123301170 10 57696731 GGTATAACAAGAAAACTAGAGATCAGTATCCCCTG[C/T]GAGCATGCACATGAAAGTCTCTAACGTGACGTTAA Y 2 1 2 1 201000 r 74 goat snp25119-scaffold259-1888262 10 41648274 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38412757 Affx-122950518 AX-123283106 10 57774707 CATACTTTCTGCATGTGTGATGCAGGGGTCTCCCC[A/G]AAAGGGTGGAGTTTTAGCTATAAGGGGCCCTTTCT R 2 1 2 1 202000 r 74 goat snp25117-scaffold259-1810286 10 41569261 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409827 Affx-122952947 AX-123280178 10 57872131 ACATGTCATGTACATCCTGAAACACCATCAAAGGC[A/G]CCCATCTCTACTGTACCAAGAACCCCCTCCATCTC R 2 1 2 1 101000 f 74 goat snp25115-scaffold259-1712862 10 41472332 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780407 Affx-122940140 AX-385267500 10 57922514 TCCTCAGGGAGCTACAGAGCACTGCATATACAGTA[C/T]AGATGCATTCTTAGAGAGAAGCCCTGCTTACCTGA Y 2 1 2 1 101000 f 74 goat snp25114-scaffold259-1662479 10 41421817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801360 Affx-122965132 AX-385288271 10 57979165 AGAAGGACCTAAGCTCAGTTAAAAATTCAAACTAT[A/G]CTTGTAATTCAGTAAGTAGACCATTAATAGAAATA R 2 1 2 1 101000 f 74 goat snp25113-scaffold259-1605828 10 41364573 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392611 Affx-122966046 AX-123262968 10 58063283 CAATGTTAGGGTGGCAGCAGCAAAGTTAAGCCAGT[C/T]GGGAGGCATTCCAATGCAATGGGAAGAACCGAACC Y 2 1 2 1 201000 r 74 goat snp25111-scaffold259-1521710 10 41280765 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437398 Affx-122932429 AX-123307736 10 58128771 AGGGCGTGCCTCTTACAAATCTCTCCTGTAATGAC[C/T]GGCCTTGGTAGGGGCATGTATTTCTTTCTTTCTTC Y 2 1 2 1 101000 f 74 goat snp25110-scaffold259-1456222 10 41215663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426017 Affx-122941128 AX-123296363 10 58196646 TGACACAAAGTTTGTGGGAAAAGGAGGATTCAAGC[A/G]TCATATGATTCACTGGACTAGATGACCCTTAAAGA R 2 1 2 1 101000 f 74 goat snp25109-scaffold259-1388347 10 41147639 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784033 Affx-122972745 AX-385271086 10 58238053 GAGTAGTAGAGGAGACTCACAGGGAAGAAAGACAT[A/G]GTAGGAGAGAACTAGGCTTTTGTCTACACAGGAAG R 2 1 2 1 101000 f 74 goat snp25108-scaffold259-1346940 10 41105840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799124 Affx-122944312 AX-385286054 10 58427610 CCCTAAGTATACATTTTGTGATACATAGGGCAGGC[C/T]AGAGGTATCAATACTGGGAAGTGGAGACAACTGGG Y 2 1 2 1 101000 r 74 goat snp25104-scaffold259-1157383 10 40916392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383127 Affx-122973258 AX-123253485 10 58466727 CCATCTCTCATCTGATCTAGACTTGATACCCCTCC[A/G]TCCTTGCCTTTACCTGAGCCCCACAATCCGATCTC R 2 1 2 1 101000 f 74 goat snp25103-scaffold259-1118266 10 40877011 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387540 Affx-122970301 AX-123257898 10 58551404 TCAGATTTGAAACGAAATATTTGCACAAACAGATT[A/G]CCAGACCCCACCCCAGACCTAATCAGAATTAGAAG R 2 1 2 1 101000 f 74 goat snp25102-scaffold259-1033589 10 40792222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452150 Affx-122921663 AX-123322483 10 58592577 CAGTTCGAGAAAAAGTATTTGGACATCTCAGAAAT[A/G]TTTGCAAACGTTAGGGGCTTCCCTAGTGGCTCAGA R 2 1 2 1 101000 f 74 goat snp25101-scaffold259-992416 10 40750713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422111 Affx-122943564 AX-123292458 10 58623533 TTGCATCCCACCTTTCCTGGTCAAGTCTCAGCCAG[A/C]TGTGACCCTCTATTCTCTTTCTTAATTCAGCAAGC M 2 1 2 1 202000 f 74 goat snp25100-scaffold259-961460 10 40718753 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442722 Affx-122927858 AX-123313059 10 58699451 TTTCCTATATTAGCAGGACCTTGCAGAGCAAGACC[A/G]TCCTAGGAAGGAAATTCTAGAGCAAGTCCTTTTGT R 2 1 2 1 101000 f 74 goat snp25098-scaffold259-885542 10 40641756 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803318 Affx-122931287 AX-385290158 10 58746746 ATCTTAGTTCCTAATCTATTTAATATTGTAAGTCC[A/G]CTTTTTCTTCTATTCATGCATCAAAGGAAATAAAT R 2 1 2 1 101000 r 74 goat snp25097-scaffold259-838247 10 40595391 C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788152 Affx-122975058 AX-385275171 10 58778503 AATTTGGTCAGTGTTTCAAATAAGTGATGTCAGTG[A/C]GGTGCAAACAATTCAGATATAGGATGTTGGGAAAA M 2 1 2 1 101000 f 74 goat snp25096-scaffold259-806490 10 40563363 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429380 Affx-122938549 AX-123299722 10 58810861 GTTGTTTCACAATCACTGGCATTTATTAGCCTATG[A/C]TGGGAAAGATTAAAGGCAAGAGGAAAAGGGGACAA M 2 1 2 1 101000 f 74 goat snp25095-scaffold259-774132 10 40530971 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775342 Affx-122940467 AX-385262473 10 58840904 TTGAATGACAGCGTATTACTGGAAGAGATTGAAGC[A/G]TACAACCATGCAAAGTAGGTATATTATACCAGAAC R 2 1 2 1 101000 f 74 goat snp25094-scaffold259-744089 10 40500597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796212 Affx-122969049 AX-385283163 10 58900868 TTATAAGGAGAATTAGAAGTGATCTAATCTTTATC[A/G]TTATAGCATTTCATCACCTAACTGTCAGGATGTGA R 2 1 2 1 201000 f 74 goat snp25093-scaffold259-684125 10 40440923 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379139 Affx-122976732 AX-123249498 10 58935653 TTTTGAGAAAGCTTGATTCAGGATGAAAATATCAT[C/T]GATTTACTATTGTTTGATTTAAAAAGGATAACTTG Y 2 1 2 1 101000 f 74 goat snp25092-scaffold259-649340 10 40407035 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399993 Affx-122960812 AX-123270348 10 59033685 CTCTTATGAAACCTAGTGATGCGGTCAGTGGACAT[C/T]GGGACCTCTCTCTGTTCTCCTGCTAACTGACATCG Y 2 1 2 1 101000 f 74 goat snp25090-scaffold259-551308 10 40308603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413160 Affx-122950349 AX-123283509 10 59067970 GGTGTTCTTCCTTCCTTAAAGGACTCTCTGTTCTC[A/G]TTAAAGAGACAGAAGAGAAGTGTCACCACCCATGT R 2 1 2 1 201000 f 74 goat snp25089-scaffold259-517023 10 40274092 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379007 Affx-122976377 AX-123249366 10 59107922 GTGGGAGACCCGAGGAGACTCTAGACACTCAGGTC[A/G]CATTGGAAGCACACTCAGGTTCCCTGCTTCTAGAG R 2 1 2 1 101000 r 74 goat snp25088-scaffold259-477071 10 40235379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426925 Affx-122940437 AX-123297270 10 59146024 CTCCATACGATTTAAAATATTAACAATTAATTTTT[A/G]CTCTGATTTTAGAGACCCTTCAGAATACAGAAGTG R 2 1 2 1 101000 r 74 goat snp25087-scaffold259-438969 10 40197124 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791497 Affx-122920912 AX-385278488 10 59200681 GAATGAATTAGCATGCCAAAATCATTAGTTATCTA[C/T]AAGTATGTAGGAAAGTTTTTGAATAATCAGTTCCA Y 2 1 2 1 101000 r 74 goat snp25086-scaffold259-384312 10 40142227 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380234 Affx-122975470 AX-123250592 10 59244351 AATCTTGCCAGATACATTGGCATAAATTCTTTACA[C/T]GAGAATAGTTTGTGCATTTATAAACATTTAAAACA Y 2 1 2 1 101000 f 74 goat snp25085-scaffold259-340642 10 40098260 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375535 Affx-122979105 AX-123245894 10 59297340 GAATTAGAAGGCCATGTTTTCCCAGTGCAAAGATT[A/G]TAATTACAGAAACAATTTTAGGGGCAAGATTTTGC R 2 1 2 1 101000 f 74 goat snp25084-scaffold259-287653 10 40044811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436110 Affx-122932662 AX-123306449 10 59331998 TTCTTAAGAAGTTCCTTAACTCATCCCTTAGAGTC[A/G]TGAATTCCTTGAGAGTAGAGTAAGTATGCATTTCA R 2 1 2 1 101000 f 74 goat snp25083-scaffold259-252995 10 40009997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797463 Affx-122934721 AX-385284402 10 59418469 TTAGTGCTTGTAAGGAAGCTACACAATGAACAAGA[C/T]GAGCAGGATCTGGCTCATCATCCATAGACTTGGCC Y 2 1 2 1 201000 f 74 goat snp25081-scaffold259-166524 10 39923539 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789759 Affx-122958761 AX-385276767 10 59447163 TTCGTGGAGTACACTTCTGAAAATGTTGGAAGACT[A/G]TTTACCAGTTTTAGCTTCTAAACAAGTGTCAACCA R 2 1 2 1 101000 f 74 goat snp25080-scaffold259-137830 10 39894207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377094 Affx-122978267 AX-123247453 10 59477845 GTCAGGACAGGCTGGATAGTCAGGGCAGGATGGTA[A/G]TATGATAAGAACACCAGCCCAGGCAGCTTATGCTA R 2 1 2 1 101000 r 74 goat snp25079-scaffold259-107148 10 39864143 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274015 Affx-1111833986 AX-519547619 10 59499668 ACATCTGCAGTTTGTCTTTTTATCAAGGAGAGTGC[A/G]TTCCAGGATCAACAATCTGCAGACATCATTAGTAG R 2 1 2 1 201000 f 74 goat GoatD01.012866 10 59499668 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320790633 Affx-122964354 AX-385277635 10 59535575 AAATCTGATATTGTGCAAGAAGGAAATTATTCTAT[A/G]TCTTGCTTTCTTCTAACGTAACCTGCAATCCCTAA R 2 1 2 1 101000 r 74 goat snp25078-scaffold259-49418 10 39805802 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377990 Affx-122977607 AX-123248349 10 59578332 ATTTGAGCCAACACAGAGTGTAAAGCCAAAAGTTC[A/G]TGCATTTTCTTTTTTTAAAAGGAAGATAACTGTAA R 2 1 2 1 101000 f 74 goat snp25077-scaffold259-6661 10 39762667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765888 Affx-122970747 AX-385253324 10 59585600 TCCTGCTAGTCTTCCACTTCTTAACCTAGTGTATA[A/G]ATTCAACAATCTATTCACTCAGCCCTAATCCACTG R 2 1 2 1 101000 f 74 goat snp23480-scaffold2367-566880 10 39753238 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389206 Affx-122969065 AX-123259564 10 59615931 CTGACCCATGCAGCAGACTAGCTCTAACATAAGGC[A/G]CAAGCCATCTGTCAATGAAAGACAGAAAGGAAACA R 2 1 2 1 201000 f 74 goat snp23479-scaffold2367-536549 10 39722306 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774307 Affx-122944256 AX-385261444 10 59648082 AAGCTAATGTATGATGAAGTAGCAGACATGGTTAC[C/T]ATAACAGAGCACTGACAACCTTAAAGCAAAGATTA Y 2 1 2 1 101000 r 74 goat snp23478-scaffold2367-504398 10 39690176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781623 Affx-122933689 AX-385268707 10 59678959 TTTCAGAGCTATCAATTGTAGAGCTTTGCTTATTA[C/T]ATACAGAGCTAACACATATTATTTTGACATAAAAA Y 2 1 2 1 101000 f 74 goat snp23477-scaffold2367-473521 10 39659392 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774772 Affx-122952470 AX-385261905 10 59716485 TTGGATAGAGGGAAAAAAATCTACCTTGGATTATA[C/T]TTTATACTGCTTAATCTTGGATTAGATATCAGAAG Y 2 1 2 1 201000 f 74 goat snp23476-scaffold2367-435995 10 39621939 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790344 Affx-122959725 AX-385277347 10 59757791 AACTTAGCGATTAAGTACAAGTACAAGGTGCTTTG[C/T]ACATTTTGTCTTTCACTACTACCAATGAGGTTGAA Y 2 1 2 1 101000 f 74 goat snp23475-scaffold2367-394689 10 39580675 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782532 Affx-122921418 AX-385269607 10 59788308 GCGAAATAGCTAAATAAATGTTCTTCATTTAGACA[G/T]ATAATAATCTGTTAATGGGTAAAATGATAAAGTGA K 2 1 2 1 201000 r 74 goat snp23474-scaffold2367-364172 10 39550318 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787172 Affx-122944155 AX-385274199 10 59823158 AAGATCCACCTAATTCTAAGTTTCTTGCATGGGTC[A/G]TTCTTCTAAGCATGGTCTCTTAAACTTCGATGTTC R 2 1 2 1 101000 f 74 goat snp23473-scaffold2367-329322 10 39514119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410129 Affx-122952812 AX-123280479 10 59858767 GATTAGCTTGGTGACTGTGGAGATACTCTGTGGCC[A/G]GCCTTACAGGAAAGTATATCAGACTAGAAACCCTG R 2 1 2 1 201000 r 74 goat snp23472-scaffold2367-293713 10 39478527 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397522 Affx-122962048 AX-123267877 10 59889932 GTTTTCATATCTGGCTTTTTTGGTGTATGCAGCTT[C/T]AGGAATTGTATATGACATGTTGATTATATTCTGCA Y 2 1 2 1 201000 r 74 goat snp23471-scaffold2367-262548 10 39446795 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791715 Affx-122976241 AX-385278706 10 59985810 CTCCAAATCATCAAGAGAAAAAGGACATCAAATAG[C/T]AACAATAAGTTATACAGCTATTTTTAGTGATGTAA Y 2 1 2 1 101000 f 74 goat snp23469-scaffold2367-166670 10 39352781 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387902 Affx-122970462 AX-123258260 10 60022434 ACAGTAACATTATTAGTACCCCGTAAACTCCCAGC[A/G]TAAACTCGTTGGGACTAAAATTCTTAACAGTAATG R 2 1 2 1 201000 r 74 goat snp23468-scaffold2367-130046 10 39316891 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463100599 Affx-1109813942 AX-514587900 10 60050741 AAAAGGCACTTTCTTCCTTAAAGCCAGACCAATCT[G/T]TCAGTGGAACTGAGCCTGGAAGATTTGAGAAGAGC K 2 1 2 1 102000 f 74 goat 10_60050741_AF-PAKI 10 60050741 G T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423437 Affx-122942603 AX-123293783 10 60067651 TCCATAGGGTCGCAAAGAGTCAGACATGACGGAAG[C/T]GACTTAGCACAGCACACATGGCTATTCCTTAAACC Y 2 1 2 1 303000 f 74 goat snp23467-scaffold2367-84829 10 39270920 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767951 Affx-122961108 AX-385255166 10 60115205 TGTAAAATAGAACAGGTTCTGCCATATGCCAAGGG[A/C]TTAGTAATTGTCAGTAATTATTATTACAACTATTC M 2 1 2 1 101000 f 74 goat snp23466-scaffold2367-37275 10 39223159 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793900 Affx-122946446 AX-385280869 10 60150162 CAGACAGTGTCTGTGTTTTCTATATGGTACTTGGG[C/T]GGGTACATCAATCATATTTGTTAAGTTGGACTCTA Y 2 1 2 1 101000 f 74 goat snp23465-scaffold2367-2318 10 39187797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419396 Affx-122945606 AX-123289744 10 60169099 ATACTCTCTCTCACACATAAACACTCCCTCAAACA[C/T]CAACACTGGTTGCCCATTGAAAAATTTAATCACTT Y 2 1 2 1 201000 r 74 goat snp47226-scaffold662-453682 10 39168385 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430313 Affx-122938235 AX-123300654 10 60215976 ATACAGGATGTTCTGACTTTTATGAGAGAAAGCCA[C/T]AAAAATATTTTTCTACTTCCTCTGTAAAAATCAGA Y 2 1 2 1 303000 r 74 goat snp47225-scaffold662-406805 10 39121449 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381565 Affx-122974818 AX-123251923 10 60247073 ATGTACCTAACTAATTTCGGTTAATTTCCTGTGAG[C/T]AAGCTTGGATCCCTGGGAGGCCAGTGAAAGCGGAG Y 2 1 2 1 101000 f 74 goat snp47224-scaffold662-375708 10 39089429 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388616 Affx-122969138 AX-123258974 10 60280091 CCAGAAAGTTACATAAGTTAGAGGACACGTGTATC[C/T]TAAAGAAAAGAAAATTATAACATGTTAAATGCAGA Y 2 1 2 1 101000 f 74 goat snp47223-scaffold662-342690 10 39056439 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379104 Affx-122976758 AX-123249463 10 60314393 GCCTGATTAATGGACTACTTACCCATCCTGAAATC[G/T]AGTCTTTTTCTACCACTTTTTTTCTTATAGAACTG K 2 1 2 1 101000 f 74 goat snp47222-scaffold662-308388 10 39021630 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398617 Affx-122961477 AX-123268972 10 60358177 AAGTAGAAAACAATTTGCAAGATGGTAGATTTAAA[C/T]ATGACTGTTAAAATAATCATGTTAAATAAATGCCC Y 2 1 2 1 101000 r 74 goat snp47221-scaffold662-264604 10 38977403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390286 Affx-122967731 AX-123260643 10 60388847 TAACCCTATTGAATTCCTCTTTCATGATCTTGAGT[A/G]TTATCATATTTTCTCATTTCCTCCCAAGTGTCTAT R 2 1 2 1 202000 f 74 goat snp47220-scaffold662-233934 10 38950071 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427768 Affx-122939235 AX-123298111 10 60434145 CTGCCTTTAAATGTGAAGAATTTATTAAAAGACAT[A/G]GGCTACAGGCTTGAACATTCAGCTGAAGGAACTGG R 2 1 2 1 101000 r 74 goat snp47219-scaffold662-188636 10 38904473 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381062 Affx-122974619 AX-123251420 10 60485593 CTACATCTGCCGTCGGGTCCTTTACCACTAGCACC[A/G]TCTGGGAAGCCCGATTTAAGATAAGGCATATTCAT R 2 1 2 1 201000 r 74 goat snp47218-scaffold662-137188 10 38853155 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770939 Affx-122954150 AX-385258102 10 60564695 ATTGGAGTTGTCTCTACTTCTGTTTCAATAGCAAT[A/G]TTAATGATTATAAAGGATGTACCTATGTATGATTG R 2 1 2 1 101000 f 74 goat snp47216-scaffold662-58086 10 38773907 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772468 Affx-122933835 AX-385259619 10 60622391 TAGTTTGAATGCTATTCTGTTCTCCTTCCAATATC[A/G]TTTCAAATTATTCTACTACATTTTCATTTTTTTCT R 2 1 2 1 102000 f 74 goat snp47215-scaffold662-390 10 38716284 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379508 Affx-122976457 AX-123249866 10 60625394 AGTTAGTGTCCTAGTACTTCTTGGAGTTATGTTAA[C/T]AAGCTCTTAAAGTCTATCTGAAGTTCTGCCTGTAG Y 2 1 2 1 101000 r 74 goat snp38109-scaffold475-818921 10 38713431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422744 Affx-122943247 AX-123293090 10 60655612 TCCTACTGTCTCTGGTCTCCATTTTTTCTAAGTCA[G/T]CCCTTAACACATTATTGATCAGAGAGTAATAAGTT K 2 1 2 1 101000 f 74 goat snp38108-scaffold475-788703 10 38683034 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274324 Affx-1111834133 AX-519547920 10 60702093 CTTTGTCTGCAACTTCAGGAGAG[A/G]TCTCGAGTCAGAACCACCCAGCTCAGGCAACTTCC R 2 1 2 1 102000 r 74 goat GoatD01.020569 10 60702093 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38413082 Affx-122950958 AX-123283431 10 60745546 TGATAGCCTGTGCCAAGATGAAGTATGGGTTACTA[C/T]GGGTATAACTGGGAAGGACATGTACGAGATTAATA Y 2 1 2 1 101000 f 74 goat snp38106-scaffold475-698769 10 38594419 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787526 Affx-122955389 AX-385274550 10 60783459 CCCTACATTTTATACAAAATAGCACCAGGAGGCAT[A/G]TTAGTATTTGAGTCTACACATTCAGTTTTTCCCCC R 2 1 2 1 101000 f 74 goat snp38105-scaffold475-660856 10 38556624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785853 Affx-122966027 AX-385272890 10 60822765 CAGTTTAACCTAATAACATGGAATCTAAACAAGTC[A/G]TTTTAAACAGACAGTGCTTTTCCCCGTGATTCCTT R 2 1 2 1 201000 f 74 goat snp38104-scaffold475-621550 10 38517075 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395418 Affx-122963946 AX-123265773 10 60863646 TTTGTTCTAAAAGGAAAAAGATAGGGTGTGACCTA[C/T]GTTATGGTGTCCTATGACAAGGGGAATGCCACTTA Y 2 1 2 1 201000 f 74 goat snp38103-scaffold475-580669 10 38476213 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402215 Affx-122959158 AX-123272568 10 60913782 CACTAGCAGGCCAGAGGTTTGACTGACAGGGGAGG[A/G]GGTGATGTAATCTACTGGTGATTGAAATAGAATTT R 2 1 2 1 101000 r 74 goat snp38102-scaffold475-530533 10 38426186 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391805 Affx-122967031 AX-123262162 10 60946202 CATGTGTATACTTAACCCCAGACACAATGAGTTGT[A/G]TGCATTAAATAAGTACAGCTTTTTACAGGTTGAAA R 2 1 2 1 201000 r 74 goat snp38101-scaffold475-498113 10 38393895 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390595 Affx-122967185 AX-123260952 10 60984725 GCTCCTGGAAAACTCCAGGGGCAGCTGAGGAAACG[A/C]GCATAAAGGACAAGAACTGCTGGTTTTCAAGGGAC M 2 1 2 1 101000 r 74 goat snp38100-scaffold475-459590 10 38355460 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423947 Affx-122942247 AX-123294293 10 61066317 CTGCTGAACGTGCTCATTTGCAACCTGACAAAGTC[C/T]GTGCATTGTTTCTTAAGAGTGGTTTGTGGCCCACC Y 2 1 2 1 101000 r 74 goat snp38099-scaffold475-377998 10 38273909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438933 Affx-122930418 AX-123309270 10 61101962 GTAAAGCCCTTTTCACCCCAGTCATAGCTGAGATA[A/C]AGTGGCAGTTGTCTTGTTTCTTTGAGTGGAGACAT M 2 1 2 1 201000 r 74 goat snp38098-scaffold475-342353 10 38239504 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793701 Affx-122970320 AX-385280673 10 61138438 CTAAGCAAATGCAAAAATTGGTCATATGGCACTTC[A/G]TATTCAAGTGACTGTTCTATATGTATTTTAAAAAT R 2 1 2 1 101000 f 74 goat snp38097-scaffold475-305877 10 38202580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381183 Affx-122974545 AX-123251541 10 61182140 GAAGGACCTTTGGGGAAATGACCCACACAGTCAGC[A/G]GGTGGTGGCACCTGTTCAGCATGCTCAGAACACGG R 2 1 2 1 101000 f 74 goat snp38096-scaffold475-262175 10 38158598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276551 Affx-1111835399 AX-519550061 10 61200294 TAAAATTATAGGAAAAGCAAAATATTGGGTGTCAG[A/G]GAAAGACAAAAGCTAAAATTTGTACTATCTTTCAT R 2 1 2 1 202000 r 74 goat Random2.2K-1086 10 61200294 A G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786055 Affx-122954661 AX-385273091 10 61211019 GCTACGAGCTGTCATTGCTCTTTCGTTTCCGTGAG[C/T]GGAGCTGATCTCTTCTCGCCTTTTGTTGGAGATTC Y 2 1 2 1 101000 r 74 goat snp38095-scaffold475-233296 10 38129694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392070 Affx-122966383 AX-123262427 10 61261397 TTTGAGTATTTCATGTCTGTACCAACAAAATAATG[C/T]AATTGTTAATTTTTAATGAGCTGTCTTTTAAATTC Y 2 1 2 1 101000 f 74 goat snp38094-scaffold475-182918 10 38078426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405417 Affx-122956278 AX-123275769 10 61359874 GGGGTGGATTAGAACCTCCCACACAACTGAGGTAC[A/C]GGTGTTCTAGCATTGATTCAGTTGGGGGCTAGGGT M 2 1 2 1 201000 f 74 goat snp38092-scaffold475-84441 10 37979442 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803729 Affx-986696199 AX-385290489 10 61410692 CCACAATGTAAATTGATTTCTGGTGATAAAAATTA[A/G]TTAATGTAGATTTAATTGTAACAAATGCATCAATT R 2 1 2 1 600010 r 74 goat 10_61410692 10 61410692 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38451885 Affx-122921049 AX-123322218 10 61445787 GAAGCTGTCCTAGGAGCCACAGGGGCAGAGTGAAA[C/T]AGAGTCCCATCATGAGCCCTTCAGGATTATGCCCA Y 2 1 2 1 101000 r 74 goat snp56243-scaffold88-1373 10 37893411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379035 Affx-122976356 AX-123249394 10 61495369 TTCACTTTAGGGTTTCTGAAAACACATGACACAAA[C/T]ATGCAAGCAAACTTGAAAATCTACATTGTTAAGCT Y 2 1 2 1 201000 r 74 goat snp56244-scaffold88-50955 10 37844845 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384762 Affx-122972026 AX-123255120 10 61529431 TCTTCTATGTTCAATACTTAGTTCTACAGAGCCAC[A/G]TAAACAGTCTGGCTGAGCAGTGGGAGAGCCTGAGT R 2 1 2 1 101000 f 74 goat snp56245-scaffold88-85017 10 37810796 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386165 Affx-122971386 AX-123256523 10 61563143 TCTTTAGAAATACAACCAGTGCGATCTATCACATG[A/G]AAGATCAGAAGGGGAAGCCACTGTAATTTCTGTTA R 2 1 2 1 101000 f 74 goat snp56246-scaffold88-118729 10 37776890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381980 Affx-122974096 AX-123252338 10 61592805 TGTCCTGGGTTCGAGAAGCAGATTAAATCACACAC[A/G]TTCATGCTCAGGAACTTCCATGTAAAAGCCAGTCT R 2 1 2 1 201000 r 74 goat snp56247-scaffold88-148391 10 37747088 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450904 Affx-122922197 AX-123321238 10 61651301 TATCTTGGAAAAGATTGCTTCTGTTCCCCTCAGCC[A/G]CAGGGATGGCTTTCAGAGTGGGGTATAGTCTCCCT R 2 1 2 1 202000 r 74 goat snp56248-scaffold88-206887 10 37688074 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476269 Affx-1251763776 AX-586011690 10 61787093 ATAAAAGTATATTTGCTTTTATAAACAAAACAAAA[-/CAAGAAGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGATTTTAAAATTTAAAAAAAATAAAAAATTAAAAAAAAAA]AAAACAAGATTAGATTTCTTGAAATAGCTTCTCTG - 4 1 4 1 20000 f 74 goat SV_293 10 61787093 - deletion junction SV-TF-chip 539476522 Affx-1251763776 AX-586011915 10 61787093 ATAAAAGTATATTTGCTTTTATAAACAAAACAAAA[-/CAAGAAGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGATTTTAAAATTTAAAAAAAATAAAAAATTAAAAAAAAAA]AAAACAAGATTAGATTTCTTGAAATAGCTTCTCTG - 4 1 4 1 20000 r 74 goat SV_293 10 61787093 - deletion junction SV-TF-chip 562166166 Affx-1251763776 AX-606941574 10 61787093 ATAAAAGTATATTTGCTTTTATAAACAAAACAAAA[-/CAAGAAGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGATTTTAAAATTTAAAAAAAATAAAAAATTAAAAAAAAAA]AAAACAAGATTAGATTTCTTGAAATAGCTTCTCTG - 8 1 4 1 20100 r 74 goat SV_293 10 61787093 - deletion junction SV-TF-chip 562166167 Affx-1251763776 AX-606941575 10 61787093 ATAAAAGTATATTTGCTTTTATAAACAAAACAAAA[-/CAAGAAGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGATTTTAAAATTTAAAAAAAATAAAAAATTAAAAAAAAAA]AAAACAAGATTAGATTTCTTGAAATAGCTTCTCTG - 8 1 4 1 20100 f 74 goat SV_293 10 61787093 - deletion junction SV-TF-chip 562166421 Affx-1251763776 AX-606941829 10 61787093 ATAAAAGTATATTTGCTTTTATAAACAAAACAAAA[-/CAAGAAGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGATTTTAAAATTTAAAAAAAATAAAAAATTAAAAAAAAAA]AAAACAAGATTAGATTTCTTGAAATAGCTTCTCTG - 8 1 4 1 20100 f 74 goat SV_293 10 61787093 - deletion junction SV-TF-chip 38426995 Affx-122940380 AX-123297340 10 61787789 TCCAGCTGTCAAGGGCTGGGCCTCCAGGGTCATCC[A/G]CTCAGTTTTATCTGCGCCAACCTGGTAGCTCTTCA R 2 1 2 1 101000 r 74 goat snp56251-scaffold88-343375 10 37550542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378741 Affx-122977030 AX-123249100 10 61820508 AAATCACATCATTTTAGAGCATGATTTCATATAAA[C/T]GTTTAGCTAATGTTGAAACAATACCATTTGGTGAT Y 2 1 2 1 101000 f 74 goat snp56252-scaffold88-376094 10 37517724 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388415 Affx-122969283 AX-123258773 10 61864352 AACTCCTTGAAGGACAAAAACTTGTGTTTCTTTCA[C/T]GAAAGTAATGAGCACAGTACTATTTGCACAAAGAA Y 2 1 2 1 101000 f 74 goat snp56253-scaffold88-419938 10 37473702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406298 Affx-122956068 AX-123276650 10 61914925 GACAGTATTCAAGGAAGAGGGTACAACAGCTGGGA[C/T]GGTCTGAAGTGAGGAAAGGCATGGCAGTTGAGAGC Y 2 1 2 1 101000 f 74 goat snp56254-scaffold88-470511 10 37422966 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452975 Affx-122920152 AX-123323308 10 61964921 GTAAGTTGTATCATCCCATAAGCTGTGCTTAAAAC[A/G]TACAATAATTCCCCATCAATTATAGGATAAACCTT R 2 1 2 1 101000 r 74 goat snp56255-scaffold88-520507 10 37372264 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399055 Affx-122960904 AX-123269410 10 62000716 TCTAAGGTGAGGTGTTCACTTAGGGGACTGTGGTG[C/T]ATAAAGCAGACCCGTGGACCTCATCTACCCCATCC Y 2 1 2 1 201000 r 74 goat snp56256-scaffold88-556302 10 37335949 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435691 Affx-122933322 AX-123306030 10 62073435 CTGCTCCAAGTGTCTGGCACACCATAGATGATCAA[C/T]GAAAATTTAGTAAATGAGTTGATAAATGGATAAGG Y 2 1 2 1 101000 f 74 goat snp56258-scaffold88-629021 10 37263023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389782 Affx-122968224 AX-123260139 10 62123624 CAAGGCTTCTATCCTGGTAGTGGAGAGAATGTGAC[G/T]CCATGGAAAACTGAGAAAGCTGAGAAAGGAATGAG K 2 1 2 1 101000 f 74 goat snp56259-scaffold88-679210 10 37212529 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392308 Affx-122967519 AX-123262665 10 62175889 CACTGTGGACAGCAGAGCTCTAAGTCTATAATAAT[C/T]CTAAGAACTTCCATCTTGGAAGTAGTTCAGCTCTC Y 2 1 2 1 101000 f 74 goat snp56260-scaffold88-731475 10 37160053 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429849 Affx-122938158 AX-123300190 10 62205925 TTGAAATGATTCTTGGCACCCATGACCACACATAG[C/T]GCCCACTAGAATGTCAGCTATATGTAACCAGAGAC Y 2 1 2 1 101000 r 74 goat snp56261-scaffold88-761511 10 37129978 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778667 Affx-122959338 AX-385265778 10 62255902 ACAAGTAATTACAAATATGATGGATATAACCAAAA[C/T]GAAGTGCTGCGATGTGTGCAATACAAGAAGCTGAC Y 2 1 2 1 101000 r 74 goat snp56262-scaffold88-811488 10 37079658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275500 Affx-1111834935 AX-519549072 10 62276973 GACCTTTGGACACCAGAATGAGAATGCCTCTGTAG[A/G]TAGGTGAGAGT R 2 1 2 1 101000 f 74 goat GoatD01.059234 10 62276973 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402157 Affx-122958649 AX-123272510 10 62298138 ATATGACCTCAAATGTTTCTCTTGCTTACTTTCTC[C/T]CTTTCTTTTTCTTCTGAGCCTGACTAATAGCCTCT Y 2 1 2 1 102000 r 74 goat snp56263-scaffold88-853724 10 37036815 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441108 Affx-122929601 AX-123311445 10 62358508 ATTTCCATTTTATAGGTAAAGAAATTGGGACCTAA[C/T]GGTATAAAGATGAGCTCAAATTCAAGACATCACCT Y 2 1 2 1 101000 r 74 goat snp18104-scaffold185-12822508 10 36967762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386831 Affx-122970092 AX-123257189 10 62393537 AGAGGGTATTTGACGAAATTTCCTAAAAGACAAGG[C/T]GAACTTAGCAAAAGTTCACAGTGCTTACATAAGCA Y 2 1 2 1 101000 f 74 goat snp18105-scaffold185-12857537 10 36931813 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452667 Affx-122920326 AX-123323000 10 62427021 AGAATACACTGACTCAGTCTTTAGGGGTGGGAAAA[C/T]GATACGGACCCTTGCTAAGCTTTCAGTCAAAAGTT Y 2 1 2 1 101000 f 74 goat snp18106-scaffold185-12891021 10 36883557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390680 Affx-122967956 AX-123261037 10 62492053 TTAAGAACAAGAAAATCTGTGGAATGAAAATGTAG[C/T]GACTGACCTTGAAGGAACCGATCCCTAGGGTTTGA Y 2 1 2 1 201000 f 74 goat snp18108-scaffold185-12956053 10 36817970 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795555 Affx-122927343 AX-385282510 10 62524654 AAAATCTAAATCACTGTTCTGTTACTCTGCAGTTA[C/T]GATTTGCTATTAGTGGTAAATGAAAACACCGTCTT Y 2 1 2 1 101000 r 74 goat snp18109-scaffold185-12988654 10 36784706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435687 Affx-122933325 AX-123306026 10 62554498 AACAGGATGGTAAACAGTTTCCCCTGTGACTAAGT[G/T]CTAGACAACAAAATATGATGGAAGAAAAGATTGCC K 2 1 2 1 101000 r 74 goat snp18110-scaffold185-13018498 10 36754982 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271749 Affx-1111832896 AX-519545543 10 62575634 AAATGTATCATTCACAGATATTACTCTTGAAGCAT[A/C]TGCTTAAGAATCATACTAGCTCCAAACAGACCATT M 2 1 2 1 101000 r 74 goat 10_62575634_AF-PAKI 10 62575634 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320774467 Affx-122928633 AX-385261603 10 62588518 ACTAAAATGAGGTTTGTTAACTTTTTCCCAGCAGA[C/T]GAGTTTTCCCCAGGTCAAGGTAAGAATCAAACAGG Y 2 1 2 1 101000 r 74 goat snp18111-scaffold185-13052518 10 36720811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769132 Affx-122947517 AX-385256307 10 62617826 GCCTGATTTCAGAGGAAGTGAAGGACTCAAGATAG[C/T]AAAGAAACTCACCTTTTGGAGGTAAATTAACTCTT Y 2 1 2 1 101000 f 74 goat snp18112-scaffold185-13081826 10 36691387 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424675 Affx-122941714 AX-123295021 10 62653595 GATGAAAGAGAGACAGATAAACTAAGGATGGCAAA[A/G]CAGCATGCTGGGAGGTGTGGCTCTGGGACTAAGTT R 2 1 2 1 101000 f 74 goat snp18113-scaffold185-13117595 10 36655871 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453832 Affx-122919549 AX-123324165 10 62713367 GAGGCCGAGAAGATAAGAACTTTAACCAAGGTCAC[A/G]CAGTGACCAGTCAGGAATAGTCCTAGTGGCTCCTA R 2 1 2 1 201000 r 74 goat snp18114-scaffold185-13177367 10 36595786 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398312 Affx-122962143 AX-123268667 10 62755522 AGGGTTACTACTATCAAAACTTGATAACCCAAGTA[C/T]GTAAATCCCTTAAATCTTTAAATAAGAACCTTGTT Y 2 1 2 1 101000 f 74 goat snp18115-scaffold185-13219522 10 36552704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787796 Affx-122950101 AX-385274819 10 62799540 AGAATCATTGTTTTATACCATTAAAGCTAAAGTTT[A/C]TCATTAGGATTAATGGAAATTCAGATTTTTTTCAA M 2 1 2 1 101000 r 74 goat snp18116-scaffold185-13263540 10 36508733 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796080 Affx-122967523 AX-385283032 10 62852426 TAAGAGACAACTGTGCTATATGCTTTAGGATTCTG[C/T]GTAATTTGTAGTATGTTTCACGTACAAGCTCACTA Y 2 1 2 1 101000 f 74 goat snp18117-scaffold185-13316426 10 36455603 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276552 Affx-1111835400 AX-519550063 10 62852670 TGATGTGTGCACACACACATAGTTAATTTCCAAAA[A/C]CACTGTACATTTTGACCCAAGATTGATGTCAGATT M 2 1 2 1 202000 r 74 goat Random2.2K-1088 10 62852670 A C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320782696 Affx-122935645 AX-385269768 10 62888312 ATTCGAACTTCCAACAAGGATTTTGAGAGCCTGCA[A/C]TAATTGCTGCATTATGCTTGTTTCTATGGGGCTAC M 2 1 2 1 101000 f 74 goat snp18118-scaffold185-13352312 10 36421614 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395240 Affx-122964473 AX-123265595 10 62952275 GTTGGACACAACTGAAGTGACTGAGCATGCATGCA[C/T]GTTGAATACAGTAGATAGACAAGGTCATCCTAGCA Y 2 1 2 1 101000 r 74 goat snp18119-scaffold185-13416275 10 36357755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432674 Affx-122936048 AX-123303015 10 62982220 GCCTCCCCACCAGGGGTGAGGTGAGATGGGAAAGC[G/T]CCTGCTGATTGCAGCGATCTGATGAAGCCCTGGCT K 2 1 2 1 101000 r 74 goat snp18120-scaffold185-13446220 10 36327960 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382826 Affx-122973550 AX-123253184 10 63021006 TAGCCACCTTGGGAAGGAGCATGGTGTTTCAACAA[C/T]ATTATTCCCAGACTGAAAGCCGCTCAGACCTGGAT Y 2 1 2 1 101000 f 74 goat snp18121-scaffold185-13485006 10 36287241 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436348 Affx-122933070 AX-123306687 10 63053492 TCCTCTACCCTGGGATGGGGAGTGGGAAGTATCAG[G/T]TAAATATTGTGAAAATTATCAAATAATATTAATAA K 2 1 2 1 103000 f 74 goat snp18122-scaffold185-13517492 10 36254479 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444283 Affx-122926766 AX-123314620 10 63087093 CATTTCCATAATTCTTAAGAGTGACCCGAAATGCT[A/G]TGGAGTCAGAAAATTCCTCCAGAGACAAGGGAAGA R 2 1 2 1 101000 f 74 goat snp18123-scaffold185-13551093 10 36220818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413900 Affx-122949834 AX-123284249 10 63125245 TGCCGTGAGATCTTCCAGCGTAACTTACAACTGAA[C/T]TCTGAACCGTTTGAGAATGTATTGGTTTCTACACA Y 2 1 2 1 101000 f 74 goat snp18124-scaffold185-13589245 10 36182407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417314 Affx-122948159 AX-123287662 10 63159760 GGTAAAGGAGGAGGAGGTATGTGGATGCGGTTGGA[A/G]AGAGGGCAGACCTTGTCATGAGCAGGAGTCAGGAT R 2 1 2 1 201000 r 74 goat snp18125-scaffold185-13623760 10 36147697 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426915 Affx-122940445 AX-123297260 10 63195990 GATGTGCATAGCTATTGTATTCATAGAGATAGAGG[C/T]GAGGATCTGACTGCTTCATTTTGTCTTCTGGTGTC Y 2 1 2 1 201000 f 74 goat snp18126-scaffold185-13659990 10 36111315 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394737 Affx-122964864 AX-123265092 10 63225323 CTTTGACATTGAGAAATCATAGAGTTAGCCAAACC[A/G]TCTCCACCTAAGCATTTATCAAATTTATCTCCCTT R 2 1 2 1 101000 f 74 goat snp18127-scaffold185-13689323 10 36081979 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453235 Affx-122920420 AX-123323568 10 63280722 TAGTCTAGGGAGAAATACATTTTATGCATGTTTCT[A/G]TTTAAAGAGAACAAACCAATAACCAAAAAAATGCC R 2 1 2 1 201000 r 74 goat snp18128-scaffold185-13744722 10 36026737 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770502 Affx-122925994 AX-385257667 10 63315222 GTTATGAAAAGTAACTTAACAGTGATCACTGCATC[A/G]TGTTTACTACATGCTAGGTACTCTTCAGAACCCTT R 2 1 2 1 201000 r 74 goat snp18129-scaffold185-13779222 10 35992309 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422719 Affx-122943638 AX-123293065 10 63347082 AGCTACTCAACTAGAAATTGATGAAAAGGAGTGGG[A/G]CTCTGAATGGGAATATAAAAATTTCCCCTTTAACA R 2 1 2 1 101000 f 74 goat snp18130-scaffold185-13811082 10 35960602 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449356 Affx-122922735 AX-123319691 10 63377785 AATCAGTTGGTTAGATTTAAGAAAGCAGAGAAAAA[C/T]GCAGATGAGCAGAGTAAGAGAATGAGAAATGAAAA Y 2 1 2 1 303000 f 74 goat snp18131-scaffold185-13841785 10 35929874 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407269 Affx-122955344 AX-123277620 10 63408987 TTCTATATCTGTAAGTTTGTTTCTGTTTTGGTATA[C/T]TCACTAGTTGGTTGTATTTTTTTTCACCTGGGTTC Y 2 1 2 1 102000 r 74 goat snp18132-scaffold185-13872987 10 35898284 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432105 Affx-122936474 AX-123302446 10 63441120 ATAGGAGGATGGACGCATTAGGGCCTTGCGCTGCA[C/T]GTGCTAGGAGTCATCCCGACAGGGTTTGTAAGCAA Y 2 1 2 1 201000 r 74 goat snp18133-scaffold185-13905120 10 35865810 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412860 Affx-122950445 AX-123283209 10 63516865 GCTCCTATCACCCTCCAAACACTGTCATCATTCTC[C/T]GGCAACTTCCATCCTTCTCAAGGTTAGCTCTGTTT Y 2 1 2 1 201000 r 74 goat snp18134-scaffold185-13980865 10 35789710 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380274 Affx-122975421 AX-123250632 10 63563030 GTTCTGTTCCCAACAGTTCCCCACTGCTCTCTTCC[G/T]AAACTTACCTAGGGAACAAGTAAGCATCCCTGTTT K 2 1 2 1 101000 r 74 goat snp18135-scaffold185-14027030 10 35743406 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400265 Affx-122960131 AX-123270620 10 63597932 GAAGAGCTAAAGTGTATTGTTGAATACTTCATTGG[A/G]TCCTTGCAATCTTTGCTAAGGTCTTGGCCATTAAA R 2 1 2 1 101000 r 74 goat snp18136-scaffold185-14061932 10 35708564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386041 Affx-122971478 AX-123256399 10 63630867 AAGGGCAAAATGGAAGAAAGCATCTAAGGTTTTTT[A/G]TCTTTACTAGGGAATATTTTAAAACAAATTATGCT R 2 1 2 1 103000 f 74 goat snp18137-scaffold185-14094867 10 35675623 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453029 Affx-122920090 AX-123323362 10 63684860 AGGAATCAATGACCATGCTCTGACTTTTCCTTTGC[C/T]GCCAGAAAGAGCTTTTATTAACGTAAATGTTATAG Y 2 1 2 1 201000 r 74 goat snp18138-scaffold185-14148860 10 35621717 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423661 Affx-122942341 AX-123294007 10 63725791 TAAATCTTCACATGAAAACTGTTTTTCAACTCTTA[C/T]GCAAGCGTCCATCCAACCAAAGTATTTCCCTTAAG Y 2 1 2 1 101000 r 74 goat snp18139-scaffold185-14189791 10 35580758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452862 Affx-122920713 AX-123323195 10 63771451 TCTCTAATGGTGAATTTAAGCCCTCTTTCAAATGG[C/T]AAGTTTGTAAATGAATTCCTTGTATTTAAACCCAG Y 2 1 2 1 101000 f 74 goat snp18140-scaffold185-14235451 10 35535851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411058 Affx-122951949 AX-123281408 10 63800299 CCACCATGTGACCTTAAGCACACAACCTGACCCAT[A/G]TAAATGTCAGTTTCCTCATTTATAAAATGAGAATA R 2 1 2 1 101000 f 74 goat snp18141-scaffold185-14264299 10 35508106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387996 Affx-122969578 AX-123258354 10 63835269 AAGAAATGACTCATAAAAGTGACCGCAAACTACCA[C/T]GAGGGCGCGACTTTTAAAAGCGCCAATACTCTTTC Y 2 1 2 1 101000 r 74 goat snp18142-scaffold185-14299269 10 35473089 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411142 Affx-122951888 AX-123281492 10 63884278 TCACTTCCTCAGAAACTGACGTGCATTTTGCTTGG[C/T]ATTGCCCACAGCGTGCATTTGAGATAGGAATTATG Y 2 1 2 1 101000 f 74 goat snp18143-scaffold185-14348278 10 35424028 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447499 Affx-122924080 AX-123317835 10 63924047 TTCCCTGGAGAAACCTGCTACTTACTAAAGCCCTT[A/G]GAAAGAAACTAGACAGCAGCAGAATGACCAGAGGC R 2 1 2 1 101000 f 74 goat snp18144-scaffold185-14388047 10 35384012 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413752 Affx-122949944 AX-123284101 10 63955926 CTTATTACATTCCTCCCCAGCGCTGCACTAACCAT[C/T]AGGATGGGACTGAACAAAAGCAGAATTCACTCCTG Y 2 1 2 1 101000 r 74 goat snp18145-scaffold185-14419926 10 35352137 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398800 Affx-122961413 AX-123269155 10 63998846 GAGTTGTATGGGAGTATGTGCGAACTTTTACCAAG[C/T]ACTTTGCATGAAATATTGTTTGTAACGTCTTTAAG Y 2 1 2 1 101000 f 74 goat snp18146-scaffold185-14462846 10 35310525 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413045 Affx-122950984 AX-123283394 10 64030311 TTCAAATATGTTCTCTAAGATAAATTACGATATAT[G/T]AATTGAATATAAGCTGAAGCGAAGTGATTGAAGTA K 2 1 2 1 102000 r 74 goat snp18147-scaffold185-14494311 10 35283190 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415921 Affx-122948454 AX-123286270 10 64077702 GCTATAGTCCGTGGGGTTGCAAAAAGTTGGACACT[A/G]CTACTAAGGCACGTTATACAGACAGCTTTGTGAGC R 2 1 2 1 101000 r 74 goat snp18148-scaffold185-14541702 10 35235341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401653 Affx-122959580 AX-123272006 10 64112357 GATTACAGTAAACTACCAGAGAAGGAGTTTTCTCT[A/C]TTGAAGAGTATGCATTATTCTTATATCTGTCTAGG M 2 1 2 1 101000 r 74 goat snp18149-scaffold185-14576357 10 35200343 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775895 Affx-122973236 AX-385263026 10 64181364 TATATTACCCACTTAACAACCACCAAACCTTTTTT[A/G]CACTATAAATATTTATGAATCACTATAAGACATGG R 2 1 2 1 201000 r 74 goat snp18150-scaffold185-14645364 10 35131197 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441791 Affx-122929088 AX-123312128 10 64247803 TCAGATGCAGAACAGCCTTTAAACATAGGTAGAGG[C/T]GGTAACAGCAACATTTTGAAAGGCTCAGCGAGGAC Y 2 1 2 1 101000 f 74 goat snp18152-scaffold185-14711803 10 35064356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396501 Affx-122963529 AX-123266856 10 64281783 ATTTTGCAGGAGCAGAAATATAAATGGTAAGTTAA[C/T]GCATAAAGAGAAAAGGAAAGTAAAGGGCCAAAATA Y 2 1 2 1 201000 f 74 goat snp18153-scaffold185-14745783 10 35030589 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378779 Affx-122977002 AX-123249138 10 64315638 CAAAGAGGGTCCCCGTGGGATGGAGCCTCAGCTAC[A/G]TGCAGTCATAAATTTCTCACTGATGCCCCTTAATT R 2 1 2 1 101000 r 74 goat snp18154-scaffold185-14779638 10 34997440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435778 Affx-122932867 AX-123306117 10 64353110 ATTACCTTACAAGGGTTAACTAGGCACATGTACCC[A/G]TCTCTGCCTTTTCTTTTGTCAAAGATCACCTTCCT R 2 1 2 1 201000 f 74 goat snp18155-scaffold185-14817110 10 34960264 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407431 Affx-122954804 AX-123277782 10 64417506 TTAAGGAATCTACCCGAGATTACACAGTCAACGAG[C/T]AGTAAATGGAAGAGTTGAAATCTGCTCATAACCAC Y 2 1 2 1 101000 f 74 goat snp18156-scaffold185-14881506 10 34900358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450198 Affx-122922294 AX-123320533 10 64458193 TGCCCTGACCTTTTCCTGATGTTTGAACATTTTTT[A/G]TTCCAAAAGAAAGAAGTAAAGATATCTTTTTTACA R 2 1 2 1 103000 f 74 goat snp18157-scaffold185-14922193 10 34859642 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766308 Affx-122939304 AX-385253694 10 64509492 TTGGTCAGTCAACAGTAGCATCTACAACATACCAC[A/G]CAAATCAAGGAAAGGGATCTACCAGTGATTCTTCC R 2 1 2 1 101000 f 74 goat snp18158-scaffold185-14973492 10 34808142 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406897 Affx-122955630 AX-123277248 10 64560834 ATCTACTTAAATCAAAGGAAAGATTAAAAATAAGA[C/T]GGCTAGGAAAAAAACTGCATGTTTTACAGTTCATT Y 2 1 2 1 101000 r 74 goat snp18159-scaffold185-15024834 10 34755922 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769939 Affx-122941730 AX-385257108 10 64593080 CACTTTTACTTTGAATATACTGTTGCAGGAAAAAC[G/T]TCTAAATATTGGATACTGCTGTGAAGATAAAGTAT K 2 1 2 1 101000 f 74 goat snp18160-scaffold185-15057080 10 34723687 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276554 Affx-1111835401 AX-519550065 10 64622899 AACTCTGGCAGGTATTTGCTCTGTCTTCATGGACA[C/G]AGCAAACAGAGTGTCATCTTGGGTTCCTGCCATTC S 4 1 2 1 101000 r 74 goat Random2.2K-1090 10 64622899 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38414264 Affx-122949613 AX-123284613 10 64665051 TGTGTAAAACCGTGTGTGTGCATGTGTGATTGACT[A/G]TAGGATAAAGTGTAAACTCTGCGTGGGGTAGAGAC R 2 1 2 1 201000 r 74 goat snp18161-scaffold185-15129051 10 34650975 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796491 Affx-122940360 AX-385283441 10 64693923 AACTGTGTGTAGTTCATTCTTAAAGAATAAATGGA[C/T]GGCTAAAACTTTTTTGGTTTATATGCTTATTCATT Y 2 1 2 1 101000 f 74 goat snp18162-scaffold185-15157923 10 34623179 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796257 Affx-122948072 AX-385283207 10 64751651 TAACAAAAAATCTATTAGTTATAATTTAGGTTCTC[A/G]TCATAAATATTTTTAGAACACTGTTCCTGCAGGGG R 2 1 2 1 101000 r 74 goat snp18163-scaffold185-15215651 10 34565475 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320791159 Affx-122960155 AX-385278154 10 64828926 GAAGGTTCTATAACCTTGACAGTCTAGTACAGTCC[A/G]TATTTAACAGACCTCCATTTTTTTCTCATATAATG R 2 1 2 1 101000 f 74 goat snp18164-scaffold185-15292926 10 34488069 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386724 Affx-122970153 AX-123257082 10 64859262 ACCACAAAGAGATGGGCACAACTGAACACACGTGC[A/G]CAACTGCAACCTTAGAGGCAGCTAACAAAAACCCA R 2 1 2 1 101000 r 74 goat snp18165-scaffold185-15323262 10 34458164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377699 Affx-122977410 AX-123248058 10 64893543 CAGCTGAGCTTCCTCCTGTGATCTCTCCAGTCTCA[C/T]GGAGAAGTAAGAGTGCTATGAGGATGTGCTAATGG Y 2 1 2 1 101000 f 74 goat snp18166-scaffold185-15357543 10 34424133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430709 Affx-122936907 AX-123301050 10 64936035 CTCTTTCTAACTTAGTACTTACATCTGGAAATGTT[C/T]GTATGAGCTTTGATGCTCATGTCTGCTTGCCCTTC Y 2 1 2 1 101000 r 74 goat snp18167-scaffold185-15400035 10 34381362 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412936 Affx-122951468 AX-123283285 10 64979425 AAAACTGCTGCTTTCCCCTGCTGAATATCTGGTGA[C/T]TGCGAAAACTTCCCTCCACTCATCCTGGCCTAAAC Y 2 1 2 1 101000 r 74 goat snp18168-scaffold185-15443425 10 34337955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791896 Affx-122945213 AX-385278886 10 65024299 TTAATCTAAATTGGACCTTAGCAAACCTAGAAGAA[C/T]AATGTTTGATGAACACTCTTCCCTTGCTCCTTGGA Y 2 1 2 1 101000 r 74 goat snp18169-scaffold185-15488299 10 34292590 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463104393 Affx-1109815652 AX-514591659 10 65076763 AGTCTCACATTTATTTCATCTGAGGTGCAGCCTAG[A/G]CACTGGGACCTCTGAAAGGTCTAGGTGACTTCAAT R 2 1 2 1 202000 r 74 goat 10_65076763_AF-PAKI 10 65076763 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392332 Affx-122966689 AX-123262689 10 65087037 TGATTATAATGGGTTTTAGATCAGCACACAGACCT[A/G]TGACCATTTTATTTTAATATACGGTCTTAATGATA R 2 1 2 1 101000 f 74 goat snp18170-scaffold185-15551037 10 34229375 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381902 Affx-122974154 AX-123252260 10 65128180 TCTTGAATTGAAGGATGCCTGGTTCCAAACATTGC[A/G]TGCAAAGTGCTTCTTCTGAGTTCTCTCTCTCTCTC R 2 1 2 1 101000 f 74 goat snp18171-scaffold185-15592180 10 34187810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404971 Affx-122956409 AX-123275323 10 65166025 ACTTTGCCTGCTTGTTTATTGCTCTACCCCCTCCA[C/T]GTCTAGACTGTCAAACATACTGTATGTTTTCATAG Y 2 1 2 1 103000 f 74 goat snp18172-scaffold185-15630025 10 34149995 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448469 Affx-122923629 AX-123318805 10 65228955 AAGAAGCCACAATTTTATTTTTATGACCACATACT[A/G]CAAAGGTACATAAAAAATAGAGAACCCTCCTCCAG R 2 1 2 1 103000 r 74 goat snp18173-scaffold185-15692955 10 34086958 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453797 Affx-122919576 AX-123324130 10 65269503 TAATATATGGTGATCTGAACTGACCTTATTAGAGA[C/T]GGCAAAATAAATGCCATTTTCAAAACAAGGAAACC Y 2 1 2 1 101000 f 74 goat snp18174-scaffold185-15733503 10 34046557 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397682 Affx-122962584 AX-123268037 10 65317470 AATTCTGGAATTGATCCTGTGTAAGACAAAGAAAA[C/T]GATAAAGTGAATGACTATTATACAAGGTATGAAAC Y 2 1 2 1 101000 f 74 goat snp18175-scaffold185-15781470 10 33998361 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792923 Affx-122946487 AX-385279901 10 65346811 TATCTTTCCTTATCTTTCACTTCTAATGCTTATGG[A/C]TTTCTGTTCTGTTTGAAATGTAACATTTAGCTACA M 2 1 2 1 201000 r 74 goat snp18176-scaffold185-15810811 10 33969404 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784999 Affx-122937631 AX-385272046 10 65393282 TTCTCCCTCCTTAGTCAGTGAGCAAAATGAGTTTT[A/C]TGAGATACAAATTTGGTAGTTGTAACTTCCGGTTA M 2 1 2 1 101000 f 74 goat snp18177-scaffold185-15857282 10 33922273 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768738 Affx-122968691 AX-385255916 10 65421852 GAGATCATATAGGACCATATATCCACATCTTGGCA[C/T]GTGGATATTCTCTTAATATCACAGCTGGAAATGCT Y 2 1 2 1 101000 f 74 goat snp18178-scaffold185-15885852 10 33893710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385524 Affx-122971250 AX-123255882 10 65467225 TTTATTTCAGTACTCTGCAGGTCCATCTGCAACCT[A/G]TATTTTGAATCTGATTAGTTGCATAATAACTCTTT R 2 1 2 1 201000 r 74 goat snp18179-scaffold185-15931225 10 33848097 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774907 Affx-122973460 AX-180660643 10 65497025 ATATTTTCAGTTCTATTGAATATGTGGAAGGCTAG[A/C]GTAGTGTGATTAAGACAAATTTGAGTCCGATTACC M 2 1 2 1 101000 f 74 goat snp18180-scaffold185-15961025 10 33818307 T G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783021 Affx-122962219 AX-385270089 10 65560217 TGGGAGGATTTTTGAGATTTTAGAGGGATTTTCAG[C/T]ACTGTATGATTAGAAAAAGCAAGTCATGAATATAA Y 2 1 2 1 101000 f 74 goat snp18181-scaffold185-16024217 10 33755117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387427 Affx-122970393 AX-123257785 10 65615222 GTGTCCCAGCCATGGACTCCCACACCTCCACAAAT[A/C]TCCCTCCAAAGCCCACTTCCTAGCACTTGGTCTTC M 2 1 2 1 201000 f 74 goat snp18182-scaffold185-16079222 10 33699684 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778668 Affx-122967660 AX-385265779 10 65647070 ACATTTCAGCCAGCTGATTTTTTCAGTCCTCACTT[A/G]TGACCTTAGGATGAGTAATGATAACAAAAATTAGC R 2 1 2 1 101000 f 74 goat snp18183-scaffold185-16111070 10 33668011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377350 Affx-122977658 AX-123247709 10 65707530 AAGATGAAAGAAAATGAGATATGGGAGAGAGTGAC[A/G]CAAAGGAAAGAAAATAAGAGGACTTAGCTTAAACC R 2 1 2 1 201000 f 74 goat snp18185-scaffold185-16171530 10 33607186 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766474 Affx-122939117 AX-150139246 10 65749366 AAGTCAATTGAATACCAAATGAAGTTTATTTCTTA[C/T]GTAATAGAACAAACGTTTCCTTTTACTTTGCCCAA Y 2 1 2 1 201000 f 74 goat snp18186-scaffold185-16213366 10 33565329 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797303 Affx-122966185 AX-385284242 10 65783050 TATAGAAAATAGCCTGAGTAGTACAATACATCTTG[C/T]GGCAAAACAATAGGATCTGCGTCACAATACAAGGA Y 2 1 2 1 101000 r 74 goat snp18187-scaffold185-16247050 10 33531561 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375544 Affx-122979097 AX-123245903 10 65821477 CCCATGGGGTTGGGAAAAAGTCACACATGACTTAG[C/T]GACTGAACAACAGCAACACGAGTAATAAAGAAAAG Y 2 1 2 1 103000 f 74 goat snp18188-scaffold185-16285477 10 33492487 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447067 Affx-122924508 AX-123317403 10 65854704 TTTAGTTATCTGACTAATCTTTATTGAACACCTAC[A/G]TATGTGCCAGACACTGCACCTAATACCTAGTGGAA R 2 1 2 1 101000 f 74 goat snp18189-scaffold185-16318704 10 33459438 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399411 Affx-122961239 AX-123269766 10 65883839 GGGCTACCCTGTTCCCCCCTTGAATGTTGTACTTA[C/T]GAGCTTTGTTTATATACATAGCAGTGACAGAAACT Y 2 1 2 1 201000 r 74 goat snp18190-scaffold185-16347839 10 33430261 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432732 Affx-122935461 AX-123303073 10 65918809 GGCATCTGACGTAAATGAGACACAACCCTGGTACT[C/T]GTACTAGATTCCAAACCTAGCACTGATAGTGGAAA Y 2 1 2 1 101000 r 74 goat snp18191-scaffold185-16382809 10 33394064 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802686 Affx-122932217 AX-385289585 10 66003550 CATTGGTAAAATGCTTCACAGTTTAGTTTTCACAC[A/G]TACCATTTAATTTAACCTGTAAGAACCTTCTTCAA R 2 1 2 1 101000 r 74 goat snp18193-scaffold185-16467550 10 33308413 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422726 Affx-122943259 AX-123293072 10 66064635 CATAGCTGAGGGTATGGACCTCAGCTTTAACATCA[G/T]CATTACTTAAATGTGAGAAAAATAAACAATTAAGT K 2 1 2 1 201000 r 74 goat snp18194-scaffold185-16528635 10 33246271 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781201 Affx-122926990 AX-385268286 10 66101865 AATAGCGTATGTTCAAAAAAATTCTGTTCAACAAG[C/T]AAATACAACCGAACCCAACAATCTGTTACTCTCAG Y 2 1 2 1 101000 r 74 goat snp18195-scaffold185-16565865 10 33209424 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384424 Affx-122972185 AX-123254782 10 66130989 CATTACATTTTGCTACTGTTATTTTTGTTTGGAAG[C/T]ACAATTACAATAGGATAGGGCAGCTATCAGGCAAA Y 2 1 2 1 101000 r 74 goat snp18196-scaffold185-16594989 10 33180163 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377619 Affx-122977886 AX-123247978 10 66189913 CCCTTAACTGGTCCCCAAACTTCCAACAATCACTG[C/T]AACACCACTTGCAATGAATGACAAGCAGCATTGAG Y 2 1 2 1 102000 r 74 goat snp18197-scaffold185-16653913 10 33121476 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390766 Affx-122967894 AX-123261123 10 66289950 TGGAAATGGTTACAGAATACTTGCAACAACTCCCC[A/G]GGCAACTCCAAATGAATTGATGGTGAGATGAAATC R 2 1 2 1 201000 r 74 goat snp18199-scaffold185-16753950 10 32994591 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379118 Affx-122976747 AX-123249477 10 66329524 ATGAGCTGGCCTGAGGCTCCATCTTGGAAGAGGAC[C/T]TTAGGGACTCCTAGTGGGAGCAACTGGGAAAAGCC Y 2 1 2 1 102000 f 74 goat snp18200-scaffold185-16793524 10 32954958 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402069 Affx-122958713 AX-123272422 10 66361054 TGCTGGTGTTTCTCATTAAACTTGTATTATCCTCA[A/G]CAGTAAATCAGTCTCCCCTATTCACAGATTCCTAT R 2 1 2 1 101000 r 74 goat snp18201-scaffold185-16825054 10 32923369 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782003 Affx-122970912 AX-385269082 10 66471858 ATCTATTTAAGGTTTCTGCTACCTGTAGCTAAAGG[A/C]ATCCTAGCAGATATAGAATGCACAAAGTAAAGAAT M 2 1 2 1 101000 f 74 goat snp18203-scaffold185-16935858 10 32812594 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396932 Affx-122963192 AX-123267287 10 66503930 AATATAGCCTGATAAATGCAGTTGGTAATATGCTC[A/G]CATTATTTTATACATTGTTAAGGTTCATAATTATT R 2 1 2 1 101000 f 74 goat snp18204-scaffold185-16967930 10 32779961 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416278 Affx-122947948 AX-123286627 10 66548654 CATGGAAGAGGCCCATAGCTGTTAGTTCCCTTTCT[A/G]TTTCCTCAGTGGGCAGCAAGAAGGAAGCAGTGGAG R 2 1 2 1 202000 r 74 goat snp18205-scaffold185-17012654 10 32735440 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389384 Affx-122968393 AX-123259742 10 66583860 TAAATTACTCCCCTCTCTGTTACACCCTCAGCAGT[A/G]TTAATTATAGTACATTTTAACTTTTTCTATCAATA R 2 1 2 1 201000 r 74 goat snp18206-scaffold185-17047860 10 32700127 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385866 Affx-122971610 AX-123256224 10 66635022 CCATCTGATTTCAAGACTTAACTATAAATTTAATG[G/T]AATATTATTAATAGAAAAGAAAAGTCTAAAAATAG K 2 1 2 1 303000 r 74 goat snp18207-scaffold185-17099022 10 32648808 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446516 Affx-122925029 AX-123316852 10 66693371 TTTGATGGTCCAGCAGAAGAAACTGTAAATACTCC[A/G]CTAAAGGAAGAAGAGGATGCAATGCCTCTGATTGG R 2 1 2 1 101000 f 74 goat snp18208-scaffold185-17157371 10 32590496 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276556 Affx-1111835402 AX-519550067 10 66697426 GCCTTTCCCCTTACATATAAGAAGCTGTATGTCCT[A/G]TATATAGGCCCAGAGATTGGTCGTTGGTTTGTTCA R 2 1 2 1 202000 r 74 goat Random2.2K-1093 10 66697426 A G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436087 Affx-122932685 AX-123306426 10 66722417 GAAAACTACCTACATGTGACTAACACCTGCTAACT[C/T]GTAAATAGTGAAGGCATGGGCTGCTTCTTAGCTCC Y 2 1 2 1 101000 f 74 goat snp18209-scaffold185-17186417 10 32561125 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788322 Affx-122945168 AX-385275340 10 66780546 TTGTAAGTCTTAATTTCACTCTTATCACGCATTGT[A/G]CTTATTAGTAATAAGGTCCATTTTATTCAACATGT R 2 1 2 1 101000 f 74 goat snp18210-scaffold185-17244546 10 32502758 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382928 Affx-122973387 AX-123253286 10 66834938 ATCCATGGCTGCTTCTCACTTCTGTAGTTACTTCC[A/G]CACTTTTGGGGACAGGGAGCTGGCAGCCTTTGTTA R 2 1 2 1 101000 f 74 goat snp18211-scaffold185-17298938 10 32447379 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403224 Affx-122957899 AX-123273577 10 66935133 ACCAAGATTGGGATAGATTCTAATGGTTACTGCCA[G/T]CTCTGATTTCATGTTCCTACTGAATTCTCACTCTC K 2 1 2 1 101000 r 74 goat snp18213-scaffold185-17399133 10 32345604 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441286 Affx-122929467 AX-123311623 10 67060374 ACATGAAAGAAGACACTGGGAGATTACTGAAACAG[C/T]GTCAGTGAGAATGGAAAAGAGGCAAAAGATTTAGT Y 2 1 2 1 101000 f 74 goat snp18216-scaffold185-17524374 10 32221282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776547 Affx-122943621 AX-385263674 10 67089866 TGGTGATGCCAACGAAGTGTGAAAGAGAATCTACC[C/T]TTTCTGTAAATCAAAGCTAAGGATTCACTTGAAAA Y 2 1 2 1 101000 f 74 goat snp18217-scaffold185-17553866 10 32191484 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378417 Affx-122976781 AX-123248776 10 67121571 TACCTCAAAGCCTTGGGGAATTGAGAAGGGCAAGG[C/T]GCTCTCATTGATAGGATTCTTCTACATGGGAAGTA Y 2 1 2 1 101000 r 74 goat snp18218-scaffold185-17585571 10 32159690 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783956 Affx-122970180 AX-385271010 10 67185445 ATATCATGCTGACATGAAAGTCATTCAAAATTATC[A/G]TCTAGAAAAGAAAGCCCAGAAAAGTCATTGGTTAT R 2 1 2 1 202000 r 74 goat snp18219-scaffold185-17649445 10 32094963 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768383 Affx-122960497 AX-385255563 10 67231247 ATTAGACAGATTTTCATCAAGTTGTTTTTGAGTGA[C/T]AGTGTGTGTACAAATGAAAGGAAGTAGACAGTTCT Y 2 1 2 1 201000 f 74 goat snp18220-scaffold185-17695247 10 32048127 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276558 Affx-1111835403 AX-519550069 10 67235298 GTTAAAGAGAAAGTTAGACCCCTGACTACCCCTCC[A/G]GCTCCTGTAGCCCAGCCTAACAATTGCCTCTCTTT R 2 1 2 1 102000 r 74 goat Random2.2K-1094 10 67235298 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441683 Affx-122929175 AX-123312020 10 67261310 AATCTCTTTTCAGGTTTCCATGGCAACAGTGGCAG[C/T]AATTCAGTGAGTAGCTTTTCCATTCTTCCTTCGTG Y 2 1 2 1 101000 f 74 goat snp18221-scaffold185-17725310 10 32017963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386373 Affx-122970848 AX-123256731 10 67312914 TGAACTGAACTGATATCTTGGTTATTGTAAACAAT[A/G]CTACAATAAACGTAGGAGTCCATTAATCTTTTTGA R 2 1 2 1 201000 r 74 goat snp18222-scaffold185-17776914 10 31966212 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450334 Affx-122922124 AX-123320669 10 67366002 AGAAACGTTTATAAAGGCCTATTGTTCTCCTGCCT[A/G]CTTGGTCATAACAAGAATGCAATTATGATACAACA R 2 1 2 1 101000 f 74 goat snp18223-scaffold185-17830002 10 31914855 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379984 Affx-122975620 AX-123250342 10 67405653 GGTGAGGACAGATTGTTAAATTTTAATTATGGCCA[C/T]GTCCTTGAGTGAATCTATAGGAAGGAATGTATGGA Y 2 1 2 1 101000 r 74 goat snp18224-scaffold185-17869653 10 31874367 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797188 Affx-122919429 AX-385284127 10 67442696 GCATAAATAAATATTTCACCTAATTAAGCTACTGC[A/C]ATTTCTATCAGTATCTGAAGGTCCTCTTCCTACTT M 2 1 2 1 101000 f 74 goat snp18225-scaffold185-17906696 10 31836875 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391320 Affx-122967321 AX-123261677 10 67477846 GTGGGAATAATGATTTTTTATCTCTTTTCTTGGTC[A/G]TTTCTTTTTATTCTCCAATCCTTCTATCACTTACA R 2 1 2 1 201000 r 74 goat snp18226-scaffold185-17941846 10 31801924 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798461 Affx-122926481 AX-385285394 10 67515149 CCATGAAAAACTTCAGAAATGATTTGCTCTATTCC[C/T]TTCCTGCCTCCAACCAAGTTCGATTGTAGGAGGTG Y 2 1 2 1 101000 r 74 goat snp18227-scaffold185-17979149 10 31764295 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394986 Affx-122964258 AX-123265341 10 67586766 TAATTGGCAGTTTCCATTTTATTTAGTCAAGTGGA[G/T]CAGGAATCAGTGTTCTTTGCATTGTTAAGGGACAG K 2 1 2 1 101000 f 74 goat snp18228-scaffold185-18050766 10 31698148 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404128 Affx-122957100 AX-123274480 10 67641873 CTGACTCTGCTTCTCTGAGAATACATGAAGGAAGC[A/G]CAGTAACTGGAGGAGAGTGGGTATCACTAGGTTCT R 2 1 2 1 201000 f 74 goat snp18229-scaffold185-18105873 10 31643432 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419924 Affx-122945323 AX-123290272 10 67673359 TTGTCCCACAGATGTCCAAATTGCTTGTTCCTGTG[C/T]AGCGAGATCTTTTCCAGTCACTGTGCTCACATTCT Y 2 1 2 1 201000 f 74 goat snp18230-scaffold185-18137359 10 31612175 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463106023 Affx-1109816476 AX-514593275 10 67686280 TACCCATTGGATGTTTCTGAATTTTGGCAGCATGT[C/T]TAATTTTGGTTTTTAACCTAAAATGAATCATGGCA Y 2 1 2 1 201000 r 74 goat 10_67686280_AF-PAKI 10 67686280 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450481 Affx-122922933 AX-123320815 10 67710605 ATCTGTTTCTTGTTCTAATTCCCAGTCTTGTCACT[A/G]CTGGTGTCCAGCAGAGGAGTTGCCAGTTGCTTGGC R 2 1 2 1 101000 f 74 goat snp18231-scaffold185-18174605 10 31574537 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436689 Affx-122932450 AX-123307027 10 67741520 AGTCATCACGAGGTACAGAGGAAACTGTTTTGTTA[C/T]GATCCCAATGTGAGTCTACCATCAGTGGCCTGGCA Y 2 1 2 1 201000 r 74 goat snp18232-scaffold185-18205520 10 31543369 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771483 Affx-122959848 AX-385258641 10 67772955 TATTCCAATAAGGAAAAACTCACAATGGAAAAGAA[A/G]TCCAAAATAAGAAAAATAGTTATTAGGGAAAGCTT R 2 1 2 1 202000 r 74 goat snp18233-scaffold185-18236955 10 31511695 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276560 Affx-1111835404 AX-519550071 10 67805021 GATCGTCCAAGAAAGAGGGCCTTTTCAGTCTCCCA[A/G]TGCCCAGAGTCTTAGACATAAAGTAGTCTTCTGCA R 2 1 2 1 101000 r 74 goat Random2.2K-1095 10 67805021 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421874 Affx-122944275 AX-123292221 10 67821377 CCAGTTGGTGTGCTTTATATCCGTTCCTGTCGAGT[A/G]TTGATGCTTTCTGATTGGTACACCATGCTTTACAA R 2 1 2 1 101000 r 74 goat snp18234-scaffold185-18285377 10 31462645 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417053 Affx-122947519 AX-123287401 10 67854367 TTTGAAACTCATACCCTCTTCTTTCTCTTATTTCT[C/T]CTATTTGTTGAATCAAATTTTGTGTAGCTTCCTGA Y 2 1 2 1 201000 r 74 goat snp18235-scaffold185-18318367 10 31429424 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38437670 Affx-122931781 AX-123308008 10 67901608 TAAATTATTTATTTCATAGGTTATAAGTTAAATTG[C/T]CCATTGTAGCAGGGCTTCTCAAACTTTATGTCTTG Y 2 1 2 1 201000 f 74 goat snp18236-scaffold185-18365608 10 31382018 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791638 Affx-122976843 AX-385278629 10 67930178 TTCTTTCCTTCCTCCAATCCATCTTATTCTTGGAC[A/G]TAAGCCAGTCTCCAGACAGACATTAATATCATTCA R 2 1 2 1 201000 r 74 goat snp18237-scaffold185-18394178 10 31353959 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775536 Affx-122937406 AX-385262667 10 67966278 GGACTAATTGGCTAGCCATCTGGAAAAAGACAAAA[C/T]GAAATTCCTAACTCACTATATATTTAAAAAACATG Y 2 1 2 1 101000 f 74 goat snp18238-scaffold185-18430278 10 31317540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411431 Affx-122951829 AX-123281781 10 67998181 AGAAGAAATAGCTACAGAGATTACAAAATAATACT[A/G]TGGGCAACTATGTATCAGTTATATGGAAACTAGAA R 2 1 2 1 101000 f 74 goat snp18239-scaffold185-18462181 10 31285103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385348 Affx-122971650 AX-123255706 10 68033045 GCAGTGATATGAACCCATACTCTGAATGACTCAAG[C/T]GCCCCTGCTTCAAGCTCCCTGAAAGTTGCAGGGCC Y 2 1 2 1 101000 f 74 goat snp18240-scaffold185-18497045 10 31250276 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450823 Affx-122921795 AX-123321157 10 68081715 GGTCCTTCATTCACCAGTCTTTTGCCATGCACTGC[A/G]TAAGTACTAGGGATAGAAGGTAAAAACACGTGAAG R 2 1 2 1 101000 r 74 goat snp18241-scaffold185-18545715 10 31202113 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403966 Affx-122957439 AX-123274318 10 68112995 ACAAGCTCACAGGCTTCAGCAAGGGAAGGGAAGAG[A/G]GAGGTCCGCAGCGTGAACCACCTAAGAACCTCACT R 2 1 2 1 201000 r 74 goat snp18242-scaffold185-18576995 10 31170728 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421808 Affx-122944323 AX-123292155 10 68168288 AAACATATATTCACTCCAGGACATCACAGAGAAAT[A/G]TTTTTAGAAATGTTTCTTCAAAAACTTTAATTACC R 2 1 2 1 202000 r 74 goat snp18243-scaffold185-18632288 10 31115191 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400036 Affx-122960782 AX-123270391 10 68199511 ATTCTGGATATGTAGCTTTGCCTAAACCTATTCTT[A/G]CCCCTGGACATTTGACCTGTTGCTTGTGAAGGTCA R 2 1 2 1 201000 f 74 goat snp18244-scaffold185-18663511 10 31083749 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781156 Affx-122931557 AX-385268241 10 68257598 TTAAAGTAACATTGACTTATAACATAATATGTTTC[A/G]TGTGTACAACAGTATACTTCTACTTTTGTATACAT R 2 1 2 1 201000 f 74 goat snp18245-scaffold185-18721598 10 31025326 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276411 Affx-1111835405 AX-519549937 10 68269585 TTCTAATGGCTTCATATATCTCTTAGGTTAAGGAC[A/G]AACCTCATTAACACACTCACAGGATCCAGCCTCCC R 2 1 2 1 101000 f 74 goat Random2.2K-1098 10 68269585 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779307 Affx-122976002 AX-385266411 10 68296881 AATAATAATCTCCTCACTGGTTTGGAAAAGCATAC[C/T]TTTGATAACATGCTTCATCTGCATTCCCTTTCTCT Y 2 1 2 1 101000 f 74 goat snp18246-scaffold185-18760881 10 30986016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447701 Affx-122924614 AX-123318037 10 68335175 CTCTCCTGTGGATGGTGCATCGTTTAGCCAACTGA[A/G]AGCTCCTCCCATAAAGATAACAAATGTAATTCTGC R 2 1 2 1 201000 f 74 goat snp18247-scaffold185-18799175 10 30946924 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421513 Affx-122943893 AX-123291860 10 68393810 CATCTCAGAATGAAATGAATTTTATTTTAAAACTA[C/T]ACTACAGCAAGTATTATCCTCTAATGTAGCATCAC Y 2 1 2 1 101000 r 74 goat snp18248-scaffold185-18857810 10 30887200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384211 Affx-122972388 AX-123254569 10 68482340 GGAACTACTAGGAGTGAGTCTCTACTAGTAAGATC[G/T]CTGTCTGAAGATGAAGAATCATGGGTGGGGTAAGA K 2 1 2 1 101000 f 74 goat snp57047-scaffold906-353133 10 30786170 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774735 Affx-122943748 AX-385261869 10 68512083 ACAATTATAACTGATCGATAATGTAATCCTTTCTG[C/T]GAACTCATTGTTACTGGAAGTTTTCCAGCAGAGGC Y 2 1 2 1 101000 r 74 goat snp57046-scaffold906-323390 10 30756322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412676 Affx-122950770 AX-123283025 10 68557306 GTCTGGGAGTTTTACAGTATAAAATGAACAATCCC[A/G]TTTGCATTTAAAGAGATCCTTATTCTACTGACTGT R 2 1 2 1 101000 r 74 goat snp57045-scaffold906-278167 10 30711054 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796753 Affx-122925784 AX-385283697 10 68639452 CTGTCCTTGATATTATTGCATTGAAGTGAGTCAAA[C/T]CATTGCCTAAAATGGTCTAAAACATCTGATTGGCT Y 2 1 2 1 101000 r 74 goat snp57044-scaffold906-196021 10 30628634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420418 Affx-122944914 AX-123290765 10 68673227 AAAAAGAATGGTCAGTTTAGGGGGAGGAGCTGAAG[A/C]TAACAGAGAGGAGAAAAGATAGTAAGTTTAGATTT M 2 1 2 1 101000 f 74 goat snp57043-scaffold906-162246 10 30594937 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436483 Affx-122932968 AX-123306821 10 68719692 CTTATTTCCCTCCCTTTTCCCTCTACCACACATGC[C/T]CTTCAGAACACTTCAGACTCAATTTTTCAGGTGAA Y 2 1 2 1 201000 r 74 goat snp57042-scaffold906-115781 10 30548325 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397487 Affx-122962076 AX-123267842 10 68754789 GCAATTATGGGCAGTGTTTTATTAATATTATAGTT[A/G]TCTCCTGAGGTGTTTACATTTTAGATAAAATTTAC R 2 1 2 1 101000 r 74 goat snp57041-scaffold906-80684 10 30513085 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416035 Affx-122948364 AX-123286384 10 68811708 TCCCCTTGGGGACCCTTAACACTCAGAACAGAACC[G/T]AAGCTGGGAATGCTAAGGGGTGTGATCAGCTTAAA K 2 1 2 1 101000 f 74 goat snp57040-scaffold906-23765 10 30456252 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420881 Affx-122944624 AX-123291228 10 68935262 ATACAGATTTTTTAATCAGATAGCAAACTGATAGT[A/G]TTATACTACTGAGCTCACAGTATGAGTCAAACTAT R 2 1 2 1 101000 f 74 goat snp7948-scaffold1287-1449408 10 30323357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414503 Affx-122949534 AX-123284852 10 69003226 CCAGCCCATTAAGTTCAGTAGAGTAGATACAATCA[C/T]GAAATGACTTTCCTTTCATGACTTTTCATGAAATG Y 2 1 2 1 101000 f 74 goat snp7947-scaffold1287-1381444 10 30254822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400835 Affx-122959791 AX-123271190 10 69049549 AAAATACTGCTTACCATTTTGATGCCTGTGGAAAA[C/T]GTCCCTGGTTTTACAGGTTTAGGTTTTTCAATTTG Y 2 1 2 1 101000 r 74 goat snp7946-scaffold1287-1335121 10 30206996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447096 Affx-122924487 AX-123317432 10 69080636 CCTAGTACAGTGCTTGGCACATACCAAGAATGTTT[A/G]TTTTGTAAATGAAGAAATGTTTTATAATGATCCAC R 2 1 2 1 202000 r 74 goat snp7945-scaffold1287-1304034 10 30175420 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415821 Affx-122948886 AX-123286170 10 69111548 GATACTTAATGATGAAAGACTTGAAGCATTCACCA[A/C]AAAAACAAGACACAAGAAAAACTGCAGTCATCCGA M 2 1 2 1 201000 f 74 goat snp7944-scaffold1287-1273122 10 30144421 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441779 Affx-122929099 AX-123312116 10 69146789 TCTAATAGTTACTTACTTATGCTAGCAGTATATTC[A/G]TGGTGCTGTGGCATACGTGCTTAGTTATGTCCAAC R 2 1 2 1 101000 r 74 goat snp7943-scaffold1287-1237881 10 30110249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415113 Affx-122949438 AX-123285462 10 69176965 ACTCATAGTACTTGTAGCAGTAGTGTTTCTTACAG[C/T]AAAAGAACAATAGGAACAGCCCAAGTGAATACTGA Y 2 1 2 1 101000 f 74 goat snp7942-scaffold1287-1207705 10 30079667 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769354 Affx-122945077 AX-385256525 10 69214065 CTAAAAAATAAAATCCTCATAAAAGAATTGTAACC[A/G]TTAGAAAGAGGAAGATAGGAGACTATGTTCTCTTT R 2 1 2 1 201000 f 74 goat snp7941-scaffold1287-1170605 10 30042593 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447663 Affx-122923960 AX-123317999 10 69282851 ATGGGAAAAACCCCAACAGTTGCTTATACTTAGCA[C/T]GACATTTATGCCCACAGGTTTTACAGTCAAACTTA Y 2 1 2 1 201000 r 74 goat snp7940-scaffold1287-1101819 10 29973684 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411048 Affx-122951957 AX-123281398 10 69326862 AGGATGGGCCATGGGGGAGCTGATGCTCTTGATCA[C/T]GTTCAAGCTCCAATGAGGGAGAAAGAAATGAGTTT Y 2 1 2 1 101000 r 74 goat snp7939-scaffold1287-1057808 10 29929086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409698 Affx-122953051 AX-123280049 10 69364926 CAATTTGTTTGGTTTGGTTTTTCTGTTGGTTTGGA[A/G]TCCTACTGGACTTGGGACATGGCTTTTCCTATCTC R 2 1 2 1 101000 r 74 goat snp7938-scaffold1287-1019744 10 29890822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408828 Affx-122954024 AX-123279179 10 69429389 TATGTTTTACTCTGGGACGTTTCTTCTTCCTCTCC[A/G]CATTCCCAGGGCCTTTATGCTAACAGCTAGTTGCT R 2 1 2 1 201000 r 74 goat snp7936-scaffold1287-955281 10 29826527 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320800520 Affx-122957253 AX-385287440 10 69458096 ACCAGATGACACAAGAAGGCATTAACTGAAAAGGC[A/G]TATTCACTCAATTTCCACTGTCTGGACTATCGATC R 2 1 2 1 101000 f 74 goat snp7935-scaffold1287-926574 10 29797350 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441040 Affx-122928934 AX-123311377 10 69488617 AAAAGGTAACCAGAGTGCTGGGCAGGGGAGAGACT[A/G]CTTGGGGAGAACTGTGGGAGGGGAGGACAAGGGGC R 2 1 2 1 102000 f 74 goat snp7934-scaffold1287-896053 10 29766850 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382032 Affx-122974950 AX-123252390 10 69539592 GGTCTCCAGAGGAGTATGGAGCCAGCAGGCAAGGC[A/G]CGAACACTGCCCAGATCAAAGTAATTTTCATTCTC R 2 1 2 1 101000 r 74 goat snp7933-scaffold1287-845078 10 29715960 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418879 Affx-122946114 AX-123289227 10 69601550 TGCATCAGGCCACATACAATACTTTGTGGGTGTGT[A/G]CAAGCATGTATCATCTCATGAAACCTTCACAGCAG R 2 1 2 1 201000 r 74 goat snp7932-scaffold1287-783120 10 29654340 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430522 Affx-122937210 AX-123300863 10 69635073 TTTCTTCCTTCTGAGAAGAGTGTGTGTATGTTTTG[C/T]GCAAGTGAGGGGGTATTTCTTCTTTCTCTCTGCAA Y 2 1 2 1 303000 f 74 goat snp7931-scaffold1287-749597 10 29620817 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445233 Affx-122925495 AX-123315570 10 69669252 AACAAAAACCTACCCCTTCTTTTTCACTTGTATTA[C/T]AAATATTTCCTCATGCACTTAGTCATCAAAACCGT Y 2 1 2 1 102000 f 74 goat snp7930-scaffold1287-715418 10 29586495 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406901 Affx-122955627 AX-123277252 10 69700264 GCAAAGGAAATAAAACATGGGACTCAGGGATAAGG[C/T]AATTTTCTTCCATGTGTCTTTCAGATCAAGATGGT Y 2 1 2 1 101000 f 74 goat snp7929-scaffold1287-684406 10 29554940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415982 Affx-122948408 AX-123286331 10 69741102 CCAAGAAAACATACGTTTGGAAACTAGAGTCTCTT[A/G]TTAGTGAAAGGAAAGGCAGGGAGCAAGCCCTGGAG R 2 1 2 1 101000 f 74 goat snp7928-scaffold1287-643568 10 29514092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423962 Affx-122942138 AX-123294308 10 69789454 CCAGGTGCTAATTTGAAGTAGGTACTATGATATTC[A/G]CCCCAGCCTACAGATGAGGATACTGAGGTTCAGGG R 2 1 2 1 101000 f 74 goat snp7927-scaffold1287-595216 10 29465502 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432784 Affx-122935423 AX-123303125 10 69818886 TAAGCCTACCACTAACCCCAGACGAACAGACATAA[C/T]GAATTCCCAGACGCACAGACTTGGCAATGACTGCT Y 2 1 2 1 202000 r 74 goat snp7926-scaffold1287-565784 10 29435513 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412037 Affx-122951727 AX-123282387 10 69917964 TCAATAGGTAGAAAGATTGGATGTTATCTAAACTG[C/T]ACAAAATGCTTTGTAGTGGACCACAGCAATGAACT Y 2 1 2 1 201000 f 74 goat snp7924-scaffold1287-466706 10 29335641 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276564 Affx-1111835406 AX-519550075 10 69936849 TAGTTAATGGAGTTGAATACATCTTCACATTTCAC[A/G]GCTCAGTGAATATGTACTCCATTTTCTTCCTGGCT R 2 1 2 1 101000 r 74 goat Random2.2K-1099 10 69936849 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777423 Affx-122947574 AX-385264544 10 69974335 TACACACTTTCTATGTACACAGGAATCTATTCTTT[A/C]GAAAAAAGGAATGGATCACTAATTAGAATGCTGCA M 2 1 2 1 101000 r 74 goat snp7923-scaffold1287-410335 10 29279082 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448138 Affx-122924288 AX-123318474 10 70095005 GACTGTCTTTGACATCGTATTTATAAAATTAAGAA[C/T]ACAACAGGAAAGGGGGGTGTTGTTTAATGTCTTCC Y 2 1 2 1 101000 f 74 goat snp7920-scaffold1287-289665 10 29160519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431306 Affx-122937084 AX-123301647 10 70170521 GAATATTTGAAAACATCCTTTTTACACTTCTCGTT[A/G]CACTGGCAGGGAATTTCACATAAGAAATGGGAGTA R 2 1 2 1 101000 f 74 goat snp7918-scaffold1287-214149 10 29084323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463107620 Affx-1109817289 AX-514594854 10 70225333 TCTCAGACAAATCAGTGTTACAGCTCTATTTTATT[C/T]AGAAAATAGCCGGAAAATCCATCCTCCAGGCGTGA Y 2 1 2 1 103000 r 74 goat 10_70225333_AF-PAKI 10 70225333 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320778025 Affx-122931538 AX-385265141 10 70243137 TGAGCACAAACACAGTTTAAAGCAACCAAATACCA[C/T]AAATACCACAACTGGGGCCCCAAATACCACAACTG Y 2 1 2 1 101000 r 74 goat snp7917-scaffold1287-141533 10 29010598 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448103 Affx-122924316 AX-123318439 10 70274583 AAAATATATTTCCATTAAAGGCTGTTTAGGTGTTT[A/G]TTTTTCAAAGCAATGCTTCCTTTTTGGAAAAATTT R 2 1 2 1 102000 f 74 goat snp7916-scaffold1287-110087 10 28979162 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798036 Affx-122960040 AX-385284972 10 70328978 ACCTTTAGCTTTGCTGATGTTTAGCAATATCCCAT[C/T]AATCTTCTCCCTCATAACCTCTTGCCTGGCACCTT Y 2 1 2 1 101000 r 74 goat snp7915-scaffold1287-55692 10 28924429 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429505 Affx-122937859 AX-123299847 10 70371573 CTGGAAAGTGGGAAGGGACAATCAAGTGGAGAGTA[C/T]ATTTCACAAACAATAGTTTTCACTTGGTGGAGGGA Y 2 1 2 1 101000 f 74 goat snp7914-scaffold1287-13097 10 28881929 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765928 Affx-122969313 AX-385253355 10 70385576 CATCTATGAATCCAAGAGTGACAAGCACTGACCCA[A/G]TGAATTTTTCTGAAGCCTATGCTATAGGGCAGGCA R 2 1 2 1 101000 f 74 goat snp1516-scaffold104-4109500 10 28861220 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391825 Affx-122967015 AX-123262182 10 70414789 CAGGTGGGGTTGGGACAGGGAGTTGGGTAAGGTGG[A/C]TGCCTTGGAAAAATTATTCTTTAGTCTAACCACAG M 2 1 2 1 101000 r 74 goat snp1515-scaffold104-4080287 10 28831453 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791245 Affx-122966190 AX-385278239 10 70511808 CTAAAAGAAGCAATAATATGGAAAGTTTGATTTTC[A/G]TGACTCATTCAGCCCAGTTCCTCACTCATAGACAA R 2 1 2 1 101000 r 74 goat snp1513-scaffold104-3983268 10 28734750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776821 Affx-122960566 AX-385263945 10 70550164 ATGAATAAAAAAGGCCTTCTTGCAATTGCCAAGAT[A/G]CAGATTTATCTTATGACTATTGCTAGGACCTTTAT R 2 1 2 1 201000 r 74 goat snp1512-scaffold104-3944912 10 28696239 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784935 Affx-122948264 AX-385271982 10 70580244 AAGAATACCTTTCATTTCTAGAACTCTGCCTGTGA[C/T]ACATTTCAATCAGAGAGATTGTACAAGAAGTGAGT Y 2 1 2 1 101000 f 74 goat snp1511-scaffold104-3914832 10 28666028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276566 Affx-1111835407 AX-519550077 10 70599893 GCCCGGACTATGTAAGTCAGCATTTATGCGTTGGA[A/G]CCAGTGCTGGTTAAAACTCTCTACATGATGCCAAT R 2 1 2 1 101000 r 74 goat Random2.2K-1100 10 70599893 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402933 Affx-122958184 AX-123273286 10 70623308 CTGTGAGAAAAATAAAATGGTGTTTGATTTATACC[A/G]CTCAATTTGTTGGTTAGTCAGTCATAAATACATGG R 2 1 2 1 101000 r 74 goat snp1510-scaffold104-3871768 10 28622786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433049 Affx-122935758 AX-123303390 10 70663010 ACCCTGTAGAGGACAGAGTTTGGTGAATCCGCTCA[G/T]ATTGGAAGCAAGGACAATGCAGATCCTGTTAGCTC K 2 1 2 1 101000 r 74 goat snp1509-scaffold104-3832066 10 28587734 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788817 Affx-122960474 AX-385275832 10 70747853 CACTTCTTCCTCATTCATTAGAAAACTTCATGTTA[C/T]GATTAAAATAGTTACCTTCTCATACTACCAAAGAA Y 2 1 2 1 101000 f 74 goat snp1507-scaffold104-3747223 10 28502719 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408893 Affx-122953975 AX-123279244 10 70780242 TAATATAATCATTTGTTTTGATTTGTTCTTTTTCC[A/G]TTGAAATTGCATGTGCCTCTACTGGTGGCCAGTTT R 2 1 2 1 101000 r 74 goat snp1506-scaffold104-3714834 10 28470294 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390944 Affx-122967066 AX-123261301 10 70812391 TACCACAGCAGTGAGAAGTCTAATGTGGTTAATGC[A/G]TGCAGTTCTCAGAACTAGGGTAAGTGTGATGTTTA R 2 1 2 1 101000 f 74 goat snp1505-scaffold104-3682685 10 28437747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448991 Affx-122923108 AX-123319326 10 70848072 GCAGGCTGGGTCTAATGAAAGGCCTGGATTCAGTT[A/G]CAATAACCTCCTATTTGGACGTTTGAGAAGGAAAA R 2 1 2 1 101000 r 74 goat snp1504-scaffold104-3647004 10 28403103 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776767 Affx-122963951 AX-385263891 10 70901779 GCCTGACCTTTACCTACACTGTAGTAGTAGGACTC[A/G]CCAATTCTCTTAATTATAGAATCTAATGGGTAACT R 2 1 2 1 101000 r 74 goat snp1503-scaffold104-3593297 10 28321665 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441994 Affx-122928431 AX-123312331 10 70944518 GATAAATCTATGAGACTAATAAAGCCTCTAAAACA[C/T]GAGTAAGAAGTGAAGACTTACCAGTGGCAGGTAAA Y 2 1 2 1 201000 f 74 goat snp1502-scaffold104-3550558 10 28278268 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781264 Affx-122961412 AX-385268349 10 71001019 TCCAACGCCTGTTCCACTATATCACATGGCTGTGT[C/T]CATTTTCCACAATGAACACTTGCTCACTCTCTCTG Y 2 1 2 1 101000 f 74 goat snp1501-scaffold104-3494057 10 28175847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403737 Affx-122958018 AX-123274089 10 71051099 TGGTTAATGTTGGAGATCCTGAGCTCTCACATGTG[C/T]CCTATATGTGTGACTGAGGGATTGTTCTCTACACA Y 2 1 2 1 101000 r 74 goat snp1500-scaffold104-3443977 10 28125331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787908 Affx-122972134 AX-385274930 10 71096001 CTTCTACAAGGCTGCCTGGTGGATATTTGAAACTC[A/G]TATCTTATTAAATCTTCCCGATATACATTTTGCCA R 2 1 2 1 101000 f 74 goat snp1499-scaffold104-3399075 10 28079084 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426090 Affx-122941074 AX-123296436 10 71131160 AGTTAAATAAGTAGGATGAAAATATACAGCCTTGA[C/T]GTACTCCTTTTCCTATGCATGTATAAAAGTACAGA Y 2 1 2 1 103000 r 74 goat snp1498-scaffold104-3363916 10 28043474 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801216 Affx-122958992 AX-385288129 10 71168176 ATCATAGGAGGTTGACATAGAATTTCTTTCAGACC[A/G]TCTCAACAAGCACCTTTCAGTGTCATGTTGAAAGA R 2 1 2 1 101000 r 74 goat snp1497-scaffold104-3326900 10 28005671 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411164 Affx-122951870 AX-123281514 10 71200994 CAGAGTCGGACACGACTGAAGCGACTTAGCAGCAG[C/T]AGCAGAACTGTAAGTAATGCACATAAAAGGATTTG Y 2 1 2 1 103000 r 74 goat snp1496-scaffold104-3294082 10 27971700 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393132 Affx-122965556 AX-123263489 10 71238459 CTTTCTATGCCCCACCCTTCACCATCTTTTTCCCT[A/G]CTAGGAGAGTAAATTAAGTCTTTACCCAAATGGAG R 2 1 2 1 201000 r 74 goat snp1495-scaffold104-3256617 10 27933319 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276568 Affx-1111835408 AX-519550079 10 71258523 TTCTGTTTTATTTTCAAAATGTCTTTGTGTCTGAT[A/T]GAGGATAGTCAACATGTATGTTAGGAATTTGATGT W 4 1 2 1 101000 r 74 goat Random2.2K-1101 10 71258523 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386970 Affx-122969967 AX-123257328 10 71278975 GCATCTCATTGTAATCTGACACTTAGAATGCTCTG[C/T]ACATCAGAATAAATGGATGAACAAGTTAACCCCCA Y 2 1 2 1 101000 f 74 goat snp1494-scaffold104-3216101 10 27892219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414557 Affx-122949390 AX-123284906 10 71308946 AAAGCAAACACACCTAGTAATTCCTAGTAATGCCA[C/T]ATTAGGAAACAGAATATTGCCAGAGCCTATTCAGG Y 2 1 2 1 101000 f 74 goat snp1493-scaffold104-3186130 10 27862169 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801562 Affx-122971468 AX-385288471 10 71350654 GTTTTGTGAAGCATAGTTTATCCTCTCCATTGTAC[C/T]TTAAATGTTTATTCTCTGTTGAATATTTAGGTTTT Y 2 1 2 1 101000 f 74 goat snp1492-scaffold104-3144422 10 27820374 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412286 Affx-122950877 AX-123282635 10 71392641 CAAAGTCTATAAAATAAAATAATGAGGGCCATTGA[A/G]TAGGATAGATACAAACATACTATATAGCCAAATAC R 2 1 2 1 101000 r 74 goat snp1491-scaffold104-3102435 10 27778375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777856 Affx-122933106 AX-385264973 10 71424097 GTGTCAGCTGGAAGCTCCATTTGTTGACCCATTAT[A/C]GCCTCAGGCTGTTCCTTTTAGGTACCAAAAATCAC M 2 1 2 1 201000 f 74 goat snp1490-scaffold104-3070979 10 27746774 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426107 Affx-122940637 AX-123296453 10 71466510 TTTAAACATGAGAAGTATTTAACATATTTATTTAT[C/T]CTCATTTTAGGTGAGTTGTGTGGTGGGTGATTCTT Y 2 1 2 1 103000 r 74 goat snp1489-scaffold104-3028566 10 27704061 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387193 Affx-122970606 AX-123257551 10 71519931 AGTAAGAGTTGTTAAGATGGAGAATTCTTGTGAAG[C/T]GAGAATTCCAGACAATTTTATGCAATTTTCTTTTT Y 2 1 2 1 101000 f 74 goat snp1488-scaffold104-2975145 10 27650335 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439081 Affx-122931132 AX-123309418 10 71574881 GGAATTTCCTTTCTGATCACCTTACAATGACAGAG[A/G]AAGCTTAAATGGAAAAAAGTAGTAATAAAAAATAA R 2 1 2 1 101000 f 74 goat snp1487-scaffold104-2920195 10 27595654 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794347 Affx-122953270 AX-385281311 10 71630216 GTGCTTAGAGCAATAAACATCTAAATCAGGGGGAT[A/G]CCCTTCGTAGAGGTCAAGTTGTAGTCAATCTTTAT R 2 1 2 1 101000 f 74 goat snp1486-scaffold104-2864860 10 27540525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450828 Affx-122921790 AX-123321162 10 71694142 TCTCTTGGAAATAAACATCCCAGATTATGACGTCT[A/G]TGAATATAGGTTTCCTTTTCTACTCTTTCCCTTCC R 2 1 2 1 101000 f 74 goat snp1485-scaffold104-2800934 10 27476993 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447280 Affx-122924933 AX-123317616 10 71728593 AAAAAAGGCAACCAGATTCCCCACACACATGTTCT[A/G]TTCAGGTTTCTGTCTCTTACACCATGATGCCTCCC R 2 1 2 1 201000 r 74 goat snp1484-scaffold104-2766483 10 27442582 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417738 Affx-122947426 AX-123288086 10 71757398 CCTGGATTTAGAGCTAGGAAGTTAGATATTTAAAT[A/G]TCCTTTCATCTCTATGGCCCCTAATCCTTGGAAGT R 2 1 2 1 101000 r 74 goat snp1483-scaffold104-2737678 10 27414014 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797655 Affx-122945347 AX-385284594 10 71828417 AAGCGCACTGAGTGGTTCATATTTTTGAAAATCTG[G/T]ACAGTATTTGGGAACAGTTTCTTTTACTGGAAACT K 2 1 2 1 101000 f 74 goat snp1482-scaffold104-2666659 10 27343087 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772755 Affx-122967535 AX-385259900 10 71882233 CATTTTTCTGCTCTGCCAGTTTTCATCTTGTCAGG[G/T]TCAAGTTCACAAGATGACTACAATCAGCCAATAAG K 2 1 2 1 101000 f 74 goat snp1481-scaffold104-2612843 10 27289223 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377952 Affx-122977206 AX-123248311 10 71948638 CTAAACTTACCCTCCCCCACCCTGCCCTGCAATTA[C/T]AAAGTCGAACTGAAGTTATTTCTTAGGAACTAAGA Y 2 1 2 1 201000 r 74 goat snp1479-scaffold104-2546438 10 27241358 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452321 Affx-122920666 AX-123322654 10 71988675 GGATCTTCCATCGCAATACACATGCTCTCTAGTTG[C/T]GGTGTGCAGGCATAGTTTCTTGGTGGCATGTGTGG Y 2 1 2 1 201000 r 74 goat snp1478-scaffold104-2506401 10 27200676 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796117 Affx-122952207 AX-385283068 10 72017772 AGTAACAGTTGCCCTAAGAGACAAATATATCTTGC[A/C]TATAAAAGGAATAGCCCACGGACTTATGAAATAAT M 2 1 2 1 101000 f 74 goat snp1477-scaffold104-2477304 10 27171284 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417494 Affx-122947162 AX-123287842 10 72050053 TTACTATGGGTCAGATATTGTTTGAAATGTTTATT[A/G]CCTCATTTAGTCTGCTCTTAAAACATACCAGTGTT R 2 1 2 1 101000 r 74 goat snp1476-scaffold104-2445023 10 27138995 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390925 Affx-122967082 AX-123261282 10 72086749 TATGGTCCATTTCCTACAACTAAAGTTTGTCCTGC[A/G]CTAATCTTGTTGGACAGGACTGATAATGGGATTCT R 2 1 2 1 101000 f 74 goat snp1475-scaffold104-2408327 10 27103606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375813 Affx-122978558 AX-123246172 10 72162011 TTTAGCGTTGTGATCACTGGTGGCAGAGGAGGGAG[C/T]AGAGGTGGGGAAGGAGCCAAAATCATAAACAACCC Y 2 1 2 1 202000 f 74 goat snp1474-scaffold104-2333065 10 27027972 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434895 Affx-122934335 AX-123305235 10 72203154 GACATCAATAGGCAAAAGCACAGCTTGGCTACACA[C/T]CTCTGGAAGGTGTTCAGTCTGTTCATCTTTGCAGC Y 2 1 2 1 102000 f 74 goat snp1473-scaffold104-2291922 10 26987675 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802080 Affx-122920729 AX-385288984 10 72265524 TTAAATGAAAAGAGGGGTCGGGACTGTCAAATATA[C/T]GAAAGCAATCAAATAGGATGAGGACCAAAAACCAT Y 2 1 2 1 101000 r 74 goat snp1472-scaffold104-2229552 10 26925161 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405802 Affx-122955901 AX-123276154 10 72337822 CTGTACTTGTAAGTGCTTCCCAAACATGACAGAGA[C/T]AACACTGCAGTCAAAGTTTTTCACTTATGCCCAGC Y 2 1 2 1 102000 f 74 goat snp1471-scaffold104-2157254 10 26852525 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787769 Affx-122944875 AX-385274792 10 72393355 ACTTTTCATCAACTTCCTTTGAAAACTCCTAAAAG[C/T]GAACAGTTTTAAAATTGAGAAACATTTAAGGACTT Y 2 1 2 1 101000 r 74 goat snp1470-scaffold104-2101721 10 26796546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398249 Affx-122962192 AX-123268604 10 72427056 CATATTCTGTATTTTGGCACATTTGAAGGGTCTCT[A/G]TTCATACCTGTCTATTGAAATCTGAAAGAAGAGAG R 2 1 2 1 101000 f 74 goat snp1469-scaffold104-2068020 10 26763148 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426446 Affx-122940809 AX-123296792 10 72471193 CCCCAGATGTATGGCTGTGAGGTAGATTCCCTGGA[A/C]CCCTACCTGTGTAAAATTCTCACACCTTTCAGGCA M 2 1 2 1 101000 r 74 goat snp1468-scaffold104-2023883 10 26719202 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381366 Affx-122974402 AX-123251724 10 72556336 CCATAATTATTTTAAAGTCAATATCCTTTCTCTGT[A/C]ATTTTACCATCCTCCATTCTTCTAATAAGCACAGC M 2 1 2 1 101000 r 74 goat snp1466-scaffold104-1938740 10 26633748 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388575 Affx-122969168 AX-123258933 10 72587676 AACCTGCTGCATGGTAGTGTGCTTATTGTACAGTT[A/G]CAATCTTTTTACACTCTCTTTCTTAAAATTCATTA R 2 1 2 1 101000 f 74 goat snp1465-scaffold104-1907400 10 26602521 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444993 Affx-122926652 AX-123315330 10 72617227 AGGCGTACTGTTACGTTATGTTCCATGTGAACAAC[A/G]GAGATTAAGAGAAAAATATGTTGCCCGTAAATTAC R 2 1 2 1 101000 f 74 goat snp1464-scaffold104-1877849 10 26573292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782433 Affx-122933805 AX-385269509 10 72664801 TTGGGCTTGATGGCGTCCTTCATAAGGACCGTCAA[C/T]GCTCCACTCACTCCCTACAAAACAAAGGCACGAAC Y 2 1 2 1 101000 r 74 goat snp1463-scaffold104-1830275 10 26525434 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769889 Affx-122965254 AX-385257058 10 72704717 TCACCACAGAGGATAGATTTAAATTGTTTCTGATA[C/T]GTTTAAATTTTAAATCCTAGATAGTCAAGAATAAC Y 2 1 2 1 101000 f 74 goat snp1462-scaffold104-1790359 10 26485760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421796 Affx-122944332 AX-123292143 10 72788362 TATGCTTAACTTTTTGACGAACTGACAGTTTTCTT[A/C]AGTGGTTGCAACACTTTACATTCCCATCAGGAATG M 2 1 2 1 303000 f 74 goat snp1461-scaffold104-1706714 10 26401861 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271862 Affx-1111832897 AX-519545645 10 72793257 TACCAACTGTCACAAGTTGATTATTTATATGAACT[A/G]TATGATGGACATTTAAAAACAGAGACTACTAACAA R 2 1 2 1 101000 f 74 goat 10_72793257_AF-PAKI 10 72793257 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38376390 Affx-122978100 AX-123246749 10 72819173 ACAGCCCCGTAATTCCCAGCCCCTCCCCTGGCTCT[C/T]GTACTTGGCAGCTCTATGACCTGGGCCACAGTCAT Y 2 1 2 1 201000 r 74 goat snp1460-scaffold104-1675903 10 26371280 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408726 Affx-122953417 AX-123279077 10 72886337 AAACTCACTTGATTGCTGGCTGGGTCAATTTTTGA[C/T]AGTCTCCTAGCTCTGCAAAATGAGTTTACTAGGGC Y 2 1 2 1 101000 f 74 goat snp1458-scaffold104-1608739 10 26302498 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436943 Affx-122933182 AX-123307281 10 72924324 GGTGCCAACCCTGCCCACCTCGTGGGGACGCCTTC[C/T]GGCACTTTCTGCCCTTTTACAAGTAACATTATGCT Y 2 1 2 1 101000 r 74 goat snp1457-scaffold104-1570752 10 26263769 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425141 Affx-122941205 AX-123295487 10 72981840 TATGCAGGAAGTCTGGGAGGCTCTGACCCGGTTTT[A/G]GGGAAATGTCCTGGGAGCCGCTGACTGAGAAGAAA R 2 1 2 1 101000 r 74 goat snp1456-scaffold104-1513236 10 26217678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389669 Affx-122968715 AX-123260027 10 73035011 CTGTGTGCAAAGCTGAACCTCTACCCAGACATGAA[C/T]GTGGATAAGGGGGAGCACAGAATTGGATTCAACAT Y 2 1 2 1 101000 f 74 goat snp1455-scaffold104-1460065 10 26164312 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603095 Affx-1002479333 AX-413837293 10 73062014 CGGTCCTCTCTGTCCCGCGGACCCCACGCGGAGCC[A/C]GGGCGGCTCTGGCCGCGGCCGCACACCGCGCCACG M 2 1 2 1 303000 r 74 goat UniBern-var21 10 73062014 C A 3 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region FMN1/GREM1 Wattle-variant SNP associated with wattles multi-breed 38404361 Affx-122956816 AX-123274713 10 73088672 GTACAGGGCTAAAGAAAAAAAAAAAAGACTTTGTG[A/G]TGAACTGGGCTCAGATCATCCAGAATATTTATGAA R 2 1 2 1 103000 r 74 goat snp1454-scaffold104-1406404 10 26111616 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448186 Affx-122924247 AX-123318522 10 73139915 TTCCTCTGAAAGTTGGAAACAACTTGGCTCACTCC[A/G]TTCAGAGGGTCTGAGATATGGACAAGAAACAATTC R 2 1 2 1 101000 r 74 goat snp1453-scaffold104-1355161 10 26060695 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385038 Affx-122971850 AX-123255396 10 73188585 ATCAGATGACCTGGGATATACTGGGCTGCACCTAA[C/T]AGAAGTTCTTGACTTAAATTTTAATTTGTGACCTT Y 2 1 2 1 202000 r 74 goat snp1452-scaffold104-1306491 10 26012019 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378465 Affx-122976680 AX-123248824 10 73230051 GTGAAAAGCCCTTCAACGGGGTCCTCTCTTCCTAG[A/C]TGATGTTGTCACAAAAGCTGCTCCAACATTTATTT M 2 1 2 1 201000 r 74 goat snp1451-scaffold104-1265025 10 25972321 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393062 Affx-122965615 AX-123263419 10 73263361 GTTTGTAGATGTGGTGTATATAGAATATTCCACAA[G/T]AGGAGCAGTGACATGACTATTTAAAATTTTTTAAT K 2 1 2 1 201000 r 74 goat snp1450-scaffold104-1231715 10 25938751 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389168 Affx-122969094 AX-123259526 10 73299248 GTTCCTGAGAGCTTTCTGCTGTTCAAAATATCCAT[A/G]CACGTGGTTGTTGATGTAAATTGTTTTATTAAATT R 2 1 2 1 101000 f 74 goat snp1449-scaffold104-1195828 10 25902927 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418513 Affx-122946426 AX-123288861 10 73347268 CGCTCCACGGCATGAGCTCAGAGGTGCTGCAAACC[A/G]TGGCTCTCAAATCTCCCTTCTACACCCCTGTCCCA R 2 1 2 1 101000 r 74 goat snp1448-scaffold104-1147808 10 25854668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276419 Affx-1111835409 AX-519549945 10 73348641 AAGTATGACAGCAACAAGCGCACGGTAAGTGATTC[A/G]CCCAAAGTCCTCCAGGTGGCCTACCTCAGTCCTGT R 2 1 2 1 101000 f 74 goat Random2.2K-1102 10 73348641 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383528 Affx-122972629 AX-123253886 10 73412812 GATGTAAATTGTTGCTTTCAAAACTATTTTTTCTT[A/G]AGAACTTTATCCTTTTCTCCAGCAAGATGTACAGA R 2 1 2 1 102000 r 74 goat snp1447-scaffold104-1082264 10 25789180 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788324 Affx-122973973 AX-385275342 10 73455328 ATGGATGCAGAATCCCTTTAAGAACATCTATAGGG[C/T]GACTCACTAGTGAATGCAATTGCAGAGCAGAGAGA Y 2 1 2 1 101000 f 74 goat snp1446-scaffold104-1039748 10 25746660 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381508 Affx-122974864 AX-123251866 10 73490717 CTACCCAAATATCATGGGAAATAGATATTCTCTTA[C/T]GTTTTCTTCTAGAATTTCATCATTTTGTTTTTTTT Y 2 1 2 1 103000 f 74 goat snp1445-scaffold104-1004359 10 25711639 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276571 Affx-1111835410 AX-519550082 10 73534710 TTTTAAAAAAATTACCGCTTGTCTTCTGAGAGGCA[A/G]TGAATGAAAATGAGGGCAACAAACATAAAAGCAAC R 2 1 2 1 101000 r 74 goat Random2.2K-1103 10 73534710 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796769 Affx-122972930 AX-385283712 10 73537125 AAAATCCTCCATGCAATCACTCTCATGGGATCCTA[C/T]AGTACCTTAAAATTACAAAGCCCTGTCACCAGACT Y 2 1 2 1 101000 f 74 goat snp1444-scaffold104-957951 10 25665145 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444962 Affx-122926676 AX-123315299 10 73595776 AGAGAGATTAAGGTGCCTTCCCTTTGAGGATTTTC[A/G]TTTCTGTTGACATAATTGGGGCCTAATACAATGTC R 2 1 2 1 102000 r 74 goat snp1443-scaffold104-899300 10 25605890 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448177 Affx-122924255 AX-123318513 10 73639761 TGCTATGGTACACTGTAAATTCGCCAGAGAAGTCT[A/C]GAGTTGAAGAAATTTTGGAGAACAGATACTTGAAT M 2 1 2 1 101000 f 74 goat snp1442-scaffold104-855315 10 25562137 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792721 Affx-122925041 AX-385279701 10 73714791 GAAGACATATGAGTTCCAATCAAACAGAATGAAAA[C/T]ATCACAGAAAACCTGGGATATTCAGTAGAAAGCCA Y 2 1 2 1 101000 r 74 goat snp1441-scaffold104-780285 10 25486826 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784159 Affx-122961690 AX-385271211 10 73753963 TCTGTGTAGTAACTGATACAATACTGCATAGTGAC[A/G]AAGTGTGACTTCTAATGCAGCTTCCAATTTACTCT R 2 1 2 1 101000 f 74 goat snp1440-scaffold104-741113 10 25447457 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385737 Affx-122971087 AX-123256095 10 73793965 AATGGCAGCCCACTGGAAAAATTAAAGTTTTATTT[A/G]CTGTCATAGAAAACCATCAGAATGACATGCAATAA R 2 1 2 1 101000 r 74 goat snp1439-scaffold104-701111 10 25406970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410214 Affx-122952565 AX-123280564 10 73843031 CAAAAGCATGGTTACATTTATTTATTGTTTGCCAC[A/G]AACTGTTGCTAATGAGTTATAAAATTATGTGTTGA R 2 1 2 1 201000 r 74 goat snp1438-scaffold104-652045 10 25357894 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407292 Affx-122955327 AX-123277643 10 73885454 TGCCTTATTTCACTCACTGTTGACGTGTCACTGTA[C/T]TGTTTTTAGAACACTACTAAGCACACAGTTATGAG Y 2 1 2 1 101000 f 74 goat snp1437-scaffold104-609622 10 25315453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429662 Affx-122937662 AX-123300003 10 73917305 TGATAAGAAGTGGGGATGTCAGATCCAGGGATACA[C/T]TCGCCCCCTGCAACCTACTCATGAATGAGCATCAA Y 2 1 2 1 101000 f 74 goat snp1436-scaffold104-577771 10 25283641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411996 Affx-122951760 AX-123282346 10 73955747 CTGTCTGCTTGACAGTTTGCTAGAGGGCTTGAGCT[A/G]TCTGTTTAAGGATCTCTATCTGCTTGTGAATTGTT R 2 1 2 1 101000 r 74 goat snp1435-scaffold104-539329 10 25246519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440252 Affx-122930660 AX-123310589 10 73996676 GACAGAGTTTGCTTTGGAGACCTGTCCTTCAGTGA[C/T]GACAGAGTTTCCTCTGTCAAGTTCAGTGGGGCTGT Y 2 1 2 1 101000 f 74 goat snp1434-scaffold104-498400 10 25205866 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794188 Affx-122967723 AX-385281154 10 74041415 CCAGACACTTGCTTATTATGTATAAAGACCTGTAC[A/G]GTCTTATGGGTCAGTGAGAGGTTAGAACCCACACC R 2 1 2 1 102000 r 74 goat snp1433-scaffold104-453661 10 25164538 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452356 Affx-122920638 AX-123322689 10 74080120 CTCTATCCGGCTCTGCTCTTGTCATGTATGTCTGA[C/T]CTTCGATCCCGCATGTCTGGTCCTGCCTTTTTCTA Y 2 1 2 1 101000 f 74 goat snp1432-scaffold104-414956 10 25125786 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424535 Affx-122941720 AX-123294881 10 74110193 GAGAAAACGCCATTATTACTTTAGGGTTAGAAGCC[A/G]TTCCCTTATTTTCCATGTCTCTTCAGCACCATTTT R 2 1 2 1 101000 f 74 goat snp1431-scaffold104-384883 10 25095476 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414613 Affx-122949348 AX-123284962 10 74151144 TACAATAGGAGGGACAGAGGCGATCTCCTATAGTG[C/T]GGGAAGAAAACATTGTGTTAGGACCTCTGCTTGTG Y 2 1 2 1 101000 r 74 goat snp1430-scaffold104-343932 10 25054736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410914 Affx-122952060 AX-123281264 10 74196033 CTCTGGGCTTAGATATGGACCCAAAGCTTTAAATA[G/T]CATTCATAAACTGGTTATCACAGTGCTTGGCACTA K 2 1 2 1 101000 f 74 goat snp1429-scaffold104-299043 10 25009408 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447961 Affx-122923769 AX-123318297 10 74272135 GTGTTTTCTAAAAAAGAAAAACCTAAAAAGCCAAC[A/G]CATTTTCTGTCTGGTGTGCCTCTTGGAACACTGCA R 2 1 2 1 201000 r 74 goat snp1427-scaffold104-222941 10 24933072 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276573 Affx-1111835411 AX-519550084 10 74282698 ATCTTCTTTTACTTTTGGGCTAAGTGCTCCATGAA[A/G]TTTTCTGGAGCTTAGGATGGGTTCTATAGAGAGCA R 2 1 2 1 101000 r 74 goat Random2.2K-1105 10 74282698 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409607 Affx-122953552 AX-123279958 10 74306782 AGGACTCCATTAACATGTTCCAACAGTGATGTCAT[G/T]GCTCAAAACGCCCACACATCCCCTTTTCTGGAATC K 2 1 2 1 101000 f 74 goat snp1426-scaffold104-188294 10 24898686 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774906 Affx-122927632 AX-385262040 10 74386940 ATGAAGAGAAAAGTTAGTATTAATATGGGATTCCA[C/T]ACCTGGCTCCTCCCACTTGTTAAAATCTTATCACC Y 2 1 2 1 101000 r 74 goat snp1424-scaffold104-108136 10 24818801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795113 Affx-122922985 AX-385282071 10 74425773 AATACCTTTTGCTAGTTTCCATTCTCCTTGTCTTC[A/G]TTTACTTTTAACAAGGGAGATATAGAAAGAAAGGT R 2 1 2 1 102000 f 74 goat snp1423-scaffold104-69303 10 24779886 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784036 Affx-122962230 AX-385271089 10 74455641 GAACAGTGTTTGCAAAAACATCAGTGTAGAGAAAC[A/G]TGGCTTTCATGTGGCTTTGCATGACTACTGTGCAA R 2 1 2 1 101000 r 74 goat snp1422-scaffold104-39435 10 24749850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447094 Affx-122924488 AX-123317430 10 74490734 GTAGAGCTGAGTAAGAAAAGAACAAGAAATAAATC[A/G]GAGGGACAACAGGTCCAGAACCAACCTCTACTAGG R 2 1 2 1 201000 r 74 goat snp1421-scaffold104-4342 10 24714041 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387826 Affx-122969670 AX-123258184 10 74509194 AAGTACTTAAAGTAGTGCCTGGCACATAGTAAATA[C/T]GAAAGAAAATTTAACCATTACTATTTTCATCATGT Y 2 1 2 1 303000 r 74 goat snp2134-scaffold1065-14019 10 24695861 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387349 Affx-122970484 AX-123257707 10 74567443 TCTAGTTTATCCTACTCCCCATTTTTCCAGTTGTG[C/T]ACCTGAAATCCCAGTATGACTTACCACTGAGTACA Y 2 1 2 1 201000 r 74 goat snp2135-scaffold1065-72268 10 24636905 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446589 Affx-122924819 AX-123316925 10 74641057 ATGCCAGAATGGATGTGTGTAATCAAGGGCAGAGA[C/T]AGGGACAGAAATGAGATTAAGGTTATGTTCTGTAG Y 2 1 2 1 101000 f 74 goat snp2137-scaffold1065-145882 10 24563876 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450800 Affx-122921813 AX-123321134 10 74678653 AGACTTTCAAAAACTAAGAGTATTATCTGCTATTG[C/T]AATACCTACTAGGGCTTCCCTGGTGACTCAGTGGT Y 2 1 2 1 201000 f 74 goat snp2138-scaffold1065-183478 10 24526063 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413223 Affx-122950251 AX-123283572 10 74715351 ACCATATTATTAAACTGTAAAATGTCAAAGGTGCT[A/G]CTAGAACTTGCTTATGGGGCAAAGATTATTCAGAG R 2 1 2 1 201000 f 74 goat snp2139-scaffold1065-220176 10 24489164 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380514 Affx-122975692 AX-123250872 10 74751735 TTGTTAAAATATCAATATTAGAATTACTTTTACAT[A/G]CATTATATGGTTCTTAGATTGGATTCATTAGTCAT R 2 1 2 1 101000 r 74 goat snp2140-scaffold1065-256560 10 24452380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441423 Affx-122928824 AX-123311760 10 74803720 ATTAATACCATGGTTATATTCTAGCAGAAAGTTGG[A/G]GAGAAAAGTCAGGCATATCAAAACACCTTTTCCAA R 2 1 2 1 101000 f 74 goat snp2141-scaffold1065-308545 10 24400587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383070 Affx-122973745 AX-123253428 10 74872314 GTCCTGGTTTTCAGCTTTTATTCAGTGGTCCCAAA[G/T]AATTGAATCTTTAAGCCTTAACAATAAAAAAAATT K 2 1 2 1 101000 f 74 goat snp2143-scaffold1065-377139 10 24331648 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762800 Affx-986697329 AX-385250840 10 74889894 ATGACATGAGTTGACAAAGTGGAGAGGGCCTTAGA[C/T]GAGCTACCTGAAGAGTGTTTCCGAACAGTGATGAG Y 2 1 2 1 600010 f 74 goat 10_74889894 10 74889894 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 320803162 Affx-986696201 AX-385290025 10 74889937 CTGAAGAGTGTTTCCGAACAGTGATGAGGATAAAA[A/G]CGTAGGAGACGATCAGTATGAAGAATGATCCCAGG R 2 1 2 1 600010 f 74 goat 10_74889937 10 74889937 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320803735 Affx-986696202 AX-385290494 10 74889948 TTCCGAACAGTGATGAGGATAAAAACGTAGGAGAC[A/G]ATCAGTATGAAGAATGATCCCAGGGATATGAATCC R 2 1 2 1 600010 r 74 goat 10_74889948 10 74889948 Ancestral_priority_1043 ancestry 0.61 recommended IMAGE 10K 10K ancestral 38446162 Affx-122925749 AX-123316498 10 74906896 TCTCTTGCATTTCCCAGAGGCTGGGCTAATACTTG[C/T]AGTCTGCAACACTTACCAGAGCCAAAACTCACATT Y 2 1 2 1 101000 r 74 goat snp2144-scaffold1065-411721 10 24296772 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782420 Affx-122961026 AX-385269496 10 74961959 GATTCAGAACCATGTTGCCACTTAAATATTTCATA[A/G]TTGAAGAAGGTGAGATCATTCAGAAGTTTGGGATA R 2 1 2 1 201000 r 74 goat snp2145-scaffold1065-466784 10 24241465 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386963 Affx-122969972 AX-123257321 10 74990851 AAACTAAGTCAATATTAAAAAGACAGCCAGTTTCA[C/T]GGTACAAAAATAAGGGGCATTTACTGCATGCATAA Y 2 1 2 1 101000 r 74 goat snp2146-scaffold1065-495676 10 24212570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436433 Affx-122933005 AX-123306771 10 75061611 GAGAGAGTAGCTAGACTGTAAGATAGACGGAGGAC[A/G]AGAACCAGAGCCTGTACACACACAGTTTCCTTTAG R 2 1 2 1 101000 f 74 goat snp2147-scaffold1065-566436 10 24139789 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434459 Affx-122934644 AX-123304800 10 75131178 AAATTCCTGTCCCCGTAGGCAGTACTAATTTGATT[A/C]GAATACAGAGAACATCCCATGAGTATGTCAATGTA M 2 1 2 1 101000 r 74 goat snp2149-scaffold1065-636003 10 24069853 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444440 Affx-122926557 AX-123314777 10 75166123 GCTGTTAAATAAGAGATCAACACAGTCAGCATTAG[C/T]AAAGTTGGGGTCATGTTGGAGTTTCTAAAGATTCA Y 2 1 2 1 201000 f 74 goat snp2150-scaffold1065-670948 10 24035066 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781823 Affx-122946544 AX-385268905 10 75195057 GCCGGGTTGGTGAGAAGTGGTTAGAGAATGGAATC[A/G]TTGTGAAGGTAGAAATAAAAGAATCTCCTGATGTG R 2 1 2 1 101000 r 74 goat snp2151-scaffold1065-699882 10 24006079 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405588 Affx-122955936 AX-123275940 10 75226270 CCCACCCCCTCACCACCCCTAGTTCCACGAGGTGG[A/G]ATGTATAAGCTGGGATTCTGATGAGGATTTGAAAT R 2 1 2 1 101000 r 74 goat snp2152-scaffold1065-731095 10 23974784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425155 Affx-122941069 AX-123295501 10 75265396 AGATGTATTTTAAGTAGAAAATGAACATTTTGCCT[A/G]TTGTAACTCATCTCACCTAGGCAACCCATTCCATG R 2 1 2 1 101000 r 74 goat snp2153-scaffold1065-770221 10 23935888 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394243 Affx-122964875 AX-123264598 10 75311400 TCATCATTGGCCCTGCTTACAGCTTCTGCCTCCTG[C/T]ACCTTCTCCATTACTGCTCTGCGTTAACATTCTTA Y 2 1 2 1 101000 r 74 goat snp2154-scaffold1065-816225 10 23890049 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271864 Affx-1111832898 AX-519545647 10 75319815 GACTACCAACTTTATCTTGCTTATTTACTTATCAG[A/G]TCAAAATGAACAGACAAAAAATATGAAGAAAAAAA R 2 1 2 1 101000 f 74 goat 10_75319815_AF-PAKI 10 75319815 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320770701 Affx-122969785 AX-385257865 10 75364139 TAAATCCTGGGATATCAGCATGGATCAGAATCAGC[C/T]TATATCCATATTTTTCACACCATGCACTACAACAC Y 2 1 2 1 101000 f 74 goat snp2155-scaffold1065-868964 10 23837730 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428217 Affx-122939443 AX-123298560 10 75394822 CCCCCTTCTCAGAGTACCTTAGCCAGGACAGGGCC[G/T]GCTGCCTCCAAAGTCACCCACATAAGTCCAGTCGC K 2 1 2 1 101000 r 74 goat snp2156-scaffold1065-899647 10 23806799 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762806 Affx-986697335 AX-385250843 10 75406964 GGTCACCGTATGGAGACGCTCCTCATGTGGTTTGC[A/G]CGAGGCCCTCTCTGCTCTGCCGGCGCATCACTGTG R 2 1 2 1 600010 f 74 goat 10_75406964 10 75406964 Ancestral_priority_1043 ancestry 0.474 neutral IMAGE 10K 10K ancestral 320765326 Affx-986697337 AX-385252846 10 75461498 GAAGCAGAAAGTCCCACCAAAATGAACTCAGAAAC[A/G]CTTGATCTGTTATTCAGGATATCCATTCATCCTTC R 2 1 2 1 600010 r 74 goat 10_75461498 10 75461498 Ancestral_priority_1043 ancestry 0.728 recommended IMAGE 10K 10K ancestral 38378831 Affx-122976543 AX-123249190 10 75476408 TGTCCAGTCGCATGGAGGACGCAACTGGGACGTGA[C/T]GCCTCTGGTATGGTTTTCCTGCATACCTGTTGCCC Y 2 1 2 1 101000 r 74 goat snp16836-scaffold1764-8063 10 23725245 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439681 Affx-122930582 AX-123310018 10 75535551 ATGTAAGTACTGGGAGTGATGAGATTTTATCTGTC[A/G]TTGTCAACAGCACATAGAACAATGTTTTTTTTGCA R 2 1 2 1 101000 f 74 goat snp16837-scaffold1764-67206 10 23666407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795656 Affx-122921299 AX-385282611 10 75585111 GGCTTTTTGGGTCACAGATGACCAAAGTCACTGTA[C/T]ACCTTTCATCTCACTTTTAACAAGCACTACTTGCC Y 2 1 2 1 101000 f 74 goat snp16838-scaffold1764-116766 10 23617056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762810 Affx-986697339 AX-385250845 10 75601269 TTATTCCTTAGAGTATAGATAACAGGGTTTAAAAT[A/G]GGAGTAAAGCTGGTGTAGAACACTGCAAGGACTTT R 2 1 2 1 600010 f 74 goat 10_75601269 10 75601269 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 320762812 Affx-986697341 AX-385250846 10 75601496 GAGAACCAACAGGAGGAAGGAACTCAAAGAAAGAA[A/G]GCCACTGTCTGCAACTATTAGTAGGCTGACAACAT R 2 1 2 1 600010 f 74 goat 10_75601496 10 75601496 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 38410895 Affx-122952072 AX-123281245 10 75622539 GGCAGGGTTCAGTTACGTGATTCTGCCTCTCCATG[C/T]AGAGCTGACTGTGATTACCCAAAGAGGAAATCAGA Y 2 1 2 1 101000 r 74 goat snp16839-scaffold1764-154194 10 23579815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401729 Affx-122959522 AX-123272082 10 75659694 AGCTTACAATATGAAGAGGTTCACATCCTCTCCGT[A/G]TTTTTAAGCCACTTCACCAAGCAGCTCCCTTGAAT R 2 1 2 1 201000 r 74 goat snp16840-scaffold1764-191349 10 23541991 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440642 Affx-122929947 AX-123310979 10 75712055 GGGAATTGCTGTCCCAAGTCAACCAGGCACTTCCT[A/G]TGGATCTGCCTTGGTACTTTTCTTAGTTGAGAATT R 2 1 2 1 201000 r 74 goat snp16841-scaffold1764-243710 10 23489622 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799149 Affx-122929679 AX-385286079 10 75749610 TTCTAGGGGCATAGATGTGTGAAACAAACTTTTAA[C/T]AAGAGTAGATGCTTAAAGCATTGTGATAGGCATGA Y 2 1 2 1 101000 f 74 goat snp16842-scaffold1764-281265 10 23452126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773340 Affx-122932080 AX-385260482 10 75818245 AATGTAAGAAAAAAACTTGCAAAGCCTGGAAGTCT[A/G]TGGAGGATTCGCCTCATTTTAATCATAGACATGGA R 2 1 2 1 101000 r 74 goat snp16843-scaffold1764-349900 10 23387704 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434464 Affx-122934640 AX-123304805 10 75898832 ACAGGTTGATCCTCAAAATCATTGAAAGTCACCAA[C/T]GTTCTGTCCTTGCAGTGTGGTAAAACTTGGTAATG Y 2 1 2 1 101000 f 74 goat snp16844-scaffold1764-430487 10 23306890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452383 Affx-122920617 AX-123322716 10 75941817 CAAGAGTTGGACATGACTTGGTGGCTAAACCACTA[C/T]ATGGGTGTTATTTTCTAAAGAGTGTTTTCTTCCTT Y 2 1 2 1 101000 r 74 goat snp16845-scaffold1764-473472 10 23263996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794925 Affx-122966439 AX-385281885 10 75971278 ATTTTTCCTTAATATTATATCAGGTAGATTTTTAA[C/T]ATATTCACTCTCAATCTGAAGCATGTCATTTTCCT Y 2 1 2 1 101000 r 74 goat snp16846-scaffold1764-502933 10 23233563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379254 Affx-122976257 AX-123249613 10 76046547 GCCTCCCTCCCCAGTAGCTTGCCCTTCCTGTATTG[C/T]AGTCTGTTTACTCACTTCTGAGCCAAATCTCCAAG Y 2 1 2 1 101000 r 74 goat snp16847-scaffold1764-578202 10 23158107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765336 Affx-986697343 AX-385252854 10 76079452 GGCTTCCACCTACCCAAGGTCTGACTGAGAGCAGA[C/T]CCGCGTGGTGAGTATAGAACTTAGAAGCTGCTGTC Y 2 1 2 1 600010 r 74 goat 10_76079452 10 76079452 Ancestral_priority_1043 ancestry 0.572 neutral IMAGE 10K 10K ancestral 38441933 Affx-122928586 AX-123312270 10 76093228 CATGCTATCAAACATACCTAAATCAGTTTCCCTAA[A/G]CCATGAACTATCCTTAAGACTTCCCAAAATGTTTC R 2 1 2 1 101000 f 74 goat snp16848-scaffold1764-624883 10 23111344 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765339 Affx-986697345 AX-385252857 10 76103885 AAACAGAGCCAGACAGACACAGGTCTGACCCTTCC[A/T]AAATGACTACCAGTAATTGGTCCCATCTCTCAAAG W 4 1 2 1 600010 r 74 goat 10_76103885 10 76103885 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38452915 Affx-122920200 AX-123323248 10 76125323 ATTCTCTAGATTTGTATTTCCAAAATGAAAAAAGC[A/G]CAGTGGCTATGGTTTTATTATTTTTTGTCCATAGG R 2 1 2 1 101000 r 74 goat snp16849-scaffold1764-656978 10 23079253 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451884 Affx-122921050 AX-123322217 10 76200139 GGCTTACTAAAATAATTTATAAAATACTTTGCTGT[A/G]CCCTTAGATCTTATTAAATCACAATGCCTCCCAAG R 2 1 2 1 201000 r 74 goat snp16850-scaffold1764-731794 10 23006689 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423153 Affx-122942753 AX-123293499 10 76233432 ACTAAATCCATGTCGTGATCCTTTCGTTATCTGAC[A/G]CTTTAGCAATGTCCCATAAATGTTTGTTGACTAAA R 2 1 2 1 101000 f 74 goat snp16851-scaffold1764-765087 10 22973319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417833 Affx-122946793 AX-123288181 10 76266734 TCAGTATCTCTCCAAAGCTGTCTGAAAGACATTCT[A/C]ACCACTATACCCCACTTATGGGTGATAGTTATATT M 2 1 2 1 101000 f 74 goat snp16852-scaffold1764-798389 10 22940010 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429911 Affx-122938109 AX-123300252 10 76333895 AAGGTTTAAACCATCTCTGCTTAAGAGCAAAAGAG[A/G]ATCAGCTGATAACTTATTTGCTTAGAGCAAAATAG R 2 1 2 1 101000 f 74 goat snp16853-scaffold1764-865550 10 22872987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377066 Affx-122978288 AX-123247425 10 76365341 TTTGATTAATTGGCCTGCCTGTCTCACCCTCTGTG[G/T]CTTGGTAACCCCAGTGTTAGCAGTGGTTCATCTTG K 2 1 2 1 101000 r 74 goat snp16854-scaffold1764-896996 10 22841620 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395635 Affx-122963793 AX-123265990 10 76421564 TGCCCAGTTCTAGCACAGAGTGGGCCCTCAGCAAA[C/T]GTTTACTGAATCTAATCTGTGTTTAGACAGTTGTC Y 2 1 2 1 201000 r 74 goat snp16855-scaffold1764-953219 10 22785060 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401859 Affx-122959422 AX-123272212 10 76466743 GCTTCTGGCTTCTTGCTTGTGTTCTTTATCCCACC[A/G]AGATTGGCCCTGGAGGAGCAACCCCGAGTTCCTCT R 2 1 2 1 101000 f 74 goat snp16856-scaffold1764-998398 10 22741449 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401266 Affx-122959287 AX-123271619 10 76512758 CTGTCCCAGCTGTCTCTGGGGTGAGGGCGGGGGCA[C/T]GTTCCCCTCTCCACGGTTGCACAGACGTGCCCTCT Y 2 1 2 1 101000 r 74 goat snp16857-scaffold1764-1044413 10 22695413 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392995 Affx-122965658 AX-123263352 10 76543841 CGTTTCTAAATTCTCCTCGATTACCCCTTTGGAGT[A/G]TGCCATCTGTCTCCTGCCAGGATGCTGATGGATGC R 2 1 2 1 101000 f 74 goat snp16858-scaffold1764-1075496 10 22664534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438376 Affx-122931312 AX-123308714 10 76574399 AGAGATCCCAGAAGGGGTCAGCCTTTGTGCAGTGT[A/G]TTCATATAATCTGGATAATTTGAATAACTGCTGTG R 2 1 2 1 201000 r 74 goat snp16859-scaffold1764-1106054 10 22634132 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400928 Affx-122959721 AX-123271281 10 76612881 CTCAGGCTGTAAATGAGAATAATCTCCTGCCTTAA[C/T]AGGGAGTTTTGAAATTCAACTGAGATTTCATATCT Y 2 1 2 1 201000 r 74 goat snp16860-scaffold1764-1144536 10 22596031 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399193 Affx-122960620 AX-123269548 10 76644105 CTGGGGCTGGTGGCAGCCCTGTGTCTCTTCCAAGA[A/G]GTCTCAGGGTCTCTGGTCCAAAACCCAGCACCCTT R 2 1 2 1 101000 r 74 goat snp16861-scaffold1764-1175760 10 22564657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408227 Affx-122953837 AX-123278578 10 76673107 AGAAAGGGTAACCAGATGGGATAGAAACATCCCAA[C/T]GAGGGATGGGCTGGGAAGAGACCAATTCTCCTCCA Y 2 1 2 1 101000 f 74 goat snp16862-scaffold1764-1204762 10 22535671 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393140 Affx-122965551 AX-123263497 10 76714809 TGAAGAGGAGGTGTGCGCCCCCTGGTGGCTCAGTG[C/T]GGAATAGACGTGTGGAAGCACACTCCCCAGACAGG Y 2 1 2 1 101000 r 74 goat snp16863-scaffold1764-1246464 10 22494335 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411498 Affx-122951688 AX-123281848 10 76754660 CTCAAGGCTCCTGGCCCAAAGAACTTTAGAGAAGA[C/T]GCAGGAATTAAGGATCAACCCAGCATAGACAGGAT Y 2 1 2 1 201000 r 74 goat snp16864-scaffold1764-1286315 10 22454945 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443458 Affx-122927830 AX-123313795 10 76784283 TATGGTTTAGCACTCAGGTCCACTCTTTACCAGCC[A/G]TGTGAGCTGCAGACTCGCCTCCCAAACCTCAGGTC R 2 1 2 1 101000 f 74 goat snp16865-scaffold1764-1315938 10 22425753 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395238 Affx-122964474 AX-123265593 10 76842940 AATGCACGACTGGCAATGAGCCTGTTTCTGGCACC[A/G]CTGGGAGAGAGGCACACAGTCTTTTCCCCTGGAGA R 2 1 2 1 101000 f 74 goat snp16866-scaffold1764-1374595 10 22367201 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453111 Affx-122920023 AX-123323444 10 76912461 ATGACCTTGACCACTGGCATCGAGGCAGTGTACCA[C/T]AGCTTTTCTTCTAGTGTTCAGGGTGGCTTTGAATC Y 2 1 2 1 101000 r 74 goat snp16867-scaffold1764-1444116 10 22297153 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451014 Affx-122921712 AX-123321348 10 76966485 TGTGCAAGACATAGGGAGAATATCTATCCCTCCAC[C/T]GGGAACACAGGAGAGAGCAGTCACGAAAGACTTCC Y 2 1 2 1 101000 f 74 goat snp16868-scaffold1764-1498140 10 22243137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417808 Affx-122946812 AX-123288156 10 77052515 AGAAACCTGCAGGTGGAATTGCTGGGTGGGAGGGT[A/G]TGGATATTTAATGCCAAACTGCCCACCAGCAGTGT R 2 1 2 1 101000 r 74 goat snp16869-scaffold1764-1584170 10 22156605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390196 Affx-122967798 AX-123260553 10 77130810 GCTCTGGACAGCAGCCAAAGCAGGAGGTGGAGCAG[A/G]CACAGCTGGCCTTCAGTCTTCGGGCCTCACAGCCG R 2 1 2 1 101000 r 74 goat snp16871-scaffold1764-1662465 10 22078134 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771003 Affx-122960072 AX-385258165 10 77161895 TAAATGGTAGCGTGTTTAATACTATTTTGTACTTT[A/G]GTGGTTTTAACTTAATAATATAGCTTCAAAATCTT R 2 1 2 1 201000 r 74 goat snp16872-scaffold1764-1693550 10 22047007 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783767 Affx-122969388 AX-385270823 10 77225175 TAGAAACTGCAGTTCATTTATCCAGGTTACTCATC[A/G]TCAGTCTGTTCCTTCATGTTCTGCCTCAGTTCTCG R 2 1 2 1 101000 f 74 goat snp16874-scaffold1764-1756830 10 21981966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762820 Affx-986697349 AX-385250853 10 77234909 CTCCCCTTCTGTCGCTCTTCTACAGAGCTATGGAG[C/T]AGGGCCACTGGGTTTGCTGCAATCTGGAATTGCTT Y 2 1 2 1 600010 f 74 goat 10_77234909 10 77234909 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 320787661 Affx-122971118 AX-385274684 10 77258901 AAAAAGCCTACTTCTGTTCCTCTTCTGTGTAATAA[C/T]GGAAATGGTTAAATGTAGATTCCCCCATGTCAAGT Y 2 1 2 1 101000 f 74 goat snp16875-scaffold1764-1790556 10 21948183 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782591 Affx-122953173 AX-385269665 10 77290626 GTTTTAAAGATTATTTTTCATACTGCCGAGACTCT[A/G]AGAAGGGTACATTGCTGCTTCAGGAAATTTTGAAA R 2 1 2 1 101000 f 74 goat snp16876-scaffold1764-1822281 10 21916300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418004 Affx-122946663 AX-123288352 10 77323231 CTATGAAATTAAAACCAGTCATGTAGCCCCTTTGT[A/G]CCTGAGACATCTAGATTCACCTGAGAAGACCTGAG R 2 1 2 1 201000 r 74 goat snp16877-scaffold1764-1854886 10 21883703 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796874 Affx-122964103 AX-385283817 10 77356812 CATGCTTAATGAACATATGTGTTTGTTAGTATTTC[A/G]ATCGTTACCTGTGAGTCCATCCTACAACTGAACTG R 2 1 2 1 101000 r 74 goat snp16878-scaffold1764-1888467 10 21849864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406641 Affx-122955819 AX-123276993 10 77394026 TCTCTGCCTCCTATTCTTCATTCTTTCCTTGCAGT[A/G]CCTCCACCATTGGGCACCACTCTGCCAGAGACTCC R 2 1 2 1 101000 f 74 goat snp16879-scaffold1764-1925681 10 21812064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449074 Affx-122923611 AX-123319409 10 77489281 CCAGGGCTAGCTCTCTCCGTGAGCCCCTTGGTCAT[A/G]CTCATTGAAGACCCTCATAGCTGCTTTTCCTTTAG R 2 1 2 1 101000 r 74 goat snp16880-scaffold1764-2020936 10 21718076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416219 Affx-122948227 AX-123286568 10 77518823 GTGGGCCTCAGATGGACAAATAAAAATCACGGTTG[C/T]GACTCTGTCCCTGAAGCTCAGTAGTCTGTTTTGCG Y 2 1 2 1 101000 r 74 goat snp16881-scaffold1764-2050478 10 21688341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450112 Affx-122922773 AX-123320447 10 77596223 TGGTGTTCTGTTGGGAGTAGTGATAGTTGTGGACA[C/T]TGCCAAATGAATGCCAAGATATTTACTTGCCTAGG Y 2 1 2 1 101000 f 74 goat snp16882-scaffold1764-2127878 10 21610364 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771517 Affx-122919835 AX-385258675 10 77638758 TGAGGTCTCAGTTATACCTGTTGCCTCATCTTCAC[A/G]TGTTGTATCTAGAGTTCTACCTACACATAAGTCAA R 2 1 2 1 101000 f 74 goat snp16883-scaffold1764-2170413 10 21567928 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431248 Affx-122937129 AX-123301589 10 77707272 AAGTGGGGGTGTTTCCTGCATCTCTGAGTCATAGT[A/G]CATGTTTACTGTATATGCTGTGTAATTTAACATGT R 2 1 2 1 201000 r 74 goat snp16884-scaffold1764-2238927 10 21499666 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778791 Affx-122978377 AX-385265900 10 77748719 GGTCGCTTGGTTTAATAACTTTGGAATTATTCTGG[A/G]CTTGCTTCCCAAAGGCAAATTAGTATTGTAAATTG R 2 1 2 1 101000 f 74 goat snp16885-scaffold1764-2280374 10 21458004 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408247 Affx-122953820 AX-123278598 10 77781045 CTGCACATGGATAAAGTCGCATAGAGCTACTCGCC[A/G]CCCACCCAACCAGACACCCAGCAAAAAGCACATGC R 2 1 2 1 101000 f 74 goat snp16886-scaffold1764-2312700 10 21425609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398283 Affx-122962165 AX-123268638 10 77830187 AAGGATGAATGCAGCTTCTCTCCCTTAAGCTACCA[C/T]GCCCCACCCTGGGGAGGGGAGGGGCGGGGGTGGGG Y 2 1 2 1 103000 f 74 goat snp16887-scaffold1764-2361842 10 21376587 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799511 Affx-122947513 AX-385286441 10 77878501 AGGAATTTTGTGGATAGTGATATAAGCCAAAAAGT[A/G]CAACCCTTGTTTTTGGAAATAACAGGTTTTGGTCA R 2 1 2 1 101000 r 74 goat snp16888-scaffold1764-2410156 10 21328133 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271753 Affx-1111832900 AX-519545547 10 77918758 AAACTCTGGGTAATAGAGAGAAAAGAGACAAGTTA[A/G]AAGGTAACCTGGATCAGAACAATGCTTTCCAATTT R 2 1 2 1 101000 r 74 goat 10_77918758_AF-PAKI 10 77918758 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38416689 Affx-122947575 AX-123287037 10 77933340 TGGTGGCTAAGTCCCCACTAGAGTACCCTGGGTAC[A/G]GAGAGCTGATTTGTTTAAGACCACATCCCTCTTAG R 2 1 2 1 101000 r 74 goat snp16889-scaffold1764-2464995 10 21273399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779780 Affx-122943668 AX-385266880 10 77962412 CCTCTATAAAATGGGTGTAGCACCTACCATCAAGA[C/T]GCTATGAGGATTTGAACAGGACACGTTTACCTAGG Y 2 1 2 1 101000 f 74 goat snp16890-scaffold1764-2494067 10 21244316 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795798 Affx-122970981 AX-385282751 10 77996242 CTCTTACAGCATCAGCTTCCTCATCCAGAAAATTC[A/G]TGTTGGGTTGGATAATCTCCATAGTTGCTTTGAGT R 2 1 2 1 101000 f 74 goat snp16891-scaffold1764-2527897 10 21211511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770008 Affx-122923892 AX-385257175 10 78025514 GCTGTCTTAATCAAAGATAATATCGGAGATTAACT[A/G]TTCTCTGTGTGACTTGGACATAACAGTTCTCTCCT R 2 1 2 1 101000 r 74 goat snp16892-scaffold1764-2557169 10 21182154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412824 Affx-122950469 AX-123283173 10 78064566 TGTGTTATAAGTGCATTCCAAAGTCCTTCATGCTA[C/T]AGGAGGATTATGCCCACTCAGGCTTTTCTTCTTAT Y 2 1 2 1 101000 f 74 goat snp16893-scaffold1764-2596221 10 21142546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800594 Affx-122931666 AX-385287513 10 78115650 GGTTCTACAAATATGATATTAAATAGTTAATATCA[A/G]TATCTGTTTCAGTGAATTGATACATATCAATTGTG R 2 1 2 1 202000 f 74 goat snp16894-scaffold1764-2647305 10 21090963 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387394 Affx-122970419 AX-123257752 10 78151306 AGCCTGAGCCACCAGGGATGCTCCCAACTTACAGA[C/T]GTGAGATTTAAATTCAGGTTCCAGCCCTTCTGCTC Y 2 1 2 1 101000 r 74 goat snp16895-scaffold1764-2682961 10 21058640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276575 Affx-1111835412 AX-519550086 10 78166524 CTGTCTGAGCTTTATAAGAAATATCTTATTTAATA[C/G]AACAACATTTTGGGTTACTCATTGTTACCCTCCAT S 4 1 2 1 102000 r 74 goat Random2.2K-1108 10 78166524 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320803166 Affx-986696203 AX-385290029 10 78251110 AATTGATATTGATAAAGTATTACTAAAATACAGAT[A/G]ATAACCTGATATATCAGCTTTATATGCACTCTTGT R 2 1 2 1 600010 f 74 goat 10_78251110 10 78251110 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 38419373 Affx-122945623 AX-123289721 10 78295486 TTTCTGATTGAGATTTTTCACACCCTGAGATGACT[G/T]TAGAACAGACCTCCCCTTCCCCCTTCGTTGACTCT K 2 1 2 1 101000 f 74 goat snp23141-scaffold2307-600792 10 20874403 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385717 Affx-122971104 AX-123256075 10 78337219 ATGAATAATAACACAAAATATTTTAAAAGTATTAC[A/G]TCTCTCTTAAGGTAAAATCAACCACACTTAGAGAT R 2 1 2 1 101000 r 74 goat snp23140-scaffold2307-559059 10 20834152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399304 Affx-122960532 AX-123269659 10 78384533 CGTCTTCTGACAAGTTTGAATAAATGCTGCATCCC[A/G]GAACCAGCCAAGCAGGGGAGAATTAAGACAAGCTT R 2 1 2 1 101000 f 74 goat snp23139-scaffold2307-511745 10 20787891 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382170 Affx-122974027 AX-123252528 10 78431272 GGCTCTCTGAATGGGCCTACGAGCTGCTAGAGAAA[C/T]GGATGCAGGGTGGTATCAGCTCTCCCCACCCTCGA Y 2 1 2 1 101000 f 74 goat snp23138-scaffold2307-465006 10 20740911 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411848 Affx-122951224 AX-123282198 10 78499367 CATCCCCACCCCCAGTACCTAGTTCATTCTTCATC[A/G]CCTTCCCTGAACAGTTAATAGGTTACTTCTTGTAT R 2 1 2 1 101000 r 74 goat snp23136-scaffold2307-396911 10 20671609 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276428 Affx-1111835413 AX-519549953 10 78532511 TAGGTGAAGGCAGACCCTGATTAGGAATTTGGGAG[A/C]TTTTAGGGAAAAGAAAGCAAAAATTAATTATACAG M 2 1 2 1 102000 f 74 goat Random2.2K-1110 10 78532511 T G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320764969 Affx-122930080 AX-385252548 10 78549687 TGTTTACATTATGTTTAGTTAAGAGTTGAATGTGC[A/G]TTAAATTGTGCGACTTGGATATTCTATATCCTTAG R 2 1 2 1 101000 f 74 goat snp23135-scaffold2307-346591 10 20621046 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453296 Affx-122920371 AX-123323629 10 78581988 TATTCCCAATGCCCGGAATCTGCTCCTCTTTGCTT[A/G]AAAACTTCAAACCATCCCTTAAGGCGCACCAGTCG R 2 1 2 1 101000 r 74 goat snp23134-scaffold2307-314290 10 20588704 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798990 Affx-122939862 AX-385285920 10 78622157 GTTGAGAACCTGAGTTCCAAATCATTATAAGTAGA[C/T]AGTCTCCTTCAAGGCAGTGTTAACTTTTTTTTCAT Y 2 1 2 1 101000 r 74 goat snp23133-scaffold2307-274121 10 20548902 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388391 Affx-122969302 AX-123258749 10 78656786 GGTGGTGTGTCCCCCTGGGAAGTGAATTCATTTGC[A/G]TGGGGGTTTTTATTGGCTTCTTCAGACGCAGAGGT R 2 1 2 1 201000 f 74 goat snp23132-scaffold2307-239492 10 20514644 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410701 Affx-122952732 AX-123281051 10 78735363 CAAAAAAGTTTAATAACTGCTGCCACAGAAGTTAT[C/T]CTGAACTAAATTTAAGTTGGCCCAAAAGAAAACAA Y 2 1 2 1 101000 r 74 goat snp23131-scaffold2307-160915 10 20435636 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787738 Affx-122965751 AX-385274761 10 78776877 GGGGGCAGAAAGATGGCTGCTCCTAAATGCTCACA[C/T]GTACAGTCTTCTTTGGAGTGTCACACAAAATGTGA Y 2 1 2 1 101000 f 74 goat snp23130-scaffold2307-119401 10 20393185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423977 Affx-122942127 AX-123294323 10 78824514 AAGTAACAGGATCCAACTGACAAGGCTTAAACAGT[A/G]TCATTCTCACACAACAAAGAGTGTGGAAGTTCACA R 2 1 2 1 101000 r 74 goat snp23129-scaffold2307-71764 10 20345049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424347 Affx-122941935 AX-123294693 10 78859481 ATCATACATCTATGCCACATTTTACTTATTCATTT[A/G]TTTATGGACATGTAGTTGCTTTCATCTCTTGGCTA R 2 1 2 1 101000 r 74 goat snp23128-scaffold2307-36797 10 20310021 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396821 Affx-122963277 AX-123267176 10 78978515 GACTTCTGAGAGACGAATAATAGTCTGCTCTTAAT[A/G]TGAGCATTGGCTGCATTGCTGTATCCACTTTGTAA R 2 1 2 1 101000 f 74 goat snp44978-scaffold613-650368 10 20190348 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412933 Affx-122951470 AX-123283282 10 79024728 CGGCTCCAGTGCTTAGCGTGAACTTGCAACGTTGC[A/G]CACAAGTTTCTTGATAGACACCACGGTGCTTCACC R 2 1 2 1 101000 r 74 goat snp44977-scaffold613-604155 10 20144179 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402450 Affx-122958614 AX-123272803 10 79072683 ATATTTTATTTTGAAAATTTGACACACTGCAAAGT[A/G]CAATCACTCTTAAATCATAAAAAATACAAAGATTT R 2 1 2 1 101000 f 74 goat snp44976-scaffold613-556200 10 20096216 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396737 Affx-122962795 AX-123267092 10 79104460 CAAAGATGGCAGATACATGAAAGACGTTCAAAATT[A/G]TTCACTGATAGGGAAATGCAAATTAAAGCCATGAC R 2 1 2 1 201000 f 74 goat snp44975-scaffold613-524423 10 20064501 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275081 Affx-1111834675 AX-519548661 10 79118417 ACCATTTTCTCTCATGAACTCACCCTAGCTTTCTC[A/G]CTCACCTTCTACAGGTCTTACTCAAACATCACAGC R 2 1 2 1 101000 f 74 goat GoatD01.045386 10 79118417 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38400982 Affx-122960097 AX-123271335 10 79158957 TCTCCACTAAAGAGATGAGAAACTCAGATCCTTCC[A/G]TTAACAGATTATCACTGGTAACTTTACATTTCTTA R 2 1 2 1 201000 r 74 goat snp44974-scaffold613-469926 10 20009125 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419384 Affx-122945616 AX-123289732 10 79208648 CTCTTCCATTTCCTCTAAAAAAGGCATCTTAACTC[A/C]CTGTACGGCAGGGGTCCTAAAGATACTACTAAGCA M 2 1 2 1 101000 f 74 goat snp44973-scaffold613-420235 10 19959398 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421904 Affx-122944252 AX-123292251 10 79283545 AAGCAGACACTGAGTCTGCTGAAGTGCAGGGAGGG[C/T]GACAAAGGGGCGGACTACATTTACAGACAACCAGT Y 2 1 2 1 101000 r 74 goat snp44972-scaffold613-345338 10 19884634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420938 Affx-122944990 AX-123291285 10 79353598 ATGAAATTTGATTGAGATAAATGTAAAATTTTGAA[C/T]GTAGAAGGAATACCTAAAATATTGCGTGTGAGTAT Y 2 1 2 1 101000 r 74 goat snp44970-scaffold613-275285 10 19814652 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390837 Affx-122967835 AX-123261194 10 79388924 AGGAGGTCCTTACGGGAAAAGCTAAAGAGAGAACT[A/G]CTGAAGTTTACAAAGTTCACCCACCCTCCCGGCCA R 2 1 2 1 101000 f 74 goat snp44969-scaffold613-239959 10 19778996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794393 Affx-122941893 AX-385281356 10 79422254 CCATTTTTCTCTCTCATAAATATACATGACTTTGC[A/G]TTTGTTGTTTCCAGATGTTACTGGAATCTATGAGG R 2 1 2 1 201000 f 74 goat snp44968-scaffold613-206629 10 19744408 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430301 Affx-122937274 AX-123300642 10 79452263 CAAAGTTGGGGCTCCCCACCAGCAGGGATCCTCCA[C/T]GGCAGGAGTTAGGAGTCTAATAAAGTAAAAGGCCA Y 2 1 2 1 101000 r 74 goat snp44967-scaffold613-176620 10 19714222 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421009 Affx-122944554 AX-123291356 10 79530470 TTCACCTGATCACTCCCATCCTGCACTGCTGACTC[A/G]CTGGGCAGCCATGCTAACTAAGGTGGGGCTTCTTT R 2 1 2 1 201000 f 74 goat snp44966-scaffold613-98413 10 19635480 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774246 Affx-122926497 AX-385261382 10 79580867 GTGAATAAAAGGAAAGTACACCATTTGATAACAAG[G/T]GTGAAAGTTGGAATAAATGCTCCTAATTTGGTAAA K 2 1 2 1 101000 r 74 goat snp44965-scaffold613-48016 10 19584507 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773792 Affx-122945657 AX-385260932 10 79626011 GACAGTTGGTGATATGTCATGAACTAATTAAGGTC[A/G]TTCTAATTCTGTACACTGGAGTTCCAAAGAATCAG R 2 1 2 1 101000 f 74 goat snp44964-scaffold613-2872 10 19539329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378245 Affx-122976901 AX-123248604 10 79629697 AGGCAGAGGGGAATTTATGGGTTGTAACACAGAGC[C/T]GGGGTGGGGGAACAGCTGGGGCTCAGGACCTGTTA Y 2 1 2 1 101000 f 74 goat snp9068-scaffold133-715 10 19535805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410450 Affx-122952385 AX-123280800 10 79664144 TGTGGGAGGGACGGGGTGAATTGGGGGATCGAGAC[A/G]GATGTCTGTGCACCGCCATATGTACAACAGCTAGT R 2 1 2 1 101000 r 74 goat snp9069-scaffold133-35162 10 19501320 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429358 Affx-122938565 AX-123299700 10 79702977 TTTGTAGTAACTGGGCATTGTTGCAGCTACAGAAA[C/T]ATAAAGATAATTTTCTTTTGTATAATTTTTGAATT Y 2 1 2 1 102000 f 74 goat snp9070-scaffold133-73995 10 19462559 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444768 Affx-122926359 AX-123315105 10 79738536 GGAAAATGAAGTGTGAGTTATTTTTTCCCACTGTA[C/T]GATGGGGCTTCTGTTTTGTTTTCCTCTTGTTCTTC Y 2 1 2 1 101000 r 74 goat snp9071-scaffold133-109554 10 19426755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476271 Affx-1251763778 AX-186365363 10 79761779 CTCTTGAGAGTCCCTTGGACAGCAAGGAGATCAAA[-/CCAGTCAATTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTCTCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGG]CAGTCAATCCTAAAGGAAATCAGTCCTGAATATTC - 4 1 4 1 20000 f 74 goat SV_330 10 79761779 - deletion junction SV-TF-chip 539476524 Affx-1251763778 AX-185441364 10 79761779 CTCTTGAGAGTCCCTTGGACAGCAAGGAGATCAAA[-/CCAGTCAATTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTCTCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGG]CAGTCAATCCTAAAGGAAATCAGTCCTGAATATTC - 4 1 4 1 20000 r 74 goat SV_330 10 79761779 - deletion junction SV-TF-chip 562166040 Affx-1251763778 AX-606941449 10 79761779 CTCTTGAGAGTCCCTTGGACAGCAAGGAGATCAAA[-/CCAGTCAATTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTCTCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGG]CAGTCAATCCTAAAGGAAATCAGTCCTGAATATTC - 8 1 4 1 20100 r 74 goat SV_330 10 79761779 - deletion junction SV-TF-chip 562166318 Affx-1251763778 AX-606941726 10 79761779 CTCTTGAGAGTCCCTTGGACAGCAAGGAGATCAAA[-/CCAGTCAATTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTCTCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGG]CAGTCAATCCTAAAGGAAATCAGTCCTGAATATTC - 8 1 4 1 20100 r 74 goat SV_330 10 79761779 - deletion junction SV-TF-chip 562166388 Affx-1251763778 AX-606941796 10 79761779 CTCTTGAGAGTCCCTTGGACAGCAAGGAGATCAAA[-/CCAGTCAATTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTCTCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGG]CAGTCAATCCTAAAGGAAATCAGTCCTGAATATTC - 8 1 4 1 20100 f 74 goat SV_330 10 79761779 - deletion junction SV-TF-chip 320785952 Affx-122936202 AX-385272989 10 79771563 CTAATCCCTTATAACATCCAATTTGCACATCTTTG[C/T]TCTTAGAGGCTGAGTGTTTGGTGTAAGTTCCACAG Y 2 1 2 1 101000 r 74 goat snp9072-scaffold133-142581 10 19393902 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449358 Affx-122922734 AX-123319693 10 79822461 AAATTGTACAGCGAGTACTCATGTACCTGCCACCT[A/G]TATTTTACAAGTAGCATTTTGCTGTATTTGTCTCT R 2 1 2 1 201000 r 74 goat snp9073-scaffold133-193479 10 19342585 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782200 Affx-122954300 AX-385269278 10 79872763 GATGGATTGAGAACACAGTTGCATCTTCTGAACAC[A/G]TCGCTTTGCTGACAGCTCTTAGTCTCCTGTGAAAT R 2 1 2 1 101000 r 74 goat snp9074-scaffold133-243781 10 19292250 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439813 Affx-122930480 AX-123310150 10 79922584 CCGGAAGCTGTGATCTACCAATAGAAGATAAATCC[A/G]GTCAAGCCCCTGAGACCAAGAGGGAAAATGCTGAG R 2 1 2 1 101000 f 74 goat snp9075-scaffold133-293602 10 19242450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412825 Affx-122950468 AX-123283174 10 79982844 GTGCTCATGTTACCCAAGGCTAAGTCATAACAACA[G/T]CATGCACCTCTGCCTTGTTGTCATGGGATGTTTGC K 2 1 2 1 101000 f 74 goat snp9076-scaffold133-353862 10 19182004 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378330 Affx-122977339 AX-123248689 10 80011869 AGAAGGGAAGAATGATTGGGAGAAGGGGAAAAGAA[A/G]GAAGAAAGGGAAGAGAAAAGAAGAAGACTAAAAAT R 2 1 2 1 303000 f 74 goat snp9077-scaffold133-382887 10 19152396 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274863 Affx-1111834539 AX-519548448 10 80021115 GCTCAGTTTCGCAAGAGCTATGATAGCCTCTACCC[A/G]CCCCCTGCAGAGTCCCCCAAACCGCCCGACGGGCC R 2 1 2 1 101000 f 74 goat GoatD01.040696 10 80021115 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38385755 Affx-122971072 AX-123256113 10 80045773 CAGCACTAGGCAAACCAACTTTGAGAATGCAAAAA[G/T]CTATACATTTTAGTTCCAAATTGTCCGGAAAGTCT K 2 1 2 1 101000 f 74 goat snp9078-scaffold133-416791 10 19118502 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451541 Affx-122921088 AX-123321874 10 80108836 GGCAAGTTGCTCACTTGCCCAAGGGGTACAATGAC[A/G]TCTACTGCCTGGGGTGGGCGTTGGCACTGAATGAG R 2 1 2 1 101000 f 74 goat snp9079-scaffold133-479854 10 19055536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404617 Affx-122957333 AX-123274969 10 80219584 GTTCTGTTACAAGTCATTTTGAAGGAATTCTGATC[A/G]CCTCTTTCCCCCATAAGCGTTAGGATCCTACAACT R 2 1 2 1 101000 f 74 goat snp9081-scaffold133-590602 10 18945658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451252 Affx-122921938 AX-123321585 10 80294859 TGGGAGACGGTTAAACAAGAATGTCAAAGCATTGA[C/T]CATGGAGGAAGCTGAGCTGTGGCATCAGCGGGCGG Y 2 1 2 1 101000 f 74 goat snp9083-scaffold133-665877 10 18870533 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431539 Affx-122936215 AX-123301880 10 80327100 GGACTGCCTGGGCAAGGTAGACCTCAAATCCAGAA[C/T]GTTGCCTGCTTCTTCTGGCCCAGAGGTCTCCCCGA Y 2 1 2 1 101000 f 74 goat snp9084-scaffold133-698118 10 18838375 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405829 Affx-122955879 AX-123276181 10 80359065 ATAATTATCATTAACCACAGTGAGCAAAACTCATC[A/G]CTGAAAACTTTTTTTTTCCAAGCCTCCCTCAAAAG R 2 1 2 1 201000 f 74 goat snp9085-scaffold133-730083 10 18806013 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421246 Affx-122944110 AX-123291593 10 80389074 CACTGAGAGGGCTCTGAGGATAAGGTCATTCCACA[C/T]GGTTGGGACATCACAACAGGGCTGGGGACAAGGGG Y 2 1 2 1 101000 f 74 goat snp9086-scaffold133-760092 10 18777354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423114 Affx-122942913 AX-123293460 10 80425013 CCAGTCTGAACCAGGGCCAGCTTTGAGGACAGCAG[A/C]GCGACTTGATAGGATTCTCTCTTCAAAGCATAGAG M 2 1 2 1 101000 r 74 goat snp9087-scaffold133-796031 10 18741426 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271869 Affx-1111832901 AX-519545652 10 80443786 ACACATGCATGGCCTTAGGATGATGAAGGGAGACA[A/G]GGGCAGGGGTGAGTCACAAATGCCAAGTACCTGAA R 2 1 2 1 101000 f 74 goat 10_80443786_AF-PAKI 10 80443786 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320767220 Affx-122929140 AX-385254501 10 80457509 AGGCTCAGACAATGTAGCTGCTAAATTAAATAATG[C/T]GCAATACCTATTTACACATCATACATGTCCATCGA Y 2 1 2 1 101000 f 74 goat snp9088-scaffold133-828527 10 18708968 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779613 Affx-122930564 AX-385266715 10 80489294 CTTAATACAGAGCTGCTCAAGCTGTTACTCTCTTA[C/T]GAAGTATCCTTTCAATTGCATTGTCATATTACCTT Y 2 1 2 1 101000 f 74 goat snp9089-scaffold133-860312 10 18679394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769160 Affx-122928994 AX-385256335 10 80532731 CTGTGAAATTTTTTGTGGCTGAGAAGCATCACTTC[A/G]CTAGAACTTAGAATTTTTTACTACGCTTACCACAC R 2 1 2 1 101000 f 74 goat snp9090-scaffold133-903749 10 18635959 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441797 Affx-122929083 AX-123312134 10 80572306 ACTGACCGCCCAGCCACCGGGACCAGAAAGGGTGC[A/G]TATGGAGAGTCAGGATCCTCAAGCAGCCTCTCCTC R 2 1 2 1 101000 r 74 goat snp9091-scaffold133-943324 10 18596558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777009 Affx-122954465 AX-385264133 10 80613801 CAGATGAAATACTTTGTTTCTGTCAGGATAAATCT[A/G]ATGGATGAATGCATATAAGCAGTAATGGTATTCTT R 2 1 2 1 101000 f 74 goat snp9092-scaffold133-984819 10 18554613 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782833 Affx-122944611 AX-385269904 10 80648813 CGACTGAAAGAATTCTTAGAAGACTATGATGATGA[C/T]AGAGATGATCCCAAATATTACAGGTGAAGAAGCCT Y 2 1 2 1 101000 r 74 goat snp9093-scaffold133-1019831 10 18519781 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418627 Affx-122947147 AX-123288975 10 80679627 GGTTGTTGATGTAGTTCCTCCCTGGCTCAGACATC[A/G]CCTCCCTTTCTGATGCCTTCTCCAGCTTCCCCAGC R 2 1 2 1 201000 f 74 goat snp9094-scaffold133-1050645 10 18488688 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773126 Affx-122922614 AX-385260269 10 80719961 GAGATACTGGGAAGTATAACTAAGTGAATATTGCC[A/G]TGATTTAGGTAAAAAATGGTGAAAGTCTAAATTAT R 2 1 2 1 101000 f 74 goat snp9095-scaffold133-1090979 10 18447992 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801751 Affx-122977585 AX-385288659 10 80759258 GGAGGCTCACTACGTGAGGAACAGCTTGCTTTTCC[A/G]CATGAGAACTTGAGTTCTTTCTAGGGAAAATGGCA R 2 1 2 1 201000 f 74 goat snp9096-scaffold133-1130276 10 18408438 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398124 Affx-122961700 AX-123268479 10 80806646 GCAACATCCAGGCAATTGGATATACAGATCTAAAT[C/T]CAGTAGAGAACTCTTAAGATGGAATTTTAGTTTTG Y 2 1 2 1 101000 f 74 goat snp9097-scaffold133-1177664 10 18361679 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445975 Affx-122925889 AX-123316312 10 80837402 GGCAAAAAAAAGAAAAAAGTCAAGAGCTCTTATAA[C/T]GGTTTGAGGGAGAAAACAAAGATGAGGACTTGATT Y 2 1 2 1 102000 r 74 goat snp9098-scaffold133-1208420 10 18330706 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398518 Affx-122961546 AX-123268873 10 80877406 AAAGGAGTGGTCACACAGCAACACTTTCTTTTGTG[A/C]TTGTTTCATTTCCATTTGCCTTGTATATCTTCACT M 2 1 2 1 201000 r 74 goat snp9099-scaffold133-1248424 10 18290466 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397523 Affx-122962047 AX-123267878 10 81020125 ACATTAAATTTAGAGAAACTATAGCTCCAGGAGGT[A/C]TCCATGGGATTTATGAAAGAAGCTTAGTTAGTGAG M 2 1 2 1 101000 r 74 goat snp9101-scaffold133-1391143 10 18147863 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442393 Affx-122928002 AX-123312730 10 81096785 AAAGCTAGCAGCTTCTCTAGTTGCATTTAGAAAAA[C/T]GTTTTTCTCTGGGGTAGGTTTTTCACTTTTGTCTC Y 2 1 2 1 102000 f 74 goat snp9102-scaffold133-1467803 10 18072339 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800473 Affx-122931352 AX-385287393 10 81154011 TTCATTCTTTTTGCCTGCTTTTCTTTATGCTTTAC[A/C]CTTGTCACTATCTAATACACTTAATTGTTTTGCTT M 2 1 2 1 101000 f 74 goat snp9103-scaffold133-1525029 10 18014105 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393331 Affx-122965945 AX-123263687 10 81249592 GTCCTCTTTGCAGCCAGGCCCCAAGCCAGTCACCA[C/T]GCAATTTTGCTAATTCAAACTGCTTTCCCGTTTAG Y 2 1 2 1 101000 r 74 goat snp9105-scaffold133-1620610 10 17923880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796003 Affx-122940702 AX-385282955 10 81321348 ATTGATTGGGCCTGGTAAACATATAAGTGTAAAAT[A/G]CTGAAAAGCTGAGACACCTCATTTTACTCTGTAAT R 2 1 2 1 101000 r 74 goat snp9106-scaffold133-1692366 10 17846834 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422358 Affx-122943435 AX-123292704 10 81372141 TAGGAACCCTGGGTTTAGAGTAGAATGTTCACCCC[A/G]TTGGAGACTCTCAGGCTTGTCTTCCTCATCACAGG R 2 1 2 1 101000 f 74 goat snp9107-scaffold133-1743159 10 17795996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453946 Affx-122919478 AX-123324279 10 81404959 TGTCTGGAAACATGCCTAAACAGAAACAGTGATAA[C/T]GAGTTAGAAGCATTAAGGGACTGCAATGGATAGAA Y 2 1 2 1 101000 f 74 goat snp9108-scaffold133-1775977 10 17762769 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397279 Affx-122962339 AX-123267634 10 81496803 ACATATTTGTTCAAAGGGACCTTTTTGTAGCTTCT[A/G]TTTTTCCAGAAGGTAGGGTTGTATGAAAGCTGGAG R 2 1 2 1 101000 r 74 goat snp9110-scaffold133-1867821 10 17670678 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382446 Affx-122974227 AX-123252804 10 81559421 CCTTTAAGGCCATTTCAAAGCCCACCCTCTCCTTA[C/T]AATGTCTCCCTGTTCCCTCGGGCAGAGTTAGTTTT Y 2 1 2 1 101000 r 74 goat snp9111-scaffold133-1930439 10 17608073 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404540 Affx-122957394 AX-123274892 10 81588027 CAAGGACTTACTCTTTCCACCTCCCAAAGAATTTT[A/G]TAGGAGCAAAATGTTGAGCAAGAGAGCTGCACTTG R 2 1 2 1 101000 r 74 goat snp9112-scaffold133-1959045 10 17579319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802107 Affx-122956743 AX-385289011 10 81635883 GAGGGATGGAGTCAAAAGAAAACAGCTTTTGACAC[C/T]AGATTCATTTGATGTTGAGTCTGGCCTCTGCTACT Y 2 1 2 1 101000 f 74 goat snp9113-scaffold133-2006901 10 17531306 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783946 Affx-122966807 AX-385271000 10 81684392 TTGAGGACGATGAGCACAACAGACAGGAACGTCAG[C/T]GTCTTAAATCCATTTAAGTCTTTGCTTCCTAGGAC Y 2 1 2 1 101000 r 74 goat snp9114-scaffold133-2055410 10 17482708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453929 Affx-122919493 AX-123324262 10 81713819 TGGAGTTGTAGCTCCTGTGGAGGGAAAGTGAGAAC[C/T]GCATATAAATAAAATTACTTCTGAAAAGCCTGAAG Y 2 1 2 1 201000 f 74 goat snp9115-scaffold133-2084837 10 17453294 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449934 Affx-122922912 AX-123320269 10 81760201 GTCATCTCATCTGCCTTTCCCTCCTGCATAAAGAC[G/T]CTCCAAGAACCTGCTCTCAGTACAGTTTACCTGCC K 2 1 2 1 201000 r 74 goat snp9116-scaffold133-2131219 10 17409848 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786778 Affx-122938759 AX-284797069 10 81805753 ATCCAGAGGCTATTTCTCAGTCCCTATCTGAGGCA[G/T]CCTTTCTGTAGCATTCCATCCTGGTGAGTTCCTCC K 2 1 2 1 101000 f 74 goat snp9117-scaffold133-2176771 10 17364398 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412317 Affx-122950853 AX-123282666 10 81841189 CCGCTCTCTCAGGCTCCTTGCTCCCCTTCATGTGC[A/G]TCTCTTACTAGCAAGCTAGTATCAGTCTTGCTTCT R 2 1 2 1 103000 r 74 goat snp9118-scaffold133-2212207 10 17329455 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400625 Affx-122960374 AX-123270980 10 81897865 GAGCAATTACCTGCCCAGATTATACAACAGTAAAT[A/C]AGACCCCAGGATTCCAACTCAGGGCAGCTAGACCC M 2 1 2 1 101000 f 74 goat snp9119-scaffold133-2268883 10 17272961 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404390 Affx-122956794 AX-123274742 10 82014124 TGTGGTATCAGGTGCTGGGCTAGGTGAGAGGGACC[A/C]CTATGACCTCGAGGCCCAGGCACTGCTTCTCTGGG M 2 1 2 1 101000 f 74 goat snp9121-scaffold133-2385142 10 17157918 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449687 Affx-122922552 AX-123320022 10 82045863 CAATCCCTGGTTGAAGAACTAAAATCCTATAAGCC[A/G]CGTGGCATGGCCAAAAAAGAGATGATTGTTTGGGA R 2 1 2 1 101000 f 74 goat snp9122-scaffold133-2416881 10 17126551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397594 Affx-122961991 AX-123267949 10 82199574 GTTTCATCCAAATGTGAAACCTCTGAACTTCTTCC[A/G]TTCTTATGCTTCCTGATGACTCTCTCCATCTCTTC R 2 1 2 1 101000 r 74 goat snp9123-scaffold133-2570592 10 16972733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396668 Affx-122962845 AX-123267023 10 82232314 AGGATGGATAGACGGTAGATAGATAGTTGCTCTTA[C/T]TGTAAGACACTGACTTGTGCAATCAGGGAGGCAAT Y 2 1 2 1 101000 f 74 goat snp9124-scaffold133-2603332 10 16940191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406972 Affx-122955052 AX-123277323 10 82361520 GGAGTTGATGACAGGCAAGCCCCATGCTGAGATAA[C/T]TGGGACCTTGAAAAGAGTGACAAACCTCTGGAAAT Y 2 1 2 1 101000 r 74 goat snp9126-scaffold133-2732538 10 16810033 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380055 Affx-122975569 AX-123250413 10 82473207 ACTAGGCTGCGCCCATGGGGAACGGAAAGAAGCAA[C/T]GAGACATGCGTCACAAGGGCTCAAAAAGTAGTTTG Y 2 1 2 1 101000 r 74 goat snp9129-scaffold133-2844225 10 16698277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410784 Affx-122952669 AX-123281134 10 82505021 CTTCCAGGGATGAGAACAAGTTAAAACAATGTATT[C/T]TGAATTCAATATGTAAGATATTTTGAAATTGGTAG Y 2 1 2 1 101000 f 74 goat snp9130-scaffold133-2876039 10 16666617 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411822 Affx-122951244 AX-123282172 10 82571456 CTGGGATTTAGCCCTAAATCCTGCCCAGAGATTTA[C/T]GGGAGGAGGAAGCCTGTGTCTGTCCTCCGGCTTTT Y 2 1 2 1 103000 r 74 goat snp9131-scaffold133-2942474 10 16600023 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385738 Affx-122971086 AX-123256096 10 82601784 TGTACGTGTATATGTGTGTGGATGTGTGGACATGT[A/G]TGCACACTATCAAGGGATTTTTGTTGCAATGGTTT R 2 1 2 1 101000 r 74 goat snp9132-scaffold133-2972802 10 16569899 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783079 Affx-122928203 AX-385270146 10 82632758 AAGGGGTTTATGAGACTATAATCTCATAAAGTGGG[C/T]GGGTGTGCTTGGGTCTGCTGTTACAATCTCCTCCA Y 2 1 2 1 101000 r 74 goat snp9133-scaffold133-3003776 10 16538793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380481 Affx-122975717 AX-123250839 10 82672319 TCCCATTAGGGCCCATTTTTGGAACTTGAGGTGTT[C/T]TGTGTTTTTTCTTCTACTTGTGTAAGGCAGCGCCC Y 2 1 2 1 101000 f 74 goat snp9134-scaffold133-3043337 10 16499155 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441716 Affx-122929148 AX-123312053 10 82730673 TCCAGCTACTCAGGAACAAATCTTTGTTTCAGTTT[A/G]TCAGAACTGCATTGAGAGGCAGCTTCCTCTGGGCT R 2 1 2 1 101000 f 74 goat snp9135-scaffold133-3101691 10 16440513 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381254 Affx-122974492 AX-123251612 10 82767876 AACCTCATCTGTGGGAGACCACAGACATGGCCACA[A/G]TTCTTTAAATTCTTCCCATCAAGAGATGAAGTCTC R 2 1 2 1 101000 r 74 goat snp9136-scaffold133-3138894 10 16403273 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798393 Affx-122953292 AX-385285327 10 82805284 CCAACTATGGTGAATGAAAGATTAGAACAACTTTT[A/G]TGAGACAGGTGGCTGTTGATAGAATATAATCACAA R 2 1 2 1 101000 r 74 goat snp9137-scaffold133-3176302 10 16365997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420763 Affx-122944714 AX-123291110 10 82820359 AACAGGCACAACCACTGATCCATTTCTCAGGACCA[G/T]ACAGTGCTTAAGAATATGCCCAAAGAGTCAGCTCC K 2 1 2 1 201000 r 74 goat snp20995-scaffold2058-1357 10 16294563 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379487 Affx-122976474 AX-123249845 10 82870298 CAAGTAGCCAGCCACGGGGGCAGCTGCTTCACGTG[A/G]CTTGACAATGACCACAAGCAAAAGCACATGAGCAC R 2 1 2 1 101000 r 74 goat snp20996-scaffold2058-51296 10 16344904 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393206 Affx-122965501 AX-123263563 10 82902628 TAAATAGCTGGGAGGAGGGGAACCTTACCTCCAAA[C/T]GCTCTCAAAAATTATTCTCCCTTGTTGAAAATCAC Y 2 1 2 1 102000 f 74 goat snp20997-scaffold2058-83626 10 16220885 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392908 Affx-122965722 AX-123263265 10 82936524 CCTTGTTCAAGGGTCAGAAGATCTATCTCCTGTCT[A/G]TTTTGGAGTACTATCTCTATCAAGCTGTGTCGGCT R 2 1 2 1 202000 r 74 goat snp20998-scaffold2058-117522 10 16255009 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802739 Affx-122971644 AX-385289638 10 82968542 GCCTAGAGTTTGAACATAATTGGCAACCGCTAAAT[C/T]TTTCAAAGTATTTATACATTCTCCCTCTTGGGCAG Y 2 1 2 1 101000 r 74 goat snp20999-scaffold2058-149540 10 16288071 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771444 Affx-122972984 AX-385258602 10 83001891 GAGACGAAAGGCAGCCAGGTTTACCTGGGTCTTGC[A/G]CTGTCCTACTCATTATGGTGTATTTGATCTGCAGA R 2 1 2 1 202000 f 74 goat snp18432-scaffold1868-28986 10 16162904 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271755 Affx-1111832902 AX-519545549 10 83010076 TAACAAGAACATCCTTACCTTAAATCATCCCATAA[A/G]TCATCCCTCGGATATGTCCAGAAAGAGGCAATCAG R 2 1 2 1 101000 r 74 goat 10_83010076_AF-PAKI 10 83010076 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38384273 Affx-122972307 AX-123254631 10 83066787 CATTGGTGTTTTAGAAGAAGCCAATAGTCGGGTGA[C/T]GGGGTTCACTATATTCTTTTGGTGGTTGTTTCTGC Y 2 1 2 1 101000 f 74 goat snp18433-scaffold1868-93882 10 16097804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448483 Affx-122923619 AX-123318819 10 83130191 CAGCGTTACTCCAGAAAGCTCATTTTCTTTGTTTT[C/T]CCTTCTCTGTTAGAATTTCCTTTTATCTACCAATA Y 2 1 2 1 201000 r 74 goat snp18434-scaffold1868-157286 10 16034352 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773467 Affx-122978360 AX-385260609 10 83161108 AAATAAATTAAGGATGCTTTGCTTTTATGTAGAAG[G/T]AAATAACAATGGCTACCAAGTATTGATTTATCCAT K 2 1 2 1 201000 f 74 goat snp18435-scaffold1868-188203 10 16002629 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433389 Affx-122935111 AX-123303730 10 83217011 AGTTATGATGGTGATATATTTTTGTAACTCTTCCT[A/G]TGTGCCTATACTTTCACTTGTGTTAGCTCTTTAAT R 2 1 2 1 101000 r 74 goat snp18436-scaffold1868-244106 10 15946438 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387637 Affx-122969855 AX-123257995 10 83272293 GAATAATAGTAGACAGTGTTGCTGTGTGTCTGGCA[C/T]ACTTCTGAATGCTTCACATGTCATAACTCATCTGT Y 2 1 2 1 101000 r 74 goat snp18437-scaffold1868-299388 10 15891474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443226 Affx-122927568 AX-123313563 10 83341520 AATCAACAAAATAGAACCTACCTCCAAACCTGCTC[A/G]TCTCCCAGGCCTCCTTATTTCAGTAAGAGTTACTA R 2 1 2 1 101000 f 74 goat snp18438-scaffold1868-368615 10 15822520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389925 Affx-122968101 AX-123260282 10 83372101 GGGGCTGCCTGCTGTGTAGGCGGGAACATCATCCC[A/G]GGGGTAGATCACGCGGTTGGGAATAGCATTCACGA R 2 1 2 1 201000 f 74 goat snp18439-scaffold1868-399196 10 15791660 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389493 Affx-122968314 AX-123259851 10 83430203 GCAGAGCTGTCCTTTCCGACTCAACCCCGAAGTGC[A/G]CACAGCCATGAGGTACTCACTGCAGGTCACCCTCC R 2 1 2 1 201000 r 74 goat snp18440-scaffold1868-457298 10 15743417 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395284 Affx-122964077 AX-123265639 10 83520608 TTGGTGGTTTTCAATTTCTGTATATTTGTAAAGAA[C/T]GGAGCCCTTTGGGCAAATTCTTTTGTGTAGCCCCA Y 2 1 2 1 201000 f 74 goat snp18441-scaffold1868-547703 10 15653813 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427314 Affx-122940138 AX-123297657 10 83569745 AAAATAAGGTTGGTGTCCATCCCTAGAGTATGATA[C/T]GCCAGGGGCTAATACACTTGCCTGTAGAATTTTGA Y 2 1 2 1 201000 f 74 goat snp18442-scaffold1868-596840 10 15607190 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773598 Affx-122930900 AX-385260739 10 83601210 AGAACTCCGTAAGGTATAAAAAGTGGATCATTTCC[A/G]CTATTTTACGCATTTATACTTAATTTCACTTGGGA R 2 1 2 1 101000 f 74 goat snp18443-scaffold1868-628305 10 15575909 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454131 Affx-122919340 AX-123324464 10 83666990 AAATGGCTAACAGCTCTGGTCAGTTAAGCAGACAC[G/T]AATACGAGTGCCAGAGCTAGTGTGATGGTGGGCTT K 2 1 2 1 101000 f 74 goat snp18444-scaffold1868-694085 10 15509876 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438910 Affx-122930434 AX-123309247 10 83720839 TTTCAGACCTTATAGTATATGGTGGGTCCAGCCAG[C/T]GATGAAACACAGTGGGAGAAGACTGCCGCCAACCA Y 2 1 2 1 101000 f 74 goat snp18445-scaffold1868-747934 10 15456163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432106 Affx-122936459 AX-123302447 10 83782269 TCGTGATAGACGAGGCATTCAACACTTGGACTCTG[A/C]GGTTGGGAAGCTCGTGGTGAGGGATGGACAGAGGG M 2 1 2 1 101000 f 74 goat snp18446-scaffold1868-809364 10 15394507 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377180 Affx-122978202 AX-123247539 10 83834189 TGTGTGACCAAATTACTGTGTCCCTCAGTCTCCCC[A/G]TCTTTGAAATGGGGCTGAATAGTTCTGACCTCATA R 2 1 2 1 101000 r 74 goat snp18447-scaffold1868-861284 10 15342201 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431587 Affx-122936177 AX-123301928 10 83891749 GCAGAGATAATACTTGAACTGGGCCTTCAAAGGTG[A/C]GTCCAGGATATGAACTGCCTTTGGGGATGGTTTGG M 2 1 2 1 101000 f 74 goat snp18448-scaffold1868-918844 10 15286098 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438341 Affx-122931336 AX-123308679 10 83927771 TTGAGTAGCTGGAAAGAAAAGAACCCGAACAAGAG[C/T]GGAGGTCAGAAGCTTCATCTTTCCTGAAAAGATCT Y 2 1 2 1 101000 f 74 goat snp18449-scaffold1868-954866 10 15250177 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426155 Affx-122940602 AX-123296501 10 83945062 TAAAGACAGGTTTTAATAGGTGGTTCATTTCTCAG[C/T]CACTATGGGCCCTGATTAATTTCCCTCACCTTCCA Y 2 1 2 1 201000 f 74 goat snp26061-scaffold271-13404 10 15233023 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784479 Affx-122950040 AX-385271528 10 84008232 AAAGCAGAAAAACCTCACACCAACAGTCTTTATAA[C/T]GGAGATAATCACGCAGGACAAAATCACCCAGGATT Y 2 1 2 1 101000 r 74 goat snp26062-scaffold271-76574 10 15169891 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797698 Affx-122934567 AX-385284637 10 84048661 TCCCTACCATCTGGCACTCAGTAGAGGATCAACAG[A/G]TAATGAATTTGTCTGTTATTAATGTATTACGGATC R 2 1 2 1 101000 f 74 goat snp26063-scaffold271-117003 10 15129885 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436172 Affx-122932616 AX-123306511 10 84100950 CATGAGTGTGTGTTGAAGGCTCTGCTAAAAATCAG[C/T]GCATGGCCCTCTTGCCTCTTTCCTCCCACTCGCCA Y 2 1 2 1 101000 f 74 goat snp26064-scaffold271-169292 10 15077671 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398362 Affx-122961667 AX-123268717 10 84131415 CATGAAGTACTGCTGAGAGCTGTCCAGGACTCAGG[C/T]GTCTCTCCCAGCCCTGGCCAACCTGGCTGCCTTCT Y 2 1 2 1 101000 f 74 goat snp26065-scaffold271-199757 10 15047051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790516 Affx-122951167 AX-385277519 10 84160336 GTGCTCAGAGAACTGAGGGAATTACGCCTTCTCTT[A/G]TCAATGAGGTGCTAGCTTTCTCCCAAGATGGGCAG R 2 1 2 1 101000 f 74 goat snp26066-scaffold271-228678 10 15018642 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425316 Affx-122940942 AX-123295662 10 84216173 ATGGTACCCACTCCCCCATAGAGTTGCGTGTGAAA[C/T]GGTGAACCCCAGGCCTGGCACAGGAAGTCCTTAAT Y 2 1 2 1 303000 r 74 goat snp26067-scaffold271-284515 10 14963036 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414722 Affx-122949265 AX-123285071 10 84263312 TACATAGGTTACGTGTCATTTTTCCCACTGACATG[C/T]GCGCTCTTAAAGCGCAGGGGCCCTGCCTGACTTGT Y 2 1 2 1 101000 f 74 goat snp26068-scaffold271-331654 10 14916401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377099 Affx-122978264 AX-123247458 10 84309599 CCCCTAAATTGCTCCTGATGGTCGGGTCAGCTAGT[G/T]ACTAGGGAGACTGCACTAAAGCCTTCATTTATCAG K 2 1 2 1 102000 f 74 goat snp26069-scaffold271-377941 10 14869992 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381444 Affx-122974341 AX-123251802 10 84339737 AATGCTGCCTTTGACAAGTTTAGGTTCTCAGTGGT[A/G]TTTTGGAGTGCTCAAAATTTCCATCAGCCCGCCCC R 2 1 2 1 101000 f 74 goat snp26070-scaffold271-408079 10 14840077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400630 Affx-122960371 AX-123270985 10 84377803 ATCTGGACATAGAAATTGAGAGAGTAAAGCTATGT[C/T]GAACGCTCCACCCCAGTGGAGTTGGGGACCCTACC Y 2 1 2 1 201000 f 74 goat snp26071-scaffold271-446145 10 14801887 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801306 Affx-122950847 AX-385288218 10 84411582 CCAAGGCTAGAAGCTCTTCATATAGTTTTAAAATT[A/G]CAAGGCTTCGAATTGCCTGCATTTTGTTCTCAAAT R 2 1 2 1 303000 f 74 goat snp26072-scaffold271-479924 10 14767843 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420050 Affx-122945134 AX-123290398 10 84442761 CTGAATGTCACCCTCTGGGTGACAGGTAACCTCAG[C/T]GGTCTCCTGGGTGATGGATGCATCAGAGTGGAGAG Y 2 1 2 1 202000 r 74 goat snp26073-scaffold271-511103 10 14736786 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795194 Affx-122951913 AX-385282152 10 84478049 TATTCACTAAACATTTACTCTGTATACAATAGCTC[A/G]CTTAATCCTCACAACTGCCTCTTAAAGTTGTTATT R 2 1 2 1 101000 r 74 goat snp26074-scaffold271-546391 10 14701751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463116060 Affx-1109821512 AX-514603233 10 84478733 CAGCTTGCCTTTGCTACTTGACAGTGTTAGGGGTT[A/G]AAGGGACCTAGAAATAACTCCCCTCTCTCTTCCAA R 2 1 2 1 201000 r 74 goat GoatD01.028989 10 84478733 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38416418 Affx-122947843 AX-123286767 10 84522866 CCGGGAACTCCAGACAGCAAGACTGGAGAGAAAGG[C/T]GTAATTGACAGGACTCTCAGGTGCAGAAGAAGAAA Y 2 1 2 1 101000 r 74 goat snp26075-scaffold271-591208 10 14656856 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797846 Affx-122931796 AX-385284785 10 84583183 GAGATTTTGATGTAGTAATTCCTTACTATCTTGTC[A/G]GTTCTTTATGCTTTTCAGAAGATGTTTCTACATTG R 2 1 2 1 101000 f 74 goat snp26076-scaffold271-651525 10 14596720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784804 Affx-122939968 AX-385271851 10 84645092 AATGGATCAAAGAAGCACTGACTGTTAACGAGACA[C/T]TGGTACAGAATGAAATATAACAACGTTCAGGACTT Y 2 1 2 1 101000 f 74 goat snp26077-scaffold271-713434 10 14534676 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775745 Affx-122943240 AX-385262876 10 84690201 AGATGCCAAATGAGTCATAATATAGATGGGTAAAG[C/T]GGTCCTGAAAAGTAGTACTGTTTGAGAGGTACTGG Y 2 1 2 1 101000 r 74 goat snp26078-scaffold271-758543 10 14489459 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403164 Affx-122958088 AX-123273517 10 84727736 CGGGCTACAGTCCGTGGGTCACAAAGAGTCAGACA[C/T]GACTGAGCACACATGCTGGTCCCCAAGGAGAGCCT Y 2 1 2 1 303000 f 74 goat snp26079-scaffold271-796078 10 14452120 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432347 Affx-122936278 AX-123302688 10 84773884 AAGCGACAAAGCTGTGCACAAGGAACTCCGGAACT[A/G]TGGTGGAAAAAGCAGACACTGAGTGGGCTCCAGGC R 2 1 2 1 101000 f 74 goat snp26080-scaffold271-842226 10 14405899 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428406 Affx-122938942 AX-123298749 10 84809371 TACTCTGCACCCTCAACAGCACAGCCACCACAGGG[C/T]ACAGGGTAAATGCTTGAGAAACGTGTGATAAATGA Y 2 1 2 1 101000 r 74 goat snp26081-scaffold271-877713 10 14370727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386348 Affx-122970865 AX-123256706 10 84838220 TTTCATGTGATTTGATGTATATTTATCATTTAAAA[C/T]GCAACGAAAACAGGAAAACACATTCACAAACTTAG Y 2 1 2 1 201000 f 74 goat snp26082-scaffold271-906562 10 14341770 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383722 Affx-122972466 AX-123254080 10 84889809 AAATAAGGGATTATAAACAAGTTCCTAGGATGCTA[C/T]ACAAGAGGCTCCCCATGCTATTAGGAGACTGACTA Y 2 1 2 1 101000 r 74 goat snp26083-scaffold271-958151 10 14289519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402424 Affx-122958634 AX-123272777 10 84919430 CAGTTTCTGTCAGGGGAAAACCTTTATGTAAGTGT[C/T]AGCATTTCTCTCAGCAATCTCGTTCTACAGCACTG Y 2 1 2 1 101000 f 74 goat snp2566-scaffold1076-2208 10 14259699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399016 Affx-122960933 AX-123269371 10 84968104 ACACCAGAATTAATAAAGAACAGAGTATAGTTGAA[C/T]AAAAACCAACCAAACAAAAAACACCTGGGAATATG Y 2 1 2 1 101000 f 74 goat snp2567-scaffold1076-50882 10 14210305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415960 Affx-122948425 AX-123286309 10 85009311 GGAGAGGGTGTAACCTTTCAGACATTCCCTGGTGA[C/T]GCAGCCCCCTTCAGCCCATCAGTGTTCCAGAGAAG Y 2 1 2 1 101000 f 74 goat snp2568-scaffold1076-92089 10 14169558 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777090 Affx-122950822 AX-385264213 10 85053721 ATCATTCCCACTCACTTCTTTATATCCCACTATTT[A/G]TGTATTGGTATGACCTTTTGCATTTTATTGACTCT R 2 1 2 1 201000 r 74 goat snp2569-scaffold1076-136499 10 14124049 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393169 Affx-122965528 AX-123263526 10 85140639 GGACAGCATCGGAGTTGGCCTTCCTGGATTCTTGC[A/G]CCGGCTCTGCTGCTTGAGAACTCTGTCGCTTTGGG R 2 1 2 1 101000 f 74 goat snp2571-scaffold1076-223417 10 14037119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403533 Affx-122957612 AX-123273886 10 85179729 TCTAATGCTTACCATCTTTGCTGTTCCTTGGGCTC[A/G]TGTCACCTGATTGCGTTATCTTTCTACTCCATGGC R 2 1 2 1 201000 r 74 goat snp2572-scaffold1076-262507 10 13998337 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392499 Affx-122966131 AX-123262856 10 85209327 CTTGTCTGCTATCACTTTATCAAAATTTGGGTAGC[A/G]TGACTTCTCCAGTCTTACTCTTCATTTTCCAAAAT R 2 1 2 1 201000 r 74 goat snp2573-scaffold1076-292105 10 13968512 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416874 Affx-122948085 AX-123287222 10 85246787 CTTCAATTTCTTATTTTCCTGCAGATTGTTCCCTA[C/T]AGATTGACCTTAGTCTTTAAAGACAGAACCTGCAC Y 2 1 2 1 101000 r 74 goat snp2574-scaffold1076-329565 10 13930657 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463116117 Affx-1109821822 AX-514603289 10 85300153 CTTCTTTCTGGTCACGGGAAATCATCTCAAGGTCA[A/G]TGCTGTTGCAGAGCCAGGCTTTCCAGAGCTTGCTA R 2 1 2 1 101000 f 74 goat Random2.2K-1113 10 85300153 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38423267 Affx-122942664 AX-123293613 10 85302012 AGGCCAAAAGGATTTCAAATGCTGCAAAGAAGGTG[C/T]CCTGCCTGCCAATGATAAGGCTGGAAGCTGGCGTT Y 2 1 2 1 101000 f 74 goat snp2575-scaffold1076-384790 10 13875375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437586 Affx-122931870 AX-123307924 10 85359460 AGAGTGCATGAACAGTATTTGTGCTTTGCTCATGC[A/G]TTCTCTGTGGGGTTGTGTATGTCGTTTAGCTTCAT R 2 1 2 1 201000 f 74 goat snp2576-scaffold1076-442238 10 13819587 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424937 Affx-122941282 AX-123295283 10 85391793 CTCTGAGTTGGCTTTGGGGGGAACCCTAGCTTTGG[C/T]GCAGGAGAGCTGCATGTGAATATTAGCTTTGTCGT Y 2 1 2 1 101000 r 74 goat snp2577-scaffold1076-474571 10 13786911 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396925 Affx-122963199 AX-123267280 10 85501047 TGCCGTCTCAGTGGGACAGTACTGTCCCTGCCACG[A/C]GTGTGGTATGGATATTTGCTCTGCCAGTGATGAGG M 2 1 2 1 101000 r 74 goat snp2579-scaffold1076-583825 10 13678792 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442544 Affx-122928528 AX-123312881 10 85537595 GGCTGTGGTCCCCTCTCCACACTTGCCACCCATGA[C/T]TATTACATTCTAGAAATGTGGTATTAGCCAATCAA Y 2 1 2 1 101000 r 74 goat snp2580-scaffold1076-620373 10 13642433 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789465 Affx-122945901 AX-385276475 10 85569040 AAGGAGGGCTATGGTTATTATCGATAATCCTAGTC[A/G]TTACAGAATGAATGAGTAAAACCACACTTAGGATG R 2 1 2 1 101000 r 74 goat snp2581-scaffold1076-651818 10 13610979 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438199 Affx-122931821 AX-123308537 10 85605970 GCCTTTCCACATGGAAAAGGTGCTTTGTTTTGGAT[A/G]CTAATGTAAGCTCCATGCAGATGTTTAGATCAGTG R 2 1 2 1 101000 r 74 goat snp2582-scaffold1076-688748 10 13574515 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431621 Affx-122936151 AX-123301962 10 85656278 CTTGACCAGACACCCGAAGGTTGTACTCACTTGGT[A/G]CTGACCTTGTAAAGACAGATTGCAACTTTAGGGAG R 2 1 2 1 201000 r 74 goat snp2583-scaffold1076-739056 10 13523095 C T 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426177 Affx-122940586 AX-123296523 10 85696954 TCCTGGCAGAACTTTAATCATTTGGGTTTTGGGCT[A/G]CCTCCCTGACTTTCCTCTAGTTTATTTTTGGCCTC R 2 1 2 1 101000 f 74 goat snp2584-scaffold1076-779732 10 13486759 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272648 Affx-1111832903 AX-519546358 10 85724486 CATAAAAAATTTCTTTTAAAGAAAACGCCAAATAT[A/G]TACAAAAGTGGAAAGAAAAGCACCATGAACCTCCA R 2 1 2 1 102000 r 74 goat 10_85724486_AF-PAKI 10 85724486 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423530 Affx-122942443 AX-123293876 10 85738214 ACTCTGTCTTTCACAGAAACTCGGTAATCCCTTAT[C/T]CCTTTTCTAACTCAGAAAAGTTCACCCCTTCTGGT Y 2 1 2 1 101000 f 74 goat snp2585-scaffold1076-820992 10 13445438 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399791 Affx-122960291 AX-123270146 10 85846531 TGGCATGAGCTACTAGTTTTTTGCTCTTCCCATGT[A/G]CTGGTCTGGATTGATTGGGAATTTAAGGATAAGCA R 2 1 2 1 101000 f 74 goat snp2587-scaffold1076-929309 10 13337487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788300 Affx-122956326 AX-385275318 10 85878038 TCGCTAACATATAAGGGCTTGAAATGTTTGAGTTG[C/T]AGAGACTAGACCAAAAAGTGAAATAGGACCTATTG Y 2 1 2 1 101000 r 74 goat snp2588-scaffold1076-960816 10 13306138 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432436 Affx-122935816 AX-123302777 10 85922153 TTGACCATTCAGCCTTGAGAATCCACTGCATCCCT[A/G]CAGATTCCTCTTCTAACATAGCTGCACATATATAT R 2 1 2 1 201000 r 74 goat snp2589-scaffold1076-1004931 10 13262637 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430521 Affx-122937211 AX-123300862 10 85952691 AGCATCTGAATTTTGCATTTATTTCCTGATTTTCC[A/G]TTTAGGTAGTATCATACTCAAGAAATGTCTCGGCT R 2 1 2 1 102000 r 74 goat snp2590-scaffold1076-1035469 10 13232255 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772837 Affx-122957804 AX-385259982 10 85985452 AAGACTCATTAAATTGATGAGGCTTAATAACTTGT[A/C]TTGTCTCCAAAGAGAAAATTTCCTAGCTAGAATTT M 2 1 2 1 101000 r 74 goat snp2591-scaffold1076-1068230 10 13199564 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450623 Affx-122921999 AX-123320957 10 86078758 AAACAGCCTTGCGAACAGAGTGTACTGAGCAGCCT[A/G]CAGGGCTGGCATCCCCCTGTCCCCTCCACCTTCCC R 2 1 2 1 101000 f 74 goat snp2593-scaffold1076-1161536 10 13106673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781999 Affx-122941886 AX-385269079 10 86108424 GAGGAAATACGTATATTAAGTAATATTCATCCAAT[A/G]TTTATTGAGTTCCTATATTTCTAAGTGCTGATAAG R 2 1 2 1 201000 f 74 goat snp2594-scaffold1076-1191202 10 13077085 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392114 Affx-122966350 AX-123262471 10 86140253 CTACTAATGCATCTCTCTGGATAATAATATACTTG[C/T]GATTTGCATAGAGGGCCCCAGACCTCAGCTAAACT Y 2 1 2 1 201000 f 74 goat snp2595-scaffold1076-1223031 10 13045513 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437736 Affx-122931730 AX-123308074 10 86212464 AGTGGAAAGTAGTGCTTGAACTTAGCAACTGAGTT[A/G]TGACCGGGAGAGGCCAGCAAGGAGTATATACTCGT R 2 1 2 1 101000 f 74 goat snp2596-scaffold1076-1295242 10 12973471 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274319 Affx-1111834184 AX-519547915 10 86226665 GCATCTCAGCTCCCTGCAGCGCCTTTCTCACTCCC[A/G]CCTCCAGGCCTTTGATGCTGCACTCTCGCCGCTTT R 2 1 2 1 202000 f 74 goat GoatD01.024215 10 86226665 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382190 Affx-122974011 AX-123252548 10 86248145 TAAGGATGCTATGACAAAACAGGGTCAGTTTTCCC[A/G]TTTGCATCTCGTCTTGTGATTTTTTTCACAGGTAC R 2 1 2 1 101000 f 74 goat snp2597-scaffold1076-1330923 10 12937798 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777239 Affx-122920202 AX-385264362 10 86284161 TTTGAAAAGTTCAGGATTGCAGCTTAAATTAAAAA[C/T]GCGAACCTTCCATTGAAGCAAAATGTCACCAGGGA Y 2 1 2 1 102000 r 74 goat snp2598-scaffold1076-1366939 10 12901799 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427850 Affx-122939724 AX-123298193 10 86313552 CAGACCTATGGAAGTGTTTGAGATTTGTGTATCTT[A/C]TAATTCAGATAAGAAAGGGAACCTCTGGATTTTTG M 2 1 2 1 101000 f 74 goat snp2599-scaffold1076-1396330 10 12872472 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411294 Affx-122952297 AX-123281644 10 86349867 TGCATAGGAGTTGAGCACTGGTCTATATACACTGA[C/T]AATCCTTCTCAAATGAATAAATCAGATCTTCCTTG Y 2 1 2 1 101000 f 74 goat snp2600-scaffold1076-1432645 10 12836228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382266 Affx-122973938 AX-123252624 10 86386176 AGTATATTTTGTGTTTTTGAAATAATCACAAAATC[A/G]TATCTGAGTACTGCCTTGAGTCAAGCTTCTGAACT R 2 1 2 1 101000 r 74 goat snp2601-scaffold1076-1468954 10 12800009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802197 Affx-122952457 AX-385289101 10 86430640 TTCAGTTAAATTCAGACGACAGTTATTGAGTGGCC[A/G]CTGGATACGAGTTCTAGGCTGAGACGATTGTGATG R 2 1 2 1 101000 r 74 goat snp2602-scaffold1076-1513418 10 12755635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778839 Affx-122963296 AX-385265947 10 86469558 TAGAGTTGTTGTTCAGAAAAACACATCATATGTAA[G/T]CATAAGATTTCTAAGACTATTGCAACATTTGACCA K 2 1 2 1 101000 r 74 goat snp2603-scaffold1076-1552336 NW_017214847.1 15406 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798560 Affx-122930228 AX-385285493 10 86502848 TCTGGTTTATTCAAAACCTATTCTGATTCTTATTT[A/G]CTTTTCAATTTTTATTGACATGTAGCTGGTTTACA R 2 1 2 1 201000 r 74 goat snp2604-scaffold1076-1585626 10 12702267 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770126 Affx-122965342 AX-385257293 10 86592647 AACTAGATTAAGATGTACATGATCTCTGATAGCCA[A/G]TGTAAGCTTAGAGAAGACCTATGGGAGTTTAAATG R 2 1 2 1 101000 r 74 goat snp2606-scaffold1076-1675425 10 12612742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775644 Affx-122965660 AX-385262775 10 86635650 GGGTACTTTGTCTGTTGTGATACATATGCTAAATC[A/G]CATTTTTAAAGGAGGGATTAGTTGTGCTTTAATAG R 2 1 2 1 101000 f 74 goat snp2607-scaffold1076-1718428 10 12569779 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771461 Affx-122961496 AX-385258619 10 86671490 GACTTGTACATATATGTTATGATTCTACCTATCAG[C/T]TCTCTGGTATTTTGCCTTTCTATCCTCCTTTCTGG Y 2 1 2 1 101000 r 74 goat snp2608-scaffold1076-1754268 10 12533916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422202 Affx-122943499 AX-123292548 10 86733601 AGGGGCTAAAACTATGAGCAATAAATAACCATCCA[C/T]ACTCACTGAAGGAAGTACTCCTTAGATAAGAGAAT Y 2 1 2 1 201000 f 74 goat snp2609-scaffold1076-1816379 10 12471770 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386957 Affx-122969976 AX-123257315 10 86785774 AAGGATTTACCAGTTCACAATAAAGAATACAAATG[C/T]GAATAAGGTTGATGAAAGAGTAATAAAATAGAAAT Y 2 1 2 1 101000 f 74 goat snp2610-scaffold1076-1868552 10 12419184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432450 Affx-122935807 AX-123302791 10 86820964 AGATTAGCTGAGCCATGAGAAAGGGCTTATAAAGT[A/G]TAAAATGCAAACCCAAGCAATAATAATATGCTAGT R 2 1 2 1 101000 f 74 goat snp2611-scaffold1076-1903742 10 12384096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405631 Affx-122956595 AX-123275983 10 86860878 CCAATGTATATTATAGATACGTTTTCTTAAACATG[A/C]TGTGCCTTTGTGTGGTGGAAAAGGTGGCAGAATTT M 2 1 2 1 201000 f 74 goat snp2612-scaffold1076-1943656 10 12344246 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442666 Affx-122927901 AX-123313003 10 86902566 AATTCAAGTTCCCTTCCAACCTTCTTCCCTCCCCC[A/G]CAAGAGTTATCTCCAGGTGACCTCTGAGTTTTCCA R 2 1 2 1 101000 r 74 goat snp2613-scaffold1076-1985344 10 12302280 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443245 Affx-122927553 AX-123313582 10 86933911 TCCCCCAGACAGATCATAAATACCACACTCCTAAC[C/T]GAAAGCAGAGCAAACAAAATCTTACCCTTATGGGT Y 2 1 2 1 101000 f 74 goat snp2614-scaffold1076-2016689 10 12271419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411804 Affx-122951257 AX-123282154 10 86963367 CCTCTCGGAAACTTCTCAGGGTTTCCTTTGCCCTG[A/C]GGGTGGGTCTGAACACACCTCCTTGTGTCCAGCTG M 2 1 2 1 201000 f 74 goat snp2615-scaffold1076-2046145 10 12241886 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389268 Affx-122969019 AX-123259626 10 87006978 TGTGCCAGCAGAGTTTATTTTCATGGCAGCTGAGC[A/G]TGATGGATTCAAGCCTGGGCAACTGTATGGGTATT R 2 1 2 1 201000 r 74 goat snp2616-scaffold1076-2089756 10 12199760 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412770 Affx-122950508 AX-123283119 10 87037799 AATACAAGATATTAATTCTTTGTTGAGGTCTATCC[A/G]TCACTTACAAGTAGCTGAATATTCTAGATGCCCTT R 2 1 2 1 101000 r 74 goat snp2617-scaffold1076-2120577 10 12168990 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396785 Affx-122962759 AX-123267140 10 87078661 CTTCTTTCTCCATTTGCAGTGTTTTGGAGAAAATT[A/G]TAAATACTTTACATAAAGTACCTAGCACGGTGTCT R 2 1 2 1 201000 f 74 goat snp2618-scaffold1076-2161439 10 12128390 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388136 Affx-122969473 AX-123258494 10 87132112 CTTTAAATAAATTCACTCTGCGATGCTACTTCCTG[A/C]GTAGAGATTTTAGCTTGTCTCTGAGTCTTTGGAAC M 2 1 2 1 101000 r 74 goat snp2619-scaffold1076-2214890 10 12074940 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783514 Affx-122956577 AX-385270577 10 87162087 CAGAGTGATTCTCAAATGTATTTTTACTCCTCAAA[G/T]CTACAATCCTCACGTTTGCATTTGGTGTTATTGCT K 2 1 2 1 101000 r 74 goat snp2620-scaffold1076-2244865 10 12044973 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799442 Affx-122976632 AX-385286372 10 87213961 GATGGATTACAGGTTTTGTAATACTCTGCCAGCAG[A/C]TCCTGATGACTTTAAGCTTGTTGCTTCTGTGAATC M 2 1 2 1 101000 f 74 goat snp2621-scaffold1076-2296739 10 11992703 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445642 Affx-122925082 AX-123315979 10 87247175 AATCCCAATTTGGGGCAACTCATTCTACAGTTTTA[C/T]GACTTGGCGACAGTATCTCATGAATAACAATGAAA Y 2 1 2 1 101000 f 74 goat snp2622-scaffold1076-2329953 10 11960528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443492 Affx-122927806 AX-123313829 10 87286294 AATAAAACTCCAACACGAAACGATCAACTTTCCTC[G/T]CCTCAATAACTGGCAATATGTAGGGGATTTTGCAG K 2 1 2 1 201000 f 74 goat snp2623-scaffold1076-2369072 10 11921394 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791489 Affx-122935462 AX-385278480 10 87318038 GTTTTCCTTTTGTCATAGGCTCAAATGCTTGCCTC[A/G]TTACATACCTGGTCCCTAAAGGTATTTGAACTGAC R 2 1 2 1 101000 f 74 goat snp2624-scaffold1076-2400816 10 11889927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274648 Affx-1111834342 AX-519548234 10 87332244 G[A/G]GGAGGAAGGAAGTGAGAAGACTAAGGTGTGGGGAC R 2 1 2 1 103000 r 74 goat GoatD01.030728 10 87332244 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38388555 Affx-122969181 AX-123258913 10 87361129 GCAAAAGTAGCATAATATAAAATACTGTTTCAACC[A/G]TATTTGACTGTACATACTGTTCAGTAGCTCTAAAT R 2 1 2 1 101000 r 74 goat snp2625-scaffold1076-2443907 10 11847276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396368 Affx-122963038 AX-123266723 10 87415850 TAGAAGAGGGTCAAGCACATAGTTATTCAATAAAT[A/G]CTTGCCTAGTTAGTTAATTAATCTTGAGGGTAATA R 2 1 2 1 101000 r 74 goat snp2626-scaffold1076-2498628 10 11791209 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788555 Affx-122931044 AX-385275572 10 87518421 TCAAAACTTATTACTAATTGCTAAAGAAAGGCTTT[A/G]TTCTTGGTTGGAGAAATTTCAGAAATCCTGGAGAG R 2 1 2 1 101000 r 74 goat snp2628-scaffold1076-2601199 10 11689244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765189 Affx-122922396 AX-385252736 10 87553030 TCCCTTGATATTTTATCCTGCATATTGTTTCCTTG[A/C]ATATCCACTATTCCTTGATATATTAAAGTATTTGA M 2 1 2 1 101000 f 74 goat snp2629-scaffold1076-2635808 10 11654458 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413620 Affx-122950555 AX-123283969 10 87591074 TCTCCATTTCCATGAAACAAACAAATGAATGAAAA[C/T]ATACACTTTCACCTTTTGTAGAATTTGACTATTAA Y 2 1 2 1 201000 r 74 goat snp2630-scaffold1076-2673852 10 11616638 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407698 Affx-122954574 AX-123278049 10 87625386 CAGACATTTCACTGGCCAGAACAAATTGGAATGTT[A/G]TACTCAGTTCTGGCTGCGTGTCTAGGGGAAGGTAG R 2 1 2 1 102000 f 74 goat snp2631-scaffold1076-2708164 10 11582322 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420490 Affx-122944862 AX-123290837 10 87669448 ACTTAGAGTGTTCTTTGTGCTTTCAAGTGTCTCCC[C/T]CTCACACATTCGGTGTTATTTAAAATTACACAGGC Y 2 1 2 1 201000 r 74 goat snp2632-scaffold1076-2752226 10 11537370 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399953 Affx-122960841 AX-123270308 10 87734205 TTTACCACGGTGCTTTGATTTCAGTCTTGAGCTTG[C/T]GTTCAAATTCTGCCAATTACAAGCCGCATGACTTT Y 2 1 2 1 201000 r 74 goat snp2633-scaffold1076-2816983 10 11471404 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409764 Affx-122952994 AX-123280115 10 87776447 ACTATTCAAGAAATATTTATTGGGTACCTACCAAG[C/T]GCTAGGCATTGTTTGTGTTCTTTGGGTTCAGCAGT Y 2 1 2 1 101000 r 74 goat snp2634-scaffold1076-2859225 10 11429227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425581 Affx-122941420 AX-123295927 10 87815620 GACTGTGAGTAGACAGTGTGAGTATACGTTTCTAG[C/T]AGACAGATTGGACATTATTGGTTTTCCCTGAGATT Y 2 1 2 1 101000 f 74 goat snp2635-scaffold1076-2898398 10 11389956 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415575 Affx-122948632 AX-123285924 10 87845840 GATCCCCATCCACATAAGTGGCTGAAAAGAAGGAC[A/C]AAAAAAAGCACTTTTCATGGACTTCAAGGAACATA M 2 1 2 1 101000 f 74 goat snp2636-scaffold1076-2928618 10 11359818 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773476 Affx-122964992 AX-385260618 10 87883505 CATGCACACCTGTTTTTGGGTCTCGTTTTCCTTTG[C/T]AATCCCGTGATTAGCCTATAGCAACAACTCAGCAA Y 2 1 2 1 101000 f 74 goat snp2637-scaffold1076-2966283 10 11322940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415906 Affx-122948464 AX-123286255 10 87942865 TTATGTGCCTGTAGAGTAGCTTGAAGCACAGTTAG[C/T]GCTGGACCCATACTGTGAAGGCTTCCCAGGTGGCG Y 2 1 2 1 101000 f 74 goat snp2638-scaffold1076-3025643 10 11263544 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428459 Affx-122938802 AX-123298802 10 87994086 ATGGGGGAACACAGGTGAGATCTCTGGACAGCTGA[C/T]GTTACACAATTCTGTGACAATAGACTGTGCTGTGA Y 2 1 2 1 101000 r 74 goat snp2639-scaffold1076-3076864 10 11211870 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390348 Affx-122967688 AX-123260705 10 88022671 AATTAGAATGTCAGAGCCGCAAGGACATTTATAGA[C/T]ACTAAAGTTCAAAAACAAAAAATCAGAGAGCTGAA Y 2 1 2 1 201000 f 74 goat snp2640-scaffold1076-3105449 10 11183352 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425745 Affx-122940745 AX-123296091 10 88089905 GCAGGCAACACCACCCGAGATGAAACGTGGCAGAC[A/G]AGCTACACCAGCGACTGACTCTAGCCTTGAAATGT R 2 1 2 1 101000 r 74 goat snp2641-scaffold1076-3172683 10 11115927 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421001 Affx-122944559 AX-123291348 10 88126504 TAGTTTCAAAGCATGTATTCTTACCTAGGAAAACT[A/G]CCACACACAGGAGCACTGAGCTATCAGAATATTAA R 2 1 2 1 101000 r 74 goat snp2642-scaffold1076-3209282 10 11079432 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802549 Affx-122940804 AX-385289453 10 88167452 CTGGGGGGAAAGACAATCAGGACGAAGAGCAGGCA[A/G]TGAGAAGTCGGTGTAGGAAATGGTTTTCCGTTTGT R 2 1 2 1 101000 r 74 goat snp2643-scaffold1076-3250230 10 11037239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776352 Affx-122942555 AX-385263479 10 88221821 ATCACGTTCTACATAGCTAACACTTGTAAGGAAGG[C/T]GAGTCAGTAGAGTCAGCAGTCATGCGATGCCAGGG Y 2 1 2 1 201000 r 74 goat snp2644-scaffold1076-3304599 10 10983087 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423343 Affx-122943162 AX-123293689 10 88261699 GTTATGGTAACAAGAGGGTAAAGCAGAGGGTAAAG[C/T]AAATGGCCACGCGAAAGTTTTGGAATTCAGCCTTG Y 2 1 2 1 101000 f 74 goat snp2645-scaffold1076-3344477 10 10942399 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276430 Affx-1111835414 AX-519549954 10 88299888 TTGCTCTTAAAGCTAGATGAAGACACATTTTTATT[A/G]GATCAAATGTGCTATTCTGTAACTTGCTTTTTAAA R 2 1 2 1 101000 f 74 goat Random2.2K-1117 10 88299888 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392815 Affx-122965790 AX-123263172 10 88312272 TCAAATTTTTCCAAAATTCATATGCCAGATGCTAA[C/T]AGTCTATTATTCCCAAAGGGAAATTTGAATCAGAG Y 2 1 2 1 101000 r 74 goat snp2646-scaffold1076-3395050 10 10891256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429500 Affx-122937863 AX-123299842 10 88349291 AATTCAGAACAGCCTTAAGCTTTCCCCAAATGCAC[A/G]TGGAAGCATAATAATAACTCCATTTGTTGGCTAAC R 2 1 2 1 201000 r 74 goat snp2647-scaffold1076-3432069 10 10853907 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413943 Affx-122950723 AX-123284292 10 88379929 TATAGCAGGGAAAGGGTCCAATGTAACCAAACTGG[C/T]AGCAAATGGCTGGCTGTTTTCTGAGCAAATTTGCC Y 2 1 2 1 101000 f 74 goat snp2648-scaffold1076-3462707 10 10823181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378026 Affx-122977581 AX-123248385 10 88416469 ATTGCTCATTTTTCATATCAATTTTCTATTTCCTG[C/T]GTCAGCTTAAAAGTATTCACTTTAATAGATTCTTG Y 2 1 2 1 101000 r 74 goat snp2649-scaffold1076-3499247 10 10786314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271756 Affx-1111832904 AX-519545550 10 88440156 AGAATACCTGGCATATTAGTCATCCTTCAACAAGT[A/C]TTAGCTATTTTCATCACCACTGTTGTGGATGTTGC M 2 1 2 1 101000 r 74 goat 10_88440156_AF-PAKI 10 88440156 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320782027 Affx-122968118 AX-385269105 10 88457789 ATTCTATCATTAGTGAGACAGTTGCACTGAGATAC[A/G]TAATTCTTATAATTGTATTCATATGGATGGCTTTC R 2 1 2 1 101000 f 74 goat snp2650-scaffold1076-3540567 10 10744283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405511 Affx-122955997 AX-123275863 10 88503520 TTTCTACTGATTAGAGCAGGCCGATTTTCACTTGC[A/G]GCAGTCAGAGATGAGGAGGAAAAACTGAGATGAAC R 2 1 2 1 201000 f 74 goat snp2651-scaffold1076-3586298 10 10697705 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408850 Affx-122954009 AX-123279201 10 88536128 AGTTCCTGGAGGGGTCATTGCTCCTGGATCTATGT[C/T]CAAAGACTCCAGAGACCTGAAGATAAGAGGTAGAG Y 2 1 2 1 101000 r 74 goat snp2652-scaffold1076-3618906 10 10664436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797424 Affx-122920663 AX-385284363 10 88592233 AGCAGTTCTCCCAAGCAACTCGTTCACGCTGAACA[C/T]ACAGCACTACCACATTGTTCTTTAGAGCCCCTTAC Y 2 1 2 1 101000 r 74 goat snp2653-scaffold1076-3675011 10 10607644 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415054 Affx-122949483 AX-123285403 10 88645154 ACTACCACCTGTAAAGTAGTCTTACTCATACTCCT[A/G]CCACCCCAAAATATAAACCCTGAATGTGATCAAGC R 2 1 2 1 102000 f 74 goat snp2654-scaffold1076-3727932 10 10554651 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413833 Affx-122949881 AX-123284182 10 88689742 GCTCTCGATGTACATTTTCCAGCAATGGCAACAAC[A/G]GCAAAATAACCAAACAGCTCCTTTATGCAGTAAGT R 2 1 2 1 101000 f 74 goat snp2655-scaffold1076-3772520 10 10510347 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438208 Affx-122931455 AX-123308546 10 88719700 GCAGTGTGGCGATGTGATAAATCAATCTGAAGTGA[C/T]AGTTAAAGTCTAGAGACTTCATCTATCAGCCCAGC Y 2 1 2 1 101000 f 74 goat snp2656-scaffold1076-3802478 10 10480557 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449865 Affx-122922365 AX-123320200 10 88786533 TCCCACCTCCACAGAGCTCAGTTAAATGTTCATCC[A/G]TGGAAACAGACGGAATTAGTAATGAATGTCTGAGC R 2 1 2 1 101000 r 74 goat snp2657-scaffold1076-3869311 10 10414495 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797092 Affx-122961476 AX-385284032 10 88871016 GCTAAAGGAGAAATTAGGTGGATGGCAGAAAAACA[C/T]GGAAGTTTAGTTGTTAAACGTTTACATAAACTGAA Y 2 1 2 1 101000 f 74 goat snp2658-scaffold1076-3953794 10 10330133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381646 Affx-122974757 AX-123252004 10 88908120 CAATTTTATGTTAGTTGCTACAAGAAGACTGCTTT[C/T]ATCCAAGGTTGAGAATTGCTAACTACAGTTGAGAA Y 2 1 2 1 101000 f 74 goat snp2659-scaffold1076-3990898 10 10292910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432000 Affx-122935932 AX-123302341 10 88963920 GTCTTCCTCACTCATTCTCCGTTGAGGCTGGCCTT[A/G]CTACCTGAGTGCCCTTTTGCATCCACAGTTCTTTT R 2 1 2 1 201000 f 74 goat snp2660-scaffold1076-4046698 10 10236984 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429549 Affx-122937824 AX-123299891 10 89046646 ATTGCATTTACTGCCCATTCAAGAGACACGGGTGA[C/T]GAAGGTTCGATCCCTGGGGTGGGGAAGAAACCCTG Y 2 1 2 1 101000 f 74 goat snp2661-scaffold1076-4129424 10 10152821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779454 Affx-122954382 AX-385266557 10 89076679 GCTTTAGTAAGAACTTAACACTACTTATCTCTTTC[A/G]TGTATAAGTATGTAACAGAGAGACAAATCCTTGTG R 2 1 2 1 201000 r 74 goat snp2662-scaffold1076-4159457 10 10123591 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426714 Affx-122939887 AX-123297060 10 89119484 TAGGTGTTTGATAATGTTCTGAAACAGTTTCTCAC[C/T]TCTAGACCAGCTACTTTCAGACTTACTGTCCTGTG Y 2 1 2 1 101000 f 74 goat snp2663-scaffold1076-4202262 10 10079810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394650 Affx-122964384 AX-123265005 10 89159936 TGCCTCTAGAGATGTCAACCGGTTGACCAAGGAAT[A/G]TTGTTTTATATCTAGTTAGAGAGATCAGGCATTAA R 2 1 2 1 101000 f 74 goat snp2664-scaffold1076-4242714 10 10039036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440117 Affx-122929703 AX-123310454 10 89232772 CAAGCAGATTGTCCTGATGGGTCATCATAGATGGT[A/G]CTGGGGTATGAATGTGGATTAAGTGGAAATGCAAG R 2 1 2 1 101000 f 74 goat snp38171-scaffold478-704449 10 9964798 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384447 Affx-122973098 AX-123254805 10 89289616 TATCACTACCTAAATATATGCAAGGATTGGAGAAT[A/G]CATTCTAAGTTTGGAAAGCTTAAAATTGAAAAGCT R 2 1 2 1 101000 f 74 goat snp38170-scaffold478-647605 10 9907042 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434597 Affx-122934102 AX-123304938 10 89389682 TATTTGATCATATCTAGGATCTGTATTTTTTACAG[C/T]TCTGTAGTTTGTTATTCCTATTGACTCATAGAAGC Y 2 1 2 1 101000 r 74 goat snp38168-scaffold478-547539 10 9806976 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405082 Affx-122957404 AX-123275434 10 89421231 AGAGACTAGAGCAAGTGTGTAGCAGTCATTAGCAC[A/G]TGCTTTACAGACCTCGTGCCTGGGAAGTGAACTTG R 2 1 2 1 101000 f 74 goat snp38167-scaffold478-515990 10 9776209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273678 Affx-1111833736 AX-519547291 10 89444401 TCTTTCCTCCACTCTTCCTCACCAGAAGAAGAAAT[A/C]GTTTCTTTCCTATCCCCCTAGTACTTAATTCTGCA M 2 1 2 1 101000 r 74 goat GoatD01.003127 10 89444401 T G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38451688 Affx-122921574 AX-123322021 10 89454033 TGTGTCTCAGGACGACAGACTCAGTCCCCATTCAG[C/T]AGCCTATTCTTACACCGACTACAGTCTTTCACTTT Y 2 1 2 1 101000 r 74 goat snp38166-scaffold478-483188 10 9740656 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446994 Affx-122924637 AX-123317330 10 89483530 TGTTTTTTAACCAGAGGTTGGCAGTTAATGAGAAG[C/T]ACATCATGCTGTACCTAACTCCCCTCTCTTTCAGG Y 2 1 2 1 101000 f 74 goat snp38165-scaffold478-453691 10 9711239 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769068 Affx-122978797 AX-385256243 10 89520052 AGAACAAATAGGTGCTTTGGGCATAGATATTTGCT[A/G]CTCACCAAAAATCCATGTGTTACCCTCATAGATCC R 2 1 2 1 101000 r 74 goat snp38164-scaffold478-417169 10 9674528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765617 Affx-122941598 AX-385253093 10 89579592 AAGATGGAGCCAAAGAGCCACATGCCAAGGAAAGT[A/G]GGTCATCTCTATAAACTGGAAAAAGTAAGAAAACC R 2 1 2 1 101000 f 74 goat snp38163-scaffold478-357629 10 9613355 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785115 Affx-122971613 AX-385272161 10 89636299 CCCACCAAAATATTTTTAAGAGTGTATTGAAAAAT[A/G]TTTCATTATATTCTAACTAAGGCAGTGATTTACAT R 2 1 2 1 201000 f 74 goat snp38162-scaffold478-300922 10 9555952 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416180 Affx-122948258 AX-123286529 10 89672445 TAAAAAAGCATTTTGGCATGATAATGCATTGTGAT[A/G]AGAACCAAAAGAAGGGCATGGAACCCAAAGCAAAG R 2 1 2 1 201000 f 74 goat snp38161-scaffold478-264776 10 9519525 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393119 Affx-122965567 AX-123263476 10 89728243 TTTTCTTCTGCTCATTGGGGTGGGCTTGAAGAAGA[C/T]GAACTAAAGCAGTAAGAAAGAGCTGTGGTCTGGTG Y 2 1 2 1 201000 f 74 goat snp38160-scaffold478-208978 10 9461554 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375944 Affx-122978454 AX-123246303 10 89778411 TGCAAAGCACAGGACATGACTGAGCAACTAAAGAG[C/T]AACAACAGCTAGCTCTCTACCTCTCACTTACCCTC Y 2 1 2 1 101000 r 74 goat snp38159-scaffold478-158810 10 9412264 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785570 Affx-122948589 AX-385272614 10 89809825 CAATGAAGTGGAATGTGGAATATACAAATAGATTC[A/G]TACTATATATCACACTTGAATTACAAAACTGTTAT R 2 1 2 1 101000 f 74 goat snp38158-scaffold478-127396 10 9380760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430040 Affx-122937570 AX-123300381 10 89862634 ATCTGCTACGCTGATTCCTTTTTATCTAATCCTGA[C/T]GTACCCTTTTCTTTCTTTGTTCATATGTTAATTAG Y 2 1 2 1 101000 f 74 goat snp38157-scaffold478-74587 10 9327390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375671 Affx-122978672 AX-123246030 10 89906817 TCCAGTTAGGGTGTGGAAATTCTTGGGAAGAAAAA[C/T]GTATTCCTTCACCTTTCAAGGTTTTTCTGACTGGT Y 2 1 2 1 101000 f 74 goat snp38156-scaffold478-30404 10 9281978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399386 Affx-122961326 AX-123269741 10 89936063 TTCACTAAAAAGAATAGCAAAGTTATAGTGCTTTT[A/C]TTTTTAAGTGTCTAGCAGAATATCTGATATCAAAT M 2 1 2 1 101000 r 74 goat snp38155-scaffold478-1158 10 9252872 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788171 Affx-122952364 AX-385275190 10 89963578 TCTGTTGATTAAATACACCACTAAGACTAACCGAC[A/G]TTGAAGATGAGTCAAAATAGATGTCTCTTCTGTGG R 2 1 2 1 101000 r 74 goat snp57088-scaffold908-899123 10 9225609 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762833 Affx-986697362 AX-385250862 10 90026961 GCTACTGAACACACTGTTCAGAGCAAGAATAGATA[G/T]ACATCTAGATACATCTGAATCAAGTTCCTGGACAC K 2 1 2 1 600010 f 74 goat 10_90026961 10 90026961 Ancestral_priority_1043 ancestry 0.702 recommended IMAGE 10K 10K ancestral 320765381 Affx-986697368 AX-385252894 10 90026989 ATAGATATACATCTAGATACATCTGAATCAAGTTC[A/C]TGGACACCTAAAACAGCACAGTGGAAATCTGCACT M 2 1 2 1 600010 r 74 goat 10_90026989 10 90026989 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38420580 Affx-122945268 AX-123290927 10 90073269 ATGGGTAAGGGATTTTACTGTAATGGTAGTTTATT[A/G]TTACATTTATTTAAATTTCAATTGAGCTTAAATAA R 2 1 2 1 103000 f 74 goat snp57086-scaffold908-789432 10 9115980 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453604 Affx-122920137 AX-123323937 10 90130375 CTCGTGTAGGCATGATTAATGATTAACTCCAGTCA[C/T]AGCCCTCTCCTCTCTCTGGGGAATGTTTATATCTC Y 2 1 2 1 101000 f 74 goat snp57085-scaffold908-732326 NW_017212645.1 6209 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781502 Affx-122977537 AX-385268587 10 90186203 ATATTATTAACGCTTTTAATTAGGCTCCAATATAC[C/T]TTCTCATTTACAAAACAAACTGAAAGGATTCCCTA Y 2 1 2 1 101000 r 74 goat snp57084-scaffold908-676498 10 8993361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443996 Affx-122926909 AX-123314333 10 90222269 GTGAAAAGGTTCAGACAAATGAAGAAACTGTCTTT[A/G]TACAGCTTTGTTAGTAATAAAGTTCTCTTCATCGC R 2 1 2 1 202000 r 74 goat snp57083-scaffold908-640432 10 8957394 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447422 Affx-122924390 AX-123317758 10 90253851 TAAGACTAAGATTTAAACTTGACACTAACTTTGGA[G/T]AACCTGGCTCAAGTTAGTGGTTTTAGTAGTCAATA K 2 1 2 1 101000 f 74 goat snp57082-scaffold908-608850 10 8926847 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420193 Affx-122945555 AX-123290541 10 90285431 ATCACGAGTTGAATAAAATAACCTGATGGGTGATG[C/T]AGAATGAGGAACATTCAATAAAACAACAAACTCAA Y 2 1 2 1 101000 r 74 goat snp57081-scaffold908-577270 10 8895390 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407836 Affx-122954534 AX-123278187 10 90317968 TCTAAGAACTTGCAAAATGTTTTAAAAGATTTTCA[A/G]CCACTCAGGCCTTAGCTCAGGTTGACAATCTAAAC R 2 1 2 1 101000 r 74 goat snp57080-scaffold908-544733 10 8862134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429589 Affx-122937720 AX-123299930 10 90356938 TGGAGTGCAACTCAGCAATAATCATTTGCCCCTAC[A/G]CATAACTGGATTCCCACCTAGATCTCTAACTGGGT R 2 1 2 1 201000 r 74 goat snp57079-scaffold908-505763 10 8823201 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377342 Affx-122977665 AX-123247701 10 90387416 AAGATGTATGCTAGTATTTCAGATAAGGCATAGGC[A/G]CTTGAACATAGCTATCCAGAGGCGGTGACCTCAGA R 2 1 2 1 201000 f 74 goat snp57078-scaffold908-475285 10 8792450 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427031 Affx-122939831 AX-123297376 10 90422251 TTTACCAAGGGGAAAAGCTCTGGCCAGATTCCAGC[A/G]TGCCCATAAATAAGAGGGACTACTAGAAATATGAG R 2 1 2 1 201000 r 74 goat snp57077-scaffold908-440450 10 8757440 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434619 Affx-122934009 AX-123304960 10 90468779 AAAATAAAGTTGAAAAAAGAAATATATCCAGAAAG[A/C]GCAAGATGGCAGACTGAAGAGAATAAAGCTTTAAA M 2 1 2 1 103000 r 74 goat snp57076-scaffold908-393922 10 8711286 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417732 Affx-122947432 AX-123288080 10 90536029 AAAATACTAGCCACATCTGCTCCTTCTTGGTTAAC[A/G]TATGATTGGTTTATCTGCCTTAAACTATCAAATGA R 2 1 2 1 201000 r 74 goat snp57074-scaffold908-326672 10 8646360 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391880 Affx-122966972 AX-123262237 10 90590062 CACATTTAGGTATATTTCATATTCACATTAACAAA[C/T]GTAGGAGTTGTTACCATTAACATTTTCAGTTCATT Y 2 1 2 1 101000 r 74 goat snp57073-scaffold908-272639 10 8592070 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406871 Affx-122955647 AX-123277222 10 90619540 AAAGGTGAAGGTGATGAAAGTTGCTGATTGCTTCA[C/T]CATCAATCCAAACTAGCCTGAAAGAAAATGTTCAG Y 2 1 2 1 101000 r 74 goat snp57072-scaffold908-243161 10 8562317 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773147 Affx-122964704 AX-385260290 10 90679409 CTTGGTCAGCTCTGTGATAAGTCAGCCAAATGCAG[C/T]AGATGTACAGTTGGACATCAAGTCAACTCCTCTCA Y 2 1 2 1 201000 f 74 goat snp57071-scaffold908-183292 10 8502229 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439896 Affx-122930030 AX-123310233 10 90712490 GGCTACATGGGTGGGGGGTGGGGATCAGTGACTTA[A/G]TAAAGTTAGCATTCCATACATAGTGTAAATGGCAA R 2 1 2 1 101000 r 74 goat snp57070-scaffold908-150211 10 8469733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801179 Affx-122956922 AX-385288092 10 90749686 AAAATAGCTTCCCAATGTGTGTTGTTACCCTAATA[A/G]CATATGGGAAGGTCCAAGGAAATGGCAATGCACTC R 2 1 2 1 202000 r 74 goat snp57069-scaffold908-113015 10 8432547 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406850 Affx-122955661 AX-123277201 10 90778734 ATCATTACCCATCCTTTGATAAAGAACAACAATAA[C/T]GATGGAAAGTCATTAGTTGACATGGCATTTCTTGT Y 2 1 2 1 101000 r 74 goat snp57068-scaffold908-83967 10 8402714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771965 Affx-122928982 AX-385259121 10 90873600 AGAAATAGTGACACTATTTTGGAAGACTTTTGTTA[C/T]GAAGGAGAATGGAGAAATGAGACAGCATCTAGAGG Y 2 1 2 1 102000 r 74 goat snp5133-scaffold1177-111450 10 8307922 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447928 Affx-122923792 AX-123318264 10 90905572 ACTTTTCCTGGTGGTGGGTCACCATCAGTAAAGTT[C/T]GGAGGCTATTTCACCAAGAGACTTGTGAAGCAGAA Y 2 1 2 1 101000 r 74 goat snp5132-scaffold1177-79478 10 8276242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438831 Affx-122930780 AX-123309168 10 90936746 CTCACATTCACCTATTTCTAAGTTTTTCTTTTATA[C/T]GAATTCATAGATAGATTTTCACATTCAAATTTGTA Y 2 1 2 1 101000 f 74 goat snp5131-scaffold1177-48304 10 8244351 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382730 Affx-122973612 AX-123253088 10 90977422 CAGAAGTACCACCATAGTTTCAGGTATTATATAGC[A/G]TCAGCTCTCTCAACGTTTTTCTGTACATGAACTTC R 2 1 2 1 101000 r 74 goat snp5130-scaffold1177-7628 10 8204027 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769977 Affx-122947041 AX-385257144 10 90993710 TTACATAATCATGCAAATTGCTGTTGTATCTATCC[A/G]TTCTATGCAGTGAATGATATTCAAAGTAATTCTGC R 2 1 2 1 201000 f 74 goat snp43043-scaffold572-8561 10 8181852 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271876 Affx-1111832905 AX-519545659 10 91033115 ATGGGGAAATGGTGAGGGTTAAACAAACGAATCAA[A/G]GAGGACTTTTCGTGTTGCGAGGGACAGAAACCATA R 2 1 2 1 101000 f 74 goat 10_91033115_AF-PAKI 10 91033115 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320802548 Affx-122939445 AX-385289452 10 91038330 CAGTAGATGGCACACCAGTGCTTAAATCCAGGTTT[A/G]TATGAGAAGGCTTCTAAGCTCTTTATTTCACAGTT R 2 1 2 1 101000 f 74 goat snp43044-scaffold572-53181 10 8136649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773839 Affx-122928585 AX-385260979 10 91073333 ATGCTCTGGTGTAAAGTTAGAATACTGTTTAAAGA[C/T]GGCAAACTGTAGATGGAGAACTGAAAAAATAATAA Y 2 1 2 1 101000 f 74 goat snp43045-scaffold572-88184 10 8101742 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785318 Affx-122922748 AX-385272363 10 91109117 TAAACAAATAGCAGTGCAGTCCTCCAAGTGGGTAC[A/C]TACATGCAGTATTCTTAAATGCATTTGAATATTTA M 2 1 2 1 101000 f 74 goat snp43046-scaffold572-123968 10 8065496 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400812 Affx-122959809 AX-123271167 10 91146275 AATTTAAAACCAGCCAAGCTGACTCCAGAGGGCAC[A/G]TGACTAACAACTTCCCATTTTGCGCACGTAAAGTT R 2 1 2 1 202000 r 74 goat snp43047-scaffold572-161126 10 8028331 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412917 Affx-122950399 AX-123283266 10 91201907 GTTATCAACCAAGGCATGGCTGGGACTGCACTCTT[A/G]CTGGCTCTAGCCGACCCTGGGAAGACTGTCCCTTG R 2 1 2 1 101000 f 74 goat snp43048-scaffold572-216758 10 7971418 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777870 Affx-122978367 AX-385264986 10 91242014 ATGGGGTAACTAGAAGCTTATTTATTAGCATTCTG[C/T]AAATAGACTCTTAAATAATTGTAAGTCACTGTGGA Y 2 1 2 1 102000 f 74 goat snp43049-scaffold572-256865 10 7931036 C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276581 Affx-1111835415 AX-519550092 10 91273062 GCACTGCAGCCAGACCTGTGGTTGACAGCCGCGCT[A/G]TATCCATTGCCAGGAATAGAAATCTAGCTTCCTGT R 2 1 2 1 101000 r 74 goat Random2.2K-1119 10 91273062 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378702 Affx-122977059 AX-123249061 10 91302455 CCAACAGACTGTCATCTTGAATTATGAAATATATT[C/T]ACATGGTCACTGATTCAGTGAAAATCCCACCTTTT Y 2 1 2 1 202000 f 74 goat snp43050-scaffold572-317306 10 7869596 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410703 Affx-122952730 AX-123281053 10 91344749 CTTCTCTTCTGTTTATAATTCACCTTACTAGTTGT[A/G]CAGACTCATCATTTCATTATTTTTCTACAGACTTG R 2 1 2 1 103000 f 74 goat snp43051-scaffold572-359600 10 7827321 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276583 Affx-1111835416 AX-519550094 10 91384479 AGAAGGGCAAGAAACACGCCTGCTGCAAGGACTCT[A/C]CTGCCAATAATCCTCTGTTCTCGTCTGCAGAGGAC M 2 1 2 1 102000 r 74 goat Random2.2K-1120 10 91384479 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399588 Affx-122961107 AX-123269943 10 91387563 TCACAGCTTCCATCAAGAGGCCTTCTTTTATTTTG[C/T]GACTCACAAAGAATGCAATCATCAGTAGAGGCAGA Y 2 1 2 1 101000 r 74 goat snp43052-scaffold572-402414 10 7784130 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778074 Affx-122973939 AX-385265190 10 91502402 GGCTATGAAATATTCAACATACAGAATTTTGATGC[C/T]CTCCCATCTAGAGACCTCTGTTTTTCCGAACAGAT Y 2 1 2 1 101000 r 74 goat snp43055-scaffold572-517253 10 7668303 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398504 Affx-122961557 AX-123268859 10 91533432 AACTTGATTCCTCAACAGACTTATGCTACCATAGT[A/G]TCTTAGAGCAGGGGAGAACTTGATTGATCCACTTA R 2 1 2 1 201000 f 74 goat snp43056-scaffold572-548283 10 7637316 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769099 Affx-122959869 AX-385256274 10 91564506 CAGTAAGTCTCTTGCATGTGAACCTTCAAAGGAAC[A/G]TTCAGATATGTGAATGTACCCAGAGAATGGATGGA R 2 1 2 1 101000 f 74 goat snp43057-scaffold572-579357 10 7606116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444183 Affx-122927269 AX-123314520 10 91617518 CTGTGGTGAATGGGTTTTTTACATTTTTGGATAAT[A/C]ATGGTTTTAATTTTTATCTTAAGGCTTTGCCTTTG M 2 1 2 1 101000 f 74 goat snp43058-scaffold572-632369 10 7553189 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429421 Affx-122938516 AX-123299763 10 91646408 CTTTTGCACCATTCTGCCTTCATCCTTCTCACAAA[C/T]AAACGCTAGCATCATTTGCTCCTCATCTTGCTAAG Y 2 1 2 1 201000 r 74 goat snp43059-scaffold572-661259 10 7524474 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785525 Affx-122963257 AX-385272569 10 91699152 AAAATATCGGACCAGTACTCCTCAAAATTTTGAAA[G/T]CAGTGAAAACAAGGTAAGTTGAAGAAAGTTACAGT K 2 1 2 1 201000 f 74 goat snp43060-scaffold572-714003 10 7471902 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443157 Affx-122928059 AX-123313494 10 91729330 TCACCTTATTGCAGGGTGACAATATACAGCCTTGA[C/T]GTACTCCTTTTCCAGGATGTTACAATCTTTGTGAG Y 2 1 2 1 103000 r 74 goat snp43061-scaffold572-744181 10 7441469 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430593 Affx-122936990 AX-123300934 10 91818872 TACATTACTATCAATATTTTATTTATAATCACGAA[G/T]AATATAACCAATCTTTCTCTAAGTCCACAAGCCTG K 2 1 2 1 101000 r 74 goat snp43062-scaffold572-833723 10 7374923 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393470 Affx-122965837 AX-123263826 10 91849600 TTTAAACAATATAAAATATATCATTGATGCTGTGT[A/G]AATTACTGCTTTTCTATATGGGTCTTCTCCTCAAA R 2 1 2 1 101000 r 74 goat snp43063-scaffold572-864451 10 7344430 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796477 Affx-122936562 AX-385283427 10 91897238 GCAATTATAAAAAATCTAACTTTTGATGGGCTTCC[A/G]TACTTTACACACAGATCTAACGATAGAACCATGGA R 2 1 2 1 101000 f 74 goat snp43064-scaffold572-912089 10 7296331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418029 Affx-122946643 AX-123288377 10 91949106 TCTTAGAGTCTACAATTTCCACCTGGAGGACTCAG[A/G]TAGCAAAACTCCAGCTCCTGATTCACTGTATTTGA R 2 1 2 1 101000 f 74 goat snp43065-scaffold572-963957 10 7244579 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380825 Affx-122975074 AX-123251183 10 91978801 TGCTGACTATTCTGATGATATTTGGAAATTTAAAA[C/T]AAGGTGGGAAGGGAAGTTAACAGTAATAATGTGTT Y 2 1 2 1 303000 f 74 goat snp43066-scaffold572-993652 10 7214960 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419515 Affx-122945445 AX-123289863 10 92024976 TATGTTCTATGTCATAGATTGCTCTGAAGAGTCAG[C/T]AAATTAGTATTAATAATATTAGCCACATTATTAAT Y 2 1 2 1 101000 f 74 goat snp43067-scaffold572-1039827 10 7169702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444206 Affx-122927253 AX-123314543 10 92066598 TTTCCCGCATTGGAAGTCGGGTTCTTGACCAGCAG[C/T]ATCACCTAGGAAAAACCAAGTTTGAAAGTAAAAGA Y 2 1 2 1 201000 r 74 goat snp43068-scaffold572-1081449 10 7127577 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421736 Affx-122944379 AX-123292083 10 92120459 CTCTTAGCACAGAGCTTGTTAATTTTAGCAGACAT[A/C]GCCTTGTGAGCTAAAGTATCTAAAAACTGAGAGTG M 2 1 2 1 101000 r 74 goat snp43069-scaffold572-1135310 10 7073335 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800158 Affx-122928561 AX-385287081 10 92158762 CTTCAACACCCTTTTATGCCATGTGAACTATTTTT[A/G]TTTGAATTCGGCTTACATAGAAAGTTATTTAGTTA R 2 1 2 1 101000 f 74 goat snp43070-scaffold572-1173613 10 7035213 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780859 Affx-122932517 AX-385267947 10 92188671 AAATTCCCACTTCTGTGATATGGAAAATTGTTTCT[A/G]TAACTCATTGAAGTAGAGTTAATAATACATACTTG R 2 1 2 1 101000 f 74 goat snp43071-scaffold572-1203522 10 7006280 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404601 Affx-122957347 AX-123274953 10 92218195 CAGTGGGCAGTGAGGGGAGAGAAGATAAAGTCATG[C/T]GAAGAATTCAAAAGGCCTCAACAATTTAGCAAACA Y 2 1 2 1 101000 f 74 goat snp43072-scaffold572-1233046 10 6976339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803184 Affx-122965434 AX-385290045 10 92257641 ATGAAACATCTTGGTGAGGATGATTATATGACTCT[C/T]AGGTCTTCTCTCCTCCAGGACTCTTTATATTACTA Y 2 1 2 1 101000 r 74 goat snp43073-scaffold572-1272492 10 6936586 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402541 Affx-122958470 AX-123272894 10 92296154 TCATGACAGCATTATATGTAAAAATACTGAGGGGG[A/C]TATAAAATAATTGTTCAAGAGATGACATCTCATTT M 2 1 2 1 201000 r 74 goat snp43074-scaffold572-1311005 10 6898097 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445163 Affx-122925549 AX-123315500 10 92346995 AGACATGGGATTTTTCCCATATTTGGGAAATTTGA[C/T]GGGATTCATTCAAAATTGTATAGGACAACCTTTTG Y 2 1 2 1 101000 r 74 goat snp43075-scaffold572-1361846 10 6846986 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415818 Affx-122948889 AX-123286167 10 92388050 TGGGGCCTATCTTTGAATCTATACAAAGAATGAAG[C/T]ATGTTGAGAAGGTGGAGAGTCTGTTTCTACTAATT Y 2 1 2 1 101000 f 74 goat snp43076-scaffold572-1402901 10 6805840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787892 Affx-122976272 AX-385274914 10 92422659 TATTTCAGTTTCTTTTCCTTAATGGAAGAATATGG[C/T]TACATCTCTCTTATTACCATAAATATTTTCCTATC Y 2 1 2 1 101000 f 74 goat snp43077-scaffold572-1437510 10 6771181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778634 Affx-122968826 AX-385265745 10 92466476 ATATTTTTTCTCATCTTTTCATGTGGAGTTTAATC[A/G]TCATTTTATTCCTACCTTTTTACTTATGAATATTT R 2 1 2 1 101000 f 74 goat snp43078-scaffold572-1481327 10 6727326 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276585 Affx-1111835417 AX-519550096 10 92483379 CACCAGTTCTTCACTTGCTTTCACTGTCAAATAAC[A/G]CTCCACTATAGATGCACCACATTTTATTTATCCTT R 2 1 2 1 101000 r 74 goat Random2.2K-1121 10 92483379 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386732 Affx-122970147 AX-123257090 10 92501818 GCTGCAGTGAGAGTGCTGAATGCTAACCACTAGGC[A/C]ACCAGGGAGCGTCAACCCTCAATCTAGTAGTGGGA M 2 1 2 1 101000 r 74 goat snp43079-scaffold572-1516669 10 6691769 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276587 Affx-1111835418 AX-519550098 10 92504706 TCTCATCAGTGGGTGTAAAACCAAGAAGAGAAAAA[A/G]GTAAGGAAATGGAAAACGGAAAATTCTTACATAAG R 2 1 2 1 202000 r 74 goat Random2.2K-1122 10 92504706 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425321 Affx-122940937 AX-123295667 10 92533649 AACTATCTTAATGAAACATCCAAATGACTCTCAAG[C/T]AGTGTTCCAGTGGGATTCTGAGGAATTGACATTAT Y 2 1 2 1 201000 f 74 goat snp43080-scaffold572-1548500 10 6659217 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441832 Affx-122929057 AX-123312169 10 92564788 GTTGCTGAGGTCTAGAAATTTCCTACATTGTTAAA[C/T]GATTAATTTCTTTCCAAGGGATGCACTACTAATTT Y 2 1 2 1 101000 f 74 goat snp43081-scaffold572-1579639 10 6627815 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437421 Affx-122932414 AX-123307759 10 92693097 GATTTTTTGATAAATGACAGTCAGTATGTTAATAG[C/T]TGTACATTTTCCTGATGGCTTCTTCTGAGTTCCTT Y 2 1 2 1 101000 f 74 goat snp43084-scaffold572-1707948 10 6499084 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774137 Affx-122972673 AX-385261275 10 92735879 AGAGGTACCTATATTGTGTTTGAAATAGAAGTATG[C/T]AATTGGCTTGCAGTTCTGAATTATTTTACCAAGGA Y 2 1 2 1 101000 r 74 goat snp43085-scaffold572-1750730 10 6456430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398129 Affx-122961696 AX-123268484 10 92765832 TGTTTACTGATGTTGGGTCTCTTTTCACATGTCAA[C/T]GGCTCTTAAAGCCCTGTGCCTGCATGGTGCTTTCC Y 2 1 2 1 201000 f 74 goat snp43086-scaffold572-1780683 10 6426399 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395810 Affx-122963644 AX-123266165 10 92807472 CAAGAATTGTAAATACCTATTGGCAACAGTACAAT[A/G]TTACGCCATTATGAACATCTCAGTTGTGTAACTAA R 2 1 2 1 101000 r 74 goat snp43087-scaffold572-1822323 10 6384682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438842 Affx-122930771 AX-123309179 10 92840283 TAAAATCTCCATGTGTATATTTAGCCCATAAAAAC[A/G]TTGAAGATTCATTACCTTTTATTTAAGAATTATAT R 2 1 2 1 101000 f 74 goat snp43088-scaffold572-1855134 10 6351926 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792297 Affx-122967279 AX-385279279 10 92934250 AGACTTTCCTGAGACTTCCCTCTATTACTGATTCC[A/G]TCTTTTTCTGTAGCTGCAATCTTTCTCTCTCAACA R 2 1 2 1 101000 r 74 goat snp43090-scaffold572-1949101 10 6258162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445951 Affx-122925905 AX-123316288 10 93006666 TTTAGTTAATAGTTGTACAAAAAAGCTGGTTTCAA[C/T]GTTCCTTTCTATAGAGTGGTTTCTAATTAACCATT Y 2 1 2 1 101000 r 74 goat snp43092-scaffold572-2021517 10 6185361 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783994 Affx-122950183 AX-385271048 10 93046115 TAAGATCTCTGTTGCTGTGTACAGAATATAGATAC[A/G]CCGTAATTTTAGCCATTACTCTTTTATGGATCATC R 2 1 2 1 101000 f 74 goat snp43093-scaffold572-2060966 10 6145280 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388812 Affx-122968905 AX-123259170 10 93092737 TCCAGATTCACAAGCCCACTGACACGTCTTGCTCT[C/T]GGAGTCTGTGATATTCCCCCATTTGGTCCGCACGT Y 2 1 2 1 101000 f 74 goat snp43094-scaffold572-2107588 10 6098828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437161 Affx-122932135 AX-123307499 10 93134213 ACAAGTTTTTTCCTGATCTGATTTTCTCTCTGCTC[A/G]CTAGCTGACTCAGTCCTGCTGACACTGGCTTCTTC R 2 1 2 1 101000 f 74 goat snp43095-scaffold572-2149064 10 6057729 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382543 Affx-122973784 AX-123252901 10 93175503 AAAAATTTTTTTTTCTTTTTTTCCCTGTCAACTAC[G/T]ATCAACGCCCCATGGGACAAGTAACAGCAATTCAA K 2 1 2 1 101000 r 74 goat snp43096-scaffold572-2190354 10 6016610 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443678 Affx-122927179 AX-123314015 10 93207226 AGCTTGGCTTGTTGTTGGAAACTGAATTTATTACA[A/G]ATGGATTCCACTGGGGATCTTTTGGAGGGAAAAAA R 2 1 2 1 101000 f 74 goat snp43097-scaffold572-2222077 10 5985065 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385893 Affx-122971589 AX-123256251 10 93237997 GCTGAGCATCTATTGTTAAGGAGACCCTTGTTAGC[A/G]CAGGTTTCCTTTTGTGAGCCTGGGGAGGTGAGAAG R 2 1 2 1 101000 f 74 goat snp43098-scaffold572-2252848 10 5954370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390520 Affx-122967240 AX-123260877 10 93271271 TGGACTCAGAGACCATCAGTGAGCCATTTTGTCAG[C/T]ATTGCTCACAAGCCTTATTGAACTTTGAAGGACAC Y 2 1 2 1 101000 r 74 goat snp43099-scaffold572-2286122 10 5921179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428047 Affx-122939129 AX-123298390 10 93303362 CAGTTAGTCCTGATGATTTGTTTTCGTCTGAGCCA[C/T]GTGCCGATTTGCTCCTGGTTTCTGTGTAGTGCGTT Y 2 1 2 1 101000 f 74 goat snp43100-scaffold572-2318213 10 5889171 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411602 Affx-122951605 AX-123281952 10 93331940 TACGGAAACCCTGGTTTACTATGGCCTCATCAGCA[C/T]GTTATCATTGTAACGGGGTTGGAGATGTTGCTGAT Y 2 1 2 1 201000 f 74 goat snp43101-scaffold572-2346791 10 5860739 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452263 Affx-122920765 AX-123322596 10 93379426 TTGATAATACAACTGCCTAGAAAGATTCCAAAGGA[A/G]TTATGTTTGTGATGTTTATTTGTCTCATGCTGAAA R 2 1 2 1 101000 f 74 goat snp43102-scaffold572-2394277 10 5812654 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376910 Affx-122977799 AX-123247269 10 93411098 AGGCTAGTAAGCTCAAACTTTATCCTAATTATGCT[G/T]CAGACAACTACAAATTCTCTCAGTTAAAAAAGCCA K 2 1 2 1 101000 f 74 goat snp43103-scaffold572-2425949 10 5781514 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444509 Affx-122926506 AX-123314846 10 93453985 TGGTCATCTAGTTCTTGCTTTTTTGCCATATTTTC[A/G]TTTCACTGAATCTCAGATTGTTTCTGACACCCTCT R 2 1 2 1 101000 r 74 goat snp43104-scaffold572-2468836 10 5739211 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771403 Affx-122973638 AX-385258561 10 93485850 AGTACTTTGGTCATGCAAACTTATGATTCATCAAC[A/G]TTTGTTGGATATCTACATGCCATGCACTTTTTAAA R 2 1 2 1 101000 r 74 goat snp43105-scaffold572-2500701 10 5707220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417432 Affx-122947212 AX-123287780 10 93517496 AAACTAGACTAGTTAGAGCAGCAGTTACATGAAGA[A/G]CAGTGACAAGTGAGACAGGGGTCATCCCAGTGATG R 2 1 2 1 101000 f 74 goat snp43106-scaffold572-2532347 10 5675744 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769968 Affx-122931488 AX-385257136 10 93554421 TCTGCAGTGAAGGTGGGCCTACTTACTGGTTGGTA[A/G]AGCCTTTTGGGAAAATAATATGAATGTGTGTGTGT R 2 1 2 1 101000 r 74 goat snp43107-scaffold572-2569272 10 5638374 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463123044 Affx-1109825025 AX-514610159 10 93562649 TGAAACAACAATAGAGACTGCCATCCTACCTGTTA[C/T]AGACATTGAGAGTTTCACCAAGCCATGAAAATTAT Y 2 1 2 1 101000 r 74 goat 10_93562649_AF-PAKI 10 93562649 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38383244 Affx-122972751 AX-123253602 10 93603546 GATTACAAAGTGTTGGACACAACTGAGCGACTAAG[C/T]GCACAGGCACATTAGCGAGGATAGTCTTTTTCTAA Y 2 1 2 1 101000 r 74 goat snp43108-scaffold572-2618397 10 5589173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783797 Affx-122944462 AX-385270853 10 93645279 TAGAAACCAATATTTCAAAGAGAATCTTATGACAA[C/T]AGAATACCGCTTTCTGATTTCTGACCTAAATCTTC Y 2 1 2 1 101000 r 74 goat snp43109-scaffold572-2660130 10 5547272 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789037 Affx-122939898 AX-385276050 10 93730781 GTTCTCTATAAGCTTGAAGAGCAGTGGGATCAGGT[A/G]CTGCTAATCCCAGGTGACCAATTAGAAGATGAAAA R 2 1 2 1 101000 f 74 goat snp43111-scaffold572-2745632 10 5461472 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450022 Affx-122922844 AX-123320357 10 93780933 GAGGCTTATGAGTTAGCAACTGTATTAGTTTTCTA[C/T]GGCTTTGTCCCAAGTTACTACAAACTTTGTGGCTT Y 2 1 2 1 101000 r 74 goat snp43112-scaffold572-2795784 10 5413743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771606 Affx-122963286 AX-385258764 10 93830195 CTGGTTTTTGATGTTTTCTTTGGGAAGGGTTGAAA[C/T]ATTTCTGATCAGCATGAGAGCAACTCAGCAGTTTT Y 2 1 2 1 201000 f 74 goat snp43113-scaffold572-2845046 10 5364819 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771143 Affx-122955419 AX-385258303 10 93873984 AACAAACATTTGTTTAACAGGAAGCACAAGACATT[A/C]GTCTGTAGTCACTGTCATTGGAGTCCTAGAACAAT M 2 1 2 1 101000 r 74 goat snp43114-scaffold572-2888835 10 5321050 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412646 Affx-122950793 AX-123282995 10 93903980 ATTATTTCTTTTCACTCTCACACTGACCTTTCACC[A/G]TCCTGGAAGAACAGTCTCAAAATTCAACTTTCCCT R 2 1 2 1 101000 r 74 goat snp43115-scaffold572-2918831 10 5290765 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407890 Affx-122954492 AX-123278241 10 93940994 ATTTAGACTGGAGGCCATTAAGCCAAGAGCCACAC[A/G]CTATGCCACGAATAGGCTCAGCCCAGACTCGACCA R 2 1 2 1 101000 f 74 goat snp43116-scaffold572-2955845 10 5252814 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784798 Affx-122929121 AX-385271845 10 93981846 ATTCCTTGAGAAGCTGACGATGGCTTAGGTGTGAG[C/T]ACAGTTCTCCATGCTGAGTACCCTGTTATTCCACG Y 2 1 2 1 101000 f 74 goat snp43117-scaffold572-2996697 10 5212241 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375417 Affx-122979194 AX-123245776 10 94021127 TCCCAGTTTTATAGTTTGAATTCACCAATAAAGAG[C/T]AAACCCATGAAACCCCAAGCACCCCGTTTTTCATC Y 2 1 2 1 303000 f 74 goat snp43118-scaffold572-3035978 10 5172587 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416266 Affx-122947957 AX-123286615 10 94078813 CATGACTAAACTCTCCAAACTGCAAGACATCCCCT[A/G]TGGAAGAAGCAGCAAATGGTACTCAGACTATATCA R 2 1 2 1 201000 r 74 goat snp43119-scaffold572-3093664 10 5115781 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777240 Affx-122964362 AX-385264363 10 94110794 CAATGCAGATCCTCATAATTTTCATAATTGGAAAG[A/C]GGTTTTGAAAGAATCACAACAATTTTCAGGGCCCT M 2 1 2 1 201000 f 74 goat snp43120-scaffold572-3125645 10 5083394 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378892 Affx-122976497 AX-123249251 10 94158074 TATGACATCTACTGCACAAGGGTTTTAATAGGACT[A/C]GATATTTGAAATATGTGGAGCGTGTAGCATCAGCG M 2 1 2 1 101000 r 74 goat snp43121-scaffold572-3172925 10 5035736 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790366 Affx-122922701 AX-385277369 10 94189339 GGGGTCGTCTGAGATTTGGGTAATCCATTCTTTCA[C/T]TGACTTAATGCATGTTTATGGAGCATCTACTGTGT Y 2 1 2 1 101000 f 74 goat snp43122-scaffold572-3204190 10 5004509 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803741 Affx-986696205 AX-385290499 10 94214529 TTCCCTAGATGACCCAGGGGTCTCAGGATTTGCTC[A/G]TTCTGCATATGGTTCTCATTGCAGCTTCGTTTTAG R 2 1 2 1 600010 r 74 goat 10_94214529 10 94214529 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 320793742 Affx-122920406 AX-385280714 10 94218029 ACTAACATGATAAAGTATATCACTTAATCAATAAG[C/T]AAGCATTTTACTTAAATCAAAGCACCATAGGTTTT Y 2 1 2 1 101000 r 74 goat snp43123-scaffold572-3232880 10 4976045 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415235 Affx-122948958 AX-123285584 10 94266570 TGGTCTCTAACATAAAACAAATCTGCTCATGCCTG[C/T]GGTCTCTGTCACTTGATTCCTCCCAAGGCTCTCAG Y 2 1 2 1 101000 r 74 goat snp43124-scaffold572-3281421 10 4927875 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782869 Affx-122978881 AX-385269939 10 94325477 TACTAAGTGCACCTACATCTGAGTTTGAAAATTGA[A/C]TCTGAACTGGGAAACATTTTCAATAGGAAAATGAC M 2 1 2 1 101000 r 74 goat snp43125-scaffold572-3340328 10 4869827 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392362 Affx-122966247 AX-123262719 10 94371728 GCACTTCATGTCAGAATGCTATGAGTTGAATTCAC[A/G]TGATCTTCTTTGTTGAATTTGCTTTTGTCCCCACC R 2 1 2 1 101000 f 74 goat snp43126-scaffold572-3386579 10 4824063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393729 Affx-122965230 AX-123264084 10 94434060 ACCCGATGGCTAAAGTGAATGCTTCATTTGCTTTG[C/T]TAAACTTCCAAGTTCTTTAAGTACCATGGCTTTTT Y 2 1 2 1 101000 f 74 goat snp8032-scaffold1291-43464 NW_017215795.1 12549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395709 Affx-122963721 AX-123266064 10 94485797 GTGCAAAGGTAGTCTCCTCCAACAATCCTGACTAA[G/T]CCATCTTAACTGAAATGCTACAAGGTATTAATATC K 2 1 2 1 101000 f 74 goat snp8033-scaffold1291-95201 10 4691398 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778563 Affx-122970433 AX-385265675 10 94518228 TGCATAATAAATTCAACAGAATTCTCATTTGATAT[G/T]GCAACAGATGAAACTCTAGTGATAGTTATTTATTT K 2 1 2 1 101000 f 74 goat snp8034-scaffold1291-127632 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387824 Affx-122969672 AX-123258182 10 94550188 TCCCACAAAATGACCTTTCATAATTCCATTCACTC[A/G]TATCCTAATAATACACTTGAATTCAAGTTAAAATG R 2 1 2 1 101000 f 74 goat snp8035-scaffold1291-159592 10 4650092 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797713 Affx-122970660 AX-385284652 10 94606909 CCTCAGGGGTTTTACATACTTAACAGGAATAGAAA[C/T]GAAAAGAGAGGTAACCAACCCATCAAACATTCCTC Y 2 1 2 1 101000 r 74 goat snp8036-scaffold1291-216313 10 4593099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394006 Affx-122965021 AX-123264361 10 94646581 TCTAGAGAGACAACCCAGCATCCACCAAAGGACGC[A/G]CATGGGTATCCATTTTAGAGACAGCAGAGCACCCT R 2 1 2 1 101000 r 74 goat snp8037-scaffold1291-255985 10 4552147 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791332 Affx-122936945 AX-385278325 10 94684051 TTAGCTTGGTTTGGTTAGGGATGCCCAGAAAAAAA[C/T]GGAAAACATAAACATTAGTAATACAAATCAGACTC Y 2 1 2 1 202000 r 74 goat snp8038-scaffold1291-293455 10 4514139 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401775 Affx-122959490 AX-123272128 10 94752209 TTCCTTTCCATCTCTGCGTCTTCATGAAAGTAAAT[G/T]TATCTCCCAGTGGCATCATCTGTAAAATATATTAT K 2 1 2 1 101000 f 74 goat snp8039-scaffold1291-361613 10 4445530 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424661 Affx-122942154 AX-123295007 10 94784353 CTCCTTAAGAAGTTTGTTTTTGTTTATGAAAGATG[C/T]TCATACATAAGAATACTAAGAGTTATTAAAGACTT Y 2 1 2 1 201000 r 74 goat snp8040-scaffold1291-393757 10 4413428 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789066 Affx-122932978 AX-385276079 10 94831720 AGCAGACCTGCCATTTTGATAGACCATCTAAAAGT[A/G]CCAGAAGATGTTTTACATATTCAGGTTAATTTGTT R 2 1 2 1 101000 r 74 goat snp8041-scaffold1291-441124 10 4363612 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420448 Affx-122944892 AX-123290795 10 94874404 TATTTAAATGTTTCTGTTTCTTGCAAGGGGAAGCA[C/T]GACTTTAAAATATTTTTGGACATGATCAGTAGGAC Y 2 1 2 1 101000 f 74 goat snp8042-scaffold1291-483808 10 4320664 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387838 Affx-122969659 AX-123258196 10 94962629 TGTAAATCAATTTAGTAACAGTAATTAATTCATAC[A/G]TGTCACATTTCATATACTAGAACGTAATTCACTTA R 2 1 2 1 101000 r 74 goat snp8044-scaffold1291-572033 NW_017192830.1 569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452160 Affx-122921653 AX-123322493 10 95003080 AACCATTCCCTCTTTCAAGAAATATCCTCTCTTGG[A/C]TTGGCTTTCCTCCTGTGTTATCTCTGAAGGCTTCT M 2 1 2 1 101000 f 74 goat snp8045-scaffold1291-612484 10 4194255 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411513 Affx-122951675 AX-123281863 10 95034696 AGGGAGACATACACCCTCCATCACAGAAACCCCAT[A/C]TCCAGGTGTACCTGAACAAAAATCCAACTTGTAAG M 2 1 2 1 101000 r 74 goat snp8046-scaffold1291-644100 10 4162325 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785091 Affx-122922007 AX-385272138 10 95080967 TCCTCACCTACTGATCTCCTGTTAGCCAAATTTCC[A/G]TCACAGGCATCATCATTAACACAATCCCTAGAGGA R 2 1 2 1 101000 f 74 goat snp8047-scaffold1291-690371 10 4117681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792084 Affx-122960859 AX-385279071 10 95116316 TCATCATCCCTCAGAAGGAGGTATGATAACTTAAA[G/T]ACCAAATTGAGACAAATATTTGATTTTGGCTACAC K 2 1 2 1 202000 r 74 goat snp8048-scaffold1291-725720 10 4082007 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769399 Affx-122920417 AX-385256570 10 95166471 GCAAAATGATGCATCCACTTTAGAAGACCATTTGG[C/T]AATTTTTATGGTAGTAGTAAACACACACTTACCCA Y 2 1 2 1 101000 f 74 goat snp8049-scaffold1291-775875 10 4031689 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785027 Affx-122958076 AX-385272074 10 95197668 CAAAAGCAACTGACAGTAGATGGGAATCTTCTGCT[A/G]TTCTCAATGTGTTAAACGTAATGGCTCATTAAGGT R 2 1 2 1 101000 f 74 goat snp8050-scaffold1291-807072 10 4000285 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405235 Affx-122956887 AX-123275587 10 95242740 GAATGCAATTCTGTTTTCAGGCAAACATTTAAAAG[C/T]AACACAAAATGAATCACTTATAAAGCTGTACTTCA Y 2 1 2 1 101000 f 74 goat snp8051-scaffold1291-852144 10 3955101 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443691 Affx-122927169 AX-123314028 10 95275180 GAGCAAGATGTGCCTAACATTTCATTGCACTAAAA[C/T]CCAGAGTTTTATAAAATCTGATTAAATGATTCAGA Y 2 1 2 1 101000 f 74 goat snp8052-scaffold1291-884584 10 3922574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387204 Affx-122970598 AX-123257562 10 95305898 CGCATACGCAGATGCAGAAACAAACGTTCTATAAA[C/T]AGAGGAAAGAAAAGTGAAAGCAGAAGGCGCTCAGT Y 2 1 2 1 103000 f 74 goat snp8053-scaffold1291-915302 10 3890926 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784409 Affx-122975037 AX-385271458 10 95335714 CAGAGAGAGGGCTGGAAATGAGGTATCATTTGGTC[A/G]TTCATATATGGTACACAATTCATCCACAATGAATT R 2 1 2 1 101000 f 74 goat snp8054-scaffold1291-945118 10 3860629 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780107 Affx-122924315 AX-385267204 10 95356988 TGTACAGTGCTGTGAGTCTTTAGCCTCACAGGATG[C/T]GGTCAAATGCTGTTTTTCAAAGTCACTTAGAGGAG Y 2 1 2 1 101000 f 74 goat snp27540-scaffold2944-109285 10 3840971 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428057 Affx-122939122 AX-123298400 10 95403878 TAGCGTATAAACGCTCATGTCTGTCATGGGTGTGT[A/G]TAATTGTGAAATATGCTACCTTCCAAATAGGACCA R 2 1 2 1 101000 r 74 goat snp27539-scaffold2944-62395 10 3793631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417513 Affx-122946947 AX-123287861 10 95450649 TGATATCCAAAGTCAGGTCTGTCCAGCCTCCTCCA[C/T]GCTCCCTGCATCCTTCTGTACCCCACCGCCCCGGG Y 2 1 2 1 101000 f 74 goat snp27538-scaffold2944-15624 10 3746859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396535 Affx-122962948 AX-123266890 10 95503630 TTATGATACAAGCAGGGAAGGCTATAAGATCAGCT[A/G]TTGTAAATGATGAATGAAGACAGAGTTACAAGCAG R 2 1 2 1 101000 f 74 goat snp23961-scaffold2420-140938 10 3693326 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422700 Affx-122943654 AX-123293046 10 95541485 AACATGATGAAATGTTTTAAAAAATAAGACCCTTG[A/C]GGAGGAGGTAAGAGAACTGAACATGTTCAACCTTG M 2 1 2 1 101000 r 74 goat snp23960-scaffold2420-103083 10 3655250 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428201 Affx-122939454 AX-123298544 10 95597914 GTCAAGCTTCACCTCAGCTCCATCGGATTTGTGCG[A/C]GCTAGTGCACCTTGGATTATTTTCCTAAGTAAAAG M 2 1 2 1 101000 r 74 goat snp23959-scaffold2420-46654 10 3601647 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380196 Affx-122975499 AX-123250554 10 95636601 TGATGTCACGGTTACACAAGCCTTCTAGTGTCTGA[C/T]GAGGAGCCCGTTTGGGGCCCTGGCCTCAGAATCAG Y 2 1 2 1 101000 f 74 goat snp23958-scaffold2420-7967 10 3562443 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801933 Affx-122967439 AX-385288838 10 95646513 ACAGGTAAAGTGAAGTGTCGTCTGCTTGTAAGCAT[A/C]TTCCGCTAATATAAATTACCCAAGCGAAGCATTGG M 2 1 2 1 101000 r 74 goat snp23972-scaffold2436-167705 10 3552882 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405774 Affx-122956488 AX-123276126 10 95675292 TGAGTCTTGGTAAATGGATAAACCAAGATATCAAA[C/T]GGTTTCGTCACTCCAGAAAGTTCTCTTATACCTGT Y 2 1 2 1 201000 f 74 goat snp23971-scaffold2436-138926 10 3523783 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773210 Affx-122934253 AX-385260353 10 95718479 CACACTCATAGGTAGGAAGTGAAGTTTGCTGTACT[C/T]TTGTAGTCTGCTTCCTTTTAATTCTAAAGTTCTGA Y 2 1 2 1 101000 f 74 goat snp23970-scaffold2436-95739 10 3481469 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389708 Affx-122968684 AX-123260066 10 95749448 GAAATTTAGACCATGAAAATATTCTTCCTTAGAAG[A/C]GGGACTGGGGGAGCTGGGTGATGGGCAGGAAGGGA M 2 1 2 1 101000 f 74 goat snp23969-scaffold2436-64770 10 3446026 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438297 Affx-122931390 AX-123308635 10 95778436 CCACTTGCCCTCCTGGCTTGTGAGAATGGGGAAAT[A/G]CATCTAGAACACTTAAGGCAATTTCTTTATAGTTG R 2 1 2 1 101000 r 74 goat snp23968-scaffold2436-35782 10 3416972 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38404318 Affx-122957015 AX-123274670 10 95810724 CCACTCTGGATTTTTAGCTCAAGATTATAGGATGA[A/G]GAAGTAACAAAGTCAGTACCAGAAACCAAGTTACT R 2 1 2 1 101000 f 74 goat snp23967-scaffold2436-3494 10 3384533 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433894 Affx-122934403 AX-123304235 10 95822830 GGCTGGGGAACTGGGGGGCTAATTGTGTCTCTTCC[A/G]TGAGTGCACGTCTTCCTGTGAATACTGGGGGTGGG R 2 1 2 1 201000 f 74 goat snp41400-scaffold538-655464 10 3371636 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419901 Affx-122945341 AX-123290249 10 95857613 AGGGTGGCTCTATTAATCCTAAACTCCTAGTTGAG[C/T]GGTTTGTGACTCCTTTGGTAACCATAAGTTTGTTT Y 2 1 2 1 101000 f 74 goat snp41399-scaffold538-620681 10 3339168 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788578 Affx-122977522 AX-385275595 10 95892591 AAAAGTCAGCAGATAAGGCACAAAGCATTGACTCA[A/G]TATAAGTAGACCACAAATCAGGTTTAACACATTTA R 2 1 2 1 101000 f 74 goat snp41398-scaffold538-585703 10 3304503 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436317 Affx-122933259 AX-123306656 10 95922984 TTCCCAGAGAAGAGGTGGTTCTGAGGTTTGTCTCC[A/G]TAAGTCAGGAAGGAAGAGGGGAGTGGGAGGAAGAG R 2 1 2 1 201000 f 74 goat snp41397-scaffold538-555310 10 3273965 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394838 Affx-122964784 AX-123265193 10 95958611 ATTGCTCCAAGCACTGAAGGAGGCAAAATCTTTTG[C/T]ATTTTATATGCCATCTTTGGAATCCCACTCTTTGG Y 2 1 2 1 101000 r 74 goat snp41396-scaffold538-519683 10 3239804 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276589 Affx-1111835419 AX-519550100 10 95964881 GAGTGCTATCACTCCCTAGATTCATTCAGGTGGCA[A/G]CTCAGAGTTTATAAGTTTGGTTGCTGTGGGACACG R 2 1 2 1 101000 r 74 goat Random2.2K-1123 10 95964881 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450982 Affx-122921734 AX-123321316 10 96001591 CTTATTTTTTTTCTCCTTTCATGGAAACCTACTAA[C/T]AGTTTTGTGATGATGAGAGTGTTGTGCTGATCTGT Y 2 1 2 1 101000 r 74 goat snp41395-scaffold538-476703 10 3198908 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381250 Affx-122974494 AX-123251608 10 96041722 AGTTGCTGTTCGTCTCTCTATTTCGTATAATGCCC[A/G]TCCCTGTGGTGCCCAGAATGAAATGCACCGATTTT R 2 1 2 1 101000 f 74 goat snp41394-scaffold538-436572 10 3158753 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271878 Affx-1111832906 AX-519545661 10 96067482 TTAAACTTAAAAGCTTTTGCACAACGAAGGAAACT[A/G]TAAGTAAGGTGAAAGACAGCCTTCAGAATGGGAGA R 2 1 2 1 303000 f 74 goat 10_96067482_AF-PAKI 10 96067482 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454271 Affx-122919639 AX-123324604 10 96097933 GTTCCACCAGTTAATCATGCTGCTTGGTGGATGCC[A/G]CTGGGCAGAACTGAATTTTGTTTTTATGATTTAGC R 2 1 2 1 101000 f 74 goat snp41393-scaffold538-380361 10 3102587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417500 Affx-122947157 AX-123287848 10 96132545 CCCTGCTCACCGTACCTGGAGAAAGCCCACGCACA[G/T]CCCCAAACTAAGAACATAAAAGGGAAAGCCTTTCT K 2 1 2 1 103000 r 74 goat snp41392-scaffold538-345749 10 3067927 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392806 Affx-122965967 AX-123263163 10 96173826 GAATCCAAAAGTGTTATTTTTGAAACATAGAAAGC[A/G]TTTTTATATTCAGAAAATTTTTTAATCCTAAAAGT R 2 1 2 1 103000 f 74 goat snp41391-scaffold538-304468 10 3026464 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789534 Affx-122930886 AX-385276543 10 96231447 ACATTTGTGAAAAATTCAAGACCTTCATATTTTTA[A/G]GAAAACAATTTGCCTCTGAAGTATCACTCCTTACC R 2 1 2 1 101000 r 74 goat snp41390-scaffold538-246847 10 2968299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449896 Affx-122922339 AX-123320231 10 96299383 GTGCCATCTTGCTTCTTCTGATGTTTCAAGTCTTA[C/T]AAGCACAGCAAAGTGCAACTTAAAAGATGGTTTAA Y 2 1 2 1 101000 f 74 goat snp41389-scaffold538-178911 10 2900512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782343 Affx-122971088 AX-385269420 10 96333989 GAAGCACACCACTTGGACCTAATTTATCCTCAGTC[A/G]TATGTACAGATCAAATATTTTTGACTAACAGTTAA R 2 1 2 1 101000 f 74 goat snp41388-scaffold538-144305 10 2865970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801471 Affx-122945343 AX-385288380 10 96365060 ATGAATTAATCTTAAGTCGAATTGAATTAAAATTA[C/T]GAACCAGAATATTGTACATGCTCTAAGAGGGGCCG Y 2 1 2 1 101000 r 74 goat snp41387-scaffold538-113234 10 2835013 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791457 Affx-122946769 AX-385278448 10 96414305 ATACCAGTTTGTTCCTCATAGTCATTAGCCCAGGA[C/T]GTGATCACTATTGTAAATTTTTGCTTATCTTCTAG Y 2 1 2 1 101000 f 74 goat snp41386-scaffold538-63989 10 2785342 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276591 Affx-1111835420 AX-519550102 10 96414900 GTATACTTAATAGCCCCAGCCTTCTAAGCTGGGGG[A/G]AAAACTGATGTAAGTACTTCCCTGAATTTTTGGTC R 2 1 2 1 201000 r 74 goat Random2.2K-1124 10 96414900 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38400549 Affx-122960430 AX-123270904 10 96477657 AAGTAGAAAGCTGACTGCATCCTCAGTGCCTAGAA[C/T]AGTGTTTGGACATAATACAGGCTCAAAAAAAAAAA Y 2 1 2 1 201000 r 74 goat snp41385-scaffold538-637 10 2721728 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797536 Affx-122921728 AX-385284475 10 96509142 TGTCATTCTTTTATTCACAGGAAAAGCTTTATCCC[A/G]ATGTATTAAGTATGCAGGGAGACAAAAGCATTTTT R 2 1 2 1 101000 f 74 goat snp6251-scaffold1220-29959 10 2690811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396673 Affx-122962841 AX-123267028 10 96557557 TGTGATGATGACCAGTTTCTTTGTTCACAGTTCTT[A/G]TGATTTGTGGCATATAAATTTTCAGGGAGACTTAC R 2 1 2 1 201000 r 74 goat snp6252-scaffold1220-78374 10 2642060 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406490 Affx-122955159 AX-123276842 10 96602742 CCATGAAAAGCTTTGAGTCCAAGAATGAGGTTGGC[A/G]CTTACGCTTGGCCACTGTTTACAGCCCATGTTCTG R 2 1 2 1 201000 f 74 goat snp6253-scaffold1220-123559 10 2598376 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428227 Affx-122939434 AX-123298570 10 96632035 TCCCCTGCCCTCCTTCACTTACTGCGCTCAGTGAA[C/T]GCCCCCTTCCTCTGTTGCTGGTTTCAGAGGGCACT Y 2 1 2 1 201000 f 74 goat snp6254-scaffold1220-152852 10 2569099 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447824 Affx-122923913 AX-123318160 10 96666625 CTTACACACACTGCAATCATTTTGTTCTTGTTTGC[A/G]TTTAATAGCCTGTAATCCATTTTAATTATATTCTT R 2 1 2 1 201000 r 74 goat snp6255-scaffold1220-187442 10 2537356 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376757 Affx-122977973 AX-123247116 10 96696658 ACACTCCAGTGGGTCACTCCCCTGTACGGTTTCAC[G/T]CGTCCATTCCATGTGTGATTCCGTTAACGACATAC K 2 1 2 1 101000 r 74 goat snp6256-scaffold1220-217475 10 2507434 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425856 Affx-122940658 AX-123296202 10 96744279 AACAGGATCCCCACACACGGTACAACACAGCTCCT[A/G]CCAGGTGTCTGGCGGGTGGGGTTGCGGGGTACCCC R 2 1 2 1 103000 f 74 goat snp6257-scaffold1220-265096 10 2459533 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276442 Affx-1111835421 AX-519549963 10 96752663 TCAGAATACTTATTTAAACATCATTAGCTGTATGT[A/C]TTTTTAAAGTAGAATAAATAATGGAAAGGGAATTG M 2 1 2 1 102000 f 74 goat Random2.2K-1125 10 96752663 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38389199 Affx-122969071 AX-123259557 10 96778007 GTATACCCCTACAACGGCCCGGTTCAAGAGCCTTT[A/G]CTGGAAAAATGATTAAGAGTTTCAAGAGGACAAAG R 2 1 2 1 101000 r 74 goat snp6258-scaffold1220-298824 10 2426040 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437364 Affx-122931929 AX-123307702 10 96830207 CCTGCTCGTATCCTCTGCCACGTCTCATCCAGGTC[A/C]GCGTAAGGTGCCCGTTACTAGGCTGTGCAAAAGGT M 2 1 2 1 101000 r 74 goat snp6259-scaffold1220-351024 10 2373664 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453240 Affx-122920416 AX-123323573 10 96870973 TTCCTTTACAAATGCAGTTTAAAATGTTTAAAGGA[A/G]CTTAATTAGCTAAGTTTGCAAATCAAAGCAAACAT R 2 1 2 1 103000 r 74 goat snp6260-scaffold1220-391790 10 2332953 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404652 Affx-122957304 AX-123275004 10 96912487 TATCCAAATTGCCCATGCCCGAGCCAGGCCTGCTT[A/G]TTTTTAAATTTCAAACATTTTCAAACACAGTGCTT R 2 1 2 1 201000 r 74 goat snp6261-scaffold1220-433304 10 2289543 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775892 Affx-122947396 AX-385263023 10 96918253 GTGAGATTCAGCACTTTGATAAAAGCAGGCTTTGC[A/G]GTACGACACGATCCAAGGTCGTATACTCTTTTTAT R 2 1 2 1 101000 f 74 goat snp11511-scaffold1420-4103 10 2283023 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390496 Affx-122967258 AX-123260853 10 96955132 AAGAAAATGGACACCATCCCCCGCTATAATTACTC[A/G]TCTGTAGGTAGATGGCAGTAAGACCCAAATTCTGG R 2 1 2 1 201000 r 74 goat snp11512-scaffold1420-40982 10 2247697 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769730 Affx-122925735 AX-385256900 10 97005019 GAGAGAAAAGGATGTAATTTGATTAGAGTTGCGTA[A/G]TAAGTTTGAGGGTCAGAGTTTTTAGAATTATATGC R 2 1 2 1 101000 f 74 goat snp11513-scaffold1420-90869 10 2200324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416490 Affx-122947794 AX-123286838 10 97042379 AAAACCCAAAAAGCTGAAAGTAGCGTTCTTCCTAA[C/T]GAGAGAAAGCTACTCATACAGGGAACACAAACCTT Y 2 1 2 1 101000 f 74 goat snp11514-scaffold1420-128229 10 2162808 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431428 Affx-122936517 AX-123301769 10 97073830 GTTTTATCAAACCCAATAGGAAAATCTGTGCTGAG[C/T]TGAGGCACTCGGCGTGGCCAGAACTACTTCCGCTT Y 2 1 2 1 101000 f 74 goat snp11515-scaffold1420-159680 10 2131262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432145 Affx-122936428 AX-123302486 10 97109165 AGATCCTCCTCTTCTTCCTTAGGGGAACCCCTGAC[A/G]TCGGAAAATTCATTCAAGGTCAAATGTATCCTACT R 2 1 2 1 101000 r 74 goat snp11516-scaffold1420-195015 10 2095504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398813 Affx-122961403 AX-123269168 10 97146550 ACAGCCATCTGAGGGTAGCAGAGGCTTCTCCTTCC[A/G]CCCAAAGTGAGGTCCATGCACCTGACCTACAGAGG R 2 1 2 1 101000 r 74 goat snp11517-scaffold1420-232400 10 2058746 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276444 Affx-1111835422 AX-519549964 10 97229467 TGCTTTTGCCTACTGCATTTTCTAGGTGAAACAGG[A/G]CTGCAGTGGGACACCCTCTGTTGTGCTGCTGGGCA R 2 1 2 1 101000 f 74 goat Random2.2K-1126 10 97229467 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38379034 Affx-122976357 AX-123249393 10 97243588 AGCGCCAGGCACCTGCATCGTTAGTGAAAATGCCC[A/G]CATCGGTTCTATTTCGAGTTCCAACTGGTCACATA R 2 1 2 1 201000 r 74 goat snp11519-scaffold1420-329438 10 1960522 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768890 Affx-122931450 AX-385256067 10 97288993 AAAAGAGATAGTAAAACCATGTTCTTGTAAGTTAT[A/G]GTTTAAAATTGGAAAGGGATGTGATCTCTCTACAG R 2 1 2 1 101000 r 74 goat snp11520-scaffold1420-374843 10 1915038 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409382 Affx-122954152 AX-123279733 10 97338757 AACGGCTGGATGTGGGAAGGGAATACGGAGGGGTA[C/T]AGAGGGAAGACAGGTTGTTTTTTTTTTAAGTAATG Y 2 1 2 1 101000 r 74 goat snp11521-scaffold1420-424607 10 1865715 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431972 Affx-122935954 AX-123302313 10 97394742 CCCAGCTAATGCACTTGCCTAAAGTTATATTCCCC[A/G]TAAATGGTAGATCTGGCCTTCCACCCTACAGTCTG R 2 1 2 1 201000 r 74 goat snp11522-scaffold1420-480592 10 1809053 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435401 Affx-122933560 AX-123305741 10 97452681 GTTTGTTTTGAGATGCAAATGGAGAGCTGGAATGG[A/G]CCTGGGGAGTAGGAGCTCCAGAGTGGAACCGCTCT R 2 1 2 1 101000 f 74 goat snp11523-scaffold1420-538531 10 1752303 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376376 Affx-122978110 AX-123246735 10 97497711 TCTGTGTTCCCTGCCTGTCTCCCCAGCAACTGCTA[C/T]GCTTGGCCACTTTGGGGAGCCCCTCAAGCCTTCCA Y 2 1 2 1 201000 r 74 goat snp11524-scaffold1420-583561 10 1707140 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377718 Affx-122977395 AX-123248077 10 97540430 TTCCTGCACAAAGTTGGGCAAGGTCCCATTTTCCC[A/G]TTCGATGAGGTAGCACTCTCAAGGAAAGACACTAT R 2 1 2 1 101000 r 74 goat snp11525-scaffold1420-626280 10 1665379 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387575 Affx-122970274 AX-123257933 10 97574531 ATCAGCGTGGAGTGTGTGGATTACTCAACCACTTG[C/T]GGGACAAAGGGCTCGGAGGATTCTTCGGGGGCACA Y 2 1 2 1 101000 f 74 goat snp11526-scaffold1420-660381 10 1631184 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427267 Affx-122939544 AX-123297610 10 97618231 TTCCGTTTCAGTAAGTACCACTTCTGTTCACTCAG[A/C]TGCTCAGAAAACCCAGATCATCCGTGGGATGTTCC M 2 1 2 1 101000 f 74 goat snp11527-scaffold1420-704081 10 1587396 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445126 Affx-122926179 AX-123315463 10 97656131 CAGGTCAGTCTTCCCCAGGGCTTACGGTGGTATGT[A/G]TTCATATGTAAATATATTCTCTTTCATTTATGGAG R 2 1 2 1 103000 f 74 goat snp11528-scaffold1420-741981 10 1550810 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449696 Affx-122922547 AX-123320031 10 97672802 TACAGTGCAGGTTGGCCTTTAGGCTGGCCTGTGCC[A/G]TGGAATGGGAGCTTGGCTTCCGAGTCCAGATTAGG R 2 1 2 1 201000 r 74 goat snp10858-scaffold1389-9286 10 1534740 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409875 Affx-122952912 AX-123280226 10 97715627 AAAGGCTCCGCAGAGGTCAGCAGAAAGGAAGCATC[A/G]CCTCAGAGTCAAATGGTGCAGCTACCCAGAGGCGG R 2 1 2 1 201000 r 74 goat snp10859-scaffold1389-52111 10 1502980 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772932 Affx-122941627 AX-385260076 10 97755210 TGACATTGAATTCTCTTATAAAAACTTGACATTGA[A/G]TTCTCCTATAAAAATTCAGGGCAATTTTATTAGCA R 2 1 2 1 101000 r 74 goat snp10860-scaffold1389-91694 10 1463231 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453536 Affx-122919793 AX-123323869 10 97814692 TGACCATGAGGTGCATGAAAAGCTGCTCGACTTTG[C/T]AGACATCAAGGAGGTGCCATTTAAGCCACTGCACA Y 2 1 2 1 101000 f 74 goat snp10861-scaffold1389-151176 10 1403561 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444115 Affx-122926818 AX-123314452 10 97854639 CTGTTTAAATCTCTTTCCCCAAGAAGGTCAGCTCC[A/G]TGAGCGTGGGGTCTTCATCTAACTTGTTCCTCAAA R 2 1 2 1 201000 r 74 goat snp10862-scaffold1389-191123 10 1362861 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451795 Affx-122921495 AX-123322128 10 97896266 GCCTACACTAGGTGCTGAGGTGCCTAGAGAAACTA[C/T]GGCACAGCTATGCCGTGGGCACCGCTGAGCAGAAA Y 2 1 2 1 101000 f 74 goat snp10863-scaffold1389-232750 10 1328203 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417357 Affx-122947719 AX-123287705 10 97924831 GGGTGGGGATACACTTGGGACTTGGCATTAACAGA[C/T]ACATACTATATATAAAATAGAGAAACATCAAGAAC Y 2 1 2 1 101000 f 74 goat snp10864-scaffold1389-261315 10 1299985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435764 Affx-122932878 AX-123306103 10 97971998 ATGGAAGTTGATAAGGGGAGTGCTGGGAAGAGAGA[C/T]ACCGGCAGATACATTTTTCTTACATCTTGCTTTAA Y 2 1 2 1 102000 f 74 goat snp10865-scaffold1389-308482 10 1254664 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396607 Affx-122962893 AX-123266962 10 98003989 CACAGCAGCCTACGGTTACAGTGAATGAATTTAGA[C/T]GTGTGGCTTTGTGAAAACCATCCAGCCAAGCATCA Y 2 1 2 1 101000 f 74 goat snp10866-scaffold1389-340473 10 1222212 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383679 Affx-122972501 AX-123254037 10 98064517 CCCAGCAACAGGGCACAACAGCCCAATCTCTCCAC[A/G]TCCTCCCAAAACCTCTTTCCTGTTTTCTCCCCCAT R 2 1 2 1 101000 r 74 goat snp10867-scaffold1389-401001 10 1161393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376210 Affx-122978808 AX-123246569 10 98096393 ATGGGGAGGCTCCACCAGGCCAGCAGCCAGGGCAG[G/T]GAGAAAACAAGTCAGGTTCTGAACAGATTCTGACG K 2 1 2 1 101000 r 74 goat snp10868-scaffold1389-432877 10 1133974 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38391992 Affx-122966502 AX-123262349 10 98151757 GAAATACAATGAATAGATGAGACGGCCTTCTCACT[C/T]GACTGCGGTAGTTTTGTTCCCTCCCAACCATGCCT Y 2 1 2 1 101000 f 74 goat snp10869-scaffold1389-488241 10 1078648 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379579 Affx-122976037 AX-123249937 10 98181448 CAGGTTTCCTCTGCTTTTCGGAGGGGAGGGCGGAG[A/C]TCAGCCACACTGTCTCCTGCCCCAGGCAGCATCTG M 2 1 2 1 101000 f 74 goat snp10870-scaffold1389-517932 10 1050522 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424716 Affx-122941679 AX-123295062 10 98235254 AATTAAGGGAGAGTGCAGAGGCAACCTGAGAGGAA[C/T]AAGTGGGCAGAGAAGAAACGGGATAAGCCAGAGGC Y 2 1 2 1 101000 f 74 goat snp10871-scaffold1389-571738 10 996272 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430887 Affx-122936875 AX-123301228 10 98272120 GTGTGCTAAGTAAAGCCAGTCACAAAAAGACCACG[C/T]ACCACACAAATCCGCTTGTATGAAATGTCCAGAAC Y 2 1 2 1 201000 r 74 goat snp10872-scaffold1389-608604 10 960540 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784111 Affx-122928238 AX-385271163 10 98316931 TCAGTGTAGTCCTATGGACTAAACGGAGTAATAAA[C/T]GGATAGAACACTTGGCACAGAATATACCAAGTGCT Y 2 1 2 1 102000 r 74 goat snp10873-scaffold1389-653415 10 915572 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276597 Affx-1111835423 AX-519550108 10 98349088 AGCCAATCAAAGTATTAATATTACCCTCTTGATCA[A/G]CTAGCTTACTCAAGAATCTTGGGATAGCCAGAAAG R 2 1 2 1 101000 r 74 goat Random2.2K-1128 10 98349088 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396600 Affx-122962898 AX-123266955 10 98352590 GTGACATTAAAACTGAGTTTCAAGTTGCAAAGGCA[G/T]AGAACCTGAAGCACGGGGCAGGGCCTCCTCTCCAA K 2 1 2 1 101000 f 74 goat snp10874-scaffold1389-689074 10 878943 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416098 Affx-122948317 AX-123286447 10 98428058 CAGGGATGAACATGCCCCCATATGTCTGAAAAGAG[A/C]AGCTTTTTTGAAGGAGGTCATTAACTACAGGTCTT M 2 1 2 1 101000 f 74 goat snp22722-scaffold2265-33857 10 800503 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789758 Affx-122929238 AX-385276766 10 98459478 AATGGAAAGTTTCAAGCACTGCAGTTAAATCCTAC[A/G]TCTCCTTTCCTTGATGAATTCTTTCAGCTGAATTG R 2 1 2 1 101000 r 74 goat snp22723-scaffold2265-65277 10 769041 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402889 Affx-122958217 AX-123273242 10 98540194 GTAAGCCTGGACTTTTTAGTATACGGTGTTGGGAC[A/G]TTCTCCATGCAAAAAATAAAGCCATGCAAGCACTG R 2 1 2 1 101000 f 74 goat snp22725-scaffold2265-145993 10 687756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437801 Affx-122931682 AX-123308139 10 98608478 TTGTCCCTCCACCCCCGAAATGCGAAATAAAGAAA[C/T]GAGTACATCAAGGCACGTTCTTCTCAGGCCGCGTG Y 2 1 2 1 202000 f 74 goat snp22727-scaffold2265-214277 10 619084 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271880 Affx-1111832907 AX-519545663 10 98664389 CTCTGGGATTCTTGCCCACAGTAGTAGGTGCAATG[A/G]CCATCTGAATTAAATTCACTCATTCTGGTCCATTT R 2 1 2 1 103000 f 74 goat 10_98664389_AF-PAKI 10 98664389 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450415 Affx-122922061 AX-123320749 10 98666716 TGGGGGGTCAGGGTGACATCTGGAGCAAAGGAAGC[G/T]TGATCTGAGGTCTGAAGATGAGGGAGAGGATGAAG K 2 1 2 1 202000 f 74 goat snp22728-scaffold2265-272515 10 560826 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385632 Affx-122971177 AX-123255990 10 98705414 AATGAGGGTAGGTGGCCTGGCACAGAGCCTGGCCC[A/G]CGGTGGTCTCCTCTGTGCGACTGCTGCTGCTGTCG R 2 1 2 1 101000 r 74 goat snp22729-scaffold2265-311213 10 522165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433513 Affx-122935016 AX-123303854 10 98735894 GTAAGATCAGAGACTTCCCTGTTGTTAGGCCTCCA[C/T]GCTTCCGCTGAAGAGAACACGGTTCCGTCCCTGGA Y 2 1 2 1 101000 f 74 goat snp22730-scaffold2265-341693 10 491040 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274143 Affx-1111834066 AX-514614350 10 98737850 CTCCACCAGCCAGCTGCTGGGCAGGTATGTTGCTA[A/C]CCATT M 2 1 2 1 102000 f 74 goat GoatD01.016711 10 98737850 T G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320775321 Affx-122938805 AX-385262452 10 98777813 AAACATTTGTCAGGATTCCTAAGTGTGAGCAAACT[A/G]TGTAATCAAGAGGCTCAATAATTTGATTAGGGCTG R 2 1 2 1 101000 f 74 goat snp22731-scaffold2265-383612 10 448796 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795465 Affx-122935743 AX-385282421 10 98809008 TTTTGATCATGAGAAGTTTAAGCTTGTTAACTCTG[C/T]TTCTCAGAAGGGCTACTGTTAACTGCACACGAACA Y 2 1 2 1 101000 r 74 goat snp22732-scaffold2265-414807 10 417624 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395402 Affx-122963957 AX-123265757 10 98843768 GGAAGTAAAAGAAATGTTTCTTAGTCATTTGAGTT[A/C]TTTCTTTTCTTTTTTTTAAATTCATTTCAAACATA M 2 1 2 1 303000 r 74 goat snp22733-scaffold2265-449567 10 383276 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443940 Affx-122927024 AX-123314277 10 98909249 CTTATCTCCAGTTGCCAGGCATATCAGGGACCACC[G/T]GTGTACTTTCTACCTGAAACGCACTGGAGCAAATT K 2 1 2 1 101000 r 74 goat snp22734-scaffold2265-515048 10 316415 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431646 Affx-122936131 AX-123301987 10 98950252 AATCAGACGCTACAAATGTTAACAGGAAGATGACC[A/C]CGAGCAGCAGCTACACTAGGCCTGAATCAGAGTAT M 2 1 2 1 201000 f 74 goat snp22735-scaffold2265-556051 10 275587 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454221 Affx-122919677 AX-123324554 10 99009067 TTCAGAAGATTCCAAAATGACTCTTTCTGTAGTCA[A/G]CCCCTCTCTCCTTCCCTCAACCTTTCTATTCAGGC R 2 1 2 1 201000 f 74 goat snp22736-scaffold2265-614866 10 216797 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417421 Affx-122947219 AX-123287769 10 99074095 CACAGGGGATTTCTAGAAGACATACAAATAACATG[C/T]AAGTGTGATTCACTTTGGGAGGGGGGGATCTATTT Y 2 1 2 1 101000 f 74 goat snp22737-scaffold2265-679894 10 147382 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448032 Affx-122923713 AX-123318368 10 99104430 GTAAGAAACCCTGAAATGCTAATCATGGGGAAAAG[C/T]AAGCACTAGCACATACTGGTTCATGGAGTAAATGA Y 2 1 2 1 101000 f 74 goat snp22738-scaffold2265-710229 10 116557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274081 Affx-1111834027 AX-519547684 10 99523504 CATTCCCCAAAAGTGAGGCTTCCACAGCATTAGAC[A/G]TGGTGGTACCTTCTAAAGCAGCTGCAGCAAGTCTT R 2 1 2 1 201000 f 74 goat GoatD01.015062 10 99523504 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320765400 Affx-986697384 AX-385252907 10 100154959 CATCCACACAATCAACTAGGCAGACTCTGTGTCTA[C/T]GGAATGTATAAAAGGCCACTGAGAGCTCCCACAAA Y 2 1 2 1 600010 r 74 goat 10_100154959 10 100154959 Ancestral_priority_1043 ancestry 0.582 neutral IMAGE 10K 10K ancestral 320762859 Affx-986697388 AX-385250881 10 100975945 GATGGCAGGAGAGGCAAGATAAACATTAAGATCCC[A/G]GGCGGGACTGACAGCTGCTGCAGCGCAAACTTCAA R 2 1 2 1 600010 f 74 goat 10_100975945 10 100975945 Ancestral_priority_1043 ancestry 0.56 neutral IMAGE 10K 10K ancestral 38437908 Affx-122931654 AX-123308246 11 17542 CACAGCCCTGTGGGAAAGCCTCGTGGGAAAGCCTC[A/G]TGGGAAAGCCTCGAGGGAAAGCCACAGATCCCTTG R 2 1 2 1 103000 r 74 goat snp41013-scaffold53-17542 NW_017212983.1 1480 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415321 Affx-122948804 AX-123285670 11 63994 AAGAGACACGCATGTGTGCGGAGTGTGTGCATGTG[C/T]GTGCGCACACATGCATCCACGATAGATCCAGGCAC Y 2 1 2 1 202000 r 74 goat snp41014-scaffold53-63994 NW_017190156.1 37736 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272700 Affx-1111832940 AX-519546404 11 90598 CTGATATAGAATACAGGATGGAGTGTTTTTCTGAT[A/G]GAAGTCATTCCCACATGTCAGAATGGGAAGGATTT R 2 1 2 1 101000 r 74 goat 11_90598_AF-PAKI 11 90598 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446241 Affx-122925692 AX-123316577 11 201500 GTGCACTGCTGGGACTTGAACGGTACCAGAACTCC[A/G]GCGAACATCCGTCTGTGGGTCAGCTGGGCGGTCAA R 2 1 2 1 101000 f 74 goat snp41015-scaffold53-201500 NW_017190156.1 97295 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446268 Affx-122925673 AX-123316604 11 254271 AATCATGAGCACTGAAAAATGGTCTCCCTATTTCA[C/T]TTCAGGGTCCTCAGCAAGTTGTTAAAAAAGCGGTG Y 2 1 2 1 101000 r 74 goat snp41016-scaffold53-254271 11 50944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793655 Affx-122950086 AX-385280628 11 286830 CGCCTGGCACAGAGTAGACGTAAAGGATGTCAGAT[A/G]CTACTGTTACTGTTGCTGTCGTCATTATTGCTCTG R 2 1 2 1 101000 r 74 goat snp41017-scaffold53-286830 11 83822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405114 Affx-122956975 AX-123275466 11 317286 TTTCTGAGTGGGTAAGGCCTTCACTCCTGCTCCAG[A/C]TATTTAAACTGCCTCTTTCAGGGGTTCCACAGAAG M 2 1 2 1 202000 f 74 goat snp41018-scaffold53-317286 11 115556 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396289 Affx-122963098 AX-123266644 11 351975 GGTGCAATCATGGAGTCTCAATCCCTGGATGGCCA[A/G]GGAAGTCCTTGACCATATGCTTTTGAAAAGCCAAC R 2 1 2 1 101000 r 74 goat snp41019-scaffold53-351975 11 150245 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406534 Affx-122955125 AX-123276886 11 394331 TCCACTACCTCTGCGGCTGGAAGCCCAGGATTCTG[C/T]ATTTCAAAATTCAACTGGAGCCATATGAGTTGGGG Y 2 1 2 1 101000 r 74 goat snp41020-scaffold53-394331 11 192691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437808 Affx-122932119 AX-123308146 11 435674 AAATACACACATACACACGTATTTTTAAAAACAGA[C/T]ACAGAAAAAGCTTGTTAAAAACATCTCTCTCTACT Y 2 1 2 1 201000 r 74 goat snp41021-scaffold53-435674 11 234015 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409509 Affx-122953632 AX-123279860 11 467707 GCCAACCTTTCCTGAAAAGAGAGAGAGCAGTGAAT[C/T]ATCCAAGTACCCCATGCATTGTGAAGTCAACCTGT Y 2 1 2 1 201000 r 74 goat snp41022-scaffold53-467707 11 265811 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276598 Affx-1111835424 AX-519550109 11 480342 TTCCCTTCTCTCAGGAATTCTTTTTCCTCAGTCAA[A/G]TCTAGCTAGTAGGGTTGCCACCAATTCCTTTAAGC R 2 1 2 1 101000 r 74 goat Random2.2K-1131 11 480342 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409811 Affx-122952959 AX-123280162 11 499939 AATGAAATAATGGACATAAAGTACCTAAGATGGTC[A/G]CTGACACATAGTAGGTGCTTCTTGAACATTTGCTG R 2 1 2 1 101000 f 74 goat snp41023-scaffold53-499939 11 297886 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428416 Affx-122938836 AX-123298759 11 590429 ACTTCTTAGGCCTATTAGTCCTTTAAACCTAGCAA[C/T]GCCACACAGTGAGATTACAGCTCAAAAACATTGTT Y 2 1 2 1 101000 f 74 goat snp41024-scaffold53-590429 11 389193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436216 Affx-122932581 AX-123306555 11 649343 AGAACTGATGAAATCAGAAATGCTTAGCGTTGTTG[C/T]ATTCCTGGTTCCCATCCATAAAAATGGTTTCTTCT Y 2 1 2 1 201000 r 74 goat snp41025-scaffold53-649343 11 449124 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390718 Affx-122967930 AX-123261075 11 700718 GAAGGACATAGTTCAGGACCCAAGATTCGCCTTAG[G/T]ACAGAAAAGAGTGATGCCCACCCTGAGGGAACACC K 2 1 2 1 101000 f 74 goat snp41026-scaffold53-700718 11 499229 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430692 Affx-122936917 AX-123301033 11 737352 TGGAGAGGGATTGTGGTCTTTTGCATCATTTCAAA[C/T]ATTTTTAGTTCAAGAAAAACCACCACAGCAGAACC Y 2 1 2 1 101000 f 74 goat snp41027-scaffold53-737352 11 531810 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401222 Affx-122959319 AX-123271575 11 766609 TTTGTTATCTCTCTTCCATCTCAGCTCTCTCAACT[A/G]TTAGAGGTGGTAATGGTTGGCCCCAAGTTTGGGAC R 2 1 2 1 102000 f 74 goat snp41028-scaffold53-766609 11 560918 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442946 Affx-122928224 AX-123313283 11 807286 GGCAGAGAAGACGAGGTTGATACCCCCACCTTATT[A/G]CCTTTGGATTTGATCATGTGACTTGCTTTGACCAA R 2 1 2 1 303000 f 74 goat snp42567-scaffold564-1213742 11 601450 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416857 Affx-122948095 AX-123287205 11 881568 TTTTAAACCATTGTGTGCATGCTCAGTCTCTCTAG[C/T]CATGTCTGACTCTCTGCGACCCCATGGACTTAACC Y 2 1 2 1 102000 f 74 goat snp42565-scaffold564-1139460 11 676084 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437345 Affx-122931944 AX-123307683 11 919902 GGGGAGAATTTTGATTGGGTGAAGCAAAACAAGAG[A/G]ATGCCACTGTGACTGGTTCTAGGATGGGCCCCCAA R 2 1 2 1 101000 f 74 goat snp42564-scaffold564-1101126 11 714450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787717 Affx-122924162 AX-385274740 11 977070 AAACCAAATAGCTCTCTAGTCCCCAATGAAATATG[C/T]AACAAGTACTGGAAATATGCAATATGTTAAATATT Y 2 1 2 1 101000 f 74 goat snp42563-scaffold564-1043958 11 771644 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375727 Affx-122978628 AX-123246086 11 1008334 CTTTTCTCTCTTCCCAGGAGGAAACCGGGGACTGT[A/G]CTTTCTAGGCAGGAAATACTAGGGCCCCACTGACG R 2 1 2 1 201000 r 74 goat snp42562-scaffold564-1012694 11 803091 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603230 Affx-1002479463 AX-413837411 11 1038097 TCCAACTCCTTTGCGACCCCATGGACTGTCACCCA[C/T]CAGGCTCTTCTGTCCATGGGATTCTTCCAGGCAAG Y 2 1 2 1 303000 f 74 goat 11_1038097_RH-map 11 1038097 T C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38445372 Affx-122925409 AX-123315709 11 1048021 GCACTGGTTGCTGAGACTTAGAAGCATGTAATATA[C/T]ATCTTAATAAAGGTCCCACTTTCCTAAGTCTTCCT Y 2 1 2 1 101000 r 74 goat snp42561-scaffold564-973007 11 843048 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450944 Affx-122921762 AX-123321278 11 1079365 CAGGTACACACAACTAACCAGCATATTGAAACTGC[C/T]TTTATAACTTTCTTGAAATTATTTTAAAAATCTGT Y 2 1 2 1 103000 f 74 goat snp42560-scaffold564-941663 11 874402 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603314 Affx-1002479464 AX-413837492 11 1125698 TGACTTAGTGACTGAATGACAATAGGTGTAGCTGA[C/T]AGGCTTAATGGAAAGATAGAACATCAGTCCTGAAA Y 2 1 2 1 201000 r 74 goat 11_1125698_RH-map 11 1125698 C T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603606 Affx-1002479465 AX-132431298 11 1142438 GTTCCCTTTTCTCCACACCCTCTCCAGCATTTATT[G/T]CTTGCAGATTTTTGGATCGCAGCCATTCTGACTGG K 2 1 2 1 103000 f 74 goat 11_1142438_RH-map 11 1142438 T G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38427983 Affx-122939180 AX-123298326 11 1146171 AGAATCCTGCCCCATTCGGCCAGGCCAGGAGGCTC[A/G]TGTCTCTTAGTTCCCCCACATGCAAGGGTTAATAA R 2 1 2 1 101000 r 74 goat snp42558-scaffold564-874857 11 942758 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603234 Affx-1002479466 AX-413837415 11 1211949 TAGGAGCCTTACCTCTCACTGAGAAATGGGAACAT[A/G]TCCCCCATTAAAGGAATTTCAAGCCCCAGTCAGCA R 2 1 2 1 102000 f 74 goat 11_1211949_RH-map 11 1211949 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38452194 Affx-122920823 AX-123322527 11 1220548 GGCCAAGAGCGCCATGCTTTATAGACTCAGCTTTA[C/T]GCTTCCTTGGAAGTGACTCTCGCCCTGCTCAGGAA Y 2 1 2 1 101000 f 74 goat snp42556-scaffold564-800480 11 1017345 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603236 Affx-1002479467 AX-413837417 11 1238333 GCAGCCTTGTACACCAGCGAAGAACTCCACTTCTT[C/T]ACAGGGTATAATTCTTTTTATACACTGCAAGATTT Y 2 1 2 1 102000 f 74 goat 11_1238333_RH-map 11 1238333 T C 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38394716 Affx-122964338 AX-123265071 11 1259124 GATGGAGGACCATCCATGCCTCCCTTAAGGCCTAT[A/G]TGGAGTATCTACTGGACACAGCCTGGATGCTGCAT R 2 1 2 1 201000 r 74 goat snp42555-scaffold564-761904 11 1055686 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603239 Affx-1002479468 AX-413837420 11 1273408 ATAGTAAAAATGATCCAAAACCTTGACATCAAAAT[A/G]TCTGGAGACAAGGACTGAGAAGATGCAAGAAAGGT R 2 1 2 1 303000 f 74 goat 11_1273408_RH-map 11 1273408 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38397007 Affx-122963136 AX-123267362 11 1290652 TATTTTGTGTTACAGAAATATAAAGTAGGAGTATC[A/G]TTGTCCAGAAGTTGTTGAGCATTTAGTTGAAATTT R 2 1 2 1 101000 r 74 goat snp42554-scaffold564-730376 11 1087530 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603241 Affx-1002479469 AX-413837422 11 1364085 ATAACTGCAAGTGTTTCAGACATTACGTAGTGACA[A/G]TAAGGAGCAAACATGGGATTAGTGACCTCCAAAAG R 2 1 2 1 101000 f 74 goat 11_1364085_RH-map 11 1364085 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38451891 Affx-122921044 AX-123322224 11 1365669 CTCTCCAGCCTTTTTCCAGTGTAATATAAATAAGA[C/T]TTCCTCACCTGTGGAAGCTGATGAGCTCACACCGG Y 2 1 2 1 101000 f 74 goat snp42553-scaffold564-655359 11 1162886 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603243 Affx-1002479470 AX-413837424 11 1378787 TTGCGACCCCAGGACTGTCACCCGCCAGGCTCCTT[G/T]GTCCATGGGATTCTCCAGGCAAGAATACTGGAGTG K 2 1 2 1 303000 f 74 goat 11_1378787_RH-map 11 1378787 T G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320781241 Affx-122950772 AX-385268326 11 1396853 GTAGTTTCAATTTTTATTTCTCAAGCTCCAAAGTC[G/T]ACGGCCTTTCTATTATAAGATTCCTCTAAGAATTA K 2 1 2 1 101000 f 74 goat snp42552-scaffold564-624175 11 1194119 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603246 Affx-1002479471 AX-185342279 11 1462153 TAGGTTGGTCATAGCTTTTCTTCCAAGGAGTAAGC[A/G]TCTTTTCATTTCATGGCTGCAGTCACCATCTGCAG R 2 1 2 1 103000 f 74 goat 11_1462153_RH-map 11 1462153 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603248 Affx-1002479472 AX-413837428 11 1499996 ATTCAGTTTCAGGTAGGAAGCATCAGAGTATTACA[C/T]AATTCTTCTTAGACTTCTGGGCTCCTTTGCAAAAT Y 2 1 2 1 101000 f 74 goat 11_1499996_RH-map 11 1499996 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603249 Affx-1002479473 AX-413837429 11 1515595 TAGAATCCTTTGGAAACCTGATTTGTGAAAACTTT[A/C]CTCTTAAATTTCCCAGTAGATTGCTCTAAAATAAG M 2 1 2 1 101000 f 74 goat 11_1515595_RH-map 11 1515595 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38413964 Affx-122950301 AX-123284313 11 1516843 TCCTGGGCAGTCTGTGTAACATTCAGAGCTGAGGG[C/T]GAGTCAGTGACTTGCTTCTGCTGATATGGCACCTC Y 2 1 2 1 101000 r 74 goat snp42550-scaffold564-504185 11 1314385 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603252 Affx-1002479474 AX-413837431 11 1550580 GAACTGGAACCAGTGAAGAGAGTTAACCAGTGGCA[C/T]CTTTCCATTCTACCTGCGCAAGGACAGGTGAGGAC Y 2 1 2 1 101000 f 74 goat 11_1550580_RH-map 11 1550580 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603333 Affx-1002479475 AX-413837509 11 1566892 TGTGGCCCTGGGCAAATGACTTGACCTCTCTGAGG[C/T]TCAGTTCCCATACTGATAAAAGAGGATAACAAGAC Y 2 1 2 1 102000 r 74 goat 11_1566892_RH-map 11 1566892 C T 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603255 Affx-1002479476 AX-413837435 11 1596076 TGGAATGCAAAAGAAGGAAGTCAAGAAACACCTGG[A/G]GTAACAGGCAAATTTGGCCTTGGAGAACAGAATGA R 2 1 2 1 103000 f 74 goat 11_1596076_RH-map 11 1596076 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38375627 Affx-122978705 AX-123245986 11 1603340 CTTCTCTCCGTCTTTGGAATCCTGTATGGTAATCC[A/G]CTGTGGCTGAACCCTCTCCTCGTGGACGTTTATGT R 2 1 2 1 101000 f 74 goat snp42548-scaffold564-417688 11 1402175 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381581 Affx-122974806 AX-123251939 11 1645002 GTCAAAGACCAGGTATCACACTGCCCCCACCTCCC[A/G]AGTCTAACCCACCAGCTCTGTCTCCAGAATCCTCC R 2 1 2 1 201000 r 74 goat snp42547-scaffold564-376026 11 1443046 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603258 Affx-1002479477 AX-413837438 11 1651183 TTTCTCCTTTGCATTTCACTTCTTTTCTTTTCTCA[A/G]CTATTTGCAATGCCTCCTCAGACAACCATTTTGGC R 2 1 2 1 303000 f 74 goat 11_1651183_RH-map 11 1651183 G A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38441955 Affx-122928570 AX-123312292 11 1680028 CTCTCCCTCCTAGAGAGCTGAGATTCTTCTGTGTC[A/G]GTGTGGATATGTTTTTATTCTTATTTGCCTTGTTG R 2 1 2 1 201000 f 74 goat snp42546-scaffold564-341000 11 1478121 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603259 Affx-1002479478 AX-413837440 11 1687609 CTCGACGGCTTCTAGTTTGCAGAATCCCTAGAATG[C/T]AACGCTTGAGAAGTAACGGCCTGGGTCCGCTCGCA Y 2 1 2 1 101000 f 74 goat 11_1687609_RH-map 11 1687609 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38415242 Affx-122948952 AX-123285591 11 1737118 TTCATGTAAGTGCCAAAAAGCATGCAGTATATGGT[C/T]GCAGCAACTCCAAAGTAATCAATCTAAAAAGAAAT Y 2 1 2 1 201000 r 74 goat snp42545-scaffold564-283910 11 1534574 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603341 Affx-1002479479 AX-413837517 11 1744023 ATATACATTTATTATAATAACTTTTAATGAAGTAA[A/G]ATCTATAAAATGCTGAATCACTGCGCTGTACACCT R 2 1 2 1 103000 r 74 goat 11_1744023_RH-map 11 1744023 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320773935 Affx-122969468 AX-385261074 11 1838866 TGTATTTCAAGATCACAGTTTTGAATACCAGGCTG[C/T]ACTCTGTACTCCTTACTCCTAGACGTGGGTCTTAT Y 2 1 2 1 101000 f 74 goat snp42543-scaffold564-182162 11 1632656 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775885 Affx-122924314 AX-385263016 11 1874840 TAACATGTAGATTGTTGTAAAAACTTCAAATGACA[C/T]AGAAACAATCAATAAAACCCCGAAAACTCCCTCCC Y 2 1 2 1 101000 r 74 goat snp42542-scaffold564-146188 11 1668559 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 350603343 Affx-1002479480 AX-413837519 11 1889836 TTCTCTCCAGTGTGAGTTCTCTGATGTTTAATAAG[A/G]GATGAAGTATGACCAAAGGCCCTTCCACATTCATT R 2 1 2 1 201000 r 74 goat 11_1889836_RH-map 11 1889836 A G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603266 Affx-1002479481 AX-413837446 11 1905754 GAGGTTGCCTCACATGGCACTCAGTAAAGGTTAGC[C/G]TTAATGATAGTTAATAAAAAGCTTTGTGTATGTTT S 4 1 2 1 101000 f 74 goat 11_1905754_RH-map 11 1905754 G C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38416524 Affx-122947768 AX-123286872 11 1911608 GGTAGTGGTTACATCAATCTACACATGTGAGAAAA[C/T]GGCATGGAATATAGACATAGCCTACGAACATTAGT Y 2 1 2 1 101000 f 74 goat snp42541-scaffold564-109420 11 1705577 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603268 Affx-1002479482 AX-413837448 11 1920414 TGAGTAGGATCGAAATAGCTGGAAGGGGGACTTCC[C/G]TGGTGATCCAGTGGTTAAGACTCCATGCTTCCAAA S 4 1 2 1 102000 f 74 goat 11_1920414_RH-map 11 1920414 C G 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603349 Affx-1002479483 AX-413837525 11 1960622 AGAAATACCCTCCTGTATCCCTGCGGAGGCCAGGG[A/T]AGGTGGGCACTGGTCTGTGGTGACACTGCCTTCTC W 4 1 2 1 400000 r 74 goat 11_1960622_RH-map 11 1960622 A T Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38392364 Affx-122966245 AX-123262721 11 1969359 CCCTCTGGTGGTTCTGACCCAGGACAAGCAGGGGA[A/G]TAGATGCGGGTGGGCAGCATCTTCCTTTGTCCTTT R 2 1 2 1 202000 f 74 goat snp42540-scaffold564-51669 11 1764106 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603271 Affx-1002479484 AX-413837451 11 1985244 CAGTGGTAAAGAACCTGCTTGTAATGCAGGAGACA[C/G]GTGTGTGATCCCTGGGTCAGGAAGATTCCCTGGAG S 4 1 2 1 103000 f 74 goat 11_1985244_RH-map 11 1985244 G C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38389723 Affx-122968673 AX-123260081 11 2003620 GGAATTTCAGGTCAGCTGAGACTGGCTCTGTGGCC[C/T]TTCTTCCCACTGCCCATCACTGTGTGACAGCTTTT Y 2 1 2 1 101000 r 74 goat snp42539-scaffold564-17408 11 1787448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401394 Affx-122959218 AX-123271747 11 2028368 CGCCCTCCATAGCCCAGAACTTATAAAGTAGTCCC[A/G]TCTTTATTGAAAATTATTTCCCTGCAAACATGAAA R 2 1 2 1 101000 f 74 goat snp24043-scaffold2446-7241 11 1812364 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433079 Affx-122935735 AX-123303420 11 2059738 TGGGGTGAGACTGTGTCTCGGGGGCACCTTGCCTG[C/T]AGGTCCCTAAGCTCTAAAAGGAACATCCTCCCACT Y 2 1 2 1 101000 r 74 goat snp24044-scaffold2446-38611 11 1844111 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774078 Affx-122975253 AX-385261216 11 2152590 TGGTCGACAGTCCCTGCTCCACTGTCCAGGGTGCT[C/T]TAAAGACACAGCTGCGGTGTCCTTTGTGCTCCGAC Y 2 1 2 1 102000 f 74 goat snp24046-scaffold2446-131463 11 1937343 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436402 Affx-122933028 AX-123306741 11 2219272 CCCAGCCATCATGACTTTGCTCCTGACAAGAGAAA[A/G]GAGAAATCAGGGGAAAGGAGAAAGTGGGAGTGCCT R 2 1 2 1 101000 f 74 goat snp24047-scaffold2446-198145 11 2004212 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444198 Affx-122927259 AX-123314535 11 2259473 TTTGGTCTGTGAGTCGTGGAGAATTCATTCATCAG[A/G]ACCATTTTGGTTGCAACCCAGCTCACATCGGCTTA R 2 1 2 1 101000 f 74 goat snp24048-scaffold2446-238346 11 2045835 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420452 Affx-122944889 AX-123290799 11 2307757 AAACATATTCATAAGCACCAATCAGGAAATCCTAA[C/T]ATGACATATAGTTCACCATTACTTCTTGGTTTCTT Y 2 1 2 1 201000 r 74 goat snp24049-scaffold2446-286630 11 2092293 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379643 Affx-122975948 AX-123250001 11 2318685 CCTTACTCGTACTTTTAAATTTTTAGTTTAGAAAT[A/G]CTTCGAAAATTAGAGGGAAGCTGGGGGGAAACTGC R 2 1 2 1 101000 f 74 goat snp48760-scaffold693-7801 11 2102072 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765361 Affx-986697357 AX-385252877 11 2420080 GGTCCAGTTAAGACTCCCATGCTTCCACTGCTGGG[C/G]ATGAAAGTTTGCTGCTACGAGCCAAGAACACGCCG S 4 1 2 1 600010 r 74 goat 11_2420080 11 2420080 Ancestral_priority_1043 ancestry 0.708 recommended IMAGE 10K 10K ancestral 38447227 Affx-122924972 AX-123317563 11 2427910 TGCCCTCCACCTCCTGTGTCGGGCACTTGGCACAC[A/G]CACATAGCCCACTACCACTGAGATATCTGTCTTGG R 2 1 2 1 101000 r 74 goat snp48762-scaffold693-117026 11 2207444 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443741 Affx-122927131 AX-123314078 11 2547440 GAAGACAACGAGAAGACTCTGAAGAGCTCAATCTC[A/G]CTCAGGGTCGGCTTTAGAAGCTGGTTGTAAGTCTG R 2 1 2 1 201000 r 74 goat snp48765-scaffold693-236556 11 2323750 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401972 Affx-122958782 AX-123272325 11 2577808 AAAGCACTTAGACTAAGCGCTGGCACATGCCAGCC[A/G]TATGGTAAAACAACATGCCTATTGCATAATTTTCT R 2 1 2 1 201000 r 74 goat snp48766-scaffold693-266924 11 2354349 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384181 Affx-122972412 AX-123254539 11 2614924 TCAGGAGACCAGAGTGGATGGAGGTCAGAGGTTTC[A/G]GAAGAGGTGAGGTTTGACTTGGGCCATGAAGGGTG R 2 1 2 1 201000 f 74 goat snp48767-scaffold693-304040 11 2385791 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415658 Affx-122948562 AX-123286007 11 2648276 CATGATCAATGTTGATTTCATTACTTTGCAGACAA[C/T]AGTTTTCTTCTATGGGTTTCTGAAAATAGAGCAAC Y 2 1 2 1 101000 r 74 goat snp48768-scaffold693-337392 11 2419162 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272610 Affx-1111832916 AX-519546322 11 2666158 AAGACACCTGGAAACGATTGTGTGTCCATCAGCAG[A/C]AGCTCTATCCTGGCCCCTACCAGCGGATTTCTCCA M 2 1 2 1 101000 f 74 goat 11_2666158_AF-PAKI 11 2666158 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38382562 Affx-122973769 AX-123252920 11 2693067 TTCAAGGTCCTGTTTCTCCCCTGGGATTTCTCCCC[A/G]TTCCTGGCTTTATAAGCCTTGACCTTCCTTCACAC R 2 1 2 1 101000 r 74 goat snp48769-scaffold693-382183 11 2464298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449789 Affx-122922426 AX-123320124 11 2727915 CAGCGTGCCGCTGCCCTCTGGCTCAGCTCTGCTGC[C/T]CTCCCTCCTGGGGGTCTCAGTGCAAGGACAGACTT Y 2 1 2 1 303000 f 74 goat snp48770-scaffold693-417031 11 2499033 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386364 Affx-122970854 AX-123256722 11 2762088 CATCTAGTCCTGAGTTTTATTTCCAGAAGCTAAAC[A/C]AGTCTTCCTTTGCTTTCAAACAAACTCAGCATCCT M 2 1 2 1 101000 r 74 goat snp48771-scaffold693-451204 11 2533020 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454006 Affx-122919433 AX-123324339 11 2857427 TATCAGCCCCTTGCAAGTGAGAACTCTGTGTCTGT[C/T]ACCCACAGTATTAGCAAGGAGAAGGCACTGGAGAC Y 2 1 2 1 101000 r 74 goat snp48773-scaffold693-546543 11 2627429 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392720 Affx-122966032 AX-123263077 11 2904301 TGGAAAAGTTTCATGAAAGGGGCAATACTTACCCC[A/G]TCACATGTGGTGTACTCTGTGATTTTTTGCTTTAA R 2 1 2 1 201000 r 74 goat snp48774-scaffold693-593417 11 2673804 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398675 Affx-122961876 AX-123269030 11 3012197 CACCCTGGAACTCAGCCCTGGGTTCCCTCAGCCCA[C/T]GAGTGTGTGCTGAGGTCCTGCGTGTACCAGGTACT Y 2 1 2 1 202000 r 74 goat snp48776-scaffold693-701313 11 2781893 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418396 Affx-122946554 AX-123288744 11 3077569 AAGCCAACCGTGTCATCTGCTTCCCAGGGGAGAAA[C/T]AGCACTTGTACTGGGTTCCATCCCCTCACTGTGCC Y 2 1 2 1 101000 r 74 goat snp48777-scaffold693-766685 11 2847754 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378630 Affx-122977112 AX-123248989 11 3107243 ATCTTTGTCAAACTAGTTATTTGTTGCCTTTTTGA[C/T]GATAGCCATTCTGACATGTGTGAGGTGGTATCTCA Y 2 1 2 1 303000 f 74 goat snp48778-scaffold693-796359 11 2877720 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773694 Affx-122979077 AX-385260834 11 3147069 TCAAAGTGAACATTAGATTTCCATGCTCTACTTTT[A/C]GGATCTTACTGCAATTGGAAGCACTTGTGCTATTT M 2 1 2 1 101000 r 74 goat snp48779-scaffold693-836185 11 2918371 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394078 Affx-122964965 AX-123264433 11 3176809 CTTAGAGCAAATTCTTTCAGCTTTTCACCGTTGAG[C/T]ATGATCTCTTAAGTTCGAATGCATTCCGACGGTCC Y 2 1 2 1 101000 r 74 goat snp48780-scaffold693-865925 11 2947824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410349 Affx-122952458 AX-123280699 11 3217705 TAATTATAGCACAAGGTGGGTATCTTGTGGAGAAC[A/G]TGGTGAGATGAAAGGACAAATACTGAAGAGCTGAG R 2 1 2 1 101000 f 74 goat snp48781-scaffold693-906821 11 2989021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429493 Affx-122937870 AX-123299835 11 3292383 GAGGTTCTGGCAGCCATTATTACGGGCTTAATGTT[C/T]AATGCCCACAAAGAGGACCTTCTACACGGCATGCC Y 2 1 2 1 102000 f 74 goat snp17753-scaffold1842-24597 11 3062476 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418812 Affx-122946165 AX-123289160 11 3343741 AACAAGGGCACCAGGCTAGGTGAATATACACACAC[A/G]TCTCTCCTAGCACTGGGATCCAACTGCTGAGACCA R 2 1 2 1 101000 r 74 goat snp17754-scaffold1842-75955 11 3114584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426637 Affx-122939948 AX-123296983 11 3406415 TGGTCCTCCTGGGCTGACATGTATCACACCCTTCT[A/G]CTGCAGACAGTGGGTGTCATCTATTGCCCTTTTCA R 2 1 2 1 101000 f 74 goat snp17755-scaffold1842-138629 11 3178294 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436462 Affx-122932984 AX-123306800 11 3440769 CACCAGTGGGCCCCAGGTTCATCCCTGGTCAGCGA[A/G]CTAAGATTCTGCAAGCTGTGCACACATAAACAGGA R 2 1 2 1 103000 r 74 goat snp17756-scaffold1842-172983 11 3212641 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430721 Affx-122936897 AX-123301062 11 3607915 GTTCTCTGCCTTATAGTTCTCTGAATGATACTTGT[A/G]GGAGTGGAGATCAAGTCTGAGAATGGCTTCTAGAT R 2 1 2 1 101000 f 74 goat snp17760-scaffold1842-340129 11 3381735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451656 Affx-122921596 AX-123321989 11 3640405 GATCTGAATTGTATCTCTACTGTATTTGTGTAGTC[A/G]TTCCTTTACCTTTCAATCTGTAGTTGACAGGCACA R 2 1 2 1 101000 r 74 goat snp17761-scaffold1842-372619 11 3414681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385249 Affx-122972089 AX-123255607 11 3673198 TTCCTGAGAATTTCCAGAAGGACAGAGACCCTCCA[G/T]TCCTAGGCAGAAGAGAGTCCTTCATTCATAGCAAA K 2 1 2 1 101000 r 74 goat snp17762-scaffold1842-405412 11 3447928 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407543 Affx-122954690 AX-123277894 11 3715923 TGCTCTGGGGACTTCTACCAGGCAAGAGAGGAGAA[A/C]GCAGATATAGGGTCTTTGGAAGAGATGCCCCTGAA M 2 1 2 1 101000 r 74 goat snp17763-scaffold1842-448137 11 3490537 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384771 Affx-122972018 AX-123255129 11 3782182 TGGAAAAGGACTTGGTTTCAGGCAGGGATCAGGCC[C/T]GCTGAAATCATGTGAGGGTCTCATTTTGCGGGGAA Y 2 1 2 1 101000 r 74 goat snp17765-scaffold1842-514396 11 3556766 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415871 Affx-122948492 AX-123286220 11 3820904 GGTAATTTACGTCTTTGTGGGCTAAGGGAGCTGTG[A/G]TGGGGTCTGATGGGCTCCGCTCTCTCTCCCCTTGT R 2 1 2 1 101000 f 74 goat snp17766-scaffold1842-553118 11 3595757 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452600 Affx-122920493 AX-123322933 11 3860197 TCTGCTTTTCTCATCAGCCTGCTCATCCCTCCCCC[A/G]CAAGGCATTGGTGCCTCCAAGGCCTGAAGCAATGT R 2 1 2 1 101000 r 74 goat snp17767-scaffold1842-592411 11 3632837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392664 Affx-122966433 AX-123263021 11 3895425 GTGAGCTTGGGAGTGCAGCAGCCCTGGGTGCGGGC[A/G]TGTGTGGCTGGGTCTTGATTTCATAGACTCTGTGG R 2 1 2 1 101000 r 74 goat snp17768-scaffold1842-627639 11 3667952 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450948 Affx-122921759 AX-123321282 11 3985227 TTCCTCCCTCAGACTCTGTAATGAGGCTGCAAACA[C/T]GAACAATGTGGAGAGAAAGGACTACAATTATACAA Y 2 1 2 1 101000 f 74 goat snp17770-scaffold1842-717441 11 3756589 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437374 Affx-122932448 AX-123307712 11 4023630 CAGATTTGCCTTCTGTCGATCACAGTGTTTCTAAA[G/T]ATTAAAGAGGAATGTTAGTGTTACACTAGAAAGTG K 2 1 2 1 101000 f 74 goat snp17771-scaffold1842-755844 11 3794859 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390315 Affx-122967711 AX-123260672 11 4053246 TCTTTGAAACAAAGACATGTGGTCTCATTTGCTGT[C/T]AGGGCAGAAGTGGAAAGACAGGAGAGGAAGTAGGC Y 2 1 2 1 101000 f 74 goat snp3233-scaffold1098-8780 11 3905487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384616 Affx-122972172 AX-123254974 11 4083887 CTGGGCAGGACGGTGCACTCAAAGCTGCGCGACCT[C/T]GGGCAAATTGCTTAATGTCTCGGGCTTCCTGTTCC Y 2 1 2 1 101000 r 74 goat snp3234-scaffold1098-39421 11 3936399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799539 Affx-122952836 AX-385286469 11 4153099 GATTTTCTGAAATTTCTCCCAAGCTTGGTTTACTC[A/G]CTTATAAGATGGTATCTCTTACCTCCCCTCCTACA R 2 1 2 1 101000 f 74 goat snp3235-scaffold1098-108633 11 4005532 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422317 Affx-122943467 AX-123292663 11 4182826 GGGATGAATGGACCCAAACCCTGGGGCGCGGGGAA[A/G]CTTTATGAGGGCTGGTCTGTTTTTAACTTGAATTT R 2 1 2 1 201000 r 74 goat snp3236-scaffold1098-138360 11 4035389 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425812 Affx-122940692 AX-123296158 11 4213281 GAGCAGTGGCCTGAACCTCACAATTTCCAGTACAA[A/G]TCGTGTGTGCAGAAGTGAATGTCACTTACACCTTG R 2 1 2 1 101000 f 74 goat snp3237-scaffold1098-168815 11 4065632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439578 Affx-122930077 AX-123309915 11 4251404 AAACATGTTCATAAGGCAACCCTCTTCTGCTAACT[A/G]CCAGAGCAGCTCTTCCGTGGCTCTGTCAGTGAAAT R 2 1 2 1 201000 f 74 goat snp3238-scaffold1098-206938 11 4103360 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787822 Affx-122932696 AX-385274845 11 4287049 CAATTATGTAATGATGTTTTACATAGCACTATTAA[C/T]GGTAGATGGTTACTGAGTTTTCTTACTCCCTCAAA Y 2 1 2 1 101000 r 74 goat snp3239-scaffold1098-242583 11 4134855 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789661 Affx-122926484 AX-385276670 11 4343966 TGAGTAAATAAATTCAATACTATCTCAATTCTAGA[C/T]GAACTAACAGTAGCTTTAGCCTCAGACTCTACTTC Y 2 1 2 1 101000 r 74 goat snp3240-scaffold1098-299500 11 4192529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388572 Affx-122969538 AX-123258930 11 4378387 CAGAGCACCTATAGAGCCTGCAAACCTCCCACAAA[G/T]AAAACGGAAACACTGAGGGACAGAAGGCGATCTTA K 2 1 2 1 101000 f 74 goat snp3241-scaffold1098-333921 11 4227301 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443619 Affx-122927301 AX-123313956 11 4438970 CTGTGCACCAGGATGGGTGCCACACTGGCTTGCAC[A/G]CTGCACAGCGATGCCCGAGACATACTCGTTTCTTT R 2 1 2 1 101000 r 74 goat snp3242-scaffold1098-394504 11 4288499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385815 Affx-122971027 AX-123256173 11 4471335 TCACTCTGTAGTCTGGGGAGACACTTGTGCTTGCT[C/T]GGGAGAAACACACAGTGTGAAGCCTGATCTCCCTG Y 2 1 2 1 201000 r 74 goat snp3243-scaffold1098-426869 11 4320789 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400264 Affx-122960132 AX-123270619 11 4502046 GAATCCTCTACCACTGAGCCACCAAGGAAACCCAG[C/T]TGTTGTTTTATGAAGGGACAAAAAGGAGGGACATC Y 2 1 2 1 101000 r 74 goat snp3244-scaffold1098-457580 11 4351587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422189 Affx-122943510 AX-123292535 11 4539973 CTGCATTGCAGGCAGATTCTTTACCATCTGAGCCA[C/T]AAGGGAAGCCCGATTAACGATATATTTGATCTTAT Y 2 1 2 1 303000 r 74 goat snp3245-scaffold1098-495507 11 4389414 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431019 Affx-122936668 AX-123301360 11 4571630 TCTTCCCACAGCACCTGCTTCAGCTAGACATTGTG[C/T]ACTGTGCTTGATGATTTACAGACAGAATGGGTATA Y 2 1 2 1 101000 r 74 goat snp3246-scaffold1098-527164 11 4421200 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434091 Affx-122934168 AX-123304432 11 4600369 AATTGGAGTCAATGCAATATCATGTGGTAATATCA[C/T]CAAGAAAAACAAGGAATGGACCTGTCTGAACACTG Y 2 1 2 1 101000 f 74 goat snp3247-scaffold1098-555903 11 4450628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276450 Affx-1111835425 AX-519549967 11 4647860 ACCTGCTCCCCGGTCCCAATTATCGAGAAAGACGC[A/G]GGATCACAGGCGCGGGCCCCTGGGACCAAAGTAAA R 2 1 2 1 202000 f 74 goat Random2.2K-1132 11 4647860 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416238 Affx-122948213 AX-123286587 11 4649071 CAACTTAATTCAGCGCAACGAGCAGACCCAATGTC[A/G]AGTCAGAAGCCTGGACTCTGGATTCTGCCACTCGG R 2 1 2 1 101000 f 74 goat snp3248-scaffold1098-604605 11 4499463 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405981 Affx-122955526 AX-123276333 11 4679664 TTAAAAAAAAAAATCTTAAATATCAATCGTTTACC[A/G]TGAAGTAGGAGTAATGTTCTCTGAAAGTCTGGTAC R 2 1 2 1 101000 r 74 goat snp3249-scaffold1098-635198 11 4530049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400889 Affx-122959750 AX-123271242 11 4715609 TGGAAGTGGATGCCCAGGAGCTGTCAGTCATCAAG[A/G]GAGGTAGAGTTGTCTTCCCAGCGCTCCGTGAATCA R 2 1 2 1 201000 r 74 goat snp3250-scaffold1098-671143 11 4566758 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790750 Affx-122955849 AX-385277751 11 4746703 GTTCAAGGTAGAATTTATCCTCCTCATATTTTGTC[C/T]ACTGCTCTAAAGGCAAGACCTGTTTCCTCATGCTC Y 2 1 2 1 101000 f 74 goat snp3251-scaffold1098-702237 11 4597461 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380047 Affx-122975574 AX-123250405 11 4779733 AATTTAACCCATAGATAAGAGATACTATCACCCTT[A/C]GTTTTTAGATGAGGCTCAGGGAAGTTAAGTAACAT M 2 1 2 1 201000 f 74 goat snp3252-scaffold1098-735267 11 4630390 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420646 Affx-122944831 AX-123290993 11 4822720 AAAAGTCAGGCACACAGGACTGGGAACTGGGTTCC[A/G]CGCATAAAGTATTTCGAGAGAGAATCTCATCAGAA R 2 1 2 1 101000 r 74 goat snp3253-scaffold1098-778254 11 4673305 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794766 Affx-122963652 AX-385281726 11 4855024 GGCGGCTTCCATGTAAATAGCTGCTGTTGGCTTCA[A/G]TGCCATGAAGATACAGAATTACAGCTTTAAGCGAA R 2 1 2 1 101000 r 74 goat snp3254-scaffold1098-810558 11 4705709 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389518 Affx-122968292 AX-123259876 11 4870338 GACAGCCCTGCAGGGTCAGGAGAAAACTGGACTTA[A/C]GGGAGAGCTCCCTAGGACGAAGGCTGTTAGATAAA M 2 1 2 1 201000 f 74 goat snp6057-scaffold1214-7768 11 4722758 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390091 Affx-122968026 AX-123260448 11 4905079 GGGTTTCTAGCTTCCAGAACTTAGATAATAAATTT[A/C]TCTTGTTCACGGGACCCAGTTTGTGCTACGTTGTT M 2 1 2 1 101000 r 74 goat snp6058-scaffold1214-42509 11 4757299 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387818 Affx-122969677 AX-123258176 11 4935053 CTACTGTTTCTGCTTTTACTTACAACATTCTCTTC[A/G]TGTGTGAATGCCCCAGCGCCACATGCTTTTTGGAT R 2 1 2 1 201000 f 74 goat snp6059-scaffold1214-72483 11 4787218 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380283 Affx-122975413 AX-123250641 11 4973770 TTGCTTCAATTGCACCAGACAGGGAGCCCTCATGG[C/T]GAGGGAAAGTGACTGGGGAGGGTCTAATGTGTCTG Y 2 1 2 1 101000 f 74 goat snp6060-scaffold1214-111200 11 4827281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376710 Affx-122978971 AX-123247069 11 5011269 CTGCCAGAGAAAGGAAGACAAAAGTGATTCATAAA[C/T]TAAATATGCAGATATAAATAAACCAATAATGTTGA Y 2 1 2 1 102000 f 74 goat snp6061-scaffold1214-148699 11 4865405 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452919 Affx-122920197 AX-123323252 11 5117283 TAATTTCCAGTCTACATTCTCAAGGACATGCCCCA[C/T]GTCTAGAAGGCTTTCATGAGACCTGAGAGGTACAT Y 2 1 2 1 201000 r 74 goat snp6064-scaffold1214-254713 11 4969935 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447391 Affx-122924415 AX-123317727 11 5146945 TAATTGTTTCTTTGCTCCTTAAAATTGCCTGTGAT[A/G]CCAACAGGGTATCCAACACAATCCCGATTTCGCCC R 2 1 2 1 101000 r 74 goat snp6065-scaffold1214-284375 11 4999651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775207 Affx-122966734 AX-385262338 11 5192251 GTGGTATAAATGGTGATTTTAAAATGCCCGTCATG[A/C]AAATGCTATGATTAATCAATACTTCTTAAGGGATT M 2 1 2 1 101000 f 74 goat snp6066-scaffold1214-329681 11 5044635 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781528 Affx-122929520 AX-385268613 11 5221976 AAAATTTTTCAAACTCTCTGCTGACAAGCCTCTCC[A/G]CTCATTAATTTCCCACTTAACATAGATGGCACCAC R 2 1 2 1 101000 f 74 goat snp6067-scaffold1214-359406 11 5075193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453517 Affx-122919807 AX-123323850 11 5256450 ACACTGTCTTCATTTCTGACTGGCCCTACACGGCC[A/G]TGGCCCTGAAAGACTCTGTGGTCACCTCTGTCACA R 2 1 2 1 101000 f 74 goat snp6068-scaffold1214-393880 11 5109524 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463132954 Affx-1109829981 AX-514619968 11 5271638 AGAAAATTTTCACAAATTTAACCCTCAAATAAACC[C/T]ATGAAGCAGGACCTACAAAATCATTGTTCTCATTT Y 2 1 2 1 101000 r 74 goat 11_5271638_AF-PAKI 11 5271638 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320792708 Affx-122935510 AX-385279688 11 5285319 GTGAGAGAAAATACATTAATTTGATGATAACAGTA[C/T]AAATCTAAGCAATAACCAAACCCCTGCTTCCTTCT Y 2 1 2 1 101000 r 74 goat snp6069-scaffold1214-422749 11 5138940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436387 Affx-122933040 AX-123306726 11 5318255 TGTGGGTGGAATCTAAAACATGACCAGATGAACCC[A/G]TCTATGAAACGGAAACAGACTCACAGATATAGAGA R 2 1 2 1 101000 f 74 goat snp6070-scaffold1214-455685 11 5171476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437185 Affx-122932061 AX-123307523 11 5366785 TAAACGTCTTGATGATGGTTACCTTTAGGGGTAAT[A/G]CTAATGATGAAAGCAGACACTTTTGTATAGACACT R 2 1 2 1 101000 f 74 goat snp6071-scaffold1214-504215 11 5220434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408898 Affx-122953971 AX-123279249 11 5445207 CTAAGCATAAAGTCCTAAATATTAGATGAGAATTA[A/G]ATTAAGTGCATGTTGATTCCATTTAACCCACTTAA R 2 1 2 1 101000 f 74 goat snp6073-scaffold1214-582637 11 5299491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375830 Affx-122978547 AX-123246189 11 5490578 TGGCGACTCCCACTAATGCCTCTGGAAGCTGTGAA[C/T]GGCCCTTCGAGTACACTGTGGAGAATGCAGAAGAA Y 2 1 2 1 102000 r 74 goat snp6074-scaffold1214-628008 11 5344740 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453601 Affx-122920140 AX-123323934 11 5573917 AGAACATTCCTTCCTAATCTTGCCAGGGGTCACGA[C/T]GATCCACCACTTTGTACCTGAAGATCTGGATTGTG Y 2 1 2 1 101000 f 74 goat snp6076-scaffold1214-711347 11 5422171 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771785 Affx-122964980 AX-385258942 11 5608578 TTGTGACTGTGAGAATGTCCTGATTCTTACATAAT[A/G]CATCCCACTCCTGATTGGCACAGCAGGCTCTTCAA R 2 1 2 1 202000 r 74 goat snp6077-scaffold1214-746008 11 5456711 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396133 Affx-122963400 AX-123266488 11 5653121 CTCTACCCCACACTTACACAACCAGAATCTCTAAG[C/T]GTGGAACTTGGAATATGCATTTTTCACACTCTCCA Y 2 1 2 1 201000 r 74 goat snp6078-scaffold1214-790551 11 5501152 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780503 Affx-122955523 AX-385267594 11 5686106 AGTGATGATTTTCACCTGGGCCTAGGGCAGTTCCA[C/T]GGAGGTCATAACAATGAAAGGATTAACACTCTAAC Y 2 1 2 1 101000 f 74 goat snp13686-scaffold1529-290788 11 5533703 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409704 Affx-122953046 AX-123280055 11 5744119 GTGTTGTTCTTGCTGCCTGTATACATCTCTGGAGA[C/T]GGAAAAGGAAACACTCTTGGATAAAGGAAAAACTG Y 2 1 2 1 101000 f 74 goat snp13685-scaffold1529-232775 11 5589227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433602 Affx-122934954 AX-123303943 11 5788868 ATCATGAATGAACCAGTCTATCACAATGGACAACA[C/T]AGGAGGAAACAAAATGTAAATTTTATGATCAACTA Y 2 1 2 1 101000 f 74 goat snp13684-scaffold1529-188026 11 5634038 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445265 Affx-122925472 AX-123315602 11 5824792 TATTAACTCTTACAATGCTTAATATCTGTGATAGA[A/G]TCCATGATCTAGGTAGCATTTAGAAAACCAGAGGC R 2 1 2 1 101000 r 74 goat snp13683-scaffold1529-152102 11 5669700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793929 Affx-122933983 AX-385280898 11 5882322 GTTACTCTCCAGGATACTTTTGAAATTATAGCATA[C/T]GCTGTAGATATGGAGATGACCATGTTAAGGTGACC Y 2 1 2 1 201000 r 74 goat snp13682-scaffold1529-94572 11 5722015 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802356 Affx-122954142 AX-385289260 11 5938248 GAGGTTATGGAACTGGGGCTTCACCAATAGGCAAT[A/G]ATGTATTTTTAATTAACGCCAATGAATTGACCATT R 2 1 2 1 101000 f 74 goat snp13681-scaffold1529-38646 11 5778317 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433710 Affx-122934530 AX-123304051 11 5968119 CAGTGGGTTGTGTGGGGTAGGGCTCAGTCTTATGA[A/G]AAAGGTGAGGTGGACACAGAAGCTCCAGGTGGTAG R 2 1 2 1 101000 f 74 goat snp13680-scaffold1529-8775 11 5809319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453091 Affx-122920039 AX-123323424 11 5988537 TTTCTGAGTTTCCTTCTGGTAAATGGGTGGTGTCT[C/T]CTTTCATCCAGAAACAGGAGGGCAAGAGAGTGGCA Y 2 1 2 1 101000 f 74 goat snp16689-scaffold1750-11544 11 6011479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402074 Affx-122958709 AX-123272427 11 6019379 TATAATCAGAAGCCTTTCACATTGCTGATGGGGTG[G/T]AAGATGGGATAGTCAAGGTGGAAAACACTTTCTAA K 2 1 2 1 201000 r 74 goat snp16690-scaffold1750-42386 11 6042296 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399686 Affx-122960493 AX-123270041 11 6124095 AGATGATAAGCCATGAGGACTGAAATGCCCAGCAA[C/T]GGAAACTATTTGATGAGAGAAGGTAGAAGACCTTG Y 2 1 2 1 101000 r 74 goat snp16693-scaffold1750-147102 11 6147147 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442538 Affx-122928534 AX-123312875 11 6174588 TAATCAAACATCTGGGATAATGATTTGGGTAGCAG[A/G]TAGCATTGACCTCTATATGGCAGATTGGAAAAATC R 2 1 2 1 101000 f 74 goat snp16694-scaffold1750-197595 11 6197453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803423 Affx-122958097 AX-385290254 11 6208064 GCTTTTATGATCAATTTGGCTAAAAAGGGTCCAGC[A/G]TAAGAGGGCTGGACATGATTATATGCCACACGACT R 2 1 2 1 101000 r 74 goat snp16695-scaffold1750-231071 11 6230962 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428344 Affx-122938990 AX-123298687 11 6240617 GAGTGGCCTGGCCTGAACCATGAGTAATGTGGTCT[G/T]CCCACACAGACCCCATGTGGCCTCGGGTCATCCTG K 2 1 2 1 101000 f 74 goat snp16696-scaffold1750-263624 11 6263623 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394777 Affx-122964831 AX-123265132 11 6283991 TTTCCAAAGTCTCATGCAATCCTAAAAGCAAGTGT[A/G]GGTCTTCCCTTTCAGCTGATGATTTGTGTGTGCAG R 2 1 2 1 101000 f 74 goat snp16697-scaffold1750-306998 11 6306882 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415497 Affx-122948694 AX-123285846 11 6329983 CCCTACACCCGTTGTGCGCTGGCTCTCTTTTCTGT[A/G]TCAAGACTCTGGGCATCACTTTTGCCTCTCTTCCC R 2 1 2 1 101000 r 74 goat snp16698-scaffold1750-352990 11 6353142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397657 Affx-122962603 AX-123268012 11 6387584 TTAATATAGTTCCCTGTGGTATGTAAGGTACTACT[A/G]TTTAAGGTCCTACAAAGATAAACAGTTTCGAAACT R 2 1 2 1 101000 r 74 goat snp16699-scaffold1750-410591 11 6410502 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403478 Affx-122957707 AX-123273831 11 6437469 TTTCTTTCTCTTAAAAAATTTTTATTTAAGTTGAG[C/T]GTAGTTGATAGCGGCTTCCCAAGTGGCTCACAGCT Y 2 1 2 1 101000 r 74 goat snp16700-scaffold1750-460476 11 6460372 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411502 Affx-122951685 AX-123281852 11 6470373 AGCAGTGCAGACAGTGGCCAGTTGGAGTGGATTTC[A/G]TTTGGTTCCAGTCTCAGAAGGTTTGCTGTGTCTCG R 2 1 2 1 101000 r 74 goat snp16701-scaffold1750-493380 11 6493058 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385153 Affx-122971754 AX-123255511 11 6576423 GTCCTGGACTCTCGTTGCTGAGATGAAAGGCCCAC[A/G]TTGTAGAGAACATTCTCCACTCCTGATAAACAGGA R 2 1 2 1 101000 r 74 goat snp16703-scaffold1750-599430 11 6597941 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392568 Affx-122966077 AX-123262925 11 6626551 AAAATAAAGGAAATAAAATAGTTCAAATCAAACCA[C/T]GTCCTTTCCAACGGAAGCGGCTCAGCTTTTTGAAG Y 2 1 2 1 101000 r 74 goat snp16704-scaffold1750-649558 11 6647876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413367 Affx-122950141 AX-123283716 11 6657876 TAATTATAGTAGGTGGTGTCCCTTCCTGGTGACTT[A/G]TGGAGTTGACCGGAGGGCTGAATTGAGGACCTGAG R 2 1 2 1 101000 f 74 goat snp16705-scaffold1750-680883 11 6677823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422713 Affx-122943642 AX-123293059 11 6695605 GTCTCTCATATCCATGGGGGATTGGTTCTAGGACC[C/T]GCTGTGGATGCCAAAATTCAAGGATGGCCAAGACC Y 2 1 2 1 201000 r 74 goat snp16706-scaffold1750-718612 11 6715874 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791716 Affx-122924465 AX-385278707 11 6747868 GCTTGTTTAAAAGTTCTTTTCACAATACAATAATC[A/G]CATTGAAAGGTCAGTCAGGTTTTGGCGCAAACGGC R 2 1 2 1 101000 r 74 goat snp16707-scaffold1750-770875 11 6767967 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274878 Affx-1111834550 AX-519548462 11 6751941 GTATGTTTCAGATGCAGGGTCTCTTCCTAATGCAC[A/G]CACTGCCCCTGCCGCATGCTCTGGGGACCCTGCAG R 2 1 2 1 101000 f 74 goat GoatD01.041268 11 6751941 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427413 Affx-122940065 AX-123297756 11 6812499 CTTTTCCTTTCTTATACTTTAAAATTTTTATTCAA[C/T]AGTCATTTGTTAATCTAGATAGACCAGAGTCCATT Y 2 1 2 1 101000 r 74 goat snp16709-scaffold1750-835506 11 6827926 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383013 Affx-122973320 AX-123253371 11 6858805 AAATAGCCACAACCCCAAGAAATCTACAGGTTTAA[C/T]GCAATCTTTATCATCATATGCACGGACATTTTTTT Y 2 1 2 1 101000 r 74 goat snp16710-scaffold1750-881812 11 6874594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762836 Affx-986697365 AX-385250865 11 6876119 AGGAAAGGGGTTGGGGAGGGACGAATTAGCAGTTT[G/T]GGATTAACATATGCACATCACTACATACAAAATAG K 2 1 2 1 600010 f 74 goat 11_6876119 11 6876119 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 320762838 Affx-986697367 AX-385250867 11 6876215 CACAGGGGCTGCTAATCAATATCCCGTATAACTTA[C/T]ATGGGAAAAGAATCTAAAAAAAATAGATTTCTGTG Y 2 1 2 1 600010 f 74 goat 11_6876215 11 6876215 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 320765384 Affx-986697371 AX-385252896 11 6876337 AAATGAATCAGTCATATGTATACACATACCCCCTT[C/T]TTTTGGAATTTCCGTCCCAGTTGGGTCACTTGCTT Y 2 1 2 1 600010 r 74 goat 11_6876337 11 6876337 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 320769979 Affx-122969842 AX-385257146 11 6905735 CAGAGAGTTTCCCACTTATTTCAGTTTCAAAGCCA[A/G]TACTCCCTTTGAACGTATTCATTAGTTTCCTGTTT R 2 1 2 1 101000 f 74 goat snp16711-scaffold1750-928742 11 6921624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407619 Affx-122954635 AX-123277970 11 6935338 GACCACTTAAATCACGGGCTTTAGATAGGGCGTCA[C/T]GCAACGGTGACCTGCCAGAATGAATCGGGTGCTGA Y 2 1 2 1 101000 f 74 goat snp16712-scaffold1750-958345 11 6951139 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401423 Affx-122959000 AX-123271776 11 6980890 GAGGCAGTCATTTTTAGAAGCTATGGCCTGAGATG[A/C]CAAGTCAGGTCTTCAGGTCCAGGGGCGGGGGTGAG M 2 1 2 1 101000 f 74 goat snp16713-scaffold1750-1003897 11 6996863 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386059 Affx-122971464 AX-123256417 11 7004597 TGTCTCCATATGTTTTATATTGAAAAGACCCTGAT[A/G]CTGGGGAAGACTGAAGGCAGGAGGAGAAGGGGACG R 2 1 2 1 103000 f 74 goat snp41245-scaffold536-8270 11 7020499 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801546 Affx-122920670 AX-385288455 11 7051705 AAAGGATATTTCTTCACTGGACTTGTGCAACTTTC[A/G]GTGTCTAAATACATATATCTGCCTCCTTAAAATGA R 2 1 2 1 101000 r 74 goat snp41246-scaffold536-55378 11 7067911 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276602 Affx-1111835426 AX-519550113 11 7076978 CAACTCAACTTCTCAACTGTGGGTTTTGGGTTTTT[C/G]TGTTTTGTTTTGTAAAACTAACTCCCCAAAATGTA S 4 1 2 1 201000 r 74 goat Random2.2K-1134 11 7076978 G C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382414 Affx-122974251 AX-123252772 11 7086719 AAAAGAAGACAGGAGGTGAGCCTGAAGGGGGGTGC[A/G]GAATGCACCCAACTGCTTTTACCTAGGAGGAGAGG R 2 1 2 1 101000 r 74 goat snp41247-scaffold536-90392 11 7103015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275592 Affx-1111834895 AX-519549162 11 7108712 ATCCGTCTGTGACTAGA[A/C]CACTGTTATAACTGCAGGCTGAACTCTCATCAGGA M 2 1 2 1 101000 r 74 goat GoatD01.057699 11 7108712 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320795876 Affx-122938220 AX-385282828 11 7128731 ATTGAATGAGAACTAAAGTAAACACTGGAGCATTT[A/G]TTCAGGAGAAACTAGTACAAAACAAAGACATAAAA R 2 1 2 1 101000 r 74 goat snp41248-scaffold536-132404 11 7144235 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421026 Affx-122944542 AX-123291373 11 7158769 TATCTTAAGGACACTGTGCGTGTTTGCAACTATAT[A/G]CTTGTATTGTTTGAGATTTTGAGTTGACAGAGACA R 2 1 2 1 101000 f 74 goat snp41249-scaffold536-162442 11 7174359 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449286 Affx-122923019 AX-123319621 11 7216823 CATTGCCCACTGAGGGTCTGCTCATTACTGCTGCA[C/T]GGCCATGGGAGTCCCTGGTCCTCACTAGGTCTTAC Y 2 1 2 1 201000 f 74 goat snp41250-scaffold536-220496 11 7232525 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383748 Affx-122972445 AX-123254106 11 7245974 ACTGCTCTTGCTAATCCTTGGCATGTGTCTTCCTC[A/G]TTGACCTTGTAAAGGTGTGTGTTAACGCTACCTGT R 2 1 2 1 201000 r 74 goat snp41251-scaffold536-249647 11 7261657 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396161 Affx-122963380 AX-123266516 11 7280508 AAAAGCATGGTTATTACACGTTCAGCATGTTTTGC[A/G]TTTGTTACCTCACACAAATCACGTTTATGTTAAAA R 2 1 2 1 101000 f 74 goat snp41252-scaffold536-284181 11 7295999 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406019 Affx-122955497 AX-123276371 11 7309338 GTGTATACAAGATTCATGCAAAGCGCTTTCACAGC[A/G]TAGGGACCAGAGAGGGGAATCTTCTCATTCACAAG R 2 1 2 1 101000 f 74 goat snp41253-scaffold536-313011 11 7324622 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389103 Affx-122968572 AX-123259461 11 7343361 TTCCCTAGAGTAGGAAAGATGGGCCAGACTGCGTC[G/T]TTGCCCTGCAGGAGGGCCCCGGCCAGAAGCGGACG K 2 1 2 1 101000 f 74 goat snp41254-scaffold536-347034 11 7359317 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436852 Affx-122932206 AX-123307190 11 7374459 ATGTCACAGAGATGATGGAGTCTTCTTGGTACCTT[A/G]TATCCTGGGGTGCAGGACATTAATGTCCCATTAGG R 2 1 2 1 101000 f 74 goat snp41255-scaffold536-378132 11 7389743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778392 Affx-122931998 AX-385265508 11 7428816 TAAGGTTAGAGAATAATAAGGTTTGTTTTAGTAAA[G/T]AATTAGTATGGGTATTTTTACTTTATCCCACTGAA K 2 1 2 1 102000 r 74 goat snp41256-scaffold536-432489 11 7444050 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386328 Affx-122970882 AX-123256686 11 7473854 AAAGCATCAGGTAGTTTGTATGTTTCCATTTCTCT[A/G]TTTCTTCCTGTGCAATGCAGTGTGAGTTATCGCCT R 2 1 2 1 101000 r 74 goat snp41257-scaffold536-477527 11 7489526 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425993 Affx-122941146 AX-123296339 11 7523116 GGAAAATCACAGTGATTTTATATTCAGGAGAGAGA[A/G]AAAAGAAAGAAAAGAGACCCACGCGCTGCTGTAAT R 2 1 2 1 101000 f 74 goat snp41258-scaffold536-526789 11 7538950 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449812 Affx-122922408 AX-123320147 11 7563124 CCTTAAGTTGATGAGGAATGAGTATCTTCTCTTTC[C/T]CTGGATCACATATAATTATGGCTAAAGATCCTGAG Y 2 1 2 1 101000 r 74 goat snp41259-scaffold536-566797 11 7579291 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385484 Affx-122971281 AX-123255842 11 7616921 ATATGAAAAAGTGTATTTGAGCAGAGAGCAGCGGA[C/T]GCATGGCTGTCTAGAGAGAAATGGCTACAGCCTGA Y 2 1 2 1 101000 f 74 goat snp41260-scaffold536-620594 11 7630601 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399067 Affx-122960895 AX-123269422 11 7649699 CGGAAAAGAAGGAAGGATGTAGAATTTATGATGAC[A/G]TCTCATAGGAACATAGAGTCAAGAGCAGTTAATTC R 2 1 2 1 101000 f 74 goat snp41261-scaffold536-653372 11 7663417 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770178 Affx-122942702 AX-385257345 11 7683918 AAAGTTGTCTGAGTAAGGGTGAAGGAAATAGCTGG[C/T]GGGACTTAGGAGACAGTGGGGTATGTTTCAGAGGA Y 2 1 2 1 202000 r 74 goat snp41262-scaffold536-687591 11 7697691 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385980 Affx-122971525 AX-123256338 11 7730117 AGATTACATGACTCAGAAACAATCGACTAGTCTCC[A/G]TTTCCTTCCTAGCGTAGCGTTAGTCAGTATTCTCC R 2 1 2 1 101000 r 74 goat snp41263-scaffold536-733790 11 7743756 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390387 Affx-122968179 AX-123260744 11 7766216 ACTTCATCCAAGAGATGTGGGGAGGCTATATTGAA[C/T]GGTTGGAGCCAAGGTTCCCTTCTAGTTTCCTTTTG Y 2 1 2 1 201000 f 74 goat snp41264-scaffold536-769889 11 7779784 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272639 Affx-1111832936 AX-519546350 11 7804540 TTTTGTTCTTTTTATGGCTGAATAATAGTCCATAT[A/G]TATATATATATATATCACATCTTCTTCACCCATTC R 2 1 2 1 103000 f 74 goat 11_7804540_AF-PAKI 11 7804540 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38390045 Affx-122968427 AX-123260402 11 7856723 ATTCTGTTTAAAATGATAACTGTGCTCCTTTCCCT[C/T]CAGCTGATGAAAATGCCTTCTTTTATGGATGTCAG Y 2 1 2 1 101000 f 74 goat snp41266-scaffold536-860396 11 7871691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399969 Affx-122960829 AX-123270324 11 7904543 GACCATTATGAATGAATTCTATTTATTAACCTGGT[A/G]TGTGATATTAGAATATTTCTTTAGAGATTGCTTTT R 2 1 2 1 103000 r 74 goat snp41267-scaffold536-908216 11 7918183 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780019 Affx-122938564 AX-385267118 11 7940414 CTGGAACTAAAACTTGTCAGAGAAAAAATAGGTTC[A/G]TGGAAACTATCAATAACATGTTGATAATAACTTTC R 2 1 2 1 101000 f 74 goat snp41268-scaffold536-944087 11 7954293 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276605 Affx-1111835427 AX-519550116 11 7989345 GTAGAGACTCAAAGGCGGCTGAGGCTCCCCATTGA[A/G]CACAGAAGGGCATAAATTGAAGCCCTGAGTGTGTG R 2 1 2 1 102000 r 74 goat Random2.2K-1136 11 7989345 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38379761 Affx-122975852 AX-123250119 11 8032723 GGTACCTTTGCAACTATCTGTGGAGAGGGCTTTAG[C/T]GGGTAGGTTCAGGCAGGAAGGATGGAGCAGGAGCA Y 2 1 2 1 101000 f 74 goat snp41270-scaffold536-1036396 11 8047002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420956 Affx-122944978 AX-123291303 11 8082734 CAAGGCACTGGCTGAGAGAACTTAGGAGTCGTTCC[A/G]TATTTACAGAAGTCTTGGATAATAATGATCTTGAA R 2 1 2 1 201000 r 74 goat snp41271-scaffold536-1086407 11 8097356 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422513 Affx-122943293 AX-123292859 11 8116798 AACCTGCACAAAGGAAAAAAAAGAAGTGCTTCTTA[C/T]AATACGATGATATTACCTATACAGGCCAGTAATGC Y 2 1 2 1 101000 r 74 goat snp41272-scaffold536-1120471 11 8131719 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375476 Affx-122979148 AX-123245835 11 8150493 GATATGCTCCAACCCTGCAGTGGCAAAGGAAGAAT[A/G]CCTTTCTGAAGAGGAGCTCCCACTGCAGTCCAGAT R 2 1 2 1 101000 f 74 goat snp41273-scaffold536-1154166 11 8165852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424866 Affx-122941335 AX-123295212 11 8189423 AGAGCCAAATACATTGTCCCCAAAATCTTTCTAAG[A/G]CACAATGATCTATGTTTAAAAATTATGAAACTGGA R 2 1 2 1 103000 f 74 goat snp54150-scaffold826-592686 11 8205206 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394362 Affx-122964646 AX-123264717 11 8235055 CAAGCGAGTCAATTATAATCACACGTAAAATGATG[A/G]TGATGGAGCTGGTGGTAATAGTGGTGAAAACATAG R 2 1 2 1 201000 f 74 goat snp54149-scaffold826-547054 11 8250900 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399430 Affx-122961226 AX-123269785 11 8267588 TCATAGCAAGGCTGAGAAACTTGTAGGCTCAAACT[A/G]CTTAAGGACATCTCTCCCCAAACTTTATCTGACTG R 2 1 2 1 201000 r 74 goat snp54148-scaffold826-514521 11 8283797 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423657 Affx-122942345 AX-123294003 11 8310453 AATTTCAGTTACCTCTTCAGTTCTGATTGAGAGCT[A/C]GAAGTATAGGGAAAAGGAAGCAGCATGTTCAGGGT M 2 1 2 1 101000 r 74 goat snp54147-scaffold826-471656 11 8326731 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793884 Affx-122963107 AX-385280853 11 8369676 CAGTGACAGATAATGGGAATTTCAGACTGGTGACC[A/G]TTAGAACTGACACTAATCCTGGCGTCTTGGACCAG R 2 1 2 1 101000 f 74 goat snp54146-scaffold826-412433 11 8385849 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422270 Affx-122943991 AX-123292616 11 8399944 TCTTTTGACTTTTAAAATAGGCAACCATATCATCT[A/G]TGAGTAGAGATAACTACTTCTCCTTTATAGGTTTT R 2 1 2 1 101000 f 74 goat snp54145-scaffold826-382165 11 8416098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448669 Affx-122923336 AX-123319005 11 8430797 AAAAAAAGAAAAGAAAAAAGAAATGGAAATTTCCA[C/T]GAGGACTTTTCATTAACTCAGGCTCACTCTTGGAA Y 2 1 2 1 101000 r 74 goat snp54144-scaffold826-351312 11 8447209 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398614 Affx-122961479 AX-123268969 11 8478504 CAAGTGAGCAGCTTTATAAACACACCTCAGGTACC[A/G]CTTTTCTCTTGATGTTTCCCTTGGAATAACACACA R 2 1 2 1 101000 r 74 goat snp54143-scaffold826-303605 11 8495245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398447 Affx-122961607 AX-123268802 11 8514601 CTCCTAGGAGCTCGCAGCTCCAAACATCAATTACC[A/G]TGATTATCTACCCGGTGCTTACAAAATGCACGGGC R 2 1 2 1 101000 r 74 goat snp54142-scaffold826-267508 11 8530009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411801 Affx-122951260 AX-123282151 11 8553205 AAATGTACCATCGAGTATAGAAATAGATGTTCTAT[A/G]TTCATTTAGAGTATACAAAGATAAGATTAAGAAGA R 2 1 2 1 101000 r 74 goat snp54141-scaffold826-228904 11 8568276 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773030 Affx-122938670 AX-385260174 11 8588105 CCTTGGGTTCCTTTGAACTTGAATTCTACACCCAG[C/T]AGAATTCAGAAACTTATTATTCATTAAGGAGATTT Y 2 1 2 1 102000 f 74 goat snp54140-scaffold826-194004 11 8603117 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403324 Affx-122957825 AX-123273677 11 8618534 AAGAGCTAATTATTTATGCCAAATCTCTACTCTGC[A/G]TACGTGTGAGAAACAGCTTGGAGGGCAGGCGATGA R 2 1 2 1 201000 f 74 goat snp54139-scaffold826-163575 11 8633330 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802008 Affx-122960513 AX-385288912 11 8702931 CATGCATTCTTCAAAACCATGACATCTTTTCTTCT[C/T]GCTAGATAATAGTTATTTATACACATGTCATAGTT Y 2 1 2 1 101000 f 74 goat snp54138-scaffold826-79178 11 8717944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436458 Affx-122932987 AX-123306796 11 8738312 TGCGGTGCAGACTTTCACGTTACCTTTGCTTTAAA[C/T]ACACTGACAGGCTTCTGTGAGTGGGAACCTGTTAT Y 2 1 2 1 201000 f 74 goat snp54137-scaffold826-43797 11 8753063 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776140 Affx-122977761 AX-385263270 11 8779983 GATATATCTGCCCACATTTTATCGGCTAAAGGAGG[C/T]CCCGTGGTCAAGCTCAACATCCATGGGATAAGGAA Y 2 1 2 1 101000 r 74 goat snp54136-scaffold826-2126 11 8794867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451700 Affx-122921566 AX-123322033 11 8793007 AACAAGGAGAGGGCACACTGATCAATGATGCTGTG[C/T]GTGTCTGCCTATTGGAAAGCCATTGCTGTTAGGTC Y 2 1 2 1 101000 r 74 goat snp31798-scaffold3559-250344 11 8806791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426230 Affx-122940349 AX-123296576 11 8871584 CTTGAACCTGAGTGGACTGAGGGTGGCAGGTTTGC[A/G]CACCTTATATTTCAGTGCTGGCACAAGGGAAGCTC R 2 1 2 1 101000 r 74 goat snp31796-scaffold3559-171767 11 8885409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417885 Affx-122946755 AX-123288233 11 8915036 GGAGGACAAGTAAGCATGTGGCTTTGACAGAAGAG[C/T]TCGAATGAAAGCGGGAGGGACACTTTCATTGAGAT Y 2 1 2 1 101000 f 74 goat snp31795-scaffold3559-128315 11 8928953 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276607 Affx-1111835428 AX-519550118 11 8953083 TGCAGGATTTGCCTGAAGATCTGTCTCCGAGAGGC[A/G]TGCTTTTTGTAATAGAGCCACAGTAGTAGACTCTA R 2 1 2 1 101000 r 74 goat Random2.2K-1138 11 8953083 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432129 Affx-122936442 AX-123302470 11 8955504 CGCACATCCACACCTGTGCTTTTGTTCAGATGCTC[A/G]GTTCATCAGGCATTCATTTCTGTTCTGTTTCAGTC R 2 1 2 1 101000 r 74 goat snp31794-scaffold3559-87847 11 8969446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378010 Affx-122977592 AX-123248369 11 9004789 CTGTCCAAAGTACAAAGACCCCACACATTTACAGA[C/T]AGATAGATGAATAGATGAGCTTATATATTTGGTTG Y 2 1 2 1 201000 r 74 goat snp31793-scaffold3559-38562 11 9018676 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429332 Affx-122938584 AX-123299674 11 9043000 TCCAATTATCTCCACTTGCCTTCAGGCTCCACAGT[A/G]TAGTCTGTTTACAGTTCTTTAGAAACCCCTTAACT R 2 1 2 1 201000 r 74 goat snp31792-scaffold3559-351 11 9056935 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411019 Affx-122951977 AX-123281369 11 9075233 CTAGCAATCAAAGCCGAGCCACGAGTCTTACCCTG[C/T]AGGTGGCTGTGAAGGCATGGTCATGTTCCTGGGGA Y 2 1 2 1 101000 f 74 goat snp13551-scaffold1523-1510193 11 9089118 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405485 Affx-122956016 AX-123275837 11 9129896 TGTAAACCTCTCAGCTGATGGCACTTTTTCCGGAA[C/T]GAAATGGAATATCATGAGTTAAGATCAGAAAACTG Y 2 1 2 1 101000 r 74 goat snp13550-scaffold1523-1455530 11 9141819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448526 Affx-122923444 AX-123318862 11 9163267 AGACTCTTTTGAATATATACCCAGGGGTGGGATAC[A/G]CTTCCTGTATCTTAACCCAGATGGGATTGTATTGG R 2 1 2 1 201000 r 74 goat snp13549-scaffold1523-1422159 11 9175154 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445210 Affx-122925515 AX-123315547 11 9201414 TTCCTGCTGACTGACTTTCACGAAGATGTGCAAAA[C/T]ACGAATACAGATGCAAACACGGACATGTCCTTAAT Y 2 1 2 1 102000 f 74 goat snp13548-scaffold1523-1384012 11 9213267 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424768 Affx-122941409 AX-123295114 11 9238308 TTTTCATGAGGCCATATATACCCTTGCATATTGCT[A/G]CTGCTTTGATTTTTTTAGGTATACACCCTAGGTAT R 2 1 2 1 101000 r 74 goat snp13547-scaffold1523-1347118 11 9250284 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423469 Affx-122942581 AX-123293815 11 9271954 TATCAGCCATGAGACCTGTTATGGTGCATTTTGAG[C/T]AGATGATTTTTAAAATCTTGTGTCCATTTAACTCA Y 2 1 2 1 201000 f 74 goat snp13546-scaffold1523-1313472 11 9284516 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789499 Affx-122958484 AX-385276508 11 9322138 TAAAATAGGCCTAAGTGTTATCCAAATTTCTCAGA[C/T]GATAAGAATATCTTGAATTGCTTGTTAAATGTACA Y 2 1 2 1 101000 f 74 goat snp13545-scaffold1523-1263288 11 9336258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438871 Affx-122930748 AX-123309208 11 9356386 AGACCTTCAGCCTCAGTATATACACCCATTGTGAC[A/G]TGTCAGCAGGTTAAGTGATACACGAACCAGCACAG R 2 1 2 1 101000 f 74 goat snp13544-scaffold1523-1229040 11 9370255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449172 Affx-122923535 AX-123319507 11 9409647 TTGAGAGCTCACTCTACCACAAGAACACTGGTGCT[A/G]TCTACCACCATTTGGCATCTTCCTTCTAGCCTGTT R 2 1 2 1 201000 r 74 goat snp13543-scaffold1523-1175779 11 9428222 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387278 Affx-122970542 AX-123257636 11 9443982 TTCCCAGGTAGACTGGCCCTGGAACCTGTATCATT[G/T]TGAAATGTTTCCACCCAGCATGGGGAAATGGAATT K 2 1 2 1 101000 f 74 goat snp13542-scaffold1523-1141444 11 9463577 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453535 Affx-122919794 AX-123323868 11 9499656 ACTCTTTGTTGACCGACTCTTCTTCTTTAGTGTTT[A/C]TTGATCATTCTACCTCTTTTAGGCAGGAGGCCAGC M 2 1 2 1 201000 r 74 goat snp13541-scaffold1523-1085770 11 9518297 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391542 Affx-122966642 AX-123261899 11 9561701 TAGCAGAACCATTTGCTTGGAATGCTAGGAGGGGG[G/T]ACTTACTGATATGTGTGAAAGGTAAAATCTAGAGT K 2 1 2 1 201000 r 74 goat snp13540-scaffold1523-1023725 11 9580868 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428424 Affx-122938828 AX-123298767 11 9602740 TCTGGACCCAATTTCCAGCTCTAGCCCTGCACTTG[A/C]GCCGTGTGTCTTATTACTCTTTCTCTTCACATCTG M 2 1 2 1 101000 r 74 goat snp13539-scaffold1523-982686 11 9621889 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428068 Affx-122939112 AX-123298411 11 9651133 TATCAGAGAAGGACAAACTCCTCAGCAGAACACTG[C/T]AAACCCTCATCTTCCCTCCTCTGTGATCTTTCCAA Y 2 1 2 1 101000 f 74 goat snp13538-scaffold1523-934293 11 9670232 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437219 Affx-122932037 AX-123307557 11 9687303 TTTTATTATAAAAATTTTAAAACACATTTAAAAAG[C/T]GGAAAGGATTGAACAACAAGCCCCCTTTGAATCTG Y 2 1 2 1 103000 r 74 goat snp13537-scaffold1523-898123 11 9706269 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438644 Affx-122930903 AX-123308981 11 9724666 ATCTAGTTGGTTATAGACCAAGGATGGCCAACACA[C/T]GGCATACCACACTCTGTCACTTCCCCATTCTGATT Y 2 1 2 1 101000 f 74 goat snp13536-scaffold1523-860760 11 9744018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446983 Affx-122924647 AX-123317319 11 9765729 CAACTATGCAAGGATTGCTGGTGTGGACAGCCGTG[C/T]ACTGACATCCTATCTTACCCACAATGCCCAAGTGA Y 2 1 2 1 101000 r 74 goat snp13535-scaffold1523-819697 11 9786088 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392314 Affx-122966703 AX-123262671 11 9801829 TCCCTAAAACCATATGCAAGATGCTGTCTGTACAC[A/G]TGTGTCTGTATTTTTCTCGGGGGGCAGGGGTTATG R 2 1 2 1 101000 f 74 goat snp13534-scaffold1523-783597 11 9822595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438386 Affx-122931303 AX-123308724 11 9857463 TCAGTTTTATTGCAAATTGGAGGCCTAGCAGTGTC[A/G]CTCTCAAAATGTGTCACTCTTCATTTCTCAGTCAG R 2 1 2 1 101000 f 74 goat snp13533-scaffold1523-727963 11 9878575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770001 Affx-122966380 AX-385257168 11 9887524 GCTTTGAAACAGGGAAAAAGAAGTCTGCTTCTGAT[A/G]GTGAAAGAGACACATTATTGTGTTGTCTTGATCAC R 2 1 2 1 101000 f 74 goat snp13532-scaffold1523-697902 11 9909337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391783 Affx-122967454 AX-123262140 11 9926416 ACTTTGCAGAATACCTTTGGAAGCTCAAGATAAGC[A/G]GACTCTGAAGCTCAAAGAGACTCAGTATTCTTTCA R 2 1 2 1 101000 f 74 goat snp13531-scaffold1523-659010 11 9947021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451904 Affx-122921033 AX-123322237 11 9975755 CTTCTGCAGCCACTGCCCTAGTTCAAGAATTCATT[A/G]TTTCTGACTTGAACAGTTGTAATGACCTGCTGACT R 2 1 2 1 101000 f 74 goat snp13530-scaffold1523-609671 11 9994608 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441271 Affx-122929478 AX-123311608 11 10094562 GGTCTGCAACTTCCTCAGCACTGGAGCAGCCCAGT[A/G]TGGAGAGGTGAGGTAAAAACTCCGTGATACCAAAA R 2 1 2 1 101000 r 74 goat snp13528-scaffold1523-490864 11 10112813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436775 Affx-122932269 AX-123307113 11 10124822 TCTCCCACACTGGCAGGTGGATTCTTAACCACTGG[A/G]CCACTTAAGAAATCCCTGCTTAGGATTTTTAAATG R 2 1 2 1 101000 r 74 goat snp13527-scaffold1523-460604 11 10143633 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453558 Affx-122919776 AX-123323891 11 10162837 TCGATTTGCTGAGCACAACACCTCACACCAGTCAC[A/G]TTTGTTGTTGGTTCTTAGGGCGGCTGGAAATTTGC R 2 1 2 1 201000 r 74 goat snp13526-scaffold1523-422589 11 10182849 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428151 Affx-122939049 AX-123298494 11 10222049 CCCGTGCTGCTGAGTATGATGAGAGGCTGTCCCGA[A/G]AAGAGGCAGAACAAGGAGCCAGCCATGGCAGTGCC R 2 1 2 1 201000 r 74 goat snp13524-scaffold1523-363377 11 10242322 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427432 Affx-122940050 AX-123297775 11 10254318 TCTTTAGTGTATCTTGAAACCTATTTTTGGAAAAC[A/G]TAACTTGGGCTTGATAATCATTAGGGCAGCTATGT R 2 1 2 1 101000 r 74 goat snp13523-scaffold1523-331108 11 10274749 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376936 Affx-122977779 AX-123247295 11 10372508 TTACTCATGTCTGTCTTACTTTTAGATAGGAAAAT[C/T]ACCTTTTTGCCTCCACTTTATGGGCTTATTTCATA Y 2 1 2 1 101000 r 74 goat snp13520-scaffold1523-212918 11 10392184 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 468271761 Affx-1111832909 AX-519545555 11 10382444 GCTACTCCTCATTTCCTGACCGATAGAAACTGTGA[A/G]ATAATATTTGTTGTTTCCAACTATAACATTCTGGG R 2 1 2 1 201000 r 74 goat 11_10382444_AF-PAKI 11 10382444 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38402490 Affx-122958585 AX-123272843 11 10475355 TGGTACCGTGCCCTCATCTGTGCAGGCAAGCCTCT[A/G]CCTTCTAGGAGTTTATGATGAGTGGAGGAGGTTAA R 2 1 2 1 101000 r 74 goat snp13518-scaffold1523-110071 11 10492884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398372 Affx-122961661 AX-123268727 11 10509753 GTAGGTGTGTGGCAGTCGCAGGAGTAGTGGTGATG[C/T]GATATTGAAGTTGAATGGTGAAACATGGGTAAAGG Y 2 1 2 1 101000 r 74 goat snp13517-scaffold1523-75673 11 10527345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444545 Affx-122926475 AX-123314882 11 10581725 CAGTATGATGAGATGATTCCTGGACCACCTTCCCT[A/G]TACCTTGGCAACTGACCATGATTCACCACCTTTGC R 2 1 2 1 101000 r 74 goat snp13516-scaffold1523-3701 11 10599386 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793765 Affx-122950102 AX-385280737 11 10585704 ATGTTACCTTCTTCAAATCTCAGTTTTTTTATCTA[C/T]AAAGTAGAAATTGTGATAGTACCTACTAGATGGGG Y 2 1 2 1 101000 f 74 goat snp27520-scaffold293-2248480 11 10603408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419729 Affx-122945898 AX-123290077 11 10627423 GTCCGACACAAACACACTTTCCAAGATGACCACTC[A/G]CAAACCTTTTCTAGAGTCTGCCCTTACTGCCATAT R 2 1 2 1 101000 r 74 goat snp27519-scaffold293-2206761 11 10644828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377316 Affx-122977683 AX-123247675 11 10666401 ACAGTCTTTCAAAATTTGGGGTTTAAAGTATGTAT[A/C]GAGAGTTTAACCCTTTATTTTATATTGGCGCATAG M 2 1 2 1 201000 f 74 goat snp27518-scaffold293-2167783 11 10683657 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438197 Affx-122931823 AX-123308535 11 10715150 AATTTCCAAGAGTGGGATAACATTCATGAGTTTGT[G/T]TTAGGATATAATTCTGGGGCAGCTGTTAGAATTAC K 2 1 2 1 201000 f 74 goat snp27517-scaffold293-2119034 11 10732405 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445563 Affx-122925144 AX-123315900 11 10756016 ACACCTGTTCTTTCTGTGACTCGCTCTCTGTGCCT[A/G]TCTTTGATGTGTCTGTGCAGGCTCTCCCCACACTG R 2 1 2 1 101000 f 74 goat snp27516-scaffold293-2078168 11 10773419 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797050 Affx-122932454 AX-385283991 11 10796838 AGCTATTGGGCACTGTAAACTTTCTCAAACCATGA[G/T]ATGAAATGGGACGTAACCACTCTCGCTATTTTTGT K 2 1 2 1 101000 f 74 goat snp27515-scaffold293-2037346 11 10814053 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788233 Affx-122923645 AX-385275252 11 10831765 GAAAAACTAGGGAATGATTACTGAAGTAAAGAGCT[A/G]TTGTTCTGTAGGAGAACACTGACTGAGGCTTCTTC R 2 1 2 1 101000 r 74 goat snp27514-scaffold293-2002419 11 10849219 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394856 Affx-122964769 AX-123265211 11 10892196 ATTCTTCTCTACCTGGTGTTTTTCTGGTTGTCTCC[A/G]CCTTGCCCCTTGCATCTCCTTTAAAAGGAGGTTTT R 2 1 2 1 202000 r 74 goat snp27513-scaffold293-1941988 11 10910241 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452385 Affx-122920616 AX-123322718 11 10931323 CACTCACCCCTTCATGGCATCTCAGCATCATGTGC[A/G]CTAAGTGTCCAGGTGCTTCTTCTCCAAGCCTGACA R 2 1 2 1 201000 r 74 goat snp27512-scaffold293-1902861 11 10949437 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795227 Affx-122928308 AX-385282185 11 10974459 CATCAAAGGCCTTTTGCTTGGAACATGCTGTCAGG[C/T]AACAAATTCTGTTCCAGTTGGTGTTCTTTGATTAT Y 2 1 2 1 101000 f 74 goat snp27511-scaffold293-1859725 11 10992615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783540 Affx-122966585 AX-385270602 11 11004341 TTGTATGCCACTCACTATGGGCACTATTAATTGGG[C/T]ATTGAGAGCTTTACATGTACTCACAAGTCCGTGTA Y 2 1 2 1 101000 r 74 goat snp27510-scaffold293-1829843 11 11022970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410346 Affx-122952461 AX-123280696 11 11040672 AGCCTGAGCAGCCAAGGAGCCCCTGGTGGTTACTG[C/T]AGATCCTCAGGGCGATGACACCAAGTGCTGGTGGA Y 2 1 2 1 101000 r 74 goat snp27509-scaffold293-1793512 11 11059620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381105 Affx-122974586 AX-123251463 11 11075957 GTTTCTAACGTCTCCCGGGCGATCCCCATGCTGCC[A/C]GTCCGTCACCTCATTTTGAGTAGTGTGGCGCGCAT M 2 1 2 1 101000 r 74 goat snp27508-scaffold293-1758227 11 11094886 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395647 Affx-122963782 AX-123266002 11 11134452 TTTGTGCCTGTGGGTTGGACTTCATTCTCCTGTAG[C/T]ATCTTATTACAGTGTCCTGGGCTCACAGCTCTGCC Y 2 1 2 1 201000 r 74 goat snp27507-scaffold293-1699732 11 11153528 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442524 Affx-122928543 AX-123312861 11 11199801 GAGGCCCAACGTGTGCATTCAGCTTGATGACAAGC[A/G]CTGCCCACTGAAGGTTAAGAATATGGACTTGGAGT R 2 1 2 1 101000 r 74 goat snp27506-scaffold293-1634383 11 11219400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384290 Affx-122972294 AX-123254648 11 11232236 AATGTCCTAACCCAATCAGCCAAAGAACCTCCCCC[C/T]GACCCACCAGGGATACACAAACTTAGGCTTCCTGA Y 2 1 2 1 201000 r 74 goat snp27505-scaffold293-1601948 11 11252041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407214 Affx-122955388 AX-123277565 11 11283986 TTTGGAAGTAACCTGAGACCTCTGAATTCACTGAC[A/G]GGATGCTCCTGGTCTGCCCTCCTCAGCCTTCCAGC R 2 1 2 1 101000 f 74 goat snp27504-scaffold293-1550198 11 11301768 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790650 Affx-122978629 AX-385277652 11 11393381 TTGAAATAGTTATCACTTCTTTCAGATGATAAACC[A/G]TAAAATTTTGCTTCTAACTTTGATGGCAAAGAGAA R 2 1 2 1 101000 f 74 goat snp27501-scaffold293-1440803 11 11410998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386252 Affx-122970959 AX-123256610 11 11449985 TTATATAAGTTACAAAAGTCACTGTGTGTTAGCAA[C/T]GGTGATATTTTAACGCAAGCCAGGACTGTGTTTTT Y 2 1 2 1 101000 r 74 goat snp27500-scaffold293-1384199 11 11467929 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769650 Affx-122942545 AX-385256820 11 11592674 TTCAGACTCTGGAAATTAGAAAGGACTCTGGAAAG[C/T]AGAACAATAGCTTCAGAAGGGTTTATTCATGAAAA Y 2 1 2 1 101000 f 74 goat snp27498-scaffold293-1241510 11 11610939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795682 Affx-122950061 AX-385282636 11 11650327 AAGTTAACTGGAGAAGTACTGACTGTTTAATATTA[C/T]GTAAGCCCAGAGGTGTTCATGCCTATCCTTGCCAC Y 2 1 2 1 202000 f 74 goat snp27497-scaffold293-1183857 11 11669318 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389312 Affx-122968500 AX-123259670 11 11690718 TGTAGGGGGTCTGTTCCAGTGAAGGACATACAATT[G/T]TGTAAGAATAAAAACAAAGTTTAAATAAATAATCA K 2 1 2 1 101000 f 74 goat snp27496-scaffold293-1143466 11 11709662 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377131 Affx-122978236 AX-123247490 11 11767925 TATACCACTGTACAGTTACAGTTAGTCGCTCAGTC[A/G]TGTCTGACTCTTTTGCAATCCCACGGACTGCAGCA R 2 1 2 1 103000 f 74 goat snp27495-scaffold293-1066259 11 11787072 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785359 Affx-122965026 AX-385272404 11 11817300 GTGGAATAAGAAAAACCATGGGTTAATTAGGTTTA[C/T]AAATTTCATATAATTATTCTCTACCAAATTAGAGC Y 2 1 2 1 202000 r 74 goat snp27494-scaffold293-1016884 11 11836355 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400260 Affx-122960134 AX-123270615 11 11876053 CCCTGACTTTGAAAAGAAACCAATAATGTAATTCT[A/G]CCTAAATGTTTTATAATCCTTACTATTCCAAAAGT R 2 1 2 1 101000 f 74 goat snp27493-scaffold293-958131 11 11895612 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400306 Affx-122960068 AX-123270661 11 11926983 GGGCTACTTTCTCTGACTTTGGTATCAAGATAAAA[C/T]AGATAAAATGGCCTAGTTTTTTATAGGTTACTGCT Y 2 1 2 1 201000 f 74 goat snp27492-scaffold293-907201 11 11946893 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381047 Affx-122974631 AX-123251405 11 11980918 TCGCTTCAGTCTAACAGACGTCAATTCTTAGTAGC[A/G]TCAAGATTCTACAAAAAGATGTGAGGAAAGAGATA R 2 1 2 1 101000 f 74 goat snp27491-scaffold293-853266 11 12000824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399990 Affx-122960814 AX-123270345 11 12059302 GGAATCCCCTTCCTTACCAAAACTGATGTGATTTG[C/T]TTTCTTCTTTCATATGTACATCTTCCAATGGTAAC Y 2 1 2 1 201000 r 74 goat snp27489-scaffold293-774882 11 12079630 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795399 Affx-122921045 AX-385282355 11 12107458 ACTGATAAGAATATAATGTTACTATGAAACATGGG[C/T]AATAAACATGAGGTTATTGTAAATTCCCAATAGTT Y 2 1 2 1 202000 r 74 goat snp27488-scaffold293-726726 11 12127505 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419153 Affx-122945742 AX-123289501 11 12137490 ATCCATAATGAAGACCTACCACTTGCCCCAAGAGC[A/G]CGAAGCCATAACAGAAACAAAAACTTGGTCACTGC R 2 1 2 1 101000 f 74 goat snp27487-scaffold293-696694 11 12158222 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443139 Affx-122928074 AX-123313476 11 12177652 CTTCTTAAGCAATAGGATTAGAGTGATCATTTCTT[A/G]CTCTTTTCTAATAAAGCCCAGAATTTGAGAGATGG R 2 1 2 1 101000 f 74 goat snp27486-scaffold293-656532 11 12198755 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404301 Affx-122957028 AX-123274653 11 12224489 TCCCTCATTGCCAGCACTCAAAATGCCAGTGGCAG[A/G]AGCTATTCCTCCTCCATCCCCTGACCGCTCATTTT R 2 1 2 1 101000 r 74 goat snp27485-scaffold293-609695 11 12245253 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796504 Affx-122970345 AX-385283453 11 12264326 CAGAGAATGTAGCCTATACAGTCTGTACATTTTAG[A/C]GGTTATTGATAACGTGTTTGTGACCCAGAATAAAA M 2 1 2 1 101000 f 74 goat snp27484-scaffold293-569858 11 12282980 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415590 Affx-122948621 AX-123285939 11 12313730 GGGTTCAAGTCCTTTTAAACAGTCCTTTCACTGTA[G/T]CTTTCGTGGGATATTTGGAAGGGAGCAAAATTAAA K 2 1 2 1 101000 f 74 goat snp27483-scaffold293-520454 11 12332572 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449759 Affx-122922449 AX-123320094 11 12349031 CAGCTTGGGCTCACCCGCAGTGATTTCTCAGGAGC[A/G]TTTCGCAAGCACCTGTTGGAATTTAAGCCCATTGA R 2 1 2 1 101000 r 74 goat snp27482-scaffold293-485153 11 12368378 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399597 Affx-122961100 AX-123269952 11 12404142 GCTTACTTTCAGAGAGCTGCTTTGGACCAGCACTT[C/T]GAATGGTGCCCTATGAAATTATCCCATCCCCCAAA Y 2 1 2 1 101000 r 74 goat snp27481-scaffold293-430042 11 12423733 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393091 Affx-122965593 AX-123263448 11 12455199 GAGAAAGAACTTACAAGAAGAAATATTTGAAGAGG[C/T]AGTGGCAGAGAACTTTTCCAAATTATTGAAGGACA Y 2 1 2 1 101000 r 74 goat snp27480-scaffold293-378985 11 12474572 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789538 Affx-122949635 AX-385276547 11 12510028 ATAGACACACACATAGATGCACCTATGACAGATAT[A/G]TAAAGATGTAGATGATAGCTAGCTAGCTAGATTGA R 2 1 2 1 101000 r 74 goat snp27479-scaffold293-324156 11 12530270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399292 Affx-122960540 AX-123269647 11 12580916 GTGTAGGATTGAAGCTACAAACCTGTGGCATCAAG[C/T]CCATTCCAGGAAGGATGTGCTCTCTGATCCCCCCT Y 2 1 2 1 101000 f 74 goat snp27478-scaffold293-253268 11 12601305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428905 Affx-122938921 AX-123299247 11 12627786 GAGACTCTGGTCCTTGTAAAATCTTTCCAGAAATA[C/T]AGTGACTGCTGGGTCTCAGTAAGCACGGAGGCTTC Y 2 1 2 1 201000 f 74 goat snp27477-scaffold293-206398 11 12646658 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428340 Affx-122938994 AX-123298683 11 12662498 GTGAGTTCAGACATATTTGCCTTGTTTCTGATCCT[A/G]GGCAAAAAGCATTCAGTCTTTCACCATTAAGTATG R 2 1 2 1 303000 r 74 goat snp27476-scaffold293-171686 NW_017191897.1 3160 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421822 Affx-122944314 AX-123292169 11 12710094 TCTCACTTTCTGTATCCCCAGGGCTTAAGAACTCC[A/G]CGTGTTAGATGTTCACTGTGCAGCTGGTAAGTGAG R 2 1 2 1 101000 r 74 goat snp27475-scaffold293-124090 11 12742261 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447436 Affx-122924380 AX-123317772 11 12763575 AATGTTTGGGATGAACTTACAAGGTTTGAGGATGC[C/T]GCTCAAGAGAGAAATTAGAATATTGTGAAATTTAT Y 2 1 2 1 101000 f 74 goat snp27474-scaffold293-70609 11 12794107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396195 Affx-122963367 AX-123266550 11 12797663 GATATCCTTTTTCCTCCCCAACTCTCCTAACATCA[C/T]AGGGAGTCAGGCTTAGAATGATTGTTGTCAACTTT Y 2 1 2 1 201000 r 74 goat snp27473-scaffold293-36521 11 12827048 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446477 Affx-122925059 AX-123316813 11 12831156 AGCAAGGAGTAGAGGTCAGGGGATTGGAGGTGTAG[C/T]GGAGTCAGGGAAACATTTTATAAAGGAGGGGTGGG Y 2 1 2 1 201000 f 74 goat snp27472-scaffold293-3028 11 12860509 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774752 Affx-122948133 AX-385261886 11 12844754 GGCTGCCTGATTGTTAAGAAGATGAATTATATGCT[A/G]TGTTGGCACACAACTTGGCACGTAATAAATCAATA R 2 1 2 1 101000 f 74 goat snp45596-scaffold625-10471 11 12872655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274710 Affx-1111834453 AX-519548296 11 12902540 AGGTAGGAGATGGCACAGAGAAAGAGCTGAGAGAG[A/C]CCAAGCTGGGAGCAGAGGACAGAGCCTGCAGCCAT M 2 1 2 1 102000 f 74 goat GoatD01.036557 11 12902540 G T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38376803 Affx-122977939 AX-123247162 11 12920298 CCTTAATCAGAGAAAATACACACTAAATTCAGGAT[A/G]AGGAGTCAGGAGAAGGAATCAAATGGCTTAGAACA R 2 1 2 1 101000 r 74 goat snp45598-scaffold625-86015 11 12946421 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272598 Affx-1111832911 AX-519546311 11 12961238 CCATCTGCAATGATTTTGGAGCCTAAAAAAATAAA[A/G]TCTGACTCTGTTTCCACTGTTTCCCCATCTATTTC R 2 1 2 1 303000 f 74 goat 11_12961238_AF-PAKI 11 12961238 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320798949 Affx-122973452 AX-385285879 11 12962435 AGCCAGTTGGCCCTATAATTTCATACAAGAATGGC[C/T]TAGTCGGAATCTGAGCCTAAGGGACAGCTAGGGAC Y 2 1 2 1 101000 f 74 goat snp45599-scaffold625-128152 11 12988432 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791593 Affx-122960633 AX-385278584 11 13061949 TCTTGTGATACATAATAAAGGGAAGAAGAATGAAA[C/T]AGGTGGTAATGTGAGTCAAATTTCATACAGAAATT Y 2 1 2 1 103000 f 74 goat snp45601-scaffold625-227666 11 13088865 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377554 Affx-122977452 AX-123247913 11 13092167 GGATATTCATTTCAAACTAAAAATCTTGATAGAGG[C/T]AACAAGCCAAAAACAACAAAGAAAACGCCAAGCTC Y 2 1 2 1 201000 f 74 goat snp45602-scaffold625-257884 11 13119465 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443498 Affx-122927801 AX-123313835 11 13146725 CTGAGTTAAATATATCTAAGTACACAGGGTAAATA[C/T]ATTTGAGGTGGGAAGTAGATCTAGCTTTATTCAGA Y 2 1 2 1 101000 r 74 goat snp45603-scaffold625-312442 11 13174091 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446689 Affx-122924746 AX-123317025 11 13192152 ATCTCTCATAGAAACTAACATTTGCCCCTACCAGG[C/T]AGCTGGAAGGTGAACCCCAGAGACGCGGAATATAC Y 2 1 2 1 101000 f 74 goat snp45604-scaffold625-357869 11 13219802 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276460 Affx-1111835430 AX-519549972 11 13283374 ACCTTGTCCTTTGTTGTTCTAGGATGAGAGCAGAG[A/G]CAGGCTGGAGTTGGCTTCTTACAGGGAAAGAGAGA R 2 1 2 1 101000 f 74 goat Random2.2K-1141 11 13283374 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424317 Affx-122941958 AX-123294663 11 13308695 GCTCCCTTTGTATCCAGCTCTGGGCAAGGTGCTTT[C/T]AGGGAAAACAGGCCATTTTCTGCTTTTGGAGTTTA Y 2 1 2 1 101000 r 74 goat snp45606-scaffold625-474412 11 13337520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381690 Affx-122974723 AX-123252048 11 13341232 TTTTATAATCCTAAGCTTGGGAAGAGTTTTCCAAG[A/C]AAGATGCAAACCTGGAGTGTAAAGGAAAAAAAAGG M 2 1 2 1 101000 r 74 goat snp45607-scaffold625-506949 11 13371188 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410945 Affx-122952039 AX-123281295 11 13414330 AATAACAGTCAGAAAGTCCCAGCCCTGGAAATGCC[A/G]TAAAACATAAGCAGTACTTATTTTTTATTTTTGCT R 2 1 2 1 202000 r 74 goat snp45609-scaffold625-580047 11 13444280 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274483 Affx-1111834222 AX-519548074 11 13414595 AGCCTGCAGCTCCAGCACTGTCCAGTGTCCTTGAC[A/G]TCTGCACCAACCTCTGTTGTGTTCTTCAGTCACCC R 2 1 2 1 201000 r 74 goat GoatD01.026174 11 13414595 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386444 Affx-122970790 AX-123256802 11 13450885 TTATCATATTCTGCTGTGAATGGCCTGTGTTCATT[A/G]TCCAATTTGATGTGGAGTAGGAGGGAGCTCTCAAT R 2 1 2 1 202000 f 74 goat snp45610-scaffold625-616602 11 13481049 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406432 Affx-122955200 AX-123276784 11 13515255 GTGTGTGTCTATGTCAGAGAATGGAGTTCTTGAAT[A/G]CTTGGTAATATAGATGGGAAATTGTGAGTGGGGAC R 2 1 2 1 101000 r 74 goat snp45611-scaffold625-680972 11 13545700 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434959 Affx-122933849 AX-123305299 11 13549072 GCATCCATTAGAACTCGCAGAACAATGTTTAATAA[C/T]AGATCAGAGAGGAATCATCTTTGTTTTGTTTCTGA Y 2 1 2 1 101000 f 74 goat snp45612-scaffold625-714789 11 13579860 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448604 Affx-122923389 AX-123318940 11 13600210 ATTAAAAAATGGTCGTGAGCAATTAAATAAATTTA[C/T]ACCTAAGTCTAATATTTCATTGTCAATTTAACAAA Y 2 1 2 1 103000 r 74 goat snp33623-scaffold395-37067 11 13630668 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448408 Affx-122923675 AX-123318744 11 13630538 TGATGGATGTCCATCCTGAGTGTCTCCTTCACCCC[G/T]CCAGACCTCAAAGGAGATGGAGAGACGGGGATGCA K 2 1 2 1 101000 r 74 goat snp33624-scaffold395-67395 11 13661395 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422656 Affx-122943687 AX-123293002 11 13671133 GATTTCCTGGAAGGAAGAGCTATTTTCTACATACA[A/G]AAAGGACAATCAAGGATCTGAATTCTGTGAAACCT R 2 1 2 1 101000 r 74 goat snp33625-scaffold395-107990 11 13702103 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407435 Affx-122954801 AX-123277786 11 13722265 CAATCCTTTAGGCACAAAATGCCTTCATCTTTTCA[A/G]CTTGCAGTTCAGAATCCAAGGAACCAAAACTGCAC R 2 1 2 1 101000 r 74 goat snp33626-scaffold395-159122 11 13754943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425427 Affx-122941531 AX-123295773 11 13762970 TTGAACTGTTGAACACTTGCTTACATTAGTTCAGT[A/G]CGTGTGGACATAGTCACTTGACTGAATTTCTAACT R 2 1 2 1 101000 r 74 goat snp33627-scaffold395-199827 11 13795723 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428268 Affx-122939405 AX-123298611 11 13799720 TTCTGCTCACAACAGCCAGCTTTGATCATTTCTGT[A/C]GCCACATGAGCCTCTAAGCTTGCCGAGGGCAGGAC M 2 1 2 1 101000 f 74 goat snp33628-scaffold395-236577 11 13832603 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276462 Affx-1111835431 AX-519549974 11 13816704 CCAGAGATAAATTTGAGGCAAAGCTCAACAGCTTT[A/G]AAAACACAGATGTGATTTTCGTGGCTGGGGCTTTG R 2 1 2 1 202000 f 74 goat Random2.2K-1143 11 13816704 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419839 Affx-122945812 AX-123290187 11 13838672 TGGATAGACAAAGGCAGGCTCAGAGAGAAAGCCAC[A/G]CCCTTGTGGTAATTTGAATAGCTTTTAAGGAGCTT R 2 1 2 1 101000 r 74 goat snp33629-scaffold395-275529 11 13870608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451742 Affx-122921531 AX-123322075 11 13926683 GCAGCCTCTTAGGGAGAGTTAGCAACCCAAAGGAA[C/T]GTGGCAAAGATGGGGAGATTCTGAGTTTGAGGCAC Y 2 1 2 1 201000 f 74 goat snp33631-scaffold395-363540 11 13958831 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421862 Affx-122944283 AX-123292209 11 13972924 GCATGCAGATTCTTTACAAACTGACTATGAGGGAA[A/G]CCCTTAGTTGACAGTGGTTTTGGAGTCTATCAGAT R 2 1 2 1 201000 r 74 goat snp33632-scaffold395-409781 11 14006772 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783674 Affx-122934781 AX-385270733 11 14030977 GAAACATTACTTCTAATGTAAGTTAAAAGATACAG[C/T]AGGGAAGATTTTTACACTCACTTTACCATGAGCAA Y 2 1 2 1 101000 r 74 goat snp33633-scaffold395-467834 11 14065283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395071 Affx-122964184 AX-123265426 11 14069642 GCACTTCAAAGTTTCTTCTTGTTAGTCACTCAGTC[A/G]TATCTGACTCTGCAACACCATGGACCATAGCCCAC R 2 1 2 1 103000 f 74 goat snp33634-scaffold395-506499 11 14104477 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446031 Affx-122925850 AX-123316368 11 14101407 ATTGGCAGGCAGTCTGTATCAGCAGAGAGAAAACA[C/T]CCTCTGCTCCAACAGGACTTCAGCTATACTTGTTA Y 2 1 2 1 201000 r 74 goat snp33635-scaffold395-538264 11 14133855 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445414 Affx-122925377 AX-123315751 11 14155080 ATCTCTCTGGCTTCTGTACAGAGAAAAGACCAGTG[C/T]GGAGATGGTTGTGGTAGGGGAAGGGGAATAGAATC Y 2 1 2 1 201000 f 74 goat snp33636-scaffold395-591937 11 14187908 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401114 Affx-122959400 AX-123271467 11 14197109 GAAACTAGATGAACAGAGCCTCTACAAGAAAGTGT[A/G]AAAGGACAGAATTGAGACACATTGAAGAGGCAGAG R 2 1 2 1 101000 f 74 goat snp33637-scaffold395-633966 11 14230136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404074 Affx-122957143 AX-123274426 11 14276392 TTGCCATAGCCTAGATTCTTACTAAAGAGGGATTC[A/G]TTGGGTTCTGGGCACACAGTAGACCTAAATAATTT R 2 1 2 1 201000 f 74 goat snp33639-scaffold395-713249 11 14310959 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408833 Affx-122954021 AX-123279184 11 14323008 ATACTGGGTCTTCCCACCCAGGCACAAAGTATATC[A/G]CTCCATTTATTGACCTTTTTCATGTCTGTAAGCAA R 2 1 2 1 201000 r 74 goat snp33640-scaffold395-759865 11 14358915 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784088 Affx-122950229 AX-385271140 11 14359259 AATACTCAGTACAGAGGTACTGTATAAGTGGCCTA[C/T]TGGTGATGGAAAATATGTAAACTCTGAAGAGAGAA Y 2 1 2 1 101000 f 74 goat snp33641-scaffold395-796116 11 14395560 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406034 Affx-122955485 AX-123276386 11 14390530 CCACACCATTTGAGCCAAGCCGCAAACCTGAGGAC[G/T]ACCTAGAAATCTAATAGGGAGGTCCTACGAAGGAA K 2 1 2 1 101000 r 74 goat snp33642-scaffold395-827387 11 14426841 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440222 Affx-122930684 AX-123310559 11 14459740 TTATCTAAAATGACTTATTGGATGGTTATAAAGAG[C/T]AAAGTCTTTATTTTATAATTTACCTACTTATTTTA Y 2 1 2 1 101000 f 74 goat snp33643-scaffold395-896597 11 14496064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447904 Affx-122923810 AX-123318240 11 14514212 TTGAATTGTTTTTCAAAATATTAATATTTATTAAA[C/T]GAGTACCATAAGCAAGGCATCAGGCTAGGTGTAGA Y 2 1 2 1 103000 r 74 goat snp33644-scaffold395-951069 11 14550724 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418939 Affx-122946502 AX-123289287 11 14570133 TGAAAGGAGAAGGAGAAATTTTGAAGTTTTCAGAT[A/G]CTCTGTCATACAACATGTAGACCAGTCCTCCTGTG R 2 1 2 1 101000 r 74 goat snp33645-scaffold395-1006990 11 14606552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432869 Affx-122935353 AX-123303210 11 14600759 GACCTTAGTTTTCTGAATGTTGAGCCAACTTTTTC[G/T]CTCTCTTCTCTATAGTAGTGGTTAAAGTCATGGAC K 2 1 2 1 201000 r 74 goat snp33646-scaffold395-1037616 11 14637608 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406076 Affx-122956239 AX-123276428 11 14632439 ACCTGGGGCAGTTTTTTTGAGCAAAGATTTTTAAA[C/T]CACCAGGCTGAAAGTAATGGAGTCCCCAGAGCATT Y 2 1 2 1 101000 r 74 goat snp33647-scaffold395-1069296 11 14669517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413127 Affx-122950374 AX-123283476 11 14690611 GTGTTCTTGTTTTAAAAGATCACTTTAGCTGCTGC[A/G]TTGTAAAACCAGTTAAGACGTGTTCACAGATTTCC R 2 1 2 1 201000 r 74 goat snp33648-scaffold395-1127468 11 14727833 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406219 Affx-122956122 AX-123276571 11 14746246 GTATGGGAATTGAGGCTTTTGGGATGCTGGTATGT[C/T]CTATGATCTATTTCTTTATTTGGGTGCTAATTGTG Y 2 1 2 1 101000 f 74 goat snp33649-scaffold395-1183103 11 14782183 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388238 Affx-122969793 AX-123258596 11 14803938 AATTTTTCTTTGTTTTATGTAGATAATGAATAAGT[G/T]TCTAATAGTTTTGTAATGCCTCCAAGATGAGAGAG K 2 1 2 1 101000 r 74 goat snp33650-scaffold395-1240795 11 14840090 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275058 Affx-1111834661 AX-519548640 11 14847353 TAACTGCAGGCCTGCCAATAGCAGATACCAAAGTT[A/G]AGCCACCAATGGGACACCATTTTCCAGAAGAACCA R 2 1 2 1 101000 f 74 goat GoatD01.044852 11 14847353 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802913 Affx-122975822 AX-385289810 11 14850176 TAATCTGCCCTTACAGATTTTCTTTCCAGAAAATC[A/G]TACTAGGAAAAGAGGACATACTCATAAATGTGAAA R 2 1 2 1 202000 f 74 goat snp33651-scaffold395-1287033 11 14886335 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447631 Affx-122923983 AX-123317967 11 14902197 GATGCCAGCACCCTAGGCCTTTCTCAGATCAAACT[A/G]CTGGGCCTCACTGCTTTTGGTACCACTTCTTCAGC R 2 1 2 1 201000 f 74 goat snp33652-scaffold395-1339054 11 14938136 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796917 Affx-122934919 AX-385283859 11 14941735 CCTACTTGGAATCTACTTAGTTGAATGAAATAAAT[A/G]CCAATACATAAAAGGAAGTATCATGTTTCACTTAA R 2 1 2 1 101000 r 74 goat snp33653-scaffold395-1378592 11 14977588 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777053 Affx-122959749 AX-385264176 11 15005089 TCGTCGGCGTCTTGGTCGCTCTAACTTTTACTTTC[G/T]TCTTTTTGACTCCTGTGTGACCCTCGTAGGAATCT K 2 1 2 1 101000 r 74 goat snp33654-scaffold395-1441946 11 15041564 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447056 Affx-122924518 AX-123317392 11 15034039 GGTTTTCTTGAGTTTGGTTTGCATGGAGGAAGTCT[A/G]CTGAAGGGTTTTCACAGTGAGAAGTTTGTGTTTAG R 2 1 2 1 201000 f 74 goat snp33655-scaffold395-1470896 11 15071318 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412620 Affx-122951274 AX-123282969 11 15076886 AATAAGCACTTGGTGGATGTTTGTTGAATGCCGAA[C/T]GTTGTATTTATTTATACCCTGCTTTTTACCAATAG Y 2 1 2 1 101000 f 74 goat snp33656-scaffold395-1513743 11 15114297 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417112 Affx-122947472 AX-123287460 11 15108357 GAATGCAGTGTGACTAGCTGAAGAAAGGAAATACA[C/T]GCCTGCAAGCATTGCCCTTGAGGAAGCTAGGTTTG Y 2 1 2 1 101000 f 74 goat snp33657-scaffold395-1545214 11 15146317 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427208 Affx-122939588 AX-123297551 11 15147019 TGATCTTAAGTTAGCAAATCAAATGCAAAAAGGAT[A/G]TTGGAAAGGGACAGATAGCTTACCCTTGAAAGAGG R 2 1 2 1 101000 f 74 goat snp33658-scaffold395-1583876 11 15185109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406923 Affx-122955087 AX-123277274 11 15195224 TTTCTCAGGGTCAACCCTAAATAAACTGGTGACCT[A/G]CAGATCAAAGACACGATTTTACTTGCCATCTCCTG R 2 1 2 1 101000 r 74 goat snp33659-scaffold395-1632081 11 15234104 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451564 Affx-122921697 AX-123321897 11 15236737 GCTTAACTAAGAAGTAGGTTCTCAGTAAATATAAA[C/T]ACTCATTCAAAAGAATGCCAGCCCTGTCACTTACC Y 2 1 2 1 201000 f 74 goat snp33660-scaffold395-1673594 11 15275431 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276464 Affx-1111835432 AX-519549976 11 15245800 CCTTCTTCCTGGGATCTGCTTCTGCCTTCACTCCA[A/C]CCAGTGAGGGGTGGGCTGCCTGCCTTCAGAGGTGC M 2 1 2 1 102000 f 74 goat Random2.2K-1144 11 15245800 T G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419363 Affx-122945631 AX-123289711 11 15281337 CCTGAGAAGATTAGCTCACAGATGCTGGGTATAAT[A/G]CTTCTTACCCGATAGTTCCTTTTTCCTTTCCCCTT R 2 1 2 1 101000 f 74 goat snp33661-scaffold395-1718194 11 15320201 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434493 Affx-122934619 AX-123304834 11 15316826 TCCTTTGGAACAAGTGCAGAAGTTTAGTTGAGAAG[A/G]TAGTTACATTTGTGCAGGTAATGGAGTGGACCTCT R 2 1 2 1 101000 f 74 goat snp33662-scaffold395-1753683 11 15355575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793486 Affx-122944485 AX-385280463 11 15359891 CCAGGCTAGTGGCTAAACAATTCTTAAATTTCAGT[A/G]AATACTCTATATCTGTTATGTTTTTCTCCTCTCTT R 2 1 2 1 101000 f 74 goat snp33663-scaffold395-1796748 11 15398419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400690 Affx-122959941 AX-123271045 11 15396604 CAGACTTTGAGATGGGGTTTCATGTAGTCAAAGCC[A/G]CTGTTTAGAGAGGTTGCAGTGACTAGTAAGACTAT R 2 1 2 1 101000 r 74 goat snp33664-scaffold395-1833461 11 15435838 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396037 Affx-122963466 AX-123266392 11 15438156 AGCTCTATATAGTTTCATATTTGCAATGTGTTTGC[C/T]ACTCACAGGATTGCTATAATGTAGTAAGATCTAAT Y 2 1 2 1 201000 r 74 goat snp33665-scaffold395-1875013 11 15477342 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383894 Affx-122973119 AX-123254252 11 15475583 CCGTTTAAGGTAGAAAATGCATAGCAGGACCCCAG[A/G]GGAGGAGATACCACTTCTAGCAGAGGAAGAATACT R 2 1 2 1 201000 r 74 goat snp33666-scaffold395-1912440 11 15514679 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435470 Affx-122933453 AX-123305810 11 15509107 TATTATAGATGGGTTTATTGAGACATAACCACATT[A/G]TAAGCTGAAGAAGTCCTTTGTATGCTTAAGTTAAA R 2 1 2 1 101000 r 74 goat snp33667-scaffold395-1945964 11 15548162 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272601 Affx-1111832912 AX-519546314 11 15574574 TAAGGAATCTCCACACTGTTCTCCATAGTGGCTGA[A/G]CTAGTTTGCATTCCCACCAACAATGTAAGAGGGTT R 2 1 2 1 103000 f 74 goat 11_15574574_AF-PAKI 11 15574574 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38419573 Affx-122945399 AX-123289921 11 15592339 AATGGAAAGGCATAATCACTACCACCACCACCCTA[C/T]AATAATGTTGGTGATTGTGTAATCTGTGATTTGTT Y 2 1 2 1 201000 r 74 goat snp33669-scaffold395-2029196 11 15631548 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768029 Affx-122926005 AX-385255243 11 15621830 GTGATGAGTCTTTGAGGAACAGACAATATATTTTC[A/G]TTGACAGCTTTGTTACTGCACATTTTAAAATTTGG R 2 1 2 1 101000 f 74 goat snp33670-scaffold395-2058687 11 15660968 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397358 Affx-122962290 AX-123267713 11 15664448 AGAGAGCTAGGAACCTACTCTCAGCAGTTCAGATG[C/T]GCTTGCGAGAGGGTGTTGCCAGTGAGGGCCTAGGG Y 2 1 2 1 101000 f 74 goat snp33671-scaffold395-2101305 11 15703522 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424657 Affx-122942156 AX-123295003 11 15701169 CTGTCAACACTCTTTTTTGCTTTCTCTTTAGACTC[A/G]GAAGTAGATCAACCCAGAGAAGAAAAGAAAGAATG R 2 1 2 1 101000 f 74 goat snp33672-scaffold395-2138026 11 15740099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411548 Affx-122951648 AX-123281898 11 15754347 CCACCAATCTTTCTACCACTCCCAAAACCTTCTCA[A/G]TTAATCTCAAGAGGCATGTAAGTATTAAACAAAGG R 2 1 2 1 101000 f 74 goat snp33673-scaffold395-2191204 11 15793787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789274 Affx-122962456 AX-385276285 11 15787742 GAGTTATCTTTTTACTGGTTACCTTCAGAATTGAG[C/T]AAAAGGTTATACAGTCCCTAGAGTAGACTTTCAAA Y 2 1 2 1 101000 r 74 goat snp33674-scaffold395-2224599 11 15828209 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403860 Affx-122957928 AX-123274212 11 15851664 TTATCATACATATCACTAACTGGGGTTCAGTGTTT[A/G]TTTATGCAGAATTGTATTTTACACCAGAGATATTA R 2 1 2 1 201000 r 74 goat snp33676-scaffold395-2288521 11 15891645 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770905 Affx-122975621 AX-385258067 11 15884733 TCATCGACATATCCAGCATGTAAGAATGGTGCAAG[A/C]TTCTTTCAAATATGATGAGTCTGCTTTTTGGGGGA M 2 1 2 1 101000 f 74 goat snp33677-scaffold395-2321590 11 15922469 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431742 Affx-122936738 AX-123302083 11 15943261 GGGTCAGCAGCCCTAATTCCTGCATTGTTCAAAGA[C/T]CAGCTGTACATAGAAATGAACTTAAATGCTTTCCC Y 2 1 2 1 101000 f 74 goat snp33678-scaffold395-2380118 11 15980755 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380527 Affx-122975683 AX-123250885 11 16003596 TCAGCATCTTCCACCTGAGTGGGGTCTTAGTGTCT[G/T]CAGAACAACTCATTGTTACATGTATCCCCTGAGGA K 2 1 2 1 101000 r 74 goat snp33679-scaffold395-2440453 11 16045867 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781458 Affx-122952415 AX-385268543 11 16035111 AACCTATCCCAAACCCTCAGTGAGATTGCCTTTAG[C/T]TTGCTACAGCATACATTTCCCTATTTGCATTTCCT Y 2 1 2 1 101000 f 74 goat snp33680-scaffold395-2471968 11 16075021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801615 Affx-122957098 AX-385288523 11 16081861 TGGGACCTGGCATTTTTATTAACAATATGTAACAA[G/T]CTTCTCTTGGTGATTTTACTGTGTGTGCCCAGGAT K 2 1 2 1 101000 f 74 goat snp33681-scaffold395-2518718 11 16122768 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768021 Affx-122930663 AX-385255235 11 16120664 TTGGACACCTGATCCCTGTTTTTGATTTGCCTGCA[A/C]CTGCTCTTTGAGATTCTCTCAATCACCCTCCTGTC M 2 1 2 1 101000 f 74 goat snp33682-scaffold395-2557521 11 16161655 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440238 Affx-122930671 AX-123310575 11 16169111 TATTTTTTTTTTAAAGACTGAATGAAAACATGATC[C/T]TCTAACTTGGAAAGTCCACAGTCTTCTCTTAATGT Y 2 1 2 1 101000 r 74 goat snp33683-scaffold395-2605968 11 16210788 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276467 Affx-1111835433 AX-519549979 11 16230718 TATCTCCACACTTCATTCAAAGTTTTATTATCATC[A/G]TGAAGGTGTAAACAACAGAGAACACCAGATTTGTT R 2 1 2 1 101000 f 74 goat Random2.2K-1147 11 16230718 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443285 Affx-122927475 AX-123313622 11 16257890 TTCCTAGTAAGTGAGCCTTTCCATCTGATTGCTGT[A/C]TTTTTCCTGGTCTTGGGTCTGCTCCTGGGAAGGTT M 2 1 2 1 102000 f 74 goat snp33685-scaffold395-2694747 11 16300117 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403486 Affx-122957701 AX-123273839 11 16320872 CCAGATTTTTAGTCCACAAAAACTGAGAAAATAAA[C/T]GTGTCTTTTTAAGCTGCCAAATTTATGGTAATTGT Y 2 1 2 1 103000 f 74 goat snp33686-scaffold395-2757729 11 16364535 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443058 Affx-122928136 AX-123313395 11 16364658 CATTGGGGCTTGAAAGCAGCTAAATATCTGTGACT[A/G]TGTTCCAGTAAAACTTTATTTATAAAAACAATCTA R 2 1 2 1 101000 f 74 goat snp33687-scaffold395-2801515 11 16408933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775715 Affx-122975040 AX-385262846 11 16434221 AGGAAGAGGCCTAATTTGATAAGTGAGAGAATAAC[A/G]TCCATTGTGCCATCTTGCCATTGAAGGAAGCCTAT R 2 1 2 1 101000 r 74 goat snp33688-scaffold395-2871078 11 16478956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397967 Affx-122961900 AX-123268322 11 16464316 TGAATTGTGTTTGGATGTCACCAGTGTGGTATGGC[A/G]TCTATGTGGCTGTTAGAAAATGAAAGAATTTAACA R 2 1 2 1 101000 f 74 goat snp33689-scaffold395-2901173 11 16509306 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772693 Affx-122953193 AX-385259840 11 16522501 ACATGGGGCAAGTTTCGTTTAAGAAGAAATTAATT[A/G]TTTGGTTAACCAATATTTACAAAGCAACTGCCATC R 2 1 2 1 202000 f 74 goat snp33690-scaffold395-2959358 11 16568224 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800033 Affx-122933161 AX-385286956 11 16560441 TTTTGAGGGAAATATTTGAAACATGGAATCATACA[A/G]TTGTCCTAAAAAATATCCTGAGAATATGTTATCAA R 2 1 2 1 101000 f 74 goat snp33691-scaffold395-2997298 11 16606039 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376792 Affx-122977949 AX-123247151 11 16604324 CCATGTCCAACTAGACAAAGTTCTGAAGAAAAGAG[C/T]GTTAACAAAAGTGAGATGTGGAACTTCTGGCTCAT Y 2 1 2 1 101000 f 74 goat snp33692-scaffold395-3041181 11 16651560 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38443755 Affx-122927120 AX-123314092 11 16650024 TAATATGAGGATACACTGAGAAGTGATAGCATACC[A/G]TTTAGATGGCTGTGAAGCTGCAAACCATCAGGTGA R 2 1 2 1 102000 r 74 goat snp33693-scaffold395-3086881 11 16697040 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773196 Affx-122974488 AX-385260339 11 16691877 GCTTTAAACCTACCTCTTGTTGAGGGAAGCACAGG[A/G]ACCTTGTGAATGAACTCCTGCACCCTACAATGTGC R 2 1 2 1 101000 f 74 goat snp33694-scaffold395-3128734 11 16739741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446535 Affx-122925015 AX-123316871 11 16721644 CATACTTTCTGTTTTTAAAAAACTCCGGCAATGTT[A/G]CTATTTGCTATTGTATTTTGCTTTGCAGTAAAGTT R 2 1 2 1 101000 r 74 goat snp33695-scaffold395-3158501 11 16769611 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786773 Affx-122957228 AX-385273804 11 16848621 GTACATCTATCACTTTGTCATGTGTGGTAAAAGAA[C/T]GCATCAATCAGAGCATAAGAGGAATCCGTCGTTGT Y 2 1 2 1 101000 r 74 goat snp24959-scaffold256-59052 11 16911495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426102 Affx-122940640 AX-123296448 11 16911836 CAATTGTTGCCAAGTTACTTCTGAACTCATAATGT[A/G]CTACCCGTGTATGCTCTCTTGAAAGACTTGGTTGA R 2 1 2 1 101000 r 74 goat snp48422-scaffold6876-6695 11 16972339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780845 Affx-122941112 AX-385267933 11 16929921 TGTGTGTGCTTACATGTGCTAGGAATCTGAAGCAG[A/G]CTTTGCTGACTTCTATATTACTCTCCCTTTTTGCT R 2 1 2 1 101000 f 74 goat snp45232-scaffold618-11291 11 16991545 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430669 Affx-122936933 AX-123301010 11 17020089 ATCACACAAAATCCAGGAAACCTGGCAGGAGAGGA[C/T]AGCAGAAGCATAGAAAATTGAAATATTTTAGATTT Y 2 1 2 1 101000 f 74 goat snp45233-scaffold618-101459 11 17083820 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779695 Affx-122955686 AX-385266795 11 17051401 TCTAGTATCATGCGGTTCAGAAGTAGGATGGAAGA[C/T]GTACTCAAATCCTCCTCAAGCTCAAAGCTTCATTA Y 2 1 2 1 101000 r 74 goat snp45234-scaffold618-132771 11 17114640 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770645 Affx-122945422 AX-385257810 11 17091476 CATATCTGGGAATCATGAGAGATTTGATAATCATC[A/G]TGAGTTAATTATGTGTTTCATGACTTCGTGTCAAG R 2 1 2 1 101000 f 74 goat snp45235-scaffold618-172846 11 17155202 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796499 Affx-122951150 AX-385283448 11 17148045 TACCAGCTAAATCCCACTGTTCTCAGTATGATAAT[A/C]TTCTACCTTGGGATGAGGAGCGAATAGTGAAGCAA M 2 1 2 1 101000 r 74 goat snp45236-scaffold618-229415 11 17212604 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384406 Affx-122972201 AX-123254764 11 17209618 ATTCACCCAGTTAAATCTGAGAACTGTAAACTCAC[A/G]TCAATTCAGTCAGTTAGTTCAGTCCCTCAGTCGTG R 2 1 2 1 101000 f 74 goat snp45237-scaffold618-290988 11 17275118 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438670 Affx-122930882 AX-123309007 11 17285018 TTACCCTCTCTCCTCAGGCAACTTGCTTTCCAAAT[A/G]TCACACCAATGCAACTGAAAATGGTAGTCATTCAG R 2 1 2 1 101000 f 74 goat snp45239-scaffold618-366388 11 17349305 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435864 Affx-122932800 AX-123306203 11 17338109 ATCCATAGGAGGAAGATTGTAACATGTTACCTAAG[C/T]GGAAATCAAGTTATTTTTGACAATTTTCAGCAAAT Y 2 1 2 1 101000 f 74 goat snp45240-scaffold618-419479 11 17402134 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768592 Affx-122938700 AX-385255772 11 17407042 ATTTCAAGTTAGAGAGTGAAACATAAGGCAAAAAA[A/G]TTGAATGATTTGGGGCAGGCCTTGGCTACATAGTA R 2 1 2 1 102000 r 74 goat snp45241-scaffold618-488412 11 17472069 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452398 Affx-122920606 AX-123322731 11 17446119 AATTTATGGGTCTCAAGGAGGGAACAGTATTGTGG[C/T]AAAATTGAGAAATTTGTATTTCAACACTTAAATAT Y 2 1 2 1 101000 f 74 goat snp45242-scaffold618-527489 11 17511655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789566 Affx-122937652 AX-385276575 11 17483534 GGGAACTTCAGGACACCCTCAACATGACAGGTAGG[A/G]GAATTGAATTCCTTATAGACATTAGGACTGCCTAC R 2 1 2 1 101000 f 74 goat snp45243-scaffold618-564904 11 17548605 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276469 Affx-1111835434 AX-519549981 11 17490657 CGCTATGTAAGGCAAATGGGGAGCCCTGATGATGG[A/C]ACCAGGCTTGGCCTCAGTCATCCCCTGTGCCCAAA M 2 1 2 1 202000 f 74 goat Random2.2K-1149 11 17490657 G T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778309 Affx-122967271 AX-385265424 11 17513322 ATTTGAATAAAATGATCCAACTGATGTGACAAGTA[C/T]AGTGTTCTATTAAGCTATAATTATTTGAAATCTGA Y 2 1 2 1 101000 f 74 goat snp45244-scaffold618-594692 11 17578533 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762848 Affx-986697377 AX-385250871 11 17544169 CTCCTAAGAGCTTAAGAGGAACATCCCCAATCAGA[C/T]CATTCATAAGATCCAGACATCAGACAGTTAAATAT Y 2 1 2 1 600010 f 74 goat 11_17544169 11 17544169 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 320765395 Affx-986697381 AX-385252902 11 17544175 AGAGCTTAAGAGGAACATCCCCAATCAGATCATTC[A/G]TAAGATCCAGACATCAGACAGTTAAATATTCAGAA R 2 1 2 1 600010 r 74 goat 11_17544175 11 17544175 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 320765414 Affx-986697392 AX-385252920 11 17544281 CATGTCTCCCCCTCAACATGGGGGTAAGGGGCCTC[G/T]GTTAGGAGTTGCTCAAAAAAGGGTCTTTTCAAGCC K 2 1 2 1 600010 r 74 goat 11_17544281 11 17544281 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 38380303 Affx-122975397 AX-123250661 11 17556634 CACCCACCTGAAAACTTTTGTTCATTTCGCTCATT[A/C]TTTTGTTTTTATGTCCTTTCTGTTACTCTTTGACA M 2 1 2 1 101000 f 74 goat snp45245-scaffold618-638004 11 17621576 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434836 Affx-122934383 AX-123305177 11 17601832 GTCTTCTGCGCTAGCACCACAGTAGATCAGGTGTC[A/G]TAAATGACCACTTCCTATTTCTGCTGAGGGACTGA R 2 1 2 1 202000 f 74 goat snp45246-scaffold618-683202 11 17674819 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390706 Affx-122967937 AX-123261063 11 17630664 GAACAAACAGACTCTCCTTTGTCTTTTCACAGTAG[A/G]TTAAGAAGGTCTTTATTTTCTGTTGAACTTCCTTT R 2 1 2 1 101000 f 74 goat snp45247-scaffold618-712034 11 17704073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476273 Affx-1251763780 AX-586011692 11 17647605 TCATACAGAATAAAGGGCTGAGCTACAATGCCATT[-/CATGCATTTATTTTTTTTTAATTTTTTATTTTTTTTAAATTTATGGGCTAGCAAACCAGACTGTGGGATAGCTACCATTT]ATGCATTTATATAGTGCTTTGTTTAGAAAATTTTC - 4 1 4 1 20000 f 74 goat SV_177 11 17647605 - deletion junction SV-TF-chip 539476526 Affx-1251763780 AX-586011917 11 17647605 TCATACAGAATAAAGGGCTGAGCTACAATGCCATT[-/CATGCATTTATTTTTTTTTAATTTTTTATTTTTTTTAAATTTATGGGCTAGCAAACCAGACTGTGGGATAGCTACCATTT]ATGCATTTATATAGTGCTTTGTTTAGAAAATTTTC - 8 1 4 1 20000 r 74 goat SV_177 11 17647605 - deletion junction SV-TF-chip 562165521 Affx-1251763780 AX-606940932 11 17647605 TCATACAGAATAAAGGGCTGAGCTACAATGCCATT[-/CATGCATTTATTTTTTTTTAATTTTTTATTTTTTTTAAATTTATGGGCTAGCAAACCAGACTGTGGGATAGCTACCATTT]ATGCATTTATATAGTGCTTTGTTTAGAAAATTTTC - 8 1 4 1 20100 f 74 goat SV_177 11 17647605 - deletion junction SV-TF-chip 562165527 Affx-1251763780 AX-606940938 11 17647605 TCATACAGAATAAAGGGCTGAGCTACAATGCCATT[-/CATGCATTTATTTTTTTTTAATTTTTTATTTTTTTTAAATTTATGGGCTAGCAAACCAGACTGTGGGATAGCTACCATTT]ATGCATTTATATAGTGCTTTGTTTAGAAAATTTTC - 8 1 4 1 20100 f 74 goat SV_177 11 17647605 - deletion junction SV-TF-chip 562165624 Affx-1251763780 AX-606941034 11 17647605 TCATACAGAATAAAGGGCTGAGCTACAATGCCATT[-/CATGCATTTATTTTTTTTTAATTTTTTATTTTTTTTAAATTTATGGGCTAGCAAACCAGACTGTGGGATAGCTACCATTT]ATGCATTTATATAGTGCTTTGTTTAGAAAATTTTC - 8 1 4 1 20100 r 74 goat SV_177 11 17647605 - deletion junction SV-TF-chip 562165678 Affx-1251763780 AX-606941087 11 17647605 TCATACAGAATAAAGGGCTGAGCTACAATGCCATT[-/CATGCATTTATTTTTTTTTAATTTTTTATTTTTTTTAAATTTATGGGCTAGCAAACCAGACTGTGGGATAGCTACCATTT]ATGCATTTATATAGTGCTTTGTTTAGAAAATTTTC - 8 1 4 1 20100 f 74 goat SV_177 11 17647605 - deletion junction SV-TF-chip 320797939 Affx-122973862 AX-385284875 11 17687213 AATGCTGATAATTCACAGAACTTCAAAAGAAGTCC[A/G]TTATATACTTAAGTATGTAGTAGGAGCCTTTTAAA R 2 1 2 1 101000 f 74 goat snp45248-scaffold618-768583 11 17761519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427155 Affx-122939630 AX-123297498 11 17722305 ATATACACATTACATACCTTGTGTGTATGAGTTTG[C/T]GTCTGTGTGTAATAAATTAAAATTGTGTTTGGAGA Y 2 1 2 1 201000 r 74 goat snp45249-scaffold618-803675 11 17798445 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390954 Affx-122967057 AX-123261311 11 17758047 AGATATTCTGCAGAACACATAAAACAAAATCTACC[A/G]TTTCTCGCTGCAGTGCTAGAGAACAGTGGGATTCT R 2 1 2 1 201000 f 74 goat snp45250-scaffold618-839417 11 17834795 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777456 Affx-122927129 AX-385264576 11 17811912 CTAATTATGATAGCGATTAAAATGATTTGTAAATT[A/G]TTCTTATTGTTCTTTGCTCTGGAAACTTTCCCATA R 2 1 2 1 101000 r 74 goat snp45251-scaffold618-893282 11 17888393 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789646 Affx-122929015 AX-385276655 11 17856124 AGATAGGCACAGTTAAGAAAATGACTGTTATTTTG[C/T]ATCATGCAAGATCATCCAACACTGGCCTCTGAAAA Y 2 1 2 1 202000 f 74 goat snp45252-scaffold618-937494 11 17941898 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443029 Affx-122928160 AX-123313366 11 17891903 TAATTTCTAAGCTGCACACATGTTGGACAAGAGAG[C/T]GAAAAACATGGAAAAAATCAGTTTCTAAGAGATGA Y 2 1 2 1 101000 f 74 goat snp45253-scaffold618-973273 11 17977820 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476274 Affx-1251763781 AX-586011693 11 17924461 TATTAATAGAAGACTAGGAATTATATAAAAGAATT[-/AGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGAAGAAAATAAAGTTACTACAAAACGAAAAAAAAAAAAAGAATTG]AAAGTTAGTGACATAGTCATTGTTGGCGTTGTTCA - 4 1 4 1 20000 f 74 goat SV_178 11 17924461 - deletion junction SV-TF-chip 539476527 Affx-1251763781 AX-586011918 11 17924461 TATTAATAGAAGACTAGGAATTATATAAAAGAATT[-/AGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGAAGAAAATAAAGTTACTACAAAACGAAAAAAAAAAAAAGAATTG]AAAGTTAGTGACATAGTCATTGTTGGCGTTGTTCA - 4 1 4 1 20000 r 74 goat SV_178 11 17924461 - deletion junction SV-TF-chip 562165146 Affx-1251763781 AX-606940558 11 17924461 TATTAATAGAAGACTAGGAATTATATAAAAGAATT[-/AGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGAAGAAAATAAAGTTACTACAAAACGAAAAAAAAAAAAAGAATTG]AAAGTTAGTGACATAGTCATTGTTGGCGTTGTTCA - 8 1 4 1 20100 r 74 goat SV_178 11 17924461 - deletion junction SV-TF-chip 562165302 Affx-1251763781 AX-606940713 11 17924461 TATTAATAGAAGACTAGGAATTATATAAAAGAATT[-/AGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGAAGAAAATAAAGTTACTACAAAACGAAAAAAAAAAAAAGAATTG]AAAGTTAGTGACATAGTCATTGTTGGCGTTGTTCA - 8 1 4 1 20100 f 74 goat SV_178 11 17924461 - deletion junction SV-TF-chip 562165388 Affx-1251763781 AX-606940799 11 17924461 TATTAATAGAAGACTAGGAATTATATAAAAGAATT[-/AGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGAAGAAAATAAAGTTACTACAAAACGAAAAAAAAAAAAAGAATTG]AAAGTTAGTGACATAGTCATTGTTGGCGTTGTTCA - 8 1 4 1 20100 r 74 goat SV_178 11 17924461 - deletion junction SV-TF-chip 562165480 Affx-1251763781 AX-606940891 11 17924461 TATTAATAGAAGACTAGGAATTATATAAAAGAATT[-/AGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGAAGAAAATAAAGTTACTACAAAACGAAAAAAAAAAAAAGAATTG]AAAGTTAGTGACATAGTCATTGTTGGCGTTGTTCA - 8 1 4 1 20100 r 74 goat SV_178 11 17924461 - deletion junction SV-TF-chip 562165641 Affx-1251763781 AX-606941051 11 17924461 TATTAATAGAAGACTAGGAATTATATAAAAGAATT[-/AGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGAAGAAAATAAAGTTACTACAAAACGAAAAAAAAAAAAAGAATTG]AAAGTTAGTGACATAGTCATTGTTGGCGTTGTTCA - 8 1 4 1 20100 r 74 goat SV_178 11 17924461 - deletion junction SV-TF-chip 562166563 Affx-1251763781 AX-606941971 11 17924461 TATTAATAGAAGACTAGGAATTATATAAAAGAATT[-/AGGAGAGAGGGAAAGATGGCGGAGGAATAGGACGGGAAGAAAATAAAGTTACTACAAAACGAAAAAAAAAAAAAGAATTG]AAAGTTAGTGACATAGTCATTGTTGGCGTTGTTCA - 8 1 4 1 20100 r 74 goat SV_178 11 17924461 - deletion junction SV-TF-chip 320792274 Affx-122951200 AX-385279258 11 17925974 AAGGACAGAGCTTCCTTTAGATGATTTCTTATTCT[A/G]CCCTCTCAATTTGGATCATTCTACTGCTGCCTGAG R 2 1 2 1 101000 r 74 goat snp45254-scaffold618-1007344 11 18012239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423419 Affx-122942617 AX-123293765 11 18019264 GCCACAGAACTGAATGGCTATGGAAGTGTAAAGAA[C/T]AAGATCATTGATGAAGTGGGCAAAGAAGTTTGAAG Y 2 1 2 1 101000 f 74 goat snp45256-scaffold618-1100634 11 18106423 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423305 Affx-122942635 AX-123293651 11 18056712 CAAGAGTTCAAGGACCATAAAAAATAAAGGAAATA[C/T]AACTCCACCAAAGGAACACAATACATCCTTTTCAA Y 2 1 2 1 103000 r 74 goat snp45257-scaffold618-1138082 11 18144036 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786586 Affx-122961062 AX-385273618 11 18104456 CAATTTGGAGCTGTAATGAACAGCCTTTCTATGAA[C/T]ATTCTTGTCCATGTTTCCTGGGTAGACTTCTGTGC Y 2 1 2 1 201000 f 74 goat snp45258-scaffold618-1185826 11 18191856 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431471 Affx-122936265 AX-123301812 11 18147821 AATTATAATTTCTTTTTTTCCTTTTGGAAAACTGC[A/G]TGCTAATATTTAGAGCCAATGTGAAAGATTCGGTT R 2 1 2 1 101000 r 74 goat snp45259-scaffold618-1229191 11 18235358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414139 Affx-122949702 AX-123284488 11 18186072 TGTATCTCTGATTTCATTTTCTATAATACACCAGC[A/G]TTTGAATACACCAGAACACACTTATCTACCTTACT R 2 1 2 1 101000 r 74 goat snp45260-scaffold618-1267442 11 18273832 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417440 Affx-122947206 AX-123287788 11 18215606 GAATAACATGCCTCCAAACAGCACTCGGCACTTGG[C/T]ACAACCCGAGCCCCAGTTCAGAGCTGCTAGTTAAT Y 2 1 2 1 201000 f 74 goat snp45261-scaffold618-1296976 11 18304109 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453415 Affx-122919889 AX-123323748 11 18266709 ATTGGGAGGAGGGAATAACCCCCATTTCACAGACT[A/G]TAGCTTTCAACAAAGGAATTTCACTCCCAAAAGAG R 2 1 2 1 201000 r 74 goat snp45262-scaffold618-1348079 11 18356051 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451697 Affx-122921568 AX-123322030 11 18297921 ATTTTTTTTAATGAATAAAACAGAGCTAAAATTGA[A/G]CACTATATTGCCAAAATATGAAATAATTGGGGGTA R 2 1 2 1 101000 r 74 goat snp45263-scaffold618-1379291 11 18387274 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272603 Affx-1111832913 AX-519546316 11 18317209 CTTCACGCGTCCGTGAAAGAAATGCTTTTCCTGCT[A/G]AAGGGAGTTGTCTGAGAGAAACATTCAGGTAGAGC R 2 1 2 1 202000 f 74 goat 11_18317209_AF-PAKI 11 18317209 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320778307 Affx-122955417 AX-385265422 11 18340882 CAACTGAAAGTGTTTTCTGTTACTGTTAAGAATAG[C/T]GTTTTAGAAATGTCAAGTAAGTCATGTTGGTTAAC Y 2 1 2 1 101000 f 74 goat snp45264-scaffold618-1422252 11 18431009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783996 Affx-122969550 AX-385271050 11 18370614 TAATGATCAGAAACTAGAAATTCTAATTATAATAA[C/T]TGACTCCAAATCATTTGTGGCATCTTCCCTTTGTT Y 2 1 2 1 202000 f 74 goat snp45265-scaffold618-1451984 11 18460741 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412469 Affx-122951395 AX-123282818 11 18410505 GCACACCAGTCTCCTTAAACGCATCTCTGCCTGGA[C/T]AGATCACTCAGTTAGTTGTAGTGCCAGTGGGTCCG Y 2 1 2 1 201000 r 74 goat snp45266-scaffold618-1491875 11 18500854 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445285 Affx-122925457 AX-123315622 11 18458540 AAATTCATTTTAAGAATAGAGCAGACAGGTATCCT[A/G]TTCGGAAAGGGGAGAGTTAATTATCATACAGTAGA R 2 1 2 1 201000 f 74 goat snp45267-scaffold618-1539910 11 18548789 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434810 Affx-122934808 AX-123305151 11 18534184 AGAGGCAGGCTGGTGTTTGCATAGTGTGAGTCTGC[A/G]TTTAGATGACTGCATTTCAAAAATATGTCTACTTT R 2 1 2 1 201000 r 74 goat snp45269-scaffold618-1615554 11 18621929 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428607 Affx-122938691 AX-123298949 11 18584148 TCGGGGTGCCTGGTCAGGTTTGGGGTCTAGAGAGA[A/C]GCAGTGAGTTCCTTTTATTTGGCTAATGCCAAATA M 2 1 2 1 201000 f 74 goat snp45270-scaffold618-1665518 11 18672437 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413745 Affx-122950052 AX-123284094 11 18617076 ACTCCAGCAAGCAGATGGAAAGATATTTTGAAGAG[C/T]AGAGAAGTGGAATCTAGGTCCAGTTAGGCCAGGGT Y 2 1 2 1 201000 r 74 goat snp45271-scaffold618-1698446 11 18705261 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778838 Affx-122975614 AX-385265946 11 18652407 ATGATTTTGTGGAGAGAGGACTTAATTGACTCCTT[A/G]CAGTGTTAAAATGTACGTATACTTTATAGATTCAT R 2 1 2 1 101000 f 74 goat snp45272-scaffold618-1733777 11 18740805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443627 Affx-122927295 AX-123313964 11 18692741 TGAAAGAGATGGTGGAGGAATGAGCTGGGGATGGC[A/G]TGCGGTGGGGGTTGTCACTTAGTAGTAAATCTTAC R 2 1 2 1 103000 r 74 goat snp45273-scaffold618-1774111 11 18780995 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437457 Affx-122932388 AX-123307795 11 18725340 ATTTGGCACCATCAAGGAATGAAGTCACCACAGAG[C/T]GAATTCCCCAGATGAGTGAAATTTGGGGTGTCAAG Y 2 1 2 1 101000 f 74 goat snp45274-scaffold618-1806710 11 18813319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390418 Affx-122967646 AX-123260775 11 18758339 TGTAGGTCACAACAGGAGGAGCAAAGATGTGAAAG[A/G]TGTATTCCCGAGGTAAAACGTGTGGAGAGTACAGA R 2 1 2 1 101000 r 74 goat snp45275-scaffold618-1839709 11 18846743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394396 Affx-122964620 AX-123264751 11 18790383 AATAATACCAGACAGGGTGGAGAAAGGCAGATTTC[A/G]TATTGCAGAAAGAACATGTATTTACTGTCAATACA R 2 1 2 1 201000 r 74 goat snp45276-scaffold618-1871753 11 18878063 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430900 Affx-122936866 AX-123301241 11 18823934 AGTTGAGAAGAAAAGTATAACAAAATTTTTTACTC[A/G]TCTAAAATCAATGGTTCCATGAACAGTACTTCAGT R 2 1 2 1 101000 r 74 goat snp45277-scaffold618-1905304 11 18911074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410827 Affx-122952634 AX-123281177 11 18873125 TGCTCTTATGAGCTTTTTCTTGTTTTTCTTACTTC[A/G]AATCAATGTTCTTGTTGTTACTTGCACACACGGCC R 2 1 2 1 101000 r 74 goat snp45278-scaffold618-1954495 11 18961058 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453118 Affx-122920017 AX-123323451 11 18905218 TTTTGTTTAATCAGGGAATGTGGAGGTCACGTGCA[C/T]CCATCTGGGACTCTGTAAGACTGCCGTTGTCCTGC Y 2 1 2 1 101000 f 74 goat snp45279-scaffold618-1986588 11 18993217 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773172 Affx-122927435 AX-385260316 11 18935619 TTTCAGAGCTCACATCATCAGTCTACCAGGTAACA[A/G]TTATACATGGTCTTGGTTTTTCTATCACTGCACCA R 2 1 2 1 101000 f 74 goat snp45280-scaffold618-2016989 11 19023877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395773 Affx-122963671 AX-123266128 11 18965950 GTCCTAATGATACTGAGACTTATAAACCACTCGCC[A/G]CAGGCACACAGCCCCAGAAGGACAGAACTTGGTTT R 2 1 2 1 101000 f 74 goat snp45281-scaffold618-2047320 11 19054737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777345 Affx-122974199 AX-385264467 11 19029576 CATCCCCAGTTTCAGTACAAATGGAACAGAATTGT[A/G]CATGTTCTTCTGAACTTTGTAATCTATCCAAGGGT R 2 1 2 1 201000 f 74 goat snp45282-scaffold618-2110946 11 19118805 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418253 Affx-122947025 AX-123288601 11 19082993 CTTGAAAAATACTGTTGATTTGAAGGAGCAAGGGG[C/T]AGAAGGCTTATGCTTGTTAAGTAACCAAACAAAAA Y 2 1 2 1 101000 f 74 goat snp45283-scaffold618-2164363 11 19173169 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418706 Affx-122946290 AX-123289054 11 19114049 GAAATTTTTTTTCCCCAAAATCTGTATCACATATG[A/C]GGAGAATGAGATTAGGTTATTGTGGTAGATCCAGG M 2 1 2 1 101000 r 74 goat snp45284-scaffold618-2195419 11 19204637 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426795 Affx-122940540 AX-123297141 11 19167505 ATTAACTATAAATACTGTGACATGCTGAAGAAAGT[C/T]GGTGAAACTGGAGTGGATAAGTGAAAGGGGATGAT Y 2 1 2 1 201000 f 74 goat snp45285-scaffold618-2248875 11 19258505 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379190 Affx-122976304 AX-123249549 11 19209281 AAGGAAGAGAGAGAGAATCATTGCTACTGCGTGAT[A/G]TAGTATATTCCCCAAAGCAGGAAATGATGGGGGAA R 2 1 2 1 101000 f 74 goat snp45286-scaffold618-2290651 11 19300408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777846 Affx-122928890 AX-385264963 11 19252677 AGTACTCATATCTGTAACAAGAGTAAAAGCACATT[A/C]TAACAACCTCACGTATAGCAAAAATGATGCTTTAG M 2 1 2 1 101000 r 74 goat snp45287-scaffold618-2334047 11 19344211 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449874 Affx-122922358 AX-123320209 11 19284443 AATTCTAATGTAAGATGTTAGCATAAGCAAAGACA[C/T]GGAGGCTGAAGAAAAGCTTGGAAAGAAAGCAATGT Y 2 1 2 1 201000 f 74 goat snp45288-scaffold618-2365813 11 19375976 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379513 Affx-122976079 AX-123249871 11 19313263 TACTAGGATAGGGTACTATAACTGGCCACCTTATG[C/T]CTCAGGAAGTACTAATTGCCACCCTCCAGTAGAAC Y 2 1 2 1 101000 f 74 goat snp45289-scaffold618-2394633 11 19404810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435060 Affx-122933739 AX-123305400 11 19349298 CTGAATTTAAAAAACATTGAGCTGTCATGAGAACT[A/G]TGATCCTTCTGAAGCGTCACGGCCACAGGGCTCAT R 2 1 2 1 201000 f 74 goat snp45290-scaffold618-2430668 11 19440672 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796805 Affx-122935142 AX-385283748 11 19384775 TCCATTTTAAAATAAAAGGCACATTGCATAGAAAA[C/T]GATCTTTGTATATGAAATATGAAAGTGAAAGTCAC Y 2 1 2 1 101000 r 74 goat snp45291-scaffold618-2466145 11 19476181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385255 Affx-122972084 AX-123255613 11 19436135 GTAAATAGCGAGTCCACGTGGTCTCGGTGCTCTTG[C/T]AGTCCGATCCATGGTGGTGTGGCCTTTTCAGCAGT Y 2 1 2 1 201000 r 74 goat snp45292-scaffold618-2517505 11 19527373 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454198 Affx-122919293 AX-123324531 11 19473880 TCCTAATTATCAGGACCTGGTACATACGCAGAAAA[A/G]AAACTGCAATGCTGCAATCATTTATTAGGAATTAG R 2 1 2 1 101000 f 74 goat snp45293-scaffold618-2555250 11 19565554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441150 Affx-122929568 AX-123311487 11 19528011 AAAACAAATTATCTGGTTCATCCACAATAATTCTC[A/G]CTTATCTTTGTGCTTGCAAATATATATTCCCCTAA R 2 1 2 1 101000 r 74 goat snp45294-scaffold618-2609381 11 19619495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429109 Affx-122938020 AX-123299451 11 19568278 TTTGGAATGTGCCGGGAACTGTTGCTGGATTCCCT[A/G]CATGTGGCTGGCTGACACAGCAGCAGTGCTGACAG R 2 1 2 1 303000 r 74 goat snp45295-scaffold618-2649648 11 19660202 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767895 Affx-122944414 AX-385255115 11 19597469 CTCTGGCTGGAGTACTTTCCCTCTAGATACCTTTG[A/C]GGTTAATTTCTTTATCGTCTTCCAAGCTTTGGTAA M 2 1 2 1 101000 f 74 goat snp45296-scaffold618-2678839 11 19689550 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434444 Affx-122934654 AX-123304785 11 19685256 TCACCTACATTTAGGATTCCTTTCCCAGATTTTGC[A/G]TGATTTTCCCTGGAGGAGGTTTGGGATCATGCTGC R 2 1 2 1 102000 f 74 goat snp45297-scaffold618-2766626 11 19778519 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766003 Affx-122945379 AX-385253424 11 19737634 TTGGCTCCGGGAACTTTACAGATGCCATTTCAAAC[C/T]GTAGGTGTTTGGAGCCTTGTTTAATGATATCTTGG Y 2 1 2 1 101000 f 74 goat snp45298-scaffold618-2819004 11 19830873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435239 Affx-122934079 AX-123305579 11 19803513 CGTCGGGTATAAAACATCAAACCCATTACAGTTCT[A/C]CTCAGTTTACACATTTTAATTGGCATCACCAGTAA M 2 1 2 1 101000 f 74 goat snp45299-scaffold618-2884883 11 19897105 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381983 Affx-122974093 AX-123252341 11 19840774 AATAGGCAGCATGTTTGCATAGAACTTGTCCCTTG[C/T]GTTAGGGACTATGAAATTCATGAAACAAAGAGCCC Y 2 1 2 1 101000 f 74 goat snp45300-scaffold618-2922144 11 19935195 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436025 Affx-122932736 AX-123306364 11 19903848 GGATGCTGGACACTGACCTCAACAGAAGGTTACAC[A/G]CCCCTCTACTGTCACATCTTTAATTTACCCCATTC R 2 1 2 1 101000 r 74 goat snp21914-scaffold215-1607160 11 19999307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778099 Affx-122970318 AX-385265214 11 19964260 CTGTTATCTGGGTTGCATGTAGGTAAGGAAACTGC[A/G]CAGAGAAAGTAAACTAGCTTAAGGACACTTAAACA R 2 1 2 1 101000 r 74 goat snp21913-scaffold215-1546748 11 20059567 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783564 Affx-122934456 AX-385270626 11 20003586 TCTCTCCTTTAATAGCTGAAACCTGCCTCTTCTAA[C/T]ACCTTCCCTCAAATTCTGGTCCTGTGGTCTTCAGC Y 2 1 2 1 101000 f 74 goat snp21912-scaffold215-1507422 11 20098763 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782432 Affx-122975030 AX-385269508 11 20053572 CATAGGTTGGAGCCCTCTTTCGGGTTGCCAGGAAA[G/T]ATCTTAAATCACAACGTTTAGAGTTTCCTTCGATG K 2 1 2 1 101000 f 74 goat snp21911-scaffold215-1457436 11 20148505 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450572 Affx-122922038 AX-123320906 11 20092440 TGGAACCTGTCATTCTCCTCTCACAAAGTTAGTGA[C/T]GTCACAGAGGGTTAGAGGGGGTCAGACGGCACCGC Y 2 1 2 1 101000 f 74 goat snp21910-scaffold215-1418568 11 20187706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392189 Affx-122966293 AX-123262546 11 20139847 TTCTTATTGAAAAGATATTTTAAAATGGTTATGTA[C/T]TTGGGGGAAAGCACATACTCAGGCCCACAGAAAAC Y 2 1 2 1 103000 r 74 goat snp21909-scaffold215-1371161 11 20234791 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274864 Affx-1111834540 AX-514630147 11 20156976 GTGAATGTGTTCTGAGCCCAAGGGCCAGCCAGCTT[A/G]CAGCCACCCCCTGCAGGCAGGAGGAAG R 2 1 2 1 102000 f 74 goat GoatD01.040840 11 20156976 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320771503 Affx-122956131 AX-385258661 11 20231530 TTTAAAAAGTGATGGAAGGTCGCAAAAGTACAAAG[C/T]GAAGTTTAGAGTTTTAACTTTCATTGCTCATAAAT Y 2 1 2 1 101000 f 74 goat snp21908-scaffold215-1279478 11 20327500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437941 Affx-122931628 AX-123308279 11 20302466 CTTCGCTATGTCTTTCACAACCTCATGTCTAGCCC[A/G]CTAGCAAATCCAGACAGCTCTGCTTTCAGAATCCA R 2 1 2 1 101000 f 74 goat snp21907-scaffold215-1208542 11 20396991 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440099 Affx-122929714 AX-123310436 11 20355219 TTGAACAATTCACAGATGAGAAAACTAAAGCTCAA[C/T]GAAAGCAAACAACTTTCCAAGAGAAACAAACCCAG Y 2 1 2 1 201000 r 74 goat snp21906-scaffold215-1155789 11 20449849 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411050 Affx-122951955 AX-123281400 11 20403553 CAGCAGTAGAAAGTAAAGGCATTGATAAAATCTAG[C/T]GACAATTACTAATAGAAATTCCATGTAAATTAAAA Y 2 1 2 1 101000 f 74 goat snp21905-scaffold215-1107455 11 20498191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431235 Affx-122937139 AX-123301576 11 20442229 GTATGGTGGTTAGGTCCAGCTAGTGGTGATGTTTC[A/G]AGATACATATTTGCAAATATTTTAAAGAGTATGTG R 2 1 2 1 101000 f 74 goat snp21904-scaffold215-1068779 11 20536762 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431870 Affx-122936065 AX-123302211 11 20482577 TTGTTCAGTATTCTTTAAATGGAAACAGCAAAGAT[G/T]CTATGTCATAACTGCCGGTTACTGTGGAAACAGTA K 2 1 2 1 101000 r 74 goat snp21903-scaffold215-1028431 11 20577321 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378819 Affx-122976550 AX-123249178 11 20515450 ATATAATTCTTTCAGTTCCTCTCGGTGTCCTTATT[C/T]ACTTTGGCTCAGATCAGCTTTTTGCTGTTGTTATT Y 2 1 2 1 201000 f 74 goat snp21902-scaffold215-995558 11 20609012 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387811 Affx-122969683 AX-123258169 11 20546169 GCTGCTAGGTCCAGCGTATGGAGATTCTCCAATAC[A/G]TAGTCACATAGAGGACAAGAACAGCCTCTTGTAGC R 2 1 2 1 201000 f 74 goat snp21901-scaffold215-964839 11 20640084 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443949 Affx-122927016 AX-123314286 11 20588621 GCACACATACTCACACACAGCAGGACTTCACTATT[A/C]TCTGTGTTGAGCTGATGTTTCTGCTCTCCTAAGGA M 2 1 2 1 201000 f 74 goat snp21900-scaffold215-922387 11 20682927 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406161 Affx-122956169 AX-123276513 11 20632641 CCTCAAACTAAGTGAAAAACCTCTTTGGGCCCCTT[A/G]CCTGAACTTTTTTACTTGGTTGATGAGTAGGCCTG R 2 1 2 1 201000 r 74 goat snp21899-scaffold215-878367 11 20726994 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391529 Affx-122966652 AX-123261886 11 20664777 AAACAAAACGTATCTTTTACATAGGCAAGTAAGAT[A/G]TAAGGACTAAGCATGGTATTGAGAGACTATACTAT R 2 1 2 1 101000 r 74 goat snp21898-scaffold215-846231 11 20759336 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402780 Affx-122958304 AX-123273133 11 20707899 TAATAGCAACGTTCAGCAAGGCTGGGTTTCCTTAC[A/C]AACTGAGGGGTGTGAGAACTGCATTTTAACCTGGT M 2 1 2 1 101000 f 74 goat snp21897-scaffold215-803109 11 20802673 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421413 Affx-122943970 AX-123291760 11 20766952 AGTGAAAATGCAGTACTTTTATTATCTCCTTTCCA[G/T]AAGCAGAAAAATGTTTTAAGTATATGCTGCTAGAA K 2 1 2 1 101000 f 74 goat snp21896-scaffold215-744056 11 20862017 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392272 Affx-122967547 AX-123262629 11 20886311 ACTCAGGGGTGGCTTTGGAAATTCAGCCCAATCCC[A/G]TAACTACCAACAATGTGAAGCAGTATTTAGGATGA R 2 1 2 1 201000 r 74 goat snp21894-scaffold215-624697 11 20982040 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272605 Affx-1111832914 AX-519546318 11 20895464 GGTCCTGGGAAACCTGGGCAGCATGCCTGGGCCGT[A/G]GTGGCTATCACTGCTGCCCCTTTCTCAGCGTGTGA R 2 1 2 1 303000 f 74 goat 11_20895464_AF-PAKI 11 20895464 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38427055 Affx-122939813 AX-123297400 11 20932468 GTCTCCATATGTCATCCAAACCTATTTATCAGGGA[C/T]GAGCTGCAGGCTTAATTTAATTCTGTATTTGGTGG Y 2 1 2 1 101000 f 74 goat snp21893-scaffold215-578540 11 21028410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791994 Affx-122970538 AX-385278982 11 20983603 GTCCCATTCAGAGCTTGTGGTCACCAAATATTTTG[C/T]GGAAGTGAGTCGAATTCTCATCTAATAGACTACAA Y 2 1 2 1 101000 f 74 goat snp21892-scaffold215-527405 11 21081817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446431 Affx-122925978 AX-123316767 11 21016965 TGGAGCCTGACCTGACTCCCAGAAGCAACTTTTTC[A/G]TTAGGACAAAAATGTCAAGTGCTCAACTTATTTTC R 2 1 2 1 201000 r 74 goat snp21891-scaffold215-494043 11 21115328 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412007 Affx-122951750 AX-123282357 11 21048489 ATGCTAAAGAGTTAGCCCCAGTTGTAAAGGAAAAT[A/G]TGATAATGAGGAGAGGGGATGGGCTCTTGCGCTAA R 2 1 2 1 201000 f 74 goat snp21890-scaffold215-462519 11 21146459 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397078 Affx-122962719 AX-123267433 11 21093552 GTTTGGAAGGTAAGGAACAAATGTAATGACCGATT[A/G]TTTAATTTTATTTCTTCTAATAAGGTAACAGATGA R 2 1 2 1 103000 f 74 goat snp21889-scaffold215-417456 11 21191518 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774785 Affx-122954298 AX-385261919 11 21131880 TGTCCATACACTGAGGCTGTCAAGCCCTCAGCTAA[C/T]GAAGTGTATATATAGTAAGATAGGCCATACTAAAT Y 2 1 2 1 101000 f 74 goat snp21888-scaffold215-379128 11 21229842 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435421 Affx-122933545 AX-123305761 11 21177694 TTAGGCTGGCATCAGAACTGGAGGAATGAAATGAA[C/T]GATAGAGTGTAGGGAAGAGCAAAGGGGAAGGAGTG Y 2 1 2 1 101000 f 74 goat snp21887-scaffold215-333314 11 21275319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419088 Affx-122945790 AX-123289436 11 21206271 ACCAAATGAGAAAAGGGGTGGGGGTGGATATAATC[A/G]TTTTTCTTTTAGTAATTTTTAATTCAGGTAGTGTT R 2 1 2 1 202000 r 74 goat snp21886-scaffold215-304737 11 21304297 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411980 Affx-122951776 AX-123282330 11 21262082 AAGTGAAGAGGCAGACCCCAGAGGGAGATACTAAC[A/G]TGATCTAGAGTGGTTGGGAAAATCTTCATGGAGCT R 2 1 2 1 201000 r 74 goat snp21885-scaffold215-248926 11 21360526 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391600 Affx-122966599 AX-123261957 11 21319581 CACACAGTTGCTGGATCTGTTTCCAATTCTGATGC[C/T]AAAATGTGTGGTATTTAACTTAAAAATTACAGTGC Y 2 1 2 1 101000 f 74 goat snp21884-scaffold215-191427 11 21418411 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793613 Affx-122978062 AX-385280587 11 21390413 ATGATTGTCATCCACTGTCACTGAGTGCCTTTTGA[C/T]GAATAGGAGAGATGTCAAAAGATCAGTGATCAGCA Y 2 1 2 1 102000 f 74 goat snp21882-scaffold215-120595 11 21489338 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423928 Affx-122942264 AX-123294274 11 21495972 CAACTACAGAGCTTCCGGATCATCACGTGTTGACA[C/T]GTCAGGTGTGGGAATGGAGCTTGGCCACCCTCCAC Y 2 1 2 1 101000 f 74 goat snp21880-scaffold215-15036 11 21593569 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381372 Affx-122974396 AX-123251730 11 21512371 GAAGACCCATGTTCATTCCCAGATAACAGTTCAGA[A/G]TGGTATAGACCTCTCATGGGGATGCCAGCAAGGAT R 2 1 2 1 101000 f 74 goat snp17528-scaffold1814-1264 11 21609772 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393727 Affx-122965231 AX-123264082 11 21550765 CATCGTACACACTCACTCACAGCCTCAAAGAAAAC[C/T]ACACAGCTGACTTCCCTACCTGTTGGGTGATAGTT Y 2 1 2 1 101000 f 74 goat snp17529-scaffold1814-39658 11 21647869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772967 Affx-122945153 AX-385260111 11 21606294 TGTATAAATTTCTATACTGCCTGCATTTTTTATAA[C/T]GAGCAGGTTTTATCTTTGTATTCAAAGAAAAAGAA Y 2 1 2 1 101000 r 74 goat snp17530-scaffold1814-95187 11 21703618 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791500 Affx-122946125 AX-385278491 11 21655708 GCGATCATTTGGAAGGAAGTTTTCCCAAGAACAAA[C/T]GGCTGTGTCTCTTGATGCAAGGCATAGAGATATTC Y 2 1 2 1 101000 f 74 goat snp17531-scaffold1814-144601 11 21752857 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446531 Affx-122925018 AX-123316867 11 21687989 TGCAGTGGCAAATTAGATTACTGTGTGAGGATTAC[A/G]TTACTGACACATACGTTGGGGAGGATACCTTTTGA R 2 1 2 1 201000 f 74 goat snp17532-scaffold1814-176882 11 21785188 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450385 Affx-122922085 AX-123320720 11 21747699 CTAATGGGCTAGGAACCGGGAGCTGTAGGTGAAGC[A/C]AGTTGGAGTTAGGTCTGAAGTTTGGGCAAATAGTC M 2 1 2 1 101000 r 74 goat snp17533-scaffold1814-236592 11 21846420 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417300 Affx-122947234 AX-123287648 11 21777338 GCTTTAAAAGGGCAGATAATTCAGGGCGTTCTCAT[A/G]ATGGAAATGCCCTGTGTCTGGACCATGAAAGTGGT R 2 1 2 1 101000 f 74 goat snp17534-scaffold1814-266231 11 21876083 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420889 Affx-122944617 AX-123291236 11 21831972 GTTAGAATGGACCAGGTAATGCATTACCCACTGCG[C/T]GGCAATTTGAAAGCTTCCATTTTGAAGCTATACAA Y 2 1 2 1 101000 f 74 goat snp17535-scaffold1814-320865 11 21931217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412089 Affx-122951125 AX-123282439 11 21863559 TTTTATGGCATCTAATGAAAACTGTTTATTTTACC[C/T]GGGCTTCAACATCTGACAGAGGCAAATCATCCAAT Y 2 1 2 1 101000 r 74 goat snp17536-scaffold1814-352452 11 21962391 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795603 Affx-122927118 AX-385282558 11 21909200 ATAGGTAGGATTTGATTGCCCCTGAGATTCAACGG[C/T]ATAACTCCGAATGAATTAATGGAAACAGATTGAAA Y 2 1 2 1 102000 f 74 goat snp17537-scaffold1814-398093 11 22006888 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385897 Affx-122971586 AX-123256255 11 21957087 CAGACGTGTTGGCCTGAAGGGCTGAAGAACAGACT[A/G]TATTACAAAAGGGATGCTAAGGGAAAGAGCACGGA R 2 1 2 1 101000 r 74 goat snp17538-scaffold1814-445980 11 22054661 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445948 Affx-122925908 AX-123316285 11 22039450 AGTAGGAAGCATTGATGTACCAGGCACTGTGCTAA[A/G]TAAATGCATCACTTAAGTAAATTTAATTCTCACCA R 2 1 2 1 201000 r 74 goat snp17540-scaffold1814-528343 11 22137695 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425213 Affx-122941022 AX-123295559 11 22088899 GTATTTTACCCCCCATGCTCTCCACCCACTCCCTC[A/G]GGAAGTGCATTTCCTTGGTGTGCAGAATGCTTGGG R 2 1 2 1 101000 r 74 goat snp17541-scaffold1814-577792 11 22187231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445267 Affx-122925470 AX-123315604 11 22130171 ATGGGCCTGGTTAGGATGTTTCCTGCAGGCTAAAC[A/G]CAGGTATTCTAGCTTAACACTCACACATAGGAGGC R 2 1 2 1 101000 r 74 goat snp17542-scaffold1814-619064 11 22230955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781701 Affx-122968635 AX-385268783 11 22194493 AGCTGGAAAAAAGAAAGTTTACATTTGTCTACAAC[G/T]CATGTCCACAACACCAAGTCTTTAGGCACAAAACA K 2 1 2 1 101000 r 74 goat snp17544-scaffold1814-683386 11 22295265 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436954 Affx-122933172 AX-123307292 11 22225972 AGACAGATGTGCACAGGCAAGGCAGGAAAGAGACA[C/T]GAGCTGGTGGGTTGTGTTGAAGCCTGTTGGTTCAG Y 2 1 2 1 101000 f 74 goat snp17545-scaffold1814-714865 11 22326615 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463144960 Affx-1109835930 AX-514631861 11 22382513 AACCTTTGTGCCCCTGATGATAGAATGGGGGCCAA[A/G]AACTGCAGGATGACTGACAAAACTCACCCTCAGGT R 2 1 2 1 202000 r 74 goat GoatD01.050231 11 22382513 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386268 Affx-122970947 AX-123256626 11 22386075 TACACAAACGCATCTGAAATCTGACCATGCATAAG[C/T]AGGATGGCAAGCCAGCAAGCACATGAGACTGGGGA Y 2 1 2 1 201000 f 74 goat snp17548-scaffold1814-874968 11 22487583 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413271 Affx-122950216 AX-123283620 11 22415496 GTGATATTTTCATATTTCAGATTATTTTTATAGAA[G/T]ATCACCCCAGAAGAGGTATTAATGTGTCATGGGAG K 2 1 2 1 103000 r 74 goat snp17549-scaffold1814-904389 11 22517475 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454265 Affx-122919643 AX-123324598 11 22462265 TCCTGGCAAGCTCACACGTGTGACAATGTACAACG[C/T]AGGCACCCTAACTGAGCCAGTCTGTTTCTCAGTAC Y 2 1 2 1 101000 f 74 goat snp17550-scaffold1814-951158 11 22564262 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800091 Affx-122936561 AX-385287014 11 22524598 CCCCACCTCTGTAATTCTTGCTGACTAAAAGCCTC[A/C]AAACTAAGCAATGAATCTGTTTCTAAGGCAACGGT M 2 1 2 1 101000 f 74 goat snp17551-scaffold1814-1013491 11 22626650 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441374 Affx-122928861 AX-123311711 11 22556772 TCACATAAATAACTTCTGTCCTTGTTTTTCCTTTC[A/G]GAATGCTGTCTACTTTAATTAAATCCTAATTACCA R 2 1 2 1 201000 r 74 goat snp17552-scaffold1814-1045665 11 22658926 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787877 Affx-122921405 AX-385274899 11 22587302 AGAACCAATGTGCTTGACTTTGAAATATATGGCTC[A/G]TTAGAAGGCATGAAGAGATTAGTTTCTTGCTATTG R 2 1 2 1 101000 f 74 goat snp17553-scaffold1814-1076195 11 22689377 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445358 Affx-122926378 AX-123315695 11 22628699 TATATATGAGGTTATAGAACTTACAAAGTGATTTT[A/G]CCACCAACCATTTTGCCTGATGTATGCCACCATTT R 2 1 2 1 201000 f 74 goat snp17554-scaffold1814-1117592 11 22731501 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439597 Affx-122930063 AX-123309934 11 22706040 GCCATCATCGTAAGTTGTCTTTTATATTAAAAATG[C/T]AGAGGTCAAGAAAGAAGAGCCACAGCTCTGCTCAT Y 2 1 2 1 303000 f 74 goat snp17555-scaffold1814-1194933 11 22810100 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784232 Affx-122934518 AX-385271283 11 22734777 TATCCCTAGCTTTTGCTAAAGTGCCTAGAGTGAGT[A/G]CTTAATAAACTATTTTGGTTACTAAATATAGAATA R 2 1 2 1 101000 f 74 goat snp17556-scaffold1814-1223670 11 22838872 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792946 Affx-122963233 AX-385279924 11 22778616 AGGTTTTTAAATATATGTGCACTTATCCTCACCTC[A/G]CCTATGTATTCTTTTTGAGAACAGATATGGGGAAA R 2 1 2 1 101000 r 74 goat snp9705-scaffold135-7816 11 22882993 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420341 Affx-122944971 AX-123290688 11 22840818 CAGGAGAGTGGGAGCCACGGGCCTCTTGAAGCTCA[C/T]GTTCAAAAATGGCCCAGTGATCCATTTGTCATATT Y 2 1 2 1 101000 r 74 goat snp9706-scaffold135-70018 11 22945148 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778804 Affx-122951127 AX-385265913 11 22873201 GAGTAAATAAAAGATGTCTCTATTTCCCATTCTAA[C/T]GAGGAAAGTGATGGTATAAACAAAGTGTTTGTTGT Y 2 1 2 1 101000 r 74 goat snp9707-scaffold135-102401 11 22977421 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382639 Affx-122973685 AX-123252997 11 22910147 AGAGAGTAGATGAAAAGAGTTTTTCCAGTGAATAA[C/T]GTATATAGATGTGGAGCCTACAAGACCTTTCCCTC Y 2 1 2 1 201000 r 74 goat snp9708-scaffold135-139347 11 23014317 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391885 Affx-122966968 AX-123262242 11 22959800 GCTTGGAAAAGCATCCCCTTCCACTCTGGTGGGAA[C/T]GAGACCTTATTTTAACAGACATGTTTTCAGTTGGT Y 2 1 2 1 101000 r 74 goat snp9709-scaffold135-189000 11 23064704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446456 Affx-122925073 AX-123316792 11 22999416 GGTCTGTTAGTTAATAATTAAAGACAAAATAATAG[C/T]ACAATTTCAGGCATCACAGGACTGGTGAAGAACTC Y 2 1 2 1 201000 f 74 goat snp9710-scaffold135-228616 11 23107756 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276622 Affx-1111835436 AX-519550132 11 23012356 AGAAATGGATAAAGGAATAAAGATAAAGCAAAAAT[A/G]TTACCTAGGAAAAAATTCTCTGCATATGTTAGGCT R 2 1 2 1 101000 r 74 goat Random2.2K-1150 11 23012356 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38393561 Affx-122965403 AX-123263917 11 23047634 AAGGTGATGAAATATTACCACAAGCATTTCCTGAA[C/T]AGTATCTACGTGAAACATAGCTTCCTGTCTCTTTC Y 2 1 2 1 101000 r 74 goat snp9711-scaffold135-276834 11 23157027 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768260 Affx-122940370 AX-385255441 11 23079651 CAGATTTCTTGGTTAATGAAATTTATGCTCTAAAA[C/T]AGGAAGTGGGAAATTAGAAGAGTGATTTGTTTTGT Y 2 1 2 1 101000 r 74 goat snp9712-scaffold135-308851 11 23189745 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793555 Affx-122957684 AX-385280530 11 23135995 TGCTTATGTATAGTTCTCAAATCTGTAAACTTACT[A/C]TGAGCAAGCAATAAATAACACACTGCTAAAGAGGA M 2 1 2 1 101000 r 74 goat snp9713-scaffold135-365195 11 23242539 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779760 Affx-122958547 AX-385266860 11 23165274 ATGTTCATTGAAATCCATGCCATATAATCATGTCT[A/G]CTTCTTGTGGTTTTAGAAGCTATAAATTCTAGACC R 2 1 2 1 101000 f 74 goat snp9714-scaffold135-394474 11 23272153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772588 Affx-122958327 AX-385259737 11 23202334 TGAAAGGTTTAGTGGTGAAATAATGTGGCTAAATC[A/G]TATGAGGTCACCTTGAACATTCCAAATGAGTTGAT R 2 1 2 1 101000 r 74 goat snp9715-scaffold135-431534 11 23309804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407791 Affx-122954952 AX-123278142 11 23265245 TTTTTTATGTTCAGTTCTGACTGTTATCTCAACCA[A/G]CAGGCTTATATATCTACTTGGAGTTTTAATGACCT R 2 1 2 1 101000 r 74 goat snp9716-scaffold135-494445 11 23367387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401135 Affx-122959384 AX-123271488 11 23300215 TTTGGAATTTGTTTTAAAAAGTTATTGAATTATAA[C/T]ATGGAAAGATGGGGAAGATAGAAAAGAAGCTGGCT Y 2 1 2 1 103000 r 74 goat snp9717-scaffold135-529415 11 23402673 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803194 Affx-122937071 AX-385290053 11 23333805 ATCTTTGTGGGGATATGATGATCAGAATAACTTCC[A/G]TCATTTCGGAACACTGAAAAAAAAGACCTGGGCAA R 2 1 2 1 101000 r 74 goat snp9718-scaffold135-563005 11 23436207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778498 Affx-122963542 AX-385265612 11 23363110 AAGAGTATGCTGGGCAGAATTTACTGAGGAGGATA[C/T]ATCGTTGTGATGAAGGGATATTTGTCTGTTTAGTT Y 2 1 2 1 101000 f 74 goat snp9719-scaffold135-592310 11 23465610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395455 Affx-122963918 AX-123265810 11 23399922 ATATTGTGGCCATAACATACATTTAATCAATCACC[A/G]CATACCAAATTATCTGCTCCTTTAAATTCTGAGAA R 2 1 2 1 101000 f 74 goat snp9720-scaffold135-629122 11 23503579 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781937 Affx-122976783 AX-385269018 11 23446177 GAAGTAACATCCTCCAGAAATGTAATATGCTGTGT[A/G]CATAGATACTACATGGATTAGTCAACACAGCAGCT R 2 1 2 1 101000 f 74 goat snp9721-scaffold135-675377 11 23551324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378837 Affx-122976538 AX-123249196 11 23495196 TTGCATAGTCCTATCACTACTTCCTGAACAAACAA[C/T]TTTAGGATGGGGCTAAAACATCATATGCTTGTAAT Y 2 1 2 1 101000 f 74 goat snp9722-scaffold135-724396 11 23598233 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38402565 Affx-122958450 AX-123272918 11 23535801 AACACATGTTGTGTTTTGGTTTGGGGTTTGTTTTC[A/G]TTTGTTTTTCCTGTGACCAGTTTCCAAACCCCAGC R 2 1 2 1 103000 r 74 goat snp9723-scaffold135-765001 11 23638928 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410225 Affx-122952556 AX-123280575 11 23577932 GCTAGACAGATTTTAAAGGTGTTCTCAGACTTACC[A/G]TTGTTTCACAATGGGGCACAATTTCAAACTGACTT R 2 1 2 1 101000 f 74 goat snp9724-scaffold135-807132 11 23680638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780237 Affx-122948963 AX-385267332 11 23636212 GAAACACTTTTAACTCTTTTGCAAGTAGAAAAGCA[C/T]GAACAGAGTTTGGAGCATATTCTCACTTCCCAGGA Y 2 1 2 1 101000 r 74 goat snp9725-scaffold135-865412 11 23737550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441007 Affx-122928957 AX-123311344 11 23678795 CTTCCACCCATAGGTTTCAATTCTAGCAGTTAACC[A/G]TCTTATATCCTGTGATTTTTCAAGGGTCTCCTAAA R 2 1 2 1 101000 f 74 goat snp9726-scaffold135-907995 11 23778317 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440354 Affx-122929655 AX-123310691 11 23714112 ACAAGTTAAAGGCTAAGTGATATAATTTCAGAAAG[C/T]GTTCAATGCTGTGAAGAAAATAAAACACAGGATGT Y 2 1 2 1 201000 f 74 goat snp9727-scaffold135-943312 11 23814421 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413219 Affx-122950254 AX-123283568 11 23776235 TATAGATTATATTACTGATTTTTACTGATTCTGAC[A/C]TAAAAGGTGTTCAAAACCCTCACTAAAGCAAATTT M 2 1 2 1 101000 r 74 goat snp9728-scaffold135-1005435 11 23874374 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384995 Affx-122971884 AX-123255353 11 23814789 TTGACTATGTGCTAAATACTGTGTTCACTGTGTAT[A/G]CAAAGATAAAGGCAGTGATAGCCCCCAGGTAGCAT R 2 1 2 1 101000 r 74 goat snp9729-scaffold135-1043989 11 23916994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784471 Affx-122951285 AX-385271520 11 23844026 TTCCAGGAGCTAAATAGCAGTTTCTATTTCTAGTC[A/G]ACTACTGTCTTTATCAAATTACTTCTTTGACTCAG R 2 1 2 1 101000 f 74 goat snp9730-scaffold135-1073226 11 23945928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272659 Affx-1111832915 AX-519546367 11 23883402 AATGCATTCACCATTTACCTCATGGAAATGTAACA[A/G]CTCTATACGAAGTCACCACATTTTCCCATCTTATA R 2 1 2 1 101000 r 74 goat 11_23883402_AF-PAKI 11 23883402 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389605 Affx-122968764 AX-123259963 11 23896493 GGATCACTGAGAAATAAATCACTCTACAAATCCTT[A/G]TCTATTGCTCCTCAGAATGGTAGGGAAAGACTGCA R 2 1 2 1 101000 r 74 goat snp9731-scaffold135-1125693 11 24000106 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785104 Affx-122962777 AX-385272150 11 23932585 GGTTAAATTCAGAGAACAGCACTCTGTGTGTCCAG[C/T]TATGTGCTGAGTTCTAGGTTAATAGGAACATACCA Y 2 1 2 1 101000 f 74 goat snp9732-scaffold135-1161785 11 24036266 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396448 Affx-122962980 AX-123266803 11 23961741 TTCTGAGCCTCATACACCTGACCTAGGATGGATCC[A/G]CAGGATTTTGTTAATGCTAAGCATTTTCCTCTAAA R 2 1 2 1 101000 r 74 goat snp9733-scaffold135-1190941 11 24065368 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399447 Affx-122961212 AX-123269802 11 24002433 CACAGCAAGCTCATTCCAGAATTCACAGTAATGGC[A/G]TTGCTTTGCAGAATGGTTGAAAGATTTGCTCTGAA R 2 1 2 1 101000 r 74 goat snp9734-scaffold135-1231633 11 24106336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803310 Affx-122970565 AX-385290150 11 24035837 TATGACTGAGTTTAAAGAGAAGGTCTGCTAAGAGC[G/T]CCTCCTCTCATGTCAACAGATTAGGTTGGTAATTC K 2 1 2 1 101000 r 74 goat snp9735-scaffold135-1265037 11 24139371 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802814 Affx-122933289 AX-385289713 11 24065668 TTTGTTTATACATCTGTTCACCATTTTGAAGTTCA[C/T]GTTTTATCCCTTTATGTATCTTCAGTTCCTAAAAT Y 2 1 2 1 101000 r 74 goat snp9736-scaffold135-1294868 11 24169118 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389137 Affx-122968548 AX-123259495 11 24096212 AAGGGCTACTGGGTTTCCAGGTTGCAGCAACATTA[C/T]AGAATGAGATAACATAAACGTCCAATTCTGCTACA Y 2 1 2 1 101000 f 74 goat snp9737-scaffold135-1325412 11 24199344 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380159 Affx-122975970 AX-123250517 11 24133253 GCCTAGATTAGGATATAACAGGCCAGAGGCCTCGC[A/G]ATGGCCCTTTCCACAAGGCCTATCTTGCCACAGCT R 2 1 2 1 101000 f 74 goat snp9738-scaffold135-1362453 11 24236242 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427567 Affx-122939482 AX-123297910 11 24173437 AATACACGCACATGCACACATGTGCATACACAGGC[C/T]CTATCCTCATCAAAAGCCTTAGACTGTGTTTCCAG Y 2 1 2 1 201000 r 74 goat snp9739-scaffold135-1402637 11 24276625 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785282 Affx-122936981 AX-385272327 11 24233573 TGGCTTTTAGAATTCCACCTGGAATTATAGACTGA[C/T]AAGGATTCTCAATGTCAGACAAGTTAAATTAAGGC Y 2 1 2 1 101000 f 74 goat snp9740-scaffold135-1462773 11 24336730 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276477 Affx-1111835438 AX-519549989 11 24238856 GAGCGTATCTGTGTTATCCAGAACCCAAAGTCTCT[C/G]GACTGGTCAGTGCTGGTCTACCTGTGAGGACCCAT S 4 1 2 1 201000 f 74 goat Random2.2K-1152 11 24238856 C G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399234 Affx-122960586 AX-123269589 11 24267570 GAATGAATGTAAGTCTAGCAGGCAAGCAAGTCTGG[C/T]GGCCGATGCCATCTGGGGACGTTGGGCCTGAGTGC Y 2 1 2 1 101000 f 74 goat snp9741-scaffold135-1496770 11 24370629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393503 Affx-122965812 AX-123263859 11 24333394 TTACTGTAATAGAAATAAAAATGCATTGATTATGC[A/G]TTTACTGGGTGCCAGGGCTTTACTAAATGTTTTTC R 2 1 2 1 101000 r 74 goat snp9742-scaffold135-1562594 11 24434180 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802014 Affx-122952707 AX-385288918 11 24400752 CCTATGAAAGCCAGTGGTGGAATCAGATTTGTCTT[A/G]TGGACAGTAGTCTGTTGACCCCTGCAGAGTGATGT R 2 1 2 1 101000 f 74 goat snp9743-scaffold135-1629952 11 24502034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418160 Affx-122947093 AX-123288508 11 24449342 GTTATTTCATATATTTACGCTTTATTTATAGGGAA[C/T]AGTATTCTAGGAGTCAAGATTTATGATATCTAGGA Y 2 1 2 1 101000 f 74 goat snp9744-scaffold135-1678542 11 24550490 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445515 Affx-122925181 AX-123315852 11 24537745 TCAGGCAGGCCTCGTTTCAGGTGGATGGGCACACC[A/G]TCCGATTTCTAGAGAGAGAGAATTATCAAGGACAT R 2 1 2 1 101000 r 74 goat snp9745-scaffold135-1766945 11 24636736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275243 Affx-1111834677 AX-192648967 11 24540362 TAG[A/G]TAAGTAGGTAATAAGATTTTATGAGGTTATGATCA R 2 1 2 1 101000 r 74 goat GoatD01.045510 11 24540362 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320769128 Affx-122940901 AX-385256303 11 24588426 CAGCTACCTCCATTTATGCAGGTGACCTTTGTTTT[A/G]CTTAGCCTGATCTTCTGAGCATCCGGTCTCCTCTG R 2 1 2 1 101000 f 74 goat snp9746-scaffold135-1817626 11 24687515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440487 Affx-122929369 AX-123310824 11 24625228 TCAATCTCTTAGTCTCTATGGTATATGTATTAGAG[C/T]AGCAGTTTTCACTCTTCTGGTTCTTAACCCAGTTT Y 2 1 2 1 101000 r 74 goat snp9747-scaffold135-1854428 11 24724559 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382082 Affx-122974909 AX-123252440 11 24654390 TACTGGAAGGCAAACTGCCTGAAAAATCTGTTGTG[C/T]GTCTTATAAGTCGGATAAAACATTAAGAACATCAT Y 2 1 2 1 201000 r 74 goat snp9748-scaffold135-1883590 11 24753932 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770223 Affx-122965477 AX-385257389 11 24732456 GCAAAAGAGAGAAGCGTAAGTGTCCAGCAGTAAGA[G/T]ATTGAACTAAGTAATAAATCAACTTTGTTTATATT K 2 1 2 1 101000 f 74 goat snp9750-scaffold135-1961656 11 24832316 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430998 Affx-122936684 AX-123301339 11 24765847 GGGATTCAGTTATTGTGTTATAGACAGACTTTTGA[C/T]GCTTTTCTCCTGCTTTTTTGATCTCACCCCACTTT Y 2 1 2 1 201000 f 74 goat snp9751-scaffold135-1995047 11 24866073 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777684 Affx-122970452 AX-385264803 11 24832855 AATGACATACGTCAAGACTTTGTAAGTAGAAAATT[A/G]TGAATTAAGTAAAATGTTGGAGTGGGAATATTTTA R 2 1 2 1 101000 f 74 goat snp9752-scaffold135-2062055 11 24932684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392286 Affx-122967534 AX-123262643 11 24885758 GTAAAGTGCTTCGCATGGGGCCTGGGACAGTGTTT[A/G]TTATTGCTCTGTCATCATCCTCTGCCCGCTGCCCT R 2 1 2 1 201000 r 74 goat snp9753-scaffold135-2114958 11 24985449 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379243 Affx-122976265 AX-123249602 11 24952315 CTCATGGACTCCCCTAGAAGCCTGGCTGAAGCCTT[A/G]CTCTTCCCAAGGCTCTAGAGGGTCCCTCCCCAGCC R 2 1 2 1 201000 r 74 goat snp9754-scaffold135-2181515 11 25052232 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392027 Affx-122966475 AX-123262384 11 25016422 TTTTACTTCACTCTTTTGTGACAACAGTTTGCTGA[C/T]AGTATGACTGCTTCTCCTTTGCCTAAGTTATATTG Y 2 1 2 1 101000 r 74 goat snp9755-scaffold135-2245622 11 25114578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445421 Affx-122925371 AX-123315758 11 25053466 AGACATCCAGGGAGAGGCTAGGAAGGCCACTTGCA[A/G]TTCTCTCTCTGTGTACTGCTTTGTCCTAAAGAGCA R 2 1 2 1 101000 r 74 goat snp9756-scaffold135-2282666 11 25151507 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434797 Affx-122933873 AX-123305138 11 25102950 ACATGGGCTCCAGACAAGGGCAGCTTCCTCCTGCA[C/T]GTTTCACTTGATCTTAGCCAAAAGGCCGAGAACCG Y 2 1 2 1 101000 f 74 goat snp9757-scaffold135-2332150 11 25201241 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431666 Affx-122936801 AX-123302007 11 25159077 CACTTGTGGAATCCATCCAGCTGTGCACTGTTTAC[A/G]CTAATGTATATACATTTTACTAGGTGAGCAATCCA R 2 1 2 1 101000 r 74 goat snp9758-scaffold135-2388277 11 25257927 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403158 Affx-122958092 AX-123273511 11 25193380 TCCAGCTCCAGCTCCTCTGCCATCAAGCTGGAGGC[A/G]CATGAGCAGAGACAGTCTGTCTCTCTTCTGGGCTG R 2 1 2 1 202000 f 74 goat snp9759-scaffold135-2422580 11 25291574 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431531 Affx-122936222 AX-123301872 11 25230773 TGATTTGGGTCCCTCTGGGCCTCACCCTTCTCCCT[A/G]TAAAGTGGGACAACCACAGTGACCTCACAGGGTCA R 2 1 2 1 101000 r 74 goat snp9760-scaffold135-2459973 11 25329357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379270 Affx-122976245 AX-123249629 11 25279156 AGTTCAGGCAGTCTGAGGGAAGGGGTGGAGGGAAG[C/T]GAGAGGAAGACTCCAAGGAGGACCGCAGGTTCTGG Y 2 1 2 1 201000 r 74 goat snp9761-scaffold135-2508356 11 25377529 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427302 Affx-122940149 AX-123297645 11 25353818 GTATTTTACCTGCTGCCAAAAAGCTTCAAAACTGA[C/T]GGGAAGATAAAACAACTACTAAAATGGCAAAATGC Y 2 1 2 1 101000 f 74 goat snp9762-scaffold135-2583018 11 25451674 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396614 Affx-122962888 AX-123266969 11 25410284 TACAAACTGTCTCATCACCACAAAGGAAGAAGAGC[A/G]TTATTTCTGGTATCAGAAATAATAAAACAAAGTAA R 2 1 2 1 201000 r 74 goat snp9763-scaffold135-2639484 11 25508159 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427486 Affx-122940009 AX-123297829 11 25448673 ATCTGGGCCATTAGGCCCATGGGGCCATTGACGCT[C/T]AGCATGTAAAGAGATAAAGCCCTATGACCAAAGTG Y 2 1 2 1 101000 r 74 goat snp9764-scaffold135-2677873 11 25546479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787255 Affx-122952646 AX-385274281 11 25478192 ATATTGTAGGACTAGGAGTCCCGTAAGTACTTCAT[A/C]GATACACAGATCCGCTAAGACACAAAATGTCTCGT M 2 1 2 1 101000 f 74 goat snp9765-scaffold135-2707392 11 25576113 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450151 Affx-122922742 AX-123320486 11 25513240 AAGAAATCCTAATTGAGGAAGTGTGTTCCTACCAA[C/T]CTTTTCCCACAGTCATCTGTCCTTCTGGCTCCCTT Y 2 1 2 1 201000 r 74 goat snp9766-scaffold135-2742440 11 25611318 T C 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426804 Affx-122940532 AX-123297150 11 25572134 ATAGAAATAATCAGTATTAGCATACTACAATATTT[A/G]TTTTGTTCTTAGATTTCGTAACACCCTACAGGAAA R 2 1 2 1 102000 r 74 goat snp9767-scaffold135-2801334 11 25670102 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768171 Affx-122964524 AX-385255366 11 25603420 GAAGAACTGGATCCACTGCATTTCTTCCGTGGAAA[C/T]GATTTCTGTGCTTCGATTACTTTCACAAAGCAAGC Y 2 1 2 1 101000 f 74 goat snp9768-scaffold135-2832620 11 25701631 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377740 Affx-122977379 AX-123248099 11 25644004 AAATGAATTATAAATATTTGGCAAATAAGATATGC[A/G]TTGGAAAAATCAGCAGCAGTACTTCTTAAAATTAC R 2 1 2 1 101000 r 74 goat snp9769-scaffold135-2873204 11 25742373 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402333 Affx-122959069 AX-123272686 11 25718195 CTTGTATAAAAATAGCTTCAAAACACTTTTCATTT[A/G]TTGGGATTTACAGTGATAGTTAATCATACTTCTTC R 2 1 2 1 101000 r 74 goat snp9770-scaffold135-2947395 11 25816553 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417146 Affx-122947353 AX-123287494 11 25753162 CAACCAGGTGGATGGCCCTCCGAGGACACAGTGCT[A/G]CTGATTGTGTGCGAATCTATTTGACAGTAGCCAGG R 2 1 2 1 101000 r 74 goat snp9771-scaffold135-2982362 11 25851726 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433284 Affx-122935213 AX-123303625 11 25789964 TCATGCAGAATAATGAATGCAGATGCTTCTACTAA[C/T]GCATGTCATTCTCTCCTTTCCATTCCCATTGCCCT Y 2 1 2 1 202000 f 74 goat snp9772-scaffold135-3019164 11 25886432 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774505 Affx-122951741 AX-385261640 11 25832839 CTCTATCTATTACAGGGAAGAAAAGTCCATAGATT[A/G]CCAAAGGTCACAGCATTAACAAATGGCAGAGCTGG R 2 1 2 1 101000 r 74 goat snp9773-scaffold135-3062039 11 25929688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447121 Affx-122924467 AX-123317457 11 25875346 CAGAGGATCTGAAAAGTTAATGGGGAGAAGAACCC[C/T]GAAAAACTATGGCCTCACACACCAGGAGCTTCAGA Y 2 1 2 1 101000 f 74 goat snp9774-scaffold135-3104546 11 25972227 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799370 Affx-122957189 AX-385286300 11 25904422 GTCTGGACTTTTCATGTGTTACAGGGCCACATTCC[A/G]TATATCATTCCATACTACATGTTCCTTTTCAAATA R 2 1 2 1 101000 f 74 goat snp9775-scaffold135-3133622 11 26001683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421188 Affx-122944156 AX-123291535 11 25971108 AGTGTCAACTTCCACTACATCCCACCCCACAGAGA[C/T]ACATAGGATAAAAGTACAACCTCCCAATTTCTTCC Y 2 1 2 1 101000 r 74 goat snp9777-scaffold135-3200308 11 26068779 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411285 Affx-122952304 AX-123281635 11 26031435 AATCTGACCTTTTGTTCCAAGATGGCCTTTATAAC[C/T]TTATCCAGGATCTCAGGAGCCCACTTACGCTATTA Y 2 1 2 1 201000 f 74 goat snp9778-scaffold135-3260635 11 26128497 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791098 Affx-122961400 AX-385278093 11 26067778 GAGTTTTTTGTGTCCCTAGTTGATAAGCTCCTTGA[C/T]GGCAAGAATCAAATCTTTAAGGTTTTAGTTCTAAG Y 2 1 2 1 101000 r 74 goat snp9779-scaffold135-3296978 11 26165047 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771651 Affx-122928359 AX-385258809 11 26108030 TTGTTTGGACTAAAATGGTAGGTGATAACTAGTGG[C/T]AGCTAGTAAAATAGACCCCATTTTCTAACACCGCA Y 2 1 2 1 101000 r 74 goat snp9780-scaffold135-3337230 11 26205710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782792 Affx-122930249 AX-385269864 11 26183350 TAGGGCCAGGCTTGTATATGGAAAACATATCAAGG[C/T]ATTTGCATTCCCACTGCTCTAGTCCAGGCCCTTTA Y 2 1 2 1 201000 r 74 goat snp9782-scaffold135-3412550 11 26279861 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790389 Affx-122926520 AX-385277392 11 26222398 TTATTCTTTTCGATCACCCCAAAGTTTGAAACTTG[A/C]ACATTCAATATTGAATGAAACAAGTCTGAGGACAA M 2 1 2 1 202000 f 74 goat snp9783-scaffold135-3451598 11 26318842 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405520 Affx-122955990 AX-123275872 11 26277011 GATAAGGTTAAGTACCAATTCTGCCTACAGTGGCC[A/G]TGAAGTTGACACGCATGCTGTCACACTGGCCAGTG R 2 1 2 1 101000 f 74 goat snp9784-scaffold135-3506211 11 26373377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418771 Affx-122946193 AX-123289119 11 26309284 GCAGGAGTTGGTACTATAGAGTTCCCAAACATATA[G/T]ATAGTTATTGGTGAGTTAACAAGGTAGAGATATAA K 2 1 2 1 101000 f 74 goat snp9785-scaffold135-3538484 11 26405622 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796020 Affx-122957042 AX-385282972 11 26357592 TGGTTATTCATGTAGCCAATTTGGATACATTTTGA[C/T]GGGCCAGTTGGCACTTTCTAATGTTGTAGAAGTTA Y 2 1 2 1 101000 r 74 goat snp9786-scaffold135-3586792 11 26454426 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377914 Affx-122977233 AX-123248273 11 26392998 TGTCATACTTGCCCTTCCTTTTAAAAAAAGTAGTA[C/T]GTAGTGGACCAAACACACAGTCCTGCAACAGAGGG Y 2 1 2 1 101000 r 74 goat snp9787-scaffold135-3622198 11 26490111 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398415 Affx-122961628 AX-123268770 11 26439713 TTTTGTTCTAAATCTATTTTCTTTTTTGCTTATTT[A/G]CTATAATTACAGATAGAAGTTTGGAGTTTAGCATT R 2 1 2 1 101000 r 74 goat snp9788-scaffold135-3668913 11 26537108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410523 Affx-122952170 AX-123280873 11 26504831 GATATTTTTAATTTAGTACCCCTAAAAAGAAGGGT[A/C]TGAAAAATAATTTCAGTTTTTGTATTATGTTAAAT M 2 1 2 1 103000 f 74 goat snp9790-scaffold135-3734031 11 26603091 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438290 Affx-122931395 AX-123308628 11 26547648 GCTCTTCATGTCTGACATATTTTAATATTTCCTTC[A/G]TTGCGTAATGCTATGCTTTGTATGTAGAAGGAACT R 2 1 2 1 101000 r 74 goat snp9791-scaffold135-3776848 11 26645864 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768839 Affx-122936673 AX-385256016 11 26605266 CTGTTAATAGAAACAGAAGCCAAGGACATTCTCTA[C/T]TACAAGTTCACCTGGCAGTAGAGTAGTACTACAAG Y 2 1 2 1 201000 f 74 goat snp9792-scaffold135-3834466 11 26703887 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411398 Affx-122951852 AX-123281748 11 26645106 AGGGAAGGTTGATAATCCAAGATGGTAATGCAACC[G/T]ACTATGATTTATTCTTGGTTATTTGCATCTGTATT K 2 1 2 1 201000 r 74 goat snp9793-scaffold135-3874306 11 26744510 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386548 Affx-122970718 AX-123256906 11 26699935 AAGCGTCAGTGTTTCTAGAAAAGGTGATATTTGTT[A/G]CTTCCCATTCTCCCCAGGTGTGTGGGGTCTTTGAG R 2 1 2 1 101000 f 74 goat snp9794-scaffold135-3929135 11 26799205 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272663 Affx-1111832917 AX-519546371 11 26744160 GGACAATCCAGAGCTCAGGTGCCTCCAGCACCCAG[A/G]AGCTCTTTACTGTACTTCCTATGGCCCAGCATAAT R 2 1 2 1 102000 r 74 goat 11_26744160_AF-PAKI 11 26744160 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440297 Affx-122930220 AX-123310634 11 26779485 GGAGTCGGGCCAGGTCACATCAGGGGAGGCCCACC[A/G]TCCTTAGCCCACATTATTGGAAGACCTGCTTGTTA R 2 1 2 1 101000 r 74 goat snp9796-scaffold135-4008685 11 26878322 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408460 Affx-122954435 AX-123278811 11 26813963 CTATGCAGACCGCTCGGTAGACTTCCCATCTGAAC[A/G]TCTCCCTTGTCCAGAATTGTATCAGTGTTCTTTCC R 2 1 2 1 101000 r 74 goat snp9797-scaffold135-4043163 11 26912909 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274948 Affx-1111834509 AX-519548530 11 26851378 ACTAACAGGGAGGGGGCGGCCT[A/G]CCCCGTTCTGGACACGCTAATTACGAGGATTCGGT R 2 1 2 1 101000 r 74 goat GoatD01.038977 11 26851378 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38400510 Affx-122961273 AX-123270865 11 26868540 AGAGAACAGCACAGCCAAAGCCCAGGAAGGGTGCA[C/T]ATTCCAAAGAAGGTATTTGACAATCCATCTCTGCA Y 2 1 2 1 101000 r 74 goat snp9798-scaffold135-4097740 11 26967907 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379309 Affx-122976198 AX-123249668 11 26929893 TAATTATCTCCATAAAAGTGAGAAAACTTGGTTGG[A/C]TTATTAGCACCTTTATTAGCACTAGGGAATCATTA M 2 1 2 1 101000 r 74 goat snp9799-scaffold135-4159093 11 27029189 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383888 Affx-122973123 AX-123254246 11 26967708 CACCCACAAAAGGTGGCGTTCTGTTGCAGGATGTC[A/G]CTGCCCTGAGCTCACGCCTGGATCTGTGGTGTGTG R 2 1 2 1 101000 f 74 goat snp40585-scaffold52-11016 11 27066546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414697 Affx-122949282 AX-123285046 11 26998569 AGGTGCCCTTGCACTGCTGGCACTGGCCTGGGCAC[A/C]CAGCAGTGGCTTATTGTTGATTGATGTTATGGGGC M 2 1 2 1 101000 r 74 goat snp40586-scaffold52-41877 11 27095909 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452377 Affx-122920623 AX-123322710 11 27039635 AAAGAAATGACTCCTTGAGAAGGAGGCCTTGGAGG[A/G]TGGGAAGATCAGGATAGACCAGGACATAGAGAAAA R 2 1 2 1 201000 r 74 goat snp40587-scaffold52-82943 11 27137343 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776053 Affx-122934026 AX-385263183 11 27073924 CTGCTGATCGCATACACTACCGCTTATGTCTGATT[C/T]GAAATATGCAAGCAATTTGCCTCTTTAAGAATTTA Y 2 1 2 1 101000 f 74 goat snp40588-scaffold52-117232 11 27171628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399036 Affx-122960922 AX-123269391 11 27115157 TGAAGATGTCTTCTGGCTATGACAACAGTCACCCC[A/G]TTTCTTTGCCCTCACTCCTTCCAAGAGTTCCCCTC R 2 1 2 1 101000 r 74 goat snp40589-scaffold52-158465 11 27212985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782642 Affx-122978983 AX-385269715 11 27150661 AGGGTCCATGCTCTGATTCCCTAAATGACTTCTTC[A/G]TAATTCATGACTATAATATATACCGCAGGCACAAT R 2 1 2 1 201000 f 74 goat snp40590-scaffold52-193969 11 27248678 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398207 Affx-122962224 AX-123268562 11 27185381 AGTTGCTGAGAATCATAAACAAAATACACAGAGGC[A/G]CTGAGCCAGGTGCCTTTCACAGGTAAGGATACCAG R 2 1 2 1 101000 f 74 goat snp40591-scaffold52-228689 11 27283275 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276479 Affx-1111835439 AX-519549991 11 27216471 TTTAAAAATGAAAGCAACTCAGTGGATTACTCAAG[A/G]ATGATTTCTTTTATTTTTGTTGTCTTTGGGAGTAA R 2 1 2 1 101000 f 74 goat Random2.2K-1153 11 27216471 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38428797 Affx-122938401 AX-123299139 11 27221915 CAGTCATCTCTGAAGTCATTATGTGCTGAGGGGCA[C/T]GGGGAGTTGGAGACAGTCCTGTCGGACTGAGCCCT Y 2 1 2 1 101000 f 74 goat snp40592-scaffold52-265223 11 27319802 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437073 Affx-122933078 AX-123307411 11 27262642 CTGCTTGCAACTTGAGAGGTAAAATTAAGTTGTAA[C/T]ATTCCAGCAAATAGCTATTGCTACTCAGAATGCTA Y 2 1 2 1 101000 r 74 goat snp40593-scaffold52-305950 11 27360508 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396563 Affx-122962928 AX-123266918 11 27312327 TCTTTCATCCCCAGTACCTGGCACAGGGTCTCAAG[C/T]GAAGAACCCAACAAAGTCTTTTGAATGGAAGCTTT Y 2 1 2 1 201000 r 74 goat snp40594-scaffold52-355635 11 27406553 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406609 Affx-122955842 AX-123276961 11 27356506 ACATTCTCTTTGTAAATCTTCCTCCTCTGATAAAG[C/T]ATATGAAGAGTATGCTGGAGACTCCTTTACTGCCA Y 2 1 2 1 101000 r 74 goat snp40595-scaffold52-399814 11 27450947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379086 Affx-122976318 AX-123249445 11 27391091 GACTTAATGATAAACAGCATTTATCTACAAGAAAA[G/T]AGCTCCTGTCTCCCTCTCAGTATTCAACTTTATTT K 2 1 2 1 201000 f 74 goat snp40596-scaffold52-434399 11 27485973 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785304 Affx-122969711 AX-385272349 11 27423015 TAGACTTTTTTCAGAATGTAACTTATGGCAAGATA[C/T]ATTATTCCTTTATTATCCATCCAATAACAGAAGTC Y 2 1 2 1 201000 r 74 goat snp40597-scaffold52-466323 11 27518044 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426270 Affx-122940319 AX-123296616 11 27459649 GCAGAAGTAAGACATTCAAGAGCAGTGGGACAGAT[A/G]GCAGACTATGAGACTGAGGAGTACAGATGAGCTGG R 2 1 2 1 101000 f 74 goat snp40598-scaffold52-502957 11 27554673 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774415 Affx-122975659 AX-385261551 11 27559439 ATTAAAAATCCCTGAATTATATACTCAGAAATGGT[A/G]TAAAATAATATACAGTTAAAGCTTCAAACAGCTAA R 2 1 2 1 101000 f 74 goat snp40600-scaffold52-602747 11 27655109 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391990 Affx-122966504 AX-123262347 11 27599759 AATGTAATATTTAAAGAATCACACACACACATCTG[C/T]ATGTGCTTTAAAAAAGAAAAAAGCAAGAGAGGGTG Y 2 1 2 1 303000 r 74 goat snp40601-scaffold52-643067 11 27695444 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442587 Affx-122928493 AX-123312924 11 27643435 GGAGGGCTGGCTCTTTCTTAGCCCCAGGGAAGCCA[C/T]GTGGTGTGGATGACACTGTGGGATCAAGTATTTTG Y 2 1 2 1 101000 r 74 goat snp40602-scaffold52-686743 11 27739230 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379284 Affx-122976215 AX-123249643 11 27686611 GGTGGTTGGTCCAGGCTATTTGAGTTGTTGGTTTG[C/T]ATTTGACATTTTCCATTTCTTCCCTTGAGGTCTGG Y 2 1 2 1 201000 f 74 goat snp40603-scaffold52-729919 11 27784402 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429658 Affx-122937665 AX-123299999 11 27721214 TAGCAGTGTGGTATCTGAGCAAGTCATTTAGGTCA[C/T]GAACCTCAATTTCTTCATCTCTAAAATGGGCTGAC Y 2 1 2 1 201000 f 74 goat snp40604-scaffold52-764522 11 27819085 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777459 Affx-122966904 AX-385264579 11 27775385 ATTCATCCATAGCTTTGTGAACGAAAGAGTCAGAG[C/T]AACTTGATTTCAAGAAACAAGTGGTGAATTTTCTC Y 2 1 2 1 101000 f 74 goat snp40605-scaffold52-818693 11 27874032 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274045 Affx-1111833971 AX-519547649 11 27783772 AGTCAGTGCTCCAGGAAGCCCCATAAACAGCAGGC[A/G]TCCCATCTGCAGTTCAAAGGATGCACAGTCTATTA R 2 1 2 1 201000 r 74 goat GoatD01.012241 11 27783772 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38442860 Affx-122927675 AX-123313197 11 27805389 GCTTTAATAACCTGCAGAAGGTCAAAATGGATAGC[A/G]TCGGTGTTCTTTAGGTAGGAGAACAGGCACCAATT R 2 1 2 1 101000 f 74 goat snp40606-scaffold52-848697 11 27904039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422510 Affx-122943295 AX-123292856 11 27838459 TGAACTGCACCTGTGTGCTTCTCTCTTGTGCTAGC[A/G]CAGGGCTGGGCATACCGGAGCTCCTGGATATTTGA R 2 1 2 1 201000 f 74 goat snp40607-scaffold52-881767 11 27937326 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378148 Affx-122976976 AX-123248507 11 27884596 TTGAATGTTTTGGAAAGAGTCACTGAAGATAAATC[A/G]CTAATAAAATCTGTTGAATTATGCGTGGGAGGGAA R 2 1 2 1 101000 r 74 goat snp40608-scaffold52-927904 11 27983415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439856 Affx-122930449 AX-123310193 11 27943287 AGAGAAACCAATTAAATTCTACAGTCAGTGTTCTG[A/C]TCCCTGAAAGGAAATTTCAGTGTGATTTTTATTCA M 2 1 2 1 101000 f 74 goat snp40609-scaffold52-986595 11 28042052 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453137 Affx-122920001 AX-123323470 11 27972413 GAATTGCCCACTTAAATGAATTTGCCCCTTTTCAC[C/T]TCCCAGTCCACCCCTGGTTTCTGCTGGTCCCGCGT Y 2 1 2 1 101000 f 74 goat snp40610-scaffold52-1015721 11 28071334 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419455 Affx-122945490 AX-123289803 11 28007409 AATGGGCCAGACCAGTGAAGGCAAACAGTACCCAC[A/G]CTGTGCAGCACAAGCTGTGCAAAGCCATCCTTCCC R 2 1 2 1 101000 r 74 goat snp40611-scaffold52-1050717 11 28106613 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438897 Affx-122930445 AX-123309234 11 28050074 GGATTGAACATCTCATACCCCATGACTCCAAACCC[G/T]CTCTGAAATGGGACATCTCTCAGATGAAATTTGCT K 2 1 2 1 101000 r 74 goat snp40612-scaffold52-1093382 11 28149319 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406511 Affx-122955143 AX-123276863 11 28110917 GTGGTTCCACCTGGTCTTGGAACAGCCTTGGCTAC[A/G]TACTCTGTGTCAGGACTTTTCCCAGCTGTTTTCAT R 2 1 2 1 201000 r 74 goat snp40613-scaffold52-1154225 11 28209953 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784922 Affx-122937692 AX-385271969 11 28150787 TCTCCATAGGTTAGCTTGAGTCTCCTCTTAAGATG[A/C]TTTTCACTAAGCAAGTAATCCAGGATATCAAGGAA M 2 1 2 1 101000 f 74 goat snp40614-scaffold52-1194095 11 28250056 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401065 Affx-122959643 AX-123271418 11 28194645 GTTTGTGACTCACCCAAAATTTGCTTCCCTTTCCA[A/G]ATGGGGAATTTCTAGTAGGGAGGAAACAGATTCGT R 2 1 2 1 101000 f 74 goat snp40615-scaffold52-1237953 11 28294235 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792443 Affx-122974461 AX-385279424 11 28275133 TCCAAGACAAATGTCAGGTTTATGATTAATTCATT[A/G]GCAGTTGCATAGTGAAGACATTGCTCTTAATAAGA R 2 1 2 1 101000 f 74 goat snp40616-scaffold52-1318441 11 28374441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425114 Affx-122941224 AX-123295460 11 28340249 GTATGAGCTGAGGTAGAGAGTTGCAGTTTCCAACA[C/T]GGACACAGCAGCACCAGATAGAACAGCCTGCAGAG Y 2 1 2 1 101000 f 74 goat snp40617-scaffold52-1383557 11 28439155 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402886 Affx-122958220 AX-123273239 11 28374161 TCCAATTTGTTTTACCCACTCCTGCCCACTGTCCA[C/T]AGCTCACTCAGCTCACACAGTAAACCCTGAGGGTC Y 2 1 2 1 201000 r 74 goat snp40618-scaffold52-1417469 11 28473481 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417205 Affx-122947308 AX-123287553 11 28411038 CATCCTGGCACACACCCTGGGGGCATGTGTCCTTA[C/T]GTCAGACGCACCCAGCAAATCCTCTGAGCATTTAG Y 2 1 2 1 201000 r 74 goat snp40619-scaffold52-1454346 11 28511086 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425177 Affx-122941051 AX-123295523 11 28465808 AGCAAAAAAAAAAAAAGGCTAAGCAAATGAAGGGA[G/T]CCAATGCTTAAAATCCTCCCTCTCAAGTTCACCAT K 2 1 2 1 101000 r 74 goat snp40620-scaffold52-1509116 11 28565697 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441968 Affx-122928562 AX-123312305 11 28494637 ACACAGCTGTCATCCTGGGATTTTCCCTCATCATT[A/G]TTGGGATTCCCTTTGGCTCTATCTTATGTATTACA R 2 1 2 1 201000 r 74 goat snp40621-scaffold52-1537945 11 28594443 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274211 Affx-1111834070 AX-514635843 11 28511550 ACTCATACA[A/G]TCCTCTAAATGTAGCACACCCGAGCTGAAATGTCT R 2 1 2 1 101000 r 74 goat GoatD01.016980 11 28511550 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38441076 Affx-122928908 AX-123311413 11 28551049 CTTCTATTTCATTCTTTCAGTGATGTGTCAGGGTT[A/G]CTGATTTGGTAGAAAGGAAATAGCAAAATAGTTAA R 2 1 2 1 201000 r 74 goat snp40622-scaffold52-1594357 11 28651117 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430973 Affx-122936702 AX-123301314 11 28597816 GTCAACCCCTGCTAGCGGGGTGAGCAGAAGCTAAA[C/T]GTGGGTCTGGGAGAAGCAGGGAGAAGTGCTTGATA Y 2 1 2 1 102000 f 74 goat snp40623-scaffold52-1641124 11 28698172 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448341 Affx-122924131 AX-123318677 11 28632638 AAAAAACAACAAACCATTACTCAATTTTTCATTAA[A/G]TTGATTTTCTCCATGTATTTAAAAATAATTATGGT R 2 1 2 1 303000 f 74 goat snp40624-scaffold52-1675946 11 28733132 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453800 Affx-122919574 AX-123324133 11 28673582 ATTCCAAAAAAATATAGTTACTCTGACAAAGATAT[G/T]TAGAGTATTGTGAGTGTGGTGTGTTGGAGACAGGC K 2 1 2 1 201000 f 74 goat snp40625-scaffold52-1716890 11 28775082 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395045 Affx-122964203 AX-123265400 11 28702149 GCTTTTTGGTAGTGGCAAAGAGTCTGGATGAGTCA[A/G]AACTCTCCTTGGAAAGATGCAGAGCCTATGTTCAT R 2 1 2 1 101000 f 74 goat snp40626-scaffold52-1745457 11 28803649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403112 Affx-122958127 AX-123273465 11 28735841 AGACACCCAGGGAGACCATCTCAAGTCCCCAGAAG[C/T]GAGTTTCCTGAAGGTGCCCTCACAAACCTCCTGGG Y 2 1 2 1 201000 r 74 goat snp40627-scaffold52-1779149 11 28837322 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421078 Affx-122944236 AX-123291425 11 28775196 TTTTTTGGCCATTTCATACCACTTGAAGGATCTCC[A/G]TTCCCCAACCAGGGATTGAACCCAGTGAAAGCCCA R 2 1 2 1 201000 f 74 goat snp40628-scaffold52-1818504 11 28876595 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773230 Affx-122978203 AX-385260373 11 28818176 CAAAGCATGCATACATTGATTGGATAACTAACAAA[C/T]AGGCTTGGTTCCTTTGGAGGCCAATAGTATCAAGG Y 2 1 2 1 101000 r 74 goat snp40629-scaffold52-1861484 11 28919670 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772716 Affx-122975044 AX-318317104 11 28880832 TGTAGATTCCACCAAATAGGTATCACTTTTCTACC[A/G]TCTTAAAGGTGGAAGAAGTTGCATCATCATAAGCC R 2 1 2 1 101000 r 74 goat snp40630-scaffold52-1924140 11 28982422 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276481 Affx-1111835440 AX-519549994 11 28924439 CAGAAGCCCTGTTTAACAAGGTTGTTTACTTGCCC[A/G]ATATTAAAACTTCTGTGTGTTGTTGATTTATTTTT R 2 1 2 1 101000 f 74 goat Random2.2K-1154 11 28924439 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412543 Affx-122951335 AX-123282892 11 28924608 GCAGGGGGTAGCTGAGGGTGGTGCAATGCCAGGGA[A/G]ACGGTTGATGACCCTGACCTCACTAGAACTGGGTC R 2 1 2 1 101000 r 74 goat snp40631-scaffold52-1967916 11 29026245 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430527 Affx-122937206 AX-123300868 11 28959170 CCAGCTCTTTGTTCTTGAGTGACAGTGGTCACTTC[G/T]AGGTGTCAGTGAGGCTCTGATAGGGAACCCTGGGG K 2 1 2 1 101000 f 74 goat snp40632-scaffold52-2002478 11 29058893 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432533 Affx-122935554 AX-123302874 11 29009203 TGAAACAGAGATCACTCAAGAAGCTGGAAAGTCAC[C/T]CAAAAGCAAGAGTGTTCTCAAGACACCAGGCAAAC Y 2 1 2 1 201000 f 74 goat snp40633-scaffold52-2052511 11 29106693 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388396 Affx-122969299 AX-123258754 11 29083530 CTGCTCAGGATCACCTTAACATTTGTAGGCTCAGT[A/C]GAGAGTACAAATGGAGGCTTACATAGCAATATGTT M 2 1 2 1 101000 f 74 goat snp40634-scaffold52-2126838 11 29176193 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793016 Affx-122967355 AX-385279994 11 29132644 ATATTCAAAATATGAAGCTGCTTCACAGGTAGATT[A/G]TTGGTTGTTTAAAGATATTTGCTGCCACTCCTATA R 2 1 2 1 101000 r 74 goat snp40635-scaffold52-2175952 11 29225568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375904 Affx-122978483 AX-123246263 11 29164274 GAGGACGTGGAGTATTTGCCTGTCTAGGGCTCCTT[A/G]CATTTTGTTCATTGATCCCAGGGACCCTCTAGACA R 2 1 2 1 101000 r 74 goat snp40636-scaffold52-2207582 11 29257225 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413139 Affx-122950364 AX-123283488 11 29195523 CATAATGGAGACTACTGAAGAAATAGCTCAACAAA[C/T]GGTTAAAGTTAGAAGCTTATGTTCCTAACTTAGTA Y 2 1 2 1 101000 r 74 goat snp40637-scaffold52-2238831 11 29288224 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765373 Affx-122959910 AX-385252886 11 29244865 CAATGATGTAGAATTACATAGAGGCCAGCCCAACC[A/G]TGATCCTATTAATTCTACACACTAGAGTTTTTGTG R 2 1 2 1 101000 f 74 goat snp40638-scaffold52-2288173 11 29337187 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799938 Affx-122959678 AX-385286864 11 29289572 TTATTGTTTTACTGGTTTCACCAGAAAGCCTGATT[A/G]CTGTCAGCTAAGTAGGTGAGATAGCATAGTTGGTA R 2 1 2 1 101000 f 74 goat snp40639-scaffold52-2332880 11 29382363 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381041 Affx-122974636 AX-123251399 11 29367827 CCCACTCCCCTTCCCTTGACAGAGCTGCTGGTTGC[C/T]CTTATATTCTGCCCTAGAGTTTACCTATTTGGCCA Y 2 1 2 1 101000 r 74 goat snp40641-scaffold52-2411135 11 29460748 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389717 Affx-122968677 AX-123260075 11 29417536 TGTGCTATTGGTTTCCAAACATATCAAATGATTTT[A/C]TGATGGTGAAAAGATGCATTTACAAGTGGTATTGA M 2 1 2 1 101000 r 74 goat snp40642-scaffold52-2460844 11 29510456 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389852 Affx-122968159 AX-123260209 11 29471702 AAGATCTTTGCTCTAAGGATGAGCAAACATGTTCA[C/T]GGAGGGTGGGCATGAAATAGCTGCAGAACATACTC Y 2 1 2 1 101000 f 74 goat snp40643-scaffold52-2515010 11 29564635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434811 Affx-122934807 AX-123305152 11 29510240 CACTGATGTTTCAGTCTCATGTATTCTCCAGAGAC[A/G]CATAGATAGTCAGATTTTCTTCTTCCATTTACTGC R 2 1 2 1 101000 f 74 goat snp40644-scaffold52-2553548 11 29601896 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424022 Affx-122942089 AX-123294368 11 29541863 GCCCAGTTGGCTGTGGTCAGCGTGGTAGACACTGA[A/G]ACAAGAAAAGGAGGACAGTGGAAGGAAGAGCTGCT R 2 1 2 1 101000 r 74 goat snp40645-scaffold52-2585171 11 29634064 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388058 Affx-122969531 AX-123258416 11 29574043 GAGGAACTGTGTGATTAAGAGATCTGAAAGATGTG[C/T]TTGGGTCAGGATGAGTAGAGCTGGGGACACCTGGC Y 2 1 2 1 201000 f 74 goat snp40646-scaffold52-2617351 11 29666385 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382650 Affx-122973677 AX-123253008 11 29621801 TTCCATTGCCAGCATGTAACTTTTCTTTTTTAGGC[A/C]TGCATGGTAGAAAATGAATGTGAAGATCCCAGCCA M 2 1 2 1 101000 r 74 goat snp40647-scaffold52-2665109 11 29714485 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416822 Affx-122948124 AX-123287170 11 29671500 CCAACATTAGCCGAACAACAAGAAGGTGCAGCTAA[C/T]GCTTTATCAATATGCCAGGCACTGTGATCATCATT Y 2 1 2 1 201000 f 74 goat snp40648-scaffold52-2714808 11 29764141 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784750 Affx-122954579 AX-385271798 11 29754058 AGACAATTATAAGTTGAAGCAGTATTCCAGTTATC[A/G]TCATCCAAACAGTCTCAGTTGTCAAAATTAAGAAT R 2 1 2 1 101000 f 74 goat snp40649-scaffold52-2797366 11 29846548 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393005 Affx-122965652 AX-123263362 11 29814428 CTGCAGCGCCTCTGACAATCCCAGGAGGACACTTG[C/T]GGAAGCAAAAATGTCCTTTCAGTGCCCGGCCTTAG Y 2 1 2 1 101000 r 74 goat snp40650-scaffold52-2857736 11 29907465 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38383452 Affx-122973459 AX-123253810 11 29890895 CTGGCTGTTTGTCTCAGCTGTGATCACAAACTCAG[C/T]AAAGCAAAGTTGTGAGTTTTATTTTCCACCATTTT Y 2 1 2 1 101000 f 74 goat snp40652-scaffold52-2934203 11 29984683 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391200 Affx-122967416 AX-123261557 11 29930150 AAAAACAGTAGACATAAGAACCCCCAATTATAGAG[C/T]ACCTAGCATGCTGGATTTTATCTCCAGTCCTCCAA Y 2 1 2 1 101000 r 74 goat snp40653-scaffold52-2973458 11 30024101 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387979 Affx-122969593 AX-123258337 11 29982674 AGTAGAAAACAGACTGCATCTTGTTGCTATGGCAA[C/T]GCCCTACTTATATCACATTAAGCTGATTCATGTCT Y 2 1 2 1 101000 r 74 goat snp40654-scaffold52-3025982 11 30076479 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446552 Affx-122924848 AX-123316888 11 30020815 TTTAAATGTTGATCCCAATCTATTAAACTGATTTC[A/G]TTACTCATTAATGGGTGGCAACTTACAGTATAAAA R 2 1 2 1 101000 r 74 goat snp40655-scaffold52-3064123 11 30114600 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272665 Affx-1111832918 AX-519546372 11 30067677 CATCTTTGTATGTTAAGAAGTATAGGGTCTCTCAT[A/C]GAGTAGATGCTCACTATGTGTGGAATAAATAAGTA M 2 1 2 1 101000 r 74 goat 11_30067677_AF-PAKI 11 30067677 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320794538 Affx-122972194 AX-385281501 11 30088142 ATATCATTTTTTCAAACAGAATAGCTACTTTCTAT[C/T]TAGAGTTTGAAAGGAGAAGTTAGGGCAGAGCCAGT Y 2 1 2 1 101000 r 74 goat snp40657-scaffold52-3131450 11 30180686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797401 Affx-122967752 AX-385284340 11 30120823 AGAAGCAGTATTTTATATCATGATTGCTGGATATC[A/G]TGAACATCCAGAAAAGAAATTACTACAATTTAAAA R 2 1 2 1 101000 r 74 goat snp40658-scaffold52-3164131 11 30213500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451274 Affx-122921314 AX-123321607 11 30168729 AGGAGGAAAATGGGTTGAATGAGAATTGTGTACAG[C/T]GCTCTGTTAGCAGCAGCTTACTGCTTTCCACTATG Y 2 1 2 1 101000 f 74 goat snp40659-scaffold52-3212037 11 30262065 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785089 Affx-122944136 AX-385272136 11 30231020 GACGCACCCTTTGCATCCTCACACCTAATCTAGGA[C/T]TCATTCACTGTATTTGAACTAAATATTAAGGGCTT Y 2 1 2 1 101000 f 74 goat snp40660-scaffold52-3274328 11 30323862 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320788022 Affx-122976889 AX-385275043 11 30262440 ACTTTAGGTTAAGTAGAAGAGGTATATTAGCCAAT[A/G]TGGACAGCTTTCTAGTTTACTTAAATGGTAGTATT R 2 1 2 1 101000 f 74 goat snp40661-scaffold52-3305748 11 30355365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798092 Affx-122975288 AX-385285027 11 30295964 TTGGGAAATTCAAAGTAAAGTATGCCTTTGTTTCT[A/C]TTTAGTATTCTCTTTAGTTACTAAATGACAACTTG M 2 1 2 1 102000 f 74 goat snp40662-scaffold52-3339272 11 30389206 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393767 Affx-122965203 AX-123264122 11 30398488 TATGTAAAATAATTATACTTGAATTTACCATGTAT[G/T]CCATTTGATTATGATGAAGATAAAATCTAACTGTA K 2 1 2 1 101000 r 74 goat snp40664-scaffold52-3441796 11 30492282 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768871 Affx-122958289 AX-385256048 11 30488005 AAAGAGACACAAAAGTAAAGGAACCAACTTTGCCA[C/T]ATATTACCCCCAAGCATGTGGGTGATGTCAGTGTT Y 2 1 2 1 101000 r 74 goat snp40666-scaffold52-3531313 11 30582164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384974 Affx-122971900 AX-123255332 11 30552314 TCCCCAATAATCAGTTTCCTTTTTCCTATGTCTAC[A/G]CCCTTCCTTGTCCTAGCCATCTTTCTGGAATGTCT R 2 1 2 1 101000 r 74 goat snp40667-scaffold52-3595622 11 30646416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377431 Affx-122977543 AX-123247790 11 30587147 GTTCATGCTAACCAAGTGAAACTTGAGTGCGGTAC[A/G]TTGTTTCAATGGGAGATATTAAAACCTGTGTGAAA R 2 1 2 1 101000 f 74 goat snp40668-scaffold52-3630455 11 30681930 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424386 Affx-122941830 AX-123294732 11 30629213 GAAGAAAAATCAGAGAAGCATCAGTTGTACAGACT[A/G]TTCATAAGACATTGTGTATGCATGCTAAGTCGCTT R 2 1 2 1 201000 f 74 goat snp40669-scaffold52-3672521 11 30725280 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415884 Affx-122948482 AX-123286233 11 30680473 GACATAGATGGAAAGCACGACATTTATGTCAGCCT[C/T]CTCTGTTTCTAGGCTCTCACTGGTGCACCCCCAGT Y 2 1 2 1 101000 f 74 goat snp40670-scaffold52-3723781 11 30776833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428552 Affx-122938730 AX-123298894 11 30711750 TCCTGTCTCCCTGGCATCCTCTCTCCCTCTATCAG[A/G]CAAGCCCTTGTGAGCCCCATTCTCTAAGAGGAAAG R 2 1 2 1 101000 r 74 goat snp40671-scaffold52-3755058 11 30808043 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432249 Affx-122936351 AX-123302590 11 30754142 CTAAGGGCACCTTGGGCTGACAGATCTGCACTGCT[A/G]TGCTCCTGGATGGTCTGAAAACAAAAACAGAAGCC R 2 1 2 1 101000 r 74 goat snp40672-scaffold52-3797450 11 30850823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383211 Affx-122972777 AX-123253569 11 30787202 AACAGCAGTTGCTTCTCTTCTACTACCCAGACAGA[C/T]TCAAACCCAGGCCCACATTTTCATCAAGGACTTAC Y 2 1 2 1 201000 f 74 goat snp40673-scaffold52-3830510 11 30883986 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441264 Affx-122929485 AX-123311601 11 30830672 AGGAACTTCTAAGAATGAATCTCAGCTTGTGAAGT[A/G]TTCTTTCTGATCGCACAAAGTCATAAACAGGGAGA R 2 1 2 1 101000 r 74 goat snp40674-scaffold52-3873980 11 30927453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445831 Affx-122926019 AX-123316168 11 30888786 ATGTGATGAGGAAAGTGCTGGGGTGAATATGAAAA[C/T]GGGATTGTTGCAGAGAAGATGAGAGGAGAATGATA Y 2 1 2 1 101000 f 74 goat snp40675-scaffold52-3932094 11 30985627 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444256 Affx-122927214 AX-123314593 11 30931833 TTACATTCCACTTTACAGCATAGCCATGTTTACTA[C/T]AGAATTTGTCAAAATATCTTTAATAAACATTATAT Y 2 1 2 1 101000 f 74 goat snp40676-scaffold52-3975141 11 31028376 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419700 Affx-122945919 AX-123290048 11 30971906 TCTTTCCTCTTTCCTTCATCTGTTCGTATCCTATC[C/T]ATGCTTTGGGAGGGGACATGAAATTCTAATGATCT Y 2 1 2 1 101000 f 74 goat snp40677-scaffold52-4015214 11 31067896 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380743 Affx-122975133 AX-123251101 11 31008409 TCTTTTGTGTTTTGTTTTCTTTGGATAAGGGGAAG[C/T]ATGTTATGATCTTCATTTTTAGTTAGGTTTTAAAG Y 2 1 2 1 101000 f 74 goat snp40678-scaffold52-4051717 11 31104457 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383337 Affx-122972681 AX-123253695 11 31056394 GGATGACCATATTGACTTCTTGGGTTATGATGGGC[A/G]TAGTGGATGCCCTATGGAATGTGTTTAGTATAGTA R 2 1 2 1 101000 f 74 goat snp40679-scaffold52-4099702 11 31152379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397071 Affx-122962723 AX-123267426 11 31110121 TCCACACACTGTGTGAGATGTTTGAATACCTGACA[C/T]GTGTGACATGTTGAAATGCCACTTTTAAAGGGGGA Y 2 1 2 1 101000 f 74 goat snp40680-scaffold52-4153429 11 31207137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381538 Affx-122974840 AX-123251896 11 31140931 AACTAAGGCGTGAGTCACAGCCCCGCACAAAGCAC[G/T]CGGTCTTCTAATTCATGTTATCTCCTCCGACTTGC K 2 1 2 1 101000 r 74 goat snp40681-scaffold52-4184239 11 31238084 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427454 Affx-122940032 AX-123297797 11 31173821 CTATGAGGATCATAATAGCTTATATTATATTGTCA[A/G]TATCCATTTTCTTCAAGTATTGGATTCAAGTTAAT R 2 1 2 1 101000 f 74 goat snp40682-scaffold52-4217129 11 31270763 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454056 Affx-122919394 AX-123324389 11 31204068 TACTTTGGTAGGTATTTTATTACTGAACTCTTAAT[A/G]TACACATATTCATGTAAGTCCTTCAGAGATTTATT R 2 1 2 1 101000 f 74 goat snp40683-scaffold52-4247376 11 31301345 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399984 Affx-122960818 AX-123270339 11 31257720 ATGTATAAATCTCAAAATGTAAAGAAAATAGGAAA[C/T]ATAGCCCTCCTTTGGTATACTTATAATATAAATGC Y 2 1 2 1 101000 r 74 goat snp40684-scaffold52-4301028 11 31354844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769175 Affx-122944619 AX-385256350 11 31288011 AGCCCTGCATCAAGGTCAACATGGAGTGAAACATT[A/C]TTTAATTTCACTGGTAACCTCTCGAGGTCTGACCA M 2 1 2 1 101000 f 74 goat snp40685-scaffold52-4331319 11 31384894 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406342 Affx-122955440 AX-123276694 11 31351467 TTCAAGGGTGGCTAAATCATATGATTGCAAGGGAC[A/G]TTCTGCAGAATGGCCAACTATTTGGCAATAAATTC R 2 1 2 1 101000 f 74 goat snp40686-scaffold52-4394775 11 31450153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784771 Affx-122958377 AX-385271818 11 31411967 AAACCTGCTTTACATAGATAACAATGGAGTAATAA[G/T]CAATCATAAACTTCAAAGGTCATAATAAATTGTTG K 2 1 2 1 201000 r 74 goat snp40687-scaffold52-4455275 11 31510859 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774937 Affx-122938679 AX-385262070 11 31448759 AAATTTGGAAGGACAGAGTGGCAATTAATTAAGAT[A/G]ACTTTAGTTTCCATCTAGAGAAAATAAAAGAGTAA R 2 1 2 1 101000 f 74 goat snp40688-scaffold52-4492067 11 31547653 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426573 Affx-122940161 AX-123296919 11 31479911 ACTCTTCCTTTCTCCCTTTAAAAGACTGAGATTTT[A/G]CATGTCAAATTTCAGCCCAGAGAGATGTTTTTTTC R 2 1 2 1 101000 f 74 goat snp40689-scaffold52-4523219 11 31578847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428053 Affx-122939125 AX-123298396 11 31515426 TTTAAATCAAATCACTTTTTAACTTAAACTTTTCC[A/G]TAAATTTGTATCACTCTCATCAATGCAATTCCAGT R 2 1 2 1 101000 r 74 goat snp40690-scaffold52-4558734 11 31615079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797692 Affx-122952948 AX-385284631 11 31580108 ACAGAAAACTGGAGATTCATAGTCCTGTTTTTATG[A/C]TATTTAATAAGGGATAGTCCCTGAGATCATCTAGC M 2 1 2 1 201000 f 74 goat snp40692-scaffold52-4623416 11 31680758 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393383 Affx-122965905 AX-123263739 11 31611627 CCCTAATTGAAAATGAGTATGACTGACCTAGTTCA[C/T]GCACAAGTTGCTTACCATGCAGCTTCCAAATGGAC Y 2 1 2 1 101000 r 74 goat snp40693-scaffold52-4654935 11 31712839 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426747 Affx-122939864 AX-123297093 11 31671058 AGGTGGCTCCTTCTCTTTACTTCCAAATCCAGCAC[A/G]TCAGAACAAGGCAGTTTCCTAATACAGTCTATAAT R 2 1 2 1 201000 r 74 goat snp40694-scaffold52-4714366 11 31770550 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770714 Affx-122976033 AX-385257878 11 31701883 TGAGGCTAATAATAGATGTTTCTTAAGATTTTTAT[C/T]ATCACCTTAGTCACAAAGTGTCATTGATTTCTGGT Y 2 1 2 1 101000 r 74 goat snp4263-scaffold1133-11854 11 31801444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421124 Affx-122944202 AX-123291471 11 31735582 AGGAGGTAAGAATGTTCTGAGTGAGCACAGTTGTC[A/G]CCCTGGGATTAGAGAAAAGTGGGTCTCCTCTAGAA R 2 1 2 1 101000 f 74 goat snp4264-scaffold1133-45553 11 31835407 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777786 Affx-122929626 AX-385264904 11 31772128 TAAAAAATGGAACTTGAGCTATATATTTCAGATCC[A/G]GAGGAGTAGATAAAGGTCATAAAACTCCATTATGC R 2 1 2 1 101000 r 74 goat snp4265-scaffold1133-82099 11 31869585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443266 Affx-122927489 AX-123313603 11 31812361 GAATACCAGAAAGGGAGTCAGAGTTTCTTGACACA[C/T]GGTAATAAATATTTTCACTTATAATGAATAATTTA Y 2 1 2 1 101000 f 74 goat snp4266-scaffold1133-122332 11 31910282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405993 Affx-122955516 AX-123276345 11 31851772 GTACCAACACATTCCTAAATAACAGAAGAAGAAAA[C/T]AGTTCTAGAAGATATTCTACAGAGTCTAGAAGCAT Y 2 1 2 1 101000 r 74 goat snp4267-scaffold1133-161743 11 31949661 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789038 Affx-122951586 AX-385276051 11 31886108 AATCATACATTTTTACTGGACTCCTATTATAATCA[C/T]CTTGACAGAAAAGCTGAGTTCTTTCCAATCTGACA Y 2 1 2 1 101000 r 74 goat snp4268-scaffold1133-196079 11 31984230 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766518 Affx-122973945 AX-385253880 11 31924977 CCTGGGAGTCAAAAAAGTCATGGGACTACTAATCT[C/T]TTTTAAGAATTTCTTGGGCATTCTGAGGAGAAACA Y 2 1 2 1 101000 f 74 goat snp4269-scaffold1133-234948 11 32023093 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431789 Affx-122936128 AX-123302130 11 31954000 CTCTCTGCCTCTTGTCTTTCTTTCTGGGCCCTACA[C/T]ACTACAGGGCTCACTGAGTACCATTCAGTAATAAT Y 2 1 2 1 101000 r 74 goat snp4270-scaffold1133-263971 11 32052063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380578 Affx-122975269 AX-123250936 11 32008629 TTTACAATGTTATTACTGACATCATTAATAGAATT[A/C]TAGGTAGGAATCATGAAGGAGGGACCTAGGGAGAC M 2 1 2 1 101000 f 74 goat snp4271-scaffold1133-318600 11 32106529 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770369 Affx-122968200 AX-385257535 11 32062381 TCAACCATATACTGGGGACTGAAGATCAACTCATG[C/T]ATAATTAAGATCATTCTTATTCCATATCCTATGAA Y 2 1 2 1 101000 f 74 goat snp4272-scaffold1133-372352 11 32159969 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398148 Affx-122961682 AX-123268503 11 32105003 AGATGGGGGGTGTAAATCTGAGAATAAGCAGTCTA[C/T]ACTTGCTAGCTATAATGCAGAGCAGAATTCCAGGA Y 2 1 2 1 101000 f 74 goat snp4273-scaffold1133-414974 11 32203340 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394083 Affx-122964961 AX-123264438 11 32153274 TAATCTAGACATCATGGAACCAATAGAAACAGACT[C/T]GTAAATTACTGAACTACGGAATTTCATTGAGCTTG Y 2 1 2 1 101000 r 74 goat snp4274-scaffold1133-463245 11 32251440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774188 Affx-122933350 AX-385261325 11 32292255 CTCTCAGTTCTATATGTAAGTTGCCTTAGCCTGAG[C/T]GCTGATGTTATACTGATTGTCCTTAAAAGTCACTT Y 2 1 2 1 101000 f 74 goat snp4276-scaffold1133-602226 11 32390663 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785565 Affx-122949913 AX-385272609 11 32328108 AACTGGAGACTTAAAAGCTGATAAATCCTGCTAAG[C/T]GAAGACTGTCCTACTCTGGATGAACTTGATCTGTG Y 2 1 2 1 101000 r 74 goat snp4277-scaffold1133-638079 11 32426576 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428993 Affx-122938851 AX-123299335 11 32358717 AGCACATGCAGGCGTTTTGTTCTTCACAGCATCCA[C/T]GGCAGCTTTAAGAGCTCATCCTCTGTCGTCCCCTT Y 2 1 2 1 101000 f 74 goat snp4278-scaffold1133-668688 11 32457125 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428366 Affx-122938972 AX-123298709 11 32388554 CCACCACTGCTGGCTGCCTGAGTCATGGCTCCTGG[C/T]AACAGCACTTATACCTGTAAATGACAGGAGGATGT Y 2 1 2 1 101000 r 74 goat snp4279-scaffold1133-698525 11 32485664 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386209 Affx-122970991 AX-123256567 11 32420749 TCATATTCATAAAAGAAGACCTGTTACCCCGTTAT[A/G]CTGTGTAAACTGCTTTTAGGAAGTAACATAATTCC R 2 1 2 1 201000 r 74 goat snp4280-scaffold1133-730720 11 32518066 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444452 Affx-122926549 AX-123314789 11 32455378 AATAATAAGTTCCTTGTGATCAGCAGTCATAGTCT[C/T]ACCCAGAATTTGTTTCTGTATTGCCATCTAGCAAA Y 2 1 2 1 101000 r 74 goat snp4281-scaffold1133-765349 11 32553205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413335 Affx-122950168 AX-123283684 11 32556541 ATAGAGGAACCTCAGTTTATAAACAGAGAAACAAA[C/T]GCAAATAGTGATTTCACAGAAAAGCATACTGGCTG Y 2 1 2 1 101000 r 74 goat snp4284-scaffold1133-866512 11 32654433 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272667 Affx-1111832919 AX-519546374 11 32567928 CACCATCAGGGTCTTTTCCAATGAGTTCTTTGCAT[A/G]AGGTGGCCATTGTATTGGCACTTCAGTTTCAGCAT R 2 1 2 1 202000 r 74 goat 11_32567928_AF-PAKI 11 32567928 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438462 Affx-122931241 AX-123308800 11 32640694 AAGAATTTCTTCCCTGGCATTTAGAGTTTACTTGG[C/T]ATATTCCTGATTGTTGGGACAGGAGTGGGGAGGAC Y 2 1 2 1 101000 f 74 goat snp4286-scaffold1133-950665 11 32739468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440456 Affx-122929393 AX-123310793 11 32682860 TCGGGGGGACAGTGGGTTGCATGGTCTTCTTTTCC[A/G]GCATTTAATCATTATCTCTTCCAGGTTACAGTTGG R 2 1 2 1 201000 r 74 goat snp4287-scaffold1133-992831 11 32781784 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405086 Affx-122956994 AX-123275438 11 32728208 GAGAAATATGACTTAATACTTAGTGTTCCAAATGG[C/T]ACTGCTCTTATAAGCAGTAAGTATGACCTTCTGGC Y 2 1 2 1 101000 f 74 goat snp4288-scaffold1133-1038179 11 32827284 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420516 Affx-122944842 AX-123290863 11 32766783 TAAAGGTCATTTTCTTGCTGTGTCCACAGCTATCA[C/T]TGCAACAGATGCTAAAGTTTTCAAGCTCTTTACCT Y 2 1 2 1 201000 r 74 goat snp4289-scaffold1133-1076754 11 32865286 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430026 Affx-122937581 AX-123300367 11 32830760 TCCACGAAGCTTCATTTACTCTCTAATAATTACCA[C/T]TCTCATAATTTTCACATAATTTCTACCTCTCCAAA Y 2 1 2 1 101000 f 74 goat snp4290-scaffold1133-1140731 11 32929858 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762869 Affx-986697398 AX-385250889 11 32832720 ACAATATCCCATGCAGGGGGCAGGGTGTGTTCCTA[C/G]GTGGGACTCAACACCAGATCTGAGTTAGAACTCTG S 4 1 2 1 600010 f 74 goat 11_32832720 11 32832720 Ancestral_priority_1043 ancestry 0.486 neutral IMAGE 10K 10K ancestral 320765429 Affx-986697400 AX-385252933 11 32832723 ATATCCCATGCAGGGGGCAGGGTGTGTTCCTAGGT[A/G]GGACTCAACACCAGATCTGAGTTAGAACTCTGGGA R 2 1 2 1 600010 r 74 goat 11_32832723 11 32832723 Ancestral_priority_1043 ancestry 0.61 recommended IMAGE 10K 10K ancestral 320803177 Affx-986696209 AX-385290039 11 32832763 TCAACACCAGATCTGAGTTAGAACTCTGGGATCTA[C/T]CTTTGTAATAAGGAGCCCTATTGATGCTGAGGCAG Y 2 1 2 1 600010 f 74 goat 11_32832763 11 32832763 Ancestral_priority_1043 ancestry 0.68 recommended IMAGE 10K 10K ancestral 38452483 Affx-122920991 AX-123322816 11 32866158 TAATCAGCTCTCTCGTAGTATCAAAGCAGTTACAA[C/T]AAATAAACAAATGTGCATGACTGTATTTAAAAAAA Y 2 1 2 1 101000 f 74 goat snp4291-scaffold1133-1176129 11 32965139 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453497 Affx-122919824 AX-123323830 11 32933485 ATTTAGAATAAAATTTGAAGTTAATGTCGTGGTCT[A/G]TCAAATTCTATGTAATCTGGACTTCAGTTATCACA R 2 1 2 1 101000 r 74 goat snp4292-scaffold1133-1243456 11 33032979 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792204 Affx-122926744 AX-385279189 11 32967456 TCCGAGGTGTGTGGCTTAATTATAGTTTGAGTCCT[A/G]TGGACATTTAAATTTCTAACCCTATTATATTCCTA R 2 1 2 1 101000 f 74 goat snp4293-scaffold1133-1277427 11 33066905 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803068 Affx-122929343 AX-385289939 11 33003969 TACAAATAAAAAGGAAGCATTATATATTGATTAAA[G/T]AATTAACTTCTCCAGAAAACGAAACAATTATAAGC K 2 1 2 1 101000 r 74 goat snp4294-scaffold1133-1313940 11 33104453 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785407 Affx-122961952 AX-385272452 11 33059417 AGTCACTCTTTATGGAGGAGTTAGGGAAAGATTCA[C/T]GAGGAATCTGAACTTAAATGGCGATATGAAAGATT Y 2 1 2 1 101000 f 74 goat snp4295-scaffold1133-1369388 11 33160254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409820 Affx-122952951 AX-123280171 11 33096830 ATGCAGGAGATTTTCAGGCAGAGGAAATACTTAGA[C/T]AGGGCCTGACATTGTCATGGAAGGTAGAGTAATAT Y 2 1 2 1 102000 f 74 goat snp4296-scaffold1133-1406801 11 33200573 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401315 Affx-122959844 AX-123271668 11 33145390 CTAGTAGGAAAAAAGGCAAAACAGTAATCGTGATT[A/G]CTTTAGAGGTGAGATTATGGGTGTTTTTCTGATAT R 2 1 2 1 101000 r 74 goat snp4297-scaffold1133-1455361 11 33250423 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427525 Affx-122939516 AX-123297868 11 33174175 ATAAACACAAAGCTGGAGCACATATAGGGACATCA[A/G]TAATAGGAGTCATAGGTTATTTTTCACAGTATTTG R 2 1 2 1 101000 f 74 goat snp4298-scaffold1133-1484146 11 33279330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392378 Affx-122966233 AX-123262735 11 33223448 TAATTCACTCTATATATCTCACATGACTTTCCTTT[C/T]GTCTCACTATGTGTAGGTAGCTATCCATCTTTGTC Y 2 1 2 1 101000 r 74 goat snp28685-scaffold309-2295810 11 33334485 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781189 Affx-122926784 AX-385268274 11 33284685 TAGAGAAAGGAATGAAAAAAGATGGGTTATTATGC[A/C]ATTATATAAAATCACATTCATGAAACTTTTGAAAC M 2 1 2 1 101000 f 74 goat snp28684-scaffold309-2234573 11 33395958 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791727 Affx-122954468 AX-385278718 11 33334549 TACCTTCTAATCATTTTAAGGTAGATTATGAAAAG[C/T]TGTTCCAAAGATCATTTGTAATGGGCAGCTGGTAC Y 2 1 2 1 101000 r 74 goat snp28683-scaffold309-2184709 11 33447956 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433499 Affx-122935026 AX-123303840 11 33387602 TATGACCTGTCCATCTTGATTGTCCCTGTATGGCA[C/T]GGCTTAAGCTTCCTTGAGTTATACAATCTCCTTGC Y 2 1 2 1 101000 f 74 goat snp28682-scaffold309-2131656 11 33501500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791002 Affx-122940927 AX-385277999 11 33436996 TAAGAGCCCTGTCCTGCAAAATAAAACTAGAACTG[C/T]GGCCTATTCTCAAAGGTAAAGACAATCAACCTAGG Y 2 1 2 1 101000 f 74 goat snp28681-scaffold309-2082262 11 33550529 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781149 Affx-122938351 AX-385268234 11 33477008 AGACACCATAAGGCTATACAATTGCAGATGTACAA[G/T]GTCTTAGGCCACAGCTATATTGCAGCAAATTTCAG K 2 1 2 1 101000 f 74 goat snp28680-scaffold309-2042250 11 33589295 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409437 Affx-122954095 AX-123279788 11 33531593 TGGATGCCAAGGCAGATATCACATCCAATGGAGTC[A/G]TATAACTACACCCTTAAGTACTGGTGACTTTGAAG R 2 1 2 1 201000 r 74 goat snp28679-scaffold309-1987665 11 33645244 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772883 Affx-122959924 AX-385260028 11 33622628 TTTAAGTTCTTAAGTGAGTCATTTGTTTTGTGTAA[A/G]TACTGGCTTTGCACTGCTTTTATGGGAAACTTTAA R 2 1 2 1 101000 r 74 goat snp28677-scaffold309-1896630 11 33736061 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797907 Affx-122947257 AX-385284845 11 33661705 TAAATATCTTTAACTGTTATTTATTATCCCACATA[C/T]AAAATCTCAACTTTTACCATTACTGACAGGGACTT Y 2 1 2 1 101000 r 74 goat snp28676-scaffold309-1857553 11 33775384 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476276 Affx-1251763783 AX-586011695 11 33665041 TTAGGCTTTTATGTATGATTTATTAATATGTCATG[-/TATAATTTTTCTATCTAGTAGTCTCTTATGATCCTTTGTAAAAATTAAAAAAAAAAATAAATAAAAAATAAAAAAAAATA]ATAATTTTTCTATCTATATGAAATTAGTTCATAGT - 8 1 4 1 20000 f 74 goat SV_218 11 33665041 - deletion junction SV-TF-chip 539476529 Affx-1251763783 AX-586011920 11 33665041 TTAGGCTTTTATGTATGATTTATTAATATGTCATG[-/TATAATTTTTCTATCTAGTAGTCTCTTATGATCCTTTGTAAAAATTAAAAAAAAAAATAAATAAAAAATAAAAAAAAATA]ATAATTTTTCTATCTATATGAAATTAGTTCATAGT - 4 1 4 1 20000 r 74 goat SV_218 11 33665041 - deletion junction SV-TF-chip 562166030 Affx-1251763783 AX-606941439 11 33665041 TTAGGCTTTTATGTATGATTTATTAATATGTCATG[-/TATAATTTTTCTATCTAGTAGTCTCTTATGATCCTTTGTAAAAATTAAAAAAAAAAATAAATAAAAAATAAAAAAAAATA]ATAATTTTTCTATCTATATGAAATTAGTTCATAGT - 8 1 4 1 20100 r 74 goat SV_218 11 33665041 - deletion junction SV-TF-chip 562166098 Affx-1251763783 AX-606941507 11 33665041 TTAGGCTTTTATGTATGATTTATTAATATGTCATG[-/TATAATTTTTCTATCTAGTAGTCTCTTATGATCCTTTGTAAAAATTAAAAAAAAAAATAAATAAAAAATAAAAAAAAATA]ATAATTTTTCTATCTATATGAAATTAGTTCATAGT - 8 1 4 1 20100 f 74 goat SV_218 11 33665041 - deletion junction SV-TF-chip 562166136 Affx-1251763783 AX-606941544 11 33665041 TTAGGCTTTTATGTATGATTTATTAATATGTCATG[-/TATAATTTTTCTATCTAGTAGTCTCTTATGATCCTTTGTAAAAATTAAAAAAAAAAATAAATAAAAAATAAAAAAAAATA]ATAATTTTTCTATCTATATGAAATTAGTTCATAGT - 8 1 4 1 20100 f 74 goat SV_218 11 33665041 - deletion junction SV-TF-chip 562166288 Affx-1251763783 AX-606941696 11 33665041 TTAGGCTTTTATGTATGATTTATTAATATGTCATG[-/TATAATTTTTCTATCTAGTAGTCTCTTATGATCCTTTGTAAAAATTAAAAAAAAAAATAAATAAAAAATAAAAAAAAATA]ATAATTTTTCTATCTATATGAAATTAGTTCATAGT - 8 1 4 1 20100 r 74 goat SV_218 11 33665041 - deletion junction SV-TF-chip 320779170 Affx-122932760 AX-385266274 11 33692852 TACAGCCTTTATCCAACAATAAGGTTCATAAATCA[C/T]AAGCCAGATACAACACCAAGGCCTATTTCAACACC Y 2 1 2 1 101000 r 74 goat snp28675-scaffold309-1826406 11 33807067 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431187 Affx-122937176 AX-123301528 11 33725420 AATGTATAAACATAGAGTCAAAGTAATATTAATAA[C/T]AAGAATAGCAACAATGATATTTAAAGCACATACGC Y 2 1 2 1 201000 f 74 goat snp28674-scaffold309-1793838 11 33839528 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775769 Affx-122940900 AX-385262900 11 33801512 TACTATGTTGTACCAATAGTCGACAATAGCAGGCT[A/G]TACTCTTAAAATGTTTGAGTCTAGCTTTCATGTTG R 2 1 2 1 101000 f 74 goat snp28673-scaffold309-1717746 11 33916469 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793184 Affx-122951159 AX-385280162 11 33879043 TAATACATAACAATGATCAGTCAATTCTATAGAAA[G/T]CTCCCTTCTAGATTTAATACTGAATTACCAACCTA K 2 1 2 1 201000 r 74 goat snp28671-scaffold309-1640215 11 33994548 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414119 Affx-122949716 AX-123284468 11 33927255 ATACCAGCAAATCTGTTTTTAGTTTAAGTACCTGG[C/T]ATACCTCTACTGTATTTTTTCTTTCTTCATTTGAC Y 2 1 2 1 101000 f 74 goat snp28670-scaffold309-1592003 11 34044100 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400573 Affx-122960413 AX-123270928 11 33992580 TTTTATTGAGTCTTTTCTTTATATTTTTCTTTTCC[A/G]TTCAAGTGCTATTTGTATACATATTACAGTGTGAG R 2 1 2 1 101000 r 74 goat snp28669-scaffold309-1526678 11 34109801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794310 Affx-122957402 AX-385281274 11 34030447 ATAAAAACTTATAGTACCATTTTTATGGGAAGTGA[A/G]TTCAACTCACCTTTGAAGCTGAATCCAGTACATTT R 2 1 2 1 202000 r 74 goat snp28668-scaffold309-1488811 11 34147530 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439692 Affx-122930574 AX-123310029 11 34086991 ACAATCTAGAATGATTTAGGGACTGAAATAACACA[C/T]GATTTCTTGAAGACAATGAAAAGGCAGGAAAATGA Y 2 1 2 1 101000 f 74 goat snp28667-scaffold309-1432267 11 34205296 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772050 Affx-122976268 AX-385259205 11 34118845 CTCACTGAGATAACTACTCCATTAAGGAAAATCTG[A/C]TTTTTATGATATCTCCCAAAGATGTTATATATTAG M 2 1 2 1 101000 f 74 goat snp28666-scaffold309-1400413 11 34236886 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795494 Affx-122953302 AX-385282449 11 34164303 GTACACCACACATCCCTAACATCAAATTTAAAGTG[A/C]GTCACCTCCCTTGTTGAATAAATTGAATAAGTACA M 2 1 2 1 101000 r 74 goat snp28665-scaffold309-1354955 11 34283573 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773627 Affx-122928147 AX-385260767 11 34205940 GGTTTAATTTAAATTTATTATGGTGAAATTTTCAA[C/T]GATATTCCTCTTTTGATGTTCAAGGAGTTTTCAGG Y 2 1 2 1 201000 f 74 goat snp28664-scaffold309-1313318 11 34326607 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424337 Affx-122941944 AX-123294683 11 34253456 CAGAGATTTGGTCCTTTTAGACATTTTTGGAAGAT[A/G]CAGTATTTTCTACTTTTACTCTGAGCCATGTTTTC R 2 1 2 1 101000 f 74 goat snp28663-scaffold309-1265802 11 34373761 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398379 Affx-122961654 AX-123268734 11 34288692 AATAACTGCAATCTGTATCCTAGGCAAGTTAAAAC[A/G]TAAACCAACATAAGTGTATTTTTATTTCAGGAAAT R 2 1 2 1 101000 f 74 goat snp28662-scaffold309-1230566 11 34409153 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432714 Affx-122936017 AX-123303055 11 34320434 AGTAGAGGTTTAGCAAGGAATCAGGGGAAAAAGGA[C/T]AAACCAAGTGCATGCTCTGGTACCTCCACAGGCTC Y 2 1 2 1 101000 f 74 goat snp28661-scaffold309-1198824 11 34441115 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413843 Affx-122949874 AX-123284192 11 34352826 AGCTCTAATAGTCTATTTTGTTTTTCAAAGTGTCG[A/G]CATTCAGCTTATTGGAAGGTACATGATAGAACAAT R 2 1 2 1 101000 r 74 goat snp28660-scaffold309-1166432 11 34474751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409008 Affx-122953883 AX-123279359 11 34455241 AGACTCAGTGATTTGTATGGAATCATGAAGGGATG[C/T]GCAACATGCATGTAACATATATTTTATTTTTCTTG Y 2 1 2 1 101000 f 74 goat snp28658-scaffold309-1064017 11 34578787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276632 Affx-1111835441 AX-519550142 11 34473785 ATCTGAGCCACCAATTAACATAGGGTGATATAAAT[A/C]ATGAAAGAGCTCTATGTTGCCCACCGTAAGGCCAA M 2 1 2 1 101000 r 74 goat Random2.2K-1156 11 34473785 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320783238 Affx-122961051 AX-385270304 11 34522548 AGTGGCCACCATCTCTACCCTAGATAACAGTAAAC[A/C]TGTAGACAATAATATGTGAGAAATGTCAGCCAATT M 2 1 2 1 101000 f 74 goat snp28656-scaffold309-996710 11 34647135 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789501 Affx-122957148 AX-385276510 11 34583313 ATAGTCTAATCAAATGCCCTCAGGCATTTGCTTTC[A/G]TTTAGGGAATACATTCCCCTCAGCTCCCCCAGGAA R 2 1 2 1 102000 f 74 goat snp28655-scaffold309-935945 11 34709738 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397860 Affx-122962452 AX-123268215 11 34618039 AAAAAATAAATAATTAAGAGAGTCTTAGTCCAAGT[C/T]AGCCTAAGGGAGGAAATGTATCAGGGAATCAAGCA Y 2 1 2 1 201000 f 74 goat snp28654-scaffold309-901219 11 34746445 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797443 Affx-122920289 AX-385284382 11 34648284 ATTTTGTGATTTAGGTTAATCAAAGAATAAATGAA[C/T]GTTTAAATTCATGTCAAGATTTCTTCCATGAAAAT Y 2 1 2 1 101000 r 74 goat snp28653-scaffold309-870974 11 34776693 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418401 Affx-122946550 AX-123288749 11 34700479 AATACTGATGCACCATAATTTAAAAAGTATACAGT[G/T]ATTACACAGTAAGTTATGCTCAGATTTTCACTTTG K 2 1 2 1 101000 r 74 goat snp28652-scaffold309-818779 11 34829666 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406433 Affx-122955199 AX-123276785 11 34741356 CAGACACCTGAGGAAGAATAAGTGAATTTTGTTTC[C/T]GCAAGGTAATGGATTTGGGGTATTTTGTTATGTAG Y 2 1 2 1 201000 f 74 goat snp28651-scaffold309-777902 11 34870762 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442297 Affx-122928252 AX-123312634 11 34779361 ATCTTCGGTTTGTGGCCAGATTGTTGCAGGAGCCC[A/G]TTTCTCCCAGTCATCAGTTAAATAATAAACTCTGT R 2 1 2 1 201000 r 74 goat snp28650-scaffold309-739897 11 34909119 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440045 Affx-122929754 AX-123310382 11 34824270 TGGAGTTGAAGCATCAGCCATTCATTTTTATACTG[C/T]GGAGGTTGACGTAGAGAATCAGGCACATGCAATAG Y 2 1 2 1 101000 f 74 goat snp28649-scaffold309-694988 11 34958121 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438718 Affx-122930847 AX-123309055 11 34872073 TTCATATACAGTACCTCTATTGGTCCTGTTTTACT[A/C]TCATTTTCCTGCTTCTTCTTAACAGGTGCTCTCTA M 2 1 2 1 201000 f 74 goat snp28648-scaffold309-647185 11 35006171 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395550 Affx-122964249 AX-123265905 11 34902731 AAATTACCCAGGTGTTCTTGGGTAGTAAATGGTAC[A/G]CACTAACAAAGACAAAACCATCCTTCATGGGAGAA R 2 1 2 1 201000 f 74 goat snp28647-scaffold309-616527 11 35036328 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385020 Affx-122971866 AX-123255378 11 34962192 TCTATTTCTGTAAATACTATGGTATCCCTGAAATC[A/G]ATTAATTTGTTGAAGAAAGTGCCTGGCTCTGTACC R 2 1 2 1 101000 f 74 goat snp28645-scaffold309-557066 11 35097232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444424 Affx-122926570 AX-123314761 11 35029835 AAATTGAAACAAATTAAAATGCTCCAATTAAGAGG[C/T]GGAGATTAGAAGAATGAATTAAAAATGATCTAACT Y 2 1 2 1 201000 f 74 goat snp28644-scaffold309-489423 11 35165343 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411173 Affx-122951862 AX-123281523 11 35058874 AATCATTTGCCCATTTTCATACAGTTATTATGAAG[C/T]AAACAGCTGTGCCTCACTTTAATTCACTTGCTGTT Y 2 1 2 1 101000 f 74 goat snp28643-scaffold309-460384 11 35194269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430815 Affx-122937453 AX-123301156 11 35089657 CCCTATGATGAAAGTTTAGCTAACATGCTTTTTTT[A/C]TGCAGGGTGAAAAATTTATTATTTTGCTTGTGGCA M 2 1 2 1 201000 f 74 goat snp28642-scaffold309-429601 11 35225352 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410707 Affx-122952727 AX-123281057 11 35152880 ATCAGTTATTTCTCAGTGATAGCACCAAGTGAAAA[C/T]ACTGATAGAAAACTAGTTTAAAACCTGTCCAGTAA Y 2 1 2 1 101000 f 74 goat snp28640-scaffold309-366378 11 35288701 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275413 Affx-1111834787 AX-519548986 11 35160878 TCAGCTGCAGTGATCCAGGGA[A/G]GTGGGGTATGAAAAGCAAATGAGGAGGCAGGCAGA R 2 1 2 1 103000 r 74 goat GoatD01.052917 11 35160878 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468272669 Affx-1111832920 AX-519546376 11 35161673 CACACACACACACATGCATACATACACAGCTAGTT[A/G]GTTTTTATCTACCAGATTTTTCATATCAAGCCAAA R 2 1 2 1 201000 r 74 goat 11_35161673_AF-PAKI 11 35161673 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320770142 Affx-122935305 AX-385257309 11 35202136 ATAATAGGCCAATGTGGGTAAAGGACTGTGGGATA[C/T]AGGAGAATCTTGTTCTGATCGTTCTGTGAGGAAGC Y 2 1 2 1 101000 f 74 goat snp28639-scaffold309-317122 11 35337737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800873 Affx-122946621 AX-385287788 11 35240019 AAAGTATTCAGGAAAAATGAGATCTATATCAATAC[A/G]TAAATTTCACAGGTAATACCTTAACCTGTGAGGTA R 2 1 2 1 101000 r 74 goat snp28638-scaffold309-279239 11 35375383 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428736 Affx-122938445 AX-123299078 11 35316075 CTCCAAACATTTACCTTTGATTTTTAAATGGTTCT[A/G]TTGCTCTCTTCTATCCTAAAGGAGACCAGTCCTGG R 2 1 2 1 101000 r 74 goat snp28637-scaffold309-203183 11 35431856 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425565 Affx-122941432 AX-123295911 11 35383258 ACACAGATAAGTGGTTATATGCAAGTTGGTGTGGG[C/T]AGTAGAAGAAATGGACATATGTGCAGTCCAAAATG Y 2 1 2 1 101000 f 74 goat snp28636-scaffold309-136000 11 35501004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431031 Affx-122936660 AX-123301372 11 35425255 TGTTTGGCTTTTTCTCTAAAACTTTGTATCTCTAA[C/T]GTGTGATGTGAATTTGCCCTGCTGCCTTCGTGTAG Y 2 1 2 1 201000 f 74 goat snp28635-scaffold309-94003 11 35543776 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437645 Affx-122931801 AX-123307983 11 35486561 GATGGAATATAAATATGGAAATTATGGGGAGGACT[C/T]TCAGCAAAGATTTCAGCTTTTGGTTAAATGCTCAG Y 2 1 2 1 101000 r 74 goat snp28634-scaffold309-32697 11 35606403 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446574 Affx-122924830 AX-123316910 11 35565471 CCAGGCGTGATTAAACATGCAGATTTCCAAATCCC[A/G]TTCCAGACTGTGTGACTGAGTCTCTTTGGAAGTGG R 2 1 2 1 101000 f 74 goat snp37473-scaffold457-764410 11 35692393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398378 Affx-122961655 AX-123268733 11 35603294 ACCGTAAATACTCCCTCGTCCCTGTGGTTTCCCAC[A/G]TAGAAGTAAAGCTTAAGTGAAGATATGGATTTCAT R 2 1 2 1 201000 r 74 goat snp37472-scaffold457-726587 11 35730793 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388275 Affx-122969764 AX-123258633 11 35682447 GGCATTGAAGGTTTGTTACTATTTAGAGAGTGTAG[C/T]AAGTATCTGCTTAGAACAAAGTGGCTGAATATAAA Y 2 1 2 1 101000 f 74 goat snp37470-scaffold457-647434 11 35810348 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781163 Affx-122950618 AX-385268248 11 35711282 TTAGCTGAAAGTGAAGATATTCCTTGACTCCAAGT[A/G]TTTTCTTATACAGGGAGCACTTAACATGGTTGAAG R 2 1 2 1 101000 f 74 goat snp37469-scaffold457-618599 11 35839061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443064 Affx-122928132 AX-123313401 11 35743517 TGTCAAAAGGCTACAGAATGTTCTTCAAAGCTGTT[C/T]CTTTTTCTGGGCAAGGGATGATGGTAGAGATGGTA Y 2 1 2 1 101000 r 74 goat snp37468-scaffold457-586364 11 35871225 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423519 Affx-122942453 AX-123293865 11 35773392 ATAGTGATTTCTGTACCTGTGGTGGCTGCAACAGC[A/G]GTATTGCTGGTTTGCCCCTCATTAAGGTCCAGAGG R 2 1 2 1 201000 r 74 goat snp37467-scaffold457-556489 11 35901521 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381393 Affx-122974380 AX-123251751 11 35821144 GATGGAACCCACAGAAATTGGTGGTAGATGGGATA[C/T]GGCAGGTGAGGTAAGGGATGAATACCATGACTTTT Y 2 1 2 1 101000 f 74 goat snp37466-scaffold457-508737 11 35957673 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379401 Affx-122976127 AX-123249759 11 35886163 AACCTATTTAAGGAAAAAATTAAATGTATCCTCTT[C/T]TCTTTTCCTCCTCGGACAACTACACAGACTGTTGG Y 2 1 2 1 101000 r 74 goat snp37465-scaffold457-443718 11 36023572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422899 Affx-122943058 AX-123293245 11 35917837 CTAAAAAATGTGCTGAGTTTGACAGTACAGTAACT[C/T]TTGAAAGTGTCCTAAATTTGTACTGTCCAATCACT Y 2 1 2 1 101000 r 74 goat snp37464-scaffold457-412044 11 36055010 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435543 Affx-122933394 AX-123305883 11 35972213 TCTCCTGCATTGGCAAGAGGATTCTTTACCTCTAC[C/T]GTCACCTGGGGAGCCCTATATGCACGTAGGTATAT Y 2 1 2 1 201000 r 74 goat snp37463-scaffold457-357668 11 36109653 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411221 Affx-122952352 AX-123281571 11 36018619 ACCCTGCAGAATAGTTTAGAGAGAGGAGAGAGAAC[C/T]GGTTACTTGCTGGGTTGTTACAGTGGAGGTCAGTG Y 2 1 2 1 201000 r 74 goat snp37462-scaffold457-311262 11 36156536 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448694 Affx-122923865 AX-123319030 11 36047798 TCCTGCATCAGCAGGTGGATTCTTTACCACTAGTC[A/G]CCAGGGAGGCCCATAAAGCATTCTAGGCAACAACG R 2 1 2 1 201000 r 74 goat snp37461-scaffold457-282083 11 36185895 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412818 Affx-122950474 AX-123283167 11 36084112 AATTAATTAAATCCATTTTAAGAAACATTGTCACT[A/G]TTTTAGACAACTTTAGTAGCCAAACATAGACTTTA R 2 1 2 1 101000 r 74 goat snp37460-scaffold457-245769 11 36222197 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412419 Affx-122951430 AX-123282768 11 36131632 AAAGTTATTTCTGTGTATTTTAGAAATTGTCCTCG[G/T]GATATAATTCAAGGTCTCTTGTCCAGACAGCTTAA K 2 1 2 1 101000 r 74 goat snp37459-scaffold457-198249 11 36269519 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430145 Affx-122937388 AX-123300486 11 36191982 TCATCCCTGATGCCTTTCTTGCTCTCATTCCCCAC[A/G]TTTGATATGTCAATTCAACTGTCAGCATATGTGCA R 2 1 2 1 101000 r 74 goat snp37458-scaffold457-137899 11 36330010 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772649 Affx-122961181 AX-385259797 11 36229952 TCCAACAAGTTTATGCATGCATATAAAGCATAAAA[G/T]GATGGAAAAATCATCTTGATCAGCCATTAAGCCTG K 2 1 2 1 101000 r 74 goat snp37457-scaffold457-99929 11 36367700 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413282 Affx-122950208 AX-123283631 11 36298411 AATCAACATAGGTCTCATGTCATTCTTTTCAGTGA[C/T]GTATGTTCAACATCTCTACAGTGCATTCCAAATAA Y 2 1 2 1 101000 f 74 goat snp37456-scaffold457-31470 11 36437200 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391998 Affx-122966498 AX-123262355 11 36327573 TTGCAGGAAAGCAGAAGAGATAGAAAAGTCTGCAG[A/G]GTCCCAGAGAAACTGACCCCAGAACCCTAACATAA R 2 1 2 1 201000 f 74 goat snp37455-scaffold457-2308 11 36466497 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405846 Affx-122955864 AX-123276198 11 36331443 ACAACATAGAACTGATAAAGCAAGTGGAAAGAACA[C/T]AGTAAGATACAAATTTAATTCTGAATATGTCAGTA Y 2 1 2 1 101000 f 74 goat snp2892-scaffold1086-1021591 11 36470148 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794378 Affx-122965414 AX-385281342 11 36364383 GAGGGAGGAAAACTTATGTTTCCAAATGGTCTCAA[C/T]ATTGTTTACTAAACAATCCATCTTGATCATACAGT Y 2 1 2 1 101000 f 74 goat snp2891-scaffold1086-988651 11 36503705 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448999 Affx-122923103 AX-123319334 11 36405177 TATTGCATTTCCGTAAGCATTAAAATGAGTGTGCT[A/G]CTAAGAATTAGCCGGGGTAGTAGGAACGCTGAATC R 2 1 2 1 201000 f 74 goat snp2890-scaffold1086-947857 11 36545277 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798495 Affx-122941123 AX-385285428 11 36443391 GAAAAAACTATAACTCGCAACCTTAAAATGACTCT[A/G]TTTCTTTCAATACATTTGATAGATCAGATCTTGTT R 2 1 2 1 101000 r 74 goat snp2889-scaffold1086-909643 11 36583817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782062 Affx-122927307 AX-385269140 11 36495867 GAACTCCTTTAATAAAAAGATTTCCGTTGCTAAAC[C/T]CTGTTGGCATAGAAATTTCTATCCAGAGATTAAAC Y 2 1 2 1 201000 f 74 goat snp2888-scaffold1086-857167 11 36636638 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425337 Affx-122941596 AX-123295683 11 36573763 TGTGATTGACCCAGGGCTGAATGCAGCCAAGCAGA[C/T]GGTTTGCTATGTTCTCCATACTTTTTCTGGTCCCA Y 2 1 2 1 201000 r 74 goat snp2886-scaffold1086-779271 11 36715396 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413667 Affx-122950112 AX-123284016 11 36630830 TACTTAGGCATCAGGGTGTCTGAAGGCAGCTGGTG[A/C]TGGCTCCACTGGGTGTCCACCAGCGTGGGGGTCCC M 2 1 2 1 101000 f 74 goat snp2885-scaffold1086-722204 11 36771523 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383470 Affx-122973445 AX-123253828 11 36692223 TGCCTTATAGTGATGGGTCTCTAGGGCTTCCCTTA[C/T]GGCTCAGCTGGTAAAGAATCCGCCTGCAATGAGGG Y 2 1 2 1 101000 f 74 goat snp2884-scaffold1086-660811 11 36834017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416265 Affx-122947958 AX-123286614 11 36734061 CCTCCAGTCTTCATTCTCCTATTTCCATACATAAT[A/G]CCTGGAGAGCCTCCCACACAATAACTACCTATTAC R 2 1 2 1 101000 f 74 goat snp2883-scaffold1086-618973 11 36875784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276634 Affx-1111835442 AX-519550144 11 36753619 GTTTGACACGACTGAGCGACGGAGCACACGTGCAC[A/G]TGTTTTCTACCAGTTAGCATGATGTCTCTGAGAAC R 2 1 2 1 101000 r 74 goat Random2.2K-1157 11 36753619 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320775804 Affx-122962629 AX-385262935 11 36773305 ATGAATTAGTTTATTCCCAATCTAAAGGGACCACG[C/T]AGAACTACTTCTCTTAGTTCCATCCACCTTAATTC Y 2 1 2 1 101000 f 74 goat snp2882-scaffold1086-579729 11 36915631 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790231 Affx-122950805 AX-385277235 11 36832190 GGGGCATTAAAGCCCTCAGTTTACCCTTAGAAAAC[G/T]AGACAGAAATCCGAGGTGTATTTTGTGTGGACACA K 2 1 2 1 201000 r 74 goat snp2881-scaffold1086-520844 11 36974251 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406809 Affx-122955690 AX-123277160 11 36861821 CCAGGCTGAGGCTACAACTGACCCAGGGAGGAGGG[C/T]GGGGTTGACAGGACACAGAGATATCACCTGCCGTC Y 2 1 2 1 202000 f 74 goat snp2880-scaffold1086-491213 11 37003731 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402685 Affx-122958354 AX-123273038 11 36897164 CTATCAAAAAAATAAGCTGGTATAATTCTATTCTC[A/G]TGAAATTATTTCTATTCATTTGGCTATCTGTCCAT R 2 1 2 1 101000 f 74 goat snp2879-scaffold1086-455870 11 37039425 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416023 Affx-122948373 AX-123286372 11 36952832 CAACTGCAGTAGAATAAACAGAGACCTCAGTGAAA[C/T]AGAAAATAAAACAGCAACAACAGAGTGGACTTGAG Y 2 1 2 1 101000 f 74 goat snp2878-scaffold1086-400202 11 37095423 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378925 Affx-122976442 AX-123249284 11 37009718 AGGAGGCTCGTTAAGAGATTACTGGTGGCAGGGAG[A/C]ATGGGAAGAAGAGAAAGAATGTCAGAGTCCCTGTA M 2 1 2 1 101000 f 74 goat snp2877-scaffold1086-343316 11 37152749 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392559 Affx-122966083 AX-123262916 11 37056534 CCATTATTCATAGTTTCATGCTGTTTTTAGCCGTG[C/T]ACTATTTTAAGCAATGTAAGCTTTGCTCTACTAGC Y 2 1 2 1 201000 r 74 goat snp2876-scaffold1086-296500 11 37199588 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771579 Affx-122922293 AX-385258737 11 37095953 CTTCTTAGAGTATCTGGTTTCTTTATCCTAGGCAA[C/T]GATCTGAGAGGCCTGGGATAAACTACTTGTATAGT Y 2 1 2 1 201000 r 74 goat snp2875-scaffold1086-257081 11 37239655 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426603 Affx-122939974 AX-123296949 11 37148961 GCTTTCTCACACATTCTCTGAATGCCTGTCTTGCC[C/T]GGCGCCTCTTTCTTCTGCAGTTCAGAAGCTGTCTA Y 2 1 2 1 101000 f 74 goat snp2874-scaffold1086-204073 11 37293005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426059 Affx-122941097 AX-123296405 11 37200198 TTTGTAGAGTTGGAACCATGACCCAGAGAATTTAC[A/G]TGCCTTTGCAAGGTTAAATACCTAGGTGGTATCAG R 2 1 2 1 101000 r 74 goat snp2873-scaffold1086-152836 11 37343785 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777900 Affx-122955624 AX-385265016 11 37240794 GAAGAAAAAAAAAACCAATTTGTCAGGAATTTGCT[A/G]CCTTTTATTTAGATGGAGCAGCTGTGTAATTATTT R 2 1 2 1 201000 f 74 goat snp2872-scaffold1086-112240 11 37384427 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399891 Affx-122960213 AX-123270246 11 37271598 CCTGTGTAAAAAACTGACTATGTGTATGTGGGTCT[A/G]TGAGTCTTTCTGGACTCTATTCTGTTCCATTGATC R 2 1 2 1 101000 f 74 goat snp2871-scaffold1086-81436 11 37415213 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792910 Affx-122958820 AX-385279888 11 37306098 TTATTAAAGTAATAATATGAAGTTTTGTTTTATAC[A/G]TTTCTTGTATTTCTTCCACTACTTCCCACCCCACC R 2 1 2 1 201000 f 74 goat snp2870-scaffold1086-46936 11 37450363 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439383 Affx-122930264 AX-123309720 11 37367249 AGATAATGAGCAGAGGCACTGAAATCTCACTTCAG[C/T]CAACCTCACCAAGTATTCGACTTACATACTCCCTA Y 2 1 2 1 101000 r 74 goat snp24195-scaffold247-14116 11 37514201 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399623 Affx-122961080 AX-123269978 11 37444185 TACCAATTGAAATCTAGAGGAAAAAACAGACTGAT[A/G]GTTGTATAGGCAGCCACTCCTACATTAGCAAACAA R 2 1 2 1 101000 r 74 goat snp24196-scaffold247-91052 11 37591807 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423816 Affx-122942802 AX-123294162 11 37518114 AGGCTGACCAGTAGATACGACTTTTCTGTTCTATT[C/T]AGTAGATGATTATATCTCTCAAAATACATTAATAA Y 2 1 2 1 101000 f 74 goat snp24197-scaffold247-164981 11 37666017 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453275 Affx-122920389 AX-123323608 11 37610692 CAGAACTGGTACTATTTGTCCATTTTTATTCAACA[A/G]TGCTATAAACCAGTTATAATACAATGGTCAGATAA R 2 1 2 1 101000 r 74 goat snp24198-scaffold247-257559 11 37760119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411126 Affx-122951899 AX-123281476 11 37643518 CAGAGGAGCCTCATGTAGAGAGAGGAGAAGGGATG[A/C]TGGAGATGGGGAGGATGAAGCGGGGAGGAAAGCAG M 2 1 2 1 101000 f 74 goat snp24199-scaffold247-290385 11 37793640 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776972 Affx-122931188 AX-385264096 11 37701926 AACCTTGTATTACAATAGTTCTGATCTTTAGACAA[G/T]AATTATATCTTTTTGTAGCTATAGTACCAAACAGC K 2 1 2 1 101000 r 74 goat snp24200-scaffold247-348793 11 37852418 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394617 Affx-122964412 AX-123264972 11 37769134 TCTGATGTAAAAAAATAAAAATCTTATACAGAGAG[A/C]TTATGTTGTAGTTCTTAGCTTTCCCTGGAGGCTTT M 2 1 2 1 101000 r 74 goat snp24201-scaffold247-416001 11 37920069 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276636 Affx-1111835443 AX-519550146 11 37794451 CATACATCACTTCTGCGTGCATTCCTTAAGTTCAT[A/G]CAAGTCATAAGGCTAAACCTGATGGCATAATCCTT R 2 1 2 1 101000 r 74 goat Random2.2K-1158 11 37794451 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430159 Affx-122937376 AX-123300500 11 37804396 CTATCATTACCAAAGATTCAAGGGGAGGTTAAGAT[A/C]TCCTTCAGAAAAAATACAGAAACCGAGGCACAGGA M 2 1 2 1 101000 f 74 goat snp24202-scaffold247-451263 11 37955467 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393966 Affx-122965050 AX-123264321 11 37845026 TGCCATATTCCAGTGGCTTGTTCACCTAAAGTAAG[C/T]CAGAAAAAAATAATCTAACACAAATTTCATCTATT Y 2 1 2 1 101000 f 74 goat snp24203-scaffold247-491893 11 37996717 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438445 Affx-122931256 AX-123308783 11 37876210 TTTTGATTTGGTATTTTTTAAGAGATTCCAGAAAG[A/G]AGGAACACAAATCTGTCCTTGGTCAATCTGAATGA R 2 1 2 1 101000 r 74 goat snp24204-scaffold247-523077 11 38027879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430044 Affx-122937566 AX-123300385 11 37920524 CTCTTGCAGTTTGTGGACTCCCCAGATGAGTTCTC[C/T]CATCTCCAGGTCTTTGTGCACACTCTTCCTGAGCT Y 2 1 2 1 201000 r 74 goat snp24205-scaffold247-567391 11 38072948 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386390 Affx-122970836 AX-123256748 11 37955681 GAAAGAATGCTGTGGAAGGAATGGAATACTAAACA[A/C]GTTACTTTTTGAGAGTGCCCTTCTGACACACTGAT M 2 1 2 1 101000 r 74 goat snp24206-scaffold247-602548 11 38108143 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783024 Affx-122948588 AX-385270092 11 37989059 CAAGCTCTTTTTCTAAGAGTGATTATTCTATTTGG[A/G]TATTAACCATTGGTGATAGCTTGGTTTATTGGAAA R 2 1 2 1 101000 r 74 goat snp24207-scaffold247-635926 11 38141522 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403556 Affx-122957592 AX-123273909 11 38034396 AGTCTTGGTTGGATTCCACAATATTTCTTCTTGAG[C/T]CTCAGCATCTTCTCTTTGAAAAGTTTCAGATTCAC Y 2 1 2 1 101000 f 74 goat snp24208-scaffold247-681263 11 38186957 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386274 Affx-122970943 AX-123256632 11 38095282 TCTTTCATAATGATTTGTGAATCTGATGGCTTGTC[A/G]TGTCCTCAGCAATAGTATTTATTATTATTATAGCA R 2 1 2 1 101000 f 74 goat snp24209-scaffold247-742149 11 38247691 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771559 Affx-122966004 AX-385258717 11 38173107 TGATGGTTAGAACATTGAAAGGTGGAAAACTTGGG[A/C]TGTTATATTTCATTATACTAATGAGAACTTTAAAA M 2 1 2 1 101000 f 74 goat snp24210-scaffold247-819974 11 38325919 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383752 Affx-122972442 AX-123254110 11 38386324 TTCATGGGCTTGGTTTGTGATGTTTCCAACTGAGA[A/C]GTAGAAGCTGTTCTGAAGTGGAACAGTTTTTGCTG M 2 1 2 1 101000 f 74 goat snp24214-scaffold247-1033191 11 38537627 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386040 Affx-122971479 AX-123256398 11 38415399 TGATTGTTTAACTATCCAAAAGACAAACAGGAAAA[A/G]GAAATCGTGTACATAATTCTGAAATCATATAATTA R 2 1 2 1 201000 r 74 goat snp24215-scaffold247-1062266 11 38565200 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375436 Affx-122979179 AX-123245795 11 38460911 CAGAGAAAGATTATTTGGCAGGGAAGGTGTGGGCC[A/G]AGACCCAGAGCTAAGAGAAGTTGGGGCCAGTGAAA R 2 1 2 1 201000 f 74 goat snp24216-scaffold247-1107778 11 38610700 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272620 Affx-1111832921 AX-519546331 11 38461137 GTGTGTCTCCAGAGGTGGCCGCAGTCCATAGGGTC[A/G]AAGAGTCGGGCGTGACTGAAGCGACTTAGCATGTA R 2 1 2 1 303000 f 74 goat 11_38461137_AF-PAKI 11 38461137 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38452973 Affx-122920154 AX-123323306 11 38565524 TCGTGCAGGGTTTTCCATACGATGTGAAAGTAAAA[C/T]GCAAATGAATCTTTTGGCCGGCCCAACACTTCAGT Y 2 1 2 1 101000 f 74 goat snp24218-scaffold247-1212391 11 38716272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385835 Affx-122971009 AX-123256193 11 38663792 ATTGTTTTTCTTGATATAAAATTATAGGGATTTAA[C/T]GAGAAATTAAAGTGCCTTTCTCTTTTAGCCCTTAT Y 2 1 2 1 101000 f 74 goat snp24220-scaffold247-1310659 11 38815275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476277 Affx-1251763784 AX-586011696 11 38697443 GATCAGCCCTGGGATATCTTTGGAAGGAATGATGC[-/TAAAGCTGAAACTCCAGAATCCCAGCCGTGCTCCTGCAGTAAAAAAAAATAAAAAAATTTAAAAAAAAAGAAAAAAAAAA]AAAGCTGAAACTCCAGTACTTTGGCCATCTCATGC - 8 1 4 1 20000 f 74 goat SV_233 11 38697443 - deletion junction SV-TF-chip 539476530 Affx-1251763784 AX-569619561 11 38697443 GATCAGCCCTGGGATATCTTTGGAAGGAATGATGC[-/TAAAGCTGAAACTCCAGAATCCCAGCCGTGCTCCTGCAGTAAAAAAAAATAAAAAAATTTAAAAAAAAAGAAAAAAAAAA]AAAGCTGAAACTCCAGTACTTTGGCCATCTCATGC - 4 1 4 1 20000 r 74 goat SV_233 11 38697443 - deletion junction SV-TF-chip 562165157 Affx-1251763784 AX-606940569 11 38697443 GATCAGCCCTGGGATATCTTTGGAAGGAATGATGC[-/TAAAGCTGAAACTCCAGAATCCCAGCCGTGCTCCTGCAGTAAAAAAAAATAAAAAAATTTAAAAAAAAAGAAAAAAAAAA]AAAGCTGAAACTCCAGTACTTTGGCCATCTCATGC - 8 1 4 1 20100 r 74 goat SV_233 11 38697443 - deletion junction SV-TF-chip 562165299 Affx-1251763784 AX-606940710 11 38697443 GATCAGCCCTGGGATATCTTTGGAAGGAATGATGC[-/TAAAGCTGAAACTCCAGAATCCCAGCCGTGCTCCTGCAGTAAAAAAAAATAAAAAAATTTAAAAAAAAAGAAAAAAAAAA]AAAGCTGAAACTCCAGTACTTTGGCCATCTCATGC - 8 1 4 1 20100 f 74 goat SV_233 11 38697443 - deletion junction SV-TF-chip 562165336 Affx-1251763784 AX-606940747 11 38697443 GATCAGCCCTGGGATATCTTTGGAAGGAATGATGC[-/TAAAGCTGAAACTCCAGAATCCCAGCCGTGCTCCTGCAGTAAAAAAAAATAAAAAAATTTAAAAAAAAAGAAAAAAAAAA]AAAGCTGAAACTCCAGTACTTTGGCCATCTCATGC - 8 1 4 1 20100 r 74 goat SV_233 11 38697443 - deletion junction SV-TF-chip 38441417 Affx-122928828 AX-123311754 11 38705103 AACTACTGGAAATTCTCTTAAATACAGAAGTGATG[C/T]GGGAACAAGCAAATTTGTTTTAAAAACTCAAAAAT Y 2 1 2 1 101000 f 74 goat snp24221-scaffold247-1351970 11 38857210 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791157 Affx-122948236 AX-385278152 11 38746139 TGACTTGTCAGTCTAAACGGCACATCTTTTAGATA[G/T]GAGATATCACAATAATGGGAAGCTGAAAAATGAAA K 2 1 2 1 101000 f 74 goat snp24222-scaffold247-1393006 11 38898594 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430548 Affx-122937023 AX-123300889 11 38778904 CTGGCTGTAACTTGTGGTACATAATGATGCTCAGT[A/G]GATATTAATTTGTATAAACTCTGGGAGACAGAGGA R 2 1 2 1 202000 r 74 goat snp24223-scaffold247-1425771 11 38932302 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395756 Affx-122963684 AX-123266111 11 38819631 GAAGGAATCTGACAGGAGGAGTACACAGCAATACA[C/T]ACTTCTGAAAAATCACAAGAAAATAGTTTACCATT Y 2 1 2 1 101000 f 74 goat snp24224-scaffold247-1466498 11 38973135 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798395 Affx-122941600 AX-385285329 11 38857117 TTCCCAGGGTACAGTAGCCCAAGTCCATATTTCAA[C/T]GCAAAGTCTGTGTCTTGATAAGTAGGAGTATCAAC Y 2 1 2 1 201000 r 74 goat snp24225-scaffold247-1503984 11 39011565 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801308 Affx-122939785 AX-385288220 11 38892651 AGGATTTAAAGCTGGCTCTATCTGAAACCAAATTC[A/G]TGCTCTTTCACTACAACTTGTAGTTTTCACAGCAT R 2 1 2 1 101000 f 74 goat snp24226-scaffold247-1539518 11 39047608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428881 Affx-122938334 AX-123299223 11 38938506 CAATAGGTGTTCACAGCCATAAACCCAAAGTGACA[C/T]AGCACCAAACCGTTTCTCTACCAGACGGAAGCCTA Y 2 1 2 1 101000 f 74 goat snp24227-scaffold247-1585373 11 39093672 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398210 Affx-122962222 AX-123268565 11 38977907 CTATTACTAATAAAGAATGCACTGAAAGTCCTTGG[G/T]GTCATGTCATGATGATATCTCTGATTCTTCCCCCT K 2 1 2 1 101000 r 74 goat snp24228-scaffold247-1624774 11 39133345 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385420 Affx-122971331 AX-123255778 11 39039651 ATAGCTATAAGATCTAAAGAGCCACCATTTTACAT[A/G]TAAAATCATGATTAAAATAAAATTATTTTTTTTAA R 2 1 2 1 103000 f 74 goat snp24229-scaffold247-1686518 11 39195279 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401708 Affx-122959539 AX-123272061 11 39068897 TCAGTGTCCTTATATGAAAAAAATAAAGGCATTTT[A/G]CTGAATTACCCATAAAATCACTGCCTACTCTAAAT R 2 1 2 1 101000 r 74 goat snp24230-scaffold247-1715764 11 39225483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424257 Affx-122942004 AX-123294603 11 39113246 TCAAATTGGATTTTCAAGGGGATTGTTTAAGTAAG[C/T]AGGTACAATAGAAAATACAGAAAGGAGGAAATGGG Y 2 1 2 1 201000 f 74 goat snp24231-scaffold247-1760113 11 39271919 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799176 Affx-122953379 AX-385286106 11 39151500 GAGTAAACTTAATTCCCTTATCTTTAAGTGATTCC[C/T]TTAATATTAAATGTTCCATTCATAGTGTCCACGTA Y 2 1 2 1 201000 r 74 goat snp24232-scaffold247-1798367 11 39310487 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773513 Affx-122964139 AX-385260654 11 39189440 AATTCCCTTAGTAAAACCCAATACCTCTACATTTA[C/T]GTAAGACTTCAGATTTATTATCCCTAGAAGAGAGA Y 2 1 2 1 201000 r 74 goat snp24233-scaffold247-1836307 11 39348817 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782104 Affx-122946339 AX-385269182 11 39223362 GGCAGAAATTGAGAATAAATTCTAATGTAAACTCC[A/G]TATTTCCACATAGTGATGAGCCCTGAGGGTACCTG R 2 1 2 1 101000 r 74 goat snp24234-scaffold247-1870229 11 39382851 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390863 Affx-122967818 AX-123261220 11 39257147 TTATTTGCATGACTATTTGTTTTCCTCTCATACAA[C/T]AGAGAGCAGGTATCATGCCTATCTTTGTAACCATT Y 2 1 2 1 101000 r 74 goat snp24235-scaffold247-1904014 11 39416353 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429158 Affx-122937982 AX-123299500 11 39303560 AGATAAGATTTAATTATATATGTGATATTCTTGGC[A/G]CTGAGTAATTACCTAATAAATGAGTATGATTATCC R 2 1 2 1 101000 r 74 goat snp24236-scaffold247-1950427 11 39464546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415506 Affx-122948687 AX-123285855 11 39341152 ATACAGAACAGATACACATACGATAGGACTAGCTG[C/T]GTAATTTGCAATGTCCTGAAGAAAATGAGAATGCA Y 2 1 2 1 101000 f 74 goat snp24237-scaffold247-1988019 11 39502891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776472 Affx-122970119 AX-385263599 11 39372620 GTACTTCCAAAATCTAGCAACAACCTATTCCTTTT[G/T]TGTGGTCATGTGCTCATTAATTCATTTGTTCATTC K 2 1 2 1 101000 r 74 goat snp24238-scaffold247-2019487 11 39534398 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436626 Affx-122932500 AX-123306964 11 39416906 GCTATAAGTGGAGAATGAGGTATGAGAAGGAGAAA[C/T]AAGTGACAGGAAGTTGGTAATGAGGCTGTTTCAGG Y 2 1 2 1 101000 f 74 goat snp24239-scaffold247-2063773 11 39578149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392695 Affx-122966410 AX-123263052 11 39536578 CTGTCATGTATACAGAAGAGCAATGAGTGTCATCA[A/G]TGTCTTCAAACAGGAATTTTATATGGTTAGGAGAT R 2 1 2 1 101000 f 74 goat snp24241-scaffold247-2183445 11 39697287 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383404 Affx-122973495 AX-123253762 11 39566465 TGTGTTTAATATGAACAAATTCTTGTATCTCCTTC[A/G]CCTCTCTGTATAGCTGGACAATGATGCTCCCCTAG R 2 1 2 1 101000 r 74 goat snp24242-scaffold247-2213332 11 39727688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390616 Affx-122967167 AX-123260973 11 39655326 TTCTCAAGAGGACCTAGGCAGGGGCAGAGGAATAA[C/T]GGAGTCTTAATGGGAAATGTGAGAGTTGGACTGTG Y 2 1 2 1 101000 f 74 goat snp24244-scaffold247-2302193 11 39814797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376355 Affx-122978327 AX-123246714 11 39700130 TACCTGTCTTTCTGGTTCATGATCCAGAATATAGG[C/T]TCTGAATTTCTAATTATTTGTTATGTGGGCAAAAC Y 2 1 2 1 101000 f 74 goat snp24245-scaffold247-2346997 11 39860738 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432085 Affx-122935873 AX-123302426 11 39745201 TATTTGTAAAGTTTATGGCCTACCACTTGGTTGCT[A/G]CAACTGGTATTACTGCCTAGAGCAACAGTGATTTT R 2 1 2 1 101000 f 74 goat snp24246-scaffold247-2392068 11 39905745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426720 Affx-122939883 AX-123297066 11 39792064 AGATAGAGGCAAGAGGATAAGCCTGTGTCCTGCCA[C/T]GCTGGCCATCATGCCATGTGGTCCTCTCAGAATGT Y 2 1 2 1 201000 f 74 goat snp24247-scaffold247-2438931 11 39953514 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449656 Affx-122922577 AX-123319991 11 39843315 TTGCTTCTTAGGAACAAATTGAGAGAAATAGGGAC[A/G]TTGGAAAAGACCCTGATGCTGGATAATATTGAAGG R 2 1 2 1 201000 f 74 goat snp24248-scaffold247-2490182 11 40004631 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452874 Affx-122920703 AX-123323207 11 39878893 AACCAAAGTAGATACAACCTAGGACAGAATAAAGA[C/T]ATTAAAGAACCATGATAATTCCTTTAATCTCATTC Y 2 1 2 1 101000 f 74 goat snp24249-scaffold247-2525760 11 40040113 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400755 Affx-122959888 AX-123271110 11 39907403 TTGAGGAATGAAAAAAAGTCAGAACTGATCAGGCA[A/G]ATTTATAATAAAAAATAACAAGTATAAACACACAC R 2 1 2 1 103000 f 74 goat snp24250-scaffold247-2554270 11 40068612 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444664 Affx-122926456 AX-123315001 11 39947972 TTAAAGGCAATTTGCTAAAAAATAATAATATGTAT[A/G]ACCAACTAGTTTTTATAACACAGTGGTTAAACCTT R 2 1 2 1 103000 r 74 goat snp24251-scaffold247-2594839 11 40109350 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393310 Affx-122965960 AX-123263666 11 39981308 AACAAATCATCATTTCTTTTGGAAGGAAAACTTAC[A/C]ATTGCTTTTCCTTGCTTTGGGGATATCAATAATTA M 2 1 2 1 101000 f 74 goat snp24252-scaffold247-2628175 11 40143180 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767625 Affx-122940260 AX-385254873 11 40016098 ATGTGGATAGATGGATGAAAGCATTCAAAAGAAAT[A/G]AGTGCCCTTGTTTCTGCCTATATAAGTAATGCTTC R 2 1 2 1 101000 f 74 goat snp24253-scaffold247-2662965 11 40178168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418187 Affx-122947072 AX-123288535 11 40071551 AAGGCATGAAATCCCTCAAGATCATTTAACTGCTC[A/G]CTGAAGCATCTAGAAAACAAAAGGATAACATATAT R 2 1 2 1 101000 f 74 goat snp24254-scaffold247-2718418 11 40233700 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781921 Affx-122970317 AX-385269002 11 40110376 TGCTCTATTTTGAAAACCCAGAGAAGGATCATAGT[A/G]TGAGAGTTAAATTCATATTCTCTGAAGCTAGTTGG R 2 1 2 1 101000 r 74 goat snp24255-scaffold247-2757243 11 40272703 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780618 Affx-122941842 AX-385267708 11 40140750 TGTGGTTTCCTCCTTTCATTTGATTTTCTAAGAAG[C/T]GTTCAAAAACCATTTCTACAATGTATTAACACATA Y 2 1 2 1 101000 f 74 goat snp24256-scaffold247-2787617 11 40302948 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787289 Affx-122970192 AX-385274314 11 40170961 TGAGTGTCTAATCTAGTTGGGAAGATAAGACCAAC[A/G]CAAAAGTATAGTGTGGGTTGGATAACGAACAGCTT R 2 1 2 1 102000 f 74 goat snp24257-scaffold247-2817828 11 40333481 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434325 Affx-122934742 AX-123304666 11 40212285 GTACAGCTGGCAAGGCTACTTTAAAATATTTTGAT[A/G]TTGCATGTATAGGGTTATGCTGCAGATTAAATAAC R 2 1 2 1 201000 r 74 goat snp24258-scaffold247-2859152 11 40375005 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800982 Affx-122945554 AX-385287896 11 40265265 TGATTTTAAGGAAGTCTTTGAACAGTGAAAGCACT[A/G]TACAATGACAGGTTGTTTTTGTAGACAGATGCACA R 2 1 2 1 101000 f 74 goat snp24259-scaffold247-2912132 11 40428598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765839 Affx-122969603 AX-385253286 11 40369671 CAACTAAGAACAGTGCAGCACAGCACTCACTGACT[A/G]CGAACTCCCTACTTTGTCATTGTGGATGATGTGTC R 2 1 2 1 101000 f 74 goat snp24260-scaffold247-3016538 11 40534464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802696 Affx-122956910 AX-385289595 11 40501866 CTTCTGCTTTTTAAAATTGGGACATTATTCTTCCC[A/G]TCTCTACTTCAATTCTTTCCCATCATTATAGATTA R 2 1 2 1 101000 r 74 goat snp24263-scaffold247-3148733 11 40667836 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411609 Affx-122951599 AX-123281959 11 40552869 AACCTAGCCCAAAAAGATGGGGTGAAGATTACAAA[G/T]CATCTTTTCCTTTTTGAAAACTGAAGTACTGTTTA K 2 1 2 1 103000 f 74 goat snp24264-scaffold247-3199736 11 40719284 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775706 Affx-122969069 AX-385262837 11 40608083 GAGGTCAGAAGAGGAAACTAAGGTTGAATAGATAA[C/T]GATGCCTCCCACCAAACTAATTGTCTATCTGCCTG Y 2 1 2 1 101000 f 74 goat snp24265-scaffold247-3254950 11 40774614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802388 Affx-122924151 AX-385289292 11 40646032 TGACATCTTCAAAGTTCATTCTAATGGGATTGAAT[A/G]TTTTTGAGAAGTCACTAGGCACTGTGAATCATTCT R 2 1 2 1 201000 r 74 goat snp24266-scaffold247-3292899 11 40812688 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798363 Affx-122965324 AX-385285298 11 40685141 AGTCCCCAAGATCATATTAGACTTTTATCTAAATG[C/T]AGAGGAATACCATGGCAGCAGGGAATGTCATAAAG Y 2 1 2 1 101000 r 74 goat snp24267-scaffold247-3332008 11 40851401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452183 Affx-122921229 AX-123322516 11 40755256 AGGATTTTATGGATTGAGAAAATTCTAACCTCTTC[C/T]AGATAAATGGAAGCAGGCATGATTTCAGAATGATA Y 2 1 2 1 101000 f 74 goat snp24268-scaffold247-3402123 11 40921733 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379883 Affx-122975779 AX-123250241 11 40826946 ACAGACACTGGTGATGAGCAATACCCTTTTTATTC[A/G]AGTGCAGAAACTGAATCTTGGAGGATTAGGCAGCT R 2 1 2 1 201000 f 74 goat snp24269-scaffold247-3473813 11 40993876 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276638 Affx-1111835444 AX-519550148 11 40843499 AAGACTGCTTCCTCCGGGTTTGTGAGCACCCTGGC[A/G]AATCCTTCATGGACTTGATTCTCTCCTCTTAACAG R 2 1 2 1 201000 r 74 goat Random2.2K-1161 11 40843499 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439958 Affx-122929984 AX-123310295 11 40856820 AATAAATAAATGACTGAAACCAGGTTGTGTAGACT[A/G]TAGTGTTAAAAAGGATTTACACGCTGATATTTTTC R 2 1 2 1 101000 r 74 goat snp24270-scaffold247-3503687 11 41024508 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790936 Affx-122939696 AX-385277933 11 40886097 TAGGTTATGCTTTTTTGCTTAAATTAACTCTTAAA[G/T]AATATCACATAGCAGATATAGGAGATTGGGTGGGG K 2 1 2 1 101000 r 74 goat snp24271-scaffold247-3532964 11 41053634 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770290 Affx-122959113 AX-385257456 11 40931923 ATGAAATTCAGATTTGGGAACACCTGAAAGGAGCA[G/T]AGAAGTCAGAGAACTATAGAAAGTAATATTTGATT K 2 1 2 1 201000 r 74 goat snp24272-scaffold247-3578790 11 41099498 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379851 Affx-122975804 AX-123250209 11 40970071 GTAGTGGTGGAAGGGAGCGTGTTATAAAGATGGAA[A/G]TCAAAGAAATGTTGTTATATTGACCTGAGTTTTGA R 2 1 2 1 101000 f 74 goat snp24273-scaffold247-3616938 11 41137643 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448099 Affx-122924319 AX-123318435 11 41012617 AGGGAGGGAGCAGAGTGCAGGCAACGTGGGCAGAC[A/G]CATAGGAAGAAGATCCTGGACTTTGTGAATAATTT R 2 1 2 1 101000 r 74 goat snp24274-scaffold247-3659484 11 41180291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767232 Affx-122959971 AX-385254513 11 41043617 CATCCTGTGTGTGTCTCTGGAGATATCACTGATTG[C/T]ATTTTCCCTGGTTATGAAATGTTAGAGAGATCAGC Y 2 1 2 1 101000 f 74 goat snp24275-scaffold247-3690484 11 41211273 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392965 Affx-122965680 AX-123263322 11 41158331 ATTTTTGTTAATGTCATAAGCCTAGAAATAATCCT[A/G]TCTTTATTAGAGAATAGCTGTGAGTTAAAAATAAA R 2 1 2 1 101000 f 74 goat snp24277-scaffold247-3805198 11 41326105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428348 Affx-122938986 AX-123298691 11 41217714 CTTTCTTTCTTCTTTCCTCTCTCTCTCCAAAAGGA[C/T]GTCTTATGTGCCAGGCAGTATACAAGGACTGGGTG Y 2 1 2 1 101000 f 74 goat snp24278-scaffold247-3864581 11 41385740 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428985 Affx-122938858 AX-123299327 11 41267626 AAGAATCTGGGAAATGGAATAGGTGCAGCATAATA[G/T]AGTGGCAAGAGAATGGGAGAAACTTAGAGTGAGTC K 2 1 2 1 201000 f 74 goat snp24279-scaffold247-3914493 11 41436050 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272622 Affx-1111832922 AX-519546333 11 41273766 CAAGGAAAACTTCCCTAACCCTTTGCTCTGTGGAG[A/G]AAGGACTGAAGAATAAAAAAGCATTTGGATGTTTT R 2 1 2 1 102000 f 74 goat 11_41273766_AF-PAKI 11 41273766 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320785668 Affx-122953796 AX-385272709 11 41305994 AGAACAAAGTCAGAGTTAATACAAGAGAGACTTGA[C/T]GTCGAGTCCCAGAAAACGGAATGGATGCTTCTTGA Y 2 1 2 1 101000 r 74 goat snp24280-scaffold247-3952861 11 41474060 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416730 Affx-122947544 AX-123287078 11 41344680 TCAGAATGGGGTTTCAGCACAGCAGGATGCAGGTG[G/T]CTGTCCTGTCACCCCAAATATTACAGCCTCCTCCT K 2 1 2 1 101000 r 74 goat snp24281-scaffold247-3991547 11 41512808 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440058 Affx-122929744 AX-123310395 11 41424721 CTGCTTTCAACTGGACATCTGTGGTTGCACCAGTT[A/G]TTACTTTTAAGCTTTACTTCTTGTCTTTTAAAATA R 2 1 2 1 201000 r 74 goat snp24283-scaffold247-4071588 11 41593062 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401609 Affx-122959618 AX-123271962 11 41479704 CAATTCAATTCAACATTCAGAGTTGTGCAACCATC[A/G]TCATAATCTAATTGTAGAATATTTTCATTATTCCC R 2 1 2 1 103000 f 74 goat snp24284-scaffold247-4126571 11 41647958 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386725 Affx-122970152 AX-123257083 11 41534603 CCCAAGACTGATGGGAGCAGGGTACTGATTTTTGG[C/T]GGCTGCCCTTAGTGAGGACAATGAATAATTGTGGT Y 2 1 2 1 201000 r 74 goat snp24285-scaffold247-4181470 11 41703470 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386001 Affx-122971509 AX-123256359 11 41583528 CAGATCAGTAGAAGATAATATGGATGAATTTTCAA[C/T]GTGATGGAGTCTCCTTTAGAGCAAATACTTACATA Y 2 1 2 1 101000 r 74 goat snp24286-scaffold247-4230395 11 41751980 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423793 Affx-122942821 AX-123294139 11 41620566 GCACCAAACCAGTGTTTTGTCTGTAAATCCTTAAT[A/G]CTCAAAGTGTGGTCATGGGACTGGTAGTGTTGGTG R 2 1 2 1 101000 f 74 goat snp24287-scaffold247-4267433 11 41789086 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451624 Affx-122921621 AX-123321957 11 41674839 CACTATAACTCAAATCTTGATGCCCCCAGTACTAA[G/T]CTGATTTCTGCAGAAAAATAACTTACAGAGTTCCT K 2 1 2 1 201000 r 74 goat snp24288-scaffold247-4321706 11 41843493 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387555 Affx-122970289 AX-123257913 11 41705498 TTCTCAGTACACCTCCCCGCTGCTAATGGAGGAGT[A/G]TGAACACAGGGAACTGTGCTGCACTCTCTGTATGC R 2 1 2 1 102000 r 74 goat snp24289-scaffold247-4352365 11 41874136 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409817 Affx-122952954 AX-123280168 11 41737722 CTAAATTGAATATATTGCTAGCAAACTATTTCTTA[C/T]AGGAAAAGAAAAGGGAAGCAAGGACAGCTGACATA Y 2 1 2 1 201000 f 74 goat snp24290-scaffold247-4384589 11 41906114 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433565 Affx-122934978 AX-123303906 11 41800910 AGCAACCAAAATAAAAACCAGCACAACCAAAATAA[A/G]ATAAAATAACAATTGGACATCTTTGAGTTGCTTCT R 2 1 2 1 201000 r 74 goat snp24291-scaffold247-4447777 11 41969046 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447385 Affx-122924419 AX-123317721 11 41850686 CAGCTGACTAGCTGTGACAGAGACAATACAGCCCA[C/T]ATAGCCTAAATATTAACCATCTCCTATTCTGCTTT Y 2 1 2 1 201000 r 74 goat snp24292-scaffold247-4497553 11 42018677 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802045 Affx-122968680 AX-385288949 11 41892273 AACACCTCACCATCATATGCCCAGTGTGCAACGAG[A/G]TCATCTCACCAACACTGCACCTAGTAGAATTTTTT R 2 1 2 1 202000 f 74 goat snp24293-scaffold247-4539140 11 42058686 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797802 Affx-122919943 AX-385284741 11 41935810 CTGTCCTGTGTGATCGTTGGTTTAACTCTATACAC[A/G]TAAGACGTTGTTCCATTGTCCTCTATTAGTGTGGC R 2 1 2 1 101000 f 74 goat snp24294-scaffold247-4582677 11 42102171 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453167 Affx-122920472 AX-123323500 11 41983813 TTTCTCTTACTGAGATTTTTTTAAAGGGCTGTGAT[A/G]TGCTCTAGAACAAGTCACATTTGTAAGAAGCTTTC R 2 1 2 1 101000 r 74 goat snp24295-scaffold247-4630680 11 42148862 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780126 Affx-122970812 AX-385267223 11 42026707 GACTATAAGAATTTTCTCGCCTAAAGAAAGGATGG[C/T]GGATTAAATGGCCACAGTTGTTCCTCAATCTCACA Y 2 1 2 1 101000 r 74 goat snp24296-scaffold247-4673574 11 42191593 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789409 Affx-122962081 AX-385276419 11 42070719 GATGTGAAGGCAAAGTCAAGAAGTATTAAGCGAGT[A/G]CTTTCCAATGACCAGCACTGTACTAAGTACTGCAA R 2 1 2 1 101000 f 74 goat snp24297-scaffold247-4717586 11 42235734 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418728 Affx-122946274 AX-123289076 11 42168749 TAATAGTATGAGGTGGAAGGCCGAGAGTAAGAGGT[A/G]TATACATTGTGAGAAAGTGTAAATAGCAATTGTGC R 2 1 2 1 201000 r 74 goat snp24299-scaffold247-4815616 11 42333588 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774266 Affx-122948027 AX-385261402 11 42203454 CAACTGATTATTAAAGATCTTTTTATTGAGGATTT[A/G]CAGCTATGTCATCAAATAACTGAGTAGTATTCAGG R 2 1 2 1 101000 r 74 goat snp24300-scaffold247-4850321 11 42369166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439133 Affx-122931087 AX-123309470 11 42265527 AGAAGCAATTGCCCAAAGTCACTCAATAAGTTAAC[A/G]TCAGAGCAGGAACAATTATGTTTTGAAGAAACATG R 2 1 2 1 101000 r 74 goat snp24301-scaffold247-4912394 11 42431574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274448 Affx-1111834204 AX-519548039 11 42288422 ACCAGCACTGGCTGCTGTGTGGTGA[A/G]TAGCAGGACCAAAGAAAGGCCAGGGTTGTGAAAGC R 2 1 2 1 102000 r 74 goat GoatD01.025351 11 42288422 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38418375 Affx-122946570 AX-123288723 11 42305057 AGAGACAATCAGAAAATCCTCTCTCTCTGTCGGTG[C/T]AGCACACTCCACACAGGAATGCAAGGAGCAGGACT Y 2 1 2 1 101000 f 74 goat snp24302-scaffold247-4951924 11 42470980 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393955 Affx-122965059 AX-123264310 11 42346205 TTCTGTTCCTTCTTTGACTTGTGAATGAAGTAGGA[C/T]GGACAGAGACAGAATGGAGGGAGGGGGAGAGGAGA Y 2 1 2 1 101000 f 74 goat snp24303-scaffold247-4993072 11 42512591 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425070 Affx-122941255 AX-123295416 11 42387398 GACCCATTGACAGTGATTTCAGACTTCCAGCCTCC[A/G]GAACTGTAAGAGAAGACTCTGTTTGGTAGTATGTT R 2 1 2 1 201000 r 74 goat snp24304-scaffold247-5034265 11 42553452 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276492 Affx-1111835445 AX-519550004 11 42451690 TGTCACAGAACAGAAATAATTCAGGATTAGAGCAC[A/G]GCTATTGGTTCTCCCAGATGCCTATGCAGGTAAAT R 2 1 2 1 101000 f 74 goat Random2.2K-1162 11 42451690 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419775 Affx-122945864 AX-123290123 11 42473195 TGCATGGTGTTGCAAAAGAGCTGGACATGACTTAG[C/T]GAATAAACAGCAATAGCGAAGTACCTCCTGGAACA Y 2 1 2 1 101000 r 74 goat snp24306-scaffold247-5120062 11 42639712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788906 Affx-122935857 AX-385275921 11 42547238 GCCTATAATGTATCTGCTTATGGCATTGAAATTGC[A/G]ATGGCACAATGAAGACCAGCCCCAAAGTACTCAAT R 2 1 2 1 101000 r 74 goat snp24307-scaffold247-5194105 11 42714471 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415639 Affx-122948578 AX-123285988 11 42581550 TTCAAATTAGTCTTTTGAACAATTAACATGATGGA[A/G]TTGAAGGAAATAAATAGTAGGGGAAGCCTGGGAGG R 2 1 2 1 201000 f 74 goat snp24308-scaffold247-5228417 11 42747821 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380465 Affx-122975730 AX-123250823 11 42614687 CCAGAACCTTTCTTTTTTAAACAGAGTTCACACCA[C/T]ATTTTAAACAGTGTTCTGCCATATTTTGATTAGGA Y 2 1 2 1 201000 r 74 goat snp24309-scaffold247-5261554 11 42780903 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412212 Affx-122950930 AX-123282562 11 42679050 ACTTGGCCACTAGTTGGAGACAAGGATTCAAGACA[C/T]GGACGATGAGTCCCTCTCTCTCTTTTGTACTGCCC Y 2 1 2 1 101000 f 74 goat snp24310-scaffold247-5325917 11 42844965 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773253 Affx-122953067 AX-385260396 11 42709204 ACCTAGCTCAAGGTCAGAACCCAGGCATATACTAG[C/T]TCTTAGACCTGTATCTTTCCACTATCATTAAAAGT Y 2 1 2 1 101000 f 74 goat snp24311-scaffold247-5356071 11 42875071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795669 Affx-122948400 AX-385282624 11 42748926 ATTCAGATCTTCACAGTTAGAGCAAAGCAGAAGAG[A/C]GAGGAAATTACCTATATAACTTCAGTAGGCTGCCT M 2 1 2 1 101000 f 74 goat snp24312-scaffold247-5395793 11 42915000 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798820 Affx-122943828 AX-385285750 11 42791624 ATGCTTTTCTCAAAGGGAGTTACAGAAATAGAATA[C/T]GTCACAACCATCCCGAAGATTGAGACCTGATCAAC Y 2 1 2 1 101000 r 74 goat snp24313-scaffold247-5438491 11 42957672 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441918 Affx-122928598 AX-123312255 11 42834359 CTGATGCTAATGGCATTCGGTAGTTGCAAATGCAC[A/G]TTTGTCTATCAGCTTTGCCAACAAGAGTGTAACTG R 2 1 2 1 101000 f 74 goat snp24314-scaffold247-5481226 11 43001353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378382 Affx-122976808 AX-123248741 11 42903309 CCTGACCCCTGGGTGAAGCGTAATTAGACCAAGGG[C/T]CAGGGTCAACAAGGATGGTAGATTCCAACCTCAGT Y 2 1 2 1 101000 r 74 goat snp24315-scaffold247-5550176 11 43070945 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376939 Affx-122977777 AX-123247298 11 42958774 TATTGCAAGAATTAGCCTTAGTTTAAAATGATGTA[C/T]GTTTCTTTATACAAGTAATCTGATCACATTTAACC Y 2 1 2 1 201000 f 74 goat snp24316-scaffold247-5605641 11 43127401 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452863 Affx-122920712 AX-123323196 11 43005892 TAACTATGGTGATGACCTCTCTCCATTCTTCTTCT[C/T]GTCTCTATTCTACTGAGAATGACTTCTTTCCAGTT Y 2 1 2 1 101000 r 74 goat snp24317-scaffold247-5652759 11 43172491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404698 Affx-122957267 AX-123275050 11 43065921 TGATTAAAAATTTAGGAGTCAGTCCCAGCTTTGCA[G/T]AATATTGGTTAAAGAAAAGGACAGTGATCTACTTG K 2 1 2 1 201000 r 74 goat snp24318-scaffold247-5712788 11 43233880 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783124 Affx-122955190 AX-385270191 11 43135579 GATAATCTGAAAGTTAGTTCTAGTCAAGTGATGTC[A/G]TAATCTTACCATTTCCTAATGTTCTCACATCTACA R 2 1 2 1 101000 f 74 goat snp24319-scaffold247-5782446 11 43292885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778380 Affx-122964307 AX-385265495 11 43215980 AACAGAGAATATTGATTTGTTAATTTTCAAAGATG[A/G]GAAAACAGTATTACTGTTTTGTATGAAGTATCTTT R 2 1 2 1 201000 f 74 goat snp24321-scaffold247-5862847 11 43373228 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418993 Affx-122946059 AX-123289341 11 43265284 TTTTTATATATGAGAGTCAGAGGGTGTGTTTGGGC[A/G]TGTGTAAGGGTTAAACCTTGTCAGGCCAGTCGCCA R 2 1 2 1 201000 r 74 goat snp24322-scaffold247-5912151 11 43423326 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801996 Affx-122966643 AX-385288900 11 43363036 AAAAAGTAATAGGTTTTCAAAGGTTAGTTTGCAAC[A/G]GATGTCAAATGAAAAAAACACACAATGTGAGAGTT R 2 1 2 1 201000 r 74 goat snp24324-scaffold247-6009903 11 43521357 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785523 Affx-122963122 AX-385272567 11 43438358 GTTTTCACTTTGTTATCCTTTCAGAACTTTTCTCT[A/G]CTTAAAAAGTATGTACACGTGTCTATACACAGCTT R 2 1 2 1 101000 f 74 goat snp24326-scaffold247-6085225 11 43596318 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439176 Affx-122931056 AX-123309513 11 43513225 AGTGACTGCAGAAGTGATCACAGCAAATACATAAG[C/T]GGCCTGGGAAAAGGAATCCTGGGGAAGGTTATGGA Y 2 1 2 1 101000 f 74 goat snp24328-scaffold247-6160092 11 43672285 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452003 Affx-122920920 AX-123322336 11 43545182 ATCAGTCAGTGAATGTGGGATGAATGGATGAATAG[C/T]ACTAGGTGGATCTCCTGCCTATACTTGATGATTCG Y 2 1 2 1 101000 r 74 goat snp24329-scaffold247-6192049 11 43704140 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446237 Affx-122925695 AX-123316573 11 43623546 AGGAAATAATATTATAGCAAGAGGGCTAGGAAGAG[C/T]AGGGTTACCTTAACTTAGTAAATGCCACTTAAATG Y 2 1 2 1 101000 r 74 goat snp24330-scaffold247-6270413 11 43780904 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416420 Affx-122947841 AX-123286769 11 43653011 CCTGGGCCAGCACACAGCAGGAACAGTCAGTGCTA[A/G]CACAATACAAGAAAGGGCTGAGGGCAGGGACCACC R 2 1 2 1 101000 f 74 goat snp24331-scaffold247-6299878 11 43811717 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383800 Affx-122973189 AX-123254158 11 43687025 CACCAGATCATGGAACAAAGAATGTCACAGAGATT[A/G]CATTGAAGACTGCAGTCCCACTAAATGGGACTGAG R 2 1 2 1 101000 f 74 goat snp24332-scaffold247-6333892 11 43845852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412106 Affx-122951114 AX-123282456 11 43726708 TACCACCTATGTTCAGAGGACCCCAGAACAGATTG[C/T]GTGCCACATCTGTTGTGTTGCTCACACTCCCCAAG Y 2 1 2 1 101000 r 74 goat snp24333-scaffold247-6373575 11 43886691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376877 Affx-122977824 AX-123247236 11 43760279 CTGAGCATCCAGCCCACCTTGTGGCAGCTCAGATT[C/T]TCCTGGGCCTCACAAGGCAGTCCTTGGGTTTCTTT Y 2 1 2 1 102000 r 74 goat snp24334-scaffold247-6407146 11 43920619 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375806 Affx-122978564 AX-123246165 11 43806340 TTTCACAGAACTAAACCACTGGAGAAGAAAAGAAC[A/G]CTTCCCAGGAGAGGTGGGGCTCACTTCACAGCTGG R 2 1 2 1 101000 f 74 goat snp24335-scaffold247-6453207 11 43966900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451366 Affx-122921245 AX-123321699 11 43844943 ACCTCAGATGAAGTCCCCATATCACCTCCTACTGC[A/G]TCCTGAACACTCTTTCTTGACAAACAACCTTCTGC R 2 1 2 1 101000 r 74 goat snp24336-scaffold247-6491810 11 44005261 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377926 Affx-122977224 AX-123248285 11 43873649 ACATCTGACCGGAGGCCACTGCAGATTCACTCATT[A/C]GGCAGATCCAGCCTTGCTGTAGCTCTCAAGAGCCA M 2 1 2 1 101000 f 74 goat snp24337-scaffold247-6520516 11 44033777 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765443 Affx-986697408 AX-385252944 11 43893326 TTTGAGAGTCTGCCTGATCAGCTGGTCAACAGGTC[G/T]ATCCAGCAAGGCTTCTGCTTTAATATTCTCTGTGT K 2 1 2 1 600010 r 74 goat 11_43893326 11 43893326 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 320803750 Affx-986696210 AX-385290507 11 43893896 CACATGTTAGACTTAAAGCACAGACGTATGAACTC[C/T]AGGAAAGTAATGTTCGACTGAAACTAACCATTGTG Y 2 1 2 1 600010 r 74 goat 11_43893896 11 43893896 Ancestral_priority_1043 ancestry 0.698 recommended IMAGE 10K 10K ancestral 320762881 Affx-986697410 AX-385250899 11 43902378 TTTGTACAAACATGGAGGATCTTCGAGACCAGACC[C/T]ACACAAGGCATTATGAGCTGTACCGGCGCCACAAG Y 2 1 2 1 600010 f 74 goat 11_43902378 11 43902378 Ancestral_priority_1043 ancestry 0.672 recommended IMAGE 10K 10K ancestral 38391334 Affx-122967310 AX-123261691 11 43905682 TACCATCCACCAGCATGGTGCAGAACTAATAACCC[A/G]TAAAACTAAGCCCCTATAAACAGTCCTCTCCGCTG R 2 1 2 1 201000 r 74 goat snp24338-scaffold247-6552549 11 44065319 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765450 Affx-986697412 AX-385252951 11 43921879 TTACTGCCATTTATGGGAAAATACTTTTAAGTATG[A/T]GGTCAATATATAAGCCAGACTGGATGGTATTACTT W 4 1 2 1 600010 r 74 goat 11_43921879 11 43921879 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 320762885 Affx-986697414 AX-385250902 11 43922107 ATGAATCTTTTGTGTACATACCAAAGGTATGTAAA[A/G]GTAATCTTTGGGGAATATGTTTTAAAATGTATTAT R 2 1 2 1 600010 f 74 goat 11_43922107 11 43922107 Ancestral_priority_1043 ancestry 0.776 recommended IMAGE 10K 10K ancestral 320762887 Affx-986697416 AX-385250903 11 43922156 AATATGTTTTAAAATGTATTATGTACCTGAAACTC[C/T]AGCAGCTCAAAACTTTTAAAGTTTTGATACAATTA Y 2 1 2 1 600010 f 74 goat 11_43922156 11 43922156 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320765465 Affx-986697420 AX-385252963 11 43922173 ATTATGTACCTGAAACTCCAGCAGCTCAAAACTTT[C/T]AAAGTTTTGATACAATTATCCAGTTGGAAACATGA Y 2 1 2 1 600010 r 74 goat 11_43922173 11 43922173 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320765469 Affx-986697422 AX-385252966 11 43922373 GTGTCCTCACACTGTGTGCATCAGTCTCTATTACA[G/T]AATTGTTTAAAACTGTCTTCCAGGGTAAATAAAGT K 2 1 2 1 600010 r 74 goat 11_43922373 11 43922373 Ancestral_priority_1043 ancestry 0.722 recommended IMAGE 10K 10K ancestral 38380740 Affx-122975135 AX-123251098 11 43944707 CCTGTTCACCTGGTAGTCACTGAACCCTGAGCCCA[C/T]TGCTTCCCCTGAACTGAGGAAAAGATCGTATGTCT Y 2 1 2 1 101000 r 74 goat snp24339-scaffold247-6591574 11 44081881 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438859 Affx-122930759 AX-123309196 11 43973961 CAGCATTCTGACACAGGATCGTATCTGCTCATCCC[A/G]TAATCTGACAGATTAAAGAGAAAAGCCAATTTGAT R 2 1 2 1 101000 f 74 goat snp24340-scaffold247-6620828 11 44111152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447300 Affx-122924918 AX-123317636 11 44016426 CTGCATTTCTATCCATGCTCCTGCCACATTTCTCT[A/G]AGAATAAAGCAGGAAATTGTGTGATTTAAAAACAA R 2 1 2 1 201000 r 74 goat snp24341-scaffold247-6663293 11 44152980 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794988 Affx-122974331 AX-385281947 11 44092335 TGAGACATTACATATATATTTCCTTGACCCACCGA[C/T]AGCACACCTAGGATTTTAAGATTAACCTATATAAA Y 2 1 2 1 101000 f 74 goat snp24342-scaffold247-6739202 11 44228006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404606 Affx-122957343 AX-123274958 11 44128229 CACCAGCTTCGAGTGATCCCTCACGACTGAGTGCT[A/C]GCAGCCTTAAGCTGGACCCAGTGCTGGGCTGAGTT M 2 1 2 1 101000 f 74 goat snp24343-scaffold247-6775096 11 44264079 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423003 Affx-122942982 AX-123293349 11 44221135 AACCGTGAGAAGACAGATTTTTCTTTATAAAATGC[C/T]AACTCCTTAAGCAACATATCAGACAGTAGGTTCCC Y 2 1 2 1 101000 r 74 goat snp24344-scaffold247-6868002 11 44357430 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385997 Affx-122971512 AX-123256355 11 44250651 GTGAGGCATGGGTGGGGGTGGGGGGCCCACGGCAC[C/T]GATCTCTCACCATCGTGTTCCAAAGATGTGAGGAA Y 2 1 2 1 101000 r 74 goat snp24345-scaffold247-6897518 11 44386970 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390584 Affx-122967194 AX-123260941 11 44287184 TATGTCCAGTGTGACTCTCCCTTAATCTCTCTGGC[C/T]GTTTCCCGGACGTAAACTCCATGCTCCAGATCTTA Y 2 1 2 1 101000 r 74 goat snp24346-scaffold247-6934051 11 44423752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440100 Affx-122929713 AX-123310437 11 44324702 AAACGTACGAAGCAGGCTTTGAACTAGGATCACAC[A/G]TGCGAGAGATGCTACTAATGGGAAACTTGTATTTA R 2 1 2 1 101000 f 74 goat snp24347-scaffold247-6971569 11 44461295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276641 Affx-1111835446 AX-519550151 11 44342619 CAAAAGGAAAACGTCTTCTGGCAGTGAGCAGAGCC[A/G]GGCTAGTCTCTGGTTGTTTTTCTGCCCGAATCCAT R 2 1 2 1 201000 r 74 goat Random2.2K-1165 11 44342619 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443574 Affx-122927336 AX-123313911 11 44354540 AACTGAAGGAAGATTCATAAGTCCATCCTCTCTGC[A/G]TTTTTATTACTCACAGTTGGCGTCTCCAGGTGAGC R 2 1 2 1 101000 f 74 goat snp24348-scaffold247-7001407 11 44491053 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799713 Affx-122971568 AX-385286641 11 44463249 CAGTTTATCTTTCTACTATTACAAAATGAATGGAA[C/T]GGGAGAAAATTTCACTATTCGTATTTATTCTTTTT Y 2 1 2 1 201000 r 74 goat snp24350-scaffold247-7110116 11 44600140 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765076 Affx-122930144 AX-385252640 11 44508018 AAGTTAATGATCAACTCAAGAAAGCACTTCAGAAA[C/T]GCAAATTCTCCCCCGCCCTAATTTCTGCATCAGAA Y 2 1 2 1 201000 f 74 goat snp24351-scaffold247-7154885 11 44644683 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428575 Affx-122938714 AX-123298917 11 44558015 CCTAACCACTGGACTGCCAGGGAAATCCCTATTGT[C/T]ATCTTTTAAGGTTTTGTTTTTCCACCTCAGAGATT Y 2 1 2 1 201000 r 74 goat snp24352-scaffold247-7204882 11 44694672 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422542 Affx-122943268 AX-123292888 11 44624054 AGTTCCTTTGTTACTGAAAATCAGGCCCAATTGCT[A/C]GTTGCTCAAAAGACAATACTCAAGAGGCAAGGGTG M 2 1 2 1 101000 f 74 goat snp24354-scaffold247-7270921 11 44761138 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274905 Affx-1111834567 AX-514643492 11 44642369 TATAGTGGGAGCATCTGCAGGGTTGTTCCTCCTTG[A/G]AAATACTCAAGGCTGATTGTTTCCC R 2 1 2 1 102000 f 74 goat GoatD01.041803 11 44642369 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320774508 Affx-122928339 AX-385261642 11 44659908 GCTTCCAAAATTTGCTATTTGTTGGAACACTCCTC[A/G]TAAGAATTGTACAAAGTATTTTGTTGCTATGGCTT R 2 1 2 1 101000 f 74 goat snp24355-scaffold247-7306775 11 44796747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785069 Affx-122951389 AX-385272116 11 44693432 AAAGGCCTTTTAGACTCTTTCCTTAAAAGGCCAAA[C/T]GCCTGGAGAAACTGTGCATATGCTGTGCTCCATGC Y 2 1 2 1 202000 r 74 goat snp24356-scaffold247-7340299 11 44830203 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389386 Affx-122968391 AX-123259744 11 44726809 TGCACTCTATCAGCCAAAACTGGGACAAAGGAAGC[A/G]TTCAGAAAGCAGGGACTATGATGAATTGAGACCCT R 2 1 2 1 101000 r 74 goat snp24357-scaffold247-7373676 11 44863506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433208 Affx-122935630 AX-123303549 11 44763884 CATCTTAGCTTCTCTTTAATATTCTTAAGCTGCAA[A/C]TTCAGTTTTCTTTTCTTCCAGTCAAGGTGGCATCC M 2 1 2 1 101000 r 74 goat snp24358-scaffold247-7410751 11 44901719 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800109 Affx-122946143 AX-385287032 11 44798904 AGGGGACCCTAGTATTGAGCAAAAAATTATTTTCT[A/G]TGCAAACAATCAACCTCTAGTTTATTTCGCTCATT R 2 1 2 1 101000 f 74 goat snp24359-scaffold247-7445771 11 44937489 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392573 Affx-122966074 AX-123262930 11 44847606 CGAGTTGATGTCCAACGACACTCAACTCGTTCTTC[A/G]TATTAATAATCAAAAGGAATGCTGATATACCCAGA R 2 1 2 1 201000 r 74 goat snp24360-scaffold247-7494473 11 44986665 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426490 Affx-122940225 AX-123296836 11 44896274 CCATGGGCCTGGCCAGGGCCAGTTCTATTTCATCT[A/G]CTTCGGGAAATATCCCCTAACTAACTTGTCAAGCA R 2 1 2 1 101000 r 74 goat snp24361-scaffold247-7543141 11 45035846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276643 Affx-1111835447 AX-519550153 11 44937842 GATCATGGACTGCCCCACAACTGCATGTGTTACAC[A/G]AGCTGCAGTAACTCCCAGTACTCTCACTGCATCCC R 2 1 2 1 101000 r 74 goat Random2.2K-1166 11 44937842 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38375884 Affx-122978497 AX-123246243 11 44965580 TCAAAGAACGCTATAAAGTAGGAATTATCACTTCT[A/G]TTTTACACTCAAGGCAACAGTGATGCAAGATAGCT R 2 1 2 1 101000 f 74 goat snp24362-scaffold247-7612447 11 45106360 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449646 Affx-122922585 AX-123319981 11 45024662 GTGTTTTTGTTCTGGAGGACTTAAAAAAAACAAAA[C/T]GTACAACATCTAGATGCTAGGAAAGTCCTAGTCAT Y 2 1 2 1 101000 r 74 goat snp24363-scaffold247-7671529 11 45165308 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400007 Affx-122960803 AX-123270362 11 45053374 AGCATAAATTACCCGCTCAGCTCACCTCTAGCATC[C/T]GAGTCAAACGGGCTTGGGAAAGATGAAATAGAAGC Y 2 1 2 1 201000 r 74 goat snp24364-scaffold247-7700241 11 45194014 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425756 Affx-122940735 AX-123296102 11 45090144 TGTTCAAATATGCAGGCAATTCATCTGAAATCTTA[C/T]TTTTGTAAAACAGACGTTAATTTTAAAATGTACCT Y 2 1 2 1 201000 r 74 goat snp24365-scaffold247-7737011 11 45230633 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377149 Affx-122978223 AX-123247508 11 45141794 TTTTTGTTACCCCAAAGAAGTGTTGCCAGATGAAA[C/T]ACAGATCACTCAGTTCAATTGAAATTTCAGGTAAA Y 2 1 2 1 201000 r 74 goat snp24366-scaffold247-7788661 11 45283998 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408070 Affx-122954262 AX-123278421 11 45170607 AAAGTGTTGGAGCTGAAGGTGGAGCTTTGTGAAAA[A/C]TAAAAGAAACTCCTCAACAATGAGATCTGATGGCT M 2 1 2 1 201000 f 74 goat snp24367-scaffold247-7817474 11 45312852 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410905 Affx-122952066 AX-123281255 11 45202677 ATTCCTTTTTGAGGTCGAGGGCACAGACATTAAAG[C/T]GTTACCTCCACCAGGGGAGTCATGTGGGATACAGA Y 2 1 2 1 201000 f 74 goat snp24368-scaffold247-7849544 11 45345036 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393943 Affx-122965068 AX-123264298 11 45238381 ACTAAATCCCAAAATTGTTTTAGGTCCCTATACTG[C/T]AAACATAGTTTTAAAAATGCTAGACTGTGAATCTA Y 2 1 2 1 101000 f 74 goat snp24369-scaffold247-7885248 11 45380415 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377944 Affx-122977210 AX-123248303 11 45271220 AAAGGGTGAACAAGTCCTAAAATGATAAATATCAG[A/C]GGTGCCATGGTGCCAATTACTGCCCACTGAACTAT M 2 1 2 1 201000 f 74 goat snp24370-scaffold247-7918087 11 45413623 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409139 Affx-122953296 AX-123279490 11 45338588 TCTAGATGAAATCTCCCCACTCTGCATCAGAGGGT[A/G]GACCTGAAGTGATGCCAGCTTCTGGCCGGATGTGG R 2 1 2 1 202000 r 74 goat snp24372-scaffold247-7985455 11 45481259 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395185 Affx-122964514 AX-123265540 11 45368128 AACCACTTGACCACCAATTCACGCTCCACTATAAA[C/T]GCCCACTTGTAAATTTCCCAAGTCAGACCCTCAAC Y 2 1 2 1 201000 f 74 goat snp24373-scaffold247-8014995 11 45510753 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431413 Affx-122936530 AX-123301754 11 45417846 GGGGAAGGGCAGTGATGTAGAAACCAGAGGAAGGG[C/T]GCCACCCACCTGCCTCCTCCATCACCACAGGCAGA Y 2 1 2 1 101000 f 74 goat snp24374-scaffold247-8064713 11 45559019 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276645 Affx-1111835448 AX-519550155 11 45461676 TGGCAGGCCTAACCATACAGAAGGGAGAGCTGGTG[A/G]CCATCTGGTAAGAATTTGATTAGCATCCCTCAGAG R 2 1 2 1 101000 r 74 goat Random2.2K-1167 11 45461676 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439536 Affx-122930112 AX-123309873 11 45479354 CTTTGTTTTTTAGGTGTTGGATAGCATCATACAAA[C/T]TGACAGCTTTTATTAAAGGATTGTCTTCCCACTGC Y 2 1 2 1 101000 r 74 goat snp24375-scaffold247-8126221 11 45620677 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397080 Affx-122962717 AX-123267435 11 45516320 AAGACACACAGCAATCAAAGGCCCAATAGCAAACG[C/T]GTTATACATTCAAAATATTTCAATAAAAATTGCAT Y 2 1 2 1 101000 f 74 goat snp24376-scaffold247-8163187 11 45658214 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407517 Affx-122954735 AX-123277868 11 45548794 CAAGTCTGTCCTCAAACAGCGCTCCCCCTCACTCG[C/T]TGTGCCCCCACCTCACTCAAACATGTTTTCTGGCT Y 2 1 2 1 103000 r 74 goat snp24377-scaffold247-8195661 11 45690470 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779073 Affx-122937874 AX-385266178 11 45590532 TGTTACCCTGATTAGGTGAAACTGCGTTGCCTGAT[G/T]ACTTACGAGCATATAGTAGCAAGCAGCGTATTTCT K 2 1 2 1 101000 f 74 goat snp24378-scaffold247-8237399 11 45733494 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383900 Affx-122973113 AX-123254258 11 45624309 ATAATCTGGCTGTGTGAGCACATGGTCATTAACGT[C/T]ATGAGCTGTTTTTGCTTTTGGGGGTCATCTCAGAG Y 2 1 2 1 201000 f 74 goat snp24379-scaffold247-8271176 11 45767259 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792745 Affx-122951448 AX-385279725 11 45665183 AAGAGGGCAGTGTCCTACCTCCAGTAGAGGAGACC[A/G]TTTTCAGAAATAGGTGTGGTCAGAGGGCAGAGAGA R 2 1 2 1 303000 f 74 goat snp24380-scaffold247-8312050 11 45807934 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790182 Affx-122951709 AX-385277186 11 45701476 AACTGAAAGGAAATTAGGCTTCTAAAAGTAAGATC[A/G]CTAAGCAGTTTAATTAACCTGGCTCGTTTCCAGCT R 2 1 2 1 101000 r 74 goat snp24381-scaffold247-8348343 11 45834774 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388843 Affx-122968883 AX-123259201 11 45750695 TTGTATTCAAGTGTTTTTGTCCCCTTTGGTTCTCT[C/T]ATCTTACTGTGGGTGTTGACTGTCCTCCGATATGC Y 2 1 2 1 101000 r 74 goat snp24382-scaffold247-8397562 11 45884051 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427522 Affx-122939518 AX-123297865 11 45785830 GGACTGTTCTCCCTCATTGATCCTGCTCCAGCATC[G/T]GCCTCAAGATGTGAGTAGCTGGGTCGCCTGCCCCT K 2 1 2 1 101000 f 74 goat snp24383-scaffold247-8432697 11 45919389 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392063 Affx-122966388 AX-123262420 11 45829634 GCAGAGGAAAAGTGCAGTCAGGACCAGCTCTCAGA[C/T]CCTGGTTATGTTTTTTCTATAGGACTTCCCTGGTG Y 2 1 2 1 101000 r 74 goat snp24384-scaffold247-8476501 11 45963656 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377588 Affx-122978315 AX-123247947 11 45864179 TTAACTACTCTTGGGGTGGGGCCCACATCATTGAA[C/T]GGCTCAGGGATGCTTAGGTTTTACTGGCTCTTATT Y 2 1 2 1 201000 f 74 goat snp24385-scaffold247-8511046 11 45998579 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405952 Affx-122955549 AX-123276304 11 45902273 GGGAGAGAGAACCAATTCACTTCTAGTGCAATGAC[A/G]TGCCAGATAGTACAGTGGGGTTCAGAGCAGGGAGA R 2 1 2 1 101000 f 74 goat snp24386-scaffold247-8549140 11 46037104 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796838 Affx-122934251 AX-385283781 11 45992699 CTAGAAGTCACATGACTTAATCATATGGCCACCAA[A/G]TAAGCCTGTGAGCACATATGCTAAGCTCAAGCACT R 2 1 2 1 101000 f 74 goat snp24388-scaffold247-8639566 11 46126977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381744 Affx-122974323 AX-123252102 11 46054705 CCAGGGTAGCCCTGGAAGAATGAATGAATAAATAA[G/T]CAGGTCAAAACTGGTGCATGGAGTCTAGGAAGGAT K 2 1 2 1 201000 r 74 goat snp24390-scaffold247-8701572 11 46188490 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411149 Affx-122951882 AX-123281499 11 46088893 TTTAGGAAGCTTTCACAAAAGTAGCTTCAGTGGAA[C/T]GGTGGAACCAGGAGTCAGTTGGATGAAATGGATTA Y 2 1 2 1 102000 f 74 goat snp24391-scaffold247-8735760 11 46222800 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394090 Affx-122964954 AX-123264445 11 46119793 TAAGCATTTTAATTCTCTCAAGACCCCAAGTAGGC[A/G]CTGTTACTACCACTTCCCCTCATTTCACATATGAG R 2 1 2 1 101000 r 74 goat snp24392-scaffold247-8766660 11 46253693 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796376 Affx-122939277 AX-385283326 11 46160502 TTGGGAATCACTTTTTGATACTCATGATGAATTTG[C/T]AGAGGTTGCTTACCTTCCAGGTCTGGCAAAGATTC Y 2 1 2 1 101000 r 74 goat snp24393-scaffold247-8807369 11 46293180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452270 Affx-122920760 AX-123322603 11 46197433 CTGCAACGGTCCATCCCTCAAGCCATCTGTACAAA[C/T]GTATCAGGACCCTAAAACAGTAGGACTCTCTCCTG Y 2 1 2 1 101000 r 74 goat snp24394-scaffold247-8844300 11 46330381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405406 Affx-122956287 AX-123275758 11 46253888 AAACACATGCAGAGAGATTCTAGAGTGAAGTAGCC[G/T]CTTAGAAAAAATAATCCACAAATGTCAGTTTCTCA K 2 1 2 1 101000 f 74 goat snp24395-scaffold247-8900755 11 46387271 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762866 Affx-986697395 AX-385250887 11 46254305 CGAGTTCACAGGCAGGGTAGGGGGCCAGGACCATC[A/G]ACCAAGGGCTAGATGGCTCAGATGGTAAAGAGTCT R 2 1 2 1 600010 f 74 goat 11_46254305 11 46254305 Ancestral_priority_1043 ancestry 0.414 neutral IMAGE 10K 10K ancestral 38452202 Affx-122920816 AX-123322535 11 46287896 CAGACTCACCATGGTTCCTTTTCAGCCTCCCTGTA[C/T]ATGTTTACCCTCCCACACTGATCATTAGAACCACT Y 2 1 2 1 201000 r 74 goat snp24396-scaffold247-8934763 11 46421290 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320780672 Affx-122946939 AX-385267762 11 46347827 CTACAAGGTCTGGACAACAGTGCTGACTGTATTGT[A/G]TATGCACTGTAACTCAGGCATTCAAGAATTAGCTG R 2 1 2 1 101000 f 74 goat snp24397-scaffold247-8994694 11 46482134 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433878 Affx-122934417 AX-123304219 11 46396786 CCTGGAGGCCCAAGTTTTAATTGAGATCCTCAGCC[A/G]TCACTGTATATGGCAGCAGAGCCCATCCCCAGCCT R 2 1 2 1 101000 f 74 goat snp24398-scaffold247-9043653 11 46531147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272624 Affx-1111832923 AX-519546335 11 46432132 GAACAGTGATACACATTTTTGAGATAGAGGGTTAC[A/G]CATCAGATGATATGCTGACAGTTTATACAATCCAG R 2 1 2 1 101000 f 74 goat 11_46432132_AF-PAKI 11 46432132 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449700 Affx-122922543 AX-123320035 11 46450927 CTGACCTGGAAAGGAGATGTGGGTTGACAGGCAGT[A/G]TTTACACAAGCCTGTGAACCACTGACATCTATCCA R 2 1 2 1 102000 r 74 goat snp24399-scaffold247-9097794 11 46585497 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782224 Affx-122950576 AX-385269302 11 46487183 TTGATGCTAGGCTAGAGACCACACTTGAGAAATAT[G/T]TGTAGAAAGCAAGTTTTCAAAAAGGTTCTTTCATT K 2 1 2 1 201000 r 74 goat snp24400-scaffold247-9134050 11 46621877 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399503 Affx-122961169 AX-123269858 11 46525359 GGGCCTTGGTCATATGCTCTTAACTCACTCTCTCC[C/T]CTGGCCTTTACCCAACCTTCATGCTTCAGTACCCT Y 2 1 2 1 101000 f 74 goat snp24401-scaffold247-9172226 11 46659915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411295 Affx-122952296 AX-123281645 11 46582982 CTACTGATTGAACGTGAGGACAAGTAGATGAATCT[A/G]ACTCTGCCTGTCTGTCCACTCTTCCCCAGAGTTTG R 2 1 2 1 101000 f 74 goat snp24402-scaffold247-9229849 11 46718098 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791929 Affx-122923008 AX-385278919 11 46622067 TACGCAATATTTTAGACATTGTTAAATTTCCCTCC[A/G]TAGGGTTGCACCCATTTTTTAATTACTTCTCAAAA R 2 1 2 1 101000 r 74 goat snp24403-scaffold247-9268934 11 46757166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394405 Affx-122964613 AX-123264760 11 46653291 CTTGGTACATGAGTAAATGTGTGAAGCCTTCCTAA[G/T]GCCTAAGCTCTGGACTTTTCTGATCACTTGAACTT K 2 1 2 1 101000 f 74 goat snp24404-scaffold247-9300158 11 46788523 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770736 Affx-122932839 AX-385257900 11 46721208 ATATTCAGAAGCACAATCAAATGTATTCTGGGGCC[A/G]TTATAGGTGGCAATTTTCTGAGATATGATATATAT R 2 1 2 1 101000 f 74 goat snp52890-scaffold793-1539305 11 46855539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765427 Affx-986697399 AX-385252931 11 46833556 ACCCCCTGAGCACTTGTGGCCTGGAGCCTGATTCC[A/T]TAAGAACTGGACTTAAATAAAAGCCCAGCAAGGTG W 4 1 2 1 600010 r 74 goat 11_46833556 11 46833556 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 38383691 Affx-122972492 AX-123254049 11 46849034 GTAGTGTGATGCCTGGTTCTCCTCCTTTGTACTCA[C/T]GGAATGGTTTCCTATATGGCCACCAGATGAAGACT Y 2 1 2 1 101000 r 74 goat snp52887-scaffold793-1411479 11 46983585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386966 Affx-122969970 AX-123257324 11 46901279 CTCAGAGCTCAGACACAGAGCAGCAATAGTAGTTT[A/C]GGCTCTGCCATCTGAGCAAAGACCAGCAGGAAAAG M 2 1 2 1 201000 f 74 goat snp52886-scaffold793-1359234 11 47036242 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789363 Affx-122950677 AX-385276373 11 46949473 TGATTACTATGCTAATGGATAATGTGATTTTCTAG[C/T]AAAGGGACAGTTTATGCAGCACTTTCCAGGCCTAT Y 2 1 2 1 101000 r 74 goat snp52885-scaffold793-1311040 11 47084501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799299 Affx-122962240 AX-385286230 11 46979012 ACTTTTGCTAATTGAGTTTTGGTGATGCCCACATC[G/T]ACCTGAAAATGGTATTAAAATGTTCCTCCCTTCCC K 2 1 2 1 101000 r 74 goat snp52884-scaffold793-1281501 11 47114000 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274373 Affx-1111834217 AX-519547968 11 46982284 AGTCAGGTGAGTGTTTCTGTCTTCCTCTAAGTGCT[A/G]TTCTTGGGCCCCGTCACCCAACTCTGGGGGTTACC R 2 1 2 1 102000 f 74 goat GoatD01.025935 11 46982284 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427394 Affx-122940078 AX-123297737 11 47038137 TGTCAATGGTAATGTTATCCACAGAGACTTGATGG[C/T]GGTTGGATGGAGTAGTGATAGTGGAGGTGTGAAGC Y 2 1 2 1 101000 f 74 goat snp52883-scaffold793-1222376 11 47173687 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772380 Affx-122932815 AX-385259532 11 47095867 ATTATTCCTAATCTAGGTCTCTATTAATAGAAATA[A/G]TCAGATGCCAAGAAGGAGGTTACCATAAGCATTTC R 2 1 2 1 101000 r 74 goat snp52882-scaffold793-1164646 11 47231571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445625 Affx-122925095 AX-123315962 11 47165682 TTTCAAATCTCCTTGCCAGAATCCTGGGTGAGCCA[A/G]CCCTTTAGATGAGATCTTCAATAAGGACCAAACCC R 2 1 2 1 201000 r 74 goat snp52881-scaffold793-1094831 11 47301629 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420633 Affx-122945225 AX-123290980 11 47199920 ATTCCGCTAAGACCCAGCATGCCTTGAGCCACATC[C/T]AAAGAAAGCCTGTGTGAAGACATAGTGCAGCCAAA Y 2 1 2 1 101000 r 74 goat snp52880-scaffold793-1060593 11 47335870 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433010 Affx-122935789 AX-123303351 11 47274056 GTTGCAAAGAGTCAGACACAACTGAAGTGACTTAG[C/T]GTGCATGCATATAGGTTTTTAAAATGTGGTTATTT Y 2 1 2 1 303000 r 74 goat snp52878-scaffold793-986457 11 47410272 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780445 Affx-122931110 AX-385267536 11 47329475 AAATGCAAGCTGATATAAAGCAATCATGGTCCTCC[A/G]TTCCCCATGCCAATTTCACAAAGACCTAGTTACCT R 2 1 2 1 201000 f 74 goat snp52877-scaffold793-931038 11 47465618 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380858 Affx-122975439 AX-123251216 11 47408307 GAGGAAACATAAACAAGGCACAGCGTGACAATAAA[C/T]GCAGTGGTAAGCTCTATGGAGAGAGGGTATGTGTC Y 2 1 2 1 101000 f 74 goat snp52875-scaffold793-852206 11 47544731 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450238 Affx-122922263 AX-123320573 11 47446898 GTTGACTTGCAAGTTGAATTGTGTCTTTGTTAGAA[C/T]AGACTGGGCTTAGCATTCAGAGCAGCTCTTCAGGC Y 2 1 2 1 101000 f 74 goat snp52874-scaffold793-813615 11 47583298 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414840 Affx-122949190 AX-123285189 11 47492365 ATATTCTCTCATATGCCCTGAGGCTGGGACTCCCT[A/G]CTTCCCTTCAAGATCTGTGGTAAATGCAGTTTCTC R 2 1 2 1 101000 r 74 goat snp52873-scaffold793-768148 11 47624139 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440604 Affx-122929980 AX-123310941 11 47524772 AGAATTACTGGCAGAACACCTGGCTGCTCTGGTCA[A/G]CCTACAAGAGGACCAGTCGCCATCTCCAGACAGTG R 2 1 2 1 201000 r 74 goat snp52872-scaffold793-735741 11 47657520 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417875 Affx-122946762 AX-123288223 11 47614584 AGAGAAGCCAGAAAAAGCTCCGCTTTGTCCCTCTC[A/G]CAGTGTTGGCAGCCCTATTGACAGTTTTCTGTGCA R 2 1 2 1 101000 r 74 goat snp52870-scaffold793-645929 11 47747621 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771885 Affx-122967577 AX-385259041 11 47644946 CAAGACTAGCAAATAAGTTCTAGAACTTGAATGTC[A/G]TACAGATGTCTTGAGTGTAAGGGTTTTTGATTTTT R 2 1 2 1 101000 f 74 goat snp52869-scaffold793-615567 11 47778121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404009 Affx-122957191 AX-123274361 11 47679544 AGGAAGAAGGTAACAAAGATCTCTGCCCTTACAAG[C/T]ACTATTTTTCTTTCCCTGGTTAAATTTGCATTCTC Y 2 1 2 1 101000 f 74 goat snp52868-scaffold793-580969 11 47812787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411108 Affx-122951912 AX-123281458 11 47722010 GATTGCACGAGTAATTCGTGATGTTCAGAGAAAAA[C/T]AAGAAAACATGACCAAGCAAGAAGGGACTATCATA Y 2 1 2 1 201000 f 74 goat snp52867-scaffold793-538503 11 47855052 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414821 Affx-122949204 AX-123285170 11 47775876 TCAAAGTAATCGATTAGTAAACCATGTCCAAGGTA[C/T]GTACTAAGAAACAAGGCTGGGTGTGAGGAATAAAA Y 2 1 2 1 101000 f 74 goat snp52866-scaffold793-484637 11 47909863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380926 Affx-122975016 AX-123251284 11 47838225 ACCCTTCCCAGGTCTAAGCCACAGGAAACACCACA[C/T]GCTGTCTGCCCTCTCTGGAGGAAGCAAAAAGCCAA Y 2 1 2 1 201000 r 74 goat snp52865-scaffold793-422288 11 47972211 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421576 Affx-122944509 AX-123291923 11 47870096 TCTTACTGTTTATACTCTCCTCCGCCCCCCGCCCC[C/T]CTCAATAAAGATGAACAGAGTCAGAGTAGAAGATA Y 2 1 2 1 201000 r 74 goat snp52864-scaffold793-390417 11 48004095 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411659 Affx-122951563 AX-123282009 11 47993936 AACACCTGCTCCTCAGAATAAATGCTTCAAGACAG[C/T]GCATTCTCCCAAGAAGCACAGAGGACGCTCTGTGT Y 2 1 2 1 101000 f 74 goat snp52862-scaffold793-266577 11 48128214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415492 Affx-122948698 AX-123285841 11 48033734 TTAGAGGAAAACAGAATTTATATAATTTTTCAATT[A/G]CATCTGTTCTGCTTCATGGTACAATGTCATTTATT R 2 1 2 1 103000 r 74 goat snp52861-scaffold793-226779 11 48168500 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433714 Affx-122934527 AX-123304055 11 48087549 CCTTGACCCAACTCAGTGTCCACACACTCTATTCT[A/G]CCATCCACCGGAAGCCCATGGAGCACCAAGATCAG R 2 1 2 1 101000 f 74 goat snp52860-scaffold793-172964 11 48222159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406836 Affx-122955672 AX-123277187 11 48117885 AAGGGCCACTAGGAGTGATGGATCAAGGGAAGTCC[A/G]GAGATCCAGGCAGGAATGGAAAACAAGGTTTCAAC R 2 1 2 1 101000 f 74 goat snp52859-scaffold793-142628 11 48252282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391274 Affx-122967357 AX-123261631 11 48150717 GATGACTCTAGCCCTAGCCACTCACTGCCTGACTA[C/T]AGCCTCACAAGGGATGCTGACCAAACTGGCCACCT Y 2 1 2 1 201000 r 74 goat snp52858-scaffold793-109796 11 48285122 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448227 Affx-122924219 AX-123318563 11 48182564 TTTCTATATACACAACAAACCAGAAATGGTACTTT[C/T]TGAAACGGAATAAGCTACTCAGTTTTCATCTTTTT Y 2 1 2 1 101000 f 74 goat snp52857-scaffold793-77949 11 48316964 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409802 Affx-122952966 AX-123280153 11 48218108 GGACATTTTGGAAAAGAAAAGCTATTTGACTAGAA[C/T]AGAATCTCAGGGAACAGCAAGATTTAAGGAAAGGA Y 2 1 2 1 101000 r 74 goat snp52856-scaffold793-42405 11 48351976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772037 Affx-122923013 AX-385259192 11 48254145 ATGAACCATCTGCTGTTTACTGGTAGTGTCCACCA[C/T]GGTGAAATGTGACATTCTCTCTAGCAGGCTAGACA Y 2 1 2 1 201000 r 74 goat snp52855-scaffold793-6368 11 48387776 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391559 Affx-122966628 AX-123261916 11 48300632 AGGTGCCTCCTGAATGAAACCACCAACAGTAAGAA[C/T]GAGAAGGAGCTTGTCTTAAACACAGAAGGCATCAA Y 2 1 2 1 101000 f 74 goat snp3581-scaffold1111-40020 11 48433609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276501 Affx-1111835449 AX-519550013 11 48301329 AAAGCCAAACCTAGGAGGAAGAAATCACGTGTAAC[A/G]TTCTTCGCCCACCTCAGAATCATCCATGGCTGCTT R 2 1 2 1 101000 f 74 goat Random2.2K-1170 11 48301329 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388222 Affx-122969405 AX-123258580 11 48348612 GGCTGGGGGAGGCTGATGGAGCAAGTGGAGGAGAT[A/G]TGTAGACAAGCCATGTATGACTGTAAGGAATTCAC R 2 1 2 1 101000 r 74 goat snp3582-scaffold1111-88000 11 48479379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796772 Affx-122964154 AX-385283715 11 48405972 TAAGAAGATATTTGACTGATATAAATTAACATATG[A/G]CATAATTGCAAATAGTTTTCCCCACATTGCCAGGT R 2 1 2 1 101000 r 74 goat snp3583-scaffold1111-145360 11 48536850 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399559 Affx-122961128 AX-123269914 11 48451745 CTAAGGACAAAATTATTGAACATAGTCAGCCCTCC[A/G]TGTTGACCAACTGCAGATCAAAAATACTCAAAAAG R 2 1 2 1 101000 f 74 goat snp3584-scaffold1111-191133 11 48582561 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378005 Affx-122977594 AX-123248364 11 48502615 GCCAGGAAAACAGGTGGGGGCCTTAACCTGCAGGT[A/G]AGGGGTGAACACAGTCTTCACAAGGCAGGTTCTGA R 2 1 2 1 303000 f 74 goat snp3585-scaffold1111-242003 11 48634190 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436056 Affx-122932711 AX-123306395 11 48536673 CTTTGCAGAGTCTTCTTTAGGATCAATTTCAGCTG[C/T]TGTGATCGAGATCCAAAGCTTCCTCAATTGTATTC Y 2 1 2 1 101000 r 74 goat snp3586-scaffold1111-276061 11 48667987 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408347 Affx-122953745 AX-123278698 11 48566914 GCTTCTGGGCCCTTTACCCTGACACTGAATGGCTC[C/T]ATGCCTCCTGGCTCTTCTGAGCCTCTGGTGTTGCT Y 2 1 2 1 201000 f 74 goat snp3587-scaffold1111-306302 11 48697940 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416663 Affx-122947593 AX-123287011 11 48613218 TGGTCCACATAACTGTAGAGGAAGGAGACAGGTGG[G/T]GTAGGTGGTATCACATGATACAAATCACAACACCT K 2 1 2 1 101000 r 74 goat snp3588-scaffold1111-352606 11 48744065 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802423 Affx-122977092 AX-385289327 11 48643651 ATCACTCAGCTATCATTTCATTGCTATTATCTCAT[A/G]CCTCAGCAGATATGATCTGCTTCCTTTATCCCATT R 2 1 2 1 101000 r 74 goat snp3589-scaffold1111-383039 11 48774386 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770825 Affx-122944744 AX-385257989 11 48678918 CCTGCTGTTCCTAAGGACACACGCCCAGGTTATTT[A/G]CTATGCTGGATATTTATCCCAAGTTACAAGGGAAC R 2 1 2 1 101000 r 74 goat snp3590-scaffold1111-418306 11 48809602 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388004 Affx-122969574 AX-123258362 11 48715067 CAGCTTTGAAGGCTCTCAAGTCCCCACTTTGGAGC[C/T]TCGTGTTTCTCACAATCAAAAGAAAAACAGGGGGA Y 2 1 2 1 101000 r 74 goat snp3591-scaffold1111-454455 11 48845938 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416364 Affx-122947880 AX-123286713 11 48757459 GTAGGTCTTATATTCCTAGAGAGAGAAAAGAAAAT[G/T]ATCAAGTTAGTGTTGGAGCATTAGAGCAGGAACAC K 2 1 2 1 101000 r 74 goat snp3592-scaffold1111-496847 11 48888428 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440990 Affx-122928972 AX-123311327 11 48802872 CCTCGGTCTAGGGTAGGTTTCTGGGAGACGTGAGC[G/T]GATCGCATAATCTTGAGAAGCCAAGTGTTTGAGCT K 2 1 2 1 101000 r 74 goat snp3593-scaffold1111-542260 11 48933959 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274762 Affx-1111834480 AX-519548348 11 48857412 GAGAAGAGAGCAGAGGGTAGGCCAAGTGAAGGGAC[A/C]CTGGGCTTTGTTCTGCT M 2 1 2 1 102000 f 74 goat GoatD01.037846 11 48857412 C A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38414524 Affx-122949519 AX-123284873 11 48860473 GTCATCCTAAGAAAGGTCTGGATCAAACTAGTAAA[C/T]AGTGATCTTCACCATACGAGGTTTTGAGGCTGCGA Y 2 1 2 1 101000 f 74 goat snp3594-scaffold1111-599861 11 48991484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430294 Affx-122937280 AX-123300635 11 48905410 GATTGCTTTAAGTGAATTCCTGAAGCCTTACTAGC[A/G]TTTTTTTCATTATATATTTTCTCAGTCAGATCTTA R 2 1 2 1 101000 f 74 goat snp3595-scaffold1111-644798 11 49036617 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412184 Affx-122951059 AX-123282534 11 49000470 CGGACACAGGAGGGGTGAGGTGCAGTTATCTAACC[A/G]ATTCTGTAGGTTCTTAAAATCATTTCTCCCTTCTG R 2 1 2 1 101000 r 74 goat snp3596-scaffold1111-739858 11 49131606 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272677 Affx-1111832924 AX-519546383 11 49027499 CAGGGCAAGCCGTGGGCACTGCTGGGGTCTGCCTC[A/C]GCCTGTTGCACTGGCTTCAGCTGTGAACTTGTTCT M 2 1 2 1 102000 r 74 goat 11_49027499_AF-PAKI 11 49027499 G T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38377652 Affx-122977859 AX-123248011 11 49052766 GTCGAGGGAGTTGCTCTGAGGTCTTGATTTTTCCA[A/G]AAACTAAGGGGGAAAAGATCACGTGTTTTGGGACT R 2 1 2 1 101000 f 74 goat snp3597-scaffold1111-792154 11 49183509 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385912 Affx-122971574 AX-123256270 11 49085051 TATTAAGTAAGGTTTTCTCCCATGTTTTCTTTAAG[A/C]TTTTGAGGCCTGTTTTTCTGCTTTTCTGTATGAGA M 2 1 2 1 303000 f 74 goat snp3598-scaffold1111-824439 11 49216200 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383393 Affx-122973502 AX-123253751 11 49118467 AAAACCCGGCCCCCCTCAATCTAGGTGTGTACACA[C/T]CATGTTCAGGGCACACGCAGGAGGAGGGACCTAAG Y 2 1 2 1 303000 f 74 goat snp3599-scaffold1111-857855 11 49249434 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275539 Affx-1111834960 AX-519549111 11 49171948 GCTTTGGGCTGATCCCTCACTCTGCAGTTTTAGCT[A/G]A R 2 1 2 1 101000 f 74 goat GoatD01.060038 11 49171948 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320785063 Affx-122962364 AX-385272110 11 49184325 TGTATGATGTATGATGGTCAAATAACACTATGACT[A/G]TACTTAACTATACTAACTTATGTGCACTTAAGCAT R 2 1 2 1 101000 f 74 goat snp3601-scaffold1111-923713 11 49315026 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412172 Affx-122951068 AX-123282522 11 49223688 TGCATTTAGCTCTGGGAAGAGTAGATGGTTATTTC[A/G]CCAAAAGTCACTCTCAGTCCCACTCCCATGAGACA R 2 1 2 1 101000 f 74 goat snp3602-scaffold1111-963076 11 49354003 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451910 Affx-122921030 AX-123322243 11 49254676 TATTTTTGACATCTGCTTTCTTCTGTGTTGACTTA[C/T]ATTTTCCTAACAAAATTCTAGTCAACAGCACTGAG Y 2 1 2 1 201000 r 74 goat snp3603-scaffold1111-994064 11 49384979 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400217 Affx-122960170 AX-123270572 11 49289983 TGCATACATATCTATCCCAGTCCCCCAGATCATCC[C/T]ACCCTCCCTTCCATTTCTTTGGTTATTGGTAAACA Y 2 1 2 1 201000 r 74 goat snp3604-scaffold1111-1029371 11 49420668 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435342 Affx-122933603 AX-123305682 11 49319021 TGGAATTTTATGAACCTTTAGGTCTTCTGAAGTGT[A/C]AAATTGATCATCTAAGTTAAATTAAACTGCCCTGA M 2 1 2 1 103000 f 74 goat snp3605-scaffold1111-1058409 11 49449711 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391323 Affx-122967319 AX-123261680 11 49365945 CAGTAAAGGACTAAGCATAAAAGCAAATGAGAATA[A/C]GCAGTGCCTGCACAGTTTGAAGCAACTCTCTAGGA M 2 1 2 1 101000 r 74 goat snp3606-scaffold1111-1105333 11 49497040 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393524 Affx-122965796 AX-123263880 11 49398752 ATGATCAGCCAAACTAAGGTTTAAACAAACACTGC[C/T]TTAAATGAGGACTTTGTCACCAGAAATATTTCCAA Y 2 1 2 1 101000 r 74 goat snp3607-scaffold1111-1138140 11 49529808 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446330 Affx-122925625 AX-123316666 11 49482681 TTTTGTCTGTCTCCCACACTAGGAAATGGGAGACC[C/T]CATGTGTCTCATTTACCACCAGCACCAAATGCAAT Y 2 1 2 1 103000 f 74 goat snp3608-scaffold1111-1222069 11 49614070 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376142 Affx-122978858 AX-123246501 11 49519566 TCCCTCCTCTCTTTCCCATCTCTCCTGCATGGACA[C/T]GAGGCAGGTGTTCACCCCTATCATGCCCCCAAAAC Y 2 1 2 1 201000 r 74 goat snp3609-scaffold1111-1258954 11 49651121 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276503 Affx-1111835450 AX-519550015 11 49535971 CTTGGCCACATGTCACGTGAGAATCTTAGTTCTCC[A/G]ACCAGGGATAGAGTCCACACTCCCTGCATTGGAAA R 2 1 2 1 202000 f 74 goat Random2.2K-1171 11 49535971 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38400050 Affx-122960773 AX-123270405 11 49555460 AGGCCCACCCCGTGATCATGCTGGTTCACTTCCTC[C/T]TAGACTCCTAGTGTTGCTGTGGTTGTCTGTCTTGG Y 2 1 2 1 101000 r 74 goat snp3610-scaffold1111-1294848 11 49687351 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393028 Affx-122965639 AX-123263385 11 49598349 ATTGGTTCTGTACCTCATGGTGGGGGTCCCATGAA[C/T]GAGACCTGAACCCCAAGGACGGCCTGGAATTAAAA Y 2 1 2 1 202000 f 74 goat snp3611-scaffold1111-1337737 11 49728904 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396752 Affx-122962782 AX-123267107 11 49631415 TTCCTTATTTGTAAAATAGGGATATAATGGCCTTT[A/G]CCTTATAGGGTTCTTATGAGCATTAAATCTGCTAA R 2 1 2 1 101000 r 74 goat snp3612-scaffold1111-1370803 11 49762638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428818 Affx-122938383 AX-123299160 11 49677683 GTGGTCATATTATGGATATCTCTTAAACTCCTCTC[A/G]TTCCCTCTAACAGTGTACATTTTCCAGAGTTTGTT R 2 1 2 1 202000 f 74 goat snp3613-scaffold1111-1417071 11 49809673 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275096 Affx-1111834595 AX-519548675 11 49701093 CT[A/G]TTCCTCAGTTTCCTAAAGAATGTCTCAGTTTCCTA R 2 1 2 1 101000 r 74 goat GoatD01.046446 11 49701093 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320794262 Affx-122927929 AX-385281227 11 49714006 TAGAAGCCTAATTAATACACATGAAACTGAAAGCC[G/T]ATGTTAATACCACACCACTTTGGTTTGATTGATAA K 2 1 2 1 101000 f 74 goat snp3614-scaffold1111-1453394 11 49845860 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440948 Affx-122929004 AX-123311285 11 49746881 CCATCTTTCCATTCCAAGGTTACGTTATTAACTTC[A/G]CCATACAATTCACCCATTGTAATTGATTTAGGATT R 2 1 2 1 101000 f 74 goat snp3615-scaffold1111-1486269 11 49880102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405420 Affx-122956276 AX-123275772 11 49791867 TAACACAGTCTCCCCCAAAATCCAAGCAATTTGTT[A/G]TACATATTGATAAGCTCATTTTAACATTTATATGG R 2 1 2 1 201000 r 74 goat snp3616-scaffold1111-1531255 11 49926017 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443571 Affx-122927339 AX-123313908 11 49803335 GATACCTCAGTATCCTAGAATCAACCAGTATTCCT[A/G]CTAGGACTCTGAGCTGTTACAGCAATGTCTCCTCT R 2 1 2 1 101000 f 74 goat snp164-scaffold1002-10838 11 49943745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404131 Affx-122957099 AX-123274483 11 49834798 AGTGTCATAAAATAGACATAAAATAACAGTGATTA[C/T]AGTTCATTCCCAGGGGCCAATCAGAAAACTTCTAC Y 2 1 2 1 101000 r 74 goat snp165-scaffold1002-42301 11 49975090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389664 Affx-122968719 AX-123260022 11 49884998 ATTTGGGTCAGTGTAAGACTTTAGGGCCTTGAGCC[A/G]TGATGGCAGGACACAGATTCCAAGGGCACAGATTC R 2 1 2 1 201000 r 74 goat snp166-scaffold1002-92501 11 50025516 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443604 Affx-122927311 AX-123313941 11 49932057 GGTGGCTGTTTGCTTCTGATGTCCACTTTCCGTCC[A/G]CCCGCCCACCTGTTGCTGGTCTTTTCGAGCACAAC R 2 1 2 1 101000 f 74 goat snp167-scaffold1002-139560 11 50072508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383318 Affx-122972695 AX-123253676 11 49961843 GTTCTCATTATAACATAAACCACTCTAGTGGCTCT[C/T]AATTGTCATTAATAAAATATTAGCATTTTATTAAA Y 2 1 2 1 103000 f 74 goat snp168-scaffold1002-169346 11 50102535 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426541 Affx-122940187 AX-123296887 11 50025811 CCTATTGGTCACCAAATGATACCCCCGGGATCAAG[C/T]AGGAAGAACAGAGGAGAGTGACCAGAAAGATGCTG Y 2 1 2 1 102000 f 74 goat snp169-scaffold1002-233314 11 50167014 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795829 Affx-122944390 AX-385282782 11 50080695 ATTCCCATTAACTACAGCAGTGCCTGAAACTCACT[G/T]TAGGGTTCCTGTTGAGTCAACAAACCTTCCTCAGT K 2 1 2 1 101000 f 74 goat snp170-scaffold1002-288198 11 50221287 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422211 Affx-122944441 AX-123292557 11 50112609 ACAGAACATGTTTGTATGTAGGGGACTTACTGTAA[C/T]GAGGGAAGTAATAGCATGGTTATAAGGTTGATTAT Y 2 1 2 1 101000 r 74 goat snp171-scaffold1002-320112 11 50253642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394374 Affx-122964638 AX-123264729 11 50143802 CTAGACATAAAAGCCCTCAACAAAATACTAGCATG[C/T]GAGATTATGCACCATGACCAAATGATCTAGAATAT Y 2 1 2 1 101000 r 74 goat snp172-scaffold1002-351305 11 50284715 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394572 Affx-122964446 AX-123264927 11 50177005 GAGCATTCCCTATGTGTAGGTGATAGAACAGCATG[C/T]GACCCAGGAGTTCAGGTGTCTTGCATTTAGTTGGT Y 2 1 2 1 101000 f 74 goat snp173-scaffold1002-384508 11 50317856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441713 Affx-122929150 AX-123312050 11 50209825 CAAGGCAGTTGGTACTGTACATATTATTCCTGATC[A/G]CTAAGCCCATAATCTGTTTCTTCCTTTCTCATTTA R 2 1 2 1 201000 f 74 goat snp174-scaffold1002-417328 11 50350921 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799495 Affx-122940365 AX-385286425 11 50259763 AAATGGGATGAAGAGATAGCATGGCAGAATGTTTT[A/G]CACAGAGGCCAGCTTATCTTCTTGGCAAGGTCTTT R 2 1 2 1 202000 r 74 goat snp175-scaffold1002-467266 11 50400962 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800157 Affx-122975467 AX-385287080 11 50288645 AAACCCAAATAACCCAGACTATTTTTACTACAAAG[C/T]AAAACAGAATAGAAACTTGAGCCTGATTTTTCTTG Y 2 1 2 1 102000 r 74 goat snp176-scaffold1002-496148 11 50430006 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799763 Affx-122968448 AX-385286690 11 50320655 GCTTCCCTGAAATGGCCCTAGGGATTCAAATGCCT[A/C]GTATATTAGTTGTTTGGGTCCTGAGGGCTGATCTC M 2 1 2 1 101000 f 74 goat snp177-scaffold1002-528158 11 50462695 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774693 Affx-122935320 AX-385261827 11 50349355 CACACTCTATTACAAGAGTTGGCAGACTAAGGTCC[A/G]TGATCAAAGTCTAACTTTTCACTTACTTTTGTAAG R 2 1 2 1 101000 f 74 goat snp178-scaffold1002-556858 11 50491601 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378296 Affx-122976858 AX-123248655 11 50424239 TAAGATGCATGAGTGTTTCAGAGGATATGTCAGAA[C/T]CTATTGATGTTCAGATTCAGGGAGAAAGAAATCTC Y 2 1 2 1 101000 f 74 goat snp179-scaffold1002-631742 11 50562762 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423870 Affx-122942311 AX-123294216 11 50470066 TCCACTCCAGACCACTACAACCAAGAACACATGGC[C/T]CTCATTCACCACAGCACACAGACAAAGTAGGGATG Y 2 1 2 1 202000 r 74 goat snp180-scaffold1002-677569 11 50607263 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395748 Affx-122963691 AX-123266103 11 50519365 TGGGGACAAAAACAAAGAGAAAATAATGCACAAAG[C/T]AAACATTTTTAGATCATCTTCTTAACAAGTATAAA Y 2 1 2 1 303000 r 74 goat snp181-scaffold1002-726868 11 50657410 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276650 Affx-1111835451 AX-519550160 11 50531311 AGTTGGACATGACTAAAGCGACTTGGCATGTGTGC[A/G]TGCACGCGTTAGACCGTCTTGAGTCACACTGTAAA R 2 1 2 1 101000 r 74 goat Random2.2K-1173 11 50531311 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769011 Affx-122930470 AX-385256186 11 50547837 GAATCATACTATTAGGGCCATCAAGAAGCTAAGTG[C/T]AAATGTGTGTTGCTATGTCAATTTAATCATCCCTA Y 2 1 2 1 101000 f 74 goat snp16760-scaffold1757-6370 11 51158753 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385806 Affx-122971034 AX-123256164 11 50602742 TTTATTGAATAATTTGATTATCATATCCTTCAACA[C/T]CTGAGGTACTCACCTCTGCCCCCAAGGAAACCAGA Y 2 1 2 1 201000 f 74 goat snp16761-scaffold1757-61275 11 51213598 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404966 Affx-122956412 AX-123275318 11 50637047 TGCAGTGATAACATAATACTGGTTTAAATAACAAG[C/T]AAAGCCTAAGAGCATCCTATAAAATGACAATTACT Y 2 1 2 1 201000 f 74 goat snp16762-scaffold1757-95580 11 51247428 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391763 Affx-122967470 AX-123262120 11 50686075 TCATCTGATATGTGAATGATCCCCTGTCACAAAAA[C/T]GTTTCTGAAAAACTGAAAACAAAGTTTCAAATTTT Y 2 1 2 1 103000 f 74 goat snp16763-scaffold1757-144608 11 51297246 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786583 Affx-122976362 AX-385273615 11 50732189 ATCAAAGCTATGTGCTAAATAAGCTTAAAATCAAT[A/G]GTGAGAATTAACTCTCACAAATATTGGACATTTTT R 2 1 2 1 202000 r 74 goat snp16764-scaffold1757-190722 11 51342526 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447024 Affx-122924541 AX-123317360 11 50783104 AAAAATTTTGTTTATATTTTGTAATATACAGTAAA[C/T]AATAGGTGGGTCAAATTGACTAAATGGCCAGATTA Y 2 1 2 1 202000 f 74 goat snp16765-scaffold1757-241637 11 51393675 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400475 Affx-122961299 AX-123270830 11 50859170 TTTCATTGTCTCATCTTTATTTTCTCAATGTTTGT[A/G]CTAAGCCCCATTGGTTATTATTCAACAATTTAAGC R 2 1 2 1 201000 r 74 goat snp16767-scaffold1757-317703 11 51469940 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774527 Affx-122956424 AX-385261661 11 50910103 ATTTCCCTGACCCACTGAGCAATAATTCTTTAAGA[C/T]GAATGTATGACATTCAGACATCATTTTTAAAAGGC Y 2 1 2 1 201000 r 74 goat snp16768-scaffold1757-368636 11 51521551 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448287 Affx-122924173 AX-123318623 11 50942805 CTTCACATGTGGTTCCTTACAAGGAAGGAAAGGAC[A/G]TAGGCCAGGTTCATAACTAATGCAATAATTTGGCA R 2 1 2 1 101000 f 74 goat snp16769-scaffold1757-401338 11 51554415 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770912 Affx-122945835 AX-385258075 11 50984301 TCTAAGAATATGTGTTTCCAGTTAATGTAATAAAG[C/T]AGCAGATTATACTCTTTTATCATACTCCTGATACA Y 2 1 2 1 101000 r 74 goat snp16770-scaffold1757-442834 11 51596717 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390639 Affx-122967149 AX-123260996 11 51028220 CCTGATCCTTAATAGAAAGAAGATTAAAGACAGAA[A/G]ACCCTCTACCCACTTGAGCAACAGCAACTAAGTAC R 2 1 2 1 101000 r 74 goat snp16771-scaffold1757-486753 11 51642546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779109 Affx-122977814 AX-385266214 11 51113451 CCATAAAAATCACATGAGATGCTATTGAGAATGGC[A/G]TTTATGGTCACCAGCCACGAAGAATTTTATTTGCT R 2 1 2 1 101000 f 74 goat snp16773-scaffold1757-571984 11 51727999 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389261 Affx-122969025 AX-123259619 11 51128908 TAATCTAAAAATCTGTATGAGCCTTGGACAGGGAT[A/G]CATATTTCCCTAGAGCTCAATGATTGCCTGCACCC R 2 1 2 1 101000 r 74 goat snp25065-scaffold2585-89916 11 51748329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452149 Affx-122921664 AX-123322482 11 51164273 TTCTCCAATATTGGAGATAACGCAGAAGATAAAAA[C/T]CTTAGGGGATGGAGGAGGAGACACATTCAATCAAA Y 2 1 2 1 201000 f 74 goat snp25064-scaffold2585-54551 11 51783566 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416894 Affx-122948071 AX-123287242 11 51201812 CAGTTAGAGCTTAGAGCAAGAATTAAATGTGTTTG[A/G]ACTTTATCTCCATCATTTAGCAGCTTTTTGTGGAT R 2 1 2 1 101000 r 74 goat snp25063-scaffold2585-17012 11 51820946 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779113 Affx-122957490 AX-385266218 11 51251527 CTGTCAATGTTTTCTGTATTACTCATAGAAACATC[A/G]CATTCCTTATACATAAAACCAGATTTAAATTCTGT R 2 1 2 1 101000 f 74 goat snp10731-scaffold1380-32604 11 51883664 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450194 Affx-122922297 AX-123320529 11 51296873 CCATTTTCCAGATCTGTAAATTGAAAATCTATTTT[A/G]TTGTTGCTGTACCCGATACTCATGCGTTCCTTTGG R 2 1 2 1 101000 r 74 goat snp10732-scaffold1380-77950 11 51929188 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399358 Affx-122961349 AX-123269713 11 51330226 GAATACAGTATTTGTAAGTATAAAAATACTTATAA[C/T]GTAATATCTACAATATATCACTATATATACTCCTG Y 2 1 2 1 101000 r 74 goat snp10733-scaffold1380-111303 11 51962077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454261 Affx-122919646 AX-123324594 11 51368850 CATCTCTTAAAATGTGTTAAACTTATGATTTTGTT[A/G]TTGCTATACCTTACACTTCAAACATGAAGACATGA R 2 1 2 1 101000 r 74 goat snp10734-scaffold1380-149927 11 52000792 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381442 Affx-122974343 AX-123251800 11 51403078 AACCTTGTTCTCTCTAAAGAACTAAACTTCTTTCA[A/G]CTCTTCAAATGGCAGTGGAATCTAACGATTATAAT R 2 1 2 1 101000 r 74 goat snp10735-scaffold1380-184155 11 52035283 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427989 Affx-122939175 AX-123298332 11 51438964 GAGTTAACTGCTAAGTTCATGTAACTAGCATTCTC[C/T]TCGTACAAAAGGTTCAGCTGTATTCTGTTAATCAA Y 2 1 2 1 101000 r 74 goat snp10736-scaffold1380-220041 11 52071074 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446348 Affx-122925611 AX-123316684 11 51513842 CATTGAGACTGGACTTTCTTTCATTTGTCATGTGT[A/C]TTTTATTTATTTTACTACATTAAACTTATATTTAG M 2 1 2 1 103000 f 74 goat snp10737-scaffold1380-294919 11 52144986 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424641 Affx-122942171 AX-123294987 11 51554249 CTTATTCCTCTTCCCATTAAAAAAAAAAAAAAGCT[A/G]CTCTCTTTTGACTTTTATTCTTCCCTCTGGACTAT R 2 1 2 1 101000 r 74 goat snp10738-scaffold1380-335326 11 52186249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782768 Affx-122941426 AX-385269840 11 51588011 ATAATGAAGATACGTTTATAATTGTACCCTATCTC[A/G]TAGTGCTATGAAGAGGAAATGAGGTAACATATGTA R 2 1 2 1 101000 r 74 goat snp10739-scaffold1380-369088 11 52220119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272680 Affx-1111832925 AX-519546386 11 51611496 ACATTTCCTGGACTGGCAGGCCTAAAGACGACATT[A/G]AAACTGGGTTAATGAATTTTTGCTGGCACTTATCT R 2 1 2 1 201000 r 74 goat 11_51611496_AF-PAKI 11 51611496 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435082 Affx-122933723 AX-123305422 11 51630254 TAATCACTCTTTCCCCTTGTACTGGGGAATTATTT[A/G]CTATTACAGTTTGAATAGATATTTCAATGTCTTAG R 2 1 2 1 201000 r 74 goat snp10740-scaffold1380-411331 11 52260280 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797753 Affx-122937520 AX-385284692 11 51705286 TAACACATACACAGGCCCTGGGGTTAGAATATGGA[C/T]ATCCTTTGAGAACCATCATTCTCCCTACCACATTT Y 2 1 2 1 102000 f 74 goat snp10741-scaffold1380-486363 11 52335812 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777768 Affx-122971909 AX-385264886 11 51794296 AAGCAATATTAGTTGCCAGGCACAGTAAACCCACC[A/G]TCATGTATGGATTTATTTTATCTGCGCACCAAGTG R 2 1 2 1 201000 r 74 goat snp44099-scaffold598-60686 11 52440791 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778622 Affx-122972488 AX-385265733 11 51825232 CTTTAAGAAAATTAAGCATCATTAAAAGGCTTGCC[A/G]TAAAATTACATAGTAAATTATTAAAGTTAAACCTT R 2 1 2 1 201000 r 74 goat snp44100-scaffold598-91622 11 52471215 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407749 Affx-122954983 AX-123278100 11 51868173 AAAGTTAGGCTCTTCCCCACCACCACCACCCCCTG[A/C]ACTTCTGTTTTAGAGTCTTGTAATATTGCCAGTTT M 2 1 2 1 201000 r 74 goat snp44101-scaffold598-134563 11 52511406 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398404 Affx-122961636 AX-123268759 11 51911528 TTCAAGATGGTGGTGCCTGGGGAAAGCCTGAACTT[A/G]CCTTCTCTCATTACCATAACAAATATACAGTGACC R 2 1 2 1 201000 r 74 goat snp44102-scaffold598-177918 11 52555143 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798213 Affx-122970032 AX-385285148 11 51961788 GTTCTTTTGGTTTACAAACTGGATTTCTACTATTT[C/T]TTCATCTCTGTCCATTTACTCGGTCCAGGGGAAGA Y 2 1 2 1 201000 f 74 goat snp44103-scaffold598-228178 11 52605912 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799460 Affx-122973248 AX-385286390 11 52030818 TTTATCTGTTCTACTTTTTCTTGCAAATTTATGTG[A/C]AATTCTGTGTGAAAATTTTGTGAAACTTGTAGTTG M 2 1 2 1 201000 f 74 goat snp44104-scaffold598-297208 11 52676276 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774585 Affx-122949168 AX-385261719 11 52059877 CACATACAATTTTACATATCCCTTTATGAAAACAT[C/T]CCCCTCTTAGATTTAATAACTGCAAAGATTGTATC Y 2 1 2 1 101000 r 74 goat snp44105-scaffold598-326267 11 52703285 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435374 Affx-122933579 AX-123305714 11 52104443 GGAAAGAAGAAACACTAAATGAAAGAGTATTTGAA[C/T]AAGGAATTTAAGAAATGTGAAGTATGAATTTATAG Y 2 1 2 1 101000 f 74 goat snp44106-scaffold598-370833 11 52748073 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796997 Affx-122927317 AX-385283938 11 52159762 CTAATATAATGTTGGCAAAGAGGAGAAGTGAGGCT[A/G]TTCCTTGGGACGATGTTAAGTCCATCATCCCATAG R 2 1 2 1 101000 f 74 goat snp6645-scaffold124-17862 11 52811439 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446804 Affx-122925294 AX-123317140 11 52198802 ATGTGAGAAAGGGGAGTCCTTGTGCACTATTGTTG[C/T]GAATCCAAATAGGTGCATCCACTGTGGAAAATAGT Y 2 1 2 1 101000 f 74 goat snp6646-scaffold124-56902 11 52851104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409390 Affx-122954146 AX-123279741 11 52359967 GTGGGTCTCCTAGAAAGTGTCCTGCAATACTGGAG[A/G]AGCCAAACGTCCTTGCTGAGGTCTCTTTTCTCACT R 2 1 2 1 201000 f 74 goat snp6648-scaffold124-218067 11 53019981 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415537 Affx-122948662 AX-123285886 11 52414024 CAAATTATTATCTTTATTGGATGATACAGAATAGA[C/T]TTAGTAATCTTTTAGTAGTGTTGGTCTGGCTTTGA Y 2 1 2 1 101000 r 74 goat snp6649-scaffold124-272124 11 53073284 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769900 Affx-122945636 AX-385257069 11 52498692 AGATATTTTGGTAACTATATATTAAACACAGAGAA[C/T]AGAATTTCTGTGCAAATAGGGTGTGAATGTGTATG Y 2 1 2 1 101000 f 74 goat snp6650-scaffold124-356792 11 53158894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444709 Affx-122926424 AX-123315046 11 52529271 AAACTCCAGACCTTAAAGGACACAAAGATTAACTG[C/T]CAGACATGTTTCTATTCTTTAACACAGTTCCTCTA Y 2 1 2 1 101000 f 74 goat snp6651-scaffold124-387371 11 53189159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423076 Affx-122942940 AX-123293422 11 52566185 TATTTGGAATATGTGCTTTCTACCGAAGAAATCTC[A/G]TCTATATTTCAGAGAAAAATTAACATAATTTCAGA R 2 1 2 1 103000 f 74 goat snp6652-scaffold124-424285 11 53226829 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783290 Affx-122927604 AX-385270355 11 52617066 AAAGGCTTAATTAAGATAGAGGAATTTGAGCAACT[C/T]TGACAACTTCTTTTCAATAGACTCTCTCACTGAGC Y 2 1 2 1 101000 r 74 goat snp6653-scaffold124-475166 11 53278593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424319 Affx-122941957 AX-123294665 11 52652494 ATATTTCCCCCTGTCATTTTAGACATGCTAACAAC[G/T]CAGGGATTGTCACAAAGTTGAGCAAAGTGAAATTA K 2 1 2 1 201000 r 74 goat snp6654-scaffold124-510594 11 53314114 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443699 Affx-122927162 AX-123314036 11 52663448 TCTGTTTCTTGTATCTAAAGCTACACTATGGAGTA[C/T]GAAATGGCAACCCACTCAAGTAGTCTTGCCTGGAA Y 2 1 2 1 201000 f 74 goat snp46995-scaffold656-1512654 11 53332212 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398253 Affx-122962188 AX-123268608 11 52693604 GTATGTATGTAAGTATATCTAGCATATATTAGGTG[C/T]AAAACAACTGTTACTTTCCATTTTCCTGTAATGAA Y 2 1 2 1 201000 f 74 goat snp46994-scaffold656-1482498 11 53363435 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395069 Affx-122964186 AX-123265424 11 52739342 AACATGGAATAAGTAGTGAGTCACACATTTTTCTT[A/G]TTCTGAATTTATCTTTCAAAAGCCTCAACAAAGAC R 2 1 2 1 102000 r 74 goat snp46993-scaffold656-1436760 11 53409522 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435835 Affx-122932823 AX-123306174 11 52795125 CACGTGTGTCTTAAACTCAATATTTTAGTGAAAGG[C/T]AACAATTTATATATTACTAATTAATTAAATGCTAA Y 2 1 2 1 101000 f 74 goat snp46992-scaffold656-1380977 11 53465845 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441457 Affx-122928763 AX-123311794 11 52825036 CTGCTTTGATTTTCAGCCAATTAATATTCCTTAAT[A/G]TGTATTGAGAAGGTAGAAAGAACTAAAAGAATAAC R 2 1 2 1 101000 r 74 goat snp46991-scaffold656-1351066 11 53496008 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399526 Affx-122961152 AX-123269881 11 52918657 AAGGAACAATCTGGTGACTTGTTCCATTAATGTCT[G/T]TAGAACTACTTGTTTATCTCTTTAAAGACTGTTAA K 2 1 2 1 201000 r 74 goat snp46989-scaffold656-1257445 11 53590943 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424978 Affx-122941912 AX-123295324 11 52947818 TAAAAATGCATGAATAACTCAGATGAGTCCCTGGT[A/G]TTCATATCTAAGCACTTAACAAACATTACTTGTGA R 2 1 2 1 201000 r 74 goat snp46988-scaffold656-1228284 11 53620438 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424388 Affx-122941828 AX-123294734 11 52987163 CAGAGGTCTAAATAACCAGACACATTTCTTTCTCT[A/G]TTTAACAAGGACTGTCTGAATTAACATATTGTGTG R 2 1 2 1 201000 r 74 goat snp46987-scaffold656-1188939 11 53658618 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785026 Affx-122959391 AX-385272073 11 53058583 CTATATTAGGAAAACTAAGTTTAACAAATAGAATA[G/T]CTCTCATAAAGAAACATATGATTATATTTTTACTT K 2 1 2 1 101000 r 74 goat snp46986-scaffold656-1117519 11 53730290 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776790 Affx-122919602 AX-385263914 11 53093235 GTCCATGGGTTCACAAAAGCCAGACGTGACTTAGC[A/G]TCTAAACCAACAAGCTTACAAAGGTCTTGTGTGAG R 2 1 2 1 303000 f 74 goat snp46985-scaffold656-1082867 11 53763484 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778219 Affx-122958882 AX-385265334 11 53135717 TTTTTATTTGTTTAGTGACTATTCTGAACTAATTA[G/T]TTAAAGCCAATATTCTTTGCAGTATGTGGCTTCTC K 2 1 2 1 202000 f 74 goat snp46984-scaffold656-1040385 11 53805941 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445155 Affx-122925556 AX-123315492 11 53174686 AAAGAGTAAGCACTTTTCACGTTTCTACTTGTATC[A/G]TATTTACTAACATTTCATTTACAAAAATAAGTCAC R 2 1 2 1 101000 f 74 goat snp46983-scaffold656-1001416 11 53845314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777048 Affx-122952241 AX-385264171 11 53229690 TTCATAAAATAGGAATCTTGGAATGTGCTGAGCTT[A/G]TGAAACAGGTAACCAAAATAGGAAATGGATAAGAC R 2 1 2 1 101000 f 74 goat snp46982-scaffold656-946412 11 53900513 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417921 Affx-122946725 AX-123288269 11 53263591 AAAATAAAGTAAATATTCTTTTAAAGTCTTCTGAA[G/T]CTGATTTTAACTCATGCTCTTACTCTATTAACTTT K 2 1 2 1 101000 r 74 goat snp46981-scaffold656-912511 11 53934829 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789096 Affx-122949780 AX-385276109 11 53314128 TGTCAGTTAATTCTCAGGTCTTGCCATTTTCTCTA[A/C]TCTACACACTGAGCTAAGGTTACATATAAGTGAAT M 2 1 2 1 101000 f 74 goat snp46980-scaffold656-861974 11 53987352 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273771 Affx-1111833831 AX-519547382 11 53314305 TGCTTTCAATTCATTATGCTTCACTCTTAGCTCAG[A/G]TTCAGTACTTCTCTGCAGTTTTAAGAAGGAATAAA R 2 1 2 1 201000 f 74 goat GoatD01.006346 11 53314305 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38381818 Affx-122974270 AX-123252176 11 53343166 CACTTAGAATGATAAAGTCATTTCCTTTTTTTTAT[A/G]CTAGATAAATGGAAATTACTGAAGCTTAGAAACAA R 2 1 2 1 103000 r 74 goat snp46979-scaffold656-832936 11 54016547 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276652 Affx-1111835452 AX-519550162 11 53353800 GTATGCATTGATCTCATGTTTATAGATCAATTGAA[A/G]CAAATGCCATTGGCTTATGCACAAGTATGGGTTAT R 2 1 2 1 101000 r 74 goat Random2.2K-1177 11 53353800 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436996 Affx-122933140 AX-123307334 11 53397810 CACCTGTAGATACTCTGATTAAATTAGTATGAGGT[A/G]CAATCAGGGCCATCAGGATTTATAAAATTTCACTA R 2 1 2 1 101000 f 74 goat snp46978-scaffold656-778292 11 54071323 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787865 Affx-122955802 AX-385274888 11 53428418 TCACCTGGGTACTCATGTGTTTGCTGACCTACAAC[A/G]TGCATGCTTTGCTTGTGTTTGCTTAAAATTTTTGG R 2 1 2 1 101000 f 74 goat snp46977-scaffold656-747684 11 54102819 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433368 Affx-122935128 AX-123303709 11 53457750 TGAGTTGCTTTTTCCTTCTTTCTCTGTCTCTCTCC[A/G]CTTTGTCTTATTCCTCCATTTCTGATGGAATTTAC R 2 1 2 1 201000 r 74 goat snp46976-scaffold656-718352 11 54131042 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435336 Affx-122933608 AX-123305676 11 53487886 CTCTAGCAATCCAGGGTTTCATGGCTCCTTTACAC[C/T]TTCTTCTCTTTCTTGAGACTAAAGAGTGCTAGAGT Y 2 1 2 1 101000 f 74 goat snp46975-scaffold656-688216 11 54161905 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800570 Affx-122948168 AX-385287489 11 53523547 CCAAAGAATATATTTGACTGTCAGTGAAGCACAGG[C/T]GATATTGAAGAAAAACTTCTGGACTAAGAATTAAA Y 2 1 2 1 101000 f 74 goat snp46974-scaffold656-652555 11 54197632 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442366 Affx-122928023 AX-123312703 11 53554733 GTGCTCACTCATGTTACTATGGAAGAAATATAAAG[C/T]AATATCTCACAGTCTCTGAAAAATAGATCGCTCAT Y 2 1 2 1 101000 f 74 goat snp46973-scaffold656-621369 11 54229175 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393891 Affx-122965117 AX-123264246 11 53613950 TGGTTTAGAATTGGCTAAATAGGAAAGGATATTCT[A/G]TTCCCCTTGTGTCTTTATAGAAAATTGTTCTCAAA R 2 1 2 1 101000 r 74 goat snp46972-scaffold656-562152 11 54289032 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421877 Affx-122944273 AX-123292224 11 53702182 GAACAGCTGTGAATCAAATTAGTCAAAAAGGCTGA[A/G]GGCATATGCTTGGAGTCCAAAAATGTCTCCTCTGG R 2 1 2 1 101000 f 74 goat snp46970-scaffold656-473920 11 54377837 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436819 Affx-122932234 AX-123307157 11 53733441 AATTCTGAGACTATGTCTAGGACCAGTAGAACAAA[C/T]GATTGTTATTGACTCAGCAAGCCGACTAGAGGCAA Y 2 1 2 1 101000 f 74 goat snp46969-scaffold656-442661 11 54409129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440600 Affx-122929982 AX-123310937 11 53781773 CCCTTAAAATATTGAAAATAGGGAAGTTGATTAAG[C/T]GAGAGTCTTTTAAGCCTGTACTGGTGTAACACTAC Y 2 1 2 1 101000 r 74 goat snp46968-scaffold656-394329 11 54457385 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421611 Affx-122944480 AX-123291958 11 53829371 TTCAGTTTGTTTCCAAAGCTGATATTTTGGATCTT[A/G]TGCACTCCAGCCTTCATGTCACTCATTCCTTGTCT R 2 1 2 1 101000 r 74 goat snp46967-scaffold656-346731 11 54505109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411824 Affx-122951242 AX-123282174 11 53884692 CTACAAAAAGAACAAAGCTAGGGAAAATAAGGCTA[C/T]ATCTTCTGGCTTCAAATCCATGCTCTACCACATAG Y 2 1 2 1 101000 r 74 goat snp46966-scaffold656-291410 11 54561134 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393341 Affx-122965937 AX-123263697 11 53938917 CCACCTTAATCCCTTGGGATGAGAGCTATTTAAAA[C/T]AGCACTTTGAGTTATTGTTTCTTAAGCAACCTTGT Y 2 1 2 1 101000 f 74 goat snp46965-scaffold656-237185 11 54614465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375600 Affx-122978723 AX-123245959 11 53975870 ATGAACTGCAGCCAGGGTATCTTATTATAGCTAGT[A/G]ATGTACCCTAGCAACAAAGACAGTCAGGAAAATTT R 2 1 2 1 101000 f 74 goat snp46964-scaffold656-200232 11 54652605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769542 Affx-122968133 AX-385256711 11 54007225 AAACCCGAATTAGCTGGCCACATTATGAACATTGT[A/G]AAAATTAGTCTCCCCTCCCTAAAAGATGTCTGGAC R 2 1 2 1 201000 r 74 goat snp46963-scaffold656-168877 11 54681313 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383064 Affx-122973750 AX-123253422 11 54038356 GAAAGAATGGATACAGTAGCTTTTACCTTGATGCT[A/G]CAATTCTCAGAAAAGTGTTAACTCTTTTTAGCTTT R 2 1 2 1 101000 f 74 goat snp46962-scaffold656-137746 11 54712462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395133 Affx-122964135 AX-123265488 11 54073679 AAGTTTTGCCTCTGGAGAAAGCTGTACCACTGAGA[C/T]GGCTAAAAATAACTGTTCTTGTCTTGCTGTTTTAC Y 2 1 2 1 201000 r 74 goat snp46961-scaffold656-102423 11 54748524 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424232 Affx-122942479 AX-123294578 11 54104265 ATGATGGGGCCTGGGTACCAAGAGCTGGCAGAAAC[C/T]TGAAGCATTGTAACTGCCAACCCCATGTCAAAAGG Y 2 1 2 1 101000 r 74 goat snp46960-scaffold656-71837 11 54779271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442128 Affx-122928337 AX-123312465 11 54151532 CCCCTCCCACTTCCAAAGCAAGAAGTGCAGGAGCA[C/T]GAAACGGAATGAGCTGAATTCCTCTGTTTGTGTAG Y 2 1 2 1 101000 r 74 goat snp46959-scaffold656-24570 11 54826830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272630 Affx-1111832926 AX-519546341 11 54158597 CTTGGCATTCTTTGGAACTCTCCATTCAAATAGGT[A/G]TATCTTTCCTTTTCACCTTTGCGTTTCACTTCTCT R 2 1 2 1 103000 f 74 goat 11_54158597_AF-PAKI 11 54158597 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395078 Affx-122964179 AX-123265433 11 54193889 CTTCATTCCTCAACTAAGGTACTATGTAACAATGC[A/G]CAGAGGAATTGATTCTTTCTCTTTACTAAAATTTC R 2 1 2 1 101000 f 74 goat snp52074-scaffold768-1308198 11 54868503 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418920 Affx-122946519 AX-123289268 11 54238855 ATGCGGACATGGTTAGAATAGAACTCTTTCTCCCC[A/G]TACTCTATGATGTGTGGATCCTGGGAAAATTTAAC R 2 1 2 1 202000 r 74 goat snp52073-scaffold768-1263232 11 54913498 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783545 Affx-122964873 AX-385270607 11 54279591 TTTGGATCTCATTTCAACCATTCTCTGATCACTCC[A/G]TCCAGTTCAAATGCTCCATTATCTGCTCTCTCAGT R 2 1 2 1 101000 f 74 goat snp52072-scaffold768-1222496 11 54953071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384386 Affx-122972217 AX-123254744 11 54310693 TCATTTTCAAAATGAACCCTAGCATCTTCCATGCA[C/T]GGCATTGGGAAGGACATTTCCAGTTACATAGAGAG Y 2 1 2 1 101000 f 74 goat snp52071-scaffold768-1191394 11 54984087 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792221 Affx-122960728 AX-385279205 11 54357094 CTATACCATCTCACAGTAACTCATGAAATTACAAA[C/T]AAATATCACCCCGTGGCAATTTTTCACTTGAACTG Y 2 1 2 1 201000 f 74 goat snp52070-scaffold768-1144993 11 55031136 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395013 Affx-122964226 AX-123265368 11 54385747 TAGATTTGGTTACCCATTCAAAATTGCCATCTCAC[A/G]TGTTGCAATCAAGACCTTGTCTGTCATCTTTGCCC R 2 1 2 1 101000 r 74 goat snp52069-scaffold768-1116340 11 55059593 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377478 Affx-122977505 AX-123247837 11 54449946 CTGAATTATTGAATGTGTGCTGTACGCCTATAAAA[C/T]GTGTTTATCTTATATTAAAACAATACATTATTTGT Y 2 1 2 1 101000 f 74 goat snp52068-scaffold768-1052141 11 55123778 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780489 Affx-122922087 AX-385267580 11 54507947 TCAAAGATGGAAGGATCAACACATCTTATTTAGGG[C/T]GCCACTTTCTTTGTGACTTAAGACATAGGACTTGA Y 2 1 2 1 101000 r 74 goat snp52067-scaffold768-994140 11 55182304 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801588 Affx-122948682 AX-385288497 11 54542333 GTCACTTCTAGGGTTAGCACACAGTGAGCCCAGAC[A/G]TCTATTGTTTGGCAGAAAAACCAGGAAGAATATTT R 2 1 2 1 101000 f 74 goat snp52066-scaffold768-959754 11 55216661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782410 Affx-122951435 AX-385269486 11 54579788 CATATAATTGACAGGAAAGTTCATTGTAAGACATG[A/C]ATTATTTAGGTATCTGACGAATTTGTGATTATACT M 2 1 2 1 101000 f 74 goat snp52065-scaffold768-922299 11 55254087 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386500 Affx-122970756 AX-123256858 11 54630333 AGAGGAGATGATTTCTAAAATATATGTAGAAAAAA[C/T]ATTTCTTCTTCACTTATTTTCCTATATTAACATGT Y 2 1 2 1 201000 r 74 goat snp52064-scaffold768-871754 11 55304905 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405310 Affx-122956837 AX-123275662 11 54684439 AGGGATCTAGTTCTCTGTCTTAACACCTATCACAG[A/G]ATAGCCTTGACAATGAAGATTGACAATGAAGATTC R 2 1 2 1 101000 f 74 goat snp52063-scaffold768-817648 11 55359366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397893 Affx-122961956 AX-123268248 11 54726240 TAAAATATCTGGGAGCACTACAAACAGGATTCCTT[A/G]GGTAATACCTGGGACAAATGGGACAAGTGAAGTAG R 2 1 2 1 101000 f 74 goat snp52062-scaffold768-775847 11 55401545 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444437 Affx-122926560 AX-123314774 11 54758371 CTGGGCCCCATAGCACTTACTAAGATTGTAATTGT[A/G]AGAGAAAAGATGGGGCTTCTCGGAAGATGGCCTCT R 2 1 2 1 102000 r 74 goat snp52061-scaffold768-743716 11 55433849 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383372 Affx-122972657 AX-123253730 11 54805767 CCCTCTTTCTGGAGCCCTTAACTTTTTAAAATGCT[A/G]TAATGTTTCAGCAAGAATAATAAACATAATAGCTT R 2 1 2 1 201000 r 74 goat snp52060-scaffold768-696320 11 55479696 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436108 Affx-122932664 AX-123306447 11 54856917 GTATATCTAGCTGCTTCTCTTTGTAAAAATTAAAC[C/T]GACTCACTTGGTAGTAAGAGTTCCAGATGGTTGAG Y 2 1 2 1 101000 r 74 goat snp52059-scaffold768-645170 11 55529597 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431201 Affx-122937166 AX-123301542 11 54895448 GGACAGATTTATTAGATACTTTTTACTAAGGCTAT[A/G]TTGGATAATTCTACTTGTTAACAGAATATATTGAC R 2 1 2 1 101000 f 74 goat snp52058-scaffold768-606639 11 55568414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784857 Affx-122942866 AX-385271904 11 54931881 TTTTAGACCTTGAAAAAGATGCCTGAACTTTTATA[A/G]ATTCAAGAGAGTAAAAATTTTTAACAGGCCATATT R 2 1 2 1 201000 r 74 goat snp52057-scaffold768-570206 11 55605428 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416182 Affx-122948256 AX-123286531 11 54967748 GTTGCAAGTATGTATTTGGAGGGACATTTAACTAG[C/T]TCTCTGCTTCATCTGCTTTCATTAAATGGGGAGAA Y 2 1 2 1 201000 f 74 goat snp52056-scaffold768-534339 11 55641686 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276512 Affx-1111835454 AX-519550023 11 55003119 AAACAGAAGCCGCACTTCAGTAACAAAAAGGAATT[A/T]AATTGCTGCTGCTGCTGCTGCTGCTAAGTCGTGTC W 4 1 2 1 102000 f 74 goat Random2.2K-1179 11 55003119 T A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434676 Affx-122933966 AX-123305017 11 55014355 TTCCGCAGGTGCAGTTAACAGTGGAAGAAACAACC[A/G]TGTCCATTTCCATTGCTCTTGTTAGAATAACGATG R 2 1 2 1 101000 f 74 goat snp52055-scaffold768-487732 11 55688606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379650 Affx-122975943 AX-123250008 11 55063660 GAACGCAACATTGTGCGTACTGATGCATCTAACCC[C/T]TTTATTCTTGGTTCGACGTGCATCTGAAAAGTAGG Y 2 1 2 1 101000 r 74 goat snp52054-scaffold768-438427 11 55737577 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377294 Affx-122977699 AX-123247653 11 55127848 TGATCTTGGAGACAGTGGTGAGGCTAAACTCAGCC[G/T]AAATAAAGCGCCTGGGTTGCATGGTAGAGAAGCAT K 2 1 2 1 201000 f 74 goat snp52053-scaffold768-374239 11 55802794 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276660 Affx-1111835456 AX-519550170 11 55132104 AAGAAATGACATCTGCCTACTCTTCCTTCTGCAGC[A/G]TCTCTTTATACTTCTGTTTACACAGTACAGGAATT R 2 1 2 1 201000 r 74 goat Random2.2K-1180 11 55132104 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434204 Affx-122934858 AX-123304545 11 55164268 ATTTGGGGGATGCAGGAAAGCATTTGGGGGTGTCA[A/G]AATTGCTGTGACAGAGGAAGTTCTAGCCAGGAGAC R 2 1 2 1 101000 r 74 goat snp52052-scaffold768-337819 11 55839108 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396396 Affx-122963017 AX-123266751 11 55230746 ATCACACACTTTGCTAGAAACTGGTAAATGCTGCT[A/G]TCTTATTTGATATTCACAATAGCCTCAACTATTGT R 2 1 2 1 101000 f 74 goat snp52050-scaffold768-271341 11 55907176 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276518 Affx-1111835457 AX-519550029 11 55235990 CTTTCCAAACGAACTATATCAGAACAGAATGATAC[A/G]GCACCCATTCCCTCTCCCTCCCCCTCCTTCTGCAC R 2 1 2 1 101000 f 74 goat Random2.2K-1181 11 55235990 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784764 Affx-122939141 AX-385271811 11 55304243 TCAGAACTGGACAGAAATTCCATTGCAAAATGATA[C/T]AGAGTGAGTGTATTATAAAGTACCTCGCAGGCACT Y 2 1 2 1 101000 r 74 goat snp52049-scaffold768-197844 11 55981597 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777003 Affx-122963845 AX-385264127 11 55338802 GACAGCAAAGGTAAAATGTAGGTAACACATACGGC[A/G]TTGCATCATCAATGGAAACGAGACTGGGAAATGCG R 2 1 2 1 101000 f 74 goat snp52048-scaffold768-163285 11 56016723 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410499 Affx-122952189 AX-123280849 11 55385689 CACCCAAAACTGAATTCACCTTTTTTCCCTTCAAA[G/T]AGCCTCTCCACAAATCTGCATCTGATGCATAGTTG K 2 1 2 1 101000 r 74 goat snp52047-scaffold768-116398 11 56063252 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378938 Affx-122976433 AX-123249297 11 55415938 ATCTGATCTTTCCTTTTTCTTGAGAAATCCCATTT[A/C]CTTTCCTTCCCTAAGACTCTCCTGTGAGCCCACTT M 2 1 2 1 101000 r 74 goat snp52046-scaffold768-86149 11 56094488 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423140 Affx-122942763 AX-123293486 11 55446681 CAGAAATAAACTATATTCCTCCTGCCTTTAGCTAA[C/T]ACTTTCCAGGCTTGGGAGCATGACCAGTCTGGATA Y 2 1 2 1 101000 r 74 goat snp52045-scaffold768-55406 11 56123420 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774592 Affx-122956808 AX-385261726 11 55479671 AATGCAAAGTATTTAATAGTGTATGCATATGTGAA[C/T]AGGGCAAAAATAATGAAGTGATATATGGCTAATTG Y 2 1 2 1 101000 r 74 goat snp52044-scaffold768-22416 11 56157062 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438215 Affx-122931449 AX-123308553 11 55505580 CATTTCAAACCTGATACTGTCTGTACCAATAAGAA[C/T]ACAGGTTCATCTGAAAGATTGTCTTATTGATTAAA Y 2 1 2 1 101000 f 74 goat snp20162-scaffold20-3394 11 56182648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801935 Affx-122974426 AX-385288840 11 55535046 ATTTACCTTTATATTATTTCACCAAATTCCTTATT[G/T]TTTCCTTGGTGCAGCCCAATAAAGATTTGAGATGG K 2 1 2 1 102000 r 74 goat snp20163-scaffold20-32860 11 56212485 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447097 Affx-122924486 AX-123317433 11 55586038 AGCAGCCTGCGTCTTGTTGCAGCTCATCATGGACT[G/T]GGAACCAAGTGTGAAGATCCAATTGGAAGGAGATA K 2 1 2 1 101000 r 74 goat snp20164-scaffold20-83852 11 56264463 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802489 Affx-122945183 AX-385289393 11 55647171 CCAGTTTCAGTCTCCTTGGAAAATGACTGAATTTA[C/T]ATCCCCACCAGTGAATTGCTTTCCCACACAGTGTA Y 2 1 2 1 202000 r 74 goat snp20165-scaffold20-144985 11 56325777 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777874 Affx-122973626 AX-385264990 11 55715799 ATGTATAAAATTTTAGTCTAACTCATTGTGGTGAA[C/T]GTTTACATTTTTCTACTAAGTGAAAGAGGTGGATA Y 2 1 2 1 101000 r 74 goat snp20167-scaffold20-213613 11 56395326 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453378 Affx-122919931 AX-123323711 11 55785643 AGGTGGCTCGTAAGCCAAATTCCTGATTTAACATC[G/T]AATTTTATTTGAGAAAGATTTAAATACATTTGGCC K 2 1 2 1 101000 f 74 goat snp20168-scaffold20-283457 11 56464938 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393827 Affx-122965167 AX-123264182 11 55869730 ACTGTCTTTTGTTTTGTTAAGTTGTTTCTTCTTAG[C/T]CTCACTTTCTTTTTCTGTTTCTACTCTTCATGCTC Y 2 1 2 1 303000 f 74 goat snp20169-scaffold20-367544 11 56549036 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771983 Affx-122974873 AX-385259139 11 55911780 TTGCAAAACAGGATAGTAAGTTAAGACGAAAGGAT[A/G]TGACCGAAGGAGAAATGACTGTTACCCACAGATTC R 2 1 2 1 101000 r 74 goat snp20170-scaffold20-409594 11 56591455 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406643 Affx-122955818 AX-123276995 11 56001493 TGGAAACCATGGGGCTTGAAGATGCAGGAGGAGAA[C/T]GTTACTAGAACTCGCAGACATTGCTGACATAGGAA Y 2 1 2 1 101000 r 74 goat snp20172-scaffold20-499307 11 56682403 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799402 Affx-122975061 AX-385286332 11 56047546 GTCATTGAATGGTACTTTACAGACTTTGCAGAGCG[C/T]TCATGTGGCTTCATAATTAAGCTTTTTAAATTAAT Y 2 1 2 1 101000 f 74 goat snp20173-scaffold20-545360 11 56728604 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387997 Affx-122969577 AX-123258355 11 56082137 CCACTGCTTTTGGCCTCATGTAGGGTTCTCTGCTC[A/G]TTCATTTACCTTTCTTTTCCTCACTTTATCTGAGA R 2 1 2 1 101000 f 74 goat snp20174-scaffold20-579951 11 56764291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418240 Affx-122947035 AX-123288588 11 56140679 AGTTCCCTTTGTTCAGGTGAACAGAACTATATTTG[C/T]GTTATAAAATAAAATATACAAAGAGAAAGAATATG Y 2 1 2 1 103000 f 74 goat snp20175-scaffold20-638493 11 56826134 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390890 Affx-122967110 AX-123261247 11 56176367 TTTTTGTTGTACTGCTTTCCATGTAGTGTCTAAAT[A/G]CTATTTTTAATTATTCCCTGAATATAGGGACTCTT R 2 1 2 1 101000 f 74 goat snp20176-scaffold20-674181 11 56861762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389400 Affx-122968379 AX-123259758 11 56237741 TGGAGGACAGATGTTAGAAGAAAAGGAGCAGAAAG[C/T]GGTAAGGAGGAAGAAAAGTAGGGTTCTTTGGTAGA Y 2 1 2 1 103000 f 74 goat snp20177-scaffold20-735555 11 56923240 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413762 Affx-122949936 AX-123284111 11 56284801 GCTAAGTTCTCTTTTGACAGTGATGGTGAAAGTTC[A/G]TATTTCATAAAAATGATGTAAAATGCAGTAATTTT R 2 1 2 1 201000 r 74 goat snp20178-scaffold20-782615 11 56971077 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440532 Affx-122929334 AX-123310869 11 56317091 ACTTCTAGTTCAAGGTGGAATTAGAGTATTTTCTG[C/T]ACATGTTGCATTGAATCAAACAAATTTTAAAATAT Y 2 1 2 1 101000 f 74 goat snp20179-scaffold20-814905 11 57003494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776467 Affx-122964977 AX-385263594 11 56349012 AAACTGTGCTATGATAGTATGAAAAATCCAATTTG[C/T]CATTTGTGCAATTGTGTCTCCAGCTGTGTACTATA Y 2 1 2 1 101000 r 74 goat snp20180-scaffold20-846826 11 57035424 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450087 Affx-122922792 AX-123320422 11 56383974 ACTCTTTACCTTTGGCTTATTGATCCTTGGATAGT[A/G]AAGAATCCGGGTGCAATGCAGGAGACATGGGTTCG R 2 1 2 1 101000 f 74 goat snp20181-scaffold20-881788 11 57070648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385708 Affx-122971111 AX-123256066 11 56414619 GCTGTCTCATATATGTTCTCAATGCAAATATGAGG[C/T]GACTATCTTGGCCTTGGAGATGAAGGCAAACAGAC Y 2 1 2 1 201000 f 74 goat snp20182-scaffold20-912433 11 57101353 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791674 Affx-122950063 AX-385278665 11 56464258 TTTAAATTTTTAACAAAATTACTATCAAAGACACT[A/G]ATGGGATATTATCTTCTCTTTTTAAACTAGTTATG R 2 1 2 1 101000 r 74 goat snp20183-scaffold20-962072 11 57151217 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769633 Affx-122937412 AX-385256803 11 56507393 GATCCAAGACAGTGACATAGGAGTAATGGAACTCA[C/T]CTCCTTTCATGGATACATCAAATCCACACCTACAC Y 2 1 2 1 101000 f 74 goat snp20184-scaffold20-1005207 11 57194413 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771850 Affx-122973788 AX-385259006 11 56595137 ACTGTTCTTTAAACTAGTGACTATTAAAGAATGCC[G/T]ATTGCCTACTCAAAATATTTTCTCACCGCTGCTTC K 2 1 2 1 101000 r 74 goat snp20186-scaffold20-1092951 11 57282547 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404126 Affx-122957101 AX-123274478 11 56641576 TTTTTTCCCCCAATGTAAATTAACAGCAAAAATCT[A/G]TTGATCAAATGACCATTTCTTGTAGACAGCATTGT R 2 1 2 1 102000 f 74 goat snp20187-scaffold20-1139390 NW_017193051.1 31633 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276664 Affx-1111835458 AX-519550174 11 56671063 TTTTGGTAAAATATGCTTTAATGTAGTAACTGGTA[A/T]TGTGCTATATGTCTCATTCTATATGCTACTTTTTC W 4 1 2 1 101000 r 74 goat Random2.2K-1184 11 56671063 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320768203 Affx-122944392 AX-385255390 11 56689108 AAACATCTCTCTTTTGCTGCGTGTTCCCACATATC[A/G]TGTATCCTGATAATAATAAATCTGTTTTCTGTCAA R 2 1 2 1 101000 f 74 goat snp20188-scaffold20-1186922 11 57376594 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416835 Affx-122948114 AX-123287183 11 56764338 AGTGCTATACCACATCAATTACTAAGTTATAATAA[C/T]ACAAAGCATGTGGAAAGCTTTGAAGAGCTGAAAGA Y 2 1 2 1 201000 f 74 goat snp20189-scaffold20-1262152 11 57452351 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790823 Affx-122973912 AX-385277823 11 56822796 AAAAAATAAATATTCTAAAGCTCTAGTCTATAGAA[C/T]ATCTTTTTCCATGGCTGAATCCTTTGAATTAATCT Y 2 1 2 1 101000 r 74 goat snp20190-scaffold20-1320610 11 57510174 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428579 Affx-122938711 AX-123298921 11 56864789 CACAGTGCTGTCTCTAGGTTTTTTTATTTTTTAGG[C/T]AATATATTTCCTTTAATTAATTAATTTTTTAAATG Y 2 1 2 1 103000 f 74 goat snp20191-scaffold20-1362603 11 57553595 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794562 Affx-122955945 AX-385281524 11 56928052 CAGGGTTAATATTTAGCCATGGAAAGAAGGAAATC[A/G]TGCCGTTTACAATAACATGAATGGACCTGAAGGGA R 2 1 2 1 102000 r 74 goat snp20192-scaffold20-1425866 11 57618216 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433826 Affx-122934458 AX-123304167 11 56973758 TCACTTCTATGTACATCTCTTTCTAATTATAAGAG[A/G]GCCTTGACATATAATTTTACGTAGTTGATATAGGT R 2 1 2 1 101000 r 74 goat snp20193-scaffold20-1471572 11 57663567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272632 Affx-1111832927 AX-519546343 11 57035227 TCATGGGATAGAAAAGTGAACTGAATGGTGCAGAT[A/G]TGCCCTTCTCTACAACCTTACCCAGTACCACAACA R 2 1 2 1 101000 f 74 goat 11_57035227_AF-PAKI 11 57035227 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38391913 Affx-122966946 AX-123262270 11 57071802 CTGAGAGTACAGCTATGTAGATCAAATAATCAATG[C/T]AAGCAAAGAGGAAATCAGAACACATATTCTATGGT Y 2 1 2 1 201000 f 74 goat snp20195-scaffold20-1569616 11 57762414 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438142 Affx-122931474 AX-123308480 11 57103405 CAACCTACCCCAAAGTATAAATTTCTTTATTTATA[G/T]CTGATAGGGAAATCTCCCTCATTATTAGCCAAACA K 2 1 2 1 103000 r 74 goat snp20196-scaffold20-1601219 11 57794639 T G 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1371/journal.pone.0152426" Pinkneck-variant SNP associated with pink neck phenotype multi-breed 38454229 Affx-122919671 AX-123324562 11 57157750 AGAAAATAAAGAAAAACACTTTTCACTAGCAAAGA[C/T]GTGTCTCTTATAAGTGCATTAGCCAAGAGCAAATA Y 2 1 2 1 101000 r 74 goat snp20197-scaffold20-1655564 11 57849939 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405253 Affx-122956876 AX-123275605 11 57190566 AAAAGGAGTTAAGCAAAACTAATGCAATATTTGCC[A/G]TTGTCACCTTTAAATAACAACCATCAGTGAACCAT R 2 1 2 1 101000 r 74 goat snp20198-scaffold20-1688380 11 57883076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420860 Affx-122944640 AX-123291207 11 57271967 TGAAAGTCAACTGATGGCTATCTCCTGAGACTTTC[A/G]TATCTTTAAGATGATGGATATCTCATCAGTGGCCC R 2 1 2 1 101000 r 74 goat snp54096-scaffold824-994065 11 57975458 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443750 Affx-122927125 AX-123314087 11 57316643 CCCAGCAGACACAGACTTACAGCCTTAATGTAGTC[A/G]TAAAATAGCCTCAGGGGATTTTCAGGTATACTTAT R 2 1 2 1 202000 r 74 goat snp54095-scaffold824-949389 11 58020594 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787974 Affx-122960480 AX-385274995 11 57366312 CATTATATAATTTTACCTTAGCATTAACAAATATC[C/T]GATCATAATTTCTATGAAATTAGCAAACATCTCTA Y 2 1 2 1 201000 f 74 goat snp54094-scaffold824-899720 11 58070111 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798232 Affx-122966650 AX-385285167 11 57405892 GAAAAGGTAGTGCTGTTTATCTGGTGATGGAGTCA[C/T]GTACTAGCCTTTCAAAAACTTCCTGATTTTCTCAC Y 2 1 2 1 201000 r 74 goat snp54093-scaffold824-860140 11 58109951 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791515 Affx-122937226 AX-385278506 11 57438591 AATCATATTTGTATCAACCATGATACTTAGTTGTT[C/T]TCTATTTGTTCCCTTTTCCAATGTTTGTTTGCTAT Y 2 1 2 1 201000 f 74 goat snp54092-scaffold824-827441 11 58143423 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782666 Affx-122942295 AX-385269739 11 57533316 TGGATTTGGGACATACTCAAAAAGTAATTTGTTTA[C/T]GGGATGTGAGAGTGTGTACAGAGAGTCAAGGAAGA Y 2 1 2 1 101000 r 74 goat snp54090-scaffold824-732716 11 58238526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780281 Affx-122951163 AX-385267376 11 57575293 ACTCACTAAAATATAGTTGTAACCTCAAGCCTAGT[A/G]CTTGTGGTATTTTCAAAGTCATTTACAGTCATGTA R 2 1 2 1 201000 r 74 goat snp54089-scaffold824-690739 11 58280220 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406102 Affx-122956219 AX-123276454 11 57618858 AGCATATCATTTTTAGCTTAATGATAATGTTGTTG[A/G]AATTAGCTGTTTTACAAAGGCTTTTGTAACTAATG R 2 1 2 1 101000 r 74 goat snp54088-scaffold824-647174 11 58323884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442104 Affx-122928354 AX-123312441 11 57657836 TCTCTTTTTAAGATAATGAAATAAGAACACAAGAT[A/G]TGTGAAACATATTTTTAAAAATTGAGTTAGACTCT R 2 1 2 1 201000 f 74 goat snp54087-scaffold824-608196 11 58362711 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434255 Affx-122934819 AX-123304596 11 57700384 ATTTATCCATTTTAACATTTTAAAGGAAAATTAAC[A/G]CAGAAAAAAGCCCCCAAATCATGTATACATATGTG R 2 1 2 1 103000 r 74 goat snp54086-scaffold824-565648 11 58404947 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792631 Affx-122940063 AX-385279612 11 57758024 CTTTGATTCTAAATGTCACTACTGAGGTGGCAACC[A/G]TGAAATGCCTCCAAAAATCATATTGGCCTGTGCCC R 2 1 2 1 101000 r 74 goat snp54085-scaffold824-508008 11 58462988 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785084 Affx-122962270 AX-385272131 11 57809259 CTTCACCAAACAGGTATCAAACTTAGTTTAAAAAG[C/T]GAAACAACTAGATTCCACACAAATTTTTATAAACT Y 2 1 2 1 101000 r 74 goat snp54084-scaffold824-456773 11 58514782 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388686 Affx-122968999 AX-123259044 11 57901035 GTGCCAAGATGAAAAGTTAATTCAACTAAACTCAT[A/C]GGCAAAGACGCAATAAATGCAAGTCAAAACATAAC M 2 1 2 1 201000 f 74 goat snp54082-scaffold824-364997 11 58607761 A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786441 Affx-122962353 AX-385273475 11 57946319 AACATATTTTCCCAAGTCTTGTACTCTTTTATTTC[A/G]TTAACAGTTAATATTAAAGTGGAAGAACTTGTTAT R 2 1 2 1 101000 f 74 goat snp54081-scaffold824-319713 11 58653060 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791601 Affx-122919615 AX-385278592 11 58009295 ACAAATTATTATAAATGCTTATCAGATTAGTTCAC[A/G]TCTTCAATCCTAAAGTGTAAGAAGTTAGCATTTGA R 2 1 2 1 101000 r 74 goat snp54080-scaffold824-256737 11 58716533 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395761 Affx-122963680 AX-123266116 11 58052779 AGTAAATTATTTTTATGGAATTCTTTATACTCTTA[C/T]GTTGAAAAACTAACTTGCTTATGTTGCTGTTTAGT Y 2 1 2 1 101000 r 74 goat snp54079-scaffold824-213253 11 58760736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777831 Affx-122953843 AX-385264948 11 58091749 GGCATAACATCATACACATACACTTCATTGGGAAG[C/T]GTAATACCAGGGAAGCTGAAGAGAAAAAGGGAAGT Y 2 1 2 1 102000 r 74 goat snp54078-scaffold824-174283 11 58800127 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276522 Affx-1111835459 AX-519550033 11 58149111 CTGTTCTCACAGGTCTTATATTCCTGTCTGCATGT[A/G]AGCATGTACATGTTTGTGCATGTGTATATGAGTTT R 2 1 2 1 101000 f 74 goat Random2.2K-1186 11 58149111 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38428196 Affx-122939013 AX-123298539 11 58178404 CATAATATGCTTCCTGAGGAAAGAAAACATCATCC[A/G]TATCCTTGACAAAGTGACTAAAACTCGTCTATCAA R 2 1 2 1 101000 r 74 goat snp54077-scaffold824-87628 11 58887507 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419823 Affx-122945826 AX-123290171 11 58226832 TTAGTAGTTTAACATAAAACCTCTCTCTCTCACCA[C/T]GTTCAGAATATGCTTGTTAAAGTTTTTGATCCACA Y 2 1 2 1 101000 r 74 goat snp54076-scaffold824-39200 NW_017211376.1 8284 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385018 Affx-122971867 AX-123255376 11 58315784 ATCCCTGTGGAATGCCAGTAAAATTTCCCTCTGTC[C/T]ATGCATATATAGTACTTAATAACAACAACAAATAT Y 2 1 2 1 101000 f 74 goat snp15374-scaffold1630-49653 11 59038324 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380318 Affx-122975385 AX-123250676 11 58370906 CCCAAGTTTTTCATTCCTCTGTTTCTACCATGCTT[A/G]TTGGTTTGGATTTGGATTATTGCACTTGCTACTTC R 2 1 2 1 201000 r 74 goat snp15375-scaffold1630-104775 11 59093666 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276524 Affx-1111835460 AX-519550035 11 58394869 GATTGTTCTTGAAAATCTGTGCTAATGCAGGTAAC[A/G]GAGAATGAGAAGTGACTGGAAAGGTACAGAAATAA R 2 1 2 1 201000 f 74 goat Random2.2K-1188 11 58394869 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320773831 Affx-122944566 AX-385260971 11 58407082 ATGCCAAGGAGATACAGAAGTTGAACATTCAGATC[A/G]CAGAGAGGGTATACTGATGGTTTGGAACTTCTGAA R 2 1 2 1 101000 r 74 goat snp15376-scaffold1630-140951 11 59129908 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1371/journal.pone.0152426" Pinkneck-variant SNP associated with pink neck phenotype multi-breed 468276526 Affx-1111835461 AX-519550037 11 58411657 AGACTGAGACTAGATGATATTTATGGTCTGATCCA[A/G]CTTTAACATTCTATATCTAATCTAATATTTTCTGT R 2 1 2 1 101000 f 74 goat Random2.2K-1189 11 58411657 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429094 Affx-122938268 AX-123299436 11 58443867 TTATATCAAGTGAACATGGGAGATGCAAGGGAATA[C/T]TGACCCTGGGTCCTCTGAGGCCATCAGAGTAACAG Y 2 1 2 1 101000 f 74 goat snp15377-scaffold1630-177736 11 59166307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771689 Affx-122965024 AX-385258847 11 58498814 ATCTGATGTTAATGTAAGTCCCTAGACATGGTAGT[C/T]AACTTCATTAGAAGGCAAATAGGGAGTTACTTTTT Y 2 1 2 1 101000 f 74 goat snp15378-scaffold1630-232683 11 59221573 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778921 Affx-122971963 AX-385266028 11 58590431 CAAATGTTTTTGAGTGCATACTAATATCAGATTTA[A/G]TTCTTGGCAATACAGTACTAAATGAAATGGATTGT R 2 1 2 1 101000 r 74 goat snp15380-scaffold1630-324300 11 59314601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386406 Affx-122970823 AX-123256764 11 58623997 ACCTGTTATTCCCCATTTTATTTAATGTAACTACA[C/T]ACTTTGTGTATCACACACATGAAAAGCTGAGTTAT Y 2 1 2 1 101000 r 74 goat snp15381-scaffold1630-357866 11 59348474 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771449 Affx-122919708 AX-385258607 11 58676385 GCACAGGAGACCTGTGCAATGATGTTTATTCTTCA[C/T]GTCCCTTTATAAAAGAATGGTAAATCATGTATAAT Y 2 1 2 1 101000 f 74 goat snp15382-scaffold1630-410254 11 59401438 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276530 Affx-1111835463 AX-519550041 11 58701032 GAGTTATGTGGAAGGGGTGGTATATAAATAACAGC[A/C]ACTCTATTCAAGAATCTCTCTGCAATGCAGGAGAC M 2 1 2 1 201000 f 74 goat Random2.2K-1190 11 58701032 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419402 Affx-122945601 AX-123289750 11 58707687 ATATAATTCTTTTAGTTAGGATATAAAATTGGTAG[C/T]AGACATGTAAGTATACAAAAGAACAATTACAATAT Y 2 1 2 1 101000 f 74 goat snp15383-scaffold1630-441556 11 59434248 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783469 Affx-122940139 AX-385270532 11 58750391 GCAAATCACATAACCAAGCCCAAAGTAAAATCCTG[C/T]GGAATTTCACCATGATGACATGATAAGGATGTGGA Y 2 1 2 1 101000 r 74 goat snp15384-scaffold1630-484260 11 59476660 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450876 Affx-122922217 AX-123321210 11 58881152 CTTTTATGTATGTATGTATGTGGTCCATTTCTTGA[G/T]AATTTGTAGAATTTTTGTATGTAGAAAAGTGTCCT K 2 1 2 1 101000 f 74 goat snp15214-scaffold1621-1432598 11 59619363 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437708 Affx-122931752 AX-123308046 11 58948520 GTGCTTGTGGTTTTCTTGGATAAGGTGAAGTTCTG[A/C]TAAAGTATAATTTTATTTTCACAATTTTATGTACT M 2 1 2 1 101000 f 74 goat snp15213-scaffold1621-1365230 11 59686726 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789234 Affx-122975461 AX-385276245 11 59008856 TTGAGTTTTTCTGAGACTTTGTGGGACAAAGCATC[A/G]TATTAGTCATTAATTAAACAGATCTATTTTCTTTA R 2 1 2 1 201000 r 74 goat snp15212-scaffold1621-1304894 11 59747754 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376976 Affx-122977750 AX-123247335 11 59074717 TTCCATTAGAAGAATATACTGTCAATAACTTTACC[A/G]TATAGTCTATAGAATGGGAATAACATCCACCCATA R 2 1 2 1 101000 f 74 goat snp15211-scaffold1621-1239033 11 59813497 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444849 Affx-122926297 AX-123315186 11 59110424 TCAGTTTGTGTTTTTAAAGTAATTGATCTCGTTTA[C/T]AAAACATTGAGACATAAATTTATTCACTGCTGTAT Y 2 1 2 1 101000 f 74 goat snp15210-scaffold1621-1203326 11 59849220 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383125 Affx-122973259 AX-123253483 11 59157224 CACTTATCTTGTCCATTTCCACTCAGGGCAAACAG[C/T]AGGAGCTTAATAAATATGTTTTTAAGAAAGATAGA Y 2 1 2 1 101000 f 74 goat snp15209-scaffold1621-1156526 11 59895775 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762880 Affx-986697409 AX-385250898 11 59188415 CCCAGGACAGACCGGAAACCCAAGACCTCTCTTTT[C/T]TCGCAGCCTCTTGATTGAACCTTATTCTAACTTGT Y 2 1 2 1 600010 f 74 goat 11_59188415 11 59188415 Ancestral_priority_1043 ancestry 0.57 neutral IMAGE 10K 10K ancestral 320765448 Affx-986697411 AX-385252949 11 59188435 CAAGACCTCTCTTTTCTCGCAGCCTCTTGATTGAA[A/C]CTTATTCTAACTTGTGAATAGTCACACTCGACACA M 2 1 2 1 600010 r 74 goat 11_59188435 11 59188435 Ancestral_priority_1043 ancestry 0.738 recommended IMAGE 10K 10K ancestral 468275701 Affx-1111834963 AX-519549270 11 59192808 AAGAACGT[A/G]TTAGACGGGAAGAGAGAGAGTTCAGGGCCAAGGAA R 2 1 2 1 102000 r 74 goat GoatD01.060094 11 59192808 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38400597 Affx-122960395 AX-123270952 11 59196986 GTTATAATAGATGGGAATGCTAATATCATTTGTGC[A/G]TTTTCAGCTTTATTGCAAATCTTGCATTGTATAAG R 2 1 2 1 201000 r 74 goat snp15208-scaffold1621-1116764 11 59935565 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418822 Affx-122946157 AX-123289170 11 59228716 TCCAAGTACTCACCAAGCAGTCTTAATGATCAAAT[C/T]GGAGCCTGTCTTATTTCATTTATTTCACTACTCAC Y 2 1 2 1 201000 f 74 goat snp15207-scaffold1621-1085034 11 59967719 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380280 Affx-122975416 AX-123250638 11 59297135 AATTCTCTTTCACCTCTTTATTTCTCTTTCTTCCC[A/G]TTACAAAGGCTGTTTTAGATATTAGAAGAGAGCAG R 2 1 2 1 201000 r 74 goat snp15206-scaffold1621-1016615 11 60036796 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395673 Affx-122963752 AX-123266028 11 59326299 CAGTATGCAGTCTGCTCATCTATAAGGGACATGCC[A/G]TTCAATTTGCCTGTACCACTTCCTCATGTTCCAGT R 2 1 2 1 101000 r 74 goat snp15205-scaffold1621-987451 11 60066854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438685 Affx-122930871 AX-123309022 11 59372111 CTTTCTCCCAGAAGATAAGTCCACAAGTCTTAACA[C/T]AGTGTACCGAATCCTCTCTTATCTGATCCTTGTTG Y 2 1 2 1 101000 f 74 goat snp15204-scaffold1621-941639 11 60112769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393316 Affx-122965956 AX-123263672 11 59430559 TAAGTGTGCCTGGAGGAGTTGGAGAGAATGGTCCA[C/T]GTAAGGGAAAAAGTAATATAAGGGTGGTAAGTGGA Y 2 1 2 1 101000 r 74 goat snp15203-scaffold1621-883191 11 60177406 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420920 Affx-122944594 AX-123291267 11 59478900 AAGAAGAGAAAATGGTTAAGAAACAAGTGTTATGA[C/T]GTCTAGATATACAGATTTCTCTGGGTATACAGCTA Y 2 1 2 1 201000 f 74 goat snp15202-scaffold1621-834850 11 60226087 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772233 Affx-122941209 AX-385259388 11 59532646 GTTTCTCAGGAATATTTTTGAGCAATAAAACTGCA[C/T]GTTACAAGAACAATAAAACTGCATGTGCAAGGAAA Y 2 1 2 1 101000 r 74 goat snp15201-scaffold1621-781104 11 60280238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415551 Affx-122948650 AX-123285900 11 59575846 AGACAAATGGCCAAAAGAATACAACTATGGACTTG[C/T]ACCACGATCTCAGATACTAAAATACCAAACTAACA Y 2 1 2 1 101000 f 74 goat snp15200-scaffold1621-737904 11 60323511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402025 Affx-122958745 AX-123272378 11 59613406 GGAATTGGGTGGGTCTGATAACTTGTCCATTGGAT[A/G]CTCCTCAGCTTGAATTATCTGGATAGTTATTACTT R 2 1 2 1 101000 f 74 goat snp15199-scaffold1621-700344 11 60361699 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378596 Affx-122976580 AX-123248955 11 59657332 AAAACATTTGACACTGTCAGTGCAGAAGGTGGGAG[A/G]GCTGAAGTGACCAGAGATACCGCTGGATGGCAAGG R 2 1 2 1 101000 f 74 goat snp15198-scaffold1621-656418 11 60405852 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412755 Affx-122950519 AX-123283104 11 59688257 GCCAAGCCACATACAACCTGAATAATTCAAAATAT[C/T]CACACTAAGTCTAAGGGCCATGCCCTCCTCCTTAG Y 2 1 2 1 101000 f 74 goat snp15197-scaffold1621-625493 11 60437144 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272687 Affx-1111832928 AX-519546391 11 59690020 TTTCTTAAAAAAATTTTTTTTAACCTGTAAGTTTG[A/G]TAGTAATATCCCACTTTCTGATTTTAGCTATTTAC R 2 1 2 1 101000 r 74 goat 11_59690020_AF-PAKI 11 59690020 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435109 Affx-122933701 AX-123305449 11 59754173 GTTTTTGAAACAATAAAAAAGAGCCCAAGGATGAG[C/T]GGATAAATCAACTAAATAAAAAGGCAATTGGAGTG Y 2 1 2 1 101000 f 74 goat snp15195-scaffold1621-559577 11 60503001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775820 Affx-122967130 AX-385262951 11 59784622 TAGGATTTCTTTATTGCAACAGTCCCAGGAGCAGG[A/C]AGTACCCAAGCAGTATCCAACCAATTGGACCAAAA M 2 1 2 1 101000 f 74 goat snp15194-scaffold1621-529128 11 60532216 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786473 Affx-122952414 AX-385273507 11 59813846 TTTTATGCGTAACTACTGTTGCTAGTGGTGGTGGT[A/G]TTAAATTTGTGTGGTTTGAGGGCTTTAAAGAAAAA R 2 1 2 1 102000 f 74 goat snp15193-scaffold1621-499904 11 60561498 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393921 Affx-122965084 AX-123264276 11 59844186 GATACCCCTGTGAATACACTCTTGAATGTTCTTCA[A/G]CTCTCACTTTAGCCCCTGAGCCTGTCCCAGCCTCG R 2 1 2 1 101000 f 74 goat snp15192-scaffold1621-469564 11 60592116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380832 Affx-122975069 AX-123251190 11 59875106 CCACTCCCCCTTCCTGGGGCAATCTCCCTCAAGTT[C/T]ATGTAGCTTTCTCCCTTATTTCAACCAGCTTTCTG Y 2 1 2 1 101000 r 74 goat snp15191-scaffold1621-438644 11 60623476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433731 Affx-122934516 AX-123304072 11 59950113 AATTTCATTCTTAGGAATAAGTTCAACACAAATGC[A/G]TCCCTATGTTCACTAAAAGGCATATTTTCACCAAA R 2 1 2 1 101000 r 74 goat snp15189-scaffold1621-363637 11 60697770 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1371/journal.pone.0152426" Pinkneck-variant SNP associated with pink neck phenotype multi-breed 320768009 Affx-122962056 AX-385255224 11 59987790 AAGGCAATAACAGTGAGATGGAGAGCTAGAGCAAA[C/T]ATTTGAGTGATTTTAAGAGAATAGAGTGAATATAC Y 2 1 2 1 101000 f 74 goat snp15188-scaffold1621-325960 11 60734982 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430012 Affx-122938027 AX-123300353 11 60070655 CTTTTACAAATCTTGCTGGGATATTTGAATGCTTC[G/T]CCACAAAACTATGCTATTCCACCATTCAGAGGATT K 2 1 2 1 101000 f 74 goat snp15186-scaffold1621-243095 11 60817969 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803288 Affx-122923995 AX-385290132 11 60162054 TGAGAGGAATATTGATAGATGGGCAGAAAAAATTC[A/G]AAATAATAATTATAGATACGGAGGCTTCCCTGGTG R 2 1 2 1 101000 r 74 goat snp15185-scaffold1621-151696 11 60909996 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320782704 Affx-122953652 AX-385269776 11 60201467 GACTATTATAGCAACAAGAGTAGGGAGAAAGAACT[A/G]TTGTGCTAAAAAAGTTCAGAATAGGAAACTTGCAA R 2 1 2 1 101000 f 74 goat snp15184-scaffold1621-112283 11 60948279 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775244 Affx-122959418 AX-385262375 11 60246731 AGCATTGGAAACTATCAGATTTAACATGGTGAGTG[C/T]AAGTTTTTCACAATTAGAATTTTCACTTGAAAGCT Y 2 1 2 1 101000 f 74 goat snp15183-scaffold1621-67019 11 60993553 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276677 Affx-1111835464 AX-519550187 11 60303934 ACTCCTTAGACTTAAATTACTTGAGGCACATCAGA[A/C]GTCGGCAGCAAAAAGTATTGCCGTTTATGTTTAGA M 2 1 2 1 101000 r 74 goat Random2.2K-1191 11 60303934 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320768476 Affx-122938939 AX-385255656 11 60376042 GAGTATTATTTTTGTTGGTAAATTTTTTCCTCTAA[C/T]AGTTTTATGAATGAAGTAGAAGTGAAAAAACAGGT Y 2 1 2 1 101000 r 74 goat snp18101-scaffold185-12683122 11 61186602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394021 Affx-122965009 AX-123264376 11 60436959 GATTCTTTGTACATTATCCTTTATTATCTATGTTC[A/G]TTTGTAATCTGAAGCCATTTCCATTAACTTTTTCA R 2 1 2 1 101000 r 74 goat snp18100-scaffold185-12622205 11 61247715 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447821 Affx-122923915 AX-123318157 11 60467829 ACCTGACTGTACATGTGACTCCATTTCTCCTGTCC[A/G]TCCTGCAGTGGTGCTTTCTTTATATCTGCAGTTGT R 2 1 2 1 101000 r 74 goat snp18099-scaffold185-12591335 11 61278990 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451005 Affx-122921717 AX-123321339 11 60496574 AAGATGTTAGAACAGACCAAATAAAAAAAGATACT[A/C]CACATCCAAAGACAGAGGAGAAGCCACATCTAGAC M 2 1 2 1 201000 f 74 goat snp18098-scaffold185-12562590 11 61308259 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795758 Affx-122961813 AX-385282711 11 60564735 CTTAGCGTCAGTGTTGAGGAAGTAATAGGGTATGA[C/T]GGAGACCATGGTATGAACTGGAGTATGTCTATCCC Y 2 1 2 1 101000 f 74 goat snp18097-scaffold185-12494429 11 61379222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451483 Affx-122921132 AX-123321816 11 60613509 AGTACAGCAAAAATACCTTGTATCAATAGTCCCCA[A/G]TCGTAGACAGACAGATACAGGCAGTTTTTATGCTA R 2 1 2 1 201000 r 74 goat snp18096-scaffold185-12445655 11 61428000 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409058 Affx-122953353 AX-123279409 11 60642283 AACAAAAAAAGAAAAAAAAAAAAGTTAAAACAAAT[A/G]TAGCCAGAAGATAGCTGGTTGTGGGGTAATATAGA R 2 1 2 1 103000 r 74 goat snp18095-scaffold185-12416881 11 61456896 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380760 Affx-122975121 AX-123251118 11 60703320 TAGTGCCTGGGAATTGCCAGACTTCCAAAGCCTTA[C/T]ATCAGTTCAGTTGTTCAGTCATGTCCAACTCTTTG Y 2 1 2 1 101000 f 74 goat snp18094-scaffold185-12355844 11 61515793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420727 Affx-122944770 AX-123291074 11 60768810 TTTGGCACCAGTACTTGGAAACTTATGCTTTCCCA[G/T]AGATTGTTTTTATAAAAATGTATTAATTAACTTAG K 2 1 2 1 101000 f 74 goat snp18093-scaffold185-12290354 11 61582218 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792936 Affx-122944938 AX-385279914 11 60823035 CACCTGTGGTCTTTGAAGAATACCTTACACATTGG[C/T]GGTAAATAAACTGGATTAATTTCAATATTTTTCAA Y 2 1 2 1 101000 f 74 goat snp18092-scaffold185-12236129 11 61637949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406118 Affx-122956205 AX-123276470 11 60853106 GTCTGTGCTTTCATTAGTTTGAAATTATTAAGTAG[C/T]ATGGCTTTTACTCAACTCTTCTACGCTTATTTTAA Y 2 1 2 1 101000 r 74 goat snp18091-scaffold185-12206058 11 61667958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789053 Affx-122971205 AX-385276066 11 60979864 TCCTGTTTTCTCTCCTCACATTTTAGACTGGGGGT[A/G]TTGAAGGCAGATTAATTCCATGGCTTCGTGGGGAA R 2 1 2 1 101000 f 74 goat snp18089-scaffold185-12079300 11 61795504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450849 Affx-122922237 AX-123321183 11 61009538 ATTAGAGTTTGTCAGGTGATGTGCTTTTAGCTGGC[A/G]CATAGTGCCCTTACTTCTTGCCAGAGCAGAGGGCA R 2 1 2 1 101000 f 74 goat snp18088-scaffold185-12049626 11 61825587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440658 Affx-122929937 AX-123310995 11 61065389 TATTTGACTAATGCTGTATGTTGACTAGCACAGTT[A/G]CAGATCTCCTTTACTTGCTAGAAGCACCTAACCCC R 2 1 2 1 101000 r 74 goat snp18087-scaffold185-11993775 11 61881931 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427887 Affx-122939695 AX-123298230 11 61103625 TTATTTGTCCGATTGCTGTTGTGGTTCTTGCCTGA[A/G]GATCTGTCTTTAGGATCTGAGTGGCCAGAATTACA R 2 1 2 1 101000 r 74 goat snp18086-scaffold185-11955539 NW_017189517.1 9457817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786729 Affx-122951074 AX-385273761 11 61204776 CTCTGTTACAGTGTTTTTAATTACGTGGCTTGCCA[C/T]CTCCAGATTGTATGCTACCAAATCTGAAGGAAAAC Y 2 1 2 1 101000 f 74 goat snp18084-scaffold185-11854388 11 62021482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435535 Affx-122933400 AX-123305875 11 61339728 TAATTTTTTTCCTAAAACAATTATAGTTGCTTTGT[A/G]GTAATAATCTGCTTTTGAAGCAGTCACTTCTCCAT R 2 1 2 1 101000 r 74 goat snp18081-scaffold185-11719436 11 62156371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276534 Affx-1111835465 AX-519550045 11 61348983 AGAGAGTTTGCTGTTCCCACATCATAGAGATGAAT[A/G]GAAAACACTTTAATACTGGCAAATTTGATACAACA R 2 1 2 1 101000 f 74 goat Random2.2K-1194 11 61348983 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776444 Affx-122949425 AX-385263571 11 61377741 GACAGGCCATGGAGCAATAGTCTAATATGGAGCTG[A/G]AGAGGTCTGCTAATAGCTTGAACAGGAGCTAGTGT R 2 1 2 1 101000 r 74 goat snp18080-scaffold185-11681423 11 62194566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778452 Affx-122935202 AX-385265566 11 61413746 GAATTCAAACAGAAAATCTATCTTAACCTTCTGAC[A/G]CATTCCTTCATTAGGAATTACACCTGCTTACCAAG R 2 1 2 1 101000 r 74 goat snp18079-scaffold185-11645418 11 62230440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790379 Affx-122943583 AX-385277381 11 61506079 TATCTACTATGTCCATCACTTCACACAGACATTAT[A/C]TCATTTATTCACCAAAAACCCATATCAGTGGACTA M 2 1 2 1 101000 r 74 goat snp18077-scaffold185-11553085 11 62322779 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798350 Affx-122957762 AX-385285285 11 61540807 CTGATTTTAGGGTAAACTTTTCATCTGCTCTTGGC[G/T]CTGCCTTAGTTACAAATGTGAAATCAATTAAATGA K 2 1 2 1 101000 f 74 goat snp18076-scaffold185-11518357 11 62357420 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419602 Affx-122945994 AX-123289950 11 61599017 TCAATTTAAAGGTGCCCAGGCTTGCATTTATGCTA[C/T]GTGCCAAAAGGGTCACTGAAATAATTTCCAGTCTT Y 2 1 2 1 101000 f 74 goat snp18075-scaffold185-11460147 11 62416062 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390662 Affx-122967131 AX-123261019 11 61633401 TCTGGCCCTTTGCCCTTCCATGTACATTTTATAAG[C/T]AGCTGGGCTTTTTCTGCAGAATATCCACAAAATAT Y 2 1 2 1 101000 f 74 goat snp18074-scaffold185-11425763 11 62450439 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381011 Affx-122974661 AX-123251369 11 61695912 CAGGCCATGTGTCAGACCATCCCCTGGGATGGCCT[C/T]GCCTGTCTCCTCCAGGGGTTTAGGAACAATTGCTC Y 2 1 2 1 202000 f 74 goat snp18073-scaffold185-11363252 11 62512282 T C 2 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1371/journal.pone.0152426" Pinkneck-variant SNP associated with pink neck phenotype multi-breed 320789725 Affx-122948436 AX-385276733 11 61781025 AAAGCAAAGCAGGACAAGGACGTGTCATAACAAGA[C/T]GCAGTATGCTGTACAAATAAAACCTAAATTATATA Y 2 1 2 1 201000 r 74 goat snp18071-scaffold185-11278139 11 62597978 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785873 Affx-122965073 AX-385272910 11 61818872 GGCACAAGCATACTACAGGATGTCATTCAGAAAAA[C/T]GTTGACCAACAAAAGACACATGGGAAGTAGAGGAG Y 2 1 2 1 101000 r 74 goat snp18070-scaffold185-11240292 11 62635907 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797546 Affx-122920719 AX-385284485 11 61867575 ACTTCAGAAAACCCACCAAATTCCCCAAATTCATC[A/G]TCATCATCATCCTCAGCTCCATTGTCTAGTGGTGG R 2 1 2 1 102000 f 74 goat snp18069-scaffold185-11191589 11 62684733 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774447 Affx-122951410 AX-385261583 11 61968542 ATGGGAGTAGAATTCTGTGTTTAGCCTTAAATTTC[A/G]CAAAAAGATTAGGTATCATTGTCTTAGAATAACTT R 2 1 2 1 101000 f 74 goat snp18067-scaffold185-11090622 11 62785821 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407872 Affx-122954505 AX-123278223 11 62002044 TCAGAGGATGAGGGCCAGAAGGAATGGAGATTCTG[C/T]GTTTCAGTTCAGTTCAGTTGCTCAGTCGTGTCCGA Y 2 1 2 1 201000 f 74 goat snp18066-scaffold185-11057120 11 62819190 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449649 Affx-122922583 AX-123319984 11 62041464 TGGGAACTCCCAGACATTACATTAACCCACTCCCT[C/T]GCCTCAGAGAGAACCTTTCGAAAAATGTAGCATAA Y 2 1 2 1 101000 r 74 goat snp18065-scaffold185-11017700 11 62858521 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385245 Affx-122972092 AX-123255603 11 62073910 CGCTCATATGTCTACCACCCCAGCTTAAGAAACAG[A/G]CTATTACCAGCCCCTTAGGAAGTGGCCGTGTGCCC R 2 1 2 1 201000 r 74 goat snp18064-scaffold185-10985254 11 62890935 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800362 Affx-122971617 AX-385287284 11 62129802 GGAATTGTTTTTCAAGTCTGTAAATCACTTTTAGT[A/G]CTGAACTAAGAGAAAAGAGACTGACTTTTAACGGA R 2 1 2 1 101000 r 74 goat snp18063-scaffold185-10929362 11 62945559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428064 Affx-122939115 AX-123298407 11 62162089 ATGAAAGGTCCTCCATGCCCTCACCCAATTTCCCC[A/G]GGACAAAATGTTAGGGACATTCGGGCAAAATAACA R 2 1 2 1 101000 r 74 goat snp18062-scaffold185-10897075 11 62978236 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419638 Affx-122945967 AX-123289986 11 62196411 AGTCAAAAAGATAAGAGATGGCTGCGGCTTTCTGC[A/G]CCTGCCTAGTTCACCCACCTCCCCTTCTGCCTCCG R 2 1 2 1 101000 f 74 goat snp18061-scaffold185-10862753 11 63012191 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402469 Affx-122958602 AX-123272822 11 62255976 GGAAACGGTCATCCTTTTAAGTGGCAATGTTCCTT[C/T]GTTAACATGTTACTTTCAGATGAAAAAGCTCCTGT Y 2 1 2 1 201000 r 74 goat snp18060-scaffold185-10803188 11 63072871 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381883 Affx-122974170 AX-123252241 11 62294932 GCCCATCTACCTTTCCCAATCTGTTCCCAAAGCTG[C/T]CATTCTGGCTCAGTTCTTATTTCCACACTCCTTAT Y 2 1 2 1 201000 r 74 goat snp18059-scaffold185-10764232 11 63111714 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425207 Affx-122941027 AX-123295553 11 62325830 TATTATGTGGAGGGCTGGATATGTCCAGGTGAGAG[C/T]AGGGTTCTCTTCCTTCTGAGGGCCCAGGGTCTGGA Y 2 1 2 1 201000 r 74 goat snp18058-scaffold185-10733334 11 63142599 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414467 Affx-122949563 AX-123284816 11 62357634 GTGCACCCGTTCATTTCCATTCATTTTGGGCAAAG[A/C]GCCTGGCAGTGTTCCTGGCGCGCTGCTGCCAGAGA M 2 1 2 1 101000 f 74 goat snp18057-scaffold185-10701530 11 63174227 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272636 Affx-1111832929 AX-519546347 11 62404302 AGGCAAGTGGGTCAGGTCTGTCATGTTCTAGTCAC[A/G]TGACCTTGGACAAGTCATTTCCTTTCCTCTGAGCT R 2 1 2 1 201000 f 74 goat 11_62404302_AF-PAKI 11 62404302 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320768381 Affx-122977596 AX-385255561 11 62415195 TAAACTTTGACCAGTGTATTATACCATGCCCTTTG[C/T]AATTAAGTAACTCAAGATAAAATGTTAAAGTTCAG Y 2 1 2 1 101000 f 74 goat snp18056-scaffold185-10643969 11 63232168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789588 Affx-122925172 AX-385276597 11 62446881 GAATAACCAAGTGAGATAGGAAACCTGCACTGAAT[A/C]TTCCTCAATAAGATCAATGATAAAGATAATCAGGG M 2 1 2 1 101000 f 74 goat snp18055-scaffold185-10612283 11 63263857 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383612 Affx-122972556 AX-123253970 11 62484776 AAACTGGAGTTACCTCTTTTTGGAGCTGAAAGCAT[A/G]GGAGGATATGCAATAATCCTCCCCACCCCATTCAT R 2 1 2 1 101000 f 74 goat snp18054-scaffold185-10574388 NW_017217595.1 5608 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801194 Affx-122935392 AX-385288107 11 62520452 TGGTAAATTCCATAGCAGCAGGATTTTGGCTTTGT[C/T]TACTGGTATATTCTACTTATAATGACTAACATATA Y 2 1 2 1 101000 f 74 goat snp18053-scaffold185-10538712 11 63338527 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398244 Affx-122962196 AX-123268599 11 62553601 CCTTGTTGCTAATGCTTCCTGTGTGACTCCATTAA[C/T]GAATGTAGGGCCTGAAGACCCCTGTTGGCTCAGCT Y 2 1 2 1 101000 f 74 goat snp18052-scaffold185-10505563 11 63371818 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428082 Affx-122939101 AX-123298425 11 62610372 TGTGCTGTTCTGGGTAATGCCGAACGCCTGGAAGG[A/G]TGTGTAGGAACTGCCCTGCTGTTTCCAGGCACTTG R 2 1 2 1 101000 f 74 goat snp18051-scaffold185-10448792 11 63428503 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389527 Affx-122968287 AX-123259885 11 62668853 CCAATAAATGAGGAAAGTATAGATGATCTCAATGC[C/T]AGGAGAGATGTGACTGAGAACAACTGGTCCAGCCC Y 2 1 2 1 201000 f 74 goat snp18050-scaffold185-10390311 11 63486874 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439511 Affx-122930133 AX-123309848 11 62699623 AGTAATTAAACCAAGAAGGTCAGAGAAAGAGGAAG[C/T]GGTTGTGTTGTTTCTGATGCGAATAGCATTGTTGT Y 2 1 2 1 101000 r 74 goat snp18049-scaffold185-10359541 11 63517643 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779092 Affx-122923110 AX-385266197 11 62742887 GAAAGTCCTCAAACAGCTCATGTTCTAGTTATTAG[C/T]ATATAAACTCACCTGTATCTGGCCTATGGAATCCA Y 2 1 2 1 101000 f 74 goat snp18048-scaffold185-10316277 11 63560709 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769766 Affx-122974842 AX-385256936 11 62793660 ATTTATAATTCTATAAGCAAATCAACTTGTTTGTC[A/G]TAGAGTAATATATTCTTAAATTAATAATGACATGT R 2 1 2 1 102000 r 74 goat snp18047-scaffold185-10265504 11 63611418 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387387 Affx-122970425 AX-123257745 11 62832147 CAAATAACGGACAATAACACATCACATAACAGGGA[C/T]TGAATAAACTACAAAATGGAAACTTTGTGAGAATT Y 2 1 2 1 101000 f 74 goat snp18046-scaffold185-10227017 11 63650408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421495 Affx-122943908 AX-123291842 11 62869563 ATAGGAGCTGGGTGTGTAAAGCATACTTCCCCCTT[C/T]CATAAACCCATCTGTTTTATTTACACTTCCTAAAA Y 2 1 2 1 201000 r 74 goat snp18045-scaffold185-10189601 11 63691429 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1371/journal.pone.0152426" Pinkneck-variant SNP associated with pink neck phenotype multi-breed 38411686 Affx-122951998 AX-123282036 11 62922150 GCTCTTATAATCAGTTTTGCGACTTTTGTCCTCAA[C/T]GATATAAAATGTTGAAATTGAAGAAGTTGGGAATA Y 2 1 2 1 101000 f 74 goat snp18044-scaffold185-10137014 11 63744308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776223 Affx-122921365 AX-385263351 11 62952649 TTATTTGATTGGAGATCATTGATAATGCTGACAAT[A/G]TTCTTAACCACACTGGCAAACTGCTAGCGACTCTT R 2 1 2 1 101000 r 74 goat snp18043-scaffold185-10106515 11 63774672 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437925 Affx-122931641 AX-123308263 11 62989163 TTTGCATCCCCAATGGAAAGACAGTAGAGTCTCAA[C/T]AGTAGCTCACTGCATTGAAATAAAGTGTTCAGCAT Y 2 1 2 1 201000 r 74 goat snp18042-scaffold185-10070001 11 63810893 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391842 Affx-122967000 AX-123262199 11 63061542 CCCACATAAATTCACTATTTTCACAATCTACAGAA[C/T]AGGTCTAATAGAAGTTAAAGATGAACTGAGCAGGG Y 2 1 2 1 101000 r 74 goat snp18040-scaffold185-9997622 11 63883565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405327 Affx-122956342 AX-123275679 11 63119829 ACTTAAATTGCCTCACAAAGCACTTCACTTGGTGT[A/G]CCTGGGAACAGACACAATGCAAACAATAACAATGT R 2 1 2 1 101000 f 74 goat snp18039-scaffold185-9939335 11 63942256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425752 Affx-122940739 AX-123296098 11 63159919 TGCTGTTCAGGGAATCAGGGAGCTTGAGACCACAG[C/T]ACGCTCATCGCACTGTGATTGTTAACACACACATG Y 2 1 2 1 201000 r 74 goat snp18038-scaffold185-9899245 11 63982423 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782158 Affx-122930293 AX-385269236 11 63189485 TATGTTTTATGCATTCCTTTGCAAACAGGTGTGCC[C/T]CTGCAATCAAGCTCTGGCCAATACAATCGGAACAG Y 2 1 2 1 101000 f 74 goat snp18037-scaffold185-9869679 11 64011826 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1371/journal.pone.0152426" Pinkneck-variant SNP associated with pink neck phenotype multi-breed 320786016 Affx-122967336 AX-385273052 11 63219452 ATTCTCTAAGCTCAAAAGATTTCAATTTCCTGACC[A/G]TGACCAAGCCATCAGGACAGAATCTCTCTTTATCA R 2 1 2 1 101000 r 74 goat snp18036-scaffold185-9839712 11 64041776 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772005 Affx-122962265 AX-385259161 11 63262452 CATGAGGTGGATCCTTTTGTGGTCCCTGAAGGGAA[A/G]TCTTCCATTCAAATGGAGACATTCCCATCTCTACA R 2 1 2 1 101000 r 74 goat snp18035-scaffold185-9796712 11 64084501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451047 Affx-122921438 AX-123321381 11 63355930 CAGCTTTCCAATGTGTTTGGGAGCCTCCAAGGCCA[C/T]GGGGAAGGGAGACATAAAGGAATCTAGCGCTTCCA Y 2 1 2 1 201000 f 74 goat snp18033-scaffold185-9703234 11 64178592 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430532 Affx-122937202 AX-123300873 11 63439770 CTGCAAGCTCACTGAATGAGATTCACTTTGTTAAG[C/T]GGCAAGGCATCTACAACTCTCCCTCAGATTCCAGG Y 2 1 2 1 101000 f 74 goat snp18032-scaffold185-9619394 11 64260923 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448312 Affx-122924154 AX-123318648 11 63502853 AGGGGTACACAGGTCAGTGGCATAGATCATGCGTG[C/T]AGCTCTTATTCTGTCCTGCCTTTCACAGACCTGCT Y 2 1 2 1 201000 f 74 goat snp18030-scaffold185-9556311 11 64323946 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403772 Affx-122957990 AX-123274124 11 63533854 AACAGCATGTGCCTGGCCAGAGCACTAAGGGAGGC[A/G]TGCCATGACCTTGTTTGACAAAAATGAAAGGATCT R 2 1 2 1 101000 r 74 goat snp18029-scaffold185-9525310 11 64354894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791336 Affx-122948024 AX-385278329 11 63569103 TTAAATGGGACTGCTGCCTTAAGTTCTCTTTCTGA[C/T]AGTTTATTGCTAGTGTAAGAAACACAACTGATTCT Y 2 1 2 1 102000 f 74 goat snp18028-scaffold185-9490061 11 64390074 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783793 Affx-122941276 AX-385270849 11 63624700 ACATCACTTATTCATAATTCATTCATATGGAGCTG[C/T]GAAAAATAGTTTCTGCCACGTGATAGGTCCCCATA Y 2 1 2 1 101000 f 74 goat snp18027-scaffold185-9434464 11 64445672 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430094 Affx-122937530 AX-123300435 11 63689387 TGATTTTTCTTTTCTGTGCAGCCATGTAAAGTGAA[C/T]TTGTGTGTTGGGTGGGGGAGTGTGTGCTCGGTCGT Y 2 1 2 1 101000 f 74 goat snp18025-scaffold185-9369777 11 64511313 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383271 Affx-122972731 AX-123253629 11 63733903 TGGCCTTTGGAGAACACTCATTGAAGGAGAAATGA[A/G]CCTGAGAAATTCCTGATTCCTTGTTCTGATGCGTC R 2 1 2 1 101000 r 74 goat snp18024-scaffold185-9325261 11 64555845 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379038 Affx-122976353 AX-123249397 11 63813545 ATCCCCTGAATATTGATTCTCTTAGTAGGAAACCA[C/T]GGCTATAAAAGGAAACACAGAAAAACCTATAAGAA Y 2 1 2 1 201000 f 74 goat snp18022-scaffold185-9245619 11 64635615 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382328 Affx-122973894 AX-123252686 11 63864541 AAATCAGATATCCTTCCCCCATAGTGCTCCCCTTT[A/G]TTGACAGCCCTACACCTAGCCTTTCCTTCATGATA R 2 1 2 1 201000 r 74 goat snp18021-scaffold185-9194623 11 64686896 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795777 Affx-122937225 AX-385282730 11 63903479 TTAAGATCCCATATACCACACAGTGTTGGGGAAAC[A/G]CCCTGCCCCAAAATTAATTACTATAAGCATAATTG R 2 1 2 1 201000 r 74 goat snp18020-scaffold185-9155685 11 64725921 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782123 Affx-122966851 AX-385269201 11 63940025 AAGAATGTAGCATGTCCTCGCTTTCTCTGTTGAGA[C/T]CCACGTTAGTGATCCCAGGAGGGAAAATAAACATA Y 2 1 2 1 201000 f 74 goat snp18019-scaffold185-9119139 11 64762433 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381838 Affx-122974256 AX-123252196 11 63983619 TGTTTTTGAATTCACAGTGGCACTGCTGTGTATCA[G/T]AGCAAAAGTTAATTTTACTTCTTTACCACTAAGGC K 2 1 2 1 201000 r 74 goat snp18018-scaffold185-9075545 11 64805745 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397940 Affx-122961921 AX-123268295 11 64032517 CCAGTACTACAAGATCTAAAGAAAAGGTTATTTTT[A/G]TCTCACTGCACAAGGACTTCTCACTACTTGAAGAG R 2 1 2 1 101000 r 74 goat snp18017-scaffold185-9026647 11 64855019 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400019 Affx-122960795 AX-123270374 11 64064569 GAAATTATGCACAAGCAGGGGAAAAGCTTTGTACC[A/G]TGATAACATTTAAACATAAAATGTTAAGTATCTCA R 2 1 2 1 101000 f 74 goat snp18016-scaffold185-8994595 11 64887066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418277 Affx-122947006 AX-123288625 11 64093356 GCAATAATGGGAAGCAATTATTAAATGTACTGCAG[A/C]GAACTTCTGGAGACAGAGAAGAGCCTGTGGCTGCT M 2 1 2 1 201000 f 74 goat snp18015-scaffold185-8965808 11 64916690 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452923 Affx-122920194 AX-123323256 11 64124789 AGGGATGAAATCCATCAACCCATTCATTCAATAAG[C/T]ATTTCATCTTACTACAAGACAAAGAAATGCATAGA Y 2 1 2 1 101000 f 74 goat snp18014-scaffold185-8934375 11 64948059 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446132 Affx-122925773 AX-123316468 11 64172987 CGAGACCCTTGGGTTTTTGTCATCAGTCTGTACAG[C/T]GACGTTAAAATTCTTAGGACAGCAATCGCCATCAA Y 2 1 2 1 101000 r 74 goat snp18013-scaffold185-8886177 11 64996869 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774113 Affx-122942829 AX-385261251 11 64237014 CCCCTCAAGCCGGTGTACTAGTTTCATTTCTTGCA[G/T]TCGAACATTCAGTAACATGTGTTTATATGTATATC K 2 1 2 1 101000 f 74 goat snp18011-scaffold185-8822150 11 65062056 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420202 Affx-122945549 AX-123290550 11 64293949 CCTCAGCAAGGCCAATCAGATTCTCTGTCCTTGAA[C/T]GGACAGAAGCAAACATCAAAAAACCACTGAAGCTC Y 2 1 2 1 101000 r 74 goat snp18010-scaffold185-8765215 11 65119053 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802359 Affx-122951196 AX-385289263 11 64325279 TGAGAATGTGAACATTTGCACTGTGATTACAGCAG[C/T]GACTCACTGTGTGATCTTTGATAAATCATACAATC Y 2 1 2 1 101000 r 74 goat snp18009-scaffold185-8733885 11 65150123 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415659 Affx-122948561 AX-123286008 11 64368945 ATTAAGAGATAGGCTCTATTGAGATGAAGTCAATT[A/G]TGCAATGGTTTTGCTTGCAGTTGACTTAGAGATTG R 2 1 2 1 101000 f 74 goat snp18008-scaffold185-8690219 11 65194034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425274 Affx-122940973 AX-123295620 11 64397609 TTTTCCCGAAACATTCTTTTGGGTCCTACTCTTTG[C/T]ACTGCTGTCCCCAACTTCTGTTTCAAATGCTGTGA Y 2 1 2 1 201000 r 74 goat snp18007-scaffold185-8661555 11 65222782 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381715 Affx-122974703 AX-123252073 11 64449860 AGTATGAGAAAATGTCTTCTTCATGGAGCATCCTT[A/G]CATTAAAAAAGTGATTTTAAGCATAATTACTGAGA R 2 1 2 1 201000 r 74 goat snp18006-scaffold185-8609304 11 65275541 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421600 Affx-122944489 AX-123291947 11 64489729 ATGGAAAATTGAGCTGCTCAAGAACCCTTTCTTAA[C/T]GACAAAAGAACTACAGACAGTATTTTAAAGGCAAG Y 2 1 2 1 101000 f 74 goat snp18005-scaffold185-8569435 11 65315992 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398914 Affx-122961010 AX-123269269 11 64527035 CTGAGCAAGTGTTCTCTGCTGGACCCGAATTTCTT[G/T]TAAAGCCTACTAAATGAAATTTCCTGGCCTTAAAA K 2 1 2 1 201000 r 74 goat snp18004-scaffold185-8532129 11 65353730 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276536 Affx-1111835466 AX-519550047 11 64557785 TCTGAAATGGGAAAATAGCAAATCATTGACAGGGC[A/G]AGAATAAGAATCCAATCTCATATCTCTGGAAGTGC R 2 1 2 1 101000 f 74 goat Random2.2K-1196 11 64557785 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430255 Affx-122937306 AX-123300596 11 64596987 GATTTCTCAGCATGATATTTGTATATTTTTCTATA[C/T]GCACTTTAAATGATAAGTCATGGAGCATCGCATCA Y 2 1 2 1 102000 r 74 goat snp18003-scaffold185-8462177 11 65423675 T C 1 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1371/journal.pone.0152426" Pinkneck-variant SNP associated with pink neck phenotype multi-breed 320787443 Affx-122923569 AX-385274468 11 64628677 AGATTTTCTTGTAATTGGAGAGTTACTAATTAAAA[C/T]ACTACCACACTGGTACAGGCCATCTGTATTTTCTG Y 2 1 2 1 101000 r 74 goat snp18002-scaffold185-8430487 11 65455405 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774432 Affx-122941405 AX-385261568 11 64682831 TTTCTTCTATAGTTAAGGGAGTTAAACATGCCACA[C/T]GTTTTATTTTAGCTCTCCCTTACATTCTTGTTTTA Y 2 1 2 1 101000 f 74 goat snp18001-scaffold185-8376333 11 65510140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765087 Affx-122944445 AX-385252651 11 64742725 CAGGGAAGTAAAAAGGATGCAAAAATATTAGAAAA[C/T]GGAACTATGTATGGGTAAAAAAATTTTCGAAGTAA Y 2 1 2 1 101000 f 74 goat snp18000-scaffold185-8316439 11 65570438 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391216 Affx-122967406 AX-123261573 11 64812102 GAGGGACTGGACAGCCTGTAAGGCATCTGTGCATA[C/T]GCTGATACTAACTACCTCTAAGAGCAACACACACC Y 2 1 2 1 101000 r 74 goat snp17999-scaffold185-8247062 11 65638492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794303 Affx-122969792 AX-385281267 11 64840865 TGCTTCTTTCACATGAATTGAGTGAGATGCTTTCT[C/T]ATTTGTAAGTGTCTACTAAACAAGAATATCTCTTG Y 2 1 2 1 101000 f 74 goat snp17998-scaffold185-8218299 11 65667249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419472 Affx-122945478 AX-123289820 11 64885243 CTTTTGGGATATTTCCAATACTTTCTTCCACTTTA[C/T]AAGTGGGAAAACTGAGGCTTTCAGAGAAGCCTGTT Y 2 1 2 1 202000 f 74 goat snp17997-scaffold185-8173921 11 65711849 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423183 Affx-122942729 AX-123293529 11 64915580 AGCCTAGCCAGCTGGCGTGAACTGTAAAAGTTGGC[A/G]TGTGTGTTTGTGTCATAAATTGTTCTGCATGATGA R 2 1 2 1 201000 r 74 goat snp17996-scaffold185-8143584 11 65742254 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435537 Affx-122933398 AX-123305877 11 64950744 AGTGGGTGCTGCCTCAGTGTAACCAGAACCACGCA[C/T]GAAGGGCTGCTCAATCTGGAGCTCTAGAAGATGTA Y 2 1 2 1 101000 r 74 goat snp17995-scaffold185-8108420 11 65776623 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415266 Affx-122948844 AX-123285615 11 64992154 GAAAGGAAGAGCCAGATGCTGGTTAATATCACTAG[G/T]TAAATATATTTGCATTTATGATGTTAGATTTAACA K 2 1 2 1 101000 f 74 goat snp17994-scaffold185-8067010 11 65817877 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788769 Affx-122942396 AX-385275784 11 65032403 GGCTAAGGATTCAAGCTGTAAGGAATATTTCTGAT[A/C]TCTGTTTTTAAACCAGGAAGAATAGAGACTAATGG M 2 1 2 1 101000 f 74 goat snp17993-scaffold185-8026761 11 65858430 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393448 Affx-122965854 AX-123263804 11 65079261 AGAGGGTGCTCATCATTTGAGAACACAGCCTGGAC[A/G]TTAAATACGTCACTTCCACTCACATTCTCTTGTCC R 2 1 2 1 201000 r 74 goat snp17992-scaffold185-7979903 11 65905651 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1371/journal.pone.0152426" Pinkneck-variant SNP associated with pink neck phenotype multi-breed 468271762 Affx-1111832930 AX-519545556 11 65110438 TAAGTCAGTTTTGTTTTCTATGTTGGTTAAGAAGG[A/G]ACAATAAAAAGGACAAAAGATTTAGAATTCTAAAC R 2 1 2 1 201000 r 74 goat 11_65110438_AF-PAKI 11 65110438 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454105 Affx-122919360 AX-123324438 11 65157452 TGTGATGAGCTTTATCATATCATATTATATCATAG[C/T]AGGACAAGATTCCCCAGTTTTCTTTTTCATGAATG Y 2 1 2 1 101000 r 74 goat snp17990-scaffold185-7901712 11 65980770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423885 Affx-122942297 AX-123294231 11 65200351 TTTTTTCTTGGTTGGTTTGGAGCTTCCAGAAATCC[A/G]TTTTGGTTTCTGACTTGTCAAGTCGTCTTCAGGCA R 2 1 2 1 101000 r 74 goat snp17989-scaffold185-7858813 11 66024668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447142 Affx-122924451 AX-123317478 11 65234025 CTCTTCATTTCCTCTTTCCTGAACCTCCAGGCACA[C/T]GATGCTTTGCTGCTTGTTTGGAATTTGTTGGCAGG Y 2 1 2 1 101000 r 74 goat snp17988-scaffold185-7825139 11 66058364 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401018 Affx-122959679 AX-123271371 11 65266200 AGGTTGCTGGTAGAATACATCTCAAATATTCTCAA[C/T]GCACATACACATGTGCACACACATATAGGAAATTA Y 2 1 2 1 101000 f 74 goat snp17987-scaffold185-7792964 11 66090737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440871 Affx-122929243 AX-123311208 11 65416843 TGACCTTCAGAAACGATGCCTCAGCACCCACATGT[A/G]CTAAATTTATTAGGATGATCGATTTGTCCCAGTTC R 2 1 2 1 101000 r 74 goat snp17984-scaffold185-7642321 11 66238823 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447734 Affx-122924593 AX-123318070 11 65482853 TAAAACAGGTGACTTTATCTGAATGAAAATCATAC[G/T]GTAATACAGCTATTTAAAAAATGAATTTGACAAGG K 2 1 2 1 101000 f 74 goat snp17983-scaffold185-7576311 11 66304681 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411269 Affx-122952315 AX-123281619 11 65520302 TGGAATTTTTACCGTTTTAGAGCTACTCCAGGTGG[C/T]GCTAGTGATAAAGAACCTGCCTGCCAATGCAGGGG Y 2 1 2 1 103000 f 74 goat snp17982-scaffold185-7538862 11 66342158 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780217 Affx-122966064 AX-385267312 11 65550331 ACAGACTACTCTTTAATGCTTGATTTATGGAGAAA[C/T]GATGAAAGTTAGAGAACTTAGGTTTGAGGAAGAAT Y 2 1 2 1 101000 f 74 goat snp17981-scaffold185-7508833 11 66372293 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399886 Affx-122960217 AX-123270241 11 65637588 GGACAAAGCACCGAATAGCAGGCTGTGTGCCCAGC[A/G]TCTAGACCAGCACCTGGCACATATTAAAGTTCTAC R 2 1 2 1 101000 f 74 goat snp17979-scaffold185-7421576 11 66459288 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448585 Affx-122923403 AX-123318921 11 65699264 ATTTTAGGAAGATTAATATGGTGACAACATACAGG[A/C]TGGATCAGCTAGGGGTTAAAGATAAAGCCAGGGGA M 2 1 2 1 201000 f 74 goat snp17978-scaffold185-7359900 11 66520065 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770699 Affx-122943441 AX-385257863 11 65743238 GAGGGCATGACAAAAATCACCACTCAAGTTGAACG[C/T]ATAGATATTTGTAGCTACCCTAAGTTGAGTGCTTA Y 2 1 2 1 101000 f 74 goat snp17977-scaffold185-7315926 11 66564398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441820 Affx-122929066 AX-123312157 11 65779664 TGTGTAGGTCACTCTTCACAGTTAGTAAGTACTCC[A/G]ATTCCATAATTAACAAAAATAAATATGTGAGGAAG R 2 1 2 1 101000 f 74 goat snp17976-scaffold185-7279500 11 66601399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450575 Affx-122922036 AX-123320909 11 65836316 AAACAGTACTTTAAATAGGATATATATAACAGACT[A/G]TGTAGACTAATATATATGTAGGATAAAAATACAAG R 2 1 2 1 101000 f 74 goat snp17975-scaffold185-7222848 11 66658738 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431988 Affx-122935942 AX-123302329 11 65886777 TTTAATTTTTTAAGGAACCTCTGTACTGTTTCCAA[C/T]AATGGCTTTATCATCTTTTATCCCACCAATTGTGC Y 2 1 2 1 101000 r 74 goat snp17974-scaffold185-7172387 11 66711152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444907 Affx-122926251 AX-123315244 11 65916791 CTGAAGTTGAAGGGGAAAGAAGCAGCTTGGGCTCC[A/G]AGGGGGTCAAGCAGAGGGAAATAATTGGTTGACGT R 2 1 2 1 201000 f 74 goat snp17973-scaffold185-7142373 11 66741210 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772354 Affx-122949976 AX-385259507 11 65969210 CCATAAGGGAAGTCCTGAGGTTGAAAAAATATTAA[C/T]CTCTGGTTTGCACCAAAATTCATCTGAGGAAGAAG Y 2 1 2 1 201000 f 74 goat snp17972-scaffold185-7089954 11 66793594 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424533 Affx-122941721 AX-123294879 11 66002888 AGCTTGATTAGAGACCACTCATCCTCTCTGGTTAC[C/T]GAGATAAATGGCTTCTCTGATTACTCTCAGTTTTT Y 2 1 2 1 101000 f 74 goat snp17971-scaffold185-7056276 11 66827100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402429 Affx-122958629 AX-123272782 11 66052291 CCAAATTCATGGCCAAACCAGACACCTGATCTCTG[C/T]GGAGGCCATGTTGAGGCTGGGGGGATCCTACCACC Y 2 1 2 1 101000 f 74 goat snp17970-scaffold185-7006873 11 66877031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427813 Affx-122939751 AX-123298156 11 66086543 TTTCAGAGTCTGCAGAGTTTTTTGACATTGTGAAC[A/G]TGAGCTGCAATCCTTCAGTACAGAGGAGGGGGTTG R 2 1 2 1 101000 f 74 goat snp17969-scaffold185-6972621 11 66911407 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440003 Affx-122929787 AX-123310340 11 66130057 TATTATTACTACACTTGCACAAGCCCAGTGAACTT[A/C]TTTTTTATACCAGCTCTATTGAAGCATAATTGACA M 2 1 2 1 202000 r 74 goat snp17968-scaffold185-6929107 11 66955010 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443484 Affx-122927812 AX-123313821 11 66168837 AGCCTGGGCATGGCCAGTTAGGTAAGTGGGGTTGG[A/G]TGGGGAAGCAGCCTGGTCCATGGTTTGGGTTTGCT R 2 1 2 1 101000 f 74 goat snp17967-scaffold185-6890327 11 66993823 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776042 Affx-122924046 AX-385263172 11 66220751 CATCTGAAAAAATAGCAATAGGAACATGTAGAATA[G/T]CATGTTAATAATTATTGCTATAAAGCTTCCAATTC K 2 1 2 1 101000 f 74 goat snp17966-scaffold185-6838413 11 67046252 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398350 Affx-122962117 AX-123268705 11 66282297 CTGCTCCTGCCCCGGGATCTCAGGGCACTGCGTCC[A/G]TCTCTCAGTCATCATCCTCTGATACTGGGTTGCCA R 2 1 2 1 101000 r 74 goat snp17965-scaffold185-6776867 11 67107751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444218 Affx-122927244 AX-123314555 11 66340533 TTCATAACCACAGGGAAGTGGCCCCCAATATTTCA[C/T]GAAAGCCATGCTTACTCCAAGAATGATCAGAGATA Y 2 1 2 1 201000 r 74 goat snp17964-scaffold185-6718631 11 67165894 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800144 Affx-122930644 AX-385287067 11 66377200 GAGAAAGCTGACAAGGCTGTTGGATTTCAGTGAGA[C/T]AGCAGATAAAATATGAGGCTAGAAAAGGCAGCAGG Y 2 1 2 1 101000 r 74 goat snp17963-scaffold185-6681964 11 67202364 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453299 Affx-122920368 AX-123323632 11 66430580 ATCAGCCTCGTCCATTGCTGCATGGAAGTACAGAG[C/T]AGTTGTCACTTGTGAGCCCCAGACCTGCCTCTTTC Y 2 1 2 1 101000 f 74 goat snp17962-scaffold185-6628584 11 67255733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440370 Affx-122929643 AX-123310707 11 66461446 CATCTAATTCCATTTATCTCACTGGTTCCAAAGTG[C/T]AGTCCCCAGACCAGTAGCATCAGTATCACCTGGAA Y 2 1 2 1 101000 f 74 goat snp17961-scaffold185-6597718 11 67286611 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407771 Affx-122954968 AX-123278122 11 66494445 CTAACTGTCTCCCACATCCATTTTCACTTTCTTCC[G/T]TCAAGGGTAGAACCATGGAGTTTCACTGGGCACAG K 2 1 2 1 101000 r 74 goat snp17960-scaffold185-6564719 11 67319421 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433946 Affx-122934283 AX-123304287 11 66528418 CAGCCTTGAGACTGAAGGTGACAGGCTCAGCAACC[A/C]GGGGTGAGATCTACTTATCACGGACTGAAGGAAGC M 2 1 2 1 201000 r 74 goat snp17959-scaffold185-6530746 11 67353484 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425230 Affx-122941008 AX-123295576 11 66567066 ACTTTTCTTCCAAGGCGTAAACGTCTTTTAATTTC[A/G]TGTTAATTGCTACAAAATCCCTCCTAGCCATCCTA R 2 1 2 1 201000 r 74 goat snp17958-scaffold185-6492098 11 67391907 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400134 Affx-122960708 AX-123270489 11 66630317 TTAAAAGCACCTTTATTTTTGTTGAGGCCTAGGGA[G/T]ACTACTTTGTTCTTTGAAATTAGGATATGCATAAA K 2 1 2 1 101000 f 74 goat snp17956-scaffold185-6428847 11 67453265 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383513 Affx-122972639 AX-123253871 11 66716464 GTACTACATGGCCTAGCACTGTTTTAATCACTTTA[C/T]ATCGATTATCTGGATCCATCTTTGCCTTAATCTTT Y 2 1 2 1 101000 f 74 goat snp17954-scaffold185-6342700 11 67539719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799396 Affx-122926050 AX-385286326 11 66767081 GCTGGTTCACAGGGTCCTATGTACTGCAACTTCCT[A/G]TGATTCTATAATTATTTGAGAGTTAAATCTTTCTT R 2 1 2 1 102000 f 74 goat snp17953-scaffold185-6292083 11 67591206 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768560 Affx-122921939 AX-385255740 11 66798835 TATATGTTCAGGATAGCTTGACTGTTTCACTTTGT[A/G]TAAATAGATTAAACTGATGAGCATTATACAAAGCT R 2 1 2 1 101000 f 74 goat snp17952-scaffold185-6260329 11 67622976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395158 Affx-122964118 AX-123265513 11 66836660 GGCTGTGCACTCGGGTTTTGCTCTGTGCATGGGCT[A/G]CCTCATCACCCACGGACCTTCTCAAAATGTGTCCC R 2 1 2 1 101000 r 74 goat snp17951-scaffold185-6222504 11 67660839 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770530 Affx-122928733 AX-385257694 11 66879305 ATGCTCTATCTTTGGCCAGATTATGAAGCTAAATT[A/G]TTGTTATTGTTCCATTTGTGTAATTTACAGTATTT R 2 1 2 1 101000 f 74 goat snp17950-scaffold185-6179859 11 67703499 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779702 Affx-122919707 AX-385266802 11 66914593 AGAGCCAAGAAAATGAAGTTGGTGGTGGTCAGTAA[A/G]CTATTACAATCTTTGTTCCCATTCCTCAACTGAAA R 2 1 2 1 101000 f 74 goat snp17949-scaffold185-6144571 11 67738864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437493 Affx-122932358 AX-123307831 11 66973870 ACATACTTCAACCTTGTAGTGACCAAAATGCAATT[A/G]TTTTTGTCCCTGCACTTCCCTCCAGGAGTCGTTTT R 2 1 2 1 201000 r 74 goat snp17948-scaffold185-6085294 11 67798119 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375601 Affx-122978722 AX-123245960 11 67016742 TCTGATAAACTTGTTTCCTAAACCCAGCAAGCATG[C/T]GGGAACAGGCAGAATGTTCCACTGCAGTGCTGAAA Y 2 1 2 1 101000 f 74 goat snp17947-scaffold185-6042422 11 67841491 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418212 Affx-122947055 AX-123288560 11 67064749 CTCCACAGAACACAGAGCAATGGATTCTTCTTTGA[G/T]CTCCTCACTTTTCATCTGGATGAATTTTAATCAGG K 2 1 2 1 201000 r 74 goat snp17946-scaffold185-5994415 11 67889566 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433241 Affx-122935246 AX-123303582 11 67095608 AGACCAAATGACAGTCTTAACCCTGGTGGTTCAGT[A/G]CTTCACTGCGGAGCATGGAATATCTCCTGTCCTGT R 2 1 2 1 101000 f 74 goat snp17945-scaffold185-5963556 11 67920653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433118 Affx-122935700 AX-123303459 11 67137883 ACCCTCACTCACTCATGCTACAGATCTCTGGAACC[A/G]TTTACCAGTAGGTTTTTGTGAAAAGAATAAATCCT R 2 1 2 1 201000 r 74 goat snp17944-scaffold185-5921281 11 67963405 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378198 Affx-122976938 AX-123248557 11 67170916 CTGAGTTAAAATGCTTTGGCCTTAGAATAGTCAAA[C/T]GGAAAGCACTGCTGGGGAACAGCAGGCTGCAGGGG Y 2 1 2 1 101000 f 74 goat snp17943-scaffold185-5888248 11 67996708 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446298 Affx-122925651 AX-123316634 11 67201851 TATTTTTTGGAGAAAGAAAAAATAAACCTTGTAAA[C/T]GTTAATGTATGTACCGATGGTGTAGCCCAACTTTA Y 2 1 2 1 101000 r 74 goat snp17942-scaffold185-5857313 11 68027670 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380478 Affx-122975720 AX-123250836 11 67241565 GTCACTGGTGGGAAGGAGATAGATCAAGCCATGTG[C/T]ATGGTCGTAGAGTGAATGTCAAAGGCAGAAGAGGG Y 2 1 2 1 101000 r 74 goat snp17941-scaffold185-5817599 11 68067023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379013 Affx-122976372 AX-123249372 11 67299517 GGCTTGGAGACAGACATCATTAACTGCCTTATCAG[C/T]GGTCTGGTTTCTGTTTTGAATTCCAGCATGGGACC Y 2 1 2 1 101000 f 74 goat snp17940-scaffold185-5759647 11 68125421 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380990 Affx-122974675 AX-123251348 11 67344973 CTTCAGGTCCTTGATCCATTGCAAAGACTGTGCCA[C/T]GGAAATGGCCCCTTAGAGTCAGGAGATCGATCAAG Y 2 1 2 1 101000 f 74 goat snp17939-scaffold185-5714191 11 68169588 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276683 Affx-1111835467 AX-519550193 11 67372642 ATTGTTTTTTATTATACTCAATCATTTATTTATAG[A/G]TAGCCACACATTTAAAGATTTATTTCATTCCTTCT R 2 1 2 1 101000 r 74 goat Random2.2K-1197 11 67372642 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320774634 Affx-122939045 AX-385261768 11 67437186 ATTTTTTTTGTCAATTAGCATTAGCTTTTAAGAGA[C/T]GAATGTGCTGTCCTGCATCCTGTTACTTGTATGAG Y 2 1 2 1 101000 r 74 goat snp17937-scaffold185-5621978 11 68261712 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386092 Affx-122971442 AX-123256450 11 67495748 ACTTCCAAAATGGAGTAAGGACCTTAGAAAAATCT[A/G]CCCCTACATAAAAGCAATGAGAACACTGGCAAACA R 2 1 2 1 101000 f 74 goat snp17936-scaffold185-5563416 11 68320751 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439709 Affx-122930560 AX-123310046 11 67558227 ACATCCTTGTGATTTTAAGTCCTACCAACCAGATA[C/T]ACTCAAGGGAGAGCTTGCTGAAGTGGATCATGCCA Y 2 1 2 1 101000 f 74 goat snp17935-scaffold185-5500937 11 68384026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783477 Affx-122968110 AX-385270540 11 67602487 AACAGAGATAGAAACTGTTGTACCTCTTTTGAAAA[G/T]CAATTTGGTCTAAGTATCACTCCCAATGGTTCCAT K 2 1 2 1 201000 r 74 goat snp17934-scaffold185-5456677 11 68427451 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413592 Affx-122950572 AX-123283941 11 67633676 TCCTTGGGGCTCAGTAGATCCCACATACTCGAGCT[A/G]AAAACAGAAAAGAAATGTTTTCATGGGGGAGGATG R 2 1 2 1 101000 f 74 goat snp17933-scaffold185-5425488 11 68458846 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271888 Affx-1111832931 AX-427210635 11 67663180 ACCTACTCCAGTATTCTTGCCTGGATAATCCCATG[A/G]ACAGAGGAGCCTGGCGGGCTACAGTCCATGGGGTC R 2 1 2 1 103000 f 74 goat 11_67663180_AF-PAKI 11 67663180 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395800 Affx-122963651 AX-123266155 11 67669532 CTTTCCTCCTAGCTCGCTACCTTTATTGTTCCCTC[A/G]TTTCACCTCTTCTGTCCTCTTTACCTAAAATAGCA R 2 1 2 1 101000 r 74 goat snp17932-scaffold185-5389632 11 68494584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438893 Affx-122930447 AX-123309230 11 67698617 CCGAGGAAGGCTGGGCCTGGGGTTCCAGGCTCCCC[A/G]CATCACAAGGAACCCACCAGCCCGAGAGCAGTAAA R 2 1 2 1 101000 r 74 goat snp17931-scaffold185-5360547 11 68523730 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276685 Affx-1111835468 AX-519550195 11 67702146 CACCTTGTCCCCAGCACATAGCTCCATGTCTCCAT[A/T]AGCACCCAAGAGACAGAAGGACATTCTGAAGTCAC W 4 1 2 1 102000 r 74 goat Random2.2K-1198 11 67702146 T A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439161 Affx-122931068 AX-123309498 11 67728711 TCTGGATGAAGGAGGGTGAAGGACATGTGGAACAG[G/T]CTAGGACACAACCCACAGCTTGAAACCCAGCTTAG K 2 1 2 1 101000 r 74 goat snp17930-scaffold185-5330453 11 68553777 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452180 Affx-122921231 AX-123322513 11 67762698 GCAATATGTATTTCATGCAGCTACTTCTCTGCACT[A/G]TAACAGACCCGTTCCCTGGCTCACTTGTTTGCTGT R 2 1 2 1 101000 f 74 goat snp17929-scaffold185-5296466 11 68587813 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385515 Affx-122971257 AX-123255873 11 67805733 ATTAGGCAAAATTGTCTCATTATAACATATATCTC[A/G]TGCCTGTCTCTCCGACTTGGCCACGCCCTTCTTTG R 2 1 2 1 101000 f 74 goat snp17928-scaffold185-5253431 11 68631086 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442632 Affx-122928459 AX-123312969 11 67847328 GGGATGGATGGAGAGATATGGGGTACAGCATCCCC[A/G]TCACAGCACAGTTTTTGGACCTGCATGCCAGATGC R 2 1 2 1 201000 r 74 goat snp17927-scaffold185-5211836 11 68672535 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775006 Affx-122973630 AX-385262138 11 67903544 AGTGAAGTTACCTTGACTGAGTTTCTTTTCTTAAA[C/T]GCTAGTTACTAAGGATGGATAACCACAGAACCAAT Y 2 1 2 1 101000 r 74 goat snp17926-scaffold185-5155620 11 68735016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379482 Affx-122976477 AX-123249840 11 68036077 GAATGTCCTGTTCAGACTGCTCAATGCATTGTAAG[A/G]ACAACTCAAAGCATGTGCTGTGGGGGAGAAACATC R 2 1 2 1 101000 f 74 goat snp17923-scaffold185-5023087 11 68866550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433608 Affx-122934950 AX-123303949 11 68092261 GAGCGTGGGGTCGGGAGATGGGGGACAGAGGAACC[A/G]CAGGACAGAGCCAGCAGTGGCAGCCTCTTCAAGTG R 2 1 2 1 101000 r 74 goat snp17922-scaffold185-4966903 11 68920795 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383737 Affx-122972453 AX-123254095 11 68145547 GTGCCTTCAGCCCTGCAGTGCTCTCTGCTTTAGGA[C/T]ACTGCTTGCCTGCCTCCCTGATGCTGCTGGGAGCT Y 2 1 2 1 201000 f 74 goat snp17921-scaffold185-4913617 11 68973989 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429838 Affx-122938166 AX-123300179 11 68200134 TTCATTAACTATTTGGAAACTTTGTTTAGATTACT[A/G]ATATGAACCTATTGTCGTCGTTAAATGTCGTTGTT R 2 1 2 1 101000 r 74 goat snp17920-scaffold185-4859030 11 69028513 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428961 Affx-122938878 AX-123299303 11 68238489 ATTGGGTGATTGTAAATATTAAATTAAATGCCAGT[A/G]CAGTATTGCTGCTGCCTTTTATTTCTGTAGTTCCT R 2 1 2 1 101000 r 74 goat snp17919-scaffold185-4820675 11 69065729 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406660 Affx-122955805 AX-123277012 11 68278924 TATTTATGAATAAAAGCAGTTAATGGACTTCAGTC[A/G]GAAAAACCTTGAATTAAAAAATATTTGATTTTATT R 2 1 2 1 101000 f 74 goat snp17918-scaffold185-4780240 11 69105858 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801753 Affx-122922558 AX-385288661 11 68352075 CCCCATTGCCAACTGATTTGGGTTGTTTGGACTTA[C/T]GTTGCTCATTTTGTAAATAACTGTAAGCAATTGAT Y 2 1 2 1 101000 f 74 goat snp17917-scaffold185-4707089 11 69179246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276475 Affx-1111835437 AX-519549987 11 68380649 CATGGGGACTAGTGAGTTGACCAGGCAAATAGAAG[A/G]GTCAGCCTTCCTAGAAAATAAGCGCCATGTGGCAC R 2 1 2 1 101000 f 74 goat Random2.2K-1199 11 68380649 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320790331 Affx-122961233 AX-385277334 11 68399397 ATTGATGGAACCAAGAACCCAGAAGTTGGAACTGG[C/T]AGTAGAAATTAAAACGTTGCATAAAGCCAAGAAGC Y 2 1 2 1 101000 f 74 goat snp17916-scaffold185-4659767 11 69225766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775611 Affx-122975013 AX-385262742 11 68445387 TGAGGTTGCTGCATAGTCACCATCAAGGAAAATGG[A/C]CTTGGTGGCTTTGAGTTCTGTTGGCTTTTGACTCC M 2 1 2 1 101000 r 74 goat snp17915-scaffold185-4613777 11 69271831 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377998 Affx-122977600 AX-123248357 11 68478589 GCCTCTGGCTTGGGTGCTTGGGGGATTCTGTCACC[C/T]ACTGAGATAGGAAAGGCAGGAGAAAGGGCAAACTT Y 2 1 2 1 201000 f 74 goat snp17914-scaffold185-4580575 11 69304960 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389365 Affx-122968458 AX-123259723 11 68510465 TAAAAGCAGCCAGGATAAAAAGATGATTAACTTCA[A/G]TGGAATTAGTAGCAAACTGACTCCTCAACTCTCCC R 2 1 2 1 101000 r 74 goat snp17913-scaffold185-4548699 11 69336884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413386 Affx-122950128 AX-123283735 11 68548144 TGATGGTGAAAATGTTGAGTGTTGTGTAGCGAGTA[C/T]GTTGGCATTACACATTCGGGACCCTGTACGTGCCC Y 2 1 2 1 101000 f 74 goat snp17912-scaffold185-4511020 11 69374583 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450224 Affx-122922274 AX-123320559 11 68609943 ACAGCTGGGGTCAGAATGCAGGTCCCTAGTTCCTT[A/C]TGGGTGGTGAGAGGTGGGTGAGACAGTTAAGCCCA M 2 1 2 1 201000 f 74 goat snp17911-scaffold185-4449221 11 69436715 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420332 Affx-122945005 AX-123290679 11 68638601 CTGCATTCATGATTCATGGTTCACCTTCACTCCAA[C/T]CTTTGCTTCCGTCCTCGCATCCCCTTCTCTGACTC Y 2 1 2 1 101000 f 74 goat snp17910-scaffold185-4420563 11 69465636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783130 Affx-122956040 AX-385270197 11 68670327 TATCAGCTGGGATTCAAAGACTAGGGGTGACTTGA[C/T]AGCTGAGATCTGGAACCATCTAAGGGATCCCTCAC Y 2 1 2 1 101000 f 74 goat snp17909-scaffold185-4388837 11 69498015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407314 Affx-122955310 AX-123277665 11 68732010 ATCACTTCAAGAAGCAAATGTGAGAGCATCTCTGA[C/T]ATCGGGGGCTGCCAGCACTCACAGGTTCATTCTAA Y 2 1 2 1 101000 f 74 goat snp17908-scaffold185-4327154 11 69560262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771685 Affx-122925283 AX-385258843 11 68788024 GGAGGTACATCCTTATCTTTCAAAGAAGGGCCCAA[C/T]AGATTACTTCTGGAGCTCATAAATCAAGTAATGGG Y 2 1 2 1 101000 f 74 goat snp17907-scaffold185-4271140 11 69617118 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381974 Affx-122974099 AX-123252332 11 68819617 TGTAAATCCTTGGGAGATGTTTCTCTCCGAATTCC[A/G]TAACAACAATTGTTCTTCACAGTTGACTGTATTAT R 2 1 2 1 101000 f 74 goat snp17906-scaffold185-4239547 11 69648739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408190 Affx-122954194 AX-123278541 11 68865158 CTGGGTTACCTCTTCTCCACATTCCTCTCTGTTTT[A/G]CCACTTATATCTCTGTCATTCTCATTTTTATCTTT R 2 1 2 1 201000 r 74 goat snp17905-scaffold185-4194006 11 69694713 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400431 Affx-122959969 AX-123270786 11 68898658 ATTTCCTTTGGCAATTGGAATGTATGGAGAAGTGG[C/T]GAGGTACCAGATCCAAGCAGAAGGTCTGAGAGTTC Y 2 1 2 1 101000 f 74 goat snp17904-scaffold185-4160506 11 69728598 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397264 Affx-122962350 AX-123267619 11 68930998 GGAAACTCCCACAACCCTTCTCACCTTCTTTCATC[G/T]CCACCTTTCTGCCAATCTGCTTTATTTCTTTTTCA K 2 1 2 1 101000 r 74 goat snp17903-scaffold185-4128166 11 69761310 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439317 Affx-122930952 AX-123309654 11 68959592 TACAAAGGAAAACTATGGCAATAGTGTAGTTCGTA[C/T]GAGATCTTCAGCTCAGGAAAGGACTCAAGGCTTCC Y 2 1 2 1 201000 f 74 goat snp17902-scaffold185-4099572 11 69789953 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395850 Affx-122964015 AX-123266205 11 68992368 TTCAGTCAGTGCATCTGTGTTCAGAATTTTCTCTG[C/T]ACCAGGCACTGTGCAGCTTTTAGGGTGCAAAGCAG Y 2 1 2 1 102000 f 74 goat snp17901-scaffold185-4066796 11 69822770 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396560 Affx-122962930 AX-123266915 11 69039444 TGTTAAAGATAATTCCACCACTGGAAACACTAAAT[A/G]CTTTAAAATAAGAAATTTTAAATTTTTAAGAAATT R 2 1 2 1 103000 f 74 goat snp17900-scaffold185-4019720 11 69870132 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406533 Affx-122955126 AX-123276885 11 69106267 ATGAGTCTTATGTAGGAGAAGCCTGGGAAACACCG[C/T]GTTTCACGAGTTTGATGTAATGGAAAGAACATAAA Y 2 1 2 1 201000 r 74 goat snp17898-scaffold185-3952897 11 69937305 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442282 Affx-122928262 AX-123312619 11 69137181 AAAGAGAACAGCATATGGCAAAGGTTTAACACATA[G/T]ATAGGGTTAACTGAATCTAGCAAAGTCAACGTCAG K 2 1 2 1 101000 f 74 goat snp17897-scaffold185-3921983 11 69968403 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394640 Affx-122964393 AX-123264995 11 69169461 GAATGAGACGGAGTTGTAATGTCCTGGTCTGGGGG[C/T]GTTTTGCTCTGCTTGTTTGCTATTAAGTGATTTGA Y 2 1 2 1 201000 r 74 goat snp17896-scaffold185-3889703 11 70000679 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765305 Affx-122961947 AX-385252830 11 69208064 AGATTTTAGGCCCAGTCACAATGGAGGTCTCCTTT[A/G]CTGCGGCCACTGGATATCAGGTTCACATAACTCCC R 2 1 2 1 101000 f 74 goat snp17895-scaffold185-3851100 11 70035327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450852 Affx-122922234 AX-123321186 11 69246385 CCTGCTCTTCCAGACTTTTTCACATCCACCTCCTA[G/T]AGCAGCTGTGTTTTCCTCTATATTGTCAAGGTTGT K 2 1 2 1 201000 f 74 goat snp17894-scaffold185-3812779 11 70073534 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380914 Affx-122975024 AX-123251272 11 69282150 AGGAGTTTTCTAGATACACACACATCAAGAGTCCC[A/C]GCCCAGGGGCATGTGCAAAGGCACAGAGAGGGAAA M 2 1 2 1 101000 f 74 goat snp17893-scaffold185-3777014 11 70109638 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405220 Affx-122956897 AX-123275572 11 69327649 GTTGTTCCATATACAGGGATTTCCTTCTCCACAAG[C/T]ATATTTAATTTACAAGGAGCCTCTCTTTGCGTTCT Y 2 1 2 1 201000 r 74 goat snp17892-scaffold185-3731515 11 70155061 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421985 Affx-122943793 AX-123292332 11 69361602 TCATCATGAATGAAGCCACTTAAGAGTGAGGCCCA[C/T]GACTTCCCTGTGCGGATGAATAACCAGGCAGAGTG Y 2 1 2 1 201000 r 74 goat snp17891-scaffold185-3697562 11 70188838 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797945 Affx-122929759 AX-385284881 11 69395137 TTCATATTCAAAACTGGGCCTCAACATGCAACCAA[C/T]GGCTATGTGTTATGAGCCTTCATGGCTGCTGATGA Y 2 1 2 1 101000 f 74 goat snp17890-scaffold185-3664027 11 70222418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450357 Affx-122922104 AX-123320692 11 69427352 AAACAGCATATCGGGTAGGAAAACTGAGAAGTGGA[C/T]GGGTCATGGGGGATCATGATGCTGACTACTTAATC Y 2 1 2 1 101000 f 74 goat snp17889-scaffold185-3631812 11 70254666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380992 Affx-122974673 AX-123251350 11 69480159 GGTAGACTGGTTTGATCTTGACAGTCAAGTTCAGG[C/T]ACCCAGAGGAGGCAAAAAGCAGTCTTGGAATTTGA Y 2 1 2 1 101000 f 74 goat snp17888-scaffold185-3579005 11 70306649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449019 Affx-122923088 AX-123319354 11 69515586 ATCTGTTTTCACTTTTACATCCTTGTCTCCTAGGC[A/G]CCTCACACAGTCCCTCTGGATGGGCAGGATGCCTG R 2 1 2 1 101000 f 74 goat snp17887-scaffold185-3543578 11 70343199 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767881 Affx-122920215 AX-385255101 11 69561035 CTTTCTACACTCTTACAGTGTCTCTTATTCTCTAC[A/G]TTATTTTTACATAGATTGCAACATGTCTTATACTC R 2 1 2 1 101000 f 74 goat snp17886-scaffold185-3498129 11 70388371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397353 Affx-122962293 AX-123267708 11 69596498 CAGTTGTCAAGAAATCTGCACTCATGTTACACTCC[A/G]CATACACTTACTTTCTTTTCTGCCTGTTTTCAGAG R 2 1 2 1 101000 f 74 goat snp17885-scaffold185-3462666 11 70422293 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426869 Affx-122940482 AX-123297214 11 69653249 TTCATGTAATAGAATCAACTGAACTCTTTAGCCCT[A/G]TGTAAATCTGTGAACATCTGGTTACTTTTAGACTT R 2 1 2 1 101000 f 74 goat snp17884-scaffold185-3405915 11 70479268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399701 Affx-122960482 AX-123270056 11 69683857 AGAAAAGATACATGTCCCTGTATATCCTGTAAAAT[A/G]ACCACATCACCATATGAGTCCTTTCAATGGCCAGG R 2 1 2 1 201000 f 74 goat snp17883-scaffold185-3375307 11 70509790 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377996 Affx-122977602 AX-123248355 11 69713527 CCTTGTCTGGGGAGAGGAGCTTTTAACTCTTCCCC[A/G]TCCAGGGATTTTACTTTCCTCCTTTTTGCCATTGA R 2 1 2 1 101000 r 74 goat snp17882-scaffold185-3345637 11 70539624 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407366 Affx-122955271 AX-123277717 11 69783534 GTGTGGAAGAAAGCATAGGCTAGGTGGCGCCCTCT[C/T]TTCTATACGGGGCGGCTGACTTGGTGTGAGAGAGT Y 2 1 2 1 201000 f 74 goat snp17881-scaffold185-3275630 11 70607581 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452175 Affx-122921235 AX-123322508 11 69812948 CAGGATGGATATTACAGTGCTAAAAAATTGGTAGA[C/T]GAACAGACTGAAAATGTTGCTTTGTTTTGCTTTTA Y 2 1 2 1 101000 f 74 goat snp17880-scaffold185-3246216 11 70636886 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450956 Affx-122921753 AX-123321290 11 69848584 CAGACTTTTAAAAAATACCTGCTTTTGCATAAACA[C/T]GGAAACTTAACTTTCCTACTGATTCTGAAGTAAGT Y 2 1 2 1 101000 f 74 goat snp17879-scaffold185-3210580 11 70673120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436484 Affx-122932967 AX-123306822 11 69889556 GTCATGACATTCATAGTCACTGAACACACTAGATA[A/G]CTGTGATAATATGATGGATCACATGGATTATGTTG R 2 1 2 1 101000 r 74 goat snp17878-scaffold185-3169608 11 70714618 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385720 Affx-122971102 AX-123256078 11 69933791 TCCCACCTTCAAGCCAATGCCTTTCCCACTATCCA[A/G]ATCATTTTGTGGTCATTTTCCCAAACAGCCATTAA R 2 1 2 1 101000 r 74 goat snp17877-scaffold185-3125373 11 70758947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442006 Affx-122928422 AX-123312343 11 69988007 GCCCCAGAACCATTCTAGAGTTCAGCACTTGGCTG[C/T]GAATCTGCCTCACACTACATGGTGAGGCTGGAGAT Y 2 1 2 1 101000 r 74 goat snp17876-scaffold185-3071157 11 70813401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783929 Affx-122968726 AX-385270983 11 70049560 AAGCAGCTCAGTAGGTCTTCCCATTAAATGCTTCT[A/G]TTTCATAAAAGCAAGTGGAAGGGATTTAGATCTGA R 2 1 2 1 101000 f 74 goat snp17874-scaffold185-3009604 11 70874793 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394950 Affx-122964288 AX-123265305 11 70078443 ACCTGAGCAACAGGCTCGCCAAAGCGTGCGTTTGT[A/G]CTTATTTTTAAACACTAAACATGGGCTTCTCATTG R 2 1 2 1 101000 r 74 goat snp17873-scaffold185-2980721 11 70903218 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376539 Affx-122977994 AX-123246898 11 70162537 TTTCCTCTCACACAATGTCTGATTGTCTCAGCACC[A/G]TTGAACAGTTGGTTGCTTCCTCAACTCTGTTCACG R 2 1 2 1 101000 r 74 goat snp17871-scaffold185-2896627 11 70986834 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387536 Affx-122970304 AX-123257894 11 70206894 ATAATGAGATCTGATTCCAAGGTGGTGATTCCCTG[C/T]GCAAATAACCCCATTGCCTGGGGACAGCCTCCCTG Y 2 1 2 1 101000 f 74 goat snp17870-scaffold185-2852270 11 71031074 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410832 Affx-122952629 AX-123281182 11 70260529 CCCTGGTGGGATCACAGCTCCATGATGAAACTGTT[C/T]GGAAAGTAGCAGAAGCAGACACGATAAGCTTCCTG Y 2 1 2 1 201000 f 74 goat snp17869-scaffold185-2798635 11 71084949 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271890 Affx-1111832932 AX-519545672 11 70300120 GCCATTTCCTCCTCCAGGGGATCTCCCTGACCCAG[A/G]GATTGAACCCACGTCTCCTGCAGCTCCTGCACCGC R 2 1 2 1 103000 f 74 goat 11_70300120_AF-PAKI 11 70300120 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38377982 Affx-122977613 AX-123248341 11 70302596 CAATGTCTTGGGCAGAGACTCTCCCTGGCCTTCCC[A/G]TCCCACTTTTTGGATCCACCCCTGAGAAACTCGGG R 2 1 2 1 101000 r 74 goat snp17868-scaffold185-2756568 11 71126775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414352 Affx-122950020 AX-123284701 11 70359126 CTATTTACTAGATGGGAATTGGAGTTATGTATAAA[C/T]GGTGTCTATGATGAAAATATTGACAGCTGCTTTCA Y 2 1 2 1 201000 f 74 goat snp17867-scaffold185-2700038 11 71183282 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393744 Affx-122965222 AX-123264099 11 70406777 TTCATTTCGTTTTTTCTCTATGCCTAACCCAGTCA[A/G]TTTAGCCAATGCAACTGAGTTCTAAGTTTCTGGAG R 2 1 2 1 101000 r 74 goat snp17866-scaffold185-2652387 11 71230618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393148 Affx-122965545 AX-123263505 11 70451327 GAGTGGATATCATTGTTTATTGTATTTAAATGTTT[A/C]TAGCTTTCCAGGAAAAGTATAATTTTGTATTTGCA M 2 1 2 1 101000 f 74 goat snp17865-scaffold185-2607837 11 71275565 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386094 Affx-122971441 AX-123256452 11 70483199 AACCAGGAACCCTTTGTTCTTGGATCGGAGTGGAG[A/C]TCAGATTGCCTTGTCACATGTGTCTTGGCGCTTCT M 2 1 2 1 101000 r 74 goat snp17864-scaffold185-2575965 11 71307402 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447138 Affx-122924454 AX-123317474 11 70580591 TACCTTGTTAGCACACTATCAGCTGTTTCATTTTT[A/G]AACAATAACACAGCAGTTCAATGCAGTTTAATTTT R 2 1 2 1 202000 f 74 goat snp17863-scaffold185-2478573 11 71403968 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396407 Affx-122963010 AX-123266762 11 70636064 ACCTTCAGATATCTGGCTTTCTGGTTGTTTTTCTT[A/G]CGAATGTTGGTTTATACAAAGCCATTCCATCCTAT R 2 1 2 1 101000 r 74 goat snp17862-scaffold185-2423100 11 71459439 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449760 Affx-122922448 AX-123320095 11 70686655 GACTGAGTGCCCAAACTGAACTGAACTGAAGCGTC[A/G]CTTGGGAATTCCCACATGCATAATCTTTTTAAAAG R 2 1 2 1 101000 r 74 goat snp17861-scaffold185-2372509 11 71509719 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453080 Affx-122920048 AX-123323413 11 70742550 GTCGTATGACCTTATCATACAACAAAAGGGTAACT[C/T]GCCACCATGTGGAGAATACTAACAAGTGATTAAAA Y 2 1 2 1 101000 f 74 goat snp17860-scaffold185-2316614 11 71563958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378122 Affx-122977137 AX-123248481 11 70813063 ACATTAAGGAGCCCTAACCAACAGCCTCCCAACTG[C/T]AAGGCTTGCTAGGCAGGTGTTGGTAACTCCCTGGT Y 2 1 2 1 201000 r 74 goat snp17858-scaffold185-2246101 11 71635113 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384864 Affx-122971946 AX-123255222 11 70849218 CTCCTTGACCACACCCCAAATCTTCCTTTCCTCCC[A/G]CCCAGAGTTTCAGCCCATTACCTCCACACCCTCAC R 2 1 2 1 201000 r 74 goat snp17857-scaffold185-2209946 11 71671607 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769904 Affx-122977530 AX-385257073 11 70904686 TGTTATTCATTTTAATGAGATGTCAATAGAATTGA[C/T]GGTATGACTTTGAATAGATTTCTATTTGGAAAATG Y 2 1 2 1 201000 f 74 goat snp17856-scaffold185-2154478 11 71728216 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443072 Affx-122928125 AX-123313409 11 70942831 CTGCTGTGATTTCACAGGAGATTCTGTGGGCAGCA[G/T]AAACAGTTCGAAAAAAGGACTACTGATAGATAAGC K 2 1 2 1 101000 f 74 goat snp17855-scaffold185-2116333 11 71766194 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771638 Affx-122919723 AX-385258796 11 70980699 AAAAAAAGTTCTTTTTCTGATACTCATGCCTAGCC[A/G]ATACTATCTGTTAGGCTGTTTCTCCTTGAGGCTGG R 2 1 2 1 101000 r 74 goat snp17854-scaffold185-2078465 11 71804435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430379 Affx-122937778 AX-123300720 11 71056186 TGATCAGAAAAATTTAAGTTGTAACCACTATGAAA[C/T]ATCATTACCATATATACCTAAATGGCCAAAATTAA Y 2 1 2 1 101000 r 74 goat snp17853-scaffold185-2002978 11 71880417 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444536 Affx-122926483 AX-123314873 11 71102031 ACCTGAACAGCCTATCACATGCCACCACCCCAACC[A/G]CCCACAGGGAAGGAGAGGAGGGGACACGACTGGGC R 2 1 2 1 101000 f 74 goat snp17852-scaffold185-1957133 11 71923758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380125 Affx-122975996 AX-123250483 11 71132569 TAAATGGCAGGAAAATGTGCAGCTACTGGACCAAA[C/T]GCAAGAAATCCGAACCTCACAGAAAAGTTGGGTTT Y 2 1 2 1 101000 f 74 goat snp17851-scaffold185-1926595 11 71954328 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790538 Affx-122954986 AX-385277541 11 71183897 CACTAAACCAGTCGCACTGGCAGGAAAGCATGTTT[C/T]GCTCACAAGCACTAAACCTAACCCGCCTTCTAAAG Y 2 1 2 1 101000 f 74 goat snp17850-scaffold185-1875267 11 72005770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424855 Affx-122941345 AX-123295201 11 71289983 TTCATCTATAAAGCACAGATCACACTTTCTGCCTC[A/G]CAGTGCCTGGCGCCAAGTATAAGCTCAGTAAATGT R 2 1 2 1 101000 f 74 goat snp17848-scaffold185-1769181 11 72111080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439988 Affx-122929799 AX-123310325 11 71321095 ACCTAAACTTGCCTTCCTCCATCAAATTAAGACCT[A/G]TCTGTCCTTTAATTCCAACATCTTTTGTGAATAAT R 2 1 2 1 101000 f 74 goat snp17847-scaffold185-1738069 11 72142096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410391 Affx-122952432 AX-123280741 11 71363949 AAGAATGCAACTATAACCTATATACATAGATACAC[A/G]TCTAAGTCCCAGACCAACCCCAGAGTAGGACATGA R 2 1 2 1 101000 r 74 goat snp17846-scaffold185-1695215 11 72185504 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783735 Affx-122975255 AX-385270791 11 71396728 CCTTCAAGTCTGTGCTATTAAACTGAGACAACTGC[A/G]TCAAGATAGAGTCCATCATATCATTCCCTGAAGCA R 2 1 2 1 101000 f 74 goat snp17845-scaffold185-1662436 11 72218743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401249 Affx-122959300 AX-123271602 11 71446501 ACAATAAAGCTGAAAAAAAAGAAAAACAAAGATGG[A/G]GAAACATTTGTCTTCACTCAACAACCTTTTTAACT R 2 1 2 1 101000 r 74 goat snp17844-scaffold185-1612663 11 72268646 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431283 Affx-122937099 AX-123301624 11 71505987 GTAAAAGGAGAAGGTAGTTTCTCTGTGATGCCCAG[C/T]GTTCATCTTCAGGCTGGGACCTCACCCTGATGGTT Y 2 1 2 1 101000 f 74 goat snp17843-scaffold185-1553177 11 72327238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793159 Affx-122926917 AX-385280137 11 71560765 TTAATCAACATGCCTCAACTCGAAGGCTCCTAACT[A/G]CTTACTGTGTGTACCTCATTGCCAACTTCCTTTGA R 2 1 2 1 101000 f 74 goat snp17842-scaffold185-1498399 11 72382101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775134 Affx-122937267 AX-385262266 11 71607096 AAATAGTACTGGGATCAATCTCCTTATTCACATAG[C/T]GTTATTTCATGTTTGGCTTTGTCCCTAAATTAGAT Y 2 1 2 1 101000 r 74 goat snp17841-scaffold185-1452068 11 72428670 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437596 Affx-122931863 AX-123307934 11 71644525 CCTGGGGTGTTAGCAACTTCCTGCCTGGCCAGTTC[A/G]ATGCAGAAATAGTGTGTTGCTACTGGATGAAGGAT R 2 1 2 1 101000 r 74 goat snp17840-scaffold185-1414639 11 72465713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453086 Affx-122920043 AX-123323419 11 71688382 ATAATTTGAGGCCTAGAATGGTACCTTCCTCTAGA[G/T]AGGATTAGGTATTTTTTTTCTGCAGATGCTTAGAG K 2 1 2 1 101000 r 74 goat snp17839-scaffold185-1370782 11 72509699 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385434 Affx-122971321 AX-123255792 11 71719803 CAAGAGGTGAGGACAGAGGGTGGCTGGGAGCTGAG[A/G]ACCAGGAGTAGGACTTCAAAAGCTGGGACGCCTTT R 2 1 2 1 101000 r 74 goat snp17838-scaffold185-1339361 11 72541086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448702 Affx-122923859 AX-123319038 11 71769174 CCCTCACAGTTGTTCCTCCATTCTCTTTCTTTTTC[C/T]GAGCATCCTTCATGTGTTAGGCACCACTCCAGGCC Y 2 1 2 1 201000 r 74 goat snp17837-scaffold185-1289990 11 72590723 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450453 Affx-122922954 AX-123320787 11 71818357 CTGGGTGCCCTGGTGGTGAGACTTGCTGGGGTTCA[C/T]GATTCTTTGGTCATGTAAGGCTGCAGGGGCCCTGG Y 2 1 2 1 201000 f 74 goat snp17836-scaffold185-1240807 11 72640044 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413258 Affx-122950226 AX-123283607 11 71851544 AATTATCGTAAACAAGTCTTTAGAGGCATGACCCA[C/T]GGAAACAGAGAGAACACAAGGAAACAGCAGCCATT Y 2 1 2 1 101000 f 74 goat snp17835-scaffold185-1207620 11 72673284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795241 Affx-122961751 AX-385282199 11 71882042 CCAAAGTTTGCTGGGTGGAGCTTCCAAGAAAGTTT[A/G]TTAAAGAAGAGTAGATGTCATCTGTGTGTTTCAAT R 2 1 2 1 101000 f 74 goat snp17834-scaffold185-1177122 11 72703862 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394517 Affx-122964538 AX-123264872 11 71922083 GCTCGTGGGCCAGGCTCCCTGAGTTCGAAGCCCAG[A/C]TCTATCACTTGCTGGCCGTGTGCTCTTGAAGAAGT M 2 1 2 1 101000 r 74 goat snp17833-scaffold185-1137081 11 72743647 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395213 Affx-122964491 AX-123265568 11 71957982 GGCAGTCATAATGATACGCACCCGCAATTTAGACT[A/G]CTGGTTCTCTCTAGAAAGAAGGCTTTAAAGTTAGT R 2 1 2 1 101000 f 74 goat snp17832-scaffold185-1101182 11 72779213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793667 Affx-122965242 AX-385280640 11 72007736 TTTGTAAAGGGAAGGCTAGCTAGCCATCAGATCCT[A/G]TTCTTACATTGAGGCCCAAGGGGTATTTTCCAGGA R 2 1 2 1 202000 r 74 goat snp17831-scaffold185-1051428 11 72829165 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454325 Affx-122919240 AX-123324658 11 72039344 TACAAACAGAAAGAAGAAAGCAGACTGGTAGGAAA[C/T]GGGGTATAAATGGGTCCCACCAGTCCAGTAGGACC Y 2 1 2 1 101000 f 74 goat snp17830-scaffold185-1019820 11 72860811 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417737 Affx-122947427 AX-123288085 11 72076259 TTTTGTATTGAGTTTTGTAATCTTTTCATACTTCT[A/G]CTGTTCCCCTGAAATAAAGATTTAGAGGTAAAACT R 2 1 2 1 101000 f 74 goat snp17829-scaffold185-982905 11 72897735 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391534 Affx-122966647 AX-123261891 11 72116787 ATGTGTTCCCAGCATCAGGCCTTCTCCACACTCCA[C/T]GGCCTTGGCATATGCAGGAGGAGAAAGGGACCAGG Y 2 1 2 1 101000 f 74 goat snp17828-scaffold185-942377 11 72938467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431715 Affx-122936759 AX-123302056 11 72198534 GATATACAGTTTGGGAAAAGGAGTCTCTCTCACAC[A/G]CTGGCCTTCCATACCTCTCCTACTGCTTGGTTTAG R 2 1 2 1 101000 f 74 goat snp17826-scaffold185-860630 11 73020237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276545 Affx-1111835470 AX-519550056 11 72232752 TCAGAAAGGCCTCAGTCATAAGGTGCCCTTCATAT[A/G]GCACCTTCTCCCCAGAGCTAGTAGGGTCTGAATTG R 2 1 2 1 101000 f 74 goat Random2.2K-1201 11 72232752 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439868 Affx-122930051 AX-123310205 11 72261092 GTTTCCTTTAGGAAGCTGAAGTCATCAGTTGATAA[C/T]CTATACTTGATAATTTTGTGATATTTTGCTTCTTT Y 2 1 2 1 101000 f 74 goat snp17825-scaffold185-798072 11 73065450 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795569 Affx-122970049 AX-385282524 11 72298758 ATAGAAGTATAAATAACCATTTTGCCATGGTGTTC[A/G]TGTAACTGTCCTCTTACATGTAATTTTCAAATTGT R 2 1 2 1 201000 f 74 goat snp17824-scaffold185-760406 11 73103119 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451493 Affx-122921124 AX-123321826 11 72333300 GGGAGGCTGGAGAACCAGGCTAAGGAATTGAGGTA[C/T]AGAAACAGGCCACACATGCAGCCTGCTGAGGCCAG Y 2 1 2 1 101000 f 74 goat snp17823-scaffold185-725864 11 73137569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422425 Affx-122943363 AX-123292771 11 72366131 CCTTTCTATGTTTTGGCTTACAACCTTGGCACTAG[C/T]GTGCTGAATAAAGGGGATTCCAGCCCTGTTCTCTC Y 2 1 2 1 101000 f 74 goat snp17822-scaffold185-693033 11 73170369 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404751 Affx-122957227 AX-123275103 11 72406355 GAGGGTGGCAATTTTAGTGCAAGTTATAAGAAAAA[C/T]GGCCAGGAAAAAAAAAGAAAAAGATGATCCCAGAG Y 2 1 2 1 101000 f 74 goat snp17821-scaffold185-652809 11 73210817 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431819 Affx-122936104 AX-123302160 11 72447704 ACCTTTAAAACACTAAAAACATGATAAATCAAACT[A/G]TACTAAAAGTACTAAACTGCACAATACTGCAACAC R 2 1 2 1 101000 r 74 goat snp17820-scaffold185-611460 11 73252709 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416671 Affx-122947587 AX-123287019 11 72530832 TAGACACTGATCGGAGTTGAGAACACAGTTTAAAA[C/T]ATAAATGGAATCTGTGGCTTTCAATTCTACAAAAT Y 2 1 2 1 101000 f 74 goat snp17819-scaffold185-528332 11 73336243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408724 Affx-122953419 AX-123279075 11 72587114 GGAGGAGCTGGTATTGAAGGTCAGAGGGTGAGCAC[G/T]TGGAGAGCCTGGGCGAGGCTCCTGCCAGCATTGCG K 2 1 2 1 101000 f 74 goat snp17818-scaffold185-472050 11 73392654 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421392 Affx-122943987 AX-123291739 11 72640659 AGAAAACATGCTTTACTTTCAAGAATAAAATGAAT[A/C]TGCATAAAAACTGACCTTAAAAAAATATTGACCTT M 2 1 2 1 101000 f 74 goat snp17817-scaffold185-418505 11 73446674 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443635 Affx-122927288 AX-123313972 11 72682714 AAAGACCAGGAGACATTTAGCTGTGATAGGAAATA[C/T]GAGGCCTTTGTTGGAGGAGAGAGAAAAGGTCAGGG Y 2 1 2 1 101000 f 74 goat snp17816-scaffold185-376450 11 73489054 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789427 Affx-122954924 AX-385276437 11 72714483 ATTCTCAACCAGCCTCAAGCTAATTTCTTACACAG[C/T]ACAGTCTTCATCTCAGGGTACTTGACTACAGACCC Y 2 1 2 1 101000 f 74 goat snp17815-scaffold185-344681 11 73520815 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778882 Affx-122948121 AX-385265990 11 72758026 CAGATGAGGAGCTGTTATCCCTGCCTGGAAGAATA[A/G]TGGGTTAACAGTTTTCAGGTAAAGTTACATTGAGG R 2 1 2 1 101000 f 74 goat snp17814-scaffold185-301138 11 73564462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275174 Affx-1111834637 AX-519548753 11 72776369 GCAGGTTCTCCTGGGTTTGGAGGCCCACTCCTGAG[A/G]GCTCCTCTCGCAGAATCAGGATTACAGCCCCCCAC R 2 1 2 1 202000 r 74 goat GoatD01.044149 11 72776369 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38429211 Affx-122937935 AX-123299553 11 72804187 CATCCCCTTCCCTTCCCGCTCTAAACTGGAAACTG[C/T]TTCAAGGTCCTAAGAGGGTTTTCAAAGAGAGTTCT Y 2 1 2 1 101000 r 74 goat snp17813-scaffold185-254977 11 73611207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272485 Affx-1111832933 AX-519546207 11 72846835 AGAGAAAGATGTCCTGTTGTAGTAAATGCCGTTTC[A/C]GGCTTTCTGTGCTTAGGTAAGGAATGGAACAGTCT M 2 1 2 1 101000 f 74 goat 11_72846835_AF-PAKI 11 72846835 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38436986 Affx-122933147 AX-123307324 11 72849439 TAACACACTAGCTAGAGCCGATTATGTGCGTTAAC[G/T]GTCTTGTTTTCTGTTCTAGTGTTTTCCTTCACTTA K 2 1 2 1 101000 r 74 goat snp17812-scaffold185-209725 11 73656925 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402598 Affx-122958424 AX-123272951 11 72935182 CAACTTCAATGCTGCCTTCTCCAAGAAGCCTCTCC[A/G]TACCACCCCACCTAAAGCAGGCCTTTGTTACCCTC R 2 1 2 1 101000 r 74 goat snp17810-scaffold185-123982 11 73741503 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427779 Affx-122939228 AX-123298122 11 72983800 ATGTTAACACAGAATGATTTCTGGTACATATTAAG[C/T]GCTCATTAAGTAATAACAATGATTATAATAACTAG Y 2 1 2 1 101000 f 74 goat snp17809-scaffold185-75364 11 73788677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444652 Affx-122926466 AX-123314989 11 73106943 GCTTGGTTCTCACTGGAGCTGATTAAAGACCTGGC[A/G]TAATCTTATTTATTCATGCACACACCAGGCAAGCA R 2 1 2 1 101000 f 74 goat snp20681-scaffold204-47680 11 73913234 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433150 Affx-122935676 AX-123303491 11 73139447 GGTTGACCTTGTATGAAAGGAAAGAGTAAGTTCTG[C/T]TAATTACCAGCTTGGTGGTGAATATTGACAATTAA Y 2 1 2 1 101000 f 74 goat snp20682-scaffold204-80184 11 73946015 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413528 Affx-122950620 AX-123283877 11 73196476 TTTGGTTCAGCAGGCAGTTCAGTTATTGACAGACT[A/G]CACTGAATTTGTGTAGGCTTCACTCTTTTGCTTTA R 2 1 2 1 101000 f 74 goat snp20683-scaffold204-137213 11 74003107 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795062 Affx-122926057 AX-385282021 11 73254139 TAGAGCAGTTCTGTTGTCACTATTTTCCTGACAGC[A/G]TTTGCTGACTTGTGTCTGTGGGTCACATTTTGGTA R 2 1 2 1 101000 f 74 goat snp20684-scaffold204-194876 11 74057385 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778451 Affx-122947038 AX-385265565 11 73288800 CCCATGGTGTGAAGTAAGAATTAGTGCATCCCTCC[A/G]TTCCAGCTCTCACCTCTTGGATTTCACAGCATGGT R 2 1 2 1 101000 f 74 goat snp20685-scaffold204-229537 11 74091961 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447222 Affx-122924977 AX-123317558 11 73327018 ATGAAATACCAAAAAGAAATAAGCAATTATGCTAG[C/T]AAACAAACAGAAAATGGCCCGAAGGCATCAGAGAA Y 2 1 2 1 101000 r 74 goat snp20686-scaffold204-267755 11 74130089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405936 Affx-122955562 AX-123276288 11 73357801 GGACAAAAATGTGTGAAATGAACACATTCAAGACC[A/G]TGGACAAAGGCAATGAAGGGAAGTTATTCCTCAGG R 2 1 2 1 101000 r 74 goat snp20687-scaffold204-298538 11 74160757 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380639 Affx-122975228 AX-123250997 11 73482161 AAACAACTGGAGCAAATTATGAGAGATCTCTATTG[C/T]ACCTATAAAAGCTTTGTATTCAAATACCTTGCTGC Y 2 1 2 1 101000 r 74 goat snp20690-scaffold204-422898 11 74283985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788123 Affx-122957291 AX-385275143 11 73563829 TACAGTGTGTCTCAATGTGTCTCAGAGACAGTCCT[C/T]AATAAATATTTACTGGCTTTAAAGGGTGAGGGCCA Y 2 1 2 1 101000 f 74 goat snp20692-scaffold204-504566 11 74366334 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443822 Affx-122927067 AX-123314159 11 73625150 TTCTCATTTGCAAAATAAAGGAGTTTCAGTGATCC[A/G]TTTCTTAGTTTGCTAAAATGTCTTTTCTGGAACTT R 2 1 2 1 101000 f 74 goat snp20694-scaffold204-565887 11 74428067 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415498 Affx-122948693 AX-123285847 11 73711890 TGAAACAACTTAGCGAGTAAACAACAGATTTTATA[C/T]TATTGGTGAGCACAATCACAGCGGTTGAAAACTGT Y 2 1 2 1 103000 r 74 goat snp20696-scaffold204-652627 11 74513588 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802364 Affx-122965390 AX-385289268 11 73750232 AAATGATCAGAAACTGCTGACCTAAATGATCTCTT[A/G]CAATTTCTTTCAGTTCTCTAAGACTATGGTTGTTA R 2 1 2 1 101000 r 74 goat snp20697-scaffold204-690969 11 74551995 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391768 Affx-122967467 AX-123262125 11 73786612 TATTAGGAGAACATTAGAAAGCTCTTTTTAGTTTA[C/T]GAATATTATTTGTGCGAAGTATGCAGAGAACTTTG Y 2 1 2 1 101000 r 74 goat snp20698-scaffold204-727349 11 74588309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383649 Affx-122972526 AX-123254007 11 73879551 ATTCATAACTCAGCCGCCTCAAAACCCAGCAGTCC[C/T]GAAGGGCAGCTTTGATCTGGCTACTGAACAATAGC Y 2 1 2 1 201000 r 74 goat snp20700-scaffold204-820288 11 74681564 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792537 Affx-122940560 AX-385279518 11 73970640 ATTCTTGATCTGTATTCTGTTCTGCTGATCTGTTT[A/G]TTGACTTCTGTAACAATAGAACAATACTCCTAATA R 2 1 2 1 102000 f 74 goat snp20702-scaffold204-911377 11 74772907 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432856 Affx-122935362 AX-123303197 11 74026374 TACAAATATGCTAGAAGAATTCAGTATTAAATGAA[C/T]GCTTTTGAAAGACTGAGTAAGGTAAGTGAATATCA Y 2 1 2 1 101000 r 74 goat snp20703-scaffold204-967111 11 74829760 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424927 Affx-122941289 AX-123295273 11 74126242 AGTCCCACTCCACCACCGAGCTTTTCTTTTAGTGA[A/G]CACTCGTGGGGATTTTCACTTTCATTAGGTGTCGG R 2 1 2 1 201000 f 74 goat snp20705-scaffold204-1066979 11 74930096 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424196 Affx-122942510 AX-123294542 11 74162407 AAAAACCACAAAACCTGCAAAAACAGCGTCCCTTA[C/T]GTTAGATACTCACAGCCATGGCTGGGGCGAGCTTC Y 2 1 2 1 101000 f 74 goat snp20706-scaffold204-1103144 11 74966112 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772148 Affx-122937314 AX-385259303 11 74204878 GCAGAACTTCAGAGCACAGTTGGTGAAACCTTGGA[C/T]AACTCCATGGTGAACATATAGGGAGGCAGAGCCAC Y 2 1 2 1 101000 f 74 goat snp20707-scaffold204-1145615 11 75008653 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795539 Affx-122921580 AX-385282494 11 74246062 CGCATCCCTGCTAGCTAAGTAGCTAACGCAATTTC[A/G]TCTTCTCTTATGGAGAAGGATGACTCAGTGTGAGC R 2 1 2 1 101000 r 74 goat snp20708-scaffold204-1186799 11 75049339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447553 Affx-122924039 AX-123317889 11 74276371 CACTTAAAGTGCAGGCGAAACCCATTAGCTGGGCA[C/T]GAACAGGCACAAGTCGTCTCACGATGCGTTATCAG Y 2 1 2 1 201000 f 74 goat snp20709-scaffold204-1217108 11 75078772 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392252 Affx-122967563 AX-123262609 11 74336191 TAAGAGTAAAGGAGTTCTGAGACTTGGACCTACCC[A/G]CCTTCCTCAAATTCAACATTTCATCATGAGTTGAA R 2 1 2 1 101000 f 74 goat snp20710-scaffold204-1276928 11 75137179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406497 Affx-122955154 AX-123276849 11 74366446 GAGAGGTCCACCAGAGCGTCACGACGCCCAGGATG[A/G]TAGCTCTACCACCCCATTCACCCACTTTGGCCTTT R 2 1 2 1 101000 r 74 goat snp20711-scaffold204-1307183 11 75167282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405615 Affx-122956606 AX-123275967 11 74417779 TTCAATCAAGCCAGTGACCCAGCTAAACCATAGCA[C/T]GGGGGATTGATTTTTCAGAGTCTTGATCTTGCGAT Y 2 1 2 1 201000 f 74 goat snp20712-scaffold204-1358516 11 75218472 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377677 Affx-122977841 AX-123248036 11 74454284 AGTCCCAGCTCTGCCTCTCACTGGCATGTCTTAGA[C/T]GGTACTCCTCTTCTCTGGGCCTCACTTGATCAAAC Y 2 1 2 1 201000 f 74 goat snp20713-scaffold204-1395021 11 75255122 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430642 Affx-122936953 AX-123300983 11 74503462 TTTTTTCTTTGCCTGCTTGGATGTTCTCCATCACT[A/G]CCCCCTCATAGTTTTGTTCCCAGCACTTTAGCTTT R 2 1 2 1 101000 f 74 goat snp20714-scaffold204-1444199 11 75304098 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419864 Affx-122945368 AX-123290212 11 74541286 GAGATCCATATCTATGCATTGGTGACATGACTAGG[C/T]GATGCATAACAAACACCTGGAACCACAAAACCTGA Y 2 1 2 1 101000 f 74 goat snp20715-scaffold204-1482023 11 75341509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429238 Affx-122937915 AX-123299580 11 74572990 ATCGATATAAAAATTGTCAAGAATTATGAGAATTG[C/T]CTCTGCTACCTGGTTGCCCCACAGGTGGCAGAGGG Y 2 1 2 1 101000 f 74 goat snp20716-scaffold204-1513727 11 75373106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396064 Affx-122963446 AX-123266419 11 74629368 AGAGAATTTCATATTCATGCCTGGTGGGCAGGTGG[C/T]GAGATATCACAGCATGAGAGATGGAAGACATGGAA Y 2 1 2 1 101000 r 74 goat snp20717-scaffold204-1570105 11 75430180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792171 Affx-122958807 AX-385279156 11 74669490 GAAGATGAAGCCCATATTCTAACTCCAGATTACAC[A/G]TCTGCTTGGATTGCCTGATACCTGGAAAAGTAGGA R 2 1 2 1 101000 r 74 goat snp20718-scaffold204-1610227 11 75470646 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412672 Affx-122950773 AX-123283021 11 74743056 CACAGGCCACAGCACCAAGGGGACACCTCCAGACC[A/G]CACCATGTGGCCGGCTTGGGCCTGTAATTTGAAGT R 2 1 2 1 101000 r 74 goat snp20719-scaffold204-1683793 11 75545372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798376 Affx-122945395 AX-192074689 11 74816916 AGAGTAGTCAGAGATATCAGGAGATAGAAGGAAAA[C/T]GAGCAGCATGATGCCTAGAAACTAAGAGCAGAATG Y 2 1 2 1 201000 r 74 goat snp20721-scaffold204-1757653 11 75619214 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443980 Affx-122926992 AX-123314317 11 74856427 CATTTGTAGACACTGTGGGTGAAGCAGCCATATCT[A/C]TGATGCCAAGACCTTGGCAGGGAAGGGAAAAGCCA M 2 1 2 1 101000 f 74 goat snp20722-scaffold204-1797164 11 75658713 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409950 Affx-122952859 AX-123280301 11 74916962 GAGGCCCTGAAAACAAAACATTTTCCCGTCATTAG[A/C]TGGGGTCTTTCCAGGAAGGTGGTAAAAGGACCGCT M 2 1 2 1 101000 f 74 goat snp20723-scaffold204-1857699 11 75719875 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386524 Affx-122970737 AX-123256882 11 74953797 AACACGGAGGACTTGGTGACCTACATGGGTAAGAA[C/T]AAAGCATCTTAGGTCTGTTTAGGAAGGAGATCACA Y 2 1 2 1 101000 f 74 goat snp20724-scaffold204-1894534 11 75756848 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276692 Affx-1111835471 AX-519550202 11 74986167 TACCACTGAGCCACCAGGGAAGTCCTAAACTTCAG[A/G]TTTTAAACCAGAAATCTAGCTTCTGTATCAAACAC R 2 1 2 1 101000 r 74 goat Random2.2K-1202 11 74986167 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394217 Affx-122964897 AX-123264572 11 75046265 ATTATTAAGCAATGATTTCCAGCATTTGAAAATAA[C/T]ATCAGTGTCTTGGAGGCATTTGTGCTGGCTAAAAT Y 2 1 2 1 201000 f 74 goat snp20726-scaffold204-1987002 11 75857662 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800154 Affx-122945049 AX-385287077 11 75087826 CCCTCCCATCATGCCAAAAGCAAACTTGCTCATCC[A/G]CTTAGCACGTGTTATGCACCACGTGACCGAAAATG R 2 1 2 1 101000 r 74 goat snp20727-scaffold204-2028563 11 75900066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772703 Affx-122941704 AX-385259850 11 75131680 CTATCAAACAATACTTTATCAAAGTATTCAAGACT[A/G]TGATAGGCAACCCTCTCTCAGACTTAAGTTTGACA R 2 1 2 1 101000 r 74 goat snp20728-scaffold204-2072417 11 75943468 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794484 Affx-122974169 AX-385281447 11 75168869 TAATCTAACAAAGAAGTGTGAATGTATTGATTTTT[A/G]CCTTACCTCGGTGAGGAAAATGAGAACAATCTACA R 2 1 2 1 101000 r 74 goat snp20729-scaffold204-2109606 11 75980834 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427936 Affx-122939214 AX-123298279 11 75200444 TGCTTAGCACTCAGTGAGGAAAGAGACTACCACCC[A/G]TAGAAATTTTCTTAGGAGATAGTACTGAGTCTAGG R 2 1 2 1 201000 r 74 goat snp20730-scaffold204-2141181 11 76012458 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376872 Affx-122977828 AX-123247231 11 75288096 TGCATATTATTCATCTATACTATATTTTCATACCT[A/G]TTTATTTAGGCTACTCCCTCACGTGTGGGTCGATG R 2 1 2 1 101000 r 74 goat snp20732-scaffold204-2228833 11 76100364 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405862 Affx-122955852 AX-123276214 11 75336865 GGCATGCAGAAATGTGAAGTAACTTTGACTTCTGA[C/T]GGTGTAATAATGATGATGTTGTCAGAGAAGAACCA Y 2 1 2 1 101000 f 74 goat snp20733-scaffold204-2277602 11 76137983 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271892 Affx-1111832934 AX-519545674 11 75347872 TGCATTTCTGGTCTGTGATCCTGACTCAGCTGTGA[A/G]TGCTGGGCTGCCATGGGGAAGAAGGTTGCTTTGGG R 2 1 2 1 101000 f 74 goat 11_75347872_AF-PAKI 11 75347872 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437409 Affx-122932421 AX-123307747 11 75377197 GTGAATGGCATCCTTCCCTGTTTGGTCACACTGAT[A/G]CAGTTTTCTAAAATACACATATTTTTATATAACAT R 2 1 2 1 101000 f 74 goat snp20734-scaffold204-2317934 11 76178322 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415088 Affx-122949455 AX-123285437 11 75418240 TTCCTCAAAGGTCCACCTTCAACACCTTTCCCTGA[C/T]GTTACAGGCTTCACACCCCCTATGCTTATGGAAGT Y 2 1 2 1 201000 r 74 goat snp20735-scaffold204-2358977 11 76219236 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790954 Affx-122951370 AX-385277951 11 75490366 AATAGTTTTTATCATGTTAGGGTCGACTTTTTAGT[C/T]CTTAGCTTGTATAGCTTTTCATCGGAAAGATGCAG Y 2 1 2 1 101000 r 74 goat snp20737-scaffold204-2431103 11 76292240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779326 Affx-122948078 AX-385266430 11 75527471 ATAGTTCATGAAAACTACACCCCCTTATAATTTTA[C/T]GATATTCTTAACCTGACATTGTAGCTATCTATATC Y 2 1 2 1 102000 f 74 goat snp20738-scaffold204-2468208 11 76329971 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378270 Affx-122976879 AX-123248629 11 75588510 TTGAACGTTTTTTACTGCAGTGAATATCTTAGATA[C/T]GAATATTTCAATATTTTGAAATATTCTTTCAAAAG Y 2 1 2 1 103000 f 74 goat snp20739-scaffold204-2529247 11 76391078 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430835 Affx-122937437 AX-123301176 11 75653813 GCAGGACTATAGTTAATAAGGCATAATTAATAAGT[A/C]GCTGAAATATTATCAGTTTGCATTTTTACCTATCA M 2 1 2 1 101000 r 74 goat snp20740-scaffold204-2594550 11 76456431 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798381 Affx-122969425 AX-385285315 11 75688812 TCCAAATAACTAGATCAGTTTACAGAACCACAGGT[A/G]TGAGCCCCATTTCCTTACCAACTCAACGACTTTCA R 2 1 2 1 101000 f 74 goat snp20741-scaffold204-2629549 11 76492586 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392576 Affx-122966072 AX-123262933 11 75737029 CACCTTCCACTCCTCCACCCCCTGAGGCAACTTGA[C/T]ACAAATCAAAGATTGAACAGTACTGGCAAATCATT Y 2 1 2 1 201000 r 74 goat snp20742-scaffold204-2677766 11 76541310 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407043 Affx-122954936 AX-123277394 11 75852386 TCATGCGTATCTTGTTTGCTGCTGCTTAGTAGTCA[C/T]TGAGTTGTGTCTGACTCTTTGTGACTCTGTGGACT Y 2 1 2 1 101000 f 74 goat snp20745-scaffold204-2793123 11 76656345 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780479 Affx-122975839 AX-385267570 11 75927181 GGGGCCAAATGTGTGAAAAGCAAAGTATAAAATAC[A/G]TATTTTAGCTAAAACCAAGAACTAAAAAAGGCTAA R 2 1 2 1 101000 f 74 goat snp20747-scaffold204-2867918 11 76731924 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798730 Affx-122951129 AX-385285661 11 75963973 ATAGGACAGAGAGAATTGTTGCAGTGATACATACT[A/G]TAGGCAGTGGAGTACAGCTATTTAGTGTGAAACTA R 2 1 2 1 101000 r 74 goat snp20748-scaffold204-2904710 11 76768691 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776161 Affx-122972188 AX-385263289 11 76038441 ACCAGGCTCTTGGATTGCAGAAACTATGCTAAGCA[C/T]TTTTCTGTTCCCAAGATAACAGGGCAAAGCAGAAG Y 2 1 2 1 102000 f 74 goat snp20750-scaffold204-2979178 11 76843854 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412236 Affx-122950913 AX-123282586 11 76069119 ACACCCTTTCCAGTTTCCCCACCTAATTATTCTCT[A/G]CACCACTTCATCTACCCTCTTTTCCTGTGATTTCA R 2 1 2 1 201000 r 74 goat snp20751-scaffold204-3009856 11 76874540 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391038 Affx-122966866 AX-123261395 11 76125772 TGGCCTCAAATGAGGGATGAGAGCTACTTATGGAA[C/T]GTGCTGGTGGTCTGTAAACACAGCCTCTGCTGTGT Y 2 1 2 1 101000 f 74 goat snp20752-scaffold204-3066509 11 76931451 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414561 Affx-122949387 AX-123284910 11 76165169 AAGAAAGATGATTTAATGACCTCATAGTGGGAATC[G/T]ACCACATACCTTGGGTTCAAGTGGTCAAAAGAACT K 2 1 2 1 101000 f 74 goat snp20753-scaffold204-3105906 11 76970088 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432237 Affx-122936359 AX-123302578 11 76226846 CTCTGTGGCTCAAGTCTCCCTGTCCTGTCCCTTGC[A/G]TGAGGTCAGGGAGCCCAGGAGGAAGAAGGTTTCAC R 2 1 2 1 101000 f 74 goat snp20754-scaffold204-3167583 11 77030819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799060 Affx-122950517 AX-385285990 11 76261749 CTGCTAGAAAGTTCCAGGAGCTTTGCTTAGTCAGA[C/T]ATTCATATTCTTACCACATTCCCCTTATAACCAAT Y 2 1 2 1 101000 f 74 goat snp20755-scaffold204-3202486 11 77065582 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415416 Affx-122948730 AX-123285765 11 76293852 TTATATTCCCCTGGCAGCAGTGATCCAAGAAGGTG[A/C]ATTACCACTTTTATTAGACACACTCCATCCTCCGA M 2 1 2 1 201000 r 74 goat snp20756-scaffold204-3234589 11 77097725 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437221 Affx-122932035 AX-123307559 11 76327938 TCAAGGACTTTCATATGCAAATACTTATATGTGAA[C/T]GTCATTATGCTGCTCCAATATACGGATTGAAGTTT Y 2 1 2 1 101000 f 74 goat snp20757-scaffold204-3268675 11 77131502 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404161 Affx-122957075 AX-123274513 11 76365557 TCCTTTCTCATTACACTCACTAACCACATGACATT[A/C]GCTTCATGGCCTTGTCACAAGGCCACAGATGCCCC M 2 1 2 1 101000 f 74 goat snp20758-scaffold204-3306294 11 77169212 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771636 Affx-122932186 AX-385258794 11 76401047 CACAAAAATCTGAACGCACTAAGCATTTAGGGTTG[C/T]GACATCCTGGGGAAAAGCAAGAAGTTGGAACTCAT Y 2 1 2 1 202000 r 74 goat snp20759-scaffold204-3341784 11 77205102 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395618 Affx-122963806 AX-123265973 11 76448163 CCTGACCATGTCTCAATCCTTGCCACCAATTCACC[A/G]CCGAGTCTTGCTGATATGCCTCCTAAGTGTCTCTC R 2 1 2 1 101000 f 74 goat snp20760-scaffold204-3388900 11 77252769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772057 Affx-122963279 AX-385259212 11 76548192 CAGCTCATCAGTGAGGCAAACCTACTACAACTCCC[A/G]TGAGCGAGTCTGCACAAGTACTACACTGATACTTA R 2 1 2 1 101000 f 74 goat snp20762-scaffold204-3488929 11 77353388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378435 Affx-122976769 AX-123248794 11 76601299 ACAGGACTACTGCAACAGGAGTTGCCTCAGTCACA[C/T]TGCCGTTGAGGGAGAAATACGCGGCCATTTCCCCA Y 2 1 2 1 101000 r 74 goat snp20763-scaffold204-3542036 11 77406976 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392271 Affx-122967548 AX-123262628 11 76727485 ACTGAACAACAAATCATGCCTCTCTTTAGAAACCC[G/T]CTATAAGATATCCAGAGGATATGCTTGGCATAACC K 2 1 2 1 101000 f 74 goat snp20765-scaffold204-3668222 11 77532993 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418411 Affx-122946542 AX-123288759 11 76764699 ATCAGTGTTTGTTGAATAAATCCAGGATGAATGAA[C/T]AAACAGAACAAATTATTTTTTCCTTTCCTGCCAAC Y 2 1 2 1 101000 f 74 goat snp20766-scaffold204-3705436 11 77570453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393509 Affx-122965808 AX-123263865 11 76851787 ACTCCTCCTCTGGAGCCCAGGGGCTCACACACCCT[C/T]CTCTGCGGTTCTAGACTTTGCCTTGCTCTTTCCTC Y 2 1 2 1 101000 r 74 goat snp20768-scaffold204-3792524 11 77656443 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442275 Affx-122928267 AX-123312612 11 76885391 AAGGTAACTAGAAACCCCTTTACACTTGTGGTTAC[A/G]AGATTCACCCTTGAGGACCTGCATGTTTGAATTCT R 2 1 2 1 101000 r 74 goat snp20769-scaffold204-3826128 11 77689960 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424279 Affx-122941988 AX-123294625 11 76923989 GGAAGCTCACAGTGTGATGAAGAAAACAACTACTT[A/G]TGACATAAAAGAATAAACCTAACAATCAAAGCAAG R 2 1 2 1 101000 f 74 goat snp20770-scaffold204-3864726 11 77724268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437356 Affx-122931936 AX-123307694 11 76980256 GGACCCTTACTTTCCAACTATTTCATGTCCATGAT[A/G]CCCATAGCTCACATCTTGAAGAGAGGATCTATTAG R 2 1 2 1 101000 f 74 goat snp20771-scaffold204-3920993 11 77781630 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452267 Affx-122920762 AX-123322600 11 77028417 ACTACAATAGTTCAGGGAATAATTGAGAGTCATAG[G/T]CTTCAAGGACAGAGACCTGGGTTTGAATCTCACTG K 2 1 2 1 201000 f 74 goat snp20772-scaffold204-3969154 11 77830151 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380315 Affx-122975388 AX-123250673 11 77065021 CACCCCTGCCTTTATAGTTATACAGCCACAGATTA[C/T]GCAGGACGTGTTTTTCTAAATAGCAAGAAGCAGTC Y 2 1 2 1 101000 f 74 goat snp20773-scaffold204-4005758 11 77867125 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448054 Affx-122923697 AX-123318390 11 77142975 GATTTAAAAGTGAGGCAGCCCCTAAGGACAGGAGC[A/G]TGGCCACTTCTCCTTGGAGGCCTCTTTCTAAATAG R 2 1 2 1 201000 r 74 goat snp20774-scaffold204-4083712 11 77945971 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439583 Affx-122930072 AX-123309920 11 77173366 GGAGGTTGCATGGCTGGGAAGTGGCTAAGCTGGAG[C/T]TGGAACCCACCTCGGTGCTGCCATGTAGACTTGGG Y 2 1 2 1 101000 f 74 goat snp20775-scaffold204-4114103 11 77976131 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400047 Affx-122960774 AX-123270402 11 77207970 CTCAGGGGCCTGACCTCCCAGTTTCCCACTAAACT[C/T]CAGGAACTGGGGTTGGAGAGAGGGATTTGCATGTT Y 2 1 2 1 201000 f 74 goat snp20776-scaffold204-4148707 11 78010381 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403742 Affx-122958014 AX-123274094 11 77316692 GTCCAGAAGGCAATGACACCAAACTTTTTCTCTTC[A/C]CCTCCCCCTCTTTTTTCAGTCTTGAAAGCAAGTGA M 2 1 2 1 101000 f 74 goat snp20778-scaffold204-4257429 11 78118998 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794886 Affx-122952223 AX-385281846 11 77407967 AGATCACCATTGGAGACAGGTCTTCATTTGTTGGG[C/T]ATTCAACCTAGTACTAAAATGAATTGAAAATAGCA Y 2 1 2 1 101000 f 74 goat snp20779-scaffold204-4348704 11 78210996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435348 Affx-122933597 AX-123305688 11 77459953 CAGATCAGTAAACAAGAACACTCTGAAGTGAAGGT[A/G]TGTGTTTGGGGTGTAGGGGTAGTGTGACTTTTAAA R 2 1 2 1 201000 f 74 goat snp20780-scaffold204-4400690 11 78264471 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402160 Affx-122958646 AX-123272513 11 77587806 ATAGATACCAGACCTGGGGGCTGGGATTTGAAGTC[A/G]TGATGGTGGGGGCTTGAAGGCAGGCCAGCCTCTCA R 2 1 2 1 103000 f 74 goat snp20782-scaffold204-4528543 11 78391928 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402968 Affx-122958158 AX-123273321 11 77669781 TATGTGGTCTAACAGGTATGTGAGAAGGAGACAGA[C/T]GCAGGGAGAAGAGAAATGCAGGAAGGAGAGATATA Y 2 1 2 1 101000 f 74 goat snp20783-scaffold204-4610518 11 78474195 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274742 Affx-1111834397 AX-519548328 11 77710315 CAACCGGCTTCTGCAGGACTCCTTCCCTGTGGAGA[A/C]AGAGCCGAGCTCTTCAGGGTGACTTTTAGACTTGG M 2 1 2 1 201000 r 74 goat GoatD01.033435 11 77710315 T G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38451693 Affx-122921570 AX-123322026 11 77772764 TTTACGATATGCTCAAGAGTGTGTTACTAATAGAA[C/T]AGAAAACAAGGTGTGGTGCAGGGGGAGAGATTCAG Y 2 1 2 1 201000 f 74 goat snp20785-scaffold204-4713501 11 78577786 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397981 Affx-122961807 AX-123268336 11 77889065 AATTCTCACCAGTAGCAGCATATATAACACAGCAA[C/T]AAGCTCTACAGTGTTTTTTAATTTATATGCATTTT Y 2 1 2 1 101000 f 74 goat snp20787-scaffold204-4829802 11 78694039 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801014 Affx-122976259 AX-385287928 11 77967512 GTTTTTCACCTAACGATGTACGAACCATCTGAGAA[C/T]AGAGACTATGGTTTGAATCATCCTAGCATCCCTGT Y 2 1 2 1 101000 r 74 goat snp20789-scaffold204-4908249 11 78772784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272637 Affx-1111832935 AX-519546348 11 77978166 CGTATATCTGCAATGAAGCCAAGGAGAAAGTCAGT[A/G]TTGAATTATATACAGTAGAGCTTCCTAGTGACCAA R 2 1 2 1 101000 f 74 goat 11_77978166_AF-PAKI 11 77978166 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413617 Affx-122950557 AX-123283966 11 78034505 AATCGCGACTCCGGTAACGGAGCCCTTGAGTGGAG[C/T]AGACTGTCCAATGTCAGTGGTAAGAAAATGTGAAA Y 2 1 2 1 101000 r 74 goat snp20791-scaffold204-4975242 11 78840122 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381781 Affx-122974296 AX-123252139 11 78112524 AGTGGCAGAATATTTGTCTCCTGGGTTGATACTGT[C/T]CCTCCTTAAGGTGATGGGTTCATCTTGGGCTGTGC Y 2 1 2 1 101000 f 74 goat snp20793-scaffold204-5053261 11 78918054 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782576 Affx-122943901 AX-385269650 11 78183930 AGCTCTTGGTGTGCCATTCAAGTGGTGATATCTAA[C/T]GGGTAATTAGGTCTGTTATCAGGAAGTGGTCTGAG Y 2 1 2 1 202000 f 74 goat snp20795-scaffold204-5124667 11 78988873 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415360 Affx-122948774 AX-123285709 11 78273281 AGAAAGTGAGATTGCAAGGTCTAGTAACAGAGGAA[C/T]GGGATCTTATAGGGTTCTTCAAATTCCCTTTCCAA Y 2 1 2 1 101000 f 74 goat snp20797-scaffold204-5214018 11 79077654 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399333 Affx-122961366 AX-123269688 11 78312227 TAAACATGTGTCCAGGGGAGAAAAATAGCAGCTCA[C/T]GGACTTGCTGCCTCGATGTCACTCAATCATTCAGC Y 2 1 2 1 201000 r 74 goat snp20798-scaffold204-5252964 11 79116919 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424834 Affx-122941360 AX-123295180 11 78367480 AGTAGGGAATTTTGAAGGGCAGGTGTCTCCCCTAT[A/G]TTTTTATTTCTGGGGAGTATTTTGGTGATGATTTT R 2 1 2 1 202000 r 74 goat snp20799-scaffold204-5308217 11 79172775 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413672 Affx-122950108 AX-123284021 11 78400856 GCAGGCAGATTCTTTACCATCTGAGCCACCAGGCT[A/G]TCACTGAAATAGCATGCCTCTTCTTCTGGGTTTCT R 2 1 2 1 101000 r 74 goat snp20800-scaffold204-5341593 11 79206276 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399611 Affx-122961090 AX-123269966 11 78431672 GCAGAGATTTCCCGAATAACCTTGACTCCACCCAC[A/G]CATAGCCTCCACCATCACCAGTGTCCCACACCACG R 2 1 2 1 101000 f 74 goat snp20801-scaffold204-5372409 11 79237901 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411677 Affx-122952004 AX-123282027 11 78463081 TCAAAGTGGAAACTCCTCGGATCTGATTACATTTC[A/G]TCGCAGATGGTGAATTTATGCCCTGATCTCCCACC R 2 1 2 1 101000 f 74 goat snp20802-scaffold204-5403818 11 79269347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778942 Affx-122932088 AX-385266049 11 78494272 GGAAGAAGTACTTCAAAAATTCTCATAGTGAGGGC[C/T]TATGGATGTTAAGCTCTTCTATTTCTTGGTATTTG Y 2 1 2 1 101000 f 74 goat snp20803-scaffold204-5435009 11 79300456 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444055 Affx-122926859 AX-123314392 11 78542074 TCACTCCTACTGCCAAGATGCCAGTCCATGCTCTT[A/G]GAGAAAATGCCCAGTCCTTGAAGTCATCCTAAAAC R 2 1 2 1 101000 r 74 goat snp20804-scaffold204-5482811 11 79348265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446148 Affx-122925760 AX-123316484 11 78589370 TGGTCATGCTTGGTTTAGAAAATAAGATGCTTTCC[A/G]TGGTGAACAAGCAAGGTAGAGATGTTATCCTTTCT R 2 1 2 1 101000 r 74 goat snp20805-scaffold204-5530107 11 79395604 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393572 Affx-122965395 AX-123263928 11 78627505 ATTATGTTTCACACTTTAAACATATATAGTGCTGT[A/G]TGTCAGTTAGATCTTACAAAACTGGAAGAAAAAGA R 2 1 2 1 101000 r 74 goat snp20806-scaffold204-5568242 11 79433911 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449654 Affx-122922578 AX-123319989 11 78673032 TTCACAGGAACTTGGGCTGCTTATGGGAACCTGCT[A/G]TAAGAGTAGAAAAGGAAGAAGGACTCGGGGATTAG R 2 1 2 1 201000 f 74 goat snp20807-scaffold204-5613769 11 79479631 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790215 Affx-122931187 AX-385277219 11 78705017 TAAATGTCCTGACATATAAAATCCCAGCGGATAAA[A/C]ATATATTTCACCTCCTTCATGTTTTTGCTCAAGTG M 2 1 2 1 201000 r 74 goat snp20808-scaffold204-5645754 11 79511874 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784161 Affx-122942620 AX-385271213 11 78742660 CCACATCACAGGCATCCTTATTTTAATTGGCTACA[A/G]TGACCAAGACTGGAGATTTGAGTTTCAAAAACAAA R 2 1 2 1 101000 f 74 goat snp20809-scaffold204-5683397 11 79553045 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454323 Affx-122919241 AX-123324656 11 78785862 TGTCTGTTAGTCTTCCAGGGGCCCTGTCACAACCC[A/G]TTAGCTCTATTTTACCTTCTTTTCATTCCTAACTT R 2 1 2 1 101000 f 74 goat snp20810-scaffold204-5726599 11 79596404 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767985 Affx-122965889 AX-385255199 11 78816570 ACTTCTATAGCAAAGACCAAGGACAATTGTTCTTA[C/T]TATGGAGGTGAGCTGTGATAGCAATATATTGTAAT Y 2 1 2 1 101000 f 74 goat snp20811-scaffold204-5757307 11 79626957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412073 Affx-122951699 AX-123282423 11 78858146 ATTTACTTGAATGGCCTTCTGAATGTTACTTACAT[G/T]ACTATTGAACGTATGTAGCCAACACCGGATACATA K 2 1 2 1 101000 r 74 goat snp20812-scaffold204-5798883 11 79664694 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381313 Affx-122974443 AX-123251671 11 78890880 AATACTGGACCCCAAGATCAGGAAAAGAATGCTAG[C/T]GGGACAATTAGCATAACAGGGAAGTTGGATGATAG Y 2 1 2 1 201000 r 74 goat snp20813-scaffold204-5831617 11 79697688 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432415 Affx-122935834 AX-123302756 11 78925751 AGCAATAATATTATCAATAGTATTCATAATTGTTT[A/C]TGAAGCACTTAATCTACAGTGAGCATTCTAAGGTC M 2 1 2 1 101000 r 74 goat snp20814-scaffold204-5866488 11 79732483 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408954 Affx-122953926 AX-123279305 11 79069662 TCGCCTCTGCAACAATGTATGACAGCGCCAAGGAC[A/G]TGGCTTACTGTGACACACAGCTCCGTGTGGTCTTT R 2 1 2 1 101000 f 74 goat snp20817-scaffold204-6010399 11 79877540 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393855 Affx-122965146 AX-123264210 11 79102730 AGATATGAACCTGGGCAATCTGAAGCCAGGATGCT[C/T]GGTGTGCTGGTCAGGATGGTGTCCAGATGTCACAA Y 2 1 2 1 101000 f 74 goat snp20818-scaffold204-6043467 11 79910747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778948 Affx-122940962 AX-385266055 11 79138503 TCTACAGTAATAATAGTTATCATTGAACACAGGCC[A/G]TTAAAGATTGCATAGAACTAGGTCATTAAAGATTG R 2 1 2 1 101000 f 74 goat snp20819-scaffold204-6079240 11 79946497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774022 Affx-122969172 AX-385261160 11 79211632 GTCACTGATTTTGTTCCTCTTCCTAGCCACACACC[G/T]AAATCATATTTCTTAGTTCAAATAGAGAAAATAAG K 2 1 2 1 101000 f 74 goat snp20821-scaffold204-6152369 11 80018885 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420941 Affx-122944988 AX-123291288 11 79275383 CAGCAGAAGGGGTGGGATAGAGGGTGCCAGGAGAT[A/G]CATCAGTGAGATAGGAGCCAGATCATGAAGGACCT R 2 1 2 1 101000 r 74 goat snp20823-scaffold204-6216120 11 80082849 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797508 Affx-122934273 AX-385284447 11 79283834 ACCTACATGGCAAATAAATTTCCCCACATCCTTGG[C/T]GTAACTTGAGCACCAAGTTATTATAAACTGAGGAA Y 2 1 2 1 102000 f 74 goat snp14766-scaffold1595-3825 11 80101808 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412442 Affx-122951415 AX-123282791 11 79316279 ACGCCATGGTCATATGCAAGAACTAGAGGTCAGAA[G/T]ACAGAGAATGGCTTGATAAATGCCACTTGCCCTTT K 2 1 2 1 101000 r 74 goat snp14767-scaffold1595-36270 11 80134353 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776431 Affx-122955521 AX-385263558 11 79360659 GAAGAGGACCATGGCTGCTGTGCACATGGAAATAA[A/G]CGTGGAAGGAATAATAATACTTGTCATTCAGTAGG R 2 1 2 1 101000 r 74 goat snp14768-scaffold1595-80650 11 80178947 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400524 Affx-122961263 AX-123270879 11 79414460 CCTTGCTCTCTGGAAATCTCCACTGGAGTTGACAA[C/T]AGCTGAAAAATGGACCAGGCTGAGCACGCATGCAT Y 2 1 2 1 101000 f 74 goat snp14769-scaffold1595-134451 11 80229923 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389275 Affx-122969013 AX-123259633 11 79447552 AACTATTATTAATGACCTATTCGATGGTAATCTAG[C/T]GTGGAGAAGAAGTAGTGTTTTCTAGGACTCCTGTC Y 2 1 2 1 201000 f 74 goat snp14770-scaffold1595-167543 11 80263413 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276549 Affx-1111835472 AX-519550060 11 79504046 AGAGTTTTCTTTCAAAAGGACTCGTCTTGTCATTC[A/C]CCTGTTCAATAATCTTTGATGCCTACCAGGTGTCT M 2 1 2 1 101000 f 74 goat Random2.2K-1205 11 79504046 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448181 Affx-122924252 AX-123318517 11 79531759 ATCTAGACATCCTATAGTGGAGGCGATGGTGAATG[C/T]TCCCCTTCATGGGAAAACAGCACAAAATGATTCAT Y 2 1 2 1 101000 f 74 goat snp14772-scaffold1595-251750 11 80348275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378466 Affx-122976679 AX-123248825 11 79589304 CTGAGAGACCCAGCATGGTGTGGACTCAGAGTGTA[C/T]AGTGGAGTGATTTTGGCAAGTCCATTGCCAGGAGC Y 2 1 2 1 101000 r 74 goat snp14773-scaffold1595-309295 11 80406241 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420356 Affx-122944960 AX-123290703 11 79600093 GTTCCATGGTGCTTTAAGGCCAGATGTATGAAGCA[C/T]GCAGAGAGCCCTTTTTCCAGTAGCAATTATCTGAT Y 2 1 2 1 101000 r 74 goat snp56550-scaffold893-1100083 11 80416787 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411594 Affx-122951611 AX-123281944 11 79629663 TTTTTAATTCCTGAATATTTAGATCCTGGGAAGCC[A/G]TCATTTTCCTCTTGAGACAGAGCAAAAGGAAGGAA R 2 1 2 1 201000 f 74 goat snp56549-scaffold893-1070513 11 80446362 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439314 Affx-122930954 AX-123309651 11 79662512 GAAAGCCTCAGAGAATGGGTGATAATGATACTGGA[A/G]GTTGCATTGGCATTTGCCAGATAGAGAAGGAGGCA R 2 1 2 1 101000 f 74 goat snp56548-scaffold893-1037664 11 80478484 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403118 Affx-122958122 AX-123273471 11 79731268 TCTCTAAGAAAACTATTTAGCTTCTTATGGATCTC[C/T]GCTAGTCCCTATAGACATCTACGATATTAGCTATA Y 2 1 2 1 101000 r 74 goat snp56546-scaffold893-968908 11 80548960 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450261 Affx-122922184 AX-123320596 11 79869688 GACTAGAATGGACGCAGATGTCCTACTGTTGGTAC[A/G]TGGTGAGAGTGAGAGGCAGAATTGGGATTTTGCCC R 2 1 2 1 101000 f 74 goat snp56543-scaffold893-830488 11 80686578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428589 Affx-122938704 AX-123298931 11 79924890 CAGGCCCTGACTTCAAGCTATGTAGAATGTAATGA[C/T]GAAGACAGGCAAGGAAACAATCTCTTAGAAGAGCA Y 2 1 2 1 101000 f 74 goat snp56542-scaffold893-775286 11 80741751 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789160 Affx-122952285 AX-385276172 11 79955330 GGACTTATTTGCACAACAAAGCTTTTAGACTCAAC[A/G]TCTATGTAATTCACCAGTGTATTCTCAAAACCAAA R 2 1 2 1 101000 f 74 goat snp56541-scaffold893-744846 11 80772395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463178232 Affx-1109853482 AX-514664715 11 80000662 GCCAATTGTATTTAAGGTTTGATAACATTTAGCAG[C/T]ATTTCTGATCTGTTCATCTGTAAAATGGAAATACT Y 2 1 2 1 101000 f 74 goat Random2.2K-1206 11 80000662 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38423791 Affx-122942822 AX-123294137 11 80112395 CTCCTATTGCCTCATCCATTACCTCTGATGTGAAA[C/T]GAACAACTGCAATAACCTTTTAGCTAATCTCCTTT Y 2 1 2 1 101000 f 74 goat snp56538-scaffold893-587781 11 80929546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381164 Affx-122975215 AX-123251522 11 80245430 TATGGGCAAAAAAAAGGTCATTTAAGATGTCTTCT[A/G]TAGTGGGACCTTCTCACTTTCTGTGACTAATTTTT R 2 1 2 1 101000 r 74 goat snp56535-scaffold893-454746 11 81062640 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435576 Affx-122933370 AX-123305916 11 80299798 GATTTCCTCATTGACTACAATAATAAGAGTTTTCT[A/C]ATCATTGTTATGGGGACTGAAAATGATGAAATGAA M 2 1 2 1 202000 r 74 goat snp56534-scaffold893-400378 11 81117385 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408129 Affx-122954241 AX-123278480 11 80334858 ACTAAACCCCAATGGGGCTTCACTGGGCTTCTCTC[A/G]TGGTTCAGATGATAAAGAATTTGCCTGCGATGCAG R 2 1 2 1 103000 f 74 goat snp56533-scaffold893-365318 11 81152359 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777769 Affx-122943298 AX-385264887 11 80365309 TTTTGAATGCATTGCTTTGTTCAGCATTTTGCTTC[A/G]CGCAAGGAAACAAGTCTTCATCTATCATTATTTCT R 2 1 2 1 101000 r 74 goat snp56532-scaffold893-334867 11 81183252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405043 Affx-122956356 AX-123275395 11 80403159 TACATCTCTAAGTATTAAAACACTTTACTGTGTCT[A/G]TTTATCAAACATGCCTACAAATAACAGGGCAGAAT R 2 1 2 1 101000 r 74 goat snp56531-scaffold893-297017 11 81221057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395771 Affx-122963672 AX-123266126 11 80512951 ATAGCATAACTTCACGGAAGAGGGAAATAAAGTAA[C/T]CTTTTTTTAATTGTAGGATAATGGCTTTTGCAATG Y 2 1 2 1 201000 f 74 goat snp56528-scaffold893-187225 11 81330939 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376412 Affx-122978084 AX-123246771 11 80545184 AAGATTACCTTCTCTTTCCACCTTTCCACAGAACT[A/G]CTCTCCTTCCAGTCCTTCATGATCTTTCTCTTGCT R 2 1 2 1 101000 r 74 goat snp56527-scaffold893-154992 11 81363171 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394655 Affx-122964381 AX-123265010 11 80594958 GTACCTCCTAGTCTAGGTGCTTGTATGAGAGTTAT[A/C]AAAATGGCCCTGATACCATCCAGAGACACAGCCAT M 2 1 2 1 101000 f 74 goat snp56526-scaffold893-105218 11 81413309 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424499 Affx-122941746 AX-123294845 11 80624232 TTCAATACTGAAATTTATTCACTCATTACTAAGTC[A/G]TCAGATGAGAGCCGACCAGGAGTTGGCAAAACTGA R 2 1 2 1 201000 f 74 goat snp56525-scaffold893-75944 11 81442864 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796699 Affx-122950833 AX-385283644 11 80686065 GCCCAGTCATCTAGCCAGCATCACAAACAGTTAAG[C/T]AGGGATCACTTCTGACTATACCCACTTTATAGCCA Y 2 1 2 1 101000 f 74 goat snp56524-scaffold893-14111 11 81504515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409953 Affx-122952857 AX-123280304 11 80702737 TTTTCGACTTGCAAATAAGGGAATGTAAGAAAACA[A/G]CTCACAGCTCCATTGATTATTTCTGAAGGTGCTCA R 2 1 2 1 101000 r 74 goat snp26298-scaffold2752-245433 11 81520754 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407967 Affx-122954342 AX-123278318 11 80737358 ATGTTACAAGGAGAGGCCATTCCCCTTCTACTCTG[G/T]CCATAACACATTCATTTACGCAGAATGGAGAGAGC K 2 1 2 1 201000 r 74 goat snp26297-scaffold2752-210812 11 81555022 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440147 Affx-122929681 AX-123310484 11 80770637 GAAGGCCAAAGTTCAAGAACAGCTACATAAGCAAA[C/T]AGGGCCACTGAATTCTGGGTGACATTGTGAGAAGC Y 2 1 2 1 101000 f 74 goat snp26296-scaffold2752-177533 11 81588447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420033 Affx-122945146 AX-123290381 11 80800928 AACTTTTGATCAAGACAACAGCTTGATTTCTCAGC[C/T]GGACTCCGGGCATATCTGCTGCAAGCTGCAGGATC Y 2 1 2 1 101000 f 74 goat snp26295-scaffold2752-147242 11 81618618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414544 Affx-122949502 AX-123284893 11 80834044 GCGGTTCCATCATCCATCCTTTCTTGGAGCAGTGG[C/T]CTGGGTGTGAGGCTTGTTCCCCAGGCCCTGGGACC Y 2 1 2 1 101000 f 74 goat snp26294-scaffold2752-114126 11 81651723 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272641 Affx-1111832937 AX-519546352 11 80840278 TTTTAGCCCTGAATGCTTTATAAATATGTCACATT[A/C]TTTCTTTGGGTTTTAAGACTTCAGACTTGTATTCA M 2 1 2 1 201000 f 74 goat 11_80840278_AF-PAKI 11 80840278 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38407281 Affx-122955335 AX-123277632 11 80875440 ACAGTGTTGATTTTCTCAAAAATTTTTGTTGTTCA[C/T]GAGGTGGGCACTTTCACCAACCTAGGCTTTTCCAT Y 2 1 2 1 201000 r 74 goat snp26293-scaffold2752-72730 11 81692706 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275468 Affx-1111834820 AX-519549041 11 80917849 TAAAGAAACTG[A/C]GAGAACCATGAGTTTATGTCATTTCCTAGCCATTC M 2 1 2 1 102000 r 74 goat GoatD01.054964 11 80917849 A C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38451861 Affx-122921068 AX-123322194 11 80946573 AGAGGTGCTGAGGCTGGAGATGGAAGAAGGTCATG[C/T]GTCCTGCAGGGTGGGTCTTAGCTCAGGCCCTCTTC Y 2 1 2 1 101000 f 74 goat snp26291-scaffold2752-1597 11 81763987 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453955 Affx-122919470 AX-123324288 11 80949949 GAGAGGATGGATGGCTGAACTGGGGTAGGAGGAAA[A/G]GTGAGAGAAAGTGGGCTGATCAAGGAATCGTAAGA R 2 1 2 1 201000 f 74 goat snp22594-scaffold2238-1028770 11 81767137 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392963 Affx-122965682 AX-123263320 11 81013197 ATGCTAAAGGATTCCAGGAATTTCCACATACCTGC[A/G]CTCACTCTCCTCTTACCATTAACATCTTGTAATAA R 2 1 2 1 101000 f 74 goat snp22593-scaffold2238-965522 11 81831088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420630 Affx-122945227 AX-123290977 11 81044517 CTTGAGAAAGAAACAGAGAGAAAGTGAAATCATTG[C/T]GGTGACAAAATAACATTGGGAGGAATAAAAGTACT Y 2 1 2 1 201000 r 74 goat snp22592-scaffold2238-934202 11 81862482 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395743 Affx-122963696 AX-123266098 11 81091990 GTGTGGAATTAACCCACTCACTCATACCACCTTTA[C/T]GAGCCAGGTTCTGTCTCATGTGTTAGGGATGCCAA Y 2 1 2 1 201000 r 74 goat snp22591-scaffold2238-886729 11 81909686 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437156 Affx-122932138 AX-123307494 11 81299629 CCAGCGCAGGTACTATGAATCAGGATGTAGGCCAT[A/G]CGGGCCCACCTGGCTCAAGAATTCTTTTTGTCCAG R 2 1 2 1 101000 f 74 goat snp22587-scaffold2238-679090 11 82103695 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787886 Affx-122939184 AX-385274908 11 81354014 AAATAATGCCAGTGAAATGTGACATTTTGAGTCCA[C/T]GATTCTAAAGAGTTGGATGAAAGCAGAAAAAACTC Y 2 1 2 1 101000 f 74 goat snp22586-scaffold2238-624705 11 82157684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451061 Affx-122921429 AX-123321395 11 81383557 ACTGCCTATCTGGTGGGCTGGGGGGAATCTCGAGA[A/G]TGTAAAGGTTACATAAGCACCAAACAGATGACAAG R 2 1 2 1 102000 r 74 goat snp22585-scaffold2238-595162 11 82187226 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789089 Affx-122978506 AX-385276102 11 81414340 AATAAGTTTTGATTCAAACATGACACTTTTTAACG[C/T]GGTGCAAAACTCGTTTTGTGCAAAATCCCATTATA Y 2 1 2 1 101000 r 74 goat snp22584-scaffold2238-564379 11 82218035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387545 Affx-122970296 AX-123257903 11 81464115 TTCTCTGAGATTCCTCTGTCATCTACCCTTCAGGA[C/T]GGGGCTGGGGAACTTTCCGAGGAGGTGAGTTGAAC Y 2 1 2 1 101000 f 74 goat snp22583-scaffold2238-514604 11 82267852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412003 Affx-122951754 AX-123282353 11 81502029 TGGGGAGGTGGCTCAAGCCCAAGTGATGTAATAAG[C/T]GACCTGAGAACACAGAGGCACTAAGAGGCTCTGCC Y 2 1 2 1 101000 f 74 goat snp22582-scaffold2238-476690 11 82303553 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385009 Affx-122971875 AX-123255367 11 81547174 CATGTTTAGGAGCTAGGATCTTGCCTTTCAGGAAA[C/T]AGGAGCCATTGGCAAGCTTTCACTTCTCTTTCCAG Y 2 1 2 1 101000 f 74 goat snp22581-scaffold2238-431545 11 82348817 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439275 Affx-122930982 AX-123309612 11 81612978 TTGAAGAGTTTCTTTTTAAGGACTTGCTGCCACTG[C/T]ACCTGGCTCTAAAATTCCACTGCTCCCTCCTGGTT Y 2 1 2 1 101000 f 74 goat snp22580-scaffold2238-365741 11 82414864 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439375 Affx-122930269 AX-123309712 11 81651090 AGCTAGTTCTCTCTTGTTCTGCCATCCTCAGTATA[C/T]GGCTCTCTTTCCAAGGCCCAAAATAGCTGCTCAAG Y 2 1 2 1 101000 f 74 goat snp22579-scaffold2238-327629 11 82453678 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397128 Affx-122962679 AX-123267483 11 81764682 GAACAGGAATGTGATGTTACTGAGCTGTCGCAGCG[C/T]CACTATGATGGCAGAATGAACGGCGATAGTGGAGG Y 2 1 2 1 201000 r 74 goat snp22576-scaffold2238-214037 11 82567443 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442243 Affx-122928291 AX-123312580 11 81795450 CAAAATGTCTTCCAAAAGACTGGGAAAAATTTATC[A/G]TAAGATGAGATTTGCATTTTCTCTATAAAATACAT R 2 1 2 1 201000 r 74 goat snp22575-scaffold2238-183269 11 82598005 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274313 Affx-1111834181 AX-519547909 11 81802995 GAGAAACAGGTGTTTCCTCCACTTCCTCATGCCAA[A/G]AGGCAGGTTAC R 2 1 2 1 102000 f 74 goat GoatD01.023840 11 81802995 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38428890 Affx-122938931 AX-123299232 11 81842218 AGTCTAAGATCCTGGACCATCACAGGAAGATGTCT[A/C]GGCCAGTGTCTACCTACATGACCAACTGACAGATA M 2 1 2 1 101000 f 74 goat snp22574-scaffold2238-136501 11 82645074 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774799 Affx-122927283 AX-385261933 11 81886974 AAGTGGAAACTGTGAGGACTTACCCTGTAAAGAGG[A/G]TGGCATTTGTCCCTGAAACATGGAGCCAACTGGGC R 2 1 2 1 201000 r 74 goat snp22573-scaffold2238-91745 11 82689664 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400109 Affx-122960727 AX-123270464 11 81915905 GATGCCACTACCTTAAATTTCTTCAGTAGCCGAAC[A/G]TGGGTTTCCGGTTGAATGGCGTACTTCCCAAGATC R 2 1 2 1 201000 r 74 goat snp22572-scaffold2238-62814 11 82717473 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399115 Affx-122960858 AX-123269470 11 81994658 GAATTCCAAAGAGACCTTTACCCCAGACTTTAAAT[A/C]GGATCTTCGTTATGTCAGCCTTATTTTATCCGCTC M 2 1 2 1 101000 r 74 goat snp33696-scaffold396-15840 11 82796018 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430844 Affx-122937431 AX-123301185 11 82052474 TCCCCAAATCTACAGTGGCAGAATTGGTTTTAGAC[A/G]CTGGCTGTCTCTGATTCTTAAATGAAATCAACTGT R 2 1 2 1 101000 f 74 goat snp33697-scaffold396-73656 11 82850137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419210 Affx-122945697 AX-123289558 11 82166753 GGAGATGAGCAATTTTATTCTGCTGTGAGATATCC[A/G]GAAGATGACTCCTAGCCAAAACACACACTCAAAAT R 2 1 2 1 101000 f 74 goat snp33699-scaffold396-187935 11 82964877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420467 Affx-122944878 AX-123290814 11 82211261 TGGACCACAGTTCCTTCTGGCTGAATGCCCATCAA[C/T]CCTGCTCACCTTGGACATCCTTCAGAAAATGATGC Y 2 1 2 1 101000 r 74 goat snp33700-scaffold396-232443 11 83009479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796612 Affx-122923476 AX-385283558 11 82247927 TTTAGATTCTGTGACATAATCTGAGCATGCCTGTC[A/G]TCTGCAGGTAGAATTGCTTGAACCATCATCAAAAG R 2 1 2 1 101000 f 74 goat snp33701-scaffold396-269109 11 83046186 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768404 Affx-122939350 AX-385255584 11 82334818 CAGGAGCTCTAACTATTTTCTGAAAATTGTTCACT[A/G]CATGGAGTAAAACAACACAATTTCTCACCTTAAAT R 2 1 2 1 101000 f 74 goat snp33703-scaffold396-356000 11 83133138 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786189 Affx-122953785 AX-385273224 11 82369464 GGATCTATTTCCGTATTTGCACAATACCTGTATCA[C/T]GGATTTACAGTGATGATTAAAGAAAGGTGACCATG Y 2 1 2 1 101000 r 74 goat snp33704-scaffold396-390646 11 83167892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433939 Affx-122934289 AX-123304280 11 82406158 TTACCTTTCCCCTTTCCTATAACTTGGGGAGCAGT[A/G]CCCCCATGATGAGTTAAAGATGAGTTAAGAGTAGA R 2 1 2 1 201000 r 74 goat snp33705-scaffold396-427340 11 83204992 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793069 Affx-122937969 AX-385280047 11 82439014 GTCCATGAAAGAGCTTTGAAACTTACATATCCCTA[G/T]ATGGAAGTGAGGGGTAGTCTGATGATTTTTTTCCA K 2 1 2 1 102000 r 74 goat snp33706-scaffold396-460196 11 83237873 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426527 Affx-122940198 AX-123296873 11 82497200 ATATTACAAGTGAGAAAAGATGTGCTTACCTGTCC[A/G]TTTATGCTATGTCTCCTTTAAAGCATGTTTAAATG R 2 1 2 1 201000 r 74 goat snp33707-scaffold396-518382 11 83295355 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448194 Affx-122924241 AX-123318530 11 82571511 GCTACCACATAAAGGTAGTCAATCTTTATCAGCTT[C/T]CAACCAAAATGAGCTAGAATGGTTGCAGAAATGCC Y 2 1 2 1 101000 f 74 goat snp33709-scaffold396-592693 11 83367233 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775742 Affx-122967204 AX-385262873 11 82646769 TCTACTTACCATTGTGTGCTATACTCCCACTTACC[A/G]CTTATTTTGTCAATCTGTTATATCACTATAAAATA R 2 1 2 1 101000 f 74 goat snp33711-scaffold396-667951 11 83443794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440681 Affx-122929921 AX-123311018 11 82677653 GCAGCTATGCATGGAAATGATAAGAGTGTTCTGCA[C/T]TGGACCTGGATGATGGGGAAAGCTTAGGGAAGAGA Y 2 1 2 1 101000 f 74 goat snp33712-scaffold396-698835 11 83474963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427064 Affx-122939806 AX-123297409 11 82727471 CTATGCAGACAGAATAAGCCTGCTTTAAACTTGAG[C/T]ACTGCCTTTCTTGTCTGTTAGGGTATAAGCCCCAT Y 2 1 2 1 201000 f 74 goat snp33713-scaffold396-748653 11 83525290 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779525 Affx-122932912 AX-385266628 11 82786305 GTGAGAGACAGGTGTGAAAGCTGTAGGAAATTGGA[C/T]GCTATTTTACCTGGTAGGAGTTAATTGTGCTGACC Y 2 1 2 1 101000 f 74 goat snp33714-scaffold396-807487 11 83583762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394788 Affx-122964822 AX-123265143 11 82815591 AAATCTCTGAAACTGTCCTTTATTAAGAGTAGGGG[A/G]TTTCCCTGAACCCAGAGGGACATGGTTTGGGGAGT R 2 1 2 1 101000 f 74 goat snp33715-scaffold396-836773 11 83613145 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423150 Affx-122942756 AX-123293496 11 82854645 TCACAAAGCATCCTGAAATCACCCAAGGGGAATTA[A/G]CCTTTTAAATTTCATGTTGTTCTAAAAAGAACATT R 2 1 2 1 201000 r 74 goat snp33716-scaffold396-875827 11 83653402 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390012 Affx-122968037 AX-123260369 11 82899709 TCTCTACACTCACAACAAAAATATTGTAGTAGCTG[C/T]AAATATTTCCATTCTGATGGATGTAAGTGGTACTT Y 2 1 2 1 101000 f 74 goat snp33717-scaffold396-920891 11 83698991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387112 Affx-122970667 AX-123257470 11 82928426 AATCTCAAGGACGAGCTCTCCAGGACCAGTTCATC[A/C]CTCCAAAGTACAGTCATTCACACTAGACAGACCTG M 2 1 2 1 101000 r 74 goat snp33718-scaffold396-949608 11 83728258 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404087 Affx-122957135 AX-123274439 11 82992465 TTCCTAAGGAGGAACTAGAAAAGGCAGAGGGCTTT[A/G]CATACATTCACTTTCTTTACTGGGGTCACCTTTAA R 2 1 2 1 101000 r 74 goat snp33720-scaffold396-1013647 11 83793222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272363 Affx-1111834091 AX-516151624 11 83006209 CATTTGTACTTTAATGTTTTGAAGAAGTTGAATTG[A/G]CCAGTGGTTTACTGAAAACATGGGCTTGCCTG R 2 1 2 1 101000 f 74 goat GoatD01.017751 11 83006209 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320780815 Affx-122977834 AX-385267904 11 83072777 AGGGAATCCGTATTACCAGGGACAACAGAGTCAAA[C/T]AGCATATAAATTTGGGTGATTTAAGAGTATAAAAT Y 2 1 2 1 101000 f 74 goat snp33722-scaffold396-1093959 11 83873650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414587 Affx-122949367 AX-123284936 11 83096408 CAAAGAAGAGAAGAGTGATACAATTGAAGACAAAA[C/T]GATAAAGTCAAAAAACTGGAAACAAGGAGAAAAAA Y 2 1 2 1 103000 f 74 goat snp10924-scaffold1392-6946 11 83905836 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401078 Affx-122959635 AX-123271431 11 83131235 AGGTGTCCCTGTGAAGAAGGGGAGTTTATTTCTCC[A/G]TCTTTTTTGGATTTGGCCATGTGTCTTAATTGGCC R 2 1 2 1 201000 r 74 goat snp10925-scaffold1392-41773 11 83940273 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441879 Affx-122928628 AX-123312216 11 83219893 AAATTGAACTACTCATTACCTGCTCTACCACTGTA[G/T]CATGATGAATTTTGATTTTGACCAACCTATATTCC K 2 1 2 1 101000 r 74 goat snp10927-scaffold1392-130431 11 84029134 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392215 Affx-122966273 AX-123262572 11 83250389 CAGACTGCCCAGTCCAGCACTTCAATGATTCTTGC[A/G]TCTTCCCATACATAGAGAAATGCTAAAGTCATTAA R 2 1 2 1 102000 f 74 goat snp10928-scaffold1392-160927 11 84060083 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376807 Affx-122977936 AX-123247166 11 83290612 TCTTGCAGTGAAATAGAAATTGAGAAATTTGAAGA[C/T]GTATCAGAATATAAGTGGATCACCATGGCCAGGAG Y 2 1 2 1 101000 r 74 goat snp10929-scaffold1392-201150 11 84100782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795391 Affx-122936328 AX-385282347 11 83347263 TTCCTTCTGGCACATCCATTATGTTATTAAATAGA[C/T]GTTTTAGAATGTTCTTTCAATCTCAGGAAGTAGGT Y 2 1 2 1 201000 r 74 goat snp10930-scaffold1392-257801 11 84158301 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451647 Affx-122921604 AX-123321980 11 83380534 AGAAGTTCTCAGGAAGAAAACATTTTGAGAAGCCA[C/T]GTATTCCATACTAGGGTGTTTGGATTTAACCTTGC Y 2 1 2 1 201000 r 74 goat snp10931-scaffold1392-291072 11 84191910 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802324 Affx-122945567 AX-385289228 11 83463996 CTTTTTCAAAATTATTTAGCGTATACACCTAGAAG[C/T]GGAATGACTGAGGAATGTCAGTTCAAGTGCATGGC Y 2 1 2 1 101000 r 74 goat snp10933-scaffold1392-374534 11 84276352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791682 Affx-122920358 AX-385278673 11 83492882 TAATATAGGTCTATGAATAAAGAGGGTACTTCATT[A/G]TTTGACTATGAATTTCAACTTTTAAGCTTGTGATA R 2 1 2 1 201000 r 74 goat snp10934-scaffold1392-403420 11 84309246 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453509 Affx-122919812 AX-123323842 11 83539595 TTCACAGAAGTGAGATGAGCTCCCAAATGTTTACC[A/G]ATCAGTGAAAATAAATGACTGCCATTTCACTGCTA R 2 1 2 1 101000 f 74 goat snp10935-scaffold1392-450133 11 84362609 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272643 Affx-1111832938 AX-519546354 11 83541878 TAAATATATATAATAATTATAACAATAAAGTTTCA[A/G]TTAGGAGAAGGCAATGGCAACCCGCTCCAGTACTC R 2 1 2 1 303000 f 74 goat 11_83541878_AF-PAKI 11 83541878 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435518 Affx-122933412 AX-123305858 11 83568241 TGATTGAGATTAGCTGTAAAGAAAACATAATTCAA[C/T]ATGTGAAGTGACTGAGATATAGGAGGTTGAATGCG Y 2 1 2 1 101000 r 74 goat snp10936-scaffold1392-478779 11 84391369 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436633 Affx-122932495 AX-123306971 11 83618207 CCATGTTTATTCTGCAAGGAAATCTTAGTAATGTT[A/G]CAGAACAGATACCACAGACTGGAAAAAAGTGATGT R 2 1 2 1 201000 f 74 goat snp10937-scaffold1392-528745 11 84441611 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417498 Affx-122947158 AX-123287846 11 83659583 ACCCATGTTCAAACATAACTTTGGTATTGGTACTG[C/T]AAATTTTCATGAGTCAGCTTGGCTGGGCCAAAGGA Y 2 1 2 1 101000 f 74 goat snp10938-scaffold1392-570121 11 84483226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799111 Affx-122924285 AX-385286041 11 83719137 GCCATCCATGGAATATGCCAGAATGTCAATTGTAC[A/G]TTGATCTAGATTTTGATTAAAATCAGAGAGACAAA R 2 1 2 1 101000 f 74 goat snp10939-scaffold1392-629675 11 84543214 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405740 Affx-122956513 AX-123276092 11 83764753 TAGCTGGTTTCATTAAAAAACTAAAAGCAAGGTAC[C/T]GTCTATTCACTCTTCATCATCAACAAGAAAACTGA Y 2 1 2 1 101000 r 74 goat snp10940-scaffold1392-675291 11 84589158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402891 Affx-122958215 AX-123273244 11 83797220 AGAATTCGATTTCATCATGCCTATTTATAGCTTTA[C/T]GGCTTAGTAAGTGGGTTCTCTATTTTCTGTCTCCC Y 2 1 2 1 101000 r 74 goat snp10941-scaffold1392-707758 11 84621757 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770658 Affx-122971295 AX-385257822 11 83844276 ACCCCTGCTCAGAAAATACCTAGTAGTATGCAAGT[C/T]TTTTAAGATAATAGGGTCAGGTAGTTATTTCAAAA Y 2 1 2 1 101000 f 74 goat snp10942-scaffold1392-754814 11 84668812 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452093 Affx-122920854 AX-123322426 11 83874333 AGTCCTCTCTGATTCAAAAACTGGATCGTGACTTC[C/T]CATGTTTCCAAAGAAATCCAAACTCCTTTCTGTGG Y 2 1 2 1 101000 f 74 goat snp10943-scaffold1392-784871 11 84698912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401457 Affx-122958974 AX-123271810 11 83904951 GCAGAATTTTGGGCTCAGTTTGGAGCATGTAAAAA[C/T]CAAGAGAAGAGGTGAAATCACAGAGAAGAAACAGC Y 2 1 2 1 101000 f 74 goat snp10944-scaffold1392-815489 11 84729665 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796354 Affx-122924667 AX-385283304 11 83946532 ATCTTTTGATTTCCACTTTGTTATCTAAATTTTAC[A/G]TAGATACACATTACAAGATGTGAGAGTTCATTAAG R 2 1 2 1 101000 r 74 goat snp10945-scaffold1392-857070 11 84771037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400114 Affx-122960724 AX-123270469 11 84005434 GAGTACCACCCCCAGATTTGCACTGATTGGCTGTA[C/T]AACCCCAGGCCACAATTTCCTCATCTGTATAATGG Y 2 1 2 1 303000 f 74 goat snp10946-scaffold1392-915972 11 84830238 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447241 Affx-122924960 AX-123317577 11 84052672 ACAACATAAAGCTGGGACACACAACTTGGCTCCGT[A/G]CTAGAGAATCAATGATTCCATTACAGAGAAAATCA R 2 1 2 1 101000 r 74 goat snp39364-scaffold50-4558957 11 84877018 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396142 Affx-122963393 AX-123266497 11 84087880 TTAAACAAATCTCTTTTTTAAAGTTTTCTTCAGTT[A/G]CATTAAGTGGTATGAAATGTATCTCATATAAGGAC R 2 1 2 1 101000 r 74 goat snp39363-scaffold50-4523749 11 84912806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446428 Affx-122925980 AX-123316764 11 84120122 TCACTCCCCAGGGAGGTTGGGGAAAGGCTTTGACT[A/G]TGGGGCTCATGAGCCTTGTGGAGGCAGCTGACACA R 2 1 2 1 103000 f 74 goat snp39362-scaffold50-4491507 11 84945306 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394750 Affx-122964853 AX-123265105 11 84205510 GGAGATCTTAGCTGATTCACAGAATGAATGAGTTG[C/T]AGGAGAAGCTGAAGACCTCTTGATTCTTTGCAGAC Y 2 1 2 1 201000 r 74 goat snp39361-scaffold50-4406119 11 85030333 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386545 Affx-122970721 AX-123256903 11 84244797 TGTGTGGTTTATTTAAATGACATCAGTACTATCCA[C/T]TAGAAAGTTTTAGTCCTTTTAGACAAATAAGCCTC Y 2 1 2 1 101000 r 74 goat snp39360-scaffold50-4366832 11 85069538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275077 Affx-1111834673 AX-519548658 11 84251350 ATTAAAATTGCAATATTGCTGTGGGGCAGCCAAAC[A/G]TACTGCAGCTCATGGACAGCTGTGATGCAGTGGCT R 2 1 2 1 101000 f 74 goat GoatD01.045287 11 84251350 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38411909 Affx-122951176 AX-123282259 11 84275287 AAGTGAAAAATGCCAGCATCCTAGATGCTTTTTAG[C/T]GGTCCACCTCCCAGGGCCCTCACACGTGGTGAAAG Y 2 1 2 1 101000 f 74 goat snp39359-scaffold50-4336342 11 85099657 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419612 Affx-122945987 AX-123289960 11 84332608 TGGCAGTGGGGGTCAGGATTCAGGCTGACAGGCTC[A/G]TCTTAGCCTTCTAGTGATGGGGAACGTTTAAATTC R 2 1 2 1 202000 f 74 goat snp39358-scaffold50-4279021 11 85157489 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444864 Affx-122926286 AX-123315201 11 84378783 GGAAGGGATTTGCTTCTGCATATCTTTATTGTTGC[C/T]AAGAGAAACCAGGCTCCAAGGGGGACTGAGAATGA Y 2 1 2 1 101000 f 74 goat snp39357-scaffold50-4232846 11 85203953 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436677 Affx-122932461 AX-123307015 11 84421375 CAAGGCAAGCGCTGATTTCTCTGTGCCCTCACAGC[A/G]CTGACAGTGGGTCCTTTGAGAACCTAGGAAACCAC R 2 1 2 1 202000 f 74 goat snp39356-scaffold50-4190254 11 85246914 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788645 Affx-122948365 AX-385275661 11 84459044 AAATTTTATTACCATCATATCAATCATTTGAGACC[A/G]TCTGATTTGATCCCCTTTTGATTTTTAACAATCTA R 2 1 2 1 101000 r 74 goat snp39355-scaffold50-4152585 11 85284951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421045 Affx-122944525 AX-123291392 11 84488791 AGGGAGTTGAAGATTGTGGGCAGCCTAATGAATTA[C/T]GGTTTACTCTGTGGCCTTACAATTAGCTGTGAAAA Y 2 1 2 1 101000 f 74 goat snp39354-scaffold50-4122838 11 85315272 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391628 Affx-122966578 AX-123261985 11 84543220 GTTGGTGAACATCTGCACTCCAGAGGAAACAGCAG[C/T]AGTAATAGAGGAAACTTGGCCTTTTCAGTAGAAAT Y 2 1 2 1 201000 r 74 goat snp39353-scaffold50-4068409 11 85370237 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414713 Affx-122949271 AX-123285062 11 84597977 AACCTCGTTTCTTTCCACTCTGTAGCAGCTCTGCA[C/T]GATGCACGCCTGTGTCTGACTTCATCCTGTAAACA Y 2 1 2 1 101000 f 74 goat snp39352-scaffold50-4013652 11 85425330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434675 Affx-122933967 AX-123305016 11 84689525 ATCTGCACACTTTGTATGTGGTGTTACAGCACATA[C/T]GGTCCTTTAATCTAATAGTTGTTATTGATAGCATC Y 2 1 2 1 101000 r 74 goat snp39350-scaffold50-3922104 11 85517969 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445310 Affx-122925436 AX-123315647 11 84752835 GTGAGTGGTCAGTTCTATGGAGATGGCTTGTTTGG[A/G]CTGAGGTGAGGACATGGGAACTGGTCTCATTTCAT R 2 1 2 1 101000 f 74 goat snp39349-scaffold50-3858794 11 85582635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432862 Affx-122935358 AX-123303203 11 84803672 AAACCCGGCAGGAGATGCCTCTAGTATATGAAATA[C/T]ATTATGGCTAATTATGAAGTTGCTAAAGTCTTCTA Y 2 1 2 1 101000 f 74 goat snp39348-scaffold50-3807957 11 85633531 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411499 Affx-122951687 AX-123281849 11 84844751 TTTGCGGCACGAGGCTGGAATGTCTATGCCTTAAC[A/G]CATCCATGGCAGACATTTTATGTAGAATGTGCTTT R 2 1 2 1 101000 f 74 goat snp39347-scaffold50-3766878 11 85674685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427800 Affx-122939760 AX-123298143 11 84877225 GCTGCAGTCCTGGTGCTAGGGGCCAACGATGTACC[A/G]TTCAGGAGGCTTCAGAGTACTGATGGGGAAGTGCT R 2 1 2 1 201000 f 74 goat snp39346-scaffold50-3734404 11 85706942 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389388 Affx-122968389 AX-123259746 11 84920149 CTTCTCTGTTCCTCCTCCCTCAGTGCTTCCTGACA[G/T]CAAGTGTTGGATATTTGACAGACTAGAGAGGCCTG K 2 1 2 1 101000 r 74 goat snp39345-scaffold50-3691480 11 85749696 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397987 Affx-122961803 AX-123268342 11 84951066 GCAGAAGTAAAGACTGAGAAATGTCCTTTGCATTT[A/G]CAACCTGGATGCTGTTGGCGACCTCGATGAAGACA R 2 1 2 1 201000 f 74 goat snp39344-scaffold50-3660563 11 85780494 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797007 Affx-122940978 AX-385283948 11 84995748 ATAATTAAATTCAGGGGGAAAGATGGTATTGTATC[C/T]GGGACCAAAAACACCCCAGCAATTACAGATCTTAG Y 2 1 2 1 101000 r 74 goat snp39343-scaffold50-3615881 11 85825734 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424620 Affx-122942187 AX-123294966 11 85024580 TCGCTTATGTCTTCTATGTGAATTCACAGGAGGTG[C/T]CCATTATTGGGATTTATGGAAACAGGCCAATTTCG Y 2 1 2 1 201000 r 74 goat snp39342-scaffold50-3587049 11 85854476 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445129 Affx-122926177 AX-123315466 11 85065001 GGACTAGTAGGAGAAAGAAAGGCCAGTGTTAACTT[A/G]TTCTCAATTGGTCGTTACTTAAACTCATGAAAAGT R 2 1 2 1 101000 f 74 goat snp39341-scaffold50-3546628 11 85894722 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793643 Affx-122951047 AX-385280616 11 85113978 TTATATGCAATAGGAATTTAATAAAAGATGCTATC[A/G]TCCTGTGACTACAATTTCCCTGTAAGTGTGGTTAG R 2 1 2 1 101000 r 74 goat snp39340-scaffold50-3497651 11 85943733 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424844 Affx-122941353 AX-123295190 11 85183285 TAGAATATGGAGTGGAATTTTTATGAAATGAGAAG[A/C]TTTTGGAGCCATGAGAGTAGGGGAGTGACGCAATC M 2 1 2 1 201000 f 74 goat snp39339-scaffold50-3428344 11 86013822 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452776 Affx-122920249 AX-123323109 11 85214205 AATGATCATCCATTTTCATTAGGCTCCTTACCCAG[G/T]CAGGGAAGGATGTGGTTCTTGCCTGCTCTTGTTTC K 2 1 2 1 101000 f 74 goat snp39338-scaffold50-3397424 11 86044729 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796812 Affx-122967203 AX-385283755 11 85284239 AGAGTACTGAGCACGCGCAAGTCACTGATTCCTAG[A/G]TAAATTCTCAATTCAAAAGGCTGTATAAAGGTCAT R 2 1 2 1 101000 f 74 goat snp39337-scaffold50-3327390 11 86114889 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787864 Affx-122946768 AX-385274887 11 85314176 TAAATGCTAAACTCACTATAAAACTACCTCATTTC[A/G]TCTAAATAAAACCGAATTCATGAAGCTTCATTCCT R 2 1 2 1 101000 r 74 goat snp39336-scaffold50-3297453 11 86144748 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393205 Affx-122965502 AX-123263562 11 85350517 TGAACTTTCAGTTTTCAGTGAACTAGCTTCAAAAG[C/T]ATGGAAAAAAGAAACATTTTTCATATATTACTAAA Y 2 1 2 1 101000 f 74 goat snp39335-scaffold50-3261112 11 86180985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394997 Affx-122964239 AX-123265352 11 85388421 AATTTTAATAACTTACCAGGGTTCACTTCCTGGGA[C/T]GAATGTTTAATTGTAATACAGACATAATAGGATGG Y 2 1 2 1 201000 r 74 goat snp39334-scaffold50-3223208 11 86217338 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375932 Affx-122978462 AX-123246291 11 85418308 CAACGGGCCGGGGACACAAACCAAAGGGGAAGATA[C/T]CTGAGGATGCCAGCTGAGCAGAGCAGGGGGGGCCT Y 2 1 2 1 101000 f 74 goat snp39333-scaffold50-3193321 11 86247300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779909 Affx-122966210 AX-385267008 11 85447694 AAGCTTCAGGAGCTAACACGTGAATTTTCTCTCTT[C/T]AGAAGAAAAAAAAGTTCCCAAACAAAAGCTCTGCC Y 2 1 2 1 102000 r 74 goat snp39332-scaffold50-3163935 11 86276734 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406992 Affx-122955038 AX-123277343 11 85493725 AGCCAAGAAAAGTCTCAAATCTAAAACCATGTCTG[A/G]CAATAATGTCTTCAGCATGTTTTAAGCATCAGGTC R 2 1 2 1 101000 r 74 goat snp39331-scaffold50-3117904 11 86323559 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396865 Affx-122963245 AX-123267220 11 85529345 ATGGAAGTATCTCCTACAGAAGATATTAAAGCAAA[A/G]CATCAGTAACAAAACCTCCACTCTGTTTCTGGAGT R 2 1 2 1 101000 r 74 goat snp39330-scaffold50-3082284 11 86359226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430392 Affx-122937767 AX-123300733 11 85566397 TTTTTCATCCACCTCTTTGGTGGTCTTCATAATAC[A/G]TGTTCTTTGGCATCTGTGTCCTGGTGACAAAAACC R 2 1 2 1 101000 f 74 goat snp39329-scaffold50-3045232 11 86396018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428726 Affx-122938454 AX-123299068 11 85598768 ACAGACTGCAGTTAATATGCTCATACATAGGAGAT[A/G]TGCACGGAGAATGAATTCCCTGAAGTGGGATTGCG R 2 1 2 1 201000 f 74 goat snp39328-scaffold50-3012861 11 86428495 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440351 Affx-122929658 AX-123310688 11 85646312 GACAGTTTGATAACTCACCCCCACATCTTCTTCTT[A/G]TATTTGTCCGCCAACTTCAGAAGAACTTCCAAGTA R 2 1 2 1 201000 r 74 goat snp39327-scaffold50-2965317 11 86475939 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401055 Affx-122959651 AX-123271408 11 85679669 TTCTATTCAAAATTCACCTCAGTTAAAATTAGGTG[C/T]CATTATTACATTGTATCCATCCTCAGTGTCCTCTC Y 2 1 2 1 101000 r 74 goat snp39326-scaffold50-2931960 11 86509307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402368 Affx-122959040 AX-123272721 11 85711883 GGAAGTGGGAAAAGCGAGAGGATTAATTTTGAGGG[A/G]AGGGAGTGGTGAACAGGTAGAGATATTTGACACTT R 2 1 2 1 101000 f 74 goat snp39325-scaffold50-2899746 11 86541617 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387187 Affx-122970612 AX-123257545 11 85754193 AAAAAAGAAAAAAAAGCAAATGTAAACATATAAGC[C/T]GTGTCTTGAACTGCTTCAGTATATACCACAACCAC Y 2 1 2 1 101000 r 74 goat snp39324-scaffold50-2857436 11 86584755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798204 Affx-122926274 AX-385285139 11 85810908 AAAATATGCTTACCTTCTAACAGTGGACATGTGTC[G/T]CTATACACGTGTCTCAAACCACAGCATGAACACCA K 2 1 2 1 101000 f 74 goat snp39323-scaffold50-2800721 11 86641573 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449336 Affx-122922983 AX-123319671 11 85840016 GATGTGTCCCTCCCGAAACCTGGCTGCAGGACATC[A/G]TATCTTCAAGGGCAAGGACAGAATGTTTTCTAACA R 2 1 2 1 101000 r 74 goat snp39322-scaffold50-2771613 11 86668185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437764 Affx-122931710 AX-123308102 11 85881061 CAGCCTGTGCCAGCCTGTATTTTATACAAGTGAAT[A/G]TTATCATCTACATTTTTTTCTGCAAGTGGAAAGTG R 2 1 2 1 101000 f 74 goat snp39321-scaffold50-2730568 11 86709167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422071 Affx-122943598 AX-123292418 11 85917886 ATATTCATTCAGCCTCTGGATCTATTAATAGTTTA[C/T]AATGTGCCTGGTGTCTTCCGTTCTGTCTGGTCCTG Y 2 1 2 1 101000 r 74 goat snp39320-scaffold50-2693743 11 86745984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437687 Affx-122931767 AX-123308025 11 85980882 CAACAATGACGGTAGGACCCCCGCATGTCTGTGCC[A/G]CGCTGCCGGGAGCAGAGAGGCGTTTGGGACCCTTC R 2 1 2 1 201000 r 74 goat snp39319-scaffold50-2630747 11 86809402 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439154 Affx-122931073 AX-123309491 11 86064064 CCCAGGGCTCGCTCTGTCTGTCTGACACCCCACCC[C/T]ACTCCACCAAGAGGCTTCTTCCCTCTTTGGATTGG Y 2 1 2 1 103000 r 74 goat snp39318-scaffold50-2547565 11 86881391 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451675 Affx-122921583 AX-123322008 11 86143093 GCCCTGCTCCCTCCCCTCCTGTCTCACCCACCCCC[A/G]CTGCTTCCTGTGAGCAACTTCCTTCCTTTGTGAGG R 2 1 2 1 101000 r 74 goat snp39317-scaffold50-2468536 11 86961792 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444542 Affx-122926478 AX-123314879 11 86203619 TCACCCCCTCTTTTCTTAAGCTTTCCTTTGCCCCT[A/G]CTGAGAATGCCTGAGAAAGCGCGATGACTCTTCAG R 2 1 2 1 201000 r 74 goat snp39316-scaffold50-2408010 11 87022634 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276553 Affx-1111835474 AX-519550064 11 86265000 CAGCAGCAGCAGGTATTTACGGATTCCACAATCTT[A/G]AAAACATATCTTAGTACATGAGTAGATGTTAGCAA R 2 1 2 1 101000 f 74 goat Random2.2K-1210 11 86265000 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431954 Affx-122935966 AX-123302295 11 86265051 GTTGTAAAGTTAATCCAGATTGTATGGTCCTTAAA[C/T]TTAGGCAACACAAAAATAAACACTAGCTGGCATGG Y 2 1 2 1 201000 f 74 goat snp39315-scaffold50-2346578 11 87086540 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272645 Affx-1111832939 AX-189372170 11 86265974 GACCCCATGGACTGTAGCACGCCAGGCCTCCCTGT[A/C]CACCTTCTCCCGCAGTTTGCTCAAACTCATGTCCA M 2 1 2 1 303000 f 74 goat 11_86265974_AF-PAKI 11 86265974 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38375491 Affx-122979137 AX-123245850 11 86298291 GGAAGAGAAGTGACAACCTAAGATAAGCTGTGGGG[G/T]GCTGGAGGGGAAACGGGGGTTGGCCTTCTGACAGA K 2 1 2 1 101000 f 74 goat snp39314-scaffold50-2313338 11 87118398 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413471 Affx-122950663 AX-123283820 11 86379700 GATTCAGACAGGCTCTGCCAGGCTTCTCTGCTGTA[C/T]AGTGAAACTCTTTCTCCTCTTGTAGGTGTTTTGAG Y 2 1 2 1 101000 r 74 goat snp39313-scaffold50-2231929 11 87211151 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770790 Affx-122919512 AX-385257954 11 86427983 TAAAAAATTTGACGAGATGCGACAACACCTTTAGA[C/T]GGATCTTAGTTGAGGGTGTTTTACCACTCGAACCC Y 2 1 2 1 101000 r 74 goat snp39312-scaffold50-2183646 11 87259657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796758 Affx-122935712 AX-385283702 11 86482217 GTAAGTCACATGTCTGACAAGTGGGACCAAAAGAC[A/G]TATCTGGTGAGAGATAGAAATGAAGATGAAGTTCA R 2 1 2 1 101000 f 74 goat snp39311-scaffold50-2129412 11 87314217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418574 Affx-122946378 AX-123288922 11 86527856 CTCCCATGACTGGCAGCCTCGGTCAGATCAATAGC[A/G]TCCCTGCATCTATCACACCCTCAACTGGGACATGA R 2 1 2 1 201000 f 74 goat snp39310-scaffold50-2083773 11 87359894 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419954 Affx-122945208 AX-123290302 11 86568314 CTGGGGAGGCAGGCTCTCCCAGCTCCCTCCTGTGG[A/G]GGCACAGCCAGGAAGCACAGCATCTCTGGGCATGG R 2 1 2 1 101000 r 74 goat snp39309-scaffold50-2043315 11 87400445 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767813 Affx-122953428 AX-385255037 11 86600016 CCTGACTTCCTCTGTCCTGAAAAACCAGATAAACA[C/T]GTTTGACTAAGTGTGAATCTGAGTTCCCGAAGTGG Y 2 1 2 1 101000 f 74 goat snp39308-scaffold50-2011613 11 87432099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800494 Affx-122955774 AX-385287414 11 86629000 TGATGATAGCAAGTGTTTGTCTTCTGTTCCTGATG[C/T]AAGATTCTAGGCTCCTGACAAGATTTCAGGAAAAG Y 2 1 2 1 101000 f 74 goat snp39307-scaffold50-1982629 11 87461078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788149 Affx-122970839 AX-385275168 11 86684724 GTGAAACACTAAGGTAGACATCTGTTAGGTTCCTA[C/T]TACTGCCTGGATCAGGCCCTTGTCTGTTCTGTTCA Y 2 1 2 1 101000 r 74 goat snp39306-scaffold50-1926905 11 87516785 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395092 Affx-122964169 AX-123265447 11 86736352 CACCAGGTAATTACAGTGTATTTAAAAAAGAAACT[A/G]ATCATCTCCCTAATCAGTGCTGTTCTCAATGTAAA R 2 1 2 1 201000 r 74 goat snp39305-scaffold50-1875277 11 87568354 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380929 Affx-122975014 AX-123251287 11 86830851 CTGCTCCCTTGTGAGCTTTTCAGGTTCACAGAGCC[A/G]TGGTGTCAGGGTCCTGGGCTGGTGTGTTCATCGGA R 2 1 2 1 101000 f 74 goat snp39304-scaffold50-1780778 11 87662795 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431392 Affx-122936547 AX-123301733 11 86862525 TTACGCATATCTTTGGCTCTGAAGTGTGTTTCCTG[C/T]GGGCAACCTATATTTGGGTCATTTTTTTTTAATCC Y 2 1 2 1 101000 f 74 goat snp39303-scaffold50-1749104 11 87694508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437376 Affx-122932446 AX-123307714 11 86905734 TAAGAAAGAGTCCCCTGTCATGTGAGCACAGCTCT[A/G]TTAGCGGCTCTGTCTCTCCTCCAGGGAGGGCTGTG R 2 1 2 1 101000 f 74 goat snp39302-scaffold50-1705895 11 87737577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375636 Affx-122978698 AX-123245995 11 87090674 CACGGACGTGAACCACTCCAGTCACCGGAAAATTC[A/G]TATCTTTCTTCCGGGTCCAGGGCCCATCTCCTGTG R 2 1 2 1 101000 f 74 goat snp39298-scaffold50-1520955 11 87922123 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386803 Affx-122970908 AX-123257161 11 87130708 ATTTATGCCATTCAAATAACTTTATGCACATAAAA[C/T]ACTTAATGCTTATAACATTGTAAGCTCTCAGTAAA Y 2 1 2 1 201000 f 74 goat snp39297-scaffold50-1480921 11 87964494 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388074 Affx-122969518 AX-123258432 11 87165782 CCAGCACAGAGAAGTGCCCACCACATGGAGGGGAC[A/G]TCACAACACCTGCCTGAGCTTCGAAATACCCTTTG R 2 1 2 1 101000 r 74 goat snp39296-scaffold50-1445847 11 87999632 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765707 Affx-122945711 AX-385253169 11 87221493 CTTCAAGACCAGAACAACGCCAGGTTATCTAAGCC[A/G]CAGCTCATCTTACCGCATCCAACAATGTATCACAA R 2 1 2 1 101000 f 74 goat snp39295-scaffold50-1390136 11 88055361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433785 Affx-122934473 AX-123304126 11 87269360 ACAGGCAGAATCTGAGAGATTAAGTAGTTTATTTG[C/T]AAGTTGAGATAAATAAGTATAATTCTTTACAGAAC Y 2 1 2 1 101000 f 74 goat snp39294-scaffold50-1342269 11 88102990 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451714 Affx-122921555 AX-123322047 11 87339584 GAACAAGTATAACAGACATGGAACTGATTAACTCT[A/G]TCTGTGTGGGGGCAGGGGAAATGTAAAATGTTAGA R 2 1 2 1 201000 f 74 goat snp39293-scaffold50-1272045 11 88173409 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416399 Affx-122947856 AX-123286748 11 87384856 CAGACGATAAATAATTGCTGCTAACACTCTAAGCC[A/G]CGGATGCGCACCCCGAGGGATCCGGATACCATAAA R 2 1 2 1 101000 f 74 goat snp39292-scaffold50-1226773 11 88218031 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777054 Affx-122926925 AX-385264177 11 87431689 GGGATTTTTCTGGGTAGGGAGTGGTGTGATAAAGC[A/G]CTATCTGAACTAGGTCAAGCTTGCAGTGACCCGGG R 2 1 2 1 101000 f 74 goat snp39291-scaffold50-1179940 11 88264455 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423841 Affx-122942782 AX-123294187 11 87490686 AGTGGTGCGCTGGGGTCATCCGAGCAGGTATTACT[A/G]TCTCCACTTCACATCTGGGGAAGCAGGGTTCAGGC R 2 1 2 1 101000 f 74 goat snp39290-scaffold50-1120943 11 88319536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444010 Affx-122926898 AX-123314347 11 87533848 AGCTTCCGCATCAGTCCTTCCAATGAATATTCAGG[A/G]TTGATGTCCTCCTGGGTTACCTGTCAAAAAGTGGG R 2 1 2 1 201000 r 74 goat snp39289-scaffold50-1077781 11 88361939 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400903 Affx-122959739 AX-123271256 11 87591480 AGGTGGATTCTTTACCATCTGACCCACCAGGGAAT[A/G]TTTAGAAAGAGTTGTTTTTATTTTGTATCCTCTCT R 2 1 2 1 201000 r 74 goat snp39288-scaffold50-1020149 11 88417912 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442376 Affx-122928015 AX-123312713 11 87637982 GACTGGTTAAGAGCTATAAACATGTTAAAATCCAT[A/G]TGTTTTGGTTGAGTTGCAAGGAGCTTTTAGAGATC R 2 1 2 1 101000 f 74 goat snp39287-scaffold50-973647 11 88464675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274257 Affx-1111834095 AX-519547855 11 87651275 CAGCTTCCAGTGTCTGGGGGTCAGGGGGACGCCCC[A/G]TGAATAGGTCTGCTGAATTCCAAGCCCCTGGAAAA R 2 1 2 1 101000 r 74 goat GoatD01.018109 11 87651275 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320793863 Affx-122941264 AX-385280832 11 87683126 TCTTTGATTCAGAGATTAGCCGAGCATATTAATAC[A/G]TATGTTTCCCACTTCCTGCCCACACACTTTTATCT R 2 1 2 1 101000 r 74 goat snp39286-scaffold50-928503 11 88509752 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412785 Affx-122950498 AX-123283134 11 87728672 TCTTCTGCAGGAGACCTCTGTCTTTGATTATCATC[A/G]TTGGAATCTGCTCCTCCTGCCCCATCCTCAGAAAT R 2 1 2 1 101000 f 74 goat snp39285-scaffold50-882957 11 88555262 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795073 Affx-122959463 AX-385282032 11 87774491 AAGAGTTGTTTGTGGGATATAAGAGCTCATAGGAC[A/G]TGATCCCTGCCAGGAAACTGATATTCTTCCATCAT R 2 1 2 1 101000 r 74 goat snp39284-scaffold50-837138 11 88601561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413279 Affx-122950210 AX-123283628 11 87804634 CAGGACAGCACGTACATAAACCTCCTGTGAGCACA[C/T]GGAAATCATTGCTGCTCCGGGAAAAAGTCTTTTGT Y 2 1 2 1 101000 r 74 goat snp39283-scaffold50-806995 11 88631985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430564 Affx-122937012 AX-123300905 11 87860631 TCTTTGTGAAATTCACACTCGCCTGGATGAGAGAC[A/G]TCTCAACTGAGAAGCAAGGTCACAGACGGGCAGGC R 2 1 2 1 101000 f 74 goat snp39282-scaffold50-750998 11 88687828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433975 Affx-122934259 AX-123304316 11 87896754 GAGAAGTTTTGTAGACAGTTCAGCCGTTCCCCTGG[G/T]ACAGAAGAGAAATGAGTTTCAGGTGCCATTCCCTT K 2 1 2 1 201000 r 74 goat snp39281-scaffold50-714875 11 88724313 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775201 Affx-122940408 AX-385262332 11 88014961 ATGCAGTTGAGTTTTCCCTTCATCTTTAGAGTAAT[A/G]TGTCTAATTATGTAGCTCTGACTTTTCAAGGCTCA R 2 1 2 1 101000 f 74 goat snp39278-scaffold50-596668 11 88842907 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780718 Affx-122973233 AX-385267808 11 88047802 GCAGAAGTTATAGAGATTCCAAAAGCTGTACAGTG[A/C]GGGAACAAACCAAATTGTCCTTCAGTGATGACAGA M 2 1 2 1 101000 r 74 goat snp39277-scaffold50-563827 11 88875936 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410513 Affx-122952179 AX-123280863 11 88086734 CGAGGTTCAGGACTTCTAAGTGAAAGGACATTAAC[A/G]AGTCTGCTTTGGTTCCTTTCTTTCCATGACACTTG R 2 1 2 1 101000 f 74 goat snp39276-scaffold50-524895 11 88915250 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802681 Affx-122948674 AX-385289580 11 88115242 TTTATACACACTTTGTCGCCTCGTTTCATGGAATC[A/G]CATGCGTCTCTAACCTCTACTTATGTACTAAAATG R 2 1 2 1 101000 f 74 goat snp39275-scaffold50-496387 11 88943983 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394860 Affx-122964766 AX-123265215 11 88169566 GAGAAGATCGTGTCAAAGAAGAGGACTTGAAATAG[A/C]ATAGATATTCTGAAGCACTCACACTTCGAGAAATG M 2 1 2 1 101000 f 74 goat snp39274-scaffold50-442063 11 88998357 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446159 Affx-122925753 AX-123316495 11 88199504 GTACTTCCCCACTGTATCAGGGTGCCAGGGCTGCC[A/G]TAACGAAGTTCCCTAAACTGGGGAGCTTCAAAAAG R 2 1 2 1 103000 r 74 goat snp39273-scaffold50-412125 11 89028157 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410137 Affx-122952806 AX-123280487 11 88234681 CCACACCTATCAAGTTGGTGTCAGACGATTTTTAC[A/C]AACCAGCTGACCTGTTCTTTGAGGTATTCGCGCCA M 2 1 2 1 101000 f 74 goat snp39272-scaffold50-376948 11 89063231 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405800 Affx-122955903 AX-123276152 11 88296772 ATCTCTAAAACTGATCGTGAAACATCAATCCTGCA[G/T]CCAAGTTATTCTCTCTTTTGGTATCTTGATGATAC K 2 1 2 1 101000 f 74 goat snp39271-scaffold50-314857 11 89125371 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413648 Affx-122950537 AX-123283997 11 88351402 CCTTAGGGTCACAAAGAACTGGACACAACTAAAGC[A/G]ACTTAGCATGCATGCTGTTGGACCCACCTTTTATA R 2 1 2 1 103000 r 74 goat snp39270-scaffold50-260227 11 89178952 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434876 Affx-122934353 AX-123305217 11 88389605 GCTTCAGTAAACGAAAGTAACGCATTAGAACGCAG[A/C]TTTAGGGTCTCATTTAAAAATATAATTCAGGCACC M 2 1 2 1 101000 f 74 goat snp39269-scaffold50-222024 11 89216417 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419882 Affx-122945354 AX-123290230 11 88439650 ATGGTAACTTCCAGCCTGTGGGCTGGCTCTGGAGT[A/G]CGGTGGAAAAGACCAGGGTGGCTTGGACAAAGTTA R 2 1 2 1 101000 r 74 goat snp39268-scaffold50-171979 11 89266373 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38390966 Affx-122967049 AX-123261323 11 88493947 CCGAAGCAGCATGCCGGGAAAGCTGTATGCTGACC[A/C]CTGTCCCAGGGGATGGAGGGCAGAGGTTGGAGGAG M 2 1 2 1 101000 f 74 goat snp39267-scaffold50-117682 11 89320345 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419093 Affx-122945786 AX-123289441 11 88551035 GAACCAAGCGTGATATTCTCAATATTTATAGTACA[G/T]CCCACTCTGCTACTAAAATATTCCTGACAATACCA K 2 1 2 1 101000 f 74 goat snp39266-scaffold50-60594 11 89377492 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776659 Affx-122964088 AX-385263786 11 88608842 TAGAGAGATTACTACTCATTAAGGTTCATAGAGAT[A/G]TCTGTCTACCTTCCCTGTCTCTTTACAGGACTCAG R 2 1 2 1 101000 r 74 goat snp39265-scaffold50-2787 11 89434715 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404226 Affx-122957651 AX-123274578 11 88646198 ACCAAGTGATATTTGGAGATAAAAGATTAAGAAAT[A/G]CTGAGGTTGCTCTCAGGTTTATATAGTTCAGAGAT R 2 1 2 1 201000 f 74 goat snp20825-scaffold2043-34470 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772616 Affx-122933563 AX-385259764 11 88685397 AGTTAACTTTTCATCTGCTCTTCTCATTTTGCCAG[G/T]CTTGCTCCGGAGGCTCTCGGATATTCTCTAGATTT K 2 1 2 1 101000 f 74 goat snp20826-scaffold2043-73669 11 89510735 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448380 Affx-122924100 AX-123318716 11 88720671 AAGGCCTCAGGGACATTCCAACACCGGCCAGGCTC[A/G]GGCCTGGACACCCTCCCTCCAGACCTGCGGACTTG R 2 1 2 1 101000 f 74 goat snp20827-scaffold2043-108943 11 89545622 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392997 Affx-122965657 AX-123263354 11 88752139 TCTCTTGTTTTCATTATGAAAATGTTAATTGGGCT[A/G]TATCTTTCATTTTTTTCTTGACCAACCTGCCAGAC R 2 1 2 1 101000 f 74 goat snp29756-scaffold3229-109794 11 89578166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375432 Affx-122979183 AX-123245791 11 88803765 ATAGAGGAAAGTCCTGAAACTTGAAATTCAGGGCA[C/T]GGCCTGCTGCAAACTGTGTTATCAATGATGATGCT Y 2 1 2 1 201000 r 74 goat snp29755-scaffold3229-58168 11 89629994 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777636 Affx-122955442 AX-385264754 11 88837535 TAAATGCTTGGCTTCAAAAGCCTGTACTGTTAACT[G/T]CTATTACATTACTCAATATTTGATTTGAAATGGAA K 2 1 2 1 101000 f 74 goat snp29754-scaffold3229-24398 11 89664079 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376292 Affx-122978376 AX-123246651 11 88874112 CTGTGGCGTGGGCTTCCCCTGGATTTATTAGAGAC[A/G]CAGAATATTGGGTCCCAACCCCAGACTCACTGAAA R 2 1 2 1 101000 r 74 goat snp24724-scaffold253-12080 11 89837609 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775462 Affx-122921919 AX-385262593 11 88914486 GCAAAGAGATATTTTCTTGAATTGATTTTATAGTA[G/T]ACAGTATTGGGTGACCTGGGAAATCATACACACAC K 2 1 2 1 101000 r 74 goat snp24725-scaffold253-52454 11 89878473 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793409 Affx-122936431 AX-385280386 11 88994277 GGGACAGCCAATTGTGTGTCTAATTATGACTCATC[A/G]CAGTTATGTTAATAGCAATTTTCAGCAAATGCATG R 2 1 2 1 101000 f 74 goat snp24727-scaffold253-132245 11 89957792 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388624 Affx-122969132 AX-123258982 11 89035005 TAAGAATGATTAAGACCCTGCTGTTTGCAGTTAAT[A/G]TGGTGAATAACTTGAGTTTGAGGCCAGAAAAGAAA R 2 1 2 1 101000 r 74 goat snp24728-scaffold253-172973 11 89998548 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425989 Affx-122941150 AX-123296335 11 89117243 TTCACTAAGACAGTAGCATTTTAAATTATTCTCAA[G/T]ATTTCATATCAAGGATCTAATGGATTTTGGGTACT K 2 1 2 1 101000 r 74 goat snp24729-scaffold253-255211 11 90079714 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392508 Affx-122966124 AX-123262865 11 89205285 ACGTTCTCATGGGTCATATTCACAGCCCTGTGTGA[C/T]GTGTATGCCATTTCCACTTGAAGAAGTGGAAACTC Y 2 1 2 1 101000 r 74 goat snp24731-scaffold253-343253 11 90168332 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 468276555 Affx-1111835475 AX-519550066 11 89212951 TCATGAAATACCGTGGGCTCTAAACAAAGGTTTCC[A/G]GGAAAAATAATAAAGGTCAGTTCCTTTCCACAATA R 2 1 2 1 101000 f 74 goat Random2.2K-1211 11 89212951 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 463186620 Affx-1109856882 AX-514672996 11 89229413 TTTCAGATCTAACTACTGAAGAATAAAAACCTGAG[C/T]ATAGACTCACAGATAATGATATTATTTGGCCAATC Y 2 1 2 1 101000 r 74 goat 11_89229413_AF-PAKI 11 89229413 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38404518 Affx-122956696 AX-123274870 11 89238550 AGGAGGTTCAGAGTTGGGGGTGATGGACACTTACA[A/G]CAGAAGGGCTGAGATGGACCTTCTAGAGGAGGAAA R 2 1 2 1 201000 f 74 goat snp24732-scaffold253-376518 11 90201659 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436756 Affx-122932284 AX-123307094 11 89285275 CTGGCAATGTGTAGAGCAAGAAATTAAGACTTTCA[C/T]GCAGTAAGCTTCATCATTCTTCCTGTCACTCAAGC Y 2 1 2 1 101000 f 74 goat snp24733-scaffold253-423243 11 90249262 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784021 Affx-122967614 AX-385271074 11 89318359 GCTTATGCTGAAACTAAAGGGAAAGATGCCTCTAC[A/G]TGCAAGCATTCAACGGAGTGCTGTGTGCTAAACAG R 2 1 2 1 101000 f 74 goat snp24734-scaffold253-456327 11 90282408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436744 Affx-122932293 AX-123307082 11 89356248 GTGTTTCCAGGACACTCTACCTTAGGGCCGGCTCC[A/G]CTTTGTAATCCAATCTTATCATGGGAGTGATATCC R 2 1 2 1 101000 r 74 goat snp24735-scaffold253-494216 11 90320201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402111 Affx-122958683 AX-123272464 11 89400890 AAGGTGTTGAGAGGCTCAAGGGCATCCAAGCACAC[A/G]TCTCATAAATATTAAGCCAAAGATAACCAAATAAA R 2 1 2 1 201000 r 74 goat snp24736-scaffold253-538858 11 90364686 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386786 Affx-122970920 AX-123257144 11 89447376 GACCCAAGCTAAGCACTGCCTGCACTCCTAATCTG[C/T]GGAAATCCTGAGACAGTAAATTTTAAGCTGCTTAA Y 2 1 2 1 101000 f 74 goat snp24737-scaffold253-585344 11 90411038 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408942 Affx-122953935 AX-123279293 11 89476896 TAAAGGCATCTGATTCAACAAAGACCTACTATCTT[C/T]GAAATCCTGCTGACTGTTCTGGAAACTCCATGGTC Y 2 1 2 1 201000 r 74 goat snp24738-scaffold253-614864 11 90440421 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447478 Affx-122924347 AX-123317814 11 89506104 GCTTCTCTCTAACTTTCTGCCACATGTCCCAACTA[C/T]AGCACATTCGATGTTCACCTTTGCCATGTATCCCA Y 2 1 2 1 201000 r 74 goat snp24739-scaffold253-644072 11 90469564 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398986 Affx-122960955 AX-123269341 11 89543417 CTGAGATTCCCTCTGTGATTGTTGTTGTTTTCAAG[C/T]AGAAGCTTTATTGAGGTGTAATTAACATACCTTAG Y 2 1 2 1 101000 f 74 goat snp24740-scaffold253-681385 11 90506970 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383045 Affx-122973294 AX-123253403 11 89606347 AATGAAGACTGCACCTTTTGCTTCATCTGAAAGTG[C/T]ATTTAATGTGCACCTGTAATGCACCAGATGTTGGT Y 2 1 2 1 101000 r 74 goat snp24741-scaffold253-744315 11 90569675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426195 Affx-122940571 AX-123296541 11 89644115 GGTTTCCTGCATTGGAGACTAGATGCCTTCCTACT[A/G]TGAAGGGCTGTCACAGTCTCAGGTGCTGCACGGGG R 2 1 2 1 101000 f 74 goat snp24742-scaffold253-782083 11 90607766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800999 Affx-122976004 AX-385287913 11 89692745 GATGTGTTCTCACTCTTCTAAGTGACAACTTTGTG[C/T]AGAACTGATCACATTAACATTACAGTAGAGACGTA Y 2 1 2 1 101000 f 74 goat snp24743-scaffold253-830713 11 90656237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448720 Affx-122923845 AX-123319056 11 89747676 TAAGGTCACAAATACAGGAGCTGGCTTAACAGGGA[C/T]GGGGGATCAGTCACCAGTGACAGATCCATGTGGCT Y 2 1 2 1 101000 f 74 goat snp24744-scaffold253-885644 11 90707580 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398294 Affx-122962156 AX-123268649 11 89797519 TTTCTTACAATGCATTGACCTGTCAGAATTCACAG[C/T]GACATTTTCAGCAGCAAACAGAAGAATGCATTTTT Y 2 1 2 1 101000 f 74 goat snp24745-scaffold253-935487 11 90757127 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793065 Affx-122950262 AX-385280043 11 89845242 CAAGACCCCACCTGAGTTCTGATGTCTGCAATTCC[A/G]TTTACCTACACTTTTCCCAATCTCTATTCTTTTCA R 2 1 2 1 103000 f 74 goat snp24746-scaffold253-983210 11 90804993 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430088 Affx-122937535 AX-123300429 11 89877741 ACATGTATTCATAAAATGAGGATCCAACCACGTGA[C/T]GCAAGCTGGTGTGATCATCTGATGCCCCTTCCTAG Y 2 1 2 1 101000 f 74 goat snp24747-scaffold253-1015709 11 90837128 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799311 Affx-122942285 AX-385286241 11 89908132 TAGTAGAAATACACCCATAAGGCAAAACTTTGTCC[A/G]CTGATCTGCAGGAAAACCTAGATTAAAAAAATAAA R 2 1 2 1 101000 f 74 goat snp24748-scaffold253-1046100 11 90867508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428071 Affx-122939110 AX-123298414 11 89941202 GGGTTACACCTCTGTCCAGCAGGAAGCAGCACCTC[C/T]GAGTGTTCTGAAACCCACCTTGGAGAAGTTATGAC Y 2 1 2 1 101000 r 74 goat snp24749-scaffold253-1079170 11 90901369 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452927 Affx-122920191 AX-123323260 11 89980492 CTCTTACTTGTATTTCATTTTCAGGAAATACCTTT[A/C]TTTTACATAGAAGAACTTTAACTTGAATTTAAAAT M 2 1 2 1 201000 r 74 goat snp24750-scaffold253-1118460 11 90940863 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463185501 Affx-1109857178 AX-514671893 11 89985627 TCTAAGTACGGAGTATGTGAACTTAACTGCAGTCC[A/G]CAGAAAATGATTCATTCCATAGCCTCTGGATAATA R 2 1 2 1 101000 f 74 goat GoatD01.047443 11 89985627 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320766534 Affx-122921286 AX-385253894 11 90027767 ATGCTCGTGGGAAAAATGCGTTCACCAGGAGACAT[A/G]CTAACTTTCTTATTAAACCAGAAGTTGGGACTGTC R 2 1 2 1 101000 f 74 goat snp24751-scaffold253-1165735 11 90988273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276557 Affx-1111835476 AX-519550068 11 90036709 AGCTGGCTTAGAGGGATACCCTTTCCCAGGAAGAG[A/C]TTTTACTCTTTTCTAAAAGTAAAGACCAAGAAGAC M 2 1 2 1 102000 f 74 goat Random2.2K-1213 11 90036709 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422083 Affx-122943589 AX-123292430 11 90062939 GAGATTACAAGGCAAAGAATCAGGAAAAGTTTTAG[C/T]ATCTAAAGGGAGTTCAGGCAAAGCCTATACACAGA Y 2 1 2 1 101000 r 74 goat snp24752-scaffold253-1200907 11 91023828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416409 Affx-122947848 AX-123286758 11 90097229 AAGTCTTGACTTTCAGCCCTGAATACAGATCTCTT[C/T]AGGCTCCTAGTAGTCTCTGTGGCTCATATGTGGCT Y 2 1 2 1 101000 f 74 goat snp24753-scaffold253-1235197 11 91058365 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790608 Affx-122946275 AX-385277610 11 90182326 GGGCTGATCTTTCTTACCACTTGAGGTGTCTCCAC[A/G]CCTTTCCTCTCTAGATTAGATTCTAGAATAACAAC R 2 1 2 1 101000 f 74 goat snp24755-scaffold253-1320294 11 91143976 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403849 Affx-122957935 AX-123274201 11 90222485 AGAGCTGCAAGGAGAGAAGATGAAGACGGGAAGGG[C/T]ATGTCCCAGGGGAAGAAAAGAAAGAGCATCCTCAA Y 2 1 2 1 201000 f 74 goat snp24756-scaffold253-1360453 11 91184401 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422592 Affx-122943740 AX-123292938 11 90288331 CTACTGCATTTCTGCTCCCAAATCTAAGTAGGAAT[A/G]TAATTTGATAAATTTTTTTTCAATTCTATGAAATC R 2 1 2 1 101000 f 74 goat snp24757-scaffold253-1426299 11 91250427 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412708 Affx-122950746 AX-123283057 11 90320496 GTAACATCACAGTAACTGTTACAAGGAAAAACTAC[A/G]GAAGATATTGTTTAAAGTCATATTAAATAAAACCA R 2 1 2 1 101000 f 74 goat snp24758-scaffold253-1458464 NW_017212920.1 11581 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388721 Affx-122968973 AX-123259079 11 90391116 AGATTTAGTCATTCATTTAAGACACATCTACTCAG[C/T]GCCTACCTTGTGGCTTATGCTACTAGGTCCTAGGA Y 2 1 2 1 101000 f 74 goat snp24760-scaffold253-1529084 11 91353801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453271 Affx-122920392 AX-123323604 11 90451175 GTTGGCCCCTCAAACCATCCCCAGGGAATGAGCCC[G/T]CACTGAGGGGCCATCTCTGTACTTAACAGAGAACA K 2 1 2 1 101000 r 74 goat snp24761-scaffold253-1589143 11 91415328 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413692 Affx-122950093 AX-123284041 11 90482293 ATTGACTTTTATGTAGATGTTTAACATTAGATGGC[A/G]TCACTGACTTTATGAGCATGAGTATGAGCAACCTT R 2 1 2 1 201000 f 74 goat snp24762-scaffold253-1620261 11 91446576 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416902 Affx-122948065 AX-123287250 11 90510793 GTGCACCCCTATATTCTGAACAACACTGTTCACAA[C/T]AGTGAAGACATCAAAGCAGCCTAAGTGTTCATGGA Y 2 1 2 1 101000 r 74 goat snp24763-scaffold253-1648761 11 91475519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788977 Affx-122927153 AX-385275990 11 90567308 GCATCAATCTGGATATATGTTCTCACTAATGTTTG[C/T]GGTCTTCATTTTAGTCACCCAGTTTTCAATTCTAT Y 2 1 2 1 101000 f 74 goat snp24764-scaffold253-1705276 11 91532242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377992 Affx-122977605 AX-123248351 11 90621915 TGTAGTATAACACATTTAAATTTAAAGAAAATTAT[C/T]CTTTTTCAGTAAAAACCAATGTTTCATTAAACATA Y 2 1 2 1 101000 r 74 goat snp24765-scaffold253-1759883 11 91595797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276559 Affx-1111835477 AX-519550070 11 90647270 GCAAAATGTGAGCAAAAGTGAACTGTGTCACTTCC[A/G]AAGAGAAGAATTAAGAGTCACATATGTCCACCATA R 2 1 2 1 201000 f 74 goat Random2.2K-1214 11 90647270 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390569 Affx-122967205 AX-123260926 11 90668555 GTGAGGCCTTGGGTCTGAATCCCATGTCCATCAGG[C/T]AGTGGGGTTATCGACCTCAGCAGTAGTGACTTCTG Y 2 1 2 1 201000 f 74 goat snp24766-scaffold253-1806523 11 91642719 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413016 Affx-122951005 AX-123283365 11 90697164 CATTATCTGGGGAGAACTCAGAAAAGGAGGACTTC[A/G]TAATAATCCAACTAAACTCTCCAAAATTCCTGTGG R 2 1 2 1 201000 r 74 goat snp24767-scaffold253-1835132 11 91671881 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446296 Affx-122925652 AX-123316632 11 90730991 AAAAATGGACATAGAACAAAGAAGTGCCAAGTAAG[C/T]AACCATGGTAACTCCACAGCCTGGAGGAGTATATT Y 2 1 2 1 201000 f 74 goat snp24768-scaffold253-1868959 11 91706001 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792300 Affx-122970938 AX-385279282 11 90743694 CTCGTTTCATCTCATTACATACTTCTGCACCCTGC[C/T]AGTGCAAATCCCCTGTGATGGAGGTGTCCTCAGTC Y 2 1 2 1 101000 f 74 goat snp56427-scaffold887-3466 11 91719364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782619 Affx-122962615 AX-385269692 11 90790434 GAACACTTTTAAATTCAGTAAAAGAGTTAGAAGAC[A/G]AAGTAGAAAAAACTGTGTGCCCTATTTTCCTGTTT R 2 1 2 1 101000 r 74 goat snp56428-scaffold887-50206 11 91766266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789723 Affx-122952960 AX-385276731 11 90898992 ATCAGAAGCAGCTTGCTTTTACCTGAGAGAGACAT[C/T]GGTAAACCTTAGAGGTACGTGAACTCGAGAGCTGC Y 2 1 2 1 101000 f 74 goat snp56431-scaffold887-158764 11 91875173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425154 Affx-122941070 AX-123295500 11 90942093 AGGAGCACACCTGGTTTTTAAAATATTAATTCTTA[C/T]GGCAAAAATTCCCCTTTATTAGATTCTTCCATAAA Y 2 1 2 1 201000 r 74 goat snp56432-scaffold887-201865 11 91919298 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441902 Affx-122928612 AX-123312239 11 90986495 GACAGCACGGTCTTCCAAGTGACATGGACAGGGAC[A/G]TAAACAAGTCACTCTTCTCAGCTTTCCTCTCCCCC R 2 1 2 1 101000 r 74 goat snp56433-scaffold887-246267 11 91963568 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441828 Affx-122929060 AX-123312165 11 91038534 GCAGTCTGCCTGCTGCAAGCTTCCAGCCAGAGGTA[C/T]GGTTCCTCAATTTCCTGCATTTGCACAAGTGAGCA Y 2 1 2 1 101000 r 74 goat snp56434-scaffold887-298306 11 92016251 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447625 Affx-122923987 AX-123317961 11 91111044 CAGATGAACTTCAGGTGACTTACTTGAGACAAATA[C/T]GTGTGCAAAAATCACAGGCTTATCTAATCGCTTCT Y 2 1 2 1 101000 r 74 goat snp56435-scaffold887-370816 11 92088628 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429740 Affx-122937597 AX-123300081 11 91146453 GAATCTGGCCCTTCTCTGTTCTACTCGAGCAATGC[A/G]TGAGTCCAGGGCATCTGTTGACTTAGTTCCTTCGG R 2 1 2 1 201000 r 74 goat snp56436-scaffold887-406225 11 92124255 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382792 Affx-122973576 AX-123253150 11 91213363 CCCACCCATTTCTCAGAGAGGTGAGCGGCCTTGCA[C/T]AGCATCTTGCAGCCAGCGGTCTCTGGAGCTGGATT Y 2 1 2 1 101000 r 74 goat snp56437-scaffold887-473135 11 92190919 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398545 Affx-122961526 AX-123268900 11 91270759 GGAGTGGTGTTCAGCTATCCGGCCTGGGTGTGAGC[A/G]CTCATCTGTCCAGGGAGACCGGGGACGGTGTGATG R 2 1 2 1 201000 f 74 goat snp56438-scaffold887-530531 11 92248354 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406523 Affx-122955134 AX-123276875 11 91330964 ATATAGAAAACAGAAGAACGAGCAAAGAACAAGCC[A/G]AAAAGAAACAAACAAACCCGGAATTAGCAGAGCTG R 2 1 2 1 103000 f 74 goat snp56439-scaffold887-590736 11 92303450 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405291 Affx-122956850 AX-123275643 11 91371019 GCAGAGGGAGACCCCTGTAGGCCTCTGTGAGTATA[C/T]GTCTCCATCCTCACCCTTGGAGCGCCCTGCTTTGG Y 2 1 2 1 101000 f 74 goat snp56440-scaffold887-630791 11 92343240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421114 Affx-122944210 AX-123291461 11 91400365 GCATGGTGGTTATGGGCAGAGGCTGTGGAGTCAGG[A/G]TGCCTGGGATCTTGCTGATTTCGGGCCCTTCTCAT R 2 1 2 1 101000 r 74 goat snp56441-scaffold887-660137 11 92372590 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416945 Affx-122948030 AX-123287293 11 91447438 GATAAACTGTGGCTAATTACATGAAGTATTATGCA[A/G]CAGCTAAATCATATGGATCCAGCATAGATCCAAAT R 2 1 2 1 101000 f 74 goat snp56442-scaffold887-707210 11 92420166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801335 Affx-122927437 AX-385288247 11 91485280 GGTTCTGCAGATTTTGAAACAAAAAATTTACATTG[C/T]AAGAGAGTTAACATCATGAAGAAAATTAAAAGAAA Y 2 1 2 1 101000 f 74 goat snp56443-scaffold887-745052 11 92456615 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276706 Affx-1111835478 AX-519550216 11 91495631 GTTCCTGTATATTATCAATAACAACTTCTATAGAC[A/G]TACAAATGCTGCTGCCGTTTAGTAGCTCAGTCATG R 2 1 2 1 101000 r 74 goat Random2.2K-1215 11 91495631 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391215 Affx-122967407 AX-123261572 11 91525420 GCCAAAGAAATACCCACAAGGGGTGAGAGCCTGGG[C/T]GGGTGTGAATCCTTCTGAATGGGCATTGGAGGGAA Y 2 1 2 1 101000 r 74 goat snp56444-scaffold887-785192 11 92496618 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476281 Affx-1251763788 AX-586011700 11 91543528 CTGAGCGACTGAACTGAACTGAGGTAGTGCAGTAG[-/TAAAGAATCCACCTGCCGAGGGAGAGGGAAAGATGGCGGATAAATTAAAAAAAAAATAAACTCAAAAAAAAAAAAAAAAA]AAAGAATCCACCTGCCAATGCAGGAGACACAGATT - 8 1 4 1 20000 f 74 goat SV_349 11 91543528 - deletion junction SV-TF-chip 539476534 Affx-1251763788 AX-425512077 11 91543528 CTGAGCGACTGAACTGAACTGAGGTAGTGCAGTAG[-/TAAAGAATCCACCTGCCGAGGGAGAGGGAAAGATGGCGGATAAATTAAAAAAAAAATAAACTCAAAAAAAAAAAAAAAAA]AAAGAATCCACCTGCCAATGCAGGAGACACAGATT - 4 1 4 1 20000 r 74 goat SV_349 11 91543528 - deletion junction SV-TF-chip 562165287 Affx-1251763788 AX-606940698 11 91543528 CTGAGCGACTGAACTGAACTGAGGTAGTGCAGTAG[-/TAAAGAATCCACCTGCCGAGGGAGAGGGAAAGATGGCGGATAAATTAAAAAAAAAATAAACTCAAAAAAAAAAAAAAAAA]AAAGAATCCACCTGCCAATGCAGGAGACACAGATT - 8 1 4 1 20100 r 74 goat SV_349 11 91543528 - deletion junction SV-TF-chip 562165471 Affx-1251763788 AX-606940882 11 91543528 CTGAGCGACTGAACTGAACTGAGGTAGTGCAGTAG[-/TAAAGAATCCACCTGCCGAGGGAGAGGGAAAGATGGCGGATAAATTAAAAAAAAAATAAACTCAAAAAAAAAAAAAAAAA]AAAGAATCCACCTGCCAATGCAGGAGACACAGATT - 8 1 4 1 20100 f 74 goat SV_349 11 91543528 - deletion junction SV-TF-chip 562165758 Affx-1251763788 AX-606941167 11 91543528 CTGAGCGACTGAACTGAACTGAGGTAGTGCAGTAG[-/TAAAGAATCCACCTGCCGAGGGAGAGGGAAAGATGGCGGATAAATTAAAAAAAAAATAAACTCAAAAAAAAAAAAAAAAA]AAAGAATCCACCTGCCAATGCAGGAGACACAGATT - 8 1 4 1 20100 f 74 goat SV_349 11 91543528 - deletion junction SV-TF-chip 562165771 Affx-1251763788 AX-606941180 11 91543528 CTGAGCGACTGAACTGAACTGAGGTAGTGCAGTAG[-/TAAAGAATCCACCTGCCGAGGGAGAGGGAAAGATGGCGGATAAATTAAAAAAAAAATAAACTCAAAAAAAAAAAAAAAAA]AAAGAATCCACCTGCCAATGCAGGAGACACAGATT - 8 1 4 1 20100 f 74 goat SV_349 11 91543528 - deletion junction SV-TF-chip 562166353 Affx-1251763788 AX-606941761 11 91543528 CTGAGCGACTGAACTGAACTGAGGTAGTGCAGTAG[-/TAAAGAATCCACCTGCCGAGGGAGAGGGAAAGATGGCGGATAAATTAAAAAAAAAATAAACTCAAAAAAAAAAAAAAAAA]AAAGAATCCACCTGCCAATGCAGGAGACACAGATT - 8 1 4 1 20100 f 74 goat SV_349 11 91543528 - deletion junction SV-TF-chip 562166404 Affx-1251763788 AX-606941812 11 91543528 CTGAGCGACTGAACTGAACTGAGGTAGTGCAGTAG[-/TAAAGAATCCACCTGCCGAGGGAGAGGGAAAGATGGCGGATAAATTAAAAAAAAAATAAACTCAAAAAAAAAAAAAAAAA]AAAGAATCCACCTGCCAATGCAGGAGACACAGATT - 8 1 4 1 20100 r 74 goat SV_349 11 91543528 - deletion junction SV-TF-chip 38395681 Affx-122963745 AX-123266036 11 91557386 CTTGCCTCAAGTTGGGCCACATACCTTGGGCACTT[A/G]CACTGTTCCTGCCAGACTACTTTGACTTTAAGTAT R 2 1 2 1 101000 r 74 goat snp56445-scaffold887-817158 11 92529002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406963 Affx-122955057 AX-123277314 11 91589361 TGAATCCCCCCAAAAAACAAAACTCCTCCTTATGA[C/T]GCAAGTCTGGGGTGCTGTTACAGCTGCCACTACTT Y 2 1 2 1 201000 r 74 goat snp56446-scaffold887-849133 11 92562271 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421451 Affx-122943939 AX-123291798 11 91622492 CTGTGGTTTCCGCGTCTGTGTAACGGGGACGATGA[C/T]AGTGCTTGCCTCGGGACTGCCACGAAGACTACACG Y 2 1 2 1 201000 f 74 goat snp56447-scaffold887-882264 11 92595020 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445910 Affx-122925937 AX-123316247 11 91651562 CTCTGCTACCCTGGCACCTACATGAACAGACAATT[A/G]TCTACTAGTTCTTACAGCAGGCAACTTCAGCATCC R 2 1 2 1 101000 r 74 goat snp26630-scaffold2784-22752 11 92623887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768414 Affx-122923500 AX-385255594 11 91685596 TGTGAGGACCAAGTTCACGTCTTTTGCTGAGTTCC[A/G]CAGGTCCTTAACATCCTAACATTCCTCCTGGCCAT R 2 1 2 1 101000 f 74 goat snp26631-scaffold2784-56786 11 92657640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272650 Affx-1111832941 AX-519546360 11 91752982 AAAGAGCCCTGAGATACCTATGCTGAGAGCTAAGG[A/G]GGTCAGACTGGCCAGTCCTGCCCCGAGGGTGGATG R 2 1 2 1 101000 f 74 goat 11_91752982_AF-PAKI 11 91752982 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38442263 Affx-122928275 AX-123312600 11 91756628 AGTTATTCTGTGACTTTAGTAAGTCATGATCACCC[C/T]TTAAATGTCCCCCTCCTTAGAAAAGTTTTCCCTCA Y 2 1 2 1 101000 f 74 goat snp26632-scaffold2784-127818 11 92728889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437244 Affx-122932019 AX-123307582 11 91805700 TGCATAGCATGCCACCTCGAAATTCAGTGATGTAT[A/G]TTTCAAGCATTTCTTATTCCTGTCTCTGTGGGTCA R 2 1 2 1 101000 f 74 goat snp26633-scaffold2784-176890 11 92777535 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427802 Affx-122939759 AX-123298145 11 91844882 CCCACTACAGCTGTGACTTAAATGTTGGCCTGGGA[A/G]GAAGGGACCCTCATTGCGTGAATGTGTGTGCGTCC R 2 1 2 1 101000 f 74 goat snp26634-scaffold2784-216072 11 92816509 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417216 Affx-122947301 AX-123287564 11 91943987 TACATACATGTTTTTTTGGTCATATCTGGTCACCC[A/G]GCAATGGACATTAAAATGGCCTCTGCTTCTTACTA R 2 1 2 1 201000 r 74 goat snp26636-scaffold2784-315177 11 92914184 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794503 Affx-122926910 AX-385281466 11 91975624 TATATTTTTGGTTACTGTAAAAATCTATACAATAC[A/G]CACTTACATTATCCCTCACGGTCAAATTGTCAGGC R 2 1 2 1 101000 r 74 goat snp26637-scaffold2784-346814 11 92945142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783641 Affx-122976059 AX-385270700 11 92032133 TGAAAGCATAAGTCCAGAAATACAAAGAGCAGGAC[A/G]TAGAGAGTGGTCAGAAATTTTAAGTCATGAAGTTT R 2 1 2 1 101000 f 74 goat snp26638-scaffold2784-403323 11 93002034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781007 Affx-122975369 AX-385268094 11 92070331 TTGGGGCTGAGTCCCTGAGGCCTTACTCCTATTGA[C/T]AAAAATGAATCTTCCTGCTCATTGTTCTAGTTCTT Y 2 1 2 1 101000 f 74 goat snp26639-scaffold2784-441521 11 93040976 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411747 Affx-122951509 AX-123282097 11 92103210 ATTGACACATAAAATTAACCATTCTAGTAGACTTT[A/C]TGGTTTTCATTCTGAGGATTTGGGAACCCGTTGAA M 2 1 2 1 101000 r 74 goat snp26640-scaffold2784-474400 11 93073641 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380503 Affx-122975700 AX-123250861 11 92147296 TGGTTTCAAGATAAGTGCCTAGATGATCATGTCAA[C/T]GATACTGATAATAAAATTATAATAACAATCATCTT Y 2 1 2 1 101000 f 74 goat snp26641-scaffold2784-518486 11 93118600 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771515 Affx-122974516 AX-385258673 11 92208619 CTTATTTAGCTTCTCTAATCCACACTACCCTCAAG[C/T]ATATTTGGCATAACAATCAGGACTTTTAGTTAGAT Y 2 1 2 1 101000 f 74 goat snp10204-scaffold1367-10938 11 93362956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403638 Affx-122957533 AX-123273990 11 92249419 CAGTGAGATGGGAACTGCAGGTGGAGAAGGCTTTG[C/T]GTTTTCCAGCAGCTGAGGGAATTTTGAGGACCGCA Y 2 1 2 1 103000 r 74 goat snp10205-scaffold1367-51738 11 93322040 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789937 Affx-122975916 AX-385276943 11 92296398 CATTTACTTGGAAGACTTAACTATGCCTACAACCC[A/G]TAATCTGTGTGTTTTCAATCTTGACAATAAGCAAA R 2 1 2 1 101000 f 74 goat snp10206-scaffold1367-98717 11 93275667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385070 Affx-122971815 AX-123255428 11 92330347 CACACTGCAAATCTTTGATAGGTATAACAGCACAT[A/C]TATCAGAAGGCATATGATTTTGCTCATATGTCAGA M 2 1 2 1 101000 f 74 goat snp10207-scaffold1367-132666 11 93241698 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424891 Affx-122941317 AX-123295237 11 92401651 ACATGTTTACATGCCCACCAGCAACAGAAACCTAT[A/G]CATCTCTGTGACCTTTGAAAAAAACACAGAAAACA R 2 1 2 1 102000 f 74 goat snp33886-scaffold4-58897 11 93443435 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443279 Affx-122927479 AX-123313616 11 92461930 GAGAATTTCTTGATCTGATATATCATAAAAGAGAC[G/T]ATGAAGAACAGGGCGGAAAGCCAGAAGATCACACA K 2 1 2 1 101000 f 74 goat snp33888-scaffold4-119176 11 93503556 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776338 Affx-122971243 AX-385263466 11 92496032 TGAGGATATACTGGTACTCTAGTGATAAATGGGCT[A/G]GATTTTGGAGGCACAGAATTCAGCTCTGTTCCAGC R 2 1 2 1 101000 f 74 goat snp33889-scaffold4-153278 11 93537831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796158 Affx-122927510 AX-385283109 11 92531596 ACCTCTAGATATATAAAGGGACTACTTAATAAAAA[C/T]AAGTTAAATTCAAATTAAACTATTTGTATTAATTT Y 2 1 2 1 202000 r 74 goat snp33890-scaffold4-188842 11 93574042 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421802 Affx-122944327 AX-123292149 11 92571288 CCCCGTCTTCCCAAATTCTTTTAAGTGTCTGCCCT[C/T]AGTACCTCATTGCTGTATCGTGATTCCGAGCAGCC Y 2 1 2 1 101000 r 74 goat snp33891-scaffold4-228534 11 93613817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798627 Affx-122919967 AX-385285559 11 92605982 TGGTTAAGTTTGAAATTGGATTGAAGGTGCACAAA[C/T]GATCTTAATGGTAAGTGTTGAGTACTGTATTGGAA Y 2 1 2 1 101000 r 74 goat snp33892-scaffold4-263228 11 93648434 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38415676 Affx-122948547 AX-123286025 11 92663272 TTTACCTGCCTTACAAATACAGATACATAGAACAC[A/C]GAAGGAAAGAAAAAAATCTCATAATTAGTCACTTT M 2 1 2 1 101000 f 74 goat snp33893-scaffold4-320518 11 93705693 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785147 Affx-122926851 AX-385272193 11 92692221 TTGTTTAAGCTAGGAAGTTTAGGGGTTCGGAGGAG[A/G]TGTACCCCCTCTTTTAAAGGACACTTCCTGGAATT R 2 1 2 1 101000 f 74 goat snp33894-scaffold4-349467 11 93735057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783847 Affx-122921145 AX-385270903 11 92755905 GCTGGACGTGATTCCCATGGCCAGCAAAAGAGAAA[C/T]GCTAGTTAAATTAGGATACATCTGTACAGTACACA Y 2 1 2 1 101000 f 74 goat snp33895-scaffold4-413151 11 93798947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446969 Affx-122924657 AX-123317305 11 92787086 CTGTACTTTCACCCCATGCAGCTGAAAAGAACTGC[A/G]TCAAGGCAAGAGGAGTTATCTGGTGTGATGAAAGA R 2 1 2 1 201000 r 74 goat snp33896-scaffold4-444332 11 93830314 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409107 Affx-122953317 AX-123279458 11 92846655 CAAGCATAGCTGAACTGGACTGGGCCAATCAGACT[C/T]CAGCCTGGGCCAATCAGACTCCCTCCCAGGAGCCT Y 2 1 2 1 101000 f 74 goat snp33897-scaffold4-503901 11 93890397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382059 Affx-122974928 AX-123252417 11 92892115 CGTGACTTTGCCTTGCCTCCTATCAAGAGGTGGAG[C/T]CTCTCTCCCCACCCCTTGAATCCGGGCTGGCCTTG Y 2 1 2 1 101000 f 74 goat snp33898-scaffold4-549361 11 93936211 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434269 Affx-122934785 AX-123304610 11 92923857 GAAACTCACTTAACTCCATACAGAGACTTGTCAGG[A/G]GGCGGAGCAGTATTTGGCATTCAGTCTCCATTATT R 2 1 2 1 201000 f 74 goat snp33899-scaffold4-581103 11 93967719 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448119 Affx-122924304 AX-123318455 11 92952426 CTAATAACCAATCTAACAGGTGGTCAGGAAGATCG[C/T]GGTCCCCGTTTCTTAGATGAGAAGGCTGAGGCTCA Y 2 1 2 1 101000 f 74 goat snp33900-scaffold4-609672 11 93996860 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398990 Affx-122960952 AX-123269345 11 93011864 AAATCCTAGGTGAATGATTAAGAAACTGGGTCATT[C/T]CTTAGAAGTTTTAAGACTGAAAAATCTATTAAGAA Y 2 1 2 1 101000 f 74 goat snp33901-scaffold4-669110 11 94056262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395838 Affx-122964023 AX-123266193 11 93074613 TTTCTTTAACACAAACATTGCACATGCTGTTGATC[A/G]TTCCCTTGACCTGGCAACTGTGTACTCATCCATTA R 2 1 2 1 101000 r 74 goat snp33903-scaffold4-731859 11 94119124 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416372 Affx-122947875 AX-123286721 11 93111959 AGCCAAGTGAAATCTGCATTGGGAAACCTAGAAAA[C/T]AGCAGTTACCTAACTGCCCTTAAAATAAAAACCTC Y 2 1 2 1 101000 f 74 goat snp33904-scaffold4-769205 11 94156501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407215 Affx-122955387 AX-123277566 11 93182733 GGTAGAAAAGACCTCACTTTGATGAAACATCTCCA[G/T]TCACACAGAGCCTGCCCAGCTGCCTCCTCAGGATG K 2 1 2 1 101000 f 74 goat snp33905-scaffold4-839979 11 94227301 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762913 Affx-986697442 AX-385250911 11 93219702 ATGGTGGCACCAATGTGTCCATAAGAGATCAGGAT[A/G]CATATTAATGGGAGGACGATGACGGCCACTCCTAC R 2 1 2 1 600010 f 74 goat 11_93219702 11 93219702 Ancestral_priority_1043 ancestry 0.708 recommended IMAGE 10K 10K ancestral 320765515 Affx-986697448 AX-385252999 11 93219734 GATGCATATTAATGGGAGGACGATGACGGCCACTC[C/T]TACTGTGAAAATGGCCAGCTCATTGAGGGATGTGT Y 2 1 2 1 600010 r 74 goat 11_93219734 11 93219734 Ancestral_priority_1043 ancestry 0.56 neutral IMAGE 10K 10K ancestral 38379631 Affx-122975957 AX-123249989 11 93222383 TCAAGATACACAGGAAGAATTTCAACAAAACCATT[A/G]TGACTTGAAGCCTGGTGCTCTCTCCTCTTGTCCTT R 2 1 2 1 101000 f 74 goat snp33906-scaffold4-879629 11 94267106 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440563 Affx-122929309 AX-123310900 11 93274665 ACAACACAGTATTAATTGTACAACCTGATCAAGTG[C/T]AATAGTCAATCCTGAGATGAGGATTTAAAATCCTT Y 2 1 2 1 101000 f 74 goat snp33907-scaffold4-931911 11 94320022 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782095 Affx-122926894 AX-385269173 11 93324955 AGGACAACTTTCACCTTTGGCTAAAAAATACTAAC[A/G]CAGAGCTTGAAATTGACCAAAGTGCGGAAAATAAA R 2 1 2 1 101000 r 74 goat snp33908-scaffold4-982201 11 94370766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435391 Affx-122933568 AX-123305731 11 93356386 AAGCAGTATAGGACTCTTCCTAATAGATACACGTA[C/T]AGAGAATATATACGCTGCAACACACAAACTCAAGT Y 2 1 2 1 101000 f 74 goat snp33909-scaffold4-1013632 11 94402332 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419750 Affx-122945882 AX-123290098 11 93413886 GTGCCAATTCGCAGCCAAAGCTGTTCAGGCCATTA[C/T]GTCTCCATTGTTTCTCTTTTCCTTTCACCATGAGA Y 2 1 2 1 101000 f 74 goat snp33910-scaffold4-1071132 11 94459862 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378838 Affx-122976537 AX-123249197 11 93452158 TGTTTAAAATATTTTTAAAGCTTTTTAAAAACATG[C/T]GGAAAGATACTGTGGTTTAAGTCAATGTAGGGAGA Y 2 1 2 1 101000 r 74 goat snp33911-scaffold4-1109404 11 94498281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440344 Affx-122929664 AX-123310681 11 93556540 TTCTGTTTCTCTGGACAGCCCTGACTAATACAGAA[A/C]GTGTCAAGCACAAAATAGACTCTTGATGGCATAAG M 2 1 2 1 201000 f 74 goat snp33912-scaffold4-1213786 11 94603681 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399553 Affx-122961133 AX-123269908 11 93599478 CTTTCGGGTCTCTAGGCCCCCCTTTCTCTCTCTGC[A/G]TGTGTCTCCAAGTTTCTCAGTTCCTGTCTCTTTCT R 2 1 2 1 101000 r 74 goat snp33913-scaffold4-1256724 11 94644912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794145 Affx-122929991 AX-385281111 11 93636265 CTTTGATAATGAACTCATCCTGGTTACTAGCACAA[C/T]GGTAGACAAATAAATCCATGAAACAGAAAAGAGAA Y 2 1 2 1 101000 r 74 goat snp33914-scaffold4-1293511 11 94682000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393902 Affx-122965109 AX-123264257 11 93669845 CATCAGGAACCAAGGAGGCATCTGGCCTTCGTCAG[C/T]CTTGGCCTTATTTCTTAAATTGATCAGAAATCAGA Y 2 1 2 1 101000 r 74 goat snp33915-scaffold4-1327091 11 94715583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792450 Affx-122976530 AX-385279431 11 93699704 AGCCAGGGCTGGTTCATCTGTATATACTCTCTACC[A/C]CAAGGAGCTTGTATTCTAGAAGAGACAGAAACCAT M 2 1 2 1 101000 r 74 goat snp33916-scaffold4-1356950 11 94745676 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397616 Affx-122962634 AX-123267971 11 93742969 TGGAGTTGTCCACCTGGTGACTGGCAAGCTAGGGC[A/G]CTTTGTCTTCCATTCCTCCCTGGGTGAGGGCTCTC R 2 1 2 1 201000 r 74 goat snp33917-scaffold4-1400215 11 94789872 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417466 Affx-122947185 AX-123287814 11 93788761 TGGGGGTATCTGTTACAGGGGCTCTGTGAGGATGG[A/G]AACAGACTTTACAAACCGTAGATTCTAACACAGGT R 2 1 2 1 101000 r 74 goat snp33918-scaffold4-1446007 11 94834821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417991 Affx-122946674 AX-123288339 11 93845858 ACCTTTGCTCTCAGCCTTGTGCCCTTGTATTTCTA[C/T]GCAGAGGCACACACATCTGAATATTCAGCCAGGTA Y 2 1 2 1 201000 f 74 goat snp33919-scaffold4-1503104 11 94891692 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397723 Affx-122962551 AX-123268078 11 93939004 GTCGTGGGCTCAAGATGATAAGTGGCACACAGCTA[A/G]GTAACAGAGCCACAGTTTGAACCACGCGCCTCCCA R 2 1 2 1 101000 f 74 goat snp33920-scaffold4-1596250 11 94984010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784243 Affx-122962470 AX-385271294 11 93971018 GTTTTGCATTTTCCTTACGATCAATGATGTTGAGC[A/G]TCTTTTCATGTACTCATTGTCAGTCTGTATGTCTT R 2 1 2 1 101000 r 74 goat snp33921-scaffold4-1628264 11 95016028 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420759 Affx-122944717 AX-123291106 11 94014336 CAGAGGTCCCAGTTGGTCTGCTCTGTGCCCCTCCC[A/G]TGCATGCCTCACTCTTTCGTGTATTCCTTCATTCG R 2 1 2 1 101000 r 74 goat snp33922-scaffold4-1671582 11 95063141 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421724 Affx-122944387 AX-123292071 11 94063848 CCACTGATGGGTGCAGTGACTAGATTCTCTTGGGG[C/T]CCTCTGACTGCTTTCTCTGGTCATAGCTTTTCTTA Y 2 1 2 1 101000 r 74 goat snp33923-scaffold4-1721094 11 95112670 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771429 Affx-122965636 AX-385258587 11 94115808 CTAGCAACAGACTTCAAAGGTGTGGTGATTCACAG[C/T]GGAAAAGCTGATCTACTTGTGCAGATGTCCTTGCA Y 2 1 2 1 101000 f 74 goat snp33924-scaffold4-1773054 11 95164643 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406054 Affx-122955470 AX-123276406 11 94161620 ACTCACAAAATGAACAAAACACTGAACTGCGTCAA[C/T]AAATAAAATCAGTGATTTGCAATTTATCTGTATAA Y 2 1 2 1 201000 r 74 goat snp33925-scaffold4-1818866 11 95210896 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790401 Affx-122973031 AX-385277404 11 94191560 CAAAGTCCCGGTAAACGGATACCTGGACTCAAAAC[C/T]GGGTTTAATCTCTTTCCTGAGTATTTAAGATATGA Y 2 1 2 1 101000 f 74 goat snp33926-scaffold4-1848806 11 95241139 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405059 Affx-122957423 AX-123275411 11 94234338 ATTTCTGCTAAGGTGCCAATAATTCACCCACCATC[A/G]TTTCTCAACATGAGCCCAAATGTCAACATCGCAAA R 2 1 2 1 101000 f 74 goat snp33927-scaffold4-1891584 11 95283917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444369 Affx-122926611 AX-123314706 11 94262857 TTTCTCCTGTGCCCAGGGTTTCCTGTGCATAGTGC[A/G]TGCCAGGTCTTCCTGTTGTTGGTTCTGCAGTTCTG R 2 1 2 1 201000 r 74 goat snp33928-scaffold4-1920103 11 95311962 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276708 Affx-1111835479 AX-519550218 11 94273045 CTACTATTCTATATTTTCAACCCACCTCATTTATT[A/G]ATCTACTCGACTAGAACATAAGCTTCATATGAGGA R 2 1 2 1 101000 r 74 goat Random2.2K-1217 11 94273045 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376704 Affx-122978977 AX-123247063 11 94308195 GTAGGATCACATCGCTCCCCTCTCCACTCAAATCT[A/G]CCTTTAAGGAAAGCGGGGTCTCCCCCATTAGTGAT R 2 1 2 1 202000 r 74 goat snp33929-scaffold4-1965441 11 95357757 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393539 Affx-122965420 AX-123263895 11 94347929 CACAGTGATATACAAGCCTCCTCAAAGGTCCTCCT[G/T]CTTCTGTACTTGCCTCCTTTACAGAGCATTCCTCA K 2 1 2 1 101000 f 74 goat snp33930-scaffold4-2005175 11 95397735 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771518 Affx-122942424 AX-385258676 11 94392612 CATTAATAAGAGTTTAAATGGAATTCCTAAGGAAA[C/T]ACTGGATCATGAAACCAACAATCTGATTTTTTGAC Y 2 1 2 1 101000 r 74 goat snp33931-scaffold4-2049858 11 95442394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436058 Affx-122932710 AX-123306397 11 94455406 CAGTCACTGTCTGAAATCTCTTTCCTCAAAGCACC[C/T]TGTGCAAGGGCTTTGAATATTGTTCCCACACAACT Y 2 1 2 1 201000 r 74 goat snp33932-scaffold4-2112652 11 95505466 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417797 Affx-122947377 AX-123288145 11 94496518 CCAAAGCCCCATCCCGCACTAACTCCCTCTTGCCA[C/T]CGATTCATCTGTTAGTTCCCTATGTTTTTATTGAG Y 2 1 2 1 101000 r 74 goat snp33933-scaffold4-2153764 11 95546483 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446583 Affx-122924823 AX-123316919 11 94528455 TTGTCATGCCTAAACTGTTGTTTCTGAAAGGATCC[A/G]TAAGAATCCTAATACTGGCTATCCAATATGAGGAA R 2 1 2 1 101000 r 74 goat snp33934-scaffold4-2185701 11 95578638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770601 Affx-122961841 AX-385257766 11 94574117 CTAAAATTAGGAATTGAATCTAAGTGTGTAAAATT[A/G]TCAGTGATTCATCACTTATCAAATCTCAAGAGAAT R 2 1 2 1 101000 r 74 goat snp33935-scaffold4-2231363 11 95624492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446444 Affx-122925967 AX-123316780 11 94625656 GGCTTTTGTTATTGTCCAGTGTTTTGGCTTTGTCT[A/G]TGTTTTTTATTATTTTGTACAGAAAGAGTATCTAT R 2 1 2 1 103000 f 74 goat snp33936-scaffold4-2282902 11 95676545 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272652 Affx-1111832942 AX-519546362 11 94654207 CTCCTCAAGAGTTCTCAATACGTGTACTAGTGCCA[A/G]TGTCCTCTGATCACCAAGAGAAGAACACAGTCAGT R 2 1 2 1 101000 f 74 goat 11_94654207_AF-PAKI 11 94654207 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468275004 Affx-1111834537 AX-519548586 11 94729821 GTCTCTAAGCCCCTGTCTGACTGCCACCCTCCTCA[A/G]GCACCCTCCCATTGACGCCCCTGCAGGGGCACCTG R 2 1 2 1 303000 r 74 goat GoatD01.040372 11 94729821 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38442578 Affx-122928500 AX-123312915 11 94781245 CTGGGTCTCCTCGTGAATGACAAGATAAATTGTAA[C/T]GGTGCCTTCAAAGACTTCACAATGCATTTTGTCAA Y 2 1 2 1 101000 f 74 goat snp33939-scaffold4-2438491 11 95831771 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787426 Affx-122943569 AX-385274451 11 94825183 TGTTTACAAAACTCAGATATTTGACATGTCACAGA[C/T]AGGCAGATTTATACTAAAGTTGGCTATGGTCTGAT Y 2 1 2 1 101000 r 74 goat snp33940-scaffold4-2482429 11 95876176 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786817 Affx-122938075 AX-385273846 11 94870531 CCCTCCACTTCAGTTCTCAAAACGCAGTGGTCAAG[C/T]ACCAACTCATGGGCCTCAGAGAATTCTCACTCTTG Y 2 1 2 1 101000 r 74 goat snp33941-scaffold4-2527777 11 95921674 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762921 Affx-986697450 AX-385250919 11 94885923 GCAAGCCCATCATCTAGTTCTTTGTCCTTGGCAAA[C/T]AGCCCTGGGTGACTGATGGAAGGACAGTCAACTCA Y 2 1 2 1 600010 f 74 goat 11_94885923 11 94885923 Ancestral_priority_1043 ancestry 0.592 neutral IMAGE 10K 10K ancestral 320762923 Affx-986697452 AX-385250921 11 94885973 GATGGAAGGACAGTCAACTCAGAGGCTGCAGGTAC[A/G]TCCATCTCATCCCTTTACTGTAGCCAGAGGATGTT R 2 1 2 1 600010 f 74 goat 11_94885973 11 94885973 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 320765529 Affx-986697456 AX-385253012 11 94885983 CAGTCAACTCAGAGGCTGCAGGTACATCCATCTCA[C/T]CCCTTTACTGTAGCCAGAGGATGTTGGGTAAATGA Y 2 1 2 1 600010 r 74 goat 11_94885983 11 94885983 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 38448229 Affx-122924217 AX-123318565 11 94904444 AACAGGAAGAATTAAGCTGGACAGCATGCGGGGAG[C/T]GAGGGTGCCACTGCTGATGGGCTCTGTCACGTGAG Y 2 1 2 1 101000 f 74 goat snp33942-scaffold4-2561690 11 95956303 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442877 Affx-122927662 AX-123313214 11 94954591 ACAATGCATAGGCCACGGCAGAAGCAGGGAGAGGA[C/T]AACTAATCTTTGCAGTCGGGGGAATGGAGGGAACT Y 2 1 2 1 202000 f 74 goat snp33943-scaffold4-2611837 11 96006944 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410653 Affx-122952771 AX-123281003 11 94970091 GATGAGGAGCTTAGTCTCTTGAATCAGGAAGAGCT[G/T]GTTCAAATGCCCGCTCTAACTTGCTGTGTGTCCTA K 2 1 2 1 101000 f 74 goat snp53294-scaffold804-245 11 96022864 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463190825 Affx-1109858992 AX-514677143 11 95038272 ATGCTGCAGTAGAGGCAGGAGTGGGAGGGGGCTGG[A/G]AGGACCGGAGCCCCGGCTTTACCAGGATTTACTGT R 2 1 2 1 102000 r 74 goat GoatD01.045497 11 95038272 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38432721 Affx-122935470 AX-123303062 11 95047098 CCTAAAAATAAGATTTTAACTTTACTAATGTTTAA[A/C]ATAGGAAGTGGCATGGTGGTTTGTGTTACAGGCTT M 2 1 2 1 101000 r 74 goat snp53296-scaffold804-77252 11 96126324 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408327 Affx-122953759 AX-123278678 11 95084675 TTCTTTATCTTATATCTCCAATGGTTTCAAAAGAA[C/T]AATCTAGACTATGGAATGAAGTTAAAGTCCTCTTT Y 2 1 2 1 201000 f 74 goat snp53297-scaffold804-114829 11 96163918 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451671 Affx-122921586 AX-123322004 11 95155035 ACATTATTCATTAAAAGAAATTTCTGTGGTGTTGA[A/G]AGAAATGTTGCTAAAGTGCTGGTTTCAATGAGTGG R 2 1 2 1 101000 r 74 goat snp53298-scaffold804-185189 11 96234817 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439917 Affx-122930015 AX-123310254 11 95186690 TTTTCTTCAGAGGAAGGAGACGTATATAGGCACCT[A/G]TAGGTGATTCATGTTGATGTACAGCAGAAACCAAT R 2 1 2 1 101000 f 74 goat snp53299-scaffold804-216844 11 96266472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405440 Affx-122956052 AX-123275792 11 95273653 CCACGTATTCCTTCCAAGCAGGGCTTCTCCACCTC[A/G]GCATCACTGACATCGGGCGCAGATCATTCTTTGTT R 2 1 2 1 101000 r 74 goat snp53301-scaffold804-303807 11 96352408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796139 Affx-122966996 AX-385283090 11 95327596 TCACTCTAGACACAGGCTGTAGTCACATTTGTTTC[A/G]TTCTTAGCTATTCCTGTGCCCATCTGTCCCTGATT R 2 1 2 1 101000 f 74 goat snp53302-scaffold804-357750 11 96406032 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395000 Affx-122964237 AX-123265355 11 95372638 CTTGCCTGTTCCTGAACTTTACATAAATGGAATCA[C/T]ACATGCTACACTCTTTTGTGTCTGGCTTCTGTGGC Y 2 1 2 1 101000 r 74 goat snp53303-scaffold804-402792 11 96451710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437515 Affx-122932338 AX-123307853 11 95416133 CTAAAAACTATACTCCAAAAAGAAGAAATGTGACC[A/G]TAAAAGGAAGGTTTCAGATGTATATATGAGGAATT R 2 1 2 1 201000 r 74 goat snp53304-scaffold804-446287 11 96495709 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405182 Affx-122956926 AX-123275534 11 95454497 ACCTGGATCTCTTTGTCTAGATGAGCTTGACTGCC[A/G]TTCTGTCCACTTCCCAGTGAGACCAGACATGGTCC R 2 1 2 1 101000 f 74 goat snp53305-scaffold804-484651 11 96534329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422261 Affx-122943997 AX-123292607 11 95518465 AGGCCGCCATGTGGAGCAGCAATGTCACCAAGGCC[A/G]TTAGCTGTCTGGGCAGAGCTGTAAACCATGCCTGG R 2 1 2 1 201000 r 74 goat snp53306-scaffold804-548619 11 96596976 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379588 Affx-122976031 AX-123249946 11 95586043 CTAATCACCAGCCCACATTGTCACCTGTGTGTCTA[G/T]CCAATTGGCTGTAGTTCAGGGGTTCCAATGACATC K 2 1 2 1 102000 f 74 goat snp53307-scaffold804-616197 11 96665569 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376594 Affx-122979064 AX-123246953 11 95629274 CAGGGCCTGGTGAAGTGGACTAATGAGATGCCGCG[C/T]GAGTCCGGGCCGGAGTTAATTGGCGCAGGTACGGA Y 2 1 2 1 201000 r 74 goat snp53308-scaffold804-659428 11 96709234 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404541 Affx-122957393 AX-123274893 11 95689467 TGGGATGGGGTGTATTTATCACATGTCCCAGAGAA[C/T]GCGGGGCCCTCAGTCCTCAGATCTGTCTTTCGATT Y 2 1 2 1 101000 f 74 goat snp53309-scaffold804-719621 11 96769215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432380 Affx-122935858 AX-123302721 11 95847181 AACAGTTTTGGCGAGTAATGCAGAATGGAGGGGAA[A/G]GAGGTAGGGCTGAGGCCAGGGGGTGGACACAAGCC R 2 1 2 1 101000 f 74 goat snp53312-scaffold804-877335 11 96926832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394322 Affx-122964679 AX-123264677 11 95886518 AATACATTCTTCCCAGGGCCGGGCTGAGCATGCCT[A/G]CATAGGGAGAGATGTCACTCCCTAGCTGGGGTCCA R 2 1 2 1 202000 f 74 goat snp53313-scaffold804-916672 11 96965584 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435339 Affx-122933606 AX-123305679 11 95963081 ATAATGTATTGAGAACTGTATTATGTTCTAGCATG[C/T]AGTCACTTTTTATACGTTTCCCATGTATGGATGAA Y 2 1 2 1 101000 r 74 goat snp53314-scaffold804-993235 11 97041463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378306 Affx-122976850 AX-123248665 11 96003604 AACACACATACTCATGCAAGGCACAACTACATGCC[A/G]TCAACAAGAAACTCACTTTAATTACATGGGTAGGT R 2 1 2 1 101000 f 74 goat snp53315-scaffold804-1033758 11 97081828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798180 Affx-122923747 AX-385285115 11 96081413 AATTAATCCCAGGGGTGGAAAGTCCAGTCATTTTC[A/G]AACTGGTAGAAAAGGCACATCAGGGCCTACTCCAA R 2 1 2 1 101000 f 74 goat snp53317-scaffold804-1111567 11 97159793 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428265 Affx-122939407 AX-123298608 11 96175789 GATACTTTCTAGAGCCCTCCCAAATTTATGTGAAC[A/G]TATTTGTTTCATAAATTAAACATTTTTTGTGTTGT R 2 1 2 1 103000 f 74 goat snp53319-scaffold804-1205943 11 97253152 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451646 Affx-122921605 AX-123321979 11 96227817 GGTTTCACACCTCAGAGGCTGTTGGCTCCAGAGTG[C/T]GAAAGGCTTCCTCACACTTCTAATTCCAGCAAGTA Y 2 1 2 1 101000 r 74 goat snp53320-scaffold804-1257971 11 97305252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795023 Affx-122924387 AX-385281982 11 96275357 CATTTTTTCCCTCTCAGCACACTTTTGACATCATC[A/G]CATAGTTTAACATATCATGATCTGTATGTTCTTTA R 2 1 2 1 101000 f 74 goat snp53321-scaffold804-1305511 11 97352948 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379577 Affx-122976039 AX-123249935 11 96315561 ATGGAAGACATGAGTGACCAATCTCGTTCTCTGTT[C/T]TAGACCACAACTGAACGTACATATTTCCTGCCTCG Y 2 1 2 1 101000 f 74 goat snp53322-scaffold804-1345715 11 97393041 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769049 Affx-122950543 AX-385256224 11 96346481 TGTGACTGTGTTGGTGTAAGGAGAAATACATTACC[A/G]TTATATATTGAAGCATTTTCTGACCTAAAACTCCA R 2 1 2 1 101000 f 74 goat snp53323-scaffold804-1376635 11 97424046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379352 Affx-122976162 AX-123249711 11 96400696 TATACCTTCAGGACTGCTCGCCAACACACCTTTCT[A/G]TCTTCCTTCTGTTGCCCGGTGGTTAAAAGCCAGGC R 2 1 2 1 101000 r 74 goat snp53324-scaffold804-1430850 11 97479115 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403282 Affx-122957855 AX-123273635 11 96465435 TCTGATGCATAACCAACGTCAAGCAGATTGTAAAG[C/T]CAGCTCTGTATATGTTTTTACATTTTCTAGTAGCC Y 2 1 2 1 101000 f 74 goat snp53325-scaffold804-1495589 11 97542633 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403146 Affx-122958100 AX-123273499 11 96558337 GCAAGAGCCCTAGGTGAGGCACCATCCTGAAAGCT[A/G]CCTCCCTCTTCCTCACTCTACAGAGAAAACCACTA R 2 1 2 1 201000 f 74 goat snp53326-scaffold804-1588491 11 97636408 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438609 Affx-122930932 AX-123308946 11 96608808 GAAACAAAAGACCTTCTACCAACAAGACAACGAGA[C/T]AATCAATTATTTACAAATACAGACTTTTATCATTG Y 2 1 2 1 101000 f 74 goat snp53327-scaffold804-1638962 11 97687201 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276710 Affx-1111835480 AX-519550220 11 96717243 GAAGCGTGACTCCCCACACTTTCAACCACAGTGCC[A/G]CCCTGAAAAAGCATGTGTTGAAGCACCATTTACTG R 2 1 2 1 201000 r 74 goat Random2.2K-1219 11 96717243 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38420773 Affx-122944707 AX-123291120 11 96722950 GGGAAAGTGCTTTGAGCTCCCCCAGGGAGGAACCA[C/T]GGTGTCTTGCTTTCCTGGTGTCTCCTATTCATACC Y 2 1 2 1 101000 r 74 goat snp53330-scaffold804-1753104 11 97801745 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773160 Affx-122962676 AX-385260303 11 96770790 AGGGGAAATCACAGGAATCAGGAACGATGCTGGGC[A/G]TGGCAAAGGATTTGACCTTGCTTCTCAAGGAAGGA R 2 1 2 1 101000 r 74 goat snp53331-scaffold804-1800944 11 97849731 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385502 Affx-122971267 AX-123255860 11 96934612 CCAAGACGGAGAGGGCTGCAGCATCCAGGCTGAGA[C/T]GGCAGGTATACATCTGGTGTCTAGTTCAGGGACCC Y 2 1 2 1 101000 r 74 goat snp53335-scaffold804-1964766 11 98011738 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777198 Affx-122964735 AX-385264321 11 96973151 ATTAGTTCAATAAGAATGATAGACAAAGGGCCACA[A/G]ATGTCTTTCTTCATGTAAAAAGCTTATAGAAATAA R 2 1 2 1 101000 f 74 goat snp53336-scaffold804-2003305 11 98050658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450435 Affx-122922048 AX-123320769 11 97082822 AAGCCCCCCTGGGTACCAGCAGCTCACATGCTGGG[A/G]TGTGCTGTGCCCATCCTCACAGCAATTCAGGCAGA R 2 1 2 1 103000 r 74 goat snp53339-scaffold804-2112976 11 98159691 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388168 Affx-122969445 AX-123258526 11 97119404 GGAGGATATAAGCAGGTGGGTGACAAGATCCAAAT[A/G]CCTTTTTGAAAGTTCTTGCCAGTTTTTTCCATTTT R 2 1 2 1 101000 f 74 goat snp53340-scaffold804-2149558 11 98196129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770306 Affx-122962502 AX-385257472 11 97196337 TATCACATGTATGCATCCCATATATGTTAACATAT[A/G]TATATGTGATTTCCCACATGTGCAAACATATCTGC R 2 1 2 1 202000 f 74 goat snp53342-scaffold804-2226491 11 98272796 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272653 Affx-1111832943 AX-519546363 11 97238305 GCATGTGATAGATAACCCTGGCATAACAATGACTT[A/G]AACATGTAGGAGTTTATACTATTTCATGAAAGAGT R 2 1 2 1 101000 f 74 goat 11_97238305_AF-PAKI 11 97238305 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413597 Affx-122950569 AX-123283946 11 97266068 GAGAGACAGGACAGTCAGAAGACTGAGAGGGCAGA[C/T]GCCAGAGGACCCCATAAGCCCCGAGGCTGAATGCG Y 2 1 2 1 101000 f 74 goat snp53344-scaffold804-2296222 11 98341656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451547 Affx-122921085 AX-123321880 11 97314266 CCCCACCCTCCTGCCTCTCCTGAAGACCTCACCCC[A/G]TCTCCTTGGCCTCCTTCTTGCCCTCAGAATCCCTA R 2 1 2 1 101000 r 74 goat snp53345-scaffold804-2344420 11 98388947 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396143 Affx-122963392 AX-123266498 11 97344318 CCTCCCAAAGAGCTCTCATCTACAGGATCAAACGA[C/T]GTAACCAATCTCATCGTCCAACCCCTTCATTTGCA Y 2 1 2 1 101000 r 74 goat snp53346-scaffold804-2374472 11 98418646 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380702 Affx-122975162 AX-123251060 11 97388077 AGTCCCTGCTCCTACCCTTCCCTGCCCCCCAGCAC[A/G]TACACTTCCCATCAGAGCACCTCTGTCAAGTCGCC R 2 1 2 1 101000 r 74 goat snp53347-scaffold804-2418231 11 98462293 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422063 Affx-122943602 AX-123292410 11 97479742 TCTAATTTTTATTTTAATGTGAATACCCTGGCTCC[A/G]CTAATGAATTGTAGTTGGGTCCAGGGTAGAAATAG R 2 1 2 1 201000 f 74 goat snp53348-scaffold804-2509896 11 98552786 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788099 Affx-122960117 AX-385275119 11 97539781 ACATTAGGAGGCATAGAGTACTGATGGTCTTTCCA[C/T]CTGTGATGTTAAGGTCAACTGGTGGTCTCAGAAAC Y 2 1 2 1 101000 r 74 goat snp53349-scaffold804-2569935 11 98613388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425463 Affx-122941505 AX-123295809 11 97573114 TCGGGTGCCATCGTGAAGCTTGATGAGACTGGTAA[C/T]CTGATGATCTCAGAAGGGCACTTCGCGTCCGAAAC Y 2 1 2 1 101000 f 74 goat snp53350-scaffold804-2603268 11 98646726 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394739 Affx-122964863 AX-123265094 11 97642570 ATTCATCAAATGATTATCCTACACCCCCTGAGTCA[A/G]ACACTGTGCTCCAGAGTGGCCAACACCACCAATTC R 2 1 2 1 303000 r 74 goat snp53351-scaffold804-2672724 11 98716572 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378272 Affx-122976877 AX-123248631 11 97686104 CGGAGACGAGATGCTCAAAGCCTCAAGAGAGGCAG[A/G]ACTAGCCCAAAGTGACGCCGGGGTGATAACTTTAC R 2 1 2 1 201000 f 74 goat snp53352-scaffold804-2716258 11 98760296 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772758 Affx-122954088 AX-385259903 11 97729626 TTAAGTCAACATTTATTCACTTCTTATATTTCATG[C/T]AAAGGAATGTAACCTTTGTTCTGTGCGGAGCCCGT Y 2 1 2 1 201000 r 74 goat snp53353-scaffold804-2759780 11 98803621 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404320 Affx-122957014 AX-123274672 11 97787718 GGGAGGCCAACCCTGCCTGGAGAAGGGAGCTTAAA[C/T]GCACCAGGTGACCTTCAGAACACCTTTCTGGGCAG Y 2 1 2 1 101000 r 74 goat snp53354-scaffold804-2817872 11 98861512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403611 Affx-122957554 AX-123273964 11 97832999 TCTAGCTCCAGGGTTTCCCAAGTAGCCCAAAGCTC[C/T]CTGGGAACCAGGCCTCTTTGATCATGCCATTATCG Y 2 1 2 1 201000 r 74 goat snp34603-scaffold4095-31080 11 98906837 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385039 Affx-122971849 AX-123255397 11 97903004 TTAGCCAGCGTCCAGCCATATCGCCTTTCAAAAGC[C/T]ATAAATCAATATAGTAACTTGTTCATTCATTTGGT Y 2 1 2 1 101000 r 74 goat snp34604-scaffold4095-101085 11 98977539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390521 Affx-122967239 AX-123260878 11 97952628 ACGAGGGGAGGTAAGTGTTGGGGAGATCACATACT[A/C]CTACATGATCAACTTTTGAAATCCAACCATCTGAA M 2 1 2 1 101000 r 74 goat snp46818-scaffold653-2097388 11 99026982 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409098 Affx-122953324 AX-123279449 11 98013786 CCTCACTAGGGCAGGAAGTCATCCTCCCCTTCTCT[A/G]TCCCCAGCTCCTGGGGAGAACAGTGTACCACACAT R 2 1 2 1 303000 r 74 goat snp46817-scaffold653-2036230 11 99086212 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443816 Affx-122927072 AX-123314153 11 98048268 GAGGGCCTTTGGCCAAAGCTATGGGTTGGCAACCC[A/G]GAGGGTATTCCAGTCCCTCTCTTTCTGTTTCCTAC R 2 1 2 1 101000 r 74 goat snp46816-scaffold653-2001748 11 99119355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276567 Affx-1111835481 AX-519550078 11 98078295 AAAGCATGAAGTTCCGCAGAAGGTAAGGCAGGAGC[A/G]GAGCCGGGGACGCATAGGGCAACTGAGACACAGAG R 2 1 2 1 102000 f 74 goat Random2.2K-1220 11 98078295 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388844 Affx-122968882 AX-123259202 11 98080305 AAACAGTGAAGAAAATCTTAATTCAAGTCTGTCCC[A/G]TGCAATATTGAGGACACACCTACCCTGAAAAATGA R 2 1 2 1 101000 r 74 goat snp46815-scaffold653-1969711 11 99151641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387948 Affx-122970015 AX-123258306 11 98118103 AGCCGACGAGGGGACACAAAGGCAAAATTAGGTCA[A/G]TTCTAGAAAAATCAAGATTTTCCCACACCTTGATC R 2 1 2 1 101000 f 74 goat snp46814-scaffold653-1931913 11 99189618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767414 Affx-122922388 AX-385254687 11 98168869 ACATCATAGCTTCTTTGAGAAATACAGCTGAACTG[C/T]GACAGGAGTAGGCTCCTACTGCACATTAGATCATT Y 2 1 2 1 101000 f 74 goat snp46813-scaffold653-1881147 11 99240404 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774974 Affx-122926214 AX-385262106 11 98278302 ATATTATAAAGAATACAGATAAGCTCAGTGAAGAT[A/G]TTAGTAATAAGACCGCTTTTAATCCTGTAACTTAA R 2 1 2 1 101000 r 74 goat snp46811-scaffold653-1771714 11 99347493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408718 Affx-122953423 AX-123279069 11 98308261 CGCCCATCCTGGGTGAGAATCCCACTCCACCTGCA[A/C]TGTGAAGCTTGGGCAAGACACCGAGCCCCTTTTCC M 2 1 2 1 201000 f 74 goat snp46810-scaffold653-1741755 11 99377854 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402135 Affx-122958667 AX-123272488 11 98340959 CAAGAGTTATCTTTCAGTCTCCTGCCTGGAGGTTC[A/G]TACTAAACCTGCTTGCCATTGGGGAGTATTAATAT R 2 1 2 1 102000 r 74 goat snp46809-scaffold653-1709057 11 99410352 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402379 Affx-122959031 AX-123272732 11 98401895 CTTAACCACTGGACCACCAGGAAAGTACCTGAACC[A/G]TTCTTAATACTCAGTACTCACTCAAGCAGTTGCCC R 2 1 2 1 101000 r 74 goat snp46808-scaffold653-1648121 11 99467761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392826 Affx-122965781 AX-123263183 11 98447292 TTCTGGCTCCCAGGACTGGGAGAGAACAGATTTCT[A/G]TTGTTTTAAGCCACCCAGTTCCTGGTGCTTTGTTG R 2 1 2 1 303000 f 74 goat snp46807-scaffold653-1602724 11 99512705 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274378 Affx-1111834221 AX-519547972 11 98456082 ACCTTTCAGAAGCTGCAGCTCCACAGTATCCCGTA[A/G]ATGCTTCCATTTTAGCCCGGGGGGCTTGTAGACTG R 2 1 2 1 202000 f 74 goat GoatD01.026150 11 98456082 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320769751 Affx-122945853 AX-385256921 11 98512476 CTAAGACAAATAAACCCGGCCTCTTCGTTTCTGCC[G/T]TTCTCAAGCTGTTGAGAGACACTCTCTGTTTGTTT K 2 1 2 1 101000 f 74 goat snp46806-scaffold653-1537540 11 99577135 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378747 Affx-122977025 AX-123249106 11 98588214 GGAAGTTGGAGACACAACAATGTGAATGTGCTTAA[C/T]GATACTGAACTATACACATAAAAATGGTTAAGATG Y 2 1 2 1 303000 r 74 goat snp46804-scaffold653-1461802 11 99653587 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407917 Affx-122954381 AX-123278268 11 98617852 CTCTTCCTAGTTAGCATTCCATCTTCGCTGTTTAA[C/T]AGCTGTGTGACTGAGCAAGTTACGTAACCTCCCTG Y 2 1 2 1 101000 f 74 goat snp46803-scaffold653-1432164 11 99682012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412153 Affx-122951082 AX-123282503 11 98686544 GTGACTACGGTCCATGGGGTCACAGAGTTGGACAC[G/T]ACTGGGCAGCTAACATTTGAGGCCCACCAAAATAG K 2 1 2 1 101000 r 74 goat snp46802-scaffold653-1363472 11 99751187 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403976 Affx-122957432 AX-123274328 11 98715508 CCTTCAAGTCACAGAGGCAGGAAACCAATAAAGGA[C/T]GTTGAGATGCAAAGAAACCAACCTGGAACCAGCGA Y 2 1 2 1 101000 f 74 goat snp46801-scaffold653-1334508 11 99780009 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413174 Affx-122950339 AX-123283523 11 98773664 TCAATGTATAAAGGAGCTTGATCACAGTCTAGGAC[A/G]TGAAAAAATAATTGTAAAATACTGATTAATACAGT R 2 1 2 1 101000 f 74 goat snp46800-scaffold653-1276352 11 99838189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440026 Affx-122929767 AX-123310363 11 98848060 CACGTGGCTCAAGGCTCCTGGAAAAACATGGGGGG[C/T]GGGGCGGGTGGCAGAGGGCCAGAACAACACGTTTC Y 2 1 2 1 103000 f 74 goat snp46798-scaffold653-1201956 11 99912857 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398555 Affx-122961519 AX-123268910 11 98880622 AACAAGACATCCATTTCCATGTGGGGGCAGAACGT[C/T]ACACACGGTCGAAAGCGATCATATGTGCTCGGGAT Y 2 1 2 1 201000 r 74 goat snp46797-scaffold653-1169394 11 99945113 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391145 Affx-122966786 AX-123261502 11 98932333 ACACTCACAGCACCCTGTCCCTGGCCTGGGCCTCG[A/C]AATGGTGCCCGTAGCCTCTGTGATGACAGGCCAGT M 2 1 2 1 101000 r 74 goat snp46796-scaffold653-1117683 11 99997200 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433265 Affx-122935228 AX-123303606 11 98968198 GGCTGATAGTAATGCTGACCTCCAAGTCTGTTGCC[A/G]TCAGTTGCCTAGAATCATCTCCCCCCAAAAATCCT R 2 1 2 1 101000 r 74 goat snp46795-scaffold653-1081818 11 100033291 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394528 Affx-122964528 AX-123264883 11 99025917 TGAGGAGAAGGATTAGCTCCAAGTAAATCAGAAAC[C/T]GAGGGTTTCCACTGTGCTTTCTCAGTGAGGGGCAC Y 2 1 2 1 101000 f 74 goat snp46794-scaffold653-1024099 11 100090433 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450999 Affx-122921721 AX-123321333 11 99060861 AGGGGAGAGAGGCTGGAACGCCTTCATTGGTGATG[C/T]GGTGGGTGGCAGTGGGCTGGATTCTAGGTGGCACT Y 2 1 2 1 201000 f 74 goat snp46793-scaffold653-989155 11 100125341 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801531 Affx-122974577 AX-385288440 11 99096817 ACAAAAAGGAGAAGGTAAGATGTCTGGTTAATGAC[A/G]TTTTATAATGATCACTTGATACAGCAACACTTTTT R 2 1 2 1 101000 f 74 goat snp46792-scaffold653-953199 11 100161326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401992 Affx-122958769 AX-123272345 11 99147180 GCTTTGTTAGTTCCAAGCTGCTTGGCAAATGTAGG[A/C]GCTGTCACGATCATCTTGGTGACAGTTTTGAGTTC M 2 1 2 1 101000 f 74 goat snp46791-scaffold653-902836 11 100212144 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443813 Affx-122927073 AX-123314150 11 99197649 CATTCCACCCCTGGGCTTGGCTTCTGCAGACAAAG[A/C]CCCAGAAACCAGACACCCTGACCCCCCAAGTTGCT M 2 1 2 1 103000 f 74 goat snp46790-scaffold653-852367 11 100261493 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443465 Affx-122927826 AX-123313802 11 99226985 CATTTACTCAGGTATTTATTAAGCACCTACTACCC[A/G]CCAGGCACCGGGCCAGATGCTGAGGAAACAAGGAC R 2 1 2 1 201000 r 74 goat snp46789-scaffold653-823031 11 100290891 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443685 Affx-122927173 AX-123314022 11 99266515 CCCGCACATGTCAATGGGCAGGGAAATGCTATTTC[A/G]CGGAAGTTACTTAACCTTTTGTGCTGGCTTATAAC R 2 1 2 1 201000 f 74 goat snp46788-scaffold653-783501 11 100331154 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423587 Affx-122942397 AX-123293933 11 99312619 TCAGCAAAGTATGTGTCACGGGTGTCACACACACC[A/G]TATCATTTCTGACAGCCAACTGCTCCGGCGACAAG R 2 1 2 1 101000 r 74 goat snp46787-scaffold653-737397 11 100377486 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409714 Affx-122953039 AX-123280065 11 99380168 TTTTCCCCTGGTTAGGGAACTAGATCCCAGATGCC[A/G]TGCAGAGCAGTCACAAGATGAAAAAATAGAAAAAC R 2 1 2 1 201000 r 74 goat snp46786-scaffold653-669848 11 100445120 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392572 Affx-122966075 AX-123262929 11 99426701 TGGATTCTCTCTAGAGACCTAGACTTCCCAAGTCA[C/T]GTGGGAACCATGAACACCGTGGAAGTAAGTGGTGA Y 2 1 2 1 202000 r 74 goat snp46785-scaffold653-623315 11 100491622 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381510 Affx-122974863 AX-123251868 11 99476140 AAATCGTGGAAAGTCTTGTTTGTTTTTAGTCAGAA[G/T]ATTGAATAGAGATTGAGAAATCTACAAGACAGATA K 2 1 2 1 101000 r 74 goat snp46784-scaffold653-573876 11 100540977 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418297 Affx-122946989 AX-123288645 11 99520545 AAAAAGTCAGAGGCTGAGCCAGAAGACCTTGTAGG[C/T]TGGGGTGTTTTTTTTGTAAAAGGATGCCCGGGTCC Y 2 1 2 1 201000 r 74 goat snp46783-scaffold653-529471 11 100585133 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383415 Affx-122973485 AX-123253773 11 99552522 CTCATCCCAGCCACATAAAGCTTGCAGGGCCTCTC[C/T]CACAGAACCACCCATTTTGCAGATGAGCAAAGAGC Y 2 1 2 1 101000 f 74 goat snp46782-scaffold653-497494 11 100617544 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795584 Affx-122956756 AX-385282539 11 99591932 GGAAAAACTGATGAGATTGAAAACAGAAACACAGA[C/T]GGACAGATGGCATTACCTGCGAACCTAAGCCCGAA Y 2 1 2 1 101000 f 74 goat snp46781-scaffold653-458084 11 100656802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441259 Affx-122929488 AX-123311596 11 99657625 CTCCCCATAAGCTGCGTTTCATGCTCCATCCTAAG[C/T]GGGTGCTGAAGACTCTCCAACCACTGCCAGTGGGG Y 2 1 2 1 101000 f 74 goat snp46780-scaffold653-392391 11 100719130 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415670 Affx-122948552 AX-123286019 11 99691346 ATGTCACTACCCATGTTTTCCTTTTTTATACACAG[C/T]GGGAGAACCAAAGACCCTGAGCATTTAGCCTGGGG Y 2 1 2 1 201000 r 74 goat snp46779-scaffold653-358670 11 100751202 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405565 Affx-122955952 AX-123275917 11 99721368 TCCAATTTCTCTCCCTTCCCAGAGGTAATCACGAT[A/G]CTGAACTTGGGTTTCTACCATTCTCTTGAATGTTT R 2 1 2 1 201000 r 74 goat snp46778-scaffold653-328648 11 100780936 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271894 Affx-1111832944 AX-519545676 11 99749507 TAGCTGTTACCCTCATATCTGCCTCTCTAATAAAC[A/G]TTATATTTTTTCTCAGTGTTGTGTATTTTAAATGA R 2 1 2 1 101000 f 74 goat 11_99749507_AF-PAKI 11 99749507 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38429424 Affx-122938514 AX-123299766 11 99750338 CACACTGCTTATCATATATGGACCCAGAAACTGAG[C/T]GTAGGGAGTTCATGGGACGCAGGACCACTTAAAGG Y 2 1 2 1 101000 f 74 goat snp46777-scaffold653-299678 11 100809910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387501 Affx-122970332 AX-123257859 11 99814502 CCAGAAATACAGAGGTGAAATGATTTTACTGGAAC[C/T]GTGTTGGAAGACCTGAATTCCAGGGAGGTCAGAGA Y 2 1 2 1 101000 f 74 goat snp46776-scaffold653-235514 11 100874240 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401847 Affx-122959430 AX-123272200 11 99853892 GGCCGCAGACCCAGGGGCTGCTTCTACCGCGTGGA[C/T]GTTGGCACTGCCGAGTGCCATTTTGGAAACCTTCC Y 2 1 2 1 101000 r 74 goat snp46775-scaffold653-196124 11 100913426 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794779 Affx-122941273 AX-385281740 11 99884142 TTGCACTTCTCGTTTCCAATTATTGAAATGTTTTA[C/T]GACAACCAAGTATTACTTTAACAATCAGAAAGAAT Y 2 1 2 1 201000 r 74 goat snp46774-scaffold653-165874 11 100943663 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427165 Affx-122939621 AX-123297508 11 99915259 CTAGTGGGGAAGGGGCGCTCCAGGGACAGGAAGGG[A/G]GTTATTACAACAGGAAGCCCCGGCACTGGATTCTT R 2 1 2 1 101000 r 74 goat snp46773-scaffold653-134757 11 100974990 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803766 Affx-986696218 AX-385290520 11 99917693 TCCTCTGGCTTTGGGGTTGAAGCCTGGGCCTGTCT[C/T]TCTGGATTCTAATGGACCCAGATCTCAGGTTCTTG Y 2 1 2 1 600010 r 74 goat 11_99917693 11 99917693 Ancestral_priority_1043 ancestry 0.544 neutral IMAGE 10K 10K ancestral 38429569 Affx-122937812 AX-123299911 11 99955481 GCTCTACCAGGAAAGAGCCAGTAAGGCACCAATCC[A/G]CACCAACCCAGGGGTCTGGCCCATAGGTACGTGTC R 2 1 2 1 201000 f 74 goat snp46772-scaffold653-94535 11 101015295 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424485 Affx-122941756 AX-123294831 11 99994611 AGGTGCACGGAATCGTTTGCAAACCTCCTAACACC[A/G]TGACTGAAATGCAGGAAACGCTCACGAGAATGGGC R 2 1 2 1 101000 f 74 goat snp46771-scaffold653-55405 11 101054366 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391723 Affx-122967499 AX-123262080 11 100035895 GAGTGATGAGAGCGTTCTCTGTTGGGAAAAGGACA[C/T]GGGTATCAGGTGTCAGGGAGCAAGGGTGAATGTCC Y 2 1 2 1 201000 f 74 goat snp46770-scaffold653-14121 11 101093069 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450620 Affx-122922001 AX-123320954 11 100074507 GACAGCAAATCACCATAAACGCAGCGGCACACAAC[A/G]CCAGCCGTGATAATGACTGCATTCGTAAAACCAGA R 2 1 2 1 101000 f 74 goat snp47050-scaffold658-1582188 11 101131861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274333 Affx-1111834191 AX-519547928 11 100114875 CTCTCTGCAAACGCACTGCAGCGGTCAGATGATGA[A/G]CTTAGAGAGCATGGCGGCTGCTGTGTGTCTAGCTG R 2 1 2 1 201000 f 74 goat GoatD01.024751 11 100114875 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38436169 Affx-122932618 AX-123306508 11 100134741 ACAGCCATGGGGCTCATGGCCTCACCAAGGAGCAG[A/G]GGAGCTTTGAACTCTGATCCACAGCCCGAGGAGGC R 2 1 2 1 201000 r 74 goat snp47049-scaffold658-1521954 11 101189543 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413891 Affx-122949841 AX-123284240 11 100195720 AAGCTCTCTGTGCCATGTTCCCCTCGCGCAGTCAT[C/T]GTCTCCACGGGGCTCCTCTCCCTCTGAAGAGGAGC Y 2 1 2 1 303000 r 74 goat snp47048-scaffold658-1460975 11 101248541 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276714 Affx-1111835482 AX-519550224 11 100208463 TAGGCTTCCAGCAGGGAAAGGGACACTGTGCCTTC[A/G]TGAAGCACCTGCTGAATACCCAGGCCTGAGTCAAG R 2 1 2 1 202000 r 74 goat Random2.2K-1222 11 100208463 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384313 Affx-122972276 AX-123254671 11 100240523 AAGTGCCCTGTCACGTGCAGTGTGGGGAGGGGAGT[C/T]CTGCTTCTGTCTGCAGGTCTGTCTAAAAGGGGTGG Y 2 1 2 1 201000 r 74 goat snp47047-scaffold658-1416172 11 101292851 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444807 Affx-122926333 AX-123315144 11 100278152 TTACCTCCAATAAATTCTGTATTTCTTCATTTTGC[A/G]TTCTCCTACATGTACAGTTGAATTTATTCATGAAA R 2 1 2 1 101000 r 74 goat snp47046-scaffold658-1378543 11 101330381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391557 Affx-122966630 AX-123261914 11 100318850 GTTGGGGGTAGGTGGGTGGAGTGTGGAAACCCTGG[C/T]CATTTCATGGGGAAAGTGCTGTGATCTGACCATAA Y 2 1 2 1 101000 r 74 goat snp47045-scaffold658-1337845 11 101369151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428996 Affx-122938849 AX-123299338 11 100351400 AGGCAAAGAAAACTGCTCAGAGGGCCCAGATCCAC[G/T]GTATGGATCAGCCAGTGAAGGGTGAATTTGAAGCA K 2 1 2 1 201000 f 74 goat snp47044-scaffold658-1305295 11 101402129 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454128 Affx-122919342 AX-123324461 11 100404611 AGCACAGCTCAGTTTAATCACTTTCTTCAAGGTCT[A/G]TTGTCATTCCGTCACTAGCTCGTCTCCGACCCTCT R 2 1 2 1 201000 r 74 goat snp47043-scaffold658-1252084 11 101455335 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402012 Affx-122958755 AX-123272365 11 100441598 TTTCTAAACCATTTTCAAAGTCTACAGAAATAGGG[C/T]GTTGTAGGGCCCTGCCTTTAAGCAGTACCTCTTAC Y 2 1 2 1 101000 r 74 goat snp47042-scaffold658-1215097 11 101492305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435646 Affx-122933761 AX-123305986 11 100488373 GTTCCTAGATGGATGCCTGCATTCACAGTGGGTTA[C/T]GTCACAGGAAGGGACACTGAGTCTGGGAACTCGCT Y 2 1 2 1 101000 f 74 goat snp47041-scaffold658-1168322 11 101539137 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378007 Affx-122977593 AX-123248366 11 100586196 AAGGGTCCATCCCCGGGATGTTTTGTACTTAATTA[A/C]GTATGAACATGGCAGAAAGCAGAGGCCCCTAACAA M 2 1 2 1 202000 f 74 goat snp47039-scaffold658-1070499 11 101636619 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428639 Affx-122938667 AX-123298981 11 100631089 ACCTGTACAATGAGGATTATAATAGCTGCCTGGTG[C/T]GCTTGAGCGGGAACTGAGTGAGGCAGACTATAAAT Y 2 1 2 1 101000 f 74 goat snp47038-scaffold658-1025606 11 101681897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386434 Affx-122970799 AX-123256792 11 100697651 GTCAGCGGAGGAAGAGACTAGAACGTATGAAGAGT[A/G]GACCGCCTTCTGCTCTCTCTGGTCCCCTCCCTCCC R 2 1 2 1 101000 f 74 goat snp47037-scaffold658-959044 11 101748558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380513 Affx-122975693 AX-123250871 11 100737621 AAATTCTTATCTAGCATTTCTGTTTTTTCTAACTT[C/T]CCTGAAGCTGTGATTTGTGTTTTATAAGAAAACAA Y 2 1 2 1 101000 r 74 goat snp47036-scaffold658-919074 11 101787283 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409422 Affx-122954123 AX-123279773 11 100776479 AATAGTAATTTACCTTCACTGAGTAAATTATTTGA[A/G]TGATGTGGAGAAAACATGTTATAAAACACTTTGTT R 2 1 2 1 101000 f 74 goat snp47035-scaffold658-880216 11 101827734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782729 Affx-122940326 AX-385269801 11 100822100 ACATGGCTTAGGACCAGTGATATTAACCTTGATGG[A/C]TTGGTTAAGGTTTTGTTTGCCAGGCGTCTCTGCTG M 2 1 2 1 101000 f 74 goat snp47034-scaffold658-834595 11 101873775 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419519 Affx-122945441 AX-123289867 11 100854721 TGGCACAGGGCACTGTGGGAAGAAGGAAGGTTTTC[C/T]GGATGCCCTAGAGCTTGGCCTCTGCAGTCAGACGG Y 2 1 2 1 101000 f 74 goat snp47033-scaffold658-801974 11 101906563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394533 Affx-122964525 AX-123264888 11 100933980 TACTTTTATCTCCTTGTACACATCTCCATTCTTTT[C/T]CAGCAATAGCCTACTTGGAAAAGCAGCTGCTAGGT Y 2 1 2 1 101000 r 74 goat snp47031-scaffold658-722715 11 101988051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425997 Affx-122941144 AX-123296343 11 100986928 TAACGCAAACATGCAGAGTGAAAAAGCAAGTCGCC[A/G]TGCAACGAGATTTGAATGGTTTGCATGCCTATGTG R 2 1 2 1 201000 r 74 goat snp47030-scaffold658-669767 11 102040677 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390593 Affx-122967187 AX-123260950 11 101021697 CCTCTGAGATTCAAATATCCTTAATGATCCTCTCC[A/G]TCTCCTTCAGCTAAACCTTTAAGGAGAAGGGGGTT R 2 1 2 1 101000 f 74 goat snp47029-scaffold658-634998 11 102075856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420916 Affx-122944598 AX-123291263 11 101053777 CTGTGAGCAGCGGGGCCCCAGGAGGTAACCTTGGC[C/T]CTTTGAACGGGAACGTGAAGTCTGGAGTCTGGCTG Y 2 1 2 1 101000 r 74 goat snp47028-scaffold658-602918 11 102107695 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403341 Affx-122957811 AX-123273694 11 101083408 AGACTGCTCCCACGAAGGAGGCTTTTTCTCCTCCC[A/G]CCCCGCCCTTCATTCTTCCTGCAGCAGCTTTCACC R 2 1 2 1 103000 f 74 goat snp47027-scaffold658-573287 11 102137224 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786519 Affx-122974858 AX-272431464 11 101129151 GAACCACTATATCAAAAGGATATTGTTAAACAGCT[A/G]TCTGTCTGTGTTGGCCTTGTCTGCATATTTGTTGT R 2 1 2 1 101000 r 74 goat snp47026-scaffold658-527544 11 102182294 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377312 Affx-122977686 AX-123247671 11 101165184 ACCCGGACCTGGTTGCCGCTGCTGAGCCCAGGCGT[A/C]TGTATACCTGCGCTTCCTCTGAGCCGGCCAATCAG M 2 1 2 1 101000 r 74 goat snp47025-scaffold658-491511 11 102218491 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417139 Affx-122947357 AX-123287487 11 101197615 TCTCCCAGAAAATACCTCTGCATCAATAAGGAGAC[A/G]TAAATATATGCATTCATTTTATATAGATGAAGACA R 2 1 2 1 101000 f 74 goat snp47024-scaffold658-459080 11 102250726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449401 Affx-122922702 AX-123319736 11 101235238 AATTAGAAGAGAGAGAGACTGTGGGTACAGTAACC[A/G]GTACAGTGCTTGGGGGAGCAGGAGCCTTTATTTTT R 2 1 2 1 103000 f 74 goat snp47023-scaffold658-421457 11 102288382 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392495 Affx-122966134 AX-123262852 11 101265912 ACTCGACCTTCAGGGTGCCCTTTGGAATGCCCTGG[G/T]AGAGGAGTCATTTCAGGTGTTGATCAGACCTGGTA K 2 1 2 1 101000 r 74 goat snp47022-scaffold658-390783 11 102316452 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384305 Affx-122972282 AX-123254663 11 101318272 TGGGCTGGGCCACTCAGTCCACGGAGCAAACTAGA[A/G]TCTGTTGCAGTCTTATTGTCCTACGTTTCCAGGGG R 2 1 2 1 101000 r 74 goat snp47021-scaffold658-338423 11 102368198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415378 Affx-122948761 AX-123285727 11 101367053 GACATCAAAGAGGAAGGGTCTAGGTCTGAGGGCAT[A/G]TTTCCTTTTTAATTTGGCTTCTGAAGGTAAGAACA R 2 1 2 1 101000 r 74 goat snp47020-scaffold658-289642 11 102416903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403933 Affx-122957465 AX-123274285 11 101423615 CCGCATTCTTTGAACAGACGCCCCAGTGCTCCACC[A/G]TATGGTGGGACCGTGATTCATTTAACCAGCCCTCT R 2 1 2 1 201000 r 74 goat snp47019-scaffold658-233080 11 102473603 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379595 Affx-122976025 AX-123249953 11 101466533 CAAATTTGAAACCCACTGCAGAGAATATCACCCAG[C/T]GGTGCCGCCTTCCAGACAGCTTGCGGATAGAAGGC Y 2 1 2 1 101000 f 74 goat snp47018-scaffold658-190162 11 102514029 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398105 Affx-122961711 AX-123268460 11 101527697 GGGGTCATTGGAGAAGAGCGCTCAGGAGCCATGGG[C/T]GGTAGACGTGCCAATTGGCACGGAGCTTGATACCA Y 2 1 2 1 202000 f 74 goat snp47017-scaffold658-128998 11 102572444 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437508 Affx-122932345 AX-123307846 11 101594620 TATTAGATCTGAGTGTGAGAGTTTAAAACGATGAC[A/G]TTTCTAGTAGAATAGAATATTTTTGTCCTTGGAGT R 2 1 2 1 101000 f 74 goat snp47015-scaffold658-62075 11 102636627 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450559 Affx-122922467 AX-123320893 11 101644572 CACCATGGAATTTTACTGTGTTTGGGGCATGCTTG[G/T]ATATTTATTTGGGGACCGATGTTGCCGTGGTGGCA K 2 1 2 1 101000 f 74 goat snp47014-scaffold658-12123 11 102687704 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391152 Affx-122966780 AX-123261509 11 101692709 TTTGTCGAGTTTGGGTGTTGACTGAACACTCCAAG[G/T]TAACTGGCAGATATCTCTGCTGAGTCCCTCCCTGG K 2 1 2 1 101000 f 74 goat "snp17423-scaffold1803-425853;SNPs_119" 11 102727084 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376666 Affx-122979005 AX-123247025 11 101746466 GTCAGGTGCAGACAACACCAGGGTATTGATACATA[C/T]GAGGGGACCTCCCTGAAGGCTCTAAGTGCAAAAAT Y 2 1 2 1 101000 f 74 goat snp17422-scaffold1803-372096 11 102781455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799228 Affx-122937630 AX-385286158 11 101829999 GCAGAACGCTTTCTGCGTTTTATTGATGTCCCTTA[A/G]AAGTTACAGTCCTACAGTGACCATATTAAACCTAA R 2 1 2 1 101000 f 74 goat snp17421-scaffold1803-288563 11 102865146 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405282 Affx-122956855 AX-123275634 11 101867110 AAGGTTGCAGGAAACAAAGTCAAGGTCAATGAAAC[C/T]GCCCAGAGTCACCCTCTATCCCTGCTCTTTCTATG Y 2 1 2 1 101000 f 74 goat snp17420-scaffold1803-251452 11 102901664 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375536 Affx-122979104 AX-123245895 11 101976524 CTGTCCTCTGGGGATGTTTGTCCGTCACCTAAACC[A/G]TCAGGCTGTCCGCACTCCAGTCTAGCTGTAGCATC R 2 1 2 1 101000 f 74 goat snp17418-scaffold1803-142038 11 103005568 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409212 Affx-122953166 AX-123279563 11 102009395 CTGGTCCGTGGGCCTGTGGACACATGATCTGCAGG[C/T]GGGCATTGCCCCCTCCCCAGCACTATGTTTTAAAA Y 2 1 2 1 202000 f 74 goat snp17417-scaffold1803-109167 11 103038036 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432663 Affx-122936461 AX-123303004 11 102041593 TTCAGACAAAAGCCCCGGAGGCTGATGCAAGTGTC[G/T]GCGAGGCCCAGGCCACGTCCCCATCAGCGCGTGAC K 2 1 2 1 101000 f 74 goat snp17416-scaffold1803-76969 11 103066675 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418902 Affx-122946098 AX-123289250 11 102091586 GAAGCACCAAAAGCACAGAATAAAGAGTGACGACT[A/G]ATAAGCCAACAAAGGGGATAAAATGGAAGAGTAAA R 2 1 2 1 101000 f 74 goat snp17415-scaffold1803-26976 11 103115627 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426873 Affx-122940479 AX-123297218 11 102164110 CGGCAACAACAGGCTTGTCCTTCACCATGGGCCAC[A/G]GACAAAAGGGAGGTGTTCCCGTTGGTGGAGGTTCC R 2 1 2 1 201000 f 74 goat snp25009-scaffold2571-107430 11 103186237 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798065 Affx-122939103 AX-385285001 11 102197387 TTACGAAGTAAATCCATGATAAATGATGTTTATGA[C/T]GTGATGGCATTTATTAAAGAAAGTGTTTATGTCTG Y 2 1 2 1 101000 r 74 goat snp25008-scaffold2571-74153 11 103216994 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271760 Affx-1111832908 AX-519545554 11 102255965 AAGGTGGTCGGGGCTGGCCTTTCTGATCGGAGCAC[A/G]TTGGAGCAGAGGCTTCAGCAAATCCTGGGAGGATC R 2 1 2 1 102000 r 74 goat 11_102255965_AF-PAKI 11 102255965 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38431722 Affx-122936755 AX-123302063 11 102464804 ATCTAGCCTCTGGCCATCCCTCTGCCCCTGTCCCC[C/T]GCATGTCTCACTGCAGCTGTCTCTGGGGCAGGTTG Y 2 1 2 1 103000 r 74 goat snp35279-scaffold4221-76869 11 103407941 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375675 Affx-122978669 AX-123246034 11 102545492 TGGCTGCACAAACTGAAGGTGACTCATCCCACCGA[C/T]TGTACACTTGGAAACGGCGAAGGTGACAGAGGCTC Y 2 1 2 1 201000 r 74 goat snp21250-scaffold2075-346356 11 103486441 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380168 Affx-122975523 AX-123250526 11 102611314 TAAGTTGGGCAGGAGGCTGGCGGGTCTGACACCTT[A/C]TGGACCCTCACAGTGGCAGTGGTTTGCCAGAATCT M 2 1 2 1 101000 r 74 goat snp21249-scaffold2075-280534 11 103548251 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765506 Affx-986697443 AX-385252990 11 102625050 TGCCCCTTTGCAGACTTCAGCAGGTCCTCTTGTTT[C/T]CAGATCACAGACAGCACCTGAGGCTGTGGTCTGTG Y 2 1 2 1 600010 r 74 goat 11_102625050 11 102625050 Ancestral_priority_1043 ancestry 0.548 neutral IMAGE 10K 10K ancestral 38422784 Affx-122943217 AX-123293130 11 102659209 CATTTGAATTTTTGCCAAACTTGTGGATTAATCAA[A/G]TATCTTATGGTTGGGAACATTTGCTCAACAGCAAA R 2 1 2 1 101000 r 74 goat snp21248-scaffold2075-232639 11 103596014 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 538942893 Affx-1251531455 AX-585490017 11 102721831 GGTTTGGAGGAGCTGGTGCCCAAGGCAGAGGCCAC[C/G]CTCCAGGACACACCTGTCCCCAGTGCTGGCTCTGA S 4 1 2 1 400000 r 74 goat SNPs_098 11 102721831 C G SV-TF-chip candidate gene ou candidate region PAEP 538942888 Affx-1251531456 AX-585490012 11 102721835 TGGAGGAGCTGGTGCCCAAGGCAGAGGCCACCCTC[C/T]AGGACACACCTGTCCCCAGTGCTGGCTCTGACCTG Y 2 1 2 1 400000 f 74 goat SNPs_099 11 102721835 C T SV-TF-chip candidate gene ou candidate region PAEP 538942890 Affx-1251531457 AX-585490014 11 102721893 TGGCTCTGACCTGCCCTTGTCTAAGAGGCTGACCC[C/T]GGAAGTGTTCCTGGCACTGGCAGCCAGCCTGACCC Y 2 1 2 1 400000 f 74 goat SNPs_100 11 102721893 C T SV-TF-chip candidate gene ou candidate region PAEP 538942892 Affx-1251531458 AX-585490016 11 102721979 ACCTGTGCCCCCACTTCTGGGGTCTACCAGGAACC[A/G]TCTAGGCCCAGAGGGGGACTTCCTGCTTGGCCCCG R 2 1 2 1 400000 f 74 goat SNPs_101 11 102721979 G A SV-TF-chip candidate gene ou candidate region PAEP 538942894 Affx-1251531459 AX-585490018 11 102722042 TGGCCCCGGATGGAAGAAGGCCTCCTATTGTCCTC[G/T]TAGAGGAAGCCACCCCGGGGCCCGGGGATGAGCCA K 2 1 2 1 400000 f 74 goat SNPs_102 11 102722042 G T SV-TF-chip candidate gene ou candidate region PAEP 538942896 Affx-1251531460 AX-585490020 11 102722089 ACCCCGGGGCCCGGGGATGAGCCAAGTAGGATTCC[A/G]GGAACCTCGTGGCTGGGGGCCCGGCCCGGGCTGGC R 2 1 2 1 400000 f 74 goat SNPs_103 11 102722089 G A SV-TF-chip candidate gene ou candidate region PAEP 538942905 Affx-1251531461 AX-585490029 11 102722111 CAAGTAGGATTCCGGGAACCTCGTGGCTGGGGGCC[C/T]GGCCCGGGCTGGCTGGCTGGCACGCCTCCTGTATA Y 2 1 2 1 400000 r 74 goat SNPs_104 11 102722111 C T SV-TF-chip candidate gene ou candidate region PAEP 538942907 Affx-1251531462 AX-585490031 11 102722116 AGGATTCCGGGAACCTCGTGGCTGGGGGCCCGGCC[C/T]GGGCTGGCTGGCTGGCACGCCTCCTGTATAAGGCC Y 2 1 2 1 400000 r 74 goat SNPs_105 11 102722116 C T SV-TF-chip candidate gene ou candidate region PAEP 538942909 Affx-1251531463 AX-585490033 11 102722154 GCTGGCTGGCTGGCACGCCTCCTGTATAAGGCCCC[A/G]AGCCCGCTGTCTCAGCCCTCCACTCCCTGCAGAGC R 2 1 2 1 400000 r 74 goat SNPs_106 11 102722154 G A SV-TF-chip candidate gene ou candidate region PAEP 538942911 Affx-1251531464 AX-573553320 11 102722160 TGGCTGGCACGCCTCCTGTATAAGGCCCCGAGCCC[A/G]CTGTCTCAGCCCTCCACTCCCTGCAGAGCTCAGAA R 2 1 2 1 400000 r 74 goat SNPs_107 11 102722160 G A SV-TF-chip candidate gene ou candidate region PAEP 538942887 Affx-1251531508 AX-585490011 11 102722275 GGCCTGGCCCTCGCCTGTGGCATCCAGGCCATCAT[C/T]GTCACCCAGACCATGAAAGGCCTGGACATCCAGAA Y 2 1 2 1 400000 r 74 goat SNPs_108 11 102722275 C T SV-TF-chip candidate gene ou candidate region PAEP 538942882 Affx-1251531509 AX-585490006 11 102723011 CAGGTGGCGGGGACTTGGTACTCCTTGGCTATGGC[A/G]GCCAGCGACATCTCCCTGCTGGACGCCCAGAGTGC R 2 1 2 1 400000 f 74 goat SNPs_109 11 102723011 G A SV-TF-chip candidate gene ou candidate region PAEP 538942801 Affx-1251531465 AX-585489935 11 102723017 GCGGGGACTTGGTACTCCTTGGCTATGGCGGCCAG[C/T]GACATCTCCCTGCTGGACGCCCAGAGTGCCCCCCT Y 2 1 2 1 400000 f 74 goat SNPs_110 11 102723017 C T SV-TF-chip candidate gene ou candidate region PAEP 538942797 Affx-1251531466 AX-585489931 11 102723984 TGGCTCAGAAAGCAGCTGTCTTTCAGGGAGAACGG[C/T]GAGTGTGCTCAGAAGAAGATTATTGCAGAAAAAAC Y 2 1 2 1 400000 r 74 goat SNPs_111 11 102723984 T C SV-TF-chip candidate gene ou candidate region PAEP 538942805 Affx-1251531467 AX-585489939 11 102724044 GCAGAAAAAACCAAGATCCCTGCGGTGTTCAAGAT[C/T]GATGGTGAGTGCCGGGTCCCTGGGGGACACCTACC Y 2 1 2 1 400000 f 74 goat SNPs_112 11 102724044 C T SV-TF-chip candidate gene ou candidate region PAEP 538942808 Affx-1251531468 AX-585489942 11 102726001 GACAAGGAGGCCCTGGAGAAATTCGACAAAGCCCT[C/T]AAGGCCCTGCCCATGCACATCCGGCTCGCCTTCAA Y 2 1 2 1 400000 f 74 goat SNPs_113 11 102726001 C T SV-TF-chip candidate gene ou candidate region PAEP 538942816 Affx-1251531521 AX-585489947 11 102726292 TCCCCCAGTGCCACGTCTAGGTGAGCCCCTGCCGG[A/C/T]GCCTCTGTGGTAAGCTGCCCGCTCTGCCCCACGTC H 6 1 2 1 400000 r 74 goat "SNPs_114;SNPs_115" 11 102726292 C T,A SV-TF-chip candidate gene ou candidate region PAEP 538942809 Affx-1251531469 AX-523906785 11 102726727 GCCCGGGAGCCTTGGCCCCTCTGGGGACAGACGAC[A/G]TCACCCCCGCCTCCCCCATCAGGGGGACCAGGAGG R 2 1 2 1 400000 f 74 goat SNPs_116 11 102726727 G A SV-TF-chip candidate gene ou candidate region PAEP 538942912 Affx-1251531481 AX-585490035 11 102726773 CTCCCCCATCAGGGGGACCAGGAGGGACCGGGACC[A/G]CGGTCACCTCTCCTGGGACCCAGGCCCCTCCAGGC R 2 1 2 1 400000 f 74 goat SNPs_117 11 102726773 A G SV-TF-chip candidate gene ou candidate region PAEP 538942914 Affx-1251531482 AX-585490037 11 102726775 CCCCCATCAGGGGGACCAGGAGGGACCGGGACCAC[C/G]GTCACCTCTCCTGGGACCCAGGCCCCTCCAGGCCC S 4 1 2 1 400000 f 74 goat SNPs_118 11 102726775 G C SV-TF-chip candidate gene ou candidate region PAEP 538942832 Affx-1251531487 AX-585489961 11 102726792 AGGAGGGACCGGGACCACGGTCACCTCTCCTGGGA[C/CCCAGGCCCCT]CCAGGCCCCTCCAGGCCCCTCCTGTGGCCTCCTGC - 2 1 2 1 400000 r 74 goat ins-del_010 11 102726792 C CCCAGGCCCCT SV-TF-chip candidate gene ou candidate region PAEP 38412404 Affx-122951441 AX-123282753 11 102736972 AGGGACAGCCCGCTTGGCTAGGCCACAGCTGCCTG[C/T]GGCATTGTTTCTGGCGGGGTACAGTTTTTAGTTTG Y 2 1 2 1 303000 f 74 goat snp21247-scaffold2075-154876 11 103674170 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410574 Affx-122952131 AX-123280924 11 102779398 GTCTCGTGTTTTTTGTGTTGCTCTGAGGTTCCTCC[A/G]TTTTAGCTAAAGGGCATATTTTTTAATTAAATGGG R 2 1 2 1 201000 r 74 goat snp21246-scaffold2075-112450 11 103714146 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380788 Affx-122975100 AX-123251146 11 102865742 AAGGACGAACTCAGCCCACACCTCGCCTGCCGGAC[A/G]CTTGCCCTCGCGGCTTTGTGTTAATACGAACTGAC R 2 1 2 1 101000 r 74 goat snp21245-scaffold2075-26106 11 103796048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428101 Affx-122939086 AX-123298444 11 102971672 GATGGCCATGTGTTATTAGCGCCAATTAGGAGAAA[C/T]GAGGGCAGAAAAGCTTTTGGCCTGGGGGCCCGGGC Y 2 1 2 1 101000 f 74 goat snp34797-scaffold4131-79725 11 103904644 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784590 Affx-122925782 AX-385271638 11 103001956 AAATCAGCTGCACTTCCGTACTCTAACAACAGACC[A/G]TCTGAAAAGGAGATCAGAAAAGCTTCCACGTACAG R 2 1 2 1 201000 r 74 goat snp34798-scaffold4131-110009 11 103934685 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388831 Affx-122968891 AX-123259189 11 103092987 AATTTTTGCTATTTAATGAGCAAGAACTGCTCATA[C/T]GTGAAAACTTAAAAGTCGTTGCATGACGAAAGTAG Y 2 1 2 1 101000 r 74 goat snp34799-scaffold4131-201040 11 104019680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449631 Affx-122923189 AX-123319966 11 103125065 AGTATCTGCCTTGTCTAAGGAGCAACACCACATTA[A/C]TGGGAGTATAACCTCCAGAAAGAGGGAGGCGATCG M 2 1 2 1 101000 f 74 goat snp21458-scaffold2090-30233 11 104027923 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429915 Affx-122938106 AX-123300256 11 103174462 CAGGGGGCAGTGGGAGGGACGAGCCATCAGGCAAA[C/T]GTAAGGAACTGATCATCAGGGCAGTTTAAAAGCAG Y 2 1 2 1 101000 r 74 goat snp21459-scaffold2090-79630 11 104050433 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378386 Affx-122976804 AX-123248745 11 103243153 CTGGACATCACGGACATCACCAGATCCTACAACGC[A/G]ACATTCCTCAGCTACGAAAGGATAAAGTCCTGGTG R 2 1 2 1 101000 r 74 goat snp21460-scaffold2090-148321 11 104114959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403985 Affx-122957210 AX-123274337 11 103329921 AGCAAACAAAACGAAAAATGCATCTGAACAGCCTG[C/T]AAGCAAGATGAGTGAGCAAGGGTTTCTGGAGTTCA Y 2 1 2 1 202000 f 74 goat snp21461-scaffold2090-235089 11 104197971 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400806 Affx-122959813 AX-123271161 11 103380839 GTTTCTAAGGGCTCTTGGGTTCTCTGAATGATAAA[C/T]GGAGAGAGGCTTCAGGTTCGTATCACTGGAAGCAC Y 2 1 2 1 103000 f 74 goat snp21462-scaffold2090-286007 11 104247653 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423231 Affx-122942692 AX-123293577 11 103459718 ACTGGGGACTGTTTTAGAAACGTAGAGAACGAGAA[C/T]GAGCCACGGGACGCCTGGCCTGGCCTGGCCTCCTC Y 2 1 2 1 101000 f 74 goat snp21463-scaffold2090-364886 11 104322032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450394 Affx-122922077 AX-123320729 11 103490741 TCGGAGCGGCTGCGCTAGCGTCAGGCCAAAGGGAC[A/G]TTATTAAAGACGCAGAAGGCGATAAAATGGCCAAA R 2 1 2 1 101000 r 74 goat snp21464-scaffold2090-395909 11 104352707 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437977 Affx-122931596 AX-123308315 11 103533184 AGAAATGATGCCTCACGCAGCAGGGTCAGTGATGA[G/T]AACCGTCTGTGCTCACGTGCAGTTTCTGTGCTTTT K 2 1 2 1 201000 r 74 goat snp21465-scaffold2090-438352 11 104395475 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762918 Affx-986697447 AX-385250916 11 103572275 CACAGACCACAGCCTCAGGTACTGTCTGTGATCTG[A/G]AAACAAGAGGACCTGCTGAAGTTTGCAAAGGGGCA R 2 1 2 1 600010 f 74 goat 11_103572275 11 103572275 Ancestral_priority_1043 ancestry 0.574 neutral IMAGE 10K 10K ancestral 320765517 Affx-986697449 AX-385253001 11 103572298 GTCTGTGATCTGAAAACAAGAGGACCTGCTGAAGT[C/T]TGCAAAGGGGCACTGCCCACGTCACAGGCCCTACC Y 2 1 2 1 600010 r 74 goat 11_103572298 11 103572298 Ancestral_priority_1043 ancestry 0.456 neutral IMAGE 10K 10K ancestral 320762922 Affx-986697451 AX-385250920 11 103572429 GTGCCTATGCCCGTGGGCACTCAAAAGCATCCGTC[A/C]GTCAGATCTGACAACGGCAAAGCCGGTCCTTCCAT M 2 1 2 1 600010 f 74 goat 11_103572429 11 103572429 Ancestral_priority_1043 ancestry 0.51 neutral IMAGE 10K 10K ancestral 320762924 Affx-986697453 AX-385250922 11 103572454 AGCATCCGTCCGTCAGATCTGACAACGGCAAAGCC[A/G]GTCCTTCCATCCAGCCACCAGTTCCCCAACACGGA R 2 1 2 1 600010 f 74 goat 11_103572454 11 103572454 Ancestral_priority_1043 ancestry 0.498 neutral IMAGE 10K 10K ancestral 38417644 Affx-122946848 AX-123287992 11 103603652 GTTCGTAGAGGTGCTGCAGACCGACCTGCAGGCCA[A/G]CATCTCCCTCGAGTTCTGGAATGCCATCTCTCAGC R 2 1 2 1 101000 r 74 goat snp54511-scaffold831-32090 11 106063681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420840 Affx-122944656 AX-123291187 11 103649364 AAAGGCTTGAGAGCTTCCAGGCCTGCGTCTGCTCA[C/T]GGTCATCACTAACCAGCTTCACTTAAGTGGGACGT Y 2 1 2 1 201000 r 74 goat snp54512-scaffold831-77802 11 106108792 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404946 Affx-122956425 AX-123275298 11 103699462 GGGCACGTGGCTCCTAAGGAAGCAGGAGGGAGGTG[C/T]TTGTAGCCATGGGACCCCCGACCCACAGGGAGCCT Y 2 1 2 1 103000 f 74 goat snp54513-scaffold831-127900 11 106159376 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436251 Affx-122932553 AX-123306590 11 103761172 CCTGGGAGCCGGGCAGAGGGGGTCTCAGGGGAGGC[A/G]CTGAGCAGAGGCCTGGGAGGGAAGGCCTTGGAGCT R 2 1 2 1 303000 f 74 goat snp54514-scaffold831-189610 11 106216353 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424787 Affx-122941395 AX-123295133 11 103809280 GGGAAGTCAGGGTGGGAAGCCTGGTGGGTGCTGAA[G/T]TCGGGGTGCCCTGGGTGAAGTCTAGGCGCCCTGGG K 2 1 2 1 103000 f 74 goat snp54515-scaffold831-237718 11 104502264 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420852 Affx-122944646 AX-123291199 11 103857042 CCAGGTGAAGCGAGGTGAGCGGATGGGCAGGGGGC[A/G]TGGCCAGACCTCGGGGGGTGCAACATGCTGGGCAT R 2 1 2 1 103000 f 74 goat snp54516-scaffold831-285480 NW_017189579.1 15980 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791977 Affx-122935053 AX-385278965 11 103942252 ACCTTCACGTTAACCTTGTTCGTTAATTTTTCAAG[C/T]AGGATTTCCTGAAAAACACCTGGGAGATGAAGACT Y 2 1 2 1 101000 r 74 goat snp54518-scaffold831-370690 11 104576548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386856 Affx-122970071 AX-123257214 11 104002915 GTGCCTGCCTGTCCATCACTCACATGGACCTGCGT[A/C]TATAAACACGGACTGAATGGCTTCTTATCTACCTC M 2 1 2 1 101000 r 74 goat snp26956-scaffold2851-46387 11 104640214 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430345 Affx-122937803 AX-123300686 11 104075629 TCCCCCCACAAGGGGCTGACCTCTTGGGCTCTCTC[C/T]TGGGCAGAGCTCCTGTCCTTGCAGCTAGACAGTCA Y 2 1 2 1 201000 f 74 goat snp26957-scaffold2851-119101 11 104713971 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435891 Affx-122932779 AX-123306230 11 104105615 TAAAATGGGTCAAGAAGAGGGCCACACCTGTCACC[A/G]AGTCCCGTGCCCCTCTGAAATTCTCTGTCTTCGTG R 2 1 2 1 201000 r 74 goat snp26958-scaffold2851-149087 11 104752318 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400711 Affx-122959925 AX-123271066 11 104139778 GTGTCTTCCTGACGTGACTACCCAGTGAAGGTTTC[A/G]TTTTTACAGCGTTTGATCCTCCGGCCTGGCTGCCT R 2 1 2 1 201000 r 74 goat snp26959-scaffold2851-183250 11 104787760 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452995 Affx-122920115 AX-123323328 11 104171195 TCTAGTGGCCCGAGGCAGGAGGATCCGTTCGCCCG[C/T]GCCCTTCTACCCCAGCTGGGAGAGAAAGACAGCTG Y 2 1 2 1 101000 r 74 goat snp26960-scaffold2851-214667 11 104819075 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445743 Affx-122926087 AX-123316080 11 104220108 CTCAGTTTAAAATCCGTGAGAAGAGAGTGCGCCCC[A/G]CTTCCTCTCTGAGGATGCACTGACTTCTGTTCATC R 2 1 2 1 102000 r 74 goat snp21483-scaffold2099-35819 11 104868342 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274877 Affx-1111834470 AX-519548461 11 104265808 TGTGTCGGCCTGTCCCCCGCTGCAGGCTTGGACCG[A/G]CAGACGCCAGCCCACGGCGCGTCCTCCACTCGGGG R 2 1 2 1 202000 r 74 goat GoatD01.037053 11 104265808 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38393116 Affx-122965577 AX-123263473 11 104303470 AACTAAAGCCGTTGGATTCGCCAGCATGAATTCCC[A/G]CCTGACGTCCCTTTCTTTGCAACCTTCATTCATTC R 2 1 2 1 101000 f 74 goat snp21485-scaffold2099-119181 11 104950186 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400811 Affx-122959810 AX-123271166 11 104371898 ACCTTCACAACCCCGGTGCTACCCGCACCCATCAC[C/T]TCCCAAAGCTTCCCCGTGTCCTTCTGTTCCCCTTG Y 2 1 2 1 101000 r 74 goat snp21486-scaffold2099-187609 11 105075330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425173 Affx-122941054 AX-123295519 11 104401610 TGACCGGAAGTGGTGGTGTGTGAGCAGCCTGGTTC[A/G]TTTTCAGTCTCTGGAGACACCATTCGATTTTCGCC R 2 1 2 1 101000 r 74 goat snp21487-scaffold2099-217321 11 105045622 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412526 Affx-122951349 AX-123282875 11 104433248 TGAAAGTCAGGGACACTGAGCATGTATGACAATAC[A/G]ATACAGATATTTACTTAAAACTCACAGAAACAGAA R 2 1 2 1 101000 f 74 goat snp21488-scaffold2099-248959 NW_017218984.1 15177 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418594 Affx-122946363 AX-123288942 11 104544857 GTGTTCTCAGCTCAGATAACCGGAAAGGATGAACT[A/G]CATCTAACGTTCATCCCTCTCCTGGCAAAATAACA R 2 1 2 1 101000 f 74 goat snp30331-scaffold3334-94374 NW_017189846.1 23197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276716 Affx-1111835483 AX-519550226 11 104563057 AATCACGTGGGTGCAGCTGACGCGGCCTCCCCATT[A/G]CTTTAGCCCCCACTGTCCCTCCAGGCCACCCTGGT R 2 1 2 1 202000 r 74 goat Random2.2K-1224 11 104563057 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430116 Affx-122937512 AX-123300457 11 104645929 TCCCTCATTTGGGCGGCGCTGATTCTGCTTTGCAA[A/G]CCTGGGGCCTTTTCTGAACAAACCGCTTCCTCACG R 2 1 2 1 201000 f 74 goat snp30333-scaffold3334-195446 11 105250677 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377756 Affx-122977367 AX-123248115 11 104694303 TCACGGCACGTTCCCCGGCTAAGAACACTTCTTGC[A/G]TGCCCTTGAATAATGCCCCAAGATGACTTAAAAAG R 2 1 2 1 101000 r 74 goat snp30334-scaffold3334-243820 11 105299621 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272649 Affx-1111832910 AX-519546359 11 104827193 ATTACTCCCTTCCTGATACAGCCGGGCGAAGCCGA[A/C]GCGTGCATTGCTGTGAACCCTTGTAAACCTGCCAT M 2 1 2 1 101000 r 74 goat 11_104827193_AF-PAKI 11 104827193 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38443927 Affx-122927035 AX-123314264 11 104829537 AACAGACACTGTGAAGTGTCTCTCCACTGGCCCCT[C/T]GTGCCATAGGGCTGCCCCCTCTGAGAGCTCCCCAG Y 2 1 2 1 303000 r 74 goat snp7960-scaffold1288-475685 11 105380640 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379226 Affx-122976276 AX-123249585 11 104866682 CACGTGTGTGGGTGATGAGCCCACCTGCAGAGGCT[A/G]TGTTTTGTGGAGACACAAGGTCACATTTGCTAAGG R 2 1 2 1 101000 r 74 goat snp7959-scaffold1288-438540 11 105417109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420408 Affx-122944920 AX-123290755 11 104962071 GCCCCAGGTCTGGGGTATATGAGGGAAAAACAAGA[C/T]AGAAACACAGGGAACCCATCGTGTGTCCAGAGGTC Y 2 1 2 1 101000 f 74 goat snp7958-scaffold1288-343151 11 105509468 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450010 Affx-122922852 AX-123320345 11 105012598 TTGAGTGAGCTGTGAATGTCGTGCTCTCTGGCTTG[A/G]GGGCCTGCACCTGCCAGGGCTGACCCTTCTTCAGC R 2 1 2 1 101000 f 74 goat snp7957-scaffold1288-292624 11 105561658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438057 Affx-122931540 AX-123308395 11 105045742 ATACAGTTGGGCCTCCTGCACCTGGGGCAGCAAAG[A/C]GCAAGTTCAAGACAGCCACTACTCTTTAAAAGAGT M 2 1 2 1 101000 r 74 goat snp7956-scaffold1288-259480 11 105594797 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276718 Affx-1111835484 AX-519550228 11 105048898 AAGAAATTTTAAACATTTGCAATGGTGACACCAAA[C/G]TCAAATAACTGAATAATTCTGGCAAAATATACACT S 4 1 2 1 101000 r 74 goat Random2.2K-1226 11 105048898 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452734 Affx-122920281 AX-123323067 11 105076035 CGTGAATAGTCTACGTGTGACAATTCGTGTATTTC[A/G]CATACGGCACAGGCACTTCCAAATTCTCCCTTGCG R 2 1 2 1 101000 f 74 goat snp7955-scaffold1288-229187 11 105625790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449207 Affx-122923507 AX-123319542 11 105110378 TGTTGCTGGGGAGCGTCTGTATGTCTCTCTCACGC[A/G]TGTGTGTGGTCTTTGTTGTTGGGGAGCGTCTGTAT R 2 1 2 1 103000 r 74 goat snp7954-scaffold1288-194844 11 105655879 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396383 Affx-122963027 AX-123266738 11 105156850 TCAGCCTTCTTCCCTGGCCTCTCGATAGCCCGTGA[C/T]GTTCACCTTCACGTCACGTCAGGGAGGAGTGATTG Y 2 1 2 1 101000 r 74 goat snp7953-scaffold1288-148372 11 105701508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401740 Affx-122959514 AX-123272093 11 105189226 TGTAAAGATCAGGAAGCCAAGGTGTGTGAGGAGAC[C/T]CTGTTACAGTGATCTGGTGTGTAGGACCTGTACTT Y 2 1 2 1 201000 f 74 goat snp7952-scaffold1288-115996 11 105724679 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276576 Affx-1111835485 AX-519550087 11 105209189 GCTCAGAGTCATGCCGCTCTTAAGGTGTGGACCCA[A/G]GGCCAGCAGAGGCTCGTTTGGGGTTATGCAGGACA R 2 1 2 1 102000 f 74 goat Random2.2K-1227 11 105209189 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778885 Affx-122955617 AX-385265993 11 105226545 CTGACTTGGAAAACTGCGTTATGTGCTGGCACCAT[C/T]CAACAAAACCCAACTCTACAGCACAAGTCTGGGGA Y 2 1 2 1 101000 r 74 goat snp7951-scaffold1288-78677 11 105762066 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421987 Affx-122943792 AX-123292334 11 105280016 CGGACACCAAGGGTCTCTGTCCCAAAAGCAGAGGC[C/T]GGGAGAAGGGACGTGGACGTTAAAACTGATGGGAG Y 2 1 2 1 101000 r 74 goat snp7950-scaffold1288-25206 11 105815293 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275528 Affx-1111834859 AX-519549100 11 106043132 GCAGTGTGAAGTGCTGCTCGGGGTCCAGGCCCAGC[A/G]CCTGGCAGAACTGCTGGACGTGGCTGGCCGTGTTC R 2 1 2 1 102000 r 74 goat GoatD01.056757 11 106043132 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276722 Affx-1111835486 AX-519550232 11 106126878 CAAATAAGCATAGGAAAAAATGTTTAACATCATTG[A/G]TCACTAATGAAATGGAAATAGATACCACAAGAATC R 2 1 2 1 101000 r 74 goat Random2.2K-1228 11 106126878 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38440258 Affx-122930655 AX-123310595 12 11041 ACTTGGACTCCACTTAATAAACCTAATTTGAATTG[C/T]AGGTAAAACATGCTGTGGCTTAGACATGTCCAATT Y 2 1 2 1 101000 f 74 goat snp48840-scaffold697-11041 12 85411739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422058 Affx-122943607 AX-123292405 12 47047 AGAGAGTGAACAAGTCCACCGTGGTAATGCAAAGG[C/T]AAGAAGGGAATTTTTATTTCTAGCACGCTAGGGCT Y 2 1 2 1 103000 r 74 goat snp48841-scaffold697-47047 12 85374541 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798157 Affx-122972503 AX-385285092 12 103282 CACTGCTCTGCTTCATTCCAAGAAATTTCTTCTAG[A/G]TCATTTCTAAAATCATACCATCTCTGCTCCAGCCA R 2 1 2 1 101000 f 74 goat snp48842-scaffold697-103282 12 85317267 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800220 Affx-122937571 AX-385287143 12 135519 CTTATTGAGTAAATTGTATCTACATTTTCTAAGCT[A/G]CAGCCACTTGGATTATCTACTTTGAGGCTTAGAAA R 2 1 2 1 101000 r 74 goat snp48843-scaffold697-135519 12 85284740 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420735 Affx-122944765 AX-123291082 12 164799 TCTACTGCATTGGCAGGGAGAATCTTTACCACTAG[C/T]GTCACCTGGGAAGGTTGCTTGTACCATTAGCCTAA Y 2 1 2 1 201000 r 74 goat snp48844-scaffold697-164799 12 85255770 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411133 Affx-122951894 AX-123281483 12 219453 AGAGCTGTGGGCTAGTTGCTGCTCTAGGGCTTGCA[C/T]GTGGATAGGTTAGTTGCATGCTCTCCACATTCAAA Y 2 1 2 1 101000 r 74 goat snp48845-scaffold697-219453 12 85200715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441064 Affx-122928915 AX-123311401 12 262685 GACAGATTGGATGAAATAAAAGCTTTGGTTTGACA[A/G]CAGGTTCCTCTAACCTGGCTCCAAGCAGTATTTCC R 2 1 2 1 101000 f 74 goat snp48846-scaffold697-262685 12 85156986 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451098 Affx-122921399 AX-123321432 12 299710 TTCTTGCTGTTCTCTCCCCATTTCTCTGCCCCAGT[A/G]TAGCTAGGCAGAGCCAAGTGACTACTGCTTACCAA R 2 1 2 1 303000 r 74 goat snp48847-scaffold697-299710 12 85119733 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785437 Affx-122977928 AX-385272482 12 332085 GCCCTTAGAAAACATGGAATCGCCTCCACCAGCCC[A/G]CAATAAATGGAGAGACAGCAATATTGTCAAGGGCT R 2 1 2 1 201000 r 74 goat snp48848-scaffold697-332085 12 85087240 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393702 Affx-122965250 AX-123264057 12 378596 ATGGGAGAGGGTGGGCCAGGCCATTGTTCTATTTT[A/G]TCATATGTTTTCTCACAACTGAGTGACTTTCACTT R 2 1 2 1 103000 f 74 goat snp48849-scaffold697-378596 12 85041180 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409260 Affx-122953131 AX-123279611 12 407608 CTGCCCAGAATGCTGAGTAGCCAGCTCTTATGTGT[A/G]TTCCCAGCAGAGCAAGTTGCTTATTAAAATGAGTC R 2 1 2 1 101000 r 74 goat snp48850-scaffold697-407608 12 85012071 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272719 Affx-1111832956 AX-519546422 12 422998 CTCTTCTCTTGTTAGAGTGAAGTCGAGCTTCTGTT[A/C]GTGTATTAAGCGAAATGCACACTGGGCTGTACCCT M 2 1 2 1 101000 r 74 goat 12_422998_AF-PAKI 12 422998 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320790059 Affx-122962003 AX-385277065 12 452655 GACTTTATCTGCAGGTTACAGTAGGTCTTTTAAAA[C/T]GTGTATGCAAGCAGTATCTCCCTGGCTTTCTCTTC Y 2 1 2 1 101000 r 74 goat snp48851-scaffold697-452655 12 84968223 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421334 Affx-122944073 AX-123291681 12 490687 GCTAAGAAAAAGAGAGATTCTCTTATCTGTGTGAG[C/T]TCTGACATACACTGAGCAGTAGTAAGATTTCAGAA Y 2 1 2 1 101000 r 74 goat snp48852-scaffold697-490687 12 84930101 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786791 Affx-122956303 AX-385273821 12 554825 ATCCTGATGAATGTGTAAGAGTCAAGACTTAAATC[A/G]CCCTCTACAACCAGGAATATGGACAACATATAAGA R 2 1 2 1 101000 r 74 goat snp48853-scaffold697-554825 12 84865168 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776633 Affx-122954336 AX-385263760 12 614909 GGAAAATATGAGCAGTTCAGATCTACAGAGACTTC[C/T]GCTCATTTCAACCAACCGACTGAATACCAGTGTTA Y 2 1 2 1 101000 f 74 goat snp48854-scaffold697-614909 12 84804000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414232 Affx-122949636 AX-123284581 12 675236 ATCCTTAAGAGAAAGGCAACATTTCAGTAGAGAAA[C/T]GGACAGAGTATATGATTGTTGTTATTTAGTCCCTT Y 2 1 2 1 201000 f 74 goat snp48855-scaffold697-675236 12 84743345 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446697 Affx-122924739 AX-123317033 12 704272 ACCAGACACCAAAAGACTACAAAGACTTTTGGGGA[C/T]GATTTTCAGTTCTCTTTAAAAACATAGTCCTTCGC Y 2 1 2 1 101000 f 74 goat snp48856-scaffold697-704272 12 84713411 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383846 Affx-122973154 AX-123254204 12 739174 CCTCAACAGACACCTCTCCAAAGAAGACAGACAGA[C/T]GGTCAACAGGCACACAAAGATACTCAGCATTGTCA Y 2 1 2 1 202000 r 74 goat snp48857-scaffold697-739174 12 84677647 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408888 Affx-122953979 AX-123279239 12 798668 CTATTGGTTCTCTCCACAGCTCAGAAAAGTAGAAG[C/T]GAAGACCAAGTAATTGACAGGTGACCAGATCTCTT Y 2 1 2 1 201000 r 74 goat snp48858-scaffold697-798668 12 84616642 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375526 Affx-122979112 AX-123245885 12 859618 ACCAGATCCAATGCAGATATTATTGTCCCCATTTC[A/G]TAGATGAGGAAACAGAGATTCAAGATGTTCACAGC R 2 1 2 1 303000 f 74 goat snp48859-scaffold697-859618 12 84554775 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423552 Affx-122942426 AX-123293898 12 896331 ACCTCCTGAGGAAGGGATAGGCTCCCCCTCATCAG[C/T]GAGAACTACAATAAATCTGAAATCTCATGCTTGGA Y 2 1 2 1 101000 r 74 goat snp48860-scaffold697-896331 12 84517863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382036 Affx-122974947 AX-123252394 12 935817 AGCCCAGAACTATCTTTAAGGTTCCTATTGAGATC[A/G]CTGTGATGGCAAGTTTCCCTCCTGTTTTCACACAG R 2 1 2 1 101000 f 74 goat snp48861-scaffold697-935817 12 84477821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383517 Affx-122972636 AX-123253875 12 973491 TTAGTGATCATGCTTCAGATAGGAGTCAACGTGGC[A/G]CCTTCACATTATCTCTTTCTACAACCGTGAATCCC R 2 1 2 1 101000 f 74 goat snp48862-scaffold697-973491 12 84440775 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796965 Affx-122967901 AX-385283906 12 1009571 TGTGTTTGCTCTTCTGCTGCTTTTCTTAGAAGAGT[A/G]TGTTGGTATTTTTGGATAAAACTAAAGGAAGGTGT R 2 1 2 1 101000 f 74 goat snp48863-scaffold697-1009571 12 84402122 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796553 Affx-122963865 AX-385283499 12 1046970 GCGGAGCTTTCTGTTCTGCTGTGTCCAGTTTAATA[G/T]TCACTAGTCATATGTGGCTAATGCTATTAGAGGGC K 2 1 2 1 101000 f 74 goat snp48864-scaffold697-1046970 12 84364499 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427564 Affx-122939484 AX-123297907 12 1082893 TCATTAGCTCGGTAGGCTAGAGAAGAGATCTGGTG[C/T]ACATTTGTTTCAATAGTTGGATAAAAGCCAACCCT Y 2 1 2 1 201000 r 74 goat snp48865-scaffold697-1082893 12 84328163 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274425 Affx-1111834278 AX-519548016 12 1103972 CAGAGAGGGAGATTGCATGGAAGGTCAGCAGTCTT[A/C]TTCAGTACAGTGCACCTGCTCAGTC M 2 1 2 1 101000 f 74 goat GoatD01.028604 12 1103972 A C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437037 Affx-122933110 AX-123307375 12 1124746 CCCTACTGTTAGAGTACCCCCGAATTCCTGAGGTC[A/G]TACTTTATACTGTAATTAAAATAAATTCATTTTAT R 2 1 2 1 103000 f 74 goat snp48866-scaffold697-1124746 12 84286309 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786030 Affx-122976183 AX-385273066 12 1160971 TTTTTTTTTAAAAACTAGCAATGGTTTATATTCTG[A/C]TGGTATCAATGCTTCTGAGTATCAGAAGGGCCATC M 2 1 2 1 101000 r 74 goat snp48867-scaffold697-1160971 12 84249463 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423171 Affx-122942739 AX-123293517 12 1207736 AGTCAGCTGTAATATTGAAACCAAATATAATATGG[C/T]GAATCTGCAGTTTGAATATTTAAGGAGCATACATT Y 2 1 2 1 101000 f 74 goat snp48868-scaffold697-1207736 12 84202667 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774431 Affx-122953817 AX-385261567 12 1243893 ATAAATGTTTCAAATAAACTTACAGACACAATACC[A/G]AAGACTTAAATATAGAAGAGAGTGTCACTGTGTTA R 2 1 2 1 101000 r 74 goat snp48869-scaffold697-1243893 12 84166064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768902 Affx-122967902 AX-385256079 12 1278909 CGTAATGGTTGTTCCTGAAGAACGTTTGCTCACTC[G/T]AGTGTGAGGACAGCCGTAACTGATGAAGTGAAGAG K 2 1 2 1 101000 f 74 goat snp48870-scaffold697-1278909 12 84130896 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393658 Affx-122965284 AX-123264013 12 1310508 GCTCTTACCTTCTACCATTAAATTATCATGTTGAC[A/G]TTGGATACCTCAGCCATCATGATGATGTTTAAAGT R 2 1 2 1 101000 f 74 goat snp48871-scaffold697-1310508 12 84099958 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427759 Affx-122939243 AX-123298102 12 1367902 AATTAAATCCTGATTTTTTTTCCTGCCATGTATTT[A/C]TCTGATCTCATTCATTACTCATTCGTAGGGAACAC M 2 1 2 1 101000 r 74 goat snp48872-scaffold697-1367902 12 84042548 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779833 Affx-122930810 AX-385266932 12 1391171 TGCTTTACCAGAAAAATTCTGTGCTTTATGCACTG[C/T]GAAATATAGATAGAAGTAATATGCAAGTTTTCCTC Y 2 1 2 1 101000 f 74 goat snp18548-scaffold1873-275602 12 84018788 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387697 Affx-122969813 AX-123258055 12 1425352 CCCACACAATACACAGTCAATCTGCCATCAAGCAA[C/T]CCATCCAGATGACTTGTTTACCAAAACTCAATGAA Y 2 1 2 1 101000 f 74 goat snp18547-scaffold1873-241421 12 83984496 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403881 Affx-122957913 AX-123274233 12 1478448 TCTAAAGTCCATCTACTGACTCCTTATAAATCCAG[A/C]TTCTGACCCTATGCTTTAAGAAAAGGATAGATTTA M 2 1 2 1 101000 f 74 goat snp18546-scaffold1873-188325 12 83929861 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779066 Affx-122941314 AX-385266171 12 1520996 AAATATAAAGATTATATTTCACAGATATGAAAATA[C/T]AATTTTTTCTGCACAAGTTATTACTTATGAACTAA Y 2 1 2 1 201000 f 74 goat snp18545-scaffold1873-145777 12 83886968 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789966 Affx-122947972 AX-385276972 12 1609453 CTGTGACATTGCACCCATTTACATAAAGGTATGTG[A/C]GTTCTGCAAAGAGAGGACATATATTCCTATTACAT M 2 1 2 1 201000 r 74 goat snp18543-scaffold1873-57320 12 83798153 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443150 Affx-122928064 AX-123313487 12 1641728 CCACCACATAGCTCCTTCACTGCCAACAAAGGTCT[A/G]TATAGTCAAAGATACGGTCTTTCCAGTAGTCATGT R 2 1 2 1 102000 r 74 goat snp18542-scaffold1873-25045 12 83765234 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786141 Affx-122941795 AX-385273177 12 1671854 CCTAAAAAGAAGTCTGGGTAAATATGTGGCCACAA[C/T]ACATGTTTCCCAAGGGTCCAAGAATAAAATTCATA Y 2 1 2 1 201000 r 74 goat snp9686-scaffold1347-532368 12 83734399 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417020 Affx-122947971 AX-123287368 12 1704206 AGGACTAATTTCAAGGTAACTGTCAGAGCTGACTG[C/T]GCTGTTTTGCACATAGCTCCCTTGCTCTGCTTATA Y 2 1 2 1 201000 r 74 goat snp9685-scaffold1347-500016 12 83700443 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386733 Affx-122970146 AX-123257091 12 1761637 TACAGAATGCAACGACCTGATTGGGAAGAGTAGCT[A/G]CAGAAAATGAATTATGCAAAGAAAAGAGCTTGCAT R 2 1 2 1 101000 f 74 goat snp9684-scaffold1347-442585 12 83642112 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398188 Affx-122962644 AX-123268543 12 1797369 CCTCTGTGCCCAGAGTATATAATTTCAGCAATCAG[A/G]GCTAGCTATTGGTATTTTCATATCGTGGTTTTTCA R 2 1 2 1 101000 f 74 goat snp9683-scaffold1347-406853 12 83606329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772003 Affx-122949417 AX-385259159 12 1896998 GACTCAAAACAAAGAAGTAACATAATTGTATATAC[A/G]TTTCATTAAAATATTACTGATAGCAACTGGGAAAA R 2 1 2 1 103000 r 74 goat snp9680-scaffold1347-307224 12 83505339 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424789 Affx-122941394 AX-123295135 12 1938095 CCATGTGTCCTCCCTTTATAACACTTTCTCTTTAA[C/T]GTGATTACTTAATTTTGTCCCTATTCGTCACAAGA Y 2 1 2 1 101000 r 74 goat snp9679-scaffold1347-266127 12 83463857 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388412 Affx-122969286 AX-123258770 12 1982534 TGCTCTAGAATTTACTCATTGTTAATGGATCATCA[A/G]TAGGATGATATATATATGCATATATACTTTTGTGA R 2 1 2 1 101000 f 74 goat snp9678-scaffold1347-221688 12 83418324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410536 Affx-122952160 AX-123280886 12 2014107 GAGAGGCCAGCAGTGTGTGTGAGGAGCCTCAAGCC[A/G]TGCTGAGGAACGAGCAGCAGTAACGGAAAAAACAG R 2 1 2 1 101000 r 74 goat snp9677-scaffold1347-190115 12 83387215 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393071 Affx-122965609 AX-123263428 12 2053952 TAGTGGAATGGCTTTAGAAGAAGGGGTCTCTGGGT[A/G]TGGAGAGGGTCCTTAGGTCATGAGGGTGGAGCCCT R 2 1 2 1 101000 f 74 goat snp9676-scaffold1347-150270 12 83350834 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433326 Affx-122935160 AX-123303667 12 2094898 AAGGGCATTTCATATAAAAGAACAGCAAATGCAAA[C/T]GCTCTGAGGGACAGCTCTGTCTATGTGCTTCAGGG Y 2 1 2 1 101000 r 74 goat snp9675-scaffold1347-109324 12 83309319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413892 Affx-122949840 AX-123284241 12 2144727 TTATGTCCAGACCTTCTTGGCCTTGACTTTCTTGG[C/T]ACTGCTAGATTAGTCCCTACCCTCTCTTTTCTCGT Y 2 1 2 1 201000 r 74 goat snp9674-scaffold1347-59495 12 83258754 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446273 Affx-122925670 AX-123316609 12 2202317 CCAACAGATTACAAACACCCCAAATCCTTCAAGCA[C/T]GCCTTGTCAGCAACTGGTTCCATCCACCAACAAGC Y 2 1 2 1 201000 r 74 goat snp9673-scaffold1347-1905 12 83200290 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780942 Affx-122934734 AX-385268029 12 2208945 GAAAAAAGGTATATTCTTGATAAAAATCAGAGTTT[A/C]GTAATCAAAGTGAAGGCTCCATCTCTGGTTGAAGA M 2 1 2 1 101000 r 74 goat snp3497-scaffold1108-409758 12 83193689 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425593 Affx-122940929 AX-123295939 12 2258966 CAAAGCAGAGAAGTCATTCCAGAAGGCAGGCAGCC[A/G]TGGGAAGTGCACCCAGAGGAGAGAAGCCCATTGTT R 2 1 2 1 101000 f 74 goat snp3496-scaffold1108-359737 12 83143712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384263 Affx-122972314 AX-123254621 12 2335852 TTGCTTGTGGAAATGCTCCATTATCCAATCTTTCT[A/G]AAAGGAACAGTTTGCTACCACAAATGATGAGTAAT R 2 1 2 1 101000 f 74 goat snp3494-scaffold1108-282851 12 83066598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449678 Affx-122922559 AX-123320013 12 2367141 GCAAACTGCTCAAAGCTTACTGTTCCCCCTGAAAG[C/T]GCCCTCCTTTGAGAGGAAGCCAATGAGTCTAGGCG Y 2 1 2 1 201000 r 74 goat snp3493-scaffold1108-251562 12 83035385 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276582 Affx-1111835488 AX-519550093 12 2391511 ACAGGGTTGAATTGCTGGGTAGCTTAAAGAGAGGC[A/G]TTCTTTTTGGACTTACAAGCAACACAATAGCTTTA R 2 1 2 1 101000 f 74 goat Random2.2K-1232 12 2391511 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320773919 Affx-122967846 AX-385261058 12 2415310 CATCAGTTCTACTGTCGTTTCCATCCTAGCATGGC[A/G]CTTCAGTGGCCTTGATTCAAGCCATAGCAAGTTCA R 2 1 2 1 101000 r 74 goat snp3492-scaffold1108-203393 12 82987292 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379344 Affx-122976167 AX-123249703 12 2448662 TTCATCTTTTATGCATGTAAAATGTGTTTCTGGTC[A/G]TGAAAGAGGTAACAGTTCTCTTTATCCTTCAAACT R 2 1 2 1 101000 r 74 goat snp3491-scaffold1108-170041 12 82953644 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415681 Affx-122948544 AX-123286030 12 2498748 CTGTCATCTCATACTAGGCAGAAGCAAGAAAGAAG[C/T]GAATTTTTGGTGATGCTGTCTCTTCTCACTAACAA Y 2 1 2 1 101000 f 74 goat snp3490-scaffold1108-119955 12 82903889 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395728 Affx-122963707 AX-123266083 12 2545995 ACCCATGCATTGGTTCTTTAACTTGACTTAGAATC[A/G]CTTTTGCAAATTCTTTTGGAAAATATGAATCGTGC R 2 1 2 1 101000 f 74 goat snp3489-scaffold1108-72708 12 82856668 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274983 Affx-1111834525 AX-519548565 12 2586995 CTAGTGAGGTGATTGGTTGGTAAAGTCTGCAGGGG[A/G]AGTAGGGACAAAAGATTTGCTAACCTTGACAAGAA R 2 1 2 1 201000 r 74 goat GoatD01.039712 12 2586995 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38375409 Affx-122979200 AX-123245768 12 2599163 TAACAAGCTCTCTCAAATGCATCAGTTCTATAGTA[C/T]AATACTAGGTGACTAAAATTCTTGTTTCTATTTTC Y 2 1 2 1 103000 r 74 goat snp3488-scaffold1108-19540 12 82803163 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449154 Affx-122923549 AX-123319489 12 2625268 GCATGCTTCCGTGAAGAAGGAATCCATGGACAGAA[C/T]AAGAGAGTCTTGCAAAGTGAATGGGGAAAATTATA Y 2 1 2 1 101000 f 74 goat snp8060-scaffold1293-6466 12 82775749 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782206 Affx-122922101 AX-385269284 12 2654621 AATTTTAGATGTCAAACTTGGAATACGTTTTCTTT[A/G]CTTATATAACAAACTCCAAATATAATTTTCAGTGC R 2 1 2 1 101000 r 74 goat snp8061-scaffold1293-35819 12 82745853 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453901 Affx-122919499 AX-123324234 12 2713278 TGCATCTGTAGCTGTTGATCATGCATACTAAGGAA[G/T]AAAATTTTATTCCCTAGTAGTGTCAGATAGGGGTT K 2 1 2 1 101000 f 74 goat snp8062-scaffold1293-94476 12 82686391 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799642 Affx-122954931 AX-385286571 12 2750060 AATAGACATCTGAGTAAGTCCATAAATAAGGAAGT[A/C]GTCAATGAGTGGAACAGTCAGCATAATTTATTTCA M 2 1 2 1 101000 r 74 goat snp8063-scaffold1293-131258 12 82648943 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423482 Affx-122942573 AX-123293828 12 2794121 ATTCCCTAGTTTTTTTATTGAAATAAAATTTACAT[A/G]CAACACTCCATAAGTTTAAGTTGTACATATAGCTC R 2 1 2 1 103000 r 74 goat snp8064-scaffold1293-175319 12 82604357 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400480 Affx-122961295 AX-123270835 12 2844723 CAGCATTTCCATCTTGCTCATGGCCCTGCAAATTA[G/T]ACACATTATCACACCCAAGCCTGCATATGATACTC K 2 1 2 1 101000 f 74 goat snp8065-scaffold1293-225921 12 82553677 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430853 Affx-122937425 AX-123301194 12 2911609 ATATTTATTCCCTCTGCAATTTTTCAGAAATGTTA[C/T]GCACTAATATAAAATGGCTTGTTACCTATCAAGGT Y 2 1 2 1 101000 r 74 goat snp8066-scaffold1293-292807 12 82487456 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271771 Affx-1111832952 AX-519545564 12 2942408 GCCTGTACTAAGTAATGAGATTTGCTTTAGATTTT[A/G]CAGACTTGCTTTTCTGCAAAATAAGTCTAGCATAC R 2 1 2 1 101000 r 74 goat 12_2942408_AF-PAKI 12 2942408 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38386848 Affx-122970079 AX-123257206 12 2942984 GATGTATGCATTTTTCCCATCCTTTCAGAATATTT[A/G]ACACAGAGACCTTTATAATTTTCACCCTTGTATTA R 2 1 2 1 101000 r 74 goat snp8067-scaffold1293-324182 12 82456084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384351 Affx-122972246 AX-123254709 12 3036343 ACTGTGACATTAGTGACCGCTTCAACCAGCCTCTC[A/G]AGGACTGAGCCTATATTTTTCCTTCAGGCTCTAGA R 2 1 2 1 101000 r 74 goat snp8069-scaffold1293-417541 12 82362223 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442967 Affx-122928208 AX-123313304 12 3144522 ACATATGATTCAAAATATCTCTCTTGCACTTCAAG[C/T]ACACCTTTAATTTTACCTTCTTCTTCAAGATTTGT Y 2 1 2 1 101000 f 74 goat snp8072-scaffold1293-525720 12 82253851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417172 Affx-122947331 AX-123287520 12 3188883 CACATGAAAAATGCTAATAGCCTAGAAAATCCACC[A/G]CAAGAATAATATATTGAATTTGAAATTTCTATCTG R 2 1 2 1 101000 f 74 goat snp8073-scaffold1293-570081 12 82211933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421491 Affx-122943912 AX-123291838 12 3218919 ATAAGCTATAAAATGGAGAAAAAGCATTCATTGCA[A/G]AAGTGCAACTTCATTCTGCAATTCCTAAAGACAGA R 2 1 2 1 103000 r 74 goat snp8074-scaffold1293-600117 12 82181794 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769544 Affx-122919994 AX-385256714 12 3265309 GGATTATGTTTCCTTATCTGCATATAAATATAGTT[A/G]CTTACCTTATAAGTGGTTTGAATCAAACTAGCTAA R 2 1 2 1 201000 f 74 goat snp8075-scaffold1293-646507 12 82135157 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771453 Affx-122923092 AX-385258611 12 3306938 GTCAAAATTTTAAATGAATTCTAAAAGAATGCATA[C/T]AAAAGATGATAATATTGGTGTGATACTCTGTGTAT Y 2 1 2 1 201000 f 74 goat snp8076-scaffold1293-688136 12 82093964 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768495 Affx-122935161 AX-385255675 12 3344407 ACATGCATAGGACCAAAGTATGTGTTGGTGTTATG[C/T]AAATACTTTGAGAAAATGGTATCTCCTCTTTTTGG Y 2 1 2 1 101000 f 74 goat snp8077-scaffold1293-725605 12 82055715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428422 Affx-122938830 AX-123298765 12 3376417 GCTTCTCCCATTATAGACTACTTCCACAAAATAGT[A/G]CATTTGTTACAATTGATGAACCTACATTAGCACAT R 2 1 2 1 101000 f 74 goat snp8078-scaffold1293-757615 12 82023646 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403756 Affx-122958004 AX-123274108 12 3459477 GACCCAAATTCACTCAGAACACATTAAAAATTGAT[A/G]CTGAATCCTTGTTTGTGGCTCAGCTGGTAAAGAAT R 2 1 2 1 201000 f 74 goat snp8080-scaffold1293-840675 12 81944785 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767056 Affx-122959788 AX-385254346 12 3490088 TGGTTCAGGACATTAAATCCTTGAAACTGCTGCTG[C/T]AAGTGAATTAACCAATGTGTTAAATGTGAAGCAAG Y 2 1 2 1 101000 f 74 goat snp8081-scaffold1293-871286 12 81914301 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391632 Affx-122966574 AX-123261989 12 3519398 ACATTGTAATACACTTAGTAGCTCTCTGTATTGCA[C/T]AGACAGAAAGGCACATATTCATGCAGAACAAATTA Y 2 1 2 1 101000 f 74 goat snp8082-scaffold1293-900596 12 81887040 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768736 Affx-122960879 AX-385255914 12 3558399 TTTGGGGACATTAAAGACCACTTTTATTTGCATAT[A/G]TTTATTTGTTAAACAAAATAACCATAATCAACTTT R 2 1 2 1 303000 r 74 goat snp22569-scaffold2237-24512 12 81838359 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409326 Affx-122953082 AX-123279677 12 3596709 TGTCTTGTGTCATGCAATACCAAGCAGTCCCCTTT[A/G]CATTGCCTTATGATTTATTTTATCATCCAGATAAA R 2 1 2 1 101000 f 74 goat snp22570-scaffold2237-62822 12 81800177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784314 Affx-122956814 AX-385271365 12 3611485 AAACATTCAAATGGAAGAGAGATTTCAGAAAAGTA[A/G]TATGCTTGACAGCTTCTCGTTATTCTCTTATTTGC R 2 1 2 1 201000 f 74 goat snp46516-scaffold644-3610 12 80882120 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772017 Affx-122930817 AX-385259173 12 3643168 CCTGCTATGAAATGTTTCTGTTACTTGTTCCTACG[C/T]AACTCTTTTACAAAAGTCTTGATCTGCTTACTTTT Y 2 1 2 1 101000 f 74 goat snp46517-scaffold644-35293 12 80850141 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402305 Affx-122959090 AX-123272658 12 3704094 TAGTATCCTCAGGAGGGCCAGGGTGGGCCCTATGA[C/T]GATTCTTGGAGCCAATCCCCTGCAGATACAGAGAG Y 2 1 2 1 102000 f 74 goat snp46518-scaffold644-96219 12 80789158 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445792 Affx-122926047 AX-123316129 12 3757154 TAATAAAAATGCTTTGCTTATTGAAAGAGCCCAAT[A/C]TGAAACATGGCACTCCTCTTCATACCTTAAGTGAA M 2 1 2 1 101000 r 74 goat snp46519-scaffold644-149279 12 80736575 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436248 Affx-122932556 AX-123306587 12 3807027 ATATGTTCCTGTTAAGTCAGGGTTTAAGTACCAAA[A/G]ACTATTGTATTTCATTTGTATTTTTATTACACAAA R 2 1 2 1 103000 f 74 goat snp46520-scaffold644-199152 12 80685271 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775326 Affx-122955815 AX-385262457 12 3837189 AACTGTTTACAGTAGTCTCTATTTCTTTTTCAAAC[A/G]TTACTAGGCATTTGACAATTCCCTGTTTAATTTTT R 2 1 2 1 201000 f 74 goat snp46521-scaffold644-229314 12 80654586 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408891 Affx-122953977 AX-123279242 12 3876526 ACAATAATAATATTTTACATTTAAAGGATAAATAA[C/T]TGCAAAACTGTCATGTATGCCCTTTGATACTATTT Y 2 1 2 1 103000 r 74 goat snp46522-scaffold644-268651 12 80614456 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438867 Affx-122930752 AX-123309204 12 3906665 ATGCCATGATCACACTAAATGTAGCCTCTGAAAAT[C/T]TTGTTTTAATTAAAATTATCTTTCTTGAACTTTAG Y 2 1 2 1 102000 f 74 goat snp46523-scaffold644-298790 12 80585198 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430176 Affx-122937363 AX-123300517 12 3936223 CAGATTCCTTACATTTTAGTTACTATTTGAGCACC[A/G]CTACTTGCTCTGGTGTGTTTGTTAATACTTTGTAA R 2 1 2 1 101000 f 74 goat snp46524-scaffold644-328348 12 80559393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783570 Affx-122966525 AX-385270632 12 3976307 GAAAATATGCTCAACCTCAACAATGTTCCCAATCT[C/T]TCAGCTAAAAGTTTTCATTAAAAGCCTAAGTACAC Y 2 1 2 1 201000 r 74 goat snp46525-scaffold644-368432 12 80521347 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450003 Affx-122922858 AX-123320338 12 4041103 AAGAGTATACAAGTTCCCTCTATACCATTAAAATG[C/T]ATTTTTTCTCTTAAACTGAGTTATGAGTCCATTTT Y 2 1 2 1 101000 f 74 goat snp46526-scaffold644-433228 12 80456187 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795911 Affx-122976336 AX-385282863 12 4072639 AGGAGTGGGCATGGGAATGCTTACAGCATTTTTTA[C/T]TGGCTTTTCCCTGGGCCATAGTAGACAACTTAAGA Y 2 1 2 1 101000 r 74 goat snp46527-scaffold644-464764 12 80423992 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786331 Affx-122966296 AX-385273365 12 4116323 CTATTTATTGATTCATTCTGTCCTAAAATATTTTC[A/G]TATTTTTCTACCACATAGGCCCATAGTTCTTGTGG R 2 1 2 1 101000 r 74 goat snp46528-scaffold644-508448 12 80380895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799478 Affx-122921327 AX-385286408 12 4167668 ATATGGTAGCATTTGTGATTACTAGTCATTACTTA[C/T]ATTACCATTAATATACTAATAATTCCTAAACTCAA Y 2 1 2 1 101000 f 74 goat snp46529-scaffold644-559793 12 80330224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397656 Affx-122962604 AX-123268011 12 4226926 CTTTTTAATAATATTTCTAATTCATGTAGTTTGGG[C/T]GAAGCTTGTGTATTTCTTAATGCCCTCATTTCCCA Y 2 1 2 1 101000 r 74 goat snp46530-scaffold644-619051 12 80270749 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780433 Affx-122965511 AX-185459338 12 4275035 CCTCATATAATTATTGAAAAGATCTGATAAATAAT[A/G]CAAGTAAAGTGTTTAGTAAAATTCCTTTTGGAAAG R 2 1 2 1 202000 f 74 goat snp46531-scaffold644-667160 12 80222791 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463200083 Affx-1109864629 AX-514686319 12 4330479 TCTTTCTAAACCTTCACAAGGTCCATGCCATTGCT[A/C]AGGTGTAGGACCCAGAGAATCGCAAGAATTGCTCT M 2 1 2 1 201000 f 74 goat GoatD01.016791 12 4330479 A C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320775768 Affx-122974322 AX-385262899 12 4392445 TGTGTTTGCTTGGGATTGGGACAATAGTATAACTT[C/T]TCCTTTGTATAAAAATCTTCTTTTCTGAAAATAAG Y 2 1 2 1 201000 r 74 goat snp49561-scaffold707-949585 12 80098713 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779306 Affx-122962387 AX-385266410 12 4421714 ATAATCCAAATATCTGGGCTACAAAACAAGAAAAG[C/T]AAGCACATTACTCAGAATTCCCCAGACAATGTCCT Y 2 1 2 1 101000 r 74 goat snp49560-scaffold707-920316 12 80069819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430249 Affx-122937309 AX-123300590 12 4452945 TGTCTTTCTTGTGAACTTACTTATATTCTGTTAGC[A/G]TTGTGGATAATAGAAATAATTTATTAGAAGATTGT R 2 1 2 1 101000 f 74 goat snp49559-scaffold707-889085 12 80037924 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799930 Affx-122953850 AX-385286856 12 4497015 CTCATGATGATCTTGCTAGGGAACTATAGAAACGA[C/T]AAGGATTTTAGAACCATACAGAATCAGATTTGTCT Y 2 1 2 1 101000 f 74 goat snp49558-scaffold707-845015 12 79993395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446236 Affx-122925696 AX-123316572 12 4556312 TCATGGGGATAGTCATTGCCTTCCCCTCTCTGTGA[A/G]TGTCAAAGATGCTAGTTATAACTCATTTGGATGGA R 2 1 2 1 201000 r 74 goat snp49556-scaffold707-785718 NW_017193916.1 17808 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410516 Affx-122952176 AX-123280866 12 4638761 ATCTGTAGCTAATATTTTCAAGAACAAAAATCTGT[A/G]TTGTTTTGAATTACTTCTCTACTATCTTTGGCTTT R 2 1 2 1 101000 r 74 goat snp49554-scaffold707-703269 12 79850331 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453950 Affx-122919475 AX-123324283 12 4759133 GCTGATTGCTTGCTTTATATTGATATAGCATAGTT[A/G]TAAAGAAAATAAATACAATTCAAGAGGTGTACTTA R 2 1 2 1 103000 f 74 goat snp49552-scaffold707-582897 12 79728346 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410304 Affx-122952492 AX-123280654 12 4969142 AATATCTTCTGCAATTCATGGGCAGTTCCTTTATT[A/G]CTTATGTAAATGAGTATTGAAGAACTAAAGCCATT R 2 1 2 1 201000 r 74 goat snp49547-scaffold707-372888 12 79514792 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795074 Affx-122923536 AX-385282033 12 5110974 TTATTTACTGTAGCAATGTTTTGACCACCACAATG[C/T]ATAAAGTATTGTCTTAGACATTTTGGGTTGCAAAT Y 2 1 2 1 101000 f 74 goat snp49544-scaffold707-231056 12 79368548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770280 Affx-122943294 AX-385257446 12 5140253 GATAAGAGATCTATCTCTTTGAGATAAGCCATGAC[A/C]TAAGTAGTAAGCTTTACTAAGAAAACATTTAAATT M 2 1 2 1 101000 f 74 goat snp49543-scaffold707-201777 12 79339612 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452098 Affx-122920850 AX-123322431 12 5253415 CACATTTTAGCTTTAGTTTTATGGAGGCACCATAT[A/G]CAAATTTCTTTGTGCATTTGTGTGTGTGTATGTGT R 2 1 2 1 101000 f 74 goat snp49540-scaffold707-88615 12 79224587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802396 Affx-122959431 AX-385289300 12 5326770 TAAACATAGATACATATCTCAATTCTAACCTACTT[C/T]TCATGTTCAAAGTTTAAATTCCTGTCCCCAGTGAG Y 2 1 2 1 101000 r 74 goat snp49538-scaffold707-15260 12 79150286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798443 Affx-122954346 AX-385285376 12 5350808 AATGGTTGTGGGTGTCTTTGTGGTATGCTTGTATG[C/T]ATTATCTGTGCATGATTCTGATATGGGTCTTGGCT Y 2 1 2 1 101000 f 74 goat snp49563-scaffold707-1056803 12 80207460 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388031 Affx-122969554 AX-123258389 12 5423076 ACTTCTTGTCTTTTATGTGATATGTAAAAAGTACT[A/G]TTTTGCTTCTTCAGAATTTTTAGTATAATATTGTG R 2 1 2 1 101000 r 74 goat snp49562-scaffold707-984535 12 80132996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272489 Affx-1111832962 AX-519546211 12 5508728 AGACCACGTATCCCGTTGCTTACCTAAGCTGGGTC[A/G]TGATGGGCTTACAGGCAGCAATGGTGGGTGTGCAC R 2 1 2 1 101000 f 74 goat 12_5508728_AF-PAKI 12 5508728 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445761 Affx-122926074 AX-123316098 12 5591790 GGCAGTGAAATTCTGTATGATTCTACAATGATGGA[C/T]AGATGTTACTATACATTCACTCAAACCTGTGCAAT Y 2 1 2 1 101000 r 74 goat snp49557-scaffold707-815821 12 79964503 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768443 Affx-122934625 AX-385255623 12 5662558 CACTCTTTTTTCTGGTAATCATCAATATTCTGTCT[A/G]TCTGAGTTCAGTGTTCCATATCAAAGGTATTGTAA R 2 1 2 1 101000 f 74 goat snp49555-scaffold707-745053 12 79892296 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390119 Affx-122968007 AX-123260476 12 5758188 AAGCTAAGATCAACATACTCTTGGACTAAGTCCTA[C/T]GGCCTCAGATACGCAGCAGCCAGAACTACTCAATT Y 2 1 2 1 201000 f 74 goat snp49553-scaffold707-649423 12 79796483 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431998 Affx-122935933 AX-123302339 12 5876268 TGGCTATAAAATTGTTTCCTAAATTATACACATTT[A/G]TGTATTACAAGCATCCTGAAAGTGTGTTCCTTTTA R 2 1 2 1 201000 f 74 goat snp49551-scaffold707-531343 12 79676308 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442916 Affx-122927631 AX-123313253 12 5906779 AAACCTCAGTTCTTTTTCAGATTCTTGCTTTAACT[A/G]CTAAAGTTAAAGATGTACAGAGATTTAACAGCTGC R 2 1 2 1 303000 r 74 goat snp49550-scaffold707-500832 12 79645712 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790104 Affx-122927287 AX-385277109 12 5940573 CATTGTCAGAAACCCACTTTAGGCAACAACAGAAG[C/T]AATGACAAAGGAGCGGATTATGTGCTTCTTTGGGG Y 2 1 2 1 201000 r 74 goat snp49549-scaffold707-467038 12 79610915 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450487 Affx-122922928 AX-123320821 12 6088278 TCTTTTCTATACACATTCAAAGGAATTTCTAGATC[A/G]TCCACTTATATTAGTGTGAATGACGTTTGAATCAA R 2 1 2 1 101000 f 74 goat snp49546-scaffold707-319333 12 79459010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387109 Affx-122970669 AX-123257467 12 6142157 AACATGGAATCTGGACACTGCCCCTGATAGGATGG[C/T]GACAATGACTGAGGAGAGGGAAAACTCTGAATTAA Y 2 1 2 1 101000 r 74 goat snp49545-scaffold707-265454 12 79402715 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768824 Affx-122975564 AX-385256001 12 6236579 ATTTTCCCTTATCTGAAGAGAAGGCTGCCTGCAGG[A/C]AGTCCCTTTGAGTTCTAGGAGGTTGCTATAACCTT M 2 1 2 1 202000 f 74 goat snp49542-scaffold707-171032 12 79308892 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769297 Affx-122933699 AX-385256469 12 6276535 GACTATATCTCTTTTTGCACAGTGATGTGCAAACA[C/T]AAAACCTACAGGATCACTCTTGATACACAGAAGTG Y 2 1 2 1 201000 r 74 goat snp49541-scaffold707-131076 12 79268429 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416555 Affx-122947674 AX-123286903 12 6363310 TTGGATGTTTAGTTGAAGAGATATCTAGTCACATT[A/G]CTCAAAATGTTGCTTGGCTTATCCTGGCTGCTTAC R 2 1 2 1 101000 r 74 goat snp49539-scaffold707-44301 12 79179433 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274722 Affx-1111834387 AX-519548308 12 6472500 CTGCACAGCTTGCAAATTCAGCGTTGGATTTCTCT[A/G]TGGAATCCTGCAGATGCAGAGAAATTAAATACGGT R 2 1 2 1 201000 r 74 goat GoatD01.033081 12 6472500 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320767841 Affx-122966569 AX-385255061 12 6519807 CAATAGCTATATTGGTGATAAACAACTAAAGCAAA[G/T]CTGGTAGTTTCATAAGAACCAAAACTGAAACCAGA K 2 1 2 1 201000 f 74 goat snp22546-scaffold223-1564643 12 79016952 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377166 Affx-122978212 AX-123247525 12 6567897 ACAGTTCAAGTTCTACTCACTTCTGGGGTATACAC[A/G]TGCCCTGTTGAAATATTCACTTTTTCTGCCCTAGA R 2 1 2 1 101000 f 74 goat snp22545-scaffold223-1516553 12 78970588 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783801 Affx-122924679 AX-385270856 12 6599683 TGACTTTTTGTTAATTTGTGAAGAACTTTTGTTTG[A/C]TTCTAATATGTTATAATTAGGCTTGGAGCTGTTAT M 2 1 2 1 201000 r 74 goat snp22544-scaffold223-1484767 12 78938986 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777095 Affx-122934033 AX-385264218 12 6661128 ACCGCTGAGGTCCTAAAAGCAAATTTACAGTGTCT[A/G]CTTGTACTTCTGATCCAGCCTTGAAAAAGTGTTAT R 2 1 2 1 101000 f 74 goat snp22543-scaffold223-1423322 12 78876481 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453741 Affx-122919614 AX-123324074 12 6743100 TCCATGGTGTTGCAAAGAGTTGAATACTACTTGAC[G/T]ACTAAACCACAACAAAATAACATACTGTTAAAACC K 2 1 2 1 103000 f 74 goat snp22541-scaffold223-1341350 12 78793941 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412833 Affx-122950462 AX-123283182 12 6906247 TAACCAGTTATTAAAATGATATTGCAAAGAGTCTG[C/T]ATAATGTAGATTGAGCATAATACATCTAAATTCCT Y 2 1 2 1 201000 r 74 goat snp22538-scaffold223-1178203 12 78629774 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406791 Affx-122955703 AX-123277142 12 6942093 CAGCTAAGCAATGACCTGGGTAATTTTTAAATTAC[A/G]TTTTAATACTAAGCAACAATAAACTTGCCTACAGA R 2 1 2 1 101000 r 74 goat snp22537-scaffold223-1142357 12 78593428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446634 Affx-122924787 AX-123316970 12 6979104 TGCTTGGTTTGGCTGTTTCATTTCTGTATATATCT[A/G]CTCATTTGCTTTACACATTCTGTGTGCAGATGCCA R 2 1 2 1 101000 r 74 goat snp22536-scaffold223-1105346 12 78555680 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796944 Affx-122924278 AX-385283886 12 7015304 TTCTGAGCTGTTTAATTATGTGTTAACAATTACTT[A/G]GTCTGAGCTCTTTTTCAGGTCTTATTCTACTTTGG R 2 1 2 1 101000 r 74 goat snp22535-scaffold223-1069146 12 78518702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398854 Affx-122961056 AX-123269209 12 7048404 TGTTGCTCTTTTCCCCTGGGAAGAAAACACATGCT[A/G]TAATAATATTTACTCTGAAAACAAGATTTTATTAT R 2 1 2 1 103000 f 74 goat snp22534-scaffold223-1036046 12 78484339 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766953 Affx-122971293 AX-385254256 12 7077005 CATGTCCTTTTGAAACATCTGAGCCACATTAAATA[C/T]GGTGGATAATATTTTGCTTCTTGTCTAAATGAAGA Y 2 1 2 1 101000 f 74 goat snp22533-scaffold223-1007445 12 78456024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418868 Affx-122946122 AX-123289216 12 7300862 TGGGAATAAATAATCATAAGGCTGTATCATCATCA[A/G]GATATTGTGGTCATTTTATAATTATAGATACAATT R 2 1 2 1 101000 f 74 goat snp22528-scaffold223-783588 12 78233774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380351 Affx-122975359 AX-123250709 12 7340701 TTTACCCATCAAATGGATTAACTAATTAAGATAGA[C/T]ACTTTTGAAACTCTAGTATTAAGCATAGAAAGCAC Y 2 1 2 1 101000 r 74 goat snp22527-scaffold223-743749 12 78191069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431826 Affx-122936099 AX-123302167 12 7379753 AGAAAATTTAAGTTTCTGCTATTACTTCCCCAATT[G/T]CCCTTGTGATCAACAGTCTCTCCTGCCTCCCAGCA K 2 1 2 1 303000 f 74 goat snp22526-scaffold223-704697 12 78151986 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399215 Affx-122960602 AX-123269570 12 7500415 AGATCATAACGTAATGCAGGCATGAGTTTTCACAA[C/T]ACTTCAACATGCTTTTATTACTGACTATAATACAG Y 2 1 2 1 101000 f 74 goat snp22523-scaffold223-584035 12 78030571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772007 Affx-122956329 AX-385259163 12 7578059 CTGGGTTTTAAACCATATGTATCTGATATTAAGAG[C/T]AGACAGACTATCTGTAATTTGGTTCTTTCTCAGGG Y 2 1 2 1 101000 r 74 goat snp22521-scaffold223-506391 12 77953968 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428659 Affx-122938653 AX-123299001 12 7607707 GAGATTCCATATGTCTTACAGAATTCATTTAACTG[C/T]GGCTGACAGTTGAATTCTAAAGAAAATCTGGATTT Y 2 1 2 1 303000 f 74 goat snp22520-scaffold223-476743 12 77924336 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438253 Affx-122931421 AX-123308591 12 7705063 TAAGGGTTAGACTTTCTGCCAAGAGACACCTACCC[A/G]CAGCAGAAAGCCAAGTGGCCTGAGCAGTCCCAGGT R 2 1 2 1 101000 f 74 goat snp22518-scaffold223-379387 12 77826366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769163 Affx-122940133 AX-385256338 12 7785227 TCAATGACTAACAATTCATTGATTATATTGGCAAA[C/T]ATACTGAAGACTAATAATATCCAGTGCTGGTGAGG Y 2 1 2 1 101000 r 74 goat snp22516-scaffold223-299223 12 77745266 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438669 Affx-122930883 AX-123309006 12 7816722 TCCAATTCTCTGATTCAACTATTCCCCGTTAGCAT[A/C]GCCCACCCATAAGTTATGATCCCAATGTGCCAGAA M 2 1 2 1 101000 r 74 goat snp22515-scaffold223-267728 12 77713041 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394600 Affx-122964424 AX-123264955 12 7866636 ACATAACAAAGAACTTGAGATTTCAGGTGCTTCTG[C/T]AAATGTGTGTGCTTAAGTCACTTTATCCTGTCTGT Y 2 1 2 1 101000 r 74 goat snp22514-scaffold223-217814 12 77660612 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802596 Affx-122942363 AX-385289498 12 7917112 AATAGTTACCATTTAAAAGGTTTCACTGCCCTTCC[A/G]TCAAAATTTTTCTGTAGTTACTCCTTACTGTTTTC R 2 1 2 1 101000 f 74 goat snp22513-scaffold223-167338 12 77610436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476283 Affx-1251763790 AX-586011702 12 7918883 AAGCACAGTCGAAATCACTTACAGGAGTTAATAAA[-/TTACATGAATCTTTTATTTATTTATTTTAAATTATTTTAGGTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCACACC]TACATGAATCTTTTAGAGTAGTAAGGTGAAATTTT - 8 1 4 1 20000 f 74 goat SV_148 12 7918883 - deletion junction SV-TF-chip 539476536 Affx-1251763790 AX-586011925 12 7918883 AAGCACAGTCGAAATCACTTACAGGAGTTAATAAA[-/TTACATGAATCTTTTATTTATTTATTTTAAATTATTTTAGGTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCACACC]TACATGAATCTTTTAGAGTAGTAAGGTGAAATTTT - 4 1 4 1 20000 r 74 goat SV_148 12 7918883 - deletion junction SV-TF-chip 562165492 Affx-1251763790 AX-606940903 12 7918883 AAGCACAGTCGAAATCACTTACAGGAGTTAATAAA[-/TTACATGAATCTTTTATTTATTTATTTTAAATTATTTTAGGTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCACACC]TACATGAATCTTTTAGAGTAGTAAGGTGAAATTTT - 8 1 4 1 20100 f 74 goat SV_148 12 7918883 - deletion junction SV-TF-chip 562165824 Affx-1251763790 AX-606941233 12 7918883 AAGCACAGTCGAAATCACTTACAGGAGTTAATAAA[-/TTACATGAATCTTTTATTTATTTATTTTAAATTATTTTAGGTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCACACC]TACATGAATCTTTTAGAGTAGTAAGGTGAAATTTT - 8 1 4 1 20100 r 74 goat SV_148 12 7918883 - deletion junction SV-TF-chip 562165896 Affx-1251763790 AX-606941305 12 7918883 AAGCACAGTCGAAATCACTTACAGGAGTTAATAAA[-/TTACATGAATCTTTTATTTATTTATTTTAAATTATTTTAGGTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCACACC]TACATGAATCTTTTAGAGTAGTAAGGTGAAATTTT - 8 1 4 1 20100 r 74 goat SV_148 12 7918883 - deletion junction SV-TF-chip 562166033 Affx-1251763790 AX-606941442 12 7918883 AAGCACAGTCGAAATCACTTACAGGAGTTAATAAA[-/TTACATGAATCTTTTATTTATTTATTTTAAATTATTTTAGGTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCACACC]TACATGAATCTTTTAGAGTAGTAAGGTGAAATTTT - 8 1 4 1 20100 f 74 goat SV_148 12 7918883 - deletion junction SV-TF-chip 562166103 Affx-1251763790 AX-606941512 12 7918883 AAGCACAGTCGAAATCACTTACAGGAGTTAATAAA[-/TTACATGAATCTTTTATTTATTTATTTTAAATTATTTTAGGTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCACACC]TACATGAATCTTTTAGAGTAGTAAGGTGAAATTTT - 8 1 4 1 20100 r 74 goat SV_148 12 7918883 - deletion junction SV-TF-chip 562166108 Affx-1251763790 AX-606941516 12 7918883 AAGCACAGTCGAAATCACTTACAGGAGTTAATAAA[-/TTACATGAATCTTTTATTTATTTATTTTAAATTATTTTAGGTGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCACACC]TACATGAATCTTTTAGAGTAGTAAGGTGAAATTTT - 8 1 4 1 20100 f 74 goat SV_148 12 7918883 - deletion junction SV-TF-chip 38380068 Affx-122975558 AX-123250426 12 7961049 TAATATTTGTCACTTTGGAGCCAATGAATAGCTGG[C/T]AGACGCTATGACAGCCCTGGCTTTGAGTGACCATA Y 2 1 2 1 101000 f 74 goat snp22512-scaffold223-123401 12 77566160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432207 Affx-122936381 AX-123302548 12 7991501 GTGGTTTCTTTTTTTAAAAAAATTCCTCTAGACAT[A/G]TTTGCCCCTTTCCATTTTTCTCTAATCAGAAATTT R 2 1 2 1 201000 r 74 goat snp22511-scaffold223-92949 12 77535629 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796528 Affx-122958240 AX-385283474 12 8079352 GGAATGAGAATCAATTCTATCATAAATTCCATCTG[C/T]GAAAATTAAATTTCTGCACAGTAAAATAGCTCCTT Y 2 1 2 1 101000 r 74 goat snp22509-scaffold223-5098 12 77449795 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391853 Affx-122966992 AX-123262210 12 8116839 TACAGGTGAACATTTTGAGTGTGATGGACGAACAT[A/G]TCTGAATGTTAAATATTAAGAACTGTGCGGCAAAC R 2 1 2 1 201000 f 74 goat snp1142-scaffold1030-32290 12 77410282 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389343 Affx-122968476 AX-123259701 12 8189501 AAACAGAAATGACTAATTTTTGACAATTCAGTGGA[C/T]GCAATTTCTATTCATAGTTATCCCTTGGGTTGCAA Y 2 1 2 1 101000 r 74 goat snp1143-scaffold1030-104952 12 77336194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382585 Affx-122973727 AX-123252943 12 8253347 TGGATACCTCATATGAGAGTAATTTAATTGTCAGT[A/G]CTGCTCAACCATTGTTTAATGAATTTCTAACAATT R 2 1 2 1 101000 r 74 goat snp1145-scaffold1030-168798 12 77271196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769200 Affx-122936885 AX-385256375 12 8298764 TATATCTTCCTCTTCTAGGTACTATTCTATACAAT[A/G]TTTGATATCTTAATAATTGATATACTTTCATTACT R 2 1 2 1 201000 r 74 goat snp1146-scaffold1030-214215 12 77225365 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790046 Affx-122968722 AX-385277052 12 8344890 AGCAGAAGCTACATAGTAAGAAGCACCATGGTCCT[C/T]TGAACTTGTGTTTACTGTGTAAACTTGGGAAAAGG Y 2 1 2 1 101000 f 74 goat snp1147-scaffold1030-260341 12 77178910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452252 Affx-122920775 AX-123322585 12 8382122 CCGAGCATTCTCTTCAGTTTTTAGCCGAAGACGGT[A/G]TTTAACATGAATATTTTAGTCATTTTGATGAATTA R 2 1 2 1 101000 f 74 goat snp1148-scaffold1030-297573 12 77141879 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400465 Affx-122961306 AX-123270820 12 8467502 TTAGCCCCTGCTTCTTTTTTTACAGGTCTCTGTGT[A/G]CCTTTATACAGATAATAAGATGATAAATAGAGAGG R 2 1 2 1 201000 r 74 goat snp1150-scaffold1030-382953 12 77054538 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778243 Affx-122944057 AX-385265358 12 8506394 CACAGTGTCTATTTACTGAATTGTAGTTTTCTTCA[C/T]TGGGGAGAAAACCCATTCTGATCACAATACATTTC Y 2 1 2 1 202000 r 74 goat snp1151-scaffold1030-421845 12 77016411 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772223 Affx-122977260 AX-385259378 12 8556115 GATGGAGAATAAGAAAAACTGGTAAGTAACAAAAG[C/T]GGTTTTAAAACTCAGTGATTGGTAGAGAACTTAAT Y 2 1 2 1 101000 r 74 goat snp1152-scaffold1030-471566 12 76965111 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444791 Affx-122926344 AX-123315128 12 8593208 GATGTATGTAAAGGGAAAACAAAGATAGTGTTAGA[A/G]CAGATATCAGAAACCAGGCCTTCTAATTCCTAAGC R 2 1 2 1 101000 r 74 goat snp1153-scaffold1030-508659 12 76927770 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419030 Affx-122946033 AX-123289378 12 8633461 TACCTGGAAGAGCCCTGGGTGAGGAAAGTACTGGA[C/T]GCTTCTTTCCATGTCTGCCCCCATCCAGGTAGACC Y 2 1 2 1 101000 f 74 goat snp1154-scaffold1030-548912 12 76887354 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791046 Affx-122922479 AX-385278041 12 8663718 GGAAGAGCAAAAATAACAACAGCATTTATCTGTCA[C/T]GCAGTTCTATCTTTAAGTGTGACTGGAAAAACGGT Y 2 1 2 1 201000 f 74 goat snp1155-scaffold1030-579169 12 76857294 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431077 Affx-122936628 AX-123301418 12 8700289 CACGCTTCTCCAAAAACAGCCAGGACTGTGCAGAA[C/T]GCAAGGGTATAATTCTTCTGGGTGGTGGGGTTTTG Y 2 1 2 1 101000 f 74 goat snp1156-scaffold1030-615740 12 76820476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435230 Affx-122934085 AX-123305570 12 8750120 ACCTTGGACTGGATGGATTTGGAGGCCTATGAGTT[A/G]CTACTTCTTTGCTCCACCTCAGTGGCATCTTTATT R 2 1 2 1 201000 r 74 goat snp1157-scaffold1030-665571 12 76770214 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390329 Affx-122967701 AX-123260686 12 8796708 AAGGTCAAGACTCCAAAGATCACCCCATTTCTTCT[A/G]TATACATCAAGTTTTCTCTCTCTTGCAGGGGTCCC R 2 1 2 1 201000 r 74 goat snp1158-scaffold1030-712159 12 76723714 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431036 Affx-122936657 AX-123301377 12 8875894 CAGACTAAAGCACTCTGAAAAATCAGCTTCTTAGA[C/T]GAAACCCTAAAGTGTTTCCTGGAACTCTTAGAGGA Y 2 1 2 1 101000 f 74 goat snp1159-scaffold1030-791345 12 76643864 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396215 Affx-122963354 AX-123266570 12 8925893 CTCACTGGTAACATTTTCACTTTGTGGTATCTTTC[A/G]TCATATAGAATTTCTCTCACATTATTTTGGGTATC R 2 1 2 1 201000 r 74 goat snp1160-scaffold1030-841344 12 76593975 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429102 Affx-122938261 AX-123299444 12 8955800 GGTTTGACACTTACTGATTTTACTTTTTAACTCCA[G/T]AAATAGTCTTACTTCCTTCAGGTGAATTCCTGGGC K 2 1 2 1 101000 r 74 goat snp1161-scaffold1030-871251 12 76563526 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446096 Affx-122925803 AX-123316433 12 8996967 TTCCCTCCAAGGCCCACTACTCTGTCCTTGCCCTC[A/G]TTGACCCTCTTTTGGGTTGTCTTGACTTCCTGCCC R 2 1 2 1 101000 r 74 goat snp1162-scaffold1030-912418 12 76522343 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426976 Affx-122940395 AX-123297321 12 9048405 TTTTGTATTTCTCTGTACAAGCTTTATTCTCATTT[A/G]CAAATAAATATTTCAAGGTGATTTATCAGAAGCTC R 2 1 2 1 101000 f 74 goat snp1163-scaffold1030-963856 12 76470842 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392149 Affx-122966321 AX-123262506 12 9096974 TTGCAATAGATACATTGCTCTTGAGCCTCCCTCCT[A/G]CCTCCCTCATCTTACCTAGATAGGTCATCACAGAA R 2 1 2 1 101000 r 74 goat snp1164-scaffold1030-1012425 12 76420267 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773795 Affx-122972113 AX-385260935 12 9137295 ATCTCCCCTGTTTAAATTCTAGCTCCCATACTTCA[G/T]ATCTATAACCAGAAGCAAGTTTAAGTAGCCTGCCT K 2 1 2 1 101000 f 74 goat snp1165-scaffold1030-1052746 12 76378875 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450907 Affx-122922194 AX-123321241 12 9178676 AAACCATCCTTGTTGAGCCTCACGTTTTCGTTTAC[A/G]TTGGGCTAGTCCCTCTCTTACTTTGGCCATAGATT R 2 1 2 1 103000 f 74 goat snp1166-scaffold1030-1094127 12 76337437 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423884 Affx-122942298 AX-123294230 12 9219023 TTTTTGATCTCATTTTTCTGAATCAGTGTCTCAAG[C/T]CTCCGTTCTGGTTTGCATTTGTAGACCCCAGATTG Y 2 1 2 1 101000 f 74 goat snp1167-scaffold1030-1134474 12 76296189 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38383920 Affx-122972976 AX-123254278 12 9270124 TTGCCCAACATCACACATGTCTTGCCCACCACTGG[G/T]CTCAGCAAACCAGGTGAGTGTCCTTTATCAGCATC K 2 1 2 1 101000 f 74 goat snp1168-scaffold1030-1185575 12 76244930 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403827 Affx-122957952 AX-123274179 12 9310801 TTGCAAGCTGACATGCCTTGCTTTCCTGGGGAGAG[C/T]GACTAAAAGCAATTTACACATTACAGAGGGTTGAG Y 2 1 2 1 101000 r 74 goat snp1169-scaffold1030-1226252 12 76204313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796486 Affx-122972430 AX-385283436 12 9345131 CAGGTGAGACCACAAATCAGAGGATAGGCTTAGGG[C/T]GGGAGCTGCCTGCACCAGAGAGACCAACCCTGCGA Y 2 1 2 1 202000 r 74 goat snp1170-scaffold1030-1260582 12 76170101 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796647 Affx-122950649 AX-385283593 12 9398703 TTTCCAAACCCAGAGCTGTTATTGTTTCACAGAAA[C/T]AGGGAAAATGATCCTTGTGCTATCACAGAATTTCA Y 2 1 2 1 101000 f 74 goat snp1171-scaffold1030-1314154 12 76115843 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799363 Affx-122933815 AX-385286293 12 9434140 GACAAATACACTGTACTAAACAATACCTTGTTCTC[A/G]TTCTGTTAATATTAGAGTTGACCATATTTGAATGG R 2 1 2 1 101000 f 74 goat snp1172-scaffold1030-1349591 12 76080705 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411407 Affx-122951845 AX-123281757 12 9478019 AAAATTACCTCACGGCAAAAAGCCATCCCTGGAGA[C/T]GTGATTTGGGAGCAGAGAGGCATATATTAGCTGTG Y 2 1 2 1 201000 f 74 goat snp1173-scaffold1030-1393470 12 76036388 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439272 Affx-122930985 AX-123309609 12 9531743 CAGGCCACTCAGGACATGGGCCAGTATAATACAGA[C/T]GGAAGAAAATGAGCTCTGAAACTGAGGGTAGTTTT Y 2 1 2 1 101000 f 74 goat snp1174-scaffold1030-1447194 12 75983822 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393663 Affx-122965279 AX-123264018 12 9563685 CTCTGTTGGGTTCTACTCTGCCTCTCTCATTAGCC[C/T]GTGGGCATCTTCTATGTCTGGACAACATGAAGAAT Y 2 1 2 1 101000 r 74 goat snp1175-scaffold1030-1479136 12 75951764 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415508 Affx-122948685 AX-123285857 12 9642597 GCAGTGATTTCATACCTCCACTTCCAACTGGTCAA[C/T]GATCACTGTGCTTCCAGCAAAGCCGACCTTCAGCT Y 2 1 2 1 101000 f 74 goat snp1176-scaffold1030-1558048 12 75872411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405798 Affx-122955904 AX-123276150 12 9687629 GTCATCTATATGCTCACAGAGGTAAAACCCCCAGA[C/T]GCATCTCTGACTCTTCCCTTTGCCTCATTCCCGCA Y 2 1 2 1 101000 f 74 goat snp1177-scaffold1030-1603080 12 75827247 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446076 Affx-122925816 AX-123316413 12 9721265 TCCACACCCTTGGAAGTTTTGCCACACAAAGACCC[A/G]TATTGCAGGGGTGGGGGGCAAGGGGTGTGGAACAA R 2 1 2 1 101000 f 74 goat snp1178-scaffold1030-1636716 12 75793894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387267 Affx-122970551 AX-123257625 12 9758013 TGCTATTTGAAAAATAATAAAAAGCTTATTAATTG[A/G]CATCTCCAAGGACCAGGAAAACTTCACCAGCTTCA R 2 1 2 1 101000 r 74 goat snp1179-scaffold1030-1673464 12 75757468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781144 Affx-122958010 AX-385268229 12 9814374 AAATAAGAAAAAGGCAAGAGAAGGCGGATGTAGCC[A/G]TCTTCAGATATATGAAAGGCTTTGAGAAGAACTGC R 2 1 2 1 201000 r 74 goat snp1180-scaffold1030-1729825 12 75701764 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418299 Affx-122946988 AX-123288647 12 9864418 CCTGGTCCCTGTACAAACATCTAGCATGGCCCTTG[C/T]AACTTTATTACTCTGTGTGACTCTCTTCCCCTGCC Y 2 1 2 1 101000 r 74 goat snp1181-scaffold1030-1779869 12 75652839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435098 Affx-122933711 AX-123305438 12 9919041 TGTTAGAAGTGTTTGCTTAATCCTCACACGCCTCT[A/G]TAAGTAGCACTATTGTCTAAAATGAGGCACAGAGA R 2 1 2 1 101000 r 74 goat snp1182-scaffold1030-1834492 12 75597534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386248 Affx-122970962 AX-123256606 12 9948541 CCTTCAACAGCAATGCCGTGTGGAAACACTGGGAC[A/G]TGGGGTCCTGGGAGCTGTGACCGTGAACCCTACCT R 2 1 2 1 101000 f 74 goat snp1183-scaffold1030-1863992 12 75567767 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400021 Affx-122960794 AX-123270376 12 9980097 GGGGGAGGCAGGACTCTGTCGCTTGAATTCCTTCC[A/G]TCATATGTATATTATCCAACCTTAGAAAACGCACA R 2 1 2 1 101000 r 74 goat snp1184-scaffold1030-1895548 12 75535810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420270 Affx-122945051 AX-123290618 12 10025530 CAATAGTCCTGGGAGGGCAGGGTGAAGCTTTGAAG[C/T]AGGTATGACAGGTGTGATGGGGGTGTTCAGGAGGC Y 2 1 2 1 101000 f 74 goat snp1185-scaffold1030-1940981 12 75490269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794615 Affx-122963325 AX-385281577 12 10062561 GATTCCTCAAGGCTTGTACAACCACTTCCAAGTCC[A/G]AGAAAAATAAATGAAGGGCTCCTGGTTTCAGAGCA R 2 1 2 1 101000 r 74 goat snp1186-scaffold1030-1978012 12 75452922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438265 Affx-122931412 AX-123308603 12 10100041 TACAGGGCTGCTGCTAGAACTAGGTGAGATACTAC[A/G]TTTAAAATATGTCTTAAAAAAATGCTTTAAGCTAT R 2 1 2 1 101000 f 74 goat snp1187-scaffold1030-2015492 12 75415657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393679 Affx-122965266 AX-123264034 12 10135779 ACCAACCTAGCTCTGAAAAGATGGCTGCTCAGGGT[A/G]CTCTGGGAAAGGTTTCCTTACTGATAAACAGAAGC R 2 1 2 1 101000 f 74 goat snp1188-scaffold1030-2051230 12 75379915 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409862 Affx-122952920 AX-123280213 12 10166556 GCCTTCTGCGGCAGCAGTAACAAAAGAGCTTTCCT[A/G]TCTTTGGCCCCACAGGCAACCTCTCGCTGTTACCA R 2 1 2 1 101000 f 74 goat snp1189-scaffold1030-2082007 12 75349341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377655 Affx-122977857 AX-123248014 12 10219798 AAACATATCAAAAAGTTAATAGTCAAAGATTCTGT[A/C]TTCCCCAAACAGTTCTAAGAATCAAGTGCCCGGTA M 2 1 2 1 201000 f 74 goat snp1190-scaffold1030-2135249 12 75295642 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788073 Affx-122921172 AX-385275093 12 10304795 CAGTTAAAAAGTTCAGCAAGACACTAGGTTTTGAA[G/T]AGACTATTGTGGCTAATTGGTCTGAGCTTCAACAG K 2 1 2 1 101000 r 74 goat snp52824-scaffold792-16031 12 75210084 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802380 Affx-122951299 AX-385289284 12 10361010 ACAAAGATTCAGCAGTATAAACAAAAACCAGATGA[A/G]TAAGTTCTGGATTATTAGGAGGAGTTCAAGAAAAC R 2 1 2 1 101000 f 74 goat snp52825-scaffold792-72246 12 75153190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780701 Affx-122965518 AX-385267791 12 10392050 AACAGAATCAGCAAGCGTTTATTCCAGATTTGATG[A/G]TTTAGAGCTGTGGGTTTAAAGTCTAGAGTGGAAGT R 2 1 2 1 101000 f 74 goat snp52826-scaffold792-103286 12 75121693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389337 Affx-122968482 AX-123259695 12 10444997 CATACATGCGCGATGGAATATAAAATGGTACAGCC[A/G]CCTGTCAGGCAGCTCCTCAAAAGATTAAACACGGA R 2 1 2 1 202000 r 74 goat snp52827-scaffold792-156233 12 75068494 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795326 Affx-122950998 AX-385282284 12 10515302 AAAAAATTCTCGATCTTTAGCCTTTCAAACATTCA[G/T]AAATTGTGAATAAATGATTCCTTTCTTTTGGATCC K 2 1 2 1 101000 r 74 goat snp52828-scaffold792-226538 12 75000349 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422940 Affx-122943028 AX-123293286 12 10548120 TTCATTCTCCAGAACAGAATTCTTGTTGTGGTGAG[C/T]GGGCTTAGCTGCCCTGTGGCATGTGGAATCTTAGT Y 2 1 2 1 103000 f 74 goat snp52829-scaffold792-259356 12 74967267 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419246 Affx-122945669 AX-123289594 12 10577569 CAACTTATGTAAAAACTGCTGAATGAAAACGAAGC[A/C]TGTTCAGCATTAGTTATGTAAATTTTAAAACCACA M 2 1 2 1 101000 f 74 goat snp52830-scaffold792-288805 12 74937110 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428477 Affx-122938789 AX-123298820 12 10619088 CATGCTCCCTCCACCATCCTGCTTGAATTGGTGCC[C/T]GTTTCCTCTGCCCTCCTTGCTGTGATTAGGCCAAC Y 2 1 2 1 201000 r 74 goat snp52831-scaffold792-330324 12 74895964 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463206791 Affx-1109867022 AX-514692956 12 10655034 CTTGGTTATTCTTTTTTTCTTTAATTGTGAGGAGA[A/G]GTCAGGTGGAAAGGTTGAGAATTTGTTGATTTGTC R 2 1 2 1 101000 r 74 goat 12_10655034_AF-PAKI 12 10655034 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320771313 Affx-122924795 AX-385258471 12 10671321 CAAAATTTAAAACCTAAAGGCAGCACAGCCCTGGA[C/T]GATGGCGTGCTGGCTTCAGCAGATGCCTGACCACG Y 2 1 2 1 202000 r 74 goat snp52832-scaffold792-382557 12 74843508 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276584 Affx-1111835489 AX-519550095 12 10711449 AACTCAAACCAGGGCTTTCTAAGTCTAGGTCTAAA[A/G]GTCTGTTCCTTCTATACCTGCACTGAATCAGCCCT R 2 1 2 1 201000 f 74 goat Random2.2K-1237 12 10711449 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392113 Affx-122966351 AX-123262470 12 10738470 AAAAACAGTGTGTAGGGAGGTGGTCTACCCTGCCC[A/G]TAGGCACTTTTCTTAGGTGATCAAAAAATATGTAT R 2 1 2 1 201000 r 74 goat snp52834-scaffold792-449706 12 74776704 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796478 Affx-122967649 AX-385283428 12 10799659 AGCCTTTTAGCTACTAAACTCTTAGATTATTCTTT[A/C]GTATAGAAAGATAATGATAAATTAAATGTTCCTAC M 2 1 2 1 201000 r 74 goat snp52836-scaffold792-510895 12 74717397 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772191 Affx-122931085 AX-385259346 12 10846338 GGAAGTTCCAGTAAACAGATTTGCATTATTTAATA[C/T]GTTCATTTTAGAAAGGAAGGATATTTAGAACCTAC Y 2 1 2 1 201000 r 74 goat snp52837-scaffold792-557574 12 74670701 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408088 Affx-122954719 AX-123278439 12 10890361 AATAAAGAGGGCCTAGACAAGCTGATCTCCAAACA[C/T]AATCTTATTCTAACAGTTTTTAAACCAATAACACA Y 2 1 2 1 101000 f 74 goat snp52838-scaffold792-601597 12 74626537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426558 Affx-122940174 AX-123296904 12 10945397 CGTCTAAGCATACTCAGTGAACAAAATGCAAGGCA[C/T]GCTGCCAACATTCCTGTGTCATTTATGTTTCATCT Y 2 1 2 1 101000 f 74 goat snp52839-scaffold792-656633 12 74571052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428285 Affx-122939391 AX-123298628 12 10995575 GTGAGAGCACAATTCTGGAGTAAAGTCGCAGGCTC[G/T]CCTTCTGGCTCCTGGAACACCTTGCAGCGCCTTCC K 2 1 2 1 201000 f 74 goat snp52840-scaffold792-706811 12 74522471 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275191 Affx-1111834645 AX-519548770 12 10998124 CAGGTTTCT[A/C]ACACTTGGCAGCACACAATGGAAGCTCTGTGTCCT M 2 1 2 1 101000 r 74 goat GoatD01.044372 12 10998124 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320797097 Affx-122927676 AX-385284037 12 11024196 GGTTACTATTTAAATCCAGTTTCTCATTTAAACAG[C/T]GTTATCTCTCACCTCCTTACACATCTCCTGTCTCG Y 2 1 2 1 101000 r 74 goat snp52841-scaffold792-735432 12 74494256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445860 Affx-122925996 AX-123316197 12 11056014 CAAGAATCCGGGGTCACTGGGACTTTTCCTTAGGT[A/G]TGTATCATAACTAGGGACTGGTGTCCAAAGCTCAG R 2 1 2 1 101000 r 74 goat snp52842-scaffold792-767250 12 74461945 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796008 Affx-122970271 AX-385282960 12 11175584 TTTCTGTGACTGTAGGGTTTTGACATATAATGTGG[C/T]GGATTTGATTGTTTTATCATAAGTAACGCATGGCT Y 2 1 2 1 101000 f 74 goat snp52844-scaffold792-886820 12 74341957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428024 Affx-122939146 AX-123298367 12 11232618 GTTCGGTAACTGGCTGTGACCTGAGCCAGGACTAG[C/T]TCTTCTCATGGTGGGGTGTGTGAGTAGGTGTGCAT Y 2 1 2 1 103000 r 74 goat snp52845-scaffold792-943854 12 74284314 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441594 Affx-122928665 AX-123311931 12 11307343 GGAGTACTTGGAACTCGGGAATTATTACAAAGATC[A/G]TACAAGAATTTGGAACAGAGGGTTCAACTTGAAGT R 2 1 2 1 101000 f 74 goat snp52847-scaffold792-1018579 12 74209788 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428197 Affx-122939012 AX-123298540 12 11352879 TGTAGTCTGTTTTGAAACTTTTATCTGAAAGATGG[A/C]GATCCTATCTATTTATTATACAGTGGGCTCTGTTT M 2 1 2 1 101000 r 74 goat snp52848-scaffold792-1064115 12 74164394 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276586 Affx-1111835490 AX-519550097 12 11371896 CTTTGTTGCTAACGAGAAATTTAGGAATATGTTTC[A/G]AAGAAAGGAACATGTATTATTTCAGGAAAGAAACA R 2 1 2 1 101000 f 74 goat Random2.2K-1238 12 11371896 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769589 Affx-122935384 AX-385256759 12 11384463 GCTCTTTGGATATTATCTTGACATAAAATAACACT[A/G]TCTTCCACACCCTCTATTTGGCTTCACTTACAGCT R 2 1 2 1 101000 r 74 goat snp52849-scaffold792-1095699 12 74132851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769748 Affx-122970162 AX-385256918 12 11427343 GTTCTGTAAAACTCTGTACTTGAAAATGTTGATTT[C/T]CTGTATGGTAAGGTTTTCCTCCTGTCTTTGTTTTT Y 2 1 2 1 101000 r 74 goat snp52850-scaffold792-1138579 12 74090006 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386355 Affx-122970860 AX-123256713 12 11513031 TCATTCATCAAAATTCTTGACAGCAAACTCTGTGT[A/G]TGTTTCACCCATCCCAGGCCCAAGCGTTTAACATG R 2 1 2 1 101000 f 74 goat snp52851-scaffold792-1224267 12 74010687 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273929 Affx-1111833903 AX-519547535 12 11520985 GGCGCGTGCCTGCCGGCTACGGTTGGCTCACATAT[A/G]TTGCTTTAACTTGATTAAAAATCAGTTGCCAGAGA R 2 1 2 1 201000 r 74 goat GoatD01.009936 12 11520985 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320795428 Affx-122938457 AX-385282384 12 11543945 GTAGATTCCATGTGCAGCAGGAGTGTGGGAATACA[C/T]AAAACTCAACTAGGCTTTTTAGGATATTTTCATAG Y 2 1 2 1 101000 f 74 goat snp52852-scaffold792-1255181 12 73980067 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424074 Affx-122942049 AX-123294420 12 11575597 TGCAGCTCCTGGGCCACCTCTTATAAGCTGAGTCC[C/T]TTACATGTTTTCAATTTAGTTTTAATTCTCTCTTG Y 2 1 2 1 101000 f 74 goat snp52853-scaffold792-1286833 12 73948671 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386624 Affx-122970228 AX-123256982 12 11595446 AGATGTTTACATAGTACCCTCTCTTTGCTGCTGCT[A/G]CTGCTAAGCCGCTTCAATCGTGTCCTACTCTGTGC R 2 1 2 1 103000 f 74 goat snp39081-scaffold498-18262 12 73924703 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378326 Affx-122977342 AX-123248685 12 11669980 CTTCTTTGTAGGGAGTCCCAGTATTAATGGTCTGG[C/T]GGGCTGAGAAGTCTAGCCTTCTCATGATCCTTTAG Y 2 1 2 1 101000 f 74 goat snp39083-scaffold498-92796 12 73850682 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433996 Affx-122934245 AX-123304337 12 11701321 CTTAGCAGAGTGATATTTCAGAGGCAGGAGCCCTC[G/T]AGAAAATGAGACACACTCCTTCTCCAGGGGGTTAT K 2 1 2 1 102000 r 74 goat snp39084-scaffold498-124137 12 73819313 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420379 Affx-122944941 AX-123290726 12 11739136 TGTTTGCATCAACAGTTTTCAGTACCAGTCAGACC[A/G]TGGGTGTGGGACACTGTTGTGCCCCCTGTCTATTC R 2 1 2 1 101000 f 74 goat snp39085-scaffold498-161952 12 73781393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399689 Affx-122960491 AX-123270044 12 11784264 TTCTAGATACAAGCCTCAGTCACAACCATGGGTCC[A/G]GTGAGGAAAGCCTCTGCTAGCACTGAAGCCCAGAG R 2 1 2 1 201000 r 74 goat snp39086-scaffold498-207080 12 73738510 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433043 Affx-122935761 AX-123303384 12 11824082 TTGGTCACTACCTTCCATTCCACTCACTGCTTCTC[A/G]TGTTTAACAAATCCCTCCTTTCTTTTCCACTCAAG R 2 1 2 1 101000 r 74 goat snp39087-scaffold498-246898 12 73700405 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420724 Affx-122944773 AX-123291071 12 11856546 ATTCCTCTTCAAAAGCAAGGTGATAGGATGGTGAA[C/T]GCTGCGATGCAAAGGCAGGCTTCTGGTCTTTGTTG Y 2 1 2 1 101000 f 74 goat snp39088-scaffold498-279362 12 73667298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429812 Affx-122938189 AX-123300153 12 11916741 ACTGGAAACCATGGCAAATTTCAGGGAAAGAAGTC[A/G]TGATAAACAGGAGGGTGGTGATGGCAATAGTCATG R 2 1 2 1 101000 f 74 goat snp39089-scaffold498-339557 12 73609249 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446104 Affx-122925797 AX-123316441 12 11957600 CTCTCTGCAGTAGCTCGAAAACTGGGATCACTGGC[A/G]TCAGGAACTTCACAGATGTGTGTGTTGGGTAGGGG R 2 1 2 1 101000 f 74 goat snp39090-scaffold498-380416 12 73569053 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446069 Affx-122925821 AX-123316406 12 11999374 ATCTATAGGTGTTTCTCCTATAATTTATATGGTAT[A/G]TTATCTTGGCTATTTTTTGGTTCTATTTATTTGTG R 2 1 2 1 101000 f 74 goat snp39091-scaffold498-422190 12 73527846 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451421 Affx-122921180 AX-123321754 12 12031411 ACAATCATGAGACAAAGCATCACCACAATGTCTAA[C/T]GCCTACCGTGGGTCTAGTTCTAACAGATCAACCTG Y 2 1 2 1 101000 r 74 goat snp39092-scaffold498-454227 12 73495740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392845 Affx-122965767 AX-123263202 12 12088345 TTGCCAAATTGCCTGGCTTTGAACCCTAATTCTGT[C/T]ACTTCCTAGCTATAACTTTGAGCAAATTGCCTAGT Y 2 1 2 1 201000 r 74 goat snp39093-scaffold498-511161 12 73439071 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775777 Affx-122968000 AX-385262908 12 12121479 TGTTTTGGCTCAGCTAAACAAAAGCACAAAATGTA[A/C]ATTGGATCCAGAAAATAACATATGGGTGCTGGTGC M 2 1 2 1 201000 f 74 goat snp39094-scaffold498-544295 12 73405798 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404520 Affx-122956694 AX-123274872 12 12193785 TGAGTATAATTGTTGTGTCTCTTTGTTGTTCAGTC[A/G]CTCAGTCATGTCCAACTCTCTGTGACCCATGGACT R 2 1 2 1 103000 f 74 goat snp39096-scaffold498-616601 12 73332467 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440899 Affx-122929223 AX-123311236 12 12242607 TCAGAGAGTGACTACGAGGTTATCGTGAAGATGCC[A/G]TCTCACACTCAGCATAAGGGCTGTAGGAAGTGGTG R 2 1 2 1 101000 f 74 goat snp39097-scaffold498-665423 12 73283257 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798322 Affx-122929512 AX-385285257 12 12281474 ACAAATCACAAGCTGAAGATACTCTCCAAGTTCTG[A/G]AAACGAGACTCAGAAGCAGTATGATAACTGGTTGG R 2 1 2 1 201000 f 74 goat snp39098-scaffold498-704290 12 73243493 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415257 Affx-122948850 AX-123285606 12 12310766 GGTGTGGTAGTAAAGGAAAGAGCAGGAACATTTGG[A/C]GGTAGATCCATCCACCTTCAAACCTCTCTCTCCCA M 2 1 2 1 101000 f 74 goat snp39099-scaffold498-733582 12 73214084 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411307 Affx-122952288 AX-123281657 12 12357414 GACCTCTAGGACATCTATGCTCTCTGCACACCTAA[A/G]AAATAATTTATGGAAAGGTGTCATTTCAAAGTGAA R 2 1 2 1 201000 r 74 goat snp39100-scaffold498-780230 12 73167115 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414483 Affx-122949550 AX-123284832 12 12391303 GGGACTGCGCTCTCTGGGTTTATTACACTTCAAAA[C/T]GATCCTGCCTGAACTCAACTCCGGTCTGCGTATTT Y 2 1 2 1 101000 f 74 goat snp39101-scaffold498-814119 12 73133509 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413962 Affx-122950302 AX-123284311 12 12436019 CTTTCTCCTCTTCTCCTTCTTCTGTGTTAATGTCC[A/G]TGTCACTGTGTTTTTAACTCTGGAGGAAGACCTGT R 2 1 2 1 201000 r 74 goat snp39102-scaffold498-858835 12 73088993 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788462 Affx-122946331 AX-385275479 12 12465107 AAAGAAGTCTGTACCTATGCTGTGGTTGAGTCTCC[A/G]TGGAAAATCGACAACCTGGACAACACTCTTCATAA R 2 1 2 1 201000 r 74 goat snp39103-scaffold498-887923 12 73060008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800710 Affx-122922849 AX-385287627 12 12528994 CTATCTCATTAGCCGATGATTAATTTTCACTCTGT[A/G]CGATGTTAAATGACTTCGTACAGCAGGATTGTTAC R 2 1 2 1 201000 f 74 goat snp39104-scaffold498-951810 12 72996181 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796864 Affx-122934322 AX-385283807 12 12581317 GAGTTTTCCTGAGAATTGCACAGCTTATATATAAA[C/T]GTATTTTTATAAGCCTCTTCAAAGCACTTTTCTAA Y 2 1 2 1 201000 r 74 goat snp39105-scaffold498-1004133 12 72945325 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411933 Affx-122951156 AX-123282283 12 12612058 ATGGTGCTGAAGATACAGGTGGGGGGCCAAGCTGG[C/T]GGGTTTGATCTCCACAGGAAATGAGGGCCAAGCAG Y 2 1 2 1 101000 r 74 goat snp39106-scaffold498-1034874 12 72914519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375401 Affx-122979207 AX-123245760 12 12642591 ACTGGGACCAACTTGCTGACTAAAATGTTGAATTG[C/T]AGCTTTATAACAACTAGATTCAAATAAATAAAACT Y 2 1 2 1 101000 f 74 goat snp39107-scaffold498-1065407 12 72884050 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409837 Affx-122952939 AX-123280188 12 12702395 ACAGCAGGCTCACCCTGGGCCCCGACCACCACCCG[A/C]GGTGACCATCACTCTTTAAGAGCAATCCTCTCCTG M 2 1 2 1 103000 r 74 goat snp39108-scaffold498-1125211 12 72825734 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789225 Affx-122942129 AX-385276236 12 12731042 AAGAGAGAACAGTTGTTTTGCTCAGAAACAAGCCC[A/G]TGACAGACTACATTGAAAAGAAAAGTCTGAAAGTG R 2 1 2 1 101000 f 74 goat snp39109-scaffold498-1153858 12 72796995 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425548 Affx-122941444 AX-123295894 12 12779821 GTTTTGCTGCAGACGAGACTCATTCAGAGCTCTTC[C/T]TACACAACCTACTCTCTTTCCCTTCTTGGCCATAG Y 2 1 2 1 101000 r 74 goat snp39110-scaffold498-1202637 12 72748230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415994 Affx-122948397 AX-123286343 12 12824860 TAGAACTTTAAGATAACAAATCCCTATCAAGTTGC[C/T]AAGTTTGTGGTAACTTGTTACTGCAACAATAGAAA Y 2 1 2 1 101000 f 74 goat snp39111-scaffold498-1247676 12 72702679 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417925 Affx-122946721 AX-123288273 12 12858240 GCCCATAGCTCTACAATTTCAGTGTTAACTATACA[G/T]GACTGTAAATATTTTGAGGAAAAAATAATAGTTGT K 2 1 2 1 101000 f 74 goat snp39112-scaffold498-1281056 12 72669296 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439230 Affx-122931018 AX-123309567 12 12894130 GAGGGAAAAGCTTGGGGCCCCCTAATATCACGCTG[C/T]ACCTGCAGTGCAGAATGACTTGATGGAGGCATGCC Y 2 1 2 1 101000 r 74 goat snp39113-scaffold498-1316946 12 72633244 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397769 Affx-122962519 AX-123268124 12 12928949 TGCCATTGGGGTCCTTGGCTCTGCAGAGGAAAGAA[A/G]GGAGCTTGACCCATGGGCTTGTAATGTAGATTAAA R 2 1 2 1 201000 r 74 goat snp39114-scaffold498-1351765 12 72597865 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439971 Affx-122929812 AX-123310308 12 12959403 GGCCTCCATCTTCTATCACCTTGGAATGATAGAGA[A/G]TGATGTCACTTCTGGGTGTAGATAAAGGCAACAGT R 2 1 2 1 201000 r 74 goat snp39115-scaffold498-1382219 12 72568093 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424673 Affx-122942146 AX-123295019 12 13004779 ATTACACCTTGTTTCTCTCATCAACAGACACAATG[A/C]GAGGTTTATTCATAAATGTATTATAGCATTAAAAT M 2 1 2 1 101000 f 74 goat snp39116-scaffold498-1427595 12 72522737 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784353 Affx-122963629 AX-385271404 12 13060724 ACATTATTAAAGACATTGAATGCGGTCCGATACCA[C/T]GATGGTGCCAAGGCCAAGTTCTTTTGCATAATATG Y 2 1 2 1 101000 r 74 goat snp39117-scaffold498-1483540 12 72466616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452941 Affx-122920181 AX-123323274 12 13106468 CTTTCAAATCTCACTAACCCCAGAAAAAGATCTTA[C/T]GCAGGAAATTTCATCCAGGGCATTTTGGTTCTCTC Y 2 1 2 1 101000 r 74 goat snp39118-scaffold498-1529284 12 72420265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390587 Affx-122967191 AX-123260944 12 13142843 AGTTGGGGGTTTCCACCTTGAGTAAAGGAGAAGCC[A/G]TTGCTTGGCTCACTAATCACTGCAAGTAAGGACTA R 2 1 2 1 101000 r 74 goat snp39119-scaffold498-1565659 12 72383404 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791778 Affx-122954788 AX-385278769 12 13175940 CACATTTTACAAAAATGCCTAGAGAGGTGTTAAAT[A/G]TTGTGTTCAAAGCTTTAATACTGGCAAGGAAGTAG R 2 1 2 1 101000 r 74 goat snp39120-scaffold498-1598756 12 72350460 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271896 Affx-1111832945 AX-519545678 12 13185602 GGTATAGGATTCAGGGTTAATAGTTCTTTTCTTAC[A/G]ATGTCTGAAAAATACTGTATAATTTCTTTCTGGCT R 2 1 2 1 201000 f 74 goat 12_13185602_AF-PAKI 12 13185602 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446099 Affx-122925801 AX-123316436 12 13247979 GAGATACAAATCACATGAGTTTTATTGCCACTTCC[A/G]CTCTTAGACTTTGTTTCCCTATGGATACTGAGAGG R 2 1 2 1 101000 r 74 goat snp39121-scaffold498-1670795 12 72278364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389590 Affx-122968776 AX-123259948 12 13290713 GGCTACACGCATATTCTACACCTACTTTTACCTAT[A/G]TTCCTCATAGTTTGTGGACCTGACTCATCACCTAG R 2 1 2 1 101000 f 74 goat snp39122-scaffold498-1713529 12 72234141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416126 Affx-122948296 AX-123286475 12 13346686 TTCAAGTTGAGTCCAGCCTGTGACATGAAACTTCC[A/G]TTAACCTGAGGTGTGCACCCTGGGGTCTCTTATCC R 2 1 2 1 101000 f 74 goat snp39123-scaffold498-1769502 12 72177601 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424271 Affx-122941994 AX-123294617 12 13398326 AGCTGGAATCTTCTCTGGGTGGAGGAGGCAGGGAA[C/T]GGAACCAGAGGGCAGAGAGGGAAGGAATGAATGTG Y 2 1 2 1 101000 f 74 goat snp39124-scaffold498-1821142 12 72126154 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448152 Affx-122924275 AX-123318488 12 13436723 TGAGACTTTGCTGAGGCAAAGGTGAGTTGGAGATA[C/T]GTTTGGTTTGGGTTTAATGGGATATATTTATATGG Y 2 1 2 1 101000 f 74 goat snp39125-scaffold498-1859539 12 72087279 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439823 Affx-122930471 AX-123310160 12 13465424 TACAATACCCAGATGGTGTCTGAGAACCACTTGGC[A/G]TGGGGGAAAGAAAAAATCCCACTCGTTGGAATTGG R 2 1 2 1 101000 f 74 goat snp39126-scaffold498-1888240 12 72058683 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388432 Affx-122969270 AX-123258790 12 13525989 GGAATGATTGCTTTAACAGAAGTGTCTGAGCTCTA[C/T]AGGCTGGGGAAGCATGGGAGTCAAGATCAATTAGG Y 2 1 2 1 101000 f 74 goat snp39128-scaffold498-1948805 12 71998109 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765537 Affx-986697461 AX-385253019 12 13537081 GTCTACACAGTCACGTCAAGGTTGGTCTGAGGCAG[C/T]GACATGCTGGGTAAGTGGTTCTCCCTCTGCCTTCC Y 2 1 2 1 600010 r 74 goat 12_13537081 12 13537081 Ancestral_priority_1043 ancestry 0.502 neutral IMAGE 10K 10K ancestral 38444839 Affx-122926305 AX-123315176 12 13583065 TCACTGCCTTCACATCCCAGCCTGGCAATTTGCCC[A/G]TGTCTTCTGGCATATTCTGATGAAATCACTGCTCA R 2 1 2 1 101000 r 74 goat snp39129-scaffold498-2005881 12 71940594 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762898 Affx-986697427 AX-385250908 12 13593226 CCCTGTGTTGTGAGCTCCCTCATGATGGTTGATGG[A/G]TCCTGGGATCCGGGGCTCCATCTTAACCTGACTCA R 2 1 2 1 600010 f 74 goat 12_13593226 12 13593226 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 320803772 Affx-986696221 AX-385290525 12 13597472 TGGATGATACATTTTTACAGATGCTTAGTAGACCA[C/T]GCTATAATGTGCAAATATATTAGTTTCTTACATTT Y 2 1 2 1 600010 r 74 goat 12_13597472 12 13597472 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 320765543 Affx-986697464 AX-385253023 12 13597766 AGTTTTTGATGAGTGATAACCTGTGATTCCCAAAA[A/C]ATGTGCTTTGACAGTTTGAAATTGAACTCAAGAAT M 2 1 2 1 600010 r 74 goat 12_13597766 12 13597766 Ancestral_priority_1043 ancestry 0.494 neutral IMAGE 10K 10K ancestral 320762937 Affx-986697466 AX-385250928 12 13603454 CTTTTCTTATGTTTAATCTCTATAAAGATAAATTC[A/T]TTTTTGAAATGCCATGATTGAGTTGACAGACTAAG W 4 1 2 1 600010 f 74 goat 12_13603454 12 13603454 Ancestral_priority_1043 ancestry 0.544 neutral IMAGE 10K 10K ancestral 38381764 Affx-122974309 AX-123252122 12 13624115 TGGTGTAGTAACACCAGAGATGTGACCATGCACAA[G/T]AATCCTTGAGCCCAAGTAACCACTGAGAAGCGTAA K 2 1 2 1 101000 r 74 goat snp39130-scaffold498-2046931 12 71899638 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772732 Affx-122953563 AX-385259877 12 13663229 TTTTCTTCTATTAATTTAAGATATTTGTAAGAATG[C/T]ACCAACTGAGTTTAAAGTTTATACTATAAGTCTAA Y 2 1 2 1 101000 r 74 goat snp39131-scaffold498-2086045 12 71862569 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430037 Affx-122937573 AX-123300378 12 13695915 TCTGATGTGTAACTTTTCTTCAAACTTAGTACTGA[C/T]GAAATCTATAGATTTAATTTTAAAAGATTTAAAAG Y 2 1 2 1 102000 f 74 goat snp39132-scaffold498-2118731 12 71830056 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382658 Affx-122973670 AX-123253016 12 13749051 TGAAAGACTTAACTTAGAAGGTGCCTCTACTTCTA[C/T]ACTGGAATCTGTTGATTGGACAAGAATAAGGCTCA Y 2 1 2 1 101000 r 74 goat snp39133-scaffold498-2171867 12 71776828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778167 Affx-122973469 AX-385265282 12 13811915 TTCCTGTATACAGCAGCAAACAAAAGTCTCTAAGA[A/C]AGTACTTAAATGTCATCAAAAATGACTTGTTGTGT M 2 1 2 1 101000 f 74 goat snp39135-scaffold498-2234731 12 71713772 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385763 Affx-122971065 AX-123256121 12 13865885 TAAAGTTCAAAAATGTGACCTGGAAGAGGAAATGT[A/G]TTAGCCCTGTTAATACCCACTAACAGTTTTTTACA R 2 1 2 1 201000 r 74 goat snp39136-scaffold498-2288701 12 71660179 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779405 Affx-122954828 AX-385266508 12 13894911 CCCCCAACACCGAGGCAAAATGCTGTATGGCTTTA[C/T]TGGGTGTCTCTCTCAGCTATTGCTTTAAAAAAAAA Y 2 1 2 1 101000 r 74 goat snp39137-scaffold498-2317727 12 71630642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424361 Affx-122941850 AX-123294707 12 13925466 GGTCTTACAATAAAATGTTCCAGTCTTTACCAAGT[A/G]CTTTTCTCAAAGATTTTATTATTAAATATTATTTA R 2 1 2 1 101000 f 74 goat snp39138-scaffold498-2348282 12 71600064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413580 Affx-122950581 AX-123283929 12 13984619 GCAAAGCAGGGAAGGGAAGAAAGCTAAGAAAGGGT[C/T]ATCTTCAACAAATGGGTTGCATCCCTGGGCAACTG Y 2 1 2 1 101000 f 74 goat snp39139-scaffold498-2407435 12 71540596 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391579 Affx-122966613 AX-123261936 12 14068901 AACTGGGAACCTAAGATGTTCCTTGAGACAATACC[A/G]TCCTTGTCTGGCTCACACATTCCCTCTACACATGT R 2 1 2 1 101000 f 74 goat snp39141-scaffold498-2491717 12 71455808 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795329 Affx-122928242 AX-385282287 12 14107371 CCAAGCACAATTTCACAGCTAGCTCAAATCAAGTG[C/T]CCTCTCAAACCACCTTAATTACTACACTTAAGAGG Y 2 1 2 1 101000 f 74 goat snp39142-scaffold498-2530187 12 71417360 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768735 Affx-122971965 AX-385255913 12 14157385 TGTCTGTAACCTCATCAACAGGGAGAAAATACTGA[C/T]ACTTTCCACGAGTGACCACATCACTGGTAGCGCAG Y 2 1 2 1 101000 f 74 goat snp39143-scaffold498-2580201 12 71366615 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391790 Affx-122967043 AX-123262147 12 14200782 GTTATCATTTTCCAGGAGTTTTAATTTGAGAATTC[G/T]CTAGATGCTTTAAGATGCTATCTTGGTCTTTGCAG K 2 1 2 1 101000 r 74 goat snp5116-scaffold1176-13378 12 71334147 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399468 Affx-122961197 AX-123269823 12 14233482 TCAAGAATTCAAACACCAGTCGCAAATTTAGTCAA[C/T]TAAATTCTTTGCAAATCTAATGCCTTGGATTCCTT Y 2 1 2 1 101000 f 74 goat snp5117-scaffold1176-46078 12 71301384 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762939 Affx-986697468 AX-385250930 12 14244310 GGCTTGATGAGAAAATAGGGATCAGTCACCAAGAG[C/G]AAGTTATAATCAACTCATGTCCATTTTTCATTTGT S 4 1 2 1 600010 f 74 goat 12_14244310 12 14244310 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320779244 Affx-122967062 AX-385266348 12 14263652 CTCCTTTGCAGATGGAAAGAGCTTGAAAAGATGGC[G/T]AGAGCTTGAGGTGATGTGTTTCTGCTTGGAGCGCA K 2 1 2 1 101000 f 74 goat snp5118-scaffold1176-76248 12 71270936 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791368 Affx-122951680 AX-385278360 12 14294892 TTTTCTGTTTTGATCTGAGTTGTGGTTACATGAAT[A/G]CATTCACTTTGTGAAAACTCATCGAAGCTGGAAAT R 2 1 2 1 101000 r 74 goat snp5119-scaffold1176-107488 12 71239761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428511 Affx-122938762 AX-123298853 12 14324253 CTGCATTAGGCAGAACTTACTCCAGGCCAATGGGA[A/G]TTCTTATCTGCCAACTCTTGATGGGAAATGAGGTC R 2 1 2 1 101000 r 74 goat snp5120-scaffold1176-136849 12 71210283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426592 Affx-122939984 AX-123296938 12 14433319 CAGACGCATAGTACAGGAAAGAGAGGGGGCCAAAG[A/G]GCAGAGAAGACCTTTTATGTTTAAATTTTTCTTGT R 2 1 2 1 101000 f 74 goat snp5123-scaffold1176-245915 12 71102425 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454080 Affx-122919377 AX-123324413 12 14474561 CTATAAACATTCTCCCCTCCCAGGCTACCTTGGCT[C/T]GGGGCTGAAGAAATCCCTTCCCTTTCCTTCAGCAA Y 2 1 2 1 102000 r 74 goat snp5124-scaffold1176-287157 12 71060993 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447112 Affx-122924474 AX-123317448 12 14523874 AGCTAAGAAAATAAGAATCATAGAGGCCATGAGGG[A/G]TGGGGAATGGTTAATGATTTCCTTTTGGAGTTGTT R 2 1 2 1 101000 f 74 goat snp5125-scaffold1176-336470 12 71012479 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384468 Affx-122973082 AX-123254826 12 14564843 GATCTAACAATACAAATGTTGGCAGTCTGTAAAAG[C/T]GATGGTATATGGGTAACAGAATTTGAGAGTGAATA Y 2 1 2 1 101000 f 74 goat snp5126-scaffold1176-377439 12 70971552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443688 Affx-122927172 AX-123314025 12 14604961 TATGTCAATCACTGAATGACCAGTTGTCTACATTT[A/G]TTTAATGTTAGTGTTAAAACCAAAAAAAACAGTTT R 2 1 2 1 201000 r 74 goat snp5127-scaffold1176-417557 12 70942845 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428914 Affx-122938914 AX-123299256 12 14647353 TTTTGAGTTTGCAAACATATGAGTTGCTTTTGGCT[A/C]TGTTGTTAATATTACCAATTAAAATCCACAGGGTT M 2 1 2 1 101000 r 74 goat snp5128-scaffold1176-459949 12 70900575 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412430 Affx-122951423 AX-123282779 12 14677856 TTTCCAGAGGGCCCCTCTCTGAAGGAAGGTGCCCC[A/G]TGGAGTGAACAGGCCCTGGTGCCCCTCCCCCGCCT R 2 1 2 1 201000 r 74 goat snp5129-scaffold1176-490452 12 70870027 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452060 Affx-122920878 AX-123322393 12 14683567 AATATCCTTCATCCTGTGGCAGAGGGGGGACTCTA[C/T]GATAACCCAAAAGATTAACAAAGCAAACTTGAATG Y 2 1 2 1 201000 r 74 goat snp24182-scaffold246-3376690 12 70863835 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398121 Affx-122961702 AX-123268476 12 14713754 TCCCTTCCACTCCAGACAGCCCTGGCCCTGAGTTC[C/T]GGGGAAATGCTGGGTGTGGTTATACTGTTTTCAGC Y 2 1 2 1 202000 f 74 goat snp24181-scaffold246-3346503 12 70835167 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402626 Affx-122958400 AX-123272979 12 14744879 AGACCAAATCACCCTAAGAATCTTCTGTAAAGGGA[C/T]TGCATTTTATACCATTACAGTGTCAGGCCTAGGGC Y 2 1 2 1 101000 f 74 goat snp24180-scaffold246-3315378 12 70803971 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403627 Affx-122957542 AX-123273979 12 14815505 CGTGGGTCAAAGATGACCTCAACCTTAGAGCCACC[A/G]TTTTCATCACCTCCATCCACGAGGGATGGGACACA R 2 1 2 1 201000 f 74 goat snp24179-scaffold246-3244752 12 70732402 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276731 Affx-1111835491 AX-519550241 12 14824428 ATGTCACCTCCAGGGACCCTAGCACTTGTCTGGGA[C/G]CCTGGGCACAGGATGGATCAGCTAGTTCAGCTAGA S 4 1 2 1 102000 r 74 goat Random2.2K-1244 12 14824428 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406261 Affx-122956097 AX-123276613 12 14891733 CATTTTGTTATCTGGGTATGGAATTATTACGATGC[A/G]TTCTCTGACACCTGAGAGCTCCCAAGGGTTTGTGG R 2 1 2 1 101000 f 74 goat snp24178-scaffold246-3168524 12 70657142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762941 Affx-986697470 AX-385250932 12 14897689 ATGGTCCAGAGTCCCCAGAGAGAAGATGCTAAGTG[A/G]GAAAATACCGGGCTCCGACCTGGGGAAGCAGAGAC R 2 1 2 1 600010 f 74 goat 12_14897689 12 14897689 Ancestral_priority_1043 ancestry 0.466 neutral IMAGE 10K 10K ancestral 38393694 Affx-122965255 AX-123264049 12 14931562 CCCAGAAAACTGTTGACACATCTCTGTTTGTGTTG[C/T]AGATAGGAGACTGCTCTGAGTGTGTGTGTGTGTGT Y 2 1 2 1 101000 f 74 goat snp24177-scaffold246-3128695 12 70617329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444863 Affx-122926287 AX-123315200 12 14963856 TAGAATTTGAATTGAATCCATTTGGCAACGTTTTA[C/T]AGTTGGGGGTGGGGAGCAGGTGGGGTCCATCAGGA Y 2 1 2 1 201000 f 74 goat snp24176-scaffold246-3096401 12 70584556 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434805 Affx-122934811 AX-123305146 12 15005320 TGAGGAAGGGGCTCTGGAATCCAGACTCCTCATCT[A/C]TGGTGGTGTCAGGAGAGGCCCTTTAACCCAAGACT M 2 1 2 1 101000 f 74 goat snp24175-scaffold246-3054937 12 70543142 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448462 Affx-122923634 AX-123318798 12 15045928 TATTAAATAGTTACCAACAGTGATTGGGAGAATTG[C/T]AGTCTTTTCCAACCATTATCAGTTTACTTTTTAAC Y 2 1 2 1 101000 f 74 goat snp24174-scaffold246-3014329 12 70502637 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406911 Affx-122955619 AX-123277262 12 15109170 TTCACATGATGAATGTCTGTGGGCAAATCAGATGT[A/C]GTTTAGGTGGGGGCAACTATAGCAGATAACATAGC M 2 1 2 1 101000 f 74 goat snp24172-scaffold246-2951087 12 70438733 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434086 Affx-122934172 AX-123304427 12 15142832 TTACAAGATTAAATTCCCAGATTACCCCAAGAACC[A/C]AATGTGGTATTTTTGCTTTACATTTAGAAACCAGA M 2 1 2 1 101000 f 74 goat snp24171-scaffold246-2917425 12 70405009 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276733 Affx-1111835492 AX-519550243 12 15185016 CCGGGCTGTCAGAGTGGGGACCACAGAGCTTGCGT[A/C]CTGATTGTAGACTCACCCTGTCTTCTGTGCCTGTG M 2 1 2 1 101000 r 74 goat Random2.2K-1245 12 15185016 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320771851 Affx-122941890 AX-385259007 12 15191792 ATGTTGGCAAATAGAGACCTGCCTCAGTCTTTTCA[A/G]CAGATGCATAGTATGCTGTCATATGGCTGTACCAA R 2 1 2 1 101000 f 74 goat snp24170-scaffold246-2868465 12 70356242 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395970 Affx-122963557 AX-123266325 12 15225067 GAGATAGTAGGATAATGGACCAGATGAACCTCTCA[A/G]TTCTCTTCTGGGCGTGAGAATCTGAGAGCCATGTG R 2 1 2 1 201000 f 74 goat snp24169-scaffold246-2835190 12 70322914 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382321 Affx-122973900 AX-123252679 12 15275912 GGTGAGCACAAAAGGACCCGCACCGCAGGGGATCA[G/T]CACCATGTTCATGAGGCAGTTTGATTCCAGAAAAT K 2 1 2 1 101000 r 74 goat snp24168-scaffold246-2784345 12 70272183 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436493 Affx-122932960 AX-123306831 12 15337948 ATTCTGTACTGTTCCTTTCCTCTGGACCAGCTTGG[C/T]GGTGGTTTAGTCGCTCAGTCATGTTCGACTTTTGC Y 2 1 2 1 102000 f 74 goat snp24167-scaffold246-2722309 12 70212443 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429216 Affx-122937931 AX-123299558 12 15389151 AGGGGGAGAGGAGCTATTAGGGAGGGGCAGTTGCC[A/G]TTATTTATAGGGTAACCAGGGAGGCCTATCTGAGA R 2 1 2 1 101000 r 74 goat snp24166-scaffold246-2671106 12 70161061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411827 Affx-122951240 AX-123282177 12 15465703 CCCTCTTCCTAGCAAAGCCCACAGTGAGCTGTGTC[A/G]CTGTGACCAAGTCATTCAGTTTCTCTGGAATTCAG R 2 1 2 1 102000 r 74 goat snp24164-scaffold246-2594554 12 70084635 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448489 Affx-122923470 AX-123318825 12 15550934 TAGAGCACGTCAGATAAACCCGCATCAGAAAAGAT[A/G]TTGTGTTATTTCTCAGGATGGAGATTTGGTAGATT R 2 1 2 1 101000 f 74 goat snp24162-scaffold246-2509323 12 69998937 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383711 Affx-122972476 AX-123254069 12 15608924 CTCTCCTTTTTTCTAAGAGCTCTTCAACTCTAAAA[C/T]GACAAGGCTCTAAAAACTATTCCTCAAGTTTCCTC Y 2 1 2 1 101000 f 74 goat snp24161-scaffold246-2451333 12 69940600 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385478 Affx-122971287 AX-123255836 12 15666962 CACGGCACTCATCACTTTCTGTCTCACAGCATAGA[C/T]CTGATTTTCTCCACAGGACTCCCTAATACAGAGTT Y 2 1 2 1 101000 r 74 goat snp24160-scaffold246-2393295 12 69882627 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765558 Affx-986697472 AX-385253038 12 15668497 AAGGCCATCTGGCCAGTGTTCCTCTGCCCTATCCC[A/G]TTTCGTCCCTCCTGATTCCACAATGTTGACCCCAA R 2 1 2 1 600010 r 74 goat 12_15668497 12 15668497 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 38403601 Affx-122957559 AX-123273954 12 15697507 CACGAAATACACAATGTGTTTGGTTTTAATAAAAA[C/T]GAATGCATCTTGCTGCAAAACGGTTGTGCTTGGTG Y 2 1 2 1 101000 f 74 goat snp24159-scaffold246-2362750 12 69852148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769244 Affx-122927031 AX-385256417 12 15730792 CACTTTCATAATAACGATTTACCAGAAAATTAGCA[C/T]GTGAAAAAAATTCGAGGTGGCAGACAGCCATATGT Y 2 1 2 1 101000 r 74 goat snp24158-scaffold246-2329465 12 69818841 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762949 Affx-986697478 AX-385250940 12 15734604 CCCAGTCCATGACAACTAACAACCTGGGTCCTCTC[A/G]CCTTCTAAGAGGGTCCATATTTTGACTATGGAATG R 2 1 2 1 600010 f 74 goat 12_15734604 12 15734604 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 320765572 Affx-986697480 AX-385253052 12 15734611 CATGACAACTAACAACCTGGGTCCTCTCACCTTCT[A/G]AGAGGGTCCATATTTTGACTATGGAATGTGTGTCT R 2 1 2 1 600010 r 74 goat 12_15734611 12 15734611 Ancestral_priority_1043 ancestry 0.606 recommended IMAGE 10K 10K ancestral 38408072 Affx-122954733 AX-123278423 12 15761667 CTTGGAATCAATGATCTTTGCAGAGTCTAAGGCTA[C/T]GCTTCTCTGAGTGCTAGGGAGTCCAGTCAAGGCTT Y 2 1 2 1 201000 f 74 goat snp24157-scaffold246-2298590 12 69787797 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379754 Affx-122975859 AX-123250112 12 15792854 CATCACCCGTCTTGTCTAGCCTATGAAGTGGCCAC[A/G]TCAGACCCCTGAACATCATTCTTGCTATTGTCCTT R 2 1 2 1 101000 r 74 goat snp24156-scaffold246-2267403 12 69756646 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415805 Affx-122948898 AX-123286154 12 15822709 AAACAGGGCGGAGAAAGGGTGTGGCTTACTGGGTC[A/G]CCTCTCCAACTGGGTCAGGGCTAGGGCTCTAAGCT R 2 1 2 1 101000 f 74 goat snp24155-scaffold246-2237548 12 69726746 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450970 Affx-122921742 AX-123321304 12 15869005 CATATTTCCTATGGCTGTTCCACATTCCTACCAGA[G/T]AAACATCCTCCACTCAGTAAGCCTTGAATTCATCA K 2 1 2 1 101000 r 74 goat snp24154-scaffold246-2191252 12 69680687 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276593 Affx-1111835493 AX-519550104 12 15909528 GAATTATCATATGACAGTTCTACTGTAGAGTATAA[A/G]CCCAAAAGAATTGAAAAAGTCTTGAAGAGATAGCT R 2 1 2 1 202000 f 74 goat Random2.2K-1246 12 15909528 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397093 Affx-122962708 AX-123267448 12 15928401 CATGCAAGGCAAGGAGCAAGGCACAGTTGACCCTC[A/G]AAGAACACAAGCTTGAGACCCGCATGCAGACTCCT R 2 1 2 1 101000 r 74 goat snp24153-scaffold246-2131856 12 69621057 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799912 Affx-122970401 AX-385286838 12 15986313 AATGTTGTGGGACTTCTCATAAATCTCACATGTCT[A/G]TGAACCTCCTCTATCTTCACTTTTGTCTAAATTTC R 2 1 2 1 101000 f 74 goat snp24152-scaffold246-2073944 12 69563081 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799344 Affx-122922807 AX-385286274 12 16016068 TTTTATCTTCTCAACAACCCGTTGATTTGAGCATG[C/T]GATACTGTTCACATGTTGTAAAGGAGGAGAAACTG Y 2 1 2 1 101000 r 74 goat snp24151-scaffold246-2044189 12 69532922 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798756 Affx-122943543 AX-385285687 12 16053513 GCCAGAGCGGGATGTAAGCATCTGATCTGACTTAG[A/G]GTTTGCAACAGCCTCTATCATTGTGCCCGGACAGT R 2 1 2 1 101000 r 74 goat snp24150-scaffold246-2006744 12 69495201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430151 Affx-122937383 AX-123300492 12 16131232 ACTTCCATGAAAGAAATCAAAGCAATTAATCTAAC[C/T]AAATACTAAGAGCTCAGAGCATTTAGAAATGCATT Y 2 1 2 1 101000 r 74 goat snp24149-scaffold246-1929025 12 69416113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276594 Affx-1111835494 AX-519550106 12 16171574 AGGGCAGAAACTAAGCCTTATTCATCCCTGAAACT[A/G]AAGAGGTATCTGACTTCATGTCTGATGAATGAATA R 2 1 2 1 101000 f 74 goat Random2.2K-1247 12 16171574 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320798140 Affx-122946613 AX-385285075 12 16204743 GAGCCTCCATTCTTAATCCCTTGAGAAATGTAAAC[A/G]TTCTCCTTAAATCAGCATAAGGAAGACTGAAGTTA R 2 1 2 1 101000 f 74 goat snp24147-scaffold246-1855514 12 69342507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476284 Affx-1251763791 AX-586011703 12 16221974 TCAGTGTCATCAATGATTGCAGTGAAGAATCTAAG[-/CTACTCCATTTTGTTAACAGAAAAATTCCATTTTGTAAGGTGCAAAGAAATCGAGGAAAACAGAATGGGAAAGACTAGAG]ATCTCTCCAAGATTTCGAGACTTGGGCATAACATT - 4 1 4 1 20000 f 74 goat SV_173 12 16221974 - deletion junction SV-TF-chip 539476537 Affx-1251763791 AX-586011926 12 16221974 TCAGTGTCATCAATGATTGCAGTGAAGAATCTAAG[-/CTACTCCATTTTGTTAACAGAAAAATTCCATTTTGTAAGGTGCAAAGAAATCGAGGAAAACAGAATGGGAAAGACTAGAG]ATCTCTCCAAGATTTCGAGACTTGGGCATAACATT - 4 1 4 1 20000 r 74 goat SV_173 12 16221974 - deletion junction SV-TF-chip 562165213 Affx-1251763791 AX-606940625 12 16221974 TCAGTGTCATCAATGATTGCAGTGAAGAATCTAAG[-/CTACTCCATTTTGTTAACAGAAAAATTCCATTTTGTAAGGTGCAAAGAAATCGAGGAAAACAGAATGGGAAAGACTAGAG]ATCTCTCCAAGATTTCGAGACTTGGGCATAACATT - 8 1 4 1 20100 f 74 goat SV_173 12 16221974 - deletion junction SV-TF-chip 562165312 Affx-1251763791 AX-606940723 12 16221974 TCAGTGTCATCAATGATTGCAGTGAAGAATCTAAG[-/CTACTCCATTTTGTTAACAGAAAAATTCCATTTTGTAAGGTGCAAAGAAATCGAGGAAAACAGAATGGGAAAGACTAGAG]ATCTCTCCAAGATTTCGAGACTTGGGCATAACATT - 8 1 4 1 20100 f 74 goat SV_173 12 16221974 - deletion junction SV-TF-chip 562165734 Affx-1251763791 AX-606941144 12 16221974 TCAGTGTCATCAATGATTGCAGTGAAGAATCTAAG[-/CTACTCCATTTTGTTAACAGAAAAATTCCATTTTGTAAGGTGCAAAGAAATCGAGGAAAACAGAATGGGAAAGACTAGAG]ATCTCTCCAAGATTTCGAGACTTGGGCATAACATT - 8 1 4 1 20100 r 74 goat SV_173 12 16221974 - deletion junction SV-TF-chip 562165777 Affx-1251763791 AX-606941186 12 16221974 TCAGTGTCATCAATGATTGCAGTGAAGAATCTAAG[-/CTACTCCATTTTGTTAACAGAAAAATTCCATTTTGTAAGGTGCAAAGAAATCGAGGAAAACAGAATGGGAAAGACTAGAG]ATCTCTCCAAGATTTCGAGACTTGGGCATAACATT - 8 1 4 1 20100 r 74 goat SV_173 12 16221974 - deletion junction SV-TF-chip 562165847 Affx-1251763791 AX-606941256 12 16221974 TCAGTGTCATCAATGATTGCAGTGAAGAATCTAAG[-/CTACTCCATTTTGTTAACAGAAAAATTCCATTTTGTAAGGTGCAAAGAAATCGAGGAAAACAGAATGGGAAAGACTAGAG]ATCTCTCCAAGATTTCGAGACTTGGGCATAACATT - 8 1 4 1 20100 r 74 goat SV_173 12 16221974 - deletion junction SV-TF-chip 562166417 Affx-1251763791 AX-606941825 12 16221974 TCAGTGTCATCAATGATTGCAGTGAAGAATCTAAG[-/CTACTCCATTTTGTTAACAGAAAAATTCCATTTTGTAAGGTGCAAAGAAATCGAGGAAAACAGAATGGGAAAGACTAGAG]ATCTCTCCAAGATTTCGAGACTTGGGCATAACATT - 8 1 4 1 20100 f 74 goat SV_173 12 16221974 - deletion junction SV-TF-chip 320781793 Affx-122927914 AX-385268875 12 16238175 CACCCTTATTCTTTACCTGTCCAATAATTCAACTT[A/C]GCTTTCAAGACCCAGTTAAATTTCACATTCTCTAC M 2 1 2 1 101000 r 74 goat snp24146-scaffold246-1822082 12 69308689 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452274 Affx-122920757 AX-123322607 12 16269554 CCACTCCTACTCAGCCATCCTCCTATTTTGGCCTC[A/G]TGCCCCATTCACTTTCATACCCTTTATTCTGCTTT R 2 1 2 1 101000 r 74 goat snp24145-scaffold246-1790703 12 69277221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390736 Affx-122967915 AX-123261093 12 16316993 TGTATGACAGCATGCGGATAGTACCTGGCACAGAG[C/T]GGAGACCTAGAAAAACGTTCTTTAAATGAATGAAT Y 2 1 2 1 201000 r 74 goat snp24144-scaffold246-1743264 12 69228926 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453596 Affx-122920143 AX-123323929 12 16424295 CTTCCGAGTAATACAGAAAAGATGCACAGTCCAGG[C/T]GAGGTTCAGAGAGCCTTCCTCTCCATCTGTTTTGT Y 2 1 2 1 201000 f 74 goat snp24142-scaffold246-1635962 12 69121106 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274292 Affx-1111834165 AX-519547889 12 16478579 CCACGATGGTCAATGCTTTGCTGCAGCCTCTTGGG[A/G]TGATTGGACCAG R 2 1 2 1 102000 f 74 goat GoatD01.022809 12 16478579 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38379962 Affx-122975637 AX-123250320 12 16515147 TTCTGAGCACAATGGAGTCCTAACCAGTTTAGCTG[C/T]ACCCACATATCTGAAAAGAAGTGTGGTCAGGGTTT Y 2 1 2 1 201000 r 74 goat snp24140-scaffold246-1545110 12 69028987 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271899 Affx-1111832946 AX-508221019 12 16545695 GGGCTCTGTATCAACCTAGAGGGGTGGGATGGGGC[A/G]GGAGAGGGGAGGAAGGTTCAAAAGGGAAGGGATAT R 2 1 2 1 303000 f 74 goat 12_16545695_AF-PAKI 12 16545695 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320794005 Affx-122929845 AX-385280974 12 16548586 GTGCTTTGTGAACGTTAGTAATTGTTGAGAAAGAC[A/G]AATAATGGAGAGTGTGTCTATGAATTCTCTGTGTG R 2 1 2 1 101000 r 74 goat snp24139-scaffold246-1511671 12 68995069 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795409 Affx-122926916 AX-385282365 12 16592947 TCCATGTTAAGCATAATATTTCTGTTGAGGTCAAA[G/T]AAGACCTATCTGTTGCAAATATGTCAGTTGATATG K 2 1 2 1 201000 r 74 goat snp24138-scaffold246-1467310 12 68950541 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441977 Affx-122928444 AX-123312314 12 16640968 TTCATGTGTAATGTAGATGTGCACTGCGTATTGTC[A/G]CAAAGAGGGCATGTTACTTATTTTTTCTTAGTTCA R 2 1 2 1 101000 f 74 goat snp24137-scaffold246-1419289 12 68902382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448598 Affx-122923393 AX-123318934 12 16689432 CTTTTTAAGGTCGCTGTGAGAATGAAATGAACTAA[C/T]ATATGTTAAGCACTTGAACAGTGCCTGGAACATAA Y 2 1 2 1 202000 f 74 goat snp24136-scaffold246-1370825 12 68853167 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276596 Affx-1111835495 AX-519550107 12 16706288 GAAAAAAATCAGATCCCATATGTGGGGCCCTAAAT[A/G]GGAATCCTTAAAAAAGATGGGCTAGCTTTGTGGTC R 2 1 2 1 101000 f 74 goat Random2.2K-1248 12 16706288 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320780551 Affx-122956048 AX-385267642 12 16743551 ATTTTTATCTAAAGAAAGAGGTCTGATGTGAAATT[G/T]CTTTCTTCATCACATTCTGGGCATATCTGAGAAAA K 2 1 2 1 101000 r 74 goat snp24135-scaffold246-1316706 12 68798727 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790900 Affx-122932492 AX-385277897 12 16811540 GTTTGAAAATACTGCCCTAGGGGCAAGTTTTACCT[A/C]TTGTGAATAATTGAAGTTAGGGATAGGAGAATGGT M 2 1 2 1 201000 r 74 goat snp24134-scaffold246-1248717 12 68729048 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766967 Affx-122958568 AX-385254266 12 16868650 TGTTGGTGGACCAGTGGATTGGAAAATAAAAGGGA[A/G]TTCCATGTGTACCTCAAATCAAACTGCTGTGTACA R 2 1 2 1 101000 f 74 goat snp24133-scaffold246-1191607 12 68671118 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769807 Affx-122953671 AX-385256977 12 16907185 GGAAAAGAGTGTATCTGGATATATGTTTTTGATTC[A/G]TCTCATGAGTCCACGCTACTGGTAATTATGTAGGA R 2 1 2 1 201000 f 74 goat snp24132-scaffold246-1153072 12 68632415 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796934 Affx-122933475 AX-385283876 12 16956934 TGGCTTGAACAAGATTTTGATAATGGAAATAGAAA[C/T]GGATAATAGGAACAGGACAGATTTGGCTGAGGAGA Y 2 1 2 1 101000 r 74 goat snp24131-scaffold246-1103323 12 68583047 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453461 Affx-122919853 AX-123323794 12 16985858 TATCATTTTAATATACTATATAAATTAAATATATC[A/G]TAAACTCCAACAGTCATAATTATAGCACACTAAAG R 2 1 2 1 102000 r 74 goat snp24130-scaffold246-1074399 12 68554021 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774391 Affx-122949964 AX-385261527 12 17023113 AGTAAGAAAAACTTAATGATTACGAGACATACAAC[G/T]AGTATGCAATTGTTAGAATTCTGATTCCGACCTAT K 2 1 2 1 101000 r 74 goat snp24129-scaffold246-1037144 12 68516821 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769636 Affx-122960668 AX-385256806 12 17064107 CTCTCATTTCCACTATCCTTCTCTGGGCTCCTTCA[C/T]GGTTCTTTAGTACCCCTTCATGTGTACCACATTTG Y 2 1 2 1 101000 f 74 goat snp24128-scaffold246-996150 12 68475484 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275951 Affx-1111835089 AX-519549508 12 17065165 GCGCCCGGGCCCCAGACGGGAGCGCACAGCCCAGA[C/G]AGCCGAGCAGAAGCCCCCACCCAAGAGGGCTCATG S 4 1 2 1 102000 r 74 goat ilmnseq_rs649821051 12 17065165 G C 1 neutral Goat_IGGC_65K_v2 Illumina 468276216 Affx-1111835225 AX-519549766 12 17065199 TGTCTGGGCTGTGCGCTCCCGTCTGGGGCCCGGGC[A/G]CAGTTTCCCCGGGTCTGCATGACGGTGGGCAGCCT R 2 1 2 1 102000 r 74 goat ilmnseq_rs665752882 12 17065199 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468272468 Affx-1111834974 AX-169477734 12 17065247 GTCTGCATGACGGTGGGCAGCCTGCAGGCCAAGGA[A/C]TGCTGCCCGCCGCTGGGCGCCGACCCCGCCAACGT M 2 1 2 1 202000 r 74 goat ilmnseq_rs635522438 12 17065247 A C 2 neutral Goat_IGGC_65K_v2 Illumina 468276004 Affx-1111835196 AX-519549559 12 17065408 CGACCGCGAGCGATGGCCCCGGAAGTTCTTCGACC[A/G]GACCTGCAGGTGCACAGGTGAGCAGGCAGGCGGAT R 2 1 2 1 102000 f 74 goat ilmnseq_rs662676427 12 17065408 A G 1 neutral Goat_IGGC_65K_v2 Illumina 468276085 Affx-1111835234 AX-519549637 12 17065799 TTCTGAGATGGGTTTGCACTTGTTGAAGAGGGAGG[A/G]CGGGTGATTCTTGGCATCGGTAAGACGGACGTTGG R 2 1 2 1 102000 f 74 goat ilmnseq_rs666851133 12 17065799 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275984 Affx-1111835105 AX-519549540 12 17065817 CTTCAGAACACCTACCCCCCAACGTCCGTCTTACC[A/G]ATGCCAAGAATCACCCGCCCTCCCTCTTCAACAAG R 2 1 2 1 103000 r 74 goat ilmnseq_rs652044295 12 17065817 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275662 Affx-1111835022 AX-519549232 12 17074761 TCGGGGTGTGGAGTGTACTTTGCGAGGTCTAAGGC[A/G]CCCAAGAATTGCTCCCTCTCTTGAGGGGTCAAGGA R 2 1 2 1 202000 f 74 goat ilmnseq_rs641975220 12 17074761 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276192 Affx-1111835213 AX-519549742 12 17074786 CCAGTGTTGCGTGGTGATCACGTAGTCGGGGTGTG[A/G]AGTGTACTTTGCGAGGTCTAAGGCGCCCAAGAATT R 2 1 2 1 102000 r 74 goat ilmnseq_rs663929118 12 17074786 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468275838 Affx-1111835109 AX-519549401 12 17074794 AGGCCCAGCCAGTGTTGCGTGGTGATCACGTAGTC[A/G]GGGTGTGGAGTGTACTTTGCGAGGTCTAAGGCGCC R 2 1 2 1 201000 f 74 goat ilmnseq_rs653011549 12 17074794 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468275612 Affx-1111834996 AX-519549182 12 17074869 TAATAATGGAGCCACACAAAGAAATCGTAAATGCT[A/G]CAGTTGGCGATCTGTGGTTGGGTCCCATTGGGCCC R 2 1 2 1 101000 f 74 goat ilmnseq_rs638065121 12 17074869 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275893 Affx-1111835137 AX-519549451 12 17077168 GAATGTCTGGTCATGCCCTTTGCTTTTAGCGCCTT[A/G]CTGGCAACGAGTCCTTCGCTTTGCCCTACTGGAAC R 2 1 2 1 102000 f 74 goat ilmnseq_rs655924633 12 17077168 A G 1 neutral Goat_IGGC_65K_v2 Illumina 468276185 Affx-1111835283 AX-519549735 12 17077249 AATCAGAGTCGGATCGTCTTGCCTTGCTGCCCCAA[A/G]CAGCTGGTCTGTGCACACGTCACACTCGTTACTGC R 2 1 2 1 102000 f 74 goat ilmnseq_rs671884251 12 17077249 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468275910 Affx-1111835071 AX-519549468 12 17079907 ATTTGATTTCTTTTCAACAAACCTTCATAGGTTCC[A/G]TTACACAAGGTGACTCGGCGGTTGTAGTCATTCAA R 2 1 2 1 201000 r 74 goat ilmnseq_rs647461641 12 17079907 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468276109 Affx-1111835245 AX-519549660 12 17079923 CTCACTGTTTCTTCCCATTTGATTTCTTTTCAACA[A/G]ACCTTCATAGGTTCCATTACACAAGGTGACTCGGC R 2 1 2 1 201000 f 74 goat ilmnseq_rs667569985 12 17079923 T C 2 recommended Goat_IGGC_65K_v2 Illumina 463210031 Affx-1109868624 AX-514696157 12 17080003 ACTTTAAAAGACATACAAAATTGCCTGTCTCTCAA[C/T]AAGTTTGACAGTCCTCCGTTCTTCCAGAACTCTAC Y 2 1 2 1 101000 r 74 goat ilmnseq_rs659730021 12 17080003 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276263 Affx-1111835249 AX-519549809 12 17081688 GGAAGGGTTTGGCAAAGCAGATGGGACCCTGGACT[A/C]TCAAGTGATGAGTCTTCATAACCTGGTTCATTCCT M 2 1 2 1 101000 r 74 goat ilmnseq_rs667832562 12 17081688 C A 1 recommended Goat_IGGC_65K_v2 Illumina 468275607 Affx-1111834993 AX-519549177 12 17081741 ATAACCTGGTTCATTCCTTCCTGAATGGGACAAGC[A/G]CTTTGCCGCATTCTGCTGCCAATGATCCTGTTTTT R 2 1 2 1 101000 f 74 goat ilmnseq_rs637865895 12 17081741 G A 1 recommended Goat_IGGC_65K_v2 Illumina 38429413 Affx-122938521 AX-123299755 12 17093894 CAGTGACAAGGCACTATCTGTGAATTCCCTGTGAA[G/T]AAAGAAGTGTGCCTTTACTAGAACCAGAATCTGCC K 2 1 2 1 101000 r 74 goat snp24127-scaffold246-966363 12 68446479 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276103 Affx-1111835242 AX-519549654 12 17099945 GGATTGAATCTTTTCATCCACTCATCAAAAATGGC[A/G]TCGGTGAAGGAATGAAGGACCTGCAAGACAGTTGA R 2 1 2 1 101000 f 74 goat ilmnseq_rs667376420 12 17099945 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275979 Affx-1111835102 AX-519549535 12 17099995 TCCGATTGTGACCAATGGGTGCCAGCTCCTGAGGC[A/C]AGGCATCCACAGGGGGATTGAATCTTTTCATCCAC M 2 1 2 1 101000 r 74 goat ilmnseq_rs651778975 12 17099995 G T 1 recommended Goat_IGGC_65K_v2 Illumina 463208015 Affx-1109868644 AX-514694168 12 17104256 AGACTCTTCTGCTTTAATTTCAGTTGGAGAAACTC[C/G]AGATTGGACCACAGTGCTCTCAGTGGTTACGGGGA S 4 1 2 1 101000 f 74 goat ilmnseq_rs649193758 12 17104256 C G 1 recommended Goat_IGGC_65K_v2 Illumina 320790825 Affx-122928587 AX-385277825 12 17172418 GGGACAGAACCTCCAAGGTCCTTCAACTGTGAAAA[C/T]TGTTTTCCTGGACAACAATTTTTCCACCTCAGAAA Y 2 1 2 1 201000 r 74 goat snp24125-scaffold246-887839 12 68368049 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432211 Affx-122936377 AX-123302552 12 17217680 TCAGGTGGTGGTGCCCTGGGTTAAGGTGGTCTAGC[A/G]TGGAGGTGTTGAAAGAGATCAGGGTCTGGACACAT R 2 1 2 1 201000 f 74 goat snp24124-scaffold246-842577 12 68322561 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430972 Affx-122936813 AX-123301313 12 17250883 CACTTTGCCAACATTTGGTCCTGATGTCAAGGGAT[A/C]GTGCAGGAAGTCTGACTAAAAGCTAGGCCAAGCTG M 2 1 2 1 101000 r 74 goat snp24123-scaffold246-809374 12 68289369 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390941 Affx-122967068 AX-123261298 12 17311611 TGGCATGCATTTCTTATAGTAGATGTTCAGGAAGA[A/C]GGGGAGGTTGGGTGAGAGAGCTGGTAGATGAATTC M 2 1 2 1 101000 f 74 goat snp24122-scaffold246-748646 12 68231615 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772895 Affx-122950646 AX-385260040 12 17353915 TCAACCAGCAACCTCCCAAACCAAAAAATGTCGAA[A/C]CTTTGCGAGTGAAAACAGCGACAATAAGTAGGAAT M 2 1 2 1 101000 f 74 goat snp24121-scaffold246-706342 12 68189019 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386080 Affx-122971450 AX-123256438 12 17390338 CCATCCTTAACTTCTCTCTTTCTCCCACAGCCAAC[A/G]TGCAAGCCAATAATTCCGTTTGTTCTACCTGCAAT R 2 1 2 1 201000 r 74 goat snp24120-scaffold246-669919 12 68151647 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433395 Affx-122935106 AX-123303736 12 17443135 GCCAGTGGGGTCCATATAAGTCCAGAATGAGAAGT[G/T]ACATCCAAGCGTTTGCACAGGACTGGCTTTTGCAG K 2 1 2 1 101000 f 74 goat snp24119-scaffold246-617122 12 68098323 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274135 Affx-1111834061 AX-519547739 12 17466649 ATGTACAGCTGCAGCATACACACTTGAAATATTCT[A/G]TTAGTTAGAAATATTAAAGTGTAAAGTCGCTCACA R 2 1 2 1 101000 f 74 goat GoatD01.016487 12 17466649 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320801911 Affx-122965700 AX-385288816 12 17486400 TTGCTTTCAGTCCTTGTTTGCCTGATCTGCCAAGA[A/G]CCTTCAGCACAGTCTAGGCCCCATCTCTTTCTTTC R 2 1 2 1 102000 r 74 goat snp24118-scaffold246-573857 12 68055501 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773407 Affx-122967069 AX-385260549 12 17523629 AAATCCAAGAAATGTATTTAACATCTGCTTAAAGT[G/T]AATAAATATAATTTGTTCATCTTGCTGCCCAGATA K 2 1 2 1 303000 r 74 goat snp24117-scaffold246-536628 12 68018115 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422630 Affx-122943708 AX-123292976 12 17554052 CACAAAGCACAGAAGCCTTCTTGACCTTGACATTG[C/T]CTTACACCTGAGATAAACCAGCTTTATTCTTAAGA Y 2 1 2 1 201000 r 74 goat snp24116-scaffold246-506205 12 67987458 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414777 Affx-122949239 AX-123285126 12 17585005 TGAGCTTGGGCAGCAGGGAAAGACACTGAAGATGG[C/T]GCGGGGGTCTGACTGGATTTGTGCTCAGAAAAACC Y 2 1 2 1 101000 r 74 goat snp24115-scaffold246-475252 12 67956709 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783207 Affx-122945103 AX-385270274 12 17629255 GGAGCAGTAAGGACTTTAAATATTGTTTACAGACT[A/G]TAACTTTTATCAAGCTAGGTTATTTATGTCTCTCC R 2 1 2 1 101000 f 74 goat snp24114-scaffold246-431002 12 67913298 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786344 Affx-122941257 AX-385273378 12 17661464 AATTTTTTTATGTAAATAAAAGTTTGAATACAACC[A/G]CTAGACGGCATGATGAAGTAATCATGTGCTTACAT R 2 1 2 1 201000 f 74 goat snp24113-scaffold246-398793 12 67881068 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390668 Affx-122967127 AX-123261025 12 17691989 AATGGTACTCCAGAAGAGTGACTCTTAAAAATATG[C/T]GTAATTTGGGACTTCCTTGGTGGTCCAGTGGTCGA Y 2 1 2 1 201000 f 74 goat snp24112-scaffold246-368268 12 67850346 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444453 Affx-122926548 AX-123314790 12 17778553 TTTCCACCCCATAGCAAGAAATGGGTGATCCACCA[C/T]TGACCAGAGGGGGTCCTAAAGGTGGAAAGATTCAC Y 2 1 2 1 101000 f 74 goat snp24110-scaffold246-281704 12 67763063 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451142 Affx-122921368 AX-123321476 12 17826439 GAACAAGGCTCATCTGGTCAGGTCTGGGCTTTGAT[A/G]TTACTCTACCTATAAGCTAGTAAGTTGGCCTGGTA R 2 1 2 1 101000 r 74 goat snp24109-scaffold246-233818 12 67714890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775770 Affx-122973893 AX-385262901 12 17859850 TCCACTGGTTATTTGGACTTATTACATACAGATCC[A/G]CATGCTCTACAAATGGAGATGATTGTTTTACTACC R 2 1 2 1 101000 r 74 goat snp24108-scaffold246-200407 12 67681655 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788633 Affx-122946164 AX-385275650 12 17915621 ATGCACCATTAGGAGCATCATTAGACTACTTGCAG[A/G]AATGTACTATCCATTTCTGTGGACTAGAAGTGTTA R 2 1 2 1 101000 r 74 goat snp24107-scaffold246-144636 12 67625688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443611 Affx-122927306 AX-123313948 12 17967564 AAGTTGCAAAGATAATGCCAACCACAAACGTATCA[C/T]GGCAAAATAAAGAGCAGATCCTCCCAGAGGAGACG Y 2 1 2 1 101000 f 74 goat snp24106-scaffold246-92693 12 67573673 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421478 Affx-122943921 AX-123291825 12 17997170 CCTACTTCTCATTTCCTTGGCTTTAGAGTTCAGAT[A/G]TACTTGAGCTGGATTAAGTTCTCCATTATCTTCTG R 2 1 2 1 101000 r 74 goat snp24105-scaffold246-63087 12 67544816 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762953 Affx-986697482 AX-385250944 12 17999423 GATTTTCACTTATATTCTGTTATTTGAAACTCAAA[C/T]AAAAAATGAAAGTCCCTCAAAGGTATGGCTCCAAT Y 2 1 2 1 600010 f 74 goat 12_17999423 12 17999423 Ancestral_priority_1043 ancestry 0.61 recommended IMAGE 10K 10K ancestral 320765579 Affx-986697484 AX-385253059 12 17999424 ATTTTCACTTATATTCTGTTATTTGAAACTCAAAT[A/C]AAAAATGAAAGTCCCTCAAAGGTATGGCTCCAATA M 2 1 2 1 600010 r 74 goat 12_17999424 12 17999424 Ancestral_priority_1043 ancestry 0.582 neutral IMAGE 10K 10K ancestral 38397610 Affx-122961978 AX-123267965 12 18036589 TGTCACAATTGACTGTTTATCATTATGGAATATCT[A/G]TTTCCTTCACTGGACACTGGAGTGGGCAGCCTTTC R 2 1 2 1 201000 f 74 goat snp24104-scaffold246-23668 12 67505314 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803205 Affx-986696223 AX-385290064 12 18037229 AAGTGCTTGTATTCAAGGAAGCTTATTTTACTTAA[C/T]AATACTCTAACATGAAAGAGTAGTGATACTGGCAA Y 2 1 2 1 600010 f 74 goat 12_18037229 12 18037229 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 320785473 Affx-122926308 AX-385272518 12 18094608 CATGTGGCTTCTGTAAAATGATTTCTTCACTTACA[A/G]TGAATGGGCTGTCAGATTCCCAGGTGTCCTAGAAT R 2 1 2 1 101000 r 74 goat snp41088-scaffold531-2123994 12 67446568 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452078 Affx-122920865 AX-123322411 12 18131147 AACCTCTCTGAGCCTCAGTGTCTAATCCTATAAAA[C/T]GGGAAGGATACCCACTTGGCAGAATTAGGAGAGTT Y 2 1 2 1 303000 r 74 goat snp41087-scaffold531-2087455 12 67410841 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383283 Affx-122972721 AX-123253641 12 18184849 TCATTTTTATATAAATAAGAATTTTGAAACTAAGC[A/G]TTTAAGAACATTCGAATACTTCTTGAGCATCCTAT R 2 1 2 1 101000 r 74 goat snp41086-scaffold531-2033753 12 67356900 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453412 Affx-122919891 AX-123323745 12 18261791 TGTCAGCATGGAGGTCTGTTCTATCAGTGTTTCTC[A/G]TCTGCTCTGTTGTCCTAGGGGTGCCAGCTAGGGAT R 2 1 2 1 101000 f 74 goat snp41085-scaffold531-1956811 12 67279830 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274593 Affx-1111834385 AX-519548182 12 18279471 GCTGTGGTTTGTCAACTGATGGATTTCACTGCAGG[A/G]TGGTTCAAGTAT R 2 1 2 1 101000 f 74 goat GoatD01.033012 12 18279471 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320787958 Affx-122969345 AX-385274979 12 18295269 AAACAACCATAGCTGTATTAGTCTTGCTGTATGAT[C/T]ACAGGTTTGTGTATAGTAAGGAATTGTTCTTTAAG Y 2 1 2 1 101000 f 74 goat snp41084-scaffold531-1923333 12 67245939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788104 Affx-122962714 AX-385275124 12 18337996 CAACCCGCATGCTAGTCATAGAGTTAACTTGGAAA[C/T]ACTGTTCTAACTTCCAGACCTTTATGAAAATCACA Y 2 1 2 1 101000 f 74 goat snp41083-scaffold531-1880606 12 67202626 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393033 Affx-122965635 AX-123263390 12 18405909 CAAATGAGTCTCACTAAAGTTCTTTTAAACAAATG[A/G]ATTGGTTGGTTGTACAGTTGCCATTATATTTTGGA R 2 1 2 1 101000 r 74 goat snp41082-scaffold531-1812693 12 67134820 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778518 Affx-122955251 AX-385265631 12 18450717 TTTCAGAAAGATCCATGTAAGGCGTTTGGTTGTCA[C/T]GGCTCTTAAAAGAGATGTTTTAACTTGAATTGTGG Y 2 1 2 1 101000 r 74 goat snp41081-scaffold531-1767885 12 67089977 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803354 Affx-122970916 AX-385290190 12 18510308 TTATTAACCTATCTATAGAATGACTTCATAGCAAA[G/T]ATAACAAGTAAGGAAGTTGGAAGTGAGCCAGTCTG K 2 1 2 1 101000 r 74 goat snp41080-scaffold531-1708294 12 67029891 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793131 Affx-122922979 AX-385280109 12 18540249 AAAATAAAATGAAATACAGATTATGTACACTTTGT[C/T]AAGATGCTGCTTCTATTATGCCAGTTTTGACAAAG Y 2 1 2 1 101000 r 74 goat snp41079-scaffold531-1678353 12 66999737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781740 Affx-122923184 AX-385268822 12 18579654 CAGATTTTACATTTCCCTTAGTGATTTACTATTAA[C/T]GTTCTACAGGAGTAAAATTATGACCTGAGCAAGCA Y 2 1 2 1 101000 r 74 goat snp41078-scaffold531-1638948 12 66960210 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390963 Affx-122967052 AX-123261320 12 18610965 GACAAGCCAGTGCCTCAGCCTGCTGTCCTGCCTGA[A/G]ACAACTGCTCTTGTCCACAGCTCTCCTGGCATGTA R 2 1 2 1 201000 r 74 goat snp41077-scaffold531-1607637 12 66928927 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769189 Affx-122955800 AX-385256364 12 18654067 GAACTAGTGGATGTCCAGACAGAGCCACCCAACTA[C/T]ACTAAGATAGGCACCTTTTCAGTGACCCATGTGGA Y 2 1 2 1 101000 f 74 goat snp41076-scaffold531-1564535 12 66885920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771275 Affx-122921128 AX-385258433 12 18710612 TGCTTCTGCTGTCAGTTAAACAAGCCTCACCTTTC[A/G]CATCAGAAACCTATTCTGTTCTGCTGACCAAGCAG R 2 1 2 1 101000 f 74 goat snp41075-scaffold531-1507990 12 66829586 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785709 Affx-122934719 AX-385272750 12 18787753 TTTCATTGACATGATCACAAAATTGATATTTTAAT[C/T]AAATATCTGGTTGGACCAACTGGACCGTTTGGTGC Y 2 1 2 1 201000 f 74 goat snp41073-scaffold531-1430849 12 66751645 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433862 Affx-122934429 AX-123304203 12 18817621 CCTCATCCTACGCCTTTTCTGTATGCCCACTGCAC[C/T]CTAGCTCTACAGCGATCTGATAAGGCTTGTCAACA Y 2 1 2 1 101000 r 74 goat snp41072-scaffold531-1400981 12 66721981 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795049 Affx-122924802 AX-385282008 12 18878867 CAGTTCCCCTAGAAGGACAGAATTAGGAGTAGATA[C/T]GGATTTTTCAACTCCATTGTTGTGTTACTTTGTGG Y 2 1 2 1 102000 f 74 goat snp41071-scaffold531-1339735 12 66660067 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380515 Affx-122975691 AX-123250873 12 18971056 TTCTCCATGAGACACAGTGTGAGAAATAATTTACT[C/T]AAGTATGATTATTTTCTTTGGGTAGAGATCAACAA Y 2 1 2 1 101000 f 74 goat snp41069-scaffold531-1247546 12 66566872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773662 Affx-122959259 AX-385260802 12 19010065 TTGGCAAATACCACTGGAAAATCTGTTCATATCTA[C/T]GTGTCTAGTAAAATCTATGGTTTGAGGTAACCTCA Y 2 1 2 1 101000 f 74 goat snp41068-scaffold531-1208537 12 66527311 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271901 Affx-1111832947 AX-519545682 12 19045833 ACTCCAATCCTGTACCCCATGAGGATGCTGTGAAA[A/C]GTTTCTGAGGACTGCCTTTGCTGTGGGGGCCAGGG M 2 1 2 1 102000 f 74 goat 12_19045833_AF-PAKI 12 19045833 G T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38422476 Affx-122943323 AX-123292822 12 19056655 TAAATGTCCTTTCTTTAACTGAAAGAACTAGGAAA[C/T]GTCTTAATGTCTAATGTTAAAAAAGCATAAGAAAG Y 2 1 2 1 101000 r 74 goat snp41067-scaffold531-1161947 12 66480550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419345 Affx-122945646 AX-123289693 12 19091398 TGGGTGCCATGTTGGACAGCACAGCTTTAGAAGGC[G/T]AGTCTAGATAAACTAAGTTCATGGGGCTTGTTGAA K 2 1 2 1 101000 r 74 goat snp41066-scaffold531-1127204 12 66446070 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443198 Affx-122927591 AX-123313535 12 19121491 CATGGTCTGCTTGCGGGCAGGGGGGTAGGACCCTG[A/C]TGTCCAGAACTAAAGGCCGTATGCTGAGAACAAGC M 2 1 2 1 101000 r 74 goat snp41065-scaffold531-1097111 12 66415893 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444030 Affx-122926883 AX-123314367 12 19150447 GCCTGAATCTCCTATGGACCTTCACAGGCATCTAC[C/T]GTTACAGTCTACGCTGTACGAACAAGGAAAATGAA Y 2 1 2 1 101000 r 74 goat snp41064-scaffold531-1068155 12 66387020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395588 Affx-122963832 AX-123265943 12 19209255 CGCAGAGTTCCCTGCCAGGAACTTTTCACAGGTGA[A/G]CAGATTTCCCTCTCAGAAATGCCAGCTGTTACAAT R 2 1 2 1 101000 r 74 goat snp41063-scaffold531-1009347 12 66327680 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393632 Affx-122965304 AX-123263987 12 19263166 ATTGCCTGTCTGCCTAGAATTCTCTCTCATCTGTC[C/T]GCCTGGCAAACATTTAGTCTTTGAAGACCAAATAA Y 2 1 2 1 201000 r 74 goat snp41062-scaffold531-955436 12 66273385 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426121 Affx-122940627 AX-123296467 12 19305164 AAAACTATGCATGAGAATCAACAGTTCAAAACCAG[C/T]ACTAAAGAAAACATCTTAAAAGCAGAGAGAAAACA Y 2 1 2 1 101000 f 74 goat snp41061-scaffold531-913438 12 66231303 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439714 Affx-122930557 AX-123310051 12 19353110 AGTATGTCCTTAGACTTCAAATTTAAGCATGCCAC[C/T]GAAAACGAATCAGAATCAAGCTTGAATTTCAAAGT Y 2 1 2 1 101000 f 74 goat snp41060-scaffold531-865492 12 66182536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447848 Affx-122923896 AX-123318184 12 19394848 AGAGCTAAAAATCTAAAATTTTCAAAAATCCTTCT[A/G]TACTGCCCAGTGGTAAGTTTGCCTTCAAGAGGCAT R 2 1 2 1 101000 r 74 goat snp41059-scaffold531-823754 12 66140853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781565 Affx-122968131 AX-385268650 12 19442811 TATCACATATCACATCTACATATCACAGCTATGCT[A/C]TCAGTCAAGCCATTTGTCACTAAAGCCTGCCTTCA M 2 1 2 1 101000 r 74 goat snp41058-scaffold531-775791 12 66093070 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799043 Affx-122968047 AX-385285973 12 19477235 ACAGCATTTGAGAGTCCTATCAGGGGCCTTTTTCC[C/T]GAGACCCTTTGTGAACATGAAGTTTGAGTCAAGGG Y 2 1 2 1 101000 f 74 goat snp41057-scaffold531-741367 12 66058832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450490 Affx-122922926 AX-123320824 12 19506853 CAGGGAAGATCGTAGCTTAGTGGGAGACTGTGCTA[C/T]GGAAGCCAGAGGTGAGAGTTTGGGGAACATGTATA Y 2 1 2 1 201000 f 74 goat snp41056-scaffold531-711749 12 66029218 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404291 Affx-122957034 AX-123274643 12 19546312 CTCCCTGTTTACAATCTACTCTTTAGAGCACTTTT[A/G]CCCATTCTTATTGTGTACATGTGAGTATAGTGTGT R 2 1 2 1 101000 r 74 goat snp41055-scaffold531-672290 12 65991544 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402174 Affx-122959187 AX-123272527 12 19612484 GTGCCATTAAAACTGGTTAAATGGATTAAAAAAAA[G/T]ACCCATCTGTATCTGCCTACAAGAATATCACTTAA K 2 1 2 1 103000 r 74 goat snp41053-scaffold531-606118 12 65926351 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394424 Affx-122964598 AX-123264779 12 19651837 TGAGCTACCAGGGAAGCCCTCCACACAAATTATGT[A/C]ACTTAATTCTCATAGTGATCCTCCAGGGTAGGTAT M 2 1 2 1 201000 r 74 goat snp41052-scaffold531-566765 12 65886663 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276741 Affx-1111835496 AX-519550251 12 19658845 GCAGCCTGTTACAACTTAGCGACTAAACCATGACC[A/C]CCACAAAAAATGACAGCATCCCTTAATAGTCAATA M 2 1 2 1 201000 r 74 goat Random2.2K-1249 12 19658845 A C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38377793 Affx-122977324 AX-123248152 12 19703145 GATAAAAAGTAGAAAGCTCAGTTTGCCATCCAAAC[A/G]TTTATTTTATGTGTCTGGAATAGAAGAAATGGAGG R 2 1 2 1 202000 f 74 goat snp41051-scaffold531-515457 12 65835630 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276743 Affx-1111835497 AX-519550253 12 19708640 CCACTGAAGTTTCAAATAATATTAAGAATGAAAAT[A/G]ACTTTACATTTTAAGGAAATTTATGTTAGATCATA R 2 1 2 1 101000 r 74 goat Random2.2K-1250 12 19708640 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320788760 Affx-122956363 AX-385275776 12 19758483 TTGAAGTATCTGCCACCCAAAATACTGAATGAACA[G/T]CAATCTGATCGAGCCTCGTAGCTACAGGGAAATAA K 2 1 2 1 101000 r 74 goat snp41050-scaffold531-460119 12 65780215 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276744 Affx-1111835498 AX-519550254 12 19781667 TCAATAAGCTAAGTCATATCTGAGACACCCTTAGT[A/G]TTTATGCACCAAAAAATGGGTGGGGCTTGTCCAGG R 2 1 2 1 102000 r 74 goat Random2.2K-1251 12 19781667 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38405691 Affx-122956548 AX-123276043 12 19797581 TGCACCCACGCCTCTGTGTCACCTGCATTGGCAGG[G/T]GGATTCTTTACCGCTGAGCCATACCCACCTTTACT K 2 1 2 1 303000 f 74 goat snp41049-scaffold531-421021 12 65741111 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276604 Affx-1111835499 AX-519550115 12 19808421 AGGACCTCTGCTGCACTCAGTCATTGGTTGGAGAA[A/G]AGAAAAAAATAGATTTTAGAGCAAAGTAGCAGGTA R 2 1 2 1 102000 f 74 goat Random2.2K-1252 12 19808421 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796621 Affx-122923335 AX-385283567 12 19881053 CTACCATAAATCTCACAGTCCTGGATCACGAATGC[A/G]TATTTATTTATAAAGGAAAATGTGGGTGGTAAAGG R 2 1 2 1 303000 r 74 goat snp41048-scaffold531-337549 12 65656469 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439366 Affx-122930276 AX-123309703 12 19942126 TTGGCAACCTCCTCTTTCTCTTAGATGGCCGCGTT[A/G]CTAGCCCTTAGTTAAACTGTAGCTTCAAGTTAGGG R 2 1 2 1 201000 r 74 goat snp41047-scaffold531-276476 12 65595303 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778592 Affx-122963554 AX-385265703 12 19977767 ATCATCGAATTTCCTTATCACAAAGAACAAAGCAC[A/G]TTTTCTATTTAACAACTAGAGAATTGAGAAAAATA R 2 1 2 1 101000 f 74 goat snp41046-scaffold531-240835 12 65559721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431975 Affx-122935952 AX-123302316 12 20009498 CGCTGTGCAGAGCTGCTCCCTAACAAACGGCGGGC[A/G]GCAGGGGAGAGGACGGCAGGAAAACAAGGCAAGTT R 2 1 2 1 201000 f 74 goat snp41045-scaffold531-209104 12 65527968 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423550 Affx-122942427 AX-123293896 12 20040380 ATACTGAACAAAAGAGAACTGAACTACCTATACAA[C/T]GACATAATAGGAAGAGACAGGCTTGTTTTTAAGAG Y 2 1 2 1 201000 f 74 goat snp41044-scaffold531-178222 12 65497228 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794764 Affx-122959722 AX-385281724 12 20074897 AAACTCTTATGTGACTTGCTCAAAGCTGCACAATC[A/G]CTGAGTGACAAGGACGGAATTAAAACCCTAGTCTC R 2 1 2 1 101000 f 74 goat snp41043-scaffold531-143705 12 65462991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397382 Affx-122962272 AX-123267737 12 20129368 CGGGGTGGTTGTAACGATTCAGTGAGTTACCACTT[A/G]TAATGCTCTTAGCAGAATGCCGGGTGTGTCATAAA R 2 1 2 1 101000 r 74 goat snp41042-scaffold531-89234 12 65408664 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404688 Affx-122957274 AX-123275040 12 20189862 TTCTATTGAAATTTAGCTTACAGGCACCATGGAGT[A/G]CAGCCTTTAACCCACTCCAGTATTCTTGCCTGGAG R 2 1 2 1 201000 f 74 goat snp41041-scaffold531-28740 12 65348286 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794064 Affx-122961509 AX-385281032 12 20220603 TTAATAGCCTTAATTGTACTTTCAGTGGTGACAAA[C/T]GAATTTTTCTGTCTGTTTAAATCATTAGTATCATT Y 2 1 2 1 101000 f 74 goat snp19264-scaffold1940-1902 12 65318138 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378218 Affx-122976921 AX-123248577 12 20269071 TTAGGTGGTATCAACCTTCCCTTTCCACAATGGGA[C/T]GTGCATACGACAGGAAATCCCCACAGCTGGGGCAT Y 2 1 2 1 101000 f 74 goat snp19265-scaffold1940-50370 12 65270041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404890 Affx-122956466 AX-123275242 12 20300849 AGTGGTGATGCACTCTTTCCTCTGTTAATGGACAT[A/G]TCTACCTCAACACGGAAAACATCCACGATGTTTTC R 2 1 2 1 201000 r 74 goat snp19266-scaffold1940-82148 12 65238087 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801159 Affx-122920724 AX-185198822 12 20376946 AAAACGAACAGAAGGTTAAGTATTTTGGAAGACTT[A/G]TCTGAACACTAGAGATCCTTCTAGGAAGTGTTTAG R 2 1 2 1 201000 f 74 goat snp19267-scaffold1940-158245 12 65161289 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429964 Affx-122938066 AX-123300305 12 20390708 CACTGGTTCCTCCTCATCCTTGAAGCTGAGATATT[C/T]GGTTATGGCTAAAAATCCTGCCATTTAATTGAATA Y 2 1 2 1 201000 r 74 goat snp50070-scaffold717-5767 12 65147781 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275462 Affx-1111834816 AX-519549035 12 20416164 AGTCATCCCCCAGAAATGTTGCAGGTTCGGTTCCA[A/G]AGCACTGCAGTAAAGAGAATAATGCAAAAAAGCAA R 2 1 2 1 202000 r 74 goat GoatD01.054643 12 20416164 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447060 Affx-122924515 AX-123317396 12 20426635 ACCAGGAATAATTTTAAATATTCAGTTTCCCTCTC[G/T]TCACTCTGTTTCCAAAGGAAAACACGTATCCCGTG K 2 1 2 1 101000 r 74 goat snp50071-scaffold717-41694 12 65111433 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783467 Affx-122964564 AX-385270530 12 20455202 AATCCTTATTGAAACTGTAGAGCTGATGAAGGATA[C/T]ACGCCACTTAGGTATTAGTTTGGAGACTTTCAAAA Y 2 1 2 1 101000 r 74 goat snp50072-scaffold717-70261 12 65083082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398352 Affx-122961676 AX-123268707 12 20516368 TTTTATTTTTTTTAATTCTTGATGTGAATTCCACT[A/G]TTGATTGACCATGTGTATTTATGTGAAGGTACTAT R 2 1 2 1 101000 r 74 goat snp50073-scaffold717-131427 12 65024720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451368 Affx-122921224 AX-123321701 12 20572477 AATACACAACGTTGGTATGTCCTGTTACTGGTGAT[A/G]TTATCCTTGATCACTTGGTTGAGATGGTATCTGTC R 2 1 2 1 101000 r 74 goat snp50074-scaffold717-187536 12 64968803 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391052 Affx-122966856 AX-123261409 12 20633273 AGTTGCTCTTGGTCCCAGCTGCCTCTCAGGACACC[A/G]GGCCCCTTTCTTGTTCCTGCTGCTTTGCTTTTAGT R 2 1 2 1 101000 r 74 goat snp50075-scaffold717-248332 12 64908317 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387686 Affx-122969819 AX-123258044 12 20668639 TAGGACCACGGGGTGAGGGCTAGGGAAGCATGGCA[C/T]GCATGTCAGAGCTTTACAAGCTCTCAGGCAGTATA Y 2 1 2 1 303000 f 74 goat snp50076-scaffold717-283698 12 64872873 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390982 Affx-122966913 AX-123261339 12 20697803 AGTAGAAAATTGTATAGCTAAAATAAATAGATTGG[C/T]ATCAATGAAAACTAGTATATAATAGACAATGAGGC Y 2 1 2 1 101000 r 74 goat snp50077-scaffold717-312862 12 64843796 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378976 Affx-122976402 AX-123249335 12 20730208 GATTTACAAACTTACATGCATGACTATATGTAAAC[A/G]TGCAGTTTCTATATTTGCATATTTGTGCTCAGCTG R 2 1 2 1 201000 f 74 goat snp50078-scaffold717-345267 12 64811579 G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427830 Affx-122939740 AX-123298173 12 20783363 GCTCTTTAGAGCAGAATTCTTCCTTTCTGTTTCCT[C/T]GTCTCTGGAAACAGTTGAGTATAGTTCCTCCCACA Y 2 1 2 1 101000 r 74 goat snp50079-scaffold717-398422 12 64757777 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801010 Affx-122974736 AX-385287924 12 20829446 TTTGAAGGGAAGATGAACACTGTTGATGTAAATAA[C/T]TGTTTGCCTTCCATTATTTGCGCGATCCTGCTGCT Y 2 1 2 1 101000 r 74 goat snp50080-scaffold717-444505 12 64711714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444265 Affx-122927207 AX-123314602 12 20873280 TCACTTATCAGATATTCTGAGTTGGAAATTATTAC[C/T]CATAGATCCTCATGGCTTCTACCATAAGATAATAG Y 2 1 2 1 101000 r 74 goat snp50081-scaffold717-488339 12 64667940 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38452656 Affx-122920334 AX-123322989 12 20903249 AGAGAGCCCATGACCCTTTGTACAGGCAATGACAA[C/T]GGAAACTAAAAAAAGAATGTTGCCATACATGCAAC Y 2 1 2 1 101000 f 74 goat snp50082-scaffold717-518308 12 64637939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420808 Affx-122944680 AX-123291155 12 20960970 CTCAAGGATGAGTGGGTCTCTCTGGGCTCGCAGGT[A/G]TGAAACACTTTCTCTTTTCAAGTCCTTGGGCATTT R 2 1 2 1 201000 f 74 goat snp50083-scaffold717-576029 12 64580645 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379728 Affx-122975878 AX-123250086 12 21007210 TTGACTTCATCAGCCTATGTCCTAAAAGCCACAAC[C/T]GTAGGAGGTGGATACTGATATGTGATCCCTATTGC Y 2 1 2 1 101000 f 74 goat snp50084-scaffold717-622269 12 64535242 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767152 Affx-122934910 AX-385254437 12 21043615 ATATTAAGGACTTTGGACTCTTGTCCTCTAAGTCT[A/G]TGATGTTCAGTCTTGAGGGTACATATGAGTCACCT R 2 1 2 1 101000 f 74 goat snp50085-scaffold717-658674 12 64498727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408611 Affx-122953501 AX-123278962 12 21111834 CTCCCCAGGTAGAGAGGGAGCCACACATTCACTTT[C/T]CCAGCTGCACCTGCAGCTAGGGTGGATATGGAACC Y 2 1 2 1 101000 f 74 goat snp50086-scaffold717-726893 12 64430955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798766 Affx-122939149 AX-385285696 12 21150068 TTGGTACTTCAATGCAGGAGTTCTTTGAAACCTGG[A/G]CTGAAGTCTCTTTAACTCAATTTGTGACTTCTGCT R 2 1 2 1 101000 f 74 goat snp50087-scaffold717-765127 12 64393033 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385143 Affx-122971762 AX-123255501 12 21217468 CCTACAGCCCCATCTGAAGGCGGGGGTGGCAGGGT[A/G]GCTGCTGATGTAAGAGGTGCCCGACTCAGTCCTCA R 2 1 2 1 101000 r 74 goat snp50088-scaffold717-832527 12 64325719 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411886 Affx-122951194 AX-123282236 12 21268436 AGTAGGTTGGATGAAGTTAAGTGTTAATTTTGTCC[A/G]CTAACAAAAATGGCAGCCTTCTCAGATTTTCCCTT R 2 1 2 1 101000 r 74 goat snp50089-scaffold717-883495 12 64274858 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384797 Affx-122971998 AX-123255155 12 21311885 AAAATGTCAAAGAGAAAATGTGAAGAAAAGGGAAA[C/T]GGAGGGGAGTAATGGAAAGGGCCTTCTTGTCAACT Y 2 1 2 1 303000 f 74 goat snp50090-scaffold717-926944 12 64231460 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419385 Affx-122945615 AX-123289733 12 21342468 GGCAAGCTGAAATCGAGTAGATCCATGGCTGATGC[A/G]CCAACACAGCAAATAAAACAGCTCTTCCCCAAAGT R 2 1 2 1 101000 f 74 goat snp50091-scaffold717-957527 12 64200558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776037 Affx-122968531 AX-385263167 12 21398870 GACCACAAGCAAAGGAGTATGAGACAAAGCTCAGG[A/C]TCACTACAACTCCATCTTTGAATTAGGATTTTTTT M 2 1 2 1 101000 f 74 goat snp50092-scaffold717-1013929 12 64144303 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381553 Affx-122974829 AX-123251911 12 21447517 GCACTGTTGCTTTCAAACCAATTATAGGAGCCCAT[A/C]TTATGGATCCCCCTGGTGGCTCAGACACTAAAGAA M 2 1 2 1 101000 f 74 goat snp50093-scaffold717-1062576 12 64095468 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412460 Affx-122951401 AX-123282809 12 21505479 CATTTGATTTCCAAGGACAGAGGGTTTTTTGTATT[A/G]CACTGAAATCTACAAAGTAAGGTACATTGATTTAC R 2 1 2 1 201000 r 74 goat snp50094-scaffold717-1120538 12 64037599 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383997 Affx-122972919 AX-123254355 12 21549957 GTGACTGTGATTATGTGCCCTAAATCACTTTGGGA[C/T]GAGGTCACAGAGGTTAGATCAGATTCTCTCTAGTA Y 2 1 2 1 101000 f 74 goat snp50095-scaffold717-1165016 12 63992886 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377644 Affx-122977866 AX-123248003 12 21594609 TGCCATACTTAAAATTTGCCTTTCATTAACCATTG[C/T]ATTTTCCTGCAACTTTCATTTTAACTTTATAAGAG Y 2 1 2 1 101000 f 74 goat snp50096-scaffold717-1209668 12 63947853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771747 Affx-122976289 AX-385258904 12 21626651 AAAAGAATTGGAAATTCTGTATGTACTTACATAGC[A/G]TGAGCTTCAAGATATAAGTAAGTGAAACAAAAAGT R 2 1 2 1 101000 f 74 goat snp50097-scaffold717-1241710 12 63915838 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272655 Affx-1111832948 AX-519546364 12 21634506 AATCAGACTCTAAGCTCTATCAAACTCCATAAGAG[A/G]ATTTAAACTTGATCTTTCCCACAGATTCTCTCCAT R 2 1 2 1 101000 f 74 goat 12_21634506_AF-PAKI 12 21634506 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320770971 Affx-122953897 AX-385258134 12 21677744 TTTTTATTGATTACCTTTAAATGTCTCATGCAAGA[C/T]GGCAACAGGAAGTAAATCTGAGACTCATGAGATTT Y 2 1 2 1 101000 r 74 goat snp50098-scaffold717-1292803 12 63865037 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390614 Affx-122967169 AX-123260971 12 21718751 AACAGGAACCGTATGTTGGGCTGTGTTTTATACTA[G/T]AGCCAACCATCTGTTTGCAATGAGCCCAGCATCCA K 2 1 2 1 201000 f 74 goat snp50099-scaffold717-1333810 12 63823934 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774404 Affx-122952600 AX-385261540 12 21753649 TTCCCAAATGCAAAATGTCCTTATAAGTATTAGGC[A/G]TTATTATGAATGTTACTTACAGTATTTATCAAGCA R 2 1 2 1 201000 r 74 goat snp50100-scaffold717-1368708 12 63788899 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789599 Affx-122939154 AX-385276608 12 21787516 TTTTGCCAAGGACCAAATACCTCTTTGGAATAGGG[C/T]ATTTTATTTTGGTTGCAAGCTTTTATTCAAATGGT Y 2 1 2 1 101000 f 74 goat snp50101-scaffold717-1402575 12 63754613 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439171 Affx-122931060 AX-123309508 12 21816376 GGTGGACTTGGCAATTAAATCACAGATACAGTTAC[C/T]ATCACTTTGTTGACATAATCCCATTTAGAGTTCAG Y 2 1 2 1 101000 f 74 goat snp50102-scaffold717-1431435 12 63725704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414322 Affx-122950042 AX-123284671 12 21868307 CAAAACAGCAGTCATCCTTGAAAGAAAACATGTCT[A/G]CACAGAAATTTGAGCTGCGTGGCTGGACTGGGCTG R 2 1 2 1 101000 f 74 goat snp50103-scaffold717-1483366 12 63673394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415308 Affx-122948813 AX-123285657 12 21905316 ATAAATCCATATTGATTTAATAATGATTTACCTTA[C/T]GAATTACCTAGCAAATGAAAGTCTGTATATCTGAA Y 2 1 2 1 101000 r 74 goat snp50104-scaffold717-1520375 12 63636191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379264 Affx-122976249 AX-123249623 12 21933891 AATCCCATTTAGTTAGTCAGTAATGGAAATCTTTT[A/G]CTGAAGAAAATAGAATTTTCTAAAATCACGATTGT R 2 1 2 1 303000 f 74 goat snp50105-scaffold717-1548950 12 63607614 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387310 Affx-122970513 AX-123257668 12 21981997 GATTTCTTTTTCAGTGGGTCACTGACTTCAAAGAC[G/T]CCTGGGTAATTTGCATGCACCTCAGATTTATCATG K 2 1 2 1 101000 f 74 goat snp50106-scaffold717-1597056 12 63559216 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418919 Affx-122946520 AX-123289267 12 22010585 CATTTTGGCAAGTGAACCAACAGTCCAAAACTACA[G/T]CTGTTAACAGAAACGTATTCTTTTCAATTCTTTCA K 2 1 2 1 101000 f 74 goat snp50107-scaffold717-1625644 12 63530008 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447448 Affx-122924371 AX-123317784 12 22054337 GAATGTGGGCTTGAAATAAATATATATTAATGTTT[A/C]TTTGATACTTTTGAGTTAGATCCTGAAAACCCATA M 2 1 2 1 101000 r 74 goat snp50108-scaffold717-1669396 12 63486378 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779313 Affx-122962189 AX-385266417 12 22098999 AACCTTAAAAATGATGGTTTGGTTGAATTTGGGGC[A/G]ATTTAAAACTGCAGTCACTTTTACAGGAATACTTA R 2 1 2 1 101000 f 74 goat snp50109-scaffold717-1714058 12 63442196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431266 Affx-122937113 AX-123301607 12 22130264 GTGAGTCCTAACCTGTGCTCTATACAAGTAACCTG[C/T]GCTCCATAACACCAGTTAGAAACGCTGGACACATT Y 2 1 2 1 101000 f 74 goat snp50110-scaffold717-1745323 12 63410907 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448911 Affx-122923172 AX-123319246 12 22159886 GCGCCTTAGTAAATAGAGAAAAAAAACCTAGACTG[C/T]GTGTGAAGAATTCCTATGGGAAAAATCACAAAGGC Y 2 1 2 1 201000 r 74 goat snp50111-scaffold717-1774945 12 63381016 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393958 Affx-122965057 AX-123264313 12 22190347 TCAGCTTAAGCATCTCCTCTTTGATGAAACCTTTC[A/G]TGATCCATTCAGATTAGAACTCATCATGATGACTT R 2 1 2 1 600000 r 74 goat snp50112-scaffold717-1805406 12 22190347 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788156 Affx-122965057 AX-385275175 12 22190347 TCAGCTTAAGCATCTCCTCTTTGATGAAACCTTTC[A/G]TGATCCATTCAGATTAGAACTCATCATGATGACTT R 2 1 2 1 101000 f 74 goat snp50112-scaffold717-1805406 12 63350478 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439518 Affx-122930128 AX-123309855 12 22228517 TTCCTTTATCTTATTTTTGTTTTCAAAGAGTGTAA[C/T]ATCTACATCATTAAACTAGTATTCTTCCCATGTGG Y 2 1 2 1 101000 r 74 goat snp50113-scaffold717-1843576 12 63312410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446204 Affx-122925717 AX-123316540 12 22263606 TCATATAAAGAAATGCTGAGGTCTAGAAAGTGTAC[A/G]TTACCAGAATATGAACTGGGCACAGAGGGTAGCTG R 2 1 2 1 101000 f 74 goat snp50114-scaffold717-1878665 12 63277352 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440235 Affx-122930672 AX-123310572 12 22313756 TCTAACTCCCAAGCCAGCAGATTGAATGGGCTTCT[C/T]CCTTTAGTCACTGAGTAACTCTGCACAGGTCACCT Y 2 1 2 1 101000 f 74 goat snp50115-scaffold717-1928815 12 63227514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436392 Affx-122933037 AX-123306731 12 22355725 AGCCCATATGGTCTCAGAGTTGGACATGACTTAGC[G/T]ACTAAACCACCATCACCTCTAAGCGATGCAAACAC K 2 1 2 1 103000 r 74 goat snp50116-scaffold717-1970784 12 63185488 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392187 Affx-122966294 AX-123262544 12 22406846 TGGCATAAGTGCTTGTCTTTGATAGCAAGCCTCTG[C/T]ACATGGGGGTTCCAGGAAAACCCTAACTCAGCTTC Y 2 1 2 1 101000 f 74 goat snp50117-scaffold717-2021905 12 63134608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400051 Affx-122960772 AX-123270406 12 22437489 TCTATATCTAAAATCCCAAGCAAGGTATAGAAAAA[A/G]CTAAAGAAAAGGGGAGTACATAAACTGGACAAATT R 2 1 2 1 102000 f 74 goat snp50118-scaffold717-2052548 12 63104176 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786713 Affx-122960688 AX-385273744 12 22474591 TTAGAAATACTTTTTAACTCACCACTAACTGTAGG[G/T]AGTATAAAACTGAGTTATAAATGACTACTGTGATA K 2 1 2 1 101000 f 74 goat snp50119-scaffold717-2089650 12 63066963 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396596 Affx-122962901 AX-123266951 12 22511482 AGAAAGACTGGGAGAAAAATCAGTATTTAGGATAC[A/G]TCAACATTTCTGATTCCAGTGGTTAGAATTGCATA R 2 1 2 1 101000 f 74 goat snp50120-scaffold717-2126541 12 63029248 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766272 Affx-122921461 AX-385253664 12 22561969 TCAGGAACACTGAGTCTGCAAGAATTAAAAAAGAA[G/T]ATTTTGAAAGGCTGATTTTTTAAGTCCTTTGTTAC K 2 1 2 1 102000 f 74 goat snp50121-scaffold717-2177028 12 62977816 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788762 Affx-122950248 AX-385275777 12 22598609 TTTTAAAAATATGGTAATAGCATCACTATTATATC[A/G]TTCACGTATAATTTGAAAATTTATGTAACTGGAGA R 2 1 2 1 101000 r 74 goat snp50122-scaffold717-2213668 12 62940558 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776233 Affx-122963591 AX-385263360 12 22628689 ATTATATATATTTCCATAGATGATAAATATGTGTA[A/G]GTCTCTGAAAATAACTTATACTCTGATGTTAACTC R 2 1 2 1 101000 r 74 goat snp50123-scaffold717-2243748 12 62909819 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426492 Affx-122940223 AX-123296838 12 22659474 ATTTGGCAATGGGATAGGAAGTAAGAGGAATGTAG[C/T]AAAAGGAATTTGGTGAAAAGGCAAATGCAGAAAAT Y 2 1 2 1 101000 f 74 goat snp50124-scaffold717-2274533 12 62878695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781882 Affx-122965604 AX-385268963 12 22707257 TTCTGCAGAAACTAATAACACCTACAAGTCATATG[C/T]ATCAAGTTGTAACTAGAACTTCTTAAGGGTAAGTA Y 2 1 2 1 101000 r 74 goat snp50125-scaffold717-2322316 12 62830569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381771 Affx-122974304 AX-123252129 12 22750767 GCAGGGCTACACTCATGGGATGGTGGCTTTAGAGG[A/G]CAGATAATACCTAGAACTGACAACGTTGTCATATT R 2 1 2 1 201000 r 74 goat snp50126-scaffold717-2365826 12 62786796 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440373 Affx-122929640 AX-123310710 12 22795566 TTTGTTTTCTCCCCACATCATCCACATGTGCTGTG[C/T]GGTGTAATGTTCTAAGCCTACCAATGTTTTATTTC Y 2 1 2 1 201000 r 74 goat snp50127-scaffold717-2410625 12 62742107 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400445 Affx-122959959 AX-123270800 12 22838957 TCAAAGGGTTTCATGTATCCTTTGGTTCATCTCCA[A/G]TGCAACATTGCATATCTGCTGTTTGCACTCCATCC R 2 1 2 1 101000 f 74 goat snp50128-scaffold717-2454016 12 62698350 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389095 Affx-122968579 AX-123259453 12 22871424 AAATGCTAATCTATTCTGGAAACACCCCATAGACA[C/T]ACCTAGAAAAGTTTAACCATGTATTTGGGCATTCC Y 2 1 2 1 101000 r 74 goat snp50129-scaffold717-2486483 12 62665757 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426387 Affx-122940853 AX-123296733 12 22904967 TATTTCTGGATGGAAAATGTCAATAGAAAATGTTT[A/G]TAATATTGTCCACCATTAATATGAAAAAGCTGAAA R 2 1 2 1 101000 r 74 goat snp50130-scaffold717-2520026 12 62631056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767551 Affx-122973709 AX-385254804 12 22937842 TAAAAAGCTAAGGGCATGCAGAGAAATGATGTATA[A/C]CACTCTATTGTATGTCCTGCAGCAAAAAGAGTGGA M 2 1 2 1 101000 f 74 goat snp50131-scaffold717-2552901 12 62596998 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388166 Affx-122969447 AX-123258524 12 22988129 GAGAGAAAATTAAGTCCTGTGGGTCACACATGCAA[C/T]AGAAATTTGATGCACCAACAGGTGAAATCTACAGG Y 2 1 2 1 101000 r 74 goat snp50132-scaffold717-2603188 12 62546462 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386865 Affx-122970064 AX-123257223 12 23030910 AACTTGGAAAGGAAGAGGTCTGCCAAGATGGCAGC[C/T]GGTGTGTCCTGGGCACTTGCATAGAAAGCCATCCT Y 2 1 2 1 101000 f 74 goat snp50133-scaffold717-2645969 12 62503682 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451037 Affx-122921446 AX-123321371 12 23088777 AGTTATTATACTAACTGCTGGATATTGCTTCAGTC[A/G]TACAGGCATTAGCAGAATTTCCCATCTAAAATACA R 2 1 2 1 101000 f 74 goat snp50134-scaffold717-2703836 12 62447160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407549 Affx-122954685 AX-123277900 12 23120360 ACAATCTGACATTTCTACTGGAAACCAGAAGTTAT[A/G]CAATAATAAGAATGATTTTTAAAATAAATAACACC R 2 1 2 1 101000 f 74 goat snp50135-scaffold717-2735419 12 62415653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385764 Affx-122971064 AX-123256122 12 23157030 CATTTTAAAAAGAAGTAAAGATGAACATCACAGCT[A/G]CTTGGAAAGGTAATGAGTTTCTCATCACTGTGTTC R 2 1 2 1 101000 r 74 goat snp50136-scaffold717-2772089 12 62378762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276748 Affx-1111835500 AX-519550258 12 23167914 CTTCTTCCTTCATCGCATGTTGATTTCCATGTATT[A/G]TATCTTTTTTAAATGTCTCCTCATCCCCTCAATGG R 2 1 2 1 101000 r 74 goat Random2.2K-1255 12 23167914 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320768930 Affx-122923517 AX-385256105 12 23212651 ACTTCTGATATTAGTTAGTATCCTGGTCTTTGTCC[A/G]TAATTAATTCATCCAAACAGCCTAAATACAGAGAC R 2 1 2 1 101000 f 74 goat snp50137-scaffold717-2827710 12 62323423 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422010 Affx-122943774 AX-123292357 12 23249182 TAGTGTGCAATTACACTGGAAAACTAAATCCAATG[C/T]ACTCTTCTTTGTTGCCAGTTGTTTTCAAAAGATGA Y 2 1 2 1 101000 f 74 goat snp50138-scaffold717-2864241 12 62286805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792565 Affx-122928058 AX-385279546 12 23282840 CTCCTTTTTAATACTGTACTGGAAGTTATAACTGA[C/T]GCAGTAAGTTTTATCTAATAAAACCAAAATGTTTT Y 2 1 2 1 101000 f 74 goat snp50139-scaffold717-2897899 12 62252985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276609 Affx-1111835501 AX-519550119 12 23293871 CGGGAGTAAAGAGCTCTACAAATTTCAGAAATCCG[A/C]GTACTTGGCACAAGAAGTGATGCGCAAACTATTCG M 2 1 2 1 101000 f 74 goat Random2.2K-1256 12 23293871 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320764940 Affx-122930621 AX-385252521 12 23313993 TGTTTTAGTCCTTATTCTGAGTTGGAAAACTAAAG[C/T]GATTATTTCTGGAAGGCTGGTAAAAACATATCATT Y 2 1 2 1 201000 f 74 goat snp50140-scaffold717-2929052 12 62221513 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776299 Affx-122944123 AX-385263427 12 23351183 CCTTGCATAGGATTTCTGGAAGCCAAATTCTAATC[A/G]CACAGTATCTGTTCTGCATCACCCAGTTCACTTTT R 2 1 2 1 101000 f 74 goat snp50141-scaffold717-2966242 12 62183644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423107 Affx-122942917 AX-123293453 12 23389632 TAACTGGACCACAAACAAGAGAAGCTTGGGTTCTG[C/T]GGTTTGGCATCTTCTTCATTGCTCAAGCAAAGCAT Y 2 1 2 1 101000 r 74 goat snp50142-scaffold717-3004691 12 62144727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796399 Affx-122929457 AX-385283349 12 23424735 GGAAATAGTGATTAGGTAGGTGAACTTGAGAATCC[A/G]CTGACTCTGATGACCCTTCTGGTCAAAGATAAATA R 2 1 2 1 101000 f 74 goat snp50143-scaffold717-3039794 12 62109796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796598 Affx-122976467 AX-385283544 12 23475844 CAACCTCATTTAATTTAAAGGCCCTATCTTCACAA[C/T]GTGATTGTGAGGTACCAGGCATTAGAGCTTCGATA Y 2 1 2 1 101000 f 74 goat snp50144-scaffold717-3090903 12 62057701 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400696 Affx-122959938 AX-123271051 12 23506789 GAGTTGGTAAAGACTTTATTTGAATTGGTGATAAA[C/T]GCTTCTTTGTCAAAATGTACTCTAAGGTCCTGCTA Y 2 1 2 1 101000 r 74 goat snp50145-scaffold717-3121848 12 62026915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376612 Affx-122979048 AX-123246971 12 23556643 AAAAATAAATAGCCATATATTTTTAATTTCAGGGC[A/G]TTTGATGTAGAACTGCTTTACATTGCACAGTTCTT R 2 1 2 1 101000 r 74 goat snp50146-scaffold717-3171702 12 61977299 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446400 Affx-122925575 AX-123316736 12 23586719 GATTTTGTGCAGATTTCACTGTCTTTGTAAGGGTT[C/T]GTCTGTCTTCTCGCCTTCCCCCTCCATCTGATCCT Y 2 1 2 1 201000 f 74 goat snp50147-scaffold717-3201778 12 61954264 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418416 Affx-122946539 AX-123288764 12 23616785 TTCCTCTGTCTGTTTCCCCTGCTTCTCCTTCTGCA[A/C]CTTAAGTTGGTCCCAGCTCACCCCTCAACAACACT M 2 1 2 1 201000 r 74 goat snp50148-scaffold717-3231844 12 61924212 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276752 Affx-1111835502 AX-519550261 12 23649252 ATGCTTCCCCTCAGGGTTAAACAAACTGACCTGCC[A/C]CATATTGGCAGAATTGAAGAAAGATGACCTTCCTG M 2 1 2 1 101000 r 74 goat Random2.2K-1257 12 23649252 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320770902 Affx-122937588 AX-385258065 12 23659474 TGAGCAGTAACTCCAAGGTGATGTTTAACACTACA[C/T]ACATTCATACTAAGTGCATTCGTAACACTCAGTAC Y 2 1 2 1 101000 f 74 goat snp50149-scaffold717-3274533 12 61881431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403306 Affx-122957838 AX-123273659 12 23704831 ATAATAGGCTTTTAAAAATTATCTTTAGATCTTTC[A/G]TAAGGTCTGAAGCCTTACCTGTGTGGATTGATGTC R 2 1 2 1 101000 r 74 goat snp50150-scaffold717-3319890 12 61835569 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414414 Affx-122949973 AX-123284763 12 23746672 TAACTTGGTGTTTTCCACTTTATCTTTTAAATATG[C/T]AAAATATCTTCTACTGCTGGCTCCGTTGGTTTCAT Y 2 1 2 1 101000 r 74 goat snp50151-scaffold717-3361731 12 61796398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440127 Affx-122929694 AX-123310464 12 23815727 GACAAAGAAATAGAAGGTACCAAGCCTAGAAGAGC[A/G]CAGCTGACCATGTATAATGTGAACAATAAATAAGT R 2 1 2 1 101000 f 74 goat snp50153-scaffold717-3430786 12 61727667 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802502 Affx-122948014 AX-385289406 12 23889323 GCAAAGAACTCTGGATGAGGTTGAATATTATTTTT[A/C]TAGATTTCACATATACATATCTATGTAAAATAACA M 2 1 2 1 303000 r 74 goat snp50154-scaffold717-3504382 12 61653919 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397591 Affx-122961994 AX-123267946 12 23926991 GGCAAAACATAATGTCTAGAGATTTCTATAAACTA[C/T]GAGATAAATACATAAAGGAAAAAAATGCAGACACT Y 2 1 2 1 101000 f 74 goat snp50155-scaffold717-3542050 12 61615676 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276613 Affx-1111835503 AX-519550123 12 23972288 CCCTCTTTAAATTTGGGAGGTCCTGATTAAGGAAG[A/G]TAAGATTTATTTTAAAGATAACCTTACCACATAGA R 2 1 2 1 101000 f 74 goat Random2.2K-1258 12 23972288 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779083 Affx-122946448 AX-385266188 12 23989040 TCAAGTACTATTTTGTTAGAAATAAGGAGATAAAA[C/T]TGTGAATTCTCTTAATCTTCCAAAACAGTGGGAAT Y 2 1 2 1 201000 f 74 goat snp50156-scaffold717-3604099 12 61553325 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415430 Affx-122948719 AX-123285779 12 24037402 GCAAGAAATTAAACTGACCTTTAGTTTAGTTGTTT[A/G]TGTCCTCTGTTCAGTTTTATTTTTCAGTTGCATGT R 2 1 2 1 103000 f 74 goat snp50157-scaffold717-3652461 12 61506738 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379125 Affx-122976743 AX-123249484 12 24079370 GATGGTAAGATAACTTAGAGAAGTTTGTATTCTCC[A/G]TTTACTATTTATATATATCTGGTAGGTTCCAGGAA R 2 1 2 1 303000 r 74 goat snp50158-scaffold717-3694429 12 61464775 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272711 Affx-1111832949 AX-519546415 12 24141935 GATGATAGAGGACGAGATGGTTGGATGGCATCACC[A/G]ACTGAATGGACACGCGTTTTAGCAAGCTCCAGGAG R 2 1 2 1 101000 r 74 goat 12_24141935_AF-PAKI 12 24141935 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38427857 Affx-122939719 AX-123298200 12 24171070 TACCATCCTACTCTCTAGAGACTCAAGGTCATGGG[C/T]GGGGGACTTGCAAATGTACCTCATGGTTGTACTGC Y 2 1 2 1 101000 f 74 goat snp50160-scaffold717-3786129 12 61372486 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429165 Affx-122937975 AX-123299507 12 24222945 TTCCGACGCTCCATCCTCTGCAAGGACCTTACTGT[A/C]ATGACTCCACTGTAAATGGATTCTGCTCATTTGAC M 2 1 2 1 101000 r 74 goat snp50161-scaffold717-3838004 12 61321332 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772142 Affx-122978400 AX-385259297 12 24284726 ATCATTTTTGAGAGAGTACATTTTATATTTATAGC[A/G]TTTCTAAAGCTTAATGGTTAAAGCTACAGTTTATC R 2 1 2 1 201000 f 74 goat snp50162-scaffold717-3899785 12 61259406 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386874 Affx-122970059 AX-123257232 12 24313989 GGCCCTTCGGGGTGTGGGTGGCTTAAGATTCACCT[C/T]GAGGATTAAATGAAAGAATTGAGGCAGGCCAGACA Y 2 1 2 1 201000 f 74 goat snp50163-scaffold717-3929048 12 61230144 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409320 Affx-122953086 AX-123279671 12 24347064 TTGAACACTGAAGGGCAGTATAGCACTGTACATAA[C/T]GCAAGAAGAAGTTCGTGGCTCCGTGACTTTAGAAA Y 2 1 2 1 101000 f 74 goat snp50164-scaffold717-3962123 12 61197031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423450 Affx-122942593 AX-123293796 12 24412899 AGACCCATGTGAGCTGCTTAAAAGTGCAGGGCCAG[C/T]AACAGCTGAGAAATTCACCAGGAATGCCCATGTCA Y 2 1 2 1 101000 f 74 goat snp50166-scaffold717-4027958 12 61130498 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383016 Affx-122973318 AX-123253374 12 24467948 ACCAGAACACACAGAGCTGCACACAGCCCAAGTCT[A/G]CAGAGGGTGAACTGCGTCTTGAATGTTATCAGTGT R 2 1 2 1 101000 r 74 goat snp50167-scaffold717-4083007 12 61075520 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443399 Affx-122927388 AX-123313736 12 24522867 TAGGGAAGAGGCTGGCCGGGGTGTTTGGCAAGGCG[A/G]GGTTTGTCCCAACTCAAATGTCCTCCTAAGGTTTG R 2 1 2 1 101000 r 74 goat snp50168-scaffold717-4137926 12 61020592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379156 Affx-122976717 AX-123249515 12 24592901 ATGCAACAACTGTCTGGATTTCTTTTTGGCCTGCA[C/T]ATGGATCAAACATTAATGCCCTTATAAAATCTGCA Y 2 1 2 1 101000 f 74 goat snp50169-scaffold717-4207960 12 60950723 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387314 Affx-122970510 AX-123257672 12 24632848 TTACTAGCTCATATTTTTGACTGCCTATTTCATTT[A/C]TTTAAACATATTAAATCTTTTAAAAATAAAAGAGG M 2 1 2 1 101000 f 74 goat snp50170-scaffold717-4247907 12 60910598 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424370 Affx-122941843 AX-123294716 12 24671012 TTCAAATGTTAGGTCCAAGAAGATAATAATCACTA[C/T]GTCTGGGCTCCAAGACAAGCAAAGAGCTGAAATGT Y 2 1 2 1 101000 r 74 goat snp50171-scaffold717-4286071 12 60872292 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442303 Affx-122928248 AX-123312640 12 24713474 CTGCCAAAACCAAAAGTATACACATATGCACATAC[A/G]CCTTTCATGCTGCTGTGGAATACTAAACTAGACAA R 2 1 2 1 201000 r 74 goat snp50172-scaffold717-4328533 12 60829782 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388958 Affx-122968806 AX-123259316 12 24800232 GAAGGCAAGTGTCAGGAAGTTAATATTAGAACACT[A/G]CTGTGGTCCGACAGTGAAGCACCTTGAAGATCAGA R 2 1 2 1 101000 r 74 goat snp50174-scaffold717-4415291 12 60742654 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437427 Affx-122932410 AX-123307765 12 24832297 AAACTGCTTAAAATACCTAGCAAAGATAAGAAATA[C/T]ATAGGAATAAGTATGGAATAAGGGAGAAAGAGTTA Y 2 1 2 1 101000 f 74 goat snp50175-scaffold717-4447356 12 60710601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410037 Affx-122953241 AX-123280387 12 24866266 CTCCTACATTGGCCAGGAGGTTCTTTACCACTAGC[A/G]CCACCTGGGAAGCCCTCTTCAATCACTATATATTT R 2 1 2 1 103000 f 74 goat snp50176-scaffold717-4481325 12 60676215 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385201 Affx-122971718 AX-123255559 12 24904794 GACTACAGCTCCTTGGAGCTGAGACTCAGTCTTAC[A/G]TATCTTTGTATTCCACATAGTACATAGCACAGTGG R 2 1 2 1 101000 r 74 goat snp50177-scaffold717-4519853 12 60637313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439490 Affx-122930152 AX-123309827 12 24936758 TTTAAGCATCCTCTTGCAACACCTTCACTCAATCC[A/G]TGATCTGTGCTATAGCTGCTTAGGAAATACGTTAA R 2 1 2 1 201000 r 74 goat snp50178-scaffold717-4551817 12 60605518 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784904 Affx-122931354 AX-385271951 12 24968466 GTGGAACAATTAATGCAATATAATGATAATGCTAA[C/T]AGCATCTTAGAACTTAAAATATGTTTTTCAAGAGA Y 2 1 2 1 101000 r 74 goat snp50179-scaffold717-4583525 12 60571717 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445067 Affx-122926222 AX-123315404 12 25070617 AGTATATATCAGACTCTGTTTCATGAAACATTCTT[A/G]TAAGACCCAGCACAGATGTTAGACTTAAAAGACTC R 2 1 2 1 102000 r 74 goat snp50181-scaffold717-4685676 12 60468914 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399441 Affx-122961216 AX-123269796 12 25108842 AAAGGAATAACTTCCAAACCTCTTATGGCATCATT[A/G]TGTGTAAGTTTATAGCATTTACCAGAATTTACATA R 2 1 2 1 101000 f 74 goat snp50182-scaffold717-4723901 12 60430718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790360 Affx-122963001 AX-385277363 12 25147427 TTGAGTGGTACAAAGAAATGTCAGTCTAGATATAG[C/T]CAAGCAAATGGCTGTCAAACATAATGGCTCTTGAT Y 2 1 2 1 101000 r 74 goat snp50183-scaffold717-4762486 12 60391743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383709 Affx-122972478 AX-123254067 12 25212910 CAAATTTGCTTGCATAACTAGATACTACTGGCTCA[C/T]AAATGTATAGCTTCAGCTAAGACCATCTGTACCTT Y 2 1 2 1 101000 f 74 goat snp50184-scaffold717-4827969 12 60327925 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795842 Affx-122942010 AX-385282795 12 25319474 CAAAGCCAGAGTTTAAATAGACCAGTGGTTTTAAA[G/T]ATTATGATTCAAGGTTCCTGAGTCACCACTGGATT K 2 1 2 1 102000 r 74 goat snp50186-scaffold717-4934533 12 60220258 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799394 Affx-122949733 AX-385286324 12 25369335 TCCAGTTGAAGATGTTGAATCAAGTAAGCAGAGAA[C/T]ATTATGAGTAGTTATGTGACTGGAATTCCCACTTC Y 2 1 2 1 101000 f 74 goat snp50187-scaffold717-4984394 12 60170258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766340 Affx-122969131 AX-385253720 12 25426605 GACGAGAAAGTATTAAATGGGCTTCTTGGAGAATG[C/T]GGAAAATTTGCTTATAGGAAACATTTGATTTACTG Y 2 1 2 1 101000 f 74 goat snp50188-scaffold717-5041664 12 60112730 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781008 Affx-122923392 AX-385268095 12 25458291 ATGTTCCAAAAACACAAGAACTTGATAAAGCCATC[A/G]TAGTGAGTATACAGTAGTATACTTGAAGTATATTT R 2 1 2 1 201000 r 74 goat snp50189-scaffold717-5073350 12 60081044 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375957 Affx-122978445 AX-123246316 12 25493702 TAAATACTAAAATAATAAATTATTTCATAAAGCAA[C/T]GTAGACTAGTTAAAATGGGGTAATATGAGAGGAAA Y 2 1 2 1 103000 r 74 goat snp50190-scaffold717-5108761 12 60040786 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404552 Affx-122957384 AX-123274904 12 25533311 AAACTACTTCTGTCTCCAGCAGGGCCATTATAATT[A/G]TTAAGAGGATCATTTAGGAAGCTGTGGATGCTTTG R 2 1 2 1 202000 f 74 goat snp50191-scaffold717-5148370 12 60001083 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412869 Affx-122950437 AX-123283218 12 25568174 AACCTGCATGTCTGGAGGCCAGCGGCTGCTTTCCC[A/G]TTGAAGATCTGCCAAGTTTAGAATGACCGAATTCT R 2 1 2 1 201000 r 74 goat snp50192-scaffold717-5183233 12 59965618 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793383 Affx-122928162 AX-385280361 12 25598205 GAAAGGGCAGCTCTATGGACATATTTCTGCAGACA[C/T]CAAAATACATCTTGCCAGTTTAGCCTTGGAGCCAT Y 2 1 2 1 101000 f 74 goat snp50193-scaffold717-5213264 12 59935502 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405612 Affx-122956608 AX-123275964 12 25642521 GTAAGTGGTTACTGTCTGTGTAACCTATAACAAAT[G/T]ATTTAACTGCTCTGGACCTCCTTTTCCTTATTTGT K 2 1 2 1 101000 f 74 goat snp50194-scaffold717-5257580 12 59890861 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387126 Affx-122970657 AX-123257484 12 25692479 TAAAACAGACGTAACGCTCATATATGCAGATTTCT[A/G]TTTGTGCTGGATAATCAATCCCAACCCACCAATCA R 2 1 2 1 101000 r 74 goat snp50195-scaffold717-5307538 12 59851129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381421 Affx-122974359 AX-123251779 12 25743128 GTGCAGAGCACCGAGGCTTGCCTGCTATATGAGAT[A/G]ACTGTCGATAGCATGGTGAGTGGGCTAGAAAAAAA R 2 1 2 1 101000 r 74 goat snp50196-scaffold717-5358187 12 59798703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443236 Affx-122927560 AX-123313573 12 25776981 TCAAGATCTAACATGAGGATAGTGTACCTAGTTCA[C/T]GAGCTTATTCCATTTATAATTTAGAATTTTTCTTT Y 2 1 2 1 101000 f 74 goat snp50197-scaffold717-5392040 12 59765333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441237 Affx-122929504 AX-123311574 12 25818777 CTGGCCAAAGAAGCTATTGCAAAGTTATCATTTTC[C/T]GATTTCCAGGAACAGGGTTTGGTCAGCCTCTGGAG Y 2 1 2 1 101000 f 74 goat snp50198-scaffold717-5433836 12 59723269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791795 Affx-122974474 AX-385278785 12 25859514 TATGGACTGTCCTGTTTTCATTTGAACAATTTAGA[A/G]TTTCAAAGACAAAAATATCAATTTGTCTAAATAAA R 2 1 2 1 201000 r 74 goat snp50199-scaffold717-5474573 12 59682687 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773747 Affx-122928077 AX-385260887 12 25892292 CAAGTATCAAGAAGTGGCTTTGATTCTCTAGTCAA[C/T]GGTGCCATTGATTACTACAGCAATTTTTAAATTTC Y 2 1 2 1 101000 f 74 goat snp50200-scaffold717-5507351 12 59649694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396495 Affx-122963535 AX-123266850 12 25921285 ATTCATCTGCTTAATTCTTCCCTTTGCCATCTGGA[A/G]ATTTGACTTTAAAACTTCAACAGAAAGAAAATTCT R 2 1 2 1 101000 r 74 goat snp50201-scaffold717-5536344 12 59620789 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419826 Affx-122945824 AX-123290174 12 25970535 TGAAACCCACCACTTCCCTGCCTTAAACTCAGCTG[C/T]ACATCCTTGTTCTACCAAGTTTTCTACAGGTTATG Y 2 1 2 1 101000 r 74 goat snp50202-scaffold717-5585594 12 59570669 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790271 Affx-122963258 AX-385277275 12 26015717 AAGGCAAAAATTCAACAGAAGAGCTGAAAGCTGCT[A/G]CTTAATAAATATCCTAGAAAGAATAAAAAGTTAAC R 2 1 2 1 101000 f 74 goat snp50203-scaffold717-5630776 12 59525330 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776301 Affx-122922372 AX-385263429 12 26049161 CTGTTTTATTCACCTCTGTATTCTTAATATCAGCA[A/C]CTAGGACATAATAGGTATTCCACAAGTATCTGTTG M 2 1 2 1 101000 f 74 goat snp50204-scaffold717-5664220 12 59491907 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441931 Affx-122928588 AX-123312268 12 26085041 TGGACTGGGAGATCTGTGAGGTATTTTCCAACTTA[C/T]GTAAAATTTTCACAAATTCACCAGATAGGGTCTGC Y 2 1 2 1 101000 f 74 goat snp50205-scaffold717-5700100 12 59455713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413478 Affx-122950658 AX-123283827 12 26139736 CTCTCCTAGTAGCCCTAGCAGGAGGGCTTGCTGTG[A/C]GCTCTGAAGTTGCTTGTTCATGCCTATTGTGTTCT M 2 1 2 1 101000 r 74 goat snp50206-scaffold717-5754795 12 59401079 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414033 Affx-122949791 AX-123284382 12 26169186 TACTGCTTTCTTAAGAGGTTGTTCCAATTTACCCC[A/G]CCAGCAGCCACATATGTGTGTAAGGTGCCCGTTTA R 2 1 2 1 101000 f 74 goat snp50207-scaffold717-5784245 12 59371511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450383 Affx-122922086 AX-123320718 12 26204338 GCATACATGTATTATGTGTATGTGTATTATAAAAT[A/G]TTTTCAGTCACAGGTCACCAATGTATGTCTTAGTC R 2 1 2 1 101000 r 74 goat snp50208-scaffold717-5819397 12 59336798 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793326 Affx-122974069 AX-385280304 12 26259251 TGCTCTCTGACAATGAATTATCCAACTTTGTAAAC[G/T]ATCCTACCATCTTTTACTCCTTGAAAATATATTGA K 2 1 2 1 101000 f 74 goat snp50209-scaffold717-5874310 12 59281620 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767241 Affx-122951230 AX-385254522 12 26290116 TGTCAGTATGTTTCAACTGGTACTTACACAATGCC[A/G]CTTGAATCTCACTCTAGCAATGCTGAGAGATACCA R 2 1 2 1 101000 f 74 goat snp50210-scaffold717-5905175 12 59250573 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782277 Affx-122968986 AX-385269355 12 26417236 AACTGAAACCGTACTCATTTAACACTAGCTCCTTC[A/G]CTCTGTTCCTCCAATCACCATTTTATCTTCTCTCT R 2 1 2 1 101000 r 74 goat snp50213-scaffold717-6032295 12 59123680 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409461 Affx-122954074 AX-123279812 12 26448926 GTACTACCTAGAACTGGATCCTTTGCTGGGGGAAG[C/T]AATTACCCGGATAACTTTAGAAAACATTTTTATGT Y 2 1 2 1 201000 r 74 goat snp50214-scaffold717-6063985 12 59091431 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397139 Affx-122962671 AX-123267494 12 26482642 GGAATGAGTCAGTTGGCAAATATTATTCAGTGCCT[A/G]CTCTGTGTAGAACCTTGTGAGGGTTGCTGTTTTGG R 2 1 2 1 101000 r 74 goat snp50215-scaffold717-6097701 12 59057797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415016 Affx-122949028 AX-123285365 12 26511691 GGAAGAGCTGTATATTAAAGAGGGTAAGGGTATCA[C/T]AATAGACCAAGGTTAACACCTACAAGCAAGAAAGG Y 2 1 2 1 101000 f 74 goat snp50216-scaffold717-6126750 12 59028213 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434775 Affx-122933889 AX-123305116 12 26591852 GGGAAAGGACCTCTTTTCCTTCCAGAACTGTTTAA[C/T]CAGTGGGGTCATTTTTCCTTATATACCAGTTGTAT Y 2 1 2 1 201000 r 74 goat snp50217-scaffold717-6206911 12 58947151 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428329 Affx-122939002 AX-123298672 12 26641112 ATTTATTCATTCATAATCATTTATTGATGTCCTAC[A/G]TTATGCAAAATTACAGTGCCTGGAACTGGGGACAC R 2 1 2 1 101000 r 74 goat snp50218-scaffold717-6256171 12 58897716 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772626 Affx-122928601 AX-385259774 12 26678227 GGAAGAAGGAACAGATTTGTCCTAATTCCAAATGA[C/T]GGAATTAGAACCAATGGATTGAAATTATAAGCAAA Y 2 1 2 1 201000 r 74 goat snp50219-scaffold717-6293286 12 58860219 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272712 Affx-1111832950 AX-519546416 12 26711218 ATAATAACCATCATAGATCCTGGCACATATTTGAC[A/G]TTCAGTGTATTTTAAGTGAACAAATTAACAACTTT R 2 1 2 1 101000 r 74 goat 12_26711218_AF-PAKI 12 26711218 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320777979 Affx-122936388 AX-385265095 12 26733034 AGTTCCGTATTAGGAGTTTTGTAAGTTTCACAATT[A/C]AGTATCCTGGAGTTTTCGAAAGAGGGTTACATTTT M 2 1 2 1 101000 f 74 goat snp50220-scaffold717-6348093 12 58805812 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780876 Affx-122952503 AX-385267963 12 26791452 TAATCACATTTTCTCTGTGTAACAGTTAGAATGTG[C/T]GTGTTCTCCTTCCCCTGAAATACTTGGGTGGTTGT Y 2 1 2 1 102000 r 74 goat snp50221-scaffold717-6406511 12 58747397 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393619 Affx-122965356 AX-123263974 12 26836431 GGGTGGGACGGGAAGGTTACTGTCAGAATTTGAGG[C/T]AGAACAAATAAATACCTGACAACCCTCTGGACATC Y 2 1 2 1 201000 f 74 goat snp50222-scaffold717-6451490 12 58702472 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788826 Affx-122943206 AX-385275841 12 26890959 GCTTATCTATAAAATCATCCTCAACTCCAGTGTAA[C/T]AGACTTCCCTGTTTGAAAATCAGCAAGATTTATTT Y 2 1 2 1 101000 r 74 goat snp50223-scaffold717-6506018 12 58647807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390366 Affx-122967675 AX-123260723 12 26932589 AATGGTTATTAAATTCTGGATTCCTGGAGTATAAA[C/T]AATTGCTGCTGCTGCTTTGCATTTGTTCAGTTTTG Y 2 1 2 1 201000 f 74 goat snp50224-scaffold717-6547648 12 58606715 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436297 Affx-122933272 AX-123306636 12 26995547 CTGGGTGTGGCTATACAGGGAGTAGATAGGAAGAG[A/C]AGATTAAAAAAGAAGGAAGGAAGGAGGCACCAGGT M 2 1 2 1 201000 f 74 goat snp50225-scaffold717-6610606 12 58542290 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401323 Affx-122959839 AX-123271676 12 27033703 TGACAAATAAGGTAGTTAACAATGCAATGGGGAGC[G/T]TAGCAGTTCACTCACTCACTTCACTGATTCATCAC K 2 1 2 1 201000 f 74 goat snp50226-scaffold717-6648762 12 58504320 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795311 Affx-122939083 AX-385282269 12 27085642 AATTTTTTCCAATGATATTTTTCTAAAAGTTCTAT[A/G]TGATTCTTTCAAATTTGACAGTTATTTCCTCATGC R 2 1 2 1 202000 f 74 goat snp50227-scaffold717-6700701 12 58452269 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391475 Affx-122966719 AX-123261832 12 27168032 TCTATGCAAGAAAAAAATGAAAGTCCTTTGTCTCC[A/G]TATTATGCATACAGAATGGGACAGAGTGATCGTAC R 2 1 2 1 102000 r 74 goat snp50228-scaffold717-6783091 12 58370053 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410592 Affx-122952118 AX-123280942 12 27222640 ACTAATTTAACTGCTCAGGACTACAAGGTATTTTG[A/G]TGTGAAATTTCTACTCATGCCAGAGTTTCTACCAC R 2 1 2 1 101000 f 74 goat snp50229-scaffold717-6837699 12 58315879 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451497 Affx-122921121 AX-123321830 12 27256083 TTCTGATTGTGGCCATTGCTGAAATTCAAAATTGG[C/T]ATTTCATTTAAATTTAAGCATACCTGAAATTTATA Y 2 1 2 1 103000 f 74 goat snp50230-scaffold717-6871142 12 58282189 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794589 Affx-122963214 AX-385281551 12 27299581 TGTGCATCTGCAGAGTTAGGTGTGTCACTACAGGA[C/T]ACCTACATCATCAAGGTTACAGGTGTGGAAGCAGT Y 2 1 2 1 101000 r 74 goat snp50231-scaffold717-6914640 12 58238170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402905 Affx-122958205 AX-123273258 12 27334947 GAAGAAAGTAGGGAAAACCACTAGACGATTCGGGT[A/C]TGACCTAAATGAAATCCCTTCAAGGATTAGCTCAG M 2 1 2 1 303000 r 74 goat snp50232-scaffold717-6950006 12 58195574 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790230 Affx-122965782 AX-385277234 12 27371850 ATTTTGAAATAGAAGAAGGATTTAATTTTGGGACA[A/G]GTGAAACAACTGTTAGGTATATATTTTGTGCTCCT R 2 1 2 1 201000 f 74 goat snp50233-scaffold717-6986909 12 58162996 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381345 Affx-122974418 AX-123251703 12 27448045 TTCAAAGTAGACACTTTGGGAAATTATCACTTTAG[A/C]GGTGTGTCATTGTTAAAAATATCTGTTAAAATCTT M 2 1 2 1 101000 f 74 goat snp50234-scaffold717-7063104 12 58085742 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419617 Affx-122945984 AX-123289965 12 27478926 GTTAAAGTCTTCACTGTATGTTAGAGCCAGTATAT[A/C]TAGAAATATATTTTAAAAACCCACACTATATTAGT M 2 1 2 1 101000 f 74 goat snp50235-scaffold717-7093985 12 58054856 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405277 Affx-122956859 AX-123275629 12 27508027 GCTATGAGTGAGGTTAAGGAGGCTTCCTGTTTTTT[A/G]CTTATACAAAAACCACAAGGATAGCAGGATCTGGC R 2 1 2 1 201000 r 74 goat snp50236-scaffold717-7123086 12 58025694 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441948 Affx-122928575 AX-123312285 12 27567694 TGCCTTTCTTCATTCCCAGCTTGCTCACTGAACAA[G/T]CTATAGAACTGAAGCCCTCAAGGACAGTCTTCACG K 2 1 2 1 201000 r 74 goat snp50237-scaffold717-7182753 12 57965981 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378075 Affx-122977173 AX-123248434 12 27602488 ACAGACCACGGGTGCTGCTTTAGGGGGCTTATCGG[C/T]CATGGGGTAAGAGAGACAGGAAAGCAAGTGTGTTT Y 2 1 2 1 201000 f 74 goat snp50238-scaffold717-7217547 12 57931464 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770234 Affx-122971242 AX-385257400 12 27657902 ACAGGATTTAAAATAAGCTTACCATCAGTGATTTC[A/G]AGTGAATGAATTCTGCTTATGATAAATATAGCTTT R 2 1 2 1 101000 f 74 goat snp50239-scaffold717-7272961 12 57876084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441636 Affx-122928634 AX-123311973 12 27687372 CATGGTAAGTGACAAAGAAAATTTTTCTAATTATA[C/T]TTTTAGAAATTTATGACACAGGTGCCAAATATAAT Y 2 1 2 1 102000 f 74 goat snp50240-scaffold717-7302431 12 57846734 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432480 Affx-122935597 AX-123302821 12 27729485 TGCTATGCCACTTTACATAAGAAACTTGAGTGTCT[A/G]CAGATTTTGGCATTCAGGTAGGCCAGAGGCCCTGT R 2 1 2 1 101000 r 74 goat snp50241-scaffold717-7344544 12 57804851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415557 Affx-122948646 AX-123285906 12 27763600 AATGGTCTAAGAAAACACACAGTGGAAAACAAGTG[A/G]TTTTCTCAACCTGATTTTCCTAATGACCAGGAGCT R 2 1 2 1 201000 f 74 goat snp50242-scaffold717-7378659 12 57770691 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771878 Affx-122975655 AX-385259034 12 27806498 CCCTTTTCCATGCATCTTTTGTGAGTGCATGTGTA[C/T]GAAATGACCATAGGGCGCAGAGCTGCCTATGTATT Y 2 1 2 1 101000 f 74 goat snp50243-scaffold717-7421557 12 57728019 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395436 Affx-122963933 AX-123265791 12 27835813 TTGAGAGACTGCTTTGTGCTAGCGACTATGTGAAG[C/T]GCTTTTCCTGTACCACTGCACTGAATTGTCAAAGC Y 2 1 2 1 101000 f 74 goat snp50244-scaffold717-7450872 12 57698797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792828 Affx-122971023 AX-385279806 12 27867023 ATGCAGAGCCAGTCCACAAAGACTGAGTGAGAAAA[C/T]AGCTTTACAAATGCCCAATTTTCAACAAAAGATCA Y 2 1 2 1 101000 f 74 goat snp50245-scaffold717-7482082 12 57668162 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420267 Affx-122945053 AX-123290615 12 27903822 TAACCACCTTCCCTGGGCCACATGGTCAGTCTTCA[C/T]AGAACTTGAGTCAGTGCCTTAAACCATCATTTTCA Y 2 1 2 1 201000 r 74 goat snp50246-scaffold717-7518881 12 57631192 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385231 Affx-122972100 AX-123255589 12 27945104 TATCACAAGAGATGCCAAAGCTGAAGAACTCTTAT[A/G]CCAATTATCTATTAATATTTATGTATTATATTTCT R 2 1 2 1 101000 f 74 goat snp50247-scaffold717-7560163 12 57590891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789180 Affx-122963818 AX-385276192 12 27996883 CGTGAATTCTGAATAATGGAGCTGGGACAGAACTG[C/T]ATCACTGAACTCTTGAGCTAAGAAAGCTTTTTAAG Y 2 1 2 1 101000 f 74 goat snp50248-scaffold717-7611942 12 57539004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276757 Affx-1111835505 AX-519550266 12 28082563 GAATATTCAGGACTGATTTCCTTTAGGACAGATTG[A/G]TTGGATCTCCCAATTAAAACAAGTAACTACTGTGT R 2 1 2 1 201000 r 74 goat Random2.2K-1262 12 28082563 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417083 Affx-122947497 AX-123287431 12 28090219 CAAAAAGCTACTCACTGGCAAATATATGAAGAATA[A/C]GTGCTTCCATTCAAATGCTCTTAAATGTTTTCAAA M 2 1 2 1 101000 r 74 goat snp50250-scaffold717-7705278 12 57445295 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436112 Affx-122932660 AX-123306451 12 28145471 CCCTCAGCTAGCCTGACCACTGTATTTAAAATGAC[A/G]TCAGGTCCTCTTCATACTTGACTCCTTTTGTTTTA R 2 1 2 1 201000 r 74 goat snp50251-scaffold717-7760530 12 57389946 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407219 Affx-122955384 AX-123277570 12 28205397 TTGGATTTCAAAAAAGCAGTATATTCAGAGTATAA[A/G]CCCTAAGTGCAGGAGCTTATCAGATCTCCTTGTAT R 2 1 2 1 201000 f 74 goat snp50252-scaffold717-7820456 12 57340321 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442530 Affx-122928539 AX-123312867 12 28236673 TATTTTTGGCATATAATTGATACTTTTATCAGTTT[A/G]CTGATAAGAAGGAATTTATTTCTACGGCCAAATTG R 2 1 2 1 101000 r 74 goat snp50253-scaffold717-7851732 12 57308978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785904 Affx-122972710 AX-385272941 12 28276634 AAGGGACAAGAAAGAAAGCTCATTTTTCACCCAAA[C/T]GAGGGTTATATATCAGAAATGGAAACATGGAAAAT Y 2 1 2 1 101000 f 74 goat snp50254-scaffold717-7891693 12 57268530 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426984 Affx-122940387 AX-123297329 12 28327291 GTACTACAATGAACAGAACGCTAGCAGATAAATAT[A/C]CAAACTCAAACCAAATGGATCAGGGTGTGGTTATT M 2 1 2 1 201000 f 74 goat snp50255-scaffold717-7942350 12 57217615 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453161 Affx-122920477 AX-123323494 12 28376151 CCTCCTGGTGAAGACCCCTACCCTGCAGAGTACCC[A/G]CTGCCCGGGGAACATCAGCCTTGGCTCTTCTTAGG R 2 1 2 1 201000 r 74 goat snp50256-scaffold717-7991210 12 57169441 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409709 Affx-122953041 AX-123280060 12 28409877 TGCCCAGATAGCTGACGTTGCCTGTAGAGCAGTGC[A/G]TTTACAGACATACTGCAGACTACCAGGATGGGTCA R 2 1 2 1 201000 f 74 goat snp50257-scaffold717-8024936 12 57135539 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796921 Affx-122935604 AX-385283864 12 28440537 AAGAGAAAAATAAATTCTTATTACGATTCTGTGAG[C/T]TTAATTTTCCTGTCACTTGTAACCCAATGTATTAC Y 2 1 2 1 101000 r 74 goat snp50258-scaffold717-8055596 12 57104852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385606 Affx-122971197 AX-123255964 12 28461064 ACCCTGGTAAACAAAAAAAAACTTTGTCTCGTGTT[A/G]GTCCCTTCTTTAATGGGTTAACTAAAGTGTTGATT R 2 1 2 1 101000 r 74 goat snp3200-scaffold1095-4636279 12 57084000 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429263 Affx-122937894 AX-123299605 12 28489734 GCATCTCATTTCTCATTCCATCCTCACTTCCTGTC[A/G]TGGAGACTCAGTTTTCAGGGTCCAGGGGACAAATG R 2 1 2 1 101000 r 74 goat snp3199-scaffold1095-4607609 12 57055231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443402 Affx-122927386 AX-123313739 12 28544783 GAGGAACAGGGAAGAAGTCCCTGCAGGACGAGTAC[A/G]CAGAGATGGGGATGGGCAGAGCTGAGAATGAAGGC R 2 1 2 1 101000 f 74 goat snp3198-scaffold1095-4552560 12 56999788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453243 Affx-122920414 AX-123323576 12 28595009 TGTTCTCAGCCAACCCCTGGCTGCTTCAGTGAGTC[A/G]CTTTTGCAGCTTCTCTGAGCAGAGGTAAAAATGCA R 2 1 2 1 101000 r 74 goat snp3197-scaffold1095-4502334 12 56949660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775020 Affx-122929413 AX-385262152 12 28624671 AAACGAGCAAAAAGGTCTTTTACATCTTTCACGAA[C/T]GATCCAAGCGTGAGTAAGAAGATACACTCATCTAT Y 2 1 2 1 101000 r 74 goat snp3196-scaffold1095-4472672 12 56919988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449905 Affx-122922332 AX-123320240 12 28664628 GTGTTTACAGAGTCAGTCAGTCCATCAGTTCAGTC[A/G]GCAGAGTGTCCACCACACGTGATCCCCTGAGCAGC R 2 1 2 1 201000 r 74 goat snp3195-scaffold1095-4432715 12 56879971 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406995 Affx-122955036 AX-123277346 12 28708497 GACTGTGGGTCCTAAGACTCTTTAATCAATAGGAA[C/T]TGATAAGAAGCCAGATGAGGAATATAGGCAAGGCT Y 2 1 2 1 201000 r 74 goat snp3194-scaffold1095-4388846 12 56836172 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392555 Affx-122966086 AX-123262912 12 28744348 GATGGATTCTTTATGATTGATATTCAAATCCCAAG[A/G]TTTATGCGCTGGGGAGAATGACAATGTGTGCAAGC R 2 1 2 1 101000 f 74 goat snp3193-scaffold1095-4352995 12 56800622 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390764 Affx-122967895 AX-123261121 12 28774168 AATTTCAACCTGGAAAACTCCTCAAATCTTCTGCA[A/G]TACCATCTCCTTTAGAATCTTAAGACTACAGGATT R 2 1 2 1 101000 r 74 goat snp3192-scaffold1095-4323175 12 56770767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429389 Affx-122938541 AX-123299731 12 28807968 TTTCCCTCCCCATGGCCACTGCCTTAATTCAGGCT[A/G]TCATCATCTATCTCTTGGATGACCTCTAATTGACT R 2 1 2 1 201000 r 74 goat snp3191-scaffold1095-4289375 12 56737152 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770031 Affx-122975557 AX-385257198 12 28857706 AATTCAGCATTATGTATCAAAATCCTTTTGAAAAG[A/G]CATAGCATCTGACTCAGTTTCTAGCAATGAATTCT R 2 1 2 1 101000 r 74 goat snp3190-scaffold1095-4239637 12 56688836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405109 Affx-122956978 AX-123275461 12 28906857 ATCTTAGTTTAAGTGAAATAATTGTGAGTTCTATC[A/C]GGGGATTTAAAGGACTAAAAAAAAGTCTGAAACAG M 2 1 2 1 101000 f 74 goat snp3189-scaffold1095-4190486 12 56639881 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381901 Affx-122974155 AX-123252259 12 28979537 GGATACGACTGAGCGAGTAACACACGCTAGCCAAG[C/T]GACCGGGTTCTCTGAGCTTAATTCCCTCCTCTCTA Y 2 1 2 1 101000 r 74 goat snp3188-scaffold1095-4117806 12 56567793 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401888 Affx-122958848 AX-123272241 12 29012392 TGACTCTTGTTGTTTGGTAGTTCTGTAAAGTTGCC[A/G]TGAACACTACATTAGCAATTACTGAACCACTGCTC R 2 1 2 1 101000 f 74 goat snp3187-scaffold1095-4084951 12 56534428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775847 Affx-122927449 AX-385262978 12 29042702 CATTTCAAAACACCTTACATACCAGTGGCCAAGAG[C/T]AGCACCTCATAATCAAGCATATTAATATTTCTTCA Y 2 1 2 1 101000 f 74 goat snp3186-scaffold1095-4054641 12 56504244 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409628 Affx-122953538 AX-123279979 12 29073664 AGACATTTTATTCTGCATTGTTTTACTTTTGATTA[C/T]GGTAGGGAAGCACTCTTACAGGATTAGCAAAAATG Y 2 1 2 1 101000 r 74 goat snp3185-scaffold1095-4023679 12 56473243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420412 Affx-122944917 AX-123290759 12 29137167 TTGCAGCTCTCACCCATCCTCAATCCTTAATTCTG[C/T]ATCTTCTCCCTTTCTCTTTTCTTGTTTCACACTGA Y 2 1 2 1 101000 f 74 goat snp3184-scaffold1095-3960176 12 56408843 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389956 Affx-122968080 AX-123260313 12 29170474 ACTCAGGCACTTTTCATCTTTGAGTATTACCCCTG[C/T]GGTGCACAGGACACGATTTCCAGATTAAGAAAATT Y 2 1 2 1 201000 r 74 goat snp3183-scaffold1095-3926869 12 56375431 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431475 Affx-122936261 AX-123301816 12 29199026 ATTCTACTTTAGTAGAATTCAGCCTTTGGTACCTG[C/T]AGGAGATTTATCTGGAAACTCACTTATAATGCTAG Y 2 1 2 1 101000 r 74 goat snp3182-scaffold1095-3898317 12 56346814 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413708 Affx-122950081 AX-123284057 12 29231919 CATGTTTTCCCAGCACATTTCCCAGGGCTTTTCTA[C/T]GGCTGCAGTGCATTGAGAGGGAGGCAATCTGCAAG Y 2 1 2 1 201000 f 74 goat snp3181-scaffold1095-3865424 12 56313650 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448477 Affx-122923623 AX-123318813 12 29274629 ACACTTGACTGGGCATCAGGCTGGAGCACAGCCTG[C/T]TCACACTCAAGAGATGCTGCCAACTTCTGAATGTA Y 2 1 2 1 303000 f 74 goat snp3180-scaffold1095-3822714 12 56270967 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271903 Affx-1111832951 AX-519545684 12 29284002 GAGAGGGAAGGACACTGCAAATAAATGTTTCTGGC[A/G]TGTGTTGGGAGTGCTCACAGTGTATGGAGCACACT R 2 1 2 1 102000 f 74 goat 12_29284002_AF-PAKI 12 29284002 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320795607 Affx-122937936 AX-385282562 12 29317182 CATGCATGCCTACCCTTTGTTCCAGATGAAGATAC[G/T]ATCTTTCTTTCAAGGCTGTAAGCAAGCCTAACCTT K 2 1 2 1 101000 f 74 goat snp3179-scaffold1095-3780161 12 56228274 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434253 Affx-122934820 AX-123304594 12 29363572 GGCATCAGTTGCTGCCATGTGAATGGACGTGTCAC[A/G]TGCCCACCTCCGTGTGTCGTCACGAAGCACTCAGG R 2 1 2 1 101000 f 74 goat snp3178-scaffold1095-3733771 12 56181862 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401994 Affx-122958768 AX-123272347 12 29450603 CACTCTAGTCTCACACTTTGCCTTCTTAGCACATC[G/T]AGAATGTCAAAAGGAAAAGGGTCAGGAAGACCCTC K 2 1 2 1 201000 r 74 goat snp3176-scaffold1095-3646740 12 56094322 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389523 Affx-122968290 AX-123259881 12 29481006 AAACTAGTTAAATAAATAATAATGTAGCCAGACAA[C/T]AAAATGGTGCCACATCATTTAGGATTGGATTCTAC Y 2 1 2 1 102000 r 74 goat snp3175-scaffold1095-3616337 12 56067429 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417736 Affx-122947428 AX-123288084 12 29512234 AGAAGTATAAAAATCAAGACAAAGCAATTTGCACC[A/G]ACTAGATTTCACTCTCATTGTGACTTCTATCCAGT R 2 1 2 1 101000 r 74 goat snp3174-scaffold1095-3585109 12 56037431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450408 Affx-122922066 AX-123320743 12 29545975 CGTGTTTGGTACTTGGTAGAATTTTAAAAAGCAGA[G/T]ATGTCTCAGCCCAGGTGGGACCACTGAGGCTTGAG K 2 1 2 1 201000 r 74 goat snp3173-scaffold1095-3551368 12 56003407 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782793 Affx-122952081 AX-385269865 12 29590386 ATTAATACCTAATTTTCTATGGCAATTGTTGACTT[A/C]GCATATGATCTAAATTCAAGGCCTGAGCCTACATT M 2 1 2 1 101000 r 74 goat snp3172-scaffold1095-3506957 12 55959179 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453298 Affx-122920369 AX-123323631 12 29620824 ATGGAGAAGTTGGTGTAGCCTGAACTTGATCTGTG[C/T]GGGAGCAAGGGCTAGGGATGAAGTTAGAGTTGGAT Y 2 1 2 1 101000 f 74 goat snp3171-scaffold1095-3476519 12 55928957 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401440 Affx-122958988 AX-123271793 12 29652284 TATTCCTTCTGCCTGGCATGTGATCCCCCAAGACA[C/T]TGGATGGCCCGCAATTCCCTCAGACCCCTTCCCAG Y 2 1 2 1 201000 r 74 goat snp3170-scaffold1095-3445059 12 55897222 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392627 Affx-122966461 AX-123262984 12 29742266 CTTGGAAACCCTGTCCCCAGAACCCTGGTCCAAGA[C/T]GATAGCAGAGACTCATTACTATTCTTAGCTAAAGG Y 2 1 2 1 101000 r 74 goat snp3168-scaffold1095-3355077 12 55807672 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786746 Affx-122951785 AX-385273777 12 29797420 GCTGCTGGAAAGGTGAAAGGGCTGCTCAGGAAGAA[C/T]ATGAACACAATATGAAAACTGCAGGGCTTTCTCCA Y 2 1 2 1 101000 r 74 goat snp3167-scaffold1095-3299923 12 55753287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418801 Affx-122946173 AX-123289149 12 29826735 CTTTTTTGAAAATCGTTCCTAGATTTTTATAAGTG[C/T]ATGCACGTCTGTTTATGGGGATATATGTGTCAAGT Y 2 1 2 1 201000 f 74 goat snp3166-scaffold1095-3270608 12 55723011 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405045 Affx-122956354 AX-123275397 12 29861226 GGTTTTCTTACGTGCCTTTAAAGATACAGTGTGAC[C/T]CTTATTCTAAAAATCTGATTATAGAGGGGTTTCAT Y 2 1 2 1 101000 f 74 goat snp3165-scaffold1095-3236117 12 55688790 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779882 Affx-122974140 AX-385266981 12 29902920 TTATGTGCTTTAGACAAATAGAAATATTCTGCATT[C/T]ATACTCAGTTTTCTGCATTTCAATCCAACATTGAA Y 2 1 2 1 101000 r 74 goat snp3164-scaffold1095-3194423 12 55647127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432274 Affx-122936332 AX-123302615 12 29938144 GAGAGAAGAGCCATTTTGCCTGAAGTCACACAAGT[A/G]ACCCAGAGCCAGGTTGGAGTCTGACCCAAGGGCAA R 2 1 2 1 201000 r 74 goat snp3163-scaffold1095-3159199 12 55613226 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792161 Affx-122968529 AX-385279146 12 29974754 AAAAAAGATTACAGAATTATAGTACAATAGTCCTT[A/G]CAGTCACGTGAATTCCTGACATTTTGAAACCACTT R 2 1 2 1 101000 r 74 goat snp3162-scaffold1095-3122589 12 55576427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798373 Affx-122974815 AX-385285308 12 30038082 AAAAAATAGAAATGTATCACTATGAAATACTGAAC[A/G]TATTCTTAAAGGTTTAACTTTAGGAATAGGGATTG R 2 1 2 1 201000 f 74 goat snp3160-scaffold1095-3059261 12 55513350 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375512 Affx-122979122 AX-123245871 12 30078004 TCCGTTGGTTCTCTCTATATTTCCACACCTTGTTG[A/C]TCAGTCATGTGTCCAACTCTTTGTGACCCTATGGA M 2 1 2 1 101000 f 74 goat snp3159-scaffold1095-3019339 12 55474360 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424447 Affx-122941787 AX-123294793 12 30115573 GGATTTATGTGGGATCCAGCTAAGTTTTATTGAGC[A/G]CCTGCTATGCGGAAGGCCTGGAAAAGGGATGTATG R 2 1 2 1 101000 f 74 goat snp3158-scaffold1095-2981770 12 55436402 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463217090 Affx-1109872142 AX-514703141 12 30133637 CCAGACTGATCAACTTACCTGCAGCACATAAAGCA[A/G]CTTGCTAACATATTATATATCATAAAATGGCAGGT R 2 1 2 1 201000 r 74 goat GoatD01.014214 12 30133637 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38433235 Affx-122935250 AX-123303576 12 30160138 AGTGTATACTTATGTACCTGGCATTGAGCTGGTGA[C/T]GGGGATACAGAGATAAATAAGACAAAGTTAGGGAG Y 2 1 2 1 201000 f 74 goat snp3157-scaffold1095-2937205 12 55392437 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417193 Affx-122947316 AX-123287541 12 30201454 CGCTCAGGCCCTCACTTCTGACCCCTAGAATCAGC[A/G]TCTGCATCTCAGGCTCACAGGTGACTTGTAAGCAC R 2 1 2 1 101000 r 74 goat snp3156-scaffold1095-2895889 12 55351014 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389655 Affx-122968727 AX-123260013 12 30230976 TGTTATCATCTCCCCCAAAGATGCAGACATTGGGG[A/C]TCGTAGAAGCTCAGTGTCCTGCTTAGGTTGTGTGA M 2 1 2 1 101000 r 74 goat snp3155-scaffold1095-2866367 12 55320901 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783517 Affx-122929385 AX-385270580 12 30267939 TTTCGGTACTCAGTAAACCTGAGACTGTCATACTT[C/T]TCATTTTTAAGAGTTGGACCTTTAAGGACTCAGGA Y 2 1 2 1 101000 f 74 goat snp3154-scaffold1095-2829404 12 55283477 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383669 Affx-122972508 AX-123254027 12 30299227 CTTTAACTGGTTTTAAAAGTGAAAGATGTCTGTGG[C/T]GTTCTGAGATTATAGTCCTTTCAGGCAACCATTGA Y 2 1 2 1 101000 r 74 goat snp3153-scaffold1095-2798116 12 55252245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392109 Affx-122966354 AX-123262466 12 30343574 TCCAATCTCCCTACCAATGTTGCCTGGTGAATCCA[C/T]GCAAAATATTCAGTGCAGTGCCAGATACTACTAAT Y 2 1 2 1 101000 r 74 goat snp3152-scaffold1095-2753769 12 55207910 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777743 Affx-122956902 AX-385264861 12 30379798 ATTCCTTTTTAATGTATGACTACTCATCAAAGACA[C/T]CTGCTTTACTCTAAGAGGTTTTTATATGGCCTCAA Y 2 1 2 1 101000 r 74 goat snp3151-scaffold1095-2717545 12 55179295 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441441 Affx-122928812 AX-123311778 12 30411359 CAAAAATAAAATTAAATATAAAATAGAATAAAATC[A/G]TGTCCTGGTATTATAAGGAATATATACAGCAGTAG R 2 1 2 1 101000 r 74 goat snp3150-scaffold1095-2685984 12 55147539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420550 Affx-122945290 AX-123290897 12 30440199 CTGAGCACACACACATATATGTATATATACACTCG[A/C]ATAACGCTGAGAACTACACTCCTTAGTAGAATGTA M 2 1 2 1 201000 r 74 goat snp3149-scaffold1095-2657144 12 55118111 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393896 Affx-122965113 AX-123264251 12 30472122 CAAGCTTATTCCGATTGTTTCTCAAGTCTAAACTA[C/T]ACAAAACACATTTTTTCTGGAGTTCTTTGGATTGT Y 2 1 2 1 303000 f 74 goat snp3148-scaffold1095-2625221 12 55086218 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405492 Affx-122956010 AX-123275844 12 30504720 ACCAGACGAAGCAAGAAACAAGGTGAAATCAGGGC[A/G]CGTTATGGTCCTGTGCACACAGCAACCCCACGGAC R 2 1 2 1 101000 f 74 goat snp3147-scaffold1095-2592623 12 55053317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391139 Affx-122966789 AX-123261496 12 30548290 AGTTACCTACTAAAGAGCTAGTAGGGCTTCCCAGG[C/T]GGCGCTAGTGGGAAAGAACCAGGCTGCCAATGCAG Y 2 1 2 1 103000 f 74 goat snp3146-scaffold1095-2549053 12 55009697 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393074 Affx-122965607 AX-123263431 12 30579025 CCAAAGTCTAGGCATTTGTGCTACCAAGTGAGCTC[A/G]CTAAGGATAGAATGAGATTTGTTGAAAACCACTCC R 2 1 2 1 101000 r 74 goat snp3145-scaffold1095-2518318 12 54978904 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434345 Affx-122934725 AX-123304686 12 30635831 CAAATAATCAAAGTCACATGCAGCTGGTAGATGGC[A/G]AAGCTTGAACCCAGGTCTGGCCAACTCCGTTCTGT R 2 1 2 1 101000 f 74 goat snp3144-scaffold1095-2461512 12 54922286 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396310 Affx-122963083 AX-123266665 12 30672572 CTCAAAAGTTTGGAATTTTCCTCCTCTTAACTTTC[G/T]TAACATTTGGACGTGCAGTTGTCGCCAAACTTGGG K 2 1 2 1 101000 r 74 goat snp3143-scaffold1095-2424771 12 54891161 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799984 Affx-122958141 AX-385286908 12 30707639 TTTTATTTCAGCTGTGTTTTAAAATGTGGATATTA[C/T]ATTTTATCTCACAATTCTGTGTGTTCATAGTTTTG Y 2 1 2 1 201000 f 74 goat snp3142-scaffold1095-2389704 12 54855992 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777186 Affx-122930252 AX-385264309 12 30751059 TCTATTCTCATTCACAAAAGTTGCCTGTGATGTCA[A/G]CACAGAGAGTAATTGAATTGGCTCACGATTGCACA R 2 1 2 1 101000 r 74 goat snp3141-scaffold1095-2346284 12 54812351 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431893 Affx-122936010 AX-123302234 12 30841462 TGTTTTCCAAGGGAACATTCTTGGGTGATGGAAAT[A/G]TCCCTTATCTGTGCTGTTCAACAGGGTGGTCTTTA R 2 1 2 1 101000 f 74 goat snp3139-scaffold1095-2255881 12 54721589 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407812 Affx-122954553 AX-123278163 12 30894647 CCTAAAAACTTCAAATGTCATCATGTGAAAATGAG[C/T]AAATAGTGTTAATTGTATAATCACGACTCCATGTA Y 2 1 2 1 101000 f 74 goat snp3138-scaffold1095-2202696 12 54668404 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415860 Affx-122948858 AX-123286209 12 30963544 ATAGAATAATTCCTCTTCCTCCTCTTCTCTTTCAA[G/T]CTTTCCAGCAGAACCAGACACCTCACTGCACATCC K 2 1 2 1 201000 r 74 goat snp3137-scaffold1095-2133799 12 54604461 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379144 Affx-122976728 AX-123249503 12 31020954 GGGGAGCAGGCAGGTGAGAAGATTCTAGAGGGGTC[A/G]TTCTCAGATTCAGATCCCTCCTCGAGCGGGGCCGT R 2 1 2 1 101000 r 74 goat snp3136-scaffold1095-2076389 12 54546702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442621 Affx-122928468 AX-123312958 12 31073331 AGCTGACCCTTGGTGGGTGTGGGTTCCTGACCAGG[C/T]GCACACTTCAAACAAGTCATCAGAGTTGCAAATTG Y 2 1 2 1 101000 r 74 goat snp3135-scaffold1095-2024012 12 54494131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433942 Affx-122934286 AX-123304283 12 31104457 ATTACTGGGATAATAAAAATAACCAGCACATTATA[A/G]TGCCTGCCACATGCCAAACTCATCTTTAAGCACTT R 2 1 2 1 101000 r 74 goat snp3134-scaffold1095-1992886 12 54463136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418918 Affx-122946521 AX-123289266 12 31134578 TCAGGACAGTTGAGGATCTAAGACTAGCTTATCGT[G/T]TCATCTCAAATACAGAAAAAAGTGGCACTAAAAGA K 2 1 2 1 101000 f 74 goat snp3133-scaffold1095-1962765 12 54432825 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402446 Affx-122958617 AX-123272799 12 31213204 AGTCTGGGGTCAGTTTCCAGGAAGTCTCTGTTATT[A/G]TGTTCAGATTCTATGCCTGCTGGTGATCAAAGACA R 2 1 2 1 201000 r 74 goat snp3132-scaffold1095-1884139 12 54353369 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447514 Affx-122924068 AX-123317850 12 31254456 ACAGAGGGCACTTGTAAATTAGCTCAGATTCTGAA[C/T]TAGGTTTATAAATGAAACTTTTCAAGTATGCATAC Y 2 1 2 1 101000 f 74 goat snp3131-scaffold1095-1842887 12 54311723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454150 Affx-122919329 AX-123324483 12 31319637 CTTCTTTTTTGCTGTTGTTCTTTACTTACTTGAGA[C/T]GGGATCACTGAAAAACTCCACATCCTCTGAGCACT Y 2 1 2 1 101000 f 74 goat snp3130-scaffold1095-1777706 12 54246446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419025 Affx-122946037 AX-123289373 12 31358414 CAACACCTTGTTTCTCAAGACGTAACCCGGGGCAG[A/G]TTTTTATGGTCGCGCTAGGGTTTTAGTCACTGGCT R 2 1 2 1 201000 r 74 goat snp3129-scaffold1095-1738929 12 54207484 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392468 Affx-122966153 AX-123262825 12 31433552 CAATTTTTTCCTGTAAACCTAACACTGTTCAAAAA[C/T]GAAGCCAACGAATTAAAACAAAAAAAGTCCAGTGT Y 2 1 2 1 201000 f 74 goat snp3127-scaffold1095-1663791 12 54132137 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413783 Affx-122949920 AX-123284132 12 31484014 CAAACGTTTGTTAAATAAATGTTTCCTGGACGCCA[A/G]CTAAGAACCAGGAATGAGCTTATAGCGAGGGAATC R 2 1 2 1 201000 r 74 goat snp3126-scaffold1095-1613329 12 54081722 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801370 Affx-122963515 AX-385288281 12 31535993 TATGTATTAGAAAATTAAAATGATTCTCGAAAGGC[C/T]GCTAAAAATGGAGGGACTGCACAAAAAGTAGGAAA Y 2 1 2 1 201000 f 74 goat snp3125-scaffold1095-1561350 12 54029875 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787831 Affx-122946854 AX-385274854 12 31582984 GCTCTGTTAAATGAATGAAAAAGCTGTTCTAAGTA[C/T]GGAATAATTAATAGATTATCTTATTAGCATTCTAT Y 2 1 2 1 101000 f 74 goat snp3124-scaffold1095-1514359 12 53982478 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393267 Affx-122965455 AX-123263624 12 31614207 CTAAACACTCTCAGGACTGCTGTGGAAGCAGTACA[C/T]GTCCACAAACACGAACCCCAGTCCTTCCAAACACG Y 2 1 2 1 201000 r 74 goat snp3123-scaffold1095-1483136 12 53951221 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429302 Affx-122938607 AX-123299644 12 31648493 AGACACCCCCTGTTCTTCCCTGCACCCTAATGAAA[C/T]GAGGCTCTGAGCTACAGGAGGCGCAAATCTGGCTT Y 2 1 2 1 103000 r 74 goat snp3122-scaffold1095-1448850 12 53921244 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418648 Affx-122946332 AX-123288996 12 31678999 AGCCAAAAAAATAATAAATAAATGAAACAGGAAAT[A/G]AAAAACCAAAATGGAAGAAATTAAAGACTGAATTC R 2 1 2 1 103000 f 74 goat snp3121-scaffold1095-1418344 12 53890788 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384138 Affx-122972811 AX-123254496 12 31724710 GGATTTCACGCCCTCTTTAACGTGTTTAGGAAATA[A/G]GAAAAAAGAATGGAGGTTTGCAGGACTTCCCTGGC R 2 1 2 1 101000 f 74 goat snp3120-scaffold1095-1372633 12 53845658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379509 Affx-122976456 AX-123249867 12 31807251 AGTCATTTTTAATTTTGCATAATCAAGCGCCCGCC[A/G]TACAGCTGCTCCTGAGAAAGGGGAAGGAAGTCATG R 2 1 2 1 201000 f 74 goat snp3118-scaffold1095-1290092 12 53763213 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272714 Affx-1111832953 AX-519546418 12 31837582 ACTGCCAACTCCCAAACCAGGAGCAGGAGGGCCTG[A/G]GAATGGGGCAAAGGATTCCAGAGTCCTCATCAAAG R 2 1 2 1 102000 r 74 goat 12_31837582_AF-PAKI 12 31837582 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38410521 Affx-122952172 AX-123280871 12 31839131 TTGTGAGCTGTTCCACACAGGCACGTGGGCTGTTC[A/G]TGGTTTATTTAACAGTGAAGTAAAATACCCATTTT R 2 1 2 1 201000 r 74 goat snp3117-scaffold1095-1258212 12 53731077 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450059 Affx-122922815 AX-123320394 12 31911054 GGAACGCAGGCACCATGGTTTCCTAATGAAAAAGA[G/T]ATGTTGGACCAAGGGGGCTTTTCTCAGAGTCCTCC K 2 1 2 1 101000 f 74 goat snp3115-scaffold1095-1186289 12 53663829 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439439 Affx-122930188 AX-123309776 12 31980102 AAGTTCTAAGACCTTAACTTTCTCACAGATCTGTC[A/G]TGTCTTTGGAACACATTTGCAGGGCATGGTGTAAA R 2 1 2 1 201000 f 74 goat snp3113-scaffold1095-1117241 12 53594603 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396265 Affx-122963314 AX-123266620 12 32017530 CTCTGCCTCCCTCCCCTTGGCAGCTTTTGCTCCTC[A/G]TCACTCAGGTCTACCCTTAAGCATCACCTCAGAGA R 2 1 2 1 101000 r 74 goat snp3112-scaffold1095-1079813 12 53557922 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767442 Affx-122956357 AX-385254713 12 32083268 TCTGTTCTTAAGTACCCTATCATTTTTGTTTCTAT[C/T]GTAAAATATATCCTTTTGTTACATGAGAATAAAAC Y 2 1 2 1 101000 f 74 goat snp3111-scaffold1095-1014075 12 53491645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276619 Affx-1111835506 AX-519550129 12 32105948 TGCTGTCTGAGGCTTAGTGTTTCATGAAGTTCCTT[C/G]CAAATGTTAGTTCTCTTTAGACTCTATACACTGGC S 4 1 2 1 101000 f 74 goat Random2.2K-1265 12 32105948 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376069 Affx-122978919 AX-123246428 12 32135677 TCTAACACATTTTTCGAGTTTTTGGTACTTTTCAA[C/T]CCCAGGGTTTTCATTCAGTTCTTTATTTATCTCTT Y 2 1 2 1 201000 f 74 goat snp3110-scaffold1095-961666 12 53439707 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385497 Affx-122971271 AX-123255855 12 32194921 TTTCAGTCCTTTTTTTAATGTAGAAAATCACTTTG[C/T]AATAAGATCTCTACACAAGGTAAAAAAGCACAAAA Y 2 1 2 1 102000 r 74 goat snp3109-scaffold1095-902422 12 53383664 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416370 Affx-122947876 AX-123286719 12 32229747 ACCATTATGTTTCCCCAGTATTTACACATCCGTCC[A/G]GGTGGCTCTGAGAGAACAGGGACGGGCTTTCGTGC R 2 1 2 1 101000 f 74 goat snp3108-scaffold1095-867596 12 53348740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421475 Affx-122943923 AX-123291822 12 32264583 CATCTGAGCAACAAGAGAAGCAATCAAGGGTGGAC[A/G]TAAGACTTCTGTTTTGCTTGTACAGGTCATATCAT R 2 1 2 1 201000 r 74 goat snp3107-scaffold1095-832760 12 53313885 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786062 Affx-122964188 AX-385273098 12 32303191 CCTGAAGTTGCAGTGAACCAGTCGACAGCTCTCTC[A/G]TAATGGAGCTGCACCTCTTCCCAAGATGACAGAAA R 2 1 2 1 101000 r 74 goat snp3106-scaffold1095-794152 12 53275354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405095 Affx-122956988 AX-123275447 12 32340830 GGGAAGGAGGGGGGTGAGTCTGGCTGCCTCAGTAC[C/T]GTCCTTGGATCAAAGCGATTAATTCCTCATCTTCC Y 2 1 2 1 101000 r 74 goat snp3105-scaffold1095-756513 12 53237921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400400 Affx-122959998 AX-123270755 12 32374117 AATCGGTCTCAGGACATCAGTCATGACTCACCCCT[A/G]CATCAATCTTACCCTCTAAATAAGAGCTGATTCTG R 2 1 2 1 101000 r 74 goat snp3104-scaffold1095-723226 12 53204564 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38408336 Affx-122953752 AX-123278687 12 32433610 TGCAGCATCTCATGATGCCTGGTCCTGATGGAGCC[A/G]TCAGCTTGCTCTGAGACATCAAAACTCAAGCCCTT R 2 1 2 1 101000 r 74 goat snp3103-scaffold1095-663733 12 53144376 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776123 Affx-122974014 AX-385263253 12 32491500 GTGTTAATAGCAAGAGACCACGTGATCTCTTGAGG[A/C]TGTTTGCTTCATGCCTGTGATATATCATGCCATTT M 2 1 2 1 201000 r 74 goat snp3102-scaffold1095-605843 12 53086460 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452623 Affx-122920361 AX-123322956 12 32550521 GAGGATTTGGAGCCAAGGTGAATCCCACTGTCGGG[C/T]AGTTTGGTGGATCCCAGGTATATGGTTAGTAGGAA Y 2 1 2 1 101000 r 74 goat snp3101-scaffold1095-546822 12 53027341 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436551 Affx-122932918 AX-123306889 12 32587347 TTAAGTGTGACAGCTCTCTTGGTCTCATGCAGTCC[A/G]CAGAGCAATTCTGTAGACTATCTTTTAAAATTTCT R 2 1 2 1 201000 r 74 goat snp3100-scaffold1095-509996 12 52989493 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431977 Affx-122935951 AX-123302318 12 32652007 CAAATACATGAAATTGTGTGTATCCATCATGACTC[A/G]ATTTAGCCAGGAGTTTATGGAGTCAATGCCAGAAT R 2 1 2 1 101000 r 74 goat snp3098-scaffold1095-445336 12 52924695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394097 Affx-122964947 AX-123264452 12 32695292 CTGGTGTGGTCCACTGCTCTCTAAAAACAATGTGT[A/G]ACATTGAAAAGAATCTGGAGGAGTCATCAAAATGC R 2 1 2 1 101000 f 74 goat snp3097-scaffold1095-402051 12 52880907 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427838 Affx-122939733 AX-123298181 12 32769728 ATTCATGTTTCACTGCAATTAACATGTAAATCATA[C/T]AGACAGGTCACTTTACTAGTATACAGTACAAACTG Y 2 1 2 1 101000 r 74 goat snp3096-scaffold1095-327615 12 52805992 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452691 Affx-122920310 AX-123323024 12 32827054 CCAGCTCTGCACAGAAGGAAGGGCTGGTGGGGAAG[C/T]GCTGGCTCATCAAGCGCCTGGAGCCCATGTGCGTG Y 2 1 2 1 201000 r 74 goat snp3095-scaffold1095-270289 12 52749506 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379248 Affx-122976262 AX-123249607 12 32863479 TTTGTTTTATTTTGGAAACCATGGTGACTGAGAGC[G/T]CCCATGAAGCCATACAAGATGCCCACAATACGCCA K 2 1 2 1 101000 r 74 goat snp3094-scaffold1095-233864 12 52713229 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381753 Affx-122974317 AX-123252111 12 32892925 ATTGAAAAATCATGAAACATATCTACTACCTCCCC[A/C]ACTTCAGAGAAATCTCTCTCACCCGCCAAATAGCT M 2 1 2 1 101000 r 74 goat snp3093-scaffold1095-204418 12 52683862 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425872 Affx-122940648 AX-123296218 12 32922198 TGTAAATTCCTGCATCGTGGCCTCCATGATAATCC[A/G]TTCCTGAAAGGGTTCTGGTTCCCAGCCAGGTTTCA R 2 1 2 1 101000 f 74 goat snp3092-scaffold1095-175145 12 52654461 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419378 Affx-122945620 AX-123289726 12 32953635 AGCATCATAGTAGAAAAAAGACAGGAAGTACCAGG[C/T]GTGCAGGCCTGACAGGGTATGCACAGCACAGCATG Y 2 1 2 1 101000 f 74 goat snp3091-scaffold1095-143708 12 52623066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783983 Affx-122975583 AX-385271037 12 32992049 CACTTTTTTTTCACATGATAACCTCCCTGAAATTA[C/T]GTGTCCCTCTGTTAATATATCCTGAGCACTTCCCA Y 2 1 2 1 101000 f 74 goat snp3090-scaffold1095-105294 12 52584138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419216 Affx-122945692 AX-123289564 12 33026476 CCCATCTCCTAAAAATGCAATCCTTTCAGAAACAG[C/T]AGAAAGGGCCCTTAGGAAGGGCATTGCCCACTTCG Y 2 1 2 1 101000 f 74 goat snp3089-scaffold1095-70867 12 52549741 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416611 Affx-122947631 AX-123286959 12 33062520 AAGGAAACCGCCCTGCTTCCAGCCTCCAGAATGGA[A/G]ACAATTCTGTTCTGCTGCTGAAGGGACCCAGTTTG R 2 1 2 1 101000 r 74 goat snp3088-scaffold1095-34823 12 52514382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382422 Affx-122974245 AX-123252780 12 33093609 ATGATTTTTTTTTTGATGAAACAAAGTATGCAAAT[A/G]CTTCTCAGTGAAAAATGCCCTTAAAAAGAGAAAAA R 2 1 2 1 101000 r 74 goat snp3087-scaffold1095-3734 12 52483254 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787477 Affx-122957725 AX-385274502 12 33103459 GTTAAATCACAGTTACAGTATCTTCTAAATAAATT[C/T]GTGCCGGATACCTAATAAACAACAAAGAAGGTAAT Y 2 1 2 1 101000 r 74 goat snp30449-scaffold335-2653906 12 52473414 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395150 Affx-122964122 AX-123265505 12 33165150 AACCTAAAACCACCATGTAGGAACTCACTCAACTC[A/G]GCTAGCTAGCAACCAGGCCGACCGACCCCTGCACC R 2 1 2 1 101000 f 74 goat snp30448-scaffold335-2592215 12 52412425 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387122 Affx-122970661 AX-123257480 12 33201351 TTCATCTGCATTCAAACCCAGGTCCTCACATCTCC[A/G]TCACAGGGGCCATCTGAGGAATAAGGACTGGCTAT R 2 1 2 1 201000 r 74 goat snp30447-scaffold335-2556014 12 52378469 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420553 Affx-122945287 AX-123290900 12 33241521 CTAAGTTCTGGCAACACAAGGGCCCCCCATCTCGA[G/T]CTTTCTTGACCAATTGTTTTGTTTCTCTGCCTTTT K 2 1 2 1 201000 r 74 goat snp30446-scaffold335-2515844 12 52339256 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768665 Affx-122971532 AX-385255843 12 33272862 GTTTCTGAATTTCAAAGGTTAAAAACTAGCACTGC[A/G]TAAGGTATTTTGTCAGTTAAATAACAGTAGAAATG R 2 1 2 1 101000 f 74 goat snp30445-scaffold335-2484503 12 52307684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430817 Affx-122937452 AX-123301158 12 33304012 ATACATTTAATAAGAGCAATGGCTTCAAAGGTGCT[A/G]CTCAGGCAACAGAAATCTTTCACGGTTGTAGTTTT R 2 1 2 1 201000 f 74 goat snp30444-scaffold335-2453353 12 52276216 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797712 Affx-122960065 AX-385284651 12 33335288 CATTCATCTAGGGTGGTGAATCCTTAACCTCTAAC[A/G]TGAATGAAGTATCCCCCCTGAAAATTGTCATAATA R 2 1 2 1 101000 f 74 goat snp30443-scaffold335-2422077 12 52244868 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401369 Affx-122959238 AX-123271722 12 33364644 GAGTGTCTTCCAAATACAGGCCCTTCAGGTGGTGA[C/T]TACTCAATAAATATTGAGTTGAAGAGGAGCGAGAT Y 2 1 2 1 101000 f 74 goat snp30442-scaffold335-2392721 12 52215748 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276621 Affx-1111835507 AX-519550131 12 33371939 AAGAGAGTAAGTTCTAATTTTAACCACTTGTAAAG[A/G]AAGCAGAGAAAGTGACGCAATAAAGCAAATGTCTT R 2 1 2 1 201000 f 74 goat Random2.2K-1266 12 33371939 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424812 Affx-122941377 AX-123295158 12 33401956 ATCCAGGATGAGCTCCAGTGTTTAAGAATCCTTTT[A/G]CCCATTAGATGTGGCAATACACACACACACACACA R 2 1 2 1 101000 f 74 goat snp30441-scaffold335-2355409 12 52178499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413242 Affx-122950238 AX-123283591 12 33433985 TAAAGAGGAAAAAAAAAACCACCAACAACTAGACA[C/T]GACTTAACCAGTCAACTGAGTGGACTTAATCCATG Y 2 1 2 1 101000 r 74 goat snp30440-scaffold335-2323380 12 52146173 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418960 Affx-122946083 AX-123289308 12 33471379 ACTGGATAAAATTCAGCTGGTAGGCTGGGACTGCC[C/T]GCCATCCTCCACTCAACCCTTATTCTAATTTCATT Y 2 1 2 1 101000 r 74 goat snp30439-scaffold335-2285986 12 52108685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774119 Affx-122919883 AX-385261257 12 33508893 TCTTTGATTTGAGGGTTTACTTGGCTCTGTTACTC[A/G]TGAAAACTATGCAGCTAAATTTTTTTGTTGAATAT R 2 1 2 1 101000 f 74 goat snp30438-scaffold335-2248472 12 52071741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437513 Affx-122932340 AX-123307851 12 33564089 GTTGACAGCTAAATAAAGAATTATTTGACTCAAGA[A/C]ACAATGGAGTTGGGTTGGGTTGGACACCTTGGTGA M 2 1 2 1 201000 f 74 goat snp30437-scaffold335-2193276 12 52014573 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451131 Affx-122921376 AX-123321465 12 33596180 TCCAACCTCAGTACCAATGCCCAATACCAAATTAT[A/G]TACTAAGTCTTATTAATAAAACTCTCCAGTGTCAA R 2 1 2 1 101000 r 74 goat snp30436-scaffold335-2161185 12 51982338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792478 Affx-122947563 AX-385279459 12 33649934 TCTAGCCAAGAATCCATAACTGAACTCGAGAAGTT[A/C]AGTTGTGGCTGAAAAAAACATCCTCTAAGATGAAA M 2 1 2 1 101000 f 74 goat snp30435-scaffold335-2107431 12 51928706 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393607 Affx-122965367 AX-123263963 12 33682834 GTTTTTTTGATTCAGCATGGAGGCATTAATAGCAT[A/G]CTTGCTGGGCTCACCAGAAGGCTGGGAAGTACAGA R 2 1 2 1 101000 f 74 goat snp30434-scaffold335-2074531 12 51895553 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378204 Affx-122976933 AX-123248563 12 33713322 TTACTTGTTTTTGTTTTGCATACTAGAGAATCAGG[A/C]GGTAGAGGAAGAGACTTAAAACTCTTTAGAATCAT M 2 1 2 1 101000 r 74 goat snp30433-scaffold335-2044043 12 51864987 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799878 Affx-122930271 AX-385286804 12 33766034 TATATGTGAGGTGACATGTCAGGAAATTTACAGCC[A/G]TTTAATCATAGCAAACCTACGGATTAGGGATGATA R 2 1 2 1 102000 f 74 goat snp30432-scaffold335-1991331 12 51812647 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450550 Affx-122922474 AX-123320884 12 33794699 TCCTCAGCATTGAACAAGAACTGAAAAGCAACGCA[C/T]GTATACAGAGAACGTGGTCTGCTAAATGCTGTCAG Y 2 1 2 1 101000 f 74 goat snp30431-scaffold335-1962666 12 51783809 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447796 Affx-122923937 AX-123318132 12 33825688 CTCCTGTGTCTCCACTGACAGTGGAGGTTGGCAGA[C/T]GTTTTCTGTCAATGCTGAGCTGGAGAGCGCTGCTG Y 2 1 2 1 201000 r 74 goat snp30430-scaffold335-1931677 12 51752431 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383185 Affx-122973215 AX-123253543 12 33877119 TTGATCTCTCTTTTTATTATTTATTATATAATTGA[C/T]GGGACAGGACTTTTAACAAAATAAAAAGGCATTTC Y 2 1 2 1 101000 r 74 goat snp30429-scaffold335-1880246 12 51701113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276623 Affx-1111835508 AX-519550133 12 33911568 AAGGAAAAGAGAAACCAGCAAAGGAAACAGTGGGA[A/C]CAATCAGAGAGGAAGGAGGAAAATCACGAACTGTC M 2 1 2 1 201000 f 74 goat Random2.2K-1267 12 33911568 T G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397107 Affx-122962696 AX-123267462 12 33918313 TTCAAAGCCAGAATCTAGGGAATATTTGCAACACA[C/T]GAGAAAGAAACAACACTGTTAGTCCATAAAATCAG Y 2 1 2 1 101000 f 74 goat snp30428-scaffold335-1839052 12 51659718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402893 Affx-122958214 AX-123273246 12 33966780 ACCGTGAAAGCGGCATTCCCAGCTGTGCTCCAATC[A/G]CCCGGATAAAAGAGGTGAGAACATCCTGGGTGCTG R 2 1 2 1 201000 r 74 goat snp30427-scaffold335-1790585 12 51611236 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388102 Affx-122969496 AX-123258460 12 33995714 AGATTTCAGGGTTGTGCGGGCCATTAGAAGCAAAA[C/T]GCAGACCCGTGACTGCCCTTAACCACTGTTCATTC Y 2 1 2 1 101000 f 74 goat snp30426-scaffold335-1761651 12 51582111 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423513 Affx-122942457 AX-123293859 12 34026947 CCAGCGGTGTGACCTGCCTGCTGTCCAGGTGAGGG[C/T]GGAGCAGCACCTGTCATTTGCATGTGTGTGTGCTT Y 2 1 2 1 303000 f 74 goat snp30425-scaffold335-1730418 12 51550686 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377673 Affx-122977844 AX-123248032 12 34058183 GCATCCTCGAGGGGCTTCCGTCCTTCACGGGGGAC[C/T]CGGAACCCACGTTGATTTTGCTGTTTCTAACATAA Y 2 1 2 1 101000 r 74 goat snp30424-scaffold335-1699182 12 51519415 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378691 Affx-122977068 AX-123249050 12 34091464 TCTTTTTATGATTTTTTTGTTTTAAGTAAGTTTTC[C/T]ATGCTGCAGTATCATAAAGATAAGCTCTTATGCAT Y 2 1 2 1 101000 r 74 goat snp30423-scaffold335-1665901 12 51486771 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399341 Affx-122961360 AX-123269696 12 34143365 ATCTCGACAGAGACGATCGTTGCTCACTTGGCCTT[A/G]CGCAATATCGCCCAGGACTGCAAAGTGCTCTGCTG R 2 1 2 1 101000 f 74 goat snp30422-scaffold335-1614000 12 51434902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424240 Affx-122942472 AX-123294586 12 34199327 CCACTGTGTAACTGTTTACAGAAGGATGGAACCTG[C/T]GGAAGTAGTAATCATTTATTCTGCTGTTAATTCAC Y 2 1 2 1 101000 f 74 goat snp30421-scaffold335-1558038 12 51379165 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419637 Affx-122945968 AX-123289985 12 34295846 TTCCTCTACACATTTAATGAAAGCTGGCATGTTAC[A/G]TAGTCATGGCCCCAAGCCCCAAGTAAGTGCTCTTA R 2 1 2 1 101000 f 74 goat snp30420-scaffold335-1461519 12 51283400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452372 Affx-122920625 AX-123322705 12 34326909 AGCACAGTTACAGGTCAAATAAATCTTTGCCAAAA[C/T]AAAGTTATTTGATAGCCATAACTATAAAAACATTG Y 2 1 2 1 101000 f 74 goat snp30419-scaffold335-1430456 12 51252291 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463219591 Affx-1109873382 AX-514705611 12 34343528 TGGTAAATTCTATCAAACATTTTAAAAAGAAATAG[A/G]ATCAGCTCTACACAATCTTTTCCAGATAACATAAG R 2 1 2 1 101000 r 74 goat 12_34343528_AF-PAKI 12 34343528 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38411736 Affx-122951516 AX-123282086 12 34393088 ACTGCTTCATGCTGAGAATATACAGTTGAACACAA[C/T]AGACTTCCCTCCTGCCCCCAAGGTGTTAGGTTTTG Y 2 1 2 1 201000 f 74 goat snp30418-scaffold335-1364277 12 51186124 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430501 Affx-122937227 AX-123300842 12 34478328 CTTGTCACTTTGTCTGAGGGGGCAGGATTGGTCCC[C/T]GTGGAGTGAGCAGGGGGGTCCCGGGCTTAGGGTGT Y 2 1 2 1 101000 f 74 goat snp30416-scaffold335-1279037 12 51101254 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778794 Affx-122925592 AX-385265903 12 34509187 TTGTTAATAACAGTACTAAACCAGGAATTTAAGTT[C/T]GTAAAGGACACAGACACAAATTAACATCGTAGAAA Y 2 1 2 1 101000 r 74 goat snp30415-scaffold335-1248178 12 51070357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382720 Affx-122973619 AX-123253078 12 34608201 ACACCAATGGGCACAGTGCTCGAACCTCAGCAAGT[C/T]GTGTCACATGCACCCTTCGAGGGAAAGGTCAGGAC Y 2 1 2 1 101000 f 74 goat snp30414-scaffold335-1149164 12 50971260 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405955 Affx-122955547 AX-123276307 12 34644327 TCACTTTATTCATGATATAAATCACCACAGGTTTA[C/T]ACAGGTAGAAAGTTTTTCACTTTTCAAAGTCAGGG Y 2 1 2 1 102000 f 74 goat snp30413-scaffold335-1113038 12 50937884 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436078 Affx-122932692 AX-123306417 12 34693440 CCAAAATACAGCAGATGATGGTGAAGGACATTATA[C/T]ATATGCTGTTTTTAATAACAAAATGATCTAATCAT Y 2 1 2 1 101000 f 74 goat snp30412-scaffold335-1063925 12 50888578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771173 Affx-122922992 AX-385258333 12 34732560 AAAAAATGTTATGGAAAAGAATTAGGATCAATTAT[A/G]TTCTTGTATTCTTTTGCACTAGTTATCTGAATATG R 2 1 2 1 201000 r 74 goat snp30411-scaffold335-1024805 12 50849450 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800729 Affx-122929993 AX-385287646 12 34769122 CCACCAGAAAGATGCACTGAAATACAGATTTCTTA[C/T]TATCTTCAACCAAAAGCAGCTTCATGGCAAAGAGA Y 2 1 2 1 201000 f 74 goat snp30410-scaffold335-988243 12 50813808 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406493 Affx-122955156 AX-123276845 12 34826053 AAAGCCTCCTTCTCTCTCCTCACGCATACTGGGTT[G/T]CTGTGAACCTCACTGCCATCCGTGCGCGAGGCTAG K 2 1 2 1 101000 f 74 goat snp30409-scaffold335-931312 12 50755609 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389917 Affx-122968107 AX-123260274 12 34871188 TTCCTCCAGGTACGGTGTTTGTCTCTGACTTGCTC[A/G]TGTTTGTGGCGGCCTGTGTTCAGCAGTGACCTGGA R 2 1 2 1 201000 f 74 goat snp30408-scaffold335-886177 12 50710615 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384792 Affx-122972003 AX-123255150 12 34905065 TTCTTTAGTAAACAGGGGTGTACACACCCCAGTAA[C/T]GCACCCAGCCTTCAGCACAATCAACTCGTGGGGTG Y 2 1 2 1 202000 r 74 goat snp30407-scaffold335-852300 12 50676693 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450834 Affx-122921785 AX-123321168 12 34949980 CTCGTTAACCAGAGTCTCCCGTTCACTTACATCGA[A/G]CTCCAGAGAACTGTGAACTGTTGTAGACACAGCTT R 2 1 2 1 101000 f 74 goat snp30406-scaffold335-807385 12 50631677 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391582 Affx-122966612 AX-123261939 12 34984758 GATTGTCATTTTCCCCTGACATCTCCTATTCATTT[A/G]TCCATGGAATGTCCTGAGGCCTTCTTATATCATCA R 2 1 2 1 202000 r 74 goat snp30405-scaffold335-772607 12 50596902 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399088 Affx-122960878 AX-123269443 12 35027103 AGGCTGGCCTGGCCCAGACCACTCTGGCCATCCTC[A/G]AGCTAGCCTCCCAAAATGCTCAGGGTTATTTGCTT R 2 1 2 1 101000 r 74 goat snp30404-scaffold335-730262 12 50554041 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762963 Affx-986697492 AX-385250953 12 35046018 TACTCTCCATTCTCTCCCCTATTCTGCCTTTAAAA[A/C]ACCTCCCCTGAAATCCACTGGGGAGTTCCAGACTT M 2 1 2 1 600010 f 74 goat 12_35046018 12 35046018 Ancestral_priority_1043 ancestry 0.474 neutral IMAGE 10K 10K ancestral 320765596 Affx-986697494 AX-385253075 12 35049675 ATGAGAATTTGCTGTATGACTCAGGGACCTCAAAC[A/G]TGGACTCTGCAAAAGGCTGAAGGGTGAGGTGGGGA R 2 1 2 1 600010 r 74 goat 12_35049675 12 35049675 Ancestral_priority_1043 ancestry 0.498 neutral IMAGE 10K 10K ancestral 320765539 Affx-986697462 AX-385253020 12 35049872 AAATACTTTTTGTTTTAAACAGATGTTCAGTGAAT[G/T]CCCTTCAGGCACAGGACCACTAGGCCAGACACAGA K 2 1 2 1 600010 r 74 goat 12_35049872 12 35049872 Ancestral_priority_1043 ancestry 0.436 neutral IMAGE 10K 10K ancestral 320762936 Affx-986697465 AX-319771472 12 35049949 AAACATGGGGGAGATGTCATAAGACCTCTATCTGC[A/G]CTTGATTACTGATCTGAAATTGTTCAATACTACAA R 2 1 2 1 600010 f 74 goat 12_35049949 12 35049949 Ancestral_priority_1043 ancestry 0.61 recommended IMAGE 10K 10K ancestral 320765549 Affx-986697467 AX-385253029 12 35049954 TGGGGGAGATGTCATAAGACCTCTATCTGCGCTTG[A/T]TTACTGATCTGAAATTGTTCAATACTACAACTAAA W 4 1 2 1 600010 r 74 goat 12_35049954 12 35049954 Ancestral_priority_1043 ancestry 0.778 recommended IMAGE 10K 10K ancestral 320762940 Affx-986697469 AX-385250931 12 35050011 ATACTACAACTAAAGGAACAATAACAAGTGATGGA[A/G]AGGATGTACAGAAACTGAAATTCTCATATATTGCT R 2 1 2 1 600010 f 74 goat 12_35050011 12 35050011 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320785682 Affx-122947573 AX-385272723 12 35064629 ATGATGATAAAGGTAAACAAACCTGCTCACAAGCC[C/T]TCAAATATTAAAATCACCAAGAAAGTATTTTCAAA Y 2 1 2 1 101000 f 74 goat snp30403-scaffold335-692736 12 50515821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382532 Affx-122973794 AX-123252890 12 35131985 AATTTACATTTAAGTAAATATAACAAATACAAAAT[A/G]TCTGACCGCGAAAAACTCAGAGAGGTCAACTATTG R 2 1 2 1 101000 r 74 goat snp30402-scaffold335-625380 12 50451655 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762948 Affx-986697477 AX-385250939 12 35169701 ATACTGATCATCCATTTCCTAAAAGCTGTAAAAAA[A/T]TTTTTTCAGTCATCAAGTGAACCAGCTAACTTTTG W 4 1 2 1 600010 f 74 goat 12_35169701 12 35169701 Ancestral_priority_1043 ancestry 0.452 neutral IMAGE 10K 10K ancestral 320765571 Affx-986697479 AX-385253051 12 35169703 ACTGATCATCCATTTCCTAAAAGCTGTAAAAAATT[G/T]TTTTCAGTCATCAAGTGAACCAGCTAACTTTTGTA K 2 1 2 1 600010 r 74 goat 12_35169703 12 35169703 Ancestral_priority_1043 ancestry 0.576 neutral IMAGE 10K 10K ancestral 320762952 Affx-986697481 AX-385250943 12 35169818 GTCCAGGTGTGTGGCGTTCTGCTGATGTGACTTGT[C/T]TGATGGAAGGATCTGAGGAGATAAGAGGAATGATA Y 2 1 2 1 600010 f 74 goat 12_35169818 12 35169818 Ancestral_priority_1043 ancestry 0.59 neutral IMAGE 10K 10K ancestral 320765578 Affx-986697483 AX-385253058 12 35169828 GTGGCGTTCTGCTGATGTGACTTGTTTGATGGAAG[A/G]ATCTGAGGAGATAAGAGGAATGATAAGCTCCATCC R 2 1 2 1 600010 r 74 goat 12_35169828 12 35169828 Ancestral_priority_1043 ancestry 0.652 recommended IMAGE 10K 10K ancestral 320765581 Affx-986697485 AX-385253061 12 35170042 TTGCCTGGGGAAGGGCCATTTCACATCCATATGGA[A/C]GTGGAGAGAAGGGCACCTCTTGAGGCTCTTTTCAA M 2 1 2 1 600010 r 74 goat 12_35170042 12 35170042 Ancestral_priority_1043 ancestry 0.528 neutral IMAGE 10K 10K ancestral 320765584 Affx-986697487 AX-385253064 12 35170249 TCCTATACACCCCAGGTAACCAAATGTGGTGAGCC[A/G]GTTGATTAGAACTGTTTATGTTCTCTCTAGGTGGT R 2 1 2 1 600010 r 74 goat 12_35170249 12 35170249 Ancestral_priority_1043 ancestry 0.654 recommended IMAGE 10K 10K ancestral 320803211 Affx-986696226 AX-385290069 12 35170613 GGAGCCACCAGCAAAAAGAAGGACACCTGACTGCT[A/G]TGGCCAGAAGGCATAATCCTGCCTGTGCTGTGAAA R 2 1 2 1 600010 f 74 goat 12_35170613 12 35170613 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 320762960 Affx-986697489 AX-385250951 12 35170760 CTTAATGACATTTGGCAGCTAATTATAATAGGGTT[A/T]TGAGGGGCACATTTTTGCAAAGGTGAGCATAGCAA W 4 1 2 1 600010 f 74 goat 12_35170760 12 35170760 Ancestral_priority_1043 ancestry 0.684 recommended IMAGE 10K 10K ancestral 320765595 Affx-986697493 AX-385253074 12 35171203 CTGATTATGCTCCCTCTGAGACACTGCTGTTGTGA[C/T]TAAAAGCACAACCTTGGGATTAAGAAAGTTATGTC Y 2 1 2 1 600010 r 74 goat 12_35171203 12 35171203 Ancestral_priority_1043 ancestry 0.714 recommended IMAGE 10K 10K ancestral 320762968 Affx-986697497 AX-385250958 12 35171351 GGTTCTCATGAGGATTTCTTGAACTGATGCTTGTA[A/C]ATTACTTGCTGGCCATGACCAAAGGCACTGGACCC M 2 1 2 1 600010 f 74 goat 12_35171351 12 35171351 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38448253 Affx-122924198 AX-123318589 12 35226552 GAAAGGAGATGACAACAAGCAAACATGTAAAGGGC[C/T]GGAGAAGCTGTAGTTGTCCTGGAGCGAGAAGAACA Y 2 1 2 1 101000 f 74 goat snp30400-scaffold335-530813 12 50356937 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402232 Affx-122959147 AX-123272585 12 35255437 GGCAGAGAGTGGGACATATTCATTATTCATTCATC[C/T]TGAAGGCACTTTCGATATCACAGCAATGTTCATAT Y 2 1 2 1 201000 r 74 goat snp30399-scaffold335-501928 12 50328003 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400462 Affx-122961308 AX-123270817 12 35287715 TGAAGAAACATGTTTTGGATCTCTCTCTGAACCTG[A/G]CTGGACTGCTAAGCAGCACAGAAGGTCAGCTGTTT R 2 1 2 1 201000 f 74 goat snp30398-scaffold335-469650 12 50304903 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400207 Affx-122960177 AX-123270562 12 35339239 TCATGTATACTGAGTGAACAAGCAGAGTGAACCAG[A/C]TGCTCCTAGGAATGGACTACATGCATCCTCACACG M 2 1 2 1 101000 f 74 goat snp30397-scaffold335-418126 12 50253456 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388830 Affx-122968892 AX-123259188 12 35372121 ACATCTCATTCCCCTGTCCTCTTCCTACATTGAAC[G/T]TAATTAAGCACTCTTTACCCTGCTCTGTTTTTTCA K 2 1 2 1 201000 r 74 goat snp30396-scaffold335-385244 12 50221647 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386837 Affx-122970087 AX-123257195 12 35402998 AAACCTTCCCAGGGAACCAGTTATTGTAAACCCAC[C/T]CTACTCCTCTGGCAGCCCCAGTCAGTTTCCTTGCC Y 2 1 2 1 101000 f 74 goat snp30395-scaffold335-354367 12 50190769 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382365 Affx-122973865 AX-123252723 12 35441540 AGACAGGGAAAGAGTAACTTACAAACCAAAGGAAA[C/T]GAAGAGGGAGCTGGCAGAGTGATACTCTAGAAGTC Y 2 1 2 1 201000 f 74 goat snp30394-scaffold335-315825 12 50152220 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394822 Affx-122964796 AX-123265177 12 35501931 TCTGCTGGTCCACCAACCACACTTCAAAGCACAGG[A/G]CCAGAGAGATCTATCAAGTGTTTGAAAATTAAAAC R 2 1 2 1 201000 r 74 goat snp30393-scaffold335-255434 12 50102697 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409524 Affx-122953621 AX-123279875 12 35556896 GAAACAGTGATCCCATTTCCCCAAAGGAAGCCCTG[C/T]AAGTGCTTACATCAAGTGTTTTAGGCTGGGGCCGT Y 2 1 2 1 101000 r 74 goat snp30392-scaffold335-200469 12 50047521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771985 Affx-122955657 AX-385259141 12 35586065 TACACTCAAACTGAATAAGAAGCAATATGAAATGA[A/G]AATAGCTCTGCTCAGTTCTGGCCTAAAAACAGGGC R 2 1 2 1 101000 r 74 goat snp30391-scaffold335-171300 12 50018545 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390457 Affx-122967615 AX-123260814 12 35677804 CTTATATGTCAAGCATAATATTAACATTACTCCTC[G/T]ACTGCAATCAGAGTTCTACCATCTCCAAGATGGGA K 2 1 2 1 101000 r 74 goat snp30390-scaffold335-79561 12 49926080 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439321 Affx-122930949 AX-123309658 12 35718727 TAGAATTATTATGCCGAAGTATATTACATATGGCA[C/T]ATGGGAAAATTATCACAGGAAGACTTGAGGGATAA Y 2 1 2 1 101000 f 74 goat snp30389-scaffold335-38638 12 49884737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798032 Affx-122954967 AX-385284968 12 35756657 TTTTCTGCTTTCGCCCTATATTAAGTTGTAGGTCC[A/G]TTGTACTTCTATCTCTTTGTATCCAATTTTTTTTT R 2 1 2 1 101000 f 74 goat snp30388-scaffold335-708 12 49846295 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392789 Affx-122965979 AX-123263146 12 35760337 GGCAGCTATGTATAATGAGCTAAGTTTCAAGTATG[C/T]GATATTGTTAATATGACTATTTCTCATCTATCTTT Y 2 1 2 1 101000 f 74 goat snp11126-scaffold140-2873 12 49838003 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431265 Affx-122937114 AX-123301606 12 35792679 TTAATGTAGATTTAATTCAGTCTTTCTACTTTGAT[A/C]TAGGTCTAAATTTTTCTGCAGGGATTAATGTTTTC M 2 1 2 1 101000 r 74 goat snp11127-scaffold140-35215 12 49805893 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402068 Affx-122958714 AX-123272421 12 35822640 ACATGGGGATTCCTCTCCTTCATTTAGGTGTCTGA[A/G]ATCCCTCAAGAGCACCTGGTTGATATTCTAGTTGT R 2 1 2 1 101000 r 74 goat snp11128-scaffold140-65176 12 49775119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419121 Affx-122945765 AX-123289469 12 35871865 AATCACAGAACTCCTGACCCCAGGGAAAATGAATA[G/T]ATGAGAGTCCATCAAAACCCTCCATACACACACTA K 2 1 2 1 201000 r 74 goat snp11129-scaffold140-114401 12 49724607 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445653 Affx-122926153 AX-123315990 12 35949672 ATTCCTGCACTTAAAAGTGTACCTGGAAAAATAGG[A/C]AATCTTGGACATTAGTTAAATAAATGAAAAAATAT M 2 1 2 1 101000 f 74 goat snp11130-scaffold140-192208 12 49644873 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796470 Affx-122974307 AX-385283420 12 36026497 GGATTATATTTCTGAGTTGTTTATAAAAACTCAGT[G/T]CCAGAGCAAGGCTAAACATTATTTTCCATTATGCT K 2 1 2 1 102000 r 74 goat snp11131-scaffold140-269033 12 49567177 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388782 Affx-122968928 AX-123259140 12 36108916 TTGTGGAGAAATTTTTGTTCATATTCCATTTTACC[C/T]GAAGCTCTTTTTAAACAGGACTTTCTTTTATTACC Y 2 1 2 1 101000 r 74 goat snp11133-scaffold140-351452 12 49483680 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402129 Affx-122958671 AX-123272482 12 36159974 CGATCAGCTCTCAGAATATTTCAATCTAAATAGTC[G/T]AATATTTGCTATGACCATAAATAGTTCATAATTCA K 2 1 2 1 202000 r 74 goat snp11134-scaffold140-402510 12 49430185 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390882 Affx-122967117 AX-123261239 12 36193272 GTATTGGAGAATTTACAGCTATAAATTAACTTTAC[A/G]CATAAGGTCTTACCCATTAGGAACATTATTTTTAG R 2 1 2 1 101000 r 74 goat snp11135-scaffold140-435808 12 49396619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394331 Affx-122964672 AX-123264686 12 36272893 TTTGCTTCAGGTCCTGCCTGATGGAAGGGTGGGCA[A/G]GTGTGTGGAAATTTCTCTTTTGGGGTTTCGAAGTC R 2 1 2 1 201000 f 74 goat snp11136-scaffold140-515429 12 49314534 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443332 Affx-122927440 AX-123313669 12 36323992 CCCGTCTATGCTAAAACTATCTCAACTTATTTAAG[A/G]CTTTTCAGAGAAGAAGAAATTGAAGTGGAATCTCT R 2 1 2 1 101000 f 74 goat snp11137-scaffold140-566528 12 49263299 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399853 Affx-122960243 AX-123270208 12 36361556 TTTCCTCCAGCATTGACTGGTTTGATCCCCTTGCT[A/G]TCCATGATGTAAACAAATGTTATTACTAGTATAAT R 2 1 2 1 303000 r 74 goat snp11138-scaffold140-604092 12 49225381 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275220 Affx-1111834775 AX-519548799 12 36361819 ACTTGCTCAGGGAGCATTTCTTTCCTGCAGTGACC[A/G]CATA R 2 1 2 1 102000 f 74 goat GoatD01.052326 12 36361819 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38397058 Affx-122962734 AX-123267413 12 36396086 TTCAACATGGGTTTTTCTTTTTTGTAAGTACCAGC[A/G]TCTTCCTCTGGATGGTTGTTTAACAGCTAGTTGTG R 2 1 2 1 101000 r 74 goat snp11139-scaffold140-638622 12 49190233 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407347 Affx-122955285 AX-123277698 12 36438531 ATGCACATGAGAAGCATAGAACAGGATCCAAAACA[C/T]GATGAATAGTATTAGCTTTAAAAATAACTGGGAAA Y 2 1 2 1 101000 f 74 goat snp11140-scaffold140-681067 12 49147200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399309 Affx-122960528 AX-123269664 12 36468706 TAATGGAGTAAATACAATCTCTTTCACAATTGGTT[A/C]TGAGAAAACTAATCAACCACATGTAGAAACTTGAA M 2 1 2 1 101000 r 74 goat snp11141-scaffold140-711242 12 49116771 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788509 Affx-122953430 AX-385275526 12 36518132 GGAGAATTTTCAGCTATAGAATATTCACCTCAGAG[A/C]TCCTCAAGGGTTATGCTCTGTCTTGCACTGAAACT M 2 1 2 1 101000 r 74 goat snp11142-scaffold140-760668 12 49066602 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403049 Affx-122958534 AX-123273402 12 36568049 CCTCATAAAGAAAGGCAGGATTACAAGGAGCTCAA[C/T]AGAAAGTGATCAGCTATGCTCAAGTATCAGCAGTA Y 2 1 2 1 101000 f 74 goat snp11143-scaffold140-810585 12 49015718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778890 Affx-122952962 AX-385265998 12 36603524 CAAACAAGTACTGATGCTACTTAGTGAACTGGTAA[A/G]TAGAGACAAAATAATTCATGGAGTAAAAATATAGA R 2 1 2 1 101000 f 74 goat snp11144-scaffold140-846060 12 48979088 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790546 Affx-122971029 AX-385277549 12 36639471 AATTAAATCAACTAGTTCATTTCAAGAAATATTTT[A/G]AAGTTTGTTTTTCCCCTATGGTTCTGTCTTGGAGC R 2 1 2 1 303000 f 74 goat snp11145-scaffold140-882007 12 48943060 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773163 Affx-122974722 AX-385260306 12 36688782 TAAATGTATGAAAAATTTCCTCTTGGGGAAACATT[A/G]TACAAACCCACATTGAGAAATATTCCACATGATAA R 2 1 2 1 201000 f 74 goat snp11146-scaffold140-931318 12 48893221 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768580 Affx-122933860 AX-385255760 12 36741522 CACCAATTCTTGATGATTTTTATCATCAAGGAAAA[G/T]AAATATATCCATGTTTAATTCTAACAAGTTGAGTC K 2 1 2 1 102000 r 74 goat snp11147-scaffold140-984058 12 48839311 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476285 Affx-1251763792 AX-586011704 12 36755774 TTGTTCTTGTGGCTATTTATCCCAGGAACACAAAA[-/ACTTATATTTAGGAGGAGGAGGGAAAGATGGCAGAGGAATAAAAAATAAAAAAATTAAAAAAAAAAAACAAAAAAAAAAC]CTTATATTTACATGACATCGTATGCACAAATGTTT - 4 1 4 1 20000 f 74 goat SV_226 12 36755774 - deletion junction SV-TF-chip 539476538 Affx-1251763792 AX-586011927 12 36755774 TTGTTCTTGTGGCTATTTATCCCAGGAACACAAAA[-/ACTTATATTTAGGAGGAGGAGGGAAAGATGGCAGAGGAATAAAAAATAAAAAAATTAAAAAAAAAAAACAAAAAAAAAAC]CTTATATTTACATGACATCGTATGCACAAATGTTT - 4 1 4 1 20000 r 74 goat SV_226 12 36755774 - deletion junction SV-TF-chip 562165315 Affx-1251763792 AX-606940726 12 36755774 TTGTTCTTGTGGCTATTTATCCCAGGAACACAAAA[-/ACTTATATTTAGGAGGAGGAGGGAAAGATGGCAGAGGAATAAAAAATAAAAAAATTAAAAAAAAAAAACAAAAAAAAAAC]CTTATATTTACATGACATCGTATGCACAAATGTTT - 8 1 4 1 20100 r 74 goat SV_226 12 36755774 - deletion junction SV-TF-chip 562165791 Affx-1251763792 AX-606941200 12 36755774 TTGTTCTTGTGGCTATTTATCCCAGGAACACAAAA[-/ACTTATATTTAGGAGGAGGAGGGAAAGATGGCAGAGGAATAAAAAATAAAAAAATTAAAAAAAAAAAACAAAAAAAAAAC]CTTATATTTACATGACATCGTATGCACAAATGTTT - 8 1 4 1 20100 f 74 goat SV_226 12 36755774 - deletion junction SV-TF-chip 562166084 Affx-1251763792 AX-606941493 12 36755774 TTGTTCTTGTGGCTATTTATCCCAGGAACACAAAA[-/ACTTATATTTAGGAGGAGGAGGGAAAGATGGCAGAGGAATAAAAAATAAAAAAATTAAAAAAAAAAAACAAAAAAAAAAC]CTTATATTTACATGACATCGTATGCACAAATGTTT - 8 1 4 1 20100 f 74 goat SV_226 12 36755774 - deletion junction SV-TF-chip 562166204 Affx-1251763792 AX-606941612 12 36755774 TTGTTCTTGTGGCTATTTATCCCAGGAACACAAAA[-/ACTTATATTTAGGAGGAGGAGGGAAAGATGGCAGAGGAATAAAAAATAAAAAAATTAAAAAAAAAAAACAAAAAAAAAAC]CTTATATTTACATGACATCGTATGCACAAATGTTT - 8 1 4 1 20100 r 74 goat SV_226 12 36755774 - deletion junction SV-TF-chip 562166330 Affx-1251763792 AX-606941738 12 36755774 TTGTTCTTGTGGCTATTTATCCCAGGAACACAAAA[-/ACTTATATTTAGGAGGAGGAGGGAAAGATGGCAGAGGAATAAAAAATAAAAAAATTAAAAAAAAAAAACAAAAAAAAAAC]CTTATATTTACATGACATCGTATGCACAAATGTTT - 8 1 4 1 20100 f 74 goat SV_226 12 36755774 - deletion junction SV-TF-chip 562166345 Affx-1251763792 AX-606941753 12 36755774 TTGTTCTTGTGGCTATTTATCCCAGGAACACAAAA[-/ACTTATATTTAGGAGGAGGAGGGAAAGATGGCAGAGGAATAAAAAATAAAAAAATTAAAAAAAAAAAACAAAAAAAAAAC]CTTATATTTACATGACATCGTATGCACAAATGTTT - 8 1 4 1 20100 r 74 goat SV_226 12 36755774 - deletion junction SV-TF-chip 38440218 Affx-122930687 AX-123310555 12 36783669 TGTTATCAACTGTGCTTGTGTAGTATTCAATGTAG[C/T]AAGCTTGTCATGTACCACACATCATAAGGAGACAC Y 2 1 2 1 101000 f 74 goat snp11148-scaffold140-1026205 12 48796773 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379845 Affx-122975808 AX-123250203 12 36830396 ATGGACTTCACCAGATGGCCAACACCAAAATCAGA[C/T]TGATATTTTGCTTACTAGAAACCATCAATTGAGGT Y 2 1 2 1 303000 r 74 goat snp11149-scaffold140-1072932 12 48749361 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778832 Affx-122952551 AX-385265940 12 36863067 TCTGAGTATAAATTAAAACTAAAGATGTTTAAATA[C/T]GGTTTCTTTGGTAGTTCATGCCATGAAAGAAAACC Y 2 1 2 1 202000 f 74 goat snp11150-scaffold140-1105603 12 48715785 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394472 Affx-122964569 AX-123264827 12 36893006 GTGTACTTGAATAAAGTAAAATCAATGTATAAATG[A/C]TAATTAAATGCAAGTAAATTATTCATTAATAACTG M 2 1 2 1 101000 f 74 goat snp11151-scaffold140-1135542 12 48685616 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792928 Affx-122969497 AX-385279906 12 36924085 CCCAGACTGGTTTCCCTGGATACAGGAGCTTCCCC[A/G]CTTAGAGTGACTGAATCATCAAGTGTTTCTGAATT R 2 1 2 1 202000 f 74 goat snp11152-scaffold140-1166621 12 48653706 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423945 Affx-122942248 AX-123294291 12 36970949 TCCCCCTAGGTCATCATGGAACCCCCAATTTAAGT[A/G]CCCTGAGTCATATAACAAGTTCACACTGGCTATCT R 2 1 2 1 101000 r 74 goat snp11153-scaffold140-1213485 12 48606702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786105 Affx-122949921 AX-385273141 12 37031218 TCTGTACTGTTTTGCCATATATATAATTCTACTAG[A/G]TGCTTCAATGTGGCATAAGTATTCTTAAAATTTGC R 2 1 2 1 101000 f 74 goat snp11154-scaffold140-1273754 12 48546250 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386620 Affx-122970232 AX-123256978 12 37063343 ATGATTGTGTGAGAAGCCATGAGGGAGTGAAATTA[G/T]TATTGCATCAGGTGAGAATGGGTAAACACTCAACA K 2 1 2 1 101000 f 74 goat snp11155-scaffold140-1305879 12 48513963 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450459 Affx-122922949 AX-123320793 12 37093044 ATTGTTCTGAAGGCTCCTTGATAGCAATTTATTCC[A/G]GTTTTCACTAAATTATATTATTTAGACAACAAGAG R 2 1 2 1 101000 f 74 goat snp11156-scaffold140-1335580 12 48484036 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428221 Affx-122939440 AX-123298564 12 37132649 CAGTGTCCTTGCCCTCACAGTGAACTATATCCAAC[A/C]CCCAATTTCTAAGGAGATGCTCTGGAATCCCTAAT M 2 1 2 1 101000 r 74 goat snp11157-scaffold140-1375185 12 48444074 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272664 Affx-1111832954 AX-185398816 12 37152045 TCTCATGATGTACTCTGCATATAAGTTAAATAAGC[A/G]GGGTGACAATATACAGCCTTGACATACTCCTTTCC R 2 1 2 1 303000 f 74 goat 12_37152045_AF-PAKI 12 37152045 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791763 Affx-122920813 AX-385278754 12 37185506 AACCGCGAGAGGCCTTGAAACCTTAAGAAATTCTA[A/G]GAAAAATCATTGGAGTAAAACTGATTAAGGGTTTC R 2 1 2 1 101000 f 74 goat snp11158-scaffold140-1428042 12 48389347 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398588 Affx-122961495 AX-123268943 12 37271518 ACTTATCCCATAAGAGGGGAGTCTGAGTATTAAAA[G/T]ACTGGGTGGCTGCCTCTTTTGCTTGTCAGTCAGCT K 2 1 2 1 101000 f 74 goat snp11159-scaffold140-1514054 12 48302334 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778131 Affx-122975862 AX-385265246 12 37332594 CCCAATTCTCTGATAAAGACAGCTGCTCTTGTCTT[A/G]CAAATTGAGTCTTTATAAGAACAGAAAAGCCTACC R 2 1 2 1 202000 f 74 goat snp11160-scaffold140-1575130 12 48240863 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430486 Affx-122937240 AX-123300827 12 37401948 TTATTTTCCAGTGTTTTTTTCAATAAGCACAAAAC[C/T]CCAACCTTTCTATAATTCAAATAATTCAATAATTC Y 2 1 2 1 101000 r 74 goat snp11162-scaffold140-1644484 12 48173525 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276625 Affx-1111835509 AX-519550135 12 37419033 AGGTACTTTGCGATTGTAAGCTTTGGTGCCTGTGT[A/G]GTTTCTTTGTTGGAGAAATGGGGAACTTCTTTTTT R 2 1 2 1 102000 f 74 goat Random2.2K-1270 12 37419033 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38377412 Affx-122977557 AX-123247771 12 37445061 ATACAGCAAAATAAATATTTTGACTCAAGTATTTC[G/T]AAAAGTATTGGGGTGTAAACAGTTGATTAATGCTA K 2 1 2 1 101000 f 74 goat snp11163-scaffold140-1687597 12 48130341 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404113 Affx-122957112 AX-123274465 12 37487996 TATACATAATGCTTCTATGGGGTTATATGAATATG[C/T]GTTTAAAGAAAATATTTCTTAAAATAGAATAAGAT Y 2 1 2 1 101000 f 74 goat snp11164-scaffold140-1730532 12 48086936 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782986 Affx-122923283 AX-385270055 12 37554910 GCATATTCAGGAACTGTACTTTATTGAGGATATAT[A/G]ACATAACTGAGTATGATGCTTGTTGAGGAAAGTTA R 2 1 2 1 202000 f 74 goat snp11165-scaffold140-1797446 12 48018393 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434064 Affx-122934188 AX-123304405 12 37650473 AATTTACTTCCATTTATTCCCTTTCTGCATTTTCT[A/G]TTCTCATTCTCATATATTCTATTTCTGCAGTCAGT R 2 1 2 1 101000 r 74 goat snp11167-scaffold140-1893009 12 47921163 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398030 Affx-122961770 AX-123268385 12 37690241 TTTTCTTGGAAGTCAGAAATAGACAGTATTTAGTA[C/T]ACTTTGGATGATGTTACAGTAATCTCGCAGTAAAA Y 2 1 2 1 101000 r 74 goat snp11168-scaffold140-1932777 12 47881889 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438727 Affx-122930840 AX-123309064 12 37722730 ACAGTTCTAGGAAGTTAATAAACTGACCTGTTATC[A/G]CCTTAAGATTAAATTCCATTCAAGTTTACATCATG R 2 1 2 1 101000 f 74 goat snp11169-scaffold140-1965266 12 47848532 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781392 Affx-122976961 AX-385268477 12 37754191 GCTGTCATTTATTTAAATGAGATGTCTTATAAGAC[A/G]TTTGTCACTCAAGGCCACTTCAATCATCAGTATTG R 2 1 2 1 201000 f 74 goat snp11170-scaffold140-1996727 12 47816721 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786233 Affx-122938846 AX-385273268 12 37800925 AGAGACAAATGCACAATGTAAATTAATCTACTTCC[A/G]TTAGGTAATCTATTTGAATGTCAGTAATTTTTTCT R 2 1 2 1 101000 f 74 goat snp11171-scaffold140-2043461 12 47769552 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391762 Affx-122967471 AX-123262119 12 37850013 TATCTTCTTTGGAAAATTGTCTAGATATGCTCATT[A/G]TTTTGATTGCACTGTTTGTCTTTTTCTTGACATAT R 2 1 2 1 101000 r 74 goat snp11172-scaffold140-2092549 12 47719763 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768102 Affx-122968709 AX-385255304 12 37888327 ACTTTTAATATAAATCAACTTAGTGATGATACGCA[C/T]GGATAAGATTTTCCAACTTTGTCTTAAAAGTTGAT Y 2 1 2 1 101000 f 74 goat snp11173-scaffold140-2130863 12 47681408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415133 Affx-122949423 AX-123285482 12 37925013 GGGTAGGACATGTTCCAGTTTTTCTAATCAAAGAG[C/T]GCTTAATCCTTCCATAAGCTGGTTGGCTTTGTTGG Y 2 1 2 1 101000 f 74 goat snp11174-scaffold140-2167549 12 47644110 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397797 Affx-122962498 AX-123268152 12 38001000 AGAAGCTAAACAATACATTAAACAACAAATGGATC[A/G]CTGAAGAAATCAAATAGGAAATTAAAAATAAAATG R 2 1 2 1 102000 f 74 goat snp11175-scaffold140-2243536 12 47566678 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418417 Affx-122946538 AX-123288765 12 38041208 TCATCTTGTATAGCATATATAAAAAAGTAAGCTAT[A/G]CAGAGAGGACATGTTGATAAGGGCTAACATTATGT R 2 1 2 1 101000 r 74 goat snp11176-scaffold140-2283744 12 47525212 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399759 Affx-122960315 AX-123270114 12 38082951 GGATAAAATTATGCATGTGTATGTTGTATTTAGCT[C/T]AAAATCTTATCATTTTTATTATTTTAAATTTGGGC Y 2 1 2 1 101000 f 74 goat snp11177-scaffold140-2325487 12 47483820 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423360 Affx-122943148 AX-123293706 12 38132780 GGACTGGCATAGAGTACAATACATTTTCTCTGGAG[G/T]AAGGCAGATCCATAAGGGTAGGAAGAGTGATGATA K 2 1 2 1 101000 f 74 goat snp11178-scaffold140-2375316 12 47433811 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443451 Affx-122927835 AX-123313788 12 38183822 GGCAGTTATTTTAGAATCATGAGGTTCACTAACAT[A/G]TAATGATGGTAGACTGAAAAGATAAAAACAGATAA R 2 1 2 1 101000 f 74 goat snp11179-scaffold140-2426358 12 47384048 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383086 Affx-122973733 AX-123253444 12 38255116 AAGTCTGAGATTGGAATATAATATGGTTCTTTTCC[G/T]AAGACATTTATTTTCTCATTCTTATCTTGGTCAGG K 2 1 2 1 101000 f 74 goat snp11180-scaffold140-2497652 12 47309742 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437200 Affx-122932051 AX-123307538 12 38288767 TAAGAGTGGCTTTCACAGGGTTGTTCCTGACTATA[C/T]ATAGATTGAATAGCTATGGTACATCTGAACAAAGA Y 2 1 2 1 101000 f 74 goat snp11181-scaffold140-2531303 12 47275457 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790590 Affx-122952275 AX-385277592 12 38331477 AAATGTTTTAGGGAAACAAAAATTCTCACCTACTA[C/T]ACTTCTAGGTAACTTTAGTATCTCTAAGAGACCAA Y 2 1 2 1 101000 f 74 goat snp11182-scaffold140-2574013 12 47232738 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776677 Affx-122947425 AX-385263803 12 38401403 ATTAATATTAGGTTTTCTGAGAATCACTGAAAATT[A/G]CCATAGTACATGTTCCAGAGTTTCAATGATTGATT R 2 1 2 1 101000 r 74 goat snp11183-scaffold140-2643939 12 47162387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447917 Affx-122923799 AX-123318253 12 38432766 ATAAGAGAAATTCAAAGAAATGTTTCTATCAGTGC[A/G]CATAATGCTTGCAAAACTATTTAGTTACCTCGTCT R 2 1 2 1 101000 r 74 goat snp11184-scaffold140-2675302 12 47131015 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772579 Affx-122959814 AX-385259728 12 38484372 TGCAGTCTACTGAGAGTAGTAGGCCCTATGGCTTT[A/G]TTTATCTTTTCTCAACCTTGGACTATTCAATAGAA R 2 1 2 1 101000 f 74 goat snp11185-scaffold140-2726908 12 47079481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449058 Affx-122923055 AX-123319393 12 38525732 TTATTTCTAAAACTATCTGCTCCAATTCTGAATGA[C/T]GTATATTCAATTATTTAACTTATCTCATTCTCAAC Y 2 1 2 1 101000 f 74 goat snp11186-scaffold140-2768268 12 47038098 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769287 Affx-122933820 AX-385256458 12 38561176 AGCCAATGAGATTTGAATTCAGATTTAGCAACATC[A/G]TATAAGTCTAGCTCCAGGTACCCAGGAGTTCATAT R 2 1 2 1 202000 f 74 goat snp11187-scaffold140-2803712 12 47002251 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769389 Affx-122973901 AX-385256560 12 38606800 AGAATTTCAATCCTATATAACTGTCAAAAGAAACT[A/G]CCTTTCACTAGGAGCACTGATACAGTTTTTGTGAG R 2 1 2 1 101000 r 74 goat snp11188-scaffold140-2849336 12 46956251 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797096 Affx-122960272 AX-385284036 12 38641740 AATATTGAGCTTCAATAACTGACAAAGTATATAGG[A/C]TTACTATCTCATAATTACCTTGGTCTTCAACTTAG M 2 1 2 1 201000 f 74 goat snp11189-scaffold140-2884276 12 46921252 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429312 Affx-122938599 AX-123299654 12 38672003 TCTCTCTCGAAAAGTGACATTTTCCCACATCTTTT[A/G]TAAATCTCAGAAATGCAAATAAAAATTTAAACTCA R 2 1 2 1 103000 f 74 goat snp11190-scaffold140-2914539 12 46891349 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776197 Affx-122962131 AX-385263325 12 38727118 AAGATTTTTATTAATATTCCTCATATATAACTACA[C/T]GTAACCAGCTAAACCTATTTGTGGATGCTTGGTGT Y 2 1 2 1 101000 r 74 goat snp11191-scaffold140-2969654 12 46835253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428748 Affx-122938438 AX-123299090 12 38805837 ATTCCAATTTCAATGAGTATAGAATATGTGGGTTT[A/G]TTTCCCCAATGTGATTATAGTGATTACATTTATTT R 2 1 2 1 101000 f 74 goat snp38277-scaffold481-1811139 12 46754131 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276767 Affx-1111835510 AX-519550276 12 38830934 TAATAGTAACTCAATAAATGTTGAAAATGTCATTA[A/G]CATTTGTAGTCATTTTATGTGTTATGCTATTCACC R 2 1 2 1 101000 r 74 goat Random2.2K-1271 12 38830934 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797085 Affx-122924864 AX-385284025 12 38841145 AATCTTATATTTATTATAACCTTCAGTGCATAACC[A/G]TAATATAATCTCAGTCTAAGAGATAATGTGATTAA R 2 1 2 1 101000 r 74 goat snp38276-scaffold481-1775831 12 46716990 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430383 Affx-122937774 AX-123300724 12 38882855 TAATGTAGCTGTTCACTCCAGCCTTCTGCAGGTCC[A/G]TGGTATTAATCAAGATATGACCACATTTACTCAGC R 2 1 2 1 201000 r 74 goat snp38275-scaffold481-1734121 12 46674886 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418564 Affx-122946387 AX-123288912 12 38940958 ACTACCAACTTTCTGGAAAAAGGAAAATAATTTTC[A/G]TTTAGGAAACATGTATGGGCTATGAATAAGAACTT R 2 1 2 1 103000 r 74 goat snp38274-scaffold481-1676018 12 46616806 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786809 Affx-122948399 AX-385273838 12 38995255 GTTTACATGCTCTACTGTAAATGGCCACAGAGGAT[A/G]TATTATGCCCCATCTTGCCAATAATCCATGTTTAA R 2 1 2 1 101000 f 74 goat snp38273-scaffold481-1621721 12 46561846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429638 Affx-122937683 AX-123299979 12 39030929 AGAAAAGAAAAGAACATTGGCTGATATATTAGAAC[A/G]TATCAATTTAATTTCAAAGACTTTCAAGTTGACTC R 2 1 2 1 201000 f 74 goat snp38272-scaffold481-1586047 12 46525969 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789556 Affx-122928118 AX-385276565 12 39069596 GCAGGATGAGAACCACTACTGGGCCACAGGAATTG[C/T]GGAAACGTTTCTAAGGAGGAAAACTGCATAATACA Y 2 1 2 1 101000 f 74 goat snp38271-scaffold481-1547380 12 46487076 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405339 Affx-122956333 AX-123275691 12 39124413 GGCGGGAGAGATATGGGGAGAGATATTTTTAGATA[A/G]GAGCATCTGGCTTGCCCCTCTAATCACATCCCATA R 2 1 2 1 101000 f 74 goat snp38270-scaffold481-1492563 12 46432407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416002 Affx-122948391 AX-123286351 12 39217711 GGTGGCTGGATGCATTGACATTAGTCACACATGAC[A/G]TAACATAGTCAAACTGGGATAAGTGAATATCACAC R 2 1 2 1 101000 f 74 goat snp38267-scaffold481-1399265 12 46338826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416580 Affx-122947656 AX-123286928 12 39249715 GCATAACTTGAATATTTTGAAAGTGTTTTGTTTTT[A/G]CTTTGGTGGGGTTGGAGGAGGGAGTGGAAAGGCAA R 2 1 2 1 303000 f 74 goat snp38266-scaffold481-1367261 12 46306977 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784707 Affx-122963878 AX-385271755 12 39291905 AACATGGTAGGAAGAATTCAGATTCTGGGTAATAA[G/T]TAGGCATAATTAAACCCTGCTACCTGCCATGATTA K 2 1 2 1 201000 r 74 goat snp38265-scaffold481-1325071 12 46264453 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798771 Affx-122971662 AX-385285702 12 39327496 TCTCATTGTTCTACTTCTTTAGAGACCTTTTTCCA[G/T]AGATATCCTGTGAGCAGACCAAAGTAACTAAAGAA K 2 1 2 1 101000 r 74 goat snp38264-scaffold481-1289480 12 46228594 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384619 Affx-122972169 AX-123254977 12 39379773 GGTCAACAAGTGGCATGGACTGTAAATAAAGCATG[A/G]CCACATGAAAATCATCCTAACCACATTTTAAACAT R 2 1 2 1 201000 r 74 goat snp38263-scaffold481-1237203 12 46173644 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775439 Affx-122954808 AX-385262570 12 39425241 TAAGATACTACTGGCAATGAATAAAGATAAAAGGA[C/T]AGGCTAGAGAGGTATACAAGTCAGTGGCATTTGAT Y 2 1 2 1 101000 r 74 goat snp38262-scaffold481-1191735 12 46127825 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784419 Affx-122973575 AX-385271468 12 39480169 TGAAAGGAATTAAGTCAGTACGAAGGTTCTAGAGA[A/C]TATGATGTTATTCGATAGACATAGAATTTGGAATG M 2 1 2 1 101000 f 74 goat snp38261-scaffold481-1136807 12 46072917 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790454 Affx-122921126 AX-385277458 12 39527382 TTATTTGGCTAATAAGCCTGCTGTCCAGGACTAAC[A/G]TCAGAGAATTTACAAACATGTTTTAAAAGTGTCAC R 2 1 2 1 201000 r 74 goat snp38260-scaffold481-1089594 12 46024727 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439593 Affx-122930065 AX-123309930 12 39573831 GGAGGGGAGGTGGGACTACATTTTTATCTGCAAAA[G/T]AAAAAGAAAAAGCTAAATGATCCCCAAATTCCTTG K 2 1 2 1 102000 f 74 goat snp38259-scaffold481-1043145 12 45977865 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397449 Affx-122962108 AX-123267804 12 39624281 ATGTTTTCTGCTTTGCTTCAAAATTTACTTTTAGA[C/T]ACTCAAAAAGAGAAAAATAGAATATGGAATTACTG Y 2 1 2 1 201000 f 74 goat snp38258-scaffold481-992695 12 45926587 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418108 Affx-122947132 AX-123288456 12 39654100 TTTAAGCCAACAGCTGGTTGTGGTTAATAAAAATG[C/T]AAACATTTTCCAAGATTTTAATATGATAACTACCT Y 2 1 2 1 101000 f 74 goat snp38257-scaffold481-962876 12 45896107 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272666 Affx-1111832955 AX-519546373 12 39672204 TGAGCAAGTCTAGATGTTGGCCTACAGGGAACAAG[A/G]CCTGGGTACCATTTGAATTACTATCATTTAGAACC R 2 1 2 1 101000 f 74 goat 12_39672204_AF-PAKI 12 39672204 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401285 Affx-122959868 AX-123271638 12 39697189 ACTTACTACTGGCTTTCCTACCAGAGGAGTGTACA[G/T]CTGTGCCCTATTGAAGTCAGAATAAACACAGTGTG K 2 1 2 1 101000 r 74 goat snp38256-scaffold481-919787 12 45852451 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768721 Affx-122934827 AX-385255899 12 39740727 TTGTTAACAATAATTGGCAAGTACCAATAATTTTC[A/G]TTTTATTACATAAACCAACAAAATAGTGTGTCTTA R 2 1 2 1 101000 f 74 goat snp38255-scaffold481-876249 12 45807773 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793980 Affx-122948261 AX-385280949 12 39796624 TCTAGATGCCCTTGTTTCTGGGAGTAATATGATTG[C/T]AGATTCTTAAAACAATTTTCAAGCCTTGAGATAGC Y 2 1 2 1 201000 r 74 goat snp38254-scaffold481-820352 12 45751853 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403936 Affx-122957463 AX-123274288 12 39837173 GACAATGATTCACCATTGTTTCTTCTTATGTTCTG[C/T]GTAGTTGTGACATGTGTCAGTACATGCTAGACCAC Y 2 1 2 1 101000 r 74 goat snp38253-scaffold481-779803 12 45709851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800545 Affx-122968173 AX-385287464 12 39865967 AGATTATTGAGTTTCTTTTACATATTTTGAATGGG[C/T]ACATGAGTCTAATTCTGAGAAGCTTCTAATACTTG Y 2 1 2 1 101000 f 74 goat snp38252-scaffold481-751009 12 45680574 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276769 Affx-1111835511 AX-519550278 12 39907736 ATGCATTGGCTTTAGGAACCTAAAAGGAATCATTA[C/G]AACCCGAGCTTCATTAATTTGAAGAATAAAGCCTT S 4 1 2 1 101000 r 74 goat Random2.2K-1272 12 39907736 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376327 Affx-122978350 AX-123246686 12 39916514 TCTTCCCTATATATTAGAAAATAATGAAAGAACAT[A/C]TAATGCAAAGGGGTTATCTGATCTCAACTGAAACT M 2 1 2 1 103000 r 74 goat snp38251-scaffold481-700462 12 45629263 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800558 Affx-122956839 AX-385287477 12 39962894 TAACTATTTAAACAGAAGTGTACTGATAGTTAATG[A/G]TCAAAGTATATATGTTAAAGCCAAATTTTTGTTAT R 2 1 2 1 201000 r 74 goat snp38250-scaffold481-654082 12 45582949 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441822 Affx-122929064 AX-123312159 12 39993999 TTACACATGATCAGCCCTGTGTTACAATCAGTCCT[A/G]TTTATATTAACTAAAAGAATGAAAATAATGAATTT R 2 1 2 1 103000 f 74 goat snp38249-scaffold481-622977 12 45550803 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773485 Affx-122968507 AX-385260626 12 40042909 GTTAAGAGGTTGCATAGATTACTAGATCAAGCTAC[A/G]TTTTACATCCAAATTAATGTCACAACTGTAACAAA R 2 1 2 1 101000 f 74 goat snp38248-scaffold481-574067 12 45501652 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802625 Affx-122942119 AX-385289527 12 40087719 TCATTTTGTGGAGAAAATCAGAATGCTTAACCATG[C/T]AATTACAAAATCAGAAAGGTCTCTATATCTTTAGA Y 2 1 2 1 101000 f 74 goat snp38247-scaffold481-529257 12 45456766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439228 Affx-122931019 AX-123309565 12 40119088 CAGAAATTAACAATTTATCTCAAGTATTTTCCCAC[A/G]TAGGTTAAAATTTTCTTATCATCATATATATGCAT R 2 1 2 1 303000 r 74 goat snp38246-scaffold481-497888 12 45425123 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408186 Affx-122954196 AX-123278537 12 40160353 TTGCAATGCTCTTTTCTGAAATCTTCATATGACTC[A/G]CTGCCTCATTATTCTGGTTTCAGATCAAAGATTAC R 2 1 2 1 101000 f 74 goat snp38245-scaffold481-456623 12 45383753 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443523 Affx-122927782 AX-123313860 12 40191806 AGATTGTTTATGTGAAGCTTTTAAGTGTATTCCCA[C/T]GGGCATTGTACATCAATAGATTAGAAAAGGAGAGT Y 2 1 2 1 101000 r 74 goat snp38244-scaffold481-425170 12 45352012 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796483 Affx-122924403 AX-385283433 12 40291732 GTAAATTCAGCCCAGGTACCTGGAAGTATCACATA[C/T]GCTTATGGCTAATATAACTGAACATAGATTTCAGC Y 2 1 2 1 101000 f 74 goat snp38243-scaffold481-325244 12 45251205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782079 Affx-122965892 AX-385269157 12 40359968 GTATCAAGAACTATGTCTAGACCACAAGTAGCAGT[G/T]TAAGTAACCAATCTAAAGACATAATAGTTCTGAAA K 2 1 2 1 101000 f 74 goat snp38242-scaffold481-257008 12 45182572 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384698 Affx-122972114 AX-123255056 12 40404369 CTCAAAGATGTTAAAGAGAAAAGTAAGTAACCCTG[C/T]AATAAATGAGGGCCAAGTTCTATTTTCTGTTCTCT Y 2 1 2 1 101000 r 74 goat snp38241-scaffold481-212607 12 45137289 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407737 Affx-122954993 AX-123278088 12 40458179 GTTCCTTTTTCCTCAATGTCAAAATATGAATATTT[A/G]TGATTCATTCCCTGCAATCCCATTTCCCACTCTCT R 2 1 2 1 101000 r 74 goat snp38240-scaffold481-158797 12 45084227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427943 Affx-122939209 AX-123298286 12 40551633 AGCTAGATCCTCATGAAAGGATATAAATAAAAATG[C/T]AATGAATATTTTTCAGTTGTTTGGTAGAAAGCAAG Y 2 1 2 1 303000 f 74 goat snp38238-scaffold481-65343 12 44992217 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767189 Affx-122960400 AX-385254471 12 40591979 TCCACACATTCTGCCATTTTACCCTATGACTACCA[A/G]CCTCATTTATCATGGTGACTTAAATTCTAATGTGG R 2 1 2 1 101000 f 74 goat snp38237-scaffold481-24997 12 44951635 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452096 Affx-122920852 AX-123322429 12 40620364 ACAAGAACAAACTTTGTGAATGCCATAAGTGAAAT[G/T]AGTAATGGCTATGAACTGCCAAACCTCAGAGTTAG K 2 1 2 1 201000 f 74 goat snp17454-scaffold1805-39262 12 44922437 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380261 Affx-122975430 AX-123250619 12 40670209 TAAAGGCTCTTACAATGAACCTTGTTACTTCTGAA[G/T]CATAAGCCAGGGGAAACTAATTCAATAAATCAAGC K 2 1 2 1 101000 f 74 goat snp24893-scaffold2542-10484 12 44858903 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444958 Affx-122926678 AX-123315295 12 40720223 TCTAATCTCATTCCTACTGACCTGGAGAGTTCCTC[A/C]TTCAGTATCCTATTATTTTACCTGTTCATACTGTT M 2 1 2 1 103000 r 74 goat snp24894-scaffold2542-60498 12 44807926 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400663 Affx-122960348 AX-123271018 12 40734490 CATGGCATTCTTGGCTAAACATCTTCCCACAGTTT[A/G]GTGAGAGAAGCTAGAAAAAACAGCCACTTTGCTGA R 2 1 2 1 101000 f 74 goat snp53649-scaffold817-9633 12 44789103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800127 Affx-122953568 AX-385287050 12 40809925 TGAAATCTAAGAATAGCTAATGCTATAAACCTAAG[C/T]AAAAATTAGTAATCATTTGTATTTCTATCAGGGAT Y 2 1 2 1 202000 r 74 goat snp53650-scaffold817-85068 12 44712869 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394187 Affx-122964918 AX-123264542 12 40877086 TCCATTCTTGTCTTTGATTTTTATTCAATTTTAAG[A/G]CCTTGATAGCTGGAGCCAGAATGTAAATTATTAAT R 2 1 2 1 101000 r 74 goat snp53651-scaffold817-152229 12 44644947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429181 Affx-122937962 AX-123299523 12 40910557 ACTTGTTCTCCCCATAAGCCTATTCCTTTTGTAGC[A/G]TTTAATTCTGTATAATGTCAACCATATATTTTAAG R 2 1 2 1 202000 r 74 goat snp53652-scaffold817-185700 12 44611581 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790232 Affx-122969635 AX-385277236 12 40953927 TTATTGAGGCAAAAGTCACATAAAAATTTAACATT[G/T]AAGTGTATGATTCACATAGTATCTGCATAGAGAAT K 2 1 2 1 201000 f 74 goat snp53653-scaffold817-229070 12 44567940 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411481 Affx-122951793 AX-123281831 12 40989204 CTGTCCATGGTGAGAGAGTCTGTTCTCCTGAATAT[A/G]TAATCACTGAAGAAAAGATATCTGACTTGTTTTAT R 2 1 2 1 101000 f 74 goat snp53654-scaffold817-264347 12 44532438 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427383 Affx-122940086 AX-123297726 12 41048994 GTAAAGTTAGTTGAACACAATAAAAATCCTTGAAA[C/T]AATTCTCATAAATAGGGTCAATTTACCTTTGACAA Y 2 1 2 1 101000 r 74 goat snp53656-scaffold817-324137 12 44471394 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376768 Affx-122977966 AX-123247127 12 41089191 GCTCTGGGTTAGAAGAAAATTCTCAGTTACCACTA[C/T]GGAGGTCAGTCAAAGGAAGGTAAGATATTTACCCA Y 2 1 2 1 101000 f 74 goat snp53657-scaffold817-364334 12 44429938 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428816 Affx-122938385 AX-123299158 12 41189839 TTCTTTGAAACTACATTTTTCTTTATATTTAAAGA[C/T]GATGTCTTTAGATAACATATTGCATTTTTTTTTCC Y 2 1 2 1 103000 r 74 goat snp53659-scaffold817-464982 12 44327535 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783820 Affx-122935219 AX-385270876 12 41241216 GCTTTAGACCAGCATCATGAGGACAGAATCAACTT[A/G]CTATTTCAATTGACTTTAAATCCTTAAGGTGCCAT R 2 1 2 1 101000 f 74 goat snp53660-scaffold817-516359 12 44275508 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772564 Affx-122921631 AX-385259713 12 41295422 ACAACCAGATTAGATATCAGCTTCCAAGGGAAGAA[C/T]GTGTTATACAGAGATTATGATGTGACAACTACATT Y 2 1 2 1 101000 f 74 goat snp53661-scaffold817-570565 12 44221089 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787603 Affx-122976947 AX-385274626 12 41350057 ATGACCTCCTAATGGTTTTCTATGCTTTAATTATT[A/C]TCTTCCAAATTATTCTTTAATTTTAGCTTTTGTGG M 2 1 2 1 101000 r 74 goat snp53662-scaffold817-625200 12 44165762 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443488 Affx-122927810 AX-123313825 12 41402599 GTTGTAAATATAAATATTTAATTTGTATGGATGAG[C/T]AAAATTTCCCCCACCAAAATTATTAGGAAGGGCTG Y 2 1 2 1 103000 r 74 goat snp53663-scaffold817-677742 12 44113357 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426697 Affx-122939900 AX-123297043 12 41433623 CATTGTCCTTAAGATTCTGTATTGAATGTTTCCTT[A/G]TAACTGTTAATAATGAGTACTTTTGAAACTTCCTG R 2 1 2 1 101000 r 74 goat snp53664-scaffold817-708766 12 44081879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405639 Affx-122956588 AX-123275991 12 41464239 ATGCATGTGCCATGTAAGTAATTTATTTTGGGGGT[A/G]AAGATATATTGAAGCATTCTTATTGGATGGCTTTC R 2 1 2 1 201000 r 74 goat snp53665-scaffold817-739382 12 44050432 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403789 Affx-122957978 AX-123274141 12 41501517 GGTTAATGATGCCTGTGGGTACTAAGAGAAGAAGA[C/T]GGTAGGAAACCAGGAAACTGTCTTCTTAAATTAAA Y 2 1 2 1 101000 f 74 goat snp53666-scaffold817-776660 12 44012312 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775056 Affx-122967943 AX-385262188 12 41599288 TGGCTAAACACAGCAAGTGCTATTTTTAAGAGATT[C/T]ACTTTTAAGAGATCTACAGTCAGGGCCTTGTATAG Y 2 1 2 1 101000 f 74 goat snp53668-scaffold817-874431 12 43916310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397935 Affx-122961925 AX-123268290 12 41645726 TTCTTAGGGCATTTACTTTAGAAAAACTGGCAATT[A/G]TAAACTCTTTCTCTACCTCTTTGAAATGTAAATTT R 2 1 2 1 101000 f 74 goat snp53669-scaffold817-920869 12 43869723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441001 Affx-122928962 AX-123311338 12 41707181 ATGTTGTGCAGACACAATGCTTTAAAATATTAATC[A/G]CAAGTTTAGTTTTGATGAAAATCTTTATAAATTGA R 2 1 2 1 103000 f 74 goat snp53670-scaffold817-982324 12 43807522 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798343 Affx-122967851 AX-385285278 12 41774455 ACTTTTCTTGTGTTTTAACTTGGAAGTTAAACACT[A/G]CTAGAAGTGGTATATATGGACTCCCAGATGGCAAG R 2 1 2 1 101000 r 74 goat snp53671-scaffold817-1049598 12 43739344 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762971 Affx-986697500 AX-385250961 12 41837174 CAGCATTATTCTACCCACCTTTATAGCAATTACAG[C/T]ACTACTAAATCTATATTTCTACATGCGACTTACAT Y 2 1 2 1 600010 f 74 goat 12_41837174 12 41837174 Ancestral_priority_1043 ancestry 0.806 recommended IMAGE 10K 10K ancestral 38429044 Affx-122938308 AX-123299386 12 41879272 TACTTTCCTATAAATGCCCTCTCATCAAGATACCA[A/G]CAGACAGTCATGAAAACTAAGTAGTCAGAAAAAAA R 2 1 2 1 101000 f 74 goat snp53672-scaffold817-1154415 12 43632160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396300 Affx-122963090 AX-123266655 12 41913468 AAAAGAAAAGAAAAGAAAACATGGTGGTGATTTCT[C/T]TAAAGTTTATATTAAGTCTTCTAGCTTCCATTTTT Y 2 1 2 1 103000 r 74 goat snp55336-scaffold855-17875 12 43598144 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800192 Affx-122978153 AX-385287115 12 42202746 TTTTCACAGAGAAAACAACAATACAAGCAAAAGAA[A/G]ACTAAGCAAAAAATTATCACTTATTCATGGAAATA R 2 1 2 1 101000 f 74 goat snp55341-scaffold855-307153 12 43300149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791536 Affx-122950616 AX-385278527 12 42257561 TCCAAGGATTCTTAGGTGAAATATGTGGCACATGT[A/G]CAGGCTGCATGCTCGTTTGTCACATTATTACTTGC R 2 1 2 1 201000 f 74 goat snp55342-scaffold855-361968 12 43244884 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272721 Affx-1111832957 AX-519546424 12 42358137 TATGTCTACAAGTTTGAAATGCAATGAAAATATGA[A/G]CCATGAGTAGAAGAATAATAGCTAAATAAATATGT R 2 1 2 1 101000 r 74 goat 12_42358137_AF-PAKI 12 42358137 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781315 Affx-122958475 AX-385268400 12 42432234 CTGTTGATTATACATTATCTGGTCTTGTAGACTAG[C/T]GTTCAAAAACCTTAATTCAATGTGGTTTTTATTTC Y 2 1 2 1 101000 f 74 goat snp55346-scaffold855-536641 12 43067524 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776324 Affx-122937130 AX-385263452 12 42466240 ATATTCTACTATTCTTGTTACAAGCTAAGACTGCT[A/G]CCTACATCTTGAAATGTATACAACAGCCCTTTCTC R 2 1 2 1 101000 r 74 goat snp55347-scaffold855-570647 12 43032606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791657 Affx-122933336 AX-385278648 12 42520018 TTGATAAGGTAAGACCTTTAAAGGAGGGATAATTA[C/T]AATGTCCAGCTTTCAAGGAGAGTACAATTATTATT Y 2 1 2 1 101000 r 74 goat snp55348-scaffold855-624425 12 42976564 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445577 Affx-122925134 AX-123315914 12 42579908 TTCTGTATTTTAGTGCTGTCAACTGAGTGAAAATT[A/G]CACAATGTAAAAGTTAAGAGTTAAGCTTTTTGGAA R 2 1 2 1 101000 f 74 goat snp9157-scaffold1332-785171 12 42903453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404808 Affx-122956655 AX-123275160 12 42611799 AAATTTCCTGTGAATCATTTCAAGGAGTCACAAGC[A/G]ATCCATCAGTGGTAAGTACTAGTGAGGGACTTTAG R 2 1 2 1 101000 r 74 goat snp9156-scaffold1332-753280 12 42870959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432559 Affx-122935537 AX-123302900 12 42641075 TGAGTTAACATTGGGAAATCAATTAATGTAATTCA[C/T]TACATTAATTTGTTCTGTTAAGAACAAAGGAGAAA Y 2 1 2 1 103000 r 74 goat snp9155-scaffold1332-724004 12 42841589 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392769 Affx-122965993 AX-123263126 12 42715321 TTTTGTATGTTGTTATTTGAGTGATTTATTTTCTT[A/G]CTCTTAATTTTTGTTAGAACTGCTTCAGTTATACC R 2 1 2 1 101000 r 74 goat snp9154-scaffold1332-649758 12 42767748 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387078 Affx-122969883 AX-123257436 12 42764470 CCAAAACCGAAGGGGATGATAAGGAAAAAGGAAAA[A/C]GGGAATCAATCCCATATAAGCTACTGAAAGACCTT M 2 1 2 1 201000 f 74 goat snp9153-scaffold1332-600609 12 42718034 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791815 Affx-122954362 AX-385278805 12 42813435 TTTGTTAAAGAATTGGTCTTAACTTATTACCACTA[G/T]TGAAGAACCTTGACTGACACGGAACCTGAAACTAA K 2 1 2 1 101000 r 74 goat snp9152-scaffold1332-551644 12 42668969 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772571 Affx-122946664 AX-385259720 12 42849662 ACTCTTAGCTCTGGATATATGTTTCCATATTTTTT[A/G]CCCTTTGAGCATAAAATGCTCAGTTTTTGAATACC R 2 1 2 1 303000 f 74 goat snp9151-scaffold1332-515417 12 42630983 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792642 Affx-122974232 AX-385279622 12 42899673 ACAATCTTTGATTGGAACTTCTCTTGTTTTTCAAA[C/T]GTTGCTTTGTTGTAATCAGCTTTTCTCCAGTGTCT Y 2 1 2 1 201000 f 74 goat snp9150-scaffold1332-465406 12 42581389 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393315 Affx-122965957 AX-123263671 12 42938333 TTTCCAGTTAGGTTACTAGGAATCAGGAAAAAGAG[C/T]AGAAACTAGGAGCCAGGTCCTGCTCTTTAAGTGAT Y 2 1 2 1 600000 f 74 goat snp9149-scaffold1332-426746 12 42938333 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800622 Affx-122965957 AX-385287541 12 42938333 TTTCCAGTTAGGTTACTAGGAATCAGGAAAAAGAG[C/T]AGAAACTAGGAGCCAGGTCCTGCTCTTTAAGTGAT Y 2 1 2 1 101000 r 74 goat snp9149-scaffold1332-426746 12 42542031 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425092 Affx-122941240 AX-123295438 12 43010101 TATCAGTAATGAAACATAATAGGAAAGGGGTGCCA[A/C]GATCAAAGGAACTTCCTAAACTCACCTTTGTAGTA M 2 1 2 1 101000 f 74 goat snp9148-scaffold1332-354978 12 42468588 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402317 Affx-122959082 AX-123272670 12 43049616 TAATGTTCTTTCTTCCAAGAATTTCTCACCTCTGA[C/T]GAATCCTAATCTTCCCCCAATCATGACTTGTTCAC Y 2 1 2 1 101000 r 74 goat snp9147-scaffold1332-315463 12 42428803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376780 Affx-122977957 AX-123247139 12 43083229 TAATGGAGAGGAAAAGGAAGTTGGGAGGATTATAG[C/T]AAAGAGTCTGTGACATTTTGTTTTCTGGATCTTTG Y 2 1 2 1 103000 f 74 goat snp9146-scaffold1332-281850 12 42394295 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419157 Affx-122945740 AX-123289505 12 43114876 AAGCATCTTCCTGGTCAACCTGCTTAATCTGCCTA[A/G]GAACATTCTTTGAGGTACTGAGAGCAAGGTCAGAC R 2 1 2 1 101000 r 74 goat snp9145-scaffold1332-250203 12 42361711 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393427 Affx-122965870 AX-123263783 12 43158003 CTGGTCTGAGGGAGTAGTCACTCATAATATTCATG[C/T]GCTACAAGAGGAAAAGATGAACTTGATTCTGACCA Y 2 1 2 1 101000 f 74 goat snp9144-scaffold1332-207076 12 42318433 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435905 Affx-122932769 AX-123306244 12 43201902 GATAAACCTGACAGGGAAACTGGTAGGAAGAATTC[C/T]AAAAATGCCTTTCTCTGCCAAAATCGCCTGGTTAT Y 2 1 2 1 101000 r 74 goat snp9143-scaffold1332-163177 12 42273364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275637 Affx-1111834923 AX-519549207 12 43222246 AGGCTTCTGCTATCTGTTGATTTCAATCAGTGAAA[A/G]AAGTAAATAAAAATAGTGCCTGTAATATATATCAT R 2 1 2 1 202000 r 74 goat GoatD01.058982 12 43222246 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320771010 Affx-122971999 AX-385258172 12 43231097 AGCATGAAGAGGAAAGGTCCCAAGCTACAGTATAT[A/G]CTGTTCTGTTTGTCATGTAATTTTAAGAGTTGAGT R 2 1 2 1 101000 f 74 goat snp9142-scaffold1332-133982 12 42244980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415075 Affx-122949466 AX-123285424 12 43274045 TAAATATACTAACATGGACACACTCACACATACAC[A/C]ATTTTATATGTTAGGCTTACATTTATAAGATTTTT M 2 1 2 1 303000 r 74 goat snp9141-scaffold1332-91034 12 42196499 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430639 Affx-122936956 AX-123300980 12 43343800 TGGCATTATTTGCAGGATAGACACATATTTTTCCA[C/T]AGCATAGACATCAACACTTTTATTTCCCATGTTTG Y 2 1 2 1 101000 f 74 goat snp9139-scaffold1332-21279 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449351 Affx-122922971 AX-123319686 12 43372637 TGTGAAGTTGAACAAAACTGTAGTATGCATAATGA[C/T]AATGTTAGTCATTTATGAATTTTCAGTTAGCTTGC Y 2 1 2 1 101000 f 74 goat snp6792-scaffold125-7459 12 42081126 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789530 Affx-122968688 AX-385276539 12 43403697 TGAAAACATAAATATTACAGATAATGAAAAGGGAA[A/C]AGTTAAGTGAAAATAGAAGAGCCAAAATTATTATG M 2 1 2 1 201000 r 74 goat snp6793-scaffold125-38519 12 42042481 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415482 Affx-122948704 AX-123285831 12 43500075 ATGCAGTTAACATTTCTGGTGGTTTTTCATTCCTT[C/T]GTGCCAACTGGTTTATTTTTCCTTTCCTTTAATGA Y 2 1 2 1 103000 f 74 goat snp6795-scaffold125-134897 12 41943753 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776379 Affx-122971459 AX-385263506 12 43531346 ACACATACATTCCTTCTGATTCATGGTAAGACCAA[C/T]GGCAGAGTGCTCAATCTGGTATGTTAATTCAATAC Y 2 1 2 1 101000 f 74 goat snp6796-scaffold125-166168 12 41912603 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800022 Affx-122968238 AX-385286945 12 43561186 TTTCTCATTCATAAAGTACAGATGATAATGATGAT[A/G]ATAACTAACTATACCTTCATGTAAAAGGTTGCTGT R 2 1 2 1 201000 f 74 goat snp6797-scaffold125-196008 12 41882286 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429271 Affx-122937887 AX-123299613 12 43600663 TTACGAATAGTGGATCTGTTTGGATGCTCCCTTCA[G/T]AGCAAACACACCAATTTCACTTGTTGTTAAAAAAT K 2 1 2 1 201000 r 74 goat snp6798-scaffold125-235485 12 41842476 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444426 Affx-122926568 AX-123314763 12 43647701 TGGCAATGATGTTTACAATGTGGTAAATACACATA[C/T]ATACAATGAAAAAATAAACCAAAGAAGAATATATA Y 2 1 2 1 103000 f 74 goat snp6799-scaffold125-282523 12 41794439 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767132 Affx-122948246 AX-385254418 12 43713721 GAAAAATTGATGGTTTCTCTTTATAAAAGAAAAAC[A/G]TCTATTCTTTAAATCAAACCCTAAATTAGAATTAA R 2 1 2 1 101000 f 74 goat snp6800-scaffold125-348543 12 41727035 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384095 Affx-122972843 AX-123254453 12 43742516 GAAGTAGGAACCGGGTTATACATAGAAATTAAGGC[A/G]TAAGACTAAGAAAGAGAAGAAAATTTTCTCTGCTT R 2 1 2 1 101000 f 74 goat snp6801-scaffold125-377338 12 41697635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790637 Affx-122922900 AX-385277639 12 43780535 TTCTATAAAGATGACTTATTAGTATTAGGCAAAAC[A/G]CAAATTGAAGTCACCAGCATTATCTCATATTAGTC R 2 1 2 1 101000 r 74 goat snp6802-scaffold125-415357 12 41659149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407778 Affx-122954962 AX-123278129 12 43816795 AACAGCTACACAAATTCAGCTACTTATGTTGACAA[C/T]AGCAACTTTTTAAGAAATAGATGCAAAACTACTCT Y 2 1 2 1 101000 f 74 goat snp6803-scaffold125-451617 12 41622683 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276771 Affx-1111835512 AX-519550280 12 43864584 CAAACAAAACCTTTCTCCCTGCTATGCCTCATTCC[A/G]TGAGAAATGTAATTTCTTACATAAGTAATCTTAAT R 2 1 2 1 201000 r 74 goat Random2.2K-1274 12 43864584 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443009 Affx-122928175 AX-123313346 12 43875589 TATGTGGAAACTAAAAGAAACACAAGACAAGCCCA[C/T]AGATATAGAAAATATATCAGTAGTGGTCAGAGATA Y 2 1 2 1 102000 f 74 goat snp6804-scaffold125-510411 12 41562653 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794236 Affx-122945716 AX-385281202 12 43926982 ATACTTTAAGTAACCTAGACAGAAATATGAGTTTC[A/G]TTCCTCACTGTAAACTTTCTTCAAGTTTTTCTTCT R 2 1 2 1 101000 r 74 goat snp6805-scaffold125-561804 12 41510631 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450731 Affx-122921868 AX-123321065 12 44007651 TGAACTCATCTTCCACAAACACATTGAATGAACAA[C/T]TATGCATACAACAATTCTGTCTGAAAGAAATCCAG Y 2 1 2 1 101000 f 74 goat snp6807-scaffold125-642473 12 41431916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435009 Affx-122933812 AX-123305349 12 44042854 AATTTATCAAGTTTAGATTTATGGCCCAGGATGTG[A/C]TCTATCCTGGAGAAGGTTTAATCTGACTTTCTAAA M 2 1 2 1 103000 r 74 goat snp6808-scaffold125-677676 12 41396014 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440385 Affx-122929631 AX-123310722 12 44082385 CATAAGTATTTCCTACATCTTGAATATATCCTATC[C/T]ATCACATATATTTTCATGTCAAAAACTGTTGAGGA Y 2 1 2 1 101000 f 74 goat snp6809-scaffold125-717207 12 41356342 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797898 Affx-122972310 AX-385284836 12 44116201 CTTGAACTCCCCTCAGGGTACAATGTTAGGGGCAG[A/C]TGCAGTGGTTGATGGATTGATGGCAGAGATATATT M 2 1 2 1 102000 f 74 goat snp6810-scaffold125-751023 12 41322274 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778431 Affx-122939319 AX-385265545 12 44162162 ATCAATTTTGTATCCACTGGGAAATATCTATAAGA[C/T]GCAAAGTAAAAAGTCACCAATATCAATACAGACAA Y 2 1 2 1 101000 r 74 goat snp6811-scaffold125-796984 12 41280563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432042 Affx-122935904 AX-123302383 12 44215943 TCTCAACTATAGTATAATTTTTGACTGAGTCACTA[A/C]AATATCCTTACTCCAGTTTATTCATTAATATCGTA M 2 1 2 1 101000 r 74 goat snp6812-scaffold125-850765 12 41226874 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775614 Affx-122920405 AX-385262745 12 44246762 TTACTAAGTCTATTCCATGGAAATGTTCTATTTAT[A/G]CATATTAATAGTATCCTACATAAGAAATTTTTTAA R 2 1 2 1 201000 r 74 goat snp6813-scaffold125-881584 12 41196313 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781118 Affx-122963935 AX-385268203 12 44323333 ATTCTAACCCAGGCAGTCAGGTTCAGAGTCTAAAC[G/T]CTTAACCCACGCACTGTTGCCTCTGACACAAGATT K 2 1 2 1 101000 f 74 goat snp6814-scaffold125-958155 12 41119269 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800052 Affx-122927267 AX-385286975 12 44355380 CCTAGGGAAATAATTACAGCAAGACTAGATTTCCA[G/T]CTGTAAGTTTACCATCTAGTGAAGTTAATTCACAG K 2 1 2 1 101000 r 74 goat snp6815-scaffold125-990202 12 41087268 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766179 Affx-122943007 AX-385253580 12 44405806 TCTTTGTTCTACATTTCCATTTCTCACATCAGCTC[A/G]TTTCCACTGAAATTATACTAATTTCTGACATCAAC R 2 1 2 1 101000 f 74 goat snp6816-scaffold125-1040628 12 41036196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785944 Affx-122931785 AX-385272981 12 44436735 TGGCCTCAAATGCTAACAGCTTTTTTGTGGGGACC[C/T]GTGATATGTTCTACTAGACCACAACTTGTCAACTA Y 2 1 2 1 101000 f 74 goat snp6817-scaffold125-1071557 12 41005431 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789374 Affx-122960357 AX-385276384 12 44481645 AAACATATTTAAGAAAATTAGCTTTACCTTTCCAC[A/G]TCTATATCTCCCTAATAAACATTAACCAAAGTCAC R 2 1 2 1 101000 f 74 goat snp6818-scaffold125-1116467 12 40960060 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414407 Affx-122949979 AX-123284756 12 44525316 TTATAAAGAGCTTACATCCCACAATGTTCCCACTA[C/T]AGAGTTAAGTTTGCATTCATTCATTCACTCATTCT Y 2 1 2 1 101000 f 74 goat snp6819-scaffold125-1160138 12 40916969 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414315 Affx-122949576 AX-123284664 12 44615949 AACTCCATACCCCCTTAGAAGCCTTAAACTGATAG[C/T]AATAATCCTATCAAACATTGAACACTAAATACACA Y 2 1 2 1 201000 r 74 goat snp6821-scaffold125-1250771 12 40824441 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772164 Affx-122945020 AX-385259319 12 44664324 GTGAAAGAGAGCTTTCACCAATCTTTTAAGACACG[C/T]GTTTCACTCAAGTTAGTGAAGGCAGAAGTATATTG Y 2 1 2 1 101000 f 74 goat snp6822-scaffold125-1299146 12 40776470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402693 Affx-122958349 AX-123273046 12 44751231 CTGAATCACAGTAGAGGATTTAAAGACCTCAGGAT[A/C]TGAAAAGGTCATTTTTGTTCAAGTACCTGTCTACT M 2 1 2 1 101000 f 74 goat snp6824-scaffold125-1386053 12 40688594 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431418 Affx-122936526 AX-123301759 12 44784911 AAGATTGGTGACATCTGTTTCTTCCACTTGGAAGA[C/T]GGCTACCATGTTGAACTAGCTTGAGACCCCCTATA Y 2 1 2 1 101000 r 74 goat snp6825-scaffold125-1419733 12 40655015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444701 Affx-122926429 AX-123315038 12 44840787 CTTTCTGACAAGAAAAGATATGAGATGATAGCAAA[G/T]ATAAAAATAATCAAATATGTTGATAAATATATTTC K 2 1 2 1 103000 f 74 goat snp6826-scaffold125-1475609 12 40599707 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449321 Affx-122922994 AX-123319656 12 44884537 AGCTTAAACATCTGAAAGTTCTCAGTTCATGCACT[A/G]TGTCATATTACAAAGGAAACTACCAAGTTTACATT R 2 1 2 1 201000 r 74 goat snp6827-scaffold125-1519359 12 40554980 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445952 Affx-122925904 AX-123316289 12 44930765 GATATTCACATCCATGTATATACCAATAACCACAT[A/C]TATAATTATATATGTATATGTGTGTTTTATATGTA M 2 1 2 1 103000 f 74 goat snp6828-scaffold125-1565587 12 40508225 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272672 Affx-1111832958 AX-189195636 12 44961230 TCATGATGTATTCTGCATATAAGTTAAATAAGCAG[A/G]GTGACAATATACAGTCTTGACGTACTCCTTTTCCT R 2 1 2 1 303000 f 74 goat 12_44961230_AF-PAKI 12 44961230 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38415504 Affx-122948689 AX-123285853 12 44981275 TAGAAAGTAAGCAAGCTGTTAAGTAGCAATGGCAA[C/T]ATCTCTAATCCATGTAAATACTTAGAAATCAGATG Y 2 1 2 1 101000 r 74 goat snp6829-scaffold125-1616097 12 40458395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795445 Affx-122936363 AX-385282401 12 45019698 CTTTGAGACTCATTAGTTTCATAAAGTTCTAGGTG[C/T]ATTTTGTAATCCATTTCCTGGTGTTAAAAATAAAA Y 2 1 2 1 101000 f 74 goat snp6830-scaffold125-1654520 12 40419544 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413274 Affx-122950213 AX-123283623 12 45115342 GAATCTTAGTGATGATGGACTATGCTTAATAAAAA[C/T]AGAAACATAAAAAAAGTGATGCCTTATTTGATAAA Y 2 1 2 1 101000 f 74 goat snp6832-scaffold125-1750164 12 40321275 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791074 Affx-122940769 AX-385278068 12 45148397 TCTTGTGACAAAAGATACTATACTTGGTTTACTGT[C/T]ATGGTTACTGTACTTCAAAGTTGATTAACAATGAA Y 2 1 2 1 101000 f 74 goat snp6833-scaffold125-1783219 12 40288088 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791479 Affx-122937336 AX-385278470 12 45185015 TTAGATTAAATGAGCTATTATAAAGTACATCTATA[G/T]AGTAACATGGCCTATCCTCTACAATAGATTCTGAC K 2 1 2 1 101000 r 74 goat snp6834-scaffold125-1819837 12 40251289 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413825 Affx-122949887 AX-123284174 12 45217367 CCATCCTGTCTATAAATAATAGCAAAACTCAGAAA[C/T]GAATTCCATCCTTAGATCTAGGTTTAAATGGACTA Y 2 1 2 1 101000 f 74 goat snp6835-scaffold125-1852189 12 40218830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797579 Affx-122960294 AX-385284518 12 45246581 ATTTACTGGCATTCTCTCAAGAAAGTATGTAAGGA[C/T]GTTTTACTAGTTCATCTGGGTCTCCTATGATGTTT Y 2 1 2 1 101000 r 74 goat snp6836-scaffold125-1881403 12 40189702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387022 Affx-122969928 AX-123257380 12 45276308 AGCCTTAAAAAGACGGTGACAGTTGAAGAAGACCA[A/G]AAAAGAAAAAAGCAAGATCTATGAAGAGGATTCCA R 2 1 2 1 101000 f 74 goat snp6837-scaffold125-1911130 12 40159778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424479 Affx-122941761 AX-123294825 12 45317546 TTGCTCTCTGCGCTTCAGAAACATAGACATCTTTC[A/G]CATCTTCTAACAGACATTTCCTCTTTCAAATTAGA R 2 1 2 1 101000 f 74 goat snp6838-scaffold125-1952368 12 40118649 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793263 Affx-122964271 AX-385280241 12 45353304 AATATCTAGTGATGAATGTGAAATGTTTTGGAAAG[C/T]ATAATAAATAAGAGTGATGACAATAATGAAAAAGG Y 2 1 2 1 101000 f 74 goat snp6839-scaffold125-1988126 12 40081836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796578 Affx-122948868 AX-385283524 12 45398083 ATCTTCATTGAGGTTTTATAAAGAATCAGGAAAAG[A/G]TACAGGAGCAAAAATCAAGGAGTACATATATTAGT R 2 1 2 1 201000 f 74 goat snp6840-scaffold125-2032905 12 40037182 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414278 Affx-122949602 AX-123284627 12 45452272 ATGTATCATACGTTTGAAGATTTTTGAAAGGGCTC[A/G]TTATTGACATAAAGCAAAAATAGTTTATTTAGCTT R 2 1 2 1 101000 f 74 goat snp6841-scaffold125-2087094 12 39982825 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452181 Affx-122921230 AX-123322514 12 45567994 TTAGTTAAAGAGACAATGAAAATTAATCTACAATG[C/T]AAACAAATATAAAATTTAATGTCGTGCCTGTATTT Y 2 1 2 1 103000 f 74 goat snp6844-scaffold125-2202816 12 39889298 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389221 Affx-122969055 AX-123259579 12 45626620 CTGTCTGCATTCTAGAGGTTCAGCACTTTCATTTC[A/G]CTTACTTATAATGAAAAGCTAAAAACTACACTACC R 2 1 2 1 101000 f 74 goat snp6845-scaffold125-2261442 12 39830721 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397734 Affx-122962542 AX-123268089 12 45730389 AAAGGATTAAACTCTTTGCTCAAGAATGCATCCTT[G/T]TAAGTTGTGCTTCTAACCACGACTGAGTCACTGGT K 2 1 2 1 101000 r 74 goat snp6847-scaffold125-2365211 12 39726511 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796405 Affx-122921966 AX-385283355 12 45776686 TCGTTTAACAAGTGCTGAGGATATTCACAATGTTG[C/T]AGTCACTGAGATACACGCAGGGATTGAGATGAACA Y 2 1 2 1 101000 f 74 goat snp6848-scaffold125-2411508 12 39679916 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801537 Affx-122926653 AX-385288446 12 45805883 CTTTTTTCTAGCAAAACATGGAGAAAGTACCTTTT[A/G]CTATGGCTTACAAACTATTAAGTCAATAAGACTTT R 2 1 2 1 101000 r 74 goat snp6849-scaffold125-2440705 12 39650758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441167 Affx-122929556 AX-123311504 12 45842258 GTCCTGTCTTACCACCTCAGTGTTTGGGTAGGGTT[C/T]GGGAAGGGGACTTTCTAGTCCCTCTTCTGGCTTAA Y 2 1 2 1 202000 f 74 goat snp6850-scaffold125-2477080 12 39614173 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414585 Affx-122949369 AX-123284934 12 45880400 TAACACATTTCGTGACAGACTAAGCCAGAAATAAA[C/T]GATTTCCACAAACATTATAAGATTGAATTTCAAGA Y 2 1 2 1 101000 f 74 goat snp6851-scaffold125-2515222 12 39575536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775352 Affx-122924273 AX-385262483 12 45931385 TAGGAAGTTAGGATGGGGGAAGAAAAGCTATAGCC[A/G]TGAAGATTTGTGAGCATAATCAATGAGATGACTTT R 2 1 2 1 101000 f 74 goat snp6852-scaffold125-2566207 12 39524139 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438648 Affx-122930899 AX-123308985 12 45967549 TTTTCACATTTATGTAAGTTTAAATTGTTTCACAC[A/G]GAGCATCAAGCAATAATGTTCTAGTGTAACTTTAA R 2 1 2 1 201000 f 74 goat snp6853-scaffold125-2602371 12 39487999 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787490 Affx-122978830 AX-385274515 12 46019309 ACTGTTTATTGAATCAAGAATAGCTCTAGTTCTCA[A/G]ATATTTTCATCAATTTCCTCACTAGATATATGCTT R 2 1 2 1 101000 f 74 goat snp6854-scaffold125-2654131 12 39436415 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389110 Affx-122968567 AX-123259468 12 46066272 AAGACAAGGTGAGAGAAGTGAGTAAAAAACTGGGA[C/T]GACACCTTCACTTTGGTGTATTTTACCCTTCTTTA Y 2 1 2 1 101000 f 74 goat snp6855-scaffold125-2701094 12 39389473 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797809 Affx-122926003 AX-385284748 12 46108145 GTAAACAGATACAAGTGGCAGAACATCCCTGATTA[C/T]ATTAAACTTAGGTGTTCCTCCCCAGCATATCTTCT Y 2 1 2 1 101000 r 74 goat snp6856-scaffold125-2742967 12 39347545 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394662 Affx-122964375 AX-123265017 12 46153430 GTATGATTATTCATTGTATAATAATATTTATTATT[A/G]CCATATGTTTCTACCCAAGATACATCACAGATGTC R 2 1 2 1 103000 r 74 goat snp6857-scaffold125-2788252 12 39302459 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794598 Affx-122942087 AX-385281560 12 46228175 CCTGCACTGAATGTCTCTCATCTTGGTCATTAAGA[C/T]TTCAAGAGAAATACTTTATAATCAAAGTAGTCACT Y 2 1 2 1 101000 f 74 goat snp6859-scaffold125-2862997 12 39227802 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377919 Affx-122977229 AX-123248278 12 46322345 ACTCTTTAAAAATGAAAAGAGCCTTTGTATGCAGA[C/T]AAATGTGTCATGGACTCCTATGCAGATTCCACCGT Y 2 1 2 1 101000 r 74 goat snp6861-scaffold125-2957167 12 39133764 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434630 Affx-122934000 AX-123304971 12 46361448 TTTCATATTATCACATATTAAAATATAAAAGTGTG[A/C]CAAATCTGTAATAACCATTTCCAAGTAGGCTAAGG M 2 1 2 1 101000 r 74 goat snp6862-scaffold125-2996270 12 39094930 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392484 Affx-122966143 AX-123262841 12 46393404 TCAGTGAGTGCAGGGCTAGTCTTCAGTGAGAAAGT[A/G]GAATGCTTGACCCAGGCACTATGCTATGAAGGACA R 2 1 2 1 101000 f 74 goat snp6863-scaffold125-3028226 12 39062710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449065 Affx-122923049 AX-123319400 12 46432357 ATCGTAACTTGCAAGAGGAAGAAATAAACCTTGTC[A/G]TGTTCAGTCACTAATATTTCAGGATTTATTTGTTA R 2 1 2 1 201000 r 74 goat snp6864-scaffold125-3067179 12 39023641 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437211 Affx-122932042 AX-123307549 12 46473057 TCAACCACAGATAGAGAGTTTCAAATTATTGATCA[A/G]CAAATAATCTCTCTCCTTCCCACTCTGTGAAGAGT R 2 1 2 1 201000 f 74 goat snp35909-scaffold431-5803 12 38982542 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771794 Affx-122971566 AX-385258951 12 46502415 GTAACAATTTGAGACAAGTCAAGCATCAAACAATG[C/T]TTTATATGGAACAGGTTCTCCATGTGTGTTAGTTA Y 2 1 2 1 201000 r 74 goat snp35910-scaffold431-35161 12 38952790 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385995 Affx-122971514 AX-123256353 12 46544762 AATAATTGCCCTTCAGACTTTGACGGCGTTGTTTC[A/G]TTGATTCTATTCTCAATGTTGCTGGTGAAAGATCT R 2 1 2 1 201000 r 74 goat snp35911-scaffold431-77508 12 38910699 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404306 Affx-122957025 AX-123274658 12 46580717 TGTGGTAAACAATGTAACTGTCTCCAGGAAGAGTC[A/G]TATTTACAAATTAAAGAACAACTATTTAATTAAAT R 2 1 2 1 202000 r 74 goat snp35912-scaffold431-113463 12 38874769 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398790 Affx-122961421 AX-123269145 12 46614702 TTGTATTGTTGAATCTGGAAGGACCATGTCTTAGG[A/C]GAAAAAGTAATAAAAGTGGCATTTTTTTCCCATAT M 2 1 2 1 101000 f 74 goat snp35913-scaffold431-147448 12 38840219 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439655 Affx-122930603 AX-123309992 12 46644479 TTGGATACAGAAAGAGGAGAATGGGTTGCTTAGTC[A/G]CGCTTGCTGAACTCTTCTGATGACCATGTTTCTTT R 2 1 2 1 101000 r 74 goat snp35914-scaffold431-177225 12 38810628 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399100 Affx-122960869 AX-123269455 12 46680514 TACCTTATTTCTTTTTATTTTAAATGTGAGCCAAC[A/G]TTATGAACCCTGTACTTTTCTGTGAACCTCAGGAA R 2 1 2 1 101000 r 74 goat snp35915-scaffold431-213260 12 38775296 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776658 Affx-122963777 AX-385263785 12 46711045 TCATCTTTATGAGCCATTTAATACAGAGTATTCGT[A/G]CTTGTATTTCCTGCAGTGTGTAATAGTATTTTTCA R 2 1 2 1 101000 f 74 goat snp35916-scaffold431-243791 12 38744804 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445651 Affx-122926155 AX-123315988 12 46748792 AATTAGTGACCTGGCTGTCTGTAAGCTTTATGTAT[A/G]TGTTTTTATTGGTCTGGGTATTTCCACCATTTAGT R 2 1 2 1 101000 f 74 goat snp35917-scaffold431-281538 12 38706951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797330 Affx-122958584 AX-385284269 12 46789823 GATGTTAAGTGGAATTTTCTTTGTTCAAATTTACC[A/G]TTGATATAAAAGAGATCATCTGTATGAAAACATAA R 2 1 2 1 101000 f 74 goat snp35918-scaffold431-322569 12 38665327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438412 Affx-122931282 AX-123308750 12 46845782 CAAACACTAAAGCCTTTTCCATTTAGCAGGTAAAG[C/T]GTAATTGCTTAATAAATTATCTTAATTTCACCTTG Y 2 1 2 1 101000 f 74 goat snp35919-scaffold431-378528 12 38609238 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779354 Affx-122958267 AX-385266458 12 46880548 CCCCGATCTTCTCCACATTACTGGGTGATGGACGA[C/T]ATTTCTAAATCTGATCATGTGACTCCGCTGCATGA Y 2 1 2 1 101000 r 74 goat snp35920-scaffold431-413294 12 38574406 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768791 Affx-122934270 AX-385255968 12 46916820 ACAGAATAACTACATGACAAATACTAAAGCAAACA[C/T]GCTGGAAGAATACCATAATATTCATTCGCCTCGTT Y 2 1 2 1 101000 r 74 goat snp35921-scaffold431-449566 12 38537912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789615 Affx-122936877 AX-385276624 12 46955122 ACACTTTGGAAGGGTTTGGTGGTGAAAAAGTTCTG[C/T]CAGAAAAATAACTGAAGGGAAGGCACCATGTCACT Y 2 1 2 1 101000 r 74 goat snp35922-scaffold431-487868 12 38499630 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276772 Affx-1111835513 AX-519550282 12 46973737 TTGACCTGCATACAGATTTCTCAGGAGGCAGTTTT[A/T]AACTACTGAGATGACCTAATGGAAAAGTACTGCAA W 4 1 2 1 202000 r 74 goat Random2.2K-1275 12 46973737 T A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797412 Affx-122972423 AX-385284351 12 47006014 TAGCTAGATCTATAGCATAGATATAAAAAGTACCT[A/G]TCACGTATTCATTAGTTCAGTCAAAATATTTTCTT R 2 1 2 1 101000 f 74 goat snp35923-scaffold431-538760 12 38448014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416352 Affx-122947888 AX-123286701 12 47044601 TGTGATGAAGCCATTTAAGTTAAAAAGGAAATAGC[A/G]TTATAGTTAAAATGGACAACCAACAGGATCTACTG R 2 1 2 1 202000 f 74 goat snp35924-scaffold431-577347 12 38409372 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798345 Affx-122934016 AX-385285280 12 47088808 TATTTTATTCACAACATTGCTGCCTCACACAAAAT[A/G]GGATTCTGTTGTGGAAGAAGTGGAAATAGGCATTG R 2 1 2 1 101000 r 74 goat snp35925-scaffold431-621554 12 38364375 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438327 Affx-122931346 AX-123308665 12 47122900 AGCCAAAACAGAACTCTTCATTTCTCCAACTTAAA[C/T]CAGCTCTTCCATCTCTGTTTTCTCCTCAGAGAGTG Y 2 1 2 1 201000 f 74 goat snp35926-scaffold431-655646 12 38330153 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418913 Affx-122946090 AX-123289261 12 47154338 TCTATTCATTCCAGTCCATTACATTCGTTTTTAGG[C/T]AGTTAACTCAGGGAAGAAAATTTTTTTGAGATGAA Y 2 1 2 1 101000 f 74 goat snp35927-scaffold431-687084 12 38297796 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787583 Affx-122958786 AX-385274607 12 47272693 CATAAAGTAGTCAGAGATCATTATTACATCTTTTA[C/T]GATTTGGAACAAGAAGACAGCTGAGATACAAAATC Y 2 1 2 1 101000 r 74 goat snp35930-scaffold431-805439 12 38179253 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392764 Affx-122965996 AX-123263121 12 47302880 TAAATTTGTACTGGCCAGGCCACATACACAGTGTT[A/G]CAATTATTTATTTAAACTAATTTTGTTATTGAAAA R 2 1 2 1 101000 f 74 goat snp35931-scaffold431-835626 12 38148942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400963 Affx-122960112 AX-123271316 12 47357803 TCCTAATTTTGTAGCACACCAGCAGGGATCTGAAC[C/T]GCAATTCAGCAGCCCCAACCAGGCAAGTTACAAAG Y 2 1 2 1 101000 f 74 goat snp35932-scaffold431-890549 12 38093002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391836 Affx-122967006 AX-123262193 12 47413743 CTTGTGTTAAGTCAATAAACTTGTTGCAATTTGTT[A/G]CAGCAGCAAGAGAAAATTAAGGCACAAGGGACAAG R 2 1 2 1 201000 f 74 goat snp35933-scaffold431-946489 12 38036837 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382037 Affx-122974946 AX-123252395 12 47484705 AAACTTTTTATCTAGTTCTGTGCCTTTAAAATTCT[A/G]TGATCACTCATTCCTGGTAAGTAAGGAAGGGCATC R 2 1 2 1 201000 f 74 goat snp35934-scaffold431-1017451 12 37965077 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781192 Affx-122935116 AX-385268277 12 47513392 TTTCATCCACAAATAATTGTGAAGTCCTTGTATTA[C/T]GAATTATGAAGTCTAGTTGAATAGCATCATTCAAA Y 2 1 2 1 101000 r 74 goat snp35935-scaffold431-1046138 12 37936032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789389 Affx-122935429 AX-385276399 12 47544278 AATATATTTAAAACACACCAAACAATTTTTGAGGG[C/T]GTATATGAACAGATTCAATTTATTGTGTGCATATA Y 2 1 2 1 101000 r 74 goat snp35936-scaffold431-1077024 12 37906152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276774 Affx-1111835514 AX-519550283 12 47564945 ACAATTTGGATTCCTTTTATATCTTTTTCATCTCT[A/G]ATTGCCATGGCTAGGCTTTCAAAACTTGAATTGAT R 2 1 2 1 103000 r 74 goat Random2.2K-1276 12 47564945 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793150 Affx-122951759 AX-385280128 12 47586093 GATACTGACACTTTCTTTCCAACCTCAATTTTGCT[C/T]TTAGCCTGCTTCTATGGAGCTGACATTTCTATGCT Y 2 1 2 1 101000 r 74 goat snp35937-scaffold431-1118839 12 37864250 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276637 Affx-1111835515 AX-519550147 12 47594537 GGGAAAGGAAAAGAAATGACACAAAGTCCTAAACC[A/C]AATAATTAAATACTTCAAAGATTTTTTTTTTAAAG M 2 1 2 1 102000 f 74 goat Random2.2K-1277 12 47594537 G T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38410105 Affx-122952830 AX-123280455 12 47636858 TAGAGGGCAGGAAATTATATAGTAACAGGGAACCA[C/T]GGAGATTCCCCATATATGGAGAGAAAGCTGAACTC Y 2 1 2 1 201000 f 74 goat snp35938-scaffold431-1169604 12 37813321 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798822 Affx-122967408 AX-385285752 12 47688027 TTATTCATATTTCCAGCATTCTATTCCACCTGAAT[A/G]TCCAAAAGTAATTTCAAAGTCCAGTCCTATTCTTC R 2 1 2 1 101000 r 74 goat snp35939-scaffold431-1220773 12 37762017 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390782 Affx-122967880 AX-123261139 12 47748600 CAAAATTACACTTAGCCCTCAAGGGCAAGCTCCAA[C/T]GTTATGGCTCCATAAAGCCTGCATCCATGACCTCT Y 2 1 2 1 101000 r 74 goat snp35940-scaffold431-1281346 12 37701378 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798299 Affx-122959976 AX-385285234 12 47787055 CAGTAATATGAAGAGAATAGTAATTATTAGCCCTT[G/T]CTATAAAAATATAATCAGGGGCTCACAGAGGTTAC K 2 1 2 1 102000 r 74 goat snp35941-scaffold431-1319801 12 37662239 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765330 Affx-122943953 AX-385252849 12 47872380 ATTCTGCAGCAAACAAATGATTTCTGACTTTTCCA[C/T]ATTAATTTAATTCTAACTTCAGCCACTTACACTGC Y 2 1 2 1 101000 f 74 goat snp35943-scaffold431-1405126 12 37575742 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398947 Affx-122960985 AX-123269302 12 47930193 ATAAATCTCAACATCTCTGAAAACCCTGCAAAGTG[A/C]TCTCAAAAGTCTTGTGTGTATCTTTCGTAAAGCAC M 2 1 2 1 101000 r 74 goat snp35944-scaffold431-1462939 12 37517314 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793427 Affx-122976885 AX-385280404 12 47984138 AAGAGCACACCAGAAGAGCAAGGAAGTAAAGTGAG[C/T]GGAGCAGAAGAGGAGCCTTCCTCTCCACAAAGGAA Y 2 1 2 1 202000 r 74 goat snp35945-scaffold431-1516884 12 37462836 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779096 Affx-122921161 AX-385266201 12 48033655 CAAGAAGTGGGAAGAGGTATGTCCACTGACTATGA[C/T]GTATATTCTGGGATGGATTTCTGACCAGATGGGAA Y 2 1 2 1 101000 f 74 goat snp35946-scaffold431-1566401 12 37413365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418385 Affx-122946561 AX-123288733 12 48102096 TGGTTAAGGCACATATTCCATTATTACTTGAGGGT[A/G]CTCTGGAGCAACTGAGAAACTTTGATACATGGCAC R 2 1 2 1 101000 f 74 goat snp35947-scaffold431-1634842 12 37344498 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441682 Affx-122929176 AX-123312019 12 48144240 ACTGAACCAATTTTGGAAAAAAAATTTGCTAAGCC[A/G]CCTCTGTAATTTATTTTCAGGGCATAAAGGAATTA R 2 1 2 1 101000 r 74 goat snp35948-scaffold431-1676986 12 37302205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397442 Affx-122962113 AX-123267797 12 48175112 GCATTTCATTAGTCCTAGAGAACAAAGATTAATAA[G/T]ACCAATATGTGATATTTTCTCTCAAGGGGCTAACA K 2 1 2 1 201000 f 74 goat snp35949-scaffold431-1707858 12 37271325 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421365 Affx-122944050 AX-123291712 12 48212216 TTGGTCCCATTCTGGTTGGGAGTTCCAGGATGGAA[C/T]AGAAATAGCATGTTCCTATACTCAGAGTGTCAGCA Y 2 1 2 1 102000 r 74 goat snp35950-scaffold431-1744962 12 37233664 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272673 Affx-1111832959 AX-519546379 12 48214474 AGAAAGCAAAAAAGACACAGATGTGTATAAGCAGA[A/C]TTTTGGACTCAGAGGGAGAGGGAGAGGGTGGGATG M 2 1 2 1 103000 f 74 goat 12_48214474_AF-PAKI 12 48214474 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320777350 Affx-122937893 AX-385264472 12 48270842 TTAAATTCAGTACCCAGTATCAAATATTTCTGAAA[C/T]AAGATTGTCTTCACAGCTGTGTATGAGGGCTTATT Y 2 1 2 1 102000 r 74 goat snp35951-scaffold431-1803588 12 37176964 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798969 Affx-122946992 AX-385285899 12 48311170 TTTTCTCTGACCTATCCTTCTGTTCACTATATTTT[C/T]TGTCTCCCTATGCTGCACTTTCATTTCTTTGTCTG Y 2 1 2 1 101000 r 74 goat snp35952-scaffold431-1843916 12 37136448 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439134 Affx-122931086 AX-123309471 12 48347441 AATCCTACTGATCCTTTAAGACCCACTCCTATGCC[A/G]CTTCTCCAGAGAAGACCAATTTCCACCAGTCTCCT R 2 1 2 1 101000 f 74 goat snp35953-scaffold431-1880187 12 37100369 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453017 Affx-122920100 AX-123323350 12 48399358 GTGTGGAATATATAGACTATTTTTTTCTCTTTTTT[C/T]CATTATGTCAGATCTTATATCTCTGCAGCTATCTT Y 2 1 2 1 101000 r 74 goat snp35954-scaffold431-1932104 12 37043670 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453502 Affx-122919819 AX-123323835 12 48451102 TGGAAGGCCAGAAGGCTGATTGAATCTCATTCATC[A/G]CTGATGGCACTTTGCTAGTGATGGCTGTGTTTAGG R 2 1 2 1 101000 f 74 goat snp35955-scaffold431-1983848 12 36993421 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400646 Affx-122960362 AX-123271001 12 48499844 CTTTTTTATGCAAAGGGAAGAAATTATTTTCTTTG[C/T]TGGTTTCTTCACTGATTCAACAACAGCAAAAGTAA Y 2 1 2 1 103000 r 74 goat snp35956-scaffold431-2032590 12 36945074 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411049 Affx-122951956 AX-123281399 12 48536715 AGAACAGAAAAATAAATGAAAACTCAAATTTCATG[C/T]AATAAGATGACCCTCAGAGAAAGTAAACTTTTAAG Y 2 1 2 1 103000 r 74 goat snp35957-scaffold431-2069461 12 36907728 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777283 Affx-122926356 AX-385264405 12 48573313 GTCCAAATTAGAGATAATTATATACCATTGAAGTG[C/T]TGGGCCACCATTCCCTGTTTGCTGTTTTTAATGTT Y 2 1 2 1 101000 r 74 goat snp35958-scaffold431-2106059 12 36870637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441976 Affx-122928445 AX-123312313 12 48607656 TGAGCACACATAAATTAATGAAGAAAGTGAGGATA[C/T]CTAAAAATGAAGGGCCAGTTCTTTCCATGTTAGAG Y 2 1 2 1 101000 r 74 goat snp35959-scaffold431-2140402 12 36835831 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376899 Affx-122977807 AX-123247258 12 48637463 TTACTAAGTTCCAACATGAAATTAGCATAATATCT[A/G]TTTTACTTCATTTTATTCTTGTTCAAATCCATGCC R 2 1 2 1 201000 f 74 goat snp35960-scaffold431-2170209 12 36805732 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407413 Affx-122955238 AX-123277764 12 48673095 ATTGGTAGGCAGATTCTTTACCACTAATCATATCA[C/T]GTTAGAGTTCATTAGAAAATCTACAAATGCATAAT Y 2 1 2 1 201000 r 74 goat snp35961-scaffold431-2205841 12 36770461 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383009 Affx-122973324 AX-123253367 12 48734155 GCAGGACCACATAAGAGGCAAAAAGTAGAGGGAAG[C/T]AGCACCAGCAGCCAAGAACTGGAGTCAAGACAGTT Y 2 1 2 1 201000 f 74 goat snp35962-scaffold431-2266901 12 36700328 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376267 Affx-122978760 AX-123246626 12 48789625 CAGAGTCAGACACAACTGAAGGGACTTAGCAGGCC[A/G]CAAACACAGTGACTCAACACCCTCATGCTATTTGC R 2 1 2 1 101000 r 74 goat snp35963-scaffold431-2322371 12 36643023 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783310 Affx-122949380 AX-385270375 12 48848176 GGCAACATCTTTCCAGAATGTTGTTAATATTTCAA[C/T]TTACTGTTATCCCCTAGCATCAGTGGATCCAGAAA Y 2 1 2 1 101000 r 74 goat snp35964-scaffold431-2380922 12 36584098 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391837 Affx-122967005 AX-123262194 12 48890330 GTCTTCAGTGGCCCTGTGTTTTGGCAGACAGTTTC[A/G]CTCCACAATGCAGAGATAGCTCTCATATTGAATTG R 2 1 2 1 201000 r 74 goat snp35965-scaffold431-2423076 12 36535928 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409220 Affx-122953161 AX-123279571 12 48993330 TAAAAGATCAAGAAGCACATTGGAGAGAAAGACAA[C/T]AATTTTCACTCAGAGTCGTGTTCTAGACTGGCAGA Y 2 1 2 1 101000 f 74 goat snp35967-scaffold431-2526076 12 36434449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378694 Affx-122977066 AX-123249053 12 49130062 AGAATGACAAGATAAAGAAGTACATTTAGCTTACA[C/T]TTGTGATGTAATGCGTTTAGCTTCCATTTCTGTAT Y 2 1 2 1 101000 r 74 goat snp35969-scaffold431-2662808 12 36296763 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774373 Affx-122957420 AX-385261509 12 49167668 CTTATTTATACTCTAGTCAGATTAATACACATGCC[A/G]TCAGAGAACTGCAAATACCTGCACAACTTTTATGC R 2 1 2 1 101000 r 74 goat snp35970-scaffold431-2700414 12 36258886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780560 Affx-122932996 AX-385267651 12 49215357 TTTCTTTTCTGATGAAATAAAGATTTGAATAATGA[C/T]GAGTAAGCCATATTAATGGATAGAAAGATTCAGCA Y 2 1 2 1 201000 f 74 goat snp35971-scaffold431-2748103 12 36211360 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378489 Affx-122976662 AX-123248848 12 49250575 GTGGGAGGGAGGAAAGACAATAGGGGAAGGAAGAC[A/G]AAGGAAAGGAAGGGTATTAATGGGGAAAAGGAACA R 2 1 2 1 201000 f 74 goat snp35972-scaffold431-2783321 12 36176082 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435456 Affx-122933463 AX-123305796 12 49287991 TACTGATTACCAATGCATTGCATAACAGGAGCACT[A/G]CAGAAAAAGAGTCTGGTTACAGAGAAAAAAAGGAG R 2 1 2 1 101000 r 74 goat snp35973-scaffold431-2820737 12 36138755 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445502 Affx-122925188 AX-123315839 12 49327173 GCAAGACTGAGAAATGATGATTAGCTTGAGATTGA[C/T]GATGTGACAAGAGCATGGGGTGGGTATGTTGCGGT Y 2 1 2 1 101000 f 74 goat snp35974-scaffold431-2859919 12 36099810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802560 Affx-122958031 AX-185357770 12 49380251 TTCCTAAAGATATATAAAAGTCTTATAAACTTTTC[A/G]TTCTGCTAAGAATATAGTGTTAAGCAAAAATAAAT R 2 1 2 1 201000 f 74 goat snp35975-scaffold431-2912997 12 36046073 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320770796 Affx-122931300 AX-385257960 12 49432435 CGGAAGTTCCACTTCTCGTTATAAAATAGTAGTCA[C/T]GGCACCTATTCCCCAAAATTTTTGAGATTCAGAAC Y 2 1 2 1 101000 r 74 goat snp35976-scaffold431-2965181 12 35993881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770531 Affx-122953451 AX-385257695 12 49472720 TTTGAGTCTGAATCACAACATTCTATCTATTGTGA[C/T]AGAATGAGACTGTTGGGCATCTTGGAAATGGGTGA Y 2 1 2 1 101000 r 74 goat snp35977-scaffold431-3005466 12 35953141 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381667 Affx-122974740 AX-123252025 12 49512514 CACGCCTCCCTTTAATACGGCCAACTGGGTTCCTT[C/T]CCTGGGTGTGTTTGCTCAAACTTGCCTTCCCACAC Y 2 1 2 1 201000 f 74 goat snp35978-scaffold431-3045260 12 35912824 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769914 Affx-122948007 AX-385257083 12 49571355 GATTAAAACATTCTAGAACCTTATCAGAAACTCTT[A/G]TACAGATCCATTTCCCTAGGCCACATATTTGAGAT R 2 1 2 1 101000 r 74 goat snp35979-scaffold431-3104101 12 35853482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445445 Affx-122925353 AX-123315782 12 49606307 CCCTCAATACAGAGCTCAAACCTTAAGACAGTATA[C/T]GGAAGAAAATTTTGTATCTTGTACCCAAAGCTTAG Y 2 1 2 1 101000 f 74 goat snp35980-scaffold431-3139053 12 35818404 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443159 Affx-122928057 AX-123313496 12 49638485 AGTTGCACAGCTTATAATGGTTCAGGCAGTCAGAT[A/G]TAGAGCACACACTTTTGACCTAATTGTACTGTATT R 2 1 2 1 101000 f 74 goat snp35981-scaffold431-3171231 12 35785586 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774701 Affx-122956821 AX-385261835 12 49673658 AGTAAAACCTGTTGGCCCACCTTCAGTTCATTAAT[A/C]TTCTTGTTATCTTTAAAACATCTCTAAAGAGAACT M 2 1 2 1 102000 r 74 goat snp35982-scaffold431-3206404 12 35749880 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446471 Affx-122925064 AX-123316807 12 49716469 CATTGTGAGGAAGCAGGGCACCTTGATGTTGCTTC[A/G]GCCATTTGCAAAGCACAGAAAATCTTAAAGCTTCT R 2 1 2 1 101000 r 74 goat snp35983-scaffold431-3249215 12 35706554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439479 Affx-122930161 AX-123309816 12 49812715 CCTCTTGCCTCTTGCCTTACCTACCCTAGCTTCTG[C/T]GAACAGTGGGCACAGTGTGAACAGTGAGACAGTTG Y 2 1 2 1 101000 f 74 goat snp35984-scaffold431-3345461 12 35609952 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441143 Affx-122929573 AX-123311480 12 49841514 CACCATAGGCATAATGTACCAGCAGATCTCTAGAC[G/T]TATTCATTATTTATAACTGACATTTTTAATAACTG K 2 1 2 1 101000 f 74 goat snp35985-scaffold431-3374260 12 35581309 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776978 Affx-122956439 AX-385264102 12 49872578 CTCTGATTTCATTAAATGGTATCATGGGTGATGGC[A/G]TTAAATGCTGGTCTTACTTCGCAGCTAGAGTCCCT R 2 1 2 1 101000 f 74 goat snp35986-scaffold431-3405324 12 35550361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794222 Affx-122920451 AX-385281188 12 49922382 GCTCCACTGTATTTGGAGATTTAATTACTATCCCT[A/G]TTTTTAATGCACTAATCCTGCAGCTTTTGATATTT R 2 1 2 1 101000 f 74 goat snp35987-scaffold431-3455128 12 35500487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449911 Affx-122922328 AX-123320246 12 49962035 ACATTTCACATACGATTACATTTCAGAGTTTGGAA[C/T]CTTCAATCACTCAGTAAACAGTGATGCTGAATTAA Y 2 1 2 1 101000 f 74 goat snp35988-scaffold431-3494781 12 35460937 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389897 Affx-122968123 AX-123260254 12 50020243 TGAGTTGACCCAAAGTTTAAGTCTTCTTGGATTAA[C/T]GACCAAGTGAGTCAGAAACGTGAAGGAAATTGATA Y 2 1 2 1 201000 f 74 goat snp35989-scaffold431-3552989 12 35402431 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786552 Affx-122977267 AX-385273585 12 50056977 GAATGAAGGGCTGGGTCTGCCATGCTAAAGCAATT[A/G]TACTCTATCCTTTAGGCCAGGACTTACAAGCTTGA R 2 1 2 1 101000 f 74 goat snp35990-scaffold431-3589723 12 35366350 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776461 Affx-122928760 AX-385263588 12 50088308 TTTCTGAGCCAGTCCGAGAAGAGAAGTGAACTTTT[A/G]TGTGTGATTTATGATATACTATTTTGCTTTGTCAC R 2 1 2 1 101000 f 74 goat snp35991-scaffold431-3621054 12 35335027 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383662 Affx-122972515 AX-123254020 12 50165674 TCTTTCCCTTTGAATCACTAGTTCTATACACATTT[A/G]TTCTGATCACTCCCAAAGAGAAGCACTTAAAAAAT R 2 1 2 1 101000 f 74 goat snp35992-scaffold431-3698420 12 34910328 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790029 Affx-122925767 AX-385277035 12 50226850 GGAGAAGTGAAACAGCATTATAATGAATAGCATTA[C/T]AATAAATAGCTCAACAGTGGTTCCAGTGGCAAGTG Y 2 1 2 1 101000 r 74 goat snp35993-scaffold431-3759596 12 34848353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385654 Affx-122971159 AX-123256012 12 50256169 TGCTGCCTGCTCACATTCCCTGGGGAAAATAATGT[C/T]TAGCTACATGAGGGAGGAAGTATCAGAGAAATGCT Y 2 1 2 1 101000 f 74 goat snp35994-scaffold431-3788915 12 34819019 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379527 Affx-122976071 AX-123249885 12 50339644 TATGTGTCTCAAATACAAAGAAAGATTTCTCATCA[C/T]GGTGATATTAGTTCCTGACATTGAGGTGAGAAACC Y 2 1 2 1 101000 r 74 goat snp35996-scaffold431-3872390 12 34734687 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393723 Affx-122965234 AX-123264078 12 50389643 CCTGCATCAACCCCAAGTCTGTATCTCATCTAAAT[A/G]CCACCTAAATCAAGGGTGGTTGGAACTCAAGGAAT R 2 1 2 1 202000 r 74 goat snp35997-scaffold431-3922389 12 34683596 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402724 Affx-122958346 AX-123273077 12 50462774 ACTGACAGTGTTTGGAGTCTTTCAGGTCTGTTTCT[A/G]TGTTGATTGTTTCTGCTGTTTCCCTCAAAAATGCT R 2 1 2 1 103000 f 74 goat snp35998-scaffold431-3995520 12 34608790 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387015 Affx-122969932 AX-123257373 12 50502632 GAGTGTACTGGACAGAAATACAGTGATTTTTCACC[G/T]CCTAACAACAATCCTGTTGATATTCCTGTGCCTTG K 2 1 2 1 101000 f 74 goat snp35999-scaffold431-4035378 12 34568057 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418814 Affx-122946163 AX-123289162 12 50568851 TAGAGGGTCAAATAAACTTTTTGATATGGAAGCCA[C/T]GTCGGTGCTTATTCATTTATCTTTTTGGAGTGTAA Y 2 1 2 1 101000 f 74 goat snp36001-scaffold431-4101597 12 34501852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785729 Affx-122946847 AX-385272770 12 50601768 GTCATTGAGAAAATACTTCATATGGTTACTTTTAG[C/T]ATCAGTCTGGAAAACCACCACCAAAATGCTTAATA Y 2 1 2 1 101000 r 74 goat snp36002-scaffold431-4134514 12 34468791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764951 Affx-122943693 AX-385252532 12 50632589 TGCCTGGACTTATGATTTCCTTAAGAGTGCTTCCC[A/G]TTCTAAAATGATGACAATAACTATTATTGTTGGGA R 2 1 2 1 101000 f 74 goat snp36003-scaffold431-4165335 12 34438745 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420712 Affx-122944782 AX-123291059 12 50681933 AAAATGAATCTTCTTTCTCCACTGTTAAGACTTTA[C/T]AAAAATTAAGATAAGATGATCCAAAGAAAATGCAA Y 2 1 2 1 201000 r 74 goat snp36004-scaffold431-4214679 12 34387795 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771650 Affx-122977838 AX-385258808 12 50711231 GTTTCAGTTGTTGCTGTTTAAAAGCTGGTGCAAAG[C/T]ACTATTTAAAAATGGGTTGTCAAGAGAGAAAAAGA Y 2 1 2 1 101000 f 74 goat snp36005-scaffold431-4243977 12 34358145 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786078 Affx-122955293 AX-385273114 12 50740868 GAACACAAAAGGTATACAGATACGTGAAAGCATGA[A/C]AGGCGCGGTGAACCTATAGTTAAGAGGAAATCTAT M 2 1 2 1 101000 r 74 goat snp36006-scaffold431-4273614 12 34327260 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428847 Affx-122938360 AX-123299189 12 50798628 CTTGGGCAGATCTGGTATTGCAAGCGTAAAAGGAA[C/T]TTAGGTGATTCATTGAATGAATTTTGATTAAGACA Y 2 1 2 1 101000 f 74 goat snp36007-scaffold431-4331374 12 34270339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381498 Affx-122974871 AX-123251856 12 50863072 CAAACTCATCCTCTGATAGGAGAAAGGAAGGGTCC[A/G]CAGAGTCTCACCATTTCTTCTTCCAGCAATCTTTA R 2 1 2 1 201000 f 74 goat snp36008-scaffold431-4395818 12 34209137 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379473 Affx-122976483 AX-123249831 12 50922548 CACACATCCCCATCATTGTCCACTCCTTCTCTCAA[A/G]CTGTCAGTCAGGAAGAAGTGCCATGAAGGAGATGA R 2 1 2 1 101000 r 74 goat snp36009-scaffold431-4455294 12 34149059 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376488 Affx-122978030 AX-123246847 12 50966429 AACATCTCTCTAATCCCTTCTTCCATCTCCCATGT[A/G]TTGATCCAGATTTAACTTCAGCTTCTTCAGCTCTA R 2 1 2 1 201000 f 74 goat snp36010-scaffold431-4499175 12 34105097 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441691 Affx-122929169 AX-123312028 12 50999993 GGATACAAAGTTTCAGTGCTGAAGACAGAGGTGAT[A/G]AAAAGATGCAGAGTATGAAAACAGAAGGCCGTGAT R 2 1 2 1 101000 f 74 goat snp36011-scaffold431-4532739 12 34071470 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785216 Affx-122956417 AX-385272262 12 51055629 GGGTGAGGCGGGAATTACCATCACTGATGTTCCAT[A/G]TGAATCTGATGGCTTTGGTTTCAAATTGTGACCTG R 2 1 2 1 101000 f 74 goat snp36012-scaffold431-4588375 12 34015723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776380 Affx-122921904 AX-385263507 12 51116921 TGATCAGATTATCAGTTTGGTAATCTGCCTAATAG[A/G]CCTCTGCCTTCCTCTAAGGAAAGTAACCTTGCAAT R 2 1 2 1 201000 r 74 goat snp36013-scaffold431-4649667 12 33954793 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383783 Affx-122973201 AX-123254141 12 51151390 TCCTCATATTTACCCTTTATTGTCCAAATAGCATC[A/G]TGCTCCTCGAACCTTCTATAGTTTCTATTTAAAAC R 2 1 2 1 101000 f 74 goat snp36014-scaffold431-4684136 12 33920243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418534 Affx-122946412 AX-123288882 12 51181477 AGTCACGGTTACCAAGCAAGTGGGAACACAGCCTC[A/G]TGAGCATGTCCTGTCAAGTGTGGATATAGAACAGG R 2 1 2 1 201000 r 74 goat snp36015-scaffold431-4714223 12 33890225 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439955 Affx-122929986 AX-123310292 12 51277892 AGCTCTTGTCATTTCTAAAATTTTATGAGTTACAA[C/T]AGTCAGTGCCTAGATGTCTATTAATTTAATCCCAA Y 2 1 2 1 101000 r 74 goat snp36016-scaffold431-4810638 12 33793554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398657 Affx-122961890 AX-123269012 12 51340277 GAGGAAGAACTGGAAACAAACATTACATCTGTATG[C/T]GTATGCATGCCAGGCATTTTGTAGACACTATATTA Y 2 1 2 1 101000 r 74 goat snp36017-scaffold431-4873023 12 33731132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385638 Affx-122971173 AX-123255996 12 51378502 AATGTGCACATGGAGGGAGAGCAAATAGATTTAAA[C/T]GTAGATGATTTAAGCCCCCTCTGCTCTCAAAAACT Y 2 1 2 1 201000 f 74 goat snp36018-scaffold431-4911248 12 33692822 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395165 Affx-122964112 AX-123265520 12 51420099 CTCTAAGGAAACCCCAACTCATACACTCCTCATAT[A/G]CAGCAGCCAGTTTTTCATTACCTCACAACCCTAAG R 2 1 2 1 101000 r 74 goat snp36019-scaffold431-4952845 12 33651064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434073 Affx-122934180 AX-123304414 12 51467062 GCTCCCTGGAGGCTGCATTCTGATTGGGTTTGGCC[G/T]ATGCGGATGCCTTCTCAGGAGACTGCAGCACAGGC K 2 1 2 1 201000 f 74 goat snp36020-scaffold431-4999808 12 33603915 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440233 Affx-122930674 AX-123310570 12 51504269 ATTTGTTAACAGAATTGACCTTGAAACTGCCCCTT[A/G]CCTTGTTCTACTTTGATTTCTGGACAATATAAATG R 2 1 2 1 101000 r 74 goat snp36021-scaffold431-5037015 12 33566347 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271772 Affx-1111832960 AX-519545565 12 51543299 ATGACTGGTGGGCAGCAGGGAGGGGTCTGGACAGA[A/C]CCACACTGACCTCACAGCTTACTTAGTTTCACCTG M 2 1 2 1 102000 r 74 goat 12_51543299_AF-PAKI 12 51543299 C A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435977 Affx-122933513 AX-123306316 12 51564416 GGCTTATAATTGTGGGATGACGAAGGGCTTTCTCA[G/T]CATGAAATAAAACTAGAAACCATAAAGAAAATCAA K 2 1 2 1 101000 f 74 goat snp36022-scaffold431-5097162 12 33505705 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391927 Affx-122966934 AX-123262284 12 51623449 CACAACCACATTTGGAAGTTTTAGGAAAGTTATTC[A/G]CACAAAAGTGGAATAAGATATAAACAAGGCAAAGG R 2 1 2 1 201000 f 74 goat snp36023-scaffold431-5156195 12 33446475 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767179 Affx-122972206 AX-385254462 12 51689278 AACTGAGTGTCAACGACGTCTTCTGAGTTCTCCTC[A/G]CTATGTGACACCCTCAAAATTGCTCTGTATTACTT R 2 1 2 1 101000 f 74 goat snp36024-scaffold431-5222024 12 33379746 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383084 Affx-122973735 AX-123253442 12 51742599 CTTACAGTTTATGCATAGCTGGATGTGATTTACAT[A/G]GAAGATAAAATAAGTTACAATGCTGCTATTTCTGA R 2 1 2 1 101000 f 74 goat snp36025-scaffold431-5275345 12 33329386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783199 Affx-122936764 AX-385270266 12 51789630 TCTGGAATCAACTGCACTCTTTCACATGCAGTTGC[G/T]TATTTCTTTTTTGCACAAAGCAAATATTTGTTTGT K 2 1 2 1 101000 f 74 goat snp36026-scaffold431-5322376 12 33281461 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391872 Affx-122966978 AX-123262229 12 51854749 TTAGGTTCAGGCCTGGTAAGTGAACGGCATTCACC[G/T]CTACTTAGCAGTGGCATGAACAGTTGTAGTCCTTT K 2 1 2 1 101000 r 74 goat snp36027-scaffold431-5387495 12 33215994 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404051 Affx-122957159 AX-123274403 12 51885621 TCATGTCTCCTTGGCTTTGCACGTGTGATGCAGTT[A/G]AGCAGTTACTAGGAAGTGCTCTTACAGGTATAGCT R 2 1 2 1 101000 f 74 goat snp36028-scaffold431-5418367 12 33184946 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416052 Affx-122948350 AX-123286401 12 51924271 TACATTTAGAATTTTGATGTCAGCATTTTATTGTC[A/G]TCTGGATCCCAGTGTCAGTACTCAGAAATCCCATG R 2 1 2 1 101000 r 74 goat snp36029-scaffold431-5457017 12 33150192 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410757 Affx-122952691 AX-123281107 12 51957101 AGAGCACTTTGTAGTATGTACACAACCTACTCTAC[C/T]GGTTGAATTAATGAATAAATGATCTCATGATTAGA Y 2 1 2 1 101000 f 74 goat snp36030-scaffold431-5489847 12 33117381 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799860 Affx-122919990 AX-385286786 12 52014985 TATTCATCATTTTCATTTATGGTTTCCAATTCCTA[C/T]CTTTAAGATGCTAAGAAACATAACTATGTAAAAAT Y 2 1 2 1 201000 f 74 goat snp36031-scaffold431-5547731 12 33060052 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767373 Affx-122932209 AX-385254648 12 52090807 CTGATTTTCCTTTTCAAATGCATGTAAATTCTATT[A/G]TGATTAATGTGACACAAATTTTTTGAAGCAAACTG R 2 1 2 1 201000 f 74 goat snp36033-scaffold431-5623553 12 32983765 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418691 Affx-122946300 AX-123289039 12 52154603 GTGTATAAATAATAAGCAAAAGTTTCAATAATTAA[C/T]ACAAGTAGAACACAGCAATGTAACCTCTATCTAGG Y 2 1 2 1 202000 f 74 goat snp36034-scaffold431-5687349 12 32919641 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395341 Affx-122964035 AX-123265696 12 52190596 TGGAAAGTATGTGCTGAGGAAATAAAATGTACTTT[A/G]TCTCAAATGATTTATACCTTCTCTTTATTCTTTGT R 2 1 2 1 101000 r 74 goat snp36035-scaffold431-5723342 12 32884033 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420511 Affx-122944846 AX-123290858 12 52232616 CTCTATCTCTTGCTTCTTCTTCAATGAGACAAGGT[A/G]CTACATTGAATCTCCCTCCTGTTCCCTATCTGCCT R 2 1 2 1 101000 r 74 goat snp36036-scaffold431-5765362 12 32842530 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376826 Affx-122977921 AX-123247185 12 52278154 GGGTAGGTGGCTGGTAAGAGTGGATATGATTAGAA[A/C]GAGTGGAAGGCATCTGGTATGGTCCAGAAAGAGAA M 2 1 2 1 101000 f 74 goat snp36037-scaffold431-5810900 12 32796583 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385668 Affx-122971148 AX-123256026 12 52315767 AAATCCTTGTGAACAGAAAACTTTCTCACGAGATA[C/T]AAGAACCCTTCGAGGCAGGGCAAGGGCTGTGAAAA Y 2 1 2 1 201000 f 74 goat snp36038-scaffold431-5848513 12 32758699 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403081 Affx-122958509 AX-123273434 12 52349457 CAGTTCACAGGGTCACAAAGAGTTGGATGTGACTT[A/G]TCGATTGAACAACAACCACAAAACCAAGCAAGACT R 2 1 2 1 303000 r 74 goat snp36039-scaffold431-5882203 12 32723922 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441207 Affx-122929527 AX-123311544 12 52401396 GCACCCTTCACTATAGAAGATGGTTTTGGACTCGG[C/T]GCTTGGGTTGACTTACAAGCCTGTTACTAATTCAC Y 2 1 2 1 101000 f 74 goat snp36040-scaffold431-5934142 12 32671585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434532 Affx-122934152 AX-123304873 12 52444326 TTTTTCTTTCATCTCTTTATTTACCATAAAATACC[A/G]TTCCTACAGGAAATTTGGTATACATGCTTAGGTCT R 2 1 2 1 201000 f 74 goat snp36041-scaffold431-5977072 12 32628692 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396723 Affx-122962804 AX-123267078 12 52492473 TCTGGACTCCAGAGTTCTATGTCAGGTAGAGAATT[A/G]TGTTGGAGGGGATGAAGAAATGTCTCTTTAATTGA R 2 1 2 1 101000 f 74 goat snp36042-scaffold431-6025219 12 32580707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418636 Affx-122946343 AX-123288984 12 52526222 TCTTTTATAGGTAAGCAAAAACTAAAGTTGAAAAA[C/T]GAAGATCCAAAGGAGAGTTTCAGAAGCATCAGCTT Y 2 1 2 1 101000 r 74 goat snp36043-scaffold431-6058968 12 32547221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764720 Affx-122942694 AX-385252338 12 52573003 CTAGGTATGATAGTCTTATCACATCACTGGCTACA[C/T]TGAGCCTCAATCGAAGAAAATAACATCATTGTTTC Y 2 1 2 1 101000 f 74 goat snp36044-scaffold431-6105749 12 32500272 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422436 Affx-122943355 AX-123292782 12 52602896 ACCCACCCCCATGCCCCGCTGCCTTCTTCTGGTCA[C/T]GTATATTTCTTACAGAGCTTTTTAAATACCCCAGA Y 2 1 2 1 101000 r 74 goat snp36045-scaffold431-6135642 12 32470530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451110 Affx-122921391 AX-123321444 12 52664185 TTGAAGCCTGCAATTATTGCTTAGGTGACCTGTGC[A/G]TCAGTACTTCAAACTCACTGAGGGTCTGTTTCCTT R 2 1 2 1 101000 f 74 goat snp36047-scaffold431-6196931 12 32408751 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391642 Affx-122966567 AX-123261999 12 52697702 AGTGCCTCATTTGTCCAGTATTTCTAAAGTGCTGC[A/G]TCTTAACTGCGATGGTCCCTGAGCCAGTGTTCCGA R 2 1 2 1 101000 f 74 goat snp36048-scaffold431-6230448 12 32374923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779249 Affx-122943746 AX-385266353 12 52740589 TGCACAATGGTTTGGAGAGTTATTGAGGAAGAAAT[A/G]TCCTCAACAACATGGCTCAAAGAGCTTTTGAAGGT R 2 1 2 1 101000 r 74 goat snp36049-scaffold431-6273335 12 32332127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452305 Affx-122920677 AX-123322638 12 52781646 GCCCTAGGGTATTGGATCTTTACATCCTCAAATTA[C/T]GTCACACTAGGCGCACACTTCTCCACACTTGGTTA Y 2 1 2 1 101000 f 74 goat snp36050-scaffold431-6314392 12 32291347 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443780 Affx-122927100 AX-123314117 12 52812250 GAATCTCAACAGGTTTAGCTTAGAGCAAACAAACC[A/G]CTGCTCTAGAGCACGGCAGTAGGTGCTTTAGGAGG R 2 1 2 1 101000 r 74 goat snp36051-scaffold431-6344996 12 32260738 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376346 Affx-122978334 AX-123246705 12 52848133 TCTCTGAAGTGGATAGCTACCCTGTCATTGCAATC[A/G]TCACTACAATTCAGAGGTGGGTCTGCACCTGCCCC R 2 1 2 1 101000 f 74 goat snp36052-scaffold431-6380879 12 32225045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387441 Affx-122970383 AX-123257799 12 52914349 TCCTCCCACCATCACTTCCTTCCAACCTCCCTCCC[A/C]ATCTTTCTCTTCTCCATCAGTTCCTCTGGCTATGA M 2 1 2 1 201000 r 74 goat snp36053-scaffold431-6447095 12 32158846 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450842 Affx-122922242 AX-123321176 12 52950034 CCAGACACTGTGATAGAGGTTTTAAAGGCATTACC[C/T]TAGGTATCAATTGTTTTTTCAGGAAAATCTCAATG Y 2 1 2 1 101000 f 74 goat snp36054-scaffold431-6482780 12 32122692 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383209 Affx-122972778 AX-123253567 12 52986390 CATCTGGTAATGCCAGTCAGGTAGGTGCCCAGTAC[A/G]GTGCTAGGAACTGGAGATGGAAGAATGGCTGAGAC R 2 1 2 1 101000 f 74 goat snp36055-scaffold431-6519136 12 32086056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796996 Affx-122932656 AX-385283937 12 53044413 CGGGCTCTGTTTTCCTTGCTGAACTGAGACTGAGG[C/T]AATATCAGTGTCTCATCTCTGATCTCTTCCCCAAG Y 2 1 2 1 101000 r 74 goat snp36056-scaffold431-6577159 12 32027903 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389578 Affx-122968787 AX-123259936 12 53119903 AATAGCCATGACTCTCTGTCTAATAATTCCCAAGG[C/T]TGTGTTATCTCCCCTATGAAGACCTCCCCAGGTTC Y 2 1 2 1 201000 f 74 goat snp36058-scaffold431-6652649 12 31952043 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276780 Affx-1111835517 AX-519550289 12 53127396 TTATATAAAGGGATAATTTGGACAGAGAGAGGAAC[A/G]TGGTCAGGATATCATGTGATGATAAATACAGAAGT R 2 1 2 1 101000 r 74 goat Random2.2K-1280 12 53127396 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793580 Affx-122926905 AX-385280555 12 53174934 TGCTATTATTCAATATCCTTGAGGAATATCCACTC[A/G]TTACTAATTTTAGTTCCTAATATGATATAGCACTT R 2 1 2 1 101000 f 74 goat snp36059-scaffold431-6707680 12 31897081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788693 Affx-122963003 AX-385275709 12 53250770 ATGTCTACTGTTCATGCTGAGCAATGCTCAGGATG[C/T]ATCATATGGTGGGTAATGGCAGCTAGGAGAGTTTT Y 2 1 2 1 201000 r 74 goat snp36060-scaffold431-6783516 12 31820958 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379049 Affx-122976345 AX-123249408 12 53323829 CCGTTCTTCCCTCTTTTCTCTTTTCACGTATATGC[A/G]TCTTTAAATGTTTCCTACTGCTTCTCGCTTCCATA R 2 1 2 1 201000 f 74 goat snp36061-scaffold431-6856575 12 31747499 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389643 Affx-122968735 AX-123260001 12 53388238 TTAGTGTATTATTGGTGTAGCTGGACTTACTGCTA[C/T]AATCTTTTTATTTCTATTTGTTTCATTTTTAATGC Y 2 1 2 1 101000 f 74 goat snp36062-scaffold431-6920984 12 31682535 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792369 Affx-122968472 AX-385279350 12 53463730 CATTTTCCCAATCTCTACAAAAAGCACAATAAAGG[C/T]ACCTACCTCAGAGAGGTGTCAAAATAACTCATAAT Y 2 1 2 1 101000 r 74 goat snp36063-scaffold431-6996476 12 31618407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442669 Affx-122927898 AX-123313006 12 53493002 TCAGTCGCCAATTTCCTGATAAATAACTCAGTAGA[C/T]ATTCCTCTTTGTTTAGTAAATTCCAAAAATATGCG Y 2 1 2 1 101000 f 74 goat snp36064-scaffold431-7025748 12 31588869 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773609 Affx-122922623 AX-385260749 12 53538605 CTTGTAGAAGGAGTCACTGCTGTTTAGAACCCTAC[A/G]CTTTACCTGCCCAACCCTATGCTTTACCTAACTCA R 2 1 2 1 101000 f 74 goat snp36065-scaffold431-7071351 12 31543461 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463225821 Affx-1109877751 AX-514711760 12 53566539 GATCCTAGACAGTAACACCTTCAAAGAGAGTACTC[A/G]GATTTAAATAAAATGAAACAAATTTTGTTTTGATG R 2 1 2 1 201000 f 74 goat GoatD01.021447 12 53566539 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38420616 Affx-122945238 AX-123290963 12 53572377 GGGGGTGCTGTGGGTGGGAGATCGTAAGTTAGGGT[A/G]CTTGGAGCAGCACACAACCAGTTTAGATCTGAGTT R 2 1 2 1 101000 r 74 goat snp36066-scaffold431-7105123 12 31509486 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778255 Affx-122959492 AX-385265370 12 53620959 GCTGAAACACCTGCCATGGTGATGACTAGTTCTGA[C/T]GGCCTTGCTGGAATTGGAAACCAAATTTTTACGGG Y 2 1 2 1 101000 r 74 goat snp36067-scaffold431-7153705 12 31461020 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424467 Affx-122941770 AX-123294813 12 53654483 TCTGTTTATAAGGAAAATAATTTTTTGGTCATTTC[A/G]TTGCTTGTAGTTTAATGGAAATGGCTGAAAATTAA R 2 1 2 1 103000 r 74 goat snp36068-scaffold431-7187229 12 31427609 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452589 Affx-122920501 AX-123322922 12 53686647 TACTCCAGCCTATCTACATGGCTGTACAACAGCCT[C/T]CCAGCCACCTGCAGCAAGGACAGTGAAGATGGCCT Y 2 1 2 1 101000 f 74 goat "GoatD01.043601;snp36069-scaffold431-7219393" 12 31395569 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320791353 Affx-122942541 AX-385278346 12 53721864 TTGACCAACGACTTAAGCTACCTGAATGTGACTTT[C/T]AGGTTTTATAATCAAACTACAACCCTACAGACTTG Y 2 1 2 1 101000 f 74 goat snp36070-scaffold431-7254610 12 31360050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796822 Affx-122959204 AX-385283765 12 53763582 TTCCCCTTCCTTCTCTTACTAGTGACCTTCTGTCA[C/T]TAGAGTTCAATTTTCCTATGAAAATCATGCTGTTA Y 2 1 2 1 101000 f 74 goat snp36071-scaffold431-7296328 12 31318484 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440744 Affx-122929873 AX-123311081 12 53792452 TGGAAGACCTGTCAAGTTAATCTAGTCAAGTTAAG[A/C]TGCTTTGCTCAATTCTCTTGGAGATAGTGACTGAC M 2 1 2 1 201000 f 74 goat snp36072-scaffold431-7325198 12 31289585 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770683 Affx-122934212 AX-385257847 12 53843440 TAAATTCCATAAAATTTTAGAGGACAATAAAAATA[C/T]ACATAAAACTTACAGATGAAATGACATGACATCCA Y 2 1 2 1 102000 r 74 goat snp36073-scaffold431-7376186 12 31238678 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779903 Affx-122965173 AX-385267002 12 53873048 GATCCTCAACCGTTTATCCAGCCCTAATAAAGAAA[C/T]GGGACCACATGGTCAGGATTGAGAGGATGCCAAAA Y 2 1 2 1 102000 r 74 goat snp36074-scaffold431-7405794 12 31208574 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383856 Affx-122973146 AX-123254214 12 53902074 ATCTCCTGGAAGCAGCGTGGTGGGATGGCAGAGTA[A/G]GGTGGTAGCAGGTGAGGTGGCAAGAGTACACACAT R 2 1 2 1 101000 r 74 goat snp36075-scaffold431-7434820 12 31179551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388712 Affx-122968980 AX-123259070 12 53990263 CAAGAGAAAGGAATTATCCAACAGGAGTGGGACCC[A/G]CAGGATTTCCTACCTGTGACTTTCACAGCTTGCTG R 2 1 2 1 101000 f 74 goat snp36077-scaffold431-7523009 12 31091148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402175 Affx-122959186 AX-123272528 12 54023115 TCTGGGGGGCTTGGAAAAACATTGTGTTTAAAGAA[G/T]AAATGCTTTGGACATAATATTTTAGTGATAAGAAA K 2 1 2 1 101000 f 74 goat snp36078-scaffold431-7555861 12 31057832 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790419 Affx-122976940 AX-385277422 12 54082758 CACTGAGGCTTGGAAAGAGAATGTCACTTGGCAGA[C/T]ATGATTTTTCAAGCTATTTGGGTCTTCTTGAGACT Y 2 1 2 1 101000 f 74 goat snp36079-scaffold431-7615504 12 30997251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272532 Affx-1111832961 AX-519546250 12 54119558 AGGGTCTCCCGTGCACCCTCTGAAAAGATATTTTG[A/G]GCACCCTCCATCAAACTGTCAGAGGTGTCTCTTCT R 2 1 2 1 101000 r 74 goat 12_54119558_AF-PAKI 12 54119558 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446791 Affx-122925303 AX-123317127 12 54129088 CCATACCAACTTTCAAGGAAATTTCTTCTAGAAAA[C/T]AAAATTTAAACTGTTCTTACAGAGGATCTTCTATG Y 2 1 2 1 201000 f 74 goat snp36080-scaffold431-7661834 12 30951093 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439560 Affx-122930092 AX-123309897 12 54186555 TGCCCTCTTCCCTAAAAGGAACTTAGGCTATTCTT[C/T]GCCTCATACTCCGAAGATACCAAACAAACCAATTT Y 2 1 2 1 101000 f 74 goat snp36081-scaffold431-7719301 12 30893807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397319 Affx-122962309 AX-123267674 12 54234297 GCAGACTTTACTTACAAGTTTCTCAAAAAGTGAAT[A/G]TTCCTTGATAGTTTATGTGGAGGTGTTTACAACCA R 2 1 2 1 101000 r 74 goat snp36082-scaffold431-7767043 12 30846157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799691 Affx-122941568 AX-385286619 12 54268659 AAAAGACAGTGGGTTCAGTTCCAGTCTGAATTACA[C/T]GATTTCAAAAGCCAGAGTTAATAAGTGATAGAGCT Y 2 1 2 1 102000 f 74 goat snp36083-scaffold431-7801405 12 30811695 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797683 Affx-122936636 AX-385284622 12 54299221 TAAAAATCTGAGTGTATTAACTCATAATAAAGGAA[C/T]ATGTTGACTTGCAGCTTCAGTTGCAAGGAAGAAAT Y 2 1 2 1 101000 r 74 goat snp36084-scaffold431-7831967 12 30781440 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451685 Affx-122921576 AX-123322018 12 54334795 CAGTAGGTCTCCCTAAATGAAAAATTAAGAAAGGT[C/T]AACTTTTACTATTCTTATTCACTTTAATATTAACG Y 2 1 2 1 201000 r 74 goat snp36085-scaffold431-7867541 12 30745738 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403832 Affx-122957948 AX-123274184 12 54441050 ACAAGCAAGGCCCTTACCTCGACTACTCTTCATAC[G/T]AGCAAATATTATTTCTATTATTTGCTAAATACCTG K 2 1 2 1 101000 f 74 goat snp36087-scaffold431-7973796 12 30641647 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444763 Affx-122926362 AX-123315100 12 54492432 AACTGCTAAAGGATGCAATAAGGGACTATGTAATC[A/G]AATGAAGATGTAAGAAGACCACTCTGGTCGTTGCA R 2 1 2 1 101000 f 74 goat snp36088-scaffold431-8025178 12 30589940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413624 Affx-122950552 AX-123283973 12 54538077 CTCCTAGACATCTTGTTTTCTGTACAAAAATGTTG[C/T]AGTTTTGCTCAGTGATTTTTATATCAGTTTCTTTA Y 2 1 2 1 101000 f 74 goat snp36089-scaffold431-8070823 12 30544110 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786781 Affx-122952011 AX-385273811 12 54574420 AACAGATGGTGTAGATATTATAGAAAACCATCAAG[A/C]GAGTGGCTCCAGTGAATTCCTCTCACAAGATAAAT M 2 1 2 1 101000 r 74 goat snp36090-scaffold431-8107166 12 30507770 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424308 Affx-122941966 AX-123294654 12 54605774 TGTACTTATTCTATGGTTTACTGAGAGAGAAGTGT[C/T]GGAGTCTTCAGTTTTGCTTTTAACCACACAATGCT Y 2 1 2 1 101000 f 74 goat snp36091-scaffold431-8138520 12 30477774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449051 Affx-122923062 AX-123319386 12 54643644 GTGTTCTTAAGTAAAGAAAATAAATAGCAATATAC[A/G]TTAATAGCATAGAAGGTGTTATCAGTGCTTTATAG R 2 1 2 1 201000 r 74 goat snp36092-scaffold431-8176390 12 30439405 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796810 Affx-122959593 AX-385283753 12 54697992 GAGTCAACTCTTCTCTATCTTACAGACCTCTTGGA[G/T]CTGTAAAACAGTAATCACACCACGAATAAGTTAAT K 2 1 2 1 101000 f 74 goat snp36093-scaffold431-8230738 12 30385373 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789113 Affx-122979021 AX-385276126 12 54771472 ATTAATTTTACATTTGATTAATTTACAACCAATGA[G/T]ATAGCAAGATATGATAGATGTTTGTGTTCTAGGCT K 2 1 2 1 101000 r 74 goat snp36094-scaffold431-8304218 12 30311487 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786334 Affx-122948075 AX-385273368 12 54826847 CTGTGGTAGATCGTCTCCAGTTTTCCAAAACACAT[A/G]TTTAAAATTGTCTCTTTGGTCTCTGTCCTCCAGCA R 2 1 2 1 101000 f 74 goat snp36095-scaffold431-8359593 12 30255457 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389203 Affx-122969068 AX-123259561 12 54860282 ACCAGTAATCTGATGCCAAACTGTTCTTTATTTGT[A/G]CTTTGCCACCAATAATATTCTTGGCCTTTGATCCA R 2 1 2 1 201000 r 74 goat snp36096-scaffold431-8393028 12 30221429 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790363 Affx-122934841 AX-385277366 12 54901011 GTCAACATGCTTTAGTACTCACTAAGTAATTCTCA[A/G]TTTTACCAAGTATTCAAAATATGTCTAATTTCCCT R 2 1 2 1 201000 r 74 goat snp36097-scaffold431-8433757 12 30180296 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407241 Affx-122955365 AX-123277592 12 54930667 CCCTGGCAGAATACATCTGAACTTCCAATGAGAAG[C/T]TGAATTTGTCAAAGGAGAGAATATAGGAAAATTAG Y 2 1 2 1 202000 r 74 goat snp36098-scaffold431-8463413 12 30150041 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407863 Affx-122954511 AX-123278214 12 54963532 ATTTCTTTCAATTACCACTACTTATGTAAAAATAG[C/T]GACCCATATCTTAATTATTAATGAAAGCAGGTAAA Y 2 1 2 1 101000 f 74 goat snp36099-scaffold431-8496278 12 30117040 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794935 Affx-122962084 AX-385281895 12 54993641 AGCCACTTCTGGAAGTTACTTAATTTTCTGTGGGT[A/G]TTTCTCAGGTTCACATAATAGTAAATTTTTGTTTG R 2 1 2 1 102000 f 74 goat snp36100-scaffold431-8526387 12 30087785 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800603 Affx-122927957 AX-385287521 12 55027226 GTGATTTGGGGTTATACATAGATAAAATATAACCA[C/T]GTCTGTGATAAATGATTTGTCTACATTATTAATTT Y 2 1 2 1 101000 f 74 goat snp36101-scaffold431-8559972 12 30054707 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779743 Affx-122933287 AX-385266843 12 55058983 ATTACCTCATGCTTATATTATCTTAATACATATAA[C/T]GGTTGCTTTCTAATTATGTAAAATGCTAATGAGTG Y 2 1 2 1 101000 r 74 goat snp36102-scaffold431-8591729 12 30022622 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422327 Affx-122943460 AX-123292673 12 55096841 AAAAGTTTAAATTCTGAAAGCAATCAGCCTCTACT[A/G]TTTTCTGTTATACTTGCTTTTGATCAGTAGGCCTT R 2 1 2 1 101000 r 74 goat snp36103-scaffold431-8629587 12 29984923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786462 Affx-122925062 AX-385273496 12 55141047 AGAATCTGCATAACTTCTAGTTATCTGGTGGTCAG[A/G]ATATTCCATTTTGGACACTTTTGCTATGATATGGA R 2 1 2 1 101000 f 74 goat snp36104-scaffold431-8673793 12 29939922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411344 Affx-122952262 AX-123281694 12 55179733 ATGTCTTTCATGTTGTTGAATAAATTTCTCTAGTT[C/T]AAATGAACACATTAATGAAATGATGAATAAATATG Y 2 1 2 1 101000 f 74 goat snp36105-scaffold431-8712479 12 29900923 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388870 Affx-122969314 AX-123259228 12 55209986 AAGATTTCCCATGCAACAGGATCACATAGGAAACT[A/G]CTTTGTGACTTTTTACTGATTTTTTAAAAACACCA R 2 1 2 1 103000 f 74 goat snp36106-scaffold431-8742732 12 29870792 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775195 Affx-122952208 AX-385262326 12 55244513 GTTTAAGTAAACTATCATACATATACTTATCCATA[C/T]GCTTTCCATTCTTGAATCATCTTGATTTAGTAATT Y 2 1 2 1 101000 r 74 goat snp36107-scaffold431-8777259 12 29836624 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784989 Affx-122963831 AX-385272036 12 55291944 AAAATAATGAATATGTTGTTTTACTATGCCACAAA[C/T]GTAACAACTCAAATTACATTGTTGCTTTTTTTCCC Y 2 1 2 1 101000 r 74 goat snp36108-scaffold431-8824690 12 29789001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451176 Affx-122921342 AX-123321510 12 55320547 GATGCTTCAAAGATATAGACATCTCCAAACTCAAG[C/T]GGTGCATATTAAAAATGTACAACTGTTTCTATGTC Y 2 1 2 1 101000 f 74 goat snp36109-scaffold431-8853293 12 29759835 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399945 Affx-122960846 AX-123270300 12 55353482 CCTTTAGCAGAGCTTTGAAAACACACCAAAATCTC[A/G]CAGACGTACAAAGATAAATGCCAGATATGTTCATA R 2 1 2 1 101000 f 74 goat snp36110-scaffold431-8886228 12 29727735 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437102 Affx-122932179 AX-123307440 12 55421006 TCCCTTTGGTAAAGTATTAACCATAAAACAACAAG[C/T]ACAGACATTAAAACAAACTAACAAACAAACAAAAA Y 2 1 2 1 103000 f 74 goat snp36112-scaffold431-8953752 12 29658830 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416117 Affx-122948303 AX-123286466 12 55460809 AACATTTCTCAGGTTTTAGTGACATTCAGAATCCG[A/G]AGAAAAATTCAATCTTTAAAATATTTCCCAGAACT R 2 1 2 1 101000 f 74 goat snp36113-scaffold431-8993555 12 29619896 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773554 Affx-122973587 AX-385260694 12 55501355 AATACTTCTTGAGAAGAATTGAAGTTTTCAATACC[A/G]CTATAATTTATTGTATAAACATGCTCACTGCTTAG R 2 1 2 1 201000 r 74 goat snp36114-scaffold431-9034101 12 29579052 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781398 Affx-122948120 AX-385268483 12 55554783 TTGTAAATGTGATACAAATATAACTTTGGATAAAA[C/T]GATCCTGTCTTAATAAAAGTAAAATTCCTTCTTTA Y 2 1 2 1 101000 r 74 goat snp36115-scaffold431-9087529 12 29524900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410126 Affx-122952815 AX-123280476 12 55589986 TAATGTAAAGAGCTTGTTTTAAATTTATTCTCCAA[C/T]GTTAGTTTCTAAATCAGAGTTTTTACTTTACAGAA Y 2 1 2 1 201000 r 74 goat snp36116-scaffold431-9122732 12 29490791 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788494 Affx-122927616 AX-385275511 12 55646979 AGATAATACAGATTTTGATACCAAAAGCAAGTGGG[C/T]ACTATTGTAACAAATAACTAGACATGTGGATGTGG Y 2 1 2 1 201000 f 74 goat snp36117-scaffold431-9179725 12 29433324 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386537 Affx-122970727 AX-123256895 12 55694717 GTCTTGCTCGTAGAATGTCTCATCTTTTTTTTCTC[A/G]TCTTGAATTCCTGTCAGATCACACTGCCCTTGGGC R 2 1 2 1 101000 r 74 goat snp36118-scaffold431-9227463 12 29385409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429494 Affx-122937869 AX-123299836 12 55756369 TTAACTTCATTAGTTCTTTCCTCCAGAGGGTCTAA[C/T]CTATTATTTAATCTAATCATTGAGTTGTTATTCAT Y 2 1 2 1 201000 r 74 goat snp36119-scaffold431-9289115 12 29323542 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406109 Affx-122956212 AX-123276461 12 55791414 CCACCAAATAACTGAACTCCTTCAATGAAGCAATG[C/T]ACTCAGAGCCCTCATCTGTGATTCAATAAGAAAAC Y 2 1 2 1 101000 f 74 goat snp36120-scaffold431-9324160 12 29287946 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393705 Affx-122965248 AX-123264060 12 55822554 ATGTGATTTAGTAATATTTGTCCTCTTGGTTATGG[C/T]AGAAAAATCCTTAGTCATTACTTCTTCAACATTAC Y 2 1 2 1 101000 r 74 goat snp36121-scaffold431-9355300 12 29256266 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413450 Affx-122950679 AX-123283799 12 55856260 GTGTATCTTTAGGATAAGCTTTTAGTTCCAGAGTT[A/G]TAAATCTTATGTAGAGGTTGTATTATTTTTGCAGT R 2 1 2 1 101000 r 74 goat snp36122-scaffold431-9389006 12 29222305 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420308 Affx-122945024 AX-123290655 12 55892950 GCCCTGGTGTTGTATTAGTCTTTCCACAATGTATA[C/T]GACATCTAGCTTTCTTCATACTTTATTTACAAAAC Y 2 1 2 1 101000 f 74 goat snp36123-scaffold431-9425696 12 29184959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774427 Affx-122966269 AX-385261563 12 55954584 ATGGTTGAACTCTGATAATATTATCAAACAGTAAT[A/G]TTTTTAAAGGAATGTTATAGCTATAATATTTAATG R 2 1 2 1 201000 r 74 goat snp36124-scaffold431-9487330 12 29123407 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438154 Affx-122931464 AX-123308492 12 55992724 CTGTTAGAATCTTTTTAATCAAATTCCAGCTCTAT[C/T]ATACTAAAACATTCCCTGTCTCTGTTCATGCTACC Y 2 1 2 1 101000 r 74 goat snp36125-scaffold431-9525470 12 29083944 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375970 Affx-122978436 AX-123246329 12 56022562 TGGCAAGGAGAGACCAATTCATTTCCTGTGTTTCA[A/G]AAATAAGCGAGAGCCTACAAGTACTGCAAATACCT R 2 1 2 1 201000 r 74 goat snp36126-scaffold431-9555308 12 29053897 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415878 Affx-122948486 AX-123286227 12 56082599 TAATTCATTTATATGCTCTCACAAGTATTTATTAG[C/T]AGACTGTTTCTACTGTTATTTTCTGTTAGAGATTT Y 2 1 2 1 101000 f 74 goat snp36128-scaffold431-9615345 12 28995885 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774325 Affx-122942645 AX-385261461 12 56125790 CTTGGATATGATTTTAAGACCTGTTTTTACCAAAA[C/T]AATGTACCAGAAATAGCCTTGTCCACTTGGAAAGC Y 2 1 2 1 101000 r 74 goat snp36129-scaffold431-9658536 12 28951418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417671 Affx-122946828 AX-123288019 12 56164685 GACAAAAATATAAAAGCTCAACTCTGTGAGACTAA[C/T]TGTTGTCATGTGTGTGTTTGTATCTTTCAGCAATA Y 2 1 2 1 303000 f 74 goat snp36130-scaffold431-9697431 12 28915619 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773962 Affx-122927204 AX-385261100 12 56207773 CGTACACAGAGACAGCACTGAAAGAATATTGGAAT[A/G]CAACAATAGTGAAATGTTGTGGCACAAGTGGAAAG R 2 1 2 1 101000 f 74 goat snp36131-scaffold431-9740519 12 28872723 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391309 Affx-122967330 AX-123261666 12 56237738 TGGTTGATTTACTGTTTGAGTTGTTACTAGTTGTC[C/T]TGGCCTAACTGTAATTTTTGTCACTACCTCTTCAT Y 2 1 2 1 101000 r 74 goat snp36132-scaffold431-9770484 12 28842474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800404 Affx-122946545 AX-385287325 12 56266316 TCCACTCAAGTCCTGTTAGTTTCATGAAAAAGGAG[A/G]AGTAGAAAGGAAAGTTCTCAGATTTTATTCTTCAG R 2 1 2 1 201000 r 74 goat snp36133-scaffold431-9799062 12 28813699 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773657 Affx-122928776 AX-385260797 12 56310246 CAGCATAAGTGACGATTTAACTTGGAGGGCCTTTG[C/T]GTAAATAGGGCTTGGAATTATTTATCTTCCTTCAT Y 2 1 2 1 101000 f 74 goat snp36134-scaffold431-9842992 12 28769894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425831 Affx-122940677 AX-123296177 12 56351331 ATGTATGGCAACAGTGCCTCACATTCTCATTAGAG[A/G]CAAGCTCTCATTTCCAGTTATTCTGTTTCTGATGG R 2 1 2 1 101000 f 74 goat snp36135-scaffold431-9884077 12 28728637 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767172 Affx-122922387 AX-385254456 12 56389191 GTCCCTGTTACAGGTACTCTCTTCCCACCTACAAC[A/G]TTCTCTGTGATAGTAACTATATATAAACAATACAT R 2 1 2 1 101000 f 74 goat snp36136-scaffold431-9921937 12 28690263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396503 Affx-122963528 AX-123266858 12 56469033 TTTGTTTGATTCCAGAGTCTGACTACTTACTCCTG[C/T]ATTAGGTGGATTTCCAGTGTGAAAGGACTAGAATT Y 2 1 2 1 101000 f 74 goat snp36138-scaffold431-10001779 12 28609607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437631 Affx-122931809 AX-123307969 12 56512831 ATACTTTAATGATTTGTGGGCAACTATAAGACTGA[C/T]GAAAGAAAGATGAGGGGAATTTAATATTAATAAAT Y 2 1 2 1 101000 f 74 goat snp36139-scaffold431-10045577 12 28565709 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771368 Affx-122938526 AX-385258526 12 56581925 ATAATTCCGATCAATTATCTCTTGCAGATAATATG[C/T]AAAATGTAAAATGAATCTCCTGTAGACAAAACATT Y 2 1 2 1 201000 r 74 goat snp36140-scaffold431-10114671 12 28503220 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400018 Affx-122960796 AX-123270373 12 56623043 TCTAGCCACCATGCTGTAAGAAAACCCCAAAGAGT[A/C]GATATAGAAAAACCACATGAAATGTCCCATATATA M 2 1 2 1 201000 r 74 goat snp36141-scaffold431-10155789 12 28460593 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386413 Affx-122970818 AX-123256771 12 56656645 GTCTTACCCTCAAAGGGCTATACCAAAGAGCTGCT[G/T]CCCAGTTACCACCTCTGTATCTCAGGGGGGTTTCT K 2 1 2 1 201000 f 74 goat snp36142-scaffold431-10189391 12 28428731 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789746 Affx-122966169 AX-385276754 12 56701453 TCTTGAAATATTTTTGTCCTGGTTTGCATGACACC[A/G]TAGATCTCTAATTCAACTTATTTCTCAATTGGCTC R 2 1 2 1 201000 r 74 goat snp36143-scaffold431-10234199 12 28382948 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401209 Affx-122959329 AX-123271562 12 56740703 TGATTTCTCTTTCTCTAAATATTACTATAATTATC[A/G]CCTATAAACTACTCCAGGCATATTTCACAGATCCT R 2 1 2 1 101000 r 74 goat snp36144-scaffold431-10273449 12 28343817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272536 Affx-1111832963 AX-519546254 12 56753811 AGTGCTGATGAGCTGTACCCGCGATGCTGGCTTAC[A/G]CCTCACTGTGCCTGGATTTGTAACTGGAGTACCTG R 2 1 2 1 101000 r 74 goat 12_56753811_AF-PAKI 12 56753811 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320766253 Affx-122948595 AX-385253649 12 56828660 CCTGTAAACCTTTTCTTATCTTATTCCTTCATGTC[A/G]TCTCCTATAATGATTTTTGATGATGGAACAACCAG R 2 1 2 1 201000 f 74 goat snp36146-scaffold431-10361406 12 28253796 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407653 Affx-122954609 AX-123278004 12 56858493 CATTTGATTATTCTGATGAAGTCATGTTGTCAGAC[A/G]CTGTATGTAAACAAAAATGTGTCCAGAACCTAAGA R 2 1 2 1 101000 f 74 goat snp36147-scaffold431-10391239 12 28223947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391014 Affx-122966885 AX-123261371 12 56948593 TTTACAATCAATAGTCTGTTTCAGCATGTGGTTTC[A/G]CTCTACCTTGATCTAAGTAAGCCTATTGCTGGTGG R 2 1 2 1 201000 f 74 goat snp36149-scaffold431-10481339 1 11140602 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426620 Affx-122939961 AX-123296966 12 57003852 AGCAAACTTCTGTTAGATCTTTATATAGCAAAGTG[A/G]TTGACATTATGAAATAGATTATGCTAAACTAGTGC R 2 1 2 1 101000 r 74 goat snp36150-scaffold431-10536598 12 28079378 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797755 Affx-122935673 AX-385284694 12 57051989 TTATCAATTGTTAAAACATCATCAATATTTTATAG[C/T]ATGTGCTAGAAATAATTTCAGGTGGTTTTGAGAAT Y 2 1 2 1 201000 f 74 goat snp36151-scaffold431-10584735 12 28032314 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445648 Affx-122926158 AX-123315985 12 57097474 AGCCTGAACAGATGTGGTACCAGACAGTGTGGATT[A/C]TATTAATCAGAGTAGTCAACAGACTGGCATATACT M 2 1 2 1 101000 f 74 goat snp36152-scaffold431-10630220 12 27986735 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438045 Affx-122931548 AX-123308383 12 57135404 TATCACTAATAATCCATGAAATATTCTGTAATGTC[C/T]TGAATCTATGAAGGATTAAATGGCAAGGAATAGGG Y 2 1 2 1 101000 r 74 goat snp36153-scaffold431-10668150 12 27949125 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779717 Affx-122957070 AX-385266817 12 57173603 TGGTGATTACTACAGTACCTACCTACAGAGCTGTT[C/T]CAGACTTTAGAAGTGCTTAGACCAATTCCTCACCC Y 2 1 2 1 101000 f 74 goat snp36154-scaffold431-10706349 12 27910302 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385886 Affx-122971594 AX-123256244 12 57218231 AGGGCCACCATCTCTGTTAGCACCGGCTATGAGCT[A/G]TCTGTTGCATCAATTTTAATGTTTCTTGCTGTTGA R 2 1 2 1 101000 r 74 goat snp36155-scaffold431-10750977 12 27864731 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768284 Affx-122975757 AX-385255465 12 57275511 AAGAGTTATGCACTGTAATAAATATTCACTATAAA[C/T]GAATATGCACTGTAAAGACCCAGAAATAGTATTAA Y 2 1 2 1 101000 r 74 goat snp36156-scaffold431-10808257 12 27807469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419029 Affx-122946034 AX-123289377 12 57318609 CAGGCCTTAGAGTGCTCTGGGGAGGACGTGGAAGA[C/T]GAGAGTTGCTGACAGGAAAGTGGGAAGCTGGAAGA Y 2 1 2 1 101000 r 74 goat snp36157-scaffold431-10851355 12 27764004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403012 Affx-122958564 AX-123273365 12 57353110 TTTTCATATCAGTGAGATTTCCTTCATATCTCACT[A/G]CCTTCCAACTCTCTTTAATCTCTTTTCTTTCGTCA R 2 1 2 1 101000 r 74 goat snp36158-scaffold431-10885856 12 27729122 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396013 Affx-122963485 AX-123266368 12 57402224 AATTTGTGTGTTCAGGAAATATATTAAGACTAGTC[A/G]TAAATACATAAACATGAGTTGATTGCCCCAAATAT R 2 1 2 1 101000 r 74 goat snp36159-scaffold431-10934970 12 27679509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435093 Affx-122933715 AX-123305433 12 57440504 TTTATTTCCACAAATTTTTACTACTATTAAATTTC[A/G]TCTAAGAACTCTTTAACTGCAACTCTCAAATTTTG R 2 1 2 1 101000 r 74 goat snp36160-scaffold431-10973250 12 27641043 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426006 Affx-122941136 AX-123296352 12 57474963 ATAAAAACTTCCAATCCTAAAAATATTTTCTTCTC[A/G]CAGTGATGATGAAGTGAAATTGCAGGAAGACAGTT R 2 1 2 1 101000 r 74 goat snp36161-scaffold431-11007709 12 27606442 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413266 Affx-122950220 AX-123283615 12 57540772 GTGGAAATTGGGAAAGAGAAACTGGACGAGGCATA[G/T]CTTGAATGTGACTACTGTATATAAAAGTACGTCTT K 2 1 2 1 103000 f 74 goat snp36162-scaffold431-11073518 12 27540029 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424536 Affx-122941719 AX-123294882 12 57577323 CTTAGGAGACGTTCAAATAGACTTTTTCCCGAGTG[C/T]TCACTACAAATAATTTCAATCATTAGAAAATGGAA Y 2 1 2 1 201000 r 74 goat snp36163-scaffold431-11110069 12 27503967 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452226 Affx-122920797 AX-123322559 12 57638024 TTATTTCTCTATTGTATAAACACTCCAGAGGTAAG[C/T]GGTTACTGACTCTGCTCTATAACTCTGCAGGGAAC Y 2 1 2 1 101000 r 74 goat snp36164-scaffold431-11170770 12 27443987 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790528 Affx-122935677 AX-385277531 12 57673212 GAATGTTTCTTTCCCTTATATTTGCTAAATAGCAC[A/G]TTCTGAAGTTCTCCTTTTGTTCAGAACAGTATTTC R 2 1 2 1 201000 r 74 goat snp36165-scaffold431-11205958 12 27408952 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778742 Affx-122970323 AX-385265853 12 57702739 AGAGTTTGAAAAGCCACAGTACACAAACCAGTAGG[C/T]ATTTGTTTAATGTCTAATGAAGACTTGTTATATTG Y 2 1 2 1 101000 f 74 goat snp36166-scaffold431-11235485 12 27379043 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394428 Affx-122964594 AX-123264783 12 57760813 GTCTGAACTTGTATTTTTTAAATCAGTTTCAATTG[C/T]TAACACAGTTGTCATTATAAGAGGTTGTTGGATAC Y 2 1 2 1 101000 r 74 goat snp36167-scaffold431-11293559 12 27320966 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439735 Affx-122930541 AX-123310072 12 57824893 ATTCTGTCATTTTTCTTTTCAAAAACCTTCTGTGT[A/G]CCTCATTATATACAAAATACAGCCAAATACTTTAG R 2 1 2 1 201000 r 74 goat snp36168-scaffold431-11357639 12 27256658 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449644 Affx-122922586 AX-123319979 12 57885224 TTTTGAAAAAGGAAAAAGTAGAACAATATTGGACA[A/C]AAGAATGCATTTTGTGTGTGAGTGTTGTGTGAAAA M 2 1 2 1 201000 f 74 goat snp36169-scaffold431-11417970 12 27196013 A C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38380877 Affx-122975052 AX-123251235 12 57921533 TCTGATTTTTTTCTATCAGACTTCAAGAAAACATG[C/T]ACTCCAAGGAATATAAGGCAGATGTTTTTTAAGTG Y 2 1 2 1 101000 f 74 goat snp36170-scaffold431-11454279 12 27160369 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386759 Affx-122970126 AX-123257117 12 57971984 GGAAGATAAATTCAAGCAATCTAAAAATAGGATGA[G/T]AACTAATAGTAGCAGCTGGTAATTAGATGCATTTA K 2 1 2 1 101000 f 74 goat snp36171-scaffold431-11504730 12 27109443 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780782 Affx-122919425 AX-385267871 12 58005972 TAAGAAATCTAAAATGAGAGTGTTCTGCTTTCACA[A/G]TTTCCTTGAAATATATGGAATGATAAATATTATAT R 2 1 2 1 101000 f 74 goat snp36172-scaffold431-11538718 12 27075376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406453 Affx-122955186 AX-123276805 12 58042353 TATCTAATACAAATACAACTTTTTGGGTTCCCTCT[A/C]GCACATCATTTGTCTGAGAAACAGAATCATTATCC M 2 1 2 1 101000 r 74 goat snp36173-scaffold431-11575099 12 27038812 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320762975 Affx-986697504 AX-385250963 12 58085168 ATACAATTTTTAATAACCATAAAAGCACCATTATA[C/T]AGAACACTTAAAATAATGCTTCACAAAACATTAGA Y 2 1 2 1 600010 f 74 goat 12_58085168 12 58085168 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 320803786 Affx-986696228 AX-385290535 12 58085436 ACTTTTCCTGGTTCCATGTCAGGACATCCTGGGAT[G/T]CTTCATTCCTTGTACGCCCAAAACTTTGGAGCTGC K 2 1 2 1 600010 r 74 goat 12_58085436 12 58085436 Ancestral_priority_1043 ancestry 0.754 recommended IMAGE 10K 10K ancestral 320798700 Affx-122935032 AX-385285632 12 58088840 AAAAGGAAGGCAAGCAATCCATTGTATTGTATACT[G/T]AGTTTGTACTAAATGCAGTAAAAGAGTAATAGGTT K 2 1 2 1 101000 f 74 goat snp36174-scaffold431-11621586 12 26992546 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785143 Affx-122972119 AX-385272189 12 58118311 AAGTCATGTGTAGGGCTATAGACTTTTGATAATTG[C/T]TAAATAAGTAATAATACCAACATTCCTCCTCCACC Y 2 1 2 1 101000 f 74 goat snp36175-scaffold431-11651057 12 26962862 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377140 Affx-122978231 AX-123247499 12 58154428 TTTATTTGACTCATCCTTCAGTGAAAGAATCTAGC[C/T]TTCTCAAACTTGGCAACAACAACAAAAAATACATA Y 2 1 2 1 102000 f 74 goat snp36176-scaffold431-11687174 12 26925973 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476287 Affx-1251763794 AX-586011706 12 58195739 TTTGGCTGCAAATAATATAATCAATCTGATTTCGG[-/TATTGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ATTGATCATCTGGTGATGTCCATTTATAGAGTCTT - 8 1 4 1 20000 f 74 goat SV_285 12 58195739 - deletion junction SV-TF-chip 539476540 Affx-1251763794 AX-586011929 12 58195739 TTTGGCTGCAAATAATATAATCAATCTGATTTCGG[-/TATTGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ATTGATCATCTGGTGATGTCCATTTATAGAGTCTT - 4 1 4 1 20000 r 74 goat SV_285 12 58195739 - deletion junction SV-TF-chip 562165091 Affx-1251763794 AX-606940503 12 58195739 TTTGGCTGCAAATAATATAATCAATCTGATTTCGG[-/TATTGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ATTGATCATCTGGTGATGTCCATTTATAGAGTCTT - 8 1 4 1 20100 f 74 goat SV_285 12 58195739 - deletion junction SV-TF-chip 562165133 Affx-1251763794 AX-606940545 12 58195739 TTTGGCTGCAAATAATATAATCAATCTGATTTCGG[-/TATTGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ATTGATCATCTGGTGATGTCCATTTATAGAGTCTT - 8 1 4 1 20100 r 74 goat SV_285 12 58195739 - deletion junction SV-TF-chip 562165138 Affx-1251763794 AX-606940550 12 58195739 TTTGGCTGCAAATAATATAATCAATCTGATTTCGG[-/TATTGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ATTGATCATCTGGTGATGTCCATTTATAGAGTCTT - 8 1 4 1 20100 f 74 goat SV_285 12 58195739 - deletion junction SV-TF-chip 562166028 Affx-1251763794 AX-606941437 12 58195739 TTTGGCTGCAAATAATATAATCAATCTGATTTCGG[-/TATTGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ATTGATCATCTGGTGATGTCCATTTATAGAGTCTT - 8 1 4 1 20100 r 74 goat SV_285 12 58195739 - deletion junction SV-TF-chip 320774423 Affx-122958890 AX-385261559 12 58201033 AAATCATCACTTTGTTTTTACAAAAATCACTCTAA[C/T]GGGCCTCTTTGTTATTCAAAGATAAATTGAAGATT Y 2 1 2 1 201000 f 74 goat snp36177-scaffold431-11733779 12 26879376 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390481 Affx-122967596 AX-123260838 12 58234968 CAGTTATGGATAATGTTATGTATCTAGGTAAGGTG[A/G]ATGAGTACAAGATGTTGAAAATGATGGAAAGGAGA R 2 1 2 1 101000 r 74 goat snp36178-scaffold431-11767714 12 26844851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447064 Affx-122924511 AX-123317400 12 58283603 TAAAGAGAACCAGATCAGTTTCCCAGTGCTCTGTA[C/T]GGGAATCCTTGAATAAATTCCAAGGATCTGTTTCC Y 2 1 2 1 101000 f 74 goat snp36179-scaffold431-11816349 12 26795890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437232 Affx-122932028 AX-123307570 12 58320879 AGCCCTGCAAACAAAATTTTAACTTCAACAAAAAA[C/T]AAGTTTTAGCCTCAAATGAAAAATAAGTTCAGCAA Y 2 1 2 1 201000 r 74 goat snp36180-scaffold431-11853625 12 26758276 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422977 Affx-122943002 AX-123293323 12 58427898 CAGAGAGGTTAAGTTACTTGAGCAAGCTAAAAATT[A/G]AAAAAACTATCATCTGAAGCCAAGTCTTTTGGCTT R 2 1 2 1 101000 f 74 goat snp19192-scaffold193-770938 12 26652492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412839 Affx-122950458 AX-123283188 12 58476482 GGCAAATTATTTAGTGTAAAGAAGGGAATATTATG[A/C]TAGATGGTAAAAATAGTCATTTTAGATATTAAATT M 2 1 2 1 101000 f 74 goat snp19191-scaffold193-722354 12 26603722 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379888 Affx-122975775 AX-123250246 12 58508480 AAGTTCTTCCCCGTGTGTTCCTGCCCCATAGATTG[C/T]ACTCTTGCCAGTTCCTATAACTGTATAATCACCTC Y 2 1 2 1 101000 r 74 goat snp19190-scaffold193-690356 12 26571576 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787052 Affx-122934888 AX-385274080 12 58604659 ATTTTTAGTTTCAGGAAAAGACTAAGTTCATACTT[A/G]TCTTACTTTCCTATGTAAGTGATTGCTTCCCATAT R 2 1 2 1 101000 r 74 goat snp19189-scaffold193-594177 12 26474015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781915 Affx-122930250 AX-385268996 12 58650102 GACAACTTCTGTCAATTGATACTGGTCTTCAAAAA[C/T]GCTACCCTGCGAATCATTTGGGTTCTTTTCTTATG Y 2 1 2 1 102000 r 74 goat snp19188-scaffold193-548734 12 26428183 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425045 Affx-122941863 AX-123295391 12 58753374 ATGCATTCACTCCCACATCCTTCATTCATTCCAGG[C/T]GGTTCCATGTTTAAACTGAGAATTCATAAATGGGT Y 2 1 2 1 101000 r 74 goat snp19186-scaffold193-445462 12 26324229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427626 Affx-122939347 AX-123297969 12 58797148 AGCTTTGTGCTGAGTGAACTACTGTTTTCAAGAAG[C/T]GATAATAAGAGAGAAATTGAAAGTCAAGACAAAAC Y 2 1 2 1 101000 f 74 goat snp19185-scaffold193-401688 12 26280332 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786210 Affx-122930043 AX-385273245 12 58836704 GATATGCTTAGCCAACATTCCCACATGGTAGCTTA[C/T]AGAGAACTTGATTCAAAGCTTGGAATCCCACACAG Y 2 1 2 1 101000 r 74 goat snp19184-scaffold193-362132 12 26240295 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792211 Affx-122947090 AX-385279196 12 58886437 CAAGCCAAGGACATAAATGAAGTCACTGGATTTTT[A/G]GCTTCATGATTTTTATGCTGTACAGTATTTTCATT R 2 1 2 1 101000 f 74 goat snp19183-scaffold193-312399 12 26190850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378664 Affx-122977088 AX-123249023 12 58916705 ACACCTAATTTTAATTCATTTAATTGGTCATATTT[A/C]CAAATATGGTTATGGTTATGTGGGATAATAAAATG M 2 1 2 1 103000 r 74 goat snp19182-scaffold193-282131 12 26160218 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444725 Affx-122926412 AX-123315062 12 58956634 TTTAAAGCCAGTGTGATCTTTATGTTCAGATCAGT[A/C]TTGCAGGGCTGCTGAACAAAATGAATAATGAACAC M 2 1 2 1 101000 r 74 goat snp19181-scaffold193-242202 12 26119399 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392677 Affx-122966424 AX-123263034 12 58988380 TTGCCAGAGACAATTTCAAGTGAATCAATTTTTAG[C/T]ATTTAATTTTTTCTATATTTTTTCTAAAAGAAATT Y 2 1 2 1 103000 f 74 goat snp19180-scaffold193-210456 12 26087507 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399205 Affx-122960611 AX-123269560 12 59039685 TGTGCAAGTCTGAGCTATAAAGTTTATAGTCTAAT[G/T]AGAGTATTCCACCTAACCCCAAAACATCATGGTAG K 2 1 2 1 101000 f 74 goat snp19179-scaffold193-159151 12 26034635 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382377 Affx-122973855 AX-123252735 12 59140915 CATGACAAATTATTAATCTCCTGAGCTGTAAAGTT[A/G]TCTACAAGAAAGGAAATGGAAAAGATAAAAAGCCT R 2 1 2 1 201000 f 74 goat snp19177-scaffold193-57921 12 25933399 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449917 Affx-122922924 AX-123320252 12 59199919 GGCAACTCTTCACATGAGCTGTTTCAGCTTTAGCA[G/T]CATTCCTTCCAAAGAAATCCCAGGACTGATCTCCT K 2 1 2 1 103000 f 74 goat snp57065-scaffold907-882683 12 25624323 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800387 Affx-122938553 AX-385287309 12 59257645 TTGACACTGTTCTGTTTTGCTGTATCGAATATGTC[A/G]CTACATAGACTACTAATTCTACTTTTAGCAAAGTT R 2 1 2 1 101000 f 74 goat snp57064-scaffold907-824957 12 25566680 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783618 Affx-122948660 AX-385270677 12 59312678 CTAGCTATATAGAAAATGATTTGCTAGGGTGAAAG[A/G]CTGATCAATATTCTTCTTTGAGAAGAACAGATATG R 2 1 2 1 101000 r 74 goat snp57063-scaffold907-769924 12 25510986 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774960 Affx-122947910 AX-385262093 12 59379767 AAACACAGTGAGTTTGTTAACATCTCTGTGTTAGA[C/T]ATGCTTTGTGTGGCTATTTCAGTTAGTACTTGAGA Y 2 1 2 1 101000 f 74 goat snp57062-scaffold907-702835 12 25442690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414046 Affx-122949781 AX-123284395 12 59425769 TGTTTAGTACAGAGAGTAACTTGGGACAGGTGTTA[C/T]ACTGTGGCCACAGTTGATTGTGATGTTTAACAAAG Y 2 1 2 1 101000 f 74 goat snp57061-scaffold907-656833 12 25396251 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783052 Affx-122936390 AX-272557466 12 59463421 ACACACTCAAGGCTGAATAGGAGGCTACTATGAGC[A/G]TTACATGAGCAATGAATGTAAACATCATGTCTGCT R 2 1 2 1 101000 f 74 goat snp57060-scaffold907-619181 12 25358657 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392139 Affx-122966328 AX-123262496 12 59512879 TTAAATTTTCTAATACATCCCTCCATGCTCAGAAG[A/C]AGGCCATGACAGATTTGATTAGGACATGTCCTTCC M 2 1 2 1 101000 r 74 goat snp57059-scaffold907-569723 12 25308965 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778892 Affx-122961438 AX-385266000 12 59543283 GGGAAGAAAAAGGAAGCAAATAATTAATGCATATC[A/G]CTTCTACTAAAGTTGTCTCTTTCCACACATTATGA R 2 1 2 1 101000 f 74 goat snp57058-scaffold907-539319 12 25278617 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420257 Affx-122945060 AX-123290605 12 59572087 TACAGTGCTGAGAGTTCAGTTCACAAGTTTATACT[A/G]TTAACTTTTATATCATAATTCAAGTAAAATATTAG R 2 1 2 1 101000 f 74 goat snp57057-scaffold907-510515 12 25249266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410637 Affx-122952082 AX-123280987 12 59618412 TTCTCCACTTTCCTATGGGACCTCTAATCCAGGGT[G/T]ATACAGGTGACATGTGAGCCCTCAGTGGGCTAATT K 2 1 2 1 101000 f 74 goat snp57056-scaffold907-464190 12 25201662 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388606 Affx-122969145 AX-123258964 12 59660894 AGGAAGGAGGGCTCTCAGACTCTTCCTTATCCAGG[C/T]GTTGGTGATGGACAGGGCAGCCTGGCATGCTGCAG Y 2 1 2 1 103000 f 74 goat snp57055-scaffold907-421708 12 25159201 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436124 Affx-122932651 AX-123306463 12 59832997 AAATATTCCACCATGCTGTCCAATATGATAGTCAC[G/T]GGCCATATTCAGTGATTGAGCACTTGAAATGTGGA K 2 1 2 1 201000 r 74 goat snp57053-scaffold907-249605 12 24988530 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272538 Affx-1111832964 AX-519546256 12 59856422 CAATGATGTGTAACAATGTGCCCCCACAGCACTGC[A/G]TTATTCACAGTTTCCCTTCCAACTCTAGCTAAAGC R 2 1 2 1 101000 r 74 goat 12_59856422_AF-PAKI 12 59856422 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38422564 Affx-122943761 AX-123292910 12 59873261 CCAAAGTCATACCAAGACATAATTGCAAATATTTT[A/G]CATGGCAGATACACTAGTATGTTTGCATAACCTAA R 2 1 2 1 101000 r 74 goat snp57052-scaffold907-209341 12 24948117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794335 Affx-122940095 AX-385281299 12 59923228 TGAAGGGTACCCTACTTTTTACCCTACTTTTCCTT[G/T]TTTCTTTCTGACTACTTATCCAAATAAATGAAAAA K 2 1 2 1 102000 f 74 goat snp57051-scaffold907-159374 12 24898129 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769643 Affx-122936543 AX-385256813 12 59958552 ATGTATCCATTGTTTTAGATAGATCGAAATATGGA[C/T]AAACAGATAAAGTACATTGGATCTGACCCAACCCT Y 2 1 2 1 101000 r 74 goat snp57050-scaffold907-124050 12 24862895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779131 Affx-122966816 AX-385266236 12 60008148 ATCATGCTATGCATATTTCTGAGAAAATATAGGTT[A/G]TTAGGAATCTTGAATTCAATATATATAAGGTTTTT R 2 1 2 1 101000 f 74 goat snp57049-scaffold907-74454 12 24811740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791024 Affx-122934522 AX-385278020 12 60104092 ACTTATTCAAATGGGAGTTATTCTCACCCATTGTT[A/G]TCTGCATATAATGTATTCAACTACTCAATTATCTC R 2 1 2 1 101000 f 74 goat snp7913-scaffold1286-411308 12 24715847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396402 Affx-122963013 AX-123266757 12 60178968 CAACATACAAAATTAAAAATAAGAGTCAGTTCCAC[A/G]TTTGTCTAAAATCTATATACTCTGTATCTACAGCA R 2 1 2 1 201000 r 74 goat snp7912-scaffold1286-336432 12 24640266 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407923 Affx-122954377 AX-123278274 12 60271775 AAAACATCTGTCCTTTTCAATTAGGAAGTAATATA[C/T]GGAATCATAAAGCATGACTTTTCAACCAATGGTAA Y 2 1 2 1 101000 f 74 goat snp7911-scaffold1286-243625 12 24546254 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451858 Affx-122921071 AX-123322191 12 60300407 ATTTTCCAATATATTATCTTGGTATGTTTGCATGT[A/G]AGTCCATGAATAAAAGAATAACATCTCATAATAAC R 2 1 2 1 101000 r 74 goat snp7910-scaffold1286-214993 12 24516944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788507 Affx-122941435 AX-385275524 12 60333041 AATATTTCCTCATGAGTAATGGTGGGAAACTATGT[C/T]AGATTTTGCTTGTCAAGTGCAGACACAAATGTGAT Y 2 1 2 1 201000 r 74 goat snp7909-scaffold1286-182359 12 24483774 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396239 Affx-122963334 AX-123266594 12 60367571 CCTTGTCAATGTGTGGGCTAGGTCACTTAGTAAAA[C/T]AGTGAATGGAACAGCAGTCATCCTTGTAATAAGAA Y 2 1 2 1 201000 f 74 goat snp7908-scaffold1286-147829 12 24448932 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772347 Affx-122953449 AX-385259500 12 60438196 TCTGATAGAAACTTGAAGGCAGACATAAACAAGAA[G/T]AAGTTTACAATAAAACTGTTTCTCTTTCATTCTTA K 2 1 2 1 201000 r 74 goat snp7907-scaffold1286-77204 12 24377434 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792465 Affx-122937809 AX-385279446 12 60472040 TCCACTTCTTCTTGTCTGAGATTAAAGAGACAACT[A/G]TCAGAGAAACTTCTTGTTAGCCCATCGCCAAATCT R 2 1 2 1 101000 f 74 goat snp7906-scaffold1286-43360 12 24342386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276782 Affx-1111835518 AX-519550291 12 60492535 CGAGTATACGTACACACACATATTCACCTTTATTT[A/T]AAAAAAGGCACCCAAATGCTGCCAGTTATTATGTC W 4 1 2 1 103000 r 74 goat Random2.2K-1281 12 60492535 A T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779964 Affx-122919792 AX-385267063 12 60506967 TTTTCTTTCTCAACACCCTTCCTAGATTGTTTGGT[A/G]AGGCACCTTCAAATATCATGCAGATGGGTGGAAAA R 2 1 2 1 101000 r 74 goat snp7905-scaffold1286-8433 12 24307076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777627 Affx-122948433 AX-385264746 12 60528431 TATTTTTAAAAAGTGATGACCCAATAAAGAAATTT[C/T]AAATGTGGTTTTGACTGGAAAATTAAGAAACTTAT Y 2 1 2 1 201000 f 74 goat snp3658-scaffold11194-864 12 24285717 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786168 Affx-122922565 AX-385273204 12 60537175 CTTATTCTCAAATACTGAGCCATCTGGATTTACCA[G/T]CTTTTAACTATTTTAAATTCACTATATGTGAAATG K 2 1 2 1 201000 r 74 goat snp42842-scaffold568-6771487 12 24273401 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386097 Affx-122971438 AX-123256455 12 60587163 TTTACATTAAATACTTTTCATTATTTCTCTTTTAC[A/G]TTGCTTCTCTATTCAACTTCAAGTGGTAGTAGCTA R 2 1 2 1 101000 r 74 goat snp42841-scaffold568-6721499 12 24223043 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444919 Affx-122926241 AX-123315256 12 60615710 TGCCTGAAGGCATGTCTACCTTTAGCAGAACAATG[A/C]GTAGATAAGTCAGTGTGGACATATCCTGGTGTCAA M 2 1 2 1 101000 r 74 goat snp42840-scaffold568-6692952 12 24194358 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445021 Affx-122926630 AX-123315358 12 60655516 GTTGCTCTTTGTCTCAAAACTGATATATAGACTCT[A/G]TCTTCTCTAGGCAAAATTTATAGCAATCAAAACAT R 2 1 2 1 101000 f 74 goat snp42839-scaffold568-6653146 12 24154427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769784 Affx-122919847 AX-385256954 12 60742379 AAGAATGAGAGAAAGCAGATTAAACAGTTTAGCCT[A/G]CTTATTCCAATTCATTAAGTGCATCATCACGAGAA R 2 1 2 1 101000 f 74 goat snp42837-scaffold568-6566283 12 24065798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439159 Affx-122931070 AX-123309496 12 60774603 AAAAAGGAGAGAGGCCATTAAGTAATGAAGCAAAT[A/G]TCTTTCCTCAATCAAACAAGTGCTAGAGAAAATGA R 2 1 2 1 101000 r 74 goat snp42836-scaffold568-6534059 12 24033313 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779660 Affx-122924081 AX-385266762 12 60887050 AAATTCAGTAACTATTTAATACCTAAATTATAGAA[G/T]ACACTGTATAGTGAAGAATTTCTTAAAATAGGAGA K 2 1 2 1 101000 r 74 goat snp42833-scaffold568-6421612 12 23920464 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388545 Affx-122969189 AX-123258903 12 60963809 CCTACATAGTTGTGAAGTTCAGTCTCTTTTTTCCT[A/G]TCCTGCGCTTGTTGTCTGATGTAGGTTCCCATGTC R 2 1 2 1 201000 r 74 goat snp42831-scaffold568-6344853 12 23842038 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785434 Affx-122964479 AX-385272479 12 60999361 TGACGCTACAGTGTTAAGCAATATGATGACCTGCA[A/G]ATTTCTTAAAGACTGTAAATTGTTTTCATGCTAAT R 2 1 2 1 101000 f 74 goat snp42830-scaffold568-6309301 12 23806626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375997 Affx-122978419 AX-123246356 12 61037320 GCTAATCTCTCCTCAAAAGCCATCTAGACCCACCC[A/G]TGGCTCAAAGGGGGAGAAGGGGAAGGGGAAAAGAG R 2 1 2 1 303000 f 74 goat snp42829-scaffold568-6271342 12 23768631 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450188 Affx-122922302 AX-123320523 12 61164597 ACTTAAGACAGCAATTTTAAAAGCCTGAGCTGAAA[C/T]ATTCTGTTTGTAGGAATCTCATTTCTCAGGAAATC Y 2 1 2 1 101000 r 74 goat snp42827-scaffold568-6144065 12 23639992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446721 Affx-122924722 AX-123317057 12 61205745 GACTGAGCACACACACCCACACACAATAACCATAG[A/C]GCATCTTGTTTTTCCTTTAGAAATACAAGTTAGAG M 2 1 2 1 201000 r 74 goat snp42826-scaffold568-6102917 12 23598861 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784553 Affx-122935808 AX-385271602 12 61241324 ATATTTTTTCTAATATCAAATCAAAGGAATTAAGG[C/T]AGTGCCGTGGTAGTGGAGCCCATGGAGATAAATGT Y 2 1 2 1 102000 r 74 goat snp42825-scaffold568-6067338 12 23562572 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790356 Affx-122948441 AX-385277359 12 61271712 GTTACTTAGTCAGTCTACTAAGTAAAAATTCTTAG[C/T]ATATGATTAGGGTACTCAGTAGCATCAGTCATGTC Y 2 1 2 1 101000 r 74 goat snp42824-scaffold568-6036950 12 23531403 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412508 Affx-122951364 AX-123282857 12 61314693 TATTTGTGTATGTAAAGGGCACAGGTGAAGTGATA[C/T]ATTAGCTGCTCTATTTGTTCAAGAACTCAGGTGGT Y 2 1 2 1 101000 f 74 goat snp42823-scaffold568-5993969 12 23488203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802504 Affx-122953269 AX-385289408 12 61352948 GTGAAAGCCTTTATGGAAAATATCTGTACTATAAG[C/T]AAAATATTTTGTATCAGTTATTTACATATACCTTC Y 2 1 2 1 202000 r 74 goat snp42822-scaffold568-5955714 12 23450017 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376528 Affx-122978002 AX-123246887 12 61387471 AAACGTCTACCCACCTATGAGGACCTAAAGGCTGA[C/T]TGTCACAAATGTGACCAAATTCACTTGCCCGGATG Y 2 1 2 1 101000 f 74 goat snp42821-scaffold568-5921191 12 23415206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381614 Affx-122974779 AX-123251972 12 61438044 AGAAAAATTATAAATAATTTAATTATACAACTGGT[A/G]CTAGATCCTGCTCTCAAAAAATAGAAAAAGTTTTC R 2 1 2 1 103000 r 74 goat snp42820-scaffold568-5870618 12 23363215 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413909 Affx-122949828 AX-123284258 12 61476298 TATGTTCCAGAGCAAGAGACTGTGTGCTTACAGAG[C/T]AGAAAGCCAAACTTTGAGTGCAAGTGTTTGCAGCA Y 2 1 2 1 201000 r 74 goat snp42819-scaffold568-5832364 12 23325196 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276783 Affx-1111835519 AX-519550293 12 61516134 TCTGTGTTTGTATTTGATAACATTTCTTTTTCTTT[A/C]TATATAAAGTCTTGTTTTAGTATTAAATTTGTGAT M 2 1 2 1 202000 r 74 goat Random2.2K-1282 12 61516134 T G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38375411 Affx-122979199 AX-123245770 12 61577881 CAAAAAACTACACTTCATGGTATCTCTCTTCTCCA[A/G]TTTCTGATATTAACAATCTTCAGTTCAGTCGCTCA R 2 1 2 1 101000 r 74 goat snp42817-scaffold568-5730781 12 23223440 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779101 Affx-122951471 AX-385266206 12 61651542 TGAGTTAATTGAAAACACAGCTTGATGTTCCCCTG[C/T]AGTTTAAATACAGAAACTCAATGCATAGAAAAATA Y 2 1 2 1 102000 f 74 goat snp42815-scaffold568-5657120 12 23149388 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399904 Affx-122960202 AX-123270259 12 61709698 TAAGACCTTTGGCTAATTTTGCTCTCCATTTTATC[A/G]TCAATGCCCAGTACATCCTTGCAACTCAGTAAGAA R 2 1 2 1 101000 r 74 goat snp42814-scaffold568-5598964 12 23090449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451305 Affx-122921288 AX-123321638 12 61754707 ATGCCTGTTAAATTAGGTTAAGAAACAGAACTATA[C/T]GAAACCTATGTAATATCTGTGTGTATGTTTAATTT Y 2 1 2 1 201000 f 74 goat snp42813-scaffold568-5553955 12 23045274 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799962 Affx-122943084 AX-385286888 12 61784837 TTTCTGCTTTCTTACAGGAAAGATAACTTAACTCA[C/T]GGTATCTCTATATGAGGTTCCTAATATATATGCAA Y 2 1 2 1 101000 f 74 goat snp42812-scaffold568-5523825 12 23015399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782268 Affx-122977598 AX-385269346 12 61831743 CTTCAATTTTTTTCCATGTATTAATATCTGTATGA[C/T]AAATGCTTGATAGCATTAACTTTGCACTTCTCTGG Y 2 1 2 1 201000 f 74 goat snp42811-scaffold568-5476919 12 22967741 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389485 Affx-122968319 AX-123259843 12 61865586 CTCTGAGCCACCAGGGAAGCCCAGACATCAGAGAC[C/T]GATGCTTTTAAAACAGGCCTTCATATTCTGTTTCA Y 2 1 2 1 101000 r 74 goat snp42810-scaffold568-5443076 12 22933646 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444563 Affx-122926977 AX-123314900 12 61912116 CAAGGAACACACACTTCACAAGCAGGTAACTTTTG[C/T]AAAGGATACAAGAGAGTCAATACTATGCTCACTCC Y 2 1 2 1 101000 f 74 goat snp42809-scaffold568-5396546 12 22885990 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398831 Affx-122961389 AX-123269186 12 61948738 CTTAAAAAATAAATTCTTATAATTATTTTTCAGTT[A/G]TTATGTTTCTTGGTGCCCAAAAATATACAGATATT R 2 1 2 1 103000 r 74 goat snp42808-scaffold568-5359924 12 22849007 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802569 Affx-122960970 AX-385289471 12 61980640 CACTCATTTCTTGTATCTGTGCAGCATGTTAATCA[C/T]AACCTCTTAATCACTCTACAATGTAAGCTGCAAAT Y 2 1 2 1 101000 r 74 goat snp42807-scaffold568-5328022 12 22816776 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775296 Affx-122941180 AX-385262427 12 62009689 GTGAGGTTTATCTCAGTGAAGAAAATCTCACTTCC[A/G]TTAAAATCACTTTACATTGTTATCACCAATTACAG R 2 1 2 1 101000 f 74 goat snp42806-scaffold568-5298973 12 22787621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778683 Affx-122958767 AX-385265794 12 62045530 AGGATTTGAATGATGGGCTCAGGTATTCATTGTGC[C/T]AACTCTGACTAGAGGCTTGCTGACATCAACTGAAT Y 2 1 2 1 101000 f 74 goat snp42805-scaffold568-5263132 12 22752107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768951 Affx-122958792 AX-385256126 12 62164381 TGAAAAACTTTCGATCTGGTTCAAATCAGTTAATG[C/T]ATCAATTGCTACACAGATCTAGGAGTCACAAGGCT Y 2 1 2 1 101000 r 74 goat snp42803-scaffold568-5144281 12 22633401 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276648 Affx-1111835520 AX-519550158 12 62226511 GGCACCCAGGAGTGAGAATGAGAGATATGAGCAAA[A/G]CAATGGAAAGACTGCATGACTTAAATGTCTGGAAA R 2 1 2 1 101000 f 74 goat Random2.2K-1283 12 62226511 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320773174 Affx-122951673 AX-385260317 12 62234914 AATCATTCACAAATAATGGTTTTAACAGTCTGGAG[C/T]TCTTAAAACACTCAAAACATTTCCTCTGGATTATG Y 2 1 2 1 102000 r 74 goat snp42801-scaffold568-5073748 12 22560112 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415920 Affx-122948455 AX-123286269 12 62268506 TGCTTTAAGCCACTCCAAGCAAACCTCCTTTGAAA[C/T]TGCAGAAGGTGGAAAGAGAGAAGACTGAATCTGAT Y 2 1 2 1 101000 f 74 goat snp42800-scaffold568-5040156 12 22526545 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434720 Affx-122933931 AX-123305061 12 62311062 AGTATTCAGTGAAAGAGGAAATAAAAGTACAACCC[A/G]CATTAAAAAGCACTTCTGTGCTTCAGATTCCGTAG R 2 1 2 1 102000 f 74 goat snp42799-scaffold568-4997600 12 22483559 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792281 Affx-122977299 AX-385279263 12 62382404 CATCAATAGCCATAGGTCTCCAGCAGTGCCACAAC[C/T]TTGAGGTTGAATCTTTGACCCATTTAAAGGACTGC Y 2 1 2 1 101000 f 74 goat snp42797-scaffold568-4926258 12 22410605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778651 Affx-122949541 AX-385265762 12 62417177 TGATGGAGAAAAGAGGACAGTGACACAAATGAAAC[A/G]TTCTCTAAGAAGAGGAATGTACTTGGATTATAAGA R 2 1 2 1 101000 f 74 goat snp42796-scaffold568-4891485 12 22375656 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797620 Affx-122973959 AX-385284559 12 62476787 AAGTGTGCATATATGTGAGTGTATGCATGAACATC[G/T]CTATTTCATAAAGACATAAATGGATACAAGGAAAA K 2 1 2 1 101000 f 74 goat snp42795-scaffold568-4831875 12 22315449 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271910 Affx-1111832965 AX-519545690 12 62495997 GTTGCCATTCCCTTCTCCTGGGATCTTCCTGACCC[A/G]GGGATCGAACCTAGGTTTCAAGCATTGCAAGCATA R 2 1 2 1 303000 f 74 goat 12_62495997_AF-PAKI 12 62495997 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320779136 Affx-122940492 AX-385266240 12 62539031 TCAAAAGCAAACCACAGTAATCACCAGCAAGAGAC[A/G]CTTATTGTAAACTTGAACTTGACGATAGGAGGACC R 2 1 2 1 101000 f 74 goat snp42794-scaffold568-4769631 12 22252043 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440570 Affx-122929304 AX-123310907 12 62579112 ACACTAAATAATTATATGCACAGTTGTATTTTCCC[A/G]ATGTTCAATAGTACTATTGTCTATTGGGACTCTTT R 2 1 2 1 101000 f 74 goat snp42793-scaffold568-4729550 12 22212007 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801964 Affx-122926748 AX-385288868 12 62607804 ACAGGAAATATAAGTTTGTGCCAGAAAGTATGAAC[A/G]TGGTCAAAGGATAATGGTGGTATATCAGAAGAACA R 2 1 2 1 101000 r 74 goat snp42792-scaffold568-4700858 12 22183466 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425598 Affx-122940925 AX-123295944 12 62662051 TATGCTCTTCTGTTCTTGGCACATAGTTTTGTTTA[C/T]AGTTGGTGTTTGAGCATGCTGCAAAATCCTAGCCA Y 2 1 2 1 101000 r 74 goat snp42791-scaffold568-4646611 12 22129774 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414555 Affx-122949392 AX-123284904 12 62695223 CATTGTTTGATTCAGAAGCTAACCTGATTTTCGGA[G/T]CCCTGTTTGAATGCTGGGGTCATTAGTTGTGCTGT K 2 1 2 1 201000 f 74 goat snp42790-scaffold568-4613439 12 22096113 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404332 Affx-122957003 AX-123274684 12 62749650 GGTTAACACATGCCTTTTCTATAAGCACAATTGAT[A/C]TGGTTAACTACTTAGATCTGCTCATCTGATAAGCT M 2 1 2 1 101000 f 74 goat snp42789-scaffold568-4559012 12 22040999 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275082 Affx-1111834586 AX-519548662 12 62845639 GGACTGCAGTGAGGTGAG[A/G]ATTTGCCAATAGCTTCCAGAAATTACCCTTTGACC R 2 1 2 1 101000 r 74 goat GoatD01.042293 12 62845639 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38436344 Affx-122933073 AX-123306683 12 62874215 GATGCAGTTCAAACAAACCCAAGTTCCCTGAGACC[G/T]CCAAGATCATTTTCACAGAAACAGTGACAGCGTGT K 2 1 2 1 102000 r 74 goat snp42787-scaffold568-4434447 12 21914308 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780896 Affx-122937703 AX-385267983 12 62947656 ATGGGGATCTGTATCTATGTCCTCTGTTCTGTTCC[A/G]TTTATCCTTGTGTCTCTCCTTTCACCAATTCCACA R 2 1 2 1 102000 f 74 goat snp42785-scaffold568-4361006 12 21841007 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379992 Affx-122975613 AX-123250350 12 62979845 TCAGGAAAATAATTTTGGAAAGTAAATAATACAAT[A/G]CAATGCATTAGAATATGAGACTGCAGAGTTAGCTA R 2 1 2 1 303000 f 74 goat snp42784-scaffold568-4328817 12 21808746 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412221 Affx-122950922 AX-123282571 12 63033352 TTGACCATGAGCTGTTCATGCACCCTGCAACTCTG[C/T]CCCTCACCTTGCCTTTAAAAAATTCCCTAATAGCG Y 2 1 2 1 101000 f 74 goat snp42783-scaffold568-4275310 12 21753477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795334 Affx-122923993 AX-385282292 12 63064545 CCCCAAATGAATAACCAAAGAAATCTGACAAGTTT[A/G]TGAACTCAACATACATAATAATTTATCACCCACCA R 2 1 2 1 101000 f 74 goat snp42782-scaffold568-4244117 12 21720681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398550 Affx-122961523 AX-123268905 12 63109395 CCTTGGGACAACTCTGAGTGAGGCAAAATGAAGGT[A/C]AGTCTTCATGCTGGTCCTAGAGGGGCCACCCCACA M 2 1 2 1 101000 f 74 goat snp42781-scaffold568-4199267 12 21675343 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407657 Affx-122954606 AX-123278008 12 63211859 TATTACTTGTTTTGACCACTAGAACAAAAGCTAAC[A/G]TGAAGAAGGCTGAGCACCGAAGAATTGATGGTTTT R 2 1 2 1 101000 f 74 goat snp42779-scaffold568-4096803 12 21572232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779444 Affx-122941543 AX-385266547 12 63248715 TGTATACAGCATAATTATGTATGTGGACATAGCTT[A/G]TATTATAACCTATGAATAACAGTACTCCTAATTAT R 2 1 2 1 101000 f 74 goat snp42778-scaffold568-4059947 12 21535287 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796858 Affx-122922306 AX-385283801 12 63289673 GCTAATAGAGAAGGATCACTTCATTTCTGCAACTT[A/G]CATTCTACTGAGTGATTAAAGGAAATAAATATCAT R 2 1 2 1 101000 f 74 goat snp42777-scaffold568-4018989 12 21494253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452520 Affx-122920551 AX-123322853 12 63358159 CAGTCAATGCCACCAGTGAAACCTTTTTCTCCTTC[A/G]TATGCCACATCCAGTAAACCATCAAACATTTTAAA R 2 1 2 1 201000 r 74 goat snp42776-scaffold568-3950503 12 21424378 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401728 Affx-122959523 AX-123272081 12 63389946 AAGGAATACTTATAACTGGCAACTATCTAATGTTT[C/T]AAGTGCTCCCTCTTGCATCACTGTGCACATCAAAA Y 2 1 2 1 201000 f 74 goat snp42775-scaffold568-3918716 12 21392415 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381478 Affx-122974966 AX-123251836 12 63467242 AATTCTCCAATTCCAGTGAAGGGCACAATGGCAAC[A/G]TGATCATAGCCTGATGCTCACCTCTCAGCCAAAAC R 2 1 2 1 101000 f 74 goat snp42774-scaffold568-3841420 12 21315311 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440526 Affx-122929339 AX-123310863 12 63521630 GTATATTTACATATGTGCATATGTACTTGTTGTGT[A/G]CATGGTAAAATAGCAGTAAATGAGTTGGACTAATT R 2 1 2 1 101000 r 74 goat snp42773-scaffold568-3787032 12 21260627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417231 Affx-122947287 AX-123287579 12 63578293 TACTAAAACAATGAAAGGACTCTAGGGTTGGGAAA[C/T]AGACAAGAATGCTTAAAATCACCCTATTATTGCCA Y 2 1 2 1 101000 r 74 goat snp42772-scaffold568-3730369 12 21201280 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428791 Affx-122938406 AX-123299133 12 63631693 TGGGAGTCAGAGGCTCAGCGAAGTAGAAATGTAAT[A/G]AAGTGATAGAGATATACCAGATTAATGTATTTCAC R 2 1 2 1 101000 f 74 goat snp42771-scaffold568-3676969 12 21147741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430741 Affx-122937505 AX-123301082 12 63708248 AGTGTTACATGAAACTTAAAATACTTAACATTGTT[A/G]CAGACTATAATTAAAATGAGTAATAACTGCTTCCA R 2 1 2 1 101000 r 74 goat snp42769-scaffold568-3600414 12 21070732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769573 Affx-122938177 AX-385256743 12 63739892 AATTCAGGAAAAAACCACAAACTGAACATAAGTAA[C/T]AATCAAGGTCTACATATGAAACAAAGTAAAATGTG Y 2 1 2 1 101000 r 74 goat snp42768-scaffold568-3568770 12 21037652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434755 Affx-122933904 AX-123305096 12 63802833 ATTACATTATAGCACTTAATTCATCTCATTTTCAC[G/T]AACTTAATTGTTAGAAATATTCACTTTGCAGAAAT K 2 1 2 1 101000 r 74 goat snp42767-scaffold568-3505829 12 20975807 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438988 Affx-122930377 AX-123309325 12 63843190 GACGGTTGTCTTTTTTTTCCTGGGGCATAACTGGC[A/G]TTATAGAGTACATCTTATTATTGCATTGGCCAAAA R 2 1 2 1 201000 r 74 goat snp42766-scaffold568-3465472 12 20935059 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769100 Affx-122944958 AX-385256275 12 63873916 TTTCCTCCTCAACATGCCACTTAGATCTTACTTTT[C/T]CATTGAGGATTTTCTGAAAATGAAGGGACATTTCA Y 2 1 2 1 201000 r 74 goat snp42765-scaffold568-3434746 12 20904350 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785874 Affx-122976712 AX-385272911 12 63908008 AGGCTGACATCTCCCAAAATGATTAAAAATGAAGT[A/G]TTGATTTACTGCTTCAAATCAACATAACATATAGA R 2 1 2 1 103000 f 74 goat snp42764-scaffold568-3400654 12 20869302 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441735 Affx-122929134 AX-123312072 12 63953061 AACAGGGTGTAGGCTGTTGATGGGTTTTCATGGAA[C/T]TGGGGTTGGGTAGAAAGTTTCTCATGTGGGGTTAT Y 2 1 2 1 101000 f 74 goat snp42763-scaffold568-3355601 12 20824196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431930 Affx-122935986 AX-123302271 12 63986115 GAAACTACAGATTCCTAGGAAGTTCTGGAACAGAA[C/T]CGCTTCCTTTCCCTCTGAAACTTATTCAGTTCAAT Y 2 1 2 1 101000 r 74 goat snp42762-scaffold568-3322547 12 20791103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431380 Affx-122936557 AX-123301721 12 64032233 TTAGGCTGTTAATTGCCTGGTAACAGTTACTAGAG[A/C]TGAAAACAGGGGTAATGAATTGAGACAAGATTAGC M 2 1 2 1 101000 f 74 goat snp42761-scaffold568-3276429 12 20745039 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415328 Affx-122948798 AX-123285677 12 64087392 CAGTGTTCATTGGTCCTGTCGTGGATAAGTCAAAG[A/G]ACTACTTGCTTTAATCCTATGAATTAAGTATAAGA R 2 1 2 1 101000 f 74 goat snp42760-scaffold568-3221270 12 20689005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435579 Affx-122933367 AX-123305919 12 64116839 TGTAGTATAGATGAAACCTCCAGTGTTAGGTGGAG[A/C]CAAGCTTTCCCTTTGAAGCACAGAATCACATTTTT M 2 1 2 1 201000 r 74 goat snp42759-scaffold568-3191823 12 20659426 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380093 Affx-122975539 AX-123250451 12 64154168 ACCTTTTAGCTTTTATGAAATGGGCATGTATCTTA[C/T]AATGGATGTAATCTCAAAATGGACCCTGATCAGGT Y 2 1 2 1 201000 f 74 goat snp42758-scaffold568-3154494 12 20622306 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385797 Affx-122971040 AX-123256155 12 64215198 AGCTTAAGGCTGTGTATTATGTGGCCTCTAATGTT[A/G]TTTACATCTTGTCCACCTGCCTTTCTGGGTGTGGG R 2 1 2 1 201000 r 74 goat snp42757-scaffold568-3093464 12 20560886 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378174 Affx-122976957 AX-123248533 12 64259939 ACATCCTGATCCAGTAGTGAGCAGTCCTTAAGGAT[A/G]TAAGAACTACTTCTGCCAAAACATACCAGTAACCC R 2 1 2 1 101000 r 74 goat snp42756-scaffold568-3048723 12 20515993 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389743 Affx-122968251 AX-106740834 12 64317235 TTCAGGAGTTTAAGGACTTTCCTGAAGAGCTGAGA[C/T]GCTGGGAATGGTGCAGTTTCTCAAGTGTCTTGCAG Y 2 1 2 1 101000 f 74 goat snp42755-scaffold568-2991427 12 20458910 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799059 Affx-122959769 AX-385285989 12 64372868 TTTGAATGTTAAGCAACAAAAGTTATTGCCTTTTA[A/G]AGGTTAAGTAAAATGTCCTGAATTCCAGGTCCAAA R 2 1 2 1 101000 r 74 goat snp42754-scaffold568-2935794 12 20402998 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423189 Affx-122942724 AX-123293535 12 64457463 TCAAATTCAACCCCTGGAATCAGTGACTCACAGAA[G/T]CACAAGCCTTACTAATAGTTCTAAGGATACAGGAA K 2 1 2 1 201000 r 74 goat snp42752-scaffold568-2851199 12 20321122 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428372 Affx-122938967 AX-123298715 12 64495080 CCCGAGAGTAATCTACTGCAAGGCTCGACATTGAT[C/T]CTAGCTAAGTTCCTTCTCTTCCTAATCCTACTGGA Y 2 1 2 1 101000 f 74 goat snp42751-scaffold568-2813582 12 20283284 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771890 Affx-122925545 AX-385259046 12 64529859 TGAAAAAAACGTTGAGATTCACATCTGGGTTGATG[C/T]AGCACAGTACAGAGTTATACACAGGGAGTTCAAAG Y 2 1 2 1 101000 r 74 goat snp42750-scaffold568-2778803 12 20248181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389737 Affx-122968256 AX-123260095 12 64564980 GTGTGTGTGCATGGGTGTGCACAGGAAAGCAGTCA[C/T]GCATGCACATTCTAGCCTGGCAGGTAAGCAAACTC Y 2 1 2 1 202000 r 74 goat snp42749-scaffold568-2743682 12 20213023 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389258 Affx-122969028 AX-123259616 12 64603220 AGTGAAAACAAAATGATGACATTTCAAAAATGTGA[C/T]GTAATGATTAAAACTAGAAACATCAGCTTACTATC Y 2 1 2 1 101000 r 74 goat snp42748-scaffold568-2705442 12 20175495 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426752 Affx-122939860 AX-123297098 12 64656544 GATGTATAATTAATGTTCTGATATATGTATAAATT[A/G]TGAAATAATCACCACAGTATTAATCACCTCACATA R 2 1 2 1 103000 r 74 goat snp42747-scaffold568-2652118 12 20121471 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411569 Affx-122951632 AX-123281919 12 64686742 TTGACACAACAATCTCTAAAAGGTATTTCAGGTAT[A/C]TAGAAATTGACTTAGTTATGCTTTGTATTCACTTG M 2 1 2 1 101000 r 74 goat snp42746-scaffold568-2621920 12 20090676 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433742 Affx-122934508 AX-123304083 12 64751266 AGAGTCACCTAACCTTTTCTACAGAGGCCAGAGAA[C/T]GCTTCTCAGGGTGAGCAGGATTTAAGATGAGACAA Y 2 1 2 1 101000 r 74 goat snp42745-scaffold568-2557396 12 20025591 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422276 Affx-122943495 AX-123292622 12 64858380 ATTTATAGCACATTACCAAATGTGAGATTGCCAAG[A/G]TAAAAATCACAAGCTTTGAAAACAGGCAGAATTAG R 2 1 2 1 101000 f 74 goat snp42743-scaffold568-2450282 12 19916581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403635 Affx-122957535 AX-123273987 12 64889007 CTTTGTGACATAAGTGTCTATTCAAATTCTTAGCC[A/G]CTCTGTTGGATTGTCTTCTTTTACAATTAATTCAC R 2 1 2 1 101000 r 74 goat snp42742-scaffold568-2419655 12 19885765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420051 Affx-122945133 AX-123290399 12 64929831 GAGCTTAATATTCAATGGTTCAGGAAAAAAGGAAT[A/C]TCATAAAAGTTTAAGGAGAAAAAGTACAGAGACAA M 2 1 2 1 101000 f 74 goat snp42741-scaffold568-2378831 12 19843687 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398355 Affx-122961673 AX-123268710 12 64992603 TCCATCCTCTAACAGCATGGATGGTGGGAACTCCA[C/T]GAACCTGGAGAGGGCAGAAACACAAGATGGAAGAA Y 2 1 2 1 101000 f 74 goat snp42740-scaffold568-2316059 12 19780040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789244 Affx-122977878 AX-385276255 12 65023475 GAGGAATCAGGTAAGTCATGCTGGAGGGAAGAGAA[C/T]GAGATTCAGGACTTGAAGTAAACATATGGTTCAAA Y 2 1 2 1 101000 f 74 goat snp42739-scaffold568-2285187 12 19749258 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271912 Affx-1111832966 AX-519545692 12 65055008 TACATTTCATTCAGAACAGGATGATCGTTCGTAGT[A/G]TGACGGTAGTCTCCAGTGAATGTTAACGTGTCCGT R 2 1 2 1 101000 f 74 goat 12_65055008_AF-PAKI 12 65055008 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276787 Affx-1111835521 AX-519550296 12 65081241 ACACATAGGAAATATTAGATATTTGTTAAATAATT[A/G]TTAGCAGTATCTGCTTAGAAAAAGTAAATGGTTAC R 2 1 2 1 101000 r 74 goat Random2.2K-1284 12 65081241 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441300 Affx-122929455 AX-123311637 12 65081446 CCTTAAATTTCAGACATCCTAAAGCTAAATACTCC[A/G]CAGCATGCTCAAAATCATCCTGTCTAAAATGAACT R 2 1 2 1 101000 f 74 goat snp42738-scaffold568-2227216 12 19690492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448400 Affx-122923681 AX-123318736 12 65153147 ATGTCTGATTATATATGTTTTTAAGTTTTCAATGG[C/T]GCCTAAAATTCAGAGAGCTATCAAACATTAAATAG Y 2 1 2 1 101000 r 74 goat snp42736-scaffold568-2155515 12 19618874 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419487 Affx-122945467 AX-123289835 12 65186086 TATCAGTGATTTTAGATGGAGGGCCAGTTGAAGGC[A/G]AGACCTTGGGTAGGTGAAGACTAGGCATCACATGC R 2 1 2 1 101000 f 74 goat snp42735-scaffold568-2122576 12 19584722 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788302 Affx-122971472 AX-385275320 12 65259404 CACTGAAGCAATTGTTTCTATTGCCCTCAGTATGC[A/G]TGATATGCTTCACTTCACAGCATCCCTGCTGAATA R 2 1 2 1 101000 f 74 goat snp42734-scaffold568-2049258 12 19510639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401938 Affx-122958811 AX-123272291 12 65298356 CCAGTGCTGCTGGACCACACTTGGAGAACCACTGT[A/C]TTAATCAGTATCAGTCTTCAGAAAAAAAAAATGCC M 2 1 2 1 101000 r 74 goat snp42733-scaffold568-2010306 12 19471765 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384493 Affx-122973061 AX-123254851 12 65351559 AAGATGGGGCCTGGATATGGTATTTTAAGTTCACA[C/T]ATCCTCATTAAAATTTTTAAGTTTATATTTTGAAT Y 2 1 2 1 103000 f 74 goat snp42732-scaffold568-1957103 12 19418143 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785632 Affx-122943625 AX-385272674 12 65389067 GATCAATCAGAAGAAAAAACATGAATATGGTGACA[C/T]AAATTCACTGTCTTATGCTTAGAGGAACGGGTTTT Y 2 1 2 1 101000 f 74 goat snp42731-scaffold568-1919595 12 19380504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402684 Affx-122958355 AX-123273037 12 65440509 ATTTCCTCCAGTGTATAAAATGGTAACATAAGCAC[A/G]TGTTATATACAGCAGGAAACATATGAGTTACTTTT R 2 1 2 1 101000 f 74 goat snp42730-scaffold568-1868153 12 19329187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781306 Affx-122949622 AX-385268391 12 65473877 TAAATAAGAATCTGCTTGGGTGATTTGTTTGCATA[C/T]GAAAGTTTGAGAAAAGTTTGTCTGGAGAATTTCAT Y 2 1 2 1 101000 r 74 goat snp42729-scaffold568-1834785 12 19295904 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451427 Affx-122921175 AX-123321760 12 65522019 ATTAGTCAATAGACAAGAGATCCTGATCAAAGACC[C/T]GAGGGAAGTAAGGAAGCAAAGCATGTGACTATCAG Y 2 1 2 1 201000 f 74 goat snp42728-scaffold568-1786643 12 19243647 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451356 Affx-122921252 AX-123321689 12 65555046 ATAGTAATATTTATCCAGAGATGACACACTTGTGA[G/T]AATACCAAGTAGTTTGTCTCTAAAACCAGGAACAT K 2 1 2 1 101000 r 74 goat snp42727-scaffold568-1753616 12 19210583 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778702 Affx-122969458 AX-385265813 12 65586206 CCATTAAACCACAAATAGGCTGTTTGTGTGTCTCA[C/T]GAATCCTTTGTATGGACAAACACCGTGTAAGAAAT Y 2 1 2 1 101000 f 74 goat snp42726-scaffold568-1722456 12 19179481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390410 Affx-122967652 AX-123260767 12 65648690 TAAGACTGGTCAAGATTATGGTTGATTCACATAAA[C/T]GTATCATTCCTCAGAGAAAAGGATATAAACTTTAG Y 2 1 2 1 101000 r 74 goat snp42725-scaffold568-1659972 12 19116599 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434437 Affx-122934660 AX-123304778 12 65689243 AGGAGCCAACATGCCAGGGAGAGGACTTCACAGGC[A/G]TGAATGGGAAATTCATAAGTGAGTTTTCCCTTATT R 2 1 2 1 201000 r 74 goat snp42724-scaffold568-1619419 12 19075921 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448859 Affx-122923282 AX-123319194 12 65729783 ATGTTCTGCTCATTGTCTCCTTTCTATATACTTTT[C/T]GTCCTTGTAGTTTATGCCCATTTAAAAAATTCTAT Y 2 1 2 1 101000 f 74 goat snp42723-scaffold568-1578879 12 19039245 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800187 Affx-122970995 AX-385287110 12 65764224 TTATATTATTGATATCTTTGTGATCCTCATAACTA[C/T]GCATTCAACAATGTTAACTGCCATCTTAGATTTTT Y 2 1 2 1 101000 r 74 goat snp42722-scaffold568-1544438 12 19004864 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386393 Affx-122970833 AX-123256751 12 65802643 TTCCCTTTGATATCTCAAAAGTGATCATCATCTCC[A/G]TTTCCAGAATATTCCAAAAATGAACACCAGTGAAT R 2 1 2 1 101000 f 74 goat snp42721-scaffold568-1506019 12 18965606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407436 Affx-122954800 AX-123277787 12 65857066 TGGTAGGAATAAAATAAAAAAGCTAGAGAATTAAA[A/G]TGTAGCAAGAGCTTCTCTGTAGAGTGAAAAATATC R 2 1 2 1 102000 r 74 goat snp42720-scaffold568-1451596 12 18910617 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413728 Affx-122950064 AX-123284077 12 65895562 TTATCATCAGAATATCCAATGTTGGTCCTTAAAAT[A/C]TACTGTAAGGCCCTCCATATCGAGTAACTAAACGG M 2 1 2 1 101000 r 74 goat snp42719-scaffold568-1413100 12 18871951 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776435 Affx-122948758 AX-385263562 12 65952325 TTCCATTTTCCAAAAGTACTTAACATTTTGGGGAA[C/T]GTGTTCAAAATCTAGAATATTCCAGCCTACATTCC Y 2 1 2 1 101000 r 74 goat snp42718-scaffold568-1356337 12 18814884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382079 Affx-122974911 AX-123252437 12 66000293 TCCGGTGTGCCTCGAAGACTCTGACCACTCTTCCA[C/T]GGGTCATTTTTCAAGATTGTTTATGTACCTGGTGA Y 2 1 2 1 201000 f 74 goat snp42717-scaffold568-1308369 12 18766504 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403204 Affx-122958058 AX-123273557 12 66044988 ATCAAAGAGTTTTGCAACTAACTCCTTGGAAACCA[C/T]GTTCCAACACAGATGCTAAGGTCTGGATAACATAG Y 2 1 2 1 101000 f 74 goat snp42716-scaffold568-1263674 12 18722229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773954 Affx-122923040 AX-385261093 12 66101708 TGGAAATTATCGGTGGAAAAATTTGAAAGGAAGGG[C/T]GAACCTAATGCCACCTGTAATTTTATTAACCAAAC Y 2 1 2 1 101000 r 74 goat snp42715-scaffold568-1206954 12 18664495 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402777 Affx-122958307 AX-123273130 12 66156001 TTGCCCCTTGAAGCTAAAGAATATCATCATTAAGG[C/T]ATATCTTCTTGTAGCTCTTTTTGTGTGTGTATGAT Y 2 1 2 1 101000 f 74 goat snp42714-scaffold568-1152661 12 18605384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396733 Affx-122962798 AX-123267088 12 66197096 AGACTATGAAAACTCAAGCTGAATTTCTCTTGGTC[A/G]ACAAAATCTTTCCCTCCGTTTGTAAGTAAGCTTCA R 2 1 2 1 201000 r 74 goat snp42713-scaffold568-1111566 12 18563824 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451573 Affx-122921691 AX-123321906 12 66246969 ATCCCTCCTCCCAGTCTCCCCTTGGTAACCATGAG[A/G]TTGTTTTCTGCATCTGTAGACTCTATTTCCATTTT R 2 1 2 1 303000 f 74 goat snp42712-scaffold568-1061693 12 18513856 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434479 Affx-122934630 AX-123304820 12 66290667 CATTTGTTGAACAATTCATTCAAACTTTTTTTTAA[C/T]GGGAGGAGGTGAAAAAAATGTATGTCTTCATGAGA Y 2 1 2 1 103000 r 74 goat snp42711-scaffold568-1017995 12 18469893 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412697 Affx-122950755 AX-123283046 12 66323164 ACATTTGCTCATACTAAATTTGAATTTATTGCCTG[C/T]ACATCTCAAATAAATTTATGAGAAATTCATTAAAA Y 2 1 2 1 101000 f 74 goat snp42710-scaffold568-985498 12 18436393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435990 Affx-122933505 AX-123306329 12 66364434 CTTTTTCGGCAATAGTATGCAGCATTGGTATTCTG[A/C]AGAAAAACTCCCATCCCCTTATAGACCAACCAAAC M 2 1 2 1 101000 f 74 goat snp42709-scaffold568-944228 12 18394870 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432723 Affx-122935468 AX-123303064 12 66394152 CAGGCACCTTAGAGCTGGTTGGCCATCTCATGAGT[C/T]GGAGACAAGACATTGCCAAGGGACAGGGAATGACA Y 2 1 2 1 101000 f 74 goat snp42708-scaffold568-914510 12 18364711 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382534 Affx-122973792 AX-123252892 12 66431471 ATAACATGCTAAAAATGAGCCCTGAGAAAGCTATG[C/T]AAATATAGATCATTTATTTTTAGGTCAAAATGAAT Y 2 1 2 1 101000 f 74 goat snp42707-scaffold568-877191 12 18327323 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791333 Affx-122921704 AX-385278326 12 66490899 ATCTACTTCTTACATTTCCATATTATCAACAAGAA[G/T]CACAGAGCTATTTGGTGAAATTCCGCAGGGAGATC K 2 1 2 1 101000 r 74 goat snp42706-scaffold568-817763 12 18267947 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435507 Affx-122933420 AX-123305847 12 66546025 TACTTTACTTATTACTATGTGAACTATAATTAAAA[C/T]AGGGGAATTTCTCTTAGAAGCAACAACTGGAAAAC Y 2 1 2 1 201000 f 74 goat snp42705-scaffold568-762637 12 18212857 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392329 Affx-122966692 AX-123262686 12 66632404 GGTTAGGAAGAGACATTAATATGATACCAACCTCA[C/T]GATCTGTAAGAGAAAAAAATGGAAAACCTTTTGTT Y 2 1 2 1 101000 f 74 goat snp42703-scaffold568-676258 12 18126057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786931 Affx-122920247 AX-385273960 12 66670161 TATATCCTCTCCTACAGGTACTTGAGAGTAAGACC[A/G]CATATTTTAAGTGTCTTTTTCCTAAATGCAATAAT R 2 1 2 1 201000 r 74 goat snp42702-scaffold568-638501 12 18088462 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418747 Affx-122946211 AX-123289095 12 66705167 GGTAAACAGATTAACGTCTGTAATGGGCGAGGAAC[A/G]TGGCCAGATGTTGCCTATTATTACCATTCCTATTA R 2 1 2 1 101000 f 74 goat snp42701-scaffold568-603495 12 18053409 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772335 Affx-122919894 AX-385259488 12 66734304 TACCAACTGCAACATACCACATCTTGAAACATTCA[C/T]TGGAAAGTCAATGGATTTCTGGAAGTTATAAATTT Y 2 1 2 1 101000 f 74 goat snp42700-scaffold568-574358 NW_017217176.1 10308 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389176 Affx-122969088 AX-123259534 12 66764586 GAATTGTGATATTTTCTATTTCGTAAATCATGGAA[C/T]TGAGATCACAGAAGATAATTTGCCCCAAGTTCTGC Y 2 1 2 1 201000 f 74 goat snp42699-scaffold568-544076 12 17994926 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434537 Affx-122934148 AX-123304878 12 66806818 TTAGGCTGGATCTTCAGCTGAGGACAGACAGGAGA[C/T]AGTACAACTGATAAAGGGACAAGTAATATCTTGTC Y 2 1 2 1 201000 r 74 goat snp42698-scaffold568-501844 12 17952626 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402089 Affx-122958699 AX-123272442 12 66855484 CCGCTGACAGCTAGAAATGGAAATGAAGTGATACA[C/T]GCCCGTGTTGTGTCTTTCAAATGTGTTTTAGCCAA Y 2 1 2 1 201000 r 74 goat snp42697-scaffold568-453178 12 17904359 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378000 Affx-122977599 AX-123248359 12 66888027 AATGTTAAATATAGTCGTGCTCTAATCATTTACAT[A/G]CTATTTCTGTGAATTACAGTGTAATCTTCTCATTC R 2 1 2 1 101000 f 74 goat snp42696-scaffold568-420635 12 17872035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377473 Affx-122977508 AX-123247832 12 66936375 CTCCACTTCAAATATCAAGGTTCTAAAACCCACTG[C/T]GGACATTGAGAAATAAACAATGATACAGACAAGAA Y 2 1 2 1 101000 f 74 goat snp42695-scaffold568-372287 12 17823375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795025 Affx-122953699 AX-385281984 12 66968392 CTTGCTCTAAGACTTGCTTCAAACATCTACAATAT[C/T]AAATCTTTAATAGGAGCGGTCTTAGATAAGGTTGA Y 2 1 2 1 101000 f 74 goat snp42694-scaffold568-340270 12 17791340 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770344 Affx-122951121 AX-385257510 12 67008455 GTTGGAAGCTCTTGTGGATTATATCTAAATAAGTA[A/G]TAACAAGAATTCTGAGGAAATACTCCTAATCAATA R 2 1 2 1 202000 r 74 goat snp42693-scaffold568-300207 12 17751436 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418280 Affx-122947003 AX-123288628 12 67051752 CTGCTGTAAAAGATTGTTAAGCAGCAAATGTAGGT[A/C]TATGTGCAACTCAATGTATATCCAGAAAAACAAAA M 2 1 2 1 101000 f 74 goat snp42692-scaffold568-256910 12 17707927 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446462 Affx-122925069 AX-123316798 12 67081216 CTAAACTACACACAACAATGTGCATTCTGAACATT[A/C]AAGCACTCGGGTAGTTAAACTGAAGGGTGGCATAT M 2 1 2 1 101000 r 74 goat snp42691-scaffold568-227446 12 17678481 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379977 Affx-122975626 AX-123250335 12 67133152 TGCTATCATGTGTAATACCGTTGTTCACGTGTCTA[C/T]GTATTTGTCCCTTTATTCTTTCTTTAGTCTCGAGA Y 2 1 2 1 101000 f 74 goat snp42690-scaffold568-175510 12 17625633 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415281 Affx-122948834 AX-123285630 12 67188144 TTTTTTTCATATGCACTGATCCCTGTGGATTCTTC[A/G]TTAGTTTTGGTTTTAAAAATTCACTTTGGTGACAA R 2 1 2 1 101000 f 74 goat snp42689-scaffold568-120518 12 17570133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435630 Affx-122933773 AX-123305970 12 67229008 ACACAAGTTTGGCCATGTTCTCATCAGTTGGCTGA[C/T]AGTTGAGCCATGGACTGTCATCAGCAAAGAAGAGA Y 2 1 2 1 101000 f 74 goat snp42688-scaffold568-79654 12 17529462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436727 Affx-122932307 AX-123307065 12 67258304 AGAAATCCATGCTTGTCATATTCCAAGTAGCTTTT[A/C]TATTGGCCTATAGCATCATCTTTCTTTCATGTGTT M 2 1 2 1 101000 f 74 goat snp42687-scaffold568-50358 12 17500504 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770141 Affx-122963549 AX-385257308 12 67291480 GATGCACTGTGATATAATCAACTTTTAACCAAAAA[A/C]GCATACACACATTACGGTGAGATAAATGCTTTTTG M 2 1 2 1 102000 r 74 goat snp42686-scaffold568-17182 12 17467415 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398513 Affx-122961550 AX-123268868 12 67315133 CAAGATTGGAATCCAGTACCCTGCAGCTCTCTTTT[A/C]TTTCTTTTCCTTGTCTCTTATTTTCCGTAGTTTAC M 2 1 2 1 303000 r 74 goat snp15937-scaffold1676-6372 12 17444176 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408806 Affx-122954041 AX-123279157 12 67385128 TTCATTGAATCATACTACACAGTGATTTGGGGGCT[A/G]TTGCCAAACAGATACAGAAAGGGAACTCTGCTCAA R 2 1 2 1 201000 f 74 goat snp15939-scaffold1676-76367 12 17374295 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429621 Affx-122937696 AX-123299962 12 67453327 TTTAGCAAGATGTAGCCATGGCCTGTTGAAAATCC[A/G]CTACTCATGGTCTAATGACTAACCCATTCATTCCT R 2 1 2 1 101000 f 74 goat snp15941-scaffold1676-144566 12 17306451 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436031 Affx-122932731 AX-123306370 12 67507358 GGAGTACACAGAGGAGTGGCTGACTCCAGAGACCA[C/T]GTTGCTCATTATTGCATTTTAATGATGCAGGTTCC Y 2 1 2 1 101000 r 74 goat snp15942-scaffold1676-198597 12 17252356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774711 Affx-122919782 AX-385261845 12 67564200 CGTGACAGTTCATTGCCCTTAAGTGAGTCAAGGCC[A/G]TATCTACAGAGAATATAAGAGCGATGAACTAAATC R 2 1 2 1 101000 f 74 goat snp15943-scaffold1676-255439 12 17195607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276789 Affx-1111835522 AX-519550298 12 67589345 CCGCCTGGTGGTAGTCTATGTTTTAAAAAATCTTT[A/C]TTCTATTCCTTAGGAAGATTCTGTTTCTTATAACA M 2 1 2 1 201000 r 74 goat Random2.2K-1285 12 67589345 A C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468271775 Affx-1111832967 AX-519545568 12 67669171 CCGCCGAGGAAGCCCCATACCAGCACTTTCTGTAC[A/G]TCAGAAATAAAATCACGGGCTTCCCTAGTGGCTCA R 2 1 2 1 102000 r 74 goat 12_67669171_AF-PAKI 12 67669171 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38404623 Affx-122957327 AX-123274975 12 67676497 TTTCCAGCCTAGGTGATAGTCTTCTAATTTCAGAT[A/C]GTGTAGGGAAATAGGACCAATGCAGGAGACATTGA M 2 1 2 1 201000 f 74 goat snp15945-scaffold1676-367736 12 17081546 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404987 Affx-122956398 AX-123275339 12 67707720 ATCAGTATTCACTTTATCTTCAATGACATGTTGCT[A/G]TTTCCCACTTCTATCTTTTGATCTTCTTCTGAACT R 2 1 2 1 101000 f 74 goat snp15946-scaffold1676-398959 12 17050463 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377426 Affx-122977547 AX-123247785 12 67759506 CTCTTCTGTTCTACCCCTATAGCAGCTAATTCTTA[C/T]AACTGTTGCTAGAAAGGGAGCAGTGTTTTCATTCC Y 2 1 2 1 201000 r 74 goat snp15947-scaffold1676-450745 12 16997942 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789494 Affx-122937355 AX-385276503 12 67791527 ATGTCTACAGAAACCCTATTTCTTGATATAAGAAT[C/T]TGGTGGTATAAAGTAGAATCCTGGGGGTGGGGAGA Y 2 1 2 1 102000 r 74 goat snp15948-scaffold1676-482766 12 16967985 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393510 Affx-122965807 AX-123263866 12 67851879 ACTCCAGGTACGTAAGTTTGATCCCTAAGCTGGGA[C/T]GATCCCCTGAAGAAGGAAATGGCAACTCACTCCAG Y 2 1 2 1 101000 f 74 goat snp15949-scaffold1676-543118 12 16917085 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789844 Affx-122951157 AX-385276851 12 67889306 CTTAGTCCTAATCATCCATTAGTTGAGGGTTTTTA[C/T]ACTCAACGCCTTACTCATCAAGTTTCTGTGGCTAT Y 2 1 2 1 101000 r 74 goat snp29361-scaffold317-587318 12 16880321 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418560 Affx-122946390 AX-123288908 12 67919170 AGAAATAGCTCCTAGAAGACCACCTCTCCCTTAGA[C/T]AATAACCATAAGCTTCAGACAAAATATTAAAAAAA Y 2 1 2 1 201000 r 74 goat snp29360-scaffold317-557454 12 16850271 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421422 Affx-122943963 AX-123291769 12 67957914 CTTTTGTTTTTTACTCATTCGGATGAATCAGATCC[A/G]GGAAGTCCTGAGCAAAATTAATCTGACAACATTCT R 2 1 2 1 201000 f 74 goat snp29359-scaffold317-518710 12 16811545 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419629 Affx-122945974 AX-123289977 12 67990414 ACAATAATGAAAAAATTAGTTTAGAAAAGGGAAAA[C/T]ACAGATTAATTCCACTTATTGGTGCAAAAATGCAA Y 2 1 2 1 101000 r 74 goat snp29358-scaffold317-486210 12 16778999 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783023 Affx-122922441 AX-385270091 12 68021228 TTCTGATTTAAACACACATCTTCCTGTAAATCACC[A/G]TATCTTCATTTTTACGGTTTCCATGGTGCCCTACT R 2 1 2 1 101000 f 74 goat snp29357-scaffold317-455396 12 16748178 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387597 Affx-122970255 AX-123257955 12 68053017 AACAACAGTGACCTGAGGGTGGGTGTGCATTAAGC[A/G]TCATCAATCACTTACACTGACTGCAAATGTATCTT R 2 1 2 1 101000 r 74 goat snp29356-scaffold317-423607 12 16716491 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424511 Affx-122941736 AX-123294857 12 68095976 TATTACAAAATATACAGAAGAACCAGGCTGACCCC[A/G]TGGAATCAAAGCTATTGGTTCAAATCCGACCTACT R 2 1 2 1 101000 r 74 goat snp29355-scaffold317-380648 12 16673552 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771188 Affx-122952512 AX-385258348 12 68134949 AGAAAAAGCAAATAAAACTCTTCTTAAAACGTACC[A/G]TTTCAAACATAGGGATGCCTGTATAGTCAAACTTT R 2 1 2 1 101000 f 74 goat snp29354-scaffold317-341675 12 16634611 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801572 Affx-122966175 AX-385288481 12 68169935 GGTGGGTGTTTGTGATCCACCTGGAAGGGAAGAAC[A/G]CATCCTCATTAAGTATGACAGGGAACTTGACCAGT R 2 1 2 1 101000 f 74 goat snp29353-scaffold317-306689 12 16599538 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777937 Affx-122956553 AX-385265053 12 68226817 TGTTTTTTGTTAAAACCCTGTACTTAGCATTTTAC[A/G]TGTGGATATATTGCTTCAGTCTGTTGTGGAACATG R 2 1 2 1 101000 r 74 goat snp29352-scaffold317-249807 12 16542055 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415883 Affx-122948483 AX-123286232 12 68257501 TGTCTGTGTCATCATAGTTTTGCAGTGATGTTAGT[A/G]CTTTGCTTTCTTACTTGTTTTACTGCCTGATACAG R 2 1 2 1 101000 f 74 goat snp29351-scaffold317-219123 12 16511144 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276655 Affx-1111835523 AX-519550165 12 68269923 GTGAGTCAGTAACATTAAGGATCATCTTCTTTAAT[A/T]AAGAGTAGAGTTGCAAAGAAGACAGGTGTTTGGAT W 4 1 2 1 201000 f 74 goat Random2.2K-1286 12 68269923 A T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412816 Affx-122950475 AX-123283165 12 68287371 AAATACTTCTTGTTATCACGGTCAAGTTCATAAAT[A/G]CAGTGAAAACCTATGGAATCAGAACAAATGAGATT R 2 1 2 1 101000 f 74 goat snp29350-scaffold317-189253 12 16481272 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377173 Affx-122978208 AX-123247532 12 68322779 GTGGAGAAATTCAACACTTCTTTGCAGGTTACCGG[C/T]GGACTGATTCCTTAGAGCAAAAGCTGGTGCTTCTG Y 2 1 2 1 101000 r 74 goat snp29349-scaffold317-153845 12 16445889 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388649 Affx-122969112 AX-123259007 12 68441728 TGTGAGTTCTTTTCTCAATTTGGAATTACTGTGAC[A/G]TTTGAGAGCCTATTGGCATACAAAGCTTTCCCAAC R 2 1 2 1 101000 r 74 goat snp29347-scaffold317-34896 12 16326840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406195 Affx-122956141 AX-123276547 12 68479617 GGACATTTCTGTTAGGTGTCTTAATCAGGCCTCCC[A/G]TAAACTCTGAGACAAGGATTTGAGTGAACATAGTT R 2 1 2 1 101000 f 74 goat snp30517-scaffold3369-2894 12 16292943 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276657 Affx-1111835524 AX-519550167 12 68525222 GTCATTTCTGGTTGGATATTTATCTGTAAAATGAC[A/G]TATTGGACTAAATGACCTCTCACTGCTCTTGCATA R 2 1 2 1 201000 f 74 goat Random2.2K-1287 12 68525222 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320780606 Affx-122969127 AX-385267696 12 68534871 ATCTGATCTCCACTTTTACCGGTTATTATTGTCTT[A/G]CCTTGAAAATTTCCTAACCCTGGCAAAATCAGTAA R 2 1 2 1 101000 r 74 goat snp30518-scaffold3369-58148 12 16233466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378940 Affx-122976432 AX-123249299 12 68541830 TCAACCTCTGAATCTCAGCTTCTTTGTCTGGAAAA[C/T]GAATACAGTTCTTGCTCTTGACCCATTGGTTTCGT Y 2 1 2 1 201000 r 74 goat snp21489-scaffold21-5022 12 14837846 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443670 Affx-122927184 AX-123314007 12 68579289 ATCAGTGCCAAGTACCAAAACTTGTAGTTTGCAGC[C/T]AAAGTGGGACTTAGGTGGGGGGAAAAAAAGGCTCT Y 2 1 2 1 102000 f 74 goat snp21490-scaffold21-42481 12 14801518 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793305 Affx-122940945 AX-385280283 12 68628107 AGGTATGTTTTGGTACCAAACAAAAGTTGGCTTTA[C/T]GGCAATAAATAGTAGACTGAATAATTCAGAAAATG Y 2 1 2 1 201000 r 74 goat snp21491-scaffold21-91299 12 14752099 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771694 Affx-122928295 AX-385258851 12 68710132 TAGCTCTTTCTCAGATAAGGCAATCTACAATGTAT[A/G]TAACCAGATCTACCTGATTTACAGTTCTCTTTTAC R 2 1 2 1 101000 f 74 goat snp21493-scaffold21-173324 12 14616926 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424079 Affx-122942046 AX-123294425 12 68781082 TTTCCTTATTTATGGAGTTATTTTTTTTAATGTAC[A/G]CAAGAACTATTTTATTATTGGTAGTGGTGGTTTAG R 2 1 2 1 101000 r 74 goat snp21494-scaffold21-244274 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276659 Affx-1111835525 AX-519550169 12 68814430 TGGTTCTAATGTGCAGGTAATGTTGAGAACCACCG[A/G]ATCATCAGACTGACTGGCAGATGGCTGAAGAGCAG R 2 1 2 1 101000 f 74 goat Random2.2K-1288 12 68814430 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320764809 Affx-122935901 AX-385252416 12 68877307 AAATTTTAAAGGATAGTGACATATATCCAAACTAT[A/G]CATCTCTAATTAGAATCCTACATTCAAGGATTTTG R 2 1 2 1 102000 f 74 goat snp21495-scaffold21-340499 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792291 Affx-122970805 AX-385279273 12 68995670 CAGATGAATAATTTCTTACAGTCACTGCATTAACT[A/G]TGTATCCCACCCTGCTGGATCCTTCATGCTCATGG R 2 1 2 1 101000 r 74 goat snp21496-scaffold21-458862 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393098 Affx-122965587 AX-123263455 12 69066493 TGATCCCATTTTCTTTATTTTTAGGTTGCTTATAT[A/G]CCTTTTGTTACACATAGGGATGAATACAGAGTCAC R 2 1 2 1 303000 f 74 goat snp21497-scaffold21-529685 5 53755759 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438093 Affx-122931514 AX-123308431 12 69133956 ACTGCCAAGTGTATCTCAATCCATGTGGGATTAAA[C/T]GACAAAGGACAAAAATGTTAAGGACCTAAGGGAAA Y 2 1 2 1 202000 f 74 goat snp55049-scaffold842-354938 12 13584244 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428701 Affx-122938624 AX-123299043 12 69164369 CTCGATGTAACATCACATGTGCAGGAATTGGACTT[A/G]TCTCCACGGGACAGGGTTCAGAACAGCACAGAGAT R 2 1 2 1 102000 f 74 goat snp55048-scaffold842-324525 8 65261890 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786509 Affx-122962137 AX-385273543 12 69198104 CCTGTTTCACAAGACTCTTGTGAGGATTAGTGCAA[A/G]CTATTCAGGGGAGCATCTTGTGTAGATGTATTCAA R 2 1 2 1 202000 r 74 goat snp55047-scaffold842-290790 12 13518559 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433040 Affx-122935763 AX-123303381 12 69249942 TCTTTCTCAAACATCCCCAGAAGCTTTTATCAGTT[G/T]CCCCTGTGTTAGTAGGGATTTGGTTTGCCTCTGGG K 2 1 2 1 101000 r 74 goat snp55046-scaffold842-238952 12 13466020 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792698 Affx-122949284 AX-385279678 12 69294245 TTGTCTAGCAAAAGTCATTCAAGCTGGCTTCTCTA[G/T]GCTTCCTATACAACCTCATGATTCTTTCAGGGCTT K 2 1 2 1 101000 f 74 goat snp55045-scaffold842-194649 12 13422822 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449886 Affx-122922347 AX-123320221 12 69337439 GTACATCAATGATTCTCTGAGTGTGGTCCCTGGAC[C/T]GCCAGCAGCAGCATTACCTGGGAACTTGCCACAAA Y 2 1 2 1 303000 r 74 goat snp55044-scaffold842-151455 12 13380063 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773225 Affx-122971389 AX-385260368 12 69388143 ACACGTGGAAGGCCATTTTGTGAGCGGAGTTGTAT[A/G]CAAATGTCACGCCTCTTCTTTAGAGCTGGATGGTT R 2 1 2 1 101000 r 74 goat snp55043-scaffold842-100751 12 13328593 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411707 Affx-122951535 AX-123282057 12 69449309 TTTATTTAGGAGACAGCTGAGCTTTGTATAAACAA[C/T]ATGAATAGCATAAAATTCCGCTTGTAAGCCATGAA Y 2 1 2 1 101000 r 74 goat snp55042-scaffold842-39585 12 13267494 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790016 Affx-122933222 AX-385277022 12 69483055 CAACTATAAGCTGTCTACAGGAAAGGTAAAATTTC[A/G]CACTGATCAACTAATTTCAACAAGGATGCCAAGAT R 2 1 2 1 102000 r 74 goat snp55041-scaffold842-5839 12 13233471 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387610 Affx-122970681 AX-123257968 12 69507055 TCAGGTCACAGTACATATACCTGCCTGGTGACATC[C/T]GGAGTGGTTAGGTGTGTCTGAGTGAGCATCCCCTT Y 2 1 2 1 101000 f 74 goat snp28502-scaffold305-18062 12 13208849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417463 Affx-122947187 AX-123287811 12 69543324 CAAGCCAAATTCCTCAGCATGTGTGAAGTGTGTCT[A/G]CCAGGGAAGCTCCTTAGAGACCCAGGGCCTTTACT R 2 1 2 1 101000 f 74 goat snp28503-scaffold305-54331 12 13172422 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772697 Affx-122942241 AX-385259844 12 69585956 TAGTACAAATTCAAGGTTCAGGGTTCCCTTGATTG[A/C]TTTGTTGTAGTTATTCAAACAATAACACATTGTTG M 2 1 2 1 102000 f 74 goat snp28504-scaffold305-96963 12 13129424 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434499 Affx-122934614 AX-123304840 12 69636605 CTTCCTTATTACTCAGATGCCTAACAGCAAGGTAG[C/T]ACCAAAAAAACCAGTGATATCTTCATAAAAGATGC Y 2 1 2 1 101000 f 74 goat snp28505-scaffold305-147612 12 13078788 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444797 Affx-122926340 AX-123315134 12 69675899 TCATATTAACATGTGTAGGATTAAATAGAAGTATG[C/T]AACCCTCTAATTTTTTTTACTCAAATATAGAGAAT Y 2 1 2 1 101000 f 74 goat snp28506-scaffold305-186906 12 13038788 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454296 Affx-122919264 AX-123324629 12 69741450 CTTTTCCCGCTTCTACGTTGGTCCTCCTACAGTCT[A/G]CTCTCAACCAAACAGTTAAAGTGACACTTCATAAA R 2 1 2 1 101000 r 74 goat snp28508-scaffold305-252457 12 12972509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787928 Affx-122949376 AX-385274950 12 69771780 TATAATTAGGAACAGATGAACAATACTATTCAATT[A/G]TCATACAGCTTAATTACTTGTGATCGTGCATATTA R 2 1 2 1 101000 r 74 goat snp28509-scaffold305-282787 12 12941979 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403631 Affx-122957539 AX-123273983 12 69800358 TACAGTCTTCAACAAAAGTGTAAACCAATATTGCA[C/T]GAAAGATAATATTCGCCAGGAAGAGGATGTTCCTT Y 2 1 2 1 101000 r 74 goat snp28510-scaffold305-311365 12 12913178 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434865 Affx-122934362 AX-123305206 12 69849260 TGATTTTATTTTACTTTAATTATACTACATTTGCT[A/G]TTCTAGCTGCTGCAGATTGTGAAGCCCTTGATATT R 2 1 2 1 101000 r 74 goat snp28511-scaffold305-360267 12 12863686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384133 Affx-122972815 AX-123254491 12 69882671 TGAAAACTGTCTCTAGTCTAAGAAGCAAGGGGTCC[A/G]GACTAGGAAGTAAAGAGACACAGGAAGAGCATTTT R 2 1 2 1 101000 r 74 goat snp28512-scaffold305-393678 12 12830177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411573 Affx-122951629 AX-123281923 12 69930974 GCATTCCAGTTCTCCAAAGCCACCCAGTGTCACCA[C/T]GGGTTATTTCTAAAAGGTGAAGTTATAAGGCTTAG Y 2 1 2 1 101000 r 74 goat snp28513-scaffold305-441981 12 12782647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276661 Affx-1111835526 AX-519550171 12 69951991 GAAACCCAGGGCTTTAAATGCTCCTATAAGAAAAG[A/G]ACAATAACTGGAAGCTCCATAAATTAAAAAAAGAC R 2 1 2 1 101000 f 74 goat Random2.2K-1290 12 69951991 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796661 Affx-122968733 AX-385283607 12 69983569 TAAACACTCTCTTTACATTCAAAACAATAACTGCC[A/G]CTATTTACTTTTAGGTTTTTGATAATGTCTCCTTT R 2 1 2 1 101000 f 74 goat snp28514-scaffold305-494576 12 12730333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276663 Affx-1111835527 AX-519550173 12 69991270 GTTCTCCTGGCCCTGGGTCCAAAGGTGTGTCTAAA[A/T]TCGCCACAGTCCTCGGCCTGAGAGGATGACCCCTT W 4 1 2 1 102000 f 74 goat Random2.2K-1291 12 69991270 T A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447875 Affx-122923830 AX-123318211 12 70031649 GGCAGAGCCTCTGGAATCTTAAGGAGTAACACCCA[C/T]AGCCTGTGGGCATCATGAAAAGGTCACCAGACATC Y 2 1 2 1 201000 f 74 goat snp28515-scaffold305-542656 12 12682261 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777045 Affx-122941023 AX-385264168 12 70129120 TTCACACTTCAAAATGTCAGAAATTGCTACACACC[A/G]TCCTAAACGAAAACTTCGTGCCTTAAGTTTAAGAA R 2 1 2 1 101000 f 74 goat snp28517-scaffold305-640127 12 12587799 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388410 Affx-122969288 AX-123258768 12 70181150 AAGAAACTGTCTTTGAAAAGGAAATGTCTAATAGC[A/G]TTTTTGAACTTCCTTATTAGGCTGCATTTTATAAT R 2 1 2 1 101000 r 74 goat snp28518-scaffold305-692157 12 12537454 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423060 Affx-122942953 AX-123293406 12 70217603 ATTAATGATATATAATCATGGCTCAAGATATTTAG[A/G]CTGTACACAGTTATGTCAGTAGCAGCGGCCACAGC R 2 1 2 1 201000 f 74 goat snp28519-scaffold305-728610 12 12501266 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408822 Affx-122954028 AX-123279173 12 70249083 GGGTTTAGCTTCATTTTAGCTGAGCTGGTTAAAGT[A/G]CCCTTGAGCCATAGTAATTGTGGTTTCACTGGGGA R 2 1 2 1 101000 f 74 goat snp28520-scaffold305-760090 12 12469702 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789222 Affx-122926436 AX-385276233 12 70279858 TGACATTGCAGATGAATGGTTGACATTCTAGAATT[A/G]TCTGTAGGAGACACGATGACTTTGCCATCTTGAGC R 2 1 2 1 101000 r 74 goat snp28521-scaffold305-790865 12 12439175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401821 Affx-122959451 AX-123272174 12 70314576 AAATTTATTGAGACATAAAATCCAGACTCTTCTTT[A/G]TTTCCTGTATTTTCCCCTCATCTGAGTTCCTAAAA R 2 1 2 1 101000 r 74 goat snp28522-scaffold305-825583 12 12403758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271776 Affx-1111832968 AX-519545569 12 70324489 TTTCAGAGACAAAAGATATGGGTATTAAAAGTTAC[A/G]TTAAGAGTCCAAAGCAGAACACTATAATGGCTCCC R 2 1 2 1 101000 r 74 goat 12_70324489_AF-PAKI 12 70324489 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320802187 Affx-122955700 AX-385289091 12 70401048 TAATTTCAACAGGAACACGGATGGTCAACTCCAGC[A/G]TTCCTCTATGCTCTTAAGCACATCCAGTTAAAGAG R 2 1 2 1 101000 f 74 goat snp28524-scaffold305-912055 12 12315907 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788000 Affx-122919508 AX-385275021 12 70475777 CCATATTTATTTGACATTCCTTTGTGTGACTTGAA[A/G]ATGTTTACATTTAAATGCTTCTCTCATCCTGTTTC R 2 1 2 1 101000 r 74 goat snp28526-scaffold305-986784 12 12240268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397746 Affx-122962534 AX-123268101 12 70513192 TGGTATGGACCACATATGCTCATGGACATTTTGGA[C/T]AGGACCAAATATCCAGGACCTTTGGGCATAGACCA Y 2 1 2 1 201000 r 74 goat snp28527-scaffold305-1024199 12 12202710 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800614 Affx-122944913 AX-385287533 12 70552888 ATTTACATGATGGAAGGGCCTTAGAAAAATTTTGG[C/T]AACAGCCCAAAGAGAACTGAAGTTCCATTTATAAT Y 2 1 2 1 101000 r 74 goat snp28528-scaffold305-1063895 12 12164827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407946 Affx-122954359 AX-123278297 12 70581867 TACACAGGGCTGCAGAGGTACAAAGGGCATATCAA[A/G]TCATAGGCAGGGAGTGGAGGACGTTTGGAACAACC R 2 1 2 1 101000 f 74 goat snp28529-scaffold305-1092874 12 12135226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381243 Affx-122974499 AX-123251601 12 70656190 TTGTAAGGAAGTGTTCTATGATTCAAAAACCCAAA[A/G]CCCCACAAATATAAATCAGTGATGCATCCGGATCA R 2 1 2 1 101000 f 74 goat snp28531-scaffold305-1167197 12 12060354 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433086 Affx-122935728 AX-123303427 12 70700039 ATTCATACAACATTTTCAGTAACTATCAATTGAAT[A/G]CCTGGGTTACTCTAGAATCTCCCTCCTAACTTGGG R 2 1 2 1 201000 f 74 goat snp28532-scaffold305-1211046 12 12015886 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274009 Affx-1111833983 AX-519547614 12 70730793 TGCCCACCTTGTTCTCCATGGTAGATATTCCCATG[A/G]AATCTG R 2 1 2 1 101000 f 74 goat GoatD01.012719 12 70730793 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38408586 Affx-122953657 AX-123278937 12 70738743 TCGTCTACTGAGAACTAAAAAAGTAACAGAAACTG[C/T]ATGGGCACATTATTTAGATAAATATAAGTATAATC Y 2 1 2 1 201000 r 74 goat snp28533-scaffold305-1249750 12 11977092 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789163 Affx-122938861 AX-385276175 12 70770816 AGTGGAGTCAAGCATGAATGCAAATTCATCAAAAT[A/C]GAATGTTACAGGGTAGGTCTCTCTGAACTCTACTC M 2 1 2 1 101000 r 74 goat snp28534-scaffold305-1281823 12 11944737 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388023 Affx-122969560 AX-123258381 12 70863301 TGGGACCCAGCTGTTGGTCACCAAGGACCGCCACC[G/T]CCCTAAGACGGCCCTCTCTGAGACAAGGGTCCTGG K 2 1 2 1 101000 r 74 goat snp28536-scaffold305-1374308 12 11852534 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777314 Affx-122926012 AX-385264436 12 70921421 GAAATCTGCTCGAACCAAGGCCTTTGTTTTTTTTC[A/G]CTTTCAAAAACTTTTGAGAGATTTTGAAACTAGGG R 2 1 2 1 102000 f 74 goat snp28537-scaffold305-1432428 12 11794036 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276801 Affx-1111835528 AX-519550310 12 71018352 CCAGACCACCCTTGACCAAGTGATCAGGCTTGACA[A/T]GGACATAGGATACAGTGTCTCTGGATGGAAATAGA W 4 1 2 1 102000 r 74 goat Random2.2K-1293 12 71018352 A T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797738 Affx-122968502 AX-385284677 12 71067197 ATTTCTGAGTAATTGACTCAATTTAGTCTTTTCAA[A/G]TACAATAGATGGAGCTGTTTTTTAGTGCAGAGGTT R 2 1 2 1 101000 r 74 goat snp28540-scaffold305-1578204 12 11652139 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451925 Affx-122921017 AX-123322258 12 71098734 GTTCTTTGTTTCCTTTTCTTCTTGTTGCTCAGTTG[A/C]TCAGTCGTGCCTGACTCTTTGCAACCCCATGGACT M 2 1 2 1 103000 f 74 goat snp28541-scaffold305-1609741 12 11620766 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433077 Affx-122935737 AX-123303418 12 71148689 GTTTTCCTGGAAGTTCTCACATACCTGGGAGTAAA[C/T]GGCTTCATTTCAACACCAACTCTGTGGGCAACTAC Y 2 1 2 1 101000 f 74 goat snp28542-scaffold305-1659696 12 11570802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388016 Affx-122969564 AX-123258374 12 71182388 CAATTCACCTCTCTGAGCCTGCTTCCTTACCTCCT[A/G]CACAAGAGGACTGGACTGCATGGACAACCAACCCT R 2 1 2 1 201000 r 74 goat snp28543-scaffold305-1693395 12 11537120 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377237 Affx-122978157 AX-123247596 12 71214385 TGTCTTAAACTGCAAAGGGTCAATACTGGGTCCTA[C/T]GACCAACAAGTAGGGTTCACCAGGCCAGGGTTTCA Y 2 1 2 1 101000 f 74 goat snp28544-scaffold305-1725392 12 11505123 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452735 Affx-122920280 AX-123323068 12 71251873 CCTCCAGGCATCACACTGGATAGTTGGACCATGAG[A/C]TTTGCCTGGCATGACCCCCTCTGCTCTCGATTCTT M 2 1 2 1 201000 f 74 goat snp28545-scaffold305-1762880 12 11466648 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395153 Affx-122964120 AX-123265508 12 71281453 GAAATCTGTTTTCCTCCAAGGGCTTTCAGACCCAT[A/G]CCAGTTTCTTCAACATTTTTTCAAGTATAGAAGTG R 2 1 2 1 101000 f 74 goat snp28546-scaffold305-1792460 12 11437103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407512 Affx-122954738 AX-123277863 12 71335174 AACAAGGACAGTCAAGGGACATGGGTAACAATAAT[A/G]ATGCATTCAAAAATAATCATTCAAAATGCAAAATG R 2 1 2 1 101000 f 74 goat snp28547-scaffold305-1846181 12 11383130 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276667 Affx-1111835529 AX-519550178 12 71360536 ATTTTTTTGGGCCAATTTCATAGAACCTGCTGTCC[A/G]AAGTAGCAAGCTCAGGTTAATGAATTGCTTTCTTA R 2 1 2 1 101000 f 74 goat Random2.2K-1294 12 71360536 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451918 Affx-122921024 AX-123322251 12 71385185 TTATAATAGTAACCAGCTTTGAGGCCAAAATAAAC[C/T]CTCTTGTTGTTCTTTAGGACACCCCATCTGCCGCA Y 2 1 2 1 101000 f 74 goat snp28548-scaffold305-1896192 12 11332555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800605 Affx-122926443 AX-385287524 12 71431604 ATCTACTGCAGAGAAGGTTCCCATAAAGTATTTGC[G/T]AAATAAATGCACAAGTGAAATGTGTGTTAAATAAA K 2 1 2 1 101000 f 74 goat snp28549-scaffold305-1942611 12 11285889 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420091 Affx-122945102 AX-123290439 12 71483731 ATTTTTCTATTGGTGTAACCCACCCATGTGAAGGC[A/G]AAAGGGAAATAAAATTAATTTTCCTCACTAGATGT R 2 1 2 1 101000 f 74 goat snp28550-scaffold305-1994738 12 11234473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780804 Affx-122966673 AX-385267893 12 71529854 ATATTGTGGCTATATGCAAAAATAATCATACACCC[A/G]CACACCCTCATGCATCCTACACCAAAATATTTACA R 2 1 2 1 201000 f 74 goat snp28551-scaffold305-2040861 12 11188509 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453368 Affx-122919938 AX-123323701 12 71570472 AGAACAATGCATGTATAATTAGAAGCCACTTTCCC[A/G]CCTTAACCGCTGAGTGTTTTCCATATTGAGTTTTC R 2 1 2 1 101000 r 74 goat snp28552-scaffold305-2081479 12 11147906 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424868 Affx-122941334 AX-123295214 12 71624262 CTGGTTATCCTCACTATTTGGGCAGCGTGGCTCTG[C/T]AGGCATGGACAGCCTCTCCAAGCGTCTTTCTTCTC Y 2 1 2 1 101000 f 74 goat snp28553-scaffold305-2135269 12 11094521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393113 Affx-122965579 AX-123263470 12 71653785 TACACCTGTTACACCCCTTCAGTCAGAGCATTCTT[A/G]TTCTTTGGGGAATGGGGAAGCAGGCAAAAGGGTTC R 2 1 2 1 202000 r 74 goat snp28554-scaffold305-2164792 12 11066067 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437329 Affx-122931956 AX-123307667 12 71681862 AGGAGATATAAACTGTTTATAAACAAAACCTATAG[C/T]TCCTTCAGAAAAATCAAACTTTTCATTGATGAGTG Y 2 1 2 1 101000 r 74 goat snp27917-scaffold2999-88892 12 11038159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800716 Affx-122935114 AX-385287634 12 71711711 ATGAGTGAAATGTATGATGCTATTATAGGTGGTCC[A/G]TATTTTATAATGTAGACCAGCACTGCCCAGTACAA R 2 1 2 1 201000 r 74 goat snp27916-scaffold2999-59043 12 11007919 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420322 Affx-122945014 AX-123290669 12 71755673 AGAGCACACTCTGATGTCATTTCTGAGAAGGATAC[G/T]AATCCTATGCGATCAGGGCTACACCCTTATGACCT K 2 1 2 1 201000 r 74 goat snp27915-scaffold2999-15081 12 10963814 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430917 Affx-122936852 AX-123301258 12 71780214 AAGTACCTCAAATATTTCAGTTGCCTACAAAACCC[A/G]CCTGAAATGCCTCTTACCAAACAATAGGGGAAAAA R 2 1 2 1 101000 f 74 goat snp13600-scaffold1526-9361 12 10939434 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398609 Affx-122961482 AX-123268964 12 71822750 TTTGTTTAATCGAGTTGAGAAAACATTTTTCTGTC[A/G]TGCCATGGTATGCCCTGGATGGTCAGCATGTACCT R 2 1 2 1 101000 r 74 goat snp13601-scaffold1526-51897 12 10896963 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403240 Affx-122957889 AX-123273593 12 71907099 TTAGGAATACCACATATTAAACTTCCCCTTCAAGG[C/T]GCAAAAGCTCCGAGAACACTGCAACAGAAGCCTGC Y 2 1 2 1 201000 r 74 goat snp13603-scaffold1526-136246 12 10813344 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450031 Affx-122922838 AX-123320366 12 71954243 AAAGCCCCCTACCCCTTGCCCACCACCAAAAACCA[C/T]CCTCAGATAAGCAAGTATAGCTAATCACAGGACAC Y 2 1 2 1 101000 r 74 goat snp13604-scaffold1526-183390 12 10766257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393969 Affx-122965048 AX-123264324 12 72019573 GTTGGGGAGGGGTGAGGAAGGGACAATGAGGCAAA[C/T]ATCAAAGGGTAACCAAAATAGCTGAAGGAATTGTG Y 2 1 2 1 101000 r 74 goat snp13606-scaffold1526-248720 12 10700871 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775483 Affx-122975492 AX-385262614 12 72054115 CTACTTACTTGAGACATCTGGTCACATGTCACTGT[C/T]GTTCCGGGAAAAGACACGGTCATGCTATTATTTCC Y 2 1 2 1 101000 f 74 goat snp13607-scaffold1526-283262 12 10665994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276669 Affx-1111835530 AX-519550179 12 72098931 CGTAGGGATGGTGGGACAAGAAAAGAATACACACA[A/G]TTATAATGCAGGATTCAACAAGATCACGGTCATGA R 2 1 2 1 101000 f 74 goat Random2.2K-1295 12 72098931 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432351 Affx-122936275 AX-123302692 12 72100525 GACGTGCCAGACAGGGAGAAAACTGCATGTACAGA[A/G]ATGCACGGAAGAAAGCGAGTTTAGCAGAAGCCAGA R 2 1 2 1 101000 r 74 goat snp13608-scaffold1526-329672 12 10619127 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38410591 Affx-122952119 AX-123280941 12 72180311 CCACCACCGCGAAGCCCACTTGCAGTGGGAGGAAC[C/T]GCTGCCCATCTCAGTGGATTAAGGTTATTTATTCA Y 2 1 2 1 101000 r 74 goat snp13610-scaffold1526-409458 12 10539180 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391329 Affx-122967314 AX-123261686 12 72211122 AAAACTAAACCACAGGGAAGAATAACCTAAAGTAC[A/G]CTGACCTTAGAAGCAGAGTGAAGCTGGGGGTTGGG R 2 1 2 1 101000 f 74 goat snp13611-scaffold1526-440269 12 10507910 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393812 Affx-122965171 AX-123264167 12 72243541 TGTTAGACAACAAAAGGCAAAGAACAGGTTTTAGC[A/G]TATACACAGTATGCCCCCATCAGAAAACAATGAAA R 2 1 2 1 101000 r 74 goat snp13612-scaffold1526-472688 12 10476468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784844 Affx-122922570 AX-385271891 12 72314975 CAATTTAAATGGTTAAATCAAGAGACATTAGATGG[C/T]AATCAGCGGTGTCAACACCTGCAATCTTACTCATT Y 2 1 2 1 101000 f 74 goat snp13613-scaffold1526-544122 12 10405017 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421887 Affx-122944265 AX-123292234 12 72343712 ATGATAGACACCACTTTTGCAAGGATGTTTCTCAT[A/G]CCCTTCACTGGGCAAGAGAAGGGCAAGAGAAAAGC R 2 1 2 1 101000 f 74 goat snp13614-scaffold1526-572859 12 10376268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273398 Affx-1111833579 AX-169425249 12 72395028 GGCTGCAGTCACCATCTGCAGTGATTTTGGAGCCC[A/C]AAAAAATAAAGTCTGACACTGTTTCCACTGTTTCC M 2 1 2 1 303000 r 74 goat 8_44215950_AF-PAKI 12 72395028 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401926 Affx-122958819 AX-123272279 12 72405551 ATTATCTGATTACCACGGTCTGTAAAGATATTTGA[C/T]GAAATGCAAGAGCAAACAAGGTAAATTCAATTATT Y 2 1 2 1 101000 f 74 goat snp13615-scaffold1526-634698 12 10313067 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398766 Affx-122961439 AX-123269121 12 72457197 CTGTGAACTGTCAACACGGGGTAAAGCCTGCCCCA[C/T]AGTGCCAGAACTTTTGATAACATAAAACCAGCCCA Y 2 1 2 1 101000 r 74 goat snp13616-scaffold1526-686344 12 10261398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392482 Affx-122966144 AX-123262839 12 72519894 CTCCTCAACTTCTCTGGGCTTATATCCTGCCTGTC[C/T]GCTCTGCAGGCATTCTGCTCTTGGCCATCCTGGCA Y 2 1 2 1 101000 f 74 goat snp13617-scaffold1526-749041 12 10198321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797865 Affx-122972766 AX-385284803 12 72553860 CGTGTTCAGCCTCTTATGCTGACCTCTGGGAGGAT[A/G]CCTAAGTTTATTTTTCAAGCTTGGTTAATTTGTTC R 2 1 2 1 101000 f 74 goat snp13618-scaffold1526-783007 12 10164184 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431939 Affx-122935979 AX-123302280 12 72598006 GTGGACTCACTGTTTGACTTAAATCGAAAAAGATC[A/G]TCTTTACCAACATTCAGTGAATACTGATTGCTCTC R 2 1 2 1 101000 f 74 goat snp13619-scaffold1526-827153 12 10119958 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451762 Affx-122921518 AX-123322095 12 72679624 TAATACGAAGTTACGGATGCATCTCCCACTCAGAA[A/G]ACTATGTACCTTGGAGACTCACCCAGTGGTGATCG R 2 1 2 1 101000 f 74 goat snp13620-scaffold1526-908771 12 10037767 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388108 Affx-122969491 AX-123258466 12 72731955 CTATTCCAGAGCAATTTTAGGTTAGGTTCACAGAA[G/T]AGAATTAGCAGAAAATAAAGAGACTCCCTATTCCC K 2 1 2 1 201000 f 74 goat snp13621-scaffold1526-961102 12 9985420 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798584 Affx-122934247 AX-385285517 12 72769118 ATGTGGTACGTGGAACTTGGAGTAGGAATATAGTT[C/T]TTACTCATCCACTAGAGCTGCTGGAGTGATAGTAC Y 2 1 2 1 101000 r 74 goat snp13622-scaffold1526-998265 12 9948039 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430903 Affx-122936863 AX-123301244 12 72833340 AGATCAGGAATCATGTCAATAAATGTTTGTCTGAG[A/C]TGGAAAAGAATGAGTTGGATTTGAAGGTAAAGTCA M 2 1 2 1 201000 r 74 goat snp13624-scaffold1526-1062487 12 9883651 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276807 Affx-1111835531 AX-519550316 12 72883008 CCTCTTCGTGTTACCACAGCCCATTTGTCGCAGCC[A/G]AGAAGCCAGGCCTTGTACAGCACTGTCAACTCCAG R 2 1 2 1 102000 r 74 goat Random2.2K-1296 12 72883008 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401563 Affx-122958895 AX-123271916 12 72917810 TCCCCTGCATCATTGACTCAGAAGAGATTTTAAGC[A/G]TTGCCATTAAAAGGAAAAAACCCAACTCTCATGTG R 2 1 2 1 101000 f 74 goat snp13626-scaffold1526-1146957 12 9801316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386007 Affx-122971505 AX-123256365 12 72950213 TTCTATGTTTCTGGGACATACGCCACCCATTCACC[G/T]ACCTGGAGAACTACAGTTCTGTGGACAAAGAAGCG K 2 1 2 1 101000 f 74 goat snp13627-scaffold1526-1179360 12 9769104 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399155 Affx-122960647 AX-123269510 12 72982603 CCCTGGGAAGAATGTGAACCAGTGTAGAGGACATT[C/T]GTGGTTTACCCTTGACCATCTATTTTTCTTTCCTC Y 2 1 2 1 101000 r 74 goat snp13628-scaffold1526-1211750 12 9736555 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769177 Affx-122951469 AX-385256352 12 73014686 ATCCCTGTATTGGCCAGGACTCCTGGTAGCCAACT[A/G]TAGAATCAACTGAGTTTAAGCAGAACACAAATAGT R 2 1 2 1 101000 f 74 goat snp13629-scaffold1526-1243833 12 9704697 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431967 Affx-122935958 AX-123302308 12 73043488 TGACTGCATGATTTCATAGAATCCTGTGACTCTTA[C/T]GTAATATTTTTATTTAAGGTTCTTAAAGTTTTTTT Y 2 1 2 1 201000 r 74 goat snp13630-scaffold1526-1272635 12 9675878 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438491 Affx-122931225 AX-123308829 12 73126113 ATTGATCAGTAAAATTATAATAATGGCATTCTGTT[C/T]CAGAGCGTTCCCCAGGATTTCATTGATGGAAAGGA Y 2 1 2 1 101000 r 74 goat snp13632-scaffold1526-1355260 12 9592759 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780597 Affx-122936105 AX-385267687 12 73159344 CAAGCTACCTAATCTTCTCTTTGCTCAAGATAATA[A/C]GTTTACTTCCAGGAGTCTTCTCAGTCTTCCATGTA M 2 1 2 1 101000 r 74 goat snp13633-scaffold1526-1388491 12 9558876 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378345 Affx-122976836 AX-123248704 12 73201313 GAAGTGTGACGGTGTATAGCACCAGTTCCCTAACT[A/G]TTCCTGTCTGGGGCTGTCTCTTTCACATGGTGATT R 2 1 2 1 101000 f 74 goat snp13634-scaffold1526-1430460 12 9516752 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403704 Affx-122958040 AX-123274056 12 73261784 CAGTTGAGATCCCTGGCATAGACAAAGGTCTAAGC[A/G]TGCATCTTCACCTGAGAAGTGATAACTGGAGAGGA R 2 1 2 1 101000 r 74 goat snp13635-scaffold1526-1490931 12 9455262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437266 Affx-122932002 AX-123307604 12 73313705 GGGTGCGGTCCTACCATCACTTCTCCTCGAACAGA[A/G]CGGTTCAGTTTTCTATGTGCTGTACATTTGGGGGG R 2 1 2 1 101000 r 74 goat snp13636-scaffold1526-1542852 12 9403554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766173 Affx-122942643 AX-385253575 12 73342866 GAGATAGACGACAGCAATCAGTGAGCTTGATTTGC[A/G]TTACAGTTTGATCTGGATCAAAGGTCCTTAATACA R 2 1 2 1 101000 f 74 goat snp13637-scaffold1526-1572013 12 9374259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431608 Affx-122936161 AX-123301949 12 73381493 CATTTTTTTCCTGGTAACACAGTGTGAGTAGCATC[A/G]TCACTTTGCTAGATTTCCTTAAGAGTGACATTTGA R 2 1 2 1 101000 f 74 goat snp13638-scaffold1526-1610640 12 9335177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390318 Affx-122967709 AX-123260675 12 73416600 AGGACAAATTTGCTGAGAGACTGCCTTTCTAGGTT[A/C]TTTGCTATTTACATAAAATAACTTATCAATCAAAA M 2 1 2 1 101000 f 74 goat snp13639-scaffold1526-1645747 12 9300400 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276809 Affx-1111835532 AX-519550318 12 73425186 GTAGTCAGGGAGACACCAAGGAGCTCAGTTGTTTT[C/G]TTTGTCTTACTGGTACCTGGCTCAGTCTGTAATGA S 4 1 2 1 101000 r 74 goat Random2.2K-1297 12 73425186 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275296 Affx-1111834709 AX-519548871 12 73445569 TCCCCTCACACGGTACCCATATGTATGCTGCAGTC[A/G]GTTGCCGTGTTATATTTTTGCTGTATGAAGTAGTC R 2 1 2 1 201000 r 74 goat GoatD01.047152 12 73445569 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427539 Affx-122939505 AX-123297882 12 73502960 TTTTGTGAGCTGTCAGTTACTTTCATTTGTCGTTT[A/G]TCTCTGGGGAATCCCTAGCCACTTAAAGTTTGTGA R 2 1 2 1 201000 f 74 goat snp13641-scaffold1526-1732107 12 9213050 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798531 Affx-122930824 AX-385285464 12 73544953 GGACTTAGAGGAGCCCGTCTCAGTTGGAATAACCT[A/G]TGTTCTCTATATTATACTTCTATAAGCTGTTGTTG R 2 1 2 1 101000 f 74 goat snp13642-scaffold1526-1774100 12 9173261 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444306 Affx-122926749 AX-123314643 12 73578788 CTTTATAATTTCTTGAACAAAAATATTAAAAATAT[A/G]TGTTCTTTCAGAATGATGCTGAATACATTTTTTTT R 2 1 2 1 103000 r 74 goat snp13643-scaffold1526-1807935 12 9139450 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803229 Affx-986696235 AX-385290084 12 73624493 ACTGGGTAAGCATGGAGCTGAGAGATAAACGACAC[C/G]CCCGCACATGGGAATGCCATCAACAAAAATTTAAG S 4 1 2 1 600010 f 74 goat 12_73624493 12 73624493 Ancestral_priority_1043 ancestry 0.738 recommended IMAGE 10K 10K ancestral 320765623 Affx-986697509 AX-185147094 12 73624538 GGGAATGCCATCAACAAAAATTTAAGAGGCGCCTC[A/G]TGGATCTATGAAGTCTGGTAGAAGGCTGAAGGGCT R 2 1 2 1 600010 r 74 goat 12_73624538 12 73624538 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 38432907 Affx-122935322 AX-123303248 12 73625040 AGAAGACACCGGAAACGAGGCTCAAGGCCTGGGGC[A/G]TCTTCTAGGCCATACTTGGCTGCAGGGTTCTAAAG R 2 1 2 1 101000 r 74 goat snp13644-scaffold1526-1854187 12 9093702 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433478 Affx-122935043 AX-123303819 12 73677513 GCATGCCAGGGCTCTGAAAGGACAGCGCAAGGCCC[A/G]CAATGTTGAGGATTTTTCAAATAAAAGTGTGGCCA R 2 1 2 1 101000 r 74 goat snp13645-scaffold1526-1906660 12 9041485 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389068 Affx-122968600 AX-123259426 12 73733735 AACCTGTCCACTATCTACACTAACCAGTTCAGAAA[G/T]CCAGCCTGCTCTCTGTAAGTTAGACTTGTCCAAAG K 2 1 2 1 101000 f 74 goat snp13646-scaffold1526-1962882 12 8985195 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411681 Affx-122952002 AX-123282031 12 73814592 CGCATTGGGCTAACCGGTTCCAGCAGCTGTGCCCA[C/T]GGCAACTGTAGATTTGCTTCAATCCTGGGTAATTT Y 2 1 2 1 101000 r 74 goat snp13647-scaffold1526-2043739 12 8903911 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398822 Affx-122961396 AX-123269177 12 73845041 ACAAGCTTCCATGGAGAAGGCAGTGCACACAACCA[C/T]AGCGGCTTATCCTCTCATCCTGTCTTTAGTGGACA Y 2 1 2 1 202000 r 74 goat snp13648-scaffold1526-2074188 12 8873493 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401666 Affx-122959570 AX-123272019 12 73888926 TAGCTCTGTTATTAACCCCAGGCTACTGTGCTCTC[A/G]TGCACTGTGGTTCCCTTCTTCCTGGCCCAGGCCTT R 2 1 2 1 201000 f 74 goat snp13649-scaffold1526-2118073 12 8829273 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395196 Affx-122964506 AX-123265551 12 73919331 TGAGGCAGTTTTGTGGTAATCCACCCCATAAAGCT[A/G]TTGAGAACAGATGACTCAAAAATTTTCCAGTGAGC R 2 1 2 1 201000 r 74 goat snp13650-scaffold1526-2148478 12 8798424 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276675 Affx-1111835533 AX-519550185 12 73939202 GATTCATTTGTCCTGAGGCAAACTGTGTGAATTCT[A/G]TTATTTTATCAGATTTCGTTTTGATTCAGTTTCAC R 2 1 2 1 101000 f 74 goat Random2.2K-1299 12 73939202 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416041 Affx-122948360 AX-123286390 12 73951364 CCATGAACACTGGTGTACCAGGACCTGTTTGAATC[A/G]CTGCTTTCCAATCTTGTGGGTGTATTTGCCCACAC R 2 1 2 1 101000 f 74 goat snp13651-scaffold1526-2180511 12 8767778 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395679 Affx-122963747 AX-123266034 12 73975226 TGAATAAAGCACAATTTAAAAATTGATTCTAATAC[A/G]TACACTCTCAGATTAATAGACATTCCCTAAGAGTT R 2 1 2 1 101000 r 74 goat snp9211-scaffold1336-14310 12 8744129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454234 Affx-122919667 AX-123324567 12 74029496 TTAACGTCTGATTTCTAAAACTGTTTGGCCCCTCT[A/G]TTCTAGGTGTGTGTGGGGGCATTCTGGGCAATGTC R 2 1 2 1 101000 f 74 goat snp9212-scaffold1336-68580 12 8689998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397726 Affx-122962549 AX-123268081 12 74077591 TGCTTTTACCTGGAGTTTGTGGCTTACCTTGGTTT[A/G]TTGTAAATATTGTTTATAGATTTTTGGTGTATTAT R 2 1 2 1 103000 f 74 goat snp9213-scaffold1336-116675 12 8642462 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797580 Affx-122923259 AX-385284519 12 74129668 GCTGCAGACGTGTTCAGTGACAATGCCAAGTTTCA[C/T]AATCTAGGGAAGCGGCAATAAATAGTTGCCAGATC Y 2 1 2 1 101000 f 74 goat snp9214-scaffold1336-168752 12 8591759 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793856 Affx-122956392 AX-385280825 12 74162713 AAAGTCTTTAAAATAGAAGAATGTGAACTATGAGA[C/T]TAAACCTTTTGGGAATGAGTTTCCACCAGTTGCTG Y 2 1 2 1 101000 r 74 goat snp9215-scaffold1336-201797 12 8558715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414319 Affx-122950045 AX-123284668 12 74200912 ACCCTGTAAGCTCCATGAAGAGAGGGGCCATGCTC[A/G]TCTTGTTCAGGACTATCTTTGTGTCAGTAAATATC R 2 1 2 1 101000 r 74 goat snp9216-scaffold1336-239996 12 8520166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454126 Affx-122919343 AX-123324459 12 74247934 CAGTTAAGCCCAAGTGAGGACGCTTTTGAGAGTGG[C/T]AAGAGAGGAAAAATTGATTAATGAAGACTAATCAC Y 2 1 2 1 101000 f 74 goat snp9217-scaffold1336-287018 12 8473009 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781224 Affx-122966281 AX-385268309 12 74278672 TAAGCATCAATCATTCTAGTTAGTCTTCTGAGCCT[A/G]CATCTGTAAAACTACCTTCTCCAGGTCTCAGAAAG R 2 1 2 1 101000 r 74 goat snp9218-scaffold1336-317756 12 8442575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430591 Affx-122936992 AX-123300932 12 74357395 TTAATACTCTTTAATTTCCCCACCAGCCTGTTCCC[A/G]CAGCTTGTTTACGTGCTGATACCCTTCCCTTCAAT R 2 1 2 1 101000 r 74 goat snp9220-scaffold1336-396479 12 8364138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438275 Affx-122931405 AX-123308613 12 74390866 TAAAACCGGGTATCTGCTCATTTTTAGTTTTCATC[A/G]TAATATGGGAAATAGACCGTAAGCTAGAAAAGAAG R 2 1 2 1 201000 r 74 goat snp9221-scaffold1336-429950 12 8330563 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444309 Affx-122926746 AX-123314646 12 74425173 GTGCTTGATTTTGTCACTTGTTTCATTGAACTTTT[A/G]TCTCTCTGAGTTTATGTACTAGGTTTACTCATTTA R 2 1 2 1 101000 r 74 goat snp9222-scaffold1336-464257 12 8296676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452517 Affx-122920553 AX-123322850 12 74457648 TCTCTTGGCATTAGGAGAAGGAAGTCAAGATAAAA[C/T]GGCCAAGGTGGGATATGCGGCCAGCTTCAGATAAG Y 2 1 2 1 101000 f 74 goat snp9223-scaffold1336-496732 12 8264208 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378896 Affx-122976494 AX-123249255 12 74494291 ACATCTGTTTCTCTGATTCATATTTTTATGGTAAA[C/T]TCTGAAATGAGACAATTATTGTGAACCCAGGAAAT Y 2 1 2 1 101000 r 74 goat snp9224-scaffold1336-533375 12 8227565 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795316 Affx-122976772 AX-385282274 12 74553960 CATTTACAAAAATAAATCTTGTCATAATTTTAACC[A/G]ATAAACAAGCTTGCAGGAGAGAAAAAGAAACCAGC R 2 1 2 1 101000 r 74 goat snp9225-scaffold1336-593044 12 8168529 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447885 Affx-122923822 AX-123318221 12 74596978 GGAAAGGATTTAAAACTCAGAATAATGCTTTCAAA[C/T]ATATTGGATCATAAAACGTTTAATACAGGGAAATC Y 2 1 2 1 101000 r 74 goat snp9226-scaffold1336-636062 12 8125185 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777251 Affx-122968181 AX-185528488 12 74667258 GTCTGTACTACTCAGATGATGAAATGAGAATGGCT[A/G]GCTGTGACCCTTGAGAATTATCCCTACAAGAACAT R 2 1 2 1 101000 f 74 goat snp9228-scaffold1336-706342 12 8054212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394117 Affx-122965340 AX-123264472 12 74711767 ATTACAGCCATTGCCATGTGCTCACTGATCTCAAC[A/G]GCCCCTCTGTGCCACTGCTACTCATAAATTCTGAG R 2 1 2 1 101000 f 74 goat snp9229-scaffold1336-750851 12 8009653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779582 Affx-122949301 AX-385266685 12 74742997 AAAAGCTTTAGGGTTATTAACGGCACCAGTTCACA[C/T]GCTCACTGAATGATGATTAGTAAAGTCTCGAAGCT Y 2 1 2 1 101000 r 74 goat snp9230-scaffold1336-782081 12 7978127 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786820 Affx-122941006 AX-385273848 12 74796628 TTTCATAATTAGAAATGAGGAACATTACCCTTAGC[A/G]TAATACCTGGTCTCAGAGGAAAGATAAAATCAGGG R 2 1 2 1 101000 r 74 goat snp9231-scaffold1336-835712 12 7916489 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451204 Affx-122921323 AX-123321538 12 74826934 AGCTCCATGTTCCCTTCACATCAGCTGCTGCTAGC[A/G]CAAGGACTCTGCCCACTGGAAGCTTCTATTTCTGG R 2 1 2 1 101000 r 74 goat snp9232-scaffold1336-866018 12 7886182 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783523 Affx-122934607 AX-385270586 12 74872471 TTCATTAGCAAATGTTGTCTAATCTTTACCTTTTA[C/T]GTTAGGGCTACTTGGCATCACTCACACTGGTCCAA Y 2 1 2 1 101000 r 74 goat snp9233-scaffold1336-911555 12 7840590 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424848 Affx-122941351 AX-123295194 12 74903262 ACAGGCTTCCAAGTTTCACATTTGTTCTTTACTTA[C/T]GCAGAAGATAGTCAACCTCTCCAAAGCTCTCTTTC Y 2 1 2 1 101000 r 74 goat snp9234-scaffold1336-942346 12 7809420 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406712 Affx-122955763 AX-123277063 12 74941214 TTACACAACCACGTATAGAACTCTGTGAGAGAGCG[A/G]GACTGCAGACAGACATGCACACTCACGTCAAGGCA R 2 1 2 1 201000 r 74 goat snp9235-scaffold1336-980298 12 7774729 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378637 Affx-122977106 AX-123248996 12 74970150 GATGAAGGTTCAAATCCACTCCCCTCAGTAGCTAC[A/G]TGATGGTGGGAAAATAGCATGACAGATAGTCCCTG R 2 1 2 1 101000 r 74 goat snp9236-scaffold1336-1009234 12 7745915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442331 Affx-122928051 AX-123312668 12 75011963 CATTTATAGCTTCCATTGCTTTCTCTTCTCCCAGC[A/G]TCCACAAAGAAAAGGAAAAAAGAAATTTCAACACG R 2 1 2 1 101000 f 74 goat snp9237-scaffold1336-1051047 12 7704215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398708 Affx-122961850 AX-123269063 12 75056548 AGGCGATTTCTCTCCCCAATGTCCACCTCTGCCTA[A/G]TTAGCCCAATAAACTCTTCTGCATCCGACACAACA R 2 1 2 1 101000 r 74 goat snp9238-scaffold1336-1095632 12 7660007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791076 Affx-122945123 AX-385278071 12 75093848 CTTTCTTTATCACTATCAATACCACACCATGAGGA[C/T]AGTGATCCTGGACACTTTATTCAAGTCTGTTTCCC Y 2 1 2 1 201000 r 74 goat snp9239-scaffold1336-1132932 12 7624696 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425829 Affx-122940679 AX-123296175 12 75181562 CACATCCACTTTAGCTCCTCTGCCAGGCTTCTGGA[A/C]TCCGAATTATGATTCTTCTCATCCTCCAAAGTAAA M 2 1 2 1 201000 r 74 goat snp9241-scaffold1336-1220646 12 7537396 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379620 Affx-122976007 AX-123249978 12 75211070 TGCACACACGTGTATAAAGGCTCAAGATAATTACT[A/G]CTTAACATTGACTTTGTTTTTTTAAATAAACATTG R 2 1 2 1 103000 f 74 goat snp9242-scaffold1336-1250154 12 7507874 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778953 Affx-122977730 AX-385266060 12 75245063 CTTTTAAATATCTGAGTCAGTGTGAGGTCAAGCGG[C/T]AGATTTTTGTGTTCACCATTTGTTCACTGAAATGG Y 2 1 2 1 101000 f 74 goat snp9243-scaffold1336-1284147 12 7473973 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788502 Affx-122948549 AX-385275519 12 75330636 CCGTTGCTCTGTGAGTTATTGTACGAGTCGGAATT[C/T]GACAGTCAGCTCTGGATCATATTTGACCAGAACAA Y 2 1 2 1 101000 r 74 goat snp9245-scaffold1336-1369720 12 7388757 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406729 Affx-122955749 AX-123277080 12 75388800 GCACTTTTATTAGGAGTAGCCCCAAACTAGATACT[A/G]TTCTGAGCTGTGTCTGATTCTTTGTGACCCCACGG R 2 1 2 1 103000 f 74 goat snp9246-scaffold1336-1427884 12 7331557 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438624 Affx-122930920 AX-123308961 12 75418976 AGTGAAACCGACATGGGAGAGGAAGTGGCCTTCGG[C/T]GTGGCTACTGCCAGTGGCTGACCTTGTTTCCTCAT Y 2 1 2 1 202000 f 74 goat snp9247-scaffold1336-1458060 12 7301479 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271777 Affx-1111832969 AX-519545570 12 75452058 GCAGTTTGTAAGCCACTGGCAGCAGCTGTCTGGAA[A/G]AGCAGGTTCAGAATTCTGAGGCCACGGGCAGGCTC R 2 1 2 1 202000 r 74 goat 12_75452058_AF-PAKI 12 75452058 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38391255 Affx-122967372 AX-123261612 12 75472140 AGTTGCACAGCTAGAAAGAGGCAGAAGTCAGGTTC[A/G]TATTATTTCTTGGCTTTTCGGATCACTTTGTAAAA R 2 1 2 1 201000 r 74 goat snp9248-scaffold1336-1511224 12 7247587 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452062 Affx-122920876 AX-123322395 12 75510988 TCTATTGAGTATGTTCCCTGGTCTCACTGTACCAT[C/T]ATTACTGTGTTTAGCTGGTGAATGAGTCTTGTTTT Y 2 1 2 1 101000 f 74 goat snp9249-scaffold1336-1550072 12 7208212 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428553 Affx-122938729 AX-123298895 12 75543518 TATAGTTGAACGTATAGTTCTTTAAAATGACTCCT[A/G]TTATTAGAAAGTGAAACTGAAGTCGCTCAGTCGTG R 2 1 2 1 303000 f 74 goat snp9250-scaffold1336-1582602 12 7175794 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380249 Affx-122975456 AX-123250607 12 75573111 GGACAATCTTGTCAAAATACCAAAACACTAAACAC[G/T]AAGAGAATAGAAATGGAACATGTGACTTCCAAATG K 2 1 2 1 201000 f 74 goat snp9251-scaffold1336-1612195 12 7146179 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416491 Affx-122947793 AX-123286839 12 75625884 AGAGACTGGAATAGTAGAAGTCAAAAATCTAAGGA[C/T]GCAGCTTAGAAACTCAGAGGATGGCTTTTTTCTTT Y 2 1 2 1 101000 f 74 goat snp9252-scaffold1336-1664968 12 7093284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432100 Affx-122936477 AX-123302441 12 75654770 CATGTTTCTTTTTGTTTTCCCCCCAATAGTAGAGG[C/T]AGACACAGCATAGAAACACTGAACACTCAGACAGT Y 2 1 2 1 201000 r 74 goat snp9253-scaffold1336-1693854 12 7064493 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445007 Affx-122926640 AX-123315344 12 75701730 AGAGAAAGTAGAGACCATCTGAAGATACTACAATA[C/T]AGATTGTCCCCAGGGGGTGTGCCAAAGTTTGTTCT Y 2 1 2 1 201000 f 74 goat snp9254-scaffold1336-1740814 12 7018162 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427959 Affx-122939198 AX-123298302 12 75734789 GCCAATATATTCTTCCAGGTGCTCCTGTTGAAAAA[C/T]AAGATGAAACTTTTAAGCTAGCTCTGAAATTAGCA Y 2 1 2 1 201000 r 74 goat snp9255-scaffold1336-1773873 12 6984983 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801226 Affx-122936943 AX-385288139 12 75774996 TTTTTTCCTGAGGGATTTGAGGGGCTTATAACATT[G/T]AACATCATGGAAAGAAGGACAACTGGGTTGAATAA K 2 1 2 1 101000 r 74 goat snp9256-scaffold1336-1814080 12 6944199 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275000 Affx-1111834627 AX-519548582 12 75859714 TTCCTAGTGGGGCTGTTGAGTTATTCTGTTTAGAC[A/G]CATACCCTGCAGGGGTGAGG R 2 1 2 1 101000 f 74 goat GoatD01.043856 12 75859714 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320782918 Affx-122958705 AX-385269988 12 75878821 TATTCGGGCAATTGGCCAAACTTGACTGCAGTGGT[A/C]TCAATTGTAGGTATATTATTGTATTCATTTTTACT M 2 1 2 1 102000 f 74 goat snp52077-scaffold77-78482 12 6841292 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397341 Affx-122962302 AX-123267696 12 75912029 AAAGAAAACCAGCTTTTTCATTCTCAGCTCTAGAG[A/C]CCAATCACGGTGTGTTCACTTTGTTTATGGGCTTG M 2 1 2 1 102000 r 74 goat snp52078-scaffold77-111690 12 6808093 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391972 Affx-122966519 AX-123262329 12 75947890 TGCTACAGCAGCAAAAGCAACTGGGATGGAAACAG[C/T]AACAGTGAAAAAAGTAACATGTAGCAACTACTTAC Y 2 1 2 1 101000 f 74 goat snp52079-scaffold77-147551 12 6771739 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429745 Affx-122937594 AX-123300086 12 76032682 GGGAGGTGGGGAGACAAGGGGGCTGAGCCCTATGA[C/T]GGTTCTGCTTCTAGAAGTATCTCCAGGCCATAGGA Y 2 1 2 1 101000 r 74 goat snp52081-scaffold77-232343 12 6686963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399378 Affx-122961331 AX-123269733 12 76061833 CCTGCCAACCACTTGAACTTCCAGCCTCCAGAACT[A/G]TAAGAAAGTAAATTTGGTGATTTAAGCCACGTGGT R 2 1 2 1 101000 r 74 goat snp52082-scaffold77-261494 12 6657986 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447547 Affx-122924043 AX-123317883 12 76113190 ATGTGGTCCAGACGCTGTTGGCAGTCCCTAGTCAC[A/G]GTGTCCATAGGCTGCAACCCAGAAGCACAATTTTA R 2 1 2 1 101000 r 74 goat snp52083-scaffold77-312851 12 6606561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433315 Affx-122935185 AX-123303656 12 76177399 AAAGTGCAACCAAGAACATGTTTGTTTCTACTTAT[A/G]CTTTCTGTTTTGTGCAATTATAAGCAATATTTCCT R 2 1 2 1 101000 r 74 goat snp52085-scaffold77-377060 12 6541963 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420675 Affx-122944809 AX-123291022 12 76359300 AAAAGTGAAAGTGAATTCATTTTTAGTTAAACATG[A/G]ATGGATTTAAAAGCAAGGATAATTTTTGCATTGAT R 2 1 2 1 101000 r 74 goat snp52089-scaffold77-558961 12 6359693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417904 Affx-122946740 AX-123288252 12 76474671 GTATGCCTAGTCCACCCATCCTTTAAAAAAAATGA[C/T]AGTCATTTTCAAGCCTTAGTCAGCTAGCTTTAATT Y 2 1 2 1 103000 r 74 goat snp52092-scaffold77-674332 12 6244115 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769258 Affx-122950864 AX-385256431 12 76513873 TCCTTGGGATCTTTTAAAAGTTGTTTAAAAGTCTT[A/G]GCCTTCTGGTGTAGAAGTTGTAAAAATATTAGTGT R 2 1 2 1 101000 f 74 goat snp52093-scaffold77-713534 12 6203625 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414303 Affx-122949585 AX-123284652 12 76533093 CATGTGGATTCAAAGCATACATTAACACCTACCAC[A/G]AAAATTCACATCCTCTCAAAATTAACTTGGTATGT R 2 1 2 1 101000 f 74 goat snp594-scaffold1016-927632 12 6184600 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786615 Affx-122960552 AX-385273647 12 76623154 TCAATTTATCTGATACAATCATGCTTTTTGAATGA[C/T]GCCATTCCCCCAAACTTTCTGTTTATAATCCACAA Y 2 1 2 1 101000 r 74 goat snp592-scaffold1016-837571 12 6093722 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446893 Affx-122925224 AX-123317229 12 76653244 ATATGTTTGTTGCAAAAATACTTGCCTTATGTTTT[C/T]GAAAACATTAAAAATCTAGAAATGCATCATAATTC Y 2 1 2 1 303000 r 74 goat snp591-scaffold1016-807481 12 6063504 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802477 Affx-122965878 AX-385289381 12 76695797 ATATTTCCTGATTATAGAAACCCAAAGGCAAGAAA[C/T]AAAATGCTTGCTTTAGCTTACTACCTTCCATCAGC Y 2 1 2 1 201000 f 74 goat snp590-scaffold1016-764928 12 6020804 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775461 Affx-122962062 AX-385262592 12 76743593 TTGAAAAATCCCAATTGTTAAAAATGTGCATATTG[C/T]GGAATAATTGTAGATATACAAAAATGTTGCAAAGA Y 2 1 2 1 101000 f 74 goat snp589-scaffold1016-717132 12 5972642 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389422 Affx-122968366 AX-123259780 12 76797374 AAATGAGTTGAGCTATAGAACTCCTCAAGTGCTCC[A/G]TCACTCAATCTTGTCTGACTCTTTTGCAACCTCAT R 2 1 2 1 101000 f 74 goat snp588-scaffold1016-663351 12 5918834 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442317 Affx-122928236 AX-123312654 12 76830304 GTGACTTAGCATGCACACACACAGACCTTGAAGTT[A/G]CTAATCTCTTTCTTCAGAAGTTATAGTATATAGTG R 2 1 2 1 201000 r 74 goat snp587-scaffold1016-630421 12 5885764 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777062 Affx-122940742 AX-385264186 12 76885923 GATATGGTCCACGTTAGAACAGTCTGTTTAGATTA[C/T]AATTAAATTGCACTAACACAGTACTAAATGATTGC Y 2 1 2 1 101000 f 74 goat snp586-scaffold1016-574802 12 5830748 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407751 Affx-122954981 AX-123278102 12 76925477 GAGCCACCAGGGAAGCCCTCACCGGTTAAATCCAA[A/G]CCCTCCCCCAATCCTGCCCACTTTCATTGTCTTTT R 2 1 2 1 303000 f 74 goat snp585-scaffold1016-535248 12 5791487 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448774 Affx-122923308 AX-123319110 12 76958157 TGTTTGCTGGGCAGGCAGAGAAACCCAGACATAGA[A/G]ACTACATAGTTTTTATCCTAGACTCTTCACTAACT R 2 1 2 1 101000 r 74 goat snp584-scaffold1016-502568 12 5758167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797379 Affx-122956390 AX-385284318 12 76998624 AATGACAAATAGTTTCTCTTTCATAAGTAAGAAGG[A/G]TAAAAGTTGCTCAGATGCTAGTTATGTAAAGGTTG R 2 1 2 1 201000 f 74 goat snp583-scaffold1016-462101 12 5717497 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802112 Affx-122931104 AX-385289016 12 77054600 GTGAGATTCAAATCAGTTCTTATATTGTCCTTGAA[C/T]GGTGGAAAAGGTGGGCAATGCTATCAAGCAAACTA Y 2 1 2 1 101000 r 74 goat snp582-scaffold1016-406125 12 5662521 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411809 Affx-122951253 AX-123282159 12 77122942 TCCTGTGAGTAAGCTTCCTGATGAAATGATGCAGA[G/T]ACAAAAGGCAATAGTGCATAGTCGTGGCCTGCCGC K 2 1 2 1 201000 r 74 goat snp581-scaffold1016-337783 12 5593489 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429369 Affx-122938557 AX-123299711 12 77151748 TGATTCAAAGTTAATTTCTTTTGAGGAATTGCCAT[A/G]CTAGTTTCCATATCTGCTGCATCGTTTTGCCTTCC R 2 1 2 1 101000 r 74 goat snp580-scaffold1016-308977 12 5564726 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434800 Affx-122933871 AX-123305141 12 77182112 CATCAGAATAAAGATGTGGCTTTTCATGATGCTTG[A/G]CTTCTTTGTTTTCTTCTTTTCTGCAAGGCAGCTGT R 2 1 2 1 201000 f 74 goat snp579-scaffold1016-278613 12 5534075 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445018 Affx-122926633 AX-123315355 12 77236883 CCAAGAGATAGAGAAGAAAACGCTGATTGTAGAGG[A/C]TCCAGGAGTGTGTGCAACTCTTTTGTGACCAGCTG M 2 1 2 1 101000 f 74 goat snp578-scaffold1016-223842 12 5478718 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407323 Affx-122955305 AX-123277674 12 77283414 GGAATTACAGCACTCTCTCTTTGTTGTTGCGTTGT[C/T]ACTTTTAAATGGATACAAGCTTTAAATCCTGTGGC Y 2 1 2 1 201000 r 74 goat snp577-scaffold1016-177311 12 5432199 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785429 Affx-122972650 AX-385272474 12 77334117 AATGTTTGCGTGATGTATCCATTATCTGTCTTCAC[A/G]TGCTCTGTTTTATTCTCTTTCAAAAAAGTTATTTG R 2 1 2 1 101000 r 74 goat snp576-scaffold1016-126608 12 5381587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795839 Affx-122958318 AX-385282792 12 77372524 CCTGATTACTCTGGAGGGTTTAGATAGAAGCGAAG[C/T]GGTTGTAGTTCAATCGATAGGAGACAGACTGCATG Y 2 1 2 1 101000 r 74 goat snp575-scaffold1016-88201 12 5343253 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419667 Affx-122945945 AX-123290015 12 77438024 GCCGCACTGGTGCAGCAAGTGTCCAGCCTCCTCAG[C/T]AGACATGACGATGTTGTCAGAGGCACATCGTGCTT Y 2 1 2 1 101000 r 74 goat snp574-scaffold1016-22701 12 5277693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796868 Affx-122959685 AX-385283811 12 77462523 CAGTATAGCAGATGTGAAGGAAGTAAGATTAGAGC[A/G]TGCTCAAGGAAAGAATAGGAGTCGATGACTTTGAG R 2 1 2 1 101000 r 74 goat snp31397-scaffold347-3055491 12 5253339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785050 Affx-122948862 AX-385272097 12 77511201 CTGTAGTCCACCAACTAGGGTATGCCAAATATTAA[C/T]AAATATTCATAGATTGCAGATGACTGCAAATAGCT Y 2 1 2 1 101000 f 74 goat snp31396-scaffold347-3006813 12 5204136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404513 Affx-122956699 AX-123274865 12 77543876 ATGTAAAAAAAAATTCAGACATAACATTTTCCAAC[A/G]TTGTGTAATAAGCATATGGAATGCATTGACCAAAA R 2 1 2 1 101000 r 74 goat snp31395-scaffold347-2974138 12 5171584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400131 Affx-122960711 AX-123270486 12 77581802 ACATATAAAAAAATAATACATGTCACACCTCACAC[A/G]CTCATCTCAATCCTGTCTTCCCAACATACACAAAG R 2 1 2 1 101000 r 74 goat snp31394-scaffold347-2936212 12 5133829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439715 Affx-122930556 AX-123310052 12 77619137 CCTGTGGTGTCAACATAGCATCTTGGCCACGGTCA[C/T]GAATGAAAGGGCCGTCTACACGTGTGCTTAAGATA Y 2 1 2 1 101000 r 74 goat snp31393-scaffold347-2898877 12 5096666 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414717 Affx-122949269 AX-123285066 12 77669961 TTTGTCCCAGGTGTCAAATATTTCTGTCTTTGGGG[C/T]AACTGAAGAGTGGATTTAGGATTTTTCCCATTCCA Y 2 1 2 1 201000 r 74 goat snp31392-scaffold347-2848053 12 5045410 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276680 Affx-1111835536 AX-519550190 12 77701597 AATGCTAGATTGTTACATGCAGTATATAATTAATC[A/C]AATTCTGTAATTAAGCACTTATGAACATTAGAAAC M 2 1 2 1 101000 f 74 goat Random2.2K-1300 12 77701597 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403073 Affx-122958516 AX-123273426 12 77726198 GGAGAATTGCAGGTGGATTCTCTACCCACTGAGCC[A/G]TCGGGGAAGCCCTCCCTCTCTCTACACAACCTAAA R 2 1 2 1 103000 r 74 goat snp31391-scaffold347-2791816 12 4989260 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393897 Affx-122965112 AX-123264252 12 77768031 ATGTTTGTTTGGCTTTATCATCTTCATATAGATAG[C/T]ATCTCTTAATGAATTTTGCTTTAACAAATCTAGCC Y 2 1 2 1 101000 f 74 goat snp31390-scaffold347-2749983 12 4947356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793355 Affx-122949872 AX-385280333 12 77856528 ATATTTTTGTTTCACTCAACTCAAGCTGCATTATC[G/T]AGCTTCTCTGAAGAACTGAATCCTTCTTCAAGACA K 2 1 2 1 101000 r 74 goat snp31388-scaffold347-2661486 12 4858579 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386287 Affx-122970934 AX-123256645 12 77922340 TATTTCTAAAATAAAATTTCTAAAATCCTCAAACA[C/T]GAAGACTTTTCAAAACAAGAGTCGATCATTATTTT Y 2 1 2 1 101000 r 74 goat snp31387-scaffold347-2595674 12 4792990 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383001 Affx-122973330 AX-123253359 12 77966923 CCTGGCTTTGAGAGTTAGATAATTCCAGGGATTAA[C/T]GCAATGAGAGCAGAGTGAAGTCAGCTCACGAGGAG Y 2 1 2 1 101000 f 74 goat snp31386-scaffold347-2551091 12 4747740 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385507 Affx-122971263 AX-123255865 12 78015815 TGCAAACATTGAAAATACCTAGAGAAAGAGGAACA[C/T]GTGTAGGATGTGTTCATGTGAATTCTTATTTGACT Y 2 1 2 1 101000 r 74 goat snp31385-scaffold347-2502199 12 4699173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397119 Affx-122962686 AX-123267474 12 78049986 TGTTGAAAAAGGTTTTCACTGGGAAATCAACATTC[A/G]TAATGCCTGTCACATCTTAGACTACTCTTCGAATG R 2 1 2 1 101000 f 74 goat snp31384-scaffold347-2468028 12 4664989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388590 Affx-122969156 AX-123258948 12 78083605 GAATTCTCTGGCTCCCAAGCATGAATCATTTCTTC[A/G]TGTGAAGTGGCCTGGGAGTTGCCATCTGAGGTCTC R 2 1 2 1 101000 f 74 goat snp31383-scaffold347-2434409 12 4630809 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385055 Affx-122971828 AX-123255413 12 78141671 AATTAAAGCCTGTCATTAAGTTTGAAGTTTCAACA[C/T]GGCATACAAAATCTGGCATAAGTAACACTAAATAT Y 2 1 2 1 101000 r 74 goat snp31382-scaffold347-2376343 12 4572059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403446 Affx-122957731 AX-123273799 12 78177849 GAAATAAACACACAAAGATTGACTTTTTAGTTCTG[C/T]GGTTATTGCTGAAACATCTTCAAGGCAAAATACAA Y 2 1 2 1 101000 r 74 goat snp31381-scaffold347-2340165 12 4536267 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271921 Affx-1111832970 AX-519545701 12 78201885 TGGTTCCAAATAGGAAAAGGAGCAAGTTAAGGCTA[A/C]GTATTGTCACCCTGCTTATTTAACTTTTATGCAGA M 2 1 2 1 103000 f 74 goat 12_78201885_AF-PAKI 12 78201885 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38447618 Affx-122923992 AX-123317954 12 78216808 TTTCCCTTCCTATGAGGCTTTATAAATATCTCAGC[A/G]CATGTCCGAATAGAACACCAGTTGGGCAAAAACCA R 2 1 2 1 101000 r 74 goat snp31380-scaffold347-2301206 12 4497300 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376887 Affx-122977816 AX-123247246 12 78249837 TTACTCAGACAGTCCGACTTGTTGCGACCCCAGGA[A/G]CTATAGCCCGCCAAGCTTCTCTGGCCACGGAATTC R 2 1 2 1 103000 f 74 goat snp31379-scaffold347-2268177 12 4485442 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444111 Affx-122926821 AX-123314448 12 78280862 TGTTTCTGCAAAAGCAATTTTGAAGATGCTAAGCC[A/G]TTTTCTGAATGACGTTCAGGTCTGCATGGGGGGTA R 2 1 2 1 101000 r 74 goat snp31378-scaffold347-2237152 12 4454592 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390047 Affx-122968426 AX-123260404 12 78311633 AGGTAAACACTTAGCGAACACTTAAAAAGAGTGTA[C/T]ATTCAACCAACACGGCCTACTGCACAGGCAGTAAT Y 2 1 2 1 201000 f 74 goat snp31377-scaffold347-2206381 12 4423843 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383713 Affx-122972474 AX-123254071 12 78341563 CTAGCAGGACTCTCCGGCTTTTGCTTGATAGAGTG[C/T]AAACAACCAGTTTCTTAAATAGAATTTTTACAAGT Y 2 1 2 1 101000 f 74 goat snp31376-scaffold347-2176451 12 4393751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446419 Affx-122925560 AX-123316755 12 78377667 GGTCCTGGACATGATGGTTCGACTTGGAATTCTTC[G/T]ACTTTCCTCTAGCGTGGAAGCCATACACGTGCAGT K 2 1 2 1 101000 f 74 goat snp31375-scaffold347-2140347 12 4357533 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400079 Affx-122960751 AX-123270434 12 78408677 TTTTATTTCCCCATTTTCTTCACATCACCTCTGTT[C/T]GGTATGTGTTCATTTTCATATTAAGATAACTTCAC Y 2 1 2 1 101000 r 74 goat snp31374-scaffold347-2109337 12 4326443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790200 Affx-122956453 AX-385277204 12 78441100 TGATCCCTTTGTAATTTGATGTCAATCGGCAGTTC[A/G]TGGTTTTCCAGTATATTTGGGCAGGATCATACCAC R 2 1 2 1 101000 f 74 goat snp31373-scaffold347-2076914 12 4293837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384235 Affx-122972370 AX-123254593 12 78485813 CTAAAAGAAAACAAAAATTTATTAAAAATCTGTTC[A/G]CACAGCTATTGAGTTGCTACTGTAAATTCAAATAA R 2 1 2 1 101000 r 74 goat snp31372-scaffold347-2032201 12 4251399 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798446 Affx-122956223 AX-385285379 12 78546609 TAATGTCTAAGGTCTTGAAAAATCATCACTTCGTA[C/T]ATACCTTTCTGGTTGACTAGTCGTTTCAGTTGAGA Y 2 1 2 1 101000 f 74 goat snp31370-scaffold347-1971405 12 4190851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438153 Affx-122931465 AX-123308491 12 78576333 AGACAGGGTTGTAGAGCGAGGAGAGAGCATTCCCA[C/T]GGGAACAAGTGTTTGTCCACTCGGTCTATTGATGT Y 2 1 2 1 101000 r 74 goat snp31369-scaffold347-1941681 12 4161900 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445601 Affx-122925116 AX-123315938 12 78631476 TCTGGCCCCTCTTCAAAGCCTTTCAGGGTTATGTG[C/T]ATTTTCTCTGGGCCACTGGGTGCTAAACTCTTCTG Y 2 1 2 1 101000 r 74 goat snp31368-scaffold347-1886538 12 4106898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429841 Affx-122938163 AX-123300182 12 78665752 TTTCCTCTCCTTACGCCTGCGTTCAGGCAAACACA[C/T]GACTATGCCACTTGCCAGAGCATGCTTTCACCCCT Y 2 1 2 1 101000 f 74 goat snp31367-scaffold347-1852262 12 4072349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769921 Affx-122971771 AX-385257090 12 78706092 TGCCCATTTCTGCCTCTTGACTACGGAAGACTTGT[A/G]TTCACTGAGCCTTTTCACACAGAGATGACCTCTTG R 2 1 2 1 101000 f 74 goat snp31366-scaffold347-1811922 12 4032192 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412219 Affx-122950924 AX-123282569 12 78734635 GAAAATTATGGTAGGGATCAAAAAACTAAATACCT[A/G]CTTGTGTTATTTTCCTGAAAGAAAATGTAAAGCTT R 2 1 2 1 101000 f 74 goat snp31365-scaffold347-1783379 12 4003713 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787364 Affx-122946496 AX-385274389 12 78770615 ATGAAATTTTGATTAGTGCTTTTCATGATGAAGAT[A/G]CTTTTGGAGTAATGGTGCTGTCTTGTAGCGAGTTA R 2 1 2 1 101000 r 74 goat snp31364-scaffold347-1747399 12 3967391 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450365 Affx-122922098 AX-123320700 12 78827892 AACTGAATTTCTGAAGAGATGTGGGTGATATAGGC[G/T]ATTCATGTTCATTTTTATGACTGCTTAAATTCTGA K 2 1 2 1 101000 f 74 goat snp31363-scaffold347-1690122 12 3909933 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443754 Affx-122927121 AX-123314091 12 78872754 CTGGAGAACGCGAAAACTCTGGAAAGGAAAAGCAC[A/G]CATGTTGGATGGGGACATGGAGTTCTGTCTAGCAT R 2 1 2 1 101000 f 74 goat snp31362-scaffold347-1645260 12 3865114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450403 Affx-122922069 AX-123320738 12 78930941 AGACGAAGAGAGAGAAAGCCTCCATTGCTATTAGA[C/T]GTGAACCCTGAAGCAAATTTGAGACCCTCCCTTTT Y 2 1 2 1 101000 f 74 goat snp31361-scaffold347-1587073 12 3805986 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771358 Affx-122929277 AX-385258516 12 78973496 CGTGTACCAAAGTTCTCCGCAGATTTTGCGCAAAT[A/C]CCAGCAAAGAATAGGACGGGGTGTGGAACTTTCCT M 2 1 2 1 202000 r 74 goat snp31360-scaffold347-1544518 12 3763538 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426807 Affx-122940529 AX-123297153 12 79012221 ATGCTTCTGTTTCTAATTCTCAAATCGTTTTCTTC[A/G]CAAAGTGCAATTATATATTTATTTGTACAGCTAAC R 2 1 2 1 101000 f 74 goat snp31359-scaffold347-1505793 12 3725302 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416836 Affx-122948113 AX-123287184 12 79056038 ACCCTCCAAAAAGGAGAACAGTACAACTGAACAAA[C/T]GTTTGGAGGGTAAAATGAAGAGTTTGCCTCCCATC Y 2 1 2 1 101000 f 74 goat snp31358-scaffold347-1461976 12 3681556 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377037 Affx-122977705 AX-123247396 12 79096941 GACACATCTAGAAATGACGAGAGCAACAGACAGAG[C/T]GTAGCCACAGACATGGGTTGTCAGCAGAGGTAGGA Y 2 1 2 1 101000 f 74 goat snp31357-scaffold347-1421073 12 3640677 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418937 Affx-122946504 AX-123289285 12 79147481 AGGTGTGATGCAGAGAAAAGCGGGATCACAGGCCA[C/T]GTGAGCTTTGTCTGGGATAAAAGATAACCTTCGGG Y 2 1 2 1 101000 r 74 goat snp31356-scaffold347-1370533 12 3590261 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426675 Affx-122939917 AX-123297021 12 79178596 ACTCTGGAGTGGGTTACCATGCCCTCCTCTTAGCT[G/T]CACCTTAAAATTCATATCCTCTTCTTTCTCAGATT K 2 1 2 1 201000 r 74 goat snp31355-scaffold347-1339418 12 3558148 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431764 Affx-122936720 AX-123302105 12 79212118 TGCTCTGAGTCAAATTAGAGAACCTCACTTAGACC[A/G]TTGGTCAGATGTCCTATGGGAGATATTGGACGAGA R 2 1 2 1 101000 f 74 goat snp31354-scaffold347-1305896 12 3525028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388129 Affx-122969478 AX-123258487 12 79257015 ACACGGGGACAGAGCAGACAGATGGACGGAAGAAC[A/G]CAGCAGAGCTTTCCAGGCAGACCTGAGAGAAAGAC R 2 1 2 1 201000 f 74 goat snp31353-scaffold347-1260999 12 3480483 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789254 Affx-122939819 AX-385276265 12 79287245 TTAATCCATTTCAACATTCTCAACCCACTTAAGTA[C/T]GGGACTCCAGATTGAATTTATGTCGAAGTGTTTCC Y 2 1 2 1 101000 r 74 goat snp31352-scaffold347-1230769 12 3450233 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445147 Affx-122926164 AX-123315484 12 79334817 TTCATCTGGCAGCACTAGAAATGAGATACCTTGAA[C/T]GGCAGGCATAGCAAAGTCACGATCCCAGTCCTGAC Y 2 1 2 1 201000 f 74 goat snp31351-scaffold347-1183197 12 3402672 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452942 Affx-122920180 AX-123323275 12 79367676 GCCTGCAACAACCATCAGGAAAAGTTTTAGTACTC[A/G]TTTTGCTACTAGTTCACTATACAAACTTCATCAAT R 2 1 2 1 201000 r 74 goat snp31350-scaffold347-1150338 12 3369950 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399626 Affx-122961078 AX-123269981 12 79420183 CATTCTTTTTAAAAAGAACCTCTGTTGCTACTGCT[A/G]CTACTTTTATTATGTGTTTTTGCTTCTTCTGCCCC R 2 1 2 1 101000 r 74 goat snp31349-scaffold347-1097831 12 3317028 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448325 Affx-122924144 AX-123318661 12 79463828 TTCAAGATAGCTTTATCTTTTCTTTCCATCCTTAA[C/T]GGCATGTAGATGGAGAATTTGTATTCCTGGAACAG Y 2 1 2 1 101000 r 74 goat snp31348-scaffold347-1054186 12 3274059 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273754 Affx-1111833820 AX-519547365 12 79482297 ACATAACTGAAACGACCTGGTAGCAGCATATACAC[A/G]AACACTGGAGTAGTAGTCACAGAGACAAACTGATA R 2 1 2 1 201000 f 74 goat GoatD01.005938 12 79482297 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38404503 Affx-122956707 AX-123274855 12 79560651 GGGGAGTAAACTCTGGATTTGTAGTACATCTCACA[C/T]GCGTGTTAGTTGAATGAATAAACAGACTTGCCTGG Y 2 1 2 1 101000 f 74 goat snp31346-scaffold347-957363 12 3178182 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772049 Affx-122938813 AX-385259204 12 79617866 TTTGTTTTTTAACTTATCACCAAATGTGCTTTAAA[C/T]GATTCTTCTCAGAAGATGCTAAGAAACAGAAAATG Y 2 1 2 1 101000 r 74 goat snp31345-scaffold347-900148 12 3120804 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437537 Affx-122931907 AX-123307875 12 79652636 TCTTCCACATTTAAATTACGGCTCTGCCACTTTGC[A/G]TTGTGTGACACTGGGCTTCATTTCTTTGTCTGTGG R 2 1 2 1 101000 f 74 goat snp31344-scaffold347-865378 12 3086346 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378607 Affx-122976572 AX-123248966 12 79737245 CAACACGCCATTGATGAGTCCATGCATGTTCTCCC[A/G]AGGGAATTATATTTGTATGAATGGATTTTGTTGTG R 2 1 2 1 201000 r 74 goat snp31343-scaffold347-780769 12 3002003 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780913 Affx-122971162 AX-385268000 12 79781183 AATTGTGTGAAGCAATTATTTTAAGGTGCCAGGGT[A/G]TGTCTCTACTAAGTGGATTTGTTAGCCTGTCTAGA R 2 1 2 1 101000 f 74 goat snp31342-scaffold347-736831 12 2958003 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433427 Affx-122935082 AX-123303768 12 79815771 TAGTAGGGGCTACACACACACGCACACATGCATCC[A/G]TGCAGGATGGGTCTTATACAGAAATGGAATCGTTT R 2 1 2 1 101000 r 74 goat snp31341-scaffold347-702243 12 2923363 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380107 Affx-122975528 AX-123250465 12 79851397 AAGAATTCCAGGTTCATCATTTCAAAGTCTTGTTG[C/T]GGGGTTGGGGGGTTTATGACTATGAATAAATGGTT Y 2 1 2 1 101000 f 74 goat snp31340-scaffold347-666617 12 2887440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782865 Affx-122929011 AX-385269935 12 79895390 TTCAAAATAATTGTAATGAGATATTACAGTTTTGA[G/T]CTTTGATGGAAAAAAGGCACAATAAAGTATACACA K 2 1 2 1 101000 r 74 goat snp31339-scaffold347-622624 12 2843224 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415836 Affx-122948875 AX-123286185 12 79929563 TAGGCCCTCAGATTTACTTTAAGTGGTATTAAGAC[A/G]TTTTGTCCTTGATGAGTTATTGTCATTTGGGTTCT R 2 1 2 1 101000 f 74 goat snp31338-scaffold347-588451 12 2808903 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402353 Affx-122959053 AX-123272706 12 79989473 AAAACAAACAAAGCAGACAGCAATTCAGAAGTGCA[C/T]GTGGCTTAGATGTTGATGAGTTTTATGCTTACGTG Y 2 1 2 1 101000 r 74 goat snp31337-scaffold347-528541 12 2748205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416411 Affx-122947847 AX-123286760 12 80028411 TAACAAAATACCAGAAAAATGAATTTCCTTTATTA[C/T]GTAAAGACCTCTGAGAAGAAAGGCTATCAACTAGA Y 2 1 2 1 103000 r 74 goat snp31336-scaffold347-489603 12 2709527 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447028 Affx-122924539 AX-123317364 12 80071434 TTGATCTTTCTGTGTATCTTTTTAGTCTCACACCA[C/T]GGTCATACTCTCAGCTCTTCTGACAACAGATGTGT Y 2 1 2 1 101000 r 74 goat snp31335-scaffold347-446580 12 2666537 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414862 Affx-122949149 AX-123285211 12 80116506 GTTATAAAAGATAAGTAGTATGATATTCTCAAAAA[C/T]AGTTCTTTATAAAATGAAAATCAGGACAATGTCTT Y 2 1 2 1 303000 f 74 goat snp31334-scaffold347-401508 12 2621899 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421853 Affx-122944288 AX-123292200 12 80148046 GGGCAGGATTCAATGGGAAGACACCAGGAGGAGAC[A/G]GACAGATCTTTGCAGAAGAGGATGTCAGGGCTTAT R 2 1 2 1 101000 f 74 goat snp31333-scaffold347-369968 12 2590013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796299 Affx-122966357 AX-385283248 12 80180460 TTACTTAGAAACGGTTTGGGGATATATGGCCACTC[C/T]GAGTATTCAGAGATAATTGTAGTGATTGTGATCTT Y 2 1 2 1 101000 f 74 goat snp31332-scaffold347-337554 12 2557333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446262 Affx-122925676 AX-123316598 12 80212403 ACACACAGGTTTAGAAAATCTCAAGTATTTCAAGA[C/T]AGAAGCAACAAAAATAACATGCGTTTAGTACTAGA Y 2 1 2 1 201000 f 74 goat snp31331-scaffold347-305611 12 2524844 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375643 Affx-122978692 AX-123246002 12 80261317 GCATGCACTTCCCGATTCTGTATTTATCAAATGCA[C/T]GGAATGTTAGATTCCTCTGTAATCATGCAGTACGG Y 2 1 2 1 101000 f 74 goat snp31330-scaffold347-256697 12 2475475 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376892 Affx-122977813 AX-123247251 12 80291868 AGGTAAGATTTTCAAGAAAGGGACTGCATTAAACT[A/G]TATTGAGTCTATCAAACAGCAAAACCAGAAACCAA R 2 1 2 1 101000 f 74 goat snp31329-scaffold347-226146 12 2444923 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776205 Affx-122967138 AX-385263333 12 80362440 ACAATTCACCAAACCAATCATCTCCATATTCCTAA[A/G]CCTGATGGTCAAGACCCAACCTTTATCCCACTGGA R 2 1 2 1 101000 r 74 goat snp31327-scaffold347-155574 12 2372643 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394185 Affx-122964919 AX-123264540 12 80392338 TACTTGTTACAACCAAACCTGGGACCCAGAACTAA[C/T]GGGCCACATGGCTCCTTGGAAATGTCATGTAAGCC Y 2 1 2 1 101000 f 74 goat snp31326-scaffold347-125676 12 2343280 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382123 Affx-122974879 AX-123252481 12 80427151 TAACAGGCAAATAAAGGAGTTGCAGCAGAGAAAAA[G/T]AAACCAGGGATGCCAGAAAGGTGTCATAAACCTCT K 2 1 2 1 201000 f 74 goat snp31325-scaffold347-90863 12 2308166 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411018 Affx-122951978 AX-123281368 12 80459785 CATGAAGCCAAAGGAAAAAGCTGGAAAGTCCACGG[C/T]GGGAATACAGTGGCAGCATCACCGCTTTAAAAGAC Y 2 1 2 1 201000 r 74 goat snp31324-scaffold347-58229 12 2277463 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450783 Affx-122921827 AX-123321117 12 80514232 TCATAACTTGTAAAACCACTGGTCTTATTATTAAA[G/T]AATACTCTGTCTGTGGAACTGTCATCGTACAAATG K 2 1 2 1 201000 f 74 goat snp31323-scaffold347-3782 12 2225244 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423541 Affx-122942434 AX-123293887 12 80525037 CCACAGAGTAAAGTTTAATAAATTCCCCAATTCAG[A/G]AATTGTACAGGGTTTATTCTCTGTCTACCGAGTAA R 2 1 2 1 201000 r 74 goat snp32056-scaffold3606-6924 12 2214468 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436767 Affx-122932275 AX-123307105 12 80556038 TTATACCTGAAAATAACAGATTATCCTTTTCAATG[C/T]GCTCATTTTAAAGCTGCTAATAATAAAACTACCTT Y 2 1 2 1 101000 r 74 goat snp32057-scaffold3606-37925 12 2187050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444416 Affx-122926576 AX-123314753 12 80604351 GCTCCTTTCACTGTATTTCCCTTAAGCAAATGGAC[A/G]CACTCTCTGCAGTTTCCATACGCACTCTGAGATGT R 2 1 2 1 101000 f 74 goat snp32058-scaffold3606-86238 12 2138826 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450213 Affx-122922284 AX-123320548 12 80660825 GTTGGTAGTTCACAGCACCAGCCCTTACTTCTCCA[A/C]GGAATCTTCATAGGATTTGAGCTGGTCATCACAAG M 2 1 2 1 201000 r 74 goat snp32059-scaffold3606-142712 12 2082579 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271923 Affx-1111832971 AX-519545703 12 80705912 GTGAAACCAACCCATATGAAATTCATTCACTTTCA[A/G]TGAAATAAATTGGCCATATTATTCATGAAAACAGA R 2 1 2 1 101000 f 74 goat 12_80705912_AF-PAKI 12 80705912 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38420529 Affx-122945306 AX-123290876 12 80717697 ACAGTCCCTTCTTGTATCATCCGTGGGTTCCACAC[A/G]TCCCTGCCATTCACTGTGTCTTACCGCCCTCCTAG R 2 1 2 1 201000 f 74 goat snp32060-scaffold3606-199584 12 2025751 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799179 Affx-122921585 AX-385286109 12 80748593 TACTGGTGCTGCCATGTTTTTTCAATGAACTGAGG[C/T]AAGAGACTAGAGCTCATACAAAGTCCATATTCTGA Y 2 1 2 1 101000 f 74 goat snp32624-scaffold3749-13555 12 1994298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798929 Affx-122953222 AX-385285859 12 80796142 CTTGCTTTTACATGAGAGATATCAGACTCTGGACC[A/G]ATCATTAATAGAGGCATTATTAAATTATTAAACAC R 2 1 2 1 101000 f 74 goat snp32625-scaffold3749-61104 12 1947385 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398311 Affx-122962144 AX-123268666 12 80852349 CCTCATGAAACGGCAGGATGCTGACCAGCTTCTTC[A/G]TCAGCACATGAACATCAACCGCTTGACTCTCCATT R 2 1 2 1 201000 r 74 goat snp32626-scaffold3749-117311 12 1891785 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397649 Affx-122962609 AX-123268004 12 80883535 GCTTAGGCACCGAGCGCCGTGATTTCTAGGCATAT[C/T]TCACCTGAATGAATTTCACCCACATATGTGTGGTG Y 2 1 2 1 101000 r 74 goat snp26839-scaffold2827-12974 12 1861034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434276 Affx-122934779 AX-123304617 12 80926283 GATGAAAAATTTAGACATAGGATTTTGAGCATACA[C/T]GGCCATCTCTTTTCCTTTTCCTTTTTCCCTGCTAT Y 2 1 2 1 201000 f 74 goat snp26840-scaffold2827-55722 12 1818358 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421153 Affx-122944183 AX-123291500 12 80982186 AGAAGCCCGTGGGGATCTGCTCAGATAACCACCTG[C/T]GCAGACGCCACGCCTATCCGCTCACATGTGTACTG Y 2 1 2 1 201000 r 74 goat snp26841-scaffold2827-111625 12 1762619 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410099 Affx-122952834 AX-123280449 12 81020962 TGGTCGTGAAACAGAGCACAGTTCTGATTTGCCGG[C/T]GGGGCTCTCACATCACCCTCCCTGCCTGCTAGGGG Y 2 1 2 1 101000 f 74 goat snp26842-scaffold2827-150401 12 1724468 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419149 Affx-122945745 AX-123289497 12 81090767 AGTGTAAAGACATTTCTCACAGTGGAAGGAAGTGC[C/T]GACTGACAAGAACACATCCCTGGGCTCCAAAAGCT Y 2 1 2 1 101000 f 74 goat snp26844-scaffold2827-220206 12 1654901 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438362 Affx-122931321 AX-123308700 12 81121444 GCTCTTCACCTCTGCCGAGAGGGTTTAAGTAACTC[C/T]GTGGTTACCCTACAGCACTAAAGAGACAAACTACA Y 2 1 2 1 101000 r 74 goat snp26845-scaffold2827-250883 12 1623329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432662 Affx-122936462 AX-123303003 12 81152241 TCCCTTACTCTGCTTTATCTGAGAATAAGCTGGTA[C/T]GGGAGTATTCTGCCATCCGTTTCTGTTGCTCATTT Y 2 1 2 1 101000 f 74 goat snp26846-scaffold2827-281680 12 1592388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388814 Affx-122968904 AX-123259172 12 81196458 ATCCCTGGACTCGCTCTTGCATTTGACTAGCACAA[C/T]GAGAAGTTTCTAGGGGACCATGTGAAGCTACTGGG Y 2 1 2 1 201000 f 74 goat snp26847-scaffold2827-325897 12 1547738 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445611 Affx-122925108 AX-123315948 12 81231127 TCTTGAGACGGGCAGGGCCAAGTCAGGTAGGGGCC[A/G]TGTCCTCGTAAAACCTATAGTTCAGCGAGCAAGAT R 2 1 2 1 101000 r 74 goat snp26848-scaffold2827-360566 12 1513300 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772196 Affx-122927023 AX-385259351 12 81282642 AAAAATAAAATGGCCTCAGTGGCACAGCTCTAAAC[A/G]TTCACGTCTCTTCATTTGTCTGTCCCAGGATGGCC R 2 1 2 1 101000 r 74 goat snp26849-scaffold2827-412081 12 1462152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424960 Affx-122941926 AX-123295306 12 81313259 GCTCAAAGGACATGTCTCCCTGTAACAGACACCAC[A/G]TCCGTGAACCTGGGTTTGGCTTTGGCAATACACAA R 2 1 2 1 201000 r 74 goat snp26850-scaffold2827-442698 12 1431596 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778854 Affx-122954687 AX-385265962 12 81345972 GGTTTCTTTGAAAAGTGACATTTACAACCCAAGGA[C/T]GTCTCGTGTGGTTTCTGTGCCACAGTCCTTCTTAA Y 2 1 2 1 101000 r 74 goat snp26851-scaffold2827-475411 12 1399061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801839 Affx-122938461 AX-385288746 12 81376292 TATACTTCAATTAAAAAATGTGGTTAAAATTAAAT[A/G]TAAAACTAGTAACCTGAACACCGAGGCTATTAAGT R 2 1 2 1 201000 f 74 goat snp26852-scaffold2827-505731 12 1368331 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450547 Affx-122922477 AX-123320881 12 81407148 TGAGACCCAGGGCCCGAACCAAGGACCCTCGCTCT[C/T]CCTGCAGCTCGGAAGACACCAAGAACGTGGACTTC Y 2 1 2 1 101000 r 74 goat snp26853-scaffold2827-536587 12 1337454 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420136 Affx-122946005 AX-123290484 12 81436784 CACCTGGGGAGGGACAGTGATCCTGGGGGACACTG[C/T]GCTTGTGGGTCAGAGAGGGTGTGTGGGAAAGCTCT Y 2 1 2 1 102000 r 74 goat snp26854-scaffold2827-566223 12 1307707 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420691 Affx-122944797 AX-123291038 12 81492668 GCCTTTTCAAGCATCTTCTCTCTTGCTCATTGTCA[C/T]AAATACACGTGTGCATATATGTGTGCATAATGCAA Y 2 1 2 1 101000 f 74 goat snp26855-scaffold2827-622107 12 1251641 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424582 Affx-122942215 AX-123294928 12 81531389 CTTAGGGCTTGTAGTCACCGCTTTCAAAGCTGGGC[C/T]GGGTCTTTCTCCAGGAGCTGTTCCCAGGGTGATTG Y 2 1 2 1 201000 f 74 goat snp26856-scaffold2827-660828 12 1214779 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795406 Affx-122978973 AX-385282362 12 81603093 CATGACGCTTGTCACAGTCCTGAAGATTCCTGCTC[A/G]ATTTGGTCTAGCCTCTCCGTTTAATTGAATGAAAG R 2 1 2 1 101000 f 74 goat snp26857-scaffold2827-732532 12 1144099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404490 Affx-122956716 AX-123274842 12 81651317 AGGGAGGCTCAGCTCCATCTTCCGGGATCCTGCTC[A/G]GCTACATCCCTCCTCCTCCCCGGGCAGCTGCCCTT R 2 1 2 1 101000 f 74 goat snp26858-scaffold2827-780756 12 1097678 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779014 Affx-122977322 AX-385266121 12 81721132 TTTTGGCTTGTTGCCTCATAGATCGGCTCCATAGA[C/T]GTGAAAAATCCCGAGGTGACTAACAGGGAAATACT Y 2 1 2 1 101000 f 74 goat snp23254-scaffold2325-38565 12 1028787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801138 Affx-122958130 AX-385288052 12 81767804 CAGCTTTATTAAGAGAGATTCAAAATTCTGTTAAC[A/G]GGATACACATTGTGGTATATATTTTAAAGCAGAAA R 2 1 2 1 101000 r 74 goat snp23255-scaffold2325-85237 12 981474 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397469 Affx-122962092 AX-123267824 12 81816009 TCCCTGGGCCTGCTCACGGGGACACTGGGGTGTGT[A/G]AAGCCCTCCTCCCCATCACTCCTGGAAAAGCGGCT R 2 1 2 1 101000 r 74 goat snp23256-scaffold2325-133442 12 933311 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421731 Affx-122944382 AX-123292078 12 81848725 AGTGGATTCCTTACCACTGAGCCCACCTGGGAAGC[C/T]GGGATAGCCAGTATCTTGAACTAAATATCTTAAAG Y 2 1 2 1 101000 r 74 goat snp23257-scaffold2325-166158 12 900439 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430229 Affx-122937323 AX-123300570 12 81902164 CATAATCACTTTATCAGTTATTTTCATGTGTACAC[A/G]TCTTAATACAGTGTGGAAATAAAATATTATGCCCC R 2 1 2 1 101000 r 74 goat snp23258-scaffold2325-219597 12 846957 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404079 Affx-122957140 AX-123274431 12 81935404 CCTCCGGAGCTCGGAGGGCCCTAGTGAGCACACGG[C/T]GATTCCTGTTGCTTGTGTCAGCGCTGATTCTAAAT Y 2 1 2 1 101000 r 74 goat snp23259-scaffold2325-252837 12 814217 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777530 Affx-122928953 AX-385264649 12 81965003 TCGTGCTGAGCCAGTACCTGTGTTTCTGCCATTCT[A/G]TAATATCTCTGTGTACAGTTAGTATTATAACGGAA R 2 1 2 1 101000 f 74 goat snp23260-scaffold2325-282436 12 785438 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603273 Affx-1002479485 AX-413837453 12 82002248 GACAATGAAATCGACTTTTTGAGTTGGAAACTCAT[C/T]TTAAGCATTTTAAGCAGAGGAAGAAGCGATCATAT Y 2 1 2 1 101000 f 74 goat 12_82002248_RH-map 12 82002248 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38434294 Affx-122934764 AX-123304635 12 82011141 AGGGTCCAAGGAGAGGGACAATTTCACAGAATGCC[C/T]GCTGCACGGCTGTAGCTGGGTGCTAATTTGCTCAG Y 2 1 2 1 101000 f 74 goat snp23261-scaffold2325-328574 12 738715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400361 Affx-122960029 AX-123270716 12 82040941 CTTATGGAAGAAGCCATATAGTGCAGGAGAGGTTG[C/T]TCTGTGATTGACTTGCTTTCATGACTTGGCCACTT Y 2 1 2 1 101000 f 74 goat snp23262-scaffold2325-358374 12 708771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437767 Affx-122931708 AX-123308105 12 82071184 ACCGCCTAGGCCTTTGGACTTCACGTGGGCCCTCA[C/T]GGAAAGGTTGTCCTTGGTGTCATCATACCGGCTGG Y 2 1 2 1 101000 r 74 goat snp23263-scaffold2325-388617 12 677736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415609 Affx-122948603 AX-123285958 12 82075263 CAGAACGCTCTGGTTCGGTTTGGGAAGGTAAATTG[C/T]AGTCATTATACTGGGGCACAGAAAGGCATACTAAA Y 2 1 2 1 101000 f 74 goat snp14501-scaffold1581-3389 12 673822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603355 Affx-1002479486 AX-413837531 12 82075627 TTTACTCAATTCTTTTTGGAATATAATGACATATT[C/T]TGTTCATTGTTCTACATCTTTGCATTTCTTCCTGC Y 2 1 2 1 101000 r 74 goat 12_82075627_RH-map 12 82075627 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38416337 Affx-122947899 AX-123286686 12 82115505 AGATGAAGGCTCTGAAATTCAAATGCAGTTCAGCA[C/T]GGCTGCAGTATTTTAGCCTGGAAAAAGCCCCAAAC Y 2 1 2 1 101000 f 74 goat snp14502-scaffold1581-43631 12 633447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403139 Affx-122958105 AX-123273492 12 82177363 GTGATGAGTCTGCACAGGACACATGCTTACGGATG[C/T]GAAGTTCATCCTGAGAAAGGTTTGCGAGAAGTTGG Y 2 1 2 1 101000 r 74 goat snp33724-scaffold3963-37610 12 571657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438802 Affx-122930800 AX-123309139 12 82209166 AGTCAACAGAGCAAAAGAAGGGAGACGGTAACGAA[C/T]GAGAGGCCGTGCAGCTGAAATGAAGGGAGAAAGGA Y 2 1 2 1 101000 f 74 goat snp33723-scaffold3963-5807 12 540901 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38440230 Affx-122930676 AX-123310567 12 82217838 TTATTGTTTTGAGAGAGAAGTGGAGGAGAAAATCG[C/T]ACTATAGGAAAACAGTGGCAATTTTGCCTCTTCCC Y 2 1 2 1 201000 f 74 goat snp38177-scaffold4795-1776 12 533372 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424104 Affx-122942029 AX-123294450 12 82275133 GTGATCGTCACCGAGACCCTCTAGACCAACAGGAG[A/G]TAGAGAAGCTCACTTGTCCTTGACTTGCTTAAAAG R 2 1 2 1 101000 r 74 goat snp38178-scaffold4795-59071 12 477137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276818 Affx-1111835537 AX-519550327 12 82318616 AAAATAAATAAATAAATAAAAATAAAATAAAAGCC[A/G]TTGATGTACAAGCAGATTTGTCTGTCTGGATTTGC R 2 1 2 1 101000 r 74 goat Random2.2K-1304 12 82318616 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399005 Affx-122960943 AX-123269360 12 82337806 TCTTTTCCGTCTCTCACAGCTTACAATTCTGTTTC[A/G]CTGATAGAGAAATTGACTCTCATCTCAGCACTTTT R 2 1 2 1 101000 r 74 goat snp38179-scaffold4795-121744 12 414653 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603277 Affx-1002479487 AX-413837457 12 82379148 ATCACTTCATGGCAGATAGATGGGGAAACAGTGGC[A/T]GACTTTATTTTTGGGGGGCTCCAAAATCACTGCAG W 4 1 2 1 303000 f 74 goat 12_82379148_RH-map 12 82379148 T A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38399510 Affx-122961164 AX-123269865 12 82390237 GTTCTGCTGGCATCAGTGGTCCTGTGAGAACTGAC[A/G]TTATCTGGAGCACAAGCGCCTCCAGGAGATACCTG R 2 1 2 1 101000 r 74 goat snp38180-scaffold4795-174175 12 362324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603279 Affx-1002479488 AX-413837459 12 82400895 AAGCAAAGGATCTCTAATGATAAACAAGTAGGTAT[C/T]ATGGCAAATGAATACGAAAACTATTCTAAGACATC Y 2 1 2 1 101000 f 74 goat 12_82400895_RH-map 12 82400895 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38450821 Affx-122921797 AX-123321155 12 82436195 GAACGAAAGACGGGCCTTCATCAGCTCTGCTGCAG[A/C]GAACATGCTGATATTCCAGCTGTCTTCCTGCTCAG M 2 1 2 1 101000 r 74 goat snp38181-scaffold4795-220133 12 314287 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603281 Affx-1002479489 AX-413837461 12 82441116 CCACCTGAGGACAGTCTCTGGATTAAACCTTCTAG[C/T]TAATACTGTTATCTTAAAATGTAAATTATAGGAGT Y 2 1 2 1 103000 f 74 goat 12_82441116_RH-map 12 82441116 T C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38389936 Affx-122968095 AX-123260293 12 82467982 TCCTGCTGCCTGTCCTGTCTCTCCCGGCATAATCA[A/C]CCTGAGATCCACCCATGTCCTAACGGTCTATGGGC M 2 1 2 1 201000 r 74 goat snp38182-scaffold4795-251920 12 281920 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429643 Affx-122937678 AX-123299984 12 82496597 CCCCTTAAACATGTTTGATCACGGAAGGGAACATC[A/G]CCTGGGAGGAGGGAGAGATAGAGAGAAAGCTGTTT R 2 1 2 1 101000 f 74 goat snp38183-scaffold4795-280535 12 253506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396258 Affx-122963320 AX-123266613 12 82534054 GGGTACCTCAGGTACTCAGGTCCTGAGGATGTCAG[C/T]GTGTCTTTTGAGGAGCACACGATTCAACCCGTTAT Y 2 1 2 1 101000 r 74 goat snp38184-scaffold4795-317992 NW_017190165.1 90842 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603283 Affx-1002479490 AX-413837463 12 82539175 CTGGGAATGCAAAAACTATGTAAATCTAGAAAGGA[A/C]TAGGCACATTTGGTTTGAAACTTTTTAAAGAAGTA M 2 1 2 1 101000 f 74 goat 12_82539175_RH-map 12 82539175 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38406431 Affx-122955201 AX-123276783 12 82560643 GGACGAGCAGCGGCCTTCTCTAATCTCATAAGCCC[A/G]TGAATCTGTGGACCCTCCCGTTACTTCTGCTGGTA R 2 1 2 1 101000 r 74 goat snp2036-scaffold1060-12483 NW_017190165.1 62925 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437666 Affx-122931783 AX-123308004 12 82615269 AGTTCCTGGGATTAGCTCTCAGAATGTCCGCCCAA[C/T]AGCTGGGTTCACAGAGGTCAGAGAATGCCCGCCTT Y 2 1 2 1 102000 f 74 goat snp2037-scaffold1060-67109 NW_017190165.1 13485 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603285 Affx-1002479491 AX-413837465 12 82623055 CCTTCTCCTGTTCTCTGTTATAAAAGGTATTGGTG[C/G]CTGTCTGAACCACCTCATCTAAAGAGGCAGCAGGA S 4 1 2 1 103000 f 74 goat 12_82623055_RH-map 12 82623055 C G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603366 Affx-1002479492 AX-413837541 12 82666802 TTCTTAGAATGTTTTGGTTTCTGTTTGCCTTTATT[C/T]AAGTTTTCTGCCATACCTTTCAAATTTGAAAATGC Y 2 1 2 1 101000 r 74 goat 12_82666802_RH-map 12 82666802 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38406606 Affx-122955844 AX-123276958 12 82674103 TTGGCATGCACCACGTCAGAGCTTCTGTCTCCGTA[C/T]GCTTTTGCTATTTTTTCTTCCCAGTGAGTGCTCTT Y 2 1 2 1 101000 r 74 goat snp2038-scaffold1060-125943 NW_017189796.1 49324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603290 Affx-1002479493 AX-413837470 12 82714229 GACTGCCTCTAATACACTTGGTGCAAAGTAAATGT[A/G]GAGGTTTGTTCAAATTAAACCCAGTTTTTTTAATT R 2 1 2 1 101000 f 74 goat 12_82714229_RH-map 12 82714229 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38425310 Affx-122940946 AX-123295656 12 82750833 CTGGGGGGAATGGATGATGACAGGACCCGGGGACA[C/T]GGATCAGCTTCAGTTGCGGTTTTGCTGACGCCCCC Y 2 1 2 1 201000 r 74 goat snp2039-scaffold1060-202673 NW_017189796.1 125343 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392922 Affx-122965710 AX-123263279 12 82779355 AGGATGGACTGGTTTAGGATTTGTGGCCCTTGCCC[A/G]CTTCCTGCTTGGTTCACTGAGGGTTTTTACTGTGG R 2 1 2 1 101000 r 74 goat snp2040-scaffold1060-231195 NW_017189796.1 154115 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435995 Affx-122933501 AX-123306334 12 82826182 TAGAGTCTGATCATTTGCTCTGCTCTTTCTTCACC[A/G]TTCATTGCAATTTCATCTAATTTTGTTTAGTTTTT R 2 1 2 1 201000 r 74 goat snp2041-scaffold1060-278022 NW_017189796.1 198625 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444765 Affx-122926360 AX-123315102 12 82866590 TTCACAGATGGGGAGACTGAGGCCCCACTCCTGTG[G/T]GGGGGGAGGATGCCCACCCTCTGACCTCCCTTTCT K 2 1 2 1 303000 f 74 goat snp27723-scaffold2958-504147 NW_017189796.1 235424 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276684 Affx-1111835538 AX-519550194 12 82886099 AAAGTAGAGGCCTTTTTATTCTAGGTGGGTAGACT[A/G]GGAAATCCTTTGCTAAAATCTGCTTTGAAGAACAA R 2 1 2 1 101000 f 74 goat Random2.2K-1306 12 82886099 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422860 Affx-122943089 AX-123293206 12 82897681 GGGAAGCCAGACTCCCGTGAGGACCCTCCGGGATC[C/T]GTGGTACCTGTTTTGCGCTCAGGCTCTAGGTCGGG Y 2 1 2 1 202000 f 74 goat snp27722-scaffold2958-473056 NW_017189962.1 13632 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404077 Affx-122957141 AX-123274429 12 82950110 TTACAGATGAAGTGGGGGGCAGAGAGGGTTAGCAG[C/T]GAGGCTGCGGACACCAGCCGGAGCTGGAGCCGGAG Y 2 1 2 1 103000 f 74 goat snp27721-scaffold2958-420627 NW_017189962.1 60027 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451399 Affx-122921198 AX-123321732 12 83061704 TGGAATCAGGCAGTGTCTGCCCTTCCGCGTCTGGT[C/T]GATTCCACGGAGCACAGTGTCCGAGAGGCCCAGCC Y 2 1 2 1 101000 f 74 goat snp27718-scaffold2958-309033 NW_017189962.1 170302 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392966 Affx-122965679 AX-123263323 12 83097194 CGCAGTGGCTGAAGTCGCTGGGATCGTGATTGGCA[A/G]CACAAGAGAAAGCCTGTGTAGCTATAGTTTAACCG R 2 1 2 1 201000 f 74 goat snp27717-scaffold2958-273543 NW_017189962.1 205923 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388041 Affx-122969544 AX-123258399 12 83127863 AGCCAGAGTTGGAGGGCCTTGGTGACTGCTGGAGC[A/G]GCGGGGCCCGTGGTCTCCTCTGGTGGCAACCTACC R 2 1 2 1 103000 f 74 goat snp27716-scaffold2958-242874 NW_017189962.1 235339 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378885 Affx-122976501 AX-123249244 12 83161534 GAAAGGAAAGAGATGAAGAAGAGAAGGACACAGGA[C/T]GGAACGGGCCGGGACCCAGGGGAGGCACCGAGAGC Y 2 1 2 1 101000 f 74 goat snp27715-scaffold2958-209203 NW_017189962.1 267711 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436104 Affx-122932673 AX-123306443 12 83209014 TTCTGACACCCCAGTGTTCACCATGCCCCCACCCC[A/G]GGCCCCGGGACCCAAGGACCTGGGACTCCAGGACG R 2 1 2 1 303000 r 74 goat snp27714-scaffold2958-161723 NW_017189962.1 312495 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271780 Affx-1111832972 AX-519545573 12 83247186 TACAAGGTGTGCACTACGATATTTATCATGAAAGA[A/C]GTTTGTAAAAATTTGGAAGAAGTTGAAAAGTATAT M 2 1 2 1 101000 r 74 goat 12_83247186_AF-PAKI 12 83247186 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38402655 Affx-122958378 AX-123273008 12 83294685 GCACCCTCCCCCTGCACCCTCCCACCGCTGTCAGC[A/G]GGCAGATAACCACTCACCTCCCTCCTGTGGGGCCT R 2 1 2 1 101000 r 74 goat snp27713-scaffold2958-76052 NW_017189962.1 372582 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415344 Affx-122948787 AX-123285693 12 83390664 CGGTGGGGCTTAAAGTGGAGCGCCACCTGGTGGGC[A/G]TCTGGGGAAGTTTGTAAAAATGGAACTGTGTGCCA R 2 1 2 1 101000 r 74 goat snp16369-scaffold1726-210060 NW_017189962.1 461155 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382000 Affx-122974077 AX-123252358 12 83460165 TTGAAAGTGGTCAGGGCACCCTTTTGGACAGAAGG[C/T]ATCAGAACAGCTGGGAAGTTTCTGCATGTCTCATC Y 2 1 2 1 102000 r 74 goat snp16368-scaffold1726-140559 NW_017189962.1 530271 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410876 Affx-122952599 AX-123281226 12 83492056 TCAAAGAACCACGGTCATACAGACAGTGAGGCAGC[A/G]TGGGGATTAAGCTGAGGATTAAGCAGAGGGACAGC R 2 1 2 1 101000 f 74 goat snp16367-scaffold1726-108668 NW_017189962.1 561146 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789129 Affx-122959914 AX-385276142 12 83550647 TGTTTCCAATATAATCTTCACTCATTTTTTGAAGC[A/G]CTCAATGGGACAGCAACCATGTTTTCCTTTTACAA R 2 1 2 1 101000 r 74 goat snp16366-scaffold1726-50077 NW_017189962.1 619615 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434880 Affx-122934349 AX-104088695 12 83587575 CCTTTTTTCATAGCACGACAGCAACAAATTTTGCA[A/G]TAATACTTTCCTTTTCCACGCTTCATGTATTTTGC R 2 1 2 1 600000 f 74 goat snp16365-scaffold1726-13149 12 83587575 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790601 Affx-122934349 AX-385277603 12 83587575 CCTTTTTTCATAGCACGACAGCAACAAATTTTGCA[A/G]TAATACTTTCCTTTTCCACGCTTCATGTATTTTGC R 2 1 2 1 101000 r 74 goat snp16365-scaffold1726-13149 NW_017189962.1 656511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276686 Affx-1111835539 AX-519550196 12 84217130 CAAATCTAATTGTGGATTTATCCATTTTTCCTTTC[A/G]GTTCTTCCTTTTATTTCTTGCTTCTTGTGTTTTAC R 2 1 2 1 103000 f 74 goat Random2.2K-1307 12 84217130 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320803801 Affx-986696236 AX-385290546 12 85514016 CTTTACCAATGGCTTTGCATTTTGTTGTTCCAGAC[A/G]AATCAGCATTTAAATTATCTATTACAAAGAGAGCA R 2 1 2 1 600010 r 74 goat 12_85514016 12 85514016 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 320803805 Affx-986696238 AX-385290549 12 85816264 CAGACACAGCCTGCCTACTGCATACCCACCTTCAT[A/G]GTGCTGTGGGCACATAACATCTTTTCAAAGAAGAG R 2 1 2 1 600010 r 74 goat 12_85816264 12 85816264 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320763011 Affx-986697540 AX-385250988 12 85816301 TGCTGTGGGCACATAACATCTTTTCAAAGAAGAGA[A/T]TTGGAACCAAATAAGCACTTCTTCGCTCCTTCTCC W 4 1 2 1 600010 f 74 goat 12_85816301 12 85816301 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 320765694 Affx-986697552 AX-385253157 12 85816348 TAAGCACTTCTTCGCTCCTTCTCCCAAACTCACAC[A/G]TTAGATAAATCTCCTCTCTTCTCATACGGAGGGTA R 2 1 2 1 600010 r 74 goat 12_85816348 12 85816348 Ancestral_priority_1043 ancestry 0.702 recommended IMAGE 10K 10K ancestral 320763025 Affx-986697554 AX-385250999 12 85816376 CTCACACATTAGATAAATCTCCTCTCTTCTCATAC[A/G]GAGGGTAGGACTATAAGTCCTCCCCTTGAAACTGC R 2 1 2 1 600010 f 74 goat 12_85816376 12 85816376 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320765704 Affx-986697558 AX-385253166 12 85816530 TAACTAATGATGAGAGCTTGGATAGAAGTATTATA[A/G]ACAGTAAAGAGAGATCTGTTGTGTGTTTTAAATTT R 2 1 2 1 600010 r 74 goat 12_85816530 12 85816530 Ancestral_priority_1043 ancestry 0.728 recommended IMAGE 10K 10K ancestral 468271926 Affx-1111832973 AX-519545705 12 86381143 ATCTGCAGTGATTTTGGAGCCCCCCAAAAAAATTA[A/C]GTCTGACACTGTTTCTACTGTATCCCCATCTATTT M 2 1 2 1 103000 f 74 goat 12_86381143_AF-PAKI 12 86381143 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38434486 Affx-122934624 AX-123304827 13 19267 ATCAGTTAATGTGAGCAGATGGGCTTCCCTGGTGG[C/T]GCAGACAGTAAAGAATCTGCCTGCCAATGCAGGAG Y 2 1 2 1 103000 f 74 goat snp27400-scaffold291-1335507 13 223096 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463247337 Affx-1109888882 AX-514733008 13 29672 CATGTGTCTCGTCGTTCCCATGGTGTTACAACTGG[A/G]GAATCAGGCCTTGTCTCGTGTGGAGTCATGTAAGT R 2 1 2 1 201000 f 74 goat 13_29672_AF-PAKI 13 29672 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320778045 Affx-122956916 AX-385265161 13 49110 AAGACAGATCTAAACTAAGAAAAGCACAGTCGCTG[A/G]TAAGTATTGCTTACAAAACATTCCCCTCCATAATG R 2 1 2 1 102000 f 74 goat snp27399-scaffold291-1305664 13 252654 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392641 Affx-122966452 AX-123262998 13 136962 AGTTTCCTATGTCCTTTATCTCAGTGTTAAAGTGT[C/T]ATTTCTGCCAGTATTATAAATGTGTGGTTCACCCA Y 2 1 2 1 101000 f 74 goat snp27398-scaffold291-1217812 13 340150 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766422 Affx-122927071 AX-385253798 13 182500 TGTAGAAGTCAAAGAGAGCACAGGCCTTAGATTAC[A/G]TAATGCTGCCTGTTTAATATTGTGTAGACCAGGTG R 2 1 2 1 101000 f 74 goat snp27397-scaffold291-1172274 13 385923 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781688 Affx-122935426 AX-385268770 13 236266 GTGTCTTTCAGATGGTTGACAACAGGCTATATGCC[A/G]CACCTACTGATTTTAGTATTTAGTACAGTTTAAAC R 2 1 2 1 101000 f 74 goat snp27396-scaffold291-1118508 13 440518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396750 Affx-122962784 AX-123267105 13 267416 TGAATAAAAATGAAATATCTGAATGGTTTCTTTTG[A/G]CTCTGAGAAGCAAGATGTATAAAACACAATGGGTT R 2 1 2 1 101000 r 74 goat snp27395-scaffold291-1087358 13 471103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765712 Affx-986697562 AX-385253174 13 280794 GAGGGTAGGAGATAGGGTCTTTAGAGGGCCAATGA[C/T]CAAGTCTAAGCAGAGTCCAAGCAAATCCAGTTCTT Y 2 1 2 1 600010 r 74 goat 13_280794 13 280794 Ancestral_priority_1043 ancestry 0.576 neutral IMAGE 10K 10K ancestral 320763035 Affx-986697564 AX-385251008 13 280882 AGTCAGGTAGGAACTGATAGGCATGAGGGGCAGAA[A/G]GAGAAACATTAGACAAACCCAGATCTGGTTCTGAC R 2 1 2 1 600010 f 74 goat 13_280882 13 280882 Ancestral_priority_1043 ancestry 0.606 recommended IMAGE 10K 10K ancestral 320765720 Affx-986697566 AX-385253180 13 281300 AATCAGCCATACTTCAATTAAAATTAAAAAAGAGC[A/C]TGGAAACAGTATCACTTCAAGTGGAAAACATTAGA M 2 1 2 1 600010 r 74 goat 13_281300 13 281300 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 38422140 Affx-122943544 AX-123292487 13 301759 GAAAACGATTGATTAGAAAGAGACCACTGTTCCCC[A/G]CCAAACTGGCATGGTTACCATCAGATTGATTATTT R 2 1 2 1 201000 r 74 goat snp27394-scaffold291-1053015 13 506508 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434726 Affx-122933927 AX-123305067 13 336870 AGAGTCCTGCTTGAGTTCTTCTTCACTCAGGCCTC[A/G]TTTTAGGGCAACTGACAATGTGGCATTTGCTTGCT R 2 1 2 1 102000 r 74 goat snp27393-scaffold291-1017904 13 541749 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764674 Affx-122954852 AX-385252306 13 382511 CAACAAGCTGAAGAGATGGAAAATTTGAGAGAAAC[A/G]AGAATTCCAGTTAGAATTTTGGACAGTGAAATATT R 2 1 2 1 101000 f 74 goat snp27392-scaffold291-972263 13 587933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387375 Affx-122970434 AX-123257733 13 424274 ACTTTGGCACAGACTTCGTGGGCCAAGGAGAAACA[C/T]GGACAAAGACAAAAGAAGAAGCTCCAGGGAGAAGA Y 2 1 2 1 101000 f 74 goat snp27391-scaffold291-930500 13 629578 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438675 Affx-122930878 AX-123309012 13 454116 AACTTTGTTCATAAGGGTATAGGCCAGATGAATGG[A/C]CCTACTGATCTGGGCCAACCTCAGCTGAGCTCAGC M 2 1 2 1 101000 f 74 goat snp27390-scaffold291-900658 13 660059 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788089 Affx-122935238 AX-385275109 13 501774 ACACAATACGCCTCCTTGAAAAGGAAGTTTAATCT[A/G]CATGCATGTGTTTGAATTGAGTCACTGTTAAGAAT R 2 1 2 1 201000 r 74 goat snp27389-scaffold291-853000 13 707763 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799398 Affx-122971203 AX-385286328 13 531468 GAGCAGCTTTTTGGCAATTTCCTATTTCTAATAAT[C/T]CTCTTATTTAAATCAGCCCTCAGATTTTTTTATTA Y 2 1 2 1 101000 f 74 goat snp27388-scaffold291-823306 13 737480 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436786 Affx-122932260 AX-123307124 13 560411 ATAAGGTACCAAAATGGCTATGTATGAATTACAAC[A/G]CTGTCAGTTTCAGCATTTAATTCATCAGACACTTT R 2 1 2 1 101000 f 74 goat snp27387-scaffold291-794363 13 766576 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450080 Affx-122922797 AX-123320415 13 598367 TCACAATATAACGGTGCAATCCAAGTAATCTGTTA[C/T]AATTCTATATATCTGTTTATCTTTTTCATCTTTTG Y 2 1 2 1 101000 f 74 goat snp27386-scaffold291-756407 13 804835 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448717 Affx-122923847 AX-123319053 13 642636 GAAGCTGGGTGGTTATTAGGAATGTGTGGGAGCAG[C/T]GGGAGAGACGCTGCCTGGAAAGAGCAAGATAGAAA Y 2 1 2 1 101000 f 74 goat snp27385-scaffold291-712138 13 849114 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444910 Affx-122926249 AX-123315247 13 680493 ATAATAGTGATGATAGTGGTTACTATTTAATGAGT[A/G]CTGATTATATAGTAATGATAACTTCAGGCAGTGGT R 2 1 2 1 101000 r 74 goat snp27384-scaffold291-674281 13 885345 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385262 Affx-122972079 AX-123255620 13 712733 TGGCTATCTGTAGCAATGAAAATATTAGGAGATTA[C/T]GGACTGAAAGTTAATGGCTCAATGGTAAAGAATCT Y 2 1 2 1 201000 f 74 goat snp27383-scaffold291-642041 13 917493 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276688 Affx-1111835540 AX-519550198 13 731360 TATAATAATTGTTTTTAGCTGTTCTCTTAGAATTG[A/G]AAACAAATGTCATCTAGTTTCCAAAGAGCAGTGTA R 2 1 2 1 101000 f 74 goat Random2.2K-1309 13 731360 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784311 Affx-122945401 AX-385271362 13 748698 CTAGATTCATAGCGTTAGAATTAAACACTTTTAGC[A/G]TCTATATACAGGCTTCTTTCACACTATTTCCTGGG R 2 1 2 1 101000 r 74 goat snp27382-scaffold291-606076 13 955320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454313 Affx-122919249 AX-123324646 13 807305 AAAGATGGGGAGCAAAAGAATTGCGAACTCATGAT[A/G]TTGTCTACATGGGTATTCAGGCTGTGAGAGTAAGA R 2 1 2 1 101000 f 74 goat snp27381-scaffold291-547469 13 1014847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415965 Affx-122948422 AX-123286314 13 860432 AAAACTGCTGTAAAAATAGCTCCTTATCACAAAAA[C/T]GTATTAAAATCTAATGTCCAAAATTACATGGTAAA Y 2 1 2 1 101000 f 74 goat snp27380-scaffold291-494342 13 1067255 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788012 Affx-122941078 AX-385275033 13 927798 TGTCTCAAAGTAAGGGGAGATCACACCAGTTAGCA[C/T]AAAGAGGTTTAGAAGACTTGTCATTTCAAACTTGG Y 2 1 2 1 101000 f 74 goat snp27379-scaffold291-426976 13 1134520 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375736 Affx-122978621 AX-123246095 13 971229 TTTTTTAAACACCCTCCTCTGCCCCTGCAGAAGAC[A/G]CATTTATTGGGTACCTATTATCAGTTGAGACTAAG R 2 1 2 1 201000 r 74 goat snp27378-scaffold291-383545 13 1178112 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423855 Affx-122942770 AX-123294201 13 1024230 TCAGAAGAAAACACACCCTTAGAGGATATTCTTTC[A/G]TTCCATGTAACTAACAGCTGGAATATTGCTGTTGC R 2 1 2 1 101000 f 74 goat snp27377-scaffold291-330544 13 1231572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417465 Affx-122947186 AX-123287813 13 1060813 ACACACACACACACACAGAGCCAATAAAGAAGGAA[A/C]TCAATAAATGACTGAGTAAATTAAGCAGAGTGTTA M 2 1 2 1 201000 r 74 goat snp27376-scaffold291-293961 13 1269529 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391900 Affx-122966956 AX-123262257 13 1108171 TCTGTCTGGCTTGGGTGTTTGGATTAAAGGTGATG[C/T]ATTTGGGATTTTTCATTTCTCATTTCCATTTAAAA Y 2 1 2 1 101000 f 74 goat snp27375-scaffold291-246603 13 1317301 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418079 Affx-122946605 AX-123288427 13 1156375 TGCGTTTTATTTATGAGTAAAGTGGGCTTCCGAGG[C/T]GGTACTAGGGGTAAAGAATTTGCCTGCCAGTGCAA Y 2 1 2 1 201000 f 74 goat snp27374-scaffold291-198399 13 1364780 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411634 Affx-122951580 AX-123281984 13 1202283 GGAATGCAGAAGTAATGAGTTAGCAGTCCCCTAAC[A/G]TGTTCTTTATCTTTCTTCATCATTGGTTGTGGAAT R 2 1 2 1 201000 r 74 goat snp27373-scaffold291-152491 13 1410472 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422509 Affx-122943296 AX-123292855 13 1285726 TTACAGATTAGGAGCACATACAGAAGGTGCTGATA[C/T]GGATGCGTTGTGTGTTGCACCGAGACATGTTGATC Y 2 1 2 1 101000 f 74 goat snp27372-scaffold291-69048 13 1495163 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454201 Affx-122919291 AX-123324534 13 1326780 TAGAATCCATGCAATTCACACCTGTTAGAAAAAAG[C/T]AAGCTCAATAACACTTTCCAACAGCAATGATGATT Y 2 1 2 1 101000 r 74 goat snp27371-scaffold291-27994 13 1536670 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428949 Affx-122938886 AX-123299291 13 1355172 CTTTCATTAGCTGGGCATTAAACTTCTGGGCTGCA[C/T]TGCAGGTAGGCTGAGGCAGCTTCGAGGCTCTGGCA Y 2 1 2 1 101000 f 74 goat snp22336-scaffold2206-213958 13 1565097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401160 Affx-122959366 AX-123271513 13 1392892 GTTTTAAAACTATATTGATTACTCAAGGCTCTGTA[A/C]TGAGTGGCTCAACATTTGTTCCAATTGCTTGTACT M 2 1 2 1 101000 r 74 goat snp22335-scaffold2206-176238 13 1602579 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425077 Affx-122941251 AX-123295423 13 1460673 GACGATTCTCCAGGGAATGGTATATCTATGAACTA[C/T]GAGCAGCATCACTCACGTCAGCTGAATGTCTGGAG Y 2 1 2 1 101000 f 74 goat snp22334-scaffold2206-108457 13 1673312 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390218 Affx-122967783 AX-123260575 13 1491415 AGGAAGGAGGCAGATAAGATGGAGCTGTTTCTGCC[G/T]CAAGGGGATCCCTAGACCCAGTACTATCTCAAGTA K 2 1 2 1 202000 f 74 goat snp22333-scaffold2206-77715 13 1704101 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274138 Affx-1111834029 AX-519547741 13 1512756 AAGCTGGCTGGCATGTCACTGTCCAGGGAACCACA[A/G]TACCATTTCTACTCTGATTTTGTAAATACATTTTT R 2 1 2 1 201000 r 74 goat GoatD01.015091 13 1512756 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320774224 Affx-122946646 AX-385261361 13 1536034 CAAGGTCCACATTGTTAATGTGGTTTTCCTAAAAG[C/T]GTATTTTTATAACTCAACATTTATATTATGTTCAT Y 2 1 2 1 101000 f 74 goat snp22332-scaffold2206-33096 13 1749667 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395344 Affx-122964033 AX-123265699 13 1566612 ATATCCTTCATTCCCTAAACTGCCAAATTAGACAA[C/T]AGAAAAAATGAAACAGTTTTACCCTCCACTTCAGA Y 2 1 2 1 101000 f 74 goat snp22331-scaffold2206-2518 13 1780633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776899 Affx-122972581 AX-385264023 13 1571977 AGTCTTAAGGTAGCTGCCTAAATAGGACTGGCCTA[C/T]AAATGCTCTAATGCGGTACAACATTAATAAGGCCC Y 2 1 2 1 101000 r 74 goat snp17694-scaffold1834-174736 13 1785653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431538 Affx-122936216 AX-123301879 13 1608254 TTTCTTTTTCAGTTCCCCAAACTGTAACTGATTCT[A/C]TTTCTCCAGAAAGCTCTAAAACACACATACACACC M 2 1 2 1 101000 r 74 goat snp17693-scaffold1834-138459 13 1819710 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767074 Affx-122969740 AX-385254362 13 1640279 AGTGTGGTCATAAAGAAGCAAGTTTCACTGATGTG[C/T]GATTCATTTCCAGCAGCAGGGCGAGCATTACAGAA Y 2 1 2 1 101000 f 74 goat snp17692-scaffold1834-106434 13 1851564 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784298 Affx-122924053 AX-385271349 13 1669035 CATCACTGGAGCAGCTAACACTCCAACCATAAGAA[C/T]GCATGTTCTCTGCCAACTTCCAGATGCATATGAGA Y 2 1 2 1 101000 r 74 goat snp17691-scaffold1834-77678 13 1880526 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433627 Affx-122934591 AX-123303968 13 1707232 CCGAGCCCAAAGCAGCAAAAATGCCCAGCTGGGCC[A/G]TGAGTCTGTGACCAAAAATGAATGTTTATTGCTAC R 2 1 2 1 101000 r 74 goat snp17690-scaffold1834-39481 13 1918874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390770 Affx-122967890 AX-123261127 13 1745406 ATTAACTGACAGAGCTGGAATCAGGAGACTCCATG[C/T]AGCTGGAATTCTTCTTGTGCTGACCGTAAGCAAGT Y 2 1 2 1 101000 r 74 goat snp17689-scaffold1834-1307 13 1956730 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452012 Affx-122920914 AX-123322345 13 1746888 CAATTGAAGCAACTTAGCAGACACATGCACACGTT[A/G]TATTTCTTCCTTGGTGGCTGCATTTTAGAAACACA R 2 1 2 1 201000 r 74 goat snp26126-scaffold2727-76 13 1957756 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383844 Affx-122973155 AX-123254202 13 1783978 CTCAGGAACAAGAGTGCTGTGTGAAACAGGCCTTT[A/G]TCAAAGGTTTGGTGGGAGCAGAGGCGAGTTCCAGC R 2 1 2 1 101000 f 74 goat snp26127-scaffold2727-37166 13 1995271 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447690 Affx-122924623 AX-123318026 13 1832684 CAACAAAAGCAGAAAATAGCAAATTTGGTAAGGCT[A/G]TGGAGAAATTGGAACCCTTGTGCATTGTTAGGGAG R 2 1 2 1 101000 f 74 goat snp26128-scaffold2727-85872 13 2044510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412299 Affx-122950867 AX-123282648 13 1864404 GAAATTGGTATGATTGCATTGTGGCTTTTCCCTGG[A/C]TATTCTAAACTAAAATTTTGAAATTATATTAACTC M 2 1 2 1 103000 f 74 goat snp26129-scaffold2727-117592 13 2075818 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413542 Affx-122950609 AX-123283891 13 1902191 CCCGACCTGGCTGTCTTGAGGATCGCCGTGTATGA[C/T]GACAACAACAAGCTGATCGGCCAGAGGATTCTGCC Y 2 1 2 1 101000 f 74 goat snp44850-scaffold611-24076 13 2113946 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387242 Affx-122970571 AX-123257600 13 1936509 ATTTTTTTATTCATGCAGCTTTATTGTATCTGCTT[G/T]GTACCAGCACTGGGCTCTGTGCTGGCGAGAAAAGG K 2 1 2 1 201000 f 74 goat snp44851-scaffold611-58394 13 2148472 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793289 Affx-122942668 AX-385280267 13 1977085 GCACTCAGAATTTTAGTAACTTCTTATTGAATTTC[A/G]TTTCCCCTCAAATCCCTTCTACATGTAGATTAATC R 2 1 2 1 101000 r 74 goat snp44852-scaffold611-98970 13 2190326 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448593 Affx-122923397 AX-123318929 13 2023836 CAGATGGACACAGCTTTCCATCTGTGTCTCAAAGT[A/G]CGGCTTGCAAACAGCCTGCAACAGAATCATCCCTT R 2 1 2 1 101000 f 74 goat snp44853-scaffold611-145721 13 2237463 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794173 Affx-122978386 AX-385281139 13 2141753 AAAAGAAAAACCACTTTGCCAAAATGGGCTTTAAA[C/T]ATGTACAACTTTACCCATTCATTACTTTCTATCAA Y 2 1 2 1 101000 r 74 goat snp44855-scaffold611-263638 13 2360062 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382728 Affx-122973613 AX-123253086 13 2172767 GGAACACACAAGGAAGCAGAGGTACTGCAAGCAAA[C/T]GGGCTATGTGCTTTTGAGGTGTGGTGTGATGTGTA Y 2 1 2 1 101000 f 74 goat snp44856-scaffold611-294652 13 2391746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766208 Affx-122948658 AX-385253608 13 2203102 ATGTAATTGGGCTGTTTGGAAGATTTCAGAGGTGA[C/T]ACCTATAGGACTCATAACACGGAGTCTGGCACGTG Y 2 1 2 1 101000 f 74 goat snp44857-scaffold611-324987 13 2422463 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428790 Affx-122938407 AX-123299132 13 2253522 TTCTCATTCTGCTTCCAAGGAGCTGGGGATCCCAA[C/T]GTCAGCCTGTTAGGTCTCACGCTAGATTTGGCTGT Y 2 1 2 1 201000 r 74 goat snp44858-scaffold611-375407 13 2474397 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386762 Affx-122970123 AX-123257120 13 2373109 TAGAAAGACAAATATTTACTCAAGAAAATTGCTAA[C/T]GTTATCCTTCTTCAGCTCTGATATGGAAAATAAAG Y 2 1 2 1 101000 r 74 goat snp44860-scaffold611-494994 13 2595551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431457 Affx-122936493 AX-123301798 13 2415681 AGTATAAGGGTTTTCAGAGCTGCATGATTTTGCTG[C/T]ACATTTTCATACATTCTGTGATGCCCAAGCACTAC Y 2 1 2 1 101000 r 74 goat snp44861-scaffold611-537566 13 2637212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427844 Affx-122939729 AX-123298187 13 2455817 TATCCAAAAGATTGTTAAAAGAGAGAGAAATAAGA[C/T]GAAACACAGCTGAAATTCAGTGATAGATGGACAGT Y 2 1 2 1 103000 r 74 goat snp44862-scaffold611-577702 13 2678017 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800005 Affx-122953180 AX-385286928 13 2487474 CCAGGCATTTGGGAAAACTCAACATCATAGTTACC[G/T]CTTCCATAAAATAGTTCCTGCTGTCATTCAGTCAG K 2 1 2 1 101000 f 74 goat snp44863-scaffold611-609359 13 2710350 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447788 Affx-122923943 AX-123318124 13 2545515 GAACTTGCACCATCTATGTTAGGCCACCGGCGACC[A/G]TTTGAATATCAGAGAGTGCCCCGCCTTGGGCTCTC R 2 1 2 1 303000 f 74 goat snp44864-scaffold611-667400 13 2769131 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388619 Affx-122969136 AX-123258977 13 2575475 ATGTGGTTTTATCACATTTTATCATGAAGAAATTT[A/G]TAGAAGTTCCAAGTGATATGTTAAAGTAATTTTCA R 2 1 2 1 101000 r 74 goat snp44865-scaffold611-697360 NW_017219217.1 12874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383362 Affx-122972664 AX-123253720 13 2661688 AATTGGGAGCTGTTTAACATATCTAACTGTAAACA[C/T]GTTTTGACATGGTGCTCACTAAGCACAGACACACA Y 2 1 2 1 101000 r 74 goat snp44866-scaffold611-783573 13 3008178 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407343 Affx-122955287 AX-123277694 13 2703958 CATCTTTCTTTTGACCTCCCCATTCTGGCTCAGAC[A/G]CTAAAGAATGTGCCTGCAATGCAGGAGACCCGGGT R 2 1 2 1 103000 f 74 goat snp44867-scaffold611-825843 13 3051391 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787317 Affx-122973526 AX-385274342 13 2740416 ATTTAGTTTTTTACAAGATGAGGTGAAATATCCAT[A/G]TATTCTTTACATTTGGGAGATTATTATATTCTTTG R 2 1 2 1 201000 f 74 goat snp44868-scaffold611-862301 13 3087587 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780726 Affx-122939832 AX-385267816 13 2783344 TTTCAAAGGCATTTCTATGTCTTTAAATACTGTAT[C/T]GTGATTTCTAGCTTAGGAGGATGTGTCAGAATTTA Y 2 1 2 1 101000 r 74 goat snp44869-scaffold611-905229 13 3129875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792959 Affx-122958909 AX-385279937 13 2834256 ATTCTGGTACCTTCTCAGGAGGCTATCTGGAGTGA[C/T]ACAGTATACTTGGTCAACTTTTCCTATTTGTTCCT Y 2 1 2 1 101000 f 74 goat snp44870-scaffold611-956141 13 3181325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272735 Affx-1111832979 AX-519546435 13 2842965 TTCGAAGTTCAAGAGGGAAGATGTGATTTCCCTCT[A/C]GACGCCGAGAGGAAAATGGCTTCATCTCGCTTGGA M 2 1 2 1 102000 r 74 goat 13_2842965_AF-PAKI 13 2842965 G T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38422148 Affx-122943538 AX-123292495 13 2874909 TGACTATATAATCTTCCATTTTTATAGCTCTATAT[A/G]TTATCTTTAAATTTTCTCTAGTACATACAGCTCTT R 2 1 2 1 101000 r 74 goat snp44871-scaffold611-996794 13 3223540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396815 Affx-122963283 AX-123267170 13 2926325 TACAAGATATGTCTCTGCCTCAGAGGTTTCAGGGC[A/G]CAATGAGTTTAGATTTAGAGTATTTACGTTTTCCC R 2 1 2 1 201000 r 74 goat snp44872-scaffold611-1048210 13 3274702 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425064 Affx-122941259 AX-123295410 13 2973462 AAGACTTCCAGCTCAAGCTCCTACAGCCACCCTTT[A/C]GAGGAAGCCGTTCCTCTCCAGCTGCAGGCTGGGTG M 2 1 2 1 102000 f 74 goat snp44873-scaffold611-1095347 13 3321918 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435530 Affx-122933403 AX-123305870 13 3009364 GGGAAGGCATTTTGAGAGCCAATTCCTTCCTCCCT[A/G]CTTAGGCTGAAACAATATTTTATCACAGTTTTCTT R 2 1 2 1 101000 f 74 goat snp44874-scaffold611-1131249 13 3358135 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449626 Affx-122923193 AX-123319961 13 3040028 AACAATTATATCTGTAAAGATCCTTTCCCTTGTCA[A/G]ACTAACAGTTTACAGGGATTCGTACTTAACATCTT R 2 1 2 1 101000 f 74 goat snp44875-scaffold611-1161913 13 3391460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375682 Affx-122978662 AX-123246041 13 3075485 AAAGTACCAGCTCGATTTAATTTCCTTTGGCAAAA[C/T]GTAGGAAATATATGTTTAAAACAAAAATACAAGCA Y 2 1 2 1 101000 f 74 goat snp44876-scaffold611-1197370 13 3426973 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437951 Affx-122931620 AX-123308289 13 3173512 AAACATAAAATATTGTCAGCTCCTGTTTCAGGAAT[A/C]TTTCTTCCTCCAGCAGACTTTGTTGAGCACCTTCT M 2 1 2 1 101000 r 74 goat snp44878-scaffold611-1295397 13 3526868 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778902 Affx-122920935 AX-385266009 13 3222075 AAGCAAGTGGAAAAGAACTGCTTTGTCACATAGCC[A/G]TCAGTTGTTCCACTTTTTAATGAAGCAAATTATTA R 2 1 2 1 101000 f 74 goat snp44879-scaffold611-1343960 13 3575694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445468 Affx-122925214 AX-123315805 13 3318556 ATGCCATAAAATAAATTAAATTTTCCTGGGCACTG[C/T]GGTTTCTGTCTGCCTTGGCTTTTGATTTGGCTTTT Y 2 1 2 1 101000 r 74 goat snp44880-scaffold611-1440441 13 3671784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765583 Affx-122959567 AX-385253063 13 3353555 AGAAAGCGTAGATAATTCAGCAATGAGACTGGCTC[A/G]CTTAGAATAGTTAGAGAGGGCCGATAGAATGGGGA R 2 1 2 1 101000 f 74 goat snp44881-scaffold611-1475440 13 3706660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451794 Affx-122921496 AX-123322127 13 3387795 GGTGGCTGCAATGCCCACTCAGCCCAGGGGACCCA[C/T]GGCAGCAGGACCTGGCCCACATACCTTCCTGGCAC Y 2 1 2 1 201000 r 74 goat snp44882-scaffold611-1509680 13 3740760 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436929 Affx-122933191 AX-123307267 13 3420697 CTCACCTCTGCCCCCAAATTTTCCATAACTGAAGT[A/G]CTAAGTAATGGTTTAAAAGCAAAAGGTTGGTATTG R 2 1 2 1 201000 r 74 goat snp44883-scaffold611-1542582 13 3773028 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375488 Affx-122979140 AX-123245847 13 3525496 CTTTGATTCACACACCCATCCCCAAACCAATTCCT[A/G]TGTCAGGAGGCATGTAATGCTTTTGTTGGCCAGGC R 2 1 2 1 201000 r 74 goat snp44885-scaffold611-1647381 13 3878476 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797241 Affx-122951131 AX-385284180 13 3578319 AGACAGGAGCCAGAGACGAAGTGGAAACCATGCAA[C/T]GATATTTCAAGCCTTTTCTCCCATAATGTCTGCTG Y 2 1 2 1 101000 r 74 goat snp44886-scaffold611-1700204 13 3931194 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415897 Affx-122948471 AX-123286246 13 3623732 AGTGTCATGGAGGATGGCAAAGAAGGCCACTGTGG[C/T]GGAGGCACAGAGAGCAAGGGAGAGGGTGTTAGGGG Y 2 1 2 1 101000 f 74 goat snp44887-scaffold611-1745617 13 3977212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409677 Affx-122953070 AX-123280028 13 3655000 AGAGAGACCTTCTCATATAAAATCTGCAAAATAGT[A/G]CAACGATATTGATTTCAAAGATAAACGTTGAGAAG R 2 1 2 1 101000 f 74 goat snp44888-scaffold611-1776885 13 4008245 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441216 Affx-122929521 AX-123311553 13 3687100 AACAACTCTCATCAGAAATGGCAGAATCAGCTGGT[A/G]CCTTGATCTTGTATTTCCCAGAGATAAATAAATTT R 2 1 2 1 201000 r 74 goat snp44889-scaffold611-1808985 13 4040757 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276689 Affx-1111835541 AX-519550200 13 3692358 GGGCTTTGGTTGTTCCTGGCACTGTTTCTCCACTT[A/T]TCTGGGTGTTTGAAATTTTTCCTGCTTGTGAGTAA W 4 1 2 1 102000 f 74 goat Random2.2K-1311 13 3692358 T A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417222 Affx-122947296 AX-123287570 13 3721116 TGTCCATGGGAACAAAGAGGAGGAATGTCCCTTAC[A/G]CATTTCCATGGTTTCCAACTACTTTTCACACAGAC R 2 1 2 1 201000 r 74 goat snp44890-scaffold611-1843001 13 4075406 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408845 Affx-122954013 AX-123279196 13 3796996 TCATGCTTCTGAGCTCCCATTTACTTCTATGGCAA[C/T]GGCAGGAGTTTGAGAGTGTGCTGACATGGCCCATT Y 2 1 2 1 101000 f 74 goat snp44891-scaffold611-1918881 13 4151381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433445 Affx-122935067 AX-123303786 13 3826886 GCTCATTTACAGGGCCTGAGGATGAAAAGGGGGGC[A/G]GTATTTCTTAGTCACTGAACCAGAATGATGACGAG R 2 1 2 1 101000 r 74 goat snp44892-scaffold611-1948771 13 4179145 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773099 Affx-122970846 AX-385260242 13 3857837 AATGTTAGTAGATTGATTACTCCAGGGCTTGATGC[C/T]ATCAAAAATAATTAAGACCTTTCCTTATATAAATT Y 2 1 2 1 101000 f 74 goat snp44893-scaffold611-1979722 13 4210201 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437724 Affx-122931739 AX-123308062 13 3954846 AATGTATAATGAAGAAATCTTAGGATTCTTATCAG[C/T]AGACGATATGAACTAACAAATCTATACAGAAATTC Y 2 1 2 1 101000 f 74 goat snp44895-scaffold611-2076731 13 4309630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390848 Affx-122967828 AX-123261205 13 3991998 AACCTCACACTCCATTTCAGTAGTTCTGGGGTGGG[C/T]GCTTGAGCTTGTGCATTTCTGACATGCTCCCAGAG Y 2 1 2 1 201000 r 74 goat snp44896-scaffold611-2113883 13 4346671 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424215 Affx-122942493 AX-123294561 13 4083099 CACATCTGCTCTACATGTAGAAGGTCCTGGGTTCA[A/G]TTCCCAGTGGAACCACAAGTTTGCATGTATTTCCA R 2 1 2 1 101000 f 74 goat snp44897-scaffold611-2204984 13 4438551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416007 Affx-122948387 AX-123286356 13 4124456 ATAGGTAAATTAGTGACCCCTTTTCTCCCTTCAGA[C/T]GATAAGGAGGGAGCCAGTGTAGGGACCTTGAAGAT Y 2 1 2 1 201000 r 74 goat snp44898-scaffold611-2246341 13 4480172 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450869 Affx-122922223 AX-123321203 13 4181495 GACCTTCAGCCTGATCTTCCTGGGAGGTCTGCACC[A/G]TGAATAGCAACCAGAACTTTCTCACCTTCAGGCAA R 2 1 2 1 101000 r 74 goat snp44899-scaffold611-2303380 13 4537548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797510 Affx-122939930 AX-385284449 13 4220793 TATGTTGCAAGATGGCTGAACCTCGAAGACATTAC[A/G]CTAAGTAAAATTATCTAATCACAGATACTGCGCAT R 2 1 2 1 101000 f 74 goat snp44900-scaffold611-2342678 13 4576465 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396203 Affx-122963362 AX-123266558 13 4255983 TACTCAAAGAGTAGTCCATGCACCAAGGACATCAG[C/T]ATCACTGGCACCACTTGAAAGCTAATTTCAAATGA Y 2 1 2 1 101000 f 74 goat snp44901-scaffold611-2377868 13 4612184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799119 Affx-122938495 AX-385286049 13 4302059 TGGGAAACAAACTATACCAAAGTAGGTAGAATGAC[A/G]AGAATCTATATCTCAGTTGATTTTATAAACATTGC R 2 1 2 1 101000 r 74 goat snp44902-scaffold611-2423944 13 4659467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415703 Affx-122948528 AX-123286052 13 4334712 GAACCTAGTTGGCATCTTACCCTGCAAATGTTGCC[A/G]TCATAGACATGTTTAGGGAGTGCTTGATGAGCTAC R 2 1 2 1 101000 f 74 goat snp44903-scaffold611-2456597 13 4692211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394030 Affx-122965001 AX-123264385 13 4370916 GTGTACTCACTCTGGGATATGTTAATCATCACTGC[C/T]AAGGTTTGAAGTAGTTAAAAAAAAGTCCAACCCAC Y 2 1 2 1 101000 f 74 goat snp44904-scaffold611-2492801 13 4728812 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770814 Affx-122966964 AX-385257978 13 4422785 GAGAGCTGAATGATGGATAGGAGCTACCCAGATGA[A/G]GAGGGTTAAGGAACAGCATTTCAGAAGGAAGGAAC R 2 1 2 1 101000 r 74 goat snp44905-scaffold611-2544670 13 4780783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405908 Affx-122955581 AX-123276260 13 4458086 CTCTCCAGAAGATGGCTCTCATACCTTTGCTTCCT[A/G]TTTCCATCTTGGTTGGAATAATACTTGCAAGTTTA R 2 1 2 1 201000 r 74 goat snp44906-scaffold611-2579971 13 4815970 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273935 Affx-1111833906 AX-519547541 13 4478235 GTATGAAACCTCTCCAGAGCAGAGCTCTGCAGAGT[A/G]AAGGGGCATTTTGCAACAAACGGTAGAGAGACAGT R 2 1 2 1 202000 r 74 goat GoatD01.010067 13 4478235 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38380761 Affx-122975120 AX-123251119 13 4487639 CATGTGACCTAGGAATTCGACACAGGTGTAGACAC[A/G]CAACAGAGAAACAAGCTTATATGCACTGAAAAATG R 2 1 2 1 101000 f 74 goat snp44907-scaffold611-2609524 13 4845537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417642 Affx-122946849 AX-123287990 13 4516793 GAAGGGTTCTTAAGGTTCTATTGGTTGAAATATAC[A/G]CCCAATATGTCTTTATCCATGAAGCATGAAGAAAG R 2 1 2 1 101000 f 74 goat snp44908-scaffold611-2638678 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393103 Affx-122965584 AX-123263460 13 4522350 CTCACGTGGGAGGGAATTGCCCAGCGCCTAACTAA[C/T]AGAGAGTAGGAGGCATCAGGGGTCATCTTGCAAGC Y 2 1 2 1 201000 f 74 goat snp12800-scaffold1493-5078 13 4883165 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789965 Affx-122952209 AX-385276971 13 4592668 AATGTCATGACTTCAGGCTGCATGAGCTTAACAAT[A/G]TTTTTAGTTTCAATATTATCCCTAATATTTGAAAT R 2 1 2 1 101000 f 74 goat snp12801-scaffold1493-75396 13 4952948 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402526 Affx-122958479 AX-123272879 13 4697472 AAATGTAAAAGGAAGAAACAGTAATTGAGTGGGTG[C/T]GCTTTGCTTGTTTTTTTGCTGTTGAATTCAATTAG Y 2 1 2 1 101000 f 74 goat snp12804-scaffold1493-180200 13 5057322 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766692 Affx-122975463 AX-385254036 13 4737227 GCTCATCATGGTAATGGATATATTCTAGATGCAGG[C/T]ATAATTCCTCCTTAAGAAATTAGAACTAATAGAAG Y 2 1 2 1 101000 f 74 goat snp12805-scaffold1493-219955 13 5098082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272410 Affx-1111834271 AX-519546137 13 4747629 ATTAAGTGTTTATTTTAAGCCATTGTCTTTGGGGT[A/G]TTT R 2 1 2 1 101000 f 74 goat GoatD01.028342 13 4747629 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320791983 Affx-122934392 AX-385278971 13 4792923 GTAATAAAGCCAAATATCTAATATTTGACTCTAAG[C/T]CATTGGAATCAAAATTGATTCTAACCCGCTGAAAA Y 2 1 2 1 101000 r 74 goat snp12806-scaffold1493-275651 13 5155027 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379722 Affx-122975883 AX-123250080 13 4843933 CACATTCTGCCTCTGGGCAGTTTACGCAAATGTAA[C/T]GTACAGTTTAAGGTTGAGTGGGACTTGGTGAGGAG Y 2 1 2 1 101000 f 74 goat snp12807-scaffold1493-326661 13 5205210 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382200 Affx-122974004 AX-123252558 13 4904248 CCCTGGAGCATCTGGCACCAGCACCATGCACAGGC[A/G]CCGCTCAGGGTGCAAGTGTGGCCTCGCGACATAGA R 2 1 2 1 101000 r 74 goat snp12808-scaffold1493-386976 13 5264987 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383531 Affx-122972626 AX-123253889 13 4936627 AGTTACCCCAAACTATGGGCAAGCTCGGGTGGTAA[C/T]GGAGGTGTGGAGAGAACAGAGGGCAGGCACCCTGG Y 2 1 2 1 101000 f 74 goat snp12809-scaffold1493-419355 13 5297666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414184 Affx-122949668 AX-123284533 13 4966684 AATAAGCTATAGCTTAATGAAAATAATATTCACAG[C/T]TCTACGTCTACCTTAAAAAGACCTGTAAAAAATTA Y 2 1 2 1 101000 r 74 goat snp12810-scaffold1493-449412 13 5329117 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782501 Affx-122927319 AX-385269577 13 5009174 TCTCTAGAACAGTAGAAATGTATTCTGCTTCAACA[C/T]ACCTGAGGAATAAACCCTCTTCCCTTAGTTACAAC Y 2 1 2 1 101000 r 74 goat snp25706-scaffold265-13439 13 5372978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389028 Affx-122968631 AX-123259386 13 5044330 AAATAGGATCATTTTTCCTGTCTGTCTGACTCATT[A/G]TGTTTCATGGGAGACTCACATATCCTAAGACCCAA R 2 1 2 1 201000 r 74 goat snp25707-scaffold265-48595 13 5408129 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776870 Affx-122970422 AX-385263994 13 5089853 ACTCAAAGGGAGTCAGAGAGGGCTTTCACCAAGTA[C/T]AAAATGGTAATTAATACAGCCCAGCAATTTAGCTC Y 2 1 2 1 101000 f 74 goat snp25708-scaffold265-94118 13 5453840 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448113 Affx-122924308 AX-123318449 13 5140551 TGGAAGAAAAAATTGCATATATTTAGAGAAGGGAA[G/T]CTCAATGCTCTTGGTCATTAATATGATCAATATGC K 2 1 2 1 101000 r 74 goat snp25709-scaffold265-144816 13 5505191 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437060 Affx-122933091 AX-123307398 13 5171045 CCACTTACTCATCTGCCTGTGGTCAGCTGGAGGGT[C/T]AGCTAGAGACTCACTGGTCTAGATTGATTTCACTT Y 2 1 2 1 101000 r 74 goat snp25710-scaffold265-175310 13 5536236 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430819 Affx-122937451 AX-123301160 13 5242134 AAGGAAGATGGGGCTTAGAAATGGATCCAAATCCA[C/T]GCAACCCTTGTGATCCCATGGTTAAGAATCTGTCT Y 2 1 2 1 201000 f 74 goat snp25711-scaffold265-246399 13 5608605 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439074 Affx-122930308 AX-123309411 13 5272610 GATGCAAGATCCAGACATATTCACAAAACTGACCT[A/C]GGAGGGGATCTGAAATCAAAGAAAGAATTCCCTTG M 2 1 2 1 101000 f 74 goat snp25712-scaffold265-276875 13 5639741 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418963 Affx-122946080 AX-123289311 13 5321435 ATCTTCCTTGCTCTAAAAATAAAAATTCACTTATG[C/T]GGTTGTGACTTTGGAACTTAGAGAATCTTGAAATG Y 2 1 2 1 101000 r 74 goat snp25713-scaffold265-325700 13 5688570 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38427306 Affx-122940145 AX-123297649 13 5353638 TCAATCTCATGCCATAAATGTTTCACATGCCATAA[A/G]CAAGATGGAGAATAATTTAGGCAATATGTATAGAA R 2 1 2 1 101000 f 74 goat snp25714-scaffold265-357903 13 5721030 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412151 Affx-122951083 AX-123282501 13 5412449 ACCAAGCCATTTTACTGGAGATAGGACCTGGGAGC[A/G]TGATTCACGTTGTTGGAAAAGACAGTTGCTGACTT R 2 1 2 1 101000 r 74 goat snp25715-scaffold265-416714 13 5781076 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769856 Affx-122944513 AX-385257026 13 5443307 TTCAACTTTGACTATTGGGCCTCCACAAATGACCT[A/G]TTTCCTTGTGTAAGCCTTAACCGTTTTCTTGACAA R 2 1 2 1 101000 f 74 goat snp25716-scaffold265-447572 13 5811701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272701 Affx-1111832988 AX-519546405 13 5447308 GTGTTAGATGATATACTAGATAATGGAGAACAGAT[A/G]TAAAATTTGTCAGTCAGTCAGTCAGTTCAGTTGCT R 2 1 2 1 201000 f 74 goat 13_5447308_AF-PAKI 13 5447308 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450156 Affx-122922737 AX-123320491 13 5478527 ATCACAGACTCTCAGTTCAGCTGAGTCAATCAGTC[A/G]TGTCCGACCCTTTGCGACCCCATGGACTGCAGCAC R 2 1 2 1 101000 f 74 goat snp25717-scaffold265-482792 13 5847219 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381681 Affx-122974729 AX-123252039 13 5509921 AAGTTTTATCTCTTGTGGTATGAACATTTAACAAG[C/T]GTTCTAACCTACTAAGTTTAAAATCAGGAGTGGAG Y 2 1 2 1 101000 r 74 goat snp25718-scaffold265-514186 13 5877555 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774384 Affx-122951185 AX-385261520 13 5541673 TAATTACCCACATTCCACTTCACCCTTGGGTTGAA[C/T]ATCATTTACATGATTTTCTAATGACTATTTCCAAA Y 2 1 2 1 101000 f 74 goat snp25719-scaffold265-545938 13 5910030 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802200 Affx-122953155 AX-385289104 13 5577261 TGGTGGTATAACCAGCCAACATGACTCAGGAAGAG[A/G]GTGTCAGGTATTTTTGTCCTGGGCAAAACAAATGC R 2 1 2 1 101000 f 74 goat snp25720-scaffold265-581526 13 5946625 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421313 Affx-122944089 AX-123291660 13 5622787 CTTGTATGACCCTGAAAGTGAATCTTGACAAACGA[C/T]GGATAAGAATTTGGTGGATAAATACCCCAGCTCCT Y 2 1 2 1 101000 f 74 goat snp25721-scaffold265-627052 13 5993248 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427750 Affx-122939251 AX-123298093 13 5656595 TGATGCCAGCTAAGGAACACAACACAGGCTATTCC[A/G]AAAGAGAGAGTAGTACCTCTTCTGTATCCTCTTCT R 2 1 2 1 201000 f 74 goat snp25722-scaffold265-660860 13 6027143 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388293 Affx-122969391 AX-123258651 13 5686126 CTTTAGTAGTGACATCGTGCTTTCAGAGAATGTTC[A/G]TGCAGTGGGAAGTAGAATAAAGTGTCTTCCATCTG R 2 1 2 1 101000 f 74 goat snp25723-scaffold265-690391 13 6057625 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275054 Affx-1111834659 AX-519548636 13 5734108 CCTGTGACAAGATGCAGACTACCTGCAGTAACAGC[A/G]AAAGCAAGGTG R 2 1 2 1 101000 f 74 goat GoatD01.044687 13 5734108 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320790668 Affx-122945704 AX-385277670 13 5745866 GTTTATGCACAGAATGTGACATGAATTAGAAAAAT[A/G]CAGTCTTTGTCAAATATTACTTTGAAAATGCTGGA R 2 1 2 1 101000 r 74 goat snp25724-scaffold265-750131 13 6117742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416678 Affx-122947583 AX-123287026 13 5828791 ACCTGCCCCACTGTCCTCATGCATAAGGATGGAGA[C/T]GTTCTTCATAGTTAAATTCTTCCTGCCCCTTTTAA Y 2 1 2 1 101000 r 74 goat snp25726-scaffold265-833056 13 6204399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778751 Affx-122954390 AX-187706288 13 5882829 CCAACACCTGTGTTGTGAACCTCTTTCCTGATAGA[G/T]TGGATAGAAAGAAGCCAAATGATACCAGGTGGTAA K 2 1 2 1 101000 f 74 goat snp25727-scaffold265-887094 13 6259595 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781504 Affx-122973365 AX-385268589 13 5920437 ATTATTATATCATAGACTCTGTGAGTAAATGCAGA[C/T]AAAAGGGCAATGATGTGGTGCCAAATGATGCTGTG Y 2 1 2 1 101000 r 74 goat snp25728-scaffold265-924702 13 6298130 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799654 Affx-122972071 AX-385286583 13 5998258 CCAACACAATAGTAGTATCGCTCATATAACTGATG[C/T]GGGATGTAGAGAACTACACTGCAACAAGCTGGGTC Y 2 1 2 1 101000 r 74 goat snp25730-scaffold265-1002523 NW_017189547.1 22064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785215 Affx-122934641 AX-385272261 13 6058455 ACATGATTCTGCCTCTGGATAAAATCTTACAAACA[C/T]CGAAACTACTTGACTTTACCCAAGGTTTGCATTTT Y 2 1 2 1 101000 r 74 goat snp25732-scaffold265-1062720 13 6436476 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438187 Affx-122931829 AX-123308525 13 6096733 GGAACACTCGGGGCCCTGCCTCTTCTGAGGGCTCA[C/T]GAGTGTCATTTGAGTGGAAGGTCAAACCCATAAAC Y 2 1 2 1 101000 r 74 goat snp25733-scaffold265-1100998 13 6475220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418507 Affx-122946431 AX-123288855 13 6139950 TGTAACTAACCTTGTAAATGTCTGTTTCCCAGACA[C/T]AGTACTAAGCATGTTCCTGCACTAACCCCTTTATT Y 2 1 2 1 101000 r 74 goat snp25734-scaffold265-1144215 13 6518463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379179 Affx-122976313 AX-123249538 13 6189030 CATTATGTCTTTTGTAAAGAAGGGTAAACAGAAGT[G/T]CAGGAAGTTCAGAGGTTTCACTAGGTTCCTTTGCC K 2 1 2 1 101000 f 74 goat snp25735-scaffold265-1193295 13 6567681 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447868 Affx-122923882 AX-123318204 13 6285221 ATTTGCACATGAGCTCAGAAAAGCCCCAGAACTCA[C/T]AATCCATTTTTCATCAGCATAAGCTGTGCTGTTTA Y 2 1 2 1 101000 r 74 goat snp25737-scaffold265-1289486 13 6665135 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797374 Affx-122946697 AX-385284313 13 6315050 ATCATTTATACTTTAGAATAAGTTATACATGTATT[A/G]CCCACTCTCAGGATATTTATATTTGAGATCTGTTC R 2 1 2 1 101000 r 74 goat snp25738-scaffold265-1319315 13 6694856 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405079 Affx-122957407 AX-123275431 13 6347267 TTGATTACACACAATTGATAATTCTGGGGTTGAAC[A/G]TAAGGTCGGGTGGCCTTGACCACATCCCCAGAATG R 2 1 2 1 201000 f 74 goat snp25739-scaffold265-1351532 13 6727259 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780193 Affx-122946479 AX-385267289 13 6403968 TGCAATCAGGCTTATAAACCAATCAGGCTTCATCA[A/G]TCTTATAAACCATTCCCTTGTGCTTTCTCTGATGA R 2 1 2 1 101000 f 74 goat snp25740-scaffold265-1408233 13 6784355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389957 Affx-122968079 AX-123260314 13 6510159 TTTAAGGGGGAGGATAAAAAGTGACTGATTCACTG[G/T]TAACTGATCAACTACTGCGCACCTGGCATTGTCAG K 2 1 2 1 101000 r 74 goat snp25742-scaffold265-1514424 13 6891486 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431498 Affx-122936243 AX-123301839 13 6539897 ATATTTCCACCAATGCAAGAAAAGGATCAAGGTCA[C/T]GAAGCTGCTACAACAGGTAGGCAGTTGAGGGGTCT Y 2 1 2 1 101000 f 74 goat snp25743-scaffold265-1544162 13 6921454 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384371 Affx-122972231 AX-123254729 13 6583455 ACAGTCAGAGCTGAAAACCACTGCTCTAATGGATA[C/T]GCCTAACTCCAGATACGATCAATCACTAAAATCAT Y 2 1 2 1 201000 r 74 goat snp25744-scaffold265-1587720 13 6965470 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770977 Affx-122924309 AX-385258140 13 6641929 AAAGAAGTCTCCAATAAGACAACCTAACAAGATCA[C/T]CGACTGCTTCTTCATTCTTCATTGTTAATACTGTT Y 2 1 2 1 101000 r 74 goat snp25745-scaffold265-1646194 13 7022341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424012 Affx-122942097 AX-123294358 13 6672553 TGTAACTTTGCCTAAAATAGGGGTTTCCCTGGTGG[C/T]GCATATGGTGAAGAATCTGCTTACAATGCAGAAGA Y 2 1 2 1 103000 r 74 goat snp25746-scaffold265-1676818 13 7053211 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786309 Affx-122971576 AX-385273343 13 6730025 TGGCTGAGATAATTAAGCCAGTGATGGTATCTCCT[A/G]TTGGAATTTCAGGCGAAGTCACTGCCTTCTTTGCA R 2 1 2 1 101000 f 74 goat snp25747-scaffold265-1734290 13 7110635 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382063 Affx-122974924 AX-123252421 13 6792736 GCCCATGGGGTCACAAAGAGTCTGACATGACTGAG[C/T]GATTAACGCTTTAACTTTCAACACAACTTTAGGAG Y 2 1 2 1 101000 r 74 goat snp25748-scaffold265-1797001 13 7174219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415083 Affx-122949459 AX-123285432 13 6832490 GTGAGGAAGCTGAGTCAGTCCCTAGGCACAGCAAC[A/G]CCATGAGAAACTTTGGCTTATCAGAGATAGACTGT R 2 1 2 1 101000 r 74 goat snp25749-scaffold265-1836755 13 7215069 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391914 Affx-122966945 AX-123262271 13 6862491 CATTCTTGCTCTTAGAGTCAAGTATTCATCCATCC[A/G]TTCATATATCCATCTGCTGTGTTCTGTTTATTTCT R 2 1 2 1 101000 r 74 goat snp25750-scaffold265-1866756 13 7245132 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274077 Affx-1111834025 AX-514741444 13 6908414 CTTTTAAGCTCAGCCCCACCATGACATTCATATAA[A/G]CCCCTAAAATGTCTCCAGTGCT R 2 1 2 1 102000 f 74 goat GoatD01.015011 13 6908414 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38454287 Affx-122919271 AX-123324620 13 6922349 TGGGACTGAAGGATCGACAGAGTAACTTAGAGAGT[A/G]CCAGGTTGTCATTAAAGACTTAGAGACTTAAACGC R 2 1 2 1 101000 f 74 goat snp25751-scaffold265-1926614 13 7305129 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773984 Affx-122924691 AX-385261122 13 6967390 AGTTTACCTTTCATGTCCACTGCCAGTAAATGAGT[A/G]TTTTTATTACTAGTTCAAATTTCACTTCCTTCTTG R 2 1 2 1 101000 f 74 goat snp25752-scaffold265-1971655 13 7350575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788471 Affx-122955858 AX-385275488 13 7010710 TATTAATTTTTCACTAAATATTAAGTTTGATTTTC[A/G]TATAAACCCTGACCCTAAATGTCACATTTATCTCA R 2 1 2 1 202000 f 74 goat snp25753-scaffold265-2014975 13 7394369 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418732 Affx-122946226 AX-123289080 13 7067460 CATGTGGAGTACAGTTGTTGACATTCATTTCCTTA[A/G]ATGCCTTAAGACTTGCTCATGAGTTTTCTCTGTCT R 2 1 2 1 101000 f 74 goat snp25754-scaffold265-2071725 13 7452120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771205 Affx-122946818 AX-385258363 13 7131801 TTTGGTAACCTGCTCTGTTGCTTATATTTAATATA[G/T]AAAAGTCCAGCTATGCCTTAGAAATCATGCCCAGT K 2 1 2 1 101000 r 74 goat snp25755-scaffold265-2136066 13 7517354 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402280 Affx-122959111 AX-123272633 13 7164879 TATAGCCTTAGCGTCTGAGGTGCTGTGGTTCCCCT[A/G]TAGGTGAGGATGATGCAGGTGAAGGAGTCTCCTCA R 2 1 2 1 201000 r 74 goat snp25756-scaffold265-2169144 13 7548461 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765242 Affx-122939687 AX-385252779 13 7201193 TAGAATAACAGTTAACATTTAAGAAATTCAAGTAC[A/G]TCCTCAAAAAGGACACTACTTGCCCATCATTTATG R 2 1 2 1 201000 f 74 goat snp25757-scaffold265-2205458 13 7585291 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784312 Affx-122958518 AX-385271363 13 7235048 ATAAGCAAACACCAAGAGCCTTAAGTCCTCTAAGT[A/G]TGTCACTTGATTCCTTTAGAGTGAAGGTGGCAGAA R 2 1 2 1 101000 f 74 goat snp25758-scaffold265-2239313 13 7619229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380355 Affx-122975355 AX-123250713 13 7267021 AAGCAGGCAAAAGAAAGTTTTCTAGGTTGAAATAC[G/T]AATTGACCTGGTGGAGAGGAGCACCCTGATGCTTA K 2 1 2 1 201000 f 74 goat snp25759-scaffold265-2271286 13 7653105 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420636 Affx-122945222 AX-123290983 13 7337814 CTTAAAACATAGCTTTGGAGGAATGGCTTACAGTT[A/C]TTTGGAGCAGATCAGTTCAGTTCAGTTCAGTTGCT M 2 1 2 1 201000 f 74 goat snp25760-scaffold265-2342079 13 7724751 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786730 Affx-122937245 AX-385273760 13 7415065 GGAGAATGGGATAACTCAGTAGAAAGACTGATATA[A/C]GGGTGGTAAATGATTTTTAGAACCAGGACAGCACT M 2 1 2 1 101000 r 74 goat snp25762-scaffold265-2419330 13 7802450 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389071 Affx-122968598 AX-123259429 13 7492729 GAAGGAGTCACTATGTTATTGTAACTCTCTCATCT[A/G]TCCCAAAGATATGACTTTCCCTTCCCCCCTCTCAT R 2 1 2 1 201000 f 74 goat snp25763-scaffold265-2496994 13 7880458 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409979 Affx-122953283 AX-123280329 13 7544995 AGTGTTTACTTCTTGCTCTTTTGTCGTTTCCTGTA[C/T]GAAAAATAAGTTTCTTGCCTCATTATATTGTGAGG Y 2 1 2 1 101000 r 74 goat snp25764-scaffold265-2549260 13 7933578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800408 Affx-122956229 AX-385287329 13 7591463 TTCTATCAGGGATTCTCATCCAGCTTTACTATTTA[C/T]GTAGCAACACGTCCTGTGTTTGACTGTCATAAAGA Y 2 1 2 1 101000 r 74 goat snp25765-scaffold265-2595728 13 7980930 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431461 Affx-122936490 AX-123301802 13 7620225 GGTGTTGGGACTGTCATCTTGGACTGTTGTTTAGT[C/T]GCTTCTGTCATGTCCAGCTCTTTCGTGACCCTGTG Y 2 1 2 1 101000 f 74 goat snp25766-scaffold265-2624490 13 8008702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276826 Affx-1111835542 AX-519550335 13 7645265 TTATCACATCAGTTTTTAAAGAGATTTGGGGATTT[A/G]TATATCCTTTTAGTTATACTTTATTGTGTTGAAAA R 2 1 2 1 101000 r 74 goat Random2.2K-1313 13 7645265 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380382 Affx-122975334 AX-123250740 13 7713533 GGGAATTTGGCTTCAGCCCAGGGACTCTTCTGCTG[A/C]TGTGAGAGTAGTGTCATTATTGTGGGGGTTATATT M 2 1 2 1 201000 f 74 goat snp25768-scaffold265-2717798 13 8102676 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770199 Affx-122962365 AX-385257366 13 7769881 ATTTGGGTTATAATGTCATCTTGTATAATGGGAAA[G/T]AAGCATGTGGTTCATTGCCGCATATGCAGAATTCC K 2 1 2 1 101000 r 74 goat snp32386-scaffold369-29066 13 8160750 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406233 Affx-122956114 AX-123276585 13 7825336 TGGGGCTCCTCCCATTAGACTCCTGGGAACTCTGA[A/G]TGCTCCATGAATCCCAGCATGAAAACCTTCAACTA R 2 1 2 1 202000 f 74 goat snp32387-scaffold369-84521 13 8216115 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799055 Affx-122972624 AX-385285985 13 7865562 AGAAGGCAGGGTTCAAGGTCACTCTATGCAAACTG[C/T]GTATGTTAAACTGGGAATCTAGAGTTTTTCTCATT Y 2 1 2 1 101000 f 74 goat snp32388-scaffold369-124747 13 8256959 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401000 Affx-122959693 AX-123271353 13 7894224 TATTCTTGGAGCCAAGGGAAATTCCAGTTCCAGTT[A/G]TCCAATAGTCATCTTTGAGGGTCTTAAGCAAAAAG R 2 1 2 1 101000 f 74 goat snp32389-scaffold369-153409 13 8285674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410972 Affx-122952018 AX-123281322 13 7928770 GGACGCTCAGCATGGCTTTCTGCGCTCAGGCTGGG[A/G]AAGAGTTGTCACACTCACCATGAGCAAGGCACCTG R 2 1 2 1 101000 r 74 goat snp32390-scaffold369-187955 13 8320554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770027 Affx-122943721 AX-385257194 13 7968837 TTGTTCCAGAACCTTTCTTGCTATAGCAAAGGTAC[A/G]ATTACTGTTCTTTGAACTGCACACCAGACTCCCTT R 2 1 2 1 101000 r 74 goat snp32391-scaffold369-228022 13 8360527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782486 Affx-122961082 AX-385269562 13 8004757 CCCTGGGAAAGTCAAAACATCGCAAGTCAGGGACC[A/G]TCTGTATTCTCAAATGCCAAATGATCCCAAAGGAG R 2 1 2 1 101000 r 74 goat snp32392-scaffold369-263942 13 8396239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272720 Affx-1111832997 AX-519546423 13 8022207 CTGGTAGGCTGCGGTCCATGGGGTTGCGAAGAGTC[A/G]GACACAACTGAGCAGCTTCCCTTTCACTTTTCACT R 2 1 2 1 303000 f 74 goat 13_8022207_AF-PAKI 13 8022207 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320773833 Affx-122920233 AX-385260973 13 8064095 AAACTTAACAAGAAATTTGTAAGAGGTGTAAACTA[C/T]AGGCCAATCTCGTGTGTAAACAAAAAAACATTATC Y 2 1 2 1 101000 r 74 goat snp32393-scaffold369-323280 13 8455569 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418243 Affx-122947033 AX-123288591 13 8095897 TGTAAGGGTGTGAGTGGGAGCCTCTTTAGGGTGTC[A/G]TAAGGTGAGGCGCATCATGCTCAGTGCTGTATTCC R 2 1 2 1 101000 r 74 goat snp32394-scaffold369-355082 13 8486647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801001 Affx-122940501 AX-385287915 13 8146828 TACATTTCACAGACATTATGAGAGAGAAGTATCTG[A/C]GTTGTGGGAAGTTCTCGCCTTCAGGAATTTAAGAC M 2 1 2 1 101000 f 74 goat snp32395-scaffold369-406013 13 8538228 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390038 Affx-122968432 AX-123260395 13 8202201 AACTAGGAAAATTAATGCCAAACTAAATAAAAATT[A/G]CTGAAACATTAATACAACTCTTTTTGAGGACCAAT R 2 1 2 1 101000 r 74 goat snp32396-scaffold369-461386 13 8593739 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431368 Affx-122937035 AX-123301709 13 8248766 GTTGTGTGTAGAATTTGTGGGAAAATGTGTAAAAA[G/T]ATAGGATACCGGGAAACCAGCTCAGCCAGGTCATA K 2 1 2 1 201000 f 74 goat snp32397-scaffold369-507951 13 8641964 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428287 Affx-122939389 AX-123298630 13 8318124 CCTTTTTCATGCTATAAGCAATAGATCTAAGATCT[A/G]TTAGCAATATTAAGGTAGTCTTATTACTGCCCATT R 2 1 2 1 101000 r 74 goat snp32398-scaffold369-577309 13 8711619 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384928 Affx-122972332 AX-123255286 13 8348332 TCCTGAAGGCGCAGAATGAACAGACACTTTCTGAA[C/T]GCATGTTGGGAAGAAGACATTGATCACTTTCAGGT Y 2 1 2 1 101000 r 74 goat snp32399-scaffold369-607517 13 8742094 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380044 Affx-122975576 AX-123250402 13 8418192 CTGGTGTGTCCTAGGCTTCATTCTGAGAGCTCCCA[A/C]CTTTCCTGACCAGAGTCACAGAAGGCTACCTGTGT M 2 1 2 1 201000 f 74 goat snp32401-scaffold369-677377 13 8812420 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435953 Affx-122933532 AX-123306292 13 8527255 GGAGGAAATGGTGCAAAGGGAACCTTCACCTGTGA[C/T]TGGGGAGGAGAAGTAAATATTGGGTTGAGAGTTCA Y 2 1 2 1 201000 f 74 goat snp32403-scaffold369-786440 13 8922541 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449552 Affx-122923246 AX-123319887 13 8568436 TTGATGCATCTGTATCCTTGAGGTCCCAGGGCTTC[A/G]CCTATGCAAGTGAGGATTTTTTATTTTTAGTTGAA R 2 1 2 1 101000 f 74 goat snp32404-scaffold369-827621 13 8964029 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799579 Affx-122931625 AX-385286509 13 8597282 CTTAGGCTGAGTCCTTATAGCATTATACACACTTG[A/C]TGGATTATTGTAATCAAGTTATTAAACTCTCCTTT M 2 1 2 1 101000 f 74 goat snp32405-scaffold369-856467 13 8993033 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402327 Affx-122959074 AX-123272680 13 8641027 CCAGAACATAGTATAATATTTATCTTGTTTACTTA[C/T]GCTGCTGACAGCAAGTATGTTTTCAGGGATATTTG Y 2 1 2 1 101000 r 74 goat snp32406-scaffold369-900212 13 9037082 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403640 Affx-122957532 AX-123273992 13 8697389 ACGTTGTAGCTGAAAAGGAATTCCACCTGGGGAGC[A/G]TAGGGAAGAATATGTAAAAATAGAGGATGACAGAG R 2 1 2 1 101000 r 74 goat snp32407-scaffold369-956574 13 9092505 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276693 Affx-1111835543 AX-519550203 13 8706636 CCGCCCATCTCCACAGGTTCTGCACCTATAGATGC[A/G]GAGGGTCCACTGTGTAATGTTTTCTCTATTTTTTG R 2 1 2 1 202000 f 74 goat Random2.2K-1315 13 8706636 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383103 Affx-122973276 AX-123253461 13 8749253 GCATAGTATCTGTGGGACTTGAGATGGGCCAGTCG[A/C]TCGCCAGCCTGCTTAAAATCTCTTGATATATAAAC M 2 1 2 1 101000 r 74 goat snp32408-scaffold369-1008438 13 9143485 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794491 Affx-122921428 AX-385281454 13 8783160 CATTCCCAGAGACTCTGGACGAAGTCCCACCTTTT[A/G]TGAAGAGTCCCGGGCATCATCACCCACCACAGATG R 2 1 2 1 102000 r 74 goat snp32409-scaffold369-1042345 13 9178089 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775787 Affx-122961641 AX-385262918 13 8825453 TCAGTGTTAGTATCGTGCAGTGTTACTGCACATGC[A/G]TTACTATTACCTTCCGTACAACTCCTGTTCCTGGA R 2 1 2 1 101000 f 74 goat snp32410-scaffold369-1084638 13 9220384 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794275 Affx-122927720 AX-385281240 13 8880716 CAGTAATAAAGAATTTCATTAAGATTATGCAAACC[A/G]TTTCTAGAGTACTACTCTACACAGTATGTTGTTAT R 2 1 2 1 101000 f 74 goat snp32411-scaffold369-1139901 13 9275540 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789366 Affx-122971078 AX-385276376 13 8917875 ATCCTTGAGCTTTCTTACCTCCAGGCATCTATGCA[C/T]GTTCTTTCCTTTGCTTGGAAAGCTCCGACCTGCAC Y 2 1 2 1 101000 f 74 goat snp32412-scaffold369-1177060 13 9313578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419172 Affx-122945728 AX-123289520 13 8956028 GCTCCACAAGTATTTTATCCTGCTAAGTTACATAC[A/G]GAGGGAGAAAAGGAGAACTCATCACTTTTGTTTCT R 2 1 2 1 101000 f 74 goat snp32413-scaffold369-1215213 13 9351814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802296 Affx-122945632 AX-385289200 13 9005972 GCATTAGTGGCCATATGTTGCCTGTCTTCCACCAT[A/G]CTCTATGTTTGCTTTCTTCAGAAACATAGTTACTA R 2 1 2 1 201000 r 74 goat snp32414-scaffold369-1265157 13 9401750 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427127 Affx-122939655 AX-123297470 13 9044473 AGGAGTGGAGTCCAGCCCCTATGGAGTATATGCAA[C/T]GGTGTGCCAGGTAGGACTTGAAACTCCTGTAAGGC Y 2 1 2 1 201000 r 74 goat snp32415-scaffold369-1303658 13 9440192 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440648 Affx-122929942 AX-123310985 13 9092412 AGCACTGGAAACTCTCCTCTTGGTCGCAGTTGCAC[A/G]TGATGCATTTCGGCACAAGGGAGGGTGAGAGGCTT R 2 1 2 1 101000 f 74 goat snp6079-scaffold1216-17233 13 9488147 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764811 Affx-122949196 AX-385252417 13 9121742 GAGATACCTAACAGCTTTTGAATTTATTCATGGGA[C/T]GATTCTTCTATTCAAAGAACATCTTTATATACTTT Y 2 1 2 1 101000 f 74 goat snp6080-scaffold1216-46563 13 9517484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424846 Affx-122941352 AX-123295192 13 9179149 GGACAGTGGGCAGAATTCAACCAGACTGAATGTAG[A/C]GGGGCAAGCATAAAGCATGCCCCATGGGGTCAAGA M 2 1 2 1 101000 f 74 goat snp6081-scaffold1216-103970 13 9575467 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442522 Affx-122928544 AX-123312859 13 9218502 TTCCTGGTGGGATCAATCTTATAATGGCAGAAGTC[C/T]GATTTTCCCCTCTGCTCTACTTGATTTTAAGTTGC Y 2 1 2 1 101000 f 74 goat snp6082-scaffold1216-143323 13 9615190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782417 Affx-122946359 AX-385269492 13 9260106 CCTCAAGCAGCGATGTAAATAGATAAGCCCATGCC[A/G]TTACTAAGGACTGGAACTTTTATTCTTGGGCTAAA R 2 1 2 1 101000 f 74 goat snp6083-scaffold1216-184927 13 9657478 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442072 Affx-122928378 AX-123312409 13 9288859 AGTGATGGACAAGCCTTCTTTCACAAAAGCTTACA[A/G]AGGAGGCATCTGAAACACAGCCTGTGATACTGGGT R 2 1 2 1 101000 f 74 goat snp6084-scaffold1216-213680 13 9686192 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414025 Affx-122949798 AX-123284374 13 9325660 ACTCTCCCTCCTCTACCTACACTGGCCATACTCAC[A/G]TTTCTAGAATGACCTCTTCACTCACTGGAATATTG R 2 1 2 1 101000 r 74 goat snp6085-scaffold1216-250481 13 9721248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275619 Affx-1111834912 AX-519549189 13 9392774 ATGTGCATTTGACCAGCCGCCCAGCGCTTGGAACA[A/G]CTCTACCACCTTGGTATGGGAACTGCAGCGTGACT R 2 1 2 1 202000 r 74 goat GoatD01.058509 13 9392774 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38425605 Affx-122940918 AX-123295951 13 9404699 TGAGGTGGTTGGTTGGGAAAAGGGAAGGATGCTGC[C/T]GCATGCATGTGGGATCTTGGGGCAGAGCCCTGAGA Y 2 1 2 1 101000 f 74 goat snp6087-scaffold1216-329520 13 9801577 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412314 Affx-122950855 AX-123282663 13 9438678 TTACTAGATTGCTCAAAAGGACAGTAAGAACTTCA[C/T]GGGGATCTTGTTAAGATGTAGTTTCTGATTCGGTA Y 2 1 2 1 201000 f 74 goat snp6088-scaffold1216-363499 13 9835530 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427270 Affx-122939542 AX-123297613 13 9485115 AAGTCTTTTTGGCTCAGGGCTGAGTGTCCTAGGAT[A/G]TTTTCAGTTCCTTGCCTTTTTCAAGCAGTCTTTGA R 2 1 2 1 201000 r 74 goat snp6089-scaffold1216-409936 13 9881627 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381513 Affx-122974861 AX-123251871 13 9519127 GATATCCATGGAGTTTTGGATTTTGGCCGTTCTAA[C/T]AGGTGTACAGAGATAGCTCACTGCTATTTCAATTT Y 2 1 2 1 201000 r 74 goat snp6090-scaffold1216-443948 13 9915289 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426480 Affx-122940234 AX-123296826 13 9550999 CGGTCCACGTCTCATCCAGGACAGTGATCTATTCA[C/T]GGGGAAAAGCGAAACAAACCAGCATTAATTAGAGG Y 2 1 2 1 201000 f 74 goat snp6091-scaffold1216-475820 13 9947869 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396044 Affx-122963460 AX-123266399 13 9585495 TAAACATTAAGAAAATTTAATCACACAAGCATGCC[A/G]TAATTTAAGGCGACCCTATCAATCTGAAAAGTCAT R 2 1 2 1 101000 r 74 goat snp6092-scaffold1216-510316 13 9981742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376482 Affx-122978035 AX-123246841 13 9615040 AGTTACAGACAGCGTGTGGCAGATAATCAAATTAG[C/T]ACAAGATGCTGCTTCGGAGGAGAATCACGCTGCTC Y 2 1 2 1 101000 f 74 goat snp6093-scaffold1216-539861 13 10009857 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385540 Affx-122971237 AX-123255898 13 9644086 AGGAAACTGCATTTTGAAAGGCTCCCAGGTAATGC[C/T]GACTGTGCTGATCTGGGGACACACTAAGAGCCGCT Y 2 1 2 1 101000 r 74 goat snp6094-scaffold1216-568907 13 10036660 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801099 Affx-122965094 AX-385288013 13 9673635 AGAATAGAAACTGTAACAACAACCTGCAGTGTTCA[C/T]CAATCACAGAAAGGATGTCTTCTCCAGCTTTGCAG Y 2 1 2 1 101000 r 74 goat snp6095-scaffold1216-598456 13 10066023 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424227 Affx-122942484 AX-123294573 13 9707083 CTACTATAAAATCAGAGTATGTATAATTCAAAAAT[A/G]TATCGCTTTTTCCATAACTGGAATTGCTGACTTTC R 2 1 2 1 101000 r 74 goat snp6096-scaffold1216-631904 13 10099289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385809 Affx-122971032 AX-123256167 13 9748017 AAAGAGAAAATGAGAAATTTGCTTCCCACACAGTG[C/T]AAGCAACGTACAGAGTCTCCCATCATAGTGTATGA Y 2 1 2 1 201000 r 74 goat snp6097-scaffold1216-672838 13 10140375 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378485 Affx-122976665 AX-123248844 13 9777661 CCTCTCTCCTGATCTTCGCGGCCACCAGGAAGCAC[C/T]GGCATCTCTAAGCGCTCGGTGAGATTCAGGGATGC Y 2 1 2 1 101000 r 74 goat snp6098-scaffold1216-702482 13 10169952 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439817 Affx-122930476 AX-123310154 13 9842867 CTATGAAAATTCAGACAGGGGTCATCTCTAAGGGC[A/G]CATAGTAGGTTCTTAACAAAATTCTGTGAGATTGA R 2 1 2 1 101000 f 74 goat snp6099-scaffold1216-767688 13 10236098 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434855 Affx-122934370 AX-123305196 13 9911393 ATCCCAAAGGCTCCCTTCAGCCCTCACTACAATAC[A/G]TGGGAGGTTTATGGCCACATGTCTGGGTCTGGGTC R 2 1 2 1 201000 r 74 goat snp6100-scaffold1216-836214 13 10304006 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407566 Affx-122954674 AX-123277917 13 9954996 CAGACATGCAATAGGAGAAATGTTTGTTGGATGAA[C/T]GCATGAGTGAAAGAATGAATGAAATGTATATGCCT Y 2 1 2 1 101000 f 74 goat snp6101-scaffold1216-879817 13 10346867 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783168 Affx-122960571 AX-385270235 13 9989573 ACTGGGTTTTAGTTTAAATCTGAAATTACGTTAGT[A/G]TGGAGAAGCCATTTATTCCCATAAAGGGTTTTAGG R 2 1 2 1 101000 r 74 goat snp6102-scaffold1216-914394 13 10381267 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792318 Affx-122935437 AX-385279300 13 10026281 CAAGGGAAGACAGCCAGGTGTGAGAAACCCTTCAG[C/T]TTTCTTAGTGTCAAGCATAATATATCAGCAAGCCT Y 2 1 2 1 202000 f 74 goat snp6103-scaffold1216-951102 13 10418097 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381522 Affx-122974853 AX-123251880 13 10073028 TGGCCGGAAGTAGCCAGAGAAAGCTTGACGTCTCT[A/G]TTCCCTAAGAAATGGGCCTCCTATCTCTTGAGGTG R 2 1 2 1 101000 r 74 goat snp6104-scaffold1216-997849 13 10464780 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403987 Affx-122957209 AX-123274339 13 10109187 CCACTCGTCAGCATCACTGGACCTTGTGTGGCATC[A/G]TATTTTCTCACTAGTCTTGAACCGCTCATGTGTCA R 2 1 2 1 101000 r 74 goat snp6105-scaffold1216-1034008 13 10501181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391002 Affx-122966897 AX-123261359 13 10144472 GCATACTTAAGAAAACACATAAGTCTCAAAGATCT[A/G]TTTCAAATAGATGGAAAACTATCCCAGGCAGATGG R 2 1 2 1 101000 r 74 goat snp6106-scaffold1216-1069293 13 10536317 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444484 Affx-122926526 AX-123314821 13 10183014 GCCTCAGGGTAACGCTCAGGGCAACCCCATTTTGT[A/G]TTGCTTAATGCTCACAGCTCTGGTTTCAGCATTCA R 2 1 2 1 101000 r 74 goat snp6107-scaffold1216-1107835 13 10575506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385479 Affx-122971286 AX-123255837 13 10214393 TAGTTTTAGAGAGGAATTTAGAGAGGTAAGCCCTG[C/T]CTAGGACTTGACAGTATCCATTGTAAGAGTAGGGT Y 2 1 2 1 101000 r 74 goat snp6108-scaffold1216-1139214 13 10606974 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413179 Affx-122950335 AX-123283528 13 10263185 GCTGTGAACATTGGTTTATACCTTTCTGGATGGAC[A/C]TGTTTTTATTTCCCTGTGGTGGGATTTTACCCTGA M 2 1 2 1 202000 f 74 goat snp6109-scaffold1216-1188006 13 10656880 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403483 Affx-122957704 AX-123273836 13 10316703 GAAGGGTACCCCGCCATCCAGTGTGCAAGTGTTCT[C/T]GCCCTTTCCTGTCTCCCATTTGGTTTCTTTTTGCT Y 2 1 2 1 102000 r 74 goat snp6110-scaffold1216-1241524 13 10710088 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766916 Affx-122923567 AX-385254230 13 10346477 CCAGCTCACAGTTACTAACAGATCCTAAGATCCAC[A/G]CTGTTCTGACTGTTCTACATCAGGGCAGAGAGGAC R 2 1 2 1 101000 f 74 goat snp6111-scaffold1216-1271298 13 10739730 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448626 Affx-122923372 AX-123318962 13 10392497 GGGCTTGCAAGGACAGGAAGTCATCACCTATCTGC[A/G]TCTACATCTTGTACTCCCTTGCTGATCAGTGGTGT R 2 1 2 1 101000 r 74 goat snp6112-scaffold1216-1317318 13 10785821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427744 Affx-122939255 AX-123298087 13 10432555 TGCTACTCAAAATGGGGTTCAGGCACCAGGCACTT[A/G]TTTGCACCAGAACCTCCTCCCTCACCCCAGATATC R 2 1 2 1 201000 f 74 goat snp6113-scaffold1216-1357376 13 10825888 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778213 Affx-122977368 AX-385265328 13 10472390 GCACTCCTGGTATTGTCTTTTACAGCCCTTTGGCC[A/G]TTCATCTCTCCTACTATGATTTGTCTTTAGCTTTG R 2 1 2 1 101000 f 74 goat snp6114-scaffold1216-1397211 13 10865686 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422625 Affx-122943712 AX-123292971 13 10521185 CTTGGCTATTTCCATAGAACTGCACTTAATGGTCA[C/T]GCTCTGACACTGCGGATCATTGACCCTTTCATCGT Y 2 1 2 1 101000 f 74 goat snp6115-scaffold1216-1446006 13 10914512 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419770 Affx-122945867 AX-123290118 13 10550811 AACACAGCACATTAAGGGTGATAAGTGCCAAGGGG[C/T]GGAAAATAAAACAGGAAAGAGGGACATGAAGTGTT Y 2 1 2 1 101000 f 74 goat snp6116-scaffold1216-1475632 13 10944165 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274389 Affx-1111834227 AX-519547982 13 10584416 ACGGTGACGTGATTCTTCTCACTTTGGGTCTGGTG[A/G]GTAGAGGCCTCCTCTCCGAGCTGCAGGACCCTGTG R 2 1 2 1 202000 f 74 goat GoatD01.026570 13 10584416 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38408159 Affx-122954217 AX-123278510 13 10594982 CACGTGTCCTTGTGTCTGTGTGTGTTCCTCTGTGT[A/G]TGTGTCTGTATGTGCCCTTGTGTGTGTCTATGTGT R 2 1 2 1 103000 r 74 goat snp6117-scaffold1216-1519803 13 10988207 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271928 Affx-1111832974 AX-519545707 13 10632273 AAGCAAATCATGACCATTTGACTTCTGTTGATAGA[A/G]CACGTGAGAATGATAGAAGTGGTAAGTTAGTGAAT R 2 1 2 1 101000 f 74 goat 13_10632273_AF-PAKI 13 10632273 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38405040 Affx-122956359 AX-123275392 13 10650076 CCTTTTTCCTGCTCGAATACCTGTGAAATTCGGAT[A/G]TGTCTTGGAATTCCCAGACTCTTATATTGGACAAA R 2 1 2 1 101000 f 74 goat snp6118-scaffold1216-1574897 13 11043275 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765669 Affx-986697537 AX-385253135 13 10683252 ACCATCAGGTTTCAACTGGTCTGGGGTCTACATAG[C/G]TGTAGTCAGCATGCGGTTAACTTCTTCCACCTGGT S 4 1 2 1 600010 r 74 goat 13_10683252 13 10683252 Ancestral_priority_1043 ancestry 0.66 recommended IMAGE 10K 10K ancestral 38391394 Affx-122967263 AX-123261751 13 10684090 TGTCTGACCGCTCTCTTGCCAATGGGTTCAACAAC[A/G]CTCTGCATGCTGGGTAACATTTTTTACTGACCTAT R 2 1 2 1 201000 f 74 goat snp6119-scaffold1216-1608911 13 11077121 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451777 Affx-122921508 AX-123322110 13 10712976 AAGGAAGCTTGTTGACATGGTGGAAAGTAAAACAG[C/T]GGTTTAAGGTCACCCAGTATCTCTCTGTTGAGATT Y 2 1 2 1 101000 f 74 goat snp6120-scaffold1216-1637797 13 11106583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438563 Affx-122931170 AX-123308901 13 10748951 AGCTTTGCCCTGGAGCCTGTTCTTACCCTTTCTTT[C/T]TTTCTTGGCCCAGGGCATCTGGAGACAGGTTGAAT Y 2 1 2 1 202000 r 74 goat snp6121-scaffold1216-1673772 13 11139242 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768914 Affx-122924461 AX-385256091 13 10845078 CAGTATGCTCTTCGGAGAATCATATGTTTTGAAGC[A/G]TATGTAATAAGTGCTGTAACATCCAAGATGATAGT R 2 1 2 1 201000 r 74 goat snp6123-scaffold1216-1769899 13 11233278 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419256 Affx-122946263 AX-123289604 13 10915533 TTCTGCCTAGAAGGGATTAGAGAAGGGACTGGACT[C/T]CACTTTCTCACCTTTCATCCTGCGAGTAAAATGAC Y 2 1 2 1 101000 r 74 goat snp3201-scaffold1096-18948 13 11303637 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409002 Affx-122953887 AX-123279353 13 10947104 AGGCATATATTGAGAAACAATATAAATATGTCTCA[C/T]AGCATAAAAATATATCATCCCTCTCATTTCCAGAA Y 2 1 2 1 101000 r 74 goat snp3202-scaffold1096-50519 13 11335331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409962 Affx-122954110 AX-123280313 13 10999719 AGAAGCAACAATTCTCAAGGCTGCCAGATCCTGCC[A/G]TATAATTTAAAAGTTGTTCCTAGAAGAAAGTACAA R 2 1 2 1 101000 r 74 goat snp3203-scaffold1096-103134 13 11387860 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451783 Affx-122921504 AX-123322116 13 11032648 GTGAAGATGGACTATGTCCCAAGCCGGGCTGATGC[A/G]TCTCTTCCTCGGCATATTTGCTTTGAAGCAGAGAG R 2 1 2 1 101000 r 74 goat snp3204-scaffold1096-136063 13 11426851 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786298 Affx-122978194 AX-385273333 13 11081152 TCAATGAGTTGGAAGAATCCGTGAACAGGATACAC[A/G]TGAATTCTGCCAGGAATACTAGGTTGGCAAGTGTT R 2 1 2 1 101000 r 74 goat snp3205-scaffold1096-184567 13 11475341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397534 Affx-122962039 AX-123267889 13 11137950 GTACATTTCTTTTTTTCTAGAAAATTTGTGCTGAG[A/G]GCACTGTTCATGTTATGTTCTTCCCTTTATATCAG R 2 1 2 1 101000 r 74 goat snp3206-scaffold1096-241365 13 11532612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385946 Affx-122971551 AX-123256304 13 11230846 TAAACACAACAAATGTCATATACACTCTTCTCTCT[A/G]CCCACAAAAATGAAGCACCTTGAAACATTTCTGAA R 2 1 2 1 101000 r 74 goat snp3208-scaffold1096-334261 13 11625039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408264 Affx-122953809 AX-123278615 13 11272789 TGTGCGGTTTGAGCTGTGAAGGCATCTGGCACAAT[A/G]GGAAGTGGCAAGTTTTGCCTTCAGGGTGACAGAAA R 2 1 2 1 101000 f 74 goat snp3209-scaffold1096-376204 13 11667277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426254 Affx-122940333 AX-123296600 13 11306558 TTGCCAGATGTGTTAGAACATCTGGAAAGAGTTAG[C/T]GATAAGTACGTTAAAAAAACTAAGCAAATGGAAAA Y 2 1 2 1 101000 f 74 goat snp3210-scaffold1096-409973 13 11700594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794797 Affx-122971169 AX-385281757 13 11335834 TTGATAAATAATTCTCTAGGCTGCTTACTGATGGC[A/G]CCCACCCAATCAATGATTTCCAATCTGTGGTCACA R 2 1 2 1 101000 r 74 goat snp3211-scaffold1096-439249 13 11730110 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378656 Affx-122977093 AX-123249015 13 11381286 ATAACCTGAAATGCCTAAGTCCTTGCTCTGAGGCC[A/G]TGGGCAGGGGGGAATCAACTCACCCGGGGGGCACA R 2 1 2 1 101000 f 74 goat snp3212-scaffold1096-484701 13 11775587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476289 Affx-1251763796 AX-586011708 13 11418416 CGTGAACCATGAACTACCAGATGTTCAAGCTGGTT[-/TTAAAAAAGCCAGAGGAGGAGAAGGGGTTGAGGCTGCCTGTTAAAATTTTAAAAAAAATAAAAAAAAATAAAAATAAAAA]TAAAAAAGCCAGAGGAACCAGAGATCAAATTGCCA - 8 1 4 1 20000 f 74 goat SV_160 13 11418416 - deletion junction SV-TF-chip 539476542 Affx-1251763796 AX-586011931 13 11418416 CGTGAACCATGAACTACCAGATGTTCAAGCTGGTT[-/TTAAAAAAGCCAGAGGAGGAGAAGGGGTTGAGGCTGCCTGTTAAAATTTTAAAAAAAATAAAAAAAAATAAAAATAAAAA]TAAAAAAGCCAGAGGAACCAGAGATCAAATTGCCA - 8 1 4 1 20000 r 74 goat SV_160 13 11418416 - deletion junction SV-TF-chip 562165881 Affx-1251763796 AX-606941290 13 11418416 CGTGAACCATGAACTACCAGATGTTCAAGCTGGTT[-/TTAAAAAAGCCAGAGGAGGAGAAGGGGTTGAGGCTGCCTGTTAAAATTTTAAAAAAAATAAAAAAAAATAAAAATAAAAA]TAAAAAAGCCAGAGGAACCAGAGATCAAATTGCCA - 8 1 4 1 20100 r 74 goat SV_160 13 11418416 - deletion junction SV-TF-chip 562166327 Affx-1251763796 AX-606941735 13 11418416 CGTGAACCATGAACTACCAGATGTTCAAGCTGGTT[-/TTAAAAAAGCCAGAGGAGGAGAAGGGGTTGAGGCTGCCTGTTAAAATTTTAAAAAAAATAAAAAAAAATAAAAATAAAAA]TAAAAAAGCCAGAGGAACCAGAGATCAAATTGCCA - 8 1 4 1 20100 r 74 goat SV_160 13 11418416 - deletion junction SV-TF-chip 38409689 Affx-122953059 AX-123280040 13 11422901 AAAGTGGTCCAGTCATGAAAAAGTTTAAGTTGATC[A/G]TTTCGGTCATACTAATGGAACTAAAACGCATGTTG R 2 1 2 1 101000 r 74 goat snp3213-scaffold1096-526316 13 11817058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445336 Affx-122926395 AX-123315673 13 11498177 AGGGGCATAGCTGAGCCACTCACCAGGCCAATCCA[C/T]GCCTCCATTCAGACCTAAGGAGCACTCTTACTGCA Y 2 1 2 1 101000 r 74 goat snp3215-scaffold1096-601592 13 11892401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402925 Affx-122958189 AX-123273278 13 11551134 GTGATATTGAAATAGGAAGTAACTTCAACTCTTCC[A/G]TAACCAGTTGAACTCAATAATCAATATACTGCTGG R 2 1 2 1 101000 r 74 goat snp3216-scaffold1096-654549 13 11945940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409935 Affx-122952871 AX-123280286 13 11595066 AAAGGACCCAAAAGATGATTGGCCCCCATTTCCTC[A/G]TTTATTGAGACCTGGCCATAAAGATGCATGTGACT R 2 1 2 1 101000 r 74 goat snp3217-scaffold1096-698481 13 11988576 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424339 Affx-122941942 AX-123294685 13 11659441 TAAACTTACAGCGCTGTGTATCAACTGTACCTCAG[C/T]ACAACTCGGGGGACATCAAGGGACAAAAAAAACCA Y 2 1 2 1 101000 f 74 goat snp3218-scaffold1096-762856 13 12051977 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399676 Affx-122960502 AX-123270031 13 11745083 GCACACAGCTCCACGCCCTGCCACATGTCCTCAAG[C/T]GCAGAGCACACACCTTCATCCACTGCTCTTTACGG Y 2 1 2 1 101000 r 74 goat snp522-scaffold1014-291925 13 12136140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800016 Affx-122930320 AX-385286939 13 11786737 ACTTCCTTGATTTTTTAATCTACATTAAATGAATA[G/T]TATTGTAAAGTGTTGTATATAGGACAATGTAGAAC K 2 1 2 1 201000 f 74 goat snp521-scaffold1014-250271 13 12177638 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448189 Affx-122924244 AX-123318525 13 11820336 AGCACATCAGCATCAATGTCATCGTAGATACTCAT[A/G]CTCTCTGTTGAAATGCAAAGACTGATTTAATCAAG R 2 1 2 1 101000 f 74 goat snp520-scaffold1014-216672 13 12211324 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429614 Affx-122937701 AX-123299955 13 11897131 TGTTTCTGGAATTAAGAGAAGCATGGTCTTTGCTT[A/C]GCTCTGGCATTTCAGTTCTTGATCCATAGGATAAT M 2 1 2 1 101000 r 74 goat snp518-scaffold1014-139877 13 12288213 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801605 Affx-122968124 AX-385288514 13 11943582 ACAGGTAACCTCGTGTAAGTCTGACTGCACAATGC[A/G]TCGGTTTGACACATTCGTATATTCCAATCTGATTA R 2 1 2 1 101000 f 74 goat snp517-scaffold1014-93426 13 12334335 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437798 Affx-122931685 AX-123308136 13 11980542 GTGAGCCTACTCCCCACGACCAGCCATTTGGTCCT[A/G]CAAACATCTCCTAACCAGGACCCATCCTGTGTTGA R 2 1 2 1 201000 r 74 goat snp516-scaffold1014-56466 13 12371438 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453754 Affx-122919606 AX-123324087 13 12034978 TCCACTTAATAATAATACTTAGCACGTAAACTGCC[A/G]CTTCTACGAGCCTCTTCAAAGCCTTTTACAATCAT R 2 1 2 1 101000 f 74 goat snp515-scaffold1014-2030 13 12425965 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406472 Affx-122955174 AX-123276824 13 12041567 GCCACAATCACACAGATCTTTCCAAATCTAATGTC[A/G]CCAACCAAGCCTTCAGCCACCTCTCTTAGAACTGA R 2 1 2 1 201000 f 74 goat snp56131-scaffold875-3458659 13 12432838 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384809 Affx-122971990 AX-123255167 13 12088705 AGCCTTTATTCTATTATTTTAAAAATATTTATTTG[C/T]ATATCTATCTCAGTTTATACACACATGTATATTTT Y 2 1 2 1 101000 r 74 goat snp56130-scaffold875-3411521 13 12480143 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407746 Affx-122954985 AX-123278097 13 12132125 TGTCCAGTAGGCCTGCCACTGGTCACATGTGTTGG[A/G]GCATTTGCTATGTGGTTAGTTCAAGGTGAGACAGG R 2 1 2 1 101000 r 74 goat snp56129-scaffold875-3368101 13 12524015 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406917 Affx-122955613 AX-123277268 13 12172460 CTGTTCTCCTGTAGGACAAAAGGTGGTATACCAAA[C/T]GCCTGGAGACCATTCTCCACAGCAGGCTGAAGTTC Y 2 1 2 1 101000 f 74 goat snp56128-scaffold875-3327766 13 12564922 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439899 Affx-122930028 AX-123310236 13 12246174 ATGAAACCCTTGCCCCCTATACTGAAGTGTGCAGT[A/G]CCGACATTTGTACCATCAGGGAATTCCGAAAGCAT R 2 1 2 1 303000 f 74 goat snp56126-scaffold875-3254052 13 12638410 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428629 Affx-122938676 AX-123298971 13 12274753 AGACATCACCATAGTGCGAACAAGCTCCAGATGGA[C/T]GATGGCTTCTGGCTTGTCCTGTCTTTGGTGGAGAG Y 2 1 2 1 201000 f 74 goat snp56125-scaffold875-3225473 13 12666963 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397003 Affx-122963140 AX-123267358 13 12321626 CATGGGTTTCATTACTTATTTCCAGGTAAAAGGGG[A/G]AAAAGAAGAAGAAGAAAATAGCATCTGTAATGTAA R 2 1 2 1 101000 f 74 goat snp56124-scaffold875-3178600 13 12713848 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396102 Affx-122963421 AX-123266457 13 12367019 TCCTCTGCCCGCACTAAATCCCTTCAACCTTCTAA[C/T]GTCACCGTCTCCAGGCAAGACTCAGCAGTTTTTTT Y 2 1 2 1 201000 r 74 goat snp56123-scaffold875-3133207 13 12759412 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276695 Affx-1111835544 AX-519550205 13 12418388 AGCCCTTCTAGATCTGATTTCTTTAGTCTTTGACC[A/G]CATTCAGCTGTGTGAATGGGCAACGAAGGCTCTTT R 2 1 2 1 101000 f 74 goat Random2.2K-1317 13 12418388 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422889 Affx-122943067 AX-123293235 13 12481444 GTTTTCATCTTCTCTCAAATCCTAAATCAGTTATT[C/T]GTCTCCTATTCCTCTCTCCACTGCATTCAAGCAGA Y 2 1 2 1 201000 f 74 goat snp56121-scaffold875-3018782 13 12873976 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773505 Affx-122950465 AX-385260646 13 12528250 GTAGGACATAATGACCTAGTATTTCTTTAAATGGC[A/G]TCATTCTTTATCAGGGAAGCCGATGCACTCCATTA R 2 1 2 1 101000 r 74 goat snp56120-scaffold875-2971976 13 12921456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413886 Affx-122949844 AX-123284235 13 12579519 TCCTGCCACCACAGCATGTTCAAAATTAGGAAAGC[A/G]TCTGATCATTTGATAAAGAAGTACAAGCTATTTAG R 2 1 2 1 201000 r 74 goat snp56119-scaffold875-2920707 13 12972495 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401998 Affx-122958765 AX-123272351 13 12687657 GCAAAAACAGTGAAAATTCCTTTACTTTCTAGCAC[A/G]TGAGTTTTCTAGAATTATTTTTCTACATAATTGAA R 2 1 2 1 101000 f 74 goat snp56117-scaffold875-2812569 13 13080821 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773532 Affx-122968017 AX-385260673 13 12765195 TATGGCATTGCAAATCATGTCTGGAAATCTCAAAG[C/T]AGGGCTTGATGTTCACACTTTTCAGTACTCCTATT Y 2 1 2 1 101000 r 74 goat snp56115-scaffold875-2735031 13 13159411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441472 Affx-122928752 AX-123311809 13 12830132 GAAACGTTAGCCTTATTCCTCTTTCCTCATATCTG[A/G]CTTCTCTCCTACAGTTTGATTAAAGAGAACTGTTG R 2 1 2 1 101000 r 74 goat snp56114-scaffold875-2670094 13 13224406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427815 Affx-122939750 AX-123298158 13 12871397 AGCATTCTGTCTTGTCAAGGACTCCTTATCATCAA[A/G]GAAGAATAAACACTCTAATTATTTTTTTTACTTTT R 2 1 2 1 101000 f 74 goat snp56113-scaffold875-2628829 13 13266299 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379824 Affx-122975823 AX-123250182 13 12973178 TGATGGGATTATTTGTCTTTTTAATTCCTATAATT[A/C]TGAGTTTTCTAAAAGAAAAGCATCCCAGATCAATA M 2 1 2 1 303000 f 74 goat snp56111-scaffold875-2527048 13 13370368 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412382 Affx-122950807 AX-123282731 13 13013788 TTCAACTAATTTCAAAAGAGGTTTAACAGTTCTCT[A/G]TAAGACAAGGTTTTAGGGCTTTGTGTTTGAAGAAA R 2 1 2 1 101000 r 74 goat snp56110-scaffold875-2486438 13 13410961 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435306 Affx-122934023 AX-123305646 13 13043732 CAAACAGAGGTAGGTATGGTTATAGTTGAATAAGT[A/G]TCTGTAGCAGAATCAGAATATTTCTGATTTTAGAG R 2 1 2 1 101000 f 74 goat snp56109-scaffold875-2456494 13 13441109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431047 Affx-122936650 AX-123301388 13 13092663 AACATGGGTGGAATATCCAGAACACCCAACATGAT[A/G]CTACTAGGATTTCTAGGAAGAGAGTAGGAAAAAAT R 2 1 2 1 101000 f 74 goat snp56108-scaffold875-2407563 13 13489949 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409514 Affx-122953628 AX-123279865 13 13167213 CTCCCCACCCAAGATTTCTGCTTACATCTCACTGT[C/T]CAGAACTAAGTCACAGAGCCACTGCACAGAAGACA Y 2 1 2 1 201000 f 74 goat snp56106-scaffold875-2333013 13 13564807 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786573 Affx-122921626 AX-385273605 13 13215896 GCATGAGATCTCGGCTGAATATTCAGGAAATCCCA[C/T]GTAAAACCCTTCCATTCTACAATTTGCGTTTTATT Y 2 1 2 1 101000 f 74 goat snp56105-scaffold875-2284330 13 13613132 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796118 Affx-122966553 AX-385283069 13 13255296 AAGGAATTGACTGTTAAAGTGACTCAATTAGAAAA[C/T]TCCTAAAAATCTTTGGCCCCAAATCAAGGGCAAAA Y 2 1 2 1 101000 r 74 goat snp56104-scaffold875-2244930 13 13652906 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272675 Affx-1111832975 AX-519546381 13 13287303 ATTTGAAATAGTGCCACTGGAATTCCATCACCTCC[A/G]CTAGCTTTGTTCATAGTGATGCTTTCTAAGGCCCA R 2 1 2 1 103000 f 74 goat 13_13287303_AF-PAKI 13 13287303 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38402733 Affx-122958338 AX-123273086 13 13396333 GATTATATGACAATCTCACCTCCAAATACCTCTCT[A/G]CAGAATTTTCCCCTCCTCTTCCTCATTCCTTCCAC R 2 1 2 1 201000 f 74 goat snp56101-scaffold875-2103893 13 13795178 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451612 Affx-122921629 AX-123321945 13 13450128 TTTGGAAGTCAGGAAGTCCAAGTTTAAGATGCTAG[C/T]TGATTTGGTTCTTAGTGAGAACTGTCTTGGGATGG Y 2 1 2 1 201000 r 74 goat snp56100-scaffold875-2050098 13 13849946 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276833 Affx-1111835545 AX-519550341 13 13451352 AATGGTATCCTATAAACGAGTCTGGATTTAGAAAA[A/G]TCTGTGTGCGTATATAATATTGGTATCTTAATCTC R 2 1 2 1 101000 r 74 goat Random2.2K-1318 13 13451352 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797575 Affx-122933066 AX-385284514 13 13480216 GCACAGATGGGTATGTAACATACCACATTTCATAA[C/T]GTATATTATACTATGCAAAACCTAAAATACATAAT Y 2 1 2 1 201000 r 74 goat snp56099-scaffold875-2020010 13 13880463 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276835 Affx-1111835546 AX-519550344 13 13490028 AGACTTCAGAAATAGATTTAGACGACAAATGCAAC[A/G]ACATCAGAATATGAGAGTCTGAAGAGACAGGATAA R 2 1 2 1 101000 r 74 goat Random2.2K-1319 13 13490028 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796516 Affx-122951700 AX-385283464 13 13518097 GATAAGCCATGTTTTGGCATCTTTTGAATATGAGA[C/T]TCATTTAAAGTCATTTGCAAGAGGGAAAAAAATGC Y 2 1 2 1 101000 f 74 goat snp56098-scaffold875-1982129 13 13918678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440585 Affx-122929293 AX-123310922 13 13568265 CCACTCCTCACCACTGCTGCACCAGCCAGCACTCT[A/G]GTTAGTAGCTACTCTGTCAGGGTGTATCTTAGAGT R 2 1 2 1 101000 r 74 goat snp56097-scaffold875-1931961 13 13968824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394333 Affx-122964671 AX-123264688 13 13632189 TGCTTGACTCTATCTTCCGCACCACACCCTGATTA[C/T]GGCAGAGACCCTGGGAGGAAGTGGTCCTGCAGGTA Y 2 1 2 1 101000 f 74 goat snp56096-scaffold875-1868037 13 14033388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777602 Affx-122955950 AX-385264721 13 13666375 TTGATTTCCTCAGTAGGACTGACCAGAAAACATAA[C/T]GAGGTTGAAGATTTAGCAAAAAGCTGTAAACACTG Y 2 1 2 1 101000 f 74 goat snp56095-scaffold875-1833851 13 14067452 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450659 Affx-122921923 AX-123320993 13 13697146 CCAAGGACCCCATCTCCAAATACCATCACATTGGA[A/G]ATTGTGGCATCAGTATATGAATTTTGGAGGGATGT R 2 1 2 1 103000 r 74 goat snp56094-scaffold875-1803080 13 14098680 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785344 Affx-122948759 AX-385272389 13 13733085 GGAAATTTCTCACTAGCCATGTCCCATTTTTAAGG[C/T]AGAACTTTTAGACCTATTAACAATGAACATACTTG Y 2 1 2 1 101000 f 74 goat snp56093-scaffold875-1767141 13 14135887 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388009 Affx-122969569 AX-123258367 13 13769617 GTCTTGAATTGCCTTAATTATTACTTAATTACTTA[A/C]TCACTCAGAAGTAAAAAGGAGACACAGACACACCT M 2 1 2 1 201000 f 74 goat snp56092-scaffold875-1730609 13 14172459 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765690 Affx-986697549 AX-385253153 13 13773764 GAGAATGTATGGAAAAAATCACTTGCTACTCCTGC[A/G]GCAGCAAAATCTAATTGGGAGTGTTCCATGGGCTC R 2 1 2 1 600010 r 74 goat 13_13773764 13 13773764 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320782601 Affx-122961480 AX-385269675 13 13816389 AAATATTTGTTGGTGTTTTGAAAGCATTTCCCAGC[A/G]TTTCCAGCAAATGCTTAAACATACATACAGGAAAA R 2 1 2 1 102000 f 74 goat snp56091-scaffold875-1683837 13 14220991 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790285 Affx-122957538 AX-385277289 13 14015886 TTCAAAATTAGGGAATGTTAGATAATCTCTTATCA[C/T]AGTGAATAATGATACAATTACTTAAAATAATATGG Y 2 1 2 1 201000 r 74 goat snp56086-scaffold875-1484340 13 14422221 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402768 Affx-122958314 AX-123273121 13 14047507 TCAAGGCTACATACTATCAACATGGTATCACTGTC[A/G]AAGCAGACCTTGAACACCTGACTGAGGTCATGTTT R 2 1 2 1 101000 r 74 goat snp56085-scaffold875-1452719 13 14454109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409006 Affx-122953885 AX-123279357 13 14102023 TTGTGGTGTCATTTAAAAAAAAATCGGTACACCCA[C/T]GCATACACAGAAAACACTTAGAATTATATCTTGCA Y 2 1 2 1 201000 r 74 goat snp56084-scaffold875-1398203 13 14508620 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797829 Affx-122937105 AX-385284768 13 14277064 AGATAGGAACTTTATACTAACAGAAAAGGATCAAC[A/G]TTTAACCAGTAAGAGCTAATGCTGACCTTAGTTAG R 2 1 2 1 101000 f 74 goat snp56080-scaffold875-1223162 13 14683254 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450578 Affx-122922034 AX-123320912 13 14495875 ATATGTTTCTTAATCATTCCTTTCTCTTTTTCGTC[A/G]TTTGTACATTTGGTTTTGTGGGCTTTCATATACAT R 2 1 2 1 103000 r 74 goat snp56076-scaffold875-1004351 13 14899232 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376841 Affx-122977911 AX-123247200 13 14707757 TTCCCTCTACACACCCTCCTCTCTAGACAGATGTA[C/T]GAAGAGGCACACACATGCATCTTTTGGTCTAAACA Y 2 1 2 1 202000 r 74 goat snp56071-scaffold875-792469 13 15108402 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793062 Affx-122967374 AX-385280040 13 14797414 AGAAATTAAACACATGTACAGAGAACTAAGAAATA[C/T]GAGGAGTATTTTTAATATGAAGCCTTACAATCTCA Y 2 1 2 1 101000 r 74 goat snp56069-scaffold875-702812 13 15198293 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803100 Affx-122960125 AX-385289971 13 14826276 CCCCAAAAGACAAGTCTCTTAAATGCCAAACCAAA[C/T]GGAAACAAAGGTGAGAGGATATCTATTCACATTTA Y 2 1 2 1 101000 r 74 goat snp56068-scaffold875-673950 13 15227211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397742 Affx-122962537 AX-123268097 13 14856583 AGAAAGTTTAACTTGTCAAAAATAATTAACAGCCC[A/G]TGCCTTTGTTTCATCCTCAAGGAGGGCATTGTTTA R 2 1 2 1 101000 r 74 goat snp56067-scaffold875-643643 13 15257566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438553 Affx-122931178 AX-123308891 13 14912379 ACATGAGAACCAGGGAGGTCACAGTAGAACTTGCC[A/G]TCTATTCACAGTCAGGGTGGACATAGGATGTGGGA R 2 1 2 1 101000 r 74 goat snp56066-scaffold875-587847 13 15313527 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397173 Affx-122962419 AX-123267528 13 14969884 TGAAGAGGTGGGGTTCCAAACATCACGGTCAGGAG[C/T]GCAGAGAGGGGGAGCGTGTCAGGAGGACCGCAGGT Y 2 1 2 1 101000 f 74 goat snp56065-scaffold875-530342 13 15370798 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403642 Affx-122957530 AX-123273994 13 15005783 ACAGCCTTATAGCCATACCAGGAAAGTATAGCTCT[A/G]ATCTGTGTGCCATCTGACCACGAACTGTATGCTCT R 2 1 2 1 101000 r 74 goat snp56064-scaffold875-494443 13 15406692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449281 Affx-122923023 AX-123319616 13 15038466 GCAGGCATGAACCGATGTCCCGGTCCCCATGTTTT[C/T]AGAAAGGTCTCTCCCTCCTCTACCACATCTAACCT Y 2 1 2 1 101000 r 74 goat snp56063-scaffold875-461760 13 15439322 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450492 Affx-122922518 AX-123320826 13 15103039 TTCGCGTGCACGATATAAGATAGGGGTCTAGTTTC[A/G]TTTTTGTTCAACTGGAGCATAATAGCTTTACAGTG R 2 1 2 1 201000 r 74 goat snp56061-scaffold875-397187 13 15504175 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401348 Affx-122959255 AX-123271701 13 15142833 TATCCTTTTACAGGGAAGTCAAGGGACAGAGGAAC[A/G]TATCGAAGGACATCTTGAGGGTGCAGTCTGAGAAA R 2 1 2 1 101000 f 74 goat snp56060-scaffold875-357393 13 15542784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404537 Affx-122957396 AX-123274889 13 15173983 GCATCCCAGAAGGAAGACTTAACCTTGAACCCTGC[A/G]CTCCTCTTCACCTTGGACAAAGCTTTTTACTCAGA R 2 1 2 1 101000 r 74 goat snp56059-scaffold875-326243 13 15574245 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453114 Affx-122920021 AX-123323447 13 15235796 TTTCTTAAGATGAACGGAAGCACGAGAGGTCAAAC[A/G]TCTTGACCAGGTTCTGCTTGCAGTAAATGTCAGCT R 2 1 2 1 101000 f 74 goat snp56057-scaffold875-264430 13 15636053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429088 Affx-122938272 AX-123299430 13 15271920 AGGAGAACACCAAGAACAGTTAATATTGGAAAATG[G/T]GTTTGGGAAGGGAGAATGTGGAAAGAGATCTCTTT K 2 1 2 1 101000 f 74 goat snp56056-scaffold875-228306 13 15672395 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451633 Affx-122921614 AX-123321966 13 15360928 ATAAACCCTCCACTCTTATGCACCTGTGACAGGTA[C/T]GTTTCTTTATGTGTCAGTTTCCACAGAGAATTGAG Y 2 1 2 1 201000 r 74 goat snp56054-scaffold875-139298 13 15761470 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393708 Affx-122965246 AX-123264063 13 15415877 AGCCCTGCTCGCACTCAGCAGAGCAGTCACAAAGT[C/T]GGGACTGGGAGCTGGAGGTCACCTGAAGGATGGGC Y 2 1 2 1 101000 f 74 goat snp56053-scaffold875-84349 13 15816563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766034 Affx-122922182 AX-385253451 13 15515468 AGACCTTTGTAAAGTCAGTGGAAAGAAAAGGTGAT[A/G]CATTTATTTCTACATATGGCTGTAGCTTATGAGGA R 2 1 2 1 101000 f 74 goat snp21929-scaffold2154-15143 13 15917248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785675 Affx-122923938 AX-385272716 13 15570137 GAACAGTGCCTGGTATGTAACAAGTCATTAATAAG[C/T]AGCTGTTAAGTGACAATTTAAATGAACGTGGGAAC Y 2 1 2 1 101000 r 74 goat snp21930-scaffold2154-69812 13 15971940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413566 Affx-122950592 AX-123283915 13 15627513 GGCACTCATACCTTGTCTATCAGATCACGGTTGAC[A/G]CAGTTGGGTAACTGCTGGAGGAAAGCATCTACTAT R 2 1 2 1 101000 f 74 goat snp21931-scaffold2154-127188 13 16029704 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785757 Affx-122942945 AX-385272797 13 15674430 CACATGAAAGCCCTTCTAAAACTAGGAAGAAAATC[C/T]TTCAAGACCACAACTTCCAATATCATCTATAAAAT Y 2 1 2 1 101000 f 74 goat snp20570-scaffold2022-611120 13 16077085 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434932 Affx-122933870 AX-123305272 13 15770541 GTGGCTAACTGCATTTAAACGTGGCTATTTCCAGA[C/T]AGGTTTTAATATAAACAAAACTCAAAAATAGGACC Y 2 1 2 1 101000 f 74 goat snp20568-scaffold2022-515009 13 16173028 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410203 Affx-122952573 AX-123280553 13 15843053 CCGGAATGCACCTGGCAAAAGAGTAAGAGTTGCCC[A/G]CATTTTTAACTCTAAGTGTCTCATCCATCTGCCCT R 2 1 2 1 101000 r 74 goat snp20567-scaffold2022-442497 13 16247432 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432948 Affx-122935291 AX-123303289 13 15909019 CAGTATAACACCCATTCATAAGCGATACTAGATAC[A/G]TCCACTTCCTAATATGTAACATCTTCAATATTTAT R 2 1 2 1 101000 f 74 goat snp20566-scaffold2022-376531 13 16314033 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397329 Affx-122963299 AX-123267684 13 15941645 AAAGATAAATTTGTGAATTGATGGGTGATGGGAGA[C/T]GTTAACTAGCTGGGAGTTAATCTAATTAACTAGAT Y 2 1 2 1 101000 f 74 goat snp20565-scaffold2022-343905 13 16346868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276837 Affx-1111835547 AX-519550346 13 15953170 TTTTATTTATAGGAATATTGAGGAATATTATAGGA[A/C]TAGGCAATTATGGAATTATGCAGGCTGAAATGTCT M 2 1 2 1 101000 r 74 goat Random2.2K-1320 13 15953170 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407484 Affx-122954762 AX-123277835 13 15981970 AGCCAAGGTTTTCAAAGCATTAGAGAAAATCATTA[C/T]GGAATCTGGGAGGCAAATGCAGCCCTCGAGGCTAA Y 2 1 2 1 101000 f 74 goat snp20564-scaffold2022-303580 13 16386541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272678 Affx-1111832976 AX-519546384 13 15986981 ATGTCATAGAGCTAGTAATTCTCTCTACCTTGAGA[A/C]AATCAAGATACACACAAAAATAACAATGTTATTTA M 2 1 2 1 101000 f 74 goat 13_15986981_AF-PAKI 13 15986981 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320786741 Affx-122975517 AX-385273772 13 16011647 ACATCTAAAAGGAAGGTGACGATCCACGTTCACCC[A/G]TGCCATAATAAAACTACACTGCTTTGGTCAAACAC R 2 1 2 1 101000 f 74 goat snp20563-scaffold2022-273903 13 16415681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790527 Affx-122952221 AX-385277530 13 16041961 GCATCTGTCCTGGAGCAGAGACATACTGATAGACA[A/G]ATTTTAAATCCTTTCCAGTGGGAGGAATTCACCAC R 2 1 2 1 201000 f 74 goat snp20562-scaffold2022-243589 13 16445532 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377815 Affx-122977309 AX-123248174 13 16093020 CTCCTTCATCTAACAGATATTTACCGAGTATCTCC[C/T]GCGTGCCCTGCTGGGGCTGGAAACAGAGACAGAAA Y 2 1 2 1 101000 f 74 goat snp20561-scaffold2022-192530 13 16496756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383164 Affx-122973231 AX-123253522 13 16149229 GAGACGGTGAGATGGGGCAGGATCCAGGCTGTCAT[A/C]GGTACTTCAGGGTAAGTCAGGGACTTCAGTCGTTA M 2 1 2 1 101000 r 74 goat snp20560-scaffold2022-136321 13 16550892 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776437 Affx-122976807 AX-385263564 13 16182427 TTAAAAAACGAGAATAACAGAAAACATCCCATTTT[C/T]ATAAAATTAGTTTTATTTCATCAACAAGGATACCT Y 2 1 2 1 303000 r 74 goat snp20559-scaffold2022-103123 13 16583673 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408843 Affx-122954014 AX-123279194 13 16218654 CCAACAACGAATGATCCAGCTCCAAAGGCCAACAG[C/T]GCAGCCCCTCCCCAATAGGAGGAGGCAGCAAGGAC Y 2 1 2 1 101000 f 74 goat snp20558-scaffold2022-66896 13 16620114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378842 Affx-122976533 AX-123249201 13 16277259 GGGCACACTTGGGTGTACGCTCTGTTTCAGACAAA[C/T]GCTAGCCTCCTTGATGGCCTCATGGATGAGATGAA Y 2 1 2 1 101000 f 74 goat snp20557-scaffold2022-8291 13 16678517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425148 Affx-122941198 AX-123295494 13 16580567 GAACTACACATTTTCAGTGGGTGAATTATATGTTA[C/T]ATGAATTATATTTCAATAGCCTTTTAAAAAAATTC Y 2 1 2 1 103000 f 74 goat snp46249-scaffold638-294918 13 16973956 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381571 Affx-122974813 AX-123251929 13 16616292 CCCTCCTAACAGTTCTAAGAAACCAAAATAGTGTC[G/T]AAGAGTAGAAAAAAAACTAGATGATATAAACTATA K 2 1 2 1 101000 f 74 goat snp46250-scaffold638-330643 13 17010441 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397788 Affx-122962504 AX-123268143 13 16683101 CTTAAATTTAGTAGTAATTTGTGCGAATTTACAAA[C/T]GCCATCAACTCTCTCGTCTTCCTGTGTGTGTGAAT Y 2 1 2 1 201000 f 74 goat snp46251-scaffold638-397452 13 17075263 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454178 Affx-122919308 AX-123324511 13 16712372 ACGTGGCTCCACCTCCAACCCCGGTTGGTTTGTTA[C/T]ACATGTAAGCAAGCAATACATAAAACCACTATCTC Y 2 1 2 1 103000 f 74 goat snp46252-scaffold638-426723 13 17104519 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393670 Affx-122965274 AX-123264025 13 16745908 AAATTATTTTTCTCTACCCACTTTTAAAATAAAAT[A/G]TAAGATGCTTAGTGCTTAGTCACTCAACCCTGTGG R 2 1 2 1 101000 r 74 goat snp46253-scaffold638-460259 13 17137997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797571 Affx-122967771 AX-385284510 13 16776854 TATTTAGATTTCTAAATGGTTAACTTATTTGGTTT[A/G]TATTCAGTATGTGGTATTTTGTTAATAAGGTGTCC R 2 1 2 1 101000 r 74 goat snp46254-scaffold638-491205 13 17168453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789403 Affx-122937207 AX-385276413 13 16817115 ATTTTATTAATGGAAACACTGAAGCCTTATAATAC[A/G]TAGGAATGGTGTTTTTAAAGGTTTCAGTTTTATTA R 2 1 2 1 201000 r 74 goat snp46255-scaffold638-531466 13 17209634 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423485 Affx-122942571 AX-123293831 13 16878366 CAATGTGGGCTTGACTCTGACAACTACGTGTTATA[C/T]AGCCAGGGAACTTGAAATTCAGAAAAGTCTGAAAA Y 2 1 2 1 101000 f 74 goat snp46256-scaffold638-592717 13 17271095 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766151 Affx-122953291 AX-385253553 13 16915182 TATCAGTATTCTAATTTGGTTTGGGGCCCAGTTAG[C/T]ATTTAATAAAGGGATTCTGACTATCACACTACTCT Y 2 1 2 1 101000 f 74 goat snp46257-scaffold638-629533 13 17307381 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381109 Affx-122974584 AX-123251467 13 16944284 TATCAGCACATGACACCCTGCAGCACCGTTACTGA[C/T]GTAGCAACCTGAGTACTTTTCACATCAATCAGTTT Y 2 1 2 1 101000 r 74 goat snp46258-scaffold638-658635 13 17336822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803238 Affx-986696240 AX-385290093 13 16955204 GAATAAATGAAGAAGAATATTTTTCACTATGACTG[C/T]TCATGCTTTCACATTTTTCATTAGCTATGCATAAG Y 2 1 2 1 600010 f 74 goat 13_16955204 13 16955204 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 38427142 Affx-122939642 AX-123297485 13 17005884 AAGGAATCTTACTCAAAAAAAGTTTCCCCCAATAT[A/G]TTTCATGTTGATGTGATCTGCCTTCATTTGACTCT R 2 1 2 1 101000 r 74 goat snp46259-scaffold638-720235 13 17399227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769946 Affx-122936671 AX-385257115 13 17121415 TATCTTCACAACCTCGCAGGCAGCACTGCTAATAA[A/G]TTTTAGTTTGGAAGCAAAGTCTACTGGCGTGGTTT R 2 1 2 1 202000 f 74 goat snp46262-scaffold638-835766 13 17513516 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433585 Affx-122934965 AX-123303926 13 17150818 GTCCAGCCCAGAGGAGGCCTTCAGCAGACGTCCCA[C/T]GAGTGAGTATCTTGTGGTCAGGGCTTTGGGCTTAC Y 2 1 2 1 101000 r 74 goat snp46263-scaffold638-865169 13 17542882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422715 Affx-122943640 AX-123293061 13 17211763 AGCAGCACAGTGTGCGATATCCACAGCGCAGCACA[A/G]CACTGCAGGCTGATCTGCGTGTCAACTTGAGTTCT R 2 1 2 1 201000 f 74 goat snp46264-scaffold638-926114 13 17603983 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445995 Affx-122925875 AX-123316332 13 17246772 CGAAAGAAGAGGAGACGGTCCTGGGGCACCACAGC[A/G]TTTTCTGATTTGGTCCCTATCTTCTGTGAGTTTAG R 2 1 2 1 101000 r 74 goat snp46265-scaffold638-961123 13 17639390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801220 Affx-122933468 AX-385288133 13 17290610 CAAAGTATGCTCCTGTTGTCAAATTTTGTTGGACC[A/G]CCTTCCTTGGTTTTACTAGTAATGGATGACAACTA R 2 1 2 1 101000 f 74 goat snp46266-scaffold638-1004961 13 17683141 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426009 Affx-122941134 AX-123296355 13 17353047 TTACCTTAGATTTTCTTTTTCTCTCACTTGTCTTC[A/G]CTTTTTCTCTCTTTCACTCCTACATTATGTGATCA R 2 1 2 1 103000 r 74 goat snp46268-scaffold638-1067398 13 17746180 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276839 Affx-1111835548 AX-519550348 13 17374057 GTGTGTCCTTGGAACCAGATTTTAATGCATAGCTC[A/G]GCCTACACCCAAAATGCTTCATTAGCCCTCTAAGC R 2 1 2 1 101000 r 74 goat Random2.2K-1322 13 17374057 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779842 Affx-122925975 AX-385266941 13 17408690 TAATTATTAATCTTATGATCACATTTTTGAAAAGC[C/T]GTCTAAACGTATTAATGATTTAATAGTGGACGGCA Y 2 1 2 1 101000 r 74 goat snp46269-scaffold638-1123041 13 17801525 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424636 Affx-122942174 AX-123294982 13 17448363 TTGAATCCAAGGGAATGTGTCAGCTTCTTTGGTGT[A/G]CCGCCTGGTTCTGCCAGGAGTTCATTTGCTGTCTA R 2 1 2 1 101000 f 74 goat snp46270-scaffold638-1162714 13 17840586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390843 Affx-122967832 AX-123261200 13 17477717 GAGGACATGAGTTTACTGTGTCTCACACCACATTC[A/C]TCTTGGGAATCTGTAAGGGAAACTTCTTCCTGGTG M 2 1 2 1 101000 r 74 goat snp46271-scaffold638-1192068 13 17869789 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413297 Affx-122950199 AX-123283646 13 17535362 TGAGGGGCGGGCTGACCACAGGTCACAAGGAAAGA[C/T]GTCAGCTTCCAGTTTAAGTGTCTGACCCTGAGGTT Y 2 1 2 1 101000 r 74 goat snp46272-scaffold638-1249713 13 17927445 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779861 Affx-122959497 AX-385266960 13 17568080 ATAAATTGGTCCTTATTTTGCCTAATTGTAGATTC[A/G]TGTGTTTCTTCTATTTTTAGTGCTGAATTTGGCAG R 2 1 2 1 101000 r 74 goat snp46273-scaffold638-1282431 13 17960023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782357 Affx-122928695 AX-385269433 13 17612996 AATTCTTGTAAGCATATTTTTCTAGTAGGTCCTGA[C/T]GGCACTTGGTTTGCACTTAAAACTGTATGTGGGAT Y 2 1 2 1 101000 r 74 goat snp46274-scaffold638-1327347 13 18004661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276705 Affx-1111835549 AX-519550215 13 17625458 TAAGTATTTATGAACTTCCATAATGGGGCTTCCCC[A/G]ATAGCTCAGTCGGTAAAGAATCCACCTGCAATGCA R 2 1 2 1 202000 f 74 goat Random2.2K-1323 13 17625458 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781796 Affx-122963709 AX-385268878 13 17667995 AGAAGAAGAAATATATAAGTTTAAACTGAGAAGAC[G/T]CTATTAAGAAAAAGCAATGTACTGTAGTCTCTGCT K 2 1 2 1 101000 r 74 goat snp46275-scaffold638-1382346 13 18059887 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788943 Affx-122955482 AX-385275956 13 17697035 ACATGTACATAAGTCAACCTTATGCATGTGGTCAT[A/G]CTTCTGAGTCATCAGTGTTTGGCTACATCCTTGCT R 2 1 2 1 101000 r 74 goat snp46276-scaffold638-1411386 13 18088871 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403216 Affx-122957905 AX-123273569 13 17729559 TGCATAAGAACTGTCCTGGGATCCTGATCAAGTCC[A/G]TTGGTAGTTACTTATGTTTGTCCAGGTTTCCTTAA R 2 1 2 1 101000 r 74 goat snp46277-scaffold638-1443910 13 18120710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276843 Affx-1111835550 AX-519550352 13 17739638 CACAACCTGGTGGCAGAGGACTGGCAACAAACAAG[A/C]GAACCGTACGCAGTGTTAGATGGTGACGGTGCTGT M 2 1 2 1 101000 r 74 goat Random2.2K-1324 13 17739638 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785785 Affx-122920828 AX-385272825 13 17793217 TTTTAGGTGAAAAGTAAGTTAAGCTAAAAGTATGA[C/T]GAAAAGTCACATCTGAAGTGTTTGAATTATAGCTT Y 2 1 2 1 101000 r 74 goat snp46279-scaffold638-1507568 13 18184177 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448692 Affx-122923866 AX-123319028 13 17843526 AAGGAGTGTGATGCTGATGCTATGTTAATGGTTAT[A/G]TATTTATTTCAAATTTTATCTGAAACAATTTAGAA R 2 1 2 1 103000 f 74 goat snp46280-scaffold638-1557877 13 18234424 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450463 Affx-122922946 AX-123320797 13 17893836 TGATGAAATGTGCTTATGATGCAAAGGTTTACAGT[A/C]TGTTGTTTTCCAATTTTTTTAAAGATGATTGTCCC M 2 1 2 1 101000 f 74 goat snp46281-scaffold638-1608187 13 18284539 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410415 Affx-122952416 AX-123280765 13 17955380 TTACTAGTCAGGAGAAGCCACCTCAAGGCTCACAA[C/T]GGAACGTCTTTTTTTCGTGTATTTATTGTTGGGTC Y 2 1 2 1 201000 r 74 goat snp46283-scaffold638-1669731 13 18346361 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385582 Affx-122971214 AX-123255940 13 17985868 TGCGTGTCATGACATGGAGGGGGCGATAGCTTGAG[A/C]AAGAATTCTCCCAGGATGAGCGTCTGGCCCAGTAC M 2 1 2 1 201000 f 74 goat snp46284-scaffold638-1700219 13 18377009 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420547 Affx-122945293 AX-123290894 13 18026051 TAGGCCTGTTAGAGATATACTTCAAAAATTCCTTC[A/G]TGGTCAAGCGTATACATTTTTTAATTCCAAGTGAG R 2 1 2 1 101000 r 74 goat snp46285-scaffold638-1740402 13 18417291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423635 Affx-122942362 AX-123293981 13 18086281 GTAAAAGATAAAGAGCATTCAATTTTCATGCAATG[C/T]GCTCTAAAGCAGGGAGTGGGGAGGAAATGGGAGAG Y 2 1 2 1 101000 f 74 goat snp46286-scaffold638-1800632 13 18477502 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789383 Affx-122967458 AX-385276393 13 18125429 ATGTGTTCAAAGTGGTCAGTATTGGTCAGTGAAAT[A/G]TCTGTTTCTACGTGTTAAATAAATGCTTCTCACAA R 2 1 2 1 101000 r 74 goat snp46287-scaffold638-1839780 13 18516753 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435678 Affx-122933331 AX-123306017 13 18162798 TGCTCTGTGCCAGGCATGAAGCTCACTGCCAAGGA[C/T]GCAGCAATGAAATCAGAAGTGGTCCCTCCCTGAAG Y 2 1 2 1 101000 r 74 goat snp46288-scaffold638-1877149 13 18554494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380331 Affx-122975374 AX-123250689 13 18208624 AACACGAGCATAGACACCTGTGTGGTCTTAGCCTC[A/G]GGACTCCTGGACCAGGTCTGTCCACGTCTTGTCAA R 2 1 2 1 101000 f 74 goat snp46289-scaffold638-1922975 13 18599907 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431478 Affx-122936258 AX-123301819 13 18250859 CCAGCCCACCTTCAGACTTCTTATGTGAGATAAGG[C/T]GTATCTGTGGTTGCTTAAGCCACTCCTGACTAGGT Y 2 1 2 1 101000 f 74 goat snp46290-scaffold638-1965210 13 18655131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427710 Affx-122939283 AX-123298053 13 18300710 CAGGGTTCAGGGCCGGGGGCTCAGACAGAGAACAC[A/G]GTGATGGAGGCAAGGTCTGCACCTCGGGGCCTTCA R 2 1 2 1 201000 f 74 goat snp46291-scaffold638-2015061 13 18704411 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379669 Affx-122975927 AX-123250027 13 18330093 TTGAATATGAAAACACACAAGGTGATGCTCAGTGC[A/G]TCACTGAATGTGTGTGTGTATCTTTGTGCATGCAT R 2 1 2 1 102000 f 74 goat snp46292-scaffold638-2044444 13 18734275 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770111 Affx-122943014 AX-385257278 13 18360828 ACACTGACAAGGTTTATGAACTGCTATTAATTCGT[A/C]GTAAGTTATTAATTCCTAGCATTGTTTTTATTATA M 2 1 2 1 101000 f 74 goat snp46293-scaffold638-2075179 13 18761691 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434169 Affx-122934889 AX-123304510 13 18394810 GAGGCTTAAAGAGGTCAAAAACACATAGAAAGTGG[C/T]AGGGCCAGAATTCAAACTCATTAGTCTGGCTTCAG Y 2 1 2 1 101000 f 74 goat snp46294-scaffold638-2109161 13 18795968 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433777 Affx-122934478 AX-123304118 13 18448608 ACATAGGGATTACGAATAGGAGCTCTGAAATCATG[C/T]AAGTATAGGCTTGAATTCTGACACTGTCAGTTATG Y 2 1 2 1 201000 f 74 goat snp46295-scaffold638-2162959 13 18850223 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378407 Affx-122976789 AX-123248766 13 18478923 AAGTCAAGAGTGACACCCTAGTTTCTCAGTTTGGG[A/C]GATTTATTGATACTGGAATATTTTGCTGGCAAGGG M 2 1 2 1 101000 f 74 goat snp46296-scaffold638-2193274 13 18880547 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448360 Affx-122924115 AX-123318696 13 18508288 ATTCCCACTTTTTCCTTTTCTCCGTCTTCTTCCAC[A/G]GTTAAGTCATCAAGTCCTGCTTCTTACGCATGCCT R 2 1 2 1 201000 r 74 goat snp46297-scaffold638-2222639 13 18909811 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463260807 Affx-1109895730 AX-514746312 13 18574418 TCCATTTTCCAGAGAAAATCATCCACCCATTCTGG[C/T]TCAGAAGCCCCTCTGCTGCCAGATAAAAAGATGTT Y 2 1 2 1 202000 f 74 goat 13_18574418_AF-PAKI 13 18574418 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418337 Affx-122946957 AX-123288685 13 18629591 CAGGTTTATTGTGCCATCTACTAAGTAGTCTTCTG[C/T]GTCTCCAGGACCATGGCTAATATATGCATGGGGAG Y 2 1 2 1 101000 f 74 goat snp46300-scaffold638-2343942 13 19031278 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800347 Affx-122938951 AX-385287269 13 18666418 CCTTCTCTCTAGAATATTCTCTCCCTTTTTTGTCC[A/G]CTTGTAAGTTCCTACCATTCATCCTTCAATAGGTG R 2 1 2 1 101000 f 74 goat snp46301-scaffold638-2380769 13 19067665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441376 Affx-122928859 AX-123311713 13 18757085 CAGCATCTTGCCTGTTCATCTTACTTTGTCTCCGA[G/T]CTCTGATGACTGGGCAGTGCACCTATTAATCTTAA K 2 1 2 1 101000 f 74 goat snp46303-scaffold638-2471436 13 19158916 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446291 Affx-122925656 AX-123316627 13 18800709 CACCCCGATCTGTTTTTAAGGCATAGACTCTTAAC[C/T]TAACAGAGTAACATTTGAAATGCATCTGTAATGTA Y 2 1 2 1 101000 f 74 goat snp46304-scaffold638-2515060 13 19202818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382345 Affx-122973880 AX-123252703 13 18846621 GAACTCAGACTAAAAAGATGGCAGGCTCGCTAGAC[A/G]GAAGGATCGTGGGTCCCAGAATCACTGCATGGAAG R 2 1 2 1 101000 f 74 goat snp46305-scaffold638-2560972 13 19248912 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434089 Affx-122934170 AX-123304430 13 18856802 CCAACAGTGATGGGCTCCCTATGACCAAAACACAT[A/G]TTTAGACCAAGCTTTGAGAGGACAGCATCTCTGCA R 2 1 2 1 101000 r 74 goat snp39538-scaffold503-488 13 19471223 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452109 Affx-122920839 AX-123322442 13 18900835 CAAATGTGTTATTTAGAGAGAACAGTTGTAGAGTG[C/T]GTGCATGTGTGCTAAGTCATTCAGTTGTGTCTGAC Y 2 1 2 1 201000 f 74 goat snp39539-scaffold503-44521 13 19516157 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394899 Affx-122964737 AX-123265254 13 18932594 GTTATATACTAGTCATTAACCATGCAAATACCAAA[C/T]AAAGTTGATCAAAGGTTTCATTTAGTTTTCTAGTT Y 2 1 2 1 101000 f 74 goat snp39540-scaffold503-76280 13 19548496 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790579 Affx-122919593 AX-385277582 13 18973389 CTATAAAACAGCTGGTTTTGAAAAGTTAAACAAAA[C/T]TGATAAAACTTTATCCCAACTAAAAGAAGAAAGAG Y 2 1 2 1 303000 f 74 goat snp39541-scaffold503-117075 13 19589244 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792304 Affx-122970609 AX-385279286 13 19013330 TTTTTATAAAACTTATAAAGATCCATAATGTGTCT[A/G]TCTTTCAGCCCATGAGGGCCAGTATAGGGGGGCAT R 2 1 2 1 102000 r 74 goat snp39542-scaffold503-157016 13 19630485 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784410 Affx-122957277 AX-385271459 13 19043777 TGCTACTCTTGTAACCATAGTCATTTTGATTAAGC[A/C]TAAATTAACTTTCATTATATTTAGCATAAAGAAAA M 2 1 2 1 202000 r 74 goat snp39543-scaffold503-187463 13 19661720 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445059 Affx-122926227 AX-123315396 13 19120770 TCACTGGACCTAGAAATAGTCTTGTTCTAGGAGTG[C/T]AAATAACAGTCTTCTCATGTCCTTTTCATCCTTCG Y 2 1 2 1 101000 f 74 goat snp39544-scaffold503-264456 13 19738930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415722 Affx-122948514 AX-123286071 13 19187308 TATTTGAAATGCAGTAAGTACAAGTGTTAAACTTA[C/T]GATTTATTCCAACAACATTGTGCTTTGTGCTATGT Y 2 1 2 1 101000 r 74 goat snp39545-scaffold503-330994 13 19805314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444666 Affx-122926455 AX-123315003 13 19245552 GTTTTGAATAATTAATTTTTTACTAGTTGTTACTG[C/T]AGGAGCATTGGCCTGCTGTGAAATAGCTATAAAGT Y 2 1 2 1 101000 r 74 goat snp39546-scaffold503-389238 13 19863861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396797 Affx-122962750 AX-123267152 13 19278439 AATAAATGTGAACTACATTTAATATGAGTTATTGA[A/G]TATAAAATCGAGTTAATGAAACCACTTCCACGAGT R 2 1 2 1 101000 r 74 goat snp39547-scaffold503-422125 13 19901486 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784589 Affx-122939301 AX-385271637 13 19326770 AAACTTATTACCAACACAGGAGCCAGAACATTTCT[A/G]TTAAAATGTAAATAAGATCGTGTCACTACGCTGTG R 2 1 2 1 101000 f 74 goat snp39548-scaffold503-470456 13 19950189 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417157 Affx-122947344 AX-123287505 13 19374025 AATTCTACCTTATCTTTTCTGAGGATCAAGGTTGG[C/T]GGAATTCACTGCCAAAATTATTGAATTTAGCCCTC Y 2 1 2 1 101000 f 74 goat snp39549-scaffold503-517711 13 19997573 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420335 Affx-122945002 AX-123290682 13 19429121 CTATTACTCGTAGTCTGGAGTTGGGAAGAGTAGGC[A/G]TTATCCTTCCCAACTGGATTTGGATTTAAGGCCCA R 2 1 2 1 201000 r 74 goat snp39550-scaffold503-572807 13 20052189 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775934 Affx-122944748 AX-385263065 13 19467527 TTTATCTGGAATCACAGGATATAGAGTGAGTAAGA[C/T]GGAGAAGTAAGGTTGAAGGAGGAGATCATTATTGT Y 2 1 2 1 101000 r 74 goat snp39551-scaffold503-611213 13 20089965 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389192 Affx-122969076 AX-123259550 13 19521187 CTCAACCTATACCCCGCCTCTCTCCCAAACATACA[C/T]GCATCTCTTCTTACCTCTTTACCTGACATTTTCCA Y 2 1 2 1 101000 r 74 goat snp39552-scaffold503-664873 13 20144974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405844 Affx-122955866 AX-123276196 13 19573842 GTTTGTGTGTGAAGAATTGGAGGTTAACTGGCAAA[C/T]AGATGTCTTCAAAGACAAACTGAATTGAAACATGT Y 2 1 2 1 101000 f 74 goat snp39553-scaffold503-717528 13 20197879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408259 Affx-122953812 AX-123278610 13 19609984 CACTGAACTTCTGAAAGTGACTTTAGTTCACGCAC[A/G]CTTTTCATCTATATTCATGGGCGTAGGCTAATAAT R 2 1 2 1 101000 f 74 goat snp39554-scaffold503-753670 13 20234481 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771787 Affx-122926145 AX-385258944 13 19651930 ATTTAGCTACATTTGTTATAGAGAGAAATCTTTCA[C/T]ACCATATATTGATTTTATATTCGTGAATTAGGGCA Y 2 1 2 1 101000 r 74 goat snp39555-scaffold503-795616 13 20277497 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384727 Affx-122972052 AX-123255085 13 19713550 GTCTTCTAAGTAGACAGGAGCCCAGTAGCTACACC[A/G]TCTCTCTCTTAATTCATATAGAGGAAAACACCTCA R 2 1 2 1 201000 r 74 goat snp39556-scaffold503-857236 13 20340301 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449043 Affx-122923069 AX-123319378 13 19749832 AGAGTTTCACTTTATTAGTAGAGTAACTTATTGAC[A/G]TTGGTGAGTGAAAAGAAATGTTCTTTTCATGCACT R 2 1 2 1 101000 f 74 goat snp39557-scaffold503-893518 13 20376994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795847 Affx-122962819 AX-385282800 13 19780739 CCTTCTTAAAGTATCCATCCATGTTTTCAGTATAG[C/T]GTATGTGATTTTTCCCCCTAGTGCTATATTTGTAT Y 2 1 2 1 101000 f 74 goat snp39558-scaffold503-924425 13 20407837 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801274 Affx-122934728 AX-385288186 13 19831644 TCATAGACATAGGAGGGCAACCAAAAGAGAATGAT[A/G]ATCTTAAATCAAAGGTAGAAATCTATATATCAGAG R 2 1 2 1 101000 f 74 goat snp39559-scaffold503-975330 13 20458716 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769342 Affx-122939136 AX-385256513 13 19861930 AGAAGGGACAGAAACCAAAAAACAGACTATTGGGA[C/T]GGAATGAAGAGTCTACTAATAGGTTGATATAGCTA Y 2 1 2 1 101000 f 74 goat snp39560-scaffold503-1005616 13 20489039 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276845 Affx-1111835551 AX-519550354 13 19881676 ATGTATGACCAACATGTCTGAAGGAAGAAATTCAG[A/G]ATGCTCTATATTTAACCTAATGTGTGGGAGGGTGC R 2 1 2 1 101000 r 74 goat Random2.2K-1327 13 19881676 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 539476290 Affx-1251763797 AX-586011709 13 19882988 TCAGTGGACCCTTTCCTTTACATTCTACCTGTAAG[-/ATGATATAATGATTTTTTTTTTTTTTGTTTTGTTTTTTTAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCT]TGATATAATGATTTTTAGACTTTTCCAATCTTACA - 8 1 4 1 20000 f 74 goat SV_188 13 19882988 - deletion junction SV-TF-chip 539476543 Affx-1251763797 AX-586011932 13 19882988 TCAGTGGACCCTTTCCTTTACATTCTACCTGTAAG[-/ATGATATAATGATTTTTTTTTTTTTTGTTTTGTTTTTTTAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCT]TGATATAATGATTTTTAGACTTTTCCAATCTTACA - 4 1 4 1 20000 r 74 goat SV_188 13 19882988 - deletion junction SV-TF-chip 562165187 Affx-1251763797 AX-606940599 13 19882988 TCAGTGGACCCTTTCCTTTACATTCTACCTGTAAG[-/ATGATATAATGATTTTTTTTTTTTTTGTTTTGTTTTTTTAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCT]TGATATAATGATTTTTAGACTTTTCCAATCTTACA - 8 1 4 1 20100 f 74 goat SV_188 13 19882988 - deletion junction SV-TF-chip 562165330 Affx-1251763797 AX-606940741 13 19882988 TCAGTGGACCCTTTCCTTTACATTCTACCTGTAAG[-/ATGATATAATGATTTTTTTTTTTTTTGTTTTGTTTTTTTAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCT]TGATATAATGATTTTTAGACTTTTCCAATCTTACA - 8 1 4 1 20100 f 74 goat SV_188 13 19882988 - deletion junction SV-TF-chip 562165470 Affx-1251763797 AX-606940881 13 19882988 TCAGTGGACCCTTTCCTTTACATTCTACCTGTAAG[-/ATGATATAATGATTTTTTTTTTTTTTGTTTTGTTTTTTTAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCT]TGATATAATGATTTTTAGACTTTTCCAATCTTACA - 8 1 4 1 20100 r 74 goat SV_188 13 19882988 - deletion junction SV-TF-chip 562165960 Affx-1251763797 AX-606941369 13 19882988 TCAGTGGACCCTTTCCTTTACATTCTACCTGTAAG[-/ATGATATAATGATTTTTTTTTTTTTTGTTTTGTTTTTTTAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCT]TGATATAATGATTTTTAGACTTTTCCAATCTTACA - 8 1 4 1 20100 f 74 goat SV_188 13 19882988 - deletion junction SV-TF-chip 562166337 Affx-1251763797 AX-606941745 13 19882988 TCAGTGGACCCTTTCCTTTACATTCTACCTGTAAG[-/ATGATATAATGATTTTTTTTTTTTTTGTTTTGTTTTTTTAGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCT]TGATATAATGATTTTTAGACTTTTCCAATCTTACA - 8 1 4 1 20100 r 74 goat SV_188 13 19882988 - deletion junction SV-TF-chip 320780601 Affx-122950884 AX-385267691 13 19920472 ATCCATACTTCTGATCATCACCAGAAATATTGCTC[A/G]TGTCTACTGATGAATTTTCAATTACAATGTTGCAC R 2 1 2 1 101000 f 74 goat snp39561-scaffold503-1064158 13 20547658 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424017 Affx-122942093 AX-123294363 13 19950028 TCTTTCCTTATAACCAGTTCAGCTTTACATTACAT[C/T]ATTCTTTCTAATGTTGTATCTTTTGTATTATTTTA Y 2 1 2 1 101000 f 74 goat snp39562-scaffold503-1093714 13 20577838 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380000 Affx-122975609 AX-123250358 13 19985941 ATACCACCCATCATGTTCAGGTTTCAGAAGGAAGA[C/T]GGAAAAAGATAAAAATGTGAAAAGGGAACATCACT Y 2 1 2 1 101000 f 74 goat snp39563-scaffold503-1129627 13 20613660 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424662 Affx-122942153 AX-123295008 13 20043497 AGATAATACTAAGGAAACAATCATGTATGTCTTCT[A/C]TCTTGTAATGCAGACATTTCATTGTCTGAACTTTT M 2 1 2 1 101000 r 74 goat snp39564-scaffold503-1187183 13 20671161 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387719 Affx-122969755 AX-123258077 13 20082281 TATTGTCTTGGATAAATAAAAACTAGTTTCTATTC[G/T]TAAGAAATGTGACCCACAGGGAAACACAAGCACAG K 2 1 2 1 201000 f 74 goat snp39565-scaffold503-1225967 13 20709839 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394392 Affx-122964624 AX-123264747 13 20136470 CCACAATTATGCTAGAGCTGGGAAGCAAACTGTTA[C/T]GTTTCTGAGTTCCTTTCTTATTTTTTTTTATCTGT Y 2 1 2 1 101000 f 74 goat snp39566-scaffold503-1280156 13 20764556 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404722 Affx-122957247 AX-123275074 13 20171638 CAGGCGGTTAGCATTGACATGATTGATCTGCCTCT[C/T]GCTTTTTTTGAGTCCAGTTCATGATAATCAAAGCA Y 2 1 2 1 201000 r 74 goat snp39567-scaffold503-1315324 13 20799685 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432640 Affx-122935475 AX-123302981 13 20205495 GCGACATGAAATAATTTGCATTTATTAAAAAGCAG[C/T]ATGCATCATTTTGCTGAAGCTGCTATTAAACTAGA Y 2 1 2 1 303000 r 74 goat snp39568-scaffold503-1349181 13 20833668 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383976 Affx-122972935 AX-123254334 13 20260856 ACTGTGTTTTTGAAGCGTTAAATTTAAAGCTGTCC[A/G]CATATACAAAGTAGGAGTAAGAGGCGACAGCAGTG R 2 1 2 1 101000 f 74 goat snp39569-scaffold503-1404542 13 20888506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276848 Affx-1111835552 AX-519550356 13 20279717 TTAAGATAGCATCATATATTCAATAGGCAGAAAAG[A/C]TCGAAAGATGTCTAAGTACGAAAGCCTGTCTGACA M 2 1 2 1 101000 r 74 goat Random2.2K-1329 13 20279717 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436977 Affx-122933155 AX-123307315 13 20310095 AACACAAAGGAATTCACGAATGACTGACCCAAGGG[C/T]AGGATAGAATCAGGGCTCAAACCCTAGTCCTTTTG Y 2 1 2 1 201000 f 74 goat snp39570-scaffold503-1453781 13 20937944 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424292 Affx-122941978 AX-123294638 13 20344702 GTCTAGAAGGAGTCCTGGGAAGAGAAACCTGATAG[A/G]TGTGGCTTCAGGGTGAAGCCAGAGGAGACGTGTGT R 2 1 2 1 101000 f 74 goat snp39571-scaffold503-1488388 13 20972776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417613 Affx-122946870 AX-123287961 13 20384458 CACAGAAAAAATAAAATTCTGTTCCCTCGCATGCT[A/G]TTACCTACCTAACTGTTATAGAGACAGACATAAAA R 2 1 2 1 201000 r 74 goat snp39572-scaffold503-1528144 13 21012414 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763028 Affx-986697557 AX-385251002 13 20417715 CTGGAATACTCCATTTGGAAAGGGATCCCAGCATG[C/T]TTCACCCTAGGGGCTGTCTGCAGAGTACATGGGAT Y 2 1 2 1 600010 f 74 goat 13_20417715 13 20417715 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 38388503 Affx-122969218 AX-123258861 13 20442675 AGAGTGATCTGTTGTCACGTGCAAACATAACGTCA[G/T]CATTACCTAAGGTGTGCATGGGTGGTTACACAGAA K 2 1 2 1 101000 f 74 goat snp39573-scaffold503-1586361 13 21071570 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765092 Affx-122923001 AX-385252656 13 20498592 TGGATGCCTTCTGTGTAAGCAGTGACAGGATCGTA[C/T]GTAGCCTTTTAGCTAAGCATGAGGACAGAGGGAGG Y 2 1 2 1 101000 f 74 goat snp39574-scaffold503-1642278 13 21127518 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399145 Affx-122960653 AX-123269500 13 20528851 GTGGTAGCTGACTAAATATCAGGTCCTCAAATCAT[C/T]CAGTGACCTGGACTTCAGGAAAAAAATCACTGTGT Y 2 1 2 1 101000 f 74 goat snp39575-scaffold503-1672537 13 21157825 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437824 Affx-122932107 AX-123308162 13 20611839 ACACCATGACTGATAAGAAGCAAAGATGATTCCAC[A/G]CTTTATTGATTAAAAAAGGAAATATCTTAAAAATG R 2 1 2 1 101000 f 74 goat snp39577-scaffold503-1755525 13 21241369 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803240 Affx-986696241 AX-385290095 13 20620553 AAACATGCTGGGATCCCTTTCCAAATGGAGTATTC[C/T]GGTCCCGCCTACCTCACACCACAGCTTGGAGCTGG Y 2 1 2 1 600010 f 74 goat 13_20620553 13 20620553 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 320763032 Affx-986697561 AX-385251006 13 20620726 GCACCAGCCTGGCATTATGTCTTGTATAAACAAAA[C/T]GGAGAAAGGGATGCAGCATTTGGGCTGTTTCTGGG Y 2 1 2 1 600010 f 74 goat 13_20620726 13 20620726 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 38396031 Affx-122963472 AX-123266386 13 20650342 AGTAGAGTACAACAATGGGCATACAGAGGCTGGCA[C/T]GCATGTTCACATTTTTGAAGGCTCGCAACCTGAAG Y 2 1 2 1 201000 r 74 goat snp39578-scaffold503-1794028 13 21279974 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378795 Affx-122976991 AX-123249154 13 20689603 CCGCTGTTCAGTCACCACTCGAATATTCAAGCCCC[A/G]AGTTACAAGACCTCAAATCAATGAGCTTGAGAAAG R 2 1 2 1 101000 r 74 goat snp39579-scaffold503-1833289 13 21318921 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422907 Affx-122943052 AX-123293253 13 20702087 TCAGTTGGAGCTTTGCCAACTGCTGACAACTCTCC[A/G]CAACTCCCAGGAGAGCTTCCCTGACTTACTGTAAC R 2 1 2 1 101000 f 74 goat snp58703-scaffold958-9441 13 21331197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451007 Affx-122921716 AX-123321341 13 20732016 GCTGCTCCATCTCTGGTGCCTAGAACAGTCCTGAT[A/G]TATGGCAGGAAACTCAACAAATATTTACTGAGTGA R 2 1 2 1 101000 f 74 goat snp58704-scaffold958-39370 13 21360810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405018 Affx-122956375 AX-123275370 13 20787082 GATTTTACTATATGTAAATTATATGCATCCCTCAA[C/T]GTTTGCTCCCCATCAGCAGCTGCTCATGGCTTGTC Y 2 1 2 1 201000 f 74 goat snp58705-scaffold958-94436 13 21414246 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770475 Affx-122926248 AX-385257641 13 20834027 TTGGATGTATTTACCGAGCATTAACCAGACATCAC[A/G]TCATATTGAAGGAAACGTTCCTTCTGTATCATGGC R 2 1 2 1 101000 f 74 goat snp58706-scaffold958-141381 13 21461067 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403279 Affx-122957858 AX-123273632 13 20874441 CAGTCAGGTAGGAAGGTGAATAAGGGGTCATTGTG[A/C]TCAAGGCACACATTTATAAGCACATTGAGACAGGC M 2 1 2 1 101000 f 74 goat snp58707-scaffold958-181795 13 21501477 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801192 Affx-122937568 AX-385288105 13 20908688 AGAAAACAATCTTCAGAGCTTTGCATGGCTTTCCA[C/T]AGCAATGCAGATATTTACATGTTTGAATCTCAATG Y 2 1 2 1 101000 f 74 goat snp58708-scaffold958-216042 13 21536577 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276715 Affx-1111835554 AX-519550225 13 20924627 TCTTCAAGGAAAACATTTTGTAGCACAGAAAAATT[A/C]GCAAAATATGGATGGAATATAATGTCCCCTAAGAG M 2 1 2 1 101000 f 74 goat Random2.2K-1330 13 20924627 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390551 Affx-122967217 AX-123260908 13 20993613 GAACTATACTGGAACAAATACAAGAGAAGGAAGGG[C/T]AGAAAGAGTAGCAAATTATCACATTTAAGGTATAA Y 2 1 2 1 201000 r 74 goat snp58710-scaffold958-300967 13 21622017 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785753 Affx-122936178 AX-385272793 13 21032056 AGGAAACAAGCAAGTGCTCCATAATAGTAATTATT[A/C]TCATCATTAACAGTTGTAATAAAACTGAAAAATAA M 2 1 2 1 101000 f 74 goat snp58711-scaffold958-339410 13 21660625 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379627 Affx-122975960 AX-123249985 13 21125012 CAGCGGAGAATATCCTGCCTCATGAAGCTAGTGAG[C/T]GTGGGCCCAGAGCTCACTCCAGGAAACCCTGCTTC Y 2 1 2 1 101000 f 74 goat snp58713-scaffold958-432366 13 21753725 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436227 Affx-122932574 AX-123306566 13 21160726 GAAAGTGAAACTCACTGAACCAGATTCATTAACTG[A/G]AAGAATGATAATACTGCATGAGAAACTAGAATTCT R 2 1 2 1 101000 f 74 goat snp58714-scaffold958-468080 13 21789443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396483 Affx-122963545 AX-123266838 13 21189760 ACTGTATGTGATGACCGCTGTCAACTAAATTTACT[A/G]TGGTGATCATTTCACAATATATACATGTATCAAAT R 2 1 2 1 201000 f 74 goat snp58715-scaffold958-497114 13 21818723 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779602 Affx-122964758 AX-385266704 13 21221435 ACTTATTTCCGGAAAAAAGTATATGGATAGGCAAG[C/T]GAATGAAAACATGGCCTGATGTCTAGAACCCAGGA Y 2 1 2 1 101000 r 74 goat snp58716-scaffold958-528789 13 21850684 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272679 Affx-1111832977 AX-519546385 13 21297406 GTCTAAAAACACTAGACTGAAACATTTGGTTTAGT[A/G]ATCTTTAAATTTCTTTCTTATCTCTTACTACCAAT R 2 1 2 1 201000 f 74 goat 13_21297406_AF-PAKI 13 21297406 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433480 Affx-122935042 AX-123303821 13 21319675 ACAGGAAGTTCTGTTGATGGAATTTAAAAGGCCCC[A/G]CATTGGGCTGGTCCAGGTGGCACCCTTGAGCAATT R 2 1 2 1 201000 r 74 goat snp58718-scaffold958-627029 13 21948741 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388399 Affx-122969296 AX-123258757 13 21368125 TTTTCAAGAGTCCCCAAAAGGCTTTGTCGGACCAA[C/T]ACACAGTGATGATACATTCATACTAACTAATGAAA Y 2 1 2 1 201000 r 74 goat snp58719-scaffold958-675479 13 21997144 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780570 Affx-122972839 AX-385267661 13 21418583 GGTTAAAGGAGCATCTACAAGCAAGCAAAAGAACT[A/G]CTGGGTCTCAGTTCTCTGACAAAAGCTAAAATGAC R 2 1 2 1 101000 r 74 goat snp58720-scaffold958-725937 13 22047523 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454035 Affx-122919412 AX-123324368 13 21469623 GACTTCCTTAAATAATGTGACTTCCTTAAATCTCC[G/T]CAACCTTGGAGATGAAAATTAATTATCATGATAAC K 2 1 2 1 101000 f 74 goat snp58721-scaffold958-776977 13 22098823 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395365 Affx-122963984 AX-123265720 13 21511061 AAATCATTCAATTCTTTCGAATATGGGGAGAAATT[A/G]GTATATAAGAAATCACTGGAAGTGTAACTATGGAA R 2 1 2 1 101000 f 74 goat snp58722-scaffold958-818415 13 22139009 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413960 Affx-122950304 AX-123284309 13 21543881 CCATGCGGTTGCAAAGGTTCTGACAGGACTGAGTG[A/C]CTTTCACTTTCAATTCATTTGCTCATTAATGAATG M 2 1 2 1 303000 r 74 goat snp58723-scaffold958-851235 13 22171764 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429268 Affx-122937889 AX-123299610 13 21623192 TAGTTTATCACTTAAAGCAGTAGAAGTAACCAGAG[C/T]ATCAGTATTTTTGCACAATTCCCCCAAGACCCAGT Y 2 1 2 1 101000 r 74 goat snp58724-scaffold958-930546 13 22251285 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790673 Affx-122950482 AX-385277675 13 21681678 TATTTGTTCCTAAGTAGGAAGGAATTTAACTAATT[A/G]CTATATAGCCTTGCTAAGTAATATAAGATATATAT R 2 1 2 1 201000 r 74 goat snp58725-scaffold958-989032 13 22310003 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375365 Affx-122979232 AX-123245724 13 21731771 GGTTTTACAGGTTTGTTTTGGGAGAGACAGCTTTT[C/T]ACCAGTCAGCTCTGTTGAGGTTTCTGGATGTGTCT Y 2 1 2 1 101000 f 74 goat snp58726-scaffold958-1039125 13 22360304 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440897 Affx-122929225 AX-123311234 13 21770415 AGCTCCCAGCAACACAGGGAGCTGTGTGTTACTTC[G/T]CTCATGGTCCCCTGAGAAGAAGCTGGTGACTGAGC K 2 1 2 1 202000 r 74 goat snp58727-scaffold958-1077769 13 22399293 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768813 Affx-122944398 AX-385255990 13 21808946 CCCACATAGCAGTAAGTTTTTAACTGAAAAAATTA[C/T]AGTGAAACACTAGTTAACTCAACGCATTATATACT Y 2 1 2 1 102000 f 74 goat snp58728-scaffold958-1116300 13 22437901 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445779 Affx-122926060 AX-123316116 13 21855665 CTACCCAAGAGAAATGAAAAACATTTGTTCAGAGT[C/T]TTCTGTGTGAATATACACAGCAGCACTGTTAGACA Y 2 1 2 1 103000 r 74 goat snp58729-scaffold958-1163019 13 22485296 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383378 Affx-122973513 AX-123253736 13 21944282 CGTTACAGCCTGATCTCAGACTCCTGTCAGATTCT[A/G]CATTATGGTAATATAATTATTTCATTATATATGAC R 2 1 2 1 101000 f 74 goat snp58731-scaffold958-1251636 13 22573914 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772287 Affx-122946391 AX-385259442 13 21987818 AAGAAATCTTGATTGGATTTGTGGCCCAAAGTGTT[A/G]CTAATGAAATATAGTGAACTATATAATGAAAGCAA R 2 1 2 1 101000 f 74 goat snp58732-scaffold958-1295172 13 22614184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429715 Affx-122937617 AX-123300056 13 22083945 AACAACTACCAATTAAAGAGAGGCTCCTTTCATTG[C/T]GAACTGAGAATTTGCAGATACTGAATAATTAACTT Y 2 1 2 1 101000 f 74 goat snp58734-scaffold958-1391299 13 22706181 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769942 Affx-122957613 AX-385257111 13 22139374 TCTAACAATAAGAAATTGAATGTCTCAATTCATAA[C/T]TGACTTTTTAACTGCTTCATAGAATACACGAGAGA Y 2 1 2 1 101000 r 74 goat snp58735-scaffold958-1446728 13 22761729 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380928 Affx-122975015 AX-123251286 13 22182562 CTTTTGTGAGTCACTTGTGTGCTGTGGTTGGTCTT[A/G]TGAGAGGGCTGGAGGTGTTTCCTTCCACTGGCTAC R 2 1 2 1 201000 r 74 goat snp58736-scaffold958-1489916 13 22805003 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789716 Affx-122947775 AX-385276724 13 22227010 CAATTATAAACAGTGGAATATACCCTCTCTGTAAC[A/G]TCTGGAAATAGAAGCAATTTATTGTGAGCTTCTAC R 2 1 2 1 101000 r 74 goat snp22467-scaffold2223-8704 13 22851681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417343 Affx-122947731 AX-123287691 13 22284397 CATATTAAGGCTGCTGCCGCCTGGGCCTTGGGACA[C/T]ATTGGGAGACACACTCCTGAGCACGCACGGGCCGT Y 2 1 2 1 201000 r 74 goat snp22468-scaffold2223-66091 13 22909097 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787377 Affx-122931942 AX-385274402 13 22313775 TCCTTGTCATTTAAACCCGGGAAAATCTGCTTTTC[A/C]TCTCCTGACGTTTTCATTCTAATTGGAGTCTTGGC M 2 1 2 1 101000 r 74 goat snp22469-scaffold2223-95469 13 22938705 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382784 Affx-122973582 AX-123253142 13 22352544 TCACTTTGACCTGTCAAAAATGGGATAATATATGC[A/G]TCTTCATACATTATCATGCTTAGGAAATAACAGAC R 2 1 2 1 101000 r 74 goat snp22470-scaffold2223-134238 13 22977769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431311 Affx-122937080 AX-123301652 13 22451213 CATCACCGTGAGAGGTGACATGACTTTGTGAAAAA[C/T]AAACAAACAAGCAAACACCTTATCAGGGAATTCCC Y 2 1 2 1 101000 f 74 goat snp22472-scaffold2223-232907 13 23077173 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796097 Affx-122941059 AX-385283049 13 22543773 ATTTGTAAAGAAATGTATTTCTGCATTTCTTTGAA[C/T]GGTAGCACATTTCATTAAAGGTTTTGGGTTTATAT Y 2 1 2 1 201000 f 74 goat snp22474-scaffold2223-325467 13 23169173 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391673 Affx-122966546 AX-123262030 13 22574877 CAAACCTGCACTGTGGGAGTCCCCATGGCCCCAGA[C/T]GGCTGCTCTGATGGCCACTGACTCTCTTCTTTGTT Y 2 1 2 1 101000 r 74 goat snp22475-scaffold2223-356571 13 23200291 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419570 Affx-122945402 AX-123289918 13 22613233 GGGGAGGGGTGGGGCTGTGCACAGCCTGGGAGACC[A/G]TGTTAAGGACTTAAGTCTTGATTCTACAAGCAATG R 2 1 2 1 101000 r 74 goat snp22476-scaffold2223-394927 13 23238809 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398925 Affx-122961001 AX-123269280 13 22702209 AACCCTACCCCAGAGGAAGAATGCCTTAAAAATCA[C/T]AAGAAAAAGAAAAGAATAGCTGCAAATCTCTACCA Y 2 1 2 1 102000 f 74 goat snp22478-scaffold2223-483903 13 23327526 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399632 Affx-122961075 AX-123269987 13 22786322 GGCAGATATGTCTACATTATATTACATTGCTCTCC[C/T]AGCTGTGCATGTATGATTTGGTGCTGGCAGTTATG Y 2 1 2 1 101000 r 74 goat snp22480-scaffold2223-568016 13 23412290 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772247 Affx-122979047 AX-385259402 13 22819888 TCTGTAGAGGAGATGCTCCCAATCTATAAAGCTAC[G/T]AATCTAATAAAGCTGCTACAAGGATGAAGTAAGAC K 2 1 2 1 201000 r 74 goat snp22481-scaffold2223-601582 13 23444731 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385217 Affx-122971706 AX-123255575 13 22896942 TTTGCCTGGACCGGAGGACATGACTCTCTAGGGAC[A/G]CTTGGAGGCAGATGGATAAACCAAAAAAAAATTCC R 2 1 2 1 101000 r 74 goat snp22483-scaffold2223-678636 13 23521906 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399407 Affx-122961241 AX-123269762 13 22947895 GCCATATGATGGCTCAGGCCAACCGAATGTGAACT[A/G]CAGTGATATATGCCACATTCAGGCGATGGTCTTGA R 2 1 2 1 101000 r 74 goat snp22484-scaffold2223-729589 13 23572866 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377195 Affx-122978190 AX-123247554 13 23048966 GAGAAAGGGCAGAGTTAAGGGGGAAGATGCTTTGT[A/G]CAGCTTGTCATAGTGAGTATGAGATGACCTATTTT R 2 1 2 1 101000 r 74 goat snp22486-scaffold2223-830660 13 23673587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765627 Affx-122967796 AX-385253101 13 23095203 CTTCCCAGAAGTAGAAAAATGTGGACAGGAACTTG[C/T]GCACATGGTCTTTTAGTGTGGAACTGGCTTATGTG Y 2 1 2 1 101000 f 74 goat snp23732-scaffold24-4592 13 23719908 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409061 Affx-122953351 AX-123279412 13 23193523 TCAATGTACCACACCACTTTTGTGGAATTGCCCAG[A/C]TGCACGCAAACTCACTCCTCTAATTTATAGAATTA M 2 1 2 1 101000 r 74 goat snp23734-scaffold24-102912 13 23819087 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786261 Affx-122964192 AX-385273296 13 23260619 AGAAAAATTGGGGATTTGAGGTTGCTTTCATTATC[A/G]CTCTTCAAAAATCACAAATAGCTTTTACCTTTTTC R 2 1 2 1 101000 f 74 goat snp23736-scaffold24-170008 13 23886454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410113 Affx-122952825 AX-123280463 13 23309942 CTGGTAAGCCCTCTGAAGTGTGAATGGTCCATTCA[A/G]TTTCAGGAAACAAGTCTCTTCTGTTGTCACATTTG R 2 1 2 1 101000 r 74 goat snp23737-scaffold24-219331 13 23935927 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436781 Affx-122932263 AX-123307119 13 23341365 GGCCCAGTATGTGTCAGGCATTGTGTTAGATGCTG[A/G]GTTGATAGAAATGACTCATGTGTGGTCCTAGTGTT R 2 1 2 1 201000 r 74 goat snp23738-scaffold24-250754 13 23967406 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779221 Affx-122961259 AX-385266325 13 23371277 AAAAAATCTGTGAGTCTAGGTTTTGCCTAGAAAAT[C/T]AAAATGAAAAGGTAGGAATCCTACTGATACCTTTT Y 2 1 2 1 101000 r 74 goat snp23739-scaffold24-280666 13 23997621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412245 Affx-122950905 AX-123282594 13 23410289 GAGACAGCAAATGTGCTTTATCAAAGAAGTGGGAT[C/T]GATTGCTGCTACATCCTTCTTTCATCCCCTCAGCT Y 2 1 2 1 101000 f 74 goat snp23740-scaffold24-319678 13 24037483 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448775 Affx-122923307 AX-123319111 13 23466965 TAAATGAGATTAATGAGAAATCCCTCACCACTTCT[A/G]GTATGCAGGCAGAGTTAAAAAATTATGGATTTCCT R 2 1 2 1 201000 r 74 goat snp23741-scaffold24-376354 13 24094513 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397608 Affx-122961979 AX-123267963 13 23507724 AAGGATGAGTTAGGAAGAGTTAGGTTTGGGGTAAG[C/T]GGCAGAGCAGTACAATAGAGACACTGATTGATGTG Y 2 1 2 1 101000 f 74 goat snp23742-scaffold24-417113 13 24135407 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435577 Affx-122933369 AX-123305917 13 23536384 ATACTGAAATATTTTTGTTCAGCCCCTCTCTATCC[A/G]TAACTAACAGTAGCCTTGAGAGTTCTACAAAGTGT R 2 1 2 1 201000 r 74 goat snp23743-scaffold24-445773 13 24164070 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450744 Affx-122921859 AX-123321078 13 23567836 GCTGCAGTCCATAGAGTCACAGAGTCGGACACAAC[A/G]TGCACGCACTTGTATTAAAGGAATGCACTTTTGTC R 2 1 2 1 101000 r 74 goat snp23744-scaffold24-477225 13 24195609 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402509 Affx-122958570 AX-123272862 13 23604459 AAACCATTGCCTCCTTTACTGCTCTGCAAGTCACA[C/T]GGCAGAAAGAGGGGCAAAATGAAGACAACACTTCA Y 2 1 2 1 201000 f 74 goat snp23745-scaffold24-513848 13 24232285 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429551 Affx-122937823 AX-123299893 13 23640053 GCACACCTCATTTGTTTTTATCTCTCAGCAATCAC[G/T]TTCCTGTGCTGTGCATTGTACAATGTCTGAGAACC K 2 1 2 1 101000 f 74 goat snp23746-scaffold24-549442 13 24267920 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399203 Affx-122960613 AX-123269558 13 23681747 AATGCTCTTTAAAGGAGATACAGATGTACAGGACT[A/G]TGAGGGTCAAAAGAAGAAACATTATTTAGGGAAGA R 2 1 2 1 101000 r 74 goat snp23747-scaffold24-591136 13 24310003 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415975 Affx-122948413 AX-123286324 13 23718251 CAGAGAATGAGTTCATTTCTCTACAAACATCCTCG[C/T]GTTGCTGTAAAACAGCACTGGCTGGATGATGAGAA Y 2 1 2 1 101000 f 74 goat snp23748-scaffold24-627640 13 24346906 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801920 Affx-122962740 AX-385288825 13 23749725 CAAGATTTCAAGGAAAGCAAAGCCAGAAAATAAGC[A/G]TTGACTGAGTAACCAACGTATGAGTTTCTTTTTCT R 2 1 2 1 101000 f 74 goat snp23749-scaffold24-659114 13 24378695 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449606 Affx-122923207 AX-123319941 13 23778387 AAAACCTGGATTTTTCTTAACTTGACATTTTAACC[A/G]GTTACAGATGAGCTCAAATATACTGGAAGGTATGA R 2 1 2 1 101000 r 74 goat snp23750-scaffold24-687776 13 24407215 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775921 Affx-122969064 AX-385263052 13 23833277 ATTCATTGCTTCTCAGTCCTTATTTTGTTATTCTA[C/T]TGCTGTTCAGTTTTAAACAAAGTATAATAAGGTTG Y 2 1 2 1 101000 r 74 goat snp23751-scaffold24-742666 13 24461893 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272681 Affx-1111832978 AX-371326924 13 23839152 GAGCCTTTTGATGAAAGTGAAAGAGGAGAGTGAAA[A/G]AGTTGGCTTAAAACTCAACATTCGGAAAACTAAGA R 2 1 2 1 303000 f 74 goat 13_23839152_AF-PAKI 13 23839152 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320794039 Affx-122930965 AX-385281007 13 23874629 CGGGTGAGATGCTTTAAAGCGTGGTGATGCTGTGC[A/G]TCTCTTAGGCTTTGTGTGCAAACAGCAGGGAAAAG R 2 1 2 1 101000 r 74 goat snp23752-scaffold24-784018 13 24503139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417467 Affx-122947184 AX-123287815 13 23907042 CTTGTTTTTAGCAGCTGCAAGATTCCTGTTTTCAG[C/T]GAGTGACCTGGGGAAGGTCTTAGGAGGATCACATC Y 2 1 2 1 101000 f 74 goat snp23753-scaffold24-816431 13 24535370 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375805 Affx-122978565 AX-123246164 13 23957384 CTCTGCCCTCTGCTCTGATTTTCAAGCTCTTCTTT[A/C]GCATCTCAAAATGTTGAGAAGGTCAGTGTCAGTCT M 2 1 2 1 201000 r 74 goat snp23754-scaffold24-866773 13 24585620 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776110 Affx-122944007 AX-385263240 13 24019858 TCAAAAGCCAAGGAAAACGTCCATATTTCCATAAC[C/T]GCATCCAGGTTTAAGCTCCTAGGTCAGATCTGGAT Y 2 1 2 1 101000 f 74 goat snp23755-scaffold24-929247 13 24648097 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450522 Affx-122922496 AX-123320856 13 24053379 TTCAGAGTTGTTCTTCACTTGGAACCGGTGAGTTT[C/T]GACAGCACAGAGGAAAACAGATTCTTACATTTTGG Y 2 1 2 1 101000 f 74 goat snp23756-scaffold24-962768 13 24681435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407383 Affx-122955261 AX-123277734 13 24105732 GGAGGGACGTCCAGCAGGGGCTCTTCCCACTCACC[A/G]CTCACTCTGCCCAGAGAAATAATCATTACAGCCCA R 2 1 2 1 101000 r 74 goat snp23757-scaffold24-1015121 13 24733466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765606 Affx-986697499 AX-385253085 13 24107671 TTTAAAGTGTTGGTTTCCTTGTGGCATTTCCAAAG[C/T]CTTGTTTGGCACTGACATTCTACATACTTCATTTT Y 2 1 2 1 600010 r 74 goat 13_24107671 13 24107671 Ancestral_priority_1043 ancestry 0.71 neutral IMAGE 10K 10K ancestral 320763039 Affx-986697568 AX-385251012 13 24107693 GGCATTTCCAAAGTCTTGTTTGGCACTGACATTCT[A/G]CATACTTCATTTTTTTCTTATAAATAAAATTGATG R 2 1 2 1 600010 f 74 goat 13_24107693 13 24107693 Ancestral_priority_1043 ancestry 0.68 neutral IMAGE 10K 10K ancestral 38434025 Affx-122934219 AX-123304366 13 24148565 CCAAATTGTTTTCATTATTAACCTCTTCTTGGGCT[A/G]TTCATCTTCTCTTCCATAAATCAAATGTTTCTTAA R 2 1 2 1 201000 r 74 goat snp23758-scaffold24-1057954 13 24776182 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393307 Affx-122965962 AX-123263663 13 24294717 AACCAGTGCCTTGCAATACTCAGAGGCCGTCTCCC[A/G]GGGCCTGTATCTCATAGAGCCCCTGTGGCGAAGGG R 2 1 2 1 101000 f 74 goat snp23761-scaffold24-1204106 13 24922824 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375918 Affx-122978472 AX-123246277 13 24332997 ACACCTGAGTGTAATATCAAACCCAGCTACTGTAT[A/G]TAGTCTCTAAATGAGCAAAATACAGACAATACAGT R 2 1 2 1 101000 f 74 goat snp23762-scaffold24-1242386 13 24961092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375755 Affx-122978604 AX-123246114 13 24364255 TTTCTATTGGAGCAGAGAATACCAACTAAAGGGAA[C/T]GGTCGAATTTTTCTCATCAATTCTGTAAGCTTCCT Y 2 1 2 1 101000 f 74 goat snp23763-scaffold24-1273644 13 24992651 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390214 Affx-122967786 AX-123260571 13 24413520 TTATTTTCAATTAAAATCCCCATAAATTAGAAAAC[C/T]TCTCATAAAACAGTGGAAATGGAAAAAAATGTTAT Y 2 1 2 1 201000 r 74 goat snp23764-scaffold24-1322909 13 25042314 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385331 Affx-122971660 AX-123255689 13 24446469 AATATCGTCATGTGTAAGGACTTCTTAACCACTGG[C/T]GGCCAGTGGTTGGAATCCACCTTTCAATGCAGGGG Y 2 1 2 1 101000 f 74 goat snp23765-scaffold24-1355858 13 25075471 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437529 Affx-122931913 AX-123307867 13 24486456 ATGTGGAAAACTTACAGTGACAGGCTTTGCAGGGT[A/G]CAGTGAAAACACTAACTCTTGGGATGCTGGGTCTG R 2 1 2 1 201000 r 74 goat snp23766-scaffold24-1395845 13 25115805 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769003 Affx-122931301 AX-385256178 13 24575070 GGTTTTCAATGATGTATGGTTTTATTGTTAACCAA[C/T]ACTTTAATGTTTATCTTTCAGTTCCCCAAGGAGAC Y 2 1 2 1 101000 r 74 goat snp23767-scaffold24-1484459 13 25204038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383886 Affx-122973125 AX-123254244 13 24611006 CACTTTTTTCTCTGCATCTATTGGGCAAATGTCTA[G/T]AATAGGATAAAAGCTATGCCTTTAAGACTAAGATG K 2 1 2 1 101000 r 74 goat snp23768-scaffold24-1520395 13 25240168 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798463 Affx-122961743 AX-385285396 13 24655497 CCAAGACTAGTTCCAAGGTAGGCTGCAATCTTTGC[A/G]TACTGTTACCTTCTCTGCTGTACATCAGGATTACA R 2 1 2 1 101000 r 74 goat snp23769-scaffold24-1564886 13 25285455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400665 Affx-122960346 AX-123271020 13 24716840 GGCAGGCTTCTCTGGACATGTCAGCTGCAAAGTAG[C/T]GTGGGGGAGGAGAACATTTTCTTGCTTTGAGACAG Y 2 1 2 1 101000 f 74 goat snp23770-scaffold24-1626229 13 25347319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769702 Affx-122944682 AX-385256872 13 24756877 GTTTCCTGCAAGTCAAGCAAGTTGGAGCTTTCTTA[C/T]ATAGCTTTATTTACATATCTTTAGAGTTAGGGCTT Y 2 1 2 1 101000 f 74 goat snp23771-scaffold24-1666266 13 25387363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766847 Affx-122945182 AX-385254169 13 24836019 TTCACTGCCCATAGGACCTCATGGCTTTGTCTATC[A/G]TCTTTATGCAAATGATCATAAATTATACAGCCCAG R 2 1 2 1 101000 f 74 goat snp23773-scaffold24-1745408 13 25467351 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444795 Affx-122926341 AX-123315132 13 24879971 CTGCGCAAGGCAGATGTGACAGAAACAGACAGCCG[A/C]GGAGCATCACATATAAATAATACAGGCAGCTGGAG M 2 1 2 1 201000 f 74 goat snp23774-scaffold24-1789360 13 25511099 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406010 Affx-122955503 AX-123276362 13 24917523 ATTTAATGTGATTCATCAGAATTTAATGACATGGT[A/G]TTGACTTAAAAAAAAATGCACATGAGAGTTGTGGA R 2 1 2 1 101000 f 74 goat snp23775-scaffold24-1826912 13 25548888 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797483 Affx-122939054 AX-385284422 13 24970870 TTTGCTAATGTGTACCTCTTTGCAGTTCTCTTTAT[A/G]TATTTCTATAAGTAGCATGTTTGCCATTAGATTTT R 2 1 2 1 101000 f 74 goat snp23776-scaffold24-1880259 13 25602249 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381527 Affx-122974850 AX-123251885 13 25026462 TATATATATATACATATAGTTCTGATTTTCTAGAG[A/C]GCCCTGACGCATACAAATGAGGAACTAATAGCTCT M 2 1 2 1 101000 r 74 goat snp23777-scaffold24-1935851 13 25658302 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417616 Affx-122946868 AX-123287964 13 25056846 TCAGAACTGCATGAGAAAGGGAGCTGCCTGCCGCC[G/T]ATGATTCCTGAGATGAGTGAGCAAACAGCGGTCCC K 2 1 2 1 101000 r 74 goat snp23778-scaffold24-1966235 13 25688390 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786899 Affx-122942107 AX-385273928 13 25098745 TACATCACGAGCTTTAAAATGACTGCGCACTTTGC[G/T]ACAGAAATCTATTTAAAAGTAGCACACCCTCTTTC K 2 1 2 1 101000 r 74 goat snp23779-scaffold24-2008134 13 25730453 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442936 Affx-122928230 AX-123313273 13 25136005 CATAGACCACGCCCCTATCTCTTCCGCCAGGCCCC[A/G]TCTTAGTTTCCCACCACAAAGCTAGCCCTTCTTTT R 2 1 2 1 102000 r 74 goat snp23780-scaffold24-2045394 13 25766592 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400560 Affx-122960421 AX-123270915 13 25166705 AAGTACTAAGTCAGAGATAACAGAGAAGGCCTTTC[A/G]GAAATGGAATACAAAACAAAGAAAGAGACTATAGT R 2 1 2 1 101000 f 74 goat snp23781-scaffold24-2076094 13 25797173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771402 Affx-122942371 AX-385258560 13 25225986 AGGGGTCAGAAAGGATCTGGAGGACACAGTAAGAA[C/T]GTGGATTTTGAAGGACTTTTAATGGGAAAATAATG Y 2 1 2 1 101000 f 74 goat snp23782-scaffold24-2135375 13 25856584 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778710 Affx-122940615 AX-385265821 13 25257014 TGAGTAGTATGGTTTGATCAGTTTCCATCAGCCTT[A/G]CTTTCTAGGCATTGACAGTAGAGAAAAAAGAAAAC R 2 1 2 1 101000 f 74 goat snp23783-scaffold24-2166403 13 25887509 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392721 Affx-122966031 AX-123263078 13 25285642 TAGAGGGACTAATCATCTTTGTCTATATTGAAATC[A/G]CTGGTTTTCATACCAAGAATATCTGCTTGTTTCTA R 2 1 2 1 101000 r 74 goat snp23784-scaffold24-2195031 13 25917075 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396846 Affx-122963260 AX-123267201 13 25323073 GTCTCTCCTGTTGGCAGCTCTGATGACAGATAGTT[C/T]CCCAGTCTTGACTTCTTTTGGAAAGTCTTTGACTC Y 2 1 2 1 101000 f 74 goat snp23785-scaffold24-2232462 13 25954984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392144 Affx-122966324 AX-123262501 13 25327984 TGATGTACTATTTGTGTAAAAAGTTTTACAAATCT[A/G]TTACAGTACAGAACTATATAGCTAACTGTGTTAAT R 2 1 2 1 103000 f 74 goat snp49128-scaffold7-7064010 13 25959692 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419812 Affx-122945836 AX-123290160 13 25362225 TATCATTGCAATATGTAATTTTCCATACATCCACT[A/G]TAAGTATTACTTTTTTTCCTTGAAAATTACATGAA R 2 1 2 1 101000 f 74 goat snp49127-scaffold7-7029769 13 25993823 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775610 Affx-122919494 AX-385262741 13 25409025 ACCAAAGAAAATGTTTAGGCTCAACCATTAGGCTG[A/C]ACATATTTTTTTTCGGTCCTTCTCAAAGAACTTTC M 2 1 2 1 101000 f 74 goat snp49126-scaffold7-6982969 13 26040818 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432482 Affx-122935595 AX-123302823 13 25451024 TTTTAAGAAGAGCTTTATAACTAGAGGTTACTCAA[C/T]GAAATGACAAAAACAAGCTATCATGCTGATTTTTT Y 2 1 2 1 101000 f 74 goat snp49125-scaffold7-6940970 13 26081720 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765657 Affx-122936321 AX-385253124 13 25502456 AACTTGCATTCAAACAATTGCATTCTTCTTCTACC[A/G]TAGACTTTTCATACAACCTCAAACACCACATTAAA R 2 1 2 1 101000 f 74 goat snp49124-scaffold7-6889538 13 26132710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413430 Affx-122950694 AX-123283779 13 25544289 CTATTCTCCTTAAGAAGAGACCCAAACGAGGTGGT[A/C]GGGGAGGGATGAATTAGGAATTTTAGATTAGCAGA M 2 1 2 1 101000 f 74 goat snp49123-scaffold7-6847705 13 26174493 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402790 Affx-122958294 AX-123273143 13 25576416 AGTGAAATGTTTTATTACATTCTTATATTCTACTT[A/G]CAGCCAAATTATAGCTATATAATACAAAACATATT R 2 1 2 1 101000 r 74 goat snp49122-scaffold7-6815578 13 26206712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402980 Affx-122958149 AX-123273333 13 25619216 TCTAGAATCAGTTCAGCATACTCCTGAAACCCACA[C/T]GCCTGAAACAAGAGAAGATTGTGTCAGTGGAATAG Y 2 1 2 1 101000 f 74 goat snp49121-scaffold7-6772778 13 26249588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453602 Affx-122920139 AX-123323935 13 25649739 TTTTCTTAACCAAATCCAAAATGTACTGCTTATAG[C/T]ATTGGCAGTTTACAATGGCAATTAACATCAATCCT Y 2 1 2 1 101000 r 74 goat snp49120-scaffold7-6742255 13 26280546 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801733 Affx-122927793 AX-385288641 13 25679154 ACTCCAGAGACTTCTGGAAATCATCTTTAAAAATC[A/G]TACCCGTGTCTGCAGCACGAATTGTTTGACTTATT R 2 1 2 1 101000 f 74 goat snp49119-scaffold7-6712840 13 26309877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445014 Affx-122926635 AX-123315351 13 25710468 CGAGAATGAGAAGCCTCATTTTTACCCAAATTCAT[A/G]TCATGTTGGATTTCTAAATGGAAAGCACACAAATC R 2 1 2 1 101000 f 74 goat snp49118-scaffold7-6681526 13 26342037 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403016 Affx-122958561 AX-123273369 13 25749997 TGAAGACCTCTGCCATACTCCTCACACACTTGAGA[C/T]GACCCGCTTCCATCCTTTCTTCAAATAGAATTCTT Y 2 1 2 1 101000 r 74 goat snp49117-scaffold7-6641997 13 26381236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787447 Affx-122940598 AX-385274472 13 25785459 GTAGGTGTTAGCTTATATAAATCTACCAAAAAGTT[C/T]GCATTTTAAAAATGTAACAAGGGTGCGAAGAGGAA Y 2 1 2 1 101000 r 74 goat snp49116-scaffold7-6606535 13 26416535 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380840 Affx-122975062 AX-123251198 13 25817331 ACGCCATGTGATGGTGTCATTTCACCCTCAGAATC[A/G]TCATAATGAAGGCAGGGAAGTTGCTGATTTACCAT R 2 1 2 1 101000 r 74 goat snp49115-scaffold7-6574663 13 26448798 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421801 Affx-122944328 AX-123292148 13 25846175 GACTCAGAGAGACACGGGAACCTGCTCAGCATCAG[A/G]GTCAGACCACATTACTGCCGCTGTTACATGTTTCT R 2 1 2 1 101000 r 74 goat snp49114-scaffold7-6545819 13 26477679 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784368 Affx-122955163 AX-385271418 13 25905831 TGGCTGTTCTGCAACTCTAGGTAATCTCATTGCAC[A/G]TATAAAAAATGATAGGGCACAAATAATCAATTACT R 2 1 2 1 101000 f 74 goat snp49113-scaffold7-6486163 13 26537926 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407374 Affx-122955267 AX-123277725 13 25943727 AAGCACATAAGCTCTGGCACTAACCTAATAACTTG[C/T]ACCCAGAGGCTGACAATATATCTTACTGTGTTACA Y 2 1 2 1 101000 f 74 goat snp49112-scaffold7-6448267 13 26575468 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415787 Affx-122948910 AX-123286136 13 25982762 AGGAAAAGGGGAAAATACAAGAAAAGAATCCTTTG[C/T]ACCTCATTCTGAAATTTCTCAATCACTTCTTTGAT Y 2 1 2 1 201000 r 74 goat snp49111-scaffold7-6409232 13 26615080 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766867 Affx-122923678 AX-385254186 13 26018817 AGAGTTGGTGGTTTTTCTAGAGTCAGACTTACCTG[A/G]TTCTCTTTCATATCTACATCTTTAAAATGAGAAAA R 2 1 2 1 101000 f 74 goat snp49110-scaffold7-6373177 13 26650822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431421 Affx-122936523 AX-123301762 13 26052684 ATAACTTTGCAAAATCAGAAAAAATGATTGACTTA[C/T]AGCAACCTAACTTCTTTTGTATGTCTTTAGTCATG Y 2 1 2 1 101000 r 74 goat snp49109-scaffold7-6339310 13 26684761 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434598 Affx-122934101 AX-123304939 13 26089594 ACTGTGCAGTCATGAGTGGTGTTAATATAAAAACG[A/G]CTCTGGAGAGGCAAGACCTGCAGTAACTATACTGT R 2 1 2 1 101000 f 74 goat snp49108-scaffold7-6302400 13 26721656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379767 Affx-122975848 AX-123250125 13 26139488 ACTTCTTTTGAGTCTTTTAAAATACAGACATTGCC[A/G]CAAAATAAAATTAAATGGATACTCCTATCACATAA R 2 1 2 1 101000 f 74 goat snp49107-scaffold7-6252506 13 26761040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410080 Affx-122952847 AX-123280430 13 26171957 CTTGGCCCTCACCATAATAGCATTACATTCATGGT[C/T]GGAATGACAGCTAAATGGATGAATGCAGCCTGTCT Y 2 1 2 1 101000 r 74 goat snp49106-scaffold7-6220037 13 26794231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777587 Affx-122921522 AX-385264706 13 26226018 ATGGCTTGCTTTATTTATTTGAGAGTCAATAAGTA[C/T]GAGTGGAGTATACTGTGAACATTCTTAGGCTTATG Y 2 1 2 1 101000 r 74 goat snp49105-scaffold7-6165976 13 26849622 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402556 Affx-122958457 AX-123272909 13 26255463 GAACAGATCTGGACTTCAAGATTGACTGCCTCAGA[C/T]AGTCACTATCAAGTTAAGGCAGTTTGATATAATAC Y 2 1 2 1 101000 f 74 goat snp49104-scaffold7-6136531 13 26879470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800583 Affx-122960435 AX-385287502 13 26297049 TCATTAAAAGGCTGTTTATACCACACATGCAATTA[C/T]GTGCTTCCTATTACTAGTTCTTATAGGTGCCCAGG Y 2 1 2 1 101000 r 74 goat snp49103-scaffold7-6094945 13 26921045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386295 Affx-122970929 AX-123256653 13 26345126 ATATGTGTAGAAAGAGGAGAGAGAACCAATTCATA[C/T]TGAATTTCTGAATATTCAATTAGGGCCAGATAATA Y 2 1 2 1 303000 r 74 goat snp49102-scaffold7-6046868 13 26969887 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418863 Affx-122946126 AX-123289211 13 26389054 GGCATATTAGGAAGGAAGTATTTGAGAAAAAAGTC[A/G]TGTGAAAATTTGAAAAATGTGTATGGTTTTGAACT R 2 1 2 1 101000 r 74 goat snp49101-scaffold7-6002940 13 27014003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433583 Affx-122934966 AX-123303924 13 26419337 CCAGAGGTGACTCAGAGTGGAAGGGCGAGTATCTC[A/G]ACCAACCTTTGGGGTCAGTTCACAGTGTTCAGAAG R 2 1 2 1 101000 r 74 goat snp49100-scaffold7-5972657 13 27044296 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402078 Affx-122958706 AX-123272431 13 26470456 TTTATTTTTATACCCAAACATTTTGAAAACCACTG[C/T]CTTTCTGAAGTTCCCAGGTGAGACATCAGCATTGC Y 2 1 2 1 101000 r 74 goat snp49099-scaffold7-5921538 13 27099672 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396006 Affx-122963490 AX-123266361 13 26536446 AGTTCTGTGGCACATAATTTCCAACAACAGTTTTT[C/T]TGGTGGAGGAAGAAGCCTAGCTGGAACCTGAGTTA Y 2 1 2 1 201000 f 74 goat snp49097-scaffold7-5855548 13 27167935 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786242 Affx-122972069 AX-385273277 13 26575550 AGTGAACCTAATGTATCTGCTTTGTGTAGGCCAGT[A/C]GTTTTTCACCTGTCCTGATGATCAAGCAAAAGCTC M 2 1 2 1 101000 f 74 goat snp49096-scaffold7-5816444 13 27207090 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381540 Affx-122974838 AX-123251898 13 26618086 ACTTTGCTTTTCCAGAACCACAAGGGGAAATGTAC[A/G]CTGTGGGTACCTGTTTGAAGTCAGGGCTATTTAAG R 2 1 2 1 101000 f 74 goat snp49095-scaffold7-5773908 13 27249985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385537 Affx-122971238 AX-123255895 13 26667134 GCAAAGACTCAACACAGTGCAGTAGGGAAGGAGTC[A/G]TTCCCAAAAGGAATTTGGAGTTGGAATATTCTTAG R 2 1 2 1 202000 f 74 goat snp49094-scaffold7-5724860 13 27299390 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449159 Affx-122923546 AX-123319494 13 26723491 CTTCTATATGGTCCAACTCTCATATCTGTATAGGA[C/T]GACAGGAGTAAGCTTAGAGAGGGGCCTAAGGGGAG Y 2 1 2 1 303000 r 74 goat snp49093-scaffold7-5668503 13 27356297 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777603 Affx-122961347 AX-385264722 13 26792970 AGATTCTTATTACCAAGACAGAGTCATCACCAAGA[C/T]GAATCTGCATAAACAGACCTTGTTAAAATAACCCT Y 2 1 2 1 101000 r 74 goat snp49092-scaffold7-5599024 13 27425453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380259 Affx-122975432 AX-123250617 13 26851336 CACTCTACTGCCCTTTGCTCACTCCATGCAGTACA[C/T]GACGCAGCACAGACTTTGATGCCGCTCTTGGGGGC Y 2 1 2 1 101000 f 74 goat snp49091-scaffold7-5540658 13 27483818 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405674 Affx-122956561 AX-123276026 13 26885688 TCTGATAAGTGGGTGGTTACGGTGGTGACAACTTC[A/G]TGCAGTGCCCAGTGCAGGTCTCTATAGCTTCCTGG R 2 1 2 1 101000 f 74 goat snp49090-scaffold7-5506306 13 27518058 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406794 Affx-122955701 AX-123277145 13 26962193 TGCCTAAGTTTCCGTGGTGATACGAACGTGGAAAA[G/T]ATGAACACGAGTGTTCTAAATGGATGCTGCATTTT K 2 1 2 1 101000 f 74 goat snp49089-scaffold7-5429801 13 27595508 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776391 Affx-122963304 AX-385263518 13 27021612 TCTTCACTCTACCAACAACAAGGACACAATTGTTA[C/T]GTACTGAGTTATTTGCCAGGTAGCGTGCTATACAT Y 2 1 2 1 101000 f 74 goat snp49088-scaffold7-5370382 13 27655256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415023 Affx-122949023 AX-123285372 13 27050788 AGTGACAGTCACCCCTGGGACTCGCCTCTTCATGT[A/G]CTTGGTTAACCCAGCCATGGTGAATTTCTGTGGAG R 2 1 2 1 101000 r 74 goat snp49087-scaffold7-5341206 13 27684487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383414 Affx-122973486 AX-123253772 13 27145810 GTTGGGACAATGGAACACCACCACCCCCCCTAGTG[C/T]AGTAAGCCTTGATTCAAAGACTCTCCAAAATTTAC Y 2 1 2 1 101000 r 74 goat snp49086-scaffold7-5246184 13 27768675 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448245 Affx-122924204 AX-123318581 13 27204449 ACAACATGCTGTGTCTTAATTAATTGAGCCGTGGA[G/T]AGGTACTGATAAGGGAGTGTGATTTATCTGGATAA K 2 1 2 1 101000 r 74 goat snp49085-scaffold7-5187545 13 27826944 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416797 Affx-122948145 AX-123287145 13 27250252 CTTAACCTTTTAGGCTTCCTGACACATGGTCCCCC[A/G]AGCCTTTTATGCACAGTGGTTATCACGTCTAATCC R 2 1 2 1 201000 r 74 goat snp49084-scaffold7-5141742 13 27873101 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800948 Affx-122948918 AX-385287863 13 27284949 TCTGACCGCTCTGAAAATAGTGCGAGAGTTTCCTC[A/G]TAGTAGAAGTCAACAGGCCAGTTTGCAGAATATTC R 2 1 2 1 101000 f 74 goat snp49083-scaffold7-5107045 13 27907662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763045 Affx-986697574 AX-385251015 13 27295092 AGTGAGTCCTCACACTGTCATTATGCTTTACTTGG[C/T]ACTTGTGTTGATTACAGGTGTTGGGACTGGCTCTT Y 2 1 2 1 600010 f 74 goat 13_27295092 13 27295092 Ancestral_priority_1043 ancestry 0.644 recommended IMAGE 10K 10K ancestral 38437236 Affx-122932025 AX-123307574 13 27316938 CCTTCTCAAACCCTTCCTTTCAAACTGTTTATGCT[A/G]TTGCTGCCCAGAAGTAAAGTGGGGCAGCACACAAT R 2 1 2 1 201000 f 74 goat snp49082-scaffold7-5075056 13 27939780 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380998 Affx-122974669 AX-123251356 13 27366537 TGACAAGAATCTGAAAAGTCTTTACAATGTTTCCC[A/G]TGACAAATTGTGATTCTGAAAGACATCTGGGGGAA R 2 1 2 1 101000 r 74 goat snp49081-scaffold7-5025457 13 27989473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396380 Affx-122963029 AX-123266735 13 27398260 GTGTCTGGGTTTGGATGAGTTCAGTCTCCAGTGCC[A/G]TCAAGAAAGCTCTTCTTCTGCATGTGTGCAGTAAT R 2 1 2 1 101000 r 74 goat snp49080-scaffold7-4993734 13 28021404 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435393 Affx-122933566 AX-123305733 13 27441627 TGCAGTCCACCTCTGATCAAGGGTCATGGTCCAAC[A/G]TCTTTCAAGATTCAGCCTTTTCATTGCTTTGAGAC R 2 1 2 1 101000 f 74 goat snp49079-scaffold7-4950367 13 28064922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432648 Affx-122936473 AX-123302989 13 27471451 TATATTCAAGGCCTTTTGTGTTTCGTTTAAACCAC[A/C]CAACCATAAGGCTAACCATCCAAAGATGATGAGCA M 2 1 2 1 101000 f 74 goat snp49078-scaffold7-4920543 13 28095101 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779821 Affx-122929708 AX-385266921 13 27504072 AGAGATGGTGAAGACATTTAGGTACCCATATGAAG[C/T]AGTTCATATCTATTGTTGATTAAATTTGCTTACCA Y 2 1 2 1 101000 f 74 goat snp49077-scaffold7-4887922 13 28127428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429762 Affx-122938255 AX-123300103 13 27551157 GGTATACAAAAACACACAAAGAAAATGGACCTGTA[G/T]ACCTATATATGTGTCACCCAGATTAAGAAATGAAA K 2 1 2 1 101000 r 74 goat snp49076-scaffold7-4840837 13 28174550 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397949 Affx-122961916 AX-123268304 13 27580742 CTTACAAGTGTCACCAAGGGCTGCCCTGTTGCCAT[A/G]GCACGGCTCTCAAAGCAAGGTACATCCCTGGGTCC R 2 1 2 1 201000 r 74 goat snp49075-scaffold7-4811252 13 28202931 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412504 Affx-122951368 AX-123282853 13 27637337 CATCTGACTTCTAGGTATACTAGATATATATACTA[C/T]ATGCTACTCTATCAAAAACACAAAACAAAACAAAA Y 2 1 2 1 303000 f 74 goat snp49074-scaffold7-4754657 13 28260501 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387102 Affx-122970674 AX-123257460 13 27673887 CTGAGTCAACCATCTTTGTCCCTGTTTTATTTTAT[A/G]TCCCAAATAAATGACTTCCTGTCTAGCAATTTGGG R 2 1 2 1 303000 f 74 goat snp49073-scaffold7-4718107 13 28297772 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451182 Affx-122921338 AX-123321516 13 27718906 TCAGTGGAATCTATGATTCCTGTCATACAAGTTGT[C/T]GCTCTGGGCAGGGAACATTTTGTTTCTTCCCTTTG Y 2 1 2 1 201000 f 74 goat snp49072-scaffold7-4673088 13 28342613 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767383 Affx-122931133 AX-385254656 13 27765659 TGTAGGAAAAGTAAGGATTAGGGAAACTACCAGAC[A/G]TTGGAAGAAGAGTCAAGTCATTAAGAATGTTAAAA R 2 1 2 1 101000 f 74 goat snp49071-scaffold7-4626335 13 28389905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443710 Affx-122927154 AX-123314047 13 27799716 ACATACACTCATAATTTTCCATTGTGTAAAGTGTT[A/G]TGAGGAGTGAAAGGGAAGTAATCAAAAGTGGGGAC R 2 1 2 1 101000 r 74 goat snp49070-scaffold7-4592278 13 28423936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420934 Affx-122944994 AX-123291281 13 27828614 GTCACTATGAGACTTATATAAAAATCCTGTTTCTC[A/G]TCAAACTTTCTTCTGCTGGTGTATCTGTCCATGAG R 2 1 2 1 101000 r 74 goat snp49069-scaffold7-4563380 13 28452869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395280 Affx-122964080 AX-123265635 13 27875634 GACCTGCTTAAGAGCAGTGTGCCCTTCCTCCCACG[C/T]GTACTCTCCATGCCTGACTCCTTCCCTGCACCCCC Y 2 1 2 1 201000 r 74 goat snp49068-scaffold7-4516360 13 28501212 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776323 Affx-122950194 AX-385263451 13 27915735 TTATCTATCCAGTAATTTAGACTGCACAGAAACTC[A/G]TTGAATCTGTTACATCCACCGTTTGTAAATTCCGT R 2 1 2 1 101000 f 74 goat snp49067-scaffold7-4476259 13 28541160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419754 Affx-122945879 AX-123290102 13 27950793 GGCTCCTCAAACTTTAAAGCTTAGCTCTTTCTCCT[A/G]TTTCATAACCACCACTACTGCTGCCATGTCTCTTT R 2 1 2 1 101000 r 74 goat snp49066-scaffold7-4441201 13 28576145 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396682 Affx-122962835 AX-123267037 13 28006126 TGCAATTCTCTCCCCGTTCTTGTTTCCAAACAAGG[A/C]GGGGCAGGGTGGGAAGGACAGGGTGGAACACATTG M 2 1 2 1 303000 r 74 goat snp49065-scaffold7-4385868 13 28631627 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782306 Affx-122920707 AX-385269384 13 28063708 AGCCTTCAGTCAGCTCCCTGTAATGTAACCTACTG[C/T]AGCTGGGTCGAGTTGCTAGCTTTCTCTAAAACACC Y 2 1 2 1 101000 f 74 goat snp49064-scaffold7-4328286 13 28689788 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432419 Affx-122935831 AX-123302760 13 28098439 CTTTCATTTCTGTTTTCCTTTCCCCCAGGGAAGCT[A/G]CACTCTCCTGCAGGGACCTGGTTTGTGGTAGTTCT R 2 1 2 1 201000 r 74 goat snp49063-scaffold7-4293555 13 28725108 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404378 Affx-122956802 AX-123274730 13 28138750 AGGTAGAGGAGCTCCCAGACAAACTCATAGCTGTC[C/T]CTACCAAGGTGATCTCAGAGACCCTACGCTCAGAG Y 2 1 2 1 101000 f 74 goat snp49062-scaffold7-4253244 13 28765532 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802927 Affx-122947278 AX-385289824 13 28188088 GCTGCTGTGACTGGAAACATGACAATCAAAATTTC[A/G]CTTTGTCTTCTGTTATGCTATTCATCTAATTTTCT R 2 1 2 1 201000 r 74 goat snp49061-scaffold7-4203906 13 28815147 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407170 Affx-122954834 AX-123277521 13 28239405 AACAAAACAACCCCCTTGCCCCAAACAATATAGTC[A/G]CTTCAGTCTTCAGAGTTCAAGTAATAAATGGTCTC R 2 1 2 1 201000 r 74 goat snp49060-scaffold7-4152589 13 28866216 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376736 Affx-122978952 AX-123247095 13 28270961 ATGTTTTCAGATCATATGAAAGGATTAAGAGCCCC[G/T]AGCTTGAAAAGAAGGTTGGAATGCAGGTAATTTTT K 2 1 2 1 201000 r 74 goat snp49059-scaffold7-4121033 13 28898189 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797081 Affx-122944690 AX-385284021 13 28308242 CCTGTTACTCGGTTCATCATGAGTTTATCTCCTTG[A/G]CTGGATGGTGGGTCCCCTGGTGGGAAGGTTGTATT R 2 1 2 1 202000 r 74 goat snp49058-scaffold7-4083752 13 28935639 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388989 Affx-122968657 AX-123259347 13 28380967 TGTACATTAGAGAAAATACCTTTTCCAAACAACAA[C/T]ACTATAAATAGTGATGCTTTCACTCAGAGCATCAA Y 2 1 2 1 101000 f 74 goat snp49056-scaffold7-4011027 13 29008963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387568 Affx-122970279 AX-123257926 13 28430001 GGCAAAAGAGAGAGGCCTGTCCTGCCTGACTTCTG[A/G]CTTGTCCCCACCTTTACGCTGTCATCCTAGGCATT R 2 1 2 1 201000 r 74 goat snp49055-scaffold7-3961993 13 29058054 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767343 Affx-122970583 AX-385254619 13 28459050 GCGCAACTAAGAGACTGAAGGAGTATGCTAGGCAC[A/G]CTCTCTGGCTTTGTTACAAGCCCATGAAGTTGATT R 2 1 2 1 101000 f 74 goat snp49054-scaffold7-3932944 13 29087338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399076 Affx-122960886 AX-123269431 13 28509026 TTTGGAATTAAATGCTTGTTGGGCTTTCTGGAGTT[C/T]GCAGGGGATGTGGTTTGTTTTATGTTGCTTTTGTT Y 2 1 2 1 201000 f 74 goat snp49053-scaffold7-3882968 13 29137736 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395975 Affx-122963516 AX-123266330 13 28556074 TGTAATAAGCATGGGCTGCTTGGGTGGGTCCTTTG[C/T]AGGTCAGTGTCCAATGCTCTCAAACCCTGCCCTCA Y 2 1 2 1 101000 r 74 goat snp49052-scaffold7-3835920 13 29185432 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427384 Affx-122940085 AX-123297727 13 28594514 TGTTCAGATAATTTTTAATGCACACTTTGTGTTTT[A/C]TTTAGACCCGATTCTTGTGCTGCAGCTTACGTTTT M 2 1 2 1 102000 r 74 goat snp49051-scaffold7-3797480 13 29224497 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791681 Affx-122971772 AX-385278672 13 28625969 TTACCATAACGAGGTGTATATCATCTTCACCTTCA[C/T]TCCTCTTCATAAATTTGACTGCTCACTGGTCAGTC Y 2 1 2 1 101000 f 74 goat snp49050-scaffold7-3766025 13 29255938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770641 Affx-122963631 AX-385257805 13 28662345 TCTCAAGATCTCCTACCACTGGGACTTATTTAGAT[A/C]TAGCAATAATTTTCACCTATTCTTCTAAATTTTTC M 2 1 2 1 101000 f 74 goat snp49049-scaffold7-3729649 13 29291896 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452191 Affx-122920826 AX-123322524 13 28762525 AAATGGCAGAGATCATCTTTGTAAGCGAGGATAAC[A/G]ATTTATTTATTTATTTTCCATGACTCTAGGGTGAC R 2 1 2 1 103000 f 74 goat snp49047-scaffold7-3629469 13 29391917 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409252 Affx-122953137 AX-123279603 13 28794361 ACCTGGTGTAATGTCTCTGGCTCTCTGTGCAGCCG[A/G]CTGCCCCCCGGGAGGACACCCCTGAGCTGAGTGCA R 2 1 2 1 101000 f 74 goat snp49046-scaffold7-3597633 13 29423970 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769756 Affx-122949286 AX-385256926 13 28827299 TGGAGTGTAAATACAGGCAGCTTATGTCCAGCTAC[A/G]TGTTTCTAAAATAATGGTGATCTACAGCCTACGAG R 2 1 2 1 101000 f 74 goat snp49045-scaffold7-3564695 13 29457077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770586 Affx-122921423 AX-385257750 13 28885853 GTGTTCTTATGGCTTAGGGTGTCAAGATAAGACTT[A/G]TAATGCACTGAATGCTATAGATTGCCATATTCCCA R 2 1 2 1 101000 f 74 goat snp49044-scaffold7-3506141 13 29516118 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450040 Affx-122922830 AX-123320375 13 28927264 TGTGTGCTGTTGGGGTTGCTATGGAGTAATATGTA[C/T]GCTGAAATGTTTTAAAACGCATATGTACAAAAATC Y 2 1 2 1 101000 f 74 goat snp49043-scaffold7-3464730 13 29557000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415003 Affx-122949038 AX-123285352 13 28963403 CACCTCCTCCCATAGGTGGAGGACTTGTTCATGAC[A/G]TCCCCACCTGTTTGTAGGAGATCTTTGAAGTCCTT R 2 1 2 1 101000 r 74 goat snp49042-scaffold7-3428591 13 29593649 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463271150 Affx-1109899020 AX-514756528 13 28985243 CACTTGCCTGGGAGAGCCCCAAGAGGTTCCAAGGA[A/G]CAAGGGGAGGCCGCAGCCGTTCACACCTCCCTCTC R 2 1 2 1 303000 r 74 goat 13_28985243_AF-PAKI 13 28985243 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320793913 Affx-122921603 AX-385280882 13 29009500 AAAATACATACATAATACCTCCCAGTTGATTAATT[A/G]CCCAAATACATTCACTTCTTGATGCTTCTACTTAG R 2 1 2 1 101000 r 74 goat snp49041-scaffold7-3382494 13 29639715 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437920 Affx-122931644 AX-123308258 13 29054460 TGTCCCCAGATATGTCAAAAGAAGGCATGTTTACT[A/G]CAGCTTAGAGCATTGAGGGGGAAAAATATAATATA R 2 1 2 1 101000 f 74 goat snp49040-scaffold7-3337534 13 29685243 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450296 Affx-122922155 AX-123320631 13 29118234 TAGGAAATGACATTTTATGTCATACCTGAGCATGA[C/T]AGTGGTGGATTTATAAGGAACTGAGACATGTTTAG Y 2 1 2 1 201000 r 74 goat snp49039-scaffold7-3273760 13 29748491 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412715 Affx-122950741 AX-123283064 13 29186826 GTGAGGGAAAAAAGGTTTCAAAGATGGATTTAATG[C/T]GGGTAGACATTTGTAAAGAGTCAAGAATGTCATAA Y 2 1 2 1 101000 r 74 goat snp49037-scaffold7-3205168 13 29817225 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778884 Affx-122966932 AX-385265992 13 29235004 TACTTGAAAAAGACAAGCATTAATGAAATAATATC[A/G]CTAGGTTTTTCTATGTGGTTGCTATCCATAGTTTT R 2 1 2 1 101000 f 74 goat snp49036-scaffold7-3156990 13 29866986 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453115 Affx-122920020 AX-123323448 13 29271538 TTAACTAATTAAAGCGGTGAATGTCCTGTAACTAA[A/G]TCGGAGGAAACTAAGTCTGCTTCTCTTTCCTCCAG R 2 1 2 1 101000 f 74 goat snp49035-scaffold7-3120456 13 29903771 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426401 Affx-122940843 AX-123296747 13 29362003 CCATTAGTACCTGCTATAAGCCTTGCAGTGTAAAA[G/T]TCTAGCCTCATAGAGCTTGAAGTAATCTTAGAGCG K 2 1 2 1 101000 f 74 goat snp49033-scaffold7-3029991 13 29996246 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395017 Affx-122964222 AX-123265372 13 29403657 TACTTATAAAACAAATAATATGTATATAAAGCCAC[G/T]GACAACTCTGCATTTGTAGGTGATAGAGATGTGTA K 2 1 2 1 101000 r 74 goat snp49032-scaffold7-2988337 13 30038158 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392692 Affx-122966413 AX-123263049 13 29454428 ATACTAGTCATTTTATATATGTTTCCCCTATTTAA[C/T]GTAATTGTCATTAAAAAATCTATATGAGTCAGAGA Y 2 1 2 1 101000 r 74 goat snp49031-scaffold7-2937566 13 30089400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390459 Affx-122967613 AX-123260816 13 29491596 CACCCAAGTCTAATAATCTGCACCCTTGAGCAGTC[A/G]CTTCCTTCCTTTACATGCTTCCCAGGGCTCCTCAT R 2 1 2 1 101000 f 74 goat snp49030-scaffold7-2900398 13 30125212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420255 Affx-122945062 AX-123290603 13 29531380 TTGGAAATCTGTAACTTAGACTTCACCAAAACACA[C/T]TGAGGGGACTTCCCTGGTTAGGACTCTGTGCTTCC Y 2 1 2 1 101000 f 74 goat snp49029-scaffold7-2860614 13 30165145 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437860 Affx-122932075 AX-123308198 13 29565336 GATTAATTGCTAAAACAGGGGTTTAGGTCATAGAG[G/T]ACCTTCAAAATATATAGCAAATGCCAATAATTGTG K 2 1 2 1 101000 f 74 goat snp49028-scaffold7-2826658 13 30199907 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448507 Affx-122923456 AX-123318843 13 29611905 ACACATTTTCTGTGAGCTGTCAGAGCAGTGAAGCC[A/G]TCACACAGCAGGTGGTCCCTGAAAAGCTCCACTGT R 2 1 2 1 101000 f 74 goat snp49027-scaffold7-2780089 13 30246334 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790218 Affx-122935572 AX-385277222 13 29680972 GAAGGAAGGTAAAAATATTTACTGTATTCGAAACT[A/G]TTAAAATTCTATGCGTTAAATATACATGTTGAGTT R 2 1 2 1 101000 f 74 goat snp49026-scaffold7-2711022 13 30315997 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793633 Affx-122969185 AX-385280607 13 29738231 TATTACAAATCTAAACTACCTTCACAATTTATTTT[A/G]GTTTCAAATTAAATCTATTTTTACACTGTTTAAGA R 2 1 2 1 101000 r 74 goat snp49025-scaffold7-2653763 13 30360976 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440996 Affx-122928966 AX-123311333 13 29799962 ATTTTTAAAATCCGCCTTACATTTTGTATTTTTTT[A/G]TGTAGTTTAATATCTGTCCTAAGCCAGCTACAGAT R 2 1 2 1 101000 r 74 goat snp49024-scaffold7-2592032 13 30422625 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406429 Affx-122955202 AX-123276781 13 29830356 TCACCCTGGACCCTGCTTAGGGTCCCAGGGTTGTG[C/T]GATTCTGGCCCACCCAGGGCAGGACAAATGCCTTT Y 2 1 2 1 102000 r 74 goat snp49023-scaffold7-2561638 13 30453159 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391094 Affx-122966824 AX-123261451 13 29882736 AAGAAGAACCAATTTTTCCTAACTAAAGCCTTCAG[A/G]CATAAAGATTGTTTTTTTTAAAAGCTGACTGTGTA R 2 1 2 1 201000 f 74 goat snp49022-scaffold7-2509258 13 30505345 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387925 Affx-122970441 AX-123258283 13 29941942 ATAAGGTACAGGAGAACCACCTAGGTCCGAGATGG[C/T]GGACAAGTTGACTTTTATTAGACTTCGAGCCTCAT Y 2 1 2 1 201000 r 74 goat snp49021-scaffold7-2450052 13 30564503 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380056 Affx-122975568 AX-123250414 13 29986038 TTCAGATTGCCCATCTTATTACCGTGTTAGAGAAA[C/T]GACTTAACCTTTCTGAGCCTCGAGTGCCTCATCAT Y 2 1 2 1 102000 f 74 goat snp49020-scaffold7-2405956 13 30608629 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790305 Affx-122969616 AX-385277308 13 30017390 GGAGCTTAAAGTTGATTGCACAGTTAAAGGATGAT[A/G]CATGCGAATCAACACCAGGTAGTTCAGGAGAGCTG R 2 1 2 1 101000 r 74 goat snp49019-scaffold7-2374604 13 30639831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779846 Affx-122938423 AX-385266945 13 30047988 ATATTCAGTTGGTTCCCCTATGATTATGGAAAAGC[A/G]TTTAATATCATTATCTTCTTATGGTTTTGTCACCA R 2 1 2 1 102000 f 74 goat snp49018-scaffold7-2344006 13 30670229 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776232 Affx-122952411 AX-385263361 13 30144932 GAGTAGCACGGTCAAAGCTGGAAGCTCTTTTGTCT[C/T]ATGCCACAGCCTATGCTTTACTTGGTATGCCATTA Y 2 1 2 1 101000 f 74 goat snp49016-scaffold7-2247062 13 30764696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773132 Affx-122962620 AX-385260275 13 30188385 TGAAAGGAAAAAGATTAAGTACTTTTTCTCCATTT[A/G]TAATTGGGTGTATAAAATTTCAGGTCAACAATAAA R 2 1 2 1 101000 f 74 goat snp49015-scaffold7-2203609 13 30808794 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398183 Affx-122962649 AX-123268538 13 30230541 CATTGCTACAAATTTCTTTGTTTTCCCAGTGTTCT[A/G]TTATTAATGCTATAATATTCCTTTGCCCCTAAATT R 2 1 2 1 101000 r 74 goat snp49014-scaffold7-2161453 13 30851746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429403 Affx-122938530 AX-123299745 13 30261547 GGCTCATCTGCAGCATTCTCCTGCTCAAATCAGGC[A/G]TCACCCTCCACAGGAAAACTTCCCTTCTCTTACAA R 2 1 2 1 101000 r 74 goat snp49013-scaffold7-2130447 13 30883056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800499 Affx-122975187 AX-385287419 13 30292792 TGTGCAGACTTGTGCTTATAAACTAGGAGATAAAA[C/T]ATAGCTTTGTGGAAAAATCTTGGCATATATCCATG Y 2 1 2 1 101000 r 74 goat snp49012-scaffold7-2099202 13 30914348 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445171 Affx-122925543 AX-123315508 13 30338229 CTTCATTTAAGCAACAAAGATCATAGCCTTTTAGC[A/G]CATACATGACCCTCATAGACTATGGCATGTTCCTT R 2 1 2 1 101000 f 74 goat snp49011-scaffold7-2053765 13 30960313 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384475 Affx-122973076 AX-123254833 13 30367120 CTCAATACTGGAGAATAGAAAAAATGATTGTTTAC[A/G]TACTACAGAAATAAGGCAGGAAAGATAAGAAATAA R 2 1 2 1 101000 r 74 goat snp49010-scaffold7-2024874 13 30989979 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797656 Affx-122959632 AX-385284595 13 30418746 AAAGTTGAGACCAGGAGTGGTCAGAGAAAACAGGT[A/G]GTTAGATGAAATTTGCAAGCCAGGGCTCCATGAGG R 2 1 2 1 101000 r 74 goat snp49009-scaffold7-1973248 13 31040139 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782270 Affx-122922588 AX-385269348 13 30493681 ATCATTTTATGATTTGATGAAAAGCAGTTAGGCCA[C/T]GTAAGTGGTCAAAATGGGATCACTTTATATATGCA Y 2 1 2 1 101000 f 74 goat snp49008-scaffold7-1898313 13 31115688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451423 Affx-122921178 AX-123321756 13 30594631 CAACATACATGTTTTCATCCCTGGTATTTTGCTCC[A/G]TGTGTAAGCTTAATGTAGTGTATGTGCTTACCTGG R 2 1 2 1 101000 r 74 goat snp49006-scaffold7-1797363 13 31217101 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776335 Affx-122957849 AX-385263463 13 30652982 ACTTTAACTGCACAGACAAAAGGTCAAAGAAAACT[A/G]TTAAAGAGAAACAAATAAAAGTGCCTGTGGAAGAA R 2 1 2 1 303000 r 74 goat snp49005-scaffold7-1739012 13 31272356 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411487 Affx-122951788 AX-123281837 13 30712212 GGGCTCCCTGGGTGGGGTGAGCTGGTTCCAGGGCA[A/G]CTTTGGGTTGAGGCCAGAAATCTCTCTTGTCTCTT R 2 1 2 1 101000 r 74 goat snp49004-scaffold7-1679782 13 31332729 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796277 Affx-122920645 AX-385283227 13 30759048 CAACTGATTTTTGTGTAGTACTTTTGTATCATGCA[A/G]CTTTACTCAGTTCATGTATTATTTCTACCTTTTGG R 2 1 2 1 201000 r 74 goat snp49003-scaffold7-1632946 13 31380206 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794867 Affx-122940119 AX-385281827 13 30788222 GGGTTGTATTATTTCTTAAACTATAACTTGGGGCA[C/T]GTGGTATTTGCCAGTATTTGTCTTCAGATTGTGCC Y 2 1 2 1 101000 r 74 goat snp49002-scaffold7-1603772 13 31410027 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415372 Affx-122948765 AX-123285721 13 30822466 ATAGTAAGAAGCAACAGGAGAATGCCCACTTTTAC[A/G]CTACTATTTAATGACAATCTTAGTGCTAAAGTCAC R 2 1 2 1 101000 r 74 goat snp49001-scaffold7-1569528 13 31444470 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422319 Affx-122943466 AX-123292665 13 30893997 AGTCTTCCTGTTTCAAATGCATATTTAATTTAACC[C/T]GAAGGAAACCCACTGGCCTACCAGCTCCCCCTCCA Y 2 1 2 1 101000 r 74 goat snp49000-scaffold7-1497997 13 31514735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450939 Affx-122921767 AX-123321273 13 30926404 TGAAAGTTGTATCTATAATATTCCTATTCTGCAGA[C/T]ACCCATCCATCAGAGTCTCTTGGGAGCTGCCTTTG Y 2 1 2 1 102000 r 74 goat snp48999-scaffold7-1465590 13 31546952 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789243 Affx-122945829 AX-385276254 13 30972706 AAGGAAGTGGTCAGTGGGCAACTGTTCCTCAAAGA[C/T]GTCCTAAATTAGTATTAAAATCAATCTAAAGGGAT Y 2 1 2 1 101000 f 74 goat snp48998-scaffold7-1419288 13 31594543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426892 Affx-122940463 AX-123297237 13 31014010 GAGCCATTCATTCCTCAGAGGAGGGCAAAACTCAT[A/G]ATGCAATCAGGAGAAAAATGTGTTGACACAGGGCA R 2 1 2 1 101000 f 74 goat snp48997-scaffold7-1377984 13 31635655 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406651 Affx-122955811 AX-123277003 13 31046762 AAGTCCTCTCCAAAAGTCTAAACACTGTTTCTGAG[C/T]TCTATGATTCTGCACTGAATATTCCAGCATTCAAG Y 2 1 2 1 101000 r 74 goat snp48996-scaffold7-1345232 13 31667994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430866 Affx-122937417 AX-123301207 13 31089753 AATAACACAAACACACAGACAAACCTGTAGCCCGG[C/T]ATTTCCTGGAGGGAGTCAAACCTTGCCAGGTGAAT Y 2 1 2 1 201000 r 74 goat snp48995-scaffold7-1302241 13 31710652 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444211 Affx-122927249 AX-123314548 13 31139738 TTAATGACACTAGCTAGTAAGATGATAATAAGCTT[A/G]TAATGTGAAGAGGACCTTTATTAAATTATACACTC R 2 1 2 1 101000 r 74 goat snp48994-scaffold7-1252256 13 31761331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776897 Affx-122947172 AX-385264021 13 31185665 GGTATGAGTTCTATCATGGTGTTGGAAACTTAAAA[C/T]GAAAATTCAATTTATACACTACAGAAACAAAATTA Y 2 1 2 1 201000 r 74 goat snp48993-scaffold7-1206329 13 31807409 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443526 Affx-122927780 AX-123313863 13 31294465 CCTGAAGAGCTCTGGAGCATCTCTCTGATAGTCTG[C/T]GGAAATCTGACCCAGACTTCAAATCCCTTCTCGAA Y 2 1 2 1 101000 r 74 goat snp48991-scaffold7-1097529 13 31918186 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440337 Affx-122929670 AX-123310674 13 31343085 CTGGGGAGGGTGACCTTTACAACATCACCAGCTTC[A/G]TGACTATAGGACCCAAGATGAAAGGCTAGTCTTAT R 2 1 2 1 101000 r 74 goat snp48990-scaffold7-1048909 13 31966423 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788285 Affx-122949251 AX-385275303 13 31374248 TGATATTCAGCACATGAACTGCTCAAGAAAATTAA[C/T]GGTTTTGGAAATACTAGTTTCTAAGTTTAAAGGAA Y 2 1 2 1 101000 f 74 goat snp48989-scaffold7-1017746 13 31997583 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413144 Affx-122950360 AX-123283493 13 31429438 GCTATTGGGTTCATGTAGCCAAATCACAAAACTAA[C/T]GAACTGTTAAATTTGCTCGGTTGTTAAACGTGAGA Y 2 1 2 1 101000 f 74 goat snp48988-scaffold7-962556 13 32052619 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417250 Affx-122947271 AX-123287598 13 31489880 TGCCACACACACACATTTAAAGGACACTGAGAAAG[C/T]GACCTTGAGAAAGTTACATGTATTTCATTGTAATT Y 2 1 2 1 101000 f 74 goat snp48987-scaffold7-902114 13 32113407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783628 Affx-122951234 AX-385270687 13 31524017 CTAAATTGTATTAAAGAGATGGATGACAAGCTTAT[C/T]GTTCCATGGTGGTCATGCTGTACTGAATTCGATAA Y 2 1 2 1 101000 r 74 goat snp48986-scaffold7-867977 13 32147588 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789257 Affx-122942486 AX-385276268 13 31561794 CCCGTGTGGAGAGCTGAGGACAATTAAAGTCAGAT[C/T]TGCCTTCCCAGTCATTGTAAAGGTATGCACTCCAC Y 2 1 2 1 101000 r 74 goat snp48985-scaffold7-830200 13 32185510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802745 Affx-122933557 AX-385289644 13 31602351 CTAAACCCAGATATAAATTATTAAGAGATTATCTA[C/T]GTCAATCCTCCATTTGGTTAACATGTGAAATATAA Y 2 1 2 1 201000 r 74 goat snp48984-scaffold7-789643 13 32226075 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423871 Affx-122942310 AX-123294217 13 31633995 GTAAAGTCTGGACCAGTGAGGGGTGGGAAGGGGAG[A/G]GGTTACGTGCAAATGATTCGTGTAGACTTTGAGAA R 2 1 2 1 101000 r 74 goat snp48983-scaffold7-757999 13 32257698 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397102 Affx-122962700 AX-123267457 13 31676938 GATGGATCTATATGTTTAGATTTTTGGTTTCTGTC[C/T]TTTGGAACTTAAAACACTTACAATGTCAGGTTTAT Y 2 1 2 1 101000 r 74 goat snp48982-scaffold7-715056 13 32300817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439939 Affx-122929999 AX-123310276 13 31714822 CTCTTTCAGATGAGTTCTGGATCACTCCCAAATGA[C/T]AGTCACCCTTCACTGTATTTTCTTTTTCCTTCATG Y 2 1 2 1 101000 f 74 goat snp48981-scaffold7-677172 13 32338894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272685 Affx-1111832980 AX-519546390 13 31739735 GAGAGGGAAACAGCAACCCACTCCAGTATTCTAGC[A/G]TGCAAAATTCCATGGACAGAGGAGCCTGGTGGGAT R 2 1 2 1 103000 f 74 goat 13_31739735_AF-PAKI 13 31739735 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38430048 Affx-122937563 AX-123300389 13 31747399 GTTAAATGGAGAAGGCAGTAAAGAAAGAATAACTT[A/C]GTGCCTGCTTTTATCTTCCCACTGCCTCCCAGCGC M 2 1 2 1 201000 f 74 goat snp48980-scaffold7-644595 13 32370726 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778108 Affx-122955291 AX-385265223 13 31834452 AATCAGGTTGCTGACACAGTGTTCTAGAACCACAT[A/G]TACCATCACTATTCACTCTCTGAATATTCTGTTTG R 2 1 2 1 101000 f 74 goat snp48978-scaffold7-557542 13 32458860 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377613 Affx-122977890 AX-123247972 13 31864473 GTAAGTCAGGGAAATAACTGCCTCTTTAAAATACA[C/T]AGAGGCTCACAATGTACAGGCTCAAAGAAGTCTTG Y 2 1 2 1 201000 f 74 goat snp48977-scaffold7-527521 13 32488843 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419470 Affx-122945480 AX-123289818 13 31925400 TTCCTCTGATGAGTTAACTCAGTGTCCTAGTTATA[C/T]GACATTTCTTAGCCTATTTAATCCTATTTCTCAGT Y 2 1 2 1 101000 f 74 goat snp48976-scaffold7-466594 13 32550624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414929 Affx-122949100 AX-123285278 13 31976242 AGGTCCATTATAATTTTACCCCTAGAGATTTTAAA[C/T]CCATCAATAAAAAATCAAGATGCAGCAGAACCCTA Y 2 1 2 1 101000 r 74 goat snp48975-scaffold7-415752 13 32601414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768807 Affx-122963520 AX-385255984 13 32007538 TACATAACTTCTACTGTTACTACTTTCAGGTGTAA[C/T]GGTGGTAATGTGTTTACATTAAAAAATCATTGTAG Y 2 1 2 1 101000 r 74 goat snp48974-scaffold7-384456 13 32633133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770072 Affx-122944043 AX-385257239 13 32084935 TTTCCTTTTATTTGTCTCCTAAGCAGAGCTGTCTA[A/G]GGACAGTACAGTATTGAAAGGAAGTCAACCCTGCA R 2 1 2 1 101000 r 74 goat snp48973-scaffold7-307059 13 32710520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276717 Affx-1111835555 AX-519550227 13 32089942 TCTTCTCAGGGCTAAGCATGTAAACACGCACATCA[C/G]AGATCACCGCTGTAATTACCCAGTCTATGGAGGCG S 4 1 2 1 101000 f 74 goat Random2.2K-1332 13 32089942 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769566 Affx-122940756 AX-385256736 13 32157133 ATTCTAAGCTTCCAATCATTCAGCCTTTACTTTCA[C/T]GCATTACCAGAACATTAGTCACTAGGAGCGTTAAT Y 2 1 2 1 101000 r 74 goat snp48971-scaffold7-234861 13 32783113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790278 Affx-122958643 AX-385277282 13 32212893 CTTTTCTTTAATTGTTGAATAGAAGCACTGACAGG[A/G]AAGTTATAGTCTAAGACCTAATTCTAATGGCAAAG R 2 1 2 1 101000 r 74 goat snp48970-scaffold7-179101 13 32838629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440210 Affx-122930692 AX-123310547 13 32262112 CTCTTTCCTGCTCCTCTCACAGACACCGTATCCTT[A/G]CAGATCCTGGAGCTGGTGGAGCTTTATCCACAGTC R 2 1 2 1 201000 r 74 goat snp48969-scaffold7-129882 13 32888453 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413354 Affx-122950152 AX-123283703 13 32305751 AGGCCACGTGTGAGTAATCCATGTAGGATGAACAT[A/G]CCTGAGAATCCCTTTTAGATAAGGAGCCCCGTTCA R 2 1 2 1 101000 f 74 goat snp48968-scaffold7-86243 13 32932320 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395544 Affx-122964253 AX-123265899 13 32335311 TGTATGTGTTTTTTTTTTGCAATTTCTGGTTTTCC[A/G]TTAAAACATGTTTTGGCCTCTGGTTGAATACAGTG R 2 1 2 1 101000 r 74 goat snp48967-scaffold7-56683 13 32961818 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423430 Affx-122942609 AX-123293776 13 32381126 TCAGGAGTAGAACTGCATTGCATTTATAAATTAAC[A/G]TAGAAGAAATATGAACTTTACAACATTAACCCTTT R 2 1 2 1 101000 f 74 goat snp48966-scaffold7-10868 13 33007568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774321 Affx-122975977 AX-385261457 13 32405749 GTTCTGAAAATATTTAGTGGATTCCTGAGCATCCT[A/G]TAATGGTTACCTTTGAGTTCCTTTTTCTTTTTTTA R 2 1 2 1 101000 f 74 goat snp21378-scaffold2086-13656 13 33034368 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452314 Affx-122920671 AX-123322647 13 32444143 TTCAGTCTCTCAGTCCCTCTCAGTCTGTATCAGGC[A/G]CTGACTTTGATGGAAGGGATTCACTTTTCTAAAAG R 2 1 2 1 101000 r 74 goat snp21379-scaffold2086-52050 13 33070786 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434861 Affx-122934365 AX-123305202 13 32529808 AAAAGCATTAAAATAGATCCCCCCTCTCACCAACA[C/T]TTAACTTCTATAAATCTGAAAAGGAAACTTTTAGG Y 2 1 2 1 201000 r 74 goat snp21381-scaffold2086-137715 13 33158242 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451096 Affx-122921400 AX-123321430 13 32558657 GTCTTACTGGTAATCACTGATGTAAAAATTCCAAA[C/T]AAAATATTAAATCCAGGATTATATTAAAAGAATAA Y 2 1 2 1 101000 f 74 goat snp21382-scaffold2086-166564 13 33187136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404956 Affx-122956419 AX-123275308 13 32609305 TCTACAGGTTATTGCTTCCCCCAAGACTGTATTTA[C/T]CACATATATTTTATGTATGTATTTATGTGAAATTA Y 2 1 2 1 103000 f 74 goat snp21383-scaffold2086-217212 13 33237817 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420482 Affx-122944869 AX-123290829 13 32640271 GCAACTAAATATTGCTTATAACATTTTACATAAGA[C/T]AATACATTTTTATCATCATTTAATATATTAATTTT Y 2 1 2 1 201000 r 74 goat snp21384-scaffold2086-248178 13 33268944 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403053 Affx-122958530 AX-123273406 13 32671613 CCCAGGATGCCTTTGCTCCTCTCCCAGCTCCACGT[A/C]TTGGCTCACTTCCTTCTCTACCAGCTCTGTCACTA M 2 1 2 1 101000 r 74 goat snp21385-scaffold2086-279520 13 33300702 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448279 Affx-122924179 AX-123318615 13 32711940 ACTGTTAGATTGTTTTTGGAAAACTGGACAGAGCT[A/G]TGTGCCAAGTAAGATAAAAACAGATCAAATATTAA R 2 1 2 1 201000 r 74 goat snp21386-scaffold2086-319847 13 33340891 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378601 Affx-122976577 AX-123248960 13 32764888 TGGCCAGCTCAGGGCTGTTACGTGTCACCATGGCC[A/G]TGTGCTCTGCCAGCCTTTAGGGCATCCGCCTCCTA R 2 1 2 1 201000 f 74 goat snp21387-scaffold2086-372795 13 33394270 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441788 Affx-122929091 AX-123312125 13 32821324 AATTCGGGAGAAGAAACTTGGCTGAATATATCCAT[C/T]TGCAAACTGTTAGCTCATGGATGGTGTATTAGTCA Y 2 1 2 1 101000 r 74 goat snp21388-scaffold2086-429231 13 33452380 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448767 Affx-122923314 AX-123319103 13 32953170 TTATTTTCATCCATAAGGTAAATCCTTGAAAGAGA[C/T]AGTAAAGAATTCAAAATGTACTTCATGTTCTACCA Y 2 1 2 1 101000 f 74 goat snp21391-scaffold2086-561077 13 33584903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273908 Affx-1111833925 AX-519547516 13 32991696 CCCTGAATTCACACTCCACCCAAAGGGTAGATGCC[A/G]GGGCCAGGCCTCTTTGGACCACTCTGCAGGGACAT R 2 1 2 1 201000 f 74 goat GoatD01.010608 13 32991696 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38396905 Affx-122963215 AX-123267260 13 33047118 AATCATTCAAAAGCTAATTTTGGCTGAGGCTGTCA[G/T]CCAGAGTGCCTACACCTACCTTCTCCAGGGTGACA K 2 1 2 1 201000 f 74 goat snp21393-scaffold2086-655025 13 33684781 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389241 Affx-122969040 AX-123259599 13 33138758 GCCAGAAAAGAGAGAGAGGGAGCAAGAGTAGAAAA[C/T]GAATGTCTACTGCGAAACTGATGTGTGGTAGGCCC Y 2 1 2 1 201000 r 74 goat snp21394-scaffold2086-746665 13 33777093 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414576 Affx-122949377 AX-123284925 13 33257003 TTACTGCATATACTTTGCTTGATATCACACCAGAA[C/T]TTTCTTAAGTATTTCCTTAGATAATATTTGCTCAA Y 2 1 2 1 101000 f 74 goat snp21396-scaffold2086-864910 13 33896058 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421190 Affx-122944154 AX-123291537 13 33290430 TTGAATACATGAAATACAGGTTGACACACATACAG[A/G]ACAACATAAGAAAAGTGAACAATTACTAAGCAGTT R 2 1 2 1 101000 f 74 goat snp30516-scaffold3368-597859 13 33930279 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415049 Affx-122949487 AX-123285398 13 33323498 CTGCCCATATAAAATAGTTGTTGTAGAAAAAAGCA[C/T]GTGAGTTCCGGAAAACCTTCTAATAACTCACCTTC Y 2 1 2 1 101000 f 74 goat snp30515-scaffold3368-564791 13 33961572 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427181 Affx-122939609 AX-123297524 13 33375250 GTTACTATCAGATCCTGAGAAACCACACTCTTGTC[A/G]CTTGTCAAATTACAGCAGTGCAAATATCTGTTATC R 2 1 2 1 101000 r 74 goat snp30514-scaffold3368-513039 13 34013143 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431724 Affx-122936753 AX-123302065 13 33456918 CCAATGTCATGTAGTCATAGTTTTTAGATTAGCCC[A/G]CAAAAGCCAGATTAAAAGTCATGCTAAAGCTGATA R 2 1 2 1 101000 f 74 goat snp30512-scaffold3368-431371 13 34094393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432996 Affx-122935255 AX-123303337 13 33505113 ATTTCTGAAGATTCTACAGCAGGTCCTTGTTATCC[A/G]AGGATAATTAGAACCAGGAAAAGGCCATTTCAATG R 2 1 2 1 101000 r 74 goat snp30511-scaffold3368-383176 13 34142705 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402899 Affx-122958209 AX-123273252 13 33548457 AGTAATTCAAAGGTAACACAGCTTTGAATCCAAGC[A/C]GGTTGGCTCTGCAACTCTCAGAGGATGGAGAAGCA M 2 1 2 1 202000 r 74 goat snp30510-scaffold3368-339832 13 34186239 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390545 Affx-122967221 AX-123260902 13 33617128 TCCTGATGAGTTTGAGCAGGATGCATGTACCGGGA[A/G]CAAATGAAGTGATGGTGATGATTTGCGACATCTAC R 2 1 2 1 202000 r 74 goat snp30508-scaffold3368-271161 13 34255019 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381172 Affx-122975208 AX-123251530 13 33675718 AGATGAACAAAATAGCCTTAGCTTCTCTGTTACTC[A/G]TAAGGCAGATCTGATTCAACTCAACAAAACCCTTT R 2 1 2 1 101000 f 74 goat snp30507-scaffold3368-212571 13 34314099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418492 Affx-122946442 AX-123288840 13 33706702 CAGCCTACCTGAAGCACAGATCAGACTCTGTCGGG[C/T]AGTAACTCCTGGGAAAAGATTTATTTTCTAAGAAA Y 2 1 2 1 101000 r 74 goat snp30506-scaffold3368-181587 13 34345139 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396539 Affx-122962945 AX-123266894 13 33770316 TTTCCCAAGAAGAATCAGGTTGGACTGTTTGAACA[C/T]GAGATTTCAGGAAGAACAGCGTGAACAGGTGTCTC Y 2 1 2 1 101000 f 74 goat snp30504-scaffold3368-117973 13 34408507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799964 Affx-122946943 AX-385286890 13 33878610 CCCTCCATCTCTTCAAAAACATTAGGTATGGTGCC[A/G]TCAGACTTCTTTTTATAAACAACAAGATTTTTTGA R 2 1 2 1 101000 f 74 goat snp30502-scaffold3368-9679 13 34516378 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423748 Affx-122942853 AX-123294094 13 33904442 AAATGTTGCTCCAGGGGCACTTTGCACTGCTGTTC[A/G]TCATTGCGTTTCCTCACCTGTCCCTCGACTTAATG R 2 1 2 1 101000 r 74 goat snp5251-scaffold1180-1542480 13 34541877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441083 Affx-122928903 AX-123311420 13 33991899 TGTTAACAGAAGAATCTCATGATGCAACGGAGATC[A/C]CACGTGGCACAACTAAGACCTGAGGCAACCAAACT M 2 1 2 1 101000 f 74 goat snp5249-scaffold1180-1455023 13 34629774 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376408 Affx-122978087 AX-123246767 13 34176342 TCCACTGTGAGCTCCAAAAGGCAGGGCTTCCCTCG[C/T]AGCTCAGCTGGTAAATAATCCACCTGCAATGCAGG Y 2 1 2 1 201000 f 74 goat snp5245-scaffold1180-1270580 13 34815065 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450208 Affx-122922287 AX-123320543 13 34206617 CAGGGAGCCATAAAATATTCCCCAGCAAATTCCTT[A/C]AGAGCAGGAAATAAACTTTTGATTTCTTGTAGACA M 2 1 2 1 101000 f 74 goat snp5244-scaffold1180-1240305 13 34845457 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801762 Affx-122959475 AX-385288670 13 34258787 GGACTGTAGGAAATTTCCACTGTAAATAAGTTAGG[C/T]GACCTTAGAACTGTCTATAAATAGGTGGTATATGC Y 2 1 2 1 101000 r 74 goat snp5243-scaffold1180-1188135 13 34897707 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408562 Affx-122953674 AX-123278913 13 34301549 ATTCCCACCTGCACAATGGAGAAAACAATTCTTAC[A/G]TAACAGGATTATTGCATGAATAAATGAAATTGCTA R 2 1 2 1 101000 f 74 goat snp5242-scaffold1180-1145373 13 34940308 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272739 Affx-1111832981 AX-519546439 13 34322426 TCACTGAGTTAGCAAGTCTCTTCTCTAGTTCTCAC[A/G]GTGTATCTCATGCCCCAAGTCTTGAAGCAAGTTTT R 2 1 2 1 201000 r 74 goat 13_34322426_AF-PAKI 13 34322426 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38381457 Affx-122974332 AX-123251815 13 34441255 TTGTCTCAAATAAATCAATAATTTCACTCAGCTTC[A/G]TTGCTCTGTGCATGGTGTGCTCTCGACAGATGGAT R 2 1 2 1 102000 r 74 goat snp5239-scaffold1180-1005667 13 35082374 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449650 Affx-122922582 AX-123319985 13 34471118 TTCTTGGGGCGGAGCCAGTACACGTTAGGTGCTCA[A/G]TAGTGATTAGCAATTGATTCAGGACTAGGAACCTG R 2 1 2 1 101000 r 74 goat snp5238-scaffold1180-975804 13 35112230 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409938 Affx-122952869 AX-123280289 13 34515379 GGGGCAGCCACATAGGAGAGATGGACAACCTTCCA[G/T]CTGCTCCTAGTCTGTGACTGACAACAGCGATGGTG K 2 1 2 1 202000 r 74 goat snp5237-scaffold1180-931543 13 35156479 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783122 Affx-122940880 AX-385270189 13 34561357 AGCAAATATGACAAACGTATTACAGGGTTTCCTTG[C/T]TTGTACTCAAGTAGTAAATGTACTACCTCTTTAAA Y 2 1 2 1 101000 f 74 goat snp5236-scaffold1180-885565 13 35202433 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790079 Affx-122943813 AX-385277085 13 34604283 TGGGGCTCTTGCAGTCTAAGTGCTTTGTATTATAC[C/T]GGTTTATTTTGAATCCTTCCCCACCACTGTCTGAG Y 2 1 2 1 101000 f 74 goat snp5235-scaffold1180-842639 13 35244915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788463 Affx-122927221 AX-385275480 13 34647079 AACCTGGACTTTTTGCTGCTGATAAGGGCTGTGTG[A/G]ATGGCAAAGAGGCAACTTACTCATTTCTTTAGAAT R 2 1 2 1 101000 f 74 goat snp5234-scaffold1180-799843 13 35288662 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451247 Affx-122921943 AX-123321580 13 34700259 AGGTCCTGAACCATTCTTGTGATAATTTTTAGGCT[A/C]TGATGCCTACACCCAGAAGGCTGACATCTTCCTAA M 2 1 2 1 101000 f 74 goat snp5233-scaffold1180-746663 13 35342059 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276857 Affx-1111835556 AX-519550366 13 34807158 GGTGTGTGGCTACTTTTTGTAATGTCCACCCCTGA[A/T]TCCCTCTTGTTCAGTTCCATGACCCTCTGTGTCAT W 4 1 2 1 201000 r 74 goat Random2.2K-1335 13 34807158 A T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320773835 Affx-122960712 AX-385260975 13 34834407 GTCTGAATATGCCATCTTGATATTGTTTCATTAAC[A/G]TCCTTTTGTGGAGCAGAATTTACCGTTGTGATACT R 2 1 2 1 101000 r 74 goat snp5230-scaffold1180-612515 13 35476488 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776569 Affx-122965464 AX-385263696 13 34925417 CTGTCTTTCCTGGCTGCTCCAGAAGTACCTTAATC[A/G]TTATACAGTACCAAACCCATGGATGAGACCAAATG R 2 1 2 1 101000 f 74 goat snp5228-scaffold1180-521505 13 35567327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435961 Affx-122933526 AX-123306300 13 35025090 CTGCGGGAGCAGAGTGAGACAAGTTCTTCTTCCCC[A/G]TAAGTCTGCTCTGGATGTTTTTCTAATATCTGTCC R 2 1 2 1 101000 r 74 goat snp5226-scaffold1180-421832 13 35668625 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783800 Affx-122972228 AX-385270857 13 35145135 ATCCCCTAGTGTTTCAAGCAGGGGAAGGAGAAAAG[C/T]AACCATTTTGCAATACAAAGGCCAAGAGCTCTCTC Y 2 1 2 1 102000 f 74 goat snp5223-scaffold1180-301787 13 35788791 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451255 Affx-122921935 AX-123321588 13 35210682 ACAATCTAAGTACCAAAAGTTGAAGTCCAGGAAGT[A/G]TTGAGTCAGATGGCTTTTATGAGATTCTGTTACAT R 2 1 2 1 101000 f 74 goat snp5221-scaffold1180-236240 13 35857527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411230 Affx-122952346 AX-123281580 13 35242851 GATGAGCCTGTCCCGCCCAGAGTCTGCTTGTCACC[A/G]TGCACTGTCCTGCACTATACCATCATGGGACCTAA R 2 1 2 1 101000 r 74 goat snp5220-scaffold1180-204071 13 35889692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445297 Affx-122925448 AX-123315634 13 35304762 TGAGTGTAAACTGGCATGATATTCCGAGAAGAAAA[C/T]ACATCAGTCTCTCTCAGAATTTAAAATATACATAC Y 2 1 2 1 101000 f 74 goat snp5219-scaffold1180-142160 13 35951605 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423116 Affx-122942912 AX-123293462 13 35451072 AGCTGGTACAAGGCCTGGGCTGTTGCTCTGTGCAC[A/G]TTGGTGTCATTTGATTTCAGGTACCGCACTAAGGG R 2 1 2 1 101000 r 74 goat snp25882-scaffold267-1023951 13 36098518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768276 Affx-122978423 AX-385255457 13 35496192 GTGATTTGTGTTATCTGGTACAGTGACAGTTATAC[A/G]TTGTCTTCTCAGATGTTTGATAGCTGTAGGAGAAA R 2 1 2 1 101000 r 74 goat snp25881-scaffold267-978831 13 36143389 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449791 Affx-122922425 AX-123320126 13 35565375 TCTTGTAGTATTTAGTCTAGTAGAGGACAAGTGAA[C/T]TTCATTGTTTAGTCTTAACGGTATTTACTCAAATG Y 2 1 2 1 101000 f 74 goat snp25880-scaffold267-909648 13 36213084 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420329 Affx-122945008 AX-123290676 13 35623705 GAAAGCTTAAGCATATATACCAAGAACGACTGATA[C/T]ATAAATCCTTGTAAAAATTAACCTCTCGGAGAGGT Y 2 1 2 1 101000 r 74 goat snp25879-scaffold267-851318 13 36271581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272205 Affx-1111833387 AX-185312215 13 35679486 ATTCAGAAGGAGATCAACCCTGGGATTTCTTTGGA[A/G]GGAATGATGCTAAAGCTGAAGCTCCAGTACTTTGG R 2 1 2 1 303000 f 74 goat 3_42416565_AF-PAKI 13 35679486 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38375710 Affx-122978642 AX-123246069 13 35683645 GCAAAATAGAAAGACGCATGCAGACTTCATGAACA[A/G]TGCTTCTAAGCCAACATAGGATGAAGCAAGCCTCT R 2 1 2 1 101000 f 74 goat snp25878-scaffold267-791378 13 36331304 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274507 Affx-1111834333 AX-519548098 13 35715096 TAGCTGTGTATTCAGCATTGCTAGGATCTGCAGGA[A/G]TGTGTTTTTATTTCCTACTCTAAATGTCAGTCTAA R 2 1 2 1 101000 f 74 goat GoatD01.030293 13 35715096 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38393042 Affx-122965629 AX-123263399 13 35717540 TAACACTGTTTTGAGTTTTGATTACTGTAACTTTG[C/T]AGTAAGTTTTGAAATCAGGATTATTCTTCCTTTAA Y 2 1 2 1 303000 r 74 goat snp25877-scaffold267-757483 13 36365236 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796760 Affx-122949903 AX-385283704 13 35746415 TGTTTCCTCTCATTTTTCTGTGGTTTTATTCATAT[A/G]TAAATAAAATCAATTCCTCTCCCCGTTGGATGCAC R 2 1 2 1 201000 f 74 goat snp25876-scaffold267-728608 13 36394404 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428883 Affx-122938936 AX-123299225 13 35800945 GCACTAGTTTTGATAATGGGTAATTTAAACAACAT[A/G]TGGTAACATTTACAAAAATGTGTAAGTCATCAAAT R 2 1 2 1 101000 f 74 goat snp25875-scaffold267-674078 13 36449428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378653 Affx-122977095 AX-123249012 13 35866817 CTGTTTTATCGTCAGGGCTTAGAATAATGTCTTCC[A/G]CACTATAGACACTTAATATTTGTTCAGTGCGTGAA R 2 1 2 1 101000 f 74 goat snp25874-scaffold267-608206 13 36516087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400340 Affx-122960044 AX-123270695 13 35906855 ATGGATTTCATCAACTTGTCAAGTTTCTGGTAGAC[A/G]TTAAGGCTAGGAAACCCAGACTCAAGCAATCATGT R 2 1 2 1 201000 f 74 goat snp25873-scaffold267-568168 13 36556975 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426513 Affx-122940208 AX-123296859 13 35988007 GGGAAACAGAGAAGGAAGGTTGGGAAAGGAAGTGA[C/T]GCTGCTCCAGAACTGAAGCTCGGGACAGTAATAGA Y 2 1 2 1 201000 f 74 goat snp25872-scaffold267-487016 13 36640180 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768781 Affx-122943056 AX-385255958 13 36017334 CCCTGTATAACACTTTACACTTTTTATATTTTGTC[A/G]TGTTTTAGCTATCCAGAATGTTTTTTAATTAAACA R 2 1 2 1 101000 f 74 goat snp25871-scaffold267-457689 13 36667250 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386671 Affx-122970191 AX-123257029 13 36048882 TACCCTGCACTTTGGTGTGTGCCCCTGTGAGTTTC[A/G]AGCAGGTCCTGAGGTATCTTGAGTCTCAATGGCAA R 2 1 2 1 101000 r 74 goat snp25870-scaffold267-426141 13 36698784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789342 Affx-122950084 AX-385276352 13 36108293 CCAGCATGGTAGCAACATGGAATGGCTTAAATTTA[A/G]ATGTACTTGAAAGTTCAGCTCCTTAGGTTCACTGG R 2 1 2 1 101000 r 74 goat snp25869-scaffold267-366730 13 36758649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395293 Affx-122964072 AX-123265648 13 36145313 AGCAGGAAGTCACGTTGTGGGTGGACTTGTGTTGC[A/G]CTTTGGTATACCTGTCAGGCTGCAGATTCCTCCCA R 2 1 2 1 101000 f 74 goat snp25868-scaffold267-329710 13 36795659 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385204 Affx-122971716 AX-123255562 13 36186933 TCAGTGCTTGTAAATAACACAAATAAATCGATAAA[C/T]GCAGCAATCTCTTGCTTAACCCTGCGTTTGGAGGG Y 2 1 2 1 101000 r 74 goat snp25867-scaffold267-288090 13 36837302 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463275577 Affx-1109901239 AX-514760904 13 36236435 TGTTGTCTACTCATCTAGGTCGTCATGTGGGTGAG[A/G]TTTAAGAAACAGTGCAGATTTAGATCCAGTGATTT R 2 1 2 1 201000 r 74 goat Random2.2K-1338 13 36236435 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778369 Affx-122954689 AX-385265484 13 36250448 CATTATTAACTCAGATATTGAACTTAAGAGTCCCT[G/T]GAATTTTCTCTCTCAAACCTGTATATTCAAACCAT K 2 1 2 1 101000 r 74 goat snp25865-scaffold267-224575 13 36901268 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424006 Affx-122942102 AX-123294352 13 36284028 CAGAATTTGCACCAAGAGTGAACCCTAAGGTAAAC[G/T]ATGAATTTCTGGCATTATGATGTGGCAATATAGGG K 2 1 2 1 201000 r 74 goat snp25864-scaffold267-190995 13 36934416 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449746 Affx-122922457 AX-123320081 13 36317955 TTAGAATTATTTAAGATGTTGGAGTATTTCCCCAA[C/T]CAAAGGATTCTGGAGCAAAGTCATCTATTTATTAT Y 2 1 2 1 201000 f 74 goat snp25863-scaffold267-157068 13 36968061 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771281 Affx-122975608 AX-385258439 13 36364213 GTTGAAGAATGTGCTCGTGCATTTCTTCAGCAGCT[A/G]TCTATTTGGTGCCTAATATGTGCTGGGACTTCTGC R 2 1 2 1 101000 f 74 goat snp25862-scaffold267-110810 13 37013793 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765749 Affx-986697582 AX-385253205 13 36405062 ATGAAATTATATGAAATAGAATAGTTCTTTTTTTC[C/T]TTAGGTTATATCACATTTCCAAGTATTTCGACAAG Y 2 1 2 1 600010 r 74 goat 13_36405062 13 36405062 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 320763055 Affx-986697584 AX-385251022 13 36405829 GAAAACAGACTATGTAACAATCTTCTTTTGTGATT[C/T]CCATATTTTCTCACTCGAATTTGTTTTAACATTCT Y 2 1 2 1 600010 f 74 goat 13_36405829 13 36405829 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 320765756 Affx-986697586 AX-385253211 13 36405834 CAGACTATGTAACAATCTTCTTTTGTGATTTCCAT[A/G]TTTTCTCACTCGAATTTGTTTTAACATTCTTATTC R 2 1 2 1 600010 r 74 goat 13_36405834 13 36405834 Ancestral_priority_1043 ancestry 0.71 recommended IMAGE 10K 10K ancestral 320763058 Affx-986697587 AX-385251025 13 36405866 CATATTTTCTCACTCGAATTTGTTTTAACATTCTT[A/G]TTCATTTGGGTAAATTCTACCCACTCATCCATTTC R 2 1 2 1 600010 f 74 goat 13_36405866 13 36405866 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 320765759 Affx-986697588 AX-385253215 13 36405874 CTCACTCGAATTTGTTTTAACATTCTTATTCATTT[G/T]GGTAAATTCTACCCACTCATCCATTTCTAGCTTAT K 2 1 2 1 600010 r 74 goat 13_36405874 13 36405874 Ancestral_priority_1043 ancestry 0.626 recommended IMAGE 10K 10K ancestral 320763061 Affx-986697590 AX-385251028 13 36405942 TATCGTTCTTTACTGTGTTTTCCACAGTCTCTACT[A/G]TCCCTTGTGAGCCCTCCAATTTCATCTTCACTTCA R 2 1 2 1 600010 f 74 goat 13_36405942 13 36405942 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 320798972 Affx-122975968 AX-385285902 13 36461509 TCAACATCTTGGCCTGGCTGAGAAGGTGTGCCACC[C/T]ATCCATCAACCAGCCAATCAATATTTATGGAATGC Y 2 1 2 1 202000 f 74 goat snp25860-scaffold267-13514 13 37112561 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769147 Affx-122968140 AX-385256322 13 36499354 GCCCATCTGGCTTAACAATGAAGCCTTAATTAAAA[C/T]GTTTTCTTTGCTTGCACATCCTTTGTCTGATTAAC Y 2 1 2 1 101000 r 74 goat snp11754-scaffold1433-526494 13 37333997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413659 Affx-122950117 AX-123284008 13 36547616 TATCAGACCCTCACTCTGCACTCTTGGCAGTATAT[A/G]TACATGAGGCAATCTGGAAAGAGAGGGGCTTCCTT R 2 1 2 1 201000 f 74 goat snp11753-scaffold1433-478232 13 37383050 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433055 Affx-122935753 AX-123303396 13 36580508 GAGCCTGTCTCCCAAGGCCACCCCACCCCAAGGGA[C/T]GGCCATTCTGTCATTTAAACAGTCACTACACAAAC Y 2 1 2 1 101000 r 74 goat snp11752-scaffold1433-445340 13 37415958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795063 Affx-122950955 AX-385282022 13 36617640 GGAAGTCTAATACAATTTAGTGTAATTATGTGAGA[C/T]GGTTTTAGTAGACATGTATCAGGATGACACTCCCC Y 2 1 2 1 101000 r 74 goat snp11751-scaffold1433-408208 13 37451382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405888 Affx-122955598 AX-123276240 13 36661629 ATTGCATTCATGAAAGGGGCCCCCTTGTGAGACCC[C/T]AGCCCAGAGCTGAGATGGGAAGGGGGCTTAGCTTG Y 2 1 2 1 103000 f 74 goat snp11750-scaffold1433-364219 13 37495396 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382877 Affx-122973424 AX-123253235 13 36746333 ATTTTACTCAGCCCTCAGTGAGCTGGTCTGCCAGT[A/G]CCTTAAGGCCTCGGCACTCGTTGTTAGTCGCTCAG R 2 1 2 1 102000 f 74 goat snp11749-scaffold1433-279515 13 37579537 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423041 Affx-122942970 AX-123293387 13 36787363 ATCTCTGGGACCACCATCAGCACCACTCCAGTCTC[A/G]CAGAACCCGATGTACAGTCAACACTCAACAAACAT R 2 1 2 1 101000 r 74 goat snp11748-scaffold1433-238485 13 37621174 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431041 Affx-122936654 AX-123301382 13 36820674 TTCATCTCACCCTCCCAGCACGGTCACTTCTGACG[C/T]ATTTTGTTAACTTATAAGATTCAAGGGGAGGGCTA Y 2 1 2 1 102000 r 74 goat snp11747-scaffold1433-205174 13 37654113 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407093 Affx-122954895 AX-123277444 13 36857031 ATCATGAATCTCCTATATTCTAACTGACAAGCATG[A/G]GTATTTTAGAATTAAAAAAATATTCAATGTAGCAA R 2 1 2 1 101000 f 74 goat snp11746-scaffold1433-168817 13 37690226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393825 Affx-122965169 AX-123264180 13 36895957 ACAAAGTGAAGGGGGCTCGGGGAGCACTGTGGGCT[A/G]CTGGTACGGTCAGTTGGAGTAAACATGGAGCTGCC R 2 1 2 1 101000 r 74 goat snp11745-scaffold1433-129891 13 37729028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272741 Affx-1111832982 AX-519546441 13 36915915 AATAAGAAATAAGAGGGTTCCCCCCGCCCCGCCAG[A/C]CACTTAACTATATGCAATACATCCAGAGCAGGGGA M 2 1 2 1 101000 r 74 goat 13_36915915_AF-PAKI 13 36915915 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320773963 Affx-122921794 AX-385261102 13 36989240 GGTTAATATCCATAATCCAACATCCAAAAGAAAAG[C/T]GAACAAAAGACAAGAGCAGGTAGTCTTGTATAAAA Y 2 1 2 1 101000 r 74 goat snp11744-scaffold1433-36608 13 37822883 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772244 Affx-122936516 AX-385259399 13 37058931 GTGCTGAAAATGCACTTATTTTTGCTTAAAATAAC[A/G]CAGTCGTTGCCAGCACTTGTGCTTTTCAGCTTGCT R 2 1 2 1 303000 f 74 goat snp15403-scaffold1634-32984 13 37901214 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381180 Affx-122975201 AX-123251538 13 37100789 TACGCAGCCACTAACACGATAGCATATACCCGGTG[C/T]GTCTCGGCGTACCTGGAGAGACAGGAATGACGTAG Y 2 1 2 1 101000 f 74 goat snp15404-scaffold1634-74842 13 37943028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794972 Affx-122952354 AX-385281932 13 37175355 TGATTCCAGCCTGTGATTCATGCCCTTTTTTGGTT[C/T]TACTTTCCCTTTAAACAGATGTAAAACAACTTTCT Y 2 1 2 1 102000 f 74 goat snp15406-scaffold1634-149408 13 38017438 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414404 Affx-122949981 AX-123284753 13 37231858 TAGGGATCTTAGCAGGTCAATAGATTCATCCGTCA[C/T]GTTCTCACTCACCCCACTATCCTTCTCCCTGTGTC Y 2 1 2 1 101000 f 74 goat snp15407-scaffold1634-205911 13 38072045 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386163 Affx-122971388 AX-123256521 13 37277285 TAAGGGACGTCTCCATGGCAACATGCTCAGTTCTA[C/T]GTTTACCTGAGTGTCCTGCAAGTTGGAGAGATGAC Y 2 1 2 1 101000 r 74 goat snp15408-scaffold1634-251338 13 38117881 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384967 Affx-122971905 AX-123255325 13 37308190 AGCAATTAACCTAACCTGTCCACTTGGCCACAGCC[A/G]CTGTTTAGGAATAAATAAGTGACTATCCATGGGGC R 2 1 2 1 201000 r 74 goat snp15409-scaffold1634-282243 13 38149246 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383545 Affx-122972616 AX-123253903 13 37341616 TGCAAGGCAATTATCCTGTCCTCTGAAACCCCAGC[A/G]CTTTGATCTTCTTCCGTATTCTCCCAGTGAACTGG R 2 1 2 1 101000 r 74 goat snp15410-scaffold1634-315669 13 38182963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412905 Affx-122950410 AX-123283254 13 37396120 ATGCGTGAGCGTGTTATGTAAACTTTAAAAATTAT[A/G]TGTCATATAGCCTTAAAGATTATATGTCAAACAAC R 2 1 2 1 201000 r 74 goat snp15411-scaffold1634-370173 13 38237313 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418371 Affx-122946573 AX-123288719 13 37444989 GATGCTGGAACTTGGAAAATAAAGGAGTTAGGTTG[G/T]TCAAGAGAGGACAAAAACACAAATGTACAGAAAAA K 2 1 2 1 101000 f 74 goat snp15412-scaffold1634-419042 13 38286362 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427362 Affx-122940101 AX-123297705 13 37486210 GACTCCGTGTGTTTGAGTGTGGCTTAAGGGGAAAG[A/G]TAAGCTGGGGCTGCTTGATAAGCCCAGGCCTTGCC R 2 1 2 1 101000 f 74 goat snp15413-scaffold1634-460263 13 38327707 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429868 Affx-122938142 AX-123300209 13 37514796 CACTTTCAACCTATGGGATGCCAGGTGAGTTTCCT[A/G]AATTCTTTGAATCTCTTTTCTGCCATCTGTAAAAT R 2 1 2 1 201000 r 74 goat snp15414-scaffold1634-488849 13 38356257 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790478 Affx-122951246 AX-385277481 13 37620358 GGTGTAATAAATTAGATCCATAGTATAAAATATTG[C/T]GCCACTAAATCATGGCTATGAAGAGTTTTAATAAC Y 2 1 2 1 101000 r 74 goat snp15416-scaffold1634-594411 13 38462294 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453436 Affx-122919871 AX-123323769 13 37679147 ACCTTTGACCTTTTAATCTTGAGGCCAAGGTGCCC[A/G]CACTTTAGTTGCCTGCATCACCTAGTCACTTGTTT R 2 1 2 1 101000 r 74 goat snp15417-scaffold1634-653200 13 38521144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797560 Affx-122972123 AX-385284499 13 37709026 TATGTTATTAGTGCTTTGATGGGTCTCATTTTACA[G/T]ACAAAGGTAGGAGCCTGAGGATCTACTTTTTCTCT K 2 1 2 1 101000 r 74 goat snp15418-scaffold1634-683079 13 38551139 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425457 Affx-122941511 AX-123295803 13 37750732 ACACCCTCCCCCTCACTCCCTGAAACCTAGGTCCC[A/G]TGTCCTTCCTTAAAGTTCACAGAAAATCCAGTGAA R 2 1 2 1 101000 r 74 goat snp15419-scaffold1634-724785 13 38592849 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433605 Affx-122934952 AX-123303946 13 37797942 ACAAGTGCGAGTAGAATTCAGAGGAGGATGTGTCT[A/G]TTTCTTCAGTTTCTCCCTGTCCAGTGGGGGCATCA R 2 1 2 1 101000 f 74 goat snp15420-scaffold1634-771995 13 38639598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788248 Affx-122963415 AX-385275267 13 37851838 ATTTTATTTCCTCAATTGTAGGGATGAGCATTCCT[C/T]ATACATCAGTAGCTCCTGAGAGCGTTGCTGTATTT Y 2 1 2 1 101000 r 74 goat snp15421-scaffold1634-825891 13 38693578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763063 Affx-986697592 AX-385251030 13 37873340 TGCTTATTGACAGAAGTCACTGGCCAAGTTCAGTT[C/T]CCAACGGTGGGGCCTTCAGCTCCAGGAGGCCACCA Y 2 1 2 1 600010 f 74 goat 13_37873340 13 37873340 Ancestral_priority_1043 ancestry 0.644 recommended IMAGE 10K 10K ancestral 38401986 Affx-122958773 AX-123272339 13 37882097 CAAAGGAGCAGGAGGAGGACTGGATCCAGAGGACA[C/T]GCTGTTGGCATGGAAGCCAAGAGAAAACGGGGTTT Y 2 1 2 1 101000 r 74 goat snp15422-scaffold1634-856150 13 38723939 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796095 Affx-122968520 AX-385283047 13 37929719 CATGCCTGTGGACTTTATGGCTGATTTCCATCTTC[A/G]TGAATGCACAAGGACCAGGCAGAAAGTACCACTGC R 2 1 2 1 101000 f 74 goat snp15423-scaffold1634-903772 13 38772036 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403588 Affx-122957569 AX-123273941 13 37966742 GTGATTCTAAACTCTTCAGGGTGGCTAGTAAAGAA[G/T]AAATAGGAAGAGAGACTGCTTTTTGTATTTTTAAG K 2 1 2 1 101000 f 74 goat snp15424-scaffold1634-940795 13 38809418 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388342 Affx-122969352 AX-123258700 13 38044535 AAAGTGTAAGGATGGCTTTTCCATGAAGGGGATCA[C/T]AAAGGCACCAAATTCCAAGGCAGAAGGGATGGGTT Y 2 1 2 1 201000 f 74 goat snp15426-scaffold1634-1018588 13 38887580 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274132 Affx-1111834059 AX-519547735 13 38050027 GACTGCAGCAGGTGCCCCGCCTCTGAGGGTTCCGC[A/G]GGCTGGCTCGGGGCTTCGGGCTGAGGTGGGTGCCC R 2 1 2 1 303000 f 74 goat GoatD01.016227 13 38050027 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38380725 Affx-122975144 AX-123251083 13 38083232 AAGGTCAAGTTCATGACCATGCAGAAGATGTATTC[A/G]CCAGAAAAGAAGGTCATGCTGCTGTTGAGAGTTTG R 2 1 2 1 101000 f 74 goat snp15427-scaffold1634-1057285 13 38926527 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395212 Affx-122964492 AX-123265567 13 38138915 GTTAACAAAGTTAGAGCCAGAGATTGCCAAAGACC[A/G]TTTTTTTCTGAAGTCATTTTGACTGTGACCAATAA R 2 1 2 1 303000 r 74 goat snp32551-scaffold371-2535321 13 38981915 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435101 Affx-122933708 AX-123305441 13 38194623 ACACCATCAGTTATTTCACCACAACTTACCTCTAC[A/G]CTAACAATGAACTTCTGAAGGTAGACATTCTGAAT R 2 1 2 1 101000 r 74 goat snp32550-scaffold371-2479613 13 39038236 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427274 Affx-122939539 AX-123297617 13 38231344 TGACCCACTGCCATGGCCACAAGGGAGACATCCCC[A/G]TTGGAGACACGCACATGGGTTTTGAGGGACATTCC R 2 1 2 1 201000 r 74 goat snp32549-scaffold371-2442892 13 39074930 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448151 Affx-122924276 AX-123318487 13 38262032 AATAAACTCAGAAGGCTTTATGAAAATCACTAAAA[C/T]GTGGAAGACTTTTAATCCACCTGAGCTCAATTTGA Y 2 1 2 1 201000 f 74 goat snp32548-scaffold371-2412204 13 39105875 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798217 Affx-122970114 AX-385285152 13 38317962 CGGTGGTTACTGACAGGGCAGTATGGCCAAGAGAA[A/G]GCTTAATAGGTCTACAGAGTAGAAGGAAACTAAAA R 2 1 2 1 101000 f 74 goat snp32547-scaffold371-2356274 13 39162362 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398062 Affx-122961745 AX-123268417 13 38375642 ACCTAGTGTCACACAGCTAACAAGTGGCTGAACTG[C/T]GTCTTAATCATTATTCTGCTTGATCTGACAGTTTC Y 2 1 2 1 201000 r 74 goat snp32546-scaffold371-2298594 13 39220110 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385343 Affx-122971653 AX-123255701 13 38407142 CACAGCAGTGTGGGTGGCACTTGGCTGCAGATGGC[C/T]GGACGCACCCTGGCCAGCTGAAGGAAATAAATTAT Y 2 1 2 1 101000 r 74 goat snp32545-scaffold371-2267094 13 39251953 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434256 Affx-122934818 AX-123304597 13 38440923 AATCTGTTTTTCCCCCATCTCTATTTACTCTGTTC[A/G]TTTCCTGTGAATTATGCTTAAACTTGGTTACATGG R 2 1 2 1 101000 r 74 goat snp32544-scaffold371-2233313 13 39285815 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447151 Affx-122924443 AX-123317487 13 38484022 CCACTGACCAACCGGGGCCTTAGTGTCTGGTCCCA[C/T]GTGGGCCGAGGCTTTGCTCAAGTCCGCTTCCGTCC Y 2 1 2 1 101000 r 74 goat snp32543-scaffold371-2190214 13 39328762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382342 Affx-122973882 AX-123252700 13 38581011 CAGAGTCGGACGCGACTGAGCGACTGAGCCTGCAC[A/G]CACACCCACTGGCATTAATCCACACAGTTTCTCCA R 2 1 2 1 101000 r 74 goat snp32541-scaffold371-2093225 13 39425849 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417816 Affx-122946807 AX-123288164 13 38635298 GTCTTGTCTGATGAATCTTTGCCTAACCCAAGATC[A/G]CAAAAGATCTGTGTTTTCTCCTAGAGAGTGTGCAG R 2 1 2 1 101000 r 74 goat snp32540-scaffold371-2038938 13 39480116 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776819 Affx-122975270 AX-385263943 13 38680856 AGTCTTTATTTGTAGGGACTAGATTTTTGTGCACA[C/T]GTCTGAGGCATTCTGATTCATACTGTTTAGTGTAA Y 2 1 2 1 101000 r 74 goat snp32539-scaffold371-1993380 13 39525416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450537 Affx-122922484 AX-123320871 13 38710970 CTTCACAAGCCACCTCCTGCTTGTATGTGAAATCT[A/G]TAGCATGTGAAATCTTCCCACACCAGGGATCGAAC R 2 1 2 1 201000 f 74 goat snp32538-scaffold371-1963266 13 39555298 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765770 Affx-986697594 AX-385253226 13 38727368 CGAACTAAAATGTGGTGACCTGGAAGAAGAACTCA[A/G]GAATGTCACTAACAACCTGAAGTCACTAGAGGCTG R 2 1 2 1 600010 r 74 goat 13_38727368 13 38727368 Ancestral_priority_1043 ancestry 0.698 recommended IMAGE 10K 10K ancestral 38376156 Affx-122978848 AX-123246515 13 38744705 AAATAGGGATTTTTTTAAACCCTTAAGGTTTGGGG[C/T]ACTTTGTTATGCAGCAATGGTAACTGCTACATGAC Y 2 1 2 1 202000 r 74 goat snp32537-scaffold371-1929531 13 39589017 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783927 Affx-122949985 AX-311553811 13 38778663 GCTGAGAATTACCCTGGCTCCATGAAGATGCCTTC[A/G]TCGTTTTGAAGGAAAGCCACCCAAATTACAGTGTG R 2 1 2 1 101000 f 74 goat snp32536-scaffold371-1895573 13 39623428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789625 Affx-122944643 AX-385276634 13 38856460 ATTTCTAAGTCCAGTAGTTCCAACCTCTTCTCTTG[C/T]ATCCCTCAGCCCTACAATGGTAGTGATTTCCTGCA Y 2 1 2 1 101000 f 74 goat snp32534-scaffold371-1817776 13 39701836 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780210 Affx-122953030 AX-385267306 13 38907629 GTGTGTCTGAATTTTAGATGCTGTCATCCATATCT[A/G]TGTTTTAAATGCTTAGCCTAATTGTCACTTCCTTA R 2 1 2 1 101000 f 74 goat snp32533-scaffold371-1766607 13 39752739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410772 Affx-122952680 AX-123281122 13 38936879 GTCGGCCTCTCTCAGACAACTGTCTGGAGGGAGGA[C/T]GGGCAGTGTGCCCACCTCATTTGGCGTTAGGAGAC Y 2 1 2 1 202000 r 74 goat snp32532-scaffold371-1737357 13 39782117 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431758 Affx-122936726 AX-123302099 13 39015930 CTAAATGGATAACTGAACTATTTTGCACCATAAGA[C/T]GAGTCTGCTTTTATTCGACCAGGGATTTCTCCTAA Y 2 1 2 1 101000 r 74 goat snp32531-scaffold371-1658306 13 39858762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393649 Affx-122965290 AX-123264004 13 39058753 GCAAACAGAGGAGACTGTCCTGGATGGTCAGTGAC[C/T]CAGACAACTTAACTTCTCACTAGTCCCTGGTGATG Y 2 1 2 1 101000 r 74 goat snp32530-scaffold371-1615483 13 39901859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780996 Affx-122973372 AX-385268083 13 39097987 CCTATGTGAGACTTGGAGACTGGTTTGTTCTGGTG[A/G]CAGGAATGGGAATTATTGCATTTGTTGTTCAGTTG R 2 1 2 1 101000 f 74 goat snp32529-scaffold371-1576249 13 39941181 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440159 Affx-122931138 AX-123310496 13 39144911 TCATTCCCAGTTTTCAAGCTCAAAAATCAACAGAA[C/T]TGAACATTTTAAATAAACTGGGATAATTCTATTAA Y 2 1 2 1 101000 f 74 goat snp32528-scaffold371-1529325 13 39989161 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792402 Affx-122977521 AX-385279383 13 39230563 AAGAAGCTTTAATGCAGCACAATTTCAATGATTGT[C/T]AGAAAATTGGTAGTTCTCAGCAGCACCTAAGATTC Y 2 1 2 1 101000 r 74 goat snp32526-scaffold371-1443673 13 40074658 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795082 Affx-122941294 AX-385282041 13 39304045 TTTATTTTACTTATACATAGTGACTCATATTTGTG[C/T]AGTTAAAATTGAGACATACATGCAACAAATTGTTA Y 2 1 2 1 101000 f 74 goat snp32525-scaffold371-1370191 13 40148974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452970 Affx-122920157 AX-123323303 13 39336036 GCCCTGGGCTGCACATGCTGGACCCATTTCACTGC[A/G]TCTGGGTCCTTGTATGGGCTCCACTTGAAAGAAAG R 2 1 2 1 101000 r 74 goat snp32524-scaffold371-1338200 13 40180944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411867 Affx-122951211 AX-123282217 13 39383052 GAAACAGGGCTGCGTGGTGCCATCTGAAAGACTCC[C/T]GGGTTCACCACCAAGATTGTTGCTCCGTAGCTTTG Y 2 1 2 1 202000 r 74 goat snp32523-scaffold371-1291184 13 40227632 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272690 Affx-1111832983 AX-314465065 13 39442961 AGGCTATGGTTTTTCCAGTAGTCATGTACGGATGT[A/G]AGAGTTGGACTGTGAAGAAAGTTGAGTGCCAAAGA R 2 1 2 1 103000 f 74 goat 13_39442961_AF-PAKI 13 39442961 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38410954 Affx-122952032 AX-123281304 13 39457162 GACTGATGCTTGCGATGCACTTTGTCACTGCATGT[C/T]ACCCACGGCCGCAGTTCTGAGACCCGCTGGGTTCC Y 2 1 2 1 101000 f 74 goat snp32522-scaffold371-1217074 13 40301787 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407691 Affx-122954581 AX-123278042 13 39497530 TGGCCAGGAGCTTCCTGTTCCCTACTCTGCAAAAC[A/C]AAAGTGAATAGTGATGTGTGGAAAATTAGACCTAG M 2 1 2 1 201000 r 74 goat snp32521-scaffold371-1176706 13 40342302 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771607 Affx-122943001 AX-385258765 13 39586263 ACCTAACATGAAGCTCATGAAGCACCACCAACTAC[A/G]TTCAGCTGTTCCCCAGTGATGAAAAGTTTCAGACA R 2 1 2 1 101000 r 74 goat snp32519-scaffold371-1087973 13 40426539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415237 Affx-122948956 AX-123285586 13 39627248 GGGGAATTGGGTTGCTAGCCGAGAGCCATCTTCTG[A/C]GAGCAGAGCCAAGGCTCCCAGCAACGCTTATCTCC M 2 1 2 1 101000 f 74 goat snp32518-scaffold371-1046988 13 40467419 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425569 Affx-122941430 AX-123295915 13 39656527 TTTGTGGGCCTATGGTCTCTGTCACAAATTATCCA[A/G]CTATGCCATAGGAGCAAGAAAGCAACCAGAGCCAA R 2 1 2 1 101000 r 74 goat snp32517-scaffold371-1017709 13 40496988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431180 Affx-122937182 AX-123301521 13 39714572 TGCACAGCTAGGTTAAAAAAACTCTCATTTATTCC[A/G]TATAGATATCCTTCCTCAAACCTTTTCCTCTCCTT R 2 1 2 1 101000 r 74 goat snp32516-scaffold371-959664 13 40555753 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449242 Affx-122923479 AX-123319577 13 39748468 GTTTGACAGCCACACAGCAGGATAGAAAAAGGCAC[A/G]TAAGGCATGAATTAACGTGGTATGAAAAGCAAAGT R 2 1 2 1 101000 r 74 goat snp32515-scaffold371-925768 13 40590432 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426134 Affx-122940618 AX-123296480 13 39778650 CAGCCAGGCCCTCCTTTTCCAAGGGCAGGAAAAGA[C/T]GCTGTGGGGTTAAGGGAACTCATTGAAGTTGGAGA Y 2 1 2 1 202000 r 74 goat snp32514-scaffold371-895586 13 40620628 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409786 Affx-122952976 AX-123280137 13 39823888 GTTAAGTACAATGTTAGGGACATGGCTGGGCCCTA[C/T]GTTCTTTTTCTTTCTCTTTGAAGGTATTGACCTGA Y 2 1 2 1 201000 f 74 goat snp32513-scaffold371-850348 13 40665745 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436639 Affx-122932490 AX-123306977 13 39873069 GTACAAGAAGGAGGTTGGGAACGGGATAATGTGAC[A/G]TCTATTCCCAGAAGAACCGCTTATCGGGTTTAAAT R 2 1 2 1 101000 r 74 goat snp32512-scaffold371-801167 13 40714509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276721 Affx-1111835557 AX-519550231 13 39888019 ATTTTATAGGCTCTGTAATCACAGTGACATCCTAC[A/G]AGAAGGCCCTGATGCCTGCGGAGCCGGTGTCCTTC R 2 1 2 1 101000 f 74 goat Random2.2K-1341 13 39888019 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432173 Affx-122936407 AX-123302514 13 39902635 GTACCCATTCTTCAAACCTCAAGATCAGATGTCCC[A/G]TCCCCCATGAGTCTTGTAGGTAACTCTGGCCTCTC R 2 1 2 1 101000 f 74 goat snp32511-scaffold371-771601 13 40744114 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432623 Affx-122935488 AX-123302964 13 39941674 ATTTGGATAAATGGTCTAGATATTTGATGTTATCA[C/T]GGAAATATTTTTATTTTAATAATTTAAATAATTCT Y 2 1 2 1 101000 f 74 goat snp32510-scaffold371-732562 13 40783248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430990 Affx-122936690 AX-123301331 13 39973634 AGCCATTCAGTTTTCGGAGTTCCAGACAACAGAGT[A/G]CAGGTAGAGGATGCCAGCTCAGAATCTGACAGCTC R 2 1 2 1 201000 f 74 goat snp32509-scaffold371-700602 13 40815210 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398713 Affx-122961846 AX-123269068 13 40015647 TAATTTAGACAACAATTAGACCCCAAAAGCAATTG[C/T]GTACACGAGCTAGTTTGTCTCCATTGGAGAATTCA Y 2 1 2 1 101000 r 74 goat snp32508-scaffold371-658589 13 40856995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433712 Affx-122934528 AX-123304053 13 40045726 CAGTTTCCTAGGTTCCAGAGGAGTTGAGCAGCAGC[C/T]GGGGGCTGGGGGCTCATCCTCCTCTGTTAACTGAC Y 2 1 2 1 103000 f 74 goat snp32507-scaffold371-628510 13 40887084 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407660 Affx-122954604 AX-123278011 13 40092665 AGTTATAGCCTGTTTGGGGGAAGCCAATGGCCAAC[A/G]TGGAGACTGAAAACAACTCCTAGATGCTGTGGGTC R 2 1 2 1 201000 r 74 goat snp32506-scaffold371-581571 13 40933789 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450274 Affx-122922175 AX-123320609 13 40131336 AGGTGAATGGCCCTGCTCCCAGGCCAGGGTGTGGT[A/C]TGTGCATCTGGTGGGTTTTCACCCCTGGTGTGGAA M 2 1 2 1 101000 r 74 goat snp32505-scaffold371-542900 13 40972381 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403918 Affx-122957476 AX-123274270 13 40183391 GGAATGAGCCATTCCTCTTGGAGCAGCTTACAACC[A/G]TGCTTGCCCTCCAGGGCTCTAACCACTTATCACTT R 2 1 2 1 101000 f 74 goat snp32504-scaffold371-490845 13 41024263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408414 Affx-122954471 AX-123278765 13 40223345 TTTTTTATTTAGGCATATTATAAACATTTGAGCCA[C/T]AGCATTTAGTAAGTCATTCAGCTGTGTCTCTGTGA Y 2 1 2 1 201000 f 74 goat snp32503-scaffold371-450891 13 41064395 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389901 Affx-122968120 AX-123260258 13 40254362 ATAGACGTCAGAGAAGGCATGTTTATACAAGCTAC[A/G]TGACCGGCACCTCGGATCTCACAAATGATGTTTCT R 2 1 2 1 101000 f 74 goat snp32502-scaffold371-419874 NW_017214525.1 12751 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765036 Affx-122972806 AX-385252606 13 40295750 GCAAGATCAGTAAATTCTCTGCAGAACATTTTCTC[A/G]TGAGAGTTTAGATCGCACTCCAAGTTTCTTTTCTT R 2 1 2 1 101000 f 74 goat snp32501-scaffold371-378486 13 41134095 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432891 Affx-122935335 AX-123303232 13 40330735 TGTCCCTGGGCCACCAGTGACCTTGGGCCTCCTTA[C/T]GTCAGCCAGCCTCTCAGCTGCAGTTTCTATTCCTG Y 2 1 2 1 101000 r 74 goat snp32500-scaffold371-343501 13 41168779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416027 Affx-122948370 AX-123286376 13 40367682 TCCCCACAAAACGAGGGTCTTGTGTTGTCATGTTC[A/G]AATCCAAAGACAAGATTTTCCAAGGATTGACCAGA R 2 1 2 1 101000 f 74 goat snp32499-scaffold371-306554 13 41205200 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785393 Affx-122929635 AX-385272438 13 40412765 CCCAACACTCATAACTAGAAACTCTGAGTTAAATC[A/G]AAATAAATTTGTTTTACCGAATTCTGTGGAACCAG R 2 1 2 1 101000 f 74 goat snp32498-scaffold371-261471 13 41250382 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450248 Affx-122922256 AX-123320583 13 40441403 CTGGCTGGATATGACCTCTACGTCCACCTCCATCC[A/G]TAGGTCCAGGGTGGGCTACATCACAGTGGACCTGT R 2 1 2 1 201000 r 74 goat snp32497-scaffold371-232833 13 41279511 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408876 Affx-122953987 AX-123279227 13 40495001 CCCCTAAGGTCATTCACTGGCCAGATGACTTAGGC[A/G]TGGCCACGAAAAGCCAGACATGGCATTCTATGCAC R 2 1 2 1 202000 r 74 goat snp32496-scaffold371-179235 13 41333145 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423614 Affx-122942378 AX-123293960 13 40527510 AGGCAAACACTCTTTTGGGGAAGATCCCCAGTGTT[A/C]TCTTTATTTCCTGCAAGTAATACATTCCTCCTTCT M 2 1 2 1 101000 r 74 goat snp32495-scaffold371-146726 13 41365083 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797200 Affx-122945472 AX-385284139 13 40556252 TTAGACGTGCTCTTGTTTCCTGAATCTCTTCTAAG[C/T]GATTTGTTTGATGTGCATTTATTGCTAGGTAATGG Y 2 1 2 1 101000 f 74 goat snp32494-scaffold371-117984 13 41393805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408192 Affx-122954193 AX-123278543 13 40607283 GGAATGCTGCATTAAAGGGGTGCCCTTTCACGGAT[A/G]TCACATTAGCAGTGAGAAATAAGCACCCCCACCCA R 2 1 2 1 101000 r 74 goat snp32493-scaffold371-66953 13 41445104 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378724 Affx-122977044 AX-123249083 13 40664554 ATATTCCAGGCTTTGCAGCACAGATACAGCCCAGA[C/T]GGCATTCAAAAAGTGTGCCTGGCAGTGTCCTAATA Y 2 1 2 1 101000 r 74 goat snp32492-scaffold371-9682 13 41501812 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441383 Affx-122928854 AX-123311720 13 40682100 CCCCTACTCTGTCCCTGTGCTTGTTCCCACAGACC[A/G]TCACCTGCTTCTTCACTGTCGACGCTGAACCCTGG R 2 1 2 1 101000 r 74 goat snp5752-scaffold1202-7765 13 41519616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391538 Affx-122966645 AX-123261895 13 40782341 GGCCAGTCTGAATTAGAACATTACCAGTCACTACC[A/G]TGCCAACCCTGCATCCTCAGCTGGTCCCGGCCTCA R 2 1 2 1 101000 f 74 goat snp5755-scaffold1202-108006 13 41619867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276723 Affx-1111835558 AX-519550233 13 40806329 ACTGTTCTCAAACTTTGCTCTTGGAGCTGCTTTAC[A/G]TTTTTAAAAATTCCTGAACACCCCAAAGAGCTTTA R 2 1 2 1 101000 f 74 goat Random2.2K-1343 13 40806329 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38405998 Affx-122955512 AX-123276350 13 40812232 ACCCTCTTCCTACTGAAGCACAAAGCTTTGCTTCT[A/G]TAAGTAGCTTTTGTTCCATGCCTTGCCGGTTAGAT R 2 1 2 1 101000 r 74 goat snp5756-scaffold1202-137897 13 41649964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417211 Affx-122947303 AX-123287559 13 40843017 GTGTTCATACCCCAACCTTCTTCATCAGACAGTAC[A/G]CTTTCTGAGCAGGTGTCTTCTTAGGCACGAAATCA R 2 1 2 1 102000 f 74 goat snp5757-scaffold1202-168682 13 41680762 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400991 Affx-122960090 AX-123271344 13 40900950 AGTGCACTCATCCCAGGACTCAGAAAAGGGGTCTC[G/T]TCCCTTTCTCCGCAATTCCCAGGCCACATCTGCAA K 2 1 2 1 201000 f 74 goat snp5758-scaffold1202-226615 13 41738246 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450268 Affx-122922179 AX-123320603 13 41004614 TCTGATCTGCTCCACTGGCTGCTCCTTGGTCCCCC[A/G]ATGCAGCGTCTCCAGGTGGACCATATCCCACGTGC R 2 1 2 1 101000 r 74 goat snp5760-scaffold1202-330279 13 41841839 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276864 Affx-1111835559 AX-519550373 13 41016987 AGCCTGGGCTCTGTGGAGCAGAAGTTCCCAAGTGA[A/G]GGCCCACCTTCCTGCTGCATCGAAGGTGATTGTTT R 2 1 2 1 202000 r 74 goat Random2.2K-1344 13 41016987 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407809 Affx-122954555 AX-123278160 13 41033539 TGACTGACAGTTGCAAGGACCCCTGGTTGGGTACC[A/G]CGTGGGATGCTGTTGGATGCTCTCCTCCTGCTTAG R 2 1 2 1 201000 f 74 goat snp5761-scaffold1202-359204 13 41870680 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434899 Affx-122934332 AX-123305239 13 41071978 GACCATTCAGGCCAAACCACCAGGTATTCCCACTA[C/T]GGTGTTTGCATCTCGTGTCAACAGTGGCTTCTGGG Y 2 1 2 1 101000 f 74 goat snp23209-scaffold2318-21647 13 41908344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446199 Affx-122925722 AX-123316535 13 41108121 GCGCAGCCCTCGGCTCCCGGCTCCCAACCAAGAAA[C/T]GTTCAGGGTCAGTGCGCTTGAGCTGTGTTTTCATG Y 2 1 2 1 101000 r 74 goat snp19442-scaffold1962-14397 13 41943486 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398039 Affx-122961763 AX-123268394 13 41160584 CATACCTGACTCCATCATTCCTCACCACAAAGGCT[C/T]TCATCTGTTGACTGGTAGAAGCTTCCCCAGCCTCC Y 2 1 2 1 201000 r 74 goat snp19443-scaffold1962-66860 13 41995334 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441085 Affx-122928901 AX-123311422 13 41215567 GGGGAAAGTGTTGGGGGTACAAGATCCAGCCACGA[C/T]GTTCTGGCTCTCGGCCCGGCAGAGCAGGAGTTCCT Y 2 1 2 1 101000 f 74 goat snp19444-scaffold1962-121843 13 42045581 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398427 Affx-122961621 AX-123268782 13 41227216 GTATTTGAAACTTTTTACTGCCTCTGGGTGGAGAG[C/T]ATCTCACGGGAAGGGAGGGAGACTGAGCTTGGGGG Y 2 1 2 1 101000 f 74 goat snp15100-scaffold1613-5678 13 42057503 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426549 Affx-122940182 AX-123296895 13 41256063 GCTGAGCAGCTGCTGGTTTCTGGCCTTGTGTGGTC[A/G]GGAAATCAGGATGAGTGAGCTGGTCCCTGCTTGCA R 2 1 2 1 102000 r 74 goat snp15101-scaffold1613-34525 13 42085766 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398626 Affx-122961469 AX-123268981 13 41286027 AAAGCTGCCTGTTTGACGGAGCCTGTTTTTGGTAC[G/T]TAAGCTCTTTCTAGCTTTTACTGCTGACCTAGGGA K 2 1 2 1 101000 f 74 goat snp15102-scaffold1613-64489 13 42112571 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418969 Affx-122946076 AX-123289317 13 41349339 TTCATAAACCAGATACTTCTACCCTTTTTCCTCCC[A/G]CTTGTCCAAAAGGAAACATATAACATGAAAAACAA R 2 1 2 1 101000 f 74 goat snp15103-scaffold1613-127801 13 42175731 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276866 Affx-1111835560 AX-519550375 13 41351136 CTGAAAGCTCAACCCTCTGGTGAGAGGCTGGGACC[A/C]AATCATGTGGTTGGGTCCCCATCCTTAGGCGTTTC M 2 1 2 1 102000 r 74 goat Random2.2K-1345 13 41351136 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438703 Affx-122930858 AX-123309040 13 41412966 CACATCTGATGGTTTCTCCCACTTGCAGACTGATC[A/G]TCTCCACTTGCGGTGGAGCATACATGGTCCCACAC R 2 1 2 1 101000 f 74 goat snp15104-scaffold1613-191428 13 42239879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798586 Affx-122939085 AX-385285519 13 41466558 CAGAGGGGAAAGAAACCCATCATAAAGCAGGTAAA[C/T]GTAGGAGCTTCTTCTGTATCCCAGATGTGGCTTCT Y 2 1 2 1 202000 r 74 goat snp15105-scaffold1613-245020 13 42293478 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774497 Affx-122928548 AX-385261632 13 41509304 AGAATCTGTACACTATATGCATTCAGGGCACAAAG[C/T]AAGTTTCTGTATAGCAATTGTGTTTCAGTTAATAT Y 2 1 2 1 101000 f 74 goat snp15106-scaffold1613-287766 13 42336791 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763069 Affx-986697598 AX-385251035 13 41511291 CAGACGACCCCTCAGTGTCCTTTGGAATGCCGTCA[C/T]CATCACTGCCCACACCGCCTGCCCTGATGCAGTGT Y 2 1 2 1 600010 f 74 goat 13_41511291 13 41511291 Ancestral_priority_1043 ancestry 0.504 neutral IMAGE 10K 10K ancestral 38376432 Affx-122978069 AX-123246791 13 41564166 AATGCTTATGCACTGTGACTGTTAAGGTGAATTAG[A/C]GTTACATCAGTTCAGTTCAGTTGCTCAGTCATTTT M 2 1 2 1 201000 f 74 goat snp15107-scaffold1613-342628 13 42391924 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406093 Affx-122956226 AX-123276445 13 41632185 ACCTCTGAGGTTGGGGTCCTGGGTCCACGTTTTCA[C/T]GTTCCCAGCTGTTCCCTTTGCTGCCTCAGCCTCGG Y 2 1 2 1 201000 f 74 goat snp15108-scaffold1613-410647 13 42460193 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439231 Affx-122931017 AX-123309568 13 41695657 TGAGTCTGAGGGACTCTTGACTCTAACAATGCTCT[A/C]TTAAAATCCAATGGCTGAAAAAGGTCCCTTGTGAC M 2 1 2 1 101000 r 74 goat snp15109-scaffold1613-474119 13 42523401 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391804 Affx-122967032 AX-123262161 13 41744907 ACAGGCCTCTGTATTAGTTTGTACTAATAGTGATC[A/G]CTGACATGACACATTTGTATGAATAATGATTACTG R 2 1 2 1 101000 f 74 goat snp15110-scaffold1613-523369 13 42573015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412745 Affx-122950524 AX-123283094 13 41823871 TAACATTTTAAAAAATGCTTATTAAACACCTTTGG[A/C]TTGTGTAATTTGTGTATTTGTGTATGTTTGTACTG M 2 1 2 1 201000 f 74 goat snp15112-scaffold1613-602333 13 42653057 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409617 Affx-122953545 AX-123279968 13 41852935 ATGCAGGTGATGATGAGTGGGGCTGTGGGCAGAGG[A/G]CTCCTCAGGAATATCCTTCACAAGGGCTCTCAGAC R 2 1 2 1 101000 r 74 goat snp15113-scaffold1613-631397 13 42681951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400828 Affx-122959797 AX-123271183 13 41884010 ATGAAACTGTGTACATGAAGGAAGACCATGAAAAC[A/G]TGGAGAGGGAAGTAAATACAGAAAAAAACCAGGTG R 2 1 2 1 202000 r 74 goat snp58737-scaffold959-2661 13 43111098 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420483 Affx-122944868 AX-123290830 13 41965700 CAGTATAAATTGTATCCATGACTATAACTTTATGC[C/T]AAGTCTTACAATTTTTTCCAGAAAATCACTGAATC Y 2 1 2 1 101000 f 74 goat snp58739-scaffold959-84351 13 43194781 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782546 Affx-122939854 AX-385269621 13 42000428 GGAATTTTGCTACTCATCTTGTCTTTACAGTATGT[A/G]TTGAATAGTTGTATGACAAGGTTCTGGTCCTTAAA R 2 1 2 1 101000 f 74 goat snp58740-scaffold959-119079 13 43229994 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787093 Affx-122975665 AX-385274120 13 42035726 GAAAAAGCTGTCATGAGAGCAATTGATGTTGGCTA[C/T]CACCATATTGACTCAGCATATATTTACCAAAATGA Y 2 1 2 1 101000 f 74 goat snp58741-scaffold959-154377 13 43265876 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439873 Affx-122930048 AX-123310210 13 42068693 ACATAATCACCAAGTCACTATTACATACTCCCTTG[A/C]GATTACTGATATAAAATTGAATTTGGGCATCTCTT M 2 1 2 1 101000 f 74 goat snp58742-scaffold959-187344 13 43298935 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439932 Affx-122930004 AX-123310269 13 42102954 TTTACAGTTGGTCATGCTCAAGTCTGTTGTTTCCA[A/G]CTCTCCCCTGGCTTAAGACCCTCTGTGGGCAAAGG R 2 1 2 1 101000 f 74 goat snp58743-scaffold959-221605 13 43333325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395917 Affx-122963599 AX-123266272 13 42134067 CTGCGTATCCAAGGCTCTGGACCCTGAGTGAAATC[G/T]TGTCATCCATGTCATATTTTAGGTCATAGTTAAAG K 2 1 2 1 201000 r 74 goat snp58744-scaffold959-252718 13 43364472 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777912 Affx-122955091 AX-385265028 13 42162828 GCATGTTTGAACAACAACTCAATGAATGTATTAAA[C/T]GGTGCATGATGCAATTCTAATACCTTACTCAAACG Y 2 1 2 1 102000 r 74 goat snp58745-scaffold959-281479 13 43393535 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395302 Affx-122964065 AX-123265657 13 42196446 GTGGGCTATAGTCCATGGGGTCACAGAGTAGGGTT[A/G]CAACGGAACAGAGCAGACACATGCACCTCAAAACA R 2 1 2 1 101000 r 74 goat snp58746-scaffold959-315097 13 43427147 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272744 Affx-1111832984 AX-519546444 13 42232654 CGCCAGCAGCTCGAGGAGGTGCAGGTGGAGAGTGT[A/G]TGACTCAGAGGTCACAGTTGTGTTTCTGTTGTTAT R 2 1 2 1 102000 r 74 goat 13_42232654_AF-PAKI 13 42232654 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433690 Affx-122934544 AX-123304031 13 42253643 ATATCCATTCATGGGGAGGTTTAGGGAATGCCCTT[C/T]TCTCAGGTCTTATGCACTTAGCCTGTGATATGAAG Y 2 1 2 1 101000 r 74 goat snp58747-scaffold959-372294 13 43484328 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396646 Affx-122962863 AX-123267001 13 42298826 GTCCCTCATTACACATCCACTCTGAGTTAGCACAT[A/G]TGCCTAGAATGACATGCTTGTTAATAAGAAATAGA R 2 1 2 1 101000 f 74 goat snp58748-scaffold959-417477 13 43529592 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403369 Affx-122957790 AX-123273722 13 42332313 TTGCTTTGGGGGTTACAGATATTTGCACATTTTGT[A/G]TGTCACCAAGGAGCCAAACGGTGAACTGTATCGTT R 2 1 2 1 101000 r 74 goat snp58749-scaffold959-450964 13 43563123 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441279 Affx-122929473 AX-123311616 13 42380723 GCTGCACAGACTTGATGAGGGCAGAGGTTGCACCC[A/G]TCTTCCTTATGACTATATTGGATGCCTGGTCCAGA R 2 1 2 1 101000 r 74 goat snp58750-scaffold959-499374 13 43611526 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275475 Affx-1111834919 AX-519549048 13 42387647 CAGCTTGAGGAAGGAGTGCAGCATCCTTCAGCATA[A/G]TAAGAGCCAGGACAGAACTGCAGACACCTCCCCTT R 2 1 2 1 201000 f 74 goat GoatD01.058827 13 42387647 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38451724 Affx-122921547 AX-123322057 13 42434067 TCCATGAGAGTGGAGATTTCAACGGACTCAGGAAA[C/T]AGGAAGGTGTTGATACCACCACAGGCACACTCATG Y 2 1 2 1 101000 f 74 goat snp58751-scaffold959-552718 13 43665371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415190 Affx-122948995 AX-123285539 13 42498088 CATCTGATAAAATTCCACTTCAGTCTCCAAGCGGC[A/G]TGCAGAGCAGTAAGGGTCTTTCTAGACACAACCAA R 2 1 2 1 201000 r 74 goat snp58752-scaffold959-616739 13 43729967 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786521 Affx-122967481 AX-385273554 13 42545773 AAAAAAAAAACTTTATCGAGTTCATTCTGTGAACA[C/T]GAACTAAGAAGATCAGAAATAATTAATAATATAAA Y 2 1 2 1 201000 r 74 goat snp58753-scaffold959-664424 13 43777687 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418587 Affx-122946368 AX-123288935 13 42580247 TCGATCTGCAGAGGGAGGTGGGAGGAAGCCCAGGC[A/G]TGTCATGGACCTGGAGAGCACCTGCCACAGACAGA R 2 1 2 1 101000 r 74 goat snp58754-scaffold959-698898 13 43812059 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418639 Affx-122946340 AX-123288987 13 42629905 ACTCTGTTTTTTAGTGGACTACTTCACTTGTATCT[A/G]GAGATGAAGATAGAAAACACCACCTCAATCAAGAG R 2 1 2 1 101000 f 74 goat snp58755-scaffold959-748556 13 43862418 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765780 Affx-986697600 AX-385253236 13 42648341 CAAGCTTCCTGATGGGAGGGACTGACTGTGGGGAA[A/T]ACTGAGTCTTACTCTGGTAGACAGTGTCATGCTCA W 4 1 2 1 600010 r 74 goat 13_42648341 13 42648341 Ancestral_priority_1043 ancestry 0.574 neutral IMAGE 10K 10K ancestral 320765779 Affx-986697599 AX-385253234 13 42662104 ACGTTTTCCTTGTCAACTCTGCCACATATCAAGTG[C/T]CCATAAGTACATTTCTGCCCACTCTTGTCTATTTA Y 2 1 2 1 600010 r 74 goat 13_42662104 13 42662104 Ancestral_priority_1043 ancestry 0.64 recommended IMAGE 10K 10K ancestral 38432028 Affx-122935914 AX-123302369 13 42669243 GCTCAGTGGGTTAAGTGACAAGACAGGAAACCTTG[A/G]GAGGAAAGTGAGTTACTTACTGTCAAGGTGTCCAA R 2 1 2 1 101000 r 74 goat snp58756-scaffold959-787894 13 43901880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765782 Affx-986697601 AX-385253237 13 42707748 TTTTTGCGGGAAGATCATGAGTTCAGTTATAGATA[C/T]GCATCTTTCAAATGCCTTTAGGTATCCAAGTGAAG Y 2 1 2 1 600010 r 74 goat 13_42707748 13 42707748 Ancestral_priority_1043 ancestry 0.698 recommended IMAGE 10K 10K ancestral 38416766 Affx-122948179 AX-123287114 13 42741677 ACCTCTATGGATACAATTTTAAATAGAATTGCTTA[C/T]ACATTTTGTACGCATCTTATGGAAAAAGCTTTCCT Y 2 1 2 1 101000 r 74 goat snp58758-scaffold959-860328 13 43974735 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402695 Affx-122959614 AX-123273048 13 42814453 ATCTAGTCTGGAGTGGGCTAAAAGATTCATAGGTC[A/G]GCTATTTCAAACTGCACAGACAGCAGAGAAAGCTT R 2 1 2 1 101000 f 74 goat snp58759-scaffold959-933104 13 44047706 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395634 Affx-122963794 AX-123265989 13 42862565 CAAAGTACCTTAATCTCAACATACCATGTTGTGGG[A/G]GCTGGGTTTTCCTTGCCCTCTCTCTCCTATGTTCA R 2 1 2 1 101000 f 74 goat snp58760-scaffold959-981216 13 44096461 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800549 Affx-122922362 AX-385287468 13 42894869 CTCTCAACTTTCTGACTCCAGTCATAACCTTCTCT[A/G]CACACTTTTATTCAGTTGTCTATTTGGCAGATCCA R 2 1 2 1 101000 f 74 goat snp58761-scaffold959-1013520 13 44128645 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392264 Affx-122967554 AX-123262621 13 42951607 GATATCGCCCTTGAATCGCAGCCCCCAGCAGCCGT[A/G]TAGGAATGTCTTCATGTCTCCATGTCTGTGACCAG R 2 1 2 1 101000 r 74 goat snp58762-scaffold959-1070258 13 44185790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378256 Affx-122976891 AX-123248615 13 42986036 CACACTACTCCTTGGCCACAATGATTAACTGTGGT[A/G]TTTCTGTGGTTGTTTAATATATATTCAGCACTCGC R 2 1 2 1 101000 f 74 goat snp58763-scaffold959-1104687 13 44220589 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417315 Affx-122948158 AX-123287663 13 43016788 AAACCCACCACCAGGAAACCCAATGTGAGGTGATA[G/T]ATCCCTCCTTACTAATTCTAACAGGGAACCGAATG K 2 1 2 1 201000 r 74 goat snp58764-scaffold959-1135439 13 44251708 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447411 Affx-122924399 AX-123317747 13 43077684 TACGGCAGCAATAGGAAACTAATACATTCACCCAA[C/T]GTATGTTTTTTCATGTTGAGGTTTGATGGCAAAAC Y 2 1 2 1 101000 f 74 goat snp58765-scaffold959-1196335 13 44312156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse590 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320765784 Affx-986697602 AX-385253239 13 43117609 AAACTGGAGTATTCCAAGGACTAATACTCTTCTCT[A/T]TGTGTCCTGCTTGAAACTGTTCTTCTATCAAGGCT W 4 1 2 1 600010 r 74 goat 13_43117609 13 43117609 Ancestral_priority_1043 ancestry 0.584 neutral IMAGE 10K 10K ancestral 38435356 Affx-122933592 AX-123305696 13 43129042 TGGAGCCGATGGGGCCTGGTTCTCATATGCCTTGC[A/G]TGGCGGGGACCTGACACGAGCTAACCAATTGTAGG R 2 1 2 1 201000 r 74 goat snp58766-scaffold959-1247693 13 44363866 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422816 Affx-122943196 AX-123293162 13 43174002 TCCAGGGACCATCCTTCCCAGCCAGGCTGCCTGAG[C/T]GTCTAGAGTGAAGCACGCTCTGGCCTCTTCTCCCT Y 2 1 2 1 101000 r 74 goat snp58767-scaffold959-1292653 13 44409714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399888 Affx-122960216 AX-123270243 13 43206738 GATGACCCTTTACAACACTTGACACCGAATTCACT[A/G]AGCACATGACCAGGTCTCCATAGCCCTCACTTGGT R 2 1 2 1 101000 f 74 goat snp58768-scaffold959-1325389 13 44441528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392192 Affx-122966291 AX-123262549 13 43237690 TCCATATGTATTTTTTTTCCTCTTCAACAAGTTAT[A/G]TCAGTGTCCTCATTTATCTTTGGCCTGTTTTCTTT R 2 1 2 1 101000 r 74 goat snp58769-scaffold959-1356341 13 44472638 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396299 Affx-122963091 AX-123266654 13 43267298 CTGAGATGTTTGATCAGTCGAGGCCCACAGGCAGC[C/T]TTTCCTTGCTGTGTCCCTTAAGCACCCTTTCTGGT Y 2 1 2 1 201000 r 74 goat snp58770-scaffold959-1385949 13 44502514 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442882 Affx-122927658 AX-123313219 13 43315301 TTTTAGCCTGCTCCATTGAAAGCCCTGAGCCCAGT[A/G]CGGCTGTCACCCTGGAAGGCGAGGGTGATAAGCCT R 2 1 2 1 102000 f 74 goat snp58771-scaffold959-1433952 13 44554246 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433694 Affx-122934541 AX-123304035 13 43355368 TTGACCGTTTTTATACTTTAAATGTAATACAGTGG[C/T]AGTGTGCAGCCAACTAAGATCTGATAGCAAGAACA Y 2 1 2 1 101000 r 74 goat snp58772-scaffold959-1474019 13 44594354 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437562 Affx-122931889 AX-123307900 13 43386310 CTACTTAGTGCCCAGGCCACAGTCCAGTTTCCTCC[A/G]CTGTCCCAGCAGTATCCTTTTGCAGTGGACCTCTT R 2 1 2 1 101000 r 74 goat snp58773-scaffold959-1504961 13 44625228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452711 Affx-122920298 AX-123323044 13 43433610 GAGTTTTTCCCCCTTGAAGTTTGCTGTGTTTGTTT[A/G]CTGCCTGTCAGCTGTTTAAGCTTTGGTGAGTATTA R 2 1 2 1 101000 r 74 goat snp58774-scaffold959-1552261 13 44672626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443853 Affx-122927523 AX-123314190 13 43494989 AATCCATGTTTATACTGAGGCAATACTAAGGTGAT[A/C]TACAATATTATGTAATAAAATACTGTCCCAAAATA M 2 1 2 1 101000 f 74 goat snp58775-scaffold959-1613640 13 44734041 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386141 Affx-122971405 AX-123256499 13 43510541 TGAGTGTTCCAAGCAAAGGAGAAAATGATCGAGGA[C/T]GTGGAGGCCCAGGAGAGCATGAATCTTCTTTTGGA Y 2 1 2 1 201000 r 74 goat snp36372-scaffold4364-4157 13 44749270 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440267 Affx-122930647 AX-123310604 13 43540013 TCCTAGCTGAAGATCATTTTCCTGTGTCCTCCGGT[A/G]CTCTGTATATATTGTAGAGAAGATCTCTGTGTCGA R 2 1 2 1 201000 r 74 goat snp36373-scaffold4364-33629 13 44778799 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435019 Affx-122933804 AX-123305359 13 43575548 TTGAAACTGACATCCAAGGAAGCCCCATGTCGATG[A/G]TGACCGCTCCTTCTCCCAGGCTCCCTGAGAGGTTT R 2 1 2 1 101000 f 74 goat snp36374-scaffold4364-69164 13 44814477 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276730 Affx-1111835561 AX-519550240 13 43598106 GAATTTGAACTGGCTGTGCTCTTCAGCCAGTCTAT[A/G]TAGACTAATTGAATAATCTTAATTGAGCTACAAAT R 2 1 2 1 101000 f 74 goat Random2.2K-1348 13 43598106 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452406 Affx-122920599 AX-123322739 13 43608490 ATTGATTCTTGTGTAGGGAGGATTGCTAATGACTT[A/C]CTGCTTGTTTTTATGGGATTCATCTTTAGAGAGTT M 2 1 2 1 101000 f 74 goat snp56265-scaffold881-26795 13 44847360 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276870 Affx-1111835562 AX-519550379 13 43610585 TTGACGTCTCCACTCAGAGGTCTTAGCCTCTCTAC[A/G]TAGAGGCTCCTCAAAAGCAACATGATCAAAATAGA R 2 1 2 1 201000 r 74 goat Random2.2K-1349 13 43610585 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794446 Affx-122935564 AX-385281409 13 43673944 ATTTTCTTATCTGACTCGGACACAGATGAAATAAT[A/G]AGTGAGATCAGACAGACTCTGTTCCCCTTGGCTAA R 2 1 2 1 101000 r 74 goat snp56266-scaffold881-92249 13 44912794 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454208 Affx-122919286 AX-123324541 13 43704352 TTCTTACAGAAATCCCACTTGATGGCTTCAGCACC[A/G]CGTGTGTCTCTTGCTTGTCAGTGACGACTGTGTTG R 2 1 2 1 201000 r 74 goat snp56267-scaffold881-122657 13 44943598 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423290 Affx-122942647 AX-123293636 13 43733272 TAATACTCCTTGACTTAACACATCCAGATCCTCTC[A/G]TTTGGATGGATGTCTAAAAGGATGAGCAGCTAGGA R 2 1 2 1 201000 r 74 goat snp56268-scaffold881-151577 13 44973404 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396172 Affx-122963775 AX-123266527 13 43773470 ACAGTTTCCAACCTGATTTCTCATGGAGAAGGGGC[A/G]TCTCTGCCTCCTGTAAACAGAGATGAGTACCTTTT R 2 1 2 1 202000 r 74 goat snp56269-scaffold881-191775 13 45013585 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse591 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38418867 Affx-122946123 AX-123289215 13 43823068 TCTTTTTTGTTTCTATAGTGATATTGTTGGTAGCA[C/T]AGAAAAAGAGAGAGAAAAAATCAACAGTGAGAGGG Y 2 1 2 1 201000 f 74 goat snp56270-scaffold881-241373 13 45063041 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411076 Affx-122951935 AX-123281426 13 43856400 TTCAGTGCATAAAAATGACAAAGAGTGAAAAACAA[C/T]AGCAAAGTTTTCTCAGAATACTAGGCTTTCACAAA Y 2 1 2 1 201000 f 74 goat snp56271-scaffold881-274705 13 45096455 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410678 Affx-122952750 AX-123281028 13 43921386 TTCGTAGCTGCCTCGGGCTGATACTGCAGGAAGAG[G/T]GAACTCTGTAGAAAAGGACTTTATGTCCAGGACCT K 2 1 2 1 101000 r 74 goat snp56272-scaffold881-339691 13 45161337 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796454 Affx-122943090 AX-385283404 13 43965190 CAGAAAGACTAGGAACGGCCTGTTCAGACAGAAAA[C/T]GAAGGGTCTATGGATTAGTAAATTTGTCAAAGACA Y 2 1 2 1 201000 r 74 goat snp56273-scaffold881-383495 13 45204685 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422663 Affx-122943681 AX-123293009 13 44017234 TCAGATGTGAGTGTAAAACTACTGGGCAGAGAGGA[C/T]GCTTCAGAGCACTGAGGGTCTCCCTCCCCCAGTTT Y 2 1 2 1 101000 f 74 goat snp56274-scaffold881-435539 13 45256717 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773703 Affx-122947106 AX-385260843 13 44057988 AAAATATGATGAATCTTAGGAACGTATGTCTACTT[A/G]AACCCAATGAATGGTGACATTTAAAAAATAAAAGC R 2 1 2 1 101000 r 74 goat snp56275-scaffold881-476293 13 45297664 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417554 Affx-122946916 AX-123287902 13 44102494 AGACTGCGCTCTGAGCACCTGTCTCAGAATCTGAC[A/G]TGAGAGGCCCAGCTCTCAGGTGGCGCTCGCTAGGA R 2 1 2 1 101000 f 74 goat snp56276-scaffold881-520799 13 45342293 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803198 Affx-122961821 AX-385290057 13 44135768 AAATAGTAGGTGAAAATGCTGTATCTGACAAGTGA[C/T]GAACAGCATAGGCAGAAAATCAGCCAGCTTATCAA Y 2 1 2 1 101000 r 74 goat snp56277-scaffold881-554073 13 45375851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401584 Affx-122958878 AX-123271937 13 44194245 AGAGGGACTGTGGCTGTCACATCCTGAAACTTCCC[A/G]TAAGAAAAAGGCTCCGATGCATTTCTAAGCACAGC R 2 1 2 1 101000 r 74 goat snp56278-scaffold881-612550 13 45434387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439338 Affx-122930295 AX-123309675 13 44232507 TCCCACTCAGGCAACGGGCCAGTAAGTTCAACTGA[C/T]GTGAAAAGAGAGAAAAGATAAGCCAAAACTGGACA Y 2 1 2 1 201000 f 74 goat snp56279-scaffold881-650812 13 45472513 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411021 Affx-122951976 AX-123281371 13 44284193 GGAACATGAGGGACCAGGACAGGGTGTCATGGAGA[C/T]GGAGGGTCAGGGCCACTCCCTGTGTCAGAATCAGG Y 2 1 2 1 102000 f 74 goat snp56280-scaffold881-702498 13 45521834 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389981 Affx-122968061 AX-123260338 13 44313635 GAAGCCCCCAAAGAACAGTTTATCAAGTGTGATGA[C/T]GGTACTTTCTCTGACAGGAGATCATAAAAGCATAT Y 2 1 2 1 101000 r 74 goat snp56281-scaffold881-731940 13 45550944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439948 Affx-122929992 AX-123310285 13 44353117 GAGAGAAAAAAAGACTGCACAAACACACGAGAAAG[C/T]AGCATTTACCCCAATCTGTCACAAAGCCAGCACTG Y 2 1 2 1 101000 f 74 goat snp56282-scaffold881-771422 13 45589712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434504 Affx-122934610 AX-123304845 13 44385209 ACAAGATCTGATTTCAGGTCTCTTTGCCAGAGTGA[C/T]GAGAATACAACTTTATTAAATTCTCTACTGCCCAG Y 2 1 2 1 101000 f 74 goat snp56283-scaffold881-803514 13 45621792 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse592 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38385673 Affx-122971143 AX-123256031 13 44414908 GGACATGGGCTTGCCGCCCGGTGCTGTCTGGCTTG[C/T]GCAGTTTGGACACCAGAACCAGGGGCTTTTCTTAA Y 2 1 2 1 201000 f 74 goat snp56284-scaffold881-833213 13 45651709 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse593 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38435657 Affx-122933345 AX-123305997 13 44445011 AAAGTCTGACAAGGGCCTGTCACCTTTGCTGGCAG[A/G]AGCCGACATGTACCCAGAGCAGCTTTCATTTTGGA R 2 1 2 1 201000 r 74 goat snp56285-scaffold881-863316 13 45681874 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442395 Affx-122928001 AX-123312732 13 44562098 AGCACTTGGCACAGACCTTGAGGTAGAGCAGGGAC[A/G]TGGTGAGGGCTACCAGGGCCCAGGAGGGAAATCAA R 2 1 2 1 202000 f 74 goat snp56287-scaffold881-980403 13 45798473 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447728 Affx-122924598 AX-123318064 13 44610560 AGTGGAGTTCTGAATGCATCAACTTCGATCACTTT[G/T]GCATCTGTTGCTGCTAAGTCACTTTAGTCATGTCC K 2 1 2 1 101000 f 74 goat snp56288-scaffold881-1028865 13 45846713 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376259 Affx-122978767 AX-123246618 13 44665221 TCGATGCTATTGCGAGGACCATCCTAGACTTTGCC[A/G]TATACATACAGGAAATAGAAGTCATGGCCTCTGTG R 2 1 2 1 201000 r 74 goat snp56289-scaffold881-1083526 13 45901909 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448870 Affx-122923274 AX-123319205 13 44698770 TTGCTTTCATATTTATCTTCAATCAGGATTCATAT[A/G]AAGAGAATTCTTTAAGTTAGTCATCATTTTATTAA R 2 1 2 1 101000 f 74 goat snp56290-scaffold881-1117075 13 45931985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443411 Affx-122927380 AX-123313748 13 44732667 TTCTGTCTACCTGGAAGAGCAGAGGCCATTTAGTC[A/G]CCCAGGTGGGCTGTTGGGACAGGGTTTGTACCTGT R 2 1 2 1 101000 f 74 goat snp56291-scaffold881-1150972 13 45964488 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772877 Affx-122966459 AX-385260022 13 44791734 TTGTCTGCAGACTCCTGAGTGAATTTTACTTACAC[A/G]TTTGATCTTTAATTTCATCACGAGCAGGAGTCCCA R 2 1 2 1 101000 f 74 goat snp56292-scaffold881-1210039 13 46023812 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380146 Affx-122975978 AX-123250504 13 44861752 TGTTTTTATCAACCTTTTTTTGGCTTTAGACACTT[A/G]TTTTCAGAACTGCCCCAGTGTATAGTCCTTGGAAC R 2 1 2 1 101000 r 74 goat snp56293-scaffold881-1280057 13 46091494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse594 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468272695 Affx-1111832985 AX-519546399 13 44864473 GAACAGTCTTTTGGACTCTGTGGGAGAAGGCGAGG[A/G]TGGGATGATTTGAGAGGGTAGCGTTGAAACGTGTA R 2 1 2 1 103000 f 74 goat 13_44864473_AF-PAKI 13 44864473 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320770414 Affx-122943699 AX-385257580 13 44896145 AAAGTTGCTTTTTAGCAATGTGAGAAACAGAAGCA[C/T]GTTATCTCCAGTCATTAAGTAAGTGCTCTGGTGTA Y 2 1 2 1 101000 r 74 goat snp56294-scaffold881-1314450 13 46125818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse595 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38377891 Affx-122977251 AX-123248250 13 44944169 TGTTGCCTTCTTGGATGTATTTTGCAAAGCTGCCA[A/G]GAATGTCTGACTTGCAGGGACTCTGTTAAATATAA R 2 1 2 1 101000 f 74 goat snp56295-scaffold881-1362474 13 46174021 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse596 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38433173 Affx-122935659 AX-123303514 13 45000741 GTCCGCCTCAGTTTGCACTGAGGTGTAAGTAGCCA[G/T]CTCAGCCTTCTGTTTTTGTATTTTTTTAAGAAAAT K 2 1 2 1 101000 f 74 goat snp56296-scaffold881-1419046 13 46230843 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453900 Affx-122919500 AX-123324233 13 45038878 GCCTTCCACGACATTCACACCAGAGTCAGTGCCTA[C/T]TGGCCAAACCAGAACATTGATATGCCTTGAGAAAA Y 2 1 2 1 201000 r 74 goat snp56297-scaffold881-1457183 13 46269216 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453622 Affx-122919752 AX-123323955 13 45099361 GAAATATTCTGTTTCTTTAAAACCCAGCACTGTGG[C/T]ATATAGTATTTAAGATATTCTTTTTTATTCTCTTC Y 2 1 2 1 101000 f 74 goat snp56299-scaffold881-1517666 13 46329866 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276872 Affx-1111835563 AX-519550381 13 45116195 GTTATTCTGCTCTGCGGTAGCAAAGAACGTCCAAC[A/T]GCTTTGATTTTGAAGGAGCTGACCCTTTGTTTTCA W 4 1 2 1 202000 r 74 goat Random2.2K-1350 13 45116195 A T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391801 Affx-122967034 AX-123262158 13 45149694 CTATCTGGAATTTAGAATGTCTGGGAAAGCCTGGC[A/G]TTTTCACGTCTTAGAGACTAGGCTCTTCCTGCTAG R 2 1 2 1 202000 r 74 goat snp56300-scaffold881-1567999 13 46377549 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787742 Affx-122951235 AX-385274765 13 45181921 GCCAAGGGACTTCCCATCAAAAAATGGCAAGTAGA[C/T]GTGTGGTCCTAAAGAAGGGAAAAATGACCCTATGA Y 2 1 2 1 101000 f 74 goat snp56301-scaffold881-1600226 13 46410991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse597 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320792430 Affx-122963518 AX-385279411 13 45229418 TGATATAAGGTCAAGTTTTCCATTTAAAAACTGGT[A/G]CATACTAGCTGTCCCATAAAAATTTATTTAATGAT R 2 1 2 1 101000 f 74 goat snp56302-scaffold881-1647723 13 46458619 A G 1 recommended GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 snp-genphyse598 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320797371 Affx-122948939 AX-385284310 13 45230023 TGACAATCTTGTAGGAAAAGGGGACAGTGATCTTT[A/C]TGTTTGTCAGTTGAATCTTTCTGGGAGTGTCTGCC M 2 1 2 1 101000 f 74 goat snp56304-scaffold881-1648328 13 46459226 A C 1 recommended GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 snp-genphyse599 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38409944 Affx-122952865 AX-123280295 13 45236372 CTGAGCGACTGAACTGAACTGAACAGTAGGTTCTC[A/G]CCTCATTTCCTTTTTAAGGTTGAGTTTGTTATTTG R 2 1 2 1 201000 r 74 goat snp56306-scaffold881-1654677 13 46465604 A G 2 recommended GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 38407003 Affx-122955030 AX-123277354 13 45239220 AAGATGTCCCAGTGCTGAGGATGACTAATGTCAGC[A/G]TTATAACATATGCCATTTTTGGTTTTGTGGCAAAT R 2 1 2 1 201000 r 74 goat snp56308-scaffold881-1657525 13 46468452 A G 2 recommended GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 snp-genphyse600 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38424730 Affx-122941668 AX-123295076 13 45240588 GGCGGAGGATGGAACACTGGGGGGAGCCGATACCC[A/G]GGACAGGGCAGTCCTGGAGGCAACCGCTATCCACC R 2 1 2 1 201000 f 74 goat "ch-rs268292977;Ch-rs268292977;snp56310-scaffold881-1658893" 13 46469820 G A 2 recommended GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 532567201 Affx-122949968 AX-579205694 13 45240841 TGGCAGGAGCTGCTGCAGCTGGAGCAGTGGTAGGG[A/G]GCCTTGGTGGCTACATGCTGGGAAGTGCCATGAGT R 8 1 2 1 104000 f 74 goat "ch-rs268292978;Ch-rs268292978;PRP-G127-S127-1;PRP-G127-S127-10;PRP-G127-S127-11;PRP-G127-S127-12;PRP-G127-S127-13;PRP-G127-S127-14;PRP-G127-S127-15;PRP-G127-S127-16;PRP-G127-S127-2;PRP-G127-S127-3;PRP-G127-S127-4;PRP-G127-S127-5;PRP-G127-S127-6;PRP-G127-S127-7;PRP-G127-S127-8;PRP-G127-S127-9;snp56311-scaffold881-1659146;snp-genphyse775;UniBern-var22" 13 46470073 "A;G" "A;G" 1 wobble probeset GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38429442 Affx-122938501 AX-123299784 13 45240876 GGCCTTGGTGGCTACATGCTGGGAAGTGCCATGAG[C/T]AGGCCTCTTATACGTTTTGGCAATGACTATGAGGA Y 2 1 2 1 400000 f 74 goat "ch-rs268292979;Ch-rs268292979;snp56312-scaffold881-1659181" 13 46470108 T C wobble probeset GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 38443269 Affx-122927487 AX-123313606 13 45240923 ACGTTTTGGCAATGACTATGAGGACCGTTACTATC[A/G]TGAAAACATGTACCGTTACCCCAACCAAGTGTACT R 2 1 2 1 400000 r 74 goat "ch-rs268292981;Ch-rs268292981;PRP-H154-R154-1;PRP-H154-R154-10;PRP-H154-R154-11;PRP-H154-R154-12;PRP-H154-R154-13;PRP-H154-R154-14;PRP-H154-R154-15;PRP-H154-R154-16;PRP-H154-R154-2;PRP-H154-R154-3;PRP-H154-R154-4;PRP-H154-R154-5;PRP-H154-R154-6;PRP-H154-R154-7;PRP-H154-R154-8;PRP-H154-R154-9;snp56314-scaffold881-1659228;UniBern-var25" 13 46470155 "A;G" "A;G" wobble probeset GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 532567216 Affx-122929352 AX-579205709 13 45241094 GAACTTCACCGAAACTGACATCAAGATAATGGAGC[A/G]AGTGGTGGAGCAAATGTGCATCACCCAGTACCAGA R 8 1 2 1 101000 r 74 goat "ch-rs268292982;PRP-R211-Q211-1;PRP-R211-Q211-10;PRP-R211-Q211-11;PRP-R211-Q211-12;PRP-R211-Q211-13;PRP-R211-Q211-14;PRP-R211-Q211-15;PRP-R211-Q211-16;PRP-R211-Q211-2;PRP-R211-Q211-3;PRP-R211-Q211-4;PRP-R211-Q211-5;PRP-R211-Q211-6;PRP-R211-Q211-7;PRP-R211-Q211-8;PRP-R211-Q211-9;snp56315-scaffold881-1659399;snp-genphyse778;UniBern-var26" 13 46470326 "A;G" "A;G" 1 wobble probeset "not_recommended;recommended" GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 SNP in PRP gene multi-breed 532567204 Affx-122960826 AX-579205697 13 45241126 AGCGAGTGGTGGAGCAAATGTGCATCACCCAGTAC[A/C]AGAGAGAATCCCAGGCTTATTACCAAAGGGGGGCA M 12 1 2 1 104000 f 74 goat "ch-rs268292983;Ch-rs268292983;PRP-Q222-K222-1;PRP-Q222-K222-10;PRP-Q222-K222-11;PRP-Q222-K222-12;PRP-Q222-K222-13;PRP-Q222-K222-14;PRP-Q222-K222-15;PRP-Q222-K222-16;PRP-Q222-K222-2;PRP-Q222-K222-3;PRP-Q222-K222-4;PRP-Q222-K222-5;PRP-Q222-K222-6;PRP-Q222-K222-7;PRP-Q222-K222-8;PRP-Q222-K222-9;snp56316-scaffold881-1659431;snp-genphyse779;UniBern-var27" 13 46470358 "A;C" "A;C" 1 wobble probeset GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 SNP in PRP gene multi-breed 38388019 Affx-122969562 AX-123258377 13 45241180 ATTACCAAAGGGGGGCAAGTGTGATCCTCTTTTCT[C/T]CCCCTCCTGTGATCCTCCTCATCTCTTTCCTCATT Y 2 1 2 1 201000 f 74 goat "Ch-rs268292984;snp56317-scaffold881-1659485;snp-genphyse780;UniBern-var28" 13 46470412 "C;T" "C;T" 2 recommended GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 38400553 Affx-122960427 AX-123270908 13 45241717 GGTAACACAGCCATCTATTGCATCAAGAATGGATA[G/T]TCATGCAACCTTTGACTTATGGGCAGAGGACATTT K 2 1 2 1 101000 f 74 goat snp56318-scaffold881-1660022 13 46470949 T G 1 recommended GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 snp-genphyse605 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320792540 Affx-122949977 AX-385279521 13 45243961 TTAGTCAATAGAAAACAATCTTCAATCAGGATAAC[A/G]CAAGACTACATATTTCTTTGATAACCCAGCATGGC R 2 1 2 1 101000 r 74 goat snp56319-scaffold881-1662266 13 46473193 A G 1 recommended GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 snp-genphyse606 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38434242 Affx-122934830 AX-123304583 13 45243990 GATAACACAAGACTACATATTTCTTTGATAACCCA[A/G]CATGGCTGGGAGGTTCTGATTCATCTGTTGTATTC R 2 1 2 1 201000 f 74 goat snp56320-scaffold881-1662295 13 46473222 A G 2 recommended GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 snp-genphyse607 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38418961 Affx-122946082 AX-123289309 13 45244203 TTATGACGTTGCCTGAAAAATGGCAGAAGGTAGTG[G/T]AACAAAAGAGTGACTATGTTGTTTGGTAAAGTTCT K 2 1 2 1 303000 r 74 goat snp56321-scaffold881-1662508 13 46473435 T G 3 not_recommended GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 38392000 Affx-122966497 AX-123262357 13 45244315 CCAAAGGCACATTTTGGCCAACCCAATACTGAATA[C/T]TTAAAGGAAACTCTTCTGTGTTGTCCTTAGCCTTA Y 2 1 2 1 103000 r 74 goat snp56322-scaffold881-1662620 13 46473547 T C 1 not_recommended GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 snp-genphyse608 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38393369 Affx-122965916 AX-123263725 13 45273812 TGAATTAAGGTTTGGAGCTTTCAGTCCCAACCTCT[A/G]ATTTCTGGGGAGAGAAGGGCGCTGGAGGTTGAATT R 2 1 2 1 103000 f 74 goat snp56323-scaffold881-1692117 13 46503168 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse609 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38427217 Affx-122939580 AX-123297560 13 45303347 TGTCCTACAGAGTGAAGCTGACGAAACAGACAGTG[C/T]GATAAGAAAGCACTGAGGAAAGGCTGTATCCTGAT Y 2 1 2 1 101000 f 74 goat snp56324-scaffold881-1721652 13 46533051 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429710 Affx-122937622 AX-123300051 13 45334284 TGAAATCCCAGATAGTAGGGATTTCCCTGGTGGTC[C/T]AATGATTAAGAAGCTGCCCGCCAACATAGAGGGCA Y 2 1 2 1 201000 r 74 goat snp56325-scaffold881-1752589 13 46564206 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405140 Affx-122956958 AX-123275492 13 45363348 AGCAACTAGGTGGAGGGCAAGCAGTTTCCTCTGGG[A/C]GCTTGATTAAAGAGGAACTTAAAGCATTTTCCGTA M 2 1 2 1 101000 r 74 goat snp56326-scaffold881-1781653 13 46593326 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse610 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38393845 Affx-122965154 AX-123264200 13 45452254 CTGAGTCCAAGTACTGGGTGTCTGAGTACCAGGGG[C/T]GGGTCCCCACTCTACTGAGGTCTGAGTGTCAACCT Y 2 1 2 1 201000 f 74 goat snp56328-scaffold881-1870559 13 46681444 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433581 Affx-122934967 AX-123303922 13 45491632 CCGAGTGAACTAAAGTTTTTGTCTCTCAAGTAGAG[C/T]AGGGCAGGGTAAATGGTCTGCTGAGCAAATGGTGC Y 2 1 2 1 101000 f 74 goat snp56329-scaffold881-1909937 13 46720686 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398592 Affx-122961493 AX-123268947 13 45607628 ACCCCAGGGCTGGGCACACATAACCAGTGAAAGGA[C/T]TGCCAGAGGATCTGGATGCCACACTGATAGTAACT Y 2 1 2 1 101000 f 74 goat snp56331-scaffold881-2025933 13 46837001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse611 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38376742 Affx-122978948 AX-123247101 13 45639329 TGTACCAGTGAGCCACCAGGGAAACCCTTAACCAG[G/T]ATGCCATTTGTCAGATTGGTGAGTTAGGAAAACGT K 2 1 2 1 101000 r 74 goat snp56332-scaffold881-2057634 13 46869185 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429199 Affx-122937946 AX-123299541 13 45735857 TAAGCAGTCTTGATAGGAGGTTTCTCAAGAGGTGA[C/T]GGGACTACAGCATGAAAAGGATTTCAGACAGATTA Y 2 1 2 1 201000 r 74 goat snp56334-scaffold881-2154162 13 46966710 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772753 Affx-122958441 AX-385259898 13 45784137 TGTTTGAACCCACTCCTGTAAACAAACTCAGTTTC[A/G]TAAAATCTGTTTGTAATTGTCAACCTTTTCCCCAT R 2 1 2 1 101000 f 74 goat snp56335-scaffold881-2202442 13 47015750 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411903 Affx-122951181 AX-123282253 13 45826946 AACGGCATCAGGTGACCTATAGACACATGAAAAGA[C/T]GCTCAACATCACTAATTACTAGAGTAATGTAAATC Y 2 1 2 1 103000 f 74 goat snp56336-scaffold881-2245251 13 47059562 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426313 Affx-122940287 AX-123296659 13 45859612 TAATTTCCTATCTTGTTTCTCTCAACTATTTTGAT[A/G]CTCAATGACTTCCATTAATTCTCATCCCCAGTTCA R 2 1 2 1 101000 f 74 goat snp56337-scaffold881-2277917 13 47092961 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428946 Affx-122938888 AX-123299288 13 45898113 ACCCGAGGGTGTGGGAAGTTCACTCTGGGGCCAGG[C/T]GGCTGGTAGAAGCTGGAGAAAGGAGCAACTGGAAC Y 2 1 2 1 101000 r 74 goat snp56338-scaffold881-2316418 13 47131718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387412 Affx-122970406 AX-123257770 13 45928658 AGAACCTGGACTACAGCACTCAATGCTCCTCTGAA[C/T]GAACTTCCTGCTAGAAAACTTATTTGGGAAAAACT Y 2 1 2 1 101000 f 74 goat snp12980-scaffold150-13862 13 47162785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396828 Affx-122963272 AX-123267183 13 45981221 AAGCTCTACTCAGCAAATTGTACTGTTGAGGAAAC[C/T]GACCCCTACATCACTTCCTTTCCTGTTCCTCTTCT Y 2 1 2 1 201000 f 74 goat snp12981-scaffold150-66425 13 47215305 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414450 Affx-122949945 AX-123284799 13 46030177 AAGATCAATTATCGCAAGTATGCAAGGAACTAGAA[A/G]GCATCATAAAGTTCTTCATTTCAAGTATTTAAAAA R 2 1 2 1 101000 f 74 goat snp12982-scaffold150-115381 13 47264123 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447683 Affx-122924629 AX-123318019 13 46064837 ATGTATTTATAGAAATATATGTTAGTATACTACTT[G/T]TAAAAGGCTCAGTGAATACACAAAAAAGTAGTGGA K 2 1 2 1 103000 r 74 goat snp12983-scaffold150-150041 13 47299337 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436153 Affx-122932627 AX-123306492 13 46121664 ATAAGGAGGAAATGACTCTTAGCCTCTTAAGTAAC[A/G]TAATAGGAAACTCTAAATGTAAACAAGGCTTTCTT R 2 1 2 1 101000 f 74 goat snp12984-scaffold150-206868 13 47356557 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411674 Affx-122951551 AX-123282024 13 46182512 AGACTGGTTTTTATGAGCCATATTACATAGAAAAA[C/T]GTGAAAATCAAAATTGTACACTGATTATCAAAGTA Y 2 1 2 1 201000 f 74 goat snp12985-scaffold150-267716 13 47417329 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse612 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38423420 Affx-122942616 AX-123293766 13 46219811 AAACCAGGCAGTATAACTTTCATGGCTGCACAGAA[C/T]ATGTAGAAATGAACAAATTCATTCAAGAAAAGAGC Y 2 1 2 1 101000 f 74 goat snp12986-scaffold150-305015 13 47453846 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse613 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38402076 Affx-122958707 AX-123272429 13 46263284 AAAGCAAAATAAAAAGCAATTAGTTAGGAGGGACT[A/G]TCTAAGTAGGATTGTCTAAAGTGAAAACCTGTAAA R 2 1 2 1 101000 r 74 goat snp12987-scaffold150-348488 13 47497338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445859 Affx-122925997 AX-123316196 13 46299365 GTGCCAGGGAAAGGCCATGGTCAGGAATGCAGAGT[A/G]CACCCTCTTCAGTGGCACTAGCTTAGCTGCTCATG R 2 1 2 1 201000 f 74 goat snp12988-scaffold150-384569 13 47533695 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439776 Affx-122930510 AX-123310113 13 46329093 CATTATGAATTACTGAGAAATAAAATATTCATAAG[C/T]ATAAAACTGAAATTAGCCTACATGGAGTTTTTCTG Y 2 1 2 1 201000 r 74 goat snp12989-scaffold150-414297 13 47563895 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401754 Affx-122959506 AX-123272107 13 46387807 CGTGTTCCTCAGACACAGCAGCGTGGTCACCATGC[C/T]GGAATTTGGCATTTGCTGCTCCTTCCACCTGGAAT Y 2 1 2 1 101000 r 74 goat snp12990-scaffold150-473011 13 47622836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415572 Affx-122948635 AX-123285921 13 46418538 AGCTAGGCACCAAAGCTTCACTTAGGTTGTGTGCT[A/G]TATCAGTCCAGAGTACACTGTTGACATAGTAGGGT R 2 1 2 1 101000 f 74 goat snp12991-scaffold150-503742 13 47653443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388599 Affx-122969151 AX-123258957 13 46459619 AGGCTCAGTATATTTTCAGAAATGTGACTTGCACT[C/T]CCAGTGTGTCTGATCCTGTCATACTGCCCTCTCCT Y 2 1 2 1 101000 f 74 goat snp12992-scaffold150-544823 13 47695031 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602767 Affx-1002479211 AX-413837128 13 46469996 TGGTGGAGGCTGGGGTCAAGGTGGTAGCCACAGTC[A/G]GTGGAACAAGCCCAGTAAGCCAAAAACCAACATGA R 2 1 2 1 102000 f 74 goat ch-rs644831537 13 46469996 A G 1 neutral Goat_IGGC_65K_v2 Illumina PRP-variant SNP in PRP gene multi-breed 350603625 Affx-1002479212 AX-413837773 13 46469998 GTGGAGGCTGGGGTCAAGGTGGTAGCCACAGTCAG[G/T]GGAACAAGCCCAGTAAGCCAAAAACCAACATGAAG K 2 1 2 1 201000 r 74 goat "ch-rs665266215;Ch-rs665266215" 13 46469998 T G 2 recommended Goat_IGGC_65K_v2 Illumina 350602769 Affx-1002479213 AX-413837130 13 46470041 GCCCAGTAAGCCAAAAACCAACATGAAGCATGTGG[C/T]AGGAGCTGCTGCAGCTGGAGCAGTGGTAGGGGGCC Y 2 1 2 1 201000 f 74 goat "ch-rs640592763;Ch-rs640592763" 13 46470041 C T 2 recommended Goat_IGGC_65K_v2 Illumina 532567195 Affx-1002479236 AX-579205688 13 46470120 TACATGCTGGGAAGTGCCATGAGTAGGCCTCTTAT[A/G]CATTTTGGCAATGACTATGAGGACCGTTACTATCG R 8 1 2 1 304000 r 74 goat "ch-rs268292980;Ch-rs268292980;PRP-I142-M142-1;PRP-I142-M142-10;PRP-I142-M142-11;PRP-I142-M142-12;PRP-I142-M142-13;PRP-I142-M142-14;PRP-I142-M142-15;PRP-I142-M142-16;PRP-I142-M142-2;PRP-I142-M142-3;PRP-I142-M142-4;PRP-I142-M142-5;PRP-I142-M142-6;PRP-I142-M142-7;PRP-I142-M142-8;PRP-I142-M142-9;snp56313-scaffold881-1659193;UniBern-var23" 13 46470120 A G 3 wobble probeset GoatSNP50 chip candidate gene ou candidate region PRP 10.1371/journal.pone.0086227 SNP in PRP gene multi-breed 532567223 Affx-1002479215 AX-579205716 13 46470122 CATGCTGGGAAGTGCCATGAGTAGGCCTCTTATAC[A/G]TTTTGGCAATGACTATGAGGACCGTTACTATCGTG R 16 1 2 1 303000 f 74 goat "Ch-rs667226700;PRP-H143-R143-1;PRP-H143-R143-10;PRP-H143-R143-11;PRP-H143-R143-12;PRP-H143-R143-13;PRP-H143-R143-14;PRP-H143-R143-15;PRP-H143-R143-16;PRP-H143-R143-2;PRP-H143-R143-3;PRP-H143-R143-4;PRP-H143-R143-5;PRP-H143-R143-6;PRP-H143-R143-7;PRP-H143-R143-8;PRP-H143-R143-9" 13 46470122 A G 3 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region 538942992 Affx-1002479273 AX-585490107 13 46470130 GAAGTGCCATGAGTAGGCCTCTTATACATTTTGGC[A/G]ATGACTATGAGGACCGTTACTATCGTGAAAACATG R 16 1 2 1 304000 r 74 goat "PRP-N146-D146-1;PRP-N146-D146-10;PRP-N146-D146-11;PRP-N146-D146-12;PRP-N146-D146-13;PRP-N146-D146-14;PRP-N146-D146-15;PRP-N146-D146-16;PRP-N146-D146-2;PRP-N146-D146-3;PRP-N146-D146-4;PRP-N146-D146-5;PRP-N146-D146-6;PRP-N146-D146-7;PRP-N146-D146-8;PRP-N146-D146-9" 13 46470130 A G 3 wobble probeset Goat_IGGC_65K_v2 candidate gene ou candidate region 532567198 Affx-1002479293 AX-579205691 13 46470131 AAGTGCCATGAGTAGGCCTCTTATACATTTTGGCA[A/G]TGACTATGAGGACCGTTACTATCGTGAAAACATGT R 8 1 2 1 304000 r 74 goat "PRP-N146-S146-1;PRP-N146-S146-10;PRP-N146-S146-11;PRP-N146-S146-12;PRP-N146-S146-13;PRP-N146-S146-14;PRP-N146-S146-15;PRP-N146-S146-16;PRP-N146-S146-2;PRP-N146-S146-3;PRP-N146-S146-4;PRP-N146-S146-5;PRP-N146-S146-6;PRP-N146-S146-7;PRP-N146-S146-8;PRP-N146-S146-9;SNPs_057;UniBern-var24" 13 46470131 A G 3 wobble probeset Goat_IGGC_65K_v2 candidate gene ou candidate region 532652008 Affx-1002479297 AX-579205701 13 46470146 GCCTCTTATACATTTTGGCAATGACTATGAGGACC[A/G]TTACTATCATGAAAACATGTACCGTTACCCCAACC R 4 1 2 1 400000 r 74 goat "ch-rs643104127;Ch-rs643104127;PRP-H151-R151-1;PRP-H151-R151-10;PRP-H151-R151-11;PRP-H151-R151-12;PRP-H151-R151-13;PRP-H151-R151-14;PRP-H151-R151-15;PRP-H151-R151-16;PRP-H151-R151-2;PRP-H151-R151-3;PRP-H151-R151-4;PRP-H151-R151-5;PRP-H151-R151-6;PRP-H151-R151-7;PRP-H151-R151-8;PRP-H151-R151-9" 13 46470146 A G Goat_IGGC_65K_v2 candidate gene ou candidate region PRP 350602879 Affx-1002479216 AX-413837198 13 46470197 CATGTACCGTTACCCCAACCAAGTGTACTACAGAC[A/C]AGTGGATCAGTATAGTAACCAGAACAACTTTGTGC M 2 1 2 1 201000 r 74 goat "ch-rs642397303;Ch-rs642397303" 13 46470197 C A 2 recommended Goat_IGGC_65K_v2 Illumina 350602775 Affx-1002479217 AX-413837134 13 46470231 CCAGTGGATCAGTATAGTAACCAGAACAACTTTGT[G/T]CATGACTGTGTCAACATCACAGTCAAGCAACACAC K 2 1 2 1 201000 f 74 goat "ch-rs668619276;Ch-rs668619276" 13 46470231 G T 2 recommended Goat_IGGC_65K_v2 Illumina 350602883 Affx-1002479218 AX-413837200 13 46470346 TCAAGATAATGGAGCGAGTGGTGGAGCAAATGTGC[A/C]TCACCCAGTACCAGAGAGAATCCCAGGCTTATTAC M 2 1 2 1 303000 r 74 goat "ch-rs644548938;Ch-rs644548938" 13 46470346 A C 3 not_recommended Goat_IGGC_65K_v2 Illumina 38380558 Affx-122975283 AX-123250916 13 46517642 CTTACTTCTGGAAATGAAGGACCCGTAGGTGAGGC[A/G]TGTCTTGAAAGATATATGTATGGACAGAAGTAAGT R 2 1 2 1 201000 r 74 goat snp12993-scaffold150-602846 13 47753426 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787115 Affx-122956755 AX-385274141 13 46569264 ATTTTCTTTGTTTCCTTCCAGAGGAAGGTACCAAC[A/G]TTCCCATACCTGTAGTGCTGCAAAGATCAACATTT R 2 1 2 1 101000 f 74 goat snp12994-scaffold150-654468 13 47804580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387335 Affx-122970495 AX-123257693 13 46612275 CAAGTAAATAAGAAATAGCTATATCAAGTTACAGC[A/G]CTAAGAAATGTGATATCACTGTGGAAATATACAAA R 2 1 2 1 101000 f 74 goat snp12995-scaffold150-697479 13 47847044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448519 Affx-122923449 AX-123318855 13 46688815 GAGGTAGGCTCTAAGACAAGGATTCTAGAGCAATT[A/G]TTTAATAAGGTGATCCCAGGAAATACCAACAGGGC R 2 1 2 1 201000 r 74 goat snp12997-scaffold150-774019 13 47924709 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781237 Affx-122941100 AX-385268322 13 46738092 TTGCTATGTTGAATTTCTGTTCAATGGACATACTT[A/G]TTAGCCTTTGCTGACCATGTAGGAGGAAATGAAGG R 2 1 2 1 101000 r 74 goat snp12998-scaffold150-823296 13 47974231 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451370 Affx-122921223 AX-123321703 13 46779231 TGGAAGAATGAGATAAAACACACACAAGTAACTAA[C/T]AACCTAGAGGTCTAGCTGCCTATATGGGACATGTG Y 2 1 2 1 101000 r 74 goat snp12999-scaffold150-864435 13 48014928 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435368 Affx-122933583 AX-123305708 13 46810626 GGTACTGAGAAGAAACTTTTCCTGTTCTTTGATTT[A/G]TATAGTGTCCTTCCAAAATGTAAACAACTTAGAGG R 2 1 2 1 101000 f 74 goat snp13000-scaffold150-895830 13 48046695 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383214 Affx-122972775 AX-123253572 13 46894747 AAATCTCTGAAAATAGTGATTCTAAAACTCTTTTG[A/C]TGAACCATTGGTTATTTTCTGTTATTTCATGATTA M 2 1 2 1 101000 f 74 goat snp13002-scaffold150-979951 13 48133203 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396615 Affx-122962887 AX-123266970 13 46935293 ATTTGGAGAAAGTCCAACCTGCCCCAGAATAACTG[C/T]ACTTTTTAAATGTAGATCTTTCTTTATTCTGGAGC Y 2 1 2 1 201000 r 74 goat snp13003-scaffold150-1020497 13 48174448 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384103 Affx-122972837 AX-123254461 13 46971154 TGGCTGGCGCAGCAACTGTAGCAGTAGACACAACA[G/T]AACACAGCACAATACCTCTCTCCTCTTGGCTGACA K 2 1 2 1 101000 f 74 goat snp13004-scaffold150-1056358 13 48210524 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765898 Affx-122949236 AX-385253331 13 47045032 ATGAGGAACATAGAGGTTAGTGGCTCTACAAAGGT[A/G]TTGCTAATACCCCTTGTAGTAATCTGGTTATTTTA R 2 1 2 1 101000 f 74 goat snp13005-scaffold150-1130236 13 48285941 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433610 Affx-122934948 AX-123303951 13 47097627 CACACACAGAAAATAAATGCAATAGAAAATAAACC[C/T]TGTTGGCTATGCTTGCAAGTAAAGACCATCATGTA Y 2 1 2 1 101000 r 74 goat snp13006-scaffold150-1182831 13 48337682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779263 Affx-122921765 AX-385266367 13 47169666 TACTAAAAGTATTAATACAAAGTGAGTGACACTCC[C/T]AGTCTTCTATATGATATTTGTACCTTACAGATATA Y 2 1 2 1 101000 f 74 goat snp13007-scaffold150-1254870 13 48409925 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446600 Affx-122924810 AX-123316936 13 47198662 ACTGACCCATTTTCCTTTTCTCACCCATATATCTC[G/T]CAACTGACAGTCCCAAGGAGAAGATGCCTGAGGCT K 2 1 2 1 101000 f 74 goat snp13008-scaffold150-1283866 13 48439041 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411577 Affx-122951625 AX-123281927 13 47249234 ACAGCCCTAGAAAAAGCTGTTTCCACCTTTTTCCT[C/T]TTCCTAGCACAATAGAAACCTTCAAGAAATGGAGA Y 2 1 2 1 201000 r 74 goat snp13009-scaffold150-1334438 13 48490254 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382754 Affx-122973593 AX-123253112 13 47300313 GACTGCAAGCCTCAGATAGCATCTAACCAAATCTG[A/G]TCTGTCATTCCCATTTAGCCATTTCTGATTGGGTT R 2 1 2 1 101000 r 74 goat snp13010-scaffold150-1385517 13 48541460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772047 Affx-122975898 AX-385259202 13 47353274 AAGTTGACTGAGGAATTTTAATGAGTCTTGTTTTA[C/T]ATCTAAAAGTATATCCAAGTGAATTCTCCATGTTT Y 2 1 2 1 101000 f 74 goat snp13011-scaffold150-1438478 13 48594834 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438305 Affx-122931364 AX-123308643 13 47392084 TCCCTCAGGCAGCCTTCTGAGAATGCCCAGGTTGG[A/G]CTGCATACCTCTCCTCTCCATGTACAAGATAATTT R 2 1 2 1 101000 r 74 goat snp13012-scaffold150-1477288 13 48633595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421092 Affx-122944226 AX-123291439 13 47426348 GATACTGAGGCACAGAGAGATAAAGTAACTGTCCC[A/G]AGGTTAAACAGCAAGGTACAGCCAAGATTTTCAGA R 2 1 2 1 201000 r 74 goat snp13013-scaffold150-1511552 13 48667587 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463283938 Affx-1109905458 AX-514769167 13 47440891 AGCTGATGGACTTGAGCTCCCTGCCTCTTAGATAC[A/G]TGTTCCCTTTGTCTTTTGTTACTGGGCTCAAAGAA R 2 1 2 1 101000 r 74 goat 13_47440891_AF-PAKI 13 47440891 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38447440 Affx-122924377 AX-123317776 13 47455636 ATTGACAGTGTAGATGATTAAGTTAGAACTTTGCT[G/T]TTGGGAGAGAGGTTGAATGTCATTTTTACCTTATT K 2 1 2 1 201000 f 74 goat snp13014-scaffold150-1540840 13 48697129 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425539 Affx-122941452 AX-123295885 13 47487504 ATGAACAAACACATGTTATACTTGTTATCTGTGTG[A/C]TTAGGCCTTGGTTACTTAGTTATTATTTATATTAT M 2 1 2 1 201000 r 74 goat snp13015-scaffold150-1572708 13 48728716 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790707 Affx-122925327 AX-385277708 13 47547009 ATACCTCTCAACAGTGTCATCCATCTGCAAAATTA[C/T]ATGATACTTTCCCCCAGTATTTGACTGCTTGTGTG Y 2 1 2 1 101000 r 74 goat snp13016-scaffold150-1632213 13 48788405 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385344 Affx-122971652 AX-123255702 13 47579569 ATCATCTGCAGGTGCAACTTGAGCAGATGAACAGG[A/C]CACAGATAATGTTGTGGTGAGGGTATGGACTTTGA M 2 1 2 1 101000 f 74 goat snp13017-scaffold150-1664773 13 48821002 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420321 Affx-122945015 AX-123290668 13 47608455 GGGACACAGCTAGATGGCAAGAGTGTCAAATAAGG[A/C]AGAGAAAGGATGCCACTCAGGAAAGACTGATAAAG M 2 1 2 1 201000 f 74 goat snp13018-scaffold150-1693659 13 48850705 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377364 Affx-122977648 AX-123247723 13 47638673 TGCCCTGATTGCACTATGGTGTCCTGAGGAACTAG[C/T]GGGGGCAGAAAACCTGCTGCTAACACAGCCAAGTT Y 2 1 2 1 201000 f 74 goat snp13019-scaffold150-1723877 13 48881699 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796155 Affx-122930117 AX-385283106 13 47706822 CTGAACACTTTGGTGAGCATTCCTCATGCTTTGAC[A/G]AAGATTCAAGATTCTTTATAGGAAAGGATGAGCTG R 2 1 2 1 101000 f 74 goat snp13020-scaffold150-1792026 13 48951166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442517 Affx-122928549 AX-123312854 13 47741653 TAAATGTTGAGAAGAAAAGTGGCTTTGTCAAATCC[C/T]ATGACTTTTTTAAAGCTTCCCATTTATATTCCAAA Y 2 1 2 1 101000 f 74 goat snp13021-scaffold150-1826857 13 48986425 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411171 Affx-122951864 AX-123281521 13 47773204 CCTATGTTTGCTTTTGGTATATTTTTATTGTCTCT[A/G]GGTTCTTGGTGTGGAAATTTACATTAATGATTTGA R 2 1 2 1 101000 r 74 goat snp13022-scaffold150-1858408 13 49018511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450862 Affx-122922227 AX-123321196 13 47802104 AACAAGCAATGCCTCACTTCAGCTTGATCTTTTTT[A/C]TTGGAAGAAAAAATATACCATCCTTCTGCAGCCTC M 2 1 2 1 101000 f 74 goat snp13023-scaffold150-1887308 13 49047556 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785788 Affx-122925634 AX-385272828 13 47871806 GGCAGCTGAATGCAATCTTCACTAATGAATAAGCA[A/C]ATACATATCTTGCACACCTGCTCTTGCTGTTGCAG M 2 1 2 1 101000 r 74 goat snp13024-scaffold150-1957010 13 49118354 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790357 Affx-122953206 AX-385277360 13 47960841 CCCATACACTTAACTGATAGCCCTGCCTCTCGTTG[C/T]CATTTAGATGGTAAATTGCAAAATACATCTTAGGG Y 2 1 2 1 101000 f 74 goat snp13026-scaffold150-2046045 13 49202211 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432595 Affx-122935508 AX-123302936 13 47992077 TACATCACTCAGTTCCTGACATGAGAAGAAAGGCA[A/G]TGAGATCTGCTTTAGAATATTTTGTTTTGGTCTTA R 2 1 2 1 101000 f 74 goat snp13027-scaffold150-2077281 13 49233352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439671 Affx-122930589 AX-123310008 13 48049877 GCTTAGTCATAGAAAGCCATGGAAGAGACTAGCAA[C/T]GCTGGAAACTGGCCCTGGATTAGGGTATCGGATAC Y 2 1 2 1 101000 f 74 goat snp13028-scaffold150-2135081 13 49294016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396816 Affx-122963282 AX-123267171 13 48131781 TAAAAATAAGGGAAAGAAGAAAGTGAACATTCTAG[A/G]ATAGGTGAAGGATTTGAATGATACTTGAGAATGTC R 2 1 2 1 201000 r 74 goat snp13030-scaffold150-2216985 13 49376986 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398658 Affx-122961889 AX-123269013 13 48162003 CAGACAGCTCTGCCTATAGATGCTCATTCATGATT[C/T]GGGGAAGCTCAGCACAAGAACCAGAGCTAAGACGG Y 2 1 2 1 101000 f 74 goat snp13031-scaffold150-2247207 13 49406577 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437607 Affx-122931855 AX-123307945 13 48260082 TGGGTGTTTTAGTGCCAATCTTCTCTCATTTATAT[A/G]TCTATGTATAAAATTCTGCTTTACTCCAAATTCCA R 2 1 2 1 101000 f 74 goat snp13032-scaffold150-2345286 13 49505629 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414445 Affx-122949950 AX-123284794 13 48293313 CAACGTGGGATGGCTCCTCTAGGCCCTCCTGCGCC[A/C]GTGTAGGCACCGCTCCAGAAACAGTTCTAATGACT M 2 1 2 1 101000 r 74 goat snp13033-scaffold150-2378517 13 49539341 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425823 Affx-122940684 AX-123296169 13 48334261 TGCTGATCCAAAAGCCTATAAAAATGTCATTTTCA[C/T]ATGACTTGTTGGAAGGTAAGGGGCATGAGCCATTT Y 2 1 2 1 303000 f 74 goat snp13034-scaffold150-2419465 13 49580527 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395986 Affx-122963509 AX-123266341 13 48403697 GTTTTGGTTCCCCTCCCAGGTATAGAACCAGAGCC[A/G]GCTGAAGTGCATCCATCCTGAGGGCAAAGAGTGCT R 2 1 2 1 201000 r 74 goat snp13035-scaffold150-2488901 13 49652061 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770233 Affx-122929965 AX-385257399 13 48452265 TCATTTATATTCTTATCTATTCCAGAAGTATAGAA[A/G]CACTCCGACAAATGATTTACCATTTCTAGACCAAG R 2 1 2 1 101000 r 74 goat snp13036-scaffold150-2537469 13 49701677 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777248 Affx-122949806 AX-385264371 13 48531810 TACCCTTGATGGGGCAATCTGATGAAATATATTAA[C/T]GTTTCATTGAACATGCACAGAAACAAATATTCTTA Y 2 1 2 1 202000 r 74 goat snp13038-scaffold150-2617014 13 49781608 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377103 Affx-122978260 AX-123247462 13 48567198 CTTAACTCTAGTGCTTCTTTCTTCTTTAAGTGTAA[A/C]TTATCCTCTCTACTAGATTTTTTCCATCAGTACAA M 2 1 2 1 101000 r 74 goat snp13039-scaffold150-2652402 13 49817487 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803249 Affx-986696246 AX-385290102 13 48571567 TGCGGATCAAATAACAGTTTTATACCAATCGTTCT[C/T]GAACTAGTCCCACTAAAATACTTTGAAAAATGATC Y 2 1 2 1 600010 f 74 goat 13_48571567 13 48571567 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 320763079 Affx-986697608 AX-385251044 13 48571637 CTGCATCAATATTATAAAATCATCAAGAAGCTATG[C/T]CAGCGTTAACCTTTTAAGTTAAAGACTGAGAGCAT Y 2 1 2 1 600010 f 74 goat 13_48571637 13 48571637 Ancestral_priority_1043 ancestry 0.69 recommended IMAGE 10K 10K ancestral 320765801 Affx-986697612 AX-385253255 13 48572022 CAACAATGAATACTTCAACTTGTATCAAAACAAAT[A/G]ATAAGTATTCACAACACCAAAGGACAAACATGAAC R 2 1 2 1 600010 r 74 goat 13_48572022 13 48572022 Ancestral_priority_1043 ancestry 0.684 recommended IMAGE 10K 10K ancestral 38388043 Affx-122969543 AX-123258401 13 48602812 TTATAGGCACCCATTTTCACTCTCACTTGAATATA[C/T]GACAACCTAAGTGTCCAGAATAAAACAGATTAAAT Y 2 1 2 1 101000 f 74 goat snp13040-scaffold150-2688016 13 49846156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393151 Affx-122965544 AX-123263508 13 48638726 ATTCCATATGTGTGTGTGTAATCATGTTTGTGTGC[A/G]TTTTAAACTAATAGACTATATTTTTAAAAGAGTCT R 2 1 2 1 303000 r 74 goat snp13041-scaffold150-2723930 13 49882074 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse614 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320779614 Affx-122948703 AX-385266716 13 48686858 GTGTAAGTGGAGTGTAAGTGGCAACAGAAGACAAT[A/G]TTCTAAGAACAACTATTTTCTCCTATCATGTGATC R 2 1 2 1 201000 r 74 goat snp13042-scaffold150-2772062 13 49930593 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427298 Affx-122940152 AX-123297641 13 48727169 ATTTCCACCAGATCCATCAGTGGTGAATTTGCATA[C/T]TGAAGTTTGAGAAACATAAAACATTAGTTTCTGTT Y 2 1 2 1 101000 f 74 goat snp13043-scaffold150-2812373 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781713 Affx-122960898 AX-385268794 13 48823695 ATTAGCAAAGCTAGGATGCCATTTCTTTTGATTCT[A/G]TTAAACAAAGTTTGTTAACTTTGTCCACACACTAG R 2 1 2 1 102000 f 74 goat snp13045-scaffold150-2908899 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768496 Affx-122973185 AX-385255676 13 48870168 CTGTCTCATGTTCAGAAATATATGACCAAAATGGA[C/T]ACTGCTAAACACTGGCCAATAAAATATATGTGGGG Y 2 1 2 1 101000 r 74 goat snp13046-scaffold150-2955372 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412987 Affx-122951026 AX-123283336 13 48913673 TTCCATCTTAGTAAAAATGAGAGGTTCTACCAGCT[A/G]CAGATTAAATAGAAACTCAGACTGTATTTGATGAA R 2 1 2 1 101000 f 74 goat snp13047-scaffold150-2998877 13 49975754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408456 Affx-122954439 AX-123278807 13 48970668 TTTTACTGGGTATATATTATGCAGAATAATTCTGA[C/T]AAGAGCAGATAAAATAACTAAATATAGTGAACAAG Y 2 1 2 1 101000 f 74 goat snp13048-scaffold150-3055872 13 50031215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801928 Affx-122921809 AX-385288833 13 49000315 AACTGAAGGTTATATTATCTATGGATAATTAATCT[A/G]TTTCCTCCAAGTGTTCCTTTGAGAATTTCTCTCTT R 2 1 2 1 201000 f 74 goat snp13049-scaffold150-3085519 13 50061091 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449915 Affx-122922325 AX-123320250 13 49042684 ATTTTAAAAGAGAGGAGATAATTTTCAATTATCTG[A/G]GCAAGTCCTAAATGTAATCATAAAGGATTTTTTGA R 2 1 2 1 303000 f 74 goat snp13050-scaffold150-3127888 NW_017204967.1 4122 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375381 Affx-122979221 AX-123245740 13 49101200 GAAAACTCAAATATTGACCTGAGCTGCTGTGGTAA[C/T]GAGGAGAAAAATGTAGCAGTGTGGGGTTTTTTTGG Y 2 1 2 1 201000 f 74 goat snp13051-scaffold150-3186404 13 50164079 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418323 Affx-122946969 AX-123288671 13 49154907 CAAATGAGTGAGTACTTGCTGAAATAAAATGAGTC[A/G]TGTGTAAAGTACTTTATACCATGCCAGATATATAG R 2 1 2 1 101000 r 74 goat snp13052-scaffold150-3240111 13 50218538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441344 Affx-122928883 AX-123311681 13 49183741 ATTCCTCTGGGAGAGAGCATGACCCACCTCAGACT[A/G]TAACAACATCTGGTGGGTCTCTACTGCCTAAGGCA R 2 1 2 1 101000 r 74 goat snp13053-scaffold150-3268945 13 50247634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391408 Affx-122966774 AX-123261765 13 49217446 AGAGTACAAACAAGAGACAGTGGGGAGGCTGCTGA[A/C]TTATTCAAGGAGCGAGATGATGGTGTCTCAGACAG M 2 1 2 1 201000 r 74 goat snp13054-scaffold150-3302650 13 50281022 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400613 Affx-122960383 AX-123270968 13 49256593 TATCTTTCTATGAATGGTGGTTAGTGCCACTATAC[A/G]TATGTATGCATAAACACCTCTATAACTATTCCTGG R 2 1 2 1 101000 f 74 goat snp13055-scaffold150-3341797 13 50320022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417308 Affx-122948162 AX-123287656 13 49305074 TAATGAAACTTTATCCCTTGACCACCCTCCAGAAT[C/T]GACTGATCTGTTTTCTGTCCCTATAGTTTTACCTC Y 2 1 2 1 101000 f 74 goat snp13056-scaffold150-3390278 13 50368909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406451 Affx-122955187 AX-123276803 13 49338306 CCCAAGGGCAGGAGGTCAGGAATGGTAGAGCAGAG[A/C]GCCACAAGCAAGCCAGGTCTCCCATCCCTCATTCA M 2 1 2 1 101000 r 74 goat snp13057-scaffold150-3423510 13 50402328 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse615 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38431712 Affx-122936762 AX-123302053 13 49371582 TACATAAAACCTTTCCTCCTTGTGAATCATTTCTT[A/G]CAAAGCTGCCTTCCTGCTAGATTCCACCCATCAGG R 2 1 2 1 101000 f 74 goat snp13058-scaffold150-3456786 13 50435750 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405390 Affx-122956297 AX-123275742 13 49403109 ACTCTTGTTGGTGGATTTCCAAGAGTAAAAGAATA[C/T]AGTCCATGTCTTCTCAGTGATGAGGAAACCACTGT Y 2 1 2 1 201000 f 74 goat snp13059-scaffold150-3488313 13 50467342 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381573 Affx-122974812 AX-123251931 13 49471937 AGGTATTGTTTAATCTGAATTTATAGAAATCCCAC[A/G]TCTCATGGTAAGACACTCTTGTTGAATAACTCCAC R 2 1 2 1 101000 r 74 goat snp13060-scaffold150-3557141 13 50537426 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778467 Affx-122949281 AX-385265580 13 49517632 AGGTATGATGAGCAACTTTATCACTATAGCGTATC[A/G]CCTAAAGAAGGGGGCAACCTTCGTTCATGGTATTT R 2 1 2 1 102000 r 74 goat snp13061-scaffold150-3602836 13 50583540 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276875 Affx-1111835564 AX-519550384 13 49548370 TCACATGGATCACACTCCCCAAGGTGGACCAACTC[A/G]TGTCGTATGTCAAATCATTGTTGAATAAAGTAAGA R 2 1 2 1 201000 r 74 goat Random2.2K-1353 13 49548370 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447551 Affx-122924040 AX-123317887 13 49586129 CAGCCAAAGGACTGAAAGTGGCCAGGGGACTTCCC[C/T]GGTATCCAGTGGTTAAGATTCCACCTTCCAACACA Y 2 1 2 1 103000 f 74 goat snp13062-scaffold150-3671333 13 50652685 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389803 Affx-122968204 AX-123260160 13 49625448 TACCATAGTGCACGGTAGGAAGCAAGGGACCTTAA[G/T]GCCTGAATAACTCCATCCCAAGGAGACTCCTATAA K 2 1 2 1 201000 f 74 goat snp13063-scaffold150-3710652 13 50692078 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390696 Affx-122967944 AX-123261053 13 49685898 GAGAGGAAAGAACAATCGAACCCTGGAAGGTCAGC[A/G]TCACTGAGGACTGGGACAGGGCCTTTGGATTTTAA R 2 1 2 1 101000 f 74 goat snp13064-scaffold150-3771102 13 50752928 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 coat-colour SNP associated with coat colour multi-breed 320796328 Affx-122965189 AX-385283278 13 49768890 GATGCTCAATAAAACGGGCTCTAGTATCATGACAG[C/T]ATCACAACCATGGCAAGATCTTCCCTCTTCTGCTT Y 2 1 2 1 101000 f 74 goat snp13065-scaffold150-3854094 13 50835713 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416123 Affx-122948299 AX-123286472 13 49828571 GGCTTCACTAGTGTTTAGAATGTTTTGTGCACAAA[C/T]TCAGTTATTGAAAGTCAATTCCATTATTGCCTTTA Y 2 1 2 1 101000 r 74 goat snp13066-scaffold150-3913775 13 50895072 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433209 Affx-122935629 AX-123303550 13 49879477 TGGAAAGACTGATTCCCCCGTGTCGTTTCTTTCTC[A/G]CTCCCCGTTTTCCTGGCTGAATTCCCATCTGAAAT R 2 1 2 1 103000 f 74 goat snp13067-scaffold150-3964681 13 50946271 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400514 Affx-122961270 AX-123270869 13 49917322 GATATTTTAACTTTTGCTAGTTACAAAACAAAATG[C/T]ACAGTATTTCCATTCTGGGGAGGAAAAAATAAACA Y 2 1 2 1 201000 f 74 goat snp13068-scaffold150-4002526 13 50984436 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789606 Affx-122969430 AX-385276615 13 49955689 GAAGAAGGGATAGGATGTTTGTTCAACAAGTTTTT[A/G]ATATGAAGACAGAACTCTAGGAACCCAATGACCAT R 2 1 2 1 101000 r 74 goat snp13069-scaffold150-4040893 13 51022681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386346 Affx-122970867 AX-123256704 13 50023944 GTTTACCAAGTTAAACAGGCTGAAGCCAGATCAGC[A/G]TATCAAAAATGGCTCAAGTAACAGGGAGAGTCCAG R 2 1 2 1 101000 r 74 goat snp13070-scaffold150-4109148 13 51091041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272748 Affx-1111832986 AX-519546446 13 50067514 CCTCAATTTGACACCCTGAATGTTGGAATCTATAG[A/G]TTAGCCTTTGACTTCTTGCTGTCACACTTTGATAT R 2 1 2 1 101000 r 74 goat 13_50067514_AF-PAKI 13 50067514 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412876 Affx-122950431 AX-123283225 13 50076658 AAAATCCAGCACAATTAATTTAAAAATATGCATGC[A/G]TGGCATAGCATCATGACATTTTTGAGCACTATAAA R 2 1 2 1 101000 r 74 goat snp13071-scaffold150-4161862 13 51144969 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427117 Affx-122939662 AX-123297460 13 50112920 TACAGATATAACTTAATTTTTTAAACTTCTCTTTT[A/C]TTGATGCTTATACCCAGAGGAAAACCCGTAACTCA M 2 1 2 1 101000 r 74 goat snp13072-scaffold150-4198124 13 51181284 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794058 Affx-122923406 AX-385281026 13 50180099 GCTTTACAGATGTTGCTGTACTCTCCTGTCTTCTT[A/G]CTTACATTATTTCTGAGCAGAAGTCTACTGTCATT R 2 1 2 1 101000 f 74 goat snp13073-scaffold150-4265303 13 51248503 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774884 Affx-122962164 AX-385262018 13 50209993 TGCAAGTTTGTGTGTTCTGAGTATTTTCTTTGCAG[C/T]TCTTTAAAGTGAGTAGCTTAATGACCCTCTAACCT Y 2 1 2 1 101000 f 74 goat snp13074-scaffold150-4295197 13 51278398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274014 Affx-1111833951 AX-519547618 13 50242906 CTGCAGATCCCAGCCTTTGGCCAGATGCATTATCT[A/G]TAGATAATAATATATGAGCCCCTTGTGACTTGCTG R 2 1 2 1 101000 r 74 goat GoatD01.011449 13 50242906 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38376112 Affx-122978882 AX-123246471 13 50264977 TTCAAGGCAGCTATTCCCAATTTATTATGGAAGCA[A/G]GTACCTTCTGGAATTTTTATTTGCTGTATTTAAAA R 2 1 2 1 101000 f 74 goat snp13075-scaffold150-4350181 13 51333112 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434584 Affx-122934111 AX-123304925 13 50326724 CTTGAGTTCAATCGATACCCAGAACACCTGCTCAC[A/G]TGCTTGCTGGGCCTGGCGTTTTCTGAGTACTTTCC R 2 1 2 1 101000 f 74 goat snp13077-scaffold150-4411928 13 51395028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427307 Affx-122940144 AX-123297650 13 50430821 AGAGAGTGTGTGAACATAATAAGCACTATATGAAC[A/G]AAGACTGGGCCACTCTGTAATACTGGGACAGGTGG R 2 1 2 1 101000 f 74 goat snp13079-scaffold150-4516025 13 51495761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446487 Affx-122925052 AX-123316823 13 50477163 CTCTTTTTATTCTTTTATGCTCTGTCAATTAAAAC[A/G]CCAGCTCCTGCTGTTCAAAAACATATCAAAGATCA R 2 1 2 1 101000 f 74 goat snp13080-scaffold150-4562367 13 51542031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802172 Affx-122942417 AX-385289076 13 50515650 TAAGGAATACAAAGAAACCTGACGTGCTCTCTCTT[A/C]TGTGTTTCTTTCATTACTTCCCATTCCATCTCCAC M 2 1 2 1 101000 f 74 goat snp13081-scaffold150-4600854 13 51580534 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789790 Affx-122952558 AX-385276797 13 50585249 TTCTGTATCCTAAGCACTTTGTCTGGCAAATAGAA[C/T]GCCATGAATGTAGTACAGTCAGAGAAGTGGCTTTT Y 2 1 2 1 101000 r 74 goat snp13083-scaffold150-4670453 13 51650515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416753 Affx-122948189 AX-123287101 13 50666960 TCGGGCTCTAGAGCTTAGGCTCAATGTAACCATTA[C/T]GGTGCATGGGCTTAGTTACTCAGCTGTATGTGGAA Y 2 1 2 1 102000 f 74 goat snp13084-scaffold150-4752164 13 51732144 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414634 Affx-122949333 AX-123284983 13 50755484 CAACTGGTGAGATGATGGCACTTCAGGAAGAGTAA[A/G]AAAGGAGTATCCCCCTCACCTGCTCCCCTTGGTGC R 2 1 2 1 101000 f 74 goat snp13086-scaffold150-4840688 13 51821265 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448707 Affx-122923855 AX-123319043 13 50796568 TTAACGTCTTCAGTGTCGGACACACGATTGTTCAG[C/T]GAGAATTGATGAAAAGAATAACAAATACGAGGACA Y 2 1 2 1 101000 f 74 goat snp13087-scaffold150-4881772 13 51862607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381079 Affx-122974607 AX-123251437 13 50896932 TCTCAAGGTTATGCATGTAATGTAGCAGCCACAGA[A/G]AGTTTTCCTCACTGCTTCCCTGATCCCTGAGCTTT R 2 1 2 1 101000 f 74 goat snp13090-scaffold150-4982136 13 51962771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276077 Affx-1111835229 AX-519549629 13 50905594 CACGGCTCCAGGGCAATGGGCTTGGGAACAGTCTG[A/G]TCGAAGAAAATAAAGAATTACCTAAAATGGTGTTC R 2 1 2 1 202000 f 74 goat ilmnseq_rs666359849 13 50905594 G A 2 neutral Goat_IGGC_65K_v2 Illumina 468275801 Affx-1111835092 AX-519549365 13 50905596 GGGAACACCATTTTAGGTAATTCTTTATTTTCTTC[A/G]ACCAGACTGTTCCCAAGCCCATTGCCCTGGAGCCG R 2 1 2 1 202000 f 74 goat ilmnseq_rs649971158 13 50905596 C T 2 neutral Goat_IGGC_65K_v2 Illumina 38387570 Affx-122970278 AX-123257928 13 50926071 AAAGGGACCCAGGTTAGAGCCACTTGCTCAAGGAG[C/T]GAGAAAAAGAGAACAACATAGGTACTTTAAAACTC Y 2 1 2 1 101000 r 74 goat snp13091-scaffold150-5011275 13 51992064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276043 Affx-1111835135 AX-519549597 13 50957280 CAACAGGCATCTCTTCTCCAGCTTGGGTTCCAGCT[A/G]TTAGGAAGAATAGAATGAAATAAGAGATTTTTTTC R 2 1 2 1 201000 r 74 goat ilmnseq_rs655826019 13 50957280 A G 2 recommended Goat_IGGC_65K_v2 Illumina 468275876 Affx-1111835128 AX-370815643 13 50961155 GATGACCGCTATTACACAGCCATCAATTTTGTGGC[A/G]ACACCTGATGAAGTAAGATATAAAAGTCTTCTTAG R 2 1 2 1 101000 f 74 goat ilmnseq_rs655099833 13 50961155 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275600 Affx-1111834990 AX-519549170 13 50968855 TGCAATGGGCATGCGTCACTATGCAATACCAACAC[C/G]GGCAAGTGCTTCTGCACCACCAAGGGCGTCAAGGG S 4 1 2 1 101000 f 74 goat ilmnseq_rs637215083 13 50968855 G C 1 recommended Goat_IGGC_65K_v2 Illumina 468275928 Affx-1111835079 AX-519549486 13 50971981 TTCTATGGTGATCCAACCAACGGTGGAAAATGTCA[A/G]CGTAAGTCAAATTTTTCAGGGTCACTGATTGCAAA R 2 1 2 1 101000 r 74 goat ilmnseq_rs648822360 13 50971981 T C 1 recommended Goat_IGGC_65K_v2 Illumina 38436825 Affx-122932229 AX-123307163 13 50975896 GGCCCCCAGCTCCCAAGGCCCCTTCCTGTTGCTCA[A/G]TCTTAAGGAAATGGCTGCCTCCTCTGAACCTCCAC R 2 1 2 1 101000 r 74 goat snp13092-scaffold150-5061100 13 52042269 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276120 Affx-1111835177 AX-519549670 13 50980365 TACAGGAAATTCCTACCCACAGCCTCTTCTCAATT[A/C]CAGCATGTGTCTGGAGGACAGCAGATATAACTGGT M 2 1 2 1 102000 r 74 goat ilmnseq_rs660195053 13 50980365 G T 1 neutral Goat_IGGC_65K_v2 Illumina 468275724 Affx-1111834976 AX-519549292 13 50981158 AAAGGGAAGGAGGCCACGTAGGCATTGGAGTCCAC[A/G]CACTGCTTCATGTTGCTGCACCACATGCACTCCGA R 2 1 2 1 202000 r 74 goat ilmnseq_rs636124223 13 50981158 A G 2 neutral Goat_IGGC_65K_v2 Illumina 468275981 Affx-1111835103 AX-519549538 13 50981270 AAGGGGTCCGACACTGCTTGGCACTGTGGTTAGCT[A/G]GGAAGTAAACCCAAGAGAGACATTTAAAGCTCCCA R 2 1 2 1 101000 r 74 goat ilmnseq_rs651849368 13 50981270 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275983 Affx-1111835185 AX-187659409 13 50983654 GTACTGGGTTCTGACAAGATCCCACAGAATCCAGC[A/G]TCACTGGGCTCAGACGGCATCCACTGTAGTGAACT R 2 1 2 1 102000 f 74 goat ilmnseq_rs661547639 13 50983654 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275903 Affx-1111835142 AX-519549461 13 50983681 TGGGAAGATATGTCCCCGTTCACAAATAGTTCACT[A/T]CAGTGGATGCCGTCTGAGCCCAGTGACGCTGGATT W 4 1 2 1 101000 f 74 goat ilmnseq_rs656081983 13 50983681 T A 1 recommended Goat_IGGC_65K_v2 Illumina 468276153 Affx-1111835266 AX-519549703 13 50983780 CAAGACATTGATTATATTCATAGTCTGTTTTGCCT[A/G]CAGTCCAAGCTCACCTTAACCCCATGGGTTGGCCT R 2 1 2 1 201000 f 74 goat ilmnseq_rs669293499 13 50983780 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275753 Affx-1111834991 AX-519549319 13 50987535 CTAGATCTCCATTTTCAAGTATGATCAGTGCCCCA[A/G]GGATAACCCGATGTATTATTGTAACAAGAAGACCA R 2 1 2 1 101000 r 74 goat ilmnseq_rs637571634 13 50987535 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275922 Affx-1111835152 AX-519549480 13 50988486 AACTGACCTGGCCTTCTGTGCAGCTGTGGTTCATA[A/G]GGACACAATGGTCATTGCACCACTGGCAGCCATTG R 2 1 2 1 102000 f 74 goat ilmnseq_rs657289384 13 50988486 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275740 Affx-1111834984 AX-519549307 13 50992176 TTTTAAGAAGAGGAACAAAAAAACATACCTCTTTT[A/T]GAAAAACATTCTGACTTTATCTTTTCTTGTGCTTC W 4 1 2 1 102000 r 74 goat ilmnseq_rs636693570 13 50992176 T A 1 neutral Goat_IGGC_65K_v2 Illumina 468275784 Affx-1111835083 AX-519549350 13 50992335 GGTGGTTTTAATAGTCTCCTCCTCAGTGACATCCT[A/T]GTATTCACATCGGAACAGTGTGAAGCACACCAGAG W 4 1 2 1 101000 f 74 goat ilmnseq_rs649409970 13 50992335 T A 1 recommended Goat_IGGC_65K_v2 Illumina 468276069 Affx-1111835150 AX-519549621 13 50999495 ACAAGGGCACCCTGGGTGTGTAATATACTCCACGT[A/G]TTCTTATCTGGAAAGAGAGCAAACAGTTCAAGGCA R 2 1 2 1 101000 r 74 goat ilmnseq_rs656947120 13 50999495 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276197 Affx-1111835216 AX-519549747 13 51016255 TTTTGTTAGGTCCTGGATGTTCAGTTCCTGTACCA[A/G]CTAATCAGTCATTTTGGACACGAGAGGAATATTCT R 2 1 2 1 101000 r 74 goat ilmnseq_rs664393015 13 51016255 C T 1 recommended Goat_IGGC_65K_v2 Illumina 38398660 Affx-122961887 AX-123269015 13 51018072 GACTCTGAGAGGGAAGTTCTTGCCCAGTAAGAAAG[C/T]AAGTTCCTCTTCTACTCTCATCAGGAGAACTTGTT Y 2 1 2 1 101000 f 74 goat snp13093-scaffold150-5103276 13 52084337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409063 Affx-122953349 AX-123279414 13 51086182 AGACAAAGCAGTCCCCATGTCTCTGGGGACTGTCC[A/G]TTTCTTTTTTCAGAGGATGTTTCCTGCTTGCGCTT R 2 1 2 1 101000 r 74 goat snp13094-scaffold150-5171386 13 52152409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399747 Affx-122960324 AX-123270102 13 51148863 TCTTCATAGTACAGCAACATCTATTTTAGTTACAA[C/T]GAAATTTCTAAAACTATCTAATTTTTAAAAAAACT Y 2 1 2 1 101000 f 74 goat snp13095-scaffold150-5234067 13 52215465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse616 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320795168 Affx-122943321 AX-385282126 13 51198145 GCATCTTATCATGGAAAAGATATGCCCATGCAAGT[G/T]CAAGATTTTGACTCATGAGGAGCTTCACTGAACAT K 2 1 2 1 101000 r 74 goat snp13096-scaffold150-5283349 13 52265216 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405108 Affx-122956979 AX-123275460 13 51233754 TGCCTCATCTTGTCTCCTGCATGATTCTGCTGCCT[A/G]ATACTAAAATCAGCTCACCATTTCGGGTCGGTCAC R 2 1 2 1 101000 r 74 goat snp13097-scaffold150-5318958 13 52300672 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452138 Affx-122921673 AX-123322471 13 51291926 AGAAGCAGAATGACTGCAGCTATGTGAATACAGAA[C/T]AGGAGGCAGTCCTGCCTGAGGAGTAGGGTAAGGTG Y 2 1 2 1 101000 f 74 goat snp13098-scaffold150-5377130 13 52358598 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430577 Affx-122937002 AX-123300918 13 51323983 ACCCGGGATTGAATACTCTACAGAAACTGTATCTG[C/T]GAGGGCCCAGATTTAGTGGCCACGGTATAGGGGAA Y 2 1 2 1 101000 f 74 goat snp13099-scaffold150-5409187 13 52391019 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398118 Affx-122961703 AX-123268473 13 51352661 AACTGAGCAGCGTGTCACAATCAGCCCTTGGCAGC[A/G]TGGGGCAAGGTAGAGCTTAAGAGCAGGGGCCCTGG R 2 1 2 1 101000 f 74 goat snp13100-scaffold150-5437865 13 52420213 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402349 Affx-122959057 AX-123272702 13 51447700 TTAAGCCTCAAAATAGTCTTCACATTTTACAGGTG[C/T]AGAAATTGAGACTCAGAGAGGTTAGACAACCTACC Y 2 1 2 1 201000 f 74 goat snp13101-scaffold150-5532904 13 52515229 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425504 Affx-122941475 AX-123295850 13 51491777 ACATTGTAATTTCCAAGAAAAGGAGACTGTTGATC[C/T]CAAGATGATGAACTTATGATGACCACACCTACATA Y 2 1 2 1 101000 r 74 goat snp13102-scaffold150-5576981 13 52559212 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775532 Affx-122974292 AX-385262663 13 51567107 CCTGTGGCCTTTGGCACCTCATCTAAACTTCTTCA[C/T]ATAGAAGATGGGATTCAGAGTAATACCTGCCTCAT Y 2 1 2 1 101000 f 74 goat snp13103-scaffold150-5652311 13 52634552 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802381 Affx-122940450 AX-385289285 13 51619582 AGGCATACAAATATTAGTGTTATCTCAAGTCTTTT[A/G]TAAATTTCCCTCTTAAATACTCTGTATCATATTTA R 2 1 2 1 303000 r 74 goat snp13104-scaffold150-5704786 13 52687015 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427823 Affx-122939745 AX-123298166 13 51676407 CCTGGGTTGAGAGGGCCTTCCTACTCACTCAGACC[A/G]TCCTGTTCAGACCAGAGCTTCATCACTGGGGAAAT R 2 1 2 1 101000 r 74 goat snp13105-scaffold150-5761611 13 52744318 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408693 Affx-122953441 AX-123279044 13 51731064 TACTCTGCGAAATTCTGAAAGAGGAACCCCGAGGA[C/T]ATGAAGTTAGAATTGCACCAGGCACCCAGGTGACT Y 2 1 2 1 201000 r 74 goat snp13106-scaffold150-5816268 13 52799552 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse617 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38381117 Affx-122974579 AX-123251475 13 51802338 ACAGAGAGTGTTTCAGAAAGGACTGAGTTAACTAA[A/G]AATAAAGGTCAGAGATAATGAGGACACTGGAAGCA R 2 1 2 1 202000 f 74 goat snp57653-scaffold924-31639 13 52871209 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775468 Affx-122934285 AX-385262599 13 51831711 GAAGTCACCATTAAGTTTTAAATGATTCTCAGAAT[A/G]CAGGGACTAAAGTGATGAGCATGTTTTAATTCATC R 2 1 2 1 101000 r 74 goat snp57654-scaffold924-61012 13 52900582 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409676 Affx-122953071 AX-123280027 13 51897980 CCTGTGAAACAGCACTTGGATTATCCCTTTAGTTA[C/T]AGCATCAAATACATATGGCACTGACTGTGTACAAA Y 2 1 2 1 101000 f 74 goat snp57656-scaffold924-127281 13 52967113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378561 Affx-122976605 AX-123248920 13 51926944 GCCCAGGGTCTGGACTGCCCCTAGTGTCATAATCA[C/T]AGGACACGTGGGGACTGTGAGTGGGGACGTGTCCC Y 2 1 2 1 101000 f 74 goat snp57657-scaffold924-156245 13 52996105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397841 Affx-122962468 AX-123268196 13 52093220 CAAGTCCGCGGTGCAGCACTTTCAGCTGAGGCTCC[A/G]TGGGAAGGTGCAATCTGTGGGGAGTCTTGTTCCAG R 2 1 2 1 101000 r 74 goat snp1640-scaffold10469-208327 13 53160981 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409624 Affx-122953541 AX-123279975 13 52247422 AGGGCAATCTGCCCAAAGCCGCCCAGGCCCCACCC[A/G]CCATGTGTCCATCTTCATGGCAGCTCCGGTTGCTT R 2 1 2 1 101000 r 74 goat snp1639-scaffold10469-54125 13 53305623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418414 Affx-122946540 AX-123288762 13 52357979 TCTGAAACCATATCAATAAACTTCATACTCTTACA[C/T]TGGATAGAGGGGTGTGTACTGAGCTTGAATACAAC Y 2 1 2 1 201000 f 74 goat snp3082-scaffold10942-56333 13 53415593 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407463 Affx-122954778 AX-123277814 13 52441420 GGAGACCAGGGCTTGGCAGATTGTCTCTGGCCGCC[C/T]GTCTGGAGACCTCAGGCCTCCTTGTAGGATTTCCC Y 2 1 2 1 303000 f 74 goat snp3083-scaffold10942-139774 13 53499191 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385856 Affx-122971618 AX-123256214 13 52485704 GGTGACCTGCGTGCCGCCCGTTTTCCAGGGACAGC[C/T]GCCCAGGGAAAGAATCTAGTTTTCTACGGACCAGC Y 2 1 2 1 101000 r 74 goat snp3084-scaffold10942-184058 13 53543394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803251 Affx-986696247 AX-385290104 13 52552851 GTCCTGGAATATCCTGTCAAGTCCAAGCTTTCAGG[C/T]CCATCAGCAGAGCAAGTGCCCACCTTCAGGAGCCC Y 2 1 2 1 600010 f 74 goat 13_52552851 13 52552851 Ancestral_priority_1043 ancestry 0.618 recommended IMAGE 10K 10K ancestral 320763090 Affx-986697619 AX-385251048 13 52555325 GTCGCCCTGTTCTCCTTTCCGGAACTTCACACAGT[A/G]GTAGACACCAGTGTCTGCTGGGGTGATGTTACTGA R 2 1 2 1 600010 f 74 goat 13_52555325 13 52555325 Ancestral_priority_1043 ancestry 0.668 recommended IMAGE 10K 10K ancestral 320763092 Affx-986697621 AX-385251050 13 52555345 GGAACTTCACACAGTGGTAGACACCAGTGTCTGCT[G/T]GGGTGATGTTACTGATGCGGATGGAAAAGTCCATG K 2 1 2 1 600010 f 74 goat 13_52555345 13 52555345 Ancestral_priority_1043 ancestry 0.586 neutral IMAGE 10K 10K ancestral 320765821 Affx-986697623 AX-385253268 13 52555356 CAGTGGTAGACACCAGTGTCTGCTGGGGTGATGTT[A/C]CTGATGCGGATGGAAAAGTCCATGTTGTATCTCTT M 2 1 2 1 600010 r 74 goat 13_52555356 13 52555356 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 320763096 Affx-986697625 AX-385251054 13 52555385 GATGTTACTGATGCGGATGGAAAAGTCCATGTTGT[A/T]TCTCTTTGTGGCATCTGCAACACTTGTTACTCGGG W 4 1 2 1 600010 f 74 goat 13_52555385 13 52555385 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38399069 Affx-122960893 AX-123269424 13 52557686 GGCAGGCTCCAGGAAGGAATCACGTCCTTTCTCTC[A/G]GTGGTTTTCTCTCACTCAAGCACCCTCCTGAAGCT R 2 1 2 1 101000 r 74 goat snp3086-scaffold10942-256040 13 53615692 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444135 Affx-122926803 AX-123314472 13 52600416 ATCTTAGTGCCTGGAAGGGCAACCTGGAGAGGGGG[A/C]TCCATAGATTGGGTGCACCTTGGGCTTAGCTTGAC M 2 1 2 1 201000 r 74 goat snp47987-scaffold677-32710 13 53941885 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773475 Affx-122969612 AX-385260617 13 52639190 GAAAGAGATTAGATGATGAACAGCGAGACTGACAA[C/T]ACCCATGGTCTTTCCCCAACAGGCTTCCAAATGCA Y 2 1 2 1 101000 r 74 goat snp47988-scaffold677-71484 13 53980640 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272750 Affx-1111832987 AX-519546448 13 52649906 AAAGTGTTTCTCACTGCTTTTGGGTAGACAGAGAA[A/G]AGACTGGCTCATTTTAGCCACGTGAAGAGTTTGTG R 2 1 2 1 101000 r 74 goat 13_52649906_AF-PAKI 13 52649906 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38379740 Affx-122975870 AX-123250098 13 52679327 CTATCTCACCTCCTCCAGGAAGTCCTCCAGAACCA[C/T]ACCTCCTGTCTTCCCTCTTCTTTGCCCCTGGAAGC Y 2 1 2 1 201000 r 74 goat snp47989-scaffold677-111621 13 54020822 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414038 Affx-122949787 AX-123284387 13 52773891 ACGAACCTATGTGTCCACAGTGACTTGTACACCCA[C/T]GTGGCCCCCCAGCCCCTCCCCATTGTACCTCTGGA Y 2 1 2 1 101000 f 74 goat snp47990-scaffold677-206185 13 54114268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396047 Affx-122963457 AX-123266402 13 52810257 CTTCTAAGCAGGAGAGACCTGTTTGCATCAGGGTC[A/G]CAACCATGTGTGCACCCAGATCTTAGGACTGAGCC R 2 1 2 1 101000 f 74 goat snp47991-scaffold677-242551 13 54148637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420020 Affx-122945157 AX-123290368 13 52871209 GGTGGAATTCCAGAGATGACTGCCGCATTCACCAT[A/C]TTCCCTTTAGGAAAAGGAGCTTGTTGCTTCTTCCT M 2 1 2 1 101000 r 74 goat snp47992-scaffold677-303503 13 54234782 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426294 Affx-122940302 AX-123296640 13 52950207 AAAGAGACGGACACTGGGCTGTTGCTACATTCAGC[A/G]CCTTGGAGGGCTTGCATGCTTTTAATCCCCCTGCT R 2 1 2 1 101000 r 74 goat snp47993-scaffold677-382501 13 54283366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400244 Affx-122960147 AX-123270599 13 53008495 CTGGAAGTCACAGGGTGTTGTTTTGAGCTCCCATT[A/G]TCTTGTCTTCATTTATCCTTGAAGATGAGGACATG R 2 1 2 1 101000 r 74 goat snp59143-scaffold97-1334327 13 54343975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445464 Affx-122925217 AX-123315801 13 53040550 TATGGCATCAGATGAACAGCACATCAACTATTACC[A/G]GGAGACCCATGGCTCTCTGCTTACGGCTGACACTA R 2 1 2 1 101000 f 74 goat snp59142-scaffold97-1302272 13 54375964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442155 Affx-122928316 AX-123312492 13 53078603 CACCAAGGAAACACCTGCAGGCCTGCTGGCCAGAG[A/C]GCCAGGAGATAGAGTTGGGGCAGTGATACCCTGTG M 2 1 2 1 101000 f 74 goat snp59141-scaffold97-1264219 13 54413988 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387931 Affx-122970029 AX-123258289 13 53108661 GTCGGCACGAGCCACACGATTTATGGACATGATGG[C/T]ACTGATGAAAAAGCAAATGAAGAGAAAATCCTGGC Y 2 1 2 1 201000 f 74 goat snp59140-scaffold97-1234161 13 54443967 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375618 Affx-122978711 AX-123245977 13 53181694 AAGAAATGAGGTCGCTGCAGACACACATCTGGGGT[C/T]GCCTCTCTTTGCAAACTTCCACCCCAATTTTACAA Y 2 1 2 1 101000 r 74 goat snp59139-scaffold97-1161128 13 54517209 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785819 Affx-122963412 AX-385272857 13 53211842 AAGGGTCATTTTGATTCATGAGTGATGCCCTGTGC[A/G]ATACTGGGAACATACGCACAGTAAAGGTGTTGCCT R 2 1 2 1 101000 f 74 goat snp59138-scaffold97-1130980 13 54547771 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406062 Affx-122956248 AX-123276414 13 53272204 GAACCAGTGATGTGGGCTTGGTCACCGGATCAGGG[C/T]CGGGCTGTTGGTTCTGAGAAAGTTGTGACACCTTA Y 2 1 2 1 101000 r 74 goat snp59137-scaffold97-1070618 13 54608139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424963 Affx-122941924 AX-123295309 13 53303214 CATGTATCTGCTCCTCTCTTCATGGTGCTGGGTGT[A/G]TGAGGAGCCCCCGTACCCCGGAGCTGGGAGGGACC R 2 1 2 1 101000 f 74 goat snp59136-scaffold97-1039608 13 54639237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412995 Affx-122951020 AX-123283344 13 53366871 GATGGGCCACCTGCCCAAGCCCCACCCGGGGCACT[A/G]TCCCTCCTCGCCCTTTCTCAAGTGAGAACTCCTAC R 2 1 2 1 101000 r 74 goat snp59135-scaffold97-975951 13 54702701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453251 Affx-122920409 AX-123323584 13 53396908 TGCAACCTCCCCACTGGCCCCCTTTGTTCATGTCA[A/G]TGGTTTAGCACTAGGACGGTGACTCTCCCAAAAGT R 2 1 2 1 101000 r 74 goat snp59134-scaffold97-945914 13 54732713 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783441 Affx-122942330 AX-385270504 13 53428548 TATTCATTGCATGATTGGTGTTCAGAGCACTGTGC[A/G]TAATGAATACATGCAGTTTAATAACTGTTGACATG R 2 1 2 1 101000 f 74 goat snp59133-scaffold97-914274 13 54764358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791906 Affx-122951379 AX-385278896 13 53460986 GCCCTGAGATCGCTTCCGTTGGCATGAATTATGCT[A/G]GCGGCAGAATGTGTACTGGGCTAATTTATTTTAAA R 2 1 2 1 101000 r 74 goat snp59132-scaffold97-881836 13 54796772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274258 Affx-1111834145 AX-519547856 13 53516283 CAGGCCAGTGCCCAGCCTGTAGTAAAGGCCAGTCA[A/G]TGCCAAAGGTCCACTGGATCCCCGGTACTTGGGAA R 2 1 2 1 202000 f 74 goat GoatD01.021356 13 53516283 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38397335 Affx-122963294 AX-123267690 13 53544139 GGAGAAAAAGCAGCAGATAAAACTATAGCAATCCC[A/G]TACCACCTCTGACCTCCCCGCCAAACAGGATTAGA R 2 1 2 1 101000 f 74 goat snp59130-scaffold97-798683 13 54879784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443148 Affx-122928066 AX-123313485 13 53592149 TAGCATTAATATTGACTGTCTATTAAGGAAGCCTT[A/G]TCCACTCAACAGCTTCATTAATAAACCATGAATCA R 2 1 2 1 101000 r 74 goat snp59129-scaffold97-750673 13 54927702 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454244 Affx-122919659 AX-123324577 13 53740306 TGCTTTCTGCCAGAGTTCACAGCCCATCCACCCGC[C/T]GTCCCCATACAGATGTGACTTAAGCATCGAGAATC Y 2 1 2 1 101000 r 74 goat snp59126-scaffold97-602516 13 55074581 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789520 Affx-122965891 AX-385276529 13 53787128 GTTGGGAAAGGCAGCCAAATGTGCTAAAAAGGAAG[A/G]GAAAGTGGGCGTGACTCACCAAAATTAAAGAAACA R 2 1 2 1 101000 r 74 goat snp59125-scaffold97-555694 13 55121535 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448883 Affx-122923264 AX-123319218 13 53828312 ATCACACTTGCACCAGGTCAAGGGCACAGTTCAAC[A/G]ATTTTCAGTGACTTTACCGAGGGGTGCGACCGTCA R 2 1 2 1 101000 f 74 goat snp59124-scaffold97-514510 13 55162605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427565 Affx-122939483 AX-123297908 13 53861010 TCACATCCTCACTGCACACCTTCCATGAGCTTCTC[C/T]GCACTTGGAAGACTTCTTAGAAACGTACAAGGATC Y 2 1 2 1 201000 r 74 goat snp59123-scaffold97-481812 13 55195156 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390995 Affx-122966902 AX-123261352 13 53896082 TGAAGGAGATGGTCTATGACAATCTACTTCCTTTC[A/G]TCCTCTTAGCAAATGTCTTATCAAATGTATTCTGT R 2 1 2 1 101000 f 74 goat snp59122-scaffold97-446740 13 55230229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426172 Affx-122940590 AX-123296518 13 53946366 TTGGAACTTATTGAAAATAACGTAATTCGCTGTAG[C/T]GCATGTTCTCTTCTGAGAATGCTACTATTTGTTTA Y 2 1 2 1 101000 f 74 goat snp59121-scaffold97-396456 13 55279693 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429167 Affx-122937973 AX-123299509 13 54004277 AGGTGACGGTGGTAGTATTGATACCTTGGGCTTTA[C/T]GGATGGTATTACGTCATGAGAGTGGAGCCCTTGTG Y 2 1 2 1 101000 f 74 goat snp59120-scaffold97-338545 13 55337214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388754 Affx-122968949 AX-123259112 13 54042017 CAACCATCGTCCCCATCGTCACTCCTGCCAGTTGA[C/T]AGACGGGTGTGGGGCCATCATTTGTGGCTTTCTGA Y 2 1 2 1 201000 f 74 goat snp59119-scaffold97-300805 13 55373851 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792238 Affx-122920427 AX-385279222 13 54092887 TTCTTCCATTAGTCCCTTCTAAAAAGTCTAGTTTG[C/T]ATTTCAGCCACGAAAAATAGTCTTATATTTTTAAT Y 2 1 2 1 101000 f 74 goat snp59118-scaffold97-249935 13 55424760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395382 Affx-122963972 AX-123265737 13 54197129 TGAGACATGGGGCAGTTGGTGGCCGAGGCAACACA[A/G]CACAGCACTGACCTGCGTGGGACATTTCTCCTGCT R 2 1 2 1 101000 f 74 goat snp59116-scaffold97-145693 13 55529444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426234 Affx-122940346 AX-123296580 13 54229955 GAGAAAATGTACAGTATATTTTTTCTTTACCAAAT[A/G]TATTGCTTTGAATATGTTTTTTTACAGTTAGAGCT R 2 1 2 1 303000 f 74 goat snp59115-scaffold97-112867 13 55562344 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433236 Affx-122935249 AX-123303577 13 54263479 TCCGGTTTGTGTCACATTCAACCAAAAGGGCCCTG[A/G]CTAATACATTAGTCTGTCTCTCGCTCCCCAATCTT R 2 1 2 1 101000 f 74 goat snp59114-scaffold97-79343 13 55595763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425955 Affx-122941176 AX-123296301 13 54326644 CAGCTGTGTGTTATTTATTCTGGGGCAGCTCTGCA[C/T]GATCCATGAGAAAACATTTTCTTTTTCCCCCATGG Y 2 1 2 1 101000 f 74 goat snp59113-scaffold97-16178 13 55659321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386582 Affx-122970696 AX-123256940 13 54393360 AAAATGAATGTGCTCAGAATGGGGCTGGCACAGAG[C/T]GTCCACTGAACCAATTCTGACTAGTATCGAGGTTA Y 2 1 2 1 201000 r 74 goat snp51639-scaffold758-2053604 13 55726105 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401148 Affx-122959374 AX-123271501 13 54474579 ACAGTTCAAGCGATACGTTCAGAATTCTGAAATTC[A/G]TGTCAGCCCCTTTACTCCTCTCAGCTTCGTGTTAC R 2 1 2 1 101000 r 74 goat snp51637-scaffold758-1972385 13 55807681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447359 Affx-122924869 AX-123317695 13 54508110 ACACTAAATGGACCCAGTTATGAAATGTTTGTGCT[A/G]GACGAGAGTTTAGAGATCCTGTAACAGAGGAAGCC R 2 1 2 1 101000 f 74 goat snp51636-scaffold758-1938854 13 55839990 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785487 Affx-122964949 AX-385272532 13 54542370 ATCTGCAAATTAGAATTGTAATAAGAGTTGTCTTA[G/T]GAACCCAGATTCCCAGGCATACATGGTTGTATATC K 2 1 2 1 101000 r 74 goat snp51635-scaffold758-1904594 13 55874257 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401654 Affx-122959579 AX-123272007 13 54662948 CATGATATTCCTTGGTGACTTTTGTCAATGAAATG[G/T]AAAAATGAGAAAACAGAAAGCCCCATCATTATTTC K 2 1 2 1 103000 f 74 goat snp51633-scaffold758-1784016 13 55995332 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419984 Affx-122945181 AX-123290332 13 54766771 ACAGGAACTGGAGGCAGGGAGTGGATGGGTGGAGA[A/G]GGAAACCTTATGCTTTTTCTCGCACCGGGACACCT R 2 1 2 1 101000 r 74 goat snp51631-scaffold758-1680193 13 56099409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383473 Affx-122973443 AX-123253831 13 54798392 CAAAATGAACCCAGTAACAGCTGAGTTCACTCTTT[A/G]CCTCCTTCAGGCAGACATACACTTTCTAATTCCCC R 2 1 2 1 101000 f 74 goat snp51630-scaffold758-1648572 13 56130926 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276877 Affx-1111835565 AX-519550386 13 54808946 CCGTCTCCGAGGATGCTGTCCCTGAACCTCCCCTA[A/C]CTAGCACCCACTCCAGTCCTTACTGCATGGGTTCT M 2 1 2 1 102000 r 74 goat Random2.2K-1359 13 54808946 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38420871 Affx-122944633 AX-123291218 13 54850495 CCCATATGTGTCTCAACAGAGATGGTGTCAGGCCT[A/G]CCTGAGTCCCCTGTGATCTTTTATCCCTTCCTTTT R 2 1 2 1 101000 r 74 goat snp51629-scaffold758-1596469 13 56182596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444739 Affx-122926401 AX-123315076 13 54908432 CCTGTTACATTTAGGGAAACACAACCCAGACTCTA[C/T]AATGATAGCTGTGAGAAGTCAGTTACAAAGGCGAT Y 2 1 2 1 101000 f 74 goat snp51628-scaffold758-1538532 13 56240713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388601 Affx-122969149 AX-123258959 13 54945128 GATTGTCCTTTTCTCTCTGAGAGGGACCCAGCTTA[C/T]ATCCACAGAGACATGGAACATTTATGAAGCTTCCT Y 2 1 2 1 101000 f 74 goat snp51627-scaffold758-1501836 13 56277390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395885 Affx-122963622 AX-123266240 13 54982409 TCCAGGTAAGAATACTGGGATGGATAGCCATTCCC[A/G]TCAACACTTTGCTCACACTCTAAACCTTCAAAACT R 2 1 2 1 101000 r 74 goat snp51626-scaffold758-1464555 13 56314706 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407973 Affx-122954337 AX-123278324 13 55013963 TGTGGACAGGGCCTCTGTTCTTCAGGACTTCTTTC[C/T]TTTCTTCGACGGCCCCTGTGTCAGGTTGCCCAGGC Y 2 1 2 1 101000 f 74 goat snp51625-scaffold758-1433001 13 56346317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443528 Affx-122927778 AX-123313865 13 55097919 ATCCCAAAATCTTTGTGGGCAATCCTGCTGGGGAT[A/G]ACTCCCAAATTCAACCTCCAGACTGTGGTTGAGTC R 2 1 2 1 101000 r 74 goat snp51624-scaffold758-1349045 13 56429947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389477 Affx-122968326 AX-123259835 13 55129879 GAGAGTAAGGTTCCCTTGAATGGGAGATGATATTT[G/T]GTGGGGACTGTCAAGGCCATGTCTTTGTCGCCTCT K 2 1 2 1 101000 f 74 goat snp51623-scaffold758-1317085 13 56462259 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452458 Affx-122920562 AX-123322791 13 55200326 CCTCTGGCTTTTCTCCTTCCCACTTCCTCCCAACC[A/G]AAGGATGGTCCTCATCAGAGTCCCCTTAGGGTTTA R 2 1 2 1 101000 r 74 goat snp51621-scaffold758-1246638 13 56532878 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398775 Affx-122961432 AX-123269130 13 55261545 CTGAGAGGCAAGACAGGGTGGTGGCCTAAAGCTCA[C/T]GCTGAGAATCACAAAAGCCTGAGCTCAGAGGACCC Y 2 1 2 1 101000 r 74 goat snp51620-scaffold758-1185419 13 56593964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 coat-colour SNP associated with coat colour multi-breed 38380700 Affx-122975163 AX-123251058 13 55309024 TGTTAAATCAATGGACAATCCTAGTGATAGTTCTT[C/T]AAAAGCAGAATTAAATTAAGGTGCTGCCTTGGTTT Y 2 1 2 1 101000 f 74 goat snp51619-scaffold758-1137940 13 56641398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389972 Affx-122968068 AX-123260329 13 55370279 ACTGGGCTCCCAAGACCCCTTAGGCTGTAGCCAGC[C/T]GTCAGCCCTGGGGTGGTAGAATTCAGAGACTGAGA Y 2 1 2 1 101000 r 74 goat snp51618-scaffold758-1076685 13 56703224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276742 Affx-1111835567 AX-519550252 13 55376999 GTGAAGGGTCGCCATGAGGCTCCTATGTGTCTGTC[A/G]GGGAAGGGCACCACATGTGGGTGGGAAGGGAATGG R 2 1 2 1 102000 f 74 goat Random2.2K-1361 13 55376999 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272703 Affx-1111832989 AX-519546407 13 55384478 GCGCCACGAACCAAATTTTTGCTGAAAGGAACACA[A/G]GGAAACCTACAACAGCATTGAAAAGGGAAACTTAG R 2 1 2 1 201000 f 74 goat 13_55384478_AF-PAKI 13 55384478 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433558 Affx-122934983 AX-123303899 13 55400873 AAAATTCCCCTGGACTGCCAGGGAATTCCCAACAG[C/T]CTCGTGTCTGATAAACAATGAAGGTAAGAAGTAAC Y 2 1 2 1 101000 r 74 goat snp51617-scaffold758-1046091 13 56734095 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430625 Affx-122936965 AX-123300966 13 55459516 CCGCACTGCCCATCACACTCATGCACATGTACATA[C/T]ACGCATGCCAGGTAACCCTCTCCAAGCACTGCTCT Y 2 1 2 1 101000 f 74 goat snp51616-scaffold758-987448 13 56792284 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380633 Affx-122975232 AX-123250991 13 55495132 TCCTTTTCCTTCATTGTCTAAAATGGGCACCAGAT[A/G]CTAAAAACTGAGAGGAGCCTTTAACTAAGGGCTTG R 2 1 2 1 101000 f 74 goat snp51615-scaffold758-951832 13 56828045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798842 Affx-122965745 AX-385285772 13 55525198 GACAAGCTTTAAGTAGTTAACAGGTGCTTTTGGAG[C/T]TGGGTGAATTTTTGAACAACCGGCAGAAAAAAGTG Y 2 1 2 1 101000 f 74 goat snp51614-scaffold758-921766 13 56858046 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275276 Affx-1111834809 AX-519548852 13 55530387 CACTATCTGGATGCTGAGTCAGCGAGGGGAGTTGG[A/G]TGGAGAGATGGGGAAGACGGAAGAACTCCCTCCCC R 2 1 2 1 102000 f 74 goat GoatD01.054269 13 55530387 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447865 Affx-122923883 AX-123318201 13 55687050 GGGGCCATACTGTTTCTTCCTTTCTAAAGACTGCA[C/T]GGAGACCTTGTCAGCTGCCTTCCAGAACCTTCTGG Y 2 1 2 1 101000 f 74 goat snp51611-scaffold758-759914 13 57019683 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435958 Affx-122933529 AX-123306297 13 55764605 TGAAAATATGGGACGGGAAGGAGGAAAATATGGGA[C/T]GGAAATATCTTGAAAATATCATCATTAAGATGGAT Y 2 1 2 1 101000 f 74 goat snp51609-scaffold758-682359 13 57097150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse618 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38398157 Affx-122962667 AX-123268512 13 55823334 TGAGAAAAAGAGGAAATAGTCAGCTAGGGCTGGGG[A/C]TAAACTCCCGGCTTAGTCTTATTTTTGTCAGTCAT M 2 1 2 1 101000 r 74 goat snp51608-scaffold758-623630 13 57155574 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383553 Affx-122972609 AX-123253911 13 55870100 TGCGCCAGGGAGACAGAGGTTGGTGTTCTGGTCCC[A/G]TCTGCCAAGAGGAGCCTTGCTGCCTCCGTGCTCCT R 2 1 2 1 201000 f 74 goat snp51607-scaffold758-576864 13 57201977 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451144 Affx-122921366 AX-123321478 13 55909772 AAAGTAAATGTGACATTGTACAGTTTGGATGAAAC[A/G]CTACCTTGGGTGGTGTCTGCTGAGACCTGCTTTAC R 2 1 2 1 201000 f 74 goat snp51606-scaffold758-537192 13 57241503 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448733 Affx-122923834 AX-123319069 13 55939729 TAGAATAGACCTGTTAAGTGTTAACTAACGTCACT[A/G]TTGTTTGATTTTTTCTTTTTTCAAGATATATCATT R 2 1 2 1 201000 f 74 goat snp51605-scaffold758-507235 13 57271374 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441313 Affx-122929445 AX-123311650 13 55978862 CCCCCATTATATACACACTTCCTGGGTGCCTCCTC[A/G]CATCTGAGAGGACTGGACCCTTTGTGCCAGAGGCT R 2 1 2 1 201000 f 74 goat snp51604-scaffold758-468102 13 57310878 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422658 Affx-122943686 AX-123293004 13 56011677 TCTGGATCAGCTCATGATCTGTTGGTGTTTACTCT[C/T]TTTTTTCCTTTTGACCTTGGATCACATTTCTTTGC Y 2 1 2 1 201000 r 74 goat snp51603-scaffold758-435287 13 57344137 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450054 Affx-122922819 AX-123320389 13 56045525 GTTAAGAACTCCTGTTTTAAAAGTAACAAACAATA[G/T]CTAGGCTTTCTTCAGAAAACTCTATTTATCAGAGA K 2 1 2 1 101000 r 74 goat snp51602-scaffold758-401439 13 57378168 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386510 Affx-122970748 AX-123256868 13 56098431 TTCTTGCAGCATGCCGAGGTCTGTAACATTCCCCC[A/G]CTTTGGTTCTAGGGCAGCGAAAAAGGTAAGATCTT R 2 1 2 1 101000 r 74 goat snp51601-scaffold758-348533 13 57430994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413090 Affx-122950951 AX-123283439 13 56215814 CCATCTTCTACAAACCAAATTAGCCACCAGTTCCC[A/G]TTCATTAAAAAAAAATAAAATGTGAAAAGTGCTAT R 2 1 2 1 102000 f 74 goat snp51599-scaffold758-231150 13 57548423 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426819 Affx-122940519 AX-123297164 13 56246114 CTCGCCTGCCTTGTTCCACCAGCTCAGTGACCAGC[A/G]TGTAGTAGGTGCTCAATAAGTGCACGCCAACCAAC R 2 1 2 1 201000 f 74 goat snp51598-scaffold758-200850 13 57578658 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400656 Affx-122960355 AX-123271011 13 56298097 CATCTTCCCAGTTGTGCAGCAGGGAAGCCAGACCC[A/G]CAGAGGAACAGAGCACAGTGCTAAGTGTGCCTCCA R 2 1 2 1 201000 r 74 goat snp51597-scaffold758-148867 13 57630509 G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377189 Affx-122978195 AX-123247548 13 56365935 TGTTAGCTGAGTCCTGCGAGGTGGGTGTGATTCTC[A/G]TACCATTTTAGATCCCAGGGAAAGCACCCAGGGAA R 2 1 2 1 101000 r 74 goat snp51595-scaffold758-81029 13 57697239 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387755 Affx-122969728 AX-123258113 13 56405346 GCCCCCCTCCTGATTCTCTGTCTGCCTGGCCCCAC[C/T]GCTCTTCATGGTGCCAGGTTCTTGATCAGCACTGG Y 2 1 2 1 101000 r 74 goat snp51594-scaffold758-41618 13 57736535 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377260 Affx-122978140 AX-123247619 13 56442157 TGGGCGGGTGGGGACATTGAGGCTCGTGGACCCAG[A/G]AGGGAGGTGGAGCGGAATGTGAATTCAGGGACTTT R 2 1 2 1 101000 r 74 goat snp51593-scaffold758-4807 13 57773710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403209 Affx-122957910 AX-123273562 13 56454934 TCCTTGGCCTGCCCCGGTGTTCGCTAGAGGTGGAG[A/G]GGAGTCGCTTTCAGCTCCTGGCAAAAACGTGAGGG R 2 1 2 1 101000 r 74 goat snp48732-scaffold691-4056627 13 57835405 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451362 Affx-122921248 AX-123321695 13 56504230 GGTGTAAGTTCTAGAGTGGAGAACACTGCAGGTGA[G/T]GGTGGCTGCACCCCTGCTCAGGAAAAAAACTCAAC K 2 1 2 1 201000 r 74 goat snp48731-scaffold691-4007331 13 57885102 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405244 Affx-122956881 AX-123275596 13 56542785 GCTGACCTTGGTGTCAGGTGGATTCTTGGACAGGC[A/G]GCTCACCCTTACCTGTGGACCAGCCGTGGCACCCA R 2 1 2 1 101000 f 74 goat snp48730-scaffold691-3968776 13 57923951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426349 Affx-122940262 AX-123296695 13 56619654 AAGGACTTGTCTCCCAGAAGGGTCTGTGAGGCCAG[C/T]GAGGCATTAAGAAGTATCTTTCATCGAACTTTAAT Y 2 1 2 1 101000 r 74 goat snp48728-scaffold691-3891907 13 58000714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445069 Affx-122926220 AX-123315406 13 56666578 TCCTGGATGGTTGGTTACCCATGAGGGGACACTCA[G/T]ATGGCCTTTTGCACAGATGGGGAAACTGAGACACA K 2 1 2 1 201000 f 74 goat snp48727-scaffold691-3844983 13 58047440 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452201 Affx-122920817 AX-123322534 13 56699161 GTCTGTACCTCTAAGGAGATTCAAATCATTATAGA[C/T]GTCCTTAGATTCACATGGGTGCCTGCCAGGTATTT Y 2 1 2 1 101000 f 74 goat snp48726-scaffold691-3812400 13 58079960 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408184 Affx-122954197 AX-123278535 13 56740339 TTACCTGAGTGGAGGTGGATAATTGAGGGCAGAGA[C/T]GTGCTGCCTGGGAGGAGGGCTCAGGCCACCCCTTC Y 2 1 2 1 101000 f 74 goat snp48725-scaffold691-3771222 13 58121230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385298 Affx-122971686 AX-123255656 13 56786923 GATTCTGCACTTTCACCCAGTACCCAGAGGGGTGC[A/G]ATGCTGCTGGTTCAAGGACCCCAAATGTCTAAAGT R 2 1 2 1 101000 r 74 goat snp48724-scaffold691-3724638 13 58167906 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378733 Affx-122977036 AX-123249092 13 56834880 AGGTCACCAGGAAGAAGCAAGGTATAAGAAACCCA[C/T]AGGCAAGAGGTGCCCAAGGAGACGTGACGACCAAA Y 2 1 2 1 101000 f 74 goat snp48723-scaffold691-3676681 13 58216050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391481 Affx-122966715 AX-123261838 13 56868911 GAGTCCATCTGGCAGGGCGCCCTGCTCTTAGAAAA[C/T]ATCACCAATCACAGTAACTGTATTTTTGATTTTCC Y 2 1 2 1 101000 r 74 goat snp48722-scaffold691-3642650 13 58250188 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385716 Affx-122971105 AX-123256074 13 56904950 GGAAATAGGAGAGAATGTCCAGGAATACAGAAAAC[C/T]AGCCGCAAGGATCATGAGATGCAGCTCAGGCCCCT Y 2 1 2 1 101000 f 74 goat snp48721-scaffold691-3606611 13 58286192 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452288 Affx-122920691 AX-123322621 13 56933620 CTTAGCACGACTTTAAGAAAGGAGCCGGTTCTCAG[C/T]GGGCCTGATCTGACCAGGTGAACCCTGGAAAGAGA Y 2 1 2 1 101000 f 74 goat snp48720-scaffold691-3577941 13 58315185 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424537 Affx-122941718 AX-123294883 13 56989033 GCAAGCCCCAGTTTAGTCATTCTGCTGGTGCCTAG[A/C]GAGACTGCCATGTGCTGACCCAGGGCTAGATGCCA M 2 1 2 1 101000 f 74 goat snp48719-scaffold691-3522528 13 58370998 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397175 Affx-122962418 AX-123267530 13 57019890 TTTATTCAAAAATTGAATTGGCCGGGCTTTAAAAA[C/T]GGGGAGCTTTCACTCTCTAAAATGAAATATCCAAA Y 2 1 2 1 201000 f 74 goat snp48718-scaffold691-3491671 13 58401792 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765101 Affx-122931067 AX-385252663 13 57061982 CCAGAGCAGAAGCGATAGAATCTGCAGAAATGTCG[C/T]TGCCTCCTAATTTTTAGTTTATGCATTGGCTCCCC Y 2 1 2 1 101000 f 74 goat snp48717-scaffold691-3449579 13 58443543 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453759 Affx-122919603 AX-123324092 13 57092557 GAGTCACTGGCTGCCCAGCACTTTCTCCAAAGAAG[A/G]GGGGCTCACAGACTGTTAGGCTCAAGAGACTTTGT R 2 1 2 1 201000 r 74 goat snp48716-scaffold691-3419004 13 58474029 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385560 Affx-122971223 AX-123255918 13 57122540 TTCTGCATTAGAATAAAAACTGAAGCCAAACACGT[C/T]CTTCAGATTCTGTGCACATAGATGTCCATGGGGCG Y 2 1 2 1 201000 r 74 goat snp48715-scaffold691-3389021 13 58504371 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435895 Affx-122932776 AX-123306234 13 57172558 TGCATCATTTTGTCCTTTCCTTTGTGGTGTCTGCC[A/G]TCAGGAGACTGGAAAAGTCTGTCAGGGGAATGATG R 2 1 2 1 201000 f 74 goat snp48714-scaffold691-3339003 13 58554327 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395861 Affx-122964008 AX-123266216 13 57236266 GGGGACGGAATCAGGGGTCTGCCTCCTTCTTCAGC[A/C]GTGAGTCCTTCCATGATAGTTTATAGACCCACGAG M 2 1 2 1 101000 r 74 goat snp48713-scaffold691-3275295 13 58617673 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427795 Affx-122939765 AX-123298138 13 57269485 TTTAACCACAAGACAGGAAAAATTCAGTGGTGGCA[A/G]GCACCAACTGTTTAAGAAGATCTTTAGAAAGACAG R 2 1 2 1 201000 r 74 goat snp48712-scaffold691-3242076 13 58651015 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772375 Affx-122972200 AX-385259529 13 57298580 AGGTCAGCTGGGATGCAACGGACAAAAGCAAGAAG[C/T]GGTAAACAATTCTAATGTGGCAGCGTTCATAAATA Y 2 1 2 1 101000 f 74 goat snp48711-scaffold691-3212981 13 58677105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417641 Affx-122946850 AX-123287989 13 57329447 GAGGCACCTTCTTCCACTGGTCCCCCCAGCCCTCA[G/T]CTGCTCCCCACCCCCACCTGCTTGAGAACCCAGAT K 2 1 2 1 103000 r 74 goat snp48710-scaffold691-3182114 13 58708550 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443572 Affx-122927338 AX-123313909 13 57359677 TGTACAGCTGAGCAGATCTCTCCAGATGTGTATTG[C/T]ATGAGGCATAAGTGTGCAGCCAGAAACACCTAGGC Y 2 1 2 1 101000 f 74 goat snp48709-scaffold691-3151884 13 58737526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428054 Affx-122939124 AX-123298397 13 57389954 CTGAATTTTTTTTTTTTTCTTAAGGGAATCAGATA[C/T]AACCATTTTTCTCTTGGTGGTTCTTGGCCTTTGTG Y 2 1 2 1 103000 r 74 goat snp48708-scaffold691-3121607 13 58768359 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375445 Affx-122979172 AX-123245804 13 57526100 TGAATTATTCCATATAATCAAACTGCCCCTGAAGT[A/G]CTGAATATGCCTACTGATGTAAAATAACTATAGGA R 2 1 2 1 201000 r 74 goat snp48705-scaffold691-2985461 13 58903739 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377326 Affx-122977677 AX-123247685 13 57579855 ACCGGAAGCGAAACAAGATTTTAAAAATGTATATA[C/T]GGCATGCTGCAAGCTTCTTTAATGTACATCATGGT Y 2 1 2 1 101000 r 74 goat snp48704-scaffold691-2931706 13 58957898 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770063 Affx-122936421 AX-385257230 13 57637845 AACTACTGGTGGGTCAAAGAAGGGTACCATGTTTT[A/G]GAGGGCAATGTGAAGATCTTTTGAGCTACCTGTTG R 2 1 2 1 101000 r 74 goat snp48703-scaffold691-2873716 13 59016707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412916 Affx-122950400 AX-123283265 13 57678299 TCACCAAACAGAACTGGAGATTTAACCAGTGTGGA[C/T]AGAGGGATTTCTGTCTCTTTTTCAGAATATGCTTT Y 2 1 2 1 101000 f 74 goat snp48702-scaffold691-2833262 13 59057691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431300 Affx-122937089 AX-123301641 13 57713678 ACTCCAGGGATGGGAGGCCCAGACCCGAGTCCAGC[C/T]GCCTTCCAGATCTTTACTACCTCCCGCTGGTTGAA Y 2 1 2 1 101000 r 74 goat snp48701-scaffold691-2797883 13 59092936 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276745 Affx-1111835568 AX-519550255 13 57724893 CCAGAGGCCTGAACAGCACAGGGTTTTCCAGGGAT[A/C]ATTGGCCAGGAGGTGTGGGTGCTGGGGTGGGACAC M 2 1 2 1 102000 f 74 goat Random2.2K-1363 13 57724893 G T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791635 Affx-122956942 AX-385278626 13 57786919 CCCTGCGGTACCTATAAAACAAGCCTGACAGGCTG[A/G]TAATCATTGTTTTTGAAGATTCCCAAGGTCCTGTG R 2 1 2 1 101000 f 74 goat snp48699-scaffold691-2724642 13 59166263 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436676 Affx-122932462 AX-123307014 13 57858797 CACAGATCAGTGACATCACCGAGCCCACTTGCCCC[A/G]TCGAAGAGATGGAAATAACTCTGCCCATGTGTCTC R 2 1 2 1 101000 r 74 goat snp48697-scaffold691-2652764 13 59238714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418216 Affx-122947052 AX-123288564 13 57894290 GATTTCTTATCACACACACAGATTCTGGGGATTAA[G/T]AAGTTATGGAAGATTGAGAAGGGGCCATTTTTACC K 2 1 2 1 101000 f 74 goat snp48696-scaffold691-2617271 13 59273768 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417219 Affx-122947299 AX-123287567 13 57935431 CTGACAATTTGAGAAGTCATTTGCCCAAAATTGCA[C/T]AGAGTGAGCAGTGAGGTTGAGATATAAACCAAGTT Y 2 1 2 1 101000 f 74 goat snp48695-scaffold691-2576130 13 59315015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272755 Affx-1111832990 AX-519546453 13 57960180 GCTTCTCCCCTGGGACACGGAAGACAACAGTGACC[A/G]TCTGCTGAGGTGCTCCACCCCGAAAACCTTGGTGC R 2 1 2 1 202000 r 74 goat 13_57960180_AF-PAKI 13 57960180 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38442672 Affx-122927895 AX-123313009 13 57969830 ATCTCCTCCAGGAATCAAAGGGAAAAGAAGACTTT[A/C]GGCATACAAAGATAGCATGTTCATTTTTGCTGTCT M 2 1 2 1 201000 r 74 goat snp48694-scaffold691-2541731 13 59347280 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433925 Affx-122934299 AX-123304266 13 57999029 TCCAGCATCTTGTTTCCAGGCAACATCTGCTAGAA[C/T]TCAGGCTTGATGCAGGTAGTTAGGAGGAGGGGGAC Y 2 1 2 1 101000 f 74 goat snp48693-scaffold691-2512532 13 59377507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387983 Affx-122969590 AX-123258341 13 58069794 GACCAGGATGGAGAGTGGGGAAAGGGAGAGAGAGA[C/T]AGTGAAACCACAAGTGTCAGCAGCTCAGACTGTCT Y 2 1 2 1 101000 r 74 goat snp48692-scaffold691-2441767 13 59447803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772842 Affx-122971741 AX-385259987 13 58104516 GGTGTTTATTGCAGGGCACAAAGCAAGGAGAATGG[A/G]CAGTGCATGCTCCAAAGACCCAAAATCCCTACTGG R 2 1 2 1 101000 f 74 goat snp48691-scaffold691-2407045 13 59482462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439141 Affx-122931081 AX-123309478 13 58156376 GGATGACACACTGGACTGTGAACAACTTTGAGGGG[C/T]AGAGCGCAGGTCTGATTCTTCTCCAAATGACCAAG Y 2 1 2 1 101000 r 74 goat snp48690-scaffold691-2355185 13 59534025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766234 Affx-122955211 AX-385253630 13 58240010 GCCTGGAACCCAGATTTAATGTGATAGAGAAATAC[A/G]CTTCTCTGTTTATTAAGCTTTTATAATGTGGGGCA R 2 1 2 1 101000 f 74 goat snp48689-scaffold691-2271551 13 59618031 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793890 Affx-122936925 AX-385280859 13 58303503 ATTTCCAGAGACTCCTGTGGTCCTTTGGAACCTCA[C/T]GCAAATTTTGAGGTGTTGCTTAGAAATCTTAGAAT Y 2 1 2 1 101000 f 74 goat snp48687-scaffold691-2208058 13 59691868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442840 Affx-122927693 AX-123313177 13 58335582 CATACAACCCCATGAGTGACCTCAGGCAAGATCAG[G/T]AGAACTGCCCAGATGAGTCCAGCCCAAACTGCTAA K 2 1 2 1 202000 r 74 goat snp48686-scaffold691-2175979 13 59723829 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411729 Affx-122951521 AX-123282079 13 58389798 ACTCTTGATTCTGAGACTCTGGTTCCCACAGTGTA[A/G]GCTGGACTCTGGACAGGGGAGAAGACCCAGACTCG R 2 1 2 1 101000 f 74 goat snp48685-scaffold691-2121763 13 59777948 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429098 Affx-122938264 AX-123299440 13 58433299 AGTCAAGTATGTGGGGCGGGGAAATCATTGTGACC[A/G]TCTTTATGAACAACACAGCACACTAAATGGCCATG R 2 1 2 1 101000 r 74 goat snp48684-scaffold691-2078262 13 59821569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404718 Affx-122957250 AX-123275070 13 58492896 AAATCACCCTGCCACACAGTCAGAATGTTTTCCCT[A/G]TGGTGGAGAAACATTATAAAAGAAGGCTTTAGCTT R 2 1 2 1 201000 r 74 goat snp48683-scaffold691-2018665 13 59881346 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443990 Affx-122926914 AX-123314327 13 58560560 CCCCATCTCTTATGAGTTTTCCGTGCATCTGAAAC[C/T]AGCTTCAGGGTGAAAGGTCAGAGGCCTTGTGTGTC Y 2 1 2 1 101000 f 74 goat snp48682-scaffold691-1951001 13 59949983 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273780 Affx-1111833807 AX-519547391 13 58568969 TTGGGTCATCCTTGCCTCCAGTGAGGAGAGCTGGC[A/G]CTCAGCCCCCAAGGAGAGTCTGCAGCCAATGTGTC R 2 1 2 1 102000 r 74 goat GoatD01.005639 13 58568969 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38381271 Affx-122974477 AX-123251629 13 58697225 AAATACTGGAGCTCCAGGCGAGTAACACAGGTAGC[G/T]CTGTCCTATCCACCCCACTGCACTCTCCCCAGGCA K 2 1 2 1 101000 f 74 goat snp48680-scaffold691-1814336 13 60087056 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386936 Affx-122969993 AX-123257294 13 58852426 GTATCTTTCACCAAATCTCAACCAGAGGAAGGTGT[A/G]CAATCTGTTATCAGTGTCCTTCTTCCTCTTCAGCT R 2 1 2 1 101000 f 74 goat snp48676-scaffold691-1659135 13 60244108 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437963 Affx-122931609 AX-123308301 13 58900305 TGTACAGCAGTACAACTGATACTGGTGCAATGAAT[A/G]TGCCTACTTCCATGACATTTTATCACAAGTGTAAT R 2 1 2 1 101000 f 74 goat snp48675-scaffold691-1611256 13 60292221 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413191 Affx-122950328 AX-123283540 13 59009866 AAGAGTTTTGGGATCTGTGAGGCAAGAACAGTGGA[C/T]GAAGACCCAATATATATGAAGAATATATTTTGGTT Y 2 1 2 1 101000 f 74 goat snp48673-scaffold691-1501695 13 60401655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396354 Affx-122963050 AX-123266709 13 59043230 CGACACACAGCCAATCCCTCCCCGTCTACAGAGCT[A/G]TGGGATGAATGACGACAAGGCTTTGTGATTAAGTA R 2 1 2 1 101000 r 74 goat snp48672-scaffold691-1468331 13 60434735 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405728 Affx-122956521 AX-123276080 13 59097932 TCTCTAGTTCCCGGCTCCCGCCTGGGGAAAGACTT[A/C]GGATTCCAACTTTGCTGCTGGGTGAATTTAGCTGA M 2 1 2 1 101000 r 74 goat snp48671-scaffold691-1413629 13 60489213 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782321 Affx-122921320 AX-385269398 13 59141306 CTCAGTTGTTTCATCTGTGATACGGGGCTCAGATC[A/G]CTACATCTGAGGATTCTGATGAAGGTGATGGGGAT R 2 1 2 1 101000 r 74 goat snp48670-scaffold691-1370255 13 60532632 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437438 Affx-122932400 AX-123307776 13 59180575 GGTACAAAGATGTTAAGCAGCTTATGCGGGCAGCA[C/T]GGTTAGTAAGTGGCAGAGCCTGTGAGGGTAACTTC Y 2 1 2 1 101000 f 74 goat snp48669-scaffold691-1330986 13 60571963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428204 Affx-122939452 AX-123298547 13 59209829 GAGTTGAGTTATTTTCATCTTACCCAGGGAGAAAA[C/T]ACCTCCATTCTTTTTTTCTTTTTTTCCTATACATA Y 2 1 2 1 202000 f 74 goat snp48668-scaffold691-1301732 13 60601347 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420154 Affx-122945585 AX-123290502 13 59246232 CATTGTGAGGTAGAGAAACACAGGGTTTAAGGAGA[C/T]GACAGGTTCAAATCCTGGTTCTGCATACTAGACAC Y 2 1 2 1 201000 f 74 goat snp48667-scaffold691-1265329 13 60637987 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429177 Affx-122937965 AX-123299519 13 59280057 TTCTCTGTGCAGGTACAGACCGCTCCAAACTTGCC[A/G]CTGGAGAGAGAAGAGGCTGAGAGTAAGGGAGTTCC R 2 1 2 1 201000 f 74 goat snp48666-scaffold691-1231504 13 60671784 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378487 Affx-122976663 AX-123248846 13 59320671 TCTGAGATCCAGACCAGCTTCTGTCACAGATTTGC[C/T]CTGTGACCTTGGGCAGGATCCTCCCCCTCTCTGGG Y 2 1 2 1 103000 f 74 goat snp48665-scaffold691-1190890 13 60712195 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410728 Affx-122952712 AX-123281078 13 59355431 CATTAACCCATGACCAGATTTTCATGTTTCCTTCC[A/G]TTATAAATGCAGGCATGAAATCCTAACGGTGTTAG R 2 1 2 1 201000 r 74 goat snp48664-scaffold691-1156130 13 60746940 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435748 Affx-122933279 AX-123306087 13 59390593 GCTGCGAGATGTGTAATAACCCACCCATACAAAGA[C/T]GGTTGTGAAATTCAAGGAAGGCAAGGGGTGTGAAA Y 2 1 2 1 101000 f 74 goat snp48663-scaffold691-1120968 13 60781262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407166 Affx-122954837 AX-123277517 13 59424365 CTCTAAGCCTCATTTCACCCCTTGTTGTGAACATT[C/T]GTAAACTGTAGGGGAATGTGCACATAGAGAAGGGG Y 2 1 2 1 202000 f 74 goat snp48662-scaffold691-1087196 13 60815064 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794830 Affx-122938015 AX-385281790 13 59526054 CATCACGGCTGCTGTTGGTACTGGCTCTCGGTGGC[C/T]GTGTAGAAGTCATCCAGCACACTCTGGATGTATTC Y 2 1 2 1 202000 f 74 goat snp48660-scaffold691-985507 13 60915128 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273956 Affx-1111833918 AX-519547561 13 59556806 TGCAGCTTGCAAAACTCTTCCTTGGTCTGTGTCTA[A/G]TTTCACTCTGCAGGGTAGCTGCATTACCAGGGGGA R 2 1 2 1 201000 r 74 goat GoatD01.010442 13 59556806 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407088 Affx-122954900 AX-123277439 13 59567303 TAATCACTCACTCTTAATTAAAAGGAAAGCACGTT[A/G]CAGAAGCCATGAGAGACAGGAGGGGATATCTGGAA R 2 1 2 1 101000 f 74 goat snp48659-scaffold691-944258 13 60956404 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442430 Affx-122927972 AX-123312767 13 59639680 TGCTTTTGGAGGGTCTGTGATGTATCAGGACAGCA[C/T]TTCCCAGCTTTGGTTCCTTTGAACACAAGTTTCTC Y 2 1 2 1 101000 r 74 goat snp48658-scaffold691-871881 13 61027668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778774 Affx-122956654 AX-385265884 13 59684899 GTGTCTATAGCACAGTTTACATATGCATGCTACAA[C/T]ATTAGAAGCATACATGTAAAAGCGGTAACGGTGGC Y 2 1 2 1 101000 f 74 goat snp48657-scaffold691-826662 13 61072317 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411403 Affx-122951848 AX-123281753 13 59734758 CAAGGTAAAGGAACTGTCGCACACTAAAGGAGACC[A/G]CAGAGACACGGCAGCCAAATGGAGTGTATGATTCT R 2 1 2 1 101000 f 74 goat snp48656-scaffold691-776803 13 61121835 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404115 Affx-122957110 AX-123274467 13 59773740 AATACCAATGATTAGAAAATGTAATTTATAACAAC[A/G]AATGTAAGTTACTCTGAGATAAAGCTCACAACAGA R 2 1 2 1 101000 r 74 goat snp48655-scaffold691-737821 13 61184057 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376065 Affx-122978922 AX-123246424 13 59816599 AGGAGTGTCTGTTAAATGAGTAAGTGAACAGGGGC[A/G]CAGGCTGGGCAGGTGAGCCAGTGTCCTTGGACGTC R 2 1 2 1 101000 f 74 goat snp48654-scaffold691-694962 13 61226651 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787763 Affx-122950544 AX-385274786 13 59846258 TTGTTTAATTTCTTGCTGGAGGAGATAAATATGTA[C/T]GCAGTCACACCCTCTCATAAACACATGTATTATTT Y 2 1 2 1 101000 r 74 goat snp48653-scaffold691-665303 13 61255856 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399414 Affx-122961237 AX-123269769 13 59875473 CACAGTCTCCCAGGCTGGTTGCAATGTTCAGCCCC[A/G]TCCTGGCTAGGGGAAACTTGGCAGTCGGCAAAGCA R 2 1 2 1 101000 r 74 goat snp48652-scaffold691-636088 13 61284766 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407247 Affx-122955361 AX-123277598 13 59909941 GGACCGTAATGGGCCCCAGAAAGCCGGATCTCAGA[C/T]AGTGGGAGATGCTGAGTATCACAGAGCAGGGGAAC Y 2 1 2 1 101000 r 74 goat snp48651-scaffold691-601620 13 61319042 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409972 Affx-122954101 AX-123280322 13 59951393 TTCAACCTCCGCAACCTGGTTTCTCATCCCAACCC[A/G]GCCTCCGTTTCCTAGCTGTGTGGTCTGGAGCTGTG R 2 1 2 1 303000 r 74 goat snp48650-scaffold691-560168 13 61360957 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777195 Affx-122932442 AX-385264318 13 59995904 TAAGACAGGGTTACATGTCTATCACAGGGTTATAA[C/T]GATAATAATTTCTATATTGACTCTATGTTGAAATG Y 2 1 2 1 201000 r 74 goat snp48649-scaffold691-515657 13 61405163 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377299 Affx-122977696 AX-123247658 13 60072974 TAGACAAGGTATTTAATGCAGGCATGTGTGTGTTT[A/G]AAGTGCCTCAGCTCAGGGGTAGACACTTACAGCTG R 2 1 2 1 201000 r 74 goat snp48648-scaffold691-438587 13 61482462 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384118 Affx-122972826 AX-123254476 13 60128943 CATGACCTAACCTAAATGAGACCCACTTAAATACT[A/G]CGTGCCTCAGCCTAAATAGCCAGGCCAATGGACTT R 2 1 2 1 101000 f 74 goat snp48647-scaffold691-382618 13 61538529 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419084 Affx-122945792 AX-123289432 13 60158933 TACTCCCACCAAATCAGAGGAACCAAACCGACAAG[C/T]CAGCTCCAAGCAAAATGCCACCACACCACTCCACT Y 2 1 2 1 101000 f 74 goat snp48646-scaffold691-352628 13 61568574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392117 Affx-122966347 AX-123262474 13 60266262 GATGCACAGACTGAGAACTGGAGGTGTGAAATAAT[A/G]TCCCAGGCCACTCTGCTGGGCACATGAACCAGTTT R 2 1 2 1 101000 f 74 goat snp48644-scaffold691-245299 13 61663275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399469 Affx-122961196 AX-123269824 13 60316867 TTTGCCGACAGGCAGCCTTCCTTGGTTAAACCCAC[C/T]TTCGTGTATGGTCCCATAAATGCAATTTGTGATGG Y 2 1 2 1 101000 r 74 goat snp48643-scaffold691-194694 13 61713384 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777220 Affx-122939294 AX-385264343 13 60348478 CACAAATCCTGTGGAAATTCCAAGGAGCTTGTCAA[C/T]GTTCCTAAGGAATCTAGATGTACCTGGGAAATTCT Y 2 1 2 1 101000 f 74 goat snp48642-scaffold691-163083 13 61744988 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802703 Affx-122947463 AX-385289602 13 60412099 GCTGGAAAGTCTTGGGAGTTTGTGGCTCAGAGAAG[C/T]AGGATTCATCCAAGGCTACATATGACTTGAGCCCC Y 2 1 2 1 101000 r 74 goat snp48641-scaffold691-99462 13 61809411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272706 Affx-1111832991 AX-519546410 13 60534790 GTGGTGAAGAATACCAGTGGACTGATGCAGGTGGA[A/G]TGGTCAGAGGAGGTCTCTCTGGGGGAGGGTGGGGA R 2 1 2 1 101000 f 74 goat 13_60534790_AF-PAKI 13 60534790 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38407893 Affx-122954401 AX-123278244 13 60552682 AACAGGAGGAGGGGATTCAAACTCAGCTGGCCCAG[A/C]TCTAGAGCCGGGGTATGATCACCAGCACCTCAATA M 2 1 2 1 102000 r 74 goat snp24789-scaffold2539-9319 13 62210640 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431823 Affx-122936101 AX-123302164 13 60562832 AGGTGAATCAGAGGTCTCTGCTGGTGCCAAGTGGG[C/T]GCCCATTTGGGCTTCCTGGACCCGGTGTTCAGGGT Y 2 1 2 1 102000 f 74 goat snp27796-scaffold298-732 13 62232676 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438091 Affx-122931515 AX-123308429 13 60603443 AAATGGGAAAAAAAAGCTTCCATTCTGCATCCAGG[C/T]ATGGAGAAAGTGCTTTACAAACATTTAATTCTTCA Y 2 1 2 1 101000 f 74 goat snp27797-scaffold298-41343 13 62273579 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772331 Affx-122969859 AX-187722028 13 60716743 TGTTCACTGTCTCCCTCATTTTGAGGATGGGGACC[A/G]TGAACAGTATACTCTGTGAATACTCTGTATACTCT R 2 1 2 1 202000 f 74 goat snp27799-scaffold298-154643 13 62386631 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444333 Affx-122926729 AX-123314670 13 60878797 GACTCCACAGCATATTGCTGACCTGAGTGGTTGGC[A/G]TCAGTCCTTTCTGGCAGGAAGAGAAATATGACTGG R 2 1 2 1 101000 r 74 goat snp6538-scaffold1231-784814 13 62434614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413484 Affx-122950654 AX-123283833 13 60913235 TTTGGGAACCCAGAGGAGGACCTCTAGACTTTGGC[A/G]TTAGTGGCCTGAAAAGGCTTCCAAGAGGAAGTAAA R 2 1 2 1 201000 r 74 goat snp6537-scaffold1231-750376 13 62468945 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773347 Affx-122961436 AX-385260489 13 60971124 AATGATTAAGAATTAATAATGATTAAGTGAGACAA[C/T]GTGTGCTTAGTACATAGATAACTTCTCAAGGTCAG Y 2 1 2 1 101000 r 74 goat snp6536-scaffold1231-692487 13 62527159 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420579 Affx-122945269 AX-123290926 13 61006494 GCAGCAAGAGCAGAGTATCTATTCTTGGTCTTTGC[A/G]CTGATAAAAGCAGTTTCATAAAATGAGATGTTGTT R 2 1 2 1 101000 f 74 goat snp6535-scaffold1231-657117 13 62562825 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776746 Affx-122972087 AX-187723098 13 61082066 CATGAAGACTAGTGCCTGATTTTATCACTTAACTC[A/G]CCTTGTGACTATGTCCAAGTTAATATTGACATTTG R 2 1 2 1 101000 r 74 goat snp6533-scaffold1231-581545 13 62638256 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418008 Affx-122946659 AX-123288356 13 61123452 CATCACATCCTATGGGTCAACTATGGCTTCAGAGG[C/T]GCCAAACAGAGACCATGGGAAGATCCACCCAGTGA Y 2 1 2 1 101000 f 74 goat snp6532-scaffold1231-540159 13 62680003 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434896 Affx-122934334 AX-123305236 13 61161390 ACTGGATATAATGCATATTTACTATGGAAGAGATG[C/T]GAAAGTTGAGGGGGACAAGATCCCCAGCCCCATCC Y 2 1 2 1 101000 f 74 goat snp6531-scaffold1231-502221 13 62717765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380829 Affx-122975071 AX-123251187 13 61225503 ATTTTCTGTTATTTGTAGGAGAAAACGTCCTAGCC[A/G]TCACAGCACAGCACTTGTACAACTATTTAAAACTT R 2 1 2 1 101000 f 74 goat snp6530-scaffold1231-438108 13 62783647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442824 Affx-122927705 AX-123313161 13 61262969 ACCCAAGGAAACGTACGCGCCTCCTCTGTGCTGGG[C/T]ACTCTGCTAGGCACTTTACACGTGTCGCTTTATTC Y 2 1 2 1 101000 r 74 goat snp6529-scaffold1231-400642 13 62821105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420704 Affx-122944788 AX-123291051 13 61302989 ATTTCAAATCAGTGTCACAAACTCCAGAAAGACCA[A/G]GGGAGTGGGAGTGAGGAGTGGGCCAGAGTGGGGAA R 2 1 2 1 101000 f 74 goat snp6528-scaffold1231-360622 13 62861012 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453860 Affx-122919530 AX-123324193 13 61343432 ACTGAGCAGGTTTCAGTAGCAGGTATTTTTAGGGT[A/G]AGCGGCATGACTTTGTCCTGCCTCAACTTCCCCAT R 2 1 2 1 101000 f 74 goat snp6527-scaffold1231-320179 13 62900107 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447897 Affx-122923814 AX-123318233 13 61396419 GCCATGAGACTTTCTGTGGCCAAAGGGTTTGAGGT[A/G]TACTTGTGTAGCTGGACACCCTCTCTTACAATTCA R 2 1 2 1 101000 r 74 goat snp6526-scaffold1231-267192 13 62951142 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382509 Affx-122973809 AX-123252867 13 61438988 TCATCAGGAGCAACACCTCTGAATGCAAAGGGACC[A/G]CTGCGGAGATTCAGGGGTCCTGTAACCCACAAGTG R 2 1 2 1 101000 f 74 goat snp6525-scaffold1231-224623 13 62993708 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396295 Affx-122963094 AX-123266650 13 61484339 TAGAGCTGGGGCTTTAACCATCTCTCCCCACAGTG[C/T]GGTCTGAGTATAAACGCCCCCCCCATCTTGTACTC Y 2 1 2 1 201000 r 74 goat snp6524-scaffold1231-179272 13 63039659 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787686 Affx-122951202 AX-385274708 13 61521308 TTAGTTACTCACTCTTGTGCTCTAACATAAACACC[A/G]TTTAAATGATTTAGTAAACATGTTTGTGTCTTTTG R 2 1 2 1 101000 f 74 goat snp6523-scaffold1231-142303 13 63076910 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447905 Affx-122923809 AX-123318241 13 61560368 TGCTGACTAAAATACCATAAACATTATTTTAAATA[C/T]TACATTTGAGCGCCTAAGAAATATTTTTTTTTAAG Y 2 1 2 1 303000 f 74 goat snp6522-scaffold1231-103243 13 63117582 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772805 Affx-122924632 AX-385259950 13 61616244 TGGAAAATCTTTAATCAGAACCATTAACGTGGGCA[A/G]ATTGTATCACTTGGAATTTCACCATCTGGCTTTGC R 2 1 2 1 10000 r 74 goat "snp6521-scaffold1231-47367;SV_299" 13 63174284 C T SV_299 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398918 Affx-122961006 AX-123269273 13 61671264 TAAATTGTACTGTGGTCTGGTCTCTCTCTGTATAT[A/G]GTAGATCACAGCCCTTTGAGACACTGATTAGATTC R 2 1 2 1 10000 f 74 goat "snp55190-scaffold849-277546;SV_300" 13 63229556 C T SV_300 2 preexisting CNV preexisting neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789946 Affx-122945695 AX-385276952 13 61722593 AACTAGTGAGTCCAGCGGGGCTCAGTCCTTGGCCT[A/G]CTTCTTTCTTTTCTACACTCCCTCTCTTCAGTGGT R 2 1 2 1 202000 f 74 goat snp55189-scaffold849-226217 13 63273673 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438569 Affx-122931164 AX-123308907 13 61759304 CATCCACTGCAGTCTCTGTGATGGTTTAGGCAAGC[A/G]CAATCCCTTGAGTTTCCTCTTCTGTAATATGTGTA R 2 1 2 1 303000 f 74 goat snp55188-scaffold849-189506 13 63310399 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769218 Affx-122935639 AX-385256392 13 61789330 GGTAGAGACTGAGATCTTCAAGGGGAATGCTCCAG[G/T]AGCAATAAATAGTCCCCGAAATGACCACTAAGGAG K 2 1 2 1 10000 f 74 goat "snp55187-scaffold849-159480;SV_300" 13 63340917 A C SV_300 1 preexisting CNV preexisting neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396055 Affx-122963453 AX-123266410 13 61864842 TTTGATTAGCATTTTGAGCTGCCACAATGTATCTG[C/T]GTATAACTATTCAGCATTATTAATTTTAAAAATAG Y 2 1 2 1 101000 f 74 goat snp55186-scaffold849-83968 13 63416242 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401719 Affx-122959530 AX-123272072 13 61929674 AAGGTCAGACTCATAAGAGGTGAAGCTGGAAAAAC[A/C]GCTGGCGTGTCCGCTGCAGTCTGTTTTCTGACAGT M 2 1 2 1 101000 f 74 goat snp55185-scaffold849-19136 13 63480938 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765831 Affx-986697629 AX-385253278 13 61955549 GAGTCTCCTGCCAGGTGTGCTGTGAGGATGTGGAG[C/G]GATAATGTGTGTAGGCTCCTAATACAACAGTGATG S 4 1 2 1 600010 r 74 goat 13_61955549 13 61955549 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 320763102 Affx-986697631 AX-385251060 13 61955617 ATGAAGATATTATAGTTATTGCTGGTGTCTGGTCA[C/G]TTCACTCCCCTCCACCTCAGGTGTCCCATCTGTAC S 4 1 2 1 600010 f 74 goat 13_61955617 13 61955617 Ancestral_priority_1043 ancestry 0.612 recommended IMAGE 10K 10K ancestral 320763104 Affx-986697633 AX-385251062 13 61956411 ACCAGCTGGAGCAACGTACGTAGGGGAGAAACCTC[A/G]GGCCAGCCCCTCCCACACCCTTAGCCACTACACAT R 2 1 2 1 600010 f 74 goat 13_61956411 13 61956411 Ancestral_priority_1043 ancestry 0.49 neutral IMAGE 10K 10K ancestral 320763106 Affx-986697635 AX-385251064 13 61956537 CTGGGGAGAGGCAGACGTGCACAGAAAGTACTTGG[A/C]AACAGAGCAACATGCTCTCCCTCAGGGCCACCCAG M 2 1 2 1 600010 f 74 goat 13_61956537 13 61956537 Ancestral_priority_1043 ancestry 0.624 recommended IMAGE 10K 10K ancestral 320763108 Affx-986697637 AX-385251065 13 61956565 TACTTGGAAACAGAGCAACATGCTCTCCCTCAGGG[C/T]CACCCAGGGGCAGGGTCCCCGATCTGTGTGTTACA Y 2 1 2 1 600010 f 74 goat 13_61956565 13 61956565 Ancestral_priority_1043 ancestry 0.476 neutral IMAGE 10K 10K ancestral 320763075 Affx-986697604 AX-385251041 13 61956646 CAACAACACGTCAGGGAGCATGTGTTCATCAGCTA[C/T]GATCACAAGGCATTGTTATGACACAGGGGACACGT Y 2 1 2 1 600010 f 74 goat 13_61956646 13 61956646 Ancestral_priority_1043 ancestry 0.538 neutral IMAGE 10K 10K ancestral 38395615 Affx-122963809 AX-123265970 13 61971928 ACCGTCGGGTAGGACTTGAAGATGGCGATGATGGC[A/G]ATCTGGATGAACATGAAGAAGATAGGGTGCTCCCT R 2 1 2 1 101000 r 74 goat snp12122-scaffold1449-23019 13 63523161 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421156 Affx-122944181 AX-123291503 13 62022545 ATGTTCGTCAGCTAGGATGGGTCTGTTTAGCCCTT[C/T]AGTTCAGTTTTCTGAACTACAAATGGGGGAGTAAA Y 2 1 2 1 101000 f 74 goat snp12123-scaffold1449-73636 13 63573086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429601 Affx-122937711 AX-123299942 13 62078049 TCAGAGACCCTGGAGAAGTCTGTTCCAGACTGTAT[C/T]ACTTCATGTCAGCACTACCAGCGCTTTGCCAAAAC Y 2 1 2 1 101000 f 74 goat snp12124-scaffold1449-129140 13 63628634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794783 Affx-122941759 AX-385281743 13 62136158 AAGACTGAAAATAAATCAACTAAAATACAAATAGT[A/G]ATTGTACTAGGTTGGCAAGATTGCTGGTAAATTTT R 2 1 2 1 201000 f 74 goat snp12125-scaffold1449-187249 13 63686716 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401687 Affx-122959555 AX-123272040 13 62180422 GTATGTTCTAGAATAGAGGTTGACAAACTATTGTC[A/G]TTAGGCCAAATTGGACCCTGTTTTTCTAAAATAAA R 2 1 2 1 101000 r 74 goat snp12126-scaffold1449-231513 13 63731015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765793 Affx-986697607 AX-385253248 13 62216816 TGCTGTGAGCACCCTGTTTGCCACCCACAGAGATG[C/T]TCAGTACTGGGGCCCTCAGAACTTCTGACCCTTAG Y 2 1 2 1 600010 r 74 goat 13_62216816 13 62216816 Ancestral_priority_1043 ancestry 0.514 neutral IMAGE 10K 10K ancestral 38421339 Affx-122944069 AX-123291686 13 62236122 TAATGTATAATCAGAGTACAGAGCCAGGGAGAGAG[A/G]GGTACACTCTGTATGTGTGTGTAACTGGAAGTGGG R 2 1 2 1 101000 f 74 goat snp12127-scaffold1449-287213 13 63786397 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801680 Affx-122921782 AX-385288588 13 62286336 CACGATTGAGTGGACGGCATGAAAGTAGAATGAAT[C/T]CAGCTCTTTGATGAGATGACCCTTGGCTCTGCCTG Y 2 1 2 1 201000 r 74 goat snp12128-scaffold1449-337427 13 63836592 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384034 Affx-122972890 AX-123254392 13 62316545 CTGTTCACCATCCAGTGGAACATCCGTGCCTTCAA[C/T]GCTGTCAAGAATTGGTCATGGATGAAGCTCTTTTT Y 2 1 2 1 101000 r 74 goat snp12129-scaffold1449-367636 13 63866664 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438240 Affx-122931431 AX-123308578 13 62353005 ACTAGATGGAGGTGGTGGCCGCACAAACTGCAAAT[A/G]TACTATAAGTCACTGAATTAAGTGGTTAGTTTTTT R 2 1 2 1 101000 r 74 goat snp12130-scaffold1449-404096 13 63903070 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397411 Affx-122962251 AX-123267766 13 62435763 CCTACACCAGGATTTTATACCATGCTGTCCCTCTG[C/T]GTCATAGTCTTTTTTTAATAAAAAAATTATAGATC Y 2 1 2 1 101000 f 74 goat snp12131-scaffold1449-486854 13 63986512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432507 Affx-122935575 AX-123302848 13 62467314 TGCACCGTTCTAGGTATAGAAGCAAATAAGATGGA[C/T]AGCCTCTATCCTCATGGAGCTTACATTCTGATGGG Y 2 1 2 1 201000 f 74 goat snp12132-scaffold1449-518405 13 64018420 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770184 Affx-122976310 AX-385257350 13 62521051 AGAGGTCTTCCTGGTAAAACATAGTCTGAGAAACC[A/G]CAGATCTTACTCTAGCCTCTTTTCACAAAGGTGTC R 2 1 2 1 101000 f 74 goat snp38035-scaffold4735-20143 13 57799709 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437689 Affx-122931765 AX-123308027 13 62561318 TGGGATTTAGGAGGCCTGGGCTTCTAATCCTACCA[C/T]GGTTTCTGTGACCTTGGGCCATTTCCTTCCTGAAC Y 2 1 2 1 201000 f 74 goat snp5921-scaffold1209-20025 13 64064519 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790284 Affx-122947763 AX-385277288 13 62764022 GTCTGCTCAGCAGATTTATCCTTCATAATCAAATT[A/G]CAATGTCACCACCTCTACAAAGTCAGCCACTCCAT R 2 1 2 1 101000 r 74 goat snp5925-scaffold1209-222729 13 64266955 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401482 Affx-122958955 AX-123271835 13 62793563 GTTGATCACCTTCTTCGTGGTAATGTGTGTGTCTT[A/G]CTTCTTAAGACTAAAAGCTCCTTAGAAGTAGATCT R 2 1 2 1 201000 r 74 goat snp5926-scaffold1209-252270 13 64296667 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439853 Affx-122930452 AX-123310190 13 62835562 GAAAGTGTGGGGTCTTAAGCACTGGACCACCAGCA[A/G]GGAAAAGTTTTAAGTGAGGAAAGGACAAGAATCTT R 2 1 2 1 101000 r 74 goat snp5927-scaffold1209-294269 13 64338112 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405099 Affx-122956985 AX-123275451 13 62878165 ATTTAAGGAAACCTCAGGGCCCTACTGAGTGCCAT[A/G]TGAAAACCCTGATGGTCCAGTGGTTAAGAATCCAC R 2 1 2 1 101000 f 74 goat snp5928-scaffold1209-336872 13 64380466 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439389 Affx-122930260 AX-123309726 13 62913929 CATAAATATTACTATATAAACGCACAGATAAATGT[A/G]TTAGGATATTCCTTAGAGGATTGTTTGTTATAATG R 2 1 2 1 101000 r 74 goat snp5929-scaffold1209-372636 13 64416198 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427027 Affx-122939835 AX-123297372 13 62943504 GGTGCTCCAGAGCCATTCATTCCAGCAGGCAGAGG[C/T]GCCACAGGTGGCGGGTTCAAAGGTGGCATGCCTGA Y 2 1 2 1 201000 r 74 goat snp5930-scaffold1209-402211 13 64445747 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801217 Affx-122964642 AX-385288130 13 63006018 TTAATGGACTAAACTCCCTTCAAAAAATCAGTCCC[A/G]TTTATGTTAGATAAATGTCCTCAAATTTAGTACGC R 2 1 2 1 102000 f 74 goat snp5931-scaffold1209-464725 13 64508245 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275617 Affx-1111834998 AX-519549186 13 63046139 GGCTGTTCTGTGCATAAGGGCTATGCCTTTGTCCA[A/G]TATGCCAACGAGCGCCATGCCCGGGCAGCTGTGGT R 2 1 2 1 101000 f 74 goat ilmnseq_rs638391203 13 63046139 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468276194 Affx-1111835214 AX-519549744 13 63047336 CAGTATATCGGCATCTGACTCTGCCTCTTCTCTCC[A/G]TACAGACATAAACATGGCTGGAGAGCCGAAGCCCA R 2 1 2 1 201000 r 74 goat ilmnseq_rs664031981 13 63047336 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275789 Affx-1111835010 AX-519549354 13 63052232 CCCCCATACCTGCTTACTGCAAGGCCCCATCCTCC[A/G]CGTCTGTGTCCTGGCTGTGCTCCTGAGAGGAGGAG R 2 1 2 1 103000 r 74 goat ilmnseq_rs640557920 13 63052232 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 320799484 Affx-122935341 AX-385286414 13 63053505 AACTGAGCTCCAGATGATTTTAGGAGAACATTTTC[A/G]TAGGTTGTTTAGATTGCTTACATCTTAAATTTGAG R 2 1 2 1 101000 f 74 goat snp5932-scaffold1209-512212 13 64555607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276094 Affx-1111835238 AX-519549645 13 63077479 TCTTCTGTCTGGGCATCCCCTTCCTCATCTAACAT[A/G]AAAGGCTTCTTCTTCTTCTTTTTCTTCTTGCTCAT R 2 1 2 1 102000 f 74 goat ilmnseq_rs667058957 13 63077479 G A 1 neutral Goat_IGGC_65K_v2 Illumina 38378752 Affx-122977021 AX-123249111 13 63085283 GTTTGCTGTAGAAAATTTAGAAAGCACAGAAAAGC[A/G]CATTGAAAGTAAAAATTGTTTAATTCTGTCATCTA R 2 1 2 1 101000 r 74 goat snp5933-scaffold1209-543990 13 64587700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772071 Affx-122964269 AX-385259226 13 63140941 TGTAAATCTTTGATCTGCCTGAAATTTATCCTGAT[A/G]CAGGATGAAGGCTCTCGCTACCCAGTTGTTCCAAC R 2 1 2 1 101000 r 74 goat snp5934-scaffold1209-599648 13 64643531 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408429 Affx-122954459 AX-123278780 13 63191518 AAGACAATACTATGAAATCTCCAGGTTTTTTGTGA[A/G]CATCAGGAGGTCGTGATTATTAAAGCTCTCTGCTG R 2 1 2 1 101000 r 74 goat snp5935-scaffold1209-650225 13 64694104 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431803 Affx-122936117 AX-123302144 13 63241165 GTACATGCTCGATACGTGTTACATGGTATTGGTGG[C/T]GGTGGTTCAGTTGCTAAGTCATGTTCGACTCTTGC Y 2 1 2 1 101000 f 74 goat snp5936-scaffold1209-699872 13 64743889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276012 Affx-1111835118 AX-519549566 13 63264827 CAGGCCCAGTACCTGGGCATGCCCCGTGAAGGCCC[A/G]TTCAAGCCTGATCACTACCGCTACTGAGAACCGGG R 2 1 2 1 101000 r 74 goat ilmnseq_rs654276401 13 63264827 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276174 Affx-1111835277 AX-519549724 13 63264863 AAGCTGAATGTGAAGCTGACCAAGCTGACTGAGAA[A/G]CAGGCCCAGTACCTGGGCATGCCCCGTGAAGGCCC R 2 1 2 1 10000 f 74 goat "ilmnseq_rs670924934;SV_300" 13 63264863 T C SV_300 1 preexisting CNV preexisting recommended Goat_IGGC_65K_v2 Illumina 468275754 Affx-1111835068 AX-519549320 13 63268064 AGCACCTGGTTGGTGAAGGAGTTGCTCATCACAAA[A/G]CTAGGGTGGCCCATGGCACAGCCCAGGTTGACCAG R 2 1 2 1 10000 f 74 goat "ilmnseq_rs647135908;SV_300" 13 63268064 G A SV_300 1 preexisting CNV preexisting recommended Goat_IGGC_65K_v2 Illumina 468275924 Affx-1111835153 AX-519549482 13 63269303 TGGCATCATCTTTCATCTGTTCAAAGTGCCTGTGG[A/G]GGAGCCTCAGTCCGTGAGAGAGGGTCAGCGACCAA R 2 1 2 1 102000 f 74 goat ilmnseq_rs657382501 13 63269303 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276040 Affx-1111835133 AX-519549594 13 63269589 CTGACGGCCAACCCCCGCTCTATCATACCCTCCAT[A/G]GCAGCCTGAAGTGCGTTGATGGGGTCAATCTCCGT R 2 1 2 1 10000 r 74 goat "ilmnseq_rs655646612;SV_300" 13 63269589 A G SV_300 1 preexisting CNV preexisting neutral Goat_IGGC_65K_v2 Illumina 468275653 Affx-1111835017 AX-519549223 13 63269678 CGGGCAAGGTGGCAGTGGTTGCGGGCTATGGCGAC[A/G]TGGGCAAGGGCTGTGCCCAGGCCTTGAGGGGATTC R 2 1 2 1 103000 f 74 goat ilmnseq_rs641081301 13 63269678 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275854 Affx-1111835044 AX-519549416 13 63269724 CCCGCAACCACTGCCACCTTGCCCGCAATCATGAC[A/G]TCTGTGGCCCGCTTGATGCCATCTATGAGGGACTC R 2 1 2 1 102000 r 74 goat ilmnseq_rs643909754 13 63269724 G A 1 neutral Goat_IGGC_65K_v2 Illumina 463289684 Affx-1109910537 AX-514774845 13 63270242 CCCACCTTGGTGACAGAGTCGTTGACATTGATGGC[C/T]GGCACCTTCAGGATCCCGTTGGCCATCATCTTGTA Y 2 1 2 1 10000 f 74 goat "ilmnseq_rs638964581;SV_300" 13 63270242 T C SV_300 2 preexisting CNV preexisting recommended Goat_IGGC_65K_v2 Illumina 463289685 Affx-1109910538 AX-514774846 13 63270275 GCTGGCACCTTCAGGATCCCGTTGGCCATCATCTT[A/G]TACAGGTTGTGGACCCCCGTTGTGGTCTCTTCAGA R 2 1 2 1 101000 f 74 goat ilmnseq_rs659529875 13 63270275 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276152 Affx-1111835194 AX-519549702 13 63270330 TGCTTCCTGGCCTGAAATCTGTCCCCTCCCCTCTC[A/G]TTCAGGCATCCGAGGCATCTCTGAAGAGACCACAA R 2 1 2 1 102000 r 74 goat ilmnseq_rs662666553 13 63270330 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468276315 Affx-1111835274 AX-519549848 13 63274142 GCAAGAACTGCTTCAGGCCTCACCTCAGCACCCAG[A/G]GCAACGAGGGTCTCAATGAGGACGGCGGTCTCCAC R 2 1 2 1 10000 r 74 goat "ilmnseq_rs669844416;SV_300" 13 63274142 G A SV_300 2 preexisting CNV preexisting neutral Goat_IGGC_65K_v2 Illumina 468275832 Affx-1111835032 AX-519549395 13 63274226 CAGCCGGCAATGCGGGCGCCCTTCAGAGGCTTGGA[A/G]GCCGAGTACATTTCTCGCATGTGCATCAGGCCTGG R 2 1 2 1 10000 r 74 goat "ilmnseq_rs642776386;SV_300" 13 63274226 G A SV_300 1 preexisting CNV preexisting neutral Goat_IGGC_65K_v2 Illumina 468276017 Affx-1111835203 AX-519549571 13 63274247 TTCAGAGGCTTGGAGGCCGAGTACATTTCTCGCAT[A/G]TGCATCAGGCCTGGCATCTCATTCTCTGCCAGGTC R 2 1 2 1 10000 f 74 goat "ilmnseq_rs663365766;SV_300" 13 63274247 G A SV_300 2 preexisting CNV preexisting neutral Goat_IGGC_65K_v2 Illumina 38423378 Affx-122943136 AX-123293724 13 63331394 GAAGTTGCCACAGCAAAGAAATAGAGAAGGCAAAA[C/T]AGGAAACTCCTGTAGACCAGGGAGATGGGGGGCTC Y 2 1 2 1 101000 f 74 goat snp5938-scaffold1209-790101 13 64834463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463294143 Affx-1109910564 AX-514779255 13 63343216 GCTCAAAGATATGATTGTTACAATATTCCTTGAGG[A/G]GGTGTCTAGAACTCTGTTTTATTGCTGCATTCTTG R 2 1 2 1 10000 r 74 goat "13_63343216_AF-PAKI;SV_300" 13 63343216 A G SV_300 1 preexisting CNV preexisting recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398887 Affx-122961031 AX-123269242 13 63362010 AATCCAATTTACTGGACTCAGAGATGCTGAGTCAC[A/G]CTAACCCTGGTGGGGGAGCTTGATGTATAAACCAG R 2 1 2 1 303000 r 74 goat snp5939-scaffold1209-820717 13 64864466 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276208 Affx-1111835221 AX-519549758 13 63401916 TGAAGTTGGGGGATTCAGGGCCACCACTTGGGACT[C/G]TGCCTGCTAGAGTGCCCAGATTGTCTATGTGTTGG S 4 1 2 1 101000 r 74 goat ilmnseq_rs665324166 13 63401916 G C 1 recommended Goat_IGGC_65K_v2 Illumina 468276169 Affx-1111835202 AX-519549719 13 63402930 GAAATGACTAAATAAGAGAGAAAATATTTCAGTAT[A/T]TGAGATGTTAGTCCATCCTTCAAATCAATTTAATT W 4 1 2 1 101000 r 74 goat ilmnseq_rs663184368 13 63402930 A T 1 recommended Goat_IGGC_65K_v2 Illumina 320780177 Affx-122971655 AX-385267274 13 63404565 GAAATAGGAGCTCATCCACTCTGGTTTTTCACTCC[A/G]TGCTGAACCCTCTGGAGAAAGTTTTTTCTCCCTTT R 2 1 2 1 101000 f 74 goat snp5940-scaffold1209-863272 13 64906990 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275866 Affx-1111835123 AX-519549427 13 63405311 CAAAAGCTGAGCTTATTCTTTTCTCACATACATAC[A/G]TTTCATATTGTTTGACTTTAATGTTTCATAGATAT R 2 1 2 1 101000 f 74 goat ilmnseq_rs654811277 13 63405311 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275871 Affx-1111835052 AX-519549432 13 63406400 CCATTGGGAACAACTTCAGACTCTAGTTGCAGCCC[A/G]TCAAGACAGACTGACAAATCTCCTATTGTCTCTGC R 2 1 2 1 101000 r 74 goat ilmnseq_rs645253156 13 63406400 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275732 Affx-1111834980 AX-519549299 13 63431508 TTTAAAGAGAAGAGAACGGACAGCAATGGTAGAGT[A/G]TATTTTGTCAACCACAACACTCGTATTACACAATG R 2 1 2 1 101000 r 74 goat ilmnseq_rs636390287 13 63431508 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468275974 Affx-1111835181 AX-519549531 13 63435126 CAGCCTTCAGGTAAGGGCTTTTCATTTAATTGACT[A/G]TAAAAAACATAGGAAAATATATAAACAAATAAACA R 2 1 2 1 101000 f 74 goat ilmnseq_rs660448256 13 63435126 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275771 Affx-1111835076 AX-519549336 13 63444319 GGGTTTATCTGCAAGCAGTAGTTATCCTTCCCTGC[A/G]TATTCAAACAGGCAATACATTGGGTTCAACACCTC R 2 1 2 1 101000 f 74 goat ilmnseq_rs647808390 13 63444319 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468276011 Affx-1111835200 AX-519549565 13 63444775 TTGAATAAACCAGTTGGACTGAAGGATTTAGAATC[A/G]ATTGATCCAGAATTTTACAATTCTCTCATCTGGGT R 2 1 2 1 101000 f 74 goat ilmnseq_rs663069826 13 63444775 G A 1 recommended Goat_IGGC_65K_v2 Illumina 38448358 Affx-122924117 AX-123318694 13 63454562 CCACACATACACAGAGGAGGCCGAAGATAGAGAAC[A/G]GGATGTAGGGGACTGAGGGGGTGTCTCCGTGGAAT R 2 1 2 1 201000 f 74 goat snp5941-scaffold1209-913269 13 64956089 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443476 Affx-122927818 AX-123313813 13 63497857 CTGGTAGGGCAGCCCCTGCTCAGGGCCAACTGATC[A/G]TTACTCTGGAGGTGGGGTGACCCAGTGGGGTGACA R 2 1 2 1 201000 f 74 goat snp5429-scaffold1188-2879889 13 64999358 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392871 Affx-122965748 AX-123263228 13 63530894 AAAGGCCAGACTCAAACCCAGATGTGTTCCACAAG[C/T]TCTCCACCACAGGCCCCCAGCCTCCTGCAGGAGAG Y 2 1 2 1 101000 f 74 goat snp5428-scaffold1188-2846852 13 65032395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389238 Affx-122969041 AX-123259596 13 63562358 TTCCTAGCCCCCGATTTCAAATACAGGACAGTGAT[A/G]TGGGGCTGAGTCCGTCTGTCCTGTGTCTCATCCCA R 2 1 2 1 101000 f 74 goat snp5427-scaffold1188-2815388 13 65063966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375613 Affx-122978713 AX-123245972 13 63591806 CAAGCTCTGCCTCCCACAGGCCATATAAACACAGG[C/T]GAGCCTCTTCTCTCCCTGGACCTCAGTTTCCCCAT Y 2 1 2 1 101000 f 74 goat snp5426-scaffold1188-2785940 13 65093962 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402000 Affx-122958764 AX-123272353 13 63711186 ATAGTTTGACCACACAGGGACAAGAAAACTCCCCT[A/G]TACAACCCGGAGATGAACTAATGATGAAAACATGA R 2 1 2 1 201000 r 74 goat snp5424-scaffold1188-2666560 13 65210823 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430520 Affx-122937212 AX-123300861 13 63763414 AACACATGCTGCCTTTCTCCTGGCCAGGCCCACCC[C/T]AGTCAGCCAACACCCAGGAACTGTGCTCCTGTGCA Y 2 1 2 1 101000 r 74 goat snp5423-scaffold1188-2614332 13 65263164 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790699 Affx-122958193 AX-385277700 13 63855527 GTTTTCTTCAAGGGTGCCTGGATGTTGGTAATATA[C/T]CTCATTTTTCTGTTCGTGTCAGAGAATACACAGTG Y 2 1 2 1 101000 f 74 goat snp5421-scaffold1188-2522219 13 65355406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427825 Affx-122939743 AX-123298168 13 64037414 AAGAAGTAAATAGAAGGATCACTTCCAAAGATGAT[A/G]TCTAAATATTTCGTCCTGCAGTCGGAAGACAGTTA R 2 1 2 1 101000 r 74 goat snp5417-scaffold1188-2340332 13 65537733 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391307 Affx-122967332 AX-123261664 13 64082552 AAGTCTGAAAGCAGAGGCCTCTTCTGACTTAGACA[G/T]CTCTGTGGTCACCTCCATCTTTAGTCCCATTAATG K 2 1 2 1 101000 r 74 goat snp5416-scaffold1188-2295194 13 65583229 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801244 Affx-122955840 AX-385288157 13 64156463 TAAATGAGTGAATGGAAATAGACCAAAGAAGTTAA[C/T]GGTGGTTTTCTCTGACAGGAGGATTTTAAGTGACT Y 2 1 2 1 101000 r 74 goat snp5415-scaffold1188-2221283 13 65654745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453603 Affx-122920138 AX-123323936 13 64196090 TGAGGCAAGCAACGAAGATCAACTCTGGCTCACTT[A/C]TGTTAAAAACAAAGGGATGGGGACTTCCCTGGTGG M 2 1 2 1 102000 f 74 goat snp5414-scaffold1188-2181656 13 65694500 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394530 Affx-122964526 AX-123264885 13 64330092 TGATGGGCTGGAGAGAGGTTTGTCTGTGACTGACA[A/G]GTCCCTGCCCTTACCCCCTATGTGAGATGTTCAGG R 2 1 2 1 101000 f 74 goat snp5412-scaffold1188-2047654 13 65827584 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399415 Affx-122961236 AX-123269770 13 64397047 TGTGTGGGCTTACTCAGCTATACAATCATTGCACG[C/T]GTGCACACTTAGGCAGGGGCACAGGCTCACATGGG Y 2 1 2 1 101000 f 74 goat snp5411-scaffold1188-1980699 13 65893944 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422968 Affx-122943008 AX-123293314 13 64433253 GATTCCTCAGGTTCTGCATTCAGGAGTAGAAGCAG[C/T]GAGCCCAGGAAGGAGGCGGAGCTATTATTGTCTCA Y 2 1 2 1 101000 f 74 goat snp5410-scaffold1188-1944493 13 65929867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445567 Affx-122925141 AX-123315904 13 64463031 AGACAGACAGACAGATCTTACTCAGAGCTAATACA[C/T]GCTGTTGTGGAAGGATAGATGGGCACACAGATGAA Y 2 1 2 1 101000 f 74 goat snp5409-scaffold1188-1914715 13 65959405 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792706 Affx-122933306 AX-385279685 13 64492034 GTCTGTTCCTGGCCACATTGTTTAATCACTGCTGC[A/G]TTGGTCTATGCTACCTAGTAGGGCAAATTCAATCC R 2 1 2 1 101000 f 74 goat snp5408-scaffold1188-1885712 13 65988764 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444384 Affx-122926599 AX-123314721 13 64524806 TTCACTTCCTTTGCCCTTCCTCCTGCCTTTCAGCT[A/G]TCGTGAGGAGGGGGCCTCATTGTGTCTCCCATGCA R 2 1 2 1 103000 f 74 goat snp5407-scaffold1188-1852940 13 66021570 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401515 Affx-122958930 AX-123271868 13 64598740 GATGTGGAGACAGACAGGGCAGAAGGAGGTTGGGA[C/T]GGTTCCCTGAGCATAACCTAGGTCGTGCGTTCATT Y 2 1 2 1 101000 r 74 goat snp5405-scaffold1188-1779006 13 66096055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402343 Affx-122959061 AX-123272696 13 64639648 GTGCCTCTCTGAGTCTTCTTGTTTCATTGGTAAAG[C/T]GGGTCGACGGTAAACCCTCTAATTTGGTCCCTGCC Y 2 1 2 1 101000 f 74 goat snp5404-scaffold1188-1738098 13 66136189 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382831 Affx-122973547 AX-123253189 13 64669998 TTGCTCTGGCCACTGGAACATGCTTTGCCTGACTG[C/T]GGAGCAGGTCAGAGGTGTCAGAGAATTAACAGTGC Y 2 1 2 1 101000 f 74 goat snp5403-scaffold1188-1707748 13 66166484 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449456 Affx-122922660 AX-123319791 13 64771499 ACAAATCTACATGAAGGGCTTCTGTGAACCTTGAG[C/T]AGAAAGGTTATAAGAAATAAATACCTAAACCATAA Y 2 1 2 1 101000 f 74 goat snp5401-scaffold1188-1606247 13 66268356 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774220 Affx-122923201 AX-385261357 13 64802259 GTGTCTAGCCTCGTGCTAGGCATTCAACTAATACT[A/G]CATTTGACATCCTAACTAAACAGCATGGTAACAGT R 2 1 2 1 201000 r 74 goat snp5400-scaffold1188-1575487 13 66299076 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410725 Affx-122952714 AX-123281075 13 64857302 ACATAGAGCCTGGAGCTGTGTAAGTGTTTGGTAAG[C/T]GTCAGCATCTTCTCCAGCCCAGCCCGCACATTGAG Y 2 1 2 1 101000 f 74 goat snp5399-scaffold1188-1520444 13 66353909 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382632 Affx-122973689 AX-123252990 13 64934996 CAACTAAGCACAGCACAGCATGCAAAGATGGTGAA[C/T]ACAGTGTTCGTTGAAGCAATGTTTGCATTAATAAA Y 2 1 2 1 201000 r 74 goat snp5397-scaffold1188-1442750 13 66431015 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790024 Affx-122963124 AX-385277030 13 65005360 TCCTTTAAGTCAGTGAAAACAGACAAATGCAATTA[C/T]ACATGCTGCTAATTTTATGTTAACTTGTTTTCAGT Y 2 1 2 1 101000 f 74 goat snp5395-scaffold1188-1372386 13 66501156 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276885 Affx-1111835569 AX-519550394 13 65035644 TGCTGGCGGAGAGTCAGCCACGAGTGCGAGGGGGA[A/G]GCAGGGAGGCGCATCTGGAGTCTGCTGAACAGTAG R 2 1 2 1 102000 r 74 goat Random2.2K-1367 13 65035644 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402224 Affx-122959152 AX-123272577 13 65047056 CGAGTATTAACCCCCTTTGGCTATATGGTTCACAC[A/G]TAAGTTCTTCAACTCAGGCTTTTTTTTTTCTTTTA R 2 1 2 1 101000 f 74 goat snp5394-scaffold1188-1330690 13 66543014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410598 Affx-122952112 AX-123280948 13 65078232 GAAAAGCCACTGACCACCCGCCAAACTGATTGATC[A/G]ACGTCAGAGCCCCTTTCCTGGGAGCAGGCAAAGAA R 2 1 2 1 101000 f 74 goat snp5393-scaffold1188-1299514 13 66574071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396498 Affx-122963532 AX-123266853 13 65181433 TAGAAAGTTTCTTGGAGACAGCCAAATCTGCAGTG[C/T]AACTGAAATGAACTGGCTTAACAACAAGGCAGGTA Y 2 1 2 1 101000 f 74 goat snp5391-scaffold1188-1196313 13 66677590 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418134 Affx-122947113 AX-123288482 13 65228971 GAGCAGAAGAACTGAAAATGGGTACCTGACTGTGT[A/G]CCCTTTAGACCCCCAAGACTCCTGCCCACCATCAG R 2 1 2 1 101000 f 74 goat snp5390-scaffold1188-1148775 13 66725050 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453336 Affx-122919964 AX-123323669 13 65282808 GTGGCAGGGTCATAAAAGACACTGGAATTGGGCTT[A/G]GGATCTGAACTTCCACACTAAGTGCAGGGAAGCCC R 2 1 2 1 101000 f 74 goat snp5389-scaffold1188-1094938 13 66780182 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799474 Affx-122935876 AX-385286404 13 65317647 GGGTTTACGAGGGTCAGCACACCAAACATGAGTCC[A/G]TGACAAACCTCTTCCACTTAAGTAATTAGAAGAAA R 2 1 2 1 101000 f 74 goat snp5388-scaffold1188-1060099 13 66815214 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444706 Affx-122926426 AX-123315043 13 65422798 GGAAAGGCAGGAAAAAGGATTTGGGTCCAGTGATA[G/T]GGCCTTTTGGATAACAGAAATTGCTCAGAAATGCC K 2 1 2 1 102000 f 74 goat snp5385-scaffold1188-954948 13 66914111 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393768 Affx-122965202 AX-123264123 13 65478731 CCCTACATAGCACAATAAAGCAGCTGCCTTGAGAT[A/G]ACTGAGGGAAAAAAAACCAAAACACCTAAATGTTT R 2 1 2 1 101000 f 74 goat snp5384-scaffold1188-899015 13 66969895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450279 Affx-122922170 AX-123320614 13 65525972 TGTGCCAGTCTAGAGCTAAGCACTTGACACATAAC[A/G]TTTTATTTATTTATTATAACAACCCTATGAAATAG R 2 1 2 1 103000 f 74 goat snp5383-scaffold1188-851774 13 67017173 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423831 Affx-122942790 AX-123294177 13 65599900 CTCCATGCTAAGTCCTTCCCTGGAAAGATATGAGA[A/G]GAGGTGACAGGATGAGATAAGGCCAGGTACCAGGG R 2 1 2 1 101000 f 74 goat snp5381-scaffold1188-777846 13 67090947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430572 Affx-122937006 AX-123300913 13 65653549 GGGGGATATGCATTTTGACAAGCTTCCCAGGTAGC[A/G]CCAGTGTACCCCTGCCCTACACACTCCACTTCTAC R 2 1 2 1 201000 f 74 goat snp5380-scaffold1188-724197 13 67144609 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390405 Affx-122967655 AX-123260762 13 65688239 GCTCATATGCCTGGGCTGCTCCAGGGAAGTTCTCA[C/T]GTGAGCTTAAGAGCAGGCTGAAGGCATGTTACATT Y 2 1 2 1 101000 r 74 goat snp5379-scaffold1188-689507 13 67178390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429495 Affx-122937868 AX-123299837 13 65724773 CACCAGAAATTCAACAAAGTCCAGCCATGGTGTGA[C/T]GCTGGGGTCCCTGCCACCGAGAACTCCAGTGGCCA Y 2 1 2 1 101000 f 74 goat snp5378-scaffold1188-652973 13 67214980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410347 Affx-122952460 AX-123280697 13 65757472 TTTATGAATATATTTTCAGCTGCAGAGACAAAGAT[A/G]GTGTATTTGACATGCCCCTAAACCTACCTACCGAT R 2 1 2 1 101000 r 74 goat snp5377-scaffold1188-620274 13 67247703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428915 Affx-122938913 AX-123299257 13 65795949 GAGCAGACTGGAAAGAAGTTCAGGGTGGGGGGAGA[C/T]CGTTTAGAACTCTACAGAGGGAAATGGCCTTATCC Y 2 1 2 1 101000 r 74 goat snp5376-scaffold1188-581797 13 67285796 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415731 Affx-122948507 AX-123286080 13 65850534 CTTACCTAGATAGTCACCAAACCCAGAAATTTGAG[C/T]CATTACTGACTTCACCTTCCTCTATATCTGCCTCT Y 2 1 2 1 101000 r 74 goat snp5375-scaffold1188-527212 13 67339964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417405 Affx-122947681 AX-123287753 13 65887410 TCATCCCAGTGCACAGGGTAACCCAGGTCTCCTGA[C/T]TGGATGGCTACAATTCATGTTTCACTGGACAGACT Y 2 1 2 1 101000 r 74 goat snp5374-scaffold1188-490336 13 67376398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272708 Affx-1111832992 AX-519546412 13 65914341 CCTAGATGACTCCTTCCCTGGCAGGTGTGTGTGTG[A/G]GACACGGAGTGACTGACAGGGGCCCAGTCGCCCCT R 2 1 2 1 103000 f 74 goat 13_65914341_AF-PAKI 13 65914341 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396882 Affx-122963234 AX-123267237 13 65927012 GTGTGTCACTCCTCCATTTGACACTTCAGACGAAA[C/T]GGTGGTCACACAAAACCTTGCTTTCCTGCTATAAT Y 2 1 2 1 202000 r 74 goat snp5373-scaffold1188-450734 13 67414706 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446970 Affx-122924656 AX-123317306 13 65981393 TGGGCACATATATGCAGTTACTACTGGGCACTTTT[A/C]TTTTAGAATGAAGTTTTTTTGGAGATATCATCTCC M 2 1 2 1 201000 r 74 goat snp5372-scaffold1188-396353 13 67469416 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396772 Affx-122962768 AX-123267127 13 66014345 ATCTACCCCCAGTGCGATCTAAATCTGGGGGTGAG[A/C]GGAATAGGGAGACCCTCCCAGGACCAGCCAGCTCT M 2 1 2 1 201000 r 74 goat snp5371-scaffold1188-363401 13 67502389 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789115 Affx-122928260 AX-385276128 13 66053980 CAGGAGTTCTCAAAGCATGGACCCTAGACCCATAG[C/T]ATTGACATCACCTGGGAACAAGATAGAAATCCAAA Y 2 1 2 1 201000 r 74 goat snp5370-scaffold1188-323766 13 67542078 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453349 Affx-122919953 AX-123323682 13 66086283 GGCCCCATCCCTTGAGAGGCCAAAGATGATACCAC[A/G]TGATGGGTGATGGGATGGTGGTATCACTCCCTGAG R 2 1 2 1 201000 f 74 goat snp5369-scaffold1188-291463 13 67574763 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789827 Affx-122921567 AX-385276834 13 66131017 AGAATCCGAGTGCCATGGCTGACATTTTACTGGGA[C/T]ACATTTTATTTTGGAAGACTCAACTCTGTACCGCC Y 2 1 2 1 101000 f 74 goat snp5368-scaffold1188-246729 13 67620296 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775775 Affx-122951695 AX-385262906 13 66194463 TTCTGATTTGGCTAAAACTGCATGCCAAACACTGC[A/G]TCAAGTTCTTTATTTGTATTAGCAGCTCTTTTAAT R 2 1 2 1 101000 f 74 goat snp5367-scaffold1188-183283 13 67683652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415260 Affx-122948848 AX-123285609 13 66231585 GGGCTTCTTCCACAGACACCCAAAGGGCAGAGTCA[A/G]AAATTATAAGAAGCAGATTCCAACCCTACCTCTAT R 2 1 2 1 201000 r 74 goat snp5366-scaffold1188-146161 13 67720860 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452207 Affx-122920811 AX-123322540 13 66271116 GGATAAGCATGATCACACTTAGCTCTCACAATGAC[A/G]CTGAGTTGGCATAATCCCTATTCCTAGAGAAGTGA R 2 1 2 1 101000 r 74 goat snp5365-scaffold1188-106630 13 67760636 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392595 Affx-122966056 AX-123262952 13 66306132 TCCTAGTTGACACAGACCAGGAAGCCTAGGTAAAC[A/G]TCTGAGTGACAGTGTCTTTGGCTGTGCGCTAGGTT R 2 1 2 1 101000 f 74 goat snp5364-scaffold1188-71614 13 67795978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399102 Affx-122960868 AX-123269457 13 66351413 CACACCACCTCTCCCCAACTCACATAGCATATGAA[C/T]GCTCGTCAAGAGAATAAATGTATGTTGGAGACAGA Y 2 1 2 1 102000 r 74 goat snp5363-scaffold1188-26333 13 67839448 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429968 Affx-122938063 AX-123300309 13 66387015 GCAAATTGTAGGACACAGTTTAGCAACTGAGCATG[C/T]ACGCTTCATAAGGTCACAAGCTTTACAAAGCTTTT Y 2 1 2 1 201000 r 74 goat snp7749-scaffold1278-2418733 13 67875151 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773882 Affx-122954721 AX-385261021 13 66426156 CTCCCATGCATAACTCTCCCTCAGAACTGTTTTCC[A/G]TCTTTCTTTGGGCTCTCCCATCTTATCAGATATTG R 2 1 2 1 101000 r 74 goat snp7748-scaffold1278-2379592 13 67914231 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398582 Affx-122961499 AX-123268937 13 66472098 GAGTGGATACAGGATCTGCCTATGGTTACTGAGCC[A/G]TAGTTATAATTTATTATTAACTCTCTCTTCTGTGC R 2 1 2 1 201000 f 74 goat snp7747-scaffold1278-2333650 13 67959831 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389216 Affx-122969058 AX-123259574 13 66521605 TAATTACTTCTGAATACGTCTTGCTAAAAGACACA[C/T]GAAACAAACCGAGATAAAGCACAGATGCTCACAGA Y 2 1 2 1 201000 f 74 goat snp7746-scaffold1278-2284143 13 68009284 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426543 Affx-122940186 AX-123296889 13 66550941 CATGACTAAGGATACAATAGAACTTCCTGGTCTCC[A/G]CTTTTAACCACAGGCTTCTGTCTCCTGAATGATAG R 2 1 2 1 101000 r 74 goat snp7745-scaffold1278-2254807 13 68038595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416392 Affx-122947861 AX-123286741 13 66597620 AAGTCTGCTAGAGAGTAAACAATGCAATCATTTAA[C/T]ACGCATATTTTTGTATTATACTCATAGTCTTCTTT Y 2 1 2 1 101000 f 74 goat snp7744-scaffold1278-2208128 13 68080446 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394952 Affx-122964286 AX-123265307 13 66655699 TCCTCTTTAAACTAATGTTCTTGCTTCAAATATTG[C/T]AATGATAAGACCAAGTAAATAACTAAAATAGCTCA Y 2 1 2 1 101000 f 74 goat snp7743-scaffold1278-2150049 13 68138486 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414944 Affx-122949087 AX-123285293 13 66697259 GAAGCAGGTCTATAAACATTGTTAGAGGCAGACAC[A/G]TTGCAGATTCTGCCACAACTGCCTCTCTTACGTAA R 2 1 2 1 101000 f 74 goat snp7742-scaffold1278-2108489 13 68179958 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395291 Affx-122964073 AX-123265646 13 66727822 TGTAATCTTGAAGAACCCAGGCATGGAGATAGCTG[C/T]GAGCTCATTTCTCTTGCTCCTTTTTTAAAAATCAG Y 2 1 2 1 101000 f 74 goat snp7741-scaffold1278-2077926 13 68211020 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789206 Affx-122930701 AX-385276218 13 66781624 TTGGAAACCACATATCCCATCACGGTGGAATTTTA[G/T]CATATTTTAATTTTCTGCTCTTTGCCACTCCCTCC K 2 1 2 1 202000 r 74 goat snp7740-scaffold1278-2024124 13 68264440 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413278 Affx-122950211 AX-123283627 13 66814486 TCAATAATGTCTGGATGACCAAAGGGGTATTAATG[C/T]ATCTCTGGTTAATAATGGGAGCTGACAGGCTTCTC Y 2 1 2 1 101000 f 74 goat snp7739-scaffold1278-1991262 13 68297449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381349 Affx-122974415 AX-123251707 13 66865746 GTAGTCTTGGACACAACTAATTCTGATTAAAGCTC[A/G]TATTCTGATTGTTTCTTACGCTAAGAGCCGTGCAG R 2 1 2 1 101000 r 74 goat snp7738-scaffold1278-1940002 13 68348586 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381862 Affx-122974183 AX-123252220 13 66897213 TTTTCCCTCTTTGCTTGAGGCTGATTACTCATAAG[C/T]GCATAAGTGCCAGGCTCATTTGCAAAATTTTCAGA Y 2 1 2 1 101000 f 74 goat snp7737-scaffold1278-1908535 13 68379951 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444144 Affx-122926796 AX-123314481 13 66935575 GAAGATTAGCACGATGGTGACACCGTAAAACTCGA[C/T]GGGGAGCCTGGAGAAGAGGGCCAAAGAGAAGAGAT Y 2 1 2 1 201000 f 74 goat snp7736-scaffold1278-1870173 13 68418492 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401843 Affx-122959433 AX-123272196 13 66967691 GCACACTGTCTTTTGCTATAGAATTACAGAATGAC[A/G]GAAATGGAAATATAGCAATTACTCACCAAAATATT R 2 1 2 1 101000 f 74 goat snp7735-scaffold1278-1838057 13 68450651 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783222 Affx-122932754 AX-385270288 13 67013694 TTCCCATTGACCTGCATCTATTGTGGTCAATTTCC[A/G]CTACATGAGCCTCAAGTCTAAATACCCCCTGATAT R 2 1 2 1 101000 r 74 goat snp7734-scaffold1278-1792054 13 68497025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422422 Affx-122943365 AX-123292768 13 67055118 CAAAGTGCGGCACTTGGGGTCAGAAATAGGTGGAC[A/G]TGACATCACAGGATCTGACTGATCCCTGACGCCGA R 2 1 2 1 201000 r 74 goat snp7733-scaffold1278-1750630 13 68538440 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434408 Affx-122934680 AX-123304749 13 67089697 CTGCTTGGTGTCCAAAAATATAAAAATGTTTACTC[C/T]GAGTGTTCTTTTTCCCATTGTCATTACAGAGTAGA Y 2 1 2 1 101000 r 74 goat snp7732-scaffold1278-1716051 13 68573050 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771326 Affx-122946673 AX-385258484 13 67158544 GTTCAGGCCGTAGACAACACTGGGTTTAGAACCAG[C/T]GGTTGTGTCTTGCTGGATATATATCAAATTGTAGA Y 2 1 2 1 202000 f 74 goat snp7730-scaffold1278-1647204 13 68641858 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404772 Affx-122956686 AX-123275124 13 67206872 AAACTAGGATTGCATGCCAAAATATAATTAAATGT[A/G]CATGTCTATCTTGATAAAAACAAAGGCCTTCTATA R 2 1 2 1 101000 r 74 goat snp7729-scaffold1278-1598876 13 68690287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453906 Affx-122919496 AX-123324239 13 67249264 TAGAAAATACAGAAAATAGGAGACGGGACTTCCCT[G/T]GTGGTCCAGTGACTAGGACTCCACACTTCCAATGC K 2 1 2 1 103000 f 74 goat snp7728-scaffold1278-1556484 13 68733355 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449581 Affx-122923224 AX-123319916 13 67281398 GGTCATTTGGGACAAGATGCTCAAATGCTCTTAGG[A/C]TCACGTTTCTTGTCAAAGTGACAGTGAGAACCTAG M 2 1 2 1 101000 r 74 goat snp7727-scaffold1278-1524350 13 68765575 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439674 Affx-122930587 AX-123310011 13 67322582 ATTTCACATCAACCTGAAGGCATATTATCACTGTC[A/G]TGAGTTCGAGGCTGAAGGATGGGACTTTATTTTCT R 2 1 2 1 101000 f 74 goat snp7726-scaffold1278-1483166 13 68806715 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276887 Affx-1111835570 AX-519550396 13 67352350 CTGCACCCGCTCCATGGGAAGGCAAAGTCTCAACT[A/G]CTGTACCACCAGAGAAATTCTAGGAGTTGTATTTT R 2 1 2 1 103000 r 74 goat Random2.2K-1369 13 67352350 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452455 Affx-122920563 AX-123322788 13 67358729 GCGTGATTCTACGTGAAGTTCTAGAACAGGCAACA[C/T]GAACTTACCAGGAAAGAAATCAGAGCAGTGCTAGC Y 2 1 2 1 101000 f 74 goat snp7725-scaffold1278-1447019 13 68843198 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446723 Affx-122924720 AX-123317059 13 67397197 TCCTCTTAATTATTGCTTCTAAATGTCTAAGAATC[A/G]TCCCTGCTTCTCAGTTGCAAATGACAGAATCCATA R 2 1 2 1 201000 f 74 goat snp7724-scaffold1278-1408551 13 68881440 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422777 Affx-122943222 AX-123293123 13 67429357 GGAGTTGGAGGAAGCGAGAAAGGTTGGCAAATGTA[C/T]GGACAAGTTGGCAGATGGCTGGAGGGGCTATCGGA Y 2 1 2 1 101000 f 74 goat snp7723-scaffold1278-1376391 13 68913334 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381832 Affx-122974259 AX-123252190 13 67463192 AAGTGGAAAGGCCCCTGGGAAGGGTCTGTCCTGGC[A/G]TTCAGATGACCTCTAAAAGGAGCCCATATTTACCT R 2 1 2 1 101000 r 74 goat snp7722-scaffold1278-1342556 13 68947697 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402613 Affx-122958412 AX-123272966 13 67504112 TCGCATTCTCCTAGCAAGGAGAAAAGGAGACCCTG[C/T]TTGCTCCTTGGAAAGGAAGACGGGCTGCTCCATTT Y 2 1 2 1 201000 r 74 goat snp7721-scaffold1278-1301636 13 68984721 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394156 Affx-122964942 AX-123264511 13 67538182 TATTTCAATGTGATTAACTTCACTTCTTTCCATTT[A/G]GCTGTAAGCAAAATCTTGTTTACAAGGCAAAAAAA R 2 1 2 1 101000 r 74 goat snp7720-scaffold1278-1267566 13 69018927 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38397913 Affx-122961941 AX-123268268 13 67597523 AGGCAGTGAAATCACAACCTCAAGCCTTTCCAGCT[A/G]CAAGAAATGAGGGCTTATTTATTCTATGATCAGAT R 2 1 2 1 201000 r 74 goat snp7719-scaffold1278-1208225 13 69078164 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377765 Affx-122977359 AX-123248124 13 67627080 AACGAACCTTTCCAAGTGGGTTGTGGATTTTTGCT[A/G]TTTTCTCTGCAGTCGACCTGGATTTGCTTTTCTAT R 2 1 2 1 101000 r 74 goat snp7718-scaffold1278-1178668 13 69108043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403809 Affx-122957962 AX-123274161 13 67667053 AGGTAATATAGGCTCTGATTCCAGGGCTTATGGCA[C/T]GGACATCTTTGGGGGCCATTATCTGCCTATGATGC Y 2 1 2 1 201000 f 74 goat snp7717-scaffold1278-1138695 13 69148370 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412400 Affx-122951445 AX-123282749 13 67703141 TTTAGATCTCTGAAGAATTACTTTTTGAAAATTGT[A/G]TTATAGAGTTATCTTCTTGAATCCTTGCATGGATG R 2 1 2 1 101000 r 74 goat snp7716-scaffold1278-1102607 13 69183978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422419 Affx-122943367 AX-123292765 13 67744780 TTGACCACTATGCCACCTGGGAGAATGAGAATGAG[A/C]TGAGGTCACTGTTAGGCATGCCTTGACAGTTGTAA M 2 1 2 1 101000 r 74 goat snp7715-scaffold1278-1060968 13 69225305 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411474 Affx-122951799 AX-123281824 13 67817259 GATAACCAGTCTGCCAAAAACATTATTGTTTTAAG[C/T]GTGCAAAACTTCAAAGTTGATTTTTAAAGCCAAAT Y 2 1 2 1 201000 r 74 goat snp7713-scaffold1278-988489 13 69297667 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428137 Affx-122939057 AX-123298480 13 67848577 TATTTCTAGCAGTGAGTAGCTTGTGAGCTTGCATT[A/G]TATCAGTAAAATAAAATACTACCATTGAAGTAAGT R 2 1 2 1 101000 f 74 goat snp7712-scaffold1278-957171 13 69329138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435164 Affx-122933661 AX-123305504 13 67879534 TCACACTTTTTAGGTCTCATCCTCCTGCACACCCG[C/T]GATATACTCTCAGCCCCTCGAGAGCCTCGTGTTTT Y 2 1 2 1 201000 f 74 goat snp7711-scaffold1278-926214 13 69360173 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768731 Affx-122925624 AX-385255909 13 67947057 TGGGGGTGCTTGCTATAAGGAATCATTTCTAACAT[C/T]TTTTCAAATCCCGTAGATGCGGAGTTCCCCGTCTC Y 2 1 2 1 101000 f 74 goat snp7710-scaffold1278-858691 13 69423331 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410098 Affx-122952835 AX-123280448 13 67994947 TTATTTGATTCTTATACCTGTTTTGTTTTTTGAAG[C/T]AGGGACTTTGGGTTAGATTCTGGCAAAAGATCTGA Y 2 1 2 1 101000 r 74 goat snp7709-scaffold1278-810801 13 69471219 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436128 Affx-122932647 AX-123306467 13 68033839 CAGCCAACCTTTTTTGAAATTACTTGTCAGGTCCA[C/T]GGTTAAGTGTGGACATTATCTCTCAACCTCTGGGA Y 2 1 2 1 101000 r 74 goat snp7708-scaffold1278-771909 13 69509954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429409 Affx-122938524 AX-123299751 13 68088698 AGCAGAGCTGGAAACAGGGATTCAGCAACATGCGA[C/T]TGATGGAGAGACGGCTCTCAGGAGAAACACATAAG Y 2 1 2 1 101000 f 74 goat snp7707-scaffold1278-717050 13 69564299 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411102 Affx-122951917 AX-123281452 13 68145752 ACCTCTACACAGAGAGCTCCTATGTTCTCTTCCTC[A/G]TAAACTTTTGTGTCCTTCGATCTGAAGCTCAAAAG R 2 1 2 1 201000 r 74 goat snp7706-scaffold1278-659996 13 69621267 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384941 Affx-122972321 AX-123255299 13 68202708 GAGGGAGATGGTGGGCTTAGCCAGCATAAAGGGGC[A/G]ATAGCTGAGTGGTGGAGGAGTGCAATGGAGCCATC R 2 1 2 1 201000 f 74 goat snp7705-scaffold1278-603040 13 69678182 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394207 Affx-122964904 AX-123264562 13 68291190 TGGAGAATCTCCAGCCATTTTCCTTCCAGGTGTTA[C/T]TTCTGCCTTGCTACCCCCGCTCCAGTTAGATGCTT Y 2 1 2 1 102000 f 74 goat snp7704-scaffold1278-514558 13 69766434 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782831 Affx-122954811 AX-385269902 13 68340865 TATAACAATAATAAAATATCAACTTGACAAAATTA[C/T]AAAACATTTACTCATAAGCACAGTGTGTTTCCTTT Y 2 1 2 1 101000 r 74 goat snp7703-scaffold1278-464883 13 69815734 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424466 Affx-122941771 AX-123294812 13 68380309 GGGTGGGGTTGCTGATGAGGATTAGAGGGTGTGCA[C/T]GACCTACATTCCTTCAATCTAGAGACCTAGTGTCA Y 2 1 2 1 101000 r 74 goat snp7702-scaffold1278-425439 13 69854305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426777 Affx-122940552 AX-123297123 13 68419533 GAGTTAGCAGTTTTATAGTTGAGAGCAATCCTAAT[A/C]GTAAACTCAACAGCCTTTGTACAAACCAGCAGAGT M 2 1 2 1 101000 f 74 goat snp7701-scaffold1278-386215 13 69894041 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392937 Affx-122965701 AX-123263294 13 68466806 GACTCCAGTGTCTTTTATTCCATGGCTACTTCTTG[C/T]CTGCCATTCTCAAAACATCCCACCGCCACAAGGAC Y 2 1 2 1 101000 f 74 goat snp7700-scaffold1278-338942 13 69941527 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413130 Affx-122950371 AX-123283479 13 68516144 GAGATTGTGCACATCACCCTTTAAGAGTCCCCTGA[C/T]GCATTGATCGCTTTCTCACTGCCCTGACCTGATTT Y 2 1 2 1 201000 r 74 goat snp7699-scaffold1278-289604 13 69991871 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452116 Affx-122920834 AX-123322449 13 68548149 GCACCCCAGATTGGCAGGTGGCAAAGAAACTTACA[C/T]ACGAGACTTGTCTTGGGCACTGCAGGACGGTGGAT Y 2 1 2 1 101000 f 74 goat snp7698-scaffold1278-257599 13 70024005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447698 Affx-122924617 AX-123318034 13 68588546 GTTGCCTGACTGGTTCTCAGTCTCCCCAAGTCTTT[A/C]TATCCCACAAATAATTCCTTTTCTGCTTAAATTAG M 2 1 2 1 202000 r 74 goat snp7697-scaffold1278-217202 13 70072887 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276891 Affx-1111835572 AX-519550400 13 68601992 TAGACCAATTTTGCAATGGCGCTTTGCACGCTGCA[A/G]AACTGTTCAACAAAAACATTCATCTTCTTCTCTTA R 2 1 2 1 101000 r 74 goat Random2.2K-1370 13 68601992 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320793487 Affx-122968902 AX-385280464 13 68650012 ATGGAACTGAGGCAGCAGGAGCAAGAAAATTTAGG[A/C]GTCTGGGATCAGATCCTGATCCTACTACTCACTAT M 2 1 2 1 101000 r 74 goat snp7696-scaffold1278-155736 13 70132824 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437391 Affx-122932434 AX-123307729 13 68679377 CCTTGCTTCATGGAAAAGGCAAAACTTGGAGCCTC[A/G]AATTGTACGTACCCACTCTGGTTGCCAGCCAAGCA R 2 1 2 1 201000 r 74 goat snp7695-scaffold1278-126371 13 70162542 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404564 Affx-122957376 AX-123274916 13 68716682 TGAACCACAAAGCCACCCCTGACGGTGCTGGATCT[A/G]GACTATGAAGGAAGCCAGCAGACATCCTAAGGAAC R 2 1 2 1 101000 r 74 goat snp7694-scaffold1278-89066 13 70202066 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402764 Affx-122958317 AX-123273117 13 68745702 ATCAAAGCCACAGGGAGGCTGAGCTGTGGATCCCA[C/T]ATGCATCCCAGGGTGAGATTTCTGAAAGAACCAGC Y 2 1 2 1 201000 r 74 goat snp7693-scaffold1278-60046 13 70231716 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794495 Affx-122944020 AX-385281458 13 68782454 ATGCTAATAATTACCATATAAAGCATCGAGCTAAG[A/G]TATCATAAAGAAAAGGACAGGAAGAAACTTGGTGG R 2 1 2 1 101000 r 74 goat snp7692-scaffold1278-23294 13 70268724 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408918 Affx-122953955 AX-123279269 13 68812770 CTGACCCAGAAAGTCACATTGGGAATGACAGGCAC[A/G]TCTTAGCATCCTCCTGGATGGAGATGCAGCGTCGT R 2 1 2 1 101000 f 74 goat snp58687-scaffold956-1409786 13 70298842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424249 Affx-122942466 AX-123294595 13 68849871 ATAAGGCTCCTACCTCAAGCCATTCTAATCACTCC[A/G]TCCTTTCTTTTTAGGCCTTACCAGAGGGACAGACA R 2 1 2 1 201000 r 74 goat snp58686-scaffold956-1372685 13 70335758 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405316 Affx-122956833 AX-123275668 13 68881104 TTCAGCAGGACATCTGCAAGACCCCACACACCCCC[A/G]CAGCTGTATTCCTCTCATATCCTAGTTTGCTCACT R 2 1 2 1 201000 r 74 goat snp58685-scaffold956-1341452 13 70366895 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801367 Affx-122945350 AX-385288278 13 68938922 GATTCAAGATTCCATTCGGCCACGTCTTAGGCAGA[G/T]ACCCTGCATGGGTGCTTTAAACCGTCTCTGTTCAA K 2 1 2 1 101000 r 74 goat snp58684-scaffold956-1283634 13 70424348 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276893 Affx-1111835573 AX-519550402 13 68956753 ATTTTGGGCTAGTCCCTGGAGACCTGGGATTGGTG[C/G]CCAGGGTATAAGAAAGGGGAAAATCCCTACAGTAA S 4 1 2 1 102000 r 74 goat Random2.2K-1371 13 68956753 G C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38389740 Affx-122968254 AX-123260098 13 68977645 GGACCTTAAGCAAGTTGCACAGCCTTGTTTAACTT[A/G]CAAGACCTATGGTCACACCTCCTGCAGAGTCATAT R 2 1 2 1 101000 r 74 goat snp58683-scaffold956-1244911 13 70463319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452859 Affx-122920715 AX-123323192 13 69017768 CAGTCCCTGGTGGAAGATCAAAGCCGCTCTCCACG[A/G]GACCCAGAGGAACCACGGTTCTGACATCCCAATTA R 2 1 2 1 101000 r 74 goat snp58682-scaffold956-1204788 13 70504403 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421073 Affx-122944240 AX-123291420 13 69060485 GGGTTCACATGCTGCCTGGCCCCTCCTCAGTCAAG[A/G]ACTTGCATTTTCAGTCTCTACCAGCCTGTGACCTC R 2 1 2 1 101000 r 74 goat snp58681-scaffold956-1162071 13 70546952 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405408 Affx-122956285 AX-123275760 13 69096127 CCTTAGTACAGGGTGCTCTGTACTGAGGGCAACTG[C/T]AGGGTTTCCCCTGGGCAGGACAGAGGTTGCATACT Y 2 1 2 1 101000 f 74 goat snp58680-scaffold956-1126429 13 70582307 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774905 Affx-122965684 AX-385262039 13 69126159 CTGGGCGGCACAATACCAGATGTCTTTTCAGCATC[G/T]ATTGATTCAAACATATGGCTCTCCCCATTAATTTC K 2 1 2 1 101000 f 74 goat snp58679-scaffold956-1096397 13 70611550 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424233 Affx-122942478 AX-123294579 13 69156286 TCTTGTCTTCCTCTGTCTAGGATACGCTTTCTCAA[C/T]GCCTCCTTCCTTGCTTTTAAAGGCAGTCCTTCCTT Y 2 1 2 1 101000 f 74 goat snp58678-scaffold956-1066270 13 70641749 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399015 Affx-122960934 AX-123269370 13 69194970 AGTCATGATACCTCACCCCTAAATTCTTTAGCATA[C/T]GTGACAGTTAATGATAAGGACTTGCTCCTCTGTAC Y 2 1 2 1 101000 r 74 goat snp58677-scaffold956-1027586 13 70680845 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415698 Affx-122948531 AX-123286047 13 69247921 TGACTGTATTACGAGGGAAAATGTTCAAATGCAGC[A/G]TCACAGTGAGAGATTTTACATGTCTCAGTAATTGG R 2 1 2 1 101000 f 74 goat snp58676-scaffold956-974635 13 70734205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405999 Affx-122955511 AX-123276351 13 69284911 GGATGTAAGGGCAAGTAGTCATTAGTCTTTAGGGA[C/T]GGGAGCAAGTGTAAATGTCAAAGCAAAAGTGCAAA Y 2 1 2 1 101000 f 74 goat snp58675-scaffold956-937645 13 70771187 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443778 Affx-122927101 AX-123314115 13 69314268 GCCTTGCCTTGGGTTCTTCATCTGTGTAGTGCGAT[A/G]TTAGTAGTGTCTGTCTCATAGCATTGCTGTGAAGA R 2 1 2 1 201000 r 74 goat snp58674-scaffold956-908288 13 70800150 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771462 Affx-122945720 AX-385258620 13 69385960 GAGCTAAAAAGGTTCTGATTTTGATTCCAGGCTGG[C/T]ACTTGCTAGCTGGATGAGCACGGGTGAATTATTTC Y 2 1 2 1 101000 f 74 goat snp58672-scaffold956-836596 13 70871933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406173 Affx-122956159 AX-123276525 13 69436017 GCTGTGGGGCACATGTGTTCCAGTAACATCTGAAC[A/G]TTAGTCAACCTTTTCTTTCCCTTGGCTCTGTCCCT R 2 1 2 1 101000 r 74 goat snp58671-scaffold956-786539 13 70917727 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380221 Affx-122975480 AX-123250579 13 69483086 TTCAACAGTGGAGACAGACGTTAAGCAACTAATCA[C/T]GGACTTAAATGTTTCATCACACATGCAATGAGGTT Y 2 1 2 1 101000 f 74 goat snp58670-scaffold956-739470 13 70964982 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405918 Affx-122955574 AX-123276270 13 69525651 CCATACAGTGGTTGAGGGCTGTGTAGTGAGAGAGT[A/G]TTCATATGCAAGGCAGGAAATAGAAGCCAAATATG R 2 1 2 1 101000 f 74 goat snp58669-scaffold956-696905 13 71007525 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429639 Affx-122937682 AX-123299980 13 69559219 GGCCTGTGTCCAGGTCTTACAGCTCAAGGACTTGA[A/G]TTTCTCCAAAGATGTGGCCTGACTTTTCATGTTTA R 2 1 2 1 101000 r 74 goat snp58668-scaffold956-663337 13 71040957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442463 Affx-122927945 AX-123312800 13 69599357 CTGTATTCAGATCTAACTTTCACCTTCCAGGGCTG[A/C]GTGGTATCCCATTGAATAGATGCACTGTACTTTGT M 2 1 2 1 201000 r 74 goat snp58667-scaffold956-623199 13 71081056 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401141 Affx-122959379 AX-123271494 13 69639236 GTAACTGGCAGGACAAAAAAATTTGGGTGGTGGGT[A/G]CTCAATTAGTGAACAGTCAAAACAGAGTTCGGGCT R 2 1 2 1 201000 r 74 goat snp58666-scaffold956-583320 13 71121028 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408758 Affx-122953395 AX-123279109 13 69670863 CTCTCATCTTTTCACTTTGCTTTCTTTTGACCTGG[C/T]GGAACTCCTAGGTATGCTTTCCTCCTAGGGAAGGA Y 2 1 2 1 201000 r 74 goat snp58665-scaffold956-551693 13 71152733 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399528 Affx-122961150 AX-123269883 13 69699699 ATACATGGAAAAAAAGGATTTCTAGGTAGGAGAAC[A/G]TCTGATTGGTCACTTTCTTTCAAAGGGTTGTGTGT R 2 1 2 1 303000 f 74 goat snp58664-scaffold956-522857 13 71187835 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774487 Affx-122964485 AX-385261622 13 69730846 ACTAGGATGAAAAGTCTGTTGGCCATATTTGGAAG[C/T]GTTTTTAATCTGCCAGCAATCCTGGGAGCTTTTTA Y 2 1 2 1 101000 r 74 goat snp58663-scaffold956-491710 13 71213057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450294 Affx-122922157 AX-123320629 13 69780514 CTGGGGATTAGGACTCAAAACTGTCTTTGTGAGGC[A/G]TGGGTGACACAGTTGACCCACAGCAATGATCAGTG R 2 1 2 1 101000 f 74 goat snp58662-scaffold956-442042 13 71262809 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446688 Affx-122924747 AX-123317024 13 69822514 GGAACTCTTAGACTCAGTTACAAAAATGATCCAGC[G/T]ATATATGGTTTTAAGAGGGTCACATAAATGAAAGC K 2 1 2 1 101000 f 74 goat snp58661-scaffold956-400042 13 71304570 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413795 Affx-122949910 AX-123284144 13 69871391 GACATGATGGGCCCTCCAGTCTTCTTTGGCTTTGG[C/T]ACTAGTAGGTGCATTAGGGTGTTGATGTGTCCTAG Y 2 1 2 1 201000 r 74 goat snp58660-scaffold956-351165 13 71354061 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437108 Affx-122932174 AX-123307446 13 69904519 GAATTTGATGTTATCTTATGGAATGAAAGGAGCTC[G/T]CTAGGGTATGTCTCCCCAGGACCCTTAAGACAGGA K 2 1 2 1 201000 f 74 goat snp58659-scaffold956-318037 13 71382248 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388728 Affx-122968968 AX-123259086 13 69933866 TAGAAAGTATTTCCAATTTCTTGAATATTTAGCTT[A/G]CAATTTTCATTTCAGACTGGATGGGGTGGGGAGTT R 2 1 2 1 101000 f 74 goat snp58658-scaffold956-288690 13 71411944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783452 Affx-122956076 AX-385270515 13 69974943 AAAATAAGTTGTTATCCATACCTTTCTAATGATCT[A/G]CTTAGGGATAGCTTGCTCACTTTTCAGGTGAAAAG R 2 1 2 1 101000 r 74 goat snp58657-scaffold956-247613 13 71453007 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396333 Affx-122963068 AX-123266688 13 70018510 ACAAAGCTGGACCTTGTCCATGGAGGCAGTGAAGT[A/G]CAGTGGGTGTGTGGACCCTTTAACTTGACCTCTTT R 2 1 2 1 201000 r 74 goat snp58656-scaffold956-204046 13 71498596 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394882 Affx-122964749 AX-123265237 13 70072958 GCACAAGAAAGGACCCCTGTAGAAGCAGGTTCCAA[C/T]GCCACCGAAAACCAGAGTCCCCTGGGGCACGTGAG Y 2 1 2 1 101000 f 74 goat snp58655-scaffold956-149598 13 71553257 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801200 Affx-122963944 AX-385288112 13 70123469 AAGTGACAGAATTTGCAACTCAGAAATTCAAGGAA[C/T]GTGTTAAATGATACCACAGGGATGAAACAAGCAAA Y 2 1 2 1 101000 f 74 goat snp58654-scaffold956-99087 13 71604142 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375720 Affx-122978633 AX-123246079 13 70162644 TACCTTCTGGTCCTGAGTGTGCCCCTGAGGCTGTT[C/T]AGTAACCACATCTGTTTCCCACGCATAGGTCTTTC Y 2 1 2 1 101000 r 74 goat snp58653-scaffold956-59912 13 71643504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452280 Affx-122920754 AX-123322613 13 70208022 TACCTGGCTTCCTCCTTGGCTGGGCTTGGCAGCTG[C/T]GTACTTCATCTACTTCTGGGGACTCTGGCAAACCT Y 2 1 2 1 101000 r 74 goat snp58652-scaffold956-14534 13 71688912 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446411 Affx-122925566 AX-123316747 13 70233538 AAGCTGGAGAAGGCCATGTTTTTCCAGCCAAGAGG[A/G]TCTTCTCAGACTGGCCTCTGCCTCTGGGGATCTCA R 2 1 2 1 101000 f 74 goat snp35329-scaffold423-1963810 13 71714766 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780964 Affx-122967887 AX-385268051 13 70277970 ACGTGGGAATCAGGATGAGACACCAAGGCAAAGCA[C/T]GTCTAATTGATCACACGGTGCTCTTTTCCACAGAA Y 2 1 2 1 101000 f 74 goat snp35328-scaffold423-1919378 13 71758976 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769916 Affx-122969995 AX-385257085 13 70310615 AGGTAGATAGACACATTCTTTAGAAACGTGAATGC[A/G]TTTTGCTAGATTGCCTGCCAGAAAACACTCACCTT R 2 1 2 1 101000 r 74 goat snp35327-scaffold423-1886733 13 71791606 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406505 Affx-122955147 AX-123276857 13 70343686 GATGGCTCGAACCATACTGATACTGAATGCAGGTC[C/T]ATGTGCCTGACACACAGTGAGGCCAAGCAATACCA Y 2 1 2 1 201000 f 74 goat snp35326-scaffold423-1853662 13 71824642 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404866 Affx-122956485 AX-123275218 13 70388633 GTCTTCTCTTTGGGTGAAATCTGTGATTCAGGTAC[A/G]TAGATATAAAATACATCATTAGTTGCTTTTAAGCT R 2 1 2 1 101000 f 74 goat snp35325-scaffold423-1808715 13 71869764 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447179 Affx-122924421 AX-123317515 13 70476805 AATTATCGGTCAGGCACTGTGCCAGGTGCTGGGCA[C/T]GGTTTCTGCCTGGTGGGAGCCCAAAAAACCCTGTA Y 2 1 2 1 201000 r 74 goat snp35323-scaffold423-1720543 13 71958223 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38388304 Affx-122969383 AX-123258662 13 70527633 TCCCCAGACCTAACCAATCATTCTTCAGGGCCTGG[C/T]ACATAATAGGGATCTGATGAGTATGTGTTTGTGGT Y 2 1 2 1 101000 r 74 goat snp35322-scaffold423-1669715 13 72008763 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773780 Affx-122939793 AX-385260920 13 70581312 TTATGAGAAAAAGGAGTGCAGGATAAGAAAACGGA[A/G]CAGTCCCCTGCAGGAGTGTTTGAAAATAAATAATT R 2 1 2 1 101000 r 74 goat snp35321-scaffold423-1616036 13 72062174 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398941 Affx-122960990 AX-123269296 13 70637485 AGGAGGAGCGATGTATTCAGGTGCAAGCACTGCAG[C/T]GAAGGATGCCGGATCCCAGCTTGTCTCATTCTAAG Y 2 1 2 1 101000 r 74 goat snp35320-scaffold423-1559863 13 72116792 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399636 Affx-122961072 AX-123269991 13 70667656 CTTCTTTATTTTTCTTCTTCTGACACTTCTTTCTC[C/T]TCCTCCTTCACCCCAGAGCCCAGGCATGGACCCAC Y 2 1 2 1 101000 r 74 goat snp35319-scaffold423-1529692 13 72146772 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429265 Affx-122937892 AX-123299607 13 70727951 GCTCCCCAAGTCTCCCAAGCAAGTCTCCAGGCCAG[C/T]GATCTCTCTGACTTTCAATCGGTCTCCAAGCTAAA Y 2 1 2 1 101000 r 74 goat snp35317-scaffold423-1469397 13 72206904 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378388 Affx-122976802 AX-123248747 13 70801857 TTTAAGCTGAGTCAGAGTAATTTTGCAAAATGCCT[A/G]TTTGCACTGAAACTCTCCTGACCATGCATCAGTGG R 2 1 2 1 101000 r 74 goat snp35315-scaffold423-1395491 13 72280673 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447723 Affx-122924601 AX-123318059 13 70862737 TGTCGCTAAAAGTGACAAGCCCAAGCTGAATGACC[A/G]TCAGGGAGGATGGTGAGAGGATTCTTCCAATGGAT R 2 1 2 1 101000 f 74 goat snp35313-scaffold423-1334611 13 72340754 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426863 Affx-122940486 AX-123297208 13 70895752 CTTGAACTGCTGTGTTTGGGGTAAGCTGCTGCTCC[A/G]CTCTGGGCCTCGTCTGTCTGTCTGTGTGCCTGGTA R 2 1 2 1 101000 f 74 goat snp35312-scaffold423-1301596 13 72373997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384584 Affx-122972991 AX-123254942 13 70927808 CCCCTTTCCCATGGAAGCCTGATATATAAATGAGA[C/T]AGAAAGTTATTTTATAATTTCAAACATCCAAGAAT Y 2 1 2 1 101000 f 74 goat snp35311-scaffold423-1269540 13 72405987 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433397 Affx-122935105 AX-123303738 13 70978749 AGTTAAACTTCAAAACCAGTTAAATCAAGATTGAC[A/G]TTTATAAAATTGGACGAATACTCTGTTGCTGTAGT R 2 1 2 1 202000 r 74 goat snp35310-scaffold423-1218599 13 72457290 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796560 Affx-122956192 AX-385283506 13 71027958 AATTATTGACAGGACGATTATTCTGATGCTCAGGA[C/T]GGTAACATCTTCCCCTAGAGAGGATTTTCTCACTT Y 2 1 2 1 101000 r 74 goat snp35309-scaffold423-1169390 13 72506672 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435437 Affx-122933479 AX-123305777 13 71065321 AGTGTCTGCTACTAAGAAAAAGAGTTAAATTATGA[C/T]ATCAATGGAGGGGGAGCTATACAGCCATTACAAAG Y 2 1 2 1 201000 f 74 goat snp35308-scaffold423-1132027 13 72542883 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272761 Affx-1111832993 AX-519546459 13 71092764 GAATTATAGCCAGTGTATTCCAGGGAAGGTGTGGC[A/G]GAGGAAATGCTTTTGTTCTAGTTGGGCCTTCAGAG R 2 1 2 1 101000 r 74 goat 13_71092764_AF-PAKI 13 71092764 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38393312 Affx-122965959 AX-123263668 13 71093968 GTCTATCCAAACCAAGTACAGTGCCTGACACATAA[C/T]AACTGTCTAATAAATGAGAGCGACCACTTTCATGT Y 2 1 2 1 202000 r 74 goat snp35307-scaffold423-1103380 13 72571553 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385542 Affx-122971236 AX-123255900 13 71129690 AGCTAGGACAGCCCACTTGCCTGAGCCCACCCTCA[C/T]GCTGAATGGTAAAGCTTGGAAGGGACAAGCTTTCC Y 2 1 2 1 101000 r 74 goat snp35306-scaffold423-1067658 13 72606929 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449374 Affx-122922721 AX-123319709 13 71158904 CAGCCTAGCGCAGCCTCCTCTGGCTGGCCTGGGTC[A/G]TTGGGAATGCTGGCCTGCAGGGCGGAAGCCTGGCA R 2 1 2 1 103000 r 74 goat snp35305-scaffold423-1038444 13 72636237 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426128 Affx-122940622 AX-123296474 13 71188597 GTCGCAAAGAGTCGGATACAACTGAGCAACTGGAC[A/G]AGAACAGAGAAACAATAAAACATGTGACTTCAAAC R 2 1 2 1 101000 r 74 goat snp35304-scaffold423-1008751 13 72665827 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436150 Affx-122932630 AX-123306489 13 71220897 CCCATCATGGGGGCCGGGCTGGATGCCTTAGGAGC[C/T]ACATGCCTACTGTCTTTGAGCTGCCATTTGCTTTT Y 2 1 2 1 101000 r 74 goat snp35303-scaffold423-976451 13 72698495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389215 Affx-122969059 AX-123259573 13 71270108 AGAGGTGGGCAGGGGCCCTGACAGACTGCTTGAGG[C/T]GAAAGACTAAGGGGTAGCTAATTTGTCATGGAATG Y 2 1 2 1 101000 r 74 goat snp35302-scaffold423-927240 13 72747597 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448317 Affx-122924149 AX-123318653 13 71335899 AACTTTCTCTGGGGTGGGTACAGAGAAGTGGAATT[A/G]TTCATGAAGAGCTCACGAATAGTTCCAAAAGAACT R 2 1 2 1 102000 f 74 goat snp35301-scaffold423-861449 13 72813419 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775621 Affx-122969380 AX-385262751 13 71365297 GAAGAACCCAAACACTGAGTACTTACTTCTCAAGT[A/G]AAAGATAAATCTCTGCACAACATTATTCTCAAAGG R 2 1 2 1 101000 f 74 goat snp35300-scaffold423-832051 13 72842793 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802229 Affx-122976689 AX-385289133 13 71401118 TTAAATACTGATTTTCATGCAAATGTGTCCATGCC[A/G]TGCCGTTTTAAGTACTGTTTCTTTGTAATATATCT R 2 1 2 1 101000 f 74 goat snp35299-scaffold423-796230 13 72878051 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415445 Affx-122949180 AX-123285794 13 71451398 AATGAAAAGAACCAGGAGTCAGCAGCTCATTACTG[C/T]AAAACAAACAAACCTAACAAATTACATAGGCTAGC Y 2 1 2 1 101000 f 74 goat snp35298-scaffold423-745950 13 72928172 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416276 Affx-122947949 AX-123286625 13 71498199 GGCCCAAAGGAGAGACTCCAGGGATGTGCAACCAC[A/G]TGGGTGAATCAAAAAGAGGAACACTCAGCCAAAGA R 2 1 2 1 201000 r 74 goat snp35297-scaffold423-699149 13 72975317 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403620 Affx-122957547 AX-123273972 13 71555954 TGCGATCAGCTAACACACTCCTCGCAGTTGGGTGG[C/T]GAGCTGCTTCTTGAAGGACCTCTGAGCTGCACATC Y 2 1 2 1 201000 f 74 goat snp35296-scaffold423-641394 13 73033156 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276758 Affx-1111835574 AX-519550267 13 71567087 CACACACACAGAGCCCATCATTGTCACTTGCGCAC[A/C]CCAGCCACTCCTGACCCCATGACCTTCTTCCTCCC M 2 1 2 1 102000 f 74 goat Random2.2K-1373 13 71567087 A C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444488 Affx-122926522 AX-123314825 13 71613012 GCTTCTTCTGTCTTAAAATAAGTGTTGAGCAGAAC[A/G]ACATGAACTGATTATCAGTCATGTGGGAGGACTCC R 2 1 2 1 101000 f 74 goat snp35295-scaffold423-584336 13 73092066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419007 Affx-122946049 AX-123289355 13 71644128 CCCACGGTTAAGTGGACTTTCTGCAATCTTCTCTC[C/T]TCCCTCTTGCAGGCACATCTCTTGGTTGGCTCCAA Y 2 1 2 1 101000 f 74 goat snp35294-scaffold423-553220 13 73122035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378376 Affx-122976813 AX-123248735 13 71720902 AAGGGAACTACCACCAGAACGGAGGTCCTGTGGGA[A/G]CTGGAGGGCCTGGTCATTCCTAGAGAACAGGTCGT R 2 1 2 1 201000 r 74 goat snp35293-scaffold423-476446 13 73188184 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427949 Affx-122939205 AX-123298292 13 71795751 TCTATAGAATTAGTACAGCCTCCTTTATCCCCTTC[A/G]CTCTTTTTCTTCACATCACTCATTGCCATCTGGCA R 2 1 2 1 101000 r 74 goat snp35291-scaffold423-401597 13 73263600 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429502 Affx-122937861 AX-123299844 13 71830400 CTAGGACCTGTCCAGTTATGCAGTATCCAGGTCTG[A/G]GTCTTCAGAGGTATTAATTAGCAAGTTCCTTTCCT R 2 1 2 1 101000 r 74 goat snp35290-scaffold423-366948 13 73298389 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385734 Affx-122971090 AX-123256092 13 71888250 CTGATATTTTGGGGTAGAAGAAAGAGTAAGAGAGT[A/G]GCCAGAAGGGAGCCAAGAGACTTGCATGTCTCTAC R 2 1 2 1 101000 f 74 goat snp35289-scaffold423-309098 13 73357603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441862 Affx-122929033 AX-123312199 13 71946275 AAGTCCGTACTGAATAAAATAAAACTCCAAGACAG[C/T]AAAAGGGAGGAGAAGCAAAAGGCAGAGAGGAAAAA Y 2 1 2 1 201000 f 74 goat snp35288-scaffold423-251073 13 73416198 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421115 Affx-122944209 AX-123291462 13 71981798 ACAAAAGGTAACCTAAGCCCCCAAATCAAAGGGCA[G/T]ACTGAGCCTGGATTTATCCTATCACAAATATGTGG K 2 1 2 1 201000 r 74 goat snp35287-scaffold423-215550 13 73451707 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419242 Affx-122945671 AX-123289590 13 72024187 CTGTCAACCATAAAAGATGTACAACCTGAGAGTTG[A/C]GAGTTAAGTTTTATTAGGGGCAAAATGACGACTGC M 2 1 2 1 101000 f 74 goat snp35286-scaffold423-173161 13 73494429 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452640 Affx-122920346 AX-123322973 13 72052766 TCTAAAACTGGGAAGTTCCATTTTCAACAACTCAG[C/T]AAAATGATGACCATACTCATGAAGAGCACTTACAT Y 2 1 2 1 101000 r 74 goat snp35285-scaffold423-144582 13 73523025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431935 Affx-122935982 AX-123302276 13 72106851 CATTCAGACTACCTTCTCTTTTTTGCAAAAGTTCT[A/G]TATAACCTGACTCCCTCTCCACCCCAACCCTTGCC R 2 1 2 1 103000 r 74 goat snp35284-scaffold423-90497 13 73578086 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423891 Affx-122942293 AX-123294237 13 72146282 TCATTGCGATAGAGTTGTGTATTTCTTCTTTTTGA[A/G]CATTTATTTGGTGCTTTTGTTGTTAGTTGCAGGCC R 2 1 2 1 101000 r 74 goat snp35283-scaffold423-51066 13 73617199 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792922 Affx-122929193 AX-385279900 13 72189612 CCTGCCCTTCTCAAGTGTGCTGCATGGGTTTAACT[G/T]CAAGTAAACACACAAGGATGAGCGAAAGGACTGTG K 2 1 2 1 101000 f 74 goat snp35282-scaffold423-7736 13 73661477 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377788 Affx-122977327 AX-123248147 13 72209967 CAGGAAAGTCACTGGTAACCTTCCTGCAACAGTTG[C/T]GGCAGCATCTCTACTGGAACACACAAGCTCTTTAC Y 2 1 2 1 202000 r 74 goat snp8480-scaffold1308-12520 13 73680690 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796678 Affx-122933470 AX-385283623 13 72247667 GTGGGGACCTGCCCTGTTAAGAAACAAATATAGTA[C/T]TTAATGTCATCTCCATGCCTCCATTTCTGCTCTTG Y 2 1 2 1 101000 f 74 goat snp8481-scaffold1308-50220 13 73707442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766430 Affx-122919756 AX-385253804 13 72283436 AATGAGTCTGAGTTTACCCTGATGCCAAATACGTG[A/G]TGTCTCTACCAACACTAACCAGTTATCAAACAGCC R 2 1 2 1 101000 f 74 goat snp8482-scaffold1308-85989 13 73743435 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398174 Affx-122962655 AX-123268529 13 72338335 GGCCTTCCAGCTAGGAAATGGTGGGACTTGAACTA[C/T]AAGACTCTCTGACTTCAAAGATAGCCCTCTAAAAG Y 2 1 2 1 101000 f 74 goat snp8483-scaffold1308-140888 13 73799873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394070 Affx-122964971 AX-123264425 13 72371381 CAAAGTCTTTTGTCCCAATGAACCAGTAAGAGTAC[A/G]CCTCCCATCGGGCCCTGACTTTCACATTGGTCCTT R 2 1 2 1 101000 f 74 goat snp8484-scaffold1308-173934 13 73832973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415449 Affx-122949178 AX-123285798 13 72416498 AGAACAGAGGTATAAAGGCAAGAGCAATGTAAATG[C/T]GGGAGACACCACACACAAAGACCACTTGGCCAGGT Y 2 1 2 1 101000 f 74 goat snp8485-scaffold1308-219051 13 73878160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381607 Affx-122974785 AX-123251965 13 72450947 AAACTTGCTGTTTGAAGGCCCAAGGTAAAGTCCCC[A/G]TCCTGCCAGTTAATGAATGACTTCAATTTCCTTCT R 2 1 2 1 201000 r 74 goat snp8486-scaffold1308-253500 13 73912323 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381688 Affx-122974724 AX-123252046 13 72516825 TCTAATTTCTGGTAGATGGGGTAAAGGAATGTCTA[C/T]GTAAAATACTTATTCTTCTCCAACAATAGAAATTG Y 2 1 2 1 101000 f 74 goat snp8488-scaffold1308-319378 13 73976793 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435545 Affx-122933392 AX-123305885 13 72551762 TTATCACAGCTATAGAATACTTGGACATTTTTCAG[G/T]GCCTCCATCACTGACATTTGACTTGGCTATTCTCA K 2 1 2 1 201000 f 74 goat snp8489-scaffold1308-354315 13 74011639 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776570 Affx-122973186 AX-385263697 13 72596693 CACTCTGATCACCTGTATGCCCATACGGCCTATAC[A/G]AGGGTCCTGACCTGTGAAATAGAATCGAACTAGAC R 2 1 2 1 101000 r 74 goat snp8490-scaffold1308-399246 13 74057570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420560 Affx-122945281 AX-123290907 13 72627615 TACCCCCAGCAGCATGGTAGCATTTTCAGTCCCGT[A/G]TGTGTCTATGTGTCCTTGTCCTTTAATGATGTTTT R 2 1 2 1 201000 r 74 goat snp8491-scaffold1308-430168 13 74088618 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412965 Affx-122951041 AX-123283314 13 72684801 GAGTAGGCGCTTTCAGCCTAGAATGGCAATGCTGG[C/T]AGAATCCCAGGGATCATCAAGCCTCAGGGTTCTCA Y 2 1 2 1 101000 f 74 goat snp8492-scaffold1308-487354 13 74145960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383864 Affx-122973140 AX-123254222 13 72719009 TAATGCCAAATAAATGCTAGCTATTGTGATTAGGG[C/T]CACAGATTACAAACAAACAAGGTGGGAGGGGTATA Y 2 1 2 1 202000 f 74 goat snp8493-scaffold1308-521562 13 74177652 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401521 Affx-122958925 AX-123271874 13 72774060 ACTATGTTGTAAAGCGTTTCCAAGAAAATATCTGG[C/T]GGCAGCTCACAACGGAGCACCCTCAGGAATAGGTA Y 2 1 2 1 101000 f 74 goat snp8494-scaffold1308-576613 13 74226684 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405323 Affx-122956345 AX-123275675 13 72813352 AGCTCCTTATCCTGGCACACAGTTTCTCACCCTTG[A/G]CACTATTGACAATTTGAACTGAATTATTCTTTGTT R 2 1 2 1 201000 r 74 goat snp8495-scaffold1308-615905 13 74266016 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422166 Affx-122943529 AX-123292512 13 72848958 GAAGCCGGAAGAGGAGGTATGCAGCTCGGGTAGTT[C/T]GGCTGCAACCGGTGGGAGCAGAATCTTTGGTCTCC Y 2 1 2 1 201000 r 74 goat snp8496-scaffold1308-651511 13 74300946 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432259 Affx-122936344 AX-123302600 13 72879674 CACCCAAGAACATGTATTTCCAAAGAACTGTTTCT[A/G]GTGACTCTGATGCTGTCCTAATGTAATCTTTCCAA R 2 1 2 1 101000 f 74 goat snp8497-scaffold1308-682227 13 74331843 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403686 Affx-122958052 AX-123274038 13 72931889 GTTGCCAAGCTCAGTGCTGTGGGTTGTGTGCTGCA[C/T]GAAGTTTCAGCCCAGGGAGAGTGGGGCTCCACTTG Y 2 1 2 1 303000 r 74 goat snp8498-scaffold1308-734442 13 74384271 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443785 Affx-122927097 AX-123314122 13 72964441 CTCCTTTCTGTGGCCTCCTTTCTCTGCTTCTCTGG[A/G]AAGGAAGGATTTATGGTTTCCCCCACCCTGCTCTG R 2 1 2 1 201000 r 74 goat snp8499-scaffold1308-766994 13 74416664 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274344 Affx-1111834197 AX-519547939 13 73003802 ATTTTCTACAAGGAAGGAGAAGAGTATTGACCAAC[A/G]CTGCAGAGTCTAAGACACGGGTGAAAGACTCCTGA R 2 1 2 1 101000 f 74 goat GoatD01.025065 13 73003802 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320774836 Affx-122921173 AX-385261970 13 73008928 AGCTTTACGCCCATATTTCAGATGGCCCATTCTAG[A/G]CGATTCTTCCCTCCTCTCATCTTAAAGCCAACAGA R 2 1 2 1 101000 r 74 goat snp8500-scaffold1308-811481 13 74461066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394033 Affx-122964998 AX-123264388 13 73041501 AGGGATGCCAGCAGAGTGAGGATTCTGTGGTCCAC[C/T]CGCCCCATCAGCGCAGCTGGGAGGAGGCAGAAGGG Y 2 1 2 1 101000 f 74 goat snp8501-scaffold1308-844054 13 74493379 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764927 Affx-122943504 AX-385252512 13 73075087 CTGGTCTCCAGGAAAGCTTGACAGAGATGTTTCTG[C/T]AGCTACAGGAAATTACTCTCATTGTACTTTTTTTT Y 2 1 2 1 101000 f 74 goat snp8502-scaffold1308-877640 13 74527231 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385825 Affx-122971019 AX-123256183 13 73116183 GCTGGGTGGACACTGCTGGCCTGGCACCCAACACG[C/T]CTCTTCTTCTGCGAGGATGCTTATGGTCCAGGGGG Y 2 1 2 1 101000 r 74 goat snp8503-scaffold1308-918736 13 74568427 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790012 Affx-122939176 AX-385277018 13 73146917 GCGCCATACAAAAGACCAAAGGAGGGAAGCGAGTC[A/G]TCTGGGTTGACACGTGACCTTTAATCGGAAGGAAT R 2 1 2 1 101000 r 74 goat snp8504-scaffold1308-949470 13 74599040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397403 Affx-122962257 AX-123267758 13 73205701 TGAAGTAAATAGTTTCAGTTTTGTTCTATGTCCAG[C/T]GGAAATCCACAAGAGGGTTGGAAGCAGGGGAATGA Y 2 1 2 1 101000 r 74 goat snp8506-scaffold1308-1008254 13 74656318 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796086 Affx-122952827 AX-385283038 13 73243484 AAACACAGAAAGATCCAACAATGTCCCAGAGCAAG[C/T]GGGTTTTCATCTCCACAGGATCCATCCAATTACCA Y 2 1 2 1 101000 f 74 goat snp8507-scaffold1308-1046037 13 74694028 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320787376 Affx-122969968 AX-385274401 13 73316608 ATTTTAAATCAGAAGTATTTGAAATCACTGTTCAT[C/T]TGGTGATAAGCCCCTTGGGTTTCTCTGTGAATGAA Y 2 1 2 1 101000 r 74 goat snp8508-scaffold1308-1119161 13 74766929 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418228 Affx-122947044 AX-123288576 13 73345391 TCAGAGTGAATAGGCAGCCTGAAAACCCTCTGACA[G/T]CAAATGCCCTCCCATGTCCCCCATCTCTCAACTCT K 2 1 2 1 101000 f 74 goat snp8509-scaffold1308-1147944 13 74795432 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443891 Affx-122927061 AX-123314228 13 73379300 TGTCAAAGCTTGCTGCTGGCTTTGGAAGATACGCC[A/G]CATCTATCCTGTTTTATATACCACCTGACAGGCCA R 2 1 2 1 201000 r 74 goat snp8510-scaffold1308-1181853 13 74829353 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763091 Affx-986697620 AX-385251049 13 73389295 TCCTGACTCTTGCTGTAATTTTCTTTGTCACTACA[A/G]CCTCACCTTCCTCCTCCACCCCACCAGCACTTCGA R 2 1 2 1 600010 f 74 goat 13_73389295 13 73389295 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 320803261 Affx-986696252 AX-385290111 13 73389361 TTCGAGAGTCTTTGGAACGTGGCTACCTGGATGCT[A/G]CCAGAGAGGCTGGGACCACTCCATTTCTTTGTAAA R 2 1 2 1 600010 f 74 goat 13_73389361 13 73389361 Ancestral_priority_1043 ancestry 0.596 neutral IMAGE 10K 10K ancestral 320765819 Affx-986697622 AX-385253267 13 73389389 GGATGCTGCCAGAGAGGCTGGGACCACTCCATTTC[C/T]TTGTAAATGTGATTGCCAGTCATGAAATCACATTG Y 2 1 2 1 600010 r 74 goat 13_73389389 13 73389389 Ancestral_priority_1043 ancestry 0.626 recommended IMAGE 10K 10K ancestral 320763095 Affx-986697624 AX-385251053 13 73390466 CAGGGCCAGAGTTCCTTGGTTCCAAAAACCACTAG[C/T]GTAGAGTCCCGAGTTGTGGTTGGGGTAGTTGGGTG Y 2 1 2 1 600010 f 74 goat 13_73390466 13 73390466 Ancestral_priority_1043 ancestry 0.628 recommended IMAGE 10K 10K ancestral 320763097 Affx-986697626 AX-385251055 13 73397115 ACTCATTTTGCTGGACACCGTTCTGGCCAGCATTC[C/T]GGGGGATGAAACCAGCATCCAGGTCCAGAGTAAAG Y 2 1 2 1 600010 f 74 goat 13_73397115 13 73397115 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 38442392 Affx-122928003 AX-123312729 13 73446409 AACTCAGGCGGTGCTGTCATAATTTGGAGGCCAGG[A/C]TTTACTCCACTTCCTGTCCATGGCCATTTCCAGAC M 2 1 2 1 201000 r 74 goat snp8511-scaffold1308-1248962 13 74895693 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416536 Affx-122947756 AX-123286884 13 73490954 TCACTACTAGCCCAGTGGGATGGCCTACTGCTAAG[C/T]GTCCCAGAAGATGAGGAGAGGCAAGAGGGTCCTTT Y 2 1 2 1 101000 f 74 goat snp8512-scaffold1308-1293507 13 74940249 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419017 Affx-122946044 AX-123289365 13 73584068 AAGGAAGAACACGCACTTGGGACATGACATGTACC[A/G]TTTCTTTGACTTTATTAATACTGTTTATTGAGCGT R 2 1 2 1 303000 r 74 goat snp8514-scaffold1308-1386621 13 75033640 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272763 Affx-1111832994 AX-519546461 13 73625169 GGAGCCCTCCTGCAAGGCCACCACCAAGATGAACC[A/G]ACTCTGCCTCTCCACAGTCCTTCTCTTTCTCCTGG R 2 1 2 1 102000 r 74 goat 13_73625169_AF-PAKI 13 73625169 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38441801 Affx-122929080 AX-123312138 13 73632302 ACAGCTGGGCTCCAGTGGTCTAGCTCTTAAGCCCT[A/G]TGCTGTGGTGCAGTGGTGGGCAAACAGTGTCTCAA R 2 1 2 1 201000 f 74 goat snp8515-scaffold1308-1434855 13 75081733 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419907 Affx-122945337 AX-123290255 13 73712442 CTCTGACCACCAGCCCAACTCTGGACCTCCCTTCC[A/G]TCCAGGGCTTTAAGGCAGGCACAGTTGAAGCCCAT R 2 1 2 1 101000 r 74 goat snp8517-scaffold1308-1514995 13 75153549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399524 Affx-122961153 AX-123269879 13 73765375 GAAAGTTTAAGAGATGACATGCAATTGTTTTCTGC[A/G]TCTGTGTCTCTATTTCTGCTTTGCAAATAGGTTCA R 2 1 2 1 101000 f 74 goat snp8518-scaffold1308-1567928 13 75206356 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418397 Affx-122946553 AX-123288745 13 73809676 GCTGCCTGCCTGACACACAGGCCTGATTGCTAAGC[A/G]TCTGATTTATGGTTCTGCAGGAGCTATCAGGGAGA R 2 1 2 1 101000 r 74 goat snp8519-scaffold1308-1612229 13 75250269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450071 Affx-122922805 AX-123320406 13 73856465 TGACTCGAACGCTTTCTATGGTCCTCTCTTCGGCA[A/C]ACTGAGCTGAGCGGGGCTTGTTTCTAGCTAATCTT M 2 1 2 1 201000 f 74 goat snp8520-scaffold1308-1659018 13 75297064 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411799 Affx-122951261 AX-123282149 13 73886263 GGGGGCATGCTCCTAACACCACTCACCAGAGATTT[A/G]CCCTTTTAAGGGGCCACAGGTAGTCTCCCCAAAGC R 2 1 2 1 101000 f 74 goat snp8521-scaffold1308-1688816 13 75326806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400842 Affx-122959785 AX-123271197 13 73926457 ATGCTCAAGCAAGGCATGTGAATGGGTTACCATCT[A/G]CAGTTATCCAAGCTCTTTCTCATCCAGAATAAGTT R 2 1 2 1 101000 f 74 goat snp8522-scaffold1308-1729010 13 75367491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410749 Affx-122952696 AX-123281099 13 73967953 AGAAACGCCCAGGGGGTCGGCAAGAAGATGAGAAG[C/T]GGGGTCTCCACACACAGACGGACGGGCCTGAGCAG Y 2 1 2 1 101000 f 74 goat snp8523-scaffold1308-1770506 13 75408923 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386030 Affx-122971485 AX-123256388 13 74026260 CAAAACTTCCCAAATTAAAACATAACTCTGTCCCC[A/G]TAGATCTTATGATCTAGTTGGGGGAGATTTATTAT R 2 1 2 1 102000 f 74 goat snp8524-scaffold1308-1828813 13 75467590 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398041 Affx-122961761 AX-123268396 13 74056273 GTCTTGGGCTAGGTTCCTCTCTGCTAGATACAAAG[A/C]TACTCTCTGCAGTGCAAATAGTCATCATGGAAGGT M 2 1 2 1 101000 r 74 goat snp8525-scaffold1308-1858826 13 75497963 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402676 Affx-122958361 AX-123273029 13 74101650 TCATCCCTCTGCCCAGTTTCTTCACCCGCAGAACC[C/T]GAGCTCCCTGGGAACAGACCTGTCCTGTTCAGCCT Y 2 1 2 1 201000 r 74 goat snp8526-scaffold1308-1904203 13 75543856 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419136 Affx-122945755 AX-123289484 13 74131989 ATGTTTCAATTTATTTTACATAGATTTATTGAGTG[A/C]TAGCCATGTGTTGGGCTTTTCCTTAGATGTTCAGG M 2 1 2 1 101000 r 74 goat snp8527-scaffold1308-1934542 13 75574292 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775974 Affx-122971584 AX-385263105 13 74170439 CCTTTGTATCCACAGAACCTGGAATAGCAGTCTTG[C/T]AGAATATAATTTCAGCAAACATTGTGAAGTGAATG Y 2 1 2 1 101000 f 74 goat snp8528-scaffold1308-1972992 13 75612901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419537 Affx-122945428 AX-123289885 13 74216955 TGTTAAATGCAGCAGTATTCTCAAGATGCTCTATT[A/G]TTAATGTAAAAAGGGAGAAAAATTAATGAGGAAAA R 2 1 2 1 102000 f 74 goat snp8529-scaffold1308-2019508 13 75659575 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381448 Affx-122974338 AX-123251806 13 74279123 CTTTTATTCACCCTGAGTGAGAAATGGAGACTCAC[G/T]GCCCAGTGAGGGGATGACCTTGCCAGAGGTAGAGC K 2 1 2 1 101000 f 74 goat snp8530-scaffold1308-2081676 13 75715695 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432440 Affx-122935814 AX-123302781 13 74319797 TAGGTGCTAATGCGCATTCCCACCTCTCTCTTCCT[A/G]TCTTCCCACCTCCTCACCACCTTTTGGGGTGACAG R 2 1 2 1 202000 r 74 goat snp8531-scaffold1308-2122350 13 75755144 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429091 Affx-122938270 AX-123299433 13 74361934 CCCACATAATGAAGGCAGGGCTCCCAAACCCCTAG[C/T]AGTGCCTGAAATATGGTGCCCCTGCCTAGAACAGC Y 2 1 2 1 101000 r 74 goat snp8532-scaffold1308-2164487 13 75797531 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388057 Affx-122969532 AX-123258415 13 74394817 ACTGTTGAGGAAGATTTGATGAGGGCAAAAAGTTT[A/G]AGAAGAAATTGGAAAAATAGATAAGAAATGCCAGC R 2 1 2 1 103000 f 74 goat snp8533-scaffold1308-2197370 13 75830868 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790404 Affx-122977282 AX-385277407 13 74465231 GTTGATAATTCTTTTCCTAATCCAAACAGCAACAA[C/T]AACAACAAAGAAAATGCCTGCCAATCCTCAGTTGG Y 2 1 2 1 102000 r 74 goat snp8535-scaffold1308-2267784 13 75901154 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446266 Affx-122925674 AX-123316602 13 74506296 ATCCCTCTTGTTCCAGAGAGAACCTCAGAAGAGCC[A/C]AGGAGTCCAGGCAAATATGGACTCAGCCCACTGCC M 2 1 2 1 201000 r 74 goat snp8536-scaffold1308-2308849 13 75944160 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765951 Affx-122938322 AX-385253377 13 74554726 TGCTAAACGATGCTCCTGTTTGAAGATGAAAGTTG[C/T]TGAGAATGCACCCTGGTGATCCACTCCACATCACG Y 2 1 2 1 101000 f 74 goat snp8537-scaffold1308-2357279 13 75992495 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400219 Affx-122960168 AX-123270574 13 74584538 CCATACTCCCACGATTTTTTTATGTCTAGTTATCA[C/T]GTTTTATTAAATAGATGTGTAGTAATCATTCTTCT Y 2 1 2 1 101000 f 74 goat snp8538-scaffold1308-2387091 13 76022358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384061 Affx-122972871 AX-123254419 13 74619647 TAAATGTAACTGTGCTGTAGCTAAATGTAACTAAA[C/T]GTAACTGTGGCTGCAGGGAGTTCCTGGTGGTCTCT Y 2 1 2 1 101000 f 74 goat snp8539-scaffold1308-2422200 13 76057493 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427463 Affx-122940025 AX-123297806 13 74658635 GAGGATGTCACTGTACAGCTCTTTCTTCATCTTTC[A/G]TTCACCTCTGGATCTGGGCAGAGGTCGTCCAGCTG R 2 1 2 1 101000 f 74 goat snp8540-scaffold1308-2461188 13 76096571 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429869 Affx-122938141 AX-123300210 13 74719656 TGGCATCCTTCCTTTAACCACCAAACCGCATCACC[A/G]CCTCTTTCATTTGGTTGGTGGATTACTATACAGAT R 2 1 2 1 201000 r 74 goat snp8541-scaffold1308-2522209 13 76158060 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431786 Affx-122936703 AX-123302127 13 74760709 TTAGATATTCCATTTCTCTAATAAATTTCTCCATC[A/G]TTTGAGCTTTTTATTGAATATGTTAATAATAAATG R 2 1 2 1 101000 f 74 goat snp8542-scaffold1308-2563262 13 76199229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768775 Affx-122967671 AX-385255952 13 74823375 GTAGAATATTATCAGATAGTAAATCTGTTCCTATT[C/T]TGGCTCAGATATGTAAACTTGAGCATATATTGGCT Y 2 1 2 1 101000 r 74 goat snp8543-scaffold1308-2625928 13 76262315 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378689 Affx-122977069 AX-123249048 13 74858639 CCTTCTATCAGGCGACTTAAGACCTGAGCAGGTCA[C/T]GGCTGCCCTCAATGGGCTGAGTAGGCAGCTGAACT Y 2 1 2 1 101000 f 74 goat snp8544-scaffold1308-2661192 13 76297547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409609 Affx-122953550 AX-123279960 13 74901429 TGCCCGGTGGAGCTCCATTCTGGCCTGGGGAATAG[G/T]GTGGGTAAGAAAATCAGCAAGTACTCCAAAAACAG K 2 1 2 1 101000 r 74 goat snp8545-scaffold1308-2703982 13 76340113 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419097 Affx-122945782 AX-123289445 13 74930542 ATTTATTAAATTAGCTCCCACATCCGTCCCTGCCC[C/T]CCCTCCTGCATGATTTATCTTACTGGCCTTTATGC Y 2 1 2 1 101000 r 74 goat snp31398-scaffold348-1983 13 76370360 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38409300 Affx-122953101 AX-123279651 13 74967560 AGGAAAAACAGTGTTGCAAAAACCTGAGGCCTGAC[A/G]TTGATTTTAAAACACACAGATCAGGACTTTTTTCC R 2 1 2 1 101000 f 74 goat snp31399-scaffold348-39001 13 76396540 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400209 Affx-122960176 AX-123270564 13 75008174 AAGGTCCCTAGCACAAACTGAGACGTGCTGTAAGC[A/G]TAACAGACACACTAGATTTTGAAGCTTTAGCCGTA R 2 1 2 1 101000 f 74 goat snp31400-scaffold348-79615 13 76437334 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410699 Affx-122952734 AX-123281049 13 75042554 AGTAAGTGCTCAATAAATGTCTTTACAATCAAAAC[A/G]CAAATCAGATTGTGTCACACCACGGCTTAAAACCC R 2 1 2 1 101000 r 74 goat snp31401-scaffold348-113995 13 76470493 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423355 Affx-122943152 AX-123293701 13 75083557 TACTGTCCTGTTAGGGTCCATTTCCAATGGATTCA[C/T]GGTCTGCTTTCTGGTACCAATCCGAGGCAGTGAGG Y 2 1 2 1 101000 f 74 goat snp31402-scaffold348-154998 13 76511392 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800343 Affx-122949748 AX-187812502 13 75117070 AGGAGGGGCCTTCATGCATTTTTGAGAAGATGACC[A/G]TTTTTTTCCTATCTTTGGGTGGGTTCCTCAGGGAA R 2 1 2 1 202000 f 74 goat snp31403-scaffold348-188511 13 76544822 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432975 Affx-122935270 AX-123303316 13 75177426 TTTGGGAGCATAAGAGAGCAAGGTCAGGGCAGCGC[A/G]GCTCTGGATCAGGGCCAGAGGGGTACTGTGTAAAT R 2 1 2 1 201000 f 74 goat snp31405-scaffold348-248867 13 76605207 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384645 Affx-122972151 AX-123255003 13 75222815 AGGCCTCTTCCTGCTCGCTTGGTCCAGCAGTGTCA[C/T]ACTTCTGCTCTCAGCCTCTCTCTCAACCAGTTTTT Y 2 1 2 1 201000 f 74 goat snp31406-scaffold348-294256 13 76650259 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376276 Affx-122978388 AX-123246635 13 75257073 TTTTTACAGTTCCCGTAACCACTAGTACACTTCCT[A/G]CCTGTGTAGATGTGCTGATTCTGGACATTGTTTGA R 2 1 2 1 101000 f 74 goat snp31407-scaffold348-328514 13 76684512 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783349 Affx-122956202 AX-385270413 13 75289466 CACCTGAGTTGGAAAGCATTGTTATCAGATCTCTT[A/G]CACTGCCTTTGTAGGGTTGTACCTTCAGACCCTTT R 2 1 2 1 101000 f 74 goat snp31408-scaffold348-360907 13 76716722 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432228 Affx-122936365 AX-123302569 13 75355100 TGTAATATTTTAGAAACAAGCAAAACGCATGGACA[G/T]ACATCAGATCGACGGCTGCCCAAGGGTGACGATGG K 2 1 2 1 101000 f 74 goat snp31409-scaffold348-426541 13 76783063 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792559 Affx-122957623 AX-385279540 13 75402212 TCTTATTTTCTAACCGATACGTGAAATAATAGATA[C/T]GATCTTTAGATAAAAATCAACCTCTCACAGGACCT Y 2 1 2 1 201000 f 74 goat snp31410-scaffold348-473653 13 76830197 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802466 Affx-122971261 AX-385289370 13 75472861 TATTTTCTCAGCCTCTTGCCAATACCAAATAATAG[C/T]GAAAGCATGAGTTTCATAGTCAAACAGACCTGATT Y 2 1 2 1 101000 r 74 goat snp31412-scaffold348-544302 13 76901083 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421053 Affx-122944519 AX-123291400 13 75561784 ATGAACAGAATCCATGAACGTGACTCCAAGAAAAG[A/G]GTGGCTAAGGACATTGGTCGTTTATGGCTAATGTG R 2 1 2 1 101000 f 74 goat snp31414-scaffold348-633225 13 76990271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407225 Affx-122955379 AX-123277576 13 75618331 AGGAGATAAGGCCATTGGATAGGAAAGCACCAGAA[A/C]CCTCTCCTGCTCTTCCCTTTGGACGATCATGTGGG M 2 1 2 1 101000 f 74 goat snp31415-scaffold348-689772 13 77046823 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384831 Affx-122971974 AX-123255189 13 75650377 GCACACAAAGGCTTGAGCTGCAGCCCACTCTGGCT[A/G]TTGTCCCCACCGAGTCAGCAGAAGACGCTAAAGCT R 2 1 2 1 201000 r 74 goat snp31416-scaffold348-721818 13 77078882 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426100 Affx-122940641 AX-123296446 13 75700968 TGAAAAGGAAATCTAAGCACATCCAAGTCCTGCCC[A/G]CTGCCCAGCGTATAGTGGGGGCTCAGTGATATTTG R 2 1 2 1 201000 f 74 goat snp31417-scaffold348-772409 13 77129440 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412700 Affx-122950753 AX-123283049 13 75768122 GACACAAATATGATCATGCATCTGAGATGAATCAA[G/T]CATGACAGTTGAATACTGATTTTAGTTGAGTTTCC K 2 1 2 1 101000 r 74 goat snp31418-scaffold348-839563 13 77197251 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276897 Affx-1111835575 AX-519550406 13 75772536 TAAAAGCTAACATGTTTTGAGTCTTTTGTTTATGC[A/C]AGGCATTGAACTAAAGGCTTTGCATATATTTATCT M 2 1 2 1 101000 r 74 goat Random2.2K-1376 13 75772536 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378146 Affx-122976978 AX-123248505 13 75824418 GTCTGCACCCTGATGCCTCCCAGGCTCTGGACTTG[C/T]ATATCTAATTGCCAGCCTTAAACATCCTAAAAAGA Y 2 1 2 1 101000 r 74 goat snp31419-scaffold348-895859 13 77263009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421066 Affx-122944244 AX-123291413 13 75895158 AATCAAATTCACCTTCCTCCTCTAGGGGCAGCGTC[A/G]CTGCCGCTGTGTGTGTCTGACTCTGGGACCCCACG R 2 1 2 1 102000 f 74 goat snp31421-scaffold348-966599 13 77331235 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406572 Affx-122955094 AX-123276924 13 75932785 CTGCAAAGAGCTCCCAGGAAGGACTGAGTGAGCGG[C/T]GGATAAGCCAATTCGAATGTGTCCTTCCACTGCTC Y 2 1 2 1 101000 r 74 goat snp31422-scaffold348-1004226 13 77368851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418465 Affx-122946463 AX-123288813 13 75962268 CAGGTCCTCGGCAGGCATTCCATTCCATCGTGTTT[A/G]CTTGTCCAATAAACCTTCTTTCTGAGGGTAGAGAT R 2 1 2 1 101000 r 74 goat snp31423-scaffold348-1033709 13 77393987 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408565 Affx-122953672 AX-123278916 13 75994583 GTAAGACTTCAGGTTTCCACATGTGTGAAATTGGG[C/T]AGCATGAGTGTACTTCATGGGGTTATCGAGTGGAC Y 2 1 2 1 101000 f 74 goat snp31424-scaffold348-1066024 13 77426293 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390438 Affx-122967630 AX-123260795 13 76039953 GTGGCTATACTTTTTTACTGGGGAAAGTTTTCTCC[A/G]TATTGATTCCTGACTTCTCTATTGTGTCTCATTGT R 2 1 2 1 101000 f 74 goat snp31425-scaffold348-1111394 13 77471633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406056 Affx-122955469 AX-123276408 13 76094636 GAAACACGTCTAAGGGGAAATTTGGACCAGCCTAC[A/G]CTGGTGAGGAAACAGGTGAAAGAAAATGCTACAAG R 2 1 2 1 201000 r 74 goat snp31426-scaffold348-1166077 13 77526344 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272765 Affx-1111832995 AX-519546463 13 76127538 AACTCTGGGGTCACGGGGATTTGCTCATGGCCAGG[A/G]TACCCTCTGAGGTACCACGGTGTCAGTTTAGAAAC R 2 1 2 1 101000 r 74 goat 13_76127538_AF-PAKI 13 76127538 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438443 Affx-122931257 AX-123308781 13 76147217 CTCCTGGTAACCCTGGCACTCCTTGGCTCCGTGCA[C/T]GGCTGTGACCTCTGCCTCCTTCTTCACGTGCACTT Y 2 1 2 1 101000 r 74 goat snp31427-scaffold348-1218658 13 77578640 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407441 Affx-122954796 AX-123277792 13 76183387 GAATTTGGACTTGGCTAAATGCCTGGTAGGTTTTC[A/G]GCCAAGGCTGTAGAGACATTCGATGGTCCAAGGGG R 2 1 2 1 101000 f 74 goat snp31428-scaffold348-1254828 13 77613079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439040 Affx-122930337 AX-123309377 13 76225377 CCTTAGGGAACAGAAACTGTAAGAGTAAAAAGGCC[C/T]GATACTAAGAACTGGTAAAGACGGAGAGAAACGCA Y 2 1 2 1 101000 r 74 goat snp31429-scaffold348-1296818 13 77654870 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439891 Affx-122930034 AX-123310228 13 76258745 AACCCTACAAAATACTTGACCAAACCAAACCAAAG[C/T]AAAACCCAACCCTTCCTCCAAACCCATAGGTGTAG Y 2 1 2 1 103000 r 74 goat snp31430-scaffold348-1330186 13 77687832 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777755 Affx-122967060 AX-385264873 13 76288489 GATTGAAATATACTGCAAGCATAAAGTACACATTG[C/T]GGCAGCTGCTGTTTTCTTAGTGCCAAGTATAGACC Y 2 1 2 1 101000 r 74 goat snp31431-scaffold348-1359930 13 77717724 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398156 Affx-122962668 AX-123268511 13 76326178 ATCCGTGTGATGGGTCTCTCACATTCCTGACTGTT[G/T]TGCAGCATGAGGCTTTGTAGAAAGTAAGCCCTTGA K 2 1 2 1 101000 r 74 goat snp31432-scaffold348-1397619 13 77755216 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401554 Affx-122958900 AX-123271907 13 76374388 CGTGGCGCTGGCATTCCGGTGGTCGCTCAGGGACC[A/G]TGAAGCAATACGGGGTCAGGCAGCAACGAGTTCTG R 2 1 2 1 201000 f 74 goat snp31433-scaffold348-1445829 13 77802574 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401549 Affx-122958903 AX-123271902 13 76421193 CCCATGGCACCTTGGTTGAGTCCTGCAGGGCATTC[A/G]TGGAGTAGTCAGACAAGAGATGGGGTTGGTGGGGA R 2 1 2 1 101000 f 74 goat snp31434-scaffold348-1492634 13 77849320 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453521 Affx-122919804 AX-123323854 13 76464391 GTCGAATGAATGAAGCCAGGTAATTGGTATGAGAT[A/G]CTGGACTAGGGTCTGGCACATGGGTGGAACATGAG R 2 1 2 1 101000 f 74 goat snp31435-scaffold348-1535832 13 77892594 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430923 Affx-122936849 AX-123301264 13 76501302 TCAGACCCAGGTCACAAACCTGCCTCTTCCTTGCT[A/G]TCTGCCTCAGGTTGGTCATGTAAACCTTGGTTTCC R 2 1 2 1 101000 r 74 goat snp31436-scaffold348-1572743 13 77929487 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417246 Affx-122947275 AX-123287594 13 76533174 GCTTTCTTACAGTGCTGGCATGTTATTTATTGAGC[A/G]CTCACCATATGTGGGGCCTCTGGGTTTCATGTGAA R 2 1 2 1 101000 f 74 goat snp31437-scaffold348-1604615 13 77961061 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443188 Affx-122927598 AX-123313525 13 76566792 TGGGTACATGACCAGCAGAACAAAGACAGGGTCCC[A/G]TCAGCAGAAAGGAAGGGAGAAATGGCAATTGGCAT R 2 1 2 1 201000 f 74 goat snp31438-scaffold348-1638233 13 77996024 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439579 Affx-122930076 AX-123309916 13 76613468 GTTGTTTATTAAGGAGGGCGGGGGACGACCCAGTC[C/T]GGAGGGTGAAGAACTTGGAAGTATTTAAATTTGAG Y 2 1 2 1 201000 r 74 goat snp31439-scaffold348-1684909 13 78042679 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407682 Affx-122954588 AX-123278033 13 76661279 AGTTCTGTCACGTTTCGTGGTACAGTTGTTGATCT[A/G]CTTTTTTCTAAACCACTATTGGTAGTTAACTTTTA R 2 1 2 1 101000 f 74 goat snp31440-scaffold348-1732720 13 78090382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397207 Affx-122962393 AX-123267562 13 76697507 AAGATTTAAAAGGAAAGCCCACTGCTCAGAGTGAA[A/C]GCTCAAGGCCAGCTGAGGTGTCCTTGTCTGCTCCG M 2 1 2 1 101000 f 74 goat snp31441-scaffold348-1768948 13 78126612 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437870 Affx-122932068 AX-123308208 13 76730492 CTGAGGCTCAGAGTGTGTGACTTGTCCAAGTCACG[C/T]AGTTAGAAGAAGGCAGAGGCTGGACTTGAACACAA Y 2 1 2 1 102000 r 74 goat snp48941-scaffold6986-1173 13 78158315 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429438 Affx-122938503 AX-123299780 13 76756075 TACCTATTCCGAAGGGTAATTCCCAGGGAGAAAGC[A/G]TGTTTATACTTTTCTTGGGGGGAAAATTCCATTTC R 2 1 2 1 101000 f 74 goat snp22918-scaffold2282-662405 13 78184082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440524 Affx-122929341 AX-123310861 13 76890823 CAACCCAGGTCGCTCATATGATGAACAGAATGACC[A/G]CCAAAACAGTGAAAACTTCTGGATCTCAAAATTGT R 2 1 2 1 101000 r 74 goat snp22916-scaffold2282-527657 13 78318736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429122 Affx-122938010 AX-123299464 13 76920117 TGGACAAAATTTTGGAGATGGTCTCTGTGAAGAAT[A/G]CCTTCATCCAGGGAAAGGGGCAGATGATAGAATTC R 2 1 2 1 201000 f 74 goat snp22915-scaffold2282-498363 13 78347764 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776463 Affx-122959268 AX-385263590 13 76954207 GTACCAGTAAGAAGCTATGCCAAAGATGGTACTTG[C/T]TTGCTTTTTAAGTCACATAAGTATATTCAGTTGGG Y 2 1 2 1 101000 f 74 goat snp22914-scaffold2282-464273 13 78381745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444065 Affx-122926852 AX-123314402 13 76989664 GAACGGAGCAGGGTCTTGTGGGGCCCTCCTGGGCA[C/T]TTTTCTTTCTGGGTTCCTTTCTGTCTTAAACGCAG Y 2 1 2 1 101000 r 74 goat snp22913-scaffold2282-428816 13 78417064 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403741 Affx-122958015 AX-123274093 13 77021939 TGCATTCATTCTCAAGGGGAAGGGGGAGGCTGGAA[C/T]AGGTTGTTGGATAAGAAGAAAAGGCGTTTAGAAAG Y 2 1 2 1 101000 r 74 goat snp22912-scaffold2282-396541 13 78449067 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792391 Affx-122923594 AX-385279372 13 77054569 GATTTGGTCAGAGATTACCTTTGATACACATTCCT[A/G]TGTGTGCAAGAAGACACGTCCAAAGATGGTCCCTG R 2 1 2 1 101000 f 74 goat snp22911-scaffold2282-363911 13 78481945 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422999 Affx-122942985 AX-123293345 13 77087531 TCCCCCGGAGGAATGCAGGAGGGGAGCAGGAGAGA[C/T]GACCGCGGGGCCTGAAAAGATTTCTTGAGACTGTG Y 2 1 2 1 101000 r 74 goat snp22910-scaffold2282-330949 13 78514862 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273608 Affx-1111833723 AX-519547222 13 77155374 ACTTGTCACCATTGGATAAAGCCGAGAAGAAGATA[A/G]A R 2 1 2 1 101000 f 74 goat GoatD01.002504 13 77155374 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447473 Affx-122924350 AX-123317809 13 77188392 CTTGCAGTTCGTATTCAAACTGCAAGGAGATTGCA[A/G]TCCTGTTCCTCTTAAAGGTGAACCAGTATCCACAG R 2 1 2 1 101000 r 74 goat snp22908-scaffold2282-230088 13 78614491 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422662 Affx-122943682 AX-123293008 13 77226728 ACATTCATGACCTAACATGTCACAAACATAAGCAA[C/T]GTATGAACCCAAATAATCTTTAGGAATAGTGAATG Y 2 1 2 1 101000 f 74 goat snp22907-scaffold2282-191752 13 78652758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442490 Affx-122927924 AX-123312827 13 77256953 AGGCTCATCACTGCCAGTTTCCCTGAACCTCAAAA[G/T]ATCACAGGCTCTGTATCTGTCAGCTTTTGCTGTGT K 2 1 2 1 101000 r 74 goat snp22906-scaffold2282-161527 13 78683487 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392823 Affx-122965784 AX-123263180 13 77285916 CCCCATCCATCTTCCCCTGCCTGTCTTGTCTGTGC[A/G]TCTTCCCATCCTCTCCTTTCCTCACAGAGACTCTG R 2 1 2 1 101000 r 74 goat snp22905-scaffold2282-132564 13 78712906 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379393 Affx-122976135 AX-123249751 13 77318285 ATCCCACCTGCCACCCACGCTCCTTTGCCTTTCGA[A/C]CTTTTTTCTCACTTTTGCCTTTCCCTTGACGTGCT M 2 1 2 1 101000 r 74 goat snp22904-scaffold2282-100195 13 78748468 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420457 Affx-122944884 AX-123290804 13 77347171 AGCTGACCAATGGCGTGGACTTCGTCTTTAGCCAC[A/G]TAGGGAAACAGAGCTGTGTTCTTGGTTCCTGGGGA R 2 1 2 1 101000 f 74 goat snp22903-scaffold2282-71309 13 78776932 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772901 Affx-122923176 AX-385260046 13 77411318 TAATTTGCATTTTCCTGTTTACAAGGCAAGTTGAA[C/T]GTCTTTTCTGTGCTCATGGTCATTCGTTTTCCTGT Y 2 1 2 1 101000 r 74 goat snp22901-scaffold2282-7162 13 78839672 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767333 Affx-122941614 AX-385254609 13 77423273 AGAAAACGCAGCTCAGCTCACATAAATGTTCCACT[A/G]AAGACAGTGCCATCTGGGCGAGGCATAAACTCTGG R 2 1 2 1 101000 f 74 goat snp26910-scaffold2849-4694 13 78851134 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276899 Affx-1111835576 AX-519550408 13 77429535 GCTGTGAAGAGTCAGGGGCAGGGAAGGGGGGGAAA[A/G]GTGGACGATCTCAACCAGGAGGCCTTTGCAATAAT R 2 1 2 1 202000 r 74 goat Random2.2K-1379 13 77429535 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38440840 Affx-122929265 AX-123311177 13 77466876 CAGAAGACTAAACACCACCACAGGGACACTGCTGG[C/T]AAAGCTCGTCACACAGAGGCCAGTGCAAGAAAAAC Y 2 1 2 1 201000 r 74 goat snp26911-scaffold2849-48297 13 78893502 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390789 Affx-122967876 AX-123261146 13 77501854 GCTGCCAGATGGAAGCAGCTCAGGGCCCTGAGGAT[C/T]ATGGCCCCTCCACATCAGCCCTGGCCCTCCCACCC Y 2 1 2 1 101000 f 74 goat snp26912-scaffold2849-83275 13 78927248 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391634 Affx-122966573 AX-123261991 13 77551050 TATTGGCCGAGATGCCCAGGCTCTTCTGAGCCCCT[G/T]CTGGAGCAGACGAAGCTGGGGTGGAGGGCATTGTT K 2 1 2 1 103000 f 74 goat snp37983-scaffold471-371550 13 78976313 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431196 Affx-122937170 AX-123301537 13 77631845 TTTCCACTGGCTCTCTAATTTTCCATATGGTCATA[C/T]AGATGTGCTGTGTTTTATTTAACCAGTTTATTGCG Y 2 1 2 1 101000 r 74 goat snp37981-scaffold471-290755 13 79057077 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420618 Affx-122945237 AX-123290965 13 77680356 GTGATTTTTAATAAATACATATGGCTGGGCAGCCA[G/T]CAGTTTGTACTTGCCTTTTTTTCCACTTGTGGTAG K 2 1 2 1 101000 r 74 goat snp37980-scaffold471-242244 13 79105039 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410999 Affx-122951992 AX-123281349 13 77726633 GAGGTGGGGGCCTTTCGCAGAAGCTGCAGCACCAC[A/G]CTGTTACCGACTGTGCTGATCTAGCCCTGTTCGTC R 2 1 2 1 201000 r 74 goat snp37979-scaffold471-195967 13 79151769 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394704 Affx-122964346 AX-123265059 13 77801225 CAGTTTAAACCTTTAGTCCAGCACCTCTGTTTGCC[A/G]TTCCTCCTGGTATCCTATCTGCTCTTGGTCGCAAG R 2 1 2 1 101000 r 74 goat snp37978-scaffold471-121375 13 79223154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397859 Affx-122962453 AX-123268214 13 77843399 ACGGCCAAAGCACACTGCCTTTTCTTTCCTCCTGA[G/T]CCACTGGCCCTCCAGAAACAAATTTCCAACAGATT K 2 1 2 1 201000 r 74 goat snp37977-scaffold471-79201 13 79265531 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398638 Affx-122961459 AX-123268993 13 77884386 ACCTGCACGTGATCAATTCTCAATAAATGGTAACC[G/T]TCCCTTCTCTGTCATTTCAGGGAAAAGGGGCAAAC K 2 1 2 1 101000 f 74 goat snp37976-scaffold471-38214 13 79306196 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419389 Affx-122945611 AX-123289737 13 77919139 CACTGAGCATGAATGCCTGCAAACAACTAGAATCC[C/T]CTTTAAAACTTTAACTTCATCTTCACGCCTTAAAA Y 2 1 2 1 101000 f 74 goat snp37975-scaffold471-3461 13 79340887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450218 Affx-122922279 AX-123320553 13 77945042 CAGTGACACCCGAGGTTGGTGATGGCTGGGGCTCA[C/T]ATCCCAGTGAGACTATCATTTTGAAAAAGCATCCG Y 2 1 2 1 101000 r 74 goat snp19334-scaffold1952-22343 13 79368270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771574 Affx-122920585 AX-385258731 13 77994621 ATTCAAATGATAATAACTTAGTTATTATCACACTG[A/G]AGTCAAATGGCAGAAATTTTGAGGCACTGATATGC R 2 1 2 1 101000 r 74 goat snp19335-scaffold1952-71922 13 79418476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407042 Affx-122954937 AX-123277393 13 78065152 TTTATTGAACCTGTTTTCTTTTTGTGGAATTCTTA[C/T]AAGCTGTGTTCAGGAATGCAGAGTTCTAATGGTTC Y 2 1 2 1 101000 r 74 goat snp19337-scaffold1952-142453 13 79488846 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388338 Affx-122969355 AX-123258696 13 78120150 CTTCAAGCACACTGTAAATAATTTATGTTCATACT[C/T]GTGTGATTTCAAATTTGTTTATTAATGTTATCTCG Y 2 1 2 1 101000 f 74 goat snp19338-scaffold1952-197451 13 79544295 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400764 Affx-122959881 AX-123271119 13 78156750 AAGAATGGTAGGACCTCGTCCTGTACGGAAGCATG[A/C]GGGGTTTGCATCTGGGGAGTAGACGCGGTGGCGGC M 2 1 2 1 103000 f 74 goat snp19339-scaffold1952-234051 13 79580880 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401158 Affx-122959368 AX-123271511 13 78188746 GTCTTGGCCAACCCCAGTCGGCAGCGCTGGCGTGT[A/G]TACTGCCCCTCGGAGTGCTCTGTGGTTTTGTTTGT R 2 1 2 1 101000 r 74 goat snp19340-scaffold1952-266047 13 79613525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375955 Affx-122978446 AX-123246314 13 78257581 TTTCTTTCAATGTCTTATTTTTTGGGCTCTTCTTA[C/T]AAGCTGTTATAACCTTGACATTTTTAGAAGACATC Y 2 1 2 1 101000 r 74 goat snp19342-scaffold1952-334882 13 79682529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771768 Affx-122953631 AX-385258925 13 78288095 TGCTTGCTGGATGCATGTCCCAGATAAGTTACTTG[C/T]ACTTACGTCTCTGTCTTAGGGCTTGCTTTTGGGAG Y 2 1 2 1 101000 f 74 goat snp19343-scaffold1952-365396 13 79713765 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380154 Affx-122975973 AX-123250512 13 78345494 ACTCCGCCTGTTGCTCAGAGGTGCGAACTCCTGGC[A/G]ATTGGCATTCACAGCTGGAGCAGCTCCTGAATTCA R 2 1 2 1 101000 r 74 goat snp19344-scaffold1952-422795 13 79770866 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409078 Affx-122953339 AX-123279429 13 78377815 TCGCCCTCGTCTGCATCACTGACCTCGATTAACCC[A/G]TTCAGCTCAAAGCAAGAAGGAAGGAGGGTAAAATG R 2 1 2 1 201000 f 74 goat snp19345-scaffold1952-455116 13 79803573 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438548 Affx-122931182 AX-123308886 13 78440675 GAGGTCACTGGGAAGATGGAAGCTGGGGCTGGGGG[A/G]TGAAGGTGAAAGAAGATCCTCTGAGATCTGCTCAT R 2 1 2 1 101000 r 74 goat snp19346-scaffold1952-517976 13 79866195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391667 Affx-122966549 AX-123262024 13 78484767 TCCTGATCTGTCCCAAGTAATCCTTTCAGTGATAG[G/T]CTAATGTTACCTCCTCCAGGAAGCCCTCCCTGGCA K 2 1 2 1 101000 f 74 goat snp19347-scaffold1952-562068 13 79910677 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414225 Affx-122949641 AX-123284574 13 78591310 TTTTTAACAAAGACTTAAAAATAATTAGAATTTAA[C/T]GAGCACCATTACGCATTGCAGTGGTTTTAATATGT Y 2 1 2 1 101000 r 74 goat snp22420-scaffold2213-270881 13 80997846 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272718 Affx-1111832996 AX-519546421 13 78631086 CTGGCCCGGGAAATCGTCATCAGCTTCCTGTTGGG[A/G]GGAGACCTCTCTGCCCAGGGCAAGAAGCATGCCCG R 2 1 2 1 202000 f 74 goat 13_78631086_AF-PAKI 13 78631086 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320772606 Affx-122976547 AX-385259754 13 78682509 TCTATAAAACAGGCAGTGGGAATGACTGAAAAATA[G/T]CGTGAAAGGCCATCTGAAAGAGTTTTGTCAGGATT K 2 1 2 1 201000 r 74 goat snp22418-scaffold2213-179682 13 81088046 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797978 Affx-122978562 AX-385284914 13 78724186 CAAGAAATGTCATTCTGGAATGGATTTGAAGTCCC[A/G]TTTCTTATCCTCCACCATGTTCCAAATTATCTTTT R 2 1 2 1 101000 f 74 goat snp22417-scaffold2213-138005 13 81130641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408944 Affx-122953933 AX-123279295 13 78758296 CGGGTCTCAACAATATTTTTAAGGTATTTTTTAAA[A/G]GTAGTTTTAATGCCATGCTAAGGTATTTGGGCATT R 2 1 2 1 103000 r 74 goat snp22416-scaffold2213-103895 13 81164673 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438078 Affx-122931524 AX-123308416 13 78790704 AACTACTATCTTCCGTGGAGTTAAAGGTCATCCGA[G/T]ACAGAGGGCTCCATACAGACAGGAAACAGGCCAGA K 2 1 2 1 101000 f 74 goat snp22415-scaffold2213-71487 13 81196045 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421187 Affx-122944157 AX-123291534 13 78857671 AGTTGAGTCAGACCAATGGAAAAGGAGACCAATGA[C/T]GAAAAAAGAAGGTCGAGAAAAGCGGAGTGGAAATA Y 2 1 2 1 101000 f 74 goat snp22413-scaffold2213-4520 13 81263993 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782643 Affx-122942366 AX-385269716 13 78888230 TACAGAGTTGAGTACTTACAAATTGGAAAGAGAAT[A/G]CAATTTAGATATTTCAAGTCAAAAAGTTTACCTTT R 2 1 2 1 101000 f 74 goat snp45572-scaffold622-1736789 13 81297410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448331 Affx-122924139 AX-123318667 13 78940116 AAAGTGCTGAAAGAAAGAAGAGGGATACGGGAAGA[C/T]AAGGGGGGACTCTGAGACCTCATTGTTAACCTTTC Y 2 1 2 1 101000 f 74 goat snp45571-scaffold622-1684903 13 81344075 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378333 Affx-122977337 AX-123248692 13 78975940 CACTCAGGTGGTCTCCATGCCTTGGAAATTGTGAA[C/T]GATGCTCTGTGGACACTGGGGCGCATGCAACTGTT Y 2 1 2 1 101000 f 74 goat snp45570-scaffold622-1649079 13 81379895 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403232 Affx-122957893 AX-123273585 13 79019757 TCAGGCTCCTTGTGGAAGATAATGCATCACAGGGC[A/G]TCTTGGTAGGCTGAGAAAAGCCCACAAAACATGTA R 2 1 2 1 101000 f 74 goat snp45569-scaffold622-1605262 13 81424040 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411849 Affx-122951223 AX-123282199 13 79049276 CTGCCCTTTAGAGGCTTCCTCTGAAATTGAGTCCA[C/T]AGGAAAGGTGACATTTTATCATTCTGTTACAAATC Y 2 1 2 1 101000 f 74 goat snp45568-scaffold622-1575743 NW_017213564.1 3856 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422180 Affx-122943518 AX-123292526 13 79084157 GAGCTATTACTGTTGCTGTGGTTTCTGGAGTCCAA[C/T]GGCTCTGACCATCCTCAGACACAAATGCTATTATT Y 2 1 2 1 101000 r 74 goat snp45567-scaffold622-1540862 13 81488836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422755 Affx-122943241 AX-123293101 13 79126053 ATGTTTTCACCTATAAAATATTCATAAAGCATAAA[C/T]GTGATGTTGCTTTGGGAAAACAAAATTTTAAAACC Y 2 1 2 1 103000 r 74 goat snp45566-scaffold622-1498966 13 81530950 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439239 Affx-122931011 AX-123309576 13 79156292 CCAATAAATATCACTAATCGTTTCAGTGGCTGACA[C/T]GCCTGCTGGAACATGGACCTGACAGTTCTTCGTTG Y 2 1 2 1 101000 f 74 goat snp45565-scaffold622-1468727 13 81560549 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450649 Affx-122921977 AX-123320983 13 79190340 AAACGATTCTAAACTGAAAGGGCTGCAGTCGCTTA[C/T]GTATGCATGTTTGTGGGGAGAACTCATCACTGGGG Y 2 1 2 1 101000 f 74 goat snp45564-scaffold622-1434679 13 81591617 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407643 Affx-122954617 AX-123277994 13 79233269 CGAGCAACCATTGCCTGGAGACCAGAGATCCCCCC[A/G]CAGACTCCACATCACTTTCCTTCTTCCTAAGAGCT R 2 1 2 1 101000 r 74 goat snp45563-scaffold622-1391750 13 81634585 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410966 Affx-122952022 AX-123281316 13 79279366 CAAAGCAGAAGATTCTGTGATGTTATTCGAGTCCA[C/T]AGAGTCAGCTGAAGGTCTGTCTACCCCTGGGACTT Y 2 1 2 1 101000 f 74 goat snp45562-scaffold622-1345653 13 81681179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430764 Affx-122937491 AX-123301105 13 79309381 TGGTGCCCCAGAGGCAAGGAAAGGAGTCCTGCCAA[C/T]GGTGTGAGTTTGGAATAGATTCTTCCACAGTCGAG Y 2 1 2 1 101000 r 74 goat snp45561-scaffold622-1315638 13 81709567 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791084 Affx-122923921 AX-385278079 13 79360679 CGCACATCTCTTTCTTTAGAATACAGGTAAAGAGA[C/T]GAAGTAATCTGTTTGAATTATGATCTCTGGGGCCA Y 2 1 2 1 101000 r 74 goat snp45560-scaffold622-1264340 13 81761366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410073 Affx-122952851 AX-123280423 13 79411589 ATACATCCACCCATCCTATCACTTCTACAGGAATG[C/T]ACTCTGTACTTTCTATAATTGTGACCACTGAGTCC Y 2 1 2 1 101000 r 74 goat snp45559-scaffold622-1213430 13 81813202 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427210 Affx-122939586 AX-123297553 13 79470305 GAAGAATCGTCAGAAGCAGAGAAGAAAGGGGGAGC[A/G]TTGTAGGAATACCAAGATGGAGATTAGAGAGTGGG R 2 1 2 1 101000 r 74 goat snp45558-scaffold622-1154714 13 81873466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375451 Affx-122979168 AX-123245810 13 79521616 GTTTCCTGAAGGAGCACTCTCGGCACTCAGGGCTG[C/T]GGCTCATCTTTCTGCGCATGGGCCACACCTGTTTC Y 2 1 2 1 303000 r 74 goat snp45557-scaffold622-1103403 13 81922142 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803837 Affx-986696254 AX-385290573 13 79563669 AATAATCTAGTGGGGGAAGACAGAAAAGAACGGGT[A/G]TTTTTTGAAGTTTGCTGTTTTCTTGGATGTTATTT R 2 1 2 1 600010 r 74 goat 13_79563669 13 79563669 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 38415127 Affx-122949428 AX-123285476 13 79579089 ACTATTATTAAAGAAAAACAGTTTCAAAAAGTGGA[C/T]GGCTGATAGAAAGTTAAACTAGGCAGTTACACCTA Y 2 1 2 1 101000 r 74 goat snp45556-scaffold622-1045930 13 81980400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430879 Affx-122936883 AX-123301220 13 79628805 TCATGTCTGTCACCAGGCCTTCCCCCAGCCCTCCA[C/T]GATAAACCATTTAAGAATGAGTTTTACATCAGACG Y 2 1 2 1 101000 r 74 goat snp45555-scaffold622-996214 13 82031445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447323 Affx-122924898 AX-123317659 13 79665910 CTGGCCTGTCTTATCGCTCTGAGGTCATGATTCCA[C/T]GGGCTGCATCCCCCAGGCTCTCCCGCTGCCTGCTT Y 2 1 2 1 101000 f 74 goat snp45554-scaffold622-959109 13 82068951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382004 Affx-122974074 AX-123252362 13 79732426 TGCCATCCCCACTCAGAGCTTCAGTGGCCATCTCT[A/C]GTTCAGAGTTTTACTTTAGACTTCCTTTCTACTAC M 2 1 2 1 101000 r 74 goat snp45552-scaffold622-892593 13 82136290 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382310 Affx-122973907 AX-123252668 13 79773267 CTCTAACTGAAATCCTTTCCCCCAAGCCCAAAGGG[C/T]ATTGCTATCTTTCCAGGAACCATAACACAATCTGT Y 2 1 2 1 201000 r 74 goat snp45551-scaffold622-851752 13 82176806 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799652 Affx-122973874 AX-385286581 13 79824612 TTCCTTGCAGGTCAGAAATCTAGTGTGTTTAGAGC[A/G]CCTTGTTATCCAGACGTTAAAATTATGAAAGGACT R 2 1 2 1 101000 f 74 goat snp45550-scaffold622-800407 13 82228952 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396528 Affx-122962953 AX-123266883 13 79855064 CGTCTCTGCCCCTCTGAGCTCTGAACAAACCGAAA[C/T]GTAAAGAGTCAGACAGATGGAAATCAAAGTTTCAG Y 2 1 2 1 102000 r 74 goat snp45549-scaffold622-769955 13 82259656 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439935 Affx-122930003 AX-123310272 13 79905871 ACTGCAGCAGAGCTGATCCTGGCCACCCTGTCTAT[A/G]GTGAAGCTACTGTAGATGACATTTTTACCCTTTGG R 2 1 2 1 101000 r 74 goat snp45548-scaffold622-719148 13 82310508 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420839 Affx-122944657 AX-123291186 13 79945267 TTCTTCATTTTTTTTCCCTCTGGAGCACAAATTTT[A/C]ACTTTCCTGACCTCTACATTTGTAATAAATTTTGT M 2 1 2 1 201000 r 74 goat snp45547-scaffold622-679752 13 82349633 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389445 Affx-122968349 AX-123259803 13 79998336 GCATCTCGCCTGGCAGCTGGTGCCGTCATAAAGAG[C/T]GCCTATCGGCCGTTTGCAAAATACATGGGGGTTTG Y 2 1 2 1 101000 r 74 goat snp45546-scaffold622-626683 13 82403033 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603292 Affx-1002479494 AX-413837472 13 80005493 GCAAACATTCACCTGCTCACCAAATGACTAATCTG[C/G]GGTGTATTATGGAAAGTCTGATTCCCCAGACCTCA S 4 1 2 1 101000 f 74 goat 13_80005493_RH-map 13 80005493 C G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468276900 Affx-1111835577 AX-519550409 13 80020048 AAATTTATTTGAATTGAAGATCCTTTAGAATTCAT[C/G]CTAAAAGTCAACCTTCAAAGCAATGTGAGGCCTGT S 4 1 2 1 101000 r 74 goat Random2.2K-1382 13 80020048 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396073 Affx-122963440 AX-123266428 13 80029998 AAAGAACACAGACAGGGTCCCTGAGGGCAGGCAGC[A/G]TGCATTCCAGGGATGGACGCGTCCCTAGACATTAG R 2 1 2 1 101000 r 74 goat snp45545-scaffold622-595021 13 82435931 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603372 Affx-1002479495 AX-413837547 13 80044623 TGTTGATGTTTAAATCTCTGTTTATCTCCAAAGTA[A/G]TATCGACTGCAGGACTAAGAATGACTTTGGCAATT R 2 1 2 1 101000 r 74 goat 13_80044623_RH-map 13 80044623 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320783914 Affx-122935081 AX-385270969 13 80078205 CCATGTTGTGGTATTATTTTCCTGCTTAAAAGATG[A/C]AGAAGGAGGCTTTAGTGGCATTAATAAGTATCCCA M 2 1 2 1 101000 f 74 goat snp45544-scaffold622-546814 13 82484544 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603296 Affx-1002479496 AX-413837476 13 80091000 GAGGAATGAGACAGGATAAGATTTTTGGCTTCAGA[A/C]AGTCAGAGTCTACTCTCAAAAGCTGGGGGGAGGAT M 2 1 2 1 201000 f 74 goat 13_80091000_RH-map 13 80091000 C A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603376 Affx-1002479497 AX-413837552 13 80108293 ATTTTAATATCCAAGCCTTAGCTGGCTCTATAGTT[A/G]GCAATTTGAGGTATGTCTGATTCCAGAAGAACAAA R 2 1 2 1 101000 r 74 goat 13_80108293_RH-map 13 80108293 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603300 Affx-1002479498 AX-413837480 13 80124730 TAGTCACTGCATTGAGTGAGTGAAGTCGCTCAGTC[A/G]TGTCCGACTCTTTGCGACCCCATGGACTGTAGCCT R 2 1 2 1 103000 f 74 goat 13_80124730_RH-map 13 80124730 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38404549 Affx-122957387 AX-123274901 13 80139944 TTTTACCTGAACTTTATAGACTTCTTTATTTGAAG[A/C]TGTAAAGGGTGAATGCAATATTAGGATACAAGGAA M 2 1 2 1 101000 r 74 goat snp45543-scaffold622-485075 13 82549463 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603302 Affx-1002479499 AX-413837482 13 80152356 GAGTGAGGATGAAACAAGGAGCTTGGCTTGGCTGC[A/T]ACGGCAAGGCACCATAGACTGAGGGGCTTAAACAC W 4 1 2 1 303000 f 74 goat 13_80152356_RH-map 13 80152356 A T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603382 Affx-1002479500 AX-413837557 13 80175256 TTGTAAAGCAGTTTTCCTCCAATTAAAAATTAAAT[A/T]AATACACTACAAAGAAATTGTCATCACTAAAAATA W 4 1 2 1 303000 r 74 goat 13_80175256_RH-map 13 80175256 T A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38437981 Affx-122931594 AX-123308319 13 80193861 CTGCTCTGGCAGATGCAGCTTTCGGAGGTGCTTGT[A/G]TTTGTCTTGGGTTTGTATCACCCTGTCTTGTATTT R 2 1 2 1 101000 r 74 goat snp45542-scaffold622-431158 13 82604140 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603306 Affx-1002479501 AX-413837485 13 80206840 CTGAACTGAACTCTTATTAGGATGATCACAGGGTG[A/G]TGGTGTTGCGATGACTATTATTTTATGCTCTGTGA R 2 1 2 1 400000 f 74 goat 13_80206840_RH-map 13 80206840 G A Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38380820 Affx-122975079 AX-123251178 13 80230584 TTGGCCCTGAGCATTGTTTGACTTCTGATGAGTTA[C/T]GTACATCATATAGACAAATAATTCCCCTAGGATTC Y 2 1 2 1 101000 f 74 goat snp45541-scaffold622-394435 13 82640273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603608 Affx-1002479502 AX-413837757 13 80232560 GTCTTGAACAGTGTTCTGGCACATATAGACATCCC[A/C]AAAGCACATATAAATCAAGAATAAATGATTCAAAG M 2 1 2 1 101000 f 74 goat 13_80232560_RH-map 13 80232560 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603386 Affx-1002479503 AX-413837560 13 80248116 CAATCCTGTCTCTGATCCCTGCCACTCTCTTCCTG[A/G]ACCCAGACTTGTAATGCAGCCCTCTCCTGGAACAT R 2 1 2 1 202000 r 74 goat 13_80248116_RH-map 13 80248116 A G 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38436265 Affx-122932544 AX-123306604 13 80264884 CTGAATGAAACTTCCTGCTTTGTATTGCCAGCCAG[C/T]GTGGGACGGAGCGGAAACCCCAGAGAATCCTCGGG Y 2 1 2 1 101000 f 74 goat snp45540-scaffold622-360135 13 82673964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603388 Affx-1002479504 AX-413837562 13 80275452 ACACCTCCCTCCAGCCCTGTCACCCGCTGAGCCAC[A/G]CTCCTTCACGATACTGTGTCTCTCTGATAACGTAC R 2 1 2 1 101000 r 74 goat 13_80275452_RH-map 13 80275452 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603390 Affx-1002479505 AX-413837564 13 80302736 TCGCTGGTATTAATTGTGCTTGTTTTTATGCTTTC[A/G]AGGGTGTTTTGTCAATGGCAGTTTTCTTTTCTGCT R 2 1 2 1 101000 r 74 goat 13_80302736_RH-map 13 80302736 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38445166 Affx-122925547 AX-123315503 13 80308039 CTAGAAACTTGTCTGTAGTGTGGAAGACTGCTTCC[A/G]TTGGAAGAAAACATTTTTGCTGAGACAAGTATTAA R 2 1 2 1 101000 r 74 goat snp45539-scaffold622-316980 13 82716880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603391 Affx-1002479506 AX-413837565 13 80347094 CCTGAAATGCACAAGAGATGTTCCAAATGTCAGGA[C/G]ATCTATCCTGAGTCCCTTTAATACTCACACAACAG S 4 1 2 1 101000 r 74 goat 13_80347094_RH-map 13 80347094 G C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38377227 Affx-122978165 AX-123247586 13 80364479 AACACTGAGACTGCTTTAATTGTTAAATTTCATTT[A/C]TTCATGTCCATAGATCAATTAAAATCAAGTGCTGT M 2 1 2 1 101000 r 74 goat snp45538-scaffold622-260540 13 82774395 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603316 Affx-1002479507 AX-413837494 13 80374089 ACAGGACATTCTTGACATCCCGCATATACAAATCA[C/T]GGAATGTCTTTCTAACTAGCCGCTCCTGTAAATCA Y 2 1 2 1 101000 f 74 goat 13_80374089_RH-map 13 80374089 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603318 Affx-1002479508 AX-413837496 13 80393307 AGCAGAGAAACCTGCCACTGCAAAGAGTCACAGTC[A/G]AGGAGAGATTGGCAGATGCAAGAAGGAGCAAGAGG R 2 1 2 1 101000 f 74 goat 13_80393307_RH-map 13 80393307 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38407306 Affx-122955316 AX-123277657 13 80395269 CACGACTGAGGGACTGAGCTGTACTGAACTGAACC[A/G]CTTGTTGAGTTGATGAGTGCCCTTTGCTTCCAGTG R 2 1 2 1 101000 r 74 goat snp45537-scaffold622-229750 13 82804783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603396 Affx-1002479509 AX-413837571 13 80444552 ATGTAGGAATTTTTTATTTTTTACCTTTGTAAAAA[C/T]TGAGTTTATCCTATCTACAGGAGAGACTGTAAGTG Y 2 1 2 1 101000 r 74 goat 13_80444552_RH-map 13 80444552 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38401679 Affx-122959560 AX-123272032 13 80449516 AAGAACAACAGGAAGCCAGTGAGACGGTCTCCTCA[C/T]GGGGTGAAATGTCCGACTTTGGTCTTCTGGCATCA Y 2 1 2 1 101000 f 74 goat snp45536-scaffold622-175503 13 82859758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419288 Affx-122946242 AX-123289636 13 80498927 GACTGAGAATTTGATGAGGTTGGGATGACCCCAGG[C/T]GACCTCTGTCAGAACGAAACCAGAAGATTAAAGGG Y 2 1 2 1 201000 r 74 goat snp45535-scaffold622-126092 13 82910392 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603398 Affx-1002479510 AX-413837572 13 80503899 TGGCTTTTTTTGAGAATCCTTGTTAAACTTTCTAC[C/T]CAGGTACTTCCTCAAGACGCTTGTATCAACTTCCA Y 2 1 2 1 101000 r 74 goat 13_80503899_RH-map 13 80503899 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603324 Affx-1002479511 AX-413837501 13 80529652 CTCACCAGGACCATTTCTCTAGATTCCATATATAT[A/G]TGTGTGTGTTAAATACACAATATTTGTTTTCTCTT R 2 1 2 1 303000 f 74 goat 13_80529652_RH-map 13 80529652 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38377150 Affx-122978222 AX-123247509 13 80561495 AGGAGAGACCAGAGATTGTTGTTTAATTGCTAAGT[C/T]GCATCTGACTCTTGCAATTCCATGGGCAGTAGCCA Y 2 1 2 1 103000 f 74 goat snp45534-scaffold622-63524 13 82973408 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440042 Affx-122929756 AX-123310379 13 80605116 CTGCTTTTTGCAGGGAGCTGATGTTCTCATGTGCC[C/T]GGCATCAAGATGAGGGAGAATTTGGTGCCACCTTT Y 2 1 2 1 101000 f 74 goat snp45533-scaffold622-19903 13 83017195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603402 Affx-1002479512 AX-413837576 13 80619318 AGCAGCTGACGGCAGACTGGAGACAGGCCTTCAGC[A/G]CACAGGAGACCGGCACACTCACAGACCAGGGGTTT R 2 1 2 1 102000 r 74 goat 13_80619318_RH-map 13 80619318 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603327 Affx-1002479513 AX-413837503 13 80644220 GGCCTTCAGTTTCAAAGGCAAATTCAGCTTGGAAC[A/G]ACAGAGCAGCTGCCTGCTTTTCATGGGAAGAAAAC R 2 1 2 1 102000 f 74 goat 13_80644220_RH-map 13 80644220 A G 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603330 Affx-1002479514 AX-413837506 13 80687331 GGTGTGACGGAGGGAGAGGGGGGAAGTAAATCTTA[A/G]AAAAAACTTTTTTTTAATTGAAGTATAGTTAAGGA R 2 1 2 1 102000 f 74 goat 13_80687331_RH-map 13 80687331 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603332 Affx-1002479515 AX-413837508 13 80718844 GGAGAAATATCTGCTCAGATATGCAGATGACACCA[C/T]CCTTATGGCAGAAAGTGAAGAGGAACTGAAGAGCC Y 2 1 2 1 103000 f 74 goat 13_80718844_RH-map 13 80718844 T C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603410 Affx-1002479516 AX-413837583 13 80738306 AGTCAGTGATTCTTGAGAAAATTCCTCTCTCTGAT[A/G]TCATGGTTTATCCACTACAGAAGCTTCTAAAAGCT R 2 1 2 1 201000 r 74 goat 13_80738306_RH-map 13 80738306 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603668 Affx-1002479517 AX-413837804 13 80755185 CAAATTCAAAAGAAAATAAATGGATTTTTTATGGC[C/T]TAAAGGATCTATTCATTACCAAATCATTTATCTTT Y 2 1 2 1 101000 r 74 goat 13_80755185_RH-map 13 80755185 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603336 Affx-1002479518 AX-413837512 13 80788585 CTGAACCTGCTATGTGAAAGAAACAACCTTTATAT[C/G]TACCTAAGCCGATGCTGAAATTGAGTCTCTATTTC S 4 1 2 1 101000 f 74 goat 13_80788585_RH-map 13 80788585 C G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603414 Affx-1002479519 AX-413837587 13 80809992 CATTCAGTTTGGCCATCAGTACACCCAGATGAAGG[C/T]TGTTTGATCTAAGCCAGTCATGACATTCTTTGTCC Y 2 1 2 1 101000 r 74 goat 13_80809992_RH-map 13 80809992 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603340 Affx-1002479520 AX-413837516 13 80855246 AGAAGCCTGAAAAACGTTTACTTAAGCATATGGCT[A/G]ATTCAAAGAAAACATTTTTATCATCCTTCTCTCAT R 2 1 2 1 101000 f 74 goat 13_80855246_RH-map 13 80855246 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468276902 Affx-1111835578 AX-519550411 13 80873572 GGAAAGAGTGGAGAGAAGAGGCTGTACAGAGCTGA[A/G]TTCTGGAAAAGAACCATCATCCCATTCTCACCACT R 2 1 2 1 101000 r 74 goat Random2.2K-1386 13 80873572 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 350603342 Affx-1002479521 AX-413837518 13 80901192 TAAATCAACAGTTCAATGAATATAAGATAAAAAAA[G/T]ATAAGTGAACTCAAGCCAGCTTTCAGAACCTTACA K 2 1 2 1 201000 f 74 goat 13_80901192_RH-map 13 80901192 G T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603419 Affx-1002479522 AX-413837592 13 80932374 GGGACAATTTCCTTCTAAAGGAAGGAGGCAGAGTA[A/G]AAAGCTCATGTTGATTCTTTTTCCTGGCCAAGGGC R 2 1 2 1 400000 r 74 goat 13_80932374_RH-map 13 80932374 A G Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603346 Affx-1002479523 AX-413837522 13 80950889 GACATTGTTCAGTTGTTTAATCACTAACTCGCATC[A/C]AGCTCTTTGCGACCTCATGGCCTGCAGCAAGCCAG M 2 1 2 1 103000 f 74 goat 13_80950889_RH-map 13 80950889 A C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603423 Affx-1002479524 AX-413837597 13 80968816 GCTCATCAGGCCTGCTCCCTTCCAGGCACTTTGAG[A/G]AGGAGCCAGCAAGGCGCAGACTCGAACCTGTTGGA R 2 1 2 1 202000 r 74 goat 13_80968816_RH-map 13 80968816 A G 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468274330 Affx-1111834137 AX-519547925 13 81454694 AGGCGTCTGGCTCCAGGCAAAGCTGGGGCCAGGCA[A/G]AGCTTCTCTGTGTTGCAGCCTCTCCAACCCCGGAG R 2 1 2 1 202000 r 74 goat GoatD01.020641 13 81454694 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468274788 Affx-1111834421 AX-519548374 13 82976914 GGGCAGCTGTGTTCC[A/G]TGGCCTGCAGGCATTATTTGGGTAGCACGTCAATT R 2 1 2 1 102000 r 74 goat GoatD01.034833 13 82976914 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38400401 Affx-122959997 AX-123270756 14 14514 ATACCTGTAACTATAGCTACTCATTCGTATGATAA[C/T]TATGGTCTTGCTGTGTTACAACTGCGGGATTTGAT Y 2 1 2 1 201000 f 74 goat snp47867-scaffold674-1102631 14 94652387 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385318 Affx-122971671 AX-123255676 14 97190 GCTCAGAACTTGAAAGGCTTTTCTTTGAATTACAA[C/T]GAACTTGGGAAGGCTTTTCTTTGAATTACAACGAA Y 2 1 2 1 101000 r 74 goat snp47866-scaffold674-1019955 14 94567957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381144 Affx-122974560 AX-123251502 14 129540 CCTTATTCTAGAGGACAAAACTGGGGCTCTAAGAA[C/T]GGGGTAACCCAGCTATAGCAGGTTAGTGTGTACCC Y 2 1 2 1 103000 f 74 goat snp47865-scaffold674-987605 14 94534798 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404365 Affx-122956812 AX-123274717 14 170857 TGGTTTTCTTCTATTGGGGAAACCGCAGCTGTGCC[A/G]TTTGTAGGAGTGTCAAAGTCTTTTTCTCTCCCAAA R 2 1 2 1 303000 f 74 goat snp47864-scaffold674-946288 14 94493365 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450214 Affx-122922283 AX-123320549 14 213393 TGTTTGGGTTGCATCACCCTTTTGGCTGTTGTGAA[C/T]GGTGCTGATATGACTATTCATGTGCAAGTATCTGT Y 2 1 2 1 101000 r 74 goat snp47863-scaffold674-903752 14 94453466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404144 Affx-122957087 AX-123274496 14 245422 GGACACGACTGACGTGACTTAGCAGCAACATGACC[C/T]GGCTTTAAAAACGGGCTCCTCATTTTACACACCGG Y 2 1 2 1 101000 r 74 goat snp47862-scaffold674-871723 14 94421464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422778 Affx-122943221 AX-123293124 14 279463 ACTCTAGGGTATGCAGAAGAAATAATAATATTGTA[C/T]ACATGAAGCTTATATAATGTTATAAGTCAATACTA Y 2 1 2 1 101000 f 74 goat snp47861-scaffold674-837682 14 94387471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434818 Affx-122934804 AX-123305159 14 321749 ATTGGTCTCAGTGAGCCCAGCCTGGCATGGTCTCC[A/G]TCAGGAGGAAATTCGGTCACCTGGGCATCCTTAGT R 2 1 2 1 101000 r 74 goat snp47860-scaffold674-795396 14 94345272 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441025 Affx-122928944 AX-123311362 14 355108 CAAGAAGGAAACAAAGACTGTGCCCTCATCCATAA[C/T]CAACATGAAACTAAGTTAAACTAATCTGTTGGACC Y 2 1 2 1 101000 f 74 goat snp47859-scaffold674-762037 14 94312158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775124 Affx-122948129 AX-385262256 14 457276 ATTATGTGTGATTATTTGGCTTCCCACTTCCTACC[A/G]TTTTTGGTTTCAAAGCCATCCTGAAACCTGGAAAA R 2 1 2 1 101000 f 74 goat snp47857-scaffold674-659869 14 94209933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779852 Affx-122951217 AX-385266951 14 495027 TCAGGGAAAAGCAGCATCTATTCATTGATTTCAGC[A/G]CAGCAGTGCTATTCGACTGAAGTTTAACCTGTACT R 2 1 2 1 101000 f 74 goat snp47856-scaffold674-622118 14 94172382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784877 Affx-122972418 AX-385271924 14 525267 CATTGTTGACTTTTGATTACTTTCACACCAATCCA[C/T]GGTGGCTGTGAACTTGCTGGACTATCTGTTGTCTA Y 2 1 2 1 101000 r 74 goat snp47855-scaffold674-591878 14 94143743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272500 Affx-1111833013 AX-189952075 14 528238 TGTGCTTCTTCCAGCCCAGCGTTTCTCATGATGTA[A/C]TCTGCATATAAGTTAAATAAGCAGGGTGACAGTAT M 2 1 2 1 303000 f 74 goat 14_528238_AF-PAKI 14 528238 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423392 Affx-122943125 AX-123293738 14 583001 CTCTTTACCTTGCTCTGTCAGAGACTGGTTTGTGC[A/G]TGGAGTTACCAAGCCTTCATCCAGACTCCATCCTA R 2 1 2 1 101000 f 74 goat snp47854-scaffold674-534144 14 94086336 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446869 Affx-122925243 AX-123317205 14 613005 GAAATCTCTGGTCCTGTTATGAGGCAGAGCCTTCA[A/C]GGATAAGCAGAATAAAATGCGTTTAGCTTTCAGGC M 2 1 2 1 600000 r 74 goat snp47853-scaffold674-504140 14 613005 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789025 Affx-122925243 AX-385276038 14 613005 GAAATCTCTGGTCCTGTTATGAGGCAGAGCCTTCA[A/C]GGATAAGCAGAATAAAATGCGTTTAGCTTTCAGGC M 2 1 2 1 101000 f 74 goat snp47853-scaffold674-504140 14 94056346 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387367 Affx-122970470 AX-123257725 14 645021 CCATGAAACTTACAGGGTGAGCTCCCAGCTTGGGG[C/T]AGGGGAGTGGCAGCCGTACACTCATCCTTCTGGAG Y 2 1 2 1 202000 r 74 goat snp47852-scaffold674-472124 14 94024320 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383863 Affx-122973141 AX-123254221 14 681553 ATTTATTAATCTTTCCCTTCCCCACTAACTGTGAC[A/G]TTTCCTTCATTGTAAGTAAAATGACCTTTGTGTAT R 2 1 2 1 201000 r 74 goat snp47851-scaffold674-435592 14 93987561 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376217 Affx-122978802 AX-123246576 14 718589 ATAGAGTGAAGTAAGTCAGAAACAGAAAAACAAGT[A/G]TCATTTATTACTGTGGACTTTCTTTTGATCACCAC R 2 1 2 1 101000 r 74 goat snp47850-scaffold674-398556 14 93949716 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397508 Affx-122962060 AX-123267863 14 747342 GTGAACACTTCCCGTCATGCCCACTTTCTGAGGAG[A/G]ACCCCGATTCTCAGCAATATTGTGTAGTCCATCTC R 2 1 2 1 101000 r 74 goat snp47849-scaffold674-369803 14 93920860 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408008 Affx-122954312 AX-123278359 14 790085 TTGTGGTGTTTTGTCTGCTTCATTTTTGTAGTTCA[C/T]TGCATTTGTTTTATTAGCTACCTGTAACTAAAGTA Y 2 1 2 1 201000 r 74 goat snp47848-scaffold674-327060 14 93878042 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381969 Affx-122974103 AX-123252327 14 837494 CTAAGCATGATCAAATATAAATTCACAGATACACT[A/C]TGAAATGTAAAACACTACTTGTATTCTTCAATCCT M 2 1 2 1 101000 r 74 goat snp47847-scaffold674-279651 14 93831336 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781575 Affx-122973652 AX-385268659 14 877710 TTATTTTTCACCTTTTAGGATCGTTTTTAGACAAC[A/G]TAGTGTTGAGCAAAATCTGAGCTGGAAATCACTGC R 2 1 2 1 101000 r 74 goat snp47846-scaffold674-239435 14 93792119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382359 Affx-122973869 AX-123252717 14 917480 TAACCAGTTCTGTTTGTGATGTGTGTTTTAATTTG[C/T]AGCTAGATTTCAAGAATGTACAGGGCCCTGCAGAG Y 2 1 2 1 101000 r 74 goat snp47845-scaffold674-199665 14 93752516 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400581 Affx-122960407 AX-123270936 14 947461 AGAATTCAGTCCTTGGAACTTCTCTGGTTTCACAA[G/T]ATCTAAGAGCAAACTCACTGGAGGTCAACCTTACA K 2 1 2 1 101000 f 74 goat snp47844-scaffold674-169684 14 93722706 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380786 Affx-122975102 AX-123251144 14 979862 CATGAATCCAGAACTTTTGCTCCCAGTGTTGGACG[C/T]GATGAGTTACTTTACAAATGACTGTTCCCAAACTA Y 2 1 2 1 101000 r 74 goat snp47843-scaffold674-137283 14 93689706 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773150 Affx-122969000 AX-385260293 14 1014786 TGTAGAACTAAACAGAGAAATCACATATTAAACAT[A/G]GTAGGCATACTATCTAAACTGGATCTAGGAGTTAG R 2 1 2 1 101000 r 74 goat snp47842-scaffold674-102359 14 93654663 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420348 Affx-122944966 AX-123290695 14 1056236 GGTAAGTCCAGGTGACTTGGTGTTCTTTCTAGAAC[A/G]TCTGTTGTACAAGGAAGACTGTGCAATGAAGCTAA R 2 1 2 1 101000 r 74 goat snp47841-scaffold674-60909 14 93613247 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433177 Affx-122935656 AX-123303518 14 1111361 AGATCATTTCTCAGAGATTGCAGGAAGGAGTCAGA[C/T]GGGCAAAGTCAAAACTTCCCTTTGCAGGGAGACTG Y 2 1 2 1 101000 f 74 goat snp47840-scaffold674-5784 14 93557853 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425433 Affx-122941527 AX-123295779 14 1118324 TTGGCCTGTCAATCACAATGAGTTTGGCTGACAGT[C/T]TACCAGATATGCAGTCTCAGCATCATTTGAGTCAG Y 2 1 2 1 101000 f 74 goat snp16555-scaffold174-1148790 14 93550937 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776807 Affx-122954584 AX-385263931 14 1147670 AGTCGGCAAGGCCATGGTTGGCAAGTTCAGTGCAT[A/C]GTGAATGCAGAGGGCGTTCAGAGAAAAGCAACAAA M 2 1 2 1 101000 r 74 goat snp16554-scaffold174-1119444 14 93522463 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798702 Affx-122936721 AX-385285634 14 1177547 AATCTTTTCCATCAAAAGCCTGGAAGCTTTGTATC[A/G]TTGTCTTTGGCCGGTTACTATGATAGTAAATTCAT R 2 1 2 1 101000 f 74 goat snp16553-scaffold174-1089567 14 93492145 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766469 Affx-122957315 AX-385253836 14 1208903 TTCAGAAAAGAAGAGTTTGGTGTTAGCAAGGCACC[A/G]TCTAATCTATAATGAATAACTACATTCAATACTGT R 2 1 2 1 101000 f 74 goat snp16552-scaffold174-1058211 14 93460797 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780324 Affx-122975876 AX-385267419 14 1256376 GTGACTTGGGTTAACATTTGCAACATCACAGGGGA[C/T]GTTAAAACACTGCTTATAGTGACCACAATAAAGCT Y 2 1 2 1 101000 f 74 goat snp16551-scaffold174-1010738 14 93412819 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393189 Affx-122965514 AX-123263546 14 1288562 GAAAGAGAAACTGAGGGGAAGCTCCCTAGGACAAG[C/T]GAGGAGACAAAGAGGAACTTGCTCCTAATGACGGG Y 2 1 2 1 201000 r 74 goat snp16550-scaffold174-978552 14 93379768 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435829 Affx-122932828 AX-123306168 14 1318291 TTTGAAGTGTGTGTGTATGTGATTAAAAGGAAAAA[G/T]CCTGAGAGTCCCCAGGAGCTAAGGTTTAAAACAAG K 2 1 2 1 103000 r 74 goat snp16549-scaffold174-948823 14 93349104 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399217 Affx-122960600 AX-123269572 14 1378550 TCTGCTCACTATTTTTATGGAGAGCTTTTAATTGA[G/T]AATAGAAGAAACAAAACTGTGTCCCCAGAAGCTTA K 2 1 2 1 201000 f 74 goat snp16548-scaffold174-888564 14 93288271 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453692 Affx-122919697 AX-123324025 14 1436225 CTTTGTATTTCCTAGAATATGTTTTTAAAAATCAA[C/T]GTCTAATTTTATTCATGGGCTCAATAGAATTTAGT Y 2 1 2 1 101000 r 74 goat snp16547-scaffold174-830889 14 93230288 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425089 Affx-122941242 AX-123295435 14 1465081 ATTTCCACAGCTTTATCACCTGTTGAGGTGAAGCT[A/G]TTTGTTGATTCTCAACCATCTCGATGACCATTTCT R 2 1 2 1 101000 r 74 goat snp16546-scaffold174-802033 14 93202481 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796069 Affx-122948677 AX-385283021 14 1496064 ATTGGGAGAAATTAAACTGAGAACCTTTCAGATAT[A/G]TTTAATTTTAGTTATTGAGGAAAATCCAGGTGAGC R 2 1 2 1 201000 r 74 goat snp16545-scaffold174-771050 14 93171487 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796991 Affx-122930488 AX-385283932 14 1585025 GGGCAAGAAAAACGCCATGCTGGTGCTCTGTGCTG[C/T]ATTTGGAATCTCCTATTGTCAGTAAACTCTTCCTT Y 2 1 2 1 101000 f 74 goat snp16543-scaffold174-682089 14 93084062 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404091 Affx-122957131 AX-123274443 14 1618263 GATCAACCAGATTCCACTGATTACAGGATGCGTCT[A/G]TGCGTGTGCACATGTGCAAATACCCCTTCCTTCTC R 2 1 2 1 101000 f 74 goat snp16542-scaffold174-648851 14 93049636 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396325 Affx-122963073 AX-123266680 14 1658528 TATTTTTATTTTTCTCTTCTTTTCTCTCTCCCTTC[A/C]CTCCGCTTCCTTGGATGCTTTCCCAAAGGAGGACA M 2 1 2 1 101000 r 74 goat snp16541-scaffold174-608586 14 93009494 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399607 Affx-122961093 AX-123269962 14 1694351 TGTAAATCACTTTTCCCCTGGCTCCTGCCCTCCTC[A/G]TCTGTTAACTCTTGAGTCTGTGAATGTCGCCTTCT R 2 1 2 1 101000 r 74 goat snp16540-scaffold174-572763 14 92973392 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797306 Affx-122923363 AX-385284245 14 1755577 TCTCAAATAGTCCGCACAACAGCCAGAGCAAACTT[G/T]TAAAATCACAGAACTAAGTTTTCTTTGCTTCAAAC K 2 1 2 1 101000 f 74 goat snp16539-scaffold174-511537 14 92912682 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411001 Affx-122951990 AX-123281351 14 1786477 TCAAAAATGCATTTTGGTTTGCAGTTAAATGTCGA[A/G]TTAAGCCCAAAATCCAATGTCTGTATTTCCTGGCT R 2 1 2 1 101000 r 74 goat snp16538-scaffold174-480637 14 92885248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377959 Affx-122977201 AX-123248318 14 1843299 GATAAAGTCCAGGTTACTTATACCCATTCTTACAT[A/G]CAGTAGTTACTCCTAAGATAGTGCTGATGTCTTTA R 2 1 2 1 101000 f 74 goat snp16537-scaffold174-423815 14 92828698 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790821 Affx-122968468 AX-385277821 14 1881008 CCTGGGCATTCAAAAAGATCGCTTTGTGGATTAGC[A/G]TGTTTGAGGGAGAGCTTATAAACTGTTTCCAAGGT R 2 1 2 1 101000 r 74 goat snp16536-scaffold174-386106 14 92791096 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785739 Affx-122926372 AX-385272779 14 1923028 ATTCCATCCATCCTCCTTTTCAATAGAGATTGATT[A/G]TATATAGAGGAGGAATTCACTCCCATAGCGGGGAG R 2 1 2 1 202000 r 74 goat snp16535-scaffold174-344086 14 92748742 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775398 Affx-122942685 AX-385262529 14 1957847 TACTCAATTTGATAAACAGCATCTTCAAAAACCCT[A/G]CAGTTAACAGCCTACTTCATGATGAAGAGCAGGAC R 2 1 2 1 201000 f 74 goat snp16534-scaffold174-309267 14 92712755 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422757 Affx-122943239 AX-123293103 14 1989219 TGAAAATTGTGTCCATCTCTGACCATTTTTTTTCC[A/G]GACAAACTCTCCATACAGTAATATAAGTGAAGGCA R 2 1 2 1 101000 r 74 goat snp16533-scaffold174-277895 14 92680986 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394602 Affx-122964423 AX-123264957 14 2040115 CACCAGCTGGGAAGGGTGATAGATAAGCCTCTACA[C/T]GTATTTTAGCCTTTGCAGTAACCATGTGGCTTGTT Y 2 1 2 1 101000 r 74 goat snp16532-scaffold174-226999 14 92629313 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418053 Affx-122946625 AX-123288401 14 2073090 AGGGCGATGGATGTGAACATATTCAGTAACTTTTA[C/T]GTTTTGAAAATTACTTGTTTGGAAGTTTCAGATGT Y 2 1 2 1 101000 r 74 goat snp16531-scaffold174-194024 14 92596242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444361 Affx-122926709 AX-123314698 14 2132163 GCATTCTTTTTAAAAAATTAATTCTTGGAAAACAC[G/T]ACTGATGCTGAAAAATCTCAGGAGAAGTTTATTAT K 2 1 2 1 101000 r 74 goat snp16530-scaffold174-134951 14 92536988 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380251 Affx-122975454 AX-123250609 14 2164361 GCAGTTGTAAGAGGGAAGTTTATAGCAATTCAATC[G/T]CACCTGAAGAGACAGTAAAAAGCACAAGCAAACAG K 2 1 2 1 303000 r 74 goat snp16529-scaffold174-102753 14 92504604 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424359 Affx-122941852 AX-123294705 14 2193582 GGGAGTGCTGATGTTCACCAACTTTCAAGCTTCTC[A/G]CCCTCTTCCTAGATACCCACTAAACCCTTTCCTAG R 2 1 2 1 101000 r 74 goat snp16528-scaffold174-73532 14 92475802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443925 Affx-122927036 AX-123314262 14 2226285 CATCTTATTTACTTCCCGTCTCTCAGTGATCACTG[C/T]ATTTTGTTGCCCGAGGTATAGTCTTTTGAAAAACG Y 2 1 2 1 101000 r 74 goat snp16527-scaffold174-40829 14 92446872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454255 Affx-122919651 AX-123324588 14 2263186 AAGAAATAGAGGTGTTAGTTCTATATTTGGCTGCA[A/G]ACTATGCAGCTCTGACTTCAGATAGCTTGGGCCAA R 2 1 2 1 101000 r 74 goat snp16526-scaffold174-3928 14 92409536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437845 Affx-122932090 AX-123308183 14 2269692 TCTGATTAAGATTTTCTTGAGCAGACAGCTACAAG[C/T]ACTTTCTCCCTTTTCTTCATTAAAGGCAATATTTC Y 2 1 2 1 101000 f 74 goat snp1529-scaffold1041-428120 14 92388290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447588 Affx-122924014 AX-123317924 14 2304925 AACATCATTTCAACCTCTTCTTGAAGATGTGCAAC[A/G]GAGAGTGGAGGCTGGCTGCTTTCCGCATGTTTATT R 2 1 2 1 201000 f 74 goat snp1528-scaffold1041-392887 14 92352752 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451217 Affx-122921965 AX-123321551 14 2337520 ATGGCATCCAGCTATTGGTGTAGAATGTGAAAAAA[G/T]CTGACCTGGTTACTGTGGACGCAGAAACAATGGCA K 2 1 2 1 201000 f 74 goat snp1527-scaffold1041-360292 14 92321047 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777112 Affx-122931340 AX-385264235 14 2367375 GCCCTTGGCCCTTGAAGCCTCTTCTCATATATGGT[A/G]CAGATCACTTTTTAATGCTTCATTGACCAAGGTAT R 2 1 2 1 201000 r 74 goat snp1526-scaffold1041-330437 14 92291056 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783262 Affx-122947159 AX-385270327 14 2425127 TCTCCCAAAGTCAAAAGTAGAACTATTCCCAGTTC[A/G]TTTTTGTGTTATAACATAATATGTAAAAATTAAGA R 2 1 2 1 102000 f 74 goat snp1525-scaffold1041-272685 14 92232884 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430533 Affx-122937201 AX-123300874 14 2478620 CTAGCAGGAAAATGTATAAAGAGGAAAGAAAACAG[C/T]GATAGTGAGAAAAGGAAATATTTATTTTCCTTTGG Y 2 1 2 1 101000 f 74 goat snp1524-scaffold1041-219192 14 92179199 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407258 Affx-122955353 AX-123277609 14 2552660 TGATGTCTCTTCTATATTCTAGGCTTGGATCAGTG[C/T]CTTTTCCCAGCTTTAAGTTAAAGGGATAGCTCATA Y 2 1 2 1 201000 r 74 goat snp1522-scaffold1041-145152 14 92104836 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412448 Affx-122951409 AX-123282797 14 2583624 AAAATGGACCTAGAATATGCTCTTGGAGCGAACTC[A/G]TTTGTATGTAGGGGACTTACTGTAAAAACCACTTT R 2 1 2 1 103000 f 74 goat snp1521-scaffold1041-114188 14 92074025 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772772 Affx-122965532 AX-385259917 14 2633393 TTTTCATGAAACTTTAGTGTTAATAGAAGTACTTG[A/G]TTATAAATTGGTCTAAAGGAAACTGGTTTGGCAGA R 2 1 2 1 202000 r 74 goat snp1520-scaffold1041-64419 14 92024440 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416085 Affx-122948326 AX-123286434 14 2662768 CAAGGAGCTGACTATGAACCATGGAAGTCTGCTCC[C/T]CTGAACCTGACACCTTCCACGGCTGCTCTAAGACC Y 2 1 2 1 201000 f 74 goat snp1519-scaffold1041-35044 14 91994364 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276904 Affx-1111835579 AX-519550413 14 2667503 TTTCCTGAATCAGTTTGTATTCTTATTTGAAAGGC[A/G]TAGATGTCACTCTGGCTACGTTAAGCAGAGATGGA R 2 1 2 1 101000 r 74 goat Random2.2K-1388 14 2667503 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38385992 Affx-122971516 AX-123256350 14 2700070 AGACTGAGGGTGCAGCAATCTTAGAGAAAGCAGAC[A/G]CTTGCTTGGGGCCTGTAAGAACTTGACTACTTTTT R 2 1 2 1 201000 f 74 goat snp16714-scaffold1751-2159 14 91956492 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401079 Affx-122959634 AX-123271432 14 2769207 GCCCTATGTTCAGCCTCCTACTGGTACAGGGCTCT[C/T]CTTCCAGACTATTTTGAGGCTGAATTCACACAAAT Y 2 1 2 1 101000 r 74 goat snp16716-scaffold1751-71296 14 91885536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409548 Affx-122953602 AX-123279899 14 2813943 AGGCGAGCGGGGGCAGTGGTCAGGAGGGTGTAAAC[A/G]ACACCTGAAATATTCCTGCTGGGGATGCACCCCAT R 2 1 2 1 101000 r 74 goat snp16717-scaffold1751-116032 14 91840715 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428404 Affx-122938944 AX-123298747 14 2845929 TTCAGAACACAGCTCTGGGGACTGGGCCGAGTGGT[C/T]ATCCACTGGTACCACTACAGAAAGGAGACAGAAGC Y 2 1 2 1 101000 r 74 goat snp16718-scaffold1751-148018 14 91808376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776751 Affx-122967826 AX-385263875 14 2904571 GTGTCCAAAATGAAAAGTTGCTCATTGCCCATCAC[C/T]GTGTGAGATGGGTCTCGCATATTCACAAGCGTCAC Y 2 1 2 1 101000 f 74 goat snp16719-scaffold1751-206660 14 91748832 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375555 Affx-122979090 AX-123245914 14 2951624 GATTCTTAGTCACCATCTTCAGCGTCCTCCTGATA[C/T]GGCTCTAGACTCGGAATCACATCTGCGTGCACTGA Y 2 1 2 1 201000 r 74 goat snp19642-scaffold1983-869967 14 91692694 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380121 Affx-122975999 AX-123250479 14 2981696 CTGGCTGAGCTCTGCTTATCACATATGAAGACACC[A/G]TGGAGTCAGTGTAAAGACAGACATGGACATAAATG R 2 1 2 1 101000 r 74 goat snp19641-scaffold1983-839895 14 91662057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603350 Affx-1002479525 AX-413837526 14 3014042 GGACAAGTAATCAATGTTTCCAGAATCAGCTCTGC[C/T]AACTGTCAGAGATGGAACAAATAAAAGATGGTAAA Y 2 1 2 1 101000 f 74 goat 14_3014042_RH-map 14 3014042 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603352 Affx-1002479526 AX-413837528 14 3030267 ATTTTTTCCAACTCTAAGCAGAAAACTCACATGCA[A/G]CTTATGGTTAGTTCTAACTCAGATGCTTAGTTTTT R 2 1 2 1 101000 f 74 goat 14_3030267_RH-map 14 3030267 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320766766 Affx-122936080 AX-385254101 14 3038694 ATAAACCGGAAAGGAAAAAGCAAATTCCAGCAAAC[A/G]TCTTCTTCCCCACTCAGCCATCGTTAATAGCATCA R 2 1 2 1 101000 f 74 goat snp19640-scaffold1983-782897 14 91604769 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272781 Affx-1111833005 AX-519546479 14 3055919 AGTTCAGGACTGAGATGATGAGAAAGGGCATCTGC[A/G]TCAATTCCTTTCTGTGACTCCCTTCAGTGACCTTA R 2 1 2 1 101000 r 74 goat 14_3055919_AF-PAKI 14 3055919 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401129 Affx-122959389 AX-123271482 14 3069473 GTCGAACTGTTTCAGCCTTGCCTGTGATCCACAGG[A/G]TACTTCCATAAGAGGTTTTCAAACTGTGGGCACGT R 2 1 2 1 101000 r 74 goat snp19639-scaffold1983-752118 14 91574106 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428525 Affx-122938751 AX-123298867 14 3100880 GTAATTCTTCTCTTTGTTCTTTTATAATAGGTTTC[A/G]TTTCCCCCCTCTGGCTTCTTTGAGGAGTATTTCTT R 2 1 2 1 101000 r 74 goat snp19638-scaffold1983-720711 14 91543065 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603354 Affx-1002479527 AX-413837530 14 3129368 TCAATGTCCTGCATAATATTGTGTGTGTGTCCCTC[A/G]TTGAGCTGCGTCTGACTCTTTGCGACCCCACTGTC R 2 1 2 1 103000 f 74 goat 14_3129368_RH-map 14 3129368 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603356 Affx-1002479528 AX-413837532 14 3179275 CTCCAACCTCATTTTTCTTTCTCCAGATTGCTTTC[A/G]CTATTTTGTCTTTTGTTTCTGCATACAAATATTAG R 2 1 2 1 103000 f 74 goat 14_3179275_RH-map 14 3179275 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38399876 Affx-122960225 AX-123270231 14 3213608 CTTGGCCTGGTGTTAGGTCAAGATTTTGGCAACAG[C/T]GTTGGTGGATCTTATTTTGATTTCTTTTAAGAAAC Y 2 1 2 1 201000 f 74 goat snp19635-scaffold1983-607983 14 91442291 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603358 Affx-1002479529 AX-413837533 14 3218867 AAAAATCCTCAAACTGTCACCAGTACCATCCATCA[C/T]CATTATAACTACATAACACTGACAAGGAAATGTAT Y 2 1 2 1 101000 f 74 goat 14_3218867_RH-map 14 3218867 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603435 Affx-1002479530 AX-413837608 14 3237520 TCTGCCCTTTGGACTCAGGAAAGGTCTTAGAGGCT[A/G]GAGTCTTGCCTGTAAGAAACAAGGGACAGAAAGAC R 2 1 2 1 202000 r 74 goat 14_3237520_RH-map 14 3237520 A G 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38437064 Affx-122933087 AX-123307402 14 3251074 CTCACATGTTGGATTGCTGCTGAGGTCAGTAGATA[C/T]GTATTGAATAGATGTCTTTTTTATTTTGGTTTTGT Y 2 1 2 1 101000 f 74 goat snp19634-scaffold1983-570517 14 91405231 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603362 Affx-1002479531 AX-413837537 14 3288354 AAGGCTATAGCATGATCAATGAAGCAGAAGTATAT[A/C]TTTTTCTGGAATTGTCTTACTTTTTCTATGAGCCA M 2 1 2 1 103000 f 74 goat 14_3288354_RH-map 14 3288354 A C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320773745 Affx-122960505 AX-385260885 14 3322589 TTAGAGCTGCAAACTTTCATTTCATCATGTTTCAA[G/T]TTAAGTTAGTTGTTTATAAGATACAAGTGTAAATA K 2 1 2 1 101000 f 74 goat snp19633-scaffold1983-499002 14 91331985 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603439 Affx-1002479532 AX-413837612 14 3325143 AGAAAACTTCATACTTTGTTTTTTTAGTTGCTTAT[A/G]TGTTCCCTTTTTCTTTGGCCTTGAATGTAAAATCC R 2 1 2 1 101000 r 74 goat 14_3325143_RH-map 14 3325143 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603367 Affx-1002479533 AX-413837542 14 3384011 TGAAAAGGAAGACATAATTTCTCCCAACCACTGAT[C/G]TATAGGAATGTAAACAAGCTGCCCAGGAACAGCGA S 4 1 2 1 101000 f 74 goat 14_3384011_RH-map 14 3384011 G C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38431018 Affx-122936669 AX-123301359 14 3393668 AGAAGTGAACTCAGTATGCTGCCTGAGACAGACCT[A/G]TAGGTTCCTGTATGATTGTCCTGTTCTATAGGCTA R 2 1 2 1 101000 r 74 goat snp19632-scaffold1983-427923 14 91262015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603369 Affx-1002479534 AX-413837544 14 3432518 GCACTTCTACATACTAGCAGCAATTGAGGAGAAAT[C/T]GAAATAAAGAAAATAATGTCATTTAAATGACAATG Y 2 1 2 1 101000 f 74 goat 14_3432518_RH-map 14 3432518 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320776020 Affx-122923485 AX-385263150 14 3443192 CAGGAATTAGGGAGAAAAGCCAAAAGAAAGAATTT[A/G]CCAAAGAATTTGGTAACTTCTTTATTCCCAGGGCT R 2 1 2 1 101000 f 74 goat snp19631-scaffold1983-378399 14 91211538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603445 Affx-1002479535 AX-413837617 14 3451431 TGTGAAGTCGACATTCTTTCTGGGAAGCATAGCTA[A/G]TGTTAGATTATACAACAAATAACTGCACAGACAAG R 2 1 2 1 101000 r 74 goat 14_3451431_RH-map 14 3451431 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603447 Affx-1002479536 AX-413837619 14 3467362 AGTAAATGGCCCTCTTACTGAATAGTGAAAGTTGT[A/G]CTGTACTTTCTGGGTGAAGAAATTGAGACAAAGAG R 2 1 2 1 101000 r 74 goat 14_3467362_RH-map 14 3467362 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603375 Affx-1002479537 AX-413837550 14 3492747 ATGTGAAGAGTCCTCGAAAAGAGTCAAGTGACAGC[C/T]GACAACTTCCTGATAAAGGAAGAGGCGTCTGGCAT Y 2 1 2 1 101000 f 74 goat 14_3492747_RH-map 14 3492747 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320777069 Affx-122958408 AX-385264192 14 3493187 AATATGGTCTAAGTGAATTGCTCTTCCATCTTACT[A/G]TCAGCCATCATAAGCATAGCATGTATGATTGCTGC R 2 1 2 1 101000 f 74 goat snp19630-scaffold1983-328404 14 91161329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603451 Affx-1002479538 AX-413837623 14 3510892 TTAATTCATAGGTTCTTAATTTTATTTTTAAGTGC[A/G]TGTTATTCCTAATACCTTTCTCATCTGAAGAAATA R 2 1 2 1 101000 r 74 goat 14_3510892_RH-map 14 3510892 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38379936 Affx-122975654 AX-123250294 14 3532434 GCCAGATTATTCATTTGTTTACAAAAGATTCATTC[A/G]CTGATTTCAAGCAGGACTAGTTTTATTGCCCTGAT R 2 1 2 1 101000 r 74 goat snp19629-scaffold1983-289157 14 91122367 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276773 Affx-1111835581 AX-519550281 14 3539129 AAAAATAAATAAAATTTGGCCCTTCTCCTTAAAGT[A/G]TATTATTTTATATATAGCAACAAGACTTGGGACTC R 2 1 2 1 101000 f 74 goat Random2.2K-1390 14 3539129 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 350603378 Affx-1002479539 AX-413837553 14 3557869 TTCCTGACCCAGGGATCAAACCCACGTCTCTTGCA[C/T]GGGCAGCGGCTTCTTTATCATTGAGCCACTCAGGG Y 2 1 2 1 303000 f 74 goat 14_3557869_RH-map 14 3557869 T C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320770738 Affx-122962610 AX-385257902 14 3560946 TCAGTTTATGAATACCAAACAGTCCCAAGCTGTTT[C/T]GATGACTAATACCTGCATGTATTATTGTCATTCAC Y 2 1 2 1 202000 f 74 goat snp19628-scaffold1983-260645 14 91093900 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403624 Affx-122957545 AX-123273976 14 3593105 TAGTGTGGGGTTATGCTCTGTAGCAGGCAAAATAA[C/T]GGTCCTCCAAAGATTTCCACTGTCAGCTCCCAGAA Y 2 1 2 1 101000 f 74 goat snp19627-scaffold1983-228486 14 91061871 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603455 Affx-1002479540 AX-413837626 14 3607281 TCAGAACACATGCTTTAGTTAAAAATAAAAATGAA[A/T]ATTAGATGAGTTTGACATTCCCAGGCTAGTTGGAA W 4 1 2 1 101000 r 74 goat 14_3607281_RH-map 14 3607281 T A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603456 Affx-1002479541 AX-413837627 14 3637966 TTCTTTGATAAGAATTGGTTAGACTTGGCTGAATA[A/G]GCAAAAACGATCACTTCTGAAGCAAAACAAATATC R 2 1 2 1 101000 r 74 goat 14_3637966_RH-map 14 3637966 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603384 Affx-1002479542 AX-413837558 14 3676801 ATCAGGAGACTCATCAGGGCTTTTTTGTGTACCCA[C/T]TTGACGTCACTTCATCACAGAACTACACTCAATCT Y 2 1 2 1 101000 f 74 goat 14_3676801_RH-map 14 3676801 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38380253 Affx-122975453 AX-123250611 14 3686372 CCTGAATGTTACCATTCTAGGCTTCTGGCCCCACA[A/G]CTGTAGGGATCCAGAAACAGATGCTGTAGACATGC R 2 1 2 1 201000 r 74 goat snp19625-scaffold1983-135219 14 90967963 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603387 Affx-1002479543 AX-413837561 14 3691818 ATTCGGGGGTGGAAATAATTTTCAGGGGCGAATTT[C/T]GAGATGTTCTAAGAAGGTTGGTTTGATCAGTGGTA Y 2 1 2 1 101000 f 74 goat 14_3691818_RH-map 14 3691818 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38413256 Affx-122950228 AX-123283605 14 3730384 TTAGCCAGTCTGGTAAATCCCTGCAGAGCTGGAAC[A/G]AGCGTCTCAGGACACATGCTCACTACAACATGGAA R 2 1 2 1 101000 r 74 goat snp19624-scaffold1983-91207 14 90926160 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603462 Affx-1002479544 AX-413837632 14 3745601 GCCTCCTTCCCCTCCCTCCATCCCAGCCCTCCAGG[C/T]CATCACGGGACACTGGGCTGGGCTTCCTGTGTGAC Y 2 1 2 1 400000 r 74 goat 14_3745601_RH-map 14 3745601 C T Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38376519 Affx-122978010 AX-123246878 14 3764088 TAAAATCTAATCCACATTTCTTTATTTACAAGGAT[A/G]TTACATAATTTTGTCAAATGATTTGCAAAAGTCAG R 2 1 2 1 101000 r 74 goat snp19623-scaffold1983-57503 14 90893108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376522 Affx-122978007 AX-123246881 14 3798177 TGCCATAATTATCTGAATGACTCTGCCGGCAGCTC[A/G]CAGGACCTGATTTGTCTTAGAGAGAAACGCACAGT R 2 1 2 1 101000 r 74 goat snp19622-scaffold1983-23414 14 90858828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603463 Affx-1002479545 AX-413837633 14 3808143 AAGTTTTCAGAATAAATCTTAGATGTCTATGACTA[C/T]GCCCAAAGAGGATTTCTTAAGCAAATATTTTGGCT Y 2 1 2 1 101000 r 74 goat 14_3808143_RH-map 14 3808143 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320780820 Affx-122966432 AX-385267909 14 3822949 GAGGTTCAGAAAGGTTCTGAGTAAACCTAAGTTAT[C/T]AATGTTTCTCCTAAAGCAGCATTCACCCACTGTAT Y 2 1 2 1 101000 r 74 goat snp44805-scaffold61-1259 14 90834229 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603465 Affx-1002479546 AX-413837635 14 3861647 TGGGCCACTAGGGATATCCCAGGATTGAAATTAAT[G/T]CTTTAAATTTTTAGGAGAACTCATCATGAAGTCAT K 2 1 2 1 101000 r 74 goat 14_3861647_RH-map 14 3861647 G T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38452629 Affx-122920356 AX-123322962 14 3861764 CACTGAGAGAAAAATCGATAATACTCTTTAGAGAA[G/T]CTTTGGGAAATCAATTTCTTTTTCTTTTAAACACA K 2 1 2 1 101000 f 74 goat snp44806-scaffold61-40074 14 90795049 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388387 Affx-122969305 AX-123258745 14 3959543 AGTACACTACTTGGATCTGCAAATACTAATATTCA[C/T]GCAGTCATAAAAATGTGAATATTTTATATTTTTAC Y 2 1 2 1 101000 f 74 goat snp44808-scaffold61-137853 14 90696994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603397 Affx-1002479547 AX-413837570 14 3984938 AATGAGAGAGAAAGATAGAGAGAGAATACTGGGAA[A/C]TATTTTTGTTTCCAAAGGAACTGATATCAATTAAT M 2 1 2 1 101000 f 74 goat 14_3984938_RH-map 14 3984938 A C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38387024 Affx-122969927 AX-123257382 14 4009540 CAGCCAGCTGCCCTGGGACCTGACACCACTCATCA[C/T]GAGGCTGAAACAAGCTTCAGAACACCACAGACTTT Y 2 1 2 1 101000 r 74 goat snp44809-scaffold61-187850 14 90646833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421423 Affx-122943962 AX-123291770 14 4091377 GAGAGCAGCTGGAAGGCAGTCTTGACGTGATCTTG[A/C]AGCATCACAAAAGTACCAGGGAAACAGAAGACAAC M 2 1 2 1 101000 r 74 goat snp44811-scaffold61-269687 14 90564375 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796050 Affx-122943794 AX-385283002 14 4121438 TTATTTTACTTAACTGAAGATAGATGACCAATTTT[C/T]CATGGATTAGAACCTAATAAAGTACCTATGACACT Y 2 1 2 1 101000 r 74 goat snp44812-scaffold61-299748 14 90534333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400595 Affx-122960396 AX-123270950 14 4156269 AGTTCCCATCTAATTTCCCTTCATTCAGTCTGAAG[C/T]AATTCCTTTAATATTTCTTGTATGGCAGATTTTCA Y 2 1 2 1 103000 f 74 goat snp44813-scaffold61-334579 14 90498248 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793987 Affx-122954425 AX-385280956 14 4187350 CACCTGCTGACTTGGCCTCCTATGCAACTGGTAAG[C/T]GTTCTAGTCCAGAAACTAGATCACATGCCTTTCAA Y 2 1 2 1 101000 f 74 goat snp44814-scaffold61-365660 14 90467383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430408 Affx-122937756 AX-123300749 14 4240830 CCTGGTTGTATTACGGAAATAGAACAAACAAACAG[A/C]AGAAACAGGAAAGAATTCATCCTAGTGAAAATAGG M 2 1 2 1 101000 f 74 goat snp44815-scaffold61-419140 14 90412513 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775486 Affx-122960623 AX-385262617 14 4271696 CCCTGCAGTACTTGTGCCTAACCAAATCTCTGGAT[A/G]TCTTGTCAAAATTTGTATTTCTGAGGCCCAGTCTA R 2 1 2 1 201000 r 74 goat snp44816-scaffold61-450006 14 90383600 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395637 Affx-122963791 AX-123265992 14 4331749 CAAGGCCCACATCCTTACTATTGATCCTAGAAACA[C/T]GTTAAAGTCTGAGTCACTTCCAAGGAAACCACCTT Y 2 1 2 1 101000 f 74 goat snp44817-scaffold61-510059 14 90322227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770003 Affx-122924246 AX-385257170 14 4366239 TGATGCATTTGGTCATTTAGGAAATAACTGGTTCA[A/G]TGAGCTAAGCAGATCTTCGAAATAACGGATATATT R 2 1 2 1 101000 f 74 goat snp44818-scaffold61-544549 14 90287377 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276775 Affx-1111835582 AX-519550284 14 4373865 AGTATTAGTGGTAATATGGAAACAGTGGTAGTTGT[A/G]TTAGTTAACAAACCTGTCAAAGCCTTAATTGTTTT R 2 1 2 1 101000 f 74 goat Random2.2K-1391 14 4373865 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391058 Affx-122966852 AX-123261415 14 4442611 AAAATACTGGTTATAAAGAAAACATTTTGAGGATT[G/T]TTCCAATGTCTTCCTTGAAACATAAATGGGCTATT K 2 1 2 1 101000 r 74 goat snp44819-scaffold61-620921 14 90209603 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427098 Affx-122939783 AX-123297441 14 4534273 TTTACCGTGCGCACTCTGCCCTGACCGATGCTTTC[A/G]CTATCTAGGTGCTGGGCCCCATGTGAGGTTATTTT R 2 1 2 1 201000 f 74 goat snp44821-scaffold61-712583 14 90115610 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786419 Affx-122936444 AX-385273453 14 4573725 TATGGAATAGCCACTCTATTACTTGAAATAGGCTG[A/G]CCAGGACCACTGAAGGGTTAACTACAGATTATAAA R 2 1 2 1 201000 r 74 goat snp44822-scaffold61-752035 14 90074414 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427121 Affx-122939660 AX-123297464 14 4605082 GAAGCAGGACATTTTCTTACACAGTCATAACACAA[C/T]GATAACATTCAGGAAGTTTGGCACTGTTGCAACAC Y 2 1 2 1 101000 r 74 goat snp44823-scaffold61-783392 14 90042889 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773867 Affx-122929912 AX-385261006 14 4640893 ACTTTCTGATGCATCATTTTAAAGTTATCTGATTT[A/C]ACAGTGATTCACAGTATGAGAAATACCTGTAACAC M 2 1 2 1 101000 r 74 goat snp44824-scaffold61-819203 14 90006621 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792853 Affx-122949503 AX-385279830 14 4673421 TTTTGGAAAGTGGTACAGGTATGTTAGAAATTTAG[A/C]TTTGCTGATACTTGATTGCGTTGCGGACTCCTCTC M 2 1 2 1 201000 f 74 goat snp44825-scaffold61-851731 14 89973055 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388273 Affx-122969766 AX-123258631 14 4730465 CTGACAAAAGATTAGTTTCCCAAATGTGTAAGGAG[C/T]ATCTACCTTCCGTTAAGAATAGGAACACATATATC Y 2 1 2 1 101000 f 74 goat snp44826-scaffold61-908775 14 89915754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782938 Affx-122948620 AX-385270008 14 4768426 TAATATAATTGGTCTATTTAATCTGAGTTATCAAA[C/T]TCAGGGGCATGATGCTGTTTATAATATTTTACTTC Y 2 1 2 1 102000 r 74 goat snp44827-scaffold61-946736 14 89876975 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382013 Affx-122974065 AX-123252371 14 4835633 GATGCCTTATGCTAGAGACATGCTTTCAGCTGTTG[C/T]TCACTCCTGGGTTTGCTTTCCCGCATGCCTGGTCT Y 2 1 2 1 101000 f 74 goat snp44828-scaffold61-1013943 14 89809640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444927 Affx-122926236 AX-123315264 14 4877009 TTCCCCCAAATCTTCCAATAAAATCAAGTGCCCAC[C/T]GAGACAGGTCACAATCACCCAGGGTCTGTGCTGTT Y 2 1 2 1 101000 f 74 goat snp44829-scaffold61-1055319 14 89768601 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409272 Affx-122953121 AX-123279623 14 4909883 GATATTCTAGGCAGTAATTTGTGATGTCCTGGCAA[C/T]GGTGAGCTAGATCAGATCTTTTAAATGATGAAATT Y 2 1 2 1 101000 r 74 goat snp44830-scaffold61-1088193 14 89735816 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799361 Affx-122947609 AX-385286291 14 4945558 GGAAATCATTCATCAGTGAGTTTGCATCCTCTGGT[A/G]TAAGCAAGCACCATATACAGTTGCTCAAAAAGGGG R 2 1 2 1 101000 f 74 goat snp44831-scaffold61-1123868 14 89699725 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787728 Affx-122976383 AX-385274751 14 4992576 AGTTTTTTCCAAAAGAATAGCAGTTGAAGTAAAGA[C/T]GGATGAGAAAGCTATAAAGTAGTGACAACTCAAGA Y 2 1 2 1 101000 r 74 goat snp44832-scaffold61-1170886 14 89652716 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377203 Affx-122978183 AX-123247562 14 5035218 AACACTGCCTCATTTTCTTAGAAGAACATTTTAGG[C/T]AACTGTGGAAGAAAAAGGCTTCTTTCCAGTCTTTG Y 2 1 2 1 201000 f 74 goat snp44833-scaffold61-1213528 14 89610108 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788476 Affx-122933029 AX-385275493 14 5070187 TGCTTGGGATCAATATGTTACATTACATGATTACT[A/G]TCTGTCATGGTGTTAGTTTTCACATACTATTGGCT R 2 1 2 1 101000 f 74 goat snp44834-scaffold61-1248497 14 89574803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379363 Affx-122976154 AX-123249722 14 5120459 CAAACTCGCTCAGGGAGTATACAAGCTCCCACACA[C/T]ACACGCACCCCAGGGCCTTGGTGCCTGGTGCTTGC Y 2 1 2 1 101000 f 74 goat snp44835-scaffold61-1298769 14 89524454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784949 Affx-122932850 AX-385271996 14 5159227 TCCCATGTAAAATAAGTATATGCATATATTCAGGC[A/G]TATTTTTTGATAAAACAGTGCTCTATGGGTTTCGG R 2 1 2 1 201000 f 74 goat snp44836-scaffold61-1337537 14 89485500 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397492 Affx-122962072 AX-123267847 14 5230401 AAAACACAAGAGCCATGTCTCTTCATTATTAACTA[C/T]GCTTGGTGTCTTATACTCAAAATTAACATCACTGC Y 2 1 2 1 101000 r 74 goat snp44837-scaffold61-1408711 14 89412884 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423713 Affx-122942881 AX-123294059 14 5276247 GCCCTCATGTGACCAGCATCATATCAGAGGAGAGA[C/T]GGACAGGGAACAGACAAGCAAAACCAGACCAAATG Y 2 1 2 1 201000 f 74 goat snp44838-scaffold61-1454557 14 89366338 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387384 Affx-122970427 AX-123257742 14 5355517 GCTTTATTAACTGCTTATTAGACAGACTTAGTTTT[A/G]GATATAGGACAAAACACGACAGAAGAACACAGCAG R 2 1 2 1 101000 r 74 goat snp44839-scaffold61-1533827 14 89286371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416097 Affx-122948318 AX-123286446 14 5384676 TGGTGACTATGATACATTTTAATGAAAATACTATG[C/T]TTCAGTCTATTTTCTTATCTTGAGAATAACTAGTG Y 2 1 2 1 101000 r 74 goat snp44840-scaffold61-1562986 14 89257034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382945 Affx-122973376 AX-123253303 14 5428813 CGTGCAGCAAATAAAGCCACTTTCCAAAAAGCCAA[C/T]GCTCAAACATTCCCAGAAACACATTTGCAAATGAA Y 2 1 2 1 201000 f 74 goat snp44841-scaffold61-1607123 14 89212844 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392236 Affx-122967575 AX-123262593 14 5463802 GACTTAGATGAACTTTGGAGATCATGAAAACCACA[A/C]TGAGTAAGAGATTCAAATGCAGCACTTGAGTTCCA M 2 1 2 1 101000 r 74 goat snp44842-scaffold61-1642112 14 89179173 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454144 Affx-122919332 AX-123324477 14 5525174 ATCACCGCAGCTTGGGCAGAGGGTCAGGTAGAGGA[C/T]AGAGGAGGGAGAAACACTGGAGTGCCTGCCCTGTG Y 2 1 2 1 101000 f 74 goat snp44843-scaffold61-1703484 14 89118055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782105 Affx-122940802 AX-385269183 14 5566437 CTTCTTCTGTTCCTTTTTTACGACCTATGACTTAG[C/T]AGATGACAATACAAGGTATCACAGGGACACCTCAC Y 2 1 2 1 101000 f 74 goat snp44844-scaffold61-1744747 14 89076867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271787 Affx-1111833015 AX-519545578 14 5571972 GTGCATCATTTCTCTTCCAAGAGTTGGCCATGTCC[A/G]CTTTTGGGCCTGAAAATTCCCATTTGGCGTTTCTC R 2 1 2 1 102000 r 74 goat 14_5571972_AF-PAKI 14 5571972 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38376288 Affx-122978379 AX-123246647 14 5614517 CTGCAAGCTCCTAACTGAAGAAGGGCTCCCCAGTT[G/T]TACACCAGGATCCATTCTCTTCTCATCTATTTAAA K 2 1 2 1 101000 r 74 goat 14_89028417_RH-map 14 89028417 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38433088 Affx-122935726 AX-123303429 14 5646866 TTCATGGGGAGAACTTGAAAACTGCTGAATAGCCC[A/G]CATAGAGAGATAAGCACCTAAGTGAGAAGTGAATA R 2 1 2 1 201000 r 74 goat snp40-scaffold10-64257 14 88996228 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437676 Affx-122931775 AX-123308014 14 5678192 AAAGCATACCAGTGGGCAGAAACATTCATTCTGAT[A/G]GCAGCAAACCTATTATTATGTCACCCAAAAAGGAG R 2 1 2 1 201000 r 74 goat snp41-scaffold10-95583 14 88965126 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448759 Affx-122949227 AX-123319095 14 5725828 TCTACTAAATACAAAGGATTCTAGAGAGTTAAAAA[C/T]ATTAGTATCTAATGCCACATTGCTAATTCCTCTTG Y 2 1 2 1 101000 f 74 goat snp42-scaffold10-143219 14 88917212 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417593 Affx-122946886 AX-123287941 14 5760110 TTGCAGGCAGGGCACCCAGGTGACATGTTAATCCT[C/T]AGAACACTAACTGTAAAGGAATTATTCAGCAACTT Y 2 1 2 1 201000 r 74 goat snp43-scaffold10-177501 14 88882997 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434738 Affx-122933917 AX-123305079 14 5884085 CCAGTTCTGCAGACTTTTCATGTGATGGCTGGAGT[A/C]TCAGTAACCATCTTGGGTTATTTGGAGCTTTAGAG M 2 1 2 1 201000 r 74 goat snp45-scaffold10-301476 14 88748520 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378686 Affx-122977071 AX-123249045 14 5913011 GCTTTTGATCTGTGGCTGGTTTTTCCTGCCTTTGA[A/G]CTCAAGCATTGGGTCTTCCTGGGTCTTCAGCCTGA R 2 1 2 1 201000 r 74 goat snp46-scaffold10-330402 14 88719524 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381318 Affx-122974438 AX-123251676 14 5944065 TGATTCACTGGCTTTATTTCTGTTATTTCTGAAGA[C/T]TTGACACAACTGAAAATCTGACATAAAAAAAAAAA Y 2 1 2 1 201000 r 74 goat snp47-scaffold10-361456 14 88688061 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383054 Affx-122973287 AX-123253412 14 6080611 TGTGTCATGAGGTACTCACTTCATCGTGGGTTGCT[A/G]TCGGCTATATGAACTTCACCTAAAAAAACGGCAGC R 2 1 2 1 101000 r 74 goat snp49-scaffold10-498002 14 88543786 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448763 Affx-122937081 AX-123319099 14 6130506 GGATTGTAAAGTGGATGGCCAAGTTGTAGTGCATA[C/T]GAATATTATGCTTAGGAATATACTCTGTGCTGCAG Y 2 1 2 1 101000 f 74 goat snp50-scaffold10-547897 14 88493824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777368 Affx-122950757 AX-385264490 14 6166387 GCCCAAACTCCTTTCAATTTGAAGCCTCATAGCTT[A/G]CTATTCCCTGTCTCAGACTCTTAACTCTTTGACAC R 2 1 2 1 101000 f 74 goat snp51-scaffold10-583778 14 88455767 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448765 Affx-122935049 AX-123319101 14 6215979 ATTCTGCTTCTAAATGGAGGACAGGCTATCCATAG[C/T]CTCCTGTTAGTCTCAGTGACCCTCCATCCAGCCGA Y 2 1 2 1 101000 f 74 goat snp52-scaffold10-633370 14 88404062 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392869 Affx-122965749 AX-123263226 14 6248796 CAGGAACCCAGCTGGATGACTTACCAAGCTCCTCT[A/G]CCACAAATAGAAAATAAACAAGAAATTGTGATGTC R 2 1 2 1 201000 f 74 goat snp53-scaffold10-666187 14 88371198 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774942 Affx-122950713 AX-385262075 14 6296182 TCCCAGAAAGTTACACCATCAAGTGAAAAGGAGAA[G/T]ATGTTTAGGTGACCATAAACTTGTCTGGTAACTTA K 2 1 2 1 101000 f 74 goat snp54-scaffold10-713573 14 88323336 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440518 Affx-122929346 AX-123310855 14 6332995 CTGTAGATACTGGAAAATATACAAATGATTTTATT[A/C]TTTTTAATTTAAAAGACTATCATCTTCCAAGGTCT M 2 1 2 1 303000 r 74 goat snp55-scaffold10-750386 14 88285999 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801071 Affx-122958143 AX-385287985 14 6380952 ATATGGGAAATCCTTTTATATTCCTTTGGATATTG[C/T]AGTCTCAATATGCTTATCTTAGGAGAGGAAAATGA Y 2 1 2 1 101000 f 74 goat snp56-scaffold10-798343 14 88237705 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442960 Affx-122928214 AX-123313297 14 6410048 GCATATACCAGAATCACAGGGAAGAGTAGTTGAAA[C/T]GCAGACTGTTGGGCCTAATGCCCAAGGTTTCTGCT Y 2 1 2 1 101000 f 74 goat snp57-scaffold10-827439 14 88207805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788311 Affx-122942232 AX-385275329 14 6440605 ACATGTAATACTGTATGTGTAATCACTGCTGTGAT[A/G]TCAAATGGTAGTCTTCATATTTCAAAATGTCTGGG R 2 1 2 1 101000 f 74 goat snp58-scaffold10-857996 14 88176534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405431 Affx-122956060 AX-123275783 14 6519988 AATTATATTGAACATATATTGAGTTATAGCAAGAG[C/T]AACAATTATATTTTAATAAATAAATACTGAATATA Y 2 1 2 1 101000 f 74 goat snp59-scaffold10-937379 14 88095369 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772493 Affx-122935976 AX-385259644 14 6576861 ATTCTCAGCTGTCTGAAGAAACAAGCTTATTGATA[C/T]AATTGAAAACAATTTCAAAAACTACTTGAGGTAAA Y 2 1 2 1 303000 r 74 goat snp60-scaffold10-994252 14 88039405 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791721 Affx-122947306 AX-385278712 14 6616319 TGTTCATATACTGATTTTTCACCTGCTGGATTTAA[A/G]TTTCCAAACTGTTTTTTGGAATATGTTTAAACTAA R 2 1 2 1 201000 r 74 goat snp61-scaffold10-1033710 14 87999779 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417245 Affx-122947276 AX-123287593 14 6668932 AAGTAACGATTTCACAGGTACCAAAGATTAGGATA[A/C]GAAATGGGAGACCATTGTTCAGTCTACCATATTTC M 2 1 2 1 101000 f 74 goat snp62-scaffold10-1086323 14 87946978 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387216 Affx-122970590 AX-123257574 14 6697678 ATGACTCTTTACTTCAGGCTAGAAGATTCTCTTCC[C/T]ACATGCTCTAAATTGCTGGATGACTCCTGGCCTGA Y 2 1 2 1 101000 f 74 goat snp63-scaffold10-1115069 14 87913271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444475 Affx-122926533 AX-123314812 14 6737457 AGGAATCCTGACCTCAAAAGTACTGAATGTGATTA[G/T]CCTGCATGTGCATTGGGCCCATGGATTATGAATTC K 2 1 2 1 201000 f 74 goat snp64-scaffold10-1154848 14 87873144 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421175 Affx-122944166 AX-123291522 14 6771913 AAAATAAAAATAATAAAACAAAACCTAACCCCCAA[C/T]GCGCTTAGATTCTAAACAACATGACTAGATGTCAA Y 2 1 2 1 101000 r 74 goat snp65-scaffold10-1189304 14 87838354 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400121 Affx-122960720 AX-123270476 14 6810245 CGAGTCACAGTGTGAGAAGTGCCTGGCTAACATGG[C/T]GGCTGTTACAGCTTTGATTGAGATTTCCCCTGACA Y 2 1 2 1 201000 r 74 goat snp66-scaffold10-1227636 14 87799781 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454007 Affx-122919432 AX-123324340 14 6842032 TCTGGTGAATCATGCATCATTGGATTTTATTCTTG[A/G]ACTGGACTTACGGAGAACAAAAAAGCACAAGAAAT R 2 1 2 1 101000 r 74 goat snp67-scaffold10-1259423 14 87760225 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404401 Affx-122956785 AX-123274753 14 6874258 AGGTACTTAACAAAGTGATTCCCAAACAGTTTAGC[A/G]TTTCATTCTTAAAATAACCGTGGTGGGGGTGGGTA R 2 1 2 1 101000 f 74 goat snp68-scaffold10-1291649 14 87726722 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769382 Affx-122943290 AX-385256553 14 6904659 GTGTTACAGGTCTTGGCTTCTAGAACTGAAACCAG[C/T]ATAAATCCTGTGTGATTCTGAGCTGAAGGGAATTT Y 2 1 2 1 101000 f 74 goat snp69-scaffold10-1322050 14 87696355 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436547 Affx-122932921 AX-123306885 14 6970063 CTAAATTTTTCTTAAAAGTTTTCAATATTTAGAGG[A/C]TTCACATTTCATCAGTTTTTCAAATTGTTTCAAAT M 2 1 2 1 303000 r 74 goat snp70-scaffold10-1387454 14 87630477 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415194 Affx-122948992 AX-123285543 14 7061557 ATAACTGTAACACATCTATTAAAAAGAAAACAGCA[C/T]GATTCAATGAATTATCCCATCTTACTCACTATTGC Y 2 1 2 1 101000 r 74 goat snp72-scaffold10-1478948 14 87538871 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801246 Affx-122938024 AX-385288159 14 7097603 AATTATAAACTTTAGTGGCAATGTTGAAAACCATT[C/T]CTGATCTTACATGGAAGTCGAAAGTCGTTGAGCCC Y 2 1 2 1 101000 r 74 goat snp73-scaffold10-1514994 14 87502531 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445659 Affx-122926148 AX-123315996 14 7126106 TACCTAGTAGTAATAACCTTAGACACGCAGATGGC[A/G]CCACCCTTATGACAGAAAGTGAAGAGGAACTAAAA R 2 1 2 1 103000 f 74 goat snp74-scaffold10-1543497 14 87472619 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421381 Affx-122944037 AX-123291728 14 7161050 ATTTCACTAAAAAATGTTTCTTTTTACCAACTTAG[C/T]AACACACATGATTGCCATTCTTCCTCCTTTCAAAT Y 2 1 2 1 101000 r 74 goat snp75-scaffold10-1578441 14 87437509 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447016 Affx-122924547 AX-123317352 14 7215669 AATAATAAATCTCTAGTCAATCCTAAAAATAATAA[A/C]TAATAATCACTCTCTACCTCTTCTTCTTCAGTCTT M 2 1 2 1 201000 f 74 goat snp76-scaffold10-1633060 14 87382389 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394570 Affx-122964448 AX-123264925 14 7275595 TTCATTATTCAATCCTTCTTATCTTGTAATGCACA[G/T]CCCTGGAAGTTTGATACTGAAAGACTGATATACAA K 2 1 2 1 101000 f 74 goat snp77-scaffold10-1692986 14 87316417 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376227 Affx-122978793 AX-123246586 14 7315043 GACAATTTCACCTCTTTTTTTCCGATTTGGATTCC[A/G]TTTATTTCTTTTTATTCACCACTTGCTGTGGCTAG R 2 1 2 1 103000 f 74 goat snp78-scaffold10-1732434 14 87276520 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438169 Affx-122931840 AX-123308507 14 7354516 TTTTAAGGTCTCTGCTTGTCATCTTCTGTTGTCTA[C/T]AGCAGCTTGCTTTCCCTTACACACATCTTTGGGCC Y 2 1 2 1 101000 r 74 goat snp79-scaffold10-1771907 14 87236577 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432003 Affx-122935930 AX-123302344 14 7433531 CTGGCAGAATCCCCAAGGATTTGCAGGATGCAAGT[G/T]GAGAGCTACTGCTGTGTACTAACTCCCTGCCACCT K 2 1 2 1 201000 r 74 goat snp56044-scaffold874-51354 14 86306538 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789093 Affx-122976673 AX-385276106 14 7464687 CCTGAGAACAATAAGTAGTAAAGGTGAATATCTTT[A/G]CTTTGAAGATATATTTTTTAGTGATCTGTATGTTT R 2 1 2 1 201000 r 74 goat snp56045-scaffold874-82510 14 86337426 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778880 Affx-122958801 AX-385265988 14 7499289 TATACCTGTGAGTCTGCTTATGATGGTGCAATCTA[C/T]GCACTTTGGAAAGGTACCCCGTTGAAGGTATGGTG Y 2 1 2 1 101000 f 74 goat snp56046-scaffold874-117112 14 86372350 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793914 Affx-122975704 AX-385280883 14 7600068 CTAAAAAATAGTTTCCTGGTGCCTGCCAGGCAGGA[G/T]AATCTGTAGATATCTTAAGACTTAGCAGTTGCCAA K 2 1 2 1 102000 f 74 goat snp56048-scaffold874-217891 14 86469135 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410927 Affx-122952052 AX-123281277 14 7663844 CATAGTTGTATTATTTACTATACACTTGTGCTAAA[C/T]GAGCCAGATATGTGACCTAGAGTCTTGTCTATTCA Y 2 1 2 1 201000 f 74 goat snp56049-scaffold874-281667 14 86532795 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423129 Affx-122942902 AX-123293475 14 7715611 TTCAATGAGCTTTCTTTTGACACCTCAAGGAATAA[C/T]GAATAATGCTAGCTTCTAGATCCTGCTGTCTCGTA Y 2 1 2 1 201000 r 74 goat snp56050-scaffold874-333434 14 86584682 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772303 Affx-122953510 AX-385259458 14 7794085 GTCCTCCCGTTCCTGTTTCCACACATCTCTCTACA[C/T]AAGCTCATCGTTCCTGATGATTTGGTAGGCTCTTC Y 2 1 2 1 102000 f 74 goat snp56051-scaffold874-411908 14 86666267 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788333 Affx-122925397 AX-385275351 14 7850462 AGATGACTTTTCTGATAAAGATTTCAAAGCACTAG[C/T]AATAAAAATGATTATTGAACATGGAGAAAAATAGA Y 2 1 2 1 201000 r 74 goat snp56052-scaffold874-468285 14 86723270 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388218 Affx-122969408 AX-123258576 14 7890139 ATGTCCCCAGAACAAAGTCCATCAGGCATTAGCTC[A/G]TTAAATAGCAAGGCCTCTGAGTTGCTGGTTCTGGG R 2 1 2 1 201000 r 74 goat snp46736-scaffold650-416026 14 86770392 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396602 Affx-122962897 AX-123266957 14 7933978 AAGATAGCATATTAATAAGATTAAAATTATTTAAA[C/T]ATATGCAAAATAAAACAACTAGGAAGAGGTATCAA Y 2 1 2 1 103000 r 74 goat snp46735-scaffold650-372187 14 86810838 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410127 Affx-122952814 AX-123280477 14 7981727 CTCACATATGGGTCACCATAGAGAATATATCTCAG[A/G]TCACAAAAAGGGAGTGTGCTCTTGAGATGGATAGG R 2 1 2 1 101000 f 74 goat snp46734-scaffold650-324438 14 86861690 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse619 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38448863 Affx-122923279 AX-123319198 14 8019030 CCAAACCTAGCTCTTTTACCACAACACAATGCTGC[C/T]TCTGAAATCATTAACATAAATGAAAATGCTTATTT Y 2 1 2 1 101000 f 74 goat snp46733-scaffold650-287135 14 86898949 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse620 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38454281 Affx-122919275 AX-123324614 14 8056237 AAATTTTTGTGGTATTATACAGATGAAGACTGTAA[C/T]GACATAAAACATACTCTGAAAGTTAGAGAAATGAT Y 2 1 2 1 101000 r 74 goat snp46732-scaffold650-249928 14 86934545 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401049 Affx-122959655 AX-123271402 14 8136625 ACAGTGAAGGAAAGGTTACTGATGCAAAGAAGGCC[A/G]TGAAATAATGAAATTTATTTGCAAGGATGGACAGC R 2 1 2 1 101000 f 74 goat snp46731-scaffold650-169540 14 87017141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272811 Affx-1111833025 AX-519546505 14 8137221 CCTCAGATATAGCAGTTTATTTAAGATAAGAAACT[A/G]CTGTCTTAATAATTAGTAAAATGCAATAATCATCC R 2 1 2 1 101000 r 74 goat 14_8137221_AF-PAKI 14 8137221 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398301 Affx-122962151 AX-123268656 14 8167089 CAACTTGAGATTATTCAGCATTAGTGGTTTAAACA[C/T]GTACTTGGATTGTGTGATGTTACCCCACATGCCAG Y 2 1 2 1 101000 r 74 goat snp46730-scaffold650-139076 14 87047768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse621 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320792965 Affx-122934559 AX-385279943 14 8204967 TTGAGCTCAAGGTATACGCTTACTAATATTTTCTC[C/T]TCTCATCAGCATAAAGTTAACAATTGTATTGCTAA Y 2 1 2 1 101000 f 74 goat snp46729-scaffold650-101198 14 87082698 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409433 Affx-122954099 AX-123279784 14 8235839 CTCTTTCAATGGTTGATTCTATATTCATCTGTGTA[C/T]AGTTCTTCATTAGTTAGTGATTTCCATATAGTAGA Y 2 1 2 1 101000 r 74 goat snp46728-scaffold650-70326 14 87114848 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429582 Affx-122937726 AX-123299923 14 8277129 AGGACAGAGGAGACTCCAGCTGACTCTTGAGTTCT[A/C]GTTCTCTTTTTGGCACATATTATGGTGAAAGAATG M 2 1 2 1 201000 r 74 goat snp46727-scaffold650-29036 14 87157966 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397735 Affx-122962541 AX-123268090 14 8322033 TGCACTCCAACATTTTGCATTCATTTTTTGAAAAT[A/G]TTTTGCACTGCTATCACTAGCTGGAATATTCTTTC R 2 1 2 1 101000 r 74 goat snp34542-scaffold406-499340 14 85071363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377681 Affx-122977425 AX-123248040 14 8365733 TATTAATTATAGTTGATACATATAATAAAATATTT[A/G]CCAACATCCTTTGCCAAATAATCAAATACTAGTCA R 2 1 2 1 103000 r 74 goat snp34541-scaffold406-455640 14 85115932 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405303 Affx-122956842 AX-123275655 14 8407675 AGCTGTAAATGTCATAATAAACATTTACAATCATA[C/T]GTATCAATAATGGAAGAGTTATGCTGTAATTTAGC Y 2 1 2 1 101000 r 74 goat snp34540-scaffold406-413698 14 85158258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791755 Affx-122965933 AX-385278746 14 8447871 TTTAATGAACACAGCACAAATAATTTTATATGTAT[A/G]TGAAAAATGAGCTATATATGCTCCTTGGTTTTGTA R 2 1 2 1 303000 f 74 goat snp34539-scaffold406-373502 14 85198058 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764717 Affx-122941839 AX-385252336 14 8500743 GGACACATTTTGAACCTTGTCTTCTGTTTCTCATA[C/T]GTTTTGGAAACCAAGCCCAAATCATCAGGAGTAGA Y 2 1 2 1 201000 f 74 goat snp34538-scaffold406-320630 14 85253777 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434104 Affx-122934940 AX-123304445 14 8538116 GAGCACCAGCACTGGTATGTACATATAGTGTCATG[C/T]ATGTGCTGTTGATGTAAGACAAAGAGACAACCAGA Y 2 1 2 1 101000 r 74 goat snp34537-scaffold406-283257 14 85291279 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414326 Affx-122950039 AX-123284675 14 8589988 TTTGAATGGTTGCCTAGTGTCATACAACCAGTGGG[C/T]AGCAAAGGCTGTAGTGGAATGGGTGTCCTTGAATG Y 2 1 2 1 101000 f 74 goat snp34536-scaffold406-231385 14 85343375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792457 Affx-122956413 AX-385279438 14 8631495 ATCAGTCTGAATCCAGTGGTTTCACTGTCTTCAGT[A/G]CACTTGATTATCTCTTACATGTAAAAGTTATTTGA R 2 1 2 1 101000 f 74 goat snp34535-scaffold406-189878 14 85384843 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785421 Affx-122974518 AX-385272466 14 8680762 TAGAATATTTTTAGTGGCTGGATCCACTGGTCCTG[A/C]TGTCTGTCCTAACTTGACATTCACGATTTTATGTA M 2 1 2 1 101000 f 74 goat snp34534-scaffold406-140611 14 85434797 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800469 Affx-122951420 AX-385287389 14 8715981 GACATTTTGGAAGCACTTTTCTGGCCTGTAACACT[A/C]GAATACAGCCCTATAAACCAGTGGGCCTGGATCAG M 2 1 2 1 101000 f 74 goat snp34533-scaffold406-105392 14 85468909 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402523 Affx-122958482 AX-123272876 14 8756138 TTGCCTTTACCCCAGCTTCCTTTGGAGTTCTAAAT[A/G]TTTTCAGCTATACACAAAGAACTCATCACAGATTC R 2 1 2 1 201000 r 74 goat snp34532-scaffold406-65235 14 85507068 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse622 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320794530 Affx-122975536 AX-385281493 14 8817836 GAGAAATTGTCACAGAGAAGAGAAGTCCAGGGAAA[C/T]ATGTTGAATAAATGCAACATGAATAAATACCTCCT Y 2 1 2 1 201000 r 74 goat snp34531-scaffold406-3537 14 85565944 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410260 Affx-122952528 AX-123280610 14 8830339 CAATAACTATCAGAGTGCAATTAAGCAAGAAAGAG[A/G]AGGGAAAATGTAGGAGACTAGCTAGAAGAATGGAA R 2 1 2 1 201000 r 74 goat snp58157-scaffold940-8867 14 85578073 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381430 Affx-122974352 AX-123251788 14 8862635 AATGACCTTCCATATAGTCAATAATATGAGTGTAG[A/C]TTTACAGTTCGCTCTCTGCACCCAGGATTCCTCCA M 2 1 2 1 202000 r 74 goat snp58158-scaffold940-41163 14 85610686 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392841 Affx-122965770 AX-123263198 14 8906259 AATACATATAGTTAAGCTTATATCTACCTAGGTAG[A/C]TATTTCCTTGACATTGAGCAAATGCCACATACCAT M 2 1 2 1 101000 r 74 goat snp58159-scaffold940-84787 14 85655087 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437451 Affx-122932392 AX-123307789 14 8952116 ATTATAGAAAATCTCCCAAGAACATGAAAAAGAAA[C/T]GAAAGCTTCATCAAAGGACTGAACTGAATCAAGCA Y 2 1 2 1 103000 r 74 goat snp58160-scaffold940-130644 14 85704091 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437922 Affx-122931643 AX-123308260 14 9013857 CCTTGTCCTCAGACACTGACTCAATTTCTCCACAT[A/G]CATTTCTCCATATTTAAATAGGGGGGAATAAGAAT R 2 1 2 1 202000 r 74 goat snp13397-scaffold1516-1621666 14 83550667 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse626 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38450134 Affx-122922757 AX-123320469 14 9055181 GGCAGGCTATATTCCATGAGGTCACAAGAGTCAGA[C/T]ACGACTTAGGGACTAAACCATGATTTTTATTGTCT Y 2 1 2 1 303000 r 74 goat snp13396-scaffold1516-1580342 14 83511014 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435312 Affx-122934018 AX-123305652 14 9088383 GTGATTACCAGAGAAGTCTTATGGAGGTGCTTAAA[G/T]ACTTTATTGTGTTTTACTTATGTTTAACCCTTAAT K 2 1 2 1 101000 f 74 goat snp13395-scaffold1516-1547140 14 83477736 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789264 Affx-122968510 AX-385276275 14 9118842 AATAAGTTTGATCTCTCTGCTATACAGAGAAAGCA[C/T]ACTTACTGTCAGTAAAATCAAAGTTCTCTATCTTC Y 2 1 2 1 102000 f 74 goat snp13394-scaffold1516-1516681 14 83446884 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272414 Affx-1111834273 AX-519546141 14 9138562 CAGCCTTGGTAGCAGCCAGCCAAAATCCCTCTGGG[A/G]TTGCAGACCACAGCTGCAGCCAGTCCCACTGTGGG R 2 1 2 1 202000 f 74 goat GoatD01.028458 14 9138562 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320773060 Affx-122934582 AX-385260203 14 9250514 CCAGAAATGTTTAATTCTGGTTGAAGCAGTCATCC[A/G]GAAACTAAACAGAGTATAGAGCTGAATTAAAAAAG R 2 1 2 1 201000 r 74 goat snp13391-scaffold1516-1385009 14 83313046 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428274 Affx-122939400 AX-123298617 14 9295814 TATGGATTGGTTAGAAAGGGAGATGGTACTGCATA[C/T]GGAGGTGTTCTGAAACTGTAAAACTTTTTGTGAGT Y 2 1 2 1 101000 f 74 goat snp13390-scaffold1516-1339709 14 83267879 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396530 Affx-122962951 AX-123266885 14 9351093 GATGAAACAAAAGGAAAAAGTTGAGCCATTTTGTC[A/G]TCTCAGTGGCCCCTGCAAAAATATGGGAAATTATG R 2 1 2 1 101000 f 74 goat snp13389-scaffold1516-1284430 14 83212214 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802860 Affx-122926284 AX-385289758 14 9413260 AAAAATGTCTTACCTGATAAACAATGTATACTTTG[C/T]ATATCATCCACTTTAATAGTGGTGTTAATGCTTTT Y 2 1 2 1 101000 f 74 goat snp13388-scaffold1516-1222263 14 83148403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434746 Affx-122933911 AX-123305087 14 9457792 TGCACATGACCACCTGCATCACCTAGGCCTTGGCC[A/G]CATGATGAAAACACAGGCCCTGCAGGGGGACTGAA R 2 1 2 1 102000 r 74 goat snp13387-scaffold1516-1177731 14 83103207 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421894 Affx-122944260 AX-123292241 14 9508588 AACTCAGTAGAGAGTGTTCTACATTTTGGAACTCT[A/G]TGAAACAGAGATGGGGGGATGAAGTTCCAATTCCC R 2 1 2 1 201000 f 74 goat snp13386-scaffold1516-1126935 14 83053266 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397151 Affx-122962438 AX-123267506 14 9544603 GAGAAGCCCTTTACTATTGGTGAAGAGTTGATCCT[A/G]CCTCCTGCTAAGGACATTTGCCTTGAACTTTTAAG R 2 1 2 1 201000 r 74 goat snp13385-scaffold1516-1090920 14 83016605 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781685 Affx-122969048 AX-385268767 14 9599118 TATTTATGTATCTTCCTTTGGCTGAAAAAAAAATA[C/T]GGATTTTATCATGTGAAGTTTCTATGACAGAACTG Y 2 1 2 1 303000 f 74 goat snp13384-scaffold1516-1036405 14 82959809 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375582 Affx-122978737 AX-123245941 14 9668466 TTTACCATATTTCTTGAGATGGGGATCAATAGGCC[G/T]ACTAAAAATTTGAATAGATGAATGAAATTAGTGCA K 2 1 2 1 101000 f 74 goat snp13383-scaffold1516-967057 14 82889645 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385381 Affx-122971625 AX-123255739 14 9728294 CACACCTAAAGGGTGCACAAAGGTCAAGTGCATAC[A/C]TAGACCCAGCAGTGAAATAAGATATTGGGCCATAA M 2 1 2 1 202000 r 74 goat snp13382-scaffold1516-907229 14 82828695 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381588 Affx-122974801 AX-123251946 14 9862078 ATGCTCGCTGTATCTTTCTTGCTGGTTCAGAGCCT[A/G]TTTGTAAGTCATGTTTCATTAACTAACTCATAAAT R 2 1 2 1 201000 r 74 goat snp13380-scaffold1516-773445 14 82695256 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771972 Affx-122926302 AX-385259128 14 9951457 TTATTTAGTATTTGTGTGCTTAACCTCCTCTTCTG[C/T]ACAATGAGAATGACAGTAGCGTTTTTTTCTCATGG Y 2 1 2 1 101000 f 74 goat snp13379-scaffold1516-684066 14 82604435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399700 Affx-122960483 AX-123270055 14 9994552 CCTCAACTTGGAATTTTCATTAAAAAAACTTAGGT[A/G]AGACTCAGAACTAGGAGAGGTTAACTTCAATTGTT R 2 1 2 1 101000 r 74 goat snp13378-scaffold1516-640971 14 82565656 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792354 Affx-122971014 AX-385279336 14 10035586 TTTTCTAATAACTCCTTGTGAATTAGACTATGGAG[A/G]ATAGAGTCTGACATCAAGATATGATCTTGTAAGAT R 2 1 2 1 101000 r 74 goat snp13377-scaffold1516-599937 14 82523195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414191 Affx-122949663 AX-123284540 14 10065480 ATATATTCTGTTTATCTTTTCCCATATTAACATTT[A/C]GACTTGGAAAAATGTAATGAATATTTCTTCTCCTA M 2 1 2 1 101000 r 74 goat snp13376-scaffold1516-570043 14 82493002 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441328 Affx-122929434 AX-123311665 14 10099785 TCATACCCCCGGATTTCCACATTGCTCAGCATGAC[A/G]TTAGAAAGTAGGGTTTCCCTGTGGCTCGGGGAGTA R 2 1 2 1 101000 r 74 goat snp13375-scaffold1516-535738 14 82459078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse623 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38415854 Affx-122948861 AX-123286203 14 10176433 TTAGTTTAGATTAGCAGTTCCTAAAATTAGTTTTT[A/C]ATCAGTAGTTCTTCAAATTAGTTTTAGTAAAGCAG M 2 1 2 1 101000 r 74 goat snp13374-scaffold1516-459090 14 82382999 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391826 Affx-122967014 AX-123262183 14 10221934 ACAAAGAGAAGTAGACTCATTTGACCCAACAATTT[A/G]ACTCTTAGGAATATAGCCAATCAAAATGAAAACAT R 2 1 2 1 101000 f 74 goat snp13373-scaffold1516-413589 14 82335956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse627 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38453139 Affx-122920000 AX-123323472 14 10250453 ATAAAACTGCTAAGGAAATGAGAAAAATAAAAATG[A/G]ATAAAAGATTCACATAAACTTATTGGCAAATAACA R 2 1 2 1 103000 r 74 goat snp13372-scaffold1516-385070 14 82307288 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408697 Affx-122953438 AX-123279048 14 10325901 GAAAGCCAAATGGAATTATCTACATTTCTTAAGCC[C/T]GCTCTAGCCCCTGTTCTTTTCTTGAATTGCTATTT Y 2 1 2 1 101000 f 74 goat snp13371-scaffold1516-309622 14 82236963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390646 Affx-122967145 AX-123261003 14 10357238 AAATTCCTGCCTGGCCCAGAGCATGCTAAATTGTC[A/G]GGTAAATAGTGTGAGTCAAGGAGACCATTCAAGGA R 2 1 2 1 201000 r 74 goat snp13370-scaffold1516-278285 14 82205406 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790881 Affx-122947060 AX-385277879 14 10439588 ATTAGGAAGATAAGTTTGTTTTCCTAAAAAGTTTA[C/T]AGATAATGGGTTTTGAAACTGAATCAGCCTTGCTG Y 2 1 2 1 201000 f 74 goat snp13369-scaffold1516-195935 14 82121315 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774894 Affx-122960762 AX-385262028 14 10468926 CAGAAGTGTAATAATCAGGGAGAAGCAAATGTGCC[A/G]TCTCATGAGTTAAATTGTCCACTCCTTTCAGAGAC R 2 1 2 1 101000 f 74 goat snp13368-scaffold1516-166597 14 82092005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441039 Affx-122928935 AX-123311376 14 10513089 AGTAGCTTACATATTTGCCAAGAGTTGATTCATAT[C/T]GTGTGGTTAGGTGTTTTTTCAGTTGTAAAGAAGTT Y 2 1 2 1 101000 f 74 goat snp13367-scaffold1516-122434 14 82047813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449857 Affx-122922373 AX-123320192 14 10605870 GTATATTCTGTGATTATAACTTATCAAATCTCAAA[G/T]AAGATACTGATGCAGGTAATTTTCAATATCTTTCC K 2 1 2 1 101000 f 74 goat snp13366-scaffold1516-29653 14 81952406 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse575 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38409042 Affx-122953363 AX-123279393 14 10659181 TCCAAGAATCATGATTGCAGTAGCAGCTCAGCAGG[C/T]GTAATAATATTTCTGGTAACTGAAATTTCTGAGGC Y 2 1 2 1 201000 r 74 goat snp22300-scaffold2202-23559 14 81897482 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse576 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38446642 Affx-122924781 AX-123316978 14 10711445 CTCAAGGGAATAGTTCTGAATACACACGCCCAAGC[A/G]TTCCTCGATTTACTCAGTCAAAATCTACAGCGAAC R 2 1 2 1 101000 f 74 goat snp22301-scaffold2202-75823 14 81844400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272770 Affx-1111832998 AX-519546469 14 10725666 GCAATACATGAAGCACGGGGTGTTTGGGAAACACT[A/C]TTATTGAGGGCGTATTCACTGCATGTGTATCAGGT M 2 1 2 1 101000 r 74 goat 14_10725666_AF-PAKI 14 10725666 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38404146 Affx-122957086 AX-123274498 14 10798707 ACACTGGCTGTCCACTGTTCACGAGCTACCAATTG[G/T]AGCTGCTACTGGAGAGGCCAAGAGCCATTGCCCCT K 2 1 2 1 101000 r 74 goat snp22303-scaffold2202-163085 14 81755131 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424107 Affx-122942027 AX-123294453 14 10901282 GGACTGCCCAGATGTAGAGGGGCCACTGATTGGCA[A/G]TTGGGAACTAGGTTAGCTTCCATTTAGTTCCACAT R 2 1 2 1 101000 r 74 goat snp22305-scaffold2202-265660 14 81658443 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse628 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38437303 Affx-122931975 AX-123307641 14 10956949 TCAAGCGTGGCTTTGCCCCTGGGAACACTTACAGC[A/G]CAGAATCCTAATCCCAAGATGGAAATAGCTGGAAA R 2 1 2 1 101000 r 74 goat snp22306-scaffold2202-321327 14 81602949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse577 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38434497 Affx-122934615 AX-123304838 14 10989352 CTGCCTTCTCTCCTGCATGTGTGCTGAACAGGCTG[C/T]GCTCCGGCAGTGGTAACAGTGAACACGGTGTCTTA Y 2 1 2 1 101000 f 74 goat snp22307-scaffold2202-353730 14 81570407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785647 Affx-122963302 AX-385272689 14 11063580 AGAGTAACCCAAGCCCTCAACATGTACTAACTACT[A/C]TCTTCCAGGAGCATTGTTAGACATGGAGACCCCTG M 2 1 2 1 201000 r 74 goat snp22308-scaffold2202-427958 14 81508060 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425608 Affx-122940916 AX-123295954 14 11106589 TGGGTTGTCTCATCAAGCTCTAAGAATTCCTTATA[C/T]GTTTAGGGTGCTAGTCCTTTGCCAGATACAAGTCT Y 2 1 2 1 201000 f 74 goat snp41384-scaffold5372-17901 14 81472776 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434402 Affx-122934684 AX-123304743 14 11174504 AGCAGGAGCCCCAGCTCCATATGGAGACAAACCAG[A/C]GCCACTTTTCTGTTGGGTGAGAGGCAGGGGGTATA M 2 1 2 1 303000 f 74 goat snp16957-scaffold1770-47090 14 81409665 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385057 Affx-122971827 AX-123255415 14 11245516 GTGCTGGAGGCAGGAGGAGGCTCTTTGTGTTAGGG[C/T]GCCCAAATTCAAGGACAATTGCTAGCAAGTGGGCA Y 2 1 2 1 101000 r 74 goat snp23111-scaffold2304-45808 14 81347455 T C 1 recommended GoatSNP50 chip candidate gene ou candidate region DGAT1 10.1371/journal.pone.0086227 snp-genphyse629 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38421453 Affx-122943938 AX-123291800 14 11259991 CTCACCCTGCGAGGCCACGTGAAGCCTGGGTCCTC[C/T]CCTCCGGAAGGGCCAAATGGAGGTCATGGGTGGTT Y 2 1 2 1 202000 f 74 goat snp23112-scaffold2304-60283 14 81335034 T C 2 neutral GoatSNP50 chip candidate gene ou candidate region DGAT1 10.1371/journal.pone.0086227 snp-genphyse630 SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38404187 Affx-122957682 AX-123274539 14 11260595 AGGGAAGCCTGGGAGCCTCTGAGCCGGGGGCTGTG[A/G]CCCAGGGGGCACTGGAGTCTCCCCAGGGGGCGAGA R 2 1 2 1 400000 f 74 goat snp23113-scaffold2304-60887 14 81334430 A G GoatSNP50 chip candidate gene ou candidate region DGAT1 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 38401126 Affx-122959390 AX-123271479 14 11260641 ACTGGAGTCTCCCCAGGGGGCGAGAGAGAGTAGGC[A/G]GGGACGGTCCGGTGGCCTTGGGTGGGGGATGGCTA R 2 1 2 1 103000 f 74 goat snp23114-scaffold2304-60933 14 81334384 A G 1 not_recommended GoatSNP50 chip candidate gene ou candidate region DGAT1 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 38416158 Affx-122948274 AX-123286507 14 11261458 TTCGAGGCCACGGCTGGTTCAGGACTGTGGCAAGG[G/T]GGTCGTGCAGGGCAGGCCCTCAGCAGCCTGTCTGT K 2 1 2 1 102000 f 74 goat snp23115-scaffold2304-61750 14 81333756 G T 1 neutral GoatSNP50 chip candidate gene ou candidate region DGAT1 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 38436242 Affx-122932560 AX-123306581 14 11262074 CCGGCCCTCAGGACAGGCCCGCTCTTTCCCACCAC[C/T]CCACCAAGGGCGTGGACACACCCCGCCTGTGGGGA Y 2 1 2 1 202000 f 74 goat snp23116-scaffold2304-62366 14 81333140 C T 2 neutral GoatSNP50 chip candidate gene ou candidate region DGAT1 10.1371/journal.pone.0086227 selGwenGoatSNP50 SNP in casein region multi-breed 38411708 Affx-122951534 AX-123282058 14 11326293 AAGCTGATGCCCAACTGCAAGTGGGTGTCTAGCCT[A/G]GCGGTGCACCCGGCAGGTAAGGGGGTGTCTTGGTC R 2 1 2 1 101000 f 74 goat snp23118-scaffold2304-126585 14 81291826 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769367 Affx-122919890 AX-385256538 14 11359234 GGCTTATTGCTGATTAAAACTGCTTAAAAGCAAGA[A/C]ACCTGAACTCTCCTATCCAGTTGTGAGGAAATCTT M 2 1 2 1 101000 r 74 goat snp23119-scaffold2304-159526 14 81267127 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384903 Affx-122972347 AX-123255261 14 11395549 GCATTGTTGGCTGTGAGGGCCGTGGGCTAGGGGCA[A/C]GAGAGGTGGCGGGCGGGGGCCGCTATCGTGAGGCT M 2 1 2 1 103000 f 74 goat snp23120-scaffold2304-195841 14 81230542 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412908 Affx-122950407 AX-123283257 14 11435253 TAAAGAAAGGAGAGGGTCTGGCCTATAAATGGGAA[G/T]AAAAAGAACCAATCAATAGGAACTACTCCTGGGGA K 2 1 2 1 101000 f 74 goat snp21785-scaffold2137-22405 14 81199971 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse631 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38442608 Affx-122928476 AX-123312945 14 11494564 TACATCGAACAATTAAAGTTTGTTTTTAAAGCAAA[C/T]GTCTTATATTTACCAATGAAGTTTACAGTGTTTTA Y 2 1 2 1 101000 r 74 goat snp21786-scaffold2137-81716 14 81146552 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse632 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38437605 Affx-122931856 AX-123307943 14 11529076 AGGCTCTGTCCTGTGCAGGGGATGTGTTGGTTCCG[C/T]GTTGAAAAACTGACCCCAACGTGGGGAAGCCCTGA Y 2 1 2 1 201000 f 74 goat snp25943-scaffold2684-3527 14 81112809 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse633 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320798643 Affx-122954823 AX-385285575 14 11617281 TATTTAAAAACATTTTATAGTGGGGAATTTGAACA[C/T]GTACTAAAGTGAACGAGGGAGAATAAAGGACACCC Y 2 1 2 1 101000 r 74 goat snp25944-scaffold2684-91732 14 81032694 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse634 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38416780 Affx-122948167 AX-123287128 14 11671787 CAACCAAAACCCCAAACCAACACCCCTTACCAAGA[C/T]ATGTCAGATTCCATGTACAAATATGGTGAATCTCA Y 2 1 2 1 201000 r 74 goat snp17790-scaffold1849-2943 NW_017190166.1 19392 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763116 Affx-986697645 AX-385251067 14 11714905 GAAAACAGCATTTTTCTGGTATCACACCTAAAAAG[A/G]TTAATAGAATTATTTGATATACTATTCATATCTAA R 2 1 2 1 600010 f 74 goat 14_11714905 14 11714905 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320797013 Affx-122947406 AX-385283954 14 11716988 TCTGAAATCTACTTCTTCTGATGTTAATATAGTCA[C/T]TTCAGCTCTCTTTACTTAGTGTTATCCCAGCACAT Y 2 1 2 1 101000 r 74 goat snp17791-scaffold1849-48144 NW_017190166.1 61826 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse635 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38407164 Affx-122954839 AX-123277515 14 11746342 AAGCCGCCCCTGCCCTCACCATAGGTGCTGGTATT[G/T]TTAAATTAGTGTTTGTGCTATTTCTTTTTAAATAG K 2 1 2 1 201000 r 74 goat snp17792-scaffold1849-77498 NW_017190166.1 90414 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440856 Affx-122929253 AX-123311193 14 11795037 GGAAGAAAAGCAAGAAAGATCTGACCCATTAGTTC[C/T]TTTACCTTTTCTCATACTGAATGCCTCCACTGCTC Y 2 1 2 1 101000 r 74 goat snp17793-scaffold1849-126193 14 80964941 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407773 Affx-122954966 AX-123278124 14 11831514 TCCAGTTAAAATTTCAGATGAACAGCAACTCACTT[C/T]TCAATGGAAGTCTCAACAGTTTCACGGGACAAACT Y 2 1 2 1 201000 r 74 goat snp17794-scaffold1849-162670 14 80928118 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769651 Affx-122922780 AX-385256821 14 11902855 TCATCTGATGGGAAAGTGCGGAATAAACAGAAGCC[A/G]CTGTGCTTAAGCAGCCGCGTCTGCAGGCTGCGCTA R 2 1 2 1 202000 r 74 goat snp17795-scaffold1849-234011 14 80865259 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431057 Affx-122936642 AX-123301398 14 11949226 TCGGGCGCGCTCAGTGCTTGGGGTGTCTGTGCCCA[C/T]GTGTGTGCCTGTGATGAGACTCGCGTCCTATAGGT Y 2 1 2 1 202000 f 74 goat snp17796-scaffold1849-280382 14 80819952 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793286 Affx-122932870 AX-385280264 14 12001180 TTGTTAAGAGAGTAGGAAAATGGAATCTTTAATAA[C/T]GTCAAACAAAGGCACCGGAAGTTATTAAACCACCA Y 2 1 2 1 201000 f 74 goat snp17797-scaffold1849-332336 14 80768751 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404985 Affx-122956399 AX-123275337 14 12030713 CACAGACCACAAGACAGTGTTATCTTCCTGTGGCC[A/G]GTGGAGCACAGCTCACGAGCCCCGGGGTGCTGGCA R 2 1 2 1 101000 f 74 goat snp17798-scaffold1849-361869 14 80740487 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse624 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38389467 Affx-122968334 AX-123259825 14 12122571 AGGTGTGCTGGGCATGTGGGCTTGCCTTTGGTAAC[A/G]TTGGGGTAAATATGGAAGAATATTTACAGTGTAAA R 2 1 2 1 202000 f 74 goat snp17800-scaffold1849-453727 14 80647141 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376743 Affx-122978947 AX-123247102 14 12161324 ACACATGAGGCCAGCAACTCAGTGCACAGGACGCC[A/G]ACAGCACACACAGAGAACACGTCCACACAGCACAC R 2 1 2 1 201000 f 74 goat snp17801-scaffold1849-492480 NW_017192798.1 3784 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400994 Affx-122960089 AX-123271347 14 12220604 TGTGTCCAGAACTCGATCTGAGAGTGGACAGGAGC[G/T]CCTGACCAGTGCAAAACAGTATACAAAGCCGTGCA K 2 1 2 1 103000 r 74 goat snp17802-scaffold1849-551760 14 80552843 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390710 Affx-122967935 AX-123261067 14 12321716 GGGGGGAAGAAAAGGAAAGAAAAGAATCTTGACTA[C/T]ATACAGTGAGCAAGGAGTGAAGCTGGCAGCTGCTT Y 2 1 2 1 201000 r 74 goat snp17804-scaffold1849-652872 14 80450712 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782525 Affx-122973329 AX-385269600 14 12364682 CTGAGGAATACCAAAGAAAAGGTGGGACTTGAAAC[A/C]ATCTACAAGACTCTGTATCCTTGTTTTTGGAGGTA M 2 1 2 1 101000 f 74 goat snp17805-scaffold1849-695838 14 80407075 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437622 Affx-122931816 AX-123307960 14 12429920 ACCTGGGGCTGGCTGCTGACAGGCCTAGGGTTTGT[C/T]TTTGGGAGTCTTGCTACATCTGAAAACACTTCACT Y 2 1 2 1 101000 r 74 goat snp17806-scaffold1849-761076 NW_017203681.1 12947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376918 Affx-122977793 AX-123247277 14 12490799 TGCCCATCACGGGGACACAGGGACTCTCTAAAGGA[A/G]TCGTGAGACCAGGGTCCATGGCTGGTGGGGGCGGG R 2 1 2 1 101000 f 74 goat snp17807-scaffold1849-821955 14 80143621 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse625 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38376983 Affx-122977745 AX-123247342 14 12592919 TGGATAGCAGATGGTTAGATGGCTGGATGGACGAG[C/T]GGATAGCTGGATGGATGGATGGTGGATGGATGGAT Y 2 1 2 1 101000 f 74 goat snp8950-scaffold1323-76977 14 80032759 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793450 Affx-122951343 AX-385280427 14 12701029 AGACAACATACAAACGTTTGAGTTCTTTGAATAAA[C/T]GCTATTTGAGTTCTATCATGGCCTATGACGTTAGC Y 2 1 2 1 101000 r 74 goat snp8952-scaffold1323-185087 14 79925071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793392 Affx-122948320 AX-385280369 14 12745971 GCTGCTGGCGTTGCTAATATTAGCAGTGGTGGTAA[C/T]AGCAACAGGAGTGTCTGAGGCAATAGTAACTGCAG Y 2 1 2 1 201000 r 74 goat snp8953-scaffold1323-230029 14 79879596 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416353 Affx-122947887 AX-123286702 14 12782617 CTGAAGGGAGTGGTTAAAAGAACTTGTCAGACCAG[C/T]TATAGGGGACTCGCAGGCTGGGCGATTTCTTCACT Y 2 1 2 1 101000 f 74 goat snp8954-scaffold1323-266675 14 79843108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376221 Affx-122978798 AX-123246580 14 12851787 GACCCGGCACCTTCAGGACCCCCGGGGTGGTCTGT[C/T]TGGGTGAAGAGTAAAGCACGTTGGCATCCTGTGTT Y 2 1 2 1 101000 r 74 goat snp19596-scaffold1975-832789 NW_017189739.1 30852 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414392 Affx-122949991 AX-123284741 14 12907904 TCAGCTGCCCTGGGTACCCACTCTGGTAGTTTCTC[A/G]TGGTTTTGCCTTCCTGGGTGACCTTTGTTCCTCTG R 2 1 2 1 101000 r 74 goat snp19595-scaffold1975-776672 14 79749708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386312 Affx-122970893 AX-123256670 14 12964895 ATGCCCCATAAATGCAGGCAGGACAGCCCAACGAC[A/G]CACCCAGCCGAGTGGGATGCTGGTCTTTTTCTTGG R 2 1 2 1 202000 f 74 goat snp19594-scaffold1975-719681 14 79697281 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765870 Affx-986697651 AX-385253310 14 12976044 GGTTCCTCTGCCTTTTCTAAATCCAGCTTGAACAT[C/T]TGGAAGTTCATGGGCCATAAACTCTGGCTTGGAGA Y 2 1 2 1 600010 r 74 goat 14_12976044 14 12976044 Ancestral_priority_1043 ancestry 0.68 recommended IMAGE 10K 10K ancestral 38419880 Affx-122945355 AX-123290228 14 13017827 CGCACAGCTGAGCTTGAGCAGAGCTGGGGATCAAC[A/G]CAACCAGGCTGACGCTCCCATTACATTCCTGGCTG R 2 1 2 1 201000 r 74 goat snp19593-scaffold1975-666749 14 79644162 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421531 Affx-122943877 AX-123291878 14 13062215 CCAGCAGAGAAAGCGCTGCGCTCTAACCTCTGGAC[C/T]GCCAGGGAACTCCCTACACTGCTACATTTCAAGAG Y 2 1 2 1 201000 f 74 goat snp19592-scaffold1975-622361 14 79601900 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411184 Affx-122951855 AX-123281534 14 13118244 GCCTGCTAGTCTGTGTCCCAGCCTTGCAGCCGCCC[C/T]GGGGGTGTGCGTACCTCCCAGAGGTGGAGTGTGGC Y 2 1 2 1 103000 f 74 goat snp19591-scaffold1975-566332 14 79549016 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442088 Affx-122928366 AX-123312425 14 13168422 CCTGTAGGACTTTGCAGACAAGGGGCAAATCTGGG[A/G]CCAAATTCCATCTCACCTGTTTCAGTGGCGGCCAT R 2 1 2 1 101000 r 74 goat snp19590-scaffold1975-516154 14 79511077 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387592 Affx-122970259 AX-123257950 14 13202088 CTGCATCTCCTATATTGGCAGGCAGATTCTTTACC[A/G]CTGAGCCACCCTTACACACGACTTTAAGAAGAAAA R 2 1 2 1 103000 r 74 goat snp19589-scaffold1975-482488 14 79478364 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272772 Affx-1111832999 AX-519546470 14 13232070 TCTATTAAATGGTAGTTTTGGTGATACAGAATTCT[A/G]TAATTTTTCTTTGACCAACCAGAATACAATGGTAT R 2 1 2 1 101000 r 74 goat 14_13232070_AF-PAKI 14 13232070 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387894 Affx-122969617 AX-123258252 14 13255368 TGACAGCATTTCCTGTCCTTTCACCCAAGTGTACA[C/T]TCACCCCTCAGTGTCCACAGAAGGCTGGCCCCAGA Y 2 1 2 1 101000 f 74 goat snp19588-scaffold1975-429208 14 79426996 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442181 Affx-122928804 AX-123312518 14 13310971 AGCCAGGTTCGCTCCGTGTCTTGCCTGTGATCACA[C/T]GGCTGAGCAGCAGTGACGCTGGATTTTGGACTTGG Y 2 1 2 1 102000 r 74 goat snp19587-scaffold1975-373605 14 79378846 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445840 Affx-122926013 AX-123316177 14 13367975 CTCAGTGAAAGGGATAAACATGTGCTAGTTGCTGA[C/T]GTAGATTCGGTGACAGACTCCAGAGGAGTAGGAAG Y 2 1 2 1 101000 f 74 goat snp19586-scaffold1975-316601 14 79321625 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450974 Affx-122921739 AX-123321308 14 13404881 TCGCAAAGAGTCGGACACAACTGAAGCTACTGAGC[A/G]TGCACCCATTTGGACCGATCTTGTTAACTTGCTTT R 2 1 2 1 101000 r 74 goat snp19585-scaffold1975-279695 14 79284721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402981 Affx-122958148 AX-123273334 14 13438020 AGCCTTCTCAGCCTCTGGACCAGGATTAAGTTAAT[A/G]CGGGGTCCAGAGGAAAACACAGGGATGGAGCCAGA R 2 1 2 1 201000 f 74 goat snp19584-scaffold1975-246556 14 79251534 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse636 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468276912 Affx-1111835583 AX-519550421 14 13461614 TCAGTTATCAATTTTAAATATAAGGAAGGTAATTA[A/G]GCAAATGGAAAGTTTCTATTTAAATGGAGTTATAA R 2 1 2 1 101000 r 74 goat Random2.2K-1398 14 13461614 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399078 Affx-122960884 AX-123269433 14 13490074 CAACACCTAACTTCCTCAGTCTTATCTCCAACTAT[A/G]AGCACCAAGATACCCACAAGTTCACCAAGATACCT R 2 1 2 1 101000 f 74 goat snp19583-scaffold1975-194502 14 79199762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412885 Affx-122950425 AX-123283234 14 13530772 GCTAAGTGCAAGGCGCAGCTCTTGGCAAGCCATAC[C/T]GCTGGGATGGCATGTTCAAGAGTCTTTGCACGCTG Y 2 1 2 1 201000 r 74 goat snp19582-scaffold1975-153804 14 79159164 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430892 Affx-122936872 AX-123301233 14 13561825 GAACCCAGAAGGGGCTGAGGGGACGAGAAGTTGGT[C/T]GATACCCCGAATGATGGGGAAGGACGAGCTGCGGC Y 2 1 2 1 101000 r 74 goat snp19581-scaffold1975-122751 14 79128111 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438470 Affx-122931236 AX-123308808 14 13596198 TGGGTCCTGGAACCCTCCGCCTCCTCCTCTTCTTC[C/T]AAAGCAAGGTCTGGCCAGTTCAGGAATCAGCACGT Y 2 1 2 1 101000 r 74 goat snp19580-scaffold1975-88378 14 79093797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452251 Affx-122920776 AX-123322584 14 13661480 ACACAAGATAGGAGCATTAGCGAGCAGCAGTCTCG[C/T]CCTGAGGAGACAGGAGCAGAAAGCTGGGAGTCTGT Y 2 1 2 1 101000 f 74 goat snp19579-scaffold1975-23096 14 79028946 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768820 Affx-122924424 AX-385255997 14 13691013 CCCCCAGTGTCCAGTCCTGCTGGTGGGCAGTCTGA[C/T]CTAATGTCCTTCCCTTCCGGGAGGTCTTTTATCTT Y 2 1 2 1 202000 f 74 goat snp1952-scaffold1054-687207 14 79000226 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378643 Affx-122977101 AX-123249002 14 13743970 TCACTTACTTTGCTATAGCTCAAGAATCTTGCATC[A/G]TTATCAGTTTTCTAAAATATAACACCCACCCTTAC R 2 1 2 1 101000 f 74 goat snp1951-scaffold1054-634250 14 78947519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384244 Affx-122972361 AX-123254602 14 13782751 GACTGATTGTACAATGTCCTATTGATTTTTTAATA[A/C]AGCAAGTTTTATCCATTAATTATAGGCTTAAACCA M 2 1 2 1 101000 f 74 goat snp1950-scaffold1054-595469 14 78909851 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276914 Affx-1111835584 AX-519550423 14 13796831 AAAAAAGAACATCCAGTCTCACCTCGGGGTGCCCT[A/G]CTTACTACTTCTTTCCAGCTAGAAAAATCCATTCT R 2 1 2 1 201000 r 74 goat Random2.2K-1399 14 13796831 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430954 Affx-122936827 AX-123301295 14 13812928 TTATCCTTAAGTCAGACTTGCAGCATATGAGCCAG[C/T]GATAAAATTTTCAACATTCTTGTATTCAAAAATTT Y 2 1 2 1 101000 f 74 goat snp1949-scaffold1054-565292 14 78879681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401737 Affx-122959516 AX-123272090 14 13850405 CAGAGGGGCATTAAGAAGACCTACATGAAGGAGGG[C/T]GTGCCGTGGTCCATCCCAGGAGCAGACAGGTGAGG Y 2 1 2 1 101000 f 74 goat snp1948-scaffold1054-527815 14 78842294 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425090 Affx-122941241 AX-123295436 14 13889042 ATCTCAAAAAAGAGTGAAAACAACCCTAATTTCTC[A/G]CCATTTGAAGTTTTTAAACAATTTCTTACTGCGGA R 2 1 2 1 101000 f 74 goat snp1947-scaffold1054-489178 14 78803674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400239 Affx-122960151 AX-123270594 14 13950234 GAGATTATCGGAACAATTAGGTGGTGTGTAGACAA[C/T]GCTTATTACATCGCCTGGTGCAGCATCTGTCGGGT Y 2 1 2 1 101000 f 74 goat snp1946-scaffold1054-427986 14 78743655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410555 Affx-122952146 AX-123280905 14 13989781 GCACAGCTGAACTATTTATCAGATGCTCCTTCACA[G/T]AAGAAGTTGACTAATAAAACTCTTAAGAAGCAAAC K 2 1 2 1 101000 f 74 goat snp1945-scaffold1054-388439 14 78706317 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402817 Affx-122958272 AX-123273170 14 14018715 GGCAGGGCGCTGCCTTGACGCTCATCTAGGGAGCC[C/T]GAGTCTGCTGGCATCACAACCCTCATTGTGACAAC Y 2 1 2 1 101000 r 74 goat snp1944-scaffold1054-359505 14 78677358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382428 Affx-122974242 AX-123252786 14 14053113 GGACACCCAGGTCTTGTCAGAAAACCCACCTGGGG[A/C]TGGATTCTGCTAGGTCAGTAGGCATCTCACCAACC M 2 1 2 1 101000 r 74 goat snp1943-scaffold1054-325107 14 78642965 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418609 Affx-122946352 AX-123288957 14 14096503 TGATGAATTCCCGAGGAGAGACCAAGGCTTGGAAA[C/T]CTCAGCACACGTGTGACTTGTTCTGAGAAGGAACA Y 2 1 2 1 101000 f 74 goat snp1942-scaffold1054-281717 14 78601841 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450583 Affx-122922030 AX-123320917 14 14131208 CATGAATCAAGTCAAATGGCCCACGTGCACGAGCA[C/T]AGGTGGGCATGGCCAGGGCACGTCTGCACGCACGG Y 2 1 2 1 101000 f 74 goat snp1941-scaffold1054-247012 14 78566200 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421706 Affx-122944401 AX-123292053 14 14170225 GGGCTCCGGGGTTTGTCTTCCTCCTTCTTGTTTCA[C/T]GAGGCTGCAAAAACTGATGCTCCTGCTTTGGCAAA Y 2 1 2 1 101000 r 74 goat snp1940-scaffold1054-207995 14 78538109 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450854 Affx-122922233 AX-123321188 14 14229467 CACCCCCTGCCTTGTTCATGCCCATCCTCTCTGTC[A/G]TTACTACAGAATAATGTGAAATCAGTCCCAGACAC R 2 1 2 1 101000 r 74 goat snp1939-scaffold1054-148753 14 78480026 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379810 Affx-122976231 AX-123250168 14 14269367 AGACAAAGTCTACAGAAGCAGGAAAGAATTACCCA[C/T]AGTGCCACCACTCAAGAGAAGCCCTGTGAACATCT Y 2 1 2 1 101000 f 74 goat snp1938-scaffold1054-108853 14 78440312 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385920 Affx-122971569 AX-123256278 14 14390647 CTGGGGAAAGCCACTCTTGCTGATGGGACTAGCAC[A/G]TGTGCGAGAATTTTCTTTGGCTCAAAGTAAGAAAC R 2 1 2 1 101000 r 74 goat snp23208-scaffold2316-504047 14 78322053 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445762 Affx-122926073 AX-123316099 14 14426816 CCGTCGTTCAGTCATGTCTGACTCTTTGCAACACC[A/G]TGGGCTGCAAATGTAGATTACACAACCGAGTTGGC R 2 1 2 1 101000 r 74 goat snp23207-scaffold2316-467878 14 78285901 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384819 Affx-122971983 AX-123255177 14 14457838 GACTTTGGAAAACTCACTGCCGCTTTCTGGTCCTT[A/G]CTTTTTCCACCTGCTGTGTAAGCTCTTTAAATCCG R 2 1 2 1 101000 r 74 goat snp23206-scaffold2316-436856 14 78254857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424149 Affx-122942544 AX-123294495 14 14489962 TAGCATGTAGTATGGCCCACTGTAAGCACCCAGCT[C/T]GCCTTCAGTTTGGTGGATGTCCTTGATGTCTTTCG Y 2 1 2 1 101000 f 74 goat snp23205-scaffold2316-404732 14 78222145 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395138 Affx-122964130 AX-123265493 14 14521882 CAGAGGGAGGCTTTTTTCATCAAGCATTCACCATC[A/G]TGAGGGTGGTGCTGCAGTCTGAGACACGTGAACCT R 2 1 2 1 101000 f 74 goat snp23204-scaffold2316-372812 14 78191340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275374 Affx-1111834861 AX-519548948 14 14565462 GCAGTGTGATCCATCTTGATAGAAGGATTCTACTC[A/G]CCTTCAGGCAATCTTCCCTGCAGGGAG R 2 1 2 1 101000 f 74 goat GoatD01.056804 14 14565462 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38437128 Affx-122932159 AX-123307466 14 14610894 TGTTTTTCCTTGGCATGTTGACTGTTTCATAGGTT[A/G]ACACAAAATGAAGGTAGAGTTCAGAGTCATTTCCC R 2 1 2 1 101000 f 74 goat snp23202-scaffold2316-283800 14 78101743 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38377785 Affx-122977329 AX-123248144 14 14640556 GCCTCCTGTGGGTCTCCCAGGCAGGCCCCTCTTCA[C/T]GGTGCAGGATGTGGAATTCTGAGCTGGGTAACAAG Y 2 1 2 1 101000 r 74 goat snp23201-scaffold2316-254138 14 78072659 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448353 Affx-122924122 AX-123318689 14 14680010 TGCCAAGCTGCTCAAATTTTCAAGATGTGTTAAAC[A/G]GAAATAGAAAATATTCTGGGTATCATTCCTCATGG R 2 1 2 1 101000 f 74 goat snp23200-scaffold2316-214684 14 78032994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446028 Affx-122925852 AX-123316365 14 14712069 CCTTTCTCCGCGAAGATCTGACCATGTCACGTCCT[A/G]CCCAGAACCCTCAATGCCTTGCCATGCCCACAAGG R 2 1 2 1 202000 r 74 goat snp23199-scaffold2316-182625 14 78000925 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426733 Affx-122939873 AX-123297079 14 14741528 GGAACTCACCACCATGAAGCAAGTCCCCTCTCAGC[A/G]AGCAGCCCGTGAGAGTGGCTGCTGTGGTCCTGTGG R 2 1 2 1 101000 f 74 goat snp23198-scaffold2316-153166 14 77971387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411629 Affx-122951583 AX-123281979 14 14775182 ATAAATCACGGCCTATTCACACAGGGGGACGCTGT[A/G]CAGCCACTTAAGATAAATCATAGACGTCTGCAGCA R 2 1 2 1 201000 r 74 goat snp23197-scaffold2316-119512 14 77936771 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439554 Affx-122930097 AX-123309891 14 14853412 CAACCTCCAGCGAGACTTTTCCCTCACCCTTCTGG[C/T]GGGTCTTAGTGAAGTTTCAGGACCCTTCTAGAAAC Y 2 1 2 1 201000 r 74 goat snp23195-scaffold2316-41282 14 77859057 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785527 Affx-122966515 AX-385272571 14 14888732 GAAGACTAAAACTCATACTAGAATATTAACAGAGC[A/G]TTACTTCCATGTTGTAGAATTATGTTAACTCAATT R 2 1 2 1 101000 f 74 goat snp23194-scaffold2316-5962 14 77823739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384656 Affx-122972144 AX-123255014 14 14938956 GGCAGGAAGAAGATTTATTTTCTTGGTAAAAGAGG[C/T]ACAATCTTCAATGAGTCAGCCTAAGAACACCAAGC Y 2 1 2 1 101000 r 74 goat snp22503-scaffold2226-345727 14 77773593 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799806 Affx-122933464 AX-385286732 14 14970953 TCTGCTGTGACTATGGTTTACATTATCTGTTGTCC[A/G]CATGTGTAAATTATATAGGAATCCTACCAGCATCA R 2 1 2 1 101000 f 74 goat snp22502-scaffold2226-313730 14 77741515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771296 Affx-122974425 AX-385258454 14 15014692 ACAGTGGCTGTGAAATTCTGGATGGAGAATGATAG[A/C]GACTCAGCAGAAATTGTAACCGATGGAACAATCCA M 2 1 2 1 101000 f 74 goat snp22501-scaffold2226-269991 14 77696900 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444110 Affx-122926822 AX-123314447 14 15066961 ACAGCATGCATAGAGAACAGCAGAACAGTATCTGT[A/G]TTTCCAGCCCAGGATGCCCAGAAGCAAGGGTAAAA R 2 1 2 1 101000 f 74 goat snp22500-scaffold2226-217722 14 77644137 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411272 Affx-122952313 AX-123281622 14 15102888 TGGGAAAATCATTGCACCTCTCTGAGCCTCTGTTT[C/T]TTCATTTGTCAAAGAGGGGTAGCAACACCCATTTG Y 2 1 2 1 103000 r 74 goat snp22499-scaffold2226-181795 14 77607819 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775277 Affx-122970164 AX-385262408 14 15152231 GACTTTCTAGCACCAGGAGTCAGTTTTATACAGTC[A/G]TAGAAACAATAACCTAGCCAGGATTTACAGAAGAG R 2 1 2 1 101000 f 74 goat snp22498-scaffold2226-132452 14 77558357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414836 Affx-122949192 AX-123285185 14 15221728 TGTTGAATGAAGGAATCTGCCTTTTACACCTAAGC[A/G]CAGAGAAAGGTTCAGTAACTAGTCAGATGTCACAA R 2 1 2 1 101000 f 74 goat snp22496-scaffold2226-62955 14 77488200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375499 Affx-122979131 AX-123245858 14 15255609 CAGGCAGAGAAAGAAAATCGCCCCTTAATAGAGAA[G/T]AGTTATCCAAAATAAAATCCAGAGAGTGTTGAACT K 2 1 2 1 101000 f 74 goat snp22495-scaffold2226-29074 14 77454316 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771119 Affx-122931951 AX-385258279 14 15297546 AGCATGCCATTGATATAAAAAACATCCAGTTCAGA[A/G]CCCACACACCTAACCACCTACTTGTCAAACTGTCA R 2 1 2 1 101000 r 74 goat snp21457-scaffold209-2228404 14 77287974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771937 Affx-122944362 AX-385259092 14 15329669 AGCTTTAGTCTCCTTATCTTTAAGTCATCTGTAGC[A/G]TGAAGAAGTCATGACAATAATTTGAAGTTAGAGAT R 2 1 2 1 101000 f 74 goat snp21456-scaffold209-2196281 14 77255390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794029 Affx-122937266 AX-385280998 14 15367053 AATGAGGTTTATGTAGGAGGGATTTGTAAAATGCA[C/T]GATGCTATATGAATTGCCAGATTCACAGTGAATCA Y 2 1 2 1 101000 r 74 goat snp21455-scaffold209-2158897 14 77218070 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431194 Affx-122937171 AX-123301535 14 15400798 GAGTATGTACTAACCCATTTAACCATCTCTGAGAG[A/G]CATGCCGCACCCTCCAAGTCTGGGCTGGGAGCAAA R 2 1 2 1 103000 f 74 goat snp21454-scaffold209-2125152 14 77182043 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382277 Affx-122973928 AX-123252635 14 15433905 AGGAATCAGTCCTAGTAAGCAGGCCCCCACAGACT[C/T]AAGGATTTGCTCTCCTGGCAACATGACTCAATTTC Y 2 1 2 1 201000 r 74 goat snp21453-scaffold209-2092045 14 77148760 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276784 Affx-1111835586 AX-519550292 14 15453377 GCTTACTTGGCTAAAATCCGTTGAAACCCTTGGAT[A/G]TGTTATCTTGTTGATTTTCTTCTATGGTTTCAAGT R 2 1 2 1 101000 f 74 goat Random2.2K-1401 14 15453377 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781907 Affx-122929132 AX-385268988 14 15491047 TCATTTCTAGTCCTTGACTGTCCACAAGTTTCTGT[A/G]TAATATGGTACAAATTACATCCCCACTTCTCTCCA R 2 1 2 1 101000 f 74 goat snp21452-scaffold209-2034903 14 77090511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446894 Affx-122925223 AX-123317230 14 15558395 CAGAGACAGACTTGGACATCTCAGGTAGTGGGCTC[A/G]TCTGGGGAGGAGAAATGGGAAGGGAAGACAATGAA R 2 1 2 1 202000 f 74 goat snp21451-scaffold209-1967555 14 77022413 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418041 Affx-122946633 AX-123288389 14 15619505 TCTAAGCTGACACTTCTTTTTCATTGAATATGAGT[A/C]TGTTTCTCTCTCTTTCTTTTGCTGGTGGCAGTAGC M 2 1 2 1 201000 f 74 goat snp21449-scaffold209-1906445 14 76961002 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432899 Affx-122935327 AX-123303240 14 15674748 ATGATTATTTCCTTTTCTCCATTTCCTACTAGTGC[A/G]TGAGATTTTGAAGCGCAAAGCTTGGATATATTCAC R 2 1 2 1 103000 r 74 goat snp21448-scaffold209-1851202 14 76905424 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779526 Affx-122976388 AX-385266629 14 15711923 TCCTGGTTCTTTCTTATGATACCATGGACTCAAGA[G/T]AGAAGGTCACATGATGGCTTTGTTGGCAGATGTAG K 2 1 2 1 101000 r 74 goat snp21447-scaffold209-1814027 14 76868261 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771177 Affx-122943334 AX-385258337 14 15780969 AGCAACTACTATGTTGGTTTTGTTAGAAAATATAA[C/T]AACAAGTATTTCTTTAGAGTGTACGGATTCTCAAT Y 2 1 2 1 101000 r 74 goat snp21445-scaffold209-1744981 14 76799325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424740 Affx-122941660 AX-123295086 14 15814090 CTTATTTTCGATGATCCATAATTCCCTTAACTTTC[G/T]AGAGTTTAGGCAAGCATTTAATTTTGGAAGATCAC K 2 1 2 1 101000 f 74 goat snp21444-scaffold209-1711860 14 76765631 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271783 Affx-1111833000 AX-519545576 14 15819501 TTACCCTTTGGCATCAGTTGAGTTCAGCCGAGGAG[A/G]AGCCCAGGCAAGGGACTGGAGAGAATATGAGGCTG R 2 1 2 1 202000 r 74 goat 14_15819501_AF-PAKI 14 15819501 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448149 Affx-122924277 AX-123318485 14 15846166 GATGCCATGGAGAACTTTGTTCTTGGTTTCTTAAC[A/C]GAGAAAGACATGTTAAATACCAACAGTCTCTACTT M 2 1 2 1 101000 f 74 goat "Random2.2K-1463;snp21443-scaffold209-1679784" 14 76733572 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431869 Affx-122936066 AX-123302210 14 15914253 AATTGGTAGGCGGCAGGCAGGTTGAATCAGCAGGG[A/C]GCTTATATACACGCTGTTTTTTGTTAGCAAAGCCA M 2 1 2 1 101000 r 74 goat snp21442-scaffold209-1611697 14 76664608 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785768 Affx-122926989 AX-385272808 14 15990011 AAATAGTATTCAACTATTATGTTCTACACTTTTGG[A/C]AAAATTATTGAGAACATATTAGCTCATCTAACATG M 2 1 2 1 201000 f 74 goat snp21440-scaffold209-1535939 14 76587086 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425960 Affx-122941173 AX-123296306 14 16069741 AAGTAGTCCCTATGGTTTCTTCATGACACAAACTA[C/T]ATTTTTCTTTTCTAGTCATGGTTGTGGACTCTTGA Y 2 1 2 1 101000 f 74 goat snp21438-scaffold209-1456209 14 76506042 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379136 Affx-122976734 AX-123249495 14 16163343 CTTCTGTGTCATTCGAAGCTGAAAATACAAGCCTT[A/G]TCTCTGTTTTCTTGTCTCTCATTTACCCCCAATTA R 2 1 2 1 101000 f 74 goat snp21436-scaffold209-1362607 14 76411483 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786050 Affx-122978655 AX-385273086 14 16206693 AGGCACTACAGAATTTATGAAGTATTTAGAGACAT[A/G]CATTTCAAAATGATATTGTGATCAGTAAGTTAGCC R 2 1 2 1 101000 f 74 goat snp21435-scaffold209-1319257 14 76367467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438940 Affx-122930412 AX-123309277 14 16288673 GTTAAGATTTACTATTGTTAATAGATTTAAGACCA[C/T]GTATTCTCTTAGTTCTTGTGTCAATTTTAAGTTCT Y 2 1 2 1 101000 f 74 goat snp21434-scaffold209-1237277 14 76284877 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784535 Affx-122926577 AX-385271584 14 16335587 AAGTCCGAATTGAAGTGCAAAAGCAATGAAAACTG[A/C]TAAACACTTGTGGAAGTAAGATGATGTAAAACCAA M 2 1 2 1 101000 f 74 goat snp21433-scaffold209-1190363 14 76237227 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400713 Affx-122959923 AX-123271068 14 16375638 AAGCTGGGATTCAAGCTCAGGAAAATATTCCACTG[C/T]ATACATGCAAAGAAAAGAAATTCAGTATTGAGATC Y 2 1 2 1 101000 f 74 goat snp21432-scaffold209-1150312 14 76196844 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378758 Affx-122977017 AX-123249117 14 16410968 AGGAGTCACCCATCATGCAGGGGCAGCAGGCAAGC[A/G]TGGCACAGACCTCTACAACTTCTATACCTCTGACC R 2 1 2 1 101000 r 74 goat snp21431-scaffold209-1114982 14 76161460 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388678 Affx-122969006 AX-123259036 14 16457100 CTATTTCTTGAATGGAATATTTATACTCTTTACTC[A/G]TTTTCCTAACTACATATCTACGATTCCTCATTTAT R 2 1 2 1 101000 r 74 goat snp21430-scaffold209-1068850 14 76115473 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413253 Affx-122950230 AX-123283602 14 16583155 AGGTATTCTCTGTAAAGCAATTAGCGGAGTGCCTA[A/G]AGCGTACTTGCACTAAAAAATATTTGTTTTTATTT R 2 1 2 1 201000 r 74 goat snp21427-scaffold209-942795 14 75988817 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276920 Affx-1111835587 AX-519550428 14 16607367 ATTTGAGGAAAATACTTGAACAGATTCTATCAAAC[A/G]GCAAGTTAATCAGAATGGAGACCTCAAAAGAAGAC R 2 1 2 1 101000 r 74 goat Random2.2K-1402 14 16607367 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425842 Affx-122940669 AX-123296188 14 16616929 ATCAGTTCACATATGTAATAAGCCAGAATGCAGGT[A/G]CTGTGAGGGAAAGGAAGCTGTCTCATTCACTTTTT R 2 1 2 1 101000 f 74 goat snp21426-scaffold209-909021 14 75955360 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770313 Affx-122946362 AX-385257479 14 16683917 CAATATCCAAGATAGCTCTCATTCATTTATCTACT[A/C]GTTCAAGAATTAATTACTGAGTTTCTACTATATTC M 2 1 2 1 101000 f 74 goat snp21424-scaffold209-842033 14 75888374 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276923 Affx-1111835588 AX-519550431 14 16722032 ATGCCTTGTTCATCAGTGATTTGTGCAAAAGTTGT[C/G]GTCGAACACATTGTTCCCATATGACTGCCAGTCTC S 4 1 2 1 101000 r 74 goat Random2.2K-1403 14 16722032 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38423996 Affx-122942110 AX-123294342 14 16725456 AAATAAAAAGGCAAAACTGCTGAGCTACTGAATAG[A/C]GAATCTTAAGGGGAACTTTCTTATTTTCAATATCT M 2 1 2 1 101000 f 74 goat snp21423-scaffold209-800494 14 75846746 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416324 Affx-122947912 AX-123286673 14 16761620 TATTTTGCTCCCCTATTGCCCATTCTCCCCAGTCA[A/G]TTAGAGACATTGCCTTAAGAATTTTCAGAATAATC R 2 1 2 1 201000 r 74 goat snp21422-scaffold209-764330 14 75810554 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797076 Affx-122923331 AX-385284016 14 16802610 TCAGTTACAGGTCACTTTGGATGAGGATTTCTGCC[A/G]TTTGCAATTGGAAGAGTCTTGAGATACTCATAAAT R 2 1 2 1 101000 f 74 goat snp21421-scaffold209-723340 14 75769476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799307 Affx-122972913 AX-385286237 14 16835503 GTTCCAAGAAGACAGAACTCTGTCTTAATAATCAG[C/T]GTGTCCTCAGTTTTTATGAGACCAACCCATATATA Y 2 1 2 1 101000 f 74 goat snp21420-scaffold209-690447 14 75736564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403411 Affx-122957760 AX-123273764 14 16870767 AGCCACTAGACAACCAGAGAAGTCCCAAGCGTTGC[A/C]TAGGTAGGCGAGAAGAAGGGGATCTTCCTGGATGG M 2 1 2 1 201000 f 74 goat snp21419-scaffold209-655183 14 75701074 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766141 Affx-122977845 AX-385253545 14 16908569 CTTGGTGATGAACCTGTTTGGACTGTCTCATGTCC[A/G]TTCTCCCTGTCTGGCATACTTTGCCTGATTTCTGC R 2 1 2 1 101000 f 74 goat snp21418-scaffold209-617381 14 75663985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382907 Affx-122973403 AX-123253265 14 16961488 TGGGAAATGTTCAAGCTCGGGTTCACATTTGGCTC[A/G]TCATCGACCTGTGCAACCCTGGAAAACACACCTAA R 2 1 2 1 101000 f 74 goat snp21417-scaffold209-564462 14 75611199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422532 Affx-122943276 AX-123292878 14 17027015 TCACAAGCACTTTTCTCAGCTCTTTGCATGGGTCT[A/G]TCATATCCGGAAAACATCACCCTGAGTTAACACTT R 2 1 2 1 101000 r 74 goat snp21416-scaffold209-498935 14 75546082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429242 Affx-122937911 AX-123299584 14 17160208 CCAGCAACTTAGAAGCTAAATGATCTTTGGCTTCT[A/C]TGAAACAAGAATGATAACAGCCTTTCGTAGTTACT M 2 1 2 1 101000 r 74 goat snp21413-scaffold209-365742 14 75412197 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413710 Affx-122950080 AX-123284059 14 17263582 TACTGCTGAGCCACCTGGGAAGCCCATATTTTAAT[A/G]TGATTTATTTCTATTTCCTATCCTATAGCATGTCA R 2 1 2 1 201000 r 74 goat snp21411-scaffold209-262368 14 75310108 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389862 Affx-122968151 AX-123260219 14 17330533 TGTTCCTTTTGGGGCTAGCCAAAGAGTCTGGATAA[C/T]GTACAGTTTGTTTCAAGGAGCAGTGGTGATGGCAG Y 2 1 2 1 101000 f 74 goat snp21410-scaffold209-195417 14 75243044 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439586 Affx-122930070 AX-123309923 14 17365369 AGAGATGCCTGGAATCAGACACGAAATTAATTGAA[C/T]GGTGGAGAATTGACAGAATGGAGAAGAGGCACAGA Y 2 1 2 1 101000 f 74 goat snp21409-scaffold209-160581 14 75208211 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393411 Affx-122965884 AX-123263767 14 17406815 GTGGGGAGAGATGAGAGAGGGAGAGAAAGCAGGTC[A/G]CATGAAAAAGACAGGGTGTATGGGCAATAGTCTTA R 2 1 2 1 101000 r 74 goat snp21408-scaffold209-119135 14 75166790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788927 Affx-122920487 AX-385275941 14 17464679 GTCCAGTTCATTCAGAATAAGCTAAATGTCACAAA[C/T]GACTCATTCATTTGTGAGATATCACAAATGGTGTT Y 2 1 2 1 201000 r 74 goat snp21407-scaffold209-61271 14 75109496 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409154 Affx-122953211 AX-123279505 14 17497056 CTCCTGCTTTATGACCCAGGTTAGGTAAACTAATA[A/G]CCCACTGATTGGACTCTGGTTGGCAAGATAGGGAT R 2 1 2 1 101000 f 74 goat snp21406-scaffold209-28894 14 75077353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424761 Affx-122941643 AX-123295107 14 17525664 TGGGCATTTTCCTGGAGGGTATGGGTGGGCAGCCA[C/T]GGATGGGAAGCACCTTTGCTTTTCTTGCTCCTTCT Y 2 1 2 1 202000 f 74 goat snp21405-scaffold209-286 14 75048615 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447802 Affx-122923931 AX-123318138 14 17552384 ATAAAACAGAGTCCGCTCTTGGGTATCTCAGAGTT[A/C]GGGGCGGGGGGACATAAAGATGTATGATTAAGGGA M 2 1 2 1 101000 f 74 goat snp788-scaffold1020-799084 14 75022013 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409124 Affx-122953306 AX-123279475 14 17600298 CATGGCACTTTCCTCAGTTTCCTTGGGGAGCCTCA[A/G]TTTTTCCTAAAGTTGTGGTTAAAGTGTAAACACAG R 2 1 2 1 101000 r 74 goat snp787-scaffold1020-751170 14 74973583 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789523 Affx-122923555 AX-385276532 14 17641828 TTCTGCTTCTTGAAGGGGATTTTTAGGTAAGGCAG[C/T]AGTTAGGGCATCTCAAAGGCAGAGAACAACTTCCT Y 2 1 2 1 101000 f 74 goat snp786-scaffold1020-709640 14 74932159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386701 Affx-122970170 AX-123257059 14 17715581 CTGCACGACACTCCCGTGAAATGGGTTTCATTATC[A/G]TATTTCCTCAAATCTAAGACAGCATCTATCTTCAG R 2 1 2 1 101000 f 74 goat snp785-scaffold1020-635887 14 74857897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791991 Affx-122975132 AX-385278979 14 17763768 GACAACAGGAATACAGCCTCCATCTACTGATTAAA[C/T]ATTGAGTATATTTACCTGTAACCAGATAAGCATGG Y 2 1 2 1 101000 r 74 goat snp784-scaffold1020-587700 14 74809161 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777833 Affx-122938798 AX-385264950 14 17792289 AATCATGTACAAACCTCTAGACCACGTAACATGTG[C/T]CTAGACCCTCTTTAAAGTCAAAAGTGAGGAGATGT Y 2 1 2 1 202000 r 74 goat snp783-scaffold1020-559179 14 74777784 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418645 Affx-122946335 AX-123288993 14 17825905 TGGTTGTTTTTTTTTCCTATGAAGGCAAAAATGCT[A/C]AAGCTTATATCCTTATAAAAGGCGGTGTATTAAGT M 2 1 2 1 201000 r 74 goat snp782-scaffold1020-525563 14 74744063 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418256 Affx-122947023 AX-123288604 14 17885998 ATAAGGAGAACAAAGAGGGAGACAGAGCTGAGTGA[C/T]GGAACATGAGGAGGTGAGTGCTTGCCCATTGGTCC Y 2 1 2 1 201000 r 74 goat snp781-scaffold1020-465470 14 74682609 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401331 Affx-122959270 AX-123271684 14 17925480 GCTCTTACTGAGTGCTTTGGATGTGCTGGGCACTG[C/T]GCTAAGTAAGGACTTCACCAGCTTATGAGGCTCTC Y 2 1 2 1 101000 r 74 goat snp780-scaffold1020-425988 14 74642583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395686 Affx-122963742 AX-123266041 14 17955937 TCTGGATTCGCGAATTCACCTGTTCACTTAAACTG[C/T]ATTTGTAACCTCAAAAACAATAAGTGTGAGGCTTT Y 2 1 2 1 101000 f 74 goat snp779-scaffold1020-395531 14 74612121 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399610 Affx-122961091 AX-123269965 14 18015205 ATCTCATGTGTAGAAGTTCTAAACTGACTGTATTT[A/G]CTGTAATAAAAGTTAAATGAGGTCATAAAGGTGGA R 2 1 2 1 201000 f 74 goat snp778-scaffold1020-336263 14 74561299 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393125 Affx-122965563 AX-123263482 14 18052235 CACACACACACACACACACGCTTTGGCCATGTTTC[A/G]TTTTCATTTGGAGGAACAATCTCGGGGAGGGTTAA R 2 1 2 1 103000 r 74 goat snp777-scaffold1020-299233 14 74524012 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442050 Affx-122928393 AX-123312387 14 18083330 CAAAGATGGCTCCTTCTCTCCTGACATTTTTGGTT[A/C]TTCACCTGTTGAGTGATTTTAAAAATTTCATCCTG M 2 1 2 1 201000 r 74 goat snp776-scaffold1020-268138 14 74492770 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796245 Affx-122920415 AX-385283195 14 18112972 AGTGCCACAATGAGAATTAGAGATTATTTAAATAG[A/C]GCCTATGACTCAGAACCCTGAAAAGTGAATAATAA M 2 1 2 1 101000 r 74 goat snp775-scaffold1020-238496 14 74465873 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432417 Affx-122935832 AX-123302758 14 18142118 GAAATAAGATAATATGTGATAGAAACAAAAATCAG[C/T]AGGAAAACAGCAAAATGCATTCCGCAAAATAAGCT Y 2 1 2 1 201000 f 74 goat snp774-scaffold1020-209350 14 74437273 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778829 Affx-122967546 AX-385265937 14 18179406 TTTTTAACTTTTAGCTGCCTGTCAGCATAAAAGCC[G/T]TGCATCCAGGCAACTCTCTCCGAGCCTCTGATGTT K 2 1 2 1 202000 r 74 goat snp773-scaffold1020-172062 14 74399957 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780030 Affx-122958979 AX-385267129 14 18215206 TGGCTGAAAGACATCACTATGAAGTCATTATACTT[C/T]CAACACTTGGACTTGGATGACAAGAGTTTTAGGCT Y 2 1 2 1 101000 r 74 goat snp772-scaffold1020-136262 14 74366209 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792865 Affx-122968267 AX-385279843 14 18259092 GCTGCTTGATTCTGCCACATCTAGAAATCTCAGGA[C/T]GGATTCGAGACAGAAGACGAAGTTGAGACATGCAG Y 2 1 2 1 101000 f 74 goat snp771-scaffold1020-92376 14 74323574 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419267 Affx-122946255 AX-123289615 14 18300688 CACTAAATGAGTCATTGTTTAATGGTAATATCAAG[C/T]AGTGGAAGAGAGGGGAAAGCATAAGCCAAAAGTCA Y 2 1 2 1 201000 f 74 goat snp770-scaffold1020-50780 14 74281890 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271933 Affx-1111833001 AX-519545712 14 18334377 CAGTCCTGAATATGTAAAAATGAAACCACCACCCA[A/G]TGTTCACAACAGCACTGTTTATAATAGCCAGGACA R 2 1 2 1 202000 f 74 goat 14_18334377_AF-PAKI 14 18334377 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781000 Affx-122963854 AX-385268087 14 18348728 GACCTTGGAAAACTGCACAAAGAGCCTCATGTCAA[C/T]ACTCTTATGGCCAAAGAGAGCCCGCCTTCACGATT Y 2 1 2 1 101000 f 74 goat snp769-scaffold1020-2740 14 74234666 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402797 Affx-122958288 AX-123273150 14 18401304 TCCTCTTCCACACACCTCTTCATTCCCTGCCCTTC[C/T]CCAGTTTCCCGAGTTCCTCCCCTCTCTCTCTTAGT Y 2 1 2 1 101000 f 74 goat snp27532-scaffold2931-484555 14 74183520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385235 Affx-122972098 AX-123255593 14 18439645 GTCATCGTTGGAAGGCACAAGAAGTTGCATTTAGT[A/G]TTGAAGAGACTGTGCTTCAAGTTTTGCTGAGAAAC R 2 1 2 1 101000 f 74 goat snp27531-scaffold2931-446214 14 74145795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393568 Affx-122965398 AX-123263924 14 18474270 CTTGCTACAGGGACAACTGCCTGCAGTGCCCTGTT[A/G]GTTTTCCTGATTATATAGTTGGTGACTTTGGCCTT R 2 1 2 1 101000 r 74 goat snp27530-scaffold2931-411589 14 74111351 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421947 Affx-122943821 AX-123292294 14 18527487 ACAGGCAGGAAACCTGAGTGCCTGCAGGGGCAAGC[A/G]TTGGTAACTAGAAGCTGCTGGCCGTTCCACAGGTA R 2 1 2 1 101000 r 74 goat snp27529-scaffold2931-358372 14 74062185 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431694 Affx-122936777 AX-123302035 14 18568854 CAGTCAAAAGGATCTTCGGTTTTGGAGGATTTTAA[C/T]GCTGGAACATTTTTGTTTGTTTGTTTGCTTGCCTT Y 2 1 2 1 101000 f 74 goat snp27528-scaffold2931-317005 14 74020387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395831 Affx-122963628 AX-123266186 14 18607702 TGTATGTGTGTGTGTGTGTGTGATATACAATATCC[A/G]TGCAAAGACCCCTCCCTCCGGCTCTGAGCTCCTGT R 2 1 2 1 101000 f 74 goat snp27527-scaffold2931-278157 14 73981450 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416525 Affx-122947767 AX-123286873 14 18664908 AAATCACATCATTCCTATAAGTGCTGCACATCACC[G/T]ACAGAACACACCCAGGTTGATCTGTGCCTGTAATT K 2 1 2 1 101000 f 74 goat snp27526-scaffold2931-220951 14 73924272 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774046 Affx-122966145 AX-385261185 14 18701370 GAGTGAAATGCCTTGAAAACAGGTCCACGTGTATT[G/T]CAGGCTGCAGCTCAGCCCAGTGTGGTCAGGTCTCC K 2 1 2 1 303000 r 74 goat snp27525-scaffold2931-184489 14 73888275 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779021 Affx-122954903 AX-385266128 14 18733273 ATGGGCCTGAGGGAGGCTTTGTGAAAGTAGAAGCT[A/G]TACCCAGAAGCAGACTGATGTCTGAATATCAACTG R 2 1 2 1 101000 r 74 goat snp27524-scaffold2931-152586 14 73856411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409254 Affx-122953136 AX-123279605 14 18784724 AAAATGAGTCTCCAAGTGTTGGAGATACTACAAGA[C/T]GGGGTGGAAAGGACCAAGGAAAGTTGGAAGGAAAA Y 2 1 2 1 101000 f 74 goat snp27523-scaffold2931-101135 14 73804681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427226 Affx-122939574 AX-123297569 14 18858532 ACGTGATGGTTTCCCCCTAAACTATTAGAAGACTG[C/T]GAAGTCAATTAGATTGCAGGCAAGCATTTTGAATA Y 2 1 2 1 201000 r 74 goat snp27522-scaffold2931-27327 14 73731516 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407785 Affx-122954956 AX-123278136 14 18886866 CAGATCCATCGCTTCCATTTACTTGTTCATCTGAT[A/G]CATGGGTGTGGCTCATCTGTTTGGGGGGCAGGCTC R 2 1 2 1 101000 f 74 goat snp32659-scaffold3753-908 14 73703298 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449977 Affx-122922879 AX-123320312 14 18919922 GAAATGCATCATGCAATGACAGCTGAGTTTAAAAA[C/T]GTGTTGAAAAGGAGGAAACAATGTATGCAGGGTGG Y 2 1 2 1 101000 f 74 goat snp32660-scaffold3753-33964 14 73671054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427774 Affx-122939231 AX-123298117 14 18996592 GGACTACAAGGGGAAGGGCCATGGTGCTGTGACAC[A/G]TAGCATCACTTAAGGAACTGTGGATTGGTTTAAAG R 2 1 2 1 201000 r 74 goat snp32662-scaffold3753-110634 14 73595565 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401118 Affx-122959397 AX-123271471 14 19041857 GACCTGATCTTAGGATAACGCAAAGCCCAGAGAAG[C/T]GCAGAGATGGTAAATAAATTGCCCAAGGTCATACA Y 2 1 2 1 101000 f 74 goat snp32663-scaffold3753-155899 14 73550411 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399451 Affx-122961208 AX-123269806 14 19113962 GGATATAAGAAAAGAGTAGGGAGAAGCAAGTCAAG[C/T]GACAAAATAACAATTATGTCCAGGAAAAATGGTGG Y 2 1 2 1 101000 f 74 goat snp32664-scaffold3753-228004 14 73478318 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382779 Affx-122973586 AX-123253137 14 19157151 GGGAGAGCAACCAACCTCCAGGAATGCATAAGTTA[C/T]TCTCATACCTTGAAGAATTTCCATAGGTCATACGT Y 2 1 2 1 101000 f 74 goat snp32665-scaffold3753-271193 14 73435116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445682 Affx-122926131 AX-123316019 14 19212495 AGCTTCCGAGAAAAGATGGTAATAAGGGCTAACGA[C/T]TGTCGTGTTCTTGCTGCCTTCTAGGCAGTGTTCTG Y 2 1 2 1 101000 f 74 goat snp32666-scaffold3753-326537 14 73380454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451502 Affx-122921118 AX-123321835 14 19241330 AACTCTTCAGCAGCTAAAGGTATGCTTTATCTCCA[C/T]GATACGAAATTCCCAGAAAAAAATGAAAACAAGCA Y 2 1 2 1 101000 f 74 goat snp32667-scaffold3753-355372 14 73351481 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771294 Affx-122920631 AX-385258452 14 19288464 TCATTTAGAGAAAACATACTACCATAGGTCTTTCA[C/T]AAAAGCAAACTGGCGAGGGACATCTGTGTACTGGG Y 2 1 2 1 101000 r 74 goat snp37487-scaffold459-19121 14 73305147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444884 Affx-122926268 AX-123315221 14 19323694 GGCCCTCGTGGCAGTTTGAATTACTTTTATGGAAC[A/G]TTTCTTCCCGGTTCCCTTTTGTCAGTCCTTTCGAA R 2 1 2 1 303000 r 74 goat snp37488-scaffold459-54351 14 73269808 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405551 Affx-122955966 AX-123275903 14 19365932 ACATGCAGTTTTGGTGTGGGGTGGCCAGAGAAGAC[C/T]GTGAGTTTGTTAGAAGTGTGTTGGACATGTTGTTT Y 2 1 2 1 201000 r 74 goat snp37489-scaffold459-96589 14 73227488 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403550 Affx-122957598 AX-123273903 14 19418319 TCTCTTTCTCCTTCTGGGAGAGTACAGGGCCCCTC[A/G]TGTTCAGGAAGGGACTTCCTCTGCCCCTGAGAGGC R 2 1 2 1 202000 r 74 goat snp37490-scaffold459-148976 14 73176479 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378185 Affx-122976948 AX-123248544 14 19475837 CACTTTTTTCTGCTTGCCAGCTTCACTCTTGCAGC[A/G]CAGCCTTCCCACAGGAGTGGAAACATGCTTGCTAC R 2 1 2 1 101000 f 74 goat snp37491-scaffold459-206494 14 73120331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394109 Affx-122965346 AX-123264464 14 19514007 TGCAGGAAAAGTTCCACTCGCTGGTCCAAGGCCTC[A/G]TTGACTCCTGCTATGAAACTCCAGTCCCACCCAGT R 2 1 2 1 101000 r 74 goat snp37492-scaffold459-244664 14 73083616 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442211 Affx-122928785 AX-123312548 14 19548336 TGCCTCTAATTGAACTAACTTGCCATCACAGTGAC[A/G]AGATGGGGAAGGAATCAGTTGATTGCCTGGATCTG R 2 1 2 1 101000 f 74 goat snp37493-scaffold459-278993 14 73049259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425493 Affx-122941483 AX-123295839 14 19595236 TACAGGCTGCTGTTAAACCATCAAGGATGTTTGCA[C/T]GGAGACTTCCTTAGAGAGGTGGTTTTTAGTTGTGA Y 2 1 2 1 101000 f 74 goat snp37494-scaffold459-325893 14 73002344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424836 Affx-122941358 AX-123295182 14 19599177 CTGACGGTCCGGACAAACAGAAACCAACTCATGGC[A/G]TGATGGTAAGGACCATGATGTAAGGAGGTTTGGAG R 2 1 2 1 101000 r 74 goat snp16258-scaffold171-492772 14 72998388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798530 Affx-122923492 AX-385285463 14 19631788 TTGCCTGAAACCCAAGACCCTAAAGGATAATCAAA[C/T]GCAAGGCCAAGTTTATCCCTGAAACTCAAAACCCA Y 2 1 2 1 201000 r 74 goat snp16257-scaffold171-460161 14 72965810 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274552 Affx-1111834290 AX-519548142 14 19647069 GCTGGCTTTAAACCAATAGAACCGAAAAGAAATTA[A/G]GCTGCAGATAAGAAAAAGGAGCAAAAGATTCTACA R 2 1 2 1 101000 r 74 goat GoatD01.029064 14 19647069 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407568 Affx-122954673 AX-123277919 14 19678689 AGAACAGTGTGAGGCATCAAGATGAAGGCAGACTG[C/T]GGAGCTAAAGGAGGCTCAGCCTCTGCCTTCAAGTG Y 2 1 2 1 101000 f 74 goat snp16256-scaffold171-413260 14 72919046 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413995 Affx-122950279 AX-123284344 14 19733084 TGGCTCCATTGCAGCTGGCACTGTAACTTTGGCTC[C/T]TGACCAGGCAAAAACGTTTCAGCATTTAATAGGCC Y 2 1 2 1 201000 r 74 goat snp16255-scaffold171-358865 14 72866821 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451513 Affx-122921109 AX-123321846 14 19772637 TTTAAACATCTACATTTTTAATACCCTAAAAAGTC[A/G]TCATTAATTTAAAGGAGATAAGGTTGTAAGAAGCA R 2 1 2 1 101000 r 74 goat snp16254-scaffold171-319312 14 72826581 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773200 Affx-122927350 AX-385260343 14 19817586 TAGAAATTGGAACAAATACTGGACTAAACCTAAAG[C/T]GGAGCTATTTTGAGCAATTCGGGCTATAACCAAAT Y 2 1 2 1 101000 r 74 goat snp16253-scaffold171-274363 14 72781460 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450029 Affx-122922839 AX-123320364 14 19876000 ATCTCTGCACATGGTCATTGGGAGAGAGTAGAAAA[C/T]ATATTTTTAGATATTAATGTTTGCTATTAATGTTT Y 2 1 2 1 101000 f 74 goat snp16252-scaffold171-215949 14 72721903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414224 Affx-122949642 AX-123284573 14 19957395 TTGATGTTAAACATGTAGGCAGCCAGTGATGTCAA[C/T]GGTATGACCTCTAGAAAAGTATATGAAACCACACC Y 2 1 2 1 201000 r 74 goat snp16250-scaffold171-134554 14 72640337 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399649 Affx-122960522 AX-123270004 14 19993988 AGTTATTTGTAAAGACAGACTTAAACATCATTTGC[G/T]ATTAATTAGTTTGCATACTGGAGTCCCAATCACTG K 2 1 2 1 101000 f 74 goat snp16249-scaffold171-97961 14 72603792 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784022 Affx-122924732 AX-385271075 14 20030108 ATGTGGAACTGGGTCTTGCACATGGTAATCCAAGT[A/G]AAAATATAACACTGGGTAGGGGAGAATGCCCATTG R 2 1 2 1 202000 r 74 goat snp16248-scaffold171-61841 14 72567813 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771857 Affx-122922315 AX-385259013 14 20074167 TGGACACAGAAACTAGTACACTGATTAAAGTTTGT[A/C]TGTACTTATTTGATCCTCTCTAATTCCAAACCCCT M 2 1 2 1 101000 f 74 goat snp16247-scaffold171-17782 14 72523635 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784405 Affx-122973221 AX-385271454 14 20100294 AAGTTAAAAAGTGGGCTGAAATATGACAAATAAAA[C/T]ATGATCTCAGGTGTGTAAAAAAGGATGCAAGGGAG Y 2 1 2 1 202000 f 74 goat snp40975-scaffold527-1335605 14 72497694 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404160 Affx-122957076 AX-123274512 14 20178304 CAAAGCCCTCAGATCTGTTTACCGGAAAGACTGTT[A/G]CTTTGTCTTCTTCCATACTTTTCTTTCTGCTCCTA R 2 1 2 1 101000 f 74 goat snp40973-scaffold527-1257595 14 72418344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449973 Affx-122922882 AX-123320308 14 20208042 TCAGATTCAAGAAAGTACATTTGTTCTGATTTGTT[A/G]TCCTAGTTATGAAAGCTTCTTGCTTCCAGCAGAGA R 2 1 2 1 101000 r 74 goat snp40972-scaffold527-1227857 14 72388319 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276925 Affx-1111835589 AX-519550433 14 20228777 TGATGGCTAATTCACGTGTCAACTTTGATTAGGCT[A/G]CAGAGTGCCCAGATGCTGATCAAACATTATTCTGG R 2 1 2 1 101000 r 74 goat Random2.2K-1405 14 20228777 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38410539 Affx-122952157 AX-123280889 14 20249782 GGTTGAAAGTTGAGCAGGGTTAGAGGGCCGCTGGG[C/T]GCCAAAGAGGAGGGAAAAGAGCAAGGCTTTCCTCA Y 2 1 2 1 201000 f 74 goat snp40971-scaffold527-1186117 14 72345928 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796453 Affx-122937036 AX-385283403 14 20306597 CCTTCATGTTTTGGAAACCACAGTGTTTTCTGTCT[A/G]GGGAATTAATGATCTCTCTTTCGCAAACAGCTGGG R 2 1 2 1 101000 f 74 goat snp40970-scaffold527-1129302 14 72288018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408641 Affx-122953479 AX-123278992 14 20337931 TCAGAGAAGACAGGAAAAAAAGAGCAAAGAGAGAA[C/T]AAGGCTTCCATAAGTGATTTGTTTTATTTGATCCT Y 2 1 2 1 201000 r 74 goat snp40969-scaffold527-1097968 14 72256563 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449877 Affx-122922356 AX-123320212 14 20399387 GCCTGGTGCTCTGGCGTTGAGCCACTTCTAGGTCA[C/T]GGTGAAAACCACAGAAGATGGTTTTTCCAATATAT Y 2 1 2 1 101000 r 74 goat snp40967-scaffold527-1036512 14 72195770 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444996 Affx-122926650 AX-123315333 14 20451617 CTTATCAGGACAGGATGCAATGAGCTGTATGAAAT[A/G]TAACTGAGCTGGACATTTAGAGCAGACTATTTTTA R 2 1 2 1 101000 f 74 goat snp40966-scaffold527-984282 14 72143635 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400983 Affx-122960096 AX-123271336 14 20534137 CTTTGATCCCCAATTTGAATTTCACCATGATTTTA[C/T]GAAGGAAGCCAGTAAATAGAGTTCTCATGCTCTAT Y 2 1 2 1 101000 r 74 goat snp40964-scaffold527-901762 14 72061080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420463 Affx-122944881 AX-123290810 14 20564519 AACGGATCTGACTTTCCCAGCTGTTTCCTGGACCA[C/T]ATCAGGTAGGGGAAAGGGACATTTCGTACGTGTAT Y 2 1 2 1 101000 r 74 goat snp40963-scaffold527-871380 14 72030798 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415028 Affx-122949020 AX-123285377 14 20602398 AGGTTGTGAGCCGCACAGTCATCAGTGTCCAGAAT[C/T]ACAGGGTGCCAGGAGATTTGCTCCAGAGAGCGTCA Y 2 1 2 1 202000 r 74 goat snp40962-scaffold527-833501 14 71992671 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387582 Affx-122970267 AX-123257940 14 20662676 GTCTTTGTGGCCCTAGGGAGGATCTGTGGACAGAC[A/G]TGCTTTCTCAATGATTTGGATTGGTTTCCAGGTCA R 2 1 2 1 101000 r 74 goat snp40961-scaffold527-773223 14 71932036 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404984 Affx-122956400 AX-123275336 14 20697701 CTGCAGTGTTTTAGGATAATTACATTTCATTCCTA[C/T]AAACCACTATCTATTGTTCTAAAGGATCAAAATAG Y 2 1 2 1 101000 f 74 goat snp40960-scaffold527-738198 14 71897038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463320686 Affx-1109926216 AX-514805564 14 20838004 ATTTATTTATGGCTGTGCTGGGTCTTTATTGCTGC[A/G]CATGGGTTTTCTGTAGTTGCGGTGCTCAGGCTGCT R 2 1 2 1 103000 f 74 goat 14_20838004_AF-PAKI 14 20838004 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38429492 Affx-122937871 AX-123299834 14 20848383 TGCCATCTGTTTTATCAGTCATCAAGATGATATTC[C/T]GATTTCCCTCTCTCTGTGTACCTCACTTCTCTACT Y 2 1 2 1 101000 f 74 goat snp40957-scaffold527-587516 14 71743988 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779630 Affx-122922452 AX-385266732 14 20951205 ATGCAAAGTATGTGACTGTCCAATAAAACTGTGCT[G/T]AAAGTCCAAGGGTATTATTTACGTTAAAAAGCATT K 2 1 2 1 101000 f 74 goat snp40955-scaffold527-484694 14 71643117 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427912 Affx-122939675 AX-123298255 14 20982799 CATGAGGAAGCAACGGCACGGGAGTCCAGAACCCT[A/C]GTGAAGGATGCCTAGGCTCCGCCAAGGAAGCTCTG M 2 1 2 1 101000 r 74 goat snp40954-scaffold527-453100 14 71610880 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802629 Affx-122948216 AX-385289530 14 21028828 GACAAAAATATCCCCAACAATTCCTAGGATATTTG[A/C]TCCATATGTATCAAATATCTGTGTTAAACTACACA M 2 1 2 1 202000 f 74 goat snp40953-scaffold527-407071 14 71567132 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409625 Affx-122953540 AX-123279976 14 21060060 CCCCTTTAAGACCCTTAAAGCCATATAATAAGACC[C/T]GCTGGACTCAAAGCGCTAAGCCGAGTCTTGCTTTG Y 2 1 2 1 101000 f 74 goat snp40952-scaffold527-375839 14 71535890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419958 Affx-122945204 AX-123290306 14 21093624 GGTTTAAGTGATGGGAGTTAAATAAAAGGTGCTTA[G/T]AACAGTGCCTGGCAGGCGGCACATGCCCCTAAATT K 2 1 2 1 101000 f 74 goat snp40951-scaffold527-342275 14 71502050 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402295 Affx-122959098 AX-123272648 14 21123052 ATAAATCCTCACCTATCACGGCAATACAATACAGA[C/T]GAACCAAGAAGGAACAGCAAGAGGAACCTGCGGGA Y 2 1 2 1 101000 f 74 goat snp40950-scaffold527-312847 14 71472651 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425729 Affx-122940755 AX-123296075 14 21235286 AGGAAGACGCTGTAAGCCAAGGACTTGATCCCCAG[C/T]GGGAACTGAAGCCCTGTTAACAGAGGGACAGGACG Y 2 1 2 1 201000 r 74 goat snp40948-scaffold527-200613 14 71360759 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448610 Affx-122923385 AX-123318946 14 21270425 AACCATGTGAGGTTTTAGCACAAAGAAACAGGAAG[C/T]GGGCCTTCACCAGACACTAAATCTGCCAGCATCTT Y 2 1 2 1 101000 f 74 goat snp40947-scaffold527-165474 14 71325868 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779356 Affx-122959148 AX-385266460 14 21302969 AAATACAATTTACATATGTTGGGAAACAACTTTCT[A/G]TAGTTCTATGTTTTTAACATGCTGCAAGCAGAGGT R 2 1 2 1 101000 r 74 goat snp40946-scaffold527-132930 14 71293241 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389919 Affx-122968106 AX-123260276 14 21341345 ACGATCTCTGAATTTCAGATGAATAAATGAACCTG[A/G]TACAAAATACATAAAAGATTTTTCACATTATATAA R 2 1 2 1 101000 f 74 goat snp40945-scaffold527-94554 14 71254860 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413389 Affx-122950126 AX-123283738 14 21377155 AGTAACATTTTATTTATGGACACTGGAATTTGAAT[A/G]TCATGTATTTTACACATGCCACAAAATATAGTTTT R 2 1 2 1 303000 r 74 goat snp40944-scaffold527-58744 14 71219471 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451595 Affx-122921643 AX-123321928 14 21409171 TTTAGGTCTCGGAGGGGCTGAGTTGAGTTCAGACC[G/T]AAAGAATAAAAGAAGCAAGCAAGAGCAGGATGAAA K 2 1 2 1 101000 r 74 goat snp40943-scaffold527-26728 14 71190313 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435972 Affx-122933517 AX-123306311 14 21451750 AGAGGCAATCAACTCATAGGGGTTTGGATGTGTTA[C/T]GCTTTCATTCACAGAGCATGTTTATTTAGTGTCTA Y 2 1 2 1 101000 r 74 goat snp53475-scaffold810-672910 14 71146461 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399212 Affx-122960605 AX-123269567 14 21506842 GCCTTTATAAGTAAAAGAAATACAAATTTAAATAG[C/T]GTGAGGAATAGTGACAAGTTGAGGACATTTATACA Y 2 1 2 1 101000 r 74 goat snp53474-scaffold810-617818 14 71091347 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377579 Affx-122977434 AX-123247938 14 21559577 TCAAAACCCACAAAGTAAATAAATACTTCTGAGAG[A/C]AGCCAATAAAGCTGAAAATAGTGACAACCCATATA M 2 1 2 1 101000 r 74 goat snp53473-scaffold810-565083 14 71038775 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406311 Affx-122955464 AX-123276663 14 21591393 ATTCCACTACACATACTCAACTGACTGGCAAAAAT[A/C]GACGGTTACACTAGTTATTTTAGAGAGTGAGTGGA M 2 1 2 1 101000 r 74 goat snp53472-scaffold810-533267 14 71006537 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416888 Affx-122948076 AX-123287236 14 21623688 TTTTTTGTGAGGAGATTCTGGGCTCCTCAGAGCAC[A/G]CTTGAGTCTTCTATGATGTGAGAATTGTATACCTT R 2 1 2 1 201000 r 74 goat snp53471-scaffold810-500972 14 70973869 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781169 Affx-122927480 AX-385268254 14 21659750 CAAAGTATGCCATGTAAGAGATACTTTTGATGAAA[C/T]GTTTACATGTTCTAGGATCTATATTACTCTTTTGC Y 2 1 2 1 101000 f 74 goat snp53470-scaffold810-464910 14 70937733 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414256 Affx-122949619 AX-123284605 14 21690917 ATCTCAATATTGGTCTCATCTCACACTGAGCCTCA[C/T]GAATTAAATCAGAGATGTGTGATGAATCCTTTGGT Y 2 1 2 1 600000 r 74 goat snp53469-scaffold810-433743 14 21690917 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791578 Affx-122949619 AX-385278569 14 21690917 ATCTCAATATTGGTCTCATCTCACACTGAGCCTCA[C/T]GAATTAAATCAGAGATGTGTGATGAATCCTTTGGT Y 2 1 2 1 101000 f 74 goat snp53469-scaffold810-433743 14 70915840 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799618 Affx-122950392 AX-385286548 14 21751772 AACTATCATCATATGTAACTGTGTCTAATATCCTG[C/T]ATCCCTTTTCCCAAATCCAAAAATAAAACAGAAAT Y 2 1 2 1 101000 r 74 goat snp53468-scaffold810-372888 14 70854819 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406269 Affx-122956091 AX-123276621 14 21804326 TCACTATCTCCACCCTGTGGAAACTGGGGACCTCC[A/G]TACTTCAGAAGACTGGCACATCAGGTGAACTGAAC R 2 1 2 1 101000 r 74 goat snp53467-scaffold810-320334 14 70804592 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434219 Affx-122934847 AX-123304560 14 21849016 ACATTGCAGTGTCTGTCCTTTTTCATCAGAAAAAC[A/G]AAACCTCTTTGAGAATTCTGCAGGAAATTTTCATT R 2 1 2 1 102000 f 74 goat snp53466-scaffold810-275644 14 70759614 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436064 Affx-122932705 AX-123306403 14 21884949 AATCAATAAGATTCTCTGGAGGAAAGCCGTAAATG[A/G]CTTCCTTTTTAGAATTTTATCACTAGCTTTCCCGT R 2 1 2 1 101000 r 74 goat snp53465-scaffold810-239711 14 70723439 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433723 Affx-122934521 AX-123304064 14 21916953 CTGAGAAACCAGCAGTAAATACTTGTGGGGAGACA[C/T]GAGGATGAACGACAGGACCCAAGAGGGTGTTCAGA Y 2 1 2 1 201000 f 74 goat snp53464-scaffold810-207707 14 70690593 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778361 Affx-122927126 AX-385265476 14 21947734 CTTGACCCTGAATTTCCTCATTGGTGATATGGGAT[A/G]ACAGTAACCTCTCCAACAGGTTGTTATAAAAATTA R 2 1 2 1 101000 f 74 goat snp53463-scaffold810-176926 14 70659882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417813 Affx-122946809 AX-123288161 14 21977849 TCCACCCTCCCCACCCTGTTTCAGGAGCAAGCATG[C/T]ACATTCCTCATGAGCGGAGTTCTGGTTTCCTCCAG Y 2 1 2 1 101000 r 74 goat snp53462-scaffold810-146811 14 70629873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773903 Affx-122942957 AX-385261042 14 22014110 CCCCAGCTTTATATCACAATATTCCCAACCTAAAT[A/G]AGGGTAATAACAATAAGAGATAACTCTTATGATTA R 2 1 2 1 101000 f 74 goat snp53461-scaffold810-110550 14 70593612 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378127 Affx-122977132 AX-123248486 14 22042715 GGCGATGGAGGCAGAGGGAACAGAGATGAATGCTC[A/G]TGTTAAAGATCTATGGCCTTTTCTTTCTCAAGAAA R 2 1 2 1 101000 r 74 goat snp53460-scaffold810-81945 14 70563290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377130 Affx-122978237 AX-123247489 14 22086145 AAGATCCTAGTTTCTTCCTATTAACAGAAAAGTTA[G/T]AGCCCAAGGTAATACAGGATGAATTTGAGGAGCCA K 2 1 2 1 101000 f 74 goat snp53459-scaffold810-38515 14 70519636 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421349 Affx-122944062 AX-123291696 14 22114804 AGGCCATTAATTTAGAGAAAATTGAGCATATTTAT[A/G]CATACAATAAAACTTACTATTTACTGAGCACCTCT R 2 1 2 1 101000 r 74 goat snp53458-scaffold810-9856 14 70491002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412341 Affx-122950837 AX-123282690 14 22132188 AAGAATACTTGAAGACTGTTTTCTTTTTTTTCAAA[C/T]GCAACTTATTATACTGTTTGATTCTCTCCATGAGT Y 2 1 2 1 101000 r 74 goat snp43187-scaffold574-2082617 14 70473736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453703 Affx-122919688 AX-123324036 14 22162099 ATAGGCTGTGTGCTCACAGGTCTTTCTCTTAAGGA[C/T]GCCCAGAGAGGCCCCTTCCAGAAAGTGTGTCCCTC Y 2 1 2 1 102000 f 74 goat snp43186-scaffold574-2052706 14 70443617 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413575 Affx-122950585 AX-123283924 14 22215924 TCATCTTTCCTCCCTCAATGACCATCTCAAGCTTC[A/G]TCCTTAGGGGCACAGTCCCTGATCCATCCTAGTTT R 2 1 2 1 101000 f 74 goat snp43185-scaffold574-1998881 14 70389751 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404849 Affx-122956624 AX-123275201 14 22247230 TCCTGGTTGAGGACAGAACATTCCCATCTACAGGG[C/T]ATTCATTTCAGGTCTGCTGTCTGGAAACAGATCTT Y 2 1 2 1 101000 r 74 goat snp43184-scaffold574-1967575 14 70358535 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773956 Affx-122924537 AX-385261095 14 22276157 CTTTGTTGCTTATTATGTAATTGCTAACCTTTTTC[A/G]CCTGTTCCAAGACCTCATTCCATCAACCATCTTTG R 2 1 2 1 101000 r 74 goat snp43183-scaffold574-1938648 14 70329323 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780685 Affx-122942503 AX-385267775 14 22324943 TTGACTTTATGCCTTCTGCTGCTAGCAAAGCTTGT[A/G]CCAGATGTGGGCTGGTAGGCACATGGAACTCAAGC R 2 1 2 1 202000 r 74 goat snp43182-scaffold574-1889862 14 70280393 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782883 Affx-122968730 AX-385269953 14 22376646 TGATGCTTGTGATGCCAAAGCAATTGGGTTAAGAA[C/T]ATGGTTCTTCAAGAGTTTTACTAACATGGATAAGA Y 2 1 2 1 101000 f 74 goat snp43181-scaffold574-1838159 14 70228836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398261 Affx-122962183 AX-123268616 14 22409322 GCCACCGTGGAAAAGAAGGATAAAGAATGGCTTTT[A/C]AAGGAGACACCAACAATGGTTTGGCCTCTGGGTCA M 2 1 2 1 101000 r 74 goat snp43180-scaffold574-1805483 14 70197225 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791937 Affx-122948949 AX-385278928 14 22466281 AGTGCTGGTTCTCACCAGAAAGAACTGGACGAGAT[A/C]TTCACATGCACAAGATCAGAGACAATGATATTTAT M 2 1 2 1 101000 f 74 goat snp43179-scaffold574-1748524 14 70140710 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415455 Affx-122949172 AX-123285804 14 22500263 AGTGAAGAGAACAGGCATTTATAAACTTAACCATA[C/T]GGCAAGAAAAGCAAAGTATTCTGACAGGGATCCTA Y 2 1 2 1 201000 f 74 goat snp43178-scaffold574-1714542 14 70106770 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382781 Affx-122973585 AX-123253139 14 22537064 TAAAGTGTATCATTCTTATAAATTCAATGGAAAAT[A/G]CTTATAGTGTTTTAAGCTTGAAATGGTGGCATTAT R 2 1 2 1 101000 r 74 goat snp43177-scaffold574-1677741 14 70069490 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429919 Affx-122938102 AX-123300260 14 22571596 TTTATGAGGTGAGCTGATGTCAGAGGAAGTTCCTT[A/G]TTAAGTGCAGGATTCTTTGTATTCCATCTTCTTAT R 2 1 2 1 101000 r 74 goat snp43176-scaffold574-1643209 14 70035118 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451808 Affx-122921486 AX-123322141 14 22614635 AATTACATTAATGGAAATACACTGAGTAGATGACC[A/G]TCTTGCACATCTTCTTATCGCTTCTAAGGGTACTC R 2 1 2 1 101000 r 74 goat snp43175-scaffold574-1600170 14 69992004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389141 Affx-122968546 AX-123259499 14 22645409 GAATTTCCACTGTATCTTCAGAAATAAGACCATTA[A/G]AAGAGAACTTCCTATCTCTAGATTATACTGTTAGG R 2 1 2 1 101000 r 74 goat snp43174-scaffold574-1569396 14 69962419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440496 Affx-122929361 AX-123310833 14 22693537 AATTATAGTCCAGTTTGTGTTGTGGAATGGGTGTT[A/C]TACAAAGTCTGCAACTGTTATTAATACAAGCAGGT M 2 1 2 1 101000 f 74 goat snp43173-scaffold574-1521268 14 69914305 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384463 Affx-122973086 AX-123254821 14 22732246 TTCCATTCAGCAGACATCTATCGAATGCCAAAAAT[A/G]TGCTCTGCTTTTCACACACAGAGACAAATAAGAAC R 2 1 2 1 101000 f 74 goat snp43172-scaffold574-1482559 14 69875025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454018 Affx-122919424 AX-123324351 14 22762517 GAAGGTGGAGCTGGGGTGGGAAGGGGGTCAATTCT[A/G]TCAGTAAATTCAGATGCAGAAGGACAGAGAGCAAT R 2 1 2 1 101000 r 74 goat snp43171-scaffold574-1452288 14 69844733 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376667 Affx-122979004 AX-123247026 14 22806373 AGCTTGCTGCCGAACCTCACACTGGCCAAAAGGGC[A/G]CTTCTGCAGGTGGACCGCCTTTTTAAAAAATTTTT R 2 1 2 1 101000 r 74 goat snp43170-scaffold574-1408432 14 69800554 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414236 Affx-122949633 AX-123284585 14 22837272 TCTCACTTGCTTAAAGCCATTTGTGTTGTTCAGTC[A/G]CTCAGTTGTGTCCGACTCTTTGCCACCCCATGGAC R 2 1 2 1 103000 f 74 goat snp43169-scaffold574-1377533 14 69769958 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448004 Affx-122923734 AX-123318340 14 22865853 TGTCCAGCCCCAGACCAGCCTCTGGCAAGGGGAGT[A/G]CAGCAACCATGATGAGCTGTGAAGGACCGTGATTC R 2 1 2 1 201000 r 74 goat snp43168-scaffold574-1348952 14 69741297 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431486 Affx-122936252 AX-123301827 14 22901159 TTTGCAGTTCACTTCCTTGAACAGAGAGCTAATCC[A/G]CTCTGGGCTTCAGTTTCCTCAGCTCAGTGCAGGGG R 2 1 2 1 101000 f 74 goat snp43167-scaffold574-1313646 14 69706406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405605 Affx-122957425 AX-123275957 14 22957021 CTGCAAAATGATCTCTTTTCGTAGACATATTACTG[A/C]TGAGAGCACTGAAGCTCAGAGAGGTTAAGGAATTT M 2 1 2 1 201000 f 74 goat snp43166-scaffold574-1257784 14 69650544 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791514 Affx-122933444 AX-385278505 14 22994532 CGGTGGAGAAGAGAGGACCACCTTAAGGGCAGCAA[C/T]AGCAATCTGAGATGTGGCAATCACATACAGCATCG Y 2 1 2 1 101000 r 74 goat snp43165-scaffold574-1220273 14 69613298 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376246 Affx-122978778 AX-123246605 14 23025507 GGTGTTTACTGAGTCCTTACTCCTTACGGATTGCA[C/T]ATTCATTAACTTTCAGTGACTGCTAACCGCACCCA Y 2 1 2 1 101000 r 74 goat snp43164-scaffold574-1189298 14 69581914 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422110 Affx-122943565 AX-123292457 14 23086296 TGTTTCTTCTACCTTCATAGCAGGTGAACCCTGCA[C/T]GTGGGGACATCAGAGAGAGGTTCCTGTCCCTCAGA Y 2 1 2 1 102000 f 74 goat snp43163-scaffold574-1128509 14 69521419 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448682 Affx-122923873 AX-123319018 14 23135282 TGAAATCTTTGTGGATTTTTTCCGGGAGTTCTTGC[C/T]CTTTTAAAGGATTTTGTTTTCCGCGTTATCACCCT Y 2 1 2 1 201000 f 74 goat snp43162-scaffold574-1079523 14 69473220 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427075 Affx-122939799 AX-123297418 14 23171793 GAAATCTGATGTAGAGCATTTCTGTGAACTTGGGC[C/T]GCCACGCTTTTCCCCAACTCACTCCTGCCTCTTTC Y 2 1 2 1 101000 f 74 goat snp43161-scaffold574-1043012 14 69436594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801208 Affx-122939665 AX-385288121 14 23224200 TACTCATACCAAGTAGGCTCCAGACTACTGGTTAG[C/T]GTGAAATTCAAATCCTTATTTGTTTAAGCTCCTTT Y 2 1 2 1 201000 r 74 goat snp43160-scaffold574-990605 14 69384107 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793597 Affx-122940177 AX-385280572 14 23265839 ATATGCATGAACAACCTCACAACCTTGGCTGGATC[C/T]TTAAGACTGAAAGATTTAGCCATACTATAAACTGC Y 2 1 2 1 101000 f 74 goat snp43159-scaffold574-948966 14 69342458 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794955 Affx-122935183 AX-385281915 14 23317626 TGCTTTGAACTGACACATTGTGCCAGAAACTTGCC[G/T]AAGGTCTTTACCTGTAGTAAGCCACTTCCTCCTCT K 2 1 2 1 101000 f 74 goat snp43158-scaffold574-897179 14 69290613 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384362 Affx-122972238 AX-123254720 14 23432327 AAAAAATAATATTTGACATGCTAAAAAGATGAAAA[C/T]AAACCTGGACAATAATAGCAACAAAGAAACCTTTC Y 2 1 2 1 201000 f 74 goat snp43156-scaffold574-782478 14 69176663 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272775 Affx-1111833002 AX-519546473 14 23462610 AATCAATACATATAGAATTAAAGTTATTGCTGAGA[A/C]CTTGGGTTTACAAAGCTGAGCCTACCAACACAGGC M 2 1 2 1 101000 r 74 goat 14_23462610_AF-PAKI 14 23462610 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38381488 Affx-122974959 AX-123251846 14 23507498 TTTATCCAGAAAAATGAGCCTCCTGGGAAGGAATG[A/C]TGATACTTTGCTACATCAAGTGTTTTCTTAGTCTT M 2 1 2 1 201000 r 74 goat snp43155-scaffold574-707307 14 69102335 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797016 Affx-122937526 AX-385283957 14 23540647 AACTGGCTTCATTCAAGATTTACCAGTTGCTTGGC[G/T]GAATTAAACCATATGTTGGTAAGCATCTCTCTTTA K 2 1 2 1 101000 f 74 goat snp43154-scaffold574-674158 14 69069170 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421024 Affx-122944544 AX-123291371 14 23571703 TGGTATTCTTTCAGTTAGCATTTAGAGGAAACCTG[C/T]GGCTTAACTCCTGGAACAGGAAGTGTCTACAGAAA Y 2 1 2 1 101000 r 74 goat snp43153-scaffold574-643102 14 69041910 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422661 Affx-122943683 AX-123293007 14 23602158 GGTCTTCTCCAGCTCGAAGATGCTGTGACACAGAC[A/C]GCGGGACACATCTTATGTAGAAAATAATTCTAGGA M 2 1 2 1 101000 r 74 goat snp43152-scaffold574-612647 14 69011035 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386590 Affx-122970690 AX-123256948 14 23637595 AGGCTGTAACAGTCAGATGCCAGGAACTGGGAAAG[C/T]GTACCAGAAGGAAAGGAATCTTCCATCTGAGCCCA Y 2 1 2 1 201000 f 74 goat snp43151-scaffold574-577210 14 68975866 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398536 Affx-122961532 AX-123268891 14 23679474 TTCCCTCAATCTCTTTCAAATGTTGCTCCAGAGGA[C/T]GCTACCTAGGACACTTCCTGCAGACACATCTCCAC Y 2 1 2 1 101000 f 74 goat snp43150-scaffold574-535331 14 68933691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384453 Affx-122973094 AX-123254811 14 23712996 AGTTTACTCCCAGAACTCGGTATTAAATTGCTCTT[C/T]TATCCATTACCACACCAGCACTGACTATTACCACT Y 2 1 2 1 101000 f 74 goat snp43149-scaffold574-501809 14 68899982 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765889 Affx-986697661 AX-385253325 14 23741909 TTTTGAGAATGGTGCAGGAGCCACTTGTGAGCCTC[A/G]GGAGTGCCAGTTCATTTTTGACCTTCAGTCAGTAA R 2 1 2 1 600010 r 74 goat 14_23741909 14 23741909 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 320777936 Affx-122947265 AX-385265052 14 23792369 AGAAGCCTTTTCAACACCTGCTGATATTGTATTTA[C/T]TGCTCATTCCCTTACAGAAAGGTAAGATGATGAAT Y 2 1 2 1 101000 r 74 goat snp43147-scaffold574-422436 14 68820998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427503 Affx-122939997 AX-123297846 14 23841378 ATTGTTAGACAGAAGGCATCCAAGTTACCAGAAAA[C/T]GCACACTGGATCTTATTAAAACTAAATCTTCAGGT Y 2 1 2 1 101000 f 74 goat snp43146-scaffold574-373427 14 68772017 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408897 Affx-122953972 AX-123279248 14 23896419 GAACTTCCCCTGTACTGTGCATAAAATGTCAGGAC[A/C]CATTCAGTGAGGTGAGTTCTATTGTTTGTTAAGTA M 2 1 2 1 201000 r 74 goat snp43145-scaffold574-318386 14 68716981 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396689 Affx-122962830 AX-123267044 14 23937492 GACTTGCCAACAGATTCATAAACTTGCAGGCTCAA[C/T]GGAGCTCCCCCCAGGGAGAATCTTGTATCATGGAG Y 2 1 2 1 101000 f 74 goat snp43144-scaffold574-277313 14 68676029 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419504 Affx-122945454 AX-123289852 14 23966990 AATGGGAAGAAGTAACCTGCCTTGGCATTATCTAA[A/G]GGTGTAAAATTCAGATAAAAGTTTTCACTATACAT R 2 1 2 1 101000 f 74 goat snp43143-scaffold574-247815 14 68646603 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422389 Affx-122943394 AX-123292735 14 23997259 ATTTATTCAGTTCAGCATGTTGACTTGGCATCCTA[C/T]AGACAAATGTCAGGAGACCAATTTCTATCAGACTC Y 2 1 2 1 101000 r 74 goat snp43142-scaffold574-217546 14 68617050 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791502 Affx-122973873 AX-385278493 14 24034052 AGAGAGTATAGAATATTTACTCATTACTAGTAAAT[G/T]ATTGGTTCATCAAAGAATTTGAAGGATGAAATGTT K 2 1 2 1 202000 f 74 goat snp43141-scaffold574-180753 14 68579851 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377964 Affx-122977196 AX-123248323 14 24079482 TCTCTGCATTCTTCTGGTTCTGTACACCTGATTGG[C/T]CAGCCTTACCCTCAGCCTGATTGCAGGATGGCTGT Y 2 1 2 1 101000 f 74 goat snp43140-scaffold574-135323 14 68533802 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398628 Affx-122961467 AX-123268983 14 24116442 CAGATTCAATGACACTTCTTCCAGAAAGGTGTTTA[C/T]TCACCATTCAATGAATAAAATCACTCCACAGCCTC Y 2 1 2 1 101000 r 74 goat snp43139-scaffold574-98363 14 68496499 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418668 Affx-122946317 AX-123289016 14 24151482 CCTCCTGACACCCAGGGCCAGGCTGGTCTCCCTCC[A/C]TTGTGTGCCCACAGTCCTGCGTACCTTTCCTTCCT M 2 1 2 1 101000 r 74 goat snp43138-scaffold574-63323 14 68461531 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379250 Affx-122976260 AX-123249609 14 24190884 GCAAAAGGAAGAGGAATTAGATGAGAGCTTAGACT[A/C]TGTCTGGCTAACTATTTTCATTTCCTTCATGATGC M 2 1 2 1 201000 f 74 goat snp43137-scaffold574-23921 14 68421721 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376369 Affx-122978114 AX-123246728 14 24240057 TAAAAAGTTGTAGAACAAATAATGAGAAAAATAAC[A/G]GACAAGTATGTTGGAAGGTGATATTGATTGAGGTC R 2 1 2 1 101000 r 74 goat snp44961-scaffold612-2272124 14 68267926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391404 Affx-122966776 AX-123261761 14 24292582 ATGGTTGGTTTGGATCAGACTTCTCTTACTGCCTT[A/G]TAGACAGCCACCTTCTATTGTTGTTGTTGAGTCGC R 2 1 2 1 102000 f 74 goat snp44960-scaffold612-2219599 14 68186254 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447811 Affx-122923923 AX-123318147 14 24328432 GCCAGGGCAACTGTAATATAAAAAGCAGCAGTGTC[A/G]TTTTGACAGAGATTCTTACTCCACTTTGACTGATT R 2 1 2 1 101000 r 74 goat snp44959-scaffold612-2183749 14 68150079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770295 Affx-122923864 AX-385257461 14 24358627 ATATCGTATCAAGTGTGGCTAGCAATACCTTATCA[C/T]TGAAATATGCCTCAAGACAAAAATTTGACCTCAGG Y 2 1 2 1 101000 f 74 goat snp44958-scaffold612-2153554 14 68120413 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448044 Affx-122923704 AX-123318380 14 24401411 CACTTACAGCCTAAGAGTGCACTTTATGCTGAATA[C/T]GGCCAAGATTTGATTTCCTGTCAATCTTCACTCAT Y 2 1 2 1 101000 r 74 goat snp44957-scaffold612-2110770 14 68077965 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436516 Affx-122932944 AX-123306854 14 24449981 ACCTCTACTGTATTTTAAAGCAAGTTTGTCTGTAG[A/C]ACCCCCAGAATCAGGATCTTGGGCCAACTAATGTA M 2 1 2 1 101000 f 74 goat snp44956-scaffold612-2062200 14 68029426 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795775 Affx-122970222 AX-385282728 14 24481973 GGGATATACTTGTAGTATTGCAATGCAATGCCTAA[C/T]GAATAATGGACAGTAGATAAATGAATGAATGAATA Y 2 1 2 1 202000 r 74 goat snp44955-scaffold612-2030208 14 67997584 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442208 Affx-122928788 AX-123312545 14 24519127 AAAAGAAAACTTTGGTTCCACTGTGATTTTAGATG[A/G]TTTTATACAGGATTCTTTGCAGCCCTTTCCTTTAA R 2 1 2 1 101000 r 74 goat snp44954-scaffold612-1993054 14 67960249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390891 Affx-122967109 AX-123261248 14 24551771 TCTCACTCAGTCAGTATTTAGTGAGAGGCTACTAC[A/G]CACAACACTACGCCAGACTCTGAGGATACAAGACC R 2 1 2 1 101000 f 74 goat snp44953-scaffold612-1960410 14 67927678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385750 Affx-122971077 AX-123256108 14 24588209 TCAGGGGTCCATGGAAGCTGTGGCAGAAGAAAAAA[A/G]AGAAGAATGAGGAACACTGACTCAACTTTCCTGAC R 2 1 2 1 303000 f 74 goat snp44952-scaffold612-1923972 14 67890883 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413907 Affx-122949830 AX-123284256 14 24628428 TGGAAGTCGTAGGAAAATGTTCTGGATATGATTAA[C/T]GTTTCTATATTATTATATGTGTTTGAAGAGAAATA Y 2 1 2 1 101000 f 74 goat snp44951-scaffold612-1883753 14 67849973 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447444 Affx-122924374 AX-123317780 14 24665356 TCTAATCTTTCCTTACCCTGCTTTTCTCCTGCAGA[A/G]TTATTTGTCCAAAACCAGAATTGATTATACCACAT R 2 1 2 1 201000 r 74 goat snp44950-scaffold612-1846825 14 67813079 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402335 Affx-122959067 AX-123272688 14 24695664 CTGACAACCCTGTCTCAGGCTGAACAAATTATTTG[C/T]ACCCTGCCTGATTGGTTTCCGTGTTTGTAATTCAA Y 2 1 2 1 101000 r 74 goat snp44949-scaffold612-1816517 14 67782864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441581 Affx-122928676 AX-123311918 14 24730823 GCTGAGGGGGTCATATGCCCACCCTTGGGCCAACC[A/G]CTTTTTGCAGGGAGAATCATAAAAAATTTCCCACT R 2 1 2 1 101000 r 74 goat snp44948-scaffold612-1781358 14 67755434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765420 Affx-122940844 AX-385252925 14 24763013 GTTAGCAAACTAGTGAAGCACTTTGAAGACACATG[C/T]TAACTTTTTATGTCAAAACAAAGATCCACAGTGTC Y 2 1 2 1 101000 f 74 goat snp44947-scaffold612-1749168 14 67723160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788008 Affx-122944369 AX-385275029 14 24808707 TTAGTGACTATCAGTGAGTGACTAAAATGAGGTTA[C/T]ACCCATCACAAAATTGTTCACAAACAGAATTTTGT Y 2 1 2 1 101000 f 74 goat snp44946-scaffold612-1703474 14 67676611 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450085 Affx-122922793 AX-123320420 14 24865450 AGAAGAGGGATACTAAAATTCACAGAAACCATAAA[C/T]GTGCTGAGCCTGTTGTAACAATCATCAGGTCATGA Y 2 1 2 1 201000 f 74 goat snp44945-scaffold612-1646731 14 67619100 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408846 Affx-122954012 AX-123279197 14 24923459 AGGACTATGACATCTGCCTTGGTCATTTAACAAAT[A/G]TTATTGTGTTCCAGATCTATGCCTGGTGTGGTGGT R 2 1 2 1 101000 r 74 goat snp44944-scaffold612-1588722 14 67560716 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420984 Affx-122944570 AX-123291331 14 24953260 CCATGCTCTTCACCTCTATTCTAGGTTGCTCTTGT[A/G]TATTACATTAATGGAAGGGAAGAGAAGTTAATCAC R 2 1 2 1 201000 r 74 goat snp44943-scaffold612-1558921 14 67531208 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439093 Affx-122931120 AX-123309430 14 24982741 CCACAACATTCGCCTTCTCAAAGCCTCTTCTCTCT[C/T]CACCTGGTCAGGTACCTTTTGCCTTTTTTCTCTTT Y 2 1 2 1 101000 r 74 goat snp44942-scaffold612-1529440 14 67501766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395128 Affx-122964140 AX-123265483 14 25038989 GCCAGTCAGTCACTGAACCCTCAGACTTTAATGAC[C/T]CTCATCAAACTCTCTTTCTGTCCACGCTGAGTCAG Y 2 1 2 1 101000 f 74 goat snp44941-scaffold612-1473192 14 67445609 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793748 Affx-122928912 AX-385280720 14 25077350 TTGTTGGATGACATATGAGTCTCACATTCTAAATA[A/G]TTGTAATTATGCTTGCGTGCTCTGTCACTTCAGTC R 2 1 2 1 201000 f 74 goat snp44940-scaffold612-1434831 14 67407865 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388368 Affx-122969333 AX-123258726 14 25111863 GAAACTAAGAGAAACCTCTAAAAATTGTTTCTCTC[A/G]TATAATTCAGTGTATGAAAGACTGTCATCCTCATG R 2 1 2 1 101000 r 74 goat snp44939-scaffold612-1400318 14 67373328 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383082 Affx-122973737 AX-123253440 14 25145522 CCCAGTTTTATCACTTAGAAGCAGTGTAATCTTGT[G/T]CAAGCAACTATTCTCATCATCTTCATCTTAAAAAT K 2 1 2 1 101000 f 74 goat snp44938-scaffold612-1366659 14 67339766 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794709 Affx-122939378 AX-385281669 14 25204595 AGGACCAGGGAGGTGGAATACATTGCTCTTGGTCA[C/T]ACAGCTAGTAAATCTGGCAAGTCTAACTCTAGCCT Y 2 1 2 1 101000 f 74 goat snp44937-scaffold612-1307586 14 67280121 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452533 Affx-122920541 AX-123322866 14 25249620 CAAGGCACCTACATTCTACCAAACCACACCATAAA[C/T]GTGCCAAAGGAGCTTGCTAATGGCATCATGTGGGA Y 2 1 2 1 101000 f 74 goat snp44936-scaffold612-1262561 14 67234963 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401084 Affx-122959630 AX-123271437 14 25293921 GGATCTGAAGAGCTTGTTAAAAATGCAGATGGCGA[C/T]GGAGTCAGAATCCTGGTAGGCAGGTCCAGGAATCT Y 2 1 2 1 201000 r 74 goat snp44935-scaffold612-1218260 14 67190717 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381802 Affx-122974282 AX-123252160 14 25332626 GTCACAGGTTGGGTGGGAGATAGGGCTTGTCGGGT[A/G]AGGAGGGGGGAACTGGTTATGTGCAGAGTCATAAG R 2 1 2 1 303000 f 74 goat snp44934-scaffold612-1179555 14 67152288 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769687 Affx-122969760 AX-385256857 14 25394221 GCCTCCATCTGCCTACCATGTAGCATTCTGATAGT[A/C]TGATACCCCCAGTTAGATGGCTTTTTGAAGACAGG M 2 1 2 1 101000 f 74 goat snp44933-scaffold612-1117960 14 67090764 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389694 Affx-122968695 AX-123260052 14 25460885 ACACAGAGAAGCCACTCACTTGATAAGTGGGTGCT[A/G]CTTAAAAACATGACCTTTTCTTTCCAGGACAATAT R 2 1 2 1 201000 r 74 goat snp44932-scaffold612-1051296 14 67024203 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428431 Affx-122938823 AX-123298774 14 25497962 GGCTTTTGTTGACTGGTAAAGACTAAGATTGTATC[C/T]AGAGATTGAGTTCTAAATTTTATTCTCCATAGAAT Y 2 1 2 1 101000 f 74 goat snp44931-scaffold612-1014219 14 66987145 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449633 Affx-122923187 AX-123319968 14 25571019 AATATGAACATATATATACTACATGTTGTTCTATC[A/G]TTGCGTTTCCACTCTACATTCTGGAAATTTCTTGG R 2 1 2 1 101000 r 74 goat snp44929-scaffold612-941162 14 66913857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380653 Affx-122975218 AX-123251011 14 25601783 TCTTCACCAGTAAACAAACGAGGTATTATCTTATT[A/G]GACCAATTTTATAAAGATATTCCAAATATTCTAAT R 2 1 2 1 101000 f 74 goat snp44928-scaffold612-910398 14 66883004 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385239 Affx-122972095 AX-123255597 14 25665476 TGCACCGGGAGCAGGGTAGTCTTATCCACTGGACT[A/G]CCAGGGGAGCCCCAAATTCTATAATCTTCCATGTT R 2 1 2 1 101000 r 74 goat snp44927-scaffold612-846705 14 66819358 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376285 Affx-122978380 AX-123246644 14 25702803 ACCATTCCTCAGACTGTCCTGGCACAGGTTGTCCC[A/G]GGTTGGGTTCCTTGGGAAGCAGACTCTAAAATGGA R 2 1 2 1 202000 f 74 goat snp44926-scaffold612-809378 14 66781914 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376907 Affx-122977802 AX-123247266 14 25834675 GAGAACAATGCCAGCAGGGGGAAAAAAATTCTTAA[A/G]AGAATATCATTAATGGATTCCTTAAAATACTGGAA R 2 1 2 1 303000 r 74 goat snp44924-scaffold612-677506 14 66649610 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410318 Affx-122952482 AX-123280668 14 25882954 GCCCTACTAGATCCTGGGAAAACCCCTTTTACAAA[C/T]GGGGAAATCAAAGCCTGAAGAAGCGAAACAAAATT Y 2 1 2 1 102000 f 74 goat snp44923-scaffold612-629227 14 66601464 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408702 Affx-122953435 AX-123279053 14 25915763 GGGGTCCCTTCTAGGTGAGTTGGGTTCCAGGTTCA[C/T]GGTGGAGAAGGGAATAACCTCAATGCTGTTGCTAC Y 2 1 2 1 201000 f 74 goat snp44922-scaffold612-596418 14 66568721 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407962 Affx-122954347 AX-123278313 14 25945357 GGACCCCACACCCTGAATACACACACACACAAACC[A/G]CAGCTTTGAGAACCACTGTGAAAGGCACTCAAAGG R 2 1 2 1 201000 r 74 goat snp44921-scaffold612-566824 14 66539359 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276927 Affx-1111835590 AX-519550435 14 25972502 TGGTTGTAAGGTGCTGTCACGTTATGCTTGTGTGC[A/G]CCTGGTTTTTATAATAACACTCAGGCTGCTGCTGC R 2 1 2 1 101000 r 74 goat Random2.2K-1408 14 25972502 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424034 Affx-122942081 AX-123294380 14 25978057 GAGTGCAGTCAGAAAAGTGCAAAGACAACACCCCA[C/T]GGAGAGAAAGCATGAGCCAGGGGACACAGGGCTTT Y 2 1 2 1 101000 f 74 goat snp44920-scaffold612-534124 14 66506418 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451763 Affx-122921517 AX-123322096 14 26051420 AAGAACGTGTTACTTGGAAGTGTGTGGTTACGGGC[A/G]TGGGGGGTGGGGAGAGGGGTGCTTTCTCTTCCTGT R 2 1 2 1 101000 f 74 goat snp44918-scaffold612-460761 14 66433144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772025 Affx-122952630 AX-385259181 14 26106792 CTTCTCTGTCGCTTCATCCTTACCTTATTTCTTCC[A/G]TTGTACTTACCCTGATCTGGAATTATCTTGTGTAG R 2 1 2 1 101000 f 74 goat snp44917-scaffold612-405389 14 66377714 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395018 Affx-122964221 AX-123265373 14 26135923 CCCTCACTTCCTCTCCACTCTGGTCCTTAAAACTA[C/T]GCCATCTGTAGAGAAGACTGGCAGAGAGTGTTAAC Y 2 1 2 1 101000 f 74 goat snp44916-scaffold612-376258 14 66349585 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445745 Affx-122926086 AX-123316082 14 26240793 TCGGGCCCTGATGAGGAGCAGAAGGTCATGGGTTC[A/G]GGAAGCACTCACTGACTGTGCCTTGTGTTTATCTT R 2 1 2 1 101000 r 74 goat snp44914-scaffold612-271388 14 66244357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445451 Affx-122925347 AX-123315788 14 26272506 ATGAAACTCTTTTTCTATTTCTATATTCTTTTCAC[A/G]TCATTATCACTAAGTGAGAAGGCCTTTTACAGTTT R 2 1 2 1 101000 r 74 goat snp44913-scaffold612-239675 14 66212723 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424992 Affx-122941902 AX-123295338 14 26311064 AGCCCTCCCAGGATGTCCATCAGGAGAATGCTCAA[G/T]CCTGGTGGTTCTCAAATTTCATGTGCCTGAGAATC K 2 1 2 1 202000 f 74 goat snp44912-scaffold612-201117 14 66174099 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375638 Affx-122978696 AX-123245997 14 26363090 GTGCTCGACTTTCGTGGTTCATGTATTTGTATTGA[G/T]CTCCTGACCTTGGAGTTGATTTATAGCCATTTTAT K 2 1 2 1 201000 r 74 goat snp44911-scaffold612-149091 14 66122040 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410506 Affx-122952184 AX-123280856 14 26449419 CTATATATTCTGGTCCTCTCTCCCTTGGATAGATC[A/G]CTAGCTCTGCAAGGACCAAGATGATGGCTTCTTCA R 2 1 2 1 201000 r 74 goat snp44910-scaffold612-62762 14 66035490 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777118 Affx-122941284 AX-385264241 14 26516524 AGAAAGAACAGAGATAACAATCTATAAGACATACC[A/G]TTGTGCATAAGTGTTCCTGCTTCACATTTTGGGGG R 2 1 2 1 101000 r 74 goat snp3487-scaffold1107-1034411 14 65965268 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272777 Affx-1111833003 AX-519546475 14 26529541 ATATCATGGTAAATTTTAAGATGAAAATAATCTTT[A/G]TGGAGTAGGTAGAGAAGAATTCAGGATACTGTAGG R 2 1 2 1 101000 r 74 goat 14_26529541_AF-PAKI 14 26529541 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38377656 Affx-122977856 AX-123248015 14 26560841 TTGCAGCACAGTACATGGTTTTTACTAACAAAATT[A/C]GCTGCTTTTTAAAATTATACTTATTTTAATGAAGT M 2 1 2 1 101000 f 74 goat snp3486-scaffold1107-990094 14 65921188 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780036 Affx-122961833 AX-385267135 14 26606403 CTCCATTGGGTATATTTAAGCACAGTTTCCATCTT[A/C]TAAGAATATTTAGTAATTTCACCATGTAGCTACAC M 2 1 2 1 101000 f 74 goat snp3485-scaffold1107-944532 14 65875377 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452177 Affx-122921234 AX-123322510 14 26656356 GATAGACACTTGGAATCAGACCCAGACACCTTACC[A/G]TGGCCTATGGATTCCTGTTTCTGCCCTTGCTACCT R 2 1 2 1 101000 r 74 goat snp3484-scaffold1107-894579 14 65825657 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397749 Affx-122962532 AX-123268104 14 26705553 GAGCAGATGAGATTCATCCATTTTATAGGCCAGGA[C/T]TTTGTTGTTAAGTGATCTGCCCAAAGTCCTGTGCC Y 2 1 2 1 201000 r 74 goat snp3483-scaffold1107-845382 14 65776309 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423598 Affx-122942388 AX-123293944 14 26737039 CAAAGCTAACTTTCAAGAGGGTTTCCAATTACTGA[C/T]GAGAATAAGAGGATGGAGATTTGAGTCTTTGAAAA Y 2 1 2 1 101000 f 74 goat snp3482-scaffold1107-813896 14 65744784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276929 Affx-1111835591 AX-519550437 14 26756532 TTTTTTTTTATTATGATTGACAAGCTGTAAAGACA[A/G]TCATAGAACTGAAAAACTGAGATAGGATGAAGTTT R 2 1 2 1 101000 r 74 goat Random2.2K-1411 14 26756532 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424824 Affx-122941368 AX-123295170 14 26770597 CAGCATCACTGGAGGGGTGCTGCAGCAGCTTTGCC[A/G]TAGTCCTTGGGCTCTCTCGGTTCCCACCTATTTTT R 2 1 2 1 101000 r 74 goat snp3481-scaffold1107-780338 14 65711409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796216 Affx-122971301 AX-385283166 14 26811602 AGCCAGGGAAAGAGTAGCAGAGAGATAAAGATGTC[A/G]CTTCTGATCTCTACCCAGTGAAAGAAACAATAGCT R 2 1 2 1 101000 f 74 goat snp3480-scaffold1107-739333 14 65670586 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784743 Affx-122944473 AX-385271791 14 26845117 TTTTATAGACACATTTTTCAGGGAGAAAAGGGAAC[A/G]TTACTCATGTAGGGTATTGATTAATTTATATTTTT R 2 1 2 1 102000 f 74 goat snp3479-scaffold1107-705818 14 65636924 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400331 Affx-122960050 AX-123270686 14 26881883 GGGGCCTCCTGAACTTGAGGTTGGAACTCAAAGGA[A/G]TCTGCTCTGAAGTGTGGGGTAAACATACTGGTTTC R 2 1 2 1 201000 f 74 goat snp3478-scaffold1107-669052 14 65600207 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399426 Affx-122961229 AX-123269781 14 26932511 GCCAAGAGACCCTTGGAAGATCCTGCATGGTGGTT[A/G]CAAGTTTCACTAAGAGCAAAGTTCCAACGATTCTT R 2 1 2 1 201000 r 74 goat snp3477-scaffold1107-618424 14 65551300 C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406984 Affx-122955043 AX-123277335 14 27001117 CCATGGTAGAGAAGTCAGACTGGTTCTAAGAGTCC[A/G]CAAGAGCACCCCTAGTCTCCAGAGAACAGATTTAG R 2 1 2 1 201000 f 74 goat snp3476-scaffold1107-549818 14 65482445 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394940 Affx-122964296 AX-123265295 14 27029641 CAAAGACAAAGATAATGTGGTTGGAAGGGGGAGTT[A/G]GAAAAGACTTTCTGGAGGAGGCGGCATTTAAGGTG R 2 1 2 1 101000 f 74 goat snp3475-scaffold1107-521294 14 65456044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380116 Affx-122976003 AX-123250474 14 27060143 CTCCCCTTTCTTTTCTTCTTCATTACTCAAATAAC[A/G]TCAGGATATGTAAGAAAATTTAGAAGATTCAGCCA R 2 1 2 1 101000 f 74 goat snp3474-scaffold1107-490792 14 65425533 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394560 Affx-122964455 AX-123264915 14 27102747 GTAGGCAGTCCAGGGTTGGTATCCTGTCTCCAAGA[G/T]CATCAGGAAAACTGCGTCCTTGAACTTTTCTGCAC K 2 1 2 1 101000 r 74 goat snp3473-scaffold1107-448188 14 65384181 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408512 Affx-122953709 AX-123278863 14 27136003 GGAAACAAATCCTTAAAGGTGCTCTGCCTCCTCTA[C/T]GAGTCCCTGCCCCTCTCTTTCCAACACAAAAACAG Y 2 1 2 1 101000 f 74 goat snp3472-scaffold1107-414932 14 65350969 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395699 Affx-122963730 AX-123266054 14 27197929 CCGCAGCCTTCAGAATAAGAAGCTATTTGGTGACA[A/C]ACCCAGCTCTGATGGAAAAAGCCCACCTTGGCAGG M 2 1 2 1 101000 f 74 goat snp3471-scaffold1107-353006 14 65289389 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790747 Affx-122936260 AX-385277748 14 27228381 GTCTGCAGAACTGATAACAGTTAAAGATGCAGGGC[A/G]GATTGGATTACAGTTTGAAAACATACTCGCTGTGA R 2 1 2 1 101000 r 74 goat snp3470-scaffold1107-322554 14 65258821 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381556 Affx-122974827 AX-123251914 14 27273364 AGATAAATCCCTGTGGTCTCACAGCCTCTCTAAAC[A/G]TTTTGATAGCAGAATGTGATGGATTATGAATCAGA R 2 1 2 1 201000 r 74 goat snp3469-scaffold1107-277571 14 65213856 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420055 Affx-122945131 AX-123290403 14 27334706 AGGACATCATGACCTGTTTACTAGACCCGGAATTT[A/G]TTACTCATCTGCTAAATGTTTGCCGAGTGAAAAAA R 2 1 2 1 101000 f 74 goat snp3468-scaffold1107-216229 14 65152744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412675 Affx-122950771 AX-123283024 14 27364844 GAGATTAGGGTGTGGGGTTGGAAAGGATTCCTAGG[A/G]GCAGATTAGGAAGGTTGAGATGGAGGAATTTAGGA R 2 1 2 1 101000 r 74 goat snp3467-scaffold1107-186091 14 65123017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425629 Affx-122940899 AX-123295975 14 27393474 AAGCGCTCCTCTCTCCTCTACACTTACATTCAGGA[A/G]TGTTCAGATAGAGTGTTTCACCTCTCTGAGCTCTT R 2 1 2 1 201000 r 74 goat snp3466-scaffold1107-157461 14 65094798 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444294 Affx-122926759 AX-123314631 14 27426611 CCCGTGGGGTACCTTCCAGGGGCAGTGAGAAGACA[C/T]GGGTGGTTCATCTCAAGACAAAGGTGTTGGGTGTG Y 2 1 2 1 101000 r 74 goat snp3465-scaffold1107-124324 14 65061537 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451792 Affx-122921497 AX-123322125 14 27473473 CCCCCTTTTCCAAGCCAAGGGAATGGCTATGGTCT[A/G]CTACTTGAAGATACACATCTTGACTAATGACCCTT R 2 1 2 1 101000 r 74 goat snp3464-scaffold1107-77462 14 65014573 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384172 Affx-122972420 AX-123254530 14 27526531 ATAAATGGACTCCACGGTACGTCGTTGCAGTCCAA[C/T]GAACTTGACTTTAAAGCAACAGAGGGGGCTTTGCT Y 2 1 2 1 102000 r 74 goat snp3463-scaffold1107-24404 14 64962230 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393929 Affx-122965078 AX-123264284 14 27581697 GCTTTTCTAAGCATTTTCCTCCCCACCGCACCCCA[C/T]AGTCCTGCTGTCACTAGGCTCATGTCCACGGAAGA Y 2 1 2 1 201000 r 74 goat snp6204-scaffold1218-1534225 14 64906967 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273925 Affx-1111833901 AX-519547531 14 27596770 CCCC[A/G]ACCACAGGACTATGATGACCATCCTCACGGGCATC R 2 1 2 1 102000 r 74 goat GoatD01.009894 14 27596770 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38404799 Affx-122956663 AX-123275151 14 27622052 GTTCAATTGGACTGATGTCCAAAATATCTCACTCC[C/T]GTGGCTGGCAGTGGATGCTGGCAGCAGGTTGAGAG Y 2 1 2 1 101000 f 74 goat snp6203-scaffold1218-1493870 14 64866706 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449347 Affx-122922974 AX-123319682 14 27657164 CCTATGAGACCAACAACCTCTGGAAAGCTGCATCA[C/T]GTGGGCCCCTCATCCTCTGGCTTTCCCCTGGGTTT Y 2 1 2 1 101000 f 74 goat snp6202-scaffold1218-1458758 14 64831001 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394566 Affx-122964451 AX-123264921 14 27714983 CTGAGTGACTAACACACCTCCAGGTTCAAGATACC[A/G]TGCACTAGGCACATAAGCATGGCAGATAGTACAGA R 2 1 2 1 101000 f 74 goat snp6201-scaffold1218-1400939 14 64773329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449540 Affx-122923254 AX-123319875 14 27779610 AACTGAATAAAGAGCAGATCCAAGCCCATGACTGC[A/G]GTCTTCTAGCTCTTTGTCTGGTGTGGTCTCTGTAA R 2 1 2 1 101000 f 74 goat snp6200-scaffold1218-1336312 14 64708374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451915 Affx-122921026 AX-123322248 14 27838074 AACAGATTCAAGGACTTAGATATGGAAAAAGCTTC[A/G]ATTAACATAGCAAAGACACTAGTATTGGCCATTCC R 2 1 2 1 101000 r 74 goat snp6199-scaffold1218-1277848 14 64649580 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431106 Affx-122936607 AX-123301447 14 27876152 GACACAATTCAATTCACAATGTTTGCCTACTCAAA[C/T]GAGTACATGGCAACCGTCACAGGCTTTCAATTTTC Y 2 1 2 1 101000 r 74 goat snp6198-scaffold1218-1239770 14 64611131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800698 Affx-122949547 AX-385287615 14 27989023 CTTGTTTAAATCAGACCCCTATATTCTAAAATCAT[A/C]TATAATTTTTGGCTCAGTTATTTACTATTAATTCA M 2 1 2 1 102000 f 74 goat snp6195-scaffold1218-1126899 14 64509776 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770781 Affx-122959600 AX-385257945 14 28029862 GAAGACACACTTCACCCTCAATACTCTCAATATTC[A/G]TATTTTTCTCTGGCAGAATATGTTCATTTGCAAAT R 2 1 2 1 101000 f 74 goat snp6194-scaffold1218-1086060 14 64469042 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379286 Affx-122976214 AX-123249645 14 28088119 TTTATTCAGAATATCACATTCCTTGTCTGAATCCA[C/T]TGATATTGGAGGTTCCTCAAAAGTGACATCTTTGT Y 2 1 2 1 201000 f 74 goat snp6193-scaffold1218-1027803 14 64410178 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453043 Affx-122920078 AX-123323376 14 28143025 TGAATTTTTTTCTAGCTCTGTACTGTTTGCCTCAA[C/T]GGTTCTCTTGTGAGAAAGATCCTTCATTTCATGGT Y 2 1 2 1 101000 r 74 goat snp6192-scaffold1218-972897 14 64354232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393559 Affx-122965405 AX-123263915 14 28186388 AGAGAGCAGAACAGTGCAGCAGACACAAGTCAAAG[C/T]AATTCCCTGGTGATAAGTAATTGGCAACAGACATG Y 2 1 2 1 201000 r 74 goat snp6191-scaffold1218-929534 14 64310755 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429147 Affx-122937991 AX-123299489 14 28216209 TTCCAGCAGATCTGCCTATTTTGTGAATTCTCACT[A/C]TTGTTATCCTGAAAAGGTAATCAGCAACTGGCTGA M 2 1 2 1 101000 f 74 goat snp6190-scaffold1218-899713 14 64280878 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777739 Affx-122951693 AX-385264857 14 28256918 AGAAACAATTGAAAATAGACATATAAGTACACATG[C/T]ATTCTCTGTGTATTTGTTCTCAGAGGATTATACAA Y 2 1 2 1 101000 r 74 goat snp6189-scaffold1218-859004 14 64240189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445341 Affx-122926391 AX-123315678 14 28292273 AAACTCACAGTGGGGACTGTGTGTTGAAGGGTCAA[G/T]AAGAAATATAAGGAAAAATAAAGAATATATGCTTT K 2 1 2 1 103000 f 74 goat snp6188-scaffold1218-823649 14 64205816 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405227 Affx-122956892 AX-123275579 14 28322482 CTATTTCATGTTAAAAGCTTTTCTCCTAAGTTTTG[C/T]GATCTTTAAGCCCTTAAGAAGCAGACACTTATTTT Y 2 1 2 1 101000 r 74 goat snp6187-scaffold1218-793440 14 64174934 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796979 Affx-122922010 AX-385283920 14 28361823 ACTATTTCCTTCATCTGACTATCTTTGTATATATG[C/T]AGGTTGTTTCTCTTTGCAAATTTTATACCCTCTGG Y 2 1 2 1 101000 r 74 goat snp6186-scaffold1218-754099 14 64135191 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764648 Affx-122974112 AX-385252285 14 28402272 CTAAACAATATTACCATTATGTTGTGCAAATTGAC[A/G]TTTGAATGTAGGCTTGTCTCACTCCAAAACTCAAA R 2 1 2 1 101000 f 74 goat snp6185-scaffold1218-713650 14 64094933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375498 Affx-122979132 AX-123245857 14 28458779 TTCTCCACCTTTTCCTTCTCTTTCTGACTAAAGAA[C/T]ACATATACTCTTACAGTCAGAAGACACTAAGTTAG Y 2 1 2 1 303000 r 74 goat snp6184-scaffold1218-657143 14 64038283 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421320 Affx-122944084 AX-123291667 14 28490047 CCATTGAACTTGTAAGATTAGAATCTGGGAGTTAA[C/T]GCATGTTGAATGGGATGGAGTTATATAAGGCAGGC Y 2 1 2 1 101000 f 74 goat snp6183-scaffold1218-625875 14 64006342 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390517 Affx-122967243 AX-123260874 14 28538927 ATGAAAATAAAGTAGCTCCTCCTCCCTGACATCTC[A/G]TCACTGCCTGTCACCATCTCCTTTTACCCTGCATG R 2 1 2 1 101000 r 74 goat snp6182-scaffold1218-576995 14 63957552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797500 Affx-122966943 AX-385284439 14 28584160 AGCTGATTTCAGTGTTTTGGTTTAGAATTCAAAAG[C/T]GACTTGATTCTGCTAGAAAATCTAGAAAACTACTA Y 2 1 2 1 101000 r 74 goat snp6181-scaffold1218-531762 14 63912057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446143 Affx-122925764 AX-123316479 14 28617846 ATCTGCAAGAAAAATAAAAGTAAGTAAAAATAATT[A/G]CATAAAGGTGAATCTGCTGAAAATTCCAGTAAAAT R 2 1 2 1 101000 r 74 goat snp6180-scaffold1218-498076 14 63878459 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395623 Affx-122963803 AX-123265978 14 28651949 TGTCTGGTAGTTTGGGGGTAAAATATAAAGAAAAA[C/T]ACTCTGACCCCAAAGTAAAAATCTGAACACTAGAA Y 2 1 2 1 101000 r 74 goat snp6179-scaffold1218-463973 14 63844967 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396036 Affx-122963467 AX-123266391 14 28681137 TATGACCATTGAAGTAATACTAAGTCTTCCAGTCC[A/G]CAAACATGGAATTCTTTCTATTTTTGTAGAGGTTT R 2 1 2 1 101000 f 74 goat snp6178-scaffold1218-434785 14 63814837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802460 Affx-122927119 AX-385289364 14 28712099 AAAGAATCATACCCTAAATCCCACAAAAGTCATCT[A/G]CTCATCTTTGGTCATTTGTGAAAGGAATGCCAAGT R 2 1 2 1 101000 r 74 goat snp6177-scaffold1218-403823 14 63784985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439528 Affx-122930119 AX-123309865 14 28768840 TGGAGCAGAGAGTACCAGGAAGAGGTGAAGACAAA[C/T]GTAGGAAGTCAGACCTTCCTCTGTATCTATCGTAG Y 2 1 2 1 201000 f 74 goat snp6176-scaffold1218-347082 14 63727908 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781426 Affx-122957847 AX-385268511 14 28808632 GATGGGATGAGAGCTTCTACTGAGCTGTGTCCAAG[A/C]GTGTACTCAGTAGATGTTATTGTGACCAAAATGTC M 2 1 2 1 101000 f 74 goat snp6175-scaffold1218-307290 14 63687648 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781589 Affx-122952758 AX-385268673 14 28871225 TTTCTAGTAACCAGCTAATGCTAGTGATCAAATAC[A/G]TTAGTATTTAAACTTTCCATCAGTTGGGATTACAT R 2 1 2 1 201000 r 74 goat snp6174-scaffold1218-244697 14 63625472 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384601 Affx-122972574 AX-123254959 14 28905685 AGGAAGCAAAAATCTTTTCTTGAGGGGGAGGTCCA[A/G]CAGGGTTCCTGCAGCTGGAACAGGTTAGACCTTGC R 2 1 2 1 101000 f 74 goat snp6173-scaffold1218-210237 14 63589824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409389 Affx-122954147 AX-123279740 14 28948224 ATGAGTTACCATAGCTTCTCTTGAAGCAAACTGTG[C/T]AACACTTATCTAGGAAGAGTTTGAGAAAAAAAAAT Y 2 1 2 1 201000 r 74 goat snp6172-scaffold1218-167698 14 63548149 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419692 Affx-122945926 AX-123290040 14 28998234 AAAAAGAAAACTTGACAACCAGGGTGATCACATGC[C/T]GAGACAGGTTGCTGGACAAAACACAGAGGGTAAAG Y 2 1 2 1 201000 f 74 goat snp6171-scaffold1218-117688 14 63498106 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434830 Affx-122934794 AX-123305171 14 29035483 TGAGTCATGCGGAGAGGGCTACTTTGACCTGAATT[A/G]TGACTTTCAGTGCATATAGTCAAGCCCCAGCAACC R 2 1 2 1 101000 f 74 goat snp6170-scaffold1218-80439 14 63461402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272730 Affx-1111833004 AX-519546429 14 29091605 ACACTAAAATTCATGGAAATGCATATCCTAAATTA[A/C]AGTTGAATTACTGAACATTAAAATAAAACCCAAAG M 2 1 2 1 101000 f 74 goat 14_29091605_AF-PAKI 14 29091605 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791541 Affx-122965526 AX-385278532 14 29095982 GAAATATTTGTACAGTGTCAGTAAGCAATAGTGGT[A/G]TCATAGATGACAGTTTGATCAGTTTGCTGTGGTTT R 2 1 2 1 101000 r 74 goat snp6169-scaffold1218-19940 14 63400277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445329 Affx-122925423 AX-123315666 14 29129188 TTTACTACTGTAGCATCTCACCCTGTAGTTTGGCA[C/T]GGCCTCATGAGTTTCCTTGACCAGTGAAATACGAG Y 2 1 2 1 101000 f 74 goat snp13153-scaffold1501-2062871 14 63367161 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391787 Affx-122967044 AX-123262144 14 29157770 GGACACACATGTATCATGTATAAAGAAAAAGTGAT[C/T]AGAAATAGAAGCAATGGAAAAGAATTCACACCACC Y 2 1 2 1 201000 f 74 goat snp13152-scaffold1501-2034289 14 63338550 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444552 Affx-122926987 AX-123314889 14 29218066 ACTCTAATTTGTAATAATCAGACAGTATTAATGAT[A/G]ATGAAAAATTTATATCAAATTTCAAATGCATTTCT R 2 1 2 1 101000 f 74 goat snp13151-scaffold1501-1973993 14 63276718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424330 Affx-122941949 AX-123294676 14 29265739 TGATTTTGAAATGGATCTCAAGAAAGGGGCCTCCA[C/T]GGGGAAATCTCAAGCTGGCCATCTAGCTCTGTGTG Y 2 1 2 1 101000 f 74 goat snp13150-scaffold1501-1926320 14 63227719 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783638 Affx-122958466 AX-385270697 14 29338091 TTTTCAGTGTCGTTTCATTATGTTGAACTATTTAT[A/G]TCATCATAATCCAAAGCATCTTTTTTTTTATGATA R 2 1 2 1 201000 r 74 goat snp13148-scaffold1501-1853968 14 63154907 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443289 Affx-122927472 AX-123313626 14 29369854 ATGTGGCTTGCATTTGTAGTGTCTGTTATACATCC[A/G]TTGGATGTTGCTGCTCTAGAAGTATAGTCTGGTGA R 2 1 2 1 101000 r 74 goat snp13147-scaffold1501-1822205 14 63122730 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433164 Affx-122935666 AX-123303505 14 29410959 GAACATGGCCTTTGGCTGGCTCTGAAAGATGGAAT[G/T]ATCCTCATACTCCAGAAAGGGCCTCTTGGGTGAGA K 2 1 2 1 101000 r 74 goat snp13146-scaffold1501-1781100 14 63077613 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381149 Affx-122974556 AX-123251507 14 29468187 AGCCTCTCTCCTTCTGAAATAGCTCACACTCTCTG[C/T]GGCGTGTGTTTCTTTTTAAATAAATTTGCTTCTTA Y 2 1 2 1 101000 f 74 goat snp13145-scaffold1501-1723872 14 63020296 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442785 Affx-122927729 AX-123313122 14 29551278 CTTGACCTCCAGCTGCCTTGGCACTTCCAGGCCTC[A/G]TATACTCTGGTGTCTGGAAGATGGTTCTTGGTGAG R 2 1 2 1 101000 r 74 goat snp13144-scaffold1501-1640781 14 62936790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421721 Affx-122944388 AX-123292068 14 29584164 CTGCATCTGAGCTGGCTGGAGTCTGCAGATGTGGA[A/G]CCTGTAGGTACGGAGACCTGACTGTGTGCTTATAC R 2 1 2 1 201000 f 74 goat snp13143-scaffold1501-1607895 14 62903058 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395040 Affx-122964206 AX-123265395 14 29648270 AGGAGGGGCTGTTTCCATCACTGCCTGGGGAGGAA[C/T]TGTACATTGTGGGACCGGTTCCCTGAATGCCTGTT Y 2 1 2 1 201000 r 74 goat snp13142-scaffold1501-1543789 14 62838928 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396641 Affx-122962867 AX-123266996 14 29702883 TCAGTGCCTTGCTTCTGTGTGTGTATGAATAATCT[A/G]TAGATAAATACACTTGATCAGGGGACAAAATCATT R 2 1 2 1 102000 f 74 goat snp13141-scaffold1501-1489176 14 62784080 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384556 Affx-122973012 AX-123254914 14 29733461 ATCTTCTGGAGGTGGGACAAGAAAAATACCAAGTG[A/C]AACAAGTATGACTGGGTGCTGAGACTGAAGGGAAC M 2 1 2 1 101000 f 74 goat snp13140-scaffold1501-1458598 14 62753515 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789979 Affx-122963186 AX-385276985 14 29768337 GGGAAAGTCACATGTGGTCTTGTATGAAACCTGTG[A/G]ATAATCTTGTTAATGCCACTATTCATATTTATAAA R 2 1 2 1 101000 f 74 goat snp13139-scaffold1501-1423722 14 62717620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440494 Affx-122929363 AX-123310831 14 29867759 ATGATGTTCCCTAAGTGCTATGAGAACTTTATAGA[C/T]GTTTATCCCCAAATTTTCTCCTTGATTGTGATTTG Y 2 1 2 1 101000 f 74 goat snp13138-scaffold1501-1324300 14 62617968 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390484 Affx-122967594 AX-123260841 14 29903223 TTTCTATACCTGTCATAAATCTGACAGTGATTATT[A/G]TTAGTGTGAATGTTACATGTATCCAGTTTGGTAAA R 2 1 2 1 101000 r 74 goat snp13137-scaffold1501-1288836 14 62582784 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401389 Affx-122959222 AX-123271742 14 29954898 GCTCCAGACACGTCATTGTTGCCTCGAGTGTAAAT[A/G]CAACAGTGAATGCTGAAGTTCGTGGATGTAAACTG R 2 1 2 1 101000 f 74 goat snp13136-scaffold1501-1237161 14 62530578 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440093 Affx-122929718 AX-123310430 14 29998482 GTCTGAGTCAGAGGGGAATCAGGTGTGGATGGGAC[A/G]TTGAGACGAGGCTGTCCAGGTAAACCCAGTGTGAT R 2 1 2 1 201000 r 74 goat snp13135-scaffold1501-1193577 14 62486935 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391455 Affx-122966736 AX-123261812 14 30066926 GATACTGCACTTTTCTTGTGAACTCAATTTTTTCA[C/T]TTGGGTATTCAGATGATTTTTTTAAACTATAGCAA Y 2 1 2 1 101000 f 74 goat snp13134-scaffold1501-1125133 14 62417956 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423406 Affx-122942627 AX-123293752 14 30123799 AGTGCCAGTCTGCAACTGTGAACTGACCTGCTTGT[A/G]CTTGAATCTAAATGGTGTCCTGGAGCCTGAGTTTC R 2 1 2 1 101000 f 74 goat snp13133-scaffold1501-1068260 14 62360181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410398 Affx-122952428 AX-123280748 14 30177851 TGTTGGAAATTTGTTTTATTTAATAGAGAAGGAGG[C/T]ACCAGTCAGACAAGTCACCCCTTGGCTGCCTGCAG Y 2 1 2 1 201000 r 74 goat snp13132-scaffold1501-1014208 14 62305896 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424327 Affx-122941952 AX-123294673 14 30222411 ACAAAAGAGAAAGAAATGAGAGGGAAATGTAGTGG[C/T]AAGGACAGGGACAGTGTTAGAGAAATTCTGAAGGC Y 2 1 2 1 101000 r 74 goat snp13131-scaffold1501-969648 NW_017189516.1 44947713 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320797574 Affx-122978305 AX-385284513 14 30258361 CAATAGCTTTCATAATATATTGGAATAAGCCCATC[A/C]AATCTTTTAGACAAACTAAATGACACTGTATGATG M 2 1 2 1 101000 f 74 goat snp13130-scaffold1501-933698 NW_017189516.1 44911511 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399156 Affx-122960646 AX-123269511 14 30296384 GCCTCTACGACTCAGGTCAGGGCACAGAGGGACCA[C/T]GAATTGATCCTAGAAAGAGTGGAATGAAGAGAGCA Y 2 1 2 1 101000 r 74 goat snp13129-scaffold1501-895675 NW_017189516.1 44872609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770287 Affx-122938905 AX-385257453 14 30340009 CTCCTCATATTTTTGTGAGAGGAGAAAAGATGGAG[C/T]GTTGTACTCATCTTTCTAATCTTTAGGCCTCTATG Y 2 1 2 1 101000 f 74 goat snp13128-scaffold1501-852050 NW_017189516.1 44828737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391327 Affx-122967316 AX-123261684 14 30370846 AGAGACAGTGTCTGGAGTCTTGTGCACACAAGCAG[A/G]ACATCACATTGTGGATACCAGTTGAGGGTTTTAAG R 2 1 2 1 201000 r 74 goat snp12471-scaffold1476-763321 14 62276827 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793955 Affx-122923099 AX-385280924 14 30411403 ATTTTTCTCTTTCTCCAGGGGTCACTTATTCACAC[A/G]TTGGGAAAATCTGAACAACATCTGTTCAAGGGTTC R 2 1 2 1 101000 f 74 goat snp12470-scaffold1476-722764 14 62236578 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393139 Affx-122965552 AX-123263496 14 30447956 AGATCAGGAAATGCCCTGAGGCCACTGCCGAGGAT[G/T]AAATGAAGTAATGACTGAGAGGTCAAGTGAGCCCA K 2 1 2 1 101000 r 74 goat snp12469-scaffold1476-686211 14 62200111 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421132 Affx-122944198 AX-123291479 14 30479460 CCTGGGTAGAAACAGGTGAGAGAAGGACCAGTTTT[C/T]GTGCCTCAAAGCACTGGTGACTAGGGCTGCCAGGC Y 2 1 2 1 102000 f 74 goat snp12468-scaffold1476-654707 14 62168530 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379777 Affx-122975842 AX-123250135 14 30515628 TTTTGTTTTGTCCTTATGACATTTAATTGAAAACA[C/T]GATACACAGGACATGGCAACCTCAGTCCCAGATGT Y 2 1 2 1 201000 f 74 goat snp12467-scaffold1476-618539 14 62132074 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452399 Affx-122920605 AX-123322732 14 30551445 CTGTCCCAATAAACCGGCCAATCTGAAATGAAAGT[A/G]CTAGTCGCTCAGTCGAGTCCAGCTCTTTGAAACCC R 2 1 2 1 101000 f 74 goat snp12466-scaffold1476-582722 14 62097561 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397457 Affx-122962102 AX-123267812 14 30588452 CCTTTCAGTTTTTAATCATTGTATGTGGTACAGTC[A/G]CAAAGTCATGTCCGATTCTTTGCAACCCCATGGAC R 2 1 2 1 101000 f 74 goat snp12465-scaffold1476-545715 14 62060177 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776326 Affx-122961449 AX-385263454 14 30617695 CTGCTTACTAGAACACTGCTAAGGACATCGAGCCT[A/G]ATTCAAATCTCACTTGCCTAACTGCACACTGTGAA R 2 1 2 1 101000 f 74 goat snp12464-scaffold1476-516472 14 62031016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407497 Affx-122954751 AX-123277848 14 30654931 TATGTGTGTGACAAGACTATAAAATATAGCATTTT[A/G]CTTCCAATATAATGGAGAACTTATCAGAAAACCTC R 2 1 2 1 101000 r 74 goat snp12463-scaffold1476-479236 14 61992049 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440969 Affx-122928989 AX-123311306 14 30702706 TTTGTAGTTGGCAGCTATGCGGATTGTGTTGTCAG[C/T]AACTGAGATGAAAAAACAAATTGCAGGAGAAAATA Y 2 1 2 1 101000 f 74 goat snp12462-scaffold1476-431461 14 61943439 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787633 Affx-122973115 AX-385274656 14 30734482 GCTTAATATGCCACAAAGAAAATCCTGAATTACTT[A/G]CAGTTGATTTTTAAGTCTTGAATGAATATTTGAAA R 2 1 2 1 101000 f 74 goat snp12461-scaffold1476-399685 14 61911066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779470 Affx-122932537 AX-385266573 14 30764397 CAACAAATCCAAAAATTGAATGATATGGGACAAAA[C/T]AGGCTGGTATACTTAGCCAGGATCAGATTAGTTTC Y 2 1 2 1 101000 r 74 goat snp12460-scaffold1476-369770 14 61876714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410040 Affx-122953240 AX-123280390 14 30795265 GGCCACCTGCTCATTCAGGGCCCCACTTACTCTTG[C/T]GTGAGGAAAGTCAAATTTCTTTTTTGGATTTCCAG Y 2 1 2 1 101000 r 74 goat snp12459-scaffold1476-338902 14 61845849 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798507 Affx-122946584 AX-385285440 14 30826123 TGTAAAGATTTTGTGCAAAGGGACTTTTTCATTTT[A/G]TAATTTCAATGGAGTTGGAGTTATTACCATGGACT R 2 1 2 1 101000 r 74 goat snp12458-scaffold1476-308044 14 61814380 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800884 Affx-122978297 AX-385287799 14 30858542 GTAATATAAACCTCACATATCAAATGTCATGAAAA[C/T]CACACAACTACAAATTTATTAGCCACACTGAAACC Y 2 1 2 1 101000 r 74 goat snp12457-scaffold1476-275625 14 61781854 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398226 Affx-122962212 AX-123268581 14 30893281 TGTGGTCCTTGCACCTGTTCCCCACTCAGCAGACA[C/T]GTCCCAAGTTAGGTCTGACACCTTTCCTTCCAAAG Y 2 1 2 1 101000 r 74 goat snp12456-scaffold1476-240886 14 61747266 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794312 Affx-122955006 AX-385281275 14 30939932 GGTTAATTAGAATTCAATAAAAAATGCCTTTTAGA[C/T]AATTTTCCTTCTGGAAATTGATAAGGTAGAGGTTA Y 2 1 2 1 101000 f 74 goat snp12455-scaffold1476-194235 14 61700065 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399714 Affx-122960469 AX-123270069 14 30977243 AATAACGCTGAAACTATCTGTAACTTAACAAACTA[C/T]GTGTGGAAATACACACAGTGCTGACGATTTCCTAA Y 2 1 2 1 201000 f 74 goat snp12454-scaffold1476-156924 14 61663181 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766910 Affx-122936794 AX-385254227 14 31010841 TCTCCATTTGTTTTCATGAGCCCATACATCTCGCC[A/G]TATTTTCCTTAGCAGTTTAGAGGTAGAGTTCATCA R 2 1 2 1 101000 f 74 goat snp12453-scaffold1476-123326 14 61629647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400499 Affx-122961282 AX-123270854 14 31061546 TTTCTCCTCCAAGTGGATTCCATTACTCAGGTTGG[A/C]TAGAATCCCTGTCATTCATGGGGGGGATATAATCT M 2 1 2 1 201000 f 74 goat snp12452-scaffold1476-72621 14 61578995 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788146 Affx-122935192 AX-385275166 14 31111079 GGTCCTCACATAATAGACAGGGGACTACTTCCTGG[A/C]TAAACAGCTGTTGTTAGAAGATCCAGGTACATCAA M 2 1 2 1 201000 r 74 goat snp12451-scaffold1476-23088 14 61528995 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389979 Affx-122968063 AX-123260336 14 31157396 GCACATCCCCCATGGAGTGAACACTGACTCTCACC[A/G]TGAAAGCCGGACATCAGTTTCTCCTGATGTCTCCT R 2 1 2 1 101000 r 74 goat snp25076-scaffold2589-135599 14 61482899 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396864 Affx-122963246 AX-123267219 14 31219200 CCAAGGACTCGGGAACGCCAGCTGCTATAGAAGGA[A/G]GAAAACGTCTCCCTCGGTGACACCACGCCTGTCAG R 2 1 2 1 101000 r 74 goat snp25075-scaffold2589-73795 14 61420363 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445806 Affx-122926037 AX-123316143 14 31258579 TAGTATTCATACTGGTGTTTTAGAACATAACTACA[C/T]TTTCATACTATGGATACTTCTAGCAATATTCGTTG Y 2 1 2 1 101000 f 74 goat snp25074-scaffold2589-34416 9 44451584 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784905 Affx-122955896 AX-385271952 14 31299974 TTTTAAATGATATTAACTCAATAATTACAAAATTT[C/T]AATTCTTTTGTGCTTTGCAGAAATTCATCTAGAGT Y 2 1 2 1 201000 f 74 goat snp12391-scaffold1469-494295 14 61376709 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411341 Affx-122952265 AX-123281691 14 31340250 AGACCGCAAGGTTTGTGGGATTTAACCTTGTCCTG[C/T]GCCCAGTGCCATGGCATATATGAATTGCAACAGCC Y 2 1 2 1 101000 r 74 goat snp12390-scaffold1469-454019 14 61336381 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441833 Affx-122929056 AX-123312170 14 31371245 CAGTGCCTTTTGCAGAGCCTGACAAACAGTAACAC[C/T]TAGTATATAAGGTACTGAACGGAGCCTTGCGGTCC Y 2 1 2 1 101000 r 74 goat snp12389-scaffold1469-423024 14 61305461 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445430 Affx-122925365 AX-123315767 14 31409954 TTAACTTTTCGCCACGAGTAATTGAGATGTTCAAA[C/T]AAGAGACAGATAAGATTTAGTATAAGGAAAATTAC Y 2 1 2 1 101000 f 74 goat snp12388-scaffold1469-384315 14 61266633 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792802 Affx-122933551 AX-385279781 14 31462384 CACTCTTTTTTCTTTACATAAATTGAGCAGAATAC[A/G]CAATGGTAGAATGCTTAACATCTGTCTCTTCTAAA R 2 1 2 1 101000 f 74 goat snp12387-scaffold1469-331885 14 61214592 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412703 Affx-122950750 AX-123283052 14 31492183 TCTGCTGGAAAGAAGTGATGAGATGCTCCTGATTC[A/G]TCCTTTGGGTAACTGACCACATGCTCCCAGTTTCC R 2 1 2 1 101000 f 74 goat snp12386-scaffold1469-302086 14 61184789 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400256 Affx-122960137 AX-123270611 14 31520996 GAACCATGTCTTACTCATTTTTATTTTCCCTACAG[C/T]GTTTAGTCTAATACCTCAGCATAGAAAATTCTACA Y 2 1 2 1 201000 r 74 goat snp12385-scaffold1469-273273 14 61156171 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451525 Affx-122921101 AX-123321858 14 31554997 TAGTGTGTCATGTTTATTTTGATTAGAGACACCAC[A/G]TTTCCTGGAAACCACCCCCTTTTCTCTCTCCCTCC R 2 1 2 1 101000 f 74 goat snp12384-scaffold1469-239272 14 61122337 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780645 Affx-122967409 AX-385267735 14 31612636 AAATTCTAGTAAGGTTAGCAGATGAGATTAAGGAT[A/G]CCCTTAATTATTACAAATTTATGAAGAATCTACTC R 2 1 2 1 101000 r 74 goat snp12383-scaffold1469-181633 14 61064932 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769734 Affx-122973540 AX-385256904 14 31650735 CCTGCTTCTGCACAGACTCCATTTAATGTTTATGG[A/G]GATGATGGTTGACTTGAAATCAGAAGAATTTTCTT R 2 1 2 1 101000 f 74 goat snp12382-scaffold1469-143534 14 61026895 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411097 Affx-122951922 AX-123281447 14 31708518 TGGCAGGTGTGGCCAGCCCCTGAGAACACAGTCAC[G/T]AGAGTGCACAGAGAGGGCAGGTTTCCCAGAGTGGG K 2 1 2 1 201000 r 74 goat snp12381-scaffold1469-85751 14 60969335 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414908 Affx-122949113 AX-123285257 14 31747710 TTGATAAATGCATCTTGCCTGTTTTCTGAAATTTT[A/G]TTTTATGAATAACATTCAAAAAATTATACACTAGC R 2 1 2 1 103000 f 74 goat snp12380-scaffold1469-46559 14 60930118 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391940 Affx-122966926 AX-123262297 14 31792097 ATCCACTTTCAAAAGGCCAAGACGCTTTGTAAATT[A/C]TAGTGGAAAACACTACCCACGCTGAATCCAGGCAC M 2 1 2 1 101000 f 74 goat snp12379-scaffold1469-2172 14 60885777 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778597 Affx-122950914 AX-385265708 14 31829412 CTGTAGTTAAAACAATTGTATTCTTATTTATTAGC[A/G]TTGGAGTAAATTTCCTGGCTTTTCTGTATTTAACA R 2 1 2 1 101000 r 74 goat snp46143-scaffold636-404588 14 60847864 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439451 Affx-122930180 AX-123309788 14 31969984 TGACAGGTCCCATGGGCTATTTGTTGTGTGTGTGT[A/G]TGTGTATCTGTGTATCTTTGTATGTGTGTGTGTAT R 2 1 2 1 303000 f 74 goat snp46140-scaffold636-264016 14 60702098 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791965 Affx-122948623 AX-385278954 14 32061907 ATAAGCATTCTTTTCCCGTCCGATAGGGCCAGTCA[C/T]GTTTTCAGCTGAGTGCAGCAAACACTTCCACAGAC Y 2 1 2 1 101000 r 74 goat snp46138-scaffold636-172093 14 60609926 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272734 Affx-1111833006 AX-519546434 14 32140905 CTCTCAAGAGTCTTCTCCAACACTCCAGTTCAAAA[A/G]CATCAATTCTTCAGCACTCAGCTTTGTTTAAATCC R 2 1 2 1 103000 f 74 goat 14_32140905_AF-PAKI 14 32140905 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438127 Affx-122931486 AX-123308465 14 32193310 TTAGGCCCACTCCTCCAAGGACAGGCTTACACGAA[C/T]CCCATTGCTGGCCTCAATGGTGAAGATGGGGTAAC Y 2 1 2 1 201000 f 74 goat snp46134-scaffold636-40690 14 60489009 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386509 Affx-122970749 AX-123256867 14 32244541 TAACTTTGTTTTAAAAATACTTTAGGAAATGTTCT[A/G]TATTATTAAAGGACCCAGTCTAAAACCTTTATCAT R 2 1 2 1 101000 r 74 goat snp37015-scaffold449-10442 14 60437792 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427808 Affx-122939755 AX-123298151 14 32298329 ATAACACACACCCTGCTGGCTCACTTGAAGAATCC[A/G]AATTCCTTTAACAAGCTGAGCAGTAGGAACCAGCC R 2 1 2 1 101000 r 74 goat snp37016-scaffold449-64230 14 60383248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437753 Affx-122931717 AX-123308091 14 32346796 ATGACAAAGAAGATGCTTAGAACACCATGACCTCA[C/T]GAGCATTGAGGGCTGTATCTCTCTCTCCTGGGGTA Y 2 1 2 1 101000 f 74 goat snp37017-scaffold449-112697 14 60334357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772968 Affx-122965343 AX-385260112 14 32397051 CATGCACCATCTATTCTTCTCTTAAGATGTTAGTC[A/G]TTTTTCACCTGCTGTGTTAAAACAATCGCTGTTTG R 2 1 2 1 101000 f 74 goat snp37018-scaffold449-162952 14 60283447 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383231 Affx-122972761 AX-123253589 14 32444496 TTCACTGAGAGGGAGACACAAAAAGATCAATGGAA[C/T]AGAATAGAAAACTCAGAAAGCCACACAAACACAAC Y 2 1 2 1 101000 f 74 goat snp37019-scaffold449-210397 14 60235837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433038 Affx-122935765 AX-123303379 14 32477343 GGCTGTTGCAAGATTCAGACGAGGAAAAGCATTCA[C/T]AGGACTTGGGGCAGGCCCTCCACACAAAGTCTGAT Y 2 1 2 1 101000 f 74 goat snp37020-scaffold449-243244 14 60202548 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438250 Affx-122931424 AX-123308588 14 32510626 AATTAAATTTGATTTTCTCCTGTTCCTCTGTCTCA[C/T]ATCAATTTAATTCTCTGACCAGTCAAAATAACCCA Y 2 1 2 1 101000 r 74 goat snp37021-scaffold449-276527 14 60169381 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382980 Affx-122973348 AX-123253338 14 32546820 CACTTCCCCCCTCGAGTGAGCCTTTGGCGCGCATC[A/C]AGAAGACTCGGGGATTTCCGGGTCCAACCACTAAA M 2 1 2 1 101000 r 74 goat snp37022-scaffold449-312721 14 60132791 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419038 Affx-122946028 AX-123289386 14 32582040 AGATTGTGACGCACGTGTGTCTGTGTGTCAGAACT[C/T]GTGCCGTGGCTCCCCAACACTTACATGAACACTCA Y 2 1 2 1 201000 r 74 goat snp37023-scaffold449-347941 14 60098015 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774686 Affx-122944108 AX-385261820 14 32614403 ACTGCATCATTGTCTTCCTCCTTTTCCGTACAGCC[A/G]TTCCAAGGCAAATTCACAAGTCAAAGATATTCCAA R 2 1 2 1 101000 f 74 goat snp37024-scaffold449-380304 14 60065326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790452 Affx-122954067 AX-385277455 14 32658610 GTCCCTGTAGCTAATGACTCGTCAAATCAAGATTT[C/T]AAAGTATTTCCCTTAGAAACACCAAATTGCACCAG Y 2 1 2 1 201000 f 74 goat snp37025-scaffold449-424511 14 60020790 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447146 Affx-122924447 AX-123317482 14 32704018 AGCACGTGCCAAACCATCAAACCTTGTAGGCTGGC[A/G]GATTATCTGTGGAGAGGAAACATCTTGATACCTCC R 2 1 2 1 101000 r 74 goat snp37026-scaffold449-469919 14 59975951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406069 Affx-122956243 AX-123276421 14 32737623 CATCCAGATATTAGAACCTATGAAACACAAAAAGA[C/T]GTACGCTTGCTAGGTTCCTAAGGTTTTATGATTAT Y 2 1 2 1 101000 r 74 goat snp37027-scaffold449-503524 14 59942415 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393271 Affx-122965452 AX-123263628 14 32776737 GTCAGAATCATAGCCCCGAAACCCTAATCTTATAC[G/T]AATTAGAGGGGTTTAATAGGAGAATATGTTAAGAA K 2 1 2 1 102000 f 74 goat snp37028-scaffold449-542638 14 59903278 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448156 Affx-122924271 AX-123318492 14 32828107 TCATTAACAATTTACTACTTCTAATATGTTAAAGC[A/C]GTGTTTTCCAGCCCTGGAAATGGCCCCACTAGGAT M 2 1 2 1 201000 f 74 goat snp37029-scaffold449-594008 14 59852201 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777403 Affx-122930942 AX-385264524 14 32871857 AAGTCATATGTCATGGACCTCCTTGGGATTAAATA[C/T]GCTAAGGCTGTTTATCTGATGTGTACATAAAGTAC Y 2 1 2 1 101000 f 74 goat snp37030-scaffold449-637758 14 59808305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771833 Affx-122935221 AX-385258990 14 32918170 AGAACACACAGCTAGGCAAACACTTCCTATTTCTA[C/T]AGATTTTGCCCCAGATGGCGATACAGGCTCTGGTC Y 2 1 2 1 101000 f 74 goat snp37031-scaffold449-684071 14 59764976 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391107 Affx-122966812 AX-123261464 14 32994023 ATTTTACAGAGTCTGGGCTCTGATCTATGGTCAGT[A/G]CTAAGTCAGGTAATATTCTATTTCTGCAGGGAGTC R 2 1 2 1 201000 r 74 goat snp37032-scaffold449-759924 14 59688964 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795246 Affx-122934816 AX-385282204 14 33028779 GAATGGTAGCAATTACCTTAATTATCCTGATTTGC[A/G]TTGAGGCTGGTGTAAGGCATGCTTATGATTTCCAA R 2 1 2 1 101000 r 74 goat snp37033-scaffold449-794680 14 59653281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429880 Affx-122938132 AX-123300221 14 33060355 AGATTTACTGTTACTTTTCACCTTTCAGTAGGTTC[A/G]TATGGCTCAGCCAGGTGAACTTCTGAACCTCTTCT R 2 1 2 1 201000 f 74 goat snp37034-scaffold449-826256 14 59621668 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424898 Affx-122941313 AX-123295244 14 33101941 CCAGGCCCTTTATCTTGTAGACGTCTCTGCTGTCA[G/T]CTCCCCCAAAAGCTGGTGCTCTGGCCAATAGGCTT K 2 1 2 1 101000 f 74 goat snp37035-scaffold449-867842 14 59579364 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445093 Affx-122926203 AX-123315430 14 33131381 TTATAAGGAGTTGCATTCTTATTTATATGAATACA[A/G]TGTATAATATTTCTCTGCTCTTCCATGTGTGTTCT R 2 1 2 1 303000 f 74 goat snp37036-scaffold449-897282 14 59550587 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789941 Affx-122977898 AX-385276947 14 33164396 TTTTGAGTAATGCTGAGCACTTCTCTCTTTTATGA[C/T]GTTTCTTATGACAATGAAATTAAGGTAATTTCACT Y 2 1 2 1 101000 f 74 goat snp37037-scaffold449-930297 14 59517345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770488 Affx-122950929 AX-385257654 14 33225004 CTAGAACTTTGCCAGCAATAGAGACTTGACTGATG[A/G]ATTTCTTTGATCAGTTTTTAATAGCTCATCTTCCC R 2 1 2 1 101000 f 74 goat snp37039-scaffold449-990905 14 59456839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404676 Affx-122957283 AX-123275028 14 33262453 CTTGAATGGCATGTGTAATTCTGACCACCATACCA[C/T]GTGCCTTTCTTCCAGGTAGCATGGCTGGTCAGGAA Y 2 1 2 1 201000 f 74 goat snp37040-scaffold449-1028354 14 59419015 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769493 Affx-122945914 AX-385256662 14 33300429 TGACACCTACATTTCTAGTTTGCAAAGTAAAATTC[A/G]CAAGTATATTGAGAAGACAATGTCTGGCTTGAAAA R 2 1 2 1 101000 r 74 goat snp37041-scaffold449-1066330 14 59380663 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800164 Affx-122945203 AX-385287087 14 33331616 CTTTCTTACCAAGCAGAATTTTCTAGGCCCAGTGA[C/T]ATAAGGGAAATAATTACTGGGTTTCAAAGACTTAC Y 2 1 2 1 101000 f 74 goat snp37042-scaffold449-1097517 14 59349651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779084 Affx-122940169 AX-385266189 14 33378168 TAAAAAGTTATTAACATGTATGGTGCACGTGAGTA[C/T]GGACCCGAACAGATCTTAAACACACTGGAACTGCT Y 2 1 2 1 101000 r 74 goat snp37043-scaffold449-1144069 14 59302938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380463 Affx-122975731 AX-123250821 14 33421622 TCAGCCCAGGTACACTATAGCATCTCTGAAAATCC[G/T]AAAAAGTGGGTGGACCCTCATGGTTTACTGTGAAT K 2 1 2 1 101000 f 74 goat snp37044-scaffold449-1187523 14 59259378 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439115 Affx-122931102 AX-123309452 14 33452514 AAAGAGGATGTTCAAACGAGTCAGAGATTCTTAAT[C/T]AAAGGAAGCAGCTCTCAGCACTGGGGAGCGACGAA Y 2 1 2 1 101000 f 74 goat snp37045-scaffold449-1218415 14 59228427 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378052 Affx-122977189 AX-123248411 14 33487112 GTTCTGAAAAGTCATGAATGCATCAGAAATTAAAT[A/G]CATGACATCTAAGTTATCTGCCTGTAATGTGAGAA R 2 1 2 1 101000 f 74 goat snp37046-scaffold449-1253013 14 59193812 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413229 Affx-122950247 AX-123283578 14 33538853 CATCTTTCCACGGCCAGTGATTTTTTATTGGTATC[A/G]TGAATGTGAATTTTCTTGTTTTCTGTAGAAGAAAG R 2 1 2 1 101000 f 74 goat snp37047-scaffold449-1304754 14 59142047 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439012 Affx-122930357 AX-123309349 14 33595588 TTTGTAAACTTATCCTGTTCTCTGCAGAACCCCAA[G/T]CTACCTGAGGTTTTGGTATCCCGAAAGACATCATT K 2 1 2 1 201000 r 74 goat snp37048-scaffold449-1361489 14 59085194 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407623 Affx-122954632 AX-123277974 14 33624904 ACTCTTGCTCCTCTTTCCAAAGAAACAGTATCATC[A/G]TGATTGAAGAAAAAGAATCTAGTCACTTGAAATAG R 2 1 2 1 201000 r 74 goat snp37049-scaffold449-1390805 14 59055891 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801559 Affx-122956539 AX-385288468 14 33665791 GAAGTTACTGAGGTCACCAAGATGAGTCATGAAGG[C/T]GGCAGGACAAGTGTGCAGAGGAAAGGCTATAAGAG Y 2 1 2 1 102000 r 74 goat snp37050-scaffold449-1431692 14 59014501 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773623 Affx-122954558 AX-385260763 14 33698562 TCCATTGATCACTCATCCATTCTGGTGCCATATGT[G/T]TTTGTGTGTGTATGTCGTATGTTTTTGATTACTGT K 2 1 2 1 101000 f 74 goat snp37051-scaffold449-1464463 14 58981727 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770246 Affx-122976036 AX-385257412 14 33732930 AGGAACTCAGGTATTTGGCTTTTCCTGATTTCAGA[C/T]GTAGAGATAAGTTCCAAAGAGAGCACAAAGGCTTA Y 2 1 2 1 101000 f 74 goat snp58878-scaffold963-1041968 14 58947270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799776 Affx-122933311 AX-385286703 14 33777490 GCATAATGAACAGGATTTTATCAGAAATTAGCAAT[A/C]CTGAAGAACCACTGCTGTCAACCAATAGTTCAGTA M 2 1 2 1 101000 r 74 goat snp58877-scaffold963-997408 14 58902024 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431303 Affx-122937086 AX-123301644 14 33810061 GGGTGCTGCTTTGCCATAGGTAAAGCAGAGAGCGC[G/T]CCAATGCAGGTGTGGCTGCCTTGCTACACCACAGG K 2 1 2 1 101000 f 74 goat snp58876-scaffold963-964837 14 58869506 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399093 Affx-122960874 AX-123269448 14 33843165 GAAAGCTCTGATGTTTTGTAAGGCCCTAGAAGTTC[C/T]GCAGAGATTAGAATCATCTTGTTTGTCCAAACTAC Y 2 1 2 1 101000 f 74 goat snp58875-scaffold963-931733 14 58836737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438344 Affx-122931334 AX-123308682 14 33924989 CATGTCCTGACTGATCACGTGCTACTCTTTGTGCA[A/G]CCTGTTAATTTCATGTAGGTGTTTCTTCCAAACTA R 2 1 2 1 101000 f 74 goat snp58874-scaffold963-849909 14 58753764 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416601 Affx-122947639 AX-123286949 14 33981323 AGTATTCATTCCTTGTCAGCTCCTATCTAAATCCA[C/T]CATTTTTACAGCAATCAATACAAATCAAAGAATTT Y 2 1 2 1 101000 f 74 goat snp58873-scaffold963-793575 14 58698083 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393216 Affx-122965494 AX-123263573 14 34041200 CTCTTTGCAACCTCATGGACTATAACCTGCCAGGC[G/T]CCATCTGTAGAAAGAGCCAAGAAGCAGCAATTTAG K 2 1 2 1 101000 r 74 goat snp58872-scaffold963-733698 14 58637697 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424023 Affx-122942088 AX-123294369 14 34091768 ACTAAGTCACAGATCAGGACTCTGAAATTTGCAGC[A/G]TCATCATACATAATCTTTTGTTTTTCAACTAATTT R 2 1 2 1 101000 f 74 goat snp58871-scaffold963-683130 14 58586061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424680 Affx-122941709 AX-123295026 14 34128824 AGCACCTGATGATGAGAGTAAGTGGTGGATGATTC[A/G]CACCTCCAGCTTCCTCCTTTCCTGAGGCTAAGGTC R 2 1 2 1 101000 f 74 goat snp58870-scaffold963-646074 14 58548916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441131 Affx-122929585 AX-123311468 14 34171081 ATCAAGAGCATTAAAAAATAACCTTGTTTTCAAGA[C/T]GGAAGAGACTGTGACAGGCAGGTTCATTCTCTACA Y 2 1 2 1 201000 f 74 goat snp58869-scaffold963-603817 14 58506107 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415714 Affx-122948520 AX-123286063 14 34205502 AATCGCTCTCCATCTCACCCATGAAACACAAACTC[G/T]TTTAATAGGGAAATGTTATCCAGACTCAGGGAGTA K 2 1 2 1 201000 r 74 goat snp58868-scaffold963-569396 14 58471701 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446376 Affx-122925591 AX-123316712 14 34236862 CTGTGAAAGGCTGTAGGAAAGAAGAAAATGAACAC[A/G]TCCCCTCTGGACTCTGACTAGAACCAAGACTTTAC R 2 1 2 1 201000 r 74 goat snp58867-scaffold963-538036 14 58439789 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441851 Affx-122929041 AX-123312188 14 34432285 GAGAGAAAACTGGGGAAATACATCTACCAAGAGAT[G/T]ACCTAAAGGGAGGAGGTAATCAGGAGAGAGAGTTA K 2 1 2 1 101000 f 74 goat snp58863-scaffold963-342613 14 58242413 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392763 Affx-122965997 AX-123263120 14 34472193 ATAACAGCTTGAAAATAGCTTTCTGGAGACAATCT[G/T]AAGCAGGTTTAAAACGGGAACTGTTTAGAATCTAG K 2 1 2 1 101000 r 74 goat snp58862-scaffold963-302705 14 58202456 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422615 Affx-122943720 AX-123292961 14 34505507 CTCTCCCATAAGAAAGTCAAATTTTAGCAGTATTA[G/T]ACTTGGGTACCTAACACTCCCTGTACAATACCAGA K 2 1 2 1 101000 r 74 goat snp58861-scaffold963-269391 14 58169240 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384663 Affx-122972139 AX-123255021 14 34576891 TGTTGGCTATTCAGTAGTATGTGGTTAGTTTTCAC[A/G]TATTTGTGAATTTTTCAGTTTTCATTCTGCTTTTG R 2 1 2 1 101000 f 74 goat snp58859-scaffold963-198007 14 58098138 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407680 Affx-122954589 AX-123278031 14 34649223 CCGTAACCAGCCGACATGTCTCAGTGCTTGTGCTT[A/G]CTAGAAAATGAGGTGAAAAACCACAGCCTAGAGTA R 2 1 2 1 101000 f 74 goat snp58858-scaffold963-125675 14 58025978 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272786 Affx-1111833007 AX-519546484 14 34751165 CCGCAACAAAGATCCAGCACAACCATAAATAAATA[A/G]GCAAATTGAAACAAATACAAACTTTTACTCAGTGT R 2 1 2 1 201000 r 74 goat 14_34751165_AF-PAKI 14 34751165 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320782685 Affx-122953471 AX-385269757 14 34809484 TAATTTCTTCCTTTAAAAAACTGAGTGTGGATTTA[C/T]AGTTTAGATAATTTATCTAGAAGGTTAAGTTAGCA Y 2 1 2 1 201000 f 74 goat snp51300-scaffold75-6315557 14 57865866 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440428 Affx-122929418 AX-123310765 14 34843558 GGACATCCCAGAGACAATCTCTCCTTTATCTCTCT[A/G]CGGGGAATTCAGCCCTGCCCTGGAGAGGTTCATCG R 2 1 2 1 101000 f 74 goat snp51299-scaffold75-6281483 14 57831497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795535 Affx-122926812 AX-385282490 14 34899575 TAATTCGGGTATTTTCCATGGAACGACTCTAAGTG[C/T]AAATTGGAAGGAAAAGGCTAAATAAATAACTTGAG Y 2 1 2 1 101000 r 74 goat snp51298-scaffold75-6225466 14 57775183 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416673 Affx-122947586 AX-123287021 14 34934397 ATTCTGGTGATCCTTATCTGCTCAGACAGAGGCCA[A/G]AGAAGGAAGAGGTTCTCTGAAATGACGTGCAAACT R 2 1 2 1 101000 r 74 goat snp51297-scaffold75-6190644 14 57740521 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451103 Affx-122921396 AX-123321437 14 34979864 TTAAATCTGTCCAAACACCCCAGAAAGACCAGGTG[C/T]GAGAAAGAATTTCACCTCCTCTGCCAAAAAGGAGG Y 2 1 2 1 201000 r 74 goat snp51296-scaffold75-6145177 14 57694958 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786221 Affx-122927758 AX-385273256 14 35028448 TCTCATCAATGAAAACGAAAATGTGTTGAATTTGG[C/T]GAGCTTGAAAATGCCTTCCGTTCAAACATTCAGAC Y 2 1 2 1 101000 f 74 goat snp51295-scaffold75-6096593 14 57646187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785352 Affx-122931794 AX-385272397 14 35082767 AGAGGGTTCAATAAGCACCTTTATCATTGACATCA[C/T]GAGCAAGCTATTAAGTACTAGTCTTGGGACCACTA Y 2 1 2 1 101000 f 74 goat snp51294-scaffold75-6042274 14 57591690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791006 Affx-122935485 AX-385278003 14 35164912 TAGATGGCGTTATTTCCTTTGTGGCTTAAATAACC[A/G]TATATTAATCTGAATTTGAAACCCTCGGTTTCAAG R 2 1 2 1 101000 f 74 goat snp51292-scaffold75-5960129 14 57508162 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428174 Affx-122939031 AX-123298517 14 35222221 TTTACCTACTGAGACATCAGGGAAGCCCCTGTGAC[A/G]TCTCTAAGTCCATGCTAGTAAGCTGGTAATTATTT R 2 1 2 1 101000 r 74 goat snp51291-scaffold75-5902820 14 57450232 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396471 Affx-122962963 AX-123266826 14 35261456 TGCGTGCATGCTTGCTAAGCCACTTCAGCCTGCCT[A/G]CATTAGCTGCTTTTTCACTCAGTTAGCGGTTGCTG R 2 1 2 1 101000 r 74 goat snp51290-scaffold75-5863585 14 57410934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788950 Affx-122967590 AX-385275963 14 35309952 TAATGTTGTCTCTGAAACTGTCCTGGAACACTATG[C/T]GGCCAATTGACTACTCTACCCAAAGATATTACCGT Y 2 1 2 1 101000 f 74 goat snp51289-scaffold75-5815089 14 57362420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442250 Affx-122928286 AX-123312587 14 35338950 ATAGCCACAGAGAAAGGATGAGAAATACTCGCTCA[C/T]GATCTCCCCCACATTCAGCCAATCACTGCCACGAG Y 2 1 2 1 201000 r 74 goat snp51288-scaffold75-5786091 14 57332964 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769989 Affx-122945264 AX-385257156 14 35375191 ACAAAAAACTCAACTCTCATAGTGAGTCCTAAAAT[A/C]TTAATCCTGCCATGGTCTAGAAGGTCGCTTCTGTG M 2 1 2 1 101000 r 74 goat snp51287-scaffold75-5749850 14 57296709 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419801 Affx-122945844 AX-123290149 14 35425069 CAAGGAGCAGGCAACATGAGCTGCTTGACTCTCAC[A/G]TCCCACTGGAGCGATGAGGCAGTCACTAGATGTAG R 2 1 2 1 101000 f 74 goat snp51286-scaffold75-5699972 14 57246706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376034 Affx-122978943 AX-123246393 14 35457720 TCCACTGTAGGTATTTAATAAATGCTAACTATAAT[A/G]TTATAACAGAATTACCTCCTGATTTCTGTTCTCAC R 2 1 2 1 303000 r 74 goat snp51285-scaffold75-5667321 14 57213967 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402711 Affx-122959197 AX-123273064 14 35505264 GGACCTTTCAGAACTGTGAGATTTGGGTGAGAGGG[C/T]AGGGGCCGAGGGGCGGGAAGGCCCATGAAGACACA Y 2 1 2 1 101000 f 74 goat snp51284-scaffold75-5619777 14 57169038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441900 Affx-122928613 AX-123312237 14 35560543 GTCACAGGAAAGGGATCATTGGGTGCTGCAGACAC[A/C]GGCTGGATTAGACCTGGATTAACTAACTTTTCAGT M 2 1 2 1 201000 r 74 goat snp51283-scaffold75-5564498 14 57113716 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775179 Affx-122925864 AX-385262310 14 35595486 ATCACTTAAATAATTTCTAATGAGAGAACTAAAAA[C/T]GAATATTTAGTCTCACACCTGAAAAAGAAGCATTT Y 2 1 2 1 202000 f 74 goat snp51282-scaffold75-5529555 14 57078612 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777331 Affx-122926827 AX-385264453 14 35634233 TTCACTTTGGGATAATCAGCAGGAATAAACTGTGA[C/T]GCACAAACCAGTATTTGAAATTGTTGAAACCTCAG Y 2 1 2 1 101000 r 74 goat snp51281-scaffold75-5490808 14 57039648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383248 Affx-122972748 AX-123253606 14 35664899 AAATAGCAAGATATTTGAGGCACAAAGTTCCTCAC[A/G]TATCTGCAGTTCATCATTTTTCTGTCTCCTCTTTG R 2 1 2 1 101000 r 74 goat snp51280-scaffold75-5460142 14 57008956 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404096 Affx-122957126 AX-123274448 14 35708323 ATTTGTACATGGATTTCTATGCATTTGTAATACTT[A/G]CATTAATTCTATGTCTTTGAAAATCTTTGGAGAGG R 2 1 2 1 101000 f 74 goat snp51279-scaffold75-5416718 14 56965584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423699 Affx-122942891 AX-123294045 14 35753723 GGACAGGCACAGCGATCCTTTGTCAAAACCTCTGC[C/T]AGTCCTTTCACTTAACTCATTTGTTTTTCATAGCA Y 2 1 2 1 101000 r 74 goat snp51278-scaffold75-5371318 14 56920668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413212 Affx-122950259 AX-123283561 14 35808369 TGCATAAATTCCTGTGTCTCCATCTTTTCTCTGCC[C/T]CTCTCACCTCAAATGCCCACACTTGACCAGGTTTT Y 2 1 2 1 101000 f 74 goat snp51277-scaffold75-5316672 14 56866131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782823 Affx-122931933 AX-385269894 14 35863280 GAGCCAATAAAACATGTTAACTAATACTAGAGGCA[C/T]GTTTATTGAATCCTCTCCAACCACAGGAGTTAAAA Y 2 1 2 1 101000 r 74 goat snp51276-scaffold75-5261761 14 56811490 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394778 Affx-122964830 AX-123265133 14 35914602 TTCATATCATCTGGAGCTGTTACCATTTTACATAC[C/T]AAGAGACAAGACTAAATTAACCAAAATCAAGAGGG Y 2 1 2 1 101000 f 74 goat snp51275-scaffold75-5210439 14 56759582 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786975 Affx-122944673 AX-385274004 14 35945496 CATAGTCTTGTACGATCACTATTTTTATATTTCTA[G/T]CATATTATTATCAGTATGTTATTATTCTGACTGAG K 2 1 2 1 101000 f 74 goat snp51274-scaffold75-5179545 14 56728191 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780389 Affx-122955220 AX-385267483 14 35978804 TTTCTGCTTCCCACTATTAACAGCTAACTTGGAGC[A/G]CAATTCTTTACTTCTCTCACTAATCCTGAAATTTT R 2 1 2 1 101000 f 74 goat snp51273-scaffold75-5146237 14 56694773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776367 Affx-122961790 AX-385263494 14 36014191 AGTCTGAAACACACACTCTCATCCTCAAAGAGGAA[C/T]GGACATCATGTAACACTGTGCTCCTAGCGCCATAT Y 2 1 2 1 101000 r 74 goat snp51272-scaffold75-5110850 14 56659278 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783171 Affx-122943950 AX-385270238 14 36054587 TGGGGGCTCAATTTTTTCTCAGGTGATTGAACTTC[A/G]TTCGTAAAAAAAGGGCACAGTGATCTCATATTTCA R 2 1 2 1 101000 f 74 goat snp51271-scaffold75-5070454 14 56618931 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783882 Affx-122976913 AX-385270938 14 36089763 CCTTTAAGACAAATTTAAGCTTCATTTCACTGACA[C/T]GTTTAGAAAACAAGTGTCTGATTCGTATTCGTTTC Y 2 1 2 1 101000 f 74 goat snp51270-scaffold75-5035278 14 56583884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276796 Affx-1111835592 AX-519550305 14 36137864 TACTGCTCCAATCTTTATTATTCCAATCTGGAAGT[A/G]AAGGGCCTTGAGCAGGAAACAGAGGTGATAGACAT R 2 1 2 1 201000 f 74 goat Random2.2K-1418 14 36137864 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422920 Affx-122943043 AX-123293266 14 36182430 TAAAATATGGTATTCCAAGAAGGTTAACAAGCCAC[A/G]CATTATTTGTATCTTTTAAAATCCATTTGCAAATA R 2 1 2 1 101000 f 74 goat snp51268-scaffold75-4942611 14 56490776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388333 Affx-122969359 AX-123258691 14 36232049 CAGTTAGCATTTATGAGCATTCAGATCTCAGCTCC[A/G]ACTTTGGCTGCTCAGTCATTTCACTGTTAGTTCAA R 2 1 2 1 101000 r 74 goat snp51267-scaffold75-4892992 14 56441164 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412612 Affx-122951281 AX-123282961 14 36306185 CTCTTGTCCAGTGTGGTCCAAGGACACAGTGAGGG[C/T]AAGGACTTTCTGTGCTACACACCCTGCACCCCAGC Y 2 1 2 1 101000 r 74 goat snp51266-scaffold75-4818856 14 56366476 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793839 Affx-122963662 AX-385280808 14 36369374 TTTAAATGCTAAATTTAAAACCTATTTCATCTTAC[A/G]TAACAGTGGGCTAGCTTAATACTACACTAAGTATC R 2 1 2 1 201000 f 74 goat snp51265-scaffold75-4755667 14 56303254 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795104 Affx-122943634 AX-385282063 14 36412037 CCTTTCATGTGAACTAACGATAGCAATAGCTCCTA[C/T]GGTGAGAAGCAAGTGGTTTTGTATATAAAGTGCCT Y 2 1 2 1 101000 f 74 goat snp51264-scaffold75-4713004 14 56260556 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793066 Affx-122963009 AX-385280044 14 36442738 AGGAAATGTTAGATTTTTATGTTATATCAAAAAAT[A/G]CATGTTTAATATAAGCTCAGGAAAAAATTGTATTT R 2 1 2 1 201000 f 74 goat snp51263-scaffold75-4682303 14 56229807 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770505 Affx-122934704 AX-385257670 14 36506695 CTATTAAGCATGGAATTCATTCTTTTCTAGGAACC[A/G]CCAATAATTGTGCCTCCTTGAATTCAATATTCATT R 2 1 2 1 201000 f 74 goat snp51262-scaffold75-4618346 14 56165561 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447911 Affx-122923804 AX-123318247 14 36561006 ACAGGGCTAAGAGTGAGAGAGTCCTCTAGAGTATT[A/G]TTTGTCATTCCTTCACAGATAAAGTTTTATCTGCA R 2 1 2 1 101000 f 74 goat snp51261-scaffold75-4564035 14 56111120 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799047 Affx-122956242 AX-385285977 14 36611178 ATTGACCTTGTATAAAAAGTTTAGTTTACTAAATG[C/T]ATCCCTGAAGATGTAGGATAACTCCTAATGGAGCT Y 2 1 2 1 101000 r 74 goat snp51260-scaffold75-4513863 14 56061828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421358 Affx-122944055 AX-123291705 14 36653727 TAGGTTGTTTCTGTAATCTTCTTTCTAGAGTATTT[A/G]TTTGGAGTATATGAGTATCGTTATATACCTAAACT R 2 1 2 1 101000 r 74 goat snp51259-scaffold75-4471314 14 56019053 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763127 Affx-986697656 AX-385251072 14 36706915 CTTTGCATTCTTTGCATTGCATTCTTCAGTAAGAA[A/G]CCTTTCTTATCTCTTCTTGCTATTATTTGGAACTC R 2 1 2 1 600010 f 74 goat 14_36706915 14 36706915 Ancestral_priority_1043 ancestry 0.614 recommended IMAGE 10K 10K ancestral 38454175 Affx-122919310 AX-123324508 14 36733087 AGAGGGCCATTTAGAAATGAACAGCAGCCTTGACT[A/G]CTATGCTGAAATTGCAAACAGAGGAATCAGACAGT R 2 1 2 1 201000 r 74 goat snp51258-scaffold75-4391954 14 55939055 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433807 Affx-122935177 AX-123304148 14 36773502 GTGGGTCCTCAATAAATGTTTACTAAAAACCTAAA[C/T]GTCATGAGCTGTTCACTCCAGGTAGAATGAATGAG Y 2 1 2 1 101000 r 74 goat snp51257-scaffold75-4351539 14 55898613 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788051 Affx-122944939 AX-385275072 14 36802552 TCCATCTTCACCATTATGCAATAAAGATTTAAAGA[C/T]ATAGTCTTTTTACCTTTTATTTCCAATAAGCATAA Y 2 1 2 1 201000 r 74 goat snp51256-scaffold75-4322489 14 55869552 A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424389 Affx-122941827 AX-123294735 14 36856574 ACACAATTCTGTCTCTCTCTGTGTTTAAATATTCC[A/G]TAATAATGGGATAAAAACAAATGGAGTGCTCACTC R 2 1 2 1 303000 r 74 goat snp51255-scaffold75-4268467 14 55814995 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419000 Affx-122946055 AX-123289348 14 36886772 GACACTAACTTTAATTAAAATATCCGGGGAGGGGG[G/T]TTACTATTTTGATATTTTTTTGGCTTGCTGGTTGC K 2 1 2 1 103000 r 74 goat snp51254-scaffold75-4238269 14 55784448 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386744 Affx-122970138 AX-123257102 14 36942356 ATCTGTGAACTGTTCCCAGGAAGCAAGGGCAGGGA[A/G]TCCAACAGCTCTGACCACACGCAACCCTAGGATGA R 2 1 2 1 101000 r 74 goat snp51253-scaffold75-4182685 14 55730305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773599 Affx-122961486 AX-385260738 14 36989362 GGATTTTTGTAACGAATAAATAAGATATTTGATAA[C/T]ACTAAAGTAGTCATTTTCAAATCCTCAGAGGTTGT Y 2 1 2 1 101000 r 74 goat snp51252-scaffold75-4135679 14 55683462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405320 Affx-122956830 AX-123275672 14 37024561 AGGAGGGCAGAGAGACCAACCAACCAGCCAGGACA[C/T]AGCCTTAATGAAGATTCAGAACATCCAAGGAAAGG Y 2 1 2 1 101000 r 74 goat snp51251-scaffold75-4100480 14 55648282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436207 Affx-122932588 AX-123306546 14 37059761 TAAGGTAGAAAATTCACAGTCCATCTCTGCTCCAT[A/G]TTTGAGACCCACTAGGAACACGACACAGGCAGTAG R 2 1 2 1 201000 r 74 goat snp51250-scaffold75-4065280 14 55613782 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401736 Affx-122959517 AX-123272089 14 37093316 TAAGCAAATAGTCATTCTGGGGGGCAGAATTTAAA[G/T]CATCTCAAATGCCTGCTTAAAAATACCTTCCCCAT K 2 1 2 1 101000 r 74 goat snp51249-scaffold75-4031725 14 55580103 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416754 Affx-122948188 AX-123287102 14 37183477 ATTTCCACTCAGTTTTTTAAAAAAGAGATGCTGCT[A/G]TCCTTCCAACCTATTCCCCAACTTCCTGTCATCCT R 2 1 2 1 201000 r 74 goat snp51247-scaffold75-3941564 14 55490018 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769300 Affx-122965013 AX-385256472 14 37214200 ATCCTAAACATCTTGTTGTTATTAACTTACTGACT[A/G]TTGTTCACGGTTATCCCATTGGGAATAAATTCATT R 2 1 2 1 101000 f 74 goat snp51246-scaffold75-3910841 14 55459270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408064 Affx-122954267 AX-123278415 14 37259053 AAGAAAGAAATCGCACAGGTCTCCTTTAATATCAT[C/T]GGTGACATGACTCCCCCTGCCTCACACCACTGCCC Y 2 1 2 1 101000 f 74 goat snp51245-scaffold75-3865988 14 55414445 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386809 Affx-122970903 AX-123257167 14 37348750 GAGTAAGAATGTAATATTGTTCTGATTTATCTCAT[A/G]TTTTGTCAGAACCCTTTCTTCAGAATTAATGATCT R 2 1 2 1 101000 r 74 goat snp51243-scaffold75-3776291 14 55324636 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388976 Affx-122968666 AX-123259334 14 37377990 GGGGTGAGAATTGATTCTGCTGGCCTTGTGCCTCA[C/T]GGGTGCTTCAGTCTCCTGGTCCCCACTCCTTCCCT Y 2 1 2 1 101000 f 74 goat snp51242-scaffold75-3747051 14 55295809 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439610 Affx-122931146 AX-123309947 14 37421729 AGCCCTGTATTCATGTTAATACTTTAAGTATTACT[A/G]CATGTTTACCATGTACCATGCAACGAGCTGTGTAA R 2 1 2 1 101000 r 74 goat snp51241-scaffold75-3703312 14 55252088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386440 Affx-122970794 AX-123256798 14 37459617 TGAGATGTTTGGGAACATTTTCTATTGGCCTGTAA[C/T]GGAGGGAAGGTTTGGACTCTGGACATATAAGGGAA Y 2 1 2 1 101000 f 74 goat snp51240-scaffold75-3665424 14 55214188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399593 Affx-122961103 AX-123269948 14 37505797 TTTATAAATGAGACTTCTTTGTTACAAACAGAAAA[C/T]AAGTGCTGTCATGTTTGGAAATTAACTATTCTAAT Y 2 1 2 1 201000 f 74 goat snp51239-scaffold75-3619244 14 55167536 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422191 Affx-122943508 AX-123292537 14 37536219 TATTTTTTGGCCATGGTCCAAATGTACACATATAG[C/T]CATCTCTTAATTATCCCTGCAGATGAAGAGTAGGA Y 2 1 2 1 101000 f 74 goat snp51238-scaffold75-3588822 14 55136748 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376804 Affx-122977938 AX-123247163 14 37565065 TTTCCATTGAAGGACAAAGAAGGTTGCTTTCTTTA[C/T]ATCATCAAAAGGAAAAACAAAACAGTTCTTTAAAA Y 2 1 2 1 101000 f 74 goat snp51237-scaffold75-3559976 14 55107906 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401769 Affx-122959495 AX-123272122 14 37601859 AAGAACCCAGATCACAACTCTCCCCTCCTGAGTGA[C/T]GCCTCTGTTCTGTGCTGCTATTTTCCACCCTTATG Y 2 1 2 1 101000 r 74 goat snp51236-scaffold75-3523182 14 55071288 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411553 Affx-122951644 AX-123281903 14 37630974 TGTAATGGCAGTGACCTCCCCTGCCCCTTACCCTA[C/T]GAAAAAGTACGAAGTTTAATAAAACGTTATAGACA Y 2 1 2 1 201000 r 74 goat snp51235-scaffold75-3494067 14 55042545 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38376131 Affx-122978865 AX-123246490 14 37663514 TTAAAATTTGTGCTAGAATGTAGAGGAAAGGAACA[A/G]CCTGTTATATTATGCAAAAACGCTTTTCAGCACAT R 2 1 2 1 101000 r 74 goat snp51234-scaffold75-3461527 14 55011172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413584 Affx-122950579 AX-123283933 14 37714588 GATCAAAGTGGTCTCGTTTACATTTTATTTATTGT[A/G]TATGTTATAGTTCTTAATCTTCTAATTATTTATTG R 2 1 2 1 201000 r 74 goat snp51233-scaffold75-3410453 14 54959575 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801339 Affx-122924546 AX-385288251 14 37749980 TTCTAAACCTGGTCTCAAATGGAAAGAATTATTCA[A/G]GGTTGTGACAGCCCTAAAATCAATTCTGTATGCCT R 2 1 2 1 101000 r 74 goat snp51232-scaffold75-3375061 14 54924268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787249 Affx-122930612 AX-385274275 14 37780035 AATTGACTAATTCATTTCTTGGCTGTGTCCATTCC[A/G]TTACTCTTCAGACTAATGTGTGCTTTATTGAAAGT R 2 1 2 1 101000 f 74 goat snp51231-scaffold75-3345006 14 54895184 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410880 Affx-122952597 AX-123281230 14 37831987 ATTAATTAAGAAACTCATGTAAAGTCTTCAACCTA[G/T]TTTAAGTTTCAGTGTAACCCTCGTTGATCCTTAGT K 2 1 2 1 101000 r 74 goat snp51230-scaffold75-3293054 14 54842548 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431736 Affx-122936744 AX-123302077 14 37890082 TCCTATGGAGTGCTTGTCCAAGTGCCTGGCACATG[A/C]TACATGCTGAAATATAGGTATTAGTGTTATTATTC M 2 1 2 1 201000 r 74 goat snp51229-scaffold75-3234959 14 54784344 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429835 Affx-122938169 AX-123300176 14 37929880 TGTTTCCACTGAAGGCTTCCTTCTTTTTAATTTCA[C/T]GATAATTCCTCTATTCTAACAAGTGAAGCATTAAT Y 2 1 2 1 202000 r 74 goat snp51228-scaffold75-3195161 14 54743414 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447893 Affx-122923816 AX-123318229 14 37964069 TCCACCTCAGTATTATTCAAAATTCCCAGGTGGTC[C/T]CCTGTCATGAATGCCCAGGACCTCTGGTCTATTTC Y 2 1 2 1 101000 f 74 goat snp51227-scaffold75-3160972 14 54709198 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403931 Affx-122957467 AX-123274283 14 37997349 AGATCACTTCCTCGTAATGCCACATTGTAGCACAC[A/G]TCACATGCTCTTTTCCCAGCAACTGGGCACACTTC R 2 1 2 1 201000 f 74 goat snp51226-scaffold75-3127692 14 54675729 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450229 Affx-122922270 AX-123320564 14 38035034 ACTTGTCCATCAGTGTAATTTTGATGCCTGTGGAG[C/T]GATGGTTCTCTGCTGCTTTTCCTTTCATTACAGGT Y 2 1 2 1 101000 f 74 goat snp51225-scaffold75-3090007 14 54638090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421740 Affx-122944376 AX-123292087 14 38090404 AATTAATTTCTTAGGGGAAAAGATAGTTAAATGAC[A/G]TATTTCTATACTAGTGTAAGGGGAGACCTGAAAAT R 2 1 2 1 201000 f 74 goat snp51224-scaffold75-3034637 14 54583364 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784320 Affx-122929755 AX-385271371 14 38132313 CACCAAACAATTTTGCTATTTAATAATCTTTGCTG[C/T]AAACAGTTTTCCCTAAATATAGTTAGCTGCCTCAG Y 2 1 2 1 101000 r 74 goat snp51223-scaffold75-2992728 14 54541331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798943 Affx-122944122 AX-385285873 14 38174057 AAGGGCACCTTTAGTTGGGGCTGGATTTTGTCCCA[C/T]TGTTTACCTTCTGGGTCCTTTTGGTGTGCAGTATG Y 2 1 2 1 101000 f 74 goat snp51222-scaffold75-2950984 14 54499413 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396062 Affx-122963447 AX-123266417 14 38216548 CCACCTTCCCCTTAATCACTGAGCCACTTCAACAG[C/T]AGTTACCAGCAGGCTTATTGATGCTAATCCTAAGA Y 2 1 2 1 201000 r 74 goat snp51221-scaffold75-2908493 14 54457082 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453049 Affx-122920073 AX-123323382 14 38246599 GGTAGAAAGGAGGAACATGCAGGTAAGACTTGTCT[A/G]GAATAATTTGAAGTTCAATTACCGAAGGTCTTAGT R 2 1 2 1 101000 f 74 goat snp51220-scaffold75-2878442 14 54426825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418351 Affx-122946591 AX-123288699 14 38306370 TTTCCATTTTTTCCCCATCTAAATTGGACTTACAA[A/G]CATGCTCTGGGAGCAGAACTCCTTTGTATGCAGGG R 2 1 2 1 101000 r 74 goat snp51219-scaffold75-2818671 14 54367012 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798703 Affx-122959408 AX-385285635 14 38398150 AAGTGTTAGTCATTTGCTGTTGCTTTCTTAAATAA[C/T]ACTTCCTGTAAGCCATGAGCATGTCATAATTATTT Y 2 1 2 1 101000 r 74 goat snp51217-scaffold75-2726891 14 54275066 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417472 Affx-122947180 AX-123287820 14 38443080 CTCCATTTCAAACCTCCATTGGCCCTCTTTTGCCC[A/G]TGGGATTAAACACAAATTTGTAAGTAAGTCTGGAA R 2 1 2 1 201000 r 74 goat snp51216-scaffold75-2681961 14 54228759 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276798 Affx-1111835593 AX-519550307 14 38468898 AGGAAGTCTTACTGTCCAGACTATCTTTGGTTTAT[A/G]TATTTTGTCTCATGAATTTAAAGAGGAAAAGAGAT R 2 1 2 1 101000 f 74 goat Random2.2K-1420 14 38468898 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38375426 Affx-122979188 AX-123245785 14 38495284 AGAACAAATGAATTTGAACTTCCTCAGCTTCAACC[A/G]TGGCTTCATCTCCCCCTTCAAGCTTACCCCCAGCC R 2 1 2 1 101000 f 74 goat snp51215-scaffold75-2629757 14 54176090 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783499 Affx-122919711 AX-385270562 14 38603721 ACCTTACCAACAGCAAGAATTGCCCATCTCTGACT[C/T]TCCAGGCTAATACCTATTACTGAATGAACAACAGT Y 2 1 2 1 101000 f 74 goat snp51213-scaffold75-2521320 14 54067296 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385265 Affx-122972077 AX-123255623 14 38654276 ACAAAGATGCAATGATCCAAAGATGAGTCACCTCA[C/T]GAAATGATCTTGCCAGAGGAAGATTGTACGCAGAT Y 2 1 2 1 101000 f 74 goat snp51212-scaffold75-2470765 14 54015308 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418688 Affx-122946303 AX-123289036 14 38711169 CTAAGCCCCCCAAAATAGAATATAAGACCCAGGAG[A/G]ACAATTTAACAGACAACAAAAAGCAAAGACAGCAC R 2 1 2 1 202000 r 74 goat snp51211-scaffold75-2413872 14 53958508 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435888 Affx-122932781 AX-123306227 14 38761307 GCTCTGGATATAAATTCTTCTGAAGGTAGAGTCAA[C/T]AGGCTTTGCTGATGGATTGATGTGAGTGAGAAAGA Y 2 1 2 1 101000 r 74 goat snp51210-scaffold75-2363734 14 53908092 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768398 Affx-122931441 AX-385255578 14 38832825 AGGTGCACAAAACTTAGACAAGAGCCAGTTATAAG[C/T]ATGTCAGGTTTGTCATAGTCATGAAGCATTTAGGA Y 2 1 2 1 101000 f 74 goat snp51208-scaffold75-2292216 14 53836396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768489 Affx-122923090 AX-385255669 14 38866780 TAATTATTCGATTGGTCACAAAAGGACTATCATTC[C/T]ACCACCAACTCCTAGAAAGAGGCCATCATTGCTAT Y 2 1 2 1 101000 r 74 goat snp51207-scaffold75-2258261 14 53801902 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448335 Affx-122924136 AX-123318671 14 38918792 CAACAAGGTATGATAAGGACTGGATTCACTCAAAA[G/T]GCCTCCTGCCCTATCACCAAAAATACTGGGGAAAA K 2 1 2 1 101000 f 74 goat snp51206-scaffold75-2206249 14 53749697 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777028 Affx-122946156 AX-385264151 14 38956910 AACTCACTGAAACCTCAGAATCCAGATTTGTAATA[C/T]AGAGATAACATCTTTCTTGACTGCTTCACAGAGGA Y 2 1 2 1 101000 r 74 goat snp51205-scaffold75-2168131 14 53711368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784109 Affx-122949894 AX-385271161 14 38987317 TAAGTCTTTTGTCTACCATGTCTATTGATTTATTC[C/T]CAATGCACTAGAGAAGAGGCTTTTACACTGGTTCA Y 2 1 2 1 101000 r 74 goat snp51204-scaffold75-2137724 14 53680502 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801601 Affx-122934643 AX-385288510 14 39038371 TAGCAAAATTTTGTGATTGGGGCAGCCCTAGACAG[C/T]TAATGGGATCAAAAACATGGTTGACTGATTGATTC Y 2 1 2 1 101000 f 74 goat snp51203-scaffold75-2086670 14 53628574 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403842 Affx-122957940 AX-123274194 14 39092325 AAAGTTGTTGAAATTCAGATTGTGAAGCCCACTAG[C/T]CACTGGCTTATGGAATTTTTATATTGGTATATTCC Y 2 1 2 1 101000 f 74 goat snp51202-scaffold75-2032716 14 53574069 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450814 Affx-122921801 AX-123321148 14 39124747 GTAGCGCTAGAAATGTGAATTTTTCTTTGTTCTTA[A/G]TATATAGAAACTGGGTACTGCTAACAGTGCATGGG R 2 1 2 1 201000 r 74 goat snp51201-scaffold75-2000294 14 53541791 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275039 Affx-1111834649 AX-519548621 14 39161275 CTGCAGGTTTTCTTCTGGAGATCTTGTACATTTCA[A/G]GAGCTCTCTAAGGACTTGAACATTGGCAATAAAAT R 2 1 2 1 101000 f 74 goat GoatD01.044460 14 39161275 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38406536 Affx-122955123 AX-123276888 14 39166719 CAGTGCCCTATTTGGGGTGTCATATTTCTTTTATG[C/T]AAAGGCAAAAGAAAAGGTTCATAACATAGAATGCT Y 2 1 2 1 101000 f 74 goat snp51200-scaffold75-1958322 14 53499695 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432786 Affx-122935421 AX-123303127 14 39198064 CAGCAACTATACTTCAATAAAAAAAAAAAGGAGTT[A/G]CTATACCCTGGCACACATAATACATGGCACTGTGA R 2 1 2 1 101000 r 74 goat snp51199-scaffold75-1926977 14 53468352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414402 Affx-122949983 AX-123284751 14 39228116 AATCTGCATGTTTTATTTTTTTCCAGATTATCATA[G/T]ACTTTATTTTTCTACTACATTTCTTTGCTAGCAGG K 2 1 2 1 101000 r 74 goat snp51198-scaffold75-1896925 14 53438390 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379370 Affx-122976149 AX-123249729 14 39282834 GCTTTAGTTCAAGAAATATAGCTACAGGACATAAC[A/G]CTGTCATCTACTTCTGCCTAACAGGACTGTCTTAT R 2 1 2 1 101000 f 74 goat snp51197-scaffold75-1842207 14 53382805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773506 Affx-122950675 AX-385260647 14 39330152 TATTTCCAGAGGACTCATTCCTTGTCACGAGTACC[A/G]TAATATCTTTCCTGCTTACTGTCCTCAATAAAAAT R 2 1 2 1 101000 f 74 goat snp51196-scaffold75-1794889 14 53335771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771594 Affx-122950351 AX-385258752 14 39384160 AGAAGGGTAGAAAATGAAGGCAATGATTTTGGCTC[A/G]TAGAAGAGTTGAGAATTTCCATAGCGATAGAGGAT R 2 1 2 1 101000 f 74 goat snp51195-scaffold75-1740881 14 53281482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769641 Affx-122935143 AX-385256811 14 39434693 GACTTTTTCATTCCCTCTGTTGTATATTAAATTAC[A/G]TGTATCCAGTCGGTTTCTTTTTGTTGTTACTATAA R 2 1 2 1 101000 r 74 goat snp51194-scaffold75-1690348 14 53230358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773571 Affx-122969207 AX-385260711 14 39471736 TCTCTAGCAATGTTGAATGTAAAACACAACCTACT[A/G]AACTAAAATTTTAATGTTTCTGGGTTTTAAAATAT R 2 1 2 1 201000 r 74 goat snp51193-scaffold75-1653305 14 53193157 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399018 Affx-122960931 AX-123269373 14 39524234 ACGGAAGGCACGTGGTGATGTGGATGTTAGAACCA[C/T]GCTGTTTTGTAGTACTCCAAAATAGTCGCAAAGAC Y 2 1 2 1 101000 f 74 goat snp51192-scaffold75-1600807 14 53141037 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451426 Affx-122921176 AX-123321759 14 39574579 AACAAAGATTTGCAATTTGAAGAAACTTTTTGGAC[A/G]ATCCCATTATAGTCCATCTTAACAAGATATGTCAC R 2 1 2 1 101000 f 74 goat snp51191-scaffold75-1550462 14 53089605 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429887 Affx-122938126 AX-123300228 14 39616943 TCCAGGGGGTTCTGACTTACCAGGGTAGGGCTGAA[C/T]TGGAAAGACTTGAGCATAATTGATGTCAGCACTGA Y 2 1 2 1 101000 r 74 goat snp51190-scaffold75-1508098 14 53047227 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405180 Affx-122956928 AX-123275532 14 39648409 TTACCCAACCTTTATTCTTCCTTCACCTGTATATC[A/G]TCCCTTTCTTCCAAGGAAAGACTTTTCAAGCATGC R 2 1 2 1 201000 f 74 goat snp51189-scaffold75-1476632 14 53015818 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375609 Affx-122978717 AX-123245968 14 39709727 GAGTATGACTCCCTCCACATCTGCCCTATGAAATG[C/T]ATTATTCTCTCTCTCACTCCTGATACAGCACTCCC Y 2 1 2 1 101000 r 74 goat snp51188-scaffold75-1415314 14 52954757 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780244 Affx-122934401 AX-385267339 14 39762341 CTGGATCTAAAAGGGGACCCCACGTATACATATTA[C/T]TGAGAAAGGGGTTATTCACTTTCCTATGCTTTAGG Y 2 1 2 1 202000 r 74 goat snp51187-scaffold75-1362700 14 52902030 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396969 Affx-122963166 AX-123267324 14 39795927 ATTTCATTCCTTTTATGTTACTGAGATTTGTTTTT[A/G]TTCAAGAACATGGTCTATCTTGATAAATGCTCAAT R 2 1 2 1 202000 f 74 goat snp51186-scaffold75-1329114 14 52868171 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802243 Affx-122964978 AX-385289147 14 39831171 TTAATTGACTAGTGAAAAGCAATTGCTGAATTACT[A/G]CTGGAATATTTTAATCACTAAAGCATTTCTTGTTA R 2 1 2 1 101000 f 74 goat snp51185-scaffold75-1293870 14 52832811 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796793 Affx-122923159 AX-385283736 14 39898454 AATACATCGAGTAGTATGAAACCAGGAATCAAATG[C/T]AGATAGTCAGGCCCTAGACCCCATATTCCTCACTG Y 2 1 2 1 101000 r 74 goat snp51184-scaffold75-1226587 14 52765727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381661 Affx-122974746 AX-123252019 14 39930156 AGGGCTGACGTCTTCCTTTAACAAAGGGTTTCCTC[A/G]TTGTTTGCTGTCCATCAGCCCTGATCACTGGCCAG R 2 1 2 1 101000 f 74 goat snp51183-scaffold75-1194885 14 52733936 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453208 Affx-122920444 AX-123323541 14 39958817 GTTATGGATCCACTTAAGAATTGGGCTATGTTCAC[A/G]TGGAACTCTGCTCAATGTTTATGTGCAGCCTAAAT R 2 1 2 1 101000 f 74 goat snp51182-scaffold75-1166224 14 52705326 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273838 Affx-1111833849 AX-519547448 14 39982133 TTCATGGTGGCACTCATGTCTGCAATTCTCTGCAG[A/G]GATGCAGTGTTGCTTTCAGTTAAATATCCTGGTGG R 2 1 2 1 101000 r 74 goat GoatD01.007191 14 39982133 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447558 Affx-122924036 AX-123317894 14 39994114 AAGTAACGTCTCTCCTCTCATATAAACACTGGTTG[C/T]GACATTTAAGAATAAATCTTTTATTGTGGTGAGCT Y 2 1 2 1 101000 f 74 goat snp51181-scaffold75-1130927 14 52670142 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790384 Affx-122978049 AX-385277387 14 40024853 GGCAGAGTGTAGGTGCAGACAAGGTTGTCTAAAAG[A/C]GTGTTCTCACCTTCTATAGCAGGTGAGACCAAAGT M 2 1 2 1 101000 r 74 goat snp51180-scaffold75-1100188 14 52639353 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402691 Affx-122958350 AX-123273044 14 40061920 TAACTAAGGAAAACATTATTTTCTTGTCACAAATT[C/T]TACTACTTGTATCATCAGCTTCTAGAAGATACCCA Y 2 1 2 1 201000 f 74 goat snp51179-scaffold75-1063121 14 52602829 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424377 Affx-122941838 AX-123294723 14 40092737 GTGATGCTTCTTCCTGCCAGTAGCCTGAGGGGCAG[C/T]GAAGGTACCACAGAGTGAAGAAACACAGAAACCAA Y 2 1 2 1 101000 r 74 goat snp51178-scaffold75-1032304 14 52571911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421900 Affx-122944255 AX-123292247 14 40128773 TTTTTATGAAGTTGAATCCCTCTCATTTTTTTTCT[A/G]TTCCTCTTCCTTCTTTTTCAACTCTCTTAGGAAAC R 2 1 2 1 103000 r 74 goat snp51177-scaffold75-996268 14 52535799 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272738 Affx-1111833008 AX-519546438 14 40158376 AATGGAGCTAATTATACTATTTTATCTGTTCTTAC[A/G]TATGTTTGAAATATTCCAAAGAAAAAGTATTTTAA R 2 1 2 1 101000 f 74 goat 14_40158376_AF-PAKI 14 40158376 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320778530 Affx-122963746 AX-385265642 14 40161274 GAACAATTTTACAAAAACTTTCTATTAAGATCTAA[A/G]TGTTATGGAGGAAAAAATGCTAGTTAAAATAGACC R 2 1 2 1 101000 r 74 goat snp51176-scaffold75-963767 14 52503124 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387656 Affx-122969844 AX-123258014 14 40192270 CCCCAATACATTTGTTGAAAATTTGACCCCTCTTC[A/G]TCATTCCCTGGTAGTTTCTTTATCTCTATAAATAT R 2 1 2 1 201000 r 74 goat snp51175-scaffold75-932771 14 52471978 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393239 Affx-122965476 AX-123263596 14 40224017 GACTGAATATGCTAGACTGTGCCAGTTATGTGACA[C/T]GAGAGGAAGATGCTGAAGCTAGCAGCGCTGGAATC Y 2 1 2 1 101000 f 74 goat snp51174-scaffold75-901024 14 52440295 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794727 Affx-122970129 AX-385281687 14 40277439 ACATAGCCTGTCACATAGATGCAGATTGCAAAGTC[A/G]TGACAAAGTTTGGAGCTTTAAATGAAACAACTCTT R 2 1 2 1 101000 f 74 goat snp51173-scaffold75-847602 14 52386996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445691 Affx-122926124 AX-123316028 14 40307235 TCGCCATAAACAGAGGTAAATATCCAAAGGAGGAA[A/G]GAGAACCGGGAATTGGGTAAAAGCATAACTAATGA R 2 1 2 1 101000 f 74 goat snp51172-scaffold75-817806 14 52357199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384311 Affx-122972277 AX-123254669 14 40367852 CTAAATATAAAACTACTGGGAAACTGATTCGTAGG[C/T]AATATACTATTAAAAATTCACATTGTCTGGTGCTC Y 2 1 2 1 101000 f 74 goat snp51171-scaffold75-757189 14 52295159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378346 Affx-122976835 AX-123248705 14 40406778 AATGAGGGGAAATACAGAGAAAGAGCAAGGGGTAA[C/T]GAAATAGCACCAGAGACAGTACATTCCTGGTGTAG Y 2 1 2 1 101000 f 74 goat snp51170-scaffold75-718263 14 52255969 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434027 Affx-122934218 AX-123304368 14 40496346 CTTAAAAAAAAGAAATATAAAGAAATTTAAATTTT[A/C]TTCTGGAGGGAGGAAGTAACTTGCCCTGTTTCTAT M 2 1 2 1 103000 r 74 goat snp51168-scaffold75-628695 14 52166515 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791080 Affx-122959487 AX-385278075 14 40562072 AATAAAATTACAGAATCAGTAGAAATGACAAGACT[A/G]CTTTGCTAATTTACATGTTTCTTTTCAAGGTCTAC R 2 1 2 1 101000 r 74 goat snp51167-scaffold75-562969 14 52100967 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800853 Affx-122954585 AX-385287768 14 40649008 TAGAATTTCTAGGATATCTACCTCTCTGGCATAGA[C/T]AGATAAACACATCTCCCCAGTGACTGTAACCTGAG Y 2 1 2 1 201000 f 74 goat snp51165-scaffold75-476033 14 52014140 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767833 Affx-122922775 AX-385255054 14 40678235 TCTTCTTTTCTCTTGCTATTAACAACCCAACGTGC[A/G]CATTACTATCTCATGGTTCTTGACGCTTCCTTTTT R 2 1 2 1 101000 f 74 goat snp51164-scaffold75-446806 14 51984980 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445885 Affx-122925960 AX-123316222 14 40715651 AGCAATTGTAAGCTTTTTAAAAAAAACTAAATACC[A/G]CTTTCTAGCCTGTTCTCACTTAAGGTCTTGTTGCT R 2 1 2 1 101000 r 74 goat snp51163-scaffold75-409390 14 51947156 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379491 Affx-122976471 AX-123249849 14 40782639 GGGTGAGAAAAGTGAAAGGGGGTGATTGTTGAAAC[A/G]ACAATCATATTACAGAAATGAAATTGGCAAGGCTT R 2 1 2 1 101000 f 74 goat snp51162-scaffold75-342402 14 51879557 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449167 Affx-122923539 AX-123319502 14 40859700 ATGTTGATACCGTAATGTATAAACCATTTTGAAAA[G/T]CACACTAAGTGACAGCAAAGGGAATTACATTTGGG K 2 1 2 1 202000 f 74 goat snp51160-scaffold75-265341 14 51802332 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430995 Affx-122936686 AX-123301336 14 40908949 TTAAAGAATAGACATCACTAGGCACTAATTGAAGA[C/T]GGTTTTAGAAAATAATTTTACACTGACCTGTTGAG Y 2 1 2 1 201000 f 74 goat snp51159-scaffold75-216092 14 51752148 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444708 Affx-122926425 AX-123315045 14 40948854 AGACTACCTCTCCAGCATCACAGGAGAGTTCTTTC[A/G]TAAAATCAGCATCATGCTTCTCTGTTCCCAACTGC R 2 1 2 1 201000 r 74 goat snp51158-scaffold75-176187 14 51712339 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786632 Affx-122936640 AX-385273664 14 41027657 TGTCATCAGCAACTCTTCCCAGTGCCATCTATATC[A/G]TGGCACTATCTAATTTAGTTTTGAATCTTAAGCAG R 2 1 2 1 101000 f 74 goat snp51156-scaffold75-97384 14 51632567 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415193 Affx-122948993 AX-123285542 14 41061113 GTCATTAAAATGCACAGACATCTTAGCTCATAAAG[C/T]GATTTACATCTACAGTAAAAATAGGGCCCCAAAGA Y 2 1 2 1 101000 r 74 goat snp51155-scaffold75-63928 14 51599137 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771845 Affx-122927966 AX-385259001 14 41096240 GCAGACATGCTATTGGGAGGGAAAGTACAGGAATA[C/T]ATAGCATCTGGTATTATTAGTTATCCAGTTCACTG Y 2 1 2 1 101000 r 74 goat snp51154-scaffold75-28801 14 51564242 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434716 Affx-122933934 AX-123305057 14 41136566 AGATACACACAAATGCAGGCATGTGTATGTGCATG[C/T]GTAGGAAACAAAAAACTTTTCCTTCTGTGCTCTTA Y 2 1 2 1 101000 f 74 goat snp13425-scaffold1518-1212335 14 51524322 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392897 Affx-122965730 AX-123263254 14 41200867 TTCTGATCTTGGATGCTTGAAAGAAAGAGAAATAG[C/T]CACATAGAGCTACACTTAAAGGCTGCCATTGAGTC Y 2 1 2 1 101000 r 74 goat snp13424-scaffold1518-1148034 14 51460102 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430304 Affx-122937272 AX-123300645 14 41252353 ATTTTACTCAGCAGGTGTTAACTGAGTACCTATGA[C/T]GTGACAGCCCCTTTGCTAAGGGACAGGGATGCAGA Y 2 1 2 1 101000 f 74 goat snp13423-scaffold1518-1096548 14 51409639 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452833 Affx-122920734 AX-123323166 14 41304137 AAATTCAGAGGAGAGCTCAAAGGCCAGAGAGTGTT[A/G]TTAAGCTGTCTTACCTGTAGGAAGATTGCATATTT R 2 1 2 1 201000 r 74 goat snp13422-scaffold1518-1044764 14 51357828 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415817 Affx-122948890 AX-123286166 14 41336688 GTAACAGAAAAGCAAACACACCAACATCCCTCCCC[A/G]CAACTTGACCCCACCTGCATTGTGGTGGGGAAAAC R 2 1 2 1 303000 r 74 goat snp13421-scaffold1518-1012213 14 51325139 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437830 Affx-122932102 AX-123308168 14 41365818 ATGACTGAACAAGCAAGAAGATATTTGAGTACTTA[C/T]ACAGCTACAGGCAGCACTTCAAGAGCTCTCATACT Y 2 1 2 1 201000 f 74 goat snp13420-scaffold1518-983083 14 51296216 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427993 Affx-122939171 AX-123298336 14 41401874 TGGTTAGGTTTGTCTCAAATCCAAAGACTGAGCCT[C/T]CTAACTAGTGAGGAGGGATGCCTCTGAGAACTGAG Y 2 1 2 1 101000 f 74 goat snp13419-scaffold1518-947027 14 51260154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416243 Affx-122948209 AX-123286592 14 41457020 ATGCAGTGATTTGGGAACCTGCATACATGGACAGG[C/T]CAACTCATGTTATTCTGGAGTAAGTGGAGGCTCTG Y 2 1 2 1 101000 r 74 goat snp13418-scaffold1518-891881 14 51205060 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410174 Affx-122952780 AX-123280524 14 41502116 ATCACCCTACAAATACCTAGTTTTCAACACAACCA[C/T]TTACCCAAAACCTTTTCCAAGTGACCCAGGCTTTA Y 2 1 2 1 101000 f 74 goat snp13417-scaffold1518-846785 14 51159469 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452304 Affx-122920678 AX-123322637 14 41541750 GCGGTGGAGTCAGGATTAGAGCCAGCAGTGGTCTG[A/G]GTTTAGGACCGTTATCCTTTAGATCACTCTACCTC R 2 1 2 1 101000 r 74 goat snp13416-scaffold1518-807151 14 51119708 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449519 Affx-122922610 AX-123319854 14 41573971 TAGGATGTAAGCATCACAAAGGTACAAAGCATGTC[A/G]TTTTTGTTCAATACTATCTAACAGGGACCAGAACA R 2 1 2 1 101000 r 74 goat snp13415-scaffold1518-774930 14 51087066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777466 Affx-122941466 AX-385264586 14 41622004 ACTTTTCTTTGCCCAATACTTATTTCTCCATATCC[A/G]TGTTAGTTATAAATCTGGCTCAAGTAGCATTATCC R 2 1 2 1 101000 f 74 goat snp13414-scaffold1518-726897 14 51039458 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782047 Affx-122946963 AX-385269125 14 41676248 ATAATTTAAGTCTTATTAAATGTTACTATCACCTT[C/T]AATCAAAGGTGACCAAACCTATTATGGAATTTCAT Y 2 1 2 1 201000 f 74 goat snp13413-scaffold1518-672653 14 50985081 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390531 Affx-122967231 AX-123260888 14 41740181 CTATGTAGACTGGCCCCCACAATCGTTCTGAGTCC[G/T]TCTCAGTGACTCTACTTCTTGTCACTAAGCCTTTG K 2 1 2 1 101000 r 74 goat snp13412-scaffold1518-608720 14 50920894 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795840 Affx-122952660 AX-385282793 14 41794442 GAAAGGATTTTATCAAGAGATAAAAAGGTTTCATT[C/T]AGGGGAGCTAAACTAAAATGTACGGCACTTTTGTG Y 2 1 2 1 101000 r 74 goat snp13411-scaffold1518-554459 14 50866182 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408285 Affx-122953792 AX-123278636 14 41838585 TAAAAAACATATCTACCCATGAAGTCAGAAATTCA[A/G]TTCTGCACAATTGCACTCATCTCACATGCTAGTAA R 2 1 2 1 303000 f 74 goat snp13410-scaffold1518-510316 14 50821524 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276800 Affx-1111835594 AX-519550309 14 41894249 CGAGAGAGGGTCCAATTCGTACGGCAAGGCCTCCC[A/G]GGCCGAGGCTTTGAAGGCCACCTGCCTCCCTGAGC R 2 1 2 1 102000 f 74 goat Random2.2K-1422 14 41894249 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424374 Affx-122941840 AX-123294720 14 41901467 GTGATTCAAGGAGATGGGGAAGGTTAGGATCATGG[A/C]GGAGCTCAGGAGGTTGGAAATCACTACTTGACATG M 2 1 2 1 101000 r 74 goat snp13409-scaffold1518-447434 14 50758897 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782172 Affx-122973686 AX-385269250 14 41936793 ATTAATCAAAACAAGGTTTAATTACATTTAATATT[A/G]TTTGATTAGCATGTGGGACATGTTAGAAATGTTTC R 2 1 2 1 202000 f 74 goat snp13408-scaffold1518-412108 14 50723663 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438606 Affx-122930935 AX-123308943 14 41982520 AGCCCCAGTGTGCAGCATATGCTTCCTTACAAAGT[C/T]AGTGAACATGCCAGAACCAAAGCTTTTGTATGTGG Y 2 1 2 1 201000 f 74 goat snp13407-scaffold1518-366381 14 50677986 T C 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379871 Affx-122975788 AX-123250229 14 42014327 GTCCAGCGTGAATAGAAATCAACTTACTTGAAACT[A/G]AAGACAAGAGACTTCTTTTTTTTTTTTGGTATGTA R 2 1 2 1 101000 f 74 goat snp13406-scaffold1518-334574 14 50645857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389004 Affx-122968647 AX-123259362 14 42070988 CAAAAGCAGAAAAGGGCTAGAAAAGAAGGGTCTAG[C/T]GAGAAATTTAGTGGTGTAATTCATAGTCAGTTAGA Y 2 1 2 1 101000 r 74 goat snp13405-scaffold1518-277913 14 50588461 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790801 Affx-122932513 AX-385277802 14 42119694 TTTCACTGAGAGTAATGCTGACCCTGTCTTCATCT[A/G]TCTATGGTGATCACAGCTGCCAAATCCTTGTCTAG R 2 1 2 1 101000 f 74 goat snp13404-scaffold1518-229207 14 50539552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386451 Affx-122970785 AX-123256809 14 42153021 GTAGGTTCTTTACCACTGAGCCACCTGGGAAGCCC[A/G]CTCTTGCCTTACAGGGAAACAAATTATCTGTGCTT R 2 1 2 1 201000 r 74 goat snp13403-scaffold1518-195880 14 50506234 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381279 Affx-122974470 AX-123251637 14 42188652 ACTGGAGAATCCCAGTCCATGGGATCACAAAGAGT[A/C]GGACACAATTGAGTACACATACTCACGCACTCAGT M 2 1 2 1 303000 r 74 goat snp13402-scaffold1518-160249 14 50470547 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379373 Affx-122976147 AX-123249732 14 42222395 GGCCTCCAAGGTCAGAAGATAATGTACACAACATC[A/G]TTTGTGGGAAAGGTATAAAAGTCCTTTTAAAAAAT R 2 1 2 1 103000 f 74 goat snp13401-scaffold1518-126506 27 38519724 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787489 Affx-122945962 AX-385274514 14 42254960 GAAGTGGAATGAACTAGATGTGGTAATGGATTGAA[C/T]GTTGCTAAAGGAGAAGGAAGTTTCAAAGACAAGGT Y 2 1 2 1 101000 r 74 goat snp13400-scaffold1518-93941 14 50403208 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801298 Affx-122947376 AX-385288210 14 42300563 TCCATAAGGTTCCCTATTGTATTATTAAGTGAGAA[A/G]AGTAAAGTGGCAAATGCTTGCAGTTATCAGAATGT R 2 1 2 1 201000 r 74 goat snp13399-scaffold1518-48338 14 50357634 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431244 Affx-122937132 AX-123301585 14 42338818 CTGAGCACTTCTTTGTCTCCCTCCCTAGATCCTTC[C/T]CCAGTGCCTCCCGCCACCTCCACCCCAGCACAGAG Y 2 1 2 1 101000 f 74 goat snp13398-scaffold1518-10083 14 50318083 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772738 Affx-122936035 AX-385259883 14 42407840 TTCATGCCAAGGAGGCAGCATTTGAGATGCATTTA[C/T]AGTCCATAAGATCGCCTACTTACAAGATTTCTTAT Y 2 1 2 1 101000 f 74 goat snp26648-scaffold2792-46975 14 50248470 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394303 Affx-122964693 AX-123264658 14 42479622 CTCTCTTTTCTCTGGAGAACTCTTAGTATTCAGAC[A/G]TAATTCCTCTTACACAGATCTTCTAAATTTGTTTT R 2 1 2 1 201000 r 74 goat snp22767-scaffold227-621423 14 50173175 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386737 Affx-122970143 AX-123257095 14 42556639 ATGATTAAGTCAGACAGTGAGTATAAAGTACCCAG[A/C]TGAGCATCAGGCACTACCAAACACTCATTTCCTAG M 2 1 2 1 101000 r 74 goat snp22766-scaffold227-544406 14 50095869 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784700 Affx-122951108 AX-385271748 14 42637959 TCACTCTGCATCTCCCAAGTCTAAAGAGGTATCAC[A/G]TATGCTCTCAGCTTCTAATGGACCCCCTTCATCAT R 2 1 2 1 101000 f 74 goat snp22764-scaffold227-463086 14 50014608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276802 Affx-1111835595 AX-519550311 14 42670673 TTCCAGTCATCTTGCCTCAACATATACAATCGGGG[A/C]CCTGTATACATGGGCTTCTCATCCATGGATTCAAC M 2 1 2 1 201000 f 74 goat Random2.2K-1423 14 42670673 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38404925 Affx-122956440 AX-123275277 14 42685409 TTCATGGAATGGTTCTCAAACTCAAAGGGGTCAAC[A/G]GCAGTCATGGAAAGAGAGTGAACAGATATGACAGT R 2 1 2 1 101000 f 74 goat snp22763-scaffold227-415636 14 49967066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271935 Affx-1111833009 AX-187720472 14 42712129 GTTCAGTTCAGTCACTCAGTCGTGTCCGACTCTGC[A/G]ACCCCATGAATCGCAGCACGCCAGGCCTCCCTGTC R 2 1 2 1 103000 f 74 goat 14_42712129_AF-PAKI 14 42712129 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433072 Affx-122935741 AX-123303413 14 42728687 GTTGACCCTATGAACTGCCAGTTCTGGACCTCAGG[C/T]TTCTCAAATGGAAAGCAGCTGTGCCTCTGAGAACT Y 2 1 2 1 201000 r 74 goat snp22762-scaffold227-372358 14 49923878 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774413 Affx-122924503 AX-385261549 14 42820732 ATACTCTTTCTCTTACTGAAAAAGAGTAAAGGATG[C/T]TCCTCACCTTTCACCCACAAACGACTTTCTCAGAG Y 2 1 2 1 101000 f 74 goat snp22761-scaffold227-280313 14 49829578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803098 Affx-122964694 AX-385289969 14 42849768 TGAGGACCCTTCTTGAGCCAGATCCTCATTCCATT[A/C]ACTAAATTTCATTTCACTGAAATCTTCTGGTTTGT M 2 1 2 1 201000 r 74 goat snp22760-scaffold227-251277 14 49800624 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772293 Affx-122950441 AX-385259448 14 42885557 TAAAATCTTAAGGATCTAGAGCAAGACAAAGAGGC[A/G]TTAGGCATGATGCCAATAGCACAATCGATAAAAGG R 2 1 2 1 101000 f 74 goat snp22759-scaffold227-215488 14 49765946 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388451 Affx-122969255 AX-123258809 14 42914619 TGTCCTGGGGTCTTCTTGGATTCTTGTTTTTGTTC[A/G]TTTAATTGTGTGTGATGGGAAAAGAAAGGTGATTA R 2 1 2 1 102000 f 74 goat snp22758-scaffold227-186426 14 49736718 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775725 Affx-122922280 AX-385262856 14 42946858 TGGAAGAACACCTGACTCTGGGACATGAATTGGCC[A/G]TAAGATTTAAGCTGCCCATCATGAACTGGGTATTC R 2 1 2 1 101000 f 74 goat snp22757-scaffold227-154187 14 49704613 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439456 Affx-122930176 AX-123309793 14 42979819 GTTTCTGTCCATCTCTTAGCTCCACCATATGCTTT[A/G]TCATTTGCATATGGTTTTCTCTACATCCTGGGAAA R 2 1 2 1 101000 f 74 goat snp22756-scaffold227-121226 14 49671704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419863 Affx-122945369 AX-123290211 14 43014715 GTGAAGCACTAGTGATGGGTACAGAGAAAGCAAAG[C/T]AAGCAGAAAACAACCCAATTATTGATTCTAGAAAC Y 2 1 2 1 101000 f 74 goat snp22755-scaffold227-86330 14 49636345 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412507 Affx-122951365 AX-123282856 14 43047837 ATGGTTTTCTTCTCCTTATACAGTACACTTCAACT[A/C]TTTAAATAATTTAAAAGTTATTTCTCATGGAAACA M 2 1 2 1 103000 f 74 goat snp22754-scaffold227-53208 14 49602952 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427531 Affx-122939512 AX-123297874 14 43085454 CTGCTATTTTGTTTTGGCTTCACCTGACCTCTAAT[A/C]ATTAGGCTAGCAGCTTTATCTTCTGGGGAATTAAT M 2 1 2 1 101000 f 74 goat snp22753-scaffold227-15591 14 49566712 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276939 Affx-1111835596 AX-519550448 14 43096316 ACCGTCTGAGCCACCAGGGAAGTCTAAGGTTTAAA[A/C]TACTGATAGTGTTTATCTTCTAGTGATACTGTGAA M 2 1 2 1 101000 r 74 goat Random2.2K-1424 14 43096316 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779744 Affx-122920800 AX-385266844 14 43111754 CTGAGAGATGGCTACTATTGCTTTCTATTACTATT[A/G]CTAAAGTATTACTTTCTGACCAGAAGTGCTTTGAG R 2 1 2 1 201000 f 74 goat snp35355-scaffold424-1045046 14 49540726 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414553 Affx-122949394 AX-123284902 14 43150050 GCCCCCTCATGGCTGAAGCAGGACATGCCATCCTG[C/T]GGATTCTCTGGTGCTTTCTCAGAAATGGACCAGGG Y 2 1 2 1 101000 r 74 goat snp35354-scaffold424-1006750 14 49502353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801855 Affx-122935750 AX-385288762 14 43195999 TTATTGGCATCCTAAATCTGTGAATGACGAAAGCT[A/G]TGGAAAAATTCTATAGGGTAGAGGGAAAATGAAAC R 2 1 2 1 101000 f 74 goat snp35353-scaffold424-960801 14 49456512 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412858 Affx-122950446 AX-123283207 14 43224503 AGTTCTTTACCATCTGAGCCACCAGGGAAGCCCAA[C/T]GGTGAGATAAAAAAGGACTTTAAAAAGCCTGTAAC Y 2 1 2 1 101000 r 74 goat snp35352-scaffold424-932297 14 49428026 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423156 Affx-122942750 AX-123293502 14 43288874 TATATTCTCAGGTTATGGGAGCTGAGAAATCAACA[C/T]GTGAGATTGGATGGAGAGTTCAGTGGACAGTGGAG Y 2 1 2 1 101000 f 74 goat snp35351-scaffold424-867926 14 49363951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382602 Affx-122973714 AX-123252960 14 43322450 GCAATGGGCAGAGGGGAACCGGAGCCACATTGAGA[A/G]TAAGAGTGACTGTTTCTTGGTGGCCTTGGAAATCA R 2 1 2 1 101000 r 74 goat snp35350-scaffold424-834350 14 49330269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425647 Affx-122940887 AX-123295993 14 43394277 ATGAAAAATAAAAGATTAATTTGCCATTTCTGCTG[C/T]AAAGGAACCAAGGTGATATTTTGACATCAAACAAG Y 2 1 2 1 101000 r 74 goat snp35349-scaffold424-762523 14 49258377 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437288 Affx-122931986 AX-123307626 14 43439094 GTGTGTACTGCAGACCCCAAAAGTTCTGGAGTTAG[C/T]GGTAACAGACACCTCTTGAAGTGGAAGGGAGGCTT Y 2 1 2 1 201000 r 74 goat snp35348-scaffold424-717706 14 49212683 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784625 Affx-122975502 AX-385271673 14 43479567 ACGACCCCTACGTTCCAATAACTCAGTGTATTTCT[A/G]CTCTTCTCTTGTGTGGTAAACTTTCTTCCTTATGC R 2 1 2 1 201000 r 74 goat snp35347-scaffold424-677233 14 49171822 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783549 Affx-122927234 AX-385270611 14 43517609 AGTCTCTTCAGAGGCTTTCAAGTTTTAAGGAAAAG[C/T]AACAACCCAATTGATACATGGGCAAACACTGATAG Y 2 1 2 1 101000 f 74 goat snp35346-scaffold424-639191 14 49133453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792255 Affx-122944708 AX-385279238 14 43588001 GAATAGATGCTTGTATTGCTTTTCCTGACTTTATA[G/T]CCAATGTTGAAAACCAAAAGATAATAAAACTTTCT K 2 1 2 1 201000 r 74 goat snp35344-scaffold424-568799 14 49062649 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426901 Affx-122940458 AX-123297246 14 43617464 GCACTGCTGATAAATCTTTTATTTAATAAAAGTGT[A/G]TTGAGAAATCACAGAGCATCAATCACTGGTGATAT R 2 1 2 1 101000 r 74 goat snp35343-scaffold424-539336 14 49033122 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433230 Affx-122935612 AX-123303571 14 43657495 TAAGATCTTTTATTCTGTCAGTTTTATTCATGGCA[G/T]GTATGTGACAAATTCCCAACAATTTGCAATCTATT K 2 1 2 1 101000 r 74 goat snp35342-scaffold424-499305 14 48992633 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451261 Affx-122921931 AX-123321594 14 43717186 TCTCTATTCTTAGCAAATAAAATGTTTAAAGAAAA[C/T]ACCGTAAAACATATCTCTATATTTGGCAATATACT Y 2 1 2 1 101000 r 74 goat snp35341-scaffold424-439614 14 48932314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413688 Affx-122950096 AX-123284037 14 43758969 CTGTGCTTCATCCTTCTAACAGTTTTATTTATCCT[A/G]TTTATTTTGTTTTCTATAGCAAAGTTGAATATTCA R 2 1 2 1 303000 r 74 goat snp35340-scaffold424-397831 14 48890284 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443224 Affx-122927569 AX-123313561 14 43804167 AGATAACCACATTTATAGCACTGAGTCATCAGGAC[A/G]TTTTTTTCTTAGGTTTCCAGACACCAGGAATCCAA R 2 1 2 1 101000 f 74 goat snp35339-scaffold424-352633 14 48845282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448647 Affx-122923354 AX-123318983 14 43853981 TGGGCAGAGAACAGATCATTGTGTGTGACCTGATT[C/T]CATTTCAGTGAGTGTCCTCGTAAAGAATGACATCA Y 2 1 2 1 201000 r 74 goat snp35338-scaffold424-302819 14 48795303 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405752 Affx-122956504 AX-123276104 14 43924063 GTGCTACTCCAACTTTAAAAATTACCTGGAGAGTA[C/T]GTTATGTCATAGAAGAATCTGCATTTCTAACAAGC Y 2 1 2 1 101000 r 74 goat snp35337-scaffold424-232737 14 48725041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411576 Affx-122951626 AX-123281926 14 43970081 ATCTTCTGCCTGGGACCTGGGAATGGCATTTCATA[C/T]GCATATTGATGTGACTGAGTGGAAAAATCTGGACT Y 2 1 2 1 201000 r 74 goat snp35336-scaffold424-186719 14 48679228 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408075 Affx-122954731 AX-123278426 14 43999919 AGCCAGGAACCCATCACTTGGAGCACTTTTAGTCT[C/T]ATTGGCTTGGTTTTGCTCATGGTGGCTGTTCAGCA Y 2 1 2 1 101000 r 74 goat snp35335-scaffold424-156881 14 48649439 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408824 Affx-122954026 AX-123279175 14 44038447 TCAGTATTAAAAAGTGTGAATTTAAAAGGCTGAGA[A/G]GTAGGGCTCTGTGTCTGAAGGTAGGGCTTGTCATT R 2 1 2 1 201000 f 74 goat snp35334-scaffold424-118353 14 48610999 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391343 Affx-122967301 AX-123261700 14 44068842 TTTCTTAGTGGTTTCAAAGGTGATCAAATAACTGT[A/G]CCTAAGGCTTTGTTTATTAATAAAGTGCATTTAAG R 2 1 2 1 101000 f 74 goat snp35333-scaffold424-87958 14 48580476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377465 Affx-122977514 AX-123247824 14 44152544 GCAGCTTTCCATGTAGAAGTGATGTGGTTGTAGAC[A/G]TGACCCAGCAATCTTTACACACATTCAGTGCCCGA R 2 1 2 1 101000 f 74 goat snp35331-scaffold424-4256 14 48496177 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441856 Affx-122929038 AX-123312193 14 44185279 TGGCATCTTAATATAAGGTGTGAATTTAACATAAA[C/T]CCATCCTAACAGAAATCCTAGAAGACCTGAACAGA Y 2 1 2 1 202000 f 74 goat snp23485-scaffold237-28380 14 48463599 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426680 Affx-122939914 AX-123297026 14 44214759 TCACTCCTCCCAGGAAAGAGGCCAAGAGCTTCCTT[C/T]AATTGACTCCCTCCTGCCCCCTTTCATTAACATAT Y 2 1 2 1 102000 r 74 goat snp23486-scaffold237-57860 14 48433418 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789923 Affx-122942732 AX-385276929 14 44268709 AGCAAAAAAACAAAGGCATCAGGGAGACATGAGGG[C/T]AAATGCCTCATGTACACACTGACTTTGAGATTCTG Y 2 1 2 1 101000 f 74 goat snp23487-scaffold237-111810 14 48379239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413012 Affx-122951008 AX-123283361 14 44302233 TGGCAAAACTGAAACTCTGTACCCATGACTCATTC[A/G]CTCTCTTTTCCTTATCACCCCCAAACCACGATTCT R 2 1 2 1 201000 r 74 goat snp23488-scaffold237-145334 14 48345819 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774167 Affx-122966249 AX-385261304 14 44334247 TCAAAATAAAACAAGTATTGCCTTCAGTAAGGACT[A/G]TACCATGTTTTGTGCGTTCTTTAGTCCCTGTTCTC R 2 1 2 1 101000 f 74 goat snp23489-scaffold237-177348 14 48313668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785544 Affx-122975784 AX-385272589 14 44363637 ATAACGCCAATCACAAAGGTTACATTCACTTTTTT[C/T]TGTTTGTTTTGTAGGAAATTCAACATCAATTCTAC Y 2 1 2 1 101000 f 74 goat snp23490-scaffold237-206738 14 48284305 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436372 Affx-122933054 AX-123306711 14 44453987 GTTTAATGTCTTCCACTCGACTGTATGTTTCATAA[C/T]GACAAGGATGATCTGCCCAGCATTGTGCTTAAAGT Y 2 1 2 1 201000 f 74 goat snp23492-scaffold237-297088 14 48193994 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441322 Affx-122929438 AX-123311659 14 44496884 AGCTGTTTTTATGAGGCACCTGTGTGCACAGAATT[A/C]TGTCACTTGGCTCCCTGGGCCTTCTTCCTCAAGAG M 2 1 2 1 101000 f 74 goat snp23493-scaffold237-339985 14 48150979 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432811 Affx-122935400 AX-123303152 14 44530378 TCTTAGTATGGGAAGTCTAGGATAGGCCTTTTTAC[G/T]ATTCTTTTAGAAAACCTATTTTTAAAGAGAGGAAC K 2 1 2 1 101000 f 74 goat snp23494-scaffold237-373479 14 48117504 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390056 Affx-122968418 AX-123260413 14 44703425 GTGGTTGTTTGACAAACTTAAGTCTTCCGCTTTAG[C/T]ATTGGTGTAGGTATATTGTGGTGCACATGTTCCTA Y 2 1 2 1 101000 r 74 goat snp23498-scaffold237-546526 14 47946114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417908 Affx-122946736 AX-123288256 14 44739838 AACTTCTTTTTCAGTAGATGTTTTATTGAAGTATT[A/G]TATTTACAGAAAGGTTCAGCCAAATAATTTTTTGT R 2 1 2 1 101000 r 74 goat snp23499-scaffold237-582939 14 47909609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795139 Affx-122970214 AX-385282097 14 44814405 ATAGATTTCTAAGATTGTATACTTACATCCAACAC[A/G]TATTCTTGAATTATGGCATGAATAATTATCGCCAC R 2 1 2 1 101000 r 74 goat snp23501-scaffold237-657506 14 47834466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791262 Affx-122938138 AX-385278256 14 44897616 TTCTGTATAAGTGTTTTGCTATTAAGTGTGTTCTT[A/G]CTGCTTAGTGGTCTGTGGAGTAGAACAATTCATTT R 2 1 2 1 101000 r 74 goat snp23503-scaffold237-740717 14 47753461 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799091 Affx-122974834 AX-385286021 14 44959478 TTTTGCCTTATTTTGGATAGAAGACAGCAGTAGAG[A/C]TTAATTTAAGTCAGACAAACTGGCTTAAATGGTTT M 2 1 2 1 102000 f 74 goat snp23504-scaffold237-802579 14 47691204 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779361 Affx-122960956 AX-385266465 14 45003435 TTTTTCAAGTAGAAGTGAAAAATACTTGTAAAAAT[A/G]ATAGTTCTTTTTGCCTGCCAAGGGCAAAACATTGT R 2 1 2 1 303000 f 74 goat snp23505-scaffold237-846536 14 47646699 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391021 Affx-122966880 AX-123261378 14 45033168 GATCTGAGTCAAAAATCTTTAGAAATCTTTTCCAG[C/T]AGGATCTCTAGTTTAGTGTTTTATCTTTCTGTCAT Y 2 1 2 1 201000 r 74 goat snp23506-scaffold237-876269 14 47616268 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418698 Affx-122946295 AX-123289046 14 45093484 GACAACATCGTTTCATGGGCACTGATTTTATTGTA[A/C]GGCCAGGAGGATGGCGAAGTGGGGGATGGTTTTAG M 2 1 2 1 101000 f 74 goat snp23507-scaffold237-936585 14 47556959 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383257 Affx-122972741 AX-123253615 14 45141276 TGACTAAGTGACTGAACAACAAACCACAGCAATGC[A/G]TCAGGCGTGTAATAAGCCCTTCATGTGTGTTATCC R 2 1 2 1 201000 r 74 goat snp23508-scaffold237-984377 14 47509319 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442387 Affx-122928007 AX-123312724 14 45181403 ACTAAAGTGGAGATGGGAAATAAGACATTTGTTAC[C/T]TCTAATCTGTTATTTACTCAGTTCTGTGCTAGGCA Y 2 1 2 1 101000 f 74 goat snp23509-scaffold237-1024504 14 47469219 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385659 Affx-122971155 AX-123256017 14 45212984 CTCAATTCCTCTACCTTTTATTCTCTCACTCTCTT[C/T]AGACATCTTCCCCTCAGCCTAAAACAAGCACATAT Y 2 1 2 1 101000 r 74 goat snp23510-scaffold237-1056085 14 47437780 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435506 Affx-122933421 AX-123305846 14 45244694 ATATGGCAACCTTTATTCTATGTCTATGGAAGATG[A/C]TCTCAATAAAATGCATAGAAATTTAAAGAAATGGG M 2 1 2 1 101000 f 74 goat snp23511-scaffold237-1087795 14 47405968 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404410 Affx-122956779 AX-123274762 14 45276758 ATATACTAGTGAGCTGGACTGAGGTGAGCTGGAGC[A/G]TGCAGAAAGAATGTGTCCAATGGCCTCTGTTTACC R 2 1 2 1 101000 r 74 goat snp23512-scaffold237-1119859 14 47373926 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382303 Affx-122973911 AX-123252661 14 45330886 CAGTCACTCGACACAGTAGTGAACACCCCTCATTC[C/T]GGAAATACTATTCTCCAGGTCTTTGTGATGCCTCG Y 2 1 2 1 201000 r 74 goat snp23513-scaffold237-1173987 14 47319825 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444687 Affx-122926441 AX-123315024 14 45375576 TTCCTGCCTCTGTGCTTGCTATTTCCTCTGCTTAT[A/G]AAACTCTTTCTCCTGATGGGCACATTATCCACTGG R 2 1 2 1 201000 r 74 goat snp23514-scaffold237-1218677 14 47275104 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401536 Affx-122958914 AX-123271889 14 45405315 AAAATATTCTTTTCATTTCAGTGGCTAAGAGATGA[C/T]AGTATGAGAGCTTAGATGTCAGCACAAAAGGAAAG Y 2 1 2 1 101000 r 74 goat snp23515-scaffold237-1248416 14 47245345 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788499 Affx-122924156 AX-385275516 14 45453582 ACGACTGAAATGACGGAGCATGCACGATACTGTAT[A/G]TGGCCCACGAAAAAGAGAACCCTGTTTTGATTCAC R 2 1 2 1 201000 r 74 goat snp23516-scaffold237-1296683 14 47196845 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445474 Affx-122925209 AX-123315811 14 45492799 TCAACACATAGCTCCAAAAAAAAACTAATTCTGGG[C/T]TTGGCAAATGGGGCACTAACAAGGATGATGCAAGC Y 2 1 2 1 102000 f 74 goat snp23517-scaffold237-1335900 14 47157602 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454188 Affx-122919302 AX-123324521 14 45522387 TTTTTCTGCTACTTTGAAATATAAGATAAAAAGTG[C/T]GAGGGAAGGAGTTAAAAGATACCTACTACTTCGTA Y 2 1 2 1 101000 r 74 goat snp23518-scaffold237-1365488 14 47127972 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402148 Affx-122958657 AX-123272501 14 45581834 TCATAGAACTGATGCTATCACAATGTACAAGTTGA[A/G]AACAATATTAGTATATATTAATACAATGGTTTCAC R 2 1 2 1 101000 f 74 goat snp23519-scaffold237-1424935 14 47066817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384328 Affx-122972262 AX-123254686 14 45613552 GAGTACCGTAGATTTGCATGGAGTTTGAAAAAACC[A/G]AGCTTGTAAGTCAAGTTTTCTGGAAACTGAAAATA R 2 1 2 1 101000 f 74 goat snp23520-scaffold237-1456653 14 47035091 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447770 Affx-122924565 AX-123318106 14 45672499 AAAATTTTCAATAAGAATGTAAATGTCTTTTGCAA[C/T]GCAAGCCAAAATCCAATAAAACATATATTCACAAT Y 2 1 2 1 201000 f 74 goat snp23521-scaffold237-1515600 14 46979836 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768579 Affx-122947511 AX-385255759 14 45801724 TCCTGGTATTATTTGGAAGCAAATCCAAAACACAG[C/T]ATGAGTTCATCAGTAAGTATTTCAGTATATTCATC Y 2 1 2 1 101000 f 74 goat snp23523-scaffold237-1644825 14 46849668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778582 Affx-122922305 AX-385265693 14 45837202 TTCTCTCAATGCCAGGACAGTTTGCCTCAAAGGGA[A/G]ATCTCATCATTTGCTCCTTCCTGTCTTCTGGGTAA R 2 1 2 1 101000 f 74 goat snp23524-scaffold237-1680303 14 46814400 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768379 Affx-122920360 AX-385255559 14 45867241 GGGTACCATTTGCTTTCTCTGCTCCTAAGTAAAAA[C/T]GTTTATGATTCAGGAGAAAAGACTATAGTGATTCC Y 2 1 2 1 101000 f 74 goat snp23525-scaffold237-1710342 14 46784208 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379773 Affx-122975845 AX-123250131 14 45904383 CTAGAGCGAATCGAGGACAGAGTCACAGCGCTGTG[C/T]GTTTCAGGAGTTGACATGGCTTTTCCAAACTGGAA Y 2 1 2 1 101000 r 74 goat snp23526-scaffold237-1747484 14 46745837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447378 Affx-122924856 AX-123317714 14 45934084 TGCCTGTTTCAACTTTATATAAATAGAGTCCTGCT[A/C]TGTGTTTCTGCAGGGTTGGTTTTTTTTTTTTTTTT M 2 1 2 1 101000 f 74 goat snp23527-scaffold237-1777185 14 46715541 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796577 Affx-122944228 AX-385283523 14 45995371 TCCTTTTCAGATCACTTTCACATAGTTATACCACT[C/T]GATCCTTTTGGAGTGATGAGTCTAATAAGTCTTAT Y 2 1 2 1 101000 r 74 goat snp23528-scaffold237-1838472 14 46654071 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272540 Affx-1111833010 AX-519546257 14 46026014 CCTACTGCGAGCCCTGGAGGCAGAGAGCCGAGACT[A/G]CTTGTGAACAGCATTAATGACTGCGAAACTGCCTA R 2 1 2 1 101000 r 74 goat 14_46026014_AF-PAKI 14 46026014 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38442766 Affx-122927743 AX-123313103 14 46042923 TTAGCTTGTGACTTATTGCTCTTTATCCAGTTTCA[C/T]GGAATTTCACCCTGCATGTGTGTGCACTGGTTGTC Y 2 1 2 1 101000 f 74 goat snp23529-scaffold237-1886024 14 46606155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424184 Affx-122942520 AX-123294530 14 46079051 AGGCAATCATGTGTGACCTATTGCTCACTGATGAA[C/T]ATGCTAAGAGCAGCAGTGTGGTGGTGGTTTTTTTT Y 2 1 2 1 101000 f 74 goat snp23530-scaffold237-1922152 14 46568912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443998 Affx-122926908 AX-123314335 14 46111787 GAAGATTTGACAATTGCCTGGGGTGGGTATGGGAA[G/T]CCAGTAGCAGAGGTTTCAGCACACCACTGTAAGCC K 2 1 2 1 201000 r 74 goat snp23531-scaffold237-1954888 14 46536287 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430988 Affx-122936692 AX-123301329 14 46141764 CTTCCACGTAGGGAAATGAACTCATTTAAGGTAAA[C/T]GAAAGTTCTTAATTGATCTAGAACAGTGCTATCCA Y 2 1 2 1 202000 r 74 goat snp23532-scaffold237-1984865 NW_017193372.1 3583 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409598 Affx-122953561 AX-123279949 14 46188982 GAAGAGGCTTATCTTCATGGGCCAGTGCTGAGTTT[A/G]TTAATCAACAGAGCTGGTGTAGTTGTGGAGTGGAA R 2 1 2 1 101000 r 74 goat snp23533-scaffold237-2032083 14 46457263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400156 Affx-122960692 AX-123270511 14 46221333 TGGTTGCAAATCAGGCAGTGCCCTAAGCCACCCTG[A/C]GTACTCACTCTCGGCTTCATCTCTCTTCTTACCCC M 2 1 2 1 101000 r 74 goat snp23534-scaffold237-2064434 14 46424626 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437256 Affx-122932010 AX-123307594 14 46286858 GGTCTACTGAGGACACTGATGCCTCTGCTCCCTGA[A/G]TAGTAACCAGAGAATGCTGAGAGTTTTCTATGTGA R 2 1 2 1 201000 r 74 goat snp23535-scaffold237-2129959 14 46350423 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802558 Affx-122971284 AX-385289461 14 46342972 ATGAATATAGCCTAATTCCTTTATTCACTAGTGAC[A/G]ATATGCTAGTAAAAGGAAATATACTCTTATAGTCA R 2 1 2 1 101000 f 74 goat snp23536-scaffold237-2186073 14 46294644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476298 Affx-1251763805 AX-586011717 14 46356772 CTAATATTATAAATAAACTATATTTCAATTTAAAA[-/TATTAAGGAGGGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAATAAAGTCGTTTGTTATTTTGGTAAAAAAAAAATAC]ATTAAAAAATAACAAAGCACATTTGTAAAGTATAA - 8 1 4 1 20000 f 74 goat SV_260 14 46356772 - deletion junction SV-TF-chip 539476551 Affx-1251763805 AX-586011938 14 46356772 CTAATATTATAAATAAACTATATTTCAATTTAAAA[-/TATTAAGGAGGGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAATAAAGTCGTTTGTTATTTTGGTAAAAAAAAAATAC]ATTAAAAAATAACAAAGCACATTTGTAAAGTATAA - 4 1 4 1 20000 r 74 goat SV_260 14 46356772 - deletion junction SV-TF-chip 562165568 Affx-1251763805 AX-606940979 14 46356772 CTAATATTATAAATAAACTATATTTCAATTTAAAA[-/TATTAAGGAGGGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAATAAAGTCGTTTGTTATTTTGGTAAAAAAAAAATAC]ATTAAAAAATAACAAAGCACATTTGTAAAGTATAA - 8 1 4 1 20100 r 74 goat SV_260 14 46356772 - deletion junction SV-TF-chip 562165648 Affx-1251763805 AX-606941058 14 46356772 CTAATATTATAAATAAACTATATTTCAATTTAAAA[-/TATTAAGGAGGGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAATAAAGTCGTTTGTTATTTTGGTAAAAAAAAAATAC]ATTAAAAAATAACAAAGCACATTTGTAAAGTATAA - 8 1 4 1 20100 f 74 goat SV_260 14 46356772 - deletion junction SV-TF-chip 562165677 Affx-1251763805 AX-606941086 14 46356772 CTAATATTATAAATAAACTATATTTCAATTTAAAA[-/TATTAAGGAGGGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAATAAAGTCGTTTGTTATTTTGGTAAAAAAAAAATAC]ATTAAAAAATAACAAAGCACATTTGTAAAGTATAA - 8 1 4 1 20100 f 74 goat SV_260 14 46356772 - deletion junction SV-TF-chip 562166289 Affx-1251763805 AX-606941697 14 46356772 CTAATATTATAAATAAACTATATTTCAATTTAAAA[-/TATTAAGGAGGGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAATAAAGTCGTTTGTTATTTTGGTAAAAAAAAAATAC]ATTAAAAAATAACAAAGCACATTTGTAAAGTATAA - 8 1 4 1 20100 r 74 goat SV_260 14 46356772 - deletion junction SV-TF-chip 320799772 Affx-122922250 AX-385286699 14 46403212 AATTAACAATAATATCCGATATACTATTTCCCACA[C/T]GAACCTGAGACAACCTGTGAAACAGGAAGGAAGAT Y 2 1 2 1 101000 r 74 goat snp23537-scaffold237-2246313 14 46234012 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773062 Affx-122931163 AX-385260205 14 46450774 ATTTTAAATTGCATGGCATGTTTACAAAATGCTAA[G/T]CACCTACACTTTTTTTTCCCAAAGTTTTGTATATA K 2 1 2 1 102000 r 74 goat snp23538-scaffold237-2293875 14 46186613 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432420 Affx-122935830 AX-123302761 14 46532989 CCGACCTGCCCTGCATCCCTGTAAACACACTCGCC[G/T]CATGCTTTTTTGCAGCAAGGGGGTTGGCAGGATAC K 2 1 2 1 201000 f 74 goat snp23539-scaffold237-2376090 14 46104261 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401392 Affx-122959220 AX-123271745 14 46563932 CTTTACTATTTGAGCCACAAGGGAAGCCAATCTTA[C/T]AGATCATTCTTATTTGAAAGACATTTTATGCACCC Y 2 1 2 1 201000 r 74 goat snp23540-scaffold237-2407033 14 46073451 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385794 Affx-122971042 AX-123256152 14 46628306 AAAGCACTTTAGATTGGCAGCACAGACACCCTCTG[C/T]ACAGGGCAGCTTCAGTGAGAAAATGAGCTTACATC Y 2 1 2 1 101000 f 74 goat snp23542-scaffold237-2471407 14 46009052 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799266 Affx-122940480 AX-385286196 14 46657313 TTCGAAAGCAGTGTTTCTAAACAGAGATCTAAATA[C/T]AGCTATATAATCACAGAGCTAATGAATGACTCACC Y 2 1 2 1 101000 f 74 goat snp23543-scaffold237-2500414 14 45980027 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802039 Affx-122923388 AX-385288943 14 46701049 TGAGAAAATATGGTTTTATCTTAGAACTCCATAGA[C/T]GGTCCATTACCTTCTGTTGGTGGTTTCGTCTCTAT Y 2 1 2 1 101000 r 74 goat snp23544-scaffold237-2544150 14 45936241 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769331 Affx-122959155 AX-385256502 14 46742265 CAAATCCTCTAAGAATGAGGAATCTATATTCACCC[A/G]TTCTTTAATTCTTTAAACCTAGAAAGTCCTAGTAC R 2 1 2 1 201000 r 74 goat snp23545-scaffold237-2585366 14 45894719 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400129 Affx-122960713 AX-123270484 14 46770883 CCTGAATACTTTCATCAAGAGACTTGGTGATTTTT[A/G]AGATGCTGTTTTTACTGAGAATCTTTTCCTTTTCT R 2 1 2 1 103000 r 74 goat snp23546-scaffold237-2613984 14 45866255 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386009 Affx-122971504 AX-123256367 14 46802792 GTGGGCTAGAAAGTGGGGATAAAGCCAAAGCCATC[A/G]TTTCCCACCCTCAGCTTTGTTCCACTCCACTGTCA R 2 1 2 1 101000 f 74 goat snp23547-scaffold237-2645893 14 45834341 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796898 Affx-122931302 AX-385283840 14 46813147 TCATTAATTCAAAAGCTCCTGTCTCTAGTACTCCC[G/T]CTCATTTGAGTTGTCCTGATCTCCACCCGCTGAAA K 2 1 2 1 101000 f 74 goat snp15522-scaffold1641-4624 14 45822652 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435922 Affx-122932758 AX-123306261 14 46859244 ATTTTTCTCCGAGCTACATTTATTTACTTAGCGAC[A/G]TATGTGTGCCACGATCTTCACAAAGCCATAAAATA R 2 1 2 1 101000 r 74 goat snp15523-scaffold1641-50721 14 45776094 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408797 Affx-122953364 AX-123279148 14 46897363 AGAGTGTCTTGTCCAAGACCTGCCTCTGACCATTA[C/T]ACCTGTGTGACTTTGGGCAAATTGCTTAACCTCTC Y 2 1 2 1 201000 f 74 goat snp15524-scaffold1641-88840 14 45738044 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276806 Affx-1111835597 AX-519550315 14 46914776 GTAGTTTAAAAGAGGAATGACCAGTATCAGCAAAC[A/G]GAGCCAGGGTGCCGAGTCAGCGTGCAGAATCGGTA R 2 1 2 1 101000 f 74 goat Random2.2K-1426 14 46914776 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390141 Affx-122967990 AX-123260498 14 46983001 TTCTAGCATCTCCATAATTCAGAATACCAACCAAA[C/T]GAAGTTGCTCAGTTGTGTCCAACTCTTTGCAACCT Y 2 1 2 1 101000 f 74 goat snp15526-scaffold1641-174478 14 45652554 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383961 Affx-122972946 AX-123254319 14 47028238 GCCGAGAAATGGTGATGGCAAAGTAAGAAATATTA[C/T]ATCAGTTATAAATAACAGAAAACCCATCTTTTTTA Y 2 1 2 1 101000 f 74 goat snp15527-scaffold1641-219715 14 45607321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422417 Affx-122943369 AX-123292763 14 47079728 ATAGGCAAGGCAAATGTCTCTAAATTATATCAATA[A/C]GAAAATCTGGGGGAAAGTATCTGTGTATTCACCAA M 2 1 2 1 101000 f 74 goat snp15528-scaffold1641-271205 14 45555414 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437195 Affx-122932054 AX-123307533 14 47175083 TGTAAAGATTCTTTTGAAAGTTTTATTCACATTGT[A/G]GAACAGCAAATGACATTTTTACAGTATTTTTTTGT R 2 1 2 1 101000 f 74 goat snp15529-scaffold1641-366560 14 45459456 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440731 Affx-122929884 AX-123311068 14 47223547 TAATCCACCCCAAGAATAAACAGTAAAAGGGATGA[C/T]GATTTTCTAGGAAGCACAGAATCTGGCTGCAAGTA Y 2 1 2 1 101000 r 74 goat snp15530-scaffold1641-415024 14 45411375 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778215 Affx-122945571 AX-385265330 14 47262047 TCTTACCTGCCACTGGCAATGAGACCTTTGGCTAT[A/G]TTCCCTACTAATAATAAGATTGGTTTTATGAAACC R 2 1 2 1 101000 f 74 goat snp15531-scaffold1641-453524 14 45374394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784194 Affx-122948853 AX-385271245 14 47314559 AACAAAAAGTTCAAATTCAAAAATGTCAATTTAGA[C/T]GGGATTTTCCCCCTCTAACACATACTGAACAAAAT Y 2 1 2 1 201000 f 74 goat snp15532-scaffold1641-506036 14 45321890 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274398 Affx-1111834176 AX-519547991 14 47331773 GCACAATGCTTCCTTGCAAAGAA[A/C]AGGCTGCAGATTACCCATGGCTACAGCACAGGACA M 2 1 2 1 101000 r 74 goat GoatD01.023432 14 47331773 T G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38389610 Affx-122968760 AX-123259968 14 47364018 CAGGTATCCATTAAATGAGCCCAGACTATTTTCTA[C/T]TGTTCAAGGATTTTTTCGCTGTTTTGAAAGCCTAA Y 2 1 2 1 101000 r 74 goat snp15533-scaffold1641-555495 14 45272091 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431873 Affx-122936062 AX-123302214 14 47452159 CACTCAGAGAACCTCTGTATCAGCTTTCTCACCTC[C/T]ACAATACTGGGAAGGGGCCAGGGAGCATTCTTCTT Y 2 1 2 1 201000 f 74 goat snp15535-scaffold1641-643636 14 45183491 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781103 Affx-122925957 AX-385268188 14 47503265 CAGGGAGACATGTTGTCAGATTCAGGCAATGCAAG[C/T]AGTCTCAGATTATTGATAATAATCATTAAAGGGTC Y 2 1 2 1 101000 f 74 goat snp15536-scaffold1641-694742 14 45132241 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416498 Affx-122947787 AX-123286846 14 47555560 GGATGGTCTTCCTTGCCTGCTCCGTTTCTCTCTAC[A/G]TTCTCCCCTGCATCCAACTAATTCAATTTCAAAAC R 2 1 2 1 201000 r 74 goat snp15537-scaffold1641-747037 14 45079937 G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792228 Affx-122963560 AX-385279212 14 47637330 ATTAAAGACACCTTCACAGACCTTAACTATGCAAA[A/G]GTATCAGCATAAAAGAATAGTGCAGTAGCTGGCTT R 2 1 2 1 101000 f 74 goat snp15538-scaffold1641-828807 14 44999474 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436904 Affx-122933211 AX-123307242 14 47689024 TTGAAGTAAAGCTCTGTCACTAGAAAAATACTATC[A/G]CTACCATACATAGAACAAAGGGCTTAATGTTCACC R 2 1 2 1 101000 r 74 goat snp15539-scaffold1641-880501 14 44946820 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789876 Affx-122924996 AX-385276883 14 47743287 CGTTAGATGAAAATGTACCTGTATTTTCAAGGGAA[C/T]AGTAACAATTTGTGAACATAGCAGCACATTCAAAT Y 2 1 2 1 101000 f 74 goat snp15540-scaffold1641-934764 14 44891995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801451 Affx-122921624 AX-385288360 14 47769541 AATATGTGATAAGTTAGCATGAAGACTGCTATTTT[A/G]TAAAAGGTACTATCCATCTGTATGGGTAGGATCGT R 2 1 2 1 101000 r 74 goat snp41241-scaffold535-546074 14 44867139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376652 Affx-122979017 AX-123247011 14 47817972 AACCTTGCGTAAGGTAACCACCATCTAAGCCTCTC[C/T]TGGCTTTTGTTAACCTGGGCCTTCTGGCTTATTTG Y 2 1 2 1 101000 r 74 goat snp41240-scaffold535-497643 14 44818781 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412005 Affx-122951752 AX-123282355 14 47857988 AGATATAATATGACCAAGACTCATGTACCACTGTA[C/T]ATAAGAAACACAACACTTAAATAAAGCTGAAACTC Y 2 1 2 1 101000 f 74 goat snp41239-scaffold535-457627 14 44778059 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382837 Affx-122973543 AX-123253195 14 47887286 AAGCTCCCACACACATGAACTAACCTTTAAAGTTC[A/G]CAACTTGAAGGTTCATACACACAGGACTAACTGTA R 2 1 2 1 303000 f 74 goat snp41238-scaffold535-428329 14 44748941 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784502 Affx-122940470 AX-385271551 14 47945506 CCCAACTTCTTCCACTCGGTTCCTCTGAGTTGAGC[A/G]TACTGACAAAATACACCTATGAGCCATCAAGGCCA R 2 1 2 1 101000 f 74 goat snp41237-scaffold535-370109 14 44690618 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446041 Affx-122925843 AX-123316378 14 47982867 ATAAGAAGGGTCTAAGAGGGTCTATAAATCACACC[G/T]ATAGCAAGAAAACAGTCACCTCCAAAGAAATGTTT K 2 1 2 1 101000 f 74 goat snp41236-scaffold535-332748 14 44653066 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391845 Affx-122966997 AX-123262202 14 48034536 GGCGTGAACTACCTCTTCTCCTGAAAGAATGCTGC[G/T]AAGTGCTGTGGAAAATACAAAATTAAATTCCCTTC K 2 1 2 1 201000 f 74 goat snp41235-scaffold535-281079 14 44600871 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389033 Affx-122968627 AX-123259391 14 48069837 TGATTGACAGTCCCCATAAAAAATACCTAATTTCC[A/G]TGTAATGACTTCTGATGTTGCTACAAGCATGTGCA R 2 1 2 1 201000 r 74 goat snp41234-scaffold535-245778 14 44565484 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408910 Affx-122953961 AX-123279261 14 48102135 AAGATCATCGAGGGAGGAATGTGAGGGGATAATTG[C/T]GGACCGAGTGAAGTCAGCCTTGGGGTCGGTCCCAC Y 2 1 2 1 101000 f 74 goat snp41233-scaffold535-213480 14 44533124 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434661 Affx-122933978 AX-123305002 14 48211631 AGTTTGTATGCAAATACCCAGGGAAACAAACTGCC[A/G]TGTTTTGTGAAACTTTGCTTTATTTGAAAGCCATA R 2 1 2 1 101000 f 74 goat snp41231-scaffold535-103984 14 44424025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417167 Affx-122947336 AX-123287515 14 48248341 AGCCTTTGTACACAAAAGTGATAGGGTGTTATTCC[A/G]TATGTAAGGGGATCCATGATAGCATATAGGTTTCC R 2 1 2 1 101000 f 74 goat snp41230-scaffold535-67274 14 44388968 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429668 Affx-122937657 AX-123300009 14 48286579 AAGATAGAGATGCACGGAGACCAGGAGTATTTTGT[A/G]GGAAAAATTAATAAAGTTTGGTGATGGACTGAATG R 2 1 2 1 101000 f 74 goat snp41229-scaffold535-29036 14 44351306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431734 Affx-122936746 AX-123302075 14 48327886 ATTTTGCCCAGATGCTAGTTTTTCAACCCCTTCTT[A/C]GGATCCTTAAGGTGGCACTAATATCTACTACTCTT M 2 1 2 1 201000 r 74 goat snp59982-scaffold998-2242139 14 44309679 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397687 Affx-122962579 AX-123268042 14 48357132 TAGCTAGTCAATCATTCAGTAAGTGATAAACTTGG[A/C]TTCTAATCTTAATTTCTGGATTTCTCATCCAGGCC M 2 1 2 1 101000 f 74 goat snp59981-scaffold998-2212893 14 44278971 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388075 Affx-122969517 AX-123258433 14 48414746 ATGAGCTGAGAGAGCTAGCAGTAATAGAATGGAAG[C/T]ATAAGTAGGTGGATATGTGATCATAAGGAGGGAAT Y 2 1 2 1 101000 r 74 goat snp59980-scaffold998-2155279 14 44222554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393854 Affx-122965147 AX-123264209 14 48469135 GGTATACAAATTTTTACATTGTTTTCTATGCCTAA[C/T]GATAATGAACATGAACATGATAATGATAATACTGG Y 2 1 2 1 101000 r 74 goat snp59979-scaffold998-2100890 14 44169624 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791133 Affx-122932437 AX-385278128 14 48506190 TGTGGATGCTAGATTTGCAAAACTCAGAGAACACT[A/G]TTAGATAACATATGTGGTATTTTCTAACATCTTTA R 2 1 2 1 101000 f 74 goat snp59978-scaffold998-2063835 14 44131835 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397056 Affx-122962735 AX-123267411 14 48536870 TCCAAGAAGCCAAAATTCTACTGTTCCCTTTGTAG[C/T]TGTTTGAAAATAAAGCAACCAGCTGGGATCCCTTT Y 2 1 2 1 201000 f 74 goat snp59977-scaffold998-2033155 14 44101495 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272497 Affx-1111833011 AX-519546218 14 48538830 CAGTGCAAACCCTGAGGCTGGATGTGCCTTAGAAC[A/G]AAGACTTCACATTTTACAAAAGTAAATGGCAAGTG R 2 1 2 1 101000 f 74 goat 14_48538830_AF-PAKI 14 48538830 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276944 Affx-1111835598 AX-519550452 14 48563119 AAATTTCTCCAGAGAACACTTTTTACCTTCATCAG[A/G]GGTATGGCATTAAGAAGGTAGACAGCCTAAGAAAA R 2 1 2 1 101000 r 74 goat Random2.2K-1430 14 48563119 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407284 Affx-122955332 AX-123277635 14 48609098 GAGAAATAGAACTGGCTTCCATTGTAACTTACAAA[G/T]TCTAGGCAGTATAAGAAGGGCATTCTCTGGAATGA K 2 1 2 1 101000 r 74 goat snp59975-scaffold998-1960927 14 44028973 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777025 Affx-122934153 AX-385264148 14 48644717 AGATAATTGTTGGAAGCACCTCCATCTGTAAAACA[G/T]AAGGACTTTATTGTTAAACAAGGAAAAGGCAGTGC K 2 1 2 1 102000 f 74 goat snp59974-scaffold998-1925308 14 43994550 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394301 Affx-122964695 AX-123264656 14 48674432 GTTGTTTTTCTGTAGATTCTATTGAGAAAACTAAG[C/T]TGGCTTTTTAAAAAATTCAACTCAGGGGCTATAGG Y 2 1 2 1 201000 f 74 goat snp59973-scaffold998-1895593 14 43964903 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775995 Affx-122922703 AX-385263125 14 48707160 CTGCTTAACATACACTGACTAGTCTACTTTGCCAA[C/T]GTGTGTTATCTCCTGCATGTTTCAGCAGGAGGAGT Y 2 1 2 1 101000 r 74 goat snp59972-scaffold998-1862865 14 43931892 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417366 Affx-122947713 AX-123287714 14 48755326 CTATATACAAAATTGAGTAGTGGTTGAGAACACAA[G/T]CTGGAGTTAACTTGTCTGGGTTCAAATCCTGGCTT K 2 1 2 1 201000 f 74 goat snp59971-scaffold998-1814699 14 43883872 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410033 Affx-122953245 AX-123280383 14 48788335 CTTTCCTCTGGAAGTGAATTCTCTCTTTCATTTTA[C/T]CTATATGGTAACCAGATGTCAAGATGGTCCCAAAT Y 2 1 2 1 101000 r 74 goat snp59970-scaffold998-1781690 14 43850558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770998 Affx-122932491 AX-385258160 14 48845182 TTGCCCAGAAAAGTGCACCCATGTGCCTAGATGTA[C/T]AAGCTTGTGGACAGGAGCAAAAAAAAATCACAAAA Y 2 1 2 1 202000 r 74 goat snp59969-scaffold998-1724843 14 43793208 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779947 Affx-122935644 AX-385267046 14 48879332 TGAATTAATATTTAATGTTCAAGACGACTGGTTTT[A/G]TGGCATAGACATCAGAAACATATACTATCAATAAG R 2 1 2 1 101000 r 74 goat snp59968-scaffold998-1690693 14 43758981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774809 Affx-122929244 AX-385261943 14 48920131 GAAATTCAATTATGCTTTACTTAGGTGATTATCCT[A/G]TAATATTCATAAAATTTAAATTGCCTAAATAATAG R 2 1 2 1 303000 r 74 goat snp59967-scaffold998-1649894 14 43718365 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779269 Affx-122943870 AX-385266373 14 48958856 GTTACTGACCTCAACTCAAATTTAAAAATGCAGTG[C/T]AAAGGCTAATGTTTAATTATTAGCATCAGAATAGC Y 2 1 2 1 102000 f 74 goat snp59966-scaffold998-1611169 14 43679622 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418481 Affx-122946450 AX-123288829 14 49019008 AAAAGCAGGTTCATTCATTCATTCAGCAGGTTGAG[C/T]GTAAGAAATATCCCTTTTTCTTTAATATTTCATGA Y 2 1 2 1 101000 f 74 goat snp59965-scaffold998-1551017 14 43619176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415988 Affx-122948403 AX-123286337 14 49056854 TAGTTGGCTGACCAGAAAATCTGGCCTCAAGCTAC[A/G]CCTACCCACAAACTGTTTGAAGCTTTCTTTCCAGC R 2 1 2 1 101000 r 74 goat snp59964-scaffold998-1513171 14 43580377 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772082 Affx-122967628 AX-385259237 14 49092619 CATGAGAGAAAAAAAGTCTTTAGAAGACGTCTCTG[C/T]AATTTTTCCTCTCAGTATAAAAATTCTGTTAAGTA Y 2 1 2 1 101000 f 74 goat snp59963-scaffold998-1477406 14 43543571 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431952 Affx-122935967 AX-123302293 14 49123167 TAGTGGAGGATGCTGACTACAGGGAATATTCTGCA[C/T]GGATGGAGAGACGGGGGTATTTAGGAATTCTCTGT Y 2 1 2 1 201000 f 74 goat snp59962-scaffold998-1446858 14 43512875 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448326 Affx-122924143 AX-123318662 14 49154590 ACCTTTCCCCATCTGAAACACATTAACTCCTGGGA[C/T]GGAGATATTCCTAGAACTTTCAGATAGTTGTTTCC Y 2 1 2 1 201000 r 74 goat snp59961-scaffold998-1415435 14 43480995 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790627 Affx-122966710 AX-385277629 14 49216115 GAGACCATCAAGCTCAGATGTGTTCAAACATTTAA[A/C]GAAGCCATTCTACCAATGCCCTAAAAATCTCTTTT M 2 1 2 1 101000 f 74 goat snp59960-scaffold998-1353910 14 43420960 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794697 Affx-122943395 AX-385281656 14 49248360 CCCGTGTTCTAACCACTGAACTAGATACTCGGGAT[A/G]TTCCTCGTCTACACTGTTCACCTAAGCACTTCATG R 2 1 2 1 101000 f 74 goat snp59959-scaffold998-1321665 14 43388855 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766872 Affx-122978252 AX-385254190 14 49285209 TTTCTAAAAAAGGAATTAGGCCTAAAGATGGCCCA[A/G]ATAAGATATAACATCAAGTAAAAACTTGAAATGAA R 2 1 2 1 101000 f 74 goat snp59958-scaffold998-1284816 14 43351920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384757 Affx-122972030 AX-123255115 14 49319019 TTCTGCATATTTGTTTAGAGTGGAAAATACAGCAA[C/T]AGAGAAAAGGAAAGAAAATGTACCTCCAATTACTT Y 2 1 2 1 201000 f 74 goat snp59957-scaffold998-1251006 14 43318144 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794002 Affx-122952404 AX-385280971 14 49359289 ATGTAAAGATTATTGTGATTAAATGAGAACATAGG[C/T]GTATAGCATTTTTCATCAATAATGTTAATTATCAT Y 2 1 2 1 101000 f 74 goat snp59956-scaffold998-1210736 14 43277538 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390845 Affx-122967830 AX-123261202 14 49399886 GTCTGCCAACACTGAAATAGTGTTATGAGCACACT[A/G]CTTATGTGGAATTAAACTTCCTTAAGATGGAAAGA R 2 1 2 1 101000 r 74 goat snp59955-scaffold998-1170139 14 43236250 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380480 Affx-122975718 AX-123250838 14 49436318 CCTGCCTTCTACTGCTTTTTGTGTCCATTTTGTGC[A/G]CTTCTCTCTAAATGCCCTTGGCACTCTTTTTACAA R 2 1 2 1 201000 r 74 goat snp59954-scaffold998-1133707 14 43199779 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795012 Affx-122947163 AX-385281971 14 49494078 TCTGACTGGAAAACTGTCTCTTATGATGTAACATT[A/G]CAACTATTGTATATGCTATTCTATTTAGAATCAGA R 2 1 2 1 101000 f 74 goat snp59953-scaffold998-1075947 14 43141918 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775435 Affx-122956811 AX-385262566 14 49537193 TCAGTACAACACTGATAGAAGGCAAAGCTTGCATC[G/T]TTTATTTTCTTAGCAAGATGAAATAAAGAAAAAAA K 2 1 2 1 201000 r 74 goat snp59952-scaffold998-1032832 14 43099032 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789840 Affx-122922837 AX-385276847 14 49588262 TATTTATATCCCACGGAATCAAGGAAGAGTAATAA[C/T]GACTCTCAGCTTGAAAATCTAGGAGTTTCAAGTTG Y 2 1 2 1 101000 r 74 goat snp59951-scaffold998-981763 14 43047523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792069 Affx-122923414 AX-385279056 14 49643361 ACAAGTTAAAGGTCATTGTCAAGAAATGTGAGCCT[A/G]CTTTCTAACCTTAGAGACTCAAATGCTAGTTCAAA R 2 1 2 1 101000 f 74 goat snp59950-scaffold998-926664 14 42992382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391591 Affx-122966605 AX-123261948 14 49697472 TAATGTTTCATTGTTTTAAGCTATTAGTCTGTGGT[A/G]CTTTATTATGATAGCCCTAGGAAACTAATACAAAT R 2 1 2 1 303000 f 74 goat snp59949-scaffold998-872553 14 42938397 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790610 Affx-122978364 AX-385277611 14 49729644 AAAGAGTATGACTAGCTAACAAATAAGTTAATGTA[C/T]GAGTAAAATTATCAGTATATCTGGTCCCTTTCTCC Y 2 1 2 1 101000 r 74 goat snp59948-scaffold998-840381 14 42905906 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420921 Affx-122944593 AX-123291268 14 49787579 ACAGCAACAGAAGCAGAAAATAGAATGGTCATGAA[A/G]AGCATTGCAAGTGAAGTATTGGTATACACATGAGG R 2 1 2 1 201000 r 74 goat snp59947-scaffold998-782446 14 42847645 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396938 Affx-122963187 AX-123267293 14 49854933 GTTTGGGCATACAGACTTTAATCTGGGTCCATTAA[C/T]ATCGCCTAGTGTGATTTGGAGCAAGAGGAACTGAT Y 2 1 2 1 201000 f 74 goat snp59946-scaffold998-715092 14 42779965 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786631 Affx-122963340 AX-385273663 14 49896773 TGAAAATACTGTGTGTCAATTGGAAGAATTTTATA[G/T]TTAAATTTATTTTGAAGTTCACAATTTGTTTTTAT K 2 1 2 1 201000 r 74 goat snp59945-scaffold998-673252 14 42737617 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766139 Affx-122929594 AX-385253543 14 49957799 TGTGCTTTTTCAGAATCATTTTATCCTCATTAAGA[C/T]GTTTCCTTCTGCTCCCTCAGACTGAAGTTAAATCA Y 2 1 2 1 201000 f 74 goat snp59944-scaffold998-612226 14 42683730 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452745 Affx-122920273 AX-123323078 14 49988313 AGGCTTGCACAAGGCATGCGCATTTATCAATGTTT[A/C]TCCCTCATTCACCTAGGCTGCAGCACTTGTGAAGG M 2 1 2 1 201000 f 74 goat snp59943-scaffold998-581712 14 42653133 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766882 Affx-122925074 AX-385254200 14 50027274 AGATATTTTAGTTTGAAACATTCTTCAGACAGTTG[A/G]GAAAAAGAACCAGATTGACACTGTAACCAAGGAAA R 2 1 2 1 101000 f 74 goat snp59942-scaffold998-542751 14 42614186 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780589 Affx-122940824 AX-385267680 14 50060185 ATCAAAACCTACGAAGCTCTAATAGCAAATGTAGA[C/T]GGGAAAGTATCTCTTTGAACTCCCATATTAATACT Y 2 1 2 1 101000 r 74 goat snp59941-scaffold998-509840 14 42580779 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775794 Affx-122929218 AX-385262925 14 50094104 GCAGAAAAATGTGTATGATTTGATGCAAACTTTCA[C/T]GTGATCCCAATAAATGTTTTCTCTAAAACAGAGGG Y 2 1 2 1 101000 r 74 goat snp59940-scaffold998-475921 14 42551201 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780716 Affx-122931545 AX-385267806 14 50132685 AAGATAAATTTGTTCTGCCAGGATTAAGATTATAG[C/T]AGAAGTGCAAACTTCCCTGTTAACTCAGTGGGTAA Y 2 1 2 1 102000 r 74 goat snp59939-scaffold998-437340 14 42512695 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786132 Affx-122951323 AX-385273168 14 50190150 GAATGCTCACAATACAGAACTGGTCAGAAGGTCTC[A/G]TTTCATACATGGGCAAATCTGAAAACCAGAGGTGT R 2 1 2 1 101000 f 74 goat snp59938-scaffold998-379875 14 42455225 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421712 Affx-122944396 AX-123292059 14 50225857 CTGTGAAAGTTACTGTGACTCAAGGGTGCTGTGTG[G/T]GTGTTAGTTGCTCATTTGTGTCTGACTCATTGCAA K 2 1 2 1 101000 f 74 goat snp59937-scaffold998-344168 14 42419170 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797763 Affx-122925143 AX-385284702 14 50269992 CTTGGAATACAATGAAGTCATCACTTTAGATGTAC[A/G]CTTTGGTTGGCATATTGGCAAGGACCTTCAGGAAT R 2 1 2 1 101000 r 74 goat snp59936-scaffold998-300033 14 42374922 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394113 Affx-122965344 AX-123264468 14 50323047 GTCAGTGTCCTTTCTTTTTGCCTTTCATATTCTTC[A/G]TGGGTGTGCATATGCATAACTGGCTGAATTTGTTG R 2 1 2 1 101000 r 74 goat snp59935-scaffold998-246978 14 42321896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427478 Affx-122940014 AX-123297821 14 50369466 TTTTAAATGGTCAAATTTGTTAATATAGTCCATTG[C/T]GATTCTATTTATAATATCACATTAAAAAATTTTGG Y 2 1 2 1 102000 f 74 goat snp59934-scaffold998-200559 14 42274885 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795937 Affx-122940356 AX-385282889 14 50427522 ATACTGTAATACATATTTCTTGCCTTGTGAATGCA[C/T]ATTTGTGCTGGAGTAGCCATGTTCTAACACATGGT Y 2 1 2 1 101000 r 74 goat snp59933-scaffold998-142503 14 42216739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377067 Affx-122978287 AX-123247426 14 50457854 TTGCAATTGGCTAACACCGACGATAACAAGTTACA[A/G]TGGGTTCTAGCAAATTCATGGTGGTTCTAAGAGCT R 2 1 2 1 101000 f 74 goat snp59932-scaffold998-112171 14 42186267 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376993 Affx-122977738 AX-123247352 14 50492115 TCTTGTTCACACATACACACACACAGACACACACA[C/T]AGACTCACCCCCTTATGAGAGAAACAGAGAGTAAA Y 2 1 2 1 201000 r 74 goat snp59931-scaffold998-77910 14 42151342 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429631 Affx-122937688 AX-123299972 14 50555957 TTTGAAGTTATTTAATAGAAAAAATAAATGTCCAG[C/T]AGTGCATCTTTATCACTATTTCCTTTAGTTCTATC Y 2 1 2 1 101000 r 74 goat snp59930-scaffold998-14068 14 42087384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414903 Affx-122949117 AX-123285252 14 50571932 AATTGATGCTCCACGTGAAAAACTAAAGATGTTTC[A/C]GTTGCTATCCTTCGCTTCCTCTTTCAGTTCAGTTC M 2 1 2 1 101000 r 74 goat snp10334-scaffold1370-1808 14 42070609 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276946 Affx-1111835599 AX-519550454 14 50628902 CTTTACCACTGAGCCACCAGGAAGCCCTGCCCTTT[A/G]CCTTGGACTCATTTTGTATGGAATAGAAGTCACAA R 2 1 2 1 101000 r 74 goat Random2.2K-1432 14 50628902 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38404479 Affx-122956725 AX-123274831 14 50639262 TCTTTTCAGGGGTGGCCTCCCTGGTCAGGGGCTTC[A/G]TTCCTTGACTACCAACCATGAGTGCATATATATGT R 2 1 2 1 101000 r 74 goat snp10335-scaffold1370-69138 14 42003132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777397 Affx-122921989 AX-385264519 14 50699441 ATAAACAAAACAAAGAGAAAGATATTACTGGGACC[A/G]TATCTTCATTATCTTATGAATAGGATGAAACCTAT R 2 1 2 1 101000 f 74 goat snp10336-scaffold1370-129317 14 41942839 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419702 Affx-122945918 AX-123290050 14 50759230 GCTAGGAGAGGAGAAAAACCATTAAGAAACAAACA[C/T]ATGAACAGGAGTGAACAAATGAAAAATCCCAGGAC Y 2 1 2 1 101000 f 74 goat snp10337-scaffold1370-189106 14 41882980 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406111 Affx-122956210 AX-123276463 14 50793470 AGGCCAGAGGTATATGTTTGACACAGGAAAGGACA[C/T]GGGGAGACACACTCAGTCTGCGGGTTTCTCTCTTC Y 2 1 2 1 101000 f 74 goat snp10338-scaffold1370-223346 14 41848208 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274723 Affx-1111834459 AX-519548309 14 50794174 GAGCATCTAGTGAAGGTGCACAGCCTGCGTGGAAC[A/G]CAGAACGGCCAAAGGTCAGCAGCCTGCAGGCCCAG R 2 1 2 1 202000 f 74 goat GoatD01.036738 14 50794174 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320790831 Affx-122958091 AX-385277831 14 50834582 GGCTCTCACCTGAACTCATGTGACTCCTGGTAAGT[A/G]CTATTCAATGGTGTGGATGGGCTGGTTCCTGTGAT R 2 1 2 1 101000 r 74 goat snp10339-scaffold1370-264458 14 41806693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795143 Affx-122945988 AX-385282101 14 50873209 AAGAATTAGACAAAGCTACTTAACTCAATTCATTT[C/T]ACATGCATCTCACACAACACTAGACTGACTGTGGA Y 2 1 2 1 101000 r 74 goat snp10340-scaffold1370-303085 14 41768047 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429501 Affx-122937862 AX-123299843 14 50917989 TGGTCAGTGTCGAGATTAGGGGTACCATGGTTATC[A/G]TTTTGCAGCTCCTACCTATAGATTTAGTATCTTCT R 2 1 2 1 101000 f 74 goat snp10341-scaffold1370-347865 14 41722533 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775827 Affx-122920821 AX-385262958 14 50969062 GAGAGAAAGTTACACTTACTTTCCATAGATTTATT[A/G]TCTGAAAAGATTTCACATTTTCACCAATGTGTCTC R 2 1 2 1 101000 r 74 goat snp10342-scaffold1370-398938 14 41670700 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401240 Affx-122959306 AX-123271593 14 51006343 TATGGTACTCAAGATGGTTTAAATGTATTTATGGC[A/G]TTAGGCTACTACTCTCTCAGTTAAAGAATGCCTCT R 2 1 2 1 101000 r 74 goat snp10343-scaffold1370-436219 14 41633416 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405429 Affx-122956061 AX-123275781 14 51036494 TATGTGGGAAATGTTCTGAAGAATTAAATAATTGC[A/G]TAGGAAGTCAATATTATAAATTAAAACAAGTATCT R 2 1 2 1 101000 f 74 goat snp10344-scaffold1370-466370 14 41602580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398503 Affx-122961558 AX-123268858 14 51115518 ACACCTTGAGGACCAGTCAGTTGAGAAACCACTCA[A/C]ATAACCAAAAATCAGGAAGAACTTGATATGTCTTC M 2 1 2 1 101000 f 74 goat snp10345-scaffold1370-545394 14 41522201 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414902 Affx-122949118 AX-123285251 14 51159024 GCAGGTGAATTCTTTACTGCTGAACTGGATGAGAT[A/G]TTTACATGGACAAAAAGATTGAGAAGCAAAAACAC R 2 1 2 1 201000 r 74 goat snp10346-scaffold1370-588900 14 41478263 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272544 Affx-1111833012 AX-519546261 14 51184150 TACTTTCTGTATTAGACTCAAGAGAAAAACTACAG[A/G]GAAGTGTCAGGTCAAACTCCCTAAACTGCTAGCAT R 2 1 2 1 101000 r 74 goat 14_51184150_AF-PAKI 14 51184150 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38453606 Affx-122920135 AX-123323939 14 51187803 GTCCAGCAAATTCCTGTTCCAGAAGACAGCTTTTA[C/T]ATTTCCTTATGTTATGTTGGAACTCTGCTTAAATA Y 2 1 2 1 101000 r 74 goat snp10347-scaffold1370-617679 14 41448810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379484 Affx-122976476 AX-123249842 14 51225632 CTTAGCATAATGCCCCCTGCCCCCAGTTGTTGCCC[A/G]CATGTCTGTCTCCTATGCCTGGATCTCTAGTCCTA R 2 1 2 1 101000 r 74 goat snp10348-scaffold1370-655508 14 41411034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403606 Affx-122957556 AX-123273959 14 51274422 TTCTAACTTCAAAGCAGAAAAGACAGAGTATGTAA[C/T]GGTGTCTTTTCTCTCCAAATCTGATTACCATGATC Y 2 1 2 1 201000 f 74 goat snp10349-scaffold1370-704298 14 41361824 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797192 Affx-122949217 AX-385284131 14 51303010 TATTAAACTTTTTAAATCCATAGAATTTTGGCCCA[A/G]GTACTATTTAAGGAATGGACAATTCCTAAGAAAAA R 2 1 2 1 201000 f 74 goat snp10350-scaffold1370-732886 14 41332977 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796814 Affx-122946022 AX-385283757 14 51333493 TAGAAGGTAGATTGCACCAAGAATCATGATGAGAA[C/T]GTTAAAAATGAAGAGTGAGCATGTTATGTAAAAGA Y 2 1 2 1 101000 f 74 goat snp10351-scaffold1370-763369 14 41301980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449883 Affx-122922349 AX-123320218 14 51418811 GTTGAGACTAAGAAGAAACTTTTATGGAAAACAAA[A/G]ATTTCTAAAAAATAAGTATTTGAAAATTTGTTTTC R 2 1 2 1 103000 f 74 goat snp10353-scaffold1370-848687 14 41216276 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383113 Affx-122973268 AX-123253471 14 51460996 ATGATCATTTCCTTATCAAATATTGAAAACAAAAT[A/G]TAAAGTAATTTGGGATTCTGTAACTGTTTTTGACA R 2 1 2 1 103000 r 74 goat snp10354-scaffold1370-890872 14 41173017 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392653 Affx-122966443 AX-123263010 14 51494850 GTGGGGTCACACAGAGTCGGACACGACTGAAGTAA[C/T]GCAGTCACAAACTGTATCTGAAACATTTGATTCAT Y 2 1 2 1 201000 r 74 goat snp10355-scaffold1370-924726 14 41138596 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773652 Affx-122937046 AX-385260792 14 51533348 TGTGCTGTGCTGTGTCTAAGCATGTCTTGCTATTG[C/T]AACTGCAAAATGGCAGCTCTATTATGTTTTTGTTA Y 2 1 2 1 101000 f 74 goat snp10356-scaffold1370-963224 14 41100018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432021 Affx-122935919 AX-123302362 14 51574182 CCCCTGGGGAGGAGTACCTGAGGCTTGTTTCCCAG[C/T]GGGAGCACTTTGTTTCCCTCCACTCCATATCACAG Y 2 1 2 1 101000 r 74 goat snp10357-scaffold1370-1004058 14 41058959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769085 Affx-122927687 AX-385256260 14 51660692 TATCCAAGAACCTTAAGAAGTGAATAAAAAATGCT[A/G]CACCCAGCTCTCTACTATTTCTTAGAGTTTCGGAT R 2 1 2 1 101000 r 74 goat snp10358-scaffold1370-1090568 14 40971260 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452767 Affx-122920256 AX-123323100 14 51708810 CCCCAGTCACTTGTTTAGCTTTTACTTAATATTTC[A/G]TACTAACTACCACATCCCCTTTGCACTGTGTGTGA R 2 1 2 1 101000 r 74 goat snp10359-scaffold1370-1138686 14 40922417 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415412 Affx-122948733 AX-123285761 14 51784314 TCTACTACTGTCTACTTACCCAAGGGAGACAGGAA[A/G]GAAGGAAAGGAAAGCAGGCAGAAAGGGAGGGAAGG R 2 1 2 1 303000 r 74 goat snp10360-scaffold1370-1214190 14 40846512 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420878 Affx-122944626 AX-123291225 14 51830357 ATGAGCAGATTTCAGGATTCCAGTACACTAGCAAC[A/G]TGATAGAAATAATGAATTTAAAAAGTATCTCACTC R 2 1 2 1 101000 f 74 goat snp10361-scaffold1370-1260233 14 40799704 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412505 Affx-122951367 AX-123282854 14 51867624 GGTGCAAACTCCCCTCAACAAACAACAGCTCCTTC[A/G]TGATCTCCAAGCCTATCAATTACATTTTATTATTT R 2 1 2 1 201000 r 74 goat snp10362-scaffold1370-1297500 14 40761995 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442568 Affx-122928508 AX-123312905 14 51923176 GTGGCTTCTAATCTTTGTCCTCATGCACAGTCCCA[C/T]GAATGTTCACTAAAAATATGTTTAAGAACTATTTC Y 2 1 2 1 101000 f 74 goat snp10363-scaffold1370-1353052 14 40706379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453211 Affx-122920441 AX-123323544 14 51953028 CTATGCCAGGTAATTTCAACATATTTGTCATCTCA[G/T]CTTTGACATCTGTTCAATGTCTTTTACTAGAGGAG K 2 1 2 1 101000 r 74 goat snp10364-scaffold1370-1382904 14 40676024 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788845 Affx-122954546 AX-385275860 14 51986719 CAATTATAAGAGAAAATCAGATAACTTTTAGGAGA[A/G]TTTCTAAATGATACTAAAGTGTCAGTCTTCACTTC R 2 1 2 1 101000 r 74 goat snp10365-scaffold1370-1416595 14 40641883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385782 Affx-122971052 AX-123256140 14 52036006 TAATTTGCTTATATTGCAGAAATGAGAAAGAATAC[A/G]TTTTTACATAGTACAAGGAATCAGAAGCTGATGAC R 2 1 2 1 101000 r 74 goat snp10366-scaffold1370-1465882 14 40592462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440528 Affx-122929337 AX-123310865 14 52168860 CCTGCTCCTATTTAAGGCACTTTAAATAGGAAAAA[G/T]AAATAGAAGAAAAGTTAAGACAAAACTTCCCCAGG K 2 1 2 1 103000 f 74 goat snp10369-scaffold1370-1598736 14 40457557 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779091 Affx-122940840 AX-385266196 14 52216364 GCAGTGCAGGAAGAATGAAACAGTGAATAAAAGGG[C/T]AGATTTTCGAACAAGAGAAATTCTTCAAGGCTTCC Y 2 1 2 1 101000 f 74 goat snp10370-scaffold1370-1646240 14 40410165 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781831 Affx-122922051 AX-385268913 14 52288426 CTATAAGGGTCTATAGCCATGGTCATGTTCACTTC[A/G]TCATCTCTTCTATTCCCAGTTCCTTCAGTTACTTC R 2 1 2 1 101000 f 74 goat snp10372-scaffold1370-1718302 14 40337378 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388271 Affx-122969768 AX-123258629 14 52329533 AATCCAAAGTAAACTCCTTTGCCTGGCTCTCTAGA[C/T]ACTTCAGCTAATTAACCTATCTCTAGAACTTCATC Y 2 1 2 1 102000 r 74 goat snp10373-scaffold1370-1759409 14 40296079 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426859 Affx-122940488 AX-123297204 14 52364787 GTACTTCCATGAACGTTTATTTTAATGTTTCCTAG[C/T]ACACATGTGCAAGATTTTATTTAACATAAGTAAAA Y 2 1 2 1 101000 f 74 goat snp10374-scaffold1370-1794663 14 40260726 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435982 Affx-122933510 AX-123306321 14 52399895 ATTTTCTTCTCTGGAATCAAATTTCTTACAGTGCT[A/G]TATGATACTACTAACATTTGGAGGACAGCTTATCT R 2 1 2 1 101000 r 74 goat snp10375-scaffold1370-1829771 14 40225632 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437163 Affx-122932134 AX-123307501 14 52455638 TACCTGAACTATATTAAGTATTAAATGATGTAACA[C/T]ATATTAAGCATTTGGAAAACTGCCTAGTACATAGG Y 2 1 2 1 101000 r 74 goat snp10376-scaffold1370-1885514 14 40169543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424134 Affx-122942007 AX-123294480 14 52487226 ATTGTTTTTATTGGAACATGGCTGCACATGGCTAA[C/T]GGTGAATTGTCTGTGACTGCATTCATGCTATAGTG Y 2 1 2 1 101000 f 74 goat snp10377-scaffold1370-1917102 14 40137939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421323 Affx-122944082 AX-123291670 14 52536539 CCAGTTTTATGGGATCATTCTGCTTTATACCAGAA[C/T]GACAGCTTGTTTGGTTAGCTCCCCCTTGCATTCTT Y 2 1 2 1 101000 r 74 goat snp10378-scaffold1370-1966415 14 40088123 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772851 Affx-122936268 AX-385259996 14 52603437 GTATCAACTCTTTTTGGAAAAAGATTTTGCCAACT[A/G]TATGAGTAGAAAGACCTATGGAATAAAGCTTTATG R 2 1 2 1 101000 f 74 goat snp10379-scaffold1370-2033313 14 40020810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402427 Affx-122958631 AX-123272780 14 52649279 AAGGCATTCCAAGGAAGGTACCAATGTCAACAGAG[A/G]GAGGAGGGAGTGTGACAAGTCAAGTCCGGAAGTTG R 2 1 2 1 101000 f 74 goat snp10380-scaffold1370-2079155 14 39977799 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276948 Affx-1111835600 AX-519550456 14 52655905 ACAACATGTGTCATAAAAATAATCCATTATCTACA[A/G]AAGTTTTCTCCCACCTACTTTCTTTGTTAAGAACA R 2 1 2 1 101000 r 74 goat Random2.2K-1436 14 52655905 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38404083 Affx-122957137 AX-123274435 14 52656749 TCCAAAATAGCCTGCCAGTGGAAGGTGGAGAGGTT[A/C]TTGTGGTTATTTCTGTTTCTTCCACACTGGTTCCA M 2 1 2 1 101000 f 74 goat snp52760-scaffold791-6037 14 39955702 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798208 Affx-122957355 AX-385285144 14 52713952 GTGTCTCTGACAAACTGCTCTAACTTGATGGACAA[C/T]GTGATAAGACCACCATTCAGCAATCTGATGTGAGT Y 2 1 2 1 101000 f 74 goat snp52761-scaffold791-63240 14 39897879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783155 Affx-122972343 AX-385270223 14 52784784 ATGTTACCCATAAGAGAATACAGCTTGCAGGTTTG[C/T]AATTGTAGATAATGATGTATTTGTAAAAGGTTTTC Y 2 1 2 1 101000 f 74 goat snp52762-scaffold791-134072 14 39825837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400877 Affx-122959760 AX-123271230 14 52846848 TTGGCTCTCATTTTTTATATTATTATAAACTTTTT[A/C]TCCTTGTGATTGAAAATTCACATGTATTCTTCATT M 2 1 2 1 103000 r 74 goat snp52763-scaffold791-196136 14 39763082 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400296 Affx-122960076 AX-123270651 14 52894897 AGGGACACAGGAAGAGGATCAGTTGTATTAATTAC[A/G]TAGAGGTGAGAGGTTGTGATGGGGGTGGGAAAAGA R 2 1 2 1 101000 f 74 goat snp52764-scaffold791-244185 14 39714220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412773 Affx-122950505 AX-123283122 14 52929789 TGATAGTTGTGATTAGGTTGGGTTTTAGTTACTTA[C/T]AGATCTGTCTTTCTCAGTAGTCTGTGAGTTCCATG Y 2 1 2 1 101000 f 74 goat snp52765-scaffold791-279077 14 39678168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427731 Affx-122939267 AX-123298074 14 52998907 AGCCTGTATACTCTCCCAGTTGGGACTGTATTCTA[C/T]GGATCTAGGCTTTCATTGTCATATCTGTGATTATA Y 2 1 2 1 101000 f 74 goat snp52767-scaffold791-348195 14 39607859 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422185 Affx-122943514 AX-123292531 14 53088572 CATGTTTCACTACATTCTAGTGGACTTGGTGCCGA[C/T]GGTGTGAATAAGGTTTCATCTTCTCACTTATTGCT Y 2 1 2 1 101000 r 74 goat snp52769-scaffold791-437860 14 39516388 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768307 Affx-122925175 AX-385255487 14 53122399 TTTTGCTATTGCCTACCCAATCTACTCTTCCTTAT[G/T]TTCTTACAAACAGACCTTGATTTTGTTTGAAATGG K 2 1 2 1 101000 r 74 goat snp52770-scaffold791-471687 14 39482309 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781560 Affx-122928701 AX-385268645 14 53151585 CACGTGGGGCTCTTGCATGACTTCAATAACTGGCA[C/T]GGTTAGACCACAGAAGCTGAATTTGTAGGCTCCTG Y 2 1 2 1 101000 r 74 goat snp52771-scaffold791-500873 14 39453596 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428831 Affx-122938372 AX-123299173 14 53206114 AAAAAGATCTGGAAAACCATCTCTCAAGATCATGC[A/G]TGCTCGTGTGCAGTCGCTTTAGTCATTGTCTGACT R 2 1 2 1 101000 f 74 goat snp52772-scaffold791-555402 14 39399049 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449053 Affx-122923060 AX-123319388 14 53275332 GATCAGTAAATCTGTATAAACTCTGTGGAAGGAGA[A/G]TCCCTGTGCCTCACCCAAGGCTGGGAATGCTATAT R 2 1 2 1 101000 f 74 goat snp52774-scaffold791-624620 14 39330797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776697 Affx-122947496 AX-385263823 14 53305119 TTTATATGGAGGCTTTAAGGGTTCAGTCATATACA[C/T]AGTTTGAATGGCTGAAACATTACAATGCTGTCTCA Y 2 1 2 1 101000 f 74 goat snp52775-scaffold791-654407 14 39300418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779824 Affx-122938040 AX-385266925 14 53394595 AACCACTCCAGTAAACTATAACTGGCACACTGACC[A/G]TGTCGGCACTATCAACTCCAAACTCACTGAACCTC R 2 1 2 1 101000 f 74 goat snp52777-scaffold791-743883 14 39210390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407849 Affx-122954522 AX-123278200 14 53440154 TTTCCAGGATCACACAGCTATTAACAGACCTCCTG[G/T]ATCAGATCCTTTTACTTTATTCAGCAAAAGCCCCA K 2 1 2 1 201000 r 74 goat snp52778-scaffold791-789442 14 39164874 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417488 Affx-122947167 AX-123287836 14 53498694 TCCTGTGCCTTCTAACTGTTGCGTCATCCAGCTCA[C/T]ACTTCTCATGCTGTTCAGGAGATGGGGGAACACTT Y 2 1 2 1 201000 f 74 goat snp52779-scaffold791-847982 14 39106078 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781449 Affx-122973820 AX-385268534 14 53559138 GCTTCATAGTAGTAATAAAAGCAGAATGCCTTGCC[C/T]CATTTTGTCTTTCTATTAAGTCATCCTTCCCAAGG Y 2 1 2 1 101000 f 74 goat snp52780-scaffold791-908426 14 39044946 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444570 Affx-122926971 AX-123314907 14 53594268 GACCATTGGTGACAGGGAAGCCTGGCTACAGTTCA[C/T]GGTATCAAATAGTCAGACATGACTGAGTGACTGAA Y 2 1 2 1 201000 f 74 goat snp52781-scaffold791-943556 14 39009893 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798611 Affx-122970755 AX-385285544 14 53638071 CCTCAGAACTGGCTACCAAAACCATCTGTTCTGTA[C/T]ATGGGCCCTATATTCTAATCCTATGTTTGTTCTTT Y 2 1 2 1 101000 f 74 goat snp52782-scaffold791-987359 14 38965868 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443208 Affx-122927583 AX-123313545 14 53687991 ACACATAGGTTAAATGTATCTTCTTTACAGCTTCA[A/G]CTTTGGCTTATTCTTTGCACTGGAAGGAGATCAGT R 2 1 2 1 101000 r 74 goat snp52783-scaffold791-1037279 14 38915316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789818 Affx-122975125 AX-385276825 14 53729670 CATTAACGGAGACCACAGTTTAGATTTAATAGGTC[A/C]GATGACAATGCAGCCAAACGCATTTAGCCTATGAT M 2 1 2 1 101000 r 74 goat snp52784-scaffold791-1078958 14 38873561 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417476 Affx-122947177 AX-123287824 14 53774248 CCACAGTCAAGTCACTGGATGTTCCGTCACCACAA[C/T]GATCCCTTGTGCTGTCCTTCCACTCCTTATCTCCC Y 2 1 2 1 101000 f 74 goat snp52785-scaffold791-1123536 14 38828674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786083 Affx-122974209 AX-385273119 14 53821188 ATGTTATGCCCATTAATTAAATGATATGCCCATTA[A/G]TTAAAAATGGGCTTGCAGCAATTTAAAAAACAGGC R 2 1 2 1 201000 r 74 goat snp52786-scaffold791-1170476 14 38781313 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271937 Affx-1111833014 AX-185303291 14 53852222 TGCCTGGAGAATCCCAGGGACGGGGGAGCCTGGTG[A/G]GCTGCCGTCTATGGGGTCGCACAGAGTCGGACACG R 2 1 2 1 303000 f 74 goat 14_53852222_AF-PAKI 14 53852222 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320774439 Affx-122924944 AX-385261575 14 53853344 TTAAAATTATGTCAGCCATCAGATTAGAAATGTTA[C/T]ATTAGGATTTTAGGAAATACTCCCTATGGGAATGC Y 2 1 2 1 201000 f 74 goat snp52787-scaffold791-1202632 14 38749119 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378744 Affx-122977027 AX-123249103 14 53909502 ACATCAAATGCTGAAAGGGTACAGTCATCAAAAAG[C/T]ACAGTTTGAAGATACTTTTTTAATGGTACATTAAA Y 2 1 2 1 101000 f 74 goat snp52788-scaffold791-1258790 14 38693015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399417 Affx-122961235 AX-123269772 14 53947299 AGGAAGTAGAGAGAAGGGACTGTGTGTGGAAAGGC[A/G]TAGAAGGAAACAGAGCAGCAATAACCACCCGCTTC R 2 1 2 1 101000 f 74 goat snp52789-scaffold791-1296587 14 38655320 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800193 Affx-122919676 AX-385287116 14 53988721 TTATGGAATGACTCTAAGCCTCAACTTGAATTATA[C/T]GGATATATTCCTATGCTTTATATATTCCACTATTT Y 2 1 2 1 101000 r 74 goat snp52790-scaffold791-1338009 14 38613412 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765328 Affx-122944045 AX-385252847 14 54027563 GTGATAGACATACTCTGGGTTTTGATATATGTTTC[G/T]CACTGATTATCTTATCTCTTACAAAATAGATCCCT K 2 1 2 1 101000 f 74 goat snp52791-scaffold791-1376851 14 38574533 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423350 Affx-122943157 AX-123293696 14 54092200 TGTTGGTTCTACCTGTTCCTTGAAAGATTTTGACT[A/G]CTTACACTGATGACTCTTGACCATGGGGTGTTACA R 2 1 2 1 201000 f 74 goat snp52793-scaffold791-1441488 14 38509610 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768960 Affx-122932719 AX-385256135 14 54151648 AATTGCACTTAGTTCAGCTTGTACTATAATTAGGC[A/G]ATTTCTCATGGACCAATCTATGCTTTCTCTAGACA R 2 1 2 1 101000 f 74 goat snp52794-scaffold791-1500936 14 38450435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379966 Affx-122975635 AX-123250324 14 54200880 TCACATCACACTGGATACAGGATGCTCCTCCTCTA[C/T]GACTGCTTGTAGGGCCCTCTCAGGCATTTCCCTAT Y 2 1 2 1 201000 r 74 goat snp52795-scaffold791-1550168 14 38400318 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788844 Affx-122924872 AX-385275859 14 54277980 TTGATTTCACAACTTACTAGTTGATCTTAATGAAT[A/C]GTTTGAAAAATACTGCCCTAGTCTATGGTGCAGCA M 2 1 2 1 101000 r 74 goat snp52797-scaffold791-1627268 14 38322988 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441864 Affx-122929032 AX-123312201 14 54314323 TGGGTGGAGTCAAACAGGAGGCCCAAGAAGAAAAT[A/G]CCAATCAATCAAGAGGAAAGCTTGGGATTGGCGGG R 2 1 2 1 101000 f 74 goat snp52798-scaffold791-1663611 14 38286181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390402 Affx-122967657 AX-123260759 14 54343150 GAGTAAGAAATTTTGAAATACTTTTGGCATATCCA[A/G]TATCCCAGGGGAGTGTAATATGTACCAGGAAATGA R 2 1 2 1 101000 r 74 goat snp52799-scaffold791-1692438 14 38257170 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411712 Affx-122951531 AX-123282062 14 54381616 CTAATGGGTAAGACCGCTCTGTCCTAGCTTTTCCT[G/T]TGATGTTATCTGCATACTTGACTAATTAGTCTAGC K 2 1 2 1 101000 f 74 goat snp52800-scaffold791-1730904 14 38217979 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399546 Affx-122961138 AX-123269901 14 54431835 AGCCAAGCTCTAACAGAATTACATGGTCTGTTATG[C/T]AAGCTCACACCTTGATAGCATTAACAAAACCAAAC Y 2 1 2 1 101000 r 74 goat snp52801-scaffold791-1781123 14 38170412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769413 Affx-122951657 AX-385256584 14 54460686 GAGACAAGGTGGCAATGAATGGGTACCTCTCTGCA[C/T]GGAGACATGTTAACAACCACGACCCTGCCAAGATG Y 2 1 2 1 101000 f 74 goat snp52802-scaffold791-1809974 14 38141523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386377 Affx-122970844 AX-123256735 14 54568754 GGGAGCACAGCCTATTTCACAAGATTTGGACAGTG[C/T]TCAGAGAAGGGGAACTCCCTGGATAGCTCGAGAGA Y 2 1 2 1 101000 f 74 goat snp52804-scaffold791-1918042 14 38033032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787494 Affx-122945848 AX-385274519 14 54599271 AGTACTTATAGCAAAGTATGACAGCCTTAGCAAAC[G/T]AAGGTTATACAAGGAACAGTAAAAACTATGGTTTT K 2 1 2 1 101000 f 74 goat snp52805-scaffold791-1948559 14 38002487 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424250 Affx-122942465 AX-123294596 14 54629632 GCACAACCACCCACATCGGGACCCACTTTCCCTAC[A/C]TTCTCTTTAACTCAATGGAAGAAGGGTCTCTGCTT M 2 1 2 1 101000 r 74 goat snp52806-scaffold791-1978920 14 37972029 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451809 Affx-122921485 AX-123322142 14 54679503 TTGGCAATCACTCAAATGCAACAATATCAACTCAA[A/G]TTGGAGTCCTTTGGTTCGAAACACAGTAAGTGGAT R 2 1 2 1 101000 r 74 goat snp52807-scaffold791-2028791 14 37922297 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407727 Affx-122955000 AX-123278078 14 54708710 GAGTTTTCAGCAAATCCCTTCTTGAAGGCCTCACA[C/T]GGAAGGACACACAGATTCGGATCATATATGTTTAA Y 2 1 2 1 101000 f 74 goat snp52808-scaffold791-2057998 14 37892989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404610 Affx-122957340 AX-123274962 14 54762633 TTCCCCTTCCTTTTCTTCATCCTGTTCAAGTATCA[C/T]GTCCTCAGAGAAGTCTCTCTGACCAACCATCCCAC Y 2 1 2 1 101000 f 74 goat snp52809-scaffold791-2111921 14 37839082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800348 Affx-122951653 AX-385287270 14 54809782 GAAAAATGAGATACAGGCTCTAATTTATATAAATC[A/C]CTTGTCAGATGCCTTTTAAAAAGAGACTTAAGCTT M 2 1 2 1 102000 r 74 goat snp52810-scaffold791-2159070 14 37791988 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404730 Affx-122957242 AX-123275082 14 54840991 AAATAAAGATAACAGGGATTGGCAGCGAGATGGGC[A/G]TAGGGCCCACAGCTTAGATCCCAAGCAGCTTTCCA R 2 1 2 1 101000 f 74 goat snp52811-scaffold791-2190279 14 37760716 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772726 Affx-122939933 AX-385259872 14 54880060 TGGTCTAGAATCTAGAACAGAGTTTTCCTTCTGCA[G/T]GAGAATCACTTTTGTAGCTATCTGAAAATATCTCC K 2 1 2 1 101000 f 74 goat snp52812-scaffold791-2229348 14 37721739 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430129 Affx-122937401 AX-123300470 14 54948371 TTGTTAGTTTAATAGGAGAAAAGGTCTCAGATTCA[C/T]AGCTGCATGCATTTCAAGTAATAAAATAAGGAGCA Y 2 1 2 1 101000 f 74 goat snp52813-scaffold791-2297659 14 37653484 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391421 Affx-122966762 AX-123261778 14 54989874 CGCCTCTGCCACACTCTAGTCACCATCCGATTTCT[A/G]TCACATTCTCTAGGTCTCTTCCTAAATGTAACCTC R 2 1 2 1 101000 r 74 goat snp52814-scaffold791-2339162 14 37611894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796648 Affx-122961968 AX-385283594 14 55047209 TCAGATGTCTTATTTTGATTCCAAACCTACTCTTA[C/T]GGTATCCTCCATTTCAATCCAATTCTTTGGCTAAA Y 2 1 2 1 101000 r 74 goat snp52815-scaffold791-2396497 14 37554620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801230 Affx-122938479 AX-385288143 14 55192165 TGCTGAAATAATTACTTCATCTTCCTCATTATCAG[C/T]GTAATTCCACTTTTCCTGTTATGAGAGCAAAAGTT Y 2 1 2 1 101000 r 74 goat snp52817-scaffold791-2541453 14 37408037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382821 Affx-122973555 AX-123253179 14 55253027 GATCTAATCCAATAATGAACCTGTTTGGGGTGGGA[G/T]AAGGCAGGTAGGAGAGGAACTTTCCTATGGATGGA K 2 1 2 1 101000 f 74 goat snp52818-scaffold791-2602315 14 37350970 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407313 Affx-122955311 AX-123277664 14 55283185 TCTAAGAGGAGGCACATTGGGAAGACACAGTAACA[C/T]GTCCATGTTCATGGAATTCATATTGTGAAACATGA Y 2 1 2 1 101000 f 74 goat snp52819-scaffold791-2632473 14 37320583 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801245 Affx-122931849 AX-385288158 14 55326405 TCTCTGCTTTCAGTCCTGAAGCCTGAAAGCAATAT[C/T]CTAGTAACCTAGCAAAGGATCTGCATGGGCAGGAG Y 2 1 2 1 101000 f 74 goat snp52820-scaffold791-2675693 14 37277049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443653 Affx-122927200 AX-123313990 14 55369974 CATCATGGAATTTGTTCAAAGTATCGTAGCACAGA[C/T]GATAAATGGAAGAACTGGGACCAAGACCTAGGGCC Y 2 1 2 1 101000 f 74 goat snp52821-scaffold791-2719262 14 37232666 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451603 Affx-122921637 AX-123321936 14 55414054 CTAGCTTAAGATGGAATTTTGCAACTTGAATTTTA[C/T]AGTCTTAGCTTATACACGATTTTCACTGAGGAGGC Y 2 1 2 1 101000 r 74 goat snp52822-scaffold791-2763342 NW_017210038.1 4428 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399840 Affx-122960253 AX-123270195 14 55447131 ACCCATGGGATGCCCAGTGGCCTCCTTACAGTCAC[A/G]TGGACATCTCTGCTTCTAGTTTCCTGTGCTTTCTG R 2 1 2 1 101000 r 74 goat snp52823-scaffold791-2796419 14 37160165 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801130 Affx-122971749 AX-385288044 14 55475207 TTTATGAAACTTTTTACTGCAAATTGGTGGAGTCA[C/T]AGAAGGAGAGCAATTGTTAGACGTCACAATTATGA Y 2 1 2 1 101000 r 74 goat snp34933-scaffold416-2914028 14 37131233 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439945 Affx-122929994 AX-123310282 14 55635213 GGATGAAAATTAACAATTTATTTACAGATGCACAA[C/T]GCTGCCTTCTCAAAGCAACACATTCTATAACTAGG Y 2 1 2 1 101000 f 74 goat snp34930-scaffold416-2754022 14 36970402 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786990 Affx-122958754 AX-385274018 14 55677969 TGACCTTCTGATATGGGTCCATGGTCATTCTGTGA[C/T]GTCTACTTGTTTCTATTAGAATAATGTTTGAAAAT Y 2 1 2 1 101000 f 74 goat snp34929-scaffold416-2711266 14 36927591 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429119 Affx-122938012 AX-123299461 14 55710912 TGACTTGAGGAAGTTTTGAAATGTTAGAATTCAGA[C/T]AAGCAATATGGAAAGTCAAAACAATATACCAAATT Y 2 1 2 1 101000 f 74 goat snp34928-scaffold416-2678323 14 36894868 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401304 Affx-122959854 AX-123271657 14 55845877 TGTGTAAACCTGGGTATAAAGTATATTGTGTTGAG[C/T]ACTCTAATTTGGAACTCAAATATTTTTTCAATAAG Y 2 1 2 1 101000 f 74 goat snp34926-scaffold416-2543358 14 36759395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418332 Affx-122946961 AX-123288680 14 55888662 TTTAATGATGGATTAATATGGGAGTTGAATGAAAG[C/T]GAGAAATGGAAAACATTCTCAGAGGAAGCTTTAAA Y 2 1 2 1 101000 f 74 goat snp34925-scaffold416-2500573 14 36716437 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404442 Affx-122956753 AX-123274794 14 55960782 ATGTAGCAGGAGCAGCAGGATTAAAGGAACTTGCC[A/G]TCAGCCTGAGGGGACCTCCCTAGGTTTTTTAATTT R 2 1 2 1 101000 f 74 goat snp34923-scaffold416-2428453 14 36645073 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446068 Affx-122925822 AX-123316405 14 55991344 ATGGCGCTTTTGTGGGGGATTAAAGATGGTCTGTA[C/T]GTCATTGTTCCTCCGCTCCTGAGATGCGTGGCCGC Y 2 1 2 1 101000 f 74 goat snp34922-scaffold416-2397891 14 36614506 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423800 Affx-122942815 AX-123294146 14 56070477 CTCCTCTTTGATTTCTTTCTTTTTTTCTGATAGCC[A/G]TAATCATCTGCTAACTGACATACCCTCATACATGA R 2 1 2 1 201000 r 74 goat snp34920-scaffold416-2318758 14 36534706 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381600 Affx-122974791 AX-123251958 14 56128220 ACATGGCGAAGATCCTGGAGATTGAGTAGTGTCTT[A/G]CAACCATAAAACTGAGAAGCTTTGAACTTCCAATT R 2 1 2 1 101000 f 74 goat snp34919-scaffold416-2261015 14 36476464 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788372 Affx-122950308 AX-385275390 14 56167267 TTACATTCTTTTATATCACCCAGTGAGTGCTATTC[A/G]CAGAGCTGAGTTTATCACCAGTGCACAATGAATGT R 2 1 2 1 101000 f 74 goat snp34918-scaffold416-2221968 14 36436987 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430978 Affx-122936698 AX-123301319 14 56247710 CAAATCTAGGAGATTGTGCAATGCCCAACCTACAC[A/G]ACCAAATGCATCAGCCCTGCCAACTGCCCATGCAC R 2 1 2 1 201000 f 74 goat snp34916-scaffold416-2141525 14 36355472 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776063 Affx-122973391 AX-385263193 14 56295308 ACAATGTATCCAGTATACTGGACAATACTGGACAA[C/T]ACTCCCACAGGACTCAGAATCACAACACAGAATAT Y 2 1 2 1 202000 r 74 goat snp34915-scaffold416-2093927 14 36308214 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418810 Affx-122946166 AX-123289158 14 56338175 AACTGAGCCACATGAAACTTAGTTCAATGAGGGCC[A/G]TTACAGACTAAGTGTCTGCATCTCCAACACATATG R 2 1 2 1 101000 f 74 goat snp34914-scaffold416-2051060 14 36265255 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380724 Affx-122975145 AX-123251082 14 56395555 CTCCAAAAATTAATTTAAGAAACCTTAAACATTTT[A/G]TTTGGGGATTCTGTTTTAGACCCTGGGAAGACTCA R 2 1 2 1 103000 r 74 goat snp34913-scaffold416-1993680 14 36209138 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773498 Affx-122937468 AX-385260639 14 56449134 CCAGGATTTTCCTTCTGGGGAAGGAAACTGAACAT[C/T]AGGATGTTACCAAAGAAAACTGCCCACTATCATTT Y 2 1 2 1 101000 f 74 goat snp34912-scaffold416-1940101 14 36155577 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272790 Affx-1111833016 AX-519546488 14 56476787 AGAAGCAACTCAAAAAAAAAAATAATAATAAAATA[A/C]ACAATGCAAAGGGGGAAATGTCTTTGGTTATTTCA M 2 1 2 1 102000 r 74 goat 14_56476787_AF-PAKI 14 56476787 A C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426971 Affx-122940399 AX-123297316 14 56506263 GCCCTGTCCATCTTCCCTCCTGTTTCAATACCTCC[C/T]GGCGATTTGGTGATTACAGCTCTCAATATAAATAT Y 2 1 2 1 201000 r 74 goat snp34911-scaffold416-1882972 14 36098764 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416992 Affx-122947993 AX-123287340 14 56546498 AGAGTTACCAGGCTTTTTCCTCTATTAGAAATCCA[C/T]TGGCAAAGAACACATAAAATATCTGTCCTCTTCCC Y 2 1 2 1 101000 f 74 goat snp34910-scaffold416-1842737 14 36058111 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276951 Affx-1111835601 AX-519550459 14 56563124 CTGGCTCTTAGACTCTTAGAACACTCAGGGTCTAA[A/G]AAGAATAACATTAACTTTGGCAATGAGCTCAGAAT R 2 1 2 1 101000 r 74 goat Random2.2K-1438 14 56563124 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443483 Affx-122927813 AX-123313820 14 56585432 CCAAGCAAGAAGTCTTAGGAGAAATAGTTCCTTTG[C/T]GATGGGCCCTTTCACCCTGGGGTATGTCTAGCAGG Y 2 1 2 1 101000 f 74 goat snp34909-scaffold416-1803803 14 36019393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390151 Affx-122967984 AX-123260508 14 56637383 GATTATAGGCTAGAGTGACATCTCTGTTTCCCATC[A/G]TCCAAATCTCTCTAATGCATAAATTCATTCACCAC R 2 1 2 1 201000 r 74 goat snp34908-scaffold416-1751852 14 35967712 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432572 Affx-122935527 AX-123302913 14 56672828 CTTCCGGGCTCTCCAGCAACCCCTTAGAATTAAAG[C/T]GACTTGGTTTCACAATCGGTGTTTCAGCAGTTCTG Y 2 1 2 1 201000 r 74 goat snp34907-scaffold416-1716407 14 35931876 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377370 Affx-122977643 AX-123247729 14 56704012 GAAACAGCAGAGGAGTGAGCAGAGGCTGCTTCTCT[A/C]GCAGAGCTGTCAGGAAAGCCCACCACACTTCCCTA M 2 1 2 1 101000 f 74 goat snp34906-scaffold416-1685223 14 35900802 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434054 Affx-122934196 AX-123304395 14 56740857 TACATACAATCATAACCTTGTACCCAATGTATAAG[C/T]ACTCAATAAATATGGGATAAGATTACTGTTAATAT Y 2 1 2 1 101000 f 74 goat snp34905-scaffold416-1648378 14 35864022 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395363 Affx-122963985 AX-123265718 14 56776035 GAATAAAGTGTGTCCCATCATTTATGAAGGAAAAC[A/G]CCTGGGGAGACAGTAAGGGTCAAATACTTTGATCC R 2 1 2 1 201000 f 74 goat snp34904-scaffold416-1613200 14 35828905 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415252 Affx-122948943 AX-123285601 14 56825521 AAAGAATTCCTGACACAGTAATTAACAGTGAAGTC[A/G]CCTTAACTCAGTATCTAGGATCTTTAAAGGGGTAT R 2 1 2 1 101000 r 74 goat snp34903-scaffold416-1563714 14 35779585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397321 Affx-122962307 AX-123267676 14 56882732 GAAGATGCCGGCTTGTCCAAGGAACTCCTGCTCAC[A/G]CAAGGGTCTTGGCCTCCCTTGCTTGCCGGTCCCTT R 2 1 2 1 101000 f 74 goat snp34902-scaffold416-1506503 14 35722356 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276817 Affx-1111835602 AX-519550326 14 56902490 TTAATATGAATGTGATTTTTCACATCAAATGTTTG[A/G]TTTTGTTTTTACAATGAAATTCTGACCTATTGATG R 2 1 2 1 102000 f 74 goat Random2.2K-1439 14 56902490 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276822 Affx-1111835604 AX-519550331 14 56963758 AATTCTGTACAATATCTTACCATCATTGAGATACT[A/G]TCATCAGTCTTCTCTGATAATATATTGGCATTATT R 2 1 2 1 101000 f 74 goat Random2.2K-1440 14 56963758 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781760 Affx-122947120 AX-385268842 14 56970213 TAGCCAAATCCCAAGCAGGACAGAGTGCAACACAG[C/T]CGAAGGTATGCACAACTTGACCCTGGTGTTAGAGA Y 2 1 2 1 101000 f 74 goat snp34900-scaffold416-1419022 14 35635028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416505 Affx-122947781 AX-123286853 14 57010320 ATAAACTCTTTTGAGAAATGCCAGTCTAATAAATG[A/C]TTTGTCAGCCAGAAATTCATGACCTTTTCATAGCA M 2 1 2 1 101000 r 74 goat snp34899-scaffold416-1378915 14 35594345 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396136 Affx-122963397 AX-123266491 14 57046014 ACAACCATTATAATATTCAGTTATTCGACAAATAC[G/T]AAACCACCCTTTAGGTGCCAGGTACTGTGCGAAGT K 2 1 2 1 201000 f 74 goat snp34898-scaffold416-1343221 14 35558237 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425150 Affx-122941197 AX-123295496 14 57106890 AGGGTACAAAATTATATACACATGATGCTTATAGC[G/T]ATGTGAACACATGCAAATAAAGACAGACTGGAAAT K 2 1 2 1 101000 f 74 goat snp34896-scaffold416-1282345 14 35497993 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38421177 Affx-122944164 AX-123291524 14 57271489 TCTTTTTTTAACAATAGTTTCAGTTGCCAGGCATT[C/T]AAATGGGGCGATACATTATGGCACTACTGCATTAC Y 2 1 2 1 201000 f 74 goat snp34892-scaffold416-1117746 14 35334008 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276959 Affx-1111835605 AX-519550467 14 57275736 AAATAAGGAAAAAAATCCCTTACCTAATCAATGTC[A/G]GGTTTAAAAAGGATTAGGGTTACAGTATGGTCTTC R 2 1 2 1 101000 r 74 goat Random2.2K-1441 14 57275736 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38410578 Affx-122952128 AX-123280928 14 57374443 GTAAAATTTGTAAGGTCTAGTCTGGAAACTATGAA[G/T]AAATTACTTTTTTAAGAGTAAGCATCTTTTGGTGA K 2 1 2 1 102000 f 74 goat snp34890-scaffold416-1014792 14 35229010 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409867 Affx-122952917 AX-123280218 14 57430109 GTCATATCTTCTCACTCCCTTTATCCCTGCTTTCT[A/G]CTTCTCGAAAATGCACTACTGAATAAAGCATCAGC R 2 1 2 1 201000 r 74 goat snp34889-scaffold416-959126 14 35172825 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447369 Affx-122924862 AX-123317705 14 57471791 TCTGTGAATGCAATATACATCCTTAACTTTTCAGC[A/G]TCTGAGTTACTATTGTCCCCTTCTTGTAAAATGTA R 2 1 2 1 101000 f 74 goat snp34888-scaffold416-917444 14 35131175 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438481 Affx-122931228 AX-123308819 14 57502184 ATATGTTTGCTTTTCAGGAGAATATATAAACATTC[A/G]TATACCTCAATAAGAAGAGAGAGGCAACCTAATAA R 2 1 2 1 201000 f 74 goat snp34887-scaffold416-887051 14 35100561 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440846 Affx-122929261 AX-123311183 14 57535964 CAGAGTCAGACACGACTGAGTGACTTTCACTTTAA[C/T]GTATTTTCCATCAGGATGACTTCCTGTCTGTCAAC Y 2 1 2 1 201000 r 74 goat snp34886-scaffold416-853271 14 35067336 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403939 Affx-122957460 AX-123274291 14 57565908 CACATTTCTAGGGTCCCTGACAGTTTGAAAATTCT[C/T]GGTTTTGGACATGAAAACCCAGCTGACACGCTCTA Y 2 1 2 1 101000 f 74 goat snp34885-scaffold416-823327 14 35037348 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442591 Affx-122928489 AX-123312928 14 57595240 TAAACTTGAGGTGGGAATATGGTTTTCATAACATA[C/T]GGTGATTTCTTATTCTAAATTCCACATTATATGTA Y 2 1 2 1 101000 f 74 goat snp34884-scaffold416-793995 14 35008012 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777106 Affx-122946146 AX-385264229 14 57625816 AGAATAAAGTCCTTTGTCAACCATAGGATAAACTA[C/T]GGTTGACAATGTCTTCCATGACCCTCGTCTCCAGC Y 2 1 2 1 102000 r 74 goat snp34883-scaffold416-763419 14 34977515 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440623 Affx-122929963 AX-123310960 14 57686627 TTTCTCACTAGGGAATTAGTCTTGACAGAGGGAGA[A/G]GGAGCTCAGGACTCAGAGGTGGAGGGTCTATGCCC R 2 1 2 1 101000 f 74 goat snp34882-scaffold416-702608 14 34916722 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449924 Affx-122922919 AX-123320259 14 57727093 TCCCCCTTGTATTCATTTCTGCATATATCTTTTCC[C/T]CAAGTATAACCTATTACTTACAGACCCTGAGAGTG Y 2 1 2 1 201000 r 74 goat snp34881-scaffold416-662142 14 34875591 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427634 Affx-122939340 AX-123297977 14 57767134 AATTCATATGCCAGTGAAACACAGAATACAGAGTA[C/T]AGGAAGGTTTTACCTTGGGTATAGGGGGAACCGTC Y 2 1 2 1 201000 f 74 goat snp34880-scaffold416-622101 14 34835044 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384203 Affx-122972395 AX-123254561 14 57818765 CTCTTTGAGCAGTCATCAGGGAATCAATTATTAAA[C/T]AGGACGAAGGGGATGATTTTACAAATACAATGACA Y 2 1 2 1 201000 f 74 goat snp34879-scaffold416-570470 14 34783051 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790552 Affx-122945044 AX-385277555 14 57931432 TTAAAGATTTGGACAGATTTTAAACTAACACGTAC[A/G]TCTTGAAATAAGAACAGATCTATTAATACTAATCT R 2 1 2 1 101000 f 74 goat snp34877-scaffold416-457803 14 34671998 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375769 Affx-122978594 AX-123246128 14 57967153 GAAATCTGTATTGTGGGTAAAGTAGAACCAAGCCA[C/T]GTTTTAGCCAGAAAGCACCATCTACAGAATATAGA Y 2 1 2 1 101000 r 74 goat snp34876-scaffold416-422082 14 34636198 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787345 Affx-122959405 AX-385274370 14 58000817 TAACGATCCTAAGGATATGTTTCCAAAAAGCAACC[A/G]CTGACAACCCTGAAGCCATTGTTCAGAGTTCTGAC R 2 1 2 1 101000 f 74 goat snp34875-scaffold416-388418 14 34602569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797440 Affx-122921292 AX-385284379 14 58051279 ACCTGCTTCTCTGTTTGTTGTTATGTGATGTTGCT[A/G]TGTTTTAAAACATTAGCCTGCAGTGTCAGTGGTGC R 2 1 2 1 101000 f 74 goat snp34874-scaffold416-337956 14 34552038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396803 Affx-122962745 AX-123267158 14 58114940 TGACAAGCAAGATGCATAAGAGTGGCATTCAAGAA[C/T]GACGCCTGACAAGAAACATAAACCTACGAGTTATC Y 2 1 2 1 101000 f 74 goat snp34873-scaffold416-274295 14 34488549 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383569 Affx-122972598 AX-123253927 14 58155943 ACAAAATAATGGAATTATCCTGAATCGAAAATCCA[C/T]AGATGTGTAGATTTACAGACACATATTTATAATCC Y 2 1 2 1 101000 f 74 goat snp34872-scaffold416-233292 14 34446973 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381311 Affx-122974444 AX-123251669 14 58187259 CCATTTTCATCTGCATTTTGGGAGGACAGAGAAAT[C/T]AGGAAACTGGGGAAGAGAATCAGAGGTAGTATCCA Y 2 1 2 1 201000 f 74 goat snp34871-scaffold416-201976 14 34415818 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417905 Affx-122946739 AX-123288253 14 58230513 TGTGGAAACTCTTGTGTCCCCATATACACCCTTCC[G/T]CACTTTGCAAACCCCAAATTCTTATGCTTAAAAGC K 2 1 2 1 101000 r 74 goat snp34870-scaffold416-158722 14 34372548 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778865 Affx-122952988 AX-385265973 14 58265989 AGAGAAAAAGAATCTTATGCTTAGATCTACAAAGG[C/T]GATATGATTTCACAGTAGTGAGCAGATATTCCATT Y 2 1 2 1 101000 r 74 goat snp34869-scaffold416-123246 14 34337057 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407570 Affx-122954672 AX-123277921 14 58308882 TCTGCTCCCATTTAAAGACTTAAATTCATACACTG[C/T]ATTAAGGGATTGATTTTTGGTTTTGATTTTCCTAC Y 2 1 2 1 201000 f 74 goat snp34868-scaffold416-80353 14 34293790 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450542 Affx-122922481 AX-123320876 14 58402111 CAAAGGGAGCTGGACTGGGGACAGTCATCCTGTAA[C/T]GACAACAGGGACACAGGCTCCATTGGTGTAAGGAG Y 2 1 2 1 201000 r 74 goat snp51548-scaffold755-2087765 14 34200640 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443539 Affx-122927767 AX-123313876 14 58464136 CCTCACTGCAGTTACTTGGCCTCAGAAAGAATCCC[A/G]CTCAAGGGAAACACTGGATGGTCCAATCAGGCAAC R 2 1 2 1 201000 f 74 goat snp51547-scaffold755-2025740 14 34138631 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390241 Affx-122967766 AX-123260598 14 58541203 CTCATCCCCAAATACTTGTCCTATGACCTAGATGC[C/T]GTCCAGCTCAGATTCAACCCATACCTCCCCCACCA Y 2 1 2 1 201000 r 74 goat snp51545-scaffold755-1948673 14 34061639 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381698 Affx-122974715 AX-123252056 14 58684138 CTCAATGGCTTCTCTCTGCCTCCAGCACAAGCAGA[C/T]TGAAGTTTAGCTTGTGGGGAATTATGACTACTGTT Y 2 1 2 1 202000 f 74 goat snp51542-scaffold755-1805738 14 33918681 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797148 Affx-122969233 AX-385284088 14 58749115 TAAATAATTGATAGTTAGTGTTTTAATTAAAGCCA[C/T]GAAAATGTTTAACTCAGGGTCCCTCAAGTGATATC Y 2 1 2 1 101000 r 74 goat snp51540-scaffold755-1740761 14 33853696 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795045 Affx-122956037 AX-385282004 14 58876024 TATACTCTGGTCCTTTACCCAAATCCAGAAAGGCA[C/T]ATTGGGAGATACTGAACATAAGCAATTATTTCAGC Y 2 1 2 1 101000 f 74 goat snp51538-scaffold755-1613852 14 33730364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786711 Affx-122933209 AX-385273742 14 58907268 CATTGAAGCAGACATTCTACTGGGAAGTTTATATA[C/T]GGAATTTCTTGACCTTACATACCCCTTTTATCAGT Y 2 1 2 1 202000 f 74 goat snp51537-scaffold755-1582608 14 33699209 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424344 Affx-122941937 AX-123294690 14 58970677 AACTGCAAAGTGATTCATACATTTAAATCCTTACA[A/G]TAGACGTTTAACAAGGATTTGGGGAAGAAAGTTTA R 2 1 2 1 201000 f 74 goat snp51535-scaffold755-1519199 14 33635408 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404748 Affx-122957230 AX-123275100 14 59021312 AATCATATACTTGGATTACTCCAGAACAAGTCAAA[A/G]CATACACAATGCTGGTATCACCAGCTCATTCTCCT R 2 1 2 1 201000 f 74 goat snp51534-scaffold755-1468564 14 33584773 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774626 Affx-122942386 AX-385261760 14 59070850 TGGTGTAATTTAGGGCTATTTTGAAATTAGTTCAT[C/T]AAGGGACCCAGCAAATCCATTCTCCTAGTTACCTA Y 2 1 2 1 101000 r 74 goat snp51533-scaffold755-1419026 14 33534857 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421038 Affx-122944530 AX-123291385 14 59115887 GTGACATTTTTTCTCAACATGTAATTCCATTTGCC[A/G]GTTGGGTCATGGGCTGTAGTTTTATAGGTTGAATG R 2 1 2 1 201000 f 74 goat snp51532-scaffold755-1373989 14 33489599 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379112 Affx-122976751 AX-123249471 14 59209873 ACTATTAATTTCATTCATAGTAAAAGAATGTAATG[C/T]GGTCAAGAGCAGTAGAAACATTTAAGGTAGATCAG Y 2 1 2 1 101000 r 74 goat snp51530-scaffold755-1280003 14 33395042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272742 Affx-1111833017 AX-519546442 14 59211219 AGGGCAGTGGAGAAAACTGCCCTTCCCAAAACATC[A/G]TCCCACTGACCAGGAAATACTGCTGCTGATTTTTA R 2 1 2 1 201000 f 74 goat 14_59211219_AF-PAKI 14 59211219 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433533 Affx-122935003 AX-123303874 14 59347618 TCTGTTTACCGAACTAAAATTGATCCCTATTTGCA[A/G]TAAAGTACCACATGCTATCTATCACTCTGGAAGTG R 2 1 2 1 101000 r 74 goat snp51527-scaffold755-1142258 14 33257501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802577 Affx-122941999 AX-385289479 14 59400204 CTTCGGAGCAGTGTACAGTAAAATACCAGCATACA[C/T]AATTCTGAAAATGGAGTAGAACTTAAAACACTCTA Y 2 1 2 1 101000 f 74 goat snp51526-scaffold755-1089672 14 33204642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408123 Affx-122954247 AX-123278474 14 59482604 TTTCCCATAAAGCACGTCTCAACACTGTATTCTTG[C/T]GTCCAACTCAGCACCAATAAGATTTAAGAAATGTG Y 2 1 2 1 101000 f 74 goat snp51525-scaffold755-1007272 14 33122189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443340 Affx-122927434 AX-123313677 14 59536928 CTCAAGATATTTAAATTTATCTTATTATCCATGTC[A/G]CTGAGCGCTTGTATTTTTTGCACTTCCTGATAACA R 2 1 2 1 101000 r 74 goat snp51524-scaffold755-952948 14 33068598 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797503 Affx-122933768 AX-385284442 14 59577374 TTTCTTTTGTTGTTCTTCAGACTGGCTAAAACTAT[A/G]TTCTGTATATAGTGAAGACCTGATAAAGAAATTTG R 2 1 2 1 201000 r 74 goat snp51523-scaffold755-912502 14 33028022 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778714 Affx-122956156 AX-385265825 14 59614583 AGAAGAACAGGGCAGATCTATACATATGAACCCAA[A/G]AGGATTATGCCATGTATATTTGAGTTATTTTTCTA R 2 1 2 1 101000 f 74 goat snp51522-scaffold755-875293 14 32990299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793682 Affx-122950909 AX-385280654 14 59650451 ATTTCAGAAACACAGACTTTCATGAAAAGTTTTCC[A/G]TTTACTTTGAAAGAAGGACCTTGAAGTGTTTTGAC R 2 1 2 1 101000 f 74 goat snp51521-scaffold755-839425 14 32954196 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436042 Affx-122932722 AX-123306381 14 59692973 TTTAAGCAACTGTTTTTTCCTGTAATATCTTTTCT[A/G]CATATCTGTTAGGGAGAATTCCACAATTGATGTTC R 2 1 2 1 101000 r 74 goat snp51520-scaffold755-796903 14 32911218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771149 Affx-122942239 AX-385258309 14 59728231 ATAATATCCTACTGAAGAATTTCCAGCACCAAGAA[C/T]AGTGTCTAGCATATTAATAAGTTCTCAATATATTT Y 2 1 2 1 101000 f 74 goat snp51519-scaffold755-761645 14 32875998 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401889 Affx-122958847 AX-123272242 14 59767846 AGGAGGAAGAAGGGAAAGAGGATAATATGAAGGGC[A/G]TGACATGTATCTATAATTTTCTTCAGATGTCCAGC R 2 1 2 1 201000 f 74 goat snp51518-scaffold755-722030 14 32836364 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377487 Affx-122977499 AX-123247846 14 59888890 TGTTTAAGGATATATTAACTATTAATATGAAAATA[C/T]GTACACAATGCCCACTAGCATCATTTTGTTTTTCA Y 2 1 2 1 101000 r 74 goat snp51516-scaffold755-600986 14 32713910 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422695 Affx-122943657 AX-123293041 14 59920946 CCAATATGGAGGAGAAATGTTGGTAAGACAGACAA[C/T]GAGAGAGACTGGCATAGCATTCACCCCACACTTTT Y 2 1 2 1 101000 f 74 goat snp51515-scaffold755-568930 14 32680173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795156 Affx-122975949 AX-385282114 14 60027000 GAATTCCGAGTCATATTTGACTCCTTCAAGTTTTC[G/T]TCATTTAATGGCAGAATGACTGCTCCACCAAATCC K 2 1 2 1 202000 r 74 goat snp51513-scaffold755-462876 14 32573286 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393268 Affx-122965454 AX-123263625 14 60061122 TTCAATGGCAGTAAGCTATTTTTAATGTTAAAACA[C/T]AGCTATATGTTTTCTTTGAAATATATTAATCATAG Y 2 1 2 1 103000 f 74 goat snp51512-scaffold755-428754 14 32539137 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769465 Affx-122978101 AX-385256635 14 60094095 TAAGAGGAGTCCAAAGAATTGACTTCAAAAAATAA[A/G]CTTCTTCTTGAAGAAATCACTAGACTTTGGCAGAT R 2 1 2 1 102000 r 74 goat snp51511-scaffold755-395781 14 32505675 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437436 Affx-122932402 AX-123307774 14 60158781 ATCAATGAGCAGATTTTTTGCAGAAACCCTATGAG[C/T]CAGGAAGAAGAGGAATGACATTCTCAAAACACTGA Y 2 1 2 1 101000 f 74 goat snp51510-scaffold755-331095 14 32440782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790669 Affx-122939540 AX-385277671 14 60194798 AATGATAAAGTATCCATATGTATACACACCATAAG[C/T]GTACTATTTAATGTTATAATTAGTAAAATGTACAC Y 2 1 2 1 101000 f 74 goat snp51509-scaffold755-295078 14 32404387 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428585 Affx-122938706 AX-123298927 14 60236242 TCAGGCTGTCATCCAAGTTGACATCAGATCATGGC[C/T]GAAAGCATCAAGAAATATCCCTTTGGTATGCTGAT Y 2 1 2 1 201000 f 74 goat snp51508-scaffold755-253634 14 32362603 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796870 Affx-122968203 AX-385283813 14 60270649 AAATGTCGCATTTCTTGATGTCCTAAGATTGTAAA[C/T]ATGGAAAGCCTCTTTTCCATAGTATCCTAAATATT Y 2 1 2 1 202000 r 74 goat snp51507-scaffold755-219227 14 32327825 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800894 Affx-122977397 AX-385287809 14 60320806 AACAAGCTGTAAGTGAACCCATCCAGGGTTTAGCA[C/T]TTTGGTAGGATAGATAGATAAGGAAGCAAGTAATT Y 2 1 2 1 101000 f 74 goat snp51506-scaffold755-169070 14 32277901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773887 Affx-122956831 AX-385261027 14 60376359 CCTTAGGAATTGCTTGCTTTTGGAAGATAAGATTA[C/T]AAACTGAATAAAATAGTTTCCCTATTAAGATTCAT Y 2 1 2 1 101000 f 74 goat snp51505-scaffold755-113517 14 32229374 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429450 Affx-122938494 AX-123299792 14 60475583 CTTGGTTTCCTTGGGTAGTACATCACTAAAGTGAA[A/G]AGTAGTTAGATAGTGAATGGTCCCAAAGCATTTTA R 2 1 2 1 101000 f 74 goat snp51503-scaffold755-14293 14 32129718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426586 Affx-122939988 AX-123296932 14 60520347 ATTGTAGGCAGAGGTAACAACAAGAATAAAGACAA[C/T]AGTCAACTGTCTGGAGAACAAATACTACAAATGTG Y 2 1 2 1 101000 f 74 goat snp53673-scaffold818-30372 14 32084176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434874 Affx-122934355 AX-123305215 14 60570528 GTATTCTGAATCCCAGCTCTCCATTTCAGGAGCAT[A/G]GACCTAGTTTTGGGGAATAGTCAAGAAAGATTTCC R 2 1 2 1 202000 r 74 goat snp53674-scaffold818-80553 14 32033351 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775018 Affx-122936395 AX-385262150 14 60601603 AATATTTAGTAATTAATTGAATATTAGCACCTACT[G/T]CCAAAATGAATAACCCTAACTCCTGTCCTGAATGA K 2 1 2 1 101000 r 74 goat snp53675-scaffold818-111628 14 32002025 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430100 Affx-122937525 AX-123300441 14 60639921 TAAGAGGAATGAGAAGAAAAAAATCATTCTGTGAT[A/G]CTAGTGAGAGTCAAGTCTATTTTTATAGTTTAAAG R 2 1 2 1 101000 r 74 goat snp53676-scaffold818-149946 14 31963399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778328 Affx-122931069 AX-385265443 14 60702110 AAGGAATACACAATATAAATCTATTGAGGCAAATG[C/T]AGAGGTACTAAATCCAAAAGTCAAGGATTTGTTTT Y 2 1 2 1 101000 r 74 goat snp53677-scaffold818-212135 14 31898816 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782342 Affx-122927927 AX-385269419 14 60737608 TGTTTCCACAAGCCCTGATTGAATCTAAAGTTCTA[C/T]GTCAGTAGAATGAAGTCATCCATTCCTCCATTAGC Y 2 1 2 1 201000 r 74 goat snp53678-scaffold818-247633 14 31863031 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387127 Affx-122970656 AX-123257485 14 60770856 AAGAACAGTCAGACTAATCTATGGTTATATAAGTC[A/G]TAAAAGTGGATTTCCTGTGAGAGGGGAAGTGAGAA R 2 1 2 1 201000 f 74 goat snp53679-scaffold818-280881 14 31827877 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274327 Affx-1111834188 AX-500172704 14 60813330 GGAAACACACTGGCTGATACCAAGAGGAATCTCCC[A/G]CTGCAGTCGGTTCCCTTCACTCCCTGCATGCATCC R 2 1 2 1 202000 f 74 goat GoatD01.024608 14 60813330 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38376909 Affx-122977800 AX-123247268 14 60882894 ACTGGATAAAGAGGGATGGGGCTCAGTATCACAAA[C/T]AGGCAAATTCCATTCAGTTTTCCTGTTCCTAAAGA Y 2 1 2 1 101000 f 74 goat snp53681-scaffold818-392919 14 31713928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413377 Affx-122950136 AX-123283726 14 60918895 CTGAATATGACTTAGCAACTGAATAACAACAAACT[A/C]GGACCAAATGCTCACTCTTCACTCAAATGAAGGTG M 2 1 2 1 201000 r 74 goat snp53682-scaffold818-428920 14 31677603 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787261 Affx-122928153 AX-385274287 14 60949658 CCTGAGTGGAACCTGGAACATTGTGCACAAGGCTG[C/T]AGGTCTATTTCTGGAAGATTTTATCAGTGGTAAAC Y 2 1 2 1 101000 f 74 goat snp53683-scaffold818-459683 14 31645944 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386898 Affx-122970040 AX-123257256 14 61010003 TTTTGATTCTTCTACTCAGCCCCTCCTACGTGGGG[C/T]ATATGACTCTGAAGGAACAATAACCCTCAGAATGT Y 2 1 2 1 101000 r 74 goat snp53684-scaffold818-520028 14 31585638 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320789642 Affx-122964701 AX-385276651 14 61012928 ACCTAAGACTCCACCTTCAAGATGTTAATAACAAG[A/C]CACTAATTTAATCACAGTATGATTTACTGAAATGA M 2 1 2 1 101000 f 74 goat snp23143-scaffold231-1792 14 31580480 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792695 Affx-122974271 AX-385279675 14 61049167 CAACCAAAATTTGAAAACTCATTAGATAAACTCAG[C/T]AGCAGAAGGGAGCTGAGAGAGGAAATAACTAGGGA Y 2 1 2 1 102000 r 74 goat snp23144-scaffold231-38031 14 31544037 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417857 Affx-122946774 AX-123288205 14 61095042 ATTTCCACATATACATATGTGTGTATATATTATAC[A/G]TAGGTAAAAGTATTTCTAGTCACTAGGGATTAAAA R 2 1 2 1 103000 r 74 goat snp23145-scaffold231-83906 14 31499063 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435171 Affx-122933656 AX-123305511 14 61184084 GGAAGAGAATTATCAGATCAGGACCTAGGTGCCTG[C/T]GAGGGGACTCATGGGGAAGATGATATCACATGGGA Y 2 1 2 1 101000 f 74 goat snp23146-scaffold231-172948 14 31409221 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775337 Affx-122951771 AX-385262468 14 61221625 GGTATCTGCCTAAAACATTGCCAGTGATTCATGGC[A/G]TAGCATGATGATTTTCATGTAGTATATATTCAACA R 2 1 2 1 101000 f 74 goat snp23147-scaffold231-210489 14 31371073 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451729 Affx-122921542 AX-123322062 14 61279201 ACGGCTAGGGATCTTCAGAAACCTTGACAGATAGC[G/T]CTATAAAGCCTGAAGACAAGGAGAGCAAGGTAATA K 2 1 2 1 101000 f 74 goat snp23148-scaffold231-268065 14 31313493 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765449 Affx-122928244 AX-385252950 14 61318548 TGTGGGGAGCCTGTGAAGGAACCAGTCATTTTTAA[C/T]AGAATAATCTGTCTATACTTGAGTATAACAGATAG Y 2 1 2 1 101000 f 74 goat snp23149-scaffold231-307412 14 31274045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801642 Affx-122959276 AX-385288550 14 61368564 TCTCAGTATATTGAAGTAGAAATGGTAGGTAACAT[A/C]GTGACACATGATTCTTCATGATTTCTCCAGCTTAA M 2 1 2 1 101000 r 74 goat snp23150-scaffold231-357428 14 31223316 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417170 Affx-122947333 AX-123287518 14 61425165 TTCAGTATGATCTATGATCACATCCTCCCACACTT[A/G]TCCACTCTTCAAGAGATCTAGCAGGTTTTTCGGCA R 2 1 2 1 101000 r 74 goat snp23151-scaffold231-414029 14 31166847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451343 Affx-122921264 AX-123321676 14 61469122 AGAATTTTTATAAGCATCGAGTTTAGTGGCTGTTC[A/G]TCTTATTATATGCATGATCATTTAATTATTCTATT R 2 1 2 1 201000 r 74 goat snp23152-scaffold231-457986 14 31122803 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771915 Affx-122972413 AX-385259071 14 61549589 TTACTGGAAGTTAGACTCAAAATATCTAAATTATT[A/G]TATCATTTGATTCTGATGTCACCTTCCCTTAATTT R 2 1 2 1 201000 f 74 goat snp23154-scaffold231-538453 14 31037610 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389940 Affx-122968092 AX-123260297 14 61587252 ATCTACCTTATGTTTAATAAGTGATGTCCACTATA[G/T]GGTTTATTATCATTTTCCATGTGATATTACTGTAA K 2 1 2 1 101000 f 74 goat snp23155-scaffold231-576116 14 31000267 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793276 Affx-122957208 AX-385280254 14 61648511 CTTGTAAAGGATACTCTGTATATGTTCTCAGACAT[A/G]TGATGCAGGGTCATTGGTACAAATGTATTCTTGAT R 2 1 2 1 101000 f 74 goat snp23156-scaffold231-637375 14 30938689 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375655 Affx-122978684 AX-123246014 14 61690043 ATTCAAAAATTTTGATTGGGATTATATTAAAATTA[C/T]GGATTAATCTGGGGAGAATTGGCGTTTTTAGGTTA Y 2 1 2 1 202000 f 74 goat snp23157-scaffold231-678907 14 30896242 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399070 Affx-122960892 AX-123269425 14 61726776 AATACATAGTCAAAAAGAAGCATAATTAGCATAAT[A/G]TTTAGCAAGAAGATCATAGTCTTGCAAGAATAAAC R 2 1 2 1 201000 r 74 goat snp23158-scaffold231-715640 14 30858829 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272745 Affx-1111833018 AX-423098144 14 61832810 GACTACAGCACACCAGACTTCCCTGTCCATCACCA[A/G]CTCCAGAACATGCTCAAACTCATGTCCATCAAATT R 2 1 2 1 303000 f 74 goat 14_61832810_AF-PAKI 14 61832810 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403152 Affx-122958096 AX-123273505 14 61919077 AGGCTACAGGCCATGGGGTTGTAAAAAATCAGACA[C/T]AGCTGAGCATGAGCACAGACAGGCATATAGGGGGA Y 2 1 2 1 103000 r 74 goat snp23161-scaffold231-907941 14 30665545 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799892 Affx-122968052 AX-385286818 14 61988180 TCAGTGAAGACATGGATTAGACCTTCATTCTTCTG[C/T]AGATGACACTCAGATCTATTTGATGATTAGTCCTA Y 2 1 2 1 101000 f 74 goat snp23162-scaffold231-977044 14 30594872 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770465 Affx-122956006 AX-385257631 14 62028204 AAATGGGTGTCCAAAATTTGTAGAACATGATTAAA[C/T]GATAATGACTATCAAGGGTTTGGCATAGAAATAGC Y 2 1 2 1 101000 r 74 goat snp23163-scaffold231-1017068 14 30554988 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428244 Affx-122939423 AX-123298587 14 62080342 TAGAATTTGGACAGCAAGACGAGTGTGTTTAGATG[A/G]CAAGTTCATTTGAGTACTTGATGGAATTCCTGGAT R 2 1 2 1 101000 f 74 goat snp23164-scaffold231-1069206 14 30503856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764756 Affx-122974387 AX-385252370 14 62124166 AAGCCTATTTGCAATTTATCAATTTTCCCATGTAT[A/G]TTCTATAATAACTGGGCTGTTATTGTTATAAGCTC R 2 1 2 1 201000 f 74 goat snp23165-scaffold231-1113030 14 30459782 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775508 Affx-122951579 AX-385262639 14 62207881 AAAAAGCTTTGAAGTCTTCAAAAGCAGTAGCCACC[A/G]CATGAAACCAAAAGGTATTTTCCTCACTAACTATA R 2 1 2 1 101000 f 74 goat snp23167-scaffold231-1196745 14 30374597 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428248 Affx-122939419 AX-123298591 14 62240882 ATCTCTCACAACTTTGTCCCTCTTTCATACCACTG[C/T]GCTCAAGCTACACAGGTCTCCTGGCTTTTCTTCAT Y 2 1 2 1 201000 f 74 goat snp23168-scaffold231-1229746 14 30341750 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452683 Affx-122920314 AX-123323016 14 62271212 CTGAATGTTACCTTCTTACTCCTATCCTCACCCCA[C/T]AAGTTCATCTATCTAATTTATTCTTCAGATTCGCC Y 2 1 2 1 201000 r 74 goat snp23169-scaffold231-1260076 14 30310703 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417156 Affx-122947345 AX-123287504 14 62327928 CTCTCTGAGCTTCTGTATGTATTACAGTTTCCTTA[A/G]CTTTCTAAATTTCTGAAAACTAAAAATAGATATTA R 2 1 2 1 103000 f 74 goat snp23170-scaffold231-1316792 14 30253209 A G 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38412897 Affx-122950417 AX-123283246 14 62364476 AGAAATGCTGATTCAAAAATAAATATATAAATTTT[A/C]GTAGATCAATACTAGTTTCTGCTTTTGCTGCTCAT M 2 1 2 1 103000 r 74 goat snp23171-scaffold231-1353340 14 30216319 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422924 Affx-122943040 AX-123293270 14 62435323 AACACAGCACATTTGGGGCTGAGGTAGTAAAAATG[C/T]ACCATCTCTATGCACCATCAGCAACTCCTGATTTA Y 2 1 2 1 201000 f 74 goat snp23172-scaffold231-1424187 14 30145662 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404220 Affx-122957657 AX-123274572 14 62465026 TCTCTCTTGAGAAGTGTAAGGTTTCATTGCAGGGA[C/T]GAGAAAGCCCACCATAAAAATATACATAGTACTAA Y 2 1 2 1 101000 f 74 goat snp23173-scaffold231-1453890 14 30116013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770339 Affx-122976242 AX-385257505 14 62503934 GTCTAATATCTGTCTATGTTATTGATGACCTTTTC[G/T]CTTATTTTAATCCTTTGCATTAGAATTAACTTCCT K 2 1 2 1 101000 f 74 goat snp23174-scaffold231-1492798 14 30076997 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771137 Affx-122920374 AX-385258297 14 62550452 TGGAAATTGTTTCCTAGTACTTTATATTGTTAAAT[G/T]ACTTCTTTAGAAAAACTTGGCAGAGTGTAACTTAT K 2 1 2 1 101000 r 74 goat snp23175-scaffold231-1539316 14 30030299 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434833 Affx-122934792 AX-123305174 14 62626950 TCATTTATCAGTTGCAGTATACTGGATAGGAGGTC[A/G]CCCTCTTTTTCCTTTCTTTCAATGTCAGGAAGCTT R 2 1 2 1 201000 f 74 goat snp23177-scaffold231-1615814 14 29953977 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445610 Affx-122925109 AX-123315947 14 62663048 ATTAAGCCTGAATATTTTCTAAGACTGGGAAAATA[C/T]ATCTGTGGCCAGCTTTTAGGTTTAATCAAACTTAT Y 2 1 2 1 101000 r 74 goat snp23178-scaffold231-1651912 14 29917415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409003 Affx-122953886 AX-123279354 14 62717132 TTCCTCTTGTCTGGCATTTATCACTCTCTCCTTTG[C/T]GGTATGGTTATTTTTGAGAATTTCTTACTTCCCAG Y 2 1 2 1 101000 f 74 goat snp22067-scaffold218-40822 14 29863268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791289 Affx-122937742 AX-385278283 14 62755017 TCCAGCCTTGCAGTGTACCACTGCAGTAACTCTTA[C/T]ATCCAAGTCTCCCCTCTCTACTCTTTCTGTCCTCA Y 2 1 2 1 101000 f 74 goat snp22068-scaffold218-78707 14 29825021 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778658 Affx-122925762 AX-385265769 14 62794036 TTTTGTTTCTGATAGCTTTTGATAATACTTTACTC[A/G]TTTGAGTCCTATATATCAGGTCACTCTGGTTTATT R 2 1 2 1 101000 r 74 goat snp22069-scaffold218-117726 14 29786620 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408647 Affx-122953474 AX-123278998 14 62841521 TGTACTCTGTACTATTTTACCATGCCATTCAAAAT[C/T]ACTCTTGGAATTTTCCTCTCCATTTCTGGTTGTTT Y 2 1 2 1 201000 f 74 goat snp22070-scaffold218-165211 14 29737181 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400106 Affx-122960729 AX-123270461 14 62888021 AATTATATATATCTTGTGAATTGTATTTATTGGTG[C/T]ATTTTCATATTTATGTGCTTCAAAGGAGCAAGAGA Y 2 1 2 1 201000 f 74 goat snp22071-scaffold218-211711 14 29691451 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452421 Affx-122920587 AX-123322754 14 62930493 TTTCACAAATATACATCAATTCACAGCTTCTATGG[A/G]TACTCAGGGAGTTTGAAGTCTCATAGTAATGGATC R 2 1 2 1 101000 r 74 goat snp22072-scaffold218-254183 14 29647575 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423644 Affx-122942354 AX-123293990 14 62962534 TGATGGATTTGAATCCAGTAGAAAAAATAAACTTG[A/C]AAGCTTTAATACATAGTATAATTCCAAAGAATAAA M 2 1 2 1 101000 f 74 goat snp22073-scaffold218-286224 14 29614915 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377320 Affx-122977680 AX-123247679 14 62992957 AACTTGTAATGCATTTTATTGTGAAATCAAATATT[A/G]CTTGTTTTCAAAGTGCTTTCACATATCTCAAAAGT R 2 1 2 1 303000 f 74 goat snp22074-scaffold218-316647 14 29583507 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785830 Affx-122959078 AX-385272867 14 63056420 TACCCAACTGTTCACAGAGAGCTCTTGTTGGAGCC[A/G]CCTCTCAAGCTTCCTGATTTGGAGTTAATTAGGTT R 2 1 2 1 101000 f 74 goat snp22075-scaffold218-380110 14 29519826 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381914 Affx-122974145 AX-123252272 14 63141358 ACTGTCTATAGATGAGGAAACTAAGACTAAACACT[A/G]TTCAGCTGATCACTAGATTATCATTGCTAAGCACA R 2 1 2 1 201000 r 74 goat snp22076-scaffold218-465048 14 29434001 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781331 Affx-122969123 AX-385268416 14 63188759 ACTCCTTATGCCAGACTTTCTAAGGACCTCTTTAG[C/T]AAATTTTCAGATCTAGACATTACTCATCACTCCCA Y 2 1 2 1 101000 f 74 goat snp22077-scaffold218-512449 14 29386346 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776846 Affx-122930149 AX-385263970 14 63225849 TTTTATGAGAGTATCTCACATTATCCAGATTTAAC[C/T]GTATAAATCAATCCAATATGATACATTACATTAAT Y 2 1 2 1 201000 r 74 goat snp22078-scaffold218-549539 14 29348967 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407354 Affx-122955279 AX-123277705 14 63256956 TGAGATCTAGCTTAAGGAGAAATATTTGTAATTTG[C/T]AAGAACATGAAAATATTCCACTGTAACAAGAGGGA Y 2 1 2 1 201000 r 74 goat snp22079-scaffold218-580646 14 29316877 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798932 Affx-122934587 AX-385285862 14 63306521 CAATAAGGTTATTAATAAGCTCTATTGTTTAAGAG[A/C]AAATACATGGGTCCTCAAACTCTAAAGCAAAGCAA M 2 1 2 1 101000 r 74 goat snp22080-scaffold218-630211 14 29268499 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422950 Affx-122943020 AX-123293296 14 63337811 TAGAACAATTCATAAAATAAAACATAAAAACTGAT[A/G]TCCTTGGCTTTTAACATTGACCTGAAACTTCTGTA R 2 1 2 1 101000 r 74 goat snp22081-scaffold218-661501 14 29237139 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453012 Affx-122920104 AX-123323345 14 63371139 AATGTCTTTCAGGCCTAGTGTGTATTTTTTGGCAA[C/T]AGCTTTCATTATAATAATACACTAAAAGTTGGGAG Y 2 1 2 1 101000 r 74 goat snp22082-scaffold218-694829 14 29202819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429925 Affx-122938097 AX-123300266 14 63409342 GAAACTTGCAGGGTAGCATTCCCAAGAAGAGAGAG[C/T]AGCTCCAAAGAGGAGCCCAAAATTTGGCAGGGAGT Y 2 1 2 1 101000 f 74 goat snp22083-scaffold218-733032 14 29164585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419226 Affx-122945684 AX-123289574 14 63476935 CTGCCAAACTCACCCTGAGAAGGAATTACGCAAGA[C/T]TGTGTCTATTTGGTGAGGTCACCCTGTGTGCATGT Y 2 1 2 1 101000 f 74 goat snp22084-scaffold218-800625 14 29095234 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767745 Affx-122968216 AX-385254973 14 63507292 TAATGTGTACTGGGTGAAGAGAAAGCAGTTGGACA[G/T]CAGCACCCTTGAAATTACATCCCTCTGCCTTTGTT K 2 1 2 1 101000 f 74 goat snp22085-scaffold218-830982 14 29064688 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383208 Affx-122972779 AX-123253566 14 63547294 TTCAAGAGTCCTGCTTTAGACTAGCCCTAATAAAA[G/T]CTTTTTGAAAGCCTTAAAATACTCACACTGATTCA K 2 1 2 1 101000 f 74 goat snp22086-scaffold218-870984 14 29023526 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409489 Affx-122954052 AX-123279840 14 63603400 TGGGTGGCTTACACAACAGAAACTTATGAGGACAG[C/T]TGTCTTCTCACTGTGTCATTACCTGGCCTCATCTC Y 2 1 2 1 101000 f 74 goat snp22087-scaffold218-927090 14 28967081 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451412 Affx-122921187 AX-123321745 14 63650118 CCTTGATTTGGGGGCAAACAGAGGGAATATACATT[A/G]TACTGCAGAGTTTTCTCACTTTGAAGGAAGGTGGC R 2 1 2 1 101000 f 74 goat snp22088-scaffold218-973808 14 28919430 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795804 Affx-122952300 AX-385282757 14 63686497 GTCATTTATGAATAGACTTCTCAATGACCTAAGTG[C/T]GATTTTTGGTCATTTAACTTACATACTTAGCACAT Y 2 1 2 1 101000 f 74 goat snp22089-scaffold218-1010187 14 28882969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392703 Affx-122966405 AX-123263060 14 63739835 TCTTATTAAGGGAAATTTCCCTCACTCCTGCCTCT[A/G]TCTCCTAACCAGGATACTTTCACAGTGGCCCTGCA R 2 1 2 1 201000 r 74 goat snp22090-scaffold218-1063525 14 28829279 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772676 Affx-122931284 AX-385259823 14 63776456 AATAAAATATCAGAACTGTCAGAAGGACCCTAAGC[C/T]GTATGCCAGAGTTTAGATATTTTGGGTAAGAAAAG Y 2 1 2 1 101000 f 74 goat snp22091-scaffold218-1100146 14 28792289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431460 Affx-122936491 AX-123301801 14 63822146 AAGCAAATACATATTAAATAATTTTCCCCAGCCTA[C/T]AGAAACCTTACCATTAGTGTTTTATTAAATGTATA Y 2 1 2 1 201000 r 74 goat snp22092-scaffold218-1145836 14 28745518 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433354 Affx-122935138 AX-123303695 14 63854124 GGCAGCAAGTTGGAATTCAGAGATTCAATCTATTC[G/T]ATCAACTAGAATATATTTAAACTAAAATTGTAATG K 2 1 2 1 101000 f 74 goat snp22093-scaffold218-1177814 14 28713403 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426685 Affx-122939910 AX-123297031 14 63889141 TAGTGACTGAAATGTATTCAGAAAAACTCTGTATT[A/G]TTTAGGATAATAATTGCTTAAATTTCTAAATATTA R 2 1 2 1 202000 r 74 goat snp22094-scaffold218-1212831 14 28676763 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788867 Affx-122961113 AX-385275882 14 63960586 ACATGAAACTTACAATATCTTTGAGAATTAAAAAT[A/G]TTAACATATTATATAAGACATCCACTGTATAATCT R 2 1 2 1 101000 f 74 goat snp22095-scaffold218-1284276 14 28605041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775735 Affx-122931417 AX-385262866 14 64002844 CATGAAAATCATTAAGTATGATCACCACAGACAAT[A/G]TAAATAATACTTAAGAAAGTATTATATCTTAAAGC R 2 1 2 1 201000 r 74 goat snp22096-scaffold218-1326534 14 28562132 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381712 Affx-122974705 AX-123252070 14 64058961 GCAATCCTACTTCATAGAGAAGCGACTATTATAAA[G/T]ATTGGGGCTCATGCACAAAGACATAAAAAGAATGC K 2 1 2 1 101000 f 74 goat snp22097-scaffold218-1382651 14 28505043 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450189 Affx-122922301 AX-123320524 14 64093925 ATATCCGTGGAAGGTAGCAGTGCTTTTATCTCTCT[A/C]TCTGTTTTGTAGGTCTGTTTGCCTCTGTTTTACTT M 2 1 2 1 201000 f 74 goat snp22098-scaffold218-1417615 14 28469933 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782700 Affx-122954404 AX-385269772 14 64144630 AACCTGTGTATAGATACTTGGCCTCAAGCACTCAC[C/T]ATGCCAGGTGTATTGGACAAAGCAAAACTCCTTAA Y 2 1 2 1 101000 f 74 goat snp22099-scaffold218-1468320 14 28418847 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775365 Affx-122957130 AX-385262496 14 64247053 CCAAGCAACTGTTTGTTTTATAATACATTCAGTGA[G/T]CATAAGTTTTGCTTCAAAAAGAGTGGAATTTTTAT K 2 1 2 1 101000 f 74 goat snp22101-scaffold218-1570743 14 28318602 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436536 Affx-122932929 AX-123306874 14 64281975 CAAGATTCATTAGTCCATTCAGAATGGTTTCTCTC[A/G]ATTGCCTGTGCTATGTGGGGTGAATAAAGTAGAAA R 2 1 2 1 101000 f 74 goat snp22102-scaffold218-1605665 14 28283589 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802895 Affx-122978941 AX-385289792 14 64324096 TGTTCTGCCTGCCCCAACATTGTACAATGTAATTA[C/T]GCAGGCATAGTAATACACATGCAATTTATTGATAT Y 2 1 2 1 202000 f 74 goat snp22103-scaffold218-1647786 14 28241147 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394401 Affx-122964616 AX-123264756 14 64352603 GTGAAACAATACCTCATTTAGAATCAGACATATTG[C/T]GTTCAGTGGCCATTTAAGTAGCTATGCATTAAAAA Y 2 1 2 1 101000 r 74 goat snp22104-scaffold218-1676293 14 28212076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272747 Affx-1111833019 AX-519546445 14 64376797 ATCATGAATTAAACAAATGGCTTCAAGGAAGGATA[A/C]ATCCACAAAGAAGATAGAAGCACATTAAATTGTAG M 2 1 2 1 101000 f 74 goat 14_64376797_AF-PAKI 14 64376797 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38399669 Affx-122960507 AX-123270024 14 64386595 CCAATATAAATGGAGAAGACTGCACATAGGTGAGA[C/T]AAGTAACTCCAGAGCTTACCTCAGACCTTCTCCAG Y 2 1 2 1 101000 f 74 goat snp22105-scaffold218-1710285 14 28177773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417196 Affx-122947313 AX-123287544 14 64470846 CAGTTCAGTTAGAAGAAAGGTGATGGCAAACCTAT[A/C]GATATGTGCTACTGGTGGCATGGGGGTTCAGAAAA M 2 1 2 1 201000 f 74 goat snp22107-scaffold218-1794536 14 28092970 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787385 Affx-122970124 AX-385274410 14 64565585 AAATGGTTTCAGTGTTATGCTTGTGTATATAAATA[G/T]AAAATAATTCCTATCATAATTCTTAAGATTTTCAG K 2 1 2 1 101000 r 74 goat snp22108-scaffold218-1889275 14 27997814 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418733 Affx-122946225 AX-123289081 14 64616382 ATCTCTAGTAGTCAATTTTTTGCCGTATAGCACAC[G/T]ATCTGTTCTGTACTCTCAGAAAATTACGAAGATTA K 2 1 2 1 101000 f 74 goat snp22109-scaffold218-1940072 14 27947085 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801502 Affx-122959093 AX-385288411 14 64689952 ATAGGAAAAGTACATTAGAGTGATCAGAATACTCT[A/G]TGTAGGACATAGATAATAACTAAAGGCCTGGAGAA R 2 1 2 1 201000 f 74 goat snp22110-scaffold218-2013642 14 27873407 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427874 Affx-122939704 AX-123298217 14 64790190 AAAATATATTTCCCAAGCATTGGAAGGGTGTATTT[A/C]TTTCAAACATGAATTAACCAAGAGAGAAGAAACAT M 2 1 2 1 101000 r 74 goat snp22112-scaffold218-2113880 14 27773211 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430105 Affx-122937521 AX-123300446 14 64800586 TGATATGAATATTCATGTACAAAATTTTGTGTGTA[C/T]ATGTTTTCCTTTCTCTCCTTACACAACTAAGAGTG Y 2 1 2 1 101000 r 74 goat snp48342-scaffold6864-3121 14 27762766 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390896 Affx-122967105 AX-123261253 14 64827713 TGACTTCACTGCCGAGTTTAATTCCCACTTCACTT[A/C]AGTATTTTTAAAAAGTTAGACTAATCACCAGGTTG M 2 1 2 1 101000 f 74 goat snp23456-scaffold2365-9014 14 27735671 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419605 Affx-122945992 AX-123289953 14 64885713 CATAGAAGGCTTTCAAGAGGTAGATGAAATGAATC[A/G]TTTGTGTTTTAAACTGCCAGCTCTGTTGTGAGTGT R 2 1 2 1 101000 r 74 goat snp23457-scaffold2365-67014 14 27677340 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376077 Affx-122978912 AX-123246436 14 64940864 TCAAGATCTGTCCATTACTGGGAATTCTCCCTGCC[C/T]TCTATCTTGTCCAAAATGGATTAGCATCTTCAGGG Y 2 1 2 1 201000 r 74 goat snp23458-scaffold2365-122165 14 27622050 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792424 Affx-122929552 AX-385279405 14 64975025 AATCCTACATAATGAACTTTGGAGGAAGTCTCTAA[C/T]AGATATATCTAAAGCAAAATATCCCAAATCAAGAT Y 2 1 2 1 101000 f 74 goat snp23459-scaffold2365-156326 14 27587536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793785 Affx-122948606 AX-385280757 14 65014994 TATGAATGCAAGATAGCTTTCTTAGTTCAAATTGC[A/G]CTGTCTCTCTATTATATCCCCTAATAATTCTGCTT R 2 1 2 1 101000 f 74 goat snp23460-scaffold2365-196295 14 27547091 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383066 Affx-122973748 AX-123253424 14 65045687 AAATACACAGTGCTTTCACATTTTTCAATACTTCT[A/C]GAATAATCTCTAAATATAATGCCTTGATCACACTC M 2 1 2 1 101000 r 74 goat snp23461-scaffold2365-226988 14 27516546 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434645 Affx-122933989 AX-123304986 14 65093413 GCCCCCAGCATACGCAGGTGAGCTGAGAGGCCGAC[C/T]GAGCGAATGAATGTGGGGGACTGGGAGGTATCTCG Y 2 1 2 1 201000 f 74 goat snp23462-scaffold2365-274714 14 27468521 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413123 Affx-122950377 AX-123283472 14 65135112 CACAGTTAAGTGAGGTGAGCTTCAGGAAACTGGCC[A/G]CAGTGGACTTACAATCCAAGCCGTTTTGAATTCAA R 2 1 2 1 101000 r 74 goat snp23463-scaffold2365-316413 14 27426108 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406544 Affx-122955116 AX-123276896 14 65186133 TGTGGACAGGATCATCTGACCCCATAGAAAGAAGT[A/G]CCTCAAAGTTGCTTTCCATAATTTGGGTGCCTGTG R 2 1 2 1 101000 r 74 goat snp23464-scaffold2365-367434 14 27375355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415474 Affx-122948710 AX-123285823 14 65215818 CTTAGACCCATTGTCCTGACATTTGTGTGCTCAGT[C/T]GCTCAGTCCTGCCCGACTTTTTGAGACCCCATATC Y 2 1 2 1 102000 f 74 goat snp12348-scaffold1466-9588 14 27345494 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447781 Affx-122923948 AX-123318117 14 65285853 TTTACTTAATAAGCATCTCCTTAGGGTGTAGCACT[A/C]TACTAGATGTTTTGGGGATAACAGAATGCAAATTA M 2 1 2 1 101000 f 74 goat snp12350-scaffold1466-79623 14 27274711 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773567 Affx-122949085 AX-385260707 14 65320529 TCCAGAATTTATTACATGGATCATAAGCATTCCAA[C/T]AGCTTGAAGATGATCAGAAACAGCACAGCACAGTG Y 2 1 2 1 101000 r 74 goat snp12351-scaffold1466-114299 14 27239928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413295 Affx-122950200 AX-123283644 14 65363908 TCATACCTCAAATCTGGAATTCCTGATTCCTGAGG[G/T]TCCCTGCCCATCATCCAACTGGCTATTCAGAATTA K 2 1 2 1 101000 r 74 goat snp12352-scaffold1466-157678 14 27196103 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790306 Affx-122922759 AX-385277309 14 65395186 AAGGCACTGGTTATTGAGAAGTAAAGCAATAAGAA[C/T]AATCATTTAAAATTGTAACATCACATTGGTACAAT Y 2 1 2 1 101000 f 74 goat snp12353-scaffold1466-188956 14 27164508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274105 Affx-1111834042 AX-519547708 14 65413005 GCACTGATGGGGGGCAGAGGAGTGAGACAGCAAGG[A/G]GAGGGGAGCTGCTGCAGGTGTGTTAAGGAGCAGGT R 2 1 2 1 303000 f 74 goat GoatD01.015752 14 65413005 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320793479 Affx-122966870 AX-385280456 14 65454855 GAATGAATAAATATAAGTCAGTCAGTACTCAAGAT[A/G]GGTATTAGAAGTAGGGACAGGTGAGCATTTGGGGA R 2 1 2 1 101000 r 74 goat snp12354-scaffold1466-248625 14 27104446 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380130 Affx-122975992 AX-123250488 14 65483444 ACTGAAAGGAAGTTCCTAGGGGATAGAATCACTTA[C/T]GTTTTCTCAGTCTTGAATGAATGAATGAAGGTAAT Y 2 1 2 1 101000 f 74 goat snp12355-scaffold1466-277214 14 27075325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796484 Affx-122938087 AX-385283434 14 65525504 GCAGTCAGATATCAATCAACATAAATAAGCATATC[A/G]TCAGACTAAAGAAGAAAACTATTTGACCATTCTAG R 2 1 2 1 101000 r 74 goat snp12356-scaffold1466-319274 14 27033268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433534 Affx-122935002 AX-123303875 14 65601582 AAAGACCTTGGTGCTGTCCCCTCTTACCTAGAGCA[C/T]GACTCACGTGCACACAGGGCTGTCATCCCACAACA Y 2 1 2 1 101000 f 74 goat snp12358-scaffold1466-395352 14 26956231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796310 Affx-122934737 AX-385283260 14 65630824 ATGAGAATATTAGATGAGACAAAGAGATACTGCAT[A/G]TTTTAAAGGTAAAAGAGACTTTATAGTAGACAAGT R 2 1 2 1 101000 f 74 goat snp12359-scaffold1466-424594 14 26926922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398724 Affx-122961836 AX-123269079 14 65661301 ACCTACATGTTTTTACTTAATGCAAGTGTGGGAGC[A/G]ACTTCCATTGTCTTAGAGGAAAGCAGTCAGTTTTT R 2 1 2 1 101000 r 74 goat snp12360-scaffold1466-455071 14 26896623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401385 Affx-122959226 AX-123271738 14 65728228 CAGGTGTCTGAGTGAGACATCCTCAGTTATACTCA[C/T]GTTTTTCCTGAATTATGTGGAAACCAATGCTTCAG Y 2 1 2 1 101000 r 74 goat snp12361-scaffold1466-521998 14 26829469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389314 Affx-122968499 AX-123259672 14 65765425 AGGGAAATATATGTAATGTTAAAAATAATTATGCA[G/T]AATATCAAATGATGTCAAGCTAAAATCAACATAAC K 2 1 2 1 103000 r 74 goat snp12362-scaffold1466-559195 14 26791861 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448231 Affx-122924216 AX-123318567 14 65813112 AAGTTTTTTAGGGTAAATCTAGAACAGCCTTTACT[C/T]AAAGACTAGATAAACTCTACTCCCAAGACCTGGAT Y 2 1 2 1 101000 f 74 goat snp12363-scaffold1466-606882 14 26743880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415006 Affx-122949035 AX-123285355 14 65843607 GAGTATTGAAAATCAGTAGGTAATTCCTAACAGGC[A/G]TTTCCAAAAGTTTTTGAAAGTTGGATTTCATTTGT R 2 1 2 1 101000 f 74 goat snp12364-scaffold1466-637377 14 26713127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398601 Affx-122961487 AX-123268956 14 65878755 TGATACCTGTAGTCACATAGAAATTTTAAGTAATC[A/G]TACACACTCCTAGCTCTTTCAGCAAGCTAGAGATA R 2 1 2 1 101000 r 74 goat snp12365-scaffold1466-672525 14 26677426 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412699 Affx-122950754 AX-123283048 14 65919571 AATTTCTCCTGGAATCCAGCATGTGGAACACATTT[A/G]TATCTGTTGTTCAACTGGTTTGCTACCTACCGTTA R 2 1 2 1 101000 r 74 goat snp12366-scaffold1466-713341 14 26636332 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793525 Affx-122965216 AX-385280502 14 65955795 AAAAGTCGGCACAATCTAACCTTGACTTTTATTCC[A/G]TTTCTTTGTGCTGCTTTAGCATCTTGCCTTCTCCC R 2 1 2 1 101000 f 74 goat snp12367-scaffold1466-749565 14 26599598 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774608 Affx-122948580 AX-385261742 14 65985848 ATCTACTTTAGTGTTGCTAATATACTTCTTTAGCT[A/C]ATTGGTACTTTAATTAACTCCTTTATTTAGTTACT M 2 1 2 1 101000 f 74 goat snp12368-scaffold1466-779618 14 26569438 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412309 Affx-122950858 AX-123282658 14 66015480 ACTAAGAGGCTTTCATTTTGAGACTGAGAGAAAAA[C/T]AAGACTTAGTGGGGTCAGTAGCTTACTCAGGAGTC Y 2 1 2 1 101000 f 74 goat snp12369-scaffold1466-809250 14 26539624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423723 Affx-122942874 AX-123294069 14 66094428 TGTTTTATTTTTGTCCCATACAATCTACCCTGGGA[C/T]GATGTCATCCTGAGAACTTATCTGAAATCTCTTTG Y 2 1 2 1 101000 r 74 goat snp56865-scaffold90-2297518 14 26458452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794046 Affx-122932597 AX-385281014 14 66138982 TCCCATGCTCTCACCAATGGCTCTCTGGAACATTC[A/G]AACTATTAAAGAAGAATAGGTAATGTCACTCAGCT R 2 1 2 1 101000 f 74 goat snp56866-scaffold90-2342072 14 26413403 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798869 Affx-122951612 AX-385285799 14 66165115 AAATTTAGAATTTCCAGGATGTTAATGCAATAGAG[C/T]AGCAGAGATCCCTAACGCATATAAGACTGTTAGAT Y 2 1 2 1 101000 r 74 goat snp1897-scaffold1052-2976319 14 26377065 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775567 Affx-122946417 AX-385262698 14 66197833 TTTTTTTGAAATTTTTGTTGGTCACCTTTAAAGCT[A/G]CATCAGTCTTGGTAATGGAAAAAAAGTCGATGTAA R 2 1 2 1 101000 r 74 goat snp1896-scaffold1052-2943601 14 26344290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435627 Affx-122933775 AX-123305967 14 66227307 TTTTGCCTGTCACCACTACAAATCCTAGGGAACTG[C/T]AAGAATGTCATTAGGGGTTATTTCACTAATGTTTT Y 2 1 2 1 101000 f 74 goat snp1895-scaffold1052-2914127 14 26314121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387642 Affx-122969852 AX-123258000 14 66280824 AAATAGATTAGAAGAAATAAAAATGAAGGGATTAC[A/G]CAAATTTTTATCCAGATAATGGCAGTATTTTGGAA R 2 1 2 1 101000 r 74 goat snp1894-scaffold1052-2860610 14 26259989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463347615 Affx-1109939857 AX-514832265 14 66281851 ATTCTAGAACACATCTGGCTCCAAGAGTTTGGCTT[A/G]AGGAATTATATTCTGGGGCTTCTCTGGTGGCTCAT R 2 1 2 1 101000 f 74 goat Random2.2K-1446 14 66281851 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376009 Affx-122978409 AX-123246368 14 66324516 TTCTACCACTTTTTAAAACATCTTCCTTCATTTCC[A/G]CAATTCCCTTGCAGCTACTACCCATTTCTCTCTGT R 2 1 2 1 101000 r 74 goat snp1893-scaffold1052-2816918 14 26216986 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772952 Affx-122935089 AX-385260096 14 66376468 CTGGTGAATTGGACACTTCATTCTACCTTAACTAT[A/G]TAAAAAAGGGATCTTTTTTCTGGATTAGGTACACT R 2 1 2 1 201000 f 74 goat snp1892-scaffold1052-2764966 14 26164130 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380547 Affx-122975292 AX-123250905 14 66435567 AACCACCTCTTAGCTTGCTTAAGCAATATTTTCCT[A/G]TTTTGCTTAAGACTTTTTTAAAAGAAGTAAAACAT R 2 1 2 1 103000 f 74 goat snp1891-scaffold1052-2705867 14 26104453 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795557 Affx-122946251 AX-385282512 14 66480563 AGTTATATTTACTTATAGAAGGAGAAGACATGAGC[C/T]CACCACTCACAAGCACTTGACAAAAACAAGGCATA Y 2 1 2 1 101000 r 74 goat snp1890-scaffold1052-2660871 14 26058983 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792094 Affx-122970673 AX-385279080 14 66537828 GTCAGAGCAAAGAAATCACTACAGATCTTCCTTGA[C/T]GTTCCAATAAAGCCACTGTGAGTTAAAAATACTAA Y 2 1 2 1 101000 f 74 goat snp1889-scaffold1052-2603606 14 26001573 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406845 Affx-122955666 AX-123277196 14 66576909 CTCAGGATAAAAGAGCATTTGGGTAATAAATCATG[C/T]GGATCGTATTTTCAATACTTTATCATGAAGAGCCA Y 2 1 2 1 101000 r 74 goat snp1888-scaffold1052-2564525 14 25963807 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381461 Affx-122974982 AX-123251819 14 66606951 ATCAGAGTGGTAGCACTGAAAGAGTTGTGGACAGT[A/C]GTGAAATTCTGAATATTTTCTGAATGCAGAACTAG M 2 1 2 1 101000 f 74 goat snp1887-scaffold1052-2534483 14 25933466 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410919 Affx-122952057 AX-123281269 14 66671653 CTTGCCACTAGGAGATTCATGATTTGCTTTGTTTT[C/T]AAAAGTTGTGATAATTTTAAGCAGATCTACGCGAC Y 2 1 2 1 201000 r 74 goat snp1885-scaffold1052-2469781 14 25868448 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793860 Affx-122946427 AX-385280829 14 66711052 GAACCACATACCAGGCAATGTTCTAACCAATTTAT[A/G]TACATATTAACTCATATACTAAGACATGAGTTAAC R 2 1 2 1 101000 f 74 goat snp1884-scaffold1052-2430382 14 25828701 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435000 Affx-122933819 AX-123305340 14 66751290 CTGTCAAGTGAGTCCAACAGCGTGAGGACAAACTC[A/G]TCATTGATGAGTTCTCATTGTAGAAAGATGAGAAC R 2 1 2 1 101000 f 74 goat snp1883-scaffold1052-2390144 14 25788529 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798331 Affx-122927371 AX-385285266 14 66852125 AGATAGATTCTTTATAGACTGCTGATTAAACAACT[A/G]TTCTGTTCAAGGCTATTCCTCACTTAGGTTTTAGA R 2 1 2 1 101000 r 74 goat snp1881-scaffold1052-2289309 14 25687957 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417054 Affx-122947518 AX-123287402 14 66901300 AACGAAGACAGGAAATGCTCAATAAGTTGTTGAGG[C/T]GGTAGAATCAAGTAGAAAGTCACTCAGTTATGTCC Y 2 1 2 1 101000 f 74 goat snp1880-scaffold1052-2240134 14 25638703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432431 Affx-122935821 AX-123302772 14 66970909 TCAATATGGTTTCAACTGACATCTTCCTTTCTACC[C/T]GTGGAGCTGAGCATCTTTTCATGGGCTTAGTGGTC Y 2 1 2 1 201000 f 74 goat snp1879-scaffold1052-2170525 14 25567955 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445712 Affx-122926110 AX-123316049 14 67001604 TTCCCATTCTCATTTTCCTCACCTGATTCACCCAG[A/C]GCTTAGCTAACAGTTAATTATCCTTCCCCTGCAAT M 2 1 2 1 201000 r 74 goat snp1878-scaffold1052-2139830 14 25542377 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401743 Affx-122959513 AX-123272096 14 67058790 TAGTCTACTTTTTATCCTGATTTCATAAATATATT[A/G]CTACTCAAATGAGAATATTTACTGTCCCCTGGGAA R 2 1 2 1 101000 r 74 goat snp1877-scaffold1052-2082644 14 25484719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442209 Affx-122928787 AX-123312546 14 67105091 ACTCCTGAAATATAATTAAAAAAAAAAAAAAGAAA[C/T]AGCCAATTCACTTTGTAAATTAAGCTGTTAAGAAA Y 2 1 2 1 103000 r 74 goat snp1876-scaffold1052-2036343 14 25438355 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450104 Affx-122922779 AX-123320439 14 67172439 ACTTTCCATCGTGCTATCAGAAAAAGTGGTCCAAA[C/T]CTCCACACAGGACATGAAAATAAAACTCATACTTG Y 2 1 2 1 101000 f 74 goat snp1875-scaffold1052-1968995 14 25370044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415803 Affx-122948900 AX-123286152 14 67201109 TTGGCTATCTGTGCAAAAGCTTTTAAAGTTTGATT[A/G]GGTCCCACTTGCTAATTTTGGCTTTTATTTTTTTT R 2 1 2 1 103000 r 74 goat snp1874-scaffold1052-1940325 14 25341384 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793981 Affx-122938367 AX-385280950 14 67270764 CTGGTTATGATTTCATAATTCATCCCCTTTCCTCC[A/G]TTGCTCATTTAGTTGAAATAGCATAATTTGCCCCC R 2 1 2 1 101000 f 74 goat snp1872-scaffold1052-1870670 14 25270666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434757 Affx-122933902 AX-123305098 14 67304903 GGTGGGACTCAAGATACATTTTTAAGGAAAAAGAT[A/G]ATGTGAACATGTTTATCATTTTAGAGGAGGGGAAG R 2 1 2 1 103000 r 74 goat snp1871-scaffold1052-1836531 14 25236271 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272799 Affx-1111833020 AX-519546495 14 67343237 AACATATCAGTCACACATCAGCCCACCCAGAGGAC[A/G]ATTGCCTTTGTGTAAATAAACAATCCCTTGTACAA R 2 1 2 1 201000 r 74 goat 14_67343237_AF-PAKI 14 67343237 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418705 Affx-122946291 AX-123289053 14 67387060 ATGCTAATACTCTATAATAAGATTCAGTAATTTAC[A/G]TTCCGTCTTCTGTCAGATTGGGGGAGGGGGGAATA R 2 1 2 1 201000 f 74 goat snp1870-scaffold1052-1754374 14 25153525 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448924 Affx-122923162 AX-123319259 14 67426475 GTCAGTGTCAGCTAACACAAATTTCTAAAGAAATG[C/T]AAAACATCAAATAGCAACTTAAGTTAAAGCTTGTA Y 2 1 2 1 101000 f 74 goat snp1869-scaffold1052-1714959 NW_017218073.1 5170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409421 Affx-122954124 AX-123279772 14 67474817 TACATAATTTAAGTCCTCATTCCAAAGGGATGCTG[C/T]ATGACTATTACTGAACACATCCTGATCCCTCAGCC Y 2 1 2 1 101000 r 74 goat snp1868-scaffold1052-1666617 14 25065776 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777773 Affx-122972682 AX-385264891 14 67511042 TTTAATTTCTAAAAGACACTTGTTTGCTCAATTAA[A/C]TACTGACTTGGGATCTTGTGCAGCATTATAAGCTG M 2 1 2 1 201000 f 74 goat snp1867-scaffold1052-1630392 14 25029059 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795715 Affx-122922195 AX-385282668 14 67570583 AGTGTTTGCAGACAAAGATTAGACAAAAATAAGTG[C/T]GTTACCCAGAAGTCTTAAAAAACAGACACAATTCA Y 2 1 2 1 101000 r 74 goat snp1866-scaffold1052-1570851 14 24968957 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391439 Affx-122966747 AX-123261796 14 67618058 GGGGACCGATAAAATGAGAAGAATATCCCCAAACT[A/G]TAAATATAAAGTATATTTATAAATATAATGGCAAG R 2 1 2 1 103000 f 74 goat snp1865-scaffold1052-1523376 14 24921334 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788796 Affx-122959542 AX-385275811 14 67716105 AGCAGTGACGCTCCCAAGAGAGTCATAAGTGAATT[G/T]GTGGTAACACAAGCAGTTTTTGACGACCAGCAATG K 2 1 2 1 201000 r 74 goat snp1863-scaffold1052-1425329 14 24823607 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434051 Affx-122934198 AX-123304392 14 67756712 ACCACAGCCCTCACTCTCACCTCATATGGTAGACA[C/T]ATGGGGCAGGACCCTCCATTTCCCACAGACACAGT Y 2 1 2 1 101000 f 74 goat snp1862-scaffold1052-1384722 14 24782176 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799475 Affx-122919971 AX-385286405 14 67792627 ACTTTGAATGTATAACTGCACATTCTATAACTTGT[A/C]TAATCTGAATCATGGCCCCAGTTCTATAGACTATT M 2 1 2 1 101000 r 74 goat snp1861-scaffold1052-1348807 14 24746178 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403519 Affx-122957624 AX-123273872 14 67827751 TTTTTTTAAGTGAAATACCATACCATGAAGACGAG[C/T]GTCAATACTTAAAAGTTTTCTCTGAGCCTGCTAAA Y 2 1 2 1 101000 f 74 goat snp1860-scaffold1052-1313683 14 24710539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443805 Affx-122927081 AX-123314142 14 67864944 AAGAGACTGACAATACTTTAACTTCTTATATTTCC[A/G]TTGATTAATTCACGGATGCAAATTCCAAGTTGGAC R 2 1 2 1 101000 r 74 goat snp1859-scaffold1052-1276490 14 24673375 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400909 Affx-122959736 AX-123271262 14 67916143 GGAAAGCGTTGCCATTTCCTTTTCCAAAATGGTCT[A/G]TTAGCTTCTGAAATTCAAATTGGCTCTATATTTGG R 2 1 2 1 201000 r 74 goat snp1858-scaffold1052-1225291 14 24622211 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389346 Affx-122968474 AX-123259704 14 68058545 AACTGGGAACTAGACCCCTTTCACTTCTGGTTTTC[A/G]TTTATTTATCCAGTCATTCATTTGTGGCTGCGCTG R 2 1 2 1 103000 r 74 goat snp1855-scaffold1052-1082889 14 24477405 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778908 Affx-122973382 AX-385266015 14 68112458 GTCTAGCTGAAAGGACTTACATGGAAGGAACTCTT[A/G]CTCAACATGCTTGCCAAGATAGGCGAATAAGCATC R 2 1 2 1 101000 f 74 goat snp1854-scaffold1052-1028976 14 24423556 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441600 Affx-122928659 AX-123311937 14 68163778 CTGCAAGGTTGTAGCTGGAGTGGGTTTGCCTCCAA[C/T]AGAAATGGATGTTTCAGTTGTCAGACATTCTGGAA Y 2 1 2 1 103000 r 74 goat snp1853-scaffold1052-977656 14 24372471 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397310 Affx-122962316 AX-123267665 14 68193101 GTAAACCCCAGAGAGAAGCTTAAAGATTCAAGGTA[C/T]GGAGGAGGAAATAGCATGTCTTACTGAGGTGAAAC Y 2 1 2 1 201000 f 74 goat snp1852-scaffold1052-948333 14 24343105 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763161 Affx-986697690 AX-385251099 14 68210146 CCATGTATGTGTGAGTGTATCTGTATCTGCATATA[C/T]ATGTTTATATATCTGTGGTTAAAACCCACTCCAGT Y 2 1 2 1 600010 f 74 goat 14_68210146 14 68210146 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 320799604 Affx-122973991 AX-385286534 14 68222718 ATTTGAGGAGAATTCTTATTGTAATAGACCACAGT[A/G]CACATGGTCTTCAGGTTTGGGCATATGCTTTCATC R 2 1 2 1 101000 r 74 goat snp1851-scaffold1052-918716 14 24313512 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802668 Affx-122973290 AX-385289567 14 68295855 TAACTATGATTGTATTAGAACTAGAGATGTTTTCC[G/T]CTGTGAAGATTAATGTTACATGCCTCAAACTTAGT K 2 1 2 1 101000 r 74 goat snp1849-scaffold1052-845579 14 24240092 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406482 Affx-122955167 AX-123276834 14 68345696 CCATCTTAATGATCTTTCTGAAACGTATTAATGGA[A/C]CTGATTGGTTCTCTCTTTTAAAAATCCTCTTAAAA M 2 1 2 1 201000 f 74 goat snp1848-scaffold1052-795738 14 24190788 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786540 Affx-122966251 AX-385273573 14 68401088 AAATTGGAAATTACACTGAACATATTTCTTCAAGT[A/G]ACAGTTTTTAAGTTACTGTCTCACAGATCCAAATC R 2 1 2 1 101000 r 74 goat snp1847-scaffold1052-740346 14 24135681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780546 Affx-122920094 AX-385267637 14 68436335 CCTTTTCAAGTCTTTATGAATACCTCTCGTTGATG[C/T]AATCTAAATGGAAAGCTTACTAACAGGAGAATATA Y 2 1 2 1 101000 f 74 goat snp1846-scaffold1052-705099 14 24100554 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773871 Affx-122959527 AX-385261010 14 68468284 GAACTTTAACACCTAAATAAAGTGTTTGAGATAAT[A/G]CAAATAAGTTGCATTGCCCACTTTTATGTACCAGT R 2 1 2 1 101000 r 74 goat snp1845-scaffold1052-673150 14 24068916 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435704 Affx-122933313 AX-123306043 14 68511662 TTTTTTGAACATAAAAGGCAATATTGCCTAGTTCT[C/T]CAGTGAACTGTTTTGGTAGCTCTAGTAAAAATAGG Y 2 1 2 1 101000 r 74 goat snp1844-scaffold1052-629772 14 24026246 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389941 Affx-122968091 AX-123260298 14 68571214 TGCCTTCAAGTGAAAGTATATTATAGTCCCAAGCC[C/T]GGTTTCCCTGCTCTTGCTTCTTCCCTAGTCTCCCT Y 2 1 2 1 101000 f 74 goat snp1843-scaffold1052-570220 14 23966565 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802354 Affx-122979156 AX-385289258 14 68650539 AAACTTTGCATATAACAACAATTTGTCCCAAGGAA[C/T]GCCTTTTTCAGTATCTGCTGTGAGCTAATCAATAT Y 2 1 2 1 101000 r 74 goat snp1842-scaffold1052-490895 14 23886566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403276 Affx-122957861 AX-123273629 14 68746528 AGCCATAGTAGGAGGCAGTGGGCTGGCTGGTACAG[A/G]TGGTTAGAGTGAAGCAGAATTTCAAATCATTTTCG R 2 1 2 1 101000 r 74 goat snp1840-scaffold1052-394906 14 23789698 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421954 Affx-122943816 AX-123292301 14 68777153 TATTCTCATCAAGCCTTTGACAAATTTTCATACTA[A/G]TGGAAAAATACATATCACAGCCTGTATTATCTGAA R 2 1 2 1 101000 r 74 goat snp1839-scaffold1052-364281 14 23758847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401613 Affx-122959616 AX-123271966 14 68809244 ATTTATTGAGTGCCTACTATGGCAAGGGTAATTCT[A/G]TAAGGTACTATGGGTAAAAAGGTCTCACAGAGAAG R 2 1 2 1 101000 r 74 goat snp1838-scaffold1052-332190 14 23726867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401220 Affx-122959321 AX-123271573 14 68854688 AAAAAAAAAAAAAAGCCCTCAGTGCCTCTCTGCAG[C/T]ACCTAAAATAAAATCCATTCCCTGTCTAGAACTTA Y 2 1 2 1 101000 r 74 goat snp1837-scaffold1052-286746 14 23680789 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378147 Affx-122976977 AX-123248506 14 68890909 ACCCATAATGGCTTGTAACAGATATTCAATTATTG[C/T]AAGTGGAATAATTGGTTAGGGGAATGAGGAATTTG Y 2 1 2 1 201000 f 74 goat snp1836-scaffold1052-250525 14 23644785 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400180 Affx-122960672 AX-123270535 14 68929984 GTTGGTGATACTTGGCATGAATTAGGTGATCAGTG[C/T]ATTTTGTTGGGGATCAATGAATGAAGCTGCATATC Y 2 1 2 1 101000 f 74 goat snp1835-scaffold1052-211450 14 23605003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406758 Affx-122955729 AX-123277109 14 68965218 GAGGGGTTGTGCATGTTGGATAGTAATTCAGTGTC[A/C]AGTTGCCATGGACAAAAGAATAAATGATGTTTAAA M 2 1 2 1 101000 f 74 goat snp1834-scaffold1052-176216 14 23569489 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802691 Affx-122957609 AX-385289590 14 69028998 CTTGCTCCTCTGTGAAGGCTAGTTCAATAAATCTA[C/T]GTCAAATTTCCCACCATTCATCTAAGGCTTTATTC Y 2 1 2 1 101000 f 74 goat snp1833-scaffold1052-112436 14 23504505 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799024 Affx-122966514 AX-385285954 14 69063283 GATAGTGGGGGAAGCCTGTGTCTCATTTTCCAAAT[A/G]CTGTGGAATTGACTACTCAAGGTGCATCTTTCATG R 2 1 2 1 101000 f 74 goat snp1832-scaffold1052-78151 14 23469918 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789561 Affx-122969915 AX-385276570 14 69102655 TGGACCAAGTTGGAAGACAGCTAACTTATGCAGGA[C/T]GAGTTCCCAGATGTCATTAAGAGAATCACTGGGGA Y 2 1 2 1 101000 r 74 goat snp1831-scaffold1052-38779 14 23430224 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437367 Affx-122931927 AX-123307705 14 69135296 CCTAAAAATGGCAATCTGTCTTATTTTGAGAAATA[C/T]ATATACATTCCCTATCCACTTTACTGAGCATTCAA Y 2 1 2 1 101000 r 74 goat snp1830-scaffold1052-6138 14 23397413 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402653 Affx-122958379 AX-123273006 14 69143723 CACTGAGCCACCTGGGAAGCCTGAGAGGGCAGCAG[C/T]ATTGTATTATTGTTCAGGATGGTAAGAGGGGATGT Y 2 1 2 1 101000 r 74 goat snp11125-scaffold14-2350075 14 23389138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382589 Affx-122973723 AX-123252947 14 69184472 TTAATGGGAAACCTGTTGATGTCAAAAACCCCAGC[A/G]TCCCCTTAGTGGATGGGGAGAGTGACCCAAATAAG R 2 1 2 1 101000 f 74 goat snp11124-scaffold14-2309326 14 23348065 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275277 Affx-1111834696 AX-519548853 14 69219087 AGATTCTCACTTCTGCAGTCACAGTGCTGCTGTCT[A/G]TGTTCAGGTCTTCTTTAGCTACTGCGTGTGTGTGT R 2 1 2 1 101000 r 74 goat GoatD01.046654 14 69219087 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38405033 Affx-122956364 AX-123275385 14 69222253 TTTTTACCGATTTGGGGAGCAACTAAGTGGTCGGT[A/G]TACAGTATGTCACTTACATCCCTTCTGAACACAGT R 2 1 2 1 101000 r 74 goat snp11123-scaffold14-2271545 14 23310121 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276963 Affx-1111835607 AX-519550471 14 69240464 GCACTTTTTTGGAAACATGAATTTGTCTCAGCACA[A/C]CTGATGTATCAGAGAACCACTGGAGCATGGGGCAG M 2 1 2 1 101000 r 74 goat Random2.2K-1451 14 69240464 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431080 Affx-122936626 AX-123301421 14 69265770 TTTTTTAAATCAAGCAGTCTGTGTGGCTGAAGTGT[G/T]AGATTCATGAAGAGATGTCATGAGAGATGAGATCA K 2 1 2 1 101000 r 74 goat snp11122-scaffold14-2228028 14 23268261 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417874 Affx-122946763 AX-123288222 14 69303527 CAGTTCATTCACCAGTCCAGCCTGTCATCTCTCCA[C/T]GTGGCAACCCAGGTGCAAGGAGAGGAGACGCACCT Y 2 1 2 1 202000 r 74 goat snp11121-scaffold14-2190271 14 23230474 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389536 Affx-122968279 AX-123259894 14 69337012 GCAGCATTCACAGATTGCATTTCTGTTTTGTCTCC[A/G]TGACGCTAGGCCTAGTATGTAGCTCCATAGTTGGC R 2 1 2 1 201000 r 74 goat snp11120-scaffold14-2156786 14 23197104 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413391 Affx-122950124 AX-123283740 14 69372832 TGTTTGTTTGTTTTTTGTCTTGTGATTGTCTAAAG[C/T]AGTAATAACAAGGAGACAGTCTAAAAGGTGGCCAG Y 2 1 2 1 201000 f 74 goat snp11119-scaffold14-2120966 14 23162521 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796281 Affx-122965596 AX-385283231 14 69417673 TTGATTTCTTTAGTCAATCATCCACTATCAGGTAC[C/T]ACTGCCCTGATTAGCAGGCTGAAGAAAAAGAGCAT Y 2 1 2 1 101000 r 74 goat snp11118-scaffold14-2076125 14 23117787 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795470 Affx-122928282 AX-385282426 14 69470782 GACATTCTCCTAATACATGGCCAGCCTCCTAAGAA[C/T]GGCATTTGGCACTTATAATTTTCCCCACAGTGATC Y 2 1 2 1 101000 f 74 goat snp11117-scaffold14-2023016 14 23064028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799587 Affx-122937853 AX-385286516 14 69503095 AAAGTATAAAAACATATAAATTGGTATGATTGAAG[C/T]AGATTCCTTTCAGAGGTATATTGTAAGAAATAATT Y 2 1 2 1 201000 f 74 goat snp11116-scaffold14-1990703 14 23031129 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787402 Affx-122924449 AX-385274427 14 69549277 AATTTAATCAGTCTCTTCATGTCTAAAGAGATATC[A/G]CATTTGGGCAGAATCTTTGTGAACAAGGGTTTGGT R 2 1 2 1 101000 r 74 goat snp11115-scaffold14-1944521 14 22984336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391982 Affx-122966510 AX-123262339 14 69614604 TTGTATGTCTCTTCAGATGTGGAAAGGAGGCCTCA[C/T]AGAAAATAAAGCTGCAGAATTAATGCCTTCTATCA Y 2 1 2 1 101000 f 74 goat snp11114-scaffold14-1879194 14 22918819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799419 Affx-122970404 AX-385286349 14 69674112 CATTTTCCCTATAGATAAAATGGTCCAGTTTTTAC[A/G]TAAAAGCAAAACAGTATTTAATTAATGGAGAAAAT R 2 1 2 1 201000 r 74 goat snp11113-scaffold14-1819686 14 22859205 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399918 Affx-122961320 AX-123270273 14 69755974 GAAGATCCTCAAAGGCTCTGGGGCTAGTGAACAAA[C/T]GGGTACAGGACCCACAGTTGAACTCTTTATCACTC Y 2 1 2 1 101000 r 74 goat snp11112-scaffold14-1737824 14 22776618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794104 Affx-122934707 AX-385281071 14 69810859 AAAATAGAAGAGTGGAAGTTACCATTAATACATTG[C/T]AATTTATATGATCATGTATATCTACACCCTTTCTG Y 2 1 2 1 101000 f 74 goat snp11111-scaffold14-1682939 14 22720173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788193 Affx-122973990 AX-385275212 14 69842396 TGAGAACTGAGTGACCAGTGGTCTTGACTCAGAAA[C/T]AATGATTATCACTCTATGGTGAGTGCTGGAGTTTC Y 2 1 2 1 101000 f 74 goat snp11110-scaffold14-1651402 14 22688179 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274811 Affx-1111834434 AX-519548396 14 69886710 GCTAGAAGGTAAGCCCCGAGAACACTGCAGGCCTT[A/G]CTAGGAAGAGTTTGCATCTATTTCCAGCATTTCCT R 2 1 2 1 202000 r 74 goat GoatD01.035666 14 69886710 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320796844 Affx-122967108 AX-385283787 14 69894618 CATATTCTTAGAGAGGAAACAGATATGCACAATTA[C/T]TGTACCAGAAAATGTGCTCTAAATATTTGTATACA Y 2 1 2 1 101000 f 74 goat snp11109-scaffold14-1599180 14 22635865 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793866 Affx-122974972 AX-385280835 14 69937236 GAATGCCTTAACATGGGCATGTTTGTATTCAGAGA[C/T]AAAAGTGTAAGTGATGAAGGAAGTTCTGTTTGGAA Y 2 1 2 1 101000 f 74 goat snp11108-scaffold14-1556562 14 22593476 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445118 Affx-122926186 AX-123315455 14 69983661 AGACCGGGAGGTGTTTTAACACAGTGGAAGGGGCA[C/T]GAGTTATGATATCATGCAATAATGTGAAATTACTG Y 2 1 2 1 201000 r 74 goat snp11107-scaffold14-1510137 14 22546893 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439263 Affx-122930992 AX-123309600 14 70040213 GAGATATCAGGACTGTGCCGCTGAATTTTTTATTT[A/G]TTTGAATGGGTTCAGTGCTTATTCATAGTTTTCTT R 2 1 2 1 101000 f 74 goat snp11106-scaffold14-1453585 14 22493945 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272752 Affx-1111833021 AX-519546450 14 70051221 TCCCTACGTGATTAGAAAGATCAAAGCTTGAGCCC[A/G]AGTACAGTGTGGAGGTGAAATGTATGCCTTGCAAA R 2 1 2 1 101000 f 74 goat 14_70051221_AF-PAKI 14 70051221 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38388956 Affx-122968807 AX-123259314 14 70079225 TTTCTTTAATGCATGTGTGTTGGATATTTACTAAC[A/G]CTCTTTAACGTGCTGATTTGTTATATTTTTGTTGA R 2 1 2 1 101000 r 74 goat snp11105-scaffold14-1414573 14 22454915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276965 Affx-1111835608 AX-519550473 14 70100311 TCATTTGAAACTATTTTTTCGAGTTTATTGAAGAT[A/G]TAAGAGTCTATGAAGGCTTCATCCCCCTGTCTATC R 2 1 2 1 101000 r 74 goat Random2.2K-1452 14 70100311 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381425 Affx-122974356 AX-123251783 14 70132125 CTTGATATAACTAAAGGGATACAAAAACACCAAGT[C/T]ACAGATCATCATAGAAAAAACATTTATGGAAAGGG Y 2 1 2 1 101000 f 74 goat snp11104-scaffold14-1361673 14 22401685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788742 Affx-122949712 AX-385275758 14 70164780 GGAATCTAGTCTTTCATTCCTGACTCAGAGAGAGA[C/T]GATTAGATGAAAGTTAAGGCTTAATTGGCTGTTTA Y 2 1 2 1 101000 f 74 goat snp11103-scaffold14-1329018 14 22369243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396936 Affx-122963189 AX-123267291 14 70217524 TCAGGTAGGATCTTCAGGCTACTTAACTGTTGGTG[C/T]GACATAGGCCAGTAACAGTGAGAACAGAAGGCAGC Y 2 1 2 1 101000 f 74 goat snp11102-scaffold14-1276274 14 22315925 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420048 Affx-122945135 AX-123290396 14 70271076 TGAGGTTGTTAATGTCATCTTTTGCACATTGAAAT[A/C]AAAGCATAAAGAAAATCCTGGAACAACAATGGAGC M 2 1 2 1 101000 f 74 goat snp11101-scaffold14-1222722 14 22262541 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777078 Affx-122962422 AX-385264201 14 70330589 ACTACTGTTAAAGAGGACTTTCTAAAACATGAATT[A/G]CATCATGTAATCACCTTTCTAACAAACACACTTAC R 2 1 2 1 201000 f 74 goat snp11100-scaffold14-1163209 14 22202830 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452911 Affx-122920203 AX-123323244 14 70381343 AGAACCATACTAAACCTTTAGAAGACTGAAAGGTC[A/G]CAAACATTTATTAAATCAGTGATGTTCTTTTTGGA R 2 1 2 1 101000 f 74 goat snp11099-scaffold14-1112455 14 22151740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394654 Affx-122964382 AX-123265009 14 70414159 CAAAGTGCCTAGTGGTTTGTTTTACTCAAATGATG[C/T]ATCAGGCACAGTACCCAGACAGATAAATCCAGTAC Y 2 1 2 1 101000 r 74 goat snp11098-scaffold14-1079639 14 22119072 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797170 Affx-122940683 AX-385284110 14 70446020 TAAAGATGAGATTTTTGTCACTAATCAGAAGCTTA[C/T]GGTTCATAACTTCAAGATCTGTAAATATACTCAAA Y 2 1 2 1 101000 r 74 goat snp11097-scaffold14-1047778 14 22087218 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399162 Affx-122960642 AX-123269517 14 70479832 ACTGCTAGAGTTACTGAATCTTCTAAGATACATCA[A/G]TTTTTTCAAAGGCAAAATAATATTCAGATCCTTAG R 2 1 2 1 303000 r 74 goat snp11096-scaffold14-1013966 14 22052796 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417310 Affx-122948161 AX-123287658 14 70529325 CGCATAAAGAGGTCAGATGCCTCATTTAGAATGCC[A/G]TTTCTGGAAAAAAATTAACTTTTTCTCTGGACTCT R 2 1 2 1 101000 f 74 goat snp11095-scaffold14-964473 14 22002737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406248 Affx-122956106 AX-123276600 14 70633042 TCCTGGTCAGCAGGTGCTGCCTGGCCCCTGTCCCT[C/T]CCACTCCTGGGCTGCATCTCAGAGTTGATTACTCT Y 2 1 2 1 101000 r 74 goat snp11093-scaffold14-860756 14 21899048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426518 Affx-122940205 AX-123296864 14 70664336 TCAAGGACCAAGCACAGAATGTGAACTGAAATGGA[C/T]GGACCTCCAGAAAGTACAGTTGTCAGGGGCTGTGG Y 2 1 2 1 101000 f 74 goat snp11092-scaffold14-829462 14 21868253 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375693 Affx-122978654 AX-123246052 14 70708697 TCCTTCCCCAATCATGGCTTACCTCTCTTCAGGTT[A/G]CTCTCCTTCAGGAAATTCCAATGCCACTGCCAAAA R 2 1 2 1 201000 r 74 goat snp11091-scaffold14-785101 14 21823613 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380100 Affx-122975533 AX-123250458 14 70757967 GATACTCAGTGATTTTTGGAGTAAATAACAGAAAC[A/C]AGACACCACATGGATGTCTTACTGGGTAATAAATA M 2 1 2 1 201000 f 74 goat snp11090-scaffold14-735831 14 21774148 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789479 Affx-122965305 AX-385276489 14 70815208 GTTACTATTTCACTAGCCTAAAATTGTAGATGGTC[A/G]TTTGAGTAAATGAAATGTTGTCTATTAAATTATAA R 2 1 2 1 101000 f 74 goat snp11089-scaffold14-678590 14 21717752 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387398 Affx-122970416 AX-123257756 14 70863732 CCAAGACTTTAATGATCTCCAGGCAGCACAGTTTT[A/C]AGCTGAGATCCTGATATCCTATGCAGTAAACCTTC M 2 1 2 1 201000 r 74 goat snp11088-scaffold14-630066 14 21668827 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779438 Affx-122943280 AX-385266541 14 70941015 AATAGTGTTTCAAAAACCAAGACAGTGTCAAGAAA[C/T]AGAGGTTGACAATCAGTGTCTAAAGCCATAGATAA Y 2 1 2 1 101000 f 74 goat snp11087-scaffold14-552783 14 21591522 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439307 Affx-122930959 AX-123309644 14 70972443 TAAGTTTATTAGTTCTTGTGTGCCAAATTTCTGTG[C/T]GTAACAGTTATGTCTTACATTTAGTTATGTCATAC Y 2 1 2 1 101000 f 74 goat snp11086-scaffold14-521355 14 21559830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397464 Affx-122962096 AX-123267819 14 71011405 AGTTTTTATTTTGGTGATATTTTATTTGAATTTCA[A/G]TGTTACTGATTTGAACAACAGCAGGTACAATGTAA R 2 1 2 1 101000 r 74 goat snp11085-scaffold14-482393 14 21520797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439204 Affx-122931036 AX-123309541 14 71083433 GTTAATTAGTTCTTGCAATTTCCCTCTCTCTACAC[A/G]TGTCTATTGGAAAATGAATTTCATCTTGATTTTTA R 2 1 2 1 101000 f 74 goat snp11083-scaffold14-410365 14 21447862 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780644 Affx-122945644 AX-385267734 14 71114429 TTACTTCACACATAAAGTAAATATTATTCATTGTC[A/G]TTACAAATATTATTCAAGGAGAGTGAAAAAACTGG R 2 1 2 1 101000 f 74 goat snp11082-scaffold14-379369 14 21415983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799694 Affx-122957915 AX-385286622 14 71143093 TTGTCTCTCTTTCTACTTGCTTTTAACTTTGGAAA[C/T]ACTAATTTCTTTTCCCTGTATATTCACGTGCAGGT Y 2 1 2 1 101000 r 74 goat snp11081-scaffold14-350705 14 21387305 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389409 Affx-122968374 AX-123259767 14 71192303 ACTTGCCTAGTACTCCAGTGCTTCTAGAATGAAAA[C/T]AAAGCACTTGCTCTAATTTTTTTCTTCTTTCTCTT Y 2 1 2 1 103000 f 74 goat snp11080-scaffold14-301495 14 21338164 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412291 Affx-122950873 AX-123282640 14 71225973 TGTCTAATGGGCTGACTGCTAGTTTTTTTCTTAGC[A/G]TGTTTGCTGTTATCTTGAGAGCCATAGTCATGCTT R 2 1 2 1 101000 f 74 goat snp11079-scaffold14-267825 14 21306723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425013 Affx-122941887 AX-123295359 14 71302849 ACAGTGGCCAACTGATGCTCTCATTGTCACCAGCC[A/G]TTTAGAATATTCCTATATTGATAGGTGCATGGAAG R 2 1 2 1 202000 r 74 goat snp11077-scaffold14-190949 14 21232585 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778879 Affx-122945698 AX-385265987 14 71375597 TTGTTGTAGATTGAAGGTAATGTTGTTACAAGAAA[C/T]AGTATTTTCCCCAAGGCTGTTGAAGAAATTCGTGG Y 2 1 2 1 101000 r 74 goat snp11075-scaffold14-118201 14 21158919 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766727 Affx-122975346 AX-385254067 14 71473023 ATCTCAGAACGATGTTACTGTTTGTATTTGCTTAG[C/T]AGTTAGTAGTCATGATCTTCCTGTATTGGGCCTGT Y 2 1 2 1 101000 f 74 goat snp11073-scaffold14-20775 14 21064667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783591 Affx-122938950 AX-385270650 14 71541174 ATTTTTCAAGTTGTGTGGGAGGAGAGACTGTTAGA[A/G]GAATCTTCATTTTCGATTTATGAAGATTCTTCTGT R 2 1 2 1 101000 f 74 goat snp35403-scaffold425-1832715 14 20994663 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415390 Affx-122948750 AX-123285739 14 71597526 AGTTATCTTCACAGTGGTTATGTATATGAGGCTGT[C/T]GCTTGAAGAAAATCAGAAGAAAGCACATGACCAAA Y 2 1 2 1 201000 f 74 goat snp35402-scaffold425-1776363 14 20937867 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440205 Affx-122930696 AX-123310542 14 71626287 GAAGTTTGCCTGCACATCCAGTGGTTTTCCTACCA[C/T]GATCACAGGAGGGCTTGCCCAGCTGGAAGGTCTAG Y 2 1 2 1 202000 r 74 goat snp35401-scaffold425-1747602 14 20909268 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416736 Affx-122947539 AX-123287084 14 71663684 TCTATACTGTTCTCAGGCTGCCACTGCCCACAGGA[C/T]GTCGTCCAAACTCCTTGACAAGGTTTGACACCCAT Y 2 1 2 1 201000 r 74 goat snp35400-scaffold425-1710205 14 20871824 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385113 Affx-122971783 AX-123255471 14 71703839 TATACTTAGGTAAAAACTTTATATGGGTCCAATGA[C/T]GAATCTGCAAAACAAGCTCTGTTTAAGAAGTCTAA Y 2 1 2 1 201000 f 74 goat snp35399-scaffold425-1670050 14 20831290 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388411 Affx-122969287 AX-123258769 14 71740317 AACTTGAACCTGGAGCAGTGGAGGCAGGAACTGCT[A/G]TATTCAGGATGCCTCCGATGCCTGAGCCTATACAT R 2 1 2 1 101000 r 74 goat snp35398-scaffold425-1633572 14 20794823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798330 Affx-122919763 AX-385285265 14 71780374 ACTTTTTCTGCTGTACCACCTTCTCAAGATCCTTC[C/T]TTCAGTACTCATCTCATACCTACTGTGTGTCTATA Y 2 1 2 1 101000 f 74 goat snp35397-scaffold425-1593515 14 20754685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377833 Affx-122977296 AX-123248192 14 71810121 CAGTTTAGAGGGTCTAGGAGACCCTCACCGAGGAC[G/T]CAGGGTCCCTGTGACGGGGAAAAAACGGGATTCCA K 2 1 2 1 101000 f 74 goat snp35396-scaffold425-1563768 14 20724963 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440325 Affx-122930200 AX-123310662 14 71846569 ATCTGGTATTAGCACTCTCCTTCCTTTAGGATGGG[C/T]GCTCCTGCCGCCACTCTCTGTTTGTGTGTTCTGAG Y 2 1 2 1 102000 f 74 goat snp35395-scaffold425-1527320 14 20688138 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780057 Affx-122958345 AX-385267155 14 71939792 TGCCAATAGGTGTAAAAGACTGAATGAATTAGATC[A/G]TTGATAAAGACAAGTCACTCAAAAAACAATGGGTA R 2 1 2 1 101000 f 74 goat snp35393-scaffold425-1434097 14 20595552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380131 Affx-122975991 AX-123250489 14 71978886 TTTGCCCACTCCTGCTTCCCATGTCCTAGGAGCAC[G/T]TCCAATCAACCTGCACACAGCTGTTTCCATCTGTG K 2 1 2 1 101000 r 74 goat snp35392-scaffold425-1395003 14 20556565 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430556 Affx-122937017 AX-123300897 14 72052410 GTACACAGCCTCATTCATTTCTCTCAACAAATCTA[C/T]GAAGTCATCATTTTACCAGTGAGGAATCTGAGGCT Y 2 1 2 1 201000 f 74 goat snp35390-scaffold425-1321479 14 20482701 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375551 Affx-122979092 AX-123245910 14 72145935 AAGGATTGGAAGTGCCTGCCTAATGTTGGAAAAAG[G/T]TTACCACAACCACACAGATAAGGCCACGTCATCCT K 2 1 2 1 101000 f 74 goat snp35388-scaffold425-1227954 14 20388558 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380920 Affx-122975020 AX-123251278 14 72257647 AATGTCTGATGCATTCTCTAGGGTTTTGGCCACAG[A/C]GCTGCCAGTGTGAATGCTGCTGACGGGAAGCTATG M 2 1 2 1 101000 f 74 goat snp35385-scaffold425-1116242 14 20276464 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773897 Affx-122935333 AX-385261036 14 72296158 ACCACAGACTTGAGTGAGTCAGGGTGTAAGCCTTC[A/G]TGTCCATCGAAGAAAAACTTCAAGTCAACCGTATG R 2 1 2 1 101000 f 74 goat snp35384-scaffold425-1077731 14 20238029 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445843 Affx-122926010 AX-123316180 14 72327765 AGAGAATTCGTTAGGTTGAACCATGGAAAACTGTC[C/T]GTATCTGACCATTTTTGATCTACAGAAACAACAGT Y 2 1 2 1 101000 f 74 goat snp35383-scaffold425-1046124 14 20206252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436617 Affx-122932507 AX-123306955 14 72370272 ACTTAAAAAACAAAAGCCAAACACGCACACACACA[C/T]ACACACACAAATGTGGTGCTTTTAGACAGTGTGTG Y 2 1 2 1 303000 r 74 goat snp35382-scaffold425-1003617 14 20163752 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781341 Affx-122939727 AX-385268426 14 72401642 TGTAAGACTGTTGTTTTAAAACTGCTTCCAAATAG[C/T]AGGCATTTGCAGTACAGTCTTAATATAAAATGGCA Y 2 1 2 1 201000 f 74 goat snp35381-scaffold425-972247 14 20132289 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428430 Affx-122938824 AX-123298773 14 72454866 AGTGCTTGAAAAACATATGCCACATGCTTCAGTGA[A/G]CAGACATCCAAAACTGGAAGAACGTCGGAATGCTC R 2 1 2 1 101000 r 74 goat snp35380-scaffold425-919023 14 20078657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425364 Affx-122941576 AX-123295710 14 72513689 CTAAGGTCACATTGCTAGCAAGTGGTGGAATCGGG[A/C]TTCAAACCCAGGTAGTGTGGCTGCAGCCTCCATCT M 2 1 2 1 101000 f 74 goat snp35379-scaffold425-860200 14 20019972 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773927 Affx-122957119 AX-385261066 14 72546110 GTGTGGTAGATAGCCTATGATTTTTCTCCTAAAAG[A/C]GCATTCTTTTATTGTCTTAACATGTGATAAATATA M 2 1 2 1 101000 f 74 goat snp35378-scaffold425-827779 14 19988692 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380175 Affx-122975516 AX-123250533 14 72578630 TCAACTCTTATGGGAAAATACACCCTTCTCTTTTC[C/T]TCCTTCTTCGGTAAGATTTTTTTCAGAGATTGCGA Y 2 1 2 1 101000 r 74 goat snp35377-scaffold425-795259 14 19957692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796105 Affx-122931437 AX-385283057 14 72625914 AAATAATATCTTCAGGGGGAGAGAGTCGGGGCAGG[C/T]GAAAAAGAACATTCCAAACTACAAGATACTTAGAT Y 2 1 2 1 102000 f 74 goat snp35376-scaffold425-747975 14 19910152 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452675 Affx-122920320 AX-123323008 14 72678798 AATGTAATCTGGGGGACCCCATCTTTTCACTCTCC[A/G]TCCGCCTCACTATGAGACAGCATATTAAAAAGCAG R 2 1 2 1 201000 f 74 goat snp35375-scaffold425-695091 14 19856635 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272754 Affx-1111833022 AX-519546452 14 72753620 GAACTGAATATTTTGATGTAACAACTGCTTCTAAA[A/C]AGCATTTGCTTCTGTTTGTTTACACACTCCACTAA M 2 1 2 1 201000 f 74 goat 14_72753620_AF-PAKI 14 72753620 A C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781626 Affx-122963108 AX-385268710 14 72760914 CATGGAGGATGGGAATTTGAGAAGAAAGGGAGTCA[G/T]CGCTGATCCACCTCCATCATCATCCCATTAGTACA K 2 1 2 1 101000 r 74 goat snp35373-scaffold425-612975 14 19773885 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400548 Affx-122960431 AX-123270903 14 72796404 TCTGTTTTTCAAAAACCCCTTCTCATTCCTCATAC[A/G]CTATTTATCCCACTTCGTTTTCTAGTTCTCTTGAA R 2 1 2 1 201000 r 74 goat snp35372-scaffold425-577485 14 19738696 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802917 Affx-122974025 AX-385289814 14 72824974 TGCCTGCCATTTTCAAGGTAGTTTCCACTTGATGA[C/T]GTCATTCAATCCTCCTGACAATTCCATGAGGCACC Y 2 1 2 1 101000 f 74 goat snp35371-scaffold425-548915 14 19710091 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276832 Affx-1111835609 AX-519550342 14 72854221 GAGCCCCGTCAGCATGACTGATACGCATAATGAAT[A/G]TAAGTAAAACCTGAAACCGTGACTTAGTTCTTCTC R 2 1 2 1 101000 f 74 goat Random2.2K-1455 14 72854221 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38410433 Affx-122952400 AX-123280783 14 72855517 CATGACGGTACAGCATCCTAGCTTTCCTAGGACCC[A/G]TCTGTCCATTCCTAAGCTCTTCCACTATCTCCTCT R 2 1 2 1 101000 r 74 goat snp35370-scaffold425-518372 14 19679401 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451378 Affx-122921216 AX-123321711 14 72885264 ATTTCCTATTAATACAGGTTAGACATAATCATCCT[A/G]TAAATGCTAAAAAGTGATCAAGATCTGATCCAAGC R 2 1 2 1 101000 r 74 goat snp35369-scaffold425-488625 14 19648917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422973 Affx-122943005 AX-123293319 14 72922699 CCAAAGGCGGCAAGCAGATGCTAGGGATCCTTGAA[C/T]GGACAAAGGTGCCTGAGTCCATGATGACATAATGA Y 2 1 2 1 101000 r 74 goat snp35368-scaffold425-451190 14 19611517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781529 Affx-122952389 AX-385268614 14 72981362 ATTTTATCACAATAAAAAGTCCCTATTTCTTAAAT[A/C]TAGATATGATTCAGCATGATTGCAATGAGCTCTCT M 2 1 2 1 101000 r 74 goat snp35367-scaffold425-392527 14 19553142 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780476 Affx-122934376 AX-385267567 14 73026013 AAGCGTAATCTGAAAAGAGGGAAGGTGAAAATATA[G/T]CCACAAAGTGATAGCAATGCAATAAATTCAAAAAG K 2 1 2 1 101000 r 74 goat snp35366-scaffold425-347876 14 19508903 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431401 Affx-122936540 AX-123301742 14 73083088 GATAGAGGCCACAGAAAGATGGGCCATAAAGAGAT[C/T]GTGTGCCCACCTTAAAGGAATTCAAATATGATGGG Y 2 1 2 1 101000 f 74 goat snp35365-scaffold425-290801 14 19451809 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428935 Affx-122938897 AX-123299277 14 73131184 AAAAGAAGTAAAAAAAATATAAATTTTTCTGCACT[C/T]TCCTGGATTTCTTTACTGAAGCCCTGAAGACACTG Y 2 1 2 1 101000 r 74 goat snp35364-scaffold425-242705 14 19403909 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800331 Affx-122974073 AX-385287254 14 73181173 ATAGGACAGTGCTGAATCTATTATTTCCTTGTCTC[A/G]TGGTAAAGAAGATTCAACTATATTGGCATGACTCT R 2 1 2 1 101000 f 74 goat snp35363-scaffold425-192716 14 19353878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400415 Affx-122959984 AX-123270770 14 73247891 TGGCCTTCACAAACTCTCCTTGTTATAGGTCCAGT[A/G]CCTCACTCCTGATGATTCCCTCGATACACCCAAGT R 2 1 2 1 101000 f 74 goat snp35361-scaffold425-125998 14 19287187 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381685 Affx-122974726 AX-123252043 14 73289305 CTCTGGATAAAGATGAGGTCAAACCACCAGGCAGC[A/G]GCTGAGTGCCCAGGGAGACTCCTGAGGGTGAAATG R 2 1 2 1 101000 f 74 goat snp35360-scaffold425-84584 14 19245438 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453820 Affx-122919557 AX-123324153 14 73333905 GTGAGTCCAGTTAAACTGACCACGACACAGGCAGG[A/G]CCTGCATAACTGAGATTCCCTTCCTATCTATAAAT R 2 1 2 1 101000 r 74 goat snp35359-scaffold425-39984 14 19200938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276834 Affx-1111835610 AX-519550343 14 73343252 CCAGTCTATGAATCCTTGGATCTGATTACTGCAGC[A/G]TTCCTGGTGGTGGGTAAGGTGGGCCTGTCCTAGGG R 2 1 2 1 101000 f 74 goat Random2.2K-1457 14 73343252 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434689 Affx-122933956 AX-123305030 14 73371640 TTCTGCCCCTTGAAAAGCCAGGCAATCAGTTCATG[A/C]TTGCAGGTGTAGTGTTTCATTTTAAAAGAGGCATA M 2 1 2 1 201000 r 74 goat snp35358-scaffold425-2249 14 19163600 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784920 Affx-122958168 AX-385271967 14 73387627 CTCTAAAAGTAACCAGTTTCCCAACTTAACTGTAG[A/G]TTTGTTTGGCCAGCTTTTTATCTTTATGTAAATGG R 2 1 2 1 101000 f 74 goat snp34546-scaffold4078-41371 14 19148627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453053 Affx-122920070 AX-123323386 14 73418361 AGCAAAGCCTCACCTGGCTAAAAAGGTATGCAAAT[A/G]CCCAGCCAGTTTTTAAAATTCAAAATTGGACAGTT R 2 1 2 1 102000 f 74 goat snp34545-scaffold4078-10637 14 19118069 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397133 Affx-122962674 AX-123267488 14 73439825 AGTGAATACCCTGGTTCAGTAAGTAAATCTGGTAG[C/T]AGACTTCAGATCAGCCGACAAGGGAGGTTCAGTTC Y 2 1 2 1 101000 f 74 goat snp42581-scaffold566-10728 14 19096235 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798554 Affx-122929971 AX-385285487 14 73504456 CATGCAAATATTTACTGGTATTGCTTAGAGCCGCA[A/G]ATCTGATCCTGTGGATTGATTACAAAATGCATTCC R 2 1 2 1 101000 r 74 goat snp42582-scaffold566-75359 14 19031193 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381951 Affx-122974117 AX-123252309 14 73548380 TCAAAAGGAAACAAGGGTGCAGTCCTGTGGTTCTG[C/T]GTACTTGCCACTTCCTTTCCAAATTCTCCCAAGCC Y 2 1 2 1 201000 r 74 goat snp42583-scaffold566-119283 14 18987323 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452391 Affx-122920611 AX-123322724 14 73592303 GAAAAGCAGAATTGATTGATTCTCTGAGGCCTGCC[C/T]GAAAGAAGAGAAGCAGCTTCAGGCCTGAAAGAAAA Y 2 1 2 1 101000 f 74 goat snp42584-scaffold566-163206 14 18943436 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789040 Affx-122952452 AX-385276053 14 73676171 TTCTAAATGGATCAAAGATGTCAATGTAGAAAGTG[A/C]GAGCTTAAAGTCACTAAGAGAAAAGCATAGATGAA M 2 1 2 1 101000 r 74 goat snp42586-scaffold566-247074 14 18860964 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444474 Affx-122926534 AX-123314811 14 73711718 CCATGAAACAAGCTAACCCAAGCCTCCTCAGGGTG[C/T]TGGTCTCATATAAGCCGTGACCCCTCTATCTGTTC Y 2 1 2 1 201000 r 74 goat snp42587-scaffold566-282621 14 18825377 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402699 Affx-122959611 AX-123273052 14 73755072 ATTGCAGTCCATAAATGTCTCATTAGAAGTTGATT[A/G]TTTTGCTTTGATATTCTGGGACTATTTAGTATTTG R 2 1 2 1 101000 f 74 goat snp42588-scaffold566-325975 14 18781968 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422633 Affx-122943706 AX-123292979 14 73799130 AAATTTTGCCGATCATACAAAAAAAATGTCATTTA[C/T]GGTAAAAGAAAATCCTGGGTCACATATTGTATTCA Y 2 1 2 1 101000 r 74 goat snp42589-scaffold566-370033 14 18737910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771329 Affx-122978823 AX-385258487 14 73908424 TATCTAAGAATCAATCAAATTCAGTAATAATGCTC[C/T]ACTTGCAGACTGAACCCAATCCGAACTTCGGAATC Y 2 1 2 1 101000 r 74 goat snp42591-scaffold566-479327 14 18627872 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276971 Affx-1111835611 AX-519550479 14 73949816 TGTTTGAGGGCAGACTGGCAGCATGTAAATGAGGA[A/G]TAGAGGTTACAGAATCTGAGCCTTAGACCCTATGG R 2 1 2 1 101000 r 74 goat Random2.2K-1458 14 73949816 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320801372 Affx-122945167 AX-385288283 14 73957772 GTGCATTTTGAGACACAAGAAGCAGCTGAAAGAGC[C/T]ATTGAAAAAATGAATGGGATGCTTCTAAATGATCG Y 2 1 2 1 101000 f 74 goat snp42592-scaffold566-528675 14 18578517 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418195 Affx-122947067 AX-123288543 14 74001880 ATTGATTGGAAAACAAAACAAGAACCTACTACAAA[C/T]AATAAATGCTGGAAAGGGTATGGAGAAAAGGGAAC Y 2 1 2 1 303000 f 74 goat snp42593-scaffold566-572783 14 18532999 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387801 Affx-122969691 AX-123258159 14 74031265 CAGGTTCCTAGCTCCAAGTTACTGGGGCTATTGAA[C/T]GGGCGTGATGTACATCACAGCCCAGCATCCAGCAA Y 2 1 2 1 101000 f 74 goat snp42594-scaffold566-602168 14 18503705 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422506 Affx-122943299 AX-123292852 14 74102784 GGAGGACTAATTTAGTACTTTACTTAATAGCTGCC[A/G]TTCTTAGAACTCTCTCTGTCTTGTTTATTATGCTA R 2 1 2 1 101000 f 74 goat snp42596-scaffold566-673687 14 18433044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412265 Affx-122950892 AX-123282614 14 74132627 ATATGAGATCTGGTCTAAAGAAGCGAGGACTGAGC[G/T]CTGGGATTTTCTTTCCGTGTTCAGGGGTTGGAACC K 2 1 2 1 101000 f 74 goat snp42597-scaffold566-703530 14 18403289 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802111 Affx-122945206 AX-385289015 14 74167975 CATACTTGGTGTAAATACAGCAAAAAGCAGTGGAC[A/G]TTAGAATGGAGAACACTTCAGATTAAAAGCTTTGG R 2 1 2 1 101000 f 74 goat snp42598-scaffold566-738878 14 18367373 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276973 Affx-1111835612 AX-519550481 14 74199906 GAACTGAATGTCTGCCCTCCCGTTTGGAAGTCCTG[A/C]GTGGAGTTAGGAATGAGTGTGCGGAGCACAGGTGC M 2 1 2 1 202000 r 74 goat Random2.2K-1459 14 74199906 C A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320799788 Affx-122949809 AX-385286715 14 74201862 GACAAATCAGTACGAAAACCATGCTCTCTCTGTTG[C/T]TGAAATCCCTAAAAGAGGGCCAGTATAGAATAAAG Y 2 1 2 1 101000 f 74 goat snp42599-scaffold566-772765 14 18333410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412216 Affx-122950927 AX-123282566 14 74232311 GGGATCAAACCCACATGGTGGGCAGGTTCTTTACC[A/G]TCTGAGCCAAATAACAGTATGTAAGCTGTGGCCCG R 2 1 2 1 101000 r 74 goat snp42600-scaffold566-803214 14 18302569 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446259 Affx-122925678 AX-123316595 14 74296334 TATATGATTTGTTTTCTTCCTTCATCCTCATATTT[C/T]CCAAAATGTCTACAAAAAGTAGGTATTATTCTTAG Y 2 1 2 1 201000 f 74 goat snp42601-scaffold566-867237 14 18238455 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789574 Affx-122919481 AX-385276583 14 74339157 TCATGACGACGAAACGTAGAGGGAACATTTAAGAA[C/T]AGAAACCATTTGTGACGGGAGTGCAGGAGAGAAAT Y 2 1 2 1 101000 f 74 goat snp42602-scaffold566-910060 14 18195469 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786136 Affx-122963513 AX-385273172 14 74389368 TTAACATTTTCAGCCTCTGTCCTCTCTGGAGACCC[A/G]TGAATACTTACATAATAATGTAAGTAATATATCTC R 2 1 2 1 102000 f 74 goat snp42603-scaffold566-960271 14 18145634 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407127 Affx-122954867 AX-123277478 14 74431855 TTCCCAGGGCTCATTCTCAGATTTATCTATATTCT[C/T]TAGGTAATCTCTATTAAATAATATATATAGACAGA Y 2 1 2 1 101000 f 74 goat snp42604-scaffold566-1002758 14 18103763 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276977 Affx-1111835614 AX-519550485 14 74432332 TGGCCATTTGATACAAAAGCATACAAAAGCTGTGA[A/G]TTCTGGTACGTTAAGAGGAAAACATTGATGGGTCC R 2 1 2 1 101000 r 74 goat Random2.2K-1460 14 74432332 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451776 Affx-122921509 AX-123322109 14 74474429 GTATCATACTTAGATTTTAAAACAAAACTAAATTA[C/T]GTCTGGGATAAATCTGGTTTTAAAAAAAGGTGCTC Y 2 1 2 1 102000 r 74 goat snp42605-scaffold566-1045332 14 18061263 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416424 Affx-122947839 AX-123286773 14 74519367 TTTTAATTGAAGGAAACAGAAAAGAGCAGTAGTAA[C/T]TGAGGAATACAGATCTTAAGAGAGTAAGTTTTGCT Y 2 1 2 1 101000 r 74 goat snp42606-scaffold566-1090270 14 18015754 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382763 Affx-122973980 AX-123253121 14 74555218 CTTCAATTTCCTACTCACGTAACACGGAAAACTCT[C/T]TAGGCCTCTCCAAATTCCGACTCTCCTCTAACCCG Y 2 1 2 1 101000 f 74 goat snp42607-scaffold566-1126121 14 17980662 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398133 Affx-122961693 AX-123268488 14 74585658 CCCGTGTCTGAGTCCCCACTACTCAGTCTAGTACC[A/G]AAGCATTGAATAGAAGATCACCGTTTGCCAGAAGG R 2 1 2 1 101000 r 74 goat snp42608-scaffold566-1156561 14 17949917 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440148 Affx-122929680 AX-123310485 14 74620191 CAGTATAGATACATATAACCACATTCTCGAGCTAA[A/G]AGAGCTCTTAGGTCATCTAGATTTCTGAGACCTTC R 2 1 2 1 101000 f 74 goat snp42609-scaffold566-1191094 14 17915284 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424431 Affx-122941798 AX-123294777 14 74664108 AGTAAATAATGTTGCTTCAATGTGACATTCCCAGA[A/G]CACAGAAATGAAAAGTTTCATCCAGCCTCAAATAA R 2 1 2 1 101000 f 74 goat snp42610-scaffold566-1235011 14 17870449 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276844 Affx-1111835615 AX-519550353 14 74690073 ACTGTGTATCTTCTGTCCTGCTTCCCAAGAAGTCA[A/G]TTAGGCTTTCAAGGAAAGAAAAAAAAAAATGGTTG R 2 1 2 1 102000 f 74 goat Random2.2K-1461 14 74690073 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38428763 Affx-122938427 AX-123299105 14 74713340 ATCAGACCCATGCCCCCTGCACTGCAAGTGGGGAC[C/T]CCTAACCACTGAACCTTCAAGGATTCCCAGAAATA Y 2 1 2 1 101000 r 74 goat snp42611-scaffold566-1284243 14 17821005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766584 Affx-122941502 AX-385253940 14 74776183 AAGGAACCACCATACTCTTAAATAGTGGCTGCACT[A/G]TTTTACACTTCACCAACTTTAGTGTGCAAGGATCT R 2 1 2 1 202000 f 74 goat snp42612-scaffold566-1347086 14 17757900 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451508 Affx-122921113 AX-123321841 14 74812721 TGATGCTGATGATGTATATTATCAATTCAGTCCAC[A/G]CCTGGGCCCTTTTTATTATTAGAACAGCAAATAAA R 2 1 2 1 101000 f 74 goat snp42613-scaffold566-1383624 14 17721544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779778 Affx-122923548 AX-385266878 14 74881431 CATATCCTGCTTATTAAATTCACATTTCTCATTGG[C/T]AATAATTACACTGTATATGAGCATTATATACACAA Y 2 1 2 1 101000 f 74 goat snp42614-scaffold566-1452334 14 17652326 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795055 Affx-122935978 AX-385282014 14 74974119 TGAACTTTAATAAATGGATTATTTTCAATGTTTAG[A/C]TTTTAAGAATGTGTAGCAATAGTGAATTTCCCAGC M 2 1 2 1 202000 f 74 goat snp42615-scaffold566-1545022 14 17558711 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391196 Affx-122967418 AX-123261553 14 75016634 GGTAAGTGTACGGAGATGAATTCCAAATTACAGAA[C/T]GAGAAAACTCCACACCTGGAATGAGCCTTGTTGGT Y 2 1 2 1 201000 f 74 goat snp42616-scaffold566-1587537 14 17515752 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792795 Affx-122922659 AX-385279774 14 75048082 AAGCCTAGAAGAAATGAGAGTAGAAAGTTGTTTAT[A/G]AATCTTTCAGTGTGATGGATGTCTAAGTCCAGGCT R 2 1 2 1 101000 r 74 goat snp42617-scaffold566-1618985 14 17483894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386651 Affx-122970207 AX-123257009 14 75111305 TTTGTAGCGTCTAATATAACAGTATTAATGGCAAA[C/T]GTCTGCCAGAACGTAGAGCAACAGCAGCTCTCACC Y 2 1 2 1 101000 f 74 goat snp42618-scaffold566-1682208 14 17420233 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453407 Affx-122919895 AX-123323740 14 75196465 TTACTGATGAATGTGAGCTACTGAGAAGAGAACAA[C/T]GTATGTAGCTATTATATTAAATATGTTTAGGCAGC Y 2 1 2 1 101000 f 74 goat snp42620-scaffold566-1767368 14 17334855 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429387 Affx-122938543 AX-123299729 14 75240511 AGAGAATATCAACAAGGTTTCCTGAGAACTGATAA[C/T]GGTGGGCATCCAAAGAGCACAATACATTGGTCATA Y 2 1 2 1 201000 f 74 goat snp42621-scaffold566-1811414 14 17290939 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391233 Affx-122967392 AX-123261590 14 75274086 ACTGGATTTTGAGGCACAGGTCCCATGTTCAGTCC[C/T]GGAACTACCCTGTGAGATCAATCCCCCTTGAGCTA Y 2 1 2 1 101000 f 74 goat snp42622-scaffold566-1844989 14 17258865 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443581 Affx-122927331 AX-123313918 14 75368813 CAAGGATGTTCCCATAATGGCACTGTTCTTAATAG[C/T]AAAAAATAAATGCCAAGATACGGATGACCCTTGAA Y 2 1 2 1 101000 f 74 goat snp42624-scaffold566-1939716 14 17163102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272756 Affx-1111833023 AX-519546454 14 75396670 ATATCCTGCCTCTTCCCTGTTTCTTTAATGTGAGA[A/C]GCCCCCCATGGCGGGCCCCTGAGCTGCCTACATTC M 2 1 2 1 101000 f 74 goat 14_75396670_AF-PAKI 14 75396670 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38380106 Affx-122975529 AX-123250464 14 75406393 CAAAGCAACATGTCTAAGATTCCACAACTAGTAAA[C/T]GGAACTAGGTAAGAAGGAGCTGGGTGAGAGAATTT Y 2 1 2 1 201000 f 74 goat snp42625-scaffold566-1977296 14 17125147 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786803 Affx-122971862 AX-385273832 14 75466670 TGACATAAAACACTTGTAATAGATCATTAAAACAA[C/T]GGCACCTAAAGAATCATACTATCCTGTGTCTACAC Y 2 1 2 1 101000 r 74 goat snp42626-scaffold566-2037573 14 17064927 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780408 Affx-122922704 AX-385267501 14 75516619 ATGAGTCCACAAATAACCATGAGTTAATCTTTAAG[C/T]AAAATGATTTACCATTATCCAACCGGATTCTCAAA Y 2 1 2 1 101000 r 74 goat snp42627-scaffold566-2087522 14 17014893 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776827 Affx-122975075 AX-385263951 14 75554996 TTATAAAAGGCAAAAGAAAATGTTGACTGTTAAAA[C/T]AAGTGGGTCATCCTAAGGTAACCAAAAGAAATGAT Y 2 1 2 1 201000 f 74 goat snp42628-scaffold566-2125899 14 16975961 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404312 Affx-122957020 AX-123274664 14 75586972 GTCTAAAGTTCTAAAAACCCTGATTCTACTACTGT[A/G]CTAATTAAGTTATACCTGAAAAGAGCACCTGGGAA R 2 1 2 1 101000 r 74 goat snp42629-scaffold566-2157875 14 16942957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276846 Affx-1111835616 AX-519550355 14 75606126 TCAGACTCTGGACCAGGATCACAGAAGGGGAGAGG[A/G]CAGGGGTCCCAGGAAACAGCCTCGCTGTGATAACT R 2 1 2 1 102000 f 74 goat Random2.2K-1462 14 75606126 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406422 Affx-122955207 AX-123276774 14 75681930 CCTACGTGAAAAGCTCCTTCCCCGGTATTTCCTTC[A/G]CGGCACTCAGATGCATGTGGACACCTTGTCCCAGG R 2 1 2 1 101000 f 74 goat snp42631-scaffold566-2252833 14 16847895 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787671 Affx-122967728 AX-385274694 14 75718637 ATAAGTTTTGTGGACTGAACCAATGTCAATTTCCC[A/G]ATTTTGATACTGTGTTAAAGTCAAGTAAGATTTTA R 2 1 2 1 101000 f 74 goat snp42632-scaffold566-2289540 14 16811310 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406646 Affx-122955816 AX-123276998 14 75755254 AAGACAAAGATCTGTGTGTGTTTTGTTCACTGTGG[C/T]GCCCCCAGCACTGTTAACAGTGTCTGGCACGTAGT Y 2 1 2 1 303000 r 74 goat snp42633-scaffold566-2326157 14 16774507 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786725 Affx-122953197 AX-385273756 14 75790236 TTTATTCATTGTTCTTTAAGGGGCTGAGATATAGC[A/G]TATATTGGCACTGAAGAATTTGTTAGGATGTAAAG R 2 1 2 1 201000 r 74 goat snp42634-scaffold566-2361139 14 16739237 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433985 Affx-122934252 AX-123304326 14 75820563 ACAGAGGAGCCTGGTGGGCTACAGCACATGGGGTC[A/G]ATAAGAATTGGGCAACTGAGTATGCATGCAAAGTA R 2 1 2 1 101000 r 74 goat snp42635-scaffold566-2391466 14 16708585 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381125 Affx-122974574 AX-123251483 14 75875099 CTTGCTACTCTGTGCTTATATTGAGGCTAATTCAT[A/G]CATTCATGCTTGTGTGAAACTCATATAAAAGACTC R 2 1 2 1 101000 f 74 goat snp42636-scaffold566-2446002 14 16652453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784647 Affx-122950408 AX-385271695 14 75904865 CCATCTATGTAAACCCATGCCAGAGAGTGTCTTTT[A/G]TTCTAAAATTTCTACTTTCAGTTTTTGGAAGATTG R 2 1 2 1 201000 r 74 goat snp42637-scaffold566-2475768 14 16622714 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432413 Affx-122935836 AX-123302754 14 75948949 GTGTGGTGGTGCGTTGCCTTCTGTTCTGTGTTCTA[A/G]CACAGTGATTCTCGGTGTTGGCTGTATGTGAGGAT R 2 1 2 1 101000 r 74 goat snp42638-scaffold566-2519852 14 16578335 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435572 Affx-122933372 AX-123305912 14 75992289 TCACTTCAGATGCTTCTCACAAGTGTAGGCCTCCC[A/G]TACCTGGACCAACTGGCTATAAGTCAGGGTTCCAT R 2 1 2 1 101000 f 74 goat snp42639-scaffold566-2563192 14 16535164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789540 Affx-122968819 AX-385276549 14 76056130 CTGTCCTCATGGTTTTTAAGATGCTGTTTTGATTT[A/G]TGAACCCATGTCCTTTGGTACATTAATATTAACTT R 2 1 2 1 101000 f 74 goat snp42640-scaffold566-2627033 14 16472293 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793072 Affx-122939052 AX-385280050 14 76091167 GAAATTTAGATATGCCATGAATTTTCATATGTGGA[A/C]CACATAATTCCCTAACAATGCCAGCTAATGGTTCT M 2 1 2 1 101000 r 74 goat snp42641-scaffold566-2662070 14 16437186 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437699 Affx-122931759 AX-123308037 14 76129545 GGCCTTGTTTCCTCTTTTCACAAGTGTTCTGGTCA[A/G]TGACTGTGGATACTATGCTCAGTGACCCAATACCA R 2 1 2 1 201000 r 74 goat snp42642-scaffold566-2700448 14 16398793 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785906 Affx-122948496 AX-385272943 14 76191330 CACTTCCTATTCCAGTTTAGCTAATGTCTATTCAG[C/T]ACCTTTTATGTGTGAGGCGTTGTCCTAAAGTACTT Y 2 1 2 1 101000 f 74 goat snp42643-scaffold566-2762233 14 16336453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410166 Affx-122952786 AX-123280516 14 76227457 CACTGCATTTTTTCACCTCTGTGTCTCAGCCCCAC[C/T]GCACCAAGCAATCTCTAAATATTTACTGAACAGAT Y 2 1 2 1 101000 r 74 goat snp42644-scaffold566-2798360 14 16299735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791626 Affx-122925620 AX-385278617 14 76301118 AAACACAAACACTTAAGAACAGTGTTGGATACACA[G/T]TGCAGTGTTTGACACAGTGACAAATCTGGCTATCA K 2 1 2 1 201000 r 74 goat snp42646-scaffold566-2872021 14 16226731 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393737 Affx-122965226 AX-123264092 14 76334108 TAAACACAAAATTCAATGTAGTGCTTCCTGGGGAG[A/G]TCACAGAAGAAGGGGAGAGCAACTGTGAAGGGAAG R 2 1 2 1 101000 f 74 goat snp42647-scaffold566-2905011 14 16193578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452504 Affx-122920976 AX-123322837 14 76373219 TACCTAAGGAGCACATTCTACCTGCCTGGTGCTGC[A/G]TTGGGTGTAAGGAAGGCAAGCCCAGGGACCCAGCT R 2 1 2 1 201000 r 74 goat snp42648-scaffold566-2944122 14 16154294 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419718 Affx-122945907 AX-123290066 14 76407846 GTAGAGACAGAAAATTCAGACAGTCTCAAAGGGGC[A/G]TGAGATCTGACATATTCTAGAACCTGGAACCACTG R 2 1 2 1 101000 r 74 goat snp42649-scaffold566-2978749 14 16122628 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387138 Affx-122970647 AX-123257496 14 76449826 TAAATATGTCTGCAATGAAGAATTGAGCTAGGTAG[C/T]CAGCTATTCAATTTTTTGTTTTTCCCTGAGTTAGT Y 2 1 2 1 201000 f 74 goat snp42650-scaffold566-3020729 14 16080676 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418553 Affx-122946396 AX-123288901 14 76480916 AATATATACTGTAGAGGATCCAAAGGATGGTTGGT[A/G]TTGGATAATGAATATATTTTTAAGAAGAATAAATG R 2 1 2 1 101000 f 74 goat snp42651-scaffold566-3051819 14 16049536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387845 Affx-122969652 AX-123258203 14 76510076 GTGGGCAAGAGTGGGAGCCAAACTCCTTAATGCAC[A/G]TCTTTTCGTATTGTTTTGATTTTTAAACTATGTAT R 2 1 2 1 101000 f 74 goat snp42652-scaffold566-3080979 14 16020071 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391854 Affx-122966991 AX-123262211 14 76546602 ACACAGTTATGGTGAAGTCCTGAGCCCGGGTACCT[A/G]TGAATGTGATCTTATTTGGAAACTGGCGTCTCTGC R 2 1 2 1 201000 f 74 goat snp42653-scaffold566-3117505 14 15983429 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768843 Affx-122970930 AX-385256020 14 76602856 GCACCACTGTCGAGCAAAAATGCCTAGTATTCCAC[A/G]CCATCCAAGGAGAAGTTACATTTTCCCCATTTTCA R 2 1 2 1 101000 r 74 goat snp42654-scaffold566-3173759 14 15926328 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801690 Affx-122973013 AX-385288598 14 76639416 GTCGGGAGCTTCAGATTAAATGGAAAGTTTTGCAA[G/T]AGAAGAGGTTTTCACTTGAAAACCAATGTACAACC K 2 1 2 1 201000 f 74 goat snp42655-scaffold566-3210319 14 15889266 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405459 Affx-122956038 AX-123275811 14 76674452 TGTCGTTCTTGCTCCGCCCGACTTCCAGGCTCAGG[C/T]AGACACGTACGGGGGCGGCGGCTCCTTGGTGGCGC Y 2 1 2 1 101000 f 74 goat snp42656-scaffold566-3245355 14 15854131 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382797 Affx-122973573 AX-123253155 14 76732915 CTTACTTTGGAATTTCAGTCTTTTACAATCTAATA[C/T]AGTCAGGAAAACACCAGGTAATAAGACTTACCGAC Y 2 1 2 1 101000 r 74 goat snp42657-scaffold566-3303818 14 15795857 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437738 Affx-122931729 AX-123308076 14 76800557 AGGAAAATCTGTTATAAGGGGCCTTTGTCATCTCA[A/G]ACTTCGCTATACCCACCTGTGCAATGAAAGGCTTT R 2 1 2 1 201000 r 74 goat snp42658-scaffold566-3371460 14 15727483 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784871 Affx-122934331 AX-385271918 14 76865550 GTGTTTTACATGTAGATGAAGTAGTTCCTTCGTTG[A/C]GTTCTATTTTAAGCTTTTGTGGAAGATCACAGAGA M 2 1 2 1 101000 f 74 goat snp42659-scaffold566-3436453 14 15662545 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785451 Affx-122978023 AX-385272496 14 76941323 AGACTGGGTTTTCTGTTATATGCAGCTGAGCCAAG[C/T]GCTAACTTACACACTGCCATTTTGCTATTCTTCTC Y 2 1 2 1 101000 f 74 goat snp42660-scaffold566-3512226 14 15585477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434315 Affx-122934750 AX-123304656 14 76970551 AGTGATAAAGGCATGGGTGAAGAGTAATCACAGGC[A/G]ACAGACACTTAGTGAGTGTTAGCAGCTGTCATATC R 2 1 2 1 101000 f 74 goat snp42661-scaffold566-3541454 14 15556129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796363 Affx-122972192 AX-385283313 14 77002637 TACTGTTGCTTTATAAAGTAAATTCTAATGATTTC[A/G]GGAGAATTTTTGATGGTTTATGGAATCTCCAGACT R 2 1 2 1 101000 r 74 goat snp42662-scaffold566-3573540 14 15524050 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399979 Affx-122960823 AX-123270334 14 77093667 GATGAATTTTGTGTTGCTTGAATCAGGTCTGTCAG[A/C]GGCCACTTGACTTGTAGGGGGCCCATCAAGAGACT M 2 1 2 1 101000 f 74 goat snp42664-scaffold566-3664570 14 15433163 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384039 Affx-122972886 AX-123254397 14 77129116 ACTGAGCCTCTGACAAATCCTGCTCACAGGACCTC[C/T]ATCAAGATATACTCCTGCCTGGTAGTCTGGGGCAG Y 2 1 2 1 101000 r 74 goat snp42665-scaffold566-3700019 14 15397979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798794 Affx-122978044 AX-385285725 14 77165228 TCCCCGTGACGTTCTTGCTTTCTCTTTACATTAGT[A/G]TCATATGTTATATGATCTCGCCCCTCCTGTTTATA R 2 1 2 1 101000 f 74 goat snp42666-scaffold566-3736131 14 15362200 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439580 Affx-122930075 AX-123309917 14 77206453 TCAGAGTTGAATTAGACGTCATCCCTGCCACTGAT[A/G]CTCTCACAGGCCCGAACTGCTAAGAGGATGTGAGA R 2 1 2 1 101000 f 74 goat snp42667-scaffold566-3777356 14 15320421 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430218 Affx-122937332 AX-123300559 14 77237636 CCTTTTTAGGACTCCTAAACTGTCACAGATGAGCC[A/G]CAATCAATCTGCTGCCTGAAGCCAGAACAGAGCTG R 2 1 2 1 101000 f 74 goat snp42668-scaffold566-3808539 14 15289559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433991 Affx-122934248 AX-123304332 14 77268368 CCCTATCACCTTTCAGGACTCAGCTCAAATGTCCC[C/T]TCTTTGAGAGAGACCGTCTGAGCCCATCCTCTCAG Y 2 1 2 1 201000 r 74 goat snp42669-scaffold566-3839271 14 15258729 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769436 Affx-122953174 AX-385256606 14 77315048 CTTCAGCGAATAAAGGGATAAAGCAGCAATTAAAA[C/T]GCTCTCTCTTGACAGGATACTGTTGATTAAATCAG Y 2 1 2 1 101000 r 74 goat snp42670-scaffold566-3885951 14 15211172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380384 Affx-122975333 AX-123250742 14 77343865 TAATGCTGTGTTACAGGTTTACTATGAAAAGAATC[A/C]ACAGGAGGGGCACCAAACAGCCTTACATACTAAAT M 2 1 2 1 201000 f 74 goat snp42671-scaffold566-3914768 14 15182580 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765962 Affx-986697704 AX-385253386 14 77349818 TCTTCACAGAGCATTCATTTCTGTTCTCCGCCTCT[C/T]CCACACTTTACGATGGCATGCTAAGTGGGCCAGAC Y 2 1 2 1 600010 r 74 goat 14_77349818 14 77349818 Ancestral_priority_1043 ancestry 0.626 recommended IMAGE 10K 10K ancestral 320765966 Affx-986697706 AX-385253390 14 77370918 TGTTAACACGTTCAATTTCATACATATGCGACTTG[C/T]GAGTTGATGTAGCTGTAGTTCACAATTGTTCTTCA Y 2 1 2 1 600010 r 74 goat 14_77370918 14 77370918 Ancestral_priority_1043 ancestry 0.652 recommended IMAGE 10K 10K ancestral 320765970 Affx-986697708 AX-385253394 14 77382963 GAGAGGAGCACTGCAAGCTTGAGCAAGGAGAGCAG[A/G]CGCAGTTATTTTTCAATGTTTGCACCCTGTGACAT R 2 1 2 1 600010 r 74 goat 14_77382963 14 77382963 Ancestral_priority_1043 ancestry 0.592 neutral IMAGE 10K 10K ancestral 320789348 Affx-122957860 AX-385276358 14 77394568 AATGTTTGGAAGATGTCCTAAGGTGGTACCCAGGA[C/T]AGCCTCTGATCTGAAGTCAATCTTTTAAACAGTGA Y 2 1 2 1 201000 r 74 goat snp42672-scaffold566-3965471 14 15131909 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276983 Affx-1111835617 AX-519550491 14 77483767 ATATCCCCAAAGGTCAAGAGGATCGGTTTGACCCC[A/C]AAGGCCCCTGTTGTCTGGATGGCAGGACTGACAAC M 2 1 2 1 102000 r 74 goat Random2.2K-1465 14 77483767 G T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38440977 Affx-122928983 AX-123311314 14 77497059 CCAGGCAGTGACACATGCTGTGAAATAATAAAATC[A/G]CATGATGTGTAAAGAATGGTGAGGGGCTCGTTGGC R 2 1 2 1 101000 f 74 goat snp42674-scaffold566-4067962 14 15028973 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789950 Affx-122938071 AX-385276956 14 77526057 AATCAGATTTAAGCATGTTCTACTGTCCTATTTAA[G/T]CATGCAATATCTAAAAGCCTTTCAGGTTCAGAGAG K 2 1 2 1 101000 r 74 goat snp42675-scaffold566-4096960 14 15000038 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440453 Affx-122929396 AX-123310790 14 77561170 CTGTCTCTGTCAATATATCCACCTATTTATCTTTC[A/G]CTCTTCTGCAGCAAATGAATCACTCCAAGCATGCC R 2 1 2 1 101000 f 74 goat snp42676-scaffold566-4132073 14 14964742 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393270 Affx-122965453 AX-123263627 14 77599348 AAGGCAGAGTTCCAGACTCGTTCCCCTATGTACTC[C/T]TGCTTCTCCCCCAATATTTCTGTTTATAGCCCTTA Y 2 1 2 1 201000 r 74 goat snp42677-scaffold566-4170251 14 14926584 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777075 Affx-122955443 AX-385264198 14 77633359 TACTGTAACCACCACTGTGGCCAAGTCTACACTCT[A/G]CTGCATTAATCTATTGTATTTGTTATTGCATTTAT R 2 1 2 1 101000 f 74 goat snp42678-scaffold566-4204262 14 14892277 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792629 Affx-122928759 AX-385279610 14 77662628 ATAAGAAACATAAGTAAGTATATAAAAAGCTGCCT[A/G]AAGTTATCCTTTATTTTCCCTGCATCTTGTTCATA R 2 1 2 1 101000 r 74 goat snp42679-scaffold566-4233531 14 14862995 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375962 Affx-122978441 AX-123246321 14 77683331 GGAGAAAAACATCATCACATACTTGGGCGGTATCA[C/T]GAGATATCCTCTGTGGTGGCCATCTGTTGTTTGCT Y 2 1 2 1 101000 f 74 goat snp5326-scaffold1184-6696 14 14842718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419817 Affx-122945831 AX-123290165 14 77742080 AATAATAATTACTTCCAAAACAGAGGTTCAGAGAA[C/T]ATCAGGTGATGTGCTTATGCAATCTGAGTGATTTG Y 2 1 2 1 101000 r 74 goat snp5328-scaffold1184-65445 14 14784076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782710 Affx-122976171 AX-385269782 14 77782362 ATTGACCAGGGCTGTTCTAAGAACTGTCTGAATCA[C/T]GTATTCACTATTATCCATGTCTTCATTAAGTGACA Y 2 1 2 1 101000 f 74 goat snp5329-scaffold1184-105727 14 14743386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425382 Affx-122941563 AX-123295728 14 77870664 TCCCTGTGGGGGTTGTCCTCAGCCTAATATTGTGA[C/T]GGATTCCAAGAATCAAAGACAAATGAAACACTGTC Y 2 1 2 1 101000 f 74 goat snp5331-scaffold1184-194029 14 14654159 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276985 Affx-1111835618 AX-519550493 14 77918927 CCTATTCCCTGTAATTTTTTCTTCTCTTTTAAATT[A/G]CCACCCAACACATTGTTTGGATAAATGTCTATGGT R 2 1 2 1 101000 r 74 goat Random2.2K-1467 14 77918927 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468274535 Affx-1111834352 AX-519548126 14 77995671 GAGCAGTGAAATGCATTCCACCTCACACGTAAGAA[A/C]GCCCCTCTGTGTGTGTGTGAGTGTAGTCATGGTAA M 2 1 2 1 201000 f 74 goat GoatD01.031393 14 77995671 A C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38433994 Affx-122934246 AX-123304335 14 78061685 TCTCTTCTCTCACTGGACCAAGCCATTTGCACTGC[A/G]TTCGTTAGTTGTTCAAGAAATGCTGCTTGCTGTTT R 2 1 2 1 201000 r 74 goat snp5335-scaffold1184-385050 14 14462519 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769152 Affx-122958306 AX-385256327 14 78168514 TGCTGATGCCACCGGAGTGGATAAAGCATCTCTTT[C/T]CTTCAATTCCAGTTTGTAAACTTCCAGGGAAGACA Y 2 1 2 1 101000 f 74 goat snp5337-scaffold1184-491879 14 14355020 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407703 Affx-122954570 AX-123278054 14 78237156 TTTGAAGGGTGAGAAGTGGCCCAAGGTCACTCATC[C/T]CCCCACTTACACCCCACATTAACCCCTGTGGGCAT Y 2 1 2 1 201000 f 74 goat snp5338-scaffold1184-560521 14 14285853 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389508 Affx-122968300 AX-123259866 14 78306221 CATGGTGTGCCAGTAAACTAGAAACTAGATGGCAA[A/C]TATTTAGGCAATCATTATCCTTGAAAGATGGACAT M 2 1 2 1 101000 f 74 goat snp5340-scaffold1184-629586 14 14221772 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446665 Affx-122924764 AX-123317001 14 78337557 AATAACTGAGTTAGTGAAACAACTTGTGCTCAGAC[A/G]CTCAGGCATATCCAGCTCTTTGCAACCCCACTAAC R 2 1 2 1 101000 f 74 goat snp55065-scaffold843-753121 14 14188554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390333 Affx-122967699 AX-123260690 14 78403830 GTTCTCTTTGTGTTTATGAAAGAAATATATTTGAA[G/T]CCCCAGAGCAACTTCTATTCCCAGGCTGATGTCCA K 2 1 2 1 101000 r 74 goat snp55064-scaffold843-686848 14 14122512 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422980 Affx-122942999 AX-123293326 14 78495901 TCCTAGCAATCCCATGAGGTGGATTCTTATTATCC[A/G]CAGTTTGTAGACTGGGAAACTGAAGCACAGAGCCA R 2 1 2 1 101000 f 74 goat snp55062-scaffold843-594777 14 14029696 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430332 Affx-122938219 AX-123300673 14 78525428 TAATGTATAAATATTGAAAACGGGTACATGTAAGT[A/G]ACCAACTACTGTGTTTTGTGTTTTTTTTTTTTTTT R 2 1 2 1 101000 f 74 goat snp55061-scaffold843-565250 14 14000364 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424132 Affx-122942008 AX-123294478 14 78643848 TATTCTAACTAAACTGAGGCTTAGTTTTCTCATCT[A/G]TAAAATGGGGATAATACTGCTTGCCTTGATTTTCA R 2 1 2 1 303000 f 74 goat snp55059-scaffold843-446830 14 13886310 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276987 Affx-1111835619 AX-519550495 14 78665834 CAGGGGGGCATGGTTTCGATCCCCAGTCAGGGAAC[A/G]AAGATTCCACATGTCCAGTGTTGTAGCCAAAGAAA R 2 1 2 1 102000 r 74 goat Random2.2K-1468 14 78665834 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784452 Affx-122942032 AX-385271500 14 78683395 AAAATTCGAGAATTGCTTGGTGTGGAAAAACCCAC[A/G]TATCTGGTATCAGATCTCTGGGTGATATATGGCAA R 2 1 2 1 102000 f 74 goat snp55058-scaffold843-407283 14 13847154 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449882 Affx-122922350 AX-123320217 14 78739809 ATAGATGTATATGATGTCATAGATATAGATAACCA[C/T]ATGCATATCATATATACAGAAAGAGTTGATAGATA Y 2 1 2 1 101000 f 74 goat snp55057-scaffold843-350869 14 13795052 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433664 Affx-122934563 AX-123304005 14 78788927 AGCCCTTGAGGTCACAGGAAATATCTAATCTTTTA[C/T]GTTTAACTTCAAATTTTTTTCTTAAAATATTTGTG Y 2 1 2 1 101000 f 74 goat snp55056-scaffold843-301751 14 13745526 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802175 Affx-122966318 AX-385289079 14 78818160 TTTATCAAAAGGATTTGTTGACTGACGGGCTTTCA[C/T]GGTTCTAATGGGCTGTTTGATACTTTTAAGAGACA Y 2 1 2 1 101000 f 74 goat snp55055-scaffold843-272518 14 13716273 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443944 Affx-122927020 AX-123314281 14 78891688 ATACATGGTCCTTTACTTCAAAAGACAAAGACTAA[C/T]GAATAAAACGTTCTAATGCAGTAAATTGCATTTAT Y 2 1 2 1 101000 r 74 goat snp55054-scaffold843-198990 14 13641670 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385669 Affx-122971147 AX-123256027 14 78937054 TGTAAGAGCAGAAGTTTTAAAATTTATTCATTGCT[A/G]TATCCACAGGTCTGAAAACAATAGCTGGAATATAG R 2 1 2 1 101000 r 74 goat snp55053-scaffold843-153624 14 13596552 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451092 Affx-122921404 AX-123321426 14 79002610 CCCATTGTTCTGCATTTTCACCAATGTTTAATATC[A/G]TTAGACTTTAAAATATTTGCTCATCAGGTGAGTAT R 2 1 2 1 101000 f 74 goat snp55052-scaffold843-88068 14 13534996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797717 Affx-122957665 AX-385284656 14 79044383 AGCCCGCAGACACATTAGAAGATCCAAATATTCAG[A/G]AGTCCTAGGTTCCACTCCTTGTCAGAGTCTTGGGA R 2 1 2 1 202000 r 74 goat snp55051-scaffold843-46295 14 13492848 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799403 Affx-122944524 AX-385286333 14 79106998 TAAGATGTTAAATATCTTAAGGCTTAAACATCTTC[A/G]TTATGATTCCAAAGACTGTAACACAGGCCTTCACT R 2 1 2 1 101000 r 74 goat snp56185-scaffold877-1483968 14 13430074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450819 Affx-122921798 AX-123321153 14 79149261 AAAGGCCATACCTGGATTTCAGTGAAGCCTGTGTC[G/T]AAGTCTAAACGAATCCCATCAACAAGGAAAAAAGC K 2 1 2 1 101000 r 74 goat snp56184-scaffold877-1441705 14 13387620 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380325 Affx-122975380 AX-123250683 14 79199811 GTATAAAAAATCATTTTATAAAGGAGATGGTTTAA[C/T]GGTATGTCAGACTTTCAAATGTGAGTGCACCCTGG Y 2 1 2 1 101000 r 74 goat snp56183-scaffold877-1391155 14 13336381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390722 Affx-122967926 AX-123261079 14 79235916 ATTCCCTTTCTTTGAACTCTTCAAATGCTTCCAAA[C/T]GCCCTTGAGATGAACTGTGTGATTGTGCCTGCCTG Y 2 1 2 1 101000 f 74 goat snp56182-scaffold877-1355050 14 13300025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418039 Affx-122946635 AX-123288387 14 79268760 TGGTTGGTTGGTAAGTGTTTTGATATCATGCCTAT[A/G]CATGAGAGCACGTTCTGGAGAGAGATTCAGACTAA R 2 1 2 1 101000 f 74 goat snp56181-scaffold877-1322206 14 13267061 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383505 Affx-122972645 AX-123253863 14 79315779 ATCCTCCTGGGACTTGGAATTTAAGTGAGTGATGG[A/G]AAATTGAGAGAAACCGTTGGAATTTCCTTATCATA R 2 1 2 1 101000 f 74 goat snp56180-scaffold877-1275187 14 13220033 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445316 Affx-122925432 AX-123315653 14 79363623 CAAGTCTGAATATCAGCCAATTCAAAAGAAACAGC[A/G]TGGTCCTGGAGAAGTGGCCAGGCCAGAGGCTTTTC R 2 1 2 1 101000 f 74 goat snp56179-scaffold877-1227343 14 13173537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777921 Affx-122927688 AX-385265037 14 79402382 CACAAAACCAGGCAATGAGATGTGAAAAGGCTTCC[A/G]TTTCCTAGCTTTCCCCCCGAACACATCAGCATATG R 2 1 2 1 101000 f 74 goat snp56178-scaffold877-1188584 14 13135079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412452 Affx-122951407 AX-123282801 14 79441749 GTTTCCCTGTCCCATAGCAGTGCAGATGCAGGTGG[C/T]ACCAGGCTGGTGGGATGGCTCAACCTTGCAGGGTC Y 2 1 2 1 101000 f 74 goat snp56177-scaffold877-1149217 14 13095668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432110 Affx-122936456 AX-123302451 14 79473763 AAAAATCCTAGGTGATTCCAAATGAATTCTGAAAC[G/T]CATAGTGGGAGAGGAACAATAAGAAAATGGCCAGG K 2 1 2 1 101000 r 74 goat snp56176-scaffold877-1117203 14 13063401 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384723 Affx-122972055 AX-123255081 14 79510166 CCATTTATAAGTGCGGAAACCTGAGGTCACACAGC[A/G]TTTGATGATTCCAGAGCAGTTAGCATCTTTAGAAT R 2 1 2 1 201000 r 74 goat snp56175-scaffold877-1080800 14 13025597 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450243 Affx-122922259 AX-123320578 14 79564743 TGGGGTCAGCTGGGCTCAGAATGAGCATCTCTTGC[A/G]TGTATTTTTTTGCACAAATATTTGGAAAAGTATTA R 2 1 2 1 101000 f 74 goat snp56174-scaffold877-1026223 14 12970675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791451 Affx-122924719 AX-385278442 14 79599171 GTCTGGCTGACTTGAAGGCTTTTACTTCTTTGTTT[A/G]CCTTTCTGCTTCACTCTCTGTCATCGAGCAGTATC R 2 1 2 1 201000 f 74 goat snp56173-scaffold877-991795 14 12937376 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375684 Affx-122978661 AX-123246043 14 79665450 TTAGGGAATCAAACAACATTATTTGCTTCCAGTTG[A/G]CATTTGATAAATGTTGCTTCTGCTACTTAATTGAT R 2 1 2 1 201000 r 74 goat snp56171-scaffold877-925516 14 12870670 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417013 Affx-122947976 AX-123287361 14 79706576 CTTTTTATTTTTCTGTGGGCCTGTGAAAGCTGTTA[C/T]GGAGTTCACACTCACTTCATCCAGACTGGCCCCAT Y 2 1 2 1 201000 f 74 goat snp56170-scaffold877-884390 14 12829545 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414273 Affx-122949606 AX-123284622 14 79794777 ACCTCCTTCCTCCCTTGAAATTCTTTATTCCTTTG[A/G]CTTCCTTGACATCCTTTTTAACTCCCTGACTCTTC R 2 1 2 1 101000 r 74 goat snp56168-scaffold877-796189 14 12741906 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779819 Affx-122972706 AX-385266919 14 79830982 TAGGAATTTGAAAAAGGAATGAGTATCTGTTGGCT[C/T]AGGTTGGTTTGGTGCAAATGGAAATAAACGATGTG Y 2 1 2 1 101000 f 74 goat snp56167-scaffold877-759984 14 12705774 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786140 Affx-122940784 AX-385273176 14 79860189 TAAAACACAACTGCTGTTCCTTGTGAAATGGTGAT[A/G]TGGTTTTCAGCATGAAGAACAAAATGACAATTATC R 2 1 2 1 101000 f 74 goat snp56166-scaffold877-730777 14 12676311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768269 Affx-122972830 AX-385255450 14 79897036 GGTATTTTTCAGCTTTCTCACATGATACATAGACA[C/T]GCCAAACTGTTTTTCATATCTAATCTAAATCAGTG Y 2 1 2 1 101000 r 74 goat snp56165-scaffold877-693930 14 12639426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801989 Affx-122936126 AX-385288893 14 79933544 CACCTTCTCTATTTTCTGGGCAAATTCACTAACTT[A/G]CTTCTGCATTCTTCTTTGGAGCTACCAGCTTCTAA R 2 1 2 1 101000 f 74 goat snp56164-scaffold877-657422 14 12602948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390777 Affx-122967884 AX-123261134 14 79978798 AGTCACATTGGTCACGGTTGGCCCTGAGTACTGGA[A/G]TTGTTTCTACACATCTACTCTGAAAAGACAAGCAT R 2 1 2 1 101000 r 74 goat snp56163-scaffold877-612168 14 12557642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441568 Affx-122928684 AX-123311905 14 80012647 GTTGAATCAGCATTTTTTTTTTTCCTGAAAATATC[A/G]TTAGTGAAACACCAGCAGTTAACAATATTTAACAA R 2 1 2 1 201000 r 74 goat snp56162-scaffold877-578319 14 12523973 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385448 Affx-122971312 AX-123255806 14 80042448 AGGCTGACCTCACAGAAAAGGAAGTTCCTCCTCCA[G/T]CTCTTGAAGGAGAGGAAGGAATTTATGGATAGAGA K 2 1 2 1 202000 r 74 goat snp56161-scaffold877-548518 14 12493993 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435444 Affx-122933473 AX-123305784 14 80082103 CACGTGAGAATGTAAACAGGTGTGGCCGTTTGAGG[C/T]CAGAGTCACAGTGAGGTGCAGTATCTTAGCATGAT Y 2 1 2 1 101000 f 74 goat snp56160-scaffold877-508863 14 12455632 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431558 Affx-122936198 AX-123301899 14 80115492 AGCATTAATTTACATAAATCTTTTTTTATAGACTT[A/G]CCTAGTAGAGTTTAAAGCCTATTTAATTTGCATTA R 2 1 2 1 101000 r 74 goat snp56159-scaffold877-475474 14 12421901 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393179 Affx-122965521 AX-123263536 14 80151061 TGTCATATATGAAAGAAAACTTAAGTAGTTTCAAA[C/T]CTTTAGAACAGAGCCCTATTTTAAACATCTCAACA Y 2 1 2 1 101000 r 74 goat snp56158-scaffold877-439905 14 12386317 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407118 Affx-122954874 AX-123277469 14 80195663 GAATTCTAAACGAGTGTTGGATAAAACAAACAGAC[A/G]CAGACCAAAAAACAGAGTCAAGAATAAGCAGATAT R 2 1 2 1 101000 f 74 goat snp56157-scaffold877-395303 14 12341239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412511 Affx-122951361 AX-123282860 14 80305677 TAGCTACTACTATATTGTACTATATACCTTTTTTG[C/T]ATGTTTAAAGTATTTCATAATTTTAAAAACAAAAA Y 2 1 2 1 103000 f 74 goat snp56155-scaffold877-285289 14 12230926 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774573 Affx-122954229 AX-385261707 14 80367135 ACCTTGTGATCATCAGCGAGCAAATTCATGCTGCT[A/G]TATTTTTCCAGTGAAACGTGCAGCAGTAGAAATGA R 2 1 2 1 201000 r 74 goat snp56153-scaffold877-223831 14 12169105 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407857 Affx-122954516 AX-123278208 14 80397623 TCGCTGCCATATTCTTTACTTGCAGAGATTTTACC[A/G]TTCAGAACTTCTTTTAATTTCTATGAACTATCTAG R 2 1 2 1 101000 f 74 goat snp56152-scaffold877-193343 14 12138820 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765199 Affx-122925538 AX-385252741 14 80445199 ACTATGGCTCATTAAACCTTGACTGAGTTGATCTC[A/G]GTGTCCAACAAAAAAGCAGTAATAAGAACACAGAG R 2 1 2 1 101000 f 74 goat snp56151-scaffold877-145767 14 12091524 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272808 Affx-1111833024 AX-519546503 14 80447932 GTTTTCCCCCTGGAAGATGCTATAGCTTTATCCCA[A/G]TGTTTCGTTGTGTATTGTTTTGTGTTTTGTGTAGA R 2 1 2 1 201000 r 74 goat 14_80447932_AF-PAKI 14 80447932 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38416249 Affx-122948205 AX-123286598 14 80482297 GAGCACCACCTTGCCCAAGATTTATTAAATAAAAA[C/T]AAAGAATGCCTGGTTAAATTGGAATTTCAGATAAA Y 2 1 2 1 103000 f 74 goat snp56150-scaffold877-108669 14 12054988 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408545 Affx-122953685 AX-123278896 14 80513925 GGAATTTGCCCCCTCAAGGAAGTGCTAGATGGTCC[A/G]TGTGACTAATGTATGGTGAGTAAGAGGGAGGAGGC R 2 1 2 1 101000 r 74 goat snp56149-scaffold877-77041 14 12023714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765914 Affx-986697675 AX-385253346 14 80515964 CTATGCCCCGGTGTCCTGGCAACAAGTGGATGCGG[A/G]TGCTGCAGATCTGGAAGGAGCAGGGCTCTGAGAAC R 2 1 2 1 600010 r 74 goat 14_80515964 14 80515964 Ancestral_priority_1043 ancestry 0.52 neutral IMAGE 10K 10K ancestral 320765922 Affx-986697680 AX-385253350 14 80541303 GGTTAGGCTGCGTAGTGGGTCTCCCATCTACCCCC[A/G]GCACATTCTTTCGTGCTTCTGACAAGATCCGTTCG R 2 1 2 1 600010 r 74 goat 14_80541303 14 80541303 Ancestral_priority_1043 ancestry 0.628 recommended IMAGE 10K 10K ancestral 320792154 Affx-122968654 AX-385279138 14 80550444 AGATATGTTAGGACACAGATTCAGATCTTTTGCCA[G/T]ATTTGAAATACCTTTTCATGCTATGCATTGAAAAT K 2 1 2 1 101000 f 74 goat snp56148-scaffold877-40522 14 11986958 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797570 Affx-122955045 AX-385284509 14 80583322 GTAGTATGCCATTTGATAGCTTTGATATTTTAAGT[A/G]CTTAAATTTAGAAGCTGCAAAGTATTCTTCCCCTG R 2 1 2 1 101000 f 74 goat snp56147-scaffold877-7644 14 11952658 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419531 Affx-122945432 AX-123289879 14 80592158 TGGCTAACCCAATGTTTTTAATAAAAGCATTAGTT[C/T]GAGACTTGCCTGGTGATCTAGTGGCTAAGACTCCA Y 2 1 2 1 303000 f 74 goat snp10397-scaffold1371-770329 14 11943816 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420343 Affx-122944969 AX-123290690 14 80696965 CCAGGAAAACAACACGTCCTTATTTATTACCCTGA[C/T]AAAATGTGGCCACGGATCAACAATGCAGTAAAAAA Y 2 1 2 1 101000 f 74 goat snp10395-scaffold1371-665522 14 11836387 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415582 Affx-122948627 AX-123285931 14 80737418 CTTAAAGAACTGCCACAAGAGATTAACATTAGTTC[A/G]TGTGTTTTCAGTTGTATAACAGGATGTTGAGCTGT R 2 1 2 1 101000 r 74 goat snp10394-scaffold1371-625069 14 11795442 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411923 Affx-122951164 AX-123282273 14 80794826 CTAGAAATGAGCAGAACTGGAATTTGAACCCAGAA[C/T]AATTAGAAATCAGCAGAACAAAAAAAAGAAAAAGA Y 2 1 2 1 303000 r 74 goat snp10393-scaffold1371-567661 14 11737066 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386260 Affx-122970953 AX-123256618 14 80833676 GATGACTCCAGCTGAGTTCCGGAGAATGGATTAGA[C/T]GGTGGCAAGAGTATGTACATGTAGAGAGAGGTTAA Y 2 1 2 1 101000 f 74 goat snp10392-scaffold1371-528811 14 11697720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797629 Affx-122978017 AX-385284568 14 80872814 CAAGTTGATTTCTTCACACTTCATTGCTTCTCTCT[A/G]TGGAGACACTATGTACATTTGTCAACTGTTTACTG R 2 1 2 1 101000 f 74 goat snp10391-scaffold1371-489673 14 11658531 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391769 Affx-122967466 AX-123262126 14 80954203 CTAAAAGGGAATTACAATAATCAAGCCAGAGCTCC[A/G]TCAGGGCGTGTGTTACTGCAGCAAAATTAAATACA R 2 1 2 1 101000 f 74 goat snp10390-scaffold1371-408284 14 11575536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387890 Affx-122969621 AX-123258248 14 81019338 ATAAATTGGGAGACTGGGACTGATATATATACACT[A/G]CTATACATAAAATAGACAACTATTAGATAACTAAT R 2 1 2 1 303000 r 74 goat snp10388-scaffold1371-343149 14 11510334 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383579 Affx-122972589 AX-123253937 14 81049147 ATTGCACCAAAAACAAAGGCTGAATTTTCTTGCTG[C/T]GGAGGGGGAAGAAACTGACTTTTCCCTCCTTCTAT Y 2 1 2 1 101000 f 74 goat snp10387-scaffold1371-313340 14 11480637 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381067 Affx-122974616 AX-123251425 14 81106076 TCTTTACTAGATACATATAATTTTCTAACAACTTT[A/G]CATGCTTTATCTCATTTCTATCCTCATAACAATCC R 2 1 2 1 101000 r 74 goat snp10386-scaffold1371-256411 14 11422714 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401720 Affx-122959529 AX-123272073 14 81161323 TTCAGCTTTCTAGCCAGACTGTGTACAAAATAAAA[C/T]GAATCACACAGCCTCCTGATTGTTCCACAGGGGTT Y 2 1 2 1 201000 f 74 goat snp10385-scaffold1371-201164 14 11367443 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413835 Affx-122949879 AX-123284184 14 81215874 ACTCTTATTCTGGAGGGGGTTGGGAGTTTTAGGAA[C/T]TCTCAAACAAGAACCATGGGGAGTGGCTTTTGTGC Y 2 1 2 1 201000 f 74 goat snp10384-scaffold1371-146613 14 11314665 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387322 Affx-122970504 AX-123257680 14 81251059 GCCTGTGTGTCCCAAGGGTCCCTGATTCTAATGTC[A/G]TCATTGTTAAAGAGCTGGAGGTGGGCCAACAGAAG R 2 1 2 1 201000 f 74 goat snp10383-scaffold1371-111428 14 11279795 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403337 Affx-122957815 AX-123273690 14 81292029 AATGACAAGCCTGCTGGCTCAGTCTTCGGATACAA[C/T]GCCCAACTGCGTTTTTTAAGTACAATTGAGTTTCA Y 2 1 2 1 201000 r 74 goat snp10382-scaffold1371-70458 14 11238132 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603145 Affx-1002479366 AX-413837268 14 81330701 CCCTGTCCTAGCTGCCCACTTGCTGCTGCCCCGCC[A/G]GAGCATGGGCTTGTAGAAGTGTCTGGGGGGGGAAG R 2 1 2 1 304000 r 74 goat "INRA-CHI14-DGAT1-R396W;SNPs_058;UniBern-var29" 14 81330701 "C;G" "A;T" 3 Goat_IGGC_65K_v2 candidate gene ou candidate region DGAT1 10.1038/s41598-017-02052-0 350603047 Affx-1002479367 AX-413837263 14 81331159 AAGGCTACTTACCGCCAGCTTCAGGAGGCGCTCCA[C/T]GATGCGGGAGTAGTCCATGTCCTGTGGGCACAGGG Y 2 1 2 1 202000 f 74 goat "SNPs_059;UniBern-var30" 14 81331159 C T 2 neutral SV-TF-chip candidate gene ou candidate region DGAT1 538942849 Affx-1251531490 AX-585489973 14 81331549 GAGTCGCCGCAGCAGGAAGCGCTTTCGGATGCGGG[G/T]GGAGCGGGGGAAGTTGAGCTCGTAGCACAGGGTTG K 2 1 2 1 400000 f 74 goat SNPs_060 14 81331549 G T SV-TF-chip candidate gene ou candidate region DGAT1 350603149 Affx-1002479368 AX-413837269 14 81331681 GGCAGCCCCCCCAGCCCCAGGCAGGATCCTCACCG[A/C]GGTAGGTCAGGTTGTCGGGGTAGCTCACGGTGCGC M 2 1 2 1 303000 r 74 goat "INRA-CHI14-DGAT1-R251L;SNPs_061;UniBern-var31" 14 81331681 "C;G" "A;T" 3 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region DGAT1 10.1038/s41598-017-02052-0 350603051 Affx-1002479369 AX-413837266 14 81338369 GGCCTGGGGCACCAGGTTGGGTCGCAGTGGCCCCA[C/T]ATCAGGGGTCAAAGGTTAGGGGTCACGCGCACCGC Y 2 1 2 1 303000 f 74 goat "SNPs_062;UniBern-var32" 14 81338369 T C 3 not_recommended SV-TF-chip candidate gene ou candidate region DGAT1 320789082 Affx-122936180 AX-385276095 14 81348225 AAACACCACTTCATTATTAAGCAATTAATATGGTT[A/G]TTAATAAACAATTCTGTTATAAGCAATAACATAAC R 2 1 2 1 101000 f 74 goat snp10381-scaffold1371-14262 14 11180815 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433124 Affx-122935695 AX-123303465 14 81366670 TCACATCTCTGAGCTCTGAAGTCTGTTTGCTCTCC[A/G]CATCCTAGCAGCAGGGCTCATCTTGGTTTCGTTCT R 2 1 2 1 101000 f 74 goat snp8358-scaffold1300-4084 14 11162180 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778480 Affx-122964021 AX-385265594 14 81404364 GTCATTTCTAGTTAGTTTCATTGCCTGAATTTAAG[C/T]GTATTTCTTTGGAGATGGGACTAGAAAAGGGGGTC Y 2 1 2 1 101000 r 74 goat snp8359-scaffold1300-41778 14 11125136 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423859 Affx-122942317 AX-123294205 14 81453760 GAAAGCTTAAGTGACAATGTGTGATTGGCTGTTTC[A/G]TCTTTAGAGTTGTTTTTCTTTCTTCTTTTTTTTAA R 2 1 2 1 103000 f 74 goat snp8360-scaffold1300-91174 14 11075809 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437280 Affx-122931992 AX-123307618 14 81508299 TTGTTGATTTATAAGTGTTTGTAAGAAAGAGCTTG[C/T]ATTTTAGAAGGCCATTCTTCTTGTCACTACTGGTT Y 2 1 2 1 101000 r 74 goat snp8361-scaffold1300-145713 14 11020858 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427129 Affx-122939653 AX-123297472 14 81541707 TCACTAGCTGCTCCTTGTCAATTTTTCTGGAGCAC[C/T]TTGCCATGGTTCAGGCTTCTCTCATAGCTCAGTTG Y 2 1 2 1 101000 f 74 goat snp8362-scaffold1300-179121 14 10987561 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409674 Affx-122953073 AX-123280025 14 81574685 GGAGGGAAATTCAGTGGCAGTTTGACAGGATGTGG[C/T]GTTGGTCACCACTGTGAGTAGTGGGTCAGACATTC Y 2 1 2 1 201000 f 74 goat snp8363-scaffold1300-212099 14 10953656 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763156 Affx-986697685 AX-385251094 14 81586976 CCAGTCCTGTGGGATCAGGGCCCTGTGTTTATGAC[C/T]TCATCCAACCTTAATCACCTCCCTGAAGGCCGCAT Y 2 1 2 1 600010 f 74 goat 14_81586976 14 81586976 Ancestral_priority_1043 ancestry 0.55 neutral IMAGE 10K 10K ancestral 320803287 Affx-986696265 AX-385290131 14 81586999 TGTGTTTATGACTTCATCCAACCTTAATCACCTCC[C/T]TGAAGGCCGCATTTTTAAATGCAGGCTCAGCAGGG Y 2 1 2 1 600010 f 74 goat 14_81586999 14 81586999 Ancestral_priority_1043 ancestry 0.588 neutral IMAGE 10K 10K ancestral 38426164 Affx-122940595 AX-123296510 14 81624125 ATATGGTTGCAGACTTTTTTTCTATAGTTTTAAAT[A/G]CTAGATGACAACAGAGAAATATTTTTAGAGTTAAA R 2 1 2 1 201000 f 74 goat snp8364-scaffold1300-261539 14 10904210 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790919 Affx-122968914 AX-385277916 14 81655805 CAAAATTTGAAAAGTCGGACAAGTAACATTGGAAA[C/T]GTGGCATTTTCAAATTTTCTCTTAGAAACTGACAA Y 2 1 2 1 101000 r 74 goat snp8365-scaffold1300-293219 14 10872659 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387312 Affx-122970512 AX-123257670 14 81694292 GCAAGTTGACTTATTTTTTGCAGATAATCCTGCTG[C/T]GCTCTAAATCAATGCAATTTCATGTATCAAATGTA Y 2 1 2 1 101000 r 74 goat snp8366-scaffold1300-331706 14 10833628 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798115 Affx-122949396 AX-385285050 14 81732322 GACACCTTCTGAATGAGGCAAACCCTAACTAGTCT[A/G]CTTAAAATTGCAACCTGATGCCATATCCTCTCCCC R 2 1 2 1 101000 f 74 goat snp8367-scaffold1300-369736 14 10795843 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763174 Affx-986697703 AX-385251110 14 81738476 AGCCTGCGCGGCTTCGTGTGTGACACATGGCTCAC[A/G]GAGGGTGCTGGTGACCGGCTCGTGAGAGGAGACGT R 2 1 2 1 600010 f 74 goat 14_81738476 14 81738476 Ancestral_priority_1043 ancestry 0.456 neutral IMAGE 10K 10K ancestral 320765964 Affx-986697705 AX-385253388 14 81742800 CCAGAGACCTCGACGCAGAGGTGGGGAGGCAGCCA[C/G]TCACGGTCTCGCCAGTGCTCTGCTCTTGCTCACGC S 4 1 2 1 600010 r 74 goat 14_81742800 14 81742800 Ancestral_priority_1043 ancestry 0.426 neutral IMAGE 10K 10K ancestral 320765972 Affx-986697709 AX-385253395 14 81786920 AGGGAGGGGAGATGGGAGGGAAGACAGGTGTGGAT[C/T]GGGGAGATTCCAGACTTTCAGCTCCTGTGCAGCAC Y 2 1 2 1 600010 r 74 goat 14_81786920 14 81786920 Ancestral_priority_1043 ancestry 0.468 neutral IMAGE 10K 10K ancestral 38442634 Affx-122928457 AX-123312971 14 81792019 GGAAAGAAGGGTTCAGTTAGGAAGGACTGCGCTTA[C/T]GGTGGGAGTAGGTTACTAAGTGGATAATTGATGGA Y 2 1 2 1 201000 f 74 goat snp8369-scaffold1300-429433 14 10735661 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398663 Affx-122961885 AX-123269018 14 81829769 ATATTCAAAGTCTGAGTGAGATCTTCTTTCATTCC[A/G]TCTATTCAGTTGGAGGAAGACAATTTCAGAGAGTG R 2 1 2 1 101000 r 74 goat snp8370-scaffold1300-467183 14 10697876 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763183 Affx-986697712 AX-385251117 14 81862332 AAAAGAAACCCTGCATCCCTTAGCCACCACCCGTG[G/T]CCTCCCGTCTCCCTCAGCCCCAGGAAACCCCCAGT K 2 1 2 1 600010 f 74 goat 14_81862332 14 81862332 Ancestral_priority_1043 ancestry 0.432 neutral IMAGE 10K 10K ancestral 320802393 Affx-122928055 AX-385289297 14 81886999 TATTAGAATCTGAGGTGACAGGTGTGTCTTTTGCC[A/G]TGTATTGTATCTACCTACTGATCGGAATCGCCTTA R 2 1 2 1 101000 f 74 goat snp8371-scaffold1300-524413 14 10640232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768410 Affx-122948534 AX-385255590 14 81959121 TAATTTCCAGGTTATAGCTTGGGTACTAAGTGGGT[A/G]GCAATGCCAGTTATTAAACATTGATTATAAGTAAA R 2 1 2 1 101000 f 74 goat snp8373-scaffold1300-596535 14 10568037 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381525 Affx-122974851 AX-123251883 14 82040302 ACACACCTACTCTGAGTTTAAGTGTATTTTCATTG[A/G]CAAAATAAAGTAATAATACCCAGCTATCTCATCTG R 2 1 2 1 101000 f 74 goat snp8375-scaffold1300-677716 14 10486531 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794279 Affx-122926221 AX-385281244 14 82074837 GTCCCATATCTTTATTGTCAATTAGTGGTCACATG[C/T]AGAATGCTATAGTGAGTGTTGAAAACAAGTAGTTT Y 2 1 2 1 101000 f 74 goat snp8376-scaffold1300-712251 14 10451902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417957 Affx-122946700 AX-123288305 14 82113761 TGGATAGTCAAAGATGAACGGTATTTATGGCCTCT[A/G]CTCTTGAAGAGCACTCTAGAGAGCATGAAAGATTC R 2 1 2 1 101000 f 74 goat snp8377-scaffold1300-751175 14 10412533 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392758 Affx-122966001 AX-123263115 14 82150616 AATGTTTCAGGGGTCTTTGACTATCTGTTCACAGA[C/T]GGAATATAAAACAATTTTGTTTCTTAGGGAGAGGA Y 2 1 2 1 101000 f 74 goat snp8378-scaffold1300-788030 14 10375636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797963 Affx-122973937 AX-385284899 14 82179271 AAACCCATAAGATCAGTTTTCCTATGGATTTATTA[G/T]CATAGCTGAAGAAGATAGTTTCTGTAAGCAGAGGC K 2 1 2 1 101000 r 74 goat snp8379-scaffold1300-816685 14 10346656 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763185 Affx-986697714 AX-385251119 14 82186579 TGCAGAGGACTTTCACCTTTGCGACAAGAGAGGCA[A/G]GTCCACCGACATGGGGACAGTTGAAGAAGCTGACT R 2 1 2 1 600010 f 74 goat 14_82186579 14 82186579 Ancestral_priority_1043 ancestry 0.514 neutral IMAGE 10K 10K ancestral 38393550 Affx-122965411 AX-123263906 14 82223369 GCTCCCTTCTGTAGCTCTGAGAGCTTAGTATCTCT[A/G]TATGTTATTTCCAAAATGAATGAATGAGACACGCT R 2 1 2 1 103000 f 74 goat snp8380-scaffold1300-860783 14 10302583 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377216 Affx-122978174 AX-123247575 14 82271832 GCGTGAATCCCTACCAAAAGACAAGGAAATAAAAA[C/T]AGCATCATGCTTTGATGGAATTTTTCAAAATCATG Y 2 1 2 1 103000 f 74 goat snp8381-scaffold1300-909246 14 10253764 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378920 Affx-122976447 AX-123249279 14 82310104 AAAATAAAATGTGTTTTTAAGTCACTAAGATGCTG[C/T]GGCTGTTCATTACTGCAGCAGAACTTTGACTGAAT Y 2 1 2 1 101000 r 74 goat snp8382-scaffold1300-947518 14 10215508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390018 Affx-122968450 AX-123260375 14 82345582 AATTGGTGGTACTTGAAAGCATGAAATATTCTACT[A/G]GCAAAATGCTGTAAGAGAAAGGAGATGAAAGAATT R 2 1 2 1 101000 r 74 goat snp8383-scaffold1300-982996 14 10179874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445569 Affx-122925140 AX-123315906 14 82454168 GAGAACTGTGTCCACCCCTTGACTCCATGCTATAC[G/T]CCTTTCTAAACAGTGTCATTGAGATCACTGATCAG K 2 1 2 1 101000 r 74 goat snp8385-scaffold1300-1091582 NW_017212664.1 8393 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443478 Affx-122927817 AX-123313815 14 82496361 ACCAGCTGAGCCACAAGAAAAGCCTGTTCTGCTGG[C/T]GTTCATTTCCAGCTCACTATTGATAAAAATTTAAC Y 2 1 2 1 101000 r 74 goat snp8386-scaffold1300-1133775 14 10028201 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407233 Affx-122955372 AX-123277584 14 82534721 CTTCAAATGATCCTGGTTACAAAACATTAGATGAC[A/G]GATAGATAACTAGGTCAAATGTGGCAAAATGTCAA R 2 1 2 1 101000 r 74 goat snp8387-scaffold1300-1172135 14 9989498 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416367 Affx-122947878 AX-123286716 14 82579678 TATAACTATTGAACCTGCTCACTTTTTGAAGATTT[A/G]CAGGGAAGTAGTACCTCCTTCTCTTCTCAGTGATA R 2 1 2 1 201000 f 74 goat snp8388-scaffold1300-1217092 14 9944679 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793160 Affx-122951761 AX-385280138 14 82610104 AGAGCAGGGGGGTCTTAATGACCATTCATCAATGC[C/T]CGTTGGCTGATCACTGAGTGCCTTCCCATTCAGTT Y 2 1 2 1 101000 r 74 goat snp8389-scaffold1300-1247518 14 9914286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376869 Affx-122977830 AX-123247228 14 82614116 TCTGTTCTCAAGCAGAGCCTTCACTGGCAACGATC[A/G]CAGAAACACTCTGGGCTCCAAAAATAATATTTTTC R 2 1 2 1 101000 f 74 goat snp4115-scaffold1129-1971623 14 9909949 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423728 Affx-122942870 AX-123294074 14 82668345 ATCAGAGCATCTTGGCTCAGGATGAACAGCTAAGA[C/T]GGGTAGTGTGCTGTATTAATGAGGCCAAAGGTCTG Y 2 1 2 1 101000 f 74 goat snp4114-scaffold1129-1917394 14 9855739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785422 Affx-122969378 AX-385272467 14 82765681 TATTAGAAGTAACAAACCCTAATTCTTAAGATGTA[C/T]GCTTTTATCTTCAACATTTAGATGACAAAATGAAG Y 2 1 2 1 101000 r 74 goat snp4112-scaffold1129-1820058 14 9760431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397097 Affx-122962704 AX-123267452 14 82804388 TTGCCAACAGATTTAGGATGGCTTTTGAAGGTCAA[A/G]TAGAGCACAGTAGTGGTCCCTTCCCTAATCCTTAA R 2 1 2 1 101000 f 74 goat snp4111-scaffold1129-1781351 14 9720987 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404524 Affx-122956692 AX-123274876 14 82862790 GGAAAACACGGAGTGCCACAAGGGCAGAGACAAGG[G/T]CATGTTGCCCCATATTTATCTTTCAAGGAAAGTTC K 2 1 2 1 101000 r 74 goat snp4110-scaffold1129-1722949 14 9663908 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778698 Affx-122976505 AX-385265809 14 82899522 AAGATGGGAGACAAAAGTGATCTTCCCTTTTTATC[A/G]TAAAATATAACCTCAGCATATGTAAATCCAGCTAT R 2 1 2 1 101000 f 74 goat snp4109-scaffold1129-1686217 14 9626883 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402010 Affx-122958756 AX-123272363 14 82940045 AGGCTTAGATAAAAATTATTTTATTTTTCTCCTCC[C/T]TCCACTGCAGAGTATAGCCACTCTCTCTTCTCTGT Y 2 1 2 1 101000 r 74 goat snp4108-scaffold1129-1645694 14 9586516 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408892 Affx-122953976 AX-123279243 14 82987315 CTAGAAGTTATGGCCGTGACTTTGCTGTTCTTTCC[A/G]TACATTAATCAGTATTTCAGAGTGAAAAGTACAGA R 2 1 2 1 201000 r 74 goat snp4107-scaffold1129-1598424 14 9538936 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423767 Affx-122942841 AX-123294113 14 83025686 TGAACCAGTTTTTTAAAAAAAGAGTCAAGAAAATG[C/T]TCCATCTAAAGATATAGAACCAAAAGAAAGCTTCA Y 2 1 2 1 102000 r 74 goat snp4106-scaffold1129-1560053 14 9499147 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272762 Affx-1111833026 AX-519546460 14 83040875 TGACAAGAGTTCACAAATGCTTACACAAATCTGTA[A/G]TGGTTAAAAAAGACACTGACTCTCTGGGCAATGCA R 2 1 2 1 101000 f 74 goat 14_83040875_AF-PAKI 14 83040875 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320782997 Affx-122927088 AX-385270065 14 83068763 TCTACAGCCAAGTGCAGAGACCCTTAGAATACAAC[A/G]TTATCCTTCCTGTAGCTGCTAAGCATTGTTACCAT R 2 1 2 1 101000 f 74 goat snp4105-scaffold1129-1516976 14 9456016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777857 Affx-122932562 AX-385264974 14 83120035 AACACTTTGTTCTGTGACAAAAGTTTTGTAAAAAT[A/G]CAGGATAATTGTTAAAGTTTCTCTTTTGACAGCAA R 2 1 2 1 101000 r 74 goat snp4104-scaffold1129-1465704 14 9403773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801715 Affx-122928062 AX-385288623 14 83168781 AACCGTTGTAGCTCATAATGCATATCCTACCTTGA[C/T]GATGCCAGTTCAACCACTGGCATGTGGATAAGAAA Y 2 1 2 1 101000 r 74 goat snp4103-scaffold1129-1416958 14 9355125 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438129 Affx-122931485 AX-123308467 14 83220448 GGAAATATTGGCATGCCATGGCCATTTCATTGATG[C/T]GGGACATGGGCTTGTGTGTTAGAGTCAATGAGTGT Y 2 1 2 1 201000 f 74 goat snp4102-scaffold1129-1365291 14 9303108 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441480 Affx-122928746 AX-123311817 14 83285249 CTACACTTAATCCCTTGTTTTCAGAAGGTGCTTTA[C/T]AATCCTTTGTGCCTGGTGTCCTGGTGACAATCTTT Y 2 1 2 1 201000 f 74 goat snp4101-scaffold1129-1300490 14 9236647 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436482 Affx-122932969 AX-123306820 14 83334753 CAGTTTACAAAATCACCAGTCATCCGTAGAGTTCT[A/G]TGCAATATGCTCTTCATATTCTCATTTTCCCAGCT R 2 1 2 1 101000 f 74 goat snp4100-scaffold1129-1250986 14 9208442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448985 Affx-122923113 AX-123319320 14 83394164 CACATCTTAGCTGGATAACTAGTTCTAGGATCTGG[A/C]TTTTAAGTATTTGTTTGCTCAAGCTGCTACTACTT M 2 1 2 1 201000 r 74 goat snp4099-scaffold1129-1191575 14 9148843 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766947 Affx-122957667 AX-385254251 14 83430814 TTAGAGTTATTTTTTTCTGATTAAGGGGATGTTTA[C/T]AGTATCTAATGAGACATAAACCATACAGCAATGTA Y 2 1 2 1 101000 f 74 goat snp4098-scaffold1129-1154925 14 9112516 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392092 Affx-122966367 AX-123262449 14 83472604 AACACATCTGGAGAAGGCAATAAGAGAGGAAGAAG[A/G]TTGGTCAAAGCCAAATAAAATTTTTTATCAAATTT R 2 1 2 1 101000 f 74 goat snp4097-scaffold1129-1113135 14 9069870 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763189 Affx-986697718 AX-385251123 14 83476763 TGTGGAACATTTATGCAGCTGCTAGCTTGAGTTTT[G/T]GTTGGGATAACTTGGCTTACAGTTCAAAAGCAAAG K 2 1 2 1 600010 f 74 goat 14_83476763 14 83476763 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320795719 Affx-122938154 AX-385282672 14 83509278 ATTTGAATTAACCATGATTATCCCATCCAATCCCA[C/T]GACATCGATCATGCATGGATGGTCCTCTAGAATAA Y 2 1 2 1 101000 r 74 goat snp4096-scaffold1129-1076461 14 9033192 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448583 Affx-122923404 AX-123318919 14 83546906 GTGTTCACCGTGGTATGTGGACTGTTCCTTGCATC[A/G]CTTGGCCTTTCTCTGGGGGCTACACATGGGCTTAG R 2 1 2 1 102000 f 74 goat snp4095-scaffold1129-1038833 14 8995395 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392019 Affx-122966480 AX-123262376 14 83589408 TGAAGTAAGTGCCAGTGGAATTATGTCTGTTTTCT[A/G]TCTCCCAAAGATTCTTTCTATTTTAATGATAGAAA R 2 1 2 1 101000 f 74 goat snp4094-scaffold1129-996331 14 8951965 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435358 Affx-122933590 AX-123305698 14 83693241 CTGACTTTCCTAACCAGGCTAAATCTTTTCATGAT[A/C]TCTTCTGTACTCTCAGGGCATGGGATATATTTTTA M 2 1 2 1 101000 f 74 goat snp4093-scaffold1129-892498 14 8848135 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404255 Affx-122957060 AX-123274607 14 83725343 TTAAGTCCACTGTTGATACCTACGGCTGAAAAAAA[A/G]AATTCCTTTCAAAATATTACCTCCTATGGATAATG R 2 1 2 1 201000 f 74 goat snp4092-scaffold1129-860396 14 8815744 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775133 Affx-122962217 AX-385262265 14 83761676 ATTGCTTAGATTTAAAGCAAGCAATTGTGATAGCT[C/T]AATTAAAAAGTGAGTATAAATGTGAAGCTATTACA Y 2 1 2 1 101000 f 74 goat snp4091-scaffold1129-824063 14 8780507 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387302 Affx-122970521 AX-123257660 14 83810260 GTGTGTCTGTGTCTGGTCATTTCTAAATGTGAAAA[C/T]GCTATGAAACAACACCTGGCTCAACTGTTTTAATT Y 2 1 2 1 101000 f 74 goat snp4090-scaffold1129-775479 14 8731852 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414308 Affx-122949580 AX-123284657 14 83910799 AAGTCTAAACCAGATTTTGTTGTGTAACTTAAGTG[C/T]AAGAAGAAAAGTCCAGCAGAATATAGGAAATATGA Y 2 1 2 1 101000 f 74 goat snp4088-scaffold1129-674940 14 8630411 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777164 Affx-122952961 AX-385264287 14 83945652 TCTTATGCTAGTATTCTCTATTCATTAAATGAAAA[C/T]AGGTATCACTGATTAAGAACCACATGTAAATAGGA Y 2 1 2 1 101000 r 74 goat snp4087-scaffold1129-640087 14 8595230 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780294 Affx-122940689 AX-385267389 14 83982497 GTATTTCCTTATCAGTGTATAGCCAGTATGAAGCA[C/T]ATTTCACTAGAGGCTGGATTAGCTTTTAGGTTTGA Y 2 1 2 1 101000 f 74 goat snp4086-scaffold1129-603242 14 8558078 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378014 Affx-122977589 AX-123248373 14 84026447 TCTTTGTAATGCTATGTGATTTACATTGCTTTTTT[G/T]TGTGTGTGTTTTTCTGAAGAGTGTAAGATTCTGGA K 2 1 2 1 101000 r 74 goat snp4085-scaffold1129-559292 14 8513421 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399499 Affx-122961172 AX-123269854 14 84104732 CGCTTTTATTACTATTTAGTATATTTCTAAAAACA[C/T]TTCAAACACTGCACTCTTGTTGCATTTTAAAGGAA Y 2 1 2 1 101000 r 74 goat snp4084-scaffold1129-481007 14 8434248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781746 Affx-122950842 AX-385268828 14 84189599 TCATGCTTTTCACTGTACACGGGGCAAGTATAAAT[A/G]CCTTCATCTCCGTAAGGCCGCTGTCAAAATACACA R 2 1 2 1 101000 r 74 goat snp4083-scaffold1129-396140 14 8354618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413676 Affx-122950106 AX-123284025 14 84222706 TTTGCTTTGTCTTTTCAGTTCCCTTTTCTCTCCTT[A/G]CAACTTGCTGCTCTTCTGCCAAGCAAAGGTGGATA R 2 1 2 1 101000 r 74 goat snp4082-scaffold1129-363033 14 8321594 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434627 Affx-122934003 AX-123304968 14 84270815 CCCATAACCCTGTTAGGACATTCTTCACTATAAAG[C/T]ACTCTTTCTTTACTTTTGTTTTCCCATTCACCTCC Y 2 1 2 1 101000 f 74 goat snp4081-scaffold1129-314924 14 8273552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431614 Affx-122936156 AX-123301955 14 84370086 CCAAAGTGAATTCTTTCCACTCACCTCTTTTAACC[A/G]GGGCTTCCTTGATGGCTCAATGGTAAAGAATCCTC R 2 1 2 1 101000 f 74 goat snp4079-scaffold1129-215653 14 8172905 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443761 Affx-122927115 AX-123314098 14 84420503 TTTTTTTGGCTCCCCACACTAGTTCAAAGATTTCC[A/G]CCTCAAGTAAAACATCTGCTGAACACCTCCACCCA R 2 1 2 1 101000 r 74 goat snp4078-scaffold1129-165236 14 8122806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765988 Affx-122937676 AX-385253412 14 84481981 ATATTTCAAGTTAATGAGCTACCTAATGCTGAGAC[A/G]CTTTCCACTGTAGATATAGATTGCTATATCTGTCT R 2 1 2 1 101000 f 74 goat snp4077-scaffold1129-103758 14 8063437 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776639 Affx-122950680 AX-385263766 14 84537787 AAAGCTAAGAACAGCTTTTGTCAAAGAGTTAGGAT[A/G]CATATCAGTGGAAATGATATACATGGGTGATCAGT R 2 1 2 1 101000 r 74 goat snp4076-scaffold1129-47952 14 8007674 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403191 Affx-122958069 AX-123273544 14 84573834 GTAATGCTTACAAATCTGAATTAACTGGTCCCTAA[C/T]GGTTTCCTGAATAGGAACCTAGAATGTTAGGTCCA Y 2 1 2 1 201000 f 74 goat snp4075-scaffold1129-11905 14 7971786 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788441 Affx-122937481 AX-385275458 14 84590588 ACATTAATAGATTTTTCAACCACTTCAAACATGGC[A/G]TTGACTCAAATAGCAACCTGTGAGCAGTATCAGTA R 2 1 2 1 101000 r 74 goat snp9809-scaffold1351-4750 14 7886783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416513 Affx-122947776 AX-123286861 14 84629844 TATTGAATTGCTATTAACCTTCACCAGTGGCAATT[A/G]TTTGTTTCTTCTGACTTCCTTATTCATTTTCTGTT R 2 1 2 1 101000 r 74 goat snp9810-scaffold1351-44006 14 7847667 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797914 Affx-122951738 AX-385284852 14 84663940 AATGAACTAATCTGTTTGCAATATATTTTTTTCAA[C/T]TTGGGAACAGATGTAGCTACAGAGTGTTGGTAAAC Y 2 1 2 1 201000 f 74 goat snp9811-scaffold1351-78102 14 7813461 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792087 Affx-122933456 AX-385279074 14 84723924 ACATATGCTGTATAGTAGGAAATATATCTGTTGAA[C/T]ATTTCTACTTGAAATATTCCAATGTAATTTCTCAA Y 2 1 2 1 101000 f 74 goat snp9812-scaffold1351-138086 14 7751805 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38422044 Affx-122943614 AX-123292391 14 84760727 TTATATTAACCACTGCTTTTCCTCTAGTTGTTTCG[C/T]ATATGTGAGTGCTTCTTTTCTTTATGTAGACTCTA Y 2 1 2 1 101000 f 74 goat snp9813-scaffold1351-174889 14 7715304 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798548 Affx-122976944 AX-385285481 14 84835257 GGAAGATGTTACCTGTGTATCTTGCTTATATCATT[C/T]ATAAAGACTTTTGGCTGAGTTGTCAGAGGAATTGT Y 2 1 2 1 101000 r 74 goat snp9815-scaffold1351-249419 14 7639933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425510 Affx-122941471 AX-123295856 14 84886598 CAGAACAAGTCATCAAACAAGTCTACATATGTAAG[C/T]ACCGAATCCAGGTGTTTAAAGGGTGGGCAGAAAAA Y 2 1 2 1 201000 f 74 goat snp9816-scaffold1351-300760 14 7587165 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397955 Affx-122961910 AX-123268310 14 84934538 AATATTTTGCTTCTGTTTTCCATTTTGTAGCCACC[A/G]TGGTGAGAATTTATTCAGTTTACAATGGAAATACT R 2 1 2 1 101000 r 74 goat snp9817-scaffold1351-348700 14 7539432 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375564 Affx-122978750 AX-123245923 14 84965472 AGAGAAGGTTTCCTCTGGAAGGAAATTTGCACAGA[G/T]ACCTAAATCTCATTTTAAATTTATTCTCTCTGCAA K 2 1 2 1 101000 f 74 goat snp9818-scaffold1351-379634 14 7508156 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394966 Affx-122964274 AX-123265321 14 85000896 TGTTCAAATCAGAAAAAAACATTGTTGCGAGAGCA[C/T]AGTAAGTCAGTGGTTGAAGAGGTCCCATAGGTAGG Y 2 1 2 1 101000 r 74 goat snp9819-scaffold1351-415058 14 7472072 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426580 Affx-122939992 AX-123296926 14 85064885 TAGAACACACACCTTTATTGAGTTACAAAATGACC[A/G]TTTTTCGGCCTACTGGAACACAAAACAAAGCTCTC R 2 1 2 1 101000 r 74 goat snp9820-scaffold1351-479047 14 7408054 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390888 Affx-122967112 AX-123261245 14 85104869 GAGCTTCAATACCTTCCTGAATACAATGGGATTCT[A/C]TGGGGCTGTTGAATTGATGAATTAAGATAATAGCT M 2 1 2 1 201000 f 74 goat snp9821-scaffold1351-519031 14 7367858 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392800 Affx-122965971 AX-123263157 14 85207838 AGACTTTCTTGCTATAATTGGAATCATGTCCACTT[C/T]GTCAGGAAATGTCACAGACTGGGTGACTTAAGCTA Y 2 1 2 1 101000 f 74 goat snp9823-scaffold1351-622000 14 7262850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773480 Affx-122961250 AX-385260622 14 85298968 TTTTTTAAACAAGTTAGTTCAATTCAGATTTTTCA[A/G]TACAGCACATAACTACCTTAATCTTACCAATGACA R 2 1 2 1 101000 r 74 goat snp9825-scaffold1351-713130 14 7172756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781381 Affx-122956664 AX-385268466 14 85331822 AATCCATATTATCATCGTCATTGTACAATGCTGCT[A/G]CTCCATAGTCCTTCAGTTTCCTGAATAACGCTACT R 2 1 2 1 101000 r 74 goat snp9826-scaffold1351-745984 14 7139531 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447301 Affx-122924917 AX-123317637 14 85416232 ATTTATAACATGAAGAAATATGATAACTGTGTAAA[C/T]GTTTCCAAATTATTGGGGAAGAGATCAAGGAGGAA Y 2 1 2 1 201000 f 74 goat snp9828-scaffold1351-830394 14 7053758 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399109 Affx-122960863 AX-123269464 14 85471609 TTTTCAGGGAGTGTAAACAGCTCTAGGCTTTTGTT[A/G]CCTAAACTATAAGAACATTGGCATCTATGAACTTT R 2 1 2 1 201000 r 74 goat snp9829-scaffold1351-885771 14 6997887 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407276 Affx-122955339 AX-123277627 14 85517894 ACTTGTAGGTTACTCAGGTGTTTGGGCCTCAAGGG[C/T]AGGGAATGTGAGAAAGACTGTGAACTGAACGGGAG Y 2 1 2 1 201000 r 74 goat snp9830-scaffold1351-932056 14 6951568 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405008 Affx-122956383 AX-123275360 14 85556284 ACACATTTTTTCTATGTTTTCCTCCAGAAGATTTA[C/T]GGCTCTAGGTTTTACAGTTACTTTATCTGTCTTAA Y 2 1 2 1 101000 r 74 goat snp9831-scaffold1351-970446 14 6913040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774029 Affx-122933265 AX-385261167 14 85608782 ATTGTATTGAAGAGAACTAAAGGGGAAAGGTGAAA[C/T]AATAAAGGCACTTATCTACAAGACACTGTAGACAA Y 2 1 2 1 201000 f 74 goat snp9832-scaffold1351-1022944 14 6860377 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440457 Affx-122929392 AX-123310794 14 85637828 AACCACTGAAATGAACTGTTGAGAATTCTATTATC[A/G]TTTTTAAAAGAACTGGTATCTTCATAATATAATCA R 2 1 2 1 101000 f 74 goat snp9833-scaffold1351-1051990 14 6831543 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797859 Affx-122953908 AX-385284797 14 85668514 TTATAATGGTGCTATGACATCCTAGTTTACACAGA[A/G]GCTTTTAATCCACCTGAATGCATTTGTCTCTTTTT R 2 1 2 1 101000 f 74 goat snp9834-scaffold1351-1082676 14 6800341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276853 Affx-1111835620 AX-519550362 14 85701197 ATAAAATCATAGTCTTCTGACTGAAAACTGTAGGA[A/C]TATTGAATTAGGGGATGCATGGGAAATGCCAAATG M 2 1 2 1 201000 f 74 goat Random2.2K-1476 14 85701197 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779891 Affx-122950799 AX-385266990 14 85748270 TGCTTATCAAACATGACTTTGTTTTAGTCTTCAGG[A/C]TATCCCAATATTCTGCTTGCCCTATAGCTTAAAAT M 2 1 2 1 101000 f 74 goat snp9835-scaffold1351-1162432 14 6719445 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773646 Affx-122949435 AX-385260786 14 85884176 GTGTTACACCTTTGTTTCCAGTATAAGTTATTGAT[C/T]ATCCCTGGGAATTTTTCACTGATGAAATGATTTTT Y 2 1 2 1 101000 r 74 goat snp9837-scaffold1351-1298338 14 6585443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428311 Affx-122939372 AX-123298654 14 85912880 AACACTGATCGAGGAAAACAGCCAGACTGAAGTAT[A/G]CGGAATGAAAAATACACAGAGAGTGAGTTATCAAG R 2 1 2 1 101000 f 74 goat snp9838-scaffold1351-1327042 14 6556734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272764 Affx-1111833027 AX-519546462 14 85920927 CATTATGTACTCTGCATATAAGTTAAAACAGCAGG[A/G]TGACAATATACAGCCTTGAGGTACTCCTTTTCCTA R 2 1 2 1 103000 f 74 goat 14_85920927_AF-PAKI 14 85920927 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320770725 Affx-122968409 AX-385257889 14 85954960 AAGTACAACAAGGGGCAACTAAATTTCACAAGCTA[A/G]GAGAAAACTAGCATAAAGATGGAAACTATTTATTC R 2 1 2 1 201000 r 74 goat snp9839-scaffold1351-1369122 14 6514446 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787295 Affx-122951710 AX-385274320 14 86003610 GAGAGAAACATTTTGTATTTCTTAACAGTCACATG[A/C]TTGTATTCATTACACATTTTTACTTGCCTGATTTT M 2 1 2 1 101000 f 74 goat snp9840-scaffold1351-1417772 14 6465569 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788706 Affx-122970988 AX-385275722 14 86041527 TTGAATTTAAATAAATATTGTTTGTTAAATTATAA[C/T]GGAAAATTAGAACATTGTTCTATATGTCAGACAAA Y 2 1 2 1 201000 f 74 goat snp9841-scaffold1351-1455689 14 6426505 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430895 Affx-122936870 AX-123301236 14 86076912 GTTCTAATTACCTCTGAGTATCAGTTACATCCATC[A/G]CTTTAACTACGTGTACTCTCCTCTTTTGTGTCTTT R 2 1 2 1 101000 r 74 goat snp9842-scaffold1351-1491074 14 6391437 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788184 Affx-122938748 AX-385275203 14 86084632 TCATCGAGTGTTTATTCAACCTTGTACCTACAGGG[C/T]GAAGTGTAATGACTGAGACATATTAAGAACTCCAT Y 2 1 2 1 101000 f 74 goat snp2969-scaffold1090-3672 14 6383833 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771476 Affx-122952844 AX-385258634 14 86140268 TGTATAGAAGGTGCTTAGTCAAGTCAATTTTGACA[C/T]GATAAAGTGGTCTAAGAAAGGTTACTAAATGACTG Y 2 1 2 1 201000 r 74 goat snp2970-scaffold1090-59308 14 6327417 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393850 Affx-122965150 AX-123264205 14 86179029 ACCTACACCATGCCCAGCCTAAAATCAAGTCTTGC[A/G]TACAATGAATAACGACTCATAAAAGTTAATAAGAC R 2 1 2 1 201000 r 74 goat snp2971-scaffold1090-98069 14 6287060 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768874 Affx-122968855 AX-385256051 14 86209637 ACTCTGAAGTAAATATTAGACTCTCAAAACTGAGA[C/T]AAGTATTTATATTATACCTGTAACGGTTGGCGTTT Y 2 1 2 1 101000 r 74 goat snp2972-scaffold1090-128677 14 6256530 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443799 Affx-122927086 AX-123314136 14 86239979 TTTCACAGTTTTTTGTTGTATATTCTCAAACAAGA[C/T]GGGGAAATGTGTTCAGTAAATTCACAGTTCTCTGA Y 2 1 2 1 202000 f 74 goat snp2973-scaffold1090-159019 14 6226284 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433381 Affx-122935119 AX-123303722 14 86268740 TCATTAATAGTTGTAATTTAGGTGAATTCAGGGAC[G/T]ATTACTCCTCCATTTTGACCACACCTTCCCTGGAA K 2 1 2 1 101000 r 74 goat snp2974-scaffold1090-187780 14 6197257 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384689 Affx-122972121 AX-123255047 14 86362388 CTTAAGTTCTTGTTTAAGGTCCCAGCAAACAGAGG[C/T]AGACCTGGAATTAGAATCCATTCCATTGTTTTCCG Y 2 1 2 1 101000 f 74 goat snp2976-scaffold1090-281428 14 6103811 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415444 Affx-122949181 AX-123285793 14 86399023 CAATCTGCCCTTAATACACAACAGAGTGTCTGGGA[G/T]GTAGGTAAGGGCCTAGAAAGCCTACAGAAACTCCC K 2 1 2 1 202000 r 74 goat snp2977-scaffold1090-318063 14 6068092 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439417 Affx-122930239 AX-123309754 14 86433604 CATGACTTAGCGACTAAAAAGCAACAAAGACACAG[C/T]AAAGCTGCTGGCCAGATATTCAGCACTGGTTGGAT Y 2 1 2 1 201000 r 74 goat snp2978-scaffold1090-352644 14 6033072 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411219 Affx-122952353 AX-123281569 14 86478333 CATTTGGGTTGCTGAGAAAAACACGGTCATACTTT[C/T]GTGGAGCCAAATGACCCTTGGCAATTCCATCATCC Y 2 1 2 1 101000 f 74 goat snp2979-scaffold1090-397373 14 5985256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406258 Affx-122956100 AX-123276610 14 86507117 CAAACTGAGAAGGCTGCCTTCTATTCCTAGTGTGA[C/T]GAAGAGTTTTTATACAGAATGACTGTTTTATCTTC Y 2 1 2 1 201000 r 74 goat snp2980-scaffold1090-426157 14 5955890 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788663 Affx-122938992 AX-385275679 14 86552493 AATGAAATAGAATGACTGTCAAAGCCTTTCTAAAA[C/T]GAGCATTCAAAATTCTTATAGTTCTCATGAAAAAG Y 2 1 2 1 201000 r 74 goat snp2981-scaffold1090-471533 14 5910520 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276991 Affx-1111835621 AX-519550499 14 86568174 ATGTATTATTATGCACATGGAAGAAAATAATAACA[A/C]TATCAAAGTCTTTAGCCAAACCTTTATTAAATCAT M 2 1 2 1 101000 r 74 goat Random2.2K-1480 14 86568174 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376337 Affx-122978341 AX-123246696 14 86593689 TTTCATTATGCTCAGTTTGAGAACCTGGAGTTCCT[A/G]TTCAGCCTAGAGCCTCAGTAAAGAATCTCTAGACA R 2 1 2 1 101000 f 74 goat snp2982-scaffold1090-512729 14 5869219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773357 Affx-122976273 AX-385260499 14 86627599 ATGATGAAAAAGTGTAAAAGACTGTAATATATAAA[A/C]TATGGTATTCTTCTTAGCACCAGCAAGGGGTAAAA M 2 1 2 1 102000 r 74 goat snp2983-scaffold1090-546639 14 5834963 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442595 Affx-122928486 AX-123312932 14 86675440 TAAAAACATTCATGTATTCCTTTATTTTAAAATAA[C/T]AATAACAATAAACTTGTCACATGTTAACATAGCAA Y 2 1 2 1 103000 r 74 goat snp2984-scaffold1090-594480 14 5787336 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448960 Affx-122923133 AX-123319295 14 86705300 GTTTGCTGCTGATATTTTCATTTTTGCAGGTTCAG[C/T]CTTACAGCTTCAAATTCACATTATTAGCAGCTATT Y 2 1 2 1 201000 r 74 goat snp2985-scaffold1090-624340 14 5757264 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441326 Affx-122929435 AX-123311663 14 86734116 AGCAAATCTCAACCCATGACTTGTTGCATGCAATG[C/T]GAAATGCACATCTTTTATTATATTTTGTGTCTTAT Y 2 1 2 1 101000 f 74 goat snp2986-scaffold1090-653156 14 5728491 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377339 Affx-122977668 AX-123247698 14 86804609 ACTTCTATACACATTATTCTTTTTTAATTCCCAAA[C/T]AGCTCTTCTCTGTAGAAAACTAGGAAAATACCACT Y 2 1 2 1 101000 r 74 goat snp2987-scaffold1090-723649 14 5657782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410268 Affx-122952522 AX-123280618 14 86872453 ACAGTGCACTGGATTGCAAAGTGTCAGACAAGCAC[A/G]TGCTCTTAAATCCTTTCGGTGCAATATTCCTTAGG R 2 1 2 1 201000 r 74 goat snp2989-scaffold1090-791493 14 5590584 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443786 Affx-122927096 AX-123314123 14 86905623 CATCTGTGCGTCTGCCACTCTGAGACCCTGAAGTC[A/G]TTAAGACCATAAATCTGAACACAAGTGGTTTTCTC R 2 1 2 1 101000 r 74 goat snp2990-scaffold1090-824663 14 5552616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418956 Affx-122946086 AX-123289304 14 86948462 AACAGATAGACGAGTCCTCAGAGTTTTCTGAAAGA[C/T]GGTCTTCTAGGTTATAATCCTCAGTTAGGCGTGAA Y 2 1 2 1 201000 r 74 goat snp2991-scaffold1090-867502 14 5511103 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415355 Affx-122948778 AX-123285704 14 87015751 CAATGCTTGACAGCAATAGTCATCGGCAATTTTTC[A/G]TTTTATGATTCTGCCTCAGGAATCTCAGCAGTGCA R 2 1 2 1 201000 r 74 goat snp2992-scaffold1090-934791 14 5445897 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401570 Affx-122958889 AX-123271923 14 87071523 CGAGCCTCGGTGCTCATAAAATGTTCTTACTGTAG[C/T]GTGTGCTAATTCTTTGTTCTTCGGCTCTCCTGACT Y 2 1 2 1 201000 r 74 goat snp2993-scaffold1090-990563 14 5390168 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799153 Affx-122938758 AX-385286083 14 87111248 ACCATCTCAATTTTCTATGTTAGGTAAAAGTTGAT[A/C]ACGGTTAGCCTGAAAGAAAAAGATTGCCTGCCCTA M 2 1 2 1 101000 r 74 goat snp2994-scaffold1090-1030288 14 5350522 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422338 Affx-122943452 AX-123292684 14 87141568 GGGAGGGTGCAACCACTGACACAACTGTTCACCTC[A/G]TTTTGAGAGGATATTTGCAAATTCCATTCAGTTCT R 2 1 2 1 201000 r 74 goat snp2995-scaffold1090-1060608 14 5319748 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393285 Affx-122965444 AX-123263641 14 87171650 GGTCCCATCTCACATCCTAAGTGGTTCCATGGAGG[A/G]CAAGCGTCCATCTATGTATTAAATATTTTTGAAGA R 2 1 2 1 101000 f 74 goat snp2996-scaffold1090-1090690 14 5289318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435936 Affx-122932748 AX-123306275 14 87215019 GGGGTCTTTAAAAGAATTGAATTAAAGTGCAAAGT[A/G]TTCTGAAAAATATGAAGCCTTATTAGCAAACATTT R 2 1 2 1 101000 r 74 goat snp2997-scaffold1090-1134059 14 5245576 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442064 Affx-122928383 AX-123312401 14 87269941 TGGAGTTCTTTGGGACTTTTCAGGGAATACCTCAC[G/T]AACTGAGAAGGAAACAGTTTTAAACTCTGCAGGTA K 2 1 2 1 101000 f 74 goat snp2998-scaffold1090-1188981 14 5190487 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428759 Affx-122938430 AX-123299101 14 87320762 TTTCACATGAGTTGAGGGAGTATGGTAGAAATACA[C/T]GGACATGCTTAAACATTTCATGACCAAAATATTTT Y 2 1 2 1 101000 f 74 goat snp2999-scaffold1090-1239802 14 5141171 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433324 Affx-122935179 AX-123303665 14 87358325 ACATGGTTCCTGCCCTAAGCTCTCTTAACATCCCC[A/G]TTGCCTCTCAGTTTATTTTTCCCTCTCTTATGCTC R 2 1 2 1 101000 r 74 goat snp3000-scaffold1090-1277365 14 5103515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384913 Affx-122972341 AX-123255271 14 87403561 GTATATTGGTACATCTTTCTCCTGTGCTGCCCTTG[A/C]GCTGCTCACTCATATTTTTATCTATAAAACCTAGC M 2 1 2 1 202000 r 74 goat snp3001-scaffold1090-1322601 NW_017216578.1 12582 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783971 Affx-122958241 AX-385271025 14 87429939 TCAATCTAAGGGTGTCTGTCATTCCTTGCAGAAAC[A/G]TCAGGAAGGTGATATCCTTTAAGCTTCCAGAGTCA R 2 1 2 1 101000 f 74 goat snp9281-scaffold1337-988203 14 4891304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476301 Affx-1251763808 AX-586011719 14 87449978 GATAATATAAATAGGTAATATTTTCAATTAATATG[-/TTAAAGTATATCCGGGGGAGAGGGAAAGATGGCGGAGGAAAACAACAACAACAAAAAAATAAATAAATAAAAAATAAAAA]TAAAGTATATCCAGCATTTCTGTCTCTCTGAATTT - 8 1 4 1 20000 f 74 goat SV_340 14 87449978 - deletion junction SV-TF-chip 539476554 Affx-1251763808 AX-586011940 14 87449978 GATAATATAAATAGGTAATATTTTCAATTAATATG[-/TTAAAGTATATCCGGGGGAGAGGGAAAGATGGCGGAGGAAAACAACAACAACAAAAAAATAAATAAATAAAAAATAAAAA]TAAAGTATATCCAGCATTTCTGTCTCTCTGAATTT - 4 1 4 1 20000 r 74 goat SV_340 14 87449978 - deletion junction SV-TF-chip 562165198 Affx-1251763808 AX-606940610 14 87449978 GATAATATAAATAGGTAATATTTTCAATTAATATG[-/TTAAAGTATATCCGGGGGAGAGGGAAAGATGGCGGAGGAAAACAACAACAACAAAAAAATAAATAAATAAAAAATAAAAA]TAAAGTATATCCAGCATTTCTGTCTCTCTGAATTT - 8 1 4 1 20100 r 74 goat SV_340 14 87449978 - deletion junction SV-TF-chip 562165338 Affx-1251763808 AX-606940749 14 87449978 GATAATATAAATAGGTAATATTTTCAATTAATATG[-/TTAAAGTATATCCGGGGGAGAGGGAAAGATGGCGGAGGAAAACAACAACAACAAAAAAATAAATAAATAAAAAATAAAAA]TAAAGTATATCCAGCATTTCTGTCTCTCTGAATTT - 8 1 4 1 20100 r 74 goat SV_340 14 87449978 - deletion junction SV-TF-chip 562165410 Affx-1251763808 AX-606940821 14 87449978 GATAATATAAATAGGTAATATTTTCAATTAATATG[-/TTAAAGTATATCCGGGGGAGAGGGAAAGATGGCGGAGGAAAACAACAACAACAAAAAAATAAATAAATAAAAAATAAAAA]TAAAGTATATCCAGCATTTCTGTCTCTCTGAATTT - 8 1 4 1 20100 f 74 goat SV_340 14 87449978 - deletion junction SV-TF-chip 562165813 Affx-1251763808 AX-606941222 14 87449978 GATAATATAAATAGGTAATATTTTCAATTAATATG[-/TTAAAGTATATCCGGGGGAGAGGGAAAGATGGCGGAGGAAAACAACAACAACAAAAAAATAAATAAATAAAAAATAAAAA]TAAAGTATATCCAGCATTTCTGTCTCTCTGAATTT - 8 1 4 1 20100 r 74 goat SV_340 14 87449978 - deletion junction SV-TF-chip 562165968 Affx-1251763808 AX-606941377 14 87449978 GATAATATAAATAGGTAATATTTTCAATTAATATG[-/TTAAAGTATATCCGGGGGAGAGGGAAAGATGGCGGAGGAAAACAACAACAACAAAAAAATAAATAAATAAAAAATAAAAA]TAAAGTATATCCAGCATTTCTGTCTCTCTGAATTT - 8 1 4 1 20100 r 74 goat SV_340 14 87449978 - deletion junction SV-TF-chip 562166228 Affx-1251763808 AX-606941636 14 87449978 GATAATATAAATAGGTAATATTTTCAATTAATATG[-/TTAAAGTATATCCGGGGGAGAGGGAAAGATGGCGGAGGAAAACAACAACAACAAAAAAATAAATAAATAAAAAATAAAAA]TAAAGTATATCCAGCATTTCTGTCTCTCTGAATTT - 8 1 4 1 20100 r 74 goat SV_340 14 87449978 - deletion junction SV-TF-chip 38392699 Affx-122966407 AX-123263056 14 87459579 TGTCTGAGGCAATTTAAAATTTACCCTGCCAACCA[C/T]AATGTGAGCACAAAGCCAGCCAACTCGCCACCCAA Y 2 1 2 1 101000 f 74 goat snp9280-scaffold1337-958563 14 4861540 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796387 Affx-122971857 AX-385283337 14 87522569 ATACACAAAAATGATTTCTCAGTCACAACACTAAC[A/C]GTATTATCAAAATTAAATCTGGCAGTAAAGTTCAA M 2 1 2 1 101000 f 74 goat snp9279-scaffold1337-895573 14 4797942 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389148 Affx-122968541 AX-123259506 14 87561818 CCCAGTAATGCCAGTGGCTCTCACTTTGAATTCAG[G/T]ACCACTGAGCCCAACGGGGCCTTAGTGGGGCCGAG K 2 1 2 1 101000 f 74 goat snp9278-scaffold1337-856324 14 4757596 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407957 Affx-122954350 AX-123278308 14 87603577 GTGACTCAGTTACTTGTTCACAAAAGTAGCTGCTT[A/G]CATGGTTACTGTGGTTTTAGGTTCTCAAACACCCA R 2 1 2 1 101000 r 74 goat snp9277-scaffold1337-814565 14 4714899 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430713 Affx-122936903 AX-123301054 14 87635320 ACCCTGTCATTAGGCACACTAAAGCCCCAAACAGG[C/T]AGTTCTGTGCCATAGTAGGCTTGTCTTTGCCTTTC Y 2 1 2 1 101000 r 74 goat snp9276-scaffold1337-782822 14 4683060 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378964 Affx-122976412 AX-123249323 14 87672749 GGGCTTTTCAGGCTTATCAATTTAAATGTCTATCA[A/G]TGTATAAGTCTCCAGCTTTAATGGCCAATACAGAA R 2 1 2 1 101000 f 74 goat snp9275-scaffold1337-745393 14 4645563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411444 Affx-122951820 AX-123281794 14 87710149 CTAACTCGTATTTCCCAAACACCCAGTGCCGTCTA[C/T]GTCTCTGTTTTCATGTGTATTTCTACTCCCTGGGA Y 2 1 2 1 101000 r 74 goat snp9274-scaffold1337-707993 14 4607878 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476302 Affx-1251763809 AX-586011720 14 87761889 TGAAGTTCTGATTGGGATAAATAATATTCTACTAT[-/TAAGAAAACCTTAGGAGAGGGAAAGATGGCGGAGGAATAGTAAATAAATAAAAATAAAAATAAAAATAGGAAAAAAAAAA]AAGAAAACCTTATGAAGTAAATAATATAAATTTGT - 8 1 4 1 20000 f 74 goat SV_341 14 87761889 - deletion junction SV-TF-chip 539476555 Affx-1251763809 AX-586011941 14 87761889 TGAAGTTCTGATTGGGATAAATAATATTCTACTAT[-/TAAGAAAACCTTAGGAGAGGGAAAGATGGCGGAGGAATAGTAAATAAATAAAAATAAAAATAAAAATAGGAAAAAAAAAA]AAGAAAACCTTATGAAGTAAATAATATAAATTTGT - 8 1 4 1 20000 r 74 goat SV_341 14 87761889 - deletion junction SV-TF-chip 562166201 Affx-1251763809 AX-606941609 14 87761889 TGAAGTTCTGATTGGGATAAATAATATTCTACTAT[-/TAAGAAAACCTTAGGAGAGGGAAAGATGGCGGAGGAATAGTAAATAAATAAAAATAAAAATAAAAATAGGAAAAAAAAAA]AAGAAAACCTTATGAAGTAAATAATATAAATTTGT - 8 1 4 1 20100 r 74 goat SV_341 14 87761889 - deletion junction SV-TF-chip 562166202 Affx-1251763809 AX-606941610 14 87761889 TGAAGTTCTGATTGGGATAAATAATATTCTACTAT[-/TAAGAAAACCTTAGGAGAGGGAAAGATGGCGGAGGAATAGTAAATAAATAAAAATAAAAATAAAAATAGGAAAAAAAAAA]AAGAAAACCTTATGAAGTAAATAATATAAATTTGT - 8 1 4 1 20100 f 74 goat SV_341 14 87761889 - deletion junction SV-TF-chip 38436346 Affx-122933072 AX-123306685 14 87767000 CACAGTTAATGATCTAATTATAATACCATGTCTCC[A/G]TTTAGAGAGAAGATATTTATGTCTTTTTCTGCATG R 2 1 2 1 201000 r 74 goat snp9273-scaffold1337-651142 14 4549901 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406515 Affx-122955140 AX-123276867 14 87812059 TAGAGTAAAAGTGAAGAAGTGACCATATAAAAAGA[C/T]GACATTAAAGGCTGATGGTAATCCTTCAATTGAAA Y 2 1 2 1 101000 f 74 goat snp9272-scaffold1337-606083 14 4505178 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788282 Affx-122964261 AX-385275300 14 87842651 AATTTCTTGAGTAAACACTCACACATTTGCTTGCA[G/T]GCAAGCACCAGAGTGACCACAAAGTTAATGTCAAA K 2 1 2 1 101000 r 74 goat snp9271-scaffold1337-575491 14 4474891 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399889 Affx-122960215 AX-123270244 14 87904425 ACTTTATTTTTGCATAAACTTTTTCCTAAAGTAAC[A/G]TATATCTGGACCTTGTTTTTGAAAGCAATATGAAA R 2 1 2 1 101000 f 74 goat snp9269-scaffold1337-513717 14 4412858 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476303 Affx-1251763810 AX-586011721 14 87920167 TTCACCCTGAAGTTTGCTTTCTAAAGAATGACTCT[-/TGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAGACAAATTAAATAAAATTAAAAAAAGAAAAGAATGACTCTTAA]GTCTTAGAGAAGATGTGGATAGAAAAATGTACATT - 4 1 4 1 20000 f 74 goat SV_342 14 87920167 - deletion junction SV-TF-chip 539476556 Affx-1251763810 AX-586011942 14 87920167 TTCACCCTGAAGTTTGCTTTCTAAAGAATGACTCT[-/TGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAGACAAATTAAATAAAATTAAAAAAAGAAAAGAATGACTCTTAA]GTCTTAGAGAAGATGTGGATAGAAAAATGTACATT - 8 1 4 1 20000 r 74 goat SV_342 14 87920167 - deletion junction SV-TF-chip 562166101 Affx-1251763810 AX-606941510 14 87920167 TTCACCCTGAAGTTTGCTTTCTAAAGAATGACTCT[-/TGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAGACAAATTAAATAAAATTAAAAAAAGAAAAGAATGACTCTTAA]GTCTTAGAGAAGATGTGGATAGAAAAATGTACATT - 8 1 4 1 20100 r 74 goat SV_342 14 87920167 - deletion junction SV-TF-chip 562166226 Affx-1251763810 AX-606941634 14 87920167 TTCACCCTGAAGTTTGCTTTCTAAAGAATGACTCT[-/TGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAGACAAATTAAATAAAATTAAAAAAAGAAAAGAATGACTCTTAA]GTCTTAGAGAAGATGTGGATAGAAAAATGTACATT - 8 1 4 1 20100 r 74 goat SV_342 14 87920167 - deletion junction SV-TF-chip 562166250 Affx-1251763810 AX-606941658 14 87920167 TTCACCCTGAAGTTTGCTTTCTAAAGAATGACTCT[-/TGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAGACAAATTAAATAAAATTAAAAAAAGAAAAGAATGACTCTTAA]GTCTTAGAGAAGATGTGGATAGAAAAATGTACATT - 8 1 4 1 20100 f 74 goat SV_342 14 87920167 - deletion junction SV-TF-chip 562166279 Affx-1251763810 AX-606941687 14 87920167 TTCACCCTGAAGTTTGCTTTCTAAAGAATGACTCT[-/TGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAGACAAATTAAATAAAATTAAAAAAAGAAAAGAATGACTCTTAA]GTCTTAGAGAAGATGTGGATAGAAAAATGTACATT - 8 1 4 1 20100 r 74 goat SV_342 14 87920167 - deletion junction SV-TF-chip 562166331 Affx-1251763810 AX-606941739 14 87920167 TTCACCCTGAAGTTTGCTTTCTAAAGAATGACTCT[-/TGAGAGAGGGAAAGATGGCGGAGGAATAGGATGGGAAGACAAATTAAATAAAATTAAAAAAAGAAAAGAATGACTCTTAA]GTCTTAGAGAAGATGTGGATAGAAAAATGTACATT - 8 1 4 1 20100 f 74 goat SV_342 14 87920167 - deletion junction SV-TF-chip 320801918 Affx-122953662 AX-385288823 14 87940084 GAAATACTTGATGAGACATTTTTCTCAGAAATTGG[A/C]TACATTATCATAACATGCAGGAGGTATTTCAATAA M 2 1 2 1 101000 f 74 goat snp9268-scaffold1337-478058 14 4377361 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796958 Affx-122969495 AX-385283899 14 87979726 AATCGTTCCATGCTGTTGAGATCGCTTATCATCCA[A/G]TTTATCTGGCCCTGTCCCAGATACATATCTTCATT R 2 1 2 1 101000 f 74 goat snp9267-scaffold1337-438416 14 4338014 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394166 Affx-122964935 AX-123264521 14 88019941 AACTTCTAATTATCCTTCTTTTGAGTCCTGTGTTC[A/G]TTTATCTTACAAACCATTTTTAAACACTTATTATG R 2 1 2 1 201000 r 74 goat snp9266-scaffold1337-398201 14 4295522 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400953 Affx-122959699 AX-123271306 14 88081490 TTGGCAAAGGTTTGGAACATCTTGAACTGCCATGC[A/G]TATCTGGTAAGAATGTAAATTAGTATAAGCACTTT R 2 1 2 1 101000 f 74 goat snp9265-scaffold1337-336652 14 4233921 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450391 Affx-122922080 AX-123320726 14 88113374 CTATAAAGATTGCTTTCATTGTACTTTTATAAAGC[A/G]TACCAAAAATCTATAGGCTTCAACTGACTTACCAC R 2 1 2 1 101000 r 74 goat snp9264-scaffold1337-304768 14 4202214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772719 Affx-122925121 AX-385259865 14 88145570 TGTGATTGATTGAATGCAAATTTTGTCAACGTTTC[A/G]CCGAAAGTTTCAACTTTCATCTTAGGTTAGAAGGA R 2 1 2 1 201000 f 74 goat snp9263-scaffold1337-272572 14 4169843 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772200 Affx-122938298 AX-385259355 14 88183308 TCTTTTTAAATAGAGAATATGTTTTATTATCATAG[C/T]ACAAATCATTATTCCTCTTGTCTCCACAATCTTTA Y 2 1 2 1 201000 f 74 goat snp9262-scaffold1337-234834 14 4131507 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476304 Affx-1251763811 AX-586011722 14 88228523 TTACTGGGTATACACACTGAGGAAACCAGAATCAA[-/AAGAGACTCATGTGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTAAAAAAAAATAAAAAATTAAAATAAAAAAAAAAG]AGAGACTCATGTATCCCAATGTTCATTGGAGCACT - 4 1 4 1 20000 f 74 goat SV_343 14 88228523 - deletion junction SV-TF-chip 539476557 Affx-1251763811 AX-586011943 14 88228523 TTACTGGGTATACACACTGAGGAAACCAGAATCAA[-/AAGAGACTCATGTGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTAAAAAAAAATAAAAAATTAAAATAAAAAAAAAAG]AGAGACTCATGTATCCCAATGTTCATTGGAGCACT - 4 1 4 1 20000 r 74 goat SV_343 14 88228523 - deletion junction SV-TF-chip 562165594 Affx-1251763811 AX-606941005 14 88228523 TTACTGGGTATACACACTGAGGAAACCAGAATCAA[-/AAGAGACTCATGTGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTAAAAAAAAATAAAAAATTAAAATAAAAAAAAAAG]AGAGACTCATGTATCCCAATGTTCATTGGAGCACT - 8 1 4 1 20100 r 74 goat SV_343 14 88228523 - deletion junction SV-TF-chip 562165760 Affx-1251763811 AX-606941169 14 88228523 TTACTGGGTATACACACTGAGGAAACCAGAATCAA[-/AAGAGACTCATGTGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTAAAAAAAAATAAAAAATTAAAATAAAAAAAAAAG]AGAGACTCATGTATCCCAATGTTCATTGGAGCACT - 8 1 4 1 20100 f 74 goat SV_343 14 88228523 - deletion junction SV-TF-chip 562165814 Affx-1251763811 AX-606941223 14 88228523 TTACTGGGTATACACACTGAGGAAACCAGAATCAA[-/AAGAGACTCATGTGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTAAAAAAAAATAAAAAATTAAAATAAAAAAAAAAG]AGAGACTCATGTATCCCAATGTTCATTGGAGCACT - 8 1 4 1 20100 r 74 goat SV_343 14 88228523 - deletion junction SV-TF-chip 562166071 Affx-1251763811 AX-606941480 14 88228523 TTACTGGGTATACACACTGAGGAAACCAGAATCAA[-/AAGAGACTCATGTGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTAAAAAAAAATAAAAAATTAAAATAAAAAAAAAAG]AGAGACTCATGTATCCCAATGTTCATTGGAGCACT - 8 1 4 1 20100 r 74 goat SV_343 14 88228523 - deletion junction SV-TF-chip 320797642 Affx-122970132 AX-385284581 14 88241612 CAGTACTTCCTTCGCAACATTTGCATGGGCTACAA[C/T]GTCTGGTTCCCTAAGATAAGCGATCCTAGATAAAC Y 2 1 2 1 101000 f 74 goat snp9261-scaffold1337-176530 14 4072264 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783428 Affx-122953107 AX-385270491 14 88306782 AAAAACATACATTAATGTTTGATATACACAATAAA[G/T]ACTAAGATCTTCACTTTAGCTCTTCCTTGGGGAAA K 2 1 2 1 101000 r 74 goat snp9260-scaffold1337-111360 14 4007381 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422528 Affx-122943279 AX-123292874 14 88346800 GTGCTGAAGACTTGACACTATCATCTGTGGGGAAA[C/T]GGGGCAGAGAACTGACCCGCGAAGTTGTAAGAAGT Y 2 1 2 1 101000 f 74 goat snp9259-scaffold1337-71342 14 3967270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788303 Affx-122970106 AX-385275321 14 88384489 AGTGAGTTTGGTTTTGCTGAAGGTCATTGAAAACT[A/G]GGATAATTGTTTTCCCAGTTTGCCGTATTGTAACA R 2 1 2 1 101000 r 74 goat snp9258-scaffold1337-33653 14 3929608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413342 Affx-122950162 AX-123283691 14 88417565 CCCCTCTAGCTACGTCCCTTCGTGCACCTCTTGTA[A/G]AGTCTAGCATTTGGAAATTTTGCCCCTGCTTTTTA R 2 1 2 1 101000 r 74 goat snp9257-scaffold1337-577 14 3899299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272818 Affx-1111833028 AX-519546512 14 88428574 ATGCTTGAAGAAAATCATAAACAAAAGACATATGC[A/G]CACCTGTGTTCGTTGCTGAACTACTTAAAATGGCA R 2 1 2 1 101000 r 74 goat 14_88428574_AF-PAKI 14 88428574 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38452855 Affx-122920717 AX-123323188 14 88433486 TTTTACTGAACAACTCACACATTTTCCCATTTACA[C/T]GATTCATGGTCGATATACGCTAAAGCACCAAACAC Y 2 1 2 1 101000 r 74 goat snp5476-scaffold1192-15245 14 3883536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412284 Affx-122950878 AX-123282633 14 88482030 CCTTAAATACAGGAATATTATTATCAATATTCTTC[A/G]CAAAAAATAAAGTCAAGATGGCTCTTTAGTAACTT R 2 1 2 1 303000 f 74 goat snp5477-scaffold1192-63789 14 3834916 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442772 Affx-122927738 AX-123313109 14 88523582 ACATCACACACAATTATATTTTTCTCCTCTCATCT[C/T]TCCTTCCCTCTTTTCTCTTCAACTCTTCATTCCTC Y 2 1 2 1 101000 f 74 goat snp5478-scaffold1192-105341 14 3793454 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444187 Affx-122927266 AX-123314524 14 88552672 ATTAAGTGGGTCTTCATTTCCTCCAAGTCTCATTG[C/T]TCTAACTATGACCCTTCAACTCCAGGCATAGCCTT Y 2 1 2 1 201000 r 74 goat snp5479-scaffold1192-134431 14 3763998 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476305 Affx-1251763812 AX-586011723 14 88563071 TTCTTTTGCCAAATAATTCAAGGATCTCAAGATGT[-/TTAAATTCTATCCACTGGGGGGAGAGGGAAAGATGGCGGAATTAAAGATTTTAAAATTTAAAAAAAATAAAAAATAAAAA]TAAATTCTATCCACTACCCTTCATTTAGTAAATGT - 8 1 4 1 20000 f 74 goat SV_346 14 88563071 - deletion junction SV-TF-chip 539476558 Affx-1251763812 AX-586011944 14 88563071 TTCTTTTGCCAAATAATTCAAGGATCTCAAGATGT[-/TTAAATTCTATCCACTGGGGGGAGAGGGAAAGATGGCGGAATTAAAGATTTTAAAATTTAAAAAAAATAAAAAATAAAAA]TAAATTCTATCCACTACCCTTCATTTAGTAAATGT - 8 1 4 1 20000 r 74 goat SV_346 14 88563071 - deletion junction SV-TF-chip 562165143 Affx-1251763812 AX-606940555 14 88563071 TTCTTTTGCCAAATAATTCAAGGATCTCAAGATGT[-/TTAAATTCTATCCACTGGGGGGAGAGGGAAAGATGGCGGAATTAAAGATTTTAAAATTTAAAAAAAATAAAAAATAAAAA]TAAATTCTATCCACTACCCTTCATTTAGTAAATGT - 8 1 4 1 20100 r 74 goat SV_346 14 88563071 - deletion junction SV-TF-chip 562165178 Affx-1251763812 AX-606940590 14 88563071 TTCTTTTGCCAAATAATTCAAGGATCTCAAGATGT[-/TTAAATTCTATCCACTGGGGGGAGAGGGAAAGATGGCGGAATTAAAGATTTTAAAATTTAAAAAAAATAAAAAATAAAAA]TAAATTCTATCCACTACCCTTCATTTAGTAAATGT - 8 1 4 1 20100 r 74 goat SV_346 14 88563071 - deletion junction SV-TF-chip 562165498 Affx-1251763812 AX-606940909 14 88563071 TTCTTTTGCCAAATAATTCAAGGATCTCAAGATGT[-/TTAAATTCTATCCACTGGGGGGAGAGGGAAAGATGGCGGAATTAAAGATTTTAAAATTTAAAAAAAATAAAAAATAAAAA]TAAATTCTATCCACTACCCTTCATTTAGTAAATGT - 8 1 4 1 20100 f 74 goat SV_346 14 88563071 - deletion junction SV-TF-chip 562165574 Affx-1251763812 AX-606940985 14 88563071 TTCTTTTGCCAAATAATTCAAGGATCTCAAGATGT[-/TTAAATTCTATCCACTGGGGGGAGAGGGAAAGATGGCGGAATTAAAGATTTTAAAATTTAAAAAAAATAAAAAATAAAAA]TAAATTCTATCCACTACCCTTCATTTAGTAAATGT - 8 1 4 1 20100 r 74 goat SV_346 14 88563071 - deletion junction SV-TF-chip 562165815 Affx-1251763812 AX-606941224 14 88563071 TTCTTTTGCCAAATAATTCAAGGATCTCAAGATGT[-/TTAAATTCTATCCACTGGGGGGAGAGGGAAAGATGGCGGAATTAAAGATTTTAAAATTTAAAAAAAATAAAAAATAAAAA]TAAATTCTATCCACTACCCTTCATTTAGTAAATGT - 8 1 4 1 20100 f 74 goat SV_346 14 88563071 - deletion junction SV-TF-chip 562166083 Affx-1251763812 AX-606941492 14 88563071 TTCTTTTGCCAAATAATTCAAGGATCTCAAGATGT[-/TTAAATTCTATCCACTGGGGGGAGAGGGAAAGATGGCGGAATTAAAGATTTTAAAATTTAAAAAAAATAAAAAATAAAAA]TAAATTCTATCCACTACCCTTCATTTAGTAAATGT - 8 1 4 1 20100 r 74 goat SV_346 14 88563071 - deletion junction SV-TF-chip 38380695 Affx-122975167 AX-123251053 14 88596708 TGATTATTGTACTTTTACAGCCAACCATATCATTA[C/T]GAAAAAATGCAAGATAAATATATTCCACCTCACCT Y 2 1 2 1 101000 f 74 goat snp5480-scaffold1192-178467 14 3719770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773422 Affx-122964070 AX-385260564 14 88655149 TTCTAATGGTTCCCTCCAATCATAGTAGCAAACAG[C/T]AATTTCTTCCTTTGCTGAATCCATCACACTTGGCA Y 2 1 2 1 101000 r 74 goat snp5481-scaffold1192-236908 14 3661312 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407376 Affx-122955265 AX-123277727 14 88747192 GAAGATGTGGAGCTCCACTCTGACCTTGCTTGGAA[C/T]AGGGAGGCCCCTAGAATCAGTGGGACTGATCCCCA Y 2 1 2 1 101000 f 74 goat snp5483-scaffold1192-328951 14 3572943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476306 Affx-1251763813 AX-586011724 14 88795566 TAGCAGAGGAGAAATTTTAGATAACTATAAGTGTG[-/GTGATTCTTTTTTTTTTTTTTAAGAATATATTTGTTTTTATGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TGATTCTTTTTTAGATACAACACCAAAGACACAAT - 4 1 4 1 20000 f 74 goat SV_347 14 88795566 - deletion junction SV-TF-chip 539476559 Affx-1251763813 AX-586011945 14 88795566 TAGCAGAGGAGAAATTTTAGATAACTATAAGTGTG[-/GTGATTCTTTTTTTTTTTTTTAAGAATATATTTGTTTTTATGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TGATTCTTTTTTAGATACAACACCAAAGACACAAT - 8 1 4 1 20000 r 74 goat SV_347 14 88795566 - deletion junction SV-TF-chip 562165295 Affx-1251763813 AX-606940706 14 88795566 TAGCAGAGGAGAAATTTTAGATAACTATAAGTGTG[-/GTGATTCTTTTTTTTTTTTTTAAGAATATATTTGTTTTTATGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TGATTCTTTTTTAGATACAACACCAAAGACACAAT - 8 1 4 1 20100 r 74 goat SV_347 14 88795566 - deletion junction SV-TF-chip 562165433 Affx-1251763813 AX-606940844 14 88795566 TAGCAGAGGAGAAATTTTAGATAACTATAAGTGTG[-/GTGATTCTTTTTTTTTTTTTTAAGAATATATTTGTTTTTATGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TGATTCTTTTTTAGATACAACACCAAAGACACAAT - 8 1 4 1 20100 r 74 goat SV_347 14 88795566 - deletion junction SV-TF-chip 562165615 Affx-1251763813 AX-606941026 14 88795566 TAGCAGAGGAGAAATTTTAGATAACTATAAGTGTG[-/GTGATTCTTTTTTTTTTTTTTAAGAATATATTTGTTTTTATGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TGATTCTTTTTTAGATACAACACCAAAGACACAAT - 8 1 4 1 20100 r 74 goat SV_347 14 88795566 - deletion junction SV-TF-chip 562166036 Affx-1251763813 AX-606941446 14 88795566 TAGCAGAGGAGAAATTTTAGATAACTATAAGTGTG[-/GTGATTCTTTTTTTTTTTTTTAAGAATATATTTGTTTTTATGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TGATTCTTTTTTAGATACAACACCAAAGACACAAT - 8 1 4 1 20100 r 74 goat SV_347 14 88795566 - deletion junction SV-TF-chip 562166257 Affx-1251763813 AX-606941665 14 88795566 TAGCAGAGGAGAAATTTTAGATAACTATAAGTGTG[-/GTGATTCTTTTTTTTTTTTTTAAGAATATATTTGTTTTTATGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TGATTCTTTTTTAGATACAACACCAAAGACACAAT - 8 1 4 1 20100 f 74 goat SV_347 14 88795566 - deletion junction SV-TF-chip 562166396 Affx-1251763813 AX-606941804 14 88795566 TAGCAGAGGAGAAATTTTAGATAACTATAAGTGTG[-/GTGATTCTTTTTTTTTTTTTTAAGAATATATTTGTTTTTATGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TGATTCTTTTTTAGATACAACACCAAAGACACAAT - 8 1 4 1 20100 f 74 goat SV_347 14 88795566 - deletion junction SV-TF-chip 562166516 Affx-1251763813 AX-606941924 14 88795566 TAGCAGAGGAGAAATTTTAGATAACTATAAGTGTG[-/GTGATTCTTTTTTTTTTTTTTAAGAATATATTTGTTTTTATGGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TGATTCTTTTTTAGATACAACACCAAAGACACAAT - 8 1 4 1 20100 f 74 goat SV_347 14 88795566 - deletion junction SV-TF-chip 38407288 Affx-122955330 AX-123277639 14 88889986 GCCTGTTTTACCCCACCTTTCCCCCCTGGTATAAG[C/T]GACTCAAGAAAATGATGACTTTAGTAAAATAAACA Y 2 1 2 1 201000 r 74 goat snp5487-scaffold1192-471745 14 3428807 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397920 Affx-122961936 AX-123268275 14 88929650 GGCTGCAAAGAGTTGGAGATGTCTGAGTGACTGAA[C/T]GACAGCAAGTATTGTTAAGTACCTCATGCACATTT Y 2 1 2 1 201000 r 74 goat snp5488-scaffold1192-511409 14 3388867 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375416 Affx-122979195 AX-123245775 14 88967996 TCTATTCTTTTCTGAGACAATAATATGAAGATCCC[A/G]TATAGACCTAATTCTAAGTCTGTGCTCACCAACGT R 2 1 2 1 101000 r 74 goat snp5489-scaffold1192-549755 14 3350535 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463364912 Affx-1109947407 AX-514849250 14 88982149 GTAAAATGACTTAGCAGAACTTTTGCTACAATAGA[A/C]AACACAGACATGGACATGGAAGTCTAAAATTTGAG M 2 1 2 1 101000 f 74 goat Random2.2K-1482 14 88982149 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 350603469 Affx-1002479548 AX-413837639 14 89003172 TTATACTGCCTTGAATAATGACTTGTGTTAAAATT[G/T]TTTCCCTCGTTTTATTTGCTTCTATCAGGTTCTTT K 2 1 2 1 400000 r 74 goat 14_89003172_RH-map 14 89003172 G T Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38450004 Affx-122922857 AX-123320339 14 89012394 AAAACGGACTTAAGTAAGATATACAGAGGCTTGCA[C/T]GCCTGAAGAAATGGACTTCAAGCTGAACTTTCAGG Y 2 1 2 1 101000 f 74 goat snp5490-scaffold1192-594153 14 3306135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393582 Affx-122965386 AX-123263938 14 89052150 TTTTTTCCTTTTTCAATTTCCCAAGTTTTTCTGCC[A/G]CTTGAATCCGATCTTTACGGTTTTGTGGAATCTGG R 2 1 2 1 101000 r 74 goat snp5491-scaffold1192-633909 14 3265986 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603471 Affx-1002479549 AX-413837641 14 89061553 CATATAATGATCATAAATATCTGTTTTCTGCAGAA[C/T]ATGTCAGTTTTGACTCTGCTTTGTGATTCTCATAC Y 2 1 2 1 101000 r 74 goat 14_89061553_RH-map 14 89061553 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603404 Affx-1002479550 AX-413837578 14 89145966 GGAGCCTGGTGGGTACAGTGCATGGGGTTGCAAAG[A/C]GTTGGACACCACTGAGCCACTAACACTTTGACTTT M 2 1 2 1 303000 f 74 goat 14_89145966_RH-map 14 89145966 A C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320773976 Affx-122967484 AX-385261114 14 89152610 TCCTTACAAAGTGCCTGATAATCGCTTTCAGAATT[A/C]AGTGGATCAATCATCATGTTAGTAGTCATGAAAAG M 2 1 2 1 101000 f 74 goat snp5493-scaffold1192-734369 14 3164531 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603406 Affx-1002479551 AX-413837580 14 89162750 TTGCTTTTGAGTATGCCATATGCATACTTCAAATT[G/T]AGAGTGATAATTATATCTGTAGAAGCTTAAATTTT K 2 1 2 1 101000 f 74 goat 14_89162750_RH-map 14 89162750 T G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320772997 Affx-122948803 AX-385260141 14 89228643 TAACTGACTTGTAGTGTATACATGCTAATATCATT[G/T]CTTAAATTGAGGGCAAATAAAGACTAAGCTTTAAA K 2 1 2 1 201000 f 74 goat snp5495-scaffold1192-810402 14 3087775 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603408 Affx-1002479552 AX-413837581 14 89231093 TATTTATTATGCAGTGGTCATTCTTGAATTAATTC[C/T]CTGGAAATTGTCATTTATTCACTTATTCTATTCCT Y 2 1 2 1 201000 f 74 goat 14_89231093_RH-map 14 89231093 C T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320792722 Affx-122935936 AX-385279702 14 89258123 TAGTGTTTTGAATCTTATTCATGAAATCATTTAAA[C/T]GAATTGCTCCAATAGTTTCTGTCATTACTTGGAAA Y 2 1 2 1 202000 f 74 goat snp5496-scaffold1192-839882 14 3059749 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384006 Affx-122972912 AX-123254364 14 89331591 TGTAGGCGGATTCTTGTCCACTGAGTGACCTGGGA[C/T]GTCCCACCTGTATCCCTCCCACCTCTATCCCTCCC Y 2 1 2 1 103000 f 74 goat snp5498-scaffold1192-913350 14 2985668 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603409 Affx-1002479553 AX-413837582 14 89337208 AAAAAGTGGGTTAGAAGTTAACGAAGGGAGAATAA[G/T]CATATTTTTAAAAACCCTGTGGAAATTTAACTTAA K 2 1 2 1 101000 f 74 goat 14_89337208_RH-map 14 89337208 T G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320785849 Affx-122962028 AX-385272886 14 89368151 CTAGGGCTTATTTGGTAAACGCTGTGACAGTTCGG[C/T]ATCTGGATATGCTAGAAAGAAATGATTTTAAGCTA Y 2 1 2 1 101000 f 74 goat snp5499-scaffold1192-949910 14 2947960 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767712 Affx-122931772 AX-385254946 14 89426455 TAGCAAAAAGCTGAGAAGCTGGGATAGGAATGCAA[C/T]GAACAAAGCCTATTGAAGAATCCCCCTTAGCAGGA Y 2 1 2 1 101000 f 74 goat snp5500-scaffold1192-1008214 14 2889753 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603481 Affx-1002479554 AX-413837650 14 89428169 CATGCATATATAATAAATGTCTGACATTCAGTATT[C/G]CAAATTGACTTTGTTATTCACAATTTCTAGTATGT S 4 1 2 1 101000 r 74 goat 14_89428169_RH-map 14 89428169 C G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38437526 Affx-122931916 AX-123307864 14 89454963 GATCTGACATTTCTTCAAATACAAAAATGTGTCTA[C/T]GTGGTATTGTAGGGTCTGCCAGCATAGCAATCTAT Y 2 1 2 1 101000 r 74 goat snp5501-scaffold1192-1036722 14 2861193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388927 Affx-122968831 AX-123259285 14 89486756 ATTCTATAGGATTTGTGTCCTTATAAGAAGATACA[G/T]CAGAATGGGCTTGTACTCTCTTGCACAAATAAAAG K 2 1 2 1 101000 r 74 goat snp5502-scaffold1192-1068515 14 2829140 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603483 Affx-1002479555 AX-413837652 14 89506881 ATATAATGGGAGAATAATTAATTTTAAGAGCATAC[A/G]TGAGCAGATGGACAATAAGGAAATATAAGCTAGTT R 2 1 2 1 101000 r 74 goat 14_89506881_RH-map 14 89506881 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320773157 Affx-122940506 AX-385260300 14 89534541 TTTTCACCTGGGAATTTTGGTTTGCTCAAAAATAC[A/G]CTCTTGTCAAACTCTAAGTGGTAAATACTTGAAGC R 2 1 2 1 101000 f 74 goat snp5503-scaffold1192-1116300 14 2781526 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603416 Affx-1002479556 AX-413837588 14 89541467 TCCTAAAGGATATCAGTCCTGAACATTCACTGGAA[A/G]GACTGATGCTAAAGTTGAAATTCCAATACTTTGGC R 2 1 2 1 103000 f 74 goat 14_89541467_RH-map 14 89541467 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603418 Affx-1002479557 AX-413837591 14 89559328 GAAGAAACGTGGATTCCCTTTTAATTCTTTGACAT[A/G]TGAGGCATATGACTGATGGTGAAGAAAAGGGGAAA R 2 1 2 1 201000 f 74 goat 14_89559328_RH-map 14 89559328 A G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320790149 Affx-122927595 AX-385277154 14 89583111 ACCAATTTAAAAATTCTCTTTGGGTTTAATTTAGC[A/G]CATTTCCCCTCTGTCCCTACATTTTATTTCTCATG R 2 1 2 1 201000 f 74 goat snp5504-scaffold1192-1164870 14 2732253 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424380 Affx-122941835 AX-123294726 14 89613027 TCACTAGCAGGGCCATGTGAAATTCATCAGGAGCC[A/G]TGAAGTCTAAAGAATCATATCGAAACACCTGGCCC R 2 1 2 1 101000 r 74 goat snp5505-scaffold1192-1194786 14 2700900 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603420 Affx-1002479558 AX-413837593 14 89636658 TTACTTTGCTAGCATGTGAGATGAGTGAAACTTTG[C/T]GGTAGTTTGAACATTCTTTGTCATTGCTTTTCTTT Y 2 1 2 1 103000 f 74 goat 14_89636658_RH-map 14 89636658 C T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38396322 Affx-122963075 AX-123266677 14 89665428 CCTGTTATGTTTTCCCTATTTCTTTCATTCTTAGG[C/T]CATCTCTATTTTCTATATTAATTCAAGAAATATGT Y 2 1 2 1 201000 r 74 goat snp5506-scaffold1192-1247187 14 2645600 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603422 Affx-1002479559 AX-413837595 14 89679320 GATGGTGAGCAGCAGCCTTTGGGTTCTCTGCAACT[C/T]GCTCTGACACTTCCCACGTTGGCCCTCTTTCACGT Y 2 1 2 1 101000 f 74 goat 14_89679320_RH-map 14 89679320 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603493 Affx-1002479560 AX-413837661 14 89715041 AAACTTAGCATTTAAATAATTCAGGATTTTACATT[G/T]TTTTAGATAACCCTGTATTGACAGTTTATAAATCA K 2 1 2 1 101000 r 74 goat 14_89715041_RH-map 14 89715041 G T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320778847 Affx-122965285 AX-385265955 14 89761930 AGCTTTATGGAAACACTAGAAATAGGAATTTGTTA[C/T]GAATAGTTAATATGTCATGAGTTCCCCAAAAAAGT Y 2 1 2 1 101000 f 74 goat snp5508-scaffold1192-1343689 14 2550371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603425 Affx-1002479561 AX-413837598 14 89793829 TCAGAGTCTCTTCTCACTTGAAGTGTCTCTAATTC[C/G]AAAGAAGGATTTGACATATTCAATTTATAATCACT S 4 1 2 1 101000 f 74 goat 14_89793829_RH-map 14 89793829 G C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603427 Affx-1002479562 AX-413837600 14 89824943 AGTAGGGTCTGTCTTTGAAGTACATCCTCCTCTAT[A/T]ATTCTCAGCCAGAAACATGGGTCATCTTTATAAAG W 4 1 2 1 101000 f 74 goat 14_89824943_RH-map 14 89824943 A T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38428467 Affx-122938795 AX-123298810 14 89825772 AACTGGACTGGAGTGAAGACTGGCAGTGGGAAAGT[A/G]TGTCCCCTTCCCTGATTGGTCTCAGTTCAGTCCAG R 2 1 2 1 101000 f 74 goat snp5509-scaffold1192-1407531 14 2487097 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603499 Affx-1002479563 AX-413837667 14 89849902 AATAAGCACACCAACCCACTGAAAGCTATTCAACC[A/C]AAAGTGCCCCTCAAATGTGATGCTAATTGCTATGT M 2 1 2 1 400000 r 74 goat 14_89849902_RH-map 14 89849902 A C Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603432 Affx-1002479564 AX-190042675 14 89941109 GAAAACAACAGAATGGGAAAGACTAGAGATCTCTT[C/T]AAGAAAATTAGAGATACCAAGGGAATATTTCATGC Y 2 1 2 1 103000 f 74 goat 14_89941109_RH-map 14 89941109 T C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38414080 Affx-122949755 AX-123284429 14 90033239 GAGAGCTGCTGAGTGACTAAGAGGTGAATAAATGC[A/G]TACAGGTGAATAAAATGTATACAGCATACATTCAC R 2 1 2 1 101000 f 74 goat snp53168-scaffold8-784628 14 2278076 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420217 Affx-122945539 AX-123290565 14 90062453 CTTTTAAAATTATTTATTCTGAAATATCCTAGAGA[C/T]GTGTGTCCTTAAAGGTATTTCTAGTTTCAATGTCT Y 2 1 2 1 101000 r 74 goat snp53167-scaffold8-755414 14 2250299 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276993 Affx-1111835622 AX-519550501 14 90110452 CAGACATGACTGAGTGAATAATATATACATGTTAA[A/G]TCTCTATGAAAAACATAAGGTTCCCCTTCCCTCAA R 2 1 2 1 101000 r 74 goat Random2.2K-1483 14 90110452 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320780660 Affx-122936748 AX-385267750 14 90174722 AATGAACCATGAATCTGAGACAGAATACTGGAAGA[C/T]GAAGGTGTATAGAGAATAAGATAATACATTTATTT Y 2 1 2 1 101000 f 74 goat snp53164-scaffold8-643145 14 2136404 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421409 Affx-122943974 AX-123291756 14 90204585 GATACAGGGTGAGCTGAAATATCTCATGCAGTGAG[C/T]GAAAGGGCGTACAATTGACCCTTGAGCAACTCAGT Y 2 1 2 1 101000 f 74 goat snp53163-scaffold8-613282 14 2105752 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392347 Affx-122966258 AX-123262704 14 90240375 GTTCTAGTACTCTGGGGTTGGGGATGTCTCGACTG[C/T]AGCCCCAGTTCTGTTCCTGGGAGTGACTCCCCGGT Y 2 1 2 1 101000 f 74 goat snp53162-scaffold8-577492 14 2071197 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450386 Affx-122922084 AX-123320721 14 90276481 CTTTCCTTCTGGACAGGATGAATGGAGAAGCCTTG[C/T]GATTTGATGTGGAAGAAGAGGATTCTGGGGACTCC Y 2 1 2 1 202000 f 74 goat snp53161-scaffold8-541386 14 2034835 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787232 Affx-122978795 AX-385274258 14 90307584 CTCCTCCCTATTTGAATATTCAATATATCTTTTAC[A/G]TCACATCATCTCATGCAAAACCTGATTTTTCAGAA R 2 1 2 1 101000 f 74 goat snp53160-scaffold8-510283 14 2003900 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385146 Affx-122971760 AX-123255504 14 90341877 GAAACTTCTTGCAGAATTGCCCTCATCCCGAGTAG[C/T]ACTGGGAAGCTGTCTGCCTAAGTGGATTATTGCAT Y 2 1 2 1 201000 f 74 goat snp53159-scaffold8-475990 14 1969663 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447325 Affx-122924897 AX-123317661 14 90424185 GGAAGATGGTATGAGCCCCGTCAACAAGTGCACAC[A/G]GCACCTTTTACAGCTTTCCTTTTTTTTCAAGTACG R 2 1 2 1 102000 r 74 goat snp53158-scaffold8-393682 14 1886177 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791936 Affx-122971601 AX-385278926 14 90474285 GGATGAGCACGTGTTTGAGGTCTGACATCTCACCG[G/T]GCTATTTATTGTCTTGGAAAATTATTTAACATCCA K 2 1 2 1 101000 f 74 goat snp53157-scaffold8-343582 14 1836428 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417069 Affx-122947508 AX-123287417 14 90511149 AATATAAACATAAGCCTTATCATGGTAGTATTTTG[G/T]TAATTGTGAGGGTAAAACCAATATTTAATAAAACC K 2 1 2 1 101000 r 74 goat snp53156-scaffold8-306718 14 1798432 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392385 Affx-122966227 AX-123262742 14 90617597 TTACTTTATGGCAAGTTCTGTATGAAATGCCTTGC[A/G]TTTCAGGTTAATGCTGTTGATCACCAGGGAGGACA R 2 1 2 1 101000 r 74 goat snp53153-scaffold8-200270 14 1691233 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402449 Affx-122958615 AX-123272802 14 90659348 TACATTTATAGTTGAGATTTTTGGTAATATCTTCC[A/G]CCTTCTCTTCCTTTTCATCTCTCCCTCCCTCATTG R 2 1 2 1 201000 f 74 goat snp53152-scaffold8-158519 14 1650559 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376690 Affx-122978987 AX-123247049 14 90711976 AAACATTTTATTACATATTGTAATATTACAAGAGG[C/T]AGGTCTCAAATTTGTTGCTGAGCTATCTAGTAACC Y 2 1 2 1 101000 r 74 goat snp53151-scaffold8-105891 14 1597088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400746 Affx-122959896 AX-123271101 14 90764775 GTGCTGTCTCCTTGTGTGGAGAATACACCAAAGAA[C/T]GTGGGCGATCCGTCTGTATGGGTAACTCAGACTGA Y 2 1 2 1 101000 f 74 goat snp53150-scaffold8-53092 14 1544554 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376549 Affx-122977985 AX-123246908 14 90823740 CATAGAAACAGAGAAAGTTAAACAAAATGAGGAGA[A/C]AGAAAATATGTTCCCTATGGAACAACAAGATAAAA M 2 1 2 1 103000 r 74 goat snp49598-scaffold708-1484160 14 1480502 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784584 Affx-122922923 AX-385271632 14 90858090 GGACTGAGAATGCTGCTGCAGACAGTTTTGGAACA[C/T]ACAATCTGCCACACATTGTCAAATCCTTCACTTAT Y 2 1 2 1 101000 f 74 goat snp49597-scaffold708-1449810 14 1445127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400790 Affx-122959827 AX-123271145 14 90886676 AGAAGACTTACTTGATGGGCTCCATCAGGCATGAA[C/T]GTTCTAGGATTCGGAGCTAATGAAGTAGAGTCTGT Y 2 1 2 1 101000 r 74 goat snp1-scaffold708-1421224 14 1416623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272820 Affx-1111833029 AX-519546514 14 90936785 CTAAACATTCATTTCTTAATTAGAGGCTTTTGACT[A/G]TTTGACAGATGTACAGATGGCTGTACAGATATTCT R 2 1 2 1 101000 r 74 goat 14_90936785_AF-PAKI 14 90936785 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425557 Affx-122941438 AX-123295903 14 91072849 CAGCAGTTGAAACCCCATGGGGAAAATGCCCAAGT[A/G]TTTTTTAATTAGAGGAGGTAAGAAATGATAACAGC R 2 1 2 1 201000 r 74 goat snp49593-scaffold708-1235051 14 1231628 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389729 Affx-122968669 AX-123260087 14 91118118 AATCTGTATCAGCCAGTAATGGTGAGGACAACGGC[A/G]TGAATCCCTTTCTGTCTGGAGCACACGCTTCCTTT R 2 1 2 1 101000 f 74 goat snp49592-scaffold708-1189782 14 1188745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791486 Affx-122977184 AX-385278477 14 91148000 GAAATTGCATTCTGGGAAAAGTAAGAAACATACAG[C/T]ATTGTTTTTATGTACATCACATATACATATATTTT Y 2 1 2 1 101000 f 74 goat snp49591-scaffold708-1159900 14 1158546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780341 Affx-122956085 AX-385267436 14 91194385 TGATGTCGAGAAGGAGGAAAAAAGCAGGATTCTAA[C/T]GAGTCAAAAGCCAAGCAAGCATAAAGGGAAGAAGG Y 2 1 2 1 101000 f 74 goat snp49590-scaffold708-1113515 14 1112000 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423985 Affx-122942120 AX-123294331 14 91251788 CCCTCAGGGCCTCGTGTGCACGGGCAGCCCCCATC[A/G]CATCATGGTCTCCGTGTGCACTGCCAAAGTCAATT R 2 1 2 1 101000 r 74 goat snp49589-scaffold708-1056112 14 1054697 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419999 Affx-122945172 AX-123290347 14 91285324 TGCTGGTAATAGCAAGTAGGGACAGAAATTATAAA[C/T]GTAGCTTATCATGTGTTCATTTATGTTTTCAAGTC Y 2 1 2 1 201000 f 74 goat snp49588-scaffold708-1022576 14 1020939 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800172 Affx-122974514 AX-385287095 14 91341219 GACAGTGTTCCCAGCTTAAGGAAGTCCCATCAGCT[A/G]TTGTAGCATTAGTTATGTTGTGGCATTAGCTAACT R 2 1 2 1 101000 f 74 goat snp49587-scaffold708-966681 14 964531 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777806 Affx-122961984 AX-385264924 14 91381407 CAATGAATACATTTGGTGAAAGTCATTTTCATTTA[C/T]GGAAATGTTAAAGAGCAAAGGTAAGTAGAATTTCT Y 2 1 2 1 201000 r 74 goat snp49586-scaffold708-926493 14 923405 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419619 Affx-122945982 AX-123289967 14 91438250 AGCTGTTTGGTTACTATATGTCAGTGAAACGCTAG[C/T]GTATCCTAAAAAGGTCACCCTTTGCCAACAAACAC Y 2 1 2 1 101000 r 74 goat snp49585-scaffold708-869650 14 868624 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393040 Affx-122965630 AX-123263397 14 91467763 GCAATGATAGTACAGACAGTTCTCCTAGGCTTTTC[A/G]CCCAGTACCCCTTGATGGTCACAAGCACAGCACAC R 2 1 2 1 201000 f 74 goat snp49584-scaffold708-840137 14 839871 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436987 Affx-122933146 AX-123307325 14 91501588 GGCGTGAAGTTGGGACTCAAACATTGGGTGTCTGA[C/T]ACCCAAGCTGTGCACTCCATGACCCAAGCAAGCAA Y 2 1 2 1 101000 f 74 goat snp49583-scaffold708-806312 14 805253 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320785382 Affx-122924660 AX-385272427 14 91575589 ATCTGATCTTTGAAAGCAGATTTATTCCTGGTGTA[C/T]AATTTGTATTCCTTTGTAACATGATTTTATTTTCA Y 2 1 2 1 101000 f 74 goat snp49581-scaffold708-732311 14 730230 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447306 Affx-122924913 AX-123317642 14 91659455 ACAACACTATCCTTGAATCTGCTCACACAGCCATA[G/T]AAGCCCTTTGGGGAAAGGCAAAGACAATACATGTT K 2 1 2 1 101000 f 74 goat snp49579-scaffold708-648445 14 645494 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785960 Affx-122940738 AX-385272996 14 91702345 TCGTATAAGTTAAAATATTGAAACATATTCCCCAC[A/G]TTAACTCCCACCCCTGGCTATCAATTAGGAACTGT R 2 1 2 1 202000 f 74 goat snp49578-scaffold708-605555 14 602760 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763203 Affx-986697732 AX-385251134 14 91704916 CCGTATGTGGGTGTAGTGAACCCAGGTGGATATGT[C/T]GTCAACCTTGAGAGCAGTGGGTGCCGTCAAGACAG Y 2 1 2 1 600010 f 74 goat 14_91704916 14 91704916 Ancestral_priority_1043 ancestry 0.594 neutral IMAGE 10K 10K ancestral 320772325 Affx-122968607 AX-385259479 14 91733750 CATCTACCCCTTTACCGAGCTCTTCCCCTGGAAAA[C/T]ACATAATCATATTTTAGGAGAAGTTTTTTCCTTGA Y 2 1 2 1 103000 f 74 goat snp49577-scaffold708-574150 14 571433 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423120 Affx-122942909 AX-123293466 14 91775383 TCCAGGAAAAAACTACTGCTGTTTCTGAATTTATT[G/T]AAAGCCCATGTTTAAAGTCTGCTCCAGAGCTACAC K 2 1 2 1 201000 f 74 goat snp49576-scaffold708-532517 14 529231 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447600 Affx-122924005 AX-123317936 14 91830883 GCCTGGCAGTAGGTGCAGAAGTGACTGTGTGAGCC[A/G]TGACTGGCGTCCACCTGGGGGACACGGTAACGGTA R 2 1 2 1 303000 f 74 goat snp49575-scaffold708-477017 14 473795 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276995 Affx-1111835623 AX-519550503 14 91846508 CAGATTGTTGGTGAATGTTAGTTTTTTTTTTTTTA[A/G]TTTCTCAGTTATCCCTTTACTCAACTTCTGCATTT R 2 1 2 1 101000 r 74 goat Random2.2K-1484 14 91846508 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779435 Affx-122952498 AX-385266538 14 91943623 CAAGAGAACTATACTTGTGTATTGTAAATAACATG[A/G]AAATACAGAAATTAGTGCCAATAGTTCAATAATAT R 2 1 2 1 101000 r 74 goat snp49573-scaffold708-364277 14 360747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799199 Affx-122964183 AX-385286129 14 91972452 AAAATCTTGGCAGGGTAACTATTAAAATACTGTTC[A/G]TGTTTCAATAAAACCTCAATAATCAGAATACAAGT R 2 1 2 1 101000 f 74 goat snp49572-scaffold708-335448 14 332124 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404932 Affx-122956436 AX-123275284 14 92002964 CTGGCACTGCCTCCCTGGTGGCTCTGCAATCCGGC[A/G]CCCTGTCCCCTCATGTCCAAAGGTGGCTCGTCTTT R 2 1 2 1 101000 r 74 goat snp49571-scaffold708-304936 14 301561 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275392 Affx-1111834872 AX-519548966 14 92012059 AGGCCCTGGCTTGCAGCAAATATCTGTGACTAACA[A/C]GACTGGATGAGCCTCACCCCCTGCAGGCTGGCAGT M 2 1 2 1 201000 f 74 goat GoatD01.057210 14 92012059 A C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38411879 Affx-122951199 AX-123282229 14 92042329 CATTGTTTGGCTTTGTGAGAGCCTTTGAGAGAGTG[A/C]GAGGGGAAGAAAATTACTCTTTTATTGTGAGGTTT M 2 1 2 1 101000 f 74 goat snp49570-scaffold708-265571 14 261296 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385601 Affx-122971201 AX-123255959 14 92077279 GTCAGATTGGAAACAAAGTGCACAGCAAATGTCAC[A/C]TGCTTGACTCGTCCTGGAACCACCCTGCCGCCACC M 2 1 2 1 201000 r 74 goat snp49569-scaffold708-230621 14 226444 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411375 Affx-122952238 AX-123281725 14 92134644 GGAAGTGACTCGAGTGTTGTTAAAAGCTGAAGTGT[C/T]AATTAGGTGGCAAGCAGTGGAGACTAGAGGGGACT Y 2 1 2 1 101000 f 74 goat snp49568-scaffold708-173256 14 168999 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415195 Affx-122948991 AX-123285544 14 92169707 TCCTTTCTGTCTTTACTCTGATTTCTTTCTACAGC[A/G]TCATAGTATTGGGTTACCCAAAAAGTTTGTTTGGA R 2 1 2 1 303000 r 74 goat snp49567-scaffold708-138193 NW_017215793.1 10422 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377170 Affx-122978209 AX-123247529 14 92225701 ACCACAGCTGCTAAGAATAAAGTGGTGTCTGTTCT[A/G]CTGGCAGAAGGCACAATGGCCCACTCATGTCATCA R 2 1 2 1 101000 f 74 goat snp49566-scaffold708-82199 14 77734 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433490 Affx-122935035 AX-123303831 14 92298181 GCACAAACAGATCCCAGCATCGATGCGTCCAAGAC[G/T]AACTGATTCTCCGATAGGGTAAAAAATTTTAAATA K 2 1 2 1 201000 r 74 goat snp49564-scaffold708-9719 14 5443 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272771 Affx-1111833030 AX-519546468 14 93528448 ACCCAATAAAAGAATCATTAATTGGAATATGGGAC[A/G]TACTAAAAACCAAACTAAAATGCACTTAAGGTCAT R 2 1 2 1 101000 f 74 goat 14_93528448_AF-PAKI 14 93528448 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276860 Affx-1111835624 AX-519550369 14 93944058 TAAATTTGAGGCTTATATACTCAGTGCATAAACTT[C/G]CTCATTAAAAATTTTCAAGACTCTCTTATGATAAT S 4 1 2 1 101000 f 74 goat Random2.2K-1485 14 93944058 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468274802 Affx-1111834502 AX-519548387 14 94219280 ACACGAGCATCTGGTGACAAGAACCTCTGCAGGGC[A/G]GACATGCCTTCTGCCCTAAGACAGCCCTTGGCCGG R 2 1 2 1 102000 f 74 goat GoatD01.038595 14 94219280 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38430908 Affx-122936860 AX-123301249 14 GCCCACATTAGAATATTAGTTCTGTGAGACCAAGG[A/G]TTCTTGTTTTTCTTTAATTGATGTATCTTCACTTC R 2 1 2 1 101000 f 74 goat snp35531-scaffold428-1317257 NW_017189517.1 48403580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392200 Affx-122966284 AX-123262557 15 1102 AGTATAAAAGAAAAAAAAATCAGACCTTCAAAATG[C/T]AAACACCCTTTTTGTGTGTGTGTGCCATCCACCAT Y 2 1 2 1 201000 f 74 goat snp16099-scaffold1694-477121 15 81898742 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438791 Affx-122931370 AX-123309128 15 36965 TTTATTAAGTATTGAGAGTGGAGGACAGATGTGGA[C/T]GGAATCCTGAGTTCTTGGTGTTAACGGTGCTTTGC Y 2 1 2 1 101000 r 74 goat snp16098-scaffold1694-441258 15 81863346 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795200 Affx-122956947 AX-385282158 15 74598 ATGACCAGATTTAAGTTCACATGGTTTTCTCCATG[C/T]AAACCTATCTGTATCTGAATTTCTTTTTTAATAAG Y 2 1 2 1 201000 r 74 goat snp16097-scaffold1694-403625 15 81825592 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406585 Affx-122956265 AX-123276937 15 116652 CAATGGTAATCATGGCACCAGTATTCTAATAAAGA[C/T]GGACAGTGGACAAATGGAATAAAATAGAAAGTCTA Y 2 1 2 1 303000 f 74 goat snp16096-scaffold1694-361571 15 81782744 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407277 Affx-122955338 AX-123277628 15 146834 AAATACCTTCTTTTATCAAGTTAAATGCTAGATGG[C/T]AAAATACTACATTATTATTTGAGGTTGATTTCTAT Y 2 1 2 1 101000 f 74 goat snp16095-scaffold1694-331389 15 81752008 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272833 Affx-1111833037 AX-519546526 15 244123 CAGACTCTTACATCTTCCATACACAGAAAAGCACC[A/G]GGTCCCCTAACTTGGAAGGTCTGATTTCCTTTAAT R 2 1 2 1 201000 r 74 goat 15_244123_AF-PAKI 15 244123 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468274468 Affx-1111834214 AX-519548059 15 317590 TATGAGCTTTGAGGGTGGTTTTGAAAGAGCTCCCC[A/G]TGCCTGCAGCAACAGAAAGGCGATGTTCAGCTTCA R 2 1 2 1 201000 r 74 goat GoatD01.025881 15 317590 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38436752 Affx-122932287 AX-123307090 15 320110 ATCAGCATAACAAAACTCACTGTACAGATGGCCCC[A/G]CTGTTGGACACCAAGAGTAGGTTGGTCACATAGGT R 2 1 2 1 201000 r 74 goat snp16093-scaffold1694-158113 15 81574781 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425447 Affx-122941519 AX-123295793 15 348672 AGGGAATCTTCACCCATGCCTGAAGAAAGTTACGC[A/G]TCCTTGCAAATGTCATCTGCTGACACCCTCGACAC R 2 1 2 1 201000 r 74 goat snp16092-scaffold1694-129551 15 81545741 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403007 Affx-122958566 AX-123273360 15 431280 GCTCATTGAGCAACCCATGTATTTTTTCTTTTATT[A/G]TATCTCAAAGCAAAATGGCTGTCTAAGGAGGCAAT R 2 1 2 1 303000 f 74 goat snp16091-scaffold1694-46943 15 81462712 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412307 Affx-122950860 AX-123282656 15 470808 CCCTCCCAGACACTGATCTTGGGGTCATATGTCCA[C/T]AGTTTCCATGATGATCACCTTCTCAAAGACCCTCT Y 2 1 2 1 101000 r 74 goat snp16090-scaffold1694-7415 15 81422578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441907 Affx-122928608 AX-123312244 15 523056 TGAAGAAATGTAGTCATTAAAAAGAATGTAAATTA[C/T]GCCTAGAGCACCACTTTATAGAATACCATTAAATT Y 2 1 2 1 103000 r 74 goat snp30071-scaffold329-1489801 15 81371836 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766321 Affx-122969451 AX-385253706 15 704555 TTGTGAGTAACTCTATTTCCCACCAATGGTCCAGG[A/G]TAAGTGGAAAGCTTCTATACCACTTTCCCTGCCCA R 2 1 2 1 101000 f 74 goat snp30067-scaffold329-1308302 15 81185246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429719 Affx-122937614 AX-123300060 15 781676 CATAATTTTGAGGAGTAGAGGATAGTAGTAGATAC[A/G]TGTTAATATATGCTAAGAACTATGATAATACAAGC R 2 1 2 1 101000 f 74 goat snp30065-scaffold329-1231181 15 81107430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778673 Affx-122953016 AX-385265784 15 908716 TCTTAGCTTATTTGTTTTGCTTTAGCCTGGTCTCC[C/T]TCAAGCGTCTAAAAGGCAGAAAAGGCTGTTTTGCC Y 2 1 2 1 101000 f 74 goat snp30062-scaffold329-1104141 15 80963850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803868 Affx-986696269 AX-385290594 15 925923 TAACCACGATAACTTATGGCCCCACCGTGAATTAG[C/T]TTCATTGTATTCCTTTTTGCTTAAATGTCTCATTT Y 2 1 2 1 600010 r 74 goat 15_925923 15 925923 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 38448243 Affx-122924206 AX-123318579 15 1149488 AAACTTCCTGAATGGAACTTCATAGCCTACAAATA[C/T]AAAACATAAGAAAAAGTTAGGTATGTCCTGAATGA Y 2 1 2 1 101000 f 74 goat snp30059-scaffold329-863369 15 80723040 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401645 Affx-122959586 AX-123271998 15 1210267 GTCAAACCCAATAGAATTTTTCTAAGAATAAGAAG[C/T]ACACCTGAAGTTATGCCAGATAAATGTGCTCAATT Y 2 1 2 1 201000 r 74 goat snp30058-scaffold329-802590 15 80661801 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441170 Affx-122929554 AX-123311507 15 1257037 AATTTCCCCACTTTGCTATTGAACAAAAATAACTG[C/T]ACCAGATAAAAGTCTGTGCGTATCATTGTATTAAC Y 2 1 2 1 202000 r 74 goat snp30057-scaffold329-755820 15 80614876 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403099 Affx-122958495 AX-123273452 15 1289183 ATGGCAAATGATTACATGTGTAGATTTTCTTTTTC[A/G]TTCATAGGTTCAAATTCAAGGACTAACAGGAAATG R 2 1 2 1 101000 r 74 goat snp30056-scaffold329-723674 15 80582343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404543 Affx-122957391 AX-123274895 15 1369118 CAAAGAAAAAGGTCTGTCTCGCATACAGAGTTATC[A/G]TTACCATCTTTCTAAATTCCATATATATGCATTAG R 2 1 2 1 103000 f 74 goat snp30055-scaffold329-643739 15 80464328 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426868 Affx-122940483 AX-123297213 15 1397650 AAGAAAAACAATAGATTCACATAATCCCTGGCAAA[C/T]GGAAGAAAAGTCAGGATTAGACACAGGGAATTTAT Y 2 1 2 1 101000 f 74 goat snp30054-scaffold329-615207 15 80435546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415442 Affx-122948711 AX-123285791 15 1491228 CTTAGTTAGGCATAGATATGACATATAAAGGGCTT[G/T]TCAGGTGGCACTAGTAGTATAGAATCTGCCTGAAA K 2 1 2 1 201000 f 74 goat snp30052-scaffold329-521629 15 80341848 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276999 Affx-1111835625 AX-519550507 15 1493263 ACGTGGAGTAGAATATATTTTGAACTTGGGGTAGA[A/G]TCCCAATTCTTATCCTGTTGGAGAGATTCATGTTT R 2 1 2 1 101000 r 74 goat Random2.2K-1487 15 1493263 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396318 Affx-122963077 AX-123266673 15 1527201 CTAATATATTCGACTATTTGGGGCACAAGTTTAAT[A/G]TTCTCCAAAGCAAATATTTCACTCTGTCTTGAAAA R 2 1 2 1 101000 f 74 goat snp30051-scaffold329-485656 15 80305772 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786698 Affx-122974222 AX-385273731 15 1605514 ATACATATATAGAATATGACACACATATAGAATAC[A/G]GATGATAAACTGCTCTAGCTTGCTACAGCCTTATA R 2 1 2 1 101000 r 74 goat snp30050-scaffold329-407343 15 80227563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766018 Affx-986697736 AX-385253437 15 1650985 CTCCCAAAGTGATGGCTGGCTTCCTCGTGGGAGAC[A/G]AGGCCATTTCCTACAAAGCTTGTGCTGCTCAGCTT R 2 1 2 1 600010 r 74 goat 15_1650985 15 1650985 Ancestral_priority_1043 ancestry 0.592 neutral IMAGE 10K 10K ancestral 320783220 Affx-122934775 AX-385270286 15 1700197 TAGCCTGAGTAGTTAGTACCAGATGTTTGTGTATT[A/G]CCAAAGTAGCTAGAATGAACCAAAACCTAGCCAGC R 2 1 2 1 101000 r 74 goat snp30048-scaffold329-312660 15 80132018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404527 Affx-122956689 AX-123274879 15 1775931 AATGATTCCCTCTCCCTGGTAAGCCTCTTCACCAG[C/T]GGGGAGACCAGGTGGAAGAGAAAGGTAGCTTCAGA Y 2 1 2 1 103000 f 74 goat snp30046-scaffold329-236926 15 80055071 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402059 Affx-122958721 AX-123272412 15 1875378 GGTTTTGTAATCAAACTCAAGTACTAACTTTCCCA[C/T]GATACTTTACTTGATGATGTCTATCCTTCAGTAAG Y 2 1 2 1 101000 f 74 goat snp30043-scaffold329-137479 NW_017215297.1 11761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797418 Affx-122951800 AX-385284357 15 1926063 AGAAGAATTTATCACTATAAAGATAAATAGACCCA[C/T]AAATAGATCCTCTATCTATGAGGTTATAGACAAAC Y 2 1 2 1 201000 f 74 goat snp30042-scaffold329-86794 15 79902196 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400374 Affx-122960018 AX-123270729 15 1977218 AGTGAGAGGGTCTGTCATCAGAGGGATTGAGTAAG[C/T]ATTCATTAATATAGAAATAATGAAGAGACAGGGAG Y 2 1 2 1 101000 f 74 goat snp30041-scaffold329-35639 15 79849652 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277001 Affx-1111835626 AX-519550509 15 2114069 CAGTTTCTCCCCGAGTTGTCCTTACCTACGAGGCT[A/G]TGAGACCCCTCAGTCATGCAGCCCAGCACCCCCAA R 2 1 2 1 202000 r 74 goat Random2.2K-1489 15 2114069 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448648 Affx-122923353 AX-123318984 15 2127160 TTAGCCTATGAGCAGAAGGTTAATTTGGACTTAGG[C/T]GATTCCCACTTTTCTTTGTCTACTACTTAAAACTT Y 2 1 2 1 101000 f 74 goat snp45978-scaffold630-163291 15 79343716 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419624 Affx-122945977 AX-123289972 15 2158079 TAATTACATTCAACATGTTCCTTGTCTTTACTGAT[A/G]CTCAAATTTATGCAGTGTAAGATTGTCCTTGGCAA R 2 1 2 1 101000 r 74 goat snp45977-scaffold630-132372 15 79312743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390671 Affx-122967124 AX-123261028 15 2206964 TTTGCCATAGGCTCCCTTTGACTTTTTATTTCATT[A/G]TGATTTCATCCATTCTTATGATGTTAAAATAATAG R 2 1 2 1 201000 r 74 goat snp45976-scaffold630-83487 15 79263147 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449989 Affx-122922872 AX-123320324 15 2275521 GAAGGAGGGCCAGGCACTCCTGATCCTCATCTGCA[A/G]CAAATAATTTGTTTATCTTTCTAAATGATACGAGG R 2 1 2 1 202000 r 74 goat snp45974-scaffold630-14930 15 79195030 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431150 Affx-122936572 AX-123301491 15 2300419 AGGTATATGCCTAAGAGTGGTATTTTTTTCTCATA[G/T]AGTATCCCTGTGTGTGCATGTTAAGTCATCTAGAT K 2 1 2 1 303000 f 74 goat snp48116-scaffold680-429466 15 79164040 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419548 Affx-122945418 AX-123289896 15 2335418 AAGATAATTGTGGTTATCCATGAATGATGCTATTA[C/T]GAATAAATTTTAGCTTTTTCTCTGTCCTCTGTATC Y 2 1 2 1 101000 f 74 goat snp48115-scaffold680-394467 15 79128090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795254 Affx-122938875 AX-385282212 15 2366064 ATATTTGTGGACAATCGACTTTTGACAAAGACTCC[A/G]TGACAAGTCAATGGAGAAAAAATAGTCTTTTAAGT R 2 1 2 1 101000 r 74 goat snp48114-scaffold680-363821 15 79097611 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448247 Affx-122924203 AX-123318583 15 2406216 TTGAAATTTTAGAAGTACTACATTAAAAAAAATTA[C/T]ACACTTGCTCAGCCAAGTGAAAAATAGCAAAAGTG Y 2 1 2 1 103000 r 74 goat snp48113-scaffold680-323669 15 79058701 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450604 Affx-122922014 AX-123320938 15 2436510 TGCTGCAGTCATTTTAGGCCAATGGATGTCACTTA[C/T]GGATGTCTTGTATATGAAAAGAAAAACATTTGTTA Y 2 1 2 1 101000 f 74 goat snp48112-scaffold680-293375 15 79026872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277005 Affx-1111835628 AX-519550513 15 2489404 GCCCAAACTGGAAACAACCCGCAAGTTCATCAACA[A/G]GAGCACAGATAAATGCGTTATGGCTGATTTATACA R 2 1 2 1 101000 r 74 goat Random2.2K-1490 15 2489404 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785828 Affx-122973643 AX-385272865 15 2499091 TGGCATATGCAAATATAAGAACAAAGCCACTCTGC[A/G]CTTCAACATTTAATGGAATCTTCAAGTTAATAAGC R 2 1 2 1 101000 f 74 goat snp48111-scaffold680-230794 15 78964195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785628 Affx-122949975 AX-385272670 15 2565380 ATACTTCAGTCATGAGAAAGTATGAAATATGGATT[A/G]TTTATTCCTAGAAATGAGTTTATATCATTATATAC R 2 1 2 1 101000 f 74 goat snp48110-scaffold680-164505 15 78895608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787117 Affx-122973118 AX-385274143 15 2608632 CAGACTCTTATGAGTCTACTCATGGTCCCAGCATG[C/T]ATCCCTAAATCTTGAGCCCTGGTAGGAATAGGTCT Y 2 1 2 1 101000 f 74 goat snp48109-scaffold680-121253 15 78850734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403882 Affx-122957912 AX-123274234 15 2637596 GGTTTGGGATTTCAGCTATTTCTTTAAGGTGCTAT[A/G]CTCAGTCACTCAGTCATGTCCAAATCTTTATGCCA R 2 1 2 1 201000 f 74 goat snp48108-scaffold680-92289 15 78822475 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766021 Affx-986697738 AX-385253440 15 2665142 GATAAGGAGCCGGAAGGCCTGTCTCTGACTTGTCC[A/T]GTGGTTTTGGGCGACTTATTTCCGCTCTCTGAGAG W 4 1 2 1 600010 r 74 goat 15_2665142 15 2665142 Ancestral_priority_1043 ancestry 0.596 neutral IMAGE 10K 10K ancestral 38445977 Affx-122925888 AX-123316314 15 2671958 TAGAAGACAGAGCAGGCTCTGCTGGTCAGTGACAA[A/C]TTTGAGGCAAAGAATCAGAGGTGTTGGTGGTTGGA M 2 1 2 1 101000 r 74 goat snp48107-scaffold680-57927 15 78787149 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399859 Affx-122960238 AX-123270214 15 2716158 ACAATTCATTGGAACTTAGGAAGATAATGTATGTC[A/G]TGATATTGGGGTGAGGCAGTATCATGTGAAAATAT R 2 1 2 1 201000 f 74 goat snp48106-scaffold680-13727 15 78742587 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792823 Affx-122973317 AX-385279801 15 2735711 CCTTAAATGAAGAGTACAAGAATAACTTCAACTGA[A/G]ATTTAAGGCCTTAGTACAAATTAGCAAGGCTTGTT R 2 1 2 1 201000 f 74 goat snp12167-scaffold1451-5727 15 78720096 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389927 Affx-122968100 AX-123260284 15 2777256 CTTTCCTTCTTTAATTTCATTCTTGTCTTACCTAT[A/G]CTTGACTTTTTCATTTTTCTTAATACCAACATGTA R 2 1 2 1 101000 f 74 goat snp12168-scaffold1451-47272 15 78675089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383947 Affx-122972957 AX-123254305 15 2832097 TTCACTGTATCTTCAGCACATAATATACTTTAGTC[A/G]TATGTATATCATGGTTAGATCATTTCACTATTCTG R 2 1 2 1 101000 r 74 goat snp12169-scaffold1451-102113 15 78618989 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426442 Affx-122940812 AX-123296788 15 2891645 TGTGACTCCTCCATTGTTGGTGGTTTGGGAACTGC[C/T]GTTATTTTACTAAACTGAAGCTTGATCCTCTCAGA Y 2 1 2 1 201000 r 74 goat snp12170-scaffold1451-161661 15 78559172 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272839 Affx-1111833040 AX-519546531 15 2908243 GTTATTCCCTTCTCATTCAGTTCCAGCCACACGTC[A/G]CCTACTACTAGCTTTTCCCTGAAAACATCAAGCAT R 2 1 2 1 201000 r 74 goat 15_2908243_AF-PAKI 15 2908243 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437531 Affx-122931911 AX-123307869 15 2913425 GAGAGTAAGAAATATGCATGTTCAAATTTACAACA[G/T]AATACCAGAGTATTTCAGAGTTGGTTAGACTGATT K 2 1 2 1 101000 f 74 goat snp32205-scaffold365-11004 15 78529341 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781511 Affx-122939818 AX-385268596 15 2965698 TCGAATGGCAATACATGTGAGATACACCATTAATT[A/G]CAATAGTCAATAGCTATTTGAATAAATACAAAGCA R 2 1 2 1 201000 f 74 goat snp32206-scaffold365-63277 15 78476695 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801057 Affx-122945703 AX-385287971 15 3007774 CACTCAGTTTAACAAGAACCAGGATCTTTTGTTAA[C/T]GCAACTTTCTTTCTCTAATAGATAATTCTTTTCAT Y 2 1 2 1 201000 f 74 goat snp32207-scaffold365-105353 15 78433637 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432700 Affx-122936029 AX-123303041 15 3054630 TCTTGACTATCAAAAAGAATACACTTGACAATACT[A/G]CACCCTCTTACAGGGAGTTCCTCTGAGGATGCTTA R 2 1 2 1 101000 r 74 goat snp32208-scaffold365-152209 15 78384837 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792645 Affx-122925516 AX-385279625 15 3117477 TACTGTAAGAAGAGGGTAATAGGGAACAGAATAGA[C/T]GAGACAAGTGAAAGGATACTCAGAGAATTTGGTTT Y 2 1 2 1 101000 r 74 goat snp32209-scaffold365-215056 15 78321038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425929 Affx-122941605 AX-123296275 15 3158574 TTAAATTGTAACATTAATAAAATTGAACTGTTTGC[G/T]CCTGCTATTGAACTCAGTCAAACATTTCTGGTTCA K 2 1 2 1 101000 r 74 goat snp32210-scaffold365-256153 15 78279873 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379607 Affx-122976016 AX-123249965 15 3175241 TTATGTGAATTGAACACATTTGCCTCTCTTACCTT[A/G]CCTTCTTAGAAATAACAAAGAGGCATTTTAAAACA R 2 1 2 1 101000 f 74 goat snp24679-scaffold2510-257248 15 78262653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377088 Affx-122978272 AX-123247447 15 3204525 TACCTGCTGCTTCCCACTTTTCCTCTTCCTTCTGT[A/G]TTCTTCACCTGAGTTGTTATTTAGTTTGAATTTTT R 2 1 2 1 201000 r 74 goat snp24678-scaffold2510-227964 15 78233727 A G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393301 Affx-122965432 AX-123263657 15 3258793 ATATTACTATACGCATCATCAATGCTTATAAGAAA[C/T]AAGGCATGCTTCATTCTTTTTCTGAAAAAGAAATT Y 2 1 2 1 101000 f 74 goat snp24677-scaffold2510-173696 15 78179664 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777285 Affx-122954371 AX-385264407 15 3290074 TATCAAAATGTGCTACAGAGTTTCACTTAAAATTC[A/G]TGCCCAAACCCATCTCTATGGAAAACAGATGCCCT R 2 1 2 1 101000 r 74 goat snp24676-scaffold2510-142415 15 78147676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428966 Affx-122938874 AX-123299308 15 3341475 ACATGATAAATTAATAACATGCAAGTGGATATAGG[C/T]AATGAATTATTTTTACTTCTTCATGAACTATGTGA Y 2 1 2 1 101000 f 74 goat snp24675-scaffold2510-91014 15 78095766 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405204 Affx-122956909 AX-123275556 15 3371507 CCAGTGGGAGGGAAACTGAGGAAGCTAGAGAGAAC[A/C]AGGGTAACACAAGGAGCACAGTCCTCAGGTTCAGG M 2 1 2 1 101000 f 74 goat snp24674-scaffold2510-60982 15 78066160 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445351 Affx-122926384 AX-123315688 15 3407865 ACAAGTTCATTCTCTATGTCTGCATCTCTATTCTT[A/G]CCCTGCAAACAGGTTTATTAGGATCACTTTTACAG R 2 1 2 1 201000 r 74 goat snp24673-scaffold2510-24624 15 78029455 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276869 Affx-1111835629 AX-519550378 15 3464112 TGTGAAGGAAGAGTCCATGTTCCTAATCACAATTG[A/G]TACAGAACAAGCAAGGAGTTATATGGCAGGAAAGA R 2 1 2 1 201000 f 74 goat Random2.2K-1492 15 3464112 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421295 Affx-122944103 AX-123291642 15 3479787 CAACATAATAACATTCCTAGAGGATGAATAGTAAA[C/T]GGTAGATGGCTATTCTGAGAGATGAGAGTAGTGGA Y 2 1 2 1 201000 f 74 goat snp10986-scaffold1394-318123 15 77955531 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419760 Affx-122945875 AX-123290108 15 3522859 CTGACCACACTCTCAGGATATTCCACCCACATCTG[C/T]TGAGTGCTTTACAGCCTTCAGAGGCTTTCATTGTC Y 2 1 2 1 101000 r 74 goat snp10985-scaffold1394-275051 15 77912790 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276871 Affx-1111835630 AX-519550380 15 3543263 TTCAGGTAAAGATGGAGACATAGTCAGGCCAGCAG[A/G]GCCAAGGTGCTGGGATATGTGCATTGGAACTGGAG R 2 1 2 1 101000 f 74 goat Random2.2K-1493 15 3543263 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432528 Affx-122935558 AX-123302869 15 3561709 CTTTTTGAAATAGTTTTCTATTTCTTGGTCCACAG[A/C]AGCCCCTGTTTGTTGGCCTATGTCCTGCCTTCTCA M 2 1 2 1 101000 r 74 goat snp10984-scaffold1394-236201 15 77874151 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781961 Affx-122925230 AX-385269041 15 3604531 CTGCCCTTATAACTGTTTACAGAGAAAACGACATG[C/T]ATATTGTACGAAAGCACATTTTGTTTCTGTGATTA Y 2 1 2 1 101000 f 74 goat snp10983-scaffold1394-193379 15 77830128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380731 Affx-122975140 AX-123251089 15 3639407 TTATTGGGACCGTCTACATGCAAGGCCAGATGCTG[C/T]AAGAGACAGATGGAAATTCACTAATTATTTACTTT Y 2 1 2 1 102000 f 74 goat snp10982-scaffold1394-158503 15 77795612 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783835 Affx-122931299 AX-385270891 15 3692760 CACACAGTACTTTGCCATATGGCCTTGGCCAATTT[A/G]GTTAACATCTCTACTTGTTTGTGACAATTACAGAG R 2 1 2 1 101000 f 74 goat snp10981-scaffold1394-105150 15 77736807 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772332 Affx-122951645 AX-385259485 15 3750169 GCTTTCTTTTTAATGCTCTCCTTATTTCATTATTC[C/T]AAAGCTAATCTACTTTAAAAGAAGCAGTTAATTTC Y 2 1 2 1 101000 r 74 goat snp10980-scaffold1394-47741 15 77679732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784018 Affx-122923602 AX-188486839 15 3788090 TTCAAAGGGAATTATGCCAGAGGGCACAAGAAAAA[G/T]AAAAATAAAAATCATCCTGTTCCCTACTTTGAAAA K 2 1 2 1 102000 r 74 goat snp10979-scaffold1394-9820 15 77642148 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394459 Affx-122964579 AX-123264814 15 3849855 TTTTCGTATGGGCAAGGCTATTTTAAGTTTACAGA[C/T]AAGACCAAAATCCTGTAAGGAAAATATCAGGAAAT Y 2 1 2 1 101000 f 74 goat snp22565-scaffold2236-51846 15 77579885 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276873 Affx-1111835631 AX-519550382 15 3975431 TAATATTTGCATAACAACTTCTATTACTCTCTTGG[A/G]TCTCTATTGAGAGTCTAATATAAACACAACCATGA R 2 1 2 1 101000 f 74 goat Random2.2K-1494 15 3975431 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320764980 Affx-122967483 AX-385252558 15 3999022 TCAAGGAATTTCTTCTCTCCAAATCAATAGAACCA[C/T]AGAACCAGTATGAGTGTATCAGCTGCTAAAAACAC Y 2 1 2 1 101000 f 74 goat snp22567-scaffold2236-201013 15 77432182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801424 Affx-122976338 AX-385288333 15 4051535 TGGAAGTGGTTTTAGTCACTGACCTAATAAATATG[C/T]ATTGAGCTCCAATGTAAATAAACCCAGCAATGTAT Y 2 1 2 1 101000 r 74 goat snp22568-scaffold2236-253526 15 77379208 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403714 Affx-122958032 AX-123274066 15 4064253 TCAAAAATGGTAGGACCAAGGCATTCCGTACAGAA[A/G]GGGACGTAGTTTTGAATGCATGGAGATATGAGAAG R 2 1 2 1 101000 f 74 goat snp24896-scaffold2544-35525 15 77366408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405379 Affx-122956304 AX-123275731 15 4096449 ATAAAATATGGGAGTCGAACTATGGATGGAGGTTC[A/G]TGACACTGTACAGGAGGCAGTGATCAAGACCAATC R 2 1 2 1 303000 f 74 goat snp24895-scaffold2544-3329 15 77333667 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377875 Affx-122977263 AX-123248234 15 4127495 TCAACAATGTATGGAAAATAGAAATTATAAGATAA[C/T]AAATCTTACAGTGGAAAGGATCTAAGAAAACATCT Y 2 1 2 1 101000 r 74 goat snp5094-scaffold1175-27618 15 77303126 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763213 Affx-986697742 AX-385251143 15 4250025 TTTGGCTTAAATATACCTTAAAACATGCAAGATTC[C/T]TTATATTTTTCCACTCTTATTGTTGGCACTTTTTG Y 2 1 2 1 600010 f 74 goat 15_4250025 15 4250025 Ancestral_priority_1043 ancestry 0.696 recommended IMAGE 10K 10K ancestral 38403792 Affx-122957976 AX-123274144 15 4252329 AAAATTTCAACTGATCATCTACATAATTAACTAGG[C/T]GAAAGAAAAACAGTAAGAAAAGTAGGCCACTGGAT Y 2 1 2 1 201000 f 74 goat snp5096-scaffold1175-152452 15 77177924 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402060 Affx-122958720 AX-123272413 15 4308196 GATATCCTGGCAAGGGAGAACAGATGGCAGAGGAG[C/T]AGGTGGACGTGGAGTACATCTCTCTCCACGGACAC Y 2 1 2 1 103000 f 74 goat snp5097-scaffold1175-208319 15 77121080 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772308 Affx-122939631 AX-385259463 15 4341837 GCTTTGTTTATCATAACAACGGGTAAAGCTGCTAA[C/T]AGGGTACACGTTCTGTGCTAACGACACTAATAGAG Y 2 1 2 1 201000 r 74 goat snp5098-scaffold1175-241960 15 77086652 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428805 Affx-122938396 AX-123299147 15 4377115 AATTTTATTTTGTATTTTAAAATTCCTTAAATTTT[A/G]CCATCTTCACAAATCAGAACTACTTTGGAAATCTC R 2 1 2 1 103000 r 74 goat snp5099-scaffold1175-277238 15 77051284 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799716 Affx-122954854 AX-385286644 15 4508986 AATCTTATACTTGATGCTTGTGTATATTCTACAAA[A/G]TCTTTCATTGGTAGCCTTAACTTGTTTTGCTTTGT R 2 1 2 1 101000 f 74 goat snp5101-scaffold1175-409109 15 76917492 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426783 Affx-122940549 AX-123297129 15 4552876 GTTCTCTTGGGTAAACCTCAGTGTGGGATGAGGGG[C/T]GCTCTGAAGGACATCGCTTTCTCCCTACCTGCCCC Y 2 1 2 1 201000 r 74 goat snp5102-scaffold1175-452999 15 76872660 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406208 Affx-122956130 AX-123276560 15 4586471 AAGTGAGACAATTTCTTTCCCTGCCATTGTCCTCT[A/C]TATAAAGCTGTTGGTTAGTATGCTGCCTCCTATTT M 2 1 2 1 101000 r 74 goat snp5103-scaffold1175-486594 15 76845597 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437166 Affx-122932132 AX-123307504 15 4616634 TTCTCTTGGCTTCTGTTCACTTCTTCCCAGCAGAT[A/G]TATCTGAACTAAAACACAAGACTGATGAAAATAAC R 2 1 2 1 201000 r 74 goat snp5104-scaffold1175-516757 15 76814966 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793688 Affx-122965989 AX-385280660 15 4704854 GACATAATTATGAGATACCACACGATATTAAGAGT[A/G]TATTTCAGTTACATGCAGCAATATGAACTTCAGAG R 2 1 2 1 101000 r 74 goat snp5106-scaffold1175-604977 15 76728469 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476307 Affx-1251763814 AX-586011725 15 4707923 ATTGGATCATTTCTCATCTGAAATTGCACTCCTGT[-/TTAAAAACATTCTAGGGAGAGGGAAAGATGGCGGAGGAATTAAATAAAAAATAAAAAAAATAAAAATAAAAAAATAAAAA]TAAAAACATTCTAAGAGTTCTAGAAAAAAATATAT - 8 1 4 1 20000 f 74 goat SV_136 15 4707923 - deletion junction SV-TF-chip 539476560 Affx-1251763814 AX-586011946 15 4707923 ATTGGATCATTTCTCATCTGAAATTGCACTCCTGT[-/TTAAAAACATTCTAGGGAGAGGGAAAGATGGCGGAGGAATTAAATAAAAAATAAAAAAAATAAAAATAAAAAAATAAAAA]TAAAAACATTCTAAGAGTTCTAGAAAAAAATATAT - 8 1 4 1 20000 r 74 goat SV_136 15 4707923 - deletion junction SV-TF-chip 562165679 Affx-1251763814 AX-606941088 15 4707923 ATTGGATCATTTCTCATCTGAAATTGCACTCCTGT[-/TTAAAAACATTCTAGGGAGAGGGAAAGATGGCGGAGGAATTAAATAAAAAATAAAAAAAATAAAAATAAAAAAATAAAAA]TAAAAACATTCTAAGAGTTCTAGAAAAAAATATAT - 8 1 4 1 20100 r 74 goat SV_136 15 4707923 - deletion junction SV-TF-chip 562165911 Affx-1251763814 AX-606941320 15 4707923 ATTGGATCATTTCTCATCTGAAATTGCACTCCTGT[-/TTAAAAACATTCTAGGGAGAGGGAAAGATGGCGGAGGAATTAAATAAAAAATAAAAAAAATAAAAATAAAAAAATAAAAA]TAAAAACATTCTAAGAGTTCTAGAAAAAAATATAT - 8 1 4 1 20100 f 74 goat SV_136 15 4707923 - deletion junction SV-TF-chip 562166009 Affx-1251763814 AX-606941418 15 4707923 ATTGGATCATTTCTCATCTGAAATTGCACTCCTGT[-/TTAAAAACATTCTAGGGAGAGGGAAAGATGGCGGAGGAATTAAATAAAAAATAAAAAAAATAAAAATAAAAAAATAAAAA]TAAAAACATTCTAAGAGTTCTAGAAAAAAATATAT - 8 1 4 1 20100 f 74 goat SV_136 15 4707923 - deletion junction SV-TF-chip 562166105 Affx-1251763814 AX-606941513 15 4707923 ATTGGATCATTTCTCATCTGAAATTGCACTCCTGT[-/TTAAAAACATTCTAGGGAGAGGGAAAGATGGCGGAGGAATTAAATAAAAAATAAAAAAAATAAAAATAAAAAAATAAAAA]TAAAAACATTCTAAGAGTTCTAGAAAAAAATATAT - 8 1 4 1 20100 r 74 goat SV_136 15 4707923 - deletion junction SV-TF-chip 562166115 Affx-1251763814 AX-606941523 15 4707923 ATTGGATCATTTCTCATCTGAAATTGCACTCCTGT[-/TTAAAAACATTCTAGGGAGAGGGAAAGATGGCGGAGGAATTAAATAAAAAATAAAAAAAATAAAAATAAAAAAATAAAAA]TAAAAACATTCTAAGAGTTCTAGAAAAAAATATAT - 8 1 4 1 20100 f 74 goat SV_136 15 4707923 - deletion junction SV-TF-chip 38381633 Affx-122974765 AX-123251991 15 4764407 CAACTCTACTTTAGCTATTACCACAATACAGTTTC[A/G]TTCTGTCCTTCTTACATAATGTGACCTATCCAAAA R 2 1 2 1 101000 f 74 goat snp5107-scaffold1175-664530 15 76668748 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768075 Affx-122947663 AX-385255280 15 4860050 GAATTTTTGTCATGTTTGTCAGTCAACCTCTGTTT[A/G]TCATATCGCTGAACATATTGTGGTTAACTTCTTTT R 2 1 2 1 101000 f 74 goat snp5109-scaffold1175-760173 15 76572924 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449187 Affx-122923523 AX-123319522 15 4890032 TCTTTATCCCTCATTATATTTATTGGGATATAATC[A/G]TTTTCCCATGGTGTGTTAGTTTCTGCTGCACAGTG R 2 1 2 1 103000 r 74 goat snp5110-scaffold1175-790155 15 76542991 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766032 Affx-986697744 AX-385253449 15 4958446 TAGGCCATGACAACCAACAAGACAATCTCGGCTCC[A/T]GCAAAGAAATGTTCAGCAAAGACCTGAGTCATGCA W 4 1 2 1 600010 r 74 goat 15_4958446 15 4958446 Ancestral_priority_1043 ancestry 0.522 neutral IMAGE 10K 10K ancestral 38422124 Affx-122943554 AX-123292471 15 4984234 CTGTTCTTGATGCTAGGATCAATAGAAGAAGGTAC[A/G]CAGAAAACCTCAGGAAAAAGCAGGAAATTAAAACC R 2 1 2 1 101000 f 74 goat snp5112-scaffold1175-884357 15 76460411 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422485 Affx-122943316 AX-123292831 15 5025784 TTTATGGCACAAGAGACTGAGTAATTTATGATACT[A/G]GAGATGCTGGATTTTTAGTGAAGATACTATAGGAA R 2 1 2 1 101000 r 74 goat snp5113-scaffold1175-925907 15 76419046 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777949 Affx-122941042 AX-385265065 15 5065997 GGGCTTTGCTTTAACATAACTGAAAATGGATTTCC[A/G]AATGGGAGTCCTTGGTTCTTATTTTTTGGGGCCCT R 2 1 2 1 101000 r 74 goat snp5114-scaffold1175-966120 15 76378998 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415693 Affx-122948536 AX-123286042 15 5072178 TTAAATATCTGAGTCAAAATATGTGGAACTCTAGA[C/T]AGCCCATATAAGGACTCTAAAACTGTCGCTTTTGA Y 2 1 2 1 101000 r 74 goat snp80-scaffold100-532 15 76373221 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803297 Affx-986696270 AX-385290140 15 5080304 GAATGGTTCCTCAAGTTGACCAGGATGACAATGTA[G/T]GAGGACACCAAGAGGAGGAAGGAGAAGACAGAGAT K 2 1 2 1 600010 f 74 goat 15_5080304 15 5080304 Ancestral_priority_1043 ancestry 0.716 recommended IMAGE 10K 10K ancestral 320763181 Affx-986697710 AX-319880036 15 5092766 AATGAGGCCATTGCCCACCACCGTGGCCAAGTACA[C/T]GGGCAGAAACACCACAAAGCACGCTCTCTGCACCT Y 2 1 2 1 600010 f 74 goat 15_5092766 15 5092766 Ancestral_priority_1043 ancestry 0.43 neutral IMAGE 10K 10K ancestral 320765979 Affx-986697713 AX-385253403 15 5092767 ATGAGGCCATTGCCCACCACCGTGGCCAAGTACAT[A/G]GGCAGAAACACCACAAAGCACGCTCTCTGCACCTC R 2 1 2 1 600010 r 74 goat 15_5092767 15 5092767 Ancestral_priority_1043 ancestry 0.474 neutral IMAGE 10K 10K ancestral 320787254 Affx-122959767 AX-385274280 15 5138285 ACAAAAAGCAAACACAGAGGAAGTTTCTGGGAAGA[C/T]AGTGGAATAGGAAGCCTCAGAAATGTATCTCCCCA Y 2 1 2 1 101000 r 74 goat snp81-scaffold100-66639 15 76306241 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800762 Affx-122953388 AX-385287679 15 5175691 AGATAACTTCCAGAAAGGGAAATACAAATGGCTAA[C/T]GAAATATACAATGGTATGTCATCTTAGTTAATAAA Y 2 1 2 1 101000 f 74 goat snp82-scaffold100-104045 15 76268191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277012 Affx-1111835632 AX-519550520 15 5202353 TTCCTGGGGTTTTCATGGGGTTCTCCAAATTCTTT[A/G]CATAAGATATTTAAGGAAACAGCCAAGTCCTACGA R 2 1 2 1 201000 r 74 goat Random2.2K-1495 15 5202353 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38411130 Affx-122951896 AX-123281480 15 5252880 ATTGCCAGAAAGTTATCATGATAATTCTCAGAAGG[C/T]AAATATGTATTCTTCTTTTCTACATCTCCGTGTAG Y 2 1 2 1 101000 f 74 goat snp83-scaffold100-181234 15 76189552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449211 Affx-122923504 AX-123319546 15 5282247 TAATTGGAAAGCAGCATCACTGAAGGGTATGGTGC[C/T]GTCTGGTCATTCAAATAAGGAGCTTGTCTCAGCAC Y 2 1 2 1 101000 r 74 goat snp84-scaffold100-210601 15 76160958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793841 Affx-122972675 AX-385280810 15 5337309 TGGGAATGCGACCCCTTGCAAGAAAGCTTCTGTTA[C/T]ACCAGAACTTGGCGTTCTGTCTTAAAAGACTTTTG Y 2 1 2 1 202000 f 74 goat snp85-scaffold100-265663 15 76105387 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445117 Affx-122926187 AX-123315454 15 5393113 GAAGGCAGCAGACACAGAGTTTGCAGGAGGCTCTG[C/T]AGCGGTACTGGTAGAACTCTGGAGCCAGATGACCT Y 2 1 2 1 101000 r 74 goat snp86-scaffold100-321467 15 76049374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425767 Affx-122940726 AX-123296113 15 5430715 ATTCACTAGCACTAGGTGTGAGGTATCAGGTGTCT[G/T]GAGGGAAATAGTAACTCATGGGCAGATCTTGTTAG K 2 1 2 1 101000 f 74 goat snp87-scaffold100-359069 15 76011633 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272794 Affx-1111833049 AX-519546490 15 5451542 CTCCATTTTCTAAAGGTTAGAGGCAAGTTATAAGA[A/C]CGAAAATGACACAAGAAGATTGAAAGCAATAGATA M 2 1 2 1 101000 f 74 goat 15_5451542_AF-PAKI 15 5451542 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320792798 Affx-122963844 AX-385279777 15 5489158 AGCAAGTCTTATAAGTAAAAACAATTTTGTAGGCA[A/G]TATTTCAATGTAGTGTTTAATGTGTTCATTATAAA R 2 1 2 1 101000 f 74 goat snp88-scaffold100-417512 15 75951911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791946 Affx-122975958 AX-385278936 15 5535993 GACTGGTACAAAAAAAGAATGTAGTGACTGTTGCC[G/T]CTTTTCTCACCCATATTTCTAATTAAAGAAGTAAA K 2 1 2 1 101000 f 74 goat snp89-scaffold100-464347 15 75905698 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401149 Affx-122959373 AX-123271502 15 5609984 TCTAGCTATTAGAGTTTAAGAATAATCTCAAACTT[A/G]TAAACTTTAGAATACACAAGTAAGCACTCTTAGCA R 2 1 2 1 101000 r 74 goat snp90-scaffold100-538338 15 75830152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776843 Affx-122972663 AX-385263967 15 5661486 ACCTGTGCTTTCTCTACTTCTATATCCCTTGATAA[C/T]GGCTATGTTGAACCACCTATATCTTTATCTTAATC Y 2 1 2 1 101000 f 74 goat snp91-scaffold100-589840 15 75778441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438252 Affx-122931422 AX-123308590 15 5729876 TCGCTCACATAAATTTTCAGATTAGTTTGTTAAGT[C/T]TTAATGTTTTAGCTGGGATTGCATTCAATAGTTAA Y 2 1 2 1 101000 f 74 goat snp92-scaffold100-658230 15 75709254 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789671 Affx-122925250 AX-188612374 15 5781238 TTCTGCCCTTCTTCCTGGCCTGCCTTAAAAATTTC[A/G]TACTTGCTTAGATTTCCTGTTCCTCATATTTATGT R 2 1 2 1 101000 f 74 goat snp93-scaffold100-709592 15 75656786 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802679 Affx-122936677 AX-385289578 15 5854353 CACAGTAACATAACAGAGTAAAATATTTGATGCCC[A/G]TAATAATGATTCTAAGGCATGAACAAAAGATCAAA R 2 1 2 1 101000 f 74 goat snp94-scaffold100-782707 15 75583426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772363 Affx-122927768 AX-385259515 15 5886533 TGTATTACGGAGTTTAAGCATTCATCCTGGATCTA[C/T]AATCATCTTGGAAATACTGACCCTAACCTGAGGAT Y 2 1 2 1 101000 r 74 goat snp95-scaffold100-814887 15 75550923 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394445 Affx-122964591 AX-123264800 15 5918553 AAGCAATTGAAATAGATGCGAGAGCCAGAGGACTT[A/C]TTTGATTATATATAAACAAATATCCATTTCCTGCA M 2 1 2 1 103000 f 74 goat snp96-scaffold100-846907 15 75518506 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406501 Affx-122955150 AX-123276853 15 5985826 AGAATTCAGTCCTGGTGTGAATGTTCTAGAGTGGG[A/C]TAACTGGGAGCTGTGGACCATTAGGCCTTCCTGAA M 2 1 2 1 101000 f 74 goat snp97-scaffold100-914180 15 75448126 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786191 Affx-122956232 AX-385273226 15 6020862 CCCCAATTGTTGAGAATATTAGTTACTATTGGCAC[A/G]TAGCAATGTCCCTTGTCCTTAGAGAACTGAATCAT R 2 1 2 1 101000 r 74 goat snp98-scaffold100-949216 15 75412653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449796 Affx-122922421 AX-123320131 15 6059991 TTTCAATATATATATTGTCTTCATTTTTCGATTTT[A/G]CTCCTCTTATTGTGCAATACTCGGCACTTCTAACT R 2 1 2 1 101000 r 74 goat snp99-scaffold100-988345 15 75372847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429040 Affx-122938310 AX-123299382 15 6146404 TTGGTCCCTGATAATTGCTACCTAACTACCTGTAA[C/T]AAAAAGCCATGTTCTCAAGGCCTATATGTCCTTGG Y 2 1 2 1 101000 f 74 goat snp101-scaffold100-1074758 15 75286105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389233 Affx-122969046 AX-123259591 15 6194176 TTTGAAGGTGAGTAATGTTGGCCAAGATCATCTTC[C/T]AGGTGGGGCACAGTTGGAGCCCCAGGAGATCTGGA Y 2 1 2 1 101000 f 74 goat snp102-scaffold100-1122530 15 75240063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385417 Affx-122971333 AX-123255775 15 6243903 TGTTATATAAAACACTTTACAAAGTAATTTGCCAG[C/T]AGAGACAAGACGCAATGGCAGAAGTTAATTGTATC Y 2 1 2 1 201000 f 74 goat snp103-scaffold100-1172257 15 75191800 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798133 Affx-122944589 AX-385285069 15 6306903 CGTTCTATGGACTCTTGCTAAAATATTCTTTTTCA[C/T]AGTTCACTTTTGTAGAAAGATTTTCTTACATATAT Y 2 1 2 1 101000 f 74 goat snp104-scaffold100-1235257 15 75127718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397081 Affx-122962716 AX-123267436 15 6343068 GAAATTGGGTGATTTCCCACGGTTTCTTCTCTTCC[A/G]CTTGTGTACCTTTTCTTTGTTCAGTTCTTTATTTT R 2 1 2 1 101000 f 74 goat snp105-scaffold100-1271422 15 75101779 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420029 Affx-122945149 AX-123290377 15 6385561 ATTAATGTATCGTATGCAGACATACACATATGCAC[A/G]TATACATACCCCATTTCACAAATGCATATAGTCTC R 2 1 2 1 201000 r 74 goat snp106-scaffold100-1313915 15 75057793 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417191 Affx-122947317 AX-123287539 15 6414911 CTGCTCGTGGTCTTCAAATTCTTTTGCTTCCTTTT[C/T]ACCAGGAAAACATTTGAAAAATGCTGTCCTCATGA Y 2 1 2 1 201000 r 74 goat snp107-scaffold100-1343265 15 75028424 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410928 Affx-122952051 AX-123281278 15 6463506 CACTTTGGTGGTCTCTAGCATTAACTTTTCAGACA[C/T]AGAGTCTGAAAGAACAGCATACATTGAGTCTCTGC Y 2 1 2 1 101000 f 74 goat snp108-scaffold100-1391860 15 74980485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775010 Affx-122939201 AX-385262142 15 6525025 GAAAAACAATCACTCTTTCCTTTGGAAGAAAATCA[C/T]GCTATTGCCAGTATAGCAATTTGATAAAAGTCCAC Y 2 1 2 1 102000 f 74 goat snp109-scaffold100-1453379 15 74918028 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442874 Affx-122927664 AX-123313211 15 6570566 GGGAAGCCCAAGACATGGCTTTTTCCAAACCGCAT[A/G]CTTCCCTGGCTTCAGATCAGTAATCAAGTAATACA R 2 1 2 1 101000 r 74 goat snp110-scaffold100-1498920 15 74872341 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385488 Affx-122971277 AX-123255846 15 6607030 TAATGCCCATATACCTAGCTGAACTAGAAGCCCTC[A/G]GATGTTAGCATTAAAATTGTGCCTGTATTGCTTGT R 2 1 2 1 201000 r 74 goat snp111-scaffold100-1535384 15 74835562 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792780 Affx-122967251 AX-385279759 15 6639999 TTAGAAAAATTTGGTTGTTGTTTTGATGGAGAGAA[C/T]GGTAAAGAAATTTTGTAAGAGAGGAATGGAAAGAA Y 2 1 2 1 101000 r 74 goat snp112-scaffold100-1568353 15 74801474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782122 Affx-122947288 AX-385269200 15 6687058 ATTAATTGTGTGTTTTAGTACATTACTAAGTATGT[A/C]TATCTTACATATAAGCCACTGCAGGCTTAACTTAG M 2 1 2 1 101000 r 74 goat snp113-scaffold100-1615412 15 74753995 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434802 Affx-122934813 AX-123305143 15 6734977 GGAAGCTCACCCTCAGAGGCTACTGAATCTAATTA[A/G]AAACAAAGAGGAATTTATTCATAATATCAGAGATT R 2 1 2 1 101000 f 74 goat snp114-scaffold100-1663331 15 74705932 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766441 Affx-122977935 AX-385253813 15 6763491 CAATAAAAACAGTCATCAGAGTAAAGGAGGGAGAA[C/T]TTTTATCACCAAAATATTCTATCTAAAGATGTATA Y 2 1 2 1 102000 f 74 goat snp115-scaffold100-1691845 15 74677496 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768134 Affx-122948705 AX-385255333 15 6814027 CTAGCTAGTGTTAAAATGCTTAAGAGTTGAAAATC[A/G]TATCTTCAATGTTATCACGACATTTTCTGGGAAGA R 2 1 2 1 101000 f 74 goat snp116-scaffold100-1742381 15 74626137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440537 Affx-122929330 AX-123310874 15 6886242 CCTTCCAACACTCTCCCATCCTCACCTTCATCTGT[A/G]CTTCCTAACTTTCTGAAAACACTTCCAGAAAATGC R 2 1 2 1 101000 r 74 goat snp117-scaffold100-1814596 15 74553117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795134 Affx-122931522 AX-385282092 15 6936790 TATATTTCTTGTGCTTATTACACATTTCCACCTAC[A/G]TGAGCTTCCAAGCCAACATGACCTTCTACTCCATA R 2 1 2 1 101000 r 74 goat snp118-scaffold100-1865144 15 74502414 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799668 Affx-122927909 AX-385286596 15 6995883 AAAGAACAAAACGCGTTCTGTAACGAGTCCACCTC[C/T]AACTTCAGTCAACAAAGTACAAATCAAGAAGGGGT Y 2 1 2 1 101000 f 74 goat snp119-scaffold100-1924237 15 74443262 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785844 Affx-122933972 AX-385272881 15 7037552 TCTCCAAGAACGTGCAAAAACAACCAAAACCAAGC[A/G]CAATTTTGGGTCACTTGGTTTTATAGGAATGTGTA R 2 1 2 1 201000 f 74 goat snp120-scaffold100-1965906 15 74401256 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383757 Affx-122972439 AX-123254115 15 7080885 TAAAAGAGTCTTGGACGGGGAAACGGGCTACACGC[A/G]TGCCTCTTCAGAGGAGAGAGTTACTACAGCTGTGG R 2 1 2 1 101000 r 74 goat snp121-scaffold100-2009239 15 74357167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406715 Affx-122955760 AX-123277066 15 7111266 ATTCCTAACCATAGTAATCAGAGAACCCTGGGAAA[G/T]CTAGTCAGATACGTATAAAAGAGTTACACATAAAT K 2 1 2 1 201000 r 74 goat snp122-scaffold100-2039620 15 74326903 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380209 Affx-122975488 AX-123250567 15 7140249 CAGTTCCATTAATTATATTCTCACAAGGCACCATG[C/T]ACTTCTGTTCCACAATCCTCAGTGCATTTGTAAAC Y 2 1 2 1 101000 f 74 goat snp123-scaffold100-2068603 15 74297708 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779772 Affx-122967343 AX-385266872 15 7179192 AACAATTATTAAATGAGCAGTGAGTCCACATTAGT[G/T]GAGTAATTATGAAGTATTTCAATTTTCCAGGAGAA K 2 1 2 1 101000 f 74 goat snp124-scaffold100-2107546 15 74259030 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769419 Affx-122920047 AX-385256590 15 7240925 CTGGACTTTCCAATAGTTTCCAAGATTACATAGAA[C/T]GAATGAGCTTTGCTTCATATTAATGACTAATATTT Y 2 1 2 1 101000 f 74 goat snp125-scaffold100-2169279 15 74197938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416084 Affx-122948327 AX-123286433 15 7297816 CCATCACAACCAAAGCATGGAGACCACTTCCCCCA[A/G]AGAGACACATAAAGAACAGTGATCTTGCTCTAAAG R 2 1 2 1 101000 r 74 goat snp126-scaffold100-2226170 15 74141365 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454065 Affx-122919387 AX-123324398 15 7397955 TAAATAAATCAATAATTTCTTTTCATGACAACATT[A/G]CCCATGTTTTTTTGAAAAATAGTAGTTTATGTATG R 2 1 2 1 303000 f 74 goat snp128-scaffold100-2326309 15 74040265 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427047 Affx-122939820 AX-123297392 15 7497083 TTTCAAGCTTGCTACTGTATTTATTGCCAATCAGC[A/G]TTCAGAGTTTACTAGGGCACTAATGGATCTTGATC R 2 1 2 1 101000 r 74 goat snp130-scaffold100-2425437 NW_017213028.1 18738 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443057 Affx-122928137 AX-123313394 15 7537270 CTGAGCTAAACCATAGTTTCTGTGACTTGAAAACT[C/T]CCAGGGAGACATATGACATTTGGAAGTGTGAGCAT Y 2 1 2 1 201000 f 74 goat snp131-scaffold100-2465624 15 73882882 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420299 Affx-122945030 AX-123290647 15 7573882 ATAAATTAAAATGTACAAATTTTGACCCTGAAATC[A/G]TTCCATGTGAGAAGATGGCTCCATTATTGGACCAG R 2 1 2 1 101000 r 74 goat snp132-scaffold100-2502236 15 73851371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380018 Affx-122975596 AX-123250376 15 7621011 CACAATATATGCTCAAAGTCCACTTAGTCGATTTG[C/T]AATTTGAAAATTTACAGAGAGGGGAAATGGAGATA Y 2 1 2 1 101000 f 74 goat snp133-scaffold100-2549365 15 73805395 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784915 Affx-122929107 AX-385271962 15 7655607 ATTTCTATTTCAAAGAGCTTATAGTCTAATTGGAG[C/T]GATGAAAACCCAACACATGTGAAAGCTTACCATTT Y 2 1 2 1 101000 r 74 goat snp134-scaffold100-2583961 15 73770704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375825 Affx-122978551 AX-123246184 15 7700247 ATTTATAGTTCTAAGGAAGGTCTATTATGACTACA[C/T]GTTAGAAGTATTTTAAATTAATTCTCTGAATGTTT Y 2 1 2 1 101000 f 74 goat snp135-scaffold100-2628601 15 73724580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782447 Affx-122929303 AX-385269523 15 7762662 ATGGTAAACAGAGTTTTAGAACTACAGATTAGGAC[A/G]CAGAATTAGCTTGTGTATATAGGTCAGTAAACTAA R 2 1 2 1 101000 r 74 goat snp136-scaffold100-2691016 15 73662277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276876 Affx-1111835633 AX-519550385 15 7764914 GAACAAAAGTACAAAATGGCTTGAGCAGTGCCTGT[A/G]TGGGTGTGTGTGTTCTCAACTGGGGCCTCAGCTGG R 2 1 2 1 101000 f 74 goat Random2.2K-1498 15 7764914 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419996 Affx-122945174 AX-123290344 15 7816678 CTAGGTTAATGGAAGAACAAAGAAACAGAATTTGT[A/C]TTAGGGAGAAATGCAATCTCAATCAGATATTTGGG M 2 1 2 1 101000 r 74 goat snp137-scaffold100-2745032 15 73608004 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780581 Affx-122971628 AX-385267672 15 7897116 TTAATAAAAATATTCCTAAGTGTTATGCACTTGGC[A/G]TATCTGTGGAACAGAAAGAATTCTGCTGTGGTTTA R 2 1 2 1 201000 r 74 goat snp139-scaffold100-2825470 15 73527703 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384780 Affx-122972011 AX-123255138 15 7943096 TGCTTTAAATAATACTAGTCAGCTGATGTAGCTAC[A/G]TAACATTTGAGAAGTAAGGTGTAAATATGGACAGT R 2 1 2 1 101000 r 74 goat snp140-scaffold100-2871450 15 73481721 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272803 Affx-1111833058 AX-519546498 15 7963987 TGGGAGATGTTCCTGGACCTTCCCATCAGACCAAC[A/G]TGGTCAGAAAGACCACCCTTTTATCTTGGACATCC R 2 1 2 1 102000 f 74 goat 15_7963987_AF-PAKI 15 7963987 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438289 Affx-122931396 AX-123308627 15 7991445 AATGGCAGGATTCTTGAGACCCAAATCCCAAGGGT[A/G]CCTGATATTACAGACCATGTAGGCTAAAGTGGGTC R 2 1 2 1 101000 r 74 goat snp141-scaffold100-2919799 15 73432398 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793439 Affx-122969285 AX-385280416 15 8049093 GCAGCAAAGAGTTACATGGAAAATGATAGGGAATT[A/C]TTGCTCTGAGTGACCAGTAAATGTTTTAGAGCAGA M 2 1 2 1 101000 f 74 goat snp142-scaffold100-2977447 15 73374299 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397206 Affx-122962394 AX-123267561 15 8081866 CCATCTGAATTATAGCCCATTTTCTCTGTAACTGG[C/T]ACCCACCCTCCTTGGTCTAGAAATGAAAATTGGTA Y 2 1 2 1 201000 r 74 goat snp143-scaffold100-3010220 15 73340844 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442036 Affx-122928401 AX-123312373 15 8134331 TGATACAGGGTTTTCTTCCCAGTTGAAGTGGGCTA[C/T]GTCAGGAGCTCAGCATATGGAAAGAGAATGTCTCA Y 2 1 2 1 101000 r 74 goat snp144-scaffold100-3062685 15 73289955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419158 Affx-122945739 AX-123289506 15 8174675 TTCATTTGAATGCTTCTTTCTATCAAAATCTTCTT[A/G]CTGTTAGAAATGGTAAGTAAAATGCCTCAGAAGTA R 2 1 2 1 101000 r 74 goat snp145-scaffold100-3103029 15 70802777 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766356 Affx-122964245 AX-385253736 15 8253719 ATTCTGATGGGTTTTGTCATGTATACATGGTCCTT[A/G]CTTATACATTGGGATATCTACCAGCTATCTGTTGG R 2 1 2 1 101000 f 74 goat snp147-scaffold100-3182073 15 73174398 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443753 Affx-122927122 AX-123314090 15 8297488 ATAGTTTCCTGAAATTCTGTAGAACTGATATGTCT[A/G]TTTGCTTATGGCGCATTTTTCCTTAAACTTGCTAT R 2 1 2 1 101000 r 74 goat snp148-scaffold100-3225842 15 73130762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783300 Affx-122926564 AX-385270365 15 8351904 TTTGTCTCCATGGCAAAAGCCAAGGGGAAAAATAA[C/T]ATATGTTATAAGCAAAGATGAAGAATATCATTTTG Y 2 1 2 1 201000 r 74 goat snp149-scaffold100-3280258 15 73074723 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798502 Affx-122978530 AX-385285435 15 8368080 CTAACATCTAGATTTTAGTCTCTATAAATAACATG[C/T]ATTACAGTCAATGTAAAGTAACTGAATATATACTT Y 2 1 2 1 201000 f 74 goat snp24184-scaffold2464-12027 15 73058892 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801745 Affx-122934064 AX-385288653 15 8412130 AAAGGCATTTCCCAAGAGAGTTCATATGGTAAACA[C/T]TACTCAGGGTTCAGAATCTATCTTTACTTATCACT Y 2 1 2 1 101000 f 74 goat snp24185-scaffold2464-56077 15 73015380 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793378 Affx-122958333 AX-385280356 15 8461140 CATATGCATGTGAATGCTTTTTTCATCACCTTTAT[A/G]TTCTTGTTCTCTCTTTATAATTTAATGATTATCAC R 2 1 2 1 201000 r 74 goat snp24186-scaffold2464-105087 15 72966736 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782445 Affx-122943069 AX-385269521 15 8523533 TAACCAATCGTATTTGTTAGCTGAATCTGAGTATG[C/T]AAAACACACAGATATGACCAACTGTGGGATGTGAG Y 2 1 2 1 101000 r 74 goat snp24187-scaffold2464-167480 15 70780563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416494 Affx-122947790 AX-123286842 15 8556250 GGGAAGTTGTGATACCAGTTCCTTCACCTTCAATT[A/G]CAGATGCATTCACCAAAGTGTGAGAAAGAAAAACA R 2 1 2 1 101000 f 74 goat snp24188-scaffold2464-200197 15 72871129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768909 Affx-122925454 AX-385256086 15 8585966 TCAGTTAAGCATAAGAGTCATTCACTCTAGATTCC[A/G]TAATCTCTGTCACAATTTTTATCTAATGTTTTTTA R 2 1 2 1 101000 f 74 goat snp24189-scaffold2464-229913 15 72840324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441141 Affx-122929575 AX-123311478 15 8628116 ATTAATGGCTAAGTGTTAACAGCAGATCTAAATTG[C/T]AACTGAGAAATAAGATTTCATCTTGAGAAAAATCA Y 2 1 2 1 101000 f 74 goat snp24190-scaffold2464-272063 15 72797541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423784 Affx-122942827 AX-123294130 15 8639018 AGTATATATATTTTTTGTATTAGGGTGAAACAAAT[A/G]TATAATCTAAAACCGAAAACATTTACATCTTAAGG R 2 1 2 1 101000 r 74 goat snp14012-scaffold1553-820427 15 72786768 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771859 Affx-122947783 AX-385259015 15 8670337 AAAAAATATATAAATGCATTCACCTTTCATAGGTT[A/G]CATATCAAAATGTAACTTTAGAAGAGGACTGTTAC R 2 1 2 1 201000 f 74 goat snp14011-scaffold1553-789108 15 72755173 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413511 Affx-122950632 AX-123283860 15 8704822 ATAAGACACCATGTAATTTGCAAGCATATTTCAAA[C/T]CACTGTGTCATGTTTACTAATGCCTCATTGACTGA Y 2 1 2 1 101000 r 74 goat snp14010-scaffold1553-754623 15 72722523 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396891 Affx-122963227 AX-123267246 15 8738238 TTCCCATTATTGTAATATATCTTAAATCTTAGATG[A/C]TCTTTCTTTTGTGATAGTGTTGAAGTGATAACACA M 2 1 2 1 101000 r 74 goat snp14009-scaffold1553-721207 15 72688791 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404136 Affx-122957094 AX-123274488 15 8789349 AATGTTCATTGTAATCAGAAACATTTTACACAGCT[A/G]TAAAAAGTAGGATGCATTTGACAAGTTACAGCTGT R 2 1 2 1 101000 r 74 goat snp14008-scaffold1553-670096 NW_017189771.1 18649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378494 Affx-122976658 AX-123248853 15 8836828 CCCTAAATTCTGGCTTTGTATGTGAATATTATATC[A/G]TAATGGCACCTCCTTTTCACATTTGCACCTTATTG R 2 1 2 1 101000 f 74 goat snp14007-scaffold1553-622617 15 72589306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393261 Affx-122965459 AX-123263618 15 8900568 ATAGTATTGAGGTATGAAAATAATTTGTCATTTCC[A/G]TGATTTTTCCCATTTCTGAGTGATAATGCATTGCA R 2 1 2 1 101000 r 74 goat snp14006-scaffold1553-558877 15 72525244 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452219 Affx-122920802 AX-123322552 15 8960268 CAAAGGAGAAAGAAATATGCTGAGCTGATAATCAT[A/G]TCTCTTGTCTGATGAATATTTCAAAAATAACACTT R 2 1 2 1 101000 f 74 goat snp14005-scaffold1553-499177 15 72464806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799664 Affx-122941931 AX-385286592 15 8996700 TTTGTTTTTCTAAAATTGATCTCTGTTTCTTTGGA[G/T]CCCATATTCCTAAAGTCAGAACAAAGAAAACAAGA K 2 1 2 1 101000 f 74 goat snp14004-scaffold1553-462745 15 72428149 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769087 Affx-122927575 AX-385256262 15 9045167 TGTCACTCAAGATCTACTAAGCATCATTTTTTGGA[C/T]GAATGTGGCCAAAGGATATCTGTGCAAAACCAGTT Y 2 1 2 1 101000 r 74 goat snp14003-scaffold1553-414278 15 72379167 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405144 Affx-122956955 AX-123275496 15 9088595 TTCAATTAACTCCTTGCTATTACAAGTGGGTTATA[C/T]ATGACTATGGAGGATTAACGCACATTGAAAGAGAG Y 2 1 2 1 101000 r 74 goat snp14002-scaffold1553-370850 15 72333164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418153 Affx-122947098 AX-123288501 15 9123965 ACAGCATGGATATATACACAAGAGCACTATTTCTT[A/G]TTTAGTTAAACTGTCAAACACAAATTTAAATATTT R 2 1 2 1 201000 r 74 goat snp14001-scaffold1553-335480 15 72297345 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780893 Affx-122926189 AX-385267980 15 9156515 TATATGATGAGGTTGGCCTCAGTACCAGAAGTTTA[C/T]AGACTTATGATAGAAGGGCACTTTTGATATTGTCA Y 2 1 2 1 101000 r 74 goat snp14000-scaffold1553-302930 15 72263729 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793424 Affx-122937154 AX-385280401 15 9185947 GTTAGAAAGATTATTCACTATTTTCTGGCAAGACC[A/G]CAGTTATACTTGCCTTGAAGTTAGCAGAATGTGAT R 2 1 2 1 201000 f 74 goat snp13999-scaffold1553-273498 NW_017214224.1 7332 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433057 Affx-122935752 AX-123303398 15 9218066 CACTACTGTTACAAGTTTATCTTTTTCTTCTCTTT[A/G]TGTTTTAGTTCTGTTTTTATGAGAAAAATTTTGTT R 2 1 2 1 303000 r 74 goat snp13998-scaffold1553-241379 15 72202844 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767710 Affx-122929256 AX-385254945 15 9265715 TCAGGAACCTAGATCAACATCAAAAGCAGCATCAG[C/T]AGGTAATGTCAACCCCTTAGGGAACTTGATGGAAC Y 2 1 2 1 101000 f 74 goat snp13997-scaffold1553-193730 15 72152539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450417 Affx-122922060 AX-123320751 15 9294238 CACTGGTGAATAGGTAAAAAATATAGCCCTATAAT[A/G]TTAAGAAGAAGTAATTTCCTAACAATGTAATTTTA R 2 1 2 1 101000 f 74 goat snp13996-scaffold1553-165207 15 72124753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396274 Affx-122963308 AX-123266629 15 9333358 CTTGTATGTGGTCTTATCAGTTATATTCAGTATTT[C/T]GTGGTGGATATAGAAACTAACATCCTCATACATTT Y 2 1 2 1 101000 r 74 goat snp13995-scaffold1553-126087 NW_017214192.1 21275 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782838 Affx-122972012 AX-385269909 15 9384411 TTGACTCTTCCTGGACTCTTGCCTTGTGTTAGCCA[C/T]GATTCTAGCAGAGTTCCCCTCTTTAGCTGGCATCA Y 2 1 2 1 101000 f 74 goat snp13994-scaffold1553-75034 15 72029428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380084 Affx-122975546 AX-123250442 15 9436716 AAGGCAGAAAAATCATTTGAATTTTGTATAAATAT[A/G]CATGGGTACAATCATTCTAGTTTTCCAAATATGAG R 2 1 2 1 101000 r 74 goat snp13993-scaffold1553-22729 15 71976544 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449160 Affx-122923545 AX-123319495 15 9460175 TGCCAATGTAATACCAAATCAGTAATTCTATTTAG[C/T]GCTTAAAATGTAGTGCTAGATTACTTGATGATGCT Y 2 1 2 1 101000 r 74 goat snp37650-scaffold4630-27704 15 71953061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798122 Affx-122923486 AX-385285057 15 9507585 TAAAGTGATCTGACATATTACAGCAGATAATGCTT[A/G]CACAGACCATGTCAATTCTGTCTCAAGTGTGGCTC R 2 1 2 1 101000 r 74 goat snp53225-scaffold801-592498 15 71780525 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451606 Affx-122921635 AX-123321939 15 9543607 GACTACTGGAAAAACCATTGCTTTGACTATAGGGA[C/T]ATTTGTCAGCAAAGGTCTATTTTGAGGAGCAGATA Y 2 1 2 1 201000 r 74 goat snp53224-scaffold801-556476 15 71744253 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277018 Affx-1111835635 AX-519550525 15 9546514 TTTCTGAAGTATTTGGTGGTGTGGCACGTGGCAGT[A/C]AAGATAGGAAATGGGAAGACACATCTTTAATCTTA M 2 1 2 1 201000 r 74 goat Random2.2K-1500 15 9546514 A C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403122 Affx-122958119 AX-123273475 15 9578398 TTTAACCTATAAATTTCAACTTAAGTATAAATTTC[A/G]TTTTGACAGTGTTCTAGACTAGAGCATATACTAAA R 2 1 2 1 101000 r 74 goat snp53223-scaffold801-521685 15 71711247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800049 Affx-122926252 AX-385286972 15 9689409 TAAGTCCAGGCTAAATCTTCAGCAAAACAAGGTTT[C/T]GTCTTTGATTTGTCACAATTGATTCTTGGTATTTC Y 2 1 2 1 101000 f 74 goat snp53220-scaffold801-410674 15 71598765 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416920 Affx-122948049 AX-123287268 15 9744867 TGATGGAAAGAGTCATATTCATGCATATCTATCCA[C/T]GTAAACATATTGGTGATCAACAGAGATTTCAAACA Y 2 1 2 1 101000 f 74 goat snp53219-scaffold801-355216 15 71543017 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377933 Affx-122977219 AX-123248292 15 9806431 ATGAAATATTTTCCATTTGCTCAATTAATCCTTTA[C/T]ATTAAAAATATCACATCCCTCTTGAAAACTTTTGG Y 2 1 2 1 101000 r 74 goat snp53218-scaffold801-293652 15 71480275 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440277 Affx-122930639 AX-123310614 15 9875674 ATCACTGTAGTTCCTTTCAACACTGGGTAGGGTTG[A/G]CCTATGGCACCAATAGGATATTGTGGAAATGATGA R 2 1 2 1 101000 f 74 goat snp53216-scaffold801-224409 15 71409807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401601 Affx-122958866 AX-123271954 15 9907114 TGTGAGATACCATACTGAGTCTCAGCCACCCAGTG[A/C]TTGGGAGACTTGAACACTCAATTTTCATTCATTAC M 2 1 2 1 201000 r 74 goat snp53215-scaffold801-192969 15 71378488 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404272 Affx-122957048 AX-123274624 15 9945624 ATTTATTCATCCCTTTATCTGACAAACAATAATTT[A/G]AGACACAGCTTCACCTGGGAAGTTTTTCAAATTCC R 2 1 2 1 201000 f 74 goat snp53214-scaffold801-154459 15 71339635 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440490 Affx-122929366 AX-123310827 15 9997070 AAACAGAATATCACAATTTTTAGAAGTATTGAAAA[A/C]ATTTCATTTTGTTATTCTCTCTTTTTTAAAAACAA M 2 1 2 1 103000 f 74 goat snp53213-scaffold801-103013 15 71287722 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439045 Affx-122930332 AX-123309382 15 10095405 ATACTATATACTCACAAATATACAATTCTCTATTT[A/G]TATCCTCATTGCATGTTTCATATCAAATAAAAAGT R 2 1 2 1 101000 r 74 goat snp53210-scaffold801-4678 15 71187919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767724 Affx-122921616 AX-385254958 15 10106417 TCTATTCTCAAAGAAAAATGCATTTGCAATTCAAC[A/G]TGTAGAATCAAAAGACTCTTTTGACAGTTCTAAAT R 2 1 2 1 101000 f 74 goat snp6687-scaffold1240-1468772 NW_017211974.1 6373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402437 Affx-122958622 AX-123272790 15 10193749 TAGAACTGATAAATTTCCAATTGACAAATACCGTT[A/G]CTCACAGTCAGTATTCATTATTTCCTCAGGCCATA R 2 1 2 1 201000 f 74 goat snp6686-scaffold1240-1381440 15 70520146 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800391 Affx-122929075 AX-385287313 15 10231563 TGAAAACTATAATCTTCTACTACCATCATTATCCC[A/G]CTGTATCGGGATAATATATTGTAGGTACAAGAGAT R 2 1 2 1 101000 f 74 goat snp6685-scaffold1240-1343626 15 70480461 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398127 Affx-122961697 AX-123268482 15 10271485 ACCTGTTAAAAGCAAAAGAAAAAGAAATTAATTTT[A/C]TTTTTTGGGGGGGAGATACATGCACAAATCCCTTT M 2 1 2 1 303000 f 74 goat snp6684-scaffold1240-1303704 15 70440674 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771649 Affx-122925511 AX-385258807 15 10300792 GTCAGACAAGACACCTGTATAATGTATCTCAAAGT[A/G]TCTTTTTGTTCACTGACTCCCTTGCCACCAACACT R 2 1 2 1 101000 r 74 goat snp6683-scaffold1240-1274397 15 70412066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803250 Affx-122948322 AX-385290103 15 10354652 AAAAATCAAATTGTGCTTAGCATCTAACTTAGATT[A/G]TCCCAGTTAATTCTCACTGTAGTATAGAAGTGAGA R 2 1 2 1 101000 r 74 goat snp6682-scaffold1240-1220537 15 70358568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389428 Affx-122968361 AX-123259786 15 10391491 CTGAGTAGAGCAAGTTCTCAAAGAACTCCTCAAAG[A/C]AAGATCATCCTCACCAGTCCTTCTAACCTCACTGG M 2 1 2 1 201000 r 74 goat snp6681-scaffold1240-1183698 15 70320698 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428886 Affx-122938934 AX-123299228 15 10436579 AATGAAGATGGTTACCTGAAAACTTATTAAAAGCA[G/T]TACAAGCCGTGTGTGATCGCATCCCTTTAATGCTA K 2 1 2 1 101000 r 74 goat snp6680-scaffold1240-1138610 15 70275499 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272773 Affx-1111833031 AX-519546471 15 10479701 TGACCCTAAAAGGAGTCACAGGCTTCCCAGGTTAC[A/C]CCTGCCAATGCAGGAGATGCCAAAAGACCTGGGTC M 2 1 2 1 103000 f 74 goat 15_10479701_AF-PAKI 15 10479701 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433287 Affx-122935210 AX-123303628 15 10481992 TGAGGACGTGTGCTGTGTTTAAGTGAGTCTGCAAA[C/T]ATAGGTATGTAACTCATTATAAAATACGTTACCCA Y 2 1 2 1 101000 r 74 goat snp6679-scaffold1240-1093197 15 70229522 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391242 Affx-122967384 AX-123261599 15 10565575 CCAGTAGTGTTGGTGTTTTGCTGAGAATAGGAAAC[A/G]TTAAATGGTAAGAAGACACACACACACACAAACAT R 2 1 2 1 101000 f 74 goat snp6677-scaffold1240-1009614 15 70144420 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405414 Affx-122956281 AX-123275766 15 10599397 AAAAAGCACATCTGGTGAGCAAAAATGGGAGAGAA[A/G]ATGAGAAAATGGTTTACTTTGGCTTAGGTTGAGTA R 2 1 2 1 101000 r 74 goat snp6676-scaffold1240-975792 15 70109261 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799136 Affx-122951043 AX-385286066 15 10643237 ATCATGCACATAACTGTGTATCTCAGGAACACTAT[A/G]AAAATAAACATGATTAGAGCAAAGTGAGCAAAAGA R 2 1 2 1 101000 f 74 goat snp6675-scaffold1240-931952 15 70064226 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429370 Affx-122938556 AX-123299712 15 10718361 TCAGCTTCCTCTTGCTGGATGTGAAAAGCTTGAAT[A/G]AGAAAGGGTTAAAACAATTCTAAGAGGTTCACAAA R 2 1 2 1 101000 f 74 goat snp6674-scaffold1240-856828 15 69988075 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396114 Affx-122963413 AX-123266469 15 10756503 TAAATTTCTTTATTATAAAACTTTAAAATTATACT[C/T]AGTAGGTAGAATTTATGTGCTTTAATCATCAGCAC Y 2 1 2 1 103000 r 74 goat snp6673-scaffold1240-818686 15 69949720 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436779 Affx-122932265 AX-123307117 15 10817088 GGAATTGATTGACTGCATTCAGTAATATATAAATG[C/T]GTTTAATAAATACTTATTAAGCTTCTCTTCTGAGA Y 2 1 2 1 101000 f 74 goat snp6672-scaffold1240-758101 15 69889695 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781174 Affx-122979011 AX-385268259 15 10870537 CTGTCCTGTGGGACAGTGGTGTAGTACAATTGTAC[A/G]CTGTGGCCAGTCAAGTCGTATACTCTCTTCTATTT R 2 1 2 1 101000 r 74 goat snp6671-scaffold1240-704652 15 69847911 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400045 Affx-122960776 AX-123270400 15 10901699 TTTTTTTTCATCAAACTTTGATTTTTGTTTCTGAG[C/T]ACAGAATAATCTATGTTACCAAGTATTCCCATTAA Y 2 1 2 1 101000 r 74 goat snp6670-scaffold1240-673490 15 69816350 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402471 Affx-122958601 AX-123272824 15 10939381 CTGACCAGGAAGTGCAGCAGTATTTGTCCTTTATC[A/G]TTGTTAGCACAAAGTCAGTAAACTATGGGCCCACA R 2 1 2 1 202000 r 74 goat snp6669-scaffold1240-635808 15 69778606 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415954 Affx-122948430 AX-123286303 15 10986305 TGCCATGTGAATGTGCACAGGGAGCAGGTCACAGA[A/G]TGGTGAAAATGTGAATAAGGCAAACAGGTTTCTAG R 2 1 2 1 101000 r 74 goat snp6668-scaffold1240-588884 15 69731407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438272 Affx-122931407 AX-123308610 15 11023114 GCAACTTTCATTTCTGGTACGTTGGTTTTATATAG[G/T]AAGTCCATTTTAGCATGTTTATTTCTTCAGGCCCT K 2 1 2 1 101000 f 74 goat snp6667-scaffold1240-552075 15 69694249 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401106 Affx-122959407 AX-123271459 15 11084785 ATCCCGAAAACTTGTTCAGTCTCCCCTGTGACCTT[A/G]TGAAGGAGAGAAAACATGTCCCTTTGTCACCTAAA R 2 1 2 1 201000 r 74 goat snp6666-scaffold1240-490404 15 69632262 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393907 Affx-122965105 AX-123264262 15 11124635 TCTTTGATATTTTGCCATCTCTGTCATAAGAGGAG[G/T]CCAGTGAGGATAAATGCAATGGGATGGGACAAAGT K 2 1 2 1 201000 f 74 goat snp6665-scaffold1240-450554 15 69592581 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792998 Affx-122938390 AX-385279976 15 11160100 GAAAACCAGTAGAATTATATACCTTAAACATTTTC[A/G]TAACCCCAGGTGAATAAATGAAATCTCAGCAACTT R 2 1 2 1 101000 r 74 goat snp6664-scaffold1240-415089 15 69555512 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440869 Affx-122929245 AX-123311206 15 11202145 TATATGGTATATCAAGAAAAGATTTTTATGTTCAA[C/T]TTCAGTCAAGGCTTTTAAAACATTTGTACAATTGC Y 2 1 2 1 101000 r 74 goat snp6663-scaffold1240-373044 15 69516599 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435935 Affx-122932749 AX-123306274 15 11240216 AAAGGGTTAGACCTTGGACTTGAAATTCTCACATC[A/G]TCTGCTCTGTCCAATCTATTGGTAACTTGGTCAAA R 2 1 2 1 201000 r 74 goat snp6662-scaffold1240-334973 15 69477729 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426447 Affx-122940808 AX-123296793 15 11296660 ATCATAGTTAATGGTGAATGATTGCAAATATTTGC[A/G]TTAAGCACAGTCTCTTGCCTGCCCATACCAGTCCT R 2 1 2 1 101000 r 74 goat snp6661-scaffold1240-278529 15 69420599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797145 Affx-122972853 AX-385284085 15 11340216 GCAACAGTGATCATATCACTTTGATGGGAAGCACC[A/G]TTATGAAAATGAAGGTAAGCCACAGAAGAACTGTG R 2 1 2 1 101000 f 74 goat snp6660-scaffold1240-234973 15 69377172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437074 Affx-122932671 AX-123307412 15 11379041 ATGATTCCCTAGTTTTAAGCCAAACTTGTCCCTGC[C/T]TTTGGGCTGATAGTGCTCTCCTTGATACACAAGCT Y 2 1 2 1 201000 r 74 goat snp6659-scaffold1240-196148 15 69337767 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386206 Affx-122970993 AX-123256564 15 11428556 GATAGAGAGAAGGGAGGCATAAAACTGGGACATAA[G/T]AGTGGAGGTAGAGATCTGTGGTCAGATTCTTAATG K 2 1 2 1 201000 f 74 goat snp6658-scaffold1240-146633 15 69291589 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447613 Affx-122923996 AX-123317949 15 11457213 AAAAAAGATTTCTATTATTGGTCATACTAAATTTA[G/T]AAAACTTCAGGGTGCATTCTTTTTAGGAGCAAAAC K 2 1 2 1 101000 r 74 goat snp6657-scaffold1240-117976 15 69261887 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277019 Affx-1111835636 AX-519550526 15 11471464 ACTGAGTGACTACCATCAGGAATAGTTCTAATGAA[A/C]ACAGGCCCAAATCCTTGCTCTTATGTTTAAGGGAG M 2 1 2 1 101000 r 74 goat Random2.2K-1502 15 11471464 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434285 Affx-122934771 AX-123304626 15 11515634 ATTCATAATATTCTTTATCTACCATGGCCTAGTTT[A/G]TATTCCCCTCTTCAAAACTACTCATGGTCTGTACA R 2 1 2 1 101000 r 74 goat snp6656-scaffold1240-59555 15 69202021 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787347 Affx-122940780 AX-385274372 15 11544329 ACATTAAGAGATAGAGAAGCTTTCTAAAATGGAAA[G/T]AAATTCATAATTCATCAGGCTGTTGTTTCATTAGG K 2 1 2 1 201000 f 74 goat snp6655-scaffold1240-30860 15 69173246 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799451 Affx-122926890 AX-385286381 15 11600431 CCCCGACCCTGCTTCTTTGTAGACTTGAAATGCAG[C/T]ACCATGTATTGCTAAAATACGAAGAGGTCAAGGAG Y 2 1 2 1 101000 r 74 goat snp5354-scaffold1186-380494 15 69115713 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381355 Affx-122974409 AX-123251713 15 11713235 CCAAAAAAAGAGGGGGGGAGCAGAAAACAAAGACA[C/T]GAGAGGAATCTGAAGCCTCTGGCACATACACTTAT Y 2 1 2 1 101000 f 74 goat snp5352-scaffold1186-267690 15 69002054 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795087 Affx-122935040 AX-385282046 15 11808759 ATTTGAATAATGAAGGTTATTTTGGGTGCACAGGA[A/G]CAAGGGTGTGTATTTGTGGTGAAGACCATATGTTT R 2 1 2 1 101000 r 74 goat snp5350-scaffold1186-172166 15 68908629 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415189 Affx-122948996 AX-123285538 15 11864271 AAATCAAATAAACATTTTCTCTTAGAAAAGATCTC[A/G]TCTAGTTATTTGGATCCTACATTTTACAAAATATC R 2 1 2 1 101000 r 74 goat snp5349-scaffold1186-116654 15 68852642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408613 Affx-122953499 AX-123278964 15 11936690 CAATATTCCTGGGTCCTTTACATAGTACCATCTCA[A/G]CAGCACATCTTAGTAGTCTTATTATCATGGATTTC R 2 1 2 1 101000 f 74 goat snp5347-scaffold1186-44235 15 68771004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780694 Affx-122938395 AX-385267784 15 11965529 TTCTGAAAACGATTGATCTTGAGGTACTTATAGAT[A/G]TTTAGATAAATTACACTCTGGACTATGTTTGTAGC R 2 1 2 1 101000 f 74 goat snp5346-scaffold1186-15396 15 68741014 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450675 Affx-122921911 AX-123321009 15 11984219 GGAATCTGAAAATTCACTGTAGAAAAGTAATAAGA[C/T]AGGTAATCAGATTTAGCAACTGACACAAAAGGATC Y 2 1 2 1 101000 r 74 goat snp32419-scaffold37-3195 15 68722456 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396916 Affx-122963206 AX-123267271 15 12030012 ACTGTCTCTCCCCAAGGTCCCTTTGGTGTTCTCTT[A/C]TGAGCTGTGTGTATATACATGCTTTCATTATATAA M 2 1 2 1 103000 f 74 goat snp32420-scaffold37-48988 15 68676601 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379071 Affx-122976327 AX-123249430 15 12107890 AGCAGTTAAGGGAAAACCCAGAACATAGGGGGCAG[A/G]GAATGGTGCTTACCTAGTGATATTTGATTGAAAAC R 2 1 2 1 101000 r 74 goat snp32422-scaffold37-126866 15 68596430 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797587 Affx-122968121 AX-385284526 15 12146054 GCCTACCTATTCATTTCCCTCCTTTCTGTAGATAC[A/G]TTGATTGAGTTATTTAGAAGCTGACGTGTAGCCTA R 2 1 2 1 101000 f 74 goat snp32423-scaffold37-165030 15 68558089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398902 Affx-122961019 AX-123269257 15 12196200 AACCTCTCTTTGGAATAAAAACCAAAGTGTAAGTA[C/T]TTTCATATTTTTTGAAACTATGGTTTTTAGGAAAT Y 2 1 2 1 303000 r 74 goat snp32424-scaffold37-215176 15 68508062 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277021 Affx-1111835637 AX-519550528 15 12201884 TGAGTGGCAAGCCAAGACTGAAATCCATGTGTCCA[A/G]ACGGTATTCAGAATTACTCTTCTTTCTGTGGTACT R 2 1 2 1 101000 r 74 goat Random2.2K-1503 15 12201884 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38410191 Affx-122952582 AX-123280541 15 12275821 CTGCATTCACCCAGTGTGTGTCTTCATAAATTCTA[C/T]ACTTCACTGTAGTCCCAGTCCTACTGACAGGAAAG Y 2 1 2 1 101000 f 74 goat snp32426-scaffold37-294797 15 68428541 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425984 Affx-122941154 AX-123296330 15 12320054 TTCTTCTTCCTACCCCCATCCTTCTAGACTCTTCT[A/G]CGTGGCCCCCAACACAAACACACCACACAGAGTGA R 2 1 2 1 201000 r 74 goat snp32427-scaffold37-339030 15 68384148 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476308 Affx-1251763815 AX-586011726 15 12386286 TAAGCATGCAAATTGGTAAAATTTTGCAGATTTTA[-/ACACCTGACTTTGTTTTTTTTTTTATTTATTATTTTATTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CACCTGACTTTGTTTTATGCCCTTCCCCTCTCCTG - 4 1 4 1 20000 f 74 goat SV_163 15 12386286 - deletion junction SV-TF-chip 539476561 Affx-1251763815 AX-586011947 15 12386286 TAAGCATGCAAATTGGTAAAATTTTGCAGATTTTA[-/ACACCTGACTTTGTTTTTTTTTTTATTTATTATTTTATTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CACCTGACTTTGTTTTATGCCCTTCCCCTCTCCTG - 4 1 4 1 20000 r 74 goat SV_163 15 12386286 - deletion junction SV-TF-chip 562165079 Affx-1251763815 AX-606940491 15 12386286 TAAGCATGCAAATTGGTAAAATTTTGCAGATTTTA[-/ACACCTGACTTTGTTTTTTTTTTTATTTATTATTTTATTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CACCTGACTTTGTTTTATGCCCTTCCCCTCTCCTG - 8 1 4 1 20100 f 74 goat SV_163 15 12386286 - deletion junction SV-TF-chip 562165225 Affx-1251763815 AX-606940637 15 12386286 TAAGCATGCAAATTGGTAAAATTTTGCAGATTTTA[-/ACACCTGACTTTGTTTTTTTTTTTATTTATTATTTTATTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CACCTGACTTTGTTTTATGCCCTTCCCCTCTCCTG - 8 1 4 1 20100 r 74 goat SV_163 15 12386286 - deletion junction SV-TF-chip 562165611 Affx-1251763815 AX-606941022 15 12386286 TAAGCATGCAAATTGGTAAAATTTTGCAGATTTTA[-/ACACCTGACTTTGTTTTTTTTTTTATTTATTATTTTATTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CACCTGACTTTGTTTTATGCCCTTCCCCTCTCCTG - 8 1 4 1 20100 f 74 goat SV_163 15 12386286 - deletion junction SV-TF-chip 562165674 Affx-1251763815 AX-606941083 15 12386286 TAAGCATGCAAATTGGTAAAATTTTGCAGATTTTA[-/ACACCTGACTTTGTTTTTTTTTTTATTTATTATTTTATTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CACCTGACTTTGTTTTATGCCCTTCCCCTCTCCTG - 8 1 4 1 20100 r 74 goat SV_163 15 12386286 - deletion junction SV-TF-chip 562166306 Affx-1251763815 AX-606941714 15 12386286 TAAGCATGCAAATTGGTAAAATTTTGCAGATTTTA[-/ACACCTGACTTTGTTTTTTTTTTTATTTATTATTTTATTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CACCTGACTTTGTTTTATGCCCTTCCCCTCTCCTG - 8 1 4 1 20100 f 74 goat SV_163 15 12386286 - deletion junction SV-TF-chip 562166416 Affx-1251763815 AX-606941824 15 12386286 TAAGCATGCAAATTGGTAAAATTTTGCAGATTTTA[-/ACACCTGACTTTGTTTTTTTTTTTATTTATTATTTTATTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CACCTGACTTTGTTTTATGCCCTTCCCCTCTCCTG - 8 1 4 1 20100 f 74 goat SV_163 15 12386286 - deletion junction SV-TF-chip 562166444 Affx-1251763815 AX-606941852 15 12386286 TAAGCATGCAAATTGGTAAAATTTTGCAGATTTTA[-/ACACCTGACTTTGTTTTTTTTTTTATTTATTATTTTATTTGTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCC]CACCTGACTTTGTTTTATGCCCTTCCCCTCTCCTG - 8 1 4 1 20100 f 74 goat SV_163 15 12386286 - deletion junction SV-TF-chip 320795597 Affx-122978141 AX-385282552 15 12389605 TTCAGGACAGGCCCTCAGTACTTAAATTAAACCCT[C/T]TTTACACACGAGCCCCTGTTAGATTTCTTCTCTCC Y 2 1 2 1 101000 f 74 goat snp32428-scaffold37-408581 15 68314654 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447732 Affx-122924595 AX-123318068 15 12418848 TTACATTTAGAAAGATCACTGCTTTGCAGTAAGAT[G/T]CAAGGGACCTTAACACTCTGAACCAGAACTGATCA K 2 1 2 1 201000 f 74 goat snp32429-scaffold37-437824 15 68285434 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774469 Affx-122970780 AX-385261605 15 12484402 GCCAGGAATTAGGAGTTGCTGAGGGTTTTATTATT[A/G]TTATTTTACAAAAGGGGGGAGCTTTCCAGTATCCA R 2 1 2 1 202000 r 74 goat snp32430-scaffold37-503378 15 68219265 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793003 Affx-122940218 AX-385279981 15 12538700 GTAGGTATCAAATGTAGGAGTCAATTAAGGGAGGT[G/T]TCAATGTGTTAGTATCTTGTTTGTCTTGAAAAGTA K 2 1 2 1 101000 f 74 goat snp32431-scaffold37-557676 15 68165216 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381151 Affx-122974555 AX-123251509 15 12584499 AAGTTTCACCCAAAATGGACTACCATGTGCTACCA[G/T]ATCCTTCTAACATTCGGGTCTTCTGAATCTGACCT K 2 1 2 1 101000 r 74 goat snp32432-scaffold37-603475 15 68119016 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443567 Affx-122927342 AX-123313904 15 12613088 CCTTACCTTAAAGGCAAGGTCATTTTCTCCCACCT[A/G]TTACCTAAGTATGTGCTCATCCCTTCTGTATTCTC R 2 1 2 1 201000 r 74 goat snp32433-scaffold37-632064 15 68090244 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320794146 Affx-122976746 AX-385281112 15 12654474 GAAAAGAGTATCCGATGCAGTTGCATTTATAATCC[G/T]CATATTTTGTACACCAGAATCTCTAACTCCAAAGG K 2 1 2 1 101000 f 74 goat snp32434-scaffold37-673450 15 68048060 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439454 Affx-122930178 AX-123309791 15 12712501 AAACCATCTATGGTGAAGGATCTTGGAATAGCAAC[A/G]CAACCAACAAAAATGTCTGAGAAGAGGAGCTCATA R 2 1 2 1 101000 f 74 goat snp32435-scaffold37-731477 15 67989970 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427647 Affx-122939330 AX-123297990 15 12756143 AAGGTGGATCAATACTTAGAACTGAGTTTCTTCTG[C/T]GTGCTATTAACAGTGTTAGGTTTACTCATTTATTT Y 2 1 2 1 201000 r 74 goat snp32436-scaffold37-775119 15 67946316 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787952 Affx-122978393 AX-385274973 15 12861959 ATTAGCATTTACCAGTGAGGGTCATTTTGGCTCCA[A/G]TTATTTATGTATTAATAGCCTGTGAATATTGCAGT R 2 1 2 1 101000 f 74 goat snp32438-scaffold37-880935 15 67840278 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428652 Affx-122938658 AX-123298994 15 12900069 ATGAGGGCATTGCAACTGGAGGTTTTTAACTATTC[A/G]TGGCATGATGAATTCCTTGTCATACTCCATCAAGG R 2 1 2 1 101000 f 74 goat snp32439-scaffold37-919045 15 67802308 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394465 Affx-122964574 AX-123264820 15 12930523 TACTTTTGTAACCCCTTGACCCAGCTTTAGACTTG[C/T]AAAAATATACTCACTGTATTTGAGACCCCTTGCTA Y 2 1 2 1 201000 r 74 goat snp32440-scaffold37-949499 15 67771513 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796539 Affx-122919866 AX-385283486 15 12979393 TTAAGAAGGGATTTAGATAACCATATTTAGTGTTA[C/T]GTAACTCCGCCTCACCACAGCCTAGAAGTCAGCAT Y 2 1 2 1 102000 r 74 goat snp32441-scaffold37-998369 15 67722385 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272774 Affx-1111833032 AX-519546472 15 12984159 CTCTTCGTGGGCCTCAAAATCACTGTGGATGGTGA[A/C]TGCACCGACAAAATCAGAAGATGATTGCTTCTTGG M 2 1 2 1 303000 f 74 goat 15_12984159_AF-PAKI 15 12984159 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320763188 Affx-986697717 AX-385251122 15 13015458 GTATAACCTGACAAGGAGGGAAAAATTTTTCTCAG[G/T]CTTAAATATTTAGCCATTTTTCCCTCCTTGTCAGG K 2 1 2 1 600010 f 74 goat 15_13015458 15 13015458 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320765989 Affx-986697719 AX-385253413 15 13015472 GGAGGGAAAAATTTTTCTCAGTCTTAAATATTTAG[A/C]CATTTTTCCCTCCTTGTCAGGTTATACAAGTTGGA M 2 1 2 1 600010 r 74 goat 15_13015472 15 13015472 Ancestral_priority_1043 ancestry 0.692 recommended IMAGE 10K 10K ancestral 38387238 Affx-122970574 AX-123257596 15 13038124 ATAATTTACTCATTTATTCAAAAATATTACCAAAA[C/T]ACTGCTAAAAATGGCAATAATTTTTTTCCTTTTGC Y 2 1 2 1 101000 r 74 goat snp32442-scaffold37-1057100 15 67662165 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277023 Affx-1111835638 AX-519550530 15 13079649 ATTGAATAACCTAGAGAACTATTTCATCTTCTTTT[A/C]CGAGCATTGAATAATATCTGATCCAAAAGGCTCTA M 2 1 2 1 101000 r 74 goat Random2.2K-1504 15 13079649 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451999 Affx-122920922 AX-123322332 15 13118324 TAATTTCTCTCCTTTCCAACTGGGAATTTGAATTG[C/T]AGATATTTTCTTTCCCCCTCCATATTGCATGTTCT Y 2 1 2 1 101000 r 74 goat snp32444-scaffold37-1137300 15 67581603 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784374 Affx-122956153 AX-385271424 15 13153610 AATTCATTGATTTGGGAACACTTCCTTGGAACCTG[A/C]GATTTAACATCTTCAGGAACCTCAGGTATGGGACA M 2 1 2 1 201000 f 74 goat snp32445-scaffold37-1172586 15 67548551 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433856 Affx-122934434 AX-123304197 15 13187546 AATTGCTATCTTTCTTTTTCTTCCAGGTTTTATAG[C/T]GACTTGTTTAGTTTTAGGTCATCAGCCAGAGAGGA Y 2 1 2 1 101000 r 74 goat snp32446-scaffold37-1206522 15 67514636 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772779 Affx-122960005 AX-385259924 15 13218926 CTTGACAGAAACCATTACATAACCAGGTAAAGGGA[C/T]TGAGAGAGGAGGAATGGGTGTTTATTGAGCAAAGT Y 2 1 2 1 202000 r 74 goat snp32447-scaffold37-1237902 15 67482760 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377007 Affx-122977726 AX-123247366 15 13254040 AATAGTACTAACTGCTTCTTACTGATTTAAATTCA[G/T]ACCATTGTGATGGTTGGAGAGTGCTGTTCAAGTGA K 2 1 2 1 201000 f 74 goat snp32448-scaffold37-1273016 15 67445619 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438766 Affx-122930811 AX-123309103 15 13289604 TGTACTTATTGTTCTTAAGGGAGATGGCCTCTAGA[C/T]AATTTAGGAAACTTGCCTTAAGCCAGTCAGATAAA Y 2 1 2 1 101000 r 74 goat snp32449-scaffold37-1308580 15 67410124 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382713 Affx-122973624 AX-123253071 15 13329438 CCTGGTTTGTGTAGACAGCATAAGGAATCAGCGGT[A/G]GGAAATGGACATACGCAGACCTTTTATTGGGCACA R 2 1 2 1 101000 r 74 goat snp32450-scaffold37-1348414 15 67370211 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382406 Affx-122973832 AX-123252764 15 13363236 GGCTGTTACTCCTTAGAATACAAACACTTATAACC[A/G]CTTGGTATATTATATAGCACACAAATAAGAGAGAG R 2 1 2 1 101000 f 74 goat snp32451-scaffold37-1382212 15 67336314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435210 Affx-122933631 AX-123305550 15 13419478 TCACCTGGGAAGCTCCTGGAGAGGCTCAGGCTCAG[A/G]GGAAAAGCTGTGAGATCTCGGTCTCCAGGAGCCAG R 2 1 2 1 201000 r 74 goat snp32452-scaffold37-1438454 15 67280484 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422609 Affx-122943725 AX-123292955 15 13456489 ATAAAGACAGGGACTTGGTTTACCACATTCAGCAT[A/C]TTCCCAAGTCCTAACACAATACCTGACACATCACA M 2 1 2 1 101000 f 74 goat snp32453-scaffold37-1475465 15 67243362 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441688 Affx-122929172 AX-123312025 15 13486447 CAAGGTGGGATACAGAGGTGACTAGAGAGGCAAAG[A/C]CCTTATTCTTGGGAGCTCACATTCTGCATGAATAA M 2 1 2 1 101000 r 74 goat snp32454-scaffold37-1505423 15 67213483 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451095 Affx-122921401 AX-123321429 15 13514997 GAAAAAAAAGTTTTCAATTTCTCCCTTACAGAGTT[A/C]TTAGGTAACACATTTCAGGTCATAGCTGAAGTTCC M 2 1 2 1 101000 r 74 goat snp32455-scaffold37-1533973 15 67184928 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797169 Affx-122920520 AX-385284109 15 13546974 TCATAAAAGGAAGATATTGTTTCCAATTAAGTCAA[C/T]ACTAAATCTCTACTCTTTAGAGATAATAATGACAA Y 2 1 2 1 101000 r 74 goat snp32456-scaffold37-1565950 15 67153115 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387207 Affx-122970596 AX-123257565 15 13607083 AAAGAACACATTAAAATATGATCTGTGGTGGTATC[C/T]GGGTGCCTTCCACGCCCATTTGTGAACACCCCAAC Y 2 1 2 1 101000 f 74 goat snp32457-scaffold37-1626059 15 67092645 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276888 Affx-1111835639 AX-519550397 15 13635491 GCATATTTGTGCCTGTTTAATTGTACGCATTCCCA[A/G]AGATATCTGTTAGCAAGAAAGTCAATAAAAGTTTT R 2 1 2 1 101000 f 74 goat Random2.2K-1505 15 13635491 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794161 Affx-122963875 AX-385281127 15 13658909 AATCTTAATGAGAACTGGTTTGAAATGCCTCTAGG[C/T]ATCACCTTGCCTACAAATTATACCCCCCACAACAA Y 2 1 2 1 101000 f 74 goat snp32458-scaffold37-1677885 15 67040800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383465 Affx-122973448 AX-123253823 15 13706305 TAAAGACAGTAACAACGGTGTAAAATCTTACTTGA[C/T]GAGATGTGTTGATGCCGTGGCTCATAAATTAGAAT Y 2 1 2 1 101000 f 74 goat snp32459-scaffold37-1725281 15 66993601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773931 Affx-122932318 AX-385261070 15 13758669 CTTGAAATTCTTGTTTATTTATGTGTGGATTCATT[C/T]ATTGGGATGTATCCATGACTTAACCATGTGAAATA Y 2 1 2 1 201000 f 74 goat snp32460-scaffold37-1777645 15 66941876 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420225 Affx-122945532 AX-123290573 15 13789853 TTTATCAAATTCTAAGACTCTTCTATTATACCATA[C/T]ACAAAAATGAATTCCTGGTAGAACTGTGAAAGGCC Y 2 1 2 1 101000 f 74 goat snp32461-scaffold37-1808829 15 66910502 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388512 Affx-122969212 AX-123258870 15 13820497 CTCAGAAAGGCTGCTCTCCCTCCCCACACCCTGTG[C/T]CTGCTATTTCTATGAAGCTCACTTCCTCTCCTGGG Y 2 1 2 1 101000 r 74 goat snp32462-scaffold37-1839473 15 66880170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423165 Affx-122942743 AX-123293511 15 13850094 ATGCCTACCAATATACTCATCCAAAGTGTCTGCTG[C/T]AGCACCACTGGGAGAAGTTGCCACTGCCCCATTTT Y 2 1 2 1 101000 f 74 goat snp32463-scaffold37-1869070 15 66853179 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424223 Affx-122942487 AX-123294569 15 13881515 GTGAGATCACAGGGGGCACACAGAAGCACACCCAC[C/T]GGCACCAGGGCACATACGCTGGCTGTATGGCTTTG Y 2 1 2 1 101000 r 74 goat snp32464-scaffold37-1900491 15 66822052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770260 Affx-122953859 AX-385257426 15 13919373 AGGTATGTCAGAGCCATCTGAAAAAGTCATCTCTT[A/G]GGAGATGCCAAGGGTAAGTCCTATAAATGATACCA R 2 1 2 1 101000 f 74 goat snp32465-scaffold37-1938349 15 66784462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796362 Affx-122966440 AX-385283312 15 13948004 CAAATCACTGACTTCTTTATATCAAAGGGTTGAGC[A/G]CCTTCTAGTCCGTAACAGTTTCATGTGTTACCTCC R 2 1 2 1 101000 f 74 goat snp32466-scaffold37-1966980 15 66756267 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420715 Affx-122944780 AX-123291062 15 13994215 TTTCCCCCATCACCAGGATGAACAACCTGGTGGCC[A/G]TGATACTAGGAGGCCATCCCTCAGGAAACAGCCTC R 2 1 2 1 201000 r 74 goat snp32467-scaffold37-2013191 15 66709816 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388748 Affx-122968953 AX-123259106 15 14029752 CTGTCACTGAAGACCCTCAATGGAACACCATTCCA[C/T]ATGCAGCTCCAAAACAAATCACTAAATAATTCAAA Y 2 1 2 1 201000 r 74 goat snp32468-scaffold37-2048728 15 66674680 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404905 Affx-122956454 AX-123275257 15 14079185 CCAGCGAAGTAAGCATTATCATTTCCATTTCACAG[C/T]TGAGGAAAATGAGTCTCAAGAAAATTTAACCAGTT Y 2 1 2 1 101000 r 74 goat snp32469-scaffold37-2098161 15 66623953 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433070 Affx-122935742 AX-123303411 15 14120570 CCACTGTGAAGCCATCCCAGGAGGGCCTCTTCCAG[C/T]TCTGCTTGAACGCTTGACATTTCACTACCTGAAGT Y 2 1 2 1 101000 r 74 goat snp32470-scaffold37-2139546 15 66582433 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407291 Affx-122955328 AX-123277642 15 14157317 TACAGTCCATGCAGTCCCAAAGAGACACAATTTAG[C/T]GACTAAGCAACAGCATATATCAATATATTTCATCA Y 2 1 2 1 201000 r 74 goat snp32471-scaffold37-2176293 15 66544280 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276890 Affx-1111835640 AX-519550399 15 14158633 GTTGTCACTAGTATGGAGGAAATATGGTGAGGTTC[A/G]CACTTTTAAAAGTAATTGGGATCTCAGTTCAGTTC R 2 1 2 1 101000 f 74 goat Random2.2K-1506 15 14158633 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388061 Affx-122969529 AX-123258419 15 14198168 GTAACTGTATTAAAAGGGTAATGTGCATCATGCCT[A/G]TAACTTACTCTCAAATGTTCAAGAAAAAATAAATA R 2 1 2 1 101000 f 74 goat snp32472-scaffold37-2217144 15 66503189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423309 Affx-122942631 AX-123293655 15 14258909 TCAGATGAGCGAGGCCCTCTTCCTTGAGCTGTTGT[C/T]TGTGGGCAGATCTGCGTATGAATATGTCATTACTC Y 2 1 2 1 101000 r 74 goat snp21714-scaffold2126-180139 15 66429062 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449270 Affx-122923031 AX-123319605 15 14305387 ACAGGAGGGGCATGTGACCTACCCCAGATGTATGC[A/G]TATGGATGTCCAGGAGGGCTTCCTGGAGAAAGAGA R 2 1 2 1 101000 f 74 goat snp21713-scaffold2126-133661 15 66381975 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376300 Affx-122978369 AX-123246659 15 14341439 TTTCAGAGGCTTTACACGTTCTGTCAGATAAGCCA[C/T]TGGGCCTGGATCTACAGAATCTCATCATCCTGAAA Y 2 1 2 1 101000 f 74 goat snp21712-scaffold2126-97609 15 66345089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418585 Affx-122946369 AX-123288933 15 14373066 GCAAAGAATCCATTAGTTGGAAAACATGAGAGCCA[G/T]AGTAATTTTTTTTTAAGTTTGTGGATTTATACAAC K 2 1 2 1 101000 f 74 goat snp21711-scaffold2126-65982 15 66312852 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427062 Affx-122939808 AX-123297407 15 14406565 CAAGTCTCCAATAAGGTGAAAATGAAAGTATTGTG[C/T]AGGACATTCTGAAAGTTAAGAAAAAGAGGACATCC Y 2 1 2 1 101000 r 74 goat snp21710-scaffold2126-32483 15 66279441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784658 Affx-122925264 AX-385271706 15 14435879 CTACCTCAAGATACAAGGACTGCATCTTTTATGAG[A/G]TTTATTCCCTGTTTTCAGGAAGGCAGAGAGGAGGG R 2 1 2 1 101000 r 74 goat snp21709-scaffold2126-3169 15 66250548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395208 Affx-122964495 AX-123265563 15 14449206 TGCACAGAATCTTGAGGGACTACTGCTGAAGATGA[A/C]CTAGATGGTTCAAAATTGCTGTCCTTGCTATGAAA M 2 1 2 1 101000 f 74 goat snp56198-scaffold878-575794 15 66232521 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387975 Affx-122969596 AX-123258333 15 14493978 TGCCTGTGTGGACCTAGCATGTCTTCAGTGCATTT[A/G]GGAAAATGAAGTCACTGAAAAATACCCAAACTTTT R 2 1 2 1 202000 r 74 goat snp56197-scaffold878-531022 15 66187871 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444295 Affx-122926758 AX-123314632 15 14561254 AAGAACAACACTATTACTCTTATCAGAAAAGGGCT[A/G]TAAAATGTTAATTGGCCTTCTGGCCAGAAGATAAT R 2 1 2 1 103000 f 74 goat snp56196-scaffold878-463746 5 53500585 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430199 Affx-122937346 AX-123300540 15 14633095 GATAGTCTACCAACTTGTGGCAAATTCCAGTGTTT[C/T]AAAGCAAAGACATACATTCTTTTCACAAAGAAAAA Y 2 1 2 1 101000 f 74 goat snp56195-scaffold878-391905 15 66046990 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390779 Affx-122967883 AX-123261136 15 14693100 TTCCTACTGCCCCTACTCAACACAAAGAAACAATG[C/T]ATAGGAAGATAGCTGGGAAGAGAAGGCAGCCATCT Y 2 1 2 1 102000 r 74 goat snp56194-scaffold878-331900 15 65986550 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420426 Affx-122944908 AX-123290773 15 14725900 CCAACTTGAATGATGTCTATGAATAAATAAATGAA[C/T]AAGTGAATGAATAAGTTAAGGCATAGAAGAAATGT Y 2 1 2 1 303000 r 74 goat snp56193-scaffold878-299100 15 65950651 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422864 Affx-122943086 AX-123293210 15 14762166 ACCTTGGAGAATGACCTTTTGTAGGGGAATTCTTA[C/T]GCTTTCCAGCAGTGCACTCATTCCTGATCCCAGAG Y 2 1 2 1 101000 f 74 goat snp56192-scaffold878-262834 15 65913271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415162 Affx-122949400 AX-123285511 15 14803896 AACAAAGCATCAAAGCCATTAAAAAAGTCCTGCAA[C/T]GTGCCACCTACAGCTCGAAGGACTCTCTCATTGTC Y 2 1 2 1 201000 f 74 goat snp56191-scaffold878-221104 15 65871523 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453276 Affx-122920388 AX-123323609 15 14866511 TTAAATGACCCCTCTGACTCAAAAAAATTAAGATG[C/T]ATAAGCAATTCTATTTTGGATTCCAGAAGCCCAGC Y 2 1 2 1 201000 r 74 goat snp56190-scaffold878-158489 15 65810907 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389291 Affx-122968517 AX-123259649 15 14907897 AGAGAACAGTAACTTAATTATGTTGATATATAGAT[G/T]GTTGTACAAAGACCTCATTTCAGCTACAAACAAAA K 2 1 2 1 101000 r 74 goat snp56189-scaffold878-117103 15 65771699 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777841 Affx-122950170 AX-385264958 15 14954212 ATACCCTTGGACCTATAATGAATTTCTGAATCTTC[A/G]CTTCAAGATCCATTATCTGATGCTAGAAAATGGAA R 2 1 2 1 101000 f 74 goat snp56188-scaffold878-70788 15 65725090 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407267 Affx-122955345 AX-123277618 15 14986862 TGATGAGGTTAACCAATAATATTTTATTCCTTATA[C/T]GTATTGCAAAAAATTATCCTAGCTGTGGTTAAATT Y 2 1 2 1 101000 r 74 goat snp56187-scaffold878-38138 15 65692821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765601 Affx-122948888 AX-385253080 15 15166837 CTCAAGGAAAGAAGACTTTATGGTGGTCCCTTCCC[A/G]CTCTGTGTTTGCCTCCCAATAATGGTGCTTTACCT R 2 1 2 1 101000 f 74 goat snp29145-scaffold313-40369 15 65514739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423340 Affx-122943164 AX-123293686 15 15198379 GTTCAATGGACAAATAAGAGAGAGGGGGGCAGGTG[A/G]TAGGGGTTGAGGGGGAGGCTTTCAGAGTCTCCAAA R 2 1 2 1 103000 f 74 goat snp29146-scaffold313-71911 15 65483580 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404000 Affx-122957198 AX-123274352 15 15316045 TTATTTGGATATGAATTCATTTATAAAGATTGAAA[C/T]AACATACACTAAACTGTTAACTGTATTACTTCTGA Y 2 1 2 1 201000 f 74 goat snp29148-scaffold313-189577 15 65357473 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431236 Affx-122937138 AX-123301577 15 15349532 GAGGTAGGACAGGAAAGATGGGTTGTCCTACCTAT[A/G]TAATGGAAGACTTTCCACCATTCTGTTGTGTACGC R 2 1 2 1 101000 f 74 goat snp29149-scaffold313-223064 15 65324176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410581 Affx-122952126 AX-123280931 15 15393086 TGCTTGGTTTGTGTTCTTGGAGATTATTTACTTTG[C/T]AGGTGTCTATTGCCAATCTTCTTCAAGCTAGATTT Y 2 1 2 1 101000 r 74 goat snp29150-scaffold313-266618 15 65280515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407045 Affx-122954935 AX-123277396 15 15428995 TAATATAGCAATAGCATTTGGAATAATGTCTATTC[A/G]TGATAGATTTATACCCACTACTTTTAGAAGGCAGC R 2 1 2 1 101000 r 74 goat snp29151-scaffold313-302527 15 65246855 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276892 Affx-1111835641 AX-519550401 15 15454333 CAACAACGTTTTCCTAAGGATACAGAAGCAGGAGT[A/G]TATGAATTCTTCTCGACAAGTATATCTGAAATGTT R 2 1 2 1 101000 f 74 goat Random2.2K-1508 15 15454333 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320774896 Affx-122938458 AX-385262030 15 15528277 AGGTACTGGAACAAAAACTTCTAAATAATACCTTA[C/T]GTAATCTTATTCCTAAAAAATGACACTATAGTCTA Y 2 1 2 1 101000 f 74 goat snp29153-scaffold313-401809 15 65146613 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380759 Affx-122975122 AX-123251117 15 15590598 ACATGCCCCCCAGTCTTAGATTCTATTAAAGGTTT[A/G]AAGACAATTCAAATCACAGTGATAAATGCAATGAT R 2 1 2 1 101000 r 74 goat snp29155-scaffold313-464130 15 65082292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272829 Affx-1111833033 AX-519546522 15 15625499 CTCTGACTCTCCCCTGGAACAGGCTCAACTCAAGC[A/G]TCACATCACATGTGTTCTTCACCTCTCCCTGATCC R 2 1 2 1 101000 r 74 goat 15_15625499_AF-PAKI 15 15625499 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38431669 Affx-122936798 AX-123302010 15 15648958 GCAGGTCACTACCCACATCTTTCTAGGATCCTGTA[C/T]AGCCTGGCACTAAGACCAATCCTACTGAAAGGCCA Y 2 1 2 1 201000 r 74 goat snp29156-scaffold313-522490 15 65015922 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272463 Affx-1111836717 AX-519546186 15 15657159 CTCAGGGTGATGAAGAGCCAGAAGGGCCTGCAGAG[A/G]T R 2 1 2 1 103000 f 74 goat GoatD01.007241 15 15657159 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38444873 Affx-122926279 AX-123315210 15 15703282 TGGAAAATATCTGCTTTCAACAGAAAATTAAGCCA[A/G]TGGTAAGTTTGGAAAAACAGCCTAGTGGCATCATT R 2 1 2 1 101000 r 74 goat snp29157-scaffold313-576814 15 64960498 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792800 Affx-122926172 AX-385279779 15 15751842 CAAAAAAAGTGTGTTTAGAGAGAGAAGAAATCTCA[C/T]GTCTAGGAAGCTATGAGATATTCCTGGTATTAATA Y 2 1 2 1 102000 f 74 goat snp29158-scaffold313-625374 15 64911933 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434786 Affx-122933881 AX-123305127 15 15787310 CCAGATCTAATGTAAGCTATGGTGTGAAGTGGGTA[A/G]GGTGGAGGCACTCTCACTGGAAAATAAACTGGTGA R 2 1 2 1 101000 f 74 goat snp29159-scaffold313-660842 15 64875111 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438453 Affx-122931250 AX-123308791 15 15879062 TGCTATACCAAGGAAAAAGAGGATTGGGCTAAAAA[C/T]AGAGGGTTAATACATCAAAGGGGATGTTACATGTT Y 2 1 2 1 101000 f 74 goat snp29161-scaffold313-752594 15 64783016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445227 Affx-122925501 AX-123315564 15 15916432 AGGCTACAGACTGTGGGGTCACAAAGAGTCGAACA[C/T]GGCTTAGTGCTTAAACAACACAATAACAATACACC Y 2 1 2 1 201000 r 74 goat snp29162-scaffold313-789964 15 64744842 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797645 Affx-122959272 AX-385284584 15 15966371 TTTTTCTTTTTTTGTTAATCTGAAAGTTTACTTCC[A/G]TTAGTGGTTCCTTTCTACTTTCACTCTCAATCAGA R 2 1 2 1 101000 r 74 goat snp29163-scaffold313-839903 15 64694718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789800 Affx-122961518 AX-385276807 15 15999740 GGAATTACATAACAAAAGTCAGAACTGTTCCTATT[A/G]CTTTCATTAAACTTCAGTGAAGTAGCATTAATTGT R 2 1 2 1 101000 r 74 goat snp29164-scaffold313-873272 15 64661212 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794077 Affx-122934445 AX-385281044 15 16086506 CAGATGTAAAGAAAAAAACACCAGAGGGGAATAGG[A/C]TAGCAAAGGATAAGGAACAACAGGGAGTGATGATG M 2 1 2 1 101000 f 74 goat snp29165-scaffold313-960038 15 64574093 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801095 Affx-122936214 AX-385288009 15 16151982 GTGTCACTTTAAAATTGATTCTCAAAATCAAAGCT[A/G]CAATTCACTTCCCAGCTTTATTTATATGTGTGAAA R 2 1 2 1 101000 r 74 goat snp29167-scaffold313-1025514 15 64508050 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792361 Affx-122958860 AX-385279342 15 16229638 GGAAGTCAAGTTGTCACCTATGTGCAGGGAAACTC[A/G]CTAATTTTTCCTCTGATATTAATCAGACTTTGCCA R 2 1 2 1 101000 f 74 goat snp29169-scaffold313-1103170 15 64430480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450017 Affx-122922847 AX-123320352 15 16264627 GAGAATTTGGTAAATCTAAAGTGATCAGGAAAAGT[A/G]TAAAAGCAAAATACAAATCAACAGTTTACAAACAT R 2 1 2 1 101000 f 74 goat snp29170-scaffold313-1138159 15 64394851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440910 Affx-122929215 AX-123311247 15 16294681 CCTGCCCCTAAAGAGAGGGCCTTGTTTTGGGAGCT[C/T]CTTGGCCCTGAGAATGAGCACAGGCTCAGAAAGGA Y 2 1 2 1 101000 f 74 goat snp29171-scaffold313-1168213 15 64364756 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774796 Affx-122966026 AX-385261930 15 16304262 AACATTATTAATCTACTCTTCAACCTTGAATGATA[C/T]GCTGTAAAACTCCTGTCTTATTCAGGCTGTGAAAA Y 2 1 2 1 101000 r 74 goat snp34605-scaffold41-401 15 64340039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403135 Affx-122958108 AX-123273488 15 16338948 TTGGAATTTTTAAAAGATATTAGCAAAGTAAAGTG[C/T]ATGTGGAATCTATCACAGAATTTAACATCTTAATG Y 2 1 2 1 101000 r 74 goat snp34606-scaffold41-35087 15 64305715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794379 Affx-122919338 AX-385281341 15 16370752 TAAGAAGAAAAGTTCTATACATTTACTTACACAGT[G/T]ACCATTTTTGGTGTTCTTCATTCTTGTATGGATCT K 2 1 2 1 101000 r 74 goat snp34607-scaffold41-66891 15 64274133 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398109 Affx-122961709 AX-123268464 15 16428956 GCTGCAGATCTAAACCAAGTTTGCTTTGCTTGAGT[G/T]TCAAATGTTTCACTCTTGGCAATGTTTTAGTTTGT K 2 1 2 1 201000 r 74 goat snp34608-scaffold41-125095 15 64215010 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771969 Affx-122946579 AX-385259125 15 16480597 GACCCTCACAATACAAGAACTAGGATGGTGTGTTT[C/T]CTGTAGTTCTATCAGGTTAGCTTTGCTGCAGCCTA Y 2 1 2 1 101000 f 74 goat snp34609-scaffold41-176736 15 64163319 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390386 Affx-122968180 AX-123260743 15 16527859 AGTGACACTGTAGGTTGATTACAAAGCAGGCCTGC[A/G]CAGTTCCTTTCATGGCTGAAGGCATACTCCTTTGT R 2 1 2 1 101000 r 74 goat snp34610-scaffold41-223998 15 64116152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419271 Affx-122946252 AX-123289619 15 16591057 CTTTTCAATATTCATTCTTTGGAAATTCTTCTGAA[G/T]AGTGATTCTGCCTACTTCCATTATGGTTGCTTTTC K 2 1 2 1 101000 r 74 goat snp34611-scaffold41-287196 15 64053729 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446047 Affx-122925839 AX-123316384 15 16626401 AGGCAACTGTACCCAGGAGAAGGGAGATGTTTATG[C/T]AGTGGAAATAGTCCCAAGGGAGCAAAGAGGTTAAC Y 2 1 2 1 101000 r 74 goat snp34612-scaffold41-322540 15 64018632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378490 Affx-122976661 AX-123248849 15 16664176 TTCCTGAGCCCCTGACTTGTGTATCCATTTGACTT[A/C]TAGATATTTCCATTTGGGTAAGCAATTTAAGATTT M 2 1 2 1 201000 r 74 goat snp34613-scaffold41-360315 15 63980937 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276894 Affx-1111835642 AX-519550403 15 16690246 AGGCCTCTCATTGAAAGAAGCTAAGTGAGTTGCCC[A/C]AGGTTAACTGCCTGGAGCCAGGATTTGGTCCTTCT M 2 1 2 1 202000 f 74 goat Random2.2K-1509 15 16690246 T G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444058 Affx-122926857 AX-123314395 15 16696228 GAAAAACTTATAGATGTTCAGAAAAAATTGGAATC[A/G]TTTTTAGCTCAAGATCAAGATTTAAAAGAAAGAGC R 2 1 2 1 101000 r 74 goat snp34614-scaffold41-392367 15 63948887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275378 Affx-1111834863 AX-519548952 15 16712089 CTTTTAAGAAATACCAGACACATCAATGACATATA[A/G]ACATCACCACAATACAGTGGAAAGATATCTGCTTT R 2 1 2 1 201000 f 74 goat GoatD01.056913 15 16712089 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320782615 Affx-122958363 AX-385269688 15 16768316 TTTTTTTTTGCTTCTGAAATAAGTCTTCTACATAA[C/T]TAATCACACAAGGAGGGACAACTACAAAATGCAGA Y 2 1 2 1 101000 r 74 goat snp34615-scaffold41-464455 15 63876991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444495 Affx-122926517 AX-123314832 15 16824176 ATCAATTATGTACCAGACTGGATTTCTATCTACAA[C/T]GCATATGTATTATTTTTTTTAATGTTAGGTTTTAA Y 2 1 2 1 101000 f 74 goat snp34616-scaffold41-520315 15 63820872 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788915 Affx-122975739 AX-385275929 15 16856260 TGCTCTAGGGAGTACAAAGATCTGAAACAGAGAGC[C/T]GTTTTTAATAGCTATCAATATTGATCCATTATGTA Y 2 1 2 1 101000 f 74 goat snp34617-scaffold41-552399 15 63788886 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413469 Affx-122950664 AX-123283818 15 16903576 TCAACATACATACTGAAACCCCATCTTGTCAGTGT[G/T]TTTTTGCTCCATTAACTCCAGCATAGGTTGTTTTT K 2 1 2 1 201000 r 74 goat snp34618-scaffold41-599715 15 63741848 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423442 Affx-122942600 AX-123293788 15 16938617 GATGTGAAGAAGAAGAAGTTAAAGAATGACTTCCA[G/T]GCTTTTAGTAGGGGTATTACTCTTTGCTTGGAGGG K 2 1 2 1 101000 r 74 goat snp34619-scaffold41-634756 15 63705914 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384703 Affx-122972110 AX-123255061 15 16968317 CAAGTAACTCCATTTTACAGATAGGGTCACTGAGG[C/T]GTAGTGAGAGGAAATGACCTGCCTGAAGTCATAGA Y 2 1 2 1 101000 r 74 goat snp34620-scaffold41-664456 15 63676241 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375965 Affx-122978439 AX-123246324 15 17024970 ATCTCTCCCACTGCCCCTCTGATTTCCTCACCTCT[A/G]TCTGTTCTAAATCACTTGAAAATTGCCACGCAAAC R 2 1 2 1 101000 r 74 goat snp34621-scaffold41-721109 15 63618938 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765799 Affx-122948490 AX-385253254 15 17083113 TTGGCTTCAGTGTGCTCATAGGCCTCTTTGCACAT[A/G]GAAGTTAATAACATGTGGAAACTCGATTTAAAAAC R 2 1 2 1 101000 f 74 goat snp34622-scaffold41-779252 15 63560380 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388643 Affx-122969117 AX-123259001 15 17172091 TGCCTTTCTGGGTCTCAGCTTACTCACCTGTAAAA[C/T]GGCTACGGTTTCTTCTTGATGGTAAATCCCTCTTA Y 2 1 2 1 201000 r 74 goat snp34624-scaffold41-868230 15 63470338 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780427 Affx-122966849 AX-385267519 15 17201810 TAATGCTTATATTTACTGAATACCAAGTATGTTCC[A/G]GGTAACTTACATTTCTTGTCATTCTTATGGTAGTA R 2 1 2 1 101000 r 74 goat snp34625-scaffold41-897949 15 63440725 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442650 Affx-122927911 AX-123312987 15 17251818 TTCCTTCTCTTCTGCATCATGTAGCTTACAGAGTA[A/G]TGGTGATACAGCCAAAGGTCAAGGCTGACCCTCCA R 2 1 2 1 101000 f 74 goat snp34626-scaffold41-947957 15 63390587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384425 Affx-122972184 AX-123254783 15 17307136 ACATAGAATATTTCCAGTTATTAAGACCCTGGTGT[A/G]CCCTCTGCAACACAACTTCTACTTTCCCCCAATCT R 2 1 2 1 201000 f 74 goat snp34627-scaffold41-1003275 15 63334422 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763196 Affx-986697725 AX-385251129 15 17349592 CATCTTAACTATGTTGAATTTTCCAGTCCACAAAT[A/G]CAGCATCCATGTCTATTTATTTAGGTCTCCTTCGA R 2 1 2 1 600010 f 74 goat 15_17349592 15 17349592 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 320766016 Affx-986697735 AX-385253435 15 17349667 TTTCATCAGCATTTTGTGCTTTTCAGCATACAAGT[C/T]TTGTACATTGTTTGTTAAGTTTACATCCAAGTGCT Y 2 1 2 1 600010 r 74 goat 15_17349667 15 17349667 Ancestral_priority_1043 ancestry 0.746 recommended IMAGE 10K 10K ancestral 320763208 Affx-986697737 AX-385251139 15 17349719 AAGTTTACATCCAAGTGCTTAATTTTTTTGAACAA[C/T]TGTAAATATTTTACATTTTGCTATCGACATATTCA Y 2 1 2 1 600010 f 74 goat 15_17349719 15 17349719 Ancestral_priority_1043 ancestry 0.594 neutral IMAGE 10K 10K ancestral 320766027 Affx-986697741 AX-385253445 15 17349740 ATTTTTTTGAACAACTGTAAATATTTTACATTTTG[A/C]TATCGACATATTCATTGTTAGTGTTTAGAAATATG M 2 1 2 1 600010 r 74 goat 15_17349740 15 17349740 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 38426698 Affx-122939899 AX-123297044 15 17354635 TTTAGGGTTGCACCAGGCAAAATAAAGGAAAGCAA[C/T]AAGCAAATGAACAAAAGTTTATGGTGTTCTTATTG Y 2 1 2 1 101000 f 74 goat snp34628-scaffold41-1050774 15 63286640 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38408026 Affx-122954297 AX-123278377 15 17400816 TCTCTTTGTTGACATTCTCATTTTATTCAGCTATC[A/G]TTTTCATGATTTTCTTCTGTTCTTTGTCCAGTTTT R 2 1 2 1 103000 f 74 goat snp34629-scaffold41-1096955 15 63239640 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794105 Affx-122938995 AX-385281072 15 17450230 CTTTTAAGTAAAGTCTATCTTTACCAAAGTCCAGG[A/C]TTACTTTTTTATTTGGCAAGCAGGATATGAAAGAA M 2 1 2 1 201000 r 74 goat snp34630-scaffold41-1146369 15 63191377 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775264 Affx-122969320 AX-385262396 15 17526001 CTGGGGGGATCTGATGGAAATGAGTAGCTGTGACT[A/G]TTCAAAAGCATGACCCAAGTCAAGTCAGGGCCAGT R 2 1 2 1 101000 r 74 goat snp34632-scaffold41-1222140 15 63114205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388811 Affx-122968906 AX-123259169 15 17567569 AGGAACTTCTATACTGTTTCCATAGAAGCTTCATC[A/G]TTTTACAGTCCCACCAAAATTTCACAAGTTTTCCA R 2 1 2 1 202000 r 74 goat snp34633-scaffold41-1263708 15 63071738 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426264 Affx-122940325 AX-123296610 15 17615412 CAATACGGAGGAGAAACCGCACAAGCTACCAAATA[C/T]GTAAAAGGCATTGACCCCTGGAACAAAGGGAGTGG Y 2 1 2 1 101000 f 74 goat snp34634-scaffold41-1311551 15 63022829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277032 Affx-1111835643 AX-519550539 15 17646667 ATATGGCTACTGGCAGCCCCAAGTTAATGTCTTTC[A/G]TAGGATGTAGTCCCTCATTCAGCATCCATATCAGT R 2 1 2 1 101000 r 74 goat Random2.2K-1510 15 17646667 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444258 Affx-122927213 AX-123314595 15 17700789 CCACAGCTAAAGTAACAGAAAAAGGAACCACAATG[A/C]GACAGGCAGGTAGCATGGTATAGTTAATAGTCAAC M 2 1 2 1 101000 r 74 goat snp34635-scaffold41-1396928 15 62936490 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802826 Affx-122969706 AX-385289725 15 17752993 CTTATTTTTAGTCCTCTTCTCCCAATTACTGCTTT[C/T]GACATGTTTTAAATCTTTCTGTTTTATGAGTCCCT Y 2 1 2 1 101000 r 74 goat snp34636-scaffold41-1449132 15 62885241 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798009 Affx-122938718 AX-385284945 15 17802801 CCTGCAGTGGGTTTTCATGAACAAGGGTTGAAGCT[A/G]TACATATTCTGCCTCTGAAATTGAGGGATTTATTT R 2 1 2 1 101000 f 74 goat snp34637-scaffold41-1498940 15 62834355 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396930 Affx-122963194 AX-123267285 15 17832533 AAGAAGAGAAAGGGACTGACAATTTATAGGCCAGA[C/T]ACCTTCATAAACAATCTCTTCTTATATTTCACCAT Y 2 1 2 1 101000 f 74 goat snp34638-scaffold41-1528672 15 62804928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274973 Affx-1111834612 AX-519548555 15 17861990 TCTGCAGGTGACTAAAATAATGCCTGGCCCTGAAT[A/G]GAAGGATGGAAAAGGAGTGGTTGTTGGATCTCCCT R 2 1 2 1 201000 f 74 goat GoatD01.043044 15 17861990 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320796573 Affx-122922079 AX-385283519 15 17863107 AAAACTGGAATGCTTGGTCGTCTCCCTTTAAAAAA[C/T]GGTTTCATACTATAATTTGTGTGTATTTTGGAATG Y 2 1 2 1 201000 r 74 goat snp34639-scaffold41-1559246 15 62774224 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389368 Affx-122968455 AX-123259726 15 17895835 CTGAAGCAGTACCAGCAAACACCTTCTAATGATTA[C/T]AGCTTGTTATATAAGAAAAGCAAACCCTTGTTTGT Y 2 1 2 1 101000 f 74 goat snp34640-scaffold41-1591974 15 62738750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443313 Affx-122927455 AX-123313650 15 17934120 CAGGAGTAAAGACAGAATGAAATAAAAATGCAAGG[C/T]ACGATTCTTCATGAAAACATGGGGACAGGAATAGA Y 2 1 2 1 303000 r 74 goat snp34641-scaffold41-1630259 15 62699120 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448350 Affx-122924124 AX-123318686 15 17968734 AGACCATCGTTTACTACAGAGGAAAAATAAGAATA[C/T]AAATGTTGGGGTAAGAGAAACAAGGGAAGCCTGCA Y 2 1 2 1 201000 f 74 goat snp34642-scaffold41-1664873 15 62664639 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399336 Affx-122961364 AX-123269691 15 18001881 TCTGATAGATATTTATGAGGTCTCTGATCCATAGC[A/G]TCACAAGGAGTCAGGCACAACTGAAGCAACTTAGC R 2 1 2 1 101000 f 74 goat snp34643-scaffold41-1698020 15 62630618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414881 Affx-122949136 AX-123285230 15 18070527 TTTATCCTGTGAGGTAGTTACTATTATTATTTCAG[C/T]TTTACAAATGGGAAAATTCAGGTCAGCAATACCAG Y 2 1 2 1 101000 r 74 goat snp34645-scaffold41-1766666 15 62562006 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784678 Affx-122965159 AX-385271726 15 18124440 CAGATGTCCTAGTCTTGCCAAATCTGATACATTTC[A/G]TGAGAGCACATTTCTCCTGTGATTTAAACAGCACC R 2 1 2 1 101000 r 74 goat snp34646-scaffold41-1820579 15 62507534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271942 Affx-1111833034 AX-519545718 15 18140328 AAAGAGGGGCGCCAGAGCTCTGCTAAGGGTGTCAG[A/G]GCGGCAGTGCCTCACAGGGACATGTGGCCTGGCCT R 2 1 2 1 102000 f 74 goat 15_18140328_AF-PAKI 15 18140328 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413884 Affx-122949845 AX-123284233 15 18156882 TTAGCCCCTGCATGCTCACTATCTGGTGGGAACAA[C/T]GGTCATATAAATGACAAAAACAAAGCGTGACAAGT Y 2 1 2 1 101000 f 74 goat snp34647-scaffold41-1853021 15 62473645 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410997 Affx-122951993 AX-123281347 15 18189021 AGTCCATGGGGTTGCAAGAGTCTAACACAACTTAG[C/T]GACTGAACAAAAACATATTAATCAAAATTGGCAAC Y 2 1 2 1 303000 r 74 goat snp34648-scaffold41-1885160 15 62441453 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446152 Affx-122925757 AX-123316488 15 18242077 GCTTTTCTGTTTTCAGAGATCTCATTATGTTTCTT[A/G]TTTCTCAAAAGAATCCTTATGCCAAAAAGGCATAT R 2 1 2 1 101000 f 74 goat snp34649-scaffold41-1938216 15 62387850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408995 Affx-122953894 AX-123279346 15 18295755 ATACTAGATCACAAGTCTTGATCAAGGCAGTAGCA[C/T]TGAATCCTTAATGAGTGTGAGATGGGCTGCACTCA Y 2 1 2 1 101000 f 74 goat snp34650-scaffold41-1991894 15 62333124 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451002 Affx-122921719 AX-123321336 15 18301481 GGTGCTTCAGAGATGTGGAATGATGTTCTGGCTCT[A/G]TTACTAACTAGCTCTGTGACCCTGATGTAATTAAC R 2 1 2 1 101000 f 74 goat snp26596-scaffold277-2628547 15 62327429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376782 Affx-122977956 AX-123247141 15 18333631 TGTTTCATGGTCCTGGATTTTTGAACCACTTCTTC[A/G]TATCTGGACTGTTCTTTTCCCCTGTTACTCCTTTC R 2 1 2 1 101000 f 74 goat snp26595-scaffold277-2596397 15 62295436 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409441 Affx-122954091 AX-123279792 15 18379725 CTGTGACCTTGAAAGTTAGCCAACTAATGTATAGA[A/C]GTCCAACTTTCCTTATTTGTAGAATAGGGATAATA M 2 1 2 1 101000 f 74 goat snp26594-scaffold277-2550303 15 62248490 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440726 Affx-122929888 AX-123311063 15 18436254 AACATTTAGTGAATGTTTTCTATGTTCCAGGCACT[A/G]TTCTGAGCACTTTGCATATATTCTTTCACATAGCA R 2 1 2 1 101000 r 74 goat snp26593-scaffold277-2493774 15 62191966 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388908 Affx-122968846 AX-123259266 15 18495021 ATACGGTTAATCATATTTGAAGGACAAAACAGAAA[C/T]AGACTAACTTGCTTTGTAGGTGCTGGAGGCTATAA Y 2 1 2 1 201000 f 74 goat snp26592-scaffold277-2435007 15 62132431 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377285 Affx-122978121 AX-123247644 15 18528679 CTCGGTGAGAATATATTTGAGACAATACTTTAAGA[C/T]GTGGAATAACTTATTTTTTAGATTCTTTTCATGTG Y 2 1 2 1 101000 f 74 goat snp26591-scaffold277-2401349 15 62100336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429212 Affx-122937934 AX-123299554 15 18636842 GTAAGATAGTGTGAATAGCATGAAATATCACAGTT[A/G]CAACAGAAGACTCTCATTTGTTTTTTTTTTTTTCT R 2 1 2 1 101000 f 74 goat snp26589-scaffold277-2293186 15 61992015 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38413784 Affx-122949919 AX-123284133 15 18679809 AGTAGAATCCTTACTGTGCTATGTTAGACTGTCTA[C/T]GGGCTGGTCTTTGCCTGCCTTTCTGCTTACCTTCC Y 2 1 2 1 201000 f 74 goat snp26588-scaffold277-2250219 15 61949123 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771290 Affx-122940686 AX-385258448 15 18713871 TTTTTTAGCTAGGTGTGTCCTTATTATAGTTTTTG[A/C]TAGTTGTGCACAAGTGGAAGTGATGTGTGCAACCA M 2 1 2 1 101000 r 74 goat snp26587-scaffold277-2216157 15 61914972 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394399 Affx-122964618 AX-123264754 15 18748031 ATATTTAAAAATGCTCTTCTCCAGGCTGAGCATAC[A/G]CAGGTCCTTCAGATTTTTCTTACATAGTAACATAG R 2 1 2 1 201000 r 74 goat snp26586-scaffold277-2181997 15 61880291 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437971 Affx-122931603 AX-123308309 15 18777606 AAAAAGAAGAAAAGAAACTTTTAAACAGCACATTC[A/G]TCTCAAAATGGCTGAGACATCCACCTCTAAAAGAA R 2 1 2 1 201000 r 74 goat snp26585-scaffold277-2152422 15 61842635 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783802 Affx-122941711 AX-385270858 15 18815062 ACGTATGAAAAGGAAGACTTCAACATTCTAAAGTA[C/T]TTTGTAACTCTCTTGGGCCTGATTCCCCAGCTCAC Y 2 1 2 1 201000 f 74 goat snp26584-scaffold277-2114966 15 61804607 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795886 Affx-122978285 AX-385282838 15 18871353 TCAATCTATAATTTACACCTTAGTTTAACCAGACT[A/G]TTCCTTGTATACTTCACTTAGCAACTGAATTCATA R 2 1 2 1 101000 r 74 goat snp26583-scaffold277-2058675 15 61748386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412362 Affx-122950821 AX-123282711 15 18904409 TATGGAAACACTCATAGGCAGGATGCAGAGGACCA[A/G]CCTCTCTGACTTTTTGTTTGGTTTCGAGAATGGTC R 2 1 2 1 101000 f 74 goat snp26582-scaffold277-2025619 15 61715211 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445054 Affx-122926231 AX-123315391 15 18943692 GGAAGCCAGGATCTTTGGGGGCTATCTTGGTAGGC[C/T]ATGGTAGAGGTTTACATTTTATTCCAATGGTTTTA Y 2 1 2 1 201000 r 74 goat snp26581-scaffold277-1986336 15 61675408 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277034 Affx-1111835644 AX-519550541 15 18973635 CAAGCTGAACTGCTAATACAGGCATAGAGCGCTAC[A/G]CCCAATACAACATGCAAAAGTGCAGGGTACATTTA R 2 1 2 1 101000 r 74 goat Random2.2K-1512 15 18973635 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320788733 Affx-122939298 AX-385275749 15 18994276 ATCCTTAAGCAGTACTAGGAGGTCAATTTCCAGAC[C/T]TCTTCAGGATTACTGAATGTCTAGATAGACATGCT Y 2 1 2 1 101000 r 74 goat snp26580-scaffold277-1935752 15 61623837 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452876 Affx-122920701 AX-123323209 15 19048959 TAGGTTCAATACCAAGTGCCCATTCTTCTCCATTA[C/T]GTAGATCTCATATTTATTTTATTTCAAAGTGCTTA Y 2 1 2 1 101000 f 74 goat snp26579-scaffold277-1881069 15 61569001 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403593 Affx-122957566 AX-123273946 15 19112664 ATTGTATTATAACTGCTTTTTATTCCTAAGATTTT[A/G]TTTATCTTTTTTTCATGATGTTTCAACATGTGCAT R 2 1 2 1 101000 r 74 goat snp26578-scaffold277-1817364 15 61504686 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417864 Affx-122946770 AX-123288212 15 19141344 TTGTCCCTTCAGTACAAACATTCCCGTTTGGTTTT[A/G]TAACTGGGGAAGGAGGAGGTGGGAGCCAAGGCTAA R 2 1 2 1 102000 f 74 goat snp26577-scaffold277-1788684 15 61475398 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416706 Affx-122947561 AX-123287054 15 19221101 ATTTCTCGTCCTGGAGATGAAAATGTCAGGTCAAC[A/G]TTATTCAGGTGAAAAGAAATGAAACAGAACTAAAG R 2 1 2 1 101000 f 74 goat snp26575-scaffold277-1708927 15 61394182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426836 Affx-122940507 AX-123297181 15 19256616 TGAGAGAATGGTGACATGGGGCAGGAGAGAGAGCC[A/G]CAAAAGTTCAGCCAATTCAGAAAGGCAGAGGCAGA R 2 1 2 1 201000 r 74 goat snp26574-scaffold277-1673412 15 61358535 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396127 Affx-122963404 AX-123266482 15 19293771 GCTCTGAGTATGGTTGCCACAATTGTATAAGATAA[A/C]TGATCAGGGCTAGAAAATATTTTATAGATAATCTG M 2 1 2 1 101000 f 74 goat snp26573-scaffold277-1636257 15 61320831 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441123 Affx-122929590 AX-123311460 15 19332432 ACCACTCTGCAGACTTCAGCCAGTTTCACACACGC[C/T]CCAGCTGACAGCATCCACCTTGGGCCCTCGCATCC Y 2 1 2 1 101000 f 74 goat snp26572-scaffold277-1597596 15 61281423 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429292 Affx-122938613 AX-123299634 15 19474629 ACATTGCCAAATTGCTCTCAAAGTTTTCAGAAATG[C/T]ATATTCCCTCCAAAAGGATATGATGGGAGTCTTAC Y 2 1 2 1 101000 r 74 goat snp26569-scaffold277-1455399 15 61138399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379662 Affx-122975933 AX-123250020 15 19530761 TTGAGAAAAGAAGTGGAGGTGGTGGTACCCATTCT[A/G]TGGGCTGGGAGGTCTGGAGACATTGTGTAAAGGAA R 2 1 2 1 101000 f 74 goat snp26568-scaffold277-1399267 15 61082464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799746 Affx-122928496 AX-385286673 15 19567181 CCTTTAGATATTATTCCAAATCCTTATCATTTACT[A/G]CAAGCTACCTATACAACTCTTGCTTCTTTTGCTTT R 2 1 2 1 101000 r 74 goat snp26567-scaffold277-1362847 15 61046006 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421831 Affx-122944307 AX-123292178 15 19636545 GCGATGTATTCTACATACATTATCTGGGTGTTCAA[C/T]GCTCATTGTGTAGTTCAGTACAAATAAGAAATTAT Y 2 1 2 1 101000 f 74 goat snp26566-scaffold277-1293483 15 60976285 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390522 Affx-122967238 AX-123260879 15 19703640 AAACACCACTGTTGTCTATAACTGCTCTTGTCCAG[C/T]AGTAATGATTTCAAGCTGCTAAGAATTGACAAATA Y 2 1 2 1 201000 r 74 goat snp26564-scaffold277-1226388 15 60906956 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273618 Affx-1111833703 AX-519547231 15 19710822 AGAAGCCAAAATCAGCGGATGCTCAAGCCCCTTAT[A/C]TAAAACAGTGTATGACGGTAAAGACTCAGCCTGAG M 2 1 2 1 201000 r 74 goat GoatD01.001965 15 19710822 C A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802213 Affx-122926225 AX-385289117 15 19765462 GTTGTAGGTGGTGAACACCACTAATCCTTTTGAAT[A/C]GGGGAGTATTATGACTTAACCATATTTAGAAAGAA M 2 1 2 1 101000 r 74 goat snp26563-scaffold277-1164566 15 60845809 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390979 Affx-122966916 AX-123261336 15 19803482 CTGTTTTGAGTGGCTTTGGGCCCCCAGGAGACGGA[A/G]GAAAAAAGCACTGGATTAGGAGAAGCCTGAAGGGT R 2 1 2 1 101000 r 74 goat snp26562-scaffold277-1126546 15 60807707 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793233 Affx-122945013 AX-385280211 15 19842810 TTCACTTGGGATGGGTAATCCTGAGAAAGTTGTGC[A/G]AACATTTTAAGTCCCAATCCTTTGAATAACTGCAT R 2 1 2 1 101000 f 74 goat snp26561-scaffold277-1087218 15 60768433 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444662 Affx-122926457 AX-123314999 15 19880059 GCTTCTCCCCTTCAAGCACCATCCAGGCCTGGGTT[A/G]CAGGACCCCTGTCCCTCCATGCCTACCCGCTGCTC R 2 1 2 1 101000 f 74 goat snp26560-scaffold277-1049969 15 60730839 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440597 Affx-122929285 AX-123310934 15 19954881 GTGAAGTGTCTTGCACATAAGCTTTGTCCAAGAGC[A/G]TTAGTGCCTGAGAGCCAGGCTTTACCCGTGTGCTT R 2 1 2 1 101000 f 74 goat snp26559-scaffold277-975147 15 60656170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385843 Affx-122971003 AX-123256201 15 19988642 AAAAGGTGGAAGACAGGGGACAGACTTTCTTGAAA[C/T]ACCTCCATGTGCCAGAATCTAAGCTCAGAACTCCA Y 2 1 2 1 101000 f 74 goat snp26558-scaffold277-941386 15 60621874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392505 Affx-122966126 AX-123262862 15 20045209 GTATTTGATTTCTGGGCGTTTGGTGATTAGGGAGA[C/T]GGGGATGTTGTACTAAGGAAAGGAAGTGAGATTAG Y 2 1 2 1 101000 f 74 goat snp26557-scaffold277-884819 15 60565897 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395738 Affx-122963699 AX-123266093 15 20081433 TACAAACGTGCTTTCAGAATGGAACTTGTTTGTAC[A/G]TACTAGCAATGACATAGCCCATGTTAATACCTGAC R 2 1 2 1 101000 r 74 goat snp26556-scaffold277-848595 15 60529746 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771539 Affx-122960529 AX-385258698 15 20125595 CATCCTGGATCCAAGGAAAGCTATCTTTGTGGTTG[C/T]GAAACTGGTGTTTTCTAGCCTCACTAGTGAGGTTA Y 2 1 2 1 101000 r 74 goat snp26555-scaffold277-804433 15 60486859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384232 Affx-122972372 AX-123254590 15 20160713 CAGGTGAGGAATCAACCCCTTGGAAACAAAGGAAA[C/T]TGCCAAGATCACACTGGTAATGCTAAAGTTAGGAT Y 2 1 2 1 201000 r 74 goat snp26554-scaffold277-769315 15 60451318 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785945 Affx-122938546 AX-385272982 15 20347543 AGAAGAGTTCCCTCCTTGGAGAGGGAACATAAACT[C/T]GGGTCCCACTGACTGCTTTAAGGACTTCTGGCATT Y 2 1 2 1 102000 r 74 goat snp26550-scaffold277-582485 15 60264259 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387280 Affx-122970540 AX-123257638 15 20395922 AGATGAATTTAGAGAAACCCTTAAATCGTTTCCTC[A/G]CAGTTCAGTAGGCGAGAGAATTCTAAAATATTTTT R 2 1 2 1 101000 r 74 goat snp26549-scaffold277-534106 15 60216233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442506 Affx-122928555 AX-123312843 15 20449802 GCATGCATGTTTAATCATTCAGTGGTGTCTTGACT[C/T]TCTGCAAGAGAGTAACATTTGTAACATTATTCTCA Y 2 1 2 1 103000 f 74 goat snp26548-scaffold277-480226 15 60161573 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381340 Affx-122974421 AX-123251698 15 20515734 TCATCCTCATACCCAGTCAATAACGTTGATATTAT[C/T]GGCCCCATGTAGGAAAACTTGCTCCAGATAACAGC Y 2 1 2 1 101000 f 74 goat snp26546-scaffold277-414294 15 60095574 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435565 Affx-122933377 AX-123305905 15 20546912 CAATTCTGCATTTTTGCTCCCTAAGGCATCCTGGA[C/T]AGAACAAGAAGGAAAACATATTTGCAGAGAGGTGT Y 2 1 2 1 101000 f 74 goat snp26545-scaffold277-383116 15 60064524 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785988 Affx-122970067 AX-385273024 15 20576854 GGATTGAATATAGGGCATAAAGATAACTTCCTTAA[C/T]GTACAACCATCCTGGTCAAAAAGAGCTGAGAAGTT Y 2 1 2 1 101000 r 74 goat snp26544-scaffold277-353174 15 60035602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798574 Affx-122936408 AX-385285507 15 20632858 GTGATAATAAACTGGAGAAACCATTAGGGAGGAGT[A/G]TTGAGGGCCAAGTTAAGTATGCTATGTGTGGACCT R 2 1 2 1 101000 r 74 goat snp26543-scaffold277-297170 15 59979518 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271944 Affx-1111833035 AX-519545720 15 20650283 GGGAAGTCACAATAATAGAATTATAGAACCCACAG[A/G]ATAGGACTATCATTTATCAGTGTCTTACTACTTAT R 2 1 2 1 101000 f 74 goat 15_20650283_AF-PAKI 15 20650283 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398347 Affx-122962118 AX-123268702 15 20669278 AGCTGTTTCGCAGCAACTACTTCCCGGGAGGCAAA[C/T]CTGCCCCCAGAAAAAATGATGAGGCCAGTTTCCAG Y 2 1 2 1 201000 f 74 goat snp26542-scaffold277-260750 15 59942778 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277035 Affx-1111835645 AX-519550543 15 20670474 ATACCACGTTCAAGAATACTTTGAATCTTTTATTT[C/G]TAGTTCCATTTCAGGTGTAAATCACTTTTCTAGCC S 4 1 2 1 101000 r 74 goat Random2.2K-1515 15 20670474 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38442453 Affx-122927954 AX-123312790 15 20730185 GAAAAAGGACTAACAACTTGTCCTTGAGCTTCAGG[A/C]TGAAGAGCACAGTTCACGTTTAGCTCATCTAAAAG M 2 1 2 1 101000 r 74 goat snp26541-scaffold277-199843 15 59882676 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433909 Affx-122934393 AX-123304250 15 20820858 CACTTACAATATAAATGTTTCCCAGGCGTTGACTG[C/T]ATGGGAGATAAACACTCTAACCTCTAGCACTTCAC Y 2 1 2 1 101000 r 74 goat snp26540-scaffold277-109170 15 59790664 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431754 Affx-122936730 AX-123302095 15 20878208 GCAGAGAAGCTGCCTGTAGCTAAGAGCCTGCAGGA[C/T]GGGTGCTCTTAGCCCCACTGTTATTGAACCAAACC Y 2 1 2 1 201000 r 74 goat snp26539-scaffold277-51820 15 59731793 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418158 Affx-122947094 AX-123288506 15 20926067 AAATAAAAGCAAGGACCAAGGAGCCCAGGCCCTGG[A/C]TGTTAGGGCCACACCCACTGGGGGAACCACAGAGA M 2 1 2 1 103000 f 74 goat snp26538-scaffold277-3961 15 59684416 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394191 Affx-122964915 AX-123264546 15 20932318 AGCATTTTTGGCACTTTCTATGAGTGGGGCAGGCA[C/T]GTGAGAGGAAGCACAGAGCAGGGGAAACTCGGTTG Y 2 1 2 1 101000 f 74 goat snp16004-scaffold1685-2191 15 59678271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400849 Affx-122959781 AX-123271204 15 21014996 CCCAACAGTCATACTCCCTGCAGAGTCCACATGCC[A/G]CAGAGCCCATCTGGGCAGAGAAGAACATTCTAACT R 2 1 2 1 201000 f 74 goat snp16006-scaffold1685-84869 15 59595115 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410702 Affx-122952731 AX-123281052 15 21045899 ACAGAGAAGCTCATTGAATTCAAGAGGAAAGTTTT[A/G]CTTATTCTAAAAGAAAAAGAAAATCCATTCTGGGA R 2 1 2 1 103000 f 74 goat snp16007-scaffold1685-115772 15 59563555 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768760 Affx-122956462 AX-385255937 15 21074603 AATTGCTACCATGAAACACGTATTATGCTAAATGC[A/G]TACCCTGCATTGTCACATGTAATACTCGCATCAAC R 2 1 2 1 101000 r 74 goat snp16008-scaffold1685-144476 15 59536024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386985 Affx-122969955 AX-123257343 15 21122563 GTGGAGCTGCTTTGTGAAACAAGCTGGGCTGGACC[A/G]TTCACTAGGTTCAGGCTATGGCACATGCTGGCGTG R 2 1 2 1 101000 r 74 goat snp16009-scaffold1685-192436 15 59487906 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451139 Affx-122921370 AX-123321473 15 21162333 AAGATTCAAAGACTAAATGCTGAGAAAAAAGGTAC[A/G]TATGTAGCTGGTGACTTTTAGAAACATCCAGAGGC R 2 1 2 1 101000 r 74 goat snp16010-scaffold1685-232206 15 59448182 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379555 Affx-122976053 AX-123249913 15 21167441 TTTAAACATTTTTTTCTCTATAACCTAAAATAAGA[C/T]GTATATTTAGCATCACAACCCACTATACAATTATG Y 2 1 2 1 201000 f 74 goat snp57877-scaffold937-2017 15 59442881 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421962 Affx-122943809 AX-123292309 15 21220194 CTCCAAACCACCAGCCATCCAGATGCTCCCAGAAG[C/T]TGAATCCTGGGCCCGAGCCCCTGTGGTTCTGATTA Y 2 1 2 1 201000 r 74 goat snp57878-scaffold937-54770 15 59390562 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427071 Affx-122939802 AX-123297414 15 21250697 ATGCTCCCTGGCCCTCATCTGCATTCCAGCCAGCC[A/G]TCTCCTGCCAGTGCCTAAGATACATTACCCGTTGG R 2 1 2 1 101000 r 74 goat snp57879-scaffold937-85273 15 59360283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790493 Affx-122925958 AX-385277496 15 21304320 CACAGAAAATAGTGTCAGAATTCAACATCAACACC[A/G]TCAATGACAGTCTAAAGTTCAAGATTTTTTGCAGT R 2 1 2 1 101000 f 74 goat snp57880-scaffold937-138896 15 59306699 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276903 Affx-1111835646 AX-519550412 15 21344568 CCGCCCGATGCTGCCAGGTAGAATTATGAACTGTT[A/G]CTGTTTTTCTGGTTTTCGGTTAGTTATCTCTTGCC R 2 1 2 1 101000 f 74 goat Random2.2K-1516 15 21344568 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436187 Affx-122932605 AX-123306526 15 21359533 CTTGAGATTTGTTATTTTGCTGAAATAGTGTATGA[C/T]GACTATTGACAAACGTTTGTCCATCTTTAAACTTT Y 2 1 2 1 101000 f 74 goat snp57881-scaffold937-194109 15 59251547 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441598 Affx-122928661 AX-123311935 15 21395306 GAGAAAAAACTAGCGAATGGACAAAAGAGAGCCAT[C/T]AACTGCTGATTATTATTTCAAAATGTTTGATAAGT Y 2 1 2 1 101000 f 74 goat snp57882-scaffold937-229882 15 59215297 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770239 Affx-122971248 AX-385257405 15 21425500 TTGGAACTTTTGGTAAAATACATACCATGAGCTGA[C/T]TCTTCTCTGTGTTTTGCCAAGAAGGTGTCACATTG Y 2 1 2 1 101000 r 74 goat snp57883-scaffold937-260076 15 59184593 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275343 Affx-1111834846 AX-519548918 15 21488516 TGCTCTTCTGCAGTGGTGGACACACACCATCATGC[A/G]TTTCTCAAAATCCA R 2 1 2 1 102000 f 74 goat GoatD01.056292 15 21488516 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320764713 Affx-122941374 AX-385252332 15 21502498 AGGCTTGTCTAAAACATCTTGTATTTATAACAGTC[C/T]ACTTTAATCTGATAGTAACTTAACTTTGATAGCAC Y 2 1 2 1 101000 f 74 goat snp57885-scaffold937-337074 15 59107714 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787057 Affx-122922676 AX-385274085 15 21536158 TTGTTAAGAATCAAATGAAATCATGAACATGAGAG[G/T]GACTTGAAAATGTGAAGACCTCTATAGAAATGTAA K 2 1 2 1 101000 f 74 goat snp57886-scaffold937-370734 15 59073782 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794289 Affx-122938175 AX-385281253 15 21592373 GTGTATTTGTGCTTATTCTGCTCAATAATACAGAC[A/G]CATTTTGAACTGGAGCATTCATGTCTTTCTTCAAT R 2 1 2 1 101000 f 74 goat snp57887-scaffold937-426949 15 59020656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425931 Affx-122941603 AX-123296277 15 21627895 AGAGAACAGCAGTTACTGGACCCAGCCACTGCCAC[A/G]TGAGGACACAGAAGGTGGCAAGGCATGGTGAGGGC R 2 1 2 1 101000 f 74 goat snp57888-scaffold937-462471 15 58984832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382456 Affx-122974219 AX-123252814 15 21666329 GGTCTTTGTTGCTGTCAACAATTCGTCCTGAGACA[C/T]GGGAATGTCAATCACAGCTGAAAAAAACTAAAAAC Y 2 1 2 1 101000 f 74 goat snp57889-scaffold937-500905 15 58945902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273835 Affx-1111833873 AX-519547446 15 21705092 TGAATGGGGTAAGTGAGGAAGGGAAAGGCCCCATG[A/G]CCTTGTCCCTTCCCCCTGCTCCTGCAGCAGGAACT R 2 1 2 1 102000 f 74 goat GoatD01.008670 15 21705092 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38441468 Affx-122928756 AX-123311805 15 21744706 ATCTTCTGGGGACACCTCACTTCTAATCCTGCCCA[C/T]TATACAGTGCTTTTCCAGAGAGCAGATTCCTCCAA Y 2 1 2 1 201000 r 74 goat snp57891-scaffold937-579282 15 58868391 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779976 Affx-122921067 AX-385267075 15 21800373 TGCATTATTTATACCCCTTGATACGAAAATATATC[A/G]CAAATGAATTTCAATGAGAGAGAGAATATTTCTTC R 2 1 2 1 201000 r 74 goat snp57892-scaffold937-634949 15 58811928 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428887 Affx-122938933 AX-123299229 15 21887665 GGGGACTTCTTGAGTTTTCCCTTCAGGCTCCTGGT[A/G]TGTTTTTGCACCAGGTGTCCTCAGGATTGTGGTGA R 2 1 2 1 101000 r 74 goat snp57894-scaffold937-722241 15 58726041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799729 Affx-122932044 AX-385286656 15 21931710 TAAACCACTGTTTGCTCTTAAGTGCCAAACACTTT[A/G]CTCCCTTTTGAAAATTGGGACATTTGCATGTCTTC R 2 1 2 1 101000 r 74 goat snp57895-scaffold937-766286 15 58683772 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384707 Affx-122972107 AX-123255065 15 21963720 TCTATTATGTTTGCCTTTTACAAGCCTGACTGTTA[G/T]AAAAAGGAAATTTGTATCTGTATTTGCAAATTTCA K 2 1 2 1 101000 f 74 goat snp57896-scaffold937-798296 15 58651612 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398044 Affx-122961758 AX-123268399 15 22017988 GCTCCCATCATGTGTGTTATGTGGATCGAATGTAC[A/G]TCTCAGGGCTCAAACCACAGGAGGATGCCTCTTGG R 2 1 2 1 101000 f 74 goat snp57897-scaffold937-852564 15 58597468 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438916 Affx-122930429 AX-123309253 15 22071366 GCAGCTTCTGGGGGTAGATCTCAATTTGCAGTATT[C/T]GGATTTCTTTTCTTTTCCTTTTCTTTCTCCTTTTT Y 2 1 2 1 101000 f 74 goat snp57898-scaffold937-905942 15 58543754 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776560 Affx-122952475 AX-385263687 15 22156061 TCTTGACCTTTCGCTCGTGGTCACATAAGGCTGCT[A/G]CAACTCCAAGCACCGCATCCCTCTTTAAGACAGAT R 2 1 2 1 101000 r 74 goat snp57900-scaffold937-990637 15 58458746 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384017 Affx-122972902 AX-123254375 15 22203146 AGCAGCTCCCTTCACGGACAAATACTAAAGGCAGG[G/T]ATCACACCTAAAACAGATGGATGCATAGTGAAATT K 2 1 2 1 101000 f 74 goat snp57901-scaffold937-1037722 15 58411775 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403110 Affx-122958128 AX-123273463 15 22239451 GCCTGAGAAGTCAGAGACACACTCCCTTCCCCCAC[A/G]ATCCTGACTGCACCTCTGCCCTGCTCCCACCTCTT R 2 1 2 1 101000 r 74 goat snp57902-scaffold937-1074027 15 58377301 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401562 Affx-122958896 AX-123271915 15 22302265 CTTCCTCATCTTTCCCCATCCTGCCTAGCTCCCAG[C/T]AGCATCCATCAAGGCTCTCTAGAGGGCATTGGCTT Y 2 1 2 1 101000 r 74 goat snp57903-scaffold937-1136841 15 58314655 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397416 Affx-122962247 AX-123267771 15 22337243 ATATTGGCAAATTTTCTCCCCATGAAACTACCAAG[C/T]GAGACATTTTTGTAAAATAATTTTCTCTACCAATT Y 2 1 2 1 103000 f 74 goat snp57904-scaffold937-1171819 15 58279545 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415977 Affx-122948411 AX-123286326 15 22388904 ACAAACAAACAAAGGTTAGCAATTTCCATTATAGG[A/G]TCCCTTAGGGCAGGAGCTATGCCTTTTCTAGGTTC R 2 1 2 1 201000 f 74 goat snp57905-scaffold937-1223480 15 58226949 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383534 Affx-122972625 AX-123253892 15 22495131 GCCATCAGATGCCAGAGCTTCCTCAGAAGAGAAGA[C/T]GCTCAGAAGATAAGCCTAGTCCTGTGGAAGCCCTG Y 2 1 2 1 201000 r 74 goat snp57907-scaffold937-1329707 15 58120209 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436930 Affx-122933190 AX-123307268 15 22519029 AAAAGAACACAGGCATTATCAGCCATTCTCTGGGA[C/T]GAACAGTAATTGCCAGTGACTTCACACTGAGTGTT Y 2 1 2 1 101000 f 74 goat snp22031-scaffold2168-145520 15 58094822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795962 Affx-122942549 AX-385282914 15 22580352 GCTGTTTTAAATTGATGTAGAAGAAATTTTAATGA[C/T]GTGAAAAATGTTTTTGATATGTTAAGTGACAAAAA Y 2 1 2 1 101000 r 74 goat snp22030-scaffold2168-84197 15 58034166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438864 Affx-122930755 AX-123309201 15 22634208 ATAAATAGCTTTCATTTATTAATCTTCTGCTGTGG[C/T]TTATGCTTTTTGTTTAAGAACTCCTATACCATGAC Y 2 1 2 1 201000 r 74 goat snp22029-scaffold2168-30341 15 57979795 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786758 Affx-122970809 AX-385273789 15 22664416 GAGACTTTTGTCAATTTTGTGAGGACCACAGAAAC[G/T]CTATTAGAGAATGAGGATGGTATGCTTTTGAGCTT K 2 1 2 1 101000 f 74 goat snp22028-scaffold2168-133 15 57949491 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401362 Affx-122959243 AX-123271715 15 22666875 AGAGTTACAGCCCCTTAAGAGCATGAGACTCCAGG[C/T]AGGGAATTCATTCACTCTAGGCTACCCTCTATTCC Y 2 1 2 1 201000 r 74 goat snp5325-scaffold1183-2762796 15 57947094 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389778 Affx-122968227 AX-123260135 15 22696928 CAGGGTATTAAAGTAAAAAAAGTGGAATTGTCAGG[C/T]GATATGCAGTAAGGCTTCTTAAATATCGCCTGGGA Y 2 1 2 1 101000 f 74 goat snp5324-scaffold1183-2732743 15 57915510 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405645 Affx-122956583 AX-123275997 15 22800728 GGAAGAACACAGATAGGGTAGGGAAATCTCCTCTG[C/T]GGAGATGACATGAGCTGAGGCAGACAAGCAGAGAA Y 2 1 2 1 101000 f 74 goat snp5321-scaffold1183-2628943 15 57807514 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386119 Affx-122971421 AX-123256477 15 22835741 ATAGTCATGGTTCCTATGTGCACAATCCATGAATG[C/T]GTTCCTTTGGGGGTTAGTAACGGTGACGATCTTAC Y 2 1 2 1 101000 f 74 goat snp5320-scaffold1183-2593930 15 57772532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395561 Affx-122963853 AX-123265916 15 22995078 GAAAGTCTCCCCTGCTACCCACGTCCTCTATCAGG[A/C]CGTGGTGAACACAGACAGTGGTTGTGACCCCTGAG M 2 1 2 1 201000 r 74 goat snp5317-scaffold1183-2434593 15 57612235 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419525 Affx-122945438 AX-123289873 15 23084054 AGGGCAGGGCCTGGTTGGACTCAGTCACTGCATCC[C/T]TAGATATAGAATAGGCCCAGCAGGGAGCAGCCGCG Y 2 1 2 1 101000 r 74 goat snp5315-scaffold1183-2345617 15 57524718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424542 Affx-122942243 AX-123294888 15 23131506 CTGAACAAAGCCACTTTAGTTTAACATTCAGCCAG[A/C]GGGGCAGGGTTCCCTGGGACAAGCCAATATGTATG M 2 1 2 1 101000 f 74 goat snp5314-scaffold1183-2298165 15 57477241 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420132 Affx-122946007 AX-123290480 15 23164572 TCTTTAAACAACTATGTCGCCCTTTAATGGGACTA[G/T]AGCACTTTCCCCCTGTTCATGCAGAGTTATGAACA K 2 1 2 1 101000 f 74 goat snp5313-scaffold1183-2265099 15 57444484 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768643 Affx-122979034 AX-385255822 15 23255440 CCAAATTAAACGTAAATTCAGTCTTATTCTAAAAC[A/G]TGTTCTTCATTGTGAAGCAAAGATATTGCTTTATC R 2 1 2 1 101000 r 74 goat snp5311-scaffold1183-2174231 15 57353632 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272831 Affx-1111833036 AX-519546524 15 23278396 AATTTGCATTTCTATATTCTTCAGTTAAGTTTACT[A/G]TATTTTCCCCATTACATTATGAACTCAGACTGAAG R 2 1 2 1 101000 r 74 goat 15_23278396_AF-PAKI 15 23278396 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38400557 Affx-122960424 AX-123270912 15 23353799 GTGGGGCTAAATAAATAAACAAATGAGTGAATAAA[C/T]AAGCACCCTATTTGACTCATTTGGGGAGAAGGCAA Y 2 1 2 1 103000 r 74 goat snp5309-scaffold1183-2075872 15 57254259 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430605 Affx-122936980 AX-123300946 15 23389403 TATTGACACAACTAAAATCTATTCTTTGAAAAGAC[G/T]AAAAAGAAAGACAAGTCTCTTAAAGACTGATTGAG K 2 1 2 1 101000 f 74 goat snp5308-scaffold1183-2040268 15 57218371 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407821 Affx-122954545 AX-123278172 15 23423645 GTAGTCTTAAACTTTCTACATATTTACATACTTAC[A/G]TAGTGAATTTCCCTTGCTTATTCCCTCATTTCCCT R 2 1 2 1 101000 r 74 goat snp5307-scaffold1183-2006026 15 57184184 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779300 Affx-122958112 AX-385266404 15 23459913 AATCTAGAGAAAATCTTATAAAGTCATTTGAAGTC[A/G]TCTCAAGGAGACCTCCTCTCATGCTTTTATGATCA R 2 1 2 1 101000 r 74 goat snp5306-scaffold1183-1969758 15 57147063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782326 Affx-122942016 AX-385269403 15 23494921 AGACAATTTGTGAACCTGGAGCATTCAGATGAAAC[A/G]TGGTATGATGCTCCAGGGTAAGGAGACAGTAGCAG R 2 1 2 1 101000 r 74 goat snp5305-scaffold1183-1934750 15 57118531 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453395 Affx-122919917 AX-123323728 15 23524978 CAAGTGTGCTGGGCTAGAACACAGAGACTGAGCCC[C/T]GTGGGCATAAGCTGTTGGTTAAAGATTCTGCAGGA Y 2 1 2 1 101000 r 74 goat snp5304-scaffold1183-1904693 15 57088542 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795153 Affx-122929415 AX-385282111 15 23625912 AATACAGCAGAAAGGACTTTAGAAAGGACTCAAAG[C/T]AGAAACACAACAATGTTGAGACTGGTGTAACCCAG Y 2 1 2 1 101000 r 74 goat snp5302-scaffold1183-1803759 15 56987439 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443976 Affx-122926996 AX-123314313 15 23661338 AACCTGCCTAGGAAGCCTGTCTGTGGGATCACATG[C/T]GAGCAGGAGTGATAAAGCCTAAGGCTGCACCCAGC Y 2 1 2 1 201000 r 74 goat snp5301-scaffold1183-1768333 15 56951826 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795170 Affx-122969871 AX-385282128 15 23713931 GAAAGAGTGAGATATTACAATATCAGGTGATAAAT[A/G]CAGGTACGTGTCTTATGACAACATGGTCAAGGCAC R 2 1 2 1 101000 r 74 goat snp5300-scaffold1183-1715740 15 56899039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434707 Affx-122933941 AX-123305048 15 23775299 TGGATGACAAATTCTGTATTTCTTTCATTCAAAAC[A/G]TATTTATTAATGGTGACTATGGAGTTATATTAGTT R 2 1 2 1 303000 r 74 goat snp5299-scaffold1183-1654372 15 56837604 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425679 Affx-122940863 AX-123296025 15 23810297 TCCATTAACCAGAGACAGAACTCAACACACTTCTG[A/G]AAGATGCAAAACCCAGGCCCCCACCCCCCAAAAGT R 2 1 2 1 101000 f 74 goat snp5298-scaffold1183-1619374 15 56802727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379220 Affx-122976280 AX-123249579 15 23846667 TGAACACCTAAGAGGTGCCAGGACTTTTCTGTAGT[A/G]CTGGTAACAGCGCGATGAACAAGACACACAACACT R 2 1 2 1 101000 f 74 goat snp5297-scaffold1183-1583004 15 56765744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450301 Affx-122922151 AX-123320636 15 23945929 TTGCAAGAAACTTACAGGGGGGTACCTGAAAACCT[A/G]GATGGCAGTTTTCTTTTAAATCTTAATTTCATTTG R 2 1 2 1 101000 f 74 goat snp5295-scaffold1183-1483742 15 56666620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398882 Affx-122961033 AX-123269237 15 23980036 CATCTTCGGGGACCGCCCGTCTTTCTGTTTCGACA[C/T]GTGTACAGTAGTGCAGTGCCCCGACGTGACTCTAT Y 2 1 2 1 201000 f 74 goat snp5294-scaffold1183-1449635 15 56634197 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780332 Affx-122957296 AX-385267427 15 24026280 GGTTATAACATTTGATTTATGAACATAATTAAAGC[A/G]TAAATGATGAGCTCTGGACTATTCCATCAGCCATC R 2 1 2 1 101000 r 74 goat snp5293-scaffold1183-1403391 15 56587971 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774793 Affx-122971720 AX-385261927 15 24061741 TGTCTTAGCACCAGTAGCTTTCTCAAAACTCTTGC[C/T]GTTAGTAATCAAGGACGGAATTATCTTCCAGAAGT Y 2 1 2 1 101000 f 74 goat snp5292-scaffold1183-1367930 15 56552609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276907 Affx-1111835648 AX-519550415 15 24153567 CATGTGCTGTTTTAGCATATCTTCAGCCCAAAGAA[A/G]CATCTTTAGTGCTCTCAATAGACCTATAATAATTT R 2 1 2 1 101000 f 74 goat Random2.2K-1520 15 24153567 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320771788 Affx-122969379 AX-385258945 15 24197669 AACACCAAGGATCTTGCTTGAAGCCATTTAGCAAC[A/G]TGACTTTCAACTCACTTTGGCTTTTTCAAAATAGG R 2 1 2 1 101000 f 74 goat snp5289-scaffold1183-1232002 15 56416982 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394628 Affx-122964403 AX-123264983 15 24242947 AGGAAAGCAGGGAACGATTGGCCAAAGATGCACAG[A/C]TTTTGAATATGATTCCTGCTTTTCACAGAAATATG M 2 1 2 1 201000 r 74 goat snp5288-scaffold1183-1186724 15 56371099 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768390 Affx-122962264 AX-385255570 15 24273527 CAGCAGCAAGCAGTACATCTTTATAATTTTATTAC[A/G]TTTCTTGTCAGTAGTTTTCTGTCTGATGACATGAT R 2 1 2 1 101000 f 74 goat snp5287-scaffold1183-1156144 15 56340506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788720 Affx-122937644 AX-385275736 15 24308623 TTTTCAAAAAAATTTAGACCACAACCCATGCAGTC[A/G]TATACACAATAAATTGCTATGTTCAGTGTGCCTTG R 2 1 2 1 101000 f 74 goat snp5286-scaffold1183-1121048 15 56305616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790723 Affx-122977892 AX-385277724 15 24353378 ATGGAGGCCATTGTAAGTTGCACTGTATCCTGGGA[C/T]AACTGACCAACATTTCTAGAAAGAGTGGCAGGATG Y 2 1 2 1 101000 r 74 goat snp5285-scaffold1183-1076293 15 56260178 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782519 Affx-122962886 AX-385269595 15 24403993 TTTTCCACTACTATGAACAACACAGAGTAACCATC[A/C]TTGTGACTGAATTTCTGGGAGCAATCGTACAAATA M 2 1 2 1 101000 f 74 goat snp5284-scaffold1183-1025678 15 56209692 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384737 Affx-122972043 AX-123255095 15 24434060 GCATGCCGCGGGCAACAAAGACAGACAAATCCCCC[A/G]CTCATTGTCCCTAATCAAATGTGTGCAAAGTTTAG R 2 1 2 1 101000 r 74 goat snp5283-scaffold1183-995611 15 56179538 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792230 Affx-122947246 AX-385279214 15 24521367 CTCATCTTTGAGCTTTTCTCACACCTACTGACTGC[A/G]GCAAATCCATCAACTAGTATTTAATAAGCACCTAT R 2 1 2 1 101000 f 74 goat snp5281-scaffold1183-908304 15 56091786 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408984 Affx-122953904 AX-123279335 15 24552958 TGCAAGGCAAAACATTGGACATTAGGGGGCTTTCC[A/G]TTGGTCTAGCGGTTAAGAATCTGCCTGTCAATGCA R 2 1 2 1 201000 f 74 goat snp5280-scaffold1183-876713 15 56060223 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446365 Affx-122925597 AX-123316701 15 24583405 GCCCAGAGGCCTTCTCCATGGAACCCATCTTGGCT[A/G]AGAGATGCATGTATGCACATGGGAGGATCCTGAGA R 2 1 2 1 201000 f 74 goat snp5279-scaffold1183-846266 15 56029871 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800782 Affx-122973342 AX-385287698 15 24683606 CGAGAATAATTTCAGCCATTGAACTCTGAAAAGAG[C/T]TACATAAAGTTGTCCGTGACTAAATATAGGTTTCA Y 2 1 2 1 201000 r 74 goat snp5277-scaffold1183-746065 15 55929598 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802588 Affx-122920033 AX-385289490 15 24731894 ACGACCATAAGGCACCATCCAGTGACGGCTTCTCA[C/T]GATCTGGTTTCAGCAGACAGGGACATCTAAAGGTC Y 2 1 2 1 101000 r 74 goat snp5276-scaffold1183-697777 15 55880954 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393888 Affx-122965120 AX-123264243 15 24817501 TAACTACTAAAGTTGTATGAGAGTCAGTTTTGTTC[A/G]TCCCACTTTATAGATGAGTCGACTGAGACTGAGGT R 2 1 2 1 201000 f 74 goat snp5274-scaffold1183-612170 15 55796131 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389086 Affx-122968587 AX-123259444 15 24847573 TATTTCCAACTCAAACTTCCTTTCCTGAGTGCCAC[A/G]TCCCCATACACAACAATTTGCAGGTGATCTCCCAC R 2 1 2 1 101000 r 74 goat snp5273-scaffold1183-582098 15 55766068 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790327 Affx-122946923 AX-385277330 15 24907699 GAATGATCCTAGAATAGGGAAGTCTCTCCTGACAC[A/G]TCAATAAACTTCGCACTAACTTCCTAGAGGGTCCC R 2 1 2 1 101000 f 74 goat snp5272-scaffold1183-521972 15 55705402 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411340 Affx-122952266 AX-123281690 15 24956565 TAAACAGGCTTCAGAAAGAAGCAGAAAAATGTCTT[A/C]TGTTTCATGTCTTATAGTATAGTCCAGCTGAGCAA M 2 1 2 1 303000 r 74 goat snp5271-scaffold1183-473106 15 55657107 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388739 Affx-122968959 AX-123259097 15 25052745 AGATAACAATTCTTTATGGTGATATTATACTTCCT[A/G]TGGAGGCTTTGGGGACAGCTTTGCAAATAAGACTG R 2 1 2 1 201000 f 74 goat snp5269-scaffold1183-376926 15 55561089 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397068 Affx-122962726 AX-123267423 15 25106198 TGGAAAGGAGTATGGTGAAGAGGTGACATGCATGC[A/G]TGAGAAGTTGTTGGAGATGAAGTTACTGACTGTCC R 2 1 2 1 101000 r 74 goat snp5268-scaffold1183-323473 15 55508645 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789533 Affx-122921290 AX-385276542 15 25202385 TCACACTGCTTTATCTCTCAGGCACTTAACACTTC[A/G]TGTTGTGTATACATCTTAATTTTAGTTTTTGGTCC R 2 1 2 1 101000 f 74 goat snp5266-scaffold1183-227286 15 55412557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392792 Affx-122965977 AX-123263149 15 25238177 GCTTCAGGATTTCCTATCAATCCTACATTGAATGC[C/T]TAGGTTTTTCAGGTAAAGTACTAGGCGCTGAAGAA Y 2 1 2 1 101000 f 74 goat snp5265-scaffold1183-191494 15 55377073 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784854 Affx-122951450 AX-385271901 15 25349111 TGGGGGCAGCTTCCCTCTTGCCTCTTCATTCATAC[A/G]TTCAACAAATAGTACTAATCATGTTGAATGAGCCA R 2 1 2 1 102000 f 74 goat snp5263-scaffold1183-80560 15 55265862 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414200 Affx-122949656 AX-123284549 15 25439797 TCGATAAACTCAGATACAACACGTAACTAGGGTGC[G/T]GAAAGACACAAAGAGAAGACAGCCATGGCACAGAG K 2 1 2 1 101000 f 74 goat snp4847-scaffold1162-10027 15 55177265 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439937 Affx-122930001 AX-123310274 15 25501271 CAGCCCTTGCTGTGCCCTGACCCACTGCAGAAATC[A/G]TAAGGGTCTATCAGGTCCCAACATTATCTCCTGGC R 2 1 2 1 101000 r 74 goat snp4848-scaffold1162-71501 15 55114921 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384803 Affx-122971994 AX-123255161 15 25530296 ATGTGCTCTTGTGCTCGTCTGCCTTCCCCTCTGAA[C/T]TGCAAGGTCCTCAAGGGTGAGGACCATGCCTTACT Y 2 1 2 1 103000 f 74 goat snp4849-scaffold1162-100526 15 55086044 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407238 Affx-122955367 AX-123277589 15 25576504 ACCTAATTAGGCTGTCTTAGAGCCGTCTCTGCCTT[A/C]GGGTGTGCTGAGGGAGGCTGGGCATTTCTCCCCTA M 2 1 2 1 101000 f 74 goat snp4850-scaffold1162-146734 15 55039348 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413970 Affx-122950297 AX-123284319 15 25628222 CTGTTTCCAAAACCCATGCTCTCTACCACCAAGGG[C/T]AGTGATGGTGGACCCCTGACACCACAAGCCTGCCT Y 2 1 2 1 201000 r 74 goat snp4851-scaffold1162-198452 15 54986514 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376623 Affx-122979038 AX-123246982 15 25667949 AATTGTTCATTTGAAATGACCTGAAAATACACTGC[A/G]TGATTTAGGCAGGCACACAAATGACCAGCAAAGCA R 2 1 2 1 101000 r 74 goat snp4852-scaffold1162-238179 15 54946732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426928 Affx-122940434 AX-123297273 15 25707859 TATAGTGAAATAAATGACTTACTCAAAACCAAAAA[A/C]ATATCTAAATCAGCCCAGAGTCAGGCCTGAGATTT M 2 1 2 1 201000 f 74 goat snp4853-scaffold1162-278089 15 54906385 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276909 Affx-1111835649 AX-519550418 15 25735007 GAGGAAAGATAAATTTCCCAAAGAAACTATAGTCT[A/G]TAGAAATACAGTTTTATTACAATTTATACTGTTTT R 2 1 2 1 101000 f 74 goat Random2.2K-1521 15 25735007 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424790 Affx-122941393 AX-123295136 15 25754924 AGATTGTTTGAGATGCTGATGGAAAGGACGTGAGC[G/T]CCGGCAGCTCCAGCAGATCCTGGCTGGCCCTGTGA K 2 1 2 1 101000 f 74 goat snp4854-scaffold1162-325154 15 54858385 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413739 Affx-122950056 AX-123284088 15 25785690 AGGCTCTTGCACTGCAGAAACCCACTCGAGGGATA[C/T]TGGGTCCAGGAGCTGAGCTGCCAACATCAGAGAGA Y 2 1 2 1 101000 f 74 goat snp4855-scaffold1162-355920 15 54831761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439498 Affx-122930145 AX-123309835 15 25825536 TTAAATACAAATTCTACCCCAAAACGCTGGTTTCC[A/G]CAAATTATTGTAATGTTCTGGAACAGAAGGGAAGC R 2 1 2 1 201000 r 74 goat snp4856-scaffold1162-395766 15 54791916 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432330 Affx-122936291 AX-123302671 15 25879038 ACCCCCTTATTAAAGACAGTGAAACTCATTGCACA[A/G]TCCACAGCTCCACACAGAGTCTGCCAGTTGCTTAG R 2 1 2 1 101000 f 74 goat snp4857-scaffold1162-449268 15 54737855 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272782 Affx-1111833038 AX-519546480 15 25894250 TTCTTTCTGCCTTACTTCACTCTGTATAATCGGCT[A/C]CAGTTTCATCCACCTCATTAGAACTGATTCAAATG M 2 1 2 1 103000 f 74 goat 15_25894250_AF-PAKI 15 25894250 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320768997 Affx-122966276 AX-385256172 15 25934935 AAATGTGCGAACCAACTTGAAATCTCCAAGCCAAA[C/T]CTTTGTGCTAAGGCCACTAAATTGTGTTGTAGTTA Y 2 1 2 1 101000 r 74 goat snp4858-scaffold1162-505165 15 54682989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778695 Affx-122936495 AX-385265806 15 25973926 ACCCTGTATATGTCAATATGACTGAAAGCAATAAG[C/T]ATCTATCATTCCAAGTAGGAGAGAAGTTATAAATT Y 2 1 2 1 101000 r 74 goat snp4859-scaffold1162-544156 15 54643986 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382370 Affx-122973860 AX-123252728 15 26006938 AGTGATTAAAACATGTAGTACAGGTACACAGTAAG[C/T]AGCCTTTATTAAGAGTATATGTTAACGAGACCATT Y 2 1 2 1 101000 f 74 goat snp4860-scaffold1162-577168 15 54611075 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445751 Affx-122926081 AX-123316088 15 26052512 TGAGACAGGATATGTTATTATCCCCATTTTGCAGA[C/T]AAGGAAAATGAGGCACAGAAGGATTAAGGGAGTTG Y 2 1 2 1 103000 f 74 goat snp4861-scaffold1162-622742 15 54565345 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414802 Affx-122949218 AX-123285151 15 26128376 GCCAGATAGTACGTGGCTCTGATTCATCAAGACAG[C/T]ACCTGTTCCAACTCTGTTTCTTATGTGTACTAGGG Y 2 1 2 1 101000 f 74 goat snp4863-scaffold1162-698606 15 54488559 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416075 Affx-122948333 AX-123286424 15 26160400 GTCTATCTTTACCAGAGGCCTGCTCTGTGCCAGGC[A/G]CCGTGAGAGTGGAGAGGATCATGTAGGGAGAAAAC R 2 1 2 1 101000 r 74 goat snp4864-scaffold1162-730630 15 54458690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394163 Affx-122964937 AX-123264518 15 26197717 GTCTAACAGTAGGCTATTTTATCTGCATTCCCCCA[A/G]TTATTAAATTTGACACCACCCAATTTCTGGGTTCC R 2 1 2 1 101000 r 74 goat snp41944-scaffold548-17230 15 54420265 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447657 Affx-122923964 AX-123317993 15 26242144 GATTCATTTTTTATCTTGTAATCTTCAGATTTTAT[C/T]TCCCCTCAACTTTGCAGCAGCCTTCGGGCCTTTTG Y 2 1 2 1 201000 f 74 goat snp41945-scaffold548-61657 15 54375861 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398112 Affx-122961707 AX-123268467 15 26286316 TTTCCCTCCGGTTCATCTCCACACCGTTCACTGAA[C/T]AGCTCATCCTTTGCCCACTGGTTGAGTGCCGCGTG Y 2 1 2 1 101000 f 74 goat snp41946-scaffold548-105829 15 54332128 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382584 Affx-122973728 AX-123252942 15 26329916 ATATATCTCAGAGTAACTCGGCTGGCAGCCTGAAA[C/T]GACATTCTGCTGAGCCTCCTCTTGGCCACTCGCTG Y 2 1 2 1 101000 f 74 goat snp41947-scaffold548-149429 15 54288501 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442436 Affx-122927967 AX-123312773 15 26376619 AATGTACCATCTTAGCAGAGTGTTCTTATGGAGCA[A/G]GACATCAACTACCTCTCTGCCTCCTCTCATCTCTT R 2 1 2 1 201000 f 74 goat snp41948-scaffold548-196132 15 54241723 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420958 Affx-122944976 AX-123291305 15 26412638 CATCCGTTCCCTAGGATACCTTTTTCAGTTGTCAC[A/G]TAATTTAGTTTGTGGTATATTACATGTGATTGGAG R 2 1 2 1 101000 f 74 goat snp41949-scaffold548-232151 15 54205686 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438591 Affx-122930946 AX-123308928 15 26443560 AAATATATGAGTGAGAATGCAGGAGAAGGCTGAGC[C/T]GAGAGGCAGGGGCCAGTCACGGGCTGTTGTTCCCT Y 2 1 2 1 101000 f 74 goat snp41950-scaffold548-263073 15 54175459 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420612 Affx-122945241 AX-123290959 15 26501346 AAGGGAGGTCTGGCCAGGAGGCAGAGTGAGACCAA[C/T]GAGTTGTTAAGTCTGGACTGTGTGTGCACTCTGTG Y 2 1 2 1 101000 r 74 goat snp41951-scaffold548-320859 15 54117726 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421970 Affx-122943803 AX-123292317 15 26530680 CAACAACAATTTTGACCATTGCTGTATTTGTTCCA[A/G]ATAGTTTTTTGACTTGTAGTTTGCCTTTTAACTTC R 2 1 2 1 101000 f 74 goat snp41952-scaffold548-350193 15 54089635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437110 Affx-122932173 AX-123307448 15 26567601 TAGTTTAAGATTGAGAGAGAAAGGGTGACTTCATA[C/T]GGAAGCTTGTAAACTTAGGGGTCATCTAGCCCCTA Y 2 1 2 1 101000 f 74 goat snp41953-scaffold548-387114 15 54052871 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436682 Affx-122932457 AX-123307020 15 26604863 GAAGGCAGCTTGTCCAAGATCCCATTGTTATTAAA[C/T]GGCTGAAATGGAAATCAGACCCATACTTACTCACT Y 2 1 2 1 201000 f 74 goat snp41954-scaffold548-424376 15 54016375 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443716 Affx-122927149 AX-123314053 15 26679254 AGTACCCCTGTATCTCCTGTTCTTCAGCATAACCA[C/T]GCACTTGACCCCTGGCCTGGTTCCGTGGGAGAGCA Y 2 1 2 1 101000 f 74 goat snp41955-scaffold548-498767 15 53941736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422575 Affx-122943752 AX-123292921 15 26775537 CGCTGTTTCACTGAGCACCTATTATGTGCCCAGCA[A/G]TGTATTAGGTTCTGGAGATAACTAGGAAGATAGAC R 2 1 2 1 201000 r 74 goat snp41957-scaffold548-595050 15 53845885 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444565 Affx-122926976 AX-123314902 15 26832246 ATTTTCCAAAGATGTTTCCAAAGATGGCCCCTCCC[A/G]TCCCACAGGCTCATCTGTAGTAAACCTTGGTCACT R 2 1 2 1 201000 r 74 goat snp41958-scaffold548-651759 15 53790557 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414897 Affx-122949123 AX-123285246 15 26892646 AGACACTGCTGTGGCCACGAGACTCCCACATCAGA[C/T]AGCAACGTCTCTACTCCTCTCTGATCCATCTGAGA Y 2 1 2 1 101000 r 74 goat snp41959-scaffold548-712159 15 53729601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416629 Affx-122947620 AX-123286977 15 26927903 TAGCTAGGATTAGGGGTAAAGGATGGGGAGGAGGC[A/G]CAACAGACTGACCCCTGCAGAGTCCTTAAACCCAC R 2 1 2 1 201000 r 74 goat snp41960-scaffold548-747416 15 53695526 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422234 Affx-122944016 AX-123292580 15 26961006 ATATGAAGATTCAAGAGAGAGGGGGTCCGAAGCTG[C/T]GGAATGGGTGGGAGTTTGGGCCGGGTCTCCTCCCT Y 2 1 2 1 101000 f 74 goat snp41961-scaffold548-780519 15 53662253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453421 Affx-122919884 AX-123323754 15 26992976 GGTTTGTTTTTGTTAAGCTTGGGGGCAAAGACTTA[C/T]ACACAGATGCAAAAATAAACCCTCTTTTACAACTC Y 2 1 2 1 101000 f 74 goat snp41962-scaffold548-812489 15 53629843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380070 Affx-122975556 AX-123250428 15 27026608 GTGCTCAGTGAATGGCTGATGAGTGAGAGAATCCC[A/G]CAGAGCCTGGGGTGAGGTCAAGGGATAGTCTGGGC R 2 1 2 1 101000 f 74 goat snp41963-scaffold548-846121 15 53597133 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407593 Affx-122954655 AX-123277944 15 27061447 CAAGCCATTCGTATTACTTTGTGGCACTATAGTTC[A/G]TGTGTTTTGACTGCAGCATAATATTCTATTGTGTG R 2 1 2 1 101000 r 74 goat snp41964-scaffold548-880960 15 53562111 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277045 Affx-1111835650 AX-519550552 15 27084550 CTATCCATTACCACACCCTCATTCTCACATGAGCC[A/G]AGTGTTGTTTGTCCTTCTTAAATGCCAAAGGTGTT R 2 1 2 1 201000 r 74 goat Random2.2K-1522 15 27084550 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401783 Affx-122959482 AX-123272136 15 27122020 TTTGGTAGGACTTCAGATTGAGGTGGTACAAATAA[C/T]GGGATGGGCAGGAAGACAGGGGAATGAGGAAGAGC Y 2 1 2 1 101000 f 74 goat snp41965-scaffold548-941533 15 53505986 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377400 Affx-122977565 AX-123247759 15 27150865 AGAGAAATCAAGCATCTGTCAAGCCAGGGACAGAC[A/G]GATGGCCTCAAGCCCTCCCTCCGCCTGACGACTGT R 2 1 2 1 101000 f 74 goat snp41966-scaffold548-970378 15 53476894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800874 Affx-122948999 AX-385287789 15 27195088 TAAAAGAATCTCCACCCTCCTGAAGATTACTGTGA[C/T]ATCATTTCTGTGCCTGGGCCATAACTCTTTTTGTC Y 2 1 2 1 101000 f 74 goat snp41967-scaffold548-1014601 15 53432370 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413990 Affx-122950284 AX-123284339 15 27223829 CTCCTGGACCCCTACCGCACAACCTGGACTCCACT[A/G]CCACCTCTAATAAAAGGTAGTATTGTCTTAAACCT R 2 1 2 1 101000 r 74 goat snp41968-scaffold548-1043342 15 53403629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785979 Affx-122963434 AX-385273015 15 27272545 CCAAATGCCTCTAATTATAAAATTGGGAGAATGAA[G/T]ATCTTGTGAAGGGTATGTGCTCCCTAAGGATCCTT K 2 1 2 1 101000 r 74 goat snp41969-scaffold548-1092058 15 53354719 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382745 Affx-122973602 AX-123253103 15 27305523 TTCGTTCCTTCCCCAGTGGATATTACTATTCCCTT[G/T]GGTTCCCTCTTTCTCCTGCAGAGAAATTGCCCCAT K 2 1 2 1 201000 r 74 goat snp41970-scaffold548-1125036 15 53321355 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276913 Affx-1111835651 AX-519550422 15 27454041 TATTAACAAATCATTTTGGCAATTCAAAGATGTGT[A/G]TGGATATACCACATTTTATTCATCTGTTCATCAGT R 2 1 2 1 201000 f 74 goat Random2.2K-1523 15 27454041 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38445847 Affx-122926006 AX-123316184 15 27540820 GAGGCTGAACCCTCAGGGAGTCTTTGTGCCAATCC[C/T]GTGGGCCCTAAACTGTCAGGGAGACTCCAGTCTCA Y 2 1 2 1 101000 f 74 goat snp41973-scaffold548-1360333 15 53087176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381985 Affx-122974091 AX-123252343 15 27590256 GTGCTGCGGGGGCATGGGGGAGCACAGCTGGGCGC[C/T]GCAGTGGTGACATTCGCAACAGGTGCTGAAGGTGA Y 2 1 2 1 101000 r 74 goat snp41974-scaffold548-1409769 15 53037573 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423654 Affx-122942347 AX-123294000 15 27621540 TCTATTTCATGACCCACGACAAGGTGCTTGGTTTA[C/T]GTGATCTGTTCACTGTCGTTTGTGTTTTATGGACG Y 2 1 2 1 101000 r 74 goat snp41975-scaffold548-1441053 15 53006242 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797244 Affx-122972701 AX-385284183 15 27651776 CTCTCCATAACAGCTTCTACTGAGCCTCTTTACAC[A/G]CTATACCATCAGCTCAGGATTAAGGAATTTCCGCT R 2 1 2 1 101000 f 74 goat snp41976-scaffold548-1471289 15 52976721 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420216 Affx-122945540 AX-123290564 15 27696729 TCTTCTATTCCCCTTCACTAATTTAGTCCCAACAC[C/T]GTGGGAATGAGCAGATAGATATCTATGAGGGGTTG Y 2 1 2 1 202000 r 74 goat snp41977-scaffold548-1516242 15 52930935 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415694 Affx-122948535 AX-123286043 15 27738097 GGTCAACCACAAGCTAAATATGAACCAACAGCTTA[C/T]AACATAATGTTAAGCAGTATCGATAAAAGTGCAAC Y 2 1 2 1 101000 f 74 goat snp41978-scaffold548-1557610 15 52889394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388655 Affx-122969108 AX-123259013 15 27811582 TATTCTGCTAAACCTAGCAGCAGTTAAATTGCTCT[C/T]TGCAAACCCTAAATCAGCCTCCTTCTCTGCCTCTC Y 2 1 2 1 101000 f 74 goat snp41979-scaffold548-1631095 15 52816544 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436500 Affx-122932956 AX-123306838 15 27858834 TTATAGCTTTCCCTTTACAGCTTTACAGGGGCAGC[A/G]TTCAGATCGCCCCTGTAGCAGCATGGGTGTGAGTG R 2 1 2 1 101000 f 74 goat snp41980-scaffold548-1678347 15 52768732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777987 Affx-122931342 AX-385265103 15 27982797 GGTTCTTATACTTGTAAGTATGAAAGATTTTATGC[A/G]TTTTGTATTTTCTAGGGTTTTCCCCTTTCATTGTA R 2 1 2 1 101000 f 74 goat snp41983-scaffold548-1802310 15 52646682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387690 Affx-122969817 AX-123258048 15 28012395 GGAATGAAGGGGCAGATCCTGGTCAACGGGAAGCC[A/G]CGGGAACTGAGGACCTTCCGCAAGATGTCCTGTTA R 2 1 2 1 201000 f 74 goat snp41984-scaffold548-1831908 15 52617160 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431290 Affx-122937095 AX-123301631 15 28049550 CCTGGTCTGTAAGCTTTCCCAGCCAGTGTTTTCTT[C/T]AAGCTCTTATTCTTAGTGGGTAGGCATGGTTGTAC Y 2 1 2 1 101000 r 74 goat snp41985-scaffold548-1869063 15 52579963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772168 Affx-122970268 AX-385259323 15 28095789 AAAAGATAGTGATTCATGCTGCTGTTATTTTGATA[C/T]AGTTTCTTTTAGAAAGAGTGACTTGATGTTATACT Y 2 1 2 1 101000 r 74 goat snp41986-scaffold548-1915302 15 52533810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427613 Affx-122939358 AX-123297956 15 28142119 ATGGCTTTGGGAATGTAGCATTTCCTTCTTCCTCC[C/T]CGTCCCCATTCTTTTTCCCTCTAGCTCTCAGATGC Y 2 1 2 1 101000 f 74 goat snp41987-scaffold548-1961632 15 52487583 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392392 Affx-122966221 AX-123262749 15 28181290 GGGTCAAGAATTACCCCCCAGGTGTGTGTGTATAT[A/G]TGTATGTTTGCACCTGGCTTTGGGACCATGTACCC R 2 1 2 1 201000 r 74 goat snp41988-scaffold548-2000803 15 52449476 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419620 Affx-122945981 AX-123289968 15 28221633 ACCTCCAAGAAAAGGCAAAGATATGGGGCCCCCAG[A/G]CAGTACTGGAATTCTTAAATTCTGTTTTCTAACCA R 2 1 2 1 201000 r 74 goat snp41989-scaffold548-2041146 15 52409326 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420867 Affx-122944636 AX-123291214 15 28253094 GATGAAATGGGAAAAACAAGGACGTTGTGGAGTAC[G/T]CTGAACATACCTGTCAGGCTGCTACATGGTTTTGA K 2 1 2 1 101000 f 74 goat snp41990-scaffold548-2072607 15 52378340 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381852 Affx-122974189 AX-123252210 15 28285398 CCAGTTCACATACACAGTACCCTTGTTGATAGACA[C/T]GGTCCCGCCATGGGAGAGCTGCCTGGAGGGAATGT Y 2 1 2 1 101000 f 74 goat snp41991-scaffold548-2104911 15 52346142 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422878 Affx-122943075 AX-123293224 15 28331388 TATTTAGAATCTGTCTTACATTCATTGGCTATAAA[C/T]AGAACCACGGCTAACAGACATGAGGTGGATTTGAA Y 2 1 2 1 201000 f 74 goat snp41992-scaffold548-2150901 15 52300320 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415655 Affx-122948565 AX-123286004 15 28360100 AAACCCATACATGATGTCAGAAGTGCTGTGAGTGA[C/T]GTGATAGAGTGAGAGTAAAGGAGAAACGCAGGAAG Y 2 1 2 1 201000 f 74 goat snp41993-scaffold548-2179613 15 52271614 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272784 Affx-1111833039 AX-519546482 15 28415394 GTGTCTATGCTGTGTATTTACCCACCCATTAGTGT[A/C]GGAAAAAACTTAGTATACATAGTTTCCCATCTGCT M 2 1 2 1 101000 f 74 goat 15_28415394_AF-PAKI 15 28415394 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38439184 Affx-122931050 AX-123309521 15 28435914 AGACACATGTCTTTACATGGTCTCTTCTATTAGAC[A/G]CTTGAGCCTAGATGTAATGCCTGGAACTGTGGCAG R 2 1 2 1 101000 r 74 goat snp41994-scaffold548-2255427 15 52194633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449597 Affx-122923213 AX-123319932 15 28476942 TCCCATAGTTGAGGTAGGGCACTGATGGGCACACC[A/G]CAGGGGGACCTTAGCCTCTCAGATGAATCCTGTGT R 2 1 2 1 201000 r 74 goat snp41995-scaffold548-2296455 15 52153936 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411975 Affx-122951778 AX-123282325 15 28521367 TCAAGGCAGAATGAAGACACTGCTTTTCAGGCTCA[C/T]GAAGATGGGGAAACCTAGTGCCTCTCTGAATCTCT Y 2 1 2 1 201000 f 74 goat snp41996-scaffold548-2340880 15 52109757 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428375 Affx-122938964 AX-123298718 15 28554179 CACAGGACCAAGTTTCTGGTCCTTACTGTTAAACT[A/G]GAAGGAAGCCCAGGGGTTATTCTTGCTTCTTCCCT R 2 1 2 1 201000 f 74 goat snp41997-scaffold548-2373692 15 52076730 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402413 Affx-122959007 AX-123272766 15 28588003 TTCTTGATGAGCCAGTTTCTTTTCTCTCTATTTCC[A/G]TGTTTCTCAAGTTTCTATAGACAGGGACTGTTTCT R 2 1 2 1 201000 r 74 goat snp41998-scaffold548-2407516 15 52042891 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789371 Affx-122942188 AX-385276381 15 28621045 TATTAAGTCCTTGATTTACCCTAATTTGTGTGGCC[A/G]TTGGTTTCCCATGGAGACTGATACTGGTTCATCCA R 2 1 2 1 101000 r 74 goat snp41999-scaffold548-2440558 15 52010144 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412324 Affx-122950848 AX-123282673 15 28683410 GTGCCGACTGAGCTCTCTCTGCACCTTAAGATTTA[C/T]GACACTGGTCTGAGCCCCCGTCACACATCCGATGG Y 2 1 2 1 101000 f 74 goat snp42000-scaffold548-2502923 15 51948535 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451715 Affx-122921554 AX-123322048 15 28737577 AGCCCTTTCTTCTGTGCCCTCTGGTCCCACATCTC[A/G]CAGCCCCATGGGGCTACAGGGCTGTCCCTGTCTGA R 2 1 2 1 103000 f 74 goat snp42001-scaffold548-2557090 15 51894566 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384906 Affx-122972346 AX-123255264 15 28776772 TCCCTCACTCACCATACCTGGGGATCCCAGAGATG[C/T]GTCTTACCATTGTTCTTACTCGATGTCAACCATCC Y 2 1 2 1 101000 r 74 goat snp42002-scaffold548-2596285 15 51855591 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416015 Affx-122948380 AX-123286364 15 28828858 GAACTGTAAGCCAGATCTGCCTGGGTCCAAAGCCC[A/G]CAACTGTAAGCCTCACTTACAGTCTCTCTCCTCTC R 2 1 2 1 101000 r 74 goat snp42003-scaffold548-2648371 15 51803736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384275 Affx-122972305 AX-123254633 15 28868385 GCTTTCAAGCAAGTCAGTTTCAACCCAAGTTTGTC[A/C]CTTTCTAATAGGAGTTTGCTGCCAGTCTCTTCAGG M 2 1 2 1 101000 f 74 goat snp42004-scaffold548-2687898 15 51764572 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399157 Affx-122960645 AX-123269512 15 28920538 AGCCAAGTAGCTCCTTTATTACCTCCCCAGCTCAC[A/G]TGTCAGGCTAGGTCTGAGCATCCATCACTTGCAGT R 2 1 2 1 101000 r 74 goat snp42005-scaffold548-2740051 15 51713036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426167 Affx-122940593 AX-123296513 15 28979343 GTCTGAAGCTCCCACCATTTAAGTCACTCCAGAGG[A/G]TCAGACATTTCCCCCTGAGGCCCTGTAAGGCACAC R 2 1 2 1 101000 f 74 goat snp42006-scaffold548-2798856 15 51654710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408789 Affx-122953370 AX-123279140 15 29013300 CGTGCTCTTAGATATTTTGAGCTCCTTAAACAAAC[A/G]GAATTGTGAGAGCTCTCTTTTGTCCAAATATGTAG R 2 1 2 1 101000 f 74 goat snp42007-scaffold548-2832813 15 51620468 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784867 Affx-122975018 AX-385271914 15 29044934 AAACACAGAGCTTGCTCTGAGAACTTGATTGAAGA[C/T]CTAAAGCTCAGAAGATAACCTGAAATAAATATTGA Y 2 1 2 1 101000 f 74 goat snp42008-scaffold548-2864447 15 51588814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766786 Affx-122946808 AX-385254118 15 29120524 GTAGGCTTCGGTTAAAGACACATCTGGGTAAACTA[C/T]GAGGAAGGACTTCCAGCCAATGAGCTTTATCAAAC Y 2 1 2 1 101000 f 74 goat snp42009-scaffold548-2940037 15 51513118 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375677 Affx-122978667 AX-123246036 15 29183287 CACATCTAATACGTGCATTGTATTACTTGTGTCTC[A/G]TAGTCCAAGGTCAGTCATCACTGGGAGATTATTGA R 2 1 2 1 201000 f 74 goat snp42010-scaffold548-3002800 15 51450394 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277048 Affx-1111835652 AX-519550555 15 29213456 GCGACCCCATAGACGGCAGCCCACCAGGCTCCCCC[A/G]TAAGATGAGGAGCCTATTAATATGCATCATGCTGT R 2 1 2 1 101000 r 74 goat Random2.2K-1524 15 29213456 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320788878 Affx-122961334 AX-385275893 15 29215591 TGAGATAGAACAGAGGAAAACGAGTCCAGGACGAC[C/T]CCCAAATTGCTGGGTGTTTAATTGAAAATTTTGAG Y 2 1 2 1 101000 r 74 goat snp42011-scaffold548-3035104 15 51418216 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417449 Affx-122947199 AX-123287797 15 29261661 ATCAGCCTAGTGTTGGGATACTATGTTGCTTAGAA[C/T]ATGGCCGTTTCTCAGCCTTCAGCCTCCCTTTCTGT Y 2 1 2 1 101000 f 74 goat snp42012-scaffold548-3081174 15 51372003 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390287 Affx-122967730 AX-123260644 15 29309496 GTTTAGATTAACTTACATATTCTAGGTTAAGGTCA[A/G]CTCTTGCTGCTTTGTGTGTTCATTGTAGTTTGGAA R 2 1 2 1 201000 f 74 goat snp42013-scaffold548-3129009 15 51323599 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381562 Affx-122974821 AX-123251920 15 29354057 CAACTTTGATCGACCGTTAGAAAGCATGAGTCCCT[C/T]TCAAAAATATTTTTTGTTAATTTTGTCCTTGGAGG Y 2 1 2 1 101000 f 74 goat snp42014-scaffold548-3173570 15 51278676 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419413 Affx-122945524 AX-123289761 15 29405697 TGTGTTCAGGCAAAGGGAATGTGCCCAAACCCTGC[A/G]CCCTAAGTAGATCATGCTCGAGCCGGGTAGGGGGG R 2 1 2 1 201000 r 74 goat snp42015-scaffold548-3225210 15 51228544 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769634 Affx-122952109 AX-385256804 15 29476621 TTGCTGAATTATAATAGCAAATTGATTTTATAGCC[A/G]CCAGTGTCTGTAACACATTCCAAGTCAACTTGGGA R 2 1 2 1 101000 r 74 goat snp42016-scaffold548-3296134 15 51157954 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441889 Affx-122928620 AX-123312226 15 29516781 GTTGTGGATCTCAGTCTAATGCAGGCACAAAACTC[A/G]TGCTGCTAACGGCTACCTTACACTACCCTCCTCTG R 2 1 2 1 201000 f 74 goat snp42017-scaffold548-3336294 15 51117879 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276917 Affx-1111835653 AX-519550425 15 29518286 AGCTCTAAGACCTTTGGATTGACTGTGTAACTTCA[A/G]GGTAGCCATATCCTCATCTGTGTAACAGGAGAAAT R 2 1 2 1 101000 f 74 goat Random2.2K-1525 15 29518286 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444338 Affx-122926726 AX-123314675 15 29576322 AGCGCATCTGTGCTAAAGTGTGTCTGCCCCAGTGA[C/T]GACTGGGAAAAGAGATGCTCCTGCATAGCCAGTCT Y 2 1 2 1 201000 r 74 goat snp42018-scaffold548-3395835 15 51058269 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773546 Affx-122973705 AX-385260687 15 29615685 GGAACTAGACCTTCAACCTAAGTGTCAATTTTCCC[A/G]CAGAAAGTCACAAATAAAGCTTGCCACATACCATA R 2 1 2 1 201000 r 74 goat snp42019-scaffold548-3435198 15 51019036 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433770 Affx-122934485 AX-123304111 15 29651164 TGGCTGAGCAGGAATGAAAGGAAGGAAAACCACCA[A/G]GGACGAAAAATGAAGAGAAGCTGAAACTACAGTGG R 2 1 2 1 101000 r 74 goat snp42020-scaffold548-3470677 15 50983831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410994 Affx-122951995 AX-123281344 15 29687398 AGAACCACTGCTCTGGGTTGCCCCACTTCCCTTCT[A/G]CTCCCAGAGTCTTCTTCCTGGGATAGCGCAATGTA R 2 1 2 1 101000 r 74 goat snp42021-scaffold548-3506911 15 50947339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403221 Affx-122957902 AX-123273574 15 29724191 GTCCCTTAGTCCCCCTGCCAAGGGCAGATCAGAAC[A/G]TATGTTTCCCCTGCAGTAGCTGATTTCTGCCTGGA R 2 1 2 1 101000 r 74 goat snp42022-scaffold548-3543704 15 50910808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424160 Affx-122942535 AX-123294506 15 29808689 AAGGATGCTTTTCCTGAACCTGGGGCCAGGGCCCT[A/G]CTCACCCTATTTAAGTGCTTCCCATCCTCAGGCAC R 2 1 2 1 101000 r 74 goat snp42024-scaffold548-3628202 15 50826175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447793 Affx-122923939 AX-123318129 15 29838895 GCTGGCGTGAACAGCTCACACTAAGCAGAACTGAC[A/G]GTTTATGCATTTATTCAACAAATATTTACTTGCAT R 2 1 2 1 101000 f 74 goat snp42025-scaffold548-3658408 15 50796518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792792 Affx-122974060 AX-385279771 15 29933436 AATGGGAGAAAAGTGAAAGAATCCATGCCAATATA[C/T]GATTAATTACCCACTGAATATTTTAGGTAATGGAT Y 2 1 2 1 201000 f 74 goat snp42027-scaffold548-3752949 15 50702174 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402623 Affx-122958403 AX-123272976 15 29993193 CTCTTTCTTTGATATATGTTTTTCTGGATCCACCA[C/T]GTTTACCGATGGGAGACTTGAAAAGGACTTAGTGC Y 2 1 2 1 101000 r 74 goat snp42028-scaffold548-3812706 15 50641812 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434998 Affx-122933821 AX-123305338 15 30022757 GTTGAATGAGTGGATGAGTGAATGAAAGAACACAT[C/T]GGCAAATGAGCAAGAGTGTTGCCCAGTTACCTGAG Y 2 1 2 1 201000 r 74 goat snp42029-scaffold548-3842270 15 50612351 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783260 Affx-122955767 AX-385270325 15 30079850 CTACTTTGAATTTCAATCTGAGTTGAATGTGGATT[A/G]TCTACAAATGAAAGGAGATAATGAGAATTACTAAA R 2 1 2 1 101000 f 74 goat snp42030-scaffold548-3899363 15 50555586 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395536 Affx-122963859 AX-123265891 15 30109105 CAGGTAATTGACTCAGAAATCAAGTGATGGTATCA[A/G]TGGTATCAGTATTAACTAACATTAATTGTTATTAA R 2 1 2 1 101000 f 74 goat snp42031-scaffold548-3928618 15 50526372 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765629 Affx-122961158 AX-385253102 15 30142212 CAAAAAGGTAGGGATGGAACTGAAGAACAAAGAGG[C/T]ATTTCCAGCAACTCGAAAAGCTAGAGTCCAGGCTA Y 2 1 2 1 101000 f 74 goat snp6688-scaffold1243-29555 15 50486361 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378789 Affx-122976995 AX-123249148 15 30210123 TCCAAGTTTTAAAAAAATCTTGAGATTTGACCTTT[A/G]CCATTCACAATTTTGTAAAGAAAGGAAAGGGACTG R 2 1 2 1 101000 r 74 goat snp6689-scaffold1243-97466 15 50417283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403913 Affx-122957479 AX-123274265 15 30270932 TCAGCCCTTGTGTTGGCTGCCTGCTGCCCAGACAG[C/T]GGGGTGAAGTCAGGACAGAGCCCCTGTTTCAGCAT Y 2 1 2 1 103000 f 74 goat snp6690-scaffold1243-158275 15 50357664 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410931 Affx-122952049 AX-123281281 15 30326555 TCCCCTGAACCACAGTGTCATCCAAAGGTCACCTG[C/T]ACTTGTCCTGGGTCTCATTCCCCACACTGAGTTGA Y 2 1 2 1 101000 r 74 goat snp6691-scaffold1243-213898 15 50301653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430636 Affx-122936958 AX-123300977 15 30390340 AACGGCACCCTTTGTTTCACAATGCTTGGCAGCCT[A/G]GGAGCAGCAGCAGTGAGGAAAAACCAGTGATTCAT R 2 1 2 1 101000 f 74 goat snp6692-scaffold1243-277683 15 50237580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441537 Affx-122928707 AX-123311874 15 30455936 CATTACCAATTGTCATGAATGAACCCTGTTTCCCA[A/G]CCTGCAGGCCAGGATGGCATAGGCTAAACTTTGGC R 2 1 2 1 102000 f 74 goat snp6693-scaffold1243-343279 15 50171954 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768715 Affx-122925724 AX-385255893 15 30484605 TTCCTTTGAAAATATTGAGATGTTTCCTAAAGAAA[C/T]GTCAGACATCTTTCAGCTTGACTATTCATCTGTTT Y 2 1 2 1 201000 r 74 goat snp6694-scaffold1243-371948 15 50143437 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402525 Affx-122958480 AX-123272878 15 30516648 GAGTTTCATTCAAAACTCCGAGCCCTACCACCTTC[C/T]CTTTTAAATAAGCACTTTAAGTAACTGAAAGATGA Y 2 1 2 1 201000 r 74 goat snp6695-scaffold1243-403991 15 50111468 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379475 Affx-122976481 AX-123249833 15 30557428 TGACAAATGTATGGACCCATGTCAGCACCACCACC[A/G]TCAAGGTCTAGAACATTTTCATTACTTAACACATC R 2 1 2 1 103000 f 74 goat snp6696-scaffold1243-444771 15 50070925 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399575 Affx-122961118 AX-123269930 15 30601245 CTGAGCCACGTAAGTGACGCCCAGGCAAATTGTCT[A/G]CCAGGCTTCAGTCTGCCATAGGAAAGAAGTAGAAT R 2 1 2 1 101000 r 74 goat snp6697-scaffold1243-488588 15 50026514 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398701 Affx-122961855 AX-123269056 15 30630928 GTACCAAAGTCTTTTTTTCTTCTTCTTACACCCCC[A/G]TCTCTCTTTGTGTCTCTTCTCTGTCTTCCCCAGGT R 2 1 2 1 101000 r 74 goat snp6698-scaffold1243-518271 15 49998130 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445275 Affx-122925465 AX-123315612 15 30698722 TTTATAAAATTTAGACTCCAGAAACATCTACATAC[A/G]TCTGTTGAAAGTAAAATAAAAATGGAGAGAGCTGA R 2 1 2 1 101000 f 74 goat snp6700-scaffold1243-586065 15 49930040 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776405 Affx-122968496 AX-385263532 15 30737675 AACTTGAGCTCTTTTTGTAATAGTTATAGACATTG[C/T]ACACATATTGGGTAAAGTATGAAAGCATCTTTAAC Y 2 1 2 1 101000 r 74 goat snp6701-scaffold1243-625018 15 49890899 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451549 Affx-122921709 AX-123321882 15 30780182 GACCTTGCTGGATCTTTGTAGCAGCTTCTGTAAAA[C/T]GAAGGGCTTTATTGTAAAGATCCCTAACATCCCTT Y 2 1 2 1 101000 f 74 goat snp6702-scaffold1243-667525 15 49848106 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416541 Affx-122947754 AX-123286889 15 30809823 GATGGACCAACAACTTGGGAACAGACTCTGCCTCC[A/G]CAGAGATGTGACAACCTCAGAGAAAAGAGCAGGCC R 2 1 2 1 101000 r 74 goat snp6703-scaffold1243-697166 15 49817973 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384288 Affx-122972296 AX-123254646 15 30896775 GCCTTACACTCTGAATGCACGAAATCACACAGCCT[A/C]TTTCTACACAAAGCTCCACACTCCCCAGCAAGGAC M 2 1 2 1 101000 f 74 goat snp36782-scaffold445-3970317 15 49730485 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420011 Affx-122945162 AX-123290359 15 30935723 ATTAAAATAGACCAACCTTCTCTGTGTTCTCAGTG[A/C]CTCAAGTGGAGTAAAGGTGGGTGAGAATTCCGTTT M 2 1 2 1 102000 r 74 goat snp36781-scaffold445-3931369 15 49691731 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437168 Affx-122932130 AX-123307506 15 30967889 CCAATGTGAGGCTTACTTTTTAGCCTTGATCTTCT[C/T]GATCCTGGCTACTGCCCTGTTTTTGTTTTGTGTTT Y 2 1 2 1 201000 f 74 goat snp36780-scaffold445-3899203 15 49659305 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406367 Affx-122955418 AX-123276719 15 30999298 AGTGTGGACCAAGGATCAGGACCTCTTACTCAACC[A/G]CTTGTACTCACCATGGAAAGGGCTCAGAAAGTTGT R 2 1 2 1 201000 r 74 goat snp36779-scaffold445-3867794 15 49627021 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384665 Affx-122972138 AX-123255023 15 31040979 AGCATGAGCTTGCATTTCACCAATGGAAACATTCT[A/G]TCTGGGTGATCAAGGAGCGCCATACCAAGTACATG R 2 1 2 1 101000 f 74 goat snp36778-scaffold445-3826113 15 49584533 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272787 Affx-1111833041 AX-519546485 15 31045778 CCAGATGCATCAACAGCTAGTGTTATTAAGCAATA[A/G]TGGTAACGTTTGCTGTCTGATAGGAGCCTTGCTGG R 2 1 2 1 101000 f 74 goat 15_31045778_AF-PAKI 15 31045778 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38428222 Affx-122939439 AX-123298565 15 31069692 AGCACAGATACATTACCCCTTGGAAGCAGTTTTCC[A/G]TGGAAATATTTGAGTAGGCAGTTGAAATCAAGGTA R 2 1 2 1 201000 r 74 goat snp36777-scaffold445-3797400 15 49555677 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376038 Affx-122978940 AX-123246397 15 31102774 ATCATGATCTTTTTTTGGAAAGTGACAGAGACTTG[C/T]GTACAAGACCTGTTTCACCCTGCTTTGGGTTCTAC Y 2 1 2 1 101000 r 74 goat snp36776-scaffold445-3764318 15 49522671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430038 Affx-122937572 AX-123300379 15 31136629 AAGAGATGATCTGGCTTGGGCCATGGGTTTATTGA[C/T]CACTAGAGATGGTGAGAAGCAGTTCAGTTGTGTAT Y 2 1 2 1 101000 f 74 goat snp36775-scaffold445-3730463 15 49489050 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424058 Affx-122942061 AX-123294404 15 31173744 CTTTGCACGTATCAAGGCTGGTGAAGGAAGGAAGG[C/T]AACCCCTAGGTCCTCTGAGGGGAACTTCAGTGTTC Y 2 1 2 1 201000 f 74 goat snp36774-scaffold445-3693348 15 49451938 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768279 Affx-122946986 AX-385255460 15 31208812 CAGGGATAATTTTAGTGTGCATGGTCCTGAAGCCA[C/T]ATAATGCAGTGACTGCTCTTGGTCATTTTTGGAAC Y 2 1 2 1 101000 f 74 goat snp36773-scaffold445-3658280 15 49416648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425135 Affx-122941210 AX-123295481 15 31253562 ATATTAAAATGGCAGAGAATTTGAAAGTCATTTCT[A/G]TTTAGCTGTGGAAGTTAGAGATTGGAGGCTCTCTC R 2 1 2 1 101000 r 74 goat snp36772-scaffold445-3613530 15 49371721 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417744 Affx-122947421 AX-123288092 15 31314225 ATATTTAAGAGGAAAATCTGCTTTCAACAACTTCA[A/G]TGAGAGGGTGATTTTTTTTTAATCTTATAAAGCTT R 2 1 2 1 101000 f 74 goat snp36771-scaffold445-3552867 15 49311149 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410967 Affx-122952021 AX-123281317 15 31370939 CCCTCCACATTCACTGCCTATGCTCAGTATTCTAG[C/T]GTAGCCCACAATTCTACACAACATCTTTACCCATG Y 2 1 2 1 101000 r 74 goat snp36770-scaffold445-3496153 15 49254217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797697 Affx-122975988 AX-385284636 15 31402117 GAAAAAAATTGAGATTATGGTGAGGAAATGAAAAG[A/G]CATGTATTTTGAGCATAGTCATCTTCTGCAGTGGA R 2 1 2 1 101000 r 74 goat snp36769-scaffold445-3464975 15 49223306 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764829 Affx-122976569 AX-385252432 15 31432456 CTTAACAAAGTAAAAGTCCCTGAGACTGGAAGCTC[A/G]TATCTATATAAGGTCCATACCACAAAAATTTGGGC R 2 1 2 1 101000 f 74 goat snp36768-scaffold445-3434636 15 49193161 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390998 Affx-122966900 AX-123261355 15 31462931 AAAAGCCATGTGAGTATCACTTTGAATACATCTAG[A/G]CATAGTTTTAAGTATACATAAAATATACTGTCTTT R 2 1 2 1 201000 r 74 goat snp36767-scaffold445-3404161 15 49162428 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453220 Affx-122920433 AX-123323553 15 31506850 AACCTGGATGAAGCAGGAAGTCTGCAGAGAGAAGA[C/T]GGAAGAAGCATGAAGGCTGTGACGAGCCACTAGAA Y 2 1 2 1 201000 r 74 goat snp36766-scaffold445-3360242 15 49117731 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423987 Affx-122942118 AX-123294333 15 31552103 AGGAGAGGAGGGATCAGGAAAAGGAGAAAGCAAGA[C/T]AGCAGGGAAGAGCAGCCTTCCCTGATAATGATGGC Y 2 1 2 1 103000 f 74 goat snp36765-scaffold445-3314989 15 49071744 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442804 Affx-122927717 AX-123313141 15 31584090 TGGGCAGAGAATTGGAACCAGCACTGCCTGTGTAC[A/G]CTGGTTCAGGAGAGTCACTTCCAGCGCTCTAGCTT R 2 1 2 1 101000 f 74 goat snp36764-scaffold445-3283002 15 49039806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386121 Affx-122971419 AX-123256479 15 31613500 TAGGCTGAGTGCAGCTATAAGGGAAAGAAGGGTAG[C/T]GAGGATGATCCCCTCTTGTCAGCCCAGGCTGGGGG Y 2 1 2 1 101000 f 74 goat snp36763-scaffold445-3253592 15 49010309 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436142 Affx-122932636 AX-123306481 15 31644207 CTGGTACTGCTCCATGCCTTCAAGAGCTGCTATAA[C/T]GTCAGCCAACCAGAAGGCCTTTGACTTCCCACAAC Y 2 1 2 1 101000 f 74 goat snp36762-scaffold445-3222885 15 48979937 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802077 Affx-122933257 AX-385288981 15 31694724 TTCCATGCTAATAGGAATATTTCAAGACTGGGCAA[C/T]GGAAGACCCAGATACCCTCTCTGGCTAAAAACAAC Y 2 1 2 1 101000 r 74 goat snp36761-scaffold445-3172368 15 48932313 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800965 Affx-122928154 AX-385287880 15 31734748 TATATATACTATCAATATGTACGTATGTACACATG[C/T]ACACGCCAGGGAGGTCCCAAGTATTCTTGACCCCA Y 2 1 2 1 102000 r 74 goat snp36760-scaffold445-3132344 15 48892271 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378120 Affx-122977139 AX-123248479 15 31784584 GTACATGTTTTTGGAACGAAGTGTCCTGGTAAAAA[C/T]ATGGCCTACCAGGTCAACTATTGTGATTTAGCAAG Y 2 1 2 1 101000 r 74 goat snp36759-scaffold445-3082508 15 48842540 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800959 Affx-122922728 AX-385287874 15 31830158 TCTGGCTACTAAACAAGTCTTGAATAAAAGCAAGC[A/G]CTGAATATGCACTAGCTAAGTATTGGCTGACTGTG R 2 1 2 1 101000 r 74 goat snp36758-scaffold445-3036934 15 48796480 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413438 Affx-122950688 AX-123283787 15 31867810 TTAGGTGATGGAAATTTAGAAATGGCCAAGTATGC[A/G]ACTTCCACTGATCCCTGCTCACTAGAAATTGAGCT R 2 1 2 1 101000 r 74 goat snp36757-scaffold445-2999282 15 48758224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783720 Affx-122964963 AX-188423144 15 31897111 ATCCGTATGGAATATGACGCTCCCACTTCTTGGAG[C/T]GCTGTAGTTTGGGGCCTAATTGATTCTGGTAATTA Y 2 1 2 1 201000 r 74 goat snp36756-scaffold445-2969981 15 48728463 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801257 Affx-122951014 AX-385288170 15 31928209 GGGTCTTTTTTTCTCTTGGTTGCACAGCCTTCATG[A/C]TCTTATTTCTCCAACCACGGATCAAATCCATGCTC M 2 1 2 1 101000 f 74 goat snp36755-scaffold445-2938883 15 48697288 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448142 Affx-122924283 AX-123318478 15 31972316 GCTACCAAAGATGCTGGAACTATTGCTGGTCTCAA[C/T]GTACTTCGAATCATCAATGAGCCAACTGCTGCTGC Y 2 1 2 1 101000 r 74 goat snp36754-scaffold445-2894776 15 48653130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414317 Affx-122950047 AX-123284666 15 32001678 TACCATCCTTTCTGCCTCGGCTGCACTCAACCACT[A/G]TACCTTGGCTCAACCTAGGTCTTCTGGCATAACTA R 2 1 2 1 101000 r 74 goat snp36753-scaffold445-2865414 15 48623034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435417 Affx-122933548 AX-123305757 15 32032550 ACTGTTACACTGGAAATGAAAACCTATGGGCAGTC[A/G]TCTTACTTCAAACAATTCAATATCCAGCCTGCATC R 2 1 2 1 101000 f 74 goat snp36752-scaffold445-2834542 15 48592229 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412506 Affx-122951366 AX-123282855 15 32065763 TTTCTCAGGCATGGTCCTGGTTTGGTCTGTCTTTG[C/T]ATCCCATGCAGTGTAGTAGTACACATAGTGGTTGT Y 2 1 2 1 101000 r 74 goat snp36751-scaffold445-2801329 15 48558610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389528 Affx-122968286 AX-123259886 15 32102394 AAATAGAAAAAACTCTTGAGAACCACAAATACATA[C/T]GGCAAATTGGTACATAATCAAGTTGGAATCACTAA Y 2 1 2 1 101000 r 74 goat snp36750-scaffold445-2764698 15 48522087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430146 Affx-122937387 AX-123300487 15 32153016 CACAGCCTGTGAGTAGCTTTTCTGCCTGAAATCTC[A/G]CCAGATCCCTTTCCCTATCTACCCTCCACACAGCT R 2 1 2 1 101000 f 74 goat snp36749-scaffold445-2714076 15 48471244 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427542 Affx-122939502 AX-123297885 15 32206143 GAAAAGGTGGGCACAGGAGTGGTGAGGATAGAACC[C/T]GGATAAAAGTGTGTTATTGGTTTAATACTAATTTT Y 2 1 2 1 201000 r 74 goat snp36748-scaffold445-2660949 15 48418342 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437940 Affx-122931629 AX-123308278 15 32244569 AGCTAATCAGAAATCTGGTTAATTAGCTTTGCAAC[A/G]TGAAGTGTCTCACAGAGAAAAATCTTATCAGGTTC R 2 1 2 1 101000 f 74 goat snp36747-scaffold445-2622523 15 48379718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396180 Affx-122963770 AX-123266535 15 32292441 TCTGGGAGTTAGAGAGTTCTGAGATGATTTTTGGC[A/G]CAATGGTAGAAAACAAACCATTCTGAAAGGAGTTA R 2 1 2 1 101000 r 74 goat snp36746-scaffold445-2574651 15 48331434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402378 Affx-122959032 AX-123272731 15 32321066 GAAAGTTTTATGAGCAATAGACCTTCCTTAGGCAA[C/T]AGAATTATAAGCCTGAAAGAAACATCAGATACTTA Y 2 1 2 1 101000 f 74 goat snp36745-scaffold445-2546026 15 48302903 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431197 Affx-122937169 AX-123301538 15 32378265 TACTCAAGAGAAAGAAAGGCTGTTTGGACATTTTA[C/T]GATACTAGCTGAACCTAAAGCTGGTGATCAGTCAT Y 2 1 2 1 101000 r 74 goat snp36744-scaffold445-2488827 15 48245043 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432383 Affx-122935856 AX-123302724 15 32423034 AAAGGAGACAGGACCATCCTGGGCCCTGCTCTGTA[C/T]GGCAATGAAAACCCCAAAGGGGACTGGACTCCTGC Y 2 1 2 1 101000 r 74 goat snp36743-scaffold445-2444058 15 48207513 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414371 Affx-122950005 AX-123284720 15 32456833 TACTGCATCTCTCCCATGAGGGGCAGTGATGTCTA[C/T]ATAATTAAAATCTGAAGCAAGAAATGGCCAGAAGG Y 2 1 2 1 101000 r 74 goat snp36742-scaffold445-2410259 15 48173819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423911 Affx-122942276 AX-123294257 15 32505897 GAGCCAGTCTCCCTGACTCAGCAGGAATCTGCTGA[C/T]ACTAACAGTGGCCTCGCAGGCCCCAATGGATCAGA Y 2 1 2 1 202000 f 74 goat snp36741-scaffold445-2361195 15 48125216 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400619 Affx-122960379 AX-123270974 15 32552596 CAGGGAAGGAGAAAGGACTTGTAGAGAACTCTTAT[A/C]TCGTGAGTTTGGTCTTCTAGTGCTTGTTGTAGCTC M 2 1 2 1 101000 r 74 goat snp36740-scaffold445-2314496 15 48078195 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776553 Affx-122956279 AX-385263681 15 32588470 TATATTTTAATGCATTATCTAATATAATCCTCATC[A/G]CTGTTGGTTCTCTTGACTAGGGATCAATGTCTGAT R 2 1 2 1 101000 r 74 goat snp36739-scaffold445-2278622 15 48042227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424050 Affx-122942069 AX-123294396 15 32623163 CGATTATTATAGCTTTATTTACAGTTTTCATGTTT[A/G]TATTTACTCTCAATTACATTTTTAGACCTTGACCC R 2 1 2 1 101000 r 74 goat snp36738-scaffold445-2243929 15 48007700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763219 Affx-986697748 AX-385251147 15 32667469 AGGGCCTGGGAGGCGTTTGGGTAGGTTCTCGAGCG[A/G]GGGTGTGGGCGGGCTGAATGGGGGCGTGGGTGGGC R 2 1 2 1 600010 f 74 goat 15_32667469 15 32667469 Ancestral_priority_1043 ancestry 0.428 neutral IMAGE 10K 10K ancestral 320766061 Affx-986697760 AX-188521137 15 32667541 CTCGTGGCACTAGGACTGAATTGGGCCCTATGCCC[C/T]GATTTGGACCGATCTGTATGGGTCCTACTTTCAAC Y 2 1 2 1 600010 r 74 goat 15_32667541 15 32667541 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 38445010 Affx-122926638 AX-123315347 15 32672105 CTGACATTTACGGCCAGTATGATCATGGGAAAGTT[A/G]TTTACTCTCTTCATACCTCAGTTTCCTTATTAATA R 2 1 2 1 201000 r 74 goat snp36737-scaffold445-2194987 15 47958967 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476309 Affx-1251763816 AX-586011727 15 32714235 CAATATCTAACCTTTCCCTCTTTTTCTCTTTTCTT[-/TAAAATCCTTGAAGCAGAGAGGGAAAGATGGTGGAGGAATAATAAATAAATAAAAAAAATAAAAAATAAAACACTTAAAA]AAAATCCTTAAATATTGGAGTGGCTCAGTTTCAAC - 8 1 4 1 20000 f 74 goat SV_217 15 32714235 - deletion junction SV-TF-chip 539476562 Affx-1251763816 AX-586011948 15 32714235 CAATATCTAACCTTTCCCTCTTTTTCTCTTTTCTT[-/TAAAATCCTTGAAGCAGAGAGGGAAAGATGGTGGAGGAATAATAAATAAATAAAAAAAATAAAAAATAAAACACTTAAAA]AAAATCCTTAAATATTGGAGTGGCTCAGTTTCAAC - 8 1 4 1 20000 r 74 goat SV_217 15 32714235 - deletion junction SV-TF-chip 562165373 Affx-1251763816 AX-606940784 15 32714235 CAATATCTAACCTTTCCCTCTTTTTCTCTTTTCTT[-/TAAAATCCTTGAAGCAGAGAGGGAAAGATGGTGGAGGAATAATAAATAAATAAAAAAAATAAAAAATAAAACACTTAAAA]AAAATCCTTAAATATTGGAGTGGCTCAGTTTCAAC - 8 1 4 1 20100 r 74 goat SV_217 15 32714235 - deletion junction SV-TF-chip 562165400 Affx-1251763816 AX-606940811 15 32714235 CAATATCTAACCTTTCCCTCTTTTTCTCTTTTCTT[-/TAAAATCCTTGAAGCAGAGAGGGAAAGATGGTGGAGGAATAATAAATAAATAAAAAAAATAAAAAATAAAACACTTAAAA]AAAATCCTTAAATATTGGAGTGGCTCAGTTTCAAC - 8 1 4 1 20100 f 74 goat SV_217 15 32714235 - deletion junction SV-TF-chip 562165967 Affx-1251763816 AX-606941376 15 32714235 CAATATCTAACCTTTCCCTCTTTTTCTCTTTTCTT[-/TAAAATCCTTGAAGCAGAGAGGGAAAGATGGTGGAGGAATAATAAATAAATAAAAAAAATAAAAAATAAAACACTTAAAA]AAAATCCTTAAATATTGGAGTGGCTCAGTTTCAAC - 8 1 4 1 20100 r 74 goat SV_217 15 32714235 - deletion junction SV-TF-chip 38387352 Affx-122970481 AX-123257710 15 32715761 TAGTGAAAATATTTCAATGCCAAACAAAAACAAGA[C/T]AAGGCTGGAGGAGAAGGGCATGAGTATAATACCAA Y 2 1 2 1 201000 f 74 goat snp36736-scaffold445-2151331 15 47915185 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442537 Affx-122928535 AX-123312874 15 32758643 TTGAATTAGCATCCAATAAACAGTAGCATATATTT[C/T]GTTTTCTATTTACTGTATGAGCATAATTTATGCCA Y 2 1 2 1 101000 f 74 goat snp36735-scaffold445-2108449 15 47871828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453245 Affx-122920412 AX-123323578 15 32799035 ACTCCATCGTCTATGCTCTTCCATCTGTATCCCAA[C/T]AGCAACACGTGAGGCAGAAACACCTGGAATTCTGA Y 2 1 2 1 201000 f 74 goat snp36734-scaffold445-2068057 15 47831648 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766065 Affx-986697762 AX-385253481 15 32815463 CTTATTTTGGGCCTTGTTTTCTTTTCAGAATATGC[A/G]TTATATTCTTCTATTAGTTATCCTCTGAGGACATG R 2 1 2 1 600010 r 74 goat 15_32815463 15 32815463 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 320766068 Affx-986697764 AX-385253484 15 32823095 TCCCAGTGGGAGGGCTCTCAGTGGCAACACTCCTC[A/G]TCGTGCCTCCATGTTGTTCATGTTTGATCTTGTGT R 2 1 2 1 600010 r 74 goat 15_32823095 15 32823095 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320763237 Affx-986697766 AX-385251165 15 32826442 TCCAACGTGGTTCTCCATTCCTACTGTGAGCACAT[A/G]GCTGTGGCCAAGTTGGCTTGTGCTGACCCCAGGCC R 2 1 2 1 600010 f 74 goat 15_32826442 15 32826442 Ancestral_priority_1043 ancestry 0.594 neutral IMAGE 10K 10K ancestral 38400591 Affx-122960398 AX-123270946 15 32828971 AGATAGGTACTCTTACCAGCCCCTTCTTACTGACA[G/T]GGAGAAGGTTCTAGGGGTGAGGAGAGGGGATAAGC K 2 1 2 1 101000 f 74 goat snp36733-scaffold445-2038121 15 47801762 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416058 Affx-122948344 AX-123286407 15 32875152 ACTACAGTCGTGAGGCCTTTATGTCCCTTATCATA[C/T]GATAAGAATATGTATGTATGTGCTGTAGTTCTCAC Y 2 1 2 1 102000 f 74 goat snp36732-scaffold445-1991940 15 47754646 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395074 Affx-122964182 AX-123265429 15 32919873 GGGATAGCAGTGGTGAAGAGCACTGAACACAGACA[C/T]GATTTAGGCTACCCACCAGCACCTGAAATTCCACC Y 2 1 2 1 101000 r 74 goat snp36731-scaffold445-1947219 15 47708684 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434564 Affx-122934128 AX-123304905 15 32963695 GTCCATGGGGTGGCAAAGAGTCAGACATGACAGAG[C/T]GACTAACACTTTCAAACACTTAACTCCTCTTTCCC Y 2 1 2 1 303000 r 74 goat snp36730-scaffold445-1903397 15 47665053 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429847 Affx-122938159 AX-123300188 15 33018781 ACTTCCACTGAGTTCTTAAGGTACCCAGAGCTCTC[C/T]AAGCACACACACCACACTCCTCCTGGATCTAGACG Y 2 1 2 1 101000 f 74 goat snp36729-scaffold445-1848311 15 47609919 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399739 Affx-122960332 AX-123270094 15 33053372 AATTGCCTTTCTGATTTATAGTTTTAGGGGTGGGG[C/T]TACGATAAAAATAACTTGGTGATTTATAAAACATC Y 2 1 2 1 201000 r 74 goat snp36728-scaffold445-1813720 15 47575709 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437785 Affx-122931695 AX-123308123 15 33085256 TTGGCTTCAGGACTCCCTTCACCTCTTTCTAGCCC[A/G]TATTCTGCCTTAGTTCATTCTTCATCACTCCCATC R 2 1 2 1 101000 r 74 goat snp36727-scaffold445-1781836 15 47545609 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426673 Affx-122939919 AX-123297019 15 33134895 TTTTAAAACATATTGCTCTTATTTCAATTATTTCC[A/G]TATTTTTATTCCTGCTACTCCCTAAATTTCCAAAT R 2 1 2 1 101000 r 74 goat snp36726-scaffold445-1732197 15 47496589 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430230 Affx-122937322 AX-123300571 15 33173985 AGGAGCCTGTGCAAAAGAAGACCCTAAAGCTTATG[C/T]GTCAAGAGCATCATTTCAAATCTGTCTCTCAGGAT Y 2 1 2 1 101000 f 74 goat snp36725-scaffold445-1693107 15 47457448 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395345 Affx-122964032 AX-123265700 15 33211763 TTTTGCACCAACGTGCTGCCCCATAGCCTTTATCA[C/T]CTGGCTCATCAGGCGCATGGATTCTTGTCTTGGGT Y 2 1 2 1 303000 f 74 goat snp36724-scaffold445-1655329 15 47418075 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384875 Affx-122971937 AX-123255233 15 33250112 GTCCACTGCTGCTGCACAGAGATGCCGTTTTTGTC[C/T]CTGGCTCAGTGTACAATGCCGGCCCTGAGAGAGAC Y 2 1 2 1 101000 f 74 goat snp36723-scaffold445-1616980 15 47379799 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380233 Affx-122975471 AX-123250591 15 33285299 ACAGAGGTGGATGAAGGTGTAGCCACTTCAGCTCA[G/T]CTGGCAGGCCCTGGTCATCAATCACGTGCTTCCCG K 2 1 2 1 101000 f 74 goat snp36722-scaffold445-1581793 15 47344506 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399852 Affx-122960244 AX-123270207 15 33330279 AAGTTCTCACCTCCAAGTGCTGTGCTGATTACATC[A/G]CTTCTAAACTGCCTGCAAAATTCAACTCAAACACT R 2 1 2 1 101000 r 74 goat snp36721-scaffold445-1536813 15 47299222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387084 Affx-122969878 AX-123257442 15 33363951 TGACAGAGAGCAGAAGGCAGGAAGTCCAGGAGGAC[A/G]TAAATGAAAACACACTCAAAGGCAATAACTGCAGC R 2 1 2 1 101000 r 74 goat snp36720-scaffold445-1503141 15 47265496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795120 Affx-122974108 AX-385282078 15 33398654 TACCAAGGGATTCCAGATCAACCAGGCAAAAAGCC[A/G]TTTATACAGATCTTGATCCTTGCGGGCAAGGTAAT R 2 1 2 1 101000 f 74 goat snp36719-scaffold445-1468438 15 47231174 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450402 Affx-122922070 AX-123320737 15 33467319 CTCCTATACTACCTTCTGTTAGACAGTATGCTATA[C/T]GGAAGAAGCTTTTATTTATATTTTTAAGCACATCT Y 2 1 2 1 101000 f 74 goat snp36717-scaffold445-1399773 15 47164576 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379028 Affx-122976361 AX-123249387 15 33498206 TTATTTTTCTCCACCACAAAAGCATCTTTACTGGT[A/G]TAGATGCTGTTGCCTGCTTTACAGGCACATGACAT R 2 1 2 1 101000 r 74 goat snp36716-scaffold445-1368886 15 47133715 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407584 Affx-122954662 AX-123277935 15 33538360 GTACAAATAACACAAAAGAGGTTGAGTGAGGTGCC[A/G]GGCACTGCAGATAAACAAGTCTGCTCAGCTCAAGC R 2 1 2 1 101000 f 74 goat snp36715-scaffold445-1328732 15 47093344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419691 Affx-122945927 AX-123290039 15 33570752 CCACATGTGAGTGGAAGAACTCTGGAGCCTGAGGC[A/G]TTATCTGTCCATGTGAATGCATGCATGCTAAGTTG R 2 1 2 1 101000 r 74 goat snp36714-scaffold445-1296340 15 47060743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797638 Affx-122953308 AX-385284577 15 33609624 CCAAAGAATATGCAGGTAACTAACAGAATTACATG[C/T]TGGAGCTTAGCAAGGTTGCTGGAAATGATATTGAA Y 2 1 2 1 101000 r 74 goat snp36713-scaffold445-1257468 15 47021344 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272842 Affx-1111833042 AX-519546534 15 33625655 TAAAAGTCAATTCTATAAAGGATATAAATTGTAAC[A/G]GTCTTAATTAGCCTTGAAGGTTAGTCAGGGAGGGT R 2 1 2 1 101000 r 74 goat 15_33625655_AF-PAKI 15 33625655 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38376314 Affx-122978359 AX-123246673 15 33661183 GTAATTCTTAGAAAAAACATGAAGGTATTTGATGG[A/C]TCGAGTATCCATTTAAAGACCAAGGTAACAGTGGA M 2 1 2 1 101000 r 74 goat snp36712-scaffold445-1205909 15 46969528 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763239 Affx-986697768 AX-385251167 15 33688916 CCTCCTCTCTGAGAAATCTTCAGTCAGCAGGCTGG[C/T]AATCATAACTAGGACTTCAACCCTGAGGCTCAGAG Y 2 1 2 1 600010 f 74 goat 15_33688916 15 33688916 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 320766079 Affx-986697770 AX-385253495 15 33688918 TCCTCTCTGAGAAATCTTCAGTCAGCAGGCTGGTA[A/G]TCATAACTAGGACTTCAACCCTGAGGCTCAGAGTT R 2 1 2 1 600010 r 74 goat 15_33688918 15 33688918 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 38426591 Affx-122939985 AX-123296937 15 33709689 ATTTTACCCACAATCTGAAAGTGATTTAAAGAGCA[G/T]GTTTGTGCTCTATACAAGTCTACAGAGGTACCACC K 2 1 2 1 101000 r 74 goat snp36711-scaffold445-1157403 15 46920679 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770889 Affx-122920218 AX-385258052 15 33749012 TCTTGCATCATCTACTTCGCCTTCTCTACTGGATC[A/G]TTCCCATCCAAACAAAACATGCTCTGTAATCTCCC R 2 1 2 1 101000 f 74 goat snp36710-scaffold445-1118080 15 46881346 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437193 Affx-122932055 AX-123307531 15 33796476 CAAAGAGTGGTTCTCTGGATGGAAAAATAATTAGC[A/G]CAATTTCTGTTTTTCCCCTCTGTGCTTTTCCTCTG R 2 1 2 1 101000 f 74 goat snp36709-scaffold445-1070616 15 46833472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430646 Affx-122936949 AX-123300987 15 33883427 CGCAACACTACAAGTCAATCTTCTTGCCAAGGCTC[A/G]TCACACTTGACCCTCACACACATGCATGCTTATCT R 2 1 2 1 101000 f 74 goat snp36707-scaffold445-983665 15 46747112 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412024 Affx-122951737 AX-123282374 15 33930712 TAAGAATAAATAAATAATGCTAAATGTTTAGGCAG[C/T]GTTTTAAAGCATAAGAAGGCCTTAAGAACCATGGC Y 2 1 2 1 101000 r 74 goat snp36706-scaffold445-936380 15 46699879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779202 Affx-122972622 AX-385266306 15 33980287 AACAAGTTTGGCTTTGTTCAGATTTCAGTTTGGCC[A/C]TTGATTTTCAAATAACTAGCCTGTAGGGTTGCTTA M 2 1 2 1 102000 f 74 goat snp36705-scaffold445-886805 15 46650335 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795347 Affx-122924562 AX-385282303 15 34038628 AAACTGTCACTTTTCAGATGACATCTTCTTTTCCC[G/T]AGAATAACGTTTTTACCCAAAAACACATCACACAA K 2 1 2 1 101000 f 74 goat snp36704-scaffold445-828464 15 46589558 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277054 Affx-1111835655 AX-519550561 15 34086535 TAAAAGTGTTTTTAAACACTCAAAATGTTTAAATA[A/T]AAAGAAGATATTGTAAAGAGCAAACAGAAAAAAGA W 4 1 2 1 101000 r 74 goat Random2.2K-1530 15 34086535 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378462 Affx-122976683 AX-123248821 15 34106580 GACTTCAAAAACACCAATTGATATATATGCACCCC[G/T]AAACTATATTTAAACAAATAGCTCTTAGAACAACC K 2 1 2 1 303000 r 74 goat snp36703-scaffold445-760512 15 46520685 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763243 Affx-986697772 AX-385251171 15 34114844 AGTATCTGTGTGGAAGGATGTGAAAGCCAGACAAG[A/G]AGAGTCTTTATGTTGAGTTTGGTCAATTCCTTTGT R 2 1 2 1 600010 f 74 goat 15_34114844 15 34114844 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320782505 Affx-122954843 AX-385269581 15 34179765 AAAAATCTAAACATAATATATCTGAATAATCTAAG[C/T]CCAAATGAAATTCATTCTCAATATCAACTCCTAGT Y 2 1 2 1 102000 r 74 goat snp36701-scaffold445-687327 15 46446796 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801489 Affx-122949643 AX-385288398 15 34214239 AGTACAAATCAATTAGTACAGTCTCCTGGCACTTA[C/T]TGTACTCAATAAATGGCAGCAATTATTACTATTAT Y 2 1 2 1 101000 r 74 goat snp36700-scaffold445-652853 15 46411335 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418225 Affx-122947046 AX-123288573 15 34257138 GGTGCTGCTGGGGGACAGTGTCAGTCTGTTCACTC[C/T]GGACACTACACACTAATGCACAACTTGTTATCCTA Y 2 1 2 1 101000 r 74 goat snp36699-scaffold445-609954 15 46368830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386085 Affx-122971446 AX-123256443 15 34305227 AGCACCCCATAATACTAAAGAAACCAAGCTGGAGT[A/G]TGGTTTTGACCTGTAATCAGAGGGGAAATGACTAT R 2 1 2 1 101000 f 74 goat snp36698-scaffold445-561865 15 46320649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378311 Affx-122976845 AX-123248670 15 34347257 ATTCTGGTTAATTACTAAGTTGTTGCTATTCAGTC[A/G]CTCAGTCATGTCTGACTCTTTGCAACCCCATGGAC R 2 1 2 1 303000 f 74 goat snp36697-scaffold445-519835 15 46278213 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414018 Affx-122949802 AX-123284367 15 34380613 GGAGTGTGTGTTACTCAGAAAAATGCAAAAGAAAC[G/T]CATGACAGAATAAAAAGGAGTTTTATTGAATTGAA K 2 1 2 1 101000 f 74 goat snp36696-scaffold445-486479 15 46244394 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799970 Affx-122965462 AX-385286896 15 34458066 ATATGTAAAAGCCTTTCACAAACTGCAAACTACCA[C/T]GTACAATTAGAGTGTTATTAATCTAACAAACTAAG Y 2 1 2 1 101000 f 74 goat snp36695-scaffold445-409026 15 46166321 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801297 Affx-122923441 AX-385288209 15 34507810 GAGTAAAATTATGTTCAATAATAGAAAAAATTATG[C/T]CTATTATTAATTCCTTCAGATGTAGAGTGAAGCAC Y 2 1 2 1 202000 f 74 goat snp36694-scaffold445-359282 15 46117301 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394177 Affx-122964925 AX-123264532 15 34550816 GGAAAGAATGGTTCCTGGAAGATGGAAAATGAAGT[A/G]CAATGTAGAGGATAATGAAAAGGTGACACCAACCT R 2 1 2 1 101000 f 74 goat snp36693-scaffold445-316276 15 46074283 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777007 Affx-122926730 AX-385264131 15 34618412 TTCTAGACACTTAGAATATAAGGAGGTAATATTGG[C/T]AAAGGGCTTGCAATGTTGTTAGCATATAATAAGTA Y 2 1 2 1 101000 f 74 goat snp36692-scaffold445-248680 15 46006018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387009 Affx-122969938 AX-123257367 15 34671354 ATGCTTCACAGTACTGCCCCAGTCTCTAGATTCTT[A/G]CTTATCTACTGCAATCTCACTGATACTGCGTGAGA R 2 1 2 1 201000 r 74 goat snp36691-scaffold445-195738 15 45953109 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446109 Affx-122925793 AX-123316446 15 34720106 AATATTAACCTTCAGATTGCAGAGGCAAAAACTAA[C/T]GCTATAAGAAGTTAAGTAACTTGCCCAAGGCGACA Y 2 1 2 1 101000 f 74 goat snp36690-scaffold445-146986 15 45902193 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781653 Affx-122935910 AX-385268737 15 34783846 CGCTTTCCTCCAAGATGAAGAACAATGCAAGAGAT[A/G]CCCACTCTTACCACTGTTAATCAACATTCTACTGT R 2 1 2 1 101000 f 74 goat snp36689-scaffold445-83246 15 45838473 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424595 Affx-122942206 AX-123294941 15 34813611 AAAATTTGCTCAAGGGTGTATTCAGTGCCCTCAGC[A/G]TCCCAAGGGCCACACCCGCAGTGTTGCTAGAGGAA R 2 1 2 1 202000 r 74 goat snp36688-scaffold445-53481 15 45808683 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442642 Affx-122928450 AX-123312979 15 34844105 TCCAATGACAGTACCATGTCACTCAGGGTGACTGT[A/C]GTAAAGCATTTGAACATTCTTTTGATGTTTCCTAT M 2 1 2 1 303000 f 74 goat snp36687-scaffold445-22987 15 45777806 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402120 Affx-122958676 AX-123272473 15 34877045 AATGCTCACAGCAACCTGTGAGGTAGTTACTATTA[C/T]TATCACTCCATTTTGTAGAAAAAGAAACCGAAGCA Y 2 1 2 1 303000 f 74 goat snp46422-scaffold643-9854 15 45745006 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408491 Affx-122954412 AX-123278842 15 34906682 ACAATTTGAAAGCTTGAATTCTGTTCCCTGTCTTA[C/T]GGGAAGAAAACAGATATTTCAGAAATGTGTAGATT Y 2 1 2 1 101000 r 74 goat snp46423-scaffold643-39491 15 45715810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452430 Affx-122920580 AX-123322763 15 34941229 GTATCCTATGCCCCTGGACACAGCAAGAAATCAAT[A/G]CCTGTTCCAACCCTGGACAAAGTCTTTCCTCAGGA R 2 1 2 1 201000 r 74 goat snp46424-scaffold643-74038 15 45681061 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396159 Affx-122963381 AX-123266514 15 34989948 TTAAACCTTGACATGGCTTTGTTTCTATTGCTGCC[A/G]TTTACTTATAAGCAATTTGGGGTCAGAAGTCCTAA R 2 1 2 1 102000 f 74 goat snp46425-scaffold643-122757 15 45632315 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437826 Affx-122932105 AX-123308164 15 35025541 TTTCCTGTGTGGCATCTTTCTCTCGTAATTCTAAC[A/G]CAATTCCAAGGGGTACATGAAATCCTGGCTCTTTT R 2 1 2 1 201000 f 74 goat snp46426-scaffold643-158350 15 45596714 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424394 Affx-122941823 AX-123294740 15 35070494 GGGTAGGACCTGATAGGATGTAGAGCCAAGATACC[A/G]CCATCAGGGATGAAGAAGCCCCCATGATGGCTGTA R 2 1 2 1 101000 f 74 goat snp46427-scaffold643-203303 15 45551825 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377664 Affx-122977850 AX-123248023 15 35127054 TTGCCTGAGGCATCCCTTCAACGAAGGGCCTGGTA[C/T]GCTGATTGCTGGGAGCGTCATCAGCAGGCAGTCTT Y 2 1 2 1 101000 f 74 goat snp46428-scaffold643-259863 15 45495690 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395375 Affx-122963977 AX-123265730 15 35156214 TAAAGGTGTGAAATCTGGTGATGGAAGTGGTAAGT[A/G]CTATCAACAATAGTGGCAATGCTGGGAAGCTGAGC R 2 1 2 1 101000 f 74 goat snp46429-scaffold643-289023 15 45466536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449364 Affx-122922729 AX-123319699 15 35200215 GTGAAGATGTGGAGCAGAGGAAAGAGGTTGCAAAC[A/G]TTTATGAAGCCACCCAAACCTTCAAGAGTCTTCTC R 2 1 2 1 201000 r 74 goat snp46430-scaffold643-333024 15 45422483 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429837 Affx-122938167 AX-123300178 15 35262781 GAGGGATCCATGGGTCAGGTGTGCATTCAGATTAG[C/T]AGTGTGACCAGTGAGGAGCAGTCCCCGCATATCTC Y 2 1 2 1 101000 f 74 goat snp46431-scaffold643-395590 15 45359550 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411802 Affx-122951258 AX-123282152 15 35328245 TTTATTCCTCGGGTATCTTGGTGTTGCTTGTCTAG[C/T]AGTTGCGGCCATGGCACCAGGAGGGATCAGGGTCA Y 2 1 2 1 101000 f 74 goat snp46432-scaffold643-461054 15 45292377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424298 Affx-122941973 AX-123294644 15 35356844 AGTGTGGCCCCTTCCCCACATCTGCCTAATGGAAA[C/T]GGAATTCTCTAAGAAATTGCAGAAGCAGGAGATAC Y 2 1 2 1 201000 r 74 goat snp46433-scaffold643-489653 15 45263681 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378295 Affx-122976859 AX-123248654 15 35451533 GCTACCTGACCCTGGGCAAGTCACTTAACCTCCAA[C/T]GGCCTAATTGTCTTCGTCTCTAAAAAGAACAAGTT Y 2 1 2 1 101000 r 74 goat snp46435-scaffold643-584342 15 45167304 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399427 Affx-122961228 AX-123269782 15 35508621 GACTGAAACAAACGCATGCCTGTCCACTGCCTCTG[C/T]GGGGCCTTCCCACAATACCAGATGCCTGGGGATGG Y 2 1 2 1 101000 f 74 goat snp46436-scaffold643-641430 15 45110538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379246 Affx-122976263 AX-123249605 15 35640796 TTTAGATCCTGTTAATGAAAATTACTTCCTCTTTA[C/T]AGAACCTGTACCCCATGTGGTTTTCTGAGGTGCAG Y 2 1 2 1 101000 r 74 goat snp46438-scaffold643-773605 15 44977954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376129 Affx-122978867 AX-123246488 15 35703778 AAAACCCCGTGGATAATATTTACAACAAAACTAGA[C/T]GGTAAAGGATTCCTACAAATCTCAAATTGCAAGCA Y 2 1 2 1 101000 r 74 goat snp46439-scaffold643-836587 15 44915301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780565 Affx-122923660 AX-385267656 15 35734052 AAAAGGAAAGCGAAAGCAGCAAGCAAGAATAACAA[G/T]CCAGGATGGAAGGGAGTTTTCGCCCTGAGAACATC K 2 1 2 1 202000 r 74 goat snp46440-scaffold643-866861 15 44885180 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378324 Affx-122977343 AX-123248683 15 35765223 ATGGCTGCTCAGTTCAGGACAGTGGGGGTTGACAA[A/G]CAGCCCTACCTTCCTCTTGACCCTCTCCTGCATCC R 2 1 2 1 101000 f 74 goat snp46441-scaffold643-898032 15 44853136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401383 Affx-122959228 AX-123271736 15 35795499 TGAGCTTCAAGGCATCCCAATCAAACCAACTATCA[C/T]GAGGATTTACAGCGAATGGTTTCCCAGGAATAATC Y 2 1 2 1 101000 f 74 goat snp46442-scaffold643-928308 15 44822527 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452893 Affx-122920217 AX-123323226 15 35844193 TCCAGATTAATATGGATAGAATCTACTTGACTTTC[A/C]TCCCTATTTATTCATCAATATACTAATCTTTTGAT M 2 1 2 1 101000 f 74 goat snp46443-scaffold643-977002 15 44773603 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452619 Affx-122920364 AX-123322952 15 35880577 AGGATCCTATCTTCAGTATGCGAGGTAGAATGAGT[A/G]CCTGGAGAAATGTGAATACTCTGTCCAGGGCTCTG R 2 1 2 1 101000 f 74 goat snp46444-scaffold643-1013386 15 44736635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439795 Affx-122930497 AX-123310132 15 35916965 CTCTAAAAATGAACAAAATTTTCTCAAGTGAACAA[C/T]GCAGCTAGGGAAGTAAGAGGTAAACAGAGCCTGAA Y 2 1 2 1 101000 r 74 goat snp46445-scaffold643-1049774 15 44699474 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436602 Affx-122932516 AX-123306940 15 36009127 TAGATATCAGCTTTTTATGTAAAAATAAAATATAA[G/T]ATGTGAATCTAGGTAGTTTCTCCATAGTCTATAAT K 2 1 2 1 103000 r 74 goat snp46446-scaffold643-1141936 15 44607233 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450633 Affx-122921991 AX-123320967 15 36060924 GCCTGGTACAAGACCAGGATGCTGAGGACCAAGAA[C/T]GGGGGGAACTTCCAGAACCCCATGACACCTCTCTG Y 2 1 2 1 201000 f 74 goat snp46447-scaffold643-1193733 15 44555583 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271946 Affx-1111833043 AX-519545722 15 36126109 GCAGAATTTTCTGATAAACACTGTCAACTGTTGCA[A/G]AAACATGTCCATTTATGAAACTAAATTTATTAAAT R 2 1 2 1 101000 f 74 goat 15_36126109_AF-PAKI 15 36126109 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38411084 Affx-122951931 AX-123281434 15 36129597 TCCCCCGCTCCGCAATGCCGCTGCAGTTCTTGCCG[C/T]GCTGAGGGTCTCTACAGGCTATGTGGATTGTGTGC Y 2 1 2 1 101000 r 74 goat snp46448-scaffold643-1262406 15 44486699 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787273 Affx-122962895 AX-385274298 15 36194217 TATAAGACAGGAAAAATAGTATCAATCTAGTCATA[C/T]TGCCTGAGGATTAACGAATGAAAAATGCACAGTTT Y 2 1 2 1 101000 r 74 goat snp46449-scaffold643-1327026 15 44421415 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419268 Affx-122946254 AX-123289616 15 36234655 AATCTCAGGCTAGGAATTGGGGCAGTATTCCACAG[G/T]CACGATAAAGGTTCATAAACTTAATGATTAGAAAA K 2 1 2 1 201000 r 74 goat snp46450-scaffold643-1367464 15 44381020 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432657 Affx-122936467 AX-123302998 15 36264827 ATAACAGATGATAGTTTTTTTTTCTCTGATTGCCC[A/G]TTATAACTTATCTGAGAACAGATATAAAGTTAAGA R 2 1 2 1 303000 r 74 goat snp46451-scaffold643-1397636 15 44349944 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763247 Affx-986697776 AX-385251175 15 36265434 TTCTGTAAGTATGTAATTAAAGTTAACTTTGTCCT[G/T]TTAATCTGTTTTATATCAATTCAAATATTAGATCA K 2 1 2 1 600010 f 74 goat 15_36265434 15 36265434 Ancestral_priority_1043 ancestry 0.732 recommended IMAGE 10K 10K ancestral 320766094 Affx-986697778 AX-385253510 15 36265459 ACTTTGTCCTGTTAATCTGTTTTATATCAATTCAA[A/G]TATTAGATCAGCAAAATATTATATTAGATGAGCAT R 2 1 2 1 600010 r 74 goat 15_36265459 15 36265459 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320803879 Affx-986696275 AX-385290599 15 36265575 ACCTTCCTTTATTCTTCCAGGTCCAGTTAGTTCCC[C/T]TCTTCCCTGTATTTACCATAGCACCTCTTACTTAC Y 2 1 2 1 600010 r 74 goat 15_36265575 15 36265575 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 320766097 Affx-986697780 AX-385253512 15 36265659 AAGTAAACTTTTCATGAGTCCTTTGCTCTTGGAAA[G/T]CAGTGATGGTTAAAAGAAATCCATGCAACCTTTTG K 2 1 2 1 600010 r 74 goat 15_36265659 15 36265659 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 320763217 Affx-986697746 AX-385251145 15 36265783 TAGGACTCATTTATGTATTCCCCTATTACTTATAA[A/G]GAGGCCAGACACAGACCCAATTTTTAAAAATTAAC R 2 1 2 1 600010 f 74 goat 15_36265783 15 36265783 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 320803309 Affx-986696276 AX-385290149 15 36265958 GAAACTTTCACTGAGCTGTTTGTCCCCCTGATCAA[C/T]TGCAGTGTTTGAAACTAAACATTAATTAAACTTCT Y 2 1 2 1 600010 f 74 goat 15_36265958 15 36265958 Ancestral_priority_1043 ancestry 0.442 neutral IMAGE 10K 10K ancestral 320766040 Affx-986697749 AX-385253457 15 36265971 AGCTGTTTGTCCCCCTGATCAACTGCAGTGTTTGA[A/G]ACTAAACATTAATTAAACTTCTCTGCTTTTTAGCC R 2 1 2 1 600010 r 74 goat 15_36265971 15 36265971 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 320763222 Affx-986697751 AX-385251150 15 36266887 TAATTGTGTTTACACTGTGATTCCTGGGTGTTAAG[G/T]TTATTGCAAATGGAAGACTAATGTGGGGGGGAGTG K 2 1 2 1 600010 f 74 goat 15_36266887 15 36266887 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 320803311 Affx-986696277 AX-385290151 15 36269199 GAGTAAACTTTCTGTGTATGGTAAGATTTCAGTAA[A/T]TATATAAATTAATGAAGGCGTAAAAGCAACCCCTT W 4 1 2 1 600010 f 74 goat 15_36269199 15 36269199 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 320766048 Affx-986697753 AX-385253465 15 36269201 GTAAACTTTCTGTGTATGGTAAGATTTCAGTAATT[A/G]TATAAATTAATGAAGGCGTAAAAGCAACCCCTTAA R 2 1 2 1 600010 r 74 goat 15_36269201 15 36269201 Ancestral_priority_1043 ancestry 0.732 recommended IMAGE 10K 10K ancestral 320763226 Affx-986697755 AX-385251154 15 36269229 AGTAATTATATAAATTAATGAAGGCGTAAAAGCAA[C/T]CCCTTAAAATAAAATCAGATTTGAAACCAAGTTTA Y 2 1 2 1 600010 f 74 goat 15_36269229 15 36269229 Ancestral_priority_1043 ancestry 0.722 recommended IMAGE 10K 10K ancestral 320766056 Affx-986697757 AX-385253472 15 36269236 ATATAAATTAATGAAGGCGTAAAAGCAACCCCTTA[A/G]AATAAAATCAGATTTGAAACCAAGTTTATTTCACC R 2 1 2 1 600010 r 74 goat 15_36269236 15 36269236 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 320766059 Affx-986697759 AX-385253476 15 36269354 AGACTTTTGCTTTCTTTTTCACTTTTCTCTCAGTT[C/T]CAGGAAATGTTTGTTTTTAACATGAACTTCCGTTG Y 2 1 2 1 600010 r 74 goat 15_36269354 15 36269354 Ancestral_priority_1043 ancestry 0.612 recommended IMAGE 10K 10K ancestral 320763232 Affx-986697761 AX-385251160 15 36269393 GAAATGTTTGTTTTTAACATGAACTTCCGTTGAAT[A/G]ACTAGTGAATGTTTTTGAAAGATGTTTTACCCAGG R 2 1 2 1 600010 f 74 goat 15_36269393 15 36269393 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 320763234 Affx-986697763 AX-385251162 15 36269423 TGAATAACTAGTGAATGTTTTTGAAAGATGTTTTA[C/T]CCAGGCTTTTTTGTTTCTTTTTCTATTGCCAGTTT Y 2 1 2 1 600010 f 74 goat 15_36269423 15 36269423 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320766070 Affx-986697765 AX-385253486 15 36269446 AAAGATGTTTTACCCAGGCTTTTTTGTTTCTTTTT[C/T]TATTGCCAGTTTTTAACTTAAGTTCTCTTTGAAAA Y 2 1 2 1 600010 r 74 goat 15_36269446 15 36269446 Ancestral_priority_1043 ancestry 0.76 recommended IMAGE 10K 10K ancestral 320763238 Affx-986697767 AX-385251166 15 36271528 TTTCAAGAACCCTGTTTTATGAATTGGGACAAAGA[A/T]CAACTATACATTTCTTATTATAAATAACTATATTA W 4 1 2 1 600010 f 74 goat 15_36271528 15 36271528 Ancestral_priority_1043 ancestry 0.68 recommended IMAGE 10K 10K ancestral 320763240 Affx-986697769 AX-385251168 15 36271622 TGGATCCTGCCTTCAGTGGGCTTCTCCCTCTCCCT[C/G]TCTGGTCGGTGCCCAGCTGCAACCAGCAGGGCTTT S 4 1 2 1 600010 f 74 goat 15_36271622 15 36271622 Ancestral_priority_1043 ancestry 0.49 neutral IMAGE 10K 10K ancestral 320763242 Affx-986697771 AX-385251170 15 36272008 TTTTCAGTAACTAAGTTGGACCCTGTAGGGCTTTC[C/G]CAAAACCAAACTGCCCACCCTCCCATGTGCTCCAT S 4 1 2 1 600010 f 74 goat 15_36272008 15 36272008 Ancestral_priority_1043 ancestry 0.596 neutral IMAGE 10K 10K ancestral 320766085 Affx-986697773 AX-385253501 15 36272114 CTCCCCTGAGTCACAAAAGGCTGGCTCCAGGCTTG[A/C]TTTAAAGACTGTGAATTTGTAGTAACTAAAAATAG M 2 1 2 1 600010 r 74 goat 15_36272114 15 36272114 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 320763246 Affx-986697775 AX-385251174 15 36272144 GCTTGCTTTAAAGACTGTGAATTTGTAGTAACTAA[A/G]AATAGCAGCTGGGGCAGGAGAACGGGTAACAGTTT R 2 1 2 1 600010 f 74 goat 15_36272144 15 36272144 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 38402948 Affx-122958172 AX-123273301 15 36304920 CTTCCCCTCCTGTCCTTACTCTGCCTTCTTTTATT[A/G]TATGGCTCTTTCCTTTTATCACCATTTTAATAATT R 2 1 2 1 101000 f 74 goat snp46452-scaffold643-1437729 15 44309542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777810 Affx-122919411 AX-385264927 15 36334737 ATGGTGAATAGATGTTGCTCCTATTTAATTTTAAA[C/T]GGTTTGATCTTCATAAACACATTTTGGTTTGCATA Y 2 1 2 1 101000 r 74 goat snp46453-scaffold643-1467546 15 44278942 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412771 Affx-122950507 AX-123283120 15 36365694 GCTTGTACAGAAGGGCATGGCAAGCTAGTGTCAGC[A/G]TCACTGAAATGCCCATTATAAATTCTCATTGGAAA R 2 1 2 1 201000 r 74 goat snp46454-scaffold643-1498503 15 44248079 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404679 Affx-122957281 AX-123275031 15 36401615 AAAGAAATTTGCAAAGAGAATTTTTAGTTCTATAG[A/C]TCGGTTAACAGGGATCGAGGTTGTGACTTGATTCC M 2 1 2 1 101000 r 74 goat snp46455-scaffold643-1534424 15 44212040 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769450 Affx-122979124 AX-385256620 15 36441826 TCAAAGTATGTTTAGAATCCCTTCTCACCTTTCCC[A/G]CTTCAATCACTTTGCTCCAACTGCACTGCCTCTCA R 2 1 2 1 101000 r 74 goat snp46456-scaffold643-1574635 15 44177090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402951 Affx-122958170 AX-123273304 15 36536117 TCTCAGATTGATTTTGTTGCCCAAGGTAAGATCAG[C/T]GGCAGAATAGGAACTACTAAAACACTTTCTCCCTT Y 2 1 2 1 101000 f 74 goat snp46458-scaffold643-1668926 15 44082929 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448869 Affx-122923275 AX-123319204 15 36573846 AAATTATTAAAACATTTTTCTGAAGAATCTGATCC[A/G]TCAAAGGAGAAACAAATAGAGCTACTGACATTGGG R 2 1 2 1 101000 r 74 goat snp46459-scaffold643-1706655 15 44045293 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444381 Affx-122926602 AX-123314718 15 36628784 TAGTTTTTCTAGCCCTGCCTGTAACTCACTGGTAC[A/G]TTTATTCTGGGAGCAGTGTAAGCAAGCCTATTTGA R 2 1 2 1 201000 r 74 goat snp46460-scaffold643-1761593 15 43990639 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406587 Affx-122956263 AX-123276939 15 36663932 ATTTTCTGAGATATTGTATAGTTACTTAAAAACAA[G/T]AATGTGCTCTAAATTGACTTAAGTATGTACTCAGA K 2 1 2 1 101000 r 74 goat snp46461-scaffold643-1796741 15 43955342 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421180 Affx-122944161 AX-123291527 15 36735327 TGTGTTGGAAGGTTTAAAAAAACTCAAGCCTGGGA[C/T]TGCTCTTGAGGCCAGTTTTGCTGCTGTGGTTCTTA Y 2 1 2 1 201000 f 74 goat snp46462-scaffold643-1868136 15 43883936 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430357 Affx-122937795 AX-123300698 15 36785738 GATCTTTGCTATGTGTCTCAAGACACTAAGGCACC[A/G]CAAGAAGATGATAAGGTGCAATTTCTGAGGACACA R 2 1 2 1 201000 f 74 goat snp46463-scaffold643-1918547 15 43833948 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386935 Affx-122969994 AX-123257293 15 36826038 CGAATTTTTGTGCACGATGATGCTCTTCCCGTATC[A/G]AGGACAATTTCCTAAGAATAGATTCTGAGAAGTGG R 2 1 2 1 101000 f 74 goat snp46464-scaffold643-1958847 15 43793000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453985 Affx-122919448 AX-123324318 15 36871713 TGAGCCAGTAAAATCAGGGAGGACTAGACAGTCTA[C/T]AGGAGTCAGTTTGGTGAAGAAAAAAGCTCCAGTTT Y 2 1 2 1 101000 r 74 goat snp46465-scaffold643-2004522 15 43747756 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453839 Affx-122919544 AX-123324172 15 36924703 AGCACAGAGCCTTTCAAGCAGGACACACTGAAGAT[A/G]TGCTGTTCTGATGTGTTTTCATGGACTGATTTGAC R 2 1 2 1 101000 r 74 goat snp46466-scaffold643-2057512 15 43694742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452680 Affx-122920317 AX-123323013 15 37042166 TACAAGAAGAAAAAAGCAAATGTAAATAAGGACCC[A/G]CTTCAGACTTAGTGTCCCAAGATATGTCAGTTATT R 2 1 2 1 101000 r 74 goat snp46468-scaffold643-2174975 15 43578284 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768397 Affx-122974397 AX-385255577 15 37083485 ATCTTGCTTCCTTTTATGACAGCTTTACAGTTTAA[C/T]AGCAATGTTCAGATATCTAAGGATGACTAGCTAAG Y 2 1 2 1 101000 r 74 goat snp46469-scaffold643-2216294 15 43537320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407661 Affx-122954603 AX-123278012 15 37116546 AAGTAAGAAGTGGGGGAACTCGGGAAGGAGACAGC[A/G]TGAAGTATGAAGAGTGACCTCTTTTGTAAAGCTCA R 2 1 2 1 201000 r 74 goat snp46470-scaffold643-2249355 15 43503978 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274117 Affx-1111834016 AX-519547720 15 37125709 CAGCAGCTCCAGTATTCACCCCTCACCTGCAGCAC[A/G]CCCACCGCAGCCTCTTCTGCTCACCTACTTCCTGT R 2 1 2 1 103000 r 74 goat GoatD01.014051 15 37125709 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38433018 Affx-122935782 AX-123303359 15 37147003 TTATTTCCTCCCTGAGTGTTCACTACTCTCTGAGA[C/T]GCTTCCATTTACTTCCCGTTCCTTTCTGCTGGAGC Y 2 1 2 1 201000 r 74 goat snp46471-scaffold643-2279812 15 43473127 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380667 Affx-122975189 AX-123251025 15 37190777 GTAAAAATTATGAAGGTGGCCTGAGACTAGAAATG[A/C]GTGAAGTGAGTCTCTTATCTGAGTCTCCCAGTTTG M 2 1 2 1 201000 f 74 goat snp46472-scaffold643-2323586 15 43428974 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375701 Affx-122978648 AX-123246060 15 37222621 TGACCTCAAGGCTCACCTGGAACTCACTGCAGGGT[A/C]TCGCCATACCTACAGCAGTGGTGCTCTAAGGCAGC M 2 1 2 1 201000 r 74 goat snp46473-scaffold643-2355430 15 43396588 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780249 Affx-122940654 AX-385267344 15 37266587 TTGTCTGAGGCTGCAGAATCGAGTAGTTATAAGGT[A/G]GAAGCTACATTTAACAGCAGAGGTAAAAAGCTGCA R 2 1 2 1 101000 r 74 goat snp46474-scaffold643-2399396 15 43352718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452848 Affx-122920723 AX-123323181 15 37295247 CAAGTGCATGGGAGTCTGTGGCAACGGGGAGAATA[C/T]TGGTAGAGTATAACTACCCTTGTGAGCTATATAGT Y 2 1 2 1 101000 r 74 goat snp46475-scaffold643-2428056 15 43323547 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790617 Affx-122957197 AX-385277619 15 37342726 GAGTTAACCAAACAGGCTAGAAATCAAGACACAAA[A/C]TGACAAGCAGCATTCTCATTGTCCAACCTTGCCAG M 2 1 2 1 101000 r 74 goat snp46476-scaffold643-2475535 15 43275897 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783969 Affx-122938617 AX-385271023 15 37378776 ATAAATTTAAAACAAAGTTCCTCGAGTCAAATTTT[A/G]TCAAGTTGCCCATATTCAATTAAGCTTTGGATTCC R 2 1 2 1 101000 r 74 goat snp46477-scaffold643-2511585 15 43239434 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453643 Affx-122919735 AX-123323976 15 37427998 TCAACAGTCAACTTCTTTGGATCTAAATTTCATCA[C/T]ACTTGAAATGAGGTCTTTTGGTAAATGTTCTTTTT Y 2 1 2 1 101000 f 74 goat snp46478-scaffold643-2560807 15 43189334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798227 Affx-122950869 AX-385285162 15 37471509 TGAAATGCAGACTAAGGTAAGACTTTTCTATTTTG[C/T]GATAAAAAGCTGAAAAGCAAAAGAGCAAAATTCTA Y 2 1 2 1 202000 r 74 goat snp46479-scaffold643-2604318 15 43145553 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787136 Affx-122955474 AX-385274162 15 37516202 AGGTTTAAATAATTGTTATTTGCAGGAGACTTGCA[C/T]GATCATTTCTCTCAGCTGTGCAGGAAGTTCCTTCT Y 2 1 2 1 101000 r 74 goat snp46480-scaffold643-2649011 15 43101013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796475 Affx-122958427 AX-385283425 15 37599505 AAGAGTTGGAACACTTTATTTTCAGATAATGTCTC[A/G]TTTCACTCGACTGCCTCAAGCCTTCCAGACACAGC R 2 1 2 1 101000 f 74 goat snp46482-scaffold643-2732314 15 43016836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406292 Affx-122956073 AX-123276644 15 37648909 CCCATCCCAGAGTTATGCACACTTACTAAGGCTCC[A/G]CCCTCGGCACATCACGGGGAGAGCGTATTAATCCT R 2 1 2 1 101000 f 74 goat snp46483-scaffold643-2781718 15 42967280 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412997 Affx-122951018 AX-123283346 15 37680692 TTAAACAGATCAACAGATGGTGTTTTAAAGAATCC[A/G]TTTCAAATGATTTATAAAATGATGACTATTCAGGA R 2 1 2 1 101000 f 74 goat snp22145-scaffold2185-1126099 15 42935298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430296 Affx-122937278 AX-123300637 15 37721733 AATCATGCCTCTGGTATCAAAGCCACATCCTTGAG[C/T]ATCTCATCAAAAACTTTACCCAGCAAACCTAAAGT Y 2 1 2 1 101000 r 74 goat snp22144-scaffold2185-1085058 15 42894086 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398022 Affx-122961777 AX-123268377 15 37763982 AGATTTTAGTAATTTGCCCAAGATTCTGTAGCAAG[C/T]AGTGGAAGAACCAGTTTGAGATTTCATTGATCTTC Y 2 1 2 1 201000 r 74 goat snp22143-scaffold2185-1042809 15 42851934 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404618 Affx-122957332 AX-123274970 15 37809894 CTTTTTCCCAATAGTTCCTGGACAGGAAACAGCAA[C/T]AGGTGTCAACTACCATGTCCAGAATGAGTGGGAGC Y 2 1 2 1 101000 f 74 goat snp22142-scaffold2185-996897 15 42805709 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273756 Affx-1111833822 AX-519547367 15 37843083 GCTAGTAGAGACTGGCTGAGGAGCATGGCTTCTTG[A/G]AAAC R 2 1 2 1 102000 f 74 goat GoatD01.005974 15 37843083 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38454289 Affx-122919269 AX-123324622 15 37848767 GGCTACTCCTTCGATCATTTGTTCTCAAATTTCAA[C/T]ATGTGAAAAATCACCTACAGTGCTTATTAAAACAC Y 2 1 2 1 101000 f 74 goat snp22141-scaffold2185-958024 15 42766740 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433020 Affx-122935780 AX-123303361 15 37906990 AAGATACTCTGCTGAGGTTTTCCTTTCTCCATGGA[C/T]CAGATGTCTTTTTGGAAAGAGCCTTGGATTTGGAA Y 2 1 2 1 101000 r 74 goat snp22140-scaffold2185-899801 15 42708600 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408882 Affx-122953983 AX-123279233 15 37945534 GGAGTTGGACTTTTGGAAGTTTTCTTTCCAGGGTA[G/T]AAATGCAGCTGCAGTTTCCTGAGAACAGACTTTAA K 2 1 2 1 101000 f 74 goat snp22139-scaffold2185-861257 15 42669885 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400085 Affx-122960747 AX-123270440 15 38013247 GCTAGAACTGGGAGAGGGCCAGGTCCATGGTCCAG[A/G]CAGCAGCTGATCACCACCTACGTGAGGACTCATGG R 2 1 2 1 101000 r 74 goat snp22138-scaffold2185-793544 15 42601951 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398869 Affx-122961044 AX-123269224 15 38045457 AATATTTGAAATGGCATTTATTTTCCCTCTCTGTT[C/T]GTCATTAAGTGGGGTCAGATTACAAAAGATTCCAC Y 2 1 2 1 303000 f 74 goat snp22137-scaffold2185-761334 15 42570153 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788419 Affx-122931854 AX-385275437 15 38091041 TACCCCAGGATCTAGTTAATCTCCCATAATAAACC[A/G]CCACAACAGTAGTCTTAGCAGCTACGATTTATTGA R 2 1 2 1 101000 r 74 goat snp22136-scaffold2185-715750 15 42524849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386217 Affx-122970986 AX-123256575 15 38148356 TACCAGCAACAGGCTGGACCTGTGTCTCCTGCTCC[A/G]CCTGCATCTCTTCATCTGCAGCCTTGCACAATCAC R 2 1 2 1 101000 r 74 goat snp22135-scaffold2185-658435 15 42467681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396876 Affx-122963238 AX-123267231 15 38199770 TCCACAGACCTTGGGAAAGCTAGTGTAGTCCCTCT[A/G]TTCATAGTCAGTGTACTTTCTGAGGGCTGTTCATG R 2 1 2 1 101000 r 74 goat snp22134-scaffold2185-607021 15 42416193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276922 Affx-1111835656 AX-519550430 15 38222555 CCATCTACACTGTTTCTTCTGCCCAACAATCCCCC[A/G]GGGGAAGAACCCCACCCACAGCCTCTGATGATGAG R 2 1 2 1 103000 f 74 goat Random2.2K-1533 15 38222555 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38414148 Affx-122949695 AX-123284497 15 38232328 GGTGATAAATTCATTGACATTGTTACCCAAAGAGT[A/G]TTCCCATCATTTGTTTGTTGGTTCACTCTTTATTT R 2 1 2 1 101000 f 74 goat snp22133-scaffold2185-574463 15 42384026 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422880 Affx-122943074 AX-123293226 15 38291141 TAACAACAAAGTGCTTTTTTTCCTCCGACTCAAGC[A/G]ACCAACAGGCAAACTACAAAGAAGACATTTATCTG R 2 1 2 1 101000 r 74 goat snp22132-scaffold2185-515650 15 42325825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404485 Affx-122956721 AX-123274837 15 38330430 ATAAGACCTTGCACAGGAGTGGAGGAATGAATGGC[A/G]TCAGATAGAAGAATTTGGTATTGAGAGCCACTAGT R 2 1 2 1 201000 r 74 goat snp22131-scaffold2185-476361 15 42286500 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429891 Affx-122938123 AX-123300232 15 38359308 GGGCCTCTGGCATCATCCCAGATTCCCACTGTGAC[C/T]GAATGTCACCTGCTATGACCTTACGTTGGACAATA Y 2 1 2 1 101000 r 74 goat snp22130-scaffold2185-447483 15 42255684 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784248 Affx-122967512 AX-385271299 15 38469717 GGGCTGAACAGGGGTGACTAGGAGGACAAGAAGCG[C/T]CGGGCAAATACTTGCACACTTACCATACAGGGGGA Y 2 1 2 1 202000 f 74 goat snp22128-scaffold2185-337074 15 42144212 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420902 Affx-122944608 AX-123291249 15 38500747 CTTCCTCTTCACTTTTCAAGGGCAGGGAAGGGGAC[A/G]TGTGGGGTCTGTCTGCAAGTTTCACCGCCAAGTCA R 2 1 2 1 202000 r 74 goat snp22127-scaffold2185-306044 15 42113997 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390230 Affx-122967774 AX-123260587 15 38590918 ACCACACTGTTTTGATTACTGTAGTATCAAAATTG[C/T]AGCTAAAATACTAGTTTTGCAGTATTGTATGAAGT Y 2 1 2 1 201000 r 74 goat snp22125-scaffold2185-215873 15 42024708 A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404421 Affx-122956770 AX-123274773 15 38622924 ACTTAGCAGGTTGAAAAAGATGAGGGTTGGCTTGG[C/T]GGTGCTCTGAGCATAGTTTATTCCATCCTCAACAT Y 2 1 2 1 101000 f 74 goat snp22124-scaffold2185-183867 15 41992778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778336 Affx-122923590 AX-385265451 15 38679798 TTCCTTGGAGTAAAAAATAGGGCTAATAATCCTCA[C/T]ATTACTAGATCATTTTGAGAATTAAGGGCATTGGT Y 2 1 2 1 101000 f 74 goat snp22123-scaffold2185-126993 15 41936078 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400511 Affx-122961272 AX-123270866 15 38738155 TCCCCCTGCTGACTCTGCCTGGAGCAGCGGGATAC[C/T]CACAGTGCTTTTAAAGAGAAACACCACACCTAGTC Y 2 1 2 1 101000 r 74 goat snp22122-scaffold2185-68636 15 41878229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271948 Affx-1111833044 AX-185454983 15 38763665 TGCCTGGAAAATCCCATGGATGGAGGAGCCTGGTG[A/G]GCTGCAGTTCATGGGGTTGCTGAGGGTCGGACACG R 2 1 2 1 103000 f 74 goat 15_38763665_AF-PAKI 15 38763665 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38441426 Affx-122928821 AX-123311763 15 38790351 AGAGAATCATTTTATACTGTTGATGGTACTGGCTT[A/G]CTGTGAAGTATAATACGCTAGAAGGAGGACCGCAT R 2 1 2 1 101000 r 74 goat snp22121-scaffold2185-16440 15 41826046 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776069 Affx-122927930 AX-385263199 15 38809941 CCTCAAATTATATTAAGTTAGAATGTAGACAGATT[A/G]TCTGCAGCTGATTAGAAATGCTGATGAGCAGTGAA R 2 1 2 1 101000 r 74 goat snp16469-scaffold1737-3051 15 41805953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382805 Affx-122973566 AX-123253163 15 38852837 TAGTTGCATACCAGAAGATTTATCAGGAAGCATCC[C/T]AAAATACAGCTTCCTAGGCCCACTCCCATACAGTC Y 2 1 2 1 101000 f 74 goat snp16470-scaffold1737-45947 15 41763149 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426847 Affx-122940498 AX-123297192 15 38911973 AACAGTATCTCTCATTCTATATCCTCTTTTGAAAC[A/G]TGATCTTGCCATTTCCCCATCAAGAGATAACATCT R 2 1 2 1 101000 f 74 goat snp16471-scaffold1737-105083 15 41704087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445923 Affx-122925927 AX-123316260 15 38946286 CAACCATAGCAGTGGAAGGCAGTGTACTAAGAAGT[C/T]GAGAACTTTTTGAAATTCTAAAGAATATCCTATGT Y 2 1 2 1 101000 f 74 goat snp16472-scaffold1737-139396 15 41669790 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781316 Affx-122955375 AX-385268401 15 38980513 CATTCAAAATTTTATAGTGGCCTGTTTTCCAACCT[A/G]CCATATGTCTAAGTGTCCCTTGGTCCAAAGTCTTG R 2 1 2 1 101000 r 74 goat snp16473-scaffold1737-173623 15 41637063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428702 Affx-122938623 AX-123299044 15 39030987 AAGACGTTTCCCCAAAGTTAAACTACATGTAACTA[C/T]GTGTCAACTCCAAAAATTAAACTGGGACTTACAAG Y 2 1 2 1 201000 r 74 goat snp16474-scaffold1737-224097 15 41588363 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432290 Affx-122936320 AX-123302631 15 39098797 AGCACCATGCATGTTTGTTTTGGGAAAACTGGGGC[A/G]TATATAAGAATAAGCCGTTGTTCTTATGGATATTT R 2 1 2 1 102000 f 74 goat snp16475-scaffold1737-291907 15 41520292 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781225 Affx-122959005 AX-385268310 15 39127405 TAGGTCCTAGAGTACAACCAACTACAGATATCCAG[C/T]ATGCAGGTGGAAATCTGAAACTAGAAGAAAGATCA Y 2 1 2 1 101000 f 74 goat snp16476-scaffold1737-320515 15 41491680 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451901 Affx-122921035 AX-123322234 15 39163753 AATAAAAAGCATGGCGAACTCTTCCCCACCTGCCT[C/T]ACAACCACCCCTCTCCAAAACAAACAAACAAAAAA Y 2 1 2 1 101000 f 74 goat snp16477-scaffold1737-356863 15 41455242 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440410 Affx-122929612 AX-123310747 15 39211684 AGCCTCCAAGGGCCAGGCCCTTGCCTGTCTTGTTC[A/G]CCAGTTCATCTAGACCAGCACCTGGCTCAGAGTGA R 2 1 2 1 102000 r 74 goat snp16478-scaffold1737-404794 15 41406969 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786823 Affx-122948008 AX-385273853 15 39248189 GGACTGCTCAGATGTAGAAGAATACTGAATTCTGG[A/C]GGAGGGAAGCAAGATAGAATTAATAAGATGAGAGG M 2 1 2 1 101000 f 74 goat snp16479-scaffold1737-441299 15 41370578 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404616 Affx-122957334 AX-123274968 15 39284269 ATTTTACAAAATTGGACAATCTTCATGTTTCTGTC[A/G]CCCAGTCACAGAGGAAACTCATAGCCCCTTTAGTT R 2 1 2 1 201000 f 74 goat snp16480-scaffold1737-477379 15 41334745 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391895 Affx-122966960 AX-123262252 15 39369753 TACACGCCTGGCACAGAGTCAAGTCCATGAGGGGT[A/G]TTCAGAAGCAGCCACAGAAAAGCCTGGATTGGTGC R 2 1 2 1 101000 r 74 goat snp31963-scaffold358-1022275 15 41251553 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449406 Affx-122922699 AX-123319741 15 39401658 CAGCTCTGATGCACTGGGAGCTTCTCTGATGCCCA[A/G]CTTCTTGTGCATTCTGCATCCGCCTGCCTCCTTGT R 2 1 2 1 201000 r 74 goat snp31962-scaffold358-990370 15 41219971 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381809 Affx-122974277 AX-123252167 15 39434306 AAGAAGACACCGTCTCAGAATATCAAGGAAGTTGA[C/T]GGCAGACTAGGATTTGCACTACACAAATGTGATAT Y 2 1 2 1 101000 r 74 goat snp31961-scaffold358-957722 15 41187072 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431441 Affx-122936506 AX-123301782 15 39463412 CGTTCACTGGCCTGTGTTCTGCACAGGGCAACTCC[A/G]TCCTCTGTGAAAAATGGAAGGTCCTGTTCATGATG R 2 1 2 1 101000 r 74 goat snp31960-scaffold358-928616 15 41157974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403262 Affx-122957872 AX-123273615 15 39498542 GACAGATAGGATAGAGCACATAGGAAAAAAACCCA[C/T]GCTAAATACTAATGTAATTATTTTTTCTAAAAAGG Y 2 1 2 1 101000 f 74 goat snp31959-scaffold358-893486 15 41123188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376615 Affx-122979045 AX-123246974 15 39568541 GAAGCAAGAGGGCTCTTTCTTGGGGGTCCATTCTA[C/T]AAGGTCTGCAGTAAAAGACAGGAAGATATTTTCTT Y 2 1 2 1 201000 r 74 goat snp31957-scaffold358-823487 15 41053331 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775349 Affx-122951941 AX-385262480 15 39599454 GAATCTAGAATTGATGTACCCATTAATATCATAAT[A/C]GCTTAAGGTCACATTAACTCTGCTTACTTTTGATA M 2 1 2 1 101000 r 74 goat snp31956-scaffold358-792574 15 41022099 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388832 Affx-122968890 AX-123259190 15 39640820 GAGACAAGTGATTGCAGAGGAGTTATGTGTCTGGT[A/G]AAGCCCAACAGACAACAGATGTGTTACCCTCCAGA R 2 1 2 1 101000 f 74 goat snp31955-scaffold358-751208 15 40980610 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408948 Affx-122953931 AX-123279299 15 39680574 ACAGCAAATGGCAGAGCTGGGAGCTGAACTCGGGT[C/T]ATCTGGCTCCATAGCCCAGCTCTCACTCACTCCAA Y 2 1 2 1 101000 r 74 goat snp31954-scaffold358-711454 15 40941061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393506 Affx-122965810 AX-123263862 15 39735010 CTGTTGATGTACTTTTAAGTTGCTTCCATATCCTG[A/G]CCCCCTCACTATTTTTATTTATGATGTAAAGCATA R 2 1 2 1 201000 r 74 goat snp31953-scaffold358-657018 15 40887103 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777562 Affx-122972432 AX-385264682 15 39779877 AGAATAAATACCTGTTTTATCTCTTTGGGAAATGC[C/T]ATCTGATTCGTCAAAAGGATATTTTTATTAGGTAG Y 2 1 2 1 101000 f 74 goat snp31952-scaffold358-612151 15 40842374 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38433638 Affx-122934583 AX-123303979 15 39837325 CTTACCCCCTACCATTATACTATGATCTTTTCAAT[C/T]TCATTTAATGTTCTTTCTTTGAATTCAACATTTTC Y 2 1 2 1 303000 r 74 goat snp31951-scaffold358-554703 15 40784874 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404592 Affx-122957353 AX-123274944 15 39875303 CCACATTTTGACAACTTTTATGCTGTCTTGGTGCA[C/T]GTTTGCTTTGTATCAGCCCTGCTGATACATTAATA Y 2 1 2 1 101000 f 74 goat snp31950-scaffold358-516725 15 40746814 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802503 Affx-122971557 AX-385289407 15 39904805 AAACAGGTAAGCCAGAGGTGTTCTGCCATTCTGCA[C/T]ATCCTACAAAGACTGATCCAAAGAACAAAGGCCTC Y 2 1 2 1 101000 f 74 goat snp31949-scaffold358-487223 15 40717267 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423894 Affx-122942290 AX-123294240 15 39953035 GACAAATGGGGGAAAGGCATTCCAGGTAGAGAGGA[C/T]AGCTTGAGCAAAGTTGTGAAGGAAGCATGAAGAAC Y 2 1 2 1 201000 r 74 goat snp31948-scaffold358-438993 15 40669111 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412091 Affx-122951124 AX-123282441 15 39996900 TGAGGGATTTCAAGACTGACTCTGGCTTCTGTCCT[A/G]CAGACAATGTTCCCTTCATTCTTATTTTCTCTAAG R 2 1 2 1 101000 r 74 goat snp31947-scaffold358-395128 15 40624952 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378178 Affx-122976953 AX-123248537 15 40054560 ATAGCAGACCAGGACCCAGGGGTTCTCAAAACTTC[A/G]CTCTTTGTTACCAAAAATAAAAATGAGAAATGGGG R 2 1 2 1 101000 f 74 goat snp31946-scaffold358-337468 15 40567080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434216 Affx-122934850 AX-123304557 15 40108734 ACTTCCCTCTGGTAAGGTCATGGGCCAACTCACAG[C/T]AATAATAGTTAACAAACAATAAGTGCCTAGGGCTT Y 2 1 2 1 101000 r 74 goat snp31945-scaffold358-283294 15 40512859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397630 Affx-122962624 AX-123267985 15 40140474 AACAGTAACACTCATGAACCAGGCCAGAGAAGAGC[A/G]CCTTTAAAGGAGACCAAGGAAAAGCCTGAGAGGAA R 2 1 2 1 102000 f 74 goat snp31944-scaffold358-251554 15 40480238 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791762 Affx-122943768 AX-385278753 15 40180627 CAGCTGATTCATGACTGAAGAGCAGTTTTCTCATA[C/T]GACTTCCATATTCCCCCAAATTCTTGCATATTTTC Y 2 1 2 1 101000 f 74 goat snp31943-scaffold358-211401 15 40439981 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412053 Affx-122951714 AX-123282403 15 40222308 GGTCACTGTGGGGTGTGGAAAGAAGAGGTCAGGTG[G/T]CTCCAGAGTTTTGATCCGATCCCTGGACAGGTAAA K 2 1 2 1 101000 r 74 goat snp31942-scaffold358-169720 15 40398485 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38394598 Affx-122964425 AX-123264953 15 40259656 ACCACTGGGGAGCAGAGTCAGGACCAAAACCTGGG[C/T]CTCCTGTGCCCAAAATGGGGTACTTTTTCTTCTCA Y 2 1 2 1 102000 r 74 goat snp31941-scaffold358-132372 15 40361457 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439697 Affx-122930570 AX-123310034 15 40291153 ACCGCTAAACCACTTCCCTGAGGAGATGTAACTTT[A/G]TTCATCAGGGCTCAGACTCTGAGCATCTAACTTGC R 2 1 2 1 201000 f 74 goat snp31940-scaffold358-100875 15 40329976 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399866 Affx-122960232 AX-123270221 15 40333235 AGGTCCTCTATGTAAATGACTCTTTCCTGAGAACT[A/C]AGTGTTTGGATTGAGCTGAAGGAACCCCTATGCAT M 2 1 2 1 101000 f 74 goat snp31939-scaffold358-58793 15 40287941 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426484 Affx-122940230 AX-123296830 15 40366739 ACAGCTGCTGAGCTATATCTTCAAGCTGGATAACA[C/T]GCATGTGCTGGAATAGTAGGGAAGTTTGGATGGTA Y 2 1 2 1 101000 f 74 goat snp31938-scaffold358-25289 15 40254207 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783053 Affx-122955401 AX-385270120 15 40405536 AATTAAATTGTATGTGTATAGTCAAAACATTTTCT[A/G]TCCCTGTATTTTAAGAATCTAACTATTACAATCAC R 2 1 2 1 101000 r 74 goat snp45751-scaffold628-13409 15 40215209 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394801 Affx-122964811 AX-123265156 15 40447103 TGAAAGACACCTCTATCACATCCCTATCAAACTAA[C/T]AGTAACCAGCTGGGAACTGCTTGTGGACAGAAAGT Y 2 1 2 1 101000 f 74 goat snp45752-scaffold628-54976 15 40173658 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410294 Affx-122952501 AX-123280644 15 40498739 GTTAAATAAGCAGGGTGACAATAGACAGCCTTGAC[A/G]TACTCCTTGCCCTACTTAGAGGTACCAATATCTGT R 2 1 2 1 201000 r 74 goat snp45753-scaffold628-106612 15 40122384 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383818 Affx-122973176 AX-123254176 15 40532655 AGTAGGCAGAGCCAGGGAGAGGAACAAGAGAGGAC[A/G]GAAAGAGCTTCCTCATTAACCCTGAGCCAGAGGTT R 2 1 2 1 101000 r 74 goat snp45754-scaffold628-140528 15 40085892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386396 Affx-122970831 AX-123256754 15 40621641 CTGAGCATACCACTGAAGCCATTCTGGTTTCCAGT[C/T]CTACCAGCCTCATGTAAATCTCTCAGAACCACAGG Y 2 1 2 1 201000 r 74 goat snp45756-scaffold628-229514 15 39998099 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406875 Affx-122955644 AX-123277226 15 40667412 GCATCTTGGAAAATATTTATCTAGTAAAAATTTCA[C/T]ATGACTGTCTTTTTCTGCTATAGTTTCACCTAAAC Y 2 1 2 1 101000 r 74 goat snp45757-scaffold628-275285 15 39952414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272375 Affx-1111834245 AX-519546104 15 40712717 AAAGAAGTCACAACTTATCCTGCAGAGCAAAAGCC[A/G]AGGTGTAACGGAGACTCGATGTGAAAGCCAAGAAA R 2 1 2 1 201000 f 74 goat GoatD01.027288 15 40712717 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38432257 Affx-122936345 AX-123302598 15 40762662 TCCTGCAGCCTTGCTAAAATTACTTATTAGTTCTG[C/T]GAGTTTGTGTTCATTTTCCTTGTGGGCTTTTACTT Y 2 1 2 1 101000 f 74 goat snp45759-scaffold628-370535 15 39855896 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434651 Affx-122933984 AX-123304992 15 40791363 CATATGTGTATCTGCTTCCAAGTCTTGTCCTGACA[G/T]TTGCCTTTTTGCATTTTTTCTTTGTTGTGCTTCAG K 2 1 2 1 101000 f 74 goat snp45760-scaffold628-399236 15 39826993 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771049 Affx-122949740 AX-385258209 15 40827953 TATTGATCCAAATTTACAATACTTTCAGTTGTTCA[G/T]ATCCCAAAAGCATAAATCACATTCTGGGTACTCCT K 2 1 2 1 101000 r 74 goat snp45761-scaffold628-435826 15 39790266 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778994 Affx-122938449 AX-385266101 15 40906954 GTGTCTCCTTATGTGAAGAGTACTCTAAGTAGAGT[A/G]CAAAGACAGATTGCATGACACTTTTCAGGGAGTTT R 2 1 2 1 101000 r 74 goat snp45762-scaffold628-514827 15 39710460 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402124 Affx-122958674 AX-123272477 15 40950950 ATGTTAAGAATACCAGTCAACAACTTTCCCCCTTC[A/G]GTTCCTAGAACTCCGGGAGGCTTCCCTCAAGCAGA R 2 1 2 1 202000 r 74 goat snp45763-scaffold628-558823 15 39665713 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401144 Affx-122959377 AX-123271497 15 40997531 CTCTTCAAAAACAGAAAATGAAATTTATGAGACTC[A/G]CACTTCTGAGATCTGGCAGGTCATACTGAGCATCC R 2 1 2 1 201000 r 74 goat snp45764-scaffold628-605404 15 39618349 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404464 Affx-122956735 AX-123274816 15 41035129 TTTCCACATCCTTGGATTCAATCCATGTAGATCAT[A/G]TAATACTGTAGTACATATTGAATAAAAAAATTCCA R 2 1 2 1 101000 f 74 goat snp45765-scaffold628-643002 15 39580570 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384753 Affx-122972033 AX-123255111 15 41088329 AATTAGCTGCTAATCAACTTTATTCTTACTTTTCA[A/G]TTATGCTAAAGAGCTTCACTGTGCTCAAGTCCTCT R 2 1 2 1 101000 r 74 goat snp45766-scaffold628-696202 15 39527673 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376274 Affx-122978390 AX-123246633 15 41121263 GAGTGTCTCACTCTACCACAGTGATATGATACTTA[C/T]GTTCAGTGCCCTAAATCTGGGGGAAATTACTGGGT Y 2 1 2 1 101000 f 74 goat snp45767-scaffold628-729136 15 39494706 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408500 Affx-122954405 AX-123278851 15 41181572 TCTCTTAGCACAGGGACCTTATAAAAACAGGCTGC[G/T]CACTGAATTCAGCCAGTAAGCTGTAGTCAGCCAAC K 2 1 2 1 101000 r 74 goat snp45768-scaffold628-789445 15 39435107 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398470 Affx-122961584 AX-123268825 15 41240588 GGACTGTTCCGCCCGTTAGAGGTCAAAGCACAGCT[A/G]TGTAAGTCTTTGAGACAAAGGGTTTTATATCAGAA R 2 1 2 1 101000 r 74 goat snp45769-scaffold628-848461 15 39376355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422289 Affx-122943485 AX-123292635 15 41275804 GCCCTACAGCCTGTGCGCCACAAGAAAAGCCACCG[C/T]AACGAGAAGCCCACAACTAGAAAGTGCAGGCTTTC Y 2 1 2 1 102000 r 74 goat snp45770-scaffold628-883677 15 39341423 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376238 Affx-122978785 AX-123246597 15 41373661 TGCAAATATGGAATGTGAGAAGGAAAGAAAGAGCT[A/C]TGTGGGATGAACTGGAATTGGAGGTACTGATGTGA M 2 1 2 1 101000 r 74 goat snp45772-scaffold628-981534 15 39244126 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271950 Affx-1111833045 AX-519545724 15 41386967 GAGAGGTTACAGCACTCTAATGGAGCACAGAAATG[A/G]GAAAAAAATATGGCGTAAAGGGTAAGAAGAACAGT R 2 1 2 1 101000 f 74 goat 15_41386967_AF-PAKI 15 41386967 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395752 Affx-122963687 AX-123266107 15 41403207 TGAGGAATTTCTTAGTATAGCAACATAAAAATAGT[A/C]GGCTATTCTGTAACTTTGTAGTTTGCTGATTTAGT M 2 1 2 1 101000 f 74 goat snp45773-scaffold628-1011080 15 39214760 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412069 Affx-122951702 AX-123282419 15 41448459 TACTTCATGCAATCCACATTTCCTCTTTTAGCAGA[C/T]AGGCAAATTTCTCATCTGGCTGATTTGGTTAGTTT Y 2 1 2 1 101000 r 74 goat snp45774-scaffold628-1056332 15 39169614 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430616 Affx-122936971 AX-123300957 15 41488035 TGGGTGAGCTCTGTTCTATCTTTGCAGTAACTCTG[C/T]AAACCTAAAGCTATTCTAAAATAAAAAGTTCAAAT Y 2 1 2 1 101000 f 74 goat snp45775-scaffold628-1095908 15 39129664 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792666 Affx-122970980 AX-385279646 15 41518414 TAGGTTAAGTGGCTGGGAAGAGAGAATTGACAGAA[C/T]GTGTTTGAAAGGCAGTGATAAGGAAGAATAAAATT Y 2 1 2 1 101000 f 74 goat snp45776-scaffold628-1126287 15 39099199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800960 Affx-122929883 AX-385287875 15 41587133 CTTGGCTCTCGAGTTGATGGGAATAGTAAGGGGCT[A/G]TGTTCACAGCCTAAGGGCTGCAGCACATATAAGGT R 2 1 2 1 101000 f 74 goat snp45777-scaffold628-1195006 15 39029468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379410 Affx-122976120 AX-123249768 15 41703083 GTGCTGTGTCTCACTTTCTACTGTGTTTTGTTTTA[G/T]AATCTGCTGCAAATCCTTTTTCGAATGACATAGAA K 2 1 2 1 201000 r 74 goat snp45779-scaffold628-1310956 15 38912628 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782072 Affx-122971425 AX-385269150 15 41741477 CAGCCATTTTTAACTCAGTGCTGTGGTTTCCATTC[C/T]TCCCTGCTCTTTCTTAAGCCACAGAACCACACTTT Y 2 1 2 1 101000 r 74 goat snp45780-scaffold628-1349350 15 38873767 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418251 Affx-122947027 AX-123288599 15 41776075 GAGCAAAGGACACTAGTGCCATAGGGATAAAAAAT[C/T]GGGGACAGACGAAAGGGACCCAGGTATAGGGTGCT Y 2 1 2 1 101000 f 74 goat snp45781-scaffold628-1383948 15 38839826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770324 Affx-122953334 AX-385257490 15 41811217 GTTGGTCTTCTACCTTGACCCGTGCTTAACAGCAG[C/T]GAAGGTGTAAGTCTGGCTGAGGAAGATCTCTGAGA Y 2 1 2 1 101000 r 74 goat snp45782-scaffold628-1419090 15 38804779 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436566 Affx-122932905 AX-123306904 15 41840466 GCAAGTGAATTGTCTAAGCTCATATACTGTCAGTG[A/G]CAGAGGGCACCTAGAACTCAGACCAGACAAGCCAA R 2 1 2 1 101000 f 74 goat snp45783-scaffold628-1448339 15 38775149 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409185 Affx-122953186 AX-123279536 15 41930268 GAAGATTATTATGACATATGTGTATAGGAATGTAA[C/T]GTGCTTATCTTAGGTAACCTGCAAGATGTAGTTCT Y 2 1 2 1 101000 r 74 goat snp45785-scaffold628-1538141 15 38684866 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771877 Affx-122931893 AX-385259033 15 41976141 AAAGGAAACATACAGGCAAGTTTAGTAAGAGTGAC[A/G]TTCACTGTAGGCTTGGAGCCTTGTAAATGATCCTT R 2 1 2 1 101000 r 74 goat snp45786-scaffold628-1584014 15 38639124 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787435 Affx-122970333 AX-385274460 15 42037357 CTTTTTTTCAAGGCATTTACAGTTTGGATCGATGA[C/T]GTTGGCACCCAGATTTTTTAGTCGGACCTTCTAAT Y 2 1 2 1 101000 r 74 goat snp45787-scaffold628-1645230 15 38578193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439622 Affx-122930628 AX-123309959 15 42077886 CTCAGCTACCCCCACCACCCCCAGCTTCCATGTCT[C/T]CTCTGATCTGTTTCTCCCCATATCCCTCTTCCTTG Y 2 1 2 1 201000 r 74 goat snp45788-scaffold628-1685759 15 38537277 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435894 Affx-122932777 AX-123306233 15 42109125 CTTTGTCTTCCCTTCAGATTCTTCTAATTTTATCC[A/G]CCATTTAAATCTTGGTGTTCTTCAGCCTTCTGCCT R 2 1 2 1 101000 r 74 goat snp45789-scaffold628-1716998 15 38506683 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402788 Affx-122958296 AX-123273141 15 42146131 ACACAGTACTTAGCTCCAACACAGATCCAGGCTCA[A/G]TCCTGTCCAGAGTGGCCTGGCTTAGTCCTGTCCTT R 2 1 2 1 101000 f 74 goat snp45790-scaffold628-1754004 15 38469843 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383831 Affx-122973165 AX-123254189 15 42175255 CCAAGAGTGATACTGTGGTTACAGAGAAAAAAGGC[A/C]TTGTCTTTAGGTGGTCGATGCTTAAGTGTTCAGGG M 2 1 2 1 101000 r 74 goat snp45791-scaffold628-1783128 15 38440772 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421253 Affx-122944759 AX-123291600 15 42234729 AACTGAAAAGATGCATATAAATTACATTTTTATAA[A/G]TGAATTCCTGAATTCCTGCAGGCTTACATTATATT R 2 1 2 1 103000 r 74 goat snp45792-scaffold628-1842602 15 38381298 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390152 Affx-122967983 AX-123260509 15 42282198 TGTAGACAGAGGCTCATTAACTTTTGAAACCACAG[C/T]AATGTGTGTTTTATACAAGTATTTTAAAGCCTTTT Y 2 1 2 1 101000 f 74 goat snp45793-scaffold628-1890071 15 38332203 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392313 Affx-122966704 AX-123262670 15 42334269 GCACTAGGGCTCCCCTGTGGACAGGGCATGTTCAA[G/T]CAGCCGGCAGTAACCAGATAAAGGTTCAGTCCAGG K 2 1 2 1 101000 r 74 goat snp45794-scaffold628-1942142 15 38279070 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800000 Affx-122938550 AX-385286923 15 42390211 CTTTCCTGAAGCCCAGATCTGTAGAATCATGGACC[A/G]TCTACACTGTTTCTTCTGCCCAACAATCCCCCAGG R 2 1 2 1 101000 f 74 goat snp45795-scaffold628-1998084 15 38222588 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446817 Affx-122925284 AX-123317153 15 42431663 TTTGGGGGCTTGAGGTATTTCCAGAAGTTCCTGAC[A/G]TGATTTGTGCTCACAGGGACAGCCAACCGAGCCAG R 2 1 2 1 101000 f 74 goat snp45796-scaffold628-2039536 15 38181339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451114 Affx-122921388 AX-123321448 15 42472428 TGTCTCCTCCTGTACAGACCATTGTCATTGTTTGC[G/T]GCTGTGACTTGATGGGGCTGATGTAGTAGAGGAAT K 2 1 2 1 101000 f 74 goat snp45797-scaffold628-2080301 15 38140676 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405933 Affx-122955564 AX-123276285 15 42505793 TGCCTCTACGGCTTCCATTTTCTCCAGTGACCCAG[C/T]GTAGACTCTTCATATGGTATCTGTCCTTTTGCTCT Y 2 1 2 1 101000 r 74 goat snp45798-scaffold628-2113666 15 38107264 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420898 Affx-122944610 AX-123291245 15 42542160 CAAGTCTCCTGGACCAGCCCAGGGAGAGCAAATAG[C/T]GTGAGTATTCCTTAAGGAAGGGAGAGGTGAGTCAG Y 2 1 2 1 202000 f 74 goat snp45799-scaffold628-2150033 15 38070887 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797361 Affx-122920188 AX-385284300 15 42579779 AATGTTGCTTACTGTTTAACAACAGAGTAATTTCT[A/G]TCAAATTAAAAATAAGACCAGAACATACTCTAACA R 2 1 2 1 201000 r 74 goat snp45800-scaffold628-2187652 15 38035643 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406191 Affx-122956144 AX-123276543 15 42626449 CAGTGCTGTGCTTTTAAAAATATGTTCATGCTTCT[A/G]TAGGTACATCTAAAGTGTGTTTTCTGAAAGCTACA R 2 1 2 1 101000 r 74 goat snp45801-scaffold628-2234322 15 37988932 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431396 Affx-122936544 AX-123301737 15 42693212 CCATCGACAAATCTCTTCCCAGTTCTCCTGCCCTC[A/G]ATGTACCAATCCGGAGAAGGCAATGGCAACTCAGT R 2 1 2 1 201000 f 74 goat snp45802-scaffold628-2301085 15 37922751 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428019 Affx-122939150 AX-123298362 15 42728736 AACCTCTCCTACCTAAAGCAGTGGACAGTGAGAAC[C/T]GAAAGGAGCAGGCCCAACAGGAAGTGGGAGAGCAG Y 2 1 2 1 202000 r 74 goat snp45803-scaffold628-2336609 15 37887380 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411425 Affx-122951833 AX-123281775 15 42790540 GGAGTTTAATATATACTTTTGCGTACTAGAAATGG[C/T]ACTTAAAAAGTTTATTTTTCCAGTAGAGTTTACTA Y 2 1 2 1 103000 f 74 goat snp45805-scaffold628-2398413 15 37825854 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382683 Affx-122973649 AX-123253041 15 42852237 ACATTATGGAAAAGCCTGGATGAACTTTTTGACAA[C/T]TGATGGTAATGGACAATGGACAAAGATAGAGCTAG Y 2 1 2 1 101000 r 74 goat snp45806-scaffold628-2460110 15 37763043 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442981 Affx-122928196 AX-123313318 15 42891266 ATTATTTGGTTGAAGAGTTGGTTTATCAGTTTCTT[A/G]CTTGGTCAATTAGTTGGCCAGTCAATTCAGAAGTT R 2 1 2 1 101000 r 74 goat snp52409-scaffold781-14292 15 37420712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403280 Affx-122957857 AX-123273633 15 42934199 TCTGAGCTGCCCAGCAAGACTTCCAGAAAGCTGAC[A/G]GAGCCTGTCTCTACTTTATCAGCAAATCAGCCACA R 2 1 2 1 101000 r 74 goat snp52410-scaffold781-57225 15 37378293 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427650 Affx-122939328 AX-123297993 15 42965758 CAAGCCTGGGCCATTCCCTCAGTAGGAGTCGAGAA[C/T]AGTCTGCCCAGCCCTGTTTTCAGGGCAGAACTTTA Y 2 1 2 1 201000 f 74 goat snp52411-scaffold781-88784 15 37347608 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389255 Affx-122969030 AX-123259613 15 42995874 CCAAGTCCATCATTCTGATTGCCCCAGTTCAGAAA[G/T]CAGAACCCTTCCTTTCCAAAGTCCCACCCATAGAG K 2 1 2 1 201000 r 74 goat snp52412-scaffold781-118900 15 37317706 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444229 Affx-122927235 AX-123314566 15 43104143 TTCCAGATCCCACATGTTATTGCCCTAGTGGACCC[A/G]CAGTCCTCAGAAAATGTTAGTCTGTTCTTTAGAAC R 2 1 2 1 201000 r 74 goat snp52415-scaffold781-227169 15 37209494 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412439 Affx-122951416 AX-123282788 15 43135681 ATATAGAAACTAAATACCTTTCAGAGAAGGAAAAT[A/C]ATTTATCAAAATGTAACTTGTACAAAAGCAAGGCG M 2 1 2 1 101000 r 74 goat snp52416-scaffold781-258707 15 37177861 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435594 Affx-122933354 AX-123305934 15 43179915 TTCAGCTGGACCTGGCTCCACACAGTTAGAGGTCT[A/G]TTTCTGGGTCTTATTGTTCTAGGACCCAGGGAATT R 2 1 2 1 101000 r 74 goat snp52417-scaffold781-302941 15 37132634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386259 Affx-122970954 AX-123256617 15 43212160 AAAGAATACACTTCCTACCCTCCACTGAAATCAGA[C/T]GTAACCTTATGACTAAGTTCTGTGACTAAATTAAA Y 2 1 2 1 101000 r 74 goat snp52418-scaffold781-335186 15 37100324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404976 Affx-122956406 AX-123275328 15 43245353 TGCACCAGAGCTCCACCCAAACTGCTCTCAGGAGG[C/T]ACCCTCCACGTAACTGAAGACAGTGGACATTTCTC Y 2 1 2 1 101000 r 74 goat snp52419-scaffold781-368379 15 37067219 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441517 Affx-122928718 AX-123311854 15 43293721 AGACATAAAAATTAAAGGTAAGCTATTATAAATCT[A/G]TATATGGATTCAGTTAGAGAAGGTTGGACACTGGT R 2 1 2 1 101000 r 74 goat snp52420-scaffold781-416747 15 37018087 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444976 Affx-122926664 AX-123315313 15 43332016 TCTTTGGATGTTTCCAAAGAACTAATTTTTGCCAT[C/T]AGCATTCCTGAAAATATTTTCATTGCATATGCCCC Y 2 1 2 1 201000 f 74 goat snp52421-scaffold781-455042 15 36980054 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798795 Affx-122923663 AX-385285726 15 43382979 CTGGCAGAACTTACTTGTTCTTTCCTCTACCTTAG[A/G]CATACCTTCACTCCAGCTAGCCCCTTCCTTTTCTT R 2 1 2 1 101000 f 74 goat snp52422-scaffold781-506005 15 36929414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407799 Affx-122954562 AX-123278150 15 43414620 GTCATATGGCTATTGTGAGGAATAAATGAATTAGT[A/G]TACATAAATGGCTAAGAAGAGTATTCAGCATACAG R 2 1 2 1 201000 r 74 goat snp52423-scaffold781-537646 15 36897253 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405051 Affx-122956350 AX-123275403 15 43458330 AGCAATAAGTGTCCATATTCTCTCTTTGACCGTCT[A/G]CGGTTGATGGCTTGGCCTTTTACCTCCGCAGAAGA R 2 1 2 1 201000 f 74 goat snp52424-scaffold781-581356 15 36852618 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801657 Affx-122970705 AX-385288565 15 43539873 GAAAACTGGTTAAGGCACTTAGTCCTGATCAGCTA[C/T]ACAGCTTGGACAACAGTTGCCTCTACAGTTATGAT Y 2 1 2 1 101000 r 74 goat snp52426-scaffold781-662899 15 36770200 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795908 Affx-122975431 AX-385282860 15 43587084 TACCTCAGTTTTTTATAAGTAAATGGAAATAACAG[C/T]ATCTACGTAGGATTGTTGGAGACTAAATGAGCTGG Y 2 1 2 1 201000 f 74 goat snp52427-scaffold781-710110 15 36722936 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765282 Affx-122924214 AX-385252812 15 43641565 GGGAGCTGAGTATCTGAACTCAGGCTCAAGGCACT[C/T]GCACACTTATATGCTGAATGCTGCTTACCTACTGA Y 2 1 2 1 101000 f 74 goat snp52428-scaffold781-764591 15 36668365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777701 Affx-122932389 AX-385264820 15 43670376 ACCTTCTTGGGTTTTGTATGTTCTGATATGAGGGT[A/G]TTAAAGTTCATGTGAACTTTACTAAATGGCTATAC R 2 1 2 1 201000 r 74 goat snp52429-scaffold781-793402 15 36639713 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385451 Affx-122971309 AX-123255809 15 43713822 TCAGACACAACTGAGCATGCACATGTATATACACA[C/T]GCACATAGCACTCTACACGGCACACTCTTTTTAGT Y 2 1 2 1 201000 r 74 goat snp52430-scaffold781-836848 15 36596130 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384561 Affx-122973008 AX-123254919 15 43743812 TTCTGAATGCAGTAACTGTGTTTTATGGCCTTTTG[C/T]ACTTTCACAGCAGCATACACAAAAGTTGAAAATTA Y 2 1 2 1 101000 f 74 goat snp52431-scaffold781-866838 15 36567678 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438178 Affx-122931834 AX-123308516 15 43785431 TAAATAGCTTGAACTTGATTGTGTAGACAGTGTGG[C/T]ACCATGGAAGGTTTTAAGCAGGGGAATGAAATGCT Y 2 1 2 1 101000 f 74 goat snp52432-scaffold781-908457 15 36525682 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402594 Affx-122958428 AX-123272947 15 43843942 CTCCGTCATGTCCGCGTCTGCAGTCATTAATCTAC[A/G]TTCTTTCCTGTGCTTGTCTTTCTACACCAAATGCC R 2 1 2 1 101000 r 74 goat snp52433-scaffold781-966968 15 36466274 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784787 Affx-122975001 AX-385271834 15 43908135 ATCCTGCTCCAAAGATTATTTGAGAAACTAAGTTA[C/T]AAACAACAGCAACTAGTTAAACATGCTGCTGCCTC Y 2 1 2 1 101000 r 74 goat snp52434-scaffold781-1031161 15 36400655 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271952 Affx-1111833046 AX-519545726 15 43919291 GTGTTAGTCGCTCTGTCATGTCCGACTCTTTGCAA[A/C]TCCCTGGACTGTAGCCCACCAGGCTCCTCTGTCCA M 2 1 2 1 303000 f 74 goat 15_43919291_AF-PAKI 15 43919291 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448308 Affx-122924158 AX-123318644 15 43955834 TGTTGGCTGTGGAGGGGAGCCTGATTACAGTGACA[G/T]GAATCATGAACGGGAGAAAAGGACCAGAGGTATAG K 2 1 2 1 101000 r 74 goat snp52435-scaffold781-1078860 15 36355858 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773256 Affx-122940040 AX-385260399 15 43994785 CTCTTTCCTCATCATTCTCTATTGCTCTATTATGA[C/T]TGCTCTCTGACTTGCTCGTGTCACTCTGTCTTTGT Y 2 1 2 1 101000 r 74 goat snp52436-scaffold781-1117811 15 36320823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442510 Affx-122928553 AX-123312847 15 44047346 CTGCCTCTAGCCCAGAAGTCCTTCACTGTAGGCAA[C/T]AGCAAAGTAGACAAGAACTAAAAGAATCTTTTGTT Y 2 1 2 1 102000 f 74 goat snp52437-scaffold781-1170372 15 36004343 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445320 Affx-122925430 AX-123315657 15 44088935 GGGAAACTGAGTATGAGGTTCTCCTCCAAGAAGAC[A/G]TGTGCAAACATACACAGCTTGAAACAGAGGAACAA R 2 1 2 1 202000 r 74 goat snp52438-scaffold781-1211961 15 36017927 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800878 Affx-122966180 AX-385287793 15 44148963 GACATGCAGAGACAACTCAACATAAAGGGAGCACT[A/G]TCTCACAGGAAAAGTCTCCCAGATAGAGAACTGGT R 2 1 2 1 201000 r 74 goat snp52439-scaffold781-1271989 15 35988792 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796794 Affx-122932752 AX-385283737 15 44179298 CAACAACTTCAAGGAAAGAAAATTTTCACCATCTC[C/T]ATTTCTTTCCTATCATTGTTATTCCATTCATTTTG Y 2 1 2 1 102000 f 74 goat snp52440-scaffold781-1302324 15 35959271 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791760 Affx-122944501 AX-385278751 15 44230569 CCTTTTTCTTCTCATTTAGATTTTCCAAGTGTCCT[A/G]CAGTCAGGTTGTCCAAAGCGACATTCAGCCATTGG R 2 1 2 1 202000 f 74 goat snp58568-scaffold953-1146096 15 36123766 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435323 Affx-122933618 AX-123305663 15 44266205 TCCAACTTGCTGAGATTGTCAGGAAGCTTTGAGCT[A/G]TTCAAACTCAAGATGTCTTCTCTCAGAAATAGGAA R 2 1 2 1 102000 f 74 goat snp58567-scaffold953-1110460 15 36088096 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800685 Affx-122946420 AX-385287603 15 44340367 TAATGGAAAAACTGACATTAAGCAAAATAAATTTC[A/G]TAAGTAATTGCAACTGAGATCATAGGAATCAGGTC R 2 1 2 1 201000 f 74 goat snp58566-scaffold953-1036298 15 36011362 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769409 Affx-122968285 AX-385256580 15 44396450 TTTAGTTTTTCTAACCTACCATTCTCAGTATCATC[G/T]TCAGCCTTGAGCCAGTTCCCTGTTTATCAGAATAA K 2 1 2 1 102000 r 74 goat snp58565-scaffold953-980215 15 35954334 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429876 Affx-122938135 AX-123300217 15 44429135 GCATCAGAGGCATACACCTGCAAGACTGGACTGCC[A/G]GGGGCCAGGCTCTCGGACACTGCAGCATGGTAGCG R 2 1 2 1 101000 f 74 goat snp58564-scaffold953-947530 15 35921658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423479 Affx-122942575 AX-123293825 15 44512017 CTCCTTCCACTCCCTCAGGTCCACTCACTGGCACA[C/T]GGTGTCTTCAGGATACAGAATGCCCTGGAAAATCT Y 2 1 2 1 101000 r 74 goat snp58562-scaffold953-864648 15 35838461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452789 Affx-122920238 AX-123323122 15 44550701 TTTATTGAATTCACTTTGTTGAAATGCTGAATACC[A/G]TTTCTGTTTTCCTGACTGGACTCTGATGTAATACT R 2 1 2 1 202000 f 74 goat snp58561-scaffold953-825964 15 35800093 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400754 Affx-122959889 AX-123271109 15 44608629 CTGAGTTCTCTCATCCCAGTTACTTCTCACTTCCA[C/T]GAGTGCTGTGTGTGCTGAGCACTCCAGGCAGCAGA Y 2 1 2 1 101000 f 74 goat snp58560-scaffold953-768036 15 35742176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435338 Affx-122933607 AX-123305678 15 44666063 CCTGGGTACTGGGCATAGTCAGGGTGAAGCAGGGC[A/G]TGGATGGGCTGCTGGCTGAATAACTTATCTTCTGT R 2 1 2 1 101000 r 74 goat snp58559-scaffold953-710602 15 35685305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380756 Affx-122975124 AX-123251114 15 44715748 ACCCTTCTGCTCCTTGGGAACCTGAGGGAATCACC[A/G]TCTCCTTCAGTGGATTTATATTTGCTCAGAAAGAC R 2 1 2 1 101000 r 74 goat snp58558-scaffold953-660917 15 35635743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408359 Affx-122953737 AX-123278710 15 44746939 AAACCCCACCCCGCAAAGAACTCAATTTGGGTTCC[A/G]TTTGCACGTGCATTTTAATGTTCCTAATCCGTAAA R 2 1 2 1 101000 r 74 goat snp58557-scaffold953-629726 15 35604455 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439644 Affx-122930610 AX-123309981 15 44797394 TTCAGAGTTCTTCATGTGTACCAATTCATTTAATT[A/C]TCACAGCAGTCCTATAAAGTAGATACTATTATTCA M 2 1 2 1 101000 f 74 goat snp58556-scaffold953-579271 15 35554394 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429946 Affx-122938081 AX-123300287 15 44836471 ATCTCTCCCTTCACCAAAAGAGAACTACTGGTTAA[C/T]GGTTAAAGCTGGAGTCAGGCAGGTGTAGATCTGAA Y 2 1 2 1 102000 f 74 goat snp58555-scaffold953-540194 15 35514928 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437690 Affx-122931764 AX-123308028 15 44912479 CTTCGTGAAAAATGACAGTCTTGCGGAAGTGGTCA[C/T]TGCTGACAGTGAACATCCATCCTGGGGGTCTTTTA Y 2 1 2 1 101000 f 74 goat snp58553-scaffold953-464186 15 35438051 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382640 Affx-122973684 AX-123252998 15 44944035 TACAAAACTTCGTATTTCAGTGTTGAACATTCTAC[A/G]CAATGAGAAAGTTAATTCCCTCTTAACTACTTCCT R 2 1 2 1 101000 r 74 goat snp58552-scaffold953-432630 15 35406493 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447460 Affx-122924361 AX-123317796 15 44986238 GTTATAGAACATGACCAAAAGTCTTTTAAGTGACA[C/T]GGGAAAGAAATGTCCCTTTCAGACCTCCAATAACA Y 2 1 2 1 101000 f 74 goat snp58551-scaffold953-390427 15 35364081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383530 Affx-122972627 AX-123253888 15 45024714 CCAGCCTCCATATTGATATGAGCCAATTTTTTTAC[A/G]TATATAAAAGTATATATATATATATGTGTGTGTGT R 2 1 2 1 103000 f 74 goat snp58550-scaffold953-351951 15 35326304 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802022 Affx-122940612 AX-385288926 15 45065299 AAGTTGTTTCTTCCAGGAATTAGGAATCCAACTAA[C/T]ATGAAGACCTAAGAAATAGAGTGAACAAAAGGCAA Y 2 1 2 1 101000 f 74 goat snp58549-scaffold953-311366 15 35284859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782150 Affx-122937738 AX-385269228 15 45107484 TGGAGAGACTATATTCAATTTCTGGTAGTCAGGAG[A/G]ATCTCCAGGGTAGCCATATATAATTAGTGATACTA R 2 1 2 1 101000 f 74 goat snp58548-scaffold953-269181 15 35245069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378840 Affx-122976535 AX-123249199 15 45138648 TGATCATTTAATTAATAGTGGCCAGAGTCAAGAGC[A/G]AGTTAAGCACATCTGCTACATAAATAAATCTGCTT R 2 1 2 1 101000 f 74 goat snp58547-scaffold953-238017 15 35213865 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794825 Affx-122943756 AX-385281785 15 45168283 ATTCTCGCCACACAAACAAAACATGACATAGCATA[C/T]GGGATTAAAGCAGATGACCACAGGTGAGAAAACAG Y 2 1 2 1 101000 r 74 goat snp58546-scaffold953-208382 15 35186091 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792055 Affx-122962636 AX-385279043 15 45203879 TTCTTTGAAGCTAAGGAAGTTAGGGGACATCACAG[C/T]ACATTGTTCCCTTAAGGTTTTAGGAAATATATGTA Y 2 1 2 1 101000 f 74 goat snp58545-scaffold953-172786 15 35152130 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792948 Affx-122954626 AX-385279926 15 45251775 ATATAAGTATTTCAGCTTTTCTGCAAAATAACCAT[A/G]CAACTTTAAACTTTTCCCAATATTGTGTTAGAGTA R 2 1 2 1 101000 r 74 goat snp58544-scaffold953-124890 15 35103720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779916 Affx-122976827 AX-385267015 15 45366821 CAATTTTGGTATATATGGAAACACCTTCTTATATG[A/G]TAAACTCATGTTAGTCTTTGTCAATAATGAAAATT R 2 1 2 1 101000 f 74 goat snp58542-scaffold953-9844 15 34993303 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411845 Affx-122951226 AX-123282195 15 45463696 CATCCACCAGAAGACAGACAGCAAAAGCAAGACTA[C/T]AATCCATCAGCCTATAGAATGGAAACAACAATCAG Y 2 1 2 1 201000 r 74 goat snp2043-scaffold1062-86932 15 34686657 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438538 Affx-122931190 AX-123308876 15 45496336 AGTCAATCTCATTCCTCAACCTGGATTCACATGGC[C/T]GGTAATTATAGTCTAGACTCAAAAGTTCTGTCAAG Y 2 1 2 1 201000 r 74 goat snp2044-scaffold1062-119572 15 34653364 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427852 Affx-122939723 AX-123298195 15 45539762 AAGAAAGGATAAACTGAGATGCAGGAGAGACTTGG[A/G]GTACAAGGTATCAACTCAGGATGTTTACGAGCTTG R 2 1 2 1 201000 r 74 goat snp2045-scaffold1062-162998 15 34609427 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384557 Affx-122973011 AX-123254915 15 45571128 AATGCTTCTTAAAGCGCCATCCCCAGGCCAGCATC[A/G]TCAGCATCACCAGGGATCTTGCAGGTTCTCGGACC R 2 1 2 1 303000 f 74 goat snp2046-scaffold1062-194364 15 34578037 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789731 Affx-122945608 AX-385276739 15 45604261 ACCCAGGCAGGGTTAATATAGTCTTCTTTATACTC[C/T]TCCCTTGAGAGTGAGAAGAGAAGGTGTTAGAGTCC Y 2 1 2 1 202000 r 74 goat snp2047-scaffold1062-227497 15 34543465 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792664 Affx-122976453 AX-385279644 15 45675594 CTATATACACACACACACCGCTCCACATACTCTGT[C/T]GATGCTGATGAAGTCAGCCTCACAGTGTAGAACTA Y 2 1 2 1 102000 f 74 goat snp2048-scaffold1062-298830 15 34473899 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421443 Affx-122943947 AX-123291790 15 45749782 TCCATTTTGCAGAAACATGGAAAGATGACTCATGG[C/T]GTTATGCTGATAGTGTAATTATGGTAAAGACATTA Y 2 1 2 1 201000 r 74 goat snp2050-scaffold1062-373018 15 34399403 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779736 Affx-122920892 AX-385266836 15 45782156 AAGCCAAAAATACACACCGAGAGAGAAAGGATGTG[A/C]GTGTCCTCCATAATGAGGAGGTGATTTAAATCACT M 2 1 2 1 101000 r 74 goat snp2051-scaffold1062-405392 15 34367365 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408087 Affx-122954720 AX-123278438 15 45815862 CCACTCAGACTTGATCCAGCTGCCTTGTGCTGACA[C/T]TAAGCTCAATAGCATCCTGGGTTTGGCCATTGTCT Y 2 1 2 1 101000 r 74 goat snp2052-scaffold1062-439098 15 34333622 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273740 Affx-1111833810 AX-519547351 15 45832176 AAATGGGAAGTTTTAATCTCCTGCAGACTGATCAT[A/G]GTAGATTTTT R 2 1 2 1 101000 f 74 goat GoatD01.005722 15 45832176 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38438083 Affx-122931520 AX-123308421 15 45855381 TTCCTGTTTTTTTCCATCTTTCTCTTATTCCCATG[C/T]AATCTTTTACTTTGATGACATCAAATCTCAGCAAG Y 2 1 2 1 201000 r 74 goat snp2053-scaffold1062-478617 15 34293380 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786825 Affx-122938909 AX-385273854 15 45891577 CTCAATCAGTTCTAGCTCTCTTGAGGAGTGGATTA[C/T]AGCCAAGCTCTGGATTATAGTTTTCCAGGGATGAA Y 2 1 2 1 201000 r 74 goat snp2054-scaffold1062-514813 15 34259986 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447215 Affx-122924981 AX-123317551 15 46009669 AGAAATTTGCCTTGGAAACCAAGAGCCCTAAGTCT[A/G]CTGATTAATATATCAAACATAATTCAAAAAGACAC R 2 1 2 1 101000 f 74 goat snp2056-scaffold1062-632905 15 34144973 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799071 Affx-122942662 AX-385286001 15 46080952 ATCTTCACTTCAGTCATCCTTGTGCTTATATCCTA[C/T]GGTCACAGCTTGGGATGAGACTGAAATACCCTGAA Y 2 1 2 1 101000 r 74 goat snp2057-scaffold1062-704188 15 34072378 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390206 Affx-122967791 AX-123260563 15 46112929 TACTTCTGACTCTTGAGGAGAAGGCTACTGTCATT[A/G]CCTTGTGGAGCAAGATGAGGGTGGCTGAAGTTGGT R 2 1 2 1 101000 f 74 goat snp2058-scaffold1062-736165 15 34040018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393399 Affx-122965894 AX-123263755 15 46145346 TAATATACTGAACTGCAGTAGAATCAAGGGGTGAA[G/T]AGGTATTTGTTCCTAAAGCTCACATGCCTTCTCAG K 2 1 2 1 101000 f 74 goat snp2059-scaffold1062-768582 15 34007030 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799689 Affx-122936938 AX-385286617 15 46343366 GTTAATATGTTTGAATTAAGACCCTGGAAAAGGAT[A/G]TTATGTTGAAGATTTAGAGGAAGAAAAGGGGCTCT R 2 1 2 1 101000 r 74 goat snp41645-scaffold542-63986 15 33685678 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429921 Affx-122938100 AX-123300262 15 46431704 TAGACCATAATTAATTTCATATGAAAAATCACTGG[C/T]AACTAGGATTAGAAGGGACCTCAAAGATTATCTGG Y 2 1 2 1 101000 r 74 goat snp41646-scaffold542-152324 15 33597099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402989 Affx-122958144 AX-123273342 15 46467425 AATCAATGGAGTCAGTGCAATTAAATGTTTATATC[G/T]TCTCCTTGTAGCTTTCTCCTTTAATTAGTAGTGCT K 2 1 2 1 101000 r 74 goat snp41647-scaffold542-188045 15 33560708 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407918 Affx-122954380 AX-123278269 15 46519038 TTTAAGTTTTTCTGCTTAAATTACAAATATACATG[C/T]ATGCACACCCACACACAGACAACTTTCCAAACCAT Y 2 1 2 1 201000 f 74 goat snp41648-scaffold542-239658 15 33508802 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384559 Affx-122973010 AX-123254917 15 46551844 TATAGGATATTCCTGCAGGCCTCAGGTCCCCCAGG[A/G]TAGGAAGTTTAATGGCACCTGCTCTAGATATAGTA R 2 1 2 1 101000 r 74 goat snp41649-scaffold542-272464 15 33475915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401459 Affx-122958973 AX-123271812 15 46587440 AAAAAATAGAACAGTTGTAAAGAAAAATGCAGATG[C/T]AGTAAACAGATCTCTCAATTTTGACCCATTCATAA Y 2 1 2 1 101000 r 74 goat snp41650-scaffold542-308060 15 33440095 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393876 Affx-122965130 AX-123264231 15 46664260 AGGATAGGCCCAACTATGATGTTTGCTAGGTTAGA[C/T]GTATTATATGCATTTTTGACTTATGATGGGTTTAT Y 2 1 2 1 102000 f 74 goat snp41651-scaffold542-384880 15 33373465 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392528 Affx-122966109 AX-123262885 15 46702749 CAAGATGATATTTCATGACCTGGGTCTTTCTGAGC[A/G]TTTTAAAGAATAAGCTTGAAAGTGAAAGTGAAGTC R 2 1 2 1 101000 f 74 goat snp41652-scaffold542-423369 15 33337904 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272844 Affx-1111833047 AX-519546536 15 46723880 TTATTTTGTGTTCTGTTTTACAGCACGGTTGTGTA[A/G]AGAAAACTTTGTACAAGCCTCTGCACGTGTGAGGC R 2 1 2 1 101000 r 74 goat 15_46723880_AF-PAKI 15 46723880 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406221 Affx-122956121 AX-123276573 15 46733286 CCTTTTCTCTCTTATAAAAGCTTTTTTCTTCCCTT[A/G]CCATATGGAAACTTGCACATGGCTCACCATGGTTG R 2 1 2 1 102000 f 74 goat snp41653-scaffold542-453906 15 33307456 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793058 Affx-122962171 AX-385280036 15 46783806 AGTGTAACACTTTACACTAATATGAGGTCATAATT[A/G]TCCTTCAGAGTAACTTTGCAGACAGTCACCAACAT R 2 1 2 1 101000 r 74 goat snp41654-scaffold542-504426 15 33256842 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401208 Affx-122959330 AX-123271561 15 46871622 ACACTAATAATGAAAAAATAGAGAAATTATGTATT[A/C]TGATTTTCTGTCATAAACTGCCAGTGTGACAATAA M 2 1 2 1 103000 r 74 goat snp41656-scaffold542-592242 15 33168073 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777886 Affx-122956227 AX-385265002 15 46900159 CAGCTACAGATTTCTTTTTGCCTGCTCCATGATGA[C/T]GGTGTTGGATTCTGTGACTATTTCTCTTCTGCCAG Y 2 1 2 1 202000 f 74 goat snp41657-scaffold542-620779 15 33139425 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415031 Affx-122949018 AX-123285380 15 46934193 AGCAGAAAGTGCAGAGAGGAAAGAGAGGCACCTCT[C/T]AAGAAGCTCCCATCTTCCACTTAGACTTGAATTTC Y 2 1 2 1 101000 r 74 goat snp41658-scaffold542-654813 15 33104688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781131 Affx-122944119 AX-385268216 15 46988552 ATCTCTTCCAAATGAATTATAGATGTACATGCAAA[C/T]GGTAAAAAAATAAAGTTCCTGTAGATAACACTGGG Y 2 1 2 1 101000 r 74 goat snp41659-scaffold542-709172 15 33049988 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796610 Affx-122975004 AX-385283556 15 47018589 GCTAAATAACAGGCCTGACATACTGTGGAATTCTA[C/T]GAATGATAGGTCTTAACTTCCTTTCAAAATAACTT Y 2 1 2 1 101000 f 74 goat snp41660-scaffold542-739209 15 33018077 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426522 Affx-122940202 AX-123296868 15 47060976 AGGAATTTTACCACTGTACAACTTACAAGACAGCA[A/G]CTCAACTAATGAGCATATGAAAACATATTCCACAT R 2 1 2 1 101000 f 74 goat snp41661-scaffold542-781596 15 32975565 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438499 Affx-122931219 AX-123308837 15 47134976 AATGTAAAACGTTGTAGAGGCTTTACTGTGTATCA[C/T]GAATTAGTAAGGTGAAAATAGAGGAGAAAAAGAAT Y 2 1 2 1 101000 f 74 goat snp41663-scaffold542-855596 15 32902700 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431511 Affx-122936235 AX-123301852 15 47169750 CTTCTCTTCATACACTATAATGGTATGATTCACAC[A/G]TGCTAAGTCACTTCAGTCATGTCCGACTCTTTGTG R 2 1 2 1 101000 f 74 goat snp41664-scaffold542-890370 15 32867470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407445 Affx-122954792 AX-123277796 15 47202924 CCTCCCTGTTCTGCCTGGTGTTGTGAGGAGGGGCC[A/G]CTCACTGACTCCATCCCTAGCCAAGCCCCCTTCCC R 2 1 2 1 101000 f 74 goat snp41665-scaffold542-923544 15 32834318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802457 Affx-122944911 AX-385289361 15 47297601 CTGTTAGTTCTACTATAGATTAAGACCAACTACTC[A/G]TAATCCCTAGTTTCTTTATCCCCAGTCATTCAATA R 2 1 2 1 101000 f 74 goat snp41667-scaffold542-1018221 15 32738686 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405736 Affx-122956516 AX-123276088 15 47328453 TAGAAGTCTCTAGATTTTCCTCAGGTTCCAGAGAA[G/T]TAGAATCCTCTCAAGAGTAAAAATCAGATTCTTTC K 2 1 2 1 201000 r 74 goat snp41668-scaffold542-1049073 15 32711645 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396783 Affx-122962760 AX-123267138 15 47363774 TCTGTCCTTGGGACATTGCCCCTAGTTCTTGTCAC[G/T]ATCCAGCAATGCCAGCAGGTTGGCAACCTGTAGTC K 2 1 2 1 101000 f 74 goat snp41669-scaffold542-1084394 15 32675979 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433429 Affx-122935080 AX-123303770 15 47407147 ATTCTTATTCTCAGTCTTCTCTCCTTTTCACCCTT[A/G]TCTCCTCTCCATCTAGTGTCTCTCCTTCTTGAATT R 2 1 2 1 201000 r 74 goat snp41670-scaffold542-1127767 15 32631529 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429634 Affx-122937685 AX-123299975 15 47448088 TCTTGAGCATGTTGGATAGTTATTTTGTAGAACTA[A/G]CTTCAGCCGTTCCCTCTTCCTTTCCCTCCAGTGTG R 2 1 2 1 201000 f 74 goat snp41671-scaffold542-1168708 15 32589689 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777299 Affx-122977666 AX-385264421 15 47495848 AATCAGGGTGACCTTAAGCTTTGTGAGGGTTTCAC[A/G]AGGTGCTAGAACCTTGTGAAACATTGGTGAACGGG R 2 1 2 1 201000 r 74 goat snp41672-scaffold542-1216468 15 32541564 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428272 Affx-122939402 AX-123298615 15 47525043 ATTTCCTTTTGTCCTTTTGGCGTGGTGTGTCGATA[C/T]GACGGCTTGTTTTTTCTTAAGTGGGGTGGGAATAT Y 2 1 2 1 202000 f 74 goat snp41673-scaffold542-1245663 15 32511574 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419547 Affx-122945419 AX-123289895 15 47557301 CTGTATGATTGTGTGATCACATGTATATGCAATGG[C/T]AAAAAGATAGAAGCAAAAGTATTTTGGCTGTGATT Y 2 1 2 1 201000 f 74 goat snp41674-scaffold542-1277921 15 32478751 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394825 Affx-122964794 AX-123265180 15 47589089 ATCCAGTCGCCCAACTCGACCGCCAGGAGGTGCCC[A/G]TCCGGCTCCCTTGCCACCCCAGAGTCCTTTGCCAG R 2 1 2 1 103000 r 74 goat snp41675-scaffold542-1309709 15 32433697 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430783 Affx-122937477 AX-123301124 15 47647092 TCCGACAGAAGCAGGTGAAAGCCGAAATTCAGCCC[A/G]CATTACACTTACCAAGCCATCAGAAAGGGAGCATT R 2 1 2 1 101000 r 74 goat snp41676-scaffold542-1367712 15 32374172 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407604 Affx-122954648 AX-123277955 15 47813926 AAAAGGGCTTTTCTATACATACACACACACCAGTG[C/T]ACAGGGCTCCAAAAAACAAAAAACCTTCCCTTCCC Y 2 1 2 1 201000 r 74 goat snp41677-scaffold542-1534546 15 32206548 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447082 Affx-122924497 AX-123317418 15 48022762 GTTTCCTTGGTCAGGGAACTAAGACCCTGCAAGCC[A/G]TACATTGCTGCAAGAAGAAAGAAAGACTACCAGTA R 2 1 2 1 101000 r 74 goat snp41679-scaffold542-1743382 15 31998062 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443479 Affx-122927816 AX-123313816 15 48053705 AAAGAGTGAAAGACACTTTTCTAATGTGGGAGGTG[C/T]AGGGTAGGAATGTTGGAAAGCTTGGGGTCAGTCCT Y 2 1 2 1 101000 f 74 goat snp41680-scaffold542-1774325 15 31967742 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414337 Affx-122950031 AX-123284686 15 48084407 CTCTGGTCCCGTGTTCTGTGCCTGCAGGCCTAGCT[A/G]TCCAGACAGTATAGAACAGTTTCTGTTCCAGTAGC R 2 1 2 1 101000 r 74 goat snp41681-scaffold542-1805027 15 31937042 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798046 Affx-122930255 AX-385284982 15 48115307 GCCAGGTAGGCTGTAAATGATTAGATGATAATTAT[C/T]AAGAAGACCAGATAATTCTATGAGTTCCAAGAGCA Y 2 1 2 1 101000 r 74 goat snp41682-scaffold542-1835927 15 31906148 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790842 Affx-122968215 AX-385277841 15 48144096 TTAAAGTTGTCGGAATGTCTTTAGATGGGATCTCT[C/T]TTCAAATATTTACCTGCCCTTTCACTCACGTTTCT Y 2 1 2 1 101000 r 74 goat snp41683-scaffold542-1864716 15 31877551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799849 Affx-122948407 AX-385286775 15 48201654 AGTCATGTTTATTTCTCTTCCCATTAAATGTGCAG[C/T]AAATACTTGATGGATGAGTGAGAGTGAACACTGCC Y 2 1 2 1 201000 f 74 goat snp41684-scaffold542-1922274 15 31819625 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427203 Affx-122939592 AX-123297546 15 48231061 GAGAGCCAAGAGCCAGGGCTGGAGGGGTTCTTCGG[C/T]CCCACCCATTCCCAGCAGAGCCAAGAGTCTGCCAG Y 2 1 2 1 103000 r 74 goat snp41685-scaffold542-1951681 15 31790218 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447402 Affx-122924406 AX-123317738 15 48278296 GTGATATAGGGAATTTACAAGATAGTATGTATGGA[A/G]AAAGTGCTTAGGACAGTACCCAGCACAGAGGTTGA R 2 1 2 1 201000 f 74 goat snp41686-scaffold542-1998916 15 31742920 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391099 Affx-122966820 AX-123261456 15 48316057 TCCTGCCCCCTGGATCACAGTGCTGTCAGTGTGGT[A/G]CCCCTGAACCCCTTCAAAGGTAAATGAAATGCTAG R 2 1 2 1 101000 r 74 goat snp41687-scaffold542-2036677 15 31705078 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413277 Affx-122950212 AX-123283626 15 48346877 CACCATCTGAGCTCTGCTTTCTGGGGGTCTGTTGT[A/G]CTCCTGTGTGCTTTTGTGTGTTTCTCAGTAGTGTG R 2 1 2 1 101000 r 74 goat snp41688-scaffold542-2067497 15 31673667 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446629 Affx-122924791 AX-123316965 15 48377568 GAGGCAAGACACTGCGCCCGCAGAGAAGGGGAGGC[A/G]AGGCTGGTCTCAAGGGAAGATCCCTAAAGCAGCTC R 2 1 2 1 101000 r 74 goat snp41689-scaffold542-2098188 15 31642569 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379840 Affx-122975812 AX-123250198 15 48420509 ACGGTTGTGTACATTTGTGTTTATGTAGGGATCAG[A/G]TATCTGACAAGGAGCCGGGGCCAGAGGAACTGATG R 2 1 2 1 101000 f 74 goat snp41690-scaffold542-2141129 15 31598933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442304 Affx-122928247 AX-123312641 15 48467084 AATAACAGCAAGTCACAGGCCCTGTGGTTAGAACC[A/G]TAGGCATCAATATGGACTCATCGTTTTTAATAATA R 2 1 2 1 201000 r 74 goat snp41691-scaffold542-2187704 15 31552835 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437023 Affx-122933121 AX-123307361 15 48519311 TAAGTAAAGCCTCTGGCTTGAATGAGAAGCATCAG[C/T]ACATCAGAGCGGTGGTTGAGCCAGGCTCACTGGCA Y 2 1 2 1 101000 f 74 goat snp41692-scaffold542-2239931 15 31500201 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414735 Affx-122949727 AX-123285084 15 48552518 ACTTCCCTTCAGTACTGACCACAGGCTGAGCCCCA[C/T]AGAAATATCTATTAGAAAGTTAGTGAACTAGATGG Y 2 1 2 1 201000 r 74 goat snp41693-scaffold542-2273138 15 31466993 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382606 Affx-122973710 AX-123252964 15 48585014 AATGCCTTGTGTCTCGACTCCTGGCGCTGGCACAG[C/T]GGCTCAGGGGCTGGACAAATGCATGCCTGTGGCAT Y 2 1 2 1 201000 f 74 goat snp41694-scaffold542-2305634 15 31434491 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415080 Affx-122949462 AX-123285429 15 48634956 AGAATTATCTGGCAGTCTGTTTTAGGTCAACAAAG[C/T]GTACTAGGAGGAAGAAAATGAAAGATGGACAGACT Y 2 1 2 1 101000 r 74 goat snp41695-scaffold542-2355576 15 31384863 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420186 Affx-122945561 AX-123290534 15 48697714 TACTGTTATAAGCTCTTTTGTACAGTTATGCTTTT[C/T]ATTTTGCTTTTAAACCATGTGCCGACATAACTTTG Y 2 1 2 1 101000 f 74 goat snp41696-scaffold542-2418334 15 31321091 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398298 Affx-122962153 AX-123268653 15 48727568 TGGACATGGGGAACACCTGGCTGAACCATGCTCTC[C/T]GCTGGGCTGAGTCTTGCTGCCAGCTTTGGGGCTGA Y 2 1 2 1 101000 f 74 goat snp41697-scaffold542-2448188 15 31291737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408170 Affx-122954208 AX-123278521 15 48761118 TGGCAAGGTACCTCCTAAGGCAAGCTGTGTTACTG[C/T]GACTGGCCATACATGCTGATTTATCCACCTCTGCC Y 2 1 2 1 101000 f 74 goat snp41698-scaffold542-2481738 15 30844429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414134 Affx-122949705 AX-123284483 15 48821507 CAGCCTGGCATAATTCCCTGCACTGTCAGGGTAAG[C/T]ACAGACCCCACCACACCATGGGTGACAGGCCTTTG Y 2 1 2 1 201000 f 74 goat snp41699-scaffold542-2542127 15 30784678 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402184 Affx-122959181 AX-123272537 15 48857056 AGGTGAATTATTCCAAGTAACCCGATTTTTAGTAA[C/T]GCCTTCCTTTGTGCCAGGTACTGTGCTAGCATCTA Y 2 1 2 1 101000 f 74 goat snp41700-scaffold542-2577676 15 30748956 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389416 Affx-122968370 AX-123259774 15 48897076 GAATGGATGCATGATATAATCTCACTTTGGGGCCG[C/T]GGGGGAAATCTATGCACAGAAAAGGCCTGGGAAGC Y 2 1 2 1 101000 f 74 goat snp41701-scaffold542-2617696 15 30709115 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380983 Affx-122974682 AX-123251341 15 49005674 ATTACTGCATCTTTCAGTATGTGCTAAACTACAAA[C/T]ATCTCATTATTATTGTTACTGGCTATTGCTGTTTT Y 2 1 2 1 101000 r 74 goat snp41703-scaffold542-2726294 15 30600898 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430938 Affx-122936836 AX-123301279 15 49050248 CAGCTTTGATAACATCAGGAATAGGTACTTTTGCA[C/T]ACTGTTTTTCAGGGTATAAATTGATATAATCTTTG Y 2 1 2 1 101000 r 74 goat snp41704-scaffold542-2770868 15 30556148 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389997 Affx-122968048 AX-123260354 15 49081945 CATAAGTCCTACCCACGGGCTAAAAGAGAGACCAC[A/G]TATGGAAAAGAAAACTTCAAAATAAATTCTGTCAT R 2 1 2 1 101000 f 74 goat snp41705-scaffold542-2802565 15 30524359 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783625 Affx-122977735 AX-385270684 15 49124792 TCTCAAAGAAGTTTTCCACGAAGTTATTCCTGTAC[G/T]TTAAGAATGACCCTCCAATGTCTTTCTTTTACATA K 2 1 2 1 101000 f 74 goat snp41706-scaffold542-2845412 15 30481122 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790467 Affx-122944109 AX-385277470 15 49163798 GCTTAAAAATAAAACATTAATATTCTTATAGGAAA[C/T]TGAAAGTAGCAAGAAACCTGAAAAAATTCAGGGCT Y 2 1 2 1 202000 f 74 goat snp41707-scaffold542-2884418 15 30441681 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795291 Affx-122937632 AX-385282249 15 49213336 AGTGGAGTGTTAAGTGTGGGCAGCCAGATAATAGA[A/C]TAGAAGGCCCAGTACATCTCCCTAAGGGAGGGGGT M 2 1 2 1 101000 r 74 goat snp41708-scaffold542-2933956 15 30393312 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410974 Affx-122952017 AX-123281324 15 49295597 TCAGACTGGCAAAACTCAAAGTTTGCTATCACAGC[A/G]TTGGTGAGACTATGAAGGAGTAAAGTCTCTCATAC R 2 1 2 1 101000 r 74 goat snp41709-scaffold542-3016217 15 30310304 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432390 Affx-122935852 AX-123302731 15 49356588 GTGCTCCAGGCAAATCTCTGCCCCTCTCTGGACTC[A/G]CACTCTGTCTCTACAATGGAACATCAGGGTTGGTC R 2 1 2 1 101000 r 74 goat snp1695-scaffold1048-23888 15 30251358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795768 Affx-122961629 AX-385282721 15 49394693 AGGGTCAATCACATCCCTGATTTTTGCCTCACCTT[C/T]GCCTTCTGTAAGTAATGATCTCTACCTGGCAGGCT Y 2 1 2 1 101000 f 74 goat snp1696-scaffold1048-61993 15 30213176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404635 Affx-122957318 AX-123274987 15 49443057 GGCCTCCAGACCACAAGTCTGGAGATGTGACTTTC[A/G]GTAACTCCCAGGTCTTTTCTGGGGTTTGGTGTCCT R 2 1 2 1 201000 f 74 goat snp1697-scaffold1048-110357 15 30165076 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451036 Affx-122921447 AX-123321370 15 49478883 CCAAGGGCTGGAGTCAGGTATAGGATGAGAGGTCC[A/G]GATGTCTTCACAGAATTTCCAAATGCTATTTCCTC R 2 1 2 1 101000 r 74 goat snp1698-scaffold1048-146183 15 30129621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768777 Affx-122956080 AX-385255954 15 49513777 TTCTGGATACTCAATACAATTCCAGTGATCCATAC[A/G]TCTATCCTTATGCCTGAACCATGCTGTCTTGATTA R 2 1 2 1 101000 f 74 goat snp1699-scaffold1048-181077 15 30094732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394101 Affx-122965352 AX-123264456 15 49546949 CACAACAGGTCCTATAAATATCTGAGCACTCTCCT[A/G]CTGAGAAGCTACTCTTTGTTGCTGATTGGACGAAG R 2 1 2 1 101000 f 74 goat snp1700-scaffold1048-214249 15 30061112 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409952 Affx-122952858 AX-123280303 15 49644837 ATGAGGTACCCAAAAGAAGGCAGGGTTTGGGGTCT[A/G]TATCAGTCCACCAGTTACTAACTGCTTAACGATGG R 2 1 2 1 101000 r 74 goat snp1702-scaffold1048-312137 15 29961877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450113 Affx-122922772 AX-123320448 15 49698681 TCCCCAGTACTAACCCCATACAAGGCGCATAGAAG[C/T]ATTTGGTAAAAATTGGTTAAACTCATGAGTAAGTC Y 2 1 2 1 201000 r 74 goat snp1703-scaffold1048-365981 15 29907730 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786621 Affx-122976711 AX-385273653 15 49745828 AAGACAACAAAGAAGTGTTTTAAACTTAATATTTA[C/T]GATTTATGACAAGTATTTATACAATGTGTACTAGG Y 2 1 2 1 202000 f 74 goat snp1704-scaffold1048-413128 15 29860457 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440190 Affx-122930707 AX-123310527 15 49795513 CAGCTTTCACAGGGGTACTGTGGAGCACAGCTCAG[C/T]AAGCAGTAAAATACAGGAGCTCCTTGTTTAAAGTC Y 2 1 2 1 101000 r 74 goat snp1705-scaffold1048-462813 15 29810447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407972 Affx-122954338 AX-123278323 15 49824221 CAAATTGTAACTTGCCTAAAATGCCAAGAGAAACC[A/G]TCTTTTTGTGGACATATTTCTGGATTTTTGAATTT R 2 1 2 1 101000 f 74 goat snp1706-scaffold1048-491521 15 29781069 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388182 Affx-122969436 AX-123258540 15 49880046 CCTGTCTCATGTTTCTTCTGTGTCCTCAGTGTCCA[G/T]CCCAGGGCCTGGCATCAAGTAGAGGACAATAAACA K 2 1 2 1 101000 r 74 goat snp1707-scaffold1048-547346 15 29724897 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419641 Affx-122945965 AX-123289989 15 49909980 TCTTCAGAAGATAATTGCTAGCAAAGGAAGAAATC[C/T]CCCCTGCTTCCTCTGCCTACTTCAAGTCCCTGCTG Y 2 1 2 1 101000 f 74 goat snp1708-scaffold1048-577280 15 29693125 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272792 Affx-1111833048 AX-185159758 15 49946693 TCAGTCGTGTCCGACTCTGTGTGACCCCATAGATG[A/G]CAGCCCACCAGGCTCCACCGTCCCTGGGATTCTCC R 2 1 2 1 103000 f 74 goat 15_49946693_AF-PAKI 15 49946693 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320792529 Affx-122971537 AX-385279510 15 49958788 TTTGAAATAATTTCAAACTAGCAGATAAGCTATAA[G/T]AATAGTTCAAAGGATTCCAGTATATCCCCACACAT K 2 1 2 1 101000 r 74 goat snp1709-scaffold1048-626088 15 29644242 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406981 Affx-122955046 AX-123277332 15 50012822 GTGGACCCCCTGGCTGCAAGGCCACAGGCCCAGTG[A/C]GGGGATATGGTGCCTCGTTCCAGTGGTCTAGAGGA M 2 1 2 1 201000 r 74 goat snp1710-scaffold1048-680122 15 29590342 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418165 Affx-122947089 AX-123288513 15 50058803 ATTGCAGTGTCTGTTACATTCCTCGGTTTGAGTCT[A/G]TCTCTTGGAATAGAAAGCAGATTCTGGAAGGCTGA R 2 1 2 1 101000 f 74 goat snp1711-scaffold1048-726103 15 29544343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439271 Affx-122930986 AX-123309608 15 50108565 GCATCTTAATGCACAAGTTATCAAGGACTGAGAAA[C/T]GGCTTTAGTCCTAATTTACAGTGAAAAAAAATCTC Y 2 1 2 1 101000 f 74 goat snp1712-scaffold1048-775865 15 29493919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420169 Affx-122945575 AX-123290517 15 50163129 TATACTCCTTTGTATTTCTAGCACCTCTCAACTTG[A/G]GAAACTTTAAAAATTATCAGTACCTAGGCCACATC R 2 1 2 1 103000 f 74 goat snp1713-scaffold1048-830429 15 29439337 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799487 Affx-122949164 AX-385286417 15 50225075 TTTTAATTAGTACTTTTCACTGTGGTAAACATAAA[C/T]TTACCATCTTAATCATTTCCAAGTGTACAGGTCAG Y 2 1 2 1 102000 r 74 goat snp1714-scaffold1048-892375 15 29377271 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794524 Affx-122948016 AX-385281487 15 50254562 TGGAAGGGAAGGACACAAAAAATTCAACAGGAGGT[A/G]GCCTCTGAGAAGGCAAAGTAGACTATAAAGACAGC R 2 1 2 1 101000 r 74 goat snp1715-scaffold1048-921862 15 29347621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772764 Affx-122929419 AX-385259909 15 50293110 ATTGAGTTTAAAGAATTTCCTCAGAATAAGATCTA[C/T]TGTTTGCCAGTATTGATTAGAATCATATCTATTGA Y 2 1 2 1 101000 f 74 goat snp1716-scaffold1048-960410 15 29309013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393332 Affx-122965944 AX-123263688 15 50378144 ACACATGAGCTGCTGCTCAGGGATCAGCTAACAGT[A/G]CAGTCTAAAACATCCCCTTTTGGGTTTAAGAAACA R 2 1 2 1 101000 r 74 goat snp1718-scaffold1048-1045444 15 29223207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436701 Affx-122932326 AX-123307039 15 50414042 AGACAGTCTTATCATCTGCAAATAGGGACAGTTCT[A/G]TTTTCTTCCTTTCTGATGAATATGCATCAGAATTA R 2 1 2 1 202000 r 74 goat snp1719-scaffold1048-1081342 15 29189646 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763261 Affx-986697790 AX-385251183 15 50438885 CAAACCTATGTTTCTACTTGAACAAAGCACAAGTT[A/G]TCATATCAACACAGTAAGTCCCCTACATACAAAAC R 2 1 2 1 600010 f 74 goat 15_50438885 15 50438885 Ancestral_priority_1043 ancestry 0.648 recommended IMAGE 10K 10K ancestral 38429001 Affx-122938847 AX-123299343 15 50474203 CCTTGTAGGCACAGCATAGTTTGGCTTCTTCCTTC[A/G]TCTCATCTCTCCTCGTGTCCTTTTCTCCCGACATT R 2 1 2 1 101000 r 74 goat snp1721-scaffold1048-1141503 15 29129621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401915 Affx-122958827 AX-123272268 15 50516156 GAAAGTAATGATGTATTCAACCCCACCAGGACTTA[C/T]GTAGAGTCAGCACTGATGATATTAGAGGACTTGTC Y 2 1 2 1 201000 r 74 goat snp1722-scaffold1048-1183456 15 29087396 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451329 Affx-122921274 AX-123321662 15 50544860 TGGATTGTTCTTTTCTCCTCTTCCCAGTCCTCCTT[G/T]TCTCCTTCACTTGGCTAACTCCTACTCATTCTTTA K 2 1 2 1 101000 r 74 goat snp1723-scaffold1048-1212160 15 29059989 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442899 Affx-122927646 AX-123313236 15 50591083 GAAATCGAGATAGCAGGGGTTTCTCCCACCAGTGC[A/G]CAGATGCACTAAGCCCAAGGGTGAGGATGACATGC R 2 1 2 1 101000 r 74 goat snp1724-scaffold1048-1258383 15 29014167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430511 Affx-122937219 AX-123300852 15 50662267 CAGTACCAGAAGAAACTGTGATAGAATTTGTTACT[A/G]TATTTTGGCCCGAGGAAGGTCTTTCCAAATATGAT R 2 1 2 1 101000 f 74 goat snp1725-scaffold1048-1329567 15 28942656 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381795 Affx-122974287 AX-123252153 15 50693833 GGTGTAGAACAAGTAATTTCATTTAGTTTAGCCAA[C/T]GATACATTCATTGGGACTGAAGAGAAGTTCAAGTG Y 2 1 2 1 101000 r 74 goat snp1726-scaffold1048-1361133 15 28911250 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409065 Affx-122953347 AX-123279416 15 50775985 CTCTGTCACACACTTCTTTAAAAACACCCTTCAAA[C/T]TCCATGCATTCAAAACTGAATTCATCCTATTTATC Y 2 1 2 1 101000 f 74 goat snp1728-scaffold1048-1443285 15 28828703 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421118 Affx-122944206 AX-123291465 15 50857039 TCTATATGAAGCTGCTGTCAGAGAAGACCTCGGTC[A/G]CTTTGGCAAGTGGCAGGGGCTGCAATTTCAGAATG R 2 1 2 1 101000 f 74 goat snp1729-scaffold1048-1524339 15 28748023 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277057 Affx-1111835657 AX-519550565 15 50877032 CAGCCACTCCGTTTGACATGACAGATGGCAGGTGA[C/G]CATCTTGCTTTGTAGCTGAGCAGAAACACAGCTCT S 4 1 2 1 101000 r 74 goat Random2.2K-1537 15 50877032 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450406 Affx-122922067 AX-123320741 15 50905405 CTACTTTCAGGACACTATGAAGGCCTAGACACCAG[C/T]GGTAAATTTCCTGCATGACTGATATTGACACGTTG Y 2 1 2 1 101000 r 74 goat snp1730-scaffold1048-1572705 15 28699424 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793035 Affx-122936792 AX-385280013 15 50944894 AACAGACATAGGGTATTTGGAGTGAAACACAATTA[C/T]GTGAAAATTACTCCAGGAGTTTTGTTTGCATTTTC Y 2 1 2 1 101000 r 74 goat snp1731-scaffold1048-1612194 15 28661615 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430288 Affx-122937284 AX-123300629 15 50997643 CCTGAAAAACAGGGATTATACTGTTCTTAAGAAAG[C/T]TGCTGTGGGGTTTCAGTGAGTTAACGGACTTGTCA Y 2 1 2 1 101000 f 74 goat snp1732-scaffold1048-1664943 15 28608799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453689 Affx-122919699 AX-123324022 15 51027707 TGTCAAGTCTACCAAATGAGGAACTGGTGAAAGAA[C/T]CAGGAGTATTCAGCCTGGAGAAAAATCAGGGTTGA Y 2 1 2 1 101000 f 74 goat snp1733-scaffold1048-1695007 15 28578778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439121 Affx-122931096 AX-123309458 15 51071563 GTAGTCCTGGGCCCAAAGAGGAAATAAAAGGTTAA[A/G]TAGGCCCATGATGCTTTTTGCAGCTGGAAAATTTC R 2 1 2 1 201000 r 74 goat snp1734-scaffold1048-1738863 15 28536329 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432501 Affx-122935580 AX-123302842 15 51103040 CATACAGGAGAGAAACCCTATGAATGGGCCACCTA[C/T]GGGAAATCATTTAGCCAAACATGTCTTACACAACA Y 2 1 2 1 201000 r 74 goat snp1735-scaffold1048-1770340 15 28505095 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452962 Affx-122920164 AX-123323295 15 51144500 CCATGTCGAAGGGGTAAGAGGAGATACGGGAGAAA[C/T]GTCCATCTGAACTGAAGGGAGCTGGTGGAGCGAAA Y 2 1 2 1 101000 f 74 goat snp1736-scaffold1048-1811800 15 28463543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779038 Affx-122959350 AX-385266145 15 51194828 GATGGATTGGGAAATAGGGGGACCTACAAAGGCAT[C/T]TGTAATGATCTATTTCTTAAGTTAGGTTGTGGGAA Y 2 1 2 1 101000 f 74 goat snp1737-scaffold1048-1862128 15 28412969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423172 Affx-122942738 AX-123293518 15 51233372 GGGAGCTCAGTCTCTGGGCAGAGCGGGGTGGCCCC[A/G]TGGGCCACGTGATACAGTCAGGTAGTTTAAGTCCC R 2 1 2 1 101000 r 74 goat snp1738-scaffold1048-1900672 15 28375602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395216 Affx-122964489 AX-123265571 15 51281203 CCTTTTCGAAAAGGTTTCCAACCCAAACTATTAGA[C/T]GGTTGTTTTAAAAGGGAACAGGGAGCAGGAGGAAG Y 2 1 2 1 101000 f 74 goat snp1739-scaffold1048-1948503 15 28327691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434178 Affx-122934881 AX-123304519 15 51312046 GACAGTGAGGAGACAGTTCCTGGAATCTGAAGAGA[C/T]GGGATGAAGGTTTGATTCCTCTGGGAAGGAAGCAA Y 2 1 2 1 101000 f 74 goat snp1740-scaffold1048-1979346 15 28298204 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385636 Affx-122971175 AX-123255994 15 51354703 GGCTCCAGGACCACAGGGCCTTGATCCTTGACAGG[C/T]GCTGCAATCACAAAATCATGATCCTTCAGAAGTTC Y 2 1 2 1 101000 r 74 goat snp1741-scaffold1048-2022003 15 28255675 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386531 Affx-122970732 AX-123256889 15 51401471 GGAGAGTCACAGGTGCCTGTGTCTGTGTGTGCTGT[A/G]CTAGCAAGTGCCAGGACAGTGTCTCCGATGAAGGG R 2 1 2 1 201000 r 74 goat snp1742-scaffold1048-2068771 15 28209018 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431904 Affx-122936004 AX-123302245 15 51432609 ATATATATTACAGGGAGAAATGGTGAGAAAGCAGC[C/T]TGGAAGGGCTGAGGCTGCAGCAGAGGGAGAATTCT Y 2 1 2 1 101000 f 74 goat snp1136-scaffold103-5440 15 28178361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395460 Affx-122963914 AX-123265815 15 51484227 CTGCTTCTCCCCCAGAGAGGATTTCTCAGCCCTGA[C/T]ACTACTGACAATGGTGGGACACTGGACACTGCAGA Y 2 1 2 1 101000 r 74 goat snp1137-scaffold103-57058 15 28127072 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407062 Affx-122954920 AX-123277413 15 51517927 TCTTAAGGTCATGTGGTGAGCAAATGACCTTGGGC[A/G]TCCCAAAAGTAGGTTTTGCTTTCTTGAGCGAGAAG R 2 1 2 1 201000 r 74 goat snp1138-scaffold103-90758 15 28093572 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379572 Affx-122976042 AX-123249930 15 51560045 TTGCCTTTGCATTTGTACAGCCCAAAAGTCAAGAA[C/T]GGTTTTTACAGTTTAAATGCTTGAAATGATTTTGT Y 2 1 2 1 101000 f 74 goat snp1139-scaffold103-132876 15 28050978 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431996 Affx-122935935 AX-123302337 15 51631744 CCTCCCAGAGCATCACCTTTGCTTCAGGCCTGCAA[C/T]GGGGACTAGGCTCGTCAGATATGCTGTATCTAATC Y 2 1 2 1 101000 r 74 goat snp1140-scaffold103-204575 15 27912733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398002 Affx-122961792 AX-123268357 15 51687786 AAGTGTTTGTCCTAAAACTGAAAGTTTTCCCCATT[A/G]TTAACAACTTGGTTTTATTCTCTAGAGCTGGTTTT R 2 1 2 1 101000 r 74 goat snp1141-scaffold103-260617 15 27854619 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773135 Affx-122942636 AX-385260278 15 51740231 GTAGGAACACATCACTTGCAGGAGACATATTTAAA[C/T]ATAATGACACATAAATATGGGAGAAATGATAGAAA Y 2 1 2 1 101000 r 74 goat snp14414-scaffold1574-28641 15 27805863 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430011 Affx-122938028 AX-123300352 15 51770559 GTGTGGAACACCACTCACTTCTGCTCAAGATGCGA[C/T]GCTTGAGGTCATCTGCTGGGATTTCATGGGCAAAC Y 2 1 2 1 201000 r 74 goat snp14415-scaffold1574-58969 15 27776309 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425327 Affx-122940934 AX-123295673 15 51801273 CTGAGAGAGATTCTTATCCTCTCTTTATGTCTTTT[A/G]TCTTGTTTGGCTGCGCCGGGTGTTCACTGTGGCAT R 2 1 2 1 202000 r 74 goat snp14416-scaffold1574-89683 15 27745276 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792844 Affx-122938568 AX-385279822 15 51875929 GAAGAGAGGAGCTCTGTTTAAATAATGTTTGTGAC[A/G]TGTTGTTTTACTGGCACTCTTAGTCCCCTTTCCAC R 2 1 2 1 101000 f 74 goat snp14417-scaffold1574-164339 15 27670405 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410205 Affx-122952572 AX-123280555 15 51911892 ACTTCTGTAGCCATTTGACATTATTGTGCCTTTTT[A/G]TTGTGTTTTATTAAAGTATCAGCTCACAGTGGATT R 2 1 2 1 101000 r 74 goat snp14418-scaffold1574-200302 15 27634379 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397298 Affx-122962324 AX-123267653 15 51968092 TTTAAGTTAAACTTAGATTTTAGCACATGGATGGT[A/G]TTATGAAAAAAATCTGGGAATGATTTAGCCTGCTT R 2 1 2 1 101000 r 74 goat snp14419-scaffold1574-256502 15 27578321 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439236 Affx-122931013 AX-123309573 15 52012126 CTTTTCTGCCATTGGGAATCTTTGTAGACTGGTAA[C/T]GAGATCTGAGGAATTGGAGAGAAAAGGTGACTGTA Y 2 1 2 1 101000 f 74 goat snp14420-scaffold1574-300536 15 27533903 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802336 Affx-122932161 AX-385289240 15 52060770 AATCAAAGGATTATGAAAGGATATTAATACCATCA[G/T]ATTTCAGCCAGGTAAGCAGAATCACTATGAATATT K 2 1 2 1 101000 r 74 goat snp14421-scaffold1574-349180 15 27485214 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382423 Affx-122974244 AX-123252781 15 52107472 GAGCTCTGCCACCTGCGAGGTACCGTGTGCCTACT[A/G]CTGCCCAGTGTTCTCACGCTGCTCTGTTACAGCCT R 2 1 2 1 101000 f 74 goat snp14422-scaffold1574-395882 15 27438033 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450187 Affx-122922303 AX-123320522 15 52153328 CTCTGCTGATTTCCCCTAATGTGCCTGGGTGTCTG[C/T]AGCTACACATTTCCACTCTGGCCCAAGCCTCCGTC Y 2 1 2 1 201000 r 74 goat snp14423-scaffold1574-441738 15 27392749 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441837 Affx-122929052 AX-123312174 15 52197049 GTACATTTAAAATAGTTCAACCTGCTGCTTCATGG[C/T]GTATATCCCTGACAGGAGACAACTTCCATCTTGAG Y 2 1 2 1 101000 r 74 goat snp14424-scaffold1574-485459 15 27348918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398586 Affx-122961497 AX-123268941 15 52248568 ACTTCACGGCCCCTCAGGTGGCAAGCATACCATCA[C/T]CCCAGTGCTCTCCAGCCTCTTGTCCTTTCCCCCCC Y 2 1 2 1 101000 r 74 goat snp14705-scaffold1592-16593 15 27305018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379711 Affx-122975892 AX-123250069 15 52282189 CACAGAATGGGCCAACAGCTTTGCAATTTTTAAAG[A/C]ACTTTTAAGTTGCATGTGGAGGAGTGAATGAAGGA M 2 1 2 1 303000 r 74 goat snp14706-scaffold1592-50214 15 27271074 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382597 Affx-122973717 AX-123252955 15 52312887 TAAATTTTTCTCTCCCACTTCCCCAGAGTTGCTGT[A/G]CAGATAAACTGGGATAAAGCCCACGATGGGCCTGT R 2 1 2 1 201000 r 74 goat snp14707-scaffold1592-80912 15 27240320 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408497 Affx-122954408 AX-123278848 15 52345125 TTTTCTCAGGGTTATGTCTTTCTTCGTCTCTGTTT[C/T]ACACACAGCATCATCGTCTTCATCTAGTATGTTTT Y 2 1 2 1 201000 r 74 goat snp14708-scaffold1592-113150 15 27208047 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792199 Affx-122925648 AX-385279184 15 52410456 CTGAAGTACAAGAAAGAAATGACTTCTCAATGATA[C/T]GCAGTTTAAAAGACTATTACAATATTCCTGTTCCC Y 2 1 2 1 101000 f 74 goat snp14709-scaffold1592-178481 15 27143005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407117 Affx-122954875 AX-123277468 15 52452429 TTCTGAGCCTTTGGTTCCTCGGCTGTACATTGGGA[C/T]AAGCTGAATATTGCCTACCCAGCCTACATCCTACA Y 2 1 2 1 101000 f 74 goat snp14710-scaffold1592-220454 15 27100843 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452993 Affx-122920116 AX-123323326 15 52497498 TACATAAAGAAAAATTTTAAACTTTGGGAGTATTA[G/T]ACCTGATTTCTGTGAATTTAGCCAAAATGGTCTTT K 2 1 2 1 101000 r 74 goat snp14711-scaffold1592-265523 15 27055602 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793019 Affx-122975326 AX-385279997 15 52547246 TTTTAGTCTGAGTGCATATGCGTTCTTGCTGTGCT[A/G]CTGAGTATGCTTGTACAAGTTGTGCACTCTATAGC R 2 1 2 1 101000 f 74 goat snp14712-scaffold1592-315271 15 27005762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775007 Affx-122944699 AX-385262139 15 52584488 TCTTTTCTATAACGTGGGGGCATCACCATCAAGAG[C/T]GCTTCTTAGGCATTCATGTGCTGGTGAATTGCTGG Y 2 1 2 1 101000 r 74 goat snp14713-scaffold1592-352513 15 26968662 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419693 Affx-122945925 AX-123290041 15 52636414 GGCACTTCCATGCTTTACTACATTCCATCCGTACC[A/G]TGATTCCACATGGTGGGCCACGCAGCTCCCTGTTC R 2 1 2 1 101000 f 74 goat snp14714-scaffold1592-404439 15 26918319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433890 Affx-122934406 AX-123304231 15 52674623 AGGGGATTTGCCCAGGACAGAAGAGCTTTTCCCAG[C/T]TGCCCACCCCAGGTTCCCCACACATATACATATTC Y 2 1 2 1 201000 f 74 goat snp14715-scaffold1592-442648 15 26880468 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432892 Affx-122935334 AX-123303233 15 52710804 GAGCGAGAAGGGACAGTTTGATGTAATTAATAACC[A/G]TCCTACAACTCCAGCAGCAGAAAGGTGACCAGGCA R 2 1 2 1 101000 f 74 goat snp14716-scaffold1592-478829 15 26844687 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414989 Affx-122949049 AX-123285338 15 52757647 CGAATAAATTCAATACTTCCATACCAAAATCAAAG[C/T]TGATGTGATAAAGGAAAATTGTGAGCTTATAGAGT Y 2 1 2 1 101000 f 74 goat snp14717-scaffold1592-525672 15 26798069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399948 Affx-122960845 AX-123270303 15 52799621 ATTGTACCTGCCAAGCTTCCTACACCTCCCACTGT[A/G]TTCTCCTAGGCCATGCAATCAGGCTCCTGCCTCAG R 2 1 2 1 201000 r 74 goat snp14718-scaffold1592-567646 15 26755560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392906 Affx-122965723 AX-123263263 15 52852407 TGTTAACTGTGCTTGAATAACTGCCCACACCCTCA[C/T]GCCTAGCACAAAGTCTGGCCTTGTGAACTGAGAAT Y 2 1 2 1 201000 f 74 goat snp14719-scaffold1592-620432 15 26705879 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779305 Affx-122923904 AX-385266409 15 52893387 TGTCTTGCATGCCTTCTAATAACCTGAAGATTCTC[C/T]CAGTATAAACAGTTTGAATTACATAGTTCTGAACA Y 2 1 2 1 101000 f 74 goat snp14720-scaffold1592-661412 15 26664476 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417799 Affx-122947375 AX-123288147 15 52923577 TATTTAAATAGTATTTTCCTGTGTTTTATAGGTCA[A/G]GAAACTAAGACTTAAGCATAAATAAATTGCCAAGT R 2 1 2 1 101000 r 74 goat snp14721-scaffold1592-691602 15 26634252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424627 Affx-122942181 AX-123294973 15 52956242 TCTGACTGGAAGTTAGGGACAAGATTAGGATGCAC[A/G]TTTGTTTTGTTTTGTTTCATTTTAGGACTTTATCT R 2 1 2 1 101000 f 74 goat snp14722-scaffold1592-724267 15 26600973 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463404781 Affx-1109967558 AX-514888644 15 52959577 GCTGGAAGAATTTTGTTGTGGTTGGAAAAAGTATG[A/G]AGATAAAGTTATACCTCATTAGGCAGTCTGAGTGC R 2 1 2 1 101000 f 74 goat 15_52959577_AF-PAKI 15 52959577 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423580 Affx-122942401 AX-123293926 15 52997337 GCCTTAAATTTCTTTGTTGTTAAAATAGCTAGTCC[C/T]GGCTTCTTTCAGTAAATATTGGTATGGTATGTATT Y 2 1 2 1 101000 f 74 goat snp17390-scaffold1801-201895 15 26559138 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420824 Affx-122944669 AX-123291171 15 53070793 GAAAATTTGGTAATACCGAATGAAATTAAATACAT[A/G]CTCACCCTTGAACCCAGCAACTCCACTTCTAGGAA R 2 1 2 1 201000 f 74 goat snp17388-scaffold1801-128439 15 26485021 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381211 Affx-122974524 AX-123251569 15 53151823 AACGGATTTAGAAGAACCACCTTTCAGCACTGGCA[G/T]CAAACACGCACGTACTGAGCACCTACTAGGTACAA K 2 1 2 1 101000 f 74 goat snp17387-scaffold1801-47409 15 26403994 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431145 Affx-122936576 AX-123301486 15 53190951 GTCCACACGGGAGGAACCGCAGTGAGCCAAGCACA[C/T]GCGCACAGGTGCATACATGCACACACACATCGGCA Y 2 1 2 1 201000 r 74 goat snp17386-scaffold1801-8281 15 26366246 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435770 Affx-122932874 AX-123306109 15 53241172 ACCAGAGGCTCTCAAGGAAACCACTAAACCAACCA[C/T]GCATCCCAAGGATGATGTTAGACAACCTGTGGCCA Y 2 1 2 1 201000 r 74 goat snp54763-scaffold837-3660638 15 26313326 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433132 Affx-122935690 AX-123303473 15 53292305 ATGGGGTCTCAAAGAATGACTGAAGTGACTGAACT[A/G]TAGAATTTTCTTCAGCTCCTGATACTAATTTGTCT R 2 1 2 1 201000 r 74 goat snp54762-scaffold837-3609505 15 26260720 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442850 Affx-122927683 AX-123313187 15 53330219 TTATCCCTTATCCTTGACACAGATGCTACTAATTT[A/G]TGTATTTTAGGAATTGAAACATATTTTTGCAGGGT R 2 1 2 1 101000 f 74 goat snp54761-scaffold837-3571591 15 26222983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790969 Affx-122952985 AX-385277966 15 53380129 CTCTTCCTTTGTGAAGCAATATCCTCCCTTGTTGG[C/T]AGTCATATTAATACAAGAATCAGAGCCCCTTTCAT Y 2 1 2 1 101000 f 74 goat snp54760-scaffold837-3521681 15 26172883 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445878 Affx-122925965 AX-123316215 15 53422590 CCTGTAGGAGATATAGGGGAACAGATGGGAAGAAA[C/T]GGGGAGAAACCCCTTTCCAGTCTGGCTTAGCCAGC Y 2 1 2 1 101000 f 74 goat snp54759-scaffold837-3479220 15 26125655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798955 Affx-122975801 AX-385285885 15 53519984 ACTTTCAAGACAAAGCCAGAAGAAAAAATGACCAC[A/G]CTCTCTACGATTACTCTATAGTATTTCATTTGAAA R 2 1 2 1 101000 f 74 goat snp54757-scaffold837-3381826 15 26027934 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410515 Affx-122952177 AX-123280865 15 53581213 CCTCAAGGAGCTCTCAGCTTAATGGAGGGAATAAA[C/T]GTATATGGTTGCTGTACAAGATGATAAGCCTACCA Y 2 1 2 1 101000 f 74 goat snp54755-scaffold837-3320597 15 25973564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797164 Affx-122956330 AX-385284105 15 53614150 GTGCGTGGACTCATGCCCAAGTAAAAGCAAACTTT[A/G]CGTTTGTCCTCTAATATAGCACCTGAATTGAAACA R 2 1 2 1 201000 r 74 goat snp54754-scaffold837-3287660 15 25940767 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402567 Affx-122958448 AX-123272920 15 53654642 TCACAGTGCTTAACACAGTGCTTCACATGAGTGAA[C/T]GAATGAACAAAAGGAAGAAAGCAATAAAAAGGGGA Y 2 1 2 1 201000 f 74 goat snp54753-scaffold837-3247168 15 25900291 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277059 Affx-1111835658 AX-519550566 15 53663366 AAGAGATCTTTAAAAATGTATATTAAATTTATGAC[A/G]AAATTGTTGAAACAGAATGTAAACAAAGATAATGA R 2 1 2 1 101000 r 74 goat Random2.2K-1539 15 53663366 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436141 Affx-122932637 AX-123306480 15 53700943 TTTTAAGGATTCTTTTGTTAAAGTACTACCTGATT[A/C]TGGTTAAAATATATTTTAATGTATTTCCTGGACTG M 2 1 2 1 101000 f 74 goat snp54752-scaffold837-3200867 15 25853248 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399677 Affx-122960501 AX-123270032 15 53763054 ATACATAGAGATCAATATGTGCTCATTTGAACCAT[A/G]TGAAAGTTGCTATTTTGTAGGTCACAAGTGAATGA R 2 1 2 1 101000 f 74 goat snp54751-scaffold837-3138756 15 25791059 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402845 Affx-122958253 AX-123273198 15 53806156 TGAAGTTAAGAAAAAAATATCAACCTTGTAAGACT[A/G]TTGTTATGACTAAATGAGGCATTGCATACAGAGTA R 2 1 2 1 101000 r 74 goat snp54750-scaffold837-3095654 15 25748408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443156 Affx-122928060 AX-123313493 15 53889184 ACTAAAGGAAAAACTATTGCTAAACATGGTCTGAT[A/G]CAGAACTTTTTGAGCTACATAATCTGCAACATCCT R 2 1 2 1 101000 f 74 goat snp54748-scaffold837-3012626 15 25665524 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436691 Affx-122932334 AX-123307029 15 53922508 GTGATGCAAATTACCTCTTATCTAGTAACAGCTTT[A/G]CAACATAAGTATTACTATTGCCAGTGTACAGATGA R 2 1 2 1 101000 f 74 goat snp54747-scaffold837-2979302 15 25632281 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768917 Affx-122926625 AX-385256094 15 53961481 TGAGTTCAATTGAAATATGATCTTCCAGAGAGTAA[C/T]TTTTCTAAAGGTCCTAAATTCTTAGAAACAGAAAA Y 2 1 2 1 102000 f 74 goat snp54746-scaffold837-2940329 15 25593656 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443367 Affx-122927413 AX-123313704 15 54013911 TGCCTCCAATGAGTTGGTCATCTACAACCACTTAG[C/T]GGCTCCTACAAATACATACATACAGAGTCTTTAAA Y 2 1 2 1 101000 f 74 goat snp54745-scaffold837-2887899 15 25541528 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388888 Affx-122968860 AX-123259246 15 54047735 TTATTGGTCTCTCTGTCTCCATGCTCTTCTCATGC[C/T]AAGTTATTACCATGCAATTGCTGAATCAATCTAAA Y 2 1 2 1 201000 r 74 goat snp54744-scaffold837-2854075 15 25507116 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378683 Affx-122977073 AX-123249042 15 54083436 CAAAATTTGCACTGCACTATATGTAGGAAGCACAA[C/T]TCACATATACCTCAGGCTTAAAGCAGCTTCTCCTT Y 2 1 2 1 101000 r 74 goat snp54743-scaffold837-2818374 15 25470635 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434577 Affx-122934115 AX-123304918 15 54122276 TCTTCCTTTTCAATTTTTCAGATGAAGAATCAGAG[G/T]CTCTGAAATTTTTAATATTTTTTCCAGGGTGCTCT K 2 1 2 1 103000 f 74 goat snp54742-scaffold837-2779534 15 25432022 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768786 Affx-122972040 AX-385255963 15 54173242 TATTAGAACAATGATTTGAATTTCAATATCAAGAA[G/T]CATAATTTAGAGTAATGGATTAAAGAGAGAAATGT K 2 1 2 1 201000 r 74 goat snp54741-scaffold837-2728568 NW_017190912.1 4685 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406869 Affx-122955648 AX-123277220 15 54215833 CAAAGAGATTTCATAACCTGAGGCTACAAAAGTGC[A/G]TGTATGCAGACTTGTGTGTATGTGCAAACAAACAC R 2 1 2 1 101000 f 74 goat snp54740-scaffold837-2685977 15 25336410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444860 Affx-122926289 AX-123315197 15 54244674 GTGGGCCCCACTGAAATGACTGGGATTTTATTCCC[G/T]GCCCTGACTAATGATATTAATAGTATCTGAGCTCT K 2 1 2 1 101000 r 74 goat snp54739-scaffold837-2657136 15 25307741 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430790 Affx-122937472 AX-123301131 15 54280595 CTGAAAAATAGTGTGGCTCTCCAAAACCACTTTCA[C/T]GTGATCTTTGTTTTAAATTATCTGTTTGCTCTCAA Y 2 1 2 1 101000 f 74 goat snp54738-scaffold837-2621215 15 25271295 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407514 Affx-122954737 AX-123277865 15 54333208 CTCATGAATGGTTGCATTTGTTTTGTTGTTTATTT[A/G]TTTATAATTATTCATTTATTTCCAATAATGACAGA R 2 1 2 1 303000 r 74 goat snp54737-scaffold837-2568602 15 25218593 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423160 Affx-122942747 AX-123293506 15 54379254 CCTGGGGTTTAAGAATGGATGAAGGATGGGGCAAC[A/G]TTTAGGGATATGGGTGAACTATTATGTGGGAATTG R 2 1 2 1 101000 r 74 goat snp54736-scaffold837-2522556 15 25172024 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769310 Affx-122942735 AX-385256481 15 54439326 AATCATCTGAGAATTTTGAGAAAATTCTGCTCTCC[A/G]TGAACGTTTACTTAATCCACATATAAATTTAACGA R 2 1 2 1 101000 f 74 goat snp54734-scaffold837-2462484 15 25113515 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445364 Affx-122925416 AX-123315701 15 54471875 GCCACTAGATGTTGATCCAAATACTTCTGCTGGCT[A/G]CGTTAATGACTGTTAAATGAAACACTAACTTCGTT R 2 1 2 1 101000 r 74 goat snp54733-scaffold837-2429935 15 25081178 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425256 Affx-122940986 AX-123295602 15 54516926 TGACTGATAGTGCCTAAGCCATAAAGATGGTAAAC[C/T]ATCTTCTGTAATATGAAGACTGGAAGTAAGTACTC Y 2 1 2 1 101000 f 74 goat snp54732-scaffold837-2384884 15 25035816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424343 Affx-122941938 AX-123294689 15 54560711 AATTGAATTCAGTGTCACCCTGGTCCCTAACCCCT[A/G]CAGCTGAGTTTGCTAACACATAAGCTATCTCTTTT R 2 1 2 1 201000 r 74 goat snp54731-scaffold837-2341099 15 24992022 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392456 Affx-122966162 AX-123262813 15 54592928 TTGGGATAGGGACATGACCAAAGAGGAGAGCTGGA[C/T]GTGTCAGTAACCAGCACTAATGATTCCACAAAGGG Y 2 1 2 1 101000 r 74 goat snp54730-scaffold837-2308882 15 24959933 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393834 Affx-122965162 AX-123264189 15 54635616 GAAATAGACACCAAGACATAGTTAGGCAAAGGATT[A/G]TTTGAGTAATAGCCTATGAGAGAAAACAGGGAAGG R 2 1 2 1 101000 r 74 goat snp54729-scaffold837-2266194 15 24916902 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392283 Affx-122967537 AX-123262640 15 54712552 TGCAGACAAATTAGCTACAAGGAGAATTTAATTGC[A/G]TGATTTAGTGACATTATATGGTTAATTGTATGGTT R 2 1 2 1 101000 f 74 goat snp54728-scaffold837-2189258 15 24839787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765107 Affx-122955552 AX-385252667 15 54745388 TGAGTTTCAGGACATCACCACCATTTTCTGGGGAA[C/T]GGTTTCGAGAATGATGTGTTTTGTAGAAGCTGTTT Y 2 1 2 1 101000 f 74 goat snp54727-scaffold837-2156422 15 24806761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380164 Affx-122975966 AX-123250522 15 54789461 ACAGAGTCACCCAGTACAAGTGGGAACATCTGACT[A/G]CCCTGAAGAGCTTGACTGGAGCTGTTTTCCTAGTG R 2 1 2 1 201000 f 74 goat snp54726-scaffold837-2112349 15 24763108 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446283 Affx-122925662 AX-123316619 15 54847956 ATGACCTGTTTAAAGAGCCTAGCATGAGACCCCAC[A/G]TAGGGTAGACACTGATGAATACTACTTCCTTGTGC R 2 1 2 1 201000 r 74 goat snp54725-scaffold837-2053854 15 24704361 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387727 Affx-122969750 AX-123258085 15 54961093 CTCTGCAGATGGCCTTTGGTCCATTGACACAAGCA[C/T]GTGGGTTGGACAGAGCTGGGTAGATCAGAGGTGAA Y 2 1 2 1 101000 f 74 goat snp54723-scaffold837-1940717 15 24590467 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417487 Affx-122947168 AX-123287835 15 55001043 TCAAAATATAAGACACCACATCCACATCTGACCCC[A/G]TATGGATAAAAGCATGCAAGCCAGCCGGGTTCACA R 2 1 2 1 201000 r 74 goat snp54722-scaffold837-1900767 15 24550607 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430122 Affx-122937407 AX-123300463 15 55069718 AAATCCAGGTACGGGACATTGAACACATTCCTTAA[C/T]GAGTCCCCCGATTATACTTAAACTAAAAGCCCCAC Y 2 1 2 1 101000 f 74 goat snp54720-scaffold837-1832092 15 24481572 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775037 Affx-122970866 AX-385262169 15 55098883 ATCTATGGGCAGCTTTTAGAGCCAATACCATTGAC[A/G]TGAGTCCTAAACAATGGATTTATTGTTTCCTGTGG R 2 1 2 1 101000 r 74 goat snp54719-scaffold837-1802927 15 24452369 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381647 Affx-122974756 AX-123252005 15 55138335 ATAGCCAACCTACTGCAACTTCTAACCATTGGTAC[C/T]GACATCTGATGTAGCCAAATAAAATGCATTCTGTT Y 2 1 2 1 101000 f 74 goat snp54718-scaffold837-1763475 15 24413213 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794795 Affx-122931553 AX-385281755 15 55187617 CTGTGAGGAAATCGGTGAATAGGGTCTCACTGACA[C/T]GGGACTTTGATGGGTAGATCGGATCTAATCAGGCA Y 2 1 2 1 101000 r 74 goat snp54717-scaffold837-1714193 15 24363029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440475 Affx-122929379 AX-123310812 15 55219183 CTCCCCAGGATCCTAACTGTTGTTGCTGTTTAGTC[A/G]CTCAGTTATGTCCGACTTTTTTGCAACTCCATGGA R 2 1 2 1 103000 f 74 goat snp54716-scaffold837-1682627 15 24331452 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389753 Affx-122968246 AX-123260110 15 55285889 AATCCTGTTCTAATTTTTTTCTCAACTTTCTTCCA[A/G]TGATTTTAGTCATTTTCATCATTTGGGGTTTCTTT R 2 1 2 1 101000 r 74 goat snp54715-scaffold837-1615921 15 24264929 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412240 Affx-122950910 AX-123282590 15 55335450 AATAAAAAGATTAAAATACAGAGAAGAGCAAAAAA[G/T]AGATCTATGGTACACAGACCTAGCATGTATACGTT K 2 1 2 1 101000 r 74 goat snp54714-scaffold837-1566360 15 24215477 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449269 Affx-122923032 AX-123319604 15 55371131 GGACATGTCAATCAACTTCCTTAGGCGTCACTTTC[A/G]TGCTCTGTCAAAATAACAAGTTTATTTCTCTAAAG R 2 1 2 1 101000 r 74 goat snp54713-scaffold837-1530679 15 24179831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800942 Affx-122977697 AX-385287857 15 55428873 AGCCACATAATCCGATTGGTAGCTAGGAGCATTCA[A/G]TTCCAACCAATATCATTTATCACTACACGGTTCCA R 2 1 2 1 101000 f 74 goat snp54712-scaffold837-1472937 15 24122288 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421966 Affx-122943806 AX-123292313 15 55458813 AAAATATAAAACTAATTCTATCACTTCCTTGCACT[A/G]TGAAGTTGGGCGATTCATTTTCCTTCTCTAAACCT R 2 1 2 1 101000 f 74 goat snp54711-scaffold837-1442997 15 24091585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799167 Affx-122973297 AX-385286097 15 55585801 AAATCACTTATTCCAATTATTTAACTGATGTTTCA[A/G]TCTTTTCCCTTTCCACCATCACTGCTGGGGGGGCA R 2 1 2 1 202000 r 74 goat snp54709-scaffold837-1316009 15 23964340 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417508 Affx-122946952 AX-123287856 15 55644363 GATTATAATAGGGCCACACTCTCCTCTCCTTTTGC[G/T]CAGGGTCATGAACACATGCAGTTTGAGAAACTGAC K 2 1 2 1 101000 r 74 goat snp54708-scaffold837-1257447 15 23905684 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271794 Affx-1111833050 AX-519545583 15 55664825 AAGGTCAGGGTCATGGAAGAAGGGGAGGGATAGGG[A/G]TGAATGCTGCTAGGGTCAAGCAAGGAAATTCACTC R 2 1 2 1 101000 r 74 goat 15_55664825_AF-PAKI 15 55664825 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38414072 Affx-122949759 AX-123284421 15 55683448 TATATGTGGGAACATTCATCTTTCTGGGGATCCAC[A/G]CCACACCTTTCAACAGATTCTCAAATGGCAGCTTT R 2 1 2 1 101000 f 74 goat snp54707-scaffold837-1218362 15 23866519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415665 Affx-122948557 AX-123286014 15 55716481 GTAGTGACATTTCAAAAGTTATAGCACAGAAAGCC[A/G]TGCAACTTCATGAGACCGTGAGGAGTATGCGCAGG R 2 1 2 1 101000 r 74 goat snp54706-scaffold837-1185329 15 23833279 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422520 Affx-122943286 AX-123292866 15 55745007 GAGCAGATGTTTAAAGATGTCCCACAATAAATCAC[A/G]CCTTTCAGGATCCATGCTCTTGTGAGATCCCCATC R 2 1 2 1 101000 f 74 goat snp54705-scaffold837-1156803 15 23804333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773272 Affx-122973173 AX-385260415 15 55815240 TTTGAAACATAAGACTTATTTTCTCCATACTTAAC[A/G]TTGTTCAGTCCATATATACAAAACTTTAAAATGAT R 2 1 2 1 101000 f 74 goat snp54704-scaffold837-1086570 15 23733850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406279 Affx-122956083 AX-123276631 15 55852417 CGTGATCTGGCTCCTCCTCACCTCAGCTCCATCTC[A/G]TAAGGCATCATGGCACCTTCCTACTGGATCTTCAG R 2 1 2 1 101000 r 74 goat snp54703-scaffold837-1049393 15 23696814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430774 Affx-122937484 AX-123301115 15 55976239 AGGGTGACTGCAGGATTAAATAAAATGCCAAGAAA[C/T]GGTTGGCAGGCTGCATTCAGAAGGTGTTAAGATGT Y 2 1 2 1 201000 r 74 goat snp54701-scaffold837-925571 15 23571780 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377994 Affx-122977603 AX-123248353 15 56076584 TAAGGGACATTTCAAACCCTCCAGTAGCCATTCTT[A/G]TTACAAATTCTATTTTAAGAATAAAAGTGTAATTA R 2 1 2 1 103000 f 74 goat snp54699-scaffold837-825226 15 23470442 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384155 Affx-122972799 AX-123254513 15 56133158 AGAATGAATAATTCTTGACCACCTGTGCTCATATC[A/G]TCTCATTTTCTCCTCATAGCAAACTAAGATATATA R 2 1 2 1 101000 f 74 goat snp54698-scaffold837-768652 15 23413351 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773002 Affx-122929470 AX-385260146 15 56236678 AATTACTTGATAGAAGAGCAGATTCTGAAACCTTC[C/T]TCTTAGGGCCACAGTCTATAAATGTAGATTTCTGA Y 2 1 2 1 101000 f 74 goat snp54696-scaffold837-665132 15 23309336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451811 Affx-122921483 AX-123322144 15 56276120 TATGATCGTGTATTGAGACTTTCCATTTCTCTTCA[G/T]ATTAGCTTCACAGTCCCAGTAAGGATTTTTAAGCC K 2 1 2 1 101000 r 74 goat snp54695-scaffold837-625690 15 23269625 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399197 Affx-122960616 AX-123269552 15 56306620 ATTCATGTTTCCACACTTTGCCACATAACTGGGGA[G/T]CTGAATATTCAGAAGACATCCAGTCTAAGAGATCT K 2 1 2 1 101000 f 74 goat snp54694-scaffold837-595190 15 23238825 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416746 Affx-122948195 AX-123287094 15 56366306 TCTGGATAAACACAGTGAGAATATTATACTTTGCT[A/G]TTGTTGAGGATGTAGGGTCATAATGAAACTAGACA R 2 1 2 1 101000 r 74 goat snp54693-scaffold837-535504 15 23178933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448340 Affx-122924132 AX-123318676 15 56398303 CAAAGTAGTCACCCAGAGAGGAATAGCTTTCTAAC[A/G]TCGTAAACTTTAGCTTTCTTCTTTGTTTTCAGAAC R 2 1 2 1 101000 f 74 goat snp54692-scaffold837-503507 15 23146535 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386385 Affx-122970840 AX-123256743 15 56435458 TAAAAAACATTAATGTATTAATATATGGTGCAAAT[A/C]TTTAAGAAAATAAAACCAAATAGCCTGAAAGAAAC M 2 1 2 1 102000 r 74 goat snp54691-scaffold837-466352 15 23109525 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274590 Affx-1111834311 AX-519548179 15 56480095 ACTCAGGCTGCAGGA[A/G]CTCAGCCTCCTCCTTTCTGCTTCATAGTCCCCAGG R 2 1 2 1 102000 r 74 goat GoatD01.029793 15 56480095 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38410687 Affx-122952743 AX-123281037 15 56527420 TTCAACAATCATAGGCTCAGTTGTCCAAACTTACT[A/G]TAATAATTTAGAACACTGTTCACCTGGTGGGAGCA R 2 1 2 1 101000 r 74 goat snp54690-scaffold837-374390 15 23019233 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414913 Affx-122949111 AX-123285262 15 56568152 TAACTCTTTCAAAAGTATCAATTTATTAATAAAAT[A/G]TTGACTATTCTATAAAATTCTAGAATAAAACTTTT R 2 1 2 1 103000 r 74 goat snp54689-scaffold837-333658 15 22978102 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781512 Affx-122967075 AX-385268597 15 56618960 GTACTATACAGGTTTGCATAAGTCAGGTTTGAAGA[C/T]AGCTCAAAACTGAATGTTCAGTGATGAATTCTTTT Y 2 1 2 1 201000 r 74 goat snp54688-scaffold837-282850 15 22927058 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415896 Affx-122948472 AX-123286245 15 56657584 GTGACTAGTCATACAAGGTGATACAGTTTCTTCCT[A/G]GAAGCTCACTCTTAGCCCCTAGTCGTCAGGCTCTG R 2 1 2 1 101000 f 74 goat snp54687-scaffold837-244226 15 22887924 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793690 Affx-122977908 AX-385280662 15 56741223 AAGGCTGGATTCATAATCTGGGAAACACTAGAAGA[C/T]GGTTTTTAAAGGTAGTGGGTAGGCGCAAATGAAAA Y 2 1 2 1 101000 r 74 goat snp54685-scaffold837-160587 15 22803524 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790351 Affx-122961815 AX-385277354 15 56776128 ATATATAAAGTGGTATGATAATGAACAGCTTTAAT[A/G]GCTAGATCTGGAACGTCTTTTTAAGATGAAATTGC R 2 1 2 1 101000 r 74 goat snp54684-scaffold837-125682 15 22768501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794376 Affx-122972386 AX-385281339 15 56807645 AGCCAAGGATTACTCCTAGATTTTTTAGTAGGGAA[A/G]TTGGAATAATGCATCTTTCAATGTTTTTGCTCATG R 2 1 2 1 101000 f 74 goat snp54683-scaffold837-94165 15 22736123 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274435 Affx-1111834283 AX-519548026 15 56834127 TTTCTTTCTTGCCTCCCATCTCCTCCTAGGGAGGC[A/G]GGATGGCCAGTCGGCATCCCCACCGCCCGTGCCTG R 2 1 2 1 202000 f 74 goat GoatD01.028732 15 56834127 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38401652 Affx-122959581 AX-123272005 15 56841914 ATATCTATGTGTCTATCCCAATATACTTGATTTCA[C/T]CATTTTTGCCTTTAATCTTAACAGTAGCTTACTGA Y 2 1 2 1 201000 f 74 goat snp54682-scaffold837-59896 15 22702593 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 468277063 Affx-1111835660 AX-519550570 15 56885843 CTCCTAACACACAGCACTCTCTTCCCCATCACTAC[A/G]TTCTCTCCAAAGCCTTGGGCCCAGCCTGGGCTGTG R 2 1 2 1 303000 r 74 goat Random2.2K-1541 15 56885843 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38387071 Affx-122969890 AX-123257429 15 56888851 CAACCATATTTTAAATTTCTTGAAAATAAAAGTCC[A/G]CCTTGTAACACGATTATCAAGTAGTGCTAATTAAC R 2 1 2 1 201000 r 74 goat snp54681-scaffold837-12959 15 22655373 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801034 Affx-122933490 AX-385287948 15 56902723 GTCCCTAGGCAGTAAAACATATCTGACGGTTTTAA[C/T]GTTCTCACTCTTAGATTCTGAATTTAGTAGTAACA Y 2 1 2 1 201000 r 74 goat snp42992-scaffold57-6360664 15 22635926 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789594 Affx-122957233 AX-385276603 15 56940249 ACTTAAAATCAAATAGTACACAATGAAATAAGAGT[A/G]CCACACTTTAGAAAAGACTTGTCTAGCAGATAGTA R 2 1 2 1 101000 r 74 goat snp42991-scaffold57-6323138 15 22598500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450159 Affx-122922324 AX-123320494 15 56970382 TCTCTAACCTGTTAGGTAAATCACCGTTGAATGTG[C/T]GTGTGTTTTGGAACTTGCATTCCAAATTTTGTGCT Y 2 1 2 1 101000 f 74 goat snp42990-scaffold57-6293005 15 22568393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388305 Affx-122969382 AX-123258663 15 57037949 GTTTCTGTCTTAGTTATTATTGTGCCATTAAAAAA[C/T]ACTGCAACTTAGTAGCTTTAAACAGCAAATTTATT Y 2 1 2 1 101000 f 74 goat snp42989-scaffold57-6225438 15 22500744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432269 Affx-122936335 AX-123302610 15 57080219 GCAGAGTCAGACATGACTGAGTGACTGAACTGAAC[C/T]GATTACTAGAAAAATGTCTGATCTTGATACAATAG Y 2 1 2 1 201000 r 74 goat snp42988-scaffold57-6183168 15 22458422 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447610 Affx-122923997 AX-123317946 15 57114697 ATCTGCTAGGTCCATGCATGAATAATGCCTGCAGC[A/G]CTGCAGCCAGCCCCTGGACCGAACTCTTCAACCTG R 2 1 2 1 101000 f 74 goat snp42987-scaffold57-6148690 15 22423113 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430825 Affx-122937446 AX-123301166 15 57157099 TCCGAGGCAGGTTGTTAAGATACCAACCAAAGCAA[C/T]GACAGACTAGATGTCTTCATGGAAACGCTGAAACT Y 2 1 2 1 101000 f 74 goat snp42986-scaffold57-6106288 15 22381400 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447247 Affx-122924955 AX-123317583 15 57188087 TTTCTACCAGTTCTATCTTTGGTGGGGGAAGTAGC[A/G]CAGCTGTATTCTGGGGTTTTCCCAATGTACTCTCT R 2 1 2 1 101000 f 74 goat snp42985-scaffold57-6075300 15 22350391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785409 Affx-122920535 AX-385272454 15 57246058 GACTTTGAAGGTTGATTGTGTAAACAAATTGTGTT[A/G]TAAAACATTCACATATAACAGAAGGTGCAATAATA R 2 1 2 1 101000 f 74 goat snp42984-scaffold57-6017329 15 22291634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377333 Affx-122977671 AX-123247692 15 57285678 TTGCTTTCCATTTATTTTATGACACTTTCCACATT[C/T]ACCCTCAGAGATTTTCTCATTTCTATTTATTAGCT Y 2 1 2 1 101000 f 74 goat snp42983-scaffold57-5977709 15 22250965 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452731 Affx-122920283 AX-123323064 15 57319879 ATCAGTCAGATTCTTTACCATTGAACCACCAGGGA[C/T]GCCCTTCCTAGGTTTATACCCATCCATAAGAGGGC Y 2 1 2 1 202000 r 74 goat snp42982-scaffold57-5943508 15 22216581 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786229 Affx-122969152 AX-385273264 15 57354655 AGTTTCCTTTTATTGAAAAAGAGGACACATAGTGC[A/G]TTTGTTATGTCACGGAGATTTTACAGAAGGCAAAT R 2 1 2 1 101000 f 74 goat snp42981-scaffold57-5908732 15 22181847 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38387348 Affx-122970485 AX-123257706 15 57406929 TCTTTTACCACTACACCACCTGGGAAGCCCATTTC[A/G]TTATATGTTTAAGGTAATAATTCAGTTCCATGTAC R 2 1 2 1 201000 r 74 goat snp42980-scaffold57-5856458 15 22129506 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439556 Affx-122930095 AX-123309893 15 57456995 GACATTCCAATACTTTCATTTCCTTCTTCTGAATA[C/T]GAGGCTGGGTATGGAGGGTGAGATATGGAAAAGAT Y 2 1 2 1 201000 f 74 goat snp42979-scaffold57-5806392 15 22079562 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427920 Affx-122939224 AX-123298263 15 57509043 CCTGGCCCAGAAGTATCATCATTGCCAAAGAGAAA[C/T]GCATAATAGTTGTGATTCATGGACTGACTGGCAAT Y 2 1 2 1 101000 f 74 goat snp42978-scaffold57-5754344 15 22027038 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382058 Affx-122974929 AX-123252416 15 57556304 GGCTGTGTATCTTACAGGAGATTACGTTCCATTTC[A/G]TTCTCCTACTCCATCATCTTGAGAACTCCTTCTCC R 2 1 2 1 101000 f 74 goat snp42977-scaffold57-5707083 15 21979772 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413056 Affx-122950976 AX-123283405 15 57597698 CAGAAACCAGCCCCACCTTGTTAGTACACATTGGG[C/T]AAATGGCTGATATCACTTCTCAGGTACTGAAAATT Y 2 1 2 1 101000 r 74 goat snp42976-scaffold57-5665689 15 21938347 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385602 Affx-122971200 AX-123255960 15 57655677 GTGGTCAGTCCTCTTACCTCTTAGTGTCTTCCCAC[A/G]AATGTGATCTCTTTCTTAAAAGATTTTATGTGGCT R 2 1 2 1 101000 f 74 goat snp42975-scaffold57-5607710 15 21880254 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796976 Affx-122929425 AX-385283917 15 57697797 AAATTTAAACTATCTAACCAGAAAATTCAAACCTT[A/G]TAAGAGAAAGATAGGAAAACAATACAGATGTGAGG R 2 1 2 1 101000 r 74 goat snp42974-scaffold57-5565590 15 21837793 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774876 Affx-122957714 AX-385262010 15 57726725 GTATTTTTGGCAATGAGTCAGATGATTCAGGAGAC[A/G]TATTTGGTGTATACTAATATGCCTTTGCAGCTTTC R 2 1 2 1 101000 r 74 goat snp42973-scaffold57-5536662 15 21808382 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385305 Affx-122971680 AX-123255663 15 57782538 TTATTGGAAAAATGTTTCTTGAGCACTTCCTATGT[A/G]TTCACAGTGTTTTAGGTGCAGGAACTGAAGTACTA R 2 1 2 1 101000 r 74 goat snp42972-scaffold57-5480849 15 21752538 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779701 Affx-122967064 AX-385266801 15 57832181 AAGGAACAACTGCTTACAAGGGTTTAGCCACAGAC[A/G]TCAGGTGACACGACTGTTTATCATTCAGAGGCAGG R 2 1 2 1 101000 r 74 goat snp42971-scaffold57-5431206 15 21702876 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376687 Affx-122978990 AX-123247046 15 57868321 GATTTTTACTGAATGCTTACCGTATATCAGCTTAT[A/C]GTCTACTAATTTAAATGTTCTCTTTGAATCTTGTC M 2 1 2 1 101000 f 74 goat snp42970-scaffold57-5395066 15 21666370 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453670 Affx-122919714 AX-123324003 15 57925712 GCAAACCACTCTAGTCTTCTTGTCGTGAGAACTGC[A/G]TAAACAGTACAAAAAGGGGAATTATGTTAGACCCT R 2 1 2 1 303000 r 74 goat snp42969-scaffold57-5337675 NW_017212051.1 9692 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381785 Affx-122974294 AX-123252143 15 57972052 TTTATAGATCTTATTTGCATTGCTTTCACTTATCT[A/G]CAAGTTACAAAGTTGTATAATAGCCCACAGACTAA R 2 1 2 1 101000 r 74 goat snp42968-scaffold57-5291335 15 21564552 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382192 Affx-122974009 AX-123252550 15 58003891 GCATTTACCTTGCATTGCTTGCTTCCCTGATGAAA[C/T]GTCCTTAAAATTTCTGTAGTTTTTTCCCCCCTATA Y 2 1 2 1 101000 f 74 goat snp42967-scaffold57-5259496 15 21532850 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423126 Affx-122942904 AX-123293472 15 58035575 GTTAAGTATAAAAGCCATAGCTCAGATATTGCAAC[A/G]TCATTAGATGTGCCTGCAGAAATGCATTGTGCTAC R 2 1 2 1 101000 r 74 goat snp42966-scaffold57-5227812 15 21500856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795796 Affx-122930338 AX-385282749 15 58112079 TTTGAGCTACTGTCAAGAACATAATAGGTTTCTCC[C/T]ATTAGCATACATAGTTTCTCTCATACATAGTTAAC Y 2 1 2 1 101000 f 74 goat snp42965-scaffold57-5151308 15 21423011 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406997 Affx-122955035 AX-123277348 15 58145805 AGGAAAGTTAAAGGCCAGCTTCTTTTCTTTATTTC[A/G]TTTTTTTTTTCCTCTTTCCTGTATCTTTACATAAA R 2 1 2 1 303000 r 74 goat snp42964-scaffold57-5117582 15 21389300 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271795 Affx-1111833051 AX-519545584 15 58173186 CCCCAGGGTCTGCCAGTGCAGTGCCCCATGGCCAG[A/C]AGTCTCATGACCCAGTCTCATGACCCAGTCTCATG M 2 1 2 1 101000 r 74 goat 15_58173186_AF-PAKI 15 58173186 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387201 Affx-122970600 AX-123257559 15 58183703 GAGAGGAAACAGCTTCTTCCCTGACCAGCCTCCCC[A/G]TCCTGTTCACTAACTCCTTGGCTGCTGCCCACCTC R 2 1 2 1 201000 r 74 goat snp42963-scaffold57-5079684 15 21351875 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420198 Affx-122945551 AX-123290546 15 58216284 ATCCCTTTTGGTAGGGTGATGGCAGAAAAACTTCA[C/T]GGAGGTGGGGTTCAAGTTGAACCCTGAAGGGTGGG Y 2 1 2 1 101000 f 74 goat snp42962-scaffold57-5047103 15 21318440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376973 Affx-122977753 AX-123247332 15 58256315 GAAACTCTCCTTGGCCTCTAGAAACACCACCCGCT[A/G]TCACAGTTCTCTTGCTGCCTGTCAGATTTTCATAT R 2 1 2 1 101000 r 74 goat snp42961-scaffold57-5007072 15 21278990 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440558 Affx-122929312 AX-123310895 15 58305165 CTCCCACGCCTTGGGAAGACTATGCTCCCCTCGCC[A/G]TGCAGTCTGTTTTGTCACTCCTGTGTTCACAGAGA R 2 1 2 1 101000 r 74 goat snp42960-scaffold57-4958222 15 21229768 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397529 Affx-122962043 AX-123267884 15 58339592 ATCTCCAAAGTCTGTGACATCTGATAGTTTGGATG[A/G]TATAGATCCATCTTTGCTCACCCTCATCCTCAGAA R 2 1 2 1 101000 r 74 goat snp42959-scaffold57-4923795 15 21195399 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790887 Affx-122920779 AX-385277884 15 58399401 AGACTATATTAGAAAACATATAGGCTAAGCTGCTC[C/T]GACAGGCACTCCAAAACTTTTAGGCTCATACAGAA Y 2 1 2 1 101000 r 74 goat snp42958-scaffold57-4863986 15 21135701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773851 Affx-122933614 AX-385260991 15 58459981 CTAAATGCTTGCTAAATGTTATTTACATGATCTTC[A/G]GCAAGTAACTTACCTTTGTCTCTCAGTTTCTCAGG R 2 1 2 1 101000 r 74 goat snp42957-scaffold57-4803406 15 21074855 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795356 Affx-122978770 AX-385282312 15 58488745 TTGGCACAGATTCTGGCCTATCGATAGATACTGGC[A/G]TATCAATTCTGGCTAGATGATCATTTGTAACTATT R 2 1 2 1 101000 f 74 goat snp42956-scaffold57-4774642 15 21046105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438762 Affx-122930813 AX-123309099 15 58523751 GTAATATGAAAAATCAAGTCAGCATAGCATTTACC[C/T]GGCTTACAAAACATAGCTGTATGAGCCAAATATGA Y 2 1 2 1 101000 f 74 goat snp42955-scaffold57-4739636 15 21010735 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417100 Affx-122947482 AX-123287448 15 58602900 TGAATTCTGTTATAACCTCAAAGACAGAAGCTATT[A/G]TGGTGGTCTCCCTGTCTTGATAAATGGCTTAGTTT R 2 1 2 1 201000 f 74 goat snp42954-scaffold57-4660487 15 20932614 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785876 Affx-122962792 AX-385272913 15 58656074 ACCAGTTTATGTCCCAGAAGCTTAAAAACAAAAGG[C/T]ATGTATGATAAAATGCTTGCTTAAGATTCTCCCCC Y 2 1 2 1 101000 f 74 goat snp42953-scaffold57-4607313 15 20879224 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276931 Affx-1111835661 AX-519550439 15 58692597 AATAAGTGAAGTGTCCTCTCTAGAACATCGCTTAC[A/C]TCTAAATTAATGCTAACAAACACATGAAAAGATGC M 2 1 2 1 101000 f 74 goat Random2.2K-1542 15 58692597 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800996 Affx-122928460 AX-385287910 15 58719549 GAGTAAGGAAGCATTCTCAGAAGTTGGAAAATTCT[A/G]CTTTCTAAAGGTAAATAAGGGGAAACACCTGGCAG R 2 1 2 1 102000 r 74 goat snp42952-scaffold57-4543838 15 20815744 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384358 Affx-122972241 AX-123254716 15 58804245 CAAATATGCAAGTCCACATTCAAAACTGGTAGCCA[C/T]AAAGTGTGTTTATCCATTCAAAAAAGGCTCATGAT Y 2 1 2 1 101000 f 74 goat snp42951-scaffold57-4459142 15 20730265 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450812 Affx-122921802 AX-123321146 15 58833877 CTCTGGAAGCATACTTAAAAACAATACGATAAATA[C/T]GTCCAACTGAAATTAACTGATTAAATTCACTAGTT Y 2 1 2 1 101000 f 74 goat snp42950-scaffold57-4429510 15 20700170 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441397 Affx-122928844 AX-123311734 15 58868444 GCAGACTTGCTCTGGAGTAAAGTGCATGATGTTCT[A/G]TTTTTCAGTGATATAGATGTTCCTGTACTTCAGCA R 2 1 2 1 201000 r 74 goat snp42949-scaffold57-4394943 15 20665378 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390094 Affx-122968024 AX-123260451 15 58903636 AACTAAATAATGACTTAAAACTTATGAAAATGTTA[A/C]GATAGAAAAGTTGATTCATAGTGTCTTTCATGCTT M 2 1 2 1 101000 r 74 goat snp42948-scaffold57-4359751 15 20630079 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431535 Affx-122936219 AX-123301876 15 58959482 CCAGCCTATCATATCATTCATTTATTCATGCACTC[A/G]TTCATTCACTGTGCCTGTATACAGTCCCCTTGATT R 2 1 2 1 101000 r 74 goat snp42947-scaffold57-4303905 15 20573832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433112 Affx-122935705 AX-123303453 15 59003386 ACAGAGTAGGCTCTTAACTTGTTTTACTAAGTAAG[C/T]GACAATTTCGTAATTCAGAGAAGAAACAGACATTC Y 2 1 2 1 201000 f 74 goat snp42946-scaffold57-4260001 15 20529731 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393542 Affx-122965417 AX-123263898 15 59045492 GAGAGAGAGAGAGAGAGAGGGAGGGAATAAGCATT[C/T]ATATTTTTATGAATTCATATTACTGTGCTAACCAT Y 2 1 2 1 303000 r 74 goat snp42945-scaffold57-4217895 15 20487198 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768641 Affx-122951784 AX-385255820 15 59094686 AACTACTGTTTGTAACAATCTTCTGAATAGGCATT[A/C]TTATCATTATTTCACACAAAGCTCTGGAGTAGAGA M 2 1 2 1 101000 r 74 goat snp42944-scaffold57-4168701 15 20437978 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446608 Affx-122924806 AX-123316944 15 59126581 TTTCCCCACTTTATGATAAATTAAAATACCATAAA[A/G]TATAAAAGAAAGTTTTAAAAAACTACAAGTGCCCT R 2 1 2 1 303000 f 74 goat snp42943-scaffold57-4136806 15 20406078 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376448 Affx-122978059 AX-123246807 15 59155941 TGCACTCCTCATGGTCAAAGGTATGCTCTCCTAGG[C/T]GGTGTATATTTCACTTGCTCCAAACTTAAATTAAA Y 2 1 2 1 101000 r 74 goat snp42942-scaffold57-4107446 15 20376352 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388492 Affx-122969227 AX-123258850 15 59193563 GAAGTGTCCCTCTGTTCCCTTTATGGGTTGGTGAG[C/T]TGTTGGTACCTTTGGTTGGAAGCTCTGTTGCTAGT Y 2 1 2 1 101000 r 74 goat snp42941-scaffold57-4069824 15 20338401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412130 Affx-122951099 AX-123282480 15 59243105 GCAGGTATCTGAACAGGTGGGAGGTTTCTCTGCAC[G/T]ACTGAGACAATCAACTGCCCTTTGTTTTCCCCCAG K 2 1 2 1 101000 r 74 goat snp42940-scaffold57-4020282 15 20288598 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414126 Affx-122949710 AX-123284475 15 59277242 GTGCCATCAGAAGAACCGGAGGATGAGAGGCAAAC[A/G]CTGTGGTAGTAACCCTTGTTCAGGGGCTTTTTATG R 2 1 2 1 201000 f 74 goat snp42939-scaffold57-3986145 15 20254464 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416308 Affx-122947925 AX-123286657 15 59305867 AAGTAGGACGAATAGACAGTAACAGATATGCCAGA[G/T]AGGCAGCCACCAGGGAAGGAAAAAGAACAGAGCTG K 2 1 2 1 101000 f 74 goat snp42938-scaffold57-3957520 15 20229986 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389966 Affx-122968073 AX-123260323 15 59361642 CTAGTTGTCATATTGCTTTCCCTTTTAAGACCGGG[C/T]AAACTGAATTCCAGCAATATTTCCTCATAATTTCC Y 2 1 2 1 201000 r 74 goat snp42937-scaffold57-3901745 15 20174073 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787226 Affx-122933994 AX-385274252 15 59403948 GTGCTTCTTCTTTCATTATATCCCAACAAGGGGTC[A/G]TTAAAGCCTCCTCTAATGCTGAATTCTCTGGGTGC R 2 1 2 1 101000 f 74 goat snp42936-scaffold57-3859439 15 20131935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442599 Affx-122928483 AX-123312936 15 59433797 CCCTAGGGGTTATCTCGGTCTCCGCTCCAGCACTG[C/T]GGCCTGTGTTTTTTCCCATGGGCTGGTACTCCTGC Y 2 1 2 1 101000 r 74 goat snp42935-scaffold57-3829590 15 20101793 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405719 Affx-122956528 AX-123276071 15 59485085 TTTCTCAAGTATAAAAAAGTATTTACCATTTTCCT[A/G]TAGTTCTTCAAATGCCTGACATTCATCTTTTCTCC R 2 1 2 1 101000 r 74 goat snp42934-scaffold57-3778302 15 20052445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451652 Affx-122921600 AX-123321985 15 59531210 GCAGAAGCGGATTTGCTGATGATTAAGAAGGAAAA[C/T]AGAGGGAGAAAAGTTCTTATTACATAAAATGATGC Y 2 1 2 1 101000 f 74 goat snp42933-scaffold57-3732177 15 20006206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784661 Affx-122934119 AX-385271709 15 59575486 CGAGTGGCTGAGTACTTTCGCCCTGTTTTGGATGA[C/T]GGTTTTTGTAAGTGACATTTTGTTGCAAAGTCTTG Y 2 1 2 1 101000 f 74 goat snp42932-scaffold57-3687901 15 19961600 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402319 Affx-122959081 AX-123272672 15 59605020 GGTTTTTTTTTTTTGGTCTCAATCTGTTTTGGTCC[G/T]CTCACCTGACATATGGTTTTCTTTTGGCTTTGAAA K 2 1 2 1 201000 r 74 goat snp42931-scaffold57-3658367 15 19931759 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399444 Affx-122961214 AX-123269799 15 59664063 GCATCCTGGTTTGAGCTTCTTTCATAATCTCAGGT[A/G]TCGCGCTTCTGCTCTGGAGACTTCTGAATCCTTGG R 2 1 2 1 101000 f 74 goat snp42930-scaffold57-3599324 15 19872770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392436 Affx-122966186 AX-123262793 15 59740265 CAAAGCTGACTGTAAGATTCCTCCTCACTCGCCTG[G/T]CAGAGAAGGAAATGGCAGTTGATCTTTCTTCATCC K 2 1 2 1 201000 f 74 goat snp42928-scaffold57-3523122 15 19796794 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797606 Affx-122961156 AX-385284545 15 59769407 CATCAAGTGACTCCAATAGATAGTCTTATAAGAGT[A/G]CTGTAACTCTCTGGAGAACAAAAAGTTAAAATTGT R 2 1 2 1 101000 f 74 goat snp42927-scaffold57-3493980 15 19767659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786816 Affx-122964294 AX-385273844 15 59800246 CACTTTAGATCTATCTGTGATAGACATAATTAGAA[C/T]TGTGTTTAGCAAATACAACTGCCTTGAGGAGATGG Y 2 1 2 1 102000 r 74 goat snp42926-scaffold57-3463141 15 19736572 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414118 Affx-122949729 AX-123284467 15 59841089 TGAAGTGGCAAGGGCAAGAGAGAATTATGAAAAGG[C/T]ATGTATAATTTCAGTCTATGTCTGAATTTGGGAAC Y 2 1 2 1 101000 f 74 goat snp42925-scaffold57-3422298 15 19697557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453642 Affx-122919736 AX-123323975 15 59880792 GTAGCGTTCCATTACTTATAAATTAGGGTGACCGA[C/T]AGTGTTGGTTTGCCTTGAGCACTCTGAGTTTATGT Y 2 1 2 1 101000 f 74 goat snp42924-scaffold57-3382595 15 19657471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378777 Affx-122977003 AX-123249136 15 59937064 ACTTTAAAATTACATCCTGCTTCTCTCTATGGCCA[A/G]TCCTTGCTTCTGCCCCTCTCACTAAGTAGGAAAAA R 2 1 2 1 201000 f 74 goat snp42923-scaffold57-3326323 15 19601437 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450319 Affx-122922136 AX-123320654 15 59974906 ATGCCCTCATCCGAACTGTTTCATCCTTTAAACTT[A/C]TGTACTTTCCTAAACTTTTCCTGTTAAAACACTCA M 2 1 2 1 101000 f 74 goat snp42922-scaffold57-3288481 15 19563480 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782955 Affx-122954716 AX-385270025 15 60014163 CTTGTATAGGCCTTATTGTAATTTTGTGATATTTT[A/G]TAATCACTAGAAATATAGGTTATAGTACAGTTACA R 2 1 2 1 303000 f 74 goat snp42921-scaffold57-3249224 15 19523931 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401809 Affx-122959462 AX-123272162 15 60063347 AAATGAAAATTGAGTAAGAATCTGTTCAGTGTGGA[A/G]CCCTTTACATCCTGTCTGTCATACTTCTATCACAA R 2 1 2 1 101000 r 74 goat snp42920-scaffold57-3200040 15 19474087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382021 Affx-122974059 AX-123252379 15 60118145 GGGGTTTTAAAGCACTGTTTATTTTACTGATGCAC[A/G]CTAATAGCTTTAGTAGAGTTTATGGATCTCATTTG R 2 1 2 1 101000 r 74 goat snp42919-scaffold57-3145242 15 19418824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431912 Affx-122935999 AX-123302253 15 60159998 GGAACTAAGATCCCGCAGAAAAAAAAGGAAAAACA[A/G]CAATCAGAAATGAAGTAAGCCCCACTATCATTTTC R 2 1 2 1 201000 r 74 goat snp42918-scaffold57-3103389 15 19376688 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379507 Affx-122976458 AX-123249865 15 60197904 GTTCACTGGAAAATCAATAATTAACACCACTCTCA[A/G]CCACACTACCATCATGACAAAACTATAAAAAGTGA R 2 1 2 1 101000 f 74 goat snp42917-scaffold57-3065483 15 19338767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377091 Affx-122978269 AX-123247450 15 60227485 AATGTATGAGTTAACATATACATATCTCTTCTTTT[C/T]ACTTCTACACTTAAATTACTATAAAATTCTGGTCT Y 2 1 2 1 101000 r 74 goat snp42916-scaffold57-3035902 15 19309260 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797413 Affx-122951255 AX-385284352 15 60285750 AAGATGAGTTAGAGTCTAGCTGAAACTAAAATGCA[A/G]CCACTTATCCTCGTGAGACATGGAAGGAGTATTTC R 2 1 2 1 101000 r 74 goat snp42915-scaffold57-2977637 15 19250673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801007 Affx-122920560 AX-385287921 15 60322306 CTCAACACTGATACACAATATTCTTCCTTTTGGAA[C/T]CAGTGCTATTAAATAGAAATGTACTAAATAGCCAT Y 2 1 2 1 201000 f 74 goat snp42914-scaffold57-2941081 15 19214086 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396851 Affx-122963256 AX-123267206 15 60378571 TTTATTTTAAAGAGTAAAGGCCCCATTCTTGTTTA[C/T]GATTAGAAGGGAAATGTTCACTTTTGAAGATCAGA Y 2 1 2 1 201000 r 74 goat snp42913-scaffold57-2884816 15 19157680 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788130 Affx-122943199 AX-385275150 15 60431853 ACTTAGCACAATGAGTGGCATATGAGTTTGTTTTC[A/G]ATACTGCTTTTCTAAGCCCCCCTTTTTTACAGTTT R 2 1 2 1 101000 f 74 goat snp42912-scaffold57-2831534 15 19106453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789030 Affx-122942299 AX-385276043 15 60498216 ACTTGAGAGCAGAAGATAAGATTCATGCAAAAGTC[A/G]TAGAAGAAAAATGTAGAGAGTAGAAACTTGAGAAA R 2 1 2 1 101000 f 74 goat snp42911-scaffold57-2765171 15 19039095 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410116 Affx-122952822 AX-123280466 15 60532753 CTAAGAACACAGAAATTGAGATAGGAAAAACAAAC[G/T]AGGAATTTTATGTAAAAGCACTTGAGAAAAGTACC K 2 1 2 1 101000 f 74 goat snp42910-scaffold57-2730634 15 19004730 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787296 Affx-122964141 AX-385274321 15 60587125 ACTCGGGTACGCCTTTATCAAAAAGGACTGTTATA[C/T]TATGAAAACACTGAAGTTTATCATTTACTGTCAAT Y 2 1 2 1 201000 r 74 goat snp42909-scaffold57-2676262 15 18951952 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381612 Affx-122974780 AX-123251970 15 60622912 ATATAGGACTAGGACTGAGACTGGAGGGTGGACAC[A/G]TAAATGGAAAAGTCCTGCCAACTCTGGCTGCAGTG R 2 1 2 1 101000 r 74 goat snp42908-scaffold57-2640475 15 18916240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388867 Affx-122969316 AX-123259225 15 60665716 TCTCCCAGAAGGGCTGTTTTACCCATCGCAGTTCA[G/T]CAAAAGAGGGGTGCATGTCCATATACCTCATTATC K 2 1 2 1 101000 f 74 goat snp42907-scaffold57-2597671 15 18874246 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765667 Affx-122959450 AX-385253133 15 60695274 AGACCTGGAGTTAGAAATGTTTGTAAATTAAGGAT[A/C]GGGTATAAACAAGCGTATGAACAAGGGTATGATTG M 2 1 2 1 101000 f 74 goat snp42906-scaffold57-2568113 15 18844614 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429186 Affx-122937957 AX-123299528 15 60730288 GAGAAAAGAGGTCGTTAGTAATCTTCTCAGATGAC[G/T]CTGTCCTTGCTGGAACCTGACCTCAACACATTCAC K 2 1 2 1 101000 f 74 goat snp42905-scaffold57-2533099 15 18809336 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778672 Affx-122949175 AX-385265783 15 60766465 CTTGAACTTAAAAACATACACTATTATCTGCAGAA[C/T]AAATAACATACAATTCCCTCTTCTACCCTGAATTG Y 2 1 2 1 201000 r 74 goat snp42904-scaffold57-2496922 15 18773510 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384778 Affx-122972013 AX-123255136 15 60846210 GTTGGTCCTTTCATTTCTATTTGAAACTTTCAAAG[C/T]GCAACCTCACTGAACAGGAACCTGTGGTCAAAGAG Y 2 1 2 1 101000 r 74 goat snp42902-scaffold57-2417177 15 18693265 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436627 Affx-122932499 AX-123306965 15 60886976 CTACAATCGTGGTTCTTGGGAGAATCTGATGTCCA[C/T]TCATAAGGGCAATCCCTCTTCCCTCTGTATCATCT Y 2 1 2 1 101000 f 74 goat snp42901-scaffold57-2376411 15 18654211 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434147 Affx-122934907 AX-123304488 15 60933415 CAAGAGGGGATGATGGTAGCATTGGTGGTTACAGA[C/T]AGTAGGAACTAATGCAAGAGAAAGAAACAAAGGAG Y 2 1 2 1 101000 f 74 goat snp42900-scaffold57-2329972 15 18607508 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271796 Affx-1111833052 AX-519545585 15 61003755 ATTCTGGTTTATCCTTTTAAAGAATTATTTTTTTT[A/G]TGCTGTGGTATGAGGGTTTAATAAAGAATAAGAAG R 2 1 2 1 101000 r 74 goat 15_61003755_AF-PAKI 15 61003755 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320783134 Affx-122976563 AX-385270201 15 61005623 GTGAAAAATTATTGTGGATTTCACTGGTGCCTGCC[A/G]TTCCATATTTTACTTAATGCCAGTGCTTTCCCCCT R 2 1 2 1 101000 f 74 goat snp42898-scaffold57-2257764 15 18535218 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789898 Affx-122970082 AX-385276905 15 61034482 TTTTCCTTAATTTGTACATATCTGGCTTCTCTAAA[C/T]GTACTTGTTCTTCTACAACTTGAGTGGAATGATTT Y 2 1 2 1 201000 r 74 goat snp42897-scaffold57-2228905 15 18506424 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452794 Affx-122920235 AX-123323127 15 61076836 CTGGCAGGCTATAGTCCATGTGGTCACAGAGAGTC[C/T]GACACAGGCTAAGTGACTAACACAGTCACAGTTGG Y 2 1 2 1 303000 f 74 goat snp42896-scaffold57-2186551 15 18465696 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444626 Affx-122926935 AX-123314963 15 61109654 AGGATTTTGTACAAACTGCAGGATGATTGCTATTA[C/T]CGAGCACTCACTGTGTGCCAGGCTCTGTGCTCTGC Y 2 1 2 1 101000 f 74 goat snp42895-scaffold57-2153733 15 18433127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443982 Affx-122926991 AX-123314319 15 61146968 ACACAGAACCCTGGTTTTCTGCAGATGAATATATG[G/T]CAGAGTTGGGTTTTAGATGCTTGGGAAGTAAAAAA K 2 1 2 1 101000 f 74 goat snp42894-scaffold57-2116419 15 18395833 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792243 Affx-122970017 AX-385279227 15 61183352 GCTAAATATTGAATGCGGAGGAGGGAGAAGGTAAG[C/T]GCCTGGGCCCAAATCAAGTACACCAAAGCCTGTAG Y 2 1 2 1 202000 r 74 goat snp42893-scaffold57-2080035 15 18359138 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766893 Affx-122940357 AX-385254211 15 61212226 TGCAGTATTAACGTTTGGTCAAAGGTGCTCGTGGC[A/G]TTTCACAGATGTAATGAAGAACCCATATTGTCCAA R 2 1 2 1 101000 f 74 goat snp42892-scaffold57-2051161 15 18330407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794613 Affx-122959883 AX-385281575 15 61264885 AAAGGCTTGAATTAAAACAATGTTAGAGCTGAATT[A/C]TAAGGATACTCATAGATAGAATCATCAAGGAAGGA M 2 1 2 1 101000 r 74 goat snp42891-scaffold57-1998502 15 18277356 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386521 Affx-122970740 AX-123256879 15 61308947 TCTAAATGGTTCTCTAAATGTCACTATGGCTTATC[C/T]GGCCATTAAAGGGTTTCTGGCCCTAAAATATAATA Y 2 1 2 1 101000 f 74 goat snp42890-scaffold57-1954440 15 18232968 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800054 Affx-122945189 AX-385286977 15 61355682 AATGGATGAAATAACAGGTATTGGGGACTCAGATA[G/T]CATATCGTTCCCTAAGTTGAGAAGTCAAGCTTTTC K 2 1 2 1 101000 r 74 goat snp42889-scaffold57-1907705 15 18186215 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801641 Affx-122941410 AX-385288549 15 61386265 ATCTTTTTGCTTACCCTTCAGTCTCCAGTGCTGGT[A/G]GATTACATAAAGCCTTCCCCTTGAATCAGGACTGA R 2 1 2 1 101000 f 74 goat snp42888-scaffold57-1877122 15 18155738 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402978 Affx-122958151 AX-123273331 15 61415262 AGATGAGAGAGGCAGAGGATGCCTGGATCTTGTCT[A/G]CTTCTTCCCTGCCTCTCACGCAGTAGTTCATTTCA R 2 1 2 1 202000 r 74 goat snp42887-scaffold57-1848125 15 18126865 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275272 Affx-1111834807 AX-519548848 15 61441396 CTCCAAATTAATTCAAGTTCCTGAGCATCTCCTAG[A/G]GGCCT R 2 1 2 1 101000 f 74 goat GoatD01.054246 15 61441396 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38428358 Affx-122938978 AX-123298701 15 61477442 TGAGCTTAGGATGATGATTATTAAGTAGAGGACTT[A/G]CTTCAGCCTCAACTGATCCCCAGAGTAATTCTCAG R 2 1 2 1 101000 r 74 goat snp42886-scaffold57-1785945 15 18067816 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402774 Affx-122958309 AX-123273127 15 61509511 CAGCCTTGTCAAGAGGGTTCAGGCTTCAAGGGTGG[A/G]TATCTGGCATGAAGGCTGGACTCTGCCATTCATCA R 2 1 2 1 101000 r 74 goat snp42885-scaffold57-1753876 15 18035808 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398194 Affx-122962640 AX-123268549 15 61571213 GACTAAAACCTAAGCAATCAGGTCACTGTATTCCA[C/T]CGGCTGAGTAATGGCTTTAGGGATGGGAACATGAC Y 2 1 2 1 101000 f 74 goat snp42884-scaffold57-1692174 15 17974123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449066 Affx-122923048 AX-123319401 15 61622104 AAAACAGCATGTTTCTTGTTGCTTCTGAAGGCACG[C/T]TGGGTATCATAACATCGAGCAGTCAGGCAGACTTC Y 2 1 2 1 201000 r 74 goat snp42883-scaffold57-1641283 15 17923407 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276934 Affx-1111835662 AX-519550442 15 61644384 TGTCTAGTACTTGTCACCATAATCACTGATGGATT[A/G]CTGCTTATAAACATAGACATTTCCAAGAAGCATTC R 2 1 2 1 101000 f 74 goat Random2.2K-1544 15 61644384 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418439 Affx-122946483 AX-123288787 15 61655911 CACTTGCACTTTTCACCTTGCTCGGCCACTTACTC[A/G]TTGTGTAACCTCCAGAAGGGCTTTCACCATTCTCT R 2 1 2 1 101000 r 74 goat snp42882-scaffold57-1607476 15 17889691 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396578 Affx-122962915 AX-123266933 15 61684566 GGATTAAGCAAAATCAAAGAGGTTTCTTTACTAGA[C/T]GAATTCTCAGAGATTTTAATATACCCTCGTGAGCT Y 2 1 2 1 101000 f 74 goat snp42881-scaffold57-1578821 15 17860833 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771977 Affx-122950813 AX-385259133 15 61729793 GATGCCCAGGATCAGTAGGCTTCCTACTAGTCCAT[A/G]TATGTGGGCAGCCCACCTACTGAATCAGAGCTCTT R 2 1 2 1 102000 r 74 goat snp42880-scaffold57-1533594 15 17815286 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388627 Affx-122969129 AX-123258985 15 61790957 ATAATTCCATATTTGGGGGAAATCCAAATGAAATC[G/T]CCCCACATGTATCATGGCATATGTATGATTTTTCT K 2 1 2 1 101000 r 74 goat snp42879-scaffold57-1472430 15 17753852 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408792 Affx-122953367 AX-123279143 15 61819510 ACCTAGAGCTTTGCAAGCACTTAGCTCTGTGATAA[C/T]GTTATAAATCAACTGGTTTCTCCAATAAGACACTG Y 2 1 2 1 101000 f 74 goat snp42878-scaffold57-1443877 15 17725297 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379758 Affx-122975855 AX-123250116 15 61855465 GCCTTCTGTGATTCTCACCCTGAATTCTAGTAATA[C/T]CTGATATTTACAATCTTTAAAACAATAGTCCAGCT Y 2 1 2 1 101000 f 74 goat snp42877-scaffold57-1407922 15 17689377 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476312 Affx-1251763819 AX-586011729 15 61857166 CAATGCTGTTCTAAGACTGCAGAGATAGATGCAAA[-/ACCAGATGCCGGGAGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTTAAAAAAAAAATCAAAAAAAAAAAAAAAAAAAC]CCAGATGCCTTTCAAGGCAAGAAAACCGTAACTCA - 4 1 4 1 20000 f 74 goat SV_295 15 61857166 - deletion junction SV-TF-chip 539476565 Affx-1251763819 AX-586011951 15 61857166 CAATGCTGTTCTAAGACTGCAGAGATAGATGCAAA[-/ACCAGATGCCGGGAGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTTAAAAAAAAAATCAAAAAAAAAAAAAAAAAAAC]CCAGATGCCTTTCAAGGCAAGAAAACCGTAACTCA - 4 1 4 1 20000 r 74 goat SV_295 15 61857166 - deletion junction SV-TF-chip 562165127 Affx-1251763819 AX-606940539 15 61857166 CAATGCTGTTCTAAGACTGCAGAGATAGATGCAAA[-/ACCAGATGCCGGGAGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTTAAAAAAAAAATCAAAAAAAAAAAAAAAAAAAC]CCAGATGCCTTTCAAGGCAAGAAAACCGTAACTCA - 8 1 4 1 20100 f 74 goat SV_295 15 61857166 - deletion junction SV-TF-chip 562165129 Affx-1251763819 AX-606940541 15 61857166 CAATGCTGTTCTAAGACTGCAGAGATAGATGCAAA[-/ACCAGATGCCGGGAGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTTAAAAAAAAAATCAAAAAAAAAAAAAAAAAAAC]CCAGATGCCTTTCAAGGCAAGAAAACCGTAACTCA - 8 1 4 1 20100 r 74 goat SV_295 15 61857166 - deletion junction SV-TF-chip 562165191 Affx-1251763819 AX-606940603 15 61857166 CAATGCTGTTCTAAGACTGCAGAGATAGATGCAAA[-/ACCAGATGCCGGGAGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTTAAAAAAAAAATCAAAAAAAAAAAAAAAAAAAC]CCAGATGCCTTTCAAGGCAAGAAAACCGTAACTCA - 8 1 4 1 20100 f 74 goat SV_295 15 61857166 - deletion junction SV-TF-chip 562165363 Affx-1251763819 AX-606940774 15 61857166 CAATGCTGTTCTAAGACTGCAGAGATAGATGCAAA[-/ACCAGATGCCGGGAGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTTAAAAAAAAAATCAAAAAAAAAAAAAAAAAAAC]CCAGATGCCTTTCAAGGCAAGAAAACCGTAACTCA - 8 1 4 1 20100 r 74 goat SV_295 15 61857166 - deletion junction SV-TF-chip 562165581 Affx-1251763819 AX-606940992 15 61857166 CAATGCTGTTCTAAGACTGCAGAGATAGATGCAAA[-/ACCAGATGCCGGGAGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTTAAAAAAAAAATCAAAAAAAAAAAAAAAAAAAC]CCAGATGCCTTTCAAGGCAAGAAAACCGTAACTCA - 8 1 4 1 20100 r 74 goat SV_295 15 61857166 - deletion junction SV-TF-chip 562166456 Affx-1251763819 AX-606941864 15 61857166 CAATGCTGTTCTAAGACTGCAGAGATAGATGCAAA[-/ACCAGATGCCGGGAGGGGGGGAGGGAAAGATGGCGGAGGAAAAATTTTAAAAAAAAAATCAAAAAAAAAAAAAAAAAAAC]CCAGATGCCTTTCAAGGCAAGAAAACCGTAACTCA - 8 1 4 1 20100 f 74 goat SV_295 15 61857166 - deletion junction SV-TF-chip 38392882 Affx-122965741 AX-123263239 15 61930029 TCATTTTCAACACTCACCTTTGAAAACTGCCCCAC[G/T]CATCCAGGTAGTTGCCAAGATGCTTTGAATCCACC K 2 1 2 1 101000 r 74 goat snp42875-scaffold57-1333358 15 17614621 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387276 Affx-122970544 AX-123257634 15 61986642 CAACTCCATTCATTTTTATGGCTGAGTAATATAAC[A/G]TGGTATATGGCATACACCACAAATTGTTGGATTAA R 2 1 2 1 103000 r 74 goat snp42874-scaffold57-1276745 15 17558339 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426613 Affx-122939966 AX-123296959 15 62024866 AAGTGTGGCAGTAAGCCTTTGGAGAAAATGAAATT[A/G]TTTACATTTCCAAGGCTTGGCTGCTATCAGTCCAA R 2 1 2 1 101000 r 74 goat snp42873-scaffold57-1238521 15 17520415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436948 Affx-122933177 AX-123307286 15 62059147 TCAGTCTCCTCAATGTAAGACCTGCCTGCCTATGG[C/T]GAGCCTGCATCTTCCCTGCAGTTCTTCTGTGCATT Y 2 1 2 1 201000 f 74 goat snp42872-scaffold57-1204240 15 17486335 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453474 Affx-122919843 AX-123323807 15 62128299 AATACTTGAGTCACATGTTGTCAGACCGCCAGCCC[A/G]CATCAATCACAGGCGAGGGTCACTCACACAGGTCA R 2 1 2 1 201000 r 74 goat snp42870-scaffold57-1135088 15 17419180 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792622 Affx-122936577 AX-385279603 15 62179562 ACTTTGAAACCACTGAAACTGCTCACATCGAGACC[A/G]TTGCTCCTTTCATGTTGTCCAGCCTGTGGTTTCTC R 2 1 2 1 101000 f 74 goat snp42869-scaffold57-1083825 15 17367895 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400732 Affx-122959908 AX-123271087 15 62213504 AACCCTTTCAGTATTTAATGGCTTAAAATAACAAA[C/T]ATTCCTTGTTTCTCACAAGTCTACAGGTCAGCTGG Y 2 1 2 1 101000 r 74 goat snp42868-scaffold57-1049883 15 17333784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436067 Affx-122932702 AX-123306406 15 62250552 AATAATAAGTATTTGTCATCTCTGATGAGGATGGA[A/C]TACTAAGTTGTATTAGTCAGGATAGTGTGGGTTAT M 2 1 2 1 101000 r 74 goat snp42867-scaffold57-1012835 15 17296683 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399884 Affx-122960219 AX-123270239 15 62285735 ACAATTCTTGATAAACTGGCCAGCCATTCACTGTA[C/T]CACCGGTAACAGCCACTCAAGACTCCCAGTTAGGA Y 2 1 2 1 101000 f 74 goat snp42866-scaffold57-977652 15 17263686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399875 Affx-122960226 AX-123270230 15 62368120 TCCAAATCATGTTTCCCTGAATTCTGAAGGCATGA[A/G]GAAATGTCAGTTCACCCAGTCCCACGGATGTTGTT R 2 1 2 1 101000 r 74 goat snp42864-scaffold57-895267 15 17181713 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433874 Affx-122934420 AX-123304215 15 62397115 GCCATCCTATTTTTTCCAAGTCAGAACTTGAGAAA[C/T]GGATTTGAGGAAGGAGTTTTCTCAGCCCTTCCTGG Y 2 1 2 1 101000 f 74 goat snp42863-scaffold57-866272 15 17152587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439980 Affx-122929805 AX-123310317 15 62451158 TATCCTTGTTATCCCTGTTACTAGGTGCATTCAGT[A/G]ACCAGCATCCACATAACTGGGGATGTGTGTAAAGT R 2 1 2 1 101000 f 74 goat snp42862-scaffold57-812229 15 17097193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438317 Affx-122931353 AX-123308655 15 62484036 AGGAGGAAAGGACCAGAGATGAAGAAGACAGCTTC[A/G]TAGGTTTCAAAGCATAAAACCATCTGAATTATTGA R 2 1 2 1 201000 r 74 goat snp42861-scaffold57-779351 15 17064450 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802195 Affx-122937054 AX-385289099 15 62513072 AGGTACACGGGGTTGAATTGGAAGCTTGACTCCAC[A/G]TCTTACTTGCTGTGTGGTCTTGCACAGTTGTTCCA R 2 1 2 1 101000 r 74 goat snp42860-scaffold57-750315 15 17035373 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450221 Affx-122922277 AX-123320556 15 62612650 GCCGAAGGAAAAAGTATGCTATCAGCTCAAGGAAA[C/T]GCCGGTTATCTCAAAACAGTTCAGAAGCCTGGATC Y 2 1 2 1 101000 f 74 goat snp42858-scaffold57-650737 15 16936530 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800326 Affx-122937033 AX-385287249 15 62645400 TTAGAACGAGCTCAACCCTGTGCTAAGGATCTTAT[A/G]TACATAATCTCATTAAATTCTCCAAATAGTCCACA R 2 1 2 1 201000 r 74 goat snp42857-scaffold57-617987 15 16902478 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411752 Affx-122951504 AX-123282102 15 62681341 GATATGCTCTGCTGAATCTCAGCCTTTTCTTATAT[A/G]ACCTGGAGGTGGATGAACAGGATGCATGGGGAAGG R 2 1 2 1 101000 f 74 goat snp42856-scaffold57-582046 15 16866847 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393489 Affx-122965822 AX-123263845 15 62745177 GCATAGTATATTGCACTAAAAAGGTGCTCAGTAGC[A/G]TTTAATTTTTTGTCTTTTGGTTTAACTTCTGAGAT R 2 1 2 1 103000 f 74 goat snp42855-scaffold57-518210 15 16801617 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393864 Affx-122965140 AX-123264219 15 62791968 TGGGACTTTTAGAAATATGTGGTGTGTTCCTAAAG[C/T]ACATAAGAATCTCCTAATTATGTAGGTGATAGCTC Y 2 1 2 1 101000 f 74 goat snp42854-scaffold57-471419 15 16754905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452331 Affx-122920658 AX-123322664 15 62843422 CAAGAACTCTAGATGAGTGAAACAACGGTCTCCCA[C/T]GTTCCCTGCCAGGACGACACCAGCAGTACCCGCCT Y 2 1 2 1 101000 f 74 goat snp42853-scaffold57-419965 15 16703221 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427790 Affx-122939770 AX-123298133 15 62874903 CTGACTGAGCTCCGTCTTCCTCCTTTATTCTCAAA[C/T]GCGGCCACTCACTAAGTTCTCGCCAGTCCCCATCC Y 2 1 2 1 101000 f 74 goat snp42852-scaffold57-388484 15 16672219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445369 Affx-122925412 AX-123315706 15 62914391 TAATTAATTTATTTTTATTTTCCTGCTCTGGCACC[A/G]GTTCTGCTGTTTCTGGTGTGTTCTCGGGCCTTATA R 2 1 2 1 101000 r 74 goat snp42851-scaffold57-348996 15 16632835 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454297 Affx-122919263 AX-123324630 15 62949249 TCATGGGATCCCTTAATGAACTCCCCTCTCCCTAA[C/T]GGCATATCTGCTGCTGATTCCTGTTTGCAGGGTTG Y 2 1 2 1 201000 r 74 goat snp42850-scaffold57-314138 15 16596683 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767024 Affx-122937944 AX-385254316 15 62995251 AAAATATTAAAGGAAGTTCTTGGGCAAAAGGAAAA[C/T]GATTCCATAAGATATCAGATCCTATAGAAAAAGAG Y 2 1 2 1 101000 f 74 goat snp42849-scaffold57-268136 15 16550493 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787946 Affx-122933364 AX-385274967 15 63026815 CTTGAGCCCGGGAATTGTTCTATCTCTGAAGCAAG[C/T]CTTGTTTCAAGATGCTCAGTTATGATTCAGGAGAT Y 2 1 2 1 101000 f 74 goat snp42848-scaffold57-236572 15 16518818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421665 Affx-122944432 AX-123292012 15 63068313 TCCTCCACTTCCCTCTAAGATTATATTGATTGATG[C/T]GCTTCCTTCCTCGAATCATTTGTGTTGTCTCAGTA Y 2 1 2 1 101000 r 74 goat snp42847-scaffold57-195074 15 16477377 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422703 Affx-122943651 AX-123293049 15 63114214 TGTGAAACGCGTCTCCATGGGCAACCACTGCATTC[G/T]CACATCTAAACCACCATAGCCCATGTTTTCCTGGA K 2 1 2 1 101000 r 74 goat snp42846-scaffold57-149173 15 16431250 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405633 Affx-122956593 AX-123275985 15 63161784 GGGGGCAGCCGATAAAAGAGAGGCCCCAAGAATGA[C/T]GCCTAAGTTTCTGTCCATAACAAGGTAAGACCATC Y 2 1 2 1 201000 r 74 goat snp42845-scaffold57-101603 15 16383770 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448410 Affx-122923674 AX-123318746 15 63206489 TAACTTCCTAGCACTCCTCACCCGGGGGAAGGTGG[A/G]CAGGCCTCATTAGTCTTTCTGTCTGAGAGGAGAAC R 2 1 2 1 101000 r 74 goat snp42844-scaffold57-56898 15 16339068 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277068 Affx-1111835663 AX-519550575 15 63237017 CCAAATAAGAGTACACTAAATTTTTCGTCATAATT[A/G]TTGTTTTGCTTAGGTCTGTCCTTCACATGAAACTT R 2 1 2 1 101000 r 74 goat Random2.2K-1545 15 63237017 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38377702 Affx-122977408 AX-123248061 15 63252846 GGTGTGACAGTCTTAGAGATCAAAAGTGGGATTCT[G/T]TGTGCTGACTGACACTCTGGAAGAATGCCAGAGAT K 2 1 2 1 101000 f 74 goat snp42843-scaffold57-10541 15 16293133 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437242 Affx-122932020 AX-123307580 15 63266107 AAAAAGATGAGAGTTTTGAAAAAGTAGAATGAAAA[G/T]AAATGATTTCCTTTTTCAAGAGCACTTTCCTAGAA K 2 1 2 1 103000 f 74 goat snp42257-scaffold5554-71655 15 16279858 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418326 Affx-122946967 AX-123288674 15 63325678 GTATCTGGCTGGGCCTTGGGAAGTAGGGGGTGAGG[A/G]CAGCCCAGGAATGGGGAGCTCTCGTGGCAGGTACT R 2 1 2 1 101000 r 74 goat snp42256-scaffold5554-12084 15 16221696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430889 Affx-122936873 AX-123301230 15 63348128 AAAGAATGGAAGTCAGGGGCAACAGCAGAAGTGGC[A/G]ATGTGGGTTGGGGGGATATCTGGAGTCCCTGTGAA R 2 1 2 1 101000 f 74 goat snp10876-scaffold139-10267 15 16199482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437563 Affx-122931888 AX-123307901 15 63382995 GTTTGCCTGTTGTTCCTTGGCTTTTGCCCAGTTCA[A/G]TGAAGATGGAATTGCCCAGTGGTGACAGGGAAGGA R 2 1 2 1 201000 f 74 goat snp10877-scaffold139-45134 15 16164769 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783388 Affx-122961795 AX-385270451 15 63423240 CCAGAGAGGAAAATCTAGTTGACTTGAAAGATTTA[C/T]AGCTTTCAGGAAGATTCCGGAAGACCGATCCAGAT Y 2 1 2 1 101000 r 74 goat snp10878-scaffold139-85379 15 16124379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398436 Affx-122961615 AX-123268791 15 63486574 AGAACTTAACATTAGGCCCATGCCGGTTGTCAGAC[G/T]ACCCGAGGGTGGGAACATCTAAGTAACCTCCAGTC K 2 1 2 1 101000 f 74 goat snp10879-scaffold139-148713 15 16064632 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440549 Affx-122929318 AX-123310886 15 63533719 CAGTGTACAAGTGCTCTGAGTGGGGAAGTCCAGGG[C/T]CCACAGCAAGAGGACTTCACCTGGACTGGGCAATC Y 2 1 2 1 101000 f 74 goat snp10880-scaffold139-195858 15 16017690 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271797 Affx-1111833053 AX-519545586 15 63553040 GATGTGTTCCATTGCAAGTGACAGAAACCTCATTC[A/G]AACTAACTAGAGTTTAAAAGGAATGTATTAACTCA R 2 1 2 1 201000 r 74 goat 15_63553040_AF-PAKI 15 63553040 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403595 Affx-122957564 AX-123273948 15 63651170 GTGGTCAGTTAAAGAATACAAGTCAGTGTCATTAC[A/C]GAGTAAAATAATCTTCATTCCACAGAGGAGATAAA M 2 1 2 1 101000 f 74 goat snp10882-scaffold139-313309 15 15899972 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408063 Affx-122954268 AX-123278414 15 63693223 GAAGAATTGGACATTAACCAGATAGTCACAAATAT[A/G]TAATTACGAATTGCTCTAGATCTTATGAGAGCACA R 2 1 2 1 101000 f 74 goat snp10883-scaffold139-355362 15 15857742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423014 Affx-122943421 AX-123293360 15 63724333 GTTGAGCTTGGTGTTCCTTTGGGAAGAGATGGCTC[A/G]TCCTGATGACATGGCATCCATGATACATACCTGTA R 2 1 2 1 201000 r 74 goat snp10884-scaffold139-386472 15 15826639 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770090 Affx-122935451 AX-385257257 15 63757546 CCAGACATTTCCTGCAGTTTAAAGGTCAGCAGCCC[A/G]TATTTACCTATAACCGATAAAAGAGTCTCTGTTTC R 2 1 2 1 101000 f 74 goat snp10885-scaffold139-419685 15 15793359 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447539 Affx-122924050 AX-123317875 15 63797112 TAAATATAGTACATGAAATTAAGATTCTGATATAT[A/G]TACTCCTATCAATTCAGCCTAGATCAGTGTAGTAA R 2 1 2 1 101000 r 74 goat snp10886-scaffold139-459251 15 15753497 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396083 Affx-122963432 AX-123266438 15 63868093 GGTCTTCTCTGATGCCTTTGATTTGCAGGCAGGGC[A/C]GTGTGGTTTAGAAAGGAGCAGTGACTTGTCTGGGA M 2 1 2 1 101000 f 74 goat snp10888-scaffold139-530232 15 15682349 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403130 Affx-122958113 AX-123273483 15 63910235 ACTTTGATTGTCCTGTGCTCAGTTTGTAAGATGTA[G/T]CTGATCTAGTAAATGCCAGTTTCCCCTCTCCACAC K 2 1 2 1 101000 r 74 goat snp10889-scaffold139-572374 15 15640095 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413264 Affx-122950221 AX-123283613 15 63974240 ACCATGTGGAGCTGAAACAGAAGACTAGGGGTAAA[C/T]GGAGGAGGCTGTTTGAATGTCATGGAAATTTTAGG Y 2 1 2 1 201000 f 74 goat snp10890-scaffold139-636379 15 15576160 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445641 Affx-122925083 AX-123315978 15 64005414 TAACTAGATCAGCTTCCTACCTTCTACTGACCTCT[A/G]CCTTCCTAGCACCTGTTTGCAAATCTGTTATTTAT R 2 1 2 1 201000 r 74 goat snp10891-scaffold139-667553 15 15544909 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410051 Affx-122953232 AX-123280401 15 64041134 TAATGAGAAAGCACCTCTAAGCTTCATCATGGGCT[A/G]CAAATGTAAATAGCCAGGAAATGAAAATTTTTTAC R 2 1 2 1 101000 f 74 goat snp10892-scaffold139-703273 15 15509314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450121 Affx-122922767 AX-123320456 15 64091440 TAGGACGTCTGGCCCCATCTTTTCAAGCAGCAAAT[A/G]GGTTAATATATAGATCTTGGGGCACCAAATGATGG R 2 1 2 1 201000 r 74 goat snp10893-scaffold139-753579 15 15458038 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439244 Affx-122931006 AX-123309581 15 64128755 ACCACTATCTATGTCCCTACTTTGCCAAGACTCAC[C/T]AAGTTGCTTGGCTATATAATGTACTCAGCATTTCA Y 2 1 2 1 201000 r 74 goat snp10894-scaffold139-790894 15 15420976 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453273 Affx-122920391 AX-123323606 15 64166163 GTGCAAAATTAAAATTCAAGGCCCCTTGAGCAACC[A/G]TTATTCAACATTTCAGGAGGATGGCAACAGAACAT R 2 1 2 1 201000 r 74 goat snp10895-scaffold139-828302 15 15383394 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778205 Affx-122978081 AX-385265320 15 64200661 TTATAATGTATTTAATTCTAATGCTGTGGTTCTTA[C/T]AAGTTATATGCTATTTTGAGGAACCATGGTGAATT Y 2 1 2 1 101000 r 74 goat snp10896-scaffold139-862800 15 15349504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428764 Affx-122938426 AX-123299106 15 64238530 GAAAGTCTCCAGGTTAGTTGAGATGTAACTTTATA[C/T]GGATCTCTGAATATTTTGTCACCATGTGTGTCCTT Y 2 1 2 1 201000 f 74 goat snp10897-scaffold139-900669 15 15311766 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771415 Affx-122939606 AX-385258573 15 64268891 TCTCAATTACAGAGTGCTGGCTTATGGCTCCATTT[A/G]TAACTCCAGTTTTAGAACGTGCTTTTTACTACTAA R 2 1 2 1 101000 f 74 goat snp10898-scaffold139-931030 15 15281453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436580 Affx-122932895 AX-123306918 15 64309596 TATATCCCTCATTTAACAACTTATATACATCATTT[A/G]TTATCCATCTTTGGTTTGATCTTGAGTAATATAAT R 2 1 2 1 101000 r 74 goat snp10899-scaffold139-971735 15 15244363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384741 Affx-122972041 AX-123255099 15 64378143 AAGCACATTTTTTAAAAGGAAGGAAAAATAAAGTG[C/T]GATCCTCTCAAGAGTTTTGTAGAGTTTAATAAGAA Y 2 1 2 1 201000 r 74 goat snp10901-scaffold139-1040282 15 15175712 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410087 Affx-122952842 AX-123280437 15 64406723 ATATATCACCCTTTCACCGCATTTCTGAACTTAAA[C/T]ACTATCCAAAACAACATGTGGCAGGTTCTCTAATT Y 2 1 2 1 101000 f 74 goat snp10902-scaffold139-1068862 15 15147303 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408165 Affx-122954212 AX-123278516 15 64448814 ACAGATGGTATTGCATATCTAAACCTGAGATTCTA[A/G]AGCAATAGCCCATTGTGGGCAGCAGACAGCAGACA R 2 1 2 1 101000 f 74 goat snp10903-scaffold139-1110953 15 15104280 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774408 Affx-122961656 AX-385261544 15 64505726 AGCCATCAGCAATTCATTCTTGAAAAGAAACAACC[A/G]TGATGAGCCCTATGATTATAAAGTTTATTTCCAGG R 2 1 2 1 101000 f 74 goat snp11206-scaffold1400-582048 15 14994525 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425328 Affx-122940933 AX-123295674 15 64534998 ACACGACTGAGCGACTAAACAACAACAAACATTAG[C/T]GTTATTTAGTTTCTCTCTTTGATGATTGCCAAGTC Y 2 1 2 1 201000 r 74 goat snp11207-scaffold1400-611320 15 14965320 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402259 Affx-122959125 AX-123272612 15 64567934 GAAAACATGTGAATATTTCTTTCATGCAATCACGT[A/G]TATTGTATTTTCTTCCAAAACGAAAGCAATTCCTA R 2 1 2 1 101000 r 74 goat snp11208-scaffold1400-644256 15 14932136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789719 Affx-122933202 AX-385276727 15 64626276 AGAGGTTACGTGAAATTCTCCAGTTGCTGTAACTC[A/G]TTGTATTATCACTTCCAGGTTTTGTGTTTTTTTAC R 2 1 2 1 101000 f 74 goat snp11209-scaffold1400-702598 15 14874260 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799482 Affx-122959458 AX-385286412 15 64667526 TTACCTAAGCTATATTCTGAATTAGAACATTTCTC[A/G]TATTATGTCTTAAACTCTCCAAGAAGAGTAGATGG R 2 1 2 1 101000 f 74 goat snp11210-scaffold1400-743848 15 14832697 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413096 Affx-122950947 AX-123283445 15 64700536 ATACTTCCCAGGGGCAGACGAGGGCTATTGTTGAA[A/C]AAGAAGTTCAGGTCTGTCTGTGTCTGTGTGTCAAA M 2 1 2 1 201000 f 74 goat snp11211-scaffold1400-776858 NW_017196749.1 5458 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794298 Affx-122976097 AX-385281262 15 64733088 GGAGTTCTCATCTTGTAAAGGTCTACTCTTCAGGT[A/C]TGTGTTCTGATTCTGGGATAAGAATGAAAACCATT M 2 1 2 1 101000 f 74 goat snp11212-scaffold1400-809410 15 14767084 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773843 Affx-122931925 AX-385260983 15 64770399 TGATAAAAATGTGTATCAAAGAAGGCTAAGTTTGC[A/G]TCTTTTGGTTTCCCGAATTCTTGTGTGGAGTAGGA R 2 1 2 1 101000 f 74 goat snp11213-scaffold1400-846721 15 14729164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793201 Affx-122953528 AX-385280179 15 64814936 CATTCAGACAAAGTAAGCCTCAAAAAATGATTTGA[A/G]CTGAAGGTATCCTCCTTCTGTAAAGAATTGTTGGT R 2 1 2 1 101000 r 74 goat snp11214-scaffold1400-891258 15 14684388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397875 Affx-122961971 AX-123268230 15 64845847 AGAGGACTCCATGTGTTAAAGAGAAAAAATGAAAG[C/T]GCTTCATGGAAGATAGGATCCAGTCTGGATTTTGA Y 2 1 2 1 303000 r 74 goat snp11215-scaffold1400-922169 15 14653282 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432588 Affx-122935513 AX-123302929 15 64896275 TTGCTTTGTATGAGAGAGATATAAAAACGTGACAT[A/G]CATTTTGGAAATAGAACATCCTTTGGAAAATGAAA R 2 1 2 1 101000 f 74 goat snp11216-scaffold1400-972597 15 14601462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393880 Affx-122965127 AX-123264235 15 64930138 AAATATAGGCTGCTGAAGGAATGCTTAAAAATACA[C/T]CCACAGTCACAGAAATTTGGGGAAAAAATGGAACA Y 2 1 2 1 201000 f 74 goat snp11217-scaffold1400-1006460 15 14568604 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777316 Affx-122946641 AX-385264438 15 64943196 TATTCCATCTCAAAGAGCTTCAATACATTTTTACC[A/G]TTTGGGTCTCCAAGTACCTGCTGATTTTCTACTGA R 2 1 2 1 101000 r 74 goat snp19080-scaffold1918-397288 15 14553526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775036 Affx-122975146 AX-385262168 15 65010579 AGTAAAATTGCTAATTAATATTATCATAATTAGAA[C/T]GTTATAAATCCATGTTGACTGATTTCCTGGCAGTT Y 2 1 2 1 202000 f 74 goat snp19078-scaffold1918-329905 15 14485946 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409855 Affx-122952926 AX-123280206 15 65055911 CACACTACCAACAGCAGCACATAAGGGACACCCCA[A/G]TACTGTATATGCTCTGGCTGGGACCACCCCTTCTT R 2 1 2 1 201000 r 74 goat snp19077-scaffold1918-284573 15 14440023 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476313 Affx-1251763820 AX-586011730 15 65057754 TTTTCTGAATGTTGAGTTTTAATTCAACTTTTTCA[-/CTCTCCTCTTTCACTTTTTTTTTCTTTTTTTCTTTTTTTCTATTCCTCCGCCATCTTTCCCTCTCCCCGGCTTGCCATTT]TCTCCTCTTTCACTTTCATCAAGATACTCTTTAGT - 4 1 4 1 20000 f 74 goat SV_302 15 65057754 - deletion junction SV-TF-chip 539476566 Affx-1251763820 AX-586011952 15 65057754 TTTTCTGAATGTTGAGTTTTAATTCAACTTTTTCA[-/CTCTCCTCTTTCACTTTTTTTTTCTTTTTTTCTTTTTTTCTATTCCTCCGCCATCTTTCCCTCTCCCCGGCTTGCCATTT]TCTCCTCTTTCACTTTCATCAAGATACTCTTTAGT - 8 1 4 1 20000 r 74 goat SV_302 15 65057754 - deletion junction SV-TF-chip 562165134 Affx-1251763820 AX-606940546 15 65057754 TTTTCTGAATGTTGAGTTTTAATTCAACTTTTTCA[-/CTCTCCTCTTTCACTTTTTTTTTCTTTTTTTCTTTTTTTCTATTCCTCCGCCATCTTTCCCTCTCCCCGGCTTGCCATTT]TCTCCTCTTTCACTTTCATCAAGATACTCTTTAGT - 8 1 4 1 20100 r 74 goat SV_302 15 65057754 - deletion junction SV-TF-chip 562165853 Affx-1251763820 AX-606941262 15 65057754 TTTTCTGAATGTTGAGTTTTAATTCAACTTTTTCA[-/CTCTCCTCTTTCACTTTTTTTTTCTTTTTTTCTTTTTTTCTATTCCTCCGCCATCTTTCCCTCTCCCCGGCTTGCCATTT]TCTCCTCTTTCACTTTCATCAAGATACTCTTTAGT - 8 1 4 1 20100 f 74 goat SV_302 15 65057754 - deletion junction SV-TF-chip 562166349 Affx-1251763820 AX-606941757 15 65057754 TTTTCTGAATGTTGAGTTTTAATTCAACTTTTTCA[-/CTCTCCTCTTTCACTTTTTTTTTCTTTTTTTCTTTTTTTCTATTCCTCCGCCATCTTTCCCTCTCCCCGGCTTGCCATTT]TCTCCTCTTTCACTTTCATCAAGATACTCTTTAGT - 8 1 4 1 20100 f 74 goat SV_302 15 65057754 - deletion junction SV-TF-chip 562166464 Affx-1251763820 AX-606941872 15 65057754 TTTTCTGAATGTTGAGTTTTAATTCAACTTTTTCA[-/CTCTCCTCTTTCACTTTTTTTTTCTTTTTTTCTTTTTTTCTATTCCTCCGCCATCTTTCCCTCTCCCCGGCTTGCCATTT]TCTCCTCTTTCACTTTCATCAAGATACTCTTTAGT - 8 1 4 1 20100 r 74 goat SV_302 15 65057754 - deletion junction SV-TF-chip 320777822 Affx-122941664 AX-385264939 15 65086461 ATTGTTTCTCTGACCTTTTCTAATGAAAATGTGTA[C/T]GTAACTCTAGGAAATAAATCATATAGGATAAAAAT Y 2 1 2 1 101000 f 74 goat snp19076-scaffold1918-254023 15 14409635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418493 Affx-122946441 AX-123288841 15 65144000 ACTTCCTATTTTTCCCAGATGTCTATAGATCATAA[C/T]AGAGTTAGGAAAGGGAGATTTATTTCCTGCTCACT Y 2 1 2 1 101000 f 74 goat snp19075-scaffold1918-196484 15 14351490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404107 Affx-122957118 AX-123274459 15 65186330 ACTTCATTTTCTTGCATAATATGAATTTGGGTGTA[C/T]ATAAGATTATTAATTTGAGTTTTCTAAAAGAGGTA Y 2 1 2 1 101000 f 74 goat snp19074-scaffold1918-154154 15 14309547 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435889 Affx-122932780 AX-123306228 15 65215394 CACAGAAGTTCCTACAGAATGGTCAGACCATATTG[C/T]TTGATTGTGTGAGTGAAAAAAAACAGGTTTCTGTT Y 2 1 2 1 600000 r 74 goat snp19073-scaffold1918-125090 15 65215394 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767089 Affx-122932780 AX-385254378 15 65215394 CACAGAAGTTCCTACAGAATGGTCAGACCATATTG[C/T]TTGATTGTGTGAGTGAAAAAAAACAGGTTTCTGTT Y 2 1 2 1 101000 f 74 goat snp19073-scaffold1918-125090 15 14280932 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386449 Affx-122970786 AX-123256807 15 65245950 TCACTACCTCTAAGGGATCCAGGCTCTACTGGGAA[C/T]AGTCAGATTGTGAGACAGTGAGAAGAAAATACCAT Y 2 1 2 1 201000 r 74 goat snp19072-scaffold1918-94534 15 14251614 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277069 Affx-1111835664 AX-519550577 15 65256045 TTCACCATTTTATTTAGAGTGCCCTCCAGAGATGG[A/G]GTTAGGGACGTATTATTCATTTGTTTGGAGTACTT R 2 1 2 1 101000 r 74 goat Random2.2K-1547 15 65256045 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398963 Affx-122960973 AX-123269318 15 65284080 CCAACTGATGACTGACTTAATAGCAAAGAGGAGAA[C/T]AAGTACCAGCTTAACAAAATCAAGGAGCTGCTCAT Y 2 1 2 1 101000 f 74 goat snp19071-scaffold1918-56404 15 14213208 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408434 Affx-122954454 AX-123278785 15 65357136 GTGATGACTATGACTGGATTGAGTCAGATGTATAA[C/T]ACTAGTTAAGAAATGTCTGTTTTTAATAATTTTAT Y 2 1 2 1 101000 f 74 goat snp26162-scaffold2731-174332 15 14138733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416237 Affx-122948214 AX-123286586 15 65393910 GCTAAAAATATACACTATGGACAATAAAAGTTACC[A/G]TTGGAAAATAACTTAGAAACTCAGTTTCCTCAATG R 2 1 2 1 101000 f 74 goat snp26161-scaffold2731-137558 15 14102372 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476314 Affx-1251763821 AX-586011731 15 65411310 AAGTTCAAGGCCAGCTTTTAGATGCTTTTAGTCAA[-/AATTTGTGTGCCGGGGTCCAGCCCCGGTGGATCCAGGGAAGACCTTGTCACGGGCGGGATTCCTCACACTGGCTTCCGGC]ATTTGTGGATTTAAGTGATCTTCCCTTTACATAAT - 8 1 4 1 20000 f 74 goat SV_303 15 65411310 - deletion junction SV-TF-chip 539476567 Affx-1251763821 AX-586011953 15 65411310 AAGTTCAAGGCCAGCTTTTAGATGCTTTTAGTCAA[-/AATTTGTGTGCCGGGGTCCAGCCCCGGTGGATCCAGGGAAGACCTTGTCACGGGCGGGATTCCTCACACTGGCTTCCGGC]ATTTGTGGATTTAAGTGATCTTCCCTTTACATAAT - 4 1 4 1 20000 r 74 goat SV_303 15 65411310 - deletion junction SV-TF-chip 562165416 Affx-1251763821 AX-606940828 15 65411310 AAGTTCAAGGCCAGCTTTTAGATGCTTTTAGTCAA[-/AATTTGTGTGCCGGGGTCCAGCCCCGGTGGATCCAGGGAAGACCTTGTCACGGGCGGGATTCCTCACACTGGCTTCCGGC]ATTTGTGGATTTAAGTGATCTTCCCTTTACATAAT - 8 1 4 1 20100 r 74 goat SV_303 15 65411310 - deletion junction SV-TF-chip 562165503 Affx-1251763821 AX-606940914 15 65411310 AAGTTCAAGGCCAGCTTTTAGATGCTTTTAGTCAA[-/AATTTGTGTGCCGGGGTCCAGCCCCGGTGGATCCAGGGAAGACCTTGTCACGGGCGGGATTCCTCACACTGGCTTCCGGC]ATTTGTGGATTTAAGTGATCTTCCCTTTACATAAT - 8 1 4 1 20100 r 74 goat SV_303 15 65411310 - deletion junction SV-TF-chip 562165768 Affx-1251763821 AX-606941177 15 65411310 AAGTTCAAGGCCAGCTTTTAGATGCTTTTAGTCAA[-/AATTTGTGTGCCGGGGTCCAGCCCCGGTGGATCCAGGGAAGACCTTGTCACGGGCGGGATTCCTCACACTGGCTTCCGGC]ATTTGTGGATTTAAGTGATCTTCCCTTTACATAAT - 8 1 4 1 20100 r 74 goat SV_303 15 65411310 - deletion junction SV-TF-chip 562166118 Affx-1251763821 AX-606941526 15 65411310 AAGTTCAAGGCCAGCTTTTAGATGCTTTTAGTCAA[-/AATTTGTGTGCCGGGGTCCAGCCCCGGTGGATCCAGGGAAGACCTTGTCACGGGCGGGATTCCTCACACTGGCTTCCGGC]ATTTGTGGATTTAAGTGATCTTCCCTTTACATAAT - 8 1 4 1 20100 f 74 goat SV_303 15 65411310 - deletion junction SV-TF-chip 562166296 Affx-1251763821 AX-606941704 15 65411310 AAGTTCAAGGCCAGCTTTTAGATGCTTTTAGTCAA[-/AATTTGTGTGCCGGGGTCCAGCCCCGGTGGATCCAGGGAAGACCTTGTCACGGGCGGGATTCCTCACACTGGCTTCCGGC]ATTTGTGGATTTAAGTGATCTTCCCTTTACATAAT - 8 1 4 1 20100 f 74 goat SV_303 15 65411310 - deletion junction SV-TF-chip 38405471 Affx-122956028 AX-123275823 15 65430782 ATCCTTTTGCCCTATGGAAGCTTTACAATGAAGAA[C/T]GAAGATCATGGCATCTGGTTCCATCACTTCATGGG Y 2 1 2 1 201000 f 74 goat snp26160-scaffold2731-100686 15 14065427 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402444 Affx-122958618 AX-123272797 15 65481897 GCGTTTTTACTCTGTTGATTGTTTCCTTTGCTGTG[C/T]GGAAACTTTTTACTTTGATGCAGTTCTACACATCT Y 2 1 2 1 303000 r 74 goat snp26159-scaffold2731-49571 15 14012913 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781727 Affx-122972945 AX-385268809 15 65525739 CACAAACAAAGGTCTACACTCATATACACAAAGAA[G/T]CATGTATATACACGAGTTCAACTACATGTACACAC K 2 1 2 1 101000 f 74 goat snp26158-scaffold2731-5729 15 13969158 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433815 Affx-122935170 AX-123304156 15 65538758 CTTTACCACTAAGCTACCTGGGAAGCCATTTACTA[C/T]GATAAACTCTTCAAAGAGATGTGCATCAAACCTTG Y 2 1 2 1 303000 r 74 goat snp57965-scaffold939-1278260 15 13956523 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452779 Affx-122920246 AX-123323112 15 65585474 ACACAATCAATTCTTGGGACTTTGCATTGACCACC[A/G]CCATGTTATTCTGGTCTCAGAACCTGAATTAATCC R 2 1 2 1 101000 r 74 goat snp57964-scaffold939-1231544 15 13911096 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777642 Affx-122929137 AX-385264761 15 65655881 AGACAAATACTAAGTGATTCTATTCAGGCTCTTCT[A/G]TCTCCCTCTTCTAATATCAAAGCTTCTTCCCATAT R 2 1 2 1 101000 f 74 goat snp57962-scaffold939-1161137 15 13840245 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414430 Affx-122949960 AX-123284779 15 65690390 GAAAGGACAATGTCAAAATCGATTTGATTTAAAGT[C/T]TGTTATTTCTACTCTGCAAATATATGCTTTCTCAA Y 2 1 2 1 101000 r 74 goat snp57961-scaffold939-1126628 15 13805710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422833 Affx-122943110 AX-123293179 15 65719043 TTCCAGGAGCATGAAGCTGGACAGGTATAGACATG[C/T]AGAAAATCGTAAAATGACTTTTTTTTCTGGCTGGG Y 2 1 2 1 101000 f 74 goat snp57960-scaffold939-1097975 15 13777136 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429565 Affx-122937814 AX-123299907 15 65764005 TATTATTGATGCCAGTGCTTTACTTCCCATGGAGT[C/T]CTCATTCTTTTAGAAATAAAATTAGAGGAAGTAGA Y 2 1 2 1 101000 f 74 goat snp57959-scaffold939-1053013 15 13733577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782656 Affx-122938474 AX-385269729 15 65807455 TTGATGTGAACTAAGAATGGAGATAATTTATAATT[A/C]TGTATGTTTTAATATTCTGAACACTGAATTATAAT M 2 1 2 1 201000 r 74 goat snp57958-scaffold939-1009563 15 13689629 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379610 Affx-122976013 AX-123249968 15 65844836 GGTGCTACTCTGTGCTAGGACACAGGATTTAAACA[C/T]GAAAATAATGGGGCCTCAATCTAGCCATAAGAAAC Y 2 1 2 1 101000 f 74 goat snp57957-scaffold939-972182 15 13651633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453144 Affx-122919996 AX-123323477 15 65879488 GTAGTACTGGACAACAGTAAACAAAGAACACCATT[A/G]CTAATACGGAAAAACCAGTTGCTACTAACATGAGT R 2 1 2 1 101000 r 74 goat snp57956-scaffold939-937530 15 13616947 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423660 Affx-122942342 AX-123294006 15 65969966 TTAACAATTAAAAAAAATAATGTTCAAAAAAGTCA[C/T]AGAAGGTTAAACTTGAGATATATAGGAGACTATTT Y 2 1 2 1 101000 r 74 goat snp57954-scaffold939-847052 15 13527277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384683 Affx-122972125 AX-123255041 15 66085740 TCATGGCATTCTATTGTTGCCAAAATGTCTACAAA[C/T]GTTCATAATATTTTGATTATAACTGAAAAGTCTCA Y 2 1 2 1 101000 f 74 goat snp57951-scaffold939-731278 15 13413427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784523 Affx-122950276 AX-385271572 15 66148867 TATACATATAATTGCATAATTATAAAACATAATTA[C/T]AATTTCAATGATCACATTTTGCATTAGGATGATAC Y 2 1 2 1 303000 f 74 goat snp57950-scaffold939-668151 15 13351279 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778353 Affx-122930753 AX-385265468 15 66177807 CAGATTTTTTCTGTTATTACATTGTGGTAGCATGT[A/G]TTTTCCATATGAAATTCCATTAGAAGGAAATTTCC R 2 1 2 1 101000 f 74 goat snp57949-scaffold939-639211 15 13322661 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413104 Affx-122950389 AX-123283453 15 66208045 CACCCTCTCATTTCTTCCTCTGCCATCCCTGATCT[A/G]GGTTTGCTACAGTGGAGTTTCTTATAAAAGGAAAG R 2 1 2 1 201000 r 74 goat snp57948-scaffold939-608973 15 13292486 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797675 Affx-122937141 AX-385284614 15 66236879 TTCCATAGAGACTTTTATCTCTAGAATTAAGTGAT[A/G]CTGAAGTTTTATGACTCTAATATGGCTAAGGAATA R 2 1 2 1 101000 r 74 goat snp57947-scaffold939-580139 15 13263035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381841 Affx-122974197 AX-123252199 15 66267168 ATGCATATTTATAATATTTATTTTATTCATATTGA[A/G]CATTTGCTTTCCAGAAATATTGTGTCAGTTTTTGC R 2 1 2 1 303000 f 74 goat snp57946-scaffold939-549850 15 13234567 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379567 Affx-122976045 AX-123249925 15 66303962 TGAATTTATCCTCCATTTCTACAAACCCAACAGAA[C/T]AGACAAATGAGAAAGAAGGAGAGAATACCAGACAT Y 2 1 2 1 101000 f 74 goat snp57945-scaffold939-513056 15 13200344 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272796 Affx-1111833054 AX-519546492 15 66308647 TTTCAAAGCAGAGCCCAATTGCCAGGATCACACCC[A/G]GTATGCTTCCTTGCAGTGTCTCAGCACTGAAAGTA R 2 1 2 1 202000 f 74 goat 15_66308647_AF-PAKI 15 66308647 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440049 Affx-122929752 AX-123310386 15 66336315 TTACTTGTTATTTAATGGAGAATTTTAGAACACAT[A/G]TTTTCATACTGTGGAAAATAATACAGAAAGAGTAA R 2 1 2 1 201000 r 74 goat snp57944-scaffold939-480703 15 13167589 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776240 Affx-122928784 AX-385263368 15 66385138 ATGACCCTTTCACTCCTCATACCAATTCTTATTAA[C/T]AAGATAAATAAGAGCAAGCATTTTTATCTATGAAA Y 2 1 2 1 201000 r 74 goat snp57943-scaffold939-431880 15 13118343 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775075 Affx-122930926 AX-385262207 15 66463081 ATATTAACAAATATAAAGGAACCAATGTGAATCCC[A/G]TGAGTGAAATATAAATCTGTACAAATAAAATCTGG R 2 1 2 1 101000 f 74 goat snp57942-scaffold939-353937 15 13039910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407150 Affx-122954850 AX-123277501 15 66531062 AATACCTTAACACACAGTGAATGTTTGTTTTCATC[A/G]TATCATAACCCAGATCAGTGGGGATCTGTTCTACT R 2 1 2 1 201000 f 74 goat snp57941-scaffold939-285956 15 12971887 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776043 Affx-122946738 AX-385263173 15 66575684 AGATTTGGAAAATGAGCCACAAGTACTCGAAAAAA[C/T]GTATTCTCTATTTTTTGACTACAAATTTAATACCT Y 2 1 2 1 202000 r 74 goat snp57940-scaffold939-241334 15 12926995 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394959 Affx-122964280 AX-123265314 15 66637232 TGACATTTTTTTCATATTTTATATATTTCCATTTC[A/G]CATAAAGCCTTATACACTGATATAGACTCCTCTTT R 2 1 2 1 101000 r 74 goat snp57939-scaffold939-179786 15 12865628 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415057 Affx-122949480 AX-123285406 15 66687370 TGAGAGAAAGTCAAATAGCAGATGAGAAATAAGCT[C/T]GGGGAAATATTATCACTCTCCTCTAAGACTGCCAC Y 2 1 2 1 201000 f 74 goat snp57938-scaffold939-129648 15 12815362 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434241 Affx-122934831 AX-123304582 15 66727774 GGATTATGGGGGAGAAATTCAAACATCCCATGGGT[A/C]ATAAAGAATTCCCACTCCTCCAACACTGAGAAATC M 2 1 2 1 101000 f 74 goat snp57937-scaffold939-89244 15 12774406 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797178 Affx-122922535 AX-385284118 15 66767177 TCTTTATTTTCTTTACCCTGATATAGCTGGGCAGC[A/G]AAAGAAGCCTTTCGAGTTGAATTAGTGATTACCTC R 2 1 2 1 101000 f 74 goat snp57936-scaffold939-49841 15 12734316 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773516 Affx-122955397 AX-385260657 15 66805034 CTTTACACTCCATGATTAAGATTCACTGCAGTGAG[C/T]GCTCAACTTGAAAATATGGACCCAAATTTTCCTCT Y 2 1 2 1 101000 f 74 goat snp57935-scaffold939-11984 15 12695097 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426943 Affx-122940420 AX-123297288 15 66835501 CTTTGACTCCCAACTCTTTGTTTCCCTCTCTACAC[A/G]TACTCATTCCTACCCACTGCCTTACTCTCACATTA R 2 1 2 1 201000 r 74 goat snp18502-scaffold187-1560839 15 12565425 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399995 Affx-122960810 AX-123270350 15 66873036 TCTTGTGGTTGTTTACTTACACATGCATCTCCTTC[A/G]TGAAGATCTGTTGTTAGACGTATCATGGAAGACAG R 2 1 2 1 101000 r 74 goat snp18501-scaffold187-1523304 15 12527848 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425128 Affx-122941214 AX-123295474 15 66927703 TTTTGAAGAGATGGTTGAAGGAGAGAAGAGAAGAA[C/T]GAGCTGGGAGATATGAGTTAATGGAAAAAAGGAGA Y 2 1 2 1 101000 r 74 goat snp18500-scaffold187-1468637 15 12477109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398710 Affx-122961848 AX-123269065 15 66962518 GAAAGAAGGGAAAAAGGAAGGAAGGGGAAGGAAGG[C/T]GGAAGGAAGGAAAGAAGAAAGCACTCGTTTAATGT Y 2 1 2 1 103000 f 74 goat snp18499-scaffold187-1433822 15 12441878 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383106 Affx-122973273 AX-123253464 15 67011826 AAATCCTGTGGCATTTGACTGCACAGGCACTGTGA[A/G]GCACCCTTCTATGGCTTGAAGCTGAGTTTAATGGT R 2 1 2 1 101000 f 74 goat snp18498-scaffold187-1384514 15 12385268 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429267 Affx-122937890 AX-123299609 15 67044324 AAATGATAATGGCTGGCTTATTCATTATTCTACCA[C/T]AGAATCTAATACATATTCTAGAACATAGTTGGTGT Y 2 1 2 1 101000 f 74 goat snp18497-scaffold187-1352016 15 12352383 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406944 Affx-122955070 AX-123277295 15 67086322 AAAGCCAATGTACAGTGGCAATTAAATATGACTCA[G/T]CCCACATTAAAACTTTGCAAAGAATTTGCTAAAAT K 2 1 2 1 101000 f 74 goat snp18496-scaffold187-1310018 15 12310377 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423641 Affx-122942357 AX-123293987 15 67137940 CCCAGAGCAATCCCACACCTACTTAAGTTCCAACC[A/G]CATTAACTTTATTTCTGCCCCACAAACACTTTATT R 2 1 2 1 201000 r 74 goat snp18495-scaffold187-1258400 15 12258597 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399692 Affx-122960489 AX-123270047 15 67167355 TAAAGACTTTGGGTTGCAAAGTGTTGAAACCCAGC[A/G]CAGAATCATCTAGAGATATAACTTCAGGCATTCTT R 2 1 2 1 201000 r 74 goat snp18494-scaffold187-1228985 15 12229222 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384184 Affx-122972410 AX-123254542 15 67205186 ATCATTAAGTGACCAAGTAAAATTTACTTTTCCAA[C/T]GAACCAAGTGTTCAATAGTACACATGACAGAGCTG Y 2 1 2 1 201000 f 74 goat snp18493-scaffold187-1191154 15 12191023 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431978 Affx-122935950 AX-123302319 15 67271942 TTAAAAGATAAGGTCATCTTCTGTTAGTAAAGTTC[A/G]TTCATTTCCTCGCTTTCATTTATTCCACCATGGCC R 2 1 2 1 101000 r 74 goat snp18492-scaffold187-1124398 15 12123727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429683 Affx-122937643 AX-123300024 15 67332237 TGAGTAAGCGTGCCCCACATCATTACTGATTTTTT[A/G]TAATTGCAAGGAATATCATCTCCATATTTCAAAAT R 2 1 2 1 201000 r 74 goat snp18491-scaffold187-1064103 15 12063070 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380027 Affx-122975589 AX-123250385 15 67376717 ATACAGGAGGGGAGAGGGGGACACACATTACTTAC[A/G]CCACATTTTACACAACTTCATTTAATCTGCAAAAT R 2 1 2 1 201000 r 74 goat snp18490-scaffold187-1019623 15 12021073 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779010 Affx-122924726 AX-385266117 15 67409207 TACCTTACAGTTGTATAACTCCAGGCTTTGTAGGA[A/G]TTCCCTCTTCTGTTAGAGACTTGTCAGTTTCTACT R 2 1 2 1 101000 f 74 goat snp18489-scaffold187-987133 15 11987453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763277 Affx-986697806 AX-385251192 15 67421477 ATACCATTTATATGAATGGCTAAAGACGATGTAGT[A/G]TGTATGTGTGTGTGTGTGTGTGTGTGTATAAAGAA R 2 1 2 1 600010 f 74 goat 15_67421477 15 67421477 Ancestral_priority_1043 ancestry 0.696 recommended IMAGE 10K 10K ancestral 38394200 Affx-122964910 AX-123264555 15 67438858 TGTAAAGACCCCTGAAAGGCTCAAATGCATCTGTT[A/G]TAGACACTATGGTGTTAGGGAGAGCCCCCAGACAA R 2 1 2 1 201000 r 74 goat snp18488-scaffold187-957482 15 11957747 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427642 Affx-122939335 AX-123297985 15 67475260 GAGGAGGAAGCAAAGATATAAGCCAGCTTGATTTG[A/C]TTGGAAAGCCAGTGCCCTTTCTGATGTCCCTCCCT M 2 1 2 1 202000 r 74 goat snp18487-scaffold187-921080 15 11921217 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405276 Affx-122956860 AX-123275628 15 67547326 GCCACAGGAAAGGAGAGCAAGGTGTCTAGCCTCAC[A/G]TGGTCATGAGTATGCAGTAGGAGCTTGAGGAAGTT R 2 1 2 1 101000 r 74 goat snp18486-scaffold187-849014 15 11847783 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796954 Affx-122953874 AX-385283895 15 67577635 AAGTGATAATTTCATGGAGTATTTAGTCTGTATCC[A/G]TTATTGTCAACTCAGTAACAAGGAAATATATATAA R 2 1 2 1 101000 f 74 goat snp18485-scaffold187-818705 15 11817487 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442112 Affx-122928349 AX-123312449 15 67610954 CATATGCCAGAGACATACACTCCTGTATAGCATAG[C/T]GCCCACCTACCACCAGCCCATTTACTACAGCCCCC Y 2 1 2 1 101000 f 74 goat snp18484-scaffold187-785386 15 11783575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781752 Affx-122966947 AX-385268834 15 67655449 TTAATTATTTTCATTTTTTCTAGCACAAGAAATGG[C/T]ATTTTTCTGTGGTGATAGTAAGTTTGTGTAAATAT Y 2 1 2 1 101000 f 74 goat snp18483-scaffold187-740891 15 11738905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407592 Affx-122954656 AX-123277943 15 67688543 TCCCCACCCCCAGTTGAAGCCCATTTCAAATGATG[C/T]AACAGACCCTATCTGTCTGTATAATGTCTCTGATG Y 2 1 2 1 101000 r 74 goat snp18482-scaffold187-707797 15 11705189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392578 Affx-122966070 AX-123262935 15 67724513 AGGTGGGAAGAGAGAAATGGAGTGATCTGAGGGCT[A/C]GCCCAGAGATGAAAGCTGATTTTAGTGATAGATGC M 2 1 2 1 201000 r 74 goat snp18481-scaffold187-671827 15 11668443 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438229 Affx-122931439 AX-123308567 15 67754386 CGGTAGGTGTTCTTGGCTCTTTATAACCATAGTCT[C/T]CCCCAGACAACTAACTCCCTGCTTACTATTTACCT Y 2 1 2 1 101000 f 74 goat snp18480-scaffold187-641954 15 11638657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426850 Affx-122940495 AX-123297195 15 67791917 AGAAGGCACAACATAGTTCTGTAAACTTTGTGATT[A/G]TTACTTCCTTCTAGTAGACACAATGGCCATGAAGT R 2 1 2 1 101000 r 74 goat snp18479-scaffold187-604423 15 11601138 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453595 Affx-122920144 AX-123323928 15 67821978 GGTTATCAGTAACACAGTAGTCCTTGATGGAATGT[C/T]AATGAACACAATGATATTTTATTACACTATAGTAA Y 2 1 2 1 101000 f 74 goat snp18478-scaffold187-574362 15 11571178 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774782 Affx-122934075 AX-385261916 15 67876820 ATGTTTGAAAGCTGACAAAAACGATAGACAAAACT[A/G]TTGGAAGTTACCTAGTTTATCTTGCCACATGCTGT R 2 1 2 1 101000 r 74 goat snp18477-scaffold187-519520 15 11516225 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428557 Affx-122938726 AX-123298899 15 67931820 TAATTGTCAGATTTCTGTGGTTTGCCATCTAATCA[C/T]ATGGTAGTGGACACAAGTACTGGTTAAGCGTAGCA Y 2 1 2 1 101000 r 74 goat snp18476-scaffold187-464520 15 11461303 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416632 Affx-122947618 AX-123286980 15 67963464 GAGGCTCACAGAGAATTCATAACTTGTCCAAGATC[A/G]TCTAACATCAAGTAATCAAGAGTGAATGACCCCGC R 2 1 2 1 201000 r 74 goat snp18475-scaffold187-432876 15 11430000 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379271 Affx-122976244 AX-123249630 15 68000068 GCAGAAGCAAAAAGAGGTGGTAAGATGCTATGTCA[G/T]AAAGAGTTATCTGGATTTCACTCTGAATAGGATAG K 2 1 2 1 101000 f 74 goat snp18474-scaffold187-396272 15 11392352 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393860 Affx-122965143 AX-123264215 15 68057901 AATAAAGACAAAGAATTGCATACTAAAATTGATGC[A/G]TAGAAAGATGGGAAGTCCCTGGGGTCCTGATGACA R 2 1 2 1 201000 f 74 goat snp18473-scaffold187-338439 15 11335250 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425182 Affx-122941047 AX-123295528 15 68095609 TTAGATGGATAGATTATGCTTCTTTGTTACAAGTG[A/G]TAGAAACCAAGTTTGGTCTCATTAATCAATAGCTT R 2 1 2 1 101000 r 74 goat snp18472-scaffold187-300731 15 11297620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765256 Affx-122966670 AX-385252792 15 68127738 ATTGTGGCTATCTACAAATGGGCTTATCTGCAGAG[C/T]AATGAGCTTCTCATGAAACCCAGCTGAATTTTAGA Y 2 1 2 1 101000 f 74 goat snp18471-scaffold187-268602 15 11265568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792875 Affx-122968922 AX-385279853 15 68225414 TAATATATATGAGCAAAAATGTCTGCATTTTAAGT[A/G]TTTGACAGTGAACTATTCCAGTATGGGAGATTTAA R 2 1 2 1 101000 r 74 goat snp18469-scaffold187-170926 15 11167799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438702 Affx-122930859 AX-123309039 15 68257777 TTCACCAAGCTCCTGCTATCACCAGCCTGAGATAC[A/G]AAGTTCTGTCCTGAGATATAAAGTCGAACCCCTCT R 2 1 2 1 101000 r 74 goat snp18468-scaffold187-138563 15 11135160 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797548 Affx-122954003 AX-385284487 15 68288996 CCAGTCCTTTTTTTTCTAATTCAAGACAGCATCTT[A/G]TCATAGAGGTAAAAGTGAGAGTGATGTTTTTTACA R 2 1 2 1 101000 f 74 goat snp18467-scaffold187-107344 15 11104013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275193 Affx-1111834646 AX-519548772 15 68309932 ACATGGCCAAACCTCACTGCAGGCACCACCTTCTT[A/G]CGTGAGCACCTGTGACAACATATTGGAAACAGGCT R 2 1 2 1 201000 r 74 goat GoatD01.044376 15 68309932 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320776561 Affx-122964145 AX-385263688 15 68322719 AGCTTAATGAATATTTGTTCAGATCTGGTCTCAAA[C/T]GTGATAGGACATGCATCATCTGGCCAGATGTTGGA Y 2 1 2 1 201000 f 74 goat snp18466-scaffold187-73621 15 11067530 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440052 Affx-122929749 AX-123310389 15 68352066 AGTCATAGCAACAAAGTCAACTTTAATATTCTATG[A/C]TATTGGATCAGTATGGGGAGGAGCACATTGATGGT M 2 1 2 1 201000 f 74 goat snp18465-scaffold187-44274 15 11038108 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795212 Affx-122930123 AX-385282170 15 68391778 TTGTATTCAGAGGAATAGTGTCTTGTTACTATTAC[A/G]TTGCCATATTTGCTCTCCAGTCTGATGTGGCTTAG R 2 1 2 1 101000 r 74 goat snp18464-scaffold187-4562 15 10998377 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433569 Affx-122934975 AX-123303910 15 68402886 GTATCCTCCTTTTAGTAGCAAAAGTAGGAAGCTCC[A/G]TTATACGATATGAATGTTAATCTCCAAATCACTCT R 2 1 2 1 201000 r 74 goat snp50632-scaffold728-841977 15 10987310 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452470 Affx-122921003 AX-123322803 15 68438643 AAAGGCAAATACAGTCCTTTGTCGCACTTGTAATG[A/G]GCTATGAAACAATTCATAAAGAAGTGGAATTTGGC R 2 1 2 1 101000 f 74 goat snp50631-scaffold728-806220 15 10950867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375400 Affx-122979208 AX-123245759 15 68478005 CTGTGATAAGAAGAAGAAAGGGAAGTTTACAGGAG[C/T]AACCCTGAAGAGTGTGCTTTTAATAATACCCTGTT Y 2 1 2 1 201000 r 74 goat snp50630-scaffold728-766858 15 10911458 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448499 Affx-122923461 AX-123318835 15 68507269 CAAGTAAGTAGACATGGTGAGCTTCCACGCTCCAC[A/G]TGGGAATTCAGCCAGAAAAGAAGAGAACAAGAAAA R 2 1 2 1 303000 f 74 goat snp50629-scaffold728-737594 15 10885714 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774775 Affx-122942259 AX-385261909 15 68538501 TCAACTCCACATTCCTATCTCACTTCTGAAAAAGT[A/G]TTTCTAAATTCGAGTGATTGAGAAACAATTCTGGG R 2 1 2 1 202000 r 74 goat snp50628-scaffold728-706362 15 10854315 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410148 Affx-122952798 AX-123280498 15 68586480 GTAACTATTAAGGAAAACTTAAGATTCTTATAGAG[C/T]GTCAGGAAATCAAATAAACAGCAACAGGGACTGAT Y 2 1 2 1 201000 f 74 goat snp50627-scaffold728-658383 15 10806623 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796078 Affx-122959574 AX-385283030 15 68631422 AAATCCAGAAACTCATCAACTCAAGGATATTAGGT[A/G]TCTGCACTTCTTAATCCAGAACTCTTGTTCTAAAT R 2 1 2 1 101000 f 74 goat snp50626-scaffold728-613441 15 10761886 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463419617 Affx-1109972846 AX-514903268 15 68635611 GTGCATGGTGTAGACAGTTCCCACTGTCTTTCTTC[A/G]GTGTGTGGTATCTCATTTCCTTGGCATCATTTATT R 2 1 2 1 201000 r 74 goat Random2.2K-1548 15 68635611 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38385352 Affx-122971648 AX-123255710 15 68699260 TTAAGTATTATCCCTGTTTGACAGAATGGGAAACA[C/T]AAGCTGAGGCGGGAAGTAGCAGATTGAGAATTCAA Y 2 1 2 1 101000 r 74 goat snp50624-scaffold728-545603 15 10692521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776310 Affx-122927741 AX-385263438 15 68771403 CATATTTCTTAGATGTCAAAGAATATGCAGTCTCC[A/G]CAAGGTGATGAAACTAAATTTGAATCAAATGAAGA R 2 1 2 1 101000 f 74 goat snp50622-scaffold728-473460 15 10619806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476315 Affx-1251763822 AX-586011732 15 68819984 ATATAAACTGCTCTAAATTTATCTCTTTATTTTGG[-/GCACATGATGCTCTTCTTTTTTTTTTTTAATTGGGGAAATGATCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTC]CACATGATGCTCTTCTAAGTCATGTTTTTTAATTC - 8 1 4 1 20000 f 74 goat SV_316 15 68819984 - deletion junction SV-TF-chip 539476568 Affx-1251763822 AX-586011954 15 68819984 ATATAAACTGCTCTAAATTTATCTCTTTATTTTGG[-/GCACATGATGCTCTTCTTTTTTTTTTTTAATTGGGGAAATGATCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTC]CACATGATGCTCTTCTAAGTCATGTTTTTTAATTC - 8 1 4 1 20000 r 74 goat SV_316 15 68819984 - deletion junction SV-TF-chip 562165476 Affx-1251763822 AX-606940887 15 68819984 ATATAAACTGCTCTAAATTTATCTCTTTATTTTGG[-/GCACATGATGCTCTTCTTTTTTTTTTTTAATTGGGGAAATGATCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTC]CACATGATGCTCTTCTAAGTCATGTTTTTTAATTC - 8 1 4 1 20100 r 74 goat SV_316 15 68819984 - deletion junction SV-TF-chip 562165543 Affx-1251763822 AX-606940954 15 68819984 ATATAAACTGCTCTAAATTTATCTCTTTATTTTGG[-/GCACATGATGCTCTTCTTTTTTTTTTTTAATTGGGGAAATGATCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTC]CACATGATGCTCTTCTAAGTCATGTTTTTTAATTC - 8 1 4 1 20100 r 74 goat SV_316 15 68819984 - deletion junction SV-TF-chip 562165878 Affx-1251763822 AX-606941287 15 68819984 ATATAAACTGCTCTAAATTTATCTCTTTATTTTGG[-/GCACATGATGCTCTTCTTTTTTTTTTTTAATTGGGGAAATGATCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTC]CACATGATGCTCTTCTAAGTCATGTTTTTTAATTC - 8 1 4 1 20100 f 74 goat SV_316 15 68819984 - deletion junction SV-TF-chip 562165912 Affx-1251763822 AX-606941321 15 68819984 ATATAAACTGCTCTAAATTTATCTCTTTATTTTGG[-/GCACATGATGCTCTTCTTTTTTTTTTTTAATTGGGGAAATGATCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTC]CACATGATGCTCTTCTAAGTCATGTTTTTTAATTC - 8 1 4 1 20100 f 74 goat SV_316 15 68819984 - deletion junction SV-TF-chip 562166336 Affx-1251763822 AX-606941744 15 68819984 ATATAAACTGCTCTAAATTTATCTCTTTATTTTGG[-/GCACATGATGCTCTTCTTTTTTTTTTTTAATTGGGGAAATGATCTTCCCGTCCTATTCCTCCACCATCTTTCCCTCTCTC]CACATGATGCTCTTCTAAGTCATGTTTTTTAATTC - 8 1 4 1 20100 r 74 goat SV_316 15 68819984 - deletion junction SV-TF-chip 320802748 Affx-122941226 AX-385289647 15 68825416 ACTCAAAATTGTCTCATTCCAGAACCATAACCCAC[A/G]TCTTAATTGATCATCTACCTTAATTTCCTAAATAT R 2 1 2 1 101000 f 74 goat snp50621-scaffold728-419447 15 10565255 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444216 Affx-122927245 AX-123314553 15 68856271 TTGAGTAGCAGCAACTGCGGCTTATAAATGTTGCC[A/G]TTCTGTAACTCCCTGAAAGACTTGCTGATCGTGTG R 2 1 2 1 101000 f 74 goat snp50620-scaffold728-388592 15 10534250 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792882 Affx-122927293 AX-385279859 15 68898661 ATTCATTCTAAAACTTGACTACTAATTAAAATCTA[A/G]CATTTGCTTAATGTGGATGGGTTGATAATTAAAGG R 2 1 2 1 201000 f 74 goat snp50619-scaffold728-346202 15 10491973 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426768 Affx-122940559 AX-123297114 15 68961392 CACTGCTGTGAGCCTGACACAGCCACGTGTCTTCC[A/G]TTATCTCCCTATCCCTTTCTTTTGGAGTGAAAATA R 2 1 2 1 101000 r 74 goat snp50617-scaffold728-283471 15 10429208 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437898 Affx-122931663 AX-123308236 15 68995535 TTAGGTGTACGATTCTTTCTATCATCATTCTGATT[A/G]TTATTATCATTATTCACATCCTATTAGCTTTTCAC R 2 1 2 1 101000 r 74 goat snp50616-scaffold728-249328 15 10395045 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401334 Affx-122959267 AX-123271687 15 69035215 ATTAATTTTGCTTAGTGTCTGTGAAATGAAGAGAC[A/G]TTAACAGTGGTTCAGAGAAGCTCTTAGCTAAGGAA R 2 1 2 1 202000 f 74 goat snp50615-scaffold728-209648 15 10355682 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407794 Affx-122954566 AX-123278145 15 69094983 TTCTTAGAACACAAAAGGGGTTGGGTTTCTTAACC[A/G]TCACAGTTTTCCAGGAGCACAGAGCTTAGGTAAAG R 2 1 2 1 101000 f 74 goat snp50614-scaffold728-149880 15 10295718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378144 Affx-122976980 AX-123248503 15 69127989 TTGCAGTTATTTTGATGATTTAATGCGATAATTAA[C/T]GCAGGTGCCTGGCACATTATAGGCTGTTCATAAAT Y 2 1 2 1 201000 f 74 goat snp50613-scaffold728-116874 15 10262615 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277071 Affx-1111835665 AX-519550578 15 69159984 GCTAGATTTTATTTCTAGGATATTCAATTATCAAA[A/G]AGCAATATGTAAAACTTGAACTTATATACTGCTAC R 2 1 2 1 101000 r 74 goat Random2.2K-1550 15 69159984 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38385694 Affx-122971123 AX-123256052 15 69182969 ACTAAGTGGTTTATAAGCATTATCTAATTTGATCC[A/G]TACAATCACTCTATAGAATTCATTTATTTACTTAA R 2 1 2 1 101000 f 74 goat snp50612-scaffold728-61894 15 10209496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417634 Affx-122946855 AX-123287982 15 69226230 TTAATAAATGGTATGATTTCCCCATAAAATATTTC[A/G]TTTACTCTAAATCCTACCTGAAGTACCAGACTCAA R 2 1 2 1 101000 r 74 goat snp50611-scaffold728-18633 15 10168488 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386942 Affx-122969990 AX-123257300 15 69268239 TCTCGCTATAAAGATGAAGAAACTGAGGATGAGAG[C/T]GGTTAACTAACTCACCCAGGTCACGTGGCTACTAG Y 2 1 2 1 201000 r 74 goat snp21404-scaffold2088-101629 15 10126920 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379687 Affx-122975912 AX-123250045 15 69304921 TAAGATATGCTTTCTAGTTGCTACCAATTGGACTC[A/G]CTAACGGGTTGAATGTAGGAGCTGAGGAAAAAAGG R 2 1 2 1 201000 f 74 goat snp21403-scaffold2088-64947 15 10090115 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793037 Affx-122963716 AX-385280015 15 69340003 CAGTGGTGATGTGCCATAACACATTTTAGGAAGAA[C/T]GTGTGGGATAGTGTATAGAGTGGTATGATCACCTT Y 2 1 2 1 201000 r 74 goat snp21402-scaffold2088-29865 15 10054944 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389147 Affx-122968542 AX-123259505 15 69378206 GCCTTTCTTTACTTGCCCCACCCTTCCTGTCAGGC[A/G]TGCAGTTCTGATGTCTAGAAGGGCAGGAGCCATCT R 2 1 2 1 201000 r 74 goat snp22049-scaffold2172-8239 15 9882771 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447883 Affx-122923823 AX-123318219 15 69417519 CAAGTGTTTCTTTCTTGTTCTGCCCCTTCCAGGTA[C/T]GGAACCAAGACCTCCCATATCCAGGCAAGAGGGGA Y 2 1 2 1 102000 f 74 goat snp22050-scaffold2172-47552 15 9843527 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438888 Affx-122930735 AX-123309225 15 69472400 GGGAAAGGAGGCTACCCTTGCTACTCCTAAGTCTA[C/T]GACCAAGTCTGCTGCAGCTTTTAAGGGCACACAAA Y 2 1 2 1 101000 f 74 goat snp22051-scaffold2172-102433 15 9788662 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382861 Affx-122973525 AX-123253219 15 69504987 TCAGAAGAAGCCTTGGAGTGCTTCTTAAGGGAAAG[C/T]CATCTCTTGTGAGTAAGGCATAGGTCCCAGTCGAA Y 2 1 2 1 101000 f 74 goat snp22052-scaffold2172-135020 15 9755045 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442094 Affx-122928361 AX-123312431 15 69546391 CCTAAGAGAGAATTTCTGTTTTATTTGTCCTAATG[C/T]CTCCTTAAATGCACTTGCCAAGTATGACCAGAGTT Y 2 1 2 1 101000 r 74 goat snp22053-scaffold2172-176424 15 9713428 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320775562 Affx-122939633 AX-385262693 15 69577512 AGGATCCAAAGAGATAATGGATGAAGCAGTCCTTG[A/C]TTCCACATCAGTTCTCCAATAAAAGAAGGTGAATT M 2 1 2 1 101000 f 74 goat snp22054-scaffold2172-207545 15 9682178 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432981 Affx-122935267 AX-123303322 15 69625759 TAAAATAAAATAATAAAAGATAGACATTTGTAATC[A/G]TCAGGCAGCAGTTAAGAGCTCCTTCCTTAGCTGCA R 2 1 2 1 101000 r 74 goat snp22055-scaffold2172-255792 15 9633655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802071 Affx-122930679 AX-385288975 15 69658293 TTCCAGTTAGGATGCTTGTAAACACACCACGTTAA[C/T]GCGTTCAAATGTTAATGGCAGCAGCTTTGTGGAGA Y 2 1 2 1 101000 r 74 goat snp22056-scaffold2172-288326 15 9600706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774854 Affx-122971917 AX-385261988 15 69689750 CCCCAGATCACTTTCCTATTTTTATACAAACACTT[A/C]ACACTATATTGAGTACCTAATGTAGTGGATGAGAT M 2 1 2 1 101000 f 74 goat snp22057-scaffold2172-319783 15 9569306 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784970 Affx-122920641 AX-385272017 15 69733923 CAGGAGGTTATGGTGCAGATGGGTCACTGAACATT[A/G]TGAGAAATTCAGTTTTAGATCTTGCTCTTCCTTTG R 2 1 2 1 101000 r 74 goat snp22058-scaffold2172-363956 15 9524866 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444514 Affx-122926502 AX-123314851 15 69764113 ATGCAAGCCAGACACACCCTGGGAACAAAAAATCC[A/G]CACTTTTCAGCTAACACTGGCAGAAAGACTACATG R 2 1 2 1 101000 r 74 goat snp22059-scaffold2172-394146 15 9494821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391784 Affx-122967453 AX-123262141 15 69816938 TAAGAATTAATAAAACTGATAATGCATAATTGACT[C/T]CATTTCCCACTTTGGTGAGGTCTACTAGACTAGAA Y 2 1 2 1 101000 r 74 goat snp22060-scaffold2172-446971 15 9441632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786188 Affx-122940826 AX-385273223 15 69840742 CACTTTTAAACATTGCTGGTAGGACTGTAACTTGT[C/T]GTAAAACCTTTAGGAAGCAATTTGACTTTCTCTTG Y 2 1 2 1 101000 f 74 goat snp13922-scaffold1544-23083 15 9417384 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409773 Affx-122952986 AX-123280124 15 69875064 GAATGTACTGCACAATCTGTTCTCTTTGATGGACT[A/G]TAAATACGTTTGGTAAAGAATCCACCTGCCAAGGA R 2 1 2 1 201000 f 74 goat snp13923-scaffold1544-57405 15 9382750 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399409 Affx-122961240 AX-123269764 15 69944871 CTCCCCACTTGGTGATGAGACACAGGACAGCCAGA[G/T]ATCCAGTGCTTGGGCATGGTCCTTGATGGCTTAGC K 2 1 2 1 101000 r 74 goat snp13924-scaffold1544-127212 15 9314277 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798400 Affx-122950959 AX-385285334 15 70020936 AATCCCTTTGGGGAGGTGGGGGAATAGGTAAAATA[C/T]AGTGGAAACACATGTATAGTACTGTGCATTACACA Y 2 1 2 1 102000 f 74 goat snp13925-scaffold1544-203277 15 9238241 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421988 Affx-122943791 AX-123292335 15 70080316 TGGCTCTTTCTTTATTTAGTTTTTATTTTGTCTCT[A/G]TTGTCTTTGAAATCTGAGTAGAAGGTTCCAGGGAA R 2 1 2 1 101000 r 74 goat snp13926-scaffold1544-262657 15 9179052 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408884 Affx-122953982 AX-123279235 15 70122890 GAGTTCTCTTCATTCCAGTCCAGGAAACCTAACTG[A/G]GCAGTAAGCTAGGGCAACCGTAAGGGTCACTTTAT R 2 1 2 1 101000 f 74 goat snp13927-scaffold1544-305231 15 9136192 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802358 Affx-122951233 AX-385289262 15 70162568 TTGCAATGAGTTTACTTTTTCCAAAAGATTCTCAC[C/T]GTTGTGCAAGTTTATGGAAATAACATTTGAGAGCA Y 2 1 2 1 101000 f 74 goat snp13928-scaffold1544-344909 15 9096546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780069 Affx-122972730 AX-385267167 15 70212212 ACTAAAATACGCTTTCCTCTAATACAGATGTCCTC[C/T]CAGTTTAATCGTGTGTAAACACTGAATGCCCTGTG Y 2 1 2 1 101000 f 74 goat snp13929-scaffold1544-394553 15 9046514 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411463 Affx-122951807 AX-123281813 15 70241601 GAAGCTTCTAGAACTTGTTTTTTTCTGATTCTGTT[C/T]GGCATCTGTTCTTTCCATCATCTTTTTGTTGTCAC Y 2 1 2 1 101000 r 74 goat snp13930-scaffold1544-423942 15 9016826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379912 Affx-122975756 AX-123250270 15 70278507 GGGGCAGCCCTTGGAGGACTGGTATGGATGTTCTC[C/T]CATGTCGCACCAGCCAGGTGACTGGGTATGTGGAG Y 2 1 2 1 201000 f 74 goat snp13931-scaffold1544-460848 15 8980038 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388851 Affx-122968877 AX-123259209 15 70308598 GAACTGATATGGAAAAGTCCTTGAGATATATTTTT[A/G]TGTAAAAGAAGCAAGGTGAGGAACAGCACATCTGT R 2 1 2 1 101000 r 74 goat snp13932-scaffold1544-490939 15 8949874 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443353 Affx-122927423 AX-123313690 15 70375608 GGGGAGTTTGTTCATTGAGTGCAAGAGTTTAGAAG[A/G]TGGGCTTGGGGTCAGCCACAGGAGTTTCTTGTTTT R 2 1 2 1 201000 f 74 goat snp13933-scaffold1544-557949 15 8884087 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783791 Affx-122942993 AX-385270847 15 70411529 TTCCTTATGAGACCCGCTGGGCCAGATATTCTCCA[A/G]GAGACCTAACTCTTTGATAATGTCTATGGAAACTG R 2 1 2 1 101000 f 74 goat snp13934-scaffold1544-593870 15 8848482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428549 Affx-122938731 AX-123298891 15 70454915 ATTAGGGAATAACAAGAGCTTTGGCAGATGAAGGG[C/T]GAAAAGTAATGGCAGAAGAAAGGAGAAAAATGATT Y 2 1 2 1 101000 f 74 goat snp30378-scaffold334-1410199 15 8804953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376550 Affx-122977984 AX-123246909 15 70490366 TGGGCAGAATTTGCTCCTTTTTACCTCCCTGGTGT[C/T]TTCTTAGCCTTTTATAAATCCATAAAAGATGATAC Y 2 1 2 1 103000 f 74 goat snp30377-scaffold334-1374748 15 8769620 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770660 Affx-122972137 AX-385257824 15 70535391 GAGCTTCCCATCAGTTTTCAGCGGCTCACTCAAAT[A/G]CGAATAGACTGCTGAAAAACATCAGGTATTTGAAG R 2 1 2 1 101000 f 74 goat snp30376-scaffold334-1329723 15 8724565 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449481 Affx-122922639 AX-123319816 15 70565795 ATAACTGTGACAAAGAAGTAGTTCTGGGCTCCCAC[A/G]TAACCCCCTAGGACATAAATTTTTATTAACTGATT R 2 1 2 1 101000 f 74 goat snp30375-scaffold334-1299319 15 8694124 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396210 Affx-122963358 AX-123266565 15 70681226 CAAGCGCCCTTGGTTATCAGTCTCTCCTTGCGTCT[C/T]GGGCATCCAGGGTTACTCAACAAGTGCTTGTCTCC Y 2 1 2 1 101000 r 74 goat snp30373-scaffold334-1183888 15 8580018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783032 Affx-122926397 AX-385270100 15 70767538 AAAGTTCATATGTCTCATCCTGAGAACCAGATACA[C/T]GTCTTTCCATTTGGCAGATGAGAATAAAACAGAAG Y 2 1 2 1 101000 r 74 goat snp30372-scaffold334-1097576 15 8493447 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398466 Affx-122961587 AX-123268821 15 70805258 TGAGTCAAATCCATGTATTTACTTTTTTCCACACA[C/T]CGGGGATGCCCACTCAAAATGGGGAGCTGAGTCGG Y 2 1 2 1 101000 f 74 goat snp30371-scaffold334-1059856 15 8455796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409451 Affx-122954083 AX-123279802 15 70842846 ATTTATACTTCTACCAGCAATGAACAAAGAGGCCC[A/G]TTTCCCTACCTCCTAGTCAGCTTGGAGTATTTGAT R 2 1 2 1 101000 r 74 goat snp30370-scaffold334-1022268 15 8418409 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446802 Affx-122925295 AX-123317138 15 70886345 CTACGCTCAGAGCATTTAGCAGAGTGTCATACTTA[C/T]GAGCTGCCACCAGGTGTCGCCCTTGTCTCTGAAAT Y 2 1 2 1 101000 f 74 goat snp30369-scaffold334-978769 15 8375391 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407620 Affx-122954634 AX-123277971 15 70923926 CCTGGTGAGGTTTACATGATTTCGTATCTGTAAAG[C/T]GCCTGGCACCCAGTATGTGTCTAATAAATGCCACC Y 2 1 2 1 101000 f 74 goat snp30368-scaffold334-941188 15 8337960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377280 Affx-122978125 AX-123247639 15 70974519 CGCAATCCAACTTCTCAGTGACCCACAGTTGATCA[A/G]GTTCATGGAAGCTGATTCACACTTAGTGTGAATGA R 2 1 2 1 101000 r 74 goat snp30367-scaffold334-890595 15 8287092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413555 Affx-122950600 AX-123283904 15 71013858 GCCTGGACTGTGTACGGCAGGTTGGCTAAGCCTGT[A/G]GGCTCTGGACCCAGCTTGCCTGTGTTCAAATTGTG R 2 1 2 1 201000 f 74 goat snp30366-scaffold334-851256 15 8247584 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802018 Affx-122931812 AX-385288922 15 71045756 TAGACTCCTAATCTTTAACAGGAGGAATGTACACC[A/G]TATGACAGGCATTGTGATAAGGCTGTTAAAGCACC R 2 1 2 1 101000 f 74 goat snp30365-scaffold334-819358 15 8216285 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38448046 Affx-122923703 AX-123318382 15 71081929 AGTCTTCCTGGAAGAGGCAGCAAGAAAAGGAGAGA[C/T]GGAAGAAGGTGATCAGCTCAATGATGAGCCTTTTC Y 2 1 2 1 101000 r 74 goat snp30364-scaffold334-783185 15 8180022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409670 Affx-122953507 AX-123280021 15 71110802 TACTATGAGTATGCTCTGGAATAAATGATGGGTAG[A/C]TTAATAAGCGAATGGATGGATGGATAGATGGCTGG M 2 1 2 1 101000 f 74 goat snp30363-scaffold334-754312 15 8151401 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447078 Affx-122924499 AX-123317414 15 71143260 CTCTTCAAACAGTGTGGCTGGAAACCCTCTGGAAA[C/T]GGCTCCCACGGGTAGTGCTCCTGCTGCGGATTTCA Y 2 1 2 1 101000 f 74 goat snp30362-scaffold334-721854 15 8119040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438274 Affx-122931406 AX-123308612 15 71187981 TAAGCTTACTACATGTCCTGTTCTAAGGGCTTTTC[A/G]TATATTACTTCATTTTATCTTCACCAGAAACCCAA R 2 1 2 1 201000 r 74 goat snp30361-scaffold334-677133 15 8075189 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435861 Affx-122932802 AX-123306200 15 71242072 CTTTACAGTGAGATGATTACTTCCTGTGAGATTAT[G/T]ACTTCTTATGTGCTTGCTGCTTGCTTATCATCTGC K 2 1 2 1 101000 r 74 goat snp30360-scaffold334-623042 15 8021151 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387319 Affx-122970506 AX-123257677 15 71271722 GAAGTAGAATTTCCTTGTCTGAAAATAATAGCAAC[A/G]TGATTTTTGAGCGTTCACCAGAGATCAGCACTGTT R 2 1 2 1 101000 r 74 goat snp30359-scaffold334-593392 15 7991621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422455 Affx-122943342 AX-123292801 15 71326212 TGTGTTCCCTCCTGGCCCACTCATAACGCTCCAGC[A/G]CTGTCACAGACTCATTCTAGACAGAAATGGCATCA R 2 1 2 1 101000 r 74 goat snp30358-scaffold334-538902 15 7937202 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405421 Affx-122956275 AX-123275773 15 71363070 ACACTGTCTTGGCCTCTGCTAAATGCCACCTAGAG[C/T]GGAACCTCTCGAATTCTCTGGGATTAATCAGGCTG Y 2 1 2 1 101000 r 74 goat snp30357-scaffold334-502044 15 7900386 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277073 Affx-1111835666 AX-519550580 15 71378411 AGTGCCTCTTTAATCTCAAATGAAGGAAACAGATA[A/G]ACAAACACATTCTACAGAGCAGCAAGGCTTCTAGC R 2 1 2 1 101000 r 74 goat Random2.2K-1552 15 71378411 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38410549 Affx-122952150 AX-123280899 15 71462586 CCCAAGCGTGTTTGGCTTTGAACACAAGCCCGTTG[A/G]GGCAGTGTGTCTGAAGGTATGGTCAGGTCACCTTT R 2 1 2 1 201000 f 74 goat snp30355-scaffold334-402528 15 7801390 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783361 Affx-122975304 AX-385270425 15 71517399 ACTATTAGTCTATGTTGTTCTTTTGTGGGTAATCC[A/G]TCTACAGTAAATTCTAAGACTTCCTTTTTATGCTT R 2 1 2 1 101000 f 74 goat snp30354-scaffold334-347715 15 7747492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416927 Affx-122948044 AX-123287275 15 71564842 TCACTCCCCATCTGCTGCGATCTCTTCTTTGCCTC[A/G]TTTTCCTCTCTTTCCCAGGCTCAGAAAATTGATGA R 2 1 2 1 101000 f 74 goat snp30353-scaffold334-300272 15 7699846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421277 Affx-122944740 AX-123291624 15 71612401 AGGGAAGCACAGGGCAAACTAGAGGGAGAGATGAG[C/T]GACTTCAAGGTCAGTGTTTCCCATTCCTGTGCCGG Y 2 1 2 1 101000 f 74 goat snp30352-scaffold334-252713 15 7652627 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439047 Affx-122930330 AX-123309384 15 71645422 GCGTTGGGTATAGGGCCCACCTGGTTAATCAGAGA[C/T]GATCCTGAGATCCTTAACTTCATTATGTCTGCAAA Y 2 1 2 1 101000 f 74 goat snp30351-scaffold334-219692 15 7622091 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803323 Affx-986696283 AX-385290161 15 71663966 TGTGCTGCAGCAGCTGTCAGTCCCACCGGGATCTC[A/G]ATGCTTATCTTGCCTCTCCTGCCGGCAGGCAACAG R 2 1 2 1 600010 f 74 goat 15_71663966 15 71663966 Ancestral_priority_1043 ancestry 0.432 neutral IMAGE 10K 10K ancestral 38389265 Affx-122969021 AX-123259623 15 71677229 ACACACACACACACACACACACACAACCATAAGGC[A/G]TAACTAGACCCTTAAGACATCAAGAGCAGGCATGC R 2 1 2 1 201000 r 74 goat snp30350-scaffold334-187885 15 7589894 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782552 Affx-122961970 AX-385269626 15 71706199 ACATTTCCACAGAAGTAACTTCAGGACTCCAAAAG[C/T]AAAGATATAGTCCAGACCATCCCCTCATCCAGAGA Y 2 1 2 1 101000 f 74 goat snp30349-scaffold334-158915 15 7560610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386485 Affx-122970760 AX-123256843 15 71759765 TATTTTTGTGAGGACTAAAGGTGACATATGTAAGC[A/G]TCTCAGGCACACAGTAGGAATCCATAAATAATGAG R 2 1 2 1 101000 f 74 goat snp30348-scaffold334-105349 15 7506887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272798 Affx-1111833055 AX-519546494 15 71778571 CCTGGAGTCTGTTATTCCGGACCCTGGAGACTTAC[A/C]CTCAACTTCTTCTCATATCTACTGCTAAAACCTTG M 2 1 2 1 101000 f 74 goat 15_71778571_AF-PAKI 15 71778571 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38424172 Affx-122942527 AX-123294518 15 71804927 CTCAGATCTGTCCTCATTATGTCACTCACTCCTCC[A/G]CTTTGAGGAAAAAGAACATTTTTCCCGGTCTCAGG R 2 1 2 1 101000 f 74 goat snp30347-scaffold334-60187 15 7461783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422824 Affx-122943190 AX-123293170 15 71846608 CTCACTGGGACTTCAGAGGTGATCCTGGCTACCCA[A/G]TGCAAGATAGAGCAGATGGTCCCCAGCTTCTGCTT R 2 1 2 1 101000 r 74 goat snp30346-scaffold334-18506 15 7419309 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791370 Affx-122974538 AX-385278362 15 71866931 AGGTATGGACAGTTTCTGGGAAAGGAACTACCAAC[A/G]GATCTTAAGCATATGCAAGGTTGCTCATTTTCTCC R 2 1 2 1 101000 f 74 goat snp30551-scaffold338-317930 15 7399183 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381713 Affx-122974704 AX-123252071 15 71907595 GTGAGTGAATAAACGTAAAGGGTCTAGACCTGCAC[A/G]AAAAGGGCAACCACTTGGTGCCTGTGGGTACTGAG R 2 1 2 1 101000 f 74 goat snp30550-scaffold338-277266 15 7358511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390606 Affx-122967177 AX-123260963 15 71952849 CCTATGCGTCTACTCAAAGCAGCATGTGGTGCGTG[C/T]AGGAGCAAGTGACAGAGTTGGACCCAGCTCTTAGA Y 2 1 2 1 101000 r 74 goat snp30549-scaffold338-232012 15 7312972 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408610 Affx-122953502 AX-123278961 15 71986161 CTCTCTTTACTTTTCCAACTCACTCTGCATTGGTG[C/T]GGGGAGAGAGCATTTGATATTCATAATCTGGTTCA Y 2 1 2 1 201000 f 74 goat snp30548-scaffold338-198700 15 7279856 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388693 Affx-122968994 AX-123259051 15 72017026 CATAAGATAGCAGCATGATCCCAACAGGACCTCCA[C/T]GGAGGAACAGGGGTTTGAGTTGAAGAGATATGAGA Y 2 1 2 1 201000 f 74 goat snp30547-scaffold338-167835 15 7249243 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413166 Affx-122950346 AX-123283515 15 72049109 TCCTTCTTCACCTCTGACCTACTGCCTTCCCCTTC[A/G]CAATTAACGGGACAGCGGTTAAGCTGGGTTCTCTC R 2 1 2 1 101000 r 74 goat snp30546-scaffold338-135752 15 7216924 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449517 Affx-122922611 AX-123319852 15 72096544 AGGACTCCTCCCAGGGGACTTCCTTCTCTGACCAG[C/T]AGAAGTTGACTTGGAGGAGGGGTGGGTGCCCCTGT Y 2 1 2 1 201000 f 74 goat snp30545-scaffold338-88317 15 7169154 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417827 Affx-122946799 AX-123288175 15 72147651 GCAGCTTTATTGAGATAGAATTTACCTACCAAAAA[C/T]AGTACCCATTTAAGTGTGCAGTTCAATGCTTTATG Y 2 1 2 1 101000 r 74 goat snp30544-scaffold338-37210 15 7117696 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776718 Affx-122968869 AX-385263844 15 72229200 TGGTTACTATTTTGTTCCTGAGCCCTCTGCTTCAC[A/G]ATTCTTACCACGGGTAATTTTTTCCGAAGTTCCTT R 2 1 2 1 101000 f 74 goat snp40405-scaffold516-44240 15 7040620 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276943 Affx-1111835667 AX-519550451 15 72252426 TTTCTTTGACAACTGTATAAAGTTCTCTTGAGATG[C/G]GGATCATACACTTTATCTAGATAGAATACATTTAT S 4 1 2 1 101000 f 74 goat Random2.2K-1553 15 72252426 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795173 Affx-122943765 AX-385282131 15 72272425 AAGTCAGACACCTGCAAAGGTTTTAAATGTCCAAA[C/T]GGTTACACCAATCAAGGTTAAAATTTTGATTGAGA Y 2 1 2 1 101000 f 74 goat snp40406-scaffold516-87465 15 6997372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396153 Affx-122963385 AX-123266508 15 72329617 TTCTTAAGACTGAGTTGCTAGGTGCACTGGAGCAA[C/T]AGACATAACCAGACAGTGAACAGTATCTCCCTCTT Y 2 1 2 1 101000 r 74 goat snp40407-scaffold516-144657 15 6939699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417595 Affx-122946884 AX-123287943 15 72406130 AAAAAGAAAAATCAAGGTTTTGGGATCCCAATCTA[C/T]GCTCAGTGATGCTTTTATCAATTGTGGTTTTTTAA Y 2 1 2 1 101000 f 74 goat snp40408-scaffold516-221170 15 6862679 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396603 Affx-122962896 AX-123266958 15 72461005 ACTGACCAGGTTGCCAAAAGAACCCAGAGAAGAGG[A/C]GGTTAGGCAGGGAGGCCTTCTCAGGAAAGGGGACG M 2 1 2 1 101000 f 74 goat snp40409-scaffold516-276045 15 6807450 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787129 Affx-122954999 AX-385274155 15 72498472 CAATAAATATATATCAAACACTTCTATATTGCCAG[A/C]CAGTGTCTTAGGCACTTGACACACGGAAATAAACA M 2 1 2 1 101000 r 74 goat snp40410-scaffold516-313512 15 6769149 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775896 Affx-122968923 AX-385263027 15 72527606 TCAAGAATGAATCCTAGTATAAACTAGGGACTTCC[A/G]TTAATAATAGTATCAACATTGGTTCATCAGTTGTA R 2 1 2 1 101000 f 74 goat snp40411-scaffold516-342646 15 6740388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437991 Affx-122931586 AX-123308329 15 72557521 GAACATTTCCTGACATTTGCCAGGGCACAAAGCCC[A/G]TCTGCACACCAGGTTTCACTGGACGCCCACCAGGA R 2 1 2 1 101000 f 74 goat snp40412-scaffold516-372561 15 6710530 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447265 Affx-122924943 AX-123317601 15 72665219 GGTAGCAAGGAAGTGGTCCGCTACCTGCTGGAGCA[C/T]GGTGAGCTGTGCCCCTGGGGTCCCTGGGGCTGCTG Y 2 1 2 1 101000 f 74 goat snp40414-scaffold516-480259 15 6606588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393447 Affx-122965855 AX-123263803 15 72711841 AGGGCATGGCAGCTCCACAGAGTCCGCATCTTCCA[C/T]TGTGATTTTAGCCCCAGGAGAAAAGCATTTCATAG Y 2 1 2 1 101000 r 74 goat snp40415-scaffold516-526881 15 6560586 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417239 Affx-122947281 AX-123287587 15 72743793 AGGGGTTCTTAAGGCCACAGGCTTCCTGGGTTCAC[A/G]CTAGGAACAGTCTGTCTGCACAGATGAAATACACA R 2 1 2 1 101000 r 74 goat snp40416-scaffold516-558833 15 6528634 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415909 Affx-122948462 AX-123286258 15 72799322 CTCTCCCACCCCCAATCTTATCACATCCAAAATAG[C/T]ACCATCTAACACAACTGTCAAATTTAGTTGCTCTG Y 2 1 2 1 201000 r 74 goat snp40417-scaffold516-614362 15 6473161 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379587 Affx-122976032 AX-123249945 15 72830594 AGGGCTCTCAATCAGGCGTCCTCACAAGCCCAGAC[A/G]GACAGGATTGCTCACCAGGCAAATGAGAAAACGTA R 2 1 2 1 101000 r 74 goat snp40418-scaffold516-645634 15 6442332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452720 Affx-122920291 AX-123323053 15 72861171 CAGCTTCTGTGGGTGTACTTCCCTGGCATCGTTAG[C/T]GTCTAGCCTGTGGCCGGGTACCAAAACTGGCCTTA Y 2 1 2 1 101000 f 74 goat snp40419-scaffold516-676211 15 6411894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433081 Affx-122935733 AX-123303422 15 72900406 TGTTCGGATTTTTTTTAAAAAGCCATTGTCAACCT[C/T]TAGATGCTGCTTTCTGAACATATTTGAAATTATCA Y 2 1 2 1 101000 r 74 goat snp40420-scaffold516-715446 15 6372603 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381056 Affx-122974624 AX-123251414 15 72937470 AAACAGCGTAGTCCCGGAGAGGCAGACCAGCGACC[A/G]TTAACCTTCCAGGGACGTCATCTTAGATCTGTCTC R 2 1 2 1 101000 r 74 goat snp40421-scaffold516-752510 15 6335673 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768275 Affx-122954616 AX-385255456 15 72998924 GGACTCTCATGTCCCTGGTTATCTGCTAAAGGATG[C/T]AATTCTATGGGTTAGAGAACTCATAATGATTAGCT Y 2 1 2 1 101000 f 74 goat snp40422-scaffold516-813964 15 6274758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430883 Affx-122936879 AX-123301224 15 73037811 GAGTAACTAACATACACAAGGGGTGGATGAATAGT[A/G]CTGAGGAAGAGTGTATAGTGAGAAGAGCCCCAGGT R 2 1 2 1 101000 f 74 goat snp40423-scaffold516-852851 15 6235742 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380264 Affx-122975428 AX-123250622 15 73119351 AAGGCTTAAGGGCTGTCCTGTGTGTATCGGGACAC[A/G]ACAGCTCTCACAGCATGGGAGTGATTACAGTGGGG R 2 1 2 1 101000 f 74 goat snp40424-scaffold516-934391 15 6155460 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431635 Affx-122936140 AX-123301976 15 73156471 TATGACATTCGCTCATGAGGGTGTATGTTAGGGAA[C/T]AGGGACTCAGAGAGCTGAAGTAAAATTTCCAGCGT Y 2 1 2 1 201000 r 74 goat snp40425-scaffold516-971511 15 6118318 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419307 Affx-122946228 AX-123289655 15 73188592 CTTTCACATTGACTTTTAGTCCCTGGAGCTAAGAC[A/G]GAGAAGAAGCAGGATTTGCTTCTAAGTAGAGCTCT R 2 1 2 1 101000 f 74 goat snp40426-scaffold516-1003632 15 6086232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428106 Affx-122939082 AX-123298449 15 73242293 AAAATAAATAAATAAATAAATAAAAACTCCTTGCA[C/T]GCATCCCCTATCACACAGGTATAAATTGAAGCCTC Y 2 1 2 1 101000 r 74 goat snp40427-scaffold516-1057333 15 6032551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450911 Affx-122922191 AX-123321245 15 73284826 TTTTTTCTCTCCCTTCAAAGCCGTAAATGATGCTT[A/G]CTTCATCGAAGCTTCAGTTCAGTTCAGTTCAATCA R 2 1 2 1 103000 f 74 goat snp40428-scaffold516-1099866 15 5989326 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383808 Affx-122973183 AX-123254166 15 73344603 AGCCATGGGGAGGTGGGCCGTAAGTCTCAGCTCAC[C/T]GATGAGGGCTCGGCGACTAACACCTGAAAACTAGT Y 2 1 2 1 101000 r 74 goat snp40429-scaffold516-1159643 15 5930528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422809 Affx-122943200 AX-123293155 15 73375909 TTTAAAGGGGAATAAAAAGGATAGCATATTGAAAA[G/T]CAGAGACATTATTTTGCCAACAAAGGTCCGTCTAG K 2 1 2 1 303000 f 74 goat snp40430-scaffold516-1190949 15 5899032 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389315 Affx-122968498 AX-123259673 15 73435277 GAGTCAGCAGTTTGGACAGTCTGGCTCCTTTCATG[C/T]TTTTCTCTTGAATTGATCTCTGGTCCCTACAGAAT Y 2 1 2 1 101000 f 74 goat snp40431-scaffold516-1250317 15 5839502 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451041 Affx-122921443 AX-123321375 15 73476887 ACCTTTATGCGGCTGTCAGGCACCAGCTCCTTTCC[A/G]TTCTTCAGCCATACTCCCCGCACGTTCTCATCTGA R 2 1 2 1 101000 r 74 goat snp40432-scaffold516-1291927 15 5798596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417383 Affx-122947699 AX-123287731 15 73521730 AGGGCCCAGATCTACAAAGGGATTTCACCAACCTG[C/T]GCCTGTCCCATCCCCAACGGCCCTGGGGTGGGTAA Y 2 1 2 1 101000 f 74 goat snp40433-scaffold516-1336770 15 5754423 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400414 Affx-122959985 AX-123270769 15 73557133 TGCAAAGGGGTGGGCTCATGAACGTAACAATTTTC[A/G]TCTGGTTTTCCGACGTATGCCAAGAGCCTAGCACA R 2 1 2 1 101000 f 74 goat snp40434-scaffold516-1372173 15 5720149 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438926 Affx-122930422 AX-123309263 15 73679102 TACCCAAGTTGGGGGGGGCCTCCGGGGACTTTTGG[A/G]TTTGGATAGGGAGGTGCTGGAGGGAGGGAGGGCAA R 2 1 2 1 102000 f 74 goat snp40436-scaffold516-1494142 15 5608902 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405602 Affx-122955924 AX-123275954 15 73711965 TCTCATTTTCTTTATTTCTCAAGTGGAGATACCTA[A/C]TGTACCAAAAGCTTACATGACAGGCGGGACAGTCA M 2 1 2 1 101000 r 74 goat snp40437-scaffold516-1527005 15 5576024 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277077 Affx-1111835668 AX-519550584 15 73720595 AGGGAATTTTCTATCAGTCCTGGAGTATCCTGTGG[A/G]CTTTCTTTAGATCTTATAGTATCTCTTTTATCATT R 2 1 2 1 201000 r 74 goat Random2.2K-1554 15 73720595 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395107 Affx-122964157 AX-123265462 15 73745878 AAACTCTTATGTCTATACAGAGTTGCAGTGTTTAA[C/T]GGTTCATCAAGAAACTTCTAAAGAGTAGAGTAATG Y 2 1 2 1 101000 r 74 goat snp40438-scaffold516-1560918 15 5542316 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399012 Affx-122960937 AX-123269367 15 73780349 CTCAACATGAATGAGTTTGTATACCTCAGCACTTC[A/G]GGGGTGGCAGACTAAGAGGAAGAGGTCAGAAGGAC R 2 1 2 1 101000 f 74 goat snp40439-scaffold516-1595389 15 5508005 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399992 Affx-122960813 AX-123270347 15 73829218 GGAGTGTTATTCATAACAAACAAAAGATGGAAACA[G/T]CCAAGGTTCCATCAAAATTGTTATCAATACATCCA K 2 1 2 1 201000 r 74 goat snp40440-scaffold516-1644258 15 5459133 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798757 Affx-122966877 AX-385285688 15 73871109 GAGTAGGTGGGGGCAGAAGTCAGTAGAATTTGTTC[A/G]CTTTTTTAATGTGACTGTGCTTTTTACCCATGGGA R 2 1 2 1 101000 r 74 goat snp40441-scaffold516-1686149 15 5417241 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379549 Affx-122976056 AX-123249907 15 73928719 TTTTCTGCAGCGAATGCAATGCAGTTGCTTTGGGT[G/T]GTGATTTGAGAGTGTGGTTTACCGGCTGGGAGAGT K 2 1 2 1 101000 f 74 goat snp40442-scaffold516-1743759 15 5359931 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454299 Affx-122919261 AX-123324632 15 73993158 GAAAAAATGCACTCTGGGCATTTATGAGGACAGAT[A/G]CAGAAGCAGGGAAGCTGAGATGCTAGAAGCCTCAG R 2 1 2 1 101000 f 74 goat snp40443-scaffold516-1808198 15 5301146 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276947 Affx-1111835669 AX-519550455 15 74006205 TTTCAAGAAGACAAAATTGTAGAGATGGAAGAGAG[A/G]TTGGTGGATTTCAGAGGTTAGAGCTGGTGGCGGGG R 2 1 2 1 101000 f 74 goat Random2.2K-1555 15 74006205 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416233 Affx-122948217 AX-123286582 15 74038920 TCCTTGCTTTTGTCTATAAATTTCATGTTGCCGGC[A/G]TCTCTTCTGAACCCGCATCCCCCTTCTCTTTAATA R 2 1 2 1 202000 f 74 goat snp40444-scaffold516-1853960 15 5255379 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796207 Affx-122975573 AX-385283158 15 74085953 TTTGTGAAATGCAGATAAGAGCATCCCTTATCTCA[C/T]AGGAGTTACTAGCATGCCATGGATGAGTTTCCCAG Y 2 1 2 1 101000 f 74 goat snp40445-scaffold516-1900993 15 5208360 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388459 Affx-122969250 AX-123258817 15 74123281 AGTCATTCATAATGAAGGGTGACTGCAGGCTTCTC[A/G]TTCCATCGGTGCCCACTGTGTGCTTTTCAAATAGA R 2 1 2 1 101000 r 74 goat snp40446-scaffold516-1938321 15 5170915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779251 Affx-122977381 AX-385266355 15 74221151 GGAATATGACAGATATAACTGCTTTGGGTTAGGGA[C/T]GTTGTTTCCTCATGGCCAAGTCTTTAGCACCCATG Y 2 1 2 1 101000 r 74 goat snp40448-scaffold516-2036191 15 5072837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420158 Affx-122945583 AX-123290506 15 74249984 TAATTTCTTTACTGTCAGGTATTTCTTTCCAGACA[A/C]TTCAGGGTAAAAATAAATGTTTAAAAAAAAATGCT M 2 1 2 1 101000 f 74 goat snp40449-scaffold516-2065024 15 5044062 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796657 Affx-122963623 AX-385283603 15 74291308 CAGCGTGATGCTGCCGTTGCTCTCCATTTTCAGGC[A/G]TTTGAGGCAATTATATTCTTCCTTATTGAAGCTTC R 2 1 2 1 202000 f 74 goat snp40450-scaffold516-2106348 15 5009802 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428936 Affx-122938896 AX-123299278 15 74328920 ATTTCCTCTGCTGCTTCCTGATCAATTAGCCCAAT[A/G]CTTAAAATAATACCTGTTGAATAAATGAATGAATG R 2 1 2 1 101000 f 74 goat snp40451-scaffold516-2143960 15 4971779 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419565 Affx-122945405 AX-123289913 15 74361456 TCTTTATAACAGCTCTTTGAGCAGCATTCACTCAG[C/T]GGCCCTGGATGTTGTGTCTGGCTCAACAAGATAGC Y 2 1 2 1 101000 f 74 goat snp40452-scaffold516-2176496 15 4939496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463422612 Affx-1109974363 AX-514906222 15 74380870 GTTTTTTAATTTGGTTTAGATTACTTTTTTTCTGT[A/G]TATAGCTCTAAATATGAAACAGCATAAAGTGCTTG R 2 1 2 1 101000 r 74 goat 15_74380870_AF-PAKI 15 74380870 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401420 Affx-122959002 AX-123271773 15 74404703 TCATAGCTGATATTTATAACTACCTTCTTATTCTA[C/T]ACTTCCTTTGTATTCAGTGACCACTTCAGTTGGCC Y 2 1 2 1 101000 r 74 goat snp40453-scaffold516-2219743 15 4896830 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791824 Affx-122970342 AX-385278814 15 74440888 GTGAAGGAAGCATATTCAAATGGTTCATTCTGCCC[A/G]TGATGAATCTTGTTCTAGAGAGGTGAACAGCAACA R 2 1 2 1 101000 f 74 goat snp40454-scaffold516-2255928 15 4860046 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384023 Affx-122972897 AX-123254381 15 74498381 TCTCCCAGGTTTCACTAAGCTCTGTGTCCTCACTC[A/G]TAGGACAGAAGCTGACATGACAGAGGTGCCCAGAC R 2 1 2 1 102000 r 74 goat snp40455-scaffold516-2313421 15 4803100 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277080 Affx-1111835670 AX-519550588 15 74498707 GTAACCCATCATTTTAACACAGTGCCTGGTCCATA[A/G]TTGACTCTCCATAAATAAATGTTGCATGAACGAAT R 2 1 2 1 202000 r 74 goat Random2.2K-1556 15 74498707 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450752 Affx-122921852 AX-123321086 15 74543667 TGTGTAGCACGTTAACTTTCTATCTTACCTATCAA[C/T]CTATTTCTTTTCATTCTTCACATCAAATTTTTACC Y 2 1 2 1 101000 f 74 goat snp40456-scaffold516-2358707 15 4756543 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786865 Affx-122928567 AX-385273894 15 74585825 ACTACATTAGTTTAGCTATTATTAGTAGAAAGTAA[A/G]TACAGGTGATTTTCAAAAGCACACAGTAAAATGTA R 2 1 2 1 101000 r 74 goat snp40457-scaffold516-2400865 15 4707055 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423716 Affx-122942878 AX-123294062 15 74631936 GAGAGCAATGCTACAAAATCTGTCAAATGTAAATG[C/T]ATGTGTATTTTTTGTTTTGATAATGACATAGATTT Y 2 1 2 1 101000 f 74 goat snp40458-scaffold516-2446976 15 4660833 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786386 Affx-122972482 AX-385273420 15 74660480 ATTTCTAGCTTTGTGTTCTCAATGAAAAAGTAAGC[A/G]CAAGAACATAAGTCAATTTTTCACATGGATGCATC R 2 1 2 1 101000 r 74 goat snp40459-scaffold516-2475520 15 4631396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402269 Affx-122959118 AX-123272622 15 74695155 CCCAACCAAATAGCCAGGTAACAGAATAAGAAAAA[C/T]AAAAAGCAGAGGATCTGGACTTTCTTGTCCATAGC Y 2 1 2 1 201000 f 74 goat snp40460-scaffold516-2510195 15 4596275 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393615 Affx-122965359 AX-123263970 15 74770312 ATGCAGAGTTCACTGCATGATCGGGCACCAAAGTT[C/T]ATTATGTCCCACTGTTGGTGGGAGTAAGACTAGGA Y 2 1 2 1 103000 f 74 goat snp13974-scaffold1550-5665 15 4391002 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423413 Affx-122942622 AX-123293759 15 74823605 TAGTGTCATGGACAAAAAATACAATCCTGACAAGA[C/T]GGCCTGCAGTTGAATTATGGCTTCACCTGCCAGCT Y 2 1 2 1 202000 f 74 goat snp13975-scaffold1550-58958 15 4240578 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476316 Affx-1251763823 AX-586011733 15 74827486 GTTTAAGGAGAATAACACTGAGTAATAATATTCAT[-/ATTGATAACTTTATTTTTTTTTAATTTTTTATTTTTTTTATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TTAAGATAACTTTAAAGAACTAATCACATTGTACA - 8 1 4 1 20000 f 74 goat SV_322 15 74827486 - deletion junction SV-TF-chip 539476569 Affx-1251763823 AX-586011955 15 74827486 GTTTAAGGAGAATAACACTGAGTAATAATATTCAT[-/ATTGATAACTTTATTTTTTTTTAATTTTTTATTTTTTTTATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TTAAGATAACTTTAAAGAACTAATCACATTGTACA - 4 1 4 1 20000 r 74 goat SV_322 15 74827486 - deletion junction SV-TF-chip 562165703 Affx-1251763823 AX-606941112 15 74827486 GTTTAAGGAGAATAACACTGAGTAATAATATTCAT[-/ATTGATAACTTTATTTTTTTTTAATTTTTTATTTTTTTTATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TTAAGATAACTTTAAAGAACTAATCACATTGTACA - 8 1 4 1 20100 f 74 goat SV_322 15 74827486 - deletion junction SV-TF-chip 562165711 Affx-1251763823 AX-606941120 15 74827486 GTTTAAGGAGAATAACACTGAGTAATAATATTCAT[-/ATTGATAACTTTATTTTTTTTTAATTTTTTATTTTTTTTATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TTAAGATAACTTTAAAGAACTAATCACATTGTACA - 8 1 4 1 20100 r 74 goat SV_322 15 74827486 - deletion junction SV-TF-chip 562166301 Affx-1251763823 AX-606941709 15 74827486 GTTTAAGGAGAATAACACTGAGTAATAATATTCAT[-/ATTGATAACTTTATTTTTTTTTAATTTTTTATTTTTTTTATGGTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCC]TTAAGATAACTTTAAAGAACTAATCACATTGTACA - 8 1 4 1 20100 r 74 goat SV_322 15 74827486 - deletion junction SV-TF-chip 38419935 Affx-122945314 AX-123290283 15 74869762 AAACTCCATATGCAACTATAATATATGGAATGAAC[A/G]TCCCATAGTTTATTTTTGCTAAGAATATGTCTCAG R 2 1 2 1 201000 f 74 goat snp13976-scaffold1550-105115 15 4194731 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427134 Affx-122939650 AX-123297477 15 74915508 TGCGGAAGTTTAAGAATTATTAATTTTGATTGATT[A/G]TTTAATATACTTTTTCTCTGTAGTTTTAGCTTATT R 2 1 2 1 101000 r 74 goat snp13977-scaffold1550-150861 15 4148325 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395867 Affx-122964004 AX-123266222 15 74958960 CTCAGGTGTTTGCATTTTCCCTCTTTCTCCTGTGC[A/G]TGTATGCTTGGTCATGTCTGACTTTGCAAACCCAT R 2 1 2 1 102000 f 74 goat snp13978-scaffold1550-194313 15 4104673 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776610 Affx-122937948 AX-385263737 15 75020652 AGTTGGGAAAACTAGAGCCCATGACTCACTATTCC[C/T]CTGGCTTAAGATCTGGCTGCTGGTTCCAGGGGACT Y 2 1 2 1 202000 r 74 goat snp13979-scaffold1550-256005 NW_017189802.1 11111 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451292 Affx-122921298 AX-123321625 15 75056898 AATTTCTTCCAAAATTATGTTTCTAAATATGCACA[C/T]TGATTGCAGACCTTGATTATATCAACTCTGTATTT Y 2 1 2 1 101000 r 74 goat snp13349-scaffold1515-32888 15 3911894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795310 Affx-122958107 AX-385282268 15 75086267 GAAGGTAGCAAGTTGAAATACTTATTATATTAGCC[A/G]TTCATGCAAAGAAATTCATTTGAAAGTTTACTTTT R 2 1 2 1 201000 r 74 goat snp13350-scaffold1515-62257 15 3848744 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775211 Affx-122924439 AX-385262342 15 75128233 AGCCACCAGGGAACTGATTGAATATATCAATAGCC[A/G]CTCAGGTATTGACTGAATACCTGGTAAAATCTCAA R 2 1 2 1 101000 f 74 goat snp13351-scaffold1515-104223 15 3836870 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410373 Affx-122952444 AX-123280723 15 75173142 GCTGTTGAAAGGCTTATACTGTTGGCAGACATTTT[A/C]TAAAACATGCTAATACCAGCCAGCATGATTTGGAC M 2 1 2 1 101000 r 74 goat snp13352-scaffold1515-149132 15 3791478 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393424 Affx-122965873 AX-123263780 15 75211948 TACTTTTATTCACACTGTACCTAAACCTGCCTATG[A/C]TGATCCACAGGTAAGATGAAACTTCAGGTCATTTG M 2 1 2 1 101000 f 74 goat snp13353-scaffold1515-187938 15 3752132 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767181 Affx-122944402 AX-385254463 15 75243975 TCCTAACATAGACTCATATTAAAAAGTTTTTGTTA[G/T]AAGATCATAACAGCAAATACTTCTTTTAGTGAGAG K 2 1 2 1 201000 f 74 goat snp13354-scaffold1515-219965 15 3719906 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425837 Affx-122940674 AX-123296183 15 75282176 CTTACTTTTAGTATTTTTAACATTCAAGACATTTT[A/C]TCTACATCAAGGAGGGTGTAGGCTCACTTCTTTGT M 2 1 2 1 102000 r 74 goat snp13355-scaffold1515-258166 15 3681703 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800896 Affx-122956702 AX-385287811 15 75375087 AAAGAGTTATCACTGATCGTTTTGCAGAAACAATG[C/T]ATCATAAAACATTGTTTTGTGTCAACTACAATTTT Y 2 1 2 1 101000 f 74 goat snp13357-scaffold1515-351077 15 3589958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377729 Affx-122977387 AX-123248088 15 75441943 AATGAATCCGAGACAGGAGAGCTATGCCTTTCCCA[C/T]GTTTATCTGTTTCTACTCTCTATCCCATTTCCAGA Y 2 1 2 1 201000 r 74 goat snp13358-scaffold1515-417933 15 3521846 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775198 Affx-122937287 AX-385262329 15 75525137 TTTTTCCATTCTTTTGCCAGAATGGTAAGCTGTAG[C/T]GCCAGTAGCTCTGTTAAGATGTCTGTTTAGGAAGA Y 2 1 2 1 101000 f 74 goat snp13360-scaffold1515-501127 15 3436435 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786832 Affx-122953237 AX-385273861 15 75569719 AGAATAGATTGGCAACTGCTGATATTTTAAGATAG[C/T]AAGTGAAGAAGACAGATAAGTCATGCAGTTGATGG Y 2 1 2 1 201000 f 74 goat snp13361-scaffold1515-545709 15 3391616 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385182 Affx-122971731 AX-123255540 15 75630304 GATAAAAAGAACACTTTGACTCTGAGATTACTACA[C/T]TCCAAAATATCCCAGTTAATTCACAAAGTCACTAA Y 2 1 2 1 101000 f 74 goat snp13362-scaffold1515-606294 15 3333165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446722 Affx-122924721 AX-123317058 15 75662077 TGCCTATGGTATTGATGTTAACCACATTTTGCAAG[C/T]ACAGCATTAGGAATGTTTTGTCTTTGTTAAGTATT Y 2 1 2 1 101000 f 74 goat snp13363-scaffold1515-638067 15 3301477 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390335 Affx-122967698 AX-123260692 15 75695695 GTGGGTTTCACAACAGACCCCAAGACGCAGCTGGT[C/T]CTGTTTGTGGTTTTCCTTGGTGTGTACTCCATGAC Y 2 1 2 1 101000 r 74 goat snp13364-scaffold1515-671685 15 3267762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376496 Affx-122978025 AX-123246855 15 75740886 ATCCCACAAAAATGCATTTATCTTTTTTTCTTTAA[C/T]GGAAGGTCTTTGGTGAAGGGTCATGAGTTAATGGA Y 2 1 2 1 303000 f 74 goat snp13365-scaffold1515-716876 15 4516367 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442696 Affx-122927878 AX-123313033 15 75761662 CTTTCAAGGGATCTTCAAGGTCAAAATGATTCCCA[C/T]AATACTTCTGAGACAGTATTTGCCTTTTTCATTCT Y 2 1 2 1 202000 r 74 goat snp12015-scaffold1442-461717 15 3139934 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769364 Affx-122938410 AX-385256535 15 75792574 CGTCATCAGGGATGAAGCCTTTATTCTAGGTCTCA[C/T]GGTGAAACTTACTAGAACTTTGACCCTTTCGTTCC Y 2 1 2 1 101000 f 74 goat snp12014-scaffold1442-430805 15 3109618 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425799 Affx-122940700 AX-123296145 15 75826429 CGGGATAGCGAAGCGGGTTGTAGATGGCCACATAA[C/T]GGTCCACTGCCATAGCAGCAAGGAGGTGACAGTCA Y 2 1 2 1 201000 f 74 goat snp12013-scaffold1442-396950 15 3075024 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430675 Affx-122936929 AX-123301016 15 75882610 TTGAGTCACTTTTCTCTTATTTTGAATAGTTTCAA[G/T]TACTAGGTCTTCAAGATCACTAGCCATTTCTTTTG K 2 1 2 1 101000 r 74 goat snp12012-scaffold1442-340769 15 3018872 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401718 Affx-122959531 AX-123272071 15 75932196 CTGCCATAGCAGAATGGGAAAGGACTTTCTGCCCA[C/T]AGTTTCAGCCACACTGACCCCAACCCCTCTTTTTA Y 2 1 2 1 101000 r 74 goat snp12011-scaffold1442-291183 15 2968459 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425161 Affx-122941064 AX-123295507 15 75980700 TTCCACTTTGCAGATGAAAAAAACGGAGGCTCAGA[G/T]AGGTGGTGTAGTTCATCGAAGGTCACACAGACTCT K 2 1 2 1 201000 r 74 goat snp12010-scaffold1442-242679 15 2919132 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425968 Affx-122941167 AX-123296314 15 76032269 CGAACAGGTTCAAGCATCAGTGACCCGCTCCAGCT[C/T]GCCGAAGGTCTGGTGATAGTCCTCAAGTCTGTGCT Y 2 1 2 1 101000 r 74 goat snp12009-scaffold1442-191110 15 2868075 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418185 Affx-122947073 AX-123288533 15 76062887 AAGTCTGTGTGAGCCTCAGTTTCTCTGTCTGGGAG[C/T]AGGTAAGGTAGTCTGGTATAATTCCACACTGGTGG Y 2 1 2 1 101000 f 74 goat snp12008-scaffold1442-160492 15 2837567 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430982 Affx-122936695 AX-123301323 15 76102408 CGAAATTTAAAAAGATGGCAGATACTACAAACTCA[C/T]GAAATCCAGAAAAGTAAGACTGCAACCAGTTTTAG Y 2 1 2 1 201000 f 74 goat snp12007-scaffold1442-120971 15 2798493 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450635 Affx-122921990 AX-123320969 15 76186590 CAGGTGCTTTGGGTGGGAGTGGAAGGGAGACGCAT[A/G]TTGGCTCAATACCAGGTCACCTTTCCAATAACTGG R 2 1 2 1 101000 r 74 goat snp12006-scaffold1442-36789 15 2714187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795046 Affx-122935402 AX-385282005 15 76242530 AAGTGCATCCACCATGGCAGATTTAAGGCTGCAAG[A/C]GAGAAGCCCCTGAACACGGGTGAGGAAGAGAAGCG M 2 1 2 1 202000 r 74 goat snp33523-scaffold3938-19052 15 2642288 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385200 Affx-122971719 AX-123255558 15 76272139 TTTTCCAGTGGAACACGAATGCTGGAGGGAAGGCC[A/G]ACTCCAAACCCCCTCTCCTTTCACAGATGGGAAAC R 2 1 2 1 201000 r 74 goat snp33524-scaffold3938-48661 15 2613723 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443695 Affx-122927166 AX-123314032 15 76303410 AGTTTAACGACCACCCTGGGGAAATCTCTGCCCTG[C/T]ACCTCATTTCTTCTTGAATCTGCTCCCCTTTCTGT Y 2 1 2 1 101000 r 74 goat snp52017-scaffold7644-30499 15 2581832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446389 Affx-122925582 AX-123316725 15 76363631 GGCGATGGTTTCTTAAACATGACACCAAAGCACAG[A/C]TGTCAAAAGAAAAGATAGCTTGGACTTCACCAGTA M 2 1 2 1 201000 r 74 goat snp35587-scaffold429-46635 15 2519304 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418335 Affx-122946958 AX-123288683 15 76409846 CTAAGTTCCATGCAGTTGCTCAAGCACTCCTGCCT[C/T]AGGACGTTTGCACCTGCTGTTTTCTGGAACCCCCT Y 2 1 2 1 201000 f 74 goat snp35588-scaffold429-92850 15 2472838 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412100 Affx-122951118 AX-123282450 15 76462810 CAGTCGTGCAGGCCTCTGACGCGTTGTTTTCCCCC[A/G]TCTGCGCCCTAGATTACTTTGACTTCATCTACGAC R 2 1 2 1 101000 r 74 goat snp35589-scaffold429-145814 15 2420953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424588 Affx-122942210 AX-123294934 15 76508482 AAAAGTTTAATAGTACTGTCTGCAAACTAAGAATT[C/T]GCTCCTCACTGTGAACAAAGTTACCGAGGCCTAAA Y 2 1 2 1 201000 f 74 goat snp35590-scaffold429-191486 15 2375233 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447399 Affx-122924409 AX-123317735 15 76543134 TTGAGGCTGAAAACCTAGGTCCCTGATTGCTGGCC[A/G]TAAATCGCAGTTAATTGGTTTTGTCTGAAATAATG R 2 1 2 1 201000 r 74 goat snp35591-scaffold429-226138 15 2340699 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276950 Affx-1111835671 AX-519550458 15 76570459 TAGGTCTTATATTTTTAGTAACTTCATTTTATCAG[A/G]AGAGTGCATTATTTCCTCAGTTCAGTCTCGTGCAA R 2 1 2 1 201000 f 74 goat Random2.2K-1558 15 76570459 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399479 Affx-122961188 AX-123269834 15 76624256 TAGGTGTCCTCCGTAGTGATCTGACATTTGCATGC[G/T]CTGTGAAATGGCCAGTGTGGTAAGTCTGGTAGCCA K 2 1 2 1 101000 r 74 goat snp35592-scaffold429-307260 15 2258843 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395988 Affx-122963507 AX-123266343 15 76660475 GCTTGTAGGGCACCATGAACTTGGTCTGTGATTCA[A/G]AAAAACACTCAACAGAAGTAGCTCAGCACAGGCAA R 2 1 2 1 101000 f 74 goat snp35593-scaffold429-343479 15 2223092 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276952 Affx-1111835672 AX-519550460 15 76689715 TCTAGATGTCACCAGAAAAAAGAGAACCAGGCACA[A/G]TGCTGAGTAGTTTCATGCAACATCTGATTTAAACT R 2 1 2 1 101000 f 74 goat Random2.2K-1559 15 76689715 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431171 Affx-122937189 AX-123301512 15 76733430 TGTTCAGCTTCTGGAGGACCAGCGTTGAGAGCCCC[A/G]TAAGTGGAGAGCATTTGTAGGCATTTAAACAAGAC R 2 1 2 1 101000 r 74 goat snp35594-scaffold429-416434 15 2182412 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773773 Affx-122975281 AX-385260913 15 76771090 TCATTTCCCTGAAAGCAAATCCAACGTGACAGAAG[A/C]TGGATGAATAATGTCAATTCTACTGAAAATGTCTT M 2 1 2 1 101000 f 74 goat snp35595-scaffold429-454094 15 2144417 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785936 Affx-122952860 AX-385272973 15 76801454 TTTTTCTACGTCTTCCCTTTTATCTCACCAACTTA[C/T]GCTTATTTTTCAGGTTCCAATTTAACCAGCTCTTC Y 2 1 2 1 201000 f 74 goat snp35596-scaffold429-484458 15 2114367 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390429 Affx-122967637 AX-123260786 15 76834190 AGGGCAGGTATGAGGGGGCAGTTTCGGGGCAGAAA[C/T]GACTGCACAGTGTGGAAAGCACCCTTGAACCCACG Y 2 1 2 1 101000 r 74 goat snp35597-scaffold429-517194 15 2081371 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404038 Affx-122957170 AX-123274390 15 76867126 TCCATGGGGTCACAAAAGAAGTGGCCACAACTTAG[C/T]GAAACAATGAAAGTATGTGCGCTGTATTGTGAATG Y 2 1 2 1 101000 r 74 goat snp35598-scaffold429-550130 15 2047476 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377152 Affx-122978221 AX-123247511 15 76905451 ACCTTTCTCTTTGCCCAAACTGGTGTTAAGTGCCA[C/T]GATCTGGGGGCACCGCGTCCAAATGCTTGTCCCAT Y 2 1 2 1 101000 f 74 goat snp35599-scaffold429-588455 15 2011199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272853 Affx-1111833056 AX-502493263 15 76907357 TTATTTCTTTTCATTGATTTTTGTACACTGTTGAA[A/C]AAATTGCATTAGTTACTTATTCTCAGACAGAACTG M 2 1 2 1 101000 r 74 goat 15_76907357_AF-PAKI 15 76907357 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448000 Affx-122923736 AX-123318336 15 76934549 CACAATACATGCTTCATTTTGGAGATTTATAAAGC[A/G]TATTATCACACTAAAGCGTCCGAGAAATTATTTAA R 2 1 2 1 101000 f 74 goat snp35600-scaffold429-617553 15 1982204 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423526 Affx-122942446 AX-123293872 15 76977541 GAGAATGCCAGCAGAAGGGGAGTGTACCTCCTGGG[C/T]AAGTGCTTCTCTGTAAGTCATTTGATACCAAGAAC Y 2 1 2 1 101000 r 74 goat snp35601-scaffold429-660545 15 1941543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444901 Affx-122926255 AX-123315238 15 77022558 GAGACACTGATACACAGTCAGAGAGCCTGTTAGTT[A/C]TGTGTTTATGGCCCCATCTCTAGACAGAGGAAATG M 2 1 2 1 101000 f 74 goat snp35602-scaffold429-705562 15 1895270 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396998 Affx-122963144 AX-123267353 15 77056578 GAAGGTATGAGGCAGACAGTAAGGACGAGCTTCCT[A/G]CTCAGGCTGTTGACTAGAAGTCCCCATCCAGAAAG R 2 1 2 1 101000 f 74 goat snp35603-scaffold429-739582 NW_017189682.1 15784 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409229 Affx-122953154 AX-123279580 15 77088959 GGAGAGCTCCATGTCTCTACAATTCACTCCTGGTT[C/T]CCTTACACCAGCCTCTGAAATACCAACAACACTCC Y 2 1 2 1 101000 r 74 goat snp35604-scaffold429-771963 15 1839366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452171 Affx-122921238 AX-123322504 15 77136962 GTTTTCCTCAATGTTTCTTGCACACATCCACTCAA[C/T]GCTTTTCTAAAATTTTTATGTCCTCATAATAAAGC Y 2 1 2 1 101000 f 74 goat snp35605-scaffold429-819966 15 1790505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427012 Affx-122939845 AX-123297357 15 77181173 AATAATGATCTGATTCATACTAATAGTTCAATAAA[C/T]GTTTGTTTAAAGAATTCAGTTTGGTGCCCAGAAGT Y 2 1 2 1 201000 f 74 goat snp45522-scaffold621-13951 15 1746274 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277088 Affx-1111835674 AX-519550595 15 77222525 ATTTCTAATATCTTAGAAATGAAACAATTTTTTTT[A/T]AAATTATAGGTTCCAAAGATGTACAGTGGGAATTT W 4 1 2 1 103000 r 74 goat Random2.2K-1560 15 77222525 A T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406332 Affx-122955447 AX-123276684 15 77236019 CTTTCCTTTGCACTTGAACCTTAGACAGGATCTCC[A/G]TGATCTTGCCCTGCTCCTAGCAGTAACTGTATTTC R 2 1 2 1 101000 f 74 goat snp45523-scaffold621-68797 15 1691203 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766351 Affx-122976297 AX-385253731 15 77265146 ATCACAATGAGACTGCTTGTCTCAAAAAGTGACCC[A/G]TGGGAAATCTGTTTCTTCAATATAGCAATATTTTT R 2 1 2 1 101000 f 74 goat snp45524-scaffold621-97924 15 1662103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802377 Affx-122944135 AX-385289281 15 77304993 ACTAATAGTTAATCAGTCTGGGTGCCTAATGCCAG[C/T]AAACCACAAGGATGATCGCTGGAGTCTAGGTCCCC Y 2 1 2 1 201000 r 74 goat snp45525-scaffold621-137771 15 1621089 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779905 Affx-122964030 AX-385267004 15 77354456 GAGGCCTCAAATTTTCCAAGTTGGCAGAATCTAAG[C/T]AACCAAGGAAGTAACCAAGCAAGCAAGACCTCTTC Y 2 1 2 1 101000 r 74 goat snp45526-scaffold621-187234 15 1571017 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769109 Affx-122927917 AX-385256284 15 77409883 TGGTGCCCAAGCAGGAATTTGTGGTCATGCTATGA[C/T]GCTGGGAGCAGCTGAATAATCAGTCACTTTGCACT Y 2 1 2 1 101000 r 74 goat snp45527-scaffold621-242661 15 1515217 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446790 Affx-122925304 AX-123317126 15 77471907 TTGGTTCACTAGCCGGCGTCTATAGCCGCCACTTC[C/T]TGCCATCATCACGTTGACCTTATCCTTGGTCTCCG Y 2 1 2 1 101000 r 74 goat snp45528-scaffold621-304685 15 1452835 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274342 Affx-1111834196 AX-519547937 15 77489290 GTGTTTCCAGAGTTTGAATGTCTACTTCATGCAAC[A/G]CTGCAGGA R 2 1 2 1 101000 f 74 goat GoatD01.025059 15 77489290 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38401495 Affx-122958944 AX-123271848 15 77501886 TCCCACTCTGGTCACGGGAAGGCAGTGGAGTGAGA[C/T]AATGCAAAAAAGCTCCACCAAGGAGTGGCTCTCAA Y 2 1 2 1 101000 r 74 goat snp45529-scaffold621-334664 15 1422579 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794370 Affx-122934868 AX-385281333 15 77557581 AGATCAAGTTAAGAACTCCCTTATTCAATTAATAA[C/T]GAAAAATGTCCTGAACAAAATTACTTCCAACTCAG Y 2 1 2 1 202000 f 74 goat snp45530-scaffold621-390359 15 1367928 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787594 Affx-122975438 AX-385274618 15 77631245 AAAGAAGAAACATAATGGATAGCTTTTCATCGGGC[A/G]CTTGATTGTTTGCTAAGAATAATCATTGACTTTGG R 2 1 2 1 101000 f 74 goat snp45531-scaffold621-464023 15 1294072 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425460 Affx-122941508 AX-123295806 15 77661394 TAGAATAAATGAACAAACACACATTCTTTAGAATA[A/G]GACCCTAATTAACTGAAAGGTTGAGAAGAGACAAG R 2 1 2 1 101000 r 74 goat snp45532-scaffold621-494172 15 1264041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452544 Affx-122920533 AX-123322877 15 77690098 GGCTGCTCTTTTCTCGTCCTTGGTGCTCCACTCCA[C/T]GCCACAGTCTGCCACTCGGCACCTTGAGAGACCCA Y 2 1 2 1 101000 f 74 goat snp26883-scaffold2832-162294 15 1236640 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404436 Affx-122956758 AX-123274788 15 77744712 TGTCTTAAAGTATCCTTCTGGTTAAAGTTATAGCA[C/T]GCTTTTTGTTGTGAAGTTGTTCTTTTCAGTTTCAG Y 2 1 2 1 101000 f 74 goat snp26882-scaffold2832-107680 15 1181648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441763 Affx-122929112 AX-123312100 15 77806259 AGAGGCACAGGGAATGGGCAGGAGCTGGGAAGTGG[A/G]CTCAAGGACCTGGCAAGTTCAGTCTTGACTCTGTC R 2 1 2 1 101000 r 74 goat snp26881-scaffold2832-46133 15 1120002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443240 Affx-122927557 AX-123313577 15 77866468 ATCGTTTTAATTACATTACAGTGAAAGTGTCAGTC[A/G]CTCAGTCCTGTCCGACTCTTTTCGACCCCATGGAC R 2 1 2 1 101000 f 74 goat snp4333-scaffold1135-13308 15 1060131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376295 Affx-122978373 AX-123246654 15 77916423 GTGTATCCCCACCCACAGTGTGCAAGCATTCTCTT[A/C]TCGCCACATCCTTACCAACACCTGTGCTCTCCCAT M 2 1 2 1 303000 f 74 goat snp4334-scaffold1135-63263 15 1009937 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793680 Affx-122923988 AX-385280653 15 77932464 CTAGTGAAAATCTCCAACCAATATTTACATCAGTC[A/G]CCTTTTCTGGTACAAACCATCTTGAAAGCTGGTGA R 2 1 2 1 101000 r 74 goat snp32417-scaffold3693-14562 15 942715 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438392 Affx-122931298 AX-123308730 15 77991878 AGAGCAGGACAAACCAGGACTGGAGGAAGGTCGCA[A/G]AAGAGGTGGCTGATCACGTTGGGCCCGCAGAAACC R 2 1 2 1 101000 r 74 goat snp18913-scaffold1906-44753 15 892440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785391 Affx-122967093 AX-385272436 15 78094642 TTCTTTCCTGTATCTTTCCGGGTCTACCTGTTTAC[A/G]TTTCTTCGTTCCCACCAAACTTCCCACTCACAAGC R 2 1 2 1 101000 f 74 goat snp18915-scaffold1906-147517 15 786860 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380337 Affx-122975371 AX-123250695 15 78159727 ACCGAATGACCTGGACACATGCTAAGCCCCCCGCC[A/G]CGTGATTCCTTTCTTTTCAGTCTTACGTTGAGAGC R 2 1 2 1 101000 r 74 goat snp18916-scaffold1906-212602 15 720577 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378570 Affx-122976598 AX-123248929 15 78204197 AGTAACGTGGGACATGCAGGACTGTCACACAGAAG[G/T]TAAGAAACCAGCCGAAGTGTGAACCCAGCCACGTT K 2 1 2 1 201000 r 74 goat snp18917-scaffold1906-257072 15 676679 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423187 Affx-122942726 AX-123293533 15 78250220 TCTTTAGCTTGGCTTTAAATCATTCAGCGCTCAAA[G/T]CTCCTACTGTTTCCGCACATGAGGAAAATATCCAC K 2 1 2 1 101000 r 74 goat snp18918-scaffold1906-303095 15 632497 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394136 Affx-122965323 AX-123264491 15 78310842 AGTATAACAGGTAGAAGTTAAATATACTTGAAGAT[A/G]TTGGGGCTGAGAAATGCTGAGCAATTGAGTATAAA R 2 1 2 1 201000 f 74 goat snp18919-scaffold1906-363717 15 570810 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388253 Affx-122969782 AX-123258611 15 78354248 GAGATCAGACAATGCTTGAGTTATTTATGGGTCCA[A/G]TGTTGTTCTAGGTGTGGACCCTGGAAGGAAAAGCT R 2 1 2 1 101000 f 74 goat snp18920-scaffold1906-407123 15 527932 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415678 Affx-122948546 AX-123286027 15 78401881 TCTCGACAAAGCTTCAGTCTGACTCTGCTGTGACT[A/G]TACTGACTTCACAACTGTGTGAAGGGGTGGTCACA R 2 1 2 1 102000 f 74 goat snp18921-scaffold1906-454756 15 479510 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386412 Affx-122970819 AX-123256770 15 78436111 TCGCATCTTGGTCACAAAAACACAGTCGATTTGTC[A/G]GTGCAAACACACAGTCTCCTTTTAGGTCGTGGGTG R 2 1 2 1 101000 r 74 goat snp18922-scaffold1906-488986 15 444574 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783947 Affx-122930031 AX-385271001 15 78465067 TGGTCTCATTGAATCCTAGCAATAGCTGAGGATAC[A/G]TATAGTGAAGGAGGTTTATTTTAGATGCTTGATCT R 2 1 2 1 101000 f 74 goat snp18923-scaffold1906-517942 15 415871 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435645 Affx-122933762 AX-123305985 15 78519873 CTCGACCTCCTCACGTCAGCATCCGGGGTTGAAAC[A/G]TTCTTTCCTCCTTTCCGTTTCTGGTTGAGTCTCTC R 2 1 2 1 101000 r 74 goat snp18924-scaffold1906-572748 15 361794 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453876 Affx-122919517 AX-123324209 15 78582275 TCAGCTAAAATTAAATACGGGTGAGAGTTAAGATA[C/T]GGCTTAACCTGAGGCAAGTTCCCTCCAGCTGTGAA Y 2 1 2 1 101000 f 74 goat snp18926-scaffold1906-635150 15 299197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383515 Affx-122972638 AX-123253873 15 78631062 CCTGAGCTCCCCCATCAACAAGTTACTGAACCCCA[A/G]TAGTCCTCGGTTTCCTTCTCTGTAAAATGGGGGCA R 2 1 2 1 101000 r 74 goat snp18265-scaffold1853-29139 15 250979 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452754 Affx-122920266 AX-123323087 15 78701083 TTTACACTTCTGGGAAGTAGACAAAGTAGCGTGGT[A/G]TGAAATAATGGAACTTCCTTCTATAAAATAAAGGC R 2 1 2 1 201000 r 74 goat snp18266-scaffold1853-99160 15 180885 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424270 Affx-122941995 AX-123294616 15 78731500 AGTTTCAGTAGAATTCACAGAAAATGTATTCATCA[C/T]TCACCCTACCTAAGGACTCTTGGTTCCAGAAAGTG Y 2 1 2 1 101000 r 74 goat snp18267-scaffold1853-129577 15 150040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402170 Affx-122959191 AX-123272523 15 78803170 AGGGAAATGAAGGCTTTTCATAGCATTACAGAAAA[C/T]GTAACAGTCTGGAGAAAAATGAACATAAAAACTTC Y 2 1 2 1 201000 f 74 goat snp18268-scaffold1853-201247 15 78356 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386747 Affx-122970136 AX-123257105 15 78868614 AACACCTTCCTTCAAGAGGCAGATGGGAGGACAAG[C/T]GGTTTAGTCTAGGGATGACACTTAGACCTGAACCT Y 2 1 2 1 101000 r 74 goat snp18269-scaffold1853-266691 15 11640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415324 Affx-122948801 AX-123285673 15 78905141 TTTCAAAGATACCTCTGAAAATGCAAAAAGTAGTT[A/G]TTTCAGGGGAGTGGGATTGGAGTGATTGCTTGTGA R 2 1 2 1 202000 f 74 goat snp18270-scaffold1853-303218 15 30900595 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801783 Affx-122964551 AX-385288691 15 78972597 TTAGCTCCCTGATTCTGTCCTTCTTCAGTCTAAGA[C/T]AGAACTAAGATTTAGGGAAGAGTGCAAAGATACAA Y 2 1 2 1 201000 f 74 goat snp18271-scaffold1853-370674 15 30948421 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277090 Affx-1111835675 AX-519550597 15 79042438 GGCAAAATCAAGAAATAATCTCAATGTTCATCACC[A/T]GCTGAGTTGATACACACAATGTCAAATATCCATAT W 4 1 2 1 102000 r 74 goat Random2.2K-1563 15 79042438 A T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272801 Affx-1111833057 AX-519546497 15 79607890 AAAGAGCTTCAAGTGCTAAGATACTGACAGATGTA[A/G]ATACATTTTATGTTGTTTCTAGTGTACTTCTTCAT R 2 1 2 1 101000 f 74 goat 15_79607890_AF-PAKI 15 79607890 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276960 Affx-1111835676 AX-519550468 15 80336088 GCTAAGCACTGTTACTAGTGCTTAACAGCCCTGAG[A/G]CTGCCAGTACAAGGTAGAGAGGCTACTAAAATAGA R 2 1 2 1 101000 f 74 goat Random2.2K-1565 15 80336088 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320782896 Affx-122920603 AX-385269966 16 25565 AATGCTACTGTCTCAACGCTTTCCATTTCTCTCAG[C/T]GCCCCACTGCTCTACCATGTCTGTGTGTGGAGTGC Y 2 1 2 1 202000 r 74 goat snp45213-scaffold617-25565 28 44630919 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778389 Affx-122943715 AX-385265504 16 88766 TTTTCCTACTTGGGAACAGTATAGAACATAGAAAA[C/T]GCTTGCTTACTTACTATGGTGTTCATTATTTGGTT Y 2 1 2 1 101000 r 74 goat snp45214-scaffold617-88766 16 54847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272860 Affx-1111833060 AX-519546550 16 139182 ATACTGGGGTAACGTAGGGTGCAGACCAGGGTACT[A/G]CTTTTCACCTCGTGGGATCCCGCCTTTTACAGTGG R 2 1 2 1 102000 r 74 goat 16_139182_AF-PAKI 16 139182 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781955 Affx-122943297 AX-385269036 16 142812 TCAGTATATTTCTGGAGCTGTAAACTGTAGTAGCC[A/G]TTCATTGAGAACATATTATCATTGAGAACATTATC R 2 1 2 1 101000 f 74 goat snp45215-scaffold617-142812 16 109745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797796 Affx-122941221 AX-385284735 16 198946 GAGCAGCACTGTTTATACTTACTGGGCAACTGCAG[C/T]AATAGTAGACTGGACTGATCAGTTACAGTCTGTTG Y 2 1 2 1 201000 f 74 goat snp45216-scaffold617-198946 16 168847 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411015 Affx-122951980 AX-123281365 16 245419 TCCAGGGGCAATATAAAAGGCAGCCTCCAAAGACT[A/G]CTTCTACTCTTAGTAAGGGGCAAGCCAGATATCCT R 2 1 2 1 201000 f 74 goat snp45217-scaffold617-245419 16 216009 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443669 Affx-122927185 AX-123314006 16 273933 AAAAGCTTTTGACAAAGCTCAACAGTCATTTATGA[G/T]AAATTAAAAAAACAAACCGTTCAGAAAGTGGGCTT K 2 1 2 1 103000 f 74 goat snp45218-scaffold617-273933 16 244654 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384091 Affx-122972847 AX-123254449 16 352662 AGGGGTGGTGGTAACAGGAGGCACCAGTTGCTACT[A/C]TTCACAGAGGGGCCTTGTGTTCACAGTGAGCTCGC M 2 1 2 1 201000 f 74 goat snp45219-scaffold617-352662 16 324218 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383069 Affx-122973746 AX-123253427 16 381379 TGTCTTCCCTGCTGTGTCAGACCTCAGGACACAGA[C/T]CTGTGTGTCTCACCTTTGGCCCAGATCTCAGGACT Y 2 1 2 1 201000 r 74 goat snp45220-scaffold617-381379 16 352445 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390398 Affx-122967659 AX-123260755 16 434541 TTAAAAAATTTTAAAAGTACATGGAGTTTGGGGGA[A/G]ATTCAGCAAGGGCTGTAGCTCAACTATGTGGGGTG R 2 1 2 1 101000 r 74 goat snp45221-scaffold617-434541 16 406691 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397605 Affx-122961981 AX-123267960 16 488459 CAGCTTCAGATCTGCGGCTGACCCCAAGTGCCTGT[A/G]CTCCGCTGCTGAGGTTCCAGCACTTGCAGTCACAC R 2 1 2 1 101000 f 74 goat snp45222-scaffold617-488459 16 460704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391857 Affx-122966989 AX-123262214 16 531497 TTTCTATCATTAAAACAATTTAAGATTCAGGTTAA[C/T]GCTTAGCACATTCTCATAGCCCCCAGCCTTCACAT Y 2 1 2 1 101000 r 74 goat snp45223-scaffold617-531497 16 504193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784401 Affx-122966326 AX-187122437 16 590515 GGAGACAGCCTATGGTTAGTGAGAAATTTCTGCCC[A/G]TTTTCCCACTCAGATCCTAACAGACTGTAGTAATA R 2 1 2 1 101000 f 74 goat snp45224-scaffold617-590515 16 564290 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411033 Affx-122951968 AX-123281383 16 621933 TTCAGCAAGGGCTTTGATAGATCCCAGCTCTCAGG[A/C]TGCGACCGGCCCACCTTCATCCACTGCCATGTCTT M 2 1 2 1 202000 r 74 goat snp45225-scaffold617-621933 16 595629 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772404 Affx-122966142 AX-385259557 16 717216 CTCACCTGTAGCAAGTGGGCCAGCAAAACAAGGGA[C/T]GGTAATTTGTTTTAGGCTTTGACTTCATCAGGTTA Y 2 1 2 1 101000 f 74 goat snp45227-scaffold617-717216 16 691606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436014 Affx-122932744 AX-123306353 16 771453 TGAATGCCTCTGATGTATCCTCTCCAGGTGAAAAT[A/G]TCCTCCACCAAAACAGGGAAAGACGTGATGCACGC R 2 1 2 1 101000 f 74 goat snp45228-scaffold617-771453 16 746305 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773036 Affx-122976852 AX-385260180 16 808649 CCCCACCCAAGACTTCCTATGTCAAAGGATTTTGA[A/G]CATTTCAACTTTATCCTGCAACAAGCAGCCTCAGA R 2 1 2 1 202000 f 74 goat snp45229-scaffold617-808649 16 895539 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419705 Affx-122945917 AX-123290053 16 844500 TCAGGGAGGGACAGAGAAAAAGGAGTTAGGAAGAG[C/T]AAGAGGCTGTCACCACCACCAAAATTAGCAAATCC Y 2 1 2 1 101000 r 74 goat snp45230-scaffold617-844500 16 818823 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763260 Affx-986697789 AX-385251182 16 856527 AACATCATTTACATAGTAGACTCTGCAAGAAATAG[C/G]AATGGATGAAGTAATCCAAAAAGTTCTAGTACCTT S 4 1 2 1 600010 f 74 goat 16_856527 16 856527 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 38454227 Affx-122919672 AX-123324560 16 879437 CAAACCCTTTCTCATAGCTGCTGCTGTTTGCTTCT[A/C]GTTCCCAGAGAGCTCCCATTCCCAGAGGCCAACGT M 2 1 2 1 103000 f 74 goat snp45231-scaffold617-879437 16 853287 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378811 Affx-122976556 AX-123249170 16 908894 GGTTTTACCCACGTGCCATGCTTCCTGCGTTGTTT[A/G]AATATAGTCATTCAGGACTTTTTCTGTGAGCACAA R 2 1 2 1 201000 r 74 goat snp23551-scaffold2374-27120 16 953028 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783633 Affx-122942559 AX-385270692 16 965587 AAAAGTCCAGTTCTTATTTTTCCAAATGCCTGTGA[A/G]GGTGATATAGAACTTTTCTTTAAACTGAGTAAAAG R 2 1 2 1 101000 f 74 goat snp23552-scaffold2374-83813 16 1009661 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779114 Affx-122973474 AX-385266219 16 994246 CCTAAGGAGTCATGGGAACACAAAGGCATGGGAAA[G/T]CATTCACATGAGTAGGAGTAATTCTAGGACAGAGA K 2 1 2 1 101000 r 74 goat snp23553-scaffold2374-112472 16 1039268 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433223 Affx-122935619 AX-123303564 16 1027753 TAGGTTTTATAAGGCATGTACCTCATTCAACTTTG[C/T]GACTTGAGTGTGAGTAGTGATGCCACTTACTCTGA Y 2 1 2 1 101000 f 74 goat snp23554-scaffold2374-145979 16 1072870 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786635 Affx-122929448 AX-385273667 16 1051026 CCATCTTATTAATTTCAACTTTTTGTATCTTGGAA[C/T]GTAGAGTGTATCTCTTATAGACAGTTGGATCATGT Y 2 1 2 1 101000 r 74 goat snp43836-scaffold590-278095 16 1096342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394067 Affx-122964973 AX-123264422 16 1134471 CTCACTTTTATTTTATTATCTTCTTGAAACTTCAT[A/G]TCAGTTCACTCCACTTGTGATTAGGTCTCTCTCTC R 2 1 2 1 101000 r 74 goat snp43834-scaffold590-194650 16 1180765 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391462 Affx-122966729 AX-123261819 16 1168552 CGTAATGGGATTTTTATATCTCCTCCACCATGTTT[A/G]CCCCTAGATTTCTGAGAAGCCCCTTTAGAATCACA R 2 1 2 1 101000 f 74 goat snp43833-scaffold590-160569 16 1215185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453751 Affx-122919608 AX-123324084 16 1223599 GCCTCAGTTTTCCTATCTATAAATTGGAAGTCAAC[A/G]TACACACCACCAAATTGCTTGGAGCCTCAGCACAG R 2 1 2 1 101000 r 74 goat snp43832-scaffold590-105522 16 1269819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394085 Affx-122964959 AX-123264440 16 1252612 CCTGGAATCAACCATACCTACCTTGTCTCACCGCT[A/C]GCCATCTCTAACTTAGAAATCCGTTTTCCAGCCTT M 2 1 2 1 101000 r 74 goat snp43831-scaffold590-76509 16 1296053 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381651 Affx-122974753 AX-123252009 16 1291241 TGACTGAAGAATTAATGCAGGATGATTTTCCAGAA[C/T]GGAAGGGCATGAATTTCCAGGTTGAGGGCATCCAC Y 2 1 2 1 101000 f 74 goat snp43830-scaffold590-37880 16 1333848 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405302 Affx-122956843 AX-123275654 16 1331637 AACTGAAGGCGAGAACAGCTTCTGTGAAAAGGAGA[A/C]ATATTAACTTTAAAACCTTCACAGTCTGGGAACAT M 2 1 2 1 101000 r 74 goat snp19644-scaffold1986-2417 16 1374096 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438457 Affx-122931246 AX-123308795 16 1371422 CTGCACAGCTCCTGGTGGTCAAGGATGCAAAGGCC[A/G]AATAGTGGGCAGGGAGTAAACATACATTTTCAAGT R 2 1 2 1 101000 r 74 goat snp19645-scaffold1986-42202 16 1412550 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773932 Affx-122929978 AX-385261071 16 1400680 AAAATAGTTTTTTTGAATGCCCATAGTTTCAAAAA[C/T]AACCAGGCTATACTACATATTAATTATACTGCCTA Y 2 1 2 1 102000 r 74 goat snp19646-scaffold1986-71460 16 1442060 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397465 Affx-122962095 AX-123267820 16 1440362 TACAAGACAGACGGCCATCCAACTCCTGTGTAAAT[A/C]GGTTCCTCTTCGAGCACCGAACAGTCTCCCCATTT M 2 1 2 1 101000 f 74 goat snp19647-scaffold1986-111142 16 1481710 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385978 Affx-122971526 AX-123256336 16 1488331 CCATGTAAATTCCTGAAGGTGCAAAAGCATGCCTC[A/G]CCTCCCTACACAGTCAAACCAAGCAGAAGCAAAAG R 2 1 2 1 101000 f 74 goat snp19648-scaffold1986-159111 16 1528331 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454070 Affx-122919384 AX-123324403 16 1524163 AGGTTATGAATAAAAAAATTGAGCTTTGTGGCTAC[A/G]CTGCCAAGGCTGGACTCTATCAACCTGCGGAAGGA R 2 1 2 1 101000 f 74 goat snp19649-scaffold1986-194943 16 1564150 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425776 Affx-122940718 AX-123296122 16 1564937 AAAACATCAATAGAAAATAAGTTCAGATAGGTGCA[C/T]GGTGGCAAGTTCCATCACACCCCAAATGAGTTAGG Y 2 1 2 1 201000 f 74 goat snp19650-scaffold1986-235717 16 1606308 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384589 Affx-122972988 AX-123254947 16 1594488 GTTTTCATTATAGCAAGTCATTTATTTATTTATTT[A/G]GTTATGAACTCCTTGGGAAAGGTCGGAGAAATGTT R 2 1 2 1 101000 r 74 goat snp19651-scaffold1986-265268 16 1635850 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415697 Affx-122948532 AX-123286046 16 1643782 ATCTTATTTTTAGGTAGCCTGTTTTTGAAATGTTC[G/T]TTGAATGCAATGCTGGCTTCTTTGATAGTTGCTAA K 2 1 2 1 101000 r 74 goat snp19652-scaffold1986-314562 16 1684914 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420213 Affx-122945541 AX-123290561 16 1676019 AATAACTGTCAATTACTGATTCTGAGGTACAGTTC[A/G]TCTGCAATCACAGAACTAGTGAGGGGAATAGTTGG R 2 1 2 1 101000 f 74 goat snp19653-scaffold1986-346799 16 1717272 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404645 Affx-122957309 AX-123274997 16 1708557 CTTGGAAGCTTCCGGGATAACTTGGGGAAGGTGTG[C/T]GTGTGTGGAGGAGAGGGGGTGGCTGGAATTGCTGT Y 2 1 2 1 303000 f 74 goat snp19654-scaffold1986-379337 16 1749298 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416586 Affx-122947651 AX-123286934 16 1745738 GCACAAATGAAATCTGGATAAACGCTGTGAATTTC[A/G]TCAGTGTCGGTCTCCTGGTTTTGATAATGGAACTA R 2 1 2 1 202000 f 74 goat snp19655-scaffold1986-416518 16 1786354 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430472 Affx-122937252 AX-123300813 16 1785820 GGTGAAGGCTCAATAAATGTCAGTTATTTTGACGA[C/T]GCTGATTATGATGATAGTGACTGTGGATGTTTTTA Y 2 1 2 1 201000 r 74 goat snp19656-scaffold1986-456600 16 1826059 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392971 Affx-122965676 AX-123263328 16 1872257 CAAGGTGCCGCTTAGAGCATGGTCTCCAGAGGCAC[A/G]CTGTCTGGGTTTTAATCTTTCTCAGGCCATGAGAC R 2 1 2 1 101000 r 74 goat snp19658-scaffold1986-543037 16 1913028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405770 Affx-122956491 AX-123276122 16 1914561 TTCTGAACTCCAGTCTCAGTTGTAAGTTCTTTCAT[A/G]CCTGCTTGTCCAGGTAAAGTCACTAAGTGTTCTCA R 2 1 2 1 101000 f 74 goat snp19659-scaffold1986-585341 16 1955022 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454306 Affx-122919256 AX-123324639 16 1951350 ATTACCACAGGCAATACCACCTAAAAAGTATCTCC[A/G]TCTCATCACTGTAAAGAGCCAGCAAATGATCTAAA R 2 1 2 1 101000 r 74 goat snp19660-scaffold1986-622130 16 1992124 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384611 Affx-122972176 AX-123254969 16 2008806 GTGCTCACGTTGGAAGGTGAATTCACTGCCCTGAG[A/G]CCTTGCGACAGAGACCCTGTTATTTTCAGTCTGCT R 2 1 2 1 101000 r 74 goat snp19661-scaffold1986-679586 16 2049749 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378672 Affx-122977081 AX-123249031 16 2040672 AATTTACATAGTATCCTCAAAGTTTATCCGTGTTG[C/T]AGCACGTGATAGAATTTCCTTCCTTTTTAAGGCTG Y 2 1 2 1 303000 f 74 goat snp19662-scaffold1986-711452 16 2081641 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766510 Affx-122949210 AX-385253873 16 2086959 GAAAATGTCCACTAGGCACCTACTAGGTAGAAGGT[A/G]CAGTTTGGATAACTAGGAAATGTAGTTGATGAGGA R 2 1 2 1 101000 f 74 goat snp19663-scaffold1986-757739 16 2128448 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273650 Affx-1111833721 AX-519547263 16 2104751 CACCCCTCTGCAGAAGGTGACCCCAGAATCAGAGC[A/G]GCTGAGCTGAAACCCTCAGGATGAGGGTGCAGGGA R 2 1 2 1 202000 r 74 goat GoatD01.002452 16 2104751 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447155 Affx-122924440 AX-123317491 16 2115736 TCTCGCTGGAGATTATTGAGTGTGGAGAGAGACCA[G/T]CCTAGTGGTGGGCCTCCAGTGGCAGCCGTCTGTAA K 2 1 2 1 101000 f 74 goat snp19664-scaffold1986-786516 16 2156570 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447416 Affx-122924395 AX-123317752 16 2149658 CACCCTCCCGCCTCCCTCCACTTGCCCTGAAACCA[G/T]CACCTTTCTGTGGATAAACCAGAGCTGAGGGTAAC K 2 1 2 1 101000 r 74 goat snp19665-scaffold1986-820438 16 2190225 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411445 Affx-122951819 AX-123281795 16 2189318 CAAGATGAAATTAAAAATTAGCTGCTTAATTGTCC[C/T]AGCCGCACTTCAAGGCCTCATGGCCGCATGGGATG Y 2 1 2 1 101000 f 74 goat snp19666-scaffold1986-860098 16 2226314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453574 Affx-122919764 AX-123323907 16 2220349 CTTCTGCACACCTGCTTTCTTCACTCTGGATTTTC[A/G]GAGAATTTCAAACACCTGGGGGACACAGCCATTCA R 2 1 2 1 202000 f 74 goat snp19667-scaffold1986-891129 16 2257225 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388417 Affx-122969282 AX-123258775 16 2252943 CAAGAGTTGGTATCTATACTATAAAGCAAGTCTAT[A/G]CAACAATAAGGAAAAACAATCAGAAAAAAAGCTAA R 2 1 2 1 101000 f 74 goat snp19668-scaffold1986-923723 16 2289541 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443382 Affx-122927402 AX-123313719 16 2288222 GGCTTCTGCCCTGCACTCTCCGGGTAGACACTTCT[A/G]AAGTATTCTAAGGTCCACAGCTCCCATGGATAGGC R 2 1 2 1 101000 r 74 goat snp19669-scaffold1986-959002 16 2325375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394725 Affx-122964332 AX-123265080 16 2331879 ACTCCCACGTACAGATAAAATTTAACAGTGTACTT[A/C]TGCTCTTCTCCTGCTTATCTCTTTAATGTCAGTTT M 2 1 2 1 101000 r 74 goat snp19670-scaffold1986-1002659 16 2369126 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420259 Affx-122945059 AX-123290607 16 2373647 GTTCACTGCTCTTCCTGTCTGCTTGGAGTGAAGAG[C/T]GATTCGAAACCAAAGAGCTGAGGGAAAGTCACAGC Y 2 1 2 1 101000 r 74 goat snp19671-scaffold1986-1044427 16 2411365 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420374 Affx-122944944 AX-123290721 16 2454386 TGGATCAGGGAGCAGGTTCCATTCCTACTTATCTC[A/G]GCTCCCTGGAGACAAGAGACATGAAGCCAGGGAGC R 2 1 2 1 101000 f 74 goat snp19673-scaffold1986-1125166 16 2480937 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770728 Affx-122971629 AX-385257892 16 2521742 AGAAGTGTTCTCCACTGCTCTTATCCACTCAGATC[A/G]CTCATCTGGTCTATATTTCTTGGACCCTCATATAC R 2 1 2 1 101000 f 74 goat snp19674-scaffold1986-1192522 16 2548229 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430549 Affx-122937022 AX-123300890 16 2566763 CAGATTCTGACCCTGAAGATAGGATTAGAGGGCAC[A/G]TCCAGGAGGGCATCAGTGTCCCCTGAAGGCACCAC R 2 1 2 1 101000 f 74 goat snp19675-scaffold1986-1237543 16 2593367 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451181 Affx-122921339 AX-123321515 16 2597709 CTCCCTTCGTCCCCTTCCCTGCTCTATTGCCCTTA[C/T]GGGGCTACCTGACTGCACACTACTTGCACTGTCTG Y 2 1 2 1 103000 r 74 goat snp19676-scaffold1986-1268489 16 2624296 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277093 Affx-1111835677 AX-519550600 16 2628933 ATGGATGGATGGATGGATAGGTAAACAGTAGGCGA[A/G]TGGACGAATCTGAGCCACATGACTCCACGGGGAAG R 2 1 2 1 202000 r 74 goat Random2.2K-1569 16 2628933 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38377494 Affx-122977494 AX-123247853 16 2633345 GCTCTACCCTGTCGTCCAAGAGGCCTTGGGCAGGC[C/T]GCTCCCCTTTCTGAGTCTTCCCTTCTTCACCTGGT Y 2 1 2 1 101000 r 74 goat snp19677-scaffold1986-1304125 16 2660159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451327 Affx-122921275 AX-123321660 16 2672749 AAAGTATAAAGAAGAAAATTAAAATCATTTATATG[G/T]CAACTACCCAGAAATAATCACTGATGTTTTCCTTT K 2 1 2 1 101000 r 74 goat snp19678-scaffold1986-1343529 16 2696218 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763262 Affx-986697791 AX-385251184 16 2672753 TCACCCGTTCTCATCTTTTTCACCTGTTCTCATCC[A/G]TTCTCATCCGTTGTCATCTGTGCTCACCCGTTCTC R 2 1 2 1 600010 f 74 goat 16_2672753 16 2672753 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 468272868 Affx-1111833065 AX-519546558 16 2698009 GGGCTACCTGGTTGGACTTCGTTCGCTTGTTTTGT[A/C]GGGTCAGTTTACTTACCTGAGCTGGGACTGTGCAC M 2 1 2 1 202000 r 74 goat 16_2698009_AF-PAKI 16 2698009 A C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398500 Affx-122961561 AX-123268855 16 2709797 TTAGGGGTTGTTAAAGGGGAAGGAAACGATTAAGC[A/G]TCATCTTAGGACATTTCTTAATCATAGTTCGTAGT R 2 1 2 1 101000 f 74 goat snp19679-scaffold1986-1380577 16 2733763 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396671 Affx-122962843 AX-123267026 16 2750700 ATTTTGAAGCCCTCAAAGTGTCAGCGCAGGCTCTT[C/T]CTCACCAACCTAGATTCTGTAAAATTTCTCTGCCA Y 2 1 2 1 201000 r 74 goat snp19680-scaffold1986-1421480 16 2775336 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413001 Affx-122951016 AX-123283350 16 2828632 AGCACGAATGAAGGGCACTCTGGTTCCAGAGCCGA[A/G]GCTGCTCCTCTTTCATATTAGTGATGCATGATTAG R 2 1 2 1 101000 r 74 goat snp19681-scaffold1986-1499412 16 2853174 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793274 Affx-122968262 AX-385280252 16 2879267 TTCCTGGACAGAAAGCATTTCTTCCCCAGGTCTTA[G/T]CCCACAATTATAACAGTAGGTATACCACTTAATTA K 2 1 2 1 102000 f 74 goat snp19682-scaffold1986-1550047 16 2904043 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777707 Affx-122933143 AX-385264826 16 2908806 ACCCCTTCTCCGTCCCTAATCTCTGAAGCCAATGC[A/G]GCAAGCTCTGAGGAAGGTCATGCTTAGAAATAATT R 2 1 2 1 101000 r 74 goat snp19683-scaffold1986-1579586 16 2934385 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394691 Affx-122964355 AX-123265046 16 3024959 TGACGTTCCAGGAGCTGAGCAGGGCAGAGCTAAGT[A/G]CCAGGCCCCTGAGGCCCAGAGGAGCTCCCGGTAGA R 2 1 2 1 101000 f 74 goat snp19685-scaffold1986-1695739 16 3050709 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420056 Affx-122945130 AX-123290404 16 3071249 AGATCTGTTTTCTCGGCTAATATCATAAAGAACAG[C/T]AAACCTAGTTACGGGCCGTCCTGTGAAAACTCCTT Y 2 1 2 1 101000 r 74 goat snp19686-scaffold1986-1742029 16 3096831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378589 Affx-122976584 AX-123248948 16 3121372 CACACCCCTTAGGATTGTGGTTGTGGTTCCCACAT[C/T]CCCTAGGACCTCAGTTATTCTACTATCCTGTGGAC Y 2 1 2 1 103000 f 74 goat snp19687-scaffold1986-1792152 16 3144637 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421184 Affx-122944159 AX-123291531 16 3158515 CCCTCACTCAGTAAGCATTTACTGCGGGCCTGCTA[C/T]GTTCCAGGCGCTGGCCAAGGGCTGGTCAAGTCGCA Y 2 1 2 1 101000 f 74 goat snp19688-scaffold1986-1829295 16 3181526 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376537 Affx-122977996 AX-123246896 16 3196219 TTGGATCCGTATTGACTTTTATCTTATATATTGAC[A/G]ACACAGGTACAGTGTGTCATTTAGCTGGTAAGATG R 2 1 2 1 101000 f 74 goat snp19689-scaffold1986-1866999 16 3219193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413464 Affx-122950668 AX-123283813 16 3227876 GCAGCAGGGATTGGTCGCACATCCCCTTCCCTTCA[C/T]GGGGTCCACGTGGCTCCTGCCTCTTGGGCTGCATG Y 2 1 2 1 101000 f 74 goat snp16425-scaffold173-1231017 16 3251767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786131 Affx-122952335 AX-385273167 16 3277775 AACTCTATTCCTAAAACGTATAGAAGTGTAATAGC[A/G]CACAATAGGTAGAATCTCAGTCTTCCAGTACAGAA R 2 1 2 1 101000 r 74 goat snp16424-scaffold173-1181118 16 3301870 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438233 Affx-122931436 AX-123308571 16 3309660 AAAATAAGTCTTTCTTTATACCCCAGCATATATTC[A/G]TGAAAAGGAATGACAGAAACAGGGTTTTAGACGTA R 2 1 2 1 102000 r 74 goat snp16423-scaffold173-1149233 16 3335024 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424406 Affx-122941815 AX-123294752 16 3356363 AGCCTCAGGCAAATGGAGAATTAAAGCTTGAAACC[A/G]TTCCAGATAAGTTCAAGTGGCTTTACAAAGAAGTT R 2 1 2 1 101000 r 74 goat snp16422-scaffold173-1102530 16 3381290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417516 Affx-122946945 AX-123287864 16 3385427 TGGGAAAAGGGTTAGGCCAGGCAGCAAAACACCTC[A/G]ACCAAAATGCAACTCAGGGAGTCTCCCTCCATGGA R 2 1 2 1 201000 f 74 goat snp16421-scaffold173-1073466 16 3410987 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453975 Affx-122919454 AX-123324308 16 3420252 TTAACCATGAAAGCAAATGTGGCTGCCCATAGCAA[G/T]CATGGAGAATGAAAGACGTAGGTCTAAGCCTGGGG K 2 1 2 1 101000 f 74 goat snp16420-scaffold173-1038641 16 3446051 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386894 Affx-122970043 AX-123257252 16 3455395 CAAGCCTGGCATTACTGGGATGGCTTGAGCTTCTG[A/C]GGTGCTCTACTGAGCTCTGTTTCCCTTTGGGCCAG M 2 1 2 1 201000 r 74 goat snp16419-scaffold173-1003498 16 3481128 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771519 Affx-122970603 AX-385258677 16 3528328 CAAAGTCCTTTTAACATGAACTGAATTATCTGACG[C/T]ATTCCAAACACCAATCACAAAAATGGTGAACTCTT Y 2 1 2 1 101000 f 74 goat snp16418-scaffold173-930565 16 3554166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375533 Affx-122979107 AX-123245892 16 3574992 CAGGATCGAACACTGGCTAAAGCGGTAGGGGAAAA[C/T]GGCAAATTGTTTCTTCTGGTGTGAAAGGGCATGAG Y 2 1 2 1 101000 f 74 goat snp16417-scaffold173-883901 16 3600737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441299 Affx-122929456 AX-123311636 16 3633511 GGCTATTGATGAGGATCGATTAATTAGGCTCCAAA[C/T]AGGGATTAAGATCTAGGGAATTGAAATTCTCACTT Y 2 1 2 1 101000 f 74 goat snp16416-scaffold173-825382 16 3659139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400243 Affx-122960148 AX-123270598 16 3700458 GCTGAAGAAACGTTTCTGTTTTGCAGATGAGGAAA[C/T]AGGGTCAGTACTTTGTACTGAGATAATTCGGCTGT Y 2 1 2 1 303000 r 74 goat snp16415-scaffold173-758435 16 3725696 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272181 Affx-1111833374 AX-519545933 16 3701289 GAGGAACCAGAGATCAAATTGCCAACATCGGCTGG[A/G]TCATGGAAAAAGCAAGAGAGTTCCAGAAAAACATC R 2 1 2 1 103000 f 74 goat 3_109135646_AF-PAKI 16 3701289 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38397638 Affx-122962618 AX-123267993 16 3759298 TAACTCTGCCTACAAGGAAGGCTGTCCGGGCTCTC[A/G]AGGTCTTCATTTCTGTTTGTGATCCAGAGAGGGTC R 2 1 2 1 101000 r 74 goat snp16414-scaffold173-699595 16 3785347 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404961 Affx-122956416 AX-123275313 16 3803232 GCTCTACACAGAGCAGAAGGCCTCCTCCCTTTCTC[C/T]TCAGGCACCTTTCCGATGAGGCAATCCCCACCACA Y 2 1 2 1 101000 r 74 goat snp16413-scaffold173-655661 16 3829105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401757 Affx-122959504 AX-123272110 16 3855508 ACCTTCCGCCGCCTGGAGAAGGCCCGGCAGGTTTG[C/T]GAACATTCAGCTGGCTGGGGAGATAGCTACTTTCC Y 2 1 2 1 101000 r 74 goat snp16412-scaffold173-603385 16 3878476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380660 Affx-122975195 AX-123251018 16 3895475 TTCATGCCTATTTCTAAAACTTCTCTCTCCCTTCA[C/T]GAGTCTTAGATTTCTGTCTTGACATTCCCCAAAGG Y 2 1 2 1 101000 r 74 goat snp16411-scaffold173-563418 16 3917929 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403455 Affx-122957724 AX-123273808 16 3948251 ACGAAGCTTGGAAGGTTAGTGCACATATGAAATGA[C/T]GGAATGAGAATCCTAAAATATTTTGACAACTGGAG Y 2 1 2 1 101000 f 74 goat snp16410-scaffold173-510642 16 3970638 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395031 Affx-122964211 AX-123265386 16 3985240 AGCATTTCATCATTTAATTTGGGGGGAGCCCAGGG[G/T]GACCCCTGCCACAATATCACTCCTAGAGTATTAGA K 2 1 2 1 101000 r 74 goat snp16409-scaffold173-473653 16 4008124 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412056 Affx-122951712 AX-123282406 16 4037118 ATACTTGAGTGCTCCAGGAGGAGATCTTGTAGAGA[C/T]GAGACAAAGATCTTTCAGTCATTCAACATTTATGC Y 2 1 2 1 201000 r 74 goat snp16408-scaffold173-421775 16 4060059 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440478 Affx-122929377 AX-123310815 16 4068615 GCTGGAGCTGACGCTGGCATTTGGCTAAGGCTGCA[C/T]GCCAGAGGTTAATCATTGGCCTGGTATGAAAAGTC Y 2 1 2 1 101000 r 74 goat snp16407-scaffold173-390278 16 4091765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274714 Affx-1111834455 AX-519548300 16 4097562 ATAGCGCAGAGTTGATACGCGTTTGAAGGGGTACA[A/G]GTGGCAGGAATAGCCTCACATCTCCACGCACCTGG R 2 1 2 1 201000 f 74 goat GoatD01.036634 16 4097562 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320775239 Affx-122946831 AX-385262370 16 4111886 CTCTCACTACCTATGCTCTTGGTTTAGGTAAGTCA[C/T]AGACTACACTCACATTTGAGGAAAAATCATGAGCA Y 2 1 2 1 101000 r 74 goat snp16406-scaffold173-347007 16 4134989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387344 Affx-122970489 AX-123257702 16 4170100 ATCCCAGGAAGACAGTCCCATTGGTATTAGGACTG[C/T]CATCACCTCATACACTTGGGAAATATTTATTGACA Y 2 1 2 1 101000 r 74 goat snp16405-scaffold173-288793 16 4193350 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375694 Affx-122978653 AX-123246053 16 4226219 GTTTTCTTTATCCTGATCTGGAGTTGGACAACTCC[C/T]CCTCTAAACCCCAGACAATTATCAACACAGCCTCC Y 2 1 2 1 101000 r 74 goat snp16404-scaffold173-232674 16 4249505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277096 Affx-1111835679 AX-519550603 16 4237471 CTCCTGTAGACAGAAAACCTGAGGCCCAGAAAAGG[A/G]AAGAGCTTGGCCCACAGTCCTGCAATAGAAAGTCA R 2 1 2 1 201000 r 74 goat Random2.2K-1570 16 4237471 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378496 Affx-122976656 AX-123248855 16 4258619 ATAAGTTAAGTCACCAGAATTTGTCCTTTTCCCTC[A/G]CTTGCAATGAATATGCTATTGTTCACTGGGGGAAG R 2 1 2 1 201000 f 74 goat snp16403-scaffold173-200274 16 4282942 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785839 Affx-122930918 AX-385272876 16 4287354 AAATTATTCCAAATCCCCTTAAGTTCCAAATTTCA[C/T]ATAAATTCCAAACTTCACCAAATAAACCCTTTGTT Y 2 1 2 1 101000 f 74 goat snp16402-scaffold173-171539 16 4312150 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803339 Affx-986696291 AX-385290175 16 4357284 ATGCCTCAAGGAGGCATCTTAGGATAGTACTGTAG[A/G]TACTATCATCCATCATTTTAATATTTTACTGACAT R 2 1 2 1 600010 f 74 goat 16_4357284 16 4357284 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 38428180 Affx-122939026 AX-123298523 16 4378841 AGCCTGTTTGCAGAACAGGAATAGAGATGCAGATG[C/T]ACAGAACAGACGTGATTTTGGATGTTTTGTGAGGG Y 2 1 2 1 201000 r 74 goat snp16400-scaffold173-80052 16 4404679 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420795 Affx-122944689 AX-123291142 16 4418295 ATCGCCAGGAGTAGGTTCTCAGTTTTGTTCCATAC[A/G]TTCAGAAGGCACTCAGCATAGTGTAGTTCCTGTTA R 2 1 2 1 101000 f 74 goat snp16399-scaffold173-40598 16 4444517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429142 Affx-122937994 AX-123299484 16 4454989 ATAGAGAAGACTGGAACCATATTAGCAACCAACTT[C/T]ATCTAACTGACATTTATAAGGAGTGCCACTCAGCA Y 2 1 2 1 102000 f 74 goat snp16398-scaffold173-3904 16 4482347 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375815 Affx-122978557 AX-123246174 16 4478185 TATCAAAAAACAAGTGGGAAACACAGGGACAGGGG[C/T]GGTGAGGGTGAGATGTATGGAAAGAGTAATGTGGA Y 2 1 2 1 303000 f 74 goat snp43127-scaffold573-19193 16 4602274 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793346 Affx-122975575 AX-385280324 16 4510686 ATGCAAAAAGGACAAAGCTCAAAGAAATTGATTTT[A/C]GATCTGCCCAACTCAAAAAATGTGTTTCTCTGTTC M 2 1 2 1 101000 r 74 goat snp43128-scaffold573-51694 16 4634759 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791090 Affx-122977331 AX-385278085 16 4557179 GTATCAATTTACTGTCCCAGTAATATTGCATATTT[A/G]TTCTCTGTACCATTAATGATAATGGTTATTATGAT R 2 1 2 1 201000 r 74 goat snp43129-scaffold573-98187 16 4680413 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803341 Affx-986696292 AX-385290177 16 4579169 TATATGACATCGTTGCATTATTATGACTAATAGCA[A/G]GTATATATTTTGATGTTTGGCTACAGTTCTTGGGT R 2 1 2 1 600010 f 74 goat 16_4579169 16 4579169 Ancestral_priority_1043 ancestry 0.784 recommended IMAGE 10K 10K ancestral 320787337 Affx-122926476 AX-385274362 16 4599139 ATTGCATGTTTCTGTCCACTACACCATCCACTTGC[G/T]CCTGAAAAAATAGATATGGATGTCTATTAAGAAGC K 2 1 2 1 101000 f 74 goat snp43130-scaffold573-140147 16 4722435 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408818 Affx-122954031 AX-123279169 16 4634244 GAGACTGAAAAAAGAGAGAGGACTTGGAAAGCTAT[G/T]GTAGAAGACTACATTAGAGATGATGGTGGCAGAAA K 2 1 2 1 102000 f 74 goat snp43131-scaffold573-175252 16 4758125 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802834 Affx-122951676 AX-385289733 16 4737430 TAATAGGATGGACCATTTAATTGAATGATGCTCCA[C/T]TGTTTATAGCACTTGTAATTGGTATATATAGAGAT Y 2 1 2 1 101000 f 74 goat snp43132-scaffold573-278438 16 4860248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440050 Affx-122929751 AX-123310387 16 4798240 GAAGTTCTAAAATCTATAACTTTAAGAAATCGCCA[C/T]GAGTTTTTACAAGGACTGATGTACAAATTTTGCCT Y 2 1 2 1 101000 f 74 goat snp43134-scaffold573-339248 16 4921622 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413670 Affx-122950110 AX-123284019 16 4843266 GCTTGCTATGTGAATTATAAACTCTGAATTTTTGC[A/G]TATCTTAATCCCTTTCTTTAACAAAGTCTGGGACC R 2 1 2 1 101000 r 74 goat snp43135-scaffold573-384274 16 4958469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772949 Affx-122953382 AX-385260093 16 4936177 TTTTGATAGGAGGACAGATGAAATTCTAGTAAACA[G/T]AAACATAACTCTGAATCATGAATTATGTTGTGAAG K 2 1 2 1 101000 r 74 goat snp44176-scaffold60-601506 16 5333905 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763266 Affx-986697795 AX-385251186 16 5097965 GGGGAAACAAAGGACAGGCTGTCAGTACCATTTCT[G/T]GTGCACTAATGTATCTAGACAAGACATACAAGCAC K 2 1 2 1 600010 f 74 goat 16_5097965 16 5097965 Ancestral_priority_1043 ancestry 0.588 neutral IMAGE 10K 10K ancestral 320794294 Affx-122926757 AX-385281258 16 5117694 TGACTGCAGAAACGGCCAGATTGAATCCCTTGGGT[G/T]AGTGATGTATAGACACAGAGGGAAGTATTGGAAAG K 2 1 2 1 101000 f 74 goat snp44174-scaffold60-419989 16 5515246 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424225 Affx-122942485 AX-123294571 16 5160789 AAGAATGGCAGTTCCCTACAGAAAATCAAAGAATA[C/T]AAGCTTGGAGTTAGAGGGTGTTTGCATCCTATCAT Y 2 1 2 1 101000 f 74 goat snp44173-scaffold60-376894 16 5558533 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784938 Affx-122957509 AX-385271985 16 5193441 ATAGAAGAATAAACTAAACAAGAAATCCTAAAGCA[C/T]GATGGAATGAGAAAAGCAAGATAGCACACATGTGT Y 2 1 2 1 101000 r 74 goat snp44172-scaffold60-344242 16 5591591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271971 Affx-1111833074 AX-186062412 16 5199278 AGCTAAATAAAATCCCTTATGATTATACAGTGGAA[A/G]TGAGAAATAGATTTAAGGGCCTAGATCTGATAGAC R 2 1 2 1 303000 f 74 goat 16_5199278_AF-PAKI 16 5199278 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450348 Affx-122922112 AX-123320683 16 5226468 CTGGCCCAGAACCATGGCAAGTGGAAGTGTCTGCA[C/T]AGACAGAAGAGATTTTTCTGAATTCATGATCTCAA Y 2 1 2 1 101000 f 74 goat snp44171-scaffold60-311215 16 5624964 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786562 Affx-122956522 AX-385273594 16 5286627 CATGTAAACTGGAAAATAGACCTTCTGAACCACAC[A/G]TTCTATGAGGATTAAAATATAATCCCAGAACCCTT R 2 1 2 1 101000 f 74 goat snp44170-scaffold60-251056 16 5686090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437371 Affx-122931923 AX-123307709 16 5322528 TCAAGGAAGTGTCTGTGTGGTGTTCAAAGTGATGA[C/T]GTGATCACCAAATATTTACAAAGAGTCACCTACAA Y 2 1 2 1 101000 f 74 goat snp44169-scaffold60-215155 16 5722424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777395 Affx-122969224 AX-385264517 16 5366656 AGTTTGCTTAAAAGACACATTCTTGTGTTAAAAGA[C/T]ACATTCTATTAATAAGTAGAAACTGCCTATTACTA Y 2 1 2 1 101000 f 74 goat snp44168-scaffold60-171027 16 5766691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430911 Affx-122936857 AX-123301252 16 5401333 AAATGACTGCAACAGAAATAAAATATGCATTTATC[A/G]TGTGTATGAAAAACAGAATAGCTTGGAGTGTGAAT R 2 1 2 1 101000 r 74 goat snp44167-scaffold60-136350 16 5802195 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425576 Affx-122941425 AX-123295922 16 5437580 TGTCACTAATACAATCTGGAGTTAACTACCTTGTG[C/T]AAGCAGGACTTGGTCTAGAAAATCCTTAGAACCAT Y 2 1 2 1 101000 r 74 goat snp44166-scaffold60-100103 16 5838559 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383568 Affx-122972599 AX-123253926 16 5482955 GGTTAAGTTAGAGGATGGCAATGGTTTATTCTTCA[C/T]GGAACTGGGAGAGTGGAAGTCAATGTAATTCAGGG Y 2 1 2 1 102000 r 74 goat snp44165-scaffold60-54728 16 5880542 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434318 Affx-122934747 AX-123304659 16 5537246 ATGGAGTGCTGGGCCCCACTGCAAGGTTTCTCACT[A/C]GGTAGATCTGGGGCGAGGCCTGAAAAATCTGCATT M 2 1 2 1 202000 f 74 goat snp44164-scaffold60-437 16 922140 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411277 Affx-122952309 AX-123281627 16 5547746 AGGAGAAGCAATTCCGGGGGCTGCAGAACCACATC[A/G]AGAAGGAGCAGAAGTTCTCCGTTATCTTGAATGGG R 2 1 2 1 202000 f 74 goat snp53579-scaffold815-1652564 16 6218245 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792400 Affx-122940661 AX-385279381 16 5583924 TAATGAACATAGTTCAAACAATAATTAACTTGTTA[C/T]ATTAAGAAAATCACAAAAACCACACAGTTGCTTGG Y 2 1 2 1 101000 r 74 goat snp53578-scaffold815-1616386 16 6275430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393952 Affx-122965061 AX-123264307 16 5628345 GTCACTTTGAATTCCATGCATCAGGCCAAAGCAAA[G/T]AATGATCTCATTACTAAAGTTTTAATAACTTCCTT K 2 1 2 1 101000 f 74 goat snp53577-scaffold815-1571965 16 6320735 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441147 Affx-122929570 AX-123311484 16 5685888 GATTCCTCAAGAAAATGGTGTGGCATGTGGATACC[A/G]CCAGGGGTTCCCTGCAGAAGGAAGGAGCCTCTCCA R 2 1 2 1 101000 f 74 goat snp53576-scaffold815-1514422 16 6373539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388667 Affx-122969099 AX-123259025 16 5742204 TTAACCCATTACCTCTATAGCTGTCCTCTAGGTTG[C/T]AGGACAAATGAAGTAGGGCTTTCTGAGTTTCAAAA Y 2 1 2 1 101000 f 74 goat snp53575-scaffold815-1458106 16 6427634 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796414 Affx-122951480 AX-385283364 16 5832416 ACTCCTACTGCACATCACATTTTTTGCTGTCATAA[C/T]ATTAATTTAATAATATAGAAGTATTTAAACTCATT Y 2 1 2 1 303000 r 74 goat snp53574-scaffold815-1367894 16 6518123 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793474 Affx-122954815 AX-385280451 16 5878979 GACCGTTAGCCTGGTGGTTAAAGGTCTTCCTGCTC[A/C]TCTAATGATCAGCCTAGCAGTGGTCCTCTCGGCAG M 2 1 2 1 101000 f 74 goat snp53573-scaffold815-1321331 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789179 Affx-122954676 AX-385276191 16 5908171 GGGGTACACAGATACAGAGCAGGTTAAATGGAGAA[C/T]GCAAAGCTACCTTATTAAGCTTAGATATCTGGAGA Y 2 1 2 1 201000 r 74 goat snp53572-scaffold815-1292139 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785892 Affx-122965547 AX-385272929 16 5938350 TAATAGACTTAAATGAATTAGAGACTCTACAATAA[C/T]ACTTAACAACGTTCTAGAAAATTGCTGCATTACAC Y 2 1 2 1 101000 r 74 goat snp53571-scaffold815-1261960 16 6539782 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405211 Affx-122956904 AX-123275563 16 5967084 AACTCAAATAAGGAAATAACTAAGAAAAGGGTCTG[C/T]GCGCTCATCTGAGATTCCAGAGAAAGGAGATGAGG Y 2 1 2 1 101000 f 74 goat snp53570-scaffold815-1233226 16 6579546 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771527 Affx-122966409 AX-385258685 16 5998610 CAAGTAGACACACCTGACTTTCTTTTGCAAACCTG[C/T]ATGGCCACAATATCCGTTGGAGGGTGGCAAACAAT Y 2 1 2 1 101000 f 74 goat snp53569-scaffold815-1201700 16 6618997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397013 Affx-122963131 AX-123267368 16 6034787 TTGGTGGACTTGTGAATGTCCATCCATTGCTTAGA[C/T]CTAAACACACATTTAAATGAAAAATCACTGAATTA Y 2 1 2 1 101000 f 74 goat snp53568-scaffold815-1165523 16 6656175 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381363 Affx-122974404 AX-123251721 16 6094269 AGGCAAATTTGATTATTTCACTCAGTGTATTTTCA[A/G]TAAGTAAGGAAGAGTTTACATTTAGTAGTATAGCC R 2 1 2 1 101000 r 74 goat snp53567-scaffold815-1106041 16 6716454 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799177 Affx-122964623 AX-385286107 16 6160922 TGTGGGAGAAAAAGTCCATTTTCTATGCTACACAA[G/T]TCCAGATACCCCATGGGCACTAAACATCACGCATG K 2 1 2 1 101000 f 74 goat snp53566-scaffold815-1039388 16 6785099 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439507 Affx-122930137 AX-123309844 16 6196625 GCAGAAAAAGCACACATATATGGATGTTGCTTTAC[A/G]CTATTAAAAATAAAAAAAAAATAAAAAAACTAAAC R 2 1 2 1 103000 f 74 goat snp53565-scaffold815-1003685 16 6821467 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419993 Affx-122945175 AX-123290341 16 6233852 ACTTAGGATGTAATAATCTCCAGTAAGCAATTCTC[A/G]TTTTCCAGTTTTGATTTTTCCAGTTCTTAGAAACA R 2 1 2 1 101000 f 74 goat snp53564-scaffold815-966458 16 6860187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803343 Affx-986696293 AX-385290179 16 6252152 TTGGTCATGACTTTGACCTGATGAAACTGAGTTTA[G/T]TATAATAAATGAAATTGCAAAGTTCAAGATTTTGA K 2 1 2 1 600010 f 74 goat 16_6252152 16 6252152 Ancestral_priority_1043 ancestry 0.71 recommended IMAGE 10K 10K ancestral 38395600 Affx-122963822 AX-123265955 16 6263750 CTGAGTGACTGAGCAAATGATACATACAGAATGTT[A/G]CCATCCTTCTCTTGGTTATTCCTTCTGCATTTTCT R 2 1 2 1 101000 f 74 goat snp53563-scaffold815-936560 16 6890327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803078 Affx-122962778 AX-385289949 16 6312323 AAGTTAATCATTTTTGACTTATTCAGGCTCAAGCA[G/T]AGTTATTGGGATTTCCTTATTACCAGGATTCCTAT K 2 1 2 1 101000 r 74 goat snp53562-scaffold815-887987 16 6938756 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786333 Affx-122950838 AX-385273367 16 6373753 TTTTAATACTTTTTTTTTGTAGGTATAATCACTCA[C/T]GAACATGGAGGTATAACTGTAACTGTTACACTCAA Y 2 1 2 1 101000 r 74 goat snp53561-scaffold815-826557 16 6998715 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774277 Affx-122955025 AX-385261413 16 6407943 AGTGAAAGTCTGAAGGGAAAATAGTGTGTTAGGAG[C/T]AATAAAATTGTGTTGAACAATAGTGTAAATTTGTG Y 2 1 2 1 101000 f 74 goat snp53560-scaffold815-792367 16 7030191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380679 Affx-122975178 AX-123251037 16 6481354 TCTCAGTGTGCTGTGTAGTGTTCAGTGTGCTGGTC[A/G]TGTCTCTCTGAAGGCCCTGTGTCCCTCCCTCCCTG R 2 1 2 1 202000 r 74 goat snp53559-scaffold815-718956 16 7050837 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392517 Affx-122966117 AX-123262874 16 6511375 CCAGGGAAGCCTGAAAAATTAGAAGAGTGGACTAA[C/T]GGCAAAAAATGTCAATTGACTTTTGCACTGATACA Y 2 1 2 1 101000 f 74 goat snp53558-scaffold815-688935 16 7081509 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800318 Affx-122969823 AX-385287241 16 6545994 GTAACTTAAACTCTCTAAGTTAAATCCAGTTTCCT[A/G]TCTGAAAAATGATAATTATATTCTTTCTTTGCTCA R 2 1 2 1 201000 r 74 goat snp53557-scaffold815-654316 16 7116482 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414628 Affx-122949337 AX-123284977 16 6590160 GGAGTGTTCAGTTAGATGTTTTAAAAATATATAAA[C/T]GGAGACAAAACGAGCCCTGCCAGACAAACTCAATT Y 2 1 2 1 303000 f 74 goat snp53556-scaffold815-610150 16 7161334 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476319 Affx-1251763826 AX-586011736 16 6607038 TTGCTCCTCTTTTGTCATGTCTTTCTAATTCTTCC[-/TCAGTATGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CAGTATGTTGTGGTTTTCCCTGTCCAGCAGGACCT - 4 1 4 1 20000 f 74 goat SV_144 16 6607038 - deletion junction SV-TF-chip 539476572 Affx-1251763826 AX-586011958 16 6607038 TTGCTCCTCTTTTGTCATGTCTTTCTAATTCTTCC[-/TCAGTATGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CAGTATGTTGTGGTTTTCCCTGTCCAGCAGGACCT - 8 1 4 1 20000 r 74 goat SV_144 16 6607038 - deletion junction SV-TF-chip 562165239 Affx-1251763826 AX-606940651 16 6607038 TTGCTCCTCTTTTGTCATGTCTTTCTAATTCTTCC[-/TCAGTATGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CAGTATGTTGTGGTTTTCCCTGTCCAGCAGGACCT - 8 1 4 1 20100 r 74 goat SV_144 16 6607038 - deletion junction SV-TF-chip 562165352 Affx-1251763826 AX-606940763 16 6607038 TTGCTCCTCTTTTGTCATGTCTTTCTAATTCTTCC[-/TCAGTATGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CAGTATGTTGTGGTTTTCCCTGTCCAGCAGGACCT - 8 1 4 1 20100 f 74 goat SV_144 16 6607038 - deletion junction SV-TF-chip 562165419 Affx-1251763826 AX-606940830 16 6607038 TTGCTCCTCTTTTGTCATGTCTTTCTAATTCTTCC[-/TCAGTATGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CAGTATGTTGTGGTTTTCCCTGTCCAGCAGGACCT - 8 1 4 1 20100 f 74 goat SV_144 16 6607038 - deletion junction SV-TF-chip 562166454 Affx-1251763826 AX-606941862 16 6607038 TTGCTCCTCTTTTGTCATGTCTTTCTAATTCTTCC[-/TCAGTATGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CAGTATGTTGTGGTTTTCCCTGTCCAGCAGGACCT - 8 1 4 1 20100 r 74 goat SV_144 16 6607038 - deletion junction SV-TF-chip 562166549 Affx-1251763826 AX-606941957 16 6607038 TTGCTCCTCTTTTGTCATGTCTTTCTAATTCTTCC[-/TCAGTATGTGCCGCGGCCAGCACAAGCAAGAGTCACACCTAGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCG]CAGTATGTTGTGGTTTTCCCTGTCCAGCAGGACCT - 8 1 4 1 20100 r 74 goat SV_144 16 6607038 - deletion junction SV-TF-chip 38452234 Affx-122920790 AX-123322567 16 6619833 AGAAGGGCTCTGAAATAAAGGGACTGAGAAAGCTG[C/T]GCTGAACTCTGGATGGAAAATGTTCCAAGCATAAT Y 2 1 2 1 201000 r 74 goat snp53555-scaffold815-580477 16 7191942 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392974 Affx-122965673 AX-123263331 16 6676021 GAATTAAAGATGGCTCTACTCTCCAAATGTCATTT[A/G]TTTCCTGCCTATAGAGTGGACCTCACCTACAGGTC R 2 1 2 1 101000 r 74 goat snp53554-scaffold815-524289 16 7246101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769448 Affx-122926323 AX-385256618 16 6718144 TACATCCATCTTTTTATCTACATCTATCTATATTG[A/C]TATCCAAGGCATATCCATATCTAAATGTTTCAAAC M 2 1 2 1 201000 f 74 goat snp53553-scaffold815-482166 16 7288968 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391602 Affx-122966598 AX-123261959 16 6746724 GTGCACTTTTCTAGTTTTGCCCATTGGGATGATTT[A/C]TTTTCACCACTGTCCTTTGGGGCTATCCCATAATA M 2 1 2 1 202000 f 74 goat snp53552-scaffold815-453586 16 7318301 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412386 Affx-122950803 AX-123282735 16 6816143 ACATGAATTAGAAGATTTCCATCCCATTATAGAGG[C/T]TTCAAGAATACTGAAGGAAGAGCTCTGGGGACTTC Y 2 1 2 1 201000 f 74 goat snp53551-scaffold815-384167 16 7387738 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800519 Affx-122935568 AX-385287439 16 6884927 AAATTAAGCTATACAACTTCTCTCCTCAAAATCCT[A/G]TAATGTGTCTGTATTTAATAAAAGGGAAGGTAAAA R 2 1 2 1 101000 f 74 goat snp53550-scaffold815-315383 16 7457163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763268 Affx-986697797 AX-385251187 16 6904904 TTAATGCATTTTTTCCTGATGACCAATGATATTAT[A/G]CATGCAAGTTTTTGGGTCATCCCTTTCTTTTGCCA R 2 1 2 1 600010 f 74 goat 16_6904904 16 6904904 Ancestral_priority_1043 ancestry 0.728 recommended IMAGE 10K 10K ancestral 38445581 Affx-122925131 AX-123315918 16 6918091 AATAAGCTCTGGTACCACTAGAATAGATGGACAAA[G/T]CATATGATAGGTTTAGTGCATTTCCTCTTTAACAG K 2 1 2 1 101000 f 74 goat snp53549-scaffold815-282219 16 7490928 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765603 Affx-122935083 AX-385253082 16 6946798 TGATTCAAATTGAACACCTCTGCTCCATGCTTAGG[C/T]AAGCTGTAACAAATATCACTTACTATTTCTATGTT Y 2 1 2 1 102000 f 74 goat snp53548-scaffold815-253512 16 7519867 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434191 Affx-122934870 AX-123304532 16 6996416 ATCGGATTTCAGGACAGATGAGACTTCTGAACAGA[C/T]AAGTTCTAGAAACTTCTCACCAAAGTAGAGATGTA Y 2 1 2 1 101000 f 74 goat snp53547-scaffold815-203894 16 7570379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432654 Affx-122936469 AX-123302995 16 7059512 CAACTTAGAGACTGAACAACAACAAAACTCTTACC[A/G]CTAGTGGAACAGTAAATTAAAATATTCCCAAAGTG R 2 1 2 1 201000 r 74 goat snp53546-scaffold815-140798 16 7634641 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776931 Affx-122965180 AX-385264055 16 7144509 TTTCACTTCAAACTCTCCTCTTTTCTAGGGTCATT[A/G]AAAGAAAGAGGTAGGTTCATATCACTGATACAACA R 2 1 2 1 101000 f 74 goat snp53545-scaffold815-55801 16 7718981 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392418 Affx-122966200 AX-123262775 16 7196208 ACAAGAGTGAGATTTGAAAGAGGGAAAACACATTG[C/T]GACTAAGGAAATGATAGAGTTGTGCAGAGAAGGAA Y 2 1 2 1 101000 r 74 goat snp53544-scaffold815-4102 16 7770419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794369 Affx-122935912 AX-187317311 16 7228850 TACAAAACTCCTTATTGCAGCCATAATTTTTACAC[A/G]TCCATTAGCAATTCCCTTTGCCAAAATAATAATAA R 2 1 2 1 201000 r 74 goat snp11615-scaffold1427-244932 16 7803631 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780121 Affx-122940833 AX-385267218 16 7259607 GAACACAGGATGATAGCAAAAGGTGAGGAAAAAGC[A/G]TGTGTCAACATTCAATATTCATTTGTGATTTAAAA R 2 1 2 1 101000 f 74 goat snp11614-scaffold1427-214175 16 7835398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428388 Affx-122938956 AX-123298731 16 7314189 ATCCTTCCCCTGGAATTTTTGGTAGCCAAAAATGG[A/G]TGTGATTTGTGATTTTTGAGATTTTATTTAATGTA R 2 1 2 1 201000 r 74 goat snp11613-scaffold1427-159593 16 7888805 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444316 Affx-122926741 AX-123314653 16 7362114 TGAAAGAAAAGGAAAAAGAAAGTGAGAAGAATTAT[A/G]CTTTCCATGTGTAGCACATCCTACTATGGGTCTAC R 2 1 2 1 101000 r 74 goat snp11612-scaffold1427-111668 16 7938200 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393126 Affx-122965562 AX-123263483 16 7418064 AATACATCATATTTAATACATATTCAGTTCATTGA[C/T]GTCTCCTTTGATTCACACACATATCCACCCTTATG Y 2 1 2 1 101000 r 74 goat snp11611-scaffold1427-55718 16 7994361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772688 Affx-122961430 AX-385259835 16 7451110 AATCACCAAATAGGTACAACTGATACTTTTATTTA[C/T]ATACTGTAACCACATTATTGACATGGGATAGATAC Y 2 1 2 1 101000 r 74 goat snp11610-scaffold1427-22672 16 8026581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433474 Affx-122935046 AX-123303815 16 7496245 TATAAGAAGAGGGAGGGAGACACCACAAGCACACA[C/T]GGAGCAAAGGCTGTATGTCAATACAGTAAAAGTGC Y 2 1 2 1 201000 r 74 goat snp13182-scaffold1504-22127 16 8071332 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763270 Affx-986697799 AX-385251188 16 7522229 AGGGATAGTTACTATCCAAATTTGTTTTCCAAGTG[A/G]GAAAGGAGACGCTCATGGAATGTAGAGAAACCTAA R 2 1 2 1 600010 f 74 goat 16_7522229 16 7522229 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320766140 Affx-986697805 AX-385253544 16 7522247 AATTTGTTTTCCAAGTGAGAAAGGAGACGCTCATG[G/T]AATGTAGAGAAACCTAAATAAGGTCACTTCGCCAA K 2 1 2 1 600010 r 74 goat 16_7522247 16 7522247 Ancestral_priority_1043 ancestry 0.762 recommended IMAGE 10K 10K ancestral 320763278 Affx-986697807 AX-385251193 16 7522282 GAATGTAGAGAAACCTAAATAAGGTCACTTCGCCA[A/G]TTACAGGCAGAATCAGAATTCTGTTATATTTAGGC R 2 1 2 1 600010 f 74 goat 16_7522282 16 7522282 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320766147 Affx-986697809 AX-385253550 16 7522286 GTAGAGAAACCTAAATAAGGTCACTTCGCCAATTA[A/C]AGGCAGAATCAGAATTCTGTTATATTTAGGCTTCC M 2 1 2 1 600010 r 74 goat 16_7522286 16 7522286 Ancestral_priority_1043 ancestry 0.61 recommended IMAGE 10K 10K ancestral 320763282 Affx-986697811 AX-385251197 16 7522313 GCCAATTACAGGCAGAATCAGAATTCTGTTATATT[C/T]AGGCTTCCTTCATATTCTATTTACCTTATGAAACA Y 2 1 2 1 600010 f 74 goat 16_7522313 16 7522313 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 320803920 Affx-986696295 AX-385290628 16 7522342 TATATTTAGGCTTCCTTCATATTCTATTTACCTTA[A/T]GAAACACAAATCACCATAGATTGTCTTTTAGAATA W 4 1 2 1 600010 r 74 goat 16_7522342 16 7522342 Ancestral_priority_1043 ancestry 0.554 neutral IMAGE 10K 10K ancestral 320763288 Affx-986697817 AX-385251203 16 7522366 TATTTACCTTATGAAACACAAATCACCATAGATTG[C/T]CTTTTAGAATATCTTAAGAGCTGATACTGTTTCTT Y 2 1 2 1 600010 f 74 goat 16_7522366 16 7522366 Ancestral_priority_1043 ancestry 0.648 neutral IMAGE 10K 10K ancestral 320765743 Affx-986697579 AX-385253200 16 7522371 ACCTTATGAAACACAAATCACCATAGATTGTCTTT[C/T]AGAATATCTTAAGAGCTGATACTGTTTCTTCAGGA Y 2 1 2 1 600010 r 74 goat 16_7522371 16 7522371 Ancestral_priority_1043 ancestry 0.692 recommended IMAGE 10K 10K ancestral 320763291 Affx-986697820 AX-385251206 16 7522602 ACAAAATCTGACTAGAGATGACTAAAGTCGGTTGA[A/G]CCATGTGTGCAAAATACACAAAGCAGGGTATGAAA R 2 1 2 1 600010 f 74 goat 16_7522602 16 7522602 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 320803922 Affx-986696296 AX-385290630 16 7522603 CAAAATCTGACTAGAGATGACTAAAGTCGGTTGAG[C/G]CATGTGTGCAAAATACACAAAGCAGGGTATGAAAG S 4 1 2 1 600010 r 74 goat 16_7522603 16 7522603 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 320766169 Affx-986697822 AX-385253571 16 7522692 GATCTAAAGCCCAGTGGGAAAGGATTACAGTTACT[C/T]TAGATGAAATACTATCTGTCCTAAGCAAGCACCAC Y 2 1 2 1 600010 r 74 goat 16_7522692 16 7522692 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 320763295 Affx-986697824 AX-385251209 16 7522720 AGTTACTTTAGATGAAATACTATCTGTCCTAAGCA[A/G]GCACCACATGAACTCACATGGGGAAGATTTAGAGG R 2 1 2 1 600010 f 74 goat 16_7522720 16 7522720 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 320766176 Affx-986697826 AX-385253578 16 7522722 TTACTTTAGATGAAATACTATCTGTCCTAAGCAAG[C/T]ACCACATGAACTCACATGGGGAAGATTTAGAGGAC Y 2 1 2 1 600010 r 74 goat 16_7522722 16 7522722 Ancestral_priority_1043 ancestry 0.558 neutral IMAGE 10K 10K ancestral 320763299 Affx-986697828 AX-385251212 16 7522751 AGCAAGCACCACATGAACTCACATGGGGAAGATTT[A/G]GAGGACATTACTGTTTACTGGGTAGGCAGGAAGAA R 2 1 2 1 600010 f 74 goat 16_7522751 16 7522751 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 320766188 Affx-986697833 AX-385253588 16 7522829 GTGAGGTCTTGCCTTGGCAAAACAGTTCAGGTGAG[G/T]TCACAGTGGTAGATAATGGCAAGCTGGAATCTAGT K 2 1 2 1 600010 r 74 goat 16_7522829 16 7522829 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 38424734 Affx-122941666 AX-123295080 16 7528714 CTCTGATTAGGAATATTTTCTAGTAAAATGTGTTT[A/G]CAGAACATAAGCAACCATCATGATCAGAAGAGAAG R 2 1 2 1 101000 r 74 goat snp13183-scaffold1504-54596 16 8101702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277101 Affx-1111835681 AX-519550608 16 7562615 ATTTGGTTGCATTGGGCCTTAGTTGTGGCAAGCAG[A/G]TTCTTCAGTACATCACATGGAATCTCTCTTGTGGT R 2 1 2 1 101000 r 74 goat Random2.2K-1572 16 7562615 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386075 Affx-122971454 AX-123256433 16 7591864 ATACTCCTGGAAACTTGAACAGGAAGTGAAACTGC[C/T]GAATTCCTGAGTGTGCTTCTTGGGTTTCAACCTGA Y 2 1 2 1 202000 r 74 goat snp13185-scaffold1504-117746 16 8165901 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785468 Affx-122942105 AX-385272513 16 7670577 GATAAGCATCTAAACTCCCTGTTCATTTCCCTATA[C/T]ACCCCCACCTCTAAATCATAGGATGATTTCCTTTC Y 2 1 2 1 101000 r 74 goat snp13186-scaffold1504-196459 16 8246187 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402278 Affx-122959112 AX-123272631 16 7714886 AAGTTCAGTCCAGCTTTGCCTCTTAAACTTTGAAG[C/T]GTCTAGTCAGTCCTGTTAACTCAATGCACCATGTT Y 2 1 2 1 201000 r 74 goat snp13187-scaffold1504-240768 16 8289992 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272836 Affx-1111833084 AX-519546528 16 7721856 TTTTTTCTTTATCCACTCTTCATCAGCCCTGAGAT[A/G]ATGGTCACTTTCTTCATGTATCTTTACTATATCCC R 2 1 2 1 101000 f 74 goat 16_7721856_AF-PAKI 16 7721856 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403474 Affx-122957710 AX-123273827 16 7723504 AACAACTGTTACTCCTTCCAGATTTATTGATGGAA[C/T]GATCAGATAGCACTGATGCTCTGAGAAGCATTTCA Y 2 1 2 1 201000 f 74 goat snp35027-scaffold418-140577 16 8298439 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788391 Affx-122931131 AX-385275409 16 7753811 GTTGTTATCCAAGTAATGGGGTGCTTGGAAAGCCA[C/T]GGAGCCTCAACGATAGGAAATGCCAAGCTCCTACC Y 2 1 2 1 101000 f 74 goat snp35026-scaffold418-110270 16 8329188 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380883 Affx-122975047 AX-123251241 16 7785898 CATATCCTCACCTCCTTCCTACACAGCTTAGGTTG[C/T]ATCTTCAATGTGATAATCACTCCCTTGAAGATGCA Y 2 1 2 1 201000 r 74 goat snp35025-scaffold418-78183 16 8361485 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450499 Affx-122922514 AX-123320833 16 7851241 GCTACGTGGGACTTGCGGACATCCTCCATCACTTG[C/T]AGGACATCAAGGGCTCAGGGCATTGTGAAAGCTTC Y 2 1 2 1 101000 r 74 goat snp35024-scaffold418-12840 16 8428636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773537 Affx-122943527 AX-385260678 16 7895062 AGGGTTTCCAGAAGGAATTTCTGCAAGTCACCTAA[C/T]CTATTCTCATTCATATGTAAACCTTGTGTGCCTAC Y 2 1 2 1 101000 f 74 goat snp24194-scaffold2466-139354 16 8498175 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424966 Affx-122941922 AX-123295312 16 7939999 GCCTTTCCTTTATTTTACTGATGAGACCAACAAGG[A/C]GCAAGAGTTACAGACAATAAATATCCATCTAGGAA M 2 1 2 1 201000 r 74 goat snp24193-scaffold2466-94417 16 8542911 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453978 Affx-122919452 AX-123324311 16 7982907 TGTTTTTCACTGTTCTGAAACATGGAAAAAACTTT[C/T]GTCTCCAGAGATCTTAGGTAACTGGGTTTCCCTCC Y 2 1 2 1 201000 f 74 goat snp24192-scaffold2466-51509 16 8586801 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376684 Affx-122978993 AX-123247043 16 8017466 ATTCTGCTCTTTAATCTCATCTCTATAATACTTAC[A/G]TTTAGCTATTTTATTTTTCACTTATAGGATGTTCT R 2 1 2 1 101000 f 74 goat snp24191-scaffold2466-16950 16 8621359 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765493 Affx-122952330 AX-385252981 16 8035443 GTTTGCTACCTAAAATGACTGCCTTATATTCTGTT[C/T]CCATGAAGAAGTCTAGCTAAAGACACTCTGGAACA Y 2 1 2 1 101000 f 74 goat snp19931-scaffold1993-928 16 8638832 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801371 Affx-122950471 AX-385288282 16 8096388 ATCACTACTATAAAAAGTTTCTTGGTTTGCACCAA[C/T]GCCTTGAGCTGATATTTGAACTTTTACTCTTCAGA Y 2 1 2 1 101000 r 74 goat snp19932-scaffold1993-61873 16 8699669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770421 Affx-122919312 AX-385257587 16 8153953 CATGTCTAACACAATATTCCTTAAAACGTGAGTTG[A/G]CTTTGAAGCTATTATTGCTCTCTATAACATTTTGA R 2 1 2 1 101000 f 74 goat snp19933-scaffold1993-119438 16 8757850 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774138 Affx-122950363 AX-385261276 16 8192015 CAAATGGACATTTATTATGCACAGAAAGCTATGAA[C/T]GGAATTTGAGTAGCCAGAGTGATGGAGCTTGATGG Y 2 1 2 1 101000 r 74 goat snp19934-scaffold1993-157500 16 8796252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763305 Affx-986697834 AX-385251217 16 8248985 TCTTACAGATATTAGATATTGCAGAAATCCCATAA[C/G]AAATATTCTGAAGACAGCATCACAACATGTCAGAT S 4 1 2 1 600010 f 74 goat 16_8248985 16 8248985 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 320766199 Affx-986697840 AX-385253599 16 8249003 TTGCAGAAATCCCATAAGAAATATTCTGAAGACAG[C/T]ATCACAACATGTCAGATGTAAGCAGATATCTGGGA Y 2 1 2 1 600010 r 74 goat 16_8249003 16 8249003 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 320797868 Affx-122937352 AX-385284806 16 8268871 CCTTCTATGAACCTAACACCATTCGACCATTTCAA[C/T]CACTTTTTATAAAGTGAGGAAACCAAGCTAGTGAT Y 2 1 2 1 201000 r 74 goat snp19935-scaffold1993-234356 16 8874281 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407640 Affx-122954619 AX-123277991 16 8322202 AGGAGATTTAGAATTAACATTCTTCATCTTTGTGC[A/G]CCATCATGAGATAAAGGAGGCAGAAACCCTCTTTT R 2 1 2 1 101000 r 74 goat snp19936-scaffold1993-287687 16 8927008 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424749 Affx-122941652 AX-123295095 16 8365880 TATGTTTTTCTGTTGAGTGGGTTAATTATTTTACA[A/C]CTGTTATGTTTTGTATCTTTTTTACAAAGGACTTC M 2 1 2 1 101000 f 74 goat snp19937-scaffold1993-331365 16 8971049 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796892 Affx-122961548 AX-385283834 16 8394131 AACAAAATTTTGAGACTGGACAAAGATAAAATAAT[A/C]GAGAATACAGGATTCTTTGACATACATCAAGTATT M 2 1 2 1 101000 r 74 goat snp13980-scaffold1551-27845 16 9041315 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406060 Affx-122956249 AX-123276412 16 8443959 CTAACTCATTTCAGGGAACTGAAACACCAATCTAG[C/T]AAACATATAATGTGAATTTACACCTATTAGCCATC Y 2 1 2 1 201000 r 74 goat snp13981-scaffold1551-77673 16 9090838 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780309 Affx-122972300 AX-385267404 16 8490055 AGCTACACTAGTTTTTAGAACCATGTCAGAAAATA[C/T]GGCAAAATCTGGAGCAGTTTTATATCTTGGAAAAA Y 2 1 2 1 101000 r 74 goat snp13982-scaffold1551-123769 16 9138076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782716 Affx-122943302 AX-385269788 16 8519486 TAGATCTGGGATATTAAAAGTAATAAACTCATCAG[C/T]GAAAAGATCATATACTTCTTATCACAAACCATCAA Y 2 1 2 1 101000 f 74 goat snp13983-scaffold1551-153200 16 9167502 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780798 Affx-122929221 AX-385267887 16 8559302 GCAGGGACTTTGAAATTCCTGCTAGAGATTCACTG[C/T]TCCTACCTTAGGTGGATCATTTGAGCTGTTCATGG Y 2 1 2 1 101000 f 74 goat snp13984-scaffold1551-193016 16 9207404 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402316 Affx-122959083 AX-123272669 16 8607230 TCAAACTTAAGGAAGAAATAAAAGTGACTTGCTAG[C/T]GCTATGTTCAGACAAAGGAGAGAATCAAATACCAT Y 2 1 2 1 101000 r 74 goat snp13985-scaffold1551-240944 16 9255302 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790381 Affx-122963162 AX-385277384 16 8644968 TTACATATGGTTTCCTGGATGCCAGTCTATGCAGA[C/T]GGTAAAAAGATGGCAGTCAGATATTTTTATTGTTA Y 2 1 2 1 101000 f 74 goat snp13986-scaffold1551-278682 16 9293523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802742 Affx-122938558 AX-385289641 16 8678039 CAAAGGATAGCTGGGATTTACTATGTTTATACAAA[C/T]ATAAGGAGATAATCTAAAGAGGAAAGATTCTGAAG Y 2 1 2 1 101000 f 74 goat snp13987-scaffold1551-311753 16 9326730 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428969 Affx-122938872 AX-123299311 16 8730077 ATTCTGTGAGTGCCTGTAAGGGAAGTGTGCATTGA[C/T]GTTAAGAGTCTATGTGGATGGTCCTTGCTGACCAA Y 2 1 2 1 101000 f 74 goat snp13988-scaffold1551-363791 16 9381357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274034 Affx-1111833998 AX-519547638 16 8737063 CCTGTCCTGTTAGGTTTTCCTATATAAAAATCACA[A/G]GCCAGGCAGTTTAGTAAAACTGTAATTCAGGGTCA R 2 1 2 1 201000 f 74 goat GoatD01.013308 16 8737063 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468277103 Affx-1111835682 AX-519550610 16 8766688 TTCTCAAGCCCCAGGGAAGCGGGATTCGAGCTTCC[A/G]GGCGAGTGCCACACGAAGGCAAAGCTAGACCTTGA R 2 1 2 1 102000 r 74 goat Random2.2K-1573 16 8766688 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320767924 Affx-122974711 AX-385255141 16 8773037 GTTACAGTGTCATAACATTGAGCAAGGATGCTGTG[C/T]CAATACTTTTGCATATTAAATCTGCAATTTACACA Y 2 1 2 1 101000 f 74 goat snp13989-scaffold1551-406751 16 9424994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398103 Affx-122961713 AX-123268458 16 8816683 AAAAACAAACACAATTCCAGTTTCCAGGCCCACAC[A/G]TAAGGAGCGTGGAAGTTGCTGATCCATCTAACAAA R 2 1 2 1 201000 r 74 goat snp13990-scaffold1551-450397 16 9468941 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413337 Affx-122950166 AX-123283686 16 8842954 CCTTTATATAAAATTCTCATCTCTTGATAATTTTC[A/G]TTTCTCTAAAAACCTAGGGACTTCATCACATCATT R 2 1 2 1 102000 r 74 goat snp32473-scaffold370-14524 16 9499050 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794808 Affx-122933046 AX-385281768 16 8900064 GAGAAAGAACATACTATTCTTGTATTCTAATCACC[A/G]CTGGTTGAAGAGTTAGAAATTGTCACAAAACACAA R 2 1 2 1 101000 f 74 goat snp32474-scaffold370-71634 16 9556574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797002 Affx-122955266 AX-385283943 16 8977067 TGATGGTGAAAGAGAGGGGGTTGTTATCATGCATT[A/G]TTTCTCAAAGTGAATAAGATTAATGAATATTTTTG R 2 1 2 1 101000 f 74 goat snp32476-scaffold370-148637 16 9632649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430079 Affx-122937542 AX-123300420 16 9029982 CAGCTAGAAGAGATGGTAGAATCCATTTGAAAGAA[C/T]GTAAAGAAAAGAAACAGGTAAAGAAAGAGGGTCAG Y 2 1 2 1 201000 f 74 goat snp32477-scaffold370-201552 16 9686183 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446839 Affx-122925270 AX-123317175 16 9084450 CTAACCGAAGTTTGAAAGCAAATAATATATCTGCT[A/G]TTTCTTTCATAACTTCAGTTCTGTCGCTCAGTCAT R 2 1 2 1 103000 r 74 goat snp32478-scaffold370-256020 16 9753840 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775513 Affx-122961781 AX-385262644 16 9117064 CCCAGAAGAAGCCAGTGTGCAAAAAGCTTGGATAA[C/T]GTGGTCTCTGGAGGTCAGCTGCTTAGAGAAGGCCG Y 2 1 2 1 202000 r 74 goat snp32479-scaffold370-288634 16 9786286 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390840 Affx-122967834 AX-123261197 16 9162502 GAATTCAGTAGACCACAATGTTTAGTCATTCAGGA[C/T]GTCAAATCATCTGAAAGTAAGTCATGGGATGAATA Y 2 1 2 1 101000 r 74 goat snp32480-scaffold370-334072 16 9831842 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781367 Affx-122945248 AX-385268452 16 9209078 GCACTTTTTAATAATAACAATTTTAGTTAAAATTA[C/T]GATCCATCACCCATTGCGCTAAACACTCGACATGT Y 2 1 2 1 202000 f 74 goat snp32481-scaffold370-380648 16 9878943 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389160 Affx-122968532 AX-123259518 16 9243929 CAAAAAAGGGACTACACTGAGACTGGAAGGAAACA[C/T]GGAGCCGTGGCATTGATGGGAATGTCCTGCCCCAT Y 2 1 2 1 101000 f 74 goat snp32482-scaffold370-415499 16 9913868 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789029 Affx-122941195 AX-385276042 16 9282267 AGTTTCTACTCAGTCCCAGTTCTTACATAAATAAC[A/G]TATAAATATTGTTATATGTTACATGAATAACAAAT R 2 1 2 1 202000 r 74 goat snp32483-scaffold370-453837 16 9953198 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439552 Affx-122930098 AX-123309889 16 9316149 CAGAGAAATGGAATACATTTATGATAAGAACCTAG[C/T]ATTCTTCTTCATGTGTATGTCTATGTATGTGATTA Y 2 1 2 1 101000 f 74 goat snp32484-scaffold370-487719 16 9986974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380340 Affx-122975368 AX-123250698 16 9361250 CATCACCTCTACCCCCAAGGAAACTCTGAACCTAA[C/T]AGAAAATACAGTGTGTAAACATAATTAGGCTGCAG Y 2 1 2 1 201000 r 74 goat snp32485-scaffold370-532820 16 10032429 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794045 Affx-122979023 AX-385281013 16 9402006 AGATCCTAAAATGATGTCTCGAATTTGTGTTTACA[C/T]GTCTATTCTAGCTTTGTCCTGCCTGTCCAAATCTT Y 2 1 2 1 101000 r 74 goat snp32486-scaffold370-573576 16 10073729 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800902 Affx-122953783 AX-385287817 16 9437970 CACAGGTGGAAAATTTCAAACTGTGACAAAAATAC[A/G]CTTTTTAAAGAGTGTACCTTGGGAAATGAGGACTA R 2 1 2 1 101000 f 74 goat snp32487-scaffold370-609540 16 10109702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277106 Affx-1111835683 AX-519550613 16 9440972 GCATGATACTGTTTGTTTCTTTCACTCCTTTGTGG[A/G]CTTGTGTGTAGGTTAGTCCCTGCTAATTGCATCCT R 2 1 2 1 101000 r 74 goat Random2.2K-1574 16 9440972 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417982 Affx-122946681 AX-123288330 16 9474925 TAACTGTTTGATAAGATCAATTTAATTTAATTCCA[C/T]AGTCCCAGCAAGGAAAGGAGACCCCCAACCCAAGG Y 2 1 2 1 101000 r 74 goat snp32488-scaffold370-646495 16 10144091 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453685 Affx-122919702 AX-123324018 16 9511680 TGGAATTAAGAGGTTAAGAAGGGAAACTATGCTGA[C/T]GATAGATTTTAAGCAAGAAAGTGATGTGTTCAAAA Y 2 1 2 1 101000 f 74 goat snp32489-scaffold370-683250 16 10181021 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776802 Affx-122951169 AX-385263926 16 9576636 CTTTTGATTCAAATAAATACAGACAAAAACCTAAT[A/G]TATGACCACTGTGTCTCTTATTAAGAGGATTCTTA R 2 1 2 1 201000 f 74 goat snp32490-scaffold370-748206 16 10246842 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768647 Affx-122953582 AX-385255825 16 9619066 GAAAAACTTTTGGTATCTAATGCCATAGTTTTTCC[A/G]TTTGCATAATTAGAAGATGGTCACTGTAGAGGTTC R 2 1 2 1 201000 f 74 goat snp29889-scaffold324-1873400 16 10401297 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451276 Affx-122921312 AX-123321609 16 9649707 CAGTATTCTGTTCTGTGTGGCTGAATGAAGCTTCT[A/G]TTCTTTGTCTTGATAGATGTAGGAGATAGGTTTCA R 2 1 2 1 101000 r 74 goat snp29888-scaffold324-1842759 16 10432462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476321 Affx-1251763828 AX-586011738 16 9688087 ATTGCCTTCTCTGGACTCCTTCCCTAGTTAAATTA[-/CAAAATAGGGGTTTTAGGGGGAGAGGGAAAGATGGTGGAGGACTTTAAAATTTTAAAAATAAAAAAATAAAAAAATTTAA]AAAATAGGGGTTTTACCCAATACAAGAAAATGAGG - 4 1 4 1 20000 f 74 goat SV_155 16 9688087 - deletion junction SV-TF-chip 539476574 Affx-1251763828 AX-586011960 16 9688087 ATTGCCTTCTCTGGACTCCTTCCCTAGTTAAATTA[-/CAAAATAGGGGTTTTAGGGGGAGAGGGAAAGATGGTGGAGGACTTTAAAATTTTAAAAATAAAAAAATAAAAAAATTTAA]AAAATAGGGGTTTTACCCAATACAAGAAAATGAGG - 8 1 4 1 20000 r 74 goat SV_155 16 9688087 - deletion junction SV-TF-chip 562165181 Affx-1251763828 AX-606940593 16 9688087 ATTGCCTTCTCTGGACTCCTTCCCTAGTTAAATTA[-/CAAAATAGGGGTTTTAGGGGGAGAGGGAAAGATGGTGGAGGACTTTAAAATTTTAAAAATAAAAAAATAAAAAAATTTAA]AAAATAGGGGTTTTACCCAATACAAGAAAATGAGG - 8 1 4 1 20100 r 74 goat SV_155 16 9688087 - deletion junction SV-TF-chip 562165232 Affx-1251763828 AX-606940644 16 9688087 ATTGCCTTCTCTGGACTCCTTCCCTAGTTAAATTA[-/CAAAATAGGGGTTTTAGGGGGAGAGGGAAAGATGGTGGAGGACTTTAAAATTTTAAAAATAAAAAAATAAAAAAATTTAA]AAAATAGGGGTTTTACCCAATACAAGAAAATGAGG - 8 1 4 1 20100 f 74 goat SV_155 16 9688087 - deletion junction SV-TF-chip 562165300 Affx-1251763828 AX-606940711 16 9688087 ATTGCCTTCTCTGGACTCCTTCCCTAGTTAAATTA[-/CAAAATAGGGGTTTTAGGGGGAGAGGGAAAGATGGTGGAGGACTTTAAAATTTTAAAAATAAAAAAATAAAAAAATTTAA]AAAATAGGGGTTTTACCCAATACAAGAAAATGAGG - 8 1 4 1 20100 f 74 goat SV_155 16 9688087 - deletion junction SV-TF-chip 562165644 Affx-1251763828 AX-606941054 16 9688087 ATTGCCTTCTCTGGACTCCTTCCCTAGTTAAATTA[-/CAAAATAGGGGTTTTAGGGGGAGAGGGAAAGATGGTGGAGGACTTTAAAATTTTAAAAATAAAAAAATAAAAAAATTTAA]AAAATAGGGGTTTTACCCAATACAAGAAAATGAGG - 8 1 4 1 20100 f 74 goat SV_155 16 9688087 - deletion junction SV-TF-chip 562166178 Affx-1251763828 AX-606941586 16 9688087 ATTGCCTTCTCTGGACTCCTTCCCTAGTTAAATTA[-/CAAAATAGGGGTTTTAGGGGGAGAGGGAAAGATGGTGGAGGACTTTAAAATTTTAAAAATAAAAAAATAAAAAAATTTAA]AAAATAGGGGTTTTACCCAATACAAGAAAATGAGG - 8 1 4 1 20100 f 74 goat SV_155 16 9688087 - deletion junction SV-TF-chip 562166373 Affx-1251763828 AX-606941781 16 9688087 ATTGCCTTCTCTGGACTCCTTCCCTAGTTAAATTA[-/CAAAATAGGGGTTTTAGGGGGAGAGGGAAAGATGGTGGAGGACTTTAAAATTTTAAAAATAAAAAAATAAAAAAATTTAA]AAAATAGGGGTTTTACCCAATACAAGAAAATGAGG - 8 1 4 1 20100 f 74 goat SV_155 16 9688087 - deletion junction SV-TF-chip 38397647 Affx-122962611 AX-123268002 16 9709186 TTCTTGAAGTTCAATATAAATATGCTTACTATATA[C/T]GCTGTTGTATTCTTTTATTTCCTTAGATTTCCAAA Y 2 1 2 1 201000 f 74 goat snp29887-scaffold324-1783280 16 10492512 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765220 Affx-122947309 AX-385252760 16 9777528 AACCTGGTGTCAAATATGGCTTTTCAAACCTTGTT[A/G]TGTTTTGAACACCATGGTATCAACAGAACCAAATT R 2 1 2 1 101000 f 74 goat snp29885-scaffold324-1714938 16 10558660 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436650 Affx-122932482 AX-123306988 16 9806715 CAAAGTTTAGTCAGATAATATTAACAAGAAAATGC[A/G]TCCATTACAACTCACTTCTAAAGAAAAAAGTGAAA R 2 1 2 1 101000 f 74 goat snp29884-scaffold324-1685751 16 10588856 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432810 Affx-122935401 AX-123303151 16 9843564 TCTTCCTTTATATGGTATAGGATTTTGAGTCTTCT[A/G]TTTCTAGGCATGTTCTTATCTTCCATTATCTTTAA R 2 1 2 1 201000 r 74 goat snp29883-scaffold324-1648902 16 10626112 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790957 Affx-122926648 AX-385277954 16 9883572 TTTTCTCATTTTAACCTTCCACTTCAAATGTGAGG[C/T]ATTCAGATCACTGTCTTTACTTAGACTTAAGATTG Y 2 1 2 1 101000 f 74 goat snp29882-scaffold324-1608894 16 10665491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398858 Affx-122961054 AX-123269213 16 9912644 TATAGATAACTGCATTTAAAAACATCCTTGTACAT[A/G]CACCTTCATGCGTTTATGACTACATAGCAGAGGCA R 2 1 2 1 101000 r 74 goat snp29881-scaffold324-1579822 16 10695512 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773494 Affx-122921471 AX-385260635 16 9971211 CTCAGTCAGTGAAAAAGATACTCTGTTTCTGAGGG[C/T]TAATTTACATTTACAGGATTGTTTACCATTAACCA Y 2 1 2 1 101000 f 74 goat snp29880-scaffold324-1521255 16 10754183 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424310 Affx-122941964 AX-123294656 16 10010302 CAGTTTATCTTAATCTTTTGAGTCTTAGAAAGCAG[C/T]GCTATTTTCAAACAAATGCAATCATCTTTAGCTTA Y 2 1 2 1 101000 f 74 goat snp29879-scaffold324-1482164 16 10793335 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429685 Affx-122937641 AX-123300026 16 10114924 TCCAGAAAGAATGGAGGAGAGCAGGTGTAGACAGC[G/T]CCATGAGACAGATTCAGCCCAGCCAACTCCTAAGG K 2 1 2 1 101000 f 74 goat snp29876-scaffold324-1377542 16 10899552 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445053 Affx-122926232 AX-123315390 16 10155231 ATTTCCCTAAGTGTCAGGCTTGCTTGTACTTCTCC[A/G]TTGACTATTTCCTCCAAAGCGTTAACTTCAACATT R 2 1 2 1 201000 r 74 goat snp29875-scaffold324-1337235 16 10939759 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453356 Affx-122919947 AX-123323689 16 10245348 GTTCACTAGCGTTGTTTGGTCTATGAAGCCATCTA[C/T]GTCCTGGCAACCTGCATTGGTTCAGAACAGCTGAG Y 2 1 2 1 101000 f 74 goat snp29873-scaffold324-1247118 16 11029309 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782641 Affx-122947484 AX-385269714 16 10327453 TTAGGGCCTATTTATAACTCTGAACTTCTAAAAGT[A/C]TTAATAAGAATTGATGGGTATCCTACGTTAATGAC M 2 1 2 1 101000 r 74 goat snp29871-scaffold324-1165013 16 11110286 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276976 Affx-1111835684 AX-519550484 16 10425464 AGCTGCTGCCAAAGATAATCTTCTAGTTCTGCCTC[A/T]GGAGTCCATGTTCCTAAGCCCCACCATCTACTAAA W 4 1 2 1 102000 f 74 goat Random2.2K-1576 16 10425464 A T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408486 Affx-122954416 AX-123278837 16 10466831 CACTGATTCTAATTCCTGAACTTCAGTCTGGCCCA[C/T]GCTGTAAACAGACAAACTCAATCTCCTCCTTACAG Y 2 1 2 1 201000 r 74 goat snp29868-scaffold324-1025635 16 11251133 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771648 Affx-122963582 AX-385258806 16 10571741 TAAGATGTGAGGATGCTAGTATTCCCATACAAAGC[A/G]TGCAGTTTAACAAGGCAACGCCTTATTTTAAGGAC R 2 1 2 1 101000 f 74 goat snp29866-scaffold324-920725 16 11356492 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422645 Affx-122943698 AX-123292991 16 10703539 ACAGGGAAACCTGGTGTGCTGCGATTCATGGGGTC[A/G]CAAAGAGTCGATATGACTGAAACACTAAACTGACA R 2 1 2 1 103000 r 74 goat snp29863-scaffold324-788927 16 11485190 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418659 Affx-122946323 AX-123289007 16 10733970 AGAATTTCTGGCTGTTATTCAATTTTTTTAACTGC[C/T]AATATTAGAAAAATAGATTGAATATTTTACATCAA Y 2 1 2 1 103000 f 74 goat snp29862-scaffold324-758496 16 11515838 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435969 Affx-122933520 AX-123306308 16 10763556 AAAAAAATTGTGATAATAGGGATGAAATTTGCCCC[A/G]TCTGTATTTAAGTTGCACTCTATGTGTGAATGAAG R 2 1 2 1 101000 r 74 goat snp29861-scaffold324-728910 16 11545337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774839 Affx-122966371 AX-385261973 16 10806053 ATTAGTGACTTTCTGTTAAAGAAGACACAGATTTC[C/T]GATGCAAAACTGACATAAATAATGAAGTATCTTCC Y 2 1 2 1 101000 f 74 goat snp29860-scaffold324-686413 16 11587897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790654 Affx-122938695 AX-385277656 16 10889904 GCTCAGTAACAATACTAAGAAAACAATTACAGCCA[C/T]AGTAGCCTGACAAAATCAAGATAACCAGAAACTCA Y 2 1 2 1 101000 r 74 goat snp29858-scaffold324-602562 16 11672754 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420474 Affx-122944873 AX-123290821 16 10933681 GCTTCCTCTCTCATCCCACGACCACCCAGGCCTAC[A/G]AGAGAGACCCTGACATGGAGTCAGGATTCCTGGTA R 2 1 2 1 101000 r 74 goat snp29857-scaffold324-558785 16 11716697 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407011 Affx-122955023 AX-123277362 16 11020630 CCAAGGGAATTACAAATAATAAAATGGTCCGTGAA[C/T]AGCTGTAAAAAGGAATAGAGTAACGAAGAAATGAA Y 2 1 2 1 101000 f 74 goat snp29855-scaffold324-471836 16 11802734 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454088 Affx-122919371 AX-123324421 16 11051315 GATTTACAGGAAGAACACAGGAAGCAGTGTTTCCA[C/T]AAACACTGGCTTTCTGTCTCTCCCTCTCTCAAGCA Y 2 1 2 1 103000 f 74 goat snp29854-scaffold324-441151 16 11833233 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422387 Affx-122943396 AX-123292733 16 11108827 AAATTGGATTCTGATTTCCAACTGTCAAAAAAAAA[G/T]TTATTGATCAGATGCATTATTCACAGTGGCTTTGC K 2 1 2 1 102000 r 74 goat snp29853-scaffold324-383639 16 11890859 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764837 Affx-122924261 AX-385252437 16 11212579 ACTCTTCATAAAAAGGCATTAGAGTACTTGGCACC[A/G]TATGCTGTAAAGTAGTGATGTTTCAATTCATTTAT R 2 1 2 1 101000 f 74 goat snp29851-scaffold324-279887 16 11996161 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439297 Affx-122930967 AX-123309634 16 11313477 AGAAAAATAAGTGTAAATCATTGTGCCTTTGTCTT[A/C]GACCATAGTGACTTAACACTGTACCAAAAGTGCAA M 2 1 2 1 101000 r 74 goat snp29849-scaffold324-178989 16 12096749 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442767 Affx-122927742 AX-123313104 16 11376659 CTACAGCTCACTCAATTCATAAACTCTATGGGAGA[C/T]GACTTTTTTCCATTTTGTTAATGAAGATCCCGAAC Y 2 1 2 1 101000 f 74 goat snp29848-scaffold324-115807 16 12160353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786705 Affx-122958647 AX-186580753 16 11475020 CAGATCTCTGACTTATTGAGAAGATAACCTTCCAG[C/T]ACCTCTTTGAGGAACTACACTGCCACCCCACATCA Y 2 1 2 1 101000 r 74 goat snp29846-scaffold324-17446 16 12263582 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785420 Affx-122958946 AX-385272465 16 11518091 AAAAAAAGTGCTTTGTAGATCCTTTAGTCTGAATA[C/T]GAACTGATGTGTTCAAGAGTTATGACCCTGAAGGT Y 2 1 2 1 101000 r 74 goat snp4926-scaffold1167-25526 16 12306792 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427956 Affx-122939200 AX-123298299 16 11567507 TCTTCTTATTTCTCAGTTAAACTAGCAAGTTCATC[A/G]TCTGAGAAAGAGGAGAAAGAATAATGTATCAGAGG R 2 1 2 1 103000 f 74 goat snp4927-scaffold1167-74942 16 12357195 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433330 Affx-122935157 AX-123303671 16 11598388 AATTATAAGTTATAAGAATGTGCTTTTATAGGTCC[A/G]TGTAATCTATCATTTCCAATACTTCCCACCTTCAT R 2 1 2 1 101000 r 74 goat snp4928-scaffold1167-105823 16 12388479 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769034 Affx-122966949 AX-385256209 16 11631971 ATCTGTGCCCTCAAGAAAGAAACCTTTTCATCATT[G/T]ACTGTATTTTTTCATCTCTCGAATAAATCTTAGAA K 2 1 2 1 101000 f 74 goat snp4929-scaffold1167-139406 16 12422666 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785567 Affx-122959200 AX-385272611 16 11665607 AATACATATGTCATATGAACCTAAAATCTCAGTGA[C/T]CAGAGAAAAGGAACTTTATAGGAAATCATTGTATC Y 2 1 2 1 101000 r 74 goat snp4930-scaffold1167-173042 16 12456012 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770734 Affx-122977102 AX-385257898 16 11716899 CATTTTTATTAAATATCACTTTCTACATATTCCCT[A/G]TTGTGTGAATTAATAAGACTAATTCACCTCTGAAT R 2 1 2 1 101000 f 74 goat snp4931-scaffold1167-224334 16 12508243 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429507 Affx-122937858 AX-123299849 16 11799437 TATAGAAAATTATTAGTTATTTAATTCCTTCAAAT[A/C]GTTCTACTTCCCCATTTCCTTTTTGGGAGACCAAT M 2 1 2 1 101000 r 74 goat snp4932-scaffold1167-306872 16 12591341 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450347 Affx-122922113 AX-123320682 16 11843452 AGATCTTTTTAAATTTTATTTATATCAGTAAGGGG[C/T]GAGGCTCAATCGATTTTTCTCAGGTCACAAAACTA Y 2 1 2 1 103000 r 74 goat snp4933-scaffold1167-350887 16 12634857 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798722 Affx-122934546 AX-385285653 16 11887236 TTTCTCTTTTGGGGGTTTTTCAATTTTTATACATG[C/T]ATGTGAATTAGATGTAAACAATACCTCAAAGTACA Y 2 1 2 1 201000 f 74 goat snp4934-scaffold1167-394671 16 12679510 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378161 Affx-122976967 AX-123248520 16 11952672 TTCTTTCTTGTATTGCAGATGCCAGCATTTCTGTA[C/T]AATAGAGTATTAGATCAAGCTGAAACTGAGTCCAT Y 2 1 2 1 201000 r 74 goat snp4935-scaffold1167-460107 16 12746601 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375589 Affx-122978732 AX-123245948 16 11992696 AATTGCTACTTATTAATATACCAACACATCAATAA[C/T]GCAGTCTTCATTTTCATTGCTAGATAGACTGTCAA Y 2 1 2 1 101000 r 74 goat snp4936-scaffold1167-500131 16 12787938 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445440 Affx-122925357 AX-123315777 16 12024778 TGTTGCGCCACACTAGTATATCTTTGTTACCATAC[A/C]TCTCCTTACGTGCCTTTTTCTGCAGATGCTGAAGT M 2 1 2 1 101000 f 74 goat snp4937-scaffold1167-532213 16 12818180 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798545 Affx-122955424 AX-385285478 16 12065017 CAATGTAGGCAGAGTGGGTTTCATCACTGATTAGG[C/T]AATTGAGATCATGCATGCTGTGGTATAGCCAAAAA Y 2 1 2 1 101000 f 74 goat snp4938-scaffold1167-572452 16 12858954 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384979 Affx-122971895 AX-123255337 16 12096346 CTTCTCAAAGGCCCCACTCCTATTGTCTGATCTCT[A/G]TGCTTTGACCTTGCTACTACATGTAAATGCGTGAA R 2 1 2 1 201000 r 74 goat snp4939-scaffold1167-603781 16 12890578 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794601 Affx-122942734 AX-385281563 16 12127048 GAGCAAATTACTGAAACAATGTTAAAAACATCTTC[A/G]CTAAGCAAATCTTCTTCAGAGGTTCTCATCACTGA R 2 1 2 1 101000 r 74 goat snp4940-scaffold1167-634483 16 12922309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788210 Affx-122946040 AX-385275229 16 12158018 TTACCTTTATTCCTAACTAGGGAAATATAGCCTTG[A/C]CAGAGGAGGTGATTCAGAGTTACAATTGCCTCCTA M 2 1 2 1 101000 r 74 goat snp4941-scaffold1167-665453 16 12952000 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406816 Affx-122955685 AX-123277167 16 12190234 AGGTAAGGCTTGCTGCCTTTTGAGTGGAATGAGCA[C/T]GTTAATACAGAAAATAATATCTGGAAATTAGAAAA Y 2 1 2 1 101000 f 74 goat snp4942-scaffold1167-697669 16 12984615 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413732 Affx-122950060 AX-123284081 16 12237894 AAGACTAAGTTGAAAAGCCTAACTACTTGAGAAAT[A/C]GGGATTGGAATCATAGAGATGTTCAGGGGGTTTCC M 2 1 2 1 201000 f 74 goat snp4943-scaffold1167-745329 16 13018680 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389879 Affx-122968138 AX-123260236 16 12277498 GTCCTTTGAGGATAGGGTAATCTTCTTCCCCTACT[A/G]TCCTGATTTTTAAGCCAGGATCTCCTCTTCTGCTC R 2 1 2 1 201000 r 74 goat snp4944-scaffold1167-784933 16 13070297 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776485 Affx-122959445 AX-385263612 16 12308042 ACAGAGGAGGTATTTTCATACTTTATTTATTAATA[C/T]CATAACTCTTCAAACTAGATTTTCAAATACCTTTG Y 2 1 2 1 201000 f 74 goat snp4945-scaffold1167-815477 NW_017195380.1 12522 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444032 Affx-122926881 AX-123314369 16 12338430 CCTTCAAAATGTTCTGATAAAGTGGCTTAGCAGCA[A/G]GACTTTTGCCATTGACTCAAACAACTCTGAAAAGA R 2 1 2 1 201000 r 74 goat snp4946-scaffold1167-845865 16 13132201 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276978 Affx-1111835685 AX-519550486 16 12352434 TTTCTCTGGATTTTCATACAAGAGATTGAGATAAT[A/T]AAAGGGGGTTTTCCCAGGTTTCCAAAGCTCCTTGC W 4 1 2 1 201000 f 74 goat Random2.2K-1577 16 12352434 T A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407099 Affx-122954890 AX-123277450 16 12366979 GCATCTGTATCATTGGTACTGATGTTAAAAAATCA[C/T]GAATATTCAAATATTTTACCAATGTCTTTAATTAT Y 2 1 2 1 101000 f 74 goat snp4947-scaffold1167-874414 16 13160501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380782 Affx-122975104 AX-123251140 16 12402961 CAAAGCTCTTCATCCAAGAAAAATAAACATATCAT[G/T]ATAAAAATAATTATTCTGCAGCTGACTCCAAATTT K 2 1 2 1 101000 f 74 goat snp4948-scaffold1167-910396 16 13196956 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784265 Affx-122921668 AX-385271316 16 12432644 GCCTTTCTTTCCTCTCCACACTTACGTTATTGTTG[C/T]GTTTACCTTATACTTGAAGGGAGAAAGGTGGTAGT Y 2 1 2 1 101000 f 74 goat snp4949-scaffold1167-940079 16 13226675 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381354 Affx-122974410 AX-123251712 16 12470371 TTTTATACACACTCATGAACAGTATTCTAGAAAGG[A/C]TAAATTTCCTTATATTCTCACCAGCAGAGTATGAG M 2 1 2 1 101000 f 74 goat snp4950-scaffold1167-977806 16 13264479 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392372 Affx-122966239 AX-123262729 16 12481695 TTTTCTTTTGTATTTTTCCCTTCCTGGAGTTTTAA[C/T]AGTTTTGCTTCTCTTGTCAACCTAAGGATAATACG Y 2 1 2 1 101000 r 74 goat snp58651-scaffold955-2067894 16 13275526 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800538 Affx-122974295 AX-385287458 16 12520489 ACTAGTAAATTCTAGTTATTAACTCCAACCTGAAC[G/T]CTCCTGTAGTGCTTCTCTTCCCTAAAGCACTTGAA K 2 1 2 1 101000 r 74 goat snp58650-scaffold955-2029100 16 13314118 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400947 Affx-122959704 AX-123271300 16 12566488 TTTCCTTTCAAAAAACTAGCATTTTACTTACTCTC[A/G]TCTCTTAAATTCATCTTTGTTTCTGCACTATGAAA R 2 1 2 1 101000 f 74 goat snp58649-scaffold955-1983101 16 13360450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415116 Affx-122949436 AX-123285465 16 12610897 TGCACAGGCTACACCTGGCTCTCATTGTGTTGTGT[A/C]GTACAAGTCTCTGAAACAGAATTTTTGTTGTTGCT M 2 1 2 1 201000 f 74 goat snp58648-scaffold955-1938692 16 13407432 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781222 Affx-122923295 AX-385268307 16 12651765 ACCAATATTTTCTTTATACGATCAGACTTTAATTT[A/G]CTTTCATCCCAGACACATCTACACCTGAGTGTCAT R 2 1 2 1 201000 r 74 goat snp58647-scaffold955-1897824 16 13448801 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376548 Affx-122977986 AX-123246907 16 12686760 CCTTTAGCTACCTAAGTAAGTCAAAATATTTTATG[A/G]GATCCGTTTAATCACTGCATTCTGGTTTTGTGTTG R 2 1 2 1 201000 f 74 goat snp58646-scaffold955-1862829 16 13483782 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765259 Affx-122939284 AX-385252794 16 12725794 CATTTTACTACTTAATTTACATATGAAATAATTTT[A/G]TTGTATTTAACATTAGATATTGGGAACAATTTTTA R 2 1 2 1 303000 f 74 goat snp58645-scaffold955-1823795 16 13522841 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445645 Affx-122926160 AX-123315982 16 12782770 AAATCAATTTGCCTTCCTGGTCTCAAAATAGTGTT[A/G]TTAGCATTGGTATTATTTTTGTTATTTCCCTTAAG R 2 1 2 1 101000 f 74 goat snp58644-scaffold955-1766819 16 13579950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793167 Affx-122926379 AX-385280145 16 12824234 TGCCAAATCACGCCATGGATGTCATGGACTACCAG[A/G]GTTCTCTTAACTGCTCTAAATAAAGTCATTTGTGT R 2 1 2 1 101000 f 74 goat snp58643-scaffold955-1725355 16 13623452 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277112 Affx-1111835686 AX-519550619 16 12849976 AAATTTGACAGTGATATAAATGAATACCAAACATT[A/G]TTTACCTTTAAAATGTTATGGTTTTTTCCCTTGAT R 2 1 2 1 101000 r 74 goat Random2.2K-1578 16 12849976 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38442373 Affx-122928018 AX-123312710 16 12857270 TCTAAGCCTGGTTCTGTGGGCATATTTGAGAAAAT[A/G]CGAGTTAATAAAAATCTTCCCAATAAAACCAGACT R 2 1 2 1 101000 f 74 goat snp58642-scaffold955-1692319 16 13657369 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782439 Affx-122943727 AX-385269515 16 12888125 TGATTTTCTTCTGAATAATTAGATTTTGTTCATTA[A/C]TATTTGAGGTGTTCATTTCTGAAAAAGACTATTCC M 2 1 2 1 101000 r 74 goat snp58641-scaffold955-1661464 16 13688849 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453632 Affx-122919745 AX-123323965 16 12919105 TTGAATGCAAAGCCTGAACAGTAAATCTCAAAATG[C/T]GAGGAGTGCCAAGGAAAGGCTGAAGTATGAGCCCA Y 2 1 2 1 201000 f 74 goat snp58640-scaffold955-1630484 16 13719321 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444554 Affx-122926985 AX-123314891 16 12953358 AAAAGTGTGGGTCACAAAGAGATTTCTGAGCAGAA[C/T]ATTGATATTTAGCATGAGAATAAGATATCCGAGAG Y 2 1 2 1 101000 r 74 goat snp58639-scaffold955-1596231 16 13755135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775718 Affx-122957654 AX-385262849 16 12987336 CTACATCTAGACTCAGTGCTGTAGGTCCACTTTGG[C/T]CTTTTCATTTGATTCTGAGCTTCTGCCATCCTCTT Y 2 1 2 1 101000 f 74 goat snp58638-scaffold955-1562253 16 13788679 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417031 Affx-122947536 AX-123287379 16 13017712 TGAAACCATGTTATCATCTATCAGCCCATCTATTT[A/G]TAACTTGTTTTCATAGATACTTTTCATAGATATTT R 2 1 2 1 101000 f 74 goat snp58637-scaffold955-1531877 16 13818843 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415546 Affx-122948655 AX-123285895 16 13049713 AAAGAAAGAATGTGTATAAAAATCAAATGTTCACT[A/G]AAGATCAATCATATATGAATCTCTTAGCTATGAAG R 2 1 2 1 101000 r 74 goat snp58636-scaffold955-1499876 16 13850707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393589 Affx-122965381 AX-123263945 16 13083743 TTACCACTAGTGCTGTAGAGCCAAGGCTTAACCAA[A/G]TCCTCTAAATTCAAATCTAATCTTCCTGCACAATA R 2 1 2 1 101000 f 74 goat snp58635-scaffold955-1465846 16 13884717 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379318 Affx-122976190 AX-123249677 16 13115101 AGTATGGCCATGCATCTTACTGTGATCAAAAAAGC[A/G]TGAGCATGTAGGTTAGCCTGGACAATCAGCTTGGA R 2 1 2 1 101000 r 74 goat snp58634-scaffold955-1434488 16 13916092 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272858 Affx-1111833059 AX-519546548 16 13137690 CAGCAGGTTGCCTTTCTCTGTTCAGCTGCTCCAGA[A/G]TGGACATCCCAGGCAGTAGTCTGCAGGATTGTAGA R 2 1 2 1 201000 r 74 goat 16_13137690_AF-PAKI 16 13137690 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378876 Affx-122976507 AX-123249235 16 13151013 CCTATCTTTAGTTTTTCTGCTGACACCTGCCAGAG[C/T]AACTAATTCAAGCAATCCTGGTAGGCAGTCATCAT Y 2 1 2 1 202000 r 74 goat snp58633-scaffold955-1398576 16 13951982 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427006 Affx-122939849 AX-123297351 16 13194553 GCAATGTGTATGTGTGTATGTATGTGTTGTGTGTG[C/T]GTGTGTTCTCTCCTTGAAGTCACCATTTCATTTCA Y 2 1 2 1 103000 r 74 goat snp58632-scaffold955-1355036 16 13996301 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391183 Affx-122967429 AX-123261540 16 13250210 TTCTCTATGTCATAGATTTGAGGAAGACCTGGAAG[C/T]GGTGAAGATTCTAAAGGAAGACCATGTCGGTATTC Y 2 1 2 1 101000 f 74 goat snp58631-scaffold955-1299379 16 14052292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413261 Affx-122950224 AX-123283610 16 13301300 ATCACCTGCTTTAATCCATTTGGAATTCAGGGAAT[A/G]TTTGACATCTAGAGTAGTAAATGAACATATTTTAA R 2 1 2 1 201000 r 74 goat snp58630-scaffold955-1248289 16 14103703 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392856 Affx-122965760 AX-123263213 16 13331436 TGTGCTTCGGGCATAGGGACTTGCAGTCGGAGACA[C/T]ACTGAAAATAGTTGTGATGTCTGAAGCTATAGACA Y 2 1 2 1 101000 r 74 goat snp58629-scaffold955-1218153 16 14133359 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397977 Affx-122961810 AX-123268332 16 13385544 ACTTACAACAGCTGATATAAGATTTCTATTTCATC[A/G]CACATAGTACTGAAGGGATAGGTAGGTGGTCTGAG R 2 1 2 1 101000 r 74 goat snp58628-scaffold955-1164045 16 14187490 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789378 Affx-122978366 AX-385276388 16 13431430 ACACAAAATGGGTGAAAATTCTACCCTGATTTTGC[G/T]TCCCATAAAAGAGATTCTGTGAGTAATTTAGTTAA K 2 1 2 1 101000 f 74 goat snp58627-scaffold955-1118159 16 14233134 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793572 Affx-122965382 AX-385280546 16 13490228 CCCAAGCTACAATTTCCCATGCTTGCAAAGCAGAT[A/G]TAATAATGTACAAAATTTATATTACCTGTGGTTAC R 2 1 2 1 201000 r 74 goat snp58626-scaffold955-1059361 16 14292127 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417038 Affx-122947531 AX-123287386 16 13596634 ACCACTGACCTGAGAGGAGCCTGGCAAGTTCCCCT[A/G]CTTATTAAAAACTGCTGCTTATCAAGCTGAAGCTT R 2 1 2 1 101000 r 74 goat snp58624-scaffold955-952955 16 14397353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435848 Affx-122932813 AX-123306187 16 13626741 GAAAGTGTACATAAGAATAATTTTCTCAGTTGTTT[C/T]AGGGCTAAAAATATTTTTATTTCTTCCTGTCTGAT Y 2 1 2 1 101000 f 74 goat snp58623-scaffold955-922848 16 14427282 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788131 Affx-122977195 AX-385275151 16 13663194 TCATGTTCTAGCACCTTAAGGTCTACACTGGCTCA[A/G]TGCTAATTTCATCATGTTGAAATTACCACTGTGAC R 2 1 2 1 201000 r 74 goat snp58622-scaffold955-886395 16 14463813 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798482 Affx-122965101 AX-385285415 16 13699275 CTTTGAAAGCAGTAATCATATAATCATTAAAGAAA[G/T]AACATTTTGATTCCTATTGTTGACACATTTTGAGG K 2 1 2 1 303000 f 74 goat snp58621-scaffold955-850314 16 14500095 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791553 Affx-122960012 AX-385278544 16 13732512 GAACAGAGAAGTGAGAGCTGTTCCTCATAAGATTC[A/G]CTAAGAAGTTTAAGGGTAAAATAATATTTCTTTCT R 2 1 2 1 101000 f 74 goat snp58620-scaffold955-817077 16 14533180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766202 Affx-986697842 AX-385253602 16 13750444 TGCTTTACAAAGTGGATATATATGTATATATATGT[A/G]TATATATAAATGCTTTAAAGAGTGGATATATATGA R 2 1 2 1 600010 r 74 goat 16_13750444 16 13750444 Ancestral_priority_1043 ancestry 0.58 neutral IMAGE 10K 10K ancestral 38385012 Affx-122971872 AX-123255370 16 13783800 ATATCCATTACAATCAAATTGATGAACTCTCTTGA[C/T]ATATAATCTAAAAATTAACTTAAAATACTTATGAA Y 2 1 2 1 101000 f 74 goat snp58619-scaffold955-765789 16 14584872 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784380 Affx-122940114 AX-385271430 16 13856442 CAAAAGCTCCAGGCAGAAACAGTTTGACTTTTTCT[A/G]ACTTTCTATTGTAAGTCACACAGCACCAGTTCTGC R 2 1 2 1 202000 f 74 goat snp58618-scaffold955-693147 16 14655350 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788730 Affx-122948005 AX-385275746 16 13886533 AATTTTTTTAAAAATTCAGTCAAAGTAAGTACTTT[A/G]CTTACTTCAGTAAAGTAATACTGAATTATCTTTCT R 2 1 2 1 201000 f 74 goat snp58617-scaffold955-663056 16 14685265 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797230 Affx-122937478 AX-385284169 16 13915183 AAAATTCTGATATAATCCAAAGAAACCCAAAGTAT[A/G]TTCTGTAGAAGACATTCTTGCAATGTTATCCTTTA R 2 1 2 1 101000 r 74 goat snp58616-scaffold955-634406 16 14713441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432500 Affx-122935581 AX-123302841 16 13957793 CATCTCTATCTTTAAAGCTCCAAAATAGATCAATC[A/G]CATGTGTTGTTTCTAATTGGTTAAATGAATCAGTT R 2 1 2 1 101000 f 74 goat snp58615-scaffold955-591796 16 14743391 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792395 Affx-122921515 AX-385279376 16 13996863 TGACTATCCAAGAGCGCAGAAAGATTAGCAATGCA[C/T]AGGAATTCCATGAGGTCATTTACTACACCAGGATG Y 2 1 2 1 101000 f 74 goat snp58614-scaffold955-552726 16 14782420 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441556 Affx-122928693 AX-123311893 16 14096521 GAGACAGATTTATTGTCTTTTCCAAGATCACATGG[C/T]AAACCCGAAGCTCATTAGATTCTATTTTCAAAATA Y 2 1 2 1 101000 f 74 goat snp58612-scaffold955-453068 16 14880447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769449 Affx-122925794 AX-385256619 16 14133796 CATGACATAAAATTATCTACATCTTCTTATCTTTG[C/T]AAAAAGATTTCTTAATGAGAAACTGTTTCATAAAA Y 2 1 2 1 201000 r 74 goat snp58611-scaffold955-415793 16 14918439 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451966 Affx-122920948 AX-123322299 16 14222001 GGGCCATTCTGAGGATTTCTTTTAAAACTTGTTAA[C/T]GGCAGTGTGGAGGGTAGTCCCTGAACAGGAAACTC Y 2 1 2 1 101000 r 74 goat snp58610-scaffold955-327588 16 15007208 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435818 Affx-122932836 AX-123306157 16 14255445 TTTAACTTAGTTTTCTGAATTTCTTCAAGAGACTG[A/G]CTTTGTTGCTTTCATCATTCTATGGGACGTTCCTT R 2 1 2 1 101000 r 74 goat snp58609-scaffold955-294144 16 15041079 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800527 Affx-122961648 AX-385287447 16 14359925 TCTATGAGTCAGGGTGAAGTGGGAAAAAGCCAGCC[A/G]TTACAATGTCTAAAGCACAGTTTAGAAGCATCTTA R 2 1 2 1 102000 f 74 goat snp58607-scaffold955-189664 16 15147262 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797376 Affx-122968226 AX-385284315 16 14428146 GACATAGGTTTCAGTTACTAAAACAAGTTACATAA[G/T]CACTCTGAATTTCAATGCAGTGAAAAAGTGATATC K 2 1 2 1 101000 r 74 goat snp58605-scaffold955-121443 16 15215432 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377923 Affx-122977226 AX-123248282 16 14459682 CAAAAGTAGACAATTAAATTAACCTGTTGAAAAAT[A/G]AAGTCAGACATTTTGTTTATTTATAGCTGGAGGCA R 2 1 2 1 303000 f 74 goat snp58604-scaffold955-89907 16 15239991 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802348 Affx-122936501 AX-385289252 16 14499993 AACTTCAGTGAGAAGTTAATGAGAAAGAGAGATAG[C/T]GAATGTTCTCTGTTTACTTATATATAAAGAGGTGA Y 2 1 2 1 201000 f 74 goat snp58603-scaffold955-49596 16 15281076 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383994 Affx-122972921 AX-123254352 16 14529459 CCCCGGGTTGAATTCTTCCTCTAAGGAGCCCAAGA[A/C]TTCAAGCATCTTTCATGGTTAGACAACAACCTTTC M 2 1 2 1 303000 f 74 goat snp58602-scaffold955-20130 29 18785161 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375802 Affx-122978566 AX-123246161 16 14553063 CTTCAAGAGAAGTGCAAATGTAGACTGGCCAGGTT[A/G]TCTTAGGAGAAAGGTGAGAGGCTCAGTAGGGCATC R 2 1 2 1 101000 f 74 goat snp21050-scaffold206-2202727 16 15339755 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404900 Affx-122956457 AX-123275252 16 14586924 TTTGGAAAATTCTTTAATCTTGTTGCTGAACACCT[A/G]ACTTCAGTTCATCAGTGCCAAATAGAAACCTGGAG R 2 1 2 1 201000 f 74 goat snp21049-scaffold206-2168866 16 15374253 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775445 Affx-122929918 AX-385262576 16 14623591 TTGAAGGTGTAGCCCCTATGTAAGACTTGCTTATC[A/G]CATTAGAAGTAAGTAACACAAGAGACTCAGCTAAT R 2 1 2 1 101000 f 74 goat snp21048-scaffold206-2132199 16 15411593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793194 Affx-122978418 AX-385280172 16 14664770 CTTGCAAGTCAATTCACACATTTCAAAGTATATGC[A/G]TTGCTGTATTTCATTAAGTATTTAACTATTTTTTT R 2 1 2 1 101000 f 74 goat snp21047-scaffold206-2091020 16 15452078 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392515 Affx-122966118 AX-123262872 16 14727467 ATTCTATGAGACTTGTGCAGTGCCTGCCTTGGGCA[C/T]GGGGAACATTTTCTCTTGGAGCTTTTGGTTAGGTG Y 2 1 2 1 101000 f 74 goat snp21046-scaffold206-2028323 16 15512235 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776365 Affx-122935883 AX-385263492 16 14772314 AAAGATAATCAGAGCTTTTTATGGTGTAACTCCAG[C/T]AATGAGGAGCTTACAGTTTTCCACACTACCCACCC Y 2 1 2 1 101000 r 74 goat snp21045-scaffold206-1983476 16 15552991 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399644 Affx-122961065 AX-123269999 16 14825302 AACACTAAGCAACAAAAAAGCAAAGAAAAGAAAGT[A/G]CCACCTTCTTAAAGATGCTTCCTCTACCCATTGCT R 2 1 2 1 101000 r 74 goat snp21044-scaffold206-1930488 16 15606605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392857 Affx-122965759 AX-123263214 16 14875303 GTTGCTAAACTGTAGATAAAGACTTTTTCTGACTG[C/T]AGGTTTCTGAGCTTTCTGACCTCAGCAAGAACAAA Y 2 1 2 1 201000 f 74 goat snp21043-scaffold206-1880487 16 15657566 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784815 Affx-122934561 AX-385271862 16 14915594 GAACATATTTTCCTTCATAATACTATTATGCCTTT[C/T]TTCATCTTGGAAAAGTAGAAAATAAAGGTCAGAAT Y 2 1 2 1 201000 r 74 goat snp21042-scaffold206-1840196 16 15697965 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392410 Affx-122966206 AX-123262767 16 14965014 CTGAAATGTCAGGGGGACATTTTCATTTTCTTTAA[A/G]TAGTATCTGAAACTTGTTATTACAGGTATTGAATT R 2 1 2 1 303000 r 74 goat snp21041-scaffold206-1790776 16 15747603 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421228 Affx-122944126 AX-123291575 16 15026391 AGACATCTTACTTAAGGATGGAAAAACTGAAGCAA[C/T]GGCTCCCAGAAGCACATGGACTGGAAAAAAATGAA Y 2 1 2 1 101000 r 74 goat snp21040-scaffold206-1729399 16 15809826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786694 Affx-122925014 AX-385273726 16 15061122 CAGCATAGGAAAGAGGCTGAGACCTCATCTGAGCT[A/G]CCTGTTTCATGTAAGCTCAATCAAGCTAAGAGACA R 2 1 2 1 202000 f 74 goat snp21039-scaffold206-1694668 16 15844322 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791096 Affx-122924157 AX-385278091 16 15101398 ATCAGGTATATTTAGTATCTGACCTACTACTATAT[A/G]TACATTTATTATCGCTTGTCCTTCCCAGAAGAATA R 2 1 2 1 101000 r 74 goat snp21038-scaffold206-1654392 16 15884796 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447899 Affx-122923813 AX-123318235 16 15131240 TTGTAACTTGAGAAAGTAAAAGATATGAAAACAAT[C/T]GTCAAAGGATGTGAGATGCTGAATGGTGTTATACT Y 2 1 2 1 101000 r 74 goat snp21037-scaffold206-1624550 16 15912536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276984 Affx-1111835688 AX-519550492 16 15143004 TCCATCAGAAGCATTCTACAAGAAAGCTACCTCAC[A/G]TTGGAATTTCAGCTAAAATTTGCACAAAAATTTGG R 2 1 2 1 101000 f 74 goat Random2.2K-1580 16 15143004 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320774466 Affx-122972920 AX-385261602 16 15161423 GTTGATTTGCTTCCAACTTGAGATAATCATGAAAC[G/T]AATAAGTTAGAAGTAAAATACAATCCTAGATTTTT K 2 1 2 1 101000 f 74 goat snp21036-scaffold206-1594367 16 15942937 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386289 Affx-122970933 AX-123256647 16 15217910 CAAATATTTATTATTTACTATTTTCTGGGCGTAGT[A/G]CTAGGCACTGGGAACAAAGTTAAACCAGTAGAGAT R 2 1 2 1 102000 r 74 goat snp21035-scaffold206-1537880 16 16000010 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453715 Affx-122919633 AX-123324048 16 15271233 AAAATTATCATATTGAATGTCTGAAATGGGTTTCT[A/G]CTGGTGAAATCTGTGTCTTCTGAACGTGATCACTA R 2 1 2 1 201000 f 74 goat snp21034-scaffold206-1484557 16 16053388 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778906 Affx-122972580 AX-385266013 16 15306936 CAAAAGCAAAAGATACTGACCATAAGCACTTTACT[A/G]TAGCTGATAGAGTATTTTGAGGGCATATGAGTTAA R 2 1 2 1 101000 f 74 goat snp21033-scaffold206-1448854 16 16089466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783589 Affx-122971694 AX-385270648 16 15335536 ATAAAAAATGCAAATATTTGTTAGAAAATAATTTA[A/C]AATAGCCAATTCTATCTGTATAAGGAGAATATAAC M 2 1 2 1 303000 f 74 goat snp21032-scaffold206-1420254 16 16119089 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427535 Affx-122939508 AX-123297878 16 15395360 TTCTACAGGTCCAGTTATTAGACTGTGTCCTCTTC[A/G]CTATTAGGAGCAAGTTATGCTAGTTTAATTAAATA R 2 1 2 1 201000 r 74 goat snp21031-scaffold206-1360430 16 16171690 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783933 Affx-122936084 AX-385270987 16 15510111 GTCATGTATCAATGGATTATTTTTGCATGGACAAC[A/G]CAGCCTTTGTAAACATCCTTACAGCTTCCAGTTAG R 2 1 2 1 101000 r 74 goat snp21029-scaffold206-1245679 16 16286617 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417414 Affx-122947225 AX-123287762 16 15560143 CTATCACAGAGTGAACAGAAGAAAATATTTTAAAA[C/T]GAAAGGAGTAATTTGAGTTAATTGAGAGAGCAAGT Y 2 1 2 1 103000 r 74 goat snp21028-scaffold206-1195647 16 16336688 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401252 Affx-122959298 AX-123271605 16 15598312 CCAGTTGTCACAGTCCCAAGACTGAAATCCTTAAG[C/T]AAACAATTCTCTCTCCTCTGGACGACAATGACAGC Y 2 1 2 1 101000 r 74 goat snp21027-scaffold206-1157478 16 16375035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801540 Affx-122963836 AX-385288449 16 15657146 AATAGTGCAGATTTTTGCAATATGGCAAATCAATG[C/T]ATGATTTATTTTCCAGTATATATGAGAATTGCACA Y 2 1 2 1 101000 r 74 goat snp21026-scaffold206-1098644 16 16433152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404897 Affx-122956460 AX-123275249 16 15711331 TGAGAGGTTTTTCAACTAGAAAAGGACAAGATCAC[A/G]TGATCGGATTTTAGCAATGTCAGCTTGACATATGT R 2 1 2 1 101000 f 74 goat snp21025-scaffold206-1044459 16 16489483 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393777 Affx-122965196 AX-123264132 16 15764553 CTTGAGCCCTGTTTCTAATGTTTTACTGAAGTATT[A/G]TTACTTTTTAATAAAAGAACAATATTTTCAACAGC R 2 1 2 1 103000 f 74 goat snp21024-scaffold206-991237 16 16541137 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394501 Affx-122964549 AX-123264856 16 15828485 TTTTCTCTGACTGACAACAGATGAAAAGTGATCTG[C/T]GTATACTGTTGTGTGCAGCAAGGACCAAAGGGATC Y 2 1 2 1 201000 r 74 goat snp21023-scaffold206-927305 16 16605446 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406376 Affx-122955410 AX-123276728 16 15868266 TAAAGTCAATTCTTATCCCTCCTTCACATTGTCCC[A/G]TTGTCTACCATACAGGCCAAGCCTTTCTGTATGGA R 2 1 2 1 101000 r 74 goat snp21022-scaffold206-887524 16 16645481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794888 Affx-122920267 AX-385281848 16 15898041 CTAAAGTAAAAATGGATCTAAATAGATTAAAAACA[C/T]GACTATGTTGAGAAGAAACAGTAATCCAGAGTAAA Y 2 1 2 1 101000 f 74 goat snp21021-scaffold206-857749 16 16675276 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277118 Affx-1111835689 AX-519550625 16 15904459 AAACCCAACTTTTTGCATTTTCCTTGGAAATGACT[A/G]TTTATTAAAAGTGAAAGACTCTATGTTTATAAGAC R 2 1 2 1 201000 r 74 goat Random2.2K-1581 16 15904459 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276988 Affx-1111835690 AX-519550496 16 15914773 AAAAAAGAAACTCAAAGATGATGTGCTATAGAGAA[A/G]TCATGGGTTACATGGGTAAAAAATTATTAGTTTCA R 2 1 2 1 101000 f 74 goat Random2.2K-1582 16 15914773 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796487 Affx-122947471 AX-385283437 16 15927523 ATCTCATTTCAGGGGGAAGGAACAGAAAAAGTAAG[C/T]CAATAAAGAAGTTCAAGAAGTAGCATTTTTAAAGT Y 2 1 2 1 101000 f 74 goat snp21020-scaffold206-828267 16 16704727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793797 Affx-122950671 AX-385280769 16 15962082 GGTACACTGAGACCAGCATATCTACAAGTAATTCA[C/T]GGGGCAATGATAACCTCTATCTCTCTAGGACAAAT Y 2 1 2 1 202000 r 74 goat snp21019-scaffold206-793708 16 16739942 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432798 Affx-122935411 AX-123303139 16 16012828 AATCATTGAGAGGAAATTAAGAAGAAACCCCTAAG[C/T]GGTTAAGAAATTACACTCTCACACTAGCCTCAAGA Y 2 1 2 1 101000 r 74 goat snp21018-scaffold206-742962 16 16790753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429148 Affx-122937990 AX-123299490 16 16061706 ATAGACTTTTCATGTCAGTGGTAATTTAACATGAC[A/G]CTTGTTACCACCATAAAGTTTATATTTCTTCATAC R 2 1 2 1 101000 f 74 goat snp21017-scaffold206-694084 16 16839862 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453353 Affx-122919950 AX-123323686 16 16117634 GGAGATCACCCAGATAGTTCCAAGTACCTCCTAAA[G/T]ACACCAATGAGGAGATGACAGGAGGGAGTACTGTT K 2 1 2 1 101000 f 74 goat snp21016-scaffold206-638156 16 16896160 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773016 Affx-122975553 AX-385260160 16 16146840 AAATGCCTGTATGAGACAAAAACAAGGACTTTGAG[C/T]GGGTGACTAGAACAGTACTTCTTGTGTCATCATAT Y 2 1 2 1 201000 f 74 goat snp21015-scaffold206-608950 16 16926449 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776617 Affx-122949777 AX-385263744 16 16176317 GTTAAAACATTTTGGTAGTTGTACAAATGGTAGTT[A/G]TCCCTTTTGTAGTTGTTCCTCAGATAAGGGCAACA R 2 1 2 1 101000 r 74 goat snp21014-scaffold206-579473 16 16956102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434477 Affx-122934631 AX-123304818 16 16215426 GTGCTTTAATATTCATGAAAATATTTGTTTATCTT[A/G]TATACTAGTTGTTTTTACCTAACCTAGCTCTTCAT R 2 1 2 1 101000 r 74 goat snp21013-scaffold206-540364 16 16995343 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388853 Affx-122968876 AX-123259211 16 16254655 CTCTGCCACCTTCTTTGGATTTTCTTTTCTTCCTG[C/T]ACTCTGGCTTCTGCAGTGTACCTGTGGTGGTCAAA Y 2 1 2 1 201000 r 74 goat snp21012-scaffold206-501135 16 17035106 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801409 Affx-122953518 AX-385288319 16 16303554 TTTTCCTTCCAAGTATTCACCTGTATATTTACACA[C/T]AAATGTGAATGCTATTGATTAAACAAAGTTGTATC Y 2 1 2 1 201000 r 74 goat snp21011-scaffold206-452236 16 17082557 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413150 Affx-122950355 AX-123283499 16 16333180 CATAGTGAAGTCAAAAACCATACCAATCTATTGGG[A/C]TTGACTAACTTTTTGCAGTCTGTCCCCAATTTACA M 2 1 2 1 101000 f 74 goat snp21010-scaffold206-422610 16 17112061 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790081 Affx-122920042 AX-385277087 16 16379175 AGTTTTGAACTGCTTCTCTGACTAAAAAATTGATC[A/G]TCTATCAGTTCAATGATAAGAATTCATTAAGGTTA R 2 1 2 1 101000 f 74 goat snp21009-scaffold206-376615 16 17158099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424295 Affx-122941975 AX-123294641 16 16421740 CTTGTCACCTTCCTATCTGAGAAACATTACATTGC[A/G]TCTTAATCCTTCACATGTTGTTGCAGCCAAGTTAA R 2 1 2 1 101000 f 74 goat snp21008-scaffold206-334050 16 17200604 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413787 Affx-122949916 AX-123284136 16 16516499 TGAGGTTAATTGTTCAAAATATGTTCTACAAAATT[A/G]CCAATCTGCTAAGACATCTTATCCCAAGTTACTTT R 2 1 2 1 101000 r 74 goat snp21006-scaffold206-239291 16 17296471 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438377 Affx-122931311 AX-123308715 16 16550919 AAAGAAGCTGGAGAATACTGTTGAAAAAAATCCAG[G/T]TTATACATCAAATGGGCATCTAATTCAATGTGAGA K 2 1 2 1 101000 r 74 goat snp21005-scaffold206-204871 16 17330923 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376495 Affx-122978026 AX-123246854 16 16589208 CCAAGTGTGGTAGGCAGAATAATGGCTCCCTGAAC[A/G]TGTCCTTGTCTAAATTCCTGAAAATGGTAAAAATG R 2 1 2 1 201000 r 74 goat snp21004-scaffold206-166582 16 17369133 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772724 Affx-122919806 AX-385259870 16 16622024 AAGCCTGATTCCTAGATTTTCAGCTTGGGTATAAA[C/T]GATTAGTGATACAGTGTAATAAGATGTCTTTTGAG Y 2 1 2 1 101000 f 74 goat snp21003-scaffold206-133766 16 17401829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437315 Affx-122931966 AX-123307653 16 16658241 TGGCTGCTGAGTGATCAGTTCAAGCTGGGGGCAAC[A/G]TGCTTCTGTTCAGCGGAGAGTCCTAAGGAGATTCT R 2 1 2 1 201000 r 74 goat snp21002-scaffold206-97549 16 17438060 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384295 Affx-122972290 AX-123254653 16 16695784 TTAGGTCCTGTACGAATATCCAGGAAAGAGTGAGA[C/T]GTATTTCCTTCTTCCCCTTTAGCCTCTAAGCTGAG Y 2 1 2 1 101000 f 74 goat snp21001-scaffold206-60006 16 17475559 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430491 Affx-122937236 AX-123300832 16 16728878 AAATGAAATGTCTTCAAGGATTTTCACCCACCCTT[A/C]TTAAGCCAAGACTCACTCTCCCCACCACCTAAATC M 2 1 2 1 101000 r 74 goat snp21000-scaffold206-26912 16 17508374 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769410 Affx-122929000 AX-385256581 16 16780580 CAATTTGTTGACTAGATAACTGAACGATGAAAAGA[G/T]AACTCAAGATATCATGGAGATGGCAACTGCAGGAA K 2 1 2 1 101000 r 74 goat snp22788-scaffold2276-260171 16 17559892 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383787 Affx-122973199 AX-123254145 16 16846866 CAGAGAGGGAGCCAACCTGCCTATGGCTTAGAAAG[G/T]AGAGTGACAGGCTGTTGAAAATGCAGATTTATTTC K 2 1 2 1 101000 r 74 goat snp22787-scaffold2276-193885 16 17626371 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774372 Affx-122926156 AX-385261508 16 16876318 CTAAGGTCAAGGCCTTATTAGATAATAACAGTATC[A/G]TATAAGATATGGTGGTATAATACTCTTAATAACTT R 2 1 2 1 101000 f 74 goat snp22786-scaffold2276-164433 16 17655766 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428619 Affx-122938684 AX-123298961 16 16926744 TATAAAAAACTCTTTACTAGGGATTTATAAGGTTG[C/T]AGATTTCTAATGATCTGTGTCACCTCTGTTGGGAT Y 2 1 2 1 101000 r 74 goat snp22785-scaffold2276-114007 16 17706249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429034 Affx-122938316 AX-123299376 16 16967113 TTACAGTAATCAGAATGGCCCCAAAAATTGCATTG[C/T]AGTAGTACTTAAATTATGCTAAGGGAAGTTCAGAC Y 2 1 2 1 101000 r 74 goat snp22784-scaffold2276-73638 16 17746617 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399638 Affx-122961070 AX-123269993 16 17006293 ACCATCTGCAGGATCTAAGAGGGAAAATCAGTTCA[A/G]CTTGAAATCAGGGAGCAAAAATCGATTAAGTTGTT R 2 1 2 1 101000 f 74 goat snp22783-scaffold2276-34458 16 17785839 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788692 Affx-122921144 AX-385275708 16 17063720 AAAAGTTGACCAGAAAACATAGCAGAAAAAGAGGC[A/G]TTGTGAGACAGTTATTGAAGGAAAATCATCTAAGG R 2 1 2 1 101000 f 74 goat snp13941-scaffold1547-22870 16 17842421 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800380 Affx-122930223 AX-385287302 16 17095008 GAAATCTGCCACTTATAGTAAAAACAACAATTTTA[C/T]GTTTAAAATATATATCAGTCTTTTGCTTGTGATTA Y 2 1 2 1 201000 r 74 goat snp13942-scaffold1547-54158 16 17872565 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772652 Affx-122938284 AX-385259800 16 17132586 AAACATAAAAAACAGCTCCCTTATATTGCAAAATA[C/T]TTACCCTGAGACATTATTTCTTTTCAAATCATAGC Y 2 1 2 1 101000 r 74 goat snp13943-scaffold1547-91736 16 17910746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378467 Affx-122976678 AX-123248826 16 17171719 ATGTCTACAGGGGTTGATAGATATCAAGAAATATG[C/T]ACTGTGAGAAATTTTTTTCAAGCAATTAATTTGAT Y 2 1 2 1 101000 f 74 goat snp13944-scaffold1547-130869 16 17949851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426091 Affx-122941073 AX-123296437 16 17203220 TTCCATCCTTGCTCCTTTCCACCCTAATACACACA[C/T]ACACAAACACACACACACACCCCATTCTAAAATAA Y 2 1 2 1 103000 f 74 goat snp13945-scaffold1547-162370 16 17981677 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438251 Affx-122931423 AX-123308589 16 17252301 TGACCTTGACTTTGTGCACACTTTTGACAACCTCC[G/T]AGCACGTTCCCAAGACCTACCGTCACCACTCTCAT K 2 1 2 1 101000 f 74 goat snp55088-scaffold845-854205 16 18031921 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448155 Affx-122924272 AX-123318491 16 17285944 TAATTCCTACTGATCATTAAAATGTCAACTGAGCT[A/G]TTCCTTAAATTGCTTCCCCAAAGTTTCCCCTTATC R 2 1 2 1 101000 r 74 goat snp55087-scaffold845-820562 16 18065500 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398291 Affx-122962159 AX-123268646 16 17327553 TCCTACTCCAATAAGAAATATAGTTATTTCTGTTT[C/T]AGAGAACTGCAAGGATGCTATAAAAAGGATACTGT Y 2 1 2 1 101000 r 74 goat snp55086-scaffold845-778953 16 18107266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379333 Affx-122976177 AX-123249692 16 17376845 TGATTTATATATCCTTCTTCGTAAGTAAGCCAGCA[G/T]AAGTTAATAGAGCAAATGTAACATGCTTTTGACTT K 2 1 2 1 101000 f 74 goat snp55085-scaffold845-729661 16 18155680 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780882 Affx-122920960 AX-385267969 16 17416672 AACAGATTGGCTTATGTTTAATGAGAATCTTTTAG[A/G]ATATAGTTTCATCAGAACCTTGGACTTACCAGACC R 2 1 2 1 101000 r 74 goat snp55084-scaffold845-689834 16 18196071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779398 Affx-122950778 AX-385266501 16 17473887 TTGTAAATTTGAGAGGCATTGCTCTTGAGATGAAG[C/T]GATGATCTTATGTCCATTAACAATATACAGATTCT Y 2 1 2 1 101000 r 74 goat snp55083-scaffold845-632619 16 18252533 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392548 Affx-122966092 AX-123262905 16 17511417 AGTTTTAGCTATATGATGTCATTGCCAGAAATGTA[G/T]CATACAAGTTTGGATTACATTAAGGTGATAATCTT K 2 1 2 1 101000 f 74 goat snp55082-scaffold845-595089 16 18290080 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386694 Affx-122970175 AX-123257052 16 17539970 TCCTTCCCCCAGTGTGCTCCCCTTTGAAAACCACA[C/T]GTTTGTTCTCTGTATCTGTGATGAAATCAATATTT Y 2 1 2 1 103000 f 74 goat snp55081-scaffold845-566536 16 18319104 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380009 Affx-122975603 AX-123250367 16 17570913 GAGTTGCTTTGCCTCTCCTCCTGCTTCCAGGCTGG[C/T]GGCATCATTTACTCTAGCTGTGTGGTTGAAACTTG Y 2 1 2 1 101000 r 74 goat snp55080-scaffold845-535593 16 18350406 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422704 Affx-122943650 AX-123293050 16 17616174 CAGGCTCCCTTTCTTTTCATGGACCAAATCTCAAC[A/G]CTTATATAAAAGACTTTGAGGGGTATGGGGAACTA R 2 1 2 1 201000 f 74 goat snp55079-scaffold845-490332 16 18395723 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772455 Affx-122959743 AX-385259606 16 17648940 GTGTTAGCATCTCCACTTAGAATTATGTATTGATT[C/T]ATTTGTATGTTATTCCTTTATATATTTTGAATCTC Y 2 1 2 1 201000 r 74 goat snp55078-scaffold845-457566 16 18428326 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795808 Affx-122975475 AX-385282761 16 17721758 CCAGTTTTCCTCAAATTAAGAAATTTACTAAGCCC[A/G]TATTTTGATACTGTGCAGACATTCCATAAAGACAA R 2 1 2 1 101000 f 74 goat snp55076-scaffold845-384748 16 18501137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452968 Affx-122920159 AX-123323301 16 17758505 TGACTGACTTTTTTTTTTTTGCCTGCCTTGCAAAT[A/G]TTTCCTTTACATGCTATGTTCTTCTTTCCTGGGAA R 2 1 2 1 201000 r 74 goat snp55075-scaffold845-348001 16 18537457 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765699 Affx-122945285 AX-385253161 16 17795689 GCTGGAGTCTGGGTAAGAATTTCAGGGACTAAGAC[A/G]AGATGTTAATTTGAGAACAGTAGCATAAAGATGAG R 2 1 2 1 101000 f 74 goat snp55074-scaffold845-310817 NW_017218261.1 6231 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423681 Affx-122942324 AX-123294027 16 17834720 ATCTTGTGGTTATATACACATACAGGGAAACATAC[A/G]TTTCTGGCCATTGTATATAACAGGCTCAGTGGTCT R 2 1 2 1 101000 r 74 goat snp55073-scaffold845-271786 16 18613564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411612 Affx-122951596 AX-123281962 16 17941887 ACACAGTGAATGGGGACATAGCCCTGAAGAAATAA[C/T]ATGTGACCTAAGGTCTGAAGGTGAGGCAGGAATTA Y 2 1 2 1 101000 f 74 goat snp55071-scaffold845-164619 16 18721415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392422 Affx-122966198 AX-123262779 16 17972328 TGAGGCGGGAGTTGCACTGTTGCTCATCGGTCCTC[A/G]TCTGAAGAGTGGTCATGTGGCTTGTCAGCTGCTGG R 2 1 2 1 201000 r 74 goat snp55070-scaffold845-134178 16 18751855 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396208 Affx-122963359 AX-123266563 16 18001198 AGTATTACCTCTGTTTTAATGACCCCCTGATTTTA[C/T]GGTGGCCGGCAGTGTGCCAGAGTCAGCTCCTTGGA Y 2 1 2 1 103000 r 74 goat snp55069-scaffold845-105308 16 18780632 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422851 Affx-122943097 AX-123293197 16 18042535 ATGCATATAAAGGTCAGAATAAGTTTATAGAGAAG[A/C]GATTTACTGTCTAATTTGTCTTATTATACTGGTAT M 2 1 2 1 101000 f 74 goat snp55068-scaffold845-63971 16 18822650 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402600 Affx-122958422 AX-123272953 16 18086865 TCAAATTAGTTTTGATTCTTTCAATTAGATATATT[A/G]TATTCCCTAAGTAATCACAACGCAGGCTTCCTTCC R 2 1 2 1 101000 r 74 goat snp55067-scaffold845-19641 16 18866786 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404934 Affx-122956434 AX-123275286 16 18115695 CAAGAGTAATTCCCATTGCACACCTGAACTCGTCC[C/T]GCATGGACGAGAAATATCATGTTTTTATACCACCC Y 2 1 2 1 101000 f 74 goat snp15553-scaffold1645-9090 16 18895489 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376343 Affx-122978336 AX-123246702 16 18144221 TTGAAAGCAACAAAGGCTTGCTTCCAAGCCTTGCA[C/T]GCATGCTGTTGCTCAGTCTTGTCTGACTATTTTAG Y 2 1 2 1 103000 f 74 goat snp15554-scaffold1645-37616 16 18924327 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767458 Affx-122969322 AX-385254726 16 18193431 ATCAATACAGACCTCTCTGAATAGGTGCCACGCTC[A/G]CTACCAAAGTAAACTTACAGACTAACAAACAAGAA R 2 1 2 1 101000 f 74 goat snp15555-scaffold1645-86826 16 18973417 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797350 Affx-122965733 AX-385284289 16 18233816 AAAGATAAGTAGATGGGCCATCTTTTAAATAGAAA[C/T]GATAGCTAGGAGACACAGTCATATGAAAGACATCG Y 2 1 2 1 101000 r 74 goat snp15556-scaffold1645-127211 16 19013542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382276 Affx-122973929 AX-123252634 16 18284924 TACGATGATTTCTATCATCTGTGCATAGACCAGTT[C/T]GAGTCTATTTCACCTTGAGACATAACACATGTAGA Y 2 1 2 1 101000 r 74 goat snp15557-scaffold1645-178319 16 19064561 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376934 Affx-122977780 AX-123247293 16 18299448 ATAAAGAAGGGCAAAGTATTTGCCAAACCTCATGC[G/T]AGATTTTTATTTTTCAGCAATGCATAGTACTGTAG K 2 1 2 1 101000 f 74 goat snp19866-scaffold1991-271730 16 19078838 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443522 Affx-122927783 AX-123313859 16 18359521 CTTTGGTTTGTGCAAGTTTATCCACATTTTCCCGT[A/G]TTCTTCTTGACACATCTGGCACAGAATTGTCCCGG R 2 1 2 1 101000 r 74 goat snp19865-scaffold1991-211657 16 19139545 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778575 Affx-122933519 AX-385265687 16 18391804 CTCCCTAAGGCCGGGATCTCAGATCTGTTTACTGC[G/T]AAGTCTCCAATACCCATTACGTAATAGCCACTCTA K 2 1 2 1 101000 f 74 goat snp19864-scaffold1991-179374 16 19171248 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448017 Affx-122923725 AX-123318353 16 18420864 CTCCAGTACCCAGGTGGAAAGGGATAATCGTGCTG[A/G]AGGTTAACACTCAAGTGAATGTTCTTGCCTTGCTC R 2 1 2 1 101000 r 74 goat snp19863-scaffold1991-150314 16 19200242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399293 Affx-122960539 AX-123269648 16 18450426 CTCCACAGTGTGTACATGGATTCTACACCAACCTG[C/T]GAACAAAGATCTAGAATCCTTTCACTCAGCTCCCT Y 2 1 2 1 101000 f 74 goat snp19862-scaffold1991-120752 16 19229909 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776723 Affx-122920050 AX-385263849 16 18491172 GGATGCAGAGCAATAGGCCTCTTGAGAAGCTTCTG[C/T]GTGTACTCTAGAATTAAGAATATTCTTAATAAGTC Y 2 1 2 1 102000 f 74 goat snp19861-scaffold1991-80006 16 19267974 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426834 Affx-122940508 AX-123297179 16 18530125 TCAAAATGTAATTTGCTGTGTGTCTCTGTGTGTTC[C/T]TGTATGTGTGTACATCCCTTATGTCATGTACATCA Y 2 1 2 1 201000 r 74 goat snp19860-scaffold1991-41053 16 19305246 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769188 Affx-122972255 AX-385256363 16 18590622 TTCGTGTAACGTAAGGCCTGCAAATGGAAATACGC[C/T]TGCTTCTCAAAATAGTCAAGGACCATCTCATGCTA Y 2 1 2 1 101000 r 74 goat snp39435-scaffold500-3076928 16 19365937 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401445 Affx-122958983 AX-123271798 16 18650533 AGGCATCTATCTGTTGAACTCCAAACACAGATATC[A/G]CTCCTAGCAGACAAGCTGTGGCTTCCTGGGATGCT R 2 1 2 1 201000 f 74 goat snp39434-scaffold500-3017017 16 19426339 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271799 Affx-1111833061 AX-185922986 16 18657611 TTTTTCCTATAGTCATGTATGGATGTGAGAGTTGG[A/C]CTATAAAGAAAGCTGAGCGCCGAAGAATTGATGCT M 2 1 2 1 303000 r 74 goat 16_18657611_AF-PAKI 16 18657611 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38377346 Affx-122977662 AX-123247705 16 18680532 TTGAGCAGATATTTCATGAAAGAGAAAAATCACTG[A/C]TGACATGCTTTTTAAAACCATTTCCTCCTATGCTC M 2 1 2 1 303000 r 74 goat snp39433-scaffold500-2987018 16 19455872 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453198 Affx-122920452 AX-123323531 16 18841258 AATTGCAGGTTTTGTTCATCTAAAAGTAGTGCTGC[A/G]TTTTTTTTTAACTGTGAACTGATTAATTTTTTGAT R 2 1 2 1 303000 r 74 goat snp39430-scaffold500-2826292 16 19616745 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802817 Affx-122975216 AX-385289716 16 18893357 TAAAGGTGGTATCCCAAAAGAGGAAGTAGTTACGT[A/G]ATAGGAGTTTGATTATACACAGAGGGATTATTCAA R 2 1 2 1 101000 f 74 goat snp39429-scaffold500-2774193 16 19668748 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387814 Affx-122969681 AX-123258172 16 18951757 TATCAAACAGTGTTAAGGGGTGGACTACCTACTAC[A/G]TAGAAACACCATTAAATTCTAAATAAGATTAGATG R 2 1 2 1 101000 f 74 goat snp39428-scaffold500-2715793 16 19725519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775739 Affx-122927316 AX-385262870 16 18992029 AGAAGTAAAAACAGTTCATCTTCAGGTTATGGAAA[C/T]ATAAAATTAAAACAATCTGTGTATACTCGAGAAGC Y 2 1 2 1 101000 r 74 goat snp39427-scaffold500-2675521 16 19765842 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401465 Affx-122958968 AX-123271818 16 19035135 AGGGTCTCTTGTGCCAAGGCTTCCACTGACTTGTG[C/T]TTTTGTTGACAGGCTTTTAGACCTCAAGGGATCAC Y 2 1 2 1 101000 r 74 goat snp39426-scaffold500-2632415 16 19809501 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402582 Affx-122958437 AX-123272935 16 19075791 CAGATATTTCTGAATTCAATTAGAAAAACAATATG[C/T]AGTGTCTCAAGAATCAAGGCAAACCTTCAAAGAAG Y 2 1 2 1 101000 r 74 goat snp39425-scaffold500-2591759 16 19848065 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277122 Affx-1111835691 AX-519550629 16 19077830 CACAAAAAAACCCACACGCACAGACACATAAATAC[A/G]CACCCAGAGGCGTCAATTATGCCAACGCAATAATG R 2 1 2 1 101000 r 74 goat Random2.2K-1586 16 19077830 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381887 Affx-122974166 AX-123252245 16 19124570 CTCTTAAAAAAATATTTACTTTGGCTTCTGGACAA[C/T]GGTTAATGGAAGTGCTAATTGCCTTAATCTACTGT Y 2 1 2 1 101000 r 74 goat snp39424-scaffold500-2542980 16 19898214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406301 Affx-122956066 AX-123276653 16 19176240 AATTTTGATTTGAACAAAATTTGAAAAATATTTTA[C/T]AGTTAAGTTTTTTACTGTGCCTCTCGGCTCATTTA Y 2 1 2 1 103000 r 74 goat snp39423-scaffold500-2491310 16 19949707 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430411 Affx-122937755 AX-123300752 16 19230906 AAACTCTTAGTTTACAGGATACTGAATGCAGAAGG[C/T]GGAGGCTTGTTTCTAAAATACTCAGCAATTGAGTT Y 2 1 2 1 101000 r 74 goat snp39422-scaffold500-2436644 16 20004266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789049 Affx-122962572 AX-385276062 16 19268290 TTAAGCTCGAAACTTTGAAAAGCTACCTGTATTAG[C/T]AAAATGTCCTACATTACTCAAAAGTTTTAAAAGTA Y 2 1 2 1 101000 f 74 goat snp39421-scaffold500-2399260 16 20041678 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414173 Affx-122949677 AX-123284522 16 19297398 TGTCAAGGAAGAGCAGACACATGTGTCGTGTGTAT[A/C]TCCTTTGTTTATACTTATGCTCCGTTGTAGCATCT M 2 1 2 1 101000 r 74 goat snp39420-scaffold500-2370152 16 20070797 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797113 Affx-122941961 AX-385284053 16 19354819 GCTTGCTGTATATGCGCAATGTGTCTCTGAAAGGA[C/T]TCATAAGATCTTCATACCTCTGATCCTGTTCAAAA Y 2 1 2 1 101000 f 74 goat snp39419-scaffold500-2312731 16 20129118 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391473 Affx-122966721 AX-123261830 16 19384338 ACAGAAGGATGAACTCAAATGAAATATTGAATGCT[A/G]TAGAAGAGGCACTGTAAAAATATTTTTACCACCCA R 2 1 2 1 101000 f 74 goat snp39418-scaffold500-2283212 16 20158621 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799203 Affx-122935314 AX-385286133 16 19442280 AATTCCTCCAGATCTTCTAGTAGGTTTACATTTGG[A/C]TCTGAAAAAAAGTCCTAAAGCACCTCAGTACTTTT M 2 1 2 1 101000 f 74 goat snp39417-scaffold500-2225270 16 20215969 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422955 Affx-122943017 AX-123293301 16 19476952 TAAGGTTGCACAGTACTTTCTTGTATGTATTTGTC[A/G]TAATTTTTTTATTCTTCTGGCTCCATCAAATTTTT R 2 1 2 1 201000 r 74 goat snp39416-scaffold500-2190598 16 20247532 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409248 Affx-122953140 AX-123279599 16 19524855 GTAACTGCCCAGGGACACCCAGCTAGTAAGTCAGT[A/G]CTGGGATCAGTTAGCAGCCTTGCTCTGCTCTCACT R 2 1 2 1 201000 r 74 goat snp39415-scaffold500-2142695 16 20295434 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277125 Affx-1111835692 AX-186675926 16 19556310 ACTGTCTTAGAGACTCCCCTCCTCACCAGCTTGCC[A/G]GAGCTGGGCAGACATTGCTCAGTTCCCCCTCATTT R 2 1 2 1 102000 r 74 goat Random2.2K-1587 16 19556310 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800366 Affx-122923531 AX-385287288 16 19558889 TTTAAAATTTGATAAAAATCTGAACCAAAGGTTAT[A/G]TAAGTTATGATCTCACTGCCTCCCCAAATCATGGT R 2 1 2 1 101000 r 74 goat snp39414-scaffold500-2108661 16 20329886 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401897 Affx-122958841 AX-123272250 16 19621440 ATGTCTCCTTGCCCCCACGTCTGTTCTTTTCTAAG[C/T]AAACATTCCTATTTCTTTTTATTTTGAGAGCCTTT Y 2 1 2 1 303000 r 74 goat snp39413-scaffold500-2046110 16 20392490 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277127 Affx-1111835693 AX-519550633 16 19628303 GGTTAATGTTTACGATTTATACATTTAACTTTTCC[A/G]TTAGCAAGCCAAGTTTAATGCAGTCTGGAAGTTTA R 2 1 2 1 101000 r 74 goat Random2.2K-1588 16 19628303 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390372 Affx-122967670 AX-123260729 16 19695752 AGGAGATTCTACTTTGATTTCAGGCAAATTTGATT[A/G]CTCAATCTCTGAAGAAGGAGAAAGTAAAAAAATAA R 2 1 2 1 101000 f 74 goat snp39411-scaffold500-1971798 16 20467146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426950 Affx-122940414 AX-123297295 16 19745545 GCAGGAATGAAAGAAGGAACAGAATATGCATCAAG[C/T]AGTCCTTTCTAGTAGATTCAAGCGTGCTTTCCATG Y 2 1 2 1 101000 r 74 goat snp39410-scaffold500-1922005 16 20516955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765753 Affx-122953553 AX-385253209 16 19787041 AGTTCAGTGAGATCCTCCTAGACAACCATATGTTT[A/C]TTGAAGTTTGTGAAGCACTTAACTGAAAACTCAAC M 2 1 2 1 101000 f 74 goat snp39409-scaffold500-1880509 16 20558529 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397065 Affx-122962728 AX-123267420 16 19834353 ACCAGTCACATGGATTAGGGCTCAACCTAATAACC[G/T]CATTTTAATTGATTACCTCTGTAAAAACTCTGACT K 2 1 2 1 202000 f 74 goat snp39408-scaffold500-1833197 16 20606359 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403236 Affx-122957891 AX-123273589 16 19875610 CTGGTAATTACATCTTCCAGATGTGTCCAATCTTG[C/T]ACCTAAACTCAATGCCTGGGGCCTTTTAAACAAAC Y 2 1 2 1 101000 f 74 goat snp39407-scaffold500-1791940 16 20647465 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410596 Affx-122952114 AX-123280946 16 19945813 TACTAGACAACCTGACACACCACCCTTTCAAGTGG[C/T]ACAAACAATGTTTAGAAGAGCCAAGACAAGGAAGC Y 2 1 2 1 201000 r 74 goat snp39405-scaffold500-1721737 16 20717601 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377694 Affx-122977414 AX-123248053 16 20026725 ATTCATAGATATGATAAAAGTAATAATCATACCCA[C/T]ATACCCACAAATATTTTGAATTTTTGTGCATGTAT Y 2 1 2 1 103000 r 74 goat snp39403-scaffold500-1640825 16 20798766 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769333 Affx-122920660 AX-385256504 16 20085835 CCAGTGGAGAAGAGAGCGTTTAATACTGAGTCTAC[A/G]TAGTTTGAAATCAGACCCTCACTTCAGTTAGAAAT R 2 1 2 1 101000 r 74 goat snp39401-scaffold500-1581715 16 20857999 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393770 Affx-122965201 AX-123264125 16 20126555 GGGAAGGCATATTTCCACTGAAACCATTTAAAGAT[A/G]CTGTGGGAAACACTGTGACTGAACTTTTATGACCG R 2 1 2 1 201000 f 74 goat snp39400-scaffold500-1540995 16 20898861 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785198 Affx-122927239 AX-385272244 16 20174851 CTCTCTTAACAACTACTCAGTATATCAAACAGCAG[C/T]GTTAGCTACAGTCACTGTGTAGTTCATATTGTTGT Y 2 1 2 1 201000 f 74 goat snp39399-scaffold500-1492699 16 20947918 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775346 Affx-122964772 AX-385262477 16 20209124 CTGAAGTAAGTTCAGATTCTGAGTCTTTCGGCAAA[C/T]AGTTCTAAATGAGGGTCCTTTTTTCTTCACCAGTT Y 2 1 2 1 101000 f 74 goat snp39398-scaffold500-1458426 16 20982538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449574 Affx-122923229 AX-123319909 16 20269873 ATGGCTGTTGGAAATGGCAAGAAAGAGAACTCAGA[C/T]GGGTTTGCAGGTAACGTATGTTTTTGTTGTTCCTG Y 2 1 2 1 201000 r 74 goat snp39397-scaffold500-1397677 16 21043987 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772684 Affx-122931989 AX-385259831 16 20323704 GTGGAAAATGATTCTAAGACCTTTAGCTAGTGACT[A/G]TGTGGATGATGAAGCTATTAACTAAGAAAAGTGAT R 2 1 2 1 101000 f 74 goat snp39396-scaffold500-1343846 16 21100134 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447709 Affx-122924609 AX-123318045 16 20366615 ATCATGCAGTGATTCCTCAGTTGACATGAGCAACT[A/G]CAGCCTAGAGATTATATTTCAACTTCATATCTTCC R 2 1 2 1 201000 r 74 goat snp39395-scaffold500-1300935 16 21143116 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791459 Affx-122967726 AX-385278450 16 20402256 TATAAATGGTAGTGTTGGAATTTAGTTTGCTGCTA[G/T]AGATTTAGAAATCCTTAAGGACATGTTTATTAGTT K 2 1 2 1 101000 f 74 goat snp39394-scaffold500-1265294 16 21179232 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429832 Affx-122938172 AX-123300173 16 20445643 AATATTCAGCTATACCTTCTGGATATAATGTGGCA[C/T]AATGAAAGTTTTGGTCCTGCTTATCCAGGACTATG Y 2 1 2 1 101000 r 74 goat snp39393-scaffold500-1221907 16 21222407 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396119 Affx-122963409 AX-123266474 16 20504120 TAAAAATGGATTTTTTTTTCACTTTCCATCTCTTT[C/T]CACATCTGAGTCCTACTCAAGTGAATACCCTCGAT Y 2 1 2 1 101000 r 74 goat snp39392-scaffold500-1163430 16 21281454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443871 Affx-122927508 AX-123314208 16 20533031 GAAGAACACGAGGACGCTTGTGTGGGAGGTATTTA[C/T]GGGCCATAAGTAAAAGTAGATACATCATGACTCAG Y 2 1 2 1 101000 r 74 goat snp39391-scaffold500-1134519 16 21310186 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425796 Affx-122940703 AX-123296142 16 20595642 TTGCTTTTATCAGTCAAATCCTCATTTTGTGACTA[C/T]GGGAGAGCCTGGCCTAGTCCCTCCTGGCACGGCTG Y 2 1 2 1 101000 f 74 goat snp39390-scaffold500-1071908 16 21372848 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432038 Affx-122935907 AX-123302379 16 20680166 AAAGGATCAGTGTCTTCTGACTCAGGGAGAGAAGG[C/T]ACTCTAGTGTCACACATCTGAAAAACCATGAGATA Y 2 1 2 1 201000 r 74 goat snp39388-scaffold500-987384 16 21457870 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403065 Affx-122958522 AX-123273418 16 20742203 TTCTTAATCTTTTGTCTTCATTTAGAAAACGAAGG[C/T]AATAAGAATACCTACCTCATATGTTTAGTATGAAG Y 2 1 2 1 303000 r 74 goat snp39387-scaffold500-925347 16 21519224 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787721 Affx-122975686 AX-385274745 16 20802089 TCACCCTTTCGTTTCCTCTGACTTGTGTTTTTCCC[A/G]TCCTCACTAAAGGACATTTAGGGTTCAGTTTAGGG R 2 1 2 1 102000 r 74 goat snp39386-scaffold500-865461 16 21578867 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378405 Affx-122976790 AX-123248764 16 20836487 GTATGATCACACTGACAGCTCTATTAATCTCCTGA[C/T]ACCAAACTCCTTTTAAATTTAGAAATGGTCATTTT Y 2 1 2 1 101000 f 74 goat snp39385-scaffold500-831063 16 21613425 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428732 Affx-122938448 AX-123299074 16 20868990 GGAAAAGCAGTTCTCCATAGGATGCAAGCAGCAAA[C/T]GGTATTATTCTTATTTTTTCTTACTGTCCCTTTAA Y 2 1 2 1 101000 f 74 goat snp39384-scaffold500-798560 16 21645705 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425432 Affx-122941528 AX-123295778 16 20913384 TGATAAAGTCGATGTTTAAGGGCTTATTTAAGCCC[A/G]CTGGTGAGCCACATTCCACTTGAATTAGGAGGTAT R 2 1 2 1 101000 r 74 goat snp39383-scaffold500-754166 16 21689916 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387804 Affx-122969689 AX-123258162 16 20979206 GACTCTGATGCAAGTCTGGAAATATTTGTCCTTAA[C/T]GAATCATGAATTGTTTTAACATGGTGGTTTGATAT Y 2 1 2 1 201000 r 74 goat snp39382-scaffold500-688344 16 21754949 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424700 Affx-122941693 AX-123295046 16 21015529 TCTAAGCACTTTGGAAATTCAATCAATAAAAGGGA[C/T]AAAAGTTCCTGCCTTCTGTTGTTGTTCAGTCTCTA Y 2 1 2 1 201000 f 74 goat snp39381-scaffold500-652021 16 21791620 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782984 Affx-122925408 AX-385270053 16 21057832 TTGTATCCAGCTCACATATTCTTTAAATTTGAGGA[C/T]GAATTTTAAAGACAGGTTAGAAAGAAAGAGTTTTA Y 2 1 2 1 101000 f 74 goat snp39380-scaffold500-609718 16 21835442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389869 Affx-122968146 AX-123260226 16 21101843 CTCTCACCTCTGTAGCTCTCCAGTCCTCATCCATA[C/T]ACTGGGGACAATTGCATGAGAAAGTTGTATGAGCA Y 2 1 2 1 201000 f 74 goat snp39379-scaffold500-565707 16 21879501 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380773 Affx-122975111 AX-123251131 16 21154840 GAGATTTTACATGTAGAAGAGGAGGAGGTACTGTG[A/G]CTACAGAGGCACAGACTGGAGGGATGCATCTGCAG R 2 1 2 1 101000 f 74 goat snp39378-scaffold500-512710 16 21932882 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272862 Affx-1111833062 AX-519546552 16 21213647 TTTAGACCCTAGCTGGTACTGGATCGTGAGGCTGT[A/G]CACACTGACTAGTGGGAACTCAGACTTTTCCCAGC R 2 1 2 1 101000 r 74 goat 16_21213647_AF-PAKI 16 21213647 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392851 Affx-122965764 AX-123263208 16 21223137 TTCAGGGATCAAGATCTTGAGCCCGGTGCTCCGTC[A/G]ATGGGAGCTAAAAGCCTGTGCATTCCCTTCAAGCC R 2 1 2 1 201000 r 74 goat snp39376-scaffold500-444413 16 22000618 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440796 Affx-122929834 AX-123311133 16 21254348 GCTGCACAAGGAGAAGTGGTCCGTAAACTGAAAGC[C/T]GAGAAAGCCCCTAAGGTCAGTATCCTGGAAGGAGT Y 2 1 2 1 101000 f 74 goat snp39375-scaffold500-413202 16 22030910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397607 Affx-122961980 AX-123267962 16 21290001 CATCTACAAAGTTTATAATTCTGGCTTCTGGGTAG[C/T]GGCCAGCCTGATAAGCTGTCTGTAGCATTGTGAGC Y 2 1 2 1 101000 f 74 goat snp39374-scaffold500-377549 16 22066487 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395199 Affx-122964503 AX-123265554 16 21331857 TTAAGAAAATTACTAGGGCTTGGGGATAGCCTAGT[A/G]TCTTATCAGTAGTTCAGTATGGATCAAAAGAAGTA R 2 1 2 1 101000 r 74 goat snp39373-scaffold500-335693 16 22105436 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430293 Affx-122937281 AX-123300634 16 21361366 ATTCTCATTTTTAACTCCCCCTGCTGATAAACTCA[G/T]ATTTTAATATTTAGGGGCTCCCTAAGGAATGTAAG K 2 1 2 1 202000 r 74 goat snp39372-scaffold500-306184 16 22135069 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402720 Affx-122958785 AX-123273073 16 21405594 AGGAAAGAAAAATACACTCAGATTTTAAAAGTAAA[C/T]AAATAACCCATCATCTACCTCTTCTCAACTTCCAA Y 2 1 2 1 303000 f 74 goat snp39371-scaffold500-261956 16 22180426 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414130 Affx-122949708 AX-123284479 16 21434548 ACAAAGAAATGAATGAATACCTGTTGTGTCCCAGG[C/T]ACTAGTTTTGGTGCTAGAAATACAAGGCAGACAGG Y 2 1 2 1 201000 r 74 goat snp39370-scaffold500-233002 16 22209524 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430360 Affx-122937792 AX-123300701 16 21469150 TATAAAGTAGCTATTTGGTGTTTAAGTACCAAAGA[C/T]GGGGATATTGCCACAGAGCTAATTGAGCAGAGATT Y 2 1 2 1 201000 f 74 goat snp39369-scaffold500-198400 16 22244169 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419658 Affx-122945952 AX-123290006 16 21516798 AAAATAAATATCTATAAGAAGACTGGTGCATAGTT[A/G]TTTATAATGGCACCAAACTAGAAACAACCAGAAAC R 2 1 2 1 102000 r 74 goat snp39368-scaffold500-150752 16 22293222 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414493 Affx-122949543 AX-123284842 16 21562552 ACCGTCTGAGGTCTGGGTTACAAGAATACAAAATC[A/G]GACATAGATCTTTCTCCCAAAGCACTAGCAATTCA R 2 1 2 1 101000 f 74 goat snp39367-scaffold500-104998 16 22339209 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381550 Affx-122974832 AX-123251908 16 21595976 GGACAGTGCTTCAGGGCCCCCAGTCAGCAAACAGC[A/G]CAGAAGCCTTAGTGTTTTCAGGAAAAAAATGTGAC R 2 1 2 1 101000 r 74 goat snp39366-scaffold500-71574 16 22372763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772107 Affx-122967705 AX-385259262 16 21653842 ATTTCTGCCTCTCGAATAGTCACTTTAAGCCCTTA[C/T]ACTCCAGATGCTTTTCAGACTATTGCTTTTGGGCT Y 2 1 2 1 101000 r 74 goat snp39365-scaffold500-13708 16 22431066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397868 Affx-122962446 AX-123268223 16 21688561 GTTAAATATTTTAAAATTGATCATTATATGCCAGC[A/G]CTGAGCTAGATACCAAATCATCCAAAACAAATAAA R 2 1 2 1 101000 r 74 goat snp8974-scaffold1327-20912 16 22474694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446026 Affx-122925853 AX-123316363 16 21739030 CGGTAATAGCTATTTAATTAAGGAATGACTCAGAT[A/G]TATCTCTGCACTTGAAATGGAGACAAAAGCTGAGA R 2 1 2 1 101000 f 74 goat snp8975-scaffold1327-71381 16 22525800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444527 Affx-122926491 AX-123314864 16 21823346 TTTCTCCCCATTGGTTGTTTTAGAGATTACAGAAC[A/G]CACCCATATATTACTTCAGTCTACATAGGGTGATA R 2 1 2 1 201000 r 74 goat snp8977-scaffold1327-155697 16 22609992 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419936 Affx-122945313 AX-123290284 16 21853472 ACTTATTAAAAGTAGGCATCAGGGCTAATCCACAA[C/T]GGTGTGTATATTTCTTCTATTGTTCATGCAGACAT Y 2 1 2 1 101000 f 74 goat snp8978-scaffold1327-185823 16 22640254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448130 Affx-122924295 AX-123318466 16 21892190 GTATGCCTTATAGCCTTTCTGTCCTATTAAAAAAC[A/G]TCTTAAACATGCAGAAGAATTAATTGATTAAAATG R 2 1 2 1 101000 f 74 goat snp8979-scaffold1327-224541 16 22678957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442220 Affx-122928777 AX-123312557 16 21924264 CCTTTACCACTAAAAGTTTAATTTCAGGCTTGAGA[A/G]GAAGGAGGAAAGAAAAATCTCTTTGAAGGCGCCGG R 2 1 2 1 201000 f 74 goat snp8980-scaffold1327-256615 16 22711065 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423237 Affx-122942688 AX-123293583 16 21955173 ACAGGATCCCACGCACACAGGCTGAATGAGCCTCC[A/G]GCAGCAGGAAGGAAGAAAGGGAAAGTCACTCAGTC R 2 1 2 1 201000 f 74 goat snp8981-scaffold1327-287524 16 22741582 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448463 Affx-122923633 AX-123318799 16 21986744 TCAGCCCGCCTTACCTGAAACCTGCGTCAGAATTA[C/T]GATCAGGCTTGTGACTGTGTTGGCAGCACCATCCT Y 2 1 2 1 201000 f 74 goat snp8982-scaffold1327-319095 16 22773748 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790477 Affx-122923173 AX-385277480 16 22037630 ACGAAATGGCACGTTTTTTCCCAGCTTGGGGCATT[A/G]TGGCATGAAGCTTCTGGGAACCTCAAAAAAAAAAA R 2 1 2 1 101000 f 74 goat snp8983-scaffold1327-369981 16 22824929 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763294 Affx-986697823 AX-385251208 16 22070554 ACAGATGGGAGGATCCCAAGATAAACCAAATACAG[A/C]CTCAGAACCAGGTAAAGCAAGATGATTGGCCAAAG M 2 1 2 1 600010 f 74 goat 16_22070554 16 22070554 Ancestral_priority_1043 ancestry 0.64 recommended IMAGE 10K 10K ancestral 320772736 Affx-122960285 AX-385259881 16 22074707 CTGTCTATTGACTTAGCTCCATACACAGAAAGGGA[A/G]CAAAGGCAAGAGAATAGGTGGGCGGCTGTAGACGC R 2 1 2 1 202000 r 74 goat snp8984-scaffold1327-407058 16 22862197 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450473 Affx-122922940 AX-123320807 16 22116434 CAAACATAAATATGGTCTGAGTTTCTGAGTTTCTC[A/G]TCATCTGGTCAGGGAGCATATTAGCTGGGAATGCT R 2 1 2 1 101000 r 74 goat snp8985-scaffold1327-448785 16 22903895 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400772 Affx-122959876 AX-123271127 16 22194010 TTACAGGCTTTGGCGTTTGGGCGGATGGAAATGGG[C/T]GTTGGCGGATCATGTCGGGAGTAAACGGTCCTCCT Y 2 1 2 1 201000 r 74 goat snp8986-scaffold1327-526361 16 22982223 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784473 Affx-122940309 AX-385271522 16 22277026 TTTTACCAGAGTTGGCCTCCTTTGATCCTTAAGAC[A/G]TTTGAAAAATTAGGAAGACTATTCTGCTTCTTGTT R 2 1 2 1 101000 f 74 goat snp8987-scaffold1327-609377 16 23065293 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425677 Affx-122940865 AX-123296023 16 22367844 CACATACATATATACAAACAAGCATACATACATAC[A/G]TACTCACACTCTCTTAAGGGGGATATTTAAGCAAA R 2 1 2 1 102000 r 74 goat snp8988-scaffold1327-700195 16 23157472 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783137 Affx-122940268 AX-385270204 16 22446551 AAGCACAAGTACGCTTTAAATAATTGAGGTAAAAT[G/T]TACATATCATGGAATTATGAATTTTAAGTGTACTC K 2 1 2 1 201000 r 74 goat snp8990-scaffold1327-778902 16 23236213 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387945 Affx-122970018 AX-123258303 16 22491606 GCAAAAATCTGAGAAGAGTATGCAAAAGCACTGGG[A/G]CAGAAACAAACTGATGTCTTTGAGGAACAGAAAGA R 2 1 2 1 201000 f 74 goat snp8991-scaffold1327-823957 16 23281143 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792945 Affx-122938671 AX-385279923 16 22547494 GCCAAAAGGTCATGATAACCTCATCACAGTTACAA[C/T]ATGGGCTTCCTCACTGTTCTACTTTGTGTCTATGG Y 2 1 2 1 101000 r 74 goat snp8992-scaffold1327-879845 16 23337363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386940 Affx-122969991 AX-123257298 16 22583802 TAGGAGGAGCAGTAAGTATGTTTATCTGGATATTT[C/T]GGGTTGACATAAGTAGAAATTTAAGGATGCCGATT Y 2 1 2 1 101000 r 74 goat snp8993-scaffold1327-916153 16 23372729 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784931 Affx-122960062 AX-385271978 16 22616671 CTCATCTCTATTAACAACTCAGTATATAGCCTTCT[A/G]TAGTTTTCTATGCTCATACAGATATATGTATGTAA R 2 1 2 1 101000 f 74 goat snp8994-scaffold1327-949022 16 23405841 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798860 Affx-122959831 AX-385285790 16 22707851 ATTTTAGCCTTGTCAGCAGCAAGTACTCCACTGCA[C/T]GTCTGATAAAAGCTGTTGAAGAGACTTTAACTGTA Y 2 1 2 1 101000 f 74 goat snp8996-scaffold1327-1040202 16 23497788 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775418 Affx-122946313 AX-385262549 16 22759261 AAAAAGAGGGACTCTAAAAATGAGTCACACATTAA[C/T]AAAATTCCCCATGTCTTATATCTTGCAAACAACCC Y 2 1 2 1 201000 f 74 goat snp12315-scaffold1464-24725 16 23549672 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777200 Affx-122978461 AX-385264323 16 22794948 TAAATTAGACCACTGTGGAACATCATCACTTTAAT[A/G]GTATCATGTGAGCTACTTTTCAACCTAATTACATC R 2 1 2 1 101000 f 74 goat snp12316-scaffold1464-60412 16 23585233 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430706 Affx-122936909 AX-123301047 16 22843430 TCTAATCCACAACACTTAAAACATGGCTAAATATC[A/G]TTAATGTAATGTTGAAGTCAGACACAAAAGAGTAC R 2 1 2 1 303000 f 74 goat snp12317-scaffold1464-108894 16 23634432 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449810 Affx-122922410 AX-123320145 16 22876457 AACATTTGTGAAATGAGCAACAAGCAGCTAACAAT[C/T]CTACCCTACTTACTATATACTAAGCACTAATTGTT Y 2 1 2 1 101000 f 74 goat snp12318-scaffold1464-141921 16 23668575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800694 Affx-122929034 AX-385287612 16 22905303 GGGCCCTATAATTTTTTTCAAGTGTATCTCTTAAT[A/G]CCTTGAAAAACTACCAAGACAAGTGGTTCTTAAAG R 2 1 2 1 101000 f 74 goat snp12319-scaffold1464-170767 16 23697891 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452307 Affx-122920676 AX-123322640 16 22936767 TCGTGGTTTCCCTCCTAACTAGCTGTGTTACCTTG[A/G]GGAGTTATTTAACACCTCTGCCCCTCCACTTCCAC R 2 1 2 1 201000 r 74 goat snp12320-scaffold1464-202231 16 23729217 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784309 Affx-122976862 AX-385271360 16 22984880 AGGAAGCTGAGATGAACTACATAGGGGAAGCAAGG[C/T]GTCTCCTTCACGACCTCTGCTAGGTAGTTCTGTGT Y 2 1 2 1 101000 r 74 goat snp12321-scaffold1464-250344 16 23777401 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438930 Affx-122930420 AX-123309267 16 23056540 ATCACTTCCCATTGTATCGCTAGTGTATAGCACTT[A/G]CTGGGTTGTACAAATTATTCTTCCATATGAACCTC R 2 1 2 1 101000 r 74 goat snp12323-scaffold1464-322004 16 23849096 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445663 Affx-122926144 AX-123316000 16 23104398 TCTTTACTGGGGTAGTTTTCCAGCCAAGGAAAGCC[A/C]CCTGCTGTTTCATTTTCTCCTCCACCATCTGGACC M 2 1 2 1 101000 f 74 goat snp12324-scaffold1464-369862 16 23897219 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401529 Affx-122958919 AX-123271882 16 23137663 GAAACTGCCCCTCACCTGGGAAGCTTGAAGGACAC[A/G]GTGAGTAAAGCTCAGGTCAGTGGCTCAGAAACTCA R 2 1 2 1 101000 r 74 goat snp12325-scaffold1464-403127 16 23930388 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452605 Affx-122920489 AX-123322938 16 23175541 TACATGGTCAATTCTAGGAGCTGCTGTCTGCCATT[A/G]CGGTGTAGAGAAAAAAGAGAAGTGGCCCTAGTGAT R 2 1 2 1 201000 f 74 goat snp12326-scaffold1464-441005 16 23971509 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375389 Affx-122979215 AX-123245748 16 23217201 CAGCCACTCTTTCTACCCCGCTACCAGGATGGAAC[A/G]TATAAGGAACAAAGCAGCTGCTCAGAATTTTAGGG R 2 1 2 1 201000 r 74 goat snp12327-scaffold1464-482665 16 24014262 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438601 Affx-122930939 AX-123308938 16 23254550 CAACAATTCTCCCCACTCAAGCAGACTGAGTGAAG[C/T]AGCTTCACAAAGATGAGATGACCAGGTACCCTCAG Y 2 1 2 1 201000 r 74 goat snp12328-scaffold1464-520014 16 24051659 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397424 Affx-122962242 AX-123267779 16 23305152 AGTTTTGACTAAACTCTGGTATCTTGCTTTCTATG[C/T]ATCATTGTTTTTAGGAAGAGTTTGAGATCTCTGTG Y 2 1 2 1 101000 r 74 goat snp12329-scaffold1464-570616 16 24102732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436768 Affx-122932274 AX-123307106 16 23341391 GCCCTTACCTTGTTCCTTATGGTCCTCTCTGCCTG[C/T]CCTGGGTGAGGAGGGCTCCTAGGGAGCCTGATCTG Y 2 1 2 1 101000 f 74 goat snp12330-scaffold1464-606855 16 24139677 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786891 Affx-122958204 AX-385273920 16 23389661 CCCAAGAAGCTTGTTAATAATTCAAGTTGCAGATT[A/G]TTACTCAAATGTGGAGCAGAGCCCATGACTTTGTA R 2 1 2 1 101000 r 74 goat snp12331-scaffold1464-655125 16 24188208 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432025 Affx-122935916 AX-123302366 16 23419008 CAAGGAAGACAAGCAGCCCTAGAGTTCTGTGTTCC[A/G]TCTGCCCCACTACATTTTTGAACAGACCACTTTGT R 2 1 2 1 101000 r 74 goat snp12332-scaffold1464-684472 16 24217920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789432 Affx-122929022 AX-385276442 16 23458488 GAAATCCTCTGTAAGTTAATAAGCATTGAAATATT[A/C]AGTGATTTCTCAGCCTCTTTTGTCCATTTGATAAG M 2 1 2 1 101000 r 74 goat snp12333-scaffold1464-723952 16 24258542 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800818 Affx-122941799 AX-385287734 16 23494636 ATGAAGGATGCATAGTCCCTAATAAGAGTAACCAA[C/T]AATCTAATGTCGGAAACATATAAGCAGATAAATAT Y 2 1 2 1 101000 f 74 goat snp12334-scaffold1464-760100 16 24294056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414915 Affx-122949109 AX-123285264 16 23536342 ATACCTTGGCTGGTTGGTCAGGCACTTGGAAGATG[C/T]GGACTTAAAAGATCAAGAACAAGGAGATTTAAAGA Y 2 1 2 1 101000 f 74 goat snp12335-scaffold1464-801806 16 24336277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379340 Affx-122976170 AX-123249699 16 23584372 AGAACAAGACTGTGAGGAAAGGAGGGAGCTGCTAA[C/T]GATGTAGAAGGGAAGTATGTTATCTCAAAAGCAAA Y 2 1 2 1 201000 r 74 goat snp12336-scaffold1464-849836 16 24384416 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429475 Affx-122938477 AX-123299817 16 23651686 GTATTGGACTTCCCAAGTCATGTGACTCCTTTTCC[C/T]AGAAAGCTGGGAGTGAGCAGCAGATTCTAGCCATA Y 2 1 2 1 101000 f 74 goat snp12338-scaffold1464-917150 16 24451739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427357 Affx-122940104 AX-123297700 16 23703140 CCCTCAGCGGGATTGAAGGTTTCCTCTTACATTAC[A/G]TGGGGCTGTCTGGTCACCTGTTTGCAGACCTTCTC R 2 1 2 1 101000 f 74 goat snp12339-scaffold1464-968604 16 24503416 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378089 Affx-122977162 AX-123248448 16 23754727 TTCCTCCCACAAAATCAGCATCTGGTTAATCTTAG[C/T]AACCATCTGAAACATTAACTGAGAATACTAATGCT Y 2 1 2 1 101000 f 74 goat snp12340-scaffold1464-1020191 16 24554755 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394132 Affx-122965327 AX-123264487 16 23784481 AATATAAAGATTTGGTTTGGCTACATTTCTTCCCT[G/T]GCTTTGAGGTGTAATTTCACCCAAACCAATCTAAA K 2 1 2 1 101000 r 74 goat snp12341-scaffold1464-1049945 16 24584405 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784147 Affx-122943404 AX-385271199 16 23814253 AAAAAAGCCCTGAGATTCAGGATAAGAGGTTAGAT[A/G]TTGACCTGCAAAACCCTGAAAAACCTGTTTCAGGT R 2 1 2 1 101000 r 74 goat snp12342-scaffold1464-1079717 16 24614196 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412664 Affx-122950779 AX-123283013 16 23857376 CCAGGTGTTCCACCGGGAAAACGGGACCTGCCTCT[C/T]GACCCTCGAGAATTTTTACCGCCAGGACATGCACC Y 2 1 2 1 101000 r 74 goat snp12343-scaffold1464-1122840 16 24657396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784776 Affx-122923383 AX-385271823 16 23905929 CTCAACATCAACATCCCATGAACACACTCCTGTAC[A/G]TTGTAGGGTTGTAAAAACACTGCTGGCTTCCCCAT R 2 1 2 1 101000 f 74 goat snp12344-scaffold1464-1171393 16 24706017 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377128 Affx-122978239 AX-123247487 16 23987850 AGACTAATCTGGTTCAGTAGTACTTGTCCACTTTG[C/T]GCTTAGGTAAAAACTAGACTCATATACTAAATAAC Y 2 1 2 1 201000 r 74 goat snp12346-scaffold1464-1253314 16 24787825 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441465 Affx-122928757 AX-123311802 16 24016823 GCAAACCAAACATTTAGAATTATCTGCAGTAGATC[A/G]TTTTACTCACTGGAACAAGAGAGAATGAAGCTGTT R 2 1 2 1 101000 f 74 goat snp12347-scaffold1464-1282287 16 24816811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272810 Affx-1111833063 AX-519546506 16 24041384 TGAACATTTCTGTGGCATCCAGCAATCTTTGTTCC[A/G]CGCTCTAGGCTGAGTCTAGGCTGAGATTCTTTGTA R 2 1 2 1 101000 f 74 goat 16_24041384_AF-PAKI 16 24041384 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38429935 Affx-122938090 AX-123300276 16 24051174 AGAGAGAGAACATTGCACACTAAAGCTGAAACCCT[C/T]CTAATACCACCTCTACTTTATGCCACTGCTGTTCC Y 2 1 2 1 201000 r 74 goat snp17223-scaffold18-19260 16 24853419 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793589 Affx-122956053 AX-385280564 16 24094863 ATTTAGGTAGTGCTTCTAATTTTTCATGTCTAACC[A/G]GGAGTCCTTAGGTTTAAGTTTGGCTCCAAGGGATC R 2 1 2 1 101000 r 74 goat snp17224-scaffold18-62949 16 24898037 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789041 Affx-122943697 AX-385276054 16 24154166 GTTACGTTAGTTTGCTTTTCAAACAAATTTTACTC[C/T]AAATAGAGTCAAGACTTTGAGATTCTAATAATGTA Y 2 1 2 1 101000 f 74 goat snp17225-scaffold18-122252 16 24957321 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382213 Affx-122973994 AX-123252571 16 24248433 GGTTTTCTTTCAGAAGCTAGAAACAGTGAGCAGCC[A/G]TGTGTGAATACATAATGGCGGCTGTGGAGACTAGA R 2 1 2 1 101000 r 74 goat snp17227-scaffold18-216519 16 25051019 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400837 Affx-122959789 AX-123271192 16 24287699 CTTGCGATTCCAAGCCGAGTGACTCCGATCACTAT[A/C]TTTAGGAGGGGTACTAGCTGGGGAACTCCTGCCCC M 2 1 2 1 101000 f 74 goat snp17228-scaffold18-255785 16 25090584 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405681 Affx-122956556 AX-123276033 16 24338683 ATTCTATTTTCTGTCTAGTCTGTCTTTTCAATTCA[C/T]GGCTGTCATCTTTGTTGCCTGAACTAGCCTGAAAC Y 2 1 2 1 101000 f 74 goat snp17229-scaffold18-306769 16 25141419 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786956 Affx-122924805 AX-385273984 16 24381801 TACCATGATCTGCAACCTGCTCTTCCTTGCAGCAG[C/T]GAGGAAGTAGTGGTACCTTCCTTCTATTTTACACC Y 2 1 2 1 202000 f 74 goat snp17230-scaffold18-349887 16 25183895 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411725 Affx-122951523 AX-123282075 16 24410568 AGCTAAGTGACTTGCCCTGAGCCAAACTGATTAAG[C/T]AGGAGACTCAGGATGTGAACTCAGCCAGTCGGATG Y 2 1 2 1 101000 f 74 goat snp17231-scaffold18-378654 16 25212470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430448 Affx-122937728 AX-123300789 16 24452514 CCACCATTTCTGTTCTGTCCCCCTGGGATTCAGCT[G/T]TCTTTGGTCAAAGCCACACTTCTCCTTGCTGGAAT K 2 1 2 1 101000 r 74 goat snp17232-scaffold18-420600 16 25254416 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382094 Affx-122974899 AX-123252452 16 24530515 GGCTTCCTGCTGCTTTTGCCCTGGATCTCAGTGCA[A/C]ATACATCTGCATTTAAGCCCTTAAGAGGGTTTTCT M 2 1 2 1 102000 r 74 goat snp17234-scaffold18-498601 16 25332601 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407107 Affx-122954883 AX-123277458 16 24567597 CCAGAGTAGTGGGAGAAATAGCTGCCATTTTCCCC[A/G]CAGCGGCTAAGTCCAGTTCTCTTCCTGTCTATAAG R 2 1 2 1 101000 f 74 goat snp17235-scaffold18-535683 16 25370167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439827 Affx-122930468 AX-123310164 16 24633751 TCAAAAAATTCTACTTTCCTTCCCTATCTGTAAAA[C/T]GGAACTAGTCTCACCTGCCTGTCCCTACCTTACAG Y 2 1 2 1 202000 f 74 goat snp17236-scaffold18-601837 16 25436340 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414282 Affx-122949599 AX-123284631 16 24671214 CAGAGCAATGGGCTTTTGGCAGCAAATGTCCACTC[A/G]CCCAATTAGACAAACTTCCAGTTGTGAGCAGAGAA R 2 1 2 1 201000 f 74 goat snp17237-scaffold18-639300 16 25473728 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777720 Affx-122932098 AX-284889659 16 24717643 AAGTGGCATACACCAAACCTTTTTAGACACTATTT[A/G]CCAGTGAAGGTGGGCCTCTTCTGATACAGCTCATC R 2 1 2 1 102000 r 74 goat snp17238-scaffold18-685729 16 25523264 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396919 Affx-122963204 AX-123267274 16 24763008 CCATGTCCCATCTAGTGGAAATGGGAGTCTTAACC[A/G]CTGGGCCACTAGGGAAGCCCCAGAAATAAGATCTT R 2 1 2 1 103000 f 74 goat snp17239-scaffold18-731094 16 25569188 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411350 Affx-122952258 AX-123281700 16 24791761 TGAGACCCAGCCAAGAACCCCAGTTTCCCTTTTCC[A/G]TCTGATCCTAACAACCCTTTGAGGATATGTGTGTC R 2 1 2 1 101000 r 74 goat snp17240-scaffold18-759847 16 25597869 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794065 Affx-122924776 AX-385281034 16 24829426 TCATTGGGTTAAGTAAGAGATTTTATATAACATTG[A/G]TTGGTTAACCAGCATGTCTTAACTCAAGTGCTGGA R 2 1 2 1 101000 r 74 goat snp17241-scaffold18-797512 16 25635285 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435685 Affx-122933326 AX-123306024 16 24869668 CGTCTCATGCACAGGATCAAACCAGGATGACGTCA[C/T]AGAGAACCTCATGCCTGCTTTAGTGGGAAGCTCAG Y 2 1 2 1 201000 f 74 goat snp17242-scaffold18-837754 16 25675437 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421573 Affx-122944511 AX-123291920 16 24900944 ACCCTGAGTGAAGCATGTTGTAGGAAGAGGCGATC[A/G]TTAAATTTGAGAATCTTAATTTTAAAAAGCCCTAA R 2 1 2 1 103000 f 74 goat snp17243-scaffold18-869030 16 25706810 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448879 Affx-122923266 AX-123319214 16 24936401 TGGAGCAGATGGGCACAGCAATAGGTCAGTACCAG[C/T]AGAGGAGAGAATTTCTCAGTTGGGTTACCCGCCTT Y 2 1 2 1 101000 f 74 goat snp17244-scaffold18-904487 16 25742788 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410868 Affx-122952604 AX-123281218 16 25006449 CTGTAATGTTTGTTGGGAGCCAGAGGAGTCCTGTT[C/T]CTTATTTGAAGTATTCTTTGGTATAGCTCACTTTC Y 2 1 2 1 201000 r 74 goat snp17246-scaffold18-974535 16 25813299 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390879 Affx-122967805 AX-123261236 16 25035210 TTTTTTAAAAAGGACAGAGTCCCACACTACTGGTC[A/G]TTTTCTTCTGCCATGCCAGCAACCATGAAGATGCA R 2 1 2 1 201000 r 74 goat snp17247-scaffold18-1003296 16 25842217 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424610 Affx-122942195 AX-123294956 16 25096548 GAGTTAAGGATAGCATCCGAGTGATGCGGGATTCC[A/G]TTTTATCCCAAATGAAACTGGCCTCTAGGCTTTGG R 2 1 2 1 101000 r 74 goat snp17248-scaffold18-1064634 16 25904794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401948 Affx-122958803 AX-123272301 16 25149314 GACTGACATGCACACAGTATCATATATAACATGGG[C/T]AACTAATAAGAACCTGAGGTGCAAATATAACCAAT Y 2 1 2 1 101000 f 74 goat snp17249-scaffold18-1117400 16 25957220 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781092 Affx-122933333 AX-385268178 16 25213945 TCGTTTCTCAACTTTTAGTTTTCTCTGTCGGTGCA[C/T]GTTTAAAACTTCCGTATTTTGTATAGCCGTTCGCG Y 2 1 2 1 201000 f 74 goat snp17250-scaffold18-1182031 16 26022160 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425048 Affx-122941860 AX-123295394 16 25249032 ATGTCCTGAAAAATTTCCAATTGACTCTACAAACT[C/T]ATGGATCAAACACATGAAGTAAAATTTAAGAATTC Y 2 1 2 1 101000 f 74 goat snp17251-scaffold18-1217118 16 26057428 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382960 Affx-122973363 AX-123253318 16 25279378 AGGCCCATAGCAGTACTGAGGACAAGCTTCTGAAT[A/G]AAGTCTGTAGCTTTCATGAAGGAAACAATTACTTA R 2 1 2 1 101000 r 74 goat snp17252-scaffold18-1247464 16 26087855 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399052 Affx-122960907 AX-123269407 16 25338423 CTTGACTATATTTGAGTTTCAGACCTGGGTACTGT[A/G]TGGAGGTTATCTAGTCCGGTGTTTCCTCATCCATC R 2 1 2 1 101000 r 74 goat snp17253-scaffold18-1306509 16 26146881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274903 Affx-1111834486 AX-519548487 16 25375212 CCCAGGGCAGCTCATGTCTCCCCCAGACCGCTGTG[A/G]CTGTGGCGTCACCAGGCCTGACTGCTGCCACTTGT R 2 1 2 1 303000 r 74 goat GoatD01.038152 16 25375212 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38379228 Affx-122976274 AX-123249587 16 25383098 TGGCCCTGAACATCCACTACTGTTCTGCCTGGAAA[C/T]ACAGCCTGACCTTGCCTGGGTGAAACCCGATTGAA Y 2 1 2 1 101000 f 74 goat snp17254-scaffold18-1351184 16 26191535 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386750 Affx-122970133 AX-123257108 16 25412672 CCATTAACCTCCTCCTGAAATCTCTTCAGTTTCTG[A/C]GTAAGACAATTTCCCCTGACACCACAGCTGCCTCT M 2 1 2 1 201000 r 74 goat snp17255-scaffold18-1380758 16 26221170 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277131 Affx-1111835695 AX-519550637 16 25431745 CCTCACCTGATTCCCCACCACACAGGACTGTACCT[A/G]CGCATTTCCTGGTGCACACCCGGAGATACCTGTTG R 2 1 2 1 102000 r 74 goat Random2.2K-1591 16 25431745 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402045 Affx-122958731 AX-123272398 16 25456549 TGGCCCAGCTGCCTGGCTCTGGACAGCGGCCCCTG[A/C]CCCTGCTGCCCCTGTGTGTAGCCCTGTTTTTGGCT M 2 1 2 1 103000 r 74 goat snp17256-scaffold18-1424635 16 26265153 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428669 Affx-122938646 AX-123299011 16 25510934 GAGAGAACAGGGCCTGGCCTCTTCGAACTGTCACA[C/T]CCCTTGCAGGGAGCAGCGTGTGGAGCCAGTCATCC Y 2 1 2 1 101000 f 74 goat snp17257-scaffold18-1479020 16 26319855 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451282 Affx-122921307 AX-123321615 16 25568209 CCTTGCCCCGTCACTGGTTTCCACCTCTCCAATTC[A/G]TGTGTCTTGATTATCTTGTGAGTTTAGTAATTTTA R 2 1 2 1 201000 r 74 goat snp17258-scaffold18-1536295 16 26376843 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399077 Affx-122960885 AX-123269432 16 25607666 GAAACACAAGAAAGCCCAGGACTCATAGCCATGAT[A/G]TGGTTTAGTGGATCAGCAGACCCTCACATTATTTG R 2 1 2 1 101000 r 74 goat snp17259-scaffold18-1575752 16 26416800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274729 Affx-1111834463 AX-519548315 16 25633044 GTTTTTGGTCTGTCAACTGCAGGCTGTAAATGGTT[A/G]TGAGATCCCAAACTGCACTTCTGTTTGGTTGTTCC R 2 1 2 1 101000 f 74 goat GoatD01.036879 16 25633044 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38389425 Affx-122968364 AX-123259783 16 25638134 AGCAATGGAGAATGGGAAGCTGGTCTTCAGTCACA[C/T]ACATGCACAGCTGAAAATTAAGGATTTAATCACCA Y 2 1 2 1 101000 r 74 goat snp17260-scaffold18-1606220 16 26447941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428746 Affx-122938439 AX-123299088 16 25688923 ATGAGCCACTTATCTTGAGTGGCCTTGGATGAGTC[A/G]TCTATACTCCTTCTGAGCCTCAGTTTCTTCACCTA R 2 1 2 1 201000 f 74 goat snp17261-scaffold18-1657009 16 26499689 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787552 Affx-122928927 AX-385274576 16 25721803 AATCAGCTTTAAGTTCTTTTCTGTCTAAAGTGCTG[C/T]AATTCAAACATACACTTTTGAAATTACAATCATCA Y 2 1 2 1 101000 f 74 goat snp17262-scaffold18-1689889 16 26532493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786178 Affx-122949280 AX-385273214 16 25759531 TCATGGTTGAGCAGGTCAGTCTGGGAACTGTTTAT[A/G]AATTCAGTTCAGAGGAGAATCTGTCTGATGACTTG R 2 1 2 1 101000 f 74 goat snp17263-scaffold18-1727617 16 26570422 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775691 Affx-122932065 AX-385262822 16 25818660 AATTCTAAAGCTTTTTATAATCCATATGATCTTTA[C/T]GTAGTCTCTGCCCACAGAGCTAGACATTGCAAAGA Y 2 1 2 1 101000 r 74 goat snp17264-scaffold18-1786746 16 26629680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388439 Affx-122969264 AX-123258797 16 25860476 GTGCAGCATGAGTATAGAGGCAAGAATAAGAAACT[A/C]TGAGCAGAAAGGAATAACATTAAGTCATGTGGAAC M 2 1 2 1 101000 r 74 goat snp17265-scaffold18-1828562 16 26671936 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398216 Affx-122962218 AX-123268571 16 25894070 TTTGTTAAAAACTTCTTGTAACTTCTCACTCTGTG[C/T]GTTCATTCTTCTCCCAAGTTACTTTGTTATCTTCA Y 2 1 2 1 101000 r 74 goat snp17266-scaffold18-1862156 16 26706499 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785766 Affx-122922110 AX-385272806 16 25925358 TTCCCTTTATTTTAATCCATGCTTGATTCTTATGG[A/G]AGAGTGATGTTAATAAGCCTCATTATTTTAGTACA R 2 1 2 1 101000 f 74 goat snp17267-scaffold18-1893444 16 26737996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794742 Affx-122948500 AX-385281702 16 25961143 CACTAAGAGAATTTCAATATAGATTTAATCAAACT[A/G]TAGTGGTTGAGAAGTCCTCTATGTTTAGCTAAATA R 2 1 2 1 101000 r 74 goat snp17268-scaffold18-1929229 16 26773653 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385745 Affx-122971080 AX-123256103 16 25990351 GTCGGATTGAAATAGCAGGGCCATAGCTTGAATAG[C/T]GTTAGTATCAGTGAAACACCACCGGTAGACCCAAT Y 2 1 2 1 101000 f 74 goat snp17269-scaffold18-1958437 16 26803137 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768277 Affx-122919670 AX-385255458 16 26027500 AATGGAGACTTACCAGATTCTCTCCCAAGAGACAG[A/G]TGAACTCTTAAGTAACAAACTGACCTAAAATAAAA R 2 1 2 1 102000 f 74 goat snp17270-scaffold18-1995586 16 26840726 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417780 Affx-122947391 AX-123288128 16 26067811 TTAGCTAGGCTTGGTGGGTTGGAGATGCATAAACA[C/T]AACTAGATTATGTTCAAGTCAGATTCTCTCTGAAG Y 2 1 2 1 101000 f 74 goat snp17271-scaffold18-2035897 16 26881027 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422867 Affx-122943083 AX-123293213 16 26096704 TTCTCAAGATAATTTTAATTTAGTTTAATTGTTTA[G/T]ATAAATATATATCGCAGAAGACTCCAACGGGGCAG K 2 1 2 1 101000 r 74 goat snp17272-scaffold18-2064790 16 26909821 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437904 Affx-122931657 AX-123308242 16 26130045 CGAGAAAGGAGGAAGGACCTGTCACACAGGTAATC[C/T]GAGAGACGAAATCAGTGTGCATGGCTTAGCCCTTC Y 2 1 2 1 101000 f 74 goat snp17273-scaffold18-2098131 16 26941674 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786630 Affx-122962973 AX-385273662 16 26173766 ACTGTTAAGGTCGAGCTGATTTGCCCTGGTTAAGA[A/G]TTTTCAGATTTCTCACCTAAGTGCTTTCAGTTGGA R 2 1 2 1 101000 f 74 goat snp17274-scaffold18-2141852 16 26985462 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794859 Affx-122936575 AX-385281819 16 26280744 TTCAGTGAGGCCAATAACTCAGAAATTCCATGAGA[C/T]AAGATACATGAGGTTCTGCATGACATTAATTTCTA Y 2 1 2 1 101000 f 74 goat snp17276-scaffold18-2248830 16 27090282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424303 Affx-122941970 AX-123294649 16 26313322 ACTTCAAATGATGACTATAAAAATATCTGCAATTA[C/T]ACTAAAACCTGCAGAAGCCTCCTGCGTGTGGCTCT Y 2 1 2 1 101000 r 74 goat snp17277-scaffold18-2281408 16 27122929 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395611 Affx-122963813 AX-123265966 16 26354545 TGTAGTGTTTAATCCATTTACACTTAATGCAAGTT[A/C]TACATAAACCTGGGCCTAAATCTATCACACCTTCT M 2 1 2 1 101000 r 74 goat snp17278-scaffold18-2322631 16 27164243 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781525 Affx-122957386 AX-385268610 16 26438827 GTATAACATTTACGTCCTGGCATACTGGAAAGCAT[C/T]GAGATCAAATCAATATGAATATAACCCAAAAAGCC Y 2 1 2 1 101000 r 74 goat snp17279-scaffold18-2406913 16 27248546 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381705 Affx-122974710 AX-123252063 16 26467354 GCACAACTGAGTACACACACACACAGACACTTAAT[A/G]CCTTAGGGCAGATACATTTCCTGGGCTGCTATGTG R 2 1 2 1 101000 r 74 goat snp17280-scaffold18-2435440 16 27276530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387957 Affx-122969609 AX-123258315 16 26522290 TTGGGGAAGGCTTCCCAGGGAGAACTGGGGCCTTG[C/T]AGGGCTAGTGGAAACCAGTTAGGAGTAAAGATAGT Y 2 1 2 1 101000 r 74 goat snp17281-scaffold18-2490376 16 27332072 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272812 Affx-1111833064 AX-519546507 16 26542488 CACACTTACCAGTGGATGTTTCCCCCATGTATGTG[A/G]CTTCTATTCAGTTTTCAGAGCTTTTTCCGTGTCTG R 2 1 2 1 102000 f 74 goat 16_26542488_AF-PAKI 16 26542488 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401876 Affx-122958856 AX-123272229 16 26569900 TTTGGCATTCTGACGCATAAAACACTGTTGTTGTT[G/T]TTCAGTCGCTAAGTTGTGTCCAGCTCTTTTGCCAC K 2 1 2 1 103000 f 74 goat snp17282-scaffold18-2537986 16 27379654 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783903 Affx-122968301 AX-385270958 16 26599944 CTCCAGGTCTTTCAGGGAGATAAACACAGCCCTTA[A/C]CCTCCTGCAGAAGATTCTAATCAGCCCAACCCAAT M 2 1 2 1 101000 f 74 goat snp17283-scaffold18-2568030 16 27409862 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442806 Affx-122927716 AX-123313143 16 26640028 ACTTGGTCCAGTGAGATTCCAGCAGTGTAGAGTAG[C/T]AGACGATGGTGGGGAGCAGGGCAGAGAAGGACCAC Y 2 1 2 1 101000 f 74 goat snp17284-scaffold18-2608114 16 27449962 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414067 Affx-122949763 AX-123284416 16 26702928 CCCGAGTGCATTTCTGGTTTTATTTTCAAGGAAGA[G/T]CATTTATCCATGTAGAAAGTGTGTTAGTCGCTCAG K 2 1 2 1 101000 r 74 goat snp17285-scaffold18-2671014 16 27509782 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416603 Affx-122947637 AX-123286951 16 26761762 GGAAAGGTCTTCACATTCAACGGACAACTGTGTTC[A/G]AACAGTAACTCACCTGAGAAAGAAAAACTAACAAG R 2 1 2 1 101000 f 74 goat snp17286-scaffold18-2729848 16 27568854 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783507 Affx-122929048 AX-385270570 16 26801120 TCCAATCTAGTTCGTATGGGGAAAGAGATCCCTGA[C/T]ATGTCTGATAGTAGTGTCTGAAGCCTTTCACTCCA Y 2 1 2 1 101000 f 74 goat snp17287-scaffold18-2769206 16 27608265 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789411 Affx-122953369 AX-385276421 16 26861330 TGGATGAAAACGTAACATTTATGAACGGAGAAACC[A/G]TTAGCGTGTAAACACTGCGTTTATTCTTGCCGCGT R 2 1 2 1 101000 f 74 goat snp17288-scaffold18-2829416 16 27665307 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439311 Affx-122930956 AX-123309648 16 26897091 ACAGTGCTGGGTGGGACTTAAAGGGGAGAGTCTTG[A/G]TGTGAGTCCCTGCCCATCTCAGGAGGAGTGTTTGT R 2 1 2 1 101000 f 74 goat snp17289-scaffold18-2865177 16 27700149 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772868 Affx-122939346 AX-385260013 16 26929879 AAAAAAATTAACGTTAATCAGCTATCTTCCCTATG[C/T]ATCAAATACTTTCACAGAACTATTTTCTTATTTCA Y 2 1 2 1 101000 f 74 goat snp17290-scaffold18-2897965 16 27732667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403028 Affx-122958553 AX-123273381 16 26961850 GGACAGACACCGTTCTTGGTGTTTAGCGTGGGCCT[A/G]CAGCTCGGGCTAGTGCCCATTTTATATTGACTCTG R 2 1 2 1 101000 r 74 goat snp17291-scaffold18-2929936 16 27764772 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434636 Affx-122933996 AX-123304977 16 26995308 GGTCTTATTTTCAGTACTTGCTTTTTATTATACAT[C/T]ATGCTTGGGGCCTACTATGGGGTTGGCCAGGAGGT Y 2 1 2 1 201000 f 74 goat snp17292-scaffold18-2963394 16 27798106 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781350 Affx-122925844 AX-385268435 16 27025885 GGGAATTGCACCCAGCACCTTATAACAGCCTATCA[C/T]GGAATATAAATCTGACAAAAGCACTGAATCAGTAT Y 2 1 2 1 101000 f 74 goat snp17293-scaffold18-2993971 16 27829147 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800713 Affx-122935385 AX-385287630 16 27075649 AAAGAAAAGAATTTGTCACTCAAAATGTGATAGAA[C/T]GAAAAATATAAACTTTATCATGCTGAGTGATTGCT Y 2 1 2 1 101000 r 74 goat snp17294-scaffold18-3043735 16 27879186 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385190 Affx-122971726 AX-123255548 16 27105432 CCAATAATTTGCTTCTTGATCAAACATTGTTCCTA[A/G]TTGATTCAAGCAGTATTTATTGTGTGCATCTTATG R 2 1 2 1 101000 f 74 goat snp17295-scaffold18-3073518 16 27909070 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403473 Affx-122957711 AX-123273826 16 27145531 AAGGCAATTCTCTTCCCTTCCTAGAAGAAGCGACC[A/G]TGGATGCAGGTGGCCCGACAGTGGTCAGTGTCCAG R 2 1 2 1 101000 f 74 goat snp17296-scaffold18-3113617 16 27949274 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799062 Affx-122956173 AX-385285992 16 27206749 CAAAGACTTGGGTTGCATTCACAGATGTGAATCCC[A/G]TAAACCTGGTTCCTTGGCTCAAGCACAGAAGGTCC R 2 1 2 1 101000 f 74 goat snp17297-scaffold18-3174835 16 28010011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405538 Affx-122955977 AX-123275890 16 27265522 GGAAGCTCTTTCAAACGGACTCTTACATTAGAGTT[A/G]ACTTTTCTTTTTTTAAAGAGTTTTTCAAATGCAGG R 2 1 2 1 103000 f 74 goat snp17298-scaffold18-3233608 16 28068911 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802264 Affx-122938453 AX-385289168 16 27317228 TCGGTTTTCTTTTGTTGAATGACTCATTCTTAGCA[C/T]GTGTACATGCTGAAAGTGTCTCTCATCTTTTGCAA Y 2 1 2 1 101000 r 74 goat snp17299-scaffold18-3285314 16 28120873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277133 Affx-1111835696 AX-519550639 16 27372800 CGTATCTTTCTCATGATGGCACGACATGAGACACA[A/G]TTTTCCACATCTAGAATAACTCCTACATTGAGTGC R 2 1 2 1 101000 r 74 goat Random2.2K-1592 16 27372800 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38393654 Affx-122965287 AX-123264009 16 27407249 GCAAGCTCGAGTCTTTTGGCAAATCAACACAATCT[A/G]CTGACCAGTTCCTTCTTCCCACTCACTGGCATGGG R 2 1 2 1 101000 f 74 goat snp17301-scaffold18-3375335 16 28210959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275075 Affx-1111834672 AX-519548656 16 27408245 GAGCTGGCTCCCTTATCTAAAATGCACGGAAAGGC[A/G]TCCCTGTGCTCACGTACTGCAGCCCTAAGGACTCG R 2 1 2 1 201000 f 74 goat GoatD01.045286 16 27408245 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38430718 Affx-122936899 AX-123301059 16 27437424 ATAAAACGGGGATATTATTAACTGCTCTGCTCACA[G/T]CTTTGGTTGTCAGAGTGATACGGAATAAGGCATAA K 2 1 2 1 101000 f 74 goat snp17302-scaffold18-3405510 16 28239559 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409762 Affx-122953000 AX-123280113 16 27495896 ATCCTTGTCAGTTTCCCCTCTGCCTAAATGAATCA[C/T]AGAATTAAAGTGTTTCACCTGATCAGACAAAAGCT Y 2 1 2 1 201000 r 74 goat snp17303-scaffold18-3463982 16 28298055 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412547 Affx-122951332 AX-123282896 16 27545444 GGACTCTGGAAGCATTTTCCACTATTTTCTCAGCT[C/T]TGCCTTTCTCTGTGTGCCAGCTTAATCATCAATTT Y 2 1 2 1 101000 f 74 goat snp17304-scaffold18-3513530 16 28342135 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434815 Affx-122934805 AX-123305156 16 27579346 CAGCTGTATTTGGGATTGATGTACACTGTGGTATT[C/T]ACTCCTGTTCCTCCAGCACAATTCTGCCTGGCTAG Y 2 1 2 1 201000 f 74 goat snp17305-scaffold18-3547432 16 28376066 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436891 Affx-122933224 AX-123307229 16 27610349 ACCAGAAACTTTCTGACTTTTTAAAAATGAAAGCA[A/G]TATGTGTTCACTCTAGAAAATTTGGGAAACTTTTT R 2 1 2 1 201000 r 74 goat snp17306-scaffold18-3578435 16 28407141 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770589 Affx-122954786 AX-385257753 16 27643374 CCTACACCACCTCTTAAGTTCTAGGTTGGTAGTAT[C/T]GGTACAATACATCCTAACCATCTACCAATGCAGTG Y 2 1 2 1 101000 f 74 goat snp17307-scaffold18-3611460 16 28440211 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407536 Affx-122954695 AX-123277887 16 27716055 ATTTTGGTGTTTGTGGGAAGGGTGGGACGTGGACT[G/T]CTTTTCCTGTGAAATCTGAAGGGTATCTCAGTTTG K 2 1 2 1 101000 r 74 goat snp17309-scaffold18-3684141 16 28512592 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444433 Affx-122926562 AX-123314770 16 27756685 ACTCTCCAAAAATTACTTACAAAACACATTTATTA[C/T]ATACTTTTTCTCCAGAGATCTACTGAGAATATTAT Y 2 1 2 1 101000 f 74 goat snp17310-scaffold18-3724771 16 28553652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769996 Affx-122936136 AX-385257163 16 27827889 AATCTTACATCAACCCTCCAACTAAAAAGGTAATG[C/T]GATTATAAATATTTAACCATTATCAGTTCAAAAGA Y 2 1 2 1 201000 r 74 goat snp17311-scaffold18-3795975 16 28624927 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771261 Affx-122977927 AX-385258419 16 27945198 TCAAAAATATAAAAGGTGACAGAGGAGTAATAATT[C/T]ACAGCTTTCAAAAAAGTTACTATCAACTTAAAAAA Y 2 1 2 1 201000 r 74 goat snp17314-scaffold18-3913284 16 28745382 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407040 Affx-122954938 AX-123277391 16 27973949 TATAAAGATAAATAAAATAGTGCTTTGTTCTCAAG[C/T]AAACAAACTATGCAATAAGCGTTACCCTCCCAATT Y 2 1 2 1 101000 r 74 goat snp17315-scaffold18-3942035 16 28773957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781497 Affx-122969134 AX-385268582 16 28005982 AAATCATCTTTGTATATTTCAGAATTGAAATGTAA[C/T]GTAGATACTGCTACAAAGGAAATATTACTATTGCT Y 2 1 2 1 201000 f 74 goat snp17316-scaffold18-3974068 16 28806098 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791703 Affx-122923808 AX-385278694 16 28058786 AATAAGCATATAACTTATTCCATTATAAGGGAGGA[C/T]ACTTAGCCCAGTAAATCAGGCCTAAAAACAGCAGC Y 2 1 2 1 101000 r 74 goat snp17317-scaffold18-4026872 16 28858987 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792814 Affx-122919527 AX-385279792 16 28101553 AAGTTCTCTATGTATCTTTGATGTTACACAGTTTC[A/G]CTAGGATGTGTGAATATATGTTTTTCCTCCTTGGC R 2 1 2 1 101000 r 74 goat snp17318-scaffold18-4069639 16 28902133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415056 Affx-122949481 AX-123285405 16 28154388 ATGAATTCTTCATGAAACTAAAACCTGTGTTTTGA[C/T]GGAAGAAAGACTAAGACAATCAAAAAGTGGATTTT Y 2 1 2 1 201000 f 74 goat snp17319-scaffold18-4122474 16 28955026 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403045 Affx-122958538 AX-123273398 16 28186806 GACAAGGAAAGTTTTCTTTGTTTTTTTGAAGAATC[A/G]TTGTTTTAACTAAGTCCTCAAAGTTTCTGGGTAGT R 2 1 2 1 101000 r 74 goat snp17320-scaffold18-4154892 16 28987545 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394632 Affx-122964400 AX-123264987 16 28223734 TCTTGACTTTGAACTACAGTATTTACTTTCTCTAT[A/G]CTGAGATGTCATGCTCTTTGGTAGTTTGCTCAAGG R 2 1 2 1 101000 r 74 goat snp17321-scaffold18-4191820 16 29024381 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794444 Affx-122961275 AX-385281407 16 28264555 AGAAATTAAGCTGATTTCTCCCTTGGCAAGCCCAG[C/T]TGATGGAGTCAAGAGCAAACCAAGAAAGACTGCAG Y 2 1 2 1 201000 f 74 goat snp17322-scaffold18-4232641 16 29065307 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414892 Affx-122949126 AX-123285241 16 28354530 CAATTTAAAAAACAAAGCAATTAAACTGTGAAAAC[A/G]CTAAGATGCCTCTGCAGCAAAACATTAACTGTGAA R 2 1 2 1 101000 r 74 goat snp17324-scaffold18-4322616 16 29155819 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380869 Affx-122975057 AX-123251227 16 28399193 CAGGCACTCTTCCACACACACAGATTCACAATCAC[A/G]CCAACAGGCTCACACAGGGACACTCACTTTTCATA R 2 1 2 1 201000 r 74 goat snp17325-scaffold18-4367279 16 29200996 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378731 Affx-122977038 AX-123249090 16 28460306 GTAATACTTTCACTTGTATTCAGATACTGCCAAAT[A/G]CAGACTTCTAAAACACTGATTTCTTTTCTAAAGCC R 2 1 2 1 201000 f 74 goat snp17326-scaffold18-4428392 16 29263244 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428172 Affx-122939033 AX-123298515 16 28517417 ACCAATTCTTTGTGGCCTGGCACAGAAGTCACTCC[A/G]TTTGTCTTCCCTGACTTCTACATTCTGTAAGATAT R 2 1 2 1 201000 r 74 goat snp17327-scaffold18-4485503 16 29320335 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416644 Affx-122947608 AX-123286992 16 28554105 AACCTCTCAGGTGTTCTTGCCGGGATAATTCCATG[C/T]GCAGTGGAGCCTGGTAGACTACATTCAGTCCATAC Y 2 1 2 1 103000 f 74 goat snp17328-scaffold18-4522191 16 29357258 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424990 Affx-122941904 AX-123295336 16 28598375 GGTAGTTGGATTTGTGATGATGTGGGAGAAAAATT[A/G]TGCCTTTGATCTATTTATAATGGAATTTATTACTA R 2 1 2 1 101000 f 74 goat snp17329-scaffold18-4566461 16 29400739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407482 Affx-122954764 AX-123277833 16 28628228 GCAAGAGTTATTAGCAGGGTATTTGACACAATTCC[A/G]AAAGTAGATGCTATCATATTTTGGTCATTTTCAGA R 2 1 2 1 101000 f 74 goat snp17330-scaffold18-4596314 16 29430741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438307 Affx-122931363 AX-123308645 16 28674763 AGAGAGACATGAGCACTTACTTACCCGGGGCAGCA[A/G]TTGCTGGGCACTGGCAAGAGTTTAGCTGAAGAATT R 2 1 2 1 101000 r 74 goat snp17331-scaffold18-4642849 16 29477735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441697 Affx-122929164 AX-123312034 16 28704404 AGTCATGTCATCCCAGGATTACCCTTCATCAGCCA[C/T]GCAATCAGAGTGAAGAATAAATTGACCCTGTTTAT Y 2 1 2 1 101000 f 74 goat snp17332-scaffold18-4672490 16 29507655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420350 Affx-122944964 AX-123290697 16 28777969 TTTCCTGGACTTAGAACTTCCTTTTCTAAAAATGT[A/G]TTTGGTAGACTGATGAGAATATGATAAGCTCTGAA R 2 1 2 1 101000 r 74 goat snp17333-scaffold18-4746055 16 29582139 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423062 Affx-122942952 AX-123293408 16 28820338 CTCTGTGGTCTGTACAACAGACAGACAGCTCTGCC[C/T]AGCCCTGGTGTTCTGGAAAAGCCTGCTTTACTGGC Y 2 1 2 1 101000 r 74 goat snp17334-scaffold18-4788424 16 29624585 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412408 Affx-122951440 AX-123282757 16 28898474 AGTTCAGTTCCCCCAAAATTCTCTCTTGATTTCAC[A/G]TGTTTGATATTTTTGATGCATTCTGTACAGAGCCA R 2 1 2 1 201000 r 74 goat snp17336-scaffold18-4866560 16 29703868 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453351 Affx-122919952 AX-123323684 16 28956469 AAGATCATTAATGCTGAAATTCTAGTTATGTGCCT[A/G]TCATGTTGGTTTTGAGTAGTCAAAATAGTGGCTTA R 2 1 2 1 101000 r 74 goat snp17337-scaffold18-4924555 16 29761848 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274582 Affx-1111834380 AX-519548171 16 29012898 CTAGCCTATAGACCTGGTGTCAAGTTATACCTATG[A/G]GATCCTGCAGGTATGAATTTTAAGCCAAATCCAAG R 2 1 2 1 201000 f 74 goat GoatD01.032764 16 29012898 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320795994 Affx-122936378 AX-385282946 16 29013735 GTGGACCTGAACTGTACAGTAATCTCGTATCGCAG[C/T]AATGTTGGAACTCAACTTTGCCAAATTGAGGGGGG Y 2 1 2 1 201000 f 74 goat snp17338-scaffold18-4981821 16 29819349 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376109 Affx-122978885 AX-123246468 16 29049304 TGAATCCAAATAATGACTTCTTATTGCACAATGAG[C/T]ACCCCGTAACTTAGAAAAATATACTGTGTATCAAT Y 2 1 2 1 101000 f 74 goat snp17339-scaffold18-5017390 16 29855092 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449890 Affx-122922344 AX-123320225 16 29084367 AGCTGCATCGTGTGGTATCCGCCTGTCCCAGAGGA[C/T]GCACATGTATTTGTGACCAAACAATTGACAGCATA Y 2 1 2 1 101000 r 74 goat snp17340-scaffold18-5052453 16 29890174 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445483 Affx-122925203 AX-123315820 16 29173318 TGCTAGATTCTAGTCCATCCTGTATCTATGTTGCA[C/T]AAGGCATTCAGCCTCTCTTGATTTTTTTCTATCAT Y 2 1 2 1 101000 r 74 goat snp17342-scaffold18-5141404 16 29979547 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272869 Affx-1111833066 AX-519546560 16 29207147 CTTGAATCAAGAGTCCCCCTCACTCTCTCCCTCAA[A/G]TCCTCCTTCTGGTGAGTGTTGATACCCTACGGAGA R 2 1 2 1 202000 r 74 goat 16_29207147_AF-PAKI 16 29207147 A G 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449980 Affx-122922877 AX-123320315 16 29212836 ATAAAGTGTGCCGCTCAAGGTGGCAAAGGCAAGTG[C/T]AGGGCCCGGGGCAAGGGGGGCAGAGAGGAGTGCAG Y 2 1 2 1 101000 f 74 goat snp17343-scaffold18-5180922 16 30019156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427345 Affx-122940115 AX-123297688 16 29355149 GTTCAAGTCGCTCCCTTCTCTTTCTCCAGGCTGGC[A/G]TAGCGCATCTAAGGCGCTCATTTTGGCCTTTTACA R 2 1 2 1 101000 r 74 goat snp17347-scaffold18-5323235 16 30161756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780136 Affx-122935050 AX-385267233 16 29386208 GCCCTTGACTCTGAAAATAGGACCCAGCAGTTGTC[A/G]TGTCATACTGAATAGATTTCTGTTCTCCACTTGTA R 2 1 2 1 101000 f 74 goat snp17348-scaffold18-5354294 16 30192737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408620 Affx-122953494 AX-123278971 16 29429095 AAAGGCCTGACTGGTGAGGCTGGTAAATATGGTCA[C/T]GGGCACGTGCAGCCCAATGCTGTCTGTCTGTCTGT Y 2 1 2 1 101000 f 74 goat snp17349-scaffold18-5397181 16 30236117 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412095 Affx-122951122 AX-123282445 16 29457843 TTCCTGGTGATGACAGAATGTTTGCGTTCCCCTTC[C/T]TCCATCCAAGTTCATATGCTGAATGTTCAGTGTGA Y 2 1 2 1 101000 r 74 goat snp17350-scaffold18-5425929 16 30264564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440228 Affx-122930678 AX-123310565 16 29501911 TATAAAGCAGTAAATGGTTGATGTGCAGAGTCTTT[A/G]CTTAGGGGTAGGACAAGGTGCAAAACACCAGATGT R 2 1 2 1 201000 f 74 goat snp17351-scaffold18-5469997 16 30308689 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427812 Affx-122939752 AX-123298155 16 29530674 AGGCAGTTATGCTAGGAAACAGCCTGGGCAGGAAA[C/T]AGGAGGTAGGTCTGGGTGCCTGTCTCCACTGCCAG Y 2 1 2 1 101000 f 74 goat snp17352-scaffold18-5498760 16 30337127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390050 Affx-122968423 AX-123260407 16 29568017 CAGATACTCCGAGCCCTGTGCTGGGTTTAATATTG[C/T]GTTCTCACCGCCTTGAAATTTTTAATCAATTTTGA Y 2 1 2 1 201000 r 74 goat snp17353-scaffold18-5536103 16 30376410 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446507 Affx-122925037 AX-123316843 16 29621212 AGAAAGAACAGAGGAGAGAGGAAGAGCAAAGTCTA[C/T]GAGGAGGGAATGGCCTTGGCACTTCTTGAGGAAAA Y 2 1 2 1 201000 r 74 goat snp17354-scaffold18-5589298 16 30429201 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382219 Affx-122973988 AX-123252577 16 29671072 GGGACACGTGGGCAAGGTAAGGAGGATGAAGACTG[C/T]GGATTAGTAACTAAATAAGGAGAATCATCAGAATA Y 2 1 2 1 201000 r 74 goat snp17355-scaffold18-5639158 16 30475684 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450210 Affx-122922286 AX-123320545 16 29704793 CACCACAGGGCAGCTCATGTACTTGCTCATTATTC[A/G]TTTTTCTGCAGAAGAGAGCTCCAGGCAGCTGAGCT R 2 1 2 1 101000 f 74 goat snp26290-scaffold2751-192634 16 30509337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793656 Affx-122943023 AX-385280629 16 29738413 TGCTTCTTACTTAGGAAAATTATTCCCGAAACGAG[A/G]TTCATTTTGATTCAGTAGAAACATTCTCCACCTTT R 2 1 2 1 101000 f 74 goat snp26289-scaffold2751-159014 16 30543227 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381077 Affx-122974608 AX-123251435 16 29772534 AGTCAGAGAGCTTCATCCCCATGAGTTCATGTATA[C/T]GTGTGTGACAGCTTTCAGAACCATACCTGGCACAA Y 2 1 2 1 101000 f 74 goat snp26288-scaffold2751-124893 16 30576089 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443807 Affx-122927079 AX-123314144 16 29802783 AACAAGGGTGCTGTTGGTGCTCAACTACTGTTCTC[A/G]CAATTGTTGAGTGCTCACTGTGTGCAGGAAGTGGT R 2 1 2 1 101000 f 74 goat snp26287-scaffold2751-94644 16 30606268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392821 Affx-122965785 AX-123263178 16 29834555 CTGGTATTAAAGACAGCTGCTCAGGAGGCCTCAAG[A/G]ATTGTTATTTTGTATGGGCTCCTCGAGGATTTTAT R 2 1 2 1 101000 r 74 goat snp26286-scaffold2751-62872 16 30638414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407576 Affx-122954668 AX-123277927 16 29872878 ATTATTGCATTAGAAATGTGATTTTTTAAATGGCT[A/G]AGGCTGGTAATTTGTCAGCATTTGGCAGGATTAAG R 2 1 2 1 101000 r 74 goat snp26285-scaffold2751-24549 16 30676354 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398488 Affx-122961572 AX-123268843 16 29965650 TTGGGATTCAGACGCACACACAGGCTGGACTCCAC[A/G]CTCTTAACCACTGCATGCCACTATCTCTCATAAAT R 2 1 2 1 101000 r 74 goat snp55871-scaffold869-67684 16 30772608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765148 Affx-122951867 AX-385252701 16 30034076 ATTAAACTCCATAGAGATTCTACATAAGAGATTAT[A/C]TTTGTTCCTAGGAAATATATACCAAAGTATTAAGG M 2 1 2 1 201000 f 74 goat snp55873-scaffold869-136110 16 30841561 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376072 Affx-122978916 AX-123246431 16 30088891 GGTTTTTCCAGTCTCTTCCCATCTATGGGTTTCAC[A/G]CCCTCCTTCCTTTCCCTCTTGCAATTTATTGTTGA R 2 1 2 1 101000 f 74 goat snp55874-scaffold869-190925 16 30896701 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438754 Affx-122930819 AX-123309091 16 30118418 CCATGGGGTCACAGAGAGTCAGGCACGACTGAAGC[A/G]ACTGAGGATGCAAGCATGTAATACTTACCCTCAAA R 2 1 2 1 101000 r 74 goat snp55875-scaffold869-220452 16 30925416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447381 Affx-122924854 AX-123317717 16 30157071 TTCTTAAAGTTGGCAGACTCCAGTGGAAGGCTGTT[A/C]GGTACAAATCTTCGTATACAAGAGGTTGGGATTTA M 2 1 2 1 101000 r 74 goat snp55876-scaffold869-259105 16 30964286 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378441 Affx-122976700 AX-123248800 16 30211030 GTTGTGGAGGACTCAAGGGAGGAAAGAGGAGGGAC[A/G]CTGGTGGTGTCAGAAGGACAGAAAGAATTTTGTTG R 2 1 2 1 101000 r 74 goat snp55877-scaffold869-313064 16 31018869 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378290 Affx-122976863 AX-123248649 16 30285795 CAAAAAACTGCTTTTTTTTGGTTGACCATGTCACG[C/T]AGCATATAGGATCTTAGGTCCCAGACCAGGGATTG Y 2 1 2 1 101000 f 74 goat snp55879-scaffold869-387829 16 31093660 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445579 Affx-122925133 AX-123315916 16 30332340 GTAGAAAAAATGGACTTTTGTATATTGATCTTGTA[C/T]AGAGACAACTTCTTAAACTCAGTTGTTAATTTTAA Y 2 1 2 1 103000 r 74 goat snp55880-scaffold869-434374 16 31139981 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382309 Affx-122973908 AX-123252667 16 30447969 TAAAACTGGGGACATCAGTGACATCAACCCCCAAC[G/T]CAAGGTGTGTTCAAGGTTACTTAATATCTGAAGAC K 2 1 2 1 201000 r 74 goat snp55883-scaffold869-550003 16 31257334 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415978 Affx-122948410 AX-123286327 16 30524106 CCAAGTTCAACTGATGTCAGCTCCAAAATATCTCC[A/G]GGACCCATTTATTCCTTTTTGTCTTGCCTGGTGGT R 2 1 2 1 101000 f 74 goat snp55884-scaffold869-626140 16 31333900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791636 Affx-122960166 AX-385278627 16 30559352 AGACTTTATGTGAGAGACCCACTCGGAGCTAAAAG[A/C]CCTCTCTCTTTTAAAGAGCCACAATTCCTGCTTTC M 2 1 2 1 101000 r 74 goat snp55885-scaffold869-661386 16 31369054 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406124 Affx-122956201 AX-123276476 16 30663008 AGCTTCAGATGTACCCTGACTCTCTAACGGCTCTC[C/T]GCAAAATATATGCTGAGTACTATTCTCATAAAAAT Y 2 1 2 1 201000 r 74 goat snp55887-scaffold869-765042 16 31472821 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400865 Affx-122959770 AX-123271219 16 30697053 TAATGGTATTTCCTGATAGTCGTGTAATACTCTGC[A/G]TATCTGTATTCAGTTGCTCAGTCTGTCCAGCTCTT R 2 1 2 1 101000 f 74 goat snp55888-scaffold869-799087 16 31506679 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387646 Affx-122969850 AX-123258004 16 30729456 TGCTGTTTCCTGTGTGCTGACTCTGCCCAGCTCCC[A/G]TCTTACCTCCACCCCACTCTCCTTTCTATAACATG R 2 1 2 1 101000 r 74 goat snp55889-scaffold869-831490 16 31539101 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798470 Affx-122953286 AX-385285403 16 30770826 TTTGTCATCTGATTGACTGTAACTTGCAGACCTCT[A/G]TAGTATTTTAGGTACAAACTTTTCCAAAGAACCAC R 2 1 2 1 101000 f 74 goat snp55890-scaffold869-872860 16 31580375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797099 Affx-122950862 AX-385284039 16 30821787 CAACACCAACAACAGGCAGAGTTTAGCCTGGCTGT[A/G]ATAACACACACTGGTGTGCATTAAAGATGATCTTT R 2 1 2 1 202000 f 74 goat snp55891-scaffold869-923821 16 31631581 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404068 Affx-122957147 AX-123274420 16 31019338 GTAAATTCTCACCTACGCTGTGATCTCTCATGCGC[A/G]TGATGTCACAGACCCTCTTCCCTCTGTCTTGATCC R 2 1 2 1 201000 f 74 goat snp55895-scaffold869-1121372 16 31830275 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423907 Affx-122942280 AX-123294253 16 31185551 AAGACTATTTCTGTAACAGAATTATTGGGTTTTAA[C/T]GGGAGATTTCAGTTGGTGAAGAATAAATGACATGT Y 2 1 2 1 201000 f 74 goat snp55899-scaffold869-1287585 16 31997103 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395237 Affx-122964475 AX-123265592 16 31282775 AGCTCTGTGCACTCCCTGCATGCTGTTTCTTTGCC[A/G]TTACTGTTTTTTCTTTGGAGTTAATTCCTTCTATC R 2 1 2 1 201000 r 74 goat snp55901-scaffold869-1384809 16 32094118 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375562 Affx-122978752 AX-123245921 16 31322516 TAGCCCTTTCTTTTAGCCAGTTACATTGAAAAGTT[A/G]ATACATTTGAATCCTTTCCTCTTTTATAATATTAT R 2 1 2 1 101000 f 74 goat snp55902-scaffold869-1424550 16 32133840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447653 Affx-122923967 AX-123317989 16 31360203 TCTACAGCATCCTCAGCATGGGGAGGCTGGGAGAA[A/G]CAAGAACATTCAGGAAGCAGAGAAGCCAGGCCAGC R 2 1 2 1 202000 r 74 goat snp55903-scaffold869-1462237 16 32171536 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390059 Affx-122968415 AX-123260416 16 31405345 CCTTTTACACCTGAGGAGACTGAATCACCAAGAAA[C/T]GAGGAGACCTGCCTAACATCCACAGCCTGTTCCTT Y 2 1 2 1 101000 f 74 goat snp55904-scaffold869-1507379 16 32215735 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793661 Affx-122957594 AX-385280634 16 31440007 CACTTGCTTACAACTGTTCTTATCTACATCCTGAA[C/T]GGTTTTCTCTGCTTCAGTAACATAAAGTGTTTGTT Y 2 1 2 1 101000 r 74 goat snp55905-scaffold869-1542041 16 32250705 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770277 Affx-122930823 AX-385257443 16 31473464 CTTTCCTGCATTAGAAGGTGTAAGAATGAAGAATT[A/C]AGTAGCTAAAGAATGATTGGTTCTCTGCCCCTAGG M 2 1 2 1 101000 r 74 goat snp55906-scaffold869-1575498 16 32284161 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432368 Affx-122935866 AX-123302709 16 31507422 GCTTTGTAGATAATGTCAGTCTTACCATGCAGAAT[A/G]CTATGTATTCAAGTTAAGAAAATTAAAAATCATAG R 2 1 2 1 103000 f 74 goat snp55907-scaffold869-1609456 16 32318324 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430394 Affx-122937766 AX-123300735 16 31542778 TTCTTTACCAACTGAGCCACCAGGAAAGCCCTAAA[C/T]AAAGTAAGCTGTTAGTAGAGCCAAAGTACGGATCC Y 2 1 2 1 201000 r 74 goat snp55908-scaffold869-1644812 16 32354161 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376467 Affx-122978045 AX-123246826 16 31590216 AGGTGTCAAGAACCGCACCAGGTCAACTCCCAGCC[A/G]CGAGGTCCTGGTATCAAGGAGCTAGGGCACAGAGG R 2 1 2 1 201000 f 74 goat snp55909-scaffold869-1692250 16 32401549 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421691 Affx-122944411 AX-123292038 16 31694359 TCTGCAGATATAGGTTCTCGGGCAGAGGGTCGTAA[A/G]TTTGTGCAGTCCAGTGGAAGAATAAGGCAGCCTTC R 2 1 2 1 101000 f 74 goat snp55911-scaffold869-1796393 16 32505551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272817 Affx-1111833067 AX-519546511 16 31707266 GACACCGAAGCCCTTGTGCCTAGGGCCTCTGCTCC[A/G]CTACAAGAGAAGCCACAGCAGTGAGAAGCCCACGC R 2 1 2 1 303000 f 74 goat 16_31707266_AF-PAKI 16 31707266 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320768782 Affx-122941825 AX-385255959 16 31789276 GCCAGGCTTTGTACTGAAATCTCCGGGCCTCACTT[A/G]CAGCTTGGGTGTGTTGATTTGATCCTCATCACGGA R 2 1 2 1 101000 r 74 goat snp55913-scaffold869-1891310 16 32601538 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800169 Affx-122969557 AX-385287092 16 31885891 ATTTTTTGTTTTTTTAGCCTTGCCTCCAGGCTTGT[A/G]GAATCTGAGTTCCCCATCAGGATCAAACCAGTGCC R 2 1 2 1 202000 r 74 goat snp55915-scaffold869-1987925 16 32697957 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417303 Affx-122947231 AX-123287651 16 31930955 TAAAACTGGAAGATATCCAGGAACAGCATTCTCTG[C/T]AATTCTCTCTTACTCATGAAGCCAAGTCCTAGGAA Y 2 1 2 1 201000 r 74 goat snp55916-scaffold869-2032989 16 32743270 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413226 Affx-122950249 AX-123283575 16 31964833 ACTTGGATGAAGTCCTCCTGCAGTTAGTTCTGGGG[C/T]GTGTCAGGGGATGGAGTGGCAGGGGGACAAGAAGG Y 2 1 2 1 101000 f 74 goat snp55917-scaffold869-2066867 16 32776010 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401585 Affx-122958877 AX-123271938 16 32116321 GAGTCAATACTCTAGCACTTAGTAGGTGGATAAAG[C/T]GATTACTGCCCTACTTTCATCACCCCCTTATTAAT Y 2 1 2 1 101000 f 74 goat snp55920-scaffold869-2218355 16 32929239 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418404 Affx-122946548 AX-123288752 16 32154001 GCTCTGGTGAGATAGTCCTGGGCAAAGGACTCACC[A/G]TCACCAGGATGTATACTCACAGTCCTCTGTAAGAA R 2 1 2 1 101000 r 74 goat snp55921-scaffold869-2256035 16 32965860 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450626 Affx-122921997 AX-123320960 16 32189336 TAGCATTTCTGTTACATAAAGGCTGGTTCAGAGAT[A/G]TGGAAGTGTGTGGTCCAGCATTCACTCAGTGATTA R 2 1 2 1 101000 f 74 goat snp55922-scaffold869-2291370 16 33001578 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423377 Affx-122943137 AX-123293723 16 32238609 TTGAAGAGCTGTCAAACTCTTTTCCAAAGTGGCTG[C/T]ACCATTTTACATTCCCATAAAAATAAAGAGGGTTT Y 2 1 2 1 303000 r 74 goat snp55923-scaffold869-2340643 16 33051717 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781994 Affx-122922601 AX-385269074 16 32279077 TTTCCAGGAGTGGAAGATCTGCTGGGTTCCAAAGT[A/G]TTAAAATGGAGTAGAAAGCCTTTCATGTTCCCATC R 2 1 2 1 101000 f 74 goat snp55924-scaffold869-2381111 16 33091157 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770512 Affx-122939047 AX-385257677 16 32401585 TTCTCATCTGCTTCACACCCTACTAACCAGAAAAA[C/T]GTAGCCATTCCTCCTACATTAGATCATGAGCTAGT Y 2 1 2 1 101000 f 74 goat snp55927-scaffold869-2503619 16 33221254 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410015 Affx-122953259 AX-123280365 16 32496526 GAGCAAATATTCCAATGCTCCCTGCCTTTCTGTAC[A/G]CTGTCCCAAGCTGTTCTGACACGCTTGCCTTTTTT R 2 1 2 1 101000 f 74 goat snp55929-scaffold869-2598560 16 33317125 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443123 Affx-122928087 AX-123313460 16 32535539 TTAGACGATAGCCAATGAAAGAGACCAGTGACTCT[A/G]TGTCTAAATTTGTTTCTCCCTGAAACCAAAATCCA R 2 1 2 1 201000 r 74 goat snp55930-scaffold869-2637573 16 33356557 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429361 Affx-122938562 AX-123299703 16 32555697 GACTTTGATGCCTCTTCCTTTCTAGTTTTAGAACT[G/T]TTTCTGCTGACCACCTGGTCCGTTCTTAAGAAGCT K 2 1 2 1 201000 f 74 goat snp1589-scaffold1045-274 16 33376541 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272488 Affx-1111834100 AX-519546210 16 32605208 TC[A/G]TCCACCCTTTTGTTGTGTCCAGTCTGCAGAGCCAA R 2 1 2 1 101000 r 74 goat GoatD01.018345 16 32605208 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320767942 Affx-122934426 AX-385255158 16 32681348 ACTATTGGTCTGAAAGGAGGTCTGTCTCTACTACA[C/T]GGCTCTAGATTTCCACTAGAACTAATACGTGATTT Y 2 1 2 1 101000 f 74 goat snp1591-scaffold1045-125925 16 33503470 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784415 Affx-122958873 AX-385271464 16 32733936 CAAAAACGGAATCCTCAAGGCAAAGTATTTGAAGT[C/T]ATGTTGGCCTCAGACTGCTCTCACTATGCAAAATG Y 2 1 2 1 101000 f 74 goat snp1592-scaffold1045-178513 16 33556479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407197 Affx-122954814 AX-123277548 16 32795593 ATGAATGATACTTGGAAGTGAACTATAGCCAAATT[A/G]TGCCAAGAGACCCAGGAAAACTGAGTCCAAATATT R 2 1 2 1 201000 f 74 goat snp1593-scaffold1045-240170 16 33618177 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382569 Affx-122973764 AX-123252927 16 32833332 CCTGTCTTCGTTTCTTCATTCTTTACTTCCCCAAA[C/T]GTTAACTGCTAGGGCCTGTCCTTTGCTCTACATGG Y 2 1 2 1 101000 f 74 goat snp1594-scaffold1045-277909 16 33654290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425748 Affx-122940743 AX-123296094 16 32863089 TCTATAATTCTCTTTGTGACTTTTAGTCATTGGAT[A/G]CCTTTGTTAACCTATCAGTGACTGATGTATTGGGT R 2 1 2 1 101000 r 74 goat snp1595-scaffold1045-307666 16 33684351 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398357 Affx-122961672 AX-123268712 16 32892076 TACTAGAAAAGATTCTTAGACCTACTTTGGTCCCT[C/T]TGATCATTGATTTATTTCCAGTTGACCCTATTTCT Y 2 1 2 1 101000 f 74 goat snp6478-scaffold123-830829 16 33762481 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377193 Affx-122978192 AX-123247552 16 32925241 CTTATTTCTATTCGGCATCAATGGACAAGGAATCA[C/T]GATCTTGGCAATATTTATAACTTGGTGGTCATTGG Y 2 1 2 1 101000 f 74 goat snp6477-scaffold123-797664 16 33795985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382916 Affx-122973396 AX-123253274 16 32955750 ATGGGTTTATAGACATAAAGTGGTGGCCAGGAACA[C/T]GACTAGTGGGCAGCAGAGGTGAAGCTGAACTGCAC Y 2 1 2 1 101000 f 74 goat snp6476-scaffold123-767155 16 33826371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418262 Affx-122947018 AX-123288610 16 33005187 AAAGACACCTGCTTCAATATTCGTATTTATATCAA[C/T]ATCTATAATTGAGAGTTCGTAGAGATAATAGAGGG Y 2 1 2 1 101000 r 74 goat snp6475-scaffold123-717718 16 33868526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437593 Affx-122931865 AX-123307931 16 33038967 CCAAGATGAAATTAAAATGAAGACATATGAAGTAT[A/G]CAGAATAGTTAAAAGCACTTCAGATAAGATCTGTC R 2 1 2 1 101000 r 74 goat snp6474-scaffold123-683938 16 33900481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432428 Affx-122935824 AX-123302769 16 33069296 TCCAGTGACATAAATCCCAATTTGCCTAGTAAATC[A/G]CTTATCTAAATTAGCACTGTTAGTCTATTGCTCAA R 2 1 2 1 101000 f 74 goat snp6473-scaffold123-653609 16 33930714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407272 Affx-122955342 AX-123277623 16 33140695 GTGGATCATGGCAAGGGTCTGAAATGTGAGGTAGT[A/C]GGTAGATGTTTATGAAATGTACATTTTATGCATTT M 2 1 2 1 101000 f 74 goat snp6472-scaffold123-582210 16 34002813 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770648 Affx-122974118 AX-385257812 16 33212253 ACACAAAATTTCAAAGAATGGTAGATCATCTCATC[A/C]AATTATTCGGCCTTCTTTCCTCTTGAAGATGAAGA M 2 1 2 1 101000 f 74 goat snp6471-scaffold123-510652 16 34075494 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800923 Affx-122968956 AX-385287838 16 33252150 ATATCATAGGTTTCCAGGAAAAGATGTTTTATGAA[A/G]TGTCTTGTCCTATAACTAGTGAATAAAATACAAAC R 2 1 2 1 101000 f 74 goat snp6470-scaffold123-470755 16 34115584 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793725 Affx-122955932 AX-385280697 16 33288188 CCTATGCAACTTGGCCTTCCAAGATCTAAAAATGG[C/T]GATGTATCAAGTTGACACAGTACCATCTCACCAAA Y 2 1 2 1 101000 f 74 goat snp6469-scaffold123-434717 16 34152026 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799768 Affx-122944129 AX-385286695 16 33319797 TGAAGAAGCAACAAAATTACCTGATCACCTGAAAA[C/T]GATTATGCTCTTTATTTTGAAAGAATACCAAAAAA Y 2 1 2 1 202000 r 74 goat snp6468-scaffold123-403108 16 34183983 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780239 Affx-122937999 AX-385267334 16 33366327 CAGTCCTGAACAGAAAGCTGGTTTTGATGTAAGAA[C/T]ATGGTTGAATTAACGAATTCCTTAGCTTTTTTTTG Y 2 1 2 1 101000 f 74 goat snp6467-scaffold123-356578 16 34231317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768944 Affx-122924555 AX-385256119 16 33396398 AGACAGCAGAAGTTACTGGGCCAACCAAGTAACTA[C/T]AGTCATTTCCCAAACATGAAGACTGCTCAACCTAT Y 2 1 2 1 202000 r 74 goat snp6466-scaffold123-326507 16 34261424 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387962 Affx-122969606 AX-123258320 16 33427549 GGAACCCTGCTTATTTTTCACAGTTGAGCATCTAT[C/T]TAGGGAAAATATACAAGCAGCCATTGGAAAATGTC Y 2 1 2 1 101000 f 74 goat snp6465-scaffold123-295356 16 34293062 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766122 Affx-122958485 AX-385253531 16 33474450 TAAATTATTTTCTGTGTAAGCCATGCCATTTCCTC[A/G]TGTTTAGCACTAAAACATTAATCTATCATGAAGTG R 2 1 2 1 101000 f 74 goat snp6464-scaffold123-248455 16 34338659 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441176 Affx-122929549 AX-123311513 16 33514029 AAGAGGGAGGGGCCAACAGGTTTGCTGTGGTCTGG[A/C]TTTGCTTCTCTTTCTCAGAGATACGCTAGGACCAA M 2 1 2 1 201000 f 74 goat snp6463-scaffold123-208876 16 34377653 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453961 Affx-122919464 AX-123324294 16 33555818 ATGAGGGTTCTACACTGACGAGTTTCTTAGATATC[A/G]TGGTCATTCAGAGGAGTTCTTCCAGAGATTATGAG R 2 1 2 1 101000 r 74 goat snp6462-scaffold123-167087 16 34419322 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400111 Affx-122960726 AX-123270466 16 33589760 AAGAATTTTTTTTTTTAATATGGTCTTTATCAATA[G/T]CCTGCTTATCTGCCTGCAGCTCTCTGCTATTTCTC K 2 1 2 1 101000 r 74 goat snp6461-scaffold123-133145 16 34451483 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380654 Affx-122975200 AX-123251012 16 33631286 CCTGCAGGGAGAGAAGCTGTCAAAGGTGAGTGTTG[C/T]CACCTTTAAACGTCGTTTTCACAATTTCGCTTGGT Y 2 1 2 1 101000 r 74 goat snp6460-scaffold123-91619 16 34492916 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444447 Affx-122926552 AX-123314784 16 33665472 GAGTCTACACTGCGGGGCTGGGGAGCACAAATCCC[A/G]CGGGTGAGTCACTGGGAAGGGGAGGAAGCCGGACC R 2 1 2 1 101000 f 74 goat snp6459-scaffold123-57433 16 34527223 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794842 Affx-122953733 AX-385281802 16 33700979 ACCTCATAGTGTTAGTGGAAAGAATTAAAAAATAG[C/T]ATGTAAAGAATCTGGTTTAATGCCTGATAGTCAAT Y 2 1 2 1 101000 f 74 goat snp6458-scaffold123-21926 16 34561226 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782859 Affx-122976490 AX-385269929 16 33794800 ACCCTTTTCATGTACTTCAGTGAAAATCTTGAAGA[C/T]GCTTATAATTAAGATGATACAACATTTTTTAGTGA Y 2 1 2 1 201000 r 74 goat snp29478-scaffold32-71796 16 34654022 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768828 Affx-122976351 AX-385256005 16 33853388 ATGATGGCTAGGAGGCCAATGTAATGGATGAGATG[C/T]ATCTAGAGTGTGTATCTAGAAGATGGTCATTGGAT Y 2 1 2 1 101000 f 74 goat snp29479-scaffold32-130384 16 34712765 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406500 Affx-122955151 AX-123276852 16 33912252 TTGGGCCCTAAAATAGAAGCAGAGCCCCAGGTCTA[C/T]ACTCTTACCTTCATCTCTACCAGGACCTTGCTGTG Y 2 1 2 1 101000 r 74 goat snp29480-scaffold32-189248 16 34771803 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447923 Affx-122923794 AX-123318259 16 33960418 CTAAACTATACATTGAAAAGAAGTAGATCCCCCAG[A/G]GCAGCCTTTCCCATCCAGAAAATGGAAACCAATCA R 2 1 2 1 101000 f 74 goat snp29481-scaffold32-237414 16 34820092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420068 Affx-122945119 AX-123290416 16 33997087 GGTGGAATTCTAAGAAAATGTAAGGAACATGCAAA[C/T]GGAAGAAACTCCCAGAGAAGGAAAAAATTAGCAGT Y 2 1 2 1 201000 f 74 goat snp29482-scaffold32-274083 16 34856902 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277002 Affx-1111835697 AX-519550510 16 34013428 AGATTACTTGAAATTGGCCACAAAGGGAGAACATA[A/C]TTCACAGAAATCAAGAAATATGAAAATCAGGGCTT M 2 1 2 1 101000 f 74 goat Random2.2K-1594 16 34013428 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38375786 Affx-122978579 AX-123246145 16 34053804 GTGAGCACAGGGAAGGTAGGTACCAGGTACAGGGT[A/G]TAATTTGCATAAAGTTAAGTGGCAATCAGTGCAGG R 2 1 2 1 101000 r 74 goat snp29483-scaffold32-330800 16 34913935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387336 Affx-122970494 AX-123257694 16 34088701 ACCCAACAAATGACTGTATTGTCAATGTAATAAAC[G/T]ACTCTACAGCTTTCTATAGTGAACTTGAGCATACA K 2 1 2 1 101000 r 74 goat snp29484-scaffold32-365697 16 34949375 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428130 Affx-122939063 AX-123298473 16 34135396 AAGAATCCTAGTCTAAATGTGTGGGAGAGTCATTC[A/G]TACACAACAATGTACTTCAGAAGAGTCTGGAGGCT R 2 1 2 1 101000 f 74 goat snp29485-scaffold32-412392 16 34996877 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796073 Affx-122933117 AX-385283025 16 34177622 AAAGCAAATAGTGACTTATTTAATTGAACTTCTGG[C/T]AGTCCTTAAAGACTGGAGAGGTTCTAGCCTTCTAT Y 2 1 2 1 101000 r 74 goat snp29486-scaffold32-454618 16 35039979 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413103 Affx-122950390 AX-123283452 16 34212399 AGGTGGGAAACTGGAGAGGAAGAAACCAGCTCAGC[C/T]AAGACTTTCCATAGGGAGTTGACTAGCTGACCCAC Y 2 1 2 1 102000 r 74 goat snp29487-scaffold32-489395 16 35074601 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429734 Affx-122937602 AX-123300075 16 34255277 TGTTCTTTTGTACTTTACCCTTCTGTCACTTAACA[C/T]AGTCTCCTGGTAATCACTGTTCAATACTTTCACAG Y 2 1 2 1 101000 f 74 goat snp29488-scaffold32-532273 16 35117555 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410990 Affx-122952006 AX-123281340 16 34286429 CTAGTTCCCATATCTTCCCCTTCCCATCCACTCTC[A/G]CAATTTTCAAAAACTTCAAAGCATTTCTCTACTCT R 2 1 2 1 201000 r 74 goat snp29489-scaffold32-563425 16 35148637 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426959 Affx-122940407 AX-123297304 16 34331048 CCTGGTGAAAAGCAAGAATCCTCTGATTCTGGATA[C/T]AAAAGAGTACCAAAGAGGAGAGAGAAAAATTGCTT Y 2 1 2 1 103000 f 74 goat snp29490-scaffold32-608044 16 35193039 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799120 Affx-122940447 AX-385286050 16 34385163 CTTGCCCAGTTATGCCAAAAATCAGTGGTGAGGCT[A/G]TGATTAGAATTGTCTCCCAAGTGCCAGGAGCTCTA R 2 1 2 1 101000 f 74 goat snp29491-scaffold32-662159 16 35247221 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780401 Affx-122921665 AX-385267494 16 34446393 ACTATCTGAGGCAGTGCTGTGTAGCATTGCTCAAA[C/T]GTTTATCTAGGAAGTCATGTAAATGGCAGAGGCTT Y 2 1 2 1 101000 f 74 goat snp29492-scaffold32-723389 16 35308781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402960 Affx-122958163 AX-123273313 16 34488766 GGGTTGTTCTCATCCTAAAATAGTGATGGAAAGAA[C/T]AACACAGATGTTTTGTTATTAGGGTTTCTGGGTGC Y 2 1 2 1 201000 f 74 goat snp29493-scaffold32-765762 16 35349999 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780410 Affx-122934037 AX-385267503 16 34530169 ACTTCTGCTTCTAGACGCAGGGATGCCCTTAAACT[C/T]AACGGCTCCAATGGCAACTCCTGATACCAGGTTAT Y 2 1 2 1 101000 r 74 goat snp29494-scaffold32-807165 16 35390115 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272819 Affx-1111833068 AX-519546513 16 34545810 AAAGCACTATCAATTGCTTTCCACACTGGTCAACA[A/G]GACAGGGAGCAATTTCTGGATTCTTCTTGCTCTTT R 2 1 2 1 201000 f 74 goat 16_34545810_AF-PAKI 16 34545810 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468272408 Affx-1111834270 AX-519546135 16 34566841 ACAAGACTGAGACTGTTTCATTAATTTTAGATGAG[A/G]ATGGGA R 2 1 2 1 101000 f 74 goat GoatD01.028327 16 34566841 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38375676 Affx-122978668 AX-123246035 16 34568019 TCAATTATTCATGGATGAATGAATGAAAGAAAAGT[A/G]TCTAAGAATCCCCATCAGTCAGGTTTTCTTTCCTC R 2 1 2 1 101000 r 74 goat snp29495-scaffold32-845015 16 35427355 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417711 Affx-122947448 AX-123288059 16 34605399 GGATAGAATCACCCTCCTCCAACATGAAATCTTTC[A/G]TATCTTTTTCCACATATTTATTCCTTTCCACTTTG R 2 1 2 1 201000 r 74 goat snp29496-scaffold32-882395 16 35463503 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799513 Affx-122969773 AX-385286443 16 34642978 AGGCCGATTCTTTTCAAGCCACCAGGGGCTTGACG[C/T]GATGCTTTAAGATCTTATGGGCCCATTAAGAAATA Y 2 1 2 1 102000 f 74 goat snp29497-scaffold32-919974 16 35502763 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400094 Affx-122960739 AX-123270449 16 34689885 GGAGTATCAGTCATTGAAGAAAGTACTACATGCAC[A/G]CTCAAGTGATGCAGATTCAAAGGGCTATAAGCAAA R 2 1 2 1 101000 f 74 goat snp29498-scaffold32-966881 16 35549746 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403546 Affx-122957600 AX-123273899 16 34735986 CAAAAGAAAAGTATGGTAAGGAAAGACAGTAATAA[C/T]GGGAGATGTGAGGAGAAAGGAATAAACTCCTAGAA Y 2 1 2 1 201000 f 74 goat snp29499-scaffold32-1012982 16 35595909 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450966 Affx-122921746 AX-123321300 16 34813296 CTTGCTTGCATATTTTCTGGAGCCCTAGAATGAGA[A/G]CTCCATAAAAGAAGTGACTTTTTGTTTGTTGCACT R 2 1 2 1 101000 f 74 goat snp29501-scaffold32-1090292 16 35673938 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783561 Affx-122950307 AX-385270623 16 34870719 AGGGAAACCTTAGTGTGATTTGCAAAGTCCTGATA[G/T]CTTCTCTCTAGTTGGAAAACTGGAAACCTCTTATC K 2 1 2 1 101000 r 74 goat snp29502-scaffold32-1147715 16 35731542 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432060 Affx-122935892 AX-123302401 16 34919414 ACCCAATTAATTCATTCATGTTTTCATCAAATTGC[A/G]CTACCACTGTGTTTTGCTAGGTAGCAGACATTTCA R 2 1 2 1 101000 r 74 goat snp29503-scaffold32-1196410 16 35780258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438019 Affx-122931569 AX-123308357 16 35020941 ATGTGTCCTTCTTTGGCTGGGTGCAGGAAAACAGG[C/T]GTATCTGAAGCCTCTTTGTCCCTGGCTTTGACTTA Y 2 1 2 1 101000 r 74 goat snp29504-scaffold32-1297937 16 35881813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407418 Affx-122955235 AX-123277769 16 35066264 GTAACCACTGTGGAAACCAGGATTCAGCCCCACTA[A/G]AGTACTGGGAGATACCTCAGAGTATTCTCAAGGAA R 2 1 2 1 201000 r 74 goat snp29505-scaffold32-1343260 16 35927329 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453027 Affx-122920091 AX-123323360 16 35125369 CTGTGATAAGGATCAAATTACCTTCTTGAGTGTCA[A/G]CTTATATATAAAATGGAGACAGTAATTGTAACTCA R 2 1 2 1 102000 f 74 goat snp29506-scaffold32-1402365 16 35987821 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429104 Affx-122938259 AX-123299446 16 35184321 GGGGAGGGGTTCTTCATGATTGGCAAGCTCTGACT[A/G]CGCTGGCTGCAGGTGACATGCACAGGAGAATCTGA R 2 1 2 1 201000 f 74 goat snp29507-scaffold32-1461317 16 36047526 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405525 Affx-122955987 AX-123275877 16 35220026 GCCAAGCAGACCTGAAAGCAAACAGAGAACATTTC[A/C]AAACGCTGAGTATCTGAGCTGTGAGCCAGAGACAG M 2 1 2 1 101000 f 74 goat snp29508-scaffold32-1497022 16 36083357 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274594 Affx-1111834313 AX-519548183 16 35257434 TTAAGCCTGAGGTCCAGGGCTGCAGGAACTGGCAT[A/G]GTTTGTTTATAAAGACCCCAGAAACCCTGGTGGAG R 2 1 2 1 201000 r 74 goat GoatD01.029820 16 35257434 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402256 Affx-122959128 AX-123272609 16 35270171 CCCATGTGTGGATATAAGCATTAAAAATTATTTTG[C/T]AACTGATAGGTGAAAATGGAAACTGGCTGCTTTAT Y 2 1 2 1 103000 r 74 goat snp29509-scaffold32-1547167 16 36133925 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780205 Affx-122953195 AX-385267301 16 35300094 GCAAAAGAATAAATAGGCACCTCACTTTATCTGCC[A/G]TATTAACAGCCAATAAACACAAATAGGTACTAATT R 2 1 2 1 101000 f 74 goat snp29510-scaffold32-1577090 16 36163836 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380505 Affx-122975698 AX-123250863 16 35344225 TGAACTATGTTCTTGTTCCTCATCTTCAGCTCTGT[A/G]CGTGTATCCTCAGCAAGATTCAGAAGCAAATAAAG R 2 1 2 1 201000 r 74 goat snp29511-scaffold32-1621221 16 36208243 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440338 Affx-122929669 AX-123310675 16 35416490 TAAAGTTTTGAGATTTTCTCAAAATTTTTGAACCC[A/G]CAGCTTTCTCTGTTCGCTGAAGGATACTCTATACT R 2 1 2 1 101000 r 74 goat snp29512-scaffold32-1693486 16 36280645 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391896 Affx-122966959 AX-123262253 16 35471231 TTCCGGATGCCTACTATGTGCCACACACTGCTCTA[C/T]GGTCTCAGGATACACAGGGAGTAAAAGCCAAAAAT Y 2 1 2 1 201000 r 74 goat snp29513-scaffold32-1748227 16 36335659 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791845 Affx-122932469 AX-385278835 16 35518684 ATTTCTCTGGATCCATGTTTTGGCTCTGGCAGTCC[C/T]AACTACTATAACATAAATAATTCTTATAGATTTTT Y 2 1 2 1 102000 f 74 goat snp29514-scaffold32-1795680 16 36383174 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447534 Affx-122924054 AX-123317870 16 35551099 ACTGTTGAAAAAATTCCAAATCCCTTCGCTTGCTG[C/T]TCAATGCTATCTTTAATCCAGCCACAATCTACCTT Y 2 1 2 1 201000 r 74 goat snp29515-scaffold32-1828095 16 36415539 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436562 Affx-122932908 AX-123306900 16 35606482 TCCTTGGGGAGATAGAGTAGTTATACATTGTATAG[C/T]AGTAGATTTTCAGTAGGCTCTGAAGTTTTTCTAGG Y 2 1 2 1 101000 f 74 goat snp29516-scaffold32-1883478 16 36470514 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793563 Affx-122948756 AX-385280538 16 35635965 TTCTTGAATGTATCAGTTAGTACAACATCTGGAAA[C/T]AATAGTGATCTTTGCACAACACCATTTAATATTAA Y 2 1 2 1 101000 f 74 goat snp29517-scaffold32-1912961 16 36500593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772637 Affx-122939816 AX-385259785 16 35721503 AGAGGGATATTTCAAAATATTAAGTGGGTCAATTC[A/G]TCTAGGAACACAGATCTTGGATAATCCCTAGCAAG R 2 1 2 1 101000 f 74 goat snp29519-scaffold32-1998499 16 36586725 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792449 Affx-122940935 AX-385279430 16 35750378 TTTGTAATCCATTGCATCAAGACCTTTCCCTTGCA[C/T]TTTCTACCAATCCTGAAATTCTTACCCAATCCTAA Y 2 1 2 1 101000 f 74 goat snp29520-scaffold32-2027374 16 36615591 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463451024 Affx-1109988769 AX-514934246 16 35777564 AGTAATTGACCCTCGGGGCAATGGAAGCTGCAGGT[C/T]GATCCATAGCTGAAATTTCCCCAAGGGTTGGAGCA Y 2 1 2 1 201000 r 74 goat GoatD01.042710 16 35777564 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434014 Affx-122934228 AX-123304355 16 35789034 GAGCTAGCACGCCACTGAATTAACTTTTCAGCCTG[A/G]TTTCATTCACGCATAGCCTTGGAAAGAGAAAATGG R 2 1 2 1 101000 r 74 goat snp29521-scaffold32-2066030 16 36654229 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398398 Affx-122961640 AX-123268753 16 35826203 GCAGTCCATGGGGTTGCAGTCGGACATGACTAAGC[A/G]ACTGAACAACAACAAGCAGCAGGATGAAGATCTGA R 2 1 2 1 303000 f 74 goat snp29522-scaffold32-2103199 16 36691356 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444723 Affx-122926413 AX-123315060 16 35873394 AGGGCTATTGGATGGGGGTGGGATGGGTAAAAAGC[A/G]TTCACCCATGCATAGGAAAAATATTTCTAAAATGC R 2 1 2 1 303000 r 74 goat snp39080-scaffold4978-12454 16 36737215 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381423 Affx-122974357 AX-123251781 16 35917147 GAGCTCAGGAAGCTCACTAGTTCTCAGGTAGAGAG[C/T]CGGAGGGTGGAGGCAATTTCTGGTAGTATAGAGCC Y 2 1 2 1 201000 f 74 goat snp50549-scaffold727-19513 16 36780322 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395159 Affx-122964117 AX-123265514 16 35949803 TTCTAAACATTTATCAAGTGAAAATCTTATCACTT[A/G]TCAAGCATCTAGGATATTGCAAAACTCATTCATTA R 2 1 2 1 101000 r 74 goat snp50550-scaffold727-52169 16 36813205 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427450 Affx-122940035 AX-123297793 16 35979698 GGTAGCTGAGGTACAGTGGAAATGCAAATAGAAAT[A/G]CTAAGAATCAGAAGCCTGAGTTCCACTTTACTTCT R 2 1 2 1 101000 f 74 goat snp50551-scaffold727-82064 16 36843310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776734 Affx-122960738 AX-385263859 16 36024810 AGATGGCTGAAATTTAATCCTCTACCATTTTCAAT[A/G]CACTGAGTAGCATAAATCCTAACCAGGTTTTAATT R 2 1 2 1 101000 r 74 goat snp50552-scaffold727-127176 16 36888410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381186 Affx-122974544 AX-123251544 16 36056188 GATTAGGAGGCAAGATAATGGAGCAGAAGGACTTG[C/T]GCTCATCTGTTCTCAGGAAAACACTAAAATCCCAA Y 2 1 2 1 201000 r 74 goat snp50553-scaffold727-158554 16 36920243 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446807 Affx-122925291 AX-123317143 16 36100886 AGCTTTGGTGTCATATATTCAGTTTCAAATCTTGT[A/G]CTGCCTATTATATGTCTGGCATTATACATATGCTG R 2 1 2 1 101000 r 74 goat snp50554-scaffold727-203252 16 36965206 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777984 Affx-122929232 AX-385265100 16 36131337 TAATGGAGAATATCTTTGGGTCAGGCTGTACACTA[C/T]AGGACAATAATAAAATGAAGGAATTTAATGAATAA Y 2 1 2 1 201000 r 74 goat snp50555-scaffold727-233703 16 36995935 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441761 Affx-122929114 AX-123312098 16 36173211 ATATGAATATGACAGCTTCATCACCTGTTCTGCTC[A/G]TGGTTTTTTGTGTTTATGTACTGATAATACTGTAT R 2 1 2 1 201000 r 74 goat snp50556-scaffold727-275577 16 37036053 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453458 Affx-122919855 AX-123323791 16 36224588 GTTTGCAGCATTTTGATACTGATGTGGTATGCAGC[C/T]GGTTCCGAGTCAAGTGTGGTCCCCCATGTACTGAA Y 2 1 2 1 201000 f 74 goat snp50557-scaffold727-326954 16 37089031 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776077 Affx-122967037 AX-385263207 16 36259611 AAAAGCATTAGCATAATGAGGTAGCATTCACTTGC[A/G]TCTACAAATAAATGAGTCTAAAGGATCCTTTCTGG R 2 1 2 1 101000 f 74 goat snp50558-scaffold727-361977 16 37124140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453435 Affx-122919872 AX-123323768 16 36305677 TTTACCTTCATTTTACATCATTCTTGGCCATTGTC[G/T]CAGCCTTTTGGGATTCATAATCTCTGCATATAAGC K 2 1 2 1 101000 r 74 goat snp50559-scaffold727-408043 16 37171670 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401162 Affx-122959364 AX-123271515 16 36354745 ATCTGATCCTCTAGATTTCCCAGGCAGGAGGCAGG[C/T]AGACAAAGTTCCTCTCTCTAAGTGATTGAATGGAG Y 2 1 2 1 101000 r 74 goat snp50560-scaffold727-457111 16 37220674 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423615 Affx-122942377 AX-123293961 16 36389870 GGAATCAGACACAAGAAAAGCTATCTGCCCAAAAG[C/T]AGGACAGAAATTCACAAAGAACAAAGGTTAATACC Y 2 1 2 1 101000 f 74 goat snp50561-scaffold727-492236 16 37253285 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799573 Affx-122932535 AX-385286503 16 36422470 AAAGCTTCTGATTACCTCCCAGCACACAATCTACA[C/T]AGAAAACTACTGTCAGCGCACTCAAAGGCAAAAAC Y 2 1 2 1 101000 f 74 goat snp50562-scaffold727-524836 16 37286538 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408209 Affx-122953851 AX-123278560 16 36573112 AGTGTAATTTAAATGAAATTGACAATATTAAAGAA[A/G]AATTAGGAGGCAAACCACATTTCCTAAGTTCTTTC R 2 1 2 1 303000 f 74 goat snp50565-scaffold727-675478 16 37435494 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778596 Affx-122935531 AX-385265707 16 36613794 GTTTATCCCTGATTTCCTTCATTCTCTCACACATC[C/T]GATCCTTTAATACATCCCTTATTTTCCAAATTTAT Y 2 1 2 1 101000 f 74 goat snp50566-scaffold727-716160 16 37476136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274609 Affx-1111834320 AX-519548197 16 36641410 AGGGG[A/G]AAATCTGCCATCTTCCTGCAGAATCTGACAGTTCT R 2 1 2 1 101000 r 74 goat GoatD01.029939 16 36641410 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320767087 Affx-122940976 AX-385254376 16 36680840 GTTGACTCATAAATTCTGTTTTAGTAATGTTGTTT[A/G]AACTGGTTCTTAGTGTTATTTATTAGCAAAATAAT R 2 1 2 1 101000 f 74 goat snp50567-scaffold727-783206 16 37542962 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393313 Affx-122965958 AX-123263669 16 36726457 GTTGTTTTTAAGGAGAGTCCGTCAACACCCCAAAT[G/T]AGAAGATGTTTTTCTTAAATGTTTCACTAGTGTGT K 2 1 2 1 101000 f 74 goat snp50568-scaffold727-828823 16 37588584 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782454 Affx-122920279 AX-385269530 16 36783789 TGATAAAATATTATTCAAATATTCCTATTGTATTA[A/C]TTTTAGTCTCATAGCAGAAGACTAATCATCAACCT M 2 1 2 1 303000 f 74 goat snp50569-scaffold727-886155 16 37645922 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379241 Affx-122976266 AX-123249600 16 36822667 AAACTGGATTTGGCCCATAGGTTATAGTCTGCCAA[C/T]CCCTGGTCCAGGTACAAATATGATAATCATTTAAA Y 2 1 2 1 101000 r 74 goat snp50570-scaffold727-925033 16 37684895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399176 Affx-122960631 AX-123269531 16 36908549 TCAGGAAGCTTACAATACTATCCGACTTGCACACA[C/T]AGGTATAAAATAATATAGAACACCTAGTTAAGGTA Y 2 1 2 1 101000 f 74 goat snp50572-scaffold727-1010915 16 37769750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802943 Affx-122963156 AX-385289834 16 36989007 GAACCCAGTGATTCTACAAATCTTGTACCATCACC[C/T]CTGAGACCTAATAAAGCTAAAAGAAACAAGTTGTT Y 2 1 2 1 201000 r 74 goat snp50573-scaffold727-1091373 16 37850457 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799787 Affx-122947715 AX-385286714 16 37021960 ACTAAGATATTAGTTTAAATGGTCTTAGGAAATTA[C/T]TGGTAAATTGAAAGCTATCTTGCCTGTACTTTCTG Y 2 1 2 1 101000 r 74 goat snp50574-scaffold727-1124326 16 37883958 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409049 Affx-122953358 AX-123279400 16 37076196 TCCAGAAACATGAACCATAATAGAGAGAGTAGCGC[A/G]TTTGATTCCTGGACTTTGAGAAATGTACACATAGG R 2 1 2 1 101000 f 74 goat snp50575-scaffold727-1178562 16 37938610 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414249 Affx-122949625 AX-123284598 16 37124737 TGTATTGGAGTAATATGGTGACAATAAAGACAGTT[C/T]CAGATGGCACAGTGAAAAGGATTGGCAGAAAGGTA Y 2 1 2 1 101000 f 74 goat snp50576-scaffold727-1227103 16 37991757 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406769 Affx-122955720 AX-123277120 16 37165440 AATTTTGTCAATTTCTCTGTGAAATGGGATGATGA[C/T]GATGATAATGGTTATAATATCACCTCAGAGAAGAT Y 2 1 2 1 101000 r 74 goat snp50577-scaffold727-1267806 16 38032539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396551 Affx-122962936 AX-123266906 16 37196563 CTTAAATACATCATGGGAGATTATAAAAGATTGCC[A/G]TTTTGAGCAACTGTTCTAAGTGTGGTGTTGATTTC R 2 1 2 1 101000 r 74 goat snp50578-scaffold727-1298929 16 38063833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385543 Affx-122971235 AX-123255901 16 37236803 TATGAAGAGACCATAGTCAATCCCATTTGTCTTAA[C/T]GTTCTTTTAAAATTTTATTAGTTTTTGCCTTTTCT Y 2 1 2 1 101000 f 74 goat snp50579-scaffold727-1339169 16 38104493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395573 Affx-122963843 AX-123265928 16 37269296 TCAAAGAGCTCACAGTTACTTCTGACATTAGGAAT[A/G]CTAATCTGTGACCAAGGTCAGTTGGAAAAAGTCTG R 2 1 2 1 101000 f 74 goat snp50580-scaffold727-1371662 16 38137288 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392563 Affx-122966080 AX-123262920 16 37298459 TCTGGATCATATGGCCAGGACCAAGCTAGCATGGC[A/G]GTATTTAGAGTCCACATACCTCGGAGGAAATTAGC R 2 1 2 1 101000 r 74 goat snp50581-scaffold727-1400825 16 38166643 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410636 Affx-122952083 AX-123280986 16 37335777 GCCCCTTGCACACGAACTGACTATATTTCAGGCCA[A/G]CAGAACTAGAAATGACAGGCTAGCCTTGCTTCACT R 2 1 2 1 101000 f 74 goat snp50582-scaffold727-1438143 16 38204323 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376044 Affx-122978936 AX-123246403 16 37418952 ATAAGGTCAAATAAACTTGGAGGATTCTACTTAGC[A/G]TGTTCTTTTCCTAATTTCCAATGTATATTGGCCTA R 2 1 2 1 101000 f 74 goat snp50584-scaffold727-1521318 16 38288558 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445931 Affx-122925921 AX-123316268 16 37463190 GACACAAAAGTGAAAAGTAAATTAGAATAAATACT[A/C]TTAAGCATATCTCAATGATTTGGGGAGTGTAGGGT M 2 1 2 1 103000 r 74 goat snp50585-scaffold727-1565556 16 38333923 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776528 Affx-122939623 AX-385263655 16 37502577 GTTGATCTTGTGGCCTACAAATATGCCTTTCACAC[A/G]TACGTATTGATCCAAAGTTAACACTTATTTATAGA R 2 1 2 1 101000 f 74 goat snp50586-scaffold727-1604943 16 38373523 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399659 Affx-122960515 AX-123270014 16 37532797 CATTAAAAAATGCTGGGTGAGTGAAAAGTGACAGT[A/G]TTAAGTTATTACAGATGGCAGCCGTCCCTGCTGGC R 2 1 2 1 101000 r 74 goat snp50587-scaffold727-1635163 16 38403741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277004 Affx-1111835698 AX-519550512 16 37549637 GAGTCCCTAACCCGTTCGCCTAAAACTATCACAAC[A/G]TTATTTGTTAATTGGCTATATGCAATACAAAATAA R 2 1 2 1 103000 f 74 goat Random2.2K-1597 16 37549637 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383496 Affx-122973426 AX-123253854 16 37563736 AAAAGGCAGTTGTGCAAGCGTAACTAAACTGAGGA[A/G]GCTGAAGGAGGAGAACAGTTCTTTTGGCTTCATTT R 2 1 2 1 101000 f 74 goat snp50588-scaffold727-1666102 16 38434781 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774092 Affx-122974532 AX-385261230 16 37622003 TTTAAGTCTATAGATGTGTATCTAGTTCAGGCAAC[C/T]AGCTAGATTTAAAGCCTTGGGAAGGAAGAAGGGCT Y 2 1 2 1 101000 r 74 goat snp50589-scaffold727-1724369 16 38493124 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440340 Affx-122929667 AX-123310677 16 37654750 CTGGAGAAATCGGACAGTTGGAGTCTCCATTCTCC[C/T]ATTTGTCTGGATGCTTTCTGGAGAAGGTAGTTTCG Y 2 1 2 1 201000 f 74 goat snp50590-scaffold727-1757116 NW_017189866.1 14906 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272821 Affx-1111833069 AX-519546515 16 37662908 TCACCAAAATTACAGTTTGATTTTAGTTCTGACAT[A/G]GAGCAATTGCTTCACATTTGTCACATGATAATCGA R 2 1 2 1 101000 f 74 goat 16_37662908_AF-PAKI 16 37662908 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38447092 Affx-122924489 AX-123317428 16 37697607 TAAGTCCCTAGCCAAATTGAGAGGAAGGTCCAGAG[A/G]TCTGCCATATACCCGCTGTCCCCACATGTGTTAGT R 2 1 2 1 101000 r 74 goat snp50591-scaffold727-1799973 16 38561879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389674 Affx-122968711 AX-123260032 16 37835781 TGGGTCTGGCTTTCCTCATTTGAGGCGGTATGCAG[C/T]AGACAGTTCCCTACTGCTCTGCAGTGGAGGGGCTT Y 2 1 2 1 101000 f 74 goat snp50593-scaffold727-1938147 16 38700137 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797335 Affx-122947146 AX-385284274 16 37870270 GATAATCATTAGGATTGGCATTATTCTGAGTCTCC[A/G]AAAGTTCTTTTTGGTTCACAGCTCACTTACACAGT R 2 1 2 1 101000 f 74 goat snp50594-scaffold727-1972636 16 38735725 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431689 Affx-122936781 AX-123302030 16 37965699 TGAAAATTTGTTTTGCTATTTTCACTTGATGAAGT[A/G]ATAAACATCATACTTGTTTTTAGGCACTTTTAGAC R 2 1 2 1 101000 r 74 goat snp50596-scaffold727-2068065 16 38831204 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445699 Affx-122926119 AX-123316036 16 38007838 GCTGAAGGGGAAAAACAGTAAAAAGAAGAGTATTC[A/G]ATAACATCAGGGAGGATTGGTGGGGTATAGATATT R 2 1 2 1 101000 f 74 goat snp50597-scaffold727-2110204 16 38875051 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399113 Affx-122960860 AX-123269468 16 38051458 TCTAAAAATGGGAACAAGTTAAAAAAAAAAACAAA[C/T]GAGAAATCTGAATAAAGTCTCTAGTTAACAGTCTT Y 2 1 2 1 103000 r 74 goat snp50598-scaffold727-2153824 16 38918784 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388529 Affx-122969200 AX-123258887 16 38095931 TCCTGCCCAATCAGTGAGTTTGTAGGAACCATGCC[A/G]TTGGTGAGCCCTGTGCTCTTTCCAGAGAAATGGCA R 2 1 2 1 201000 f 74 goat snp50599-scaffold727-2198297 16 38963999 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397109 Affx-122962694 AX-123267464 16 38143821 TATTTACCTTTGTATCATATCCAAGAGGGAGTTTC[A/G]CATTTAATACTCAAATATTTATTAAATGATTTGTT R 2 1 2 1 101000 f 74 goat snp50600-scaffold727-2246187 16 39012122 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782260 Affx-122958893 AX-385269338 16 38172552 TCTGGTTTAAACAAATCTCATAAATAAAACAGTTT[A/C]TATCCTTCTCACATAGCATGCAGATATATTGACTC M 2 1 2 1 201000 f 74 goat snp50601-scaffold727-2274918 16 39040893 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448724 Affx-122923841 AX-123319060 16 38207229 CACTTTGCCCATTGATTTGCGGAACTGCCTTTGCT[A/G]CATGTACATGAGCCTGTCTCTCTGGGATCCATGTC R 2 1 2 1 101000 f 74 goat snp50602-scaffold727-2309595 16 39076304 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795767 Affx-122955340 AX-385282720 16 38273125 CATTCTCCTGAAGAGGAAGTGCTCATATGCAATAA[A/G]TGGGTATGGAAAGGTCTCCAGAATTTGAAGTGAGA R 2 1 2 1 101000 r 74 goat snp50603-scaffold727-2375491 16 39139449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446692 Affx-122924744 AX-123317028 16 38304995 GCACCTAGTCCATTTAGGTTGTTCATGTGCTTAAA[C/T]GAGTTAAGTCTCATAAAGGATTTTGCCCAGATATT Y 2 1 2 1 102000 f 74 goat snp50604-scaffold727-2407361 16 39172643 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390204 Affx-122967793 AX-123260561 16 38342093 TCATATTTATCCACATTTTAGCTCTTATTACCCCA[C/T]AGTATAACCATCTGCTTCCTTATACATCTTCTCCA Y 2 1 2 1 101000 r 74 goat snp50605-scaffold727-2444459 16 39210318 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274930 Affx-1111834583 AX-519548512 16 38430515 AGTTAGATGTCAGACACTACCCATTTCACATGGAA[A/G]TCCACGTTTCTGCTACCGTTGGAAATACAGACAGG R 2 1 2 1 101000 f 74 goat GoatD01.042255 16 38430515 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38423741 Affx-122942859 AX-123294087 16 38438080 AAGGTCTCTTCCCCATTTGAAGTCAGTAACCTCAA[A/C]TTTATTTTTCTCATAGCATTAATATTTTTATTTCT M 2 1 2 1 303000 r 74 goat snp50606-scaffold727-2540446 NW_017195895.1 8362 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379430 Affx-122976106 AX-123249788 16 38468236 TTAAAGCATTTCAAAAGTTTATCATTAGGCTGGTC[G/T]AAGCATTTGGAACAAATGAAGCCATCAATCAGAGA K 2 1 2 1 101000 r 74 goat snp50607-scaffold727-2570602 16 39342045 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434020 Affx-122934223 AX-123304361 16 38505527 TGAATTTTATAGGAAACAGAGAAAGAAAAGAATTC[A/G]TTTGGCTAGTAACCCACTCCAGTGTTCTTGCCTGG R 2 1 2 1 201000 f 74 goat snp50608-scaffold727-2607893 16 39379171 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390856 Affx-122967823 AX-123261213 16 38580330 AGGGGAGATTTCCAAGATATATGTCCTAGCTACCA[G/T]AAGTAGTCTTAGAATAAATTGATATGATGATACAA K 2 1 2 1 101000 f 74 goat snp50609-scaffold727-2682696 16 39454707 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790548 Affx-122931611 AX-385277551 16 38620211 TCAAACCAGATTGGAGATTATTTCCCTAGCCACAC[C/T]GAAGACAGCTCCTACGAGACATTCAGAGAGAGAAA Y 2 1 2 1 101000 f 74 goat snp50610-scaffold727-2722577 16 39494496 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793588 Affx-122955004 AX-385280563 16 38632289 TATCCTAATTCCCAGAACCTGTAAACATGTTGCCT[G/T]GTGTGATGAAAGGTACTTCACTGATGTGATTAAAC K 2 1 2 1 101000 f 74 goat snp3966-scaffold1125-804912 16 39506431 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386212 Affx-122970989 AX-123256570 16 38675213 TTCGTAAAGCAGTAAGATGTCAGCCTTCTTTCTCT[A/C]GTGAACTTATATCTTGATCTCACTTTTACAAAGAA M 2 1 2 1 201000 r 74 goat snp3965-scaffold1125-761988 16 39549566 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397644 Affx-122962613 AX-123267999 16 38720363 CACACCAAAAGGTAGGGGCCAGACCCTGTCTGTAG[A/G]CTGTAGTTGACTACTTCCACCACCATCAAGCAAAC R 2 1 2 1 101000 r 74 goat snp3964-scaffold1125-716838 16 39594024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779506 Affx-122919347 AX-385266609 16 38796275 TTTAAAAAACTGTGATGACAGACAAATTTATCTGT[A/G]CTGGCTTCTGAGGACCATCTGAGGCAAGAAAACAT R 2 1 2 1 102000 r 74 goat snp3963-scaffold1125-640926 16 39669871 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421135 Affx-122944195 AX-123291482 16 38838549 TCATGGAGCTTACGTTCCAGGTGGAGAGCCAAGCA[A/G]TAAGCAAATATTTTTATTTAAGTGGGATGTGAAGC R 2 1 2 1 101000 f 74 goat snp3962-scaffold1125-598652 16 39711829 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383291 Affx-122972716 AX-123253649 16 38910417 AGCCAGCCTCTGCCACTAGCCAGCCTTCTATCATA[C/T]ATACTGTGACCTGATTGAGGGCAGAGAGGTCCATC Y 2 1 2 1 101000 r 74 goat snp3960-scaffold1125-526784 16 39784019 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417238 Affx-122947282 AX-123287586 16 38969585 GTTGTTGTTTTTTTAAAAAAACATGAATTTGCATG[C/T]ATTCTCACTTGACATGGAAGCTGTCTCCTTTAAAG Y 2 1 2 1 101000 r 74 goat snp3959-scaffold1125-467616 16 39843517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782583 Affx-122944426 AX-385269657 16 39001336 TGACCACTTGTGTGGTCTTATTACATGGTTGTTTG[C/T]ATTACCTATCCTTTACCTCTGAAAACAACTGGAAG Y 2 1 2 1 101000 f 74 goat snp3958-scaffold1125-435865 16 39875415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802442 Affx-122934249 AX-385289346 16 39080859 GGTATAATAGTAGTGTCGAGTTTCTGTCTTTGGTC[A/G]CGTATTGAAGTTCTCAGACACACTGTGAAGCTAGC R 2 1 2 1 101000 f 74 goat snp3957-scaffold1125-356342 16 39955052 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425887 Affx-122941633 AX-123296233 16 39141866 TTTAGAGATGTGGAAACCGAGTCTCCGAGAGGTTA[C/T]GACATTTCCCAGGATTGTAGAACTGGAGGGTAGCG Y 2 1 2 1 101000 f 74 goat snp3956-scaffold1125-295335 16 40015684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394047 Affx-122964988 AX-123264402 16 39184234 TTGGATTTGAGGGCTGGTGTGTGTGACTCCAAAGC[C/T]GGTGCTCTGAGCTGTTACCCTGAGCTGCCTCCTAG Y 2 1 2 1 101000 f 74 goat snp3955-scaffold1125-252967 16 40058624 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375912 Affx-122978477 AX-123246271 16 39215507 GGGTTCAAGTGAGAATTAGGGGCTATACCAGCATC[A/G]TTGCAACAAGGAAGAGAGAGGAAAGTGTCCTGAAA R 2 1 2 1 101000 f 74 goat snp3954-scaffold1125-221694 16 40089752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391690 Affx-122967583 AX-123262047 16 39246435 AGCAGTGGAGCGGCTGTCTGTTGTGGGAAGCCCTA[A/G]TACTGAGTTTGGGGACTGCTTTAGGAAAATCGAGC R 2 1 2 1 201000 f 74 goat snp3953-scaffold1125-190766 16 40120683 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443446 Affx-122927838 AX-123313783 16 39301040 CGGAATTTGAAGTCATGGCCCCTGTCCCTGTTCTG[G/T]ACTCTTGGCCCTGAGGGTTCCTGAGGGTTTCACGG K 2 1 2 1 101000 f 74 goat snp3952-scaffold1125-136161 16 40175213 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453808 Affx-122919567 AX-123324141 16 39358015 TGGAACCTGGATTCACACCTAGGACTCACAACCAT[A/G]CAGTGAGGGGCCCCTGGGCAGGGTCGGGGGTGGAA R 2 1 2 1 101000 f 74 goat snp3951-scaffold1125-79186 16 40232187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786015 Affx-122945714 AX-385273051 16 39392554 CTATTCTTCTAAGTCCTCAGTTTCAAGATGACAGC[C/T]CCCACCAAGGTCATTGGAGAAACTACACAGCTGGC Y 2 1 2 1 101000 r 74 goat snp3950-scaffold1125-44647 16 40267597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422803 Affx-122943204 AX-123293149 16 39434305 TGTGCAGTGAAGTATGTGTAAGTCTGGTCCCTGAC[A/G]CAAGGGGAAGGAGATCAAACAGAGGCAAGTTCAGC R 2 1 2 1 101000 f 74 goat snp3949-scaffold1125-2896 16 40309063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410562 Affx-122952140 AX-123280912 16 39442262 CTACAGGTAAGGAAAGAGAAAGAGCAAATACACAG[C/T]GATATGTTACCAAGTTGGTCACAGCTTTGAGAAAA Y 2 1 2 1 201000 r 74 goat snp39043-scaffold4940-59277 16 40317174 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389700 Affx-122968690 AX-123260058 16 39499865 AGCCTGGGAACCTCACACCAGTCTAGCTGCCATCA[C/T]TGTATCAGAGGGTGGAGGCTAGGGCTGGGGAGAAA Y 2 1 2 1 201000 f 74 goat snp39042-scaffold4940-1674 16 40374121 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422224 Affx-122944025 AX-123292570 16 39502706 GCTCAGAGTAAGGAGACCCTCCCTCTGGGGATAAA[C/T]GAGGTCTGAAGTGCAGCGGTAAGTTAGTTACCAGC Y 2 1 2 1 101000 r 74 goat snp1217-scaffold1030-3471516 16 40377103 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273808 Affx-1111833856 AX-519547419 16 39554337 GACAAATCTTTCAAACACATATTCTCCAGGATCTT[A/C]CTTAAGACACTCCATTATGTCTTGACAGAAAATCA M 2 1 2 1 201000 f 74 goat GoatD01.007899 16 39554337 A C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38451481 Affx-122921133 AX-123321814 16 39576239 GATTTGGGCAGACTGGAGAACTGGTGTTCTGAGAC[C/T]GGAAGTGTTTAAAGGAAGCAGTAAAGCTGTTCCTT Y 2 1 2 1 101000 r 74 goat snp1216-scaffold1030-3397983 16 40449651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773081 Affx-122935175 AX-385260223 16 39617408 GACAGCCCAGGCTTTATCTCTGTAGAGAGCCTGTC[A/G]CTTTTTAGGTTGAAAAAAAAGATTACGTTGAAATC R 2 1 2 1 101000 f 74 goat snp1215-scaffold1030-3356814 16 40490960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418805 Affx-122946170 AX-123289153 16 39659190 GCTCTGCAGTGCAGAATTCATCGGATGAGGAGCCT[A/G]CTTTTCGGGGAATAATTCATTTTTCCGGTGTTGGA R 2 1 2 1 201000 f 74 goat snp1214-scaffold1030-3315032 16 40533223 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376618 Affx-122979042 AX-123246977 16 39717361 ACAGACAGGATCACCTGTAAAGTCAGGAAGAAGGA[C/T]GTCAAAAAGTTGGGGGTGGGGTAGGAAGATTTTTC Y 2 1 2 1 101000 f 74 goat snp1213-scaffold1030-3256861 16 40593623 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449821 Affx-122922401 AX-123320156 16 39769502 GTTTTTGCTTTTCCCCAGTTTGGAATTGTTTGGGT[A/G]TGAAACATTCATAAATACATAAATTAAATCAGTTA R 2 1 2 1 103000 f 74 goat snp1212-scaffold1030-3204720 16 40644585 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379336 Affx-122976174 AX-123249695 16 39800132 CAGTCTATTACTTGTTACCTGAGAAATGACAACAT[A/G]CATCTTGACTTATTACAAAGAGTACTACAAATTAT R 2 1 2 1 101000 r 74 goat snp1211-scaffold1030-3174090 16 40675381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417087 Affx-122947493 AX-123287435 16 39834772 ATTCTTACATCTCTTCTCTGCTATTATTTTGAAAA[C/T]AGCATGGCTATGTTTCCTATGGGGAAGGTGGGGAG Y 2 1 2 1 101000 f 74 goat snp1210-scaffold1030-3139450 16 40710060 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441037 Affx-122928936 AX-123311374 16 40001624 AGTTATGAGACCTGAAGCTGAGGGACCAGTTGAGC[A/G]TCGCGGAGGGTTGGGGGTGGGATTGTAGTGCATAA R 2 1 2 1 101000 f 74 goat snp1208-scaffold1030-2972598 16 40873428 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416198 Affx-122948243 AX-123286547 16 40100288 GTACTTGCCTGGTCTCTGGTGGAGAAATGCTTTTC[A/G]TAACCACACACAACGCTGTTGATGTCATCCTAAGG R 2 1 2 1 101000 f 74 goat snp1206-scaffold1030-2873934 16 40972037 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409813 Affx-122952957 AX-123280164 16 40133597 TACTTGAGGATAAATAGGCAGAAAGATCAACGATA[C/T]AGAAATTCTAGAAAGAAATTCAAGGGCATATAAGA Y 2 1 2 1 101000 f 74 goat snp1205-scaffold1030-2840625 16 41005599 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420339 Affx-122944972 AX-123290686 16 40168133 GGGCAGAGGGAGCCAGGCCACCCATCTGATCAGAG[C/T]ACCACCTCCCACAGGGAGGATGAGGGCTTTTAACA Y 2 1 2 1 303000 f 74 goat snp1204-scaffold1030-2806089 16 41040297 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411029 Affx-122951970 AX-123281379 16 40240079 TGCCCCTCTGTGAACTTTCTCCTGTTTCTGCATAC[G/T]CAGCTCTGCCCACTTGCAGCAAGCATCCCAGGCCT K 2 1 2 1 101000 f 74 goat snp1203-scaffold1030-2734143 16 41111433 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391068 Affx-122966844 AX-123261425 16 40297394 CACACTCATCCCCCACCACACACATCATACACACA[C/T]GGAGACACATCACAGGCCACTTGGTGGCCACCCCC Y 2 1 2 1 201000 r 74 goat snp1202-scaffold1030-2676828 16 41168597 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463448887 Affx-1109989817 AX-514932137 16 40316654 TTCAGATCCAGGGATGGAACCTGGGTCTCCTGCAT[C/T]GGCAGGCAGATTCTTTATAGTCTGAGCCACTAGGG Y 2 1 2 1 303000 f 74 goat 16_40316654_AF-PAKI 16 40316654 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38383014 Affx-122973319 AX-123253372 16 40344525 CCTTCCCCCAGTCTGCTCTGCAGTATCAGAAGCTC[A/G]GTCTTCTGACTCTTTTCCTTGTATCCCTCCTCCCA R 2 1 2 1 101000 r 74 goat snp1201-scaffold1030-2629697 16 41214732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424896 Affx-122941315 AX-123295242 16 40373723 TCCTGCGTACCACCACCCACTTACATGCGTGCACA[C/T]GTCACATGTGTGATCACAGACATTCAGGAACAGTC Y 2 1 2 1 101000 r 74 goat snp1200-scaffold1030-2600499 16 41243907 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383051 Affx-122973289 AX-123253409 16 40506347 CTCCCAACTCTGCTTTTCAGCCTTTCCTTCTGCCG[C/T]GTCCTTCTTTTCCTGCTGTGCTGGGTGTTGGTGAG Y 2 1 2 1 201000 f 74 goat snp1198-scaffold1030-2467875 16 41375711 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432616 Affx-122935493 AX-123302957 16 40588536 TGTTTCTGCCAAGGCACCCAAAGAAGAGGGTCGCC[A/G]TCTCCAGATAGCAGGCAGGAAGGCGCCAGGAAGGT R 2 1 2 1 101000 f 74 goat snp1196-scaffold1030-2385686 16 41457788 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764904 Affx-122972471 AX-385252495 16 40633610 CACCCCATATGGTCCAGCCGTTTCCCTCTGAAATA[C/T]ATGTATAAGGATCTTGATAGCAGTACTAATTAGAT Y 2 1 2 1 101000 f 74 goat snp1195-scaffold1030-2340612 16 41502543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448143 Affx-122924282 AX-123318479 16 40665973 AAGCCTTTAATGCCTGACTTTGAAAGATTTTTATC[A/G]TTCATTTGTTCATCCATCCAAGTATTTATTGAGTG R 2 1 2 1 201000 f 74 goat snp1194-scaffold1030-2308249 16 41535461 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442604 Affx-122928479 AX-123312941 16 40701631 ATGACATTCGAATGGCAGAGTCAGATTCTAAGGCA[G/T]CAGTGAGGTGCGTCTGCCACCCTTTCTCCCATTCC K 2 1 2 1 101000 f 74 goat snp1193-scaffold1030-2272591 16 41571215 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417052 Affx-122947520 AX-123287400 16 40749428 TTGTGCTTAGAAGTTGTTCTGTCCTCATCTTCCTT[A/G]CTTTGATTTATAATAGGTAAAAGCTACATATTTAA R 2 1 2 1 201000 r 74 goat snp1192-scaffold1030-2224794 16 41618920 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431852 Affx-122936079 AX-123302193 16 40781063 TCCAGCAATAGATTCTGAAGTCCTGGGTTTCGATC[A/G]AATGCGTCTTTTATCTTTCCCAGGAATACACTGAA R 2 1 2 1 201000 r 74 goat snp11327-scaffold141-10857 16 41652575 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416653 Affx-122947602 AX-123287001 16 40834503 GGTGATTTACTATTGGAAATGGTAGGAAGTTGCTG[C/T]GGAGTTATGAGAAAACCAAACCAATTAGGTAAGAG Y 2 1 2 1 101000 f 74 goat snp11328-scaffold141-64297 16 41706609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383501 Affx-122972649 AX-123253859 16 40879931 GTAAAAATATTGTTTAAAAGATATGGTTTGTAACC[A/G]TCTTCAGATGAAAAAGCAATAAATAAAAGTCAAGC R 2 1 2 1 303000 f 74 goat snp11329-scaffold141-109725 16 41752643 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423272 Affx-122942661 AX-123293618 16 40971371 ATTAGATGATGAAACATACTAAAGAAGATCTAAAA[A/C]GATGGAGGTGTTCTTTATTTGGGGGCAGGAAGAAA M 2 1 2 1 201000 f 74 goat snp11330-scaffold141-201165 16 41843576 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395499 Affx-122963888 AX-123265854 16 41030372 CGGCTACACATTTATTTTTTTGCTTTTATATGTCT[A/G]AATTTCATCTTTAACACTGCACATAAATGCTTTCG R 2 1 2 1 101000 r 74 goat snp11331-scaffold141-260166 16 41901673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419660 Affx-122945950 AX-123290008 16 41086604 TTCTCTAGCCCTATTTCACAGCAAGAGACCAAGAA[C/T]AGGAGGGGACTGGGACTTAAGACGAGGATCATACT Y 2 1 2 1 101000 f 74 goat snp11332-scaffold141-316398 16 41957831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403431 Affx-122957742 AX-123273784 16 41167581 ATGGTAGGATGCTGATCACGGTTTCCTAACCTCAT[G/T]TTAAAAATAAGAACATTTAACAACAACAAAACAAA K 2 1 2 1 101000 f 74 goat snp11333-scaffold141-397375 16 42038798 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398565 Affx-122961511 AX-123268920 16 41204937 TTAAAATGTCCAATAGGCCAAGGTGCCACATTTTA[C/T]GGCAGTGTATCCTGAACCCCATCGTTGCTGCTGGT Y 2 1 2 1 201000 f 74 goat snp11334-scaffold141-434731 16 42077075 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404457 Affx-122956741 AX-123274809 16 41241799 GTCTTCAAAGGTAAGGATGCTCCTTCCTTCCAGGT[A/G]TTGGGGAGGGTACATCTCATATGAGGGTTTTGTGA R 2 1 2 1 101000 f 74 goat snp11335-scaffold141-471593 16 42113927 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430350 Affx-122937800 AX-123300691 16 41320185 GTACATCCTCACCATTACCATCACCAGCATTGTTA[C/T]GTCGAGAGCAGTATCCACTAACTGAGCATGTATGC Y 2 1 2 1 201000 r 74 goat snp11336-scaffold141-549979 16 42191219 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416819 Affx-122948127 AX-123287167 16 41377256 TAATATGAATTTCAGTTCAATTTTAAGCAGCCCCA[C/T]GTGGCTGGCTTGAGCCTTGTTCACACAGCAGACCA Y 2 1 2 1 101000 r 74 goat snp11337-scaffold141-607050 16 42245853 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400492 Affx-122961287 AX-123270847 16 41407810 AGACCGTGGGTAGACGCCAATGCGGAGACAGGACC[A/G]TTCTCGCGCTGTCTGTAGCGGCCGCAGTATCACTT R 2 1 2 1 201000 f 74 goat snp11338-scaffold141-637604 16 42276224 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377583 Affx-122977431 AX-123247942 16 41486393 AGCGCCACAGTTTGGAAGCACCAGTTCTTCGGCGA[G/T]CAGCCTTCTTTAGATCAAGTACGGTAGGGTAAGTT K 2 1 2 1 101000 r 74 goat snp11339-scaffold141-716187 16 42354801 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802138 Affx-122946746 AX-385289042 16 41563251 TATGGATTCTACTGACTAATAATATGGCCAGACCC[C/T]CTGTGGTCCCTAAATTCAGAGCCTTTGATAACTTC Y 2 1 2 1 101000 r 74 goat snp11340-scaffold141-793045 16 42435151 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384440 Affx-122973103 AX-123254798 16 41659987 CACTCTGCCCCAGATTTTAAGTGAAACCATCTCAG[C/T]ATATAATTCCCATGATCACTGTGGAATCCAAAACA Y 2 1 2 1 201000 r 74 goat snp11342-scaffold141-889781 16 42532354 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423200 Affx-122942717 AX-123293546 16 41750913 GGCTTCCTGCTGTTGGAACTGTGGGGTCTGAAGGC[A/G]CTCACAAGTTTCTGCACTCACTGGGCTGAAGGTTT R 2 1 2 1 101000 r 74 goat snp11344-scaffold141-980707 16 42623026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396482 Affx-122963546 AX-123266837 16 41845819 CATAAGTGTTCTATAATTAGATAATGGTTGCGTGA[C/T]TGTGTGAATATACTAAAAACTACTGAATAGCACAC Y 2 1 2 1 101000 f 74 goat snp11346-scaffold141-1075613 16 42717000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381708 Affx-122974708 AX-123252066 16 41892978 AGGTCTACCTCTGTCCCTTTTTTGGGTAAAGTGGC[A/G]GTGTAGACTTTCGCCCGAGGCAAAGCGGGCTTGTC R 2 1 2 1 101000 f 74 goat snp11347-scaffold141-1122772 16 42764269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419021 Affx-122946041 AX-123289369 16 41933678 CTGCCGTTGATATCTACTTGCTGACACTGAGTGGT[A/G]AGTTCCCCAGTTCACTGTCCAGCTGATTTTCCCCA R 2 1 2 1 201000 f 74 goat snp11348-scaffold141-1163472 16 42805068 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441388 Affx-122928850 AX-123311725 16 41967042 AGATGAGAACCCGGGGCAGTTTCAGCCCCCCATCC[A/G]TTTCATCCCTTGTCTAGTGGTGACCTGGAGCCAGT R 2 1 2 1 103000 r 74 goat snp11349-scaffold141-1196836 16 42838846 A G 1 parentage parentage not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414975 Affx-122949061 AX-123285324 16 42026903 AAGGAGAATGATGCAAGCTGTGCTTGTTGCAAGAA[C/T]AGCATAAGATGTTAAACAGGGAGCATAGCAAAATT Y 2 1 2 1 101000 f 74 goat snp44057-scaffold597-23009 16 43006186 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392714 Affx-122966035 AX-123263071 16 42110315 ATGGGCCAACTGGGTTCCACATAAACTTAAGAGTA[A/C]GTTAATATTCAGAGAGGGGAAATGGAAACCCATCT M 2 1 2 1 102000 f 74 goat snp44058-scaffold597-106421 16 43089720 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779864 Affx-122924998 AX-385266963 16 42243541 TGTTGCTTTTTAAGGTCCTAAATGTCCTCTATTTA[A/C]AATGAAATTCTTTTGTATTAACCTCCTTTCATATG M 2 1 2 1 202000 f 74 goat snp44061-scaffold597-239647 16 43222492 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448268 Affx-122924188 AX-123318604 16 42272864 TTGTTTAAACATTTCTTAAAAGTGGAAAGTTGAAG[C/T]TGGATGCTTGATTGGCAAATGTCTGAATCAAGGTT Y 2 1 2 1 101000 r 74 goat snp44062-scaffold597-268970 16 43252318 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801785 Affx-122952360 AX-385288693 16 42305608 GCCTGACACATGACGACAGCTGGTGCTTAATATAG[C/T]GAACACTGTCTATGCTCTAGGTACTGCTTTGGTGG Y 2 1 2 1 101000 f 74 goat snp44063-scaffold597-301714 16 43285053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438288 Affx-122931397 AX-123308626 16 42335013 CCTTACTGTTGCTTCAAATAAAAAGATTATGTGTT[A/G]TTTGTTATTTAATTGGGTTGTTGATCATAACCTGG R 2 1 2 1 101000 r 74 goat snp44064-scaffold597-331119 16 43314587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769393 Affx-122938839 AX-385256564 16 42393010 TCTTTTTGTAAGAACGAGGACATTCGTGTATATAG[C/T]GACTGTATCGTTATCAAAATCAGAAGATCTGCCAG Y 2 1 2 1 101000 r 74 goat snp44065-scaffold597-389116 16 43371568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802482 Affx-122960017 AX-385289386 16 42427156 GTGGATGCTTTGTTTACTCAGTGTCAGATGTGCTC[A/G]CCCTTCCTCTATGCTCTCAAATAAAATGAAGCAAA R 2 1 2 1 101000 f 74 goat snp44066-scaffold597-423262 16 43405741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777580 Affx-122925145 AX-385264699 16 42482201 ATATATAGGGGACTTTCTGTATGTAGATTCACTGT[A/C]TAATTGGACTTGTTACTTAGGTTCACACTTTAAGA M 2 1 2 1 101000 f 74 goat snp44067-scaffold597-478307 16 43460705 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434733 Affx-122933921 AX-123305074 16 42530158 TTAGGCAGTGGAGGATTCCATTGTTATGAGAACTT[A/G]CATGTATGGGAGAGGCCCTTTTCCTTCTGATGCAT R 2 1 2 1 201000 f 74 goat snp44068-scaffold597-526264 16 43507574 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388383 Affx-122969308 AX-123258741 16 42628638 AGAGGTCAAGCAGTTACCCAAAATCCCACCATGAA[C/T]AGGAGGAAAAACACAAACCTGATTCAGGATTTCAG Y 2 1 2 1 201000 f 74 goat snp44070-scaffold597-624744 16 43606415 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429914 Affx-122938107 AX-123300255 16 42691022 AGTCCCCCTGGGGTTGCGGGTAGGGCAGATGAACA[C/T]AAGTTATTTGGAAGCCACCTCTTCCTTGTATTCTG Y 2 1 2 1 101000 r 74 goat snp44071-scaffold597-687128 16 43669009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406883 Affx-122955638 AX-123277234 16 42719822 ATTACGGTTGACGTGACTGCTATTATTTAAAAGAG[C/T]AAATCAGTTAGGAGGAAAAAACATCTTATTTCTAC Y 2 1 2 1 101000 f 74 goat snp44072-scaffold597-715928 16 43697822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786391 Affx-122935098 AX-385273425 16 42763032 ATACAATCACATTACCTAAGTCACGCTTTAACTGC[C/T]TTCAGACAAATATGCAAACAAACAGTTTCAGAAAG Y 2 1 2 1 101000 f 74 goat snp44073-scaffold597-759138 16 43740978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773312 Affx-122938278 AX-385260455 16 42801867 ATCTTTGTGTTCTACCATCTTTAGAATGTCACTTT[C/T]GGCTTTGCGGATTCTTACCTCATGGTTCAAGGTGG Y 2 1 2 1 101000 f 74 goat snp44074-scaffold597-797973 16 43779718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379853 Affx-122975802 AX-123250211 16 42854376 TCATTAGGTAAAAAGCCATTAAGAATAGATACATG[C/T]ATATGTATAACTGAATCATTTTTCTGTACATCTGA Y 2 1 2 1 103000 f 74 goat snp44075-scaffold597-850482 16 43833056 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786848 Affx-122934150 AX-385273877 16 42932199 TTCTAGAGCAGTTCATAGAAAAGAGAACTACATCC[A/G]CCCACTAGTTCAAGAATCAAGATATTTATTATGCT R 2 1 2 1 101000 f 74 goat snp44076-scaffold597-928305 16 43910417 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766214 Affx-986697849 AX-385253613 16 42940502 TTGTGGACCTCACGGTAACAAGACCGTGTTAGGTC[A/T]AATGTTATCTCTTCTATTTTACGGAGAAGAGACTG W 4 1 2 1 600010 r 74 goat 16_42940502 16 42940502 Ancestral_priority_1043 ancestry 0.554 neutral IMAGE 10K 10K ancestral 320763322 Affx-986697851 AX-385251227 16 42940894 TAAATACGTGCTGGGGGACATCAAAACAGAACTAT[A/G]CTGGTGGTGGCTGTGAAAAAGAACCTGCAAGTCAC R 2 1 2 1 600010 f 74 goat 16_42940894 16 42940894 Ancestral_priority_1043 ancestry 0.628 recommended IMAGE 10K 10K ancestral 320766220 Affx-986697853 AX-385253619 16 42940896 AATACGTGCTGGGGGACATCAAAACAGAACTATAC[C/T]GGTGGTGGCTGTGAAAAAGAACCTGCAAGTCACAG Y 2 1 2 1 600010 r 74 goat 16_42940896 16 42940896 Ancestral_priority_1043 ancestry 0.504 neutral IMAGE 10K 10K ancestral 320765747 Affx-986697581 AX-385253203 16 42978972 TGAAGCTTAGTGAAGAGAGGAGTGGGTTATGTTGG[C/T]TTTTTATAGGGCAAGAGCCATGCATGTATTGTGAT Y 2 1 2 1 600010 r 74 goat 16_42978972 16 42978972 Ancestral_priority_1043 ancestry 0.74 recommended IMAGE 10K 10K ancestral 320791392 Affx-122970388 AX-385278384 16 42981239 ATGACATCTACAGGGATAACCGTCTCCATTTCCTC[A/G]GCTCCTTTAGCCAGGATGACCAGAGCTCTTTTTGA R 2 1 2 1 101000 r 74 goat snp44077-scaffold597-977345 16 43959780 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766225 Affx-986697856 AX-272300364 16 42985835 AGGCAAGGTAGGATAAGCAGGTTTAGGACTGGCTA[C/G]TACTTCAGAGATTTCCAAGGCATCAGTGCTGGGCT S 4 1 2 1 600010 r 74 goat 16_42985835 16 42985835 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 38398012 Affx-122961784 AX-123268367 16 43062191 TCAAGGGTTAAAAAATATAACATGTTCATGGATTA[C/T]GGAATTCAGACAAGGGTGGCTTGTCCCTGCTCCAC Y 2 1 2 1 101000 r 74 goat snp44079-scaffold597-1058297 16 44040898 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398747 Affx-122961818 AX-123269102 16 43104807 ATCTATGGATGCTCACGTCCTTACATAAAATGACA[C/T]AGTCCAGTCAGCACTCAAGGGTTCCATATCCTTAC Y 2 1 2 1 101000 f 74 goat snp44080-scaffold597-1100913 16 44083432 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390833 Affx-122967838 AX-123261190 16 43233353 CCTCAAATTTGGCTGAACTTAGCAAACAAAGCAGA[A/G]AAAGGGAGGCAAGATCAAGATCACTGTCAATTGCT R 2 1 2 1 101000 f 74 goat snp44082-scaffold597-1229459 16 44213405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408564 Affx-122953673 AX-123278915 16 43358260 CCATTGTGCAGAGATTCTGGTCCAGAGGGCTGCTG[C/T]AGTGGCCCTGGGCTCCATTGCTCTTAATTTCCTAG Y 2 1 2 1 101000 r 74 goat snp44084-scaffold597-1354366 16 44337869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383327 Affx-122972689 AX-123253685 16 43412853 AATCCCTAATGGCTCTTTATTTGAGAGCCCCACAA[C/T]GGGCTGAGGCTCTCAGGACATGTGGTCCAAGTGCT Y 2 1 2 1 202000 r 74 goat snp44085-scaffold597-1408959 16 44392439 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393385 Affx-122965903 AX-123263741 16 43444181 GGATGGGTAATAAAAAGGAGGTCAGAAAAGGACCT[A/G]AAGCAGGTGGGTCTGCTGCCATGGGCCAACTACCA R 2 1 2 1 101000 f 74 goat snp44086-scaffold597-1440287 16 44423803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429059 Affx-122938297 AX-123299401 16 43496551 TCTGTCTTCAGGGAAACTCTGTCTTCAGGCTGCCT[A/G]CAGCTCCTCAGGGGCAGGCACCTACTTGTGATTCA R 2 1 2 1 101000 f 74 goat snp44087-scaffold597-1492657 16 44475565 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383435 Affx-122973471 AX-123253793 16 43529110 CCTCGACATCCCAGGAAAACCCATCTTGGGTTCAC[A/G]CAAGGACCTGGGGACAAGGTGAGAGCCAGGAGTTC R 2 1 2 1 103000 f 74 goat snp44088-scaffold597-1525216 16 44507824 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437517 Affx-122932336 AX-123307855 16 43572332 GTAACAAGAGCTGGTGCTCCTGGGTGCGTCCCATA[C/T]GCCAGGAACTGTGCTGCCTGTATGCATGCGTCTCA Y 2 1 2 1 201000 f 74 goat snp44089-scaffold597-1568438 16 44551455 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442576 Affx-122928502 AX-123312913 16 43617470 CAGAACCCACTCACCTTGGCCCCCTTTCTCCTCTC[A/G]CAGGCTTGTTGTTATCCTTTCTCAGTCACAAGCCT R 2 1 2 1 101000 r 74 goat snp44090-scaffold597-1613576 16 44596599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452762 Affx-122920259 AX-123323095 16 43649767 AATGAGAACAGGAGTGGCAGCTCCAGCTTCTATTC[A/G]CTGAAGGCCAATTCATTGAAAAACCCTGGGCTGAA R 2 1 2 1 101000 f 74 goat snp44091-scaffold597-1645873 16 44628898 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448450 Affx-122923644 AX-123318786 16 43686862 ACTCTCAGAATCACATGGCTAAATGAGACAGGTAA[G/T]CCAGGAAACACTATGGAAATTAAGACACACAGTCC K 2 1 2 1 101000 f 74 goat snp44092-scaffold597-1682968 16 44665988 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418656 Affx-122946326 AX-123289004 16 43737313 GTGTGTGAGTATGTATATCACAAACACAAGGTGTA[C/T]ATGAATGCAAACACAGAAATGATTAAGCCTGTACA Y 2 1 2 1 101000 f 74 goat snp44093-scaffold597-1733419 16 44716551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272822 Affx-1111833070 AX-519546516 16 43770024 GACTCAGAGATGAATTTATTCTTAAGAGACAAACA[A/G]CATAATGGGGGATGACCTTGACTGGACTTTCAGAG R 2 1 2 1 101000 f 74 goat 16_43770024_AF-PAKI 16 43770024 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38390382 Affx-122968183 AX-123260739 16 43773294 AAAAACTTCAAAAGGACTAGCATCAGAGAGATTGC[A/G]TTCTCCAAACAAGTATTTATTAATTAAACTAGAAA R 2 1 2 1 101000 f 74 goat snp44094-scaffold597-1769400 16 44752789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385233 Affx-122972099 AX-123255591 16 43833484 CACAAAGGGTAAATCAGTCCATGGGGTCAAATACT[A/G]TAAAGGTCAAGGGGAAAGAGGGCAGAGGAAAGGTC R 2 1 2 1 101000 f 74 goat snp44095-scaffold597-1829590 16 44813078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404889 Affx-122956467 AX-123275241 16 43884732 CTTTATAAGTCTCAACTGCACGATGCTTTTTAAAA[C/T]ATAGGTGCAATTTGGGCCTGTGGTTAATACTGTTT Y 2 1 2 1 201000 f 74 goat snp44096-scaffold597-1880838 16 44864218 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408361 Affx-122953736 AX-123278712 16 43928999 CCCAAACCCCAGAAATAAACCTCCCTGTGCTGGCT[A/G]GGTCTCAGTCTCTCTCTTACCGGGAAGCAGAATGC R 2 1 2 1 101000 r 74 goat snp44097-scaffold597-1925105 16 44908543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377912 Affx-122977234 AX-123248271 16 43954102 TTGTTGTGTTTTGTCTATTAATCCTGCTTCATGGA[C/T]GGCGGTATCTCCCATCTTTCTCTTGGGAGGACTAC Y 2 1 2 1 101000 f 74 goat snp20919-scaffold205-3081698 16 44935791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397566 Affx-122962013 AX-123267921 16 43998185 ACAGTGTGTTCTGGGAGGAAAGGGGAGCCAGAATC[A/G]TCTCCAAACAGGCAATTCAAGTAAGATCAGGGGAA R 2 1 2 1 101000 r 74 goat snp20918-scaffold205-3037615 16 44981542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416139 Affx-122948288 AX-123286488 16 44027012 AAAGGATACTTAACAGTTCTGTTTATGAAGCAGTT[A/C]GATCAAATGGCTTAAATATTTGAGTCCTAATAACA M 2 1 2 1 201000 r 74 goat snp20917-scaffold205-3008788 16 45010346 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425760 Affx-122940732 AX-123296106 16 44127282 AAAATGGGAGTGGGTAATTTGAAACTTTGACCCAA[A/G]TGTGTCAAACCTGGCAAGAAATTTGCAGCCAGGCA R 2 1 2 1 101000 r 74 goat snp20915-scaffold205-2908518 16 45111589 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396259 Affx-122963319 AX-123266614 16 44221049 AACCTGCGCAAAGCTCTCAGGATCAACCTTGTTTG[G/T]TTGTTTTTAATTCTTTTTTCATGCGAGGGGAAGAA K 2 1 2 1 101000 f 74 goat snp20914-scaffold205-2814751 16 45205910 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421914 Affx-122943844 AX-123292261 16 44251791 TAAAGGAAGAAACTTCTAGTGCAAAGTCTTGGACA[C/T]AAGAACAAGTCTGGTGTGCTCCAGGTACAGAGAGA Y 2 1 2 1 101000 f 74 goat snp20913-scaffold205-2784009 16 45236904 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390042 Affx-122968429 AX-123260399 16 44306380 AAGTTTTGAGCTACTAAATAAAATTCACAAACTGC[G/T]AAGATTCAAAGACTTAATGAGCTAAACACAAAGGG K 2 1 2 1 101000 r 74 goat snp20912-scaffold205-2729420 16 45292095 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402974 Affx-122958154 AX-123273327 16 44402479 CTGGACCTGCGTCTTGTGTACAAGCCGTCCATGTC[A/G]TCCACGAAGTCAGGGGTGAGGTCCGGCATGTATTT R 2 1 2 1 101000 f 74 goat snp20911-scaffold205-2633321 16 45381308 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435840 Affx-122932818 AX-123306179 16 44530258 TTAAGTAATTGCTGATTCAGACTTCCCGGGTGGTC[C/T]GGTGTTAAGTACGGGATACAGGTTCAATCCCTGGT Y 2 1 2 1 101000 f 74 goat snp20908-scaffold205-2505542 16 45507012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400271 Affx-122960126 AX-123270626 16 44622656 GGGGCCCATGCCCACTGCTGGCCACAGAGGGGGAG[C/T]ACTTCCTATCCTACAAGGGTTGAGACGCCCCTTGC Y 2 1 2 1 101000 r 74 goat snp20906-scaffold205-2413144 16 45599067 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397540 Affx-122962034 AX-123267895 16 44660913 GGGATACTCCAGAGCAAGTAGGAGACGGGGGCAAG[A/G]ATGGGTGCTAACCGGGCACCTTCACCTACACCAGC R 2 1 2 1 201000 r 74 goat snp20905-scaffold205-2374887 16 45637569 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442925 Affx-122927623 AX-123313262 16 44709119 CCGAGGAAGCCAGTAACCAGCTTTCCCTAAGCTAG[C/T]TTCCTGGGTGAAAAACAGCCCTGGGTTTCAGTGCC Y 2 1 2 1 101000 f 74 goat snp20904-scaffold205-2326681 16 45685814 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436555 Affx-122932914 AX-123306893 16 44795258 ACCCAACCCAGGTTGTTTCTTCATGGCTCTAACTG[A/C]TCCCCAAATAAATACCTGCTCACTCTGTAAGTAAA M 2 1 2 1 101000 r 74 goat snp20902-scaffold205-2240542 16 45770675 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402993 Affx-122958140 AX-123273346 16 44824704 TTTCTTGTTAACTTCACCCATTTTTTTTTTAAACT[A/G]TCCTCAACTCTTGCTGTTTAAAAAAAAAAAAAACA R 2 1 2 1 101000 f 74 goat snp20901-scaffold205-2211096 16 45799212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375732 Affx-122978624 AX-123246091 16 44859040 TGTCTGTCTGTCTCTGTCTTTGGCAAGTATTTCCA[C/T]ACTCCAGCCACCAGCCTTTCACCTGCTGCTATGAG Y 2 1 2 1 101000 f 74 goat snp20900-scaffold205-2176760 16 45833515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446082 Affx-122925813 AX-123316419 16 44938637 AAACCCTGATTAGAAGTGATATTCCTCATGGAAGG[C/T]GATGGTATTTGATACATTTGTGACCTTGAGATAGT Y 2 1 2 1 201000 r 74 goat snp20898-scaffold205-2097163 16 45911972 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435997 Affx-122933500 AX-123306336 16 45014449 AGAGGAAGCAGGGCATGCTGAGAGCTGTAAGGGGG[A/G]TCAGAGCCCATAACCCAGCTCTGCTCAAAGCCAGA R 2 1 2 1 101000 r 74 goat snp20896-scaffold205-2021351 16 45988492 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427951 Affx-122939204 AX-123298294 16 45046061 TCTTTTCCTGCAGTGCTCTCTTTCTCTCCTGGCTT[A/G]TAGTGGCCTTCTTCTCCCCCTCCACTTTGAAGACA R 2 1 2 1 201000 r 74 goat snp20895-scaffold205-1989739 16 46019141 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393700 Affx-122965251 AX-123264055 16 45084061 GGACAAGAAGACCCTGAGTCCACAGAGCATGTCTT[A/G]CTTTAACCAGCCGTGGTCCAGGTCCTCCACTAGCC R 2 1 2 1 201000 f 74 goat snp20894-scaffold205-1951739 16 46056984 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401428 Affx-122958996 AX-123271781 16 45113664 AACCTGGTCTAAAGCCAAGCGTCCCGCCTGGAGGA[C/T]TGAGCAGTGGCTGGGAAGGAGGACCAGCCCTGCAC Y 2 1 2 1 303000 r 74 goat snp20893-scaffold205-1922136 16 46086945 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443551 Affx-122927760 AX-123313888 16 45150446 GGGCCCTGATGGACCCCAGTACTTCTCTCATGTCT[A/G]TAGTGTGTCCATGTCCTGTGCCCTCCCAAGATTTC R 2 1 2 1 101000 r 74 goat snp20892-scaffold205-1885354 16 46123666 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444990 Affx-122926655 AX-123315327 16 45179544 AAGCAGCTCTCCTGGGCCCTGGACACCCCTTGGAA[G/T]CTGAGCTGACCACTTGAGAACTCTAGCCGTCGAGT K 2 1 2 1 101000 r 74 goat snp20891-scaffold205-1856256 16 46152887 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386218 Affx-122970985 AX-123256576 16 45270136 GCTACTTTTACCAAATTCAACTGAGGGGACACAGC[A/G]CCAAGTGACCTTGTCAGCCCCATGGTCCCCAGGTC R 2 1 2 1 101000 f 74 goat snp20889-scaffold205-1765664 16 46241546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383218 Affx-122972772 AX-123253576 16 45339566 ACAGAAGGGATGGGCAGCCATTTCCCAGACACCCA[C/T]TAAGCACTGGGAAAGTGGATGGGAAAGAGCTCTTG Y 2 1 2 1 101000 r 74 goat snp20887-scaffold205-1696234 16 46311390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428356 Affx-122938980 AX-123298699 16 45464658 CTGGCCGATTATAAATGCGTGTCATTCATTTGTCC[A/G]TCCATCAGCTCCTGAATTTATTCAGTGTTGGTGGT R 2 1 2 1 101000 f 74 goat snp20885-scaffold205-1571142 16 46435951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379903 Affx-122975763 AX-123250261 16 45507601 GGTTCAGTGCGGCCTTAAAGGTTCATTTATATCTC[A/G]TAAGCTCTTGGGGAGCCAACTCATTGGAAAAAGAC R 2 1 2 1 101000 f 74 goat snp20884-scaffold205-1528199 16 46479020 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417086 Affx-122947494 AX-123287434 16 45565993 GCGAGAGACAAAATGATGGAGACGGATGGGGAGAT[A/G]CAGGACATGACTGGAGGGCGGGGTGAGCAGGACGT R 2 1 2 1 101000 f 74 goat snp20883-scaffold205-1469807 16 46538208 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444657 Affx-122926462 AX-123314994 16 45616508 CCACATTCAAAAGGCCCCAGCACTAAGCTTAAGGC[A/G]TTGTCATTGTTGTCTTGATACTCTGAGTAATTTTC R 2 1 2 1 101000 r 74 goat snp20882-scaffold205-1419292 16 46588614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784077 Affx-122966582 AX-385271129 16 45662738 CAGGCCAATGCGAGTGCAGAGGGACTTAGAAGCAG[C/T]AATTTCAGTAGAAGGAAAATGAGACTGAGGGCTTG Y 2 1 2 1 101000 r 74 goat snp20881-scaffold205-1373062 16 46633856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440331 Affx-122929676 AX-123310668 16 45715892 AGCTGGCATATTTTGCTTCCCTTCAATATGTTCAA[C/T]GGTTCATCCTTCTTTTCCCAAGATCCCAACACAGC Y 2 1 2 1 101000 f 74 goat snp20880-scaffold205-1319908 16 46686843 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423838 Affx-122942785 AX-123294184 16 45769534 GTAGACTTTATATTACTTGATAACTACTGCATGGT[A/G]TGTGTGGAGGAGTTAACCCTGCTGTATGAGCAAGC R 2 1 2 1 201000 f 74 goat snp20879-scaffold205-1266266 16 46740748 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389436 Affx-122968356 AX-123259794 16 45819158 TGTCTCATCGTTGGCCAGATAGCCCCTTCTTTTGA[C/T]GCCTATGTCCTTTTGGAATGAACCATGGATCTTTG Y 2 1 2 1 201000 r 74 goat snp20878-scaffold205-1216642 16 46790623 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433622 Affx-122934593 AX-123303963 16 45950656 GAGAAAGCTCACTCGCGCTGTGCACAGTGATGAGA[A/G]TTGCAAGGTGGCTGGATGATTTCCCCTTAAGATGG R 2 1 2 1 101000 f 74 goat snp20876-scaffold205-1085144 16 46919920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768089 Affx-122925842 AX-385255291 16 45980606 ATAAGTGGTGTCTGCCTACTTATACACTGCTGGGC[A/G]TGGAGTAAATAAGATCGCTGGATTTGCTTGGAGCC R 2 1 2 1 101000 f 74 goat snp20875-scaffold205-1055194 16 46949758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434175 Affx-122934883 AX-123304516 16 46018309 CTTTGCATACGGCTTATAATTCCCTCTGCTTGGGT[A/G]TGGGTGGGCCTGACCTAATCAGGTGAGCCCTTTGA R 2 1 2 1 101000 f 74 goat snp20874-scaffold205-1017491 16 46987456 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433319 Affx-122935182 AX-123303660 16 46097107 CAGCCTCTCATGAGAAGTTCTATCATCCTTTTAGG[A/C]GTGACCTCTCAAAGAGAAGAAAAGATGAGACATCC M 2 1 2 1 101000 f 74 goat snp20872-scaffold205-938693 16 47066991 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277011 Affx-1111835701 AX-519550519 16 46114637 GTTCATTCAATATAAGTTTTATGTGATGTGGGAAC[A/C]TTTATAAGAAAATGAAGACTCAAAGAAACGATGAA M 2 1 2 1 101000 f 74 goat Random2.2K-1600 16 46114637 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434417 Affx-122934674 AX-123304758 16 46154815 CTACCCAACCCATCCTGCTCAAAACTTTCAAGGTC[A/G]TCCAGAGAAAGCGAGTCCGAGCGTCCATCACAGTC R 2 1 2 1 101000 f 74 goat snp20871-scaffold205-880985 16 47124596 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418096 Affx-122947139 AX-123288444 16 46186034 AGTATGTCGACAGGAGGGTTTAAGTTTTAGGGAAG[C/T]GTCTTTTAAGGGATGCCCTGGCGTGGAGACGGTTT Y 2 1 2 1 101000 f 74 goat snp20870-scaffold205-849766 16 47155494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386227 Affx-122970978 AX-123256585 16 46223214 TGTCTCTTCTTGGCTAAATTAGCCTCTTGTTCTCC[A/G]CCAGGTAATCCCAGAGTGCAGCCAGAGCCCGGCAT R 2 1 2 1 101000 f 74 goat snp20869-scaffold205-812586 16 47192259 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445614 Affx-122925106 AX-123315951 16 46275567 TGCTTCTATATAAAAGGTGTCTCTATCTCCAAGAT[C/T]CCTAAGGGAAAATGGCCACATGTAGGAAGGAAGAC Y 2 1 2 1 201000 f 74 goat snp20868-scaffold205-760233 16 47245067 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397164 Affx-122962427 AX-123267519 16 46357325 GTCTTGAAAGGTCTAAGAAGCAAAGGACAGCCAAA[C/T]GCCCAAATCTGGGTTTCTTGCCCTGTTCCCCACTG Y 2 1 2 1 101000 f 74 goat snp20866-scaffold205-678475 16 47327307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271800 Affx-1111833071 AX-519545588 16 46407103 ATAAAGCAGTAAACTTTAAGAAGAGGTGACCATCC[A/G]AGACCTGAAACATAATTTGCGATGTTCTGCAGTTA R 2 1 2 1 101000 r 74 goat 16_46407103_AF-PAKI 16 46407103 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398703 Affx-122961853 AX-123269058 16 46414869 TTAATGATCTGTTTGTGCTCATGGGAATGGAAATG[C/T]AGTTTTAATGTCTTATTTACTCACAGTCTGCTGTC Y 2 1 2 1 101000 r 74 goat snp20865-scaffold205-620931 16 47384769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435365 Affx-122933585 AX-123305705 16 46560711 GCCACTGGGGCTATACCTTTCCCCTCTCAGGTTCA[C/T]GAGAATCACATGAAACAGATTCTTCCAGTTGCCTG Y 2 1 2 1 101000 r 74 goat snp20862-scaffold205-475089 16 47530363 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277145 Affx-1111835702 AX-519550651 16 46563369 TTGCAGGACATCAGAGCAACACACAAATCAGTTGC[A/G]TTTCCATCCACCACCAATGAACCATACTGAAAGGA R 2 1 2 1 201000 r 74 goat Random2.2K-1601 16 46563369 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382118 Affx-122974882 AX-123252476 16 46593643 GTCTTTTGAGGGCTGGATTTAAATCAAAGCCTGTA[C/T]GAGGGAGAAGAAAAGCTTTGTGATCTCTTTGCTGA Y 2 1 2 1 101000 f 74 goat snp20861-scaffold205-442157 16 47564129 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274384 Affx-1111834168 AX-514940039 16 46626190 CTGCCCTTGGAGGCCCTGGTGAGCCTACATTCAAG[A/G]TCAAGTTAACAACACACACCTTCCATCTTCT R 2 1 2 1 201000 r 74 goat GoatD01.023082 16 46626190 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407674 Affx-122954593 AX-123278025 16 46656169 GAACTGCCCTCATTTTAGTAATTGGGGATGGCATT[C/T]ATCTCTGGTTAACAAATGAGCTGAAGAATCAGCTT Y 2 1 2 1 101000 r 74 goat snp20860-scaffold205-379631 16 47627822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440881 Affx-122929235 AX-123311218 16 46690120 CATTCTGGGACTTATTGGGTGGTTTCTGAGGTGGG[A/G]GGTGAGGAGGGCAGTGCAAGGGGAGTGAGGTGGGA R 2 1 2 1 103000 f 74 goat snp20859-scaffold205-345680 16 47661845 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386032 Affx-122971484 AX-123256390 16 46756396 GCAGCAGGCCTTCAGATACGCACGTAAGTGAGTGA[A/G]CTCTGGGGAGGAGGATGACAGACAATATGGTTACT R 2 1 2 1 201000 f 74 goat snp20857-scaffold205-279404 16 47728180 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447922 Affx-122923795 AX-123318258 16 46787631 AGCTACTGTTTATTTCCTTTTCTCCACCAGATTTT[C/T]CTTTCTCTCCTCTTGCCCCAAACCTTCTTCCTTCC Y 2 1 2 1 201000 r 74 goat snp20856-scaffold205-248169 16 47759469 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769502 Affx-122936168 AX-385256672 16 46841474 TAGTGGAGAGATGTAATCAGACTTCCTACAGCAAA[G/T]AATAGAGTATTTTAGAGCCAGTTTTAATCTACGTG K 2 1 2 1 101000 f 74 goat snp20855-scaffold205-194326 16 47813529 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416239 Affx-122948212 AX-123286588 16 46996840 AAAAAAAGCCAGAAACTTTCTTCAGTTGTGCATTT[A/C]TTCTACCCAGCCCCCATAAAAGGGAAGGGCATGCC M 2 1 2 1 101000 r 74 goat snp20852-scaffold205-38960 16 47966781 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437383 Affx-122932440 AX-123307721 16 47026225 ACGCCAAACACCTCTCCAGCTGGATGGACGCTCTC[A/G]GCTCTGCTTCCAGAGTCCAGTTCTAAACCTCCTCT R 2 1 2 1 201000 f 74 goat snp20851-scaffold205-9575 16 47995577 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452886 Affx-122920222 AX-123323219 16 47105083 GGGTCCCAGAAGCTTCGTTGGCAAAGCCACAAGCA[G/T]CAGAGGGGTGGAGACTGCTAGGCTCTTTGGCAGAG K 2 1 2 1 303000 f 74 goat snp37106-scaffold4500-69184 16 48073496 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406653 Affx-122955810 AX-123277005 16 47189009 CTCCCGGGAGTGGGCTCCGCCCCTCGGTTCTGGGG[A/G]CAGGGTGCCCAGAATCACCTTGGCTTTACAAACAC R 2 1 2 1 101000 r 74 goat snp37107-scaffold4500-153110 16 48143865 C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439403 Affx-122930248 AX-123309740 16 47227493 CTTCTCTAGAGAGAGCCTTTGGAAGAACTCACGGG[C/T]GCAAAGTGCTGCCCCACAAAAGTGGGCCACGCTTG Y 2 1 2 1 101000 f 74 goat snp37108-scaffold4500-191594 16 48182523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418777 Affx-122946189 AX-123289125 16 47261446 GTTGAAATGTGGGATGAGGAACACTCTCTGCAAAC[C/T]GACCCCATGTGAATGAGATCTTTACCGCAGCTTGG Y 2 1 2 1 101000 f 74 goat snp37109-scaffold4500-225547 16 48216525 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452134 Affx-122921676 AX-123322467 16 47311143 TCACACCCATAGGGGTGCTGCCATCAGAGATAGTA[C/T]GCGCATAGGGACGTCGCACCTGGTATGCCACCTTT Y 2 1 2 1 101000 f 74 goat snp14803-scaffold1599-43270 16 48264348 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399656 Affx-122960517 AX-123270011 16 47365093 TGCTGGAAAACCCAAAGACTGCATCAGCTACCACA[C/T]GTATTTATATCTGTGTGTTTGTGTGTCTGTGTGTT Y 2 1 2 1 101000 f 74 goat snp14804-scaffold1599-97220 16 48318607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404097 Affx-122957125 AX-123274449 16 47399065 CAGGATACACTTGGTTGTCACAAACAGGGTGGGGC[A/G]CTCTGGGCATCTGGTGAGTTGAACATCCTATACCG R 2 1 2 1 101000 f 74 goat snp14805-scaffold1599-131192 16 48352293 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400062 Affx-122960766 AX-123270417 16 47442653 CGTGAGCTGGGGCGAGCTTCTGTTTCCTTAGACGC[A/C]GAGAAAAATCCCCACGCAGATGTCTGATGGCTCAA M 2 1 2 1 101000 r 74 goat snp14806-scaffold1599-174780 16 48394766 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274272 Affx-1111834104 AX-519547869 16 47456951 AGGCTGGCTCACTACAGACCTCTTCCTGAGCCTCT[A/G]CAGGTTTGTGTGGACACATGTATATTGTGTATCCA R 2 1 2 1 201000 r 74 goat GoatD01.018504 16 47456951 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38429150 Affx-122937989 AX-123299492 16 47484551 GTGGGTGAACACGTGCATGTGTGCATGTATGTGCA[C/T]GCCTGTGGGAGTAAATGCTGCTGTCTGCAAACGAC Y 2 1 2 1 101000 r 74 goat snp14807-scaffold1599-216678 16 48435817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451266 Affx-122921926 AX-123321599 16 47612243 CATGGAAATGAAGGTGGCCTCAGAGAGCATCTCCA[C/T]GCCCCTCTCCTGGGGGAGCCCTCCTTGCCTGTCAT Y 2 1 2 1 101000 f 74 goat snp14809-scaffold1599-344370 16 48565329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800665 Affx-122957448 AX-385287583 16 47641599 AGTATTGCTGTATGTTTAATTATAGATAGATAAAC[A/G]TATTGTTTCAAAGTGCTAAGGTTTTATTTCACTGT R 2 1 2 1 202000 f 74 goat snp14810-scaffold1599-373726 16 48594736 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400298 Affx-122960075 AX-123270653 16 47694346 AGGGAAAGTCAAGGTCACGCAGCCATGGTCTGTGA[C/T]GACTTCTGACCGCAAACAAATATATATGAAAACGA Y 2 1 2 1 201000 r 74 goat snp14811-scaffold1599-426473 16 48647511 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436213 Affx-122932583 AX-123306552 16 47745159 TTGTCCAGTGAGAGCTGAAGCTCAGCCAGGGACAC[A/G]TGACCTGTGACTCAAAGTTTTCACAGTTCTGCACG R 2 1 2 1 101000 r 74 goat snp14812-scaffold1599-477286 16 48698775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446584 Affx-122924822 AX-123316920 16 47831361 TACCACTAGTCACAGCTAGAAGGCCACAGAGGACC[C/T]GTGTGGAATGTGCCCTCACTTTGGGGGGCGGGAGA Y 2 1 2 1 101000 f 74 goat snp14814-scaffold1599-563488 16 48784913 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430216 Affx-122937334 AX-123300557 16 47867403 GGCCAGTGGGGGAGTGGGAGAGGGCAGGCTGGTGG[C/T]GAGGCAGGCATAGCAGCGGGAGTGTGCCGGTCCAA Y 2 1 2 1 201000 r 74 goat snp14815-scaffold1599-599530 16 48820952 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377204 Affx-122978182 AX-123247563 16 47953255 GGCAGGAGGTCTGCAGTCACTCTGTGCAGCTCAAG[A/G]GTCCCTGAGCAGGACAGGGTGGAAGAGAGGGGTGG R 2 1 2 1 102000 f 74 goat snp14816-scaffold1599-685382 16 48907200 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435223 Affx-122933621 AX-123305563 16 48024028 AGAGCTGGTCCTAAGGACGCCTAAGAACTGAGGCC[A/G]TAGAGCCAGGAGGGACTGTCCAGGAGAAGCAGGCT R 2 1 2 1 101000 f 74 goat snp14817-scaffold1599-756155 16 48978064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381636 Affx-122974763 AX-123251994 16 48087625 GCAGGAGCCGGTGGGGATGCCTAGGCCAGCTCAGC[A/G]TTTCCAGAAAGGCCAACCTGCACACACAGGACCCA R 2 1 2 1 101000 r 74 goat snp14818-scaffold1599-819752 16 49040852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392832 Affx-122965778 AX-123263189 16 48155930 GGGAAGCCACCTTCTGAAACACCCTTCTCCTCACA[G/T]GTGCCCTCATGCTGAGACTCTAGCCCACGGGGTCG K 2 1 2 1 101000 f 74 goat snp14819-scaffold1599-888057 16 49104961 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445291 Affx-122925452 AX-123315628 16 48184709 GAGAGCAAAAGGGCCCGTGGGACCCGGTGAGAAGA[C/T]AGGGATGCGGATGTGGAGTCTGAGGGGGTAGCAGC Y 2 1 2 1 101000 f 74 goat snp14820-scaffold1599-916836 16 49133688 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392765 Affx-122965995 AX-123263122 16 48216376 AAAACAACACACCCCTATTTCTTCAAAAAGAAACA[C/T]AGGAAGAATAAGCACAAAAGAGGAATGAAATTGGC Y 2 1 2 1 303000 f 74 goat snp14821-scaffold1599-948503 16 49165093 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426882 Affx-122940471 AX-123297227 16 48254350 TAGGGAGTCTTGAAAACAGCAGAAATCTGTTCCCA[C/T]GGTGGAGGGCAGAAGCCTGCGGTGAGAGTGGGGCA Y 2 1 2 1 101000 f 74 goat snp14822-scaffold1599-986477 16 49202859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397908 Affx-122961945 AX-123268263 16 48324577 TTTTTTTTTTTGCTATTCAGTTGTGTGAATTCTTT[A/G]CATAGTTTGGGCATCAACCCCTTATCAATGTGATT R 2 1 2 1 101000 r 74 goat snp14823-scaffold1599-1056704 16 49273896 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446972 Affx-122924655 AX-123317308 16 48436735 CAGCCACACTGCCTCCACCAGCAAGGCCTGCTAAG[A/G]CACGCGGGACACCCAGTGGAGTTCATCGTAGTTTG R 2 1 2 1 101000 r 74 goat snp14825-scaffold1599-1168862 16 49385587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277015 Affx-1111835703 AX-519550522 16 48512960 GGGTCTGAGGGTGTCACAGAGAAATTGTGCCTGAT[A/G]CTAGTCAGCAGGACAAAGTTTCTGTGCCCCCCCAC R 2 1 2 1 101000 f 74 goat Random2.2K-1603 16 48512960 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388112 Affx-122969488 AX-123258470 16 48523810 CGTAGGTTAGAGGCAGGCTCTTCTAAAGGGGCTCC[A/G]GGAGCCCTGTTTCCGCCCAGCCAGTCTGGAGCCTC R 2 1 2 1 101000 f 74 goat snp14826-scaffold1599-1255937 16 49473334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433553 Affx-122934988 AX-123303894 16 48649969 TCTCAGAATCCTATAAACACGTGGAGCACACAGCT[C/T]AAGGCCAAATGGGCTGCTCTGGCGTCCAAGAAGAC Y 2 1 2 1 102000 f 74 goat snp14828-scaffold1599-1382096 16 49598721 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451964 Affx-122920949 AX-123322297 16 48713294 AACTCTTTGCTCCCCTGACCCCTCGTGTTCACTTA[A/C]ATTTTTAAATTCTTTTTCCTTCCTTCATTTTGAAA M 2 1 2 1 201000 r 74 goat snp14829-scaffold1599-1445421 16 49662363 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796620 Affx-122959554 AX-385283566 16 48770810 TTCTGTGTGTGTGTTGTGCTTCTGCGTGCATACAT[A/G]TTTGATGGCCCATGTGCCTGTCAGGCCTTGGCACG R 2 1 2 1 101000 f 74 goat snp14830-scaffold1599-1502937 16 49718086 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392891 Affx-122965735 AX-123263248 16 48810586 GAACAGACGGGGAAGAGGAAGACCAGAGTGTGTGT[A/C]GTTGAGGGAAAGGAAGTCATTTCCCGAGTGCTCGC M 2 1 2 1 201000 r 74 goat snp14831-scaffold1599-1542713 16 49748617 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407870 Affx-122954506 AX-123278221 16 48916418 CAGCCTCATATTTCAAACTGCCAGAGCCAAGCTGG[C/T]GCCACCCCTGCACCCTGCATGTCCACCTTCCACAC Y 2 1 2 1 101000 f 74 goat snp14833-scaffold1599-1648545 16 49853113 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271967 Affx-1111833072 AX-519545739 16 48924293 TTTACAATTATTATAAAATATTGGCTGTATTCCAC[A/G]TTGTACAGTATATCCTTGTAGACTGTCTTACACTG R 2 1 2 1 303000 f 74 goat 16_48924293_AF-PAKI 16 48924293 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38379661 Affx-122975934 AX-123250019 16 48948906 TGCCATGTATTTGCCATGTGGTCTTGTGCAAGCCC[A/G]TTTTCCACTCTTTAAAAGGAGTCTATTGTACGCGT R 2 1 2 1 101000 r 74 goat snp14834-scaffold1599-1681033 16 49885140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421384 Affx-122944035 AX-123291731 16 48987476 GTGAGTTACCAGAGGGCTGTCAGTGCCCTGGGGAG[A/G]CCAGGCGGCCAGCAGGTGTGCTCCAGCCTCCTGGC R 2 1 2 1 102000 f 74 goat snp14835-scaffold1599-1719603 16 49923293 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414554 Affx-122949393 AX-123284903 16 49027186 TGGCTTTGCTACAACTTTATTCACTACGCTGCATG[A/G]GGAGCCCTCCCTAAGGCCCTCCTGGCCCTTCCCTA R 2 1 2 1 101000 f 74 goat snp14836-scaffold1599-1759313 16 49962998 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429843 Affx-122938161 AX-123300184 16 49081361 CAATTCCTGGAGCTCCAGCTAGCTGCCTTTGCTTT[G/T]CCAAGCACAACTGACTGCACCCCCAACGTCTGGGT K 2 1 2 1 101000 f 74 goat snp14837-scaffold1599-1813488 16 50015884 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392817 Affx-122965789 AX-123263174 16 49204153 TGGGCACTCCCCTCAGTGGTCGCCTCAGGACGTTC[A/G]GGGTCAACTTTGGGTTCGTTTCTTCCCCTCTTCCC R 2 1 2 1 101000 r 74 goat snp14839-scaffold1599-1936280 16 50139871 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381616 Affx-122974777 AX-123251974 16 49253495 CTCGGAGAAAGGCAATACACTTAGCTGGTTCTGCA[A/G]TGTGCACAAAGGAAGACCTACCTGGCCCTGTTCTT R 2 1 2 1 101000 f 74 goat snp14840-scaffold1599-1985622 16 50189132 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410748 Affx-122952697 AX-123281098 16 49374608 CAGTCACCTTCTGAGGTTAGAACTTCCCTACATGA[A/C]TCCGGGGTCAGGGAGGGGACACAACACAGCCCCTC M 2 1 2 1 101000 f 74 goat snp30157-scaffold331-1670999 16 50309902 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428441 Affx-122938817 AX-123298784 16 49405821 AGATGCTCCTCTTTCTTCATTCCCAAGATGATCTC[A/G]TCCAATTCCACAGCTTTAAATACCATCCAAAGACT R 2 1 2 1 101000 r 74 goat snp30156-scaffold331-1639786 16 50340425 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779383 Affx-122921218 AX-385266487 16 49439951 TTAAAACAGGCATTATTATTAATGTCCATTGTCCT[C/T]ATCCTCTTCTGCTGTCCTGTAGTACTGACCTCGTC Y 2 1 2 1 101000 f 74 goat snp30155-scaffold331-1605656 16 50374145 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453717 Affx-122919632 AX-123324050 16 49597585 CAGGATTGTAGTTCACAGGATTCTGGGTCTCATAG[C/T]AAAGAACCATCATCCAAATTGTCAATAGCGCCACA Y 2 1 2 1 101000 f 74 goat snp30153-scaffold331-1448022 16 50532013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275661 Affx-1111834937 AX-519549231 16 49656416 TGACCTGCAGTTGGTTCCTCCGCAGTGTCTCGGAG[A/C]AGTGCTTTGGCAGGAGCACAGCCAGAGGAGAGGCT M 2 1 2 1 202000 r 74 goat GoatD01.059268 16 49656416 A C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38382970 Affx-122973355 AX-123253328 16 49693233 AAGATGGATGGCAACTTGTGTTATTTTGATGGGAG[A/G]GTAGCGTTGCCCTCATCCTCCTGTCAGCAAGCCCT R 2 1 2 1 201000 f 74 goat snp30151-scaffold331-1352374 16 50627327 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416929 Affx-122948043 AX-123287277 16 49764549 CTCGAGGTTCATTCCGGCTGAATAATGTTTCATGG[C/T]GTGTATTCCCCACAGTCTGTTTGTTCTTTTGTCCA Y 2 1 2 1 201000 r 74 goat snp30150-scaffold331-1281058 16 50699711 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386102 Affx-122971433 AX-123256460 16 49803285 GATTTATCCTCTGTTTTTGAAATTTAAATGGATGA[C/T]AAGAAATGAGGTTCCAAGACTTTCCCATACCCTTT Y 2 1 2 1 101000 r 74 goat snp30149-scaffold331-1242322 16 50738839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434203 Affx-122934859 AX-123304544 16 49842214 CTCGTTTGCACAGGGCTCTTCATCTTTTCCTGAGT[A/G]CACAGTCTACAAGAACCTGTCCTAAAAGAACAGGA R 2 1 2 1 101000 r 74 goat snp30148-scaffold331-1203393 16 50778009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440527 Affx-122929338 AX-123310864 16 49870835 CCTTGATCCTCATAATAGTTCTACAACATGGGGAA[A/G]CTGAGGTCGGAGTATGCCAGCTACTGTGCAAACAA R 2 1 2 1 101000 f 74 goat snp30147-scaffold331-1174772 16 50806561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782402 Affx-122960136 AX-385269478 16 49917608 TTTTCTTTAAAGTCCACGTCCCACAGTTGGCTCAC[G/T]TATCTTATGAGCTGTTGAATCAGTGGTGTTCAAGT K 2 1 2 1 201000 f 74 goat snp30146-scaffold331-1127999 16 50852725 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396145 Affx-122963391 AX-123266500 16 49985464 AGAGCACTGACCTCAGTGAGCAGAGCGCCTGATGT[C/T]GTGGTCACCTTCTCTTGGGTCTGTGTTTTGAGAGA Y 2 1 2 1 201000 r 74 goat snp30145-scaffold331-1060143 16 50921881 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453837 Affx-122919546 AX-123324170 16 50019856 ACATGAGGAAAAGACATAGATTGGTTAAAGAATTT[A/G]CCAGAGCCACACAGCTCATGAATGGTGGAGCTGGG R 2 1 2 1 101000 f 74 goat snp30144-scaffold331-1025751 16 50956038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432181 Affx-122936402 AX-123302522 16 50060939 CATTGACGATGGAGGCAGGGCCACGAGCCAAGGAA[C/T]GTGCATGCCCTCTCAAAGCTCAAAAAGACAGAAAC Y 2 1 2 1 101000 r 74 goat snp30143-scaffold331-984668 16 50997497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425494 Affx-122941482 AX-123295840 16 50121942 AAATGTGGTCCAGCTTTTGCCATATCTTGAAACTC[A/G]TCAAAAGAAGCCAGAAATCCTATCTTTTACATGAA R 2 1 2 1 101000 f 74 goat snp30142-scaffold331-923665 16 51057608 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412269 Affx-122950889 AX-123282618 16 50181833 GAGGCACAGGTCATCTGCACAGTCTTGCAGCTAAC[A/G]CAGATGGTGGAGATGGGATTTGAACCCAGGCAGTC R 2 1 2 1 101000 f 74 goat snp30141-scaffold331-863774 16 51117626 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384534 Affx-122973030 AX-123254892 16 50226111 TACATTAAAACAATTACATGAGGCTTGAAGGATCT[A/C]ATAGTGCATCAGTCTTTAGGATGAAGTCATTTGAA M 2 1 2 1 101000 r 74 goat snp30140-scaffold331-819496 16 51162540 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449198 Affx-122923513 AX-123319533 16 50290879 TTCTTGCCCATTTTATGCATGAGTTTGTTTCCACC[A/G]CAGTCACAGAATAGAAGCTCATTCATTCACTGAGC R 2 1 2 1 101000 f 74 goat snp30139-scaffold331-754728 16 51227567 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395220 Affx-122964487 AX-123265575 16 50326643 TGTGTGCTGGTGGGGCTTCTTCACTTCCACCCAGC[A/G]TTCTCTGCTCACAAAGCTCACCTCCACTTGTAGAT R 2 1 2 1 101000 r 74 goat snp30138-scaffold331-718964 16 51263132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427736 Affx-122939262 AX-123298079 16 50375435 CATGTTACAGACTTTTGCATGTTGGAACCAGACCT[A/G]CGTGTGGAGTTAGGAGTGGGGAAGGCTATTGGGGA R 2 1 2 1 101000 f 74 goat snp30137-scaffold331-670172 16 51311909 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434984 Affx-122933831 AX-123305324 16 50433132 GTTAAGTACTTAGCACATATGTGCTAAGGATTCCA[G/T]AAATATCACTGTGAGTTTTTAAAACTATGGCCCAA K 2 1 2 1 201000 r 74 goat snp30136-scaffold331-612475 16 51371759 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771849 Affx-122935657 AX-385259005 16 50476061 CCAAGAGCTCTTGATGTGAAGTTGGAAGATGAACA[C/T]GAGTCCCTACCCTTCCTGTATGATCTGTGTGACTT Y 2 1 2 1 101000 f 74 goat snp30135-scaffold331-569546 16 51415203 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423210 Affx-122942709 AX-123293556 16 50526622 CTCCAGTGAAGAGGATGCAGGTTTTGTCCTTTGCT[A/G]CAGGCCTCCTGAGCAAGATAAGGGCATTTAAAGAA R 2 1 2 1 101000 f 74 goat snp30134-scaffold331-518985 16 51465518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768320 Affx-122926641 AX-385255500 16 50639935 GTCTCTGTCGATACTTGGAATTCATGATGGTTTTT[A/G]TTCTCCCTTCGAATTCAAGGAGGGACAGTGTCATA R 2 1 2 1 201000 f 74 goat snp30132-scaffold331-405672 16 51578978 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425241 Affx-122940999 AX-123295587 16 50680628 CAGCTCCTGAACATCAGTGGCCAGTACATGCAGAG[C/T]ACCCAGAAACAGCACACTCCTATAACAAGAAATAA Y 2 1 2 1 202000 r 74 goat snp30131-scaffold331-364979 16 51619990 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377568 Affx-122977441 AX-123247927 16 50724071 CCAGTGTCAGTTAAGAGGTATGCCCCAAGAAACTG[C/T]ATTTAGAAATATAAAGTGTCTGGGGCTGCCCTGGT Y 2 1 2 1 201000 f 74 goat snp30130-scaffold331-321536 16 51663296 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385071 Affx-122971814 AX-123255429 16 50765043 TGCATGACAAGTTCGGAGCTGAAGTGCCTTCAGTC[A/G]TAGCAAAGAGTGGGAGAGAGCAGACAGCTCTGTAA R 2 1 2 1 101000 f 74 goat snp30129-scaffold331-280564 16 51704571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377388 Affx-122977629 AX-123247747 16 50806079 ATTGAAATTCCCAAGAGAGAAAAAGCTGATTGGCC[A/G]TTGGTCAGCCCTCACTGGTTGATCTTAAGCCAGTC R 2 1 2 1 101000 f 74 goat snp30128-scaffold331-239528 16 51745750 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447766 Affx-122924568 AX-123318102 16 50849956 TGGGTAGTTTGGTGGGTGTGTGTGTATGCGTGTTT[A/G]TGTATATGTTTGTCTATCTATGGGTGGCTTGGAGA R 2 1 2 1 201000 r 74 goat snp30127-scaffold331-195651 16 51789518 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394475 Affx-122964568 AX-123264830 16 50894236 AACAGCTGCATTCCTTTGCTTTCTTCTCTTGCACT[A/G]TGACTCTGCAGCCTTTCTCATTCAGAAGGAGAGTC R 2 1 2 1 201000 r 74 goat snp30126-scaffold331-151371 16 51832902 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416876 Affx-122948083 AX-123287224 16 50928689 TCTTTGTAGCAATTTTTATGTTACACTGAATAAGC[A/G]TGGATCTGGGGACACAGAAAGTGTTTAATGAGCAA R 2 1 2 1 201000 f 74 goat snp30125-scaffold331-116918 16 51867504 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384521 Affx-122973040 AX-123254879 16 50975509 AAAAGTACTGTGTTGGGGGGGAGTATGATGCTTCA[C/T]GACAAAGAATTCCTATATTCATTATCCCATTTCAT Y 2 1 2 1 101000 f 74 goat snp30124-scaffold331-70098 16 51914262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439732 Affx-122930542 AX-123310069 16 51021828 TGGGGAGATGAGAGTGAACACCCCTCCTTGTCTTA[C/T]AAGAAGGGCCAGGTCTGCCTTCTTACACATCTGTC Y 2 1 2 1 102000 f 74 goat snp30123-scaffold331-23779 16 51960680 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784408 Affx-122924281 AX-385271457 16 51057062 AAGCAATAGACAAAAGTCCAGACTTTGGAGTGAGA[C/T]AGCTCTGCCACTTTATGTATGTGACCTTGAGTGAG Y 2 1 2 1 101000 r 74 goat snp32668-scaffold376-3495 16 51996017 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769420 Affx-122966595 AX-385256591 16 51121915 CTGTGAATACACACCTTTTACTAGAACATTAAGGA[C/T]GTTGGTGAGAAGTCATGCAGAAGCTAAGGGTACTA Y 2 1 2 1 101000 r 74 goat snp32669-scaffold376-68348 16 52061001 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418068 Affx-122946614 AX-123288416 16 51159759 TACTACATACTGCCACACTCCTGTCTTTTTCAAAA[A/G]AGAAAGTCAAGAGAACCCAGCAAGGACCATCCTTG R 2 1 2 1 101000 f 74 goat snp32670-scaffold376-106192 16 52100105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277017 Affx-1111835704 AX-519550524 16 51190185 TCGTCTGTAATGACTGTATTTGTGGCAAAGCTGGG[A/G]GGATGCCTCCACTCTGGGGTTCCTCCAGCAACTCA R 2 1 2 1 101000 f 74 goat Random2.2K-1605 16 51190185 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390295 Affx-122967725 AX-123260652 16 51191063 GCGTCAACAGTTTAGAAGCTAAAATAGCACAGAGG[C/T]GACCACGACGCAGTACCCATGATGATCACTTTGTT Y 2 1 2 1 101000 f 74 goat snp32671-scaffold376-137496 16 52131256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786268 Affx-122975671 AX-385273303 16 51220338 TGTGTAAACAAAGTTTTGTTATTCACTTTCCTAAG[C/T]AAGTACATTAGAAAAGTCCACCATCTAATCTCGAT Y 2 1 2 1 101000 f 74 goat snp32672-scaffold376-166771 16 52166544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427172 Affx-122939616 AX-123297515 16 51280314 AATGGAGGCTGGTCCCCCATAGGGAATGAAGGGGA[C/T]ATTCCCATTTTTTCAAATGCCAATTAGCCTGAAGA Y 2 1 2 1 101000 r 74 goat snp32673-scaffold376-226747 16 52227523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423411 Affx-122942624 AX-123293757 16 51331505 CAGGAACAAATGCAAGTGTGGCAAGACTGACGGAC[A/G]CATAGAAAACAGATTCCCAATTTGGGACAGAAACA R 2 1 2 1 101000 f 74 goat snp32674-scaffold376-277938 16 52279325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382768 Affx-122973976 AX-123253126 16 51361241 CACTGCTCTCTCTGCAGGACCACCTAAGTCTCTGC[C/T]GAATTACATCTCTTTTTACTGTAGGTACTTAAGAG Y 2 1 2 1 101000 r 74 goat snp32675-scaffold376-307674 16 52308811 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782382 Affx-122974597 AX-385269458 16 51420602 GTCATTATTCAATGCATTAGTTTCCTAAACTACAC[A/G]TTCTCTAATTGAGGTTCAAGTTATAACAGATTGGA R 2 1 2 1 101000 f 74 goat snp32676-scaffold376-367035 16 52368541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380978 Affx-122974685 AX-123251336 16 51468376 AGACTCTGTGCCTAAGTCACATTTGCTTTGCTCTC[G/T]GAGTTCCCAAACATGGTGCAGCACTGATAATAACC K 2 1 2 1 101000 r 74 goat snp32677-scaffold376-414809 16 52416305 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271803 Affx-1111833073 AX-519545591 16 51485607 ATGCTGAATGCAGCTTTCCACCCAGAACATTATGA[A/C]TCTTTCTTCAGGAGCCCGGAGTGAAATCAACCTCC M 2 1 2 1 101000 r 74 goat 16_51485607_AF-PAKI 16 51485607 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38401893 Affx-122958844 AX-123272246 16 51523875 CCCATTACTGCAAAAGGTAGGGGAACAGGCCAGGC[C/T]TTCTGACTGATGGTCTACTTTTTCCTGTTTTATGA Y 2 1 2 1 201000 r 74 goat snp32678-scaffold376-470308 16 52471771 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388021 Affx-122969561 AX-123258379 16 51561508 AAGGATCTGGAAAGAGAGGTCTGTAAGTCACTTCT[A/G]AAAGTGGGATCCTCCCCTGCACCCTCAGGTGGGGG R 2 1 2 1 101000 f 74 goat snp32679-scaffold376-507941 16 52509580 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391449 Affx-122966741 AX-123261806 16 51590481 CATTTTGTTCTCCATCTTTCCAGCTTCTCTGGTGA[C/T]GTGATAGGCAGCATCTAAGATGGTGCCCAATAATC Y 2 1 2 1 201000 r 74 goat snp32680-scaffold376-536914 16 52539027 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421963 Affx-122943808 AX-123292310 16 51667336 TTGACTCACAATTCTCATGGTGTGCATTTTTTTAC[A/G]TTGACAACATTACCCTGTATTATTTTTTGCACAGC R 2 1 2 1 101000 r 74 goat snp32682-scaffold376-613769 16 52615844 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450333 Affx-122922125 AX-123320668 16 51715831 GCCTGGTGAAGATGAACCCAAACCCAAATTATAGT[A/G]CTCATTCTAAAATATTCCTCCAAGAGTCAGGATCA R 2 1 2 1 101000 f 74 goat snp32683-scaffold376-662264 16 52664817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783031 Affx-122968712 AX-385270099 16 51763480 CATATTTCTACCATGAATATAAGTGGCCTTTGCAT[A/G]AAGTAAGCTTAAATTGGATTGTACTCATTAGACAT R 2 1 2 1 101000 f 74 goat snp32684-scaffold376-709913 16 52711014 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403541 Affx-122957605 AX-123273894 16 51805260 CAGGGTTGTGAAGAGTTGGACACGACTGAAGCAAC[A/G]CCACATATATAGAAGCAAGGCCTTTCTTACTCATG R 2 1 2 1 101000 r 74 goat snp15706-scaffold1651-634458 16 52775140 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800472 Affx-122957525 AX-385287392 16 51838912 TATATGAAGAAGCATCTTGAGCTGATATAGAAATC[G/T]ACAACAGTGGACAAACTCCAAGTTGGTCATTCTCA K 2 1 2 1 101000 r 74 goat snp15705-scaffold1651-600806 16 52808766 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415577 Affx-122948631 AX-123285926 16 51869566 TGGGATCCCCAGCTTGGACTCTGCAATTTCTTAGT[A/G]TCCACTGACATCACATGAAGTCTGTTTGTCAGTCC R 2 1 2 1 101000 r 74 goat snp15704-scaffold1651-570152 16 52839672 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274161 Affx-1111834078 AX-519547762 16 51899719 CTGCAGCATTCTGTCCTATTTGCATGAGTAAGGAG[A/G]ATTTCTGCAGCTGATCCACTATATTTCACCACAAT R 2 1 2 1 101000 f 74 goat GoatD01.017316 16 51899719 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407204 Affx-122955804 AX-123277555 16 51936393 GAGAAAAACAGAATTTTATTTCTGTGCCTAATGGT[A/G]TCACCTTGATCAGACTCTGTGTTGAACATAGCTAA R 2 1 2 1 101000 r 74 goat snp15703-scaffold1651-503325 16 52906978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388205 Affx-122969419 AX-123258563 16 51971019 TGTATTTAATTCAGTCACAAGGAGGATGAAATGAT[C/T]CTGGTTGAAATAAAATTGGGCATTCTGGGTTTGAT Y 2 1 2 1 201000 f 74 goat snp15702-scaffold1651-468699 16 52941620 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440305 Affx-122930215 AX-123310642 16 52021928 TTCCTTTTAACCCAGCAGTGTGACTCAGCAGTTTC[G/T]CCAAGATGGCCATGAAGTGGAGGTCCCCACAGAGG K 2 1 2 1 101000 f 74 goat snp15701-scaffold1651-417790 16 52992905 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417893 Affx-122946749 AX-123288241 16 52053058 GACCTGGAATGAAGAGTTGATCCTTTGAAAGATTC[A/G]CATGATCTGATGAATTCTTTCTTGTTCCCCATGAT R 2 1 2 1 101000 f 74 goat snp15700-scaffold1651-386660 16 53023164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446727 Affx-122924717 AX-123317063 16 52117920 TCTGATGCCCTCTCTGGTCTAGGCAGCCTTTAAGT[A/G]ATAAGAATTCTAGATGGAGATGCTAGAGGTGGTAC R 2 1 2 1 101000 r 74 goat snp15699-scaffold1651-321798 16 53082260 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476324 Affx-1251763831 AX-586011741 16 52145391 CTAACGATTTCAGACTCTACCACCCTCTTCTCCTC[-/TTGCCTTCAATCTTTTTTTTTTTTAATTTTTTATTTTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCC]TGCCTTCAATCTTTCCCAGCGTCAGGCAGGGTCTT - 4 1 4 1 20000 f 74 goat SV_271 16 52145391 - deletion junction SV-TF-chip 539476577 Affx-1251763831 AX-586011963 16 52145391 CTAACGATTTCAGACTCTACCACCCTCTTCTCCTC[-/TTGCCTTCAATCTTTTTTTTTTTTAATTTTTTATTTTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCC]TGCCTTCAATCTTTCCCAGCGTCAGGCAGGGTCTT - 4 1 4 1 20000 r 74 goat SV_271 16 52145391 - deletion junction SV-TF-chip 562165206 Affx-1251763831 AX-606940618 16 52145391 CTAACGATTTCAGACTCTACCACCCTCTTCTCCTC[-/TTGCCTTCAATCTTTTTTTTTTTTAATTTTTTATTTTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCC]TGCCTTCAATCTTTCCCAGCGTCAGGCAGGGTCTT - 8 1 4 1 20100 r 74 goat SV_271 16 52145391 - deletion junction SV-TF-chip 562165737 Affx-1251763831 AX-606941146 16 52145391 CTAACGATTTCAGACTCTACCACCCTCTTCTCCTC[-/TTGCCTTCAATCTTTTTTTTTTTTAATTTTTTATTTTTTTTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCCCCCCC]TGCCTTCAATCTTTCCCAGCGTCAGGCAGGGTCTT - 8 1 4 1 20100 f 74 goat SV_271 16 52145391 - deletion junction SV-TF-chip 38400614 Affx-122960382 AX-123270969 16 52154893 TTATTGATGAGTAGTATTTTAAAAACAATTTACAC[C/T]GATAAAGATACAATAGGCATTCCACAAGACAGTGC Y 2 1 2 1 101000 r 74 goat snp15698-scaffold1651-284825 16 53119446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771014 Affx-122941237 AX-385258176 16 52207217 TGTGGAGCCCATTATATTCAGCTGTACTAACCCCT[A/G]CCTAGGTTGTTTTCTCTATCCAAACCTTTCTCTGG R 2 1 2 1 101000 f 74 goat snp15697-scaffold1651-232501 16 53173013 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379289 Affx-122976212 AX-123249648 16 52241039 AAATGAAAAGTCCACAGGAGACTCTGGGGGGCTCT[A/C]GGGGTGAGTTATTTCCTTGCCTTTTCCAGCTTCCG M 2 1 2 1 101000 f 74 goat snp15696-scaffold1651-198679 16 53206871 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787719 Affx-122956318 AX-385274742 16 52289552 GGTTTGATCCAGGAACTCAAACAGTATCACCAGCT[A/G]TGTTCTCTTTACTATAGTCTATGCTTATGAACTTC R 2 1 2 1 101000 f 74 goat snp15695-scaffold1651-150166 16 53256763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396648 Affx-122962861 AX-123267003 16 52323975 GACCTGCTAGATGCCAAGTAGCACCTGCGCCCCCT[A/G]TTGTGACAATCAAAAATGTCTCCAGACATTGGCAA R 2 1 2 1 303000 f 74 goat snp15694-scaffold1651-115743 16 53290590 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438787 Affx-122931372 AX-123309124 16 52403415 GTTATTCCTCCTTTTCCTTCCTAGACACAGTGCTT[A/G]CTTTCTTGATTGCCCCAGGCTTTTTTTTTGGCCCC R 2 1 2 1 101000 f 74 goat snp15693-scaffold1651-36303 16 53371942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775160 Affx-122966955 AX-385262292 16 52458306 AACTAAATTTGAGAGGTACTTTTCAGGCTATTGAA[C/T]AGAAGAATTCTCCTTAAATATATCTGTGGTAACTA Y 2 1 2 1 101000 f 74 goat snp8715-scaffold131-5959371 16 53430798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786764 Affx-122963425 AX-385273795 16 52518935 CAAATAGGGATGAAGAGCATACCATTTTTAACTAA[C/T]AGGAGGTTTTTGTTGTCAGTAAGAGTGATAGGGAC Y 2 1 2 1 101000 f 74 goat snp8714-scaffold131-5898742 16 53483524 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788697 Affx-122973127 AX-385275713 16 52574978 AGTGACAAAAACTTTACAACTCTATTTTTAACAAC[G/T]TGGGTTTATGCTGATGAAAATTACTTTATTACATG K 2 1 2 1 101000 r 74 goat snp8713-scaffold131-5842699 16 53537167 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435898 Affx-122932774 AX-123306237 16 52605366 CACTTTTATCCAAGTAATGAACTCAGTGATCCTGC[C/T]CAGGACTTTCCCAAATAGTGTTCAAGTGCCACCTG Y 2 1 2 1 101000 f 74 goat snp8712-scaffold131-5812311 16 53568085 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435582 Affx-122933365 AX-123305922 16 52649451 ATAGTCAGTATTCAGTTAGCTCTTTAAATTAAGTC[A/G]CTGTTTTCTTCAGATTGAAACTATAAGACATGGTC R 2 1 2 1 201000 f 74 goat snp8711-scaffold131-5768226 16 53612668 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402602 Affx-122958420 AX-123272955 16 52679509 CTCTGCCTTACATGAAGTTATGCCATGCACTTACA[C/T]GAACTATCTAAAAAGCATATGAGGACTTTGTTTTT Y 2 1 2 1 101000 f 74 goat snp8710-scaffold131-5738168 16 53643296 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383055 Affx-122973286 AX-123253413 16 52710313 GAGAGAACGGCATGCAAACATATAGGCAAAAAAGA[C/T]GAAGGGGGATAGCATGTCCAGGAACTGCAAGCAAT Y 2 1 2 1 101000 f 74 goat snp8709-scaffold131-5707364 16 53674210 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416867 Affx-122948090 AX-123287215 16 52743060 ACCCAGGAGGAAGTTGACTTGTTCATGGACTGCCT[A/G]TATTCACATTTCCATAGGCATTTCAAAATTCATTT R 2 1 2 1 201000 r 74 goat snp8708-scaffold131-5674617 16 53707687 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432957 Affx-122935284 AX-123303298 16 52791475 CATTTTTTTTTTCATTTACTGTGATTTAACATGAT[A/C]GTGTCTTTTTCAGGGCATTTATGATACGAGTCAGA M 2 1 2 1 101000 r 74 goat snp8707-scaffold131-5626202 16 53756442 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793109 Affx-122976317 AX-385280087 16 52848775 ATAATAAATATGTTCCCAATGGGTGAGTTTTCAAT[A/G]CTGCACTGAACAAAGTGGGTAAAGATCCCTTTGAA R 2 1 2 1 101000 r 74 goat snp8706-scaffold131-5568902 16 53813513 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277151 Affx-1111835705 AX-519550657 16 52859193 AGGAGCTCAGAACTAGAGTAGTTCAGGGTGACACC[A/G]CTCAGATTCACGCTGTTTAGCTGATTGATATTTGG R 2 1 2 1 101000 r 74 goat Random2.2K-1607 16 52859193 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383411 Affx-122973489 AX-123253769 16 52965754 CATTATCCTTGAATTCTGTAAGAAAATTCCTTGTC[A/G]TTAAGATAATTACCCTGTTTGCTTAAGTTGCCTCA R 2 1 2 1 101000 f 74 goat snp8704-scaffold131-5451923 16 53930931 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763333 Affx-986697862 AX-385251235 16 53043874 AGACGCAGTGAGACTCTGATGGCCATGGTGCAAGC[C/G]TGGCCCTTTGCCCGCCTGCCTCTAGGGGGGCTGAT S 4 1 2 1 600010 f 74 goat 16_53043874 16 53043874 Ancestral_priority_1043 ancestry 0.504 neutral IMAGE 10K 10K ancestral 38419228 Affx-122945682 AX-123289576 16 53055364 ACAGTTTACAAAACCACCTTAAAAGTACTACTGTA[A/G]TAATACTTTTAAAAGCATTTAAAAGTAAATGCCAG R 2 1 2 1 103000 f 74 goat snp8702-scaffold131-5362313 16 54021849 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389638 Affx-122968739 AX-123259996 16 53088072 ACAGATTGTTTAAAATGTAAAAATGAGAATACTAC[A/G]TATCAAAATCTTGCTGGTTTTGTTCCACAATACCT R 2 1 2 1 201000 r 74 goat snp8701-scaffold131-5329605 16 54054566 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378503 Affx-122976651 AX-123248862 16 53157913 ATACTCATTTTCTGTAATCAATAAAAGCCATACGC[A/G]CACACACACATGGAAATAGTTATCTTAAATGTGAT R 2 1 2 1 101000 f 74 goat snp8699-scaffold131-5259764 16 54125163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784143 Affx-122977932 AX-385271195 16 53214833 AAAATGCATGGTAAGTCTATTAAATAGCAACTACA[C/T]TGTATACCACAAAGCAGATTAATACTATGGAAATA Y 2 1 2 1 101000 r 74 goat snp8698-scaffold131-5202844 16 54180276 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390084 Affx-122968030 AX-123260441 16 53256689 TCAGCTCAGTTCAGCATGGCTTCTCTCTTTTATGT[A/G]AGTAATACATGACCTCTCTCCATGCCACTAATTTC R 2 1 2 1 201000 r 74 goat snp8697-scaffold131-5160988 16 54225579 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790826 Affx-122957211 AX-385277826 16 53297138 ATCTTTTAATTTTCAGTTTTTACTTCCACAAAAAT[A/C]TTAAAGGCTTTACTAGAAGTAGATTCTGATAATCT M 2 1 2 1 202000 f 74 goat snp8696-scaffold131-5120539 16 54266591 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448672 Affx-122923333 AX-123319008 16 53355401 GCCTCTGAAAAGGTAGGTAGGGGAATGAATACACT[A/G]TGGCTCTTCTCAGTCCTGGCAAAGATTTCTTCTTC R 2 1 2 1 101000 f 74 goat snp8695-scaffold131-5062276 16 54323821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766240 Affx-986697864 AX-385253636 16 53370964 CTGGGTTTCATTTTGACTTTTAGGGATTAATTGAT[C/T]TAAGTCTGTATATTGAACCATGGTCATTCTCTTTT Y 2 1 2 1 600010 r 74 goat 16_53370964 16 53370964 Ancestral_priority_1043 ancestry 0.782 recommended IMAGE 10K 10K ancestral 38376647 Affx-122979019 AX-123247006 16 53386905 GTCTGTGGGGCTGCAAAGATTCGGACACGACTGAG[C/T]GACTTCACCTTACCTTACCTTAACATGTATTTACT Y 2 1 2 1 303000 f 74 goat snp8694-scaffold131-5030772 16 54355919 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763337 Affx-986697866 AX-385251239 16 53417265 ATCCAACACCCCTCTACTACAGGTGGTCGAATGGA[C/T]AGAGAGAGGACCAACTGTTTCAACCAATGACTCTA Y 2 1 2 1 600010 f 74 goat 16_53417265 16 53417265 Ancestral_priority_1043 ancestry 0.44 neutral IMAGE 10K 10K ancestral 320803932 Affx-986696301 AX-385290638 16 53417280 ACTACAGGTGGTCGAATGGACAGAGAGAGGACCAA[C/T]TGTTTCAACCAATGACTCTATACATATGCCTTCTC Y 2 1 2 1 600010 r 74 goat 16_53417280 16 53417280 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 38447418 Affx-122924393 AX-123317754 16 53429192 GATAATGATTTGATGTTCAGTGTGGAGGAGCGAGC[A/G]TGCTCATTCATGTACAATTCTTTGGGAACCCATGG R 2 1 2 1 101000 f 74 goat snp8693-scaffold131-4988485 16 54398565 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795916 Affx-122949701 AX-385282868 16 53459228 TTGGGACATCTTTCTGAAGCAGAAAGAAAGGCAAT[A/G]CTCTAAGAATGACGGAGTACATCTATCACTTGAAG R 2 1 2 1 101000 f 74 goat snp8692-scaffold131-4958449 16 54429085 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453816 Affx-122919560 AX-123324149 16 53490685 GGAGGCTGGATGTGTGGAAAGAGGAGTTAGATGCC[A/G]CTATAGTTACAGTGCAAACAGAGGGATGGCTGAGT R 2 1 2 1 101000 f 74 goat snp8691-scaffold131-4926992 16 54460587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452264 Affx-122920764 AX-123322597 16 53523844 ATTCCATCTTATAGATCTTCACTGGCTCCTCCCTG[C/T]ACTTGGAATGAAATCCCAGGTCCTCTCGACATGGC Y 2 1 2 1 101000 f 74 goat snp8690-scaffold131-4893833 16 54494825 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452296 Affx-122920684 AX-123322629 16 53555138 CTGTCATTTACTTTTAATCCTTGTCAGAAAGCAAA[G/T]AATCTATTCTGATTAGAAGTTTTCTCTGCCAACAT K 2 1 2 1 101000 f 74 goat snp8689-scaffold131-4862539 16 54526255 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395393 Affx-122963964 AX-123265748 16 53601070 AACATTGCACGTGGTAGGATTCCTCTTAGGACCAC[C/T]CTGGGCAGATTAACCATCGATCCCATATCATTAGG Y 2 1 2 1 101000 r 74 goat snp8688-scaffold131-4816607 16 54570136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435697 Affx-122933318 AX-123306036 16 53634734 GCTGGCCTGTGTTCTACAGGTGTTCCTGACAACAG[C/T]ATGTTCCGCTCCTTAGCCCTGTGAATGGGGAAGGT Y 2 1 2 1 101000 f 74 goat snp8687-scaffold131-4782943 16 54603850 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769750 Affx-122978207 AX-385256920 16 53683816 TTTTTATAACAATAAGTAATCATTCAATCACATAA[C/T]AGGAGTATTTGAATGAGCTATTTTCAACATCTTGA Y 2 1 2 1 101000 r 74 goat snp8686-scaffold131-4733861 16 54653002 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796471 Affx-122934783 AX-385283421 16 53727006 ATACTGTGCATTCTTCTTCCAATAAAGTTTCCTTT[C/T]TGTATCTTGGAATCTAGCCATGAAGATAAAACAGA Y 2 1 2 1 101000 f 74 goat snp8685-scaffold131-4690671 16 54696392 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787145 Affx-122968675 AX-385274171 16 53779070 ACAGATCATAAGAACATGAAAGCTGCTGACTTCTG[A/G]CATATCACTGATAACCTACCTTTCCCTTTGAATCA R 2 1 2 1 101000 f 74 goat snp8684-scaffold131-4638607 16 54748373 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782538 Affx-122974383 AX-385269613 16 53828035 CCCAGTTTCACGTCTAGGGGAAGGGGAGTGAAAAG[G/T]CAGAGAAATCTTTTAAGGAGAGAGGCCATCTCTGA K 2 1 2 1 202000 r 74 goat snp8683-scaffold131-4589642 16 54797494 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785820 Affx-122975136 AX-187083743 16 53868034 AAAATCTTTAATTCTTAATAGTCACCATTTATTTC[A/G]TATCAGAAAGTGGAGGAAATAAATGCTGAAGGACC R 2 1 2 1 101000 r 74 goat snp8682-scaffold131-4549643 16 54838941 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786740 Affx-122955771 AX-385273771 16 53902153 CACACACACTATAAAAAGGTGGACTTTATAGTATG[C/T]AAATTATAACTCAATAAGTCTGTTCTTAAAAAATG Y 2 1 2 1 201000 r 74 goat snp8681-scaffold131-4515524 16 54872876 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442057 Affx-122928389 AX-123312394 16 53945720 TTCTTGACATATCTCCCAAATGCACACATGCACAA[C/T]ACCACAGGTACCCAGGCAAGTATATTCTGTTCATC Y 2 1 2 1 101000 r 74 goat snp8680-scaffold131-4471957 16 54916377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431156 Affx-122936568 AX-123301497 16 53985871 GGGTGTGCTCTAACCTGCTGTTTTGTAAGGACTGC[A/G]TCATCCACCCAGAGTGAGAACATCCTGGTCAGTCG R 2 1 2 1 101000 r 74 goat snp8679-scaffold131-4431806 16 54956728 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800580 Affx-122949935 AX-385287499 16 54019653 AAAACAACTGCAACAAATGAACCCAAAGTTAAGGA[C/T]GGATGGAAGCCTAGAGCCAATTAAAGCAAAATGGG Y 2 1 2 1 101000 f 74 goat snp8678-scaffold131-4398024 16 54990552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440641 Affx-122929948 AX-123310978 16 54102110 CCGAGCGTCTCCTGCCATGACCGCTGTGCAAATCC[C/T]GAACTCTCTACTGCAGTGGTCCTTACCTGTCTCTG Y 2 1 2 1 101000 r 74 goat snp8676-scaffold131-4315567 16 55072179 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795637 Affx-122938727 AX-385282592 16 54154963 TCATGAGGGACATGGGAACAAAAATATTGCCTGCC[A/G]TATCAGTCAACTAAGGTGCCACAGCTGTCAGCCGT R 2 1 2 1 101000 f 74 goat snp8675-scaffold131-4262714 16 55125941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274224 Affx-1111834076 AX-514944424 16 54159157 GCCTGCAGCATTAGGTACTACAGGGAGGTC[A/C]GGTTGGGATATGATTGGTAGATAAGAGATAAAGAT M 2 1 2 1 101000 r 74 goat GoatD01.017265 16 54159157 A C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38393226 Affx-122965487 AX-123263583 16 54184288 CAAGGAGTTATTAAATATAAAAACCTCCACTCAGA[C/T]GAAAGCCCGGCCTCTAGTAGGCACTTCATATTCAG Y 2 1 2 1 101000 r 74 goat snp8674-scaffold131-4233389 16 55155179 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416896 Affx-122948069 AX-123287244 16 54220584 TCTTCATGTTACAGGGCTCCTTCCTCTCCCTCTAA[A/C]AACCATGGCCCTCTCAATTCGCCATTTAACTCTGT M 2 1 2 1 201000 r 74 goat snp8673-scaffold131-4197093 16 55191511 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795467 Affx-122965848 AX-385282423 16 54326814 ATTCCTCTATACTAGTTTAAACCACATTACCTCTA[C/T]AGGTCATGCTAAGGTGGATGTTCTACGCAAGCTAC Y 2 1 2 1 101000 r 74 goat snp8671-scaffold131-4090863 16 55297902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437656 Affx-122931792 AX-123307994 16 54366328 CTCTGAGGAATGGCACAATATCCCTTGTAGGTAAA[C/T]GACAGGGAGAGCTCCTGGGTGAGGGTTACAGCCCT Y 2 1 2 1 101000 f 74 goat snp8670-scaffold131-4051349 16 55337819 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378150 Affx-122976975 AX-123248509 16 54422032 CCTGATCTGCCCTCCGTTTTGTCATTCTCCCCTTC[G/T]CCCACACTTCCTCCTTTTGGTACACCAGAGAAAGA K 2 1 2 1 101000 r 74 goat snp8669-scaffold131-3995645 16 55393509 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414616 Affx-122949345 AX-123284965 16 54478279 CCATTGGCATCATAGTGAGAGAAACAAGAATGGCT[A/G]TTCCTGTCTGCTTCACAGGTTTGTATGAGATATAA R 2 1 2 1 101000 f 74 goat snp8668-scaffold131-3939398 16 55449724 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422479 Affx-122943320 AX-123292825 16 54506828 AACCTGGGAGAACTCAGTGGATGACACTCAGACAC[A/G]CTTATGTGGTGATGCCTCCAGTCCCAGGGCATCGA R 2 1 2 1 201000 f 74 goat snp8667-scaffold131-3910849 16 55478244 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272878 Affx-1111833075 AX-519546568 16 54558949 TCACTGAGAAATGGTTCACTGTTGTTGTATAGATT[A/G]AGAGAAGACAACAAAAACTATGATTTTTTAAATCT R 2 1 2 1 201000 r 74 goat 16_54558949_AF-PAKI 16 54558949 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449547 Affx-122923249 AX-123319882 16 54561768 TCCTGAAGTATTGTAAACCCTGTAGCCACTGCGCA[C/T]CAGCATCTGTGTGGATGTTCTGTTTGCCTAAATGG Y 2 1 2 1 101000 r 74 goat snp8666-scaffold131-3855909 16 55533087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274443 Affx-1111834202 AX-519548034 16 54588852 AGTATTCTTTTTCCCTGCAGCTAATTCA[A/G]TCAGACTTAGTAAGACAAATGGTTATGCTCTTAAG R 2 1 2 1 101000 r 74 goat GoatD01.025290 16 54588852 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38415654 Affx-122948566 AX-123286003 16 54618046 TTTTCCTAGTGGTTCATCACAAGGAAACCCATCTC[A/G]CTCACCTTTTGTTACAGTGAAATTCTAGTCCCTTG R 2 1 2 1 201000 r 74 goat snp8665-scaffold131-3799631 16 55589456 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426292 Affx-122940303 AX-123296638 16 54646736 AAGAGCCTACACCCATCTACAAGGGATAGACCCAC[A/G]TGTCTATTGACCCTGTAGCTGGAGAATGTAAACAA R 2 1 2 1 201000 r 74 goat snp8664-scaffold131-3770941 16 55618158 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422946 Affx-122943024 AX-123293292 16 54679315 TCACATGGCAGATCTGAACATCCCAGCCAGGTCCA[C/T]GGGTAGCGTCATTTCAGCAACTGGATAAGCTCTTG Y 2 1 2 1 101000 r 74 goat snp8663-scaffold131-3738362 16 55650843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421918 Affx-122943841 AX-123292265 16 54729110 AAAGACTGCTGTGTTGGCTACTTTGAGCTCTTCAC[G/T]AAAGGGAATAATCCCAACTGTGGCCAACCTATGAA K 2 1 2 1 101000 f 74 goat snp8662-scaffold131-3688567 16 55700252 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431740 Affx-122936740 AX-123302081 16 54785191 CTTAAAGACTCTCGTAGGTCTTCAAAAGTGACAAA[C/T]GTGTATATATATACTATATCCTCAGAAAAAGCTTT Y 2 1 2 1 103000 f 74 goat snp8661-scaffold131-3632486 16 55756291 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384682 Affx-122972126 AX-123255040 16 54839056 GAATTCCTGTGTCATGTTTTGTTCCTGTTGTTTGG[C/T]ATTTGCTTGTTTTAGTAATAAATGACCTTGCCCAC Y 2 1 2 1 201000 r 74 goat snp8660-scaffold131-3578621 16 55810155 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377121 Affx-122978245 AX-123247480 16 54884237 CCTCATTTTTAGCCGTATTAGTCCCTGTGTAGAGT[A/G]TTCTGAAAATAGCATGTGCTCTTGTCGTATCAGTT R 2 1 2 1 101000 f 74 goat snp8659-scaffold131-3533440 16 55855478 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390452 Affx-122967618 AX-123260809 16 54940500 TGATACATTTAAATTTTACAGTTTAGTTGGGTATT[A/G]TGAAGTACAGTGCAGAAAAGTCATTTGAGCTTTTG R 2 1 2 1 201000 f 74 goat snp8658-scaffold131-3477177 16 55912227 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447461 Affx-122924360 AX-123317797 16 54974096 TAAAATAAAAATGAGATCAATTGCTTTGTTTGCCC[A/G]GAAATACTTAATAAGCACCGATCATAGGCCAGGTA R 2 1 2 1 101000 r 74 goat snp8657-scaffold131-3443581 16 55944216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766156 Affx-122922572 AX-385253558 16 55019715 ATGCCCTCCACGGGGTAATTTGTACAAATTTGTCT[A/G]TATTATATTATCCAATCTTAATCTTTTTAAATAAT R 2 1 2 1 101000 f 74 goat snp8656-scaffold131-3397962 16 55990252 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799790 Affx-122934186 AX-385286716 16 55070517 TCACTTATTCCATAGTTTTTGATGTAGTGTGGTAA[C/T]ATATAGTTAGTGTCCTGGTAGAGTTGCTTTTTTGC Y 2 1 2 1 101000 r 74 goat snp8655-scaffold131-3347160 16 56041325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383006 Affx-122973326 AX-123253364 16 55111594 AGTAGAGGGATCTGAATAAACCTTTATTGAATGAA[C/T]GAAAAAACTGAACATGAAAAAAAAGTGAATGAAGA Y 2 1 2 1 103000 f 74 goat snp8654-scaffold131-3306083 16 56082972 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277155 Affx-1111835707 AX-519550661 16 55115444 GTAGTGGATCGGACGGGCAGTAGACTACCAAACAG[A/T]GCCCATGACCTTTCACTGGCGCAAGTTTTGCTCTG W 4 1 2 1 202000 r 74 goat Random2.2K-1609 16 55115444 A T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380195 Affx-122975500 AX-123250553 16 55143429 GAAATCCCCAATGAAAATATAAATGTTATCTGGTA[A/G]AGGAAGCCTCTGAGCCATTTTTAGGCCATTAGCAG R 2 1 2 1 101000 r 74 goat snp8653-scaffold131-3274248 16 56114915 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420959 Affx-122944588 AX-123291306 16 55177804 TCTCCCTGAGGTAGAGAAATATTTCTTTTTCTCAT[A/G]CATTAAGTTCTATATGCCTGAAAAGTCTGAAACCA R 2 1 2 1 201000 r 74 goat snp8652-scaffold131-3239873 16 56148598 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441475 Affx-122928749 AX-123311812 16 55222660 TGAAGATTACTTAGGGCTTTCTATAATGCCATCAT[A/G]TTTATTTGTTAGGGCTACCATAACAAAATGTCAAA R 2 1 2 1 103000 f 74 goat snp8651-scaffold131-3195017 16 56193227 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402850 Affx-122958249 AX-123273203 16 55252535 CTCTCTTCTGCTGCACGGTTCTCTAGTCAGACACC[A/G]TCCCACAGAAACGTAACACAAGTCCTGGATGTCAT R 2 1 2 1 101000 f 74 goat snp8650-scaffold131-3165142 16 56223105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398382 Affx-122961652 AX-123268737 16 55288566 GCACCCAGAGTAACTAACCCTCAGAACACAGAAGC[A/G]TGGAATTGATGCACTTGTTTATGGTAGCAGGAATC R 2 1 2 1 101000 r 74 goat snp8649-scaffold131-3129111 16 56259183 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775518 Affx-122979116 AX-385262649 16 55334310 TATTTCTCTGATTATCAACTGTACTCCATGTTTCA[C/T]AGTTTCAGAGCCATCTGGGAGTTCAGTCACTCAAA Y 2 1 2 1 101000 r 74 goat snp8648-scaffold131-3083367 16 56324191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387292 Affx-122970529 AX-123257650 16 55416388 CCCAAATTACGTTTATAAACTCTGGTCCTGGGTGA[C/T]ACTTTGCAAAAAAAAGAAGTCTCAGTGGTTAAATG Y 2 1 2 1 101000 f 74 goat snp8647-scaffold131-3001289 16 56406610 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381082 Affx-122974604 AX-123251440 16 55474551 AGTTCCAACATTATGTTATAAAAAGACTGGCTTCC[A/G]TTTGGGGCAGATTCTCATGTACTCACCCTTTCTGG R 2 1 2 1 201000 f 74 goat snp8646-scaffold131-2943126 16 56465862 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274490 Affx-1111834323 AX-519548081 16 55488431 ACTTCCCTGAGTGACCTCCCCATAGGTCTCCCTGA[A/G]GGTCCTCATGACATGGCAGCTGGCTTCCTGCAGAG R 2 1 2 1 303000 f 74 goat GoatD01.029986 16 55488431 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38440930 Affx-122929018 AX-123311267 16 55533612 CCTGGTCTATTGCTCCTTCCCCAACTCCAAGGTCT[C/T]CCCTGGTGGCTCAGATGATAAAGAATCTGTCTGCA Y 2 1 2 1 101000 f 74 goat snp8644-scaffold131-2884065 16 56524799 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404773 Affx-122956685 AX-123275125 16 55589711 TGCATTTTATTCCTACAACTCATGAGGCACTTAAC[A/G]TGACTACTGTGTCCTCCGCTTTTGTATATGCCATC R 2 1 2 1 101000 r 74 goat snp8643-scaffold131-2827966 16 56580848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800135 Affx-122933218 AX-385287058 16 55633551 GTGCAACTGGAATTCCCATATATAATGAGGGCTCA[A/G]TAATTCCTGTCACTAAGTTACAACGGTTAATTAGG R 2 1 2 1 101000 f 74 goat snp8642-scaffold131-2784126 16 56624661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389128 Affx-122968555 AX-123259486 16 55666523 GGTCTTCTGACTTTTGCCTGATGTCAGCCAACTTT[C/T]TGATGGAAGGAAAGTCCTGGGAGGCTAAAAACAGA Y 2 1 2 1 101000 f 74 goat snp8641-scaffold131-2751154 16 56657477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801277 Affx-122944008 AX-385288189 16 55712789 TGTCCTCAAGGATCTCACAGTCCAATAGGCTTGCA[A/G]TGCAAATCAGTGTTTATAGGAATGAAGCTATGCTG R 2 1 2 1 102000 f 74 goat snp8640-scaffold131-2704888 16 56704354 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402827 Affx-122958265 AX-123273180 16 55747621 ACAAACATCTCAGTTCATCAAGGTCTTCTAATTCT[C/T]CTCTACTTTAGGTGATTCCCAGCAAGGCCACTCTT Y 2 1 2 1 101000 r 74 goat snp8639-scaffold131-2670056 16 56739083 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783606 Affx-122977851 AX-385270665 16 55787435 AAAAGCTTTCTCCGGATCCCTTAATTTTTCTGAGC[C/T]TCAGTTTCCCTTATCAGCGTAACATGGCTAATAAT Y 2 1 2 1 101000 f 74 goat snp8638-scaffold131-2630242 16 56778821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413913 Affx-122949824 AX-123284262 16 55833307 TTAAGTCAGCTTCAGTTTTGTTGTTTACAGGGTTT[C/T]CTAGCAGCTATCCTGTAGTTTAGCATGATAATCTC Y 2 1 2 1 201000 r 74 goat snp8637-scaffold131-2584370 16 56825016 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388505 Affx-122969216 AX-123258863 16 55901282 GTGGAGAAGAGGACTATAAAAGATGAATCTTTGTC[A/G]TCATCAATTGGGAAAAGCAGCAGCAGTTAAGAAAA R 2 1 2 1 101000 f 74 goat snp8636-scaffold131-2516395 16 56893479 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405912 Affx-122955578 AX-123276264 16 55936045 GTGGTGACCAGATGTCTGTGTCCAGCCCAGTGCCC[A/G]CACCTTCCCCACTCTGGCTGCGCTGCTCCATCTTT R 2 1 2 1 101000 f 74 goat snp8635-scaffold131-2481632 16 56928314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393796 Affx-122965184 AX-123264151 16 55985379 TAGCAGTGAGGAGCCACAGGAGAACCGTACTAAAA[G/T]AAAGAGCATAATGGCATTTACCAGTTTGAAAGATC K 2 1 2 1 101000 f 74 goat snp8634-scaffold131-2432298 16 56977244 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384617 Affx-122972171 AX-123254975 16 56021781 TCTAGCAAGTCTACATCTAGACAGTTACTTCAAAA[A/C]TATGCAGAAAGATTCAGCTACCAAGTTATTTATTG M 2 1 2 1 101000 f 74 goat snp8633-scaffold131-2395896 16 57013488 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803020 Affx-122962158 AX-385289897 16 56073019 TAGAGGATTTGATTTGCAGAAATTCAATTTACACC[A/G]CACCCTTAGAGAAATACACCACAGTGCAAAGCTGA R 2 1 2 1 101000 r 74 goat snp8632-scaffold131-2344658 16 57064193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451151 Affx-122921362 AX-123321485 16 56121540 CAATTTTAGCAGAGGGAGATCCCACACCATAAGAT[A/G]CAGAGTATGGAAAATGCTCCTGATGGCCACAGCAT R 2 1 2 1 101000 f 74 goat snp8631-scaffold131-2296137 16 57112766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766250 Affx-986697870 AX-385253647 16 56142629 AATGGCTGGTATTAATAGGCTACAGGGGCTGATGG[C/T]AGTGCCCCATGTGTCTTGAACCAGAGGCTGTCGTA Y 2 1 2 1 600010 r 74 goat 16_56142629 16 56142629 Ancestral_priority_1043 ancestry 0.508 neutral IMAGE 10K 10K ancestral 320796783 Affx-122975375 AX-385283726 16 56206249 TGGCCACTTGTTCTGTCAGAGAAAACGGCCTTTTC[A/G]TATGCTTCATTCTGATACTTGAGCAGGGTCCTCCG R 2 1 2 1 101000 r 74 goat snp8629-scaffold131-2211428 16 57197151 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413716 Affx-122950074 AX-123284065 16 56262360 CTTAAAATGTCTTAATTTGGGTATTAGCCATGCTC[A/G]TACATTAAAGTAAAATGAGATTAAAGAAAAGCCCT R 2 1 2 1 101000 f 74 goat snp8628-scaffold131-2155317 16 57252403 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436851 Affx-122932207 AX-123307189 16 56351606 GCCTTCAGTAGGTATTCTGTGAGAATGTTCCACAC[A/G]TAGATGTAGTTTTGATGTATTTGCGTGATGAGGTG R 2 1 2 1 201000 r 74 goat snp8626-scaffold131-2066071 16 57342142 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440974 Affx-122928986 AX-123311311 16 56384422 CTCTTTGTGTTTGGCTTACAGAAATTTGAATATGA[C/T]GTGATTAGGTGTAGAGGTTTTTGTTGTAGTAGTAG Y 2 1 2 1 101000 r 74 goat snp8625-scaffold131-2033255 16 57376551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448943 Affx-122923145 AX-123319278 16 56416291 ACTTGTACATGTGTAAGTCAGAACCATTAAAATGC[G/T]ATAACTTCGAGTGGAAATGTGAATTTTAAGAACAA K 2 1 2 1 101000 r 74 goat snp8624-scaffold131-2001386 16 57408452 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277027 Affx-1111835708 AX-519550534 16 56483120 ATTGGATGCCTGAGAGAAGGTGGGACATTGACTTT[A/G]GAAAAATTCACAAGCTGATGTCATCTTGATTTTGA R 2 1 2 1 101000 f 74 goat Random2.2K-1612 16 56483120 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38377408 Affx-122977560 AX-123247767 16 56489892 AGGCAGGAGATGATGGGGCTTTGGACAAGGCGGTA[A/G]TGATGGAAGTAAGAGAAGTATTTGCATTCTCTATA R 2 1 2 1 201000 r 74 goat snp8622-scaffold131-1927785 16 57484652 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786342 Affx-122960206 AX-385273376 16 56544019 AGTCTTTATTCTGGACCATTTGATGCATTCTATTC[A/G]TTATGAACACATATTATGTATATCTTGGATCTCTT R 2 1 2 1 101000 f 74 goat snp8621-scaffold131-1873658 16 57540058 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382287 Affx-122973921 AX-123252645 16 56590752 CCTCTGTCTTTTCTACATCTGTCTTTCCACTCCCC[A/G]TCTGTACTCTGCAGAGAATCACACAAAGCGTAGTC R 2 1 2 1 101000 f 74 goat snp8620-scaffold131-1826925 16 57584265 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799637 Affx-122970537 AX-385286566 16 56644761 TATTTAAAAACCATTAAGGAAAAAGACAAACAGCC[A/G]TCTAGAAATATGAGCAGAGGACTTGAAAAGACAAT R 2 1 2 1 101000 f 74 goat snp8619-scaffold131-1772916 16 57637892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768733 Affx-122975196 AX-385255911 16 56680750 TTGCTCAGAAAACTTGTTTGAAAGGGTGATGAAGC[A/G]TTTGGGTTGTGCTGTGGGTTTTCACTCCCCAATTT R 2 1 2 1 201000 f 74 goat snp8618-scaffold131-1736927 16 57674298 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386978 Affx-122969961 AX-123257336 16 56730355 GAGGCTGGGCATTTAGTGATGAGGATGTTGGTACT[A/G]CAAAAGGCTGTGGGAATGCTCCAGGGAAGTGAGGA R 2 1 2 1 101000 f 74 goat snp8617-scaffold131-1687322 16 57724020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424154 Affx-122942540 AX-123294500 16 56762606 TGGGCAGTGTCTGCGTCCTCATCACTCCTTTCTCT[C/T]GGGAGCAGTGAGACACTTTAGAGCCATTTCTAGGA Y 2 1 2 1 101000 r 74 goat snp8616-scaffold131-1655071 16 57756414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377690 Affx-122977417 AX-123248049 16 56801770 AAAGAAACCCAGGAATTGAAGAGGAGAAACTGGGC[A/G]CAGTATCTTTCACTGTGCAGAAAGATTGGGAGAGG R 2 1 2 1 201000 r 74 goat snp8615-scaffold131-1615907 16 57796413 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425118 Affx-122941222 AX-123295464 16 56837108 AGGTCAACAGGGCCAGGGATCTGCCGAAGGAAGAA[C/T]GGGGAAAATATCTCACATGTTTTGTTTACTTGCTT Y 2 1 2 1 102000 r 74 goat snp8614-scaffold131-1580569 16 57831491 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421799 Affx-122944330 AX-123292146 16 56903517 GCCACAAGTGTAGTTTTAAGTCCTCTAGTGACCAC[A/G]TTAAAAAAAGTAAAATGAAATAGTGATATTAATTT R 2 1 2 1 103000 f 74 goat snp8612-scaffold131-1514160 16 57898770 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407675 Affx-122954592 AX-123278026 16 56932618 TGTAAGTGTTTTGCATCTAGAAGGCCCTCGGTGAG[C/T]GCTGTTCCTCGTCTTCCTGAAGACTGCAGCCCCTT Y 2 1 2 1 101000 f 74 goat snp8611-scaffold131-1485059 16 57927838 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780052 Affx-122939097 AX-385267151 16 56992639 TCTCAGTCAATCCAGTGGGAAAACTTATTTCCCAG[C/T]AGTTCAAGCATAAGCTCTGGGAGCATGCTTTGTAG Y 2 1 2 1 102000 f 74 goat snp8610-scaffold131-1425038 16 57988041 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423216 Affx-122942705 AX-123293562 16 57021883 TTTAAATAAAAGTTAGTTTTCAAAAATATCAAGAT[A/G]CCAATTTTAGAATTTTTCTGCTACCCCTTGGGGTA R 2 1 2 1 101000 r 74 goat snp8609-scaffold131-1395794 16 58017964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435227 Affx-122934087 AX-123305567 16 57070279 AGCCTAGATCTTTGGAATGAAATACAATCCAGGAT[A/G]CACAAGAAGAGTCAGCAGCATTTTTAGCTGGACCA R 2 1 2 1 101000 f 74 goat snp8608-scaffold131-1347398 16 58066463 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388330 Affx-122969361 AX-123258688 16 57114328 CTGGTGGGCTACAGTCCACAGGGTCACAAAGAGTC[A/G]GACACGATGGAGCATATCTACTTCTACATGCATGA R 2 1 2 1 101000 r 74 goat snp8607-scaffold131-1303349 16 58109986 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272826 Affx-1111833076 AX-519546520 16 57122891 AGCAATATTACAACACAGAGAGTCAAAGTGTTAAT[A/G]TAAACTGACACAAGACCATAACTGTATACTTTTGA R 2 1 2 1 101000 f 74 goat 16_57122891_AF-PAKI 16 57122891 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320783208 Affx-122968821 AX-385270275 16 57171757 AAGTTAGCCTAATTCCAAAAACTATTCCTTCATTA[C/T]ACTACAATGTCCCACTCTCTCTTGTTCTAAAGCAA Y 2 1 2 1 101000 r 74 goat snp8606-scaffold131-1245920 16 58167376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440608 Affx-122929976 AX-123310945 16 57207855 CTGCCAGGAAGTTAGGAATGTTTTCAAACTGAAGC[A/G]CAATGATGGGGACTGTCAAAAGGAGCAAGAGCCAG R 2 1 2 1 101000 f 74 goat snp8605-scaffold131-1209822 16 58201699 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393292 Affx-122965438 AX-123263648 16 57293053 CCACAAATGAATAAGAGGGAGCAAACAACTACAAT[A/G]TAAGACTATAAAGCAGTAAAATGAAACGTTTAGCA R 2 1 2 1 101000 f 74 goat snp8603-scaffold131-1124624 16 58286994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412378 Affx-122950810 AX-123282727 16 57325437 CAACATTAAACATGGTAGGGAGTGTTAAATGTAGG[A/G]TGGTTAAAATATGTTCAAAGTTAAGAGAGCTTCAG R 2 1 2 1 101000 f 74 goat snp8602-scaffold131-1092240 16 58319571 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446586 Affx-122924821 AX-123316922 16 57354492 CTTCCTTACACCATGTTTTTGGTTTTAATAAAAAT[A/G]GTCAACACTGGCTCCAACTGGGGAAAAAAAGCTAA R 2 1 2 1 303000 f 74 goat snp8601-scaffold131-1063185 16 58348712 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802874 Affx-122927765 AX-385289772 16 57384904 AAAAATTCTGCTTGTTAATATAGTAGGAGAACAGA[C/T]ATCCCTCTGGTCACACAATCTGAACACCCACAAGT Y 2 1 2 1 101000 r 74 goat snp8600-scaffold131-1032773 16 58379284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446619 Affx-122924798 AX-123316955 16 57460349 AATTTTTCCCTTTAAATGGATTTGGTTTATAATAC[A/G]TAAATTGTACCTCAATAAAGCTGTTAAAAAATCCT R 2 1 2 1 103000 f 74 goat snp8599-scaffold131-957328 16 58454201 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797433 Affx-122922906 AX-385284372 16 57518941 CACAGTGAATATCTCTAACAGAGAGCATGGACAGA[C/T]GGTCATTAGCAGCTCACTTTGCAGAAGAAAACCTG Y 2 1 2 1 101000 r 74 goat snp8598-scaffold131-898736 16 58512776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785321 Affx-122978016 AX-385272366 16 57549759 AGCCCCCTGTTTTCTATACAGCTGATGGCACAGCA[C/T]GGCTTCTCACACTAGAGCACACTGGAGTCACCTGG Y 2 1 2 1 101000 r 74 goat snp8597-scaffold131-867918 16 58542374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447208 Affx-122924987 AX-123317544 16 57636320 AATTGATGGTGCTCTGTGCTCTGCAAAGACTTTTG[C/T]ATAATATCTCATTTGAGTCTTACCACAAGCCTCAG Y 2 1 2 1 201000 r 74 goat snp8595-scaffold131-781357 16 58627866 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450928 Affx-122921775 AX-123321262 16 57672665 TGGCAGACACAGATTGTATGTAAAGTAAAAGGACA[C/T]GGCTCACTTAAAGCACAAGTGGAAAATTGTCTCTA Y 2 1 2 1 101000 f 74 goat snp8594-scaffold131-745012 16 58664181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795581 Affx-122968662 AX-385282536 16 57721312 ATGCCTTCAATCCCATCACACCATTTATAACTACT[A/C]TGCACACAGTATTGACTAACATTGACCATATGCTT M 2 1 2 1 101000 f 74 goat snp8593-scaffold131-696365 16 58713134 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802663 Affx-122944885 AX-385289562 16 57765972 GGTAAAATATCTGGTTTCTCTCTTTTCACTTCTAA[C/T]AGAAGTTCATTAGGTAAACATGATGACAAAGGAAA Y 2 1 2 1 101000 f 74 goat snp8592-scaffold131-651705 16 58758260 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375537 Affx-122979103 AX-123245896 16 57794692 AATTTTCTGAACACCCACAGAAAGAGCTGTGAATG[C/T]TGGACCGATTAAAAAAAGAGAAAGCAAAATACGTA Y 2 1 2 1 103000 f 74 goat snp8591-scaffold131-622985 16 58786995 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434244 Affx-122934828 AX-123304585 16 57827307 TCTGACAAATATTTCACTGTTTTATTTTCCTGTCC[C/T]AAGTCTACCAAATGTTTGTGCCAAATGTTCCGCAA Y 2 1 2 1 201000 r 74 goat snp8590-scaffold131-590370 16 58819569 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801429 Affx-122973171 AX-385288338 16 57873729 AAAGACAGTTCTCTAAAATAAGACATTAACTGTAA[C/T]GGAATGAAATAATTAGATAACTATCTTGTGGTAAC Y 2 1 2 1 201000 r 74 goat snp8589-scaffold131-543948 16 58866103 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430135 Affx-122937396 AX-123300476 16 57929033 ATTCATCCAAAACACAAAGTCAATCTTGTGCCCCA[C/T]GCCACTCCCTTGGAATGCACAATCGAGAAAATAGT Y 2 1 2 1 201000 r 74 goat snp8588-scaffold131-488644 16 58921469 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431732 Affx-122936747 AX-123302073 16 57982748 CTCACCCAAGCCTGAAGTATCCACTCTCCTAGAAG[C/T]GTTATTCTCACCCACCTCCAGTCAGTACCAAGTTT Y 2 1 2 1 101000 r 74 goat snp8587-scaffold131-434929 16 58972172 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796004 Affx-122931258 AX-385282956 16 58091032 ATGTGTTGGTGAAAGGACGAGCAGGAAGGGTTTCT[A/G]TTGCGGTAACACTCACGACAGAGTAGTAGTACTGT R 2 1 2 1 101000 f 74 goat snp8585-scaffold131-326645 16 59081357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782622 Affx-122927186 AX-385269695 16 58127097 TGAAATTGAGATTGCTGAGAAGGGTGCATTGCAGG[G/T]TGTGACTGAGGTAAGGTTACATTTAGTTCTTTGAT K 2 1 2 1 101000 f 74 goat snp8584-scaffold131-290580 16 59117478 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431012 Affx-122936675 AX-123301353 16 58162545 ATTTCATGATCGGTAATCTAGGGTTGAATACTTTC[A/G]TTGTCTTTTTAATATCTGACATACCTCACAACAAT R 2 1 2 1 101000 f 74 goat snp8583-scaffold131-255132 16 59152922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386557 Affx-122970712 AX-123256915 16 58197074 ACCTGAGATTTATTTCAGAGCACTATCCTTGGGCT[A/G]CTATAGCCCTTTGTCTACAGATGTAGAAATTTGGG R 2 1 2 1 101000 f 74 goat snp8582-scaffold131-220603 16 59187675 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412929 Affx-122951473 AX-123283278 16 58229613 CTGATAAAGGGTACCTGCAGGAACCAACAGCTAAC[A/G]TTAAGTATCAGAAAAACTAAAAGCTTTCTCCCTAA R 2 1 2 1 201000 r 74 goat snp8581-scaffold131-188064 16 59219889 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771388 Affx-122970287 AX-385258546 16 58262283 CAACACATACCACAGTAGAAAATTGATGTTATATA[C/T]ACAAAATTCTCTCCAAATTTTCCTAAAGGAAAATT Y 2 1 2 1 102000 r 74 goat snp8580-scaffold131-155394 16 59252582 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277159 Affx-1111835709 AX-519550665 16 58309103 ACTAAAAATTCCCCATTTCTTCACTGCTATAACTA[C/G]AGTTACTGCTAGTGGAATTAAGAAAAGTAAAATTC S 4 1 2 1 201000 r 74 goat Random2.2K-1616 16 58309103 G C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38379332 Affx-122976178 AX-123249691 16 58364000 GAATGCCATTGGTTGGTCTCCTCTGATGTCTGTCT[C/T]GAGTCAACATTTAAATTGTTCACTGCCTTGCAGAG Y 2 1 2 1 201000 r 74 goat snp8578-scaffold131-53677 16 59354853 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795983 Affx-122933786 AX-385282935 16 58401462 ACTTTTATGTCTTTAATTTCCATGACCTTATTTTG[A/C]GCTCTACTTGTTCATCTTGCAAACTTAACCGGGTT M 2 1 2 1 101000 r 74 goat snp8577-scaffold131-16215 16 59392178 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792964 Affx-122978211 AX-385279942 16 58446275 ATGGAACATTAAGTGGTTACATACATTGAGGTTCC[A/G]TTGTACATTAGTAGTACAGGTAGTTATACTGTACA R 2 1 2 1 101000 r 74 goat snp3659-scaffold112-28499 16 59436787 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442556 Affx-122928520 AX-123312893 16 58497843 GATTAATTTGAGAACACCAGAATCATACAGAACAA[C/T]GAACCATGTAGAACAATACACTGGAACCAGTAGGC Y 2 1 2 1 101000 r 74 goat snp3660-scaffold112-80067 16 59488356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445855 Affx-122926001 AX-123316192 16 58532656 TATCCAGGGAGATCAATCAGGAGACTCGTGAAGTC[A/G]TCCAGGTGAAAGATGACAGTTGTTTAGACTGGGAT R 2 1 2 1 201000 r 74 goat snp3661-scaffold112-114880 16 59522147 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444500 Affx-122926513 AX-123314837 16 58572495 TGAGTTGCAGCTTTTGGGAAGAGAGATGTAACAAT[A/G]AATGAAAAGGCTCAACACGTCTGCAGACAAAGCAG R 2 1 2 1 101000 f 74 goat snp3662-scaffold112-154719 16 59562199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771715 Affx-122921915 AX-385258872 16 58639015 AGTAAACAGAGCATGGAACCCTGGAAGGAAAGGCA[C/T]TGAAGACTAAATCATTTGTATCTTTACCAATTATT Y 2 1 2 1 101000 f 74 goat snp3664-scaffold112-221239 16 59628851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399710 Affx-122960473 AX-123270065 16 58681932 TTTCATTAAAATAAAATATGTGCCCCCAGTTTGGA[C/T]AATGAGTTGCTCAAAAACATTCCAAAGTGATTTTA Y 2 1 2 1 201000 r 74 goat snp3665-scaffold112-264156 16 59671823 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377300 Affx-122977695 AX-123247659 16 58759049 AAGATCTTAATGACTGAGGTGAGGAATTTTTACTT[A/G]TTTTGGCAGGCACAGGCAGGCAGGGGCAAAACTCA R 2 1 2 1 101000 f 74 goat snp3666-scaffold112-341273 16 59745838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784768 Affx-122936770 AX-385271815 16 58792337 ATATGAAAAGTTATATACTATGTTACAAAATTAAC[A/G]TTAGTGACAACTATTAGATAGTAAAGCAGTAATTA R 2 1 2 1 202000 f 74 goat snp3667-scaffold112-374561 16 59779757 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448965 Affx-122923129 AX-123319300 16 58876961 CTTGCTTTAACCAAGTGGCTTATAATGTTGTTCAG[A/G]AAGCATATTTAAAGTTCTGTGCTCAGCTCTTATGC R 2 1 2 1 101000 f 74 goat snp3668-scaffold112-459185 16 59865215 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392752 Affx-122966007 AX-123263109 16 58928112 TGGCAATCCCCACAAAAAAATAAGAAATCTAGGTC[A/G]CTGTTCTACTTGCTTACATTCTGGCAGGAGGAGAC R 2 1 2 1 201000 r 74 goat snp3669-scaffold112-510336 16 59916162 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439587 Affx-122930069 AX-123309924 16 58964033 TCGTCATTTACAGTGGCCGGAGCTGATGTGCAGAC[A/G]CTTCGGGAGAGGCTCATCGATGCCCTGGAGTCCCA R 2 1 2 1 101000 f 74 goat snp3670-scaffold112-546257 16 59951725 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388538 Affx-122969194 AX-123258896 16 58996021 GACTGATATAAGCCCCACAGGTATACTCCACATAC[A/G]TGGTCTGGTATGCGTGCACTTTGAGGATGTGGTCA R 2 1 2 1 201000 r 74 goat snp3671-scaffold112-578245 16 59984202 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439832 Affx-122930465 AX-123310169 16 59024699 TGGGAAGGAATGAAGAATTCCAAGAAAAACATTTG[C/T]ATAATATTTCAATTATATATGTGTTTCCTTAAAGT Y 2 1 2 1 103000 f 74 goat snp3672-scaffold112-606923 16 60007991 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377332 Affx-122977672 AX-123247691 16 59062579 CAAGATTGAAAAGCCATGTGAAGGAAAGGAAAATG[C/T]AACTGTCTTTTTGGAGGACAGATTCTTAGGCACAC Y 2 1 2 1 101000 r 74 goat snp3673-scaffold112-644803 16 60045991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789549 Affx-122970438 AX-385276558 16 59111633 TACATTCTAGTGGTAGGGGAAGTAAAAAGCAAATA[C/T]ATCTTTTCTGTAATAGACAGTTATAAGTGCTCCAA Y 2 1 2 1 101000 f 74 goat snp3674-scaffold112-693857 16 60095181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449130 Affx-122923568 AX-123319465 16 59172784 AAAGCAGCATAGCACAAGTATGTGAGCAGAAAAAG[A/G]AAGCAACAGAAGAACAGCTAGAAATACGGTGAAAT R 2 1 2 1 101000 f 74 goat snp3676-scaffold112-755008 16 60156736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440449 Affx-122929400 AX-123310786 16 59209066 ATCAGTCATGTCACTAGATATTATGAAAGAAACTG[C/T]ATTCAATGTGTCATTTTGAAAAAATACTAGAGTCT Y 2 1 2 1 101000 f 74 goat snp3677-scaffold112-791290 16 60192893 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434842 Affx-122934379 AX-123305183 16 59251333 TATGACTACACTTATTTATTATGACTACATGCTAC[C/T]AGAAGAAATATCAAAACTAATACCCATCATATACT Y 2 1 2 1 101000 f 74 goat snp3678-scaffold112-833557 16 60235603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432379 Affx-122935859 AX-123302720 16 59316248 TGTCCATTCAGCCTCCAAATGAAGATGCTGAGTAC[A/G]CAGTTGGGTATATGAGCCTGTACTGAACTGAATCA R 2 1 2 1 201000 r 74 goat snp3679-scaffold112-898472 16 60300741 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452936 Affx-122920185 AX-123323269 16 59358223 GTAGTTTCATGCCACCTTGCCTTTGCACATGTTGA[C/T]CATGCCATTTTCGTCTATGTAACTGACACTTCTTC Y 2 1 2 1 201000 r 74 goat snp3680-scaffold112-940447 16 60343107 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773695 Affx-122945633 AX-385260835 16 59406538 TTTGAACTCTTGCATATCCTCCATCCCTGCTACTA[C/T]GACCATTTGATCCATGAGCCCATTAGCCAAGCCCT Y 2 1 2 1 101000 f 74 goat snp3681-scaffold112-988762 16 60391849 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452167 Affx-122921242 AX-123322500 16 59461662 GTCTTTAATAATTTTTAAGGGTGTATGAGAAGTCC[C/T]GAGACTAAAACAATTTTTAAATTATTGGTCTAAGC Y 2 1 2 1 101000 f 74 goat snp3682-scaffold112-1043886 16 60447085 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789799 Affx-122959961 AX-385276806 16 59500039 ACAGAAATCTAGCCAGTCTTATCACACAGACCATA[G/T]CCTTGTGTAACTCAGTGTTAAAAGTAATGGCATAT K 2 1 2 1 202000 r 74 goat snp3683-scaffold112-1082263 16 60485792 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388894 Affx-122968856 AX-123259252 16 59539883 CTTTGCCAGTTCTGGATTTTTTTTCCCACCCTTTC[A/G]TCTTTCTTCCTTTTTTTCCTCTTGATGCTAATCTT R 2 1 2 1 303000 r 74 goat snp3684-scaffold112-1122107 16 60525389 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782469 Affx-122954242 AX-385269545 16 59614934 TACCTCATGGAGCTCATGAGTTGCAGAATATTTTG[A/G]CTTTATCTAATACTCCATTTTTCATCCTGTGCAAG R 2 1 2 1 101000 f 74 goat snp3686-scaffold112-1197158 16 60600942 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379677 Affx-122975921 AX-123250035 16 59665637 ATCCTTTCCTACAGTCCTGCGTTTAACAGCGTTTC[A/G]TCTGAACTCAGACGGAGACAGGCAACAGAGGCAAA R 2 1 2 1 101000 f 74 goat snp3687-scaffold112-1247861 16 60651442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453282 Affx-122920384 AX-123323615 16 59695119 GGACATTGCAGCAACACGGCCAGAGCGCCACTGTA[A/G]CATTCAGAGCCTCGTGTCCATCCAAAAGCAGAAGA R 2 1 2 1 101000 r 74 goat snp3688-scaffold112-1277343 16 60680755 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419334 Affx-122945652 AX-123289682 16 59754088 AAGTAGCTAGGATGCAAACATCCCAGGTCCCTGAG[C/T]AGGAGCTCAAGCCAGCCTGCCTGGTGGCCTTGCCT Y 2 1 2 1 101000 f 74 goat snp3690-scaffold112-1336312 16 60740031 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272828 Affx-1111833077 AX-185286492 16 59800372 GCAGATGACACCACCCTTATGGCAGAAAGTGAAGA[A/G]GAGCTAAAAAGCCTCTTGATGAAAGTGAAAGAGGA R 2 1 2 1 103000 f 74 goat 16_59800372_AF-PAKI 16 59800372 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38436867 Affx-122932195 AX-123307205 16 59804878 TCTAGATCAGAACTACTACACAGTGCTTTTAAAAA[A/G]TGTTTAAGGAAACAAAGTTTACAGACAGAAGCCCT R 2 1 2 1 102000 r 74 goat snp3691-scaffold112-1387102 16 60790823 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389733 Affx-122968667 AX-123260091 16 59846364 ATCATTTTCTCCTTAGAAAGTACCTTGATGTGAGA[C/T]GTCCACTTTCTGATTTTATATTTCCCAGTTTTCAG Y 2 1 2 1 201000 f 74 goat snp3692-scaffold112-1428588 16 60828104 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777993 Affx-122964750 AX-385265109 16 59876249 TCAGCTCTAATAATTGCTGAATGTCTCCCTTGTAA[C/T]GGTTTTGTGTGGGAGCTCACATTTTCATATACACT Y 2 1 2 1 102000 f 74 goat snp3693-scaffold112-1458473 16 60858432 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409960 Affx-122954112 AX-123280311 16 59915448 CAAAGAAGTTGAATTTTTTATACATTTATTGTCTC[A/G]CATCTATCATCCAAGTAATAAGCTTTTAAAAGACA R 2 1 2 1 101000 r 74 goat snp3694-scaffold112-1497672 16 60898424 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412635 Affx-122950800 AX-123282984 16 59944348 CCAGTCAGGAGTAGAAGAGGGCAAGGGAACCAGAG[A/G]TGAACATAGTGGCTGGAAGTGCTGAGTATTAAATG R 2 1 2 1 101000 r 74 goat snp3695-scaffold112-1526572 16 60927794 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277161 Affx-1111835710 AX-519550667 16 59954329 CTTCTTAGCCCAGCACTGGCCTTCCCCCTGCTGGA[A/G]GAAGCGGGGAAGTGTAGGAGCTGGACCTTTCCGTT R 2 1 2 1 103000 r 74 goat Random2.2K-1619 16 59954329 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778700 Affx-122951880 AX-385265811 16 59995209 GTAGTGTGTCAGAAATTGGAATAATAATATTTTAC[A/G]TCTTTCTGATGTTTTAGATTTATAACATTCCTACC R 2 1 2 1 201000 f 74 goat snp3696-scaffold112-1577433 16 60979567 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401907 Affx-122958832 AX-123272260 16 60028385 GCAGCAGCTCTATAGACTAGGAGGGGAACCTGACC[A/G]TTTCCAATTGACAGTGTCTTGCCTGGTCCTTTAGA R 2 1 2 1 101000 r 74 goat snp3697-scaffold112-1610609 16 61013391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384598 Affx-122972576 AX-123254956 16 60059583 TTTCCAAGAAAATGGCTCATTTTCCTTCTCTTACA[C/T]GCCCTGGATGTTTAAGGCTATGCTTTCAGCTGCTC Y 2 1 2 1 101000 r 74 goat snp3698-scaffold112-1641807 16 61044674 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390733 Affx-122967917 AX-123261090 16 60146786 CTGAGTATTTGCAAGAAAGATTACATGGCCTGCAA[C/T]GTCTGAAATAATGACTATCTGGTCCTTTTACAGAA Y 2 1 2 1 101000 r 74 goat snp3700-scaffold112-1729010 16 61131204 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417964 Affx-122946694 AX-123288312 16 60201998 CAAGGAGGGAAGATGTCCTAAAGATTGGGTCATCC[A/G]CTGGGCAGCCCGGGAAGGGGAGTAGCTACCAGTCA R 2 1 2 1 101000 f 74 goat snp3701-scaffold112-1784222 16 61186311 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771378 Affx-122936593 AX-385258536 16 60236704 AATTTAAAATACACCACGTTTGCTTTTTATTCCTG[A/G]CTGTACAATGTAATTGACTAATATATATTGCCTCT R 2 1 2 1 101000 f 74 goat snp3702-scaffold112-1818928 16 61222306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417572 Affx-122946902 AX-123287920 16 60295205 TCTTTTTATAGAATACTTAAAAAGTAACACTTGCC[A/G]AAGTATCAGTAACTTCTGTGGAACACTAAGTCCTA R 2 1 2 1 101000 r 74 goat snp3703-scaffold112-1877429 16 61280880 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389904 Affx-122968117 AX-123260261 16 60352587 TTCTAAGCCCCTGACCTGAATGTCAGTAGCATTCA[C/T]TTGGTGCTTTTCGAAGATTGCCGCATCAGAAGTTG Y 2 1 2 1 101000 r 74 goat snp3704-scaffold112-1934811 16 61338762 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782771 Affx-122968363 AX-385269843 16 60406973 ACAGTCACATCAAATCAGGAGTGAAGCAATGCAAC[A/G]TTTATCTGCTTTGCACTGTGCTTGTTGCATAACCT R 2 1 2 1 201000 f 74 goat snp3705-scaffold112-1989197 16 61393581 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776044 Affx-122958116 AX-385263174 16 60438254 CTTCAGTTCCCCACTCTTTGAAGTGGGAATGGTAA[C/T]AGTTCCTAGAATATTCTTGACGTCAGTTAAACGAG Y 2 1 2 1 102000 f 74 goat snp3706-scaffold112-2020478 16 61425179 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792837 Affx-122975191 AX-385279815 16 60487544 TAGATGTTCCTTTAAGTTTTCTGCTCTGAAAACTT[A/C]TAAGGGCCAGAGCAGACTATAAACAAACACGAGAA M 2 1 2 1 102000 r 74 goat snp3707-scaffold112-2069768 16 61474445 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444588 Affx-122926959 AX-123314925 16 60530572 TCAGCAGAAGGTGTCTCCACATGCCCCTGGGGAAC[A/G]TAGCCACTCCTCACAGACCTTGAGAACCAGCACTC R 2 1 2 1 101000 r 74 goat snp3708-scaffold112-2112796 16 61517557 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413322 Affx-122950180 AX-123283671 16 60563264 CCTTAATAAAAGGGGTTCCCTATCTGACTCACATC[A/G]TGAAACACAGCAACAAAACTCCCTAGTCATCACAA R 2 1 2 1 101000 f 74 goat snp3709-scaffold112-2145488 16 61550024 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423558 Affx-122942421 AX-123293904 16 60593182 GCCAGAATGCAAAGAAGCAGGACAAATGCAACCCA[G/T]AGTTAGGAAATAAATTAATCAAATGAAATTGACTC K 2 1 2 1 303000 r 74 goat snp3710-scaffold112-2175406 16 61580438 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410681 Affx-122952747 AX-123281031 16 60623162 GACTCCTCCCAGTTAAAGACTGAACTTGGCAGAAG[C/T]AAGAAGGCCGACCAGGTCCTGGAAGACACGATTCC Y 2 1 2 1 101000 f 74 goat snp3711-scaffold112-2205386 16 61610842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802628 Affx-122967419 AX-385289529 16 60652627 TTTTTCTCAATGCCTTGGAGTCCTATGGTGGAAAA[A/G]TGAGGACTCTCCAGTTTGAGCAATTTGGCTTCTCC R 2 1 2 1 101000 r 74 goat snp3712-scaffold112-2234851 16 61640045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376063 Affx-122978924 AX-123246422 16 60688460 ATGCCACCCAGGTGGACCACTGCTACAAATAGCCA[C/T]GAAAGTGCTAACAAAACCAACACTCTCTTTGGAGC Y 2 1 2 1 101000 r 74 goat snp3713-scaffold112-2270684 16 61675900 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392103 Affx-122966359 AX-123262460 16 60740218 AATTTCACAACAACTCCAAAAGGGAGGTGTTAATA[C/T]TGTCTCCATACGTCTTCTCAAGGAAAATGAACCTT Y 2 1 2 1 101000 r 74 goat snp3714-scaffold112-2322442 16 61727235 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789137 Affx-122957681 AX-385276149 16 60781899 CTTTGTAATTCCTTGAGTAAATTTAACTAATTCTA[C/T]GGATAAAACATCTCTTTTTTCTCCCCCTAGAATGT Y 2 1 2 1 101000 r 74 goat snp3715-scaffold112-2364123 16 61766547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383457 Affx-122973455 AX-123253815 16 60812491 ATTATTTGCCCGTCTGGCCAGCCTGCAACTGGCCC[A/G]TATCAAGTAGGTACTAGACTGAACGGAATTCCGGG R 2 1 2 1 101000 r 74 goat snp3716-scaffold112-2394715 16 61797045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771190 Affx-122946801 AX-187024822 16 60841326 TAGAGCTATTTTCCCTGGGGTAACTTTTCAAATGT[C/T]TCTAACATCTCAGAAGAAACTCAATCTGAATCTTG Y 2 1 2 1 101000 r 74 goat snp3717-scaffold112-2423550 16 61825809 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383686 Affx-122972496 AX-123254044 16 60873158 AGAAAAATAAAGATATTTTATTTCCTTTTCTAAAG[A/G]TCCCTATATAATATTCAAAACAATTTTCAGCTAGT R 2 1 2 1 201000 r 74 goat snp3718-scaffold112-2455382 16 61858444 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453546 Affx-122919785 AX-123323879 16 60956281 AGATTAGAAAACTAACATAGGAAGAGACCTAATAG[C/T]AGCAGAGAAGGAAATCTGTCCAAACACCAGGAAGA Y 2 1 2 1 201000 f 74 goat snp3720-scaffold112-2538505 16 61942455 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450012 Affx-122922851 AX-123320347 16 60987321 CTGAGAGATGAGTCTTCAAGTCCACCACTTCTCCA[C/T]GGTGTAGAGAGAGGACTGTAAAGTTGGGCCAATTT Y 2 1 2 1 201000 f 74 goat snp3721-scaffold112-2569545 16 61973899 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798606 Affx-122966012 AX-385285539 16 61017141 TTTTCTGTAATCGTGCATGACAATAAAATTAAATG[C/T]CTTTACATCTGAACCCCCACAACCCACTGCCTCTT Y 2 1 2 1 101000 r 74 goat snp3722-scaffold112-2599365 16 62004093 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426569 Affx-122940164 AX-123296915 16 61050064 AGAGGCTCAGTTAGGGTGATGGCAGTGAGGGTTAA[C/T]AGAGAGAAGTGACTTCAGGACAAACTTTGAAGGTG Y 2 1 2 1 101000 r 74 goat snp3723-scaffold112-2632288 16 62037458 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402512 Affx-122958569 AX-123272865 16 61108270 CAACCAATGTCAGCCTCCCCAGAAGGGCAAGCAGG[A/G]CAGAGAGAAGCCCTGAAGTGGTAGTGAGGGAATAT R 2 1 2 1 101000 r 74 goat snp3724-scaffold112-2690494 16 62095290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796151 Affx-122950372 AX-385283102 16 61147361 TTGCCATGGCACCAATTGTTTACGTGACAACTTCT[A/G]TTCTTTCATTCCTCAAATAAACGAATTTTCATATA R 2 1 2 1 101000 f 74 goat snp3725-scaffold112-2729585 16 62134416 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380703 Affx-122975161 AX-123251061 16 61198038 CTGTGAATTTGAAGGCCAACGTCTCCACTTTCAGA[C/T]TGTTTTATCTGAGGTAGAAGGCTGTGGGGTCCCTT Y 2 1 2 1 101000 f 74 goat snp3726-scaffold112-2780262 16 62184950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375645 Affx-122978691 AX-123246004 16 61247808 AGTAAGTGGGTCCCACTGAAGGAAAAGAAACGTTC[A/G]GTGGGCTCATTCAAAACTGTGATCTTTGCTTGTTT R 2 1 2 1 101000 r 74 goat snp3727-scaffold112-2830032 16 62236053 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451230 Affx-122921955 AX-123321564 16 61287015 TCCCGTGGTCAACAATAAATAAATATTTAAACGGC[G/T]AGGAGTTCCTGGCGGGCGCCAAGAGGTTCCCAGCA K 2 1 2 1 201000 r 74 goat snp3728-scaffold112-2869239 16 62275629 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390820 Affx-122967849 AX-123261177 16 61343865 TGAGGTCTCAGCACCCAGGACTGGCCATTACATTA[C/T]GACAGCAAATCACAAATGTGATCCAGAGTCTTCTA Y 2 1 2 1 101000 r 74 goat snp3729-scaffold112-2926089 16 62332705 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777360 Affx-122948706 AX-385264482 16 61401092 GACTTGAAGCCAAAGCCTTAGAAATTATCCCCTAG[C/T]ATTCATGGAATAAATACTAAGGTAAGAGTCAATGT Y 2 1 2 1 102000 f 74 goat snp3730-scaffold112-2983316 16 62390163 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766929 Affx-122930634 AX-385254241 16 61439000 AGGGGAAGAAGTGACGGCCTATTTTTGTCAGAGCT[A/G]CTTAGACATTACCGGAATGAGAACGCTGCAGTTCA R 2 1 2 1 101000 f 74 goat snp3731-scaffold112-3021224 16 62428368 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417740 Affx-122947424 AX-123288088 16 61467594 TTCACATTCAGTTTCCCATCATGCACTGGGTGAAA[C/T]GGCAGCCTGACATGATGAGAAGCCTCCCTGAAGAC Y 2 1 2 1 201000 f 74 goat snp3732-scaffold112-3049818 16 62456898 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277036 Affx-1111835712 AX-519550542 16 61516699 AAAACCTCTTTGTACAGGCCTGCCCAACAAGTTAC[A/G]GTTGTTAGTGTCTTAAGAAATATGTGTCAGCCTGT R 2 1 2 1 101000 f 74 goat Random2.2K-1620 16 61516699 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38426813 Affx-122940523 AX-123297158 16 61531810 GCCCACCCAATATTGTTAGCTATTATTATTCCCTT[A/G]TCCTAAACAATACTTTACACAAAATCATGGGTTGG R 2 1 2 1 201000 r 74 goat snp3733-scaffold112-3114034 16 62511524 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799305 Affx-122956092 AX-385286235 16 61589440 AGTTCATATCTTCATGCTGCTGACATGTGAATGAT[A/C]TTGGACAACTTATATTTTGTCTTAGTGGCATTTTC M 2 1 2 1 101000 f 74 goat snp3734-scaffold112-3171664 16 62569129 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385898 Affx-122971585 AX-123256256 16 61641899 CTTTCTGAGTAGGTTTCTCAATCACAAAAGACTTA[C/T]AACTCTTCTCTGTCACCCCCCTGACCCCTCCTCCT Y 2 1 2 1 101000 f 74 goat snp3735-scaffold112-3224123 16 62622341 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772224 Affx-122946329 AX-385259379 16 61684554 GCTTATTTTGAGAATGTCTTTCATTTTCTGGGTCC[A/G]CATGTCACGGTAAGTCCAAGAATCCAAGAGTTGTT R 2 1 2 1 101000 f 74 goat snp3736-scaffold112-3266778 16 62664995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277167 Affx-1111835713 AX-519550673 16 61717248 GTTACTTGGGGGTTACCTGGGGGTCTGAGGCTTTG[A/G]TGGTGACCGATAGAAACCAGGATAAAACCCATAAT R 2 1 2 1 101000 r 74 goat Random2.2K-1621 16 61717248 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320774463 Affx-122945573 AX-385261599 16 61724230 CATGATACATGCCAATCTCCAGAAATACAAAGTTG[C/T]CTGTCTTTCTGGAAGCTTCCTAGACCATCCCAGAC Y 2 1 2 1 101000 r 74 goat snp3737-scaffold112-3306454 16 62705693 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431120 Affx-122936595 AX-123301461 16 61756223 ATTACTTGCTTTTGAATAAGTTATACTGTGAAACT[A/G]CTATCTTTTGGAAATCAACTATAATTTTTAAAAGG R 2 1 2 1 101000 f 74 goat snp3738-scaffold112-3338447 16 62737902 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434903 Affx-122934329 AX-123305243 16 61799841 GAAGTGATGGGTAGGCTGTTCCAGGAAGAAGGAAC[A/G]TGGGGTACAGTGGCCTCGAAGCTCGAGGGTATCTG R 2 1 2 1 101000 f 74 goat snp3739-scaffold112-3382065 16 62780970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274118 Affx-1111834050 AX-519547721 16 61855292 GTTGCTGTAAACCGGGAATTTCCAGCCAAGTACGC[A/G]GAGGATTAGCCATCAGGGCCACCAGGTGGCGATAG R 2 1 2 1 101000 f 74 goat GoatD01.015898 16 61855292 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38420097 Affx-122945097 AX-123290445 16 61871008 TAGCTTTAAAATATTTACCCAAGCTGAGAAACAAA[C/T]GAAACCTTGGAAGAAAAATCTCATGTAGAGGATTT Y 2 1 2 1 101000 f 74 goat snp3741-scaffold112-3453232 16 62852043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382254 Affx-122973947 AX-123252612 16 61921092 GATTAGGCTGAGCTGGCTGTGTGACTGTAAGCAAG[C/T]CACATAACCTTTCCAGACCCTGATTTTCCCATCTC Y 2 1 2 1 201000 r 74 goat snp3742-scaffold112-3503316 16 62902721 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774359 Affx-122941009 AX-385261495 16 61972809 TTATTATTCTCCACAGGTTCACAATAATGGGGAAA[C/T]AGAATGCTATACTGATGGCTCTAATGAGAGACAAA Y 2 1 2 1 101000 r 74 goat snp3743-scaffold112-3555033 16 62954339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413111 Affx-122950384 AX-123283460 16 62014819 GATACACAGAAAGAGGCAAAGATGAGAGATAAAAA[C/T]ACTTCAAAGATTCCCCACAGCATTCCAGATTTGGG Y 2 1 2 1 101000 r 74 goat snp3744-scaffold112-3597043 16 62995281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454320 Affx-122919243 AX-123324653 16 62061975 GGCATTGGTTAGTGGGGAAAAAAATAGGAGAGAGA[G/T]AGTTAGCAAACCAGAAACACAGAGACACAGAAAAG K 2 1 2 1 101000 f 74 goat snp3745-scaffold112-3644199 16 63039628 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386079 Affx-122971451 AX-123256437 16 62106491 TGGGCTACAGTCAAAGGGGTCGCAAACTTCGAACA[C/T]AGCTTAGCAACTGAGGAACAACAATGACGACAGAC Y 2 1 2 1 102000 r 74 goat snp3746-scaffold112-3688715 16 63084112 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780936 Affx-122948140 AX-385268023 16 62136618 GTTAGGAGACTTGGAAGACCAAAATTTTTTTGTAA[C/T]AATATTAAGACAGTATTTACTTTTTTTCACTCTCA Y 2 1 2 1 202000 r 74 goat snp3747-scaffold112-3718842 16 63114613 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431686 Affx-122936784 AX-123302027 16 62166202 ATTAATATTTTCAGTCTGTTTCCAAAAACTCCATC[C/T]GCTCACTGACTGCACTGAGTCCTTTTCCCGTCTCT Y 2 1 2 1 201000 f 74 goat snp3748-scaffold112-3748426 16 63144204 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444559 Affx-122926980 AX-123314896 16 62199820 TTCTTCTACTGAGGCAGCTCACTATCAGTTGTTGC[A/G]CTTATAAGCCTAGTAACAGGAAAGGCTAATGTGCC R 2 1 2 1 101000 f 74 goat snp3749-scaffold112-3782044 16 63177740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398607 Affx-122961483 AX-123268962 16 62239464 ATAACACTGACCTCTCTGCTCCCTTGCGCTGTTTC[A/G]CTGGCTGTCCACCTTAGCCTTTCGTGTTCTGCTCT R 2 1 2 1 101000 r 74 goat snp3750-scaffold112-3821688 16 63218267 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801384 Affx-122940772 AX-385288295 16 62278313 TGTCTTTTTACTGAGTATTTCCTGTTGACTGTAAA[C/T]ACTCTAAAAATACAGAAAGGCTGACAGAAGAAGAT Y 2 1 2 1 102000 r 74 goat snp3751-scaffold112-3860537 16 63256998 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394280 Affx-122964710 AX-123264635 16 62328798 TTTTCCAGTAAAACACATGTGCAAACATTATCCAG[A/G]GTGACATTTAAAAAAATTCTAAAATATATATCAGA R 2 1 2 1 101000 f 74 goat snp3752-scaffold112-3911022 16 63307865 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431628 Affx-122936146 AX-123301969 16 62357898 GTAGGAAGAGCATGTCATGAGAAAATGATAAGTAT[G/T]TGTGGGAAAACAGCTGAAAATGTTTTTGGCGAGAG K 2 1 2 1 101000 f 74 goat snp3753-scaffold112-3940122 16 63337429 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405899 Affx-122955589 AX-123276251 16 62391280 AGAACTATAGAAGAGTATATTTTATATTATTAGCT[A/G]CCAACTTTCCAGTGGTTGAAGCTCTCCATATATGT R 2 1 2 1 101000 r 74 goat snp3754-scaffold112-3973504 16 63371269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796132 Affx-122976733 AX-385283083 16 62423273 CACGATGACGTTAGTAATTATTAAAAATCTCTGGT[A/G]TCCCAAGCCACTGTCAGCTAAAATCGAACTGGAGC R 2 1 2 1 101000 r 74 goat snp3755-scaffold112-4005497 16 63403271 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790640 Affx-122973016 AX-385277642 16 62465830 TGCTTTGAGTGTTTGGAGGACTGGTCATCTTCAAC[G/T]AAGCATGACTGGTTCCTTACCTTTTGCAAAGCAGG K 2 1 2 1 101000 f 74 goat snp3756-scaffold112-4048054 16 63445890 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418002 Affx-122946665 AX-123288350 16 62495356 TGAAGGGAGTGGGGCTTTTGGAGGCAGACACGTTC[A/G]TAATAACAAAAATGGACAAACCAGTGGAAAGCTAT R 2 1 2 1 201000 r 74 goat snp3757-scaffold112-4077580 16 63475517 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277169 Affx-1111835714 AX-519550675 16 62514769 TGTAATGCCAGATTAATGCAATGTAACTCAACTAC[A/G]CACAAATATTAACATATCACTTCACTTGGCTGCTC R 2 1 2 1 101000 r 74 goat Random2.2K-1622 16 62514769 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320770693 Affx-122967885 AX-385257857 16 62544896 AGTTACTGGTAAAGATTTTAGTTACATATAAATAG[C/T]AGCAATCTAAGATATTGGAAATGAAAGAAAAGAGA Y 2 1 2 1 101000 r 74 goat snp3758-scaffold112-4127120 16 63523450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400205 Affx-122960179 AX-123270560 16 62592073 CATTAGTTGCGGAATCTCTTCAGACTCTTCAGATA[C/T]GGTGTTTTTCCCATTCTATCATTTGTCTTCTTCTG Y 2 1 2 1 101000 f 74 goat snp3759-scaffold112-4174297 16 63570665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450019 Affx-122922846 AX-123320354 16 62649075 TCTTAGCCCACATGGACTTGGAGTTGACCAACAGA[C/T]ATGAAACTTCTATAAAAGAGTCAGAAAGGGACAAA Y 2 1 2 1 201000 r 74 goat snp3760-scaffold112-4231299 16 63627514 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390098 Affx-122968021 AX-123260455 16 62688108 GCTTATCTCTGCAAAGAGCCAGCTTCGCTTCTTTG[A/C]TCTTTTCTATTGCTTTTAAATTCTCTATTTTGATG M 2 1 2 1 303000 f 74 goat snp3761-scaffold112-4270332 16 63666164 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271806 Affx-1111833078 AX-519545593 16 62695702 AGGAGAAGAGCCTCTGAAGAATAGGGTGTGTGCTT[A/G]TCCTGCTCTTCTCAGTTGCAACATTCATTCCCTAC R 2 1 2 1 101000 r 74 goat 16_62695702_AF-PAKI 16 62695702 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38409563 Affx-122953590 AX-123279914 16 62724752 CTTCATGAGCTCATGATGTGAGATAACTGAGCAAA[C/T]AAGAGGGTTGGAGGGAGTGTCATTTTACATCAAGC Y 2 1 2 1 202000 f 74 goat snp3762-scaffold112-4306976 16 63704065 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801398 Affx-122921725 AX-385288308 16 62772671 TTATATTTGAGCCTTCAGACATTTCCTGAGCCAGC[A/G]TTATGGATATAATGTTATTGTGTACCTTGACTCCA R 2 1 2 1 101000 f 74 goat snp3763-scaffold112-4354895 16 63752179 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377198 Affx-122978187 AX-123247557 16 62822680 GTTTTCCCTAACTCTCATTGTGAAGGCTTGCTATG[C/T]AATAGCTGTGAAAGTTTTTTGACAACCAACCATTA Y 2 1 2 1 201000 r 74 goat snp3764-scaffold112-4404904 16 63803726 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396329 Affx-122963070 AX-123266684 16 62893229 GCATGCCATATGAGAGACACTGTCCTGGTGGTTTC[A/G]TTGTGATGGTCCACGATCCTACGTTCATCGAATGT R 2 1 2 1 101000 r 74 goat snp3765-scaffold112-4475453 16 63874866 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412849 Affx-122950452 AX-123283198 16 62927264 TTTACTGAGGAACTGAGGCTCAGAAAAGTTAGTTA[A/G]CTGGCCCAAAGTTATACAGTTGGAAAGTGGTGGAA R 2 1 2 1 101000 r 74 goat snp3766-scaffold112-4509488 16 63909587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781482 Affx-122965969 AX-385268568 16 62960255 GGCAGGGAAAATGAGGTGTCATTACTGTGTTTTAT[A/G]TTAACAAGCAGAATTTTTGCACCCAGACATGCTTA R 2 1 2 1 101000 f 74 goat snp3767-scaffold112-4542479 16 63942587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389716 Affx-122968678 AX-123260074 16 62991649 TTTACTGTTTAGATTAACTAATTGAATTATCTCAG[C/T]AAACCACTAATAAAGATATTAATATCCCACATTTA Y 2 1 2 1 101000 f 74 goat snp3768-scaffold112-4573873 16 63973927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443672 Affx-122927183 AX-123314009 16 63025034 CTGTTTTGCTAAATAAACTATTTGCTCCCCTCCCC[A/G]AGAAATAAAGACATTGACAGGTACAAAACTAATAT R 2 1 2 1 201000 r 74 goat snp3769-scaffold112-4607258 16 64007673 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397038 Affx-122963109 AX-123267393 16 63062129 AATGAGAGGTACCCCAAGACCAAGTAAATGAGATA[C/T]GAATTTTCACATTAAAAGTGTTATTGGGAATTTCC Y 2 1 2 1 201000 r 74 goat snp3770-scaffold112-4644353 16 64044670 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413788 Affx-122949915 AX-123284137 16 63095767 CTAGATCCTCATTTACATCTGTCCCTAGCCCTTGA[C/T]GTTGCCACCTCCTATCTAGGAAGGATGAAAGAAGA Y 2 1 2 1 201000 r 74 goat snp3771-scaffold112-4677991 16 64078278 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380245 Affx-122975459 AX-123250603 16 63128537 TAATATCTGTTAGACTAGCACTTCTGAAACTTCTA[C/T]GTGCATAGGAGTCACTGGGGATTTTGTTAGAACTG Y 2 1 2 1 201000 f 74 goat snp3772-scaffold112-4710761 16 64110999 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394998 Affx-122964238 AX-123265353 16 63176293 AATAAAAAGTTAAAAAAAAAATAGAAATGTTTAGA[C/T]GTTGAATTTTGACCATGGCTTTCCTCCTTTGTTCT Y 2 1 2 1 101000 r 74 goat snp3773-scaffold112-4758517 16 64158143 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408118 Affx-122954250 AX-123278469 16 63218986 ATTGTGTTTGGTTACTGCTTTAGAAAATGAGAATT[A/G]GAGATATCCATGGTGGTCCAGAGGCCAAGACTCCA R 2 1 2 1 201000 f 74 goat snp3774-scaffold112-4801210 16 64200825 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388209 Affx-122969416 AX-123258567 16 63249433 GCCTTAGAAATCCTGGGCAAGTGATGTCTGCTTAG[C/T]GATAGGGCACGGTCACCCTTTCCTGGGGGGGAAAG Y 2 1 2 1 101000 f 74 goat snp3775-scaffold112-4831657 16 64231067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401231 Affx-122959313 AX-123271584 16 63283196 TGAAGGCGAGTAGTGCTCACTCCTTCGTTTGATGC[A/G]CCACATAGAGTGCATTCTCACTGCCTTTGTAATCT R 2 1 2 1 101000 f 74 goat snp3776-scaffold112-4865420 16 64264552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405837 Affx-122955872 AX-123276189 16 63343405 TGTCTCAAATATCGTGTCCCCACAGAAAGCATCTT[C/T]GTGTAGGAGTTTAACGGTCAAGAGCATGGCCTCCC Y 2 1 2 1 201000 r 74 goat snp3777-scaffold112-4925629 16 64324495 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274099 Affx-1111834004 AX-519547703 16 63368592 TAAAATAACTGCTGCAGC[A/G]AGATGCTCAACTTTCAAGCTATAAATAATAGCATT R 2 1 2 1 101000 r 74 goat GoatD01.013487 16 63368592 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38445504 Affx-122925187 AX-123315841 16 63377325 AGCAAGTGAAAATGATGAGCAAAGACTGTTTTCAC[C/T]ATGAATGCATTTGCTTCACAACCACTTAGGTCACT Y 2 1 2 1 101000 r 74 goat snp3778-scaffold112-4959549 16 64359040 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387683 Affx-122969821 AX-123258041 16 63421127 CACTCACTTCCCTGTATCAAGACAGACACGAGGTG[C/T]ACCACCCAGCTACACTTATAAATAAGTAACACCAC Y 2 1 2 1 101000 r 74 goat snp3779-scaffold112-5003351 16 64402774 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794361 Affx-122955214 AX-385281325 16 63475176 AGTAAAATGCAGAAGATGGAGGATGAAGACCCATA[G/T]TTCTTCATACTCAGTCTCTTTCTAAAAATTTTGAA K 2 1 2 1 101000 f 74 goat snp3780-scaffold112-5057400 16 64456808 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433280 Affx-122935216 AX-123303621 16 63527012 ACAGGGATGCAGGAAAAAGAGTGCTCTCATGCACT[A/G]TAGAAATGTGAATTTTTATAATTCATCTTAAGATT R 2 1 2 1 101000 f 74 goat snp3781-scaffold112-5109236 16 64508493 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772450 Affx-122932737 AX-385259601 16 63558920 ATCCTGCCTAGACTAAGCAGCTAGCAAATCGACTG[C/T]GCTCTTTGTGCACAAAACTCACACCTCACTCAGCT Y 2 1 2 1 101000 f 74 goat snp3782-scaffold112-5141144 16 64540404 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277042 Affx-1111835715 AX-519550549 16 63564032 CAGCCCTACCAAAACTTACTTATCGAGGGCATAAG[A/G]GTTGAAGAAGATGGGAATGGAGAACTTGGGAGCTT R 2 1 2 1 202000 f 74 goat Random2.2K-1624 16 63564032 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769791 Affx-122971429 AX-385256961 16 63589300 TGTTTGTACTCTTTTGTATTAAAAACCACATTGTC[A/G]TGAAGCTTTGTGAAATGATCTTAAATTGAGGTAAA R 2 1 2 1 101000 f 74 goat snp3783-scaffold112-5171524 16 64570715 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436827 Affx-122932227 AX-123307165 16 63648375 AAATACGGTGTTATAAAATAAACGCCATAAACCTA[C/T]TTTGCTAATAACTAAATGCAAGCCCCTTCTCACAA Y 2 1 2 1 101000 r 74 goat snp3784-scaffold112-5230599 16 64629493 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388068 Affx-122969523 AX-123258426 16 63690464 ACATAGTTCCCCACAAAAAGATGGTACTTTCAACA[A/G]CAGAGAACTTTAATAAAAGCATATGCCTATGAAGA R 2 1 2 1 101000 r 74 goat snp3785-scaffold112-5272688 16 64671737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768376 Affx-122959260 AX-385255556 16 63720825 GGGTGTAGGAGGAATTGTGGATGTCCTGTAACCCT[A/G]CTTTCCCCAAGTCTGGTCGATTGTGTAGTATTCTC R 2 1 2 1 101000 f 74 goat snp3786-scaffold112-5303049 16 64702688 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434605 Affx-122934095 AX-123304946 16 63754118 GGAGATATTTTGCACTTTAGCCTGGATGAAAAGTA[C/T]AAGATATGTTCAAAGCTTCCCTAATTCTTTTCTTA Y 2 1 2 1 101000 f 74 goat snp3787-scaffold112-5336342 16 64736775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787144 Affx-122950373 AX-385274170 16 63795748 TGAATGCATTTCAGAAACTGTAGTTGTAGTACCAA[C/T]GATCAATAATTGAGGTGAGAAATTAGTAATGGAAA Y 2 1 2 1 101000 r 74 goat snp3788-scaffold112-5377972 16 64778103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782708 Affx-122979089 AX-385269780 16 63830003 ATTGATCACAGACACTAATGAACTCATTTTAACTT[A/G]CAAAAAACCTAAACTAGGATTTAAAAGAATATAGA R 2 1 2 1 103000 f 74 goat snp3789-scaffold112-5412227 16 64812644 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436572 Affx-122932900 AX-123306910 16 63906238 AAAACATAGTTCTGATAAGGCTGCATTCATAAACC[C/T]AATACAGTTTAAGGTTAATTTTTTTCCCACAATCA Y 2 1 2 1 101000 f 74 goat snp3790-scaffold112-5488462 16 64889624 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377909 Affx-122977236 AX-123248268 16 63985414 AAATCACTTGAAGGAAAGTCTCCAGTGAATTACAA[C/T]ATGTCAAGTCAAGGAATATACCTATCTCAAGGAAT Y 2 1 2 1 101000 f 74 goat snp3792-scaffold112-5567638 16 64969058 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378732 Affx-122977037 AX-123249091 16 64031432 TCTCTAAAGAGGCAGCACATAAGTGAATACTCTTG[G/T]GAGTACCCATGTGAATCACTAAGCAGTTATGATAT K 2 1 2 1 101000 f 74 goat snp3793-scaffold112-5613656 16 65014935 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800156 Affx-122946764 AX-385287079 16 64066471 TGTCCAAAGTGGGGAAAAATAAAGTGATGCAGAGT[C/T]TGGTACTTAACAGATATGTAATAAGAATGTTTTGA Y 2 1 2 1 101000 f 74 goat snp3794-scaffold112-5648695 16 65050287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408830 Affx-122954023 AX-123279181 16 64103174 TGGGGTCATACGAACATCTCCCTCCTGTCTTCTCT[A/G]CTCCTGACTTTGAAAAGCAGGTGCCTTAACAGTGG R 2 1 2 1 201000 r 74 goat snp3795-scaffold112-5685398 16 65087208 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451997 Affx-122920923 AX-123322330 16 64156364 TTTGCTTTCAGTTCCACGTTGACTTTTTCGAGGAC[A/G]TGGGCCAGTGGACATAAAGGCCAAGCTATTTTCAC R 2 1 2 1 101000 f 74 goat snp3796-scaffold112-5738588 16 65130091 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794979 Affx-122928497 AX-385281939 16 64194477 CAACTGAGACCATAACATAAACAAGTCTTTATGTG[C/T]GCATTTTCTGAGACTGAATGAATTAAGAAATGCAT Y 2 1 2 1 201000 r 74 goat snp3797-scaffold112-5776701 16 65168067 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451591 Affx-122921645 AX-123321924 16 64226211 TCTTGACCTCTGCACCCCTTCTCATCTTTGCTTCC[A/G]TTCCGGTAGAGGGCTGGGGTGAGCTGTGGGTGTGT R 2 1 2 1 103000 f 74 goat snp3798-scaffold112-5808435 16 65199817 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424603 Affx-122942200 AX-123294949 16 64257039 AATTATTTCTTTAGCATCTGCTTGTGCCTGGAGCT[A/G]GGTATTATGGAGGAAGATACAAGAGGGGAAAAAAT R 2 1 2 1 101000 f 74 goat snp3799-scaffold112-5839263 16 65230587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381759 Affx-122974313 AX-123252117 16 64298216 CTGAGGGCTCTCAACTTACTGAACATAGAAACATG[C/T]AATAATTGTAATTTTTTCTTATTACTGATTTTAAA Y 2 1 2 1 101000 f 74 goat snp3800-scaffold112-5880440 16 65271574 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436952 Affx-122933174 AX-123307290 16 64329092 CTACTTCAAAATTTTATGAAACCTTGGACAAGTCA[C/T]GCTCTGGGACTCAGTTTTCTCTCTGTAAAATGAAG Y 2 1 2 1 201000 f 74 goat snp3801-scaffold112-5911316 16 65302564 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384880 Affx-122971933 AX-123255238 16 64391667 AGTCAGGAAAACTCAGTGTCAAACCTAATGAGAGA[C/T]ACAGTACGTAGGAGACAACTTGCCATCTTCTGATA Y 2 1 2 1 101000 f 74 goat snp3802-scaffold112-5973891 16 65365534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388318 Affx-122969370 AX-123258676 16 64491669 CTCTTTCTGTTACCTTGCTTTGACCCTACCTGTGA[C/T]GATAAAATTTTGTTTACTTATTTGGCTCCCAGGTA Y 2 1 2 1 102000 f 74 goat snp3804-scaffold112-6073893 16 65465262 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781347 Affx-122929085 AX-385268432 16 64538985 AGATGCACTCATGTTCCCAACATATGAGTACTTCT[A/G]TCTCTGTATGTTTTTAAGAACTTCTCTTCTACCTG R 2 1 2 1 201000 r 74 goat snp3805-scaffold112-6121209 16 65512836 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418536 Affx-122946410 AX-123288884 16 64579906 ATGTATTTGTATTATCTGTAATTTACCCATAAAGA[C/T]GAAGAGCCTCTGCGGAGTTAGTGGCTTGCCCTAGG Y 2 1 2 1 201000 f 74 goat snp3806-scaffold112-6162130 16 65553641 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409520 Affx-122953625 AX-123279871 16 64629592 AAGCCAAACCTCAGCTATGTCTTGGTTAGCGCTCT[A/G]CCTTGAGGGGTTACTTGACATATGGCAGATTCTGA R 2 1 2 1 101000 f 74 goat snp3807-scaffold112-6211816 16 65603724 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418197 Affx-122947066 AX-123288545 16 64692721 ACATTCCGCTCTCTTGAATTATTTCTGACATTTAC[A/G]TCTATAAGCAGTCCTAAAGAATCCATGCTCTTTTA R 2 1 2 1 101000 r 74 goat snp3809-scaffold112-6274945 16 65666987 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782250 Affx-122970062 AX-385269327 16 64723098 CTAAATATATTGTATTTGATTACTGATATCAAAAC[A/G]TGTTTCATTCTACTAAAACTGACTATAATTGAGGA R 2 1 2 1 101000 r 74 goat snp3810-scaffold112-6305322 16 65697505 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798899 Affx-122970398 AX-385285829 16 64751862 TCTTATGATTGTTTTCTTTTGCTCCTCATTCATTA[C/T]GTTAATAACCTAGCACATGTTCAGTACTGTGCACA Y 2 1 2 1 201000 f 74 goat snp3811-scaffold112-6334086 16 65726386 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405056 Affx-122956346 AX-123275408 16 64784637 AGTAAAAATATGCCTTATCCCAACACTTCCAGAAA[C/T]GTCCTGCAGGGAGCACTCATGAGCCCAACTTGAAA Y 2 1 2 1 101000 f 74 goat snp3812-scaffold112-6366861 16 65759102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418338 Affx-122946956 AX-123288686 16 64821220 TATCTACATGTCATTTTTGACTTTGTGAAACAACA[C/T]AGGTATTTTAGGGTTCTAGGTGTCTTCACTATAAG Y 2 1 2 1 101000 r 74 goat snp3813-scaffold112-6403444 16 65796220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441257 Affx-122929490 AX-123311594 16 64865830 TGTGAATGCTTTGGTTGACTAAAATGGGGAAAAAA[C/T]GATGACAAATATTTTATGAGTATTTGTCATTAACA Y 2 1 2 1 202000 r 74 goat snp3814-scaffold112-6448054 16 65841222 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769586 Affx-122943111 AX-385256756 16 64903661 TTATATATACCAATGACACAGGAGTCCACAAGTGA[C/T]GTAATTAACACAGCAAGGGTAGGCATATGTGGTAC Y 2 1 2 1 101000 f 74 goat snp3815-scaffold112-6485885 16 65878793 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781697 Affx-122965614 AX-385268779 16 64992227 CCCTCTGGGACATTTGGTTGAAATTTAAAGGAATT[A/G]CCACTAGATGACACCATAGATTGCATAACCAAACC R 2 1 2 1 101000 r 74 goat snp3817-scaffold112-6574451 16 65964586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786182 Affx-122969965 AX-385273218 16 65026977 TAACACAGGTGCATTTCCTAAGTCACTTCTCCTTC[A/G]TAATACTATTGGTGGGTCACAAAAAATTTTACTCC R 2 1 2 1 101000 f 74 goat snp3818-scaffold112-6609201 16 65998915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438814 Affx-122930792 AX-123309151 16 65083984 GGGCAAATTACTTAGCTTCTGAGTCCTTTTCAATA[C/T]GTAAAATGAGGGGATAACTATACCAAGATCATAGA Y 2 1 2 1 101000 f 74 goat snp3819-scaffold112-6666208 16 66056271 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389603 Affx-122968766 AX-123259961 16 65159637 GCCAGCCTGTTTTAAGCACACTTGTCACTGAGAGC[A/G]CATTTTTGATTATTTACCAAACACCATGCCTTCAA R 2 1 2 1 101000 f 74 goat snp17014-scaffold1776-5188 16 66132026 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768428 Affx-122939639 AX-385255608 16 65189223 TACAATAATAATAATTGCAGTGTCAGCAAATCAAA[C/T]GATAAGATATGATCACTTGAGGAGCATTTTTTTCT Y 2 1 2 1 101000 r 74 goat snp17015-scaffold1776-34774 16 66162007 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768378 Affx-122935044 AX-385255558 16 65218573 TAAAAGTTTCATATATAATAATTCTGGTCCTAAGT[A/G]TATTGCAGCCCAGCTATTATTTTAAAAACCCTAGA R 2 1 2 1 101000 r 74 goat snp17016-scaffold1776-64124 16 66191782 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386980 Affx-122969959 AX-123257338 16 65258705 GTCTGGTGTTAAAGCAAAGTTTGAATTTATGCCTT[A/G]CTAGGTACATGACTGGGCAAGCTAGTTGATCTGTT R 2 1 2 1 101000 r 74 goat snp17017-scaffold1776-104256 16 66231962 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271975 Affx-1111833079 AX-185837781 16 65267447 ATTCCAGTATTCTTGCCTGGAAAATTCCATGGACA[A/G]AGGAGCCTGGTGGTCTACTGTCTATGAGGTTGCAA R 2 1 2 1 103000 f 74 goat 16_65267447_AF-PAKI 16 65267447 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403307 Affx-122957837 AX-123273660 16 65289441 CTTAGCAATGAAGACCTTTAGGTGATACATACAGT[A/G]TATTTTCCAAATGTGATCAAAGGGAAGCCATCTAT R 2 1 2 1 101000 f 74 goat snp17018-scaffold1776-134992 16 66262916 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444090 Affx-122926836 AX-123314427 16 65327728 TGGATCCTGTGCATGCTTCTTCTTTGTGGGAATCA[C/T]GTGGGAAGGAATAACTGGGCAAAGACTGTGTGGAA Y 2 1 2 1 101000 f 74 goat snp17019-scaffold1776-173279 16 66301172 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395968 Affx-122963559 AX-123266323 16 65356928 CATTGCAGGCAGACTCTTTACTGTCTGAGCCACCA[C/T]GGAAGCCCCAGGAATGCAGTAGGTATTACTATTCC Y 2 1 2 1 103000 r 74 goat snp17020-scaffold1776-202479 16 66330493 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783320 Affx-122921910 AX-385270385 16 65393230 ATCTGAAAAATGACAGATGCTCTTTTCCTAACTAA[A/G]AATTCTCTGTACCCTAAGGAGAATAATTCCCTTGC R 2 1 2 1 101000 f 74 goat snp17021-scaffold1776-238781 16 66366138 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418381 Affx-122946565 AX-123288729 16 65431659 AAATTCAACTAAATGTCGCCTTATCCTGAAACACT[A/G]TCCTCTTTGCTTTCTTGTTTCCACTCTGCTGTTCT R 2 1 2 1 201000 f 74 goat snp17022-scaffold1776-277210 16 66408034 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803005 Affx-122961398 AX-385289885 16 65503108 AATCTTTATAGTCGTATTACTATTGTACTTAGACT[A/C]TCTGCTCACTCACTGAACTCAGTTAGCTTTCTGGT M 2 1 2 1 101000 r 74 goat snp17023-scaffold1776-348659 16 66479720 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433308 Affx-122935191 AX-123303649 16 65538081 ATGAACAAATATGTTTAAAAATAAGTATATAATCC[A/G]AAATCTTTCCCAGGTTCTACACACAATAGTGAATT R 2 1 2 1 101000 r 74 goat snp17024-scaffold1776-383632 16 66515081 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784058 Affx-122939397 AX-385271111 16 65568337 ACGACTAAATTTCTGGATTATTTCAAAAGCGAATT[A/G]TCATTCACAGTGTCTAGAAGCCCCTTCTAAAACTT R 2 1 2 1 101000 r 74 goat snp17025-scaffold1776-413888 16 66545436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402702 Affx-122959609 AX-123273055 16 65603812 TGTGCATATATGAAACAAAGCACACAGCCCTGGCC[A/G]CAAATCTCATTTTATAACCAAATAAGACAGCTGGC R 2 1 2 1 201000 r 74 goat snp17026-scaffold1776-449363 16 66580993 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395631 Affx-122963797 AX-123265986 16 65648437 GCCTGTCTTGTTCCCAGTTTTCAACAAATATTTTG[C/T]AGCATCCAGTTTAGGATACCAATGTTGACTTAAAA Y 2 1 2 1 201000 r 74 goat snp17027-scaffold1776-493988 16 66625473 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439999 Affx-122929790 AX-123310336 16 65685138 GTAGTGACGAGTGCATCGATTTTAAGGAAAATGTC[A/G]TTGACAACTGCTTCTTTTGGAAGACTGTCAAATTT R 2 1 2 1 101000 f 74 goat snp17028-scaffold1776-530689 16 66662256 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433107 Affx-122935710 AX-123303448 16 65734610 ATGAGATATCAGGTCAGGAGGGCAGGTGAGGATTA[A/G]ATTAGGATCTTCCTACCAGCTTTATGGAGGCATAA R 2 1 2 1 201000 r 74 goat snp17029-scaffold1776-580161 16 66711781 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436791 Affx-122932255 AX-123307129 16 65770001 TGAGTTACTTTGCAACATTTTTTCAACATCTTAAC[A/C]GTTCATAAGAGCAATTTAGGATAACAAAAGTCTGG M 2 1 2 1 101000 r 74 goat snp17030-scaffold1776-615552 16 66747006 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792113 Affx-122960663 AX-385279098 16 65882772 ACAAGAAAGCCCCGAGAAAGCAGAATCACTGAAAA[C/T]GCATGTTTGTTCTGAAGATATTATTTGAGATTTTC Y 2 1 2 1 101000 f 74 goat snp17032-scaffold1776-728323 16 66860221 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403381 Affx-122957781 AX-123273734 16 65927734 TCCTGTGTAACAGTAAGATATTGGGGGTTACATCC[A/G]TAGAGCCTAGCAGAGCCCAGCAGAGTCAGCCTCAT R 2 1 2 1 101000 f 74 goat snp17033-scaffold1776-773285 16 66905637 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388792 Affx-122968921 AX-123259150 16 65980519 ACTGAAAGTCTCATTCGAAAAAAGAAAACTGAATC[A/G]TGAACATAGAGAACAGAGGGAGAGGGATGGATTGG R 2 1 2 1 201000 f 74 goat snp17034-scaffold1776-826070 16 66959036 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450721 Affx-122921877 AX-123321055 16 66031840 GCAGACTACAGTCCAAGGGGTTGCAGAGTTGGACA[C/T]GATTGAGCATGCACACAATTTTATTTAACATGTTA Y 2 1 2 1 103000 r 74 goat snp17035-scaffold1776-877391 16 67010929 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400039 Affx-122960780 AX-123270394 16 66108349 TAAATTGGGCGGGGGGAGGGGGGAAGGTTAATGGA[A/G]GAAAAGGAAACTTTGGAGAGAGGAGACAGAGCAAG R 2 1 2 1 101000 r 74 goat snp17037-scaffold1776-953900 16 67087507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405334 Affx-122956337 AX-123275686 16 66147024 GGTTTAGAAAGACTAGATGAACTCTGTTTCTTTCA[C/T]GCTCCCAGCCCCAGGCTATGCAACACCTGCTAACT Y 2 1 2 1 201000 f 74 goat snp17038-scaffold1776-992575 16 67126223 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801046 Affx-122944006 AX-385287960 16 66178488 GCTGTGCTTCATTCACAAATATGTATCTAAGACTT[C/T]ATTTCTACCTTTGTAAGCTAGAAACACAATGAAGA Y 2 1 2 1 101000 f 74 goat snp17039-scaffold1776-1024039 16 67157594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419516 Affx-122945444 AX-123289864 16 66247564 TGGATTGATAGTCCAGCATTATTGATCCTGATCAG[C/T]ATCATTTTCTTATGTCAGCCTTAGGGATCATTTCA Y 2 1 2 1 101000 r 74 goat snp17040-scaffold1776-1093115 16 67225318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792191 Affx-122969454 AX-385279176 16 66292107 GATACTAGGGAACTTTTAGGACCAGGACCCTATTA[C/T]AAATAAAGGCTTGATCGCAAGAAACAATGAGGAGC Y 2 1 2 1 101000 f 74 goat snp17041-scaffold1776-1137658 16 67269436 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420364 Affx-122944952 AX-123290711 16 66326751 AATGGGAGAATTTTGCCTCTTTAAAATTTAAAAAG[C/T]AAGATTTGTAAATGTATAAAATATATGTATGTATA Y 2 1 2 1 103000 f 74 goat snp17042-scaffold1776-1172302 16 67304578 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421695 Affx-122944408 AX-123292042 16 66383545 TATTTAAATGTGAAATGAGTTCTGCAGCCATTAAG[A/C]GTTGGAGAAACTGAGAGGAAAGAGAGACCGCTGTT M 2 1 2 1 201000 f 74 goat snp17043-scaffold1776-1229096 16 67361723 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434981 Affx-122933833 AX-123305321 16 66414745 TTTTGCACAAGAAATTCCACTTATAACACAGAGTT[A/G]GAAATCACTGACCTGCAGAACCTCACATGCATGTG R 2 1 2 1 201000 f 74 goat snp20318-scaffold201-25359 16 67395124 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436033 Affx-122932729 AX-123306372 16 66469934 ACAAAATAAAAATAAAAAGATTTATTGTAAGGGGC[C/T]CTTGACTTCTGACATCTGTAGATTTCACTTATTGT Y 2 1 2 1 101000 r 74 goat snp20319-scaffold201-80548 16 67449823 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385054 Affx-122971829 AX-123255412 16 66545287 GGGCTCAATGAATTAGAAAACAAAAGAATCAAAAC[A/G]TAATAAATTACACAAAAATTAGATTCTTTGACAAG R 2 1 2 1 303000 r 74 goat snp20320-scaffold201-155901 16 67526942 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417584 Affx-122946894 AX-123287932 16 66585905 TTCCCACTTATTTTCATGACATCTTGCCCTAGCCT[A/G]AATGGCTTTGGGAAAGCTAACTTGGAAATTCCAAG R 2 1 2 1 101000 r 74 goat snp20321-scaffold201-196519 16 67568440 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767008 Affx-122959043 AX-385254302 16 66645671 TTGGAGATGGGGTAAGTGCTATTGGCATGTAGTGC[A/G]TGGAGGCCAGGAATTCCACGTATCCTATGGTGAAC R 2 1 2 1 101000 f 74 goat snp20322-scaffold201-256285 16 67628768 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414477 Affx-122949555 AX-123284826 16 66706972 TGATGCCTCAGGACTGAGGGAACAGTGGATGCAGA[C/T]GAAAATTAGAAATAGTTTTTGGTGATGGTGAAAAG Y 2 1 2 1 101000 r 74 goat snp20323-scaffold201-317586 16 67688973 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774281 Affx-122922269 AX-385261417 16 66742320 TCCTTTAGGTTCACTTGTGGTGAAGATGACACACC[A/G]TCATTGTTGCTAATTATACTTCATTCCTTCCTTCC R 2 1 2 1 101000 f 74 goat snp20324-scaffold201-352934 16 67724315 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768392 Affx-122958752 AX-385255572 16 66775696 GTTACAGTTTGAGTGAAATAGGGACCATAAAATCA[C/T]ACCTCCAAATGTCAAGACTGCTCTTAGTGAAAGGT Y 2 1 2 1 101000 r 74 goat snp20325-scaffold201-386310 16 67757721 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385384 Affx-122971622 AX-123255742 16 66804844 AGAGTGCTTCTGGCTTGATGGAGATGGGTGAGCCT[A/G]CCATCATTAGGAATGTGTAAAGTCTGTGATAATGT R 2 1 2 1 101000 r 74 goat snp20326-scaffold201-415458 16 67786774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770245 Affx-122951388 AX-385257411 16 66819657 GTTCTATTACAGATCCAATGCTAGGCAACAGCGAA[C/T]CCCAATCCACTAGCAAGGGAACACCAGGATGTTTC Y 2 1 2 1 202000 r 74 goat snp18375-scaffold186-823860 16 67801772 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380727 Affx-122975143 AX-123251085 16 66848501 AGGCGATACCAGACGGTCTTCATCATTAAAGCTCT[C/T]TCCCTCCCGCCTGGCTTCAGCTTGCCCCTTTAGCT Y 2 1 2 1 101000 f 74 goat snp18374-scaffold186-795016 16 67830949 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770267 Affx-122974902 AX-385257433 16 66927045 CAAGGGTCTTAATTCTGGTTTCAGAGACATTTCAC[G/T]AGTCTGTGCATAGATTCTAGGTGGCTGGTGAGCCC K 2 1 2 1 101000 f 74 goat snp18372-scaffold186-716472 16 67909519 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376606 Affx-122979053 AX-123246965 16 66966990 TGTTTTTTACGTTTAGGATATAACCGTAGACGGTG[C/T]GTTATATTTAGACACCATGTACCTGAGACAGTTCC Y 2 1 2 1 101000 r 74 goat snp18371-scaffold186-676527 16 67949427 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409014 Affx-122953878 AX-123279365 16 67012916 AAGTGAACTAACAAATTTGAAACACAGAGCCTTGT[A/G]CACAACAAGTGTCCATTAAATACCAGCTGCGTCAG R 2 1 2 1 101000 r 74 goat snp18370-scaffold186-630601 16 67997102 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439941 Affx-122929997 AX-123310278 16 67041704 TTTATTTTAAAGGGCAGTTATAAATTCCTTTGTGT[A/G]TCTTGAAACATAATATTATAGGTAGCAGTTAAGTA R 2 1 2 1 101000 r 74 goat snp18369-scaffold186-601813 16 68024511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277173 Affx-1111835716 AX-519550679 16 67048689 ATCTCCAAAGTATAGCTAATGTTCCAATTAAGCTA[A/G]GTGATGAAAACTGAGGGAGTAACACACACAATAAA R 2 1 2 1 101000 r 74 goat Random2.2K-1625 16 67048689 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795140 Affx-122934131 AX-385282098 16 67072804 TTAAATGAATTAGATATAAAGCTCAATATGAATTA[C/T]AACTGATTTTAGGTAGAAAGGTTGTTTTATTAAAA Y 2 1 2 1 201000 f 74 goat snp18368-scaffold186-570713 16 68055547 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424081 Affx-122942044 AX-123294427 16 67113879 TGATGTTCTCCACCAGATTGTAAGGTCCATCCATA[C/T]AGGAAATGGGTGTATCATAGCACTGGCTCTGTCCC Y 2 1 2 1 101000 r 74 goat snp18367-scaffold186-529638 16 68096497 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766271 Affx-986697882 AX-311996425 16 67147558 ATCAAGACAAAGGAAAGAAATTATCCAAAGAATGA[C/T]GTTACTGAAGACAGTAATGAGAGCAAATTGGTCAA Y 2 1 2 1 600010 r 74 goat 16_67147558 16 67147558 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 320766275 Affx-986697884 AX-385253667 16 67147630 AACAGACTCAAGCAAGTTTCTGCCACCCATTTGTG[A/G]CTGCCTTGTTCCTTTTTTTGCCCTATAAAATGGAG R 2 1 2 1 600010 r 74 goat 16_67147630 16 67147630 Ancestral_priority_1043 ancestry 0.634 recommended IMAGE 10K 10K ancestral 320763357 Affx-986697886 AX-385251257 16 67147943 GCTGTAGGCTCTAAGTTGGTGTCCTTGCCTCTGCC[A/T]TATCTCTTTCTAACCTTTTCCCTCCCCCTGGTCAG W 4 1 2 1 600010 f 74 goat 16_67147943 16 67147943 Ancestral_priority_1043 ancestry 0.48 neutral IMAGE 10K 10K ancestral 320803361 Affx-986696302 AX-385290196 16 67148330 GACTTTTTGGACTCTTCCTTCCAGCACCAAGTTTA[C/T]TCTTTCACCATTCCCATTTCACTGTATTACATTCT Y 2 1 2 1 600010 f 74 goat 16_67148330 16 67148330 Ancestral_priority_1043 ancestry 0.614 recommended IMAGE 10K 10K ancestral 320766222 Affx-986697854 AX-385253621 16 67148382 TTTCACTGTATTACATTCTTCCGTTTTCTGGTGCG[C/T]TCATTCTCCTTTGAAATCAGAGCGTATATCTTTCA Y 2 1 2 1 600010 r 74 goat 16_67148382 16 67148382 Ancestral_priority_1043 ancestry 0.738 recommended IMAGE 10K 10K ancestral 320766228 Affx-986697857 AX-385253626 16 67148461 ATCCACAAATTTCAGACCAGGGGCCAGCATGTAGT[A/G]GAAGTTTTAATAAATGTTTGAAGAGTGTATAAAAT R 2 1 2 1 600010 r 74 goat 16_67148461 16 67148461 Ancestral_priority_1043 ancestry 0.652 recommended IMAGE 10K 10K ancestral 38450809 Affx-122921805 AX-123321143 16 67156790 GTGAGAATAAGAAGCTCACTCTTTTCTTCTCATTT[A/C]TCCACTAGGAATGAAGATATTTGGATTTTCTAAAA M 2 1 2 1 202000 r 74 goat snp18366-scaffold186-486727 16 68139280 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393494 Affx-122965819 AX-123263850 16 67196647 CCATAGGGGGGAAAAGCATTTTTAAATTGTATATT[A/G]CCACTTCAAAATTAGAATTTGAAAAGCAAATGTAT R 2 1 2 1 201000 f 74 goat snp18365-scaffold186-446870 16 68179756 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432703 Affx-122936026 AX-123303044 16 67267050 TTCTAATAAATTAAATAAATAAAATAAACAGAGGC[A/G]TTTGTCTGGAGAAGGGGTTGGGGAGAGCCTTTCAA R 2 1 2 1 201000 f 74 goat snp18364-scaffold186-376467 16 68249555 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445520 Affx-122925176 AX-123315857 16 67311563 TCCTGATTGAGACCAAGGATGGCAAGTTTCTGCCA[C/T]GAGGGCTCCTCCTCCCCTCTTCCCCTCTGTCCTTT Y 2 1 2 1 101000 f 74 goat snp18363-scaffold186-331954 16 68294378 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389621 Affx-122968751 AX-123259979 16 67355933 TTGCCCTTAAAGTAACAGTCATCACTTCTGCTCCC[A/G]TTCCATTGGCCAGCCCTTGGGATCACATGGCCCAT R 2 1 2 1 101000 f 74 goat snp18362-scaffold186-287584 16 68339146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783574 Affx-122937208 AX-385270636 16 67391783 CATCCTTGTATTTTTAAATTGCAAGTGTCCAATTA[C/T]GTACAAGGGTCAAGACAAAATTGATCTGAAGGAGC Y 2 1 2 1 101000 f 74 goat snp18361-scaffold186-251734 16 68374935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393428 Affx-122965869 AX-123263784 16 67420907 ATCTTAGATCTTGCTGCCTGAGCGAAGTTTTCTCC[A/G]GCTTCAGGAGTCCACCCTGTCTTCTCCTATACAAA R 2 1 2 1 101000 f 74 goat snp18360-scaffold186-222610 16 68404841 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783089 Affx-122959114 AX-385270156 16 67462936 AAAATGAGTTATGCTTGTGTATTAAGAAAGAATTG[A/C]GGCTGCATCTATATTCATTGGTATGTGTTTATCAT M 2 1 2 1 101000 r 74 goat snp18359-scaffold186-180581 16 68446929 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401675 Affx-122959564 AX-123272028 16 67506717 TGCATGCCTCATACTTTCAGAGACAATATCCTTTG[A/C]TAGAGTCAAAAGCAGGTTCTGGCTGGACAGTACCC M 2 1 2 1 101000 f 74 goat snp18358-scaffold186-136800 16 68490367 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436589 Affx-122932888 AX-123306927 16 67536493 GGGATCGAACCCAGGTCTCCTGCATTTCAGGCAGA[C/T]GCTTTAACCTCTGAGCCGCCTTAGTAGGACAATGG Y 2 1 2 1 303000 f 74 goat snp18357-scaffold186-107024 16 68520219 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402639 Affx-122958390 AX-123272992 16 67578223 AAAAATTAAGAAGAAGAAGCCTCAGGTGAGTCTTG[C/T]GATCAGGAAGGTGTGGGGAGTCAGTTTTGGGCATG Y 2 1 2 1 103000 f 74 goat snp18356-scaffold186-65294 16 68562165 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391593 Affx-122966604 AX-123261950 16 67613251 GGCGGCAGCAGAGGGTGACTCCGTTAACAAGACCA[C/T]ACAGGTGAAAAATCAATTGGCAAATATTTTGTAAA Y 2 1 2 1 202000 f 74 goat snp18355-scaffold186-30266 16 68596987 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397168 Affx-122962424 AX-123267523 16 67643302 TGTGTCAGCTTGGAGCTGTGAGATGTCATTAACTA[C/T]GCAGGCCTCAGTGTTCTCCTGGGTAAAAAGGGAGG Y 2 1 2 1 101000 f 74 goat snp18354-scaffold186-215 16 68627361 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781971 Affx-122961338 AX-385269051 16 67673511 ATGGTCTTCCCAAGTCAAGAGGGTACTATAAGATT[C/T]TCTAATGCTTTGCAAAACTTTACATTTTGTAATGT Y 2 1 2 1 101000 f 74 goat snp41492-scaffold540-29895 16 68657681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387273 Affx-122970546 AX-123257631 16 67714948 TTCTCTACACTTTGCCCAGAATGGATTTTGTGTTA[C/T]GTGAGTCACTCAGCAGTGTCCGTGTCTTTGTGATC Y 2 1 2 1 101000 f 74 goat snp41493-scaffold540-71332 16 68699241 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769837 Affx-122958343 AX-385257007 16 67770366 GAGTTTTAAATCTGAATCTTGATACTGATCATTCT[C/T]AGTAGTCTGCATTTCCTTGAGTTTTCCTTTATTCA Y 2 1 2 1 101000 r 74 goat snp41494-scaffold540-126750 16 68755736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405855 Affx-122955859 AX-123276207 16 67810036 GTTGCTCTGGACAGAGAGACGGAATCAGCAGCCTG[A/C]TGGCATCACTGGGTCAAAGACCATGAGGTCATTTG M 2 1 2 1 101000 r 74 goat snp41495-scaffold540-166420 16 68795373 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774141 Affx-122954925 AX-385261279 16 67844310 GCTCGATGCAAAGATGTTTAGAATGTTCATCTTGG[A/C]GATTGTATTATTTACAGCAACTCCACACTGTGCCC M 2 1 2 1 101000 f 74 goat snp41496-scaffold540-200694 16 68829610 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451632 Affx-122921615 AX-123321965 16 67883797 ACGCCTCCAGACTTTCTCTCCCCAGCATCACTGTT[A/G]TCCGCTCATGGAACACAAGCTCATTGTTATATCGA R 2 1 2 1 101000 r 74 goat snp41497-scaffold540-240181 16 68869136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271810 Affx-1111833080 AX-519545597 16 67900784 CCTATGCATTTCTTTATAATATATTACTTTCCTAG[A/G]AAATGGGATCCATCTGAATTTTCATAAAGTTTTAT R 2 1 2 1 101000 r 74 goat 16_67900784_AF-PAKI 16 67900784 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406520 Affx-122955136 AX-123276872 16 67913305 AACCTTATTACCAACAGATATTAGTTTCATTTTTC[A/G]CCAGCTTTTTGGCATCCAACTCTTTCCCTCTGGGA R 2 1 2 1 201000 f 74 goat snp41498-scaffold540-269689 16 68899174 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796152 Affx-122950987 AX-385283103 16 67998799 TTTAAAAAAAAACAGGCATTACCTTAAAAAGTTTG[C/T]ATTCTGTTGTAAACACAGTATGATTACAGGAGCAA Y 2 1 2 1 101000 r 74 goat snp41499-scaffold540-355183 16 68984599 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429756 Affx-122937587 AX-123300097 16 68059253 GTGTAAATCAGCAGTGATATCTCTTTGATGGTCTC[A/C]CTTAGCCATGAAGCATGAAGTATAGATAAAAAGGC M 2 1 2 1 201000 r 74 goat snp41500-scaffold540-415637 16 69046082 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403133 Affx-122958110 AX-123273486 16 68092734 TCATCCAAAACTCTTTCAAAGGTATATCTTGAAGG[C/T]GCTTCTATAAAAGCAGCACTACCTGTATTCATTAA Y 2 1 2 1 101000 f 74 goat snp41501-scaffold540-449118 16 69079783 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417860 Affx-122946772 AX-123288208 16 68143626 ACCATTTAAAGCCCTGCACTCAGAGGAGCTGTTAC[A/G]CAGTGCAGCACCTCCTCACGCTCTGGCTCTAAATC R 2 1 2 1 101000 f 74 goat snp41502-scaffold540-500010 16 69131014 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449579 Affx-122923225 AX-123319914 16 68185951 GCTGGGCTTCTGACAATAATCTTACCTAAGGGAAG[C/T]ACAATCCTTAAAACTATTATAAATTAGACATGAGA Y 2 1 2 1 101000 f 74 goat snp41503-scaffold540-542335 16 69173527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406454 Affx-122955185 AX-123276806 16 68254321 CTTACAGAACAAGACTTATGGACTGTTAATGGACT[C/T]CCAAATGAAAATAACTCTTCAGATCATTTGCCTTT Y 2 1 2 1 101000 f 74 goat snp41504-scaffold540-610705 16 69242523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774661 Affx-122940010 AX-385261795 16 68330680 TTGCTATAATTTTAATATTAAGCAATGCACATAGC[A/G]CGCCCAAATCAGAATTGCTAATTCACTTCAAGGGT R 2 1 2 1 101000 r 74 goat snp41506-scaffold540-687064 16 69319019 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801708 Affx-122958775 AX-385288616 16 68377996 GCACTTTCCTGGCAAATGGGGAGATATTCTTCTAG[C/T]GATCTATTCTCAAACTATAGAGGCTGGAGGACTTC Y 2 1 2 1 101000 f 74 goat snp41507-scaffold540-734380 16 69366067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399377 Affx-122961332 AX-123269732 16 68414959 GACATCCAATGGCATGTGAAGGTATAATTGGTAGT[A/G]TTTTCTCCTTTAAGGGTCACAAAATAGTGGTCCGT R 2 1 2 1 101000 r 74 goat snp41508-scaffold540-771343 16 69403352 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787433 Affx-122929943 AX-385274458 16 68463395 ATGTGATTATTGAACTACTGAATGTAATCTGAATT[A/G]TGGTGGAATTTCAAAGTAGGAGATAATATTTTCTA R 2 1 2 1 101000 r 74 goat snp41509-scaffold540-819779 16 69452187 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397209 Affx-122962392 AX-123267564 16 68497277 AGTCTATTCATGAACCAATGAGGACAGAGTAAAAG[G/T]TACCAAGAATCAAGGTTGATCCAATTTTGTGTCCC K 2 1 2 1 101000 r 74 goat snp41510-scaffold540-853661 16 69486513 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451503 Affx-122921117 AX-123321836 16 68548995 AACTCCATGCAACTCCATCACCTGTCGCAGGTGGA[C/T]CAACCGTGACGCTGTCTGGTGTATTTAGTTTTCCA Y 2 1 2 1 101000 r 74 goat snp41511-scaffold540-905379 16 69537757 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384030 Affx-122972892 AX-123254388 16 68589569 AAAACTGCACTCAGCACTGCCCAGCCCAGTTCTCT[C/T]CTGCTAGAGCTGGCAAGCCCTTCTGGCCACCTGAA Y 2 1 2 1 101000 f 74 goat snp41512-scaffold540-945953 16 69578330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375615 Affx-122978712 AX-123245974 16 68628583 CAACTGGAGAAACTCCAGGAGAAAGACAGAGGTCA[G/T]ATTTAGGCAGGAAGAAGACAGAGGGGCAACTTAAA K 2 1 2 1 201000 f 74 goat snp41513-scaffold540-984967 16 69617700 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802838 Affx-122947043 AX-385289737 16 68663473 TGAACAGCGAACTAGAATTTTCAGTTAACTGTCAC[A/G]TATTATCCCCTAACCACTGATGAGAATTTACTGTA R 2 1 2 1 101000 f 74 goat snp41514-scaffold540-1019857 16 69652484 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419572 Affx-122945400 AX-123289920 16 68714531 ACCTCCATGGGGTTGTCCATTAAGAGACTTTAAAA[G/T]CGATTGCAAGAATCACCTCAAGGTGTGAGAAGGCG K 2 1 2 1 101000 f 74 goat snp41515-scaffold540-1070915 16 69704790 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425353 Affx-122941584 AX-123295699 16 68745495 AGGCCCAGAGATTGTGATCAGGACACTGAGGCACC[A/G]TCCTGGGACTTACTGCAGTTTGGGGACCTCTGTGC R 2 1 2 1 202000 f 74 goat snp41516-scaffold540-1101879 16 69735602 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406610 Affx-122955841 AX-123276962 16 68782532 TGATTTTCAGGTAGAATGAGACTGCGTGGAAAGAG[C/T]GTAGGATGGAAATTAGACTTGCCCTGGAATCCCAG Y 2 1 2 1 101000 f 74 goat snp41517-scaffold540-1138916 16 69772478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801070 Affx-122970149 AX-385287984 16 68845434 TTTTAAAGCCTGGAATTAAGTTTTTGCTCAAATTC[C/T]AGAGTACAGTAATATATCAAAAGGAAGGCTTAGGG Y 2 1 2 1 101000 r 74 goat snp41519-scaffold540-1201818 16 69835717 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409806 Affx-122952963 AX-123280157 16 68883862 CAACAGCCGTGACGTCCTAGGGCTTCCCATATGAC[A/G]TGGTGGTAAAGAATCCGCCAGCTAACACAGGAGAC R 2 1 2 1 201000 f 74 goat snp41520-scaffold540-1240246 16 69874411 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390511 Affx-122967247 AX-123260868 16 68930502 GTTTCCTGGAAGATTAAATGAGAAGTCTTGCAAGG[C/T]GCTTAGCATGTCATCAGGTACTCACTCAGTGGTAG Y 2 1 2 1 101000 r 74 goat snp41521-scaffold540-1286886 16 69921024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433188 Affx-122935646 AX-123303529 16 68965302 ACCCTCTCCTGCTTAAAAGTTGTGGCTGGCTCCCG[A/C]TGCCTTACATGATAAACATGCACTTTATTTATCTG M 2 1 2 1 101000 r 74 goat snp41522-scaffold540-1321686 16 69955657 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452056 Affx-122920881 AX-123322389 16 69006904 AAGCCCGAGGTGCTACACCAGCCCAGCCTGTGGTG[C/T]GTCTCCTTGGTTGAGACGATAGGGTGGAGAAATGA Y 2 1 2 1 103000 r 74 goat snp41523-scaffold540-1363288 16 69997170 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417297 Affx-122947236 AX-123287645 16 69066902 CCTGTCCTGGCACGGGGGGCCCAGGCCAGGCTGTG[A/C]GGGGCCATGTCCTGGTCTCCCACTTTCACTTCCTG M 2 1 2 1 303000 f 74 goat snp41524-scaffold540-1423286 16 70058285 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415403 Affx-122948740 AX-123285752 16 69099719 ATACATATTTTGATTAAAATTCAAGACTGAAAGGG[C/T]GAGTTTCAGTGGCTAGGTATAACACTTCAAGTGGA Y 2 1 2 1 101000 r 74 goat snp41525-scaffold540-1456103 16 70091336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277047 Affx-1111835717 AX-519550554 16 69158375 TACTGCATATGTTGTACATACTTCCATTCATGTGC[A/G]AATCTGCACATATAAGCCTTTGACTGTGTGGATCA R 2 1 2 1 201000 f 74 goat Random2.2K-1629 16 69158375 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38381021 Affx-122974654 AX-123251379 16 69163981 TTTTTTCCTTTCATTGCTATTCCGATGTCCCTTGA[C/T]GTCATTGGGGAATTGGGTCTAGTACTCCCTACTGG Y 2 1 2 1 101000 f 74 goat snp41526-scaffold540-1520365 16 70156066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772902 Affx-122964882 AX-385260047 16 69207168 GGGCAGAGCTTTACCTTTGGTTTAGATAAAACTTA[C/T]ACTCTTCCGTTGTAAGCCTTTCCTTTATCAACATA Y 2 1 2 1 101000 f 74 goat snp41527-scaffold540-1563552 16 70199614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447977 Affx-122923755 AX-123318313 16 69243194 TTGTCACATTGCCCAGCCTTCCTTGGAGTTAGATA[C/T]GGCCAACTGTTAAATGTCTCAAAGGAATGTGAGCA Y 2 1 2 1 101000 f 74 goat snp41528-scaffold540-1599578 16 70235125 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777302 Affx-122970768 AX-385264424 16 69296644 ACTGTAACATAATCATGAATATCAAGTTATTCCAG[C/T]TCTTATGTTAGGAAAAGCCAATTTTAAATTTGGAT Y 2 1 2 1 101000 f 74 goat snp41529-scaffold540-1653028 16 70288498 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415126 Affx-122949429 AX-123285475 16 69347196 TCATTATTCCTTTGTGGAGCAAGGGCACTGCTTGC[A/G]TTTTGGTAGGACAGCACTGTTGTTCTCAGTTGTCC R 2 1 2 1 102000 r 74 goat snp41530-scaffold540-1703580 16 70334737 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277051 Affx-1111835719 AX-519550558 16 69389977 TTTGCACTGTTCTGAATAGCGTGATGAAATCTCAC[A/G]CTGTCTTGCTCCATCCTGCCTGGACATGAACCATC R 2 1 2 1 201000 f 74 goat Random2.2K-1630 16 69389977 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320801558 Affx-122962026 AX-385288467 16 69409507 TTCTCTTTCTTAAACAGCCAACACACTGAAGTGAC[A/G]TAAGCCTGGAACTTCATGTGGCCATGCTCCTTTTG R 2 1 2 1 101000 f 74 goat snp41531-scaffold540-1765891 16 70396963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384308 Affx-122972279 AX-123254666 16 69438117 TTATGCAACTTACAAAGGGATGCCGAGAGCAGTGG[A/C]GTATGATGGTTCATTTGTGCCTCCTTTCGCTAGTA M 2 1 2 1 101000 r 74 goat snp41532-scaffold540-1794501 16 70425534 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449105 Affx-122923586 AX-123319440 16 69471232 AGAGCCGTCTTGGGGTCCCCATCATCTAGGCACAC[A/G]GCCTCCCCATGGTGATTGACTTCTTGTACTTGGTC R 2 1 2 1 201000 r 74 goat snp41533-scaffold540-1827616 16 70458691 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441640 Affx-122929206 AX-123311977 16 69510898 GCAAGTGTGCTGGAGGGATTCAAATTGTACCATCA[G/T]TCACGCGGAGATGTCATAAGGAAATGCTAACACTT K 2 1 2 1 101000 f 74 goat snp41534-scaffold540-1867282 16 70497634 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391435 Affx-122966751 AX-123261792 16 69543247 CTGACCCCTGCAAAGCATTTGTAGAATTAGTTAAT[A/G]GTACTCAGGCAACAGTTCAAGAGGCTGGTCCTTGC R 2 1 2 1 201000 f 74 goat snp41535-scaffold540-1899631 16 70529613 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409978 Affx-122953284 AX-123280328 16 69600077 CACGCACACAAAGGTTTAAAAATGAAAGATCATGT[A/G]TTCAGAGACCCCCAAGAAGGAAACCATATTTTCTC R 2 1 2 1 101000 r 74 goat snp41536-scaffold540-1956461 16 70586182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789299 Affx-122942408 AX-385276310 16 69662855 TGTTCTTTCCTCTAATTCTCCGCAGTCCCACTTAA[A/G]TGGGCTGCTTTGGCTTTTCTTTATAAATTTCACCT R 2 1 2 1 201000 r 74 goat snp41537-scaffold540-2019239 16 70648064 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445201 Affx-122925522 AX-123315538 16 69692109 GTTGGTGGAGAGAAGGGGGTGGTCAGGGGCTGAAG[A/G]GCACTCCCGCCCGGCTCCTGGTTCTAAGGAGGCTG R 2 1 2 1 101000 r 74 goat snp41538-scaffold540-2048493 16 70677047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444835 Affx-122926309 AX-123315172 16 69763530 GGTCACAAAGAGTCGGACACAACTGAACAACTAAC[A/G]TTTTCGCTTTCATAAAGTTGGTTGAACTTAAGCAC R 2 1 2 1 201000 r 74 goat snp41539-scaffold540-2119914 16 70748996 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454236 Affx-122919666 AX-123324569 16 69805113 ATTTTTAGAGATAATCAGTCTAGAATATAGGAACC[A/G]TAAGCTATACATCCAATTGTCTTTTTCTGAAGGGC R 2 1 2 1 101000 r 74 goat snp41540-scaffold540-2161497 16 70790771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430631 Affx-122936961 AX-123300972 16 69893114 GCTAAAAAGGCCTTTGAGCAACTGGCTAAGTGAAA[C/T]GGTAAGAGAGCATCAGTTTTTACTTCAGGAGAGAA Y 2 1 2 1 101000 f 74 goat snp41542-scaffold540-2249498 16 70878851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429607 Affx-122937706 AX-123299948 16 69925058 GACGTGGGCTCATATTATGATAAAAAAAGGAGACC[A/G]TTCAGCTCACAGCCTGTACTGTCTGTCCCTGATGC R 2 1 2 1 201000 f 74 goat snp41543-scaffold540-2281442 16 70911079 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381557 Affx-122974826 AX-123251915 16 70014133 CCTCCGGCTAGATTGAGATTAGCAACTCTAAGTTT[A/G]TAGTAAGAACCATCACCTTGTTTGTGTGATTTTTC R 2 1 2 1 101000 f 74 goat snp41545-scaffold540-2370517 16 71000524 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777809 Affx-122948964 AX-385264928 16 70053506 ATGATGCTTCTCAATCCTTTGTTAGTCCTTTGAGT[A/G]TGCTCTGCTTTATACAAATTTGAACTTGTATAAAA R 2 1 2 1 101000 f 74 goat snp41546-scaffold540-2409890 16 71039810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399731 Affx-122960455 AX-123270086 16 70098265 GAGCAGGTGTCTCTGTCCCTCGGCAGGTCTGAACG[C/T]AGAACTTCCGCTTTGGGAAGGTCTCCATGGGTTCG Y 2 1 2 1 303000 f 74 goat snp41547-scaffold540-2454649 16 71083309 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420095 Affx-122945099 AX-123290443 16 70157521 GGATGTAACTGTGTGATAAGTTGAGTTAGATTTGT[A/C]TGCTTGGGAAGTCTCATAGTCACCCTCATGGGGAC M 2 1 2 1 101000 f 74 goat snp41548-scaffold540-2513905 16 71142919 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277180 Affx-1111835720 AX-519550687 16 70199864 CTTGTTATTCACAGACAAAAGTGCTCTGGAGGTAG[A/G]GCTGGTAATGTTTCACTGGACCTGATTCATTCTAA R 2 1 2 1 101000 r 74 goat Random2.2K-1631 16 70199864 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407455 Affx-122954784 AX-123277806 16 70205583 GCCCAGCTCAGCCTCTCCTTCCCACTTCTCAGTCT[A/G]CTTCCAGCTAGAATCTCTCTCTCCTCTAATTTGTC R 2 1 2 1 101000 r 74 goat snp41549-scaffold540-2561967 16 71190867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442810 Affx-122927714 AX-123313147 16 70236031 TTCCTTAGTTCTCTCCTCACCTCCCATTCCTTCCC[A/G]CACATCTTTATTTTCCTGTTTTCTCTCCAGTAGTT R 2 1 2 1 201000 r 74 goat snp41550-scaffold540-2592415 16 71220743 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277182 Affx-1111835721 AX-519550688 16 70284301 AAAGTGCTCACCATCTTGAAAGAATGCACTGTGCA[A/G]CTTCACACATACAAACTCATGCATTTTTTTGTTGT R 2 1 2 1 101000 r 74 goat Random2.2K-1632 16 70284301 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430608 Affx-122936977 AX-123300949 16 70292173 TTCCAGGCAACCAGAACCCTAGTCTCTGTCCACAC[A/G]TGAGTAGTTTACAAAGACTATGCAATCTGCTATAC R 2 1 2 1 201000 r 74 goat snp41551-scaffold540-2648557 16 71276836 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390340 Affx-122967695 AX-123260697 16 70323792 ACTGTATAGTCCATGGGGTCACAAAGAGTCAGACA[C/T]GACTGAACGGCTTTTACTTACAACCAGGAGGAACT Y 2 1 2 1 201000 r 74 goat snp41552-scaffold540-2680176 16 71308326 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399647 Affx-122960524 AX-123270002 16 70352464 GCTAGGCATGGAGCAATTCCTGGTGAAAGACATCC[A/G]TAAAATATATTAAAGTACCAAAGAGAAATCACAGA R 2 1 2 1 201000 r 74 goat snp41553-scaffold540-2708848 16 71337647 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272830 Affx-1111833081 AX-519546523 16 70403281 CTCTCATCCAACATATGCATGGCAATCTGTGACTC[A/G]TCTTTTCATTCTCTTGATGGTATCATATGACGAGT R 2 1 2 1 101000 f 74 goat 16_70403281_AF-PAKI 16 70403281 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423522 Affx-122942450 AX-123293868 16 70465445 CACCATATGCAATCTGGCACAGAGGAAATGCTGCT[A/G]TTTTAGGATCGAGGTGATGCCAAAGATGTATATTT R 2 1 2 1 101000 r 74 goat snp41555-scaffold540-2821829 16 71452258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275186 Affx-1111834643 AX-519548765 16 70522066 AGGCA[A/G]CCTAAAAGGCTCTCATTCCCACCCCTCATGAGAAT R 2 1 2 1 102000 r 74 goat GoatD01.044321 16 70522066 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320789531 Affx-122929946 AX-385276540 16 70543029 GAGACCCAGTCACATGGAGGTCACGATCCATATCC[A/G]CTCATCATTAACAGATATTAGCGAAAGGATTTAAC R 2 1 2 1 101000 f 74 goat snp41557-scaffold540-2899413 16 71530148 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453075 Affx-122920053 AX-123323408 16 70572663 ACCACAGCTACGTTTTATTAAGTGCTATTTGATCC[A/G]TTTGGAAAAAGCCTGTTTGTTGGGATTCATTTGGG R 2 1 2 1 101000 f 74 goat snp41558-scaffold540-2929047 16 71559819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383953 Affx-122972952 AX-123254311 16 70619109 CGATGCTGATGGATGCCATGTGTGGGAGGTGAGGA[C/T]GCTCAGCTGCGGGGCTGAGTCTGGGGTCTAAGTGA Y 2 1 2 1 101000 f 74 goat snp41559-scaffold540-2975493 16 71605915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438636 Affx-122930910 AX-123308973 16 70674370 ATCGGACAGCAGAGCTGGAAGAGCTCATTTAATCT[A/G]TTTTCTCATTTTCAAGATGTAGCAGTCGAGTCTAT R 2 1 2 1 201000 r 74 goat snp41560-scaffold540-3030754 16 71660987 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795478 Affx-122929156 AX-385282433 16 70751648 ATCTTTAGGATATTATCATTCATTGGTTGTAGGGA[C/T]GGGAAGAGTGAAAGGTAACTGAGGTTTCTACTAGA Y 2 1 2 1 101000 r 74 goat snp41561-scaffold540-3108032 16 71738311 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442968 Affx-122928207 AX-123313305 16 70780535 GCATTGCATGGCAGTTCATTCTTGCCTCTTCCCCT[A/G]TGGAATGGAGCCTCAGTCCATGCGTATATCAATGG R 2 1 2 1 201000 r 74 goat snp41562-scaffold540-3136919 16 71767266 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435103 Affx-122933706 AX-123305443 16 70814647 AACTGCTATAACCTATTCTTTAACCTGAAAGATCT[A/G]TTCTGTGGATGCAAATCTCTCTTGTATATTATCCT R 2 1 2 1 101000 r 74 goat snp41563-scaffold540-3171031 16 71801410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418034 Affx-122946640 AX-123288382 16 70877672 GATCCCACGGGCTGCATGGCACGGCCAACCCCCAC[C/T]GATCCCCGTCTCCAAAACAAAAAACCCCCAAACTT Y 2 1 2 1 103000 r 74 goat snp41565-scaffold540-3234056 16 71864763 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435707 Affx-122933310 AX-123306046 16 70924261 CTAAAAAATGAAGGAAGGATATATGAGGAACTATC[A/G]TCACAAATATCATAAATAAACAATTATGATTTCAT R 2 1 2 1 101000 f 74 goat snp41566-scaffold540-3280645 16 71911595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382194 Affx-122974007 AX-123252552 16 70955488 AGGCCCCATTGATTTCAGGGTAAAATTCATATTCC[G/T]CAACAATCTTTACAGAGTCTTTCATGATTTTGACC K 2 1 2 1 101000 f 74 goat snp23283-scaffold2329-456745 16 71942873 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420917 Affx-122944597 AX-123291264 16 70995419 CCCACGCACGTCTATTTCCTGTTGTACCCTTACTT[A/G]CCCCAATTGTAGAGGATTATGCCAGTTTATATTAT R 2 1 2 1 101000 r 74 goat snp23282-scaffold2329-416814 16 71982948 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776351 Affx-122947945 AX-385263478 16 71048916 ACTGTCATACTTATTTGTCCCTTATGGAACCCTTA[C/T]GTGTCTGTCTAACTAAACTTGGCAGTGATTTAAAA Y 2 1 2 1 101000 r 74 goat snp23281-scaffold2329-363317 16 72037160 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763332 Affx-986697861 AX-385251234 16 71049502 TTGCAAAATCTTAAGAAAGTAGCTGGACAGCTCTT[C/G]CCCGTGCTCCTGTCTGGGGCTAGGGACAGAGTGCT S 4 1 2 1 600010 f 74 goat 16_71049502 16 71049502 Ancestral_priority_1043 ancestry 0.708 recommended IMAGE 10K 10K ancestral 320763334 Affx-986697863 AX-385251236 16 71054479 CCGCGGAGAGGCCGTTTTTGTGAGCCGTTCACACC[C/T]TCTCCTCGCCCCGTCGTGACCTCGGCCCAGTGTTT Y 2 1 2 1 600010 f 74 goat 16_71054479 16 71054479 Ancestral_priority_1043 ancestry 0.558 neutral IMAGE 10K 10K ancestral 320785599 Affx-122977907 AX-385272643 16 71109958 ATTCATCATTTGTACTGGTGTAAATAAATCATTGT[C/T]TTAGACTGAGGGATTTCTTGTTTAATTTTGTTGCT Y 2 1 2 1 101000 r 74 goat snp23280-scaffold2329-302275 16 72098122 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445655 Affx-122926151 AX-123315992 16 71154280 GATTTTCATCATTTCAGAGGGTTTTATCGGACACC[A/G]CTTAAACTAGACTTGGGGTTCAAATCACATTGGAA R 2 1 2 1 101000 f 74 goat snp23279-scaffold2329-257953 16 72142507 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277153 Affx-1111835706 AX-519550659 16 71324365 ACAAGCAGTTGATGACTACTCTGTAACTCAAAAGT[A/G]TCATTGCATTACGACTCCAGATCTGCAAGACCATA R 2 1 2 1 101000 r 74 goat Random2.2K-1634 16 71324365 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439800 Affx-122930492 AX-123310137 16 71333990 GGACCTTGAAAACGATAACCGTTTACACTCATCTT[C/T]GCCATCGCTAAAACAGTAAATACTCAAGTCTTCAA Y 2 1 2 1 101000 f 74 goat snp23276-scaffold2329-78243 16 72324611 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392057 Affx-122966391 AX-123262414 16 71378188 AAAAAACAGATCTGCTCTATCTACCGCACTAGGCT[A/G]TAAGATCACGTCTCTGGTTCTCCAGTTCTCATTGC R 2 1 2 1 101000 f 74 goat snp23275-scaffold2329-34045 16 72369051 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387705 Affx-122969807 AX-123258063 16 71409083 TGGCAGCAGAACAGCAGGAAACAGCTTCCTTCTTC[A/G]AGGCCTCAGCCGGTGCCTGGGGACAGGGAGCCAGG R 2 1 2 1 103000 f 74 goat snp23274-scaffold2329-3150 16 72399439 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769478 Affx-122965312 AX-385256648 16 71427644 ACCCCATGAGACTGTAAAACCTATGAGAGCAGTCA[C/T]AGTACCTATTATGTTAACGCGATATCCATCCCCAA Y 2 1 2 1 101000 f 74 goat snp52575-scaffold785-15312 16 72417815 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764975 Affx-122925088 AX-385252554 16 71461854 GCAATATAAAGTGACCAAAAAGGGAGAAGGCATTA[C/T]GAGGAAGGGTGTTACAAATAACGTAAAACGATCAC Y 2 1 2 1 101000 f 74 goat snp52576-scaffold785-49522 16 72452027 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406459 Affx-122955182 AX-123276811 16 71491257 ACTGTTGACTTGGGGAAAACTCAAGGCCATCAGGA[C/T]GTTCTCTCACCATTCACCATGATGGGGCCTTTGGA Y 2 1 2 1 101000 f 74 goat snp52577-scaffold785-78925 16 72481553 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767521 Affx-122919354 AX-385254780 16 71534524 TGGGTAAGCGTCTCAAAGGTACTTGTCTTGATATC[A/G]TTATTGTCTTGTTATGACAATAATGAACACTGTTT R 2 1 2 1 102000 f 74 goat snp52578-scaffold785-122192 16 72525028 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395567 Affx-122963848 AX-123265922 16 71569566 GTTTTTGACCCACGCTCTGGAGGAATTTTGAGTTA[A/G]AGCTGGCACATTTGGGCATCTTCCCTGTGTGTTTC R 2 1 2 1 101000 f 74 goat snp52579-scaffold785-157234 16 72559272 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277058 Affx-1111835722 AX-519550564 16 71578080 GCCAGATACAAGTACACATGTCACTTGGCAACATT[A/C]AGGAATCACTGAGAATTCAAAACATTAAAAAGTAA M 2 1 2 1 101000 f 74 goat Random2.2K-1635 16 71578080 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447322 Affx-122924899 AX-123317658 16 71615383 ATCCTCAGAAAATATCAGGCAAATATACAAATATG[C/T]ATGGGCAAGAATGTTATAACATCATTACGGGTATG Y 2 1 2 1 101000 r 74 goat snp52580-scaffold785-203051 16 72605167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389505 Affx-122968303 AX-123259863 16 71648573 AGAAGTGCAGTGTGACGCTTGCACGTCAAACCTGT[A/C]GAGAATCAGCTGCCCTTGCTTTTGCCCCTTCTTCT M 2 1 2 1 101000 f 74 goat snp52581-scaffold785-236241 16 72638153 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392453 Affx-122966165 AX-123262810 16 71744670 CAATGCCTGCCAGGCCATATCGTGCTTAGTACAAA[C/T]TGGTACGGATACAATCAAAGATTTTTGCACAGACT Y 2 1 2 1 101000 f 74 goat snp52583-scaffold785-332338 16 72735061 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390279 Affx-122967737 AX-123260636 16 71799464 AACTAGGTGAGACCTTTGGCTCTTGGGTGAAGGAG[A/G]ATGGAAATTAAGATGCAAGAGGAAGGACAGAAATC R 2 1 2 1 101000 r 74 goat snp52584-scaffold785-387132 16 72788874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385517 Affx-122971255 AX-123255875 16 71852242 GAAGGAGGCAGCTGAGACCCTGATGACGGGCAGGC[A/G]CTCTTTTCTTCAGTCCATGACAGGGGTGGGAAGTG R 2 1 2 1 303000 f 74 goat snp52585-scaffold785-439910 16 72841450 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401455 Affx-122958976 AX-123271808 16 71883579 GGCTCCTGGGCAGGGTGACAGGGCCCAGTGGAGAC[A/G]GCAGTTCTCAAAGTTGTAGTGACCCCAGTGTGTGC R 2 1 2 1 101000 r 74 goat snp52586-scaffold785-471247 16 72872774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444547 Affx-122926473 AX-123314884 16 71912201 TCTCTTTTGTTAAATTTTCCATCAAGGACAGAGTC[A/G]TATCCTATTTGTTTGGGTATTCTGAGAGTCTAGTT R 2 1 2 1 101000 r 74 goat snp52587-scaffold785-499869 16 72901702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386636 Affx-122970220 AX-123256994 16 71994463 CGTTTCTCATAAACCTCCAATATTTATTTTTATTG[C/T]GTCACTTAAGCATGTAAACATAAAACTAAGTATCA Y 2 1 2 1 101000 r 74 goat snp52589-scaffold785-582131 16 72984409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781600 Affx-122938374 AX-385268684 16 72027141 CTAACATACAGCATGTTGACAACAATTAATAAAAC[A/C]GTATTGAAACTGGGAATTTGCTGTGAAAGTGGATT M 2 1 2 1 101000 r 74 goat snp52590-scaffold785-614809 16 73018530 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441885 Affx-122928623 AX-123312222 16 72060538 CTGCATTAAACTGGCTTTGGATGAACCATTGCGTG[C/T]GTTTTTATTTTCCTGCTGTGACCCCACCTGCTTCC Y 2 1 2 1 101000 f 74 goat snp52591-scaffold785-648206 16 73052231 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784070 Affx-122939529 AX-385271123 16 72122087 CGTTCCAGTATTTCAAATTTCAAGCTCCAACTATT[A/G]TTCCTCGGCGTGGCCCTCTATATTATCAGATGCCC R 2 1 2 1 101000 r 74 goat snp52592-scaffold785-709755 16 73113536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446258 Affx-122925679 AX-123316594 16 72171391 AGCCAGGATGGTGATGCTGTTTCTGGCTGGTTAGC[C/T]GCTTTTTGTTCCAGAATGGTGCCACAGAGTTAAAC Y 2 1 2 1 101000 r 74 goat snp52593-scaffold785-759059 16 73163222 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394150 Affx-122965313 AX-123264505 16 72203743 CTGATATTTTCCAAACTTGGTTGCACTTGTTGTGT[C/T]TTCTATCTTAGTTAATAACAACTTGACCCTTTCAG Y 2 1 2 1 201000 r 74 goat snp52594-scaffold785-791411 16 73195478 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784089 Affx-122948752 AX-385271141 16 72242246 TTATTTGCCACCCTCTCTAAGTATTAAGTATTGAA[C/T]AGGGCTTCATGCCCACCTTAGCAATGGTTATTCCC Y 2 1 2 1 101000 r 74 goat snp52595-scaffold785-829914 16 73233607 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784583 Affx-122941620 AX-385271631 16 72275100 GCAGGGAGGAAGGAGGACAAGATGCTAGATGATAG[A/C]TGACAAGGGCCCATTGTTCATGCAGCTCCTCACTG M 2 1 2 1 101000 r 74 goat snp52596-scaffold785-862768 16 73266662 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392284 Affx-122967536 AX-123262641 16 72314463 CTGAGATTCTGAAATCCTAACACAGAATCAAGTGA[C/T]GCCAGTGCCACTGGTCCGTGGGCCCCACATTGAGC Y 2 1 2 1 101000 f 74 goat snp52597-scaffold785-902131 16 73305841 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406378 Affx-122955408 AX-123276730 16 72346355 TACTCAGCACTTGATACGTGCCAGTCAGATGAAAC[A/G]TTCATTTTTATGAAAACCCGTACTTTGACCTCAAC R 2 1 2 1 101000 f 74 goat snp52598-scaffold785-934023 16 73337931 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426615 Affx-122939964 AX-123296961 16 72390069 CACACGACAGGTCTTCAGAAGGACTTGGCTTCCTG[A/C]TTCTCATTCAAAAGGCTTGGTGCTCACTTCCTTTC M 2 1 2 1 101000 r 74 goat snp52599-scaffold785-977737 16 73381790 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417823 Affx-122946802 AX-123288171 16 72433874 ACTAATGAGACTCCCGATTTTCTCAGTGTCCATCG[C/T]GGCACAGACAGACCCCTTGGCCAAAACAGAAGCTG Y 2 1 2 1 101000 f 74 goat snp27812-scaffold299-13749 16 73425022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396529 Affx-122962952 AX-123266884 16 72484813 CAGGCGCCTGAACCTCTCTATTTCCAGAAAACACC[A/G]CAGGTGATTCAAAGTGTGAGATGTCTTGTTACAGA R 2 1 2 1 101000 r 74 goat snp27813-scaffold299-64688 16 73475760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395167 Affx-122964111 AX-123265522 16 72516020 CTAATTTGGATAGAATAGAGGAATTAAGAAAACCA[C/T]AAAATGCACAACATGAAGCTAGAAAGGGATTTACA Y 2 1 2 1 101000 r 74 goat snp27814-scaffold299-95895 16 73506969 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383753 Affx-122972441 AX-123254111 16 72580432 TGGGCATCCCAAGACCCAGAGGTGTAGAACTCGCC[G/T]AGGTACAGTGCTCATGGCATCTCCTCTAGAACGTC K 2 1 2 1 101000 r 74 goat snp27816-scaffold299-160307 16 73571301 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430699 Affx-122936913 AX-123301040 16 72697472 TCGGCCACCCTGCCCACTTTATGGGATGGAAACTC[G/T]GAACACTCCAGACCGAGGAGAGGCTGCCGTGGACA K 2 1 2 1 101000 f 74 goat snp27818-scaffold299-277347 16 73689013 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397779 Affx-122962511 AX-123268134 16 72729664 ACTCTTAATAAGCAATGTTTGTGGAATGAATGAAT[G/T]AATGGATACCCAGTGATCAAAAAGATATGATTATT K 2 1 2 1 101000 r 74 goat snp27819-scaffold299-309539 16 73721254 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405838 Affx-122955871 AX-123276190 16 72765829 TCTTCTCTTTTTTAAGCTGAGTGAGATCTTGGAAA[G/T]AATTTAAAAGCTCCTAAAGAGGATGTTACTAGTTA K 2 1 2 1 101000 r 74 goat snp27820-scaffold299-345704 16 73757382 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417352 Affx-122947722 AX-123287700 16 72797560 CTAGAGTGTTGCATGTATCATCTCTTTTCATCCCC[A/G]TAATGGTCCTGTGAGGTATCTGGAATCGTTATCTC R 2 1 2 1 201000 r 74 goat snp27821-scaffold299-377435 16 73789063 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439870 Affx-122930050 AX-123310207 16 72826791 CATGACTTAGAAGAGAACCCCAGCTAACGTCCCCA[A/G]CCCAGGTCAGAGTCTCTGCTCGGTACGTAGTCACC R 2 1 2 1 202000 r 74 goat snp27822-scaffold299-406666 16 73818246 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425050 Affx-122941858 AX-123295396 16 72874212 GGAGGTTCACGCCTCCTTCTTGATGCTATTAGTCA[C/T]GTGACTTTGGCAGCTCAGAGGATGGGCAGGGGGCT Y 2 1 2 1 101000 f 74 goat snp27823-scaffold299-454087 16 73859053 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272832 Affx-1111833082 AX-519546525 16 72925670 CCCCCGGAGTGATGTGGACTTGGCATTCTTGTAGG[A/G]ACTCCCTGTCACAGATGTGGAGGCAGGAGAGGTCA R 2 1 2 1 102000 f 74 goat 16_72925670_AF-PAKI 16 72925670 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438286 Affx-122931398 AX-123308624 16 72926875 TGGGTGCCCTGCCGGGTGCCCTGCCATCTAACCCT[A/G]CTGTACTAAAGAGAGAGTCTTGGAGGCAGTCTCCA R 2 1 2 1 101000 r 74 goat snp27824-scaffold299-506750 16 73911605 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405168 Affx-122956937 AX-123275520 16 72965533 ACTGCAGAGAGGAGCCCAAAGAGTTAAGGGCCAGC[A/G]GGCGGCTGGAGAGGAGGCCAAGTTGGAAAAGGCCA R 2 1 2 1 101000 f 74 goat snp27825-scaffold299-545408 16 73949012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445713 Affx-122926109 AX-123316050 16 73018464 TCTTCTCTTTCCATCAGCTAGAACCCTCAGATGTC[A/G]CCTTCTTAAGAAAACCTCCCATATCCCCCAGTGAT R 2 1 2 1 201000 f 74 goat snp27826-scaffold299-598339 16 74002360 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378516 Affx-122976639 AX-123248875 16 73078712 CCCCTCAACCACTGACACACCGGGTCTTGCTCCTC[C/T]CCTTCTGCACCGCGGCCATTTCCGGAGGAGCCATT Y 2 1 2 1 101000 f 74 goat snp27827-scaffold299-658587 16 74062735 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381251 Affx-122974493 AX-123251609 16 73110486 CATGCCCTTCGTGAACACCTTCTGAGAAGAGGTAC[A/C]TATGCAAAAGATGCCAGGCCATGGGAAGGAACCAG M 2 1 2 1 101000 f 74 goat snp27828-scaffold299-690361 16 74094451 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410082 Affx-122952846 AX-123280432 16 73189374 GGGTTCTCTGCCTTTTCAGCTCTCTCAGAGCTCTC[A/G]TGAAGACTGGCGTGTGCTCTGTCTCTGGGAAGCCA R 2 1 2 1 201000 r 74 goat snp27830-scaffold299-769249 16 74173115 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785254 Affx-122922229 AX-385272299 16 73226267 TGCTCTCTCCAATAAGTGAATATTCATCTGGTCCA[C/T]TTGAAGGATCACAACTATAAGTTACTACTTCACTG Y 2 1 2 1 101000 f 74 goat snp27831-scaffold299-806142 16 74210018 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778488 Affx-122969449 AX-385265602 16 73267714 CTTCAGAATTTCTGCAAATAGTTATTTTGAGAAGC[A/G]CTTGAGTGACGAAGAATAATCCTTGTGCTCACTCT R 2 1 2 1 101000 r 74 goat snp27832-scaffold299-847589 NW_017217806.1 2954 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277186 Affx-1111835723 AX-519550692 16 73291387 TAATATTTGTAAAAGTGTCTTATACAACATTATAC[C/G]GGTAAGACGTATTATCCGTGCTGACAGGAGGCAGA S 4 1 2 1 101000 r 74 goat Random2.2K-1637 16 73291387 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451930 Affx-122921014 AX-123322263 16 73310094 AACACCGCAGAGTGAGCAGTTACTGGACTGGCAAC[A/G]CAACCCCACCCACAAGCAGGGAAGTGTCATCTTGC R 2 1 2 1 101000 f 74 goat snp27833-scaffold299-889969 16 74304173 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446280 Affx-122925664 AX-123316616 16 73339272 GCAGACTTACTGGAGCTCTCAGTGTGACGTGGACA[C/T]GGACAAATGAAAGCCACAGGAAAATATTCTTACTA Y 2 1 2 1 101000 f 74 goat snp27834-scaffold299-919147 16 74334135 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449380 Affx-122922717 AX-123319715 16 73370565 ACAGACAGGCAGTAACTATTGCAACAGCACCAACT[A/G]CAAGAAACCAGGAAACAAATGGCAGTAACTGAAAA R 2 1 2 1 101000 f 74 goat snp27835-scaffold299-950440 16 74365827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795786 Affx-122955460 AX-385282739 16 73415103 ACAAATAGCTGAAAATTTCCTTAACATGGGAAAGG[A/G]AATAGATTTCTAGGTCCAGAAAGCAGGGTCCCAAA R 2 1 2 1 303000 f 74 goat snp27836-scaffold299-994978 16 74410640 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791092 Affx-122921598 AX-385278087 16 73475865 ACCAAGGTGGGTACAGTCTGGAAAATGAAACACAG[C/T]CTTGGATCTGGAAAATATTCTCTAAATGTGATGCT Y 2 1 2 1 101000 r 74 goat snp27837-scaffold299-1055740 16 74472163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376124 Affx-122978870 AX-123246483 16 73519351 TCTTCTTCCTTCAACTGTGTTATTCTTCAATGTGT[A/G]TTAATTCCACTTTTTTAAACTAATGAATTGGCAAC R 2 1 2 1 101000 f 74 goat snp27838-scaffold299-1099226 16 74516107 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771835 Affx-122925087 AX-385258992 16 73574079 TCATATAGGGATATTGTATCCAGTATTGCTATGTC[A/G]TCTGATTTGATAATTGTGAAATCTGTTGATCTTTA R 2 1 2 1 101000 f 74 goat snp27839-scaffold299-1153954 16 74571087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277188 Affx-1111835724 AX-519550694 16 73577317 TTATCTTCAAGACATCTCTCTCTCTCTCTCTGTCA[A/G]TTTCTCTCTCAATTTCTCAATGATTGCAGTGCTTT R 2 1 2 1 101000 r 74 goat Random2.2K-1638 16 73577317 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378937 Affx-122976434 AX-123249296 16 73625124 CGGATTCCCAGTTGAATCCAGGCATCTGCCTTTTC[C/T]GTTCCTGCATGCTGAACGGTGCTAAAGAGAAACTA Y 2 1 2 1 201000 r 74 goat snp27840-scaffold299-1204999 16 74622643 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780631 Affx-122969796 AX-385267721 16 73665930 TATCCCACATGACAAAGGTAAAAACCCTAAACAAG[A/C]TACAGGAGTTCACCAGTAAAAGACTAAAAGAAATG M 2 1 2 1 101000 r 74 goat snp27841-scaffold299-1245805 16 74663469 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769104 Affx-122978293 AX-385256279 16 73707760 TAGGACTTCTTCATTTTCAGGGAGATGCGCTTTTA[C/T]GTTTAACACAGTTACTGTATCAGTAACAAATTCTT Y 2 1 2 1 101000 f 74 goat snp27842-scaffold299-1287635 16 74705428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425570 Affx-122941429 AX-123295916 16 73759269 TAAGGTGGTGTGATTATAGCCTTATGTTTTATGGC[A/G]CTTACTTGAGAAGTAGCTCTGTACCCATTGTGTGA R 2 1 2 1 101000 r 74 goat snp27843-scaffold299-1339144 16 74756881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405951 Affx-122955550 AX-123276303 16 73808265 ATGTAATACTGTGCGTGTCTGCTGGCCATCAGCAC[A/G]CCTCACTGTTCCTTGTCTAAACACCAAAAAATAAA R 2 1 2 1 201000 r 74 goat snp27844-scaffold299-1388140 16 74805914 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400935 Affx-122959714 AX-123271288 16 73863616 TGAACACTGAAGGGTCACGAATGATGCAAATAAGA[C/T]GAGCACACGCCTTCCCGGGCCTGCTCCCTTCTGCC Y 2 1 2 1 101000 f 74 goat snp27845-scaffold299-1443491 16 74853023 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430979 Affx-122936697 AX-123301320 16 73893981 GATTTGGCTGTCTCAGCTCTAACAGTTAGGGAAGG[C/T]GTGTCACCACCTTATATACCCATTGATTTTGAAAA Y 2 1 2 1 201000 r 74 goat snp27846-scaffold299-1473856 16 74883169 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381628 Affx-122974769 AX-123251986 16 73925345 CATCAGTAAACTCAACACTATTGAGGAAAGAGTCA[A/G]TGAACTTGAAGTTAAGTAAAGAGAAATTATTCAAA R 2 1 2 1 101000 f 74 goat snp27847-scaffold299-1505220 16 74913766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390381 Affx-122967664 AX-123260738 16 73977176 GGAAAGTAACATACTAAATATAGCTCCTCTGAAAA[C/T]AAATAGGCTATTTGCAATGAAACATATTTAATCAT Y 2 1 2 1 101000 f 74 goat snp27848-scaffold299-1557051 16 74965613 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391262 Affx-122967366 AX-123261619 16 74025383 TCATAAAAGTGAAATTCCTGGAGGACTGGTGGGTT[A/C]TGACAGCTCTTCCCTTTGACCCTTGGCCAAGGCTA M 2 1 2 1 102000 f 74 goat snp27849-scaffold299-1605258 16 75013874 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409800 Affx-122952967 AX-123280151 16 74115647 GCAAGTGATGTGACCATTCGGCAGTCAGCTTCCTC[A/G]TGTCTAAACTGGTGGCTGTGATAAATGAAGCTTTG R 2 1 2 1 101000 r 74 goat snp27850-scaffold299-1695522 16 75102150 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765284 Affx-122931045 AX-385252813 16 74173850 CATTAAAATCTGTTATAGGGAACACTCGATAAGAA[C/T]GGAAAATGCGTTCATCTCAATAAATCAATACACCA Y 2 1 2 1 201000 f 74 goat snp27851-scaffold299-1753725 16 75160715 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447869 Affx-122923881 AX-123318205 16 74219812 TGAAAAAAATTAAAATCAATAGAAAAGTTAGAAAC[C/T]ACATCAAGAATATCTCCTAAGGACTAGAATAAAGA Y 2 1 2 1 101000 r 74 goat snp27852-scaffold299-1799687 16 75206653 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390468 Affx-122967605 AX-123260825 16 74269914 CATCACACTGCAAGCATTCCAAACTCCTGCAGACC[A/G]AAGCTTTTTCTAATGCAAAGTGAGGAAAATGTAGT R 2 1 2 1 201000 r 74 goat snp27853-scaffold299-1849789 16 75256577 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377107 Affx-122978256 AX-123247466 16 74325690 CTTCCTGTCTTCCACGCTGATAACACACATCAAAA[C/T]AGGAGGGAAGTTCCTCACTGACGTCTGATTTCTGC Y 2 1 2 1 101000 f 74 goat snp27854-scaffold299-1905565 16 75312474 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424600 Affx-122942202 AX-123294946 16 74357294 AAATCCCAGGCTATGCAACATAATTTATGTGGATC[C/T]GTGTGGATTCAACCTCTCCTGCAAGAAGACAGTAA Y 2 1 2 1 101000 r 74 goat snp27855-scaffold299-1937169 16 75343695 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448344 Affx-122924129 AX-123318680 16 74390820 GAAATTTCCCTTTCCGGTATCAACCCCAGAGGAAG[C/T]AGAGGGCATACCCACAAGGACCCAGGTACACGAGT Y 2 1 2 1 101000 f 74 goat snp27856-scaffold299-1970695 16 75377175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386999 Affx-122969945 AX-123257357 16 74422696 CTAATAACTCAGTTCTCTGATCTATCTAACAGGAG[C/T]AATTTATCATCTATCATATCTAATCCATAAATTTT Y 2 1 2 1 101000 f 74 goat snp27857-scaffold299-2002571 16 75408987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792422 Affx-122921811 AX-385279403 16 74538802 TTTGAGTCCCAGGAAAATCTGAGAATTTTATCTTC[A/G]TGGGTTGTCTTTATTCCCATAATAAATATTTATCT R 2 1 2 1 101000 f 74 goat snp27859-scaffold299-2118677 16 75526085 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429159 Affx-122937981 AX-123299501 16 74576272 AGGGGCTTAATTGGCTCAGCGAGAATAACTCAAGG[C/T]GAGCTCTCCCAGAGCTGAGACTCCCGTTACAGTAG Y 2 1 2 1 101000 f 74 goat snp27860-scaffold299-2156147 16 75563416 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795411 Affx-122974848 AX-385282367 16 74618888 TCAATTCAGGGTAAACGCACGAGTGTGCTTTAGCC[A/G]TCTTTACCTGAACCATAGGGCTTTCTCCTCAGAAG R 2 1 2 1 101000 f 74 goat snp27861-scaffold299-2198763 16 75606005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435424 Affx-122933489 AX-123305764 16 74655493 TTGAGAATTTTTAAACTTATACATAGAACTAATAT[A/C]GGACCATTCATTCTTAGAGTTATAAAACCTCTAGA M 2 1 2 1 101000 r 74 goat snp27862-scaffold299-2235368 16 75642683 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425873 Affx-122940647 AX-123296219 16 74691104 TCATGAGCCTGGTTTCTGGAGCCATGATCCTGGGG[C/T]GTCAGTTGCTCTCATGGTTATTTTGGGGGGCACAT Y 2 1 2 1 201000 f 74 goat snp27863-scaffold299-2270979 16 75677523 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788301 Affx-122974054 AX-385275319 16 74721271 ATTCTGGCAGTTATTTATGGTTTATATTCACATAA[C/T]GAATTTGTGAAACTTGTATTCTGATTATTTTGCAT Y 2 1 2 1 101000 r 74 goat snp27864-scaffold299-2301146 16 75707488 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770365 Affx-122976956 AX-385257530 16 74788045 CTATACTTCAGTTCCTTTATGAATTTAAATGCTCT[A/C]CTCATGATCGTGCACTATAGTATATAGCATATGTT M 2 1 2 1 101000 f 74 goat snp27865-scaffold299-2367920 16 75774883 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774878 Affx-122955145 AX-385262012 16 74823485 ATTCAATATTGAATATAAGGGCAGGTGTTTTTTTG[C/T]AGGAAGTGTCCTGTCTTTACACCCAAGAAGCATGC Y 2 1 2 1 101000 r 74 goat snp27866-scaffold299-2403360 16 75810797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388192 Affx-122969428 AX-123258550 16 74881757 AAAAGGTGGGCGTGTGCATATAAACCAACGGAAGG[C/T]GATTAAGCTGTAGAAAACAACAAAATCCTACCGTT Y 2 1 2 1 101000 f 74 goat snp27867-scaffold299-2461632 16 75867817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449932 Affx-122922913 AX-123320267 16 74938939 TTCCTTGTGGCCTGCATTTGCTCTCTTCCGGCTAC[A/C]GTTCTGGGGAAAATCTGTCATCCCGGTGTACTGAG M 2 1 2 1 201000 f 74 goat snp27868-scaffold299-2518814 16 75925242 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394927 Affx-122964308 AX-123265282 16 75032335 CAAGTATCTGTTACTACATGATAGACGCTGTTCCG[A/C]GTGGTAAGAATATTATAGGTGGGGACTTCCCTGGT M 2 1 2 1 101000 f 74 goat snp27870-scaffold299-2612210 16 76018541 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433698 Affx-122934538 AX-123304039 16 75073871 TTCCAATGGACACAGACTATCTAGTTCTCTATGTG[C/T]GTGCCTAGTCTCTCAGTCTTGTCTGGCTTGCGACC Y 2 1 2 1 101000 f 74 goat snp27871-scaffold299-2653746 16 76059766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414346 Affx-122950024 AX-123284695 16 75107675 CTTTACTGATCTGAGCCTGAGAGTGTGGTGACATA[C/T]ACTGCCTGCCTCATACTGGTGCTCTGACCCTGTGA Y 2 1 2 1 201000 f 74 goat snp27872-scaffold299-2687550 16 76091978 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399550 Affx-122961135 AX-123269905 16 75165709 ATAGATTAACTGGAGAACTGATGTTCAGAGAGGCT[A/G]TGCCACTTTTCCAAGGTCAGACAGCTGGAGAGTGG R 2 1 2 1 101000 f 74 goat snp27873-scaffold299-2745584 16 76149635 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377547 Affx-122977456 AX-123247906 16 75195211 GACTGTGGACCATCTCAGAATAGACTCTGCCCTTG[A/G]GATAGCCCTCTTGACAGCCCTTGCCCTGTAGTTTA R 2 1 2 1 201000 f 74 goat snp27874-scaffold299-2775086 16 76178894 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442420 Affx-122927981 AX-123312757 16 75236811 GAAACTGACCTTTGCACAGATATCTAAAGGGCAAG[C/T]AGGAGTTAGCAGAGTGACAGAAAGGGACATGGGTA Y 2 1 2 1 101000 f 74 goat snp27875-scaffold299-2816686 16 76219918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795703 Affx-122975180 AX-385282656 16 75270492 CTCAGCTTGCTGTTGACCTAAGAACTCTGTGATCG[C/T]CGCTTTAAACACAACCCCTCTAATATACATTATAT Y 2 1 2 1 101000 f 74 goat snp27876-scaffold299-2850367 16 76253336 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384822 Affx-122971981 AX-123255180 16 75306538 TGCAAGATATCATCATCTCTCACTGGGCCAGCACC[A/G]CCGCTATCCAACCCTGTGCTATTCCTGGGGGTACT R 2 1 2 1 101000 f 74 goat snp27877-scaffold299-2886413 16 76289195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783827 Affx-122977510 AX-385270883 16 75341789 ATCTACCCCGTATCTTCATGACAGTATAGATATTG[C/T]ACATACTTACTACCTCCTGACTTATTGAAAGGATT Y 2 1 2 1 202000 f 74 goat snp27878-scaffold299-2921664 16 76325041 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440677 Affx-122929924 AX-123311014 16 75379460 TCTGTTAATTCGGGCATTATGTGAGGCTACCCAGC[G/T]CACAGTGATTCCCACAGACTCAAGTCCTGAGCTTA K 2 1 2 1 101000 f 74 goat snp27879-scaffold299-2959335 16 76362640 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440836 Affx-122929267 AX-123311173 16 75413714 ATAGTTTAACTTTACTCCTTTGTATGTGGTAACAC[A/G]CATGTTTCACTGAATGATTCAGAAATCGCTTCTGA R 2 1 2 1 101000 f 74 goat snp27880-scaffold299-2993589 16 76397513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272834 Affx-1111833083 AX-519546527 16 75479281 AGGAAGCCTGGCGTGCTGTGGTTCATGGGGTATCA[A/G]AGAGCTGGACACAACTGAGTGACTGAACTGAACTG R 2 1 2 1 303000 f 74 goat 16_75479281_AF-PAKI 16 75479281 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320800140 Affx-122940166 AX-385287063 16 75501265 CTCTTTTTATTCTGGAATATCAACACATTTGTTTT[A/C]TATTTCAACCTTAATTTGTTGTAGTTAGCTATAGA M 2 1 2 1 101000 r 74 goat snp27882-scaffold299-3081140 16 76484524 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416437 Affx-122947829 AX-123286786 16 75556680 GCCTGCCGTGCAGGAGACCTGGGTTTGATCTAAAG[C/T]AGTGACAGTGGAAATAGAAAAAATTGAATATATTA Y 2 1 2 1 201000 r 74 goat snp27883-scaffold299-3136555 16 76540206 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431833 Affx-122936094 AX-123302174 16 75586776 TACCGAATCTGAACTTTCAGCAGAACCTGGGCACT[A/G]TCTGTCAATGGATGGGCTTGATTAGGTACATAAAT R 2 1 2 1 201000 r 74 goat snp27884-scaffold299-3166651 16 76570293 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434410 Affx-122934678 AX-123304751 16 75644886 TGCTCTTTGCCTTAGGGGAAGGACAAGGCAGAGAA[C/T]GCAAAAGTCAGCAGCCACAGTTTCATTCATTTAAA Y 2 1 2 1 101000 f 74 goat snp27885-scaffold299-3224761 16 76628726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437648 Affx-122931798 AX-123307986 16 75676797 GGCTAACTCAGACTGAGCTTCAGAGTCGCACGTAC[A/G]TATCTCCAGAAAATAAGAGCTTTCTCCTCTATTGT R 2 1 2 1 101000 f 74 goat snp27886-scaffold299-3256672 16 76660662 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440488 Affx-122929368 AX-123310825 16 75725581 CCAGAAAATAAAACACTTGGTTTTATTTTTTGCTT[A/G]CAACACCCTTAAAGATCAGTCCCACCTTCCCTTAC R 2 1 2 1 101000 r 74 goat snp27887-scaffold299-3305456 16 76709383 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783235 Affx-122962049 AX-385270301 16 75769565 TATGGGAAACATCAGTACAGATACTGAATGTGGAC[A/G]TTTTCTAATATAAATATCGATAACAATCTGGTTTA R 2 1 2 1 101000 f 74 goat snp27888-scaffold299-3349440 16 76753075 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451664 Affx-122921591 AX-123321997 16 75815330 GCTTGAGAGTGAGTAAAAACCTTTGGGAAGTAACC[A/G]GAGTTCCATGACCATATTTCTGAATGACCTTTCCG R 2 1 2 1 101000 r 74 goat snp27889-scaffold299-3395205 16 76798580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788919 Affx-122952943 AX-385275933 16 75889138 GAACAACTTGTTCTGGGCTTCTGTATATCCTGAAT[A/G]TTGGTAGTTGGATTTAGCATTTTGATCAAATTTGG R 2 1 2 1 101000 f 74 goat snp27891-scaffold299-3469013 16 76871497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444618 Affx-122926941 AX-123314955 16 75923367 GCCATTTTGCGCTTTAATATTTTAGCTTTCTTCAC[A/G]CATCCAGTTTACTGAATTAGAGACACTTAATGCCG R 2 1 2 1 101000 r 74 goat snp27892-scaffold299-3503242 16 76906077 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438611 Affx-122930930 AX-123308948 16 75954597 GGGCGTTAAACACTAAAGCCATGTCAGTTGTGACT[C/T]TATGTCTGTCAATCTGATGTTCCAGAACCTTCTGA Y 2 1 2 1 101000 r 74 goat snp27893-scaffold299-3534472 16 76937544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770179 Affx-122977837 AX-385257346 16 76014119 CAAAGTACGCACCTACTGATTACAAAGACTTGTAA[G/T]ATAAGTTATTATTTACCACCTGTTTATGGATGACC K 2 1 2 1 201000 f 74 goat snp27894-scaffold299-3593994 16 76997725 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797727 Affx-122968545 AX-385284666 16 76055237 CCCCAGCTGTTTTCCCTTGAAGTCCAGTTGACTTA[C/T]GGCCTTGTCTTAATTTCAGGTACGCAGCACAGAGA Y 2 1 2 1 101000 r 74 goat snp27895-scaffold299-3635112 16 77038159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778065 Affx-122946245 AX-385265181 16 76090211 GTGTTAAAAGAAGTCTACTCCACCAAGCCATTTAG[C/T]AAATAAAACTAGTACCTGGCCGTGAAAGAAAAATG Y 2 1 2 1 101000 f 74 goat snp27896-scaffold299-3670086 16 77074069 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425217 Affx-122941019 AX-123295563 16 76152820 AGGCCTGTTGACAACAAAAGCATAATTAAGACCTC[A/G]CTTTATTATTAGCCACTGACACGCTAGTGTGGATG R 2 1 2 1 101000 r 74 goat snp27897-scaffold299-3732695 16 77135982 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434807 Affx-122934810 AX-123305148 16 76192548 CAGTTGATATGTCAAAGCAAAAGGAGTTAAAAAGC[A/G]TTCTGGAGGGGTAAACCCAAAGCTACTTTTGGATA R 2 1 2 1 201000 f 74 goat snp27898-scaffold299-3772423 16 77175865 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410783 Affx-122952670 AX-123281133 16 76240970 GTCGCAGGACACGGGCTAGGTCATCATGTCCCTAG[C/T]ACCCAGGATACTCCATGGAAAGGAGTCTACAGGTT Y 2 1 2 1 101000 r 74 goat snp27899-scaffold299-3820845 16 77224521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774810 Affx-122936665 AX-385261944 16 76280153 TTTCCTAACAAGTTTCTGTCATACTTTGCACTTTT[A/C]TTCAGAAACACTTTTGACAATAATCCCTAGACATT M 2 1 2 1 101000 f 74 goat snp27900-scaffold299-3860028 16 77264606 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791818 Affx-122951359 AX-385278808 16 76316289 ATAAAACATATTCACTCTTTTCATCTCTGCAACCC[A/G]TGCCCTGATCCAGACTATCACCATGTTTACTGGAT R 2 1 2 1 102000 f 74 goat snp27901-scaffold299-3896164 16 77301652 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770695 Affx-122975387 AX-385257859 16 76345814 TCACTTGAGAACTCGTTATACTAAATCTAGTCAGC[A/G]CAGCCTAGACCCACACACCAGCCCTCCAGGGTGGG R 2 1 2 1 303000 r 74 goat snp27902-scaffold299-3925689 16 77330891 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434377 Affx-122934702 AX-123304718 16 76388415 GTAAATTTAACTTAGATAGCTACATGAAATAAGAT[A/G]CATAAAGTTCTCAGTTCAGGGCCTGACACAAATAT R 2 1 2 1 201000 f 74 goat snp27903-scaffold299-3968290 16 77372989 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418618 Affx-122947153 AX-123288966 16 76422847 TGCTACCCTTCCAGCACTGAGTACAGGAAAATGCC[A/G]TCTCCTGCCCTGTGTCTGCTCGTTGTCCTCAATTT R 2 1 2 1 101000 f 74 goat snp25927-scaffold2680-28694 16 77407904 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398198 Affx-122962637 AX-123268553 16 76454543 ATGATTGTTCCCGACGCAGCTGACAGGTTAGGAAG[C/T]GCAGGAGGACGGAAGCCTCGCCTTCGCAGGGGACC Y 2 1 2 1 101000 f 74 goat snp25928-scaffold2680-60390 16 77439752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436311 Affx-122933263 AX-123306650 16 76494319 TCCATCTCCATACTTCACCGTATTGATCTGGGCTC[A/G]TGGGCATGCCCCTCCTTGAACTGATCAGCTCACGG R 2 1 2 1 101000 f 74 goat snp25929-scaffold2680-100166 16 77479242 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446592 Affx-122924817 AX-123316928 16 76537196 ATTTGCAACGGCCCCAACAGTTAAACCCGCACAGG[C/T]AATTCCTACAGTGCCGATCTCTAACTGTATCCCTG Y 2 1 2 1 101000 r 74 goat snp25930-scaffold2680-143043 16 77521680 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447433 Affx-122924382 AX-123317769 16 76575339 CCAGATGGCACAAGTTCTGGTTCTGACCCAGTCTC[C/T]GATCTTGGACAGTTGAGTTTGCTTCCCTGGACCTC Y 2 1 2 1 101000 r 74 goat snp25931-scaffold2680-181186 16 77558840 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772750 Affx-122926866 AX-385259896 16 76609980 TCGAAGGAGATGTGCTCTAGCAACTTTCTTCATGG[C/T]GATATTTTCAAATACCTTGTCAAAAAGGACTCTTC Y 2 1 2 1 101000 f 74 goat snp25932-scaffold2680-215827 16 77593733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387994 Affx-122969580 AX-123258352 16 76685471 TGGATTTATATCCCAATGGTTAGCGCATGGGTCTG[C/T]GGACGCCTCATTATTACAATGAAACATTTTGGCAT Y 2 1 2 1 101000 f 74 goat snp25934-scaffold2680-291318 16 77669028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773348 Affx-122928660 AX-385260490 16 76713246 TTAGAAACACTCAGAAGCTGCCCTGAAATGTTGGC[A/G]TAAAACCTAGAGTCGCAAACGCCCATTTCTCTCCC R 2 1 2 1 101000 f 74 goat snp16011-scaffold1686-24883 16 77696552 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273786 Affx-1111833813 AX-519547397 16 76725852 TCTGTCAGCTGCAGACTGCTGTTAGGTCCCAGAGG[A/C]CATCCACTTGTCCCGGGTCTGCCTGCAGTTCCTTG M 2 1 2 1 103000 r 74 goat GoatD01.005777 16 76725852 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38391545 Affx-122966639 AX-123261902 16 76770285 CCACGACCGTGTTGACATTTCCGTTCTCAACTGAA[C/T]GGTCACTTCAGGAACCTGAAGACTGTTTCTCTTGC Y 2 1 2 1 101000 f 74 goat snp16012-scaffold1686-81922 16 77752341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427738 Affx-122939260 AX-123298081 16 76801743 AGCAGTCAAAGCACCAAGTCCTAACCACTGGACCA[C/T]CAGGAAAATCTCTGGATCAAAAATTTCCAAACATT Y 2 1 2 1 102000 r 74 goat snp16013-scaffold1686-113380 16 77784084 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426572 Affx-122940162 AX-123296918 16 76847507 AGTTTTTTTAAAAGTTCTATTCTTTTTTTGGCTTC[A/G]CAGACTTTTAGGCATTTGATATTTGACATGTGTGA R 2 1 2 1 101000 r 74 goat snp16014-scaffold1686-159144 16 77829261 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418168 Affx-122947087 AX-123288516 16 76923450 GGATGTTATGCAAGATGGAGGACTTCTCGCCTCAC[A/G]TTGGAGCAGCAACAGGATGATAGTGCTTTGCGTGG R 2 1 2 1 202000 r 74 goat snp16015-scaffold1686-235087 16 77905973 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393807 Affx-122965176 AX-123264162 16 76955095 GCTTGAAAGGTGAGCTGGGCTTGCTTGAGGGGTCA[C/T]GCTAAGGAATGTGGTGTTTATTTAGTAGATAAGTA Y 2 1 2 1 101000 r 74 goat snp16016-scaffold1686-266732 16 77936310 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382684 Affx-122973648 AX-123253042 16 76979971 CACAGTCCTCATGTTTTGCAAACAGAACAGGAAAC[A/G]AGTCAGGTTACAAGGGTAACTGTCGCGTGTGGCAG R 2 1 2 1 101000 r 74 goat snp29567-scaffold3201-188294 16 77962178 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428000 Affx-122939166 AX-123298343 16 77027706 GAAACTTCTCAGATGTGAGGAGGAGCGACAGCTTC[A/G]GTACGTGTTCACATTTTCAGGTTAAACCAAGAATT R 2 1 2 1 101000 r 74 goat snp29566-scaffold3201-140559 16 78010174 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429051 Affx-122938303 AX-123299393 16 77057360 ATTAGCCATTATTTTAACACCTACTTCAGAGCAAT[A/G]TTGTAATGATACATTGTATAACAAAGGTCTTTGAA R 2 1 2 1 101000 f 74 goat snp29565-scaffold3201-110905 16 78039816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766252 Affx-986697871 AX-385253648 16 77062050 AAATCAAACCTCAATAAATTTAAGGAAATTGAAAC[C/T]GTATCACTCATCTTCTCTAACTACAATGCTATTAG Y 2 1 2 1 600010 r 74 goat 16_77062050 16 77062050 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320803947 Affx-986696308 AX-385290653 16 77062250 CAATGAAAACACGACAACTCAAAACCCACAGGATG[C/T]AGTGAAAGCAGGTCTGAGAGGGACGCTTACAGCAA Y 2 1 2 1 600010 r 74 goat 16_77062250 16 77062250 Ancestral_priority_1043 ancestry 0.622 recommended IMAGE 10K 10K ancestral 38402180 Affx-122959184 AX-123272533 16 77094025 GCGGATAGGACTGAGCGACTGAACAACAACATCGA[C/T]ACATGAAGGCACAGCCTTGAGCAAATTAAATCCTC Y 2 1 2 1 101000 r 74 goat snp29564-scaffold3201-74240 16 78074619 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389404 Affx-122968377 AX-123259762 16 77187539 TGCATACATGCGTCTGATCTGAAACATTATTTCCC[G/T]TCTCCTCCCCACAGAAAAAGATGGTGTTCTGGCAG K 2 1 2 1 101000 f 74 goat snp27349-scaffold2907-19175 16 78139697 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433388 Affx-122935112 AX-123303729 16 77262198 AGATGTGAGCAAGTCAGAGCTCGCTTCTCTTTCCA[C/T]GGCCTCAGAGTCAGAAGGCTTTGGATCCCAGAAGT Y 2 1 2 1 101000 f 74 goat snp27350-scaffold2907-93834 16 78199266 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418982 Affx-122946068 AX-123289330 16 77315833 TCCCAGAACAGCCTTGCCCTTGCCCCTGTTTTGAA[C/T]GAGAGAGAAAGCTGCTACACGCCTTTGTGAACATG Y 2 1 2 1 201000 r 74 goat snp12255-scaffold1459-10356 16 78251590 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428402 Affx-122938946 AX-123298745 16 77354477 GGTGGGCTTCGGGCCCCCACCTCCTCCCTTCAGGT[A/C]GGAAGCTGTCTTAGTGCCGAGCCTTTGGACAGGGC M 2 1 2 1 103000 r 74 goat snp12256-scaffold1459-49000 16 78291217 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792626 Affx-122929201 AX-385279607 16 77422405 AGATGCTATATGTATTTTGTTCAGCTTTTCTAGTT[A/G]TCTGAAATAAGAAGTTTCAAATTACCTGATTGCTA R 2 1 2 1 101000 f 74 goat snp12257-scaffold1459-116928 16 78360188 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377503 Affx-122977487 AX-123247862 16 77504615 CTAACCGTGAGTGCCTTTTCACTTGCTTGTTGGCC[A/G]TTTGTGTATCTTTTTCAGAGACATGTCTATTCAAA R 2 1 2 1 201000 r 74 goat snp12259-scaffold1459-199138 16 78442514 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404080 Affx-122957139 AX-123274432 16 77625019 TGGAGATATGGACGGTCATCCTCAGCTCATTCACA[C/T]GGTCACCGAGAGACAGAGCTCAGGCAGCCTTCTGC Y 2 1 2 1 101000 f 74 goat snp5609-scaffold1198-53490 16 78561466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439650 Affx-122930605 AX-123309987 16 77674341 CAGAAACTCCAGAGATCAACCGACTCGCCTAGGGC[A/G]CCTTATCTTTGACAAAGGAGGCTGGCCAGAATATA R 2 1 2 1 303000 f 74 goat snp5608-scaffold1198-4168 16 78608650 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272892 Affx-1111833085 AX-519546580 16 78257876 TACGTTATGTCCCATTCCCGGGTGAGGGTAGTTCC[A/C]AAACTTCAATACATGTCAAAATTACTCTGAGGGCC M 2 1 2 1 101000 r 74 goat 16_78257876_AF-PAKI 16 78257876 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468272458 Affx-1111834274 AX-519546183 16 79076714 CGGAGTGCCACAGGCACTTTCCAGGACCACGCCTC[A/G]CATGCTGCCCTGAGGACGTGGCACTCAGTGGACTC R 2 1 2 1 202000 r 74 goat GoatD01.028485 16 79076714 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468273683 Affx-1111833778 AX-519547295 16 79187320 GGTGATGGTTTTGCCCGCGGGGCGGGCAGCACCCT[A/C]ACCTCAGGCCTCCTCTGCCCCTGGGGGCAGGAGCT M 2 1 2 1 303000 f 74 goat GoatD01.004549 16 79187320 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320800150 Affx-122973722 AX-385287073 17 3333 TCATCATGTTATCCCTTGCTTGAAGCCCAACTGTT[A/G]CTTCTCTTTGCTTCATGGTTAAAGGTCACAGTTGT R 2 1 2 1 101000 r 74 goat snp52379-scaffold779-2013281 17 68776309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407172 Affx-122954833 AX-123277523 17 34431 GTCTCTGGCTGACGGCTTGTGATTGGCCCCCAGCA[C/T]ATTTCTGCAGGGGAGCAGGGCTGCTTGTCAAAACC Y 2 1 2 1 103000 r 74 goat snp52378-scaffold779-1982183 17 68808303 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453662 Affx-122919719 AX-123323995 17 173336 AACAGGAGGAAAAAAAAAAAACACCCACAAATTAC[A/G]TGGCTAGCAAGGACTTCCAGAAGAGAGGTAGTCTC R 2 1 2 1 101000 r 74 goat snp52375-scaffold779-1843278 17 68947220 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377233 Affx-122978160 AX-123247592 17 229002 ATGACTCACCAGAAAATTTAAATTTTAGAACCATC[C/T]CTAAAGCCCAGACTAGTAAATCAACCTCTCCAATG Y 2 1 2 1 101000 r 74 goat snp52374-scaffold779-1787612 17 69003859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766267 Affx-986697879 AX-385253661 17 260415 GACGGACCTGTGAAGGTCATCACTGGCTCAGCCTC[C/T]GATCTGGTCTTTGTCCCTGGTGTCCTTTGCCCATG Y 2 1 2 1 600010 r 74 goat 17_260415 17 260415 Ancestral_priority_1043 ancestry 0.57 neutral IMAGE 10K 10K ancestral 38397822 Affx-122962482 AX-123268177 17 302020 CCTATTCTAATTTACCTTACTAAATGATGTTCATT[A/G]TGACAAAAGAAATGATCAAAAAGCACTCCCCCATA R 2 1 2 1 201000 f 74 goat snp52373-scaffold779-1714594 17 69071228 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793620 Affx-122970614 AX-385280594 17 336052 ATCCTTCAAAATTTTCCTAAATGTATGCAGTAAGT[C/T]CTAAATGTAGAAGAGAAAAAGTACATCCCTGTCTT Y 2 1 2 1 101000 r 74 goat snp52372-scaffold779-1680562 17 69105543 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271829 Affx-1111833095 AX-519545614 17 367315 CTCTGAATGAACCACTTTATTCATTTATACATTTG[A/G]CCATGCTGATCGGCTTATGGGATCCCAATTCCCTG R 2 1 2 1 101000 r 74 goat 17_367315_AF-PAKI 17 367315 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38441595 Affx-122928664 AX-123311932 17 381959 AAACTTCAGTGTCTAAACAGTTAGGGAAGCTCCTA[C/T]GGAATGAGTAGACAGTCATTTACACAACCAACAAG Y 2 1 2 1 101000 f 74 goat snp52371-scaffold779-1634655 17 69149852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381155 Affx-122974552 AX-123251513 17 411088 AATAACTGTGACCCCTGAACAAAGAAACAAAGAAA[G/T]AAAACTGAAGTCACAGGAAGCATTCTGTATCTCTG K 2 1 2 1 103000 r 74 goat snp52370-scaffold779-1605526 17 69179037 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434348 Affx-122934724 AX-123304689 17 474565 ACTTCACTCCCCTGCCTCCCAGCTGGTGGGTACAA[A/G]AGGAGTGCTCAGTAAAGAAGCCTTCTGAGCTCCTT R 2 1 2 1 201000 r 74 goat snp52369-scaffold779-1542049 17 69242701 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381314 Affx-122974442 AX-123251672 17 520234 TCAATTAAGAGACATCTGATTACAAAGTCCCTCAG[A/G]CTCTTCATTATATGTTATATGTCAATTAAATTTCA R 2 1 2 1 101000 f 74 goat snp52368-scaffold779-1496380 17 69288901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778958 Affx-122970531 AX-385266065 17 560411 AATTAGACATTTATCACAAATTCGATTTCCATATA[G/T]AATTTAAATCTATTTCTGGATGTTTTTCTTTTCTA K 2 1 2 1 202000 r 74 goat snp52367-scaffold779-1456203 17 69328879 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395459 Affx-122963915 AX-123265814 17 630386 ACTTTCCCATCAAGAATGTGTTAACAAGATCATAC[A/G]TCTATAGCTAGACAGCACACTACACAATGATGATT R 2 1 2 1 101000 f 74 goat snp52366-scaffold779-1386228 17 69399808 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763352 Affx-986697881 AX-385251252 17 646201 AATTGTAGTATTGCTAGTACACACTCATTTACATA[C/T]ATGTAATTTCGTGCAGGAGGACTTAATGTCTCCAT Y 2 1 2 1 600010 f 74 goat 17_646201 17 646201 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 320803948 Affx-986696309 AX-385290654 17 646205 GTAGTATTGCTAGTACACACTCATTTACATACATG[C/T]AATTTCGTGCAGGAGGACTTAATGTCTCCATTACT Y 2 1 2 1 600010 r 74 goat 17_646205 17 646205 Ancestral_priority_1043 ancestry 0.728 recommended IMAGE 10K 10K ancestral 320766273 Affx-986697883 AX-385253665 17 647156 ACTTGAGGCCAGGGACCTGAACAGGGACCCCCCGC[A/G]TCCACTACTGGCCTCAGAGAGAAGGAGAGCTGCTG R 2 1 2 1 600010 r 74 goat 17_647156 17 647156 Ancestral_priority_1043 ancestry 0.516 neutral IMAGE 10K 10K ancestral 320803376 Affx-986696310 AX-385290210 17 647415 GAATGAAGAAAGATGTGAACAGCTTTTTCTGGACC[A/T]AGTTCCGTGGTGTGACTGAGCACAGTCTTAGGCCA W 4 1 2 1 600010 f 74 goat 17_647415 17 647415 Ancestral_priority_1043 ancestry 0.628 recommended IMAGE 10K 10K ancestral 320766276 Affx-986697885 AX-385253668 17 647422 GAAAGATGTGAACAGCTTTTTCTGGACCTAGTTCC[A/G]TGGTGTGACTGAGCACAGTCTTAGGCCAAACAGAC R 2 1 2 1 600010 r 74 goat 17_647422 17 647422 Ancestral_priority_1043 ancestry 0.584 neutral IMAGE 10K 10K ancestral 320763358 Affx-986697887 AX-385251258 17 647477 CTTAGGCCAAACAGACAAATGAAGTGGCGGCCTTT[G/T]TAGAGGATGTTTCTGCCCCCAGAGCCCCGACTCTG K 2 1 2 1 600010 f 74 goat 17_647477 17 647477 Ancestral_priority_1043 ancestry 0.55 neutral IMAGE 10K 10K ancestral 320765750 Affx-986697583 AX-385253206 17 647478 TTAGGCCAAACAGACAAATGAAGTGGCGGCCTTTT[C/T]AGAGGATGTTTCTGCCCCCAGAGCCCCGACTCTGA Y 2 1 2 1 600010 r 74 goat 17_647478 17 647478 Ancestral_priority_1043 ancestry 0.448 neutral IMAGE 10K 10K ancestral 320766285 Affx-986697890 AX-385253675 17 647737 TACTGCCATAGATCAGGGTTTTGGGGGCCGATCCT[G/T]GGAGCTGTTGGTACCAGCTCACACCCAATATTCCA K 2 1 2 1 600010 r 74 goat 17_647737 17 647737 Ancestral_priority_1043 ancestry 0.544 neutral IMAGE 10K 10K ancestral 38382008 Affx-122974070 AX-123252366 17 704416 TTTCCAAATAAAACAAAAACACTAATTTGAAAAGG[C/T]ATTGCAACTCTATGTTCCTTTTAACATACCTCACA Y 2 1 2 1 103000 r 74 goat snp52365-scaffold779-1312198 17 69467360 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783868 Affx-122955413 AX-385270924 17 783360 TGTTGAACAATAATGGGAGGGGTTTATCTATTGGG[C/T]GTCAGATCCACAAGCATGTAGTAGTAGCTTTGAGT Y 2 1 2 1 101000 r 74 goat snp52363-scaffold779-1233254 17 69548063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376617 Affx-122979043 AX-123246976 17 834505 AGAATACTGTACTTAGGGAATAGCAGTTTGTAAAA[C/T]GATTCATATATCATTCCATTCTTAATTTTTGTAGA Y 2 1 2 1 101000 f 74 goat snp52362-scaffold779-1182109 17 69599867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439642 Affx-122930611 AX-123309979 17 881734 CAATCATCTCTTGTTTTGCAGGCTGTGCTCCCTGG[C/T]AGGGCAATATCCCTGGTAGCTGGGTTCTGCAGTCA Y 2 1 2 1 101000 f 74 goat snp52361-scaffold779-1134880 17 69647901 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274140 Affx-1111834030 AX-519547743 17 910515 CCTGTGGGGCCAGGCACCTTGCGCTTGTTTCTTAC[A/G]AGTCCATCTTTCATGAGATGTTGTTCCTTGTCTGT R 2 1 2 1 201000 r 74 goat GoatD01.015133 17 910515 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38393760 Affx-122965210 AX-123264115 17 924637 TTTGTGGCACTCTCTAGACCAAAATAAATGCCTAA[C/T]AATTACATTTTTAACAAGGTAAGAGTCACTGAAAC Y 2 1 2 1 101000 f 74 goat snp52360-scaffold779-1091977 17 69691034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788350 Affx-122963045 AX-385275368 17 985500 AATCCAAAGAGGCTCATGAGGCATTATACCTTTAG[C/T]GCTCTTAAGAGGGCCAGATGTAACAACTCATCCTT Y 2 1 2 1 101000 r 74 goat snp52358-scaffold779-1031114 17 69751600 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771305 Affx-122936191 AX-385258463 17 1020440 AGAAAGTGAAATTCAAACTTTGTATGAAGATTAAA[C/T]GATAAAAGTAGTTTTGGTTCTGAGACAAGTATCAT Y 2 1 2 1 101000 r 74 goat snp52357-scaffold779-996174 17 69775527 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777431 Affx-122968763 AX-385264552 17 1052751 GATGGTTTCTGTAGATTTTTAGATTATTAATATTA[A/C]TCCTCTACTCTTTCTAATTTAGCATGCCAAGTCAT M 2 1 2 1 303000 f 74 goat snp52356-scaffold779-963863 17 69808412 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420231 Affx-122945527 AX-123290579 17 1095536 TAAAAAGGGCACCATTCAACCTACATTGTGGTTCA[C/T]GGCAAAATTTTTATAGACAGAAATAAAGAGAAGTC Y 2 1 2 1 101000 f 74 goat snp52355-scaffold779-921078 17 69851239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439122 Affx-122931095 AX-123309459 17 1129549 CCCTCCTATACTGAGTTTTGTGATGGTGGGGTGCA[C/T]GTGCATCCCTCTGCATCCGGCCCTGAGTACTTGCT Y 2 1 2 1 101000 f 74 goat snp52354-scaffold779-887065 17 69885509 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792427 Affx-122933431 AX-385279408 17 1165612 TGTTCACAGGAATTTCCTGAAGATTGTAAAATAAC[A/G]AGGACAAACCTTGAAAGGATGCTATTATGATAAAG R 2 1 2 1 101000 r 74 goat snp52353-scaffold779-851002 17 69922217 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387195 Affx-122970604 AX-123257553 17 1217297 CCTGTAGTCTACTTGACCACACAAAATGAGTACCA[C/T]GGAATAGCTTAGCTAACTCTAGACCAAAAGTACAA Y 2 1 2 1 101000 f 74 goat snp52352-scaffold779-799317 17 69975672 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463480372 Affx-1110003601 AX-514963298 17 1230066 AGAGGGCAGCCAGTCACTGCAGACCCTCTCCCCCT[C/T]AGCATTCTTTAGAGGTTAGGAATGGGCTGGAGACA Y 2 1 2 1 201000 r 74 goat GoatD01.004755 17 1230066 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38417577 Affx-122946899 AX-123287925 17 1268507 ACAGGGAGAGCTTTCGTCTTTTCTTCCTTAGTTGA[A/G]CAGCCAACCACTGTGATTTCAGCACCATCTTTGTG R 2 1 2 1 201000 r 74 goat snp52351-scaffold779-748107 17 70027495 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773907 Affx-122944874 AX-385261046 17 1330739 TAGAGTTTGGTATGTGAACCTGAATTTGCTGCTAT[A/G]ATTAAAACTAAATCCCTCATGTCCTCTGTCCAATT R 2 1 2 1 101000 f 74 goat snp52350-scaffold779-685875 17 70090008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429953 Affx-122938076 AX-123300294 17 1400167 CTAAACCTGTGAAAGCATGAGTAAAGCATTTTCAC[A/G]GCCGAGCAAAGGCAGGAATCTAGACAGATAAGCAG R 2 1 2 1 201000 f 74 goat snp52349-scaffold779-616447 17 70160124 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793188 Affx-122933783 AX-385280166 17 1449081 CTAAAATGCTTAATCCTCTTACATTTTATTAATTC[A/G]TTTTATTAAAAACGATGATGTTGTCACTTAGTCTG R 2 1 2 1 101000 f 74 goat snp52348-scaffold779-567533 17 70209479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391688 Affx-122967585 AX-123262045 17 1480570 ACAGTATATATTCTTTTTATATTTTTAAACAATTT[A/C]TTTTCTTCAATTTATCTGTACTTTTCTCCTAAGAT M 2 1 2 1 103000 r 74 goat snp52347-scaffold779-536044 17 70240720 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450887 Affx-122922208 AX-123321221 17 1533737 ATAAATCTAACAAAAATTTTAATAACCTGAGAATG[C/T]AATGTGATAAATTTAAGATTCTGCTGAGTTGTCTC Y 2 1 2 1 101000 r 74 goat snp52346-scaffold779-482877 17 70294093 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797531 Affx-122961838 AX-385284470 17 1564859 CATGAGAATCTATGTAAACTTCAATGATTAATTTA[G/T]CCATCTTATCCTGAATGTCTGTATAAATTATTGGA K 2 1 2 1 201000 f 74 goat snp52345-scaffold779-451755 17 70326368 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436664 Affx-122932470 AX-123307002 17 1633485 TTAACCAAAACAATGGTTAGGGAAGGCTATTATCT[A/G]CTCCAGTATTCTGGCCTGGAGAATCCCAGGGACTG R 2 1 2 1 101000 f 74 goat snp52343-scaffold779-383129 17 70395626 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384231 Affx-122972373 AX-123254589 17 1699772 AACTTCTCTTGTAGTGCAGAGATAATTCTGGTCTT[A/G]CAGTTTTCTTTTGCTTAAACTCATATGAAACATTT R 2 1 2 1 101000 f 74 goat snp52342-scaffold779-316842 17 70462090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794270 Affx-122932449 AX-385281235 17 1736007 ATTTAAATTAATGATAGACTTATACATGTTTACAC[G/T]TCTAACATGTTTTCCATTCGACTATGTCGTATTTG K 2 1 2 1 101000 r 74 goat snp52341-scaffold779-280607 17 70498899 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387726 Affx-122969751 AX-123258084 17 1777496 TTTTAAGTGAATGTCTGCATCAGAGAATTTCATTT[A/G]CCACTTACTGTTAACTTCCTGACCCATATAAGTTA R 2 1 2 1 101000 r 74 goat snp52340-scaffold779-239118 17 70540786 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420027 Affx-122945151 AX-123290375 17 1894485 AGATCTTATTCCTACCACTCTCTAACAGTATAGGC[A/G]TCTTTTTAATGAACCATATTCTTCCATGCTAGCTC R 2 1 2 1 101000 r 74 goat snp52338-scaffold779-122129 17 70657092 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277192 Affx-1111835726 AX-519550698 17 1899300 CTGGTGAGGGTCTCTGCAGGAAGTAAGTCACGGCT[A/G]TGTCAGTACAGCAGTTTCTCCCACAGCTGGGGTGA R 2 1 2 1 102000 r 74 goat Random2.2K-1643 17 1899300 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320780148 Affx-122964305 AX-385267245 17 1948641 TTGCCTCTGGGCATCATCTCTTTTTCCTACACTCG[C/T]ATCTGGAGTAAACTTAAGAACCATGTCAGTCCTGG Y 2 1 2 1 101000 f 74 goat snp52337-scaffold779-67973 17 70710934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412200 Affx-122950940 AX-123282550 17 1982778 TATTAAAGTGGGCTCCCTGATTTCAATAGATAATG[C/T]AATCCCAATGGAATAAAGTTGAAAACTAAAATTTA Y 2 1 2 1 101000 f 74 goat snp52336-scaffold779-33836 17 70744150 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414472 Affx-122949559 AX-123284821 17 2016477 GTCTCTATTGCTGTAGCTAGATAAAGAGAGCACTC[A/G]CCTCCCATGCACAAGGAAGGACCACACTCTGCACA R 2 1 2 1 101000 f 74 goat snp52335-scaffold779-137 17 70777490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449936 Affx-122922910 AX-123320271 17 2078334 CAACACATTTATGGTCTCGTGTGTAATAACCCCAG[A/C]GGTGCTCAGCAGTTATCCTATGAGAGATTCTAAGT M 2 1 2 1 101000 r 74 goat snp53387-scaffold806-61621 17 70838351 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381131 Affx-122974569 AX-123251489 17 2126164 TAGCTTGTTCCTCTGCAGTACTCTGCTCTGAAAAT[C/T]CTAGCCACTTCAAAGTCCTTGGAGTCCTACTTCTG Y 2 1 2 1 101000 f 74 goat snp53388-scaffold806-109451 17 70887544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428116 Affx-122939074 AX-123298459 17 2169455 ATCCTGGAAAAAATCCTCTCTTTCCTGGTTTCTCA[C/T]GTAGGCAAGTGTGGGCAATGAACCATAGCTTCAGG Y 2 1 2 1 101000 r 74 goat snp53389-scaffold806-152742 17 70938983 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768952 Affx-122948518 AX-385256127 17 2213415 CCCCCACAGAGCTTGAGAGAATCATTAACTATCTT[C/T]ACATCAATGACTCAATCTCCCATTATACACAACCA Y 2 1 2 1 101000 f 74 goat snp53390-scaffold806-196702 NW_017203416.1 7643 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436925 Affx-122933195 AX-123307263 17 2249429 TGTTTTAAATTTTCCCAAATGATTCTAACATGCAG[C/T]GACATTCAAGCACCAGTGGAAATCACTGTATTAGA Y 2 1 2 1 101000 r 74 goat snp53391-scaffold806-232716 17 71020274 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431243 Affx-122937133 AX-123301584 17 2307792 TTGCTCTATGTATCTTGAGGATTTCAGCTAAGTTT[A/G]CACAGTCCAGCAATCATAAATTGACCAGGACCTGA R 2 1 2 1 101000 r 74 goat snp53392-scaffold806-291079 17 71079894 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776252 Affx-122950038 AX-385263380 17 2342632 TGTTACTTACCAACTAGCAGCTAATGATTAATCCA[C/T]AGTTGTCTAATACGAAATTCATAGTGAAGATCTGT Y 2 1 2 1 101000 r 74 goat snp53393-scaffold806-325919 17 71114869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800274 Affx-122934391 AX-385287196 17 2380125 GTTCACTGGAGTCAAAACCTATAATATTCCAAAGG[C/T]AGGGTCAGCTGACCTAGTGTTTAGTATTAAGCACC Y 2 1 2 1 101000 r 74 goat snp53394-scaffold806-363412 17 68391310 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400070 Affx-122960758 AX-123270425 17 2442031 ATCACAAGAAATAGAAGTCAATAGTAACAGAGCTA[C/T]AGGAAATGTAGATAAACTTCTCAGAACTAGACATC Y 2 1 2 1 101000 f 74 goat snp53395-scaffold806-425318 17 68328149 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429822 Affx-122938181 AX-123300163 17 2507897 TTCACATCATTTACACTTAAAAAACAATATTGTCT[A/G]TCTTGTATGTTGGTTGTCTAGATTAAATAAAATAC R 2 1 2 1 101000 r 74 goat snp53397-scaffold806-491184 17 68262556 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783544 Affx-122920294 AX-385270606 17 2550190 TTTGTTATCTACTTTCATGCATTTCAAATTCAAAG[A/G]CAAGAGAGGACAGTATGAAAATCTGATTTTATTGA R 2 1 2 1 101000 r 74 goat snp53398-scaffold806-533477 17 68219779 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383518 Affx-122972635 AX-123253876 17 2608092 CTCCCTCCTAGAAGGAGAGGATCATTTTTCTAAAC[A/G]TTTGCCTCTTGAAATCAGGATAAAATCTAGCCTTC R 2 1 2 1 101000 f 74 goat snp53399-scaffold806-591379 17 68161426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774938 Affx-122965016 AX-385262071 17 2658688 TGTTAGTCTTTGTTGTCAAATCAACAAGTTAATTT[A/G]CAGTTTGGTGGAAGTGGACAGAGATTATAAGAGTC R 2 1 2 1 101000 r 74 goat snp53400-scaffold806-641975 17 68109628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422812 Affx-122943198 AX-123293158 17 2691617 TGGGAAGAAGCAGGGGCAAACCATAGAGTATACTA[C/T]GCAAAATTTTCCCATTTCCAAGATTTTATTGGTGC Y 2 1 2 1 101000 f 74 goat snp53401-scaffold806-674904 17 68077332 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790382 Affx-122939094 AX-385277385 17 2736378 CATATCTGAGAGATGGGGCAATATGCACATTAAGG[A/C]TGTTGTGTGATTCAGTCTGGCCAGACTAGAGAGTG M 2 1 2 1 101000 r 74 goat snp53402-scaffold806-719665 17 68032148 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795419 Affx-122976941 AX-385282375 17 2794627 TATACCTGAATCCTGTGTTAGCTGTCCCTTTTCAA[A/G]TGGTTACCTTCCTTAGTTAACATTTAATTTTTTGG R 2 1 2 1 201000 f 74 goat snp53403-scaffold806-777914 17 67973412 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428753 Affx-122938434 AX-123299095 17 2823831 TCATGCTTGAATCATTGCATTTTCATATTTTATAA[C/T]GAACTGTCCTCCCCCATGTTTTTATTTCTAAAATT Y 2 1 2 1 103000 r 74 goat snp53404-scaffold806-807118 17 67945398 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377452 Affx-122977524 AX-123247811 17 2865969 TCAGAGGTCTTTGTGCTGGGGACAGAGTGGTGCTG[C/T]GGGCCTGGAAGTGCTTGTTTTAAGTGAAGGAAACC Y 2 1 2 1 101000 r 74 goat snp53405-scaffold806-849256 17 67902841 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404929 Affx-122956438 AX-123275281 17 2901253 ACAACCATCCATTCAGTCATCCATCCAACAGACAC[A/G]TAGTGAGTAAAGCCACACTATGGTAGTACTCTTCT R 2 1 2 1 202000 r 74 goat snp53406-scaffold806-884540 17 67867562 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788573 Affx-122975722 AX-385275590 17 2951228 GTAGGGAGAGAAACAGCATATTTTCAACTATCATA[C/T]TCTGTTTGAATATTTATTATTCTCTGCAAAGTTAA Y 2 1 2 1 201000 r 74 goat snp53407-scaffold806-934515 17 67820190 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420672 Affx-122944812 AX-123291019 17 2988923 ACAGGCTGAAGGCTTCCCCTCTGGAGGAGCAGACT[C/T]AGATGTTGCACAGCCGAAAGGTGACTAATAGCCAC Y 2 1 2 1 101000 r 74 goat snp53408-scaffold806-972210 17 67783298 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442512 Affx-122928552 AX-123312849 17 3018485 GACATAGTACAGAGAAGTATATGAGCCTGTGCATC[A/G]CAAGTGCACAGATCTGCAGAGTAGGATGGTACTGA R 2 1 2 1 101000 f 74 goat snp53409-scaffold806-1001772 17 67753874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375383 Affx-122979219 AX-123245742 17 3062204 TAGACACCCATTAGGCTCTCTTCCTCTTCCTCACC[A/G]CAGACACCCCAACACCCAAGGAGCAGTGGCTGATA R 2 1 2 1 101000 f 74 goat snp53410-scaffold806-1045491 17 67708992 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402428 Affx-122958630 AX-123272781 17 3094230 GCACAGTTATTTTAAAATGCATGTTTTAATGACCA[A/G]TGTAAAGCTTCATTATGGTATGCAAGTATACAAGC R 2 1 2 1 101000 r 74 goat snp53411-scaffold806-1077517 17 67676681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434163 Affx-122934893 AX-123304504 17 3138610 GCCACCATCTGCGCCATCTTTTATTCCATGTCAGT[A/G]CTCGTACGTGACGGGGGAGCCCCTGCTCTGTCCGG R 2 1 2 1 101000 f 74 goat snp53412-scaffold806-1121897 17 67631894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778802 Affx-122941179 AX-385265911 17 3211199 CCGATTATGCTATCTAGCATTGAGTATTTGAAAAA[C/T]CTTAATATCATTTTGATGTGTATAACTTGGATAAA Y 2 1 2 1 202000 r 74 goat snp53413-scaffold806-1194486 17 67558541 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765546 Affx-122929146 AX-385253026 17 3240504 ATCGCTAGCTGTCTAATTCCACTTCTGAAAGGAAG[A/G]TCATCTTCCAATTGACAATTTACTTTATTACTAAG R 2 1 2 1 101000 f 74 goat snp53414-scaffold806-1223791 17 67528727 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377716 Affx-122977396 AX-123248075 17 3274581 CCTCCCGTTCTTTCCACTTCCATGCACATTCCCAA[C/T]GACATCTTGACTGTGAGGCCCTCCTCGCTCCCTGA Y 2 1 2 1 101000 f 74 goat snp47227-scaffold663-2582 17 67473193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271825 Affx-1111833093 AX-519545612 17 3298560 CATTATGGAAATACTTTTTTCTTATGGCTGAAATT[A/G]ATTAGAAGGAAATAGAAGAAGGCAAGAGAAGGAAA R 2 1 2 1 101000 r 74 goat 17_3298560_AF-PAKI 17 3298560 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38439722 Affx-122930550 AX-123310059 17 3356665 TTAGAATCCCCTGGTATTTGTTAAAAATAAGGGTC[C/T]TGGGCCCACTGCAGACTTAATGAATTGGAATACAA Y 2 1 2 1 102000 f 74 goat snp47228-scaffold663-84666 17 67390408 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780415 Affx-122932835 AX-385267507 17 3405070 TGAGGTAATAAGTGTATTAACTAACCTTATCATGG[C/T]AATCATTTCTCAGTACAGACATACATCAAATCATC Y 2 1 2 1 101000 r 74 goat snp47229-scaffold663-133071 17 67341497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407065 Affx-122954917 AX-123277416 17 3437064 ACCTTGGGCATCCCACTTGCAGCTGGCATCTCAAG[C/T]GGGAAAGTCTTATGGGTCTGGAGCTTATAACCCAT Y 2 1 2 1 101000 r 74 goat snp47230-scaffold663-165065 17 67309211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420680 Affx-122944805 AX-123291027 17 3479687 AGAAGTGTAGGAGAGGCATGGAAGAAGTAACAACC[A/G]CAGTTCCAGTTTCATCTGCCTTCATACTGGTTCAG R 2 1 2 1 101000 f 74 goat snp47231-scaffold663-207688 17 67265021 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389452 Affx-122968345 AX-123259810 17 3514699 TGAAAAGCAGTTTGATAATACTGTTTAAAGTGTTC[A/G]CCTTATATAATCATCGATTCCACCTCTAGGAATTC R 2 1 2 1 101000 r 74 goat snp47232-scaffold663-242700 17 67229908 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406246 Affx-122956107 AX-123276598 17 3564106 AGCTCTATGACCCCACTTGAAGGTTTTAACATCAA[C/T]GAAATGTCATTATTCTATGGGATTCCCTGCCTCTT Y 2 1 2 1 201000 r 74 goat snp47233-scaffold663-292107 17 67179911 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453777 Affx-122919589 AX-123324110 17 3624810 GAACAAACCAAACAAGGAGAGAACTTGCATCTCAA[G/T]AATTAGGAAGAATGAATCCATTTGGAAAAGTGCTG K 2 1 2 1 101000 f 74 goat snp47234-scaffold663-352811 17 67118460 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415916 Affx-122948457 AX-123286265 17 3695450 CTTTATCTCACTGATATTTATGGCACACTCACTGC[A/G]CCAGGCCCTGGAGCTCCCTCTGTGTACTCAACAGA R 2 1 2 1 101000 f 74 goat snp47235-scaffold663-423451 17 67048390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391868 Affx-122966982 AX-123262225 17 3741362 AGGGAATCTCTTGGCTTTAGCAAATATCTGCAATT[A/G]TATGCCACTAGCCATTGAGAAATAAGAAATCACAG R 2 1 2 1 101000 f 74 goat snp47236-scaffold663-469363 17 67002901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420723 Affx-122944774 AX-123291070 17 3800152 GGGAGCAGGAGGCCCATACATGCTGTCTCTGAGCG[C/T]TGCCACTCTGCTGCCTCCTCGATTTTAAATTAACC Y 2 1 2 1 101000 r 74 goat snp47237-scaffold663-528153 17 66947985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443625 Affx-122927296 AX-123313962 17 3831000 ACAGTGGATTATGGCTAAAAGGGCTGCAAGCTACA[C/T]GAATTACAATGAGTTTTTAAGAAACCAAAGACAAA Y 2 1 2 1 101000 f 74 goat snp47238-scaffold663-559001 17 66917691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419252 Affx-122946267 AX-123289600 17 3921139 TAAGTCAGTACCCAGGTGGAAGAGTAACCCAGTGA[A/G]AGGGAGGGGAGAGGACTTGGGTTGCTGTGGGCAAA R 2 1 2 1 101000 f 74 goat snp47240-scaffold663-649140 17 66826806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792975 Affx-122957947 AX-385279953 17 3966798 GTTTTTTCCCAGCTCTTTCTCACTAAAAGTAATGT[A/C]TTAATTTTCAGAGCTATAACGATATAATCTGCCCA M 2 1 2 1 101000 f 74 goat snp47241-scaffold663-694799 17 66780957 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385065 Affx-122971820 AX-123255423 17 4019498 CTTATCCTAGGCCACAGGTGGACCAAGCACGTTTA[C/T]GCAACACAGTAGCTGTTCTCAAAAAAACAACTCTG Y 2 1 2 1 101000 r 74 goat snp47242-scaffold663-747499 17 66728466 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392526 Affx-122966110 AX-123262883 17 4070117 TCCAACCAACAGGCTAATTTGTAAGTCACCATCAC[A/G]GTGGATATTAGATCATTTCCCTTGGGCTAAATTAT R 2 1 2 1 101000 f 74 goat snp47243-scaffold663-798118 17 66677934 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398209 Affx-122962223 AX-123268564 17 4102358 GTCTTGTGGACTTTACAGAGTTGGTAATGCTATTT[A/G]ACTGTTGTTCAAAAGCCAGAAGTATGTCTGCAGTG R 2 1 2 1 101000 r 74 goat snp47244-scaffold663-830359 17 66645568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402281 Affx-122959110 AX-123272634 17 4142634 CATGCCTGATGGAGGGCTCAGATGAGCAAAACTTG[A/C]TTGCTAATGATTCTTTAAGAGATAGGACTACCTTG M 2 1 2 1 101000 f 74 goat snp47245-scaffold663-870635 17 66609143 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448939 Affx-122923149 AX-123319274 17 4177215 ATATTAGTCACAGTCATCTGCCCAGGGAAAGAGCT[A/G]TGGCAATACAAGAGGGACCACAAAGTGAAAAGCAG R 2 1 2 1 201000 r 74 goat snp47246-scaffold663-905216 17 66576110 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426825 Affx-122940514 AX-123297170 17 4211966 TCTCATTCACCAAATCTCCCACTGCCATTCACAGA[C/T]GCAAGGGAATCTGGGAAGATTAAGGGTTTTTGCTC Y 2 1 2 1 102000 f 74 goat snp47247-scaffold663-939967 17 66541182 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778385 Affx-122974336 AX-385265500 17 4246357 AAAGCATCCAAAATACTGCAGTACATACGTAGCTA[A/C]GAACATACAGACACTTTGATGCACAGCGTTTATTC M 2 1 2 1 101000 r 74 goat snp47248-scaffold663-974358 17 66506298 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399448 Affx-122961211 AX-123269803 17 4305685 CAAATCAATCATCGCTTCATTTGCTAGGGGCACTG[A/C]GCTCTGAATATGGGTAGGATTCCATGTCGTGACCC M 2 1 2 1 101000 f 74 goat snp47249-scaffold663-1033686 17 66448097 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399825 Affx-122960264 AX-123270180 17 4352426 CCAGCATCAACATTTAGAACCTGTGCAAATCAAAC[G/T]AAGGTTGTCTTTGGGGGATTTACAATCCAAGATGG K 2 1 2 1 101000 f 74 goat snp47250-scaffold663-1080427 17 66402116 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446568 Affx-122924835 AX-123316904 17 4383136 TCTCGCATGCTGCAACTAAGAGATCCTGCAGGCCA[C/T]AGCTAAGACCTGGTGCAGACAAAACATGTGAAAAA Y 2 1 2 1 303000 f 74 goat snp47251-scaffold663-1111137 17 66371666 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796913 Affx-122954704 AX-385283856 17 4415412 TTCCTTTGAGTAAATTACTAAGACTACTGCCTTCC[A/G]GATAACAAGTACAGGGATAATTTTAAACAGCAAAC R 2 1 2 1 101000 f 74 goat snp47252-scaffold663-1143413 17 66339275 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437107 Affx-122932175 AX-123307445 17 4448597 CCTTGAGACACAGAGCTCCACGTGGAGGAGAAACC[A/G]TGCAGGCAAAGCGGAACAGGACCTGGACAACAAAG R 2 1 2 1 101000 r 74 goat snp47253-scaffold663-1176598 17 66305983 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391932 Affx-122966931 AX-123262289 17 4480821 ACATCCTGACTGCTTTCTTCGGTCCCTCTCGGGTG[A/G]AGGCTGGTTCCTCCTCCTTTCCCTTTCTTGGTCTG R 2 1 2 1 201000 f 74 goat snp47254-scaffold663-1208822 17 66273488 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438201 Affx-122931820 AX-123308539 17 4528869 CAGGGACCGGGAACCTTTGCACTTTCCCCTTCTCT[A/G]TCGTGTCCACTCGTCACCCTGTCCCTCCCTGGGCA R 2 1 2 1 201000 r 74 goat snp47255-scaffold663-1256870 17 66235153 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434556 Affx-122934133 AX-123304897 17 4576477 TAAAGGGTCAGGCTAGTCTGAATGCTGCTCCCAAG[C/T]GGCTCACACTGTCTCTTCCCATCCTTTTGGTAGAT Y 2 1 2 1 201000 r 74 goat snp47256-scaffold663-1304478 17 66186807 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408204 Affx-122953855 AX-123278555 17 4621518 AACATTAAAAAATTTTTTTGAACTTTACTTACTGC[A/G]TTCATGATATTCCCTGCTTGTAGCACCAAGTGTAA R 2 1 2 1 101000 r 74 goat snp47257-scaffold663-1349519 17 66141881 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445123 Affx-122926181 AX-123315460 17 4705330 TTTATTCTCAACTCATATTGAATTTAATGAATTTC[A/G]CCTTTCAAGGTCAAAAGCATATCATTGGTTCATTC R 2 1 2 1 101000 r 74 goat snp47259-scaffold663-1433331 17 66057277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784640 Affx-122963754 AX-385271688 17 4770773 AGTTAGGCTGAAGGGAAAGAAGGAATGGCTAGAAG[C/T]AGAAAAACCATTTAGGAAGCATTTTACAGCGTGAG Y 2 1 2 1 101000 f 74 goat snp47260-scaffold663-1498774 17 65992241 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380440 Affx-122975295 AX-123250798 17 4805756 GTATAGTTCTCTTCAAGTTTAAACATTCTATAAAA[C/T]AGGCATCAAACATTTTAGAAGGTCAACCCTTGATC Y 2 1 2 1 201000 f 74 goat snp47261-scaffold663-1533757 17 65956760 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788835 Affx-122936228 AX-385275850 17 4880014 TGTCTCTGTGTGGACAAAGGTCTATGTCTATAGAT[A/G]CTTTTGCCTTTTATAGTCATTGTCGCCCCACTTAA R 2 1 2 1 101000 f 74 goat snp47263-scaffold663-1608015 17 65882880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791470 Affx-122921346 AX-385278461 17 4947605 CACCTTTCATAAGCAGTTCCCGAAACCAGCAGGTC[A/G]CAGGGAAAGACTGGTTACTAGACAGTGATTGAGGC R 2 1 2 1 101000 r 74 goat snp47264-scaffold663-1675606 17 65816569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435387 Affx-122933571 AX-123305727 17 5007554 TTTCCCAGCACCCTGATTGACCTTCCTGTCATCAG[C/T]ATGGCCCAGATCACACTGACTGAAATAAGTCATTT Y 2 1 2 1 101000 r 74 goat snp47266-scaffold663-1735555 17 65757082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426353 Affx-122940259 AX-123296699 17 5045155 GCATTTATAGACACTGGAAGACTGATCTTTAAGAA[A/G]TTAAAAATATTTAAAATTTTTGTGGTGAAAGTTGC R 2 1 2 1 103000 f 74 goat snp47267-scaffold663-1773156 17 65719535 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416938 Affx-122948036 AX-123287286 17 5106138 TTTTAAGAACACAGTTTTTTAAGGAAGTCCAGTTT[A/G]CTGTGTTTATCTTTGTCTTGTTTAAGAAATCTTCA R 2 1 2 1 101000 r 74 goat snp47268-scaffold663-1834139 17 65658431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410808 Affx-122952649 AX-123281158 17 5136876 CACCATATATTGCTGAGGCTCTCTCCGTGAGAAGG[C/T]CTGTCCCTAATGGCTTTCAAGCATTACTGTGCTGG Y 2 1 2 1 201000 r 74 goat snp47269-scaffold663-1864877 17 65627829 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413700 Affx-122950088 AX-123284049 17 5174461 TAGCTTAGACATGTAAATGCTTTCATTGCTATATC[A/G]TTTTTGCTTTGCCTTGTGAATTTTAAACTCTTTTT R 2 1 2 1 102000 f 74 goat snp47270-scaffold663-1902462 17 65589672 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413363 Affx-122950144 AX-123283712 17 5225894 CTACAAAGGAGTATTGTAAGTGTTTTAGTACGCAT[A/G]TTGTCTCTGCTAGCTCTATAACAATATAAAACTTA R 2 1 2 1 101000 f 74 goat snp47271-scaffold663-1953895 17 65539920 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399736 Affx-122960452 AX-123270091 17 5255955 TTTCACTACTGGCAGGCCGTATAATTTGACAGCCC[A/G]TCTTCTGTAGAAGGAAAACAGTATATTTTTAAAAT R 2 1 2 1 101000 f 74 goat snp47272-scaffold663-1983956 17 65510057 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430265 Affx-122937300 AX-123300606 17 5312146 AGTGAGCAACTGTCATTTACAATGACCTCAGATCT[C/T]TCGAACTGCTTCTCCATATTCTGCTGATTTCCGCA Y 2 1 2 1 101000 r 74 goat snp47273-scaffold663-2040147 17 65453953 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795718 Affx-122946879 AX-385282671 17 5351531 GAAATGAGAGCAAAATCATGGGGACTTAGGAGTGT[A/G]TGAGAACTTTCTAGGAAGCTGATCTATTTGTTTTA R 2 1 2 1 101000 f 74 goat snp47274-scaffold663-2079532 17 65414228 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399120 Affx-122960855 AX-123269475 17 5386321 ACATGATCAGTTACTTGGGAACCTCTTCTCCAGTC[C/T]TGTGTAAATTTGTGAGTGAGATGCGGGGCACAGCC Y 2 1 2 1 101000 f 74 goat snp47275-scaffold663-2114322 17 65379417 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388907 Affx-122968847 AX-123259265 17 5420238 AGAACTAGTCTTCGATTTCAGTAAGGTGCATTTAG[A/C]TTATAAAGTCCCTTGATTATGAAGCCAGCGTGGAA M 2 1 2 1 102000 f 74 goat snp47276-scaffold663-2148239 17 65345559 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788280 Affx-122970010 AX-385275298 17 5469840 GTGGTAAAGTCTTCCCATGAGATTTAGAAAAGATA[A/G]CTTCTTAACTGAGCCCTGAAAGATCAGATTAAAAA R 2 1 2 1 101000 r 74 goat snp47277-scaffold663-2197841 17 65299386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379557 Affx-122976052 AX-123249915 17 5528688 GCCTGTGAAGCCTCACTGGGCTTGGACAGCTCCCC[A/G]GCATCTCCCACCGTGGAGGTGCCGGCCTCTGTGTG R 2 1 2 1 103000 f 74 goat snp47278-scaffold663-2256689 17 65240243 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400351 Affx-122960036 AX-123270706 17 5580515 AGCTTTTATATTGATATGTTTCTGGAATAATTTCA[C/T]GTAAAGTCTATACTTGACCTTCTGGGGTGTATAAT Y 2 1 2 1 201000 f 74 goat snp47279-scaffold663-2308516 17 65188256 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415468 Affx-122949161 AX-123285817 17 5640442 GAGTGACTGGGACACTAGTCCTGAGCTGGGGTGAC[A/G]CTTGCCCTTTTGGATGAGGATGTCATGATATCCAG R 2 1 2 1 101000 r 74 goat snp47280-scaffold663-2368443 17 65128727 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380305 Affx-122975396 AX-123250663 17 5707314 TGCAGTCCACCTTGGAAACACTTTGGTTTGCTTCC[A/G]CAGAATCACACTGAATCTCCTGCCAGAAGGCCTCA R 2 1 2 1 101000 f 74 goat snp47281-scaffold663-2435315 17 65061470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772815 Affx-122935292 AX-385259960 17 5767252 TGTGAGAGGCATCACCCATGGTTTTGAACAAGAGA[C/T]GGTCTTTTGGAAGATGAGTTTTGCAAGGGTGCGCA Y 2 1 2 1 101000 f 74 goat snp47282-scaffold663-2495253 17 65001360 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273700 Affx-1111833789 AX-519547312 17 5793432 ATGCTGGTTTCTTGAATTCTCCTGGAGCCGCCTTT[A/G]GAA R 2 1 2 1 101000 f 74 goat GoatD01.005105 17 5793432 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443202 Affx-122927588 AX-123313539 17 5801647 TCAGAGCAGTCAGGTCGCTAATACCAGGCTCCTTC[C/T]AAGACTCAGAGGGGACTCTAGGATACCACTCACTG Y 2 1 2 1 201000 f 74 goat snp47283-scaffold663-2529648 17 64967184 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777862 Affx-122949288 AX-385264979 17 5834135 CTTTCGGTTCACCTAGGAGTATTTTCTTTAGGGAC[A/C]TTTCAGAATGCGCCTAGATAAGAAATTCTGTTTGA M 2 1 2 1 201000 f 74 goat snp47284-scaffold663-2562136 17 64934756 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392444 Affx-122966173 AX-123262801 17 5885201 GTTGAGAACCGAGAATCCTGACAGTCAGGATACCA[C/T]ATGCAGAGGAAGACCAAGGATTGCGGGCAGCCATC Y 2 1 2 1 101000 f 74 goat snp47285-scaffold663-2613202 17 64884302 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407182 Affx-122954825 AX-123277533 17 5939331 CATAAAGCTAGTAACACATTCTTTTATTTTTGGCC[A/G]TCTTGTGTGGCTTGTGGGGTTTTAGTTTCCCAACC R 2 1 2 1 201000 f 74 goat snp47286-scaffold663-2667332 17 64830392 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463483763 Affx-1110005312 AX-514966653 17 5943013 GGGCTGGCTGTAAGAAGTAAATGAATAAAACAAAT[C/T]ATGTGTTCAAGACAGAGCAGCTCTTACTTTAAGCG Y 2 1 2 1 201000 r 74 goat Random2.2K-1646 17 5943013 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320773896 Affx-122950418 AX-385261035 17 5988998 CTGAGGTTGATAAAAACCTGTTGAGGGAACCTGGA[G/T]CCCTGGTATTTATCCAGACAATTTGGAAGCATTAC K 2 1 2 1 101000 r 74 goat snp47287-scaffold663-2716999 17 64780008 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425720 Affx-122940762 AX-123296066 17 6022841 ATCCACTAACCCCACTAACTACAGCTTCTTAGGCA[C/T]GTGCAATAAGAAGCATATATTAAACCCTTTCAAGT Y 2 1 2 1 201000 r 74 goat snp47288-scaffold663-2750842 17 64745863 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277194 Affx-1111835727 AX-519550700 17 6068518 CTTCAGAGTAAAACCCTGCAATTTTTGTGTTCGTT[A/G]TTTCATTAAACCCAGATGTTCTGTGTGCTCTCCAT R 2 1 2 1 101000 r 74 goat Random2.2K-1647 17 6068518 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388774 Affx-122968935 AX-123259132 17 6070597 TGGGAAAGAGTCAGAGTTGGGCTCTATCAGGTATA[C/T]GTCTGGGTTATTTCTCCAGTACCTTGATGCCTACA Y 2 1 2 1 101000 f 74 goat snp47289-scaffold663-2798598 17 64698392 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405469 Affx-122956030 AX-123275821 17 6112118 ATGGGTCTGAATTTCAAACATGCACAAATTCTAAA[C/T]AGGAAGCTCAAATGCTTTCAGAATGAAAGATATAC Y 2 1 2 1 101000 f 74 goat snp47290-scaffold663-2840119 17 64657386 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425514 Affx-122941469 AX-123295860 17 6153976 TTTACCATCTGCGCCACCAGGGAATCCCTTAAAAA[G/T]AAAGAAAACCCCACTAAACACAAGCCATTCAAAAT K 2 1 2 1 303000 r 74 goat snp47291-scaffold663-2881977 17 64614782 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380224 Affx-122975478 AX-123250582 17 6184838 GCCTCAGCTCACAGCCAGACCTAGAGTCAGCCCTC[A/G]TGTTCACCATCCCACGGTCACTCCAAGCTGAAAGC R 2 1 2 1 101000 r 74 goat snp47292-scaffold663-2912839 17 64584001 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277072 Affx-1111835728 AX-519550579 17 6218817 GGAAACTGAAAGGTATCGATCGTGTGCGGCTTTAC[A/G]CCGCTAAGCTTGAGGAATGTTGTGATGCAGCAGTA R 2 1 2 1 201000 f 74 goat Random2.2K-1648 17 6218817 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390824 Affx-122967845 AX-123261181 17 6221152 AATGCTCCCACTAATCTGCCCTTTTGCTTCTAAAC[A/G]CAGCCCAAACCCTTCATTCCCATCCCCAGGTCTCC R 2 1 2 1 101000 f 74 goat snp47293-scaffold663-2949153 17 64546957 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452870 Affx-122920706 AX-123323203 17 6261756 ACAATGTGCTGCAGAATCACCCCCAAAAAAGTGTT[A/C]GTCACTCAGTTGTGTCCAACTCTGTGCTGCTATGG M 2 1 2 1 103000 f 74 goat snp47294-scaffold663-2989757 17 64506402 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427741 Affx-122939257 AX-123298084 17 6290799 TTTTCACTTTCACTTTCTATTACCACTCCAACCTA[C/T]ACCTTCCAACCCAGAGCTAAAGTATTATCTTCATT Y 2 1 2 1 101000 f 74 goat snp47295-scaffold663-3018800 17 64477133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427039 Affx-122939825 AX-123297384 17 6351369 GTTGGAAGCAACTCAAACATCCATCATCTGATGAA[C/T]GGATAAACAGACTGGGAAAGGCGCTCGTTTATGTT Y 2 1 2 1 103000 f 74 goat snp47296-scaffold663-3079370 17 64415706 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424504 Affx-122941742 AX-123294850 17 6384232 GATACATTACAGTTCATCTCCAGCATTTATCAAAG[G/T]GCCCAAAATATCAATGGCACTCGTACTTATTGGAC K 2 1 2 1 101000 r 74 goat snp47297-scaffold663-3112233 17 64382473 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775883 Affx-122969061 AX-385263014 17 6442535 TCCATTTGTGTCCACATACTTCTTCATAGAAGGCA[C/T]CCTTCCTGCCTTGTAAGTTGCATTGTCAAGGACAA Y 2 1 2 1 101000 f 74 goat snp47298-scaffold663-3170536 17 64323102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433139 Affx-122935684 AX-123303480 17 6472307 ATGACAATAACTGCATAGCTTATAAAATCTTGAAC[A/G]TGTCAGAATTTGTTATTCTTCTATTGTTGACCATT R 2 1 2 1 101000 f 74 goat snp47299-scaffold663-3200308 17 64293282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801500 Affx-122968714 AX-385288409 17 6510096 AAACAAGGTGAAAAATTACAGAGTATACAGGTTTT[A/G]TAGGGAAAAATCTTTTTGCAGTCAGAGATATGAAA R 2 1 2 1 101000 f 74 goat snp47300-scaffold663-3238097 17 64254227 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765457 Affx-122977509 AX-385252957 17 6591307 AACTACGTCAAAGTGATTGTAAGTAGGTTGTGCAT[A/G]TTGAAATTGGTCACATATTCAGTGGAGTCTATGTA R 2 1 2 1 101000 f 74 goat snp47302-scaffold663-3319308 17 64172375 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420260 Affx-122945058 AX-123290608 17 6599810 TGCAGACTTTCTGCATATAATTTGTTGAAGTTATG[C/T]GGGGAAAAGAGATAAAGATACCTTTAATCAATAAT Y 2 1 2 1 201000 f 74 goat snp13947-scaffold1549-7489 17 64163837 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274382 Affx-1111834223 AX-519547976 17 6630600 ACTGCATTGTGGACACTCAAGATACATTTTGTTCA[A/G]CTCCTGGAGCTGCAGTAGAGAACTGTCAGGCAAGG R 2 1 2 1 201000 f 74 goat GoatD01.026193 17 6630600 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38439233 Affx-122931015 AX-123309570 17 6631644 AGTACCGTGCATTTTTCCACACCCTTACGATGACC[A/G]ATACCCTCATGGAGTGGTTAGAGAAAACTGCACAT R 2 1 2 1 101000 f 74 goat snp13948-scaffold1549-39323 17 64132012 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440781 Affx-122929847 AX-123311118 17 6661796 AAGACTATCAGGAAAAACATTGAACGGAGTCTCTG[C/T]ATCATAGTCTAGCTTTAGCTCTTCTGAAGGTTTAT Y 2 1 2 1 101000 f 74 goat snp13949-scaffold1549-69475 17 64102016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381385 Affx-122974385 AX-123251743 17 6695893 AGGCAGAGTCCCTTGATTTACTATATAATGAAAAA[C/T]TTGTATGTCCATTTACTATCTTCAATGCCATTTTT Y 2 1 2 1 201000 r 74 goat snp13950-scaffold1549-103572 17 64068590 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768453 Affx-122927815 AX-385255633 17 6732064 ATAGTCTCCTGATTCCACTTTGTTATACTGATAAG[C/T]ATTGCCCTACATTCTGTGCCTTTTAAATTTGCTAC Y 2 1 2 1 101000 r 74 goat snp13951-scaffold1549-139743 17 64032754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767525 Affx-122970003 AX-385254783 17 6820259 GGAGTGTGTGTGCTTCTGGATATGTGTCAGTGGCT[A/G]TATGTTGTCTGTTAACATGGAGGTTTCTGTCAAGC R 2 1 2 1 101000 f 74 goat snp13953-scaffold1549-227938 17 63945713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412872 Affx-122950434 AX-123283221 17 6865673 CAAAGGAAAAAATAAATTTCATTCTCTTATATGGC[C/T]GGATATAATCCATTACATACATGTTCTTGTTTTTA Y 2 1 2 1 303000 r 74 goat snp13954-scaffold1549-273352 17 63900523 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799623 Affx-122935525 AX-385286553 17 6900909 TACTTCTCCACATGAATGCCATATTTCCTTTTTGT[A/C]TATACCTTTGGTTATATTTTAAGTTGGATAATTAA M 2 1 2 1 102000 f 74 goat snp13955-scaffold1549-308588 17 63864709 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799944 Affx-122971597 AX-385286870 17 6939147 TTTCAGGACGCTAGATCTTTCAGATATTTGCTTCC[G/T]TCCACCATTGTTTTCTGCAGTATCTCGCTCATTAT K 2 1 2 1 101000 f 74 goat snp13956-scaffold1549-346826 17 63826487 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451398 Affx-122921199 AX-123321731 17 6980447 ACACAAGCAGTTTTTTTTCTCCTTGTGCTAGAGGT[A/G]TAAATTATACCTAGTTTTTCTTCTTAATATTAATA R 2 1 2 1 303000 r 74 goat snp13957-scaffold1549-388126 17 63784312 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777561 Affx-122958642 AX-385264680 17 7027345 CTCTGGTTTATCATACATATTCTGGTTTATCTTTC[A/G]CACCTGGACTCTTTAGTCATAGTATTTCTCAGTCC R 2 1 2 1 101000 r 74 goat snp13958-scaffold1549-435024 17 63737364 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391417 Affx-122966766 AX-123261774 17 7060186 AACATGGATCATAATTCTCAAGTGCATTGCCCCGG[A/C]GGAAGAGAGAGTCAAAAGGCTCTGCATTATGTCTC M 2 1 2 1 201000 r 74 goat snp13959-scaffold1549-467865 17 63704253 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791209 Affx-122964413 AX-385278203 17 7092196 AAACGATAGAAAAACATCACAGTAGCAGTAGACGA[A/G]GCAAGAGAGGTGATACAGCTATAGTAGTGAGTATG R 2 1 2 1 101000 r 74 goat snp13960-scaffold1549-499875 17 63671739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420548 Affx-122945292 AX-123290895 17 7136796 AAAGCAAAAACATGATGGCATCTTCTCTGATGGCC[A/G]TAAATCTCTCTGTAAAGTGAAATGAAATTAATTGG R 2 1 2 1 101000 f 74 goat snp13961-scaffold1549-544475 17 63627328 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396571 Affx-122962921 AX-123266926 17 7168746 AAAATACCACTCTGATATAGAACATATGAGATCCT[C/T]ACTGTTTGAATCCAGCTTTGCCCTCCAAGTTTTAT Y 2 1 2 1 101000 r 74 goat snp13962-scaffold1549-576425 17 63595386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768796 Affx-122949015 AX-385255973 17 7242662 CCATAAAAGTTTGTTCACATTAAATCTAGGTAAAT[A/G]TAGGTTATAGACTAATATAATGGTGGAGGCAGTGT R 2 1 2 1 101000 r 74 goat snp13964-scaffold1549-650341 17 63521172 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383666 Affx-122972511 AX-123254024 17 7271794 TTTGCAGTTGTTATTTCCAGTGTGTTTCTTGCTGA[A/C]TGAATTTCTCTCTTGCAGTACAGCCTTATTTACTA M 2 1 2 1 101000 r 74 goat snp13965-scaffold1549-679473 17 63491804 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402807 Affx-122958281 AX-123273160 17 7372014 GAAGTAACTGTCTGTGAGTGAGGTGGGGAGGCAGC[C/T]GCCTCTATGAGAGTTTGTACCAAGAGTGAGGTAGC Y 2 1 2 1 101000 r 74 goat snp57745-scaffold930-66661 17 63391373 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375373 Affx-122979226 AX-123245732 17 7434414 AGATTTTTGTGTTCTTTTTTCCATTTTAAACGATC[A/G]TTGTTTGTTCATCATGTAAAGCTTAGAAATTTAGC R 2 1 2 1 101000 r 74 goat snp57746-scaffold930-129061 17 63329279 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794877 Affx-122973497 AX-385281837 17 7469499 TGAATATAACCTCTAAGGCAGCAGCTTTCAGAATG[C/T]ACTTCTACTGCTTTTGATTAGCCAGACTGATCTGA Y 2 1 2 1 101000 f 74 goat snp57747-scaffold930-164146 17 63294575 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405821 Affx-122955886 AX-123276173 17 7537899 TAGATCCCCATGTAATACAGTCATTACTTGGCCGT[A/G]CTTAAATCTCACAAGCACGTCAGGCCACATATTTA R 2 1 2 1 102000 r 74 goat snp57749-scaffold930-232546 17 63226297 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393970 Affx-122965047 AX-123264325 17 7623182 CCGCTTGCTTACATTTTTCATGATAAAGACCAAGA[C/T]GCACACGCTCCTCACAAGTACAACTAGGAGAATCA Y 2 1 2 1 201000 f 74 goat snp57751-scaffold930-317829 17 63140646 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439993 Affx-122929795 AX-123310330 17 7683236 CTTGAGTACCAAGTGACAGGCAAAGGATCAACCAT[A/G]TTGGTGCCTCTTCTCTTTTTCTTGTATTATACAAG R 2 1 2 1 101000 f 74 goat snp57752-scaffold930-377883 17 63080644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377814 Affx-122977310 AX-123248173 17 7715154 GTGGCTGGGGTTGGAGGAAGATCTCCTGCTGGGCT[A/G]CATTACAAGCTGGCAGAGACCCAGAGCAGAAGCCC R 2 1 2 1 101000 r 74 goat snp57753-scaffold930-409801 17 63051092 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782272 Affx-122968863 AX-385269350 17 7754106 TGGTAGTAAAGTTTTAAGCAACATATTTAATTATC[A/G]TTTACCTTAAGGATTTTATTTATCATGAAAAAATT R 2 1 2 1 101000 f 74 goat snp57754-scaffold930-448753 17 63012694 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387443 Affx-122970381 AX-123257801 17 7836104 CTTTCGGTTTTCTAAACTACTTGGTTAATATTTGC[A/G]TAAAAGTGGGACTTTACTTTCATGAAAGCATAGAT R 2 1 2 1 101000 f 74 goat snp11465-scaffold142-120012 17 62929320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390426 Affx-122967639 AX-123260783 17 7877496 TTGAATTCTATATGTTTGCTAAAGGGCTTTCCTAG[C/T]AGTTACTAGAAAATGTTGAATGAAAATACTGAATA Y 2 1 2 1 101000 f 74 goat snp11464-scaffold142-78620 17 62888450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779959 Affx-122947673 AX-385267058 17 7919447 GAAGTCTACACACCCACTTCTTTCTGCCTAAACAC[A/G]CTTACTAGGAGTACTCCCACCCCTTTTGCTTGTCT R 2 1 2 1 101000 f 74 goat snp11463-scaffold142-36669 17 62846087 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378522 Affx-122976634 AX-123248881 17 7954171 TTCTCTTAAGTGCCAAATCTGTAACAATAATGACA[C/T]GATAGTACTGAGCTCATCTAGCCTAACTCAAGAGT Y 2 1 2 1 101000 r 74 goat snp11462-scaffold142-1945 17 62811271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387810 Affx-122969684 AX-123258168 17 7963096 GACACCAGGAACCAACCACACTAAAATATAACTGC[A/G]TACAATAAAAGAAAAAGTATAGTAAGGAGGTATTT R 2 1 2 1 101000 f 74 goat snp32582-scaffold3721-6881 17 62791369 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390592 Affx-122967188 AX-123260949 17 7969942 TGAGAGAGAGTGTAGGAAAGAAGGAATATTTCTGA[C/T]GTGGAGGATCAGGAGAAAACTTTGTGGAGGCATTT Y 2 1 2 1 101000 r 74 goat snp12487-scaffold1479-575 17 62782166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400337 Affx-122960046 AX-123270692 17 8001358 TGCCAGCACCCCTTAGGATGCTTGGCTGGTTTTCT[A/G]CATTAAGAGGACAGTGGGACGTCTTGCTTGCCAGC R 2 1 2 1 201000 r 74 goat snp12488-scaffold1479-31991 17 62750612 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416408 Affx-122947849 AX-123286757 17 8055975 TGGTACATATTGGAACACCTGCTCAGAAATTTTGT[A/G]CTGACATTAATGGTTGGAAAATTAGAGACTTTTAT R 2 1 2 1 101000 r 74 goat snp12489-scaffold1479-86608 17 62695980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387769 Affx-122969718 AX-123258127 17 8172889 TTTTCAGTCTTTCATAGTTTATTAACTTGACAACA[C/T]ACATTAAGAACCTGCTATTTTAGATGCTAAGGACA Y 2 1 2 1 101000 r 74 goat snp12491-scaffold1479-203522 17 62582378 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452400 Affx-122920604 AX-123322733 17 8202139 CTTAGCAAATGTCACCATTCAACTAAGCAGCACTC[G/T]AAGCAGGGACCTTTTGGTTTATATTCTAAGAATAC K 2 1 2 1 101000 f 74 goat snp12492-scaffold1479-232772 17 62553123 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393319 Affx-122965953 AX-123263675 17 8235677 TCCAGCCAAGTCTACTAAATACTGCTTAACAGACA[C/T]CAAGCATGACAGCATTTTTAAACATATATGAAATG Y 2 1 2 1 101000 f 74 goat snp12493-scaffold1479-266310 17 62520336 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433802 Affx-122934461 AX-123304143 17 8310422 GGGGTTGCCAGTTCATGGAACTGTCTATTATTTCT[A/G]TCACTCAAGTTATTTGTGAGTCTGTTTGCACTGAT R 2 1 2 1 101000 f 74 goat snp12494-scaffold1479-341055 17 62445377 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274489 Affx-1111834225 AX-519548080 17 8322110 TTCAAAATATTGAAAGAGAAAGCCAAATGTAAAAC[A/G]TGTGTCTTTAAGCTAGAGCAGAAACTGTCCATCTG R 2 1 2 1 201000 r 74 goat GoatD01.026252 17 8322110 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320775139 Affx-122975908 AX-385262271 17 8364627 ATTGCCACTTTTTCAGAGATGTTGAAAATACCTAG[C/T]ACAATAATTCAAATCTACATATATCTGTCTCCCAA Y 2 1 2 1 101000 f 74 goat snp12495-scaffold1479-395260 17 62391045 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272004 Affx-1111833108 AX-519545772 17 8374298 GGGCATGCAAGAAACTGTTAACCATGGTTAGTGTT[A/G]GAGAAGGTGGAAATGCAAAGGGAAATTTTACCTTT R 2 1 2 1 201000 f 74 goat 17_8374298_AF-PAKI 17 8374298 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38388991 Affx-122968656 AX-123259349 17 8408144 TTTCAAGGTTACACTGATGGGAAGCAGCAGGGTGA[C/T]GGTCTGAACCTAGGTTGTATGGCCCAGAACTGTTC Y 2 1 2 1 201000 r 74 goat snp12496-scaffold1479-438777 17 62347717 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404559 Affx-122957379 AX-123274911 17 8457186 GAGGGGAGATATGTAATTTTGCAGAGCTCACTCAG[C/T]ACTGTACTGAATTTTCAAAGGACAGTAAGTCAGTT Y 2 1 2 1 101000 f 74 goat snp12497-scaffold1479-487819 17 62298699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379540 Affx-122976062 AX-123249898 17 8488999 TAAAAACAGGGTACAAGATTTCCTTTTTTAAAGGA[C/T]ACCTCTCTCTGTAAAATGTGTTTCTTTCTCCCATT Y 2 1 2 1 101000 r 74 goat snp12498-scaffold1479-519632 17 62267135 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783470 Affx-122933014 AX-385270533 17 8541190 GAGAAAGTGGCATTTTCCTCTGCCTCTTGAATGAT[A/G]AGTAGGAGTTGTATACAACTTTTTCAACTTAATGG R 2 1 2 1 102000 f 74 goat snp12499-scaffold1479-571823 17 62213622 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792417 Affx-122950970 AX-385279398 17 8572017 ATTATTGATTGCATATTGTTTCTCTGAAACATCTA[C/T]ATCAACACTGTTACTTGAACAGCTGTGTTTCTTAT Y 2 1 2 1 101000 f 74 goat snp12500-scaffold1479-602650 17 62182362 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772001 Affx-122931733 AX-385259157 17 8609087 ACTTTTGTTTTCTCAGATTTTTCACCGAAGACTGG[A/C]GTTTCTCATTAGAGTTCATCCCTACAAATTAAGTT M 2 1 2 1 201000 f 74 goat snp12501-scaffold1479-639720 17 62145068 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429547 Affx-122937826 AX-123299889 17 8698303 CAGAAACTCTCTAGTGCTGGAAGGAGAAGACGAGA[C/T]GGAAGTAGTAAGAGACTGTTGGGAAGCACAAATGT Y 2 1 2 1 101000 f 74 goat snp12503-scaffold1479-728936 17 62056491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800050 Affx-122976475 AX-385286973 17 8742462 ATCCAGTAATTTAAAAACACTGTGATATTAGCATA[A/G]GCATCAAGAGAACAGAACAGATAACCTTAAAACAT R 2 1 2 1 101000 r 74 goat snp12504-scaffold1479-773095 17 62011652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395425 Affx-122963941 AX-123265780 17 8775684 AAGTAATTATGTCTTTAAAAGATCTGCAGTTTGTG[C/T]ATGTTTGTTACTCTTGGGGGAATCCCCTTTCAGAA Y 2 1 2 1 202000 f 74 goat snp10169-scaffold1364-414793 17 61977473 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396016 Affx-122963483 AX-123266371 17 8813319 GCAGAGCCACTCAAAACAGAGCTAAACCTGCACTG[C/T]GCGTGCGTAGGTGCTTGCTCAGTTGTGTCATACTT Y 2 1 2 1 101000 f 74 goat snp10168-scaffold1364-377158 17 61939393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802445 Affx-122975420 AX-385289349 17 8912230 ACACACTTTCTTTCTAACTTGCATTAGACAGTGAG[A/C]TGTCTGTAAGCCCTCAATCAATGAGAATGATTCAG M 2 1 2 1 101000 r 74 goat snp10166-scaffold1364-278247 17 61839276 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772531 Affx-122948266 AX-385259682 17 8942474 TATCCGAGTGATCATATATGCCATAAATTCTCTTT[C/T]TGGAAGCCATTGGGAAATAAGGTATAAAATATATA Y 2 1 2 1 101000 f 74 goat snp10165-scaffold1364-248003 17 61808884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387855 Affx-122969645 AX-123258213 17 8993899 TGAAAAAGAATATCAAGAGTATGACCAAAATGGCA[C/T]AGTAAATTCAATAGTAATTTAGTGGTCAGGCTGCT Y 2 1 2 1 101000 r 74 goat snp10164-scaffold1364-196578 17 61757295 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422420 Affx-122943366 AX-123292766 17 9046138 CATGGTGGGATAGTTTTTATTTTGTCCAAAATAAC[A/G]CATTGTTCAATATTGAGACTGCTCAGATAGGTTTG R 2 1 2 1 101000 r 74 goat snp10163-scaffold1364-144339 17 61703580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786863 Affx-122947109 AX-385273892 17 9087331 GAGATAATTCATGTAATAGTAAAATTGAAATAGGC[A/G]CTTGCTTTTTCTTGCTTGATTTGCATCAGTTTTTA R 2 1 2 1 101000 r 74 goat snp10162-scaffold1364-103146 17 61662585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415934 Affx-122948443 AX-123286283 17 9117959 AGAAGCATCTTTGTTTGTCATTCAGTTGCTAAGTC[A/G]TGTCTGACGCTTTGAGACCCCATGGACTGCATTGT R 2 1 2 1 103000 f 74 goat snp10161-scaffold1364-72518 17 61630150 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438191 Affx-122931826 AX-123308529 17 9155366 CCATATTTTGGGGCCATTTCCTACCCAGATTGTTT[C/T]TTGAGTGTTTGGAAATTATAAAAAGAAAACAAAGA Y 2 1 2 1 101000 f 74 goat snp10160-scaffold1364-35111 17 61592282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427794 Affx-122939766 AX-123298137 17 9188304 CTGGCACAAAAAATTTAGCTCAATGGCTATGTTAT[A/G]TCTGTTGGTAAGATGCTTTGTTAGTTGTTACTATT R 2 1 2 1 101000 r 74 goat snp10159-scaffold1364-2173 17 61558521 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799707 Affx-122927576 AX-385286635 17 9213635 GCACGATGGAGTTGATTGCAAAGAAGCAGAGAAAG[C/T]AGGGAGAAAAAGTTCCTGGACATTTGAAATGAGTG Y 2 1 2 1 101000 f 74 goat snp23393-scaffold2341-332758 17 61521661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386466 Affx-122970775 AX-123256824 17 9261213 GTCTTTTCCATAAATGATCATGGAACAATTAGATA[C/T]GTACATGGAAAAAATAAACTTTGATCCCTTACAAA Y 2 1 2 1 101000 f 74 goat snp23392-scaffold2341-285180 17 61474055 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442907 Affx-122927638 AX-123313244 17 9312418 AGAATGAAGATGAGTCTTGAATATTGAAGTCATAT[C/T]GAGAGGGGATACTGAAGTGACAACATTCAACAGCT Y 2 1 2 1 201000 f 74 goat snp23391-scaffold2341-233975 17 61422805 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780997 Affx-122940633 AX-385268084 17 9362127 TATATCTTCTATGAAAGGAAGTAGCTAAAACATTT[A/C]TGCAATAGCTAAGTGTTGAGAGACCACCAGAATAA M 2 1 2 1 101000 r 74 goat snp23390-scaffold2341-184266 17 61373118 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410219 Affx-122952560 AX-123280569 17 9462466 CGTTTCTATGAGCGGTCTGTTCATGTACTTTGTCT[A/G]TTTCTTCCAATCCCTCCTGGAAGTATCCATGGTCT R 2 1 2 1 201000 r 74 goat snp23388-scaffold2341-83927 17 61272497 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800430 Affx-122978720 AX-385287351 17 9520754 ACGAGGTGGAGAAAGTCAGCTTTTCGACTCTTTCC[A/G]TGAAAATCATTATTTCTATGCCCTTGATTTTTCAC R 2 1 2 1 101000 f 74 goat snp23387-scaffold2341-25639 17 61213840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772524 Affx-122947552 AX-385259675 17 9578394 AACATACCCATACTTAAGTCCCAAAGAAGTCCAAA[G/T]GTATAACAAGTCCATTTCACTCAGTGAAAGCTTTG K 2 1 2 1 101000 f 74 goat snp55427-scaffold858-2196323 17 61156642 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430690 Affx-122936919 AX-123301031 17 9634161 CTTACTGGGCTAGCTTTCTTCCCCAAATGGCTGGA[C/T]GTTTAGGGAGAAGCAATAAGAAGCTGTGCAAGAAA Y 2 1 2 1 201000 r 74 goat snp55426-scaffold858-2140556 17 61100693 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378425 Affx-122976776 AX-123248784 17 9693792 GGGAAGGTGAGACACCAAACCGCTAAGCTGATAGC[A/G]TTCCTGGCAGGTCTGGAGTTACAGGATAACTTGCT R 2 1 2 1 101000 f 74 goat snp55425-scaffold858-2080925 17 61042191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793501 Affx-122978238 AX-385280478 17 9736385 TGCATCCACAGTCCTCGGATCGCTAGCTACACTTA[C/T]GGTTCCTTTTTGAAAAATGGGATCAAAAGGCTCCT Y 2 1 2 1 101000 r 74 goat snp55424-scaffold858-2038332 17 60999423 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438051 Affx-122931544 AX-123308389 17 9822706 TAGGTCTGCTTCCCATGCCTGTCTCTTAAGCACAA[C/T]GCTACACTATCCTGTGGCCTGCCATCAAAGGCTTT Y 2 1 2 1 201000 r 74 goat snp55422-scaffold858-1952011 17 60912972 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390956 Affx-122967056 AX-123261313 17 9878290 CCAAGCTGTCACCGTTCCCCCTCTCTCTTCCTGCC[A/G]CTGTCGTGGACAAGCCACCTGAAAGGTATGTGGTT R 2 1 2 1 101000 r 74 goat snp55421-scaffold858-1896427 17 60857357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393961 Affx-122965055 AX-123264316 17 10043369 TAAGAAGTAGGGCAAAGAGGATGGGCAGCAGTACA[C/T]GAAGCAGTCTTGACATGGTGTTTGAAACTTGGAAG Y 2 1 2 1 101000 r 74 goat snp55417-scaffold858-1731348 17 60691624 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277198 Affx-1111835729 AX-519550704 17 10064103 ATGATGTAGAGGCGGGGCGGCACTGTGTGTATGCA[A/C]ACACAAGTACACCTCGGCACACGCCAGGAGGCAAG M 2 1 2 1 202000 r 74 goat Random2.2K-1651 17 10064103 C A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398033 Affx-122961767 AX-123268388 17 10295217 ACAATACCCACACCTGGGCCTCATTTCCAAAGATG[A/C]TGCTTTAATTGGCCTGGAGTGGAGTCTGGGAATGA M 2 1 2 1 101000 f 74 goat snp55412-scaffold858-1479500 17 60439730 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389533 Affx-122968281 AX-123259891 17 10358315 GGGTGGAATGATTTGGAGGATCAGTGTAGACATAC[A/G]CCCTAGGGTTAGCTACATTGCCTTTCATGCAATAC R 2 1 2 1 101000 f 74 goat snp55411-scaffold858-1416402 17 60376067 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445506 Affx-122925186 AX-123315843 17 10423608 ATTCACTCATTCATTCAACAAGTATTTAAGAGCCT[A/G]ATAGTGTGTCAGGAGCAGACAAAGTCAGCTATTGC R 2 1 2 1 101000 r 74 goat snp55410-scaffold858-1351109 17 60310197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802916 Affx-122965275 AX-385289813 17 10464622 ACACTAACTTAAGTGACAAGGGCTCATTTCAGTGG[C/T]GATGGCTATTTTGTATCTTGCCTTGGTGTTGCTGA Y 2 1 2 1 101000 f 74 goat snp55409-scaffold858-1310095 17 60270223 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436947 Affx-122933178 AX-123307285 17 10505438 TCCTCTTTATCCAGCTAACCAAGCTAAGCAAGATG[A/C]TCCTTCTGCCTGAAGTGTTCTCCCTCATGCCTCCT M 2 1 2 1 201000 f 74 goat snp55408-scaffold858-1269279 17 60229423 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782531 Affx-122942172 AX-385269606 17 10541082 GTCCTCCACTTGAAGGAAGCCATGAATTCTATCGA[G/T]CTTAAAAATCCATCTTTGAAGAGATATCACTGGCA K 2 1 2 1 101000 f 74 goat snp55407-scaffold858-1233635 17 60193946 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435805 Affx-122932846 AX-123306144 17 10577664 CCCAAAGTAGTTAAAGCCCCGAGGCCTTATAGATC[A/G]ATATAAAGCTGGTGAAGGTAATTTAATTACAATAT R 2 1 2 1 201000 r 74 goat snp55406-scaffold858-1197053 17 60156707 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454202 Affx-122919290 AX-123324535 17 10607297 AAGTTTTCAAATAGACAGGGAAATGCCAAGAACAT[A/G]TAAAAGGTTTAAAAGGCATGGTTGCACTGGGTCTT R 2 1 2 1 303000 r 74 goat snp55405-scaffold858-1167420 17 60126550 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421138 Affx-122944193 AX-123291485 17 10648088 GATAAGATTAACGCTGGGTGTGCCAAGAATAGAAA[C/T]GGAGAGGCCAGAAACTGGGTCTACTCTAATAATTC Y 2 1 2 1 101000 f 74 goat snp55404-scaffold858-1126629 17 60084924 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774610 Affx-122948618 AX-385261744 17 10861213 AGCAGGGGCAGCAAGGGTAGTTAGCATCTAACAAA[C/T]GCCCAGTGCTAAACACTTATTATCACCTCACTTTA Y 2 1 2 1 101000 r 74 goat snp55399-scaffold858-913504 17 59870265 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445427 Affx-122925367 AX-123315764 17 11336228 TGGATGATTGCTAAGCCAGAGGGGAGGACAATGAC[A/G]TCAGCAACCCAAATGTAATTCTCACATTCCACCCT R 2 1 2 1 101000 f 74 goat snp55388-scaffold858-438489 17 59397597 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271811 Affx-1111833086 AX-519545599 17 11340854 CTATTTTCCTAAGTATGATTGTATTCATGGGGTCA[A/G]TGCAAAAGACGATTTGATACTGACTATTGCCCTAA R 2 1 2 1 101000 r 74 goat 17_11340854_AF-PAKI 17 11340854 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38439886 Affx-122930036 AX-123310223 17 11481990 CTGATCCTCACCTTAGGGTGCGTGCGTCCTAAGTC[A/G]CTTCAGTTGTGTTGGACTCTCTGCGGCCCCATGGA R 2 1 2 1 103000 f 74 goat snp55385-scaffold858-292727 17 59249949 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799368 Affx-122935968 AX-385286298 17 11529657 AATATAAAGACCAGAAGCCAAAGATGGTATCAATT[C/T]AACCTAGTACTGGCATCTAGAATCTTATGTCCTTG Y 2 1 2 1 101000 r 74 goat snp55384-scaffold858-245060 17 59204669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383512 Affx-122972640 AX-123253870 17 11566632 GAATATGGTAAGGCCACACGACTTGTTCTGGCCAA[C/T]GTAATGTGAGCAGAAGCACCACATATCACTTCCAA Y 2 1 2 1 101000 r 74 goat snp55383-scaffold858-208085 17 59169469 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772186 Affx-122936905 AX-385259341 17 11635842 TACTACCACTCCATCCTGTTCTTTTAACCCAAACC[C/T]AAGCAATATATTTTCTGTGGATTGACTATACTCCC Y 2 1 2 1 101000 f 74 goat snp55381-scaffold858-138875 17 59101272 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424125 Affx-122942014 AX-123294471 17 11675765 TTAAGATATGGGCTGGGAATTTCAGCACTTGAGCT[A/C]TTTGATAAGGAGCAGAACCCTAACCCTTGACTTGG M 2 1 2 1 101000 r 74 goat snp55380-scaffold858-98952 17 59061291 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432698 Affx-122936030 AX-123303039 17 11708683 CAAGGGAAGCCCATCATTATGAGAAAAGTCTCAAT[A/G]GGCTGGGGATGACTCAAGTGTAAGGGAAACAAAAG R 2 1 2 1 101000 f 74 goat snp55379-scaffold858-66034 17 59028310 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272372 Affx-1111833808 AX-519546101 17 11769548 C[A/G]TGTGCTTTCAACAAGGATGTGCCAGGATTCCCTGC R 2 1 2 1 101000 r 74 goat GoatD01.005672 17 11769548 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320784554 Affx-122956969 AX-385271603 17 11783789 CCATGTTTACAGACTACTTCATGTGTTCATTCTGC[A/G]TGGGTTTTTGCTTCTGCAAACATATTCACTGTGCC R 2 1 2 1 101000 f 74 goat snp32745-scaffold379-8973 17 58954114 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802941 Affx-122924836 AX-385289833 17 11814823 AACATTCACTCTCACTTTCTGTGATATATTCCATA[A/G]TCCAGCCAAGTGCTAGGTTAAAACCCATTGCATTG R 2 1 2 1 101000 r 74 goat snp32746-scaffold379-40007 17 58923429 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392100 Affx-122966362 AX-123262457 17 11892812 TACAGCAGCCTTGGAAGAGTGTTTCTCAACCTCCA[C/T]GGAATCCTCAGAGAGGAAGGACCGGCCGAGTTCAC Y 2 1 2 1 202000 r 74 goat snp32748-scaffold379-117996 17 58848262 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443103 Affx-122928102 AX-123313440 17 11926018 CCACTAGGGGCCAGGCCACGTGAAATTCCTGAGCA[A/G]TTCACAGAGTAACCCTGGGAGGTGGTGGGCAGAGC R 2 1 2 1 101000 f 74 goat snp32749-scaffold379-151202 17 58815039 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441501 Affx-122928730 AX-123311838 17 11968263 TCTAACAAGACAGAAAATAATCTGAGAATGATGTA[C/T]AGTGATGAAAGATTTCCACGGTGATGGTTCCCTGG Y 2 1 2 1 101000 r 74 goat snp32750-scaffold379-193447 17 58773126 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398502 Affx-122961559 AX-123268857 17 12010190 AGAACCACATGGGCTACAGCTGTGTTATAAGGGCA[C/T]CTGCCAGTTGGTGGTGAGGATGCTTGGTGTGAAGA Y 2 1 2 1 101000 f 74 goat snp32751-scaffold379-235374 17 58730696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445508 Affx-122925185 AX-123315845 17 12042322 AAAGGAAAAGCAAAACCAAAGCCCCCGCAAGTTTA[C/T]AGGAAGGGAACACCCCTGAGGGATGCTGGTATCAG Y 2 1 2 1 201000 r 74 goat snp32752-scaffold379-267506 17 58698058 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420211 Affx-122945542 AX-123290559 17 12085820 CCTCAGAGGCGTTCATTAATGCTCTGAGAGGGTCA[C/T]GCCCAAGGGCCATCTTCGACCACTATGTCCAATAA Y 2 1 2 1 101000 f 74 goat snp32753-scaffold379-311004 17 58654016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784249 Affx-122968916 AX-385271300 17 12114726 AAATTTCTAAAATAAGGATTTATCATAAAATCAAA[C/T]GCATATTCAGAGTAATGGAGATGTTGCCTCTTGAC Y 2 1 2 1 101000 r 74 goat snp32754-scaffold379-339910 17 58625122 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381033 Affx-122974644 AX-123251391 17 12149099 AAAGAGTTTTGACCTCAAGGACTTCTCTAGACCAC[A/G]CATTATTCTAGGGAGGGTGCTCCCCTGTCTACTAC R 2 1 2 1 201000 f 74 goat snp32755-scaffold379-374283 17 58590999 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420690 Affx-122944798 AX-123291037 17 12205921 TGAAAAGAATCTGAAAGTGGCCCTTAATCCCATCA[C/T]GTAGAAATAACCATTATTACCATGCTAATCTGTAG Y 2 1 2 1 101000 f 74 goat snp32756-scaffold379-431105 17 58534119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440733 Affx-122929882 AX-123311070 17 12238292 AGAATTGAGGATGACACCTAGGAAACGTGTTCACC[A/G]CTGGCATGCCGGTCTCTTGTATTCCTGTGCTGATT R 2 1 2 1 101000 f 74 goat snp32757-scaffold379-463476 17 58501909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780302 Affx-122929308 AX-385267397 17 12276555 AGCTTATTGTTCTTGACCAGCTGATGCTTCATTCG[C/T]AGAGTGAATTCCTTTGAAAGAGCGAAGTATAACCT Y 2 1 2 1 101000 f 74 goat snp32758-scaffold379-501739 17 58463584 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790638 Affx-122969784 AX-385277640 17 12313143 AAGAATGACAGCTCCCAGGCCTGATGGTTTTCTAA[C/T]AAAGATTTGTGAATGTTCTCCACATTGGGACATTC Y 2 1 2 1 101000 f 74 goat snp32759-scaffold379-538327 17 58426879 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440724 Affx-122929889 AX-123311061 17 12391970 ATGGGTTTTTGCTATTTTTGCCTTTCACACTGTGG[C/T]CTCTAATTCATCTGGAATGAATCTACCTGGAATTG Y 2 1 2 1 101000 r 74 goat snp32761-scaffold379-617154 17 58348696 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376417 Affx-122978079 AX-123246776 17 12426228 ATATGGTATGCTTGGCTCCATACCATAATTTTGAG[A/G]GCAGGTCTCTGTCTTAATGGGTGCTGAATAAACAT R 2 1 2 1 101000 f 74 goat snp32762-scaffold379-651412 17 58314345 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381836 Affx-122974257 AX-123252194 17 12464693 CTAATTCTATATTTTTAATTGTGTGTTATGATAGG[C/T]AAGTCACAGAAAAAAATCGCATGCTTAGAGGTAGT Y 2 1 2 1 101000 r 74 goat snp32763-scaffold379-689877 17 58275723 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773489 Affx-122944651 AX-385260630 17 12508499 ATCTTTTATATTTATAGATCAACAGAGAGAGAGCC[A/G]TCTATCCATCTGAGAGTCCTGTGTCAGAATATATG R 2 1 2 1 101000 r 74 goat snp15988-scaffold1681-725288 17 58232017 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439543 Affx-122930106 AX-123309880 17 12553422 GGCATTCTAGTGAGGTGTATGGTGAAATGATTTAG[A/C]CATGAAACCACTAAACTACAGGAATCATATAGTTT M 2 1 2 1 101000 f 74 goat snp15987-scaffold1681-680365 17 58187128 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773483 Affx-122947696 AX-385260625 17 12587492 GAATTAACAGGTCAGATAAGCAAAGAGAACCCTAT[C/T]GATTTATTATAGTTTTGGAATTCAGTAGCTTTAAT Y 2 1 2 1 101000 f 74 goat snp15986-scaffold1681-646295 17 58152998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384216 Affx-122972383 AX-123254574 17 12618329 CCTGGGTCACATGTTCCCTCATGGGAGATGATGAA[G/T]CAATGGCCGCATTTTAGTTGACGATACATTAATTT K 2 1 2 1 101000 r 74 goat snp15985-scaffold1681-615458 17 58121630 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463484370 Affx-1110007759 AX-514967251 17 12621647 GAGAGAATGTATTGCTGCAGCTAAAGGGTCTCAGA[C/T]TGTGGTCTCAGGCAACCCAGAGAGATCCTAGACCT Y 2 1 2 1 101000 f 74 goat GoatD01.025128 17 12621647 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38429162 Affx-122937978 AX-123299504 17 12693704 AAACTTCACAGTTTCTTCCCATCTCAGAGAAGGCA[C/T]ATGCACTTTCCTTTTCGAGAATGTTCCTCCACCTG Y 2 1 2 1 201000 r 74 goat snp15984-scaffold1681-540083 17 58044725 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414459 Affx-122949569 AX-123284808 17 12732384 TGGGGGAAGAATCCCATAAGTGGTCTCCTCACTTA[C/T]GTAAGTATGGTGTGAATAGGCTCCATTGTCCTGGT Y 2 1 2 1 101000 r 74 goat snp15983-scaffold1681-501403 17 58006096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386735 Affx-122970145 AX-123257093 17 12778778 TAAGCATATGAGATATGCACAAGTTCTGCATTGGT[A/G]TTATGGGGAATCAAAAAGAAGAGCCACAGAAGGAA R 2 1 2 1 101000 f 74 goat snp15982-scaffold1681-455009 17 57960794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396468 Affx-122962966 AX-123266823 17 12854403 AGAAGAATCGTTTAGGTGGAGTTCAATGTATCAAA[C/T]AATCATTACTAAACATAGGACAACATAAAGACAAC Y 2 1 2 1 101000 f 74 goat snp15981-scaffold1681-379384 17 57883790 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792116 Affx-122920383 AX-385279102 17 12891736 TACAAAGAAAGCAGTGTGCCAGGAATCACTTTAAC[A/G]TGTGGTAGAAGTTTTAGTACTAAAGGAGTCACTTT R 2 1 2 1 101000 f 74 goat snp15980-scaffold1681-342051 17 57846138 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409566 Affx-122953588 AX-123279917 17 12922206 CAGATGCTAGCATCCTGCCGCCAAGGGGTATGTGG[A/G]ACAAGCACTGAAGATCTATCTGAGAGGAAATGAAG R 2 1 2 1 202000 f 74 goat snp15979-scaffold1681-311581 17 57815641 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383092 Affx-122973284 AX-123253450 17 12968438 AGAGTTTCGCTATCATAGGTAGGAGGAACCAAAAC[A/G]CTGAGAAGGACCCACTCTGGAGACCAGGCACCCAA R 2 1 2 1 101000 f 74 goat snp15978-scaffold1681-265349 17 57769300 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390620 Affx-122967164 AX-123260977 17 13003877 CCTTCCAACCAGCAGTGAGAGTTCCTTCTGTCCCA[C/T]GTCCTTGTGAGGACTGGGTTCACTAAGTGCTCAGG Y 2 1 2 1 101000 f 74 goat snp15977-scaffold1681-229910 17 57733764 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413536 Affx-122950614 AX-123283885 17 13032590 TTACTATTATTAACCAAGCTAAGAAGAGGGAAAGA[C/T]GAATAAATGAAATGATAATTTCATCTGAGAATTAG Y 2 1 2 1 201000 r 74 goat snp15976-scaffold1681-201197 17 57704234 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418846 Affx-122946138 AX-123289194 17 13069236 TACTCCACCTCCTAGAAATACCTAATGGACTATTA[A/C]AGAATTGGCAATGAGTAAAAGAAATATTTCATAAC M 2 1 2 1 101000 f 74 goat snp15975-scaffold1681-164551 17 57671468 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437683 Affx-122931769 AX-123308021 17 13121139 TTCATGCAGAGTTCCTCATCTCTGACAGACTGAGA[C/T]AGGCCTGAGACCTGGGTGGGACCCTTTGCTGCGGC Y 2 1 2 1 101000 f 74 goat snp15974-scaffold1681-112648 17 57619309 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274556 Affx-1111834364 AX-519548146 17 13161407 AGTTTCCATCCTGAGCTGAACCTGCAGGAGGCTCT[A/G]GGTGCCAGTGGTTAGAGTCTTGCTCCTGGCTCACC R 2 1 2 1 202000 f 74 goat GoatD01.032143 17 13161407 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38419239 Affx-122945673 AX-123289587 17 13181507 TATGGTTAATAGAAAGCAAAAATATCATGGAAGGG[C/T]GAACAGAATTTCCCTTCCACTGAAAATAACAAGGA Y 2 1 2 1 202000 f 74 goat snp15973-scaffold1681-52280 17 57558777 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397193 Affx-122962404 AX-123267548 17 13210291 CGCCTGGTTCAGGGGACTCTTGCTCACGAGGAGTC[A/G]CCCCACAGGTGATTTCAGAAGTATAGACTCTCTCC R 2 1 2 1 101000 r 74 goat snp15972-scaffold1681-23496 17 57529943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395518 Affx-122963873 AX-123265873 17 13241964 AAGAAATTGGTAAGGAAACCATGTCTTTCCTGGCT[G/T]TATCTGTGATTCTTTTGTCCAGTTTTAAAGAATGG K 2 1 2 1 201000 r 74 goat snp14245-scaffold1569-607415 17 57515508 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375590 Affx-122978731 AX-123245949 17 13272197 ACAACTTCTAATTCCCTATTCATATGATCAGGTCT[A/G]TGTATTGGATTATATGGAAGGAATGGTCATAAATG R 2 1 2 1 101000 r 74 goat snp14244-scaffold1569-577182 17 57484769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420330 Affx-122945007 AX-123290677 17 13307535 CTTCTTATCAGTAGACACGGTCAACAGAAACAACA[A/G]TCTCTCATAGCCAAAGAGGAAAAACAAGGTGTCCT R 2 1 2 1 101000 f 74 goat snp14243-scaffold1569-541844 17 57448986 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784775 Affx-122938092 AX-385271822 17 13362085 AAAACCTCACTAGTTTCCTGGAGTCTATAAACTAC[A/G]CTTTGAGTTTGGCCTGTCGCCTCTCCTATCTTAGC R 2 1 2 1 101000 r 74 goat snp14242-scaffold1569-487294 17 57394817 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774178 Affx-122976020 AX-385261315 17 13404789 CGCACAGTGAATGACTATATGAATGCTATATGCAA[C/T]ATTCCAGTGCCCTGAGATCTTTTATCATCCTTAAG Y 2 1 2 1 101000 r 74 goat snp14241-scaffold1569-444590 17 57351786 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408097 Affx-122954714 AX-123278448 17 13463161 AGTCTGCTTATATTTTATCCTTCCCTCCTGGAGCC[A/G]CATTGCCACCAGCCTGTATCAGTCTAGCTTGCTTC R 2 1 2 1 201000 r 74 goat snp14240-scaffold1569-386218 17 57293539 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448222 Affx-122924222 AX-123318558 17 13500531 TTTCACTTTATATAGTATATACATTGATTTTGCCT[A/G]CTTTGACTATTAATTCATCCCAGAAGTTTTAGTCT R 2 1 2 1 101000 r 74 goat snp14239-scaffold1569-348848 17 57255805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419196 Affx-122945709 AX-123289544 17 13616935 AGGGAGATATGATTCAGTGTGAAACAAAGTTTTTC[G/T]ATCATTTGCACACCAGCATACTGTCTTGCTTTGGT K 2 1 2 1 101000 r 74 goat snp14237-scaffold1569-232444 17 57139013 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453806 Affx-122919569 AX-123324139 17 13653729 CTCTGCTTTTTTTTTTTTTTAATAAGATCTATTGT[A/G]ATTTTGAATCCTAAATAATCACACTGACTTGAACT R 2 1 2 1 101000 r 74 goat snp14236-scaffold1569-195650 17 57102206 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397783 Affx-122962507 AX-123268138 17 13692299 ACTTCGTTTGTTTCAGTCCTTCTGAATTTCTAGTC[A/G]TTTTATTTAAGGTGTGTGTGTGTGCTCAGTCATGT R 2 1 2 1 201000 f 74 goat snp14235-scaffold1569-157080 17 57063473 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444420 Affx-122926573 AX-123314757 17 13737285 CTTGCATTGCCTTGCTGCCCACTCTTGGGTCTTTA[C/T]TCCCTTGTCACACAATGGTAATGTAGGAACAGTCT Y 2 1 2 1 101000 r 74 goat snp14234-scaffold1569-112094 17 57017902 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424940 Affx-122941279 AX-123295286 17 13779317 GACGCTATTGCTGTCAAACAACGAAGTCAAAGAGA[C/T]GAATTTAGAGGTTCACATTTACAGAGATGATAGTG Y 2 1 2 1 101000 f 74 goat snp14233-scaffold1569-70062 17 56976502 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393608 Affx-122965366 AX-123263964 17 13809211 ATCATTCTCCTCTTATACATAAGAAAACAAAAGGG[C/T]GGATAAGATATTGCAAATGTATTCCCTTAACTTGA Y 2 1 2 1 101000 r 74 goat snp14232-scaffold1569-40168 17 56950270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404266 Affx-122957053 AX-123274618 17 13839458 TCTGCTAGAGATAATCCCCCCATATCAGTCCACAA[G/T]AGTATTTCATTTTCTCCTGTCTCCCAATGCCATTT K 2 1 2 1 201000 r 74 goat snp14231-scaffold1569-9921 17 56919881 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786404 Affx-122942219 AX-385273438 17 13873850 ATACACTTAGAAATACTGGCTTTATCCTTTAGATT[A/G]TTGGAGAAAGCAAACAAACTCTTTTTCCCCCCTTT R 2 1 2 1 101000 r 74 goat snp32657-scaffold375-1403142 17 56855465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399827 Affx-122960262 AX-123270182 17 13925363 TTGGATCAAGATGGTGAGGTAGGAAGATCCCACAC[A/G]TTCAACTTCAGAATATTATTTGGTGATACTTACTC R 2 1 2 1 201000 r 74 goat snp32656-scaffold375-1351629 17 56803180 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271981 Affx-1111833087 AX-519545750 17 13945369 TTAGCAGAGACTCCTTAAAATAGAAATCTATTGAC[A/G]TTTGTTCCAAAGACTTCCTTTTCCTTTCCTGGTAA R 2 1 2 1 201000 f 74 goat 17_13945369_AF-PAKI 17 13945369 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454239 Affx-122919663 AX-123324572 17 14008159 CTATTTTCTTTTCTCCTAATTCCTTGCCAACTAAT[A/G]CATATTTCACATTTCTTTCATCACAGGAAGCAGAG R 2 1 2 1 101000 f 74 goat snp32654-scaffold375-1268833 17 56721496 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408052 Affx-122954277 AX-123278403 17 14050499 TGTGTGCACATCTGTTACATTACCGTTCTCTGTCA[C/T]GCAGTTTGGGATGTAAAAACACACACATAGGCATC Y 2 1 2 1 101000 f 74 goat snp32653-scaffold375-1226493 17 56679026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427871 Affx-122939707 AX-123298214 17 14110211 AATCGACTATTATTAACTGGAACACCTCTTCAAAA[C/T]AACTTGCATGAACTTTGGTCACTTCTTAATTTTTT Y 2 1 2 1 101000 f 74 goat snp32652-scaffold375-1166781 17 56618507 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768472 Affx-122925800 AX-385255652 17 14152911 ATAAAGTAAATTTTCCTGGTAGTAGAAATTTATAC[A/C]TAAGCGTGGTACTACTACTCCAGTGTGGTATTTGG M 2 1 2 1 101000 r 74 goat snp32651-scaffold375-1124081 17 56575333 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388553 Affx-122969183 AX-123258911 17 14211604 ATTTCATAGCGCGCAGAAAGTTAGTGCTACTTGTA[C/T]AGACTTAAGTCTTTAATAGAGATACTGCACTGATT Y 2 1 2 1 101000 f 74 goat snp32650-scaffold375-1065388 17 56516964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426590 Affx-122939986 AX-123296936 17 14251005 CTATTAAAATGGCATGCTGATACAGTCATCCTGTC[A/G]TTCCTTATAAGAAATGACTTCAGAAATGCTCAGTA R 2 1 2 1 101000 r 74 goat snp32649-scaffold375-1025987 17 56477774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440365 Affx-122929647 AX-123310702 17 14286078 AACATATACAATGACAGAAAAAATTACATGGAGAG[C/T]ACACTATTTAGATATAGAGAGAAGAGATCATTGCT Y 2 1 2 1 101000 r 74 goat snp32648-scaffold375-990914 17 56443066 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438980 Affx-122930382 AX-123309317 17 14344318 CTCTGCTGACACAGCATCCCAGACATTGTGCAAAA[C/T]GTTCTGGGAAACCAACAGTCAGTTCTCAGCATCCT Y 2 1 2 1 202000 r 74 goat snp32647-scaffold375-932674 17 56379728 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775767 Affx-122972510 AX-385262898 17 14396705 TTCTACAATTTCCCACAGAGAATATCCCTGTAGGC[A/G]CTACAATCAAATTACTGTTTTAAAGGCACTGAGAA R 2 1 2 1 101000 f 74 goat snp32646-scaffold375-880287 17 56328588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408896 Affx-122953973 AX-123279247 17 14443558 ACAGATTATATTTTAACTAATTATAAATTACAGTC[A/G]TGAGGTAACATGTAAACTTCAGTATTGATATTTTA R 2 1 2 1 101000 r 74 goat snp32645-scaffold375-833434 17 56280711 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439426 Affx-122930198 AX-123309763 17 14484425 TAAGGGCCTTGTAATCAATTTTCAAACACAAATCG[C/T]ATTTCCAAAATACTGGCAAGCTTCCTCCATAGCAA Y 2 1 2 1 101000 r 74 goat snp32644-scaffold375-792567 17 56235030 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434110 Affx-122934936 AX-123304451 17 14531354 GGTAGAAAAATATATGAAACTTTTTTTAAGGCATC[A/G]TTCAAGTTTCTCTGACTCTATGCTGAATGTCTACA R 2 1 2 1 101000 r 74 goat snp32643-scaffold375-745638 17 56187776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398646 Affx-122961899 AX-123269001 17 14585293 TAACAAGGTTGGTATACATGGTAGCCAATCTACAC[A/G]TTTGGACCCACGATGAATGATGCCCCCTGGTATGT R 2 1 2 1 201000 f 74 goat snp32642-scaffold375-691699 17 56132817 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449979 Affx-122922878 AX-123320314 17 14630904 ATTAAAAAGTGGAAAAGGATTATTGGGTCCCAACC[A/G]TGCACAACTGAAATAGAATTCCCAGTGAGAAAAGC R 2 1 2 1 101000 r 74 goat snp32641-scaffold375-646088 17 56087278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377427 Affx-122977546 AX-123247786 17 14663197 GTCTTGCCTTGCTCTGCAGCGGTTCTAGGAATAAG[C/T]GCACTGCTCCTAAACTATGGCCCCGTGGTTGAGCT Y 2 1 2 1 101000 f 74 goat snp32640-scaffold375-613795 17 56054898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392447 Affx-122966171 AX-123262804 17 14752606 GTGTTTCTCTAATTTTAATCTATCCATGTCTTTCC[A/G]TCACCCTTGTGTTACTAAGTGATGTATTGGTCTTC R 2 1 2 1 101000 r 74 goat snp32638-scaffold375-524386 17 55965210 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397692 Affx-122962575 AX-123268047 17 14790643 TGTCAGAAGCTGTGTGATTGTTTCTTTTTCAGTTG[C/T]GAATATGAAATTAATGAGACTAGAGACAGAGTCTA Y 2 1 2 1 201000 r 74 goat snp32637-scaffold375-486349 17 55928327 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380486 Affx-122975713 AX-123250844 17 14820383 TCATTGCCATTACAAAAAAAATGCACATCTGCAAC[A/C]GTTTTAACCGTATCCTGCAGTATTCTCCACTTCAT M 2 1 2 1 101000 r 74 goat snp32636-scaffold375-456609 17 55898695 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277076 Affx-1111835730 AX-519550583 17 14854112 TGAGAGATTCCTTCAGTTCTCTACTAAGAGACACA[A/G]GCAATTCAGCACTATTTAGTTTGCCAGTGTCTTCT R 2 1 2 1 101000 f 74 goat Random2.2K-1653 17 14854112 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401282 Affx-122959871 AX-123271635 17 14872806 TTGACCTTCCTAGAAACATAGCTCTGAAAGCCTTA[C/T]GGCCCAGAAAAGACATTGCAGGAGGTGGCTGACCA Y 2 1 2 1 101000 f 74 goat snp32635-scaffold375-404186 17 55846086 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386702 Affx-122970169 AX-123257060 17 14920560 TATAAACATGAGTAACTGACCAGAAGTTAGAGCAG[C/T]ATTAAGCAAGCTGGATATCTCATCCACCCATGTAT Y 2 1 2 1 101000 r 74 goat snp32634-scaffold375-356432 17 55798391 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447255 Affx-122924951 AX-123317591 17 14972711 TGTAGCTTCACATGTTCAAAGTGTTTCAGTCCTGG[A/C]GGATACAAAGCTTGACACTAACATTGGTCTGGTAG M 2 1 2 1 101000 r 74 goat snp32633-scaffold375-304281 17 55751050 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377667 Affx-122977848 AX-123248026 17 15024840 GCCACAGAAAAGCTGTGCAAAGAACTCTAAAATCA[C/T]GCTGATAGAATCTGGGTGAGGAAGCTATTTGAGAT Y 2 1 2 1 101000 f 74 goat snp32632-scaffold375-252152 17 55698649 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801565 Affx-122975481 AX-385288474 17 15074329 TCATTTTACCATTATTTGATGTTTACAAAGCTAAA[C/T]GTTTGCAGAGGTAAATTACTCACTGTCTTTAGTTC Y 2 1 2 1 101000 r 74 goat snp32631-scaffold375-202663 17 55650992 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390249 Affx-122967760 AX-123260606 17 15138498 TGTTTCTACTGCTCTAGGTGGCCCAGATACATTTA[C/T]GGTGAACAGCTGTTTTTGCTTGAAGAGGAGTGGCT Y 2 1 2 1 101000 f 74 goat snp32630-scaffold375-138494 17 55586607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421055 Affx-122944518 AX-123291402 17 15195102 ACTTTTCTTTAGAAAAAACATAAATAAAAGAACTA[C/T]AAGCGACTATTTTTCCTGTTAACTTGGCTATAGAG Y 2 1 2 1 101000 r 74 goat snp32629-scaffold375-81890 17 55530452 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277202 Affx-1111835731 AX-519550708 17 15226524 AAAGTTAAAATCTGCTTTCTTAGCAACTCTGAAAT[A/C]TGCAGTACTGTATTATTAGCTATAATTGCTGTGCT M 2 1 2 1 101000 r 74 goat Random2.2K-1654 17 15226524 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320787782 Affx-122963685 AX-385274805 17 15231350 GTTCATTTATACTTTTTAACAATATTCAGTACTTT[A/G]TCTTGTCCCTGTGAAGCACCTAGTCACCTAAACCA R 2 1 2 1 101000 r 74 goat snp32628-scaffold375-45642 17 55493530 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409045 Affx-122953360 AX-123279396 17 15268205 AAGTACTAAATAGTTGCTATTAATTTATATTGATT[A/G]TCATTTCCTAATTTCCATATGTTGGAATTTGTACC R 2 1 2 1 201000 f 74 goat snp32627-scaffold375-8787 17 55458297 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434703 Affx-122933945 AX-123305044 17 15283298 TCTAGGTAGCTTTAAAACGAAATTATTGTGATATC[A/G]CTTAGTATTTTAAGAGTTCACTTATAACTCAGTCT R 2 1 2 1 101000 r 74 goat snp21226-scaffold207-5047965 17 55443139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441622 Affx-122928643 AX-123311959 17 15319068 TCTCACTAGCCCACTCCAAAGCCTGGAGGAAACTT[A/G]CTTTCTGAATTACCTGATCTTCAGAGCAATAGATA R 2 1 2 1 201000 r 74 goat snp21225-scaffold207-5012195 17 55407475 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451031 Affx-122921450 AX-123321365 17 15352018 TGCTCCTTTTTCCTAGCTACAGGTAAATATCCCAT[A/G]AACTCAGCTCAACGAGTACCTCCTCCAGGAGGTCC R 2 1 2 1 101000 f 74 goat snp21224-scaffold207-4979245 17 55374148 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792549 Affx-122931266 AX-385279530 17 15391398 ACATTTCAACTGTAAAGTCTGACATTCTTGATAGT[G/T]GATGAAATATTCATACAGCACTCTGGAAATAACCT K 2 1 2 1 101000 f 74 goat snp21223-scaffold207-4939865 17 55334347 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792442 Affx-122933095 AX-385279423 17 15446205 TATCTCATAATAAATTGCAAAATGTCCTCAGGATG[C/T]AGAGGTTATGAATGAGTGTACCAGAATTGGACTCT Y 2 1 2 1 101000 r 74 goat snp21222-scaffold207-4885058 17 55274768 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798062 Affx-122929588 AX-385284998 17 15475736 GCTACTTCCAGTAGCTGATTTAACCTGCAAAAACC[A/G]CCACATAATATTATTGACTCAGATTTTAGAGACGA R 2 1 2 1 101000 f 74 goat snp21221-scaffold207-4855527 17 55245336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794703 Affx-122919844 AX-385281663 17 15558397 GGTGTAATTGTGCATATTATATTTTTGCCCACAGG[A/G]CTTGAGATCATTATCCTCAGATACAAATGTATTAC R 2 1 2 1 101000 f 74 goat snp21219-scaffold207-4772866 17 55162734 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402241 Affx-122959140 AX-123272594 17 15594959 CTCCAGAACCCCTGAAGCAACTTAGGTTTTTCTCA[G/T]AATGTCTTTCATTAAAAATCCCATGAATGAAATGT K 2 1 2 1 101000 f 74 goat snp21218-scaffold207-4736304 17 55126745 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769484 Affx-122977889 AX-385256654 17 15628929 TCCCAAAAATTTTTGTAGTAGAATTCGGTCTTAGC[A/G]TGAAGACTGAATTGTGGTATTAAAGAAGACCCACA R 2 1 2 1 101000 f 74 goat snp21217-scaffold207-4702334 17 55092797 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383635 Affx-122972538 AX-123253993 17 15702683 TGAGAATGATGATCAGTTGTTGTTCCTCAATGAGT[C/T]CAGGGCAAGAGGAAATGAATATTAACAAACTGTTG Y 2 1 2 1 201000 f 74 goat snp21216-scaffold207-4628580 17 55018433 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798430 Affx-122939401 AX-385285364 17 15741487 TGTCAGTGGAGGTCCACTGCATACTGAAATAAACT[A/G]CTTTGATGGCTGACTCTCCAATTCTCTTTTAAACC R 2 1 2 1 101000 f 74 goat snp21215-scaffold207-4589776 17 54979624 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801439 Affx-122973253 AX-385288348 17 15796929 GGAACTCGGTAGAAACCAATAATTTCATTATTGAT[A/G]TACAAGGCCCTTCTTCTTGCTATTGTTGTTGTTTA R 2 1 2 1 102000 r 74 goat snp21214-scaffold207-4534334 17 54923058 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275368 Affx-1111834858 AX-519548942 17 15807325 TGCAGTGTCTTTACTCCTAAGAAGTCTGAGTGTGC[A/G]TCAGAGCTCC R 2 1 2 1 101000 f 74 goat GoatD01.056738 17 15807325 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320769500 Affx-122953703 AX-385256670 17 15849733 AAATTCTTAAGTTCATGATTCTAAAGAAATTAATG[C/T]AAAGTTTGGCTTACGTTTGGTTTATGAGAGCATCA Y 2 1 2 1 201000 f 74 goat snp21213-scaffold207-4481530 17 54869673 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277204 Affx-1111835732 AX-519550710 17 15879801 CTAGTCATCAGCTGATTCTGAGGAAGAAACCCCCA[C/G]GGACACTTCTTCCATCCGTGCATGCAGTAGAGAGG S 4 1 2 1 102000 r 74 goat Random2.2K-1655 17 15879801 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397314 Affx-122962313 AX-123267669 17 15881992 CATGATGGAGTTGGAAGGGCTAAAGTTTGGAAAAC[A/G]CTGTGTCCTTATGTGCCAGGCACTTGCCTGGTATA R 2 1 2 1 101000 f 74 goat snp21212-scaffold207-4449271 17 54837418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796318 Affx-122959466 AX-385283268 17 15911226 AAAGAAAGCCAAATTAGACATTTTTATGTACTAAG[C/T]ACTCAACCACAACAAATTCTCACCGAAAGAACATC Y 2 1 2 1 201000 r 74 goat snp21211-scaffold207-4420037 17 54808559 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797496 Affx-122947963 AX-385284435 17 15963988 GGAAATCAGAAGCAATCAGGTTCCTAGAGTCTAAA[C/T]GTTTCTGAATTCTAAAGCTGAACCAGTACAGGGTC Y 2 1 2 1 101000 r 74 goat snp21210-scaffold207-4367275 17 54755539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792305 Affx-122924700 AX-385279287 17 16006598 ATCTGATTGATCAGACTAGAATTGAGTTTATTTTG[C/T]ACTATATGGTAATGAATTGTCATATTTGTCATGTC Y 2 1 2 1 101000 f 74 goat snp21209-scaffold207-4324665 17 54712463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419112 Affx-122945770 AX-123289460 17 16043043 AAAGCCTCTGCAGGGTCTGCAAGGATCCATGTAAA[C/T]ATCTGAACAGAGCGCGAAGAGAAAAGAAAAAGTGC Y 2 1 2 1 201000 f 74 goat snp21208-scaffold207-4288220 17 54675756 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785123 Affx-122962900 AX-385272169 17 16083382 GACGCCTTCTCAATCTTTATCTTCTGGACTTTGCC[A/G]TACTTGATACTGTTGATGACTTTCTTCTTAAAATC R 2 1 2 1 101000 f 74 goat snp21207-scaffold207-4247881 17 54635280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274971 Affx-1111834611 AX-519548554 17 16101922 TGACCCTCAAACTTCAGTGATCTCATGTGTAAATT[A/G]GGTGTGAGGGTCTGTCACCTGCAGGGCTTGTCTCT R 2 1 2 1 201000 f 74 goat GoatD01.043012 17 16101922 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320770325 Affx-122925461 AX-385257491 17 16124496 AAAACAGTAAGAACAAACGTCTGTGACACAGTCAA[C/T]GGCAGTGATGTATGGTGAAATCTCATTTTCAAACT Y 2 1 2 1 101000 r 74 goat snp21206-scaffold207-4206767 17 54594275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431901 Affx-122936006 AX-123302242 17 16157020 CTCTCTTGAGAGAGGTGATGAATATATTTTATATG[C/T]AGAAGGAGAGAAATACACAGTCACATAATACAGAC Y 2 1 2 1 101000 r 74 goat snp21205-scaffold207-4174243 17 54561905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792080 Affx-122964692 AX-385279067 17 16196625 TTTCCTTTCAGTTCAAACACTAGAAAGTTTATAAT[A/G]CTTCTCCTCTCCCTTTGCATAAACAAAATGTTACC R 2 1 2 1 101000 r 74 goat snp21204-scaffold207-4134638 17 54521467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772357 Affx-122926944 AX-385259510 17 16252208 TCTTCTATCTCCCTAATCTAAAGTAGCCCTGAATC[G/T]CCCTCTGTCATTTCACACTATTTTAATACTGTCTA K 2 1 2 1 101000 r 74 goat snp21203-scaffold207-4079055 17 54465451 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791598 Affx-122943511 AX-385278589 17 16304105 AAACATTTCTTCTTGGGAGCCAAATAACAAGGAAC[A/G]TATCTCATCTCACAGTAAAACTAGACACACGTTTT R 2 1 2 1 101000 f 74 goat snp21202-scaffold207-4027158 17 54413799 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381026 Affx-122974649 AX-123251384 17 16348666 CATAATTGCTTGATGTCAGAAATGTTCACACCACC[A/G]TTCATAGAATTTTAACTTCATTATTTAGGAAAAGA R 2 1 2 1 101000 f 74 goat snp21201-scaffold207-3982597 17 54369564 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386127 Affx-122971415 AX-123256485 17 16388382 CCACCTTTTCAAAGACTAAATATAAAAATAGTGAG[A/C]AGCCTCATGGTTATGCTCTGGTTCAAAATGAATTC M 2 1 2 1 101000 r 74 goat snp21200-scaffold207-3942881 17 54329966 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396188 Affx-122963372 AX-123266543 17 16418690 ATTGCACATTTTCTCCTAGTGCCTCTTCTTTTTCT[A/G]CCACTACCTTCCCTCTCCCTAGTTTTCTACTCTTT R 2 1 2 1 101000 r 74 goat snp21199-scaffold207-3912573 17 54299290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271815 Affx-1111833088 AX-519545602 17 16467511 ACGCAGTCTCTGCCCCTAGAGTAACAGGGAGAACA[A/G]ACATTGAAGCAAACAATGGCAACTAAATGTGAACA R 2 1 2 1 201000 r 74 goat 17_16467511_AF-PAKI 17 16467511 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38384793 Affx-122972002 AX-123255151 17 16475515 TGGGGCTGTGCTTGTCTTGTTCATTTCTGTTCTTT[A/G]TAAGTTTCTGGCATATAACGGGTGCTGGTAAAGAT R 2 1 2 1 101000 r 74 goat snp21198-scaffold207-3855748 17 54242613 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437237 Affx-122932024 AX-123307575 17 16533442 TCTCTGTCACATTTTCAAAAGTCCTCAAACACATT[A/G]GCTCTACTTGTCCTTTAAAGTTTTTTTTAATATGA R 2 1 2 1 101000 f 74 goat snp21197-scaffold207-3797821 17 54194061 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788644 Affx-122923738 AX-284916354 17 16588102 ATCATTCTTGTACAAGTCTTTCTGTGAATGTATGC[A/G]TTCATTTCTCTAGGGTATTATATCCACCAGTGAAA R 2 1 2 1 202000 f 74 goat snp21196-scaffold207-3743161 17 54139527 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403909 Affx-122957482 AX-123274261 17 16617968 TAGAAGGGGTGGGGAGGGGCTACTGCCCAGGACCA[C/T]GCCCACTGAGGGGTTCCTGTAAGAGAAACTCCACC Y 2 1 2 1 101000 r 74 goat snp21195-scaffold207-3713295 17 54109397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384624 Affx-122972166 AX-123254982 17 16658911 ACTTAGGCAGCATCTTTTAGGGGCTGCTGGGCTAC[A/G]GCACATATAAGCAACCAATTCCTGATCTACCCGGT R 2 1 2 1 101000 r 74 goat snp21194-scaffold207-3672352 17 54068387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414824 Affx-122949201 AX-123285173 17 16689578 TAGCTGCATTCTGAAGTGTTTTCCTTTGTCTTGTA[A/G]AGAATTCCCTTCTTTCATTTATTTAATTTTTAGAA R 2 1 2 1 101000 f 74 goat snp21193-scaffold207-3641685 17 54036819 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376685 Affx-122978992 AX-123247044 17 16719462 AGATATCTACAACCAGCTTCTTGTGGAAGTAACAG[A/C]TGAAATGGTAAATAGCCAAGCCTTGTCTGCTATGG M 2 1 2 1 101000 r 74 goat snp21192-scaffold207-3611801 17 54006954 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792752 Affx-122940599 AX-385279732 17 16771611 AGCACATTGTGAAAGGCCATTTGGAGCAAACAAGA[A/C]GCCAGAGGCAACTGCAGAATGACTTGAAAAATGAC M 2 1 2 1 101000 f 74 goat snp21191-scaffold207-3559652 17 53954252 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449994 Affx-122922867 AX-123320329 17 16812272 CCATTATTTAGGCAGTTTTTGGCTCCCCTTCCGAA[C/T]GAAAGGTATCAGTGCCAAAGAAACATAATAAAGCA Y 2 1 2 1 201000 r 74 goat snp21190-scaffold207-3518991 17 53914173 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405206 Affx-122956908 AX-123275558 17 16864254 GGTCACTTTCTACACATTGGTATTTTCATCCTGAA[C/T]ATGTTTGCCACAAGCAGATTTACCCCACAACAAAC Y 2 1 2 1 101000 r 74 goat snp21189-scaffold207-3467009 17 53862352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450207 Affx-122922288 AX-123320542 17 16896761 GTGAGAAAGGGTCTGTTAGAAACGAGGAAAGGTTG[C/T]GGTCCCAACCAGCTAAGGACAGACAGGGAGAGGAG Y 2 1 2 1 101000 f 74 goat snp21188-scaffold207-3434502 17 53831389 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452158 Affx-122921655 AX-123322491 17 16945125 TTTTAGTGGAAAGAGTCATGAGGTTTAGACAGTTT[A/C]GCAACAGAAGTACTTCGAATTAGTCCAAAAGCAGA M 2 1 2 1 101000 r 74 goat snp21187-scaffold207-3386138 17 53783304 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422360 Affx-122943434 AX-123292706 17 16985309 CAAAATATGTGTACTTAATCTAATATACTTGTGAG[C/T]AGAAAAAATGTAAGTAATATAATTTATTTTTTTGC Y 2 1 2 1 101000 f 74 goat snp21186-scaffold207-3345954 17 53743825 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790019 Affx-122940773 AX-385277025 17 17018993 ATCCCTGTAACACTATGATGATTCAATTACATACA[C/T]AACCACTTCTCCATTCAAAAGCTCCAAAACCTCTG Y 2 1 2 1 101000 r 74 goat snp21185-scaffold207-3312270 17 53710306 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405462 Affx-122956036 AX-123275814 17 17102196 GACATTTTAACGAGCTTTCATGGAGTGAGGTACAT[A/G]TACAGTAATATGAAAGGGCTCTGATGAGCTTAATA R 2 1 2 1 101000 f 74 goat snp21183-scaffold207-3229067 17 53630796 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392670 Affx-122966429 AX-123263027 17 17131464 CTTTTATTGCAAGTCTTCCAGCTGCACCTAAGAGA[A/C]AAGAGTCTCAGATCCAAGAGCCTCCGCTAGTATCC M 2 1 2 1 101000 r 74 goat snp21182-scaffold207-3199799 17 53601106 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446677 Affx-122924755 AX-123317013 17 17179177 GTCTTTGGAACAAGTGGGTGTGTGCTGGCCTGTCT[A/G]TTCCCATCTTCTCCAGAACCACAGCAGCTGTTGTC R 2 1 2 1 201000 f 74 goat snp21181-scaffold207-3152086 17 53553652 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426203 Affx-122940371 AX-123296549 17 17207877 TCCCCGCAGACCCACTGACTGTTCTTTTTTCTATG[A/C]TGCCACACCACCAACCTGCCGATGTTAGGTTTTAT M 2 1 2 1 201000 f 74 goat snp21180-scaffold207-3123386 17 53524575 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413344 Affx-122950161 AX-123283693 17 17270095 TTGCTGCAGCTCCATTTCCCCCTCTGCCCACACTT[C/T]TCACCTCCTTTCTCCCTTCCTAATGCACACCTGCA Y 2 1 2 1 101000 r 74 goat snp21179-scaffold207-3061168 17 53462317 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401779 Affx-122959486 AX-123272132 17 17316127 TTTTACCCACTATGGGAGCTCTGGCATTATTATCA[C/T]GCAGCCATTCTGAAGCCAAAACTCAAGGCCAACCC Y 2 1 2 1 101000 f 74 goat snp21178-scaffold207-3015136 17 53416938 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380522 Affx-122975687 AX-123250880 17 17376516 TTACCTGTTAGTCCTAGACACAACTTTAAAGTCCT[A/G]TTTGTCTTGTTGCAACCATTTCAATGTTTTACTTG R 2 1 2 1 101000 f 74 goat snp21177-scaffold207-2954747 17 53356560 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446201 Affx-122925720 AX-123316537 17 17418012 AGAGTAATGACTTCTAAGCCATACTATCTGAGTCC[A/G]TTAACACCAGTTCAGCCACCGACTAGATGGGTGGC R 2 1 2 1 101000 f 74 goat snp21176-scaffold207-2913251 17 53315231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784340 Affx-122956261 AX-385271391 17 17447361 TCCAGGTCAACCTCCTTCTCAGTTCTTTTAAAGAA[C/T]TCACCATTCAACACTGTTCCGACTTCCCAACAGTA Y 2 1 2 1 201000 f 74 goat snp21175-scaffold207-2883902 17 53285895 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401306 Affx-122959853 AX-123271659 17 17481033 CTTCATCTTGGACTTGAAGGATGAGTAGAATTTGA[C/T]GAAGGTGGGGATCACTCTTTTTACTGAGAGTGCAG Y 2 1 2 1 201000 r 74 goat snp21174-scaffold207-2850230 17 53252383 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451937 Affx-122921009 AX-123322270 17 17559460 CCTTCTTTCTAATGAGAAATTCTCCTTTTTGCATA[C/T]AGCCCCTTCCAGGAGTACCTCCATCGCACTGATGT Y 2 1 2 1 101000 f 74 goat snp21172-scaffold207-2771803 17 53174036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448352 Affx-122924123 AX-123318688 17 17595651 GGATCTGTTGGATTCCAAAACAGGAAAATTTTCAC[A/G]AACTGTTTCTGTCTCGCTCTGATGCCCTACCTAAA R 2 1 2 1 101000 r 74 goat snp21171-scaffold207-2735612 17 53137994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409035 Affx-122953862 AX-123279386 17 17626267 ATGTGGGGCGAGAGCGAAGGCCTGCTCTTCAGCTC[A/G]TGATGCAACGGGCACTCTAGCTATTCTAGGTCATC R 2 1 2 1 101000 r 74 goat snp21170-scaffold207-2704996 17 53107665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788638 Affx-122977255 AX-385275655 17 17657704 GCCCTTAAGCATGGCAGACTGAATACATGTTTATC[G/T]CCACTTCTTTTCTACCTTGCCTCAACACTCCACAA K 2 1 2 1 101000 f 74 goat snp21169-scaffold207-2673559 17 53076210 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428481 Affx-122938786 AX-123298824 17 17694550 TCCTAGGAAGTGAAAAAAGGTGAGGGAGGGGAGGA[C/T]GGCAGGAGGAAAATCATGCTTAAGAGCTAATTGAA Y 2 1 2 1 101000 r 74 goat snp21168-scaffold207-2636713 17 53039843 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405243 Affx-122956882 AX-123275595 17 17757278 GGAGAAGACGTGAGCACCTCTTGCATCCAGAGCAC[G/T]TTGAGAACCATCAGCCTGGGATCACTAGCTCTCTG K 2 1 2 1 201000 r 74 goat snp21167-scaffold207-2573985 17 52977397 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792796 Affx-122960655 AX-385279775 17 17798729 TGCTCAATAGTGGATCCTGGAAGAGGCCTAGAAAT[A/G]TGCATGTTCGTATCACCTCAGGTGATGGTAGTGGG R 2 1 2 1 101000 f 74 goat snp21166-scaffold207-2532534 17 52935461 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385535 Affx-122971240 AX-123255893 17 17828005 TGTGCCTAAAGTCTGGTACAGAATGTAGAAAACCA[C/T]GGAACTAGTCTTTGTGAAAGTATTGCTTCCAAATA Y 2 1 2 1 101000 f 74 goat snp21165-scaffold207-2503258 17 52903665 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436671 Affx-122932465 AX-123307009 17 17858203 AGCCACTCTCACCAGTTAGGGAGGTGAGACCCCCT[C/T]CCTACATCCAAATACTCAAGGACCAGCCTGCACAG Y 2 1 2 1 201000 r 74 goat snp21164-scaffold207-2473060 17 52873729 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454233 Affx-122919668 AX-123324566 17 17895896 ACCCTTTATTGCCTTTCCAAAGCTGTTCAGGTTGC[A/G]TGCTCGTGCTGCAAGAAATCTCTGAAATCGCCTTC R 2 1 2 1 101000 r 74 goat snp21163-scaffold207-2435367 17 52835088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439990 Affx-122929798 AX-123310327 17 17924710 CTCTTACCCACAAACAGGCCAGTCACTGGGGGATA[C/T]GAACCACAGTCAAGAGATGAGAGAAAGCCATTCCA Y 2 1 2 1 102000 r 74 goat snp21162-scaffold207-2406553 17 52806268 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442937 Affx-122928229 AX-123313274 17 17966285 CTGAACCTGGGCAAGACCCTACAAGCCGTGTTACA[C/T]GTCCCTCAGCCTCAGTTTCCCCATCTGTAAAATGG Y 2 1 2 1 201000 f 74 goat snp21161-scaffold207-2364978 17 52764547 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800312 Affx-122941661 AX-385287235 17 17998942 ATTTTCCTTTATGTACTACTTAAGCTGAATCCTTA[C/T]GTTGTTTTATTGTTCTCATTGTCATTACTTTCTAA Y 2 1 2 1 201000 r 74 goat snp21160-scaffold207-2332321 17 52733969 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274464 Affx-1111834306 AX-519548055 17 18032383 CCACTGCAGGCCCTGGCAGAAGGCTGCAGGAAAGG[A/C]GCACAGGAGAGGAAGCGGGTTGGGGTGTGGGGCGG M 2 1 2 1 103000 f 74 goat GoatD01.029571 17 18032383 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320775823 Affx-122959151 AX-385262954 17 18081483 TACAGAAATGGATTGAAATTCTGTAAACAAATCCT[C/T]TCTAATCCCAAATTTGCTGAGCATGGAGGTAAGTG Y 2 1 2 1 101000 r 74 goat snp21159-scaffold207-2249780 17 52650530 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383268 Affx-122972733 AX-123253626 17 18116291 TCCTGGCAACTTAAAAGAAGGAAACCAACAGTTGA[C/T]ATTTATATTTCACAAGAGAAATGAGGACACATTAA Y 2 1 2 1 201000 r 74 goat snp21158-scaffold207-2214972 17 52615636 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390626 Affx-122967161 AX-123260983 17 18163598 GGGAGAAAAGAAACCCCAGCCGCTTCATGCTGTAT[G/T]TCTCAGACATGGAAAGAATGCAAGAAACATCCCAG K 2 1 2 1 201000 r 74 goat snp21157-scaffold207-2167665 17 52568411 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800202 Affx-122956995 AX-385287125 17 18216831 AAGACCCATTCAGTACTATTTGTCTTCTTCTTGAT[A/C]TTAACAACAGAAAATGGGATAGGAAATATTTGTAT M 2 1 2 1 102000 f 74 goat snp21156-scaffold207-2114432 17 52514679 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789428 Affx-122937879 AX-385276438 17 18260866 TCCTATTTTAGTGATAGTAACTCTGTAACCACCAA[C/T]GGTAGGGTTATTTGAGAAACCCCGGCTTTATCCAA Y 2 1 2 1 101000 r 74 goat snp21155-scaffold207-2070397 17 52470596 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392889 Affx-122965736 AX-123263246 17 18297670 GGAGGTCGGTGCAGTAAGAGAATCCCCCCAGAGCA[C/T]CTGAAGCAGAGAAAGTACTCTGAAGGTCTTGGGTG Y 2 1 2 1 201000 r 74 goat snp21154-scaffold207-2033593 17 52433522 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404411 Affx-122956778 AX-123274763 17 18329581 TTGATAACAGGTAAATTTATAAAGACAGACTAAGT[A/G]AGGAGAATCGGCCACCCTGAAATATCTTTGGCATA R 2 1 2 1 101000 r 74 goat snp21153-scaffold207-2001682 17 52401565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394810 Affx-122964805 AX-123265165 17 18419507 ACCTTAGGTAGACAGTAAATATCCAGGGAGTACAA[C/T]GGCCTTTCTCGCCCTACAACAGGAGTTTTGCCTCA Y 2 1 2 1 101000 f 74 goat snp21151-scaffold207-1911756 17 52311345 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273789 Affx-1111833815 AX-519547400 17 18499798 ACTCACCCCACACTTTGCC[A/G]CATTCGCTGTGCTTTTCTTCGGGGTCTTTCACTGG R 2 1 2 1 101000 r 74 goat GoatD01.005783 17 18499798 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38421603 Affx-122944487 AX-123291950 17 18502205 AAAAATAAATAAATAAAAGGAGAAGAAGAAGAATT[A/C]GTGAAAGGAGGCAGCAAGGAAAACCAATCTGACAT M 2 1 2 1 103000 r 74 goat snp21150-scaffold207-1829058 17 52228488 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775246 Affx-122953322 AX-385262377 17 18540551 ATATGCTGTATTGTTAACTTCTATCAAAGGGGTTC[A/C]TATCTCGGGAATCACGGGAAAGTTTCAAACATGAT M 2 1 2 1 101000 f 74 goat snp21149-scaffold207-1790712 17 52190126 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407743 Affx-122954988 AX-123278094 17 18569149 TCATAACTTTCTGACATGCTAAAAGAGGCAGTTTT[A/G]TATTGCACTTCCTGCTTCTGGATTTGAGCAATATT R 2 1 2 1 101000 f 74 goat snp21148-scaffold207-1762114 17 52161476 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386716 Affx-122970159 AX-123257074 17 18605440 TGAAAACAGACTGCACTGGGCCTCCGACACCTTTG[A/C]TGTCTGACCAGGCTCTCATCCACAGGGCCCCTGTG M 2 1 2 1 202000 r 74 goat snp21147-scaffold207-1725823 17 52125187 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274555 Affx-1111834292 AX-519548145 17 18634801 TCAGCAGCCACAGCCTGGGTCAGCACCAGGCATAG[A/C]CGAGGCACACAATAAAAGCCAACCAATGTG M 2 1 2 1 202000 r 74 goat GoatD01.029175 17 18634801 A C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38448258 Affx-122924195 AX-123318594 17 18647266 TGATTCCCCTAAAAATGCCTGCCCTGTGGACACAG[C/T]ATGTATTGATTACACCACGTATTTTGAATTGTTGA Y 2 1 2 1 201000 r 74 goat snp21146-scaffold207-1683997 17 52083396 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393015 Affx-122965650 AX-123263372 17 18688564 ATGCTACAGTTCATGGGGTCACAAAGAGAAGGACA[C/T]GACTTAGGAAACGAACAACATAGTAGCCACATATA Y 2 1 2 1 201000 r 74 goat snp21145-scaffold207-1642699 17 52042023 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427013 Affx-122939844 AX-123297358 17 18720134 TGGGAACCCCTATACTGACAGCAAAATTCTTGAAT[A/G]CTAATAAATCACAGAAAATGTATTTCTTTGAACTT R 2 1 2 1 103000 f 74 goat snp21144-scaffold207-1611129 17 52010448 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452685 Affx-122920313 AX-123323018 17 18776332 AGACATTTTTAAAAAGAAAGAAAAAATTCAGAACT[A/G]CAGAGAAGAGATGCAAAGAATATAACAGAATCTGT R 2 1 2 1 101000 r 74 goat snp21143-scaffold207-1554931 17 51953600 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390807 Affx-122967860 AX-123261164 17 18825555 GAACCAAGAAGTACTCAAAGCACGACAGGGATATA[C/T]GTCAAAGTGTGAAGCAGCTTCTACTGCCAAATCAG Y 2 1 2 1 101000 f 74 goat snp21142-scaffold207-1505708 17 51904282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787419 Affx-122925092 AX-385274444 17 18854446 ACAGACTTTGGCCACATTTGCAAAGAAACATTTTT[C/T]ACTGACTTTCCAAAGACATAGATCAATATTGTAAG Y 2 1 2 1 101000 f 74 goat snp21141-scaffold207-1476817 17 51875357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431973 Affx-122935953 AX-123302314 17 18885458 AGTAAAACAGTCTGGTATCATGCAAAATACAAAAA[C/T]AAGGCAACAGAATAGAGTCTGGAAGTTTACTCACA Y 2 1 2 1 201000 f 74 goat snp21140-scaffold207-1445805 17 51843818 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802459 Affx-122952749 AX-385289363 17 18936219 ATTAGCGATCACCTCCTTTTGTCAACACTGACTTC[A/G]TGAATTGCATTTACATTAGACCCATTTGTAAGAAG R 2 1 2 1 101000 f 74 goat snp21139-scaffold207-1395044 17 51792902 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769705 Affx-122935820 AX-385256875 17 18973175 GCACTTTTAAACTAGTTAGCTAGGTTATATTTACC[A/G]TGTTTACATAGACATTTAAACACAAGTAACAGACA R 2 1 2 1 201000 r 74 goat snp21138-scaffold207-1358088 17 51752185 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410440 Affx-122952394 AX-123280790 17 19019093 AGACTGAAATTAGCTGTACCCTAAAAAGATATCCC[A/G]CCAAAATATTTTTGTTAAAGAAATAATAAAATTGG R 2 1 2 1 101000 f 74 goat snp21137-scaffold207-1312170 17 51706040 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389784 Affx-122968222 AX-123260141 17 19060075 CTGTTTCAGATGGTGATATAATAAAGGTGGCTTCC[A/G]TGCATTTACTCATCATCTGCTCAAGAGACCTAAGC R 2 1 2 1 101000 r 74 goat snp21136-scaffold207-1271188 17 51664475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435737 Affx-122933288 AX-123306076 17 19091726 CAGGTGAGTTTTTCCCCCCCCCCCCAATTTTGTGG[C/T]GCAATGTTCAACACTATGTTAACCACTTGGAACTG Y 2 1 2 1 101000 r 74 goat snp21135-scaffold207-1239537 17 51633834 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463492658 Affx-1110009831 AX-514975453 17 19141864 GTGGTAAAGGATCTGCCTGCCAGTGCAGAAGATGC[A/C]GGATGTTCGGGTTCAGTCCTGGGGTCAGGAAGATC M 2 1 2 1 303000 r 74 goat 17_19141864_AF-PAKI 17 19141864 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320794009 Affx-122929861 AX-385280978 17 19143123 TAATTTCTGTCTGAGCTACTCTGGAGACTAAAAGC[A/G]TGAGAAATTATTACTAATCAGTAGAGCTTCAGGTA R 2 1 2 1 101000 f 74 goat snp21134-scaffold207-1188140 17 51581703 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377269 Affx-122978133 AX-123247628 17 19193033 AACAGCAAACTAGATGGCAGAGAAGACTTCACAGT[A/G]TCTTCAAACTGCTGCAGATGCAGCAATGAATGACA R 2 1 2 1 102000 r 74 goat snp21133-scaffold207-1138230 17 51531387 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791699 Affx-122977158 AX-385278690 17 19241909 TTCTGTTACCTGCATCTAATAAAGTCTAAGTAATA[C/T]GTCACAACAACCCAGTTAAGGCTGAAACATGCCCA Y 2 1 2 1 101000 r 74 goat snp21132-scaffold207-1089354 17 51482652 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418203 Affx-122947062 AX-123288551 17 19291284 TATACTCACCACATTTCAGGGGGGACCAGCGCCTT[A/G]TCTGCTGAAGTCCTTCAGGGCACATTCCTGGGCTT R 2 1 2 1 101000 r 74 goat snp21131-scaffold207-1039979 17 51432518 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391442 Affx-122966745 AX-123261799 17 19323236 AGCTACTGCTGCTTTGCTATACCCCACGAAACCTG[C/T]GCTGCTCTGGAAACATGCTGCCTGAGGGGCTACCC Y 2 1 2 1 101000 f 74 goat snp21130-scaffold207-1008027 17 51400827 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792918 Affx-122952665 AX-385279896 17 19355215 GAGCACTGCCTTAAAAGCATGAATTGGTAGCTGTG[A/C]TTGTGATACTATAATGCATGAGGGAGTAACACATC M 2 1 2 1 101000 f 74 goat snp21129-scaffold207-976048 17 51369029 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447850 Affx-122923894 AX-123318186 17 19388507 TGCTCTCAGTGGGATAGTGTGCCTATATTTTATTT[G/T]ACTCTTGCCATTAATTACCTGGGGGCCTGTATCAT K 2 1 2 1 101000 f 74 goat snp21128-scaffold207-942756 17 51335474 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388931 Affx-122968828 AX-123259289 17 19445472 TTAGCACGCATGCACTCTCCCTTGCTGAAGTCTTC[A/G]CTTTACTGTTTATCTCCCATCTGTGACCTCAGAAC R 2 1 2 1 101000 r 74 goat snp21127-scaffold207-885791 17 51277860 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410276 Affx-122952516 AX-123280626 17 19476814 TGAACAATACTATAGATCCAAATGAACATGACAGA[C/T]GTATACAGATCACTGCTGACAGCAGCAGAAGATAT Y 2 1 2 1 101000 f 74 goat snp21126-scaffold207-854449 17 51246084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781982 Affx-122930742 AX-385269062 17 19517832 ATGGTTAATGTTTAAGTGCAACAGAAACAGGAATA[C/T]AGACAAGGATATGATTTGGCTCGCTATAACTGGAG Y 2 1 2 1 101000 r 74 goat snp21125-scaffold207-813431 17 51205345 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385321 Affx-122971668 AX-123255679 17 19610166 ATCTTTATAAAAGTTATTGGTAATTATTTTGATCT[A/C]GGTTGGTTGAATCTGTGTAGAGAGAACCCAATGAG M 2 1 2 1 201000 f 74 goat snp21123-scaffold207-721097 17 51111601 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447691 Affx-122924622 AX-123318027 17 19695590 TAGTGATATCAAACATCTGTGCTTTCGGGCCGTCT[A/G]TATGTCTTCTTTGGAGAAACGTCTATTTAGATCTT R 2 1 2 1 101000 f 74 goat snp21122-scaffold207-635673 17 51024842 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429864 Affx-122938144 AX-123300205 17 19738935 CAGGGGTATTGATTGGGTTGCTGACATTGGATGGG[A/G]ATGGGAGGTGGTCTTTCCACATTCTTTGGGTTCCA R 2 1 2 1 201000 f 74 goat snp21121-scaffold207-592328 17 50981938 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769156 Affx-122927116 AX-385256331 17 19767875 ACTTCTGCCTCCCCCACAGTTGCTTGTTTTCTTCT[A/G]TTAAAAACAGAAGACATTGTCTCAAATCCAAGTGC R 2 1 2 1 102000 f 74 goat snp21120-scaffold207-563388 17 50953038 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775034 Affx-122967183 AX-385262166 17 19809135 CAAATGGCCACGTGAAAGTAAATGTGTATAACTGG[C/T]TGTTTTTCTGTAGTACCCACATTTATGGCTACTTT Y 2 1 2 1 101000 f 74 goat snp21119-scaffold207-522128 17 50911843 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783779 Affx-122935643 AX-385270835 17 19859171 TAAATAGACTTTATCCAGTTTAACAAAGTTTCATA[C/T]AGATTAAGCATGTTAATATGTTCTGTTTGCTGATT Y 2 1 2 1 101000 r 74 goat snp21118-scaffold207-472092 17 50861353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384800 Affx-122971997 AX-123255158 17 19897858 GTGTCATATACTTGTGTGTACTTAGTCACTGAGTC[A/G]TGTTGACTCTTTGTGATCCCATGGACTGCAGCCTA R 2 1 2 1 303000 r 74 goat snp21117-scaffold207-433405 17 50822586 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771463 Affx-122978504 AX-385258621 17 19933296 GATGTATCAAGAAAAGTCTAGATGATAACTAAAAG[C/T]GTAAAGAGCAGACAGGCAAAACAAGGAACTATCTA Y 2 1 2 1 101000 r 74 goat snp21116-scaffold207-397967 17 50787152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414642 Affx-122949326 AX-123284991 17 19974924 ACAAAAGAATGTTTTCAATTCCACCTTTAATGTCC[A/G]TGGCACTGGAGATCATGTTTTACTTGCTTTCAATA R 2 1 2 1 101000 r 74 goat snp21115-scaffold207-356339 17 50745363 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434790 Affx-122933878 AX-123305131 17 20004148 TTTGAGACTAACTAATTTCTCTTCCATTAGTGTCT[C/T]ACTTTCAAGAGGGCAGTGGTTAGGAATGGTAACAC Y 2 1 2 1 202000 f 74 goat snp21114-scaffold207-327115 17 50716257 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407310 Affx-122955313 AX-123277661 17 20040655 CAAATCCCCTGTCAGAGAGAAGCAAGTTGTTGAGT[A/G]TGCTTTTTGCTGTATCCCCAGCACTAGGTAAAGTG R 2 1 2 1 101000 f 74 goat snp21113-scaffold207-290608 17 50679613 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405776 Affx-122955921 AX-123276128 17 20089794 TACCTGAACTGTTATTGATTAAAAACATTGGCTTC[C/T]ACCTGTGCTGAGTATTCTGGGGTTAACAGAACTTT Y 2 1 2 1 201000 f 74 goat snp21112-scaffold207-241469 17 50629802 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375442 Affx-122979175 AX-123245801 17 20120924 TTTCCTCTGTTAACTGGCTTCGCCATTATAATCAT[C/T]TTTGCTCTCCAAATAGCCTTTTTCTTAACATGCCT Y 2 1 2 1 101000 f 74 goat snp21111-scaffold207-210339 17 50598482 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799644 Affx-122942292 AX-385286573 17 20222856 TTAGGTCTTTAAAAGAGATATGCTAAAATATTTCA[C/T]CAGTCTGTCAAGCCACATTCTGCCATCATCGCACA Y 2 1 2 1 101000 r 74 goat snp21109-scaffold207-108407 17 50496599 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377074 Affx-122978282 AX-123247433 17 20276218 ATATAACAAGATTAGATAAATAAGAAAACTGAGCA[G/T]AGTGGAGAATAACAGGTAACAGATCCATAATCCCA K 2 1 2 1 101000 r 74 goat snp21108-scaffold207-55045 17 50443050 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448374 Affx-122924104 AX-123318710 17 20309097 AAAATATAATTTCCACTGAGCAAAACAACTTGTCT[A/G]TTTTCCTCAAGGATGCAATATAAAAACTTAAAACA R 2 1 2 1 101000 r 74 goat snp21107-scaffold207-22166 17 50410190 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426359 Affx-122940255 AX-123296705 17 20395945 AGTTAAATGTGGAGAAAAGAAAGACATGAAGCATT[A/G]CTTTGCTGGCAAAGACACTGGTAGAAGTTTTGCTC R 2 1 2 1 201000 r 74 goat snp6642-scaffold1238-961963 17 50322177 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432988 Affx-122935261 AX-123303329 17 20425222 TTCCTGATTTGGATAGGTTGCACTGTGGCTTTATA[A/C]AAGGATGTTGCTGTGAAAGGAGTATCATATTGGCA M 2 1 2 1 101000 f 74 goat snp6641-scaffold1238-932686 17 50292448 A C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407016 Affx-122955020 AX-123277367 17 20494177 GGTATCCTTAGTACCTAGTGTGAATGATCAAAAAG[C/T]ATATTGAATGCATTATTAGTGAATGGCAAACAGAG Y 2 1 2 1 101000 r 74 goat snp6640-scaffold1238-863731 17 50222040 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788686 Affx-122940376 AX-385275702 17 20571962 CTATCTGCTGAGTCTGATAAAATGTGAAAATTACA[C/T]AACTTTATAGTACCTCAACATTTATCTTCTTGATT Y 2 1 2 1 101000 f 74 goat snp6638-scaffold1238-785946 17 50143790 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776554 Affx-122927007 AX-385263680 17 20607003 CTGGAAAGAGCCAGTCCCTGATTACCTCTTTAAGT[A/G]GATGTAAATGAGCAGTTAACCTAAATTACCCTACA R 2 1 2 1 101000 f 74 goat snp6637-scaffold1238-750905 17 50107917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790347 Affx-122974375 AX-385277350 17 20675377 ATGGTAATATCATGGGAAAACACATGCTTTCTTAG[A/C]TCATGATAATCAAAGTGAATTTTACACTGGTAACT M 2 1 2 1 201000 r 74 goat snp6636-scaffold1238-682531 17 50038414 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272351 Affx-1111833792 AX-519546082 17 20733308 TGCTTTATTTATACACACATTATTTTGCTATCAGC[A/G]TCTGCAGCCATCCCCAACAAACGGCTGCTGAGGTA R 2 1 2 1 201000 f 74 goat GoatD01.005210 17 20733308 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427157 Affx-122939628 AX-123297500 17 20749313 CACTGAAAAATCCGCTAGACCTCCTCTCCTTTCCT[A/G]TAAGAAAACACAATGATCATTTTCATTGAGAGGTA R 2 1 2 1 201000 r 74 goat snp6635-scaffold1238-608595 17 49963014 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769559 Affx-122947726 AX-385256729 17 20783353 AACTGAAACTCTAACTTTAGAAGGAACTTAAGAAT[C/T]AACCTGCAGTTGTAAAACCCATGGTGCCCTTACAA Y 2 1 2 1 101000 r 74 goat snp6634-scaffold1238-574555 17 49928480 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394433 Affx-122965092 AX-123264788 17 20885218 ATTTGGGGGACCGGGGTGAAATGTGAATTTAATGT[A/G]TGTGTTCTCCCCAAATGTATATGTTCATGCTCTAA R 2 1 2 1 101000 f 74 goat snp6632-scaffold1238-472690 17 49807801 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440419 Affx-122929606 AX-123310756 17 20930795 ATAAGCTGTTATCAAGATTTCTGCTATCTTCCATT[A/G]CCTCTCCACAGTATTGTAAGAAAAATTGGATCAGT R 2 1 2 1 101000 r 74 goat snp6631-scaffold1238-427113 17 49762656 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429293 Affx-122938612 AX-123299635 17 20993273 GTTACTTTAGTTCCAAAGGAAAAGAGCAATTTAAG[A/G]AGAATCTAGCAGGTACTATTCACTATTATTTAACA R 2 1 2 1 101000 r 74 goat snp6630-scaffold1238-364635 17 49700482 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277083 Affx-1111835733 AX-519550590 17 20995444 GGTCCAAAGTTGTGTGAATCTTGGGGACCCAGTAC[A/G]ACACAGCCAACAGAGCAATTTGGTTTGGGGTGATT R 2 1 2 1 201000 f 74 goat Random2.2K-1657 17 20995444 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412855 Affx-122950447 AX-123283204 17 21051289 GTTTGATCTGGCAGAAACCTTCTCAGGCCTATGCT[A/G]CTGTTTGAGAATCTGCCTATCAGTTAGCTTTCATG R 2 1 2 1 201000 f 74 goat snp6629-scaffold1238-306619 17 49641833 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791860 Affx-122920924 AX-385278850 17 21083667 TAGTTTTGCATTTTTTAGATCAAGAAAAGGCTGTA[A/G]GCAGTTGGCAATGAATAGTACATAAGGCCTGAATG R 2 1 2 1 101000 r 74 goat snp6628-scaffold1238-274241 17 49609459 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791729 Affx-122977698 AX-385278720 17 21122206 CATCGCTATTAGAAAAGACATTCACAAAAATTCAT[A/C]GATTCCAGCTAACTCTTCCTTTGAAGGCAAATAAT M 2 1 2 1 101000 r 74 goat snp6627-scaffold1238-235702 17 49571514 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788017 Affx-122976876 AX-385275038 17 21160021 ACCCTTTACTTTCTGTAATGTAAACAATATGATCA[C/T]GGTGTTACCCTTTCATGGATCATTGGTAAATATTA Y 2 1 2 1 101000 r 74 goat snp6626-scaffold1238-197887 17 49533707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794238 Affx-122944725 AX-385281204 17 21210638 TGCCACCTTGACATGTTCTCTACCAATTTAAGGAA[C/T]GCTAAGGTAGTGGACAGTTCATGGCTACTTAGGAA Y 2 1 2 1 101000 r 74 goat snp6625-scaffold1238-147270 17 49482975 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772387 Affx-122974557 AX-385259540 17 21252626 TTGAAGGTGTAATGCATTCTCCTAGCTACAAACCA[C/T]TATTTCCCCAATGTCTGATAAAAAACAACTAGTAG Y 2 1 2 1 201000 r 74 goat snp6624-scaffold1238-105282 17 49440917 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775678 Affx-122970719 AX-385262809 17 21288850 ACTGTAGTTACACCCACACAAAAAGGTTTTACTCC[A/G]TATCAATATCACTATTTTTTCCAACACTGAACAAA R 2 1 2 1 101000 f 74 goat snp6623-scaffold1238-69058 17 49404388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438853 Affx-122930764 AX-123309190 17 21333917 AACTAGCGCTGTAGGGCTCCCAATGGGCGACGAGC[A/G]TCTGAGTATTCCTCTGCTGGGAATATTCACGTGCC R 2 1 2 1 101000 r 74 goat snp6622-scaffold1238-23991 17 49357801 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787621 Affx-122950638 AX-385274644 17 21364946 TGTATGCTTGGCAACTATCCATACAGCATTGCTGA[C/T]GGTTGTGCTGCTATATATGAAAAACTTCCATCTAT Y 2 1 2 1 101000 f 74 goat snp13332-scaffold1514-6939 17 49313212 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406317 Affx-122955459 AX-123276669 17 21396734 CAAAACTCAAACTAAAACCTTCAATCTGATATCAT[A/C]TCCAGTGACTTCATTTTCACCTAACAATAAAGATA M 2 1 2 1 201000 f 74 goat snp13333-scaffold1514-38727 17 49280995 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768438 Affx-122963491 AX-385255618 17 21441642 CTAATACAAAACTGTTTTGTGAAGGGAATAAGCAT[A/G]TTATCTTTCAGTACAGTCAGAAAGATCAGCATTAC R 2 1 2 1 201000 f 74 goat snp13334-scaffold1514-83635 17 49236581 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798998 Affx-122935373 AX-385285928 17 21476095 TATGCTATTACATGTCGTGTGTAAGTTCTGAAGTG[A/G]TACAGAGCTAGGTAAGGTTTAAAGATCACACACAC R 2 1 2 1 101000 r 74 goat snp13335-scaffold1514-118088 17 49201723 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424294 Affx-122941976 AX-123294640 17 21506880 CTCATATTTCCACTCATAAATGGCTGAGTACTTAT[A/G]ATACTACCCAGCACATCTCACCTAATCTCCCCTTA R 2 1 2 1 101000 f 74 goat snp13336-scaffold1514-148873 17 49169907 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388405 Affx-122969291 AX-123258763 17 21578224 TATAATACCTTCACTCCTTTCTTTTGCCCAGGTGT[A/G]TTTGGACTATACATTTCTGCATTTTTTGTTTCTTT R 2 1 2 1 101000 f 74 goat snp13337-scaffold1514-220217 17 49098576 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450303 Affx-122922149 AX-123320638 17 21615365 AAACAGAACTCATCTGTGTCCTACCTTTTAGTCCA[C/T]AGTCTTTCTTTCCCTCTATCTATGGAACTTCATAG Y 2 1 2 1 101000 f 74 goat snp13338-scaffold1514-257358 17 49062376 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378069 Affx-122977178 AX-123248428 17 21684395 TATCATAACCCACTGGTTTTACTGCTGAATTGTGG[C/T]GACATGCTAGTCACCAGAGATTAGTATCACTTCAA Y 2 1 2 1 101000 r 74 goat snp13340-scaffold1514-326388 17 48992614 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463490771 Affx-1110010997 AX-514973586 17 21743885 GCTCCACAGAAGTTATCAACGTTACAGACTTTAAC[A/G]ATGTCAAACTCACAAAACCGATAAATATCTAGATG R 2 1 2 1 101000 f 74 goat 17_21743885_AF-PAKI 17 21743885 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378895 Affx-122976495 AX-123249254 17 21781256 ATGGTTGGAAAGGCTATATAGGACATTTAATTCAA[A/C]TCCCATTCAATGAAAAAATGTCCTTTATTCCATTT M 2 1 2 1 201000 f 74 goat snp13342-scaffold1514-423249 17 48896808 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794117 Affx-122942328 AX-385281082 17 21888720 TGGAAGTACTGTAATCAAAGCCTCCTGGCTTTCAA[C/T]CTTAGCACTTCTAAAATGTGTTGATTTCCTTTTCC Y 2 1 2 1 201000 r 74 goat snp13344-scaffold1514-530713 17 48786117 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799724 Affx-122952864 AX-385286652 17 21954880 GCTGACCATAGCCTAAAACTAACAAGGTGAAACAG[C/T]AGGTAAACAATAACCTATGTGAACTATGGAGTGAC Y 2 1 2 1 101000 f 74 goat snp13345-scaffold1514-596873 17 48719329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779663 Affx-122948332 AX-385266765 17 21997921 GTCACTCAAAGGAAAAAAATTGTAAGGAAGGATGA[G/T]TGTATACAAACAGGTTATCTAAAAAGTTATGCAGT K 2 1 2 1 102000 f 74 goat snp13346-scaffold1514-639914 17 48675419 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420431 Affx-122944904 AX-123290778 17 22045831 GATTTCTGCTACTCCACAATGGGGAAAAATACTCC[A/G]TGCATTTGTGGCCCTGTGATTAACTTCCTTGTGAA R 2 1 2 1 201000 r 74 goat snp13347-scaffold1514-687824 17 48627978 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784384 Affx-122920530 AX-385271435 17 22096222 GAGCACCTTGAAACTCACTGCTCTTTTAGCCTTGC[A/G]TTTCCTAGTGTGCTGATCAAAACCCTTGCCATAAA R 2 1 2 1 101000 f 74 goat snp13348-scaffold1514-738215 17 48577301 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386436 Affx-122970797 AX-123256794 17 22132207 TATTTTATTAAAGTGTGCTCCCCCAATCTCTGCTG[C/T]AATAATATTCAGTTTATGTGCCACGTACTGTATTA Y 2 1 2 1 201000 r 74 goat snp43337-scaffold578-11342 17 48539324 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397214 Affx-122962388 AX-123267569 17 22161598 CCACCTCTTCATATGCTTACTTGTTCTACTTAAGC[A/G]TAAATGACTATATGGCCTTCATCTGACTGAACCTT R 2 1 2 1 101000 r 74 goat snp43338-scaffold578-40733 17 48509129 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787222 Affx-122940216 AX-385274248 17 22214406 AGAGGTAGAATTGAGTGAGATTTTGTTGTTGAAAC[A/G]TTTTCTGCACGTTGACCTATATTTGAATGATGATT R 2 1 2 1 101000 f 74 goat snp43339-scaffold578-93541 17 48455984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782899 Affx-122968512 AX-385269969 17 22247022 GATAGAGAATTTAGAAGAAAGCCTATTTAAAGAGC[A/G]TGTCAACTTATGATTTGTATATACTGGGATGAAGA R 2 1 2 1 101000 f 74 goat snp43340-scaffold578-126157 17 48423464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793043 Affx-122967496 AX-385280021 17 22288836 CATTCTCTAAAGAATTTGGAGTTGTCTTTAGAGAC[A/G]TCTTCAAGGTTTTTCTTCTTCCCCAAGGTGTAAGA R 2 1 2 1 101000 r 74 goat snp43341-scaffold578-167971 17 48381568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423104 Affx-122942919 AX-123293450 17 22332579 AATTTCAGTGCAGTTGCTTCCATTTTTATCTAGTT[A/G]CTTGAATAGATAAATTTAATTACCATATATAGAAG R 2 1 2 1 201000 r 74 goat snp43342-scaffold578-211714 17 48337878 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411214 Affx-122952357 AX-123281564 17 22386032 CACATTTGTTGTATTTATTATTTATGTTTTGAAAT[A/G]TTGGCACTTTTCTATACACTTTCCTTGAGGATATT R 2 1 2 1 101000 r 74 goat snp43343-scaffold578-265167 17 48283154 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432300 Affx-122936313 AX-123302641 17 22418020 TTCCAGTCCTTGTTTTGATTTATTTCAAGTCACCT[A/G]TGTATCAAATGACAAACCAGTTGGTTGCTGACCTT R 2 1 2 1 101000 r 74 goat snp43344-scaffold578-297155 17 48250790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440357 Affx-122929653 AX-123310694 17 22470844 ATCTATTCTCTGGAGAAACTGTATATTGATAAATG[A/C]TATAACTGACAGTGTTCTTATTACCTAATTCTATT M 2 1 2 1 101000 r 74 goat snp43345-scaffold578-349979 17 48198379 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376368 Affx-122978316 AX-123246727 17 22519120 TTTAAGTATTTAATATTTTTCTAACAAATGTCAGA[C/T]GAGTAAAGAATGAATAAGACAGCAGTCTACAATGA Y 2 1 2 1 103000 r 74 goat snp43346-scaffold578-398255 NW_017196631.1 5237 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439373 Affx-122930270 AX-123309710 17 22570734 AATCATATATTTTAAAAATGTGCAGAGACCATAGA[G/T]CATTATTTTCCAAAATAAGGGTAAAGTTTTGGTTT K 2 1 2 1 103000 f 74 goat snp43347-scaffold578-449869 17 48096793 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781532 Affx-122945415 AX-385268617 17 22604241 CTTCTACTTCACCATTTTAGATCCTTTGATATAGA[C/T]GTGGAAAGTCCTTAGTCTTAACAAAAGTTCACATT Y 2 1 2 1 101000 f 74 goat snp43348-scaffold578-483376 17 48052183 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802709 Affx-122940528 AX-385289608 17 22634604 TATCATCATGGATTTATTCTAATCCTTGTTATACA[A/G]GAAAGAGAGGAAAATGAAATTTCTATCTTCTACAA R 2 1 2 1 303000 r 74 goat snp43349-scaffold578-513739 17 48021506 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419584 Affx-122945391 AX-123289932 17 22664496 TGAAGGTTTTATGTGTGTGTGCCTGTGAGAGTGTG[C/T]GAAGTGAGGAATTCGGAGTACATCTGACGTCAGAG Y 2 1 2 1 201000 r 74 goat snp43350-scaffold578-543631 17 47991630 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440605 Affx-122929979 AX-123310942 17 22699855 AGAAAAATAAGATGGTATATGAAGCTAAGCTGTGA[A/G]ATACATTGTTTTTCTACCATCATAACTGGAACAGA R 2 1 2 1 101000 r 74 goat snp43351-scaffold578-578990 17 47954912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419281 Affx-122946247 AX-123289629 17 22790307 AAACACCTGAAATCAGAAGCATCAGTTGGAAGTTC[A/G]TTGGAAGTTGAGTGAAAACCAGGACTGGGTACAAA R 2 1 2 1 101000 r 74 goat snp43352-scaffold578-669442 17 47865944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381807 Affx-122974279 AX-123252165 17 22825304 CTACTAAACCAGTAACCCTGGTATTAATCTCAGTA[C/T]AATCCCAAGCACATTGTATGAATCCTATAAATATT Y 2 1 2 1 101000 f 74 goat snp43353-scaffold578-704439 17 47830532 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390945 Affx-122967065 AX-123261302 17 22873366 CCAGAACAAACAACAAATAAAAAATAGGGCTTAAC[A/G]TCATTGTCAATTGTGTCTCACTAAGGAAGCTAGAG R 2 1 2 1 101000 r 74 goat snp43354-scaffold578-752501 17 47782394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376410 Affx-122978086 AX-123246769 17 22939249 AGAGCCCAGCTCTGACAATATATACTTTTCTACAT[C/T]TTTGTAGCATTTTTTCCCCATAATGACTGCCCATA Y 2 1 2 1 201000 f 74 goat snp43355-scaffold578-818384 17 47712955 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413817 Affx-122949893 AX-123284166 17 22976376 TAAATAATCAATTTGCCTCTGATTCAGAAACCTTG[C/T]ATTTACTGTCAGGAAAAAATAAAATATGAATATAT Y 2 1 2 1 101000 f 74 goat snp43356-scaffold578-855511 17 47675762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409466 Affx-122954070 AX-123279817 17 23019642 CAATCTCCTTCTCTTTATGAGTAATTGCAACTAAC[C/T]GATACATAGTGAACAAGAAGAGATTGGAGAATGCA Y 2 1 2 1 101000 f 74 goat snp43357-scaffold578-898777 17 47631833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419195 Affx-122945710 AX-123289543 17 23081958 CATTGATCTCCACTCTTTTATTATTTCCTTTACTC[C/T]GCTTGCTTTGGACTTAATTTGCTCTTCCATGTTGT Y 2 1 2 1 101000 r 74 goat snp43358-scaffold578-961093 17 47568931 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798982 Affx-122971747 AX-385285912 17 23095819 CCCTAGATTCCTCTCTGACACCCTGATTATGTAAC[A/G]TATACACTCTTCTACAACCTCTGCATATTGGCATT R 2 1 2 1 101000 f 74 goat snp21851-scaffold2141-673322 17 47555428 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798231 Affx-122960471 AX-385285166 17 23127012 TTCCATGTATTTTTGCTTAAATTCAGAGTATATAT[A/G]TGTCACTTAGATTTAAGCTCATTCCATTCATTATT R 2 1 2 1 201000 f 74 goat snp21850-scaffold2141-642129 17 47524144 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444196 Affx-122927260 AX-123314533 17 23165862 CTTGGGGAGATAGAAAAACAAATAGTCATTTATAG[C/T]ACAAATCAGATTGATTTAAATGTTTTAATAATGAC Y 2 1 2 1 101000 f 74 goat snp21849-scaffold2141-603279 17 47485150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429307 Affx-122938603 AX-123299649 17 23202638 ATGAGGATCTGGATATCAAATGGAGCTGATTTAAT[C/T]AATTGGAGTCATGTGATTTAGGGGGCCAGTTTAAT Y 2 1 2 1 201000 f 74 goat snp21848-scaffold2141-566503 17 47448347 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790385 Affx-122944341 AX-385277388 17 23240447 ATCTTGAGTAGATATTTATGAGATTAGAGATCAGA[C/T]AATAAGTCAGCTTTGGACTGTAGTTGTAGGAGTTA Y 2 1 2 1 201000 f 74 goat snp21847-scaffold2141-528694 17 47409918 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790164 Affx-122965388 AX-385277169 17 23285776 GTAGTAATCTTTTATAGAGTTCTTGCATTGTCTAA[C/T]GTCCTTTGATTCTTTTTTCCAAATGCTGTGTTCCC Y 2 1 2 1 101000 r 74 goat snp21846-scaffold2141-483365 17 47363503 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403899 Affx-122957488 AX-123274251 17 23328890 AAATAGAGAAAATACAGTTTGTAAGAGGGTAAAGC[A/G]CTATTTCATTTCAGTGAATTTTAATAAGCATTGAA R 2 1 2 1 101000 f 74 goat snp21845-scaffold2141-440251 17 47319619 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277085 Affx-1111835734 AX-519550592 17 23363130 TCTCATGATTAATTTGTATCTAAAGTTCCAACTCA[A/G]TTCTAATAACTAAAATTCAGGGACTTCCCTGGTGG R 2 1 2 1 201000 f 74 goat Random2.2K-1659 17 23363130 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320766274 Affx-122920031 AX-385253666 17 23365528 TTAATGACTTTAACTAGAGTGGTCTCACAAAGAAC[A/G]TCAGTTGCCCTTAATGCATATGCATTGTCTTTCAG R 2 1 2 1 201000 f 74 goat snp21844-scaffold2141-403613 17 47283060 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408930 Affx-122953945 AX-123279281 17 23422251 ATGAATGGAGCATTTGACTACATGGTATCAGTTTT[G/T]CCCCCAGAAGAGACAGAAAAATATTACTTTTAACG K 2 1 2 1 201000 f 74 goat snp21843-scaffold2141-346890 17 47225559 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778447 Affx-122926982 AX-385265561 17 23510087 CAGTGGTTAAATATGAGACTAGAGATTAACTGTGA[A/G]TGTAATCATAAAAAGCTGTGAATGTTATGATAATT R 2 1 2 1 101000 f 74 goat snp21842-scaffold2141-259054 17 47134547 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439684 Affx-122930580 AX-123310021 17 23563651 CTTAGTTTTCATGTTTAACTATGCTGTCATTTAAC[A/G]TTATCAGTTCAGTTCAATTGCTCTGTTGTGTCCAA R 2 1 2 1 201000 f 74 goat snp21841-scaffold2141-205490 17 47080026 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429478 Affx-122938475 AX-123299820 17 23596911 GTTGAAAAATACAAATTTTAGAATGTCTCCCAGAA[C/T]GGACAGAAAATTATAAAGAATATTTTAAAGATTTT Y 2 1 2 1 102000 f 74 goat snp21840-scaffold2141-172230 17 47046516 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421031 Affx-122944537 AX-123291378 17 23632689 AGTGCTCTTCTCTCAAGGGTTAATATAGTCTTACT[A/G]TTCAGTTGTGACTCTTTGAGGTTTCTAATAATTGT R 2 1 2 1 101000 f 74 goat snp21839-scaffold2141-136452 17 47010445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405598 Affx-122955928 AX-123275950 17 23668245 CAGCCATACTAGGTCCCCTTCGAAGGACCTCTGCC[A/G]TAGTTACTTTCTATGCTTGAGATTATCTTCCTTCA R 2 1 2 1 201000 r 74 goat snp21838-scaffold2141-100896 17 46974421 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410091 Affx-122952840 AX-123280441 17 23706537 AAAAAACAGCAAGTGCACTACTTGGGAGAAAGAGC[A/G]CTGGATACAAACAGCTCTCTGAACGCCAATGGCAA R 2 1 2 1 101000 r 74 goat snp21837-scaffold2141-62604 17 46935982 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793611 Affx-122951165 AX-385280585 17 23736084 TTTCTAAAGAAAGTTCTTAACGTAGGAAGAGTGAT[A/G]CGAATTTGTGTCATTCAAAGGTAAGTCTAGACAAG R 2 1 2 1 101000 r 74 goat snp21836-scaffold2141-33057 17 46906348 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451790 Affx-122921498 AX-123322123 17 23766469 GATTTCATCCTTTAAGTGAGGGATGGATGGAAGAA[A/G]AAAGCCCTGGATGTCTCAGCTGCTCTTGTCTGAAA R 2 1 2 1 101000 f 74 goat snp21835-scaffold2141-2672 17 46875384 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439972 Affx-122929811 AX-123310309 17 23777772 TAACTAGAACTTGTTTGTACAGTATTCATAAGTAC[A/G]TAAAACCGTGTATTTTCAGTAAATCTGGCTGTGTT R 2 1 2 1 101000 f 74 goat snp19702-scaffold199-8532 17 46863026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426961 Affx-122940405 AX-123297306 17 23807254 AATTAACCCTGTAGAGTCAGGTCATTTTGCAGTAT[A/G]TTTCAAAGGTAATACATATTTTACTTGAGTGACCA R 2 1 2 1 101000 f 74 goat snp19703-scaffold199-38014 17 46832863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435216 Affx-122933626 AX-123305556 17 23839023 TTTTTTCCTCAATGAGCATGGAAGTTGATAGCCTG[C/T]AAAATGTCCTTAATAAGTACCTAAAATAAATTCAC Y 2 1 2 1 101000 f 74 goat snp19704-scaffold199-69783 17 46800445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413769 Affx-122949931 AX-123284118 17 23875447 AATTATTTAATATTTCCAAGAATAAAAATAAAAGC[A/C]ATTCCAACACTATTTACTGCTAAAGAAAGGGCAAA M 2 1 2 1 101000 r 74 goat snp19705-scaffold199-106207 17 46762324 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415894 Affx-122948474 AX-123286243 17 23904338 TCTGTTTGTGCACATATATGCACATGCATATAAAC[A/G]TGTATTCCTTTTGGGAATTCATTGTGATCATATTG R 2 1 2 1 103000 r 74 goat snp19706-scaffold199-135098 17 46732993 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451665 Affx-122921590 AX-123321998 17 23936567 AAAGGAATAACCATAGTAGCAGGCTTGGTAAATAC[A/G]CCTGGGCCCAACAGGAACTGCCTCTCACTGAATCT R 2 1 2 1 201000 f 74 goat snp19707-scaffold199-167327 17 46699907 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414063 Affx-122949766 AX-123284412 17 23985761 ATGTAGTCACATGATATTCATCCTGACATTCTTGA[C/T]AGTATTGACTCTTTGATATTTCTATTTTCAACGCC Y 2 1 2 1 101000 f 74 goat snp19708-scaffold199-216521 17 46649719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799955 Affx-122944114 AX-385286881 17 24045405 TAAAGGATTTACATTTGTAAACAATTAGGAGGGTT[A/G]TTTTGCATGAGGAAGGGAAATCTTTCCTCAGGAAT R 2 1 2 1 102000 r 74 goat snp19709-scaffold199-276165 17 46589557 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419255 Affx-122946264 AX-123289603 17 24087968 ACGTTTCTGTGCTGATGGTTCTCTCTGCTTGGTAT[A/G]CTTATCCATGGTTTCCTTTCAACAGCATCAGTTTG R 2 1 2 1 201000 r 74 goat snp19710-scaffold199-318728 17 46546696 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409234 Affx-122953150 AX-123279585 17 24119352 TCAGTCTTGGGGTATGGACCAGGTAGATCCACATG[C/T]CACATCTGCTACATCAGACTAAGGAATTGATTCCA Y 2 1 2 1 101000 r 74 goat snp19711-scaffold199-350112 17 46515189 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775985 Affx-122965698 AX-190100951 17 24150775 GAAGACCTGGATAGTAAACAGAGTATTGCCTGTTA[C/T]GCTTTCATATATTTTAGACTGTATATTTGTGAATC Y 2 1 2 1 101000 f 74 goat snp19712-scaffold199-381535 17 46484721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799251 Affx-122934166 AX-385286181 17 24195708 CATGTGAATAAGTCTTACTTTAGGTTATGACAAAC[A/G]GAAAGATATGTTTAAAAAAGTCATCACTGGACAAA R 2 1 2 1 201000 r 74 goat snp19713-scaffold199-426468 17 46439756 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442230 Affx-122928301 AX-123312567 17 24231697 AAATCATTTACTTGTCAAGGCTCAAAAGAATAACC[A/G]CTAGTCTAAACTACTAGTATATATAACTACTAATA R 2 1 2 1 101000 f 74 goat snp19714-scaffold199-462457 17 46399441 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271985 Affx-1111833089 AX-519545753 17 24274026 AAGCCCAGGCCACGTGAGCAGGCCCTGGTGGATGG[A/G]ACACTGCCTGGGGGTGGGGGAGAGAAAGGAGAAAC R 2 1 2 1 303000 f 74 goat 17_24274026_AF-PAKI 17 24274026 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412134 Affx-122951096 AX-123282484 17 24328833 TCAGAAGGTTTTGCTCTCTTATTTTCTGCCATGTG[A/C]TTTCTTCTTATTTAAGAACTGCTTTCACTTTCAAT M 2 1 2 1 101000 r 74 goat snp19716-scaffold199-559593 17 46301796 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779875 Affx-122942344 AX-385266974 17 24384794 TATTAAATTTGACAATAGCAATCTGAAAACTAACA[C/T]AAATTATGAATTTGCTAAACCATGTTCAATCATTG Y 2 1 2 1 102000 r 74 goat snp19717-scaffold199-615554 17 46247156 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781065 Affx-122945321 AX-385268152 17 24419789 CATCCACCCTCAATATGTCGCTTCACTCTCCTTTA[C/T]GTCTCTATGTGTGTTTTACTTATCCAAAAAACCTT Y 2 1 2 1 101000 f 74 goat snp19718-scaffold199-650549 17 46212356 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396579 Affx-122962914 AX-123266934 17 24449376 TGTACATCTGTCTTGATATACTAATGTAGCAAATT[A/C]TTAGGAGAAGAGTTGTTTCATAGAATCTCATCTCA M 2 1 2 1 101000 f 74 goat snp19719-scaffold199-680136 17 46182508 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399808 Affx-122960278 AX-123270163 17 24480271 TGACAGAGGAATGGAAAACTATTAATTTTCTTCTT[A/C]AGTCAATAAAATAATCTTGCTTTTTGTTAGAAAAG M 2 1 2 1 303000 r 74 goat snp19720-scaffold199-711031 17 46150935 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386273 Affx-122970944 AX-123256631 17 24544357 TTGATTTAAATCCAGGAAAATTGGGAGGCAGACTA[G/T]CGAAGACTGAAGAACACCCTGTGTATCTCCTTCAA K 2 1 2 1 201000 f 74 goat snp19721-scaffold199-775117 17 46085390 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453927 Affx-122919495 AX-123324260 17 24575142 CTGTAAATGTTATAAAAGCACCAGTGATATATGAG[C/T]AGAAACTTTCAGAAAACCAAAATATAAAGATTTGC Y 2 1 2 1 101000 f 74 goat snp19722-scaffold199-805902 17 46054468 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801066 Affx-122944393 AX-385287980 17 24610413 TTCTGATACCCAGTTGCACACTCTTTCTTTGTAAT[A/G]TAACCCTTCTACCCAGATGAAGGTAGTCATGTGAC R 2 1 2 1 101000 r 74 goat snp19723-scaffold199-841173 17 46018689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422005 Affx-122943779 AX-123292352 17 24648598 CTAAAAGTAGGATAGATAGGTTTGGCCAAGTTTCT[A/G]CCAACCAGACAATTTTTTTCCTTAATGTATAAAAG R 2 1 2 1 101000 f 74 goat snp19724-scaffold199-879358 17 45979987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383330 Affx-122972687 AX-123253688 17 24686597 TGTGTTAAGGGTCTTCACAGGTATTCAAGTTACAG[C/T]AAGGTTATTAGTAAGGTGGACCCTAAGCCTATATG Y 2 1 2 1 101000 f 74 goat snp19725-scaffold199-917357 17 45939636 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399458 Affx-122961203 AX-123269813 17 24780207 CAACATCTTCTGGAAAAAAAATTCTTAACCTAAAG[C/T]AAACCCAGAAATCGTTATCACCAGTTACCACTTGG Y 2 1 2 1 101000 r 74 goat snp19727-scaffold199-1010967 17 45843934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773915 Affx-122970795 AX-385261054 17 24831444 GGTAACTCACAGCCCAGGCACTGATGAAAAAACAA[G/T]AATAATAATGAGATTAAGTGGAAGAAGTGTTGGCT K 2 1 2 1 201000 r 74 goat snp19728-scaffold199-1062204 17 45792683 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782332 Affx-122947104 AX-385269409 17 24866544 CACCTGGGAAGCCTACTATGGCAGTAAGATATTTC[A/G]TCAAGAAATATCTATTCTATGGGTTACTACAACTT R 2 1 2 1 201000 r 74 goat snp19729-scaffold199-1097304 17 45756573 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778151 Affx-122944718 AX-385265266 17 24922548 TATAAAACCATGGAATAACTAGATCTACAGTAGTA[G/T]CTATCAGCCTGAATAATGAAGTAAACTGAGTCAAG K 2 1 2 1 101000 r 74 goat snp19730-scaffold199-1153308 17 45710944 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770169 Affx-122941418 AX-385257336 17 24979904 GGGATGCAGTCTCCTACCGAAACTTACTTAAACAA[C/T]AGACACAAAGCAAATGACAGAGAATATTATGGAAA Y 2 1 2 1 202000 r 74 goat snp19731-scaffold199-1210664 17 45653350 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402289 Affx-122959103 AX-123272642 17 25027577 GGATACAATGGTGAAACAAAATTTCTTCCACCATC[A/G]ATATCACCTTTTATTCTGAGGAGAATTGCCACAGA R 2 1 2 1 101000 r 74 goat snp19732-scaffold199-1258337 17 45605528 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450761 Affx-122921845 AX-123321095 17 25098765 AAACAATAAACTGCTCTGTATCATTCAGAAGCTAC[A/G]TATCACTCAGAAGCATATTAGCATACCACTTTTCT R 2 1 2 1 101000 f 74 goat snp19733-scaffold199-1329525 17 45533460 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426183 Affx-122940581 AX-123296529 17 25166029 TATCTTTGCTATCTAGCAGACATGTCATTAATACT[A/G]TTTATATGCCTGCTTTCTTATAAAGTCCTTAGAAA R 2 1 2 1 101000 f 74 goat snp19734-scaffold199-1396789 17 45465149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421838 Affx-122944302 AX-123292185 17 25228758 CAGCATTGCTGTAACATATTAGGACCTGCATGAAA[C/T]GCCACTGGCCACCCACTTTAGGAAATCTCTCAGCA Y 2 1 2 1 101000 f 74 goat snp19735-scaffold199-1459518 17 45401819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418072 Affx-122946611 AX-123288420 17 25263330 TAATCTCTGGTTCTATCTATGTTGCTCTAAATTGC[A/G]TTATTTCATTTTTTTAATGGCTGAGTGGCATTTCA R 2 1 2 1 103000 f 74 goat snp19736-scaffold199-1494090 17 45364777 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763385 Affx-986697914 AX-385251274 17 25298649 GCACCCACAGATAAGACACTCACACAGAACATACA[C/T]GAGGAGCAGAGAGATCACAAGCAAAAGGCCCACAT Y 2 1 2 1 600010 f 74 goat 17_25298649 17 25298649 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 38396676 Affx-122962838 AX-123267031 17 25298917 CACAAGATCAAATGCCAGTAACTTACTTAGGGAAC[A/G]TAGATGTTTACAGAGACTGGGAAGCATGTATACAG R 2 1 2 1 101000 f 74 goat snp19737-scaffold199-1529677 17 45329150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431958 Affx-122935964 AX-123302299 17 25335757 CACAGAGTCATACATGACTGAGCGACTGAACTGAT[A/G]CTGATACTGAAACCATCAAAAAAAGAGACAGTTTT R 2 1 2 1 201000 r 74 goat snp19738-scaffold199-1566517 17 45292022 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415825 Affx-122948883 AX-123286174 17 25372349 AATTAATATGTCATCAGGAATGGGTTTTGTGAGCG[C/T]GTGTTGGTGGACAACCAGAAGGAGTATCGCACACA Y 2 1 2 1 101000 f 74 goat snp19739-scaffold199-1603109 17 45254926 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415066 Affx-122949473 AX-123285415 17 25430444 ATTTCATGAATGATACACTCATCATTCAGCAAATC[A/G]TCTATCTACCTTTGTGGCTTTGGGATTAGAGAGCA R 2 1 2 1 101000 r 74 goat snp19740-scaffold199-1661204 17 45195837 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437059 Affx-122933092 AX-123307397 17 25465627 CTAGGCAAATAAAATAAATGAAGTTAACTTGGATT[A/G]ATATTACATAACTGTGAACTAGAAGCTGAGACAAA R 2 1 2 1 101000 r 74 goat snp19741-scaffold199-1696387 17 45160535 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393478 Affx-122965832 AX-123263834 17 25503010 GGGAAAGACCATTAATTAATTAATTTAATTAACAG[C/T]AAGAAGAGAGGATATGGTTATCATATGATAATTAT Y 2 1 2 1 303000 r 74 goat snp19742-scaffold199-1733770 NW_017195985.1 6835 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789077 Affx-122931180 AX-385276090 17 25540171 TTAAAATTATTGATGACATCCTGAGGGATATAAAT[A/G]CAGTGAAAATGAATTTGAATTCCCATTTAGTGTCA R 2 1 2 1 101000 r 74 goat snp19743-scaffold199-1770931 17 45064036 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789619 Affx-122944886 AX-385276628 17 25590931 TACCCTGTGGATTGGTAGGTCACTTTTGATAATCT[A/G]TTGTGAGTACATGAAAGGGCCATGAGGTTGAGAAA R 2 1 2 1 101000 r 74 goat snp19744-scaffold199-1821691 17 45012516 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400326 Affx-122960054 AX-123270681 17 25626043 GGTCGCAGAGTCAGACACGACTAAGTGACTAACAC[A/G]CTAAGCACACTGAACAGAACCAACTGTCTCCTTCC R 2 1 2 1 101000 r 74 goat snp19745-scaffold199-1856803 17 44977150 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432223 Affx-122936368 AX-123302564 17 25659852 CATGACGCCTCTTATAAATATAATGGCTCTGGATA[G/T]CTCATAATTTTCTCATCATTAAAATATTTTAAAAC K 2 1 2 1 103000 f 74 goat snp19746-scaffold199-1890612 17 44942273 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452856 Affx-122920716 AX-123323189 17 25715510 TACTCACTGAAATTGTTATATTAAATAGAATATTA[C/T]GAGGTATTCTGGTATTTTTGAAACTGAACTTGAAT Y 2 1 2 1 303000 f 74 goat snp19747-scaffold199-1946270 17 44885924 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450964 Affx-122921748 AX-123321298 17 25774582 TTTATAATTGAGACATGCTAGGGTTAAAGGAATTA[C/T]GTGACTTTTTCCGAAATCATGTAATGAGAATGACT Y 2 1 2 1 101000 r 74 goat snp19748-scaffold199-2005342 17 44826447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387567 Affx-122970280 AX-123257925 17 25820711 TTTCTTACCTAGTTCTTTCAAAATAATATTAATTT[A/G]GCCTCTGGCATTTCATAAAAACATTTAGGTTAATT R 2 1 2 1 101000 r 74 goat snp19749-scaffold199-2051471 17 44779609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430470 Affx-122937253 AX-123300811 17 25890261 TCTGAACAAATGCTTAAGTGTCATTGCTATTGCTA[C/T]CTTATTAAATATTTAATACTGCCTAATAAACACAA Y 2 1 2 1 103000 f 74 goat snp19750-scaffold199-2121021 17 44708914 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376839 Affx-122977912 AX-123247198 17 25931331 AAAAATAAAAGTGAACTGATGACTATTTTTGGCTT[A/C]TTGAGGCTCTTTTCAGTAGAGAACATGGCTAAATA M 2 1 2 1 101000 r 74 goat snp19751-scaffold199-2162091 17 44671663 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391436 Affx-122966750 AX-123261793 17 25978688 TCTTAAAGACAGAAAATTATGTGTACATATACATA[C/T]ATGGGAGTGTATATAATAATTAAATCTTTAGGAAG Y 2 1 2 1 103000 r 74 goat snp19752-scaffold199-2209448 17 44623753 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440106 Affx-122929710 AX-123310443 17 26012493 GCCATGTTCCAGTACAATTTTATTTACAAAAACAC[A/G]TGGCAGCTAGGATTTGGCCACTGGCTGTAGTTGGA R 2 1 2 1 103000 r 74 goat snp19753-scaffold199-2243253 17 44589756 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448671 Affx-122923334 AX-123319007 17 26116946 TTTACTTTTCTCTTTTCTATGGTATCAGTAACAGG[C/T]GGCCAGTTTCTAGTCTCCAGCTTTGTGGCTGATGC Y 2 1 2 1 201000 f 74 goat snp19755-scaffold199-2347706 17 44483464 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774258 Affx-122951871 AX-385261394 17 26158999 TGATTTCATCTCAGCTTCTTATGTAGTGATCACAA[C/T]GTATTATGTACATTTTCGTACTTGGTTACAAGTAA Y 2 1 2 1 101000 f 74 goat snp19756-scaffold199-2389759 17 44441336 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407710 Affx-122954567 AX-123278061 17 26200403 TCCAGGAAAGAAAACATTTTCTCAAAGGCATTTTT[A/G]TAGTTAAAATAGTAAAATCATAAACTTTACTATTA R 2 1 2 1 303000 r 74 goat snp19757-scaffold199-2431163 17 44399429 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404405 Affx-122956782 AX-123274757 17 26258057 AATTCTAACTGCCAGACCTCAAATGATCTGTTATG[A/G]AATTTAAAATGTCCAGAAACTATAAATAGGCCTCC R 2 1 2 1 201000 r 74 goat snp19758-scaffold199-2488817 17 44341275 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781040 Affx-122950651 AX-385268127 17 26286606 TGTAGTCCCTGGGTATGAAAATGTTTAAAGTAAGT[A/G]TTACTGCTTAAATGAGAAAAGGGTAAATCAGAACT R 2 1 2 1 101000 f 74 goat snp19759-scaffold199-2517366 17 44312660 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776307 Affx-122978681 AX-385263435 17 26335636 GAGGTTCAGTGGTCTCTGACATGTCAGAATATCCA[C/T]GCTAAAGTGAAAAAAACACATAGTTATGTGTTTTG Y 2 1 2 1 201000 r 74 goat snp19760-scaffold199-2566396 17 44263120 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274987 Affx-1111834527 AX-519548569 17 26342817 ATGCCTCTGGGACTTGATCCCCATGCCGGGCCCTT[A/C]TTCCTGTTGGCTGCTCCCCTGCAGGGTCTGGGCCC M 2 1 2 1 202000 r 74 goat GoatD01.039891 17 26342817 T G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386623 Affx-122970229 AX-123256981 17 26426427 TTCCTCTATCTCTATGTGTACACAGTATCATTTCA[C/T]GACTATGTGATATGGTTCTAGTATATCCAAATTTA Y 2 1 2 1 101000 f 74 goat snp19762-scaffold199-2657187 17 44165284 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434962 Affx-122933846 AX-123305302 17 26484770 GAATAATTGCAAAGGGTACCTTAGAGATAGAATTT[A/G]CAGAATGAGAAGGGTGAATGGCCGTTATGCAAAAA R 2 1 2 1 201000 f 74 goat snp19763-scaffold199-2715530 17 44109762 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391188 Affx-122967424 AX-123261545 17 26541472 TGTACTCTGGTCAGACTCTATCACCTATCTCACTG[C/T]GGGTGGCAACTTCAGGAATTAGGGTTAGCTCAGAA Y 2 1 2 1 101000 f 74 goat snp19764-scaffold199-2772232 17 44052452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453031 Affx-122920088 AX-123323364 17 26571620 TATTTCACTATTAGGACTATTGCACACTATTAGGA[C/T]TGTACAAACAAGAAACTGAAGTTGATGAAACAACA Y 2 1 2 1 101000 f 74 goat snp19765-scaffold199-2802380 17 44022560 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385698 Affx-122971119 AX-123256056 17 26611788 CACTGTAATTCTGGAATTAGGAACTGATTTTGTAA[C/T]TGAACAGTGAATAGAAGGTGAGGTACAGAAATACT Y 2 1 2 1 101000 f 74 goat snp19766-scaffold199-2842548 17 43982763 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422863 Affx-122943087 AX-123293209 17 26659627 TGTTATCTAGGTTACATAGATGGAGGATAATGAGG[A/C]GATCATGGAGAAATAGAGGGAAAATCAAGGCAGGG M 2 1 2 1 201000 f 74 goat snp19767-scaffold199-2890387 17 43934833 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277089 Affx-1111835736 AX-519550596 17 26659791 CATGACATGAAAATGGCATGGCCAGTTTGATAGAA[C/G]TAGGTGGAGGGTGCACAGGTTTCTGTTCTTTCTAA S 4 1 2 1 202000 f 74 goat Random2.2K-1660 17 26659791 C G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431680 Affx-122936788 AX-123302021 17 26701540 CAAGCAATTCACACAGTAATAGATTGGAGGGAACA[A/G]CATTATGTAAAACAAAGCAACAAGCCATCTTATGC R 2 1 2 1 101000 f 74 goat snp19768-scaffold199-2932300 17 43896265 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790787 Affx-122925504 AX-385277787 17 26747105 TAGCTGTTTATTTGAAAGAATGCTTTTCAGCTTCT[A/G]TTCTGCCCTCAACCAGCACTGACTCTACTATGATT R 2 1 2 1 202000 f 74 goat snp19769-scaffold199-2977865 17 43850311 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271820 Affx-1111833090 AX-519545606 17 26779782 TGGAAAATAGCCACTGGGGTCTGGGGGGCAGAGAA[A/G]GGACCTCACAGCAGGTGACCAAATGCATTCTTCAT R 2 1 2 1 102000 r 74 goat 17_26779782_AF-PAKI 17 26779782 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450356 Affx-122922105 AX-123320691 17 26782502 GGACATGAGACTTACAAGAACTTATAAACTGAAAA[C/T]GCAAATTTTTTTTCTTAAAATGAGGTGCTATGTAA Y 2 1 2 1 201000 f 74 goat snp19770-scaffold199-3013262 17 43807000 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427327 Affx-122940128 AX-123297670 17 26824381 GGGAAAGTGTACAGATTATTAGCTAAAGGGAGATG[A/C]GAATTCAAGGGAAGGTTCTGTTTATTTTTAATATC M 2 1 2 1 101000 f 74 goat snp19771-scaffold199-3055141 17 43764652 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430251 Affx-122937308 AX-123300592 17 26862112 ATACTTTAAAATTCATATAAAAGGAAGATTATTAT[A/G]CAAAACCAACCCTTCCCTTACATAAGGTACAGTTC R 2 1 2 1 202000 f 74 goat snp19772-scaffold199-3092872 17 43726851 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773402 Affx-122969034 AX-385260544 17 26922663 AATTTTTTACTGTGAAAATCTAATCTAACTTGGCA[C/T]GTAACTAAACCATTGCTATGATAATGGTATTATGA Y 2 1 2 1 101000 r 74 goat snp19773-scaffold199-3153423 17 43665713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774875 Affx-122963872 AX-385262009 17 26957798 TTGAAATGTACGTTCCACATACTATTCTTATACTA[G/T]GAGATACTTCAAGGACGTAGTTTATACATGACCGA K 2 1 2 1 201000 f 74 goat snp19774-scaffold199-3188558 17 43630791 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799994 Affx-122965351 AX-190166211 17 27022535 AATTACAGAATTACTTCAAAAAATATCTTGTGAAC[A/G]TCTGTAATATTCCTCACATTATATAAAGTGTTAGG R 2 1 2 1 101000 f 74 goat snp19776-scaffold199-3253295 17 43565504 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396391 Affx-122963021 AX-123266746 17 27078503 GTCTCCCTTTTATGGTACTGTTTATTTTTGTGTAA[C/T]ATTATCTACTCTTTGTGCTTACCTCTAGGAAATTT Y 2 1 2 1 101000 r 74 goat snp19777-scaffold199-3309263 17 43510745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377497 Affx-122977492 AX-123247856 17 27123567 AGCAAATAACTCAGATTCATCCACAAAGTTTTGAC[A/G]TATGTACATATTCTAATGAATAAATTTATCTGAAT R 2 1 2 1 101000 f 74 goat snp19778-scaffold199-3354327 17 43466999 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792517 Affx-122920219 AX-385279498 17 27176642 ACTTCCATATAGCAGAAAGACTACAGGTGACAATC[A/G]ATAACAATCATTTACCAGTTAAAACTAAGTACACG R 2 1 2 1 101000 f 74 goat snp19779-scaffold199-3407402 17 43413219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451723 Affx-122921548 AX-123322056 17 27213345 ATGATCTTTTTACTTGAGAACAAGCTCAACCTCTT[A/G]TTGTTTATTTCTCTGAGTATGTGTTGCTTTTTCTT R 2 1 2 1 201000 r 74 goat snp19780-scaffold199-3444105 17 43375419 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379131 Affx-122976739 AX-123249490 17 27263304 CATGTGAATCTGAGAAGACAGAAAATGGGGACAGG[C/T]AGTATAGCAACCCTTGCAAAGGATTTTTCTATAAA Y 2 1 2 1 101000 r 74 goat snp19781-scaffold199-3494064 17 43324712 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798477 Affx-122951021 AX-385285410 17 27318536 AGTCCATGAGTGTTCACCAGAATATCACTAGGGAA[C/T]AGACTCATGCCTGGCGCTTAATGGGCTTCAAGTTC Y 2 1 2 1 201000 r 74 goat snp19782-scaffold199-3549296 17 43270670 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385853 Affx-122970996 AX-123256211 17 27385981 AAAAAAATAATCATGTTTCTGTCTTTATAGAAATG[C/T]GAAACTACTTTTTGGAGTAAAACATTCAGCAAACA Y 2 1 2 1 101000 r 74 goat snp19783-scaffold199-3616741 17 43204362 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436198 Affx-122932596 AX-123306537 17 27434834 AGGCCAGTGCTCAGTTATGAGGAAAAGGGCAGGTG[C/T]AGGACTGTAGCCCTAAGATAGCTGACAAAATGGAG Y 2 1 2 1 101000 r 74 goat snp19784-scaffold199-3665594 17 43154974 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765677 Affx-122972926 AX-385253141 17 27468214 CTGGGCCAGGGCATGTCTAAAAAATTCAGGGACTA[C/T]CACCATCTTGGGAATTCTTCCTTAGCTTAACCTCA Y 2 1 2 1 101000 f 74 goat snp19785-scaffold199-3698974 17 43121541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794754 Affx-122957877 AX-385281714 17 27533632 TACGAAACCCATCTTTATTCAATCTTTAAATGTAA[A/G]TTGTATGCTGGTGACACAAACTTTTCTTTGCAACA R 2 1 2 1 201000 f 74 goat snp19786-scaffold199-3764392 17 43053452 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403679 Affx-122958056 AX-123274031 17 27584615 ATCACTTCTCAAAATGGGTTTTCTCACTCACATAC[A/G]TCTCTGATGATGTAGCCACGCGTTCTGGGAAACAA R 2 1 2 1 201000 f 74 goat snp19787-scaffold199-3815375 17 43002206 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789729 Affx-122960499 AX-385276737 17 27646136 AATAATCCATTTTATCAGATAAGCATAACAGACTA[G/T]AACTAAATCCAGAGAAATATTAGTCGATAAGTCAC K 2 1 2 1 101000 r 74 goat snp19789-scaffold199-3876896 17 42941009 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400685 Affx-122959944 AX-123271040 17 27676776 AGCAAGAATTGGGATTTGAATAATAATTTCACCTA[A/C]AGACATTTCAGACATTATTTTTGTCAGCATCTGAA M 2 1 2 1 101000 f 74 goat snp19790-scaffold199-3907536 17 42910447 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771935 Affx-122958161 AX-385259091 17 27715470 CCCAGTAATCCATGGATATTAATATTTCGGTTTAT[C/T]AGTTTTGTGGATTGGTGAGCTTGACTGAGTTTCTT Y 2 1 2 1 101000 r 74 goat snp19791-scaffold199-3946230 17 42870949 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408577 Affx-122953663 AX-123278928 17 27751235 AATAACATTTCCTCTTTGAAAGTTCCCTTGACATA[C/T]CTACAATACAAGGAAAGGAAGATTTTAATGCTTCT Y 2 1 2 1 101000 f 74 goat snp19792-scaffold199-3981995 17 42835135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769014 Affx-122923465 AX-385256189 17 27787917 ATACAAATAATACTATCCTATTAAAAAGACCAGGT[A/G]TTTTCTGTTCCAAACCTGGCAAAAATATGCTTGTT R 2 1 2 1 101000 r 74 goat snp19793-scaffold199-4018677 17 42797417 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772672 Affx-122932151 AX-385259819 17 27840361 GACTATTTTGGATGGAGACAGGATCCAGATTAAAA[G/T]ACTCCTTGCAGAGGAAAGTAGGAAAGGGAATTCTA K 2 1 2 1 102000 r 74 goat snp19794-scaffold199-4071121 17 42743958 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414715 Affx-122949270 AX-123285064 17 27881038 CAGAAGCCTGGAAAAGGAACCTCATGGAGCTGGAC[A/G]CAGAACTTTGAAGAAAGACTTTTTCTTGCGGTACT R 2 1 2 1 101000 f 74 goat snp19795-scaffold199-4111798 17 42702272 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392546 Affx-122966094 AX-123262903 17 27911896 GTAGAGTACAAGTGAAAGACTTCTTTATCACGATT[G/T]CTTACATATATGTATATACTATGTATACATATATA K 2 1 2 1 103000 f 74 goat snp19796-scaffold199-4142656 17 42671347 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392734 Affx-122966020 AX-123263091 17 27940668 CTCTCTGTGTTTATGTGTGTGCATATGATAAAGAG[C/T]GAAATAGAAGCCTTAGTGGTTTTTAAGCTTTAAGA Y 2 1 2 1 201000 r 74 goat snp19797-scaffold199-4171428 17 42642230 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389125 Affx-122968557 AX-123259483 17 28072460 GCAGCCTTGATCACTGCCAGCCCAGCATACTGAAG[C/T]ACCCAAAATCAGATGATCAGAGATGATTGTGTTAG Y 2 1 2 1 201000 r 74 goat snp19799-scaffold199-4303220 17 42509012 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768934 Affx-122956302 AX-385256109 17 28127686 TATTCTCTATCATTTTGGATTATAAGAACCATGTG[A/G]CAATAAAATCTACTCTTTATATCCTCCGTGGGTAT R 2 1 2 1 101000 r 74 goat snp19800-scaffold199-4358446 17 42453573 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782900 Affx-122921994 AX-385269970 17 28222627 AAAAAATTAAATATTATAGTAAAGCAGCAGAGAGA[G/T]AGCCTGAAACCACTTACTTTCTGAATGAGAAAGAA K 2 1 2 1 101000 r 74 goat snp19803-scaffold199-4453387 17 42359107 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403893 Affx-122957492 AX-123274245 17 28260528 CACTATTTGGATTTGTGAGAACAGTTATTTGTTAA[C/T]GATTCTTCTTTCCTCAGTGAGTGTTTCATACCTTG Y 2 1 2 1 101000 f 74 goat snp19804-scaffold199-4491288 17 42320881 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409112 Affx-122953314 AX-123279463 17 28295090 TCCTGGTATTCACCCTGTGGTGGAGAATTTAAAAA[C/T]GGATCCCAAGAGATGATCAAGAGGCACAACTACAT Y 2 1 2 1 101000 f 74 goat snp19805-scaffold199-4525850 17 42285847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413076 Affx-122950962 AX-123283425 17 28342447 TCTACAAGTAAACTATGTTTAAGGATTCATCACCA[C/T]TCAGGTCCTCCTTACATTATTATAAAGTATTTGAA Y 2 1 2 1 101000 f 74 goat snp19806-scaffold199-4573207 17 42237168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789405 Affx-122928169 AX-385276415 17 28376339 ATGCCTATTATACAGCCAATTAAAGACATCGAGAA[G/T]CCACTTAAATATATGGCTTGGAGACATATTCAGCT K 2 1 2 1 101000 r 74 goat snp19807-scaffold199-4607099 17 42203384 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450722 Affx-122921876 AX-123321056 17 28408211 TAGAAGACAATGGAAAGAAATTATTTCCAACCTAG[C/T]ATCCCATAACCAACTAAACTACTATTCAAGTGCCA Y 2 1 2 1 101000 r 74 goat snp19808-scaffold199-4638971 17 42170812 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797728 Affx-122953002 AX-385284667 17 28449360 AAGAAAAGAGGGAAAGAAGGGTAAGGGATAAGAGA[C/T]GGGTATCAGCTGTGTCTATAAGGATTTATTTTTAA Y 2 1 2 1 101000 f 74 goat snp19809-scaffold199-4680120 17 42129473 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798891 Affx-122959728 AX-385285821 17 28490400 TAATTCACAGACAATACGGAAGTCAGATGCAAGCA[C/T]GGGAATGCAATTATCAAAATTCAAACTGTAAAAAA Y 2 1 2 1 101000 f 74 goat snp19810-scaffold199-4721160 17 42087594 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777137 Affx-122977861 AX-385264260 17 28541349 GATGCTTGTAAGGAAGCAAAGTTGTTTTTGTTTAA[C/T]GACTATGAATTCTTTGACCATAGAAATTGCCTTTG Y 2 1 2 1 202000 f 74 goat snp19811-scaffold199-4772109 17 42036413 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429013 Affx-122938331 AX-123299355 17 28625233 GCTGAATGCTGTTCCCAAACTGTCCCCCGAAACCA[A/G]TTTCCCTGGGTGCCTTCCTTGGAGGGGACTGTAGA R 2 1 2 1 103000 f 74 goat snp19812-scaffold199-4855993 NW_017212232.1 10380 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772178 Affx-122937085 AX-385259333 17 28663055 AAGCTGAGTTATAACACTGGAAATAACTTTGTATT[A/C]CTATTCACTATACCTTAAAGTTAATAAACATGATA M 2 1 2 1 101000 f 74 goat snp19813-scaffold199-4893815 17 41928441 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772991 Affx-122955453 AX-385260135 17 28705499 AGTTTCTGAGGTAGCTAAATCTGGGTGGTGATGCT[C/T]GTACGTCACTATATGTATAAAAATTGAGTTGTACC Y 2 1 2 1 101000 f 74 goat snp19814-scaffold199-4936259 17 41885550 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439968 Affx-122929813 AX-123310305 17 28799707 TCCATTCATGTTGGAAGGCCGGATTCCCCAGCATA[C/T]GCACTAGTGTTTGGCTCTGGAAATGAGTCGCCAGA Y 2 1 2 1 101000 f 74 goat snp19816-scaffold199-5030467 17 41789575 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404333 Affx-122957002 AX-123274685 17 28905228 GCATCACTGCTGTCTTGGAAGCCATTGTAATTTGC[A/G]TTGAGGAGTTTCCTTCTGCAGTCTTTTCTACTCAA R 2 1 2 1 101000 f 74 goat snp19818-scaffold199-5135988 17 41683983 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422854 Affx-122943094 AX-123293200 17 28940588 CCAATGAAATTCTGAGTTTTAACATGATGATGACT[A/G]TAGAAGTCTTTTTAAAAGACACAGCAAGATATAAG R 2 1 2 1 101000 f 74 goat snp19819-scaffold199-5171348 17 41648618 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441849 Affx-122929043 AX-123312186 17 28998633 TCTCCGGAGCACAAATAAACAAAATGATCATGTAC[A/G]TTGGTAAATGTGTTTGCATTATTTAGCCAAGCCAG R 2 1 2 1 201000 r 74 goat snp19820-scaffold199-5229393 17 41590667 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426351 Affx-122940261 AX-123296697 17 29037790 TTGTCCGAAAGGGGGTGGGTGGCCCCATGATTTGA[A/G]GAGCTCTGTTTCCTCTGAATGTACATTCAGGACCC R 2 1 2 1 201000 r 74 goat snp19821-scaffold199-5268550 17 41551417 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414882 Affx-122949135 AX-123285231 17 29071387 TGGGACTATAAACACCAATCTGGACATAACGGAGC[A/G]CATTTAGCCCTCTTGTTTGGAACTGTAAGGAAAAT R 2 1 2 1 101000 f 74 goat snp19822-scaffold199-5302147 17 41517805 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448008 Affx-122923731 AX-123318344 17 29137648 TCAGTTACAAATCAAGTCATCATGACGAATGTTGA[A/G]GAGGTATCCAGAGATCTTCCCAACGCTGTAGTTTC R 2 1 2 1 201000 f 74 goat snp19824-scaffold199-5368408 17 41450182 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797788 Affx-122950362 AX-385284727 17 29168933 GTTGATGTGATTAACATTACCTAATTTCTGGGATA[C/T]GCCCAATTTCTGTAGGGCAAAAGAATGTTTACCAG Y 2 1 2 1 101000 r 74 goat snp19825-scaffold199-5399693 17 41418970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802505 Affx-122963188 AX-385289409 17 29198285 CAGATGAGATGCTGAGACACCTAACTTCCTGAGGT[C/T]GAATGAGACCATCAGAAGTCAGTATTTGTAGAGGT Y 2 1 2 1 101000 f 74 goat snp19826-scaffold199-5429045 17 41389663 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777224 Affx-122954209 AX-385264347 17 29269812 TGAAGCTGAAGAAAGTTAAGCAGCGTCACCAAGTC[A/G]CTCCATTAAAATATGGGAAGGTTGGTCTTACATGC R 2 1 2 1 101000 f 74 goat snp19827-scaffold199-5500572 17 41322242 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782662 Affx-122959836 AX-385269735 17 29304272 TTTTTGTGGAATCTCATGGGACCACTGATAAAGTG[C/T]AGGTTTTGTTGTCAGAACGCCCTGACTGAGTCAGA Y 2 1 2 1 101000 r 74 goat snp19828-scaffold199-5535032 17 41287434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382975 Affx-122973352 AX-123253333 17 29336336 CCATAGAGCAATTTTGACCTGAGTGCCTATTTAAA[C/T]AAAATTTGCAGGAACAACAGCTTACAGGCTTCACT Y 2 1 2 1 201000 f 74 goat snp19829-scaffold199-5567096 17 41255927 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271989 Affx-1111833091 AX-519545757 17 29368611 TTATAGAGGTATAATTTGTACATGCTGCTGCTGCT[A/G]CTAAGTCGCTTCAGTCGTGTCCATCTCTGTGCGAC R 2 1 2 1 103000 f 74 goat 17_29368611_AF-PAKI 17 29368611 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433505 Affx-122935021 AX-123303846 17 29380262 ATGAGAGTGGACATGGATAAGTCGATGGACAACAG[C/T]AAAGGCGCCATCTAGCTCATTCAACTAAAACATGT Y 2 1 2 1 101000 f 74 goat snp19830-scaffold199-5611022 17 41211677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778077 Affx-122957805 AX-385265193 17 29413092 TTATATCAGACTGAAATTGAGTGCTGACATTGACT[A/G]CAAATGATTGTGAGGTAACTTTTAGCATGACACAA R 2 1 2 1 101000 f 74 goat snp19831-scaffold199-5643852 17 41178588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784971 Affx-122976735 AX-385272018 17 29496067 CTTTGCTACATTTCCTATGTTTCTATCTCTGGTAG[C/T]AAACTTTCTGGCAAAAATTTTATGGATGGAATTCT Y 2 1 2 1 101000 f 74 goat snp19832-scaffold199-5726827 17 41095395 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441758 Affx-122929117 AX-123312095 17 29529591 TGCAAGCCTCTACCACAAAATACTCAGCCCAGGCC[C/T]GTACATCAAACATCTCTGTAGAGGCCTTATGCTTG Y 2 1 2 1 101000 r 74 goat snp19833-scaffold199-5760351 17 41062374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449415 Affx-122922693 AX-123319750 17 29564349 TGCCACTTCCTAGAAAGGGCGTCGAGCCGCGGAGC[A/G]CCTTTGAGCCTGCGGGTTCTGGTGAATGTGTTAGA R 2 1 2 1 101000 r 74 goat snp19834-scaffold199-5795109 17 41027869 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443422 Affx-122927372 AX-123313759 17 29703343 GACTGACTGCTTATGACAGGAAACAAAACCAAACA[C/T]ACCATGGATTTATTTTAGTAATAAAACGAAGGGCC Y 2 1 2 1 101000 f 74 goat snp19836-scaffold199-5934103 17 40888133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442753 Affx-122927755 AX-123313090 17 29733825 ATATGCAGATGGAGAAAGAGGAAGGACTATTTAGA[C/T]AGGGTGGTTAGGTCAAACTCTAAGATATTAGGACA Y 2 1 2 1 101000 r 74 goat snp19837-scaffold199-5964585 17 40865553 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436655 Affx-122932478 AX-123306993 17 29808950 TTTGGCTTTGGTGACGGTTAGCTTTTTGGGGTTTA[C/T]GTAGATATTCACATCTTTGTGCTGCTGCTGGACAA Y 2 1 2 1 101000 f 74 goat snp19839-scaffold199-6039710 17 40790363 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399423 Affx-122961231 AX-123269778 17 29841666 AGTTTTGGTAGATGTTGCCAGTTTCCACTGAATGG[A/C]TTGTACCATTTTTCCGTCAGCCACCTGAAAAGTTT M 2 1 2 1 201000 r 74 goat snp19840-scaffold199-6072426 17 40757478 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774417 Affx-122952117 AX-385261553 17 29923359 AGAGGCAGAGCAAAGACCGAAACTTAGGTGTGTAT[A/G]TATTCATTACCCATGATCTTAATCATTCTGCTGGG R 2 1 2 1 101000 f 74 goat snp19842-scaffold199-6154119 17 40674761 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447702 Affx-122924613 AX-123318038 17 29963414 TTCTCTCTTTATTAATGATTTCACTGTGTCCAGAG[C/T]GTCTTTTCCTTACTCTGTGCAACTAGGACTACTGA Y 2 1 2 1 101000 r 74 goat snp19843-scaffold199-6194174 17 40632743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445087 Affx-122926207 AX-123315424 17 30021096 CTTGCACTTCTGTGGAAAAGATCCTTCACTCTGTC[A/G]TTGGGCATGGTACTGGTAGCTGGAGTGTTACCTCT R 2 1 2 1 201000 r 74 goat snp19844-scaffold199-6251856 17 40574571 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787220 Affx-122951519 AX-385274246 17 30055544 ATAATATTACCAAGTTGGTGAAGTATCAATATTGT[A/G]CTTATTGATAACTGTGGAAACAAAAAAAATGTAAT R 2 1 2 1 201000 f 74 goat snp19845-scaffold199-6286304 17 40540333 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444281 Affx-122926767 AX-123314618 17 30085453 TGTCCAAAGACCCTTAGAAACATAGCTGGACATGT[A/G]TAGACATTGTGAGACTTGGTCATGCAGGGGTCTGA R 2 1 2 1 201000 f 74 goat snp19846-scaffold199-6316213 17 40510372 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401486 Affx-122958951 AX-123271839 17 30132900 GTTAGAATGCTGACTGAGCAATTTGTCAGAGAGGT[A/C]TTGGAGAGGAACAGAAGTGAAAACTATATCATGGT M 2 1 2 1 101000 f 74 goat snp19847-scaffold199-6363660 17 40461374 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803398 Affx-122929127 AX-385290229 17 30162418 ACAGAATTTGTCTTCAGAACTCCAACTTTTTAGCC[A/G]TAGCACATCTAGTTTTTGTTTATTGGCAACCTAAA R 2 1 2 1 101000 r 74 goat snp19848-scaffold199-6393178 17 40430958 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379929 Affx-122975661 AX-123250287 17 30202942 GGCACCTTCAGCCTTCTAACAATTATTTCTGATGT[A/G]CTCTCATTTGTCATTGACAGGGTTACAAGGGGTGT R 2 1 2 1 101000 r 74 goat snp19849-scaffold199-6433702 17 40389953 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782168 Affx-122948418 AX-385269246 17 30256840 CTTGGGGTAGAGGTGGCAAGAGGGGAGAATATAGC[C/T]GTTCTCCTTTTGGAAGCTGTAAGAGAGTTTTCCAA Y 2 1 2 1 101000 f 74 goat snp19850-scaffold199-6487600 17 40335871 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413084 Affx-122950956 AX-123283433 17 30297321 TTAAATGGTTCTAATTTGAGTTTCTTACCAAATGC[A/G]CATCTTAAAAAGCTGGTTAAAGTGTATAAAAAGTT R 2 1 2 1 101000 r 74 goat snp19851-scaffold199-6528081 17 40294960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476327 Affx-1251763834 AX-586011744 17 30317353 CATTTTGGTGACTCTCCATTCTTGGTCATTTTTTT[-/AAAATTAAAGTGTCCGAGAGAGGGAAAGATGGCGGAGGAAATAAATAAACTTACAGGCACCAGAAAAATAAAATTAAATT]AAATTAAAGTGTCCTTGTTTTACAAGGTTGTGTTA - 8 1 4 1 20000 f 74 goat SV_210 17 30317353 - deletion junction SV-TF-chip 539476580 Affx-1251763834 AX-586011966 17 30317353 CATTTTGGTGACTCTCCATTCTTGGTCATTTTTTT[-/AAAATTAAAGTGTCCGAGAGAGGGAAAGATGGCGGAGGAAATAAATAAACTTACAGGCACCAGAAAAATAAAATTAAATT]AAATTAAAGTGTCCTTGTTTTACAAGGTTGTGTTA - 8 1 4 1 20000 r 74 goat SV_210 17 30317353 - deletion junction SV-TF-chip 562165638 Affx-1251763834 AX-606941048 17 30317353 CATTTTGGTGACTCTCCATTCTTGGTCATTTTTTT[-/AAAATTAAAGTGTCCGAGAGAGGGAAAGATGGCGGAGGAAATAAATAAACTTACAGGCACCAGAAAAATAAAATTAAATT]AAATTAAAGTGTCCTTGTTTTACAAGGTTGTGTTA - 8 1 4 1 20100 f 74 goat SV_210 17 30317353 - deletion junction SV-TF-chip 562165812 Affx-1251763834 AX-606941221 17 30317353 CATTTTGGTGACTCTCCATTCTTGGTCATTTTTTT[-/AAAATTAAAGTGTCCGAGAGAGGGAAAGATGGCGGAGGAAATAAATAAACTTACAGGCACCAGAAAAATAAAATTAAATT]AAATTAAAGTGTCCTTGTTTTACAAGGTTGTGTTA - 8 1 4 1 20100 r 74 goat SV_210 17 30317353 - deletion junction SV-TF-chip 38423980 Affx-122942124 AX-123294326 17 30330983 AAGAAGTCCTATTAAGAAATAGTTTTCCAAACTAA[C/T]AGTGTATACAAAATTGCAGAGAGAAATATTAAAAC Y 2 1 2 1 303000 f 74 goat snp19852-scaffold199-6561743 17 40260952 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380411 Affx-122975314 AX-123250769 17 30348402 TGCTACACAGGCCACAGAAATTAAGTGATCAGCTT[C/T]CAATAGGAGTGCAGAGAGCACTGAGTCTTCCTCAG Y 2 1 2 1 201000 f 74 goat snp16572-scaffold1747-558459 17 40243575 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417891 Affx-122946751 AX-123288239 17 30421402 TTTCAGAGAGAGAAGACTAAGGACGTGCTCATGCA[C/T]GTCTTGCTCCCCACTCACCCTAAAAACCCCAGGAC Y 2 1 2 1 201000 r 74 goat snp16570-scaffold1747-485459 17 40169961 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402186 Affx-122959179 AX-123272539 17 30547244 AGAATACACTCTTAGAGGGAAAGCCAGCAGACAGG[C/T]GAGTGGTTTCTATCCTGGGTTTTTTGGCAAGCCAG Y 2 1 2 1 101000 r 74 goat snp16567-scaffold1747-359617 17 40043019 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386878 Affx-122970056 AX-123257236 17 30579562 CAGGGAATTGTGATTTTTACTTCAGTGCCGAATAT[A/G]TGGAATAGTATCTGGCACAAAGGTGAATAAGAATA R 2 1 2 1 101000 f 74 goat snp16566-scaffold1747-327299 17 40010995 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766332 Affx-986697918 AX-385253715 17 30582375 TCCCCAATGGTAGGGATGATCCTCCCACTCATTAG[C/T]ATATGAATTCCATTCCTTCACAAAACCTAGCCAGG Y 2 1 2 1 600010 r 74 goat 17_30582375 17 30582375 Ancestral_priority_1043 ancestry 0.74 recommended IMAGE 10K 10K ancestral 539476328 Affx-1251763835 AX-586011745 17 30593392 CATCTTTCTTTTCTTCAGTTCTCATCCCCTCCCTT[-/GTCCTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCACCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCATTGTC]CTAGTTCTTTCTTGCCAATACTCACTAACTCTGAA - 8 1 4 1 20000 f 74 goat SV_211 17 30593392 - deletion junction SV-TF-chip 539476581 Affx-1251763835 AX-586011967 17 30593392 CATCTTTCTTTTCTTCAGTTCTCATCCCCTCCCTT[-/GTCCTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCACCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCATTGTC]CTAGTTCTTTCTTGCCAATACTCACTAACTCTGAA - 4 1 4 1 20000 r 74 goat SV_211 17 30593392 - deletion junction SV-TF-chip 562165434 Affx-1251763835 AX-606940845 17 30593392 CATCTTTCTTTTCTTCAGTTCTCATCCCCTCCCTT[-/GTCCTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCACCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCATTGTC]CTAGTTCTTTCTTGCCAATACTCACTAACTCTGAA - 8 1 4 1 20100 r 74 goat SV_211 17 30593392 - deletion junction SV-TF-chip 562165463 Affx-1251763835 AX-606940874 17 30593392 CATCTTTCTTTTCTTCAGTTCTCATCCCCTCCCTT[-/GTCCTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCACCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCATTGTC]CTAGTTCTTTCTTGCCAATACTCACTAACTCTGAA - 8 1 4 1 20100 r 74 goat SV_211 17 30593392 - deletion junction SV-TF-chip 562165761 Affx-1251763835 AX-606941170 17 30593392 CATCTTTCTTTTCTTCAGTTCTCATCCCCTCCCTT[-/GTCCTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCACCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCATTGTC]CTAGTTCTTTCTTGCCAATACTCACTAACTCTGAA - 8 1 4 1 20100 r 74 goat SV_211 17 30593392 - deletion junction SV-TF-chip 562165895 Affx-1251763835 AX-606941304 17 30593392 CATCTTTCTTTTCTTCAGTTCTCATCCCCTCCCTT[-/GTCCTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCACCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCATTGTC]CTAGTTCTTTCTTGCCAATACTCACTAACTCTGAA - 8 1 4 1 20100 r 74 goat SV_211 17 30593392 - deletion junction SV-TF-chip 562166018 Affx-1251763835 AX-606941427 17 30593392 CATCTTTCTTTTCTTCAGTTCTCATCCCCTCCCTT[-/GTCCTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCACCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCATTGTC]CTAGTTCTTTCTTGCCAATACTCACTAACTCTGAA - 8 1 4 1 20100 r 74 goat SV_211 17 30593392 - deletion junction SV-TF-chip 562166524 Affx-1251763835 AX-606941932 17 30593392 CATCTTTCTTTTCTTCAGTTCTCATCCCCTCCCTT[-/GTCCTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCACCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCATTGTC]CTAGTTCTTTCTTGCCAATACTCACTAACTCTGAA - 8 1 4 1 20100 f 74 goat SV_211 17 30593392 - deletion junction SV-TF-chip 320778777 Affx-122964172 AX-385265886 17 30615062 TAGCTTAAATGTGTTTCCCTCTAAACACACTGCTA[C/T]AATTTAGTTTCAGCTCTCCCAGAAAAAACATAATA Y 2 1 2 1 201000 r 74 goat snp16565-scaffold1747-291799 17 39974827 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398549 Affx-122961524 AX-123268904 17 30649427 TCTTGATGTTGTTGCTGTTGCTGTTGTTCTGTTTT[A/G]TTTTCCTCCATTGTTTTGTTGCGGCTATTTAACTG R 2 1 2 1 101000 r 74 goat snp16564-scaffold1747-257434 17 39941214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401625 Affx-122959599 AX-123271978 17 30698466 CCATGAAAATGGCTGTATTTTTAAATACTGTTAAT[A/G]TAAAATATGCAAATAAAACTGTCTATAGTCCACAT R 2 1 2 1 101000 r 74 goat snp16563-scaffold1747-208395 17 39892698 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428013 Affx-122939153 AX-123298356 17 30729262 CCCTTGCTGGAAGAGCTTTTATAGGTTCAGCTAAT[A/G]AGAAGAAAGTGAGTGAGATTTTGAAAGCTGAATGG R 2 1 2 1 101000 f 74 goat snp16562-scaffold1747-177599 17 39861867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442862 Affx-122927674 AX-123313199 17 30782445 CACTGATCACTTTTGTGTGTGTGAAGTAAATTAGC[A/G]CCACAATAAAAAGTATGAATGTTATGTTAATTCCT R 2 1 2 1 201000 r 74 goat snp16561-scaffold1747-124416 17 39809022 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420517 Affx-122944841 AX-123290864 17 30855167 AGGCGCTTATGAAAGTTCTCTGTAAAATAAAAAGC[A/G]TAGAGTTAAGATGGAATTTTGGAACTGACTCATTC R 2 1 2 1 101000 r 74 goat snp16559-scaffold1747-51694 17 39735098 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452010 Affx-122920915 AX-123322343 17 30903107 CCAAAAGAAGGAGTTCAGGAAGACTCTAGTCCAGG[C/T]ATCTGTGACCCAGATAAGCTGAAGACAGTGTTGGA Y 2 1 2 1 201000 r 74 goat snp16558-scaffold1747-3754 17 39688035 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436528 Affx-122932936 AX-123306866 17 30911312 GAAGCAAATTAAGGACACAAATAAACAAAAAGACA[C/T]ACCACGTTCATTGGTTGAAAGACTTAACGTTGTTA Y 2 1 2 1 103000 r 74 goat snp35586-scaffold428-3748502 NW_017217942.1 5222 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277092 Affx-1111835737 AX-519550599 17 31004930 TCTGCCCTATCACAGAATGTTCAGGGAAACACTTC[A/G]GTCATGGAACTTGATAACACTGATGAGAAATGATG R 2 1 2 1 101000 f 74 goat Random2.2K-1662 17 31004930 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382636 Affx-122973687 AX-123252994 17 31015420 CACCAGTATTTTCTACATTCCCTCTTCCCCATGAG[C/T]GGGCTGCTAGGGAGAATCACTATTCCACTTGACCC Y 2 1 2 1 201000 r 74 goat snp35584-scaffold428-3644394 28 6969510 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379863 Affx-122975793 AX-123250221 17 31064196 CCCATAAAGACTCCACAGCATATTAGCTCAGTCAC[A/G]TCTTGATATTCCATCTGGGCCAGGCATTATTTAAG R 2 1 2 1 101000 r 74 goat snp35583-scaffold428-3595618 28 7017689 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277216 Affx-1111835738 AX-519550722 17 31109600 AGTCTGGGAGGGCCAGGGACAGACTGAAGGCAGAA[A/G]CCTCCCAGTGTTTAGATCTCTTTTCCTTTTCAATG R 2 1 2 1 101000 r 74 goat Random2.2K-1663 17 31109600 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38393473 Affx-122965835 AX-123263829 17 31114691 AGATGAGACAGAGAAGATGCCGCATGTCCTGTGCC[A/G]CTTCCTATAGCATGAAGAAAACCCAGGTTGAGAGA R 2 1 2 1 101000 r 74 goat snp35582-scaffold428-3545123 28 7069978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792715 Affx-122930710 AX-385279695 17 31166586 TGGAAGCAATGATGTCAACCAGAAATTACATTATG[C/T]AGTGATGATACTAAAAAGCAAGTATTATAAGTTCC Y 2 1 2 1 101000 f 74 goat snp35581-scaffold428-3493228 28 7123188 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776459 Affx-122952914 AX-385263586 17 31211845 AAGAAACAGACTTTTTAAAATCCCAAAGGAAATAG[C/T]GATACTCTCACTACATTAGTTTCATTATCAAGACA Y 2 1 2 1 101000 f 74 goat snp35580-scaffold428-3447969 17 39651787 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389615 Affx-122968756 AX-123259973 17 31245072 TAAAACTACTGTAGCAACTTAGGGCTGTAATATGC[A/G]CTATTAGTGGCTGAATAGAGTGCATCAGTCTGGTA R 2 1 2 1 101000 f 74 goat snp35579-scaffold428-3414742 17 39617766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383383 Affx-122973510 AX-123253741 17 31288079 GTTCATGGGCTGTAATAAATGTAGCAATCCAAGGT[A/G]TGATCTTGATAGTACAAGAGACTGTTCAATAAATT R 2 1 2 1 201000 r 74 goat snp35578-scaffold428-3371735 17 39574788 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446485 Affx-122925054 AX-123316821 17 31316723 CTTCTGATTTAGAAACAAGGCAATTGATATTCAAA[C/T]ACAAAGGATAGGCACCCTTATCATATCCTTTCTTA Y 2 1 2 1 101000 f 74 goat snp35577-scaffold428-3343091 17 39546002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790374 Affx-122934849 AX-385277377 17 31355361 ACAAGTCTGTAAGCCTGTTCTTACGAGAGTTGGCT[A/G]GAAATTAGATCTGAGGCATTATGGAGTATAGAACC R 2 1 2 1 201000 f 74 goat snp35576-scaffold428-3304453 17 39507383 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431444 Affx-122936504 AX-123301785 17 31388838 TCTGAAACAATGGGGTTGTTTAAAGCCATAAATCC[A/G]TGAAACAAATCAAACAAAGTGTTTTAGAGATATGC R 2 1 2 1 101000 f 74 goat snp35575-scaffold428-3270976 17 39473881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424744 Affx-122941656 AX-123295090 17 31417814 AACCGATTCAGAATGCATTTTGAAGGTATTGTTAA[C/T]AGGATTGGCTAATGGACACGGAAAATAAGAGAAAA Y 2 1 2 1 101000 r 74 goat snp35574-scaffold428-3242000 17 39444728 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386474 Affx-122970769 AX-123256832 17 31470821 TCCAGTGTTTTATCAGTGTGAAATACCACAGCTTT[A/G]CTAAAACTCTTTTCTTTTTGATAGATGTATCTTAT R 2 1 2 1 101000 f 74 goat snp35573-scaffold428-3188993 17 39391442 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448037 Affx-122923709 AX-123318373 17 31502166 CTGGGTGTCAGTCCACAAGGGTGCACTGAACTCTA[C/T]GCAGCTAAGAGCAGATGTGAATGGAGGCATGCAAG Y 2 1 2 1 101000 f 74 goat snp35572-scaffold428-3157648 17 39360102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442264 Affx-122928274 AX-123312601 17 31545408 AAAAACAGGTTTGGGTCCAACTCAAGTACATATGG[C/T]AAAAATATAAATAAAATTTCATCTTTCTCACGTGC Y 2 1 2 1 101000 f 74 goat snp35571-scaffold428-3114406 17 39315678 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800402 Affx-122936745 AX-385287323 17 31586609 TCAAGATTTTTATCAGACCCTTACCCTAAACTAAC[A/G]TATGAATACTTAAGGACAAAATGTCCTGACTTGTG R 2 1 2 1 101000 r 74 goat snp35570-scaffold428-3073205 17 39274386 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415567 Affx-122948639 AX-123285916 17 31648543 TCATAAATTAAATATATTTATATGTATTTCCATAC[A/G]TATGTGTATAAGAGGAATATGTGGTATGACTTCTT R 2 1 2 1 103000 r 74 goat snp35569-scaffold428-3011271 17 39211585 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395147 Affx-122964124 AX-123265502 17 31719979 AGAAATGACTGATGAACAGACATGTCTTTTCCTCA[C/T]ACAAGGCTATAAGATGGACACAGAGAGAGCCAACA Y 2 1 2 1 202000 r 74 goat snp35568-scaffold428-2939835 17 39140078 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447261 Affx-122924946 AX-123317597 17 31753311 CTGGGAAATTATTAAAATACAGATTTTTTTCATTC[C/T]ACTCTCAGTAATTCTGATTCAGTACTTTTGTAGCA Y 2 1 2 1 101000 r 74 goat snp35567-scaffold428-2906503 17 39106756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421840 Affx-122944300 AX-123292187 17 31787749 AATAATTTTAATCACTTTGAAGCACATAGGTCATT[A/C]GGGCTAATTAAGGAGAAGGTCTTGTCATGAAAATG M 2 1 2 1 101000 f 74 goat snp35566-scaffold428-2872065 17 39072254 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445553 Affx-122925152 AX-123315890 17 31828222 TGAATTCCTATTCTGTAATAGAGGGAGTGCTTCCT[A/G]CTAATGCCAGTGGGATGTTGACAAAAATCTGAGAC R 2 1 2 1 101000 f 74 goat snp35565-scaffold428-2831592 17 39032217 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402411 Affx-122959008 AX-123272764 17 31865532 AACTATCTAGACAGCAGGGATCTGGAGACCAAACC[A/G]CTCTGGGTAATTTCTTCCCCAGGATTATGCAGAAC R 2 1 2 1 201000 r 74 goat snp35564-scaffold428-2794282 17 38994171 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436690 Affx-122932335 AX-123307028 17 31913171 TCTAGTTTTCTTCAAAACCGTGTGGAAGCTTTGAT[A/G]TGAGAGAATCTCCTTCATTAGGAGGGAGTCTAGAG R 2 1 2 1 101000 f 74 goat snp35563-scaffold428-2746643 17 38944830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791292 Affx-122975513 AX-385278286 17 31946577 TGACTGTAAATGAAATGTCTAAAATTCAGCTGACT[A/G]CCTCTCTCCCCACAACACAAATAGTTCTTGCCACT R 2 1 2 1 103000 r 74 goat snp35562-scaffold428-2713237 17 38911200 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778112 Affx-122958070 AX-385265227 17 31975221 TAAAAATGAAAGACAAGCCAGTCTGGGAAAAGAAT[A/G]TTTGCAAAATGTATCTAAGTAGTTGTACTCAGATT R 2 1 2 1 202000 r 74 goat snp35561-scaffold428-2684593 17 38882815 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785842 Affx-122936409 AX-385272879 17 32042832 CCAAAAATGGGCATATCCATGAGTTCACATGTTCT[A/G]TACTATTCTATATCAGAAATGGGTTGATGGGACTT R 2 1 2 1 201000 f 74 goat snp35560-scaffold428-2616982 17 38812744 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275646 Affx-1111834929 AX-519549216 17 32083064 AATCACACTTTCCCTTACATG[A/G]CATTGTACATCTACTATACAAAGTGGGAGTCTAAG R 2 1 2 1 101000 r 74 goat GoatD01.059089 17 32083064 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468271990 Affx-1111833092 AX-519545759 17 32084609 AAACCAAAGAATCCCAGACAAGCTAGAGTTTTCAG[A/G]TTTCCTTTGACTTAATTCCCAAATCTCCTGCTTTG R 2 1 2 1 101000 f 74 goat 17_32084609_AF-PAKI 17 32084609 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38379606 Affx-122976017 AX-123249964 17 32088911 TGTTGTCCGTTGACAGAATTCATAACAGAGACATC[A/C]TTCACCCTACTCAGGATTTTGGTGGCCTGGACGTG M 2 1 2 1 101000 f 74 goat snp35559-scaffold428-2570903 17 38766480 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802890 Affx-122964696 AX-385289788 17 32152687 TTGACCCCTGCTTTGAAAAGCAGCATAAGCATTTA[A/G]GGCTCTGTGGTGTTTAGTGTGATGTGATAAATTGC R 2 1 2 1 201000 r 74 goat snp35558-scaffold428-2507127 17 38702529 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409290 Affx-122953109 AX-123279641 17 32194204 ACACAACCCAGACGTCCCCCAGAACAGAGCCTTTC[A/G]CTGCAGTGCAGGCAGACTCATGTTCACACACAGCC R 2 1 2 1 303000 r 74 goat snp35557-scaffold428-2465610 17 38660555 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789380 Affx-122958231 AX-385276390 17 32241484 TAAATTGTGTGGGTTTGGTTTTCTTGGTACAGTTG[C/T]AGTTATTATTTCCCTTTGACCTTTGTAAATTTGTA Y 2 1 2 1 101000 f 74 goat snp35556-scaffold428-2418330 17 38612409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433054 Affx-122935754 AX-123303395 17 32273740 TTTTATTTTTTTTACTGTATGCTTTACAATTCTAG[C/T]TCCTTTCAAGTCTGGACATAAAAAATAAAAATTTT Y 2 1 2 1 101000 r 74 goat snp35555-scaffold428-2386074 17 38580116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772602 Affx-122930654 AX-385259750 17 32308177 TATCAATAAAGAGAAATACGTCTTTTTCAAGGCAG[G/T]GAAGTTTTTATAGGAAACTTCTATTTGTAATAGAA K 2 1 2 1 201000 r 74 goat snp35554-scaffold428-2351637 17 38545204 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409603 Affx-122953556 AX-123279954 17 32337725 AAAATAAGCCTTCAGTTATTTAAAATATTAGATAT[C/T]ATTCATGAAAATACAGAATCTCATAAATCGGCTGC Y 2 1 2 1 101000 r 74 goat snp35553-scaffold428-2322089 17 38515947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774818 Affx-122931563 AX-385261952 17 32369852 TTCCATAAATAACTACTTTTTTGAAGGTGATTTCT[A/C]TATTTGTACTATTATCCTTTTATTCTTCCTGTTCA M 2 1 2 1 201000 r 74 goat snp35552-scaffold428-2289962 17 38483380 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799677 Affx-122941424 AX-385286605 17 32399856 TTCGTGGGAGGTCTTCTTTTAAGTCATCTATTTGG[C/T]GTGTTTAAATATGATGAAAAGAAGGATGGAGAGCA Y 2 1 2 1 101000 f 74 goat snp35551-scaffold428-2259958 17 38453072 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401789 Affx-122959477 AX-123272142 17 32452086 AGCTAGAAGATACTTCATGTGTGTGTGGAAAGAGT[A/G]CAGGGCCAAGATTTAATGAAATAGTGTGAGTATGT R 2 1 2 1 101000 f 74 goat snp35550-scaffold428-2207728 17 38399246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769786 Affx-122950726 AX-385256956 17 32482711 ATTGATTTCTAGAAGAATCTGACTTTTTCTCAGCC[A/G]TGATTGCTGTACATAATCTCAGCTCTAATTATGTC R 2 1 2 1 101000 f 74 goat snp35549-scaffold428-2177103 17 38368662 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398712 Affx-122961847 AX-123269067 17 32534135 CTAAGTTCAAGTGAAAATTTAGATCTCTGAAATAC[G/T]AATTGTGATCAGAATTTAATATCCATTATGGTACA K 2 1 2 1 101000 f 74 goat snp35548-scaffold428-2125679 17 38316990 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789154 Affx-122951254 AX-385276166 17 32594457 TAGAAAAGACAAAAATATTGTGAAGGGATGCTTTT[A/G]TCCTATAGGTATCATCAGTACTGAAAACTTTTTTT R 2 1 2 1 201000 f 74 goat snp35547-scaffold428-2065357 17 38256941 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453681 Affx-122919706 AX-123324014 17 32623470 AGTGTTTGTACTGGGTCAGGAGACCTCAGTTCAAG[C/T]AGACACAGAGAATCTTCCATGTTCTCCTCTCTAAA Y 2 1 2 1 202000 r 74 goat snp35546-scaffold428-2036344 17 38228109 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403203 Affx-122958059 AX-123273556 17 32672670 ATTCATTCAAGGATGCATTTTTTCCTGCAACTATT[A/C]GCACAGTCAATATCCTTTGAGGAAAACATGACTGT M 2 1 2 1 101000 r 74 goat snp35545-scaffold428-1987144 17 38183606 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450093 Affx-122922787 AX-123320428 17 32716352 GACATCAATCTTTTGTGTTTCCATCTTTTAACTAT[A/G]TTTCACCTTTCTCACCCCAGTATTTCTTTTGCCTA R 2 1 2 1 103000 r 74 goat snp35544-scaffold428-1943462 17 38140082 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775951 Affx-122978261 AX-385263082 17 32776679 TCCCTCACCACACCTCTTGAATTTTACAATTTTAA[C/T]GGTGTAAATGGTGCTCTTTAAATACTTCATTTTGC Y 2 1 2 1 201000 r 74 goat snp35542-scaffold428-1883135 17 38080068 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799802 Affx-122974260 AX-385286728 17 32817364 TTTTAAACTTCAGTAGTAATGACTTCAAATGCAGA[C/T]GCACGCAGTGATCCTTTGTTGCCAGTTGTATACAG Y 2 1 2 1 101000 r 74 goat snp35541-scaffold428-1842450 17 38039282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273602 Affx-1111833694 AX-514986449 17 32817500 A[A/G]TACATATTTTGTGGTACTTGCATACCAGTACAATG R 2 1 2 1 101000 r 74 goat GoatD01.001751 17 32817500 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38389413 Affx-122968372 AX-123259771 17 32846069 CATAGAGAGTATAATTTGTAAATAATAAACTTGGA[C/T]ATTGAATTGAAATTGTTTGGCAAACAGGAACCAAG Y 2 1 2 1 101000 r 74 goat snp35540-scaffold428-1813745 17 38010277 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377682 Affx-122977424 AX-123248041 17 32898682 TAAACCAATGCTGAAGGTGTAGTGAACATAAAAGA[A/G]TTGCATGATTTATTTTATTGAGTGACATTTTTAAG R 2 1 2 1 101000 f 74 goat snp35539-scaffold428-1761132 17 37958127 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387805 Affx-122969688 AX-123258163 17 32977316 TGATCCCATGTGAACCATCATTGATTACCTTTGAT[C/T]AGTAATGTATTCATTGGCATCCACACCAGGCATGG Y 2 1 2 1 101000 f 74 goat snp35538-scaffold428-1682498 17 37879409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391512 Affx-122966667 AX-123261869 17 33022925 TCTTGGTTTGAGGGGCTTTATTAGAAAGCTGCCTG[C/T]GGGTGGTTCATAACCAGTTGTACTTATTTCAGTGC Y 2 1 2 1 101000 r 74 goat snp35537-scaffold428-1636889 17 37833347 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393367 Affx-122965918 AX-123263723 17 33065807 ACAGTGAAGCTGCCCTGGGAGGAATATGTCAGATT[A/G]CTTGTCTCGGCTTTTATTATTTAAGCCTCAGCTGT R 2 1 2 1 101000 r 74 goat snp35536-scaffold428-1594007 17 37790320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781391 Affx-122936212 AX-385268476 17 33129527 ATATGTCTCTAGTTTAACCTTTCCCAAAGCAAGAT[A/G]TTTCACAAGGTTGGCAACAACTGCTGGTCACAGCC R 2 1 2 1 101000 r 74 goat snp35535-scaffold428-1530287 17 37726351 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446963 Affx-122924662 AX-123317299 17 33185693 TCTTTTTGACATAAAACCTAATTCTGAGAATTCTC[A/G]CTGTAGGTCTCACATCTCCATTGCTTTATCTTGGA R 2 1 2 1 101000 r 74 goat snp35534-scaffold428-1474121 17 37670452 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776757 Affx-122938153 AX-385263881 17 33225915 TTATTAAGTATGTGCCATCACTGGGTTATCAAAAG[C/T]AAATCACGCTTTTTGTAACACTTTTTATTCCAAGC Y 2 1 2 1 201000 f 74 goat snp43532-scaffold581-20724 17 37625701 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412132 Affx-122951097 AX-123282482 17 33273970 CCCCCACACTTCATCCTCACTCTTCAAGCACTCAG[C/T]TCCCATTTCCCTCATCCCTTCGGCATTTAGAAATG Y 2 1 2 1 101000 f 74 goat snp43533-scaffold581-68779 17 37577208 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451601 Affx-122921639 AX-123321934 17 33307021 GATCAGAACACATATGGACCAGGAATACTCCTAAG[C/T]ACACTCAGTAATGATCATTGCTATTGGGGGAGAAG Y 2 1 2 1 101000 f 74 goat snp43534-scaffold581-101830 17 37543359 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442778 Affx-122927734 AX-123313115 17 33340382 GCCAACAAAGACCCCAGGAGGCGGATGAGAGTTCC[A/G]GGACCCTTTTCCGGGGTCTGACGAACTGTACTGGG R 2 1 2 1 201000 f 74 goat snp43535-scaffold581-135191 17 37509206 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429950 Affx-122938079 AX-123300291 17 33432388 ATGAGAAAGCAAGAGAGAGAGACAGGCAGGCAGAC[G/T]AAAGCAGAAGAGGAGATAAACAGAGACCAGTAATT K 2 1 2 1 303000 r 74 goat snp43537-scaffold581-227197 17 37416221 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776165 Affx-122933914 AX-385263293 17 33466998 TACACTGGTTCCTTCCTTGCCAGAAAATTAAGTTG[A/G]CCCTTACACAGGCACAGGCATTGGTTTTGATTCAA R 2 1 2 1 101000 f 74 goat snp43538-scaffold581-261807 NW_017199155.1 10209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795283 Affx-122920704 AX-385282241 17 33496573 AGAGCACCATGTGACAATAAGAAAAGTAATCCCAA[C/T]GCTAACAAGAAAATCACCTTACAGTTCTGGGGATA Y 2 1 2 1 101000 r 74 goat snp43539-scaffold581-291382 17 37352121 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405833 Affx-122955875 AX-123276185 17 33529229 TCTTCCTTTGAGAGAATTTGCAAAACAAATTCTTC[A/G]TACATTAGATCTCCTTCATAGACTCTTAACAGTAT R 2 1 2 1 101000 r 74 goat snp43540-scaffold581-324038 17 37320730 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433675 Affx-122934555 AX-123304016 17 33572361 CTTTATTATAGTGATTTGCTTTTTAAGAAATAAAT[C/T]CACATGGAATGAAAGAATGGGGGGAAAGGTAAAAC Y 2 1 2 1 303000 f 74 goat snp43541-scaffold581-367170 17 37276891 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390070 Affx-122968406 AX-123260427 17 33621224 TCTGAGCTACCAGGGAAGCTTGATATTTCTCCTGG[C/T]AATCCATCAATACTGTCCTGAAACACTTATTATCA Y 2 1 2 1 201000 r 74 goat snp43542-scaffold581-416033 17 37224932 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795717 Affx-122957290 AX-385282670 17 33675635 CCCAACCCACAACAACACTTGAGCGCAAGAGAGAA[G/T]AAAGGCCTATGGATGTCAGTAAGGCTTCCTCAGCC K 2 1 2 1 101000 r 74 goat snp43543-scaffold581-470444 17 37169874 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320772170 Affx-122965685 AX-385259325 17 33715432 TTATTTTACATTATTAAAATCAGGCCAGTAGAAAA[C/T]GGATATTAAGATGTTAGAATCAGCTAAGAAAATGA Y 2 1 2 1 101000 r 74 goat snp43544-scaffold581-510241 17 37130357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426871 Affx-122940481 AX-123297216 17 33761226 AGGAACATTTGTTTTAAAACTCTATAATAAACTGC[A/G]TGTGGTTTTAAAAAAGGAAAAGGAAGGGTAAATAT R 2 1 2 1 101000 r 74 goat snp43545-scaffold581-556035 17 37084338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779267 Affx-122968477 AX-385266371 17 33815631 CTGCCAGACAAGGGAGGCTAAGGTTTGTGTGGAAC[A/C]CGCAATTATACTTCTCGACACCCTCATATCTGTGA M 2 1 2 1 101000 f 74 goat snp43546-scaffold581-610440 17 37030015 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384498 Affx-122973058 AX-123254856 17 33854463 GGAGTTTCCAGGCAAGAGTACTGGAGTGGGGTGCC[A/G]TTGCCTTCCCCCTCGTTTACAGCAGAAGATGGTAA R 2 1 2 1 101000 r 74 goat snp43547-scaffold581-649272 17 36990926 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272379 Affx-1111834248 AX-519546108 17 33865962 TTGGAACTCATAATCAAAAAGTCCCCAACTTTCCA[A/G]TGGTTTTAAAAGCATTGTGAGGGAGGGGGCTGCAG R 2 1 2 1 202000 f 74 goat GoatD01.027359 17 33865962 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320780770 Affx-122946582 AX-385267859 17 33915636 GGTCAAATTCCTAGGATAAGAAACCATAATAGATG[C/T]AACTTTACTGCTGAAATCAGTGGTTTGAGGAAAGC Y 2 1 2 1 101000 r 74 goat snp43548-scaffold581-710445 17 36929440 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436131 Affx-122932645 AX-123306470 17 33963381 TATAGTGTGTTGTTTACCTACCTTATTATTTAGTC[A/G]TTTTGTTATCTTTCAATTTTCCTTCTTCTCTCACT R 2 1 2 1 101000 r 74 goat snp43549-scaffold581-758190 17 36881814 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420338 Affx-122944973 AX-123290685 17 34010023 CAAGGTCAGTCTAAATTTTAATAACTGGCTGGGAA[C/T]AGGATTTATGGAGGGGACGGAGAGGAGAAAAGGCT Y 2 1 2 1 201000 f 74 goat snp43550-scaffold581-804832 17 36835158 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772747 Affx-122924233 AX-385259892 17 34040957 TAATACTCCTCTTTCAGTGTACTTGATAGAACTAG[C/T]ATAAGCAAACTTGTGATGGATAGATATAGATTACC Y 2 1 2 1 101000 f 74 goat snp43551-scaffold581-835766 17 36804049 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775941 Affx-122978751 AX-385263072 17 34103663 CCAAGATCACTTCAGGCAGCATAGTTCTGTGACAT[C/T]TATAGATTGATCAGATATAAATATCAACTTCAGTT Y 2 1 2 1 101000 f 74 goat snp43552-scaffold581-898472 17 36747020 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451677 Affx-122921582 AX-123322010 17 34136418 GAAAGAGTGAGGGAGAGGCAGACCTTCTAGACTGC[A/G]CAGAACAAGGGACCTGGAAGTGGCAACCTAAGAAA R 2 1 2 1 101000 r 74 goat snp43553-scaffold581-931227 17 36715306 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437340 Affx-122931948 AX-123307678 17 34183324 CCTTTGAAACTCCAGAGCTTCAGGAATGCCTCAGG[C/T]ATTCTTCCTTGGATCTTGTCTACCTTGAGACTCTG Y 2 1 2 1 101000 r 74 goat snp43554-scaffold581-978133 17 36668563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770379 Affx-122932314 AX-385257546 17 34222716 TGGAGGTACAATCCCTAAGGAATTCCTTATAGGAC[G/T]ACTCTAATCTATGACAGGTATAGGTACACATCATT K 2 1 2 1 101000 f 74 goat snp43555-scaffold581-1017525 17 36629060 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418177 Affx-122947079 AX-123288525 17 34313760 TTTTTCCCAGTGTGACTATCTCGCAAATTTAATCA[C/T]AGAAATGTATGAAGAATATTTCCTTTGAGAAAATT Y 2 1 2 1 101000 f 74 goat snp43557-scaffold581-1108569 17 36537928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449776 Affx-122922436 AX-123320111 17 34368503 CTTCATCCCTCTAAATTGTCCTCCCAGCAAAGACC[C/T]CAAGCAAAGCTTTTGGAAGGACTATCATTTTTAAA Y 2 1 2 1 201000 r 74 goat snp43558-scaffold581-1163312 17 36482666 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451320 Affx-122921278 AX-123321653 17 34421469 GGGCAAAGTTTAACTTTCAATAAATAGCTGCTGGC[A/G]TGGCTTAGTTTGAACATTCTTTGGCACTGCCTTTC R 2 1 2 1 101000 f 74 goat snp43559-scaffold581-1216278 17 36429564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452360 Affx-122920635 AX-123322693 17 34467726 TGAATGCTCAATTTACTATTTAAAAAAAAATTGCA[A/G]TTAATGAGCTACTTAAAACAGGTTCTGCAGAAATA R 2 1 2 1 102000 r 74 goat snp43560-scaffold581-1262535 17 36383459 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791083 Affx-122975780 AX-385278078 17 34503572 GAGCTCAAGGGTTAAAAGTTTCAGTTCTACCACCA[A/G]CTGTCCACAGGTTAAGTCATACATTCTCTCCATGG R 2 1 2 1 101000 f 74 goat snp43561-scaffold581-1298381 17 36347473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390693 Affx-122967947 AX-123261050 17 34583641 TCTCCAGCCACATCTCTTCCCTTCTACCTCGTACT[A/G]CCTTTGCACCTTACACTCCCACAGTAGTAAACTGT R 2 1 2 1 101000 r 74 goat snp43562-scaffold581-1378450 17 36267262 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271994 Affx-1111833094 AX-519545762 17 34591861 GAGGGATTGAGGGAAAGAGGAGAAGGGAACGACCG[A/G]GGATGAGATGGCTGGATGGCATCACGGACTCGATG R 2 1 2 1 103000 f 74 goat 17_34591861_AF-PAKI 17 34591861 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426515 Affx-122940207 AX-123296861 17 34619782 CCGCACCAGCACCCACCGAGGCTCAAGTCCCTCAT[A/G]GAAATGGTGTAGGGCTGTCAGCCGTCGTCACCACA R 2 1 2 1 101000 r 74 goat snp43563-scaffold581-1414591 17 36231079 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275551 Affx-1111834966 AX-519549123 17 34621075 ATTGGATTTTTGCATTTGTAGCCATTTGTTTAGTC[A/G]ATAGGATCTTCAACAAAGTACATATCACTTCACAA R 2 1 2 1 101000 f 74 goat GoatD01.060191 17 34621075 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38376466 Affx-122978046 AX-123246825 17 34655099 ATTGTTACTTCAATTAAGAATCAGAAAATCTCTTT[A/G]TTCCACATGTCAGAATTACTGTACAAAAGGGAAGT R 2 1 2 1 101000 r 74 goat snp43564-scaffold581-1449908 17 36195366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787469 Affx-122959292 AX-385274494 17 34696773 GCCTACTGTACCTGAAAATCAATGTTTGGAAACTA[A/C]GTATGTGAGAGAGGTGGGAATAAAAAAAAGCCCCC M 2 1 2 1 101000 f 74 goat snp43565-scaffold581-1491582 17 36153574 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410261 Affx-122952527 AX-123280611 17 34745653 ACTACTTTTACCAGGATCACTTAAGAGGAAAAAAA[C/T]GGTTTGGTGATGATGCTGAACTTTTGTTCGGAAGA Y 2 1 2 1 103000 f 74 goat snp43566-scaffold581-1540462 17 36103307 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388236 Affx-122969794 AX-123258594 17 34784083 GTCCTCTTCCCTAGGAAGATTGGTTTGTGGATCCT[A/C]TTACTGAGTGACTCTCAGTGCTTCACTGTGGCAGC M 2 1 2 1 101000 f 74 goat snp43567-scaffold581-1578892 17 36064673 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320793658 Affx-122978896 AX-385280631 17 34834374 AAACCACCCAAGGAATACCTAGAAAGACTGAAATC[A/G]CTCATCCAAAAGGTATATAACAAATTACATTTGAT R 2 1 2 1 101000 f 74 goat snp43568-scaffold581-1629183 17 36014401 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380148 Affx-122975976 AX-123250506 17 34884045 TCTGCTCCTTCTGCAACTGCTTCTAGTCTTCTTTA[C/T]TTTGCAAACATCTCTCTGAAGATAATATACATTGT Y 2 1 2 1 101000 f 74 goat snp43569-scaffold581-1678854 17 35963861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398245 Affx-122962195 AX-123268600 17 34918324 CCCCAAGTCTGCAGTTGTTCAGTCACGAGGTAAAA[C/T]GAGGTCTGTATGTCATTACCTTCAGCTTATTTCTC Y 2 1 2 1 101000 f 74 goat snp43570-scaffold581-1713133 17 35929108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795004 Affx-122973223 AX-385281963 17 34957439 AGTGAGCTCCATTCTGACAAAGAAGAGAATAAGAA[C/T]TGAAGGCAACTAAAGACAATTACCTCTTATTTGCT Y 2 1 2 1 101000 f 74 goat snp43571-scaffold581-1752248 17 35890014 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446288 Affx-122925658 AX-123316624 17 35104586 TAAGTACTTGGGACACAGGCACAATCACTGGCTAA[C/T]GAAGAGTCTGAATATCAGAATATGACCTACATTCT Y 2 1 2 1 101000 f 74 goat snp43573-scaffold581-1899395 17 35743416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431594 Affx-122936173 AX-123301935 17 35160931 TGCATTTCACCTGTTTTGATCAACTGAAAATTAAA[C/T]ATATTTTGTGCCACCTGGAATATTCATTAAGCAAA Y 2 1 2 1 101000 f 74 goat snp43574-scaffold581-1955740 17 35686390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428778 Affx-122938415 AX-123299120 17 35210733 CACCCTAAAAAACAATTTATAATAATCCAAGGTAA[G/T]AAAACAGGTACAGAAGTTTGCTAGAATACTATTTA K 2 1 2 1 201000 f 74 goat snp43575-scaffold581-2005542 17 35636328 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379546 Affx-122976058 AX-123249904 17 35254297 TCATGTCCCTCCCTGCTCCATGCCCTTCTATATTG[C/T]AAGACCATTAATAAAAGAGAGAGATGAAACAATCC Y 2 1 2 1 202000 r 74 goat snp43576-scaffold581-2049106 17 35592987 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795162 Affx-122919906 AX-385282120 17 35317944 TCACTTAATCATTACAACCCTATTAGGTAGGCGTT[A/G]CCCTCATTAGATATAATGGGAAACTGAGACCAGGA R 2 1 2 1 101000 r 74 goat snp43577-scaffold581-2112753 17 35529095 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388866 Affx-122969317 AX-123259224 17 35405420 TTATGCTCTGAGACATGACTGTTTACTTAAGTTTA[C/T]GTTACACTAGGAAATAAAACAGCAGCATTTCCTTT Y 2 1 2 1 101000 f 74 goat snp43579-scaffold581-2200229 17 35441722 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772936 Affx-122976868 AX-385260080 17 35448689 GTAGCTTCTGGGGGGGAGGGTAATAAATGGCTTAC[G/T]CAGAAGAAATTCTATCTCTGTTCCATCAGTATGGA K 2 1 2 1 201000 r 74 goat snp43580-scaffold581-2243498 17 35397554 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404650 Affx-122957305 AX-123275002 17 35480219 TTCTGGTATTGGGTGGGCCAGCTTGCTTTTTGTTA[C/T]AAGCACTCTGGTTGGACCTTCCTTCTCTCTGTCAA Y 2 1 2 1 101000 f 74 goat snp43581-scaffold581-2275028 17 35366525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403488 Affx-122957700 AX-123273841 17 35522389 AGAAGGAGAAGACTACAGAAGGATATAGAAATGGG[A/G]ATTGGTAACTCAAAGTCCAGGGTAGGTATCAAAAG R 2 1 2 1 101000 r 74 goat snp43582-scaffold581-2317198 17 35324410 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788460 Affx-122932805 AX-385275477 17 35559881 CAGGGAAAATTGGCTATGTTTTGCTTTTCAAGGAA[C/T]CATTGAACCTTGAAAATTTTCTCCTGTGGTAGAAA Y 2 1 2 1 201000 r 74 goat snp43583-scaffold581-2354690 17 35288307 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800167 Affx-122959290 AX-385287090 17 35618422 AGGACATTTCAAAATAGTTTGTAAATAAGCACAGC[A/G]CCTCTACTGGTTAACCTGCATTTTAGTTTTCTCCC R 2 1 2 1 101000 r 74 goat snp43584-scaffold581-2413231 17 35228341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792394 Affx-122943506 AX-385279375 17 35691938 GGTCTACATTCCACACAAGAAATCTGACTTAGCTT[A/G]TGATGAATTTGGATGCTGTGGGCCATCCTTGAGCA R 2 1 2 1 201000 r 74 goat snp43585-scaffold581-2486747 17 35154593 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429533 Affx-122937837 AX-123299875 17 35753878 GATCAAAGATGGATGACTTCCCACACCTCTTTTCT[A/G]TTGATACATTGATTCTGGGTAAACTGTTTCCAAGC R 2 1 2 1 201000 r 74 goat snp43586-scaffold581-2548687 17 35094533 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426207 Affx-122940368 AX-123296553 17 35826412 TTTTAATCAGAACAGACCATTGGGAGGCAAAACAC[A/G]TAAAATAGTTATTATAAACATAGACCCTGAAAACA R 2 1 2 1 101000 f 74 goat snp12034-scaffold1443-780870 17 35030609 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445277 Affx-122925464 AX-123315614 17 35865966 CTTGCCCACAGAGGACAGCCACCACTAGCTTTCTC[A/G]GATGGGCCAGTGCTTCACTAGTGCATTTCTTATCT R 2 1 2 1 201000 r 74 goat snp12033-scaffold1443-741316 17 34992123 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435998 Affx-122933499 AX-123306337 17 35927306 TGGTTACGGGATAAGAAAGTCAGGATGAAAATGTC[A/G]CCTTGAATCTGCAGTTGCCTTAAGCATCCAGGAAG R 2 1 2 1 101000 f 74 goat snp12032-scaffold1443-679976 17 34930085 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422221 Affx-122944027 AX-123292567 17 35972175 TATCAAACTTTGTTCAGGGATTTATAATATCAGTT[A/G]CAAGATGTTGTTACTTATCTATGAAATGTGTAGAA R 2 1 2 1 101000 f 74 goat snp12031-scaffold1443-635107 17 34886575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436386 Affx-122933041 AX-123306725 17 36002470 TAGAATAATCATAGCTGACTTCACAGAGCCGCTTT[A/C]TTGGTTTCAGGTCACAGACAACCTGCCTTATTACC M 2 1 2 1 101000 f 74 goat snp12030-scaffold1443-604812 17 34855166 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274128 Affx-1111834057 AX-519547732 17 36049313 TTAACATGGGTAAGCGTTTTGCTACATAAGCAAGT[A/G]AGTTCAGGAACCTGAGTGCTCTGGTGGCCAGGACT R 2 1 2 1 101000 f 74 goat GoatD01.016111 17 36049313 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320798737 Affx-122921420 AX-385285668 17 36052622 TGCAGTTTATGTAATTTGAAATGAATTTAAATGCT[A/G]TAATGATTACAAAGGTGTAAATGAGAAGTGACACA R 2 1 2 1 201000 f 74 goat snp12029-scaffold1443-554660 17 34803832 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785134 Affx-122975749 AX-385272180 17 36096561 AATATTCACTGGGTCTGTAATAGTATGAGTCAGTA[C/T]GTTGAATTGATAATGTGTTTTCAGAGCATTCATAA Y 2 1 2 1 101000 f 74 goat snp12028-scaffold1443-510721 17 34762990 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376229 Affx-122978792 AX-123246588 17 36137451 CCATTTTTCAGTTTTACTAATTTTCTTTGTATGGT[A/G]TGGTTCATTTCATTATCTTGTCTCCTAATCACTAC R 2 1 2 1 101000 r 74 goat snp12027-scaffold1443-469831 17 34721891 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794178 Affx-122946227 AX-385281144 17 36199981 GTAGCTTACCAATACTTAATATTAATACATTAAAT[A/G]TTAGGTTAAGACCCTGGGTTATAAAGAAGAAATAT R 2 1 2 1 103000 f 74 goat snp12026-scaffold1443-407301 17 34658800 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794464 Affx-122925349 AX-385281427 17 36240501 GATGTGAAATAGGAATCCCAGGAATATCAGTTCTT[A/G]ATACAAAATAAGGAAGCAGCAAAACACACAGAAAG R 2 1 2 1 201000 r 74 goat snp12025-scaffold1443-366781 17 34618253 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774729 Affx-122938970 AX-385261863 17 36269074 AACAATTTAAACTTCAACAATTCTCTGTTCTGTCT[A/G]TGTATCTATCTACCATAGATCCATCCATCTATTCT R 2 1 2 1 201000 f 74 goat snp12024-scaffold1443-338208 17 34589073 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792564 Affx-122973137 AX-385279545 17 36305590 ACTCATATCAGAATGTATAGTATCCCATCACCACA[G/T]CAAGTTCACTTCTGGTTTTCCTGTCAATTTCAAAG K 2 1 2 1 101000 r 74 goat snp12023-scaffold1443-301692 17 34552421 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375836 Affx-122978542 AX-123246195 17 36366952 AATGCTTCAAACTGATAATATTTTATTTTACAAAA[C/T]ATTTATGCTACACTTTGCTATCAGGTAATACTTTC Y 2 1 2 1 103000 r 74 goat snp12022-scaffold1443-240330 17 34491027 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379953 Affx-122975642 AX-123250311 17 36408934 CAAATGTGATTTATAGGAGGCTAATAAAATGACTT[A/C]TTTCTCTTGCTTGCCTCTGGAAGTATTTAAGTTTA M 2 1 2 1 101000 f 74 goat snp12021-scaffold1443-198348 17 34449214 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392535 Affx-122966103 AX-123262892 17 36443513 TCTATGGCTTATGAAGTGAATGCATTTTCTTTATT[A/G]TGCATTTAATATCCTTTTATCTACCCATGTAAGCA R 2 1 2 1 102000 r 74 goat snp12020-scaffold1443-163769 17 34414608 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376138 Affx-122978860 AX-123246497 17 36472132 ACCTACAGAGACCTCTAACCTTTTCTACCATGTGA[G/T]GACTTAGCGAAAACACAGCCATTTATGACCAGGAA K 2 1 2 1 101000 f 74 goat snp12019-scaffold1443-135150 17 34386020 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389196 Affx-122969073 AX-123259554 17 36526365 TAGGTAAAAAGAGAAACATAAAGATATATCAGCTA[C/T]ACCAGATTAAGGTAATATAAACAGGATGAGGACAG Y 2 1 2 1 201000 f 74 goat snp12018-scaffold1443-80917 17 34332016 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387379 Affx-122970431 AX-123257737 17 36568745 AAGCATTAAAGGACAACAAAAGCATATTTTATCTC[A/G]TGTATTATATATACAAGTTTTAGTTTAAAACTTAA R 2 1 2 1 103000 f 74 goat snp12017-scaffold1443-38537 17 34289101 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793376 Affx-122943029 AX-385280354 17 36608482 GTAAATCTCCCAGCTCAAGAACTAGACAAAAGCAG[C/T]CTGCTTTATTCCTCCCCTAACCTTCACTCCTATGT Y 2 1 2 1 101000 f 74 goat snp14473-scaffold1578-1049269 17 34253327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425844 Affx-122940668 AX-123296190 17 36641797 TGTCAGCTGTGAGCCTGGGAATCTCCCTTGTAATG[C/T]ACAGGTCAAAAGCGTCTCAAGATTGATGACTAGAA Y 2 1 2 1 201000 r 74 goat snp14472-scaffold1578-1015954 17 34221798 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792197 Affx-122949080 AX-385279182 17 36673358 GACTTCCAGGAACAAGTGCAATTCTTCTTTCATCT[A/G]CTTTGTACTACTATGAGCTTTGATTATAGCTTGAT R 2 1 2 1 101000 f 74 goat snp14471-scaffold1578-984393 17 34190651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444505 Affx-122926509 AX-123314842 17 36709657 ACCTGCCATACATTAAGCAAAGGTTGTTGAGGCCA[C/T]CAAGGCATCAGCCACAGCATCTGTCCCCAGCTGTA Y 2 1 2 1 201000 f 74 goat snp14470-scaffold1578-948094 17 34154202 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418996 Affx-122946057 AX-123289344 17 36751892 CTTAAAGCTTTCAGACTTTCTTTAGACTTTATGTC[A/G]CAAGGGTATGAGAATTTAATTTTGGATATTAATTA R 2 1 2 1 101000 f 74 goat snp14469-scaffold1578-905859 17 34111494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800810 Affx-122927019 AX-385287726 17 36793587 TACACAAAGCCATATGGAAATTCACACTCCTGTGC[G/T]CCAGAATCTTCTCTTAGGTTGTGCTCCCAAATCAA K 2 1 2 1 101000 f 74 goat snp14468-scaffold1578-864164 17 34069813 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411227 Affx-122952348 AX-123281577 17 36857525 ATCTTCACATTTCAACATATAAGACCCATGCACGA[C/T]GAGGGCCTGAGCCATCAAAGGCTTCCTTGGAGGCT Y 2 1 2 1 101000 f 74 goat snp14467-scaffold1578-800226 17 34010016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387954 Affx-122969611 AX-123258312 17 36919785 TGCTCAGAATGAGAATGCCAGGTACATGTGCAAAC[A/G]TTGCCTCAATGAGAATGAAGTTTCATTAGAGGCAA R 2 1 2 1 101000 f 74 goat snp14465-scaffold1578-737966 17 33948078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379697 Affx-122975904 AX-123250055 17 36969630 TAAACAGTAGATGCATGGACAAGTGACATTAGAAG[C/T]GACTTCTTAGGAGCTCTTAGGCTTGTGACATTTGG Y 2 1 2 1 101000 f 74 goat snp14464-scaffold1578-688121 17 33897620 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445454 Affx-122925345 AX-123315791 17 37014501 TCAGAGTCAGACACAATTTAGTGACTAAATAACAA[C/T]AAATTGCTCTCATTTCACGTTCAGATTGCTACCAT Y 2 1 2 1 303000 r 74 goat snp14463-scaffold1578-643250 17 33852853 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420378 Affx-122944942 AX-123290725 17 37043695 GTACCCAGAGTATCTATTACCACCCTCTTGATCAC[A/G]TGAGTTGCTTGGGCAAGAAAACTTCAACAGTTGTC R 2 1 2 1 101000 f 74 goat snp14462-scaffold1578-614056 17 33823702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781926 Affx-122939096 AX-385269008 17 37084927 CGAGCATATCCTATTCATACTGTTCCTACTCTCCT[A/G]CAAGAGTGAATAATATCTGAATCAAATATATTCTT R 2 1 2 1 101000 f 74 goat snp14461-scaffold1578-572824 17 33781883 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450369 Affx-122922095 AX-123320704 17 37130101 TACTGCTCCCCCCAAAATTGTTTAATTGAAACATA[C/T]GAAACTAATATTTTATCAAAATAATACAAGTGTTT Y 2 1 2 1 103000 f 74 goat snp14460-scaffold1578-527650 17 33736124 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425649 Affx-122940885 AX-123295995 17 37170022 CCCTCTCATTCATTCATTTTCTGTTTATTTTGGTG[C/T]ATTATTTGAAAATAAGGAGGCTTAATTTGAAACAC Y 2 1 2 1 303000 r 74 goat snp14459-scaffold1578-487729 17 33695105 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385167 Affx-122971743 AX-123255525 17 37233282 AGCTCATGAGCCTTTTATTGTGGTCATTTTAGCAC[A/G]TAGTAACCCACAAAGTGGGGATGAGGTTTGCATTT R 2 1 2 1 101000 f 74 goat snp14458-scaffold1578-424469 17 33631511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781334 Affx-122923980 AX-385268419 17 37267591 TCTCCATAGTCATTCTGGGACTTAAAACCATGAAA[C/T]GCTTGGGATTGCTTCCTGTCTGTTAACTGTTGCAA Y 2 1 2 1 101000 r 74 goat snp14457-scaffold1578-390160 17 33596896 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271831 Affx-1111833096 AX-519545615 17 37271550 TGGCCCTGCGGTTGCATAACATTTGTTATTTTCCA[A/G]TTTCTCTGAGACCTAAATTTGAACTTAGCATGTTA R 2 1 2 1 201000 r 74 goat 17_37271550_AF-PAKI 17 37271550 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449634 Affx-122923186 AX-123319969 17 37296946 GACTAAAAGGAAATCCCTCCACCCAGCTGGTGTAC[A/G]ACTTTGGCAAAATTCTTTCACTTGAATTTAGACTT R 2 1 2 1 201000 r 74 goat snp14456-scaffold1578-360805 17 33567314 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415710 Affx-122948523 AX-123286059 17 37328018 TCAGACACTCTACTGAGACCTGTTTGCTCTGCCTT[C/T]ACAGCCAGACTTAGATTCTCACTCAGTAGTTAGGA Y 2 1 2 1 201000 r 74 goat snp14455-scaffold1578-329733 17 33543239 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772823 Affx-122965830 AX-385259968 17 37376541 TTGGTTTCTGATATTAAAAATCTAACAGGGAGGCA[C/T]AAAGTAGATTAAGAGGCTAAAGTATAGATTGGCAA Y 2 1 2 1 101000 f 74 goat snp14454-scaffold1578-281210 17 33494140 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381881 Affx-122974171 AX-123252239 17 37428309 TATTCTATGTCAATTTCTTGCATATCAGTTCTCAC[A/G]CGTGTAATCTGGTGAGGTCTCGATGCCACCACATA R 2 1 2 1 201000 f 74 goat snp14453-scaffold1578-229442 17 33441147 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785122 Affx-122936333 AX-385272168 17 37485031 AAATGAATAGTTACTGAAAAGATTTATGGGTGGGA[A/C]ACATGTGAATTTCCACCAGAGTGGAGAGGATTAAT M 2 1 2 1 201000 r 74 goat snp14452-scaffold1578-172720 17 33382932 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791186 Affx-122945224 AX-385278181 17 37519944 CTCTCCAGGGTTATCTGATCATAAAAATATAATTC[G/T]AAAACATCAAGTTGTTAATAATGAGGATAGATGTT K 2 1 2 1 101000 f 74 goat snp14451-scaffold1578-137807 17 33347560 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801493 Affx-122925685 AX-385288402 17 37568548 TACTGTAGTAAAATTGTGTATATTCTGTCAACATC[A/G]CTTGGTGGTGAGGTGTGCCACTCAACTGTATTTTG R 2 1 2 1 102000 r 74 goat snp14450-scaffold1578-89203 17 33299055 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451802 Affx-122921490 AX-123322135 17 37614911 TGTAAACTTTGGAAACTATCTCACTCAGCTCCCTC[A/G]CAGAAAGAATGGACAGAAAAGGAACACTACACAGA R 2 1 2 1 201000 f 74 goat snp14449-scaffold1578-42840 17 33251859 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403822 Affx-122957956 AX-123274174 17 37648665 TCTCCATCATGCAGATACTTTCATTTTTAATATAG[C/T]CCTGCTGCAATATTAGTTACTATGGTCTAGGATCA Y 2 1 2 1 101000 r 74 goat snp14448-scaffold1578-9086 17 33217983 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766683 Affx-122946624 AX-385254028 17 37674936 CGAATGTTGGTAGTCTTAAAGTCACCAAATACCTT[C/T]ATATAATTATTAATTGTGAGATCATGGAAATCACT Y 2 1 2 1 101000 f 74 goat snp58215-scaffold943-17086 17 33191073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766170 Affx-122962311 AX-385253572 17 37732327 GCTGATGAAGCAAGAAAGACAAATGATGGCTAGCA[C/T]GTGAATAATTTTGGTACAAGCCAAACACTTTACTG Y 2 1 2 1 101000 f 74 goat snp58216-scaffold943-74477 17 33131310 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418270 Affx-122947012 AX-123288618 17 37802134 CAAAGGAAATGTTGTATATTTCTCCAAGCACAATT[A/G]TCATTCAGCTCATGATGCTGACTAACTAGAAGCTT R 2 1 2 1 101000 r 74 goat snp58217-scaffold943-144284 17 33060950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784028 Affx-122947272 AX-385271081 17 37838444 AGCAATATATAAACAAAACATAAGATTTGTTCAAC[A/G]TCTGCAAATCCACCAATACAATTCATGATAACTAC R 2 1 2 1 201000 f 74 goat snp58218-scaffold943-180594 17 33024772 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428615 Affx-122938687 AX-123298957 17 37868573 TTATATCATTTCTGTAATATCTCTAGCACTCCTGT[A/C]TTTTTAATGTATGTCAGAAACTCATCTATGTTCAA M 2 1 2 1 101000 r 74 goat snp58219-scaffold943-210723 17 32993663 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447822 Affx-122923914 AX-123318158 17 37899364 GAAGCCAATACATTTGCTGAGAAGCACCAGGAGTG[C/T]AATATGTCATGATAATTGTATTATTATTTCCCACC Y 2 1 2 1 101000 f 74 goat snp58220-scaffold943-241514 17 32963281 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767071 Affx-122929173 AX-385254360 17 37933547 CAGTATCTGTCAGGTGAATTTTGTGGGAGGTAGCC[A/G]GAAGTATGTGCTACTTTGACGTTAGTAAAATGGCA R 2 1 2 1 101000 f 74 goat snp58221-scaffold943-275697 17 32929032 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796014 Affx-122955362 AX-385282966 17 37962546 AATTGGCAAAGCAGTTCTATAAATGGATACTCAAG[C/T]AAAAATTGTCAGCTTACCACATGGAGATCTAAAGG Y 2 1 2 1 101000 f 74 goat snp58222-scaffold943-304696 17 32899909 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408044 Affx-122954283 AX-123278395 17 37998362 TTGATGAAATTTCAGGAATATTTTCTTATTTGAAA[C/T]GGTCCTCTAAAAGTAGAAATATTCAATAGCCTTTA Y 2 1 2 1 101000 r 74 goat snp58223-scaffold943-340512 17 32864329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778657 Affx-122933976 AX-385265768 17 38027778 TTGTAAGTATAATGGAATGATCAAATTAGTCCAAA[C/T]AGTGTACCTTCCAGATCTTGACTTGATATTGCAAA Y 2 1 2 1 201000 f 74 goat snp32937-scaffold381-161884 17 32833505 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378053 Affx-122977188 AX-123248412 17 38061355 GAGAAGTAAGAGGGAAGTCAGGAGGGAGAAAGATG[C/T]ATAGAAGAGGGAGTGAGTAAAGGGCAAATGTTATC Y 2 1 2 1 102000 f 74 goat snp32936-scaffold381-128307 17 32798625 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444263 Affx-122927209 AX-123314600 17 38090495 AGAAAAGCATGGTGATTTAGACCGAGTGTTATTGA[C/T]GAAGGCTATGTAAGGAAGAATGATTGCATTTTAGT Y 2 1 2 1 101000 f 74 goat snp32935-scaffold381-99167 17 32768795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400659 Affx-122960352 AX-123271014 17 38143864 AACTATATTTTGAACATCATTTCCTTTATTCTCTA[G/T]ATTAACTTTATCCATGGCTGAATTTACATGTTCAC K 2 1 2 1 101000 r 74 goat snp32934-scaffold381-45798 17 32715781 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383596 Affx-122972567 AX-123253954 17 38181481 AAATACCAGTGTTCAGTTCAATACACAACTTAATC[A/G]TGAAATGAGGAACTTGAGGGAAAAGAAAGAATCAA R 2 1 2 1 101000 f 74 goat snp32933-scaffold381-8181 17 32683692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768164 Affx-122965877 AX-385255361 17 38271088 CACTAAAATTCTGGTCACTGCCACTTTGTATGAAG[C/T]AGATAGCACTATCACTTGCAAATAAACACATATAT Y 2 1 2 1 101000 f 74 goat snp52670-scaffold79-81327 17 32564500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432751 Affx-122935446 AX-123303092 17 38319481 ACTAGTTTTGTTTGTAGTGATGCTCATGACTACTC[A/G]TAATCATATACTGAAATGTCTGATTGACTGCACAT R 2 1 2 1 201000 r 74 goat snp52671-scaffold79-129720 17 32518119 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384258 Affx-122972352 AX-123254616 17 38352217 ACAAAATAAAGTGGATTTGGTTTTTATTTATGGGC[A/G]TCAGAGCAGGGAAGCTCTGGCATCTTTTACTTAAT R 2 1 2 1 202000 f 74 goat snp52672-scaffold79-162456 17 32485061 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776120 Affx-122925633 AX-385263250 17 38400478 CATAGCCTCTAAATACATCAAAATAAGACATGGTG[C/T]GATAGATTTTTATATAGCACTTGCTTATTCATAGG Y 2 1 2 1 101000 f 74 goat snp52673-scaffold79-210717 17 32428749 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786910 Affx-122969515 AX-385273939 17 38463524 AACTGAGGATCAGAAGAGGGAGGTGACTCAAACTG[C/T]AAGTTTGCTAGTAAAGCTGCTCTCACAATTTAGAG Y 2 1 2 1 101000 f 74 goat snp52674-scaffold79-273763 17 32365549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437832 Affx-122932100 AX-123308170 17 38524518 AGCTATGCTGTTTTTGACTTAGAGTCTACACAGCT[A/G]CAATAGGTGGAACTTCCTCCCTCCTGTCTGGTCCT R 2 1 2 1 101000 f 74 goat snp52675-scaffold79-334757 17 32304325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441219 Affx-122929518 AX-123311556 17 38563452 ACTTACAGTTAGTTTTTAAATTAAGAATGTTTTTA[C/T]GAATTAAAGTAAATCAAATGTGAAAGTGATAGGCA Y 2 1 2 1 101000 r 74 goat snp52676-scaffold79-373691 17 32264746 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439078 Affx-122931135 AX-123309415 17 38617705 TTTTGACTTGGTAAGTAATAGAAAGAGTGTTTACT[A/G]CGGCATACAGCAGAGTTCAGAAGGCCCTTTCACAC R 2 1 2 1 201000 f 74 goat snp52677-scaffold79-427944 17 32209602 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404942 Affx-122956428 AX-123275294 17 38647278 CTGTCCAGTGTAAGGGATTGCCATCAAATTACTCA[C/T]GCACTCATTGCACACACTGTTCCTTCCGTAGACAC Y 2 1 2 1 101000 f 74 goat snp52678-scaffold79-457517 17 32179661 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787934 Affx-122959099 AX-385274956 17 38688579 TCTTCAATCAATTCTCAATACAACAGTCAGCATGA[G/T]CCTGTAAATACAAAAGTGAGGTCTCACCACTAATA K 2 1 2 1 101000 r 74 goat snp52679-scaffold79-498818 17 32137921 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774863 Affx-122958748 AX-385261997 17 38720658 AATTCATCTTTGACCTAAAGATGATGAGAGTGTTC[A/G]AGCAGTTGTGGCAACAAACAGTATAGAATCTCCAC R 2 1 2 1 101000 r 74 goat snp52680-scaffold79-530897 17 32105782 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453701 Affx-122919689 AX-123324034 17 38767128 AATCAGTACAGTGACACAGATGTAGTTGGAGACTG[C/T]CTAACTTTAGAGGGAAATGCATCTTATCGGGACTT Y 2 1 2 1 101000 f 74 goat snp52681-scaffold79-577367 17 32059529 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273645 Affx-1111833719 AX-519547258 17 38805255 GAGGTCTTC[A/G]TTAGGTGTAGGTGCTTTTGTCTGCAGCTATAGCTG R 2 1 2 1 101000 r 74 goat GoatD01.002359 17 38805255 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320779378 Affx-122976951 AX-385266482 17 38833045 ACTCTGATTTTGAAACAAGAATACCTAAATCCACA[C/T]GTCATGTATGCTGAGCTTTATTATCCCTTTTGTCC Y 2 1 2 1 101000 r 74 goat snp52683-scaffold79-643284 17 31991345 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412772 Affx-122950506 AX-123283121 17 38877336 AATACTGAGTGGTCTCAGCAGTTGGTGTTAGAATA[A/G]TGACTGCTACCCAGGCCCAAGGGGCGGATGAGTGA R 2 1 2 1 101000 f 74 goat snp52684-scaffold79-687575 17 31946549 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771170 Affx-122936373 AX-385258330 17 38970168 AAAAGGATTGGAAAATCGAATGGTTCTTGAAACTG[C/T]GGACACGCTTGTGCTACCTGGTGACTAAAAGAACA Y 2 1 2 1 101000 r 74 goat snp52686-scaffold79-780407 17 31852239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277097 Affx-1111835739 AX-519550604 17 39025727 GACCCCTAATTAATAAGTAACATTCACTTTAGAGG[A/G]TAATTTAAAATAAGCTTTTAAGTTCTATTTTAGTG R 2 1 2 1 101000 f 74 goat Random2.2K-1666 17 39025727 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320781582 Affx-122922423 AX-385268666 17 39060276 TCCACAAGTTTCATATCCCAGAGTGAAGCAAGTTT[A/G]TCATTTAATTTCCAACTAGATAACTTTAATGATCT R 2 1 2 1 101000 f 74 goat snp52688-scaffold79-870515 17 31760435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449121 Affx-122923574 AX-123319456 17 39142129 CTAATATCACACTCTAAAAGAGAAGGAAAACCACA[C/T]TGCTTACGGCATTTTCTGACACATGCCCTAGCCTC Y 2 1 2 1 101000 r 74 goat snp52690-scaffold79-952368 17 31677756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384402 Affx-122972205 AX-123254760 17 39310462 CAAAGAGGCATTAGCCAGGAGCCTTGGGAGCTGCT[A/G]GTGAGAAATCCTGAGATGGAGCTGAGTAAGGAACA R 2 1 2 1 101000 r 74 goat snp52694-scaffold79-1120701 17 31511142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388402 Affx-122969293 AX-123258760 17 39384503 GGGGTCCGCAGGGCTGGAAATAGCTTGGTTGGATG[C/T]AGAGATTTGAAATGTAGACAGTGACATAAAAGGAT Y 2 1 2 1 101000 r 74 goat snp52696-scaffold79-1194742 17 31438825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273874 Affx-1111833905 AX-519547482 17 39389014 GAGGTTGAAAATGTTGGGTTTTCCTGAGAGCTGTA[A/G]TGGAGGCAGTTCTGCATCTCCCCCAGGTTCTGGAG R 2 1 2 1 101000 f 74 goat GoatD01.010026 17 39389014 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38399436 Affx-122961220 AX-123269791 17 39415205 AGCTGATCTGGAAGCCTTCTTTGCTTGATCACTCC[C/T]TCTGGTGTGACAGAGACTTCACAGAGGGAGTACTG Y 2 1 2 1 101000 f 74 goat snp52697-scaffold79-1225444 17 31410926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783620 Affx-122919658 AX-385270679 17 39536367 GAAACATACTGCTCAGGCTTGGATCATTATAAGGT[A/C]GCTCTTCTCCATATATCTGAAGGACCATGTGCGTC M 2 1 2 1 101000 r 74 goat snp52700-scaffold79-1346606 17 31289394 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385671 Affx-122971145 AX-123256029 17 39620990 TTCACATGGGAAGAATTCAGTAAATGTTTGCTATC[A/G]TTAGCTAGAAGACTTTTAAGAAATTAACCACTGTT R 2 1 2 1 201000 r 74 goat snp52702-scaffold79-1431229 17 31204289 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403245 Affx-122957885 AX-123273598 17 39704083 ACCTGAGTGTGTGCCATCCCGGTGCCCCTGCAGAT[A/G]TGGGTTGTGCTTGCCCACTGTCGCTCTCTGGTTGC R 2 1 2 1 101000 r 74 goat snp52704-scaffold79-1514322 17 31120886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397695 Affx-122962573 AX-123268050 17 39768473 GACTGGACCCTCAACAAGTTCCCAAAACCACTAGC[A/G]TGGTTACCATTTTGGAAAGTGCAGCATCAGACTTG R 2 1 2 1 101000 r 74 goat snp52705-scaffold79-1578712 17 31055982 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463502995 Affx-1110017146 AX-514985667 17 39782486 GGATGGGAGCAATTCCTAGAGCTGCTGGCTGCAGG[A/G]GCCGAAGGGTTCCAGGGCTAGTGCAGGCCTACTGG R 2 1 2 1 102000 f 74 goat 17_39782486_AF-PAKI 17 39782486 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320801581 Affx-122966517 AX-385288490 17 39798087 AATATCATTATAAATTTAGGATTATAGTTTTCCCT[A/G]TTATTCATATGTAACACTTCTGCAGTATGTCAGCT R 2 1 2 1 101000 r 74 goat snp52706-scaffold79-1608326 17 31026718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385073 Affx-122971813 AX-123255431 17 39871381 GGACACAGGAGTCCTGGCTTTCCAAGGGGTATGGT[A/G]CACCTGTAGGTCTGGTCACAAGAACTCAGGGGAAT R 2 1 2 1 101000 r 74 goat snp52707-scaffold79-1681620 17 30953351 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397162 Affx-122962429 AX-123267517 17 39902381 ACATTCATTTTCTTTATACCATTATTTACCTGTGC[A/G]TCTTCATGAACTTCTGAAATGCAGTTGTGCAGCTG R 2 1 2 1 201000 f 74 goat snp52708-scaffold79-1712620 17 30922534 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788452 Affx-122943566 AX-385275469 17 39938821 AACACAGGGTTATGTATACAGTATAACCTCGATTA[C/T]GTAGAAAAATGTGATCAAGCATTTTTTAAAAGGTT Y 2 1 2 1 101000 f 74 goat snp52709-scaffold79-1749060 17 30886128 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417228 Affx-122947290 AX-123287576 17 39971390 GGCACCTACCTCTTAGTCCAGGAGATCCATGTCCT[A/G]TTCTGTGAAATTCATGTGACCACTTTGGAAAATAA R 2 1 2 1 101000 r 74 goat snp52710-scaffold79-1781629 17 30854059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443272 Affx-122927484 AX-123313609 17 40027472 TGTCTGATAATAGGATGTTAATATCCCCTATGACA[C/T]AGTTAAGTTGAAGACTGAATAACATTGTTATGTAA Y 2 1 2 1 201000 r 74 goat snp52711-scaffold79-1837711 17 30797960 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444241 Affx-122927225 AX-123314578 17 40118917 TTTAGGGAAGAGCTCCACAGGGATAAGAGTGAAAA[A/G]TCTCGACCTTTGAGAATACAGCCTGAATATCAGCA R 2 1 2 1 201000 f 74 goat snp52713-scaffold79-1929156 17 30706701 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775217 Affx-122949941 AX-385262348 17 40149293 TCAGCAATCATTATAATGACCAAGGAACAATGATA[C/T]CATCTTGAATGACAATGCATTATTACGCCTTAATT Y 2 1 2 1 101000 r 74 goat snp52714-scaffold79-1959532 17 30676592 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399670 Affx-122960506 AX-123270025 17 40198395 TGATGCCACCTTGCTGTTCTGATCAGTATGAAGGC[A/G]CAGATTTGAAGATGATGAGAGTGTGTTGGGCCACA R 2 1 2 1 101000 f 74 goat snp50381-scaffold720-33972 17 30622682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405090 Affx-122956991 AX-123275442 17 40231854 GTTATCACTATGTAACTGCTTTTGCTCTGGCTCCC[A/G]TTCTGCTTTGATTCTAGCTCTTTCTATAGGCAACT R 2 1 2 1 201000 r 74 goat snp50382-scaffold720-67431 17 30589147 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419595 Affx-122945999 AX-123289943 17 40269842 TGAAATGGCTGAGGATGTTTTAAAAATTGGAAAAA[A/G]CTTCCGAAGTATGGCTTTCCATGACCTCTTCTGCC R 2 1 2 1 103000 r 74 goat snp50383-scaffold720-105419 17 30550717 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441768 Affx-122929108 AX-123312105 17 40315125 AAGAACAGGTGTCTTGCCATTTTCTGAAATGGCAG[A/C]GAATTCTGACTCAATCCTTTGGAACACTTGAAAAA M 2 1 2 1 101000 r 74 goat snp50384-scaffold720-150702 17 30505636 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384159 Affx-122972797 AX-123254517 17 40373892 GAAAATTATGACATTATTTTGGCAGGTTATTGGTG[A/G]CCTCCAGGATTTAATGGTCATTGAGAGCTACAGTT R 2 1 2 1 101000 r 74 goat snp50385-scaffold720-209469 17 30445315 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446777 Affx-122925313 AX-123317113 17 40414865 TGGGTGGACTGTGCTGATGCCTCAGTGAAGAGGCA[G/T]CTGACTTTTCTTAGCCATGTCCTGTCACCCTGCAA K 2 1 2 1 101000 r 74 goat snp50386-scaffold720-250442 17 30404448 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385014 Affx-122971870 AX-123255372 17 40450625 GGTGAGAGTGTGCTTATCTGAGCAGGCTGAGGAGA[C/T]GGGAGTGAGGCCACGGGAAAGCAGAAACTGAGTGG Y 2 1 2 1 101000 f 74 goat snp50387-scaffold720-286202 17 30368580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376046 Affx-122978935 AX-123246405 17 40512587 GGTGTTTCAGCAACAGGCCAGGCCAGCTTGTTGCC[A/G]CCCAGGCCTGATGTTAAGATGGGTGATAAGAGTAC R 2 1 2 1 101000 r 74 goat snp50388-scaffold720-348164 17 30299665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778607 Affx-122953377 AX-385265718 17 40557615 AGACACTCAGTACGTTTAGCGCTGGGATAAAACGC[G/T]GAGACTGTTTCCATGCCCACAAGAGTCATTAAATC K 2 1 2 1 101000 r 74 goat snp50389-scaffold720-393192 17 30254479 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768597 Affx-122938806 AX-385255777 17 40586182 AACCCAACTCTGGTCAGTTCTCCTCAAGTGAAATC[A/G]CATGACTAGAAACAGGAAATTGGAGGATATCTAAC R 2 1 2 1 101000 f 74 goat snp50390-scaffold720-421759 17 30225440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803432 Affx-122962103 AX-385290263 17 40623364 CTCCAAAATAACCATCAGAGAGGTGCAAATTTGCT[A/G]TCTTTGAAGATGGAGCAAGAAGTGATGAGCTGAAG R 2 1 2 1 202000 r 74 goat snp50391-scaffold720-458941 17 30188268 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389946 Affx-122968087 AX-123260303 17 40660145 TGGTAGTATTTTATTTTCTTGTAAGTTTCTGCTAG[A/C]TCTAACACATGAGATCAGTCTACGTTTTTCTGAAA M 2 1 2 1 201000 r 74 goat snp50392-scaffold720-495722 17 30150563 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798251 Affx-122968506 AX-385285186 17 40702676 GGCACAAAGGAAACAATAATGTTTTACTACTCAAC[A/G]TTCTGGAAGCAAAGTGCCTGAGATTATGTATTTGT R 2 1 2 1 101000 f 74 goat snp50393-scaffold720-538253 17 30099583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440867 Affx-122929246 AX-123311204 17 40752826 ACGTTATCTGCATTGTTACTTTTCAGTTTGAAAGC[G/T]AACTGTATAAAGCATTTGTGCAAAGTGAATATGTA K 2 1 2 1 101000 f 74 goat snp50394-scaffold720-588403 17 30049130 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394684 Affx-122964360 AX-123265039 17 40811715 ATTCCACTTGTTTCAAGTATTTTACTTTTATGCTT[C/T]CTAGTCCAAGGCAGTCTATTTTTTCCTTTTAAGTT Y 2 1 2 1 101000 r 74 goat snp50395-scaffold720-647292 17 29989183 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382633 Affx-122973688 AX-123252991 17 40841925 TGTTCTAACAAGGCTGGCTGCAAGGCCTACAGAGT[A/C]CTGGGTCTGTCACTGGCCTGGTGGTGTGTGTGGCT M 2 1 2 1 101000 f 74 goat snp50396-scaffold720-677502 17 29959102 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773862 Affx-122953248 AX-385261002 17 40871919 ACACTTGTCATTGTTTAGATCAAATGGAAATACCT[A/G]TTTTCAGGCATCAGGTTATTTTAACTTACTGTTTC R 2 1 2 1 101000 f 74 goat snp50397-scaffold720-707496 17 29929553 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436156 Affx-122932625 AX-123306495 17 40902045 AATGTAAATAAGGCAAAAGAAGATGCCTTGGGGAG[C/T]GAGAGACCATGGGGATTAGAGCTGGGCATAAATCA Y 2 1 2 1 101000 f 74 goat snp50398-scaffold720-737622 17 29899224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447932 Affx-122923790 AX-123318268 17 40935295 ATAATGATGGTGCATGGAGATGGAGCCTTTGAGAG[A/C]TGGGTAGGGCATTACGGTGGAGTCCTATGATTGGA M 2 1 2 1 201000 r 74 goat snp50399-scaffold720-770872 17 29865687 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782890 Affx-122919810 AX-385269960 17 40966505 AAATTATATAAAATGATATTACAGTATGACTCACA[C/T]GATTTCTTGATTGCATCTCCAAATGTTTTTCCTAG Y 2 1 2 1 101000 r 74 goat snp50400-scaffold720-802082 17 29833813 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389277 Affx-122969011 AX-123259635 17 40997380 GTGGCCTGATCAAAGAGAAAAATAGGACTTTCATG[C/T]ACTAATATGGGGAAGAGTGAAGAGGGGCAAGTATG Y 2 1 2 1 201000 f 74 goat snp21596-scaffold2113-505 17 29802359 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788518 Affx-122947065 AX-385275535 17 41035908 GAAATAAGCCTAGGACATTTGGGCATGGCCAAGTC[A/G]TCACCCCTTGATAATTTCCTATTATCACTAGAAAA R 2 1 2 1 101000 f 74 goat snp21597-scaffold2113-39033 17 29762313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444480 Affx-122926529 AX-123314817 17 41072598 ATTTATTTTTTAGGGAGGAAGGGATTAATTTGATG[C/T]AAAAGGAGAAGAGCTCAAGTTTTGTGCCTAATTTT Y 2 1 2 1 101000 f 74 goat snp21598-scaffold2113-75723 17 29725934 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425259 Affx-122940984 AX-123295605 17 41112816 AGACTTTAAAAGTCAGTTCTTATAATTGATAAAAG[C/T]AGGCAGAAAATCAGTATGAAAACACAACATAATGG Y 2 1 2 1 201000 f 74 goat snp21599-scaffold2113-115941 17 29685325 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389039 Affx-122968622 AX-123259397 17 41168390 TCCCAGATTGATTAAAGACTTTCCTATGAAGCGCT[A/G]TGGTGGGAGGGAGCTCAAAGGTCAGAAATGCAGAC R 2 1 2 1 201000 f 74 goat snp21600-scaffold2113-171515 17 29628192 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773314 Affx-122923522 AX-385260457 17 41210739 TTGCTGAGTATAGACCTGTTTCCCACATTTGACTC[C/T]AAACTCCTTGAAACTATACTCCATAATTATAAGGC Y 2 1 2 1 101000 f 74 goat snp21601-scaffold2113-213864 17 29582240 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442941 Affx-122928227 AX-123313278 17 41270465 ATATGACATTTTTTCTATTGTTGAGCCTCACAGCT[A/G]CAGAGGATATTAAAAAATAGTCTGTGTAGGCTATT R 2 1 2 1 101000 r 74 goat snp21602-scaffold2113-273590 17 29522917 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421117 Affx-122944207 AX-123291464 17 41301384 AAAACATAAAATAGATCTGGCCACATCCTATTTCC[A/G]TTAGCACAGTTTAGGAACTCCCTGAAGAATAAAGA R 2 1 2 1 101000 f 74 goat snp26695-scaffold2802-80322 17 29488581 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779369 Affx-122974642 AX-385266473 17 41368541 TTAGCAACAATCATTTATTCTAACTGCTTCTTCCC[A/G]TTCTATTTCCACCCAGAAAATAGTTCACACAAATA R 2 1 2 1 201000 f 74 goat snp26693-scaffold2802-13165 17 29421251 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437843 Affx-122932091 AX-123308181 17 41388268 GCCAGTTGTGTCTGCAGCTCATGTTGGCCCAAGCA[G/T]CAGTAATTTCAGGGGGAGATCTGTGCATGGCTGGA K 2 1 2 1 201000 f 74 goat snp51109-scaffold746-6463 17 29399374 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420595 Affx-122945254 AX-123290942 17 41436884 GTGTTATTCTCAATGTTAGAAAGCATTCAATCTTT[A/G]AACATTAAGTATAATGTAAATTGTAGGGTTTTTGT R 2 1 2 1 101000 f 74 goat snp51110-scaffold746-55079 17 29350385 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785058 Affx-122971412 AX-385272105 17 41473348 TGTGCAAGCAATTCATAGATAGTACAAATTTGTTA[C/T]GTTGAAAAATACTCATTAATTGTCCTAATATTCAT Y 2 1 2 1 101000 f 74 goat snp51111-scaffold746-91543 17 29313742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775566 Affx-122976787 AX-385262697 17 41543097 AAAGAAATATTTTCTTATAGGCTTTCACCAACCTG[C/T]ATTATGATGAGTCATGAACACACACATTTTTAAAA Y 2 1 2 1 101000 f 74 goat snp51113-scaffold746-161292 17 29242001 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446754 Affx-122925329 AX-123317090 17 41597227 TGAAAGTTGGAGAAAAGGCAAACCAAGAGTTAATA[C/T]AGGCCAAGAAGGCAGCAGAAAACTGCTACTGGATG Y 2 1 2 1 101000 f 74 goat snp51114-scaffold746-215422 17 29188537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390138 Affx-122967993 AX-123260495 17 41617367 AATGCCTTTCCTTTGCATGTTCTTGCATTTCTTGC[A/G]TTTCAGATGAGGACACAATTAAAACACCAACTGTA R 2 1 2 1 201000 r 74 goat snp46819-scaffold653-2129345 17 29168195 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419276 Affx-122946249 AX-123289624 17 41650462 CCCATCTTTCAGCAAAGCATTTTAACACAGAGTGA[C/T]GTAGTTGTAGGGGAAAAAATAACTTTGAACATATC Y 2 1 2 1 101000 f 74 goat snp46820-scaffold653-2162440 17 29134544 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413680 Affx-122950103 AX-123284029 17 41684089 AAATGCTTCAGTCGACATTAAAGCCCCTTTTAAAG[C/T]GGAAACAGAATGAGATGAAGACAGAATTTATTGTA Y 2 1 2 1 101000 r 74 goat snp46821-scaffold653-2196067 17 29100811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383660 Affx-122972517 AX-123254018 17 41728663 CCACAAGCAGGCTGCTGCCCTCAACTTTCCATTCT[A/G]TGTCTCCATCTTACATATATGCTGTACTTATTTGG R 2 1 2 1 101000 r 74 goat snp46822-scaffold653-2240641 17 29056215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429012 Affx-122938332 AX-123299354 17 41772020 CTGAGAAAATTCAACTGATGATATAAACTAAATAA[G/T]ATTCCTTAAAGAACCACCAAGCTTCACCAGTAATG K 2 1 2 1 101000 r 74 goat snp46823-scaffold653-2283998 17 28995590 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800292 Affx-122970336 AX-385287215 17 41808909 CATAGACCTGGTTTGTACAGAATTCTGACTGCTGC[A/G]TAGCCAGTTGAAGTAAAGAGATTGTTCCAGTAATA R 2 1 2 1 101000 f 74 goat snp46824-scaffold653-2320887 17 28958842 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784892 Affx-122941648 AX-385271939 17 41875233 GTTTAAGATGATTACCTGGGGAAAACTGCACAGAT[A/G]CATAATTGACTCATACTGGAACGTTACCAGTTCTG R 2 1 2 1 101000 r 74 goat snp46825-scaffold653-2387211 17 28891608 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417935 Affx-122946715 AX-123288283 17 41925241 CGGAGTTCAGCTCCTCTTACCTGCTCTCTGCCTCC[A/C]CATCAGACCTCTTATGCCACCTTCGAACTGGTGAC M 2 1 2 1 201000 r 74 goat snp46826-scaffold653-2437219 17 28841717 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772893 Affx-122935259 AX-385260038 17 42011319 TATAGATGGCTACATCTTAGGAAATGAAACAGCAG[C/T]AATTTGACAGTTAATGAGTGCTTCCTTCAAATTGC Y 2 1 2 1 101000 f 74 goat snp46828-scaffold653-2523297 17 28755520 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796072 Affx-122963382 AX-385283024 17 42058189 ACACTGGTATTACGTTCTTAAGACATTAATATTTT[A/G]AGCTTTATGAGGTAGAGTTAAATTATTTCTAAAAG R 2 1 2 1 101000 f 74 goat snp46829-scaffold653-2570167 17 28708866 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380201 Affx-122975495 AX-123250559 17 42116153 AAAAACAGTCCTCAAATATTCATTTATTTGAATAG[C/T]GCTATTAATGTATTTGAATGCTTCAAACATTAAGA Y 2 1 2 1 103000 r 74 goat snp46830-scaffold653-2628131 17 28651209 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438350 Affx-122931330 AX-123308688 17 42161088 CAAAGACTCTTGGAAAATAAATAATCATGTCTTCA[A/G]ACTCCTCTTACTGGGATGCAAGTAAAAAGCAGAAT R 2 1 2 1 101000 r 74 goat snp46831-scaffold653-2673066 17 28606126 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437160 Affx-122932136 AX-123307498 17 42200553 GTGGAGCCACACTTCCTGGCCACCCCCAGGAAGTC[A/G]TCTTGCCTGTGTCAGCAGAGGGAAATTTCTGGAAA R 2 1 2 1 103000 r 74 goat snp46832-scaffold653-2712531 17 28566538 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769248 Affx-122947008 AX-385256421 17 42249130 ACAAAATGGTTGAACTTCATAAAAGTAGAAGATAA[G/T]CTTGCTTTCTTTGCCCCATCTACTAATAGGAATTT K 2 1 2 1 101000 r 74 goat snp46833-scaffold653-2761108 17 28517685 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425413 Affx-122941541 AX-123295759 17 42319962 CCTTGGAATTACTTAGGAAAGCTTGATACCAAATA[A/G]CGTCTCTGATTCCTGTGAGTTGGGTTTGACAAGCA R 2 1 2 1 101000 f 74 goat snp46835-scaffold653-2831940 17 28452307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376049 Affx-122978933 AX-123246408 17 42349035 TGTGAAACAGGAAGTGAAGAGAACATTTACTAACG[C/T]AGGAAATGTGAAAGTAGCCTGGGAATCTTCCGAGT Y 2 1 2 1 101000 r 74 goat snp46836-scaffold653-2861013 17 28423216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765573 Affx-122926536 AX-385253053 17 42392261 TTCTAGGACACTGCAAGGCCATAGCTTATTCCTCA[A/G]TTAATTACTAAAATATAGTGTTTGGAGAAATACAA R 2 1 2 1 101000 f 74 goat snp46837-scaffold653-2904239 17 28379931 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388481 Affx-122969234 AX-123258839 17 42428686 GCGCTCAGGTAAGATTCTCTAGTTAGGGACACTCC[A/G]TGCCTATTACCATGTGTCATTATTGAGAGGAGCAA R 2 1 2 1 101000 f 74 goat snp46838-scaffold653-2940664 17 28343739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415873 Affx-122948491 AX-123286222 17 42471530 GAGTTGATCATTTGATATATATTTTCTATTTAAAA[C/T]AGAAAACAATGTTCTGTTGCTGGAGAGATGGGACA Y 2 1 2 1 103000 r 74 goat snp46839-scaffold653-2983508 17 28301528 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773232 Affx-122956178 AX-385260375 17 42505436 ATAAAAATAATTCCACTTCCAGTGAAAGTAAAAGC[A/G]TCTGAAAGCTGAAGCTGAGAAATTTGAAGGAGACT R 2 1 2 1 101000 r 74 goat snp46840-scaffold653-3017414 17 28267577 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272000 Affx-1111833097 AX-519545768 17 42559593 CCCTACAGATTCCTATGTAATCCTCTGTGGCCTAA[A/G]ATCTGAGTAGTGATTCCCACAAAGCAAGGGGAGGG R 2 1 2 1 101000 f 74 goat 17_42559593_AF-PAKI 17 42559593 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320791399 Affx-122940257 AX-385278391 17 42561055 ACCTGTGGGCAAGTGTGACCATTTCTAAATTTGTC[A/G]TAAAATATTTGCACAGAAGCAAACTTGTCCCACCT R 2 1 2 1 201000 r 74 goat snp46841-scaffold653-3073033 17 28209774 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429860 Affx-122938148 AX-123300201 17 42593722 AAAATTGTTTAGCACAATGATCATTTGAATGGAAA[C/T]CACCCAGTCTCACATGGACCCGTCCATCTTACTTG Y 2 1 2 1 201000 f 74 goat snp46842-scaffold653-3105700 17 28174604 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390661 Affx-122967132 AX-123261018 17 42631958 GATGCACACGATGTTCAGCAAACACCAGCTCTCTG[C/T]GTACATGACAGTCAGCAAACACCAGCATAGTATAC Y 2 1 2 1 101000 r 74 goat snp46843-scaffold653-3143936 17 28135883 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794323 Affx-122952314 AX-385281287 17 42678752 TTTGATGTTACCTACTTTTCTATTTTATGAGAACT[A/C]TAATTCTTACCCAAGTATGATAGCAAACTAAGTAG M 2 1 2 1 101000 r 74 goat snp46844-scaffold653-3190730 17 28088854 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791400 Affx-122950370 AX-385278392 17 42731949 AAAAAAAGACCAGCTCAGGAATAGCAAGAGGCTAA[C/T]GAAAGAATTCTTCTCTCAGATAAAGCAGAACTTTA Y 2 1 2 1 101000 f 74 goat snp46845-scaffold653-3243927 17 28035688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426831 Affx-122940511 AX-123297176 17 42773570 ATATATTTTAATAAAATTAAATGGAGAGTCAGAAC[A/G]TGAAGTGCTCTCTGAAAGGATGGATCTGGTGTGAA R 2 1 2 1 101000 r 74 goat snp46846-scaffold653-3285548 17 27993587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435126 Affx-122933688 AX-123305466 17 42824561 GATTTCATTCTCCCAATTAACCCTCCAAAAATAAA[C/T]AAAGTTCATTATAAATAAAATAAGCAAAAATACAA Y 2 1 2 1 103000 f 74 goat snp46847-scaffold653-3336539 17 27937236 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403784 Affx-122957982 AX-123274136 17 42873164 CCATGGCATTTCTTGAAACTACAAACTGTATCACA[C/T]AATTTCAGGATGGTCCTTCTCCAACACTGAATATT Y 2 1 2 1 101000 f 74 goat snp46848-scaffold653-3385142 17 27888160 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438602 Affx-122930938 AX-123308939 17 42945262 AATTATTCTTAGAATATCCAACGTTGCCCACTTCA[C/T]GGAGAAGGGGAAGGAGTCATACGAGACTGGGCACC Y 2 1 2 1 101000 f 74 goat snp46850-scaffold653-3457240 17 27816727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427728 Affx-122939270 AX-123298071 17 42985272 TTTTGGGAAAGTGCAGTCACAGTCCCACCTCAAGG[A/C]TGGGCAGTGACCATTCCTTCCATCTGCTTCTCTTT M 2 1 2 1 201000 r 74 goat snp46851-scaffold653-3497250 17 27780662 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781669 Affx-122977901 AX-385268753 17 43014480 TAAAAGCTGCTTTCCTGATTGATACAAGTACAGTC[A/G]TATCACAGGAGTTAATACAGCTGCACCAAATACTA R 2 1 2 1 101000 f 74 goat snp46852-scaffold653-3526458 17 27751522 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776818 Affx-122933605 AX-385263942 17 43155705 AACAATAAAAAAGCTAATTCACTGATCAAATAGTA[A/C]TCTATCAACAACTGGTGGTTATTGCTAAAGAGAAT M 2 1 2 1 201000 f 74 goat snp46855-scaffold653-3667683 17 27605357 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785755 Affx-122970281 AX-385272795 17 43186173 CACATCCACTAGGAAATTTGGGAATTTCTATCCTA[C/T]GGATGAGAAATTACCACATGGTTGGTATACAAGAT Y 2 1 2 1 201000 f 74 goat snp46856-scaffold653-3698151 17 27574898 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448288 Affx-122924172 AX-123318624 17 43218949 CCCTCTTTTACCCTGAAGATGACACAAAAATGAAC[G/T]AATAGAAATGAAATTGCTATTACGAATTAAAAGAG K 2 1 2 1 101000 f 74 goat snp46857-scaffold653-3730927 17 27541955 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791120 Affx-122934911 AX-385278115 17 43260996 AAGAACAAATTAATCAAGACATATAGGCCTGGCCA[C/T]GTGGAAACCAGCAAAGAGCAAAACAAGGAGACCAG Y 2 1 2 1 202000 f 74 goat snp46858-scaffold653-3772974 17 27499969 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395669 Affx-122963755 AX-123266024 17 43289883 CCACCTCCTGATCCCTGAACCCTGTGAATAGATTA[C/T]GGCACTTGGCAAGGGGGAGTTTTGTTGCTGTTGTT Y 2 1 2 1 101000 f 74 goat snp46859-scaffold653-3801861 17 27471143 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798699 Affx-122966082 AX-385285631 17 43342145 GGATTTAACAGTAAAGAACTAAAGGCAGTTATGAA[C/T]ATCCAGTCTCTACTTCTATGCTGTAGGCATTGCAG Y 2 1 2 1 101000 r 74 goat snp46860-scaffold653-3854123 17 27417649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390599 Affx-122967181 AX-123260956 17 43374000 TTATGCCTCAGTGGAAATGGCATTAAATGTCTCTC[A/G]TTCAGTGGTTGCAGGGGACTCTGCACGTGCTGTGT R 2 1 2 1 101000 f 74 goat snp46861-scaffold653-3885978 17 27384994 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421168 Affx-122944171 AX-123291515 17 43435642 GCAGAAATCAAAAAATCAAGTATTTCCAAAAGACG[C/T]GTGAATGTAGAATCCTAAAATTGAGAACAAGGTAA Y 2 1 2 1 101000 r 74 goat snp46862-scaffold653-3947620 17 27322745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774972 Affx-122939676 AX-385262104 17 43486273 AGAGCATGTTCTGCAATGTTTGATTTCATTTTGAG[A/G]TAAATGAGAAGTGAAATCTGAAGCCACATTCTGAG R 2 1 2 1 101000 r 74 goat snp46863-scaffold653-3998251 17 27270817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424213 Affx-122942495 AX-123294559 17 43533797 TTGTTTTTCAGTAGACAAGTGGTTTATTACATGTA[C/T]AGTGGTGAGGAGAGAAGTGGGAATTCCAGAGTCTC Y 2 1 2 1 102000 r 74 goat snp46864-scaffold653-4045775 17 27222763 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433720 Affx-122934524 AX-123304061 17 43586181 AGGCATTAGACTTCTATCCTCTGTCCATGGACTCA[C/T]AGTCTACTCTATGTGGGTTTGAAACAGAAATTTGA Y 2 1 2 1 201000 r 74 goat snp46865-scaffold653-4098159 17 27169391 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385445 Affx-122971313 AX-123255803 17 43625090 CTCAGTGGCAGAAATTGGAAGGCACTTCTGAAATT[G/T]CTCTTCCTCTTCAGTTTTCCCACCATTTTCTTCTT K 2 1 2 1 101000 f 74 goat snp46866-scaffold653-4137068 17 27130472 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793558 Affx-122968838 AX-385280533 17 43649406 ACTGGATTTTAGGATTACTTCTGCTGAGTAATCTT[C/T]ATCTGTGTGCAGAGACATAGACTTCTGCCATTCTT Y 2 1 2 1 201000 r 74 goat snp16273-scaffold1714-1565 17 27106267 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776787 Affx-122934074 AX-385263911 17 43680245 AGCCTAGAGAATGACTATAGACTGGACACAAGCTC[A/C]GTCAAGTAGTGATCCAATTTGCACACATGGGATTG M 2 1 2 1 101000 f 74 goat snp16274-scaffold1714-32404 17 27074941 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421958 Affx-122943812 AX-123292305 17 43719221 TTTTTCAACTGTTTGTGTCTCTAGTCACTAGTTTA[C/T]ATCTGTATGTTTGTGAACTTTTTTACAGATAATCA Y 2 1 2 1 101000 f 74 goat snp16275-scaffold1714-71380 17 27035192 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793119 Affx-122949064 AX-385280097 17 43774803 AATGTGAAGAATTCATGTCAGAGAAAGGCCTGGCA[G/T]CAAGAAGACCCATTAGGCCCTTATATCATCATTAG K 2 1 2 1 101000 f 74 goat snp16276-scaffold1714-126962 17 26979390 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408225 Affx-122953839 AX-123278576 17 43811009 GGACATTTCTGTTGGATATGGTGGTACCCTGCAGA[C/T]GCTGGTGGGCAGATGGGTAGGCATGTGTCTCAGTT Y 2 1 2 1 101000 f 74 goat snp16277-scaffold1714-163168 17 26942955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428921 Affx-122938908 AX-123299263 17 43853789 ACAACAAACCAGAGAACCCATTAGCAGACCCCCAC[A/G]TGTGCCATCATCTGATTTCAGACAAAAAGTGACAC R 2 1 2 1 201000 r 74 goat snp16278-scaffold1714-205948 17 26899766 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383307 Affx-122972702 AX-123253665 17 43886427 AAATTACAACTGAGATGGCTTGGCCCCTCAGTGGA[C/T]ACAGATGTGCTGGGCTGGGTGGGAGCTATTGGCAA Y 2 1 2 1 102000 f 74 goat snp16279-scaffold1714-238586 17 26865599 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448238 Affx-122924209 AX-123318574 17 43968904 AGCCAAGATGTCTGATGCCTGAGTCTGTTCTTTAC[A/G]TTACACTGCTCTACAGTGACATGAGGCTTTCTGGG R 2 1 2 1 101000 r 74 goat snp16280-scaffold1714-321063 17 26782979 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377036 Affx-122977706 AX-123247395 17 44009981 TAGACAGAAGTTCTTTGTTATTTTAGTTTTACTCT[A/G]TTTTGAGGGTCTTTCCTTGTCATGAGTGCACAACG R 2 1 2 1 101000 r 74 goat snp16281-scaffold1714-362140 17 26741469 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420829 Affx-122944665 AX-123291176 17 44091432 TCTGTCTATTTAAGTTTACACACAGGGGAAGTACA[A/G]TAGGAGTACTATAAAAGCATGTAGGGGATTGATAA R 2 1 2 1 201000 f 74 goat snp16283-scaffold1714-443591 17 26659949 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421604 Affx-122944486 AX-123291951 17 44125491 GTTCCTGAGATACAATTGGCACGTGAAGTAGAGTT[C/T]AAGGTGTACAAGGAGATAATTTCCCAAGGGCAACC Y 2 1 2 1 101000 f 74 goat snp16284-scaffold1714-477650 17 26625825 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424856 Affx-122941344 AX-123295202 17 44159338 GCTTGCATAGTTGAAGGATGTTGCTGCCATTAAAC[A/G]TCTGAAGGCAGTTCCAACTGACAGCGGGTGGGTTG R 2 1 2 1 101000 f 74 goat snp16285-scaffold1714-511497 17 26593096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451707 Affx-122921561 AX-123322040 17 44207328 GCCTCCCAGAGTGCAGGTCCTGTCCAAGCCTGGCC[A/G]ACCACCCCCATCAACATGGTCAGAAGTGGTTGGTG R 2 1 2 1 102000 r 74 goat snp16286-scaffold1714-559487 17 26545870 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450094 Affx-122922786 AX-123320429 17 44255073 GAAGAAGCTTCTTGGCTGGCTATGCACAGATAAAG[C/T]TCTTCTTGCCCTGGCAATGCAGGAGGCTTAAACTT Y 2 1 2 1 101000 f 74 goat snp16287-scaffold1714-607232 17 26498225 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379442 Affx-122976098 AX-123249800 17 44289388 CTCAGGCAGGCTGCATCCCAGGACGTGACCTCCAC[G/T]GCCCAGGCCTACTTGTCGAAGCTTTGCCTCTCCTT K 2 1 2 1 101000 r 74 goat snp58965-scaffold967-807788 17 26465137 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436307 Affx-122933266 AX-123306646 17 44319365 TCCTCGGTGAGAGTCTAGGTCTGGGATCAGAGCTC[A/G]TGGAGGAGCTGATGTTTGAGATGGGATTGGTGGGC R 2 1 2 1 101000 r 74 goat snp58964-scaffold967-777811 17 26434806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446390 Affx-122925581 AX-123316726 17 44356984 GCTGCTCATCTTTCAGTTAGCCTCCCTCCCAGCAT[A/G]TCAGGATTTCCTGTTTTTCTCTCTATAGTCCCATG R 2 1 2 1 201000 f 74 goat snp58963-scaffold967-740192 17 26397135 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275240 Affx-1111834786 AX-519548819 17 44392982 CTGCAGTGATATTTCAACCTAAGTATTTTACGTAT[A/G]A R 2 1 2 1 101000 f 74 goat GoatD01.052908 17 44392982 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38388836 Affx-122968887 AX-123259194 17 44394183 AATTCGTATCAAGCAGAAACTCCTAGGAATCCATA[C/T]CCTATTTCTTGGATCTAAAACACAACAGACACTAG Y 2 1 2 1 101000 r 74 goat snp58962-scaffold967-702993 17 26359642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443553 Affx-122927355 AX-123313890 17 44428338 ACAGGGTAAGAAAGGGCTTTCTTCAGTCATGACAA[C/T]GAATGCTATGAGGCAAAGGAACAGATGCAACAGGG Y 2 1 2 1 101000 f 74 goat snp58961-scaffold967-668838 17 26325347 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416534 Affx-122947758 AX-123286882 17 44465220 CTCATGGAGCAGTGGTGATCAAAGCAGGTCGTGAA[C/T]GGACAGAGTGGCAGAGAAAAGTGGGCAGTCTCACT Y 2 1 2 1 101000 f 74 goat snp58960-scaffold967-631956 17 26288498 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445109 Affx-122926191 AX-123315446 17 44504238 GTCCTTCCGTTGTGCTCTCAACATGCAGGCATTGG[C/T]GGCACACAAACAAGGCGGTGCGTGTGACCACCTCC Y 2 1 2 1 101000 f 74 goat snp58959-scaffold967-592938 17 26250273 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409535 Affx-122953612 AX-123279886 17 44538250 GAGGAGAGCACTGATGTAGGAGTGACTTTGGGTTA[C/T]AAGTCACCACTCAACCCAGACTGTCCTAAATCCTT Y 2 1 2 1 201000 f 74 goat snp58958-scaffold967-558926 17 26216223 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786476 Affx-122950455 AX-385273510 17 44574900 AATCATAGTACACTTGTCATACCAATAATAATTGT[A/G]CCAGTTTATCAACCCAGATTATTTTTGAATACTTA R 2 1 2 1 101000 r 74 goat snp58957-scaffold967-522276 17 26179499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410890 Affx-122952075 AX-123281240 17 44631174 AAGCAGCCTCCCCAGACATGGCGTTCATGACTCCT[G/T]TTGGGGTGGACAGTTCAGTTGTCAGCCCAGTCTGG K 2 1 2 1 202000 f 74 goat snp58956-scaffold967-466002 17 26123255 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440673 Affx-122929927 AX-123311010 17 44698983 CCCAGGGCCTTGTCCTCTCGCCCACACGCTCCTAT[C/T]CCTTACCCTGACTTTGCCATTGCACGGATGGTCTG Y 2 1 2 1 101000 r 74 goat snp58955-scaffold967-398193 17 26056832 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421172 Affx-122944168 AX-123291519 17 44755628 GTGTTTCAGTGGAATTTGAGGAGCAGATTCATCTG[C/T]GGGCATCACGGACTGGGGTGATACAGACAGAAACT Y 2 1 2 1 201000 f 74 goat snp58954-scaffold967-341548 17 26001310 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385907 Affx-122971578 AX-123256265 17 44797775 GCAGGTCAGGGTGACACCCGAGGAGCCGTGGGTGT[C/T]AGGCTGGATTTATTCTAAGTGCAGAGAGGAAACTG Y 2 1 2 1 101000 r 74 goat snp58953-scaffold967-299401 17 25959351 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436489 Affx-122932963 AX-123306827 17 44836021 AAGACGTTTCATGACAGAATGTATTTAAGGTCCTC[A/G]TCTGCATCAGCCTGGAAGGACGTTGTTGTTGAGCT R 2 1 2 1 101000 f 74 goat snp58952-scaffold967-261155 17 25921171 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403385 Affx-122957778 AX-123273738 17 44875779 AAATCGCAGTGCATCTCTGCGCTGAGGTGGGGACA[C/T]GCAGTGGTTACAGAGCAGCACAGCTTTGTAGACAA Y 2 1 2 1 101000 r 74 goat snp58951-scaffold967-221397 17 25880864 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790067 Affx-122964951 AX-385277073 17 44915113 TATATTTTTTTTCCATCTTCAAACTAGATTATTAA[A/C]ATATCCAGTTGAAGGAGACAAGCCCAGCTAACACT M 2 1 2 1 101000 r 74 goat snp58950-scaffold967-182063 17 25843251 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386418 Affx-122970814 AX-123256776 17 44982810 GCTGCATCAGGACCACAGAGTGGTGGGGACTCATC[A/G]CCAAATCCATCCTCCTTGTGAGCATTTCTCCACTC R 2 1 2 1 101000 r 74 goat snp58948-scaffold967-114366 17 25774903 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408240 Affx-122953826 AX-123278591 17 45017760 TAGCTTTCTTAACAAAATAAACCTTCAGATGTATC[A/G]TTTTCAAAGGGCGCAAACATGACAATCTTTTAGAA R 2 1 2 1 101000 r 74 goat snp58947-scaffold967-79416 17 25739580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445051 Affx-122926234 AX-123315388 17 45054817 GCAATGCCTGAGATGGCAGGAGCTGAAGCCGTCCC[A/G]GCAAAAGCCTTCCGCTGTTTGATGTATTGCAAGGA R 2 1 2 1 101000 r 74 goat snp58946-scaffold967-42359 17 25701833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434565 Affx-122934127 AX-123304906 17 45085738 CAAAGCATGTGGGCATAGTTTTCATACAGGTGGAA[C/T]AGCAAGTGCAAAGGCCCTAAGGTAGGAGTGAGCCC Y 2 1 2 1 101000 f 74 goat snp58945-scaffold967-11438 17 25670976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378998 Affx-122976384 AX-123249357 17 45125443 CTGGGGAATGAAGAAGACAGGCCAGGCAAAGGGAG[A/G]CAGACCTCGTGTGTGGGATACCTAAGGAGGTCTCC R 2 1 2 1 201000 r 74 goat snp4671-scaffold1150-918624 17 25631125 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795704 Affx-122935796 AX-385282657 17 45156736 TTTCATTAAGATCTTTTTCTGAGGTATTATCTTGT[C/T]CTTTCATTTGTAACATATTGCTCAGTCTCCTTGTT Y 2 1 2 1 101000 r 74 goat snp4670-scaffold1150-887331 17 25599079 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272841 Affx-1111833098 AX-519546532 17 45170626 ACAGAGAGCAGCCCACCAGGTTATGCCGTCCCTGG[A/G]ATTCTCCAGGCGAGAACACTGGAGTGGGTTGCCAT R 2 1 2 1 303000 f 74 goat 17_45170626_AF-PAKI 17 45170626 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38419926 Affx-122945322 AX-123290274 17 45196061 GGTTCTTTTATTGCCAATAGGTGTGTCAGTAAACA[C/T]GTAAAACACGTTTTGTCTCTTTCTTCACCACTCAG Y 2 1 2 1 101000 f 74 goat snp4669-scaffold1150-848006 17 25561664 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438429 Affx-122931269 AX-123308767 17 45228347 ACATCATCTCAAAGAAGCCCCACTTCCAGTAATGA[G/T]AAGGGCTCTTAGGAAGGCCTAGGAAGTGGCATGGA K 2 1 2 1 201000 r 74 goat snp4668-scaffold1150-815720 17 25528677 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406757 Affx-122955730 AX-123277108 17 45279861 TGTTTTTATAGCATTCCAAGCTGTGTGCCGCTTCA[A/G]AAGTAGCACAGCTGTCATTATAATTAGTTGCTGTC R 2 1 2 1 201000 r 74 goat snp4667-scaffold1150-764206 17 25477019 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424032 Affx-122942083 AX-123294378 17 45312379 CCCCAAATGTTCTCTCCTGGGACCTCAGGTGAGCA[C/T]AGGAGCAGGGAGGGAGGTGGACAGGACTCTGCTCC Y 2 1 2 1 303000 r 74 goat snp4666-scaffold1150-731688 17 25444106 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396702 Affx-122962822 AX-123267057 17 45350848 CATAGGGAAGCTGGATCTTGGTGTCCCGTTGTCTA[A/C]TGGTACCCTCAGGAAAGTGGGGTCTGGGATGTACA M 2 1 2 1 102000 f 74 goat snp4665-scaffold1150-693219 17 25405707 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396051 Affx-122963455 AX-123266406 17 45382173 TATGTGAGATAAAGCACGTCTTTCCTGAGAGAGTC[A/G]GCAAATGAGGGGTCCCATGGTCCAGTTTGTGCTCA R 2 1 2 1 101000 f 74 goat snp4664-scaffold1150-661894 17 25373675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776514 Affx-122947782 AX-385263641 17 45424552 GGAGAAGTAGCTTCCTAAAGACATTGAAGTAAATC[A/G]TTTTTTAGCTTCTTGTAAGGAAGGGAAATAATCTC R 2 1 2 1 201000 r 74 goat snp4663-scaffold1150-619515 17 25330183 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400798 Affx-122959820 AX-123271153 17 45456178 CAGTTGCCACAGGTAACACTTTCGACAGGAAAATT[A/G]CACACAATCTAAAAGTTTGAGAGTTATGTTTTATT R 2 1 2 1 101000 f 74 goat snp4662-scaffold1150-587889 17 25298833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404762 Affx-122957218 AX-123275114 17 45493696 CTCAGATAATGTTCCAGTCATAAGTGAGACATGAC[A/G]CTACTTGGAACCATGTGATGGAGACCATTATCTCT R 2 1 2 1 101000 r 74 goat snp4661-scaffold1150-550371 17 25261606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786527 Affx-122973964 AX-385273560 17 45553023 TCCTGACCTGAGAGTGTCTCTCTTAGCACAGGTGC[A/G]TCTAAGCTCTCCTAATCTGTCCCTAATTCCCACGT R 2 1 2 1 101000 r 74 goat snp4660-scaffold1150-491044 17 25202958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395187 Affx-122964512 AX-123265542 17 45595252 CACAAGGCTTTCTCCTTCGTCGGTGGTTGTCTAAA[C/T]GGATGATCTTTGGAGGGAAGATGGTAGAAAACTCT Y 2 1 2 1 201000 f 74 goat snp4659-scaffold1150-448815 17 25159971 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437627 Affx-122931811 AX-123307965 17 45627520 CCAAAAGCCTTGGATATGAAAGTGCAGCCCTCCTA[C/T]GTGTCCAGAGCAAGGCATCCAGCCTCAGTGACTTC Y 2 1 2 1 101000 f 74 goat snp4658-scaffold1150-416547 17 25127993 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773689 Affx-122960679 AX-385260829 17 45681199 GTATTTGAATGATACATTTCTGTCGAGAATCCTCT[A/G]TTGAAACAGACTGGGAAATCTGAGTAACAACATAG R 2 1 2 1 101000 r 74 goat snp4657-scaffold1150-362868 17 25074157 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442029 Affx-122928405 AX-123312366 17 45720420 GCAAGCTCCTCAGCTTTCCAACCTTGGTGATATTC[A/G]CAAACACGAGGAATCCATGCCTCTGTTTTGCTACA R 2 1 2 1 101000 f 74 goat snp4656-scaffold1150-323647 17 25035075 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438216 Affx-122931448 AX-123308554 17 45756670 TCTCCAAATTTTGCTCTTCATGATATCATTTCTCC[C/T]ACCCTATTTTGGTTATCACTTCCTTGTAATCATGG Y 2 1 2 1 101000 r 74 goat snp4655-scaffold1150-287397 17 24998741 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442048 Affx-122928394 AX-123312385 17 45807819 AAAGAAAAAAGGAATCCCCTTTGCCTGCCCCCAGT[A/G]CCATTACACCGTCCTCCTTGTACAGTGGATGTGTC R 2 1 2 1 101000 r 74 goat snp4654-scaffold1150-236248 17 24947741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396904 Affx-122963216 AX-123267259 17 45851687 AGGTAGTACATAAACTTCTGTTGTGTAAGTTAAAT[G/T]GTCCAGAAAATCTTAACAGCGTCATAATCCTGGGG K 2 1 2 1 201000 f 74 goat snp4653-scaffold1150-192380 17 24903518 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413216 Affx-122950256 AX-123283565 17 45952830 TTTATAGGCTTTTGTTTGGTTGGTTTTTTCTGGCC[A/C]CTCAGCATGTGGGATCTTAGGTCCCCTAGCAGGGA M 2 1 2 1 103000 f 74 goat snp4650-scaffold1150-91237 17 24802807 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429488 Affx-122937873 AX-123299830 17 45983743 TGCAGGAGCCACAGGGAGAGAAGTGAGTGCAGGAA[C/T]GGGTCAGCACCCTCCTCAGTTGCAGTGTGGCATGA Y 2 1 2 1 101000 f 74 goat snp4649-scaffold1150-60324 17 24771784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398636 Affx-122961461 AX-123268991 17 46012508 CCTCTGAAACACCCTAAGATCTCAGCTCAAATGTC[A/G]CATGTACTGACACCCTAAAGGTGGCTGATCTGACA R 2 1 2 1 201000 r 74 goat snp4648-scaffold1150-31559 17 24743424 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386575 Affx-122970701 AX-123256933 17 46045113 GGGGTGGCAAAGAGTCAGACATGACTAGTGACTAA[C/T]GCACTAGGAACAGTAGCAGGAATGAGAATTAAGCC Y 2 1 2 1 101000 r 74 goat snp7059-scaffold1260-947 17 24712091 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375797 Affx-122978570 AX-123246156 17 46074738 GTCAAGTGTGTGGAAACACGGCCTTGGTCTGAAAA[C/T]GTTGCAGAAATCCTGTGAAAGAAATCTACAAGTGC Y 2 1 2 1 101000 f 74 goat snp7060-scaffold1260-30572 17 24682374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432564 Affx-122935533 AX-123302905 17 46104451 GTTCTGGGACTAACCCTGGGCTGGTGTGGGGACCA[C/T]GAGACCTGTCCACTTGAGGGAGCTGCTCTAATCAG Y 2 1 2 1 101000 r 74 goat snp7061-scaffold1260-60285 17 24652665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407903 Affx-122954392 AX-123278254 17 46134829 CTCTGAATGCATGGATGGAGGTTCAGGCTCTGACA[C/T]GAACCAGCAGTGTGACCTCCCTTAAGTCATCTGAT Y 2 1 2 1 201000 f 74 goat snp7062-scaffold1260-90663 17 24622261 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787962 Affx-122952174 AX-385274983 17 46170164 GGTGATCATAGTCGTCAACTGAAGTGTATTACCTC[A/G]TACCTGACACCATCTTCAGAGTTCTCAGAGTGATG R 2 1 2 1 101000 f 74 goat snp7063-scaffold1260-125998 17 24586815 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432444 Affx-122935811 AX-123302785 17 46173733 ATACTGGGATAAACAGCCATGATGTTCACCAGAAG[G/T]GGATCAGTCATGTGATCATTTAAAAATGAGTCACA K 2 1 2 1 101000 f 74 goat snp3967-scaffold1126-2951 17 24580366 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390015 Affx-122968036 AX-123260372 17 46202718 TCCCTGAAACAGCATTTCATTCCCCTCGCAGGATC[A/G]CCCACCGCAGTTTGATTTGCATAGTCTCCTGGCTG R 2 1 2 1 201000 r 74 goat snp3968-scaffold1126-31936 17 24551676 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453322 Affx-122919975 AX-123323655 17 46235017 CTCCTTTGCCTGCCCAGAAGGAGGGGAGTTTCAGT[A/C]GTGGAAATGACATAGGTGACCGGCATGAGGTGTGT M 2 1 2 1 101000 r 74 goat snp3969-scaffold1126-64235 17 24520095 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436408 Affx-122933023 AX-123306746 17 46267368 GTGTAGGACACTCCCAGGTACACAGGACCTAGACT[A/G]TATCCATATCTCATGCTACTTGATTCTCTCAATTA R 2 1 2 1 201000 r 74 goat snp3970-scaffold1126-96586 17 24487106 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421377 Affx-122944040 AX-123291724 17 46297055 ACAGGTGGCTTACCTTGCAAGCACACCTTCAGCCC[A/G]TCTACTAGCTCTTGTCCTCTGTCTTGAAACACACA R 2 1 2 1 101000 r 74 goat snp3971-scaffold1126-126273 17 24457563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386392 Affx-122970834 AX-123256750 17 46349154 CACTGAATCTCTTCTAATAAGCTATATATAAAACT[A/G]TGTCAGTGCTAAACTGTTTTAATTGTTATTGGGTT R 2 1 2 1 101000 f 74 goat snp3972-scaffold1126-178372 17 24404597 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445552 Affx-122925153 AX-123315889 17 46389401 GTTGAGGCCATCCAAACCACAGTCCGATCTGTAAG[C/T]AAAGCCAAGATTTTGTCAACAGCTTAACCCTTTTC Y 2 1 2 1 101000 r 74 goat snp3973-scaffold1126-218619 17 24364585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388742 Affx-122968957 AX-123259100 17 46423947 GTTTTATTCAGCTTTATGTCCTCTGAGGCAGGGAG[C/T]AAATGCTGGATGAATGAATAATGCAACTTTAAGGT Y 2 1 2 1 101000 f 74 goat snp3974-scaffold1126-253165 17 24330010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431240 Affx-122937136 AX-123301581 17 46466263 AGGAGGGAGTTTGGTGTTGGGCAGCTGAGTGCCTG[C/T]AAACAGCTGTTGAGCCTTTTGAAGTTGGTGTTTCA Y 2 1 2 1 101000 r 74 goat snp3975-scaffold1126-295481 17 24287713 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438908 Affx-122930435 AX-123309245 17 46524301 TGTGCAATTCCAACCAGTTCTCACTATGGAGAAAG[A/G]CAACTCAGGAGGGCTGGATCTTTCGATTTTTCAGC R 2 1 2 1 101000 f 74 goat snp3976-scaffold1126-353519 17 24230781 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426537 Affx-122940190 AX-123296883 17 46571390 TTCTGCTGTTTCTTCTGATCCAGAGCTGCCATTCC[A/G]CCTTTCCCATTAAGGCCCCCTTCCAGACCATTGTT R 2 1 2 1 101000 f 74 goat snp3977-scaffold1126-400608 17 24183411 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433952 Affx-122934277 AX-123304293 17 46624667 AGGCCCTGGGGAGGAGGGGGCGCAGCCACAGTGAC[C/T]CCATGTAGATCTCTGTTCACTCAACTAATTGAGCA Y 2 1 2 1 101000 r 74 goat snp3978-scaffold1126-453885 17 24130011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413281 Affx-122950209 AX-123283630 17 46673830 CACCATGAGCAAAAGGCTCACTTCACACCAACCTT[A/G]TCACTGTCATGTCTGAACAAGTAGAACCACTGCCT R 2 1 2 1 101000 r 74 goat snp3979-scaffold1126-503048 17 24080366 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387684 Affx-122969820 AX-123258042 17 46711505 AAAGCTGTGTTTTCCAGTGATGTCTGCTGGATGCT[A/G]TTTGCATCCACATCTCTTCTTATTTTTATTGGTTG R 2 1 2 1 101000 f 74 goat snp3980-scaffold1126-540723 17 24043172 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766975 Affx-122969882 AX-385254274 17 46743387 ATAAGCATATACATAAACCCTCATCTAGACCACAA[C/T]GGAATATTCTCTTCACACAGCAAGAAAATCTATAC Y 2 1 2 1 101000 f 74 goat snp3981-scaffold1126-572605 17 24013735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451673 Affx-122921584 AX-123322006 17 46787594 ACAAAACCATCAAGAGAAAGTCATCTGTCCATGCA[A/G]AGAACAGGTAAACAGATTCTGAACTCTGGCTGCAC R 2 1 2 1 101000 f 74 goat snp3982-scaffold1126-616812 17 23969535 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392600 Affx-122966053 AX-123262957 17 46816636 GGCCTCTGGATTGTTGGTGGACGCGATCGGAAACA[G/T]CGAGACAACCCCTGTCCCAAAACACAGTAAGGGAA K 2 1 2 1 101000 f 74 goat snp3983-scaffold1126-645854 17 23941309 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382619 Affx-122973701 AX-123252977 17 46872403 GGGATGCTAGTAATAGTATTTATTTCATAGGGTCA[C/T]AGGAAAGATTTAAGGACGTCAGGCATGCATAGAGC Y 2 1 2 1 101000 r 74 goat snp3984-scaffold1126-701621 17 23887567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787903 Affx-122946984 AX-385274925 17 46937819 ATGGGCTTAGGATGAGTGCGCTTATTTTGCTAAAT[C/T]CCTATATTTAAAGCTTGTCTTCCTCCCCACTCCAT Y 2 1 2 1 101000 r 74 goat snp3985-scaffold1126-767037 17 23822433 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442136 Affx-122928330 AX-123312473 17 46975337 ATAAACCAGGCAGGGTTAGCTGTCTGCAGTGCTAA[C/T]AGGCGTCTCATTGTCCTTTTCCCCACATCAGTTCA Y 2 1 2 1 101000 r 74 goat snp3986-scaffold1126-804555 17 23785159 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776347 Affx-122948450 AX-385263475 17 47029957 TAACACATGAATTGAGGATCCAAAAGTGAAAAATA[G/T]AAATTAAACAAGAAATAGAATAGGCATACTTTAAA K 2 1 2 1 303000 r 74 goat snp3987-scaffold1126-859175 17 23730255 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275599 Affx-1111834901 AX-519549169 17 47078490 TCAGCTCAAGGCTTGATAAGCAAGTGCAAGGTAAT[A/G]ATGAAATACTAAAGATACCTGAGCACTGAGATATT R 2 1 2 1 201000 r 74 goat GoatD01.057937 17 47078490 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38397073 Affx-122962722 AX-123267428 17 47093209 TCCCTTGGTGGCATTACACCTTCAGGATCTAGCAG[A/G]CTCTTGTTCTCAACATTTCCACCTTCATTGGACTC R 2 1 2 1 101000 r 74 goat snp3988-scaffold1126-922427 17 23666358 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405547 Affx-122955968 AX-123275899 17 47142246 TTTATTTTTATCACCAGTTACCCTACTTCCTTGTT[C/T]AGGGCTCTCTTCCCTCCAGAATGTAACTTCTGCAA Y 2 1 2 1 201000 f 74 goat snp3989-scaffold1126-971464 17 23616954 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395858 Affx-122964009 AX-123266213 17 47193189 TGCCTTTGGGGATTTATTTCCAAAGAGCATTTGAT[A/G]TGAATTTGGGGGTGACATGATATGGATTTCCCTCC R 2 1 2 1 201000 f 74 goat snp3990-scaffold1126-1022407 17 23566342 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774790 Affx-122961419 AX-385261924 17 47222516 AGCCATTATCTAATACTTGGTATTTAATCTCTCCC[A/G]TGGTCGCCAACATCACTTAAGAAAATCACAGAAAT R 2 1 2 1 101000 r 74 goat snp3991-scaffold1126-1051734 17 23537147 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427637 Affx-122939338 AX-123297980 17 47259871 CTTTTATGACCATTCCACAAAAACAAATTGCTTTT[A/G]TAGTCAAAATGACAAATTTAGACCCCTTGATCAAT R 2 1 2 1 101000 f 74 goat snp3992-scaffold1126-1089089 17 23497187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775088 Affx-122950784 AX-385262220 17 47311183 GGAAATCCTTTTAAGAAAGTTTTGTCATAGACTAA[C/T]GTTGAATGCAAATGAAAGGACTTACAGGTAGCTTT Y 2 1 2 1 101000 r 74 goat snp3993-scaffold1126-1140401 17 23445713 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38453301 Affx-122920367 AX-123323634 17 47425785 GAAAATATGTAGCCAGAAATATGGTCCAGCTGCTC[A/G]CCACTCAAAAGCTGTTAAAAAGACAGAAAGGAAAG R 2 1 2 1 101000 f 74 goat snp3995-scaffold1126-1255003 17 23332727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277098 Affx-1111835740 AX-519550606 17 47476545 CTCACCTGGGCTATTCAGTCGTTGCCATCAATCAT[A/G]TTGTTGAATTTAAGGAGAAGAAACAGGAAATTGAA R 2 1 2 1 101000 f 74 goat Random2.2K-1670 17 47476545 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419076 Affx-122945799 AX-123289424 17 47484874 ACCTGTGACACAGTTTCAGTATTAAGTGAAGAAAT[A/G]CTATTTCTTTCAGCAAACATTTCAACACAGGTAGA R 2 1 2 1 101000 f 74 goat snp3996-scaffold1126-1314092 17 23274063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441284 Affx-122929469 AX-123311621 17 47534625 GCTGCTGGGTTTTTAAGAAGGCAGCAGGTCCCTCA[C/T]GGATGCATTTCAGATATTGATGAGAATATCTATTG Y 2 1 2 1 101000 r 74 goat snp3997-scaffold1126-1363843 17 23224215 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422817 Affx-122943195 AX-123293163 17 47594509 GTGGGACACTCTCACAGTCTTAGGTGTCTCACAAC[A/G]CTTATAAGTTACAAGAAGAAGAAAAAGTAGGAATT R 2 1 2 1 101000 f 74 goat snp3999-scaffold1126-1423727 17 23163588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379188 Affx-122976306 AX-123249547 17 47678736 ACAGTCAGCCTCATTAACAGGACTTACTATGGTTG[C/T]AAATATCACTGGGTTCATCCTTCAAGGGTGATGAG Y 2 1 2 1 101000 r 74 goat snp4001-scaffold1126-1507954 17 23079448 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396709 Affx-122962816 AX-123267064 17 47716480 TTAAGAAAACGCTTCAAGAATTTCACCCTGACCGT[A/G]CACCTAGATAGAGCTGTCAACTTTCCAATGACTGG R 2 1 2 1 101000 r 74 goat snp4002-scaffold1126-1545698 17 23041004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794374 Affx-122964552 AX-385281337 17 47751609 CAGGGATGGTCAAAGCCTTGAAATTGAATATATTC[A/G]TATTTAATGAAGTAATGAAAACCTCTCACTTTCAA R 2 1 2 1 201000 f 74 goat snp4003-scaffold1126-1580827 17 23005792 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273927 Affx-1111833902 AX-519547533 17 47754002 A[A/G]CTAAAAGATAATCTTGTTAAATGTCAAATTCACCT R 2 1 2 1 103000 r 74 goat GoatD01.009906 17 47754002 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38444670 Affx-122926453 AX-123315007 17 47802996 GGCTGCGTCCAAACCCACGTGGTACATCAAAGCCC[A/G]TGTGTTTCCTGCTGCACCACCATCTTCTGTGGCTA R 2 1 2 1 101000 r 74 goat snp4004-scaffold1126-1632214 17 22954356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426627 Affx-122939956 AX-123296973 17 47836203 CTTCTGAAACCAAGCAGGACCCTGTGGGGCTCCAG[A/G]GTACAGGTGCCTTTCTGTTCAATCTCCATTATCTC R 2 1 2 1 103000 r 74 goat snp4005-scaffold1126-1665421 17 22921164 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376752 Affx-122978535 AX-123247111 17 47901104 AGCTTGGGTGCCTGGGGGGATATGTGTCATCTGGT[A/G]TTAAGCTTTCATGCATTTCTCAGAATCATCGACAG R 2 1 2 1 101000 r 74 goat snp4007-scaffold1126-1730322 17 22855813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434922 Affx-122934313 AX-123305262 17 47932653 GGGAACAGCAATTTACCAAAACCCTCAGAGCATCC[A/G]TGTGCCCACAACCCGCATCCCTGGCCCTCCTCCAC R 2 1 2 1 101000 f 74 goat snp4008-scaffold1126-1761871 17 22824068 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419850 Affx-122945378 AX-123290198 17 47968097 GCCGCAAAAATTAATGCCATACTGTCCATTCTTTG[A/C]TTCATTCCTTCTTTTTTTTTAAATCCTGTTTGACC M 2 1 2 1 103000 f 74 goat snp4009-scaffold1126-1797315 17 22788618 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394108 Affx-122965347 AX-123264463 17 47998606 AGCAGTGTTTCTTCTAATTCTGGCCGCTGGACCCT[A/C]TGACAAAAGGCACAGAGTTTGAAGTGGGAGTTTTG M 2 1 2 1 101000 r 74 goat snp4010-scaffold1126-1827824 17 22758215 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272843 Affx-1111833099 AX-519546535 17 48034650 CACTCCAGGGTTCTTGCCTGAATAATCCCAGGATG[A/G]TGGAGCCTAGTGGGCTGCCATCTGCGGGGTCGCAC R 2 1 2 1 103000 f 74 goat 17_48034650_AF-PAKI 17 48034650 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38380038 Affx-122975582 AX-123250396 17 48043764 TTATCTCCACTGATTCACTTTGTTTTCAGCTACAG[G/T]TGACCATCAGCACCGTGACTGGCATGGAAGCCGGA K 2 1 2 1 201000 r 74 goat snp4011-scaffold1126-1872982 17 22713197 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783055 Affx-122931953 AX-385270122 17 48074401 CTAAATACGCAGTCTATTTGTAAAGGTGATTGAAA[C/T]GGCTCCAGAGAATTCATTACTTCCATTACAGACAC Y 2 1 2 1 101000 r 74 goat snp4012-scaffold1126-1903619 17 22682318 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415963 Affx-122948423 AX-123286312 17 48107853 AACACAATCCCTGACTTTCTCTCTGCTGTCCTTCA[C/T]GTACCAGGTCAAAGCTTTGTTCTTTCAACACAAGG Y 2 1 2 1 101000 f 74 goat snp4013-scaffold1126-1937071 17 22649044 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419721 Affx-122945905 AX-123290069 17 48158654 CGGACTCAGAGCCTCTAATGGACTTTTAGGCCCTC[A/G]TTTTTTCTTGACATGAGCAAACAAGAATCAAGAAG R 2 1 2 1 102000 r 74 goat snp4014-scaffold1126-1987872 17 22598157 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451022 Affx-122921456 AX-123321356 17 48209403 CATCCTCATATTAGAATTCTATTTAGAAAGAATGG[A/C]TAAAATGAGAACATCCAGTCTTAGACAGTAAGGGG M 2 1 2 1 101000 r 74 goat snp4015-scaffold1126-2038621 NW_017214367.1 11246 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437805 Affx-122931679 AX-123308143 17 48255009 CCACACTCCATACACCATCCTCAAGCTGTTGAATT[A/C]TAAGTGTCACATAAGACACAATGATGCCCAGAGAA M 2 1 2 1 101000 r 74 goat snp4016-scaffold1126-2084227 17 22501157 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419815 Affx-122945833 AX-123290163 17 48304342 GAATAAAAACTTTTTTCTTCCCTTCTTAATACTTA[C/T]GTGAATTCTTTTATAACCCATGTTGGCTCACCTAA Y 2 1 2 1 101000 r 74 goat snp4017-scaffold1126-2133560 17 22451933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791957 Affx-122919280 AX-385278946 17 48337737 ATATGAAATGGTTTGTTAGTTTTAGGAGCTGTGCT[A/G]TAAATGCCCGGTCTAGTCATCCCCCTTCTCACTCC R 2 1 2 1 101000 f 74 goat snp4018-scaffold1126-2166955 17 22419305 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425559 Affx-122941437 AX-123295905 17 48366264 TCCCAGCCATTCTCTCTGTCCATTTACTGAGCCAT[A/G]TTTACTGGAGGCCCGCCAGGTACGAGGCACTGTGC R 2 1 2 1 202000 r 74 goat snp4019-scaffold1126-2195482 17 22390981 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378707 Affx-122977056 AX-123249066 17 48397211 CTGCTGTGCCATGACTCAGAGGGAACAGACGACAA[C/T]ATAAGTGGGAGGGATCCTTTCCTTGCTTGAGTGAA Y 2 1 2 1 201000 f 74 goat snp4020-scaffold1126-2226429 17 22359950 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433532 Affx-122935004 AX-123303873 17 48435656 CAGTCACAGGGTCGGACACAACTGAGCAACTATGC[A/G]TGCATGCCCCACTGGAACCTAAAAATAACATGAGC R 2 1 2 1 101000 r 74 goat snp4021-scaffold1126-2264874 17 22321467 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435781 Affx-122932865 AX-123306120 17 48517659 GTGTGTGTCCTGGAGATGCCCGTGTGATGGCAGTC[A/G]TTGGTCTTGTAGACCCGGCCAGAGAAGCCTCTTCC R 2 1 2 1 201000 r 74 goat snp4023-scaffold1126-2346877 17 22239500 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771103 Affx-122974393 AX-385258264 17 48556799 TGATGCTCCTTCTTTTGTTTCATGGGAAAGTAGAA[C/T]AGGAAAAATATTCACCATAGCACCAAAAATCCTAA Y 2 1 2 1 102000 f 74 goat snp4024-scaffold1126-2386017 17 22200786 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378011 Affx-122977591 AX-123248370 17 48605329 GCAAGTGTAGAATAGCACTAATCAACTAACACTTT[A/G]ACTTTTTTGAGGAGCTTACCATGTTGTTCATTAAA R 2 1 2 1 101000 f 74 goat snp4025-scaffold1126-2434547 17 22152221 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421419 Affx-122943966 AX-123291766 17 48644172 CTTTCACTTTCGAAAACCCCAGCCTGTTACAAGCA[C/T]AGATCCTTGTGTAGCACAAGTGGTCATAACAACAA Y 2 1 2 1 201000 r 74 goat snp4026-scaffold1126-2473390 17 22112949 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419672 Affx-122945941 AX-123290020 17 48673867 TGCCTCTTCAAAGACTTTCCCATCAGAATCAACAG[C/T]GATTTTTCTCTTTACCTTGAAAATTTTCTATTCTG Y 2 1 2 1 101000 f 74 goat snp4027-scaffold1126-2503085 17 22082865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382905 Affx-122973405 AX-123253263 17 48710772 GAGGCTGGGGCACTCTGAGAGCCACTCTGAAGGAC[A/G]ACCTTGCCTCGTCTCAGGTACTAGCCCCTCAGAAT R 2 1 2 1 101000 r 74 goat snp4028-scaffold1126-2539990 17 22047279 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433821 Affx-122935164 AX-123304162 17 48776682 CTGTAGAATCAGGAGCAATGATTTAGTGCATGAGC[A/G]AGAAATGGAATAGTGCATGAAAGAGTGTTTGGTGG R 2 1 2 1 101000 r 74 goat snp4030-scaffold1126-2605900 17 21980939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447605 Affx-122924001 AX-123317941 17 48806856 CTACAAAGCAGCTCATCAGCCTTATTTTTTCCCTC[A/G]TTAAACTTAACCCAGAGTAATAACTCACCTCCTCT R 2 1 2 1 201000 r 74 goat snp4031-scaffold1126-2636074 17 21950617 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786475 Affx-122969433 AX-385273509 17 48836818 CAGAGACTGAAGCAATGAATAACGCATCTCTTATT[A/G]TATTATCTCTGTATAAATAACACTAAAGGCAATAT R 2 1 2 1 101000 f 74 goat snp4032-scaffold1126-2666036 17 21920005 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423691 Affx-122942898 AX-123294037 17 48871882 CAGCCAAAATAAAATAAATAAATAATTTTAAAAAA[C/T]AATGGCATCGTATTTGCATATACATGACGGTAACA Y 2 1 2 1 103000 r 74 goat snp4033-scaffold1126-2701100 17 21884559 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781155 Affx-122963288 AX-385268240 17 48910793 AGTTTTATGCCAACCATAAACAGAATCTTTTAACA[A/G]ATTGAAACAGTAGAATTTTTTGACAGATTGAAATT R 2 1 2 1 101000 r 74 goat snp4034-scaffold1126-2740011 17 21846193 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452547 Affx-122920531 AX-123322880 17 48945574 ACATCTGATAAGCAGTAGAGATGGTCAAGTGCCCA[A/G]CTTCAAAGAACCAGCTCTTGGCTAATGCCCCAAAT R 2 1 2 1 201000 f 74 goat snp4035-scaffold1126-2774792 17 21811615 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277100 Affx-1111835741 AX-519550607 17 49003786 GTTTTCATGAGCTCACATTTGCTGATAAAGTAGAG[A/G]GAAGGGGGTAATAAGATGGGATAAGATCTGTAACA R 2 1 2 1 101000 f 74 goat Random2.2K-1671 17 49003786 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376464 Affx-122978047 AX-123246823 17 49008726 GCTTTCTTCCCCCTCCTCCAAATACATGTACCATG[A/C]TGCTACTCCATGAATGAAGGCAGCTGGGGATTTCT M 2 1 2 1 103000 f 74 goat snp4036-scaffold1126-2837944 17 21751294 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384150 Affx-122972802 AX-123254508 17 49075026 TCCTTTATATAAATGTGTTGGAGAAAGGGTACTGG[C/T]GATGTCCATGTGTAGAGTCTTCTCTTGTGTTGTTG Y 2 1 2 1 201000 f 74 goat snp4037-scaffold1126-2904244 17 21685542 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376958 Affx-122977764 AX-123247317 17 49174868 ATGCAAGAGAAAAAAGAGAAGAGTTAGGGGCCTGT[A/G]CTTAAACAAAACTTCCTTTAGGAAAAAAAAAATCA R 2 1 2 1 103000 f 74 goat snp4039-scaffold1126-3004086 17 21585662 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434690 Affx-122933955 AX-123305031 17 49208095 CCAGAATGTTTTCAACACCAATATTTCTGAGGTCA[A/G]ACTAACTTACTTGAGGTCTAGCAATTCATTTTGGA R 2 1 2 1 101000 f 74 goat snp22426-scaffold2218-12696 17 21549906 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424382 Affx-122941834 AX-123294728 17 49237671 GTCTTCCTTCTCAAAAATAGCATAAATAAATAAAA[G/T]AAAATAGATTGCTTGCTCTTCTCATCTCACTGGGT K 2 1 2 1 103000 r 74 goat snp22427-scaffold2218-42272 17 21520257 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436088 Affx-122932684 AX-123306427 17 49288727 AAGTGTCAAAAGCCTTTGTTCAGTTCACAAATCAC[A/G]TCTGCTTGTTTATATATTTAACATCTGATGATCAG R 2 1 2 1 101000 f 74 goat snp22428-scaffold2218-93328 17 21470072 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384989 Affx-122971888 AX-123255347 17 49372859 TCACTGGACAATTAATCAACATGTAGGGTTAGCCT[A/G]CTTCGATCCAGGGATTAATAATCATTGTCTGGCAC R 2 1 2 1 101000 f 74 goat snp22430-scaffold2218-177460 17 21382745 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430452 Affx-122937268 AX-123300793 17 49443643 AATGTCAAATGCATTTCTTTCATCTCCTTATTTTC[A/G]TTCCTATTCTTGTAGTCATTGCAGCTCTGCCTTTA R 2 1 2 1 103000 r 74 goat snp22432-scaffold2218-248244 17 21314245 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386278 Affx-122970941 AX-123256636 17 49471700 AAATGAGGAATGTCTCAGATGGAAAGTGAGCAGAG[C/T]GTTTGAAGAAGAATCCAGCTGATACTCGACTAAAT Y 2 1 2 1 101000 f 74 goat snp25856-scaffold2665-12958 17 21284278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796251 Affx-122952688 AX-385283201 17 49500303 ATGTATAATTTTTTGACTGGACATGGAATCTTTCA[G/T]CCAAGCCAAAGGATCTCTAACAGTTTAAGCAGCCC K 2 1 2 1 101000 r 74 goat snp25857-scaffold2665-41561 17 21255724 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772069 Affx-122929774 AX-385259224 17 49538366 TTGTCCTCCGTTTCTCCCTGCTGCTAACAGGGAGA[C/T]GTTTTAAACTAGGAAGGCTCCTAGATTACCTCCTA Y 2 1 2 1 202000 f 74 goat snp32203-scaffold3646-71907 17 21217908 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440774 Affx-122929851 AX-123311111 17 49645887 TTCTCTCCTGTGTGAAAACCAAAAAACAGCAGATC[C/T]GGGGCCACACTGCTTAGGAGCCCTTGTAAAGGTTT Y 2 1 2 1 101000 f 74 goat snp44729-scaffold609-35515 17 21110033 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387809 Affx-122969685 AX-123258167 17 49677019 TCTCTTCTCTCTGCACCCAGCTCACACTGTCCCCA[C/T]GGTGAACTGCCTTCCTCACTCACCCCATTTCGTGC Y 2 1 2 1 101000 r 74 goat snp44730-scaffold609-66647 17 21078846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397679 Affx-122962586 AX-123268034 17 49714751 GACAGAAACTAAAAGAATGAATAATTGCCAGCACC[A/G]TGAACAAAATGTATAACTAAAAATATATGAGGCAC R 2 1 2 1 101000 f 74 goat snp44731-scaffold609-104379 17 21040898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411651 Affx-122951568 AX-123282001 17 49781872 AGCAGTAATCATGGTCATCTTTCTTGAGAGGTCCA[G/T]CCTCCTAGTCTGGCCACACTGCAAAATCCAGGTGA K 2 1 2 1 101000 f 74 goat snp44733-scaffold609-171500 17 20973376 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444862 Affx-122926288 AX-123315199 17 49842529 ACCACAGAGAGCCATAGGGACTTGTCAACGCACCC[A/G]TCAGCCTTTCAGCAGAGACATCATCAACCTTCTAG R 2 1 2 1 101000 r 74 goat snp44735-scaffold609-232157 17 20912716 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445035 Affx-122926620 AX-123315372 17 49884849 ATTCTAGCCCCATGTCCACAGAGACTGATTCAAGA[C/T]TGAAACCCAAATGAAATCAGTGACAACAGAAAGGA Y 2 1 2 1 101000 f 74 goat snp44736-scaffold609-274477 17 20870649 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421746 Affx-122944371 AX-123292093 17 49935595 TGGAAAACAATAAATCTTGATAATGAGCAAACAGC[A/G]CGGGCACCTCCACTCTCTCAGCTGCCAGATCCTGG R 2 1 2 1 101000 f 74 goat snp44737-scaffold609-325223 17 20819223 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394489 Affx-122964558 AX-123264844 17 49984528 TGAAATCTCTGCCCTCCTCCCTCCCACTCTTCCAA[C/T]TTCACTGAAGTAGTCTCTCAGCAGGCCTCTGCCTC Y 2 1 2 1 101000 r 74 goat snp44738-scaffold609-374156 17 20769892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764791 Affx-122948538 AX-385252400 17 50019213 GTGGGAATTCTAGCACTTGCAGCTGAGCCCAAATA[C/T]GTAAATCCTAAGCTCTCTTCATGTATCAACGCAGG Y 2 1 2 1 101000 f 74 goat snp44739-scaffold609-408841 17 20734954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431029 Affx-122936662 AX-123301370 17 50055409 AGGGGGTAGCCAAAATAGTTTTCCCCCTGCATTTG[C/T]GGTTCCCAAAGTATAAGATGCAGACTGATTTTAGG Y 2 1 2 1 201000 r 74 goat snp44740-scaffold609-445037 17 20700796 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767222 Affx-122948222 AX-385254503 17 50086518 TTTACAGAACACTGGCGATGTGCTAACCTGGGCAT[A/G]TACAACTGCTACATCCATTGATTATCACAATGCTT R 2 1 2 1 101000 f 74 goat snp44741-scaffold609-476146 17 20669394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394485 Affx-122964561 AX-123264840 17 50173943 TACTATTATTATTATTTTAGCACATGTTGGACAAG[C/T]GATCAACTACAGCTTGTGAGGGGCCTAACTGGGTG Y 2 1 2 1 201000 f 74 goat snp44743-scaffold609-563571 17 20581714 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405903 Affx-122955585 AX-123276255 17 50212309 TTTGTGATCTGGCCTCATCACTAAACTGGTCTCTG[A/C]TCTATGGACCCTCTGGTCACACCCATCTCCTTACT M 2 1 2 1 201000 f 74 goat snp44744-scaffold609-601937 17 20543462 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800858 Affx-122955148 AX-385287773 17 50304677 ATCAAGACAGATAATATTTCTAGCTAACACTTACA[C/T]GGTACTTATCACGTATCAGACACTGTCCTGGGCAC Y 2 1 2 1 101000 r 74 goat snp44745-scaffold609-694305 17 20452055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422765 Affx-122943232 AX-123293111 17 50336270 TTAAAAAATAAATAAAATGGGAACAGAGCTGGAAG[G/T]ACTTTCCTTTACCAAAAATCTTAAACTTGCTGTGG K 2 1 2 1 101000 r 74 goat snp44746-scaffold609-725898 17 20419879 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435139 Affx-122933679 AX-123305479 17 50365966 GGAAAATACAAAAATGGAAAATATGAAAGGCTGAA[A/G]TGCCACAAAAGCATCTTTGCCAGGATGTCAAGGAA R 2 1 2 1 101000 r 74 goat snp44747-scaffold609-755594 17 20389997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445326 Affx-122925425 AX-123315663 17 50396711 TTGAAACTGATCACACTCCGAAGTTAAACTCATCC[A/G]GCTGCTTGTATAGGATCCCTGAAGCTCAAGCTGAT R 2 1 2 1 101000 f 74 goat snp44748-scaffold609-786339 17 20360950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380894 Affx-122975039 AX-123251252 17 50470607 AGGGCTTTTTAACTGTGTTTGCCGAGAATTTCCAA[C/T]GGAGGCGAGGGGGACACAACCTCACACAGGTCCCA Y 2 1 2 1 101000 f 74 goat snp44749-scaffold609-860235 17 20287331 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452230 Affx-122920793 AX-123322563 17 50518607 ATGGGTTTGATCCCTGGTCCTGAAACTAAGATCCT[A/G]CAAGCTGAGTGGTGAGGCTGGGGAAAAAAAAAAAA R 2 1 2 1 103000 f 74 goat snp44750-scaffold609-908235 17 20239438 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794751 Affx-122961606 AX-385281711 17 50617791 TTGCATGCAACTGTATCTAATTCTAACTCCTAACA[C/T]GACTTTTCTCTGGTCCTTTGCCCTCTGGTTCGATG Y 2 1 2 1 101000 r 74 goat snp44752-scaffold609-1007419 17 20140432 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402345 Affx-122959059 AX-123272698 17 50651332 ATCCAGACCCAGCAGAGAAGAATGAGACCCAGGTC[A/G]GTGGTCTCCATCTGCTTCCTCTGCCTGTGGTCCCC R 2 1 2 1 102000 f 74 goat snp44753-scaffold609-1040960 17 20107186 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447929 Affx-122923791 AX-123318265 17 50683525 TGAGACCTAGAAGTCTGAGAGGAGACAGAGACCCC[C/T]CACTCCACCCTGGAGACCCCACTGGCCCTGCTGAG Y 2 1 2 1 101000 f 74 goat snp44754-scaffold609-1073153 17 20076652 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277102 Affx-1111835742 AX-519550609 17 50727553 TTGTTCTAGAAAATACAAATACAGTTATGCCCTAG[A/G]AAAGGTTCTTAAACCTGTAGTGTAGAATGGTACAC R 2 1 2 1 101000 f 74 goat Random2.2K-1673 17 50727553 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437491 Affx-122932359 AX-123307829 17 50732590 AGGTCCCACCTCCTAATATCATCACATAGGGGTTA[A/G]TTTCAACATAAGAACTGGGGAGGAGGGGGACCCAA R 2 1 2 1 103000 f 74 goat snp44755-scaffold609-1122218 17 20027723 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277226 Affx-1111835743 AX-519550732 17 50740596 TGCCATGTAACACTGGGAAAGTTATTTAAACTGGT[A/G]TTGAAATTTTCTGTATCTGCAAAATATGCTCTTTA R 2 1 2 1 201000 r 74 goat Random2.2K-1674 17 50740596 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38389618 Affx-122968754 AX-123259976 17 50783951 CTTGTGACCAGTTAAACCAGGAGAGGATGAAATTG[C/T]GGGGAGAGATTGAGAGGCACCCACTTTTCCCCGCT Y 2 1 2 1 101000 f 74 goat snp44756-scaffold609-1173579 17 19976894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272845 Affx-1111833100 AX-519546537 17 50789146 GCAACAGTTAGAAATTTACATGGAACAGCGGACTG[A/G]TTCAAATGGGAAAGGAGTATAACAAGGCTGTATAT R 2 1 2 1 102000 f 74 goat 17_50789146_AF-PAKI 17 50789146 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394342 Affx-122964663 AX-123264697 17 50829590 CATATCCTAATCAGCCGCAGGAAGGGAGGGTGCTG[C/T]GTGATCCCCACTTCTAAGAGGAGTTAAACTGAGGC Y 2 1 2 1 201000 r 74 goat snp44757-scaffold609-1219218 17 19934832 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400802 Affx-122959817 AX-123271157 17 50873055 GACATTGTGGTCTTTTCATGACTACAGTGTAAAAG[C/T]AGGGTTCTTTTTTTTTTTTAACTTGTATTTATTTA Y 2 1 2 1 101000 f 74 goat snp44758-scaffold609-1262683 17 19891575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430202 Affx-122937344 AX-123300543 17 50914494 CACTGTGGTTAGACTCAGAGAGGGACTTCCTTGTC[A/G]TGAACGGACAGCAGCTTGAGTCTTTACACCCAGTC R 2 1 2 1 101000 r 74 goat snp44759-scaffold609-1304122 17 19852864 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390260 Affx-122967753 AX-123260617 17 50949291 GGTGATCTGTGTGTTAAATCACTTCATCCCCACCA[A/C]CCTTATGAGGCAGATGCTGTTTCTTGTTTCTTTAT M 2 1 2 1 201000 r 74 goat snp44760-scaffold609-1338919 17 19818490 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786027 Affx-122926665 AX-385273063 17 50978847 TGGAAACACAGAGTATGAGACAGGGAGGGAAAATC[A/G]CTGCAAAGATCCTATGGCCTCACGAGCTTGTGTTC R 2 1 2 1 101000 f 74 goat snp44761-scaffold609-1368475 17 19792660 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452733 Affx-122920282 AX-123323066 17 51032505 AGGCTGAAGGCTGGATCCCCATCTCCCAGACACCA[C/T]GCCCTCCACCCTAGGATAGTAACACAGTTGGACCA Y 2 1 2 1 101000 r 74 goat snp44762-scaffold609-1422133 17 19738488 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425285 Affx-122940963 AX-123295631 17 51065081 AAAGAAAGAAACCCCTCCCATCTCCTGCTGCCTTC[A/G]CTCATGCTGGCCTTTGAACCACTTTCATTTCGCCA R 2 1 2 1 101000 r 74 goat snp44763-scaffold609-1454709 17 19705850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791980 Affx-122924630 AX-385278968 17 51120743 GAAAGTGATGATAGCTAAGAAAGTGGTCCAAGTTG[C/T]ATTATTCAAATATGACTGCTTCAGAAGGATATTCG Y 2 1 2 1 101000 f 74 goat snp44764-scaffold609-1510371 17 19649904 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420485 Affx-122944866 AX-123290832 17 51153972 AGTGGGGATTCAATTTGTGGTCTCAGAGAAGGCAA[C/T]GGCACCCCACTCCAGTACTCTTGCCTGGCAAATCC Y 2 1 2 1 103000 f 74 goat snp44765-scaffold609-1543600 17 19616701 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446597 Affx-122924813 AX-123316933 17 51191586 AGACACCCTCCAAGGAAACAGGGCCATTCTAGGGT[A/G]CCTTGTATGCCTTAAATCCAGAGGGGTGATAAAGG R 2 1 2 1 101000 r 74 goat snp44766-scaffold609-1581214 17 19578929 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433904 Affx-122934397 AX-123304245 17 51232564 GGGGGTTAAAAAGAATATGGACGGGGGCGGGGCCT[A/C]GAGGAGCGGGAGGGCATTTCCCTGGGTCAGTGTGC M 2 1 2 1 202000 r 74 goat snp44767-scaffold609-1622192 17 19537400 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443841 Affx-122927532 AX-123314178 17 51270064 CACTCACTACAGACATAGGGTTTCTCACCTGTATG[A/G]ACTCTCATGTGAATCTGCAGGTGTGAGCTCCAATT R 2 1 2 1 201000 r 74 goat snp44768-scaffold609-1659692 17 19499934 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431981 Affx-122935948 AX-123302322 17 51306155 ACTCTTGTGCTTGTGCTGCATTTTAGCTTGTTTAC[G/T]TCATTACTCAAACATGACTCAAATTTCACAGCCAG K 2 1 2 1 201000 r 74 goat snp44769-scaffold609-1695783 17 19463933 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390635 Affx-122967152 AX-123260992 17 51361808 AAACATGCGGACACACAGACAGATACACAGGGCAC[A/G]CTGGTCCTAATCGCTGCAAAGAGGTACTGACCTGT R 2 1 2 1 201000 r 74 goat snp44770-scaffold609-1751436 17 19407605 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442583 Affx-122928495 AX-123312920 17 51390939 TACAGTCTTTGGGACCCAACAAACTGGTGAATGAG[A/G]TGGACATGTCCAAAAACAATGATCAAAACAGGGTT R 2 1 2 1 101000 f 74 goat snp44771-scaffold609-1780567 17 19378103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428738 Affx-122938444 AX-123299080 17 51434709 GAGAGCTGAGACGGAAGAGAAAGTAGACGGAGAGA[C/T]GCTGAGAGAGGCCAGAGGATGACACAGGACAGATT Y 2 1 2 1 202000 r 74 goat snp44772-scaffold609-1824337 17 19333892 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422254 Affx-122944001 AX-123292600 17 51514604 TTCCCATGCCCAGATGTGCAGGTTCCTGGCACCAC[A/G]CCTCTGCAGAACAGCCAACCCCAGAGTGCTCAGTG R 2 1 2 1 201000 f 74 goat snp44774-scaffold609-1904232 17 19253625 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439769 Affx-122930514 AX-123310106 17 51545280 TTGACAGTCCATGGTGGAGCCAAACAAAAAACAAA[C/T]AAACAGATATATAAAACAAGTATTTATTACTACTT Y 2 1 2 1 202000 r 74 goat snp44775-scaffold609-1934908 17 19222988 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400359 Affx-122960031 AX-123270714 17 51603133 GTCAAGAATAAGGGTGAGAATGACCTTTCACTATC[A/G]TTTGGTGGAGCTTACATTTTATTCCATATTACACG R 2 1 2 1 101000 f 74 goat snp44776-scaffold609-1992761 17 19165274 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798834 Affx-122925072 AX-385285764 17 51642385 ATTGAGGTTTTCCTGACTGATTACTGCCTACTGGT[A/G]AAGGAATCTGCTTTATCTTATATGCCTGAGGACTT R 2 1 2 1 101000 f 74 goat snp44777-scaffold609-2032013 17 19126040 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789969 Affx-122927570 AX-385276975 17 51703901 GGCAGACATGATATGTATCAGTGATGAATGCTGCT[A/G]TATTTCTGGCCAGCTTAATTGCTTCGATTACATTA R 2 1 2 1 101000 f 74 goat snp44778-scaffold609-2093529 17 19064337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376053 Affx-122978930 AX-123246412 17 51742625 GAGAGTTCAGAGAGAAGGTAGATAGTTGTAGGGGT[A/G]GATGGGTCAGTGGATGGAAAGATGGATGCATGGCT R 2 1 2 1 101000 f 74 goat snp44779-scaffold609-2132253 17 19025438 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424459 Affx-122941777 AX-123294805 17 51826311 CAGGTCTTGGATCAAAACGACCTAGTTTTTCTTCT[A/G]CACCAGTTATTTCACCTGCTCCTAACAGTGCACCA R 2 1 2 1 101000 f 74 goat snp44780-scaffold609-2215939 17 18941673 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380970 Affx-122974985 AX-123251328 17 51920565 AACATTAGTACAGTAATCTTTTGAGGGGGTGAAGT[A/C]GGAAAGGATAGCTGTGGCAGGCAAAGGGAGACACA M 2 1 2 1 101000 f 74 goat snp44782-scaffold609-2310193 17 18847537 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433797 Affx-122934465 AX-123304138 17 51951273 AATCCAGCATCTTTCTCAAAGCTTTTCCTCCGAGA[A/G]CCCTAAACCCACAGTTCCATTTCCCTTTTGTGGGG R 2 1 2 1 201000 r 74 goat snp44783-scaffold609-2340901 17 18816678 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377042 Affx-122977701 AX-123247401 17 51999586 TCTGGTTTCCTAGTCCTCAGTGCTCACCCAAAGCC[A/G]GTCGCCTAGTGACCCCCCGCTCCGTTGAGGCTAGA R 2 1 2 1 101000 f 74 goat snp44784-scaffold609-2389214 17 18769047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275118 Affx-1111834703 AX-519548697 17 52014392 TGCAGTCAGAGAGGAGTTTGTGCAGCCTTCCAAAT[A/G]AGCCTGACAGCCTTC R 2 1 2 1 101000 f 74 goat GoatD01.046944 17 52014392 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38395803 Affx-122963649 AX-123266158 17 52049555 GCCAGAAAGATCAGGGACCACTGACCTAGGGGCTC[C/T]GCAAAGGCTCTGTCTTGGTCCCCTGCTCCCCCTGG Y 2 1 2 1 201000 r 74 goat snp44785-scaffold609-2439183 17 18719040 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426363 Affx-122940253 AX-123296709 17 52085308 CTAACCCTGATATCAGGATGTGCCCTGGATCTGGC[A/G]GGTAAGGACTGTTCTCTCAAATCCCCCAAAACAAA R 2 1 2 1 101000 r 74 goat snp44786-scaffold609-2474936 17 18683272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426839 Affx-122940505 AX-123297184 17 52179940 GCAGAGAAATTGGAATCCTTGTGTGTGACTGGTGG[A/G]AATGTGAAATGGTGCAGTTTGCTATATGCACCAAT R 2 1 2 1 201000 r 74 goat snp44788-scaffold609-2569568 17 18591576 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445818 Affx-122926029 AX-123316155 17 52243266 AAATGCCCCTCTGCTCTACAGGGTACTGTGGTCAA[C/T]GAGGAGACCTGGACAGTGCATTCCAAAGGCAAGGA Y 2 1 2 1 201000 r 74 goat snp44789-scaffold609-2632894 17 18527943 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386989 Affx-122969952 AX-123257347 17 52277732 AAACAGACTTCTTTTTACTTTTAATCTTACCTAGG[C/T]ATACATAACATTCAATAAATTTACTGAATGCCTGC Y 2 1 2 1 101000 r 74 goat snp44790-scaffold609-2667360 17 18493430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379846 Affx-122975807 AX-123250204 17 52329473 GGGTTTAACCCAGACTAGTGTGGGAGTACACTGGA[G/T]GCTTGGGGGCTGAAGGAAGAGGTATCCCCTGGGCT K 2 1 2 1 101000 f 74 goat snp44791-scaffold609-2719101 17 18440968 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445829 Affx-122926021 AX-123316166 17 52373291 CAAATGGTGACATGACATGGCACTCGGGCCATAGG[A/C]TTCTCTTACAGCACAGCACAGAGGGACACGGGGAT M 2 1 2 1 102000 r 74 goat snp44792-scaffold609-2762919 17 18397044 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405015 Affx-122956378 AX-123275367 17 52409324 AAGAATATCAGGAAAATGTATCTTCTCTGAGGGTC[A/G]CCAGAGAAGGTCACCTATAAATCCACAAACATCAA R 2 1 2 1 101000 r 74 goat snp44793-scaffold609-2798952 17 18360583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411971 Affx-122951128 AX-123282321 17 52468636 TCATCAGCAAGGACTTAAATAACTCATTTCACTGG[A/G]TCTCCAGGGCATAGAATACGAAAATGAAAAGCAAT R 2 1 2 1 101000 r 74 goat snp44794-scaffold609-2858264 17 18301311 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377887 Affx-122977254 AX-123248246 17 52508639 CTGTAATCAATCTACGTGTACTATAACTTTTTCCT[A/G]CTTTTCCTTCTTTTCCCCCCACAAAGTAAAATTTC R 2 1 2 1 201000 f 74 goat snp44795-scaffold609-2898267 17 18261328 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393391 Affx-122965900 AX-123263747 17 52541618 CTGCGAATCCCCCCCAACCCTATTCCACAGATACC[A/G]TTAACTTTTTGTCTTCAGTTCTTCAGGCAGTAACT R 2 1 2 1 201000 r 74 goat snp44796-scaffold609-2931246 17 18227995 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448422 Affx-122923665 AX-123318758 17 52574014 ACAACAGAAGACTTAAAGACCCCGAGTTTATGACC[A/G]TTCTTAGGTTCCTGATAACAACACGCCTCTGTTTC R 2 1 2 1 201000 r 74 goat snp44797-scaffold609-2963642 17 18195592 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782493 Affx-122948644 AX-385269569 17 52615504 TATCTACTGTTGAAGCATAAAGTCTTTGCTCATTG[A/C]GTTCTCTTGTGATGAAATCATGTTGGAGGTCTGTA M 2 1 2 1 101000 f 74 goat snp44798-scaffold609-3005132 17 18154209 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436703 Affx-122932324 AX-123307041 17 52651340 TAGAAGAATCTAAATCTGCTAATCCCCCAACCCTG[A/G]TACTTCTCAGTAAAAATATTTAAAATCACATTGTT R 2 1 2 1 103000 f 74 goat snp44799-scaffold609-3040968 17 18118235 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433567 Affx-122934976 AX-123303908 17 52681318 ACACATATGTGTGTATGAAACTGAAGCAAAATTTC[A/G]TTTAAAAAAAAAAACCATTCCCCTACTTCATGTGA R 2 1 2 1 102000 f 74 goat snp44800-scaffold609-3070946 17 18088007 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440533 Affx-122929333 AX-123310870 17 52750815 CACGGTTGATCAGCGCCTTCATCTTCACCTTAACC[A/G]GGGGGAAACTGAAGCCCAGAGAGAAGGTATAATTT R 2 1 2 1 201000 f 74 goat snp44802-scaffold609-3140443 17 18018356 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380573 Affx-122975273 AX-123250931 17 52786432 TCCATAAAGAAAAAGTCTTCACACACCCCCTACCA[C/T]GGCCGTCCTTCTTAGAAGACAGGTTCATGACACAG Y 2 1 2 1 201000 r 74 goat snp44803-scaffold609-3176060 17 17982670 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414012 Affx-122950267 AX-123284361 17 52827937 TTTCTAACGCGAAAGCAAGATCACTAACACTTCTC[A/G]CCTCCGCAGAGGTAAAAACTAGCTCTTTACTTAAG R 2 1 2 1 101000 f 74 goat snp44804-scaffold609-3217565 17 17942747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448033 Affx-122923712 AX-123318369 17 52890791 CACTTTATTCCAGTATTGACCTCATCATACTAGTT[A/G]CATCTGCCATGACCCTGTTTCTAAATAAAGTCACA R 2 1 2 1 101000 f 74 goat snp30012-scaffold327-2824425 17 17879328 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273533 Affx-1111833658 AX-519547148 17 53052987 CCTTCGGGAAGCGTCCCTGCCAATTGTTGCTGCAG[A/G]AAGTGCTGAATCATGAGAGCACAGTCAGAGGAAAA R 2 1 2 1 101000 r 74 goat GoatD01.000784 17 53052987 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38389353 Affx-122968469 AX-123259711 17 53111425 TGGGTGCTTAATATTGGGCACTTCATCTACATATT[A/G]CATTTAGTCCTCGCAGCAATCCTATGAGAGCAAAC R 2 1 2 1 101000 r 74 goat snp30008-scaffold327-2603791 17 17658987 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415967 Affx-122948420 AX-123286316 17 53156929 CCTGCATTTGAAGGCCGATTCTTAACTGCTAGACC[A/G]CCAGGGAAGTCCTGTGATGAATTCTTGAATAATGT R 2 1 2 1 101000 f 74 goat snp30007-scaffold327-2558287 17 17613075 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423137 Affx-122942765 AX-123293483 17 53207361 CATATCCCTTAAATGTGAACTGAGGGACTTCCCTC[A/G]TGGCCCAGTAGTTAAGAGTCTGCCTTTCTATGCGG R 2 1 2 1 201000 f 74 goat snp30006-scaffold327-2507855 17 17562921 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452530 Affx-122920544 AX-123322863 17 53275220 ATCAATATTCTGAGAAAGGTCAAGATTAAAAGAGA[A/C]TTAAGAACAGATTCTTGGAGTGGATCCTGATTTGA M 2 1 2 1 201000 f 74 goat snp30004-scaffold327-2439996 17 17495299 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277105 Affx-1111835744 AX-519550612 17 53319594 TCTCCTATTGGCCTCCATAAATGGAGACTGGAGAA[A/C]CAAAGAAAAGAGGGCTGAAAAGCAGAGTGAAAGGG M 2 1 2 1 101000 f 74 goat Random2.2K-1675 17 53319594 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401210 Affx-122959328 AX-123271563 17 53331475 TATTGTGAAACAAAGTACAAACCTGATAGACCAGT[A/C]TGAACAAGACAAATATGAAGATTCTGTTTTCCATT M 2 1 2 1 101000 f 74 goat snp30003-scaffold327-2383741 17 17439732 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383262 Affx-122972737 AX-123253620 17 53363043 CCCAGAGGCTGTCCCTTTTCATCCCCTTGAACCTC[C/T]GCTTATTTAGGCGAAGGGAGAGTTGAATCCAAGAG Y 2 1 2 1 101000 r 74 goat snp30002-scaffold327-2352173 17 17407563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272899 Affx-1111833101 AX-519546587 17 53386354 GAAAGAGACGGCTGTGACTGGTACAAACGGAGCTG[A/G]CTCTGTGAACTGTCCCTTTACCGCGAAAGAATGCC R 2 1 2 1 101000 r 74 goat 17_53386354_AF-PAKI 17 53386354 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423386 Affx-122943131 AX-123293732 17 53429532 TCAGGCCTGACTGCAGGAGCAGTTGGAGGAGGGAA[C/T]ATTAACCCTGTCTCCTAACCCTGTGTCCTACTCTG Y 2 1 2 1 101000 r 74 goat snp30001-scaffold327-2285684 17 17342864 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771072 Affx-122947460 AX-385258232 17 53509661 CATGATTATTATTTAAGTTTAACCCTGTCTAACGA[C/T]GCTGGCTATATTGTTATTTGGACAGTACCCAAGCA Y 2 1 2 1 101000 r 74 goat snp29999-scaffold327-2205555 17 17261891 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446341 Affx-122925615 AX-123316677 17 53750699 TGACAGAGTTCCCACCATCCCTGATCAGTGACTTG[C/T]AAAGGGCCGGGCCATGGGAGGGCCCCAGCAAGTTT Y 2 1 2 1 101000 f 74 goat snp29995-scaffold327-1964517 17 17019290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387478 Affx-122970352 AX-123257836 17 53799820 ATTTGAACTTGAAACTTCCTTGTTCAAGACTTCAG[A/G]AAGCCACATACCCGACAGGAAAGAATTCCAAGAGC R 2 1 2 1 201000 f 74 goat snp29994-scaffold327-1915396 17 16970130 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383884 Affx-122973126 AX-123254242 17 53831135 TTCTACAGCAAACGCTATTCTCGAGCCCTCTATTT[A/G]GGAGCCAAGGCCATTCAGCTGAACAGTAACAGTGT R 2 1 2 1 101000 f 74 goat snp29993-scaffold327-1884081 17 16938878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786794 Affx-122920992 AX-385273824 17 53875422 TTTTTAATCATTCTTGGGCCTGGAGAGCAGAAGTA[C/T]GCCTACAGTGTCAAATTCGATCCATTTTCATTAAA Y 2 1 2 1 101000 f 74 goat snp29992-scaffold327-1839794 17 16894448 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452255 Affx-122920772 AX-123322588 17 53909022 TCACTTCTCTGCTAAAAATCCTACCATGGCTCCCT[A/G]TCTCAAGGGTTAAGTATAAACAGGCATGAAGGAGT R 2 1 2 1 201000 r 74 goat snp29991-scaffold327-1806194 17 16861707 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785609 Affx-122923620 AX-385272652 17 53947967 TTTGTTGGGTTTTTGATTATTTCTGGTCAGAGGCA[C/T]GGAGCCTTATGACCCAGGTGTATTCTGTATTAGTT Y 2 1 2 1 201000 f 74 goat snp29990-scaffold327-1767249 17 16824543 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425503 Affx-122941476 AX-123295849 17 53977402 TACAAAGAGTGCTTTCTGCTTAGCGACTGAGTACT[A/G]TTTTGACTCAAGCCAGTTCCAACACATTTTTGCAC R 2 1 2 1 101000 r 74 goat snp29989-scaffold327-1737814 17 16795079 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426398 Affx-122940846 AX-123296744 17 54011115 ACTTTAATCACAAGACCACTATACACTGCACCAAG[A/C]TCAGATTTGACATTTTCCTACATTTACTCCACATT M 2 1 2 1 101000 f 74 goat snp29988-scaffold327-1704101 17 16761212 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422742 Affx-122943248 AX-123293088 17 54054715 CCTTCACTATCCGATTCACCATCATCACTGCCTCC[A/G]TCACCATGACCACCCGCACCGCCATCGGTGAGACC R 2 1 2 1 101000 f 74 goat snp29987-scaffold327-1660501 17 16717396 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784078 Affx-122948037 AX-385271130 17 54138291 GTCAGGGCTGTGAAGAGAAGATGAGATTTGAACAC[C/T]TGTGGGCAAATAAGACAATTTGCTGTGAATCAGGC Y 2 1 2 1 101000 f 74 goat snp29985-scaffold327-1576925 17 16633360 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428892 Affx-122938930 AX-123299234 17 54254719 CTCCCTCTGTTGTTTAGTTAGGTGTCCCTCTCCAG[A/G]AGCAGGAAGCCCCCAAAATCAGGATCAGAGTAAGG R 2 1 2 1 101000 f 74 goat snp29983-scaffold327-1460497 17 16516035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769263 Affx-122944276 AX-385256436 17 54290501 AGAAATAATCGCAGAAACTGGATGTTTGGGAGTTA[C/T]GTGACAGGATAGGGAAATCACTTAGCACAGAGCAT Y 2 1 2 1 101000 r 74 goat snp29982-scaffold327-1424715 17 16480152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450409 Affx-122922065 AX-123320744 17 54320820 TGTGCACTTCTCCTCTATACTCAAGAATGAGTTTG[C/T]GCCATCCAAAATTCTTCTGCTATTTTCTTTTCCCT Y 2 1 2 1 101000 f 74 goat snp29981-scaffold327-1394396 17 16449717 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407601 Affx-122954650 AX-123277952 17 54357029 TCAATGTTAATTTCCTGATTTTAATCATTGCACTG[C/T]GGCTATATAACAACATGTCCCTCAGAGAGAATATT Y 2 1 2 1 101000 r 74 goat snp29980-scaffold327-1358187 17 16413479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446404 Affx-122925573 AX-123316740 17 54401448 GGTCCAGAGAGCATCCAGGAGGCCAGAGAGAAGCT[A/G]TCTCCCCAGCCAACAAACTCTTACAGACCACCAGG R 2 1 2 1 101000 r 74 goat snp29979-scaffold327-1313768 17 16369119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453776 Affx-122919590 AX-123324109 17 54430853 TGCTAGAGCTACGAGAGAAAAGGGACTTTCTTTCC[C/T]TGAGTGTTTCCATGCTGGTGAAAGAGAGCTGTCAG Y 2 1 2 1 201000 r 74 goat snp29978-scaffold327-1284363 17 16340012 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780339 Affx-122941566 AX-385267434 17 54467125 TGAACCAGAATAGGGATGAAGAAGAACACTGAAGT[C/T]ATTAGACGTGACAAATACTGACATTTACTCTGGGT Y 2 1 2 1 101000 f 74 goat snp29977-scaffold327-1248091 17 16303877 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783506 Affx-122971549 AX-385270569 17 54500689 AATAGTAGCTCTAATTTACTGGCTGATCACTATAT[A/G]TTGGCCATTTCACCATGCACTGATTGTTTGAAACC R 2 1 2 1 101000 r 74 goat snp29976-scaffold327-1214527 17 16271228 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275326 Affx-1111834836 AX-519548901 17 54512196 GTGTTGCCTTGCCTTGGTGTAAATACCAAAAGGAA[A/G]TCTCTTTCCTCTGTCCCACATTAGGTACAGGGCAG R 2 1 2 1 201000 f 74 goat GoatD01.055900 17 54512196 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320799843 Affx-122977362 AX-385286769 17 54551652 TGCTTAGTTCCAGGACATAGGATTTGGCTGATCCA[C/T]GAATATTTGGCTTTACGTTTTAATTAAGTGTTGTT Y 2 1 2 1 101000 f 74 goat snp29975-scaffold327-1163564 17 16220050 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382104 Affx-122974891 AX-123252462 17 54583204 AACACAAGCCGTCTCAGTGCTGCCCCCTGGTGCTA[C/T]ATGAGAGGTACTACGAGGCACAGTGGTGTAGTTGC Y 2 1 2 1 101000 r 74 goat snp29974-scaffold327-1132012 17 16189735 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797155 Affx-122924658 AX-385284094 17 54612134 CACACTACTAATAATAACATCGCATGAACTGGTTA[C/T]TGAGCACAGATGATAAGCCAAACACCATGTAATCC Y 2 1 2 1 101000 r 74 goat snp29973-scaffold327-1103082 17 16160786 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801031 Affx-122976644 AX-385287945 17 54724450 TAGTAAACACCTTACAGAACAAGATGTAAGGTGAC[A/G]TTTCTATTAGTAATGATTTGCAAAATTGGACTAGT R 2 1 2 1 101000 f 74 goat snp29970-scaffold327-990766 17 16048857 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389373 Affx-122968452 AX-123259731 17 54774046 AACAGTACCTTTTATTTTTAAAAACTGCTCAAACA[A/G]AATTAGATCATTTCATTCTTTTGGATGGCACAGAC R 2 1 2 1 101000 r 74 goat snp29969-scaffold327-941170 17 15999254 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449203 Affx-122923509 AX-123319538 17 54905698 ACTATCAATAAACAACATATCAGGTCCATGGCTCT[A/G]AGCCAAGCCCTCACCCCTCCTCTGAGAGCAAAATG R 2 1 2 1 101000 f 74 goat snp29967-scaffold327-809518 17 15872720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436196 Affx-122932598 AX-123306535 17 55046010 TCTAATCACTGGGAAACCCAACAAGATCCAGTTTC[A/C]ATACATTTAGGAAGGCTGAGTTGTATGCTTTTATC M 2 1 2 1 201000 r 74 goat snp29964-scaffold327-669206 17 15730250 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772400 Affx-122923720 AX-385259553 17 55126466 AGAAAATGCAGGCAAGGAAATAATTACCAGATTAC[C/T]AAATACCCAGTGATAATTATACCTCATGGAGCTAC Y 2 1 2 1 101000 f 74 goat snp29962-scaffold327-588750 17 15650249 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377846 Affx-122977286 AX-123248205 17 55239499 CGTCTACCCATTGGTAAACTGTCATAATATACTGG[C/T]TTTGTTAGAACGAACACTTTCCCACCATGAGCTGG Y 2 1 2 1 101000 f 74 goat snp29960-scaffold327-475717 17 15536889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441871 Affx-122929028 AX-123312208 17 55275317 CACAGAACACGACAGTGTGACGCTGGCCAAGGATG[C/T]GACAACGTGGAGGAAGAGCTGTGGGCATTTCAGAC Y 2 1 2 1 201000 r 74 goat snp29959-scaffold327-439899 17 15500806 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476329 Affx-1251763836 AX-586011746 17 55290722 ACTGCAATTCCTCATCCATTTGGATTTAAATCCTA[-/TAAAAATGTCCTTAAATTTTCTTTTTTTTTTAATGTATATTTCCCATCCTATTCCTCCACCATCTTTTTCGGAAAACCTC]AAAAATGTCCTTAAATTTTCAACTCCGTACTCACC - 8 1 4 1 20000 f 74 goat SV_278 17 55290722 - deletion junction SV-TF-chip 539476582 Affx-1251763836 AX-586011968 17 55290722 ACTGCAATTCCTCATCCATTTGGATTTAAATCCTA[-/TAAAAATGTCCTTAAATTTTCTTTTTTTTTTAATGTATATTTCCCATCCTATTCCTCCACCATCTTTTTCGGAAAACCTC]AAAAATGTCCTTAAATTTTCAACTCCGTACTCACC - 4 1 4 1 20000 r 74 goat SV_278 17 55290722 - deletion junction SV-TF-chip 562165184 Affx-1251763836 AX-606940596 17 55290722 ACTGCAATTCCTCATCCATTTGGATTTAAATCCTA[-/TAAAAATGTCCTTAAATTTTCTTTTTTTTTTAATGTATATTTCCCATCCTATTCCTCCACCATCTTTTTCGGAAAACCTC]AAAAATGTCCTTAAATTTTCAACTCCGTACTCACC - 8 1 4 1 20100 r 74 goat SV_278 17 55290722 - deletion junction SV-TF-chip 562165240 Affx-1251763836 AX-606940652 17 55290722 ACTGCAATTCCTCATCCATTTGGATTTAAATCCTA[-/TAAAAATGTCCTTAAATTTTCTTTTTTTTTTAATGTATATTTCCCATCCTATTCCTCCACCATCTTTTTCGGAAAACCTC]AAAAATGTCCTTAAATTTTCAACTCCGTACTCACC - 8 1 4 1 20100 f 74 goat SV_278 17 55290722 - deletion junction SV-TF-chip 562165553 Affx-1251763836 AX-606940964 17 55290722 ACTGCAATTCCTCATCCATTTGGATTTAAATCCTA[-/TAAAAATGTCCTTAAATTTTCTTTTTTTTTTAATGTATATTTCCCATCCTATTCCTCCACCATCTTTTTCGGAAAACCTC]AAAAATGTCCTTAAATTTTCAACTCCGTACTCACC - 8 1 4 1 20100 f 74 goat SV_278 17 55290722 - deletion junction SV-TF-chip 562166206 Affx-1251763836 AX-606941614 17 55290722 ACTGCAATTCCTCATCCATTTGGATTTAAATCCTA[-/TAAAAATGTCCTTAAATTTTCTTTTTTTTTTAATGTATATTTCCCATCCTATTCCTCCACCATCTTTTTCGGAAAACCTC]AAAAATGTCCTTAAATTTTCAACTCCGTACTCACC - 8 1 4 1 20100 r 74 goat SV_278 17 55290722 - deletion junction SV-TF-chip 562166323 Affx-1251763836 AX-606941731 17 55290722 ACTGCAATTCCTCATCCATTTGGATTTAAATCCTA[-/TAAAAATGTCCTTAAATTTTCTTTTTTTTTTAATGTATATTTCCCATCCTATTCCTCCACCATCTTTTTCGGAAAACCTC]AAAAATGTCCTTAAATTTTCAACTCCGTACTCACC - 8 1 4 1 20100 r 74 goat SV_278 17 55290722 - deletion junction SV-TF-chip 320773423 Affx-122965168 AX-385260565 17 55329150 GTGAACTTGTATTCTGTAGGGAAACTGATGTGTTC[A/G]TCACCCATTCAGCCAATACAGATTTCTTGAGTTCC R 2 1 2 1 101000 f 74 goat snp29958-scaffold327-386066 17 15446912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412975 Affx-122951035 AX-123283324 17 55405936 CCATGTGTAAGTGTGGCTAAATTCCAGACAGCCCC[A/G]AGGAAAGGTCCTTCCTTTCACAGGGCTAGTGGCAC R 2 1 2 1 102000 f 74 goat snp29956-scaffold327-309280 17 15370333 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463515623 Affx-1110021409 AX-514998142 17 55420202 ACTCTCCCCAATATAAACAAACAGGTTTTAGTACA[A/G]TTTCAAAAATGCACTGTCATATTCCATGAAATTTG R 2 1 2 1 201000 r 74 goat Random2.2K-1681 17 55420202 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437865 Affx-122932071 AX-123308203 17 55471012 AGCAATTAGGTTTCTGTATATCACTTCTTATTCAG[G/T]AGAGCAGAGGTTTACTTTCTGGCCCTTTAGCTTAA K 2 1 2 1 201000 f 74 goat snp29955-scaffold327-244204 17 15305434 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377078 Affx-122978279 AX-123247437 17 55565536 TGGAGATAGAAGCAAGTTCTATCATGGGAAGAAAG[A/G]TGCAGTGAAGCCATCTGACCTGCATCTTCAGTGTT R 2 1 2 1 101000 f 74 goat snp29953-scaffold327-149680 17 15210702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416942 Affx-122948033 AX-123287290 17 55617944 GCCCTTGTTTGGAGAAAATAGGAGGCTCTGTTCCA[A/G]TTCTGCCATTGAACCTCTCTGTGACCATGGACATG R 2 1 2 1 101000 r 74 goat snp29952-scaffold327-97272 17 15158464 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443292 Affx-122927469 AX-123313629 17 55662991 AACGCTTTCTATGTGCTTTTAGGCAATCATAGTCA[C/T]AGTAATCTCTCTCTTTAGTCACTGACTCATGTCCG Y 2 1 2 1 101000 f 74 goat snp29951-scaffold327-52225 17 15112473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410125 Affx-122952816 AX-123280475 17 55710699 GACTCAAGAGCCCCTGTCCAGACTGCCTTCATCCA[C/T]GCAATTCTGGGGGACCGTTTTTGCCTGGGGCTCCT Y 2 1 2 1 101000 r 74 goat snp29950-scaffold327-4517 17 15065156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407758 Affx-122954977 AX-123278109 17 55725946 GCCACAGAGAACTTCTATAATCAAGTTTTAGGTCC[A/G]GGTCAGTGGTAGAGAGAAGGAAAGCTCTCCCCCCA R 2 1 2 1 101000 f 74 goat snp5894-scaffold1206-10631 17 15050175 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444284 Affx-122926765 AX-123314621 17 55778637 TGAAAAAAAAAATAACCACAGAACATTTCATTTCA[C/T]ATACGGCCTTGTGTATCTAAAGTGAGAGGCTCCTA Y 2 1 2 1 101000 r 74 goat snp5895-scaffold1206-63322 17 14997238 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772328 Affx-122967386 AX-385259482 17 55810439 GCGTGGAGCCTGGCATAGGTGGGTGATAAGCAAAT[A/G]CTTCCCAAAAGCTGACTCAGAACAGATCCAGAACA R 2 1 2 1 101000 r 74 goat snp5896-scaffold1206-95124 17 14965506 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406637 Affx-122955822 AX-123276989 17 55845050 AAAAGAGAGGGAGGGCCTCAGGAGCAGACAAAGAG[C/T]ACCTTGAAGGAGTTTTCTGGGTGGTTAAAAAACAG Y 2 1 2 1 101000 r 74 goat snp5897-scaffold1206-129735 17 14930575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410851 Affx-122952613 AX-123281201 17 55903508 AGAAGCAAGTGTTCACAATTCAGAGAGAGAGAAGG[A/G]AAATCAAACAGACAATTATAAAATTTTGTTCCCTT R 2 1 2 1 101000 f 74 goat snp5898-scaffold1206-188193 17 14872392 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382235 Affx-122973963 AX-123252593 17 55965537 CATCTCTCAGTCTGACTTAACCACATGGGTTCACA[C/T]GGAGAATTTCCCTTCTCCCTAAATAATGTTCTCTT Y 2 1 2 1 101000 f 74 goat snp5900-scaffold1206-250222 17 14809419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413507 Affx-122950635 AX-123283856 17 56000181 TCTCCAGCCAGCTTTAATGTGCACGTGAATCACCC[A/G]GGAGATTCTGACCCATGGTAGCTAGGGTGGGGGTA R 2 1 2 1 101000 f 74 goat snp5901-scaffold1206-284866 17 14776373 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272900 Affx-1111833102 AX-519546588 17 56009254 CCCCCATGACCACCCCCATCCCACTCCAAGAAACT[A/C]AATTCTGGCAAAGAAGCCCGGGGTACGTCTCTCCT M 2 1 2 1 102000 r 74 goat 17_56009254_AF-PAKI 17 56009254 G T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38419643 Affx-122945963 AX-123289991 17 56076962 ACTCCCATTGTGAGAGTGGAGAGGTTTTGAGACTG[C/T]GCCAGGGAGTGGGTGCTGACTCCTGCTCCCAGTCT Y 2 1 2 1 101000 f 74 goat snp5902-scaffold1206-361647 17 14698729 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447169 Affx-122924429 AX-123317505 17 56118982 TCCAGGAAGCACTCCTAGACTTTTGCAAGCTACAT[A/G]CTGCTTTTCCCTTCTCTATATCCCTATGACATTCA R 2 1 2 1 101000 f 74 goat snp5903-scaffold1206-403667 17 14656820 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795289 Affx-122945170 AX-385282247 17 56172335 TATTCTCTCCTCAATCTATCAAGCTTCTCAAAACA[C/T]CTCTTCACACTCACTGATTCCACAGCTTCAGGACA Y 2 1 2 1 101000 r 74 goat snp5904-scaffold1206-457020 17 14603408 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421789 Affx-122944338 AX-123292136 17 56350897 ATTCCCACAACTTTCCCTTGCTAAATATCATTCAA[C/T]GGCTCCCTATTACCCTTAGGCTAACGCCCAAGCTA Y 2 1 2 1 201000 f 74 goat snp5908-scaffold1206-635582 17 14409170 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393441 Affx-122965859 AX-123263797 17 56393792 TTTTACTGCCTTTTCATATCCCGTAAATCTGAGGA[C/T]GAAGCCTTAGGAGAAGGAAGACAGAAAGCGACGCA Y 2 1 2 1 201000 f 74 goat snp5909-scaffold1206-678477 17 14366463 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789079 Affx-122976989 AX-385276092 17 56459664 ATTTGAATTGCTTTGGAATTCAAGTCTTTCAGGAC[A/G]CAGAATCCTAGGGTGTTCCTATGTTAATTCTGGAG R 2 1 2 1 201000 r 74 goat snp5910-scaffold1206-744349 17 14300826 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394038 Affx-122964994 AX-123264393 17 56521579 ACATGTTTTTAATGTTTATTCTACAAATTAAATGA[C/T]GTCTACAGTCCAGGCAAACAGTCTTTTCTGAAAAG Y 2 1 2 1 101000 r 74 goat snp5911-scaffold1206-806264 17 14238175 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383913 Affx-122972982 AX-123254271 17 56557067 TAGTCCACAAACCCTGGTTCATTTTTATTTGGTTG[A/C]TTGGTTGCTTGGTGTGTTAACCATGGAATTTCCTT M 2 1 2 1 101000 r 74 goat snp5912-scaffold1206-841752 17 14201587 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430364 Affx-122937789 AX-123300705 17 56806072 AACTCAGCACTACAGTAGCATGGACAGGTTTAAAG[A/C]AAGAGAGGCCTGGATCGGGAGGGAGTGTGGGCAGA M 2 1 2 1 101000 f 74 goat snp5917-scaffold1206-1090757 17 13953815 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453853 Affx-122919535 AX-123324186 17 56855773 TTCTCTCCACCCCTGACCTAGTGAGTTGGAAAGGC[A/G]CTGACTGGGTTTCAGCTTTTGCCTGGCAGCTTTTT R 2 1 2 1 202000 r 74 goat snp5918-scaffold1206-1140458 17 13903808 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777408 Affx-122962646 AX-385264529 17 56910661 ATTGTCTAGTCCAGGTTATTTGAAACACATTTTAT[A/C]GACCATGAGTTTCACCCATGTGTGGTAGAAGTTAA M 2 1 2 1 303000 f 74 goat snp37916-scaffold469-10075 17 13849020 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766339 Affx-986697922 AX-385253719 17 56930990 TTTGGAAAATTGCCCATGTAAAGAACGATGGAGAC[C/T]CATGACAATTATACAAAGACTAATGTTCTGCTCCA Y 2 1 2 1 600010 r 74 goat 17_56930990 17 56930990 Ancestral_priority_1043 ancestry 0.57 neutral IMAGE 10K 10K ancestral 320763398 Affx-986697927 AX-385251283 17 56932089 TGTCACACAAACTAGGTATATGGAGTGACAAATGA[C/T]TAGTATCTCTAAGGCATCCTTCATCGTTCAGATGC Y 2 1 2 1 600010 f 74 goat 17_56932089 17 56932089 Ancestral_priority_1043 ancestry 0.734 recommended IMAGE 10K 10K ancestral 320763406 Affx-986697935 AX-385251289 17 56944088 AGAATGAGACCGTGAAGGCCTGAGATTGGGCTTCC[C/T]GATGGCTCAGCTGGTAGAGAATCTGCCTGCAATGC Y 2 1 2 1 600010 f 74 goat 17_56944088 17 56944088 Ancestral_priority_1043 ancestry 0.49 neutral IMAGE 10K 10K ancestral 38398899 Affx-122961021 AX-123269254 17 56980488 AGAGAGGCAAGAATTCCCCACATACCTGCTCACTA[C/T]CAGACGAGTTTTGTTCCAGGCATTGGGCAAAAATA Y 2 1 2 1 101000 r 74 goat snp37917-scaffold469-79902 17 13778291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379160 Affx-122976715 AX-123249519 17 57013553 ATAGTCCATAAGGTCATGCAGAGTCGGACACAACA[C/T]GCACAGTCTCATTTAAGCTGTAGAGCAGGATTTAG Y 2 1 2 1 101000 r 74 goat snp37918-scaffold469-112967 17 13744898 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403717 Affx-122958030 AX-123274069 17 57069246 TGAGAGAAAGCCCTGCTTCCTGTTGACAGAAGGTA[C/T]GAAGGAGGCTCCCTGGCTAAGGATGCACCCCCAGT Y 2 1 2 1 201000 r 74 goat snp37919-scaffold469-168660 17 13688601 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417128 Affx-122947367 AX-123287476 17 57101995 ACAATCTGTTCACAAACTCAGCGGGGGTAAGTAGC[A/G]CAAGTGTGGTCACATCCATTTGTCAGATAGGGAGA R 2 1 2 1 101000 f 74 goat snp37920-scaffold469-201409 17 13656482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781472 Affx-122957526 AX-385268557 17 57140110 AAAATGTCCACATGCAATGAGAAAAAACCTAAGTT[A/G]TCTAATGGAAGAAGGGTCCCTGACATCACGGAGGT R 2 1 2 1 101000 r 74 goat snp37921-scaffold469-239524 17 13618308 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778455 Affx-122970005 AX-385265569 17 57171432 TTGCTAGAAGAGCAGGAGTAACCGTAGTAATGACC[A/G]TCAGTATGAAGTACCTACTAGGTCCTGGTTGTTGT R 2 1 2 1 101000 r 74 goat snp37922-scaffold469-270846 17 13587157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381137 Affx-122974565 AX-123251495 17 57184566 CTTCTGCACAGGGTTTACAGCCCGGTCAGGGCACA[C/T]GGCCAGTGACTGACCCTTACATCTCCTTCCCTCTG Y 2 1 2 1 101000 r 74 goat snp6031-scaffold121-3848906 17 13573747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438619 Affx-122930923 AX-123308956 17 57243727 AGGTCATGAAGCCCCCTCACAGCCTCATTTTTGTA[C/T]AGCTATAAAATGAGGAAGTAATAGGGCTGCCAGCT Y 2 1 2 1 202000 f 74 goat snp6030-scaffold121-3789745 17 13514394 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448002 Affx-122923735 AX-123318338 17 57282356 ATGTGCCCCAAAGCACAAGGACTGACTCTGTTTAC[G/T]GATGATTCTTCAATTCTTAGAACAGTGCCGAAATA K 2 1 2 1 101000 r 74 goat snp6029-scaffold121-3751116 17 13476022 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392326 Affx-122966695 AX-123262683 17 57351194 TGTGGTGATTGAAGTCCAGAGAGATTAGGTAACTT[A/G]TCAAGATCACACCACCAGTGAGAAGCAGAGGAAAT R 2 1 2 1 101000 r 74 goat snp6027-scaffold121-3682278 17 13407125 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442901 Affx-122927644 AX-123313238 17 57396480 ACCAGTCACCTGTAGAGAGCAGAGAGTTCTAAAAA[C/T]GAGGGGCTGAGGAAAGTGAGTGAGTAGCTTGGTGC Y 2 1 2 1 101000 f 74 goat snp6026-scaffold121-3636992 17 13361587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382312 Affx-122973906 AX-123252670 17 57429013 ATTAAACAAGGGGCTAAGGTGCCCCCCCACCCCTC[A/G]CTGAGGAAAGGCGGTGTTTGGGGAATACACATTGA R 2 1 2 1 101000 r 74 goat snp6025-scaffold121-3604459 17 13330154 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793953 Affx-122961297 AX-385280922 17 57472675 CACTTTGAAAGCATCTATGAGTTTCACAAACTATC[A/G]TTAAATTCCTTAACCAACATACAGTAAAAAGTGAC R 2 1 2 1 101000 f 74 goat snp6024-scaffold121-3560797 17 13287940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425908 Affx-122941618 AX-123296254 17 57523385 CTGTCACACAGGGTCCCCGGTACACAGGTGCCCAC[A/G]TCATACCCTGGAAGGCCCTGTCTGTCGTTCCCTCA R 2 1 2 1 101000 r 74 goat snp6023-scaffold121-3510087 17 13237165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439125 Affx-122931092 AX-123309462 17 57556538 GTGAGGCAGGTGCTGTTACTACCGTCATCATTCTG[C/T]ATATGAGCAAAGGGAGGCAGCCTCCTGGTGTCCAC Y 2 1 2 1 101000 f 74 goat snp6022-scaffold121-3476934 17 13204471 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451407 Affx-122921191 AX-123321740 17 57598376 CTAGAGATACCCACCCAGGTTGTACAGCTTATGTT[C/T]TATTTCAGAAGTGGGAGGAAGGGGCGAATACCGTG Y 2 1 2 1 103000 f 74 goat snp6021-scaffold121-3435096 17 13170049 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789875 Affx-122945075 AX-385276882 17 57640904 ATGTAAGATGGGACATCATTACAAATCCTGTAGAT[A/G]TTAAAAAGTTAAAACGAAATATTATGAACACCTTT R 2 1 2 1 202000 r 74 goat snp6020-scaffold121-3392568 17 13127073 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452369 Affx-122920628 AX-123322702 17 57705044 GATAGTGGAAAGGGTGGGCCTCATGGAGCACCAGA[G/T]GTACGGAGGATAAGTTAGACATAATCTCTAACTGC K 2 1 2 1 101000 r 74 goat snp6019-scaffold121-3328428 17 13063158 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405665 Affx-122956568 AX-123276017 17 57734420 TTTACAATAGTCCTTATCACCCACGCTTCCATCTT[C/T]GGTTTCAACAAGTTTATTTTGACCATGGGGTTCAA Y 2 1 2 1 101000 f 74 goat snp6018-scaffold121-3299052 17 13034038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430475 Affx-122937249 AX-123300816 17 57767055 CCGATGGGCACAGCACTTCAGAGGTCAATGTTTTG[A/G]CTGTTTTGTTCTGACATGCTCTTTCAGCTGCGGTC R 2 1 2 1 201000 r 74 goat snp6017-scaffold121-3266417 17 13001579 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440828 Affx-122929274 AX-123311165 17 57813356 GGAGAGAAAGTGCAGGTGCTGGAGAATCAGGAGTT[C/T]GGTTTTGGATAAGTAAGAGGAGCTGACAATACATT Y 2 1 2 1 101000 r 74 goat snp6016-scaffold121-3220116 17 12955699 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448473 Affx-122923626 AX-123318809 17 57903410 ACTGTGCTTTGCCTGAGTTCTTGCAATGTACTTTT[C/T]TTCCACTGGACAGTGTATCTTGGACGTCCATTCCA Y 2 1 2 1 101000 r 74 goat snp6014-scaffold121-3130062 17 12865927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431684 Affx-122936785 AX-123302025 17 57942542 CAGCAGGGCTGGCACACCCTGCATGCATTGACATA[C/T]ACCAGCTCAACCACACCCCAATGGCCAAAAAGAAG Y 2 1 2 1 101000 f 74 goat snp6013-scaffold121-3090930 17 12826921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786567 Affx-122971244 AX-385273599 17 57978796 TTAACTCAAAACCAGTATACAATAAATTGTTGTTA[G/T]AGTTATTTTTACTTCCCATTCCATAGGAGGGGAAT K 2 1 2 1 101000 r 74 goat snp6012-scaffold121-3054676 17 12790331 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413838 Affx-122949877 AX-123284187 17 58010895 GGGGACAGTGGACTGGATCCTGGTTAGAAAGCCTG[A/C]TGTGGTTGAGAGCTGCCAACAGGGCTTCATCCACA M 2 1 2 1 101000 f 74 goat snp6011-scaffold121-3022577 17 12758416 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392652 Affx-122966444 AX-123263009 17 58137599 TTCTTAAAATCGTGTGGCTATGAGGAAGGCTTTCC[A/G]CAGAGAGTTGAGAGGTCAGTAATTTTGAATCCAAA R 2 1 2 1 101000 f 74 goat snp6008-scaffold121-2895873 17 12630328 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782225 Affx-122930844 AX-385269303 17 58187141 ATGATGGGAGCGAGGGGAGGGATCATGGTTTTCAT[A/G]CAACTTAATACGTTTTATGTGAACAATCTTTGTAA R 2 1 2 1 102000 f 74 goat snp6007-scaffold121-2846331 17 12580756 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786950 Affx-122957484 AX-385273979 17 58246863 TCTGCCTTTTTAAATGGTCTTATTTCCCTCTTAGA[C/T]CATGAAAAAAGGAATAATGGCCATGTGACAGTCAT Y 2 1 2 1 201000 r 74 goat snp6006-scaffold121-2786609 17 12521082 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788265 Affx-122961161 AX-385275284 17 58277656 AAATCAGCATACACCTTTCAGTAAGAAAATTTATT[A/G]CCACATTTTTCAGTTGCAATCCCACAACAATTTAC R 2 1 2 1 101000 r 74 goat snp6005-scaffold121-2755816 17 12490405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423086 Affx-122942931 AX-123293432 17 58310616 CATTGTAACACATGATCATATGAAATTATTCATTC[A/G]TTTGCTGTCTTTTATCCACACAGAACAATGCCACT R 2 1 2 1 101000 r 74 goat snp6004-scaffold121-2722856 17 12457329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386965 Affx-122969971 AX-123257323 17 58341837 GGTATATGAAAGATACTTTTAAGAAGGATAGACAG[C/T]ATCACTAAGACTCATCAGAGGCTCTTATTAAATGT Y 2 1 2 1 101000 r 74 goat snp6003-scaffold121-2691635 17 12426219 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384514 Affx-122973047 AX-123254872 17 58390809 TTAACTTTTGTGAGGACAAAAGTCAAGTTTTATCT[A/G]TCATTTTGTATTCCCACACTTAACAAGGTGGAGTG R 2 1 2 1 101000 f 74 goat snp6002-scaffold121-2642663 17 12377270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406275 Affx-122956087 AX-123276627 17 58421531 CAGACCTTGGGCCAATTCCCTCTCCAAGGTCATGA[A/G]AGAAGCAGTTTCAGGGACACAATAATCACATCAAG R 2 1 2 1 101000 r 74 goat snp6001-scaffold121-2611941 17 12346153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376366 Affx-122978318 AX-123246725 17 58456898 GAAGTTGTCTCAGGATATCATGAATTTCTTACTTT[A/C]GTCCTGGAATCCGTCATTCCTCAAAGAACTCTCAC M 2 1 2 1 101000 r 74 goat snp6000-scaffold121-2576574 17 12310712 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375393 Affx-122979213 AX-123245752 17 58500703 CCCGGGGATGAGGATGCCCTTGGAGACAGAGCTGC[A/G]TGGGGTGACACTGACTCTAGATGCAGCTGTAGTTG R 2 1 2 1 101000 r 74 goat snp5999-scaffold121-2532769 17 12266385 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272902 Affx-1111833103 AX-519546590 17 58519713 AGCACATGCGCTAATCTTTCCAAAAACCCAGGCCT[A/G]TGCATGTAAGATGCACAGTTATGGCATCAGTAGGG R 2 1 2 1 102000 r 74 goat 17_58519713_AF-PAKI 17 58519713 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38417532 Affx-122946932 AX-123287880 17 58561591 TCTAGATGCTTTTCCATCTTGGGGACTCTGGAGAT[C/T]GTAGCTGATACTGACTTGGGGACTGACTTTTTCCT Y 2 1 2 1 101000 f 74 goat snp5998-scaffold121-2471881 17 12205271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434290 Affx-122934767 AX-123304631 17 58639770 AGATATTCTACTGAGTATTCAAGAAGTGCTAATAA[C/T]CACTATTCTTACATTCTCCATAATCGATGAAGTGG Y 2 1 2 1 101000 r 74 goat snp5996-scaffold121-2393702 17 12126703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414570 Affx-122949382 AX-123284919 17 58673374 CTTCAGGGACTGCCCCCTGCCCTCACAATGAACTC[C/T]AAACCCCTCACCACGTTCTGGCTCCAATCACCTCT Y 2 1 2 1 101000 r 74 goat snp5995-scaffold121-2360098 17 12092483 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407369 Affx-122955270 AX-123277720 17 58702225 CCATGGGGTTGTCCATACAGTTAAGACCCCTTGGT[A/G]CCTTAAGGGGAACACGTGTGAAGTAGACACTGCCA R 2 1 2 1 202000 r 74 goat snp5994-scaffold121-2331247 17 12063443 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420949 Affx-122944982 AX-123291296 17 58749480 TAGCTCAAAAATATTTTAAAAAATAAATAAAACAC[A/C]AGACTAATGATCTTGATCAAAGTAGCTTCCCCCTT M 2 1 2 1 101000 r 74 goat snp5993-scaffold121-2283992 17 12016128 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386772 Affx-122970115 AX-123257130 17 58784114 CTGTGCTAAACAAGTTAGATGGGATAATGTATACA[C/T]AGTTCTTGGCATGTGAAAGATGATTAATAAATGCT Y 2 1 2 1 101000 r 74 goat snp5992-scaffold121-2249358 17 11981496 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427282 Affx-122939532 AX-123297625 17 58812943 AATAAAAAGTCTGCTGGGGGAGGATTTTAGAAACT[G/T]GATAGTTTAGTAAAAAGATATGACTGTACCTAGTG K 2 1 2 1 101000 r 74 goat snp5991-scaffold121-2220529 17 11953507 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426879 Affx-122940474 AX-123297224 17 58847751 TTATTTTTAAGAAGACTCTTAGCAGCAGGTACTCT[A/G]CTAGGCGTGTCGAACTCACTTCATGACTCCTTGAG R 2 1 2 1 101000 r 74 goat snp5990-scaffold121-2185721 17 11918704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786147 Affx-122927517 AX-385273183 17 58941920 GAGCCACTTAGAAACAGAAGAATCTGCAAAGCAAG[C/T]GATAGATGTTTGGTATCACACTAAAACTACACGAG Y 2 1 2 1 101000 f 74 goat snp5988-scaffold121-2091552 17 11824038 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424818 Affx-122941373 AX-123295164 17 58973842 AAGCAAATAAATTAAAATACTACTTTTACATGCCA[C/T]GATTTCACGTTAATGTTTCCTTTTTTACTCATTTC Y 2 1 2 1 101000 r 74 goat snp5987-scaffold121-2059630 17 11791586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801689 Affx-122930545 AX-385288597 17 59009337 AAATAATCATAATCACGGTTTCAAATAGTGAAATA[A/G]TAATAACTATTATTATTCTACAGCTCTTCCAGGAG R 2 1 2 1 201000 r 74 goat snp5986-scaffold121-2024135 17 11755960 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388609 Affx-122969143 AX-123258967 17 59060189 GGGTCAGTTTGCAACCTCTAACATCTGGTGACAAA[C/T]GACAGTGTGCTAGGGAAGGCATTTGGGCTTGGAAT Y 2 1 2 1 101000 f 74 goat snp5985-scaffold121-1973283 17 11704316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417582 Affx-122946896 AX-123287930 17 59119847 AGAGGCCTCTCTCTGGAGTTCTCCCCACATGCCCA[C/T]GCTGGAACCAGCTTGCATGATTCATGTCCTGAAGG Y 2 1 2 1 201000 r 74 goat snp5984-scaffold121-1913625 17 11644696 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425397 Affx-122941553 AX-123295743 17 59178552 CTAGGTATGTTTTTATGTGTACGTGAGTGTTTTTT[A/G]TTCCTGTGTTTGTGTATTTGTGTGTGTGTTGGCAT R 2 1 2 1 201000 f 74 goat snp5983-scaffold121-1854920 17 11585921 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405290 Affx-122956851 AX-123275642 17 59228145 TAGAAATCTCCTAAAATACTGAGTGCCCACTGGGC[A/G]CCAGGAACTGTATTCAGTACTTTGTGTCTGTCTGT R 2 1 2 1 102000 r 74 goat snp5982-scaffold121-1805327 17 11536631 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404916 Affx-122956447 AX-123275268 17 59272656 TTTCCTTAGGGCTAAGACTCTGGCTTGACCTTAAG[A/G]AACTGCCAGGATAATGAGAACACCAACAACCATCA R 2 1 2 1 101000 r 74 goat snp5981-scaffold121-1760816 17 11492179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407278 Affx-122955337 AX-123277629 17 59328496 GGACTCCATGCCGGGTACAACACTGGGGATTTGCA[C/T]TCATTTTCTTGAATCTTCCTAAGGACACTGCAAAG Y 2 1 2 1 101000 r 74 goat snp5980-scaffold121-1704976 17 11436089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453269 Affx-122920393 AX-123323602 17 59373252 CCAGGGGCCCCAATCCAAATAGCTACAGGAACCCA[C/T]GGTGAATGTCAATACATGATGATGAGTCCAACCAA Y 2 1 2 1 201000 r 74 goat snp5979-scaffold121-1660220 17 11391289 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386876 Affx-122970058 AX-123257234 17 59432020 CTTCTCCATCTTTTTTGCTCTTGTCAAAGAGTACA[C/T]GACCCCTAAGGTCATCACAGTGGAGGAAGAAAGGG Y 2 1 2 1 101000 f 74 goat snp5978-scaffold121-1601452 17 11332613 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404994 Affx-122956393 AX-123275346 17 59463018 AGATAATACAAAAATGAGCACCCAAGGTGTCATTT[A/G]TCTTTGGTTTTGGATTATGTGCAATGACTGCTTCT R 2 1 2 1 101000 r 74 goat snp5977-scaffold121-1570454 17 11301972 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392698 Affx-122966408 AX-123263055 17 59512065 AAGAAACCCAAATCTGTCCTTTCAAACTTGCCAAC[A/G]TGCAATATTTCCTCTGACTTTGACCATTGTCTCCC R 2 1 2 1 201000 r 74 goat snp5976-scaffold121-1521407 17 11253552 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453132 Affx-122920006 AX-123323465 17 59566212 TATTCATACTAAAGGGGAGGGAATTACGCAAAGCT[A/G]TGAACACTGGGTAGCAGGAAGAATGGAAGGGGGAA R 2 1 2 1 101000 f 74 goat snp5975-scaffold121-1467260 17 11199792 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772248 Affx-122954475 AX-385259403 17 59601799 CTAGGCATCAGCTGGTGGAAATGGTCCCAGAGTTC[A/G]TAATCACTGAGAGGAAGGCAGGTTTTTTTTGTTTT R 2 1 2 1 101000 f 74 goat snp5974-scaffold121-1431673 17 11164255 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409915 Affx-122952884 AX-123280266 17 59640207 CCCCATTTCTTCCCAGTTGAGGCTCAGGGCAGACA[C/T]GCCTGAATGTAATTCTAAGAGGCAGGGGAAGCCTG Y 2 1 2 1 201000 f 74 goat snp5973-scaffold121-1393265 17 11125827 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414527 Affx-122949516 AX-123284876 17 59732808 CTGCTTAGTAAAGTTTGAAATATTTCATTGAGTTC[A/G]TTCCTCAGATCACTAGCCCTTAAAAGGTGGCTTGA R 2 1 2 1 101000 r 74 goat snp5971-scaffold121-1300664 17 11034012 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434540 Affx-122934146 AX-123304881 17 59767468 TTGAAAAGGATACACCCTTCCTGGACCTCGGGGAT[A/G]TAGCAGTACCTAAACAGACCTGATCTCTTCCTTCT R 2 1 2 1 101000 r 74 goat snp5970-scaffold121-1266004 17 10999476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402434 Affx-122958625 AX-123272787 17 59810021 ATTGTTTGTAATACAATATAGGGCTCTTCCTCTAC[G/T]CCTTTATATCTGTGTGTGTCTGTCTCTATACCTCT K 2 1 2 1 201000 f 74 goat snp5969-scaffold121-1223451 17 10956972 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428724 Affx-122938456 AX-123299066 17 59842864 GCATCAGCACCTGAACCCAGGCGTCTTTGACCAGC[G/T]GTGGGAAAGCACATCGGAGGTCGGGTACCCCAAGC K 2 1 2 1 201000 r 74 goat snp5968-scaffold121-1190608 17 10924084 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449377 Affx-122922719 AX-123319712 17 59901511 TACCATGTTGACGCGATGTCAATTTCCTGTAACGT[A/G]GCAATCTCCATTGGGAAGGACTTGATTATTGCTCT R 2 1 2 1 101000 f 74 goat snp5967-scaffold121-1131961 17 10865740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787815 Affx-122956116 AX-385274838 17 59950082 TAAAGCATAAGGACATTAGAATATCTTGTGTATTA[C/T]GATGTCACATAACAGGAAAGCTCAAGGTAAAAGTT Y 2 1 2 1 101000 r 74 goat snp5966-scaffold121-1083390 17 10817506 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793015 Affx-122955768 AX-385279993 17 59985257 AATGCTGAAGCAATGCCTGGTACACAGAAAATCTT[C/T]GATAAACACTGGATGAAATTATCATAGAATAATTG Y 2 1 2 1 101000 f 74 goat snp5965-scaffold121-1048215 17 10782556 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765976 Affx-122942209 AX-385253400 17 60038084 CCATAATTCAGAAGACCGAGGCAGTTGACGTGGTA[G/T]CACACGTTTCTATGAATTAAGAAACAAACTATAGA K 2 1 2 1 101000 f 74 goat snp5964-scaffold121-995388 17 10729752 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388257 Affx-122969779 AX-123258615 17 60100906 CTACAAGGAAGATAGAGTCCCCATGGGAGAAATTA[A/G]GGCTCTTCAGCCTTCAGGGGAGAAAGTTAGATCAA R 2 1 2 1 101000 f 74 goat snp5963-scaffold121-932566 17 10667374 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407440 Affx-122954797 AX-123277791 17 60148850 CTTGAAAGTGGATTCTTTCCCCCCACCTAGATGGC[G/T]GGTGAGCTGGTGCTGTTTATCGGTTCCTTTTCAGA K 2 1 2 1 202000 r 74 goat snp5962-scaffold121-884622 17 10619514 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440657 Affx-122929938 AX-123310994 17 60191239 GAGAAAGCCAAACCAAAATATAAAGAAAAAGCTTC[C/T]GTGGACCCTCTCCAGAGGTTACCACTGGGACTAGT Y 2 1 2 1 101000 r 74 goat snp5961-scaffold121-842233 17 10576552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275882 Affx-1111835131 AX-519549442 17 60223251 ATTTGCATCGAGATGGAAACCTTTTTGCTCAGGGT[A/G]TCCTTCTGGGTGGCGCTGGTCGGAGGTGTCATCAG R 2 1 2 1 102000 f 74 goat ilmnseq_rs655476105 17 60223251 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275688 Affx-1111835035 AX-519549258 17 60223272 CTGTAGCTTTCAGCGTTATCACTGATGACACCTCC[A/G]ACCAGCGCCACCCAGAAGGACACCCTGAGCAAAAA R 2 1 2 1 102000 f 74 goat ilmnseq_rs643186608 17 60223272 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468276111 Affx-1111835246 AX-519549662 17 60223293 ACACGGATGCTTAGGTTTGTGCTGTAGCTTTCAGC[A/G]TTATCACTGATGACACCTCCGACCAGCGCCACCCA R 2 1 2 1 101000 f 74 goat ilmnseq_rs667679883 17 60223293 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275939 Affx-1111835084 AX-519549497 17 60223396 ATAGTTGTGCACTGAGCCATTGCTGGGGAGGGCCA[A/G]ATTCGTGGGTTGATGTGTGGTAACCACGAAGCTGA R 2 1 2 1 101000 r 74 goat ilmnseq_rs649444422 17 60223396 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275656 Affx-1111835019 AX-519549226 17 60223397 AATAGTTGTGCACTGAGCCATTGCTGGGGAGGGCC[A/C]AATTCGTGGGTTGATGTGTGGTAACCACGAAGCTG M 2 1 2 1 202000 f 74 goat ilmnseq_rs641376586 17 60223397 T G 2 neutral Goat_IGGC_65K_v2 Illumina 468275962 Affx-1111835094 AX-519549520 17 60223422 CCCACGAATTTGGCCCTCCCCAGCAATGGCTCAGT[A/G]CACAACTATTGCCCACAACAGACTAAGATTACTTC R 2 1 2 1 101000 r 74 goat ilmnseq_rs650183538 17 60223422 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275582 Affx-1111834982 AX-519549152 17 60223612 CTTAAATACATTGATAGGGAGATCAATGACCACAT[A/G]GATAAGGTCTCCAAGGGCAAGGCTGGCTATCAGCG R 2 1 2 1 101000 f 74 goat ilmnseq_rs636671976 17 60223612 T C 1 recommended Goat_IGGC_65K_v2 Illumina 320801280 Affx-122939701 AX-385288192 17 60234569 TAAGGATTCTGAAATAAGTAACTTGTCAAGAGATG[C/T]CAAGTCATAAAGATGGTTACTCTTGGAGATGGAAG Y 2 1 2 1 101000 r 74 goat snp5960-scaffold121-798903 17 10533173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463514843 Affx-1110023128 AX-514997374 17 60257871 TTGAACAAAATGACTTTGGCGTTTTCCTCTGCAAG[C/T]TGTTCCCCTTTTTGCAGAAGTCCTCAGTGGGGATC Y 2 1 2 1 101000 f 74 goat ilmnseq_rs671841888 17 60257871 T C 1 recommended Goat_IGGC_65K_v2 Illumina 38447972 Affx-122923759 AX-123318308 17 60279055 ACGGACACGGAAAATCACTGGCATAGTATAAGGAC[A/G]TAACAGATATAAGCTACATGGATAGATGGGGGCTT R 2 1 2 1 101000 r 74 goat snp5959-scaffold121-754417 17 10488715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276088 Affx-1111835160 AX-519549640 17 60280379 AATGCTCTTCCTCCTCTCTCCCTCCTCTCCTCTTT[C/G]CAGTTCTATCAAGATGTTAAGGACTGGTGGCTATT S 4 1 2 1 201000 r 74 goat ilmnseq_rs657684219 17 60280379 C G 2 recommended Goat_IGGC_65K_v2 Illumina 468276226 Affx-1111835230 AX-519549776 17 60280444 GCTATTTGGGTTCTACTTCTGCATGCCCCTGGTGT[A/G]CACCGCGATCTTCTACACCCTCATGACTTGTGAGA R 2 1 2 1 102000 r 74 goat ilmnseq_rs666529295 17 60280444 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275797 Affx-1111835090 AX-519549361 17 60290484 ATGCTGGTGCCATTCATGGGCACCGAGGTCATCAG[A/G]CTCTTGGACTGGTAACAGCAGCAGCAGAGGCAAGA R 2 1 2 1 202000 f 74 goat ilmnseq_rs649867027 17 60290484 C T 2 neutral Goat_IGGC_65K_v2 Illumina 38441882 Affx-122928625 AX-123312219 17 60308940 AGAAACCAGATTTTACAAATACAGGGAGAACTTCC[A/G]TTGAGCTCGTAAGGTTTTGAAGGGATCTTAAGGGG R 2 1 2 1 101000 r 74 goat snp5958-scaffold121-724532 17 10459139 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386029 Affx-122971486 AX-123256387 17 60362013 CTCTACCACTTCTTTATATCACATTCATGTTCTTA[A/C]GAATTTTCTTTATACAAATTCATTTTTTTTTGACC M 2 1 2 1 102000 f 74 goat snp5957-scaffold121-671459 17 10406092 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376563 Affx-122977974 AX-123246922 17 60391506 TTGGGAAGATTGGGATAAATCAAACAGACCTGCTT[A/G]TTACCTCCTAAAAGCTTACAGTCTAGTGCAGATAA R 2 1 2 1 101000 f 74 goat snp5956-scaffold121-641966 17 10376747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376224 Affx-122978796 AX-123246583 17 60422949 GCCCTGTTCCAACCTGCTCTGGGTTCATTCCAAGC[A/G]TTTGTACAGCCGCCTCCTACTTTTCCATCCTTATC R 2 1 2 1 101000 r 74 goat snp5955-scaffold121-610523 17 10345461 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414637 Affx-122949330 AX-123284986 17 60459126 TATAAGGAACAAGAATGGAATCAAAGGGGAATATG[C/T]GAGAGTCAGAGCAGGAAACCTTCAGACGGAGGTCG Y 2 1 2 1 201000 f 74 goat snp5954-scaffold121-574346 17 10309216 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394868 Affx-122964760 AX-123265223 17 60522993 ACTCTTCCCTTTCAATGCAGGGAGCAAGGGTTCTA[C/T]GCCTGGTGGGGGAACTAAGACCTTGGTTGGGGAGA Y 2 1 2 1 101000 f 74 goat snp5953-scaffold121-510479 17 10245215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439332 Affx-122930300 AX-123309669 17 60569315 GGAATGAGGGGACCCCTGGGGCTAAGGTGTCTGGG[A/G]GAAGGCCCCCCACTTACTCCTTCCAGGCAGCATCT R 2 1 2 1 101000 r 74 goat snp5952-scaffold121-464157 17 10198875 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414564 Affx-122949385 AX-123284913 17 60619766 TAAGTGGTGGAGACCTTGAGTCCCAGACCCAGGAC[A/G]TGAGTTGGCCTGATTCCAAGTGATACAGTGGTCTG R 2 1 2 1 101000 r 74 goat snp5951-scaffold121-413706 17 10148489 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383564 Affx-122972602 AX-123253922 17 60693145 TTTGCCGTTTGATTTTCTTTTTTTCTTGGATTCCA[C/T]GTGACACTTCCATTTCCTTGAGGTAGTCTCACTGG Y 2 1 2 1 101000 r 74 goat snp5949-scaffold121-340327 17 10076873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384577 Affx-122972996 AX-123254935 17 60728677 GCTTTGTGGGCATCCGTGGGAACAGCCTGAGTAAG[C/T]TTTCTCTAAGAAATTTCCAGAAATGCTTTGCATCC Y 2 1 2 1 101000 r 74 goat snp5948-scaffold121-304795 17 10041335 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431585 Affx-122936179 AX-123301926 17 60791000 TCCACTTGGATTCCTGGAGAACACCCCGCCCCCTG[C/T]CCCATTAAGGTGTGAGCCGGCCTGAGAAGGGCTGG Y 2 1 2 1 201000 r 74 goat snp5947-scaffold121-242472 17 9979896 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411115 Affx-122951908 AX-123281465 17 60826569 ATAGATGAGAGACCAAGGCCACTCTCCCTCCCTGG[C/T]GCACTGGTTTCCTGACTTGGTCCTGTTCGGCATTC Y 2 1 2 1 101000 r 74 goat snp5946-scaffold121-206903 17 9943995 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789074 Affx-122944391 AX-385276087 17 60869050 TTACTAATATGTTAGGCTTAAATATTATCATCTTG[C/T]AATTTACTGCATATTTATCCCACCTGTCCTTTGTT Y 2 1 2 1 101000 r 74 goat snp5945-scaffold121-164422 17 9901508 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409434 Affx-122954098 AX-123279785 17 60903522 GAGAAGATGAGGTCAGTGACATGCGGAAGAACAGA[C/T]AGGGGGGCTACCTGTGTTGGGGAACTAATGCTTCA Y 2 1 2 1 101000 f 74 goat snp5944-scaffold121-129950 17 9867087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449197 Affx-122923514 AX-123319532 17 60961999 ATCCAGCAAAGTCTTATGTTTCATTACCCGGAACC[A/G]TTGCCATGCGTTGCTTGCAGCTTAAAAGTGACTCC R 2 1 2 1 101000 f 74 goat snp5943-scaffold121-71473 17 9810287 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277234 Affx-1111835747 AX-519550740 17 60982274 CCACCCCATCTCACCCCTCTAGGTTGTCATAAATT[A/T]TCTTGTTTTTCTCTCTCGGCATTTGCTGCTACTTC W 4 1 2 1 102000 r 74 goat Random2.2K-1685 17 60982274 T A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38410566 Affx-122952137 AX-123280916 17 61004914 TGCTTTCCCTGCCTCGCCTGCCTTTCCCAGAGAAA[C/T]GACCATCAGGGTCTTGGCCTTGTTTTCCTCTAAGT Y 2 1 2 1 202000 r 74 goat snp5942-scaffold121-28558 17 9768086 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272854 Affx-1111833104 AX-519546544 17 61027710 AGAGAACAGACTATGGACAAGGGCGGGGGGGGGGG[A/G]GGAAGGAGAGGGTGAGACAAATGGAGAGAGCAGCA R 2 1 2 1 303000 f 74 goat 17_61027710_AF-PAKI 17 61027710 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38380448 Affx-122975744 AX-123250806 17 61071864 TGAAGATGACAAACATAAGTGGAAAGACAGAGTGA[C/T]GCCGGCTTTGAGGAATTGATGTTAAAATGTGCAAA Y 2 1 2 1 101000 f 74 goat snp12104-scaffold1448-38293 17 9698039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440705 Affx-122929903 AX-123311042 17 61101235 TAGAAAGCTGATGTCATTTTGTGAATTTAGTAACA[C/T]AAATTTGTATTTTTATAGCTTGGCTAATATGTTTA Y 2 1 2 1 101000 f 74 goat snp12105-scaffold1448-67664 17 9668727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400516 Affx-122961268 AX-123270871 17 61160246 TGGTGATGTAGAACTGAAGCCAGTGGGAGGCACTG[A/G]GTTAAGGGTCTGGATTTAGAAGCAAAAGGAAGAGG R 2 1 2 1 101000 r 74 goat snp12106-scaffold1448-126675 17 9609725 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377052 Affx-122978299 AX-123247411 17 61211532 AATGGAGGATCGGCCCAATGACTCATGGTCCATCC[A/G]TATCCTGCAATGAACGCTACTCAGATGAGAGTGGT R 2 1 2 1 101000 r 74 goat snp12107-scaffold1448-177961 17 9559008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418443 Affx-122946480 AX-123288791 17 61258923 AAGAAGGAAGGTCCATACCCAAGTTTATAGCTTGC[A/G]TGGCTAAATGAATGGGGAAGCCATCAATTACAAGA R 2 1 2 1 101000 f 74 goat snp12108-scaffold1448-225352 17 9511632 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799752 Affx-122967813 AX-385286679 17 61303493 AAAAGAGGCAGAAACATACATAATAATACTAGACA[A/C]TATGACCCTTTGTTATGGCACCAAAACAATCAAAT M 2 1 2 1 101000 r 74 goat snp12109-scaffold1448-269922 17 9467748 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410150 Affx-122952796 AX-123280500 17 61346483 ATGAATGACTACATGAATGAATGGATGGATGACAA[C/T]AGAATAAACAGGTGGGTGGGTAGGTGGATAGGTGA Y 2 1 2 1 101000 f 74 goat snp12110-scaffold1448-312912 17 9424857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394804 Affx-122964809 AX-123265159 17 61406313 CTTAACAGCAAAGTTGCCACGGCATTTTATTATCT[C/T]TACCATGTCCACCAATGACGCTTTAATTGAAATAC Y 2 1 2 1 101000 f 74 goat snp12111-scaffold1448-372742 17 9366238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418436 Affx-122946486 AX-123288784 17 61463201 GGAGGGGAAAAGGGCATTTGGGTTTATCAACAAGG[C/T]AGGTCCATAAAAGATGAGAAGAAACAGATAAATTT Y 2 1 2 1 101000 f 74 goat snp12112-scaffold1448-429630 17 9308918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383277 Affx-122972725 AX-123253635 17 61502911 CAGGGATTCAAATCTCAATTCTGCCAATTTCTAGG[C/T]GGGTGCAAGTCACTTAATTCTGAGCTTCAGTTCCT Y 2 1 2 1 101000 f 74 goat snp12113-scaffold1448-469340 17 9268421 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476330 Affx-1251763838 AX-586011747 17 61544942 GACTGGATTCTTCATCTGAAAAATGCAGGTGCTTT[-/TAAAAAATTATTAGAGGGAGGAGGGAAAGATGGCGGAGGAAAAAAAAACAAACAAACAAAACAACAACAACAACAACAAC]AAAAAATTATTAAACAGTGAAACATCCACCCTACT - 8 1 4 1 20000 f 74 goat SV_292 17 61544942 - deletion junction SV-TF-chip 539476584 Affx-1251763838 AX-586011970 17 61544942 GACTGGATTCTTCATCTGAAAAATGCAGGTGCTTT[-/TAAAAAATTATTAGAGGGAGGAGGGAAAGATGGCGGAGGAAAAAAAAACAAACAAACAAAACAACAACAACAACAACAAC]AAAAAATTATTAAACAGTGAAACATCCACCCTACT - 4 1 4 1 20000 r 74 goat SV_292 17 61544942 - deletion junction SV-TF-chip 562165874 Affx-1251763838 AX-606941283 17 61544942 GACTGGATTCTTCATCTGAAAAATGCAGGTGCTTT[-/TAAAAAATTATTAGAGGGAGGAGGGAAAGATGGCGGAGGAAAAAAAAACAAACAAACAAAACAACAACAACAACAACAAC]AAAAAATTATTAAACAGTGAAACATCCACCCTACT - 8 1 4 1 20100 f 74 goat SV_292 17 61544942 - deletion junction SV-TF-chip 562165884 Affx-1251763838 AX-606941293 17 61544942 GACTGGATTCTTCATCTGAAAAATGCAGGTGCTTT[-/TAAAAAATTATTAGAGGGAGGAGGGAAAGATGGCGGAGGAAAAAAAAACAAACAAACAAAACAACAACAACAACAACAAC]AAAAAATTATTAAACAGTGAAACATCCACCCTACT - 8 1 4 1 20100 f 74 goat SV_292 17 61544942 - deletion junction SV-TF-chip 562165906 Affx-1251763838 AX-606941315 17 61544942 GACTGGATTCTTCATCTGAAAAATGCAGGTGCTTT[-/TAAAAAATTATTAGAGGGAGGAGGGAAAGATGGCGGAGGAAAAAAAAACAAACAAACAAAACAACAACAACAACAACAAC]AAAAAATTATTAAACAGTGAAACATCCACCCTACT - 8 1 4 1 20100 f 74 goat SV_292 17 61544942 - deletion junction SV-TF-chip 562166319 Affx-1251763838 AX-606941727 17 61544942 GACTGGATTCTTCATCTGAAAAATGCAGGTGCTTT[-/TAAAAAATTATTAGAGGGAGGAGGGAAAGATGGCGGAGGAAAAAAAAACAAACAAACAAAACAACAACAACAACAACAAC]AAAAAATTATTAAACAGTGAAACATCCACCCTACT - 8 1 4 1 20100 r 74 goat SV_292 17 61544942 - deletion junction SV-TF-chip 562166509 Affx-1251763838 AX-606941917 17 61544942 GACTGGATTCTTCATCTGAAAAATGCAGGTGCTTT[-/TAAAAAATTATTAGAGGGAGGAGGGAAAGATGGCGGAGGAAAAAAAAACAAACAAACAAAACAACAACAACAACAACAAC]AAAAAATTATTAAACAGTGAAACATCCACCCTACT - 8 1 4 1 20100 r 74 goat SV_292 17 61544942 - deletion junction SV-TF-chip 562166537 Affx-1251763838 AX-606941945 17 61544942 GACTGGATTCTTCATCTGAAAAATGCAGGTGCTTT[-/TAAAAAATTATTAGAGGGAGGAGGGAAAGATGGCGGAGGAAAAAAAAACAAACAAACAAAACAACAACAACAACAACAAC]AAAAAATTATTAAACAGTGAAACATCCACCCTACT - 8 1 4 1 20100 f 74 goat SV_292 17 61544942 - deletion junction SV-TF-chip 320799118 Affx-122977612 AX-385286048 17 61545862 TGTATGTATCTAAAGAGGTGAGGAATCCTTAGAAA[C/T]AATCATAATCTTTCATATCTTTAACTTTTTAAAAT Y 2 1 2 1 101000 f 74 goat snp12114-scaffold1448-512291 17 9225301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387742 Affx-122969738 AX-123258100 17 61599195 AGGAACTTGCAGGTGGTAACTAGAGTACCTGTTTG[C/T]ATTTTAGAACCCATTTATAAAGTGCTTCGAAGGTG Y 2 1 2 1 101000 r 74 goat snp12115-scaffold1448-565624 17 9171990 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773106 Affx-122961322 AX-385260249 17 61630430 GTGTCTTATGTCACATAATAATACACTTCAGCCTT[A/G]CACTATGTTCTTTGTCATATGCGTGTGTGCACATA R 2 1 2 1 101000 r 74 goat snp12116-scaffold1448-596859 17 9140752 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377329 Affx-122977675 AX-123247688 17 61663534 GTTTTTGAGGACTTATTACTTGCTCCTCGCAACCA[C/T]GCCAAGGAGCAGACCCAGGAGTGCGGTGGCTGGGA Y 2 1 2 1 101000 f 74 goat snp12117-scaffold1448-629963 17 9107750 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792350 Affx-122922261 AX-385279332 17 61714357 TTTTAAACTCTCCTCAGCTTTAGGAACTATTTTCT[A/C]TGAGGATCACAGATCATATCTTCATTTGAGGGACT M 2 1 2 1 101000 r 74 goat snp12118-scaffold1448-680786 17 9057407 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422424 Affx-122943364 AX-123292770 17 61771639 AGCTATTCAGAATACTAAGATCTAGTTGTTAGATG[C/T]ATTAATTGCTATTGGGGTTTTATTGCTTCTAGTTA Y 2 1 2 1 201000 r 74 goat snp12119-scaffold1448-738068 17 8999083 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414453 Affx-122949573 AX-123284802 17 61822721 ACTTCTTATAGTCTTAGAACCAAGGAAGTGACTGG[C/T]ACATATTGATAATTTAATTACTTTCTCAATCTTTT Y 2 1 2 1 101000 f 74 goat snp12120-scaffold1448-789150 17 8947552 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382117 Affx-122974883 AX-123252475 17 61881409 AACACCCCTCCCCCACTCCTCCCATCGTCCGTTGC[C/T]CAGCTGACTCCTAATGTTCTAGACCAGGAGGCTTG Y 2 1 2 1 103000 r 74 goat snp12121-scaffold1448-847838 NW_017189638.1 25558 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445047 Affx-122926613 AX-123315384 17 61949704 ACGTCAAGTCAGAGGATGTTCGCTGCAGCAGCACC[A/G]TCAGGAGTATAGGCAGAGCTCATTTAGTTGCGCTG R 2 1 2 1 101000 r 74 goat snp16136-scaffold1699-626631 17 8797513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438415 Affx-122931279 AX-123308753 17 62004334 TCACTTCCAGTCTTTCTGCTGTCAAGAACTAGTCA[C/T]CTGACCAATTCCAGCGCAACGGAGGCAAAGAAACC Y 2 1 2 1 101000 f 74 goat snp16135-scaffold1699-572001 17 8742624 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426364 Affx-122940252 AX-123296710 17 62037156 GCCTATAGACAAAATACCTCATGTCATTAAATGCT[A/G]TTGTGATAAGAGAATATATATATATATCCTTCTAG R 2 1 2 1 101000 f 74 goat snp16134-scaffold1699-539179 17 8709870 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791550 Affx-122945098 AX-385278541 17 62074802 CAAGAGCCTTTTAACATAAGAAATATCACCCTTTA[C/T]AGAATAAAGATGAAACTAAATGTAATTTATATGTG Y 2 1 2 1 201000 r 74 goat snp16133-scaffold1699-501533 17 8671821 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447637 Affx-122923979 AX-123317973 17 62137470 GAAAGCTGGGTCTGCAGAGAATGGGAGAGCAGTGG[G/T]GTCCACCATCTAGCAGGGGAACTTTTATTTACTTA K 2 1 2 1 101000 r 74 goat snp16132-scaffold1699-438865 17 8609405 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793259 Affx-122942235 AX-385280237 17 62168264 GCCCTCTTGTTGAAAGAGTGCACGGAAGTGTATCC[A/G]TTGAAAATGCTGCATACATACATTTTTAGAGGTCT R 2 1 2 1 101000 f 74 goat snp16131-scaffold1699-408071 17 8580634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452558 Affx-122920524 AX-123322891 17 62206681 TGCCCGTCCAGAGACTGTGCTAAAGCGGGCACTTT[A/G]TATCCACTCCTGTAGTCCTTATTCCTGTGAGTCAG R 2 1 2 1 101000 r 74 goat snp16130-scaffold1699-369654 17 8542197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783805 Affx-122934924 AX-385270861 17 62257879 TAGACTTGATAAAACACTGAATCTGGGTGATGGTA[C/T]GTGGGACTCTACTTCTGTGGATTTAAAAAATTTTC Y 2 1 2 1 101000 f 74 goat snp16129-scaffold1699-318456 17 8490931 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403116 Affx-122958123 AX-123273469 17 62291164 ATAAAACAAGATGTACTAAGGTGCTTGGGTCGGGG[C/T]GAGGGGCTGCCTTAGTAGGGGTAGTCAGAGAAGGC Y 2 1 2 1 101000 f 74 goat snp16128-scaffold1699-285171 17 8457485 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800141 Affx-122975394 AX-385287064 17 62325298 CTACCTAACTTCATTCTTTTCCTTGTAGAGATTCT[A/G]TCATAATTGTTTTCAATCCTTGTTCTTGCTATCTT R 2 1 2 1 101000 f 74 goat snp16127-scaffold1699-251037 17 8423997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273607 Affx-1111833722 AX-519547220 17 62340710 ACATGCTTTCAATAAATAGACTGCAGAAGGTGGTC[A/G]AGAAGAAAGTTACTAACGTACGTCTATATGTATCT R 2 1 2 1 101000 f 74 goat GoatD01.002469 17 62340710 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38396445 Affx-122962982 AX-123266800 17 62356928 CCAACCTCAGGGCCTTGGCCCATGTTGTTCCCTCT[A/G]CCAGGAATTCCCTTCCCACTCCTTGTCTTGATAAC R 2 1 2 1 101000 r 74 goat snp16126-scaffold1699-219407 17 8392580 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777845 Affx-122931673 AX-385264962 17 62406492 GCACAAGATATTTTTCCAGGAAGAGGATCTATACC[A/G]TCCATCAGATGCACAAAAGGATTCAGAGCCCAAGG R 2 1 2 1 101000 f 74 goat snp16125-scaffold1699-169843 17 8342783 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419803 Affx-122945843 AX-123290151 17 62436199 GAAGTATCACATCTTTCCTCACAATAACTCAAAGA[C/T]GAGGAAATGGGATCACACAGCTAATAAATGATGTT Y 2 1 2 1 303000 f 74 goat snp16124-scaffold1699-140136 17 8312794 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797205 Affx-122951836 AX-385284144 17 62466275 TAGATATACAAACCTACATTGAAATGCTTTGTTTT[A/G]TGTGGGTTTTTTAACCCCAAAATGGTGTCATGCCT R 2 1 2 1 102000 r 74 goat snp16123-scaffold1699-110060 17 8282729 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783888 Affx-122920973 AX-385270943 17 62510147 TAAAAATTAGCAGAAGGATGTGAGGCACTTGGAAA[C/T]GCAGAGGTAGAACTATTTACCAATTGATATGGAAG Y 2 1 2 1 101000 f 74 goat snp16122-scaffold1699-66188 17 8239283 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429214 Affx-122937933 AX-123299556 17 62599308 TAGAATGCAGCTCTAGCTGGTAAGCCAGCACAGGC[C/T]TCCCCAGTAAACCACTACCTCACTCTGGAATAGGT Y 2 1 2 1 201000 r 74 goat snp20946-scaffold2054-22874 17 8148756 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445616 Affx-122925104 AX-123315953 17 62648800 TCATCCCTAATTTGCTACACTGATCAAAACCAAAT[A/G]AGAGTCCCCTAGAGTCCATGAGTCTATCAGTACAA R 2 1 2 1 600000 f 74 goat snp20947-scaffold2054-72366 17 62648800 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779801 Affx-122925104 AX-385266901 17 62648800 TCATCCCTAATTTGCTACACTGATCAAAACCAAAT[A/G]AGAGTCCCCTAGAGTCCATGAGTCTATCAGTACAA R 2 1 2 1 101000 r 74 goat snp20947-scaffold2054-72366 17 8099110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381827 Affx-122974263 AX-123252185 17 62755999 TAGAGAAACTGAAAATGCAGAGGTAATAAATGGAC[A/G]GGAACCAGGCTTTGAATCCAGAGAAATGTGATGAC R 2 1 2 1 201000 f 74 goat snp20949-scaffold2054-179565 17 7991399 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408330 Affx-122953757 AX-123278681 17 62807994 CTGAGGAGGAGAGGGACTTGGAGGTGGTGGGGCCA[A/G]GACCCAGACCCAGGTCCAAACTCCACATCCATTCA R 2 1 2 1 101000 r 74 goat snp20950-scaffold2054-231560 17 7939886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445476 Affx-122925208 AX-123315813 17 62836744 GTCCAGACTCTGGACTTTTGGTGTTAGCAGGATCA[G/T]CATACTGTAAGGCACCTAGGCAGCAACTCAGAAAA K 2 1 2 1 101000 f 74 goat snp20951-scaffold2054-260310 17 7911089 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452982 Affx-122920125 AX-123323315 17 62889554 GGCACATTTCGCTGGCAACAGTTAACTGTACACAC[A/G]GCCGTTTACTGGAACGGGGGCTTTGGTTTCCCTTC R 2 1 2 1 101000 f 74 goat snp20952-scaffold2054-313120 17 7859162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779379 Affx-122959009 AX-385266483 17 62934928 AGGCAGCTTATCCTCTGACTGTATAAGGGCTTTTC[C/T]GCAGTGCTATGAAATCTGATATGCCACAGGCCTGT Y 2 1 2 1 101000 f 74 goat snp20953-scaffold2054-358494 17 7813150 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433083 Affx-122935731 AX-123303424 17 62967908 AAAGAACAACGACTCGGACCCAAAGACTAAACACA[A/G]CATTTCACTGATGGGAACTGGAAACGCACAACTCA R 2 1 2 1 101000 f 74 goat snp20954-scaffold2054-391474 17 7780175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444380 Affx-122926603 AX-123314717 17 62996602 AAGGGGAGGGGGATAAGACACATGCTGGTCCACAG[A/C]GGGGTGTCATAGCCCAATGGGATAAGAAGAGTGTC M 2 1 2 1 102000 r 74 goat snp20955-scaffold2054-420168 17 7751642 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386847 Affx-122970080 AX-123257205 17 63027739 TGGGGGTGTCAGAGGGAGCCACTCTCTGCCAGGGA[A/G]GCCTGTTGTCTGCTGGACTCAGTAGTTCTCATCTG R 2 1 2 1 101000 r 74 goat snp20956-scaffold2054-451305 17 7720453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420363 Affx-122944953 AX-123290710 17 63063713 TTGCTGCGTGGAAATGTACCACATTCTAATTAACC[A/G]TTCCTCTATTCTTGGTCATTTGAGTTTGTTTCTAC R 2 1 2 1 101000 f 74 goat snp20957-scaffold2054-487279 17 7687067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451694 Affx-122921569 AX-123322027 17 63105414 GTTCACTGGCACGTTCGGGGAGCTTGTGGAGGTCA[A/G]TTCTGGGCAGCCCTGTGCAGACAGGCTGCTCTGAT R 2 1 2 1 101000 f 74 goat snp20958-scaffold2054-528980 17 7645326 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380142 Affx-122975982 AX-123250500 17 63186416 TTCACTTGCCAGAGGAAAAAACTGTGAAGAGATAC[A/G]TGTGTGATTCTTTCTACATCCTTTTCATGTGCATC R 2 1 2 1 201000 r 74 goat snp20960-scaffold2054-609982 17 7564435 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425902 Affx-122941622 AX-123296248 17 63225645 CTCTTTCTCCCAGATATCATTTAATACATCACCTC[A/G]CCGGGCTGTATGTACCTGCTCCTAATAAACCTCTA R 2 1 2 1 101000 f 74 goat snp20961-scaffold2054-649211 17 7525472 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430878 Affx-122936884 AX-123301219 17 63278993 GTTCACCTGGACAAGCTGGCACCCTGACCCATAGA[C/T]GAATGACTCCTAGGTGCTGCAATCAGCAGGTGGAA Y 2 1 2 1 101000 r 74 goat snp20962-scaffold2054-702559 17 7476739 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768356 Affx-122950747 AX-385255536 17 63308119 TACTCAGGCACTACTTCCTTTTACCTTGTGAAACC[C/T]CATGATATTGCCATTTTATAAGGCAGGAAACTGAA Y 2 1 2 1 101000 f 74 goat snp20963-scaffold2054-731685 17 7447605 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433949 Affx-122934280 AX-123304290 17 63343402 CATATCAGCAGTAGGCACAAAGGAACTCCTGGTAA[C/T]GCAGGACTCGGTGGTAAACTCAGATCTGCAGGTCC Y 2 1 2 1 101000 f 74 goat snp20964-scaffold2054-766968 17 7412275 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400873 Affx-122959764 AX-123271227 17 63393173 ACTGGAGGTGCAAAAGATTTAAGTAACTAAAGCTA[C/T]GTGAGTAGACCAAGTTTTTCAAAAACATTATATTT Y 2 1 2 1 101000 f 74 goat snp20965-scaffold2054-816739 17 7363034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445957 Affx-122925901 AX-123316294 17 63479137 CTAGAACCCTGAGGGGACAGCTATGTGACCTTGGG[C/T]AGATGGCTTTGCCTCTGAACTTCTTTCCTGACCTA Y 2 1 2 1 101000 r 74 goat snp20967-scaffold2054-902703 17 7276968 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432951 Affx-122935289 AX-123303292 17 63537661 AAAACTCTTTTTAGGCCCCAGCATCTCGGGCTGTC[A/G]GTGTGGGTCTCACAAAGCCTGATCTGATGAGAGGC R 2 1 2 1 201000 r 74 goat snp20968-scaffold2054-961227 17 7218461 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386808 Affx-122970904 AX-123257166 17 63613685 TAGGAGTTCACCAGGTTGCCAAGGGAGCAGGAAAT[C/T]TCGTAGAGAATTTGCCCTCGACACCTGCTGGATGG Y 2 1 2 1 101000 r 74 goat snp20969-scaffold2054-1037251 17 7141631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401371 Affx-122959237 AX-123271724 17 63669980 TTATATACATAGAGATAATTAAGAAACTGGAGACA[C/T]TGCTGGCCTCTGATAAGGCAGCTGTGGGATTGAGG Y 2 1 2 1 201000 f 74 goat snp20970-scaffold2054-1093546 17 7085338 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453511 Affx-122919811 AX-123323844 17 63684796 AAACGCTTCAGAGAAGTGGTTCTCAATGGGGTGAC[A/G]TTGGCAATGTCTGGAGACAGTTTCGATTGTCACAA R 2 1 2 1 101000 f 74 goat snp14534-scaffold1586-892337 17 7069842 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272906 Affx-1111833105 AX-519546594 17 63719816 TAAGATAGTCCTTTTCAGTATTAATCGCACTTAGG[A/G]TGCATTTGTAGACCTTGGTGTCCTTTTTTTAGGTA R 2 1 2 1 101000 r 74 goat 17_63719816_AF-PAKI 17 63719816 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38436272 Affx-122932539 AX-123306611 17 63728186 TCCTGTGGTCCATATGGGTGGGCCAGGGCCTCCAC[A/G]TTGTCCAACTCCTGAGGGTGCCACCCACACTGCAT R 2 1 2 1 101000 r 74 goat snp14533-scaffold1586-848947 17 7026907 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413654 Affx-122950122 AX-123284003 17 63790518 AAAGCTACGGAGGATGGTTAGAAGCTGCACCACGG[C/T]GACACAGAACTAAACTGGTGGGCCTGAAGATGCTT Y 2 1 2 1 101000 r 74 goat snp14531-scaffold1586-786615 17 6964074 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791604 Affx-122935212 AX-385278595 17 63820472 CCACATAGTGAAAAAGGGTTTCCTAAAGCAGGATA[C/T]AAAACTATAGAATCAACTAGTATGGTTCCTTTCTT Y 2 1 2 1 101000 f 74 goat snp14530-scaffold1586-756661 17 6934156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436453 Affx-122932991 AX-123306791 17 63859989 GTAGGCAAGACCCCTGCTTGAGTGACAGAAGGGGA[C/T]AAAACTTGGGGAATATTAAAATTCACCCTCCATTG Y 2 1 2 1 102000 f 74 goat snp14529-scaffold1586-717144 17 6894652 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401419 Affx-122959003 AX-123271772 17 63905232 TGGCAAAATTTTAACATCTGTTTAATCTCGTGGGT[A/G]AGCACAGGAGTGTTCTATTATGTATGACTTGTTTC R 2 1 2 1 201000 r 74 goat snp14528-scaffold1586-671901 17 6849368 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402465 Affx-122958604 AX-123272818 17 63935704 TACTGCACACACAGAGGTAGAAAGACTGGGCACAG[C/T]AGAGTCACCAGCTCTCACAGAACACGGACGGCGTA Y 2 1 2 1 201000 r 74 goat snp14527-scaffold1586-641429 17 6819061 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424851 Affx-122941348 AX-123295197 17 63966152 CATATATCTATTTTTTCAAAGCATTTTCTCATTGT[A/G]CTTTCCTTGTACTTCATGTAATTCAGAGCAGAGAG R 2 1 2 1 101000 r 74 goat snp14526-scaffold1586-610981 17 6788694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438750 Affx-122930822 AX-123309087 17 64052041 CTTTCAGAGGTTCAAAGACTTGAAACAAAGAGCAT[C/T]GTTACCTTAATTCTCTGCTCGTTAACTCGAGCTAG Y 2 1 2 1 101000 r 74 goat snp14524-scaffold1586-525092 17 6702691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417705 Affx-122947452 AX-123288053 17 64100878 CTGTTCTAGACACTGGGGTACAGAACTGAGCAAGA[C/T]AGACAAGGGGCTCTGGTCGAGGGAGATAATCAACA Y 2 1 2 1 201000 f 74 goat snp14523-scaffold1586-476255 17 6653172 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412926 Affx-122950391 AX-123283275 17 64140469 TACAAAAAGGAACCAAATGAAATTCAGAGCTGGAA[C/T]ACACAAAGGAAGGGGATTTGAAGATAGATCTATAG Y 2 1 2 1 101000 f 74 goat snp14522-scaffold1586-436664 17 6613662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442008 Affx-122928420 AX-123312345 17 64186075 AGCAGTTGCAGCAAGATACTGAATGGCTCACAAAG[A/G]CTACAGTATTTACTATCTTACCCTTTCAGAACAAG R 2 1 2 1 101000 f 74 goat snp14521-scaffold1586-391058 17 6568086 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384811 Affx-122971989 AX-123255169 17 64249439 GCACTCTTGTCAAAACCCATCTCCTTCCCCTTCCC[G/T]ATTTTTTCTGAAAGGAAGGCTGAGACCCAGAAAGG K 2 1 2 1 201000 r 74 goat snp14519-scaffold1586-327694 17 6505195 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377114 Affx-122978250 AX-123247473 17 64281603 AAGAAGTAGGAATGGTGGCAAAGAAAAGGGGACTG[C/T]ATGGCCCAGCAAGAACATCTCAGCAACCCGGGTTG Y 2 1 2 1 101000 f 74 goat snp14518-scaffold1586-295530 17 6473224 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782804 Affx-122938761 AX-385269876 17 64314306 GTTATAACACTTGGCATTACATGTTGTAACATTAA[C/T]ATGTAACACTTCCCACCCACTTCACCACACATCTC Y 2 1 2 1 201000 r 74 goat snp14517-scaffold1586-262827 17 6440192 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395116 Affx-122964150 AX-123265471 17 64366697 AAATTAGTTTTTTAATCTGCTTCAAGTTGCTAAAA[C/T]GCCCTGTCTCCCTTCCATTGTCACCTGAAGGCCTG Y 2 1 2 1 201000 f 74 goat snp14516-scaffold1586-210436 17 6387752 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378542 Affx-122976617 AX-123248901 17 64397687 GTAGACCTGACTTCTCACCTCATATCAAAAGGAAT[C/T]CCCCACCATGCATGTTAGCATTGGAAGGCCCTGCG Y 2 1 2 1 101000 f 74 goat snp14515-scaffold1586-179446 17 6356440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451500 Affx-122921119 AX-123321833 17 64460279 AACCTACAGATACTCATCCATGCACAGAATGACTC[A/G]TGTACTGAGTTATTCATTTCAGCATTATTTGTAAT R 2 1 2 1 101000 f 74 goat snp14514-scaffold1586-116854 17 6293528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397499 Affx-122962067 AX-123267854 17 64508800 GGAGGAGCGTGGCAGCACATCCCATTGTTGGGAAC[A/G]TATTTCCACCCAAAGTGGGGCCTGTAGGAACAGGA R 2 1 2 1 202000 f 74 goat snp14513-scaffold1586-68333 17 6245186 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403994 Affx-122957202 AX-123274346 17 64544033 AGTTGACACAACTCTCCAGGAAACTACCCATCCCT[A/G]CCTTGGACTCTGAAGTCTTCCCTCTGGGCGTAGTC R 2 1 2 1 101000 f 74 goat snp14512-scaffold1586-33100 NW_017189867.1 8564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447710 Affx-122924608 AX-123318046 17 64574195 TTCAAAATAACCCCCTGTAGCCATGTGCTAGTTTT[A/C]CCTCCAGTCTTCTTTTTTCTTTATCACACGTGTGT M 2 1 2 1 103000 f 74 goat snp14511-scaffold1586-2938 17 6179439 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434993 Affx-122933824 AX-123305333 17 64598213 GTGTGTCCCTGGGTTGTCCACTGCCTCTTTGTTCA[A/G]TCAATACATCTGAGCCTGCGGTCAAGACTCTTTAT R 2 1 2 1 101000 r 74 goat snp25600-scaffold264-20981 17 6136178 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417589 Affx-122946889 AX-123287937 17 64639542 CTTTGAGAGCTGAGAACTCAACTGTCTTACTAATG[C/T]ATACCCAAGATATACAATAGGCATCCACTAAATGC Y 2 1 2 1 101000 f 74 goat snp25601-scaffold264-62310 17 6094846 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424666 Affx-122942151 AX-123295012 17 64677470 AAACAGATGCGTGCAGCACCTGCTGTGTGGCTGCC[G/T]CTATGTTCAGTGCTCTGTGCTGAGTTGTCTAAGTG K 2 1 2 1 101000 r 74 goat snp25602-scaffold264-100238 17 6056912 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416833 Affx-122948116 AX-123287181 17 64764832 TATGACACCCAGTGTCACAGCTAACATCCCTGGTC[A/G]CGTGTCTTTGCATACCTGTTGCATTCGATAAGAGG R 2 1 2 1 101000 r 74 goat snp25604-scaffold264-187600 17 5970177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273810 Affx-1111833859 AX-519547421 17 64774750 GTCAGCTCTAATGAGGCAGGTGACTGCAGAGCCCA[A/C]TACATACGGTGAAGCAAGTCAGACAGAGGACAAAC M 2 1 2 1 202000 f 74 goat GoatD01.007951 17 64774750 C A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38454121 Affx-122919348 AX-123324454 17 64826899 ACCACACCTGACGTTTCGTGATCATTCACGGAGTT[A/G]TTGAGTGAATGATCTTACGTGAGACAATCCACGGA R 2 1 2 1 101000 r 74 goat snp25605-scaffold264-249667 17 5913143 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451295 Affx-122921296 AX-123321628 17 64894037 CTAATTGGGTCACTTACAGTGAGCCACTGGTGAAC[A/G]TTTAACGTTAGCCAGGTCTTTGGGGGGAAAGCCCC R 2 1 2 1 102000 r 74 goat snp25606-scaffold264-316805 17 5846647 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453329 Affx-122919970 AX-123323662 17 64931865 GGCTTCGAGTTCAGCTTTGGAAACTGTTATGGGAA[A/G]AGAATGTCTGGGAAGGGACCAGAGGTGAAGGAGGC R 2 1 2 1 101000 f 74 goat snp25607-scaffold264-354633 17 5809123 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451032 Affx-122921449 AX-123321366 17 64962649 CTTTGTAGCAACAAAAAGGTGATTTGAACTAAAAA[G/T]ACAGTTGTCATATGATCCAGCAATCTCACTCCTGG K 2 1 2 1 101000 f 74 goat snp25608-scaffold264-385417 17 5778369 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407221 Affx-122955382 AX-123277572 17 65003677 CTCCAGAATGCCTTTCCTTGCCAGGCCTGCCCGGA[G/T]ACATAAATCCTCACTCATCCCAGCTCACACATCTC K 2 1 2 1 101000 r 74 goat snp25609-scaffold264-426445 17 5737578 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419697 Affx-122945921 AX-123290045 17 65037271 TGAACAGAAATACGAATGTTGGAACAGAGCTGAAA[C/T]GGCAGTGGTTGGATGGCAAGGGAGACTGGAATTTT Y 2 1 2 1 101000 f 74 goat snp25610-scaffold264-460039 17 5704859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398010 Affx-122961785 AX-123268365 17 65093769 TGTTCACCATTAGGAAACAAGTTACGTGACTTCCC[G/T]CATTCCATCCGACGGAATGATGCAACTGGAGGGAG K 2 1 2 1 101000 f 74 goat snp25611-scaffold264-516537 17 5649002 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451540 Affx-122921089 AX-123321873 17 65136750 GTGAACCCGCACGTAGAAAGACTGAGTGCTAACTC[A/G]CAGGGCTGATTGGGTAGGGAAGGGGTGTCTGACAG R 2 1 2 1 101000 f 74 goat snp25612-scaffold264-559518 17 5605797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443406 Affx-122927384 AX-123313743 17 65191047 TGTTGAATGTCTTTCCTGGAGAGTGGGCAACTGCT[A/G]AAATCTTTGACCAGGTTTTAAATGACTGGCAGCAA R 2 1 2 1 101000 r 74 goat snp25613-scaffold264-613815 17 5551567 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419663 Affx-122945948 AX-123290011 17 65275790 ACAGGAGAGCCATGGCCGCATTAGATGTTGAAACC[C/T]GGCTTGCAGCACTTTGAGAGCAAAAGCAGTGTGCC Y 2 1 2 1 101000 f 74 goat snp25614-scaffold264-698558 17 5468461 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431649 Affx-122936129 AX-123301990 17 65307211 TTAAAGTGAGCCTGCTTTCTGCCGGGAATTCTTAA[C/T]GGGGCTCTGATGCTTTCAGTTCTTTTTCCTCTTCA Y 2 1 2 1 101000 f 74 goat snp25615-scaffold264-729979 17 5437168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771687 Affx-122973091 AX-385258845 17 65355983 GACTCTTAACGTTTTAAATTCATTTCCAAACTATA[A/G]TTTGGTTTGAAAGATAATTAATCTCTTTCTAGTGC R 2 1 2 1 101000 f 74 goat snp25616-scaffold264-778751 17 5388158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403705 Affx-122958039 AX-123274057 17 65386709 CAAGAAGATTTAGGGTCATTAGCAAAGATACTTTC[A/G]TTCTATCTCTTGCTGTCATAGCAAATTAGCTCAAA R 2 1 2 1 101000 r 74 goat snp25617-scaffold264-809477 17 5357194 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442043 Affx-122928396 AX-123312380 17 65464984 TCCACCACTTTATTACTCATATGACCTGGGGCAAA[C/T]GACCACATCTCTGGGAACTTCTTTTTCTTTCTTTC Y 2 1 2 1 101000 f 74 goat snp25619-scaffold264-887752 17 5282574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380870 Affx-122975056 AX-123251228 17 65503594 AAATAAGTCAGATGAGATGCTCAGCTATGTTTACA[C/T]GATCTTCTTTTGTATGGGAGGTAAAATTCCTTTGG Y 2 1 2 1 101000 f 74 goat snp25620-scaffold264-926362 17 5244233 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377417 Affx-122977553 AX-123247776 17 65534430 TCCTTCTCTCAGGACTTTGTAAATCCCTGCCCGTG[A/C]GTTTAATGAGTGAAGAGTTTACGATGTCACTTCTG M 2 1 2 1 101000 r 74 goat snp25621-scaffold264-957198 17 5213285 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438437 Affx-122931262 AX-123308775 17 65564943 GACAATCTCTTTTACTGCTGATCCCCAGTACCTAA[C/T]GTTGGGTCTGGCTCATCATAGGTGCTCTATAAATT Y 2 1 2 1 101000 r 74 goat snp25622-scaffold264-987711 17 5182750 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451821 Affx-122921476 AX-123322154 17 65606909 GTGTGGCCCAGCTAAGCTTTCCCCTCTCTGAGCCT[C/T]AGTTTCCCTGTGTGTGCAATGAGGGAGTTGCATGA Y 2 1 2 1 101000 r 74 goat snp25623-scaffold264-1029677 17 5140585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277113 Affx-1111835748 AX-519550620 17 65637061 ACGGGAACTAAAACTCTTCAACACTAGGGACATGG[A/G]ATTTGGCCAAAGACAGAACTAAAGAGAACTTTTGA R 2 1 2 1 101000 f 74 goat Random2.2K-1689 17 65637061 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415472 Affx-122949157 AX-123285821 17 65638283 TTTCTGCTCTTGACTTGTGCTTGGGCTCCTCTCTC[A/G]TCTTGTCCCCTGGAAGAGTCCTCTGAGCGAGACAC R 2 1 2 1 201000 f 74 goat snp25624-scaffold264-1061051 17 5113041 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450413 Affx-122922063 AX-123320748 17 65682641 GTTTTCCCGTCTGATCACTCAACTAGAGCAGAAGG[C/T]CCTTGCAGTCAGGACCTGGTCTGATTCATCTCTCC Y 2 1 2 1 201000 r 74 goat snp25625-scaffold264-1105409 17 5068454 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423291 Affx-122942646 AX-123293637 17 65712321 TGCGTGCTGTCTTGCGTGTGCGTGTTTCTAGCAAA[C/T]CCACAGCCAGCCCAAGCTCCCAGAGCCACACTGAG Y 2 1 2 1 102000 f 74 goat snp25626-scaffold264-1135089 17 5038628 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379779 Affx-122975840 AX-123250137 17 65763982 TTTCTGAATGTGAGAAGCACCAAGTACCCTCCCAT[C/T]TTCTCCACCCTACCCAGGCTCAACCATTGCGAGTC Y 2 1 2 1 101000 f 74 goat snp25627-scaffold264-1186750 17 4986735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420333 Affx-122945004 AX-123290680 17 65794994 ATTTAAAACCAGTTTCACACACTAAGAATCAACTC[A/G]TAAAACAAAAGAGAAAAGAGCTCCAAGGATATGTG R 2 1 2 1 101000 f 74 goat snp25628-scaffold264-1217762 17 4955581 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377549 Affx-122977455 AX-123247908 17 65844226 AGATCCCAGTCGGTGATCTCAAAGTTCTCCCGCTC[A/G]TCCTCGTCATCATCCATGTGGCCTTCGCCGTCCCG R 2 1 2 1 101000 f 74 goat snp25629-scaffold264-1266994 17 4906404 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436776 Affx-122932268 AX-123307114 17 65877635 CTCCGGGAACCAGGGTCACCATCTGAGACTCTGAC[A/G]CCCAGCTTGTAACTGCATTAAACGAATGGGGCCAT R 2 1 2 1 101000 r 74 goat snp25630-scaffold264-1300403 17 4872448 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453232 Affx-122920423 AX-123323565 17 65925651 GCACACAGTTGGCCCCAGTATGGGGGGTCCTGCAT[C/T]TGCGAATACAGAAGTCAGGCTGGACTATGCCGTCT Y 2 1 2 1 101000 r 74 goat snp25631-scaffold264-1348419 17 4824277 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433005 Affx-122935791 AX-123303346 17 65995730 CATTTCTTGGTCTGTCAACTGGGGGTCTTCATTGG[A/G]GGCTGCAAAGAGGATTTCACAGCAGATGATTTCAA R 2 1 2 1 201000 f 74 goat snp25632-scaffold264-1418498 17 4754504 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420152 Affx-122945587 AX-123290500 17 66064388 TGCTCCAAGCTCCCTGCAGGCCCTGAGCCAGTTCT[A/G]CCTTCTAAGGGATCTAATTAAGCCCTGGTGAGGAG R 2 1 2 1 101000 r 74 goat snp25633-scaffold264-1487156 17 4688612 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403853 Affx-122957933 AX-123274205 17 66105149 GCCCAATTTGTGATGGTTTGTTACAGCAGCTTAGG[A/G]AAATAATCCAGGAAGGGAGTTCACAGATCCCTAAG R 2 1 2 1 201000 r 74 goat snp25634-scaffold264-1527917 17 4647907 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420564 Affx-122945278 AX-123290911 17 66135755 GTCCTGGTCTTCATGGACCTCAGTCCCTGAGTGAC[C/T]GCAGGCCAGAGCCAGGAGTGGAGAGAGGAGGATTT Y 2 1 2 1 102000 f 74 goat snp25635-scaffold264-1558523 17 4617303 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442197 Affx-122928794 AX-123312534 17 66164966 TTCCCGTCATCTGAAGTTTGGTCAGAAATGAAAGG[C/T]GAGAAGTGCAGGGAGAAAAATGGGCGAAATGGAAG Y 2 1 2 1 101000 f 74 goat snp25636-scaffold264-1587734 17 4588060 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413133 Affx-122950369 AX-123283482 17 66208801 TAGTTGCATGGTGCTTTTTACATATTCTGGACACA[C/T]GTCCTTGATAGAATATACTATGGAGAAGATTTTTC Y 2 1 2 1 101000 r 74 goat snp25637-scaffold264-1631569 17 4543872 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272859 Affx-1111833106 AX-519546549 17 66219928 CAGACTGGTTGCAAATAGGAAAAGGAGTACATCAA[A/G]GCTGCATATTGTCACCCTGCTTATTTAACTTATAT R 2 1 2 1 103000 f 74 goat 17_66219928_AF-PAKI 17 66219928 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450579 Affx-122922033 AX-123320913 17 66261010 AAAAAAAAGTAAGAGAAAAAACACATCTTTGCAGA[C/T]GACTGTACAGAATATAATCCCATCTATACAAAAAA Y 2 1 2 1 101000 r 74 goat snp25638-scaffold264-1683778 17 4491761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439801 Affx-122930491 AX-123310138 17 66298495 ACATTGTGGTAGAATGTATATAATACGAAATTGCA[A/G]TTTATACCAAATTGAGCAGTGGGGTCTTGGATTCC R 2 1 2 1 201000 f 74 goat snp25639-scaffold264-1721263 17 4454224 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382682 Affx-122973650 AX-123253040 17 66327375 AAGAATCAGAGTTTTTGGGGGAGACAGTGAAGGCC[A/G]TGTTTCCTCCAAGTGGAAATCAAGTCCCAGCTCCT R 2 1 2 1 101000 r 74 goat snp25640-scaffold264-1750143 17 4424814 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277238 Affx-1111835749 AX-519550744 17 66338784 TGGTTTTAATTTCAGTCAATCATGATTCTCCACTA[A/T]GGGTATGTTAAGGTCATTTTCTTCTAATTTTGTGC W 4 1 2 1 101000 r 74 goat Random2.2K-1690 17 66338784 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789298 Affx-122928404 AX-385276309 17 66361853 TTCGTGTTCTATGCTCTATTGTATGCACGTGTCTA[C/T]GTGGGCTACTAAACTCACCTCTTTAAATAACTGAG Y 2 1 2 1 101000 f 74 goat snp25641-scaffold264-1784621 17 4390333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390039 Affx-122968431 AX-123260396 17 66408340 TGACTGTCAGATGCAGGCTGTGATCTGGGGTTGAC[A/G]TGAGGGCCCCGAAGGCAGCTGGATGAATCACGGAA R 2 1 2 1 101000 f 74 goat snp25642-scaffold264-1831108 17 4344098 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400324 Affx-122960055 AX-123270679 17 66463760 AGTAGGTTTTTTTTTTAATCCAGTAAATAATCCTC[A/G]CCAGAATCAAATATTGCAGTGGTTGCAACATGGAG R 2 1 2 1 201000 r 74 goat snp25643-scaffold264-1886528 17 4309461 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444894 Affx-122926261 AX-123315231 17 66524423 TCTCCGAACTTCCTTCCCTTCTGCCTCTGTTACAG[A/G]AGGCCCTGAAACCCCTCCCACCGTCAGGATTCAGA R 2 1 2 1 303000 r 74 goat snp25644-scaffold264-1947191 17 4248826 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449671 Affx-122922566 AX-123320006 17 66563668 TTTTCTAATTCAATCAGTGAGGGGAATAGGTAGAT[A/G]TTACAAGTGGTTCAAAAGAGAATCGGAAAAAGAGC R 2 1 2 1 101000 f 74 goat snp25645-scaffold264-1986436 17 4209322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397145 Affx-122962442 AX-123267500 17 66593293 CACACTCAGACCCTGTCTGTCTGACACCAGAACCT[A/G]TATCCCTAACAGAGTCCCCTTGCTGTTAAAATGTG R 2 1 2 1 101000 r 74 goat snp25646-scaffold264-2016061 17 4179626 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404496 Affx-122956712 AX-123274848 17 66661681 TGCTTGTATCTGAGGTTCTGACCTGTGAAGTGATC[A/G]TCCCTCCTCACGCCCCAGAAGCATCATTCCCTCCT R 2 1 2 1 101000 f 74 goat snp25647-scaffold264-2084449 17 4111637 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801290 Affx-122927037 AX-385288202 17 66719362 CGAGTTGACCAGAATCCAATCAAATGCAGGCCCTA[C/T]GACACTTTCACAGCTAATTGGTTTGACTGGTACGC Y 2 1 2 1 101000 f 74 goat snp25648-scaffold264-2142130 17 4053356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407846 Affx-122954525 AX-123278197 17 66748646 GCCACAGACCATCCTGGGACCCCGGCTAAGCCCCC[A/G]CACGACGCTAATTACTCTACATGAGCTTCTTCTGA R 2 1 2 1 101000 r 74 goat snp25649-scaffold264-2171414 17 4024003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446631 Affx-122924790 AX-123316967 17 66788528 CTTCTGAGAAGGGGGAGTGTCTCTTCCCACCCCGT[A/G]TACCCCCCAGCATAGAGGACTGGATCAAGCAAGTG R 2 1 2 1 101000 r 74 goat snp25650-scaffold264-2211296 17 3983854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383258 Affx-122972740 AX-123253616 17 66840728 CCAACTAGGAGCTCACAGAGTCCTGGGAGAGACAA[C/T]GTTTGTGGAGTGTGTAGAGTGCTTCAGATTAGAGG Y 2 1 2 1 101000 r 74 goat snp25651-scaffold264-2263496 17 3931915 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476331 Affx-1251763839 AX-586011748 17 66844807 TTAGCCATGAGAGTTTTCCACCATGACAGAACTTT[-/AAAGACATGCTTTTTTTTTTTTAATTTTAAAATCTTTAATTCTTCCCGTCCCATTCCTCCGCCATCTTTCCCTCTCTCCC]AAGACATGCTTTTTTATACTAACTAAAGATATTCA - 4 1 4 1 20000 f 74 goat SV_307 17 66844807 - deletion junction SV-TF-chip 539476585 Affx-1251763839 AX-586011971 17 66844807 TTAGCCATGAGAGTTTTCCACCATGACAGAACTTT[-/AAAGACATGCTTTTTTTTTTTTAATTTTAAAATCTTTAATTCTTCCCGTCCCATTCCTCCGCCATCTTTCCCTCTCTCCC]AAGACATGCTTTTTTATACTAACTAAAGATATTCA - 4 1 4 1 20000 r 74 goat SV_307 17 66844807 - deletion junction SV-TF-chip 562165286 Affx-1251763839 AX-606940697 17 66844807 TTAGCCATGAGAGTTTTCCACCATGACAGAACTTT[-/AAAGACATGCTTTTTTTTTTTTAATTTTAAAATCTTTAATTCTTCCCGTCCCATTCCTCCGCCATCTTTCCCTCTCTCCC]AAGACATGCTTTTTTATACTAACTAAAGATATTCA - 8 1 4 1 20100 f 74 goat SV_307 17 66844807 - deletion junction SV-TF-chip 562165629 Affx-1251763839 AX-606941039 17 66844807 TTAGCCATGAGAGTTTTCCACCATGACAGAACTTT[-/AAAGACATGCTTTTTTTTTTTTAATTTTAAAATCTTTAATTCTTCCCGTCCCATTCCTCCGCCATCTTTCCCTCTCTCCC]AAGACATGCTTTTTTATACTAACTAAAGATATTCA - 8 1 4 1 20100 r 74 goat SV_307 17 66844807 - deletion junction SV-TF-chip 562165842 Affx-1251763839 AX-606941251 17 66844807 TTAGCCATGAGAGTTTTCCACCATGACAGAACTTT[-/AAAGACATGCTTTTTTTTTTTTAATTTTAAAATCTTTAATTCTTCCCGTCCCATTCCTCCGCCATCTTTCCCTCTCTCCC]AAGACATGCTTTTTTATACTAACTAAAGATATTCA - 8 1 4 1 20100 f 74 goat SV_307 17 66844807 - deletion junction SV-TF-chip 562166434 Affx-1251763839 AX-606941842 17 66844807 TTAGCCATGAGAGTTTTCCACCATGACAGAACTTT[-/AAAGACATGCTTTTTTTTTTTTAATTTTAAAATCTTTAATTCTTCCCGTCCCATTCCTCCGCCATCTTTCCCTCTCTCCC]AAGACATGCTTTTTTATACTAACTAAAGATATTCA - 8 1 4 1 20100 f 74 goat SV_307 17 66844807 - deletion junction SV-TF-chip 562166570 Affx-1251763839 AX-606941978 17 66844807 TTAGCCATGAGAGTTTTCCACCATGACAGAACTTT[-/AAAGACATGCTTTTTTTTTTTTAATTTTAAAATCTTTAATTCTTCCCGTCCCATTCCTCCGCCATCTTTCCCTCTCTCCC]AAGACATGCTTTTTTATACTAACTAAAGATATTCA - 8 1 4 1 20100 r 74 goat SV_307 17 66844807 - deletion junction SV-TF-chip 320776242 Affx-122977369 AX-385263370 17 66886425 CTTACCAGGTACGAGTCACTGATCATAAAGCTTAA[C/T]GTATATGAACCGGTGTAGCCCCCAGCTACACTGGA Y 2 1 2 1 201000 r 74 goat snp25652-scaffold264-2309193 17 3886049 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419608 Affx-122945990 AX-123289956 17 66923942 CCCAACTTAGTGTTTTTCAAACTGCAGACTGTGAT[C/T]AATCCATAGATTATAAGTCATTTAGGAAGTGTGGT Y 2 1 2 1 201000 r 74 goat snp25653-scaffold264-2346710 17 3848431 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436208 Affx-122932587 AX-123306547 17 66982088 ATTTGACATAATTAACTGAAAAATATGGAGTAAGC[G/T]ATTTCAGAGCCTTCATTATTAGTGCTGTCAACTGG K 2 1 2 1 101000 r 74 goat snp25654-scaffold264-2404856 17 3790589 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785256 Affx-122933988 AX-385272301 17 67021116 TTCCCAAAACTAAGCAACATAGCTATAGCTAACAC[A/G]TCCTCTTAGGTACTTAAAGACAATGAGAAGCAGGA R 2 1 2 1 101000 f 74 goat snp25655-scaffold264-2443884 17 3754888 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429071 Affx-122938288 AX-123299413 17 67062511 ATGCTGAATGTTCTTTTTGGCAAACTTCTATGATA[C/T]AATGCTCTGAGAGGGGAATTCTAAGCTTATTTGGA Y 2 1 2 1 201000 f 74 goat snp25656-scaffold264-2485279 17 3713136 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441940 Affx-122928580 AX-123312277 17 67140261 CCTTGTTGAATGTGTCACAGGCACTTGAAAAGAAT[A/C]TGTACAGGCAGACCTTGGAGACAGTGTAGGTTCAG M 2 1 2 1 101000 f 74 goat snp25657-scaffold264-2563029 17 3636032 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430006 Affx-122938032 AX-123300347 17 67179116 AAACAGTTCTCATAAACTATGTTATAGCTGCTAAG[A/C]TAAGCGGTTGTTTTTACAAGCAGTTCAAAATGAGA M 2 1 2 1 101000 f 74 goat snp25658-scaffold264-2601884 17 3597108 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377315 Affx-122977684 AX-123247674 17 67221841 CCACTCCCACTTCAGATACCAGTCTCAACCTCTGT[A/G]CTTCTGACCAACAGGCTATACACAGGAGGTTCCTA R 2 1 2 1 101000 r 74 goat snp25659-scaffold264-2644609 17 3554073 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450661 Affx-122921921 AX-123320995 17 67278960 TGCTGAAACAACAAATTCAGGAAGCAATTAAATCA[C/T]GCTTTATTGATCTTGCCTTAGGAGCCTAATTTTGT Y 2 1 2 1 101000 r 74 goat snp25660-scaffold264-2701728 17 3496875 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428354 Affx-122938982 AX-123298697 17 67455615 AGCAACTAGAAAACACACTTATCTTATTAACGAGA[C/T]TGGAATTATTTTAATTAGGTATCTCCACATGCACC Y 2 1 2 1 101000 r 74 goat snp25663-scaffold264-2878383 17 3322283 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452359 Affx-122920636 AX-123322692 17 67492458 ACCACAAATGTGTTAGCACACCCAGCCAGAGACCA[C/T]GGCAATGACTGGATCTGTGAGTATTCTTACAAGTG Y 2 1 2 1 101000 r 74 goat snp25664-scaffold264-2915226 17 3285568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393218 Affx-122965492 AX-123263575 17 67525645 ACCAGAATGAGAGAATAAACCAAAAGATATGAAGA[C/T]GTGAGATCCAGGAAAAAGAAGATTCAAAAAGGTAT Y 2 1 2 1 101000 f 74 goat snp25665-scaffold264-2948413 17 3251979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782885 Affx-122925433 AX-385269955 17 67575124 GACCAACACTGCTTTGACTCACTCATAAACCGAAG[C/T]AGAGATATTATCCAGTTAGGTCAAACTACTGATTA Y 2 1 2 1 101000 f 74 goat snp25666-scaffold264-2997892 17 3201935 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402566 Affx-122958449 AX-123272919 17 67610563 TCTGGAGAGGAGGTTCCTGAGTGAAAGCATGGAAG[C/T]ATCATTAAATATAATAAATCTCTTCCTCTTACCAG Y 2 1 2 1 101000 f 74 goat snp25667-scaffold264-3033331 17 3166493 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770526 Affx-122927394 AX-189115725 17 67641316 CAATACTTTCACTGTGTTTACCACCCTCAATCCTC[C/T]GGTTTAGTCAAATGCTCAAATGGCATTAAGACTGG Y 2 1 2 1 101000 f 74 goat snp25668-scaffold264-3064084 17 3135280 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432297 Affx-122936315 AX-123302638 17 67683635 GCAGTCTGCAGAGTATCAGTTTGATCATTTCAATC[A/G]TGGCCAGCTTCAGACTACAAGACACCTAGTTTCAA R 2 1 2 1 101000 f 74 goat snp25669-scaffold264-3106403 17 3092643 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793903 Affx-122969858 AX-385280872 17 67766663 AGCCATTCATTCGTTTTAGCAAATCTTTATCATGC[A/G]TCAACTGTACATAAAGCATTTTGGCAGGAATCACC R 2 1 2 1 101000 r 74 goat snp25671-scaffold264-3189431 17 3009675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414829 Affx-122949198 AX-123285178 17 67798718 AATGTTTAAAGTAGAAATGTGTAACCAAGGTGAAG[A/C]CTGTTCCAGGAGCTGTTGCTTGCTCTAGCCAGGAC M 2 1 2 1 101000 f 74 goat snp25672-scaffold264-3221486 17 2977656 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783416 Affx-122960064 AX-385270479 17 67853349 GTGGAGCGGTCCTTTTCCACTCTTTCACATGAATT[A/G]TAAGTCTTGACTGCAGCCACCACACCTTTTAGGAA R 2 1 2 1 101000 f 74 goat snp25673-scaffold264-3276117 17 2922650 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426865 Affx-122940485 AX-123297210 17 67894189 TTGTTCTTTGAATTAGACACTAGAATATGGCCTTT[C/T]TGGGCTGAACGAGCTCCCATGATGTTTTCTAGCTT Y 2 1 2 1 101000 f 74 goat snp25674-scaffold264-3316957 17 2881833 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452604 Affx-122920490 AX-123322937 17 67933707 TGTCCTCTATGGAGAGAGGTACGGGTGGAAATAAA[C/T]TGGTTCCTCTCCTGGAAAGGGCAAAGTAATAGCTC Y 2 1 2 1 101000 f 74 goat snp25675-scaffold264-3356475 17 2841986 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396442 Affx-122962983 AX-123266797 17 67983394 ATGTCCAGCCGTCTATTCACGCAGCAGACTTCACC[A/G]AAAGCTTTTCTAGGTGCTCAGTAACTCCTCACTGG R 2 1 2 1 101000 f 74 goat snp25676-scaffold264-3406162 17 2792418 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376152 Affx-122978851 AX-123246511 17 68017586 CTACCATTCCCTTCCAGCCCCAGTTTCAGCCCCAC[A/G]CAGAAGGAAAGAACTGGCTGAGAAGGGCAGCTCCA R 2 1 2 1 101000 r 74 goat snp25677-scaffold264-3440354 17 2758218 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389715 Affx-122968679 AX-123260073 17 68086996 CTCCTCCCACATCCTTTTCCCTTTCTGGTGTCTCT[A/C]CTTTGATGAAGGTGAGGTGAAATGTTGGTTAACAT M 2 1 2 1 101000 r 74 goat snp25678-scaffold264-3509764 17 2688533 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453174 Affx-122920467 AX-123323507 17 68125380 CCTACTTGCTAACCTGCTCATCCTTTGCTCCACCA[A/G]ACAAATCTGTGGGCAGAATCTCGGGGTTTTAGTTG R 2 1 2 1 201000 f 74 goat snp9918-scaffold1354-8956 17 2651277 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787154 Affx-122937794 AX-385274180 17 68158892 GAAACACACACACTCCAGGCTAAATGGTACGTGAA[A/G]TATGTTGCCACACATCCCTGCCGAGTCCCTCGAAG R 2 1 2 1 101000 r 74 goat snp9919-scaffold1354-42468 17 2617367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388426 Affx-122969275 AX-123258784 17 68202392 TACATGACACTGTTGTTCTACTCAGTTTCAAACGG[C/T]AAAAACTGAGGGCAGCAAGAGCAAAGGGATTTGAG Y 2 1 2 1 101000 f 74 goat snp9920-scaffold1354-85968 17 2572803 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391040 Affx-122966864 AX-123261397 17 68231123 GCAGAATGGAGTAATCTGGTCACAAAGGACAACAG[A/G]GCCCAATCTTTCCCTTCATCCGTGGGAGCTCCCCT R 2 1 2 1 101000 f 74 goat snp9921-scaffold1354-114699 17 2544116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420266 Affx-122945054 AX-123290614 17 68292878 TGTTAAAGGATTAAAAGAAAATTTATTATAGTAGC[G/T]AAAAAAGTACTCCACGGTTTATACAAAACCGTCTG K 2 1 2 1 102000 r 74 goat snp9922-scaffold1354-176454 17 2484158 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407847 Affx-122954524 AX-123278198 17 68337601 CCTCTCCCTCTCAGCTTTTTGTGTGTCTAAGCGGC[A/G]TAGGACTGTAAAATTCCGTTCTTGATTCAGAACCA R 2 1 2 1 101000 r 74 goat snp9923-scaffold1354-221177 17 2439413 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396280 Affx-122963303 AX-123266635 17 68419315 TTCCCATGGCTCTCTCATCTTGTGATTCAACATAG[A/C]TTATGGGGGGACTTCCCTGGTGGTTCAGTGGTAGG M 2 1 2 1 101000 f 74 goat snp9924-scaffold1354-302891 17 2360656 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779684 Affx-122950925 AX-385266784 17 68461911 AGGGGCCCTGATTTGCTCAGGCAAATACCTGAGTA[G/T]CCAAGTTGAAACTGAAACCCAGCTCTTGTGCCTTG K 2 1 2 1 202000 r 74 goat snp9925-scaffold1354-345487 17 2318652 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389052 Affx-122968612 AX-123259410 17 68505280 CAGATTAATGGTTATCTTTGGTAGTGAGCGCAGGG[A/C]GACTGGGGTTGCTAGTTACGTTCTGTATCTTCATC M 2 1 2 1 101000 f 74 goat snp9926-scaffold1354-388856 17 2274840 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766360 Affx-986697934 AX-385253740 17 68519331 GATTTTCAAGCTCTTGCTAGGCTGCACCACGTCAG[C/G]GCCCACTCGAGTGAAACAATCACCCTGTGGCACCT S 4 1 2 1 600010 r 74 goat 17_68519331 17 68519331 Ancestral_priority_1043 ancestry 0.504 neutral IMAGE 10K 10K ancestral 320803981 Affx-986696325 AX-385290676 17 68519380 AAACAATCACCCTGTGGCACCTAGGTCGGGTATGA[A/G]GAATGTGTTCCTGTCAAAGTCAAGAATTTTCTTGA R 2 1 2 1 600010 r 74 goat 17_68519380 17 68519380 Ancestral_priority_1043 ancestry 0.714 recommended IMAGE 10K 10K ancestral 320766366 Affx-986697938 AX-385253745 17 68519643 AAGCGAGCCTCCTTTGGGAAGAAGAGGCAGCCACC[C/T]GGTGTTTGTTTGTAAGCCTCTATTAGGAAGGAACA Y 2 1 2 1 600010 r 74 goat 17_68519643 17 68519643 Ancestral_priority_1043 ancestry 0.632 neutral IMAGE 10K 10K ancestral 320763411 Affx-986697940 AX-385251294 17 68519668 GGCAGCCACCTGGTGTTTGTTTGTAAGCCTCTATT[A/T]GGAAGGAACAGGTTCGCTTATACAGCGGGAGACCT W 4 1 2 1 600010 f 74 goat 17_68519668 17 68519668 Ancestral_priority_1043 ancestry 0.63 neutral IMAGE 10K 10K ancestral 320766373 Affx-986697942 AX-385253752 17 68519768 GAGGCAGGGCCGTGTATCTCCCCTTCCCTTTGAGA[C/T]CCTTGCAAAGACATAGTGGAAGTGCCCATGAAGAA Y 2 1 2 1 600010 r 74 goat 17_68519768 17 68519768 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 38400182 Affx-122960670 AX-123270537 17 68535755 ACCACTTTTAGCAAAAGCCACATGATACTTTTCCC[A/G]TTGAACTACATAGCCTTAAAATCTGAGGATACAAT R 2 1 2 1 101000 f 74 goat snp9927-scaffold1354-419331 17 2244155 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381200 Affx-122974533 AX-123251558 17 68580203 AGGCACTTTAAGACTCTACAGATGTCCTGCTGCTC[A/G]TCAAATTTCTTCAGTGTTCATCGTTATAATGGTTG R 2 1 2 1 201000 r 74 goat snp9928-scaffold1354-463779 17 2200090 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430118 Affx-122937511 AX-123300459 17 68615548 CAGTTGTGAATTACTGCATTCCAGAGGATGAAGTC[G/T]TGTGTGTTGGTTTTCCTTCCGCCTTTTCATTGCCC K 2 1 2 1 101000 f 74 goat snp9929-scaffold1354-499124 17 2165130 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436055 Affx-122932712 AX-123306394 17 68652187 TCCAGCGTATATATTTTTTAGCACCTACCGACTTT[A/G]TTCCAGAACCACATGATGCAAATCACTGCAGATGG R 2 1 2 1 101000 r 74 goat snp9930-scaffold1354-535763 17 2128894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277241 Affx-1111835750 AX-519550747 17 68659785 TCCTGAGGCCACAAGAGCAGGTCCCTGAGATCCCC[A/G]TCATAACCAGGGAGCAACCCCAAGTTTCTTCCCAC R 2 1 2 1 102000 r 74 goat Random2.2K-1692 17 68659785 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409027 Affx-122953867 AX-123279378 17 68686670 AAGTGGGGCCTGTTTTCTCTGTTGCGGTCAGCTGC[A/G]TAGATAGCAATAGTCATGTACCCTAGAAAGAGACT R 2 1 2 1 101000 r 74 goat snp9931-scaffold1354-570246 17 2093619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791542 Affx-122929966 AX-385278533 17 68764216 GTCGTCTTTTCCATTTTGTTTAATACAGTGTTTCC[A/C]AAACAGTGTTTGATGTGATGTCTTTTCATTCTCTG M 2 1 2 1 101000 f 74 goat snp9933-scaffold1354-647792 17 2016057 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803987 Affx-986696328 AX-385290681 17 68773918 TCACCAAAGATTGCTCTACCTGATTCAGATCATTT[C/T]TCACAGTCTTCAGTTCCATTTCTAGTGCTCTAAGA Y 2 1 2 1 600010 r 74 goat 17_68773918 17 68773918 Ancestral_priority_1043 ancestry 0.68 recommended IMAGE 10K 10K ancestral 320792588 Affx-122938464 AX-385279569 17 68826824 GTTTTTCTCTTTCCTTTGAACGTCCATGAACATTT[C/T]TGCATGACTTCCATTTATGAAAACAAAGCTACTAC Y 2 1 2 1 201000 r 74 goat snp9934-scaffold1354-710400 17 1955044 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410468 Affx-122952212 AX-123280818 17 68855381 ATGTGTTGAAAACCTACGAGTCTCATCTTACTGGC[A/G]TCATAAGTAGGAGTGTATGAGGCCCTGACACAGTC R 2 1 2 1 101000 f 74 goat snp9935-scaffold1354-738957 17 1926550 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421485 Affx-122943917 AX-123291832 17 68952827 TCCCTCCGTTTGTCCAGCTAATATTTATTAAACAC[C/T]TCTTTTGAGCCAGGCACTGAGAGTATGGCATATAG Y 2 1 2 1 101000 r 74 goat snp9936-scaffold1354-836403 17 1829197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436792 Affx-122932254 AX-123307130 17 68993170 ATTATGGGAGCAAAGTAGGAGGGAGCAGAGGTGAA[C/T]ACCCAACATACCCTGGGGTGTGGACACAGAAACAA Y 2 1 2 1 102000 f 74 goat snp9937-scaffold1354-876746 17 1789078 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380973 Affx-122974688 AX-123251331 17 69057632 AGAGCTATGTGGATCTCATCTCCCCAGACTGCCAG[A/G]CTCCAAGAGGTAGCTTTTCACAGAAGCCCTGCTCT R 2 1 2 1 101000 r 74 goat snp9938-scaffold1354-941208 17 1723427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415012 Affx-122949030 AX-123285361 17 69094478 ACTTGAAAGGGAGTATTCCCTGTCGTGGCCTCCCC[A/G]CTTCCCTCCTTCCCGGGAAGTATTGGTAATTTGGT R 2 1 2 1 102000 f 74 goat snp9939-scaffold1354-978054 17 1686223 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398765 Affx-122961440 AX-123269120 17 69123957 TATTTCATCTGTTTCCTCCCAGAAGGCCCATCGCA[C/T]GTTAGGTCAGCGTTCAGTAACTTAGCCGGCCACAT Y 2 1 2 1 201000 r 74 goat snp9940-scaffold1354-1007533 17 1656833 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420388 Affx-122944935 AX-123290735 17 69180017 TTCATATAAATGTGGACCAGGAGCAACGTCTGGCT[A/G]GTCCAGAGGATGACACAGTGCCCTCTGTCACCTCC R 2 1 2 1 102000 f 74 goat snp9941-scaffold1354-1063593 17 1600382 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277242 Affx-1111835751 AX-519550748 17 69201544 TTCTTTCAGACCTCAATTTACCACGAAATTAGGAT[A/C]CTAGAAAAAATCTGTAGAACTAGCTTTGTGTTCAT M 2 1 2 1 101000 r 74 goat Random2.2K-1693 17 69201544 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38453827 Affx-122919553 AX-123324160 17 69211700 ATTTGAGTTTTTTCAAGCTTGTGTGACATTGCCAA[C/T]GAGGAGATGTCTGTCTGTCTGCTGTTCCTTGGAAA Y 2 1 2 1 201000 f 74 goat snp163-scaffold1001-670504 17 1558647 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277121 Affx-1111835752 AX-519550628 17 69279675 AAGATTTGAGCCATGCCAAGTGTTATGCCCAAGTC[A/G]CGAAATCTCCCAGTGACCACCAGGGAGCCAATATC R 2 1 2 1 103000 f 74 goat Random2.2K-1695 17 69279675 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443105 Affx-122928101 AX-123313442 17 69301771 TGACATGTTTTGCTGATACCAGCACTCCAATGGTG[A/G]TGGGGCAAATAAGGAATTGATTTTCCTTATAAAAG R 2 1 2 1 101000 f 74 goat snp162-scaffold1001-580433 17 1468095 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399958 Affx-122960837 AX-123270313 17 69360599 AGGGGCAGTATCCACTCTGAGACTCTGTTAAAGAC[A/G]TCAACTTATTTCACCCCCACATTCTTGAGAGGTGG R 2 1 2 1 101000 r 74 goat snp161-scaffold1001-521605 17 1409057 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272002 Affx-1111833107 AX-519545770 17 69393682 TTGGCAGCTGAACAACAGAGTGGCTGGCCCATCAA[A/G]TGCCTGACTGCACTGAACTACAGAGTAGGACCCCA R 2 1 2 1 303000 f 74 goat 17_69393682_AF-PAKI 17 69393682 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38407328 Affx-122955301 AX-123277679 17 69467462 TCTCATACACACACACACAGCGCACTCTAACAAGC[G/T]AGCATCTCACCAGACCTACTAGTGGCCCAAGACTT K 2 1 2 1 201000 r 74 goat snp159-scaffold1001-414742 17 1302471 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438165 Affx-122931843 AX-123308503 17 69531733 TCCCAACACCTAGAATAGTGCTTGGCACTCAGCGA[C/T]GGCTGATTCGTTTGACAGATGTCCTGAGAGGGTGA Y 2 1 2 1 201000 r 74 goat snp158-scaffold1001-350471 17 1204399 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274913 Affx-1111834571 AX-519548496 17 69551441 TTGGGAAGTTGGGCTTCTGCAGGTAAATCAATCAC[A/G]TTAGAACACACACTCATATGAACAAAAGTAAACCC R 2 1 2 1 101000 f 74 goat GoatD01.041888 17 69551441 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38420945 Affx-122944984 AX-123291292 17 69564447 TGCAAGAGGCCTGACAGGGGTTTTCTAAGTGTGGA[A/C]GGTGGACTGCAAGTTTCTGCAGGTGTCATCTTCCT M 2 1 2 1 101000 f 74 goat snp157-scaffold1001-317757 17 1171678 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375713 Affx-122978639 AX-123246072 17 69611479 GGGTGTAACTGAAAATTTCTTTCCAAAAAATGCTT[A/G]AATCTAGTTTTCAAGAAGGACTGGTAATAGAAATT R 2 1 2 1 101000 r 74 goat snp156-scaffold1001-270725 17 1124477 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775848 Affx-122942028 AX-385262979 17 69662523 ATAAATGTTGATAAACTACTCTAAATGGAAGTGAT[A/G]TTTTTATCTACTTCCCAAATTAGCTGAGTAATTTT R 2 1 2 1 201000 r 74 goat snp155-scaffold1001-219681 17 1073496 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775084 Affx-122932652 AX-385262216 17 69692330 GGACAAAAAGTACTGGCCTTCATGACCAATTTATC[A/G]TTACTTCTGACCTACTGTGGGAAAACTAAACCATC R 2 1 2 1 101000 f 74 goat snp154-scaffold1001-189874 17 1044081 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782502 Affx-122971667 AX-385269578 17 69747036 TTGATATGAGAATAAGAATGATCCAGAGATGAAAG[A/G]CAAGCTGATGCAATGAGCTATTTGCCAGGCACTTG R 2 1 2 1 101000 f 74 goat snp153-scaffold1001-135168 17 989892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795369 Affx-122930640 AX-385282325 17 69795341 CTCTGCATTTGTTTTGATTGCTTTAATAATGTAGT[A/G]TTGTGAACTACTTAAACATACTGATTTTAGCAGAT R 2 1 2 1 101000 f 74 goat snp152-scaffold1001-86863 17 941695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406974 Affx-122955051 AX-123277325 17 69837091 AGACGAGCACGTGGCCACGAAGAGCCCGTCTGTCA[C/T]GATGTGAAGAGATGGGAGGTTTTTCCAGCCAGTGG Y 2 1 2 1 101000 r 74 goat snp151-scaffold1001-45113 17 904924 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438188 Affx-122931828 AX-123308526 17 69866647 TCAATTTCAGCTGCCCCTCAAACTTGGCTTCAGCC[C/T]AATTCCAGGTGTTTTCAGAACCGAGCTGAAGGCCA Y 2 1 2 1 201000 r 74 goat snp150-scaffold1001-15557 17 875434 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380707 Affx-122975157 AX-123251065 17 69909543 CTCAAGTGGAGATAACCAAGGAGTCAACAATTGGG[C/T]GGTGGTGATGGTAGTTTCCAGACACCTGGTTCAAG Y 2 1 2 1 201000 f 74 goat snp15265-scaffold1626-205053 17 831624 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427672 Affx-122939312 AX-123298015 17 69972518 TCCCAGTCCATCAAGGAAAGTTTACATCTGATATG[A/C]GTGTGCTGTTCCCTATGCAAGGATGCCTTCTCCCC M 2 1 2 1 101000 f 74 goat snp15264-scaffold1626-142078 17 768330 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399084 Affx-122960881 AX-123269439 17 70008572 ATATGCACTTTTCAAGGGATCACTGGCTCTGGGCA[C/T]TGGGTGGAGATTGGACAAGGCTTCCAGTAAGCAGC Y 2 1 2 1 201000 r 74 goat snp15263-scaffold1626-106024 17 732457 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390583 Affx-122967195 AX-123260940 17 70065241 ATAATTCCTTATGGTAAAGATTTATGACCTTCTAG[C/T]GGTCCAGCTGGGCTCAGATCTCTGACTGTCCATTT Y 2 1 2 1 201000 f 74 goat snp15262-scaffold1626-49355 17 675466 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451955 Affx-122920956 AX-123322288 17 70241325 TATTTGCATGTATGTATGTATTTGGAAGATTTCAC[A/G]TAAGTCTCACCAGTCCACAACCCCCACGTTCCCTG R 2 1 2 1 101000 r 74 goat snp40268-scaffold5133-11721 17 256445 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277123 Affx-1111835753 AX-519550630 17 70268744 ACCATCTTAAGAATTTCTAAAGAGAAGCCTTGGAA[A/G]TGGCAACCCGCTTCAGTGTTCTTGCCTGGAGAATT R 2 1 2 1 101000 f 74 goat Random2.2K-1697 17 70268744 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38410335 Affx-122952469 AX-123280685 17 70269441 TCAGCCTTGCGTTCCTCCTGGGTCCACCGGCAGAG[A/C]GCCTCGTGCTTCACTGAGCCCTTGGGTTCAAGTGC M 2 1 2 1 101000 r 74 goat snp35280-scaffold4225-9588 17 228198 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414677 Affx-122949298 AX-123285026 17 70299375 GTTTCCACTAAAAAACGTAAATTACAAGAGATGCT[A/G]CGTGGAAACCCCCACATGCGTAGCTATGTGCCTGT R 2 1 2 1 201000 f 74 goat snp35281-scaffold4225-39522 17 198085 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410866 Affx-122952605 AX-123281216 17 70344658 TCACACTTCTGAAAAAAAGTGCTTGCCTGGTCTGA[C/T]CACAGTTTTGTGCGAGCCTGTCAACCCTTCAGGAA Y 2 1 2 1 101000 f 74 goat snp21722-scaffold2130-39201 17 152764 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431494 Affx-122936246 AX-123301835 17 70396063 CCTTTGCCTCAGCCACTGGACTCTGCAAACGTGAC[A/C]CTTGAGGCTTTAGAATCACAGAAAGGGCCTGGCCC M 2 1 2 1 101000 r 74 goat snp21723-scaffold2130-90606 17 103619 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398749 Affx-122961454 AX-123269104 17 70425323 AATGGATGTGCAGTGGTGCCGGCGTCGTTCACTGA[A/G]AAGACCATTTTCCCCGCTGGATTGCCTTGGCACCT R 2 1 2 1 201000 r 74 goat snp21724-scaffold2130-119866 17 74278 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411934 Affx-122951155 AX-123282284 17 70634024 GGTTAGGAAAAAACAGGTTCCATTGCTGAGGACAA[C/T]GCTGAACCGCAGCTGGGGGAACCGGGGCAGCACAG Y 2 1 2 1 101000 f 74 goat snp25345-scaffold2611-119717 NW_017190051.1 135262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377868 Affx-122977269 AX-123248227 17 70662556 GGAAGTCCCACTCTCCCGATTCTTAAGCAGTCTAC[A/G]CTTAAACAGTTCTAGTCAGAATCAAATCACTTGAC R 2 1 2 1 101000 r 74 goat snp25346-scaffold2611-148249 NW_017189896.1 6313 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795652 Affx-122940524 AX-385282607 17 70693209 AAGTTTTAAGAAAAGAGGATTAATGTGCTCAGATC[C/T]ATTAATTAGATAAATCATGGGTCTGTGCAGAGGGC Y 2 1 2 1 101000 f 74 goat snp25347-scaffold2611-178902 NW_017189896.1 36993 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436950 Affx-122933176 AX-123307288 17 70749845 ACACTTCTGCAGGGTAAAGACGAGTGTAAACACTC[A/G]TTCAAAGCCATTGGTTGCTATAAGGCAGGCAGCAG R 2 1 2 1 101000 r 74 goat snp25348-scaffold2611-235538 NW_017189896.1 86971 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411815 Affx-122951248 AX-123282165 17 70808662 TGTCTTTAGTGTCTCTTTGTGACTAGACGAAGCTG[A/C]GTCTCAGCCAGAACGTGGCCTGGCCGCATCCACGT M 2 1 2 1 101000 f 74 goat snp25349-scaffold2611-294355 NW_017189896.1 134859 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436887 Affx-122933227 AX-123307225 17 70891420 ACCTCCGATGGAGCACTGTCCTGTGGGCTGTGGAG[A/G]AGCCTGTCCTTAGCAAATACTCGATGACACACTTA R 2 1 2 1 101000 r 74 goat snp25350-scaffold2611-377113 NW_017189530.1 27521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476334 Affx-1251763842 AX-586011751 17 70909796 AATTAAAAAAAATAATAAAACTACTAACATAATCT[-/GTCAGATCATAGACTTTGTTTTTTTTGTTTTTTTTTTAACGTCTTGCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCAGATCATAGACTTTGAAGTGACTTGTGATCTAT - 4 1 4 1 20000 f 74 goat SV_318 17 70909796 - deletion junction SV-TF-chip 539476588 Affx-1251763842 AX-586011974 17 70909796 AATTAAAAAAAATAATAAAACTACTAACATAATCT[-/GTCAGATCATAGACTTTGTTTTTTTTGTTTTTTTTTTAACGTCTTGCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCAGATCATAGACTTTGAAGTGACTTGTGATCTAT - 4 1 4 1 20000 r 74 goat SV_318 17 70909796 - deletion junction SV-TF-chip 562165068 Affx-1251763842 AX-606940480 17 70909796 AATTAAAAAAAATAATAAAACTACTAACATAATCT[-/GTCAGATCATAGACTTTGTTTTTTTTGTTTTTTTTTTAACGTCTTGCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCAGATCATAGACTTTGAAGTGACTTGTGATCTAT - 8 1 4 1 20100 r 74 goat SV_318 17 70909796 - deletion junction SV-TF-chip 562165432 Affx-1251763842 AX-606940843 17 70909796 AATTAAAAAAAATAATAAAACTACTAACATAATCT[-/GTCAGATCATAGACTTTGTTTTTTTTGTTTTTTTTTTAACGTCTTGCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCAGATCATAGACTTTGAAGTGACTTGTGATCTAT - 8 1 4 1 20100 r 74 goat SV_318 17 70909796 - deletion junction SV-TF-chip 562165947 Affx-1251763842 AX-606941356 17 70909796 AATTAAAAAAAATAATAAAACTACTAACATAATCT[-/GTCAGATCATAGACTTTGTTTTTTTTGTTTTTTTTTTAACGTCTTGCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCAGATCATAGACTTTGAAGTGACTTGTGATCTAT - 8 1 4 1 20100 f 74 goat SV_318 17 70909796 - deletion junction SV-TF-chip 562166208 Affx-1251763842 AX-606941616 17 70909796 AATTAAAAAAAATAATAAAACTACTAACATAATCT[-/GTCAGATCATAGACTTTGTTTTTTTTGTTTTTTTTTTAACGTCTTGCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCC]TCAGATCATAGACTTTGAAGTGACTTGTGATCTAT - 8 1 4 1 20100 f 74 goat SV_318 17 70909796 - deletion junction SV-TF-chip 320798300 Affx-122958300 AX-385285235 17 71051061 CAGGTTATTTCTTCCCTTCTCTGTTAACGTAGCAC[A/G]TTACGTTAACTTGGTTTTGAGTGTTACCCTTGCAT R 2 1 2 1 101000 f 74 goat snp41404-scaffold5388-246493 NW_017189530.1 174908 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380753 Affx-122975126 AX-123251111 17 71099137 ACCACGGAGACCTGAAGCAGAGTAGTTTCAAACAC[A/G]AATCTGATGCGCAAGCGCGGGTGGGACGACAAGCT R 2 1 2 1 101000 f 74 goat snp41403-scaffold5388-198417 NW_017189530.1 222083 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418313 Affx-122946976 AX-123288661 17 71173856 CCATCTCACTGCACCACGAAAACACAAGCAGACAC[A/G]CTGAGGGGCAGTCTACAAGAGCAGTCCAGTACTCG R 2 1 2 1 101000 f 74 goat snp41402-scaffold5388-123698 NW_017189530.1 297247 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410147 Affx-122952799 AX-123280497 17 71204493 TCCCAGGAGAGGCCTCAACCTAGTCCTAATCCTCC[G/T]CGACACACTCACTTCTCGAGTTCTGAGAGAAGCCG K 2 1 2 1 101000 r 74 goat snp41401-scaffold5388-93061 NW_017189530.1 327541 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411459 Affx-122951809 AX-123281809 17 71300026 CTGTGGGGAGCCCAACAGAGAACCTCCCACGGGAG[C/T]GGGGCCAGCAGAAGTGACCTTCCTGCGCCTAAAAT Y 2 1 2 1 303000 f 74 goat snp27804-scaffold2986-241887 NW_017189851.1 213034 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413298 Affx-122950198 AX-123283647 17 71351091 CCTCCTGCTCAGGGACAAGGGGCTCCAGGCTCTTG[C/T]ACTTCCCACGTGCAGAGAAGTGCTAGCCAAACTCT Y 2 1 2 1 202000 f 74 goat snp27803-scaffold2986-190822 NW_017189851.1 261813 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424826 Affx-122941366 AX-123295172 17 71388662 TAAACTAGCAAACTGAGCCTTATAATGTGTTAAAA[C/T]GCTGCTGCTGCTGCTAAGTCGCTTCAGTCGTGTCC Y 2 1 2 1 103000 f 74 goat snp27802-scaffold2986-153251 NW_017189851.1 302831 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419819 Affx-122945830 AX-123290167 17 71495818 CAAGATATTGAATACCTTATAGTTCCCTGCGCTCC[G/T]CAGTAGGGCCTCGTGTTTACCCGTCTCGCATGCAA K 2 1 2 1 201000 r 74 goat snp27800-scaffold2986-46095 NW_017189851.1 405328 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377363 Affx-122977649 AX-123247722 17 71567840 TACCCAGCTTTCTGCCTGGCATTCAGCTCTCCCTT[C/T]ATCTTGAAGACTGCCGCGTGTTTTAAAGATGCTTT Y 2 1 2 1 101000 r 74 goat snp25887-scaffold2674-182257 NW_017189851.1 491334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449488 Affx-122922634 AX-123319823 17 71629085 TTCTCTGAAAAAAGGAACTTCCCCGTGATACTGAT[A/G]AGGAAGGGCTGCTGCAGCGGCCCAGCCTGCCCAAC R 2 1 2 1 101000 f 74 goat snp25886-scaffold2674-121012 NW_017189851.1 549970 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439058 Affx-122930323 AX-123309395 17 71715797 AGGCCGTTCCCTTGGGACAGCTCTGCTTCCTGCCC[A/G]TCGAGGCTCACGCCTGTGGCCGTGACCCAGCTGCC R 2 1 2 1 202000 r 74 goat snp25885-scaffold2674-34300 NW_017189851.1 626400 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397373 Affx-122962279 AX-123267728 17 71753047 TTTTCCAATCACCTGGAGCCGTGGGCTGCCAGCGC[C/T]GTTAATCCTGGGGATGTTATTTAAAGCCGAGACGT Y 2 1 2 1 101000 r 74 goat snp26810-scaffold2812-54948 NW_017189851.1 660389 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443724 Affx-122927144 AX-123314061 17 71840720 CAACGTCCTGCTCACCGAAGAAGTGGAAACAGCGC[A/G]CTCCCCAGGCTTCGGTAGGAAGCAACAGGGAGCAG R 2 1 2 1 101000 f 74 goat snp53476-scaffold8108-32626 NW_017189851.1 741888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391081 Affx-122966833 AX-123261438 18 4536 TAGGGGTTTTACATCAGCTTCAGGCCAGGAGGCCT[A/G]CTAACATTTTATGATCTTTCTTTCTGATAACGGTC R 2 1 2 1 303000 f 74 goat snp6125-scaffold1217-4536 NW_017190138.1 120097 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407845 Affx-122954526 AX-123278196 18 40512 ATAGCAGTTTTGTTTTCGGGCAGAACTGTAGTCTC[A/G]TGTGTGGAAACAGCCTGACTCTACTGAGAGTCAGA R 2 1 2 1 303000 f 74 goat snp6126-scaffold1217-40512 NW_017190138.1 83420 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272883 Affx-1111833127 AX-431000193 18 70366 TCCAGTACACTTGCCTGGAAAATCCCATGGACGGA[A/G]GAGCCTGGTAGGCTGCAGTCCATGGGGTTGCTAAG R 2 1 2 1 103000 f 74 goat 18_70366_AF-PAKI 18 70366 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38415040 Affx-122949494 AX-123285389 18 92138 GGGAGTCAGGCCTCGTCTCTGTGGAGACATGCAAG[C/T]CCGCTTTCCTCTCGAGCTGTAAAAGTTGTGTCAGG Y 2 1 2 1 103000 f 74 goat snp6127-scaffold1217-92138 NW_017190138.1 30640 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429904 Affx-122938114 AX-123300245 18 139176 AGTTTACAAATGAAATTCTGTCTTTATCAATGTCT[A/G]CTTAGTGAGGTCTTCCCTGAGACTGCTCTTTGAAG R 2 1 2 1 201000 f 74 goat snp6128-scaffold1217-139176 18 2018929 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410436 Affx-122952397 AX-123280786 18 198677 ATAGTGCAAGACATAGAAGCACTGCATGTCTATTC[G/T]ATTCTAAATACATGAATCTGGCTCATTCACTGCCC K 2 1 2 1 101000 r 74 goat snp6129-scaffold1217-198677 18 2079240 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420968 Affx-122944581 AX-123291315 18 236016 CCCCAGAAACAGACCTGAGACAAAGAGGCTAAGAG[C/T]ATGTCTTTTGTGTGAAAGGTGATGCCTAGAAACCC Y 2 1 2 1 101000 r 74 goat snp6130-scaffold1217-236016 18 2116157 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453962 Affx-122919463 AX-123324295 18 289696 TAGTTGGAAGCCAGCTTGACATTGAAGCCCCACTG[C/T]AAACACACCGCAATAATATGCTCAGGTGAACCCTG Y 2 1 2 1 101000 r 74 goat snp6131-scaffold1217-289696 18 2169903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387021 Affx-122969929 AX-123257379 18 340580 CTGGGCACTGAGGGTGTGCTGAGCTGTGAGCTGAA[C/T]GATGTGGAAGCTCAGGACTGCCTCAGATGTGATCC Y 2 1 2 1 101000 r 74 goat snp6132-scaffold1217-340580 18 2221452 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430795 Affx-122937467 AX-123301136 18 378463 CCAACAATCACCATATCATCGCTGGTGAACTCATA[G/T]GAGGGAACTTCAAGGTTGAGAGGTGCAGGCCCCTT K 2 1 2 1 101000 f 74 goat snp6133-scaffold1217-378463 18 2259470 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798268 Affx-122919874 AX-385285203 18 427838 GTACACATAGACAGGCTTTTTATACTGTAGAATGT[C/T]TCACAAATGGGAAAGAATGTTATTTGTATTTCAAT Y 2 1 2 1 201000 r 74 goat snp6134-scaffold1217-427838 18 2309185 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396593 Affx-122962903 AX-123266948 18 493470 ATGCAAAACCCACAGCTTAACTGACGGTCAGCCAC[A/G]CATTGTAATACCAACAGGAACAACTTCCGTGCTCT R 2 1 2 1 101000 r 74 goat snp6135-scaffold1217-493470 18 2374164 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782853 Affx-122962903 AX-180660634 18 493470 ATGCAAAACCCACAGCTTAACTGACGGTCAGCCAC[A/G]CATTGTAATACCAACAGGAACAACTTCCGTGCTCT R 2 1 2 1 600000 f 74 goat snp6135-scaffold1217-493470 18 493470 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448641 Affx-122923359 AX-123318977 18 527992 AATTCTGGAACCGTGAGGAAGGAAAGCACATTTCC[A/G]CTGAGTGGTACTGAGGGGTGCCACGGGGGTAGAGC R 2 1 2 1 101000 f 74 goat snp6136-scaffold1217-527992 18 2407935 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441158 Affx-122929562 AX-123311495 18 558982 CTTAATACATGGTATTTGTTACTGCTGCACTGGAG[C/T]TATGGGGGTTTGAATCCCCTCTCCATGGAGGAAGG Y 2 1 2 1 101000 f 74 goat snp6137-scaffold1217-558982 18 2438878 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387297 Affx-122970525 AX-123257655 18 606963 GTCCTAACTTCCTCATCTACACTAGCCCCACCACC[A/G]TCATCACCACCACAAAAACACCATTATTCTCCATC R 2 1 2 1 103000 r 74 goat snp6138-scaffold1217-606963 18 2485416 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430214 Affx-122937335 AX-123300555 18 651144 TCACCATGCCCCAAGCGATGGGATCCATGCAAAAG[C/T]AGACTCAGAGGAAAATCAATAACCTTGGCTAGTTT Y 2 1 2 1 201000 r 74 goat snp6139-scaffold1217-651144 18 2529904 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410680 Affx-122952748 AX-123281030 18 682510 GTGTCCGTGCGCCATCTGTCGCCGGTCGTGGATCG[A/G]GTTCTCTTTTGCGTAAATCAAGGGTCCCAGGCCTG R 2 1 2 1 101000 r 74 goat snp6140-scaffold1217-682510 18 2561456 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414272 Affx-122949607 AX-123284621 18 723975 AACATTTAGATGAAGCATCTTTATGAACGGGCCCC[A/G]CAGATCATCATCTCTGCTGCGTTAGTTCTAATTGC R 2 1 2 1 201000 r 74 goat snp6141-scaffold1217-723975 18 2602184 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764929 Affx-122929016 AX-385252513 18 775350 TTGGGCCTCCTGTTAGCTTTGTTTATCTCTGTGGA[C/T]AGAGCTTTTTAAATGACCCTAGCCCTCTGAACTTA Y 2 1 2 1 101000 f 74 goat snp6142-scaffold1217-775350 18 2653753 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435282 Affx-122934043 AX-123305622 18 806678 TGCACATTCCCTGGAAAGATTTTGGAACAACCAGA[C/T]GCTCCTACTGGGAGAAGGTGAAGAGTAAACACCTT Y 2 1 2 1 201000 f 74 goat snp6143-scaffold1217-806678 18 2676035 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399456 Affx-122961205 AX-123269811 18 846983 ATGAAATAACACCACACCATATAAAGGGGCCTGAA[C/T]CTGAGTGTCCTGCAGCTTGGTTAGTTTCCGCCGGG Y 2 1 2 1 101000 f 74 goat snp6144-scaffold1217-846983 18 2712442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449218 Affx-122923498 AX-123319553 18 914115 GCCTCAGACAAAGGAGCAAGATGAGCATGTGAAAG[C/T]GAAAGGCACTCAGTCGTGTCCGACTCTTACAGTCC Y 2 1 2 1 101000 f 74 goat snp6145-scaffold1217-914115 18 2777478 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390753 Affx-122967904 AX-123261110 18 958330 GAGCTACAAAAATGTTCTTGCCCTTTATCCCAAGT[A/G]TTTATTCTGGATGGAGAATAAAATCCAAGGACAGA R 2 1 2 1 202000 r 74 goat snp6146-scaffold1217-958330 18 2821205 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766821 Affx-122919345 AX-385254145 18 1013155 GCACAGACAAAGTGGCCTAAACCTAACACAGTACC[A/G]TTCTCTACATTAGTTCTCATCTTCTCCCCATTGTG R 2 1 2 1 101000 f 74 goat snp6147-scaffold1217-1013155 18 2875881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603434 Affx-1002479565 AX-413837605 18 1041942 CAGATTAAAAAATTAGGAAAACTTTATAGGAAGGA[C/T]ATCTATGAAAAACCTACAGCTAACTTTATTATAGT Y 2 1 2 1 101000 f 74 goat 18_1041942_RH-map 18 1041942 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38414076 Affx-122949757 AX-123284425 18 1051183 TAATTCTCCGGAGAAGGAGTCAGCTATGAGATGCT[A/G]GCAGCCAGCACTCATGACAGCTGGGGAATGGGTGG R 2 1 2 1 101000 f 74 goat snp6148-scaffold1217-1051183 18 2913496 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410607 Affx-122952107 AX-123280957 18 1086248 GGAAAGAAGTGGTGGGAGTAGGGATAGTGTGTCAA[C/T]CCAACAAGGCAGGAAAAGGAAAAAGAACTGAAGGA Y 2 1 2 1 201000 f 74 goat snp6149-scaffold1217-1086248 18 2948613 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603505 Affx-1002479566 AX-413837672 18 1112284 CCAATATGTTTTTAGGGGCAATAGTTAAGATAGGA[A/G]GACCCTTAATTTCCAAGACTGTTGTTCAAGTAACT R 2 1 2 1 101000 r 74 goat 18_1112284_RH-map 18 1112284 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38437755 Affx-122931716 AX-123308093 18 1146354 ACATAGGAACTTGCTAAAAACAGCGAAAGACACTC[C/T]GGGGACTGAAGCTCATTAAGGGCTCAATACATTTT Y 2 1 2 1 201000 f 74 goat snp6150-scaffold1217-1146354 18 3008975 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377394 Affx-122977626 AX-123247753 18 1190389 ATAGGAACACTCTACGGCAGCCTGAAAGTGGGGGA[C/T]CAGGTCCGGCTGTTTATTGATGAGGTGAGTTGCTT Y 2 1 2 1 101000 r 74 goat snp6151-scaffold1217-1190389 18 3052476 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603438 Affx-1002479567 AX-413837610 18 1214376 CCAGAATATGGAAAATTCTATCAAATAGAGGAAGA[C/T]CCATAAGTATTTAGTAAATAAATAAATCCAAGTTA Y 2 1 2 1 101000 f 74 goat 18_1214376_RH-map 18 1214376 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603440 Affx-1002479568 AX-413837611 18 1300238 TTCTCCAACACCACAGTTCCAAAGCAACAATTCTT[C/T]TGTGCTCAGCTTTCTTTAGAGTCCAACTCTTATGT Y 2 1 2 1 103000 f 74 goat 18_1300238_RH-map 18 1300238 T C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38434656 Affx-122933981 AX-123304997 18 1313093 TGGAGGTGGTGCACACAGGAGTCAGTCTTCTCCTG[A/G]AAGGGGGAGGGAAGTCAGCACCCTGTCTGACGAAA R 2 1 2 1 201000 f 74 goat snp6153-scaffold1217-1313093 18 3175025 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603511 Affx-1002479569 AX-413837678 18 1315914 TGTGCCACACTGTTTTATTATAATGAGAAAAATAA[C/T]AAAGAGTAAATAATCTAAAAATCACAGGCAACAGA Y 2 1 2 1 102000 r 74 goat 18_1315914_RH-map 18 1315914 T C 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603443 Affx-1002479570 AX-413837615 18 1340558 AACCATCTGGGTGAGCATAGTTGCATGTTTAAGCA[C/G]AGAAGAAACAGACCATTTCTGGTGATCTGATGGGA S 4 1 2 1 101000 f 74 goat 18_1340558_RH-map 18 1340558 C G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38444243 Affx-122927223 AX-123314580 18 1350372 GACCTTGGAGTTCCATGAAACTCCTACAGTTTGTA[C/T]GTAGGTTATGTGCATTTTTCCTGAGGAGAGTTCAT Y 2 1 2 1 101000 f 74 goat snp6154-scaffold1217-1350372 18 3212108 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763436 Affx-986697965 AX-385251318 18 1357620 CTCCAGGATGAATCTAAGCACCCAAAAGATAATGA[A/G]TTATTATTAGTTTTATTAGTATTTTCTCTTCTTCC R 2 1 2 1 600010 f 74 goat 18_1357620 18 1357620 Ancestral_priority_1043 ancestry 0.738 recommended IMAGE 10K 10K ancestral 38396451 Affx-122962978 AX-123266806 18 1383705 GCTCTGCTTCATGCAGGCAATGGGTTTCCTAGTGC[A/G]CCAGCAGTCAGACCATACGGTGCTGCTTTTACTGG R 2 1 2 1 201000 r 74 goat snp6155-scaffold1217-1383705 18 3245458 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390708 Affx-122967936 AX-123261065 18 1448737 AAATTTTCAAGATCATGTAGATGTGACATTGACCC[A/G]TGAAGTTCCAACACTTAAAATTTTTCCTTTCCTTT R 2 1 2 1 101000 f 74 goat snp6156-scaffold1217-1448737 18 3310674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785065 Affx-122922355 AX-385272112 18 1486003 ACAGAAAGAACATTTCCACAAAATAACTCAATTAA[C/T]AACTCAAAATAGAAATTTACCTATTTCCTCCAAAA Y 2 1 2 1 101000 r 74 goat snp6157-scaffold1217-1486003 18 3348388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416093 Affx-122948321 AX-123286442 18 1521214 AATGCCAGCTTCCACCACTAGTAATTCTCCCCCAC[A/G]TTCAAATCCTTCCATGTCTGTAACTCCTTATTTCT R 2 1 2 1 201000 r 74 goat snp6158-scaffold1217-1521214 18 3383486 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396021 Affx-122963480 AX-123266376 18 1560405 GACGCAGAGCTGGACCAGAGTTACAGGTCCCCGGA[C/T]GTGCCCACTCTCCTGGAAGGGGACAGGGTGGGCGG Y 2 1 2 1 102000 f 74 goat snp6159-scaffold1217-1560405 18 3422612 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448059 Affx-122923692 AX-123318395 18 1596315 TCACCTTATGAATTTCTTCTGAGACCTTTCTCTGC[A/G]TAAATCTCCTGCACAACAATCACCCTTTCAAATCC R 2 1 2 1 201000 r 74 goat snp6160-scaffold1217-1596315 18 3458759 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407521 Affx-122954706 AX-123277872 18 1650568 ACCTCCCACCTCCCTTCAACCAAAGTGGCTCTGCT[A/G]TTAAATGTTTTACATACTGAGTGCAGGAGGCAGAA R 2 1 2 1 101000 r 74 goat snp6161-scaffold1217-1650568 18 3512080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603446 Affx-1002479571 AX-413837618 18 1666113 AACTTTAAATGATGCATTAGACCAGTTAGACCTAA[C/T]TGATATCTATAGGACATTTCACCCCAAAACAATGA Y 2 1 2 1 400000 f 74 goat 18_1666113_RH-map 18 1666113 C T Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38450099 Affx-122922783 AX-123320434 18 1690187 AACAGGAAACAGAGCAAGGCCCAGACTTTAGCCTT[A/G]CTTGGCTTTGGTGAGAGTATTTGCTGGTTTGCTTC R 2 1 2 1 101000 r 74 goat snp6162-scaffold1217-1690187 18 3551826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603448 Affx-1002479572 AX-413837620 18 1752854 TGCTATCTAGGTTAGTCAAAGCTTTCCTTTCAAGG[A/G]ATAAGCATCTTTTAATTTCATGGCTGCAGTCACCA R 2 1 2 1 103000 f 74 goat 18_1752854_RH-map 18 1752854 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38384013 Affx-122972906 AX-123254371 18 1774223 TTGTAGATTCGCCTGCCTTCCTCATGCAGGTAATC[A/G]TACTACAGTGGTGTCTCTTCCCTTCTTGTCCTTGT R 2 1 2 1 101000 r 74 goat snp6164-scaffold1217-1774223 18 3635991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400848 Affx-122959782 AX-123271203 18 1830778 CCCCTGCGTGTGGGCTCTGACCCCACCAAGGCCCT[A/G]CAGTCGTGTTCTGTCAGATGCTTGCTGAAGCACCT R 2 1 2 1 101000 r 74 goat snp6165-scaffold1217-1830778 18 3691454 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603450 Affx-1002479573 AX-413837622 18 1846222 TACTGTGTGCTCCTTGACTGACCTAAAAGAATTAA[C/T]ATACAACTTCCAAATACCTTCATCAGAAAGAGAAT Y 2 1 2 1 101000 f 74 goat 18_1846222_RH-map 18 1846222 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38389212 Affx-122969060 AX-123259570 18 1888711 ATAGCCAGGCCATTTCATATAAGAAAAGGGAAACG[C/T]AAACTCCACTGTGGCACTGCCTGGACTTCATATAA Y 2 1 2 1 101000 f 74 goat snp6166-scaffold1217-1888711 18 3749751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603521 Affx-1002479574 AX-413837686 18 1891740 CAAATTAAGCTAATTCCTCACATCTGACTCTTTCT[C/T]GATATTTCAAGAAACTTTCAGAACCTTCCTTCCTC Y 2 1 2 1 101000 r 74 goat 18_1891740_RH-map 18 1891740 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38423612 Affx-122942379 AX-123293958 18 1930225 GTGATGATGAGTGCTGGGACCGATGGTGGAGGCTG[C/T]AGGCCTCGCTCTGGGAGGATAAAATGGGAAATGAA Y 2 1 2 1 102000 f 74 goat snp6167-scaffold1217-1930225 18 3788422 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603523 Affx-1002479575 AX-413837688 18 1945427 TGGACTGGTTGGATCTCCTTGCAGTCCAAGGGACT[C/T]TAAAAAGTCTTCTCCAACACCACAGTACAAAAGCA Y 2 1 2 1 103000 r 74 goat 18_1945427_RH-map 18 1945427 C T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320763438 Affx-986697967 AX-385251320 18 1967549 CATGTTTATTGCAGATTATCTGTCTTCTCCCAGCT[A/G]GACTATCAGTTCCCTGAGGATAAGTGTCTGCCTGC R 2 1 2 1 600010 f 74 goat 18_1967549 18 1967549 Ancestral_priority_1043 ancestry 0.68 recommended IMAGE 10K 10K ancestral 350603457 Affx-1002479576 AX-310729769 18 1982607 TTGTACTTTTCTAGGAATTTGTCCATTTCTTCCAC[A/G]TTGTCCATTTTATTGGCATACAACTGCTGATAGTA R 2 1 2 1 303000 f 74 goat 18_1982607_RH-map 18 1982607 G A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320788313 Affx-122929877 AX-385275331 18 1985930 AGGAAACAATAAAAAGCATTAGGAATACCCAAAAG[G/T]AGGTATTGCAATCCTAAACCCACTGCATTACCCTT K 2 1 2 1 101000 r 74 goat snp6168-scaffold1217-1985930 18 3837951 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603527 Affx-1002479577 AX-413837692 18 1999507 AGTGAAGAAGGGTTCCTGCTGGTGCCCTGAAACCC[A/G]ACTGAGAAGAAGAGGGCACCATGGGTTAATGAGCA R 2 1 2 1 101000 r 74 goat 18_1999507_RH-map 18 1999507 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320781923 Affx-122970188 AX-385269004 18 2000625 TCATTTCTGTCCTGTCACTAACCACCTAGAGTTAG[C/T]GTAGACCCCACTGGTTACTGGCTCAGTCACCCAAG Y 2 1 2 1 101000 f 74 goat snp32076-scaffold3613-8635 18 3853243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440841 Affx-122929264 AX-123311178 18 2030493 CTTTTTCATTCAGAAATGTAGACTGTTTCATGAGG[A/C]TTCTGTCATCCAGCCCCACTGCTGAATGATGGATG M 2 1 2 1 101000 f 74 goat snp32077-scaffold3613-38503 18 3883357 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603461 Affx-1002479578 AX-413837631 18 2035340 GGCAAATGCATAGTACATTAGCATAGCTTAAGATA[A/C]ACATTTCCATAAGAAAAAGGCATTGGTTATCTCTA M 2 1 2 1 103000 f 74 goat 18_2035340_RH-map 18 2035340 C A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603530 Affx-1002479579 AX-413837695 18 2060822 GCTCTCAGTTGGTCTTTGTCAACTTCCAATGGCCA[A/G]CCACTACATCTCCTTGACAAAACTTCTTGAACCAC R 2 1 2 1 101000 r 74 goat 18_2060822_RH-map 18 2060822 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38383827 Affx-122973168 AX-123254185 18 2094805 AATCAGATCATTACTCTCTATGCCTTAGACTTATA[C/T]AGTGCTGTACATCAATTACTTCTTCAATAAAACTG Y 2 1 2 1 101000 f 74 goat snp32079-scaffold3613-102815 18 3947504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423715 Affx-122942879 AX-123294061 18 2133897 CCGTCATGTTACCCAAGGTCAGAAAAATGTGAAGC[C/T]CTCCTCTGCTAGCGCTTTGCACATTTCAAAAGGTG Y 2 1 2 1 101000 r 74 goat snp32080-scaffold3613-141907 18 3986343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603466 Affx-1002479580 AX-413837636 18 2138588 CATCCTCTTCCTCTGTAAATGAGGTCAGTGGGATA[C/T]GTAGACAATTTATCTGGTTTAACTAGGACTACCTT Y 2 1 2 1 101000 f 74 goat 18_2138588_RH-map 18 2138588 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320790487 Affx-122919718 AX-385277490 18 2182702 TAGTTGTATTAAGAACTTCATTCAAACCAGAGCAG[C/T]TTTCGGAATCAAAAGCTAACATACACTTTAAAGAC Y 2 1 2 1 101000 f 74 goat snp32081-scaffold3613-190712 18 4035072 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603468 Affx-1002479581 AX-413837638 18 2184660 GCTCAGCAGAAAGGTTAGGTTTATAGGGAAAAGTT[C/G]ACTATTCAGCCCACTGAGAATCACTGAAACCTTGG S 4 1 2 1 101000 f 74 goat 18_2184660_RH-map 18 2184660 C G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38418449 Affx-122946476 AX-123288797 18 2218893 ATCCAGAACCTCCATTCTTTGGACCCCTTTGCTGA[C/T]GCAAGTAAGGGTGCTTATCTGCCTCCTGCTGGCAC Y 2 1 2 1 201000 r 74 goat snp42290-scaffold557-16583 18 4071269 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395310 Affx-122964059 AX-123265665 18 2249911 AGACTCCTGTAAGGGCTCTCTCCTGTCGGCCGGAC[A/C]TGCTCACCTCTTCCCTTTACTAACGTCCACCGAGA M 2 1 2 1 201000 r 74 goat snp42291-scaffold557-47601 18 4102232 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391926 Affx-122966935 AX-123262283 18 2282345 TTTTTCTTTTGTGCACTGTCCTCATGGCTATACCC[G/T]CCAGAGAACCTGTTCCTCTGGGAATCTTATTTAAT K 2 1 2 1 101000 f 74 goat snp42292-scaffold557-80035 18 4113183 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603470 Affx-1002479582 AX-413837640 18 2284985 CTGAAGATTCTGAAGGTCAGGTCTTGTGTTCCCCC[A/C]ACCCAGGACCCAGCTGGGGCTCTCCACTTCCTTTC M 2 1 2 1 102000 f 74 goat 18_2284985_RH-map 18 2284985 A C 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603472 Affx-1002479583 AX-413837642 18 2333575 AATCATCATACACAGAAAGAGTCTGAATCTCTTCA[G/T]TTCCCAGGGAGCTGCCTCCAATCACCCCTCATCTT K 2 1 2 1 201000 f 74 goat 18_2333575_RH-map 18 2333575 T G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38393967 Affx-122965049 AX-123264322 18 2353505 ACTCTTGCATGTGGCACACCCAGACACCAGAAGGA[G/T]GTCCACCTCACAACTATTACTTGTGCAAAACTGGT K 2 1 2 1 101000 r 74 goat snp42294-scaffold557-151195 18 4183539 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439025 Affx-122930347 AX-123309362 18 2388594 TACCGTGTCAATTAACAGGTCGAAGCTTGTACTGT[A/G]CACTAAGATGCCTTCACCTGTGGGCTCTGAAATGA R 2 1 2 1 101000 f 74 goat snp42295-scaffold557-186284 18 4218368 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447229 Affx-122924970 AX-123317565 18 2432428 GTTGATGAAAAACACACCTGTGTCTGGATTTACCT[A/G]TATCCAAGTACATTAAACCTGCATATGTACTTAGC R 2 1 2 1 101000 r 74 goat snp42296-scaffold557-230118 18 4262785 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603540 Affx-1002479584 AX-413837704 18 2463276 GAGGCCACAGACCCCACAGAGCCCCCACTTCCTCC[A/G]CCCTTCAAGCCAGATCATCCCTCCGCAAACCTCAG R 2 1 2 1 102000 r 74 goat 18_2463276_RH-map 18 2463276 G A 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38387980 Affx-122969592 AX-123258338 18 2498373 AGAAATTGATAGCTCCTGTGCTCTACCATGGTGTC[A/G]GAGCTGGATTCGGAGGCAGGTACTTGATTTCCTGC R 2 1 2 1 101000 f 74 goat snp42297-scaffold557-296063 18 4329049 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603476 Affx-1002479585 AX-311404952 18 2502090 ACTGCAGCCATGAAATTAAAAGACACTTACTCCTC[A/G]GAAGGAAAGTTATGACCAACCTAGATAGCATATTG R 2 1 2 1 103000 f 74 goat 18_2502090_RH-map 18 2502090 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603478 Affx-1002479586 AX-413837647 18 2545751 TGCAAGAATCGAGAGAATGAGGCTAACGTGCAAAG[A/G]AAAAACAGACCAGAGTCCTAACAAATTCATTTGAG R 2 1 2 1 201000 f 74 goat 18_2545751_RH-map 18 2545751 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38414500 Affx-122949537 AX-123284849 18 2550157 GAAGTTTAAAGTCTGAAACTCCTGGAATTGGTTTC[G/T]ACAGTGTATGATAGCTTGTTCAAATAATAGGTGCC K 2 1 2 1 101000 r 74 goat snp42298-scaffold557-347847 18 4379505 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790155 Affx-122947795 AX-385277160 18 2579739 GATATTGAAAACAGAGTTCTATGTGTTTTCTGTGT[A/G]CACTGAAAAACAGGTTCCCCAAAAGAACTTGTATT R 2 1 2 1 202000 f 74 goat snp42299-scaffold557-377429 18 4412372 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793148 Affx-122919821 AX-385280126 18 2610966 AGTAATTTCTCCAGAGTTAATAAGTGTAATCTATA[A/G]AATAGCTTGGTAGGAGTTTTTTTGACCTTATCAGA R 2 1 2 1 101000 r 74 goat snp42300-scaffold557-408656 18 4442871 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272552 Affx-1111833115 AX-519546268 18 2638499 AAGAATGGAGGATTGATTTGTGAATGATAGGTTGA[A/C]TTTGCCAGACAAATCATATGGAGGTCAAGTTGTTT M 2 1 2 1 101000 r 74 goat 18_2638499_AF-PAKI 18 2638499 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320779730 Affx-122957454 AX-385266830 18 2648152 ATTCACAAGTCATTATTGAATACCATATAAATTTA[A/G]TATACCCTGAAGGGAATTTGCCCTAGGGACACATT R 2 1 2 1 202000 f 74 goat snp42301-scaffold557-445842 18 4480470 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799670 Affx-122962937 AX-385286598 18 2679744 AGTAATGGTGTTTCCAAAAAGAATAAGGCAAATAT[A/G]CCTACAGTCTCTGCGTGAATCAGCACTTTAAATCA R 2 1 2 1 201000 f 74 goat snp42302-scaffold557-477434 18 4512737 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603546 Affx-1002479587 AX-413837709 18 2697619 TCCCGGGTCCTCCCTCGCAGGGAGACACCACTGCC[C/T]TCCAGCAACACAATCCTGGAAAATGCCCAGGGAGG Y 2 1 2 1 102000 r 74 goat 18_2697619_RH-map 18 2697619 T C 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38453154 Affx-122919989 AX-123323487 18 2712537 GGGAAGCTTTAGAAGTCATTCACAAGATGGGGAGG[A/G]GGGATCTGATGATGGGAGACCCCATCATGAGTCAT R 2 1 2 1 202000 r 74 goat snp42303-scaffold557-510227 18 4545926 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763440 Affx-986697969 AX-385251322 18 2717271 GTCCAGTAGCCGTCTGGGTTAGCTCCCTGACCCTC[C/T]GGAGGATGATCTGAAAAACACAAGGTCTTATCGAC Y 2 1 2 1 600010 f 74 goat 18_2717271 18 2717271 Ancestral_priority_1043 ancestry 0.442 neutral IMAGE 10K 10K ancestral 350603482 Affx-1002479588 AX-413837651 18 2752917 TCCTGAATCATTCAAGGACCTTAACATATATTTTA[A/G]CTTCGGTCACCTACCCCCTCCCCTTATAAGCTATT R 2 1 2 1 201000 f 74 goat 18_2752917_RH-map 18 2752917 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38453612 Affx-122920131 AX-123323945 18 2761761 CAAAGATGACGGGTGACTTTGGTGGAGTGTTGTGT[C/T]GGCCTGTGGGCGAGAGACAATTCTGTCAAGCTGAA Y 2 1 2 1 201000 f 74 goat snp42304-scaffold557-559451 18 4594485 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603550 Affx-1002479589 AX-413837713 18 2793803 TTATTCCCTTTATTGATATTGCTTTAGCACCATCA[A/G]TAGAGATCTGTGAGGAAAATACTTGATTGTGAAAG R 2 1 2 1 101000 r 74 goat 18_2793803_RH-map 18 2793803 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38430050 Affx-122937562 AX-123300391 18 2794183 AAGTAAGGACTGTAAAAAATAATTTGGATGTGAGA[C/T]GGCCCTTACTAACTAAATATGATTCCAGGGCTGCA Y 2 1 2 1 101000 r 74 goat snp42305-scaffold557-591873 18 4626935 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778743 Affx-122950786 AX-385265854 18 2823719 TACATACTTCACTTCAATCTAGATTTCTGATGTAA[C/T]GCCATTATGATTTATGTGGTAACTTAGTGTGTTTC Y 2 1 2 1 101000 r 74 goat snp42306-scaffold557-621409 18 4656123 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603486 Affx-1002479590 AX-413837655 18 2840471 ACTGCAAATGCAAGACAGAGTGAGAAAAGACAATC[A/T]GTGACCCAACAACGCCTGCTCTAACACTGATTCAA W 4 1 2 1 101000 f 74 goat 18_2840471_RH-map 18 2840471 A T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38394237 Affx-122964880 AX-123264592 18 2864179 TAGCTCTGCCCTGTTTTTCTGTCTTGCGCTAACTG[A/C]TCTGAGATTAGGAGATGTACAGTTCCTAGTGCTGG M 2 1 2 1 101000 r 74 goat snp42307-scaffold557-661869 18 4697107 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802355 Affx-122961571 AX-385289259 18 2924659 ATCGTTTGACATTCCTCATGAGAGGGCCTGATCTT[A/G]GTGGTAGAATAGAGTTGGTTTTGCAAGTTGACCTC R 2 1 2 1 101000 r 74 goat snp42309-scaffold557-722349 18 4757921 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603554 Affx-1002479591 AX-413837717 18 2980927 GGGTCCAAGTCCTCCTCCCTGCCTCCAGGCCCTGC[A/G]TCTTGATGGAAGTCTACATCCAGCGGGTGGGCAGG R 2 1 2 1 400000 r 74 goat 18_2980927_RH-map 18 2980927 G A Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320772734 Affx-122953919 AX-385259879 18 3016310 CCACTATACTATGAAAAACTGATATTCGGTTCATC[A/G]TATTTTGAAAAAGGAAATCTATAATATTTAGATTT R 2 1 2 1 202000 r 74 goat snp42311-scaffold557-814000 18 4849067 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389085 Affx-122968588 AX-123259443 18 3068881 GTACCTGCATCAGGAATAAGTGAAAAATAAAACTA[C/T]GATCAGGGCCTTACAGTACTGTGTGAGTGAATTTA Y 2 1 2 1 102000 r 74 goat snp42312-scaffold557-866571 18 4902436 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763442 Affx-986697971 AX-385251324 18 3099385 CGGGTGGAGAGAGCATCAGTGACGGTGTCACCACC[C/T]AGGGTTCTTGGCCTCTTTAATCAATAGAAATTGAA Y 2 1 2 1 600010 f 74 goat 18_3099385 18 3099385 Ancestral_priority_1043 ancestry 0.438 neutral IMAGE 10K 10K ancestral 38388564 Affx-122969174 AX-123258922 18 3109462 TGTAAGTGTCCTTTTGTTGTTGAGTCAGTCAGTCA[C/T]GTCTGACCCTGTGACCCCATGGACTGCAGCATGCC Y 2 1 2 1 102000 f 74 goat snp42313-scaffold557-907152 18 4942614 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419835 Affx-122945816 AX-123290183 18 3166116 TGTTCAGAGGCTTTGGAAAAGATTTAAAGAATCTA[G/T]CAGACATAATCTCATGTTTATGTAGGAAATATTGC K 2 1 2 1 101000 r 74 goat snp42314-scaffold557-963806 18 4999707 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769833 Affx-122955824 AX-385257003 18 3222592 ACTCTGAAAATTAGAGTCGGAATTCATTGTTATTA[C/T]GCACATGATCAAACAGCTAGCAAGTATGTTTCTGT Y 2 1 2 1 101000 r 74 goat snp42315-scaffold557-1020282 18 5056731 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438534 Affx-122931194 AX-123308872 18 3279194 TGGAGTCAGAATTGGCTTCTTCTGTGCAACACATA[C/T]GGGAACAAAAACACAGCTTCAAGTCGAATACCACT Y 2 1 2 1 201000 r 74 goat snp42316-scaffold557-1076884 18 5114232 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439983 Affx-122929803 AX-123310320 18 3318376 GGTTTTCTTCTGAACAGGGAGAGTGACATGATTTA[C/T]GGCTTCGCTAAAAGCAAACTTTATTGCAGAAGGAA Y 2 1 2 1 101000 r 74 goat snp42317-scaffold557-1116066 18 5153721 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441148 Affx-122929569 AX-123311485 18 3347615 CGCTGGCCCAGCACCTTTGTAGAATGCTGCCTACC[A/G]CCTGAAATACACCTGCATGCATGCATGCTAAGTCG R 2 1 2 1 303000 f 74 goat snp42318-scaffold557-1145305 18 5183561 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433682 Affx-122934550 AX-123304023 18 3397744 AGAAAGGGTAGATTGATCTCATTTTCCTCATTTAC[G/T]AAATGCTAAGAGTCATTTGATTAGCTCTAAGGCCG K 2 1 2 1 202000 f 74 goat snp42319-scaffold557-1195434 18 5234977 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436173 Affx-122932615 AX-123306512 18 3439282 CACTGAAAAATGTTAACACTCGGAACTATGACAGC[A/G]TCTTCTATGGCACAGACACATCCAGTGACACAAGG R 2 1 2 1 101000 f 74 goat snp42320-scaffold557-1236972 18 5276602 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381455 Affx-122974333 AX-123251813 18 3470824 AGAGATAAGCTATCACAATTAACGTGAGTTTAGCA[C/T]AGTCACTGGATAGAAGGGAAATAGAGCAAAAGTCA Y 2 1 2 1 101000 f 74 goat snp42321-scaffold557-1268514 18 5308481 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796350 Affx-122932108 AX-385283300 18 3516050 CAATAAAAACAAAAGCATGCACTGCAGATTTTATA[C/T]ACTTTAGTCCCTGGTTAAGGGCTGTGTGCATGCTG Y 2 1 2 1 102000 r 74 goat snp42322-scaffold557-1313740 18 5355237 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386617 Affx-122970234 AX-123256975 18 3555673 TGCAGAGGAACAAATGAAATTATTTTCACAAAATG[C/T]GCTACTTCCTTTCCCTTCTGCCTGGCAAATATGAA Y 2 1 2 1 201000 f 74 goat snp42323-scaffold557-1353363 18 5395116 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786514 Affx-122935407 AX-385273548 18 3591119 ATTGATCTCTCTGCTCCACACTTACTAAGAAATAC[A/G]TTTCAGAGACTCTAGAAGTCAGTCAAATGTTGCTC R 2 1 2 1 101000 f 74 goat snp42324-scaffold557-1388809 18 5430658 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449427 Affx-122922684 AX-123319762 18 3639413 AATTTGGTTGAGGCAACCTTTCAGCAATTAAAACT[A/G]CTCAGTAGGGAAATAACAGAAGAGTAATTAGAAAG R 2 1 2 1 101000 r 74 goat snp42325-scaffold557-1437103 18 5479292 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432433 Affx-122935819 AX-123302774 18 3674358 AATCCCCAGATACAATCCAACATATATTTTGTATG[C/T]GTTCACTTTTGCTAACTAGATAATTAACACTCCTC Y 2 1 2 1 101000 r 74 goat snp42326-scaffold557-1472048 18 5514332 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384970 Affx-122971903 AX-123255328 18 3732819 TCCAAAGGAAGCACTAATCAGGACTCCCCTGGTGG[C/T]CCAGTGGTTAAAACACTGCATTTCCAAAGCAGAGG Y 2 1 2 1 303000 r 74 goat snp42327-scaffold557-1530509 18 5572309 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395700 Affx-122963729 AX-123266055 18 3771380 ATGAATTCTTGAAAACATGGCATTTTAGACAGTCT[A/G]CTGTACTGACTTTAGATTCTGTTGCTGCCTTGTGG R 2 1 2 1 101000 r 74 goat snp42328-scaffold557-1569070 18 5611524 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406915 Affx-122955615 AX-123277266 18 3801538 TGTAATAGACATATGGGGACAATCAGGGGAAACCA[G/T]ATGTGTTGTGGGTATTTGGTGATATAAATGATCCA K 2 1 2 1 101000 f 74 goat snp42329-scaffold557-1599228 18 5641703 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391669 Affx-122966548 AX-123262026 18 3830131 CATTAAGTCCTTTTAAAACAAATACATCATAAAAT[A/G]TTAATGTCAGTATTTTTTTATGCAGTTAAACCGTT R 2 1 2 1 303000 f 74 goat snp42330-scaffold557-1627821 18 5670021 A G 3 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320785605 Affx-122938511 AX-385272649 18 3860593 CAGCAGTAGAATCAACATACACCTTGGGTAGTGAG[C/T]GCTCCATCTGCAGAGGTAATGAAACAGGTTAGGCA Y 2 1 2 1 101000 r 74 goat snp42331-scaffold557-1658283 18 5700977 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431631 Affx-122936144 AX-123301972 18 3944536 TGTGAATCCCAGTCAGACATATGCAGAATGGGAAG[A/C]GACCAGATTTAATGATAATTCATGGGAAATAAGAC M 2 1 2 1 101000 f 74 goat snp21320-scaffold208-2824940 18 5787839 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405325 Affx-122956343 AX-123275677 18 4009418 ATACTATCTTCAAATAGATTTTAAGGGGAGGTAGC[C/T]GGTTTCCCCCTCCGTCAGTTTCTCCCATCAGGAGG Y 2 1 2 1 201000 f 74 goat snp21319-scaffold208-2760058 18 5853066 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408435 Affx-122954453 AX-123278786 18 4056474 TGGAGTTTGGATGAAAGAATATTCAGATGGCATCC[A/G]TCTCTGGGCCACAGTTCACAGCCTCAGAAAGTGGC R 2 1 2 1 201000 f 74 goat snp21318-scaffold208-2713002 18 5900433 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400088 Affx-122960745 AX-123270443 18 4088202 CATGCACACTATCTGATGGTTTTTATTGTTGTTGG[C/T]ATGTGTATGTCAGAACCGTAGCAGCTTAGTACCAG Y 2 1 2 1 201000 r 74 goat snp21317-scaffold208-2681274 18 5931723 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790675 Affx-122922309 AX-385277677 18 4125980 GTGTATTCTAGGTAAAAGGTAGTGTCTGTAAGAAT[C/T]GATAAGAATACATGGGCCAGAGATGTCAAGGAAGT Y 2 1 2 1 101000 r 74 goat snp21316-scaffold208-2643496 18 5966331 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447951 Affx-122923776 AX-123318287 18 4206042 TCCTTCGAAAAACTCAGGAGTTCTGGCCCCACGTG[G/T]CTTCCTTTTTGCAAGGTGACCGTCCGCTCCAGTTG K 2 1 2 1 201000 f 74 goat snp21314-scaffold208-2563434 18 6045319 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419918 Affx-122945328 AX-123290266 18 4257911 GGGATTCGTGCTTTACATGCATTATTTTATTCGGT[C/T]CACAGCATAGCTTGTTTTGCAGATGAAGGAGCTAT Y 2 1 2 1 101000 r 74 goat snp21313-scaffold208-2511565 18 6097689 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784464 Affx-122943478 AX-385271513 18 4314904 TTCATGGACTCCAGATTAAGAATTCTTGCTGTAGA[C/T]GGCAGATGCTGATATACAGCTAGGGAGATGAAGCA Y 2 1 2 1 101000 r 74 goat snp21312-scaffold208-2454572 18 6154954 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420433 Affx-122944903 AX-123290780 18 4349663 CAGATTGTAAATACATATTTGCAAATTCCTCTACC[A/G]TTGTTCACAAACCATGTAGGCCTGTTCCTGCAGGG R 2 1 2 1 101000 r 74 goat snp21311-scaffold208-2419813 18 6189495 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452842 Affx-122920727 AX-123323175 18 4399594 CCATCTCATTCTTGCATCTGAACCTCTGAACACTA[C/T]AGTGTTCATCTTATTAACTCCATTTTGCAGTCGAG Y 2 1 2 1 101000 f 74 goat snp21310-scaffold208-2369882 18 6235991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783584 Affx-122937362 AX-385270644 18 4431573 AATGCTAGCGTTCTAAATGGCCTGCTTGCTGTTAA[C/T]AGATTCACTGGCACTGAGATCCATTTCTTTTCCGG Y 2 1 2 1 101000 f 74 goat snp21309-scaffold208-2337903 18 6267943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443414 Affx-122927379 AX-123313751 18 4461059 CCCACGATGTCAGAGGGCAACTGAGGCTGGGACTT[C/T]ACACCTGTGCCCTTTCTAGAAGAGGAGGCTTGGAA Y 2 1 2 1 101000 r 74 goat snp21308-scaffold208-2308417 18 6296918 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414276 Affx-122949604 AX-123284625 18 4519092 GTCTACTCTGCTCTTCCCTCCCCTGTTGCTGGGCT[A/G]CTGGCTATCTCTCTGGACCTGACTCCATCAGTTTC R 2 1 2 1 101000 r 74 goat snp21307-scaffold208-2250384 18 6355069 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408847 Affx-122954011 AX-123279198 18 4553310 TCAGCCAAGGAGAAGGACATAGAAATATTAAGAGT[G/T]TAAGGAAATATTGTTCTACTCCGAGGATGAGTCAT K 2 1 2 1 101000 r 74 goat snp21306-scaffold208-2216166 18 6389143 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446657 Affx-122924769 AX-123316993 18 4582075 GAATCTGGAATCGGTCAGAACCTGGATTGGGGGTC[A/G]CGCCTTGCCACTGCTGAGCTATGTGACCCTGGAGG R 2 1 2 1 101000 f 74 goat snp21305-scaffold208-2187401 18 6417531 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423125 Affx-122942905 AX-123293471 18 4644571 CCTTCAGCTCCTGCTTTTCACAAAACCCTTCCCGG[C/T]TGCTCCAATCAACATGAATTCTCCCTGGAATGAAC Y 2 1 2 1 101000 r 74 goat snp21304-scaffold208-2124905 18 6480415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794610 Affx-122945138 AX-385281572 18 4673415 CCACAGACCGTCCATGGATAAGACGCTAAATGTCG[A/C]GTCCTGGATTATCAGCTAATTCTGGTATCAAATCT M 2 1 2 1 101000 f 74 goat snp21303-scaffold208-2096061 18 6509160 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419732 Affx-122945896 AX-123290080 18 4710568 ACGGGAAACCAGCAGCATCCCCAAGGGCTTCCTGT[A/G]TGCCAGACACCGTCCTGAGCTGTCATAAACACTCA R 2 1 2 1 101000 r 74 goat snp21302-scaffold208-2058908 18 6546498 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385141 Affx-122971763 AX-123255499 18 4786575 TACACACTCACTGCTTTTCTGAGACTCTTAAATTC[A/G]CCTTGTTAAAACACCACCATCTTTCTGTTCTTTAT R 2 1 2 1 101000 f 74 goat snp21301-scaffold208-1982901 18 6622689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443603 Affx-122927312 AX-123313940 18 4823942 ATCTGGGTATTTCCTTCTTCATCCAGATGTTTGGC[A/G]TCCCCTAGGTGCAGCCTGCTATCTTTGGTTGAATA R 2 1 2 1 202000 r 74 goat snp21300-scaffold208-1945534 18 6660346 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421983 Affx-122943795 AX-123292330 18 4857491 CCACCTGAGCTGCTTCACTAAAAGGACACAACATC[A/G]TTTCTAGGATGCTCGGGCCAAATATCTGCTTTAAC R 2 1 2 1 101000 f 74 goat snp21299-scaffold208-1911985 18 6693054 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407316 Affx-122955309 AX-123277667 18 4888068 TAATATTCTACAAGAGGCATGCACCATCTTGGTGG[C/T]CACAGAACTTGTATAAAATAACATTTATATAGAAT Y 2 1 2 1 101000 f 74 goat snp21298-scaffold208-1881408 18 6723511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407259 Affx-122955352 AX-123277610 18 4933460 TCGTTGAAAAGGCACATTACCCAAGGATATAGCCC[A/C]GACCTTTGAGCTTGTGGTCATAAGACAAAATGGAC M 2 1 2 1 101000 r 74 goat snp21297-scaffold208-1836016 18 6769324 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432930 Affx-122935304 AX-123303271 18 4976576 TCCAAAGCTGTTTCTAATCACACATCGAATCCTAA[A/C]GTAAATGCAATTAATTGCCCAATAAACAGTCTCAG M 2 1 2 1 101000 f 74 goat snp21296-scaffold208-1792900 18 6812330 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780283 Affx-122926719 AX-385267378 18 5113346 GTTTCCCCATCTATTTTAGCCCTCATTCAAATCCT[A/G]ATCCTCCTTTAAGCCTACCCTGGATCTCATCTTAT R 2 1 2 1 101000 f 74 goat snp21293-scaffold208-1656130 18 6950135 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452334 Affx-122920655 AX-123322667 18 5142399 GAAATTAGCTGTCCATTCCGGCTCACACGATGCCC[C/T]GTCCGGAGGCCCAGGAATTTGATACTGGCTATTTC Y 2 1 2 1 201000 f 74 goat snp21292-scaffold208-1627077 18 6978983 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463525819 Affx-1110028684 AX-515008213 18 5150200 AGCAGGTTTGCAGGGGCTGGACGACTGCAAAGAGC[A/G]GGACAAGGGTGAGTGAGATAGACTCCAGTTCCTAG R 2 1 2 1 202000 f 74 goat 18_5150200_AF-PAKI 18 5150200 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394042 Affx-122964991 AX-123264397 18 5201995 ACTGCAATCCACACCAGGCTGCAAATGAGAGCCAC[A/G]CACAAGCACACACGCGCCTCGCGTGTGCACTTGTT R 2 1 2 1 201000 f 74 goat snp21291-scaffold208-1567481 18 7038271 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797481 Affx-122961679 AX-385284420 18 5232557 CAGCAGGTGCATCATTTTACACTGTCTTCTAATTC[A/G]TCTCAAATATATTTGATGATACATCTGAGATCCCT R 2 1 2 1 101000 f 74 goat snp21290-scaffold208-1536919 18 7066313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403552 Affx-122957596 AX-123273905 18 5294033 CATGAAAAGAGGACACGGACAAGGTCATTTAAGGG[A/G]CCACATCACAAGCTTCTATAATTGGCAGCTTCTGC R 2 1 2 1 201000 f 74 goat snp21289-scaffold208-1475443 18 7128475 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409646 Affx-122953525 AX-123279997 18 5326279 GGACAAGTTATCTGACCTGGGGTAGCAGACCTGTG[C/T]TCCCAGGAGCAGGACGATAGAAGGGAAACAGGGTG Y 2 1 2 1 101000 r 74 goat snp21288-scaffold208-1443197 18 7160293 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389858 Affx-122968155 AX-123260215 18 5356727 ATACAGGAGTTACTTCTGGGCACTGCCTCTGCAGA[C/T]GGCTGGTGTTACCTCTCTGTATGCTTCCAGCTGTG Y 2 1 2 1 101000 r 74 goat snp21287-scaffold208-1412749 18 7190782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381322 Affx-122974435 AX-123251680 18 5394946 AGGGAAGCAAGGTGCCTAAAATCTGTTTTGCTATA[C/T]ACAGATCTGGAGGATCGTTTTTTACTGTCTCTACA Y 2 1 2 1 201000 f 74 goat snp21286-scaffold208-1374530 18 7229060 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389795 Affx-122968211 AX-123260152 18 5432915 AGTTGGCAGGAGAAAGGGGTAACCTGCTCTGACCA[C/T]GCTTTGTCAAAAACTTCTGTGCTCAGTGAGGACGC Y 2 1 2 1 101000 r 74 goat snp21285-scaffold208-1336561 18 7265789 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421343 Affx-122944067 AX-123291690 18 5482462 GGAGAGGCAAGGGGAGGCCCTGGAGCCTGATCCCC[A/G]TGCCTTGTTTTCTGAAAAGTTAATACTCCCTGAAC R 2 1 2 1 101000 r 74 goat snp21284-scaffold208-1287014 18 7315544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397790 Affx-122962503 AX-123268145 18 5527482 TGACACTGTGACATTATTTTTTAAGTGAAGCACTT[A/C]AGGATATATTAAACACAAATGTGAAGTTCCTGTTA M 2 1 2 1 201000 r 74 goat snp21283-scaffold208-1241994 18 7359367 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378571 Affx-122976597 AX-123248930 18 5574845 GGCATCCCAAAGTAAACTCTGTGTATGCTTGATGT[A/G]TCAGTCAGCTTTTGCTGCATAACAAATCACCCTGT R 2 1 2 1 101000 f 74 goat snp21282-scaffold208-1194631 18 7406590 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440246 Affx-122930664 AX-123310583 18 5608163 AATGTCTTCTTCTAGTGTCCCAACTATTGATTTTA[C/T]GACTTGTATTTATACCCATAAAGTCTTCTCCTTTT Y 2 1 2 1 101000 f 74 goat snp21281-scaffold208-1161313 18 7439838 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772251 Affx-122965543 AX-385259405 18 5660769 CATGTCTGGTAGAGCCATAATTTTCTAATTCATAT[A/C]TCTGAGCTTTTTCTCGAGCAGTTGGACTTGGTTGG M 2 1 2 1 101000 f 74 goat snp21280-scaffold208-1108707 18 7492758 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401682 Affx-122959558 AX-123272035 18 5719361 CTAATTCTTTACCATTCTTAAAGATTCGGTTGCTT[A/G]TAAGTTAACCAGAATTGCCTGTTTTTCAGCACATA R 2 1 2 1 101000 r 74 goat snp21279-scaffold208-1050115 18 7549939 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427294 Affx-122940155 AX-123297637 18 5775106 ATAAAGCTGGAGAAAAAAAAGAAAAACACAAATAA[C/T]GCTTCCCACAGGAACTATACATGAAAACCAGGTCC Y 2 1 2 1 101000 r 74 goat snp21278-scaffold208-994370 18 7605007 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416700 Affx-122947566 AX-123287048 18 5832631 CTCCCTCCCCTGAGATGCTGCGTTTGTAACAGATC[A/G]GTAGGCTTGTTGAGCAGGGCTCCAGGGACTGTTGC R 2 1 2 1 101000 f 74 goat snp21277-scaffold208-936845 18 7662407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422175 Affx-122943521 AX-123292521 18 5891266 GTATATTTAGTTGTCAGGTTCCAAAGACAGATGCC[A/G]TCCGAATTATTGACTCACACTTCTGCAGTTACTGA R 2 1 2 1 101000 f 74 goat snp21276-scaffold208-878210 18 7720670 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404093 Affx-122957129 AX-123274445 18 5960612 TAACGTACGTAAATTGCTTGGTCCTAGGCACTCAG[A/C]GAAGAGTAATGTAATTATTAGTACTGCACTGTAGT M 2 1 2 1 101000 f 74 goat snp21275-scaffold208-808864 18 7789841 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392566 Affx-122966078 AX-123262923 18 6002900 AGGGTGTCCAGAAGCGACTGTAAAAGCAGCAGTCT[A/G]TAGCCAGTTGTGTGCCAAGGCTGACTTTTTTGGAC R 2 1 2 1 101000 r 74 goat snp21274-scaffold208-766576 18 7832131 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774813 Affx-122969879 AX-385261947 18 6078826 GATGTCATTGCTGTTGACAGCTGATCCTAATAAAG[C/T]AGTCGGCAGTGTAGGCCAAGGGCTCCTATACGATC Y 2 1 2 1 201000 r 74 goat snp21272-scaffold208-690650 18 8033397 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420828 Affx-122944666 AX-123291175 18 6119512 CCAGAGAAAAGGGTCGATGGTTATAAGCCACCATG[C/T]GCCATTAGCTGTGAGATGGGCAGCATGCCACGAGC Y 2 1 2 1 101000 f 74 goat snp21271-scaffold208-649964 18 8073798 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766432 Affx-986697977 AX-385253806 18 6128060 TCCCTTAGGAACTAAAAATAGAGCTACCGTGTGAT[C/T]CAGCAACTCCACTACAGAGCGTATATACAGAGGAA Y 2 1 2 1 600010 r 74 goat 18_6128060 18 6128060 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 320763450 Affx-986697979 AX-385251329 18 6128101 ACTCCACTACAGAGCGTATATACAGAGGAAACCAC[A/G]ATTCAAAAAGATACACGTAGCCCAGAGTTCACTGC R 2 1 2 1 600010 f 74 goat 18_6128101 18 6128101 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 38446715 Affx-122924725 AX-123317051 18 6154744 CCGTTGATCAGCTGCTAATGGCTGAGCTAGACCAC[A/G]TAAACACATTTACTTAAAAAAGACCAAAACATCAT R 2 1 2 1 101000 f 74 goat snp21270-scaffold208-614732 18 8108933 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400434 Affx-122959967 AX-123270789 18 6200829 GCTCCAGCCCTACACTCTTAACCATTGTGCTAATT[A/C]TTTGTCTTTGCAGTAATAAAAAATATAGGGCGGCA M 2 1 2 1 101000 f 74 goat snp21269-scaffold208-568647 18 8155235 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803212 Affx-122937145 AX-385290070 18 6229791 CGTTACTAAGAAAAATGTCCGGATAGATCGATCGA[C/T]GCAAACAGAACTAACCAGACATTGATGATTAGCAA Y 2 1 2 1 101000 r 74 goat snp21268-scaffold208-539685 18 8182421 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435714 Affx-122933305 AX-123306053 18 6278285 CATTTCATGGTTCTTGACCCCCCAAGCTGCTCACC[A/G]TCTACAACAGAATGAAGTTCTCCCAATTCCTGGTC R 2 1 2 1 101000 r 74 goat snp21267-scaffold208-491191 18 8230480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390391 Affx-122968177 AX-123260748 18 6318434 TCATGGCCAAGGGGCAAGTTCACGGGCATCCCCCA[C/T]GCAAACACAGTTGTGGAGACTCCAGGACTCCCTGC Y 2 1 2 1 101000 r 74 goat snp21266-scaffold208-451042 18 8270800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415618 Affx-122948596 AX-123285967 18 6353085 ACTTAGAGTTAACAGATGAGGAAACTGAGGCCCAG[C/T]AAAGTTCACTAACGTGCATAAGGTCACACAGCACC Y 2 1 2 1 201000 r 74 goat snp21265-scaffold208-416391 18 8304813 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446588 Affx-122924820 AX-123316924 18 6394418 ATTATAAGTGATGTTTTTCTAGTTCCTCAAATTCC[G/T]ATGATATTTATTATATTTATTTTATAATAAAGCAA K 2 1 2 1 103000 f 74 goat snp21264-scaffold208-375058 18 8345960 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799045 Affx-122928672 AX-385285975 18 6431331 TTAAGAGCAGAGCTCTTTCCATCTCAGCAGATTGC[A/G]TTCTTCAAGGAACACACAGTTCTAACAAATTAGCA R 2 1 2 1 101000 f 74 goat snp21263-scaffold208-338145 18 8383975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417490 Affx-122947166 AX-123287838 18 6483481 GCTAGAATACAGAAAAATAAGCATTCATATAAAGT[A/G]CCTGAGGGAGTTTAAGTTATACAATTGATATGGAA R 2 1 2 1 101000 r 74 goat snp21262-scaffold208-285995 18 8436067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384587 Affx-122972989 AX-123254945 18 6521428 AAGGAAGGGCTCTAGACAAAGGATAGTATTGATGG[C/T]GATGGTGGTGGTGATGATCTTGAGGTAGGCTCTGA Y 2 1 2 1 101000 f 74 goat snp21261-scaffold208-248048 18 8474313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402071 Affx-122958712 AX-123272424 18 6551075 TGCCTTAGGACCCCAGTGGCTGCTCTGAGTACAGC[A/G]TGGTCTGCTCTACCTCCTTTGGAGTCCTCCACCCT R 2 1 2 1 201000 r 74 goat snp21260-scaffold208-218401 18 8503876 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383238 Affx-122972756 AX-123253596 18 6595953 GCCTCAGAGACTCATTTGACATATGTTGAGTTCCC[A/G]TTCTATGTCAGAGACTGAATGTCTGGTCCCTAGGA R 2 1 2 1 101000 r 74 goat snp21259-scaffold208-173523 18 8548476 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433300 Affx-122935197 AX-123303641 18 6657735 CTACAAGTCTGAAGACAGATCTGCCAGGGAATGCC[A/G]CACTTATGCCCCTGTGAATGTGTATGTGTGTTTGG R 2 1 2 1 101000 f 74 goat snp21258-scaffold208-111741 18 8610391 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777440 Affx-122938959 AX-385264561 18 6718781 TTAGAAGAGTGTTTACCAAAGCTTTAAAAATTAGA[C/T]AATGTACAGCACTTCTTAGGAATATATATACATTA Y 2 1 2 1 101000 f 74 goat snp21256-scaffold208-50695 18 8671365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790456 Affx-122967975 AX-385277459 18 6753823 ATAAATTACCAATGTCTGTACGTAGTAAGTGCTAC[A/G]TACAGCTGCTAGTTGCTTCTGTTATTTTTATTATG R 2 1 2 1 101000 r 74 goat snp21255-scaffold208-15653 18 8706423 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433732 Affx-122934515 AX-123304073 18 6785147 CCTCCCCAGGATCCCAGCTTTTGCCCCAAAGACAA[C/T]GCAAGAGGGGGAAATGCTCCCCACCCAAGGGTCGG Y 2 1 2 1 101000 f 74 goat snp4470-scaffold1144-15572 18 8737330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439113 Affx-122931103 AX-123309450 18 6817778 GAGGGAAGGAGGGAGAAAGGAAAGAAGTCTCAGGG[C/T]GGGAAAGGGAGGGGACATTTTGGGGACGGCAGTTA Y 2 1 2 1 101000 f 74 goat snp4471-scaffold1144-48203 18 8768267 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407634 Affx-122954623 AX-123277985 18 6847736 AGTGGGATCAGGGAAGAGGCAGTAAGGGGTTCTTT[C/T]CCTTTTATTCAATAGTCTTCTGCACTGCTTAACTT Y 2 1 2 1 101000 r 74 goat snp4472-scaffold1144-78161 18 8798188 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790098 Affx-122940949 AX-385277104 18 6896954 AGCCACACCACATGAAACTACACTGGATCCTCATT[A/G]TTCACTGACCCCATATTTGCGAATTCTACTCACTA R 2 1 2 1 101000 f 74 goat snp4473-scaffold1144-127379 18 8847398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437500 Affx-122932352 AX-123307838 18 6940027 TGCAATTTAGCCAGTCAGCAGGGGAAAACTGGATG[A/G]AGACTTTTGAATCCATCAAAAGCATGTGGCAATCA R 2 1 2 1 102000 f 74 goat snp4474-scaffold1144-170452 18 8890444 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440693 Affx-122929911 AX-123311030 18 6979907 CTCCGAAGTTCAAGAGAAAGGTGCAAAATTCTAAG[C/T]AAGGTTCAAAGAAGAGTTTCCTGTAAAAGACTTTT Y 2 1 2 1 101000 f 74 goat snp4475-scaffold1144-210332 18 8930336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796619 Affx-122963962 AX-385283565 18 7036984 TGTTTATTACTTTTTCAGCTATTACAGGAAAATAA[C/T]AGCACCTAAACTATCTAAATGTCCAATGTTAGAGA Y 2 1 2 1 101000 r 74 goat snp4476-scaffold1144-267409 18 8987479 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416157 Affx-122948275 AX-123286506 18 7066527 CCTAGGCTTCCACCCCTTCTCCCTCCCCCACACTA[C/T]ACTGTTACAAGGTCACACAAGCCAGAGGAACCAAA Y 2 1 2 1 101000 r 74 goat snp4477-scaffold1144-296952 18 9016889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603555 Affx-1002479592 AX-413837718 18 7084488 AAACATTTTTTTACTCAATATCTTACTCCCTGTCT[A/C]TGCTTCTCTAAAGTTGTAACCCTTCACAGAAAAGC M 2 1 2 1 201000 r 74 goat 18_7084488_RH-map 18 7084488 C A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320789889 Affx-122922658 AX-385276896 18 7096309 TGCTTTCTGCTGTAAAGGTGATGTCACCTCCATCC[C/T]CTTACCTCATCCTTTAGTCTGGAACTGGTCTACTT Y 2 1 2 1 101000 f 74 goat snp4478-scaffold1144-326734 18 9047313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417670 Affx-122946829 AX-123288018 18 7130928 GGGGGTGGCAAAGAGTTGCACACAACTGAGCGATT[A/G]GCAACAACACATAAGAACCAAACCTTAATTTGAGG R 2 1 2 1 103000 r 74 goat snp4479-scaffold1144-361353 18 9081947 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414618 Affx-122949343 AX-123284967 18 7175167 TTGTGGTTAAGGTTTAAGAGCCCTAACCACTTCCT[A/G]CTTGCCTGGTGGTGGGTGCTTTGTGTGGTGCTTCT R 2 1 2 1 101000 f 74 goat snp4480-scaffold1144-405592 18 9126459 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798044 Affx-122966485 AX-385284980 18 7224112 AGGGAGACAAAGACTTGAAATGAAATCTACTTACC[A/G]TCCTTGAATTGTTTCCCTGTAGGCTCAGACCCAGT R 2 1 2 1 101000 r 74 goat snp4481-scaffold1144-454537 18 9175705 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428486 Affx-122938781 AX-123298829 18 7264040 CAAGTAAGGAAAGACATATGGGAGTGCTTTGGAAA[C/T]AGCTTAGTCATTATTTCCTGAGGCTCAGTTTTCTT Y 2 1 2 1 101000 f 74 goat snp4482-scaffold1144-494465 18 9214650 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401107 Affx-122959406 AX-123271460 18 7308697 AGGTGCATCTGAGCCATACAGGAGAGGAGTCCCCT[C/T]GGCAGTGCTCCCTGGAGACTCGTGCCCGTTGTTGT Y 2 1 2 1 201000 f 74 goat snp4483-scaffold1144-539122 18 9258746 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277124 Affx-1111835754 AX-519550631 18 7323004 TCACAAGGTTGAAAGGTATTAACGAGAACCCACGC[A/G]GTCCTGGGCAACCGTCTGCGGAAAACATTTTCCTT R 2 1 2 1 201000 f 74 goat Random2.2K-1703 18 7323004 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 350603492 Affx-1002479593 AX-413837660 18 7338805 GACCTCAGGTTCTAGATTCATCTAGATTCCAAAAC[A/G]GGTCAGCAGACTTTTGCTTAAAAAGCCAGGAAGTA R 2 1 2 1 101000 f 74 goat 18_7338805_RH-map 18 7338805 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38406066 Affx-122956245 AX-123276418 18 7346819 CTTACTGAGTCCTGAGCAATCTTTAAATCAACTGT[A/G]CCTACTCATGCTGCGCTCTGGTGGTGATGGAAAAT R 2 1 2 1 101000 f 74 goat snp4484-scaffold1144-577244 18 9288159 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603494 Affx-1002479594 AX-413837662 18 7387047 ACAGTGCCCGTCTGCAACCATGGGCTGGGAAAGCT[C/G]GCCCGGATGGAGGCCGAGAGTCCCCTTGAGTCACG S 4 1 2 1 400000 f 74 goat 18_7387047_RH-map 18 7387047 C G Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320772340 Affx-122960098 AX-385259493 18 7390650 AGAAATTTCTAAATTCATCGTTTGTTTCACTAATC[C/T]GTTCTTTGATCGCCGTCAGGAGTTGATAGTTAACA Y 2 1 2 1 101000 r 74 goat snp4485-scaffold1144-621075 18 9331698 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791547 Affx-122929005 AX-385278538 18 7423048 GCACTGCAGAGCTTTGTGCACGTAACAGGTGGTTA[A/G]GATGGAGTACACTATGTGTATTTCACCAGAATTTT R 2 1 2 1 101000 r 74 goat snp4486-scaffold1144-653473 18 9363942 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603496 Affx-1002479595 AX-413837664 18 7424827 GCTGAAAGTGAGATGAGTAACAAGCCCTGTTCCCA[C/G]CATGGGGACGTGGCCCTGGCTCTCTAGACGAGGAC S 4 1 2 1 101000 f 74 goat 18_7424827_RH-map 18 7424827 G C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603498 Affx-1002479596 AX-413837666 18 7509569 CTGAAACTTGTTAGAAAGACTTATTTGAAGAAGAG[C/G]TAAATCAAGTTGAAATATACATGAGAAATTTATAT S 4 1 2 1 101000 f 74 goat 18_7509569_RH-map 18 7509569 G C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38423963 Affx-122942137 AX-123294309 18 7512354 GTCCTCTACCTTATTCCTTCTCCTTAGCACTTACC[A/G]TAATCTAACAGACTATGCCTTTGTTATTTTATTTT R 2 1 2 1 201000 r 74 goat snp4488-scaffold1144-742779 18 9453610 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394241 Affx-122964877 AX-123264596 18 7532308 GCAAGTCTTTTGGGGGTCCCCATCTCCCTGTGTCC[A/G]CTGCCAGGGTGTAGAGGTCTGCTTCCCAAAGGTAA R 2 1 2 1 101000 r 74 goat snp5115-scaffold11756-8820 18 9473451 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409658 Affx-122953517 AX-123280009 18 7549063 GTTCCAGGGACGAGGTGAGACAGTATCTACTGAGC[A/G]CTCAGTATCTACTGCACCAGCCGCTCAGCAAGCAT R 2 1 2 1 101000 r 74 goat snp38662-scaffold490-674883 18 9490000 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603564 Affx-1002479597 AX-413837726 18 7566418 GTGTATGTGTGTGTGTGAGAGGGTGTGTGTGTGTA[A/G]GGGCATGTGTTGTACACCTGTGTATGTACATACAT R 2 1 2 1 101000 r 74 goat 18_7566418_RH-map 18 7566418 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38416220 Affx-122948226 AX-123286569 18 7586946 CTGCTGTTAACCCGTGTGACTCTCATAGCAACCTA[G/T]GAGGCTTGGTCTTAATGTGACCCCCACTGAGTTCA K 2 1 2 1 101000 f 74 goat snp38661-scaffold490-637000 18 9527490 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778638 Affx-122970041 AX-385265748 18 7620632 TCTGCTAAAGATAACTGTGCCATTATCATCTCTAT[C/T]AGATTTCTGCAGAGCCAAGGTCGTTTTTAACATTA Y 2 1 2 1 101000 r 74 goat snp38660-scaffold490-603314 18 9557079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603502 Affx-1002479598 AX-413837669 18 7642054 TGAAATACTTCTCAGCTTCACTGGACCACTAACTT[C/T]CCTCTACAACATCATCCAGAAGAATCCTTAACCCT Y 2 1 2 1 101000 f 74 goat 18_7642054_RH-map 18 7642054 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38431059 Affx-122936641 AX-123301400 18 7650925 GGAGACTTCTGGAATCGAAATGCACGGTGGCGTGG[C/T]GGGCAGAGGGACGGACGGACGAGAGAGCATTAGCG Y 2 1 2 1 101000 f 74 goat snp38659-scaffold490-573021 18 9587324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272885 Affx-1111833128 AX-519546573 18 7704330 TGGGCACTGGCTGTAGCTACAATTTGTACCCTGGC[A/G]ACTCTGTTTACTAGCTATGTGGCCTTGGGCATGTC R 2 1 2 1 201000 f 74 goat 18_7704330_AF-PAKI 18 7704330 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398605 Affx-122961484 AX-123268960 18 7714872 CTAGAGTCAGGAGAAACCTTTTGGGAAGCTACCTC[A/G]TCTCACTCATGATAAAAGAAACCGAACAAAGAGCC R 2 1 2 1 101000 r 74 goat snp38658-scaffold490-509074 18 9651356 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603504 Affx-1002479599 AX-413837671 18 7743438 GATCTTTGAACACTGAGCAAGTGAAAGGGGTGGGG[A/G]GGATGTTAAAAAAAAAAAAAGCCAGCAAGTTATGG R 2 1 2 1 102000 f 74 goat 18_7743438_RH-map 18 7743438 A G 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38436652 Affx-122932481 AX-123306990 18 7758745 ACTATCTCAAGGCTCCCAGGCCCCATGGTGGGACA[C/T]GACCCGCCCCAGCAAGACAGCTGCCTACAGATGTG Y 2 1 2 1 303000 r 74 goat snp38657-scaffold490-465201 18 9690261 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603506 Affx-1002479600 AX-413837673 18 7760780 CCACGAATATGGGGGCTCTGAGGTTAACGCACTTG[A/G]AAATGATGGATTCGTGGTGATTTGGGCCACGGGGA R 2 1 2 1 101000 f 74 goat 18_7760780_RH-map 18 7760780 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38451409 Affx-122921189 AX-123321742 18 7789949 CAAGCACTAATTATTACCTGGGTAAAAACGTGAAC[A/C]CTGCAACTCAGTCTTTTACTCCATACAACCATGTA M 2 1 2 1 101000 f 74 goat snp38656-scaffold490-433997 18 9721567 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378887 Affx-122976500 AX-123249246 18 7828685 ATGCCTTTGGCCTGGTGCACCTCTTTAATTAAATG[C/T]ACCTCTTTAAACCACGATGGGGCCACTGCACAGGG Y 2 1 2 1 101000 f 74 goat snp38655-scaffold490-395261 18 9760174 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603508 Affx-1002479601 AX-413837675 18 7854631 TGGTTTTTTGGTCCCTCTCTATTGAAGGTGTAATG[G/T]GTTGCTCAGTAGTAACCAGGAGCTGTAGAGCTCTA K 2 1 2 1 103000 f 74 goat 18_7854631_RH-map 18 7854631 G T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38450250 Affx-122922254 AX-123320585 18 7879142 TGTGTGCAGCTCATCTGGAATGGAAGTGTCTTTCC[A/G]CCTCTGTGTGTACAGTGGCATCTGGTTGTCTGAAA R 2 1 2 1 101000 f 74 goat snp38654-scaffold490-344804 18 9809975 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603510 Affx-1002479602 AX-413837677 18 7913814 AAGAGCATGGTAATCCACTCCAGAATTCTTGCCTG[A/G]AGAATCCCATGGACAGAGGAGCCTGGCAGGCTGCA R 2 1 2 1 400000 f 74 goat 18_7913814_RH-map 18 7913814 G A Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603512 Affx-1002479603 AX-318252055 18 7947507 TCCTTAGGGGATCTTCCTGACCCAGGGATCAAGCC[C/T]GCATCTCCTGCATTGCAGGCAGATTCTTTATAACT Y 2 1 2 1 303000 f 74 goat 18_7947507_RH-map 18 7947507 T C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320771864 Affx-122923020 AX-385259020 18 7948359 TCAACTAAGTCAAGGGTAGATGAAGTCTAGTAAAT[A/C]AGTAAGCTCATTCTCCATATAAATTGGTGGCATTC M 2 1 2 1 101000 r 74 goat snp38652-scaffold490-275587 18 9879842 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415065 Affx-122949474 AX-123285414 18 7978040 TGAGGGAAGGGAACATTTGGGTGTGCTGTGGGTTA[C/T]GTAAACACCCACTAAATATTGATGCAAGCATAATT Y 2 1 2 1 101000 f 74 goat snp38651-scaffold490-245906 18 9910773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603514 Affx-1002479604 AX-413837680 18 7994743 CACATGGTTTTATTAGTGAAGTCCTCCAAATATTT[A/G]AAGAATCAACACCAATCTTTCTCAAACGTTTTCAG R 2 1 2 1 201000 f 74 goat 18_7994743_RH-map 18 7994743 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38440495 Affx-122929362 AX-123310832 18 8022776 GCTGGGATTATCTTATCTCTTTATTGGTTTGTGCT[A/G]TGTTCTTCTCCACTGGAACTAAGCTTCATGAGGGC R 2 1 2 1 201000 r 74 goat snp38650-scaffold490-201170 18 9956192 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454010 Affx-122919430 AX-123324343 18 8061658 CTGTGCCTCAGCTTCCTCATCTCTAAAATGGGCTT[A/G]ATAACGGTGCCTACATCAGTTTTCATTTGTGATGT R 2 1 2 1 201000 r 74 goat snp38649-scaffold490-162288 18 9996729 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434015 Affx-122934227 AX-123304356 18 8091124 AGTTAATATTCAGACCTCTAGGGTTTGTTCTTTAG[A/C]GTGTTAGGCATCCCTCTCCCAGTGTGTGGTTTTTT M 2 1 2 1 101000 f 74 goat snp38648-scaffold490-132822 18 10026271 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403420 Affx-122957752 AX-123273773 18 8159114 GGAAGGGTAATAATGAGAATTAGAATGTCTGGTTT[A/C]GACTGCTCAAGATTTACCTCCCTGTAAGGTTGAGG M 2 1 2 1 101000 r 74 goat snp38647-scaffold490-64832 18 10094244 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780933 Affx-122978352 AX-385268020 18 8209036 TTTGTCTGCCCTATATCCACCTCCTGTCATTCACA[C/T]GCTTTCAGTCACAGTCCCCTAAACAACTTCCCTAA Y 2 1 2 1 101000 f 74 goat snp38646-scaffold490-14910 18 10143831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772689 Affx-122927896 AX-385259836 18 8243968 CTCTACATATAAATACAAGGTTACTTGTCAACATT[C/T]TTCCATTTAATCTTTATGAGAGTCACTTTATACCA Y 2 1 2 1 101000 f 74 goat snp41916-scaffold546-2652228 18 10177310 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780919 Affx-122930474 AX-385268006 18 8289876 TTTGAAATCTGATCTGAATTTTTATACCTGTAGCA[C/T]ATCATAACTGTTAAAGTGAAAGAGAGTTCTGTAAA Y 2 1 2 1 101000 f 74 goat snp41915-scaffold546-2606320 18 10223219 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399098 Affx-122960870 AX-123269453 18 8364381 GATGGCCTAAATTCTATCACAAAATTTGAAAGTGT[A/G]TCTTCTTACCATTTTAAAATTCATTGTCAAAATTA R 2 1 2 1 103000 f 74 goat snp41913-scaffold546-2531815 18 10298254 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412083 Affx-122951692 AX-123282433 18 8430190 GGTGCTAACCGAGGGAACCTGGGCTGCTTGGCAGA[C/T]TGCAGAAGTCAGCCAGATGAAGACAAGGGAAGGGA Y 2 1 2 1 101000 r 74 goat snp41912-scaffold546-2466006 18 10364230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397308 Affx-122962318 AX-123267663 18 8467411 AGAAGGTGAGCACAGCCAGCCAGGATTATCAGAGC[A/G]TATTAGCCAACCTGCAATTGACCCCAGATACACAG R 2 1 2 1 101000 r 74 goat snp41911-scaffold546-2428785 18 10401207 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780098 Affx-122964061 AX-385267195 18 8512406 TAAATTTGTCAGAAGTCCTTACTCTCGCTTCCATC[A/G]TAATTTCTCCACACCACCATGAAAGACAAAGTGAG R 2 1 2 1 101000 f 74 goat snp41910-scaffold546-2383790 18 10446591 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463528512 Affx-1110030056 AX-515010880 18 8556805 AGGAAGGAACTTGGCTGGCTTGACTGATGGGGACA[A/C]CAAACAAAGTGGGGGTCAGAGACGTAGATCAGAGC M 2 1 2 1 102000 f 74 goat GoatD01.020145 18 8556805 A C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38438651 Affx-122930897 AX-123308988 18 8563747 ACCCAGTGTATTTCAACGGTGGTAGAAAAACACAC[A/G]CATACTTGCCTGAACACCACTAAGGCCGAGTGACT R 2 1 2 1 101000 f 74 goat snp41909-scaffold546-2332449 18 10498737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791236 Affx-122937232 AX-385278230 18 8597597 CTATAAGCAGCAATTAGGCAACAGGAGCTGTTTTC[A/G]CAATGGTATTTGCTCCTGAAGGCATGTCAAGAATA R 2 1 2 1 101000 f 74 goat snp41908-scaffold546-2298599 18 10532216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443274 Affx-122927483 AX-123313611 18 8640986 TCACCAACAATGTTGCAAGTACTCAGTGAATGTTT[A/G]TTAAATAAAAGGAAGGAATGACTGTTTGCTGAGTA R 2 1 2 1 201000 r 74 goat snp41907-scaffold546-2255210 18 10575697 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788787 Affx-122951681 AX-385275802 18 8675031 CATACAAAGCACATAATAAGCACTGTCTCATTTAA[C/T]GTTCCCCAAAGTCTCCTGTGATCTCCATTTGCAGA Y 2 1 2 1 101000 f 74 goat snp41906-scaffold546-2221165 18 10609602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422443 Affx-122943349 AX-123292789 18 8717665 GAGGTCTCTGTTTTCTAGTAAAAAGTCAGCCTGCA[C/T]GTGGAATGGTGATAGGTTTTATGTCGACAGCTAGC Y 2 1 2 1 101000 f 74 goat snp41905-scaffold546-2178531 18 10652045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398615 Affx-122961478 AX-123268970 18 8746844 TAATTTTCTTGCTGATTTTCTCTGGCTTCCTACTG[C/T]ATTTTCCTGCCTTACCCCCTGCAGCACCAAATCAA Y 2 1 2 1 101000 r 74 goat snp41904-scaffold546-2149352 18 10680524 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409338 Affx-122954185 AX-123279689 18 8860972 ACTGAACTGAACTGAGACCTTATGGCCCAAAAAAA[C/T]AAAAATATTTGCTAGCTTGCCCTTTCCAGAAAAAT Y 2 1 2 1 202000 r 74 goat snp41902-scaffold546-2035224 18 10794521 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771445 Affx-122928796 AX-385258603 18 8914999 CTGCCAAAAAAGAGCTGAGTAATCCTGAGCAGAGC[A/G]TCAGTGCTTTCATCTATGAAGTAGGAATTTTATAC R 2 1 2 1 101000 r 74 goat snp41901-scaffold546-1981197 18 10847646 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768859 Affx-122954918 AX-385256036 18 8966121 CAATTCCATTTCTGGAAGACGTACAGAAAGACACC[A/G]TCATCGTGGACATGTCATTATGCGCTTTTCCCCAC R 2 1 2 1 101000 f 74 goat snp41900-scaffold546-1930075 18 10898835 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415417 Affx-122948729 AX-123285766 18 9002524 TCCAAGTGAAGACTGCATGGTATCCTCCCACACTT[C/T]CTGTCTCTTCTCTGCTTTCTGTATAGCCACCTCAC Y 2 1 2 1 201000 f 74 goat snp41899-scaffold546-1893672 18 10935226 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434536 Affx-122934149 AX-123304877 18 9055025 AGCTAATACAGTTTGAGAATTTACCAGCTGGTAGA[A/G]TATGCTCAATGACTGTCTTATTTAATCCTCAGGGA R 2 1 2 1 101000 f 74 goat snp41898-scaffold546-1841171 18 10988257 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419390 Affx-122945610 AX-123289738 18 9096229 CAAATCACACCTGTTTCTCTGGCCTCAGTATTCCT[A/C]TGACCATGGAGAGTTGGCTTCAGTTCAGTTGCTCA M 2 1 2 1 201000 f 74 goat snp41897-scaffold546-1799967 18 11029388 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782399 Affx-122942003 AX-385269475 18 9147594 CAGCTTAACTGTGGTCAACTTGCTTTGGATATGTA[C/T]GTATGTATCCTTCTATCTATGGCACAGTGTGCAGT Y 2 1 2 1 101000 r 74 goat snp41896-scaffold546-1748602 18 11080806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380419 Affx-122975308 AX-123250777 18 9182142 ACTTCTCTTGATGACTGAGAACTTCGGCTTCAAGA[C/T]GAGTATCTCAGTGGTCTCATTCATCTCACTTTAAT Y 2 1 2 1 101000 r 74 goat snp41895-scaffold546-1714054 18 11115584 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785767 Affx-122933731 AX-385272807 18 9220589 TCTCCCACTTGTTAGATTATTAATTAAAGGTCTTG[A/C]TATTATTATCAAATGTTCTTTGAAAAGCTTGCTTA M 2 1 2 1 201000 r 74 goat snp41894-scaffold546-1675607 18 11154240 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801167 Affx-122928839 AX-385288080 18 9257843 CTAGTTCTAAGTTTAATAGATCTATTTTGGTAATA[A/G]TTGTGTGAATTATGTACTCAGGTTTCTGGTTGAGC R 2 1 2 1 201000 f 74 goat snp41893-scaffold546-1638353 18 11192375 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415811 Affx-122948895 AX-123286160 18 9306740 CCTATTTTGCAGTGGTTCCCAGGCATTGAATCCCC[G/T]CAAGTCCCATGGAAGGTCATATCAAGCCCAATAAT K 2 1 2 1 101000 r 74 goat snp41892-scaffold546-1589456 18 11241049 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436302 Affx-122933269 AX-123306641 18 9344113 CAGTCTTCTGGAAACCTCCTGCTCTGCTCTGGCTC[A/G]TCCATGTCTCCCTCTGATGAACTGAAAAAACTTCT R 2 1 2 1 101000 r 74 goat snp41891-scaffold546-1552083 18 11278894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399243 Affx-122960578 AX-123269598 18 9418109 GAGAGAAGGATGCAAGTCCAGGCTGGATGAATATA[C/T]GAGCAAAGACGCGGAAACAGGAAGATACAAGGAAG Y 2 1 2 1 101000 f 74 goat snp41889-scaffold546-1478087 18 11352050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409456 Affx-122954079 AX-123279807 18 9451407 TGCCTCTTAGACACATGCAGCTGGAATAACCTAAG[C/T]GATTTCGGGTTGAGGGACACCAAAATCAAATAAAA Y 2 1 2 1 201000 r 74 goat snp41888-scaffold546-1444789 18 11385008 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277251 Affx-1111835755 AX-519550756 18 9489490 AACTCTGTTCCCCGGAGCCCTGCGTGGGCCCTACT[A/C]TGAGTCACCTAGAAAACCTGGGCCGGTGACAGCTT M 2 1 2 1 102000 r 74 goat Random2.2K-1706 18 9489490 G T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441224 Affx-122929515 AX-123311561 18 9514294 AAAAAAGTTTTGAAGGCCTTGGTGCTGGGCCTGAG[C/T]GCTTAATTAACTAAATGGTACTGACGAGGCCCTGA Y 2 1 2 1 201000 r 74 goat snp41887-scaffold546-1381902 18 11445069 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431574 Affx-122936187 AX-123301915 18 9549018 TGGTTCTGGCCCCAGAATCACCAGCAGAAGTAAAC[A/G]TACAGATTCTCAGGTCCTGACACTGGAGTTTGGTC R 2 1 2 1 101000 r 74 goat snp41886-scaffold546-1347178 NW_017204686.1 3855 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445198 Affx-122925524 AX-123315535 18 9586907 ATCTGCAGCAACCTCCTCTCCACCTGCTCTGTTGA[C/T]GGCATTGGGTGCCTTTGCATGGTTCCTCAGACTGG Y 2 1 2 1 201000 r 74 goat snp41885-scaffold546-1309289 18 11537167 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434428 Affx-122934666 AX-123304769 18 9637171 ACCACAGAGTGACCTGCCCCATGCTGGGGTTGCTG[C/T]GGGGCAAGTTTTTCTTTAGTCTAATATCTAGAAAT Y 2 1 2 1 202000 f 74 goat snp41884-scaffold546-1259025 18 11588400 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402634 Affx-122958394 AX-123272987 18 9672467 ACTCCACAGCGATGAGAATGAGCAGATTCGGCCTC[A/G]TGCAACAATATGGAGAAATATCCAAATACAGTATG R 2 1 2 1 101000 r 74 goat snp41883-scaffold546-1223729 18 11624203 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389186 Affx-122969081 AX-123259544 18 9735051 GGTGGGTGAGGCATAGATGTTGACGCTACCTCCGC[C/T]CTTCCCTGTAGCTCCCAGGTGACCTTCGGTGAGTT Y 2 1 2 1 201000 f 74 goat snp41882-scaffold546-1161145 18 11686551 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437310 Affx-122931969 AX-123307648 18 9797288 AACCGCCCCATGTAGAAGCATGTTCACAAGGCAGA[G/T]GGGCTCAGGACTGACGGTGTCTCAGCTTCCTAGCC K 2 1 2 1 101000 f 74 goat snp41881-scaffold546-1098908 18 11745209 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440613 Affx-122929973 AX-123310950 18 9855187 TCCTGTCCACAGCTGGGGATGGGAAGCAGTGGTTT[A/G]TTCTCCCCTGAGGCCTTTACGGATAAGTCAGAGAT R 2 1 2 1 101000 r 74 goat snp41880-scaffold546-1041009 18 11801703 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446183 Affx-122925734 AX-123316519 18 9887393 CGATACTGAAATATGATATAACTTGCCAGCTCTTA[C/T]AGTCTCACATGTTTCTTAAGGGAAATTATCAATGT Y 2 1 2 1 101000 f 74 goat snp41879-scaffold546-1008803 18 11833957 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394724 Affx-122964333 AX-123265079 18 9916796 CAGGCCAGGAAGATGGGCAGCTGTCCCAAAAGCAC[A/G]CAAGGCTCTGCTGATTAAGTGTAGCTTTCCCAGCA R 2 1 2 1 101000 r 74 goat snp41878-scaffold546-979400 18 11864422 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378422 Affx-122976778 AX-123248781 18 9951450 CGGTGATGCTTATCCCTTCCTGGGGCATCAGTCCC[A/G]TCTGCTGGTTCTAAGCTGGGTTGCAGGGCAGGCTG R 2 1 2 1 201000 r 74 goat snp41877-scaffold546-944746 18 11898552 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441887 Affx-122928621 AX-123312224 18 9982106 CGAGTTCATCAGTTAGAAATGGTTTTGCCTGCAAG[C/T]AACAGTGGCTGAAAATAACGTGACTTAACCTAGAA Y 2 1 2 1 101000 f 74 goat snp41876-scaffold546-914090 18 11928912 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449215 Affx-122923501 AX-123319550 18 10015836 CAGATAAGCCACTCTGGATCCCTGTGACACCAGAC[A/G]CCATCTGTGCAGGAAGCACTGTTTGGTTTCTAGAT R 2 1 2 1 101000 r 74 goat snp41875-scaffold546-880360 18 11962605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277253 Affx-1111835756 AX-519550758 18 10102275 TCAACTGCTGTTGTATTTCCATCTTTCTTTATCAA[A/G]CAGAATGATCTTTAAACTCAGGAGGCTTGAATAAA R 2 1 2 1 101000 r 74 goat Random2.2K-1708 18 10102275 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415608 Affx-122948604 AX-123285957 18 10102832 GTGAGGAATAATGGCTTATACGAGGCAGTGACCCT[A/G]CAGCACCTCTGACTTGGAACATTTTTCGGAACAGA R 2 1 2 1 101000 f 74 goat snp41874-scaffold546-793364 18 12049364 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423768 Affx-122942840 AX-123294114 18 10145279 TTATGTGACTTCAGTTCTTCTCAGTTTGTCAAGGC[A/G]TGCTTTATGGCCTAACATATGGTCTGTTCTGAAGA R 2 1 2 1 101000 f 74 goat snp41873-scaffold546-750917 18 12091788 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393710 Affx-122965245 AX-123264065 18 10203875 TGAGGTGTGAGAAGCCTCCCTCCTCCTCATCTAGG[C/T]GGGATGCAATACGATTAAGCCATTTTACAGATGTG Y 2 1 2 1 101000 r 74 goat snp41872-scaffold546-692321 18 12150483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272006 Affx-1111833109 AX-519545774 18 10206207 TCCTCCATCCGTGGGATTCTACAGGCAAGAATACC[A/G]GAGTGTGTTGCCATGCCGGTCTCCAGGGGATCTTC R 2 1 2 1 103000 f 74 goat 18_10206207_AF-PAKI 18 10206207 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387162 Affx-122970631 AX-123257520 18 10232604 GAAAGTTTTCTCCTTTTAGTGACTGATGAACTCCT[A/G]TTCATCCTTCACAACCCTGATTTTTTATCCCATTC R 2 1 2 1 101000 r 74 goat snp41871-scaffold546-663592 18 12179301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775773 Affx-122960484 AX-385262904 18 10266400 ATTTACGCTTATCTGCAGTGTGAGGTACGGATCCA[C/T]CTTTGGTTTGATTTCTAATAGCTAATTATTTCATT Y 2 1 2 1 101000 f 74 goat snp41870-scaffold546-629796 18 12213029 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767763 Affx-122969332 AX-385254990 18 10332395 ATTATCACTGAGGACACTCAAGGGCTATTTGCCTT[A/G]CACTAATCTGCCTCAGATATCCCCAAACAAATGTC R 2 1 2 1 101000 f 74 goat snp41869-scaffold546-563801 18 12271810 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450826 Affx-122921792 AX-123321160 18 10373249 ATTGAGGAAGCACAGAAAATAATTTTCCCATTTAT[C/T]AAAAAGTGAAACGTGACCAACTCAAAAGAGAGGCC Y 2 1 2 1 103000 r 74 goat snp41868-scaffold546-522947 18 12312300 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406280 Affx-122956082 AX-123276632 18 10404083 AAGCAGTCCATCTAGCAGTCACAGGAGAGCCAGGA[C/T]ACCTGGATCAATATCCATAGACTGACTCATGGCTA Y 2 1 2 1 103000 f 74 goat snp41867-scaffold546-492113 18 12343824 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427073 Affx-122939801 AX-123297416 18 10436373 TGGTCTGTCCTGCCCACACCACGGAAGAGTGTTCG[A/G]CCACAAAAAAGAGCCCAGCACGGACACAGGCTCCA R 2 1 2 1 202000 r 74 goat snp41866-scaffold546-459823 18 12376868 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379801 Affx-122976239 AX-123250159 18 10474221 TAAACACACACACAGAAACCCAGTGGGATAAAATA[C/T]GCTACATGGCCTATAGGGGTGGTTTCTGAGTTATA Y 2 1 2 1 201000 f 74 goat snp41865-scaffold546-421975 18 12415004 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430554 Affx-122937019 AX-123300895 18 10524806 GCCCCCAGCTGGCTATTTTATGCCAGCTTTCCAGG[C/T]AATTCTGAAGGACCTGGAGGCCTAGGACCCCAGTG Y 2 1 2 1 102000 r 74 goat snp41864-scaffold546-371390 18 12465589 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390383 Affx-122968182 AX-123260740 18 10573736 TTTTCTTCCCTGTGCATTATACCTGCTCTCAACTC[C/T]TGTTTCCCTCTGGTTTCTTTCTGGGGCTCTGTCTC Y 2 1 2 1 101000 f 74 goat snp41863-scaffold546-322460 18 12514191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418509 Affx-122946429 AX-123288857 18 10612553 AAGATCTCATCAGTATCAGAGACCCTGGAGAAAAC[A/G]GCCGCTTCCAAAGTTCTGCCTTATGATTTTCAATG R 2 1 2 1 201000 r 74 goat snp41862-scaffold546-283643 18 12553325 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444596 Affx-122926955 AX-123314933 18 10658109 AGGAAATTGAGAAAGGTGACTTTCCCAAGGTCACA[G/T]AGAGCTAAGGGGCCAACCCCAACTCAGCTCTGTGT K 2 1 2 1 201000 r 74 goat snp41861-scaffold546-238087 18 12598563 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424063 Affx-122942057 AX-123294409 18 10701456 GCCTGAGTTCATGCAGCCAGAAAAAGAACTATCGA[A/G]AGCGGGCCCGGCTGAGGACAGCGCGTGGGTCACTT R 2 1 2 1 101000 f 74 goat snp41860-scaffold546-194740 18 12641251 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443370 Affx-122927411 AX-123313707 18 10732739 AGCCTATACATACAAAGAGGACTGTTATTCAGTCA[C/T]GAAAAGGAGCAAAGTGCTGACACATGCTAAGCGTG Y 2 1 2 1 201000 f 74 goat snp41859-scaffold546-163457 18 12671804 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446344 Affx-122925614 AX-123316680 18 10814836 TTTCCAGTGAGTCACTGGCTGAGACGCCGGTGCTG[A/G]AGCTAGCCATGGACTGACCCTCCTGAACTCTCCCT R 2 1 2 1 201000 r 74 goat snp41858-scaffold546-81360 18 12749267 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433085 Affx-122935729 AX-123303426 18 10854559 TCAGGAAAGCCCGGATGATTTTATTTTCCTTGAGA[G/T]AACTACTTAATGTCATTTGACTTAGGTACCAAGCA K 2 1 2 1 201000 r 74 goat snp41857-scaffold546-41637 18 12788768 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427255 Affx-122939552 AX-123297598 18 10925198 GAGGACTGCCAGAGGGGAAATGAAGCCGCGGCAGC[A/G]TCCACGGGTGGCTGTTCTAAGGAGGGGTAGTCTGC R 2 1 2 1 201000 f 74 goat snp904-scaffold1023-2462266 18 12859787 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449739 Affx-122922463 AX-123320074 18 11001088 GAGTGCGTGCCCCAGGCACAGTGTAGTCCTCACCT[C/T]ACCACCCCCACTGCAACAGGTCTGGGAGTTTCTGG Y 2 1 2 1 201000 r 74 goat snp902-scaffold1023-2386376 18 12933069 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438525 Affx-122931199 AX-123308863 18 11057292 ACCTTGGGAAAGTCCCCTCGCTGCCTGACCTGCTC[C/T]GTGAGCGCCCAGGCGGCGTGTGAGAAAGCGGGCCC Y 2 1 2 1 303000 r 74 goat snp901-scaffold1023-2330172 18 12989973 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444408 Affx-122926582 AX-123314745 18 11114410 CCCACACAGAGATGTCCAAGGGGCATCTCGACTCC[A/G]GGGGCTCAGGCACGGACCAGAGCAACAAGAATGTC R 2 1 2 1 202000 r 74 goat snp900-scaffold1023-2273054 18 13040648 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418940 Affx-122946501 AX-123289288 18 11165318 ACCCCTCACCCACTAGGGATGGGAGTTAGCAGATA[C/T]ATTCCCCACCTCCCTTGTTCTTCTTCCTGGTGCTG Y 2 1 2 1 201000 f 74 goat snp899-scaffold1023-2222146 18 13091325 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449338 Affx-122922982 AX-123319673 18 11263571 CTGGTCAGGGTTCCGGGCCCACAAAGAGCATGGCT[C/T]TCCAACTCCATGCTTGGTGACTCCACGTGAGTCTC Y 2 1 2 1 101000 r 74 goat snp898-scaffold1023-2123893 18 13190280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390026 Affx-122968443 AX-123260383 18 11298894 ACCTTTACCTCTGGGAATGGGTGCACAGCTGACTC[A/G]TCAAGGGGCCCAGGGGCCTCCAACACAGGATCCGC R 2 1 2 1 101000 f 74 goat snp897-scaffold1023-2088570 18 13225681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433200 Affx-122935636 AX-123303541 18 11412067 TGGAATCAAACCTGCAATCAAGTCTGATTCAAGTC[A/G]TATCCTAGCTGTGTGAGCTTGGGCAAGTGATGGGG R 2 1 2 1 101000 f 74 goat snp895-scaffold1023-1975397 18 13339044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402386 Affx-122959027 AX-123272739 18 11474088 CTGTATTGGAAGTGCCAAGTCTTAGCCACTGGACC[A/G]CCAGTGAAGTCCCTTGAGTGGTCCTTACAAAAATG R 2 1 2 1 103000 r 74 goat snp894-scaffold1023-1913376 18 13399151 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418169 Affx-122947086 AX-123288517 18 11530367 GGGAACAGATCGGTCTCTGTGTTCTGTATTTCCTG[C/T]AGTGCGAAGCTTCGCCTTTTATTTTTAATAGCACT Y 2 1 2 1 201000 r 74 goat snp893-scaffold1023-1857097 18 13455231 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441034 Affx-122928939 AX-123311371 18 11665767 GTAAAGACGCAATCAGCCCAGAGCCCACTGCGCTG[C/T]GATAATCTGATGTAAGCCAGGCGCTGATTTATACG Y 2 1 2 1 101000 r 74 goat snp890-scaffold1023-1721697 18 13590683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377869 Affx-122977268 AX-123248228 18 11701277 CGTGATCCCCTGCAGGACACTGCAGAGAGATGGCT[C/T]GAATGAAAGAGGACGAGGAGGAGGAGGTGTCAGAA Y 2 1 2 1 103000 f 74 goat snp889-scaffold1023-1686187 18 13626437 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420577 Affx-122945270 AX-123290924 18 11730877 CCGGGTTGGAACAAGATCTTCACTCTGGCCTGTCC[C/T]GGGAGCGAAGGCATTTGGAAAGGTGTGTTAGTGAG Y 2 1 2 1 201000 f 74 goat snp888-scaffold1023-1656587 18 13655931 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451285 Affx-122921304 AX-123321618 18 11852008 GAGGGTTTGACTGACAGGGAGTAGAACAGACTTCC[A/G]GCAGAGACCAGAAAATGCAGAGCTCCCAGCAGGAA R 2 1 2 1 101000 f 74 goat snp886-scaffold1023-1535456 18 13774641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447452 Affx-122924368 AX-123317788 18 11933814 ATAAAAGGAAGCACCGAGTGCTTTAGAAACACACA[A/G]CAGGGAGAGACAAACAGCCTGGGATGGAAGATTTA R 2 1 2 1 101000 f 74 goat snp884-scaffold1023-1453650 18 13855860 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391048 Affx-122966858 AX-123261405 18 11980215 GAGTCCTTGCCGTGAGCTTTTTGGTCTGGTGTCAG[C/T]GTCCCCAGGGACCACTCTGAATCAGGCGGAATGGC Y 2 1 2 1 101000 f 74 goat snp883-scaffold1023-1407249 18 13902076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382605 Affx-122973711 AX-123252963 18 12016279 TGTTCTGACTTCAGTAGAAGGAAGTGGGCACGTAA[C/T]GTTTTGAGATGGCTCTTCCTTTGCCACCAAGCTTC Y 2 1 2 1 101000 f 74 goat snp882-scaffold1023-1371185 18 13938149 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403962 Affx-122957442 AX-123274314 18 12054423 AGCTGTGGGCACCCCCCATGCAATCGGGTTGATGC[A/G]TCTTTCCCAGCACATGACGTGCACACACCTGCCAC R 2 1 2 1 101000 r 74 goat snp881-scaffold1023-1333041 18 13975321 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422226 Affx-122944023 AX-123292572 18 12103860 GGTGCGGGCGGCTGAGGGTGGCCCAGGTTAATAAA[C/T]GGGGTGACTAGGGTGCCCACCCACAGCCTTTAGAT Y 2 1 2 1 201000 f 74 goat snp880-scaffold1023-1283604 18 14024462 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398652 Affx-122961895 AX-123269007 18 12147123 TACGGCATAAGGATCTTTTCTGTTTGTGAAATTCC[A/G]AAAGTAACCTTGGCTCACCACGTCTGTCTGCCGTT R 2 1 2 1 101000 r 74 goat snp879-scaffold1023-1240341 18 14067827 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447291 Affx-122924924 AX-123317627 18 12176866 GGGTCCGGTCTTAGAGTGTGAAGTGTTTTCCAAAC[G/T]CATTAGGTCATGGAGCTCTTCTTCATGGAGTGTTC K 2 1 2 1 101000 r 74 goat snp878-scaffold1023-1210598 18 14096377 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277257 Affx-1111835758 AX-519550762 18 12200066 AATTAGAGTATGGACATCTTTGGGGGCCACTGTCT[A/T]GCCAGCCAGAGTCATTTAATCCTCACTTTATTTCG W 4 1 2 1 202000 r 74 goat Random2.2K-1710 18 12200066 A T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785989 Affx-122948619 AX-385273025 18 12220488 GCTGTTGCAGGATAGCTCCTGTTCTCCAGCAATAC[A/G]TGGAAACTTTCTAGAAATTGCTTGAATATGGATAG R 2 1 2 1 101000 f 74 goat snp877-scaffold1023-1166976 18 14139562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403141 Affx-122958104 AX-123273494 18 12262896 TATGCCTGCTCTGGGCTCAGAACCACCTGCTTGGC[A/G]CTCCAAACCTTACTTTACCACAGTTTATTTTTTTA R 2 1 2 1 101000 r 74 goat snp876-scaffold1023-1124568 18 14181682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434724 Affx-122933928 AX-123305065 18 12294874 GTTTAGTTTAGTCCTACAAGGACCGTTTCATGGCT[A/G]TGAAGTGGAATGTGGAATGGAGCAGAAGCGTACAT R 2 1 2 1 201000 f 74 goat snp875-scaffold1023-1092590 18 14207660 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392185 Affx-122966295 AX-123262542 18 12332620 GTTAATTACTACGTGATTACCAGCACAGAGCCTGA[C/T]CTCAGGTTACTGGGGCTCACATGCCAGCTATGCAT Y 2 1 2 1 101000 f 74 goat snp874-scaffold1023-1054844 18 14245044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420228 Affx-122945530 AX-123290576 18 12388879 CAGTAGGCAGCTCTAAAAGATAAAGACTCAGAAAA[C/T]AGAGCCACAAAGACCCACAGTTGCCCTAGAAACAA Y 2 1 2 1 101000 r 74 goat snp873-scaffold1023-998585 18 14301351 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415713 Affx-122948521 AX-123286062 18 12456705 TGTGAATTTATTCAATGCTTTCTCCAGAAACCTCA[C/T]GGTACTTTTTAAACTATCACATAATCATTCTAGAA Y 2 1 2 1 101000 r 74 goat snp872-scaffold1023-930759 18 14367383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391890 Affx-122966963 AX-123262247 18 12520148 TCCTGAAAAAGCAGCCTGGTTAAATCTCTGTTTAC[A/G]TTTCTTTTTTAAGATGTTGTGTTTTGTTTTGAGCT R 2 1 2 1 103000 f 74 goat snp871-scaffold1023-867316 18 14430468 A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410067 Affx-122953218 AX-123280417 18 12551921 CCGCTTTTGAAGGCAAGAATTGGCAACAGTTTTTC[A/G]TGTGTGTGTGGCTTGCTTGTAAGCAGCTGAAATGT R 2 1 2 1 101000 f 74 goat snp870-scaffold1023-835543 18 14462618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395604 Affx-122963819 AX-123265959 18 12580426 CATACTCTGAAATACAAACTAATAAGATGGATGGA[G/T]GAGTGGATAGATGGATGGATAGACAGATGAAGGAT K 2 1 2 1 303000 f 74 goat snp869-scaffold1023-807038 18 14490598 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784664 Affx-122978263 AX-385271712 18 12612211 TCCTCCCACTATATGCCATCGTCGTGTGTGTCCCA[C/T]GAAATTTCCATAAAGATGGTCATACCATTCAAATC Y 2 1 2 1 101000 f 74 goat snp868-scaffold1023-775253 18 14523172 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388873 Affx-122969312 AX-123259231 18 12681515 AAACCCCCCCGGCCCTCAAACAACAGACAGGGAGA[C/T]GTTATCACCTCCTCTATGAAATTAAGTGGGATGAA Y 2 1 2 1 101000 r 74 goat snp867-scaffold1023-705949 18 14591756 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385356 Affx-122971645 AX-123255714 18 12738748 TGGGGTGCAGGGCATGGCCTGAATCCCACGACCTC[A/G]CCCCAGCATGTGGTCTTTACCTTTCAGGGTCAGGA R 2 1 2 1 101000 r 74 goat snp866-scaffold1023-648716 18 14647304 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791726 Affx-122956618 AX-385278717 18 12779583 AGCCCATATTCTGTTTGTGAAGTGTTTCTCTTTGA[A/G]TAAATCCACTTCTTAGTTATCAGTTTGTCTCTCGC R 2 1 2 1 101000 f 74 goat snp865-scaffold1023-607881 18 14688457 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428139 Affx-122939056 AX-123298482 18 12810278 GTTCTCCATGTGGGTCCTCTGGACAGCACCAGAAA[C/T]GGTGGGTTCTCGGGCCTGCCCAGTCAGATGCTCTG Y 2 1 2 1 101000 f 74 goat snp864-scaffold1023-577186 18 14719375 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272008 Affx-1111833110 AX-519545775 18 12820079 CGTGCACACACGTACACACAGTTCCGAACATGTAT[A/G]CATGCCATCTCTCTCTCACACACACACACACACAC R 2 1 2 1 201000 f 74 goat 18_12820079_AF-PAKI 18 12820079 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38409406 Affx-122954136 AX-123279757 18 12853236 CCAGAGAACACTTAGAGCATCAGATCATCAGATGC[A/G]CTAAGATGTTAAATCCCAGGGGGGCGCCGAGAACA R 2 1 2 1 202000 r 74 goat snp863-scaffold1023-534228 18 14762585 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433880 Affx-122934415 AX-123304221 18 12893307 ACAAGAGCAAGACAGCCGAGAGGGAGATGAACGAC[C/T]GTAATCTTGAAATGATGGAAACTTAGGCCATGCTC Y 2 1 2 1 101000 r 74 goat snp862-scaffold1023-494157 18 14802609 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400580 Affx-122960408 AX-123270935 18 12954514 GACAGAACAGCAGAGTGCCAAAGGGTGATGCTGTT[G/T]TCATTTACTTACTGTAGTGAGTGACAAGGCCCTTT K 2 1 2 1 101000 r 74 goat snp861-scaffold1023-432950 18 14862119 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432219 Affx-122936372 AX-123302560 18 13005877 TTTTAAGTAGAACCCCTAAAATCCATTCCCCTCCA[C/T]GGTCATTATCAGTTCATCAAATAATAAAAAGGACA Y 2 1 2 1 201000 r 74 goat snp860-scaffold1023-381587 18 14912897 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387329 Affx-122970498 AX-123257687 18 13069814 ATCACACATTTACTTATTTTATGGATGTTTCCTTA[C/T]ATTACACAGAGGGCACAAGAGCCCGTGCAGTAGCA Y 2 1 2 1 101000 f 74 goat snp859-scaffold1023-317650 18 14975578 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277259 Affx-1111835759 AX-519550764 18 13127279 GGGGTGGGGGCAGGGGGGAGGAAGATCTTGCAGCC[A/G]TCTTTACCTTCCCATTGTGATCAACAAACGATTGT R 2 1 2 1 101000 r 74 goat Random2.2K-1711 18 13127279 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388479 Affx-122969236 AX-123258837 18 13148327 AAAACACCGAATCCCACGTCTGCTGCCCAGGAAAC[C/T]GCTCCTCTTGGGTCAGTGTGAAGCAGACTACAGGA Y 2 1 2 1 201000 r 74 goat snp857-scaffold1023-239137 18 15053358 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399565 Affx-122961125 AX-123269920 18 13201969 AAGAGAGTGCTGGGGTCCAAGTGGACCATATGGAC[A/C]GCGTTAGCAACAGGCACCAGTGATTCCCCGGATGG M 2 1 2 1 201000 r 74 goat snp856-scaffold1023-185495 18 15107046 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391947 Affx-122966921 AX-123262304 18 13273794 AGCCCTGCTGACGCTGCAGAACCCCCGATTCTCCA[A/C]GTCCGTCCACGCGGAGGGCAGGAGGCAGCGCCATG M 2 1 2 1 103000 f 74 goat snp855-scaffold1023-113670 18 15175544 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787995 Affx-122935146 AX-385275016 18 13317255 ACCACGTGATTTGGCCTTGTACCTGCCCTGTACTA[C/T]GTGATTTGGCCAGGACCTAGCCTGTTTACCTGCTG Y 2 1 2 1 101000 r 74 goat snp854-scaffold1023-70209 18 15219243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763464 Affx-986697993 AX-385251336 18 13345145 CTAAGAAACAACAATCTTGTTCCTCCCTCTCCGAT[C/T]CAACCTGCTACTCTTATGCAGGGAGAGCACAGAGG Y 2 1 2 1 600010 f 74 goat 18_13345145 18 13345145 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 320803415 Affx-986696329 AX-385290246 18 13345167 CTCCCTCTCCGATTCAACCTGCTACTCTTATGCAG[G/T]GAGAGCACAGAGGCCCAGAGAGGGCACGTGCCTTG K 2 1 2 1 600010 f 74 goat 18_13345167 18 13345167 Ancestral_priority_1043 ancestry 0.532 neutral IMAGE 10K 10K ancestral 38394634 Affx-122964398 AX-123264989 18 13400847 TGGGAAAAGTTTGTTTCTTTAAAAAACCAAACATG[C/T]AACCACTCTATGGCCTAGCAAGTGTACTCCCAGGG Y 2 1 2 1 101000 r 74 goat snp42285-scaffold5561-13284 18 15301856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396330 Affx-122963069 AX-123266685 18 13466685 TGCCTCCAAAGGCTCAGGAGGAAGATGTGAGCAGG[C/T]GGGGCCTGAGAAGACCAGGGCTGTCCAGTGAGCCG Y 2 1 2 1 101000 f 74 goat snp42286-scaffold5561-79122 18 15363949 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427775 Affx-122939230 AX-123298118 18 13560073 CCTTGTTTATTCTCAATCACCCAGCAGACTGTCAG[C/T]CCACAGGGCAGGGCTGGCAAGGCCTGTTCCCCTCC Y 2 1 2 1 101000 f 74 goat snp42288-scaffold5561-172510 18 15457341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388737 Affx-122968961 AX-123259095 18 13567300 TAATCCCCCACCCACTGGGAGAGCAGTGGTAACCC[A/G]TCAGCTGATTGCTTCAAATCTGCTGCTGGGCCGGA R 2 1 2 1 303000 r 74 goat snp28476-scaffold3031-190741 18 15464429 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445471 Affx-122925212 AX-123315808 18 13624674 CGACAGATGCCGTTCCACCCCTCCACCACCACAGC[A/G]TTTTCTAGACCCAGGGTCAGGACCCGATATTCTAA R 2 1 2 1 101000 r 74 goat snp28475-scaffold3031-133367 18 15521154 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407393 Affx-122955255 AX-123277744 18 13658191 TCTGCTAACTCACTTTTCCTGACACTTTCTTGCCC[C/T]TCACCTGGCACAGACTGCATGGGGGAGGTTGGACG Y 2 1 2 1 101000 f 74 goat snp28474-scaffold3031-99850 18 15555229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449909 Affx-122922330 AX-123320244 18 13726818 TGTTTTGAGGTTGTAAACACTGGCTACTAGCCCAC[A/G]AAAGGTCTCAGCTCACTGTCTCCCATCCTAATAAA R 2 1 2 1 101000 r 74 goat snp28473-scaffold3031-31223 18 15623917 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387039 Affx-122969916 AX-123257397 18 13833927 GTTACAAGTTCTGACTAGAGGCGAAACCCCCAGGC[A/G]TAGGGGCATAAAGCAGGAATGGACAGACGCCTGTG R 2 1 2 1 101000 f 74 goat snp27343-scaffold2904-5676 18 15731287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386173 Affx-122971379 AX-123256531 18 13844908 GACGGGCGGGAGGTGCACCCCCCTGACCGGCACCG[A/G]AAGCACTCAGCCGACAGGCAAGCCCATGCTGAGAA R 2 1 2 1 102000 r 74 goat snp56020-scaffold873-367940 NW_017189517.1 27073675 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435554 Affx-122933384 AX-123305894 18 13881438 TTTCATCATTTGGAGGAGAGATCTTGTGTGTGAGT[A/G]TGTTTACACATGTGTACATACATGCAGAGATGGGC R 2 1 2 1 202000 f 74 goat snp56019-scaffold873-331410 18 15776603 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446829 Affx-122925276 AX-123317165 18 13940905 TAACAAGGTAAACACAGTTTATAAGTTGAGGTTAT[A/G]CAGAAGCAAGTATTAAGTGCTGATGAATCTAGGAA R 2 1 2 1 101000 r 74 goat snp56018-scaffold873-271943 18 15835471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791004 Affx-122972696 AX-385278001 18 13992967 AATATGAGGAACACCTCATGTCAGTGACCGCCTGG[C/T]AGTGTGTTACTGTAACACAGGTGTCTTATATGAAA Y 2 1 2 1 202000 f 74 goat snp56017-scaffold873-219881 18 15887136 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774060 Affx-122950662 AX-385261198 18 14031354 CCTTTCACTTAAAGCATTGGATGATCCATGCATTA[C/T]GTTAGGTGTGTGATTGAAATATGTCATTCGGAAGT Y 2 1 2 1 101000 f 74 goat snp56016-scaffold873-181494 18 15924390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409219 Affx-122953162 AX-123279570 18 14084483 GGGATCTGCTGTGGCTTGGGGCAAGAATCCATTTC[C/T]TCCTCTGGGAAGCAGACAAAAGAATAGTCCAGCAT Y 2 1 2 1 101000 r 74 goat snp56015-scaffold873-128365 18 15977631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277136 Affx-1111835760 AX-519550642 18 14116977 TTGCCTTCAGCTGTGAAGAGGGAAGCACATCTCAC[C/G]CCCGCCCCCTCGCCCCGGCTGTTTGCTGGCAGAGA S 4 1 2 1 102000 f 74 goat Random2.2K-1712 18 14116977 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419371 Affx-122945625 AX-123289719 18 14149288 ATAACAGTGAAGTCCGCTGTGTCTTCCTTTCACAG[A/C]TTCTCTCTCCGTGGCCTGCAGTGCTGGGTAATAAC M 2 1 2 1 102000 r 74 goat snp56014-scaffold873-63560 18 16041947 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413220 Affx-122950253 AX-123283569 18 14190132 TACCTCATTTGTACAATGGGGACAACATGACCTGC[A/G]CAGACAGTATGGCACACAACATCACAACAGTGCCT R 2 1 2 1 101000 f 74 goat snp56013-scaffold873-22716 18 16082409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274278 Affx-1111834107 AX-519547875 18 14242417 TCTCC[A/G]TGATTCCCATGGCTGCAGCCCAAAAGCAACCTCCA R 2 1 2 1 102000 r 74 goat GoatD01.018847 18 14242417 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38423821 Affx-122942797 AX-123294167 18 14263427 AGTTGGGTGACACTCAGGAGTGTTGTCGACCAGGA[C/T]AGGGTTTCCCCTGGGGCTGGTCACATGTCAGTCTT Y 2 1 2 1 201000 f 74 goat snp59698-scaffold99-50480 18 16155381 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441937 Affx-122928582 AX-123312274 18 14308130 TCAGTCCTAGGTGTTGGTCAGAGACTCTGGTTTGT[A/G]GACATGGCACCAACAGAAGCTTCCCGAGACACTGC R 2 1 2 1 101000 f 74 goat snp59699-scaffold99-95183 18 16198866 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763433 Affx-986697962 AX-385251315 18 14387109 CTTTCAAGAAAATAGTTTTGTCTTTATTATTCTAA[G/T]TGCTAGCTCCCATTTTCTCAGTGCTCTTTAGCAAT K 2 1 2 1 600010 f 74 goat 18_14387109 18 14387109 Ancestral_priority_1043 ancestry 0.61 recommended IMAGE 10K 10K ancestral 320766415 Affx-986697966 AX-385253791 18 14387119 AATAGTTTTGTCTTTATTATTCTAAGTGCTAGCTC[C/T]CATTTTCTCAGTGCTCTTTAGCAATTAGAAGTTTT Y 2 1 2 1 600010 r 74 goat 18_14387119 18 14387119 Ancestral_priority_1043 ancestry 0.696 recommended IMAGE 10K 10K ancestral 320766418 Affx-986697968 AX-385253794 18 14387504 TCTGAGGAAATGCCAAATGCTCTTTTAGGCTCACT[A/G]ACTGTGGTTGCTTCTGGAGAGAAATTTCATCAGAG R 2 1 2 1 600010 r 74 goat 18_14387504 18 14387504 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320763441 Affx-986697970 AX-385251323 18 14387541 CTGTGGTTGCTTCTGGAGAGAAATTTCATCAGAGA[C/G]AATACTGCTAGCAAATATTCCCAAGCTCAAGTATG S 4 1 2 1 600010 f 74 goat 18_14387541 18 14387541 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 320803991 Affx-986696330 AX-385290685 18 14387548 TGCTTCTGGAGAGAAATTTCATCAGAGACAATACT[G/T]CTAGCAAATATTCCCAAGCTCAAGTATGGGACTCG K 2 1 2 1 600010 r 74 goat 18_14387548 18 14387548 Ancestral_priority_1043 ancestry 0.734 recommended IMAGE 10K 10K ancestral 38433711 Affx-122934529 AX-123304052 18 14443108 ATTGCGTCTACTTCATGGAGGCCTGACACAGGGTG[A/C]GCATTCAATAATGGCCCACTGTTGTCATTTTGACC M 2 1 2 1 101000 r 74 goat snp59701-scaffold99-230161 18 22335031 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277263 Affx-1111835761 AX-519550768 18 14473848 TCACTAAGGTCTCCTGAGGTTGGGGCTGGTGCGGC[A/G]CCCATGCGGCGTTGTCTGTAGTCAGCGCTGCTGTC R 2 1 2 1 303000 r 74 goat Random2.2K-1713 18 14473848 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424307 Affx-122941967 AX-123294653 18 14481850 TCTTTTCCCATTTGTCATCCTAAAAAAAGAAAAAA[C/T]AGTTTAAATTACCTTAAATTCAAGATTAACTTAAG Y 2 1 2 1 303000 r 74 goat snp59702-scaffold99-268903 18 22296232 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795489 Affx-122929785 AX-385282444 18 14531916 CTCTGGGGGACAATTGTTTTTAAGATATGTTTTAC[A/G]TCCATGGTTCCAAAGAGTTCTGTTGTAAACAAAAT R 2 1 2 1 101000 f 74 goat snp59703-scaffold99-318969 18 22246313 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417862 Affx-122946771 AX-123288210 18 14575108 TGCATGATGAAATCCACCACCTTCGAGTTCTGGAG[A/C]ACGGTCCCCACCAAGGCAATGGCCTTGTCCACAGC M 2 1 2 1 101000 f 74 goat snp59704-scaffold99-362161 18 22203029 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793077 Affx-122949762 AX-385280055 18 14665092 TTCATCTCTCTGGAACCCACTTTACTTGGACCTTT[A/G]CATGACGGACTCCTAAGCATCTTTCACATACACAT R 2 1 2 1 101000 f 74 goat snp59705-scaffold99-452145 18 22112684 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792810 Affx-122961401 AX-385279788 18 14710722 TATTTTGATAACCAAGATTACATTACACCAAGTCA[A/G]CCTGGAAGGAAAAAATCGTAATCCTTCATTTCCTG R 2 1 2 1 101000 r 74 goat snp59706-scaffold99-497775 18 22065752 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770130 Affx-122960899 AX-385257297 18 14788755 GAAAAGGGAGAAACCTTCACAAATGCCTCCAGAAA[C/T]AGCTCCATAGCCATGTCTGAAACCATCAGTATTTA Y 2 1 2 1 101000 r 74 goat snp59707-scaffold99-575808 18 21987013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433160 Affx-122935668 AX-123303501 18 14835781 AAATCTATTCCTTCAAACAGGAGAGCCTGGAGTCC[A/G]CTGGAGGCCCAGAGAGGGCCCATCCTTCTGACTTG R 2 1 2 1 101000 f 74 goat snp59708-scaffold99-622834 18 21939829 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800633 Affx-122954266 AX-385287552 18 14883084 GTGTATATATTGCACATACACAGTACAGTGTTTCT[A/G]TGAACTGTGTTACAGTCTCATTTTTGTGCATGTTC R 2 1 2 1 101000 r 74 goat snp59709-scaffold99-670137 18 21894816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801131 Affx-122974345 AX-385288045 18 14957910 CTCAAGGGCAGTTTAATAGATTCTGGGGTATGTCT[A/C]GTATTTCAGCATCAAGTTGAGCAAACAGAACTGCA M 2 1 2 1 101000 f 74 goat snp59711-scaffold99-744963 18 21819526 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433135 Affx-122935688 AX-123303476 18 14989332 CAGCACTGTCAGCGTGTCGGTGAAGCTGCGGGAGC[A/G]TCACAGCCACCCCAAGTGTTATGTGTGCGCCAACT R 2 1 2 1 101000 r 74 goat snp59712-scaffold99-776385 18 21787946 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410692 Affx-122952739 AX-123281042 18 15039565 AAATGGCTTTGATTTGGACTTGTAATGTGCATGTG[C/T]GTGTATTACAGCACTGTATGTTCTTCCTAAAAGGT Y 2 1 2 1 101000 r 74 goat snp59713-scaffold99-826618 18 21737927 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435538 Affx-122933397 AX-123305878 18 15098069 ACTCCGCAAATAAACTGTAGACTTTCTGAGGATAA[C/T]GAATATAGGTCTATATTTTAATGTGAGCCGTGAAT Y 2 1 2 1 101000 f 74 goat snp59714-scaffold99-885122 18 21679633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438283 Affx-122931399 AX-123308621 18 15138907 CAATCATCAGAGAAAGAAGGTAACTTTTTATTTGC[A/G]CTGCTTCTTACCTTTTTTCCTAAACAAGTGGAAAG R 2 1 2 1 101000 f 74 goat snp59715-scaffold99-925960 18 21638976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437972 Affx-122931600 AX-123308310 18 15140986 ATTTGGTTTAGGTCCATCAGCTCCCAGTAGACTTT[A/G]AACATACGATGCGCCCCCTCACAGCTTGCATTAGT R 2 1 2 1 101000 f 74 goat snp40156-scaffold512-1729 18 21636990 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383495 Affx-122973427 AX-123253853 18 15173911 GAATTCCATCAGTGTAGCAAAAGAATAATAACATC[A/G]TGACCAGGTAGAGTTTATTCTATGAATTCATTGTC R 2 1 2 1 101000 r 74 goat snp40157-scaffold512-34654 18 21603261 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406000 Affx-122955510 AX-123276352 18 15206387 AGACAGGCTGCAATTACTAGGTATACTTACAGCTA[C/T]GAACCAATGATGAGGAGTTTCTTGACCTAATATTT Y 2 1 2 1 101000 f 74 goat snp40158-scaffold512-67130 18 21571109 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453179 Affx-122920463 AX-123323512 18 15266330 AGATTTGGTGGATAGAGTGCCTGAAGAACTATGGA[C/T]GTAAGTTTATACACACTCCTGTAAGTTTGTATAGG Y 2 1 2 1 201000 r 74 goat snp40159-scaffold512-127073 18 21505508 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797860 Affx-122959992 AX-385284798 18 15304912 GTTATAAGATAAGCAAGTGCAATATTGTTACAGAA[G/T]ACAAATATCTCTGAAAAGTTTCTCTCAGAAATATT K 2 1 2 1 101000 r 74 goat snp40160-scaffold512-165655 18 21467618 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393431 Affx-122965867 AX-123263787 18 15344339 AACCTAACAACTCAACCTCTTATAAGGGTGTTATG[C/T]TCAGTTCATTGCACAGATGCGTCACACCAAAAACA Y 2 1 2 1 101000 f 74 goat snp40161-scaffold512-205082 18 21428177 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395814 Affx-122963641 AX-123266169 18 15402776 AGTGTAATGTTTTCAAGGTTTGTCCATGTTGTGCT[A/G]TTTATCTTTCACTGCTTATTTCCTCGAGAAAATGT R 2 1 2 1 201000 r 74 goat snp40162-scaffold512-263519 18 21369880 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772786 Affx-122920127 AX-385259931 18 15438377 GTTTTGAGAACTTACTTTATTTTTAGGGTAAATCT[A/G]CTTATGACAGACCTCTTACTTTTCCTTCATCTGGG R 2 1 2 1 101000 r 74 goat snp40163-scaffold512-299120 18 21334348 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795678 Affx-122965898 AX-385282633 18 15468748 TGGAAACTTTTAGTCTCTTTTGTAAATGTAATACA[A/G]TTCTGACTTAGTATAACAACCATGCTTGGTCATAG R 2 1 2 1 101000 f 74 goat snp40164-scaffold512-329491 18 21303909 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271844 Affx-1111833111 AX-519545627 18 15485035 GGGGGAGGGGTGTGACCCCAAAAAAGACCACAGGA[A/G]CCCCTGGAATACAAGATGATCTGCTATGTACAGAG R 2 1 2 1 102000 r 74 goat 18_15485035_AF-PAKI 18 15485035 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406184 Affx-122956150 AX-123276536 18 15500995 GTCTCCCTATCCCAACCCTAGGCAACTGCGAATCT[A/G]CTTTCTGTCTATATGGATTTTCCTGTTCTGGGTAT R 2 1 2 1 303000 r 74 goat snp40165-scaffold512-361738 18 21270824 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432427 Affx-122935825 AX-123302768 18 15578154 ATAACATAGGTTAAACATTAAAATTTCATCACTTT[A/G]TTTCCTTACTGAATGTTACAGTGAAGCCCATTAAT R 2 1 2 1 101000 r 74 goat snp40167-scaffold512-438897 18 21194490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403357 Affx-122957800 AX-123273710 18 15609142 TGCAGGTCACTTTATCAAATGTAAAGAACAGTCTT[A/G]CTAGTTAATGATGCAGTCAGTGAAGTGAGCTGCTC R 2 1 2 1 101000 r 74 goat snp40168-scaffold512-469885 18 21163620 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789861 Affx-122926318 AX-385276868 18 15657640 TGTTTATGAGGACTTAGTCACTTGGCACCATGGAG[A/C]GTGCAAAATATGGTTCCTAGCTGGGTTGTACTTTC M 2 1 2 1 101000 f 74 goat snp40169-scaffold512-518383 18 21114687 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377022 Affx-122977717 AX-123247381 18 15689500 CTCCCTTTAGCCCCTGAGAGCTTTAGGCTTTTCTG[C/T]AGCATCTCAGCTCCTTTTCATTCACCTTTGCTGAA Y 2 1 2 1 101000 r 74 goat snp40170-scaffold512-550243 18 21081558 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405505 Affx-122956001 AX-123275857 18 15727018 TTGCAGATGAGTTTACTGAGGCTCAGAGAAGTCAG[C/T]AACTTTCTCAAGTTTCTTCAACTAAGGGAGCCAGT Y 2 1 2 1 303000 r 74 goat snp40171-scaffold512-587761 18 21044089 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797974 Affx-122973070 AX-385284910 18 15756571 CTTGAAAATAAGCAGTCAATGGGTCTATGCCTATG[C/T]GTCTTTCATTTCTGCCCACAAATATCCAAGGAAAT Y 2 1 2 1 101000 f 74 goat snp40172-scaffold512-617314 18 21014549 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781810 Affx-122933915 AX-385268892 18 15808917 CCCCATTTCTCTTGGTCTGCCTGACCTTGAGTTTT[A/G]CTTTAACAAATAGAATGTGATGGAATTGATATTGT R 2 1 2 1 101000 f 74 goat snp40173-scaffold512-669660 18 20961421 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442955 Affx-122928218 AX-123313292 18 15866377 ATGATGAGGCGCATGCTCTGTGTTGGAGGGCTGCT[A/G]TTTACCGCCAGCAAGGAGGAGGAAATAGACCACGT R 2 1 2 1 101000 r 74 goat snp40174-scaffold512-727120 18 20903428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274266 Affx-1111834101 AX-519547864 18 15937259 AAGTCCCACCTCTGTCCTTCAAGATGCCCCCTGCC[A/G]TGACTCCCACTGAGCTTGGAACAATAAAAACAAAC R 2 1 2 1 201000 r 74 goat GoatD01.018399 18 15937259 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38432762 Affx-122935438 AX-123303103 18 15946573 ACTTTATCTCAGTCAGTGCTCTTGGGAAACGGAGA[C/T]GAAGACACAACCAAGACACATGTTAACTCTCCAAC Y 2 1 2 1 101000 f 74 goat snp40176-scaffold512-807316 18 20823302 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433668 Affx-122934560 AX-123304009 18 16008373 CCTGCAATGATGTGCTTGGCCTAGGCTGGTTGCTC[A/G]TTCTCCTGCCCTCAGGGGCTGGCCTCCATGTTCTA R 2 1 2 1 101000 f 74 goat snp40177-scaffold512-869116 18 20761621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397064 Affx-122962729 AX-123267419 18 16047626 TGACTCCTCCAGCAAGCAGAATCTGTTCAGATTAC[A/G]TAAATGCCTAAGAGTGAGAATTGCTGGCAATGTTA R 2 1 2 1 101000 r 74 goat snp40178-scaffold512-908369 18 20722288 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395081 Affx-122964177 AX-123265436 18 16082765 GGGAAGCTCAAGGTAGGAGGTAGGGAGCAGCAAAC[A/C]TCAGCGGGGCAGACTGTGAGACCCTTGCTTTCTTC M 2 1 2 1 201000 f 74 goat snp40179-scaffold512-943508 18 20687151 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276106 Affx-1111835170 AX-519549657 18 16105310 AATGACATTGTCCAGCTGCTGTACCACGGCCGCCC[A/G]GGTGGCCAGGACACCAGCCTCCAGCAGCAGCATGA R 2 1 2 1 202000 r 74 goat ilmnseq_rs659009612 18 16105310 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468275627 Affx-1111835003 AX-519549197 18 16105339 GACACCATGGAGCTGCAGATGAGCACGTCAATGAC[A/G]TTGTCCAGCTGCTGTACCACGGCCGCCCGGGTGGC R 2 1 2 1 101000 f 74 goat ilmnseq_rs639613180 18 16105339 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275818 Affx-1111835100 AX-519549381 18 16105465 CTGGCCACCCAGATGGCTGCAATGATCCTCCACGC[A/G]CGGGGCAGTGTCACGACACTGTGGTACCGCAGGGC R 2 1 2 1 202000 f 74 goat ilmnseq_rs651729942 18 16105465 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468275554 Affx-1111834968 AX-519549126 18 16105561 ACCTACTACAACCACACGGTCGTCCTGCTGTGCCT[C/G]GTTGGCTTCTTCATAGCCATGCTGGCCCTGATGGC S 4 1 2 1 202000 f 74 goat ilmnseq_rs119103307 18 16105561 C G 2 neutral Goat_IGGC_65K_v2 Illumina 468276054 Affx-1111835219 AX-169485039 18 16105652 GCCCTGATGAATGGGGCGCTGCCTCTTCTGGAGCC[A/G]GGCGATGCCCCGGGCATGCTGGCAGGCCCGGGCCA R 2 1 2 1 103000 f 74 goat ilmnseq_rs664859254 18 16105652 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 463538913 Affx-1110033161 AX-515021191 18 16105661 CCTGCCAGCATGCCCGGGGCATCGCCCGGCTCCAG[A/G]AGAGGCAGCGCCCCATTCATCAGGGCTTTGGCCTC R 2 1 2 1 103000 r 74 goat ilmnseq_rs664274065 18 16105661 A G 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275711 Affx-1111834969 AX-519549280 18 16105667 AGCATGCCCGGGGCATCGCCCGGCTCCAGAAGAGG[A/C]AGCGCCCCATTCATCAGGGCTTTGGCCTCAAGGGC M 2 1 2 1 303000 r 74 goat ilmnseq_rs119103308 18 16105667 C A 3 not_recommended Goat_IGGC_65K_v2 Illumina 468275858 Affx-1111835046 AX-519549420 18 16105686 CCGGCTCCAGAAGAGGCAGCGCCCCATTCATCAGG[A/G]CTTTGGCCTCAAGGGCGCTGCCACCCTCACCATCC R 2 1 2 1 103000 r 74 goat ilmnseq_rs644488799 18 16105686 G A 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275560 Affx-1111834971 AX-519549131 18 16105689 GCAGGATGGTGAGGGTGGCAGCGCCCTTGAGGCCA[A/C]AGCCCTGATGAATGGGGCGCTGCCTCTTCTGGAGC M 2 1 2 1 103000 f 74 goat ilmnseq_rs268233137 18 16105689 T G 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275718 Affx-1111834972 AX-519549286 18 16105699 AGGCAGCGCCCCATTCATCAGGGCTTTGGCCTCAA[A/G]GGCGCTGCCACCCTCACCATCCTGCTGGGCGTCGT R 2 1 2 1 303000 r 74 goat ilmnseq_rs268233138 18 16105699 G A 3 not_recommended Goat_IGGC_65K_v2 Illumina 468275713 Affx-1111834970 AX-187906529 18 16105720 AAGGGGCCCCAGCAGAGGAAGACGACGCCCAGCAG[A/G]ATGGTGAGGGTGGCAGCGCCCTTGAGGCCAAAGCC R 2 1 2 1 102000 r 74 goat ilmnseq_rs119103309 18 16105720 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468275929 Affx-1111835156 AX-519549487 18 16105733 GAGGTGCAGAAAGAAGGGGCCCCAGCAGAGGAAGA[A/C]GACGCCCAGCAGGATGGTGAGGGTGGCAGCGCCCT M 2 1 2 1 102000 f 74 goat ilmnseq_rs657434682 18 16105733 G T 1 neutral Goat_IGGC_65K_v2 Illumina 463534679 Affx-1110033162 AX-515016973 18 16105786 CCCTTCTTTCTGCACCTCTCGCTCATCGTCCTCTG[C/G]CCCCAGCACCCCACCTGTGGCTGCATCTTCAAGAA S 4 1 2 1 202000 f 74 goat ilmnseq_rs669694251 18 16105786 C G 2 neutral Goat_IGGC_65K_v2 Illumina 38404883 Affx-122956472 AX-123275235 18 16124283 AGGAATTAATGATGCAACTGAACACGTGAATCACT[A/G]CCCCTCTGCCACATGCTTTATACATGCTAACTCAC R 2 1 2 1 201000 f 74 goat snp40180-scaffold512-985026 18 20645725 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778334 Affx-122953967 AX-385265449 18 16183972 TTGAGTGGACCTTTGAACCAATTCTAATTTCCTCC[A/G]TGAATATGGTGATAATGTTTTAGCCAGCCCCAAGT R 2 1 2 1 101000 f 74 goat snp40181-scaffold512-1044715 18 20586073 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444372 Affx-122926608 AX-123314709 18 16280731 CTCTGAGGTCTTTGATGAGAATTTTTAAATTCAGC[A/G]TTTTCATTTGAATAATTGTAGAAGAATTAGTAAAG R 2 1 2 1 303000 r 74 goat snp40183-scaffold512-1141474 18 20489640 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418094 Affx-122947141 AX-123288442 18 16327984 CAGTGTCCATGCATCAGGGTGGTTCAAGGCCATAG[C/T]GCCATTCGTGGACAGAGCTCCTGGGAACAGGTGGA Y 2 1 2 1 101000 f 74 goat snp40184-scaffold512-1188727 18 20441940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777779 Affx-122924084 AX-385264897 18 16362441 GTGAAGGAAAAAATAATTGTTTACTGTCTGGATTA[C/T]TTAGGCCTCTGATTTACATAGTTTCCTATTAATTG Y 2 1 2 1 101000 f 74 goat snp40185-scaffold512-1223184 18 20407181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397904 Affx-122961948 AX-123268259 18 16394555 GGCACCCAGTAAGCATAATGTTATTTTCTCATTAA[C/T]AGTATTTATTTACGTGGAGTACACTGGGATCTGAA Y 2 1 2 1 101000 r 74 goat snp40186-scaffold512-1255298 18 20375098 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392643 Affx-122966451 AX-123263000 18 16431685 GTGGCTCCGAACACCTACCAGGGGAGGCAGACCGC[A/G]AGTGTCAACACTGAGCCTGGTATTAAGAGGAGTCT R 2 1 2 1 101000 r 74 goat snp40187-scaffold512-1292428 18 20338014 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428485 Affx-122938782 AX-123298828 18 16505559 TAGCTACATCCTACTGAGCCTTTCTCATACTGTGC[G/T]CCAAGTCCTCCTCATGGATTAGCTTATTTGAAGCA K 2 1 2 1 201000 r 74 goat snp40188-scaffold512-1366302 18 20264176 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417097 Affx-122947485 AX-123287445 18 16538309 GGAGGGTGCCTGGTGTGCCCCCGAAGTCAGAGGAT[A/G]TGCTACCTGAGGTTGGCACTGTGATAAATGTATAA R 2 1 2 1 101000 r 74 goat snp40189-scaffold512-1399052 18 20230070 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436147 Affx-122932632 AX-123306486 18 16567293 CAGAGCCTCTCACACACTCTTCCAAATGCTCAGGC[A/G]TTCTTTACATGGTTGCTCCTCATCCTTTTACATCC R 2 1 2 1 101000 r 74 goat snp40190-scaffold512-1428036 18 20201089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420246 Affx-122945067 AX-123290594 18 16597497 TAGCAGCTCAGACCTGTCACCCTGTGAGCTCACCA[C/T]ACTTGTGAGTGGCGAGAGAATCTAGAATGAGTCGA Y 2 1 2 1 202000 f 74 goat snp40191-scaffold512-1458240 18 20170748 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418556 Affx-122946393 AX-123288904 18 16639061 GCTACCTGGAGAATTTCTCATGCAGAACCGTGTCT[C/T]TCCCGGTAACTTCTGTGGGGTGGGGAAGAATGTGT Y 2 1 2 1 101000 f 74 goat snp40192-scaffold512-1499804 18 20129258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420254 Affx-122945063 AX-123290602 18 16674389 TCTCAGCCCAGAGAGGTGTCCGGCCAAAGGAGGAG[C/T]GGCTCTGAGCTGTCTGGAGTCCCTGTCTTTGTGTA Y 2 1 2 1 101000 r 74 goat snp40193-scaffold512-1535132 18 20094384 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450896 Affx-122922202 AX-123321230 18 16720880 TCATGGGCCAAATCAAGTGCTATGGTCAATCTTGA[C/T]GACAGTGAAGTGGGGGAAATATAGCAAACATCTGT Y 2 1 2 1 201000 f 74 goat snp40194-scaffold512-1581623 18 20047700 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431654 Affx-122936810 AX-123301995 18 16752904 CCAGCTGACACAGGAACTGAACTCAGAGAGATTAA[A/G]TTCCTCAAGTTGACACAGCTAGTAAGGAGAACAGA R 2 1 2 1 201000 r 74 goat snp40195-scaffold512-1613647 18 20020190 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411063 Affx-122951946 AX-123281413 18 16789770 TACAGGCAACCGAGGGTTATAGGAGTTCAGAGAGC[C/T]GGCAACGCAGATGACAGGTTTTAGAATTCCCGTAG Y 2 1 2 1 201000 r 74 goat snp40196-scaffold512-1650513 18 19983298 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440381 Affx-122929633 AX-123310718 18 16827586 TGCACTCACATTTTACTTGAGGAATATGAATAAAA[A/C]TTGCTTTCTTTCCACAGTCAGTGGCCAAGCTGGAC M 2 1 2 1 201000 f 74 goat snp40197-scaffold512-1688329 18 19944334 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433915 Affx-122934387 AX-123304256 18 16858670 ACCAGACAGATAAAATACATACTCACATAGAACTC[A/G]TATTCCAGGAAGCTGGAGCTAGCCAGCAAGTGCAG R 2 1 2 1 101000 f 74 goat snp40198-scaffold512-1719413 18 19913094 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787889 Affx-122928889 AX-385274911 18 16910320 CCCCTGAAAATCTTTCACCAAAGAAATTGTGATCG[C/T]AATGGAAATCTTTACTCCTTTCAATATAGCATTTT Y 2 1 2 1 101000 f 74 goat snp40199-scaffold512-1771063 18 19861162 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38427607 Affx-122939362 AX-123297950 18 16978412 GAAGGAAGAGAAGAAACTGGCCAGGCATGAAAAAA[G/T]AGATGTTCATTACACCTGGGGTTTGTCCATTATGT K 2 1 2 1 201000 f 74 goat snp40200-scaffold512-1839155 18 19792565 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387832 Affx-122969664 AX-123258190 18 17012606 TCCCTATGTTTGAATCCCAGCTCTATTAATCACTA[A/G]TCTCATGGACTTGTCCGTGTCTCAGTTTCCTCACC R 2 1 2 1 201000 r 74 goat snp40201-scaffold512-1873349 18 19758444 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405160 Affx-122956943 AX-123275512 18 17055656 TCAATATATTTCATCAGCCACCTAGCTTATGTCTC[C/T]ACCCCACTTTCCTCTGTGTGACTATCTTCAGACTT Y 2 1 2 1 201000 f 74 goat snp40202-scaffold512-1916399 18 19714655 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277140 Affx-1111835762 AX-519550646 18 17071735 AGAGGCAGCATTACTGTGACATAGAGTTTTATGCC[A/G]TTAGTCTGTGAGCTCCCTGTTGGCTGGACCATGCC R 2 1 2 1 101000 f 74 goat Random2.2K-1714 18 17071735 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392986 Affx-122965665 AX-123263343 18 17087052 ATCACACTGAGTGGACCCCATTCCTGGCACAAGCA[A/G]TGACACCCACTGCTTTATTAACCTGCGCTGCCCAG R 2 1 2 1 101000 r 74 goat snp40203-scaffold512-1947795 18 19683059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439084 Affx-122931129 AX-123309421 18 17129983 GAATGAAATGAGCCACGAAAGTTTTCTTGGAGTAT[G/T]CAGGTTTTAAGTGATTTGACCAGGGCAAAAAGACC K 2 1 2 1 101000 r 74 goat snp40204-scaffold512-1990726 18 19640154 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381893 Affx-122974161 AX-123252251 18 17171791 TCAAACCTTTTTCAAGTTTAGTAGAAATGTTTATG[C/T]ATACAACATACAGACATATATATAGTACATGTGTG Y 2 1 2 1 202000 f 74 goat snp40205-scaffold512-2032534 18 19597870 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452299 Affx-122920682 AX-123322632 18 17208472 AGGTAAAATTCACATGTTTTAAACTTGGTCAGAAC[A/G]TAGCAGTAGGATGTTTCTCTTTCTAGTTTTTACGC R 2 1 2 1 101000 f 74 goat snp40206-scaffold512-2069215 18 19561194 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274992 Affx-1111834623 AX-519548574 18 17234158 CAGCAGAAATACTCCTACTGACCCTCTCAACCCAA[A/C]TTATTGGACACCTGCAGATTCTAAGG M 2 1 2 1 101000 f 74 goat GoatD01.043831 18 17234158 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320772474 Affx-122943353 AX-385259625 18 17242294 GACTGAACGTAAGCGTACTTATAGTTAAGCCTTTG[C/T]AGGGAAAATAGTTTACCCTTCAAGACATTATTCTT Y 2 1 2 1 101000 f 74 goat snp40207-scaffold512-2103037 18 19527252 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383399 Affx-122973498 AX-123253757 18 17304600 ATCTCAACAAACATTAAGAAACACACTTCCAAAAT[A/G]CCATGATTTAAAGACAGAAACTAATGGAAATAAGA R 2 1 2 1 101000 r 74 goat snp40208-scaffold512-2165343 18 19464798 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789562 Affx-122927326 AX-385276571 18 17348352 GTCCCCATACCCCCAGCACAATTTCTCCAAATGTC[C/T]ATATCCCAGACCAGACTGGTATATTGGTTACAGTT Y 2 1 2 1 103000 f 74 goat snp40209-scaffold512-2209095 18 19421042 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441662 Affx-122929190 AX-123311999 18 17386561 ACGCAGTGTGCAAAACATGGACTGTATCCCATGGC[A/G]TCAATGGACAAGAGAAACTTCACTTGGCCTCTGAA R 2 1 2 1 101000 r 74 goat snp40210-scaffold512-2247304 18 19381115 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387491 Affx-122970340 AX-123257849 18 17416685 ACCACGGTTTTAGGCTACAAGATGTCTTCATATAC[A/G]TGTTTATCTTCCCCTGAACCTTTTCAATTGTCATT R 2 1 2 1 101000 f 74 goat snp40211-scaffold512-2277428 18 19350897 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778769 Affx-122954835 AX-385265879 18 17478213 AAGCAATAATTATGACTTCATTCACTGATAAGCAA[C/T]GGCATTACATAAATCTGATGCGGATTTAGAACATG Y 2 1 2 1 101000 r 74 goat snp40212-scaffold512-2338956 18 19289022 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411318 Affx-122952281 AX-123281668 18 17518264 CTCTGATTGCCTTGGATCAGGGTCTCTAGCACTGA[A/G]TGCAAAGCCTGGCAGAGAACTGGCAGGTAAAGACT R 2 1 2 1 201000 f 74 goat snp40213-scaffold512-2379007 18 19248637 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772456 Affx-122958580 AX-385259607 18 17576058 TCAGAAAAAGCAAAAGGTTGGAGCACTCAGTCACA[C/T]GAAAGGCTCTTCGAAGAGATTAAGAACGTGATTCA Y 2 1 2 1 101000 f 74 goat snp40214-scaffold512-2436801 18 19191410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421222 Affx-122944131 AX-123291569 18 17679271 CCAAGTGTCAGACCCTGCACACACGGCCTCTGCTT[A/G]CCAACACAAAGACAGGATGGGCCTCAACAGCCCAA R 2 1 2 1 201000 r 74 goat snp40216-scaffold512-2540014 18 19088899 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791589 Affx-122975543 AX-385278580 18 17710117 GATGCAGAATCACATTCTTTCTCTACACAGAGCTA[C/T]AGGCCATTACTATCTATAACCAGAGTATCCACTTG Y 2 1 2 1 101000 f 74 goat snp40217-scaffold512-2570860 18 19058213 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382158 Affx-122974036 AX-123252516 18 17741092 ACTTGTCCTCAAATATCTCCTGTTTATCTTGGGAA[C/T]GGCCTACATGAATAGTCCATTTGTTGGAAGAACAT Y 2 1 2 1 101000 f 74 goat snp40218-scaffold512-2601835 18 19028699 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414171 Affx-122949678 AX-123284520 18 17801411 GTTGAAGGGCATAGCTCCTGGCAGCACCCCCACCC[A/G]CTGCTCCAGTACTTGGGGGGCTCCTGGTAACTCCA R 2 1 2 1 103000 f 74 goat snp40219-scaffold512-2662154 18 18970051 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802894 Affx-122945219 AX-385289791 18 17832471 ATTTGTTTGTTAAACCTATTCATATTAAGTATACA[A/G]CAATGGTAGAAATGTGTTTTCATCCTTCCTAATTT R 2 1 2 1 101000 r 74 goat snp40220-scaffold512-2693214 18 18938982 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415899 Affx-122948470 AX-123286248 18 17882367 AATGCACCCAGACAAAGATAAATAGTTGCTAACAA[C/T]AGAAAGACCACTAGGTATTGAGTACTTCTCAAAAG Y 2 1 2 1 101000 r 74 goat snp40221-scaffold512-2743110 18 18889137 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801840 Affx-122957019 AX-385288747 18 17960335 ACTTGCAGAAGTAGAACACTCCTTACCTGGCTTCC[A/G]GAGTTAGCAATTATCAAATCATGGTCTATTTTCTT R 2 1 2 1 101000 f 74 goat snp40223-scaffold512-2821078 18 18810438 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272011 Affx-1111833112 AX-519545778 18 18013157 TAATGACCAGCATAGGAAATAACCCCAGGTCATAA[A/G]CAGGCACTTTTGAAAAAAATGGAATATTTGGTATT R 2 1 2 1 101000 f 74 goat 18_18013157_AF-PAKI 18 18013157 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38410943 Affx-122952040 AX-123281293 18 18035510 ATCCTTTTTTGAGTTAAAAAAATTCATTACTGTAA[C/T]AAGTATCTTGCATATGAAATGCATTTCTACAGCAT Y 2 1 2 1 201000 r 74 goat snp40224-scaffold512-2896253 18 18734308 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430204 Affx-122937342 AX-123300545 18 18067883 CTGTTTGTCCTTTAAAGTGGCGTGTGGAGTGAAAT[A/G]GTTTGCAGCAGGTACTTGGTGAGTGTTTGTTTTCT R 2 1 2 1 101000 f 74 goat snp40225-scaffold512-2928626 18 18701880 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381497 Affx-122974872 AX-123251855 18 18126374 GGGATTGAGCTAGTCTCCTGCATCTGTGAAATGGG[C/T]CACGCATGGTACCCAACGTGCTGGGTAGCTGTAGA Y 2 1 2 1 201000 r 74 goat snp40226-scaffold512-2987117 18 18643554 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403906 Affx-122957483 AX-123274258 18 18161842 ATCAACCAGAGCCAGGGTGGAGCTGGGAAGGGGTC[A/G]GGGCAAGTGGCTCTGTGGGTGGGGCCTCGGCTGCC R 2 1 2 1 103000 f 74 goat snp40227-scaffold512-3022585 18 18607989 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444748 Affx-122926374 AX-123315085 18 18194524 TCTATTTCCTTTCTTTCTACCTGAAGGAGATCCTG[C/T]GCTTCACCAGAACATTAGCTTCCACCCCTGCAAAG Y 2 1 2 1 101000 f 74 goat snp40228-scaffold512-3055267 18 18575083 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388364 Affx-122969337 AX-123258722 18 18316707 GGGGTGGGTCTGGTTGGTGTTTTCTTTCCCAGCAC[A/G]TAGCTCGCTTTCCCAAAGAGACAGCGTGCTTGAGT R 2 1 2 1 101000 r 74 goat snp40230-scaffold512-3177450 18 18451895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432296 Affx-122936316 AX-123302637 18 18345407 TTAGAGAATGATCTCATCTAAATAAATATGTACTC[A/G]TATACATATAGAAACAAGTCTAAAGGGACACGGCT R 2 1 2 1 201000 r 74 goat snp40231-scaffold512-3206150 NW_017211586.1 13303 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376174 Affx-122978833 AX-123246533 18 18458116 TATATCATGAGGGCTTGGGGATGTGAGTGACTGTC[A/G]TTGGCATTGTTTTCCTATCTCATTCCTTGAGGGTT R 2 1 2 1 101000 f 74 goat snp40233-scaffold512-3318859 18 18312228 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384060 Affx-122972872 AX-123254418 18 18491218 GGCAATTGTGTGTTGTTGGTTGTGAACGAAGATGC[A/G]GAAACCTCATGTCCTGCCATTGGCAAATATATACA R 2 1 2 1 101000 f 74 goat snp40234-scaffold512-3351961 18 18279368 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419508 Affx-122945452 AX-123289856 18 18524455 TACCCAGAGTCCCACTTCCCTGCAGGGCTATTTCT[A/G]CATAATCCAGAAAGGCCATTCAAAGGACAGCTGCC R 2 1 2 1 101000 r 74 goat snp40235-scaffold512-3385198 18 18246141 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398342 Affx-122962122 AX-123268697 18 18562518 GGCTCCAAGAAGCCCCTACACAAGGTGCCCCGTGC[A/G]TGCAGATTTCTTGAGACCCTGGTTCTGACTCTAGG R 2 1 2 1 101000 r 74 goat snp40236-scaffold512-3423261 18 18208111 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418828 Affx-122946152 AX-123289176 18 18639490 TGTTAAAAATCAGGTAATTTTAAGTTGTTACATAA[G/T]CATTGGAAAAAAAGACAATCCTCATTTCCACTGCC K 2 1 2 1 201000 f 74 goat snp35010-scaffold4174-54251 18 18130972 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430955 Affx-122936826 AX-123301296 18 18697743 ACATGCACACGCATGGCTCAGCATGTAAATGTGCA[C/T]GTGCTTACGTGTGACTCAACATCCATGTGTGTTAC Y 2 1 2 1 101000 r 74 goat snp35011-scaffold4174-112504 18 18072752 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379893 Affx-122975771 AX-123250251 18 18733568 CCACAAAGTCATCCTCAAGCCTCCTCATGCTTCCT[C/T]GTAATCCCACTGGCAGAGTCATGCTCTCCTGTGGA Y 2 1 2 1 201000 r 74 goat snp35012-scaffold4174-148329 18 18036859 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452827 Affx-122920738 AX-123323160 18 18766571 CATGCTTTTAATAAGCATGGCCATAACTAGGAAAT[C/T]GGATTTCCAGGAGCTGGGAGGGAGAAAAGTTGTGG Y 2 1 2 1 101000 f 74 goat snp35013-scaffold4174-181332 18 18003923 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375972 Affx-122978434 AX-123246331 18 18808331 CCTCAGCACTTAAGAAGAAGAGTGGCAAACCCACA[C/T]GGGGAAGCAAGAGTGAATTGTTCTAAGATCTAAGT Y 2 1 2 1 101000 f 74 goat snp35014-scaffold4174-223092 18 17961754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421556 Affx-122943859 AX-123291903 18 18927052 CTAGAAGCCCTCACCCTGGACCAGGGGAATTAAGC[A/C]CTCTGATTGGCTGTGCTGGATCCCACAGCAGTCAC M 2 1 2 1 101000 r 74 goat snp35017-scaffold4174-341813 18 17842966 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439780 Affx-122930507 AX-123310117 18 18964169 ATGGTTCCTGAGTGAACACAAGAAGCAGACTTGCA[C/T]AAGGAAAAAACAGATATGTCCTGCTAAACTTGGAG Y 2 1 2 1 101000 r 74 goat snp35018-scaffold4174-378930 18 17805932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794426 Affx-122964180 AX-385281389 18 19001436 AATAACAACACGGACAAGACAGTCCTTTGAAAATC[A/G]TGATACCAGCCCACCTAATGTACACAATAAATGAA R 2 1 2 1 101000 f 74 goat snp35019-scaffold4174-416197 18 17768596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376363 Affx-122978321 AX-123246722 18 19037179 AAGGTATTTCCATCTGCCTTGTTTTCTCTTCCGCC[A/G]TTTGTCTGTGAGGCTCAGCACGTTCGTGGTGAATG R 2 1 2 1 101000 r 74 goat snp35020-scaffold4174-451940 18 17733509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383197 Affx-122972788 AX-123253555 18 19067814 ATCCAGACTCTGCCAGATAACTAATAGGCTTGGTC[A/G]GTTAAGTAGGAAGCTTGGGAAACAAGAGAGCATTG R 2 1 2 1 101000 f 74 goat snp35021-scaffold4174-482575 18 17702851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395062 Affx-122964191 AX-123265417 18 19111425 TCAGCCTGGTTTTGAGGGGACTGGTCCATGGGTCC[A/G]TGAGCCAATCTCTTGTCTCATTCTTCTCTGGAGAG R 2 1 2 1 101000 r 74 goat snp35022-scaffold4174-526186 18 17659303 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797459 Affx-122979108 AX-385284398 18 19155319 CTGGTACAGACGTAAAGGAGTAGAAAAATAAAACA[C/T]GAATTCATTGTAGGAGCAGGAAAATCATATTTAAA Y 2 1 2 1 101000 f 74 goat snp35724-scaffold43-4995518 18 17615925 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768362 Affx-122967553 AX-385255542 18 19251203 AAATGTCAGATTCAAATACGTATTTTAGTATACTT[A/G]TTTGGAACACACTTATACTACCAAGTTATTCACCT R 2 1 2 1 101000 r 74 goat snp35722-scaffold43-4899634 18 17519621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423906 Affx-122942281 AX-123294252 18 19281163 GTCACAAAGAGTCAGACACAAATGAGCAACTAACA[C/T]GCTTGGGGAAAGGATTCCCACTGAGTTAGTTAACA Y 2 1 2 1 303000 r 74 goat snp35721-scaffold43-4869674 18 17489582 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277267 Affx-1111835763 AX-519550772 18 19283213 TGAGTGAATAACTTGACGGATAGATAAATGTATAG[A/G]TAAATAGGTAGATAGATGGTGCAGAGAAGGCAATG R 2 1 2 1 101000 r 74 goat Random2.2K-1717 18 19283213 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424602 Affx-122942201 AX-123294948 18 19314714 AAATAAAACCACTAGCATTCTTGGTGATTGGTTTT[A/G]TTTTGCTTTGTTTTCTCCTATGTAATCCCTGATTC R 2 1 2 1 101000 r 74 goat snp35720-scaffold43-4836123 18 17456013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409204 Affx-122953171 AX-123279555 18 19357122 TCTCCATAACGTGGGCGAGTCTGTTCCATACAGTC[A/G]TTCAGAGGCCCAGGTTTCTGCCACCTCATTGCTCT R 2 1 2 1 101000 f 74 goat snp35719-scaffold43-4793715 18 17413377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433662 Affx-122934564 AX-123304003 18 19393343 AGGATGCTACCAGCCCTCACATCTGATTCTCTGAA[A/G]CCTGGGGACAGCTCAATCAGGTAATCCATCCTTGA R 2 1 2 1 202000 f 74 goat snp35718-scaffold43-4757494 18 17376758 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777135 Affx-122944196 AX-385264258 18 19423566 TCCAAAGTCCACATGTTCCCTGTGGGTTGGTTTGC[A/G]TGTCTCACACACAAACTAGGTGGAGGCCAGAGACC R 2 1 2 1 101000 f 74 goat snp35717-scaffold43-4727271 18 17346492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391772 Affx-122967463 AX-123262129 18 19482052 AGTCCTCTCCTGGGTAAAGGAGCAATGGTTAGAGG[A/C]TAAGGATTTCCCTTTTTGATTTGAGATTTGGGCAG M 2 1 2 1 101000 r 74 goat snp35716-scaffold43-4668785 18 17287268 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430004 Affx-122938034 AX-123300345 18 19524132 ATTGTGGATTACATATCAGTTCAGTGTCTCCCGTC[A/G]TGTTCCTGACTCTGATGCATAGATAATGTCGGGGA R 2 1 2 1 201000 r 74 goat snp35715-scaffold43-4626705 18 17245221 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409081 Affx-122953337 AX-123279432 18 19559328 GCAGATGGCATTTAATATATTCCCAGACATAAACA[C/T]GAGGCTTAAGTTGTATATGGTATATGTTCCTGAGC Y 2 1 2 1 101000 r 74 goat snp35714-scaffold43-4591509 18 17210108 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790967 Affx-122971944 AX-385277964 18 19593438 AGTTTCCTTGATGTTTCCAGATGTAGCCCATGTAT[A/G]CAAAGAACACTTCTATTCCATCCTTCCAGTAAGGA R 2 1 2 1 101000 f 74 goat snp35713-scaffold43-4557399 18 17175791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390267 Affx-122967747 AX-123260624 18 19643005 ATATTCCTGATTAATTTCTATGGGGTTCACATGGT[A/G]TTGTACAAAATAAATATGAAATAGTCTAAGACACA R 2 1 2 1 101000 f 74 goat snp35712-scaffold43-4507832 18 17126085 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783076 Affx-122941376 AX-385270143 18 19687999 TCTGCTGGGAAAACCAACAAAGAAGATGGGAATCT[A/G]TTCACAATGTAATTCTAGTTGGTGACAAACACTAT R 2 1 2 1 101000 f 74 goat snp35711-scaffold43-4462838 18 17080926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409772 Affx-122952987 AX-123280123 18 19760453 TTGGACGGGATGATGGAAATTATAGAGCCTAAGCT[A/G]CTGCCTGGGAGTCAAACTCTCTTCACAACAGTCCT R 2 1 2 1 101000 f 74 goat snp35710-scaffold43-4390384 18 17006406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414666 Affx-122949306 AX-123285015 18 19791601 ATCAGGGGCTTTTCCAATGAATTGGCTCTTCGCAT[C/T]AGGTGGCCAATATATTGGTCTTTGATTTTGGTATA Y 2 1 2 1 303000 r 74 goat snp35709-scaffold43-4359236 18 16974997 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391426 Affx-122966758 AX-123261783 18 19829261 AATTTAAAAAAAATGTTGGGAGGAAACATGAAATG[A/C]GAATACCTATCAATTCTTGTTCATGTGTACATTTA M 2 1 2 1 101000 r 74 goat snp35708-scaffold43-4321576 18 16936447 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410195 Affx-122952579 AX-123280545 18 19868595 TTGAGTTTTCCCCACAAGGATTCCATTGCCGCTCC[A/G]TGGCTTGAATATCCTGATAGTCAGTGAAGCTTCAA R 2 1 2 1 101000 r 74 goat snp35707-scaffold43-4282242 18 16896683 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277144 Affx-1111835764 AX-519550650 18 19895399 GGTCAACACATGGTGCTGCGTCTTCTCTGGACATT[A/C]CCAGCCTGACAGATGCACCCCTTGCAGTGTGACTC M 2 1 2 1 101000 f 74 goat Random2.2K-1719 18 19895399 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408615 Affx-122953497 AX-123278966 18 19927289 AGAGAATCAGACAATTACTCATCCATCCATTCATC[C/T]GTTCACCCACACAGCCATTTGTGCATCCATTGTAA Y 2 1 2 1 101000 r 74 goat snp35706-scaffold43-4223548 18 16837984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784741 Affx-122959756 AX-385271789 18 19961391 CCAGACCCACACACAAAAATGATAAACATACAACC[A/G]CAATTAGCATCTTGCAAAGTTTTCAGTTTGGAGTC R 2 1 2 1 101000 f 74 goat snp35705-scaffold43-4189446 18 16803830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277146 Affx-1111835765 AX-519550652 18 19983332 ACATGATCAAAATTCACTGTTAGATTGGATGGCTT[A/G]CAGGCAACCGAGGGTTATAGGAGTTCAGAGAGCTG R 2 1 2 1 101000 f 74 goat Random2.2K-1720 18 19983332 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779026 Affx-122929737 AX-385266133 18 19997220 TCCACAGAGTTAACTGTGTCTTCAAGTTTAGCTGG[A/C]GTTTGTTCATGTTCAATGGTGTATAACTTTTTTTT M 2 1 2 1 101000 f 74 goat snp35704-scaffold43-4153617 18 16768195 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773276 Affx-122934431 AX-385260419 18 20032489 CAGTTACATGATATAATAAAGGCATTTATGAATTG[C/T]GCTTTATACTGAAACATTAATTGAGAGAGCTCATT Y 2 1 2 1 101000 r 74 goat snp35703-scaffold43-4118348 18 16733418 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277273 Affx-1111835766 AX-519550778 18 20066622 ACAGGTTTCCTGGGCCTCCAACTTGCAGGTGGCAG[A/T]GCAGGGGAATTTTCTGCTTGCATAACCACATGGGC W 4 1 2 1 102000 r 74 goat Random2.2K-1721 18 20066622 A T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397856 Affx-122962454 AX-123268211 18 20078030 ATCCATTCAAAAAATATTTGCTTGGCACCCAACAC[A/G]TCCCACTCTGTTCTAGATCCTGGGACTGAAGCTGA R 2 1 2 1 101000 f 74 goat snp35702-scaffold43-4072807 18 16687986 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799454 Affx-122926768 AX-385286384 18 20126564 TCTGTTGGCTAGCACCTTCAAGTACTTCAGAAGCA[C/T]ACATTTATATATTGGTTATATATCAGTCACTTATT Y 2 1 2 1 101000 f 74 goat snp35701-scaffold43-4024273 18 16639380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444555 Affx-122926984 AX-123314892 18 20167011 ATTTCAAGTGCTGCTGCTCTCCAACCTACTTATTA[C/T]AGTCTTACATTGTTCCTTATCTGACCCAGATTTTG Y 2 1 2 1 101000 f 74 goat snp35700-scaffold43-3983826 18 16598184 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392417 Affx-122966201 AX-123262774 18 20206298 AGGTACCGTCAGCCTTGTAAAACTACCCCTGTTTT[A/C]TTCTCATTATGCTTTTCTTCCTCTTTCCTCATGCT M 2 1 2 1 101000 r 74 goat snp35699-scaffold43-3944539 18 16558580 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425126 Affx-122941216 AX-123295472 18 20315457 TGGGTGATCAGTTGAGATAGTTGCTCTGTGCTCCA[C/T]GTACTCTCTTAACCTTGAGTAGGCTAGCCTGAGCT Y 2 1 2 1 101000 r 74 goat snp35697-scaffold43-3835380 18 16449170 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778594 Affx-122934363 AX-385265705 18 20356726 TGGCAGCTGCTCAGAACCAGATCAAGAGAGGTTGT[A/C]TTTGACAGTTCGTAGGACACTGCCCATTTCGTTAG M 2 1 2 1 101000 f 74 goat snp35696-scaffold43-3794111 18 16408146 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386118 Affx-122971422 AX-123256476 18 20386359 CTGGAGCCACCTGCTTGAGTAACCACGGTGGGGCC[A/G]TCCCGTGGCTCATCAACGCACCATCGTGCCTGCGT R 2 1 2 1 101000 r 74 goat snp35695-scaffold43-3764478 18 16378526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382996 Affx-122973335 AX-123253354 18 20436772 TTTTCCCCCCCTTTTTGGTAAACTCTTCATAGTTA[C/T]GCCTTAAGTTATCCATTTGCTTCATTTACTCATTC Y 2 1 2 1 201000 r 74 goat snp35694-scaffold43-3714065 18 16328074 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384100 Affx-122972840 AX-123254458 18 20482896 TGATAGAATAGATTAGAGATATAAAATTAGAGATG[C/T]AAAATCAAAGGAATCTAGGTCACTTTATGAGGGCC Y 2 1 2 1 101000 r 74 goat snp35693-scaffold43-3667941 18 16281915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417707 Affx-122947450 AX-123288055 18 20512856 AGCCGCATACATGTTCCTGTGGGTGGGGAGCTTGA[C/T]GGGAGGGTTGAGGGGTGGCCCCCAAGCTAAGGAAA Y 2 1 2 1 303000 f 74 goat snp35692-scaffold43-3637981 NW_017213974.1 7361 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463538026 Affx-1110034851 AX-511444678 18 20539812 TCCACTGCAGTTCAAAAGCAAAGGTCTGTGCTTTA[C/T]GGTGAAAGTGATCATTTAAAGCTCTCCTTTATCTC Y 2 1 2 1 101000 f 74 goat 18_20539812_AF-PAKI 18 20539812 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418302 Affx-122946985 AX-123288650 18 20560183 GCTCCATAAAACCAGCCCCAGGGCTGTGTTCCTCA[C/T]GCATGAGCACAGCTTTTGTGGACAGACACAGGCCC Y 2 1 2 1 201000 r 74 goat snp35691-scaffold43-3590654 18 22508135 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277150 Affx-1111835767 AX-519550656 18 20560356 TCCTTCATTACAGCTTCCTGACAGTCTACACAGTC[A/C]AACAAACCTCTCTTAAACCAGGCCAGTACTGAAGA M 2 1 2 1 101000 f 74 goat Random2.2K-1722 18 20560356 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320772193 Affx-122971315 AX-385259348 18 20593148 GTAGCATCCCAGGTTGTGAGCCTAATACTGAACAA[C/T]TTGACAAGTCAGTACAGGACACAGTGCAAGTCATT Y 2 1 2 1 101000 f 74 goat snp35690-scaffold43-3557689 18 22541010 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385657 Affx-122971157 AX-123256015 18 20692355 CCCTGGCCATAAGTTTTGGTTCCCCATTTTGTCCT[C/T]GGAAGTTTTAGCCAATCTGGACTAGAAGCCTAGTG Y 2 1 2 1 201000 r 74 goat snp35688-scaffold43-3458482 18 22642224 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393185 Affx-122965516 AX-123263542 18 20724122 AATTTTCTTATCCATAAAATGAGGTGATTATTCTC[A/G]TTGATTTTTTAGGCTACCCTCCCACTGCCTTGCTC R 2 1 2 1 101000 r 74 goat snp35687-scaffold43-3426715 18 22674088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432112 Affx-122936454 AX-123302453 18 20752852 TGGCAAGGCTGGATTTTTCTCCTTGGTAATACTGG[A/C]GTCTGTCCAGGGGATAAGGGAGGATGTAGACACCT M 2 1 2 1 101000 f 74 goat snp35686-scaffold43-3397985 18 22702903 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769324 Affx-122953760 AX-385256495 18 20805069 AAAGGTATGTTCCACTTTCAACAACTCCAACCCAG[C/T]AGATAATCTATAGGGTATATATTTTGAACTTTTTA Y 2 1 2 1 102000 f 74 goat snp35685-scaffold43-3345768 18 22756202 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274524 Affx-1111834346 AX-519548115 18 20827189 TACCCAGGTCCTGAATGCTTAGCTATAACTGCAGG[A/G]CTGCCTCACAGATAGAGAACAGTATGGAGGGTCCT R 2 1 2 1 201000 f 74 goat GoatD01.030955 18 20827189 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38396162 Affx-122963379 AX-123266517 18 20835601 TCTTTTGCTGATGCAGGTGGTTAATGACCCTTGAG[A/G]AAAAATGGTCATGAGACCTGGGGCCGGGGGATGGG R 2 1 2 1 101000 f 74 goat snp35684-scaffold43-3315236 18 22787131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408148 Affx-122954226 AX-123278499 18 20889040 TGAGCAGCCTAACCCTTCCCCTCCAGGATCTTGTC[A/G]CATGTCAGACTTGTCGCAGGATATTTATTCTCTTA R 2 1 2 1 102000 r 74 goat snp35683-scaffold43-3261797 18 22840450 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417831 Affx-122946795 AX-123288179 18 20922080 AAGAGAGACATGGTCCTTTTTGCTTTGGAGTTTAT[A/G]GTGTAGTAAGGGAGAATACAGGGCTTCCCTGATGG R 2 1 2 1 101000 f 74 goat snp35682-scaffold43-3228757 18 22873756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443881 Affx-122927500 AX-123314218 18 20963907 GCTAAGTGTTCATCCTAATGGTGATGTGGAGTTCA[C/T]TGGAGGACTTTAGGAAGAGGAATAATGCCAAGACA Y 2 1 2 1 101000 f 74 goat snp35681-scaffold43-3186930 18 22914869 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434838 Affx-122934382 AX-123305179 18 21031432 GCAAAGGAACTGAGTCAATGTTTCTTAAAACAAGA[C/T]ATTGATAGAAATTAAGCCTCTCAGTCGGTAAAGAA Y 2 1 2 1 101000 r 74 goat snp35680-scaffold43-3119405 18 22982513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776286 Affx-122948171 AX-385263414 18 21084370 GGTGCCATAATGAAGAGTAGGATAAAATGTGATGA[C/T]ATATAAAAATGTATCCAACACTATCTGTATGACCC Y 2 1 2 1 101000 f 74 goat snp35679-scaffold43-3066467 18 23035422 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396376 Affx-122963032 AX-123266731 18 21126559 TGTCAGGGACCATGTTAAATGTTAGAAATACAAAA[C/T]GAAAAAAATCAATTGTTGTTACTGTCCTCATCATC Y 2 1 2 1 202000 f 74 goat snp35678-scaffold43-3024278 18 23077398 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777616 Affx-122933882 AX-385264735 18 21155545 AGGCATATAAACATGCCAATAGGCAAAGAGTAATA[G/T]TTTAATAAACATCTCTTTTCTAATTTACTTATTTA K 2 1 2 1 201000 r 74 goat snp35677-scaffold43-2995292 18 23106361 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794966 Affx-122940388 AX-385281926 18 21201308 ATTAGTAAGAAATAAAATCATACATAAAATGTATG[C/T]GGCTAACGGTAGAATGCCCTGCTAACTAATGTCAT Y 2 1 2 1 202000 f 74 goat snp35676-scaffold43-2949529 18 23152075 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411684 Affx-122951999 AX-123282034 18 21287035 CCTGACTTGAGACTGAATGTGCTCACTGCACCTGC[C/T]GTGTTGAGGACGGACTGAGAGGAGACGGGGGAAGC Y 2 1 2 1 101000 f 74 goat snp35674-scaffold43-2863802 18 23238360 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397932 Affx-122961927 AX-123268287 18 21335029 CACATGTGACCTGTAGGATGGACCAAAGCACAGAG[A/G]GCCATTTGGCCATTTCAACATTTCAGCTAGAGTTG R 2 1 2 1 101000 r 74 goat snp35673-scaffold43-2815808 18 23286442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411275 Affx-122952311 AX-123281625 18 21377368 ATCTTCCCAAAGTGCAGACGCTTATTTACTTTTAC[A/G]TGTTCACCGTCTTCTTCCTGGTGGGACTCAGATGA R 2 1 2 1 101000 f 74 goat snp35672-scaffold43-2773469 18 23329283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429185 Affx-122937958 AX-123299527 18 21410805 TGACACTGCAACACTGCATTGTTGTCCCAGATCAC[A/G]TCGGCTACGAAAGGCTTAGCATTTCGTCAAGGCAG R 2 1 2 1 101000 r 74 goat snp35671-scaffold43-2740032 18 23362706 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405477 Affx-122956023 AX-123275829 18 21448746 TCTTTTAAAAATATATCCAACAAGTTCCTACTGGT[A/G]TTTTGAGTACCTTAGAATTTGCCTAGTGAAAAGTT R 2 1 2 1 201000 r 74 goat snp35670-scaffold43-2702091 18 23400663 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442422 Affx-122927979 AX-123312759 18 21478975 TTCATTCAAGAGACATTTATAAATTTCTTTTATGT[A/G]TAAGACTCTCCACCAAGTACACTGGAAAGATCGAA R 2 1 2 1 101000 r 74 goat snp35669-scaffold43-2671862 18 23430850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790846 Affx-122953682 AX-385277844 18 21557107 CACATTTGCAGTTGACATGACTTTGAAACTAGATA[C/T]GATCTTAAGCATCTGAGGCCACATACTATCCTCCA Y 2 1 2 1 101000 r 74 goat snp35668-scaffold43-2593730 18 23508849 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385584 Affx-122971213 AX-123255942 18 21628445 CAACATCATCAACAATGAAGTGTACTTTAAAACAA[C/T]AGCATGTTATTTTCACCTATTAAACTGGGGAAAAC Y 2 1 2 1 101000 f 74 goat snp35666-scaffold43-2522392 18 23580651 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421654 Affx-122944450 AX-123292001 18 21730061 CCTACCATGAACCGTGAAGAATTCAGGCAGGAAAG[A/C]TTCAGATCTCAAAGTACCAGGCTCTGAAGAATAAA M 2 1 2 1 101000 f 74 goat snp35664-scaffold43-2420776 18 23682268 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443705 Affx-122927158 AX-123314042 18 21780544 GGCTCCTTAATGAGCAAGCCTGGTACTGGCCAAAA[C/T]TGCCACAGGCTGGTAGCCCCACATGGTTGAGGATG Y 2 1 2 1 101000 f 74 goat snp35663-scaffold43-2370293 18 23732804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447284 Affx-122924930 AX-123317620 18 21838759 TCTGCCTAAAGAGGAGAATAAATGTTTAAATATAT[A/G]CAGCTCAAATAGAAGTGGTAGCAATCAGAGTAACC R 2 1 2 1 101000 r 74 goat snp35662-scaffold43-2312078 18 23791703 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385544 Affx-122971234 AX-123255902 18 21892969 AAGCCCAAGTTCTAACCTCTTTCTCGTCTCTCTGG[C/T]GCTCCAGCATCATCAGGATGGGGCACTAGGGTTCT Y 2 1 2 1 101000 f 74 goat snp35661-scaffold43-2257868 18 23846099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446528 Affx-122925020 AX-123316864 18 21940416 GCTACGTGGAAAAGGGGTTAATTGTAAATGGAGCC[A/G]TGGTTATGGGGAGAACTCCAGGCAGGTACTGGTTT R 2 1 2 1 101000 f 74 goat snp35660-scaffold43-2210421 18 23894157 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432123 Affx-122936446 AX-123302464 18 21971441 TCCTACAAAAATAAAACAGGCAAACCTTGATTATC[A/G]TGTGAGATCAATTAATGAGCACTGCTATTATCCTT R 2 1 2 1 101000 r 74 goat snp35659-scaffold43-2179396 18 23925101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409931 Affx-122952874 AX-123280282 18 22003155 CTCTGGAAGCTCTGTCCTTAGCCCCTGGGAGGGAC[A/G]AGAGCTCTGAGTGGGCACATTCCCGTCCAGGCACA R 2 1 2 1 201000 r 74 goat snp35658-scaffold43-2147682 18 23956833 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603580 Affx-1002479605 AX-413837735 18 22011865 GAAGTATGCGAAGTTTATAGCAAAATTAAAAGAAT[A/G]AATATGAAATGACTACCTTTGCAGTGTTGTGATGA R 2 1 2 1 101000 r 74 goat 18_22011865_RH-map 18 22011865 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603517 Affx-1002479606 AX-413837682 18 22032962 ATTTGTCATTTCTTGCCTTTGTTTACCTATTGGTT[G/T]TATGTCTGGATGATCTGTTCATTCATGAAGTAGGG K 2 1 2 1 202000 f 74 goat 18_22032962_RH-map 18 22032962 G T 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38385029 Affx-122971858 AX-123255387 18 22084687 TTTGGGCCCAGGCCCCACTAGGGTCTGGAAGGTAC[A/G]CAAGAATGAGAAAACATCCCTGTCATGGTTATAGA R 2 1 2 1 101000 r 74 goat snp35656-scaffold43-2066150 18 24037932 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800526 Affx-122954549 AX-385287446 18 22121417 CCAGGCAACAGAATCACTTAGCCCACAGATGTCAA[C/T]AGTGCCAAGTCTGAGAAGCCCTCCCATCTACTCAG Y 2 1 2 1 101000 r 74 goat snp35655-scaffold43-2029420 18 24074733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603520 Affx-1002479607 AX-413837685 18 22135767 ACCATGATCTTAGTTTTTTGGATGTTGTGTTTTAA[A/G]CCAACTTCACTCTCCTCTTTCACCCTCATCAAGAA R 2 1 2 1 303000 f 74 goat 18_22135767_RH-map 18 22135767 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603585 Affx-1002479608 AX-413837739 18 22156466 TTATGTGTTCACTGGAATAGCACTTTTAATTTCCT[C/T]CAAGAAATTTTCCTTTGCACTCACAACTTTGCTAA Y 2 1 2 1 101000 r 74 goat 18_22156466_RH-map 18 22156466 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38387680 Affx-122969824 AX-123258038 18 22158229 TTGATCCCTCCAGCCTGGAAGAATGAGAATGGGAG[C/T]GACATCCAGCTGTTCCTGATCTCCATCTGAGTCAC Y 2 1 2 1 201000 r 74 goat snp35654-scaffold43-1992608 18 24111362 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603524 Affx-1002479609 AX-413837689 18 22176186 TTTCATACTCTGTCGTCCCCTTCTCCTCCTGCCTT[C/T]AGTCTTTCCTAGCATTAGGGTCTTTTCCAATGGAT Y 2 1 2 1 303000 f 74 goat 18_22176186_RH-map 18 22176186 T C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38392683 Affx-122966419 AX-123263040 18 22188577 TTGAACACAGTTCCCTGTGCTAAGTGTCTTTTCCT[A/G]TCTTCATAGTACCTACTCTATAGGTGGTTCATAGT R 2 1 2 1 201000 r 74 goat snp35653-scaffold43-1962260 18 24141755 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403903 Affx-122957485 AX-123274255 18 22237623 ATCAGGGCAAGGCCGGAGTAAAGCCCAAGAAAACC[A/G]CACTGGCTCTGGGGCTCTGACTGACATCATCTTTG R 2 1 2 1 202000 f 74 goat snp35652-scaffold43-1913214 18 24190891 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603526 Affx-1002479610 AX-413837691 18 22264090 TGGCTTACCACAGGACACTGAATATAGTTCCCTAC[A/T]ATACCTGCTATACATTAGGACCTTGTTGTTTATCC W 4 1 2 1 103000 f 74 goat 18_22264090_RH-map 18 22264090 A T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603591 Affx-1002479611 AX-413837743 18 22279254 GAGTGTACTCTTCATGGTGTTCTACCACAAGTCAC[C/T]GTCAACAGTTTTAGCTATTTTATTTCTAAGCTGTT Y 2 1 2 1 201000 r 74 goat 18_22279254_RH-map 18 22279254 C T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38388067 Affx-122969524 AX-123258425 18 22283452 AGTTACTTCTGCAGTTGCTCACTAAGCATCTATTA[C/T]GTACTGGGCTCAGAGGAAACAAAGATAAATAAGAT Y 2 1 2 1 101000 f 74 goat snp35651-scaffold43-1867385 18 24236881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430163 Affx-122937373 AX-123300504 18 22327198 TAATTCAGACAAAAACAAACAATTTAATTTTGTTT[C/T]TGAAATAAGGATGAAAGAGTGTAGAAATCACGTGA Y 2 1 2 1 103000 r 74 goat snp35650-scaffold43-1823639 18 24280556 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603531 Affx-1002479612 AX-413837696 18 22355034 AGACATCATTTTGCCAACAAAGATCTGTACAGTCA[A/T]AGCTATGGTTTTTCCAGTAGTCATATATGGATGGG W 4 1 2 1 103000 f 74 goat 18_22355034_RH-map 18 22355034 A T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38416329 Affx-122947907 AX-123286678 18 22357120 GTGGGTAAGAGTGCAAGCCTTCTGCAGTCCTAAGT[A/G]CAGAGTCTGCTGAAGTAGATTGTCCATCTAGTTTG R 2 1 2 1 101000 r 74 goat snp35649-scaffold43-1793717 18 24310539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603533 Affx-1002479613 AX-413837698 18 22385391 AACTCTTATGTATATGTAATTATTTTAAGTTGCTG[A/G]TCTCAATTTCAAATACATTTTTAACAACTCTGCAA R 2 1 2 1 303000 f 74 goat 18_22385391_RH-map 18 22385391 G A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38379749 Affx-122975863 AX-123250107 18 22385962 CTCTATTCCTTATTAGCCATGAGACCTTGGGTGAG[A/C]CAGTCAATTTTTCTTTGCTTCTCTGCTTTTTCTAT M 2 1 2 1 101000 f 74 goat snp35648-scaffold43-1764875 18 24339383 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603535 Affx-1002479614 AX-185233746 18 22406263 GTCTTGATTCCAGCTTGTGCTTCCTCCAGCCCAGC[A/G]TTTCTCATGATGTACTCTGCAGATAAGTTAATAAG R 2 1 2 1 103000 f 74 goat 18_22406263_RH-map 18 22406263 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38381740 Affx-122974326 AX-123252098 18 22425813 CAATGGCATTCATTCCGTGAATTCTGAAGGCCCTC[G/T]CTTATGACTCTTGTAAGAAGTATCTGGGAAGTGGC K 2 1 2 1 600000 r 74 goat snp35647-scaffold43-1725024 18 22425813 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781666 Affx-122974326 AX-385268750 18 22425813 CAATGGCATTCATTCCGTGAATTCTGAAGGCCCTC[G/T]CTTATGACTCTTGTAAGAAGTATCTGGGAAGTGGC K 2 1 2 1 101000 f 74 goat snp35647-scaffold43-1725024 18 24378849 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603669 Affx-1002479615 AX-413837805 18 22443433 ACATGAAGAAGTGCTGCCCCCTTGTGGCCTTTTAC[A/G]TTAACAACACCATGAAAAGTGGTTGTGTGTGTTAC R 2 1 2 1 101000 r 74 goat 18_22443433_RH-map 18 22443433 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38376453 Affx-122978055 AX-123246812 18 22461336 AACTGTCCCACAGACATGCCTCTTTTTTCTGGTAA[C/T]AAACGACCTTGTTCTTTCTTTGGGAAGCCATTCCT Y 2 1 2 1 201000 f 74 goat snp35646-scaffold43-1689501 18 24414360 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603615 Affx-1002479616 AX-190102488 18 22484559 TTTTTTTTTTTTAAATTTTAAAATCTTTAATTCTT[A/C]CATGCGTTCCCAAACATGAACCCCCTCCCACCTCC M 2 1 2 1 303000 f 74 goat 18_22484559_RH-map 18 22484559 C A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320795125 Affx-122949349 AX-385282083 18 22502662 ATACAATTACTTTACTAACAGTTCAAGTGGACAAG[A/G]GGATATTGCCACATCCAGTGTGCTCATCAACTTTA R 2 1 2 1 101000 r 74 goat snp35645-scaffold43-1648175 18 24455562 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443299 Affx-122927464 AX-123313636 18 22533885 TGACCCTGGAGAGATTTCCAAGCCAAAACTACCGA[A/C]CTTGTAGATTCCAGGGAACCCCAAACCAGAGGTAA M 2 1 2 1 101000 f 74 goat snp35644-scaffold43-1616952 18 24487297 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603617 Affx-1002479617 AX-187948064 18 22568643 TTGGGGGCTGTTTGGAGATGTAGTTCAGTTCAGTC[A/G]CTCAGTCATGTCTGACTCTTTGAGACCCCATGGAC R 2 1 2 1 103000 f 74 goat 18_22568643_RH-map 18 22568643 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603619 Affx-1002479618 AX-413837766 18 22587389 CTTACATTTGCTGAAGTACCCTGCTGGCTCAGATG[A/G]TATAGAATCTGCCTGCAACGCATGAGTCCTGGGTT R 2 1 2 1 303000 f 74 goat 18_22587389_RH-map 18 22587389 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38412263 Affx-122950893 AX-123282612 18 22593655 GGACCTCCAACCAGTTTTTACTGAAGTCTTGGGGG[C/T]ATCGATAGTACAACACAAAGGGGAACATTTGGTTA Y 2 1 2 1 102000 f 74 goat snp35643-scaffold43-1557182 18 24547084 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603626 Affx-1002479619 AX-413837772 18 22607883 TCTGTTATCTCCTATCCTAAAGGGGAGGTAGTCTT[A/C]TGGCAATCGAAGGTGACAGTCTTCCCATCTAGACT M 2 1 2 1 101000 f 74 goat 18_22607883_RH-map 18 22607883 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38439960 Affx-122929819 AX-123310297 18 22623118 TTGACTCACGCTTACAGTGGGAGTTTCGGTCCTCT[A/G]TGTAGAAACAAGTGAGGTTCAGGCGTGGGGCCGAT R 2 1 2 1 101000 f 74 goat snp35642-scaffold43-1527719 18 24576588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380039 Affx-122975581 AX-123250397 18 22656224 CATGATCTAAAACATTTTCTTTTTTCTTCTCAAGT[A/G]CTTAGCTACATTGTTTATGGAATGCCTTGTTTTAC R 2 1 2 1 101000 r 74 goat snp35641-scaffold43-1494613 18 24609553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379933 Affx-122975657 AX-123250291 18 22694070 AAGGCCAGACAGCACCTCCCAGGATGGAGACCTGG[G/T]ATGATAAATACTGCTGATAATAAACATTGAATATG K 2 1 2 1 101000 r 74 goat snp35640-scaffold43-1456767 18 24647265 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603679 Affx-1002479620 AX-413837814 18 22722737 TGTTATATGAGTATTAGCTTGTTGAATCACTGAAA[A/G]CATCAATGAAATTGAGTGGTGACATCATTCCTGAT R 2 1 2 1 101000 r 74 goat 18_22722737_RH-map 18 22722737 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38387182 Affx-122970617 AX-123257540 18 22766908 ATTCAGTGCCCCAGAGCTGGAGAATTCAACGTGAC[A/G]TTCATCTTCAAGGCTGGCTGGAAAAAGGTCTTTTG R 2 1 2 1 101000 r 74 goat snp35638-scaffold43-1383929 18 24719978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603680 Affx-1002479621 AX-413837815 18 22803322 CCTGATTCCCCCTCTGGTCTTGACGTTCGCAGAGT[A/G]CCAGCTTCCCTGTTGCTGTTACTAAGCTCAGCTCT R 2 1 2 1 202000 r 74 goat 18_22803322_RH-map 18 22803322 G A 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38401176 Affx-122959352 AX-123271529 18 22804292 CTAGACAGTGGTTATCTCTGGTGACAAAAGAAGGG[C/T]GGTGATTGGCTGGAGGCCTCTCGGGGGCTTCAGTA Y 2 1 2 1 101000 f 74 goat snp35637-scaffold43-1346545 18 24757303 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603637 Affx-1002479622 AX-413837779 18 22818648 CCAGGGATTGTGAGATTTACAAGAGCTTTCTATAT[C/T]GCTCAAAGAACTCCAGGGATCAACATCTATGGATG Y 2 1 2 1 101000 f 74 goat 18_22818648_RH-map 18 22818648 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38409505 Affx-122953635 AX-123279856 18 22844311 CACTACATGGTGCTTTGCGGACCCAGGCTCCTTCC[A/G]TCTTGTAGCTCTGCTGCCTCCTAGAGCCTTGTAGG R 2 1 2 1 101000 r 74 goat snp35636-scaffold43-1306526 18 24797539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446253 Affx-122925682 AX-123316589 18 22905302 AGTTATGGAGAGGGGATCTCTGAGCCCCAGTTTCA[C/T]GCCTTGAGTCTCCACCTCTCCAAGTCAAGGATGTT Y 2 1 2 1 101000 f 74 goat snp35635-scaffold43-1245535 18 24858726 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603639 Affx-1002479623 AX-413837780 18 22934290 TTCCAATAAAACTTCATTGATGGATGTTGAAATCT[A/G]GGTTTTATATCATTTTTATGGGCCACAAAATGTTA R 2 1 2 1 400000 f 74 goat 18_22934290_RH-map 18 22934290 A G Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603641 Affx-1002479624 AX-413837781 18 22950911 GAGACAGGAGTCAAGAAGGTTCTCTTAGGAGAGTA[C/T]TATATTTACTGAAGTATAAAAACAACACTTCTCCT Y 2 1 2 1 101000 f 74 goat 18_22950911_RH-map 18 22950911 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38393243 Affx-122965473 AX-123263600 18 22961488 AGGGATGGAAAAGAAAGGACTCAGGGCCTTCAGTG[C/T]GGAGCCGAGGGCACAGTTCAGGGGACATTCCTGGG Y 2 1 2 1 101000 f 74 goat snp35634-scaffold43-1189349 18 24915630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603643 Affx-1002479625 AX-413837782 18 22966814 GAAAGAGCTCTAACCTACAAATTGTTCTTAAATGT[C/T]ATAAGATGCTTATGAATTTCTCCTTTACCAATAAT Y 2 1 2 1 101000 f 74 goat 18_22966814_RH-map 18 22966814 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38425421 Affx-122941534 AX-123295767 18 22990449 CTATAGTCAGTGCTGGAAACTATCTCCTTGTCTCT[A/G]TGTGTGTTAGTCACTCAGTCGTGTCTGACTCTCTG R 2 1 2 1 201000 f 74 goat snp35633-scaffold43-1160388 18 24944615 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402494 Affx-122958581 AX-123272847 18 23021199 GACACTTACGTGTAATTGACAGATCGTGGTAGTTC[C/T]AAGAAACCTTGAGCCCCTGATAGTCCACTGAACTC Y 2 1 2 1 101000 f 74 goat snp35632-scaffold43-1129638 18 24975593 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788276 Affx-122942849 AX-385275294 18 23061877 ATGATTCTTCTTTCTGCCTATGTGTACTCCAGCTG[C/T]GGATAAGAGTACATGGGGAATGTCTATTATTTTGA Y 2 1 2 1 202000 f 74 goat snp35631-scaffold43-1088960 18 25015970 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789956 Affx-122930039 AX-385276962 18 23117536 ACTTCTTTCATCCAATTCCTATCCATGCAGCTCCC[A/G]CTCTGTGCCAGTTTTTCTCCCTACTGTGTTATCAC R 2 1 2 1 101000 f 74 goat snp35630-scaffold43-1033301 18 25071395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450652 Affx-122921975 AX-123320986 18 23153512 AAAGTAGATACATGAATAAACTAATAATCGAGGTC[A/G]TGTCTGGTGGTTGGAAGACATGTGAAGCTGGGACC R 2 1 2 1 101000 f 74 goat snp35629-scaffold43-997325 18 25107287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272548 Affx-1111833113 AX-519546264 18 23169638 GAATGGCTTTCGGGTCTCTGAGAAAGACACTCTTG[A/G]TTTGTAGATGATACAGTCAGCCCTCGGTAAACATA R 2 1 2 1 101000 r 74 goat 18_23169638_AF-PAKI 18 23169638 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38434214 Affx-122934852 AX-123304555 18 23190299 GTTTTTGGAACATCTTCAGCCTCACCAGGCTCTCC[G/T]GGGATAAGCCAGTAACTTTCTCATCTCTCCAGCTT K 2 1 2 1 101000 r 74 goat snp35628-scaffold43-960538 18 25142922 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795917 Affx-122935328 AX-385282869 18 23235350 ATATTTTAATAGGGTAGACTGACACAACACAAACT[A/G]TCATTACCCTTAATGATAGGGCTTAAAAGCTTAAT R 2 1 2 1 201000 r 74 goat snp35627-scaffold43-915487 18 25187303 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441957 Affx-122928569 AX-123312294 18 23277642 TCTTTGGTACAGTAACTGGACTGTTCCTACAGGAA[C/T]GTTTCAGGGTTTTCAGCTGACCTATCCTGGGCCCA Y 2 1 2 1 101000 r 74 goat snp35626-scaffold43-873195 18 25229494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397301 Affx-122962322 AX-123267656 18 23306241 GGCAAGGAGGAGGTTTCAGGAGGAAACAGCACCAG[A/C]GATGTTTGTCTCCTCTGACCCCTGGACCATTCTGA M 2 1 2 1 101000 r 74 goat snp35625-scaffold43-844596 18 25257829 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394587 Affx-122964434 AX-123264942 18 23349875 CTTATTTAATTTTGTAGTATTTTACCTTCATGCCA[G/T]AAAGAATACCACTACCAGATACATGACACAGGAAA K 2 1 2 1 101000 f 74 goat snp35624-scaffold43-800962 18 25301521 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772175 Affx-122953891 AX-385259330 18 23412654 CTATATTCTGCCCACAGGGAAACATGTTCTAGTCC[A/G]CAGGAGACTTCCAGGAACCAGGAGAAATCAATCAA R 2 1 2 1 102000 r 74 goat snp35623-scaffold43-738183 18 25364228 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418517 Affx-122946424 AX-123288865 18 23507835 GTCAGACACAACTGAGTGAGCACACACAGCTTTGA[C/T]GTTCATGGAAGGGGGAGAAGATGATGACCCTGTCA Y 2 1 2 1 103000 r 74 goat snp35621-scaffold43-643002 18 25456930 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452567 Affx-122920517 AX-123322900 18 23538679 AAGCTTGCTTTACGTTTGTGATAAAACGTGTACAC[G/T]ACTTAAAAATAAAGGAGTATGAGGGTGAGGGCTCT K 2 1 2 1 202000 f 74 goat snp35620-scaffold43-612158 18 25487973 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796900 Affx-122947233 AX-385283842 18 23575943 GCCCTGCTCTCACTTAATAGAGGATTTATATAAAC[A/G]TAGAATATAATAAGAGTTAAAGAACAGACATGGGA R 2 1 2 1 101000 f 74 goat snp35619-scaffold43-574894 18 25525743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415295 Affx-122948824 AX-123285644 18 23620409 TTTCATTTTTAAAAACCTTTAAAAAAATTTAACAC[C/T]CTCTACTATGGAACAAGAATTTAGATCTTAAAACC Y 2 1 2 1 101000 r 74 goat snp35618-scaffold43-530428 18 25570913 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790410 Affx-122970616 AX-385277413 18 23662862 GGTTCTCTCCTGGATGGTCTTCCCGGACACGATTA[C/T]TGTCAGCAATGTTAAGAGACATCCTGCATGTGGGG Y 2 1 2 1 101000 f 74 goat snp35617-scaffold43-487975 18 25613620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438172 Affx-122931838 AX-123308510 18 23716741 GCGGGGACCCCACTGGGTAGTGGGTGTACGTACGG[C/T]GGATAAGTGAGTGACTGGGTGGATGAACAGGTGGA Y 2 1 2 1 101000 r 74 goat snp35616-scaffold43-434096 18 25665712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436670 Affx-122932466 AX-123307008 18 23750652 AAGACCCAGTGGCGTTGAAGGTCCTGGCCCAGCAC[A/G]TCAGAATCTCAGACCCTCTTCCACCAGCTACTCCG R 2 1 2 1 201000 r 74 goat snp35615-scaffold43-400185 18 25699693 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381968 Affx-122974104 AX-123252326 18 23784917 GCAGAGCCCCCAGGAGTTACCAGCAGTGTGCAGTC[G/T]CTGCACCCTCTTTCACATCAGCGAGTGTCTGTGGC K 2 1 2 1 101000 r 74 goat snp35614-scaffold43-365920 18 25732248 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789147 Affx-122969357 AX-385276159 18 23838188 GGTTTTCTTGTAAATTGCCTATTGGGCCTGGAAGA[C/T]GTGTTAGCAACTGTTATATGAAACTCCACTATACA Y 2 1 2 1 101000 f 74 goat snp35613-scaffold43-312649 18 25785214 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427284 Affx-122940569 AX-123297627 18 23872610 ACATCTCTGCTAAAACAGAAACAGAGGTGGCAGAA[G/T]CAAAGAAAGGATGATCAAACTGAACAATCCCCAAA K 2 1 2 1 201000 r 74 goat snp35612-scaffold43-278227 18 25819581 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801347 Affx-122954344 AX-385288259 18 23933040 GAATGATACAAATCCTCCTAGTAAAAGGATGAACT[A/G]CCAATTAGAACCAGAAAGTGACACCTGGAATTACA R 2 1 2 1 101000 r 74 goat snp35611-scaffold43-217797 18 25881299 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779586 Affx-122966787 AX-385266689 18 23965026 AGATATAATTGCCTTTCATGATCTAAGATCATGGT[A/G]ATACTTCCCCAAAAGACAAGTGAAAATGAAAACCA R 2 1 2 1 102000 r 74 goat snp35610-scaffold43-185811 18 25913286 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410655 Affx-122952769 AX-123281005 18 24004929 GATCTATTCCCAGAGGTCTGTGATTATGAGAGGGA[A/G]CAGGGTAAATTTCATTGAAAATACATTCTGCAGCC R 2 1 2 1 101000 f 74 goat snp35609-scaffold43-145908 18 25953295 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772180 Affx-122969062 AX-385259335 18 24054024 CTAATGGAAATGTATGATGATATTAAAACAGAATC[A/G]TTAATATTTTGTAACTAAAACCCCAAACCCTATCA R 2 1 2 1 101000 r 74 goat snp35608-scaffold43-96813 18 26002530 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414006 Affx-122950272 AX-123284355 18 24103278 GATGATTAACTCTTGAGTGCAGGGTTGGGTGGGGG[G/T]AGGGGAGCGTTTGGAGATAATTCACAGGATGGTAG K 2 1 2 1 201000 r 74 goat snp35607-scaffold43-47559 18 26051789 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794168 Affx-122939879 AX-385281134 18 24149940 TGGGATTAATCAGACAAAGCCTCCATGATTTAGAA[C/T]GCAGCACAGGGAAATCAGAAGCCTGGGAACTCCAC Y 2 1 2 1 202000 r 74 goat snp35606-scaffold43-897 18 26098676 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441990 Affx-122928434 AX-123312327 18 24175111 TAGTCATCTGGGATGTGTCAGGACGTGTCAGACCC[A/G]CATCAGAGTCATTTTTGCTTGGAATTCTCAGACTT R 2 1 2 1 201000 r 74 goat snp14557-scaffold1589-24175 18 7967072 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447190 Affx-122924999 AX-123317526 18 24210319 CAGGGTGTTGGACTAACAGGTCCTAATGCCTGTCC[G/T]CCCACAGAAACAAATAAACAACTAGATGTTGATGA K 2 1 2 1 101000 f 74 goat snp14558-scaffold1589-59383 18 26161932 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445739 Affx-122926090 AX-123316076 18 24286844 AGAGTTAGTTCTGTTCCAGAAAGATAACTGTGTTA[G/T]AGAACAGTCTTTGTCACAGTGTTACTGGGAACACT K 2 1 2 1 101000 r 74 goat snp14559-scaffold1589-135908 18 26238979 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424942 Affx-122941278 AX-123295288 18 24365529 CTGACCCAGAGCCAGCCTCTGAAGCCCAGCATTGC[A/G]CAGCATCCTCCTGTCTGGCCGGTTCCCTCAGCTTT R 2 1 2 1 201000 r 74 goat snp14560-scaffold1589-214593 18 26314859 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410665 Affx-122952761 AX-123281015 18 24428399 TGAAGTTCTAATCCCTCTCTTTCAGAATGTGACTT[G/T]ACTTTGAAAAAAAGATTGTAGCAGATGTAATTAAT K 2 1 2 1 201000 r 74 goat snp14561-scaffold1589-277463 18 26377741 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409571 Affx-122953585 AX-123279922 18 24466885 GTTGTTGCAAAACAGACAAGAGCCATGATCCACAC[A/G]TCCGCATTCTTTATTTCCATGTGTAAATGGCTGCC R 2 1 2 1 101000 r 74 goat snp14562-scaffold1589-315949 18 26416368 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790632 Affx-122967211 AX-385277634 18 24496134 CCTAAGCTATTCATTTATCTTGTTGTGTGGTATCC[A/G]TGTAGGCCTCTCAAAGACAGACTTTACTATTACTT R 2 1 2 1 101000 f 74 goat snp14563-scaffold1589-345198 18 26445530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405487 Affx-122956014 AX-123275839 18 24579898 ATGTTGGATGGATCAGTCAAGCAAGCCCTCTACTC[C/T]CAGTTGGTTTGAGTTCACTGGGGAAAGGAATGTAC Y 2 1 2 1 201000 f 74 goat snp14564-scaffold1589-428962 18 26529141 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782951 Affx-122931754 AX-385270022 18 24619239 CCGAGCCCAATATTCAAACTGGTTTTCGTCCTGAA[C/T]ATTTCTCTGATCTTGAAAGCTACTGTTTTGGTGCC Y 2 1 2 1 101000 f 74 goat snp14565-scaffold1589-468303 18 26568459 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435076 Affx-122933726 AX-123305416 18 24668210 CTACCAAGATAGTGTTCCATGGTCTAGCTTAGCAC[A/G]AGTAGGAGATAGCAAACAGCTTTACTGGTCATACT R 2 1 2 1 101000 f 74 goat snp14566-scaffold1589-517274 18 26617502 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382407 Affx-122973831 AX-123252765 18 24733736 GACTCCTTCTTGCTGTTCTAACTAGCTGACAGACC[A/G]TCAACAAGCACAATACTTCTATTGTACCTAGGTTT R 2 1 2 1 101000 f 74 goat snp14567-scaffold1589-582800 18 26683154 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441234 Affx-122929506 AX-123311571 18 24775492 GTGATCCTACAAGGAGGTGCTATTATTTCCACTTC[A/G]CAGATGGAGAAACAGGCTCAGGACGGGGTGAGGAG R 2 1 2 1 101000 f 74 goat snp14568-scaffold1589-624556 18 26724938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277152 Affx-1111835768 AX-519550658 18 24789563 CACTGTATAAATCACAGTCTCTTGTAGTTCAAGCC[A/G]GGCCAAGGCGGCAGGGAGGAGACTCCTACTTGGAG R 2 1 2 1 101000 f 74 goat Random2.2K-1723 18 24789563 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320780273 Affx-122938128 AX-385267368 18 24841679 GGTGGAGCCAGGACTGGCAACAACATGCAGGATTC[A/G]GAATCCAAGTGCTTCCTAGCAGGGTCAGTTGCAGG R 2 1 2 1 101000 f 74 goat snp14569-scaffold1589-690743 18 26787116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413897 Affx-122949836 AX-123284246 18 24872247 ACCCAACACATCCCTCTTGTGGTCTCTCAGGCACT[C/T]TGACCATGTCTTAACCTGCCTCTGGGGCTCCCAAG Y 2 1 2 1 101000 f 74 goat snp14570-scaffold1589-721311 18 26825909 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416398 Affx-122947857 AX-123286747 18 24912657 GGATGGAGAGCATAAGGAAAGCCAGAAAAATAACA[C/T]CAACAGTGAAGCCATCTTCTGTTGGGAGAATCCAG Y 2 1 2 1 101000 f 74 goat snp14571-scaffold1589-761721 18 26844004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277279 Affx-1111835769 AX-519550783 18 24998583 TTCAAGACCTTGGAAACCTCAGTGTATATGGATCC[A/G]CTTCCCTGTTTTTGGCCAAAGTGTGATTTACCTGT R 2 1 2 1 101000 r 74 goat Random2.2K-1724 18 24998583 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436945 Affx-122933180 AX-123307283 18 25019764 GTCACAAGAAATTCCTTCCCTGGCTTCTCAGCGCC[A/G]TTGATGAAACCCCTTCAGAAGCAAACTCCCTGCTT R 2 1 2 1 101000 r 74 goat snp14573-scaffold1589-868828 18 26951243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390034 Affx-122968436 AX-123260391 18 25087025 TCTTTACCGCTGGACCACCAGGGAAGTCCCCTCAA[G/T]ACTTCTACTGTTGTATAGGGTTTTAGTTCGAAATT K 2 1 2 1 201000 r 74 goat snp14574-scaffold1589-936089 18 27017038 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409056 Affx-122953354 AX-123279407 18 25145524 AGGGCAGGTGCTCTCTGGACCGCTGGGCAGTGAAC[A/G]GGTGCTCTCTCAAGCTTGAACCAAGCCCTACATCA R 2 1 2 1 101000 r 74 goat snp14575-scaffold1589-994588 18 27075431 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788947 Affx-122946402 AX-385275960 18 25193834 ATGTACATAGATTTCATCACGATATAGGAAGAAAC[C/T]AATTTGTTGCACTGACAGTCACAGAAACAGCCAGC Y 2 1 2 1 101000 r 74 goat snp14576-scaffold1589-1042898 18 27122763 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421011 Affx-122944553 AX-123291358 18 25224983 TCATCCTTCCCTGTATACTCATTGGTTAGGTTTGG[C/T]GCCAATGAGCACCTCCAGCCGCAGGGGAGGCTGGG Y 2 1 2 1 103000 f 74 goat snp14577-scaffold1589-1074047 18 27154098 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379494 Affx-122976469 AX-123249852 18 25271382 GGTGGTTTTCTAGGAGCCCAAATAGCAGTCCCACA[A/C]CAAGACCACAACACCCATGCAGAAAGCAGCCCAAG M 2 1 2 1 101000 f 74 goat snp14578-scaffold1589-1120446 18 27200655 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390507 Affx-122967249 AX-123260864 18 25311872 ATCGATTGGCTCCAAAACACCAAAAGAAAATTGCA[A/G]TTTCAAAATGAGTAAATGTTTAATTCCTACCAAAC R 2 1 2 1 101000 f 74 goat snp14579-scaffold1589-1160936 18 27240626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272344 Affx-1111833680 AX-519546075 18 25360019 GTGAAGAATACCACCTCTTACCCTCCCATGTAAGT[A/C]AGGCATCTCTCAGTGGGG M 2 1 2 1 101000 f 74 goat GoatD01.001289 18 25360019 A C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320787208 Affx-122924099 AX-385274234 18 25381978 ATGTTTTTTAAACCTTTCTCATTTACTAATTTGGA[C/T]GAGTAACTTGACCTACAGAAGACCTTCACTTTATT Y 2 1 2 1 101000 f 74 goat snp14580-scaffold1589-1231042 18 27310810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771772 Affx-122949379 AX-385258929 18 25434012 GGATGCTTTTATTGCCTCTGGGGGACTCAAGCAAA[A/G]GAAGCAGGGTTACTACTTCATCAAGACTCTTCAGC R 2 1 2 1 101000 f 74 goat snp14581-scaffold1589-1283076 18 27362441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394926 Affx-122964309 AX-123265281 18 25476013 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAG[G/T]AGGCTACTTAACCTGGATCAGTGTGCTAGAATTCA K 2 1 2 1 101000 r 74 goat snp14582-scaffold1589-1325077 18 27404615 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788325 Affx-122929166 AX-385275343 18 25537600 TGACCCCATGGACTACATTGCAGTACAATGTAGAA[C/T]ACTCGATAAATGTTAAACCAGCTTTGGAAGGGCAA Y 2 1 2 1 201000 r 74 goat snp14583-scaffold1589-1386664 18 27465854 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769146 Affx-122966163 AX-385256321 18 25566234 GAGAAGGCAGGGCACACATAGGATTTTTATCTTAA[C/T]GTGGATTCAGAAAATGTGTGATTCAAAGAGGTCCC Y 2 1 2 1 101000 f 74 goat snp14584-scaffold1589-1415298 18 27494609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451298 Affx-122921293 AX-123321631 18 25612189 AGAGAAGAGAAGCATTGCTGGCTCTTAAAAGTGAA[A/C]GTGAAAGTCACTTAGTCGTGTCCAGCTCTTTGCGA M 2 1 2 1 303000 f 74 goat snp14585-scaffold1589-1461253 18 27540950 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395792 Affx-122963658 AX-123266147 18 25648949 AAACCTGAGTGGGTCCTTCCCAGCAGGCTGTGGGT[A/G]TGAGATTATAAATAAGTGACAGTTTCCATAGTTAC R 2 1 2 1 101000 r 74 goat snp14586-scaffold1589-1498013 18 27577672 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272550 Affx-1111833114 AX-519546266 18 25680218 TTCCCAATCCTGAACCCCCCTCCCACCTCCCACCC[A/G]GAATGTTACTTTTAAACTGAGACTGGAAAATAAGA R 2 1 2 1 101000 r 74 goat 18_25680218_AF-PAKI 18 25680218 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38411442 Affx-122951821 AX-123281792 18 25703613 GAGCCAGGAGTGAGGGGCTGCCCAGAGGGTCCAGC[A/G]CAGTCTCTCCCCTCCAGGAACATGACATCGAGACG R 2 1 2 1 101000 r 74 goat snp14587-scaffold1589-1552677 18 27632588 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277156 Affx-1111835770 AX-519550662 18 25705624 AGAGAGAAGGGGGCTGAGGGATGGCACCAGTCACC[A/G]CCGGCCACTTTGCCTGTGAGCTGCTGTGGGGATCT R 2 1 2 1 303000 f 74 goat Random2.2K-1725 18 25705624 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320799690 Affx-122962285 AX-385286618 18 25739186 AGCAACAAACTTACCTTTAAGTCATGTTCCTGATG[C/T]AGCTCAGCTAATACATTCATAATAGCCATTGTCCA Y 2 1 2 1 101000 r 74 goat snp14588-scaffold1589-1588250 18 27668368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396440 Affx-122962984 AX-123266795 18 25792379 GGGGTTATTAGTTACAATGTTAGCTTGCTCTGTCT[A/G]CTAACAGACATGAATGGGTGAAATTAAAAGTTACT R 2 1 2 1 101000 f 74 goat snp14589-scaffold1589-1641443 18 27721679 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430259 Affx-122937303 AX-123300600 18 25864216 TTGCTGAGAAAAGCGAGGGTATTGGGATGAGCAGT[A/G]AATAATGTTCTTCATTCTTTAAATAAATAAATCCT R 2 1 2 1 101000 f 74 goat snp14590-scaffold1589-1713280 18 27790392 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422142 Affx-122943542 AX-123292489 18 25915099 GAGTGTACTTACAGCCAATTGTTACAGCACTGTTT[A/G]TTGTTAAGACTATCCTTTCTGTATTGTCTGTGTGC R 2 1 2 1 101000 f 74 goat snp14591-scaffold1589-1764163 18 27841771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440595 Affx-122929287 AX-123310932 18 25957079 CCCATCCTCATCCTTCTTTAGGCATGTGTGCCCTC[A/G]TCTCTTTCTGGTTTTCTGTCCCAGGAGGTTTTCTA R 2 1 2 1 102000 r 74 goat snp14592-scaffold1589-1806143 18 27883968 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398017 Affx-122961780 AX-123268372 18 26003376 ATGAGAACTAAGAACAGACTTTGGATGTCTATGCA[C/T]GTGAGGACAGGCACCTTCCTGTATTCGCTCTTTGT Y 2 1 2 1 201000 f 74 goat snp14593-scaffold1589-1852440 18 27930474 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385854 Affx-122971619 AX-123256212 18 26047318 AATATGCTAATTGCAAGAGGGATCTGAAGATTGCG[C/T]GAAACATGGGTTTGCAAGAGTCTGTGGTATGCTAG Y 2 1 2 1 101000 f 74 goat snp14594-scaffold1589-1896382 18 27973817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777899 Affx-122933957 AX-385265015 18 26078058 AAAAAGCACTTATATTGTGGAATAAGACTTCTTAA[C/T]GGAGAAAAGGCATTAAACAGACCTTGTATTAGGCT Y 2 1 2 1 101000 r 74 goat snp14595-scaffold1589-1927122 18 28004098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766461 Affx-986697992 AX-385253828 18 26102903 GAACTTTTCTGCTTGCTAGATGGATTTCTGCTTTG[C/T]GTGTGAATCATTTGAAAAAGCAATTATATCTTCAA Y 2 1 2 1 600010 r 74 goat 18_26102903 18 26102903 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 320766464 Affx-986697994 AX-385253831 18 26102930 CTGCTTTGCGTGTGAATCATTTGAAAAAGCAATTA[C/T]ATCTTCAAATTTATGAAGTGGAGCTTTGTTTTTTA Y 2 1 2 1 600010 r 74 goat 18_26102930 18 26102930 Ancestral_priority_1043 ancestry 0.732 recommended IMAGE 10K 10K ancestral 320766468 Affx-986697996 AX-385253835 18 26111431 AATAATAATAATTATTAGCATCATAATTATTTATA[C/T]AATTTTAGAGTCTATTCTGCATTTATCTCAATACT Y 2 1 2 1 600010 r 74 goat 18_26111431 18 26111431 Ancestral_priority_1043 ancestry 0.668 recommended IMAGE 10K 10K ancestral 320803420 Affx-986696331 AX-385290251 18 26111554 TACTGTATCCCCTTGCCTTGGTGATCTGGGGACAG[C/T]TCCCCCAGGATGGAAATCAGGAGGGTCTCTATGGG Y 2 1 2 1 600010 f 74 goat 18_26111554 18 26111554 Ancestral_priority_1043 ancestry 0.498 neutral IMAGE 10K 10K ancestral 320789295 Affx-122950982 AX-385276306 18 26121129 TGATGAAAGGATTGTGGGTTTAATTGAGAGTGAAA[C/T]AATAACCGCAGTGAGTTGGAGACAGTAATCTGGTC Y 2 1 2 1 101000 r 74 goat snp14596-scaffold1589-1970193 18 28047690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763469 Affx-986697998 AX-385251340 18 26127191 TAAGAGGGAGTGTAGGGACCTACCTGCCTATCACT[A/G]GGCTTTGGCTGAAACAAAGAGTAAAGTCTCCTGGC R 2 1 2 1 600010 f 74 goat 18_26127191 18 26127191 Ancestral_priority_1043 ancestry 0.46 neutral IMAGE 10K 10K ancestral 320766475 Affx-986698000 AX-385253841 18 26127196 GGGAGTGTAGGGACCTACCTGCCTATCACTAGGCT[C/T]TGGCTGAAACAAAGAGTAAAGTCTCCTGGCAGCCC Y 2 1 2 1 600010 r 74 goat 18_26127196 18 26127196 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 320763473 Affx-986698002 AX-385251344 18 26127231 TTGGCTGAAACAAAGAGTAAAGTCTCCTGGCAGCC[C/T]AGAGCTCTTGAAGGGGGCCTGCAGTCATCCTGGGG Y 2 1 2 1 600010 f 74 goat 18_26127231 18 26127231 Ancestral_priority_1043 ancestry 0.624 recommended IMAGE 10K 10K ancestral 320803421 Affx-986696332 AX-385290252 18 26127820 ACACACACGGACTAGGACAGCTTCCCTTAACAATT[A/G]CATTATCCGCTTTACCCTCCTTGGTCTCTGGATAT R 2 1 2 1 600010 f 74 goat 18_26127820 18 26127820 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 320766496 Affx-986698012 AX-385253862 18 26127829 GACTAGGACAGCTTCCCTTAACAATTGCATTATCC[G/T]CTTTACCCTCCTTGGTCTCTGGATATGAAAGTCCA K 2 1 2 1 600010 r 74 goat 18_26127829 18 26127829 Ancestral_priority_1043 ancestry 0.684 recommended IMAGE 10K 10K ancestral 320763485 Affx-986698014 AX-385251355 18 26128012 ATGATTTCACAACTGCTTAACCTTTGTTTTAACAG[C/T]TCATGGGCTTCCCACTCTCTGCAGGCAAGATGGAC Y 2 1 2 1 600010 f 74 goat 18_26128012 18 26128012 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 320801387 Affx-122940987 AX-187979871 18 26154502 AAATTTCAGAGATTGACTGGGGATTGAGACAGCTA[C/T]GAAGAGGAAAATTGTGGACCTAAATAGAGAACCAA Y 2 1 2 1 101000 f 74 goat snp14597-scaffold1589-2003566 18 28080977 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440208 Affx-122930693 AX-123310545 18 26190166 TAGACATGTCGTGGGTCACCTAAGATAGATGTTTT[A/G]AGATATGAAGTAGTAGTGTTTGTGAATAAGAATGA R 2 1 2 1 101000 r 74 goat snp14598-scaffold1589-2039230 18 28117680 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429790 Affx-122938205 AX-123300131 18 26220784 CCAGAGGTTTTTTAATCCTAAATTTTGTATATATC[A/G]TGTCTATTAATATTTATGTACTTTTATTCATAGCT R 2 1 2 1 101000 f 74 goat snp14599-scaffold1589-2069848 18 28148106 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450656 Affx-122921925 AX-123320990 18 26252750 ATAGTAATAGAAGTTAAATTCCAGCTGAGATATCA[C/T]ACCATGCAGACATGTGGCCTCTTGGAGGTCCGAGG Y 2 1 2 1 101000 r 74 goat snp14600-scaffold1589-2101814 18 28180317 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394231 Affx-122964885 AX-123264586 18 26317563 TGCAGATGGATGATGAGAGGTCAGAGAAGGGATGA[C/T]TCTTAACTTCTTAGAGCCTGTTAGGCTGACTAGAC Y 2 1 2 1 101000 r 74 goat snp14602-scaffold1589-2166627 18 28245322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799432 Affx-122932143 AX-385286362 18 26371460 GTTAAACTGCCATCGGTTGATGTATGTCAGCTTCG[A/C]TTAATTGTGAATGAGCCTGATAACTGCCCTTCCCT M 2 1 2 1 101000 f 74 goat snp14603-scaffold1589-2220524 18 28300242 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436822 Affx-122932231 AX-123307160 18 26412018 TGAACAAGACTATCAGCGCTCCAACACCCAGTCTC[A/G]CACCGCACTGTGGATCCACTTAAGAAAAACTGGCT R 2 1 2 1 201000 r 74 goat snp14604-scaffold1589-2261082 18 28340885 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415505 Affx-122948688 AX-123285854 18 26443060 CATCTGACATGACTAAATTTGCCTTCTTTTTCTCT[A/G]TTTCCATAGATACCTGAATGAACCGTCTTAATAGT R 2 1 2 1 201000 r 74 goat snp14605-scaffold1589-2292124 18 28371997 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441046 Affx-122928930 AX-123311383 18 26526463 AGAGATATTCAGTAATATATCCTAGAGTTTTCCCC[A/G]TAGTCAGAAATTCTTCCCAGCTTCTAAATTAACAC R 2 1 2 1 101000 r 74 goat snp14607-scaffold1589-2375527 18 28455408 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794745 Affx-122978487 AX-385281705 18 26566379 GTTGGGCTCACCTTGTACATACTGTGTATATAACT[C/T]ACCAATTTGCGTAACAATAATCAGTGAACTGATTT Y 2 1 2 1 101000 f 74 goat snp14608-scaffold1589-2415443 18 28495402 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377766 Affx-122977358 AX-123248125 18 26602921 TTGAACAGAACCAGGAGGAATATAGTCTGTTTCTG[C/T]GGCATCATCAAGGCTAAAGATACTGTGGTGAGTGT Y 2 1 2 1 101000 r 74 goat snp14609-scaffold1589-2451985 18 28532305 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452540 Affx-122920536 AX-123322873 18 26634141 AACAGATAAATAGATGGCAATAGTTTCAATTTTAT[A/G]ATATTTGCCTGAGCAACGATCTGCCTGCCAAGAGA R 2 1 2 1 101000 r 74 goat snp14610-scaffold1589-2483205 18 28563635 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431929 Affx-122935987 AX-123302270 18 26669550 GGGAACCTTTAAAGCCATTTCCTGTGATTAGATTA[C/T]ACTCAGAATATTCAGAATTTAAATGGCCTATCAAA Y 2 1 2 1 101000 f 74 goat snp14611-scaffold1589-2518614 18 28599101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406540 Affx-122955120 AX-123276892 18 26713015 AAACTGGAAAAGAATGACAACAGCTATAGCTAAGT[C/T]ATATCAAATGTTTACTGTGCACTAGAGTCTTAGTG Y 2 1 2 1 101000 r 74 goat snp14612-scaffold1589-2562079 18 28643817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387607 Affx-122970248 AX-123257965 18 26747063 GCTGCTTTATATAATAAAAGGTTTGTTCCTTGTAG[G/T]AGGAAATGGTATTTAGAGACCACACTGTCTTATAC K 2 1 2 1 101000 f 74 goat snp14613-scaffold1589-2596127 18 28677945 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763487 Affx-986698016 AX-385251356 18 26773089 AGGACACAGTAGTTTAACAAGTAACGGAGTTCAAG[C/T]CCTAATGGGGGTTATAGATGAAGATTATGAGGGCA Y 2 1 2 1 600010 f 74 goat 18_26773089 18 26773089 Ancestral_priority_1043 ancestry 0.722 recommended IMAGE 10K 10K ancestral 320766515 Affx-986698022 AX-385253878 18 26773107 AAGTAACGGAGTTCAAGTCCTAATGGGGGTTATAG[A/G]TGAAGATTATGAGGGCAAATTTTCTATTATGATGA R 2 1 2 1 600010 r 74 goat 18_26773107 18 26773107 Ancestral_priority_1043 ancestry 0.694 recommended IMAGE 10K 10K ancestral 38398337 Affx-122962125 AX-123268692 18 26786698 AACAGTCATTAATTTTTCTTTCTTCATGCAATGCC[A/G]TTATCTTTTCCTCCACTCTCTTCTACTCTTAGTAT R 2 1 2 1 201000 r 74 goat snp14614-scaffold1589-2635762 18 28719311 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785399 Affx-122971830 AX-385272444 18 26822430 GTATTTATACTTGTCAATTGAGTCTTACAATAAGT[C/T]TGTGATATAAGAGCTACACATTCTTAGTTAAGATG Y 2 1 2 1 101000 r 74 goat snp14615-scaffold1589-2671494 18 28755170 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765946 Affx-122956095 AX-385253372 18 26852428 GGATTGGAATTTGTGCTCTTCCATTTGTGAGTTGA[A/G]CAACTTAGTTCCTGTTACTTTTTGAGTCTCAATTT R 2 1 2 1 101000 f 74 goat snp14616-scaffold1589-2701492 18 28785872 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425036 Affx-122941868 AX-123295382 18 26885072 ACTCTTGATCAAACATTAACAGACTTTTGGGGGCA[C/T]GCATAAATACAAATAAAGTTCTGCAAAGTCCTTCT Y 2 1 2 1 101000 f 74 goat snp14617-scaffold1589-2734136 18 28818656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451875 Affx-122921058 AX-123322208 18 26920327 ACCTTGTGACTCAACAGAGCAAGCTGACCACTTTA[C/T]AAGCTGAAACATTGTGAAGGGTTGAGGGGAGAGAG Y 2 1 2 1 101000 f 74 goat snp14618-scaffold1589-2769391 18 28854069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388260 Affx-122969777 AX-123258618 18 26965743 GCCCAGGTGCTGGATCCATGCTGGAACCAGATGCA[C/T]GTTCACATCTTTGAAAGTTGTAATCCAATGAAGAC Y 2 1 2 1 303000 f 74 goat snp14619-scaffold1589-2814807 18 28899452 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277158 Affx-1111835771 AX-519550664 18 27016532 GCTAAACCTGAACACTTCATGCCCTGAGGTTTTTC[A/G]ACTGACTGTGAGTAACTCAAGGGCTTCCCTGATAG R 2 1 2 1 102000 f 74 goat Random2.2K-1728 18 27016532 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38385894 Affx-122971588 AX-123256252 18 27016889 ATTTAGTCATCCTTGTCGAATTAAATCTTTACTGA[C/T]ACAGATTTACATATAGATTGCCAATAGAAAGAATT Y 2 1 2 1 101000 f 74 goat snp14620-scaffold1589-2865953 18 28950141 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441013 Affx-122928952 AX-123311350 18 27072928 ATGGATGATTTTGTGACAAGCCTATGAATCATTTT[A/G]CCCTACTAGCAGTGTTAGGGAATTATTAGAACTGT R 2 1 2 1 201000 f 74 goat snp14621-scaffold1589-2921992 18 29006148 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435492 Affx-122933434 AX-123305832 18 27111428 TAATATTGCTTGGAGACTTCCTCTTCTATCCAAGA[C/T]GGAATAACAGGGATCAGATTTACTGTCCCGTCTGA Y 2 1 2 1 101000 f 74 goat snp14622-scaffold1589-2960492 18 29045948 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431257 Affx-122937121 AX-123301598 18 27142986 AGTTCCTAAGTCATATGATAGTGGTAGTCAGAGTC[A/G]TTATTATGTCTTTCTCTAGGAGGCGTTTTAGAAAC R 2 1 2 1 101000 f 74 goat snp14623-scaffold1589-2992050 18 29077311 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274701 Affx-1111834449 AX-519548287 18 27177202 AGTGCTCTTTTCCTGGGCTTGGCCTGAAAGGAACA[A/G]GCATGGA R 2 1 2 1 102000 f 74 goat GoatD01.036462 18 27177202 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38397866 Affx-122962448 AX-123268221 18 27179682 TTCATGTCTGTTGCTAGAATCCTTAGTAGCAAATT[A/C]TGTTATTTTCCCTATCACATCCCTTATCAATGTGA M 2 1 2 1 101000 r 74 goat snp14624-scaffold1589-3028746 18 29114128 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423803 Affx-122942812 AX-123294149 18 27237240 CACATTTGTATCCCTAGCCTTTAGGAAAATACTTG[A/C]TACATAGTAACTGATTAAAATATTGAGTGAAAATG M 2 1 2 1 101000 f 74 goat snp14625-scaffold1589-3086304 18 29152859 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793278 Affx-122940284 AX-385280256 18 27294081 ATGACACCATGACTGCTGTCTGGTAGGAGTAACCT[A/G]CCTAAAGTCAGTTTGTGATCAGATTAACCATCACT R 2 1 2 1 101000 f 74 goat snp14626-scaffold1589-3143145 18 29209747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434334 Affx-122934733 AX-123304675 18 27332437 CATTCTAAATAATGCAGCATATCGTAACAGTCAGA[C/T]GGTGTATAATTCCCTCCATCTGAAACAAAATTGAT Y 2 1 2 1 101000 f 74 goat snp14627-scaffold1589-3181501 18 29247467 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444646 Affx-122926920 AX-123314983 18 27382070 CATCCATAAAGAGAATCAGAGCACTACTATTACTT[A/G]CAACAGTCAGTATTTACTGCTGGGCTGGGACTGGG R 2 1 2 1 101000 f 74 goat snp14628-scaffold1589-3231134 18 29297687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799582 Affx-122944676 AX-385286512 18 27420504 TAAAAGGTATTTTAGCTAAGTGTAATATTCTTGAA[C/T]ACCACTCTTCTTCCTTTCAAAAATCTAGCAATGTT Y 2 1 2 1 101000 r 74 goat snp14629-scaffold1589-3269568 18 29336602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436815 Affx-122932237 AX-123307153 18 27464696 CTTCTAGGTGGAAACATTTAATCACTAATACTTGA[C/T]GCCCCATCTCCGTCTTCCCACTGCTATTCTTAACA Y 2 1 2 1 101000 f 74 goat snp14630-scaffold1589-3313760 18 29380226 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790103 Affx-122934800 AX-385277110 18 27517701 GCATGGGCCATATATGTGGTAGAAGTCAGTTTCCT[A/G]CTATTCATTGACCTCTACCATACTCATACTCCTGC R 2 1 2 1 101000 f 74 goat snp14631-scaffold1589-3366765 18 29433894 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388225 Affx-122969402 AX-123258583 18 27578422 TCATTCTCATGATGTACTCAATACACTCCTATTAG[C/T]AGTTTGGCCTGCACTATGGAGAAGGAAATGGCAAT Y 2 1 2 1 201000 f 74 goat snp14632-scaffold1589-3427486 18 29494890 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418669 Affx-122946316 AX-123289017 18 27640701 ATGTACAAAGAAAGCTCAGTGACCAGGCAGTCCTG[A/C]TAACCAAGAGCAGAAGGGAATCTGCTTGAGGCTGT M 2 1 2 1 201000 f 74 goat snp14633-scaffold1589-3489765 18 29559861 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380762 Affx-122975119 AX-123251120 18 27656583 GGGTATGTCAGATCATGGTAGCTATGGCATAAAAC[A/G]GGGCTCTTTTCACTTAGAAAGCTAAATGTTTCCAT R 2 1 2 1 101000 f 74 goat snp46622-scaffold647-745608 18 29605642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403166 Affx-122958087 AX-123273519 18 27687162 TAGGACATTTTTAGCGTTTAACTCTCTACCCAAAT[A/G]TATTTCTGAAGAATTTGATCATAACTATTATCAAT R 2 1 2 1 101000 f 74 goat snp46621-scaffold647-715029 18 29636201 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400863 Affx-122959772 AX-123271217 18 27729111 CCCTGAAGAACAGGACTCCATATTCAATCTACAGA[C/T]GAGAACAGTTAATTCTATAAGAAATTACTCATGGA Y 2 1 2 1 101000 f 74 goat snp46620-scaffold647-673080 18 29678477 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421240 Affx-122944115 AX-123291587 18 27809301 TAACCCTATATTCCTGATAGAGCACGTGCTTAGTC[A/G]TTCAGTTGTGTCTGGTTCTTTGTGACCCCATGGAC R 2 1 2 1 103000 f 74 goat snp46618-scaffold647-592890 18 29758260 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424483 Affx-122941758 AX-123294829 18 27851662 TTTTTTTAATGTATTTAATTCTTCAAGGTCAGGGT[A/G]TATAAAATTTTCAAGCTTGGTCTTTCTTTTTAAAG R 2 1 2 1 101000 r 74 goat snp46617-scaffold647-550529 18 29800773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388552 Affx-122969184 AX-123258910 18 27894827 GAGCCAGTGTATTTGTTACTATTTTTTCTGTTTTG[C/T]GATTTATTAATGTCAGTAATCCTATATATTTAATG Y 2 1 2 1 201000 r 74 goat snp46616-scaffold647-507364 18 29844155 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451134 Affx-122921374 AX-123321468 18 27931421 ACTTATGTCAAGACTAAGAAGACTATGGCAGTTGG[C/T]AATGAAAATGGGTAAAAATCTACAAATTTAACAGT Y 2 1 2 1 101000 f 74 goat snp46615-scaffold647-470770 18 29881297 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772342 Affx-122963978 AX-385259495 18 27969249 TATCAATCATGGACAATTTTCATATAATACCCAAA[C/T]GGAAAGAGCCCTAAGAATCAATCCAAATAAACCAT Y 2 1 2 1 101000 r 74 goat snp46614-scaffold647-432942 18 29919447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429055 Affx-122938300 AX-123299397 18 28001216 GTTAATTTACCCCATGCAACGGGGTACTTAACCAT[G/T]AATTTCTATCAAGTCATTAGCTGGGGACTGATCCT K 2 1 2 1 102000 f 74 goat snp46613-scaffold647-400975 18 29951437 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785011 Affx-122977628 AX-385272058 18 28035993 ACCTATGTGAAAAGGTGGTTTATTAGGTAAAGATG[A/C]TGCCTTACTGCCAAACACAGTGACATCAACCTCTA M 2 1 2 1 101000 r 74 goat snp46612-scaffold647-366198 18 29986144 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390344 Affx-122967691 AX-123260701 18 28065738 CAGTTTGTTATTTTTCCAGTCACCCTGAGTGTGAT[A/G]TTGGGAATTCTGTAACAGCCTGTGACATATTCTGT R 2 1 2 1 101000 f 74 goat snp46611-scaffold647-336453 18 30016321 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408071 Affx-122954261 AX-123278422 18 28121349 GAGTATTTCAGAAGTAAAGATATTGGGATTTTTGT[A/G]TTTTGCTTTGAAGAAATGATTATTGAGTCAGTTCA R 2 1 2 1 101000 r 74 goat snp46610-scaffold647-280842 18 30073039 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415650 Affx-122948569 AX-123285999 18 28158581 ATAGAGATTTTATATTTTAATATTCTCCTTTTATA[C/T]ATGAGGAAACTGAGGCAGAACAAAGAAGTGACATT Y 2 1 2 1 303000 f 74 goat snp46609-scaffold647-243610 18 30117652 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780552 Affx-122949347 AX-385267643 18 28189490 TTGTTATTATTAAACTGTTTACTCACCTTTTTTTC[A/G]CTCTTCAACTCCCTTCTCCTATTTCTACTTTCTGC R 2 1 2 1 101000 r 74 goat snp46608-scaffold647-212701 18 30148435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384766 Affx-122972022 AX-123255124 18 28241968 GTCCTCTATTTTTTAAGACTATAATTAGGTGCCCT[A/G]TGGAACTTATGGAATTTGCTTTTTAGTCTCTGTGC R 2 1 2 1 101000 f 74 goat snp46607-scaffold647-160223 18 30202052 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272507 Affx-1111833116 AX-519546226 18 28263736 CACTAGTTTTCTGTCAGTTTGCTTGCTTTGTCCAT[A/C]CTGACAAATGCATGGAGAAACTTCTGTGGCAATTC M 2 1 2 1 101000 f 74 goat 18_28263736_AF-PAKI 18 28263736 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38431270 Affx-122937109 AX-123301611 18 28275588 AGCTCCATAGAATGTACTAATTTGACAGTTGATGA[C/T]ATAACCAATTAACTATTCAGAACAACATAGTGTTT Y 2 1 2 1 101000 r 74 goat snp46606-scaffold647-126603 18 30235920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406990 Affx-122955040 AX-123277341 18 28305924 CCATTAGAGGATTTTAAGTAATTTAAAATGTTGCA[A/C]ACACAAATGAGATTCCTTTGTCTACTTTTGGAGAG M 2 1 2 1 101000 r 74 goat snp46605-scaffold647-96267 18 30266036 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385476 Affx-122971289 AX-123255834 18 28359552 TTCTGAGATAATGGCTAAGTAACAACGAACACTGA[C/T]GTTATTTAATTTGTTGCTTTAGAAAAAGTGTTTGT Y 2 1 2 1 101000 f 74 goat snp46604-scaffold647-42639 18 30320752 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798080 Affx-122978694 AX-385285015 18 28397020 CAACAGTTTATTTCATTGAGATTTATTAAAACAGA[C/T]ACTTGTCATTAATCAAAAGTCAATTGATTTCTCAA Y 2 1 2 1 101000 f 74 goat snp46603-scaffold647-5171 18 30358230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434772 Affx-122933891 AX-123305113 18 28403309 CACAAAGAGATAAGAAAATATTTTGGCATTTGTGA[C/T]AGAACCATGGTTAAACATCAGAACTGAATGATTTG Y 2 1 2 1 101000 r 74 goat snp37870-scaffold467-1019 18 30363938 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453830 Affx-122919550 AX-123324163 18 28451874 CTTGCTTCAATCTATAAATAAATCCTTGCCTCACT[A/G]CATAATATCCTTTTATTCATACAAAATAGTGATAT R 2 1 2 1 101000 f 74 goat snp37871-scaffold467-49584 18 30412687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277160 Affx-1111835772 AX-519550666 18 28478002 AATTTGGATTTTAAAATACATACTTGAAACTGGAG[A/G]TAATTAGCCAATGGAATTAAGCAAAACTAAGATCT R 2 1 2 1 101000 f 74 goat Random2.2K-1729 18 28478002 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390133 Affx-122967997 AX-123260490 18 28484531 CTTCAAGTTGACCAGTTGGTCTGACATAGAAAGGG[C/T]AGATGACAAATTTAAATCACTGATTCTCAGTCTAC Y 2 1 2 1 201000 r 74 goat snp37872-scaffold467-82241 18 30445992 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791414 Affx-122922214 AX-385278406 18 28542098 ATTATTAGAAGGTTCATTATGTAGGATTGGATCCA[G/T]CCTCCAGAACTTTCTGTTTACTTCACTCAGATGAT K 2 1 2 1 102000 r 74 goat snp37873-scaffold467-139808 18 30499912 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411582 Affx-122951621 AX-123281932 18 28636861 TGTGGATAGGCCTTGTGTGTGTGTGTTTCTGTTGC[A/G]CTGATTCAGTCTTAAGTCTCAGGCAGTTTCTGTGT R 2 1 2 1 101000 r 74 goat snp37875-scaffold467-234571 18 30595657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767161 Affx-122951857 AX-385254446 18 28678315 CTGGAAAATATTTAGGGAGGAAGGCTTCATGTAAA[C/T]GATTAAAGTTATTTTGCAAGAGCTAAATTAGTAAT Y 2 1 2 1 101000 f 74 goat snp37876-scaffold467-276025 18 30637167 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442152 Affx-122928318 AX-123312489 18 28726857 ATACTACAGAAAAAAATAAAGGATGCTGGGGGGAG[C/T]GGGAAGAAAGTAGAGAAAAGCATGCTCAGTGAAAG Y 2 1 2 1 101000 f 74 goat snp37877-scaffold467-324567 18 30686092 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406986 Affx-122955042 AX-123277337 18 28782190 TCCCAAAAGGTTCCATGTACCCCTTCTAGGTCATT[A/G]TGCCCTTCAAGGTAACCTGTGCTCTGTTTCTGTTT R 2 1 2 1 201000 r 74 goat snp37878-scaffold467-379900 18 30741310 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441830 Affx-122929059 AX-123312167 18 28811735 TTTACAACCCCATAACTTTCTTCCCCCAAACCTGC[A/G]CTCTTCATTATCATGTTATGCTGAAGCCACTGAAG R 2 1 2 1 201000 r 74 goat snp37879-scaffold467-409445 18 30771229 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277287 Affx-1111835773 AX-519550791 18 28835637 TAGCAGAGAATAAAATAGACAAAAATTTTTGTCCT[A/G]GAGGAGCTTAAACTATTAAGATAACTATTAAGATA R 2 1 2 1 101000 r 74 goat Random2.2K-1730 18 28835637 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378882 Affx-122976503 AX-123249241 18 28846388 GCATGCAACTGATAAGTGAAAAGAAAAAGATAATC[C/T]TGCACAGTCAGCAACTTTTAGCAGAAGAATCTCTG Y 2 1 2 1 101000 r 74 goat snp37880-scaffold467-444098 18 30805902 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392655 Affx-122966441 AX-123263012 18 28893355 GCAAGTCAATTACAAGATAATTACTGATTAGGAGA[C/T]GCTCACAGAAGAGAATAAACAGAATAAATAGCAAA Y 2 1 2 1 101000 f 74 goat snp37881-scaffold467-491065 18 30852556 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437355 Affx-122931937 AX-123307693 18 28929634 TGGCCACCTTCTGAGCTGCCATTTGGAAAGTCCCT[A/G]TAGCAAGGAGTGGAGAGTCCACCAGAGACAGGTAG R 2 1 2 1 201000 r 74 goat snp37882-scaffold467-527344 18 30888842 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402356 Affx-122959050 AX-123272709 18 28959238 TCATGATGCCAAAGACATCCCAAACTTTCACACAT[A/C]GTGCATCATCTGGAAGTGTGAGGACCATCTCTCCT M 2 1 2 1 101000 f 74 goat snp37883-scaffold467-556948 18 30918698 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277289 Affx-1111835774 AX-519550793 18 28963291 ACATGTACCACATTTTCTTTATCCATACCTCTGTC[A/G]ATGGACATTTAGGTAAGACCGCTAAGTCACTCTCA R 2 1 2 1 101000 r 74 goat Random2.2K-1731 18 28963291 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38442063 Affx-122928384 AX-123312400 18 28991730 ATTTCATTGATGCCCTGGAAAATTACAACACCTCA[C/T]GTTGAGTCATGAAGATAAAGAAATGGAGATTTTTT Y 2 1 2 1 101000 f 74 goat snp37884-scaffold467-589440 18 30951103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797190 Affx-122937265 AX-385284129 18 29047551 ATTCTGTCAGACCTTTAAGTAACTGGAGACTTCTG[C/T]AAAACCTTGGAAGTGAATTGGTTTAGAGACGAATT Y 2 1 2 1 101000 f 74 goat snp37885-scaffold467-645261 18 31007003 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770043 Affx-122922495 AX-385257210 18 29085194 AAGTGATTAAGAATGCACAGTTATTTTCAAATTGT[A/G]CCAAATACTCTGCAAGTATTCTCTGGCATCTGCTT R 2 1 2 1 101000 r 74 goat snp37886-scaffold467-682904 18 31043184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403618 Affx-122957549 AX-123273970 18 29115449 ACCCTGACATCCACGGCCCTTTTTATCTGCCCCCC[A/G]TTTGCTTTGCTAACCAATTTCTTTTACGTCCTGTG R 2 1 2 1 101000 r 74 goat snp37887-scaffold467-713159 18 31073364 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445513 Affx-122925182 AX-123315850 18 29166415 TCTACTTTATTATGAAATTCCCTAAATCACAGAAT[A/G]CTAAAAGTTTAGGCTATCAGACACAGAGAACTGCG R 2 1 2 1 201000 f 74 goat snp37888-scaffold467-764125 18 31124215 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274745 Affx-1111834471 AX-519548331 18 29230337 AAACTCATCAGCTGCTGCAGGCTTTTTGGTCCATC[A/G]CCTTTTATTTTCTCTGCAGCCAAAGA R 2 1 2 1 102000 f 74 goat GoatD01.037130 18 29230337 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320779443 Affx-122953514 AX-385266546 18 29241057 TTGATAGTACATTTAACAGTTCATTATAAACTAGA[C/T]GAAATTGATACATTCCTTTAAAAATGCAACTTATC Y 2 1 2 1 101000 r 74 goat snp37890-scaffold467-838767 18 31198789 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793528 Affx-122924716 AX-385280504 18 29290588 CAGTTTCCTAGTTCATAAGTACAATATTTCATGCA[C/T]ATTGTATACATAGTAAGATAATATTTTGATAACTG Y 2 1 2 1 201000 r 74 goat snp37891-scaffold467-888298 18 31252177 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780667 Affx-122937618 AX-385267757 18 29351893 TTTTATTTACATTCAGCCATGGATAGAATGATGCC[A/G]CTTTTAGGGAATTAAGACAAAGGGAGCAGATTGAA R 2 1 2 1 101000 r 74 goat snp37892-scaffold467-949603 18 31313963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797569 Affx-122920917 AX-385284508 18 29393289 GACTCCTAGGAGTATCCTTGGAATCAAATAACCAG[C/T]AGGGAGATTGGTTTGATGGTCTGAACCATGCCTGA Y 2 1 2 1 101000 r 74 goat snp37893-scaffold467-990999 18 31355645 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422569 Affx-122943757 AX-123292915 18 29448378 GCATCACCTCCCAACAAATGCATGCACAAACAAAA[A/C]GTCCATTTTTATTATAAGGTTTAAGTTTTTTCTTT M 2 1 2 1 202000 r 74 goat snp37894-scaffold467-1046088 18 31411022 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444121 Affx-122926813 AX-123314458 18 29482018 ACTGTTTTTATAAAACAAAGCTTTCTTATGTTGCC[A/G]TCTTGACTGCAAAACAATATACCATTTCTTAAAAT R 2 1 2 1 101000 r 74 goat snp37895-scaffold467-1079728 NW_017213431.1 969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783176 Affx-122952377 AX-385270243 18 29510697 TTTCTGACTTCAGAGATAAGGCTAAAATAAAGAAG[C/T]GAATATGTTCATAGCATTTATCAACTCAGCTCCCA Y 2 1 2 1 101000 r 74 goat snp37896-scaffold467-1108407 18 31474126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442361 Affx-122928026 AX-123312698 18 29541386 AAGTGGGTCTGTGAAATGGACACAGCCTTTTGAGA[C/T]GGAGTCCATAACCTGTGAGGTCAGTGTTAACTATG Y 2 1 2 1 101000 f 74 goat snp37897-scaffold467-1139096 18 31504822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798601 Affx-122937246 AX-385285534 18 29596492 GGTAGAAAGATGGATCTACAGAGTGAAGTTCAAGG[C/T]AATGGATAATGCATAGATGCACAGAAGTCTAAGGA Y 2 1 2 1 101000 f 74 goat snp37898-scaffold467-1194202 18 31560053 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781613 Affx-122977108 AX-385268697 18 29636547 TTAGAACCTACATACCTTTTATTCCAAAATCAATG[A/C]TATTAACCAGTTGATCACACTTATACCTGTGAGTT M 2 1 2 1 101000 f 74 goat snp37899-scaffold467-1234257 18 31601032 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277166 Affx-1111835775 AX-519550672 18 29655195 GTATGTCTAATTTCAGATATCTTGGATCATTTCTC[A/G]AATTATTGAAAGATTTCAGAAATTTCATCACTTTG R 2 1 2 1 101000 f 74 goat Random2.2K-1733 18 29655195 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785467 Affx-122970408 AX-385272512 18 29672923 TTGTATGTAATAGAACCAAAATGATGGAGTTGAAA[G/T]CTATCTAAAAATCATAGAGTCCAACCCTTTCATTT K 2 1 2 1 101000 f 74 goat snp37900-scaffold467-1270633 18 31637457 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764601 Affx-122932382 AX-385252246 18 29715045 AATTAAAGAAATTAAAATCTCTCCATGGTGATCCC[A/G]TAATTCCTACTTTGTGCTGTAAATGTAAGATTTGG R 2 1 2 1 101000 f 74 goat snp37901-scaffold467-1312755 18 31680353 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440059 Affx-122929743 AX-123310396 18 29747201 TCTTGTGCTACAGACTTCTTGCAAAGCCTATCAAC[A/G]TAGTGCTTACTTCACCTTCTGTTTTCTAAAGACAA R 2 1 2 1 101000 f 74 goat snp37902-scaffold467-1344911 18 31712860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393887 Affx-122965121 AX-123264242 18 29804500 ACATGCTAACTGCAACCAATTCCGAGTTTTATTTT[A/G]CACTTACAGTATTTTTTTCTTTTCTGTGTTTATTG R 2 1 2 1 101000 f 74 goat snp37903-scaffold467-1402210 18 31770250 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375517 Affx-122979119 AX-123245876 18 29859002 TACAGTCCAAACGGTAATACATCAAGGCATGACCT[A/G]TCCCCTGACATGCCCCTGTTTGTTCACTGCTCCCC R 2 1 2 1 102000 f 74 goat snp37904-scaffold467-1456712 18 31824945 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377864 Affx-122977273 AX-123248223 18 29888881 ATTACATGTCAGATAATGAGCTCAACATTTTGTTT[A/C]TATTATTTAAATAAATCCCAAAACAACTATCAGAA M 2 1 2 1 201000 r 74 goat snp37905-scaffold467-1486591 18 31855012 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438811 Affx-122930794 AX-123309148 18 29931346 ATCCCTAGACCACACTTTGAGTACTGAAGCTTTAA[C/T]GGTTACTTGTTTTTATTTGGATCTTAACCACCTGG Y 2 1 2 1 101000 f 74 goat snp37906-scaffold467-1529056 18 31897579 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454058 Affx-122919392 AX-123324391 18 29994310 GTAAAGAATGGTTAAATCCACACTAGAATCACTAG[C/T]GAGCCTCACTTTGCACTTTGGAGAGTTTAATTTAG Y 2 1 2 1 101000 f 74 goat snp37907-scaffold467-1592020 18 31957909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421595 Affx-122944494 AX-123291942 18 30047035 GCCTCCTCTCAATAAACTCCAAGGGAATTAAACCA[C/T]GCAAACCCTCTTTTAAGTCTGGACCATTCTTATAG Y 2 1 2 1 101000 f 74 goat snp37908-scaffold467-1644745 18 32009351 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394706 Affx-122964345 AX-123265061 18 30092198 TGTAGGCCGAAACGCGGAGAGGCTGAAGTTTGTGG[C/T]AAACAGGGGGCTTATTCACAAGGCAGCGAAGACAG Y 2 1 2 1 101000 r 74 goat snp37909-scaffold467-1689908 18 32054388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408487 Affx-122954415 AX-123278838 18 30140667 TATGTCCTAGCGCTATCTGAAATGTGACTATCTCC[C/T]ATGGCCACCGCTTCACCTATCATTTATTAAGTGGA Y 2 1 2 1 101000 r 74 goat snp37910-scaffold467-1738377 18 32103481 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433906 Affx-122934395 AX-123304247 18 30192757 ACCTTCATCATCTCAAAATCTTTAATTTAACCACA[C/T]CTGCAATACCCCTTTTGTCACATACTACTCACAAG Y 2 1 2 1 101000 r 74 goat snp37911-scaffold467-1790467 18 32156221 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381085 Affx-122974602 AX-123251443 18 30239750 TACATCATCCTCTAGTAGCTGCTTCCTTGATTTTT[A/G]CTAATAATCAGTGAACTAGAGTAGCTTAGTCTGTG R 2 1 2 1 201000 r 74 goat snp37912-scaffold467-1837460 18 32204003 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382263 Affx-122973941 AX-123252621 18 30281319 GTCAGACCATCAGCATGCAGCCCCTGAGACAGAGC[A/G]TCAGACTGCTGTGTAATTGGTCATCTCTTTAATCA R 2 1 2 1 101000 r 74 goat snp37913-scaffold467-1879029 18 32245970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783879 Affx-122945572 AX-385270935 18 30310592 AAATCTGACCTCCATTAGTGTCTCTATTGACTAAC[A/G]TGCAGAGAGAAAGTGACTGCCAAAGCATAACCCAT R 2 1 2 1 101000 r 74 goat snp3081-scaffold1093-1662245 18 32275559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448062 Affx-122923690 AX-123318398 18 30344792 TGTTTGAAATCCGAAGAATGTTAAGAGCCTTGCCC[A/G]TATTTTCATGAAACAAGGAGCAGAGCTTAAAAAAT R 2 1 2 1 101000 f 74 goat snp3080-scaffold1093-1628045 18 32310040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450161 Affx-122922322 AX-123320496 18 30381912 AAGCTCAAGAGGAGGTAATGTTGTTGGTAGTAAAA[C/T]AAAAGATCTGTCAAACTTATGGGTTTCAAATTAGT Y 2 1 2 1 101000 f 74 goat snp3079-scaffold1093-1590925 18 32347566 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432168 Affx-122936412 AX-123302509 18 30430615 TAAGTGCAGGATCAGATACAGGACATCTCACTGTG[A/G]TAGGAGAGTAAGGAGAAAACAAGGTCTGTTTTAGA R 2 1 2 1 101000 r 74 goat snp3078-scaffold1093-1542222 18 32396294 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785692 Affx-122927114 AX-385272733 18 30527754 CAGCCTAGTTAAGCTGATTCCCAAATCCTGGTAAT[A/G]TAGAAATCTGTATTTGCTTTAGGACACAATGTTTT R 2 1 2 1 101000 f 74 goat snp3076-scaffold1093-1445083 18 32493804 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782070 Affx-122961452 AX-385269148 18 30565531 GAAAAATTGTGTAGTATTACAGTAAAAAGACTGAC[A/G]CCATTGGCTATTGAACAAGTAGGAGAATACAACTT R 2 1 2 1 101000 r 74 goat snp3075-scaffold1093-1407306 18 32530098 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770702 Affx-122934199 AX-385257866 18 30598647 CAAGAAGTGTTCAATTTCCCTTTAATAGCCAAAGA[A/G]TGACAATGAGAAATGAGATGCTACTGAAGAAGTAG R 2 1 2 1 101000 r 74 goat snp3074-scaffold1093-1374190 18 32561838 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776508 Affx-122967868 AX-385263635 18 30657316 CATGTATATTATTCCAATACATTAATCCATCTTTC[A/G]TATTTCTTGACCTTTTCCAATGCCCTTCACCAGTC R 2 1 2 1 101000 r 74 goat snp3073-scaffold1093-1315521 18 32621464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422232 Affx-122944018 AX-123292578 18 30691161 GGATGATTAACAAAAAAACATGCATTTGGCCTCAA[C/T]TGTCCTTTAAGAAGAAGGAATTGTAAGTCAAGTCA Y 2 1 2 1 101000 f 74 goat snp3072-scaffold1093-1281676 18 32655254 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411912 Affx-122951174 AX-123282262 18 30733691 CTGTTAAAGATGAAGAGTTCATAAAGTTGAGGATA[G/T]TAAGTCTTAGGTAAATATAATTTAAAGCTGATCAT K 2 1 2 1 101000 f 74 goat snp3071-scaffold1093-1239146 18 32697767 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796857 Affx-122952620 AX-385283800 18 30766185 ATTCCACAGCTCTGTGTTTTTACCATTTCCATCCA[A/G]ATATAAAACATTTCCTTAACCAAGAAGAAAATAAT R 2 1 2 1 201000 r 74 goat snp3070-scaffold1093-1206652 18 32732107 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392384 Affx-122966228 AX-123262741 18 30795258 GAGTGGCCTACCATTACACATGTATGATCGATACA[G/T]ATTAGACTTTGCTGGAGCCAACCTGGTTTAGGAGT K 2 1 2 1 101000 r 74 goat snp3069-scaffold1093-1177579 18 32760447 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272861 Affx-1111833117 AX-519546551 18 30799662 AATCTCCAGGTAACACAGGACAATCTCTGAAAATG[A/G]GGCAGATTCTCAGGAGCTGATGTTTAGAGGGTTTC R 2 1 2 1 101000 f 74 goat 18_30799662_AF-PAKI 18 30799662 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38377219 Affx-122978172 AX-123247578 18 30849014 ACAAACCCACAAGGCTTTCTTTTCAGAAGAAAGAT[A/G]TAAGGGCATAACCTCTGAGGCATATTCTGATTTTA R 2 1 2 1 201000 r 74 goat snp3068-scaffold1093-1123823 18 32814937 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407421 Affx-122955232 AX-123277772 18 30907772 CTTTTATGTCCTAAACTTCATCTTCATTGCAAATT[A/G]CCTGACCCTTGTGGAAGATTGCTGTTGGGCACACA R 2 1 2 1 101000 f 74 goat snp3067-scaffold1093-1065065 18 32874890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431512 Affx-122936234 AX-123301853 18 30943826 ACACAGGGCATGAGCAGGGATCACGGGATTGTCCC[A/G]TCTGCCTGCTCAGAGTGCTAGACCTGACCGCCACT R 2 1 2 1 201000 f 74 goat snp3066-scaffold1093-1029011 18 32911114 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788258 Affx-122977371 AX-385275277 18 31005711 TTTGTCTGGGTGGGTCTTACTTATGAGAGACTTCC[A/G]TCATACCATGAAAGCCCATGAGAACTAAAGCTGTG R 2 1 2 1 101000 f 74 goat snp3065-scaffold1093-967126 18 32974159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453863 Affx-122919528 AX-123324196 18 31052871 ACTTTTTGATAATATTAAATAAACTAACACACTGA[A/C]CTTGAAATCCCTGAGCCAGGTCTCCTAAATATTAG M 2 1 2 1 101000 r 74 goat snp3064-scaffold1093-919966 18 33021921 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392290 Affx-122967531 AX-123262647 18 31086424 AAGGCCGGTTACAAATCCTGGCTGCAACATCTTAA[G/T]CTATGCAACCTCTGGTCTTGCTTTCCTTCAAATCT K 2 1 2 1 101000 f 74 goat snp3063-scaffold1093-886413 18 33056461 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380947 Affx-122975002 AX-123251305 18 31119127 AAAGGAGAGGCTGAACATAGGGAATAAATGCCGCA[C/T]GGCGACAGCTTTGGGGGCTGTTTGTCTAACACACT Y 2 1 2 1 201000 f 74 goat snp3062-scaffold1093-853710 18 33089397 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399322 Affx-122961374 AX-123269677 18 31148137 AAGTGCAACATGCATCTCCCCGTTTCTTTTTCTTT[A/C]TTAGACTTTTTCTTTAGAATATTCAACTTTAATGG M 2 1 2 1 202000 r 74 goat snp3061-scaffold1093-824700 18 33118425 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378024 Affx-122977582 AX-123248383 18 31210908 ATGCTGACAATTCAGTGCTTCCATCTTTAAGTGTC[A/G]CTCCTAAAAAAAAAAAAAGAAGAAGAAAAAGAAGA R 2 1 2 1 101000 f 74 goat snp3060-scaffold1093-761929 18 33181213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453074 Affx-122920054 AX-123323407 18 31273023 CTCTTATTTGACTCCATGTTCTCCATAAAAAAGAT[A/G]TCAACTTCTTCTGGATGTTAGTTGAGGTAAAATGA R 2 1 2 1 101000 f 74 goat snp3059-scaffold1093-699814 18 33243585 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387353 Affx-122970480 AX-123257711 18 31314070 CTGATCCTTTAGCAATTTTCAAATTGAGTCCTATG[C/T]AGCAGTGATTTATGTTTGAGCACCATTTGTTAAGC Y 2 1 2 1 101000 r 74 goat snp3058-scaffold1093-658767 18 33284846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438313 Affx-122931357 AX-123308651 18 31366718 ACCTTTCCTTCAAAGACTGTAATTTGATTGTTTTT[A/C]TGCTGTGAATTGATAGATGGAATATTCAGAAGGGT M 2 1 2 1 101000 r 74 goat snp3057-scaffold1093-606119 18 33338361 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780879 Affx-122951134 AX-385267966 18 31437392 ATGAGTCTGCCATCCCTCTGCCTACTAGAGATTTA[G/T]TGTATCTGCCTTTTAGAGTCAATTATCTATCAAGT K 2 1 2 1 101000 f 74 goat snp3056-scaffold1093-535445 18 33410067 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443938 Affx-122927026 AX-123314275 18 31475129 CTGTGCTTCCGTTATTCTGAGTCCTTGAGTGAACA[C/T]GGTAAGTAGACTTTCCCCACCTTTCTCTGCTGACA Y 2 1 2 1 101000 f 74 goat snp3055-scaffold1093-497708 18 33444881 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773203 Affx-122969676 AX-385260346 18 31511898 CTTCTAAAAAGCCTCACTCTTCAATCAGGGGCAAA[C/T]ATTTTAGACCTAAAGGGTATTTTGGAAGAGGAGAA Y 2 1 2 1 101000 f 74 goat snp3054-scaffold1093-460939 18 33482039 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789839 Affx-122946466 AX-385276846 18 31542487 AAAACTGACATGAATTACTTCAAAGGTTCTCTCAA[A/G]TTATTCTCATGATTAGAACTACCAGTTAAAATACA R 2 1 2 1 101000 f 74 goat snp3053-scaffold1093-430350 18 33512623 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413320 Affx-122950182 AX-123283669 18 31579726 CTATACTTTGATTTCCTATTCATTCTTCAAAATCC[A/G]ATCCAAGTGTTCATCTCCCTCACAGAAGTCTTTTG R 2 1 2 1 101000 r 74 goat snp3052-scaffold1093-393111 18 33550018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392304 Affx-122967522 AX-123262661 18 31611063 CACGTTATTCAATATTGAGCCCCCCACTAAGCATG[C/T]AAGCCCCTGAAGTCTGGAATCACAATCTTCAAATT Y 2 1 2 1 201000 r 74 goat snp3051-scaffold1093-361774 18 33581475 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384882 Affx-122971932 AX-123255240 18 31693136 TTAGATTTCCTGACTTATTTTTGTTTCAGGTAACA[C/T]GAAGGTATGGATTTGGAAAGCTTAGCAGTTTGAAG Y 2 1 2 1 101000 r 74 goat snp3050-scaffold1093-279701 18 33663559 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394920 Affx-122964313 AX-123265275 18 31764288 GTATTGTCTTACATTAGGACAAGGCCTTTCTACAG[C/T]ATGCCCAAATATTTACTTTCACATTATGAACATTT Y 2 1 2 1 101000 f 74 goat snp3048-scaffold1093-208549 18 33734565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794274 Affx-122954213 AX-385281239 18 31808406 AAGATAAATTTCACCAACCACCTCATTTAAAGTCC[A/G]TCCTCGTTTCTCTCTGTCACAGAATCCTCTTTGTC R 2 1 2 1 101000 r 74 goat snp3047-scaffold1093-164431 18 33781393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411749 Affx-122951507 AX-123282099 18 31856865 CTGTATAATGAGACTAGTAATTATTATATGTAAAC[A/G]TTTATCCTAGTTCAATGACTCTCAAACATTTTTTG R 2 1 2 1 101000 r 74 goat snp3046-scaffold1093-115972 18 33829740 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412174 Affx-122951067 AX-123282524 18 31915343 TCTGGGTATGTTATTTCAGTGAAAGAACTCCAGCT[A/C]GCTGGCCAGTGCCTGCAGGAAAGACTTCTGATTAA M 2 1 2 1 101000 f 74 goat snp3045-scaffold1093-57494 18 33889027 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383167 Affx-122973228 AX-123253525 18 31957355 TGCTGGGCTTTCCTTTACCCCAGCCCATCAGACCA[C/T]GCTCCTTAGAGACTTCTTGTACGGTTTTAATGTAT Y 2 1 2 1 201000 r 74 goat snp3044-scaffold1093-15482 18 33932410 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390741 Affx-122967911 AX-123261098 18 32008777 AAACACCATGCCAAGATCCTTCCTGCACTCTATTA[A/C]ATTTTCTCAACAGTAAGAATTATTATCATTCCCGT M 2 1 2 1 201000 r 74 goat snp22688-scaffold225-2727392 18 33992926 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274918 Affx-1111834575 AX-515031430 18 32042406 GAGGTTGCCAGAATATGTCTTCACATTGGCAATCC[A/G]TACCTGCA R 2 1 2 1 101000 f 74 goat GoatD01.042032 18 32042406 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38385289 Affx-122971692 AX-123255647 18 32056345 GGCAAGAGTGGGCATCTCTGTTATGAATGTCTTTC[C/T]GGGGAGGCTTAACTAAGTCCTTGATGGTAAAGTTC Y 2 1 2 1 101000 f 74 goat snp22687-scaffold225-2679824 18 34040309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277293 Affx-1111835776 AX-519550797 18 32062044 TGAATATTTTAGGAATGTATATATTAAGTTTTTTA[A/T]AAAAATTCTCTGTTCAAAAACTTGGCCGCTTACGT W 4 1 2 1 102000 r 74 goat Random2.2K-1735 18 32062044 A T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452099 Affx-122920849 AX-123322432 18 32085185 GGATGTTTCCTTGTAATTACAGCCAGACGTTGGGC[A/G]TCATCCTGCACAAGCAGCAAGTAGCCAGCCATGGC R 2 1 2 1 101000 f 74 goat snp22686-scaffold225-2650984 18 34069158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769517 Affx-122924982 AX-385256687 18 32128153 TCATCTGTATTCCCCTTGACCCATCCTTTTTTCTC[A/G]CCCCTAATTTGTTCATCAACTGACCTTTGGACAAG R 2 1 2 1 102000 f 74 goat snp22685-scaffold225-2608016 18 34112104 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449713 Affx-122922532 AX-123320048 18 32162613 CAAAAACTCAGTAATCAAGGCCTACAGTATTTCAA[C/T]GCATGCAAAAAAACCCATGAAGGACAAAACACCAA Y 2 1 2 1 101000 f 74 goat snp22684-scaffold225-2573556 18 34146990 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38422764 Affx-122943233 AX-123293110 18 32206670 CTCCCTTCTTTCCTAGGTCTGTCTAACAACATTCT[A/C]TCTTGAGCCTCTAAGCTCCTGCTACAAGGCCCTTC M 2 1 2 1 101000 f 74 goat snp22683-scaffold225-2529499 18 34191136 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417715 Affx-122947445 AX-123288063 18 32252389 TTTCTGTAAAGCACCTCACCTGCATCAGAGTTCAA[C/T]AAATAGTCAATATCATTGCAAGTATTAAATAAAGC Y 2 1 2 1 201000 r 74 goat snp22682-scaffold225-2483780 18 34236900 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405874 Affx-122955607 AX-123276226 18 32283098 TTCCGTGTTTGTGCGTGTGTGCCCGTGCACACGCA[C/T]GCACGCACACATGCATTTGACTCTACCACAGAGGA Y 2 1 2 1 202000 f 74 goat snp22681-scaffold225-2453071 18 34267613 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768878 Affx-122958772 AX-385256055 18 32328805 AAAGTCACTAGTATTTTAATGTTCACATTAAACAA[C/T]GCCTAGAGCTAGAAACAAATGTATCAACACTTTCA Y 2 1 2 1 101000 r 74 goat snp22680-scaffold225-2407364 18 34313267 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769648 Affx-122941000 AX-385256817 18 32361907 CAATTAGTGGTCTAGCACCTGAAATTCCTCACAGC[C/T]ATCATCCACTTGCTTGTTATTTGTCCCAGTAATGC Y 2 1 2 1 101000 f 74 goat snp22679-scaffold225-2374262 18 34346410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797311 Affx-122946337 AX-385284250 18 32467526 AAGAAAGACAGCAGTCAGACGATCGCCCAAATCAA[C/T]GTGAGATTACGATTGTGAGAAATGCCACAAAGGAG Y 2 1 2 1 101000 r 74 goat snp22676-scaffold225-2268643 18 34453092 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452285 Affx-122920694 AX-123322618 18 32522782 CTCCACTGTGCTATGCCTGTGCTTTGAGACCAGGG[A/G]AAAGCCTCAGGAGAGAAGCGCAGTGTGCTAGCCTG R 2 1 2 1 201000 r 74 goat snp22675-scaffold225-2213387 18 34508792 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437091 Affx-122932188 AX-123307429 18 32585284 AGCCCAGCTCTGTCCACTTGCCTACCTTCTTCCCA[C/T]TCCTTTAATTCTCAAGCTGGCCTGTTCTAACACAC Y 2 1 2 1 101000 r 74 goat snp22674-scaffold225-2150885 18 34571530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795576 Affx-122951133 AX-385282531 18 32621122 TGACAGAACTGACCATTTTACACTAATATCAGGAT[A/G]GCAGAGGAGAATAACAACAAACCCCACAAATATTA R 2 1 2 1 101000 r 74 goat snp22673-scaffold225-2115047 18 34607765 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393094 Affx-122965591 AX-123263451 18 32658053 GAATCTAGGCCACTGCAGAGCACATCCTACAGCTG[C/T]ACTAAACAAGAAGTCAAGCAAACAGTCTTATCCAA Y 2 1 2 1 101000 r 74 goat snp22672-scaffold225-2078116 18 34644768 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777237 Affx-122945115 AX-385264360 18 32696822 ACAATGGCCACTTACAGAGTAAAGTCACTAAATTA[C/T]ACCCAACCAGCTGTCGTTAGAATAAGATGATAGGT Y 2 1 2 1 101000 r 74 goat snp22671-scaffold225-2039347 18 34684171 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385096 Affx-122971794 AX-123255454 18 32796100 GGTCTCCTTGCCTTGAGTCCCCCCTTCCTTCCCCC[A/G]CCTCTTCCACAGTTGATGACTTCGGTTTTCTGTCT R 2 1 2 1 101000 r 74 goat snp22669-scaffold225-1940069 18 34781936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377874 Affx-122977264 AX-123248233 18 32838294 GTGATGAGCTGTGGGGAGGTGTGGAATTGCCATCT[A/G]TCTAAGGGAAAATGTCCACTTAACTTGCGGGCTTA R 2 1 2 1 101000 r 74 goat snp22668-scaffold225-1897875 18 34823923 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413447 Affx-122950682 AX-123283796 18 32932201 TGAATCGTTTCATTCTGCTTTTTTAAAGTCCCTCC[A/G]AAAGGCTCCCCACTGTCTCAAAGCAGTGTCTCTCA R 2 1 2 1 101000 r 74 goat snp22666-scaffold225-1803968 18 34918419 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277170 Affx-1111835777 AX-519550676 18 32952721 ACTGTGATACTAGACAAATTGATTCATTGCTTAGC[A/G]ATACACATTTCTCATCTAAAACAAACAAGCAAGCA R 2 1 2 1 101000 f 74 goat Random2.2K-1736 18 32952721 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430935 Affx-122936839 AX-123301276 18 32980778 TAACCCCTTATAAAAATGCCGTGACTGGAATGGCT[A/G]CACTAATATCAGACAAAATAGGCTTTAACACAAAA R 2 1 2 1 101000 f 74 goat snp22665-scaffold225-1755391 18 34966899 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379082 Affx-122976321 AX-123249441 18 33014990 CATCTACCCACGTTTTTGTATACACACAGATATCT[A/C]TATCAGGTCTTCTCAGTCATGATACTAGTGACATT M 2 1 2 1 101000 r 74 goat snp22664-scaffold225-1721179 18 35000581 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387973 Affx-122969597 AX-123258331 18 33058194 AATTGAATAATATCCTGGGTGAGGCTACTCTTTCC[A/G]CCTGAATTACCCATATCTTTGACTAGCTCACTCCT R 2 1 2 1 101000 f 74 goat snp22663-scaffold225-1677975 18 35043231 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407753 Affx-122954980 AX-123278104 18 33115248 GGAGGCCAAATGCTACAGCAAAGAAAATGTAGGCT[A/G]TGGAGTTGGACAGATCCAAGTTCAAATCTCAGCCT R 2 1 2 1 101000 f 74 goat snp22662-scaffold225-1620921 18 35100357 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426779 Affx-122940551 AX-123297125 18 33177967 CATTTGTAGTGTGACCTTGGGCGAGTCGCTTCCCC[G/T]CTGTGGATGAGCTCTGATGCGTCTTCACGCCGTAG K 2 1 2 1 101000 r 74 goat snp22661-scaffold225-1558202 18 35163009 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795450 Affx-122959202 AX-385282406 18 33208017 TGATTTTTTTTAACACACACGTGGGACTGAACTCT[C/T]AAGAGTTCCTGGGAATTCTGCACAGTTTATTTAGG Y 2 1 2 1 101000 r 74 goat snp22660-scaffold225-1528152 18 35192963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417448 Affx-122947200 AX-123287796 18 33266661 TTAGATGCCAGCAGGTGACTAGCTGGTTCCTCTGT[A/G]TGAGCATTGTGCTTAAACAATGGCATTAGTAGTTT R 2 1 2 1 101000 r 74 goat snp22659-scaffold225-1469508 18 35252171 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399056 Affx-122960903 AX-123269411 18 33296352 TTTTCTCTTATTTCCGGCGTAAGACAGTTAAGCAG[C/T]GGGTTCTCTGGAAGCCATTAAATACGGCAGAATGT Y 2 1 2 1 101000 f 74 goat snp22658-scaffold225-1439817 18 35282138 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379727 Affx-122975879 AX-123250085 18 33338795 AAAGACGTTTTCCTGCAGCTGAAGAAAGACTCATC[A/G]CTTAGTGGGTCAAAGGGGCGAGGGGACAGCAGTCT R 2 1 2 1 101000 f 74 goat snp22657-scaffold225-1397374 18 35324559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427866 Affx-122939710 AX-123298209 18 33372487 TCAATGTGGGCAGCGTCCATCCACCACCCAGTCAC[C/T]ACCTAAAGTCTGAGGTTTAGGGAAGAGGGGAGGTG Y 2 1 2 1 201000 f 74 goat snp22656-scaffold225-1363682 18 35358182 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277172 Affx-1111835778 AX-519550678 18 33383351 TATGCCATTCCTTCCAATGACAGTGATCTTCGTAA[A/G]GGGCATTATTGATGTCCCTGTCCCTGAAGGCAGGT R 2 1 2 1 101000 f 74 goat Random2.2K-1737 18 33383351 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448425 Affx-122923662 AX-123318761 18 33414522 ACTTACACGTGGACAGCAAACACAGGCTGCACCCT[C/T]GTGTAGAGACACTGACCATGTGATGAGAAACCCAG Y 2 1 2 1 101000 r 74 goat snp22655-scaffold225-1321647 18 35400688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434135 Affx-122934917 AX-123304476 18 33445286 AGAGAAGCTGAGTCCCTTGCCCAGAGTCCCATGAG[C/T]AGGCAGTGGTGTGATGTTGGCCCTGCCCAGAGCTC Y 2 1 2 1 201000 r 74 goat snp22654-scaffold225-1290883 18 35432318 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400282 Affx-122960088 AX-123270637 18 33474409 ACTAGGATCTCAGTTCCATGCCTCACTTTTTTGCC[G/T]CTACAATTTACATCCACAAAACCTATTAACTTCCC K 2 1 2 1 201000 r 74 goat snp22653-scaffold225-1261760 18 35461256 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392927 Affx-122965707 AX-123263284 18 33511200 GACGACTTGCTGCCACCTGCTTCAGCTGCTAAGGG[A/G]AGCCTCACCCTCCTGGCAGTGCTGGGCTCATTACC R 2 1 2 1 101000 f 74 goat snp22652-scaffold225-1224969 18 35497926 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272863 Affx-1111833118 AX-519546553 18 33544490 ACCTTGTCTACTCCAGAACCAGGAAGGGAAAAACA[A/G]GATAATAAGAAAATGTTTCCTAGATAAGCAGATCT R 2 1 2 1 101000 f 74 goat 18_33544490_AF-PAKI 18 33544490 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38385663 Affx-122971152 AX-123256021 18 33554719 GTCCCTATCCTACCCCTAACACTCATCCGCCTTCA[C/T]GGAGCTCAGAACTGAGGAGCAGCCACTCTCTGACG Y 2 1 2 1 201000 r 74 goat snp22651-scaffold225-1181450 18 35541255 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387385 Affx-122970426 AX-123257743 18 33613084 CTTTTCTCTAAAGGACCTGTGTCAGTGTTCACTTA[C/T]GCCTACAAATGTATAGGGGTTCCTGTTTCCCATGT Y 2 1 2 1 101000 f 74 goat snp22650-scaffold225-1123085 18 35600313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450741 Affx-122921861 AX-123321075 18 33642948 TGGCAGAGAGGCTGGACAGTGCTAAGCCAAGGGTT[A/G]CCATTGTGTATAGGGGGCTCAGGAATGTTGCTTGG R 2 1 2 1 101000 f 74 goat snp22649-scaffold225-1093221 18 35630278 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448522 Affx-122923446 AX-123318858 18 33674950 CTACACGCGCATCGTTTTCGCTCCATTACTGATTC[A/G]CATGGTCTGAAAACGCAGCTTTGGGGGCAGGGTGG R 2 1 2 1 101000 f 74 goat snp22648-scaffold225-1061219 18 35662187 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390248 Affx-122967761 AX-123260605 18 33713504 GCTCCAAATCCTTTTGTAGAATGATGTCATGTGTC[G/T]TTAGAAAATAAAGTTGTTTATTAGAGAATAGAGCA K 2 1 2 1 101000 f 74 goat snp22647-scaffold225-1022665 18 35701126 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445954 Affx-122925902 AX-123316291 18 33746284 TCTAGTGGAATACTCAGAAGTGTTTCTCCAGACCC[A/G]TGCACTCTGCAGGCGTGTGTTAATGGGTGGTGTGT R 2 1 2 1 101000 f 74 goat snp22646-scaffold225-989885 18 35733828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417679 Affx-122946822 AX-123288027 18 33884587 CTATCCACACCCACAGTCTTTTCTGTGTCTGGAAG[C/T]GCCTCACCCCTCTCCTCACTTCTGTGCCACCGCTC Y 2 1 2 1 101000 f 74 goat snp22643-scaffold225-851582 18 35872324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426633 Affx-122939951 AX-123296979 18 33927185 ATTAATTAAACGAGTACTCCATTCTCACTGGCCCA[A/G]TGGATAATCCAAGACTGGGGTCTCTGGCCACCTCA R 2 1 2 1 101000 f 74 goat snp22642-scaffold225-808984 18 35914870 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412940 Affx-122951466 AX-123283289 18 33980532 CTGCTGCTTGAAATCCTCCCCCAAGCCCCCGGTTT[A/G]CCTATGCCTGAGAGGCAAAGGCCCTCAGCCCAGCT R 2 1 2 1 103000 r 74 goat snp22641-scaffold225-755637 18 35967886 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802749 Affx-122948035 AX-385289648 18 34029601 TTAATGTTATGCTACATGGGTACAGACTGAAAGAG[C/T]GATAGAATGCATATGCATCAGAAAAACAAGTTATG Y 2 1 2 1 101000 f 74 goat snp22640-scaffold225-706568 18 36016981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415400 Affx-122948743 AX-123285749 18 34066925 GTCTATATTTATTCACTATTAAGTTCAAGTTGATT[A/C]AATAAAAAGAGCGAGATCACCTATTCACTTTATAA M 2 1 2 1 101000 r 74 goat snp22639-scaffold225-669244 18 36054414 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400393 Affx-122960003 AX-123270748 18 34116011 TGTATATAGAGAAAAGCCAGTCAGGGTGTGTTTCA[G/T]AATCAGTCAGGGTAAAGACGACAATGTTGAAGAAC K 2 1 2 1 101000 r 74 goat snp22638-scaffold225-620158 18 36103703 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437495 Affx-122932356 AX-123307833 18 34173739 AGCACCTTCATCTTCTCTCAACCCTAGATCCCATC[A/G]TCAGCTGGAAGCATAAACATCTGGAAGGCTGGAAG R 2 1 2 1 101000 f 74 goat snp22637-scaffold225-562430 18 36161160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381218 Affx-122974517 AX-123251576 18 34234564 ACAAATTTATCTCTAATGATCCTGCCCATGGTAAC[A/G]TATGTAATCCTCCTAATTCAATAGGAAAAGACCAT R 2 1 2 1 101000 f 74 goat snp22636-scaffold225-501605 18 36221742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778835 Affx-122970734 AX-385265943 18 34267314 GTAAAAGATGAAGTCCTTAAGAAATTAATCTGATT[A/C]GGAAGGAAAGTCATAGAAAGACTGGTTACACTACA M 2 1 2 1 101000 r 74 goat snp22635-scaffold225-468855 18 36254587 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410923 Affx-122952054 AX-123281273 18 34296290 CTGGATGAGGGGAAAGACCTAATGAACCTTGGAGC[A/G]TTGAAAGCCCCACACAGATGGGAACTTCATCAACT R 2 1 2 1 201000 f 74 goat snp22634-scaffold225-439879 18 36283603 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384853 Affx-122971955 AX-123255211 18 34334399 ACCCAGATATGATTGAGCACAAGTACGATTACTAG[C/T]AGCCTCTGTTCGGAGCTGTAGATGGGCCAACTGGC Y 2 1 2 1 101000 f 74 goat snp22633-scaffold225-401770 18 36321686 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784842 Affx-122954660 AX-385271889 18 34373623 AGATCACCGCTAACCAAACTGTATGAACTGAAAGG[C/T]TGCACATACAGTGAATTCTAATGGTATCCTGTACA Y 2 1 2 1 101000 f 74 goat snp22632-scaffold225-362546 18 36360921 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422394 Affx-122943389 AX-123292740 18 34460996 CAAGGAACATATTAAAAAAACAGATGAAACACTGC[A/C]TTTGTTGAAGAAAGGAAAAGAACTGCCAGCTTTTC M 2 1 2 1 101000 f 74 goat snp22630-scaffold225-275173 18 36448138 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403469 Affx-122957713 AX-123273822 18 34610626 TCACTCATCTGAAGCTGTTCTAGTGCAGTCTGGAG[C/T]TGTGTCACAGTGCCCTCTTCCCTTTCCTCACCCTC Y 2 1 2 1 101000 f 74 goat snp22627-scaffold225-125543 18 36598237 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774784 Affx-122975844 AX-385261918 18 34641684 GAATGTGCTGCCTATGGTACCACTCACGTAGATCC[A/C]CTAGATCACCTAAGAATCTCACTCATGCAGAAGAT M 2 1 2 1 101000 r 74 goat snp22626-scaffold225-94485 18 36629435 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397636 Affx-122962619 AX-123267991 18 34688063 GACAGGATAGGACAACGTGGAGTTGTTATCATTAC[C/T]TGCCCTTTGGAAAGCAAATCTCAAATCAACTTCTA Y 2 1 2 1 101000 f 74 goat snp22625-scaffold225-48106 18 36674258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463550619 Affx-1110039086 AX-515032739 18 34726355 CAAACCCCACCACCCAGACTGGGGTTCACTAATGT[C/T]ATTACTAATGATATCATTACTGAGTGAGATGCCGT Y 2 1 2 1 101000 r 74 goat GoatD01.034510 18 34726355 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320773102 Affx-122969166 AX-385260245 18 34758320 AAGACTCTTCCAAGTAGTTAACCCACATTTACCTT[A/C]TCTCCTACCCGAGGCACTAGAGATTACAGAAATGA M 2 1 2 1 101000 r 74 goat snp7213-scaffold1266-2438708 18 36745438 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435788 Affx-122932860 AX-123306127 18 34799582 TTTTAAAAATCTTACCATTTTGAAAAAAAATTACC[A/G]TCACTTACTGAGTATCACTGGGCCAAGGACTGTGC R 2 1 2 1 101000 r 74 goat snp7212-scaffold1266-2397446 18 36786723 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398236 Affx-122962204 AX-123268591 18 34828231 AGAAAAGAAACAACTTCTAAGTCTATAGGTCAAAT[A/G]TTAATGGACCCAAAACTAGAATGATTTGTGTTAAA R 2 1 2 1 101000 r 74 goat snp7211-scaffold1266-2368797 18 36815453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441899 Affx-122928614 AX-123312236 18 34874865 ACTCACCCTCTAGATTCTCCAGAAGGGAGGTGGAC[A/C]TGAGAGCTCACTGTGGTTAGGCCATTTCTCTGCTG M 2 1 2 1 201000 r 74 goat snp7210-scaffold1266-2322163 18 36862118 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378359 Affx-122976826 AX-123248718 18 34944461 AAAATGACCGTTCTTCTTCAGGACTCCTTCCATCC[A/G]TCAGAATACTTCATCATTTACTAATTTTGTTGAAA R 2 1 2 1 201000 r 74 goat snp7209-scaffold1266-2252567 18 36931785 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778379 Affx-122923630 AX-385265494 18 34979033 ATGGAGAATTAACTGTAAATACTCCTAATGGCTCA[C/T]GAATTATAATTTGACAAAGCCCACTCATCTTCCCT Y 2 1 2 1 101000 r 74 goat snp7208-scaffold1266-2217995 18 36966167 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410612 Affx-122952104 AX-123280962 18 35019280 GTAGTCACTCGATCCCAGCCAACTGCAAGGGGACC[A/C]GGAGATGCAGTCTTGCCTGTCGCCCACAAAGTAGG M 2 1 2 1 101000 r 74 goat snp7207-scaffold1266-2177748 18 37006578 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419262 Affx-122946259 AX-123289610 18 35104831 GCCTCTCCCCCTGGGGAAGAGGAAGATGACAAGGA[C/T]GGAGCAGCCTCCATGGGCAGCAGAAAAAGAGCTGG Y 2 1 2 1 201000 r 74 goat snp7205-scaffold1266-2092197 18 37092200 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769745 Affx-122970899 AX-385256915 18 35153556 ATACATATAGGAAACAAGGAACAAAGAATGACAGA[C/T]GGTAGGAAAAAACTGTATAGTCAGATTTATAACAA Y 2 1 2 1 101000 f 74 goat snp7204-scaffold1266-2043472 18 37141310 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433647 Affx-122934575 AX-123303988 18 35213441 AAGTGATAATAGCAAGGCTGCAGGGCACATGGTTA[C/T]TACTTTTTTTTAAAGAAAATCACTTTCCAATATAT Y 2 1 2 1 103000 f 74 goat snp7203-scaffold1266-1983587 18 37201504 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424207 Affx-122942500 AX-123294553 18 35277057 GTGCACGGAGGACGCCTTTCTCCTGTCCTGCAGGT[A/G]CACACGGTGTTTTACCTGGACTGTTTCATCGTTCA R 2 1 2 1 101000 r 74 goat snp7202-scaffold1266-1919971 18 37264951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447428 Affx-122924385 AX-123317764 18 35308029 CCCCTCAGCTTTGCTTCTCTCCAGTAAACCACCCA[C/T]GGGAGGAGAAGAGGAATATGAAGTACAGGATGTGG Y 2 1 2 1 201000 f 74 goat snp7201-scaffold1266-1888999 18 37295931 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405885 Affx-122955600 AX-123276237 18 35358944 CCTTCCTTCCAACCTTTTAGGCCCAGAGGGAGCAA[C/T]ATCTTATCTGAAAGTGAAAGTCACCTCAGTTATGT Y 2 1 2 1 201000 f 74 goat snp7200-scaffold1266-1838084 18 37346418 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423797 Affx-122942817 AX-123294143 18 35401901 TGGGGGAAGAAATGGTTCATTTAACTCTCTCCTCC[A/G]TGAGTCAGGCCCCTTCCTAGTCACTCCCATTTCTC R 2 1 2 1 101000 f 74 goat snp7199-scaffold1266-1795127 18 37389320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397536 Affx-122962037 AX-123267891 18 35449212 CATTTGCTCAAATGGGAAAAAGATTCATTTGAAGA[C/T]GGACGTTGAAACATCACTATTGATACTATTTCAAT Y 2 1 2 1 101000 r 74 goat snp7198-scaffold1266-1747816 18 37436762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773588 Affx-122934570 AX-385260728 18 35477925 CTTGTCTTCAAATATCAACCTGACTAAAGAAAGGA[C/T]GGCTCCAGGGCAAAATTTAAATAGCTGTTCTGCAG Y 2 1 2 1 101000 r 74 goat snp7197-scaffold1266-1719103 18 37465475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795843 Affx-122974252 AX-385282796 18 35512157 GACTTCATCTCATTTCTTATTTTAGCAACACATGA[C/T]GTATCATATCAAAATAATGTCATCAATTTGATATT Y 2 1 2 1 101000 f 74 goat snp7196-scaffold1266-1684871 18 37499904 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773121 Affx-122948877 AX-385260264 18 35545601 CTTTCTAATTAACCAAACCAAGAAATTTCTCTATC[A/G]CTTTCAACAGGAAATCATATGCCATCAGCAAATAA R 2 1 2 1 101000 r 74 goat snp7195-scaffold1266-1651427 18 37533504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449757 Affx-122922451 AX-123320092 18 35602780 ACCTCCTAACATCTTTGAGGATTAAATGGGTTATA[C/T]ACATAAAGCACTCAAAGCAGCATTTATTATCAGTA Y 2 1 2 1 201000 r 74 goat snp7194-scaffold1266-1594248 18 37591000 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442579 Affx-122928499 AX-123312916 18 35645031 GTAGAAAAAGGTGGAGAACACTGTGAGCTAAGTGA[C/T]AAGGACAGGAAAACACAGGTTTGAGGCCTGTAAAG Y 2 1 2 1 101000 f 74 goat snp7193-scaffold1266-1551997 18 37633341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386300 Affx-122970925 AX-123256658 18 35689504 TAAAAACCCATGTCATCTTTTCCTGAATATGTCCT[C/T]AGCTTTCAGTTTGGCTTTTGAGATAGTGGAAAGTC Y 2 1 2 1 101000 f 74 goat snp7192-scaffold1266-1507524 18 37677870 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783899 Affx-122959153 AX-385270954 18 35734813 TTGTAAGGTGCCCTTTTTACTGAGTTTGAATGCCC[A/C]AGTGTTCTAGAGTAAGTGAAATTTTGCTAAGTTTT M 2 1 2 1 101000 f 74 goat snp7191-scaffold1266-1462215 18 37723090 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379753 Affx-122975860 AX-123250111 18 35775713 GCCAGACTGGATGATCTTGGCTCCCCTATACGGCC[A/G]TTTAGTCTTAACTGTTTACACAGTGAGAAGCATCA R 2 1 2 1 101000 r 74 goat snp7190-scaffold1266-1421315 18 37764056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427786 Affx-122939774 AX-123298129 18 35808922 CACTGCTGTCATGAACCGAAGTTATAGTATCACTC[C/T]AGGAAGATTAAAGAGCCATCAGGGGGACAGAAGGA Y 2 1 2 1 101000 f 74 goat snp7189-scaffold1266-1388106 18 37797380 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413059 Affx-122950973 AX-123283408 18 35848729 ACAAGTGACATGTGGACTGTAATCACAGAAGGCAG[C/T]TCTGAAACATAAAGGCGCTCATGGAAAAGAGTAAA Y 2 1 2 1 101000 r 74 goat snp7188-scaffold1266-1348299 18 37837426 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410582 Affx-122952125 AX-123280932 18 35900895 CTTACCCTGAGCCTAACTATGAGGCCAGGGTTAGA[G/T]CAATTAAATGAGAAGCAGACTTTGCCCTTAAAGAA K 2 1 2 1 101000 f 74 goat snp7187-scaffold1266-1296133 18 37889845 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785357 Affx-122946820 AX-385272402 18 35959100 TAATAATAATAAACTCCATTTAATTCATTTCCTCC[G/T]GTTTCCTTTTTCTCATCCTATTCTACACATCTACC K 2 1 2 1 101000 r 74 goat snp7186-scaffold1266-1237928 18 37947970 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436729 Affx-122932305 AX-123307067 18 36008697 ATCATATTCTGTGACAACCTAAACCTGTAGGAGAT[C/T]CTGGTCAACTAAAAGACCATCCAAAAAAGTAATCT Y 2 1 2 1 101000 r 74 goat snp7185-scaffold1266-1188331 18 37998276 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400424 Affx-122959975 AX-123270779 18 36052471 ATAACTGGACTAATTGTATATAAAATATATTTCTA[C/T]AGGTAGTACTGAGAATAAATTATCGTTACTAGTAA Y 2 1 2 1 103000 r 74 goat snp7184-scaffold1266-1144557 18 38042365 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408289 Affx-122953788 AX-123278640 18 36101427 CCTACCAGTACCTTCCTGCTTTGTTTTTTCTCTCC[A/G]TAATTCCTCAACTTAGCACTATCTGCCTTTCACAT R 2 1 2 1 201000 r 74 goat snp7183-scaffold1266-1095601 18 38091299 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443387 Affx-122927398 AX-123313724 18 36156066 ACATGGACAAATGGTCTTCCATCGTATTTCTAGGA[C/T]ACTTCCTAAAGATGTCTGGCATGCCATTGTAGGAA Y 2 1 2 1 101000 f 74 goat snp7182-scaffold1266-1040962 18 38146146 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426027 Affx-122941122 AX-123296373 18 36192661 TGCTTCAGCCCAGACGGGTCCCTCTGCAGAGCCCA[C/T]AGTACCTGTGGTCTCAGCTACTCAACCACACAGTC Y 2 1 2 1 101000 r 74 goat snp7181-scaffold1266-1004367 18 38182765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433415 Affx-122935092 AX-123303756 18 36227177 TTTGCTGGCTAGCAAACCCAAACCCCAAAATCCCA[C/T]GTCTGCAATGAGCCAATCACCTGCCCCTTCTCTTC Y 2 1 2 1 201000 r 74 goat snp7180-scaffold1266-969851 18 38217213 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405772 Affx-122956489 AX-123276124 18 36276606 GGTCAGCCCCAGTACAAAGAGGCTAGAGATGGACC[G/T]TGGAATGCAGAGGAGGGGCACGTGAGCTGCTGTCC K 2 1 2 1 101000 f 74 goat snp7179-scaffold1266-920422 18 38266419 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445344 Affx-122926389 AX-123315681 18 36319635 TGATGGGATATGATCTGTCTATAATGCAGCAAATT[A/C]ATGTTCTTTAGACATTTAATCTAGCAATAATGTGT M 2 1 2 1 202000 r 74 goat snp7178-scaffold1266-877393 18 38309478 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389552 Affx-122968269 AX-123259910 18 36353272 TTGTGAGGTGGCTCTATGTTTATCTAAATGAGGCC[A/G]TGGATCCTCTTCACTTTTGATATCTCCTTTGTCAA R 2 1 2 1 101000 f 74 goat snp7177-scaffold1266-843756 18 38343414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798137 Affx-122952873 AX-385285072 18 36385934 AATCTAGTTTTTTTCTCTAGATAATTGTCTTCAAA[C/T]ATCTAGCTAAAGTAAAAAGCCTTCCCAAATACATG Y 2 1 2 1 101000 r 74 goat snp7176-scaffold1266-811094 18 38376723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786107 Affx-122948525 AX-385273143 18 36421431 CACTGACAAAAGAAAATTGATCACATATTAGATCA[C/T]GAAGAAAAATCTCATTGACTCCTGTAAAGCAGAAA Y 2 1 2 1 101000 r 74 goat snp7175-scaffold1266-775597 18 38410810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768274 Affx-122920608 AX-385255455 18 36474114 ATTTTTAAAGGGCTTATAAGAAACACCTCAAAATC[A/G]TTAGAGGACAATCAACAGTTTGGTTTTACTTGCTT R 2 1 2 1 101000 r 74 goat snp7174-scaffold1266-722914 18 38464330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390011 Affx-122968038 AX-123260368 18 36573683 TAGATCATTTTTTCCAAAGATGGTGACAACAGTAT[A/G]TCCCATCCCACACGTTATTCTAACAATGTGGCACT R 2 1 2 1 101000 r 74 goat snp7172-scaffold1266-623345 18 38565330 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400949 Affx-122959703 AX-123271302 18 36605191 TCCTTCCCATTCTCCTCCTTCCCCCAACATTCATT[A/G]TGGGGAAAATTACCTACAACAGGACACTACTGGTT R 2 1 2 1 201000 r 74 goat snp7171-scaffold1266-591837 18 38596850 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410615 Affx-122952101 AX-123280965 18 36642079 CCCCACTGTCTACCAGCAGGACTTGATCATAAACA[C/T]GGGGGATTTGAGAATTCTTTACAATGCCTGTGCTT Y 2 1 2 1 101000 f 74 goat snp7170-scaffold1266-554949 18 38634334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390931 Affx-122967077 AX-123261288 18 36691346 CCATTGATGGTGAGCATCCCTGAAGGCAAAGTCCT[A/G]TTTCAGAGTCTGGTACTGACGTCCAGAAGCAGCAG R 2 1 2 1 201000 r 74 goat snp7169-scaffold1266-505682 18 38683124 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795052 Affx-122927352 AX-385282011 18 36753333 ATTATTAAAAGTCTGAGGCATTCACAAAATAAAGG[C/T]AATTAAGAAATACAAAGAGTGTAACTAATGGGCTT Y 2 1 2 1 101000 r 74 goat snp7167-scaffold1266-443695 18 38744838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797797 Affx-122926947 AX-385284736 18 36799910 CAGCACTTGTCATTCGTTTTACCAAAGTGGCTCAG[C/T]GTTGCTTCACACTGATTATCTACTAGCGCCCACTA Y 2 1 2 1 201000 r 74 goat snp7166-scaffold1266-397118 18 38791840 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776949 Affx-122938906 AX-385264073 18 36830575 TGATATGCATGCTGTGTTGTGTAGGAATAATAACC[A/G]CTCTTCATAGATGTTCACCTCCTTCTCCAGGACCC R 2 1 2 1 101000 r 74 goat snp7165-scaffold1266-366453 18 38822417 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767636 Affx-122932531 AX-385254880 18 36887567 GCACAACTGATGGACAGAAAGAGATGAATTTAAAG[C/T]ATACTTAAATTCCTGCCACTTTCCTCTTTCAGTTT Y 2 1 2 1 101000 f 74 goat snp7164-scaffold1266-309461 18 38880178 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452719 Affx-122920292 AX-123323052 18 36933191 TATGTTGTTATTTAAACATTTCCACTCTTGTGCCT[A/G]CCCCATGACCCTCACTTTCCAACCTTCAAAAACCT R 2 1 2 1 101000 r 74 goat snp7163-scaffold1266-263837 18 38928797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401184 Affx-122959348 AX-123271537 18 36984361 CATGTCTTCCCAGCTAAAAAGAACAGTGGTCATGA[C/T]GCTATACAGCAAAAAGCACCAAGATTTGTGGCATG Y 2 1 2 1 101000 r 74 goat snp7162-scaffold1266-212667 18 38979896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802256 Affx-122921100 AX-385289160 18 37046169 GAACAAGACAAATCAGAGGATGTATGTATGAATGA[C/T]GCGAAGGGACTTCCACTTTATATAATGGCAAACTA Y 2 1 2 1 101000 r 74 goat snp7161-scaffold1266-150859 18 39041786 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277174 Affx-1111835779 AX-519550680 18 37061237 GGGCACAGGGATCACATTTCTCCAGCTTGGGATAA[A/G]CCCTGTCACACAAAAATTGTGCCTGGAAAGAGGAA R 2 1 2 1 201000 f 74 goat Random2.2K-1738 18 37061237 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275308 Affx-1111834827 AX-519548883 18 37076035 TAGAATCTCAGCAGACCTTGAACTTCATATGAACC[A/G]GCTAAAGAGGCTGCTGACATGGCCACTGCAGACTT R 2 1 2 1 101000 f 74 goat GoatD01.055368 18 37076035 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38408233 Affx-122953832 AX-123278584 18 37082755 GGTGAGGAACTGGAGGCACAGACTGGTTCAGTGAC[A/G]TGCCAGAGGTCCTGGCATGAAGGAGTAGCAGGGTC R 2 1 2 1 102000 f 74 goat snp7160-scaffold1266-114273 18 39078562 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795592 Affx-122960236 AX-385282547 18 37121077 CAAGATTTCTCAGAGGGCTCTGTAATCATGTCAGG[A/G]CCACAAAATACAGTTCAAACCACTTTGTCACAAAG R 2 1 2 1 101000 f 74 goat snp7159-scaffold1266-75951 18 39116849 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385295 Affx-122971687 AX-123255653 18 37155859 AGGATTTTAGGTGGAGTGGGTGGTGTTGATGAAGT[A/G]CCTTCCTACCCTTTCCACCCTCTTGGTTGTGTTGA R 2 1 2 1 201000 f 74 goat snp7158-scaffold1266-41169 18 39151713 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789493 Affx-122957388 AX-385276502 18 37216619 AAGGCCTGTGGAAATTCTAGGTAACAGCAACACTC[A/G]TGACGCTTGACACTTCATATCTGTTCATGGGTTTC R 2 1 2 1 101000 f 74 goat snp9581-scaffold1344-19492 18 39212737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799319 Affx-122963213 AX-385286249 18 37247801 GCTGCTAAATCCACTTTCTATTTTGCATTTTCTTA[C/T]GTTGTAATGAAAAGTCATACTTTAAATCCAAGTAT Y 2 1 2 1 303000 f 74 goat snp9582-scaffold1344-50674 18 39243967 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419286 Affx-122946243 AX-123289634 18 37277937 AGCTATGTGAAGGCTGCTCTTAGAAACCAGGTCCC[C/T]GCTTAAGTCAGGGCCAAGGGGTATGGCTACATAAA Y 2 1 2 1 101000 f 74 goat snp9583-scaffold1344-80810 18 39274102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393030 Affx-122965638 AX-123263387 18 37307725 ACACCCCTCCCCTTGCAGGCAACTGCATTTCGCTT[A/G]TGGCCTTGCACAGCCTGCGGTCAGGAAAGAGCCTT R 2 1 2 1 201000 r 74 goat snp9584-scaffold1344-110598 18 39303971 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409582 Affx-122953574 AX-123279933 18 37350931 GACAGGGTGGCTGGAGGCTGATTTCCAGGCATGAA[C/T]GGCTTTGCCACACGTGCCCAGGCCAGTTCTGCCAA Y 2 1 2 1 102000 f 74 goat snp9585-scaffold1344-153804 18 39347260 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766132 Affx-122928938 AX-385253538 18 37384832 CGGCGGCTGTATATATATGCTTTTAAATTACACCC[A/G]TGTAAACTGAGTACAGCGGCTGTGAATATGGTCGG R 2 1 2 1 101000 f 74 goat snp9586-scaffold1344-187705 18 39381083 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425736 Affx-122940751 AX-123296082 18 37414766 TATGTGCTGTTTAGGTCACCAGGGGTGGGCCCTGT[C/T]GCAAGTACACCTGGTGTCTGGCCAACTCGCCCACC Y 2 1 2 1 201000 r 74 goat snp9587-scaffold1344-217639 18 39410946 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796143 Affx-122959252 AX-385283094 18 37448096 CCACATATAAATGAGTCAGGGACTGTGCCCAACGC[A/G]TGATGCCTGTTACCCCTTCCTGTATTAGTGGTAGG R 2 1 2 1 101000 f 74 goat snp9588-scaffold1344-250969 18 39444226 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420574 Affx-122945272 AX-123290921 18 37504026 GAGTCAAGATGTGGGTGTCTTGGGCATCACTGCCC[A/G]GGATTAAAGTTCTCAGGACAACGGGGTGTGCACTT R 2 1 2 1 201000 f 74 goat snp9589-scaffold1344-306899 18 39499589 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449999 Affx-122922862 AX-123320334 18 37534766 TTCTAACTCTATAAATATTAATCACAGCTGAGCCA[C/T]GTAGAGTTTTATAATTTAATTTACCTTCTTGTACA Y 2 1 2 1 101000 f 74 goat snp9590-scaffold1344-337639 18 39530371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429660 Affx-122937663 AX-123300001 18 37572252 GTGCACAGCCCTCTGCTCTGCTGAAGGGGATGAGC[A/G]AGGGCCCAGGCCACCCTAGATTCGACCCAGCAAGC R 2 1 2 1 101000 f 74 goat snp9591-scaffold1344-375125 18 39567855 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400083 Affx-122960748 AX-123270438 18 37603950 TGGCATAGATGGAGGGCACTGACAAGGTGGCATCA[C/T]AGTCCTTTAAAAGCAAGTGTTGTTTCAGGTCAGGC Y 2 1 2 1 101000 r 74 goat snp9592-scaffold1344-406823 18 39599427 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453633 Affx-122919744 AX-123323966 18 37641080 AAAAGGGAAACACTAAAATAGCGAACCAGTACTCA[C/T]GAGAATGGCTAAAACAAGGAGAGGTTTTGCAGGTT Y 2 1 2 1 101000 f 74 goat snp9593-scaffold1344-443953 18 39636695 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431668 Affx-122936799 AX-123302009 18 37681660 AGTAAATCCTTATTTATTTGTCCCAAAAGGCCAGG[C/T]GGTGCTCTTTCTTCTCAGTGCTGGTTTCTATTCAC Y 2 1 2 1 101000 r 74 goat snp9594-scaffold1344-484533 18 39666020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436351 Affx-122933069 AX-123306690 18 37720257 GATAACTTGGATCTGCAGGAAATGGCAGACATGCC[C/T]GGGGAAAAGCACTTCTAAATGCCAGATTCATGTCT Y 2 1 2 1 201000 r 74 goat snp9595-scaffold1344-523130 18 39704515 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774623 Affx-122952674 AX-385261757 18 37772006 AGATTCATCTGGTATTGTCTGTAAGGTTGAGATTT[A/C]TTTTTTGGTGCAGGACGGTAATTATTACCAGCAAC M 2 1 2 1 101000 f 74 goat snp9596-scaffold1344-574879 18 39758433 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793966 Affx-122953350 AX-385280935 18 37821318 GGCATCATCTATTTACTTAAATCTCTCCTCAGAAC[C/T]GTATCACCGAACACTTTTAAAGTGGCAACTCTCCC Y 2 1 2 1 101000 f 74 goat snp9597-scaffold1344-624191 18 39807826 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794103 Affx-122967500 AX-385281070 18 37855856 AAATATTGCATACTCCATAAATGATATATGCACCT[A/C]TATTTGCTATAGAAACCAGTATTCCTATTACTACT M 2 1 2 1 101000 f 74 goat snp9598-scaffold1344-658729 18 39842851 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407787 Affx-122954955 AX-123278138 18 37887332 ACTGTCTCCCATTTTCCTAATGAGGAAAGTAAAAC[A/G]CAAAGAGGTTCATTCACTAAGTCACCCAAGACCAC R 2 1 2 1 102000 r 74 goat snp9599-scaffold1344-690205 18 39874687 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424067 Affx-122942054 AX-123294413 18 37938422 GTGAAGCGACAAGAGGAATCCATTATGCAAATCAT[A/G]TCACTTTGCATAATGTTTCATGACTGGAATATGCA R 2 1 2 1 101000 f 74 goat snp9600-scaffold1344-741295 18 39926799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414219 Affx-122949645 AX-123284568 18 37991636 CTAGTCCCAGCTCTTTCACAGTTTCTCCTGTTACC[C/T]TCAGTAAGTCACTGCACCCCTCTGGACCTGTTTCG Y 2 1 2 1 101000 f 74 goat snp9601-scaffold1344-794509 18 39980749 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453164 Affx-122920474 AX-123323497 18 38025474 AACATGGCCCAATTACATTGCTCCTAGAATAGACT[A/G]CTTCCTAATAGCTTCCCAAATTTTATAGCCAATAA R 2 1 2 1 101000 f 74 goat snp9602-scaffold1344-828347 18 40014776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397126 Affx-122962680 AX-123267481 18 38119668 GGAGATATGAAAGTTAAATGAAATCACATACATCA[A/G]TTGAGACCAGCAAGGTGCCTGCTACTCAGTAATCT R 2 1 2 1 101000 r 74 goat snp9604-scaffold1344-922541 18 40109706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273725 Affx-1111833764 AX-519547337 18 38153533 CCACAGCATCTGGAAAGACTGCACTGCAGACAGCA[A/G]TCAGCCTGTCTGGATTTTGTGGTCTTGAGGGCTTG R 2 1 2 1 202000 r 74 goat GoatD01.003860 18 38153533 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38425072 Affx-122941254 AX-123295418 18 38157231 CAGACTGGAGATGACCCCCAGTTCTGTTTCCATTT[A/C]GCTTGAGATATGTTCTATGACCTCTGTAGCATTTG M 2 1 2 1 201000 r 74 goat snp9605-scaffold1344-960104 18 40147335 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429196 Affx-122937949 AX-123299538 18 38192394 CCATTAACTAGTAGAGTGCTTGGCACAGAGGAGGT[A/G]TACCATAATATTTGCTGAACAGATTAATTAAATGA R 2 1 2 1 201000 r 74 goat snp9606-scaffold1344-995267 18 40182617 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274506 Affx-1111834233 AX-519548097 18 38220635 CCCTCTTCAGCTCCCAGGGACTCTCAGCATACATA[A/C]TGAACAAAACCCTGACCCAGATCAGAGCTGCAGAA M 2 1 2 1 202000 r 74 goat GoatD01.026793 18 38220635 G T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38424696 Affx-122941696 AX-123295042 18 38224503 CCCTGCACAACCCAGGTCCCACGCTATCTCTTTTT[A/G]CCACCTCTAGACGTCATGGTTCCCCCTTCCCAGGG R 2 1 2 1 101000 f 74 goat snp9607-scaffold1344-1027376 18 40214780 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391629 Affx-122966577 AX-123261986 18 38274118 GTGGATGGACATGGAGAGCCTGGGACTGAAATTGT[A/G]AGGGGTGTGTGTGGAAAGAGAAAACATTAAGCTCA R 2 1 2 1 201000 f 74 goat snp9608-scaffold1344-1076991 18 40264679 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445100 Affx-122926198 AX-123315437 18 38311589 TCACGTCAGTGCATCTAATTGCTCTGAGAATATTC[A/G]TATAGTGGGTTATCATCTTCTTTCTTTCCCATTGT R 2 1 2 1 101000 r 74 goat snp9609-scaffold1344-1114462 18 40301000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416358 Affx-122947884 AX-123286707 18 38350938 AAAGACCAAGCCACCAGCTGGGTTATTTCGATGAT[A/G]CTGTCATTGCTTCAGAACACCTTCGTCAGCCAGCC R 2 1 2 1 101000 f 74 goat snp9610-scaffold1344-1153811 18 40339555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389836 Affx-122968170 AX-123260193 18 38380964 TACTGCCATGTGGTGCTTTTCTAACCTTGCAGTGC[C/T]CAATAGCCTGGGCTGCAGATCTGTTAAGACTGAGG Y 2 1 2 1 101000 f 74 goat snp9611-scaffold1344-1183837 18 40369501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409686 Affx-122953061 AX-123280037 18 38418060 TTTTTGAGAGTGTCTATCAAGTAGGGCTTCCCAGG[C/T]GGTTCAATGGTAAAGAAACTGCCGGCCAATGCAGG Y 2 1 2 1 103000 f 74 goat snp9612-scaffold1344-1220933 18 40406509 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784503 Affx-122967683 AX-385271552 18 38447411 TTTGAATTTTTGAGAAATTACAAAAAGTGTTTGAT[A/G]CAGTATTGTCTTAGACTACAAGTATACTAAATAAG R 2 1 2 1 101000 r 74 goat snp9613-scaffold1344-1250284 18 40433816 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802786 Affx-122936045 AX-385289685 18 38492576 AAGTACATTCAAGGTTTTTCTTCACTGAAGGAGTC[A/G]TTGAAAATACTTAATTTGCTATGAATTCTGGTCAC R 2 1 2 1 101000 f 74 goat snp9614-scaffold1344-1295449 18 40477594 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793059 Affx-122971626 AX-385280037 18 38524328 GGCCTTAACTAGATACTCTATTCCAGAGCTTGATT[A/G]TTATCATTAAGATATTGAAAGATCTTAAGTCTTTG R 2 1 2 1 101000 f 74 goat snp9615-scaffold1344-1327201 18 40509071 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394417 Affx-122964604 AX-123264772 18 38568558 TGAGGTGTGGGCATGAGGTAAGGTGACTCTCCTGT[A/G]GCGCTCGTTGAATGCACCATGTGCCTTCAGGCGCA R 2 1 2 1 101000 f 74 goat snp9616-scaffold1344-1371431 18 40553632 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779792 Affx-122935344 AX-385266892 18 38597622 AGTTTAGCAGTCCTTCCCTTTATTATTTTCTAGAC[A/G]CTATATTGCTTTACCTTTCAGTTTATATTCACAAG R 2 1 2 1 101000 f 74 goat snp9617-scaffold1344-1400495 18 40582641 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379634 Affx-122975955 AX-123249992 18 38628646 GAGCAAGGTGAGATCTTGATTTTTGTCTCATGACC[A/G]TTCTGTCCATCAGCATGGAACATGGGGACTGTGGC R 2 1 2 1 101000 f 74 goat snp9618-scaffold1344-1431519 18 40613734 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451241 Affx-122921947 AX-123321574 18 38668928 ATAATGTCCCAGGGATGGTGGCTGAGTGCAAAGGG[C/T]AGCCTTGGGCCAGGGAGGCTGGAACTCCAACTTGA Y 2 1 2 1 101000 f 74 goat snp9619-scaffold1344-1471801 18 40654353 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424596 Affx-122942205 AX-123294942 18 38701699 TGCTTTATGTACTTTATTTCAATGTAATTCTCCCA[A/G]CAACCCTGTGAGGCCAGTATTGGTATTATCTCCAT R 2 1 2 1 201000 f 74 goat snp9620-scaffold1344-1504572 18 40687061 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277176 Affx-1111835780 AX-519550682 18 38757007 TGTAAGTTGCAGTGTCCTTTGGGCAATCTCAGTCT[A/G]TTTCTGTATCAGGCTACCCTTCCCAAGTAGGGAGC R 2 1 2 1 101000 f 74 goat Random2.2K-1739 18 38757007 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320772500 Affx-122965531 AX-385259651 18 38772507 CTAACAGTCTAAGCATAAGATAAAGGGGCAACACC[C/T]AAAACCATCCCCAGTTAGATTCATTTTCTTCCTGC Y 2 1 2 1 101000 r 74 goat snp9621-scaffold1344-1575380 18 40753556 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393894 Affx-122965115 AX-123264249 18 38809404 GAGACATGATGATGTCACATGGGCCACAGAAGAAT[A/G]TTCTTAACAAAAGCAGCTTCCTAGAAACATGTGAA R 2 1 2 1 101000 f 74 goat snp9622-scaffold1344-1612277 18 40790948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770083 Affx-122975760 AX-385257250 18 38872365 AATAAGGTCTTGAGATAATCTTGTGTGGTGAATAC[A/G]TTTTCTTTTTAACCACAAACTTCAGAAGTGGTAGT R 2 1 2 1 101000 f 74 goat snp9623-scaffold1344-1675238 18 40854315 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406401 Affx-122955225 AX-123276753 18 38919331 ATGATTCAGTAAAATGATGCATGTAAGTTACTCTG[C/T]ACAGTGTTTGGCACGGAGTAGATGGATATTGGCTG Y 2 1 2 1 101000 r 74 goat snp9624-scaffold1344-1722204 18 40901297 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399903 Affx-122960203 AX-123270258 18 38949592 AGTTCAAACCAAAGAGTTTACCATAGCTTCATAGA[C/T]GGCTGGTGTTATACCAATGCAAGCTTCCCCAAGGT Y 2 1 2 1 101000 f 74 goat snp9625-scaffold1344-1752465 18 40931534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790686 Affx-122956164 AX-385277688 18 38982626 TGGTATATACTAGAATGTATTTGGTTTTTAGTCAG[C/T]GTTTGGGATCAGTTACTTTTCATCTGACTTATTGA Y 2 1 2 1 101000 r 74 goat snp9626-scaffold1344-1785499 18 40964354 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397142 Affx-122962669 AX-123267497 18 39018975 CAGAGGTCAGAAATCTCACTTGGTCTCCAGTTCCT[C/T]CTACTCTGTATGTCTGGACTGAGGGAGAAACAAGG Y 2 1 2 1 201000 r 74 goat snp9627-scaffold1344-1821848 18 41000718 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797465 Affx-122947235 AX-385284404 18 39094508 GTAAGCGAAGGTGTTCAATGTGAATCTGTTTATTT[A/G]TTTGGTAGCTACAGTGTAGTAGACAGTGAGACAGA R 2 1 2 1 101000 f 74 goat snp9628-scaffold1344-1897381 18 41076893 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277303 Affx-1111835781 AX-519550807 18 39124675 GAACCCCATCCATCACTGCCTGACTGATCCCCACC[A/G]ACCCTGTCAACCGGACCCTGGCAGGTCCCAGTCTA R 2 1 2 1 303000 r 74 goat Random2.2K-1740 18 39124675 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38428125 Affx-122939067 AX-123298468 18 39145838 GAAAGTGGCAGAAATAGGTTGCAAAGATGAATAGG[A/C]AACTGCCAATAACTACGCATTGTGCAAACTGAATG M 2 1 2 1 101000 f 74 goat snp9629-scaffold1344-1948711 18 41128456 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277305 Affx-1111835782 AX-519550809 18 39162562 CGTAAGGAGACACACCCGTGAGCACACACATTCGC[A/G]GCATCAAAAACTCATCAAACAGCAGCCAGTAAATT R 2 1 2 1 102000 r 74 goat Random2.2K-1741 18 39162562 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384348 Affx-122972248 AX-123254706 18 39191486 GCCAAATATGAAAAACAATGGAAATGTTAGTCATT[A/G]CCCTCAGAAGACAGTGTTTAAGGCGTCCTGCTTCT R 2 1 2 1 101000 r 74 goat snp9630-scaffold1344-1994359 18 41174298 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783656 Affx-122957092 AX-385270715 18 39222484 AAAGGTGGGAAAACTACAGCCCATTGCCTGTTTCT[A/G]TAGATAAAGTGTTATTGGACATATTTTCAGGGCAG R 2 1 2 1 101000 f 74 goat snp9631-scaffold1344-2025357 18 41205112 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435690 Affx-122933323 AX-123306029 18 39261963 ACAGTCTGCTTCTGTTTGCAGTTTAATTTAGTCCA[A/G]TTTCCTGAGATACGTTACCCCATAGGGAAATGAAT R 2 1 2 1 101000 f 74 goat snp9632-scaffold1344-2064836 18 41244668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439826 Affx-122930469 AX-123310163 18 39392865 TCTGTCCTGTCCAGTACAGTAGTCACCGGCCATGC[A/G]TGGCTGTTTACAGTTACATTATCAAGGACAAATAA R 2 1 2 1 201000 r 74 goat snp9635-scaffold1344-2195738 18 41375876 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404930 Affx-122956437 AX-123275282 18 39426762 GTGGGAAAACGCGTATCCATGTTTGAAAGCTTACC[A/G]CTGACAGCTATTAAAAAAAGAAATTAAAGAAGTCT R 2 1 2 1 101000 f 74 goat snp9636-scaffold1344-2229635 18 41410393 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437523 Affx-122931918 AX-123307861 18 39553459 AAGGCTTCCTTCCCCAGGAAAGCTGGCGCGCTCTT[A/G]TCAGAAAGAACAGCAGAGACTGGGTAGCAAGCCTG R 2 1 2 1 101000 r 74 goat snp9639-scaffold1344-2356332 18 41533171 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452946 Affx-122920176 AX-123323279 18 39599125 CTTATATTTGAAAGTGCTATGGGTTTTATTGAGGA[G/T]AATGTCCTTATTCTTAGAAGGTACAAATATTTAGG K 2 1 2 1 201000 f 74 goat snp9640-scaffold1344-2401998 18 41578991 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445398 Affx-122925390 AX-123315735 18 39628116 CCACCATCCTGAAGTCTAGGTGGATGATTTCCACA[C/T]GTATATTTAGAATTCTATCATTTATATCTGGATTC Y 2 1 2 1 101000 f 74 goat snp9641-scaffold1344-2430989 18 41607981 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439505 Affx-122930139 AX-123309842 18 39659365 TAGGATGGCAAAGAGCTGGCTCAGCTCCTTTCTGG[A/G]CAGGTTAGTTGGGCTTTGTATGTTATATTCTGGGC R 2 1 2 1 101000 r 74 goat snp9642-scaffold1344-2462238 18 41638985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419696 Affx-122945922 AX-123290044 18 39713927 CAGTATGTGCCTTTTACTGTCAGAGCCTTAAATAA[A/G]CCTCAGTTGCTCTGGATAAAACATTTCAGATGAAA R 2 1 2 1 101000 r 74 goat snp9643-scaffold1344-2516800 18 41693302 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392105 Affx-122966358 AX-123262462 18 39753443 AATTCAGATCCCAGAACTTTGTTTTACTTAAAGAC[A/G]TTTATAGTATTTGTTTAATTAATAACAGATAAACA R 2 1 2 1 201000 r 74 goat snp9644-scaffold1344-2556316 18 41732644 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416696 Affx-122947570 AX-123287044 18 39838178 TCTCCATACTTGGAGCCGTGCCACCACCATTCCCC[A/G]GTATTGGCATTCCCAGCAAGGCCGGACTCCTGGCC R 2 1 2 1 201000 r 74 goat snp9646-scaffold1344-2641051 18 41817289 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780947 Affx-122968144 AX-385268034 18 39885769 CACGCTGACACTGGTCTATACACTGAAAATGGTAA[C/T]GTTCATGTTATGCGTGTTTTACGCACCCCAAATCC Y 2 1 2 1 101000 f 74 goat snp9647-scaffold1344-2688642 18 41864751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426016 Affx-122941129 AX-123296362 18 39966582 GACATAAATGGTAATTATGGAAAACCTGGAGAAAG[C/T]GCTTTCAATAAATTTGCATTCTCTTGGACCACTGC Y 2 1 2 1 101000 r 74 goat snp9649-scaffold1344-2769455 18 41945258 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418402 Affx-122946549 AX-123288750 18 39990507 AAAGAAATGCAAGGAAGAGTCCGTGAAAGGCATGG[C/T]GTATGAAAGGAAAATAGTCAGACCTCAGTCTTGGC Y 2 1 2 1 101000 f 74 goat snp34687-scaffold410-1493626 18 41969232 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427087 Affx-122939791 AX-123297430 18 40019804 TCTTCTGAGCCTCATAAATTCCTTGCCCACGTCCC[A/G]CTTTGAAAGAGGTCACCTTCCCCTACTCGGCCTCC R 2 1 2 1 101000 f 74 goat snp34686-scaffold410-1464329 18 41998774 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420545 Affx-122945294 AX-123290892 18 40062807 ACTTCCAGATTTCTGCTTGCCTGGGATCTGATGTC[A/G]TCTAGAGATGAAACTGAGGTTCTGGTCAGGAAGAG R 2 1 2 1 101000 f 74 goat snp34685-scaffold410-1421326 18 42041885 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381343 Affx-122974419 AX-123251701 18 40135369 GAAAGTGGCACCAAAAAATAAATGAAAGAAAGCAA[C/T]GGAAAGTGAAGGAGAAAAATTAAGAGACACAGAGG Y 2 1 2 1 201000 f 74 goat snp34684-scaffold410-1348764 18 42115590 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411887 Affx-122951193 AX-123282237 18 40167959 CTTTTAGACCCAGTATGATTTCTCTCTTTCTGAAA[C/T]GCTAAGTGACAGCGCCATCGGGCAGCCCTGTGGAG Y 2 1 2 1 101000 f 74 goat snp34683-scaffold410-1316174 18 42147484 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799703 Affx-122923505 AX-385286631 18 40199265 GTGGAGAACATAATTAGGGGAGTTTTATTTTTTTA[A/C]TCTAGATTTAGTTCTAACTAATGAGGAGGAACTAG M 2 1 2 1 101000 f 74 goat snp34682-scaffold410-1284868 18 42179094 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272913 Affx-1111833119 AX-519546600 18 40314284 AATACTTTTCATTTGTTTACCCTTGCAAATAGCAT[A/G]TCCATAAACATCCATGTTCCTACATCTTTGAGTGC R 2 1 2 1 101000 r 74 goat 18_40314284_AF-PAKI 18 40314284 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425901 Affx-122941623 AX-123296247 18 40316280 GCAAAGAGATCATTCGATATAAGTTACTCAGTTTG[C/T]AGCTGAAGGAGAAACCTGGTAGGGAGGTTAAGCAT Y 2 1 2 1 101000 f 74 goat snp34680-scaffold410-1167853 18 42295379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402219 Affx-122959156 AX-123272572 18 40347966 TTTGCTGTCAGAGTTGAAACCCCTGCAGGCACCTG[C/T]GGTAGCCAAGGCTTCCTTCGGAAACTTCAGTCCCA Y 2 1 2 1 201000 r 74 goat snp34679-scaffold410-1136167 18 42327086 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782821 Affx-122966303 AX-385269893 18 40379715 TATTAACTGCATCTCCCACAACAATGGGGTTATAA[C/T]GGATTTTTGCAAATACAGATATGTTCCCAAATAAT Y 2 1 2 1 101000 r 74 goat snp34678-scaffold410-1104418 18 42358793 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277183 Affx-1111835783 AX-519550689 18 40402909 ACTTCACTTCAGTTCTGTTTAATTTGTTAGAGCTT[A/G]TTTTGTAACCCAGGATGTGGTCTATCTTCATAAAT R 2 1 2 1 202000 f 74 goat Random2.2K-1742 18 40402909 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320790742 Affx-122965537 AX-385277743 18 40416272 ATATAATTTCCCCTACTTTATTGAAATTTAATTTC[A/G]TAATTTTCATATACAGCCAATGAACTCAGAATGGC R 2 1 2 1 202000 f 74 goat snp34677-scaffold410-1067861 18 42395325 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386746 Affx-122970137 AX-123257104 18 40507731 CAAACTCTCTTTTCCCCAAAGCAGTTTAATACAGA[A/G]ATCAAGAGAGCACCTGTACACCTAGGGTAGTAGAA R 2 1 2 1 101000 r 74 goat snp34675-scaffold410-976402 18 42487279 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797594 Affx-122950957 AX-385284533 18 40537548 TTTCATATATCTTTGCATCTTTCTAGGAATTTTCC[A/G]TATCATATAAGCTACGGAATTTGTTGGCTTGGAGT R 2 1 2 1 303000 f 74 goat snp34674-scaffold410-946585 18 42517205 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416441 Affx-122947826 AX-123286790 18 40581255 CCCTATTTCACCAAGATCACTCTTCTACTAGCTGC[A/G]TCTTCACAGGCTCCACAGCCTCATCTGTACCTGTC R 2 1 2 1 101000 f 74 goat snp34673-scaffold410-902878 18 42560633 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427845 Affx-122939728 AX-123298188 18 40621899 AAGGGTGACAGAAGGGTGATGGTTGGGGAGTTGGG[C/T]GGGAAGGGAGAGAAGAAGATGAGTCTCACTTTAGA Y 2 1 2 1 201000 f 74 goat snp34672-scaffold410-862234 18 42601337 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383543 Affx-122972617 AX-123253901 18 40665574 AACAGACTGCCTCATCCTTGATCCTTCAGTAGGCC[C/T]GGCACCAGAGAACAGCTTCAGTTCAGAAGCACCAT Y 2 1 2 1 101000 f 74 goat snp34671-scaffold410-818559 18 42645274 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775336 Affx-122971752 AX-385262467 18 40720443 ACCCAGCTTATCTCAAAACCCAGGATCTGGAAATG[C/T]ATTTCTCCTGATGCACCACTGTGACGTTGTTTTGA Y 2 1 2 1 101000 r 74 goat snp34670-scaffold410-763690 18 42700657 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410118 Affx-122952820 AX-123280468 18 40759552 CATACTAGCTTTGTTTAAACGCTCTACTTCCTTAA[C/T]GGTTTTTGTTGCTTTCTTTGCAATTATTGGGACTG Y 2 1 2 1 101000 f 74 goat snp34669-scaffold410-724581 18 42742170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773133 Affx-122936592 AX-385260276 18 40789447 ATACTTGCTTCCAAGTAAACAGCACAAGTTAATAA[C/T]ATCAGACTTTTCATCTGCCCTACTAAATGCTGGAA Y 2 1 2 1 101000 r 74 goat snp34668-scaffold410-694686 18 42771991 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774071 Affx-122960021 AX-385261209 18 40901379 AATGGAATAGTTTGTACAAATGCTGGTTATCTACC[A/G]TCCTTTTAAAAGTCAAATCTGGCAACACATTTTCT R 2 1 2 1 101000 r 74 goat snp34665-scaffold410-582754 18 42883648 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439052 Affx-122930328 AX-123309389 18 40954999 AGATGACAACTCGGATAACACTTCTCACCCCGGAA[C/T]ATAATTTCCTTCTGTTCTTGCCCCATGCCTCACGA Y 2 1 2 1 101000 r 74 goat snp34664-scaffold410-529134 18 42937869 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411433 Affx-122951827 AX-123281783 18 40984679 AGAAGTTCCAGAACATACGCTGGTTTGTCCAATCC[A/G]TCTGACAATTAAGAGAGAGGCAGGACCCCCATTCT R 2 1 2 1 101000 f 74 goat snp34663-scaffold410-499454 18 42967218 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383367 Affx-122972661 AX-123253725 18 41020546 ATGTCAGACAGCTGGACTGATTGCTCTTGGTTTTC[C/T]CCAAACCCCCAGTAATACCTCCTTGCATGCACTAC Y 2 1 2 1 201000 r 74 goat snp34662-scaffold410-463587 18 43002826 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769738 Affx-122978244 AX-385256908 18 41052282 AGGCCTGCTGTACCTACATAGACCTGGGAAACACT[A/C]TGAGAGATGCCAGTAGGGATGTTTAAGTAATAATG M 2 1 2 1 101000 f 74 goat snp34661-scaffold410-431851 18 43034499 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785194 Affx-122945912 AX-385272240 18 41100340 CTTCTGGGATTCTGGAAGGGGAAGGATCACCTTCT[A/G]GAGGGCGAAGTGGCATCTTTCCTTTTTCCTGGCAT R 2 1 2 1 202000 r 74 goat snp34660-scaffold410-383793 18 43082164 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387620 Affx-122969867 AX-123257978 18 41141316 TTATTTACCTTTATTTTAAATCATTCTGATTACAA[C/T]AAAGACTCATTTTGGTGTCAGGACACCTTAAATAT Y 2 1 2 1 201000 f 74 goat snp34659-scaffold410-342817 18 43123704 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412919 Affx-122950398 AX-123283268 18 41187109 GCAGGGTTGTGGTACATGTTGACAGAATTGACTTG[C/T]AAAGAAATGGGTGAGATGCTACACAATTTGGGTTT Y 2 1 2 1 101000 r 74 goat snp34658-scaffold410-297024 18 43170038 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421955 Affx-122943815 AX-123292302 18 41243975 AGCACACATCTGGGTATGGGGGATATTCAGGACCC[A/G]CTTGCCAAAGGATGAGCTGTCTGACTCTTGGATGT R 2 1 2 1 101000 f 74 goat snp34657-scaffold410-240158 18 43222831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378790 Affx-122976994 AX-123249149 18 41278054 TTTCTTCCTGACCCTCTCAGGGTTTGGCCATACAT[A/G]CAGAAATCTAGACCATGAAATTGTGCCAAGCCCTG R 2 1 2 1 101000 f 74 goat snp34656-scaffold410-206079 18 43255581 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408002 Affx-122954316 AX-123278353 18 41328140 CAAAATTCAGGGACTTTACAATGATGTGTTACAGA[C/T]GATGTATGTGGGTTAGCTGGGGTCTGGCTGCTCTA Y 2 1 2 1 101000 r 74 goat snp34655-scaffold410-155993 18 43305427 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797157 Affx-122947289 AX-385284096 18 41389185 TTTATTCTTTTCTATTGACCTAAGCTTTAGAGTTT[A/C]TGACTTTTCCCCCTGAATCCTATTTAGCCGTATGC M 2 1 2 1 101000 r 74 goat snp34653-scaffold410-94948 18 43365632 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420291 Affx-122945036 AX-123290639 18 41441885 GGGTCTTAGCAGGTGAGCCCACCTTCTAACAGAGA[C/T]GGAGAAAGGCCTTTTGTAAACATCAGAGCAGGTTC Y 2 1 2 1 101000 f 74 goat snp34652-scaffold410-42248 18 43418771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376913 Affx-122977797 AX-123247272 18 41473003 AGAACACAAGTTATGGGGTAGAAACCGCAAGTGCC[A/G]TAAGGACTAATAAGTGCTTATTCATTGTTCCTTGC R 2 1 2 1 201000 r 74 goat snp34651-scaffold410-11130 18 43449900 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448337 Affx-122924134 AX-123318673 18 41487090 TGTGTTTGTGCCTCATCAGAGCCCTGTTTCTGGTG[C/T]ACCTGGTTTGAGACTGATGCAGGTAATTCGTGTTC Y 2 1 2 1 101000 f 74 goat snp55090-scaffold846-2858 18 43463799 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430476 Affx-122937248 AX-123300817 18 41524734 CCGTGGTCCCTGGGCAGAGAAATCTCTAAGCAGAG[C/T]TATAAATGTCCCAAGAAACTCACTACCTTTAGGTC Y 2 1 2 1 101000 r 74 goat snp55091-scaffold846-40502 18 43501669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430842 Affx-122937432 AX-123301183 18 41579140 TGTATCCAAAATCCAAAAAATTCCAGTTGTCAGGT[A/G]CCCAACCCTGGGCCTATGGGCAGCATGACCATGAG R 2 1 2 1 101000 f 74 goat snp55092-scaffold846-94908 18 43555969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776177 Affx-122924713 AX-385263305 18 41607828 ATAGTCACACTATTAGCATCATCTCCACAGAATCC[A/G]TGGTTTTAAAACTTCATGGAAATCTATAGTATGGA R 2 1 2 1 101000 f 74 goat snp55093-scaffold846-123596 18 43584727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426344 Affx-122940265 AX-123296690 18 41703705 TGTTGCCTAAGCTTCCATCACACCAGATCCTCTTA[C/T]GCCAGGACCTTTGCACATGACTTTGTCTGAATCAG Y 2 1 2 1 101000 f 74 goat snp55095-scaffold846-219473 18 43681402 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440430 Affx-122929417 AX-123310767 18 41745315 CCCGTTTATGTAGATCTTAATACAGTTATATAGTC[A/G]CAGGGCTAACGTCCCCTTTGGATGGTAATGAGGTC R 2 1 2 1 201000 f 74 goat snp55096-scaffold846-261083 18 43722474 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398019 Affx-122961779 AX-123268374 18 41775107 TTGCTTTTGTCCTGGAAGTCCTCAGCAAACGCCCC[A/G]GTCATATCTTGGAATTTCACCATAGGAGAATATCA R 2 1 2 1 101000 r 74 goat snp55097-scaffold846-290875 18 43752202 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775988 Affx-122969501 AX-385263118 18 41804537 AACTGCTGTGGTTTGGCTCTGGTGCTTCAAAAAGG[C/T]AACTTCCACACCAGTTTTCAAGCCCCGAATTTCTG Y 2 1 2 1 101000 f 74 goat snp55098-scaffold846-320305 18 43780871 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415747 Affx-122948940 AX-123286096 18 41841306 ACAAGGCCGCGGGAGGATCCCAACTGTGTCCTGCC[A/G]CATGAGAGTCAGACACAGAAGGCCCCAACTTGAGC R 2 1 2 1 201000 f 74 goat snp55099-scaffold846-357074 18 43817527 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422794 Affx-122943210 AX-123293140 18 41886789 TTCTGGCTGAATTCCCATCTGGAGCGTGGAGGCTC[A/G]CCATGTCTTCTTACTTGCCCTGGCTTCTAAGTCCC R 2 1 2 1 103000 f 74 goat snp55100-scaffold846-402557 18 43863146 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433466 Affx-122935052 AX-123303807 18 41943820 TACATATTCAATGATGGAGAAAGTGGGAAACCTCA[C/T]GAAAATCGCCCAGGTCCAGGCTGGGATGCAAGTGT Y 2 1 2 1 101000 f 74 goat snp55101-scaffold846-459588 18 43920575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397685 Affx-122962581 AX-123268040 18 41981760 CAATACAAATGTGGTGCCCAATGAAGGCAAGACCA[A/G]GAAGATAAATATGAACGGGGTGAGGGGAAAAAAGG R 2 1 2 1 101000 f 74 goat snp55102-scaffold846-497528 18 43958255 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433657 Affx-122934569 AX-123303998 18 42019804 TTTTTCCTTTGTTTTTGTTATTTTGGGAGTTTAGG[A/C]GCCAACTCATAAGAAATATGAATGCCAGTAGCACT M 2 1 2 1 103000 r 74 goat snp55103-scaffold846-535572 18 43996383 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381766 Affx-122974308 AX-123252124 18 42053485 CTTTTAGATCCGGACACCGGACAAAGGCCAGTAGA[C/T]GGGACGGTGGCAGCATATTCTAAAATGATGTCCCC Y 2 1 2 1 202000 r 74 goat snp55104-scaffold846-569253 18 44030016 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425357 Affx-122941581 AX-123295703 18 42104314 GCAAAGAAAAGGAATACAAACCACAGAAGTTTCTG[A/C]GGATTACACGGCACAAGAAGAAAATGCGAAGTTGG M 2 1 2 1 101000 r 74 goat snp55105-scaffold846-620082 18 44081336 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398009 Affx-122961786 AX-123268364 18 42158476 TTTTTATTTCCTAGAGATTTTGATGCAAACCTATA[C/T]CTGTGTGAAGAAGCATTTGGCCTTCTGCCTTTTAA Y 2 1 2 1 201000 f 74 goat snp55106-scaffold846-674244 18 44135914 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409877 Affx-122952910 AX-123280228 18 42188161 TCCCTGTACCATCATTCAGCTCAGTGATTCCTTCC[A/G]TGAGAACTTACTGAGGACCTACTCTATGATAAGGT R 2 1 2 1 101000 f 74 goat snp55107-scaffold846-703929 18 44165596 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431503 Affx-122936241 AX-123301844 18 42235186 GGAGGAATCCTGCAAGACTGGGGCTGTGGGAGGGC[A/G]TCCTCCACAAGAGGTGTGGTCTTAGGCAAAAGAAA R 2 1 2 1 101000 r 74 goat snp55108-scaffold846-750954 18 44212572 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781359 Affx-122933940 AX-385268444 18 42288508 GATTTTGAAAAAATAATCCCAGTTAACAGGTAAAT[C/T]TTACATAGAGACACTGGAAGGAGACTAGACAGCTC Y 2 1 2 1 101000 r 74 goat snp16017-scaffold1687-18703 18 44266550 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411007 Affx-122951986 AX-123281357 18 42322394 CAGAAATCTCTCTATTCGATTGATTTCAACTTTGC[A/G]ATTTCTGTGAGTACTGTCACGTTTTGGTGGTGGGT R 2 1 2 1 101000 r 74 goat snp16018-scaffold1687-52589 18 44300634 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777500 Affx-122930240 AX-385264619 18 42354486 CCAAAAAAGCTGAATTAGAATGAAGGTATTTATCC[C/T]GTGGCTCTGTTAACCTAAACACCTCTTTGTTAAAT Y 2 1 2 1 101000 f 74 goat snp16019-scaffold1687-84681 18 44332149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425304 Affx-122940950 AX-123295650 18 42416411 ATGGGGTTTGAGGCTGTGGGCTCTGCCATGAGACT[A/G]TCTGTCTGCTCCCTCCTCTGTGGCACAGGGAACAT R 2 1 2 1 101000 f 74 goat snp16020-scaffold1687-146606 NW_017213986.1 7861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801985 Affx-122925315 AX-385288889 18 42503528 CATAGTCAGTGGAATGTGCAAACTCTTTAAAAGTC[A/G]AGGATTTACAGTCTGACTGTAAAACAATTAGCAAG R 2 1 2 1 101000 f 74 goat snp16022-scaffold1687-233723 NW_017215739.1 4689 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277309 Affx-1111835784 AX-519550813 18 42514972 GATGTTGACTTGACGTCAACATAGGCTGTTCCAAG[A/G]AGATTTCCAGACACTTTTGTCTTAGAGGCTGAAAG R 2 1 2 1 101000 r 74 goat Random2.2K-1744 18 42514972 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320801620 Affx-122930400 AX-385288528 18 42541597 ACACCTGCTGCCACTTTAGTCCTCTGAAGGAAACC[A/G]TCGTGGCATAACCCAGGTATTGTCATCAATTGGGG R 2 1 2 1 101000 f 74 goat snp16023-scaffold1687-271792 18 44403934 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427453 Affx-122940033 AX-123297796 18 42583392 TCAAGGTTTACTTTCAGCTCTACAGTGTTCAGAGC[A/G]TATCTACTGACTATATGCCTGCAGTCGGCCGGCTA R 2 1 2 1 101000 r 74 goat snp16024-scaffold1687-313587 18 44445643 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403681 Affx-122958055 AX-123274033 18 42639386 AGGGGGTGGGTAACATTCCCCAGCTCAGCCTATGA[C/T]GCTGATATTACCCTGATTCAAAACCAGGGGAAACC Y 2 1 2 1 101000 r 74 goat snp16025-scaffold1687-369581 18 44501240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777762 Affx-122953797 AX-385264880 18 42670245 ACTAGGAACATTCTTTGGACTAGTATGATGTAACA[A/C]AATGATCATTACAAGGTCTCATTTTCAGAAGAGAT M 2 1 2 1 101000 f 74 goat snp16026-scaffold1687-400440 18 44531567 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392629 Affx-122966460 AX-123262986 18 42716485 AGAGAGACTTTCCAGGCTTTCCCTGCCCACTGTTT[A/G]TTAAATATCTCTCTCTCTGCCCCTATGACTAGTCC R 2 1 2 1 201000 r 74 goat snp16027-scaffold1687-446680 18 44577899 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381707 Affx-122974709 AX-123252065 18 42766350 TCTCTGTCCTGAGGGGCTGGGACTGTAGAGCCTTG[C/T]CCTCCAGGCAGACTTGTTTACCAAACTGAACAAGA Y 2 1 2 1 101000 r 74 goat snp16028-scaffold1687-496545 18 44628176 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383587 Affx-122972583 AX-123253945 18 42812064 AGCACCTGGTCCCTGTGTGCTCCTTAGAACTTCCC[C/T]CACTGAAGGAAAAAGAGAACTTGGTTGGGTCCAGA Y 2 1 2 1 201000 f 74 goat snp16029-scaffold1687-542259 18 44673794 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463551066 Affx-1110041462 AX-515033178 18 42856866 TGTGGCTTTCTTGGCATGGAACAGCTGCTTAGGCA[A/C]AGAGCTGTAGGAACCTATTAAAACTCACAGGCCTG M 2 1 2 1 101000 f 74 goat 18_42856866_AF-PAKI 18 42856866 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440826 Affx-122929275 AX-123311163 18 42869626 TCCCTGCAAGCCTGCTTGTCCCTGAGCAAGGTTCA[C/T]GCCTTGCAAGTGGGCCAGGGCTGTGGACAGGGCAG Y 2 1 2 1 103000 f 74 goat snp16030-scaffold1687-599821 18 44731202 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453108 Affx-122920026 AX-123323441 18 42884273 AAGGACATTATTAAAACTTGACAGTAACAATAAAA[C/T]GCCAGTCTGTGATGTGGGGACCAGTGGCTTTCTGG Y 2 1 2 1 201000 f 74 goat snp34725-scaffold411-1700049 18 44958084 G A 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380010 Affx-122975602 AX-123250368 18 42918938 TGGCAACAATTTGGGGCAGCAGTGTGTGGTATGGC[A/G]TGGCTTGTGCACTTAGCCACCAGCCTACCTGGTCC R 2 1 2 1 101000 f 74 goat snp34724-scaffold411-1665384 18 44992743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407558 Affx-122954680 AX-123277909 18 42955055 CCAACACATATGCATGAGCTTACACAGATGCAAGC[A/G]CCCCATACACATTTTCACTCATGCACCATGCACAG R 2 1 2 1 101000 f 74 goat snp34723-scaffold411-1629267 18 45028982 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277187 Affx-1111835785 AX-519550693 18 43012707 GCTTAATGAAAACTGAGTTGGTGACAGTGTGATGC[A/G]CTCCAACCCAGTCAAATGGGTTTGAAGGGCTGCAG R 2 1 2 1 101000 f 74 goat Random2.2K-1745 18 43012707 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396121 Affx-122963407 AX-123266476 18 43037081 GCTCCTGCTCTAGAGGGGGTCTCACCTCAGTGAAA[C/T]GGGGGCTGGAACACTCGACCTCTGTCTGGGGAAAT Y 2 1 2 1 303000 f 74 goat snp34722-scaffold411-1547241 18 45112101 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375708 Affx-122978644 AX-123246067 18 43067605 GGAGAATCGGGTCTTTCTCAGGCTCTCAGGAAGGC[A/G]CCAAGACTGTGAGTGACCTGGAAGTTCTAATGAGT R 2 1 2 1 101000 r 74 goat snp34721-scaffold411-1516717 18 45142581 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451590 Affx-122921646 AX-123321923 18 43096283 AGCTCTGTCAGCGACGCTACCGATCTTTGCTCTCT[C/T]GGGATTCTGGCATTTTCTGCTCCCCGAGGAGGGCT Y 2 1 2 1 201000 f 74 goat snp34720-scaffold411-1488039 18 45171094 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435211 Affx-122933630 AX-123305551 18 43128506 CTCTAAAGTGCCATGTTAAAAACACTGCTATTTCC[A/G]CTTTACAGATATCATGCTCATATCTCAGAAACCAA R 2 1 2 1 101000 r 74 goat snp34719-scaffold411-1455816 18 45203195 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445703 Affx-122926116 AX-123316040 18 43231462 GTTTAAAATCACAACAAGGCTCCATCCACAAACTC[A/G]TTTGGGATTATTGAGGTCAGAGTGCATGGGAAGGA R 2 1 2 1 201000 f 74 goat snp34717-scaffold411-1352860 18 45304509 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799339 Affx-122955635 AX-385286269 18 43266184 GAAATAAGAAAAAGTAAGTGTTGGAAACAGGGTTG[A/G]ACATTAGTAATGAGTATATGGTGGTTCATTTTATT R 2 1 2 1 101000 f 74 goat snp34716-scaffold411-1318138 18 45338864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277189 Affx-1111835786 AX-519550695 18 43285439 TGAACCATCATCACAGATGATGTCAGAGAAAGGAC[A/G]CTCTTATATTTGCATGTTTAAAACATTTTGTTCTG R 2 1 2 1 101000 f 74 goat Random2.2K-1746 18 43285439 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797181 Affx-122927925 AX-385284121 18 43304837 ATGCCAGAAGCAGTAGTGCCTTCAAGCACCACGTT[G/T]CCTCCTATTCCAACCTACAAAACACTTTGGAAATA K 2 1 2 1 101000 r 74 goat snp34715-scaffold411-1279485 18 45377504 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404501 Affx-122956709 AX-123274853 18 43338810 ACAAAAACAGGGAGATGTGAGAATGCTAAGGCAGA[C/T]AGAGAGGTGAGCAGGGGCCAGGTCTTTGAGTATCA Y 2 1 2 1 101000 f 74 goat snp34714-scaffold411-1245512 18 45411550 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384958 Affx-122971912 AX-123255316 18 43373432 TGTCCAAGAGATTTGGGGACTGAAAGCTTGGCATC[A/G]CAGGCTATTTGGGGATCCAGGAAGTAGGACATGTG R 2 1 2 1 101000 f 74 goat snp34713-scaffold411-1210890 18 45446528 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440155 Affx-122931141 AX-123310492 18 43426341 TATGGAGGATTGTGTGCCAAACACTGTGCTTTCTA[C/T]ACGTGTTTGTTCCTTTAGTCTTCCCAGTAACCCTA Y 2 1 2 1 101000 r 74 goat snp34712-scaffold411-1157981 18 45504321 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397835 Affx-122962473 AX-123268190 18 43460492 GCTAAATATTCTTTCATATGTTGATTTTTATGTGC[A/G]TGGTGTGTTCATGTCCTGTGCTCATTTTTCTGATT R 2 1 2 1 101000 r 74 goat snp34711-scaffold411-1123830 18 45538885 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392227 Affx-122966264 AX-123262584 18 43489517 GCCTTCTTTTGTGTTGGTATCCAGTTTTATTATTA[C/T]AGTTTCAGAAAATGAGTTGAGTGATTCCTCAGTTT Y 2 1 2 1 101000 f 74 goat snp34710-scaffold411-1094805 18 45568243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277191 Affx-1111835787 AX-519550697 18 43503789 ATCATTTCATTTATTCTGCTTACTGACATTTCCTC[A/G]TCTTTTTCTAGTTTCTTAAGCTGGAACCTGAGGCC R 2 1 2 1 201000 f 74 goat Random2.2K-1747 18 43503789 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447841 Affx-122923902 AX-123318177 18 43545928 TTCCAAGGAGTCTTCCCTGGCAGTCCACTGGTTAA[A/G]ACTCTGAGCTTTCACTGCATGAGGTGAAGGGTTGA R 2 1 2 1 303000 r 74 goat snp34709-scaffold411-1038394 18 45625048 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782753 Affx-122919916 AX-385269825 18 43607936 ATACACTTATAAGTATTATAAAGGAAGTAAAGCAG[C/T]AGAAAGTACAGCAAAGTTCTTCAATACCTTAGGGG Y 2 1 2 1 101000 r 74 goat snp34708-scaffold411-976386 18 45687403 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801430 Affx-122963877 AX-385288339 18 43710643 AAGACAGAAAAACAGGAAGACTAGTCTGTGTCTTG[C/T]GATGAAATGCTAGTTATCTATACATATGGATCAGG Y 2 1 2 1 101000 f 74 goat snp34706-scaffold411-873679 18 45788938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385966 Affx-122971534 AX-123256324 18 43741788 GAGTGAAAGGATGAGGTCAGAGAGGGAAGGAAGGC[A/G]AGAAGTCATTGTGAGAACTTTGAGTTTTATTCCCA R 2 1 2 1 101000 r 74 goat snp34705-scaffold411-842534 18 45820135 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444985 Affx-122926658 AX-123315322 18 43777152 CACAGGTGCCTCCTTTTGTTTGACTCCAGCCCCAG[C/T]GAGGACTTGGAGCTGAAACCTGGTTTACTCCTGGT Y 2 1 2 1 102000 f 74 goat snp34704-scaffold411-807170 18 45852188 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422240 Affx-122944011 AX-123292586 18 43869777 CCCACCTCCAAGAAACCATCCCACCCCAACATCAC[A/G]TACACACACACCGCAGCCTTTGTCACTTAGAGAAG R 2 1 2 1 303000 f 74 goat snp34703-scaffold411-714545 18 45943402 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423321 Affx-122943181 AX-123293667 18 43911266 CATCCACCAAATGTAGGCCTCCCAGCAACTTGAGG[A/G]GTAGGAGTAATCATGATCATCTTAAAGGGAAAATC R 2 1 2 1 101000 r 74 goat snp34702-scaffold411-673056 18 45985339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436421 Affx-122933013 AX-123306759 18 44074130 CCCATGGTCACACAGCTTGCCAGAGACAGGGCCTC[A/G]GTTTATTCTCATTCTGTCTTCTCCTGTCCCCATGC R 2 1 2 1 303000 f 74 goat snp34700-scaffold411-510192 18 46151140 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411951 Affx-122951143 AX-123282301 18 44114954 CTTCCATTCAAAGGCTGAAAGCCTCAGGGAGTTTG[C/T]GCAGGATTCCTGGGCACTGATCAGACAGCTGCCCT Y 2 1 2 1 101000 f 74 goat snp34699-scaffold411-469368 18 46192572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424379 Affx-122941836 AX-123294725 18 44170048 TACCTAAACACACTGTGAGTTGAGTCTCACATTCA[G/T]AGTGGATGTCCAGGGGCCTGGGGTTTCTTGCTTCT K 2 1 2 1 101000 f 74 goat snp34698-scaffold411-414274 18 46247348 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380545 Affx-122975666 AX-123250903 18 44200619 CCCCTGAAGACCTCCAGGAATCACTCCTGAGCCCT[A/G]CCAGGTGGTCCTCAGCAGTGTCTCCCATTCTATCC R 2 1 2 1 103000 f 74 goat snp34697-scaffold411-383703 18 46278037 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437181 Affx-122932122 AX-123307519 18 44271412 TGATTTTGTTGTGTAGTTTTCTCCTTTATTACCAT[C/T]TGGGGTAAATCTTCATCATAAATATCCTCCTTCAT Y 2 1 2 1 101000 r 74 goat snp34696-scaffold411-312910 18 46349718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391516 Affx-122966663 AX-123261873 18 44311894 TTTTACCATACTTGATTAAACAAACCCCAGGTAAC[A/G]TCTTAAAATACCCTGCCTATCAGGCCCAGAGCTTT R 2 1 2 1 101000 r 74 goat snp34695-scaffold411-272428 18 46389756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449762 Affx-122922447 AX-123320097 18 44376786 CACTGGAACTATGGAAACAAACTAGGGAGGAATTC[A/G]CAGAAGGGGAAGATAACAATGGAGAATATAGAGGG R 2 1 2 1 101000 r 74 goat snp34693-scaffold411-207536 18 46451090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406684 Affx-122955782 AX-123277036 18 44408332 CACATTGCCATTTCACACACCTCCTCCCTCTGATA[G/T]CCTAGGCAGCTCCAAATATATAACTCCAAGAAAAT K 2 1 2 1 102000 f 74 goat snp34692-scaffold411-175990 18 46483763 T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774154 Affx-122927140 AX-385261292 18 44489852 TAACTGACACATGCTAAAGGCTGTCTGGAGCCTAG[C/T]TGTGAGGTAGCAAGTTTAACAGTAAAACGAACCCC Y 2 1 2 1 101000 f 74 goat snp34690-scaffold411-94470 18 46565935 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401410 Affx-122959207 AX-123271763 18 44536754 TATTATTTGAAGCTTCTTTCAAATAACTAGGAGCC[A/G]TACTCTTGTCAGACACCTTCTGTGCCAAGCACTGC R 2 1 2 1 101000 r 74 goat snp34689-scaffold411-47568 18 46612676 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432715 Affx-122936016 AX-123303056 18 44590085 GGTGAGGATGATGGTGATGGTACCAATGATGGTGA[C/T]GCTGATGAAGCTGATGGTAGTGGTGGTGATAGTGA Y 2 1 2 1 101000 f 74 goat snp33230-scaffold389-2282621 18 46661247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407677 Affx-122954591 AX-123278028 18 44635840 CATCCTCTCCTCAACATTTCTTAACCTCAGTCTTT[A/C]TTTTATTTTCCTTCATAAGAATTATTCTTATCTAG M 2 1 2 1 201000 r 74 goat snp33229-scaffold389-2236866 18 46702022 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440179 Affx-122930715 AX-123310516 18 44679238 TGACAAAAGTCCTACAGCTCTCTCTCAGTGGCTTT[A/G]TTTGGATGATGCGCTCATTTCTGAACCCGGGGGCT R 2 1 2 1 201000 r 74 goat snp33228-scaffold389-2193468 18 46745346 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274329 Affx-1111834189 AX-519547924 18 44697780 CCTCCTCTCCTGACAGCCGCCTGCAGCGGGCAGCT[A/G]GAGCGGCACACTGCACGCCGCGGCGTCATCTACAG R 2 1 2 1 202000 f 74 goat GoatD01.024629 18 44697780 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38451744 Affx-122921530 AX-123322077 18 44741096 GGCCATCCTGGACCTGCGTTCTTACAGAGCAGCAG[A/G]GACAGAGGTGTCTTATAGATAAACACCCATGTGCT R 2 1 2 1 101000 r 74 goat snp33226-scaffold389-2131610 18 46806414 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447219 Affx-122924978 AX-123317555 18 44775856 CAGACCACGCTCTTTCTCTGACCACACCATGTAAG[C/T]GGCACCTTGCTGCACTAACCATTCACTCGCGTTTG Y 2 1 2 1 101000 f 74 goat snp33225-scaffold389-2096850 18 46841278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422122 Affx-122943556 AX-123292469 18 44804598 GCTTCCATCTTTCTTCCAGAAGACATGGACGTCCG[C/T]GGGACGGCTACTTGAGAACTCACACTGGAGGAGGA Y 2 1 2 1 202000 r 74 goat snp33224-scaffold389-2068108 18 46870221 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441097 Affx-122928893 AX-123311434 18 44861000 GGAGTCAGTCTGGAGCCGAAGTCAAGTCACGAGTG[A/G]TTCCCAGGATCCTTTGACCCTGGCTGTTACCTCGC R 2 1 2 1 201000 r 74 goat snp33223-scaffold389-2011706 18 46926412 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786997 Affx-122919597 AX-385274025 18 44906875 GCCACAGTCAAGTAAAATACTTAGCAAAGATGGAA[C/T]GCTCATAAATTGGGTGATAGGAAATGGAGTAGAGG Y 2 1 2 1 101000 r 74 goat snp33222-scaffold389-1965831 18 46972346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437320 Affx-122931963 AX-123307658 18 44959521 ACCAAATAAATATTTCACAAATGCATCTTTAGATA[A/G]AGGAGGAGTGTTTGTATCAGTGAGAACTGGGTGAA R 2 1 2 1 101000 r 74 goat snp33221-scaffold389-1913185 18 47025466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377240 Affx-122978155 AX-123247599 18 45003627 GGCATCCCTGAGTCCTCATCTTAGGAGACAGACAT[A/G]CACGTGTACAGACAGACACTCTCGGGCCCACACGG R 2 1 2 1 101000 f 74 goat snp33220-scaffold389-1869079 18 47069533 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429252 Affx-122937903 AX-123299594 18 45036737 TCACATGTTGTGCTTATATATATATATACCCCAGA[C/T]GGATAGACCTCTTTCCTTCATTTGAAAGGAAAAAG Y 2 1 2 1 201000 r 74 goat snp33219-scaffold389-1835969 18 47102398 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403001 Affx-122958135 AX-123273354 18 45069219 TCAGTCCTCTCAATCGACACAGATAATAGCAATTC[C/T]AGCTGTAACTGGACACATTGAGAAGCACATGGACT Y 2 1 2 1 101000 f 74 goat snp33218-scaffold389-1803487 18 47135262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429516 Affx-122937850 AX-123299858 18 45113952 CAAGGGTCAGCTGAGTCTCTGCTCTAGGAACAAGG[A/G]CACTACAAGGTCTCCACTGAGATAGCAGATTTCAG R 2 1 2 1 101000 r 74 goat snp33217-scaffold389-1758754 18 47179920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387481 Affx-122970349 AX-123257839 18 45148253 TGTAATTTTTTGTGGAGTTGCCTGTTTATGTGCCT[A/G]CATTACCCCTTCGATGAGATCTTCCTGAAGCCCAA R 2 1 2 1 101000 f 74 goat snp33216-scaffold389-1724453 18 47213370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394206 Affx-122964905 AX-123264561 18 45205057 AAATGGCTAAACCATCAGAATATGCCAATTAGAGG[C/T]ATGCTTATTTGTTTTATGAAAAATACTCCCTTTGT Y 2 1 2 1 101000 f 74 goat snp33215-scaffold389-1667649 18 47270826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439363 Affx-122930278 AX-123309700 18 45251683 AACGAAGACACATATGAAATCTCAGTCCAGAGGGG[A/C]GGAAACACATCCCATAATGGCAACAACTCAGAGTG M 2 1 2 1 101000 f 74 goat snp33214-scaffold389-1621023 18 47316782 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392490 Affx-122966137 AX-123262847 18 45327392 ATGAGATAGACACAAAAGTCCACTGCAAGAAACGT[A/G]TGTCATACAGTCAATCCTCATCATGGGCAGAGTCT R 2 1 2 1 101000 f 74 goat snp33213-scaffold389-1545314 18 47387424 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418877 Affx-122946116 AX-123289225 18 45361464 ACCCTAACCCCCAAATCCTATCTCATTCCTGAGAG[C/T]CCAGAATGGTGATACCCCTGCCTGAGGAAGGGGTC Y 2 1 2 1 201000 r 74 goat snp33212-scaffold389-1511242 18 47419695 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426791 Affx-122940543 AX-123297137 18 45395196 ACCACTGGCTCTCCCATTCCTAGGGGAGTGCCCTG[A/G]CCTGAGTGGTCCAAGGTTGCTCCCACCACATCCAC R 2 1 2 1 103000 r 74 goat snp33211-scaffold389-1477510 18 47451834 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406169 Affx-122956162 AX-123276521 18 45426119 CGTTGCGAAGTCTTGGCATTAGCTGAAGCCTCTCA[C/T]GTTATCACAATTATTCCAGACACTCAGGAACCCTG Y 2 1 2 1 101000 f 74 goat snp33210-scaffold389-1446587 18 47483259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797492 Affx-122925521 AX-385284431 18 45456915 GGGGGGTGGTTTAACATCAGTACATTCTGAGATAA[A/G]GCCTTGAGTGAGGTGGTTTATTTGCAATGTGATCC R 2 1 2 1 201000 r 74 goat snp33209-scaffold389-1415791 18 47514011 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438455 Affx-122931248 AX-123308793 18 45545637 ATTGTACTTATATTATGCCACATAAGAAAACTTAC[A/G]TTGCTGTTAAGTTGCTAAGTCGGGTCCGACTCTTT R 2 1 2 1 201000 f 74 goat snp33207-scaffold389-1327069 18 47603119 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413072 Affx-122950964 AX-123283421 18 45590028 ATGTTCACCTGGATTTGTCCAGTGCCATCTTTGTC[A/G]AGAGATTTGAAGGCACCTGGGGAAAGGAAGGGTTG R 2 1 2 1 101000 f 74 goat snp33206-scaffold389-1282678 18 47647221 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383561 Affx-122972604 AX-123253919 18 45631157 GACCTCGTTACGTATAAACAGGAATATCAATGTCA[A/G]TGTGTCAATATTTGTTACTTTTTCCATTAGAACCT R 2 1 2 1 101000 f 74 goat snp33205-scaffold389-1241549 18 47687419 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775870 Affx-122970395 AX-385263001 18 45684711 AATGGAGAGAGTTGACAGTCACCACCTTAACCATA[C/T]GTTCAAATTTAGCCTCATGATTTCAATCTGTACCT Y 2 1 2 1 101000 f 74 goat snp33204-scaffold389-1187995 18 47740500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438034 Affx-122931556 AX-123308372 18 45718943 TGAACATCACCAACCCCTAAAATGGCAAATCACAG[C/T]ACTATTTTTGAAATTATAAGAAACATTTTTCAAAA Y 2 1 2 1 101000 f 74 goat snp33203-scaffold389-1153763 18 47774463 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277193 Affx-1111835788 AX-519550699 18 45725703 ACTGATTTTCTTAAGCAGTCAAAGTTATTACTGTT[C/G]GTTTGTGCGCTGTTTGTGCAGTCGAAGCCAGAGCT S 4 1 2 1 101000 f 74 goat Random2.2K-1749 18 45725703 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320778331 Affx-122938355 AX-385265446 18 45794677 CCTGCTTCTGACACTAATTAGCCATGTAACCTTGG[C/T]GAGGTAGCCTAAATATTCGTTTTAGCAATCTCTTC Y 2 1 2 1 101000 f 74 goat snp33202-scaffold389-1078029 18 47850143 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433812 Affx-122935172 AX-123304153 18 45829925 AAGCAGTGCAGTGCTACAGTTATATTAGCATCGTA[C/T]TTTTCTGAGTTTAAAAGAAATCAATATATTTAAAA Y 2 1 2 1 101000 f 74 goat snp33201-scaffold389-1042781 18 47885828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784566 Affx-122931883 AX-385271614 18 45859559 TTTCATTCATGAAAGGTTTTTGCTGGCTATGGAAT[C/T]CTGGGTTGACAGTTCTTTACCAAAAAAATACTGTT Y 2 1 2 1 101000 r 74 goat snp33200-scaffold389-1013147 18 47915309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424177 Affx-122942525 AX-123294523 18 45891826 ATTATAGTATGGAGCAGTTAAGCATCTTGTTCAGT[A/G]TAACACAAGTAGGAAAGTGATGGGCTACAGATGAT R 2 1 2 1 101000 r 74 goat snp33199-scaffold389-980880 18 47947602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413758 Affx-122949939 AX-123284107 18 45920599 ATACCTAAAAAACCCTATCTTCTGTAAAATTACAC[A/G]CCAAATATTAAAGTTTATGGGGAAATTAGGAAAAA R 2 1 2 1 101000 f 74 goat snp33198-scaffold389-952107 18 47976390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773968 Affx-122920768 AX-385261107 18 45966544 AACATGAGCAGCCATTTTATGTCATACTCCTCATA[C/T]AGTCTCTGTTAAATGAACTTGGTAGAGAGCTATAC Y 2 1 2 1 101000 f 74 goat snp33197-scaffold389-906162 18 48022315 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432610 Affx-122935498 AX-123302951 18 46037955 AGCTTTCCACTGGTTGTAGTAGTGACCGAAACAGC[A/G]TTAGAATTCCTGGCCAACACTTAGTGTGTGCTCAC R 2 1 2 1 101000 r 74 goat snp33196-scaffold389-834751 18 48093388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771565 Affx-122968264 AX-385258723 18 46066834 TCCAGAGAGATCACTTAGAGCATTTTTACCAAAAG[G/T]ATCTAAATTAACTACTGCTGAATAACAAATTACTC K 2 1 2 1 101000 f 74 goat snp33195-scaffold389-805872 18 48122656 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763498 Affx-986698027 AX-385251362 18 46088700 CTTTTTCACATATGCAAAAGCTCAAAGGATTCATC[A/C]CCATCATACCTGCACTATAGGAAATACTAGAGGAA M 2 1 2 1 600010 f 74 goat 18_46088700 18 46088700 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 320766466 Affx-986697995 AX-385253833 18 46088717 AAGCTCAAAGGATTCATCACCATCATACCTGCACT[A/G]TAGGAAATACTAGAGGAAGGCCTGCAGGAGGGATT R 2 1 2 1 600010 r 74 goat 18_46088717 18 46088717 Ancestral_priority_1043 ancestry 0.548 neutral IMAGE 10K 10K ancestral 38448094 Affx-122924322 AX-123318430 18 46103425 GACATTCTTAGGACAAGAAAGTAGAGTATGGATGC[A/G]CCAGTTACAGAGATGAGGGAAGAAAAGAACTGGGT R 2 1 2 1 101000 f 74 goat snp33194-scaffold389-769281 18 48159520 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763470 Affx-986697999 AX-385251341 18 46125776 TGTGTTGCTTTCTGCCGTACTTGTCTCAAGGATGG[C/T]TCTGGCTGGAGGAACTTAAGAGACATGGGTCAAAC Y 2 1 2 1 600010 f 74 goat 18_46125776 18 46125776 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 320803424 Affx-986696333 AX-385290255 18 46163186 GTGAGGAAGTTGGTGGCTTTCAATAACACCTCCAA[A/C]AATGGCTCTTTTGTTGAAATATTTATTGACCAGAC M 2 1 2 1 600010 f 74 goat 18_46163186 18 46163186 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320766491 Affx-986698009 AX-385253857 18 46163233 TGTTGAAATATTTATTGACCAGACAGCATGTGCTA[G/T]GTCTTTTGTCCCCTGGCTTGTTGAGCTCTGTCCTT K 2 1 2 1 600010 r 74 goat 18_46163233 18 46163233 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 38399376 Affx-122961333 AX-123269731 18 46168737 CAAAGGTGGAAAATGAAAATCCTTCAGGGGCCAAG[C/T]AGGTAATGAATATGAGAGAGACAGGCAAAATGTTA Y 2 1 2 1 201000 r 74 goat snp33192-scaffold389-703969 18 48225432 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771148 Affx-122966262 AX-385258308 18 46197515 AGAGAATATATCTACTAGGAAAAAGTGACCCAAAA[C/T]GGTCAAGACTGAAACATGCCCCACTAAAATGACTT Y 2 1 2 1 101000 r 74 goat snp33191-scaffold389-675191 18 48254181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388944 Affx-122968816 AX-123259302 18 46251173 TGCACAGCATATGCATATAATTAAGGGAAGAGGGA[A/G]CACCAGTTAGAAGAGCCCAGGTGGAAATATACCTG R 2 1 2 1 201000 f 74 goat snp33190-scaffold389-621533 18 48309248 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766494 Affx-986698011 AX-385253860 18 46296905 CTTCAAGCAATGCTGCCAAAGAAGCTGAACAGTTC[C/T]TTGAAGACCTGTATGACCTTCTGGAACTAACACCA Y 2 1 2 1 600010 r 74 goat 18_46296905 18 46296905 Ancestral_priority_1043 ancestry 0.478 neutral IMAGE 10K 10K ancestral 320802983 Affx-122958546 AX-385289868 18 46316696 CAGGGATCTACCCTGGGAATCCATGATTGACCAGT[A/G]CCAATAACATGGATCATTTTGAGATTCAGCATGTT R 2 1 2 1 201000 r 74 goat snp33189-scaffold389-556010 18 48375245 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774544 Affx-122965138 AX-385261678 18 46345295 AATGCGAGGTGGCAGATGTCATATTATGGCTTATG[A/G]TAATACTAACACTGATTGCAAGAAAGTAATAACCC R 2 1 2 1 101000 f 74 goat snp33188-scaffold389-527411 18 48403885 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798199 Affx-122926604 AX-385285134 18 46389445 CTGGTCTCTAAAAATACTGTGCAAGTTTTTTACTT[A/G]TATCAGCAGTAACAAAGATTCCTTTTGTTTATAGT R 2 1 2 1 201000 r 74 goat snp33187-scaffold389-483261 18 48446730 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427507 Affx-122939531 AX-123297850 18 46424978 AAATGTAGCCTATGTTTACTGAGTCATTTTCTCAG[A/C]CTGCTTTTGGCCTGTAGATGTTTTGGCATCCAAAG M 2 1 2 1 101000 r 74 goat snp33186-scaffold389-447728 18 48482341 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451916 Affx-122921025 AX-123322249 18 46457062 ATTTCTAGATCTCTGCTGCTTGTTTGCAGTGGGGC[A/G]GGCCCTGGTGGCAAGATGCAGATAGATACTCTTCC R 2 1 2 1 201000 f 74 goat snp33185-scaffold389-415644 18 48512542 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394676 Affx-122964365 AX-123265031 18 46509486 ATTCTAATAAGTGGACCACACAGAAAACAAACCCA[C/T]ATCTGAATCTTGGGCATTGTTTCACCAGGCAGAGA Y 2 1 2 1 101000 r 74 goat snp33184-scaffold389-363220 18 48565232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463553787 Affx-1110042836 AX-515035864 18 46520456 CCAAAGGCATGTGATAATAGACAAAGATACTCCAA[A/T]ACTCCTAGGAGAAAGCATATTTTCTTTTTCTGTCT W 4 1 2 1 101000 f 74 goat Random2.2K-1750 18 46520456 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446252 Affx-122925683 AX-123316588 18 46567807 GCTTTCTAGAAGTAGGGTGAATAAATGTTGGTTAG[C/T]GAAAGAACAGATTACCACTAATCCCTCAATATTCA Y 2 1 2 1 101000 f 74 goat snp33183-scaffold389-304899 18 48624259 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449962 Affx-122922890 AX-123320297 18 46606010 CTCAGGTTCGCTATGGTTTGGCTCTTTGTAGAAGG[A/C]TGCCAGGTGCATGTTTCATAGCACATGCTCTATCA M 2 1 2 1 101000 f 74 goat snp33182-scaffold389-266696 18 48662792 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385370 Affx-122971633 AX-123255728 18 46641166 GGAAAGAAAACCCTCAGGTATCCAGTATGTAACTG[A/C]TCACAAAGCATCCAAGTGATTTCAAGCATGTTAGT M 2 1 2 1 101000 f 74 goat snp33181-scaffold389-231540 18 48697892 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797512 Affx-122926523 AX-385284451 18 46674963 TCACATGACTGGTAAGGACCACGGAGATCAAAGGT[A/G]CAAGTCTATCAACCCCCAGACCCCAGATCACACCT R 2 1 2 1 101000 f 74 goat snp33180-scaffold389-197743 18 48731565 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392003 Affx-122966494 AX-123262360 18 46717065 TGAAGACACCCAAGAAAAAAAACAAGGAAGAAGAT[A/G]CTGTCTATAATTTTTTAATTAAAAAAATTGGGCTT R 2 1 2 1 103000 f 74 goat snp33179-scaffold389-155641 18 48773912 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440175 Affx-122930717 AX-123310512 18 46757701 GCCTCTGGGGAGGGAAATTGGGTATCTTTTCCCTC[C/T]ACTCCCAGCCCCCTCCCTCCCCTGCTTCGTGTATT Y 2 1 2 1 303000 f 74 goat snp33178-scaffold389-115005 18 48814508 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393109 Affx-122965581 AX-123263466 18 46791478 TTGGCCCAAGCCTTCCCCAGGGAGAACCCAGGCTG[C/T]AGAACCCACTAGACCCCCGGTGTTTAAAGTGACAA Y 2 1 2 1 101000 r 74 goat snp33177-scaffold389-81228 18 48848178 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378884 Affx-122976502 AX-123249243 18 46837976 GTCAGCTGCTGTTCCCTCTGCCTGGAAGGGTCTTC[A/G]TCCAGATGTGTCACAAGGCTCGCCACCACCCGACT R 2 1 2 1 101000 r 74 goat snp33176-scaffold389-34730 18 48894209 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442943 Affx-122928226 AX-123313280 18 46888271 ATCTGAAGGGACCAGGGTGGTGGCCAGGGTAGCAG[C/T]GGGGGCCGTTGTTGAATTAAGACAACCTTCCCAGC Y 2 1 2 1 303000 r 74 goat snp19465-scaffold1967-15466 18 48943958 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775519 Affx-122922494 AX-385262650 18 46982967 GCAAGTAACACAATCCTGACTGGCCCTGACTGAAA[C/T]AGTAAGATGGTTATATATTGTATATCACCTGAGTT Y 2 1 2 1 101000 f 74 goat snp19467-scaffold1967-110162 18 49038045 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429556 Affx-122937820 AX-123299898 18 47053171 AGCAAAAGCAGTAATAACAATAGTAACAGGTTAAG[C/T]GGTTAAAAGCACAGACTTTGGAATCATCTGAATTT Y 2 1 2 1 201000 f 74 goat snp19468-scaffold1967-180366 18 49108197 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439243 Affx-122931007 AX-123309580 18 47102415 CATGACCTTCTAATGATTAATAAGTTTCTCCCAGT[A/G]ACCTCCCAAATGAAGCTCTGACCCTCCCAATTATT R 2 1 2 1 201000 f 74 goat snp19469-scaffold1967-229610 18 49156894 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428959 Affx-122938879 AX-123299301 18 47164826 AGTTAACGTCCAGTCCCATTCTCCCCCGATCAGTG[A/G]TGACCTTACCACCCTTCCAGGCCCCACTGTCCTCG R 2 1 2 1 201000 r 74 goat snp19471-scaffold1967-292021 18 49219534 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451507 Affx-122921114 AX-123321840 18 47196106 TGGCTTTGAATGAATGCATGCATGCATTTCCCAGG[C/T]ACCTTCTCACTCTTTCTGTGTCCTGCCCTGCAGCG Y 2 1 2 1 201000 r 74 goat snp19472-scaffold1967-323301 18 49250551 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436582 Affx-122932893 AX-123306920 18 47232529 CCTAGATGCTTGAAAGGGCAGGTCTGTGATCCTTC[C/T]ATCACCCTGACTTCTCAGTTTCCAGATTTCTTGTT Y 2 1 2 1 101000 f 74 goat snp19473-scaffold1967-359724 18 49286398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802700 Affx-122942067 AX-385289599 18 47262802 TTCCTTAGAATTTCAAATAACCCAGGGGTGATGTA[C/T]TCAGACAGGGTTGTAACGCTGTCGTTTCATGCTTT Y 2 1 2 1 101000 f 74 goat snp19474-scaffold1967-389997 18 49316679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451374 Affx-122921220 AX-123321707 18 47295631 TCCATCCCCAGCTGGAAGGACGGTCTTGCCTTCAA[C/T]GCCCTGATCCACCGGCACAGACCAGAACTGATCGA Y 2 1 2 1 201000 r 74 goat snp19475-scaffold1967-422826 18 49349386 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432665 Affx-122936460 AX-123303006 18 47333872 CCGGAGCCTGGTCTCTTTCCAGGCTGAGCATGGCC[C/T]GGGGGGCTCCTGGAATCCACAGGCCTGGTGGCAAG Y 2 1 2 1 201000 f 74 goat snp19476-scaffold1967-461067 18 49385961 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419232 Affx-122945679 AX-123289580 18 47372498 GATGACCAGATGGCTGGATGGCTGAATGGACAGGC[C/T]ATGACTGAATCAAAAAGAAAGAGACAATGAGGGAA Y 2 1 2 1 101000 f 74 goat snp19477-scaffold1967-499693 18 49424813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398180 Affx-122962651 AX-123268535 18 47403667 TGCAAGGCCTCCACAAGGTCAGCTTCCACCACACC[A/G]TCAATCAGGCCCCTGATGTGAACAACTGGGGAGGC R 2 1 2 1 201000 f 74 goat snp19478-scaffold1967-530862 18 49456035 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448915 Affx-122923169 AX-123319250 18 47442779 TCCTCCCAGGATGCCCGAGGTCCTACTACCTGTGT[A/G]TAGCAGCGCAGGAGCAGTCCTTTTTCCTTCAGCAG R 2 1 2 1 101000 r 74 goat snp19479-scaffold1967-569974 18 49495109 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418847 Affx-122946137 AX-123289195 18 47479783 AAACAAATATAGCCCCGGGAAGTACTTGGAACGGC[A/G]TCTCAAACAAAAGAGCGAGTGGCTGATGCTATTAT R 2 1 2 1 101000 r 74 goat snp19480-scaffold1967-606978 18 49530744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446221 Affx-122925706 AX-123316557 18 47608095 AGGAAGGTTGCAGTCGGCTCTGATCCAGTGAAGCC[A/G]CAAGAATGGCCAGGGAAGTGTTGAGTGGGCATGCA R 2 1 2 1 201000 f 74 goat snp19483-scaffold1967-735290 18 49660078 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422653 Affx-122943690 AX-123292999 18 47641690 GCTCGTCTGTACTTGACTTGGTTCCATCATGATGG[A/C]TATCTTACTCTCGCTCCGTGATGGGATGTTGGGTC M 2 1 2 1 101000 r 74 goat snp19484-scaffold1967-768885 18 49693270 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793106 Affx-122968414 AX-385280084 18 47675389 TTTTTCTCTCATCCCAGGTTTAATTATGTAGTAAA[C/T]GCTGTTGGCTTTTTTTTCTGACCGATCAACATGTG Y 2 1 2 1 101000 r 74 goat snp19485-scaffold1967-802584 18 49726748 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452358 Affx-122920637 AX-123322691 18 47710647 GCACATGGTGGACACGTGTTCTGTTTCTGTTGACA[A/G]AATACATGAATGCGAGATAGAACCCATGATTGGGG R 2 1 2 1 101000 r 74 goat snp19486-scaffold1967-837842 18 49762053 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441778 Affx-122929100 AX-123312115 18 47737114 ATGGATGCTGCCTGTCTCTCTGCAACAACCAACTC[C/T]TCAGAACCAAGGATTTACACCTTCTTGGGAACTAT Y 2 1 2 1 101000 r 74 goat snp34572-scaffold4085-62886 18 49782286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786102 Affx-122945683 AX-385273138 18 47765622 AGGGCCTTACTTTAAGTGCTGTTATGCGGATTATT[A/G]CATTTACTCCTTACACCAGCATCCTGAGGTGGATA R 2 1 2 1 101000 f 74 goat snp34571-scaffold4085-34378 18 49810869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393927 Affx-122965079 AX-123264282 18 47815372 GTGTGGAGAATGCCAGATATGTCCGCTTGAGAAGC[A/G]TTTCCCACTAGACTGCCACAGTTCTATGAGAGCAA R 2 1 2 1 101000 r 74 goat snp15158-scaffold162-277114 18 49861833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422245 Affx-122944009 AX-123292591 18 47878496 TCCCATCCTTTGCCCCCTTGTCCCCAGTCAGAACA[C/T]GCCCCTTGCCTGAGGGATTCAGGTTAGAATTACCC Y 2 1 2 1 101000 r 74 goat snp15157-scaffold162-213990 18 49914002 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272915 Affx-1111833120 AX-519546602 18 47903416 GAGAGGAAGTAAAATCACAGAAATAATAGAGAAAC[A/G]GACTAAATCCATATCACTGTTGCTTGACAATAGCT R 2 1 2 1 101000 r 74 goat 18_47903416_AF-PAKI 18 47903416 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38409778 Affx-122952982 AX-123280129 18 47947592 CTCTTAAGAAAGTGAATCAGACAGGGTTGCTGTTG[A/G]TTTGGATTGTGGCTCTGAGGGAAAAAAAGTCAAGA R 2 1 2 1 101000 f 74 goat snp15156-scaffold162-144894 18 49983033 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397028 Affx-122963117 AX-123267383 18 47990960 TAATTCTTTTGAGTCTCAGTGCAATCCTAGGAAGC[A/G]GGGGTTACTCTTACTGATCTTTGCAGCAGAGGAAA R 2 1 2 1 101000 f 74 goat snp15155-scaffold162-101526 18 50026217 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375745 Affx-122978614 AX-123246104 18 48025034 AAGAGGAGTTTGTACATATAGGTATGTATTCAACA[C/T]GATATCTGCCAACTAAATTAAAAGAATATATGTAA Y 2 1 2 1 101000 f 74 goat snp15154-scaffold162-67452 18 50059856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452977 Affx-122920151 AX-123323310 18 48087224 AGCAAAAATAAACATCAAACTAAACATCTCCTTCA[C/T]GGTAAACAATACCATCAAGGACATGAAAAAATAAC Y 2 1 2 1 101000 r 74 goat snp15153-scaffold162-5262 18 50150496 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785034 Affx-122970666 AX-385272081 18 48109838 CAGAATAAACCACTAGATTTTGTATCATGAATAGT[A/G]CTAGACAATTGCTTTAGATTAGATTTTAGCAGAAA R 2 1 2 1 201000 r 74 goat snp58498-scaffold951-101809 18 50133932 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435415 Affx-122933549 AX-123305755 18 48166618 GAACTTTCTCAGGATTGAAGCTGTGTTCGCCATCA[C/T]GATGGTGATCAGTGCCGGCCACAGTCCCCCAGCTG Y 2 1 2 1 101000 f 74 goat snp58497-scaffold951-45029 18 50224973 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433624 Affx-122934592 AX-123303965 18 48202678 CCCACTCTCTGCCTTTAGCTCCGGCTCCTCCCTGG[A/G]GCCCCAAGAAGCCCCCACCCCATCCTGCCCTCAGC R 2 1 2 1 101000 f 74 goat snp58496-scaffold951-8969 18 50261336 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775070 Affx-122940892 AX-385262202 18 48215517 CTGATTCCTCTTAGAAAAATCAAGTAGATTGAAGG[A/C]GTGTGTTTCTTTTAAAGGGAAGATGCACATCTTAA M 2 1 2 1 101000 r 74 goat snp21633-scaffold2118-1236119 18 50273830 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375422 Affx-122979191 AX-123245781 18 48269912 TGGCCAGTTGTTATTTGCAGAATGTTTAAAAGAGG[C/T]GTTGGCACCCAACAAGTATTCAGTAAATGTTGACT Y 2 1 2 1 101000 f 74 goat snp21632-scaffold2118-1181724 18 50327389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414571 Affx-122949381 AX-123284920 18 48336532 TGAGGACATCCGTTTCTTTGGATGCCCACTCCAAG[C/T]GGTCAGGTCATTCACTCATGACCTGGGCAGGGTCC Y 2 1 2 1 101000 f 74 goat snp21631-scaffold2118-1115104 18 50395072 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796597 Affx-122949314 AX-385283543 18 48375348 TCTGATTATTGCAGAGAATATTCCTCTTATTCACT[A/G]CCTCCAAAGTCATCTCTCTTCTTTCCCTGCGTTCT R 2 1 2 1 102000 r 74 goat snp21630-scaffold2118-1076288 18 50434116 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790153 Affx-122927884 AX-385277158 18 48419813 ATTCTAATGATATTCTCTTTAGTGGGCTAAGGTTT[A/G]CTAATTACCTAGTGTGGATATTTTTAAAAAAATAT R 2 1 2 1 101000 f 74 goat snp21629-scaffold2118-1031823 18 50478463 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392431 Affx-122966191 AX-123262788 18 48474870 GGCAGCAGTCTCCATCGAGGCTGGCAGACGTCAGT[A/C]GGATGGACTAGGTGGAAAGTGGTTTAAGGGTCGTT M 2 1 2 1 101000 r 74 goat snp21628-scaffold2118-976766 18 50530409 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379655 Affx-122975939 AX-123250013 18 48511705 GGGGCTGAGGGCAGGCAGGGTCACTTGGAGCCTCA[C/T]GAGACCGTCTTGAAGAGTGGCTTGGGCAGACTTAG Y 2 1 2 1 101000 r 74 goat snp21627-scaffold2118-939931 18 50566580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415510 Affx-122948684 AX-123285859 18 48655772 CAGTTTCCTTGTTGGTAAAATGGGATAATGAATAA[C/T]ATCTAATTTATGGGGTTATTGTGCATATTAAATGC Y 2 1 2 1 103000 f 74 goat snp21624-scaffold2118-795864 18 50710901 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428529 Affx-122938747 AX-123298871 18 48752323 CCAGGTGTCACAGTCAAGTTTAGGGGTCACAGGTC[A/G]AATACAGGGCCAGAGGACAGTTGGGACACAACTGC R 2 1 2 1 101000 f 74 goat snp21622-scaffold2118-699313 18 50807546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788940 Affx-122927123 AX-385275953 18 48784024 TTACTTCCCACTACTTTGTATCCTTCTCTTTATTT[C/T]ACAAGCATTTTCGGAATGCTTGCTTCTGTTAGGTT Y 2 1 2 1 101000 f 74 goat snp21621-scaffold2118-667612 18 50839167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438348 Affx-122931331 AX-123308686 18 48816345 AAAATGAATGAAAGAGCTAGAGCAGTGGCGATGAA[C/T]TGCAAAACCATGTTGAACACAAAGAATTTGCAGAA Y 2 1 2 1 101000 f 74 goat snp21620-scaffold2118-635291 18 50871470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766451 Affx-122960167 AX-385253821 18 48851932 TAATTTAAAAAGCGAAAGCTTCCACTGCTAGTTAT[C/T]TGTGCCAACCCCTTCACAGTTAACTCATCAAGTCT Y 2 1 2 1 201000 f 74 goat snp21619-scaffold2118-599704 18 50906545 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450144 Affx-122922749 AX-123320479 18 48900930 ACACTTGCTGCAACCCTGCTGTCTGAAGGGTCAGC[A/G]CCTTTAAGCAGAGCCCTGCCCCTAAACCTCTGCCA R 2 1 2 1 101000 r 74 goat snp21618-scaffold2118-550706 18 50955773 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778129 Affx-122968577 AX-385265244 18 48953358 AACCTCTAGAGCCTTGTGTGTTTCACAATGCCATC[A/G]TTATTGAGTTTCAAATGTCGTTAGATTTGTTTTAC R 2 1 2 1 101000 f 74 goat snp21617-scaffold2118-498278 18 51008131 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801395 Affx-122972852 AX-385288305 18 48992874 GGTTTCGCTGGTCTTTGTCTGAACTATGCAGTCTA[C/T]ACCATTGTACTGTGAACGCACCCACAGACATTCAT Y 2 1 2 1 101000 r 74 goat snp21616-scaffold2118-458762 18 51045479 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380347 Affx-122975362 AX-123250705 18 49053056 AAGTACATCATTTTTGCCAACTACTGTTTGATGTT[A/G]ACTAAGAACTTGACTTTTTAAAGTATATTGCTAAA R 2 1 2 1 101000 f 74 goat snp21615-scaffold2118-398580 NW_017193206.1 1217 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406584 Affx-122956266 AX-123276936 18 49095808 GCAACTCTTTGGGCTCCTTTCCTTCCCATGAGACT[A/G]TGGGTCCACAGGATGCAGGCAAAACTTTAGCCCAG R 2 1 2 1 201000 r 74 goat snp21614-scaffold2118-355828 18 51159270 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376914 Affx-122977796 AX-123247273 18 49125078 AAAAGTCTGGAAGGAGATCTGCCAAACAGTTAACC[A/G]TGGTTATCTCTAGAAGGACAGGTGAAGGAGGAATT R 2 1 2 1 102000 f 74 goat snp21613-scaffold2118-326558 18 51189221 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277197 Affx-1111835790 AX-519550703 18 49140630 AGTTTCCGTATTTTAACACTGGGATGACACTGGCT[C/G]GGATCTCATGGGGATTTTAGAAGCATGCAGCGCCC S 4 1 2 1 101000 f 74 goat Random2.2K-1751 18 49140630 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425372 Affx-122941570 AX-123295718 18 49161672 GACTGCCACCCTCCTTCTAAAGAGGAGAGACAGAG[A/G]GAGGTGGAAAGCCAGACCCAGGCCACAACAAGTGG R 2 1 2 1 102000 f 74 goat snp21612-scaffold2118-289964 NW_017189872.1 16335 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425775 Affx-122940719 AX-123296121 18 49217500 AATATGTTCCTGAATCATTCAGGATACATGACTGC[A/G]CACAGCATGGCCTTTTACTCCTGAATATTTCAGCA R 2 1 2 1 101000 r 74 goat snp21611-scaffold2118-234136 18 51287918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431688 Affx-122936782 AX-123302029 18 49253861 AGCCTTTGAGTGCTGATTTGAGTAAATACGATCAC[A/C]AAGTACATTTCTGGAAACTTCGGGGAAAGATGAAC M 2 1 2 1 201000 f 74 goat snp21610-scaffold2118-197775 18 51324140 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376947 Affx-122977771 AX-123247306 18 49290905 AGGCAATTCGTGTGCACACCTAGACCTGCTCACCC[A/G]TGCACACATTTACACACTGCATGGACACGTGGTCT R 2 1 2 1 101000 r 74 goat snp21609-scaffold2118-160731 18 51361615 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387981 Affx-122969591 AX-123258339 18 49322275 AACAGTGGACAACTCATTCCACTGTCTGCTTGCCC[A/G]TAAGAAATGATCAGTGATCCTATCTGATTCCTCTG R 2 1 2 1 101000 r 74 goat snp21608-scaffold2118-129361 18 51393018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446439 Affx-122925971 AX-123316775 18 49358569 AATCTGGATTTTCTTGAAGGTTATGTGACCTAGAC[A/G]CCCTGTCAGATGGAATGTTAGATTCAGTGGTCGAT R 2 1 2 1 101000 f 74 goat snp21607-scaffold2118-93067 18 51429351 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414711 Affx-122949272 AX-123285060 18 49405094 AGGGGACAGTTCCCCTGAGGAAGTGATGTGAGAGC[G/T]GGGACCTGAAGGATATCCAGGAGTCAGGGAAGGAG K 2 1 2 1 101000 f 74 goat snp21606-scaffold2118-46542 18 51475592 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453734 Affx-122919620 AX-123324067 18 49434995 TTACCACTTGGAAGTGGTGTAACATAAAATTAACC[A/G]TTTTTAAGAGTGCAGTTCAGTGGCTTTAAGTACAT R 2 1 2 1 303000 f 74 goat snp21605-scaffold2118-16641 18 51505567 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409732 Affx-122953024 AX-123280083 18 49469572 GCTCTTGCTCGGAAGCCAGCCCTGCAAGTTGTTTC[C/T]GGATCAGATCACTCACCACAGGACTGGGAAGTAGG Y 2 1 2 1 102000 f 74 goat snp26598-scaffold2775-14914 18 51614085 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429653 Affx-122937669 AX-123299994 18 49514159 CTCAATACATGTTGCCTACAATGATAACTATTATG[C/T]GGGCATCATCTGCGTTTGACAGATGTAGCAATTGA Y 2 1 2 1 101000 r 74 goat snp26599-scaffold2775-59501 18 51739525 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444548 Affx-122926472 AX-123314885 18 49618146 CACTGATGGCAGCCCAGGTGGTAGAAGAAGATGCC[A/G]TCTTCATAGCACTTTTCCTCCTGGTAGTGGGTGTG R 2 1 2 1 101000 r 74 goat snp26601-scaffold2775-163488 18 51842300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763490 Affx-986698019 AX-188122032 18 49625434 AGCCGTCCACCACGTCTCGCCAGCGCCGGCACACC[G/T]GGCGGGATTGCCGGAGCAGCGTGCTTGGGGGCAGG K 2 1 2 1 600010 f 74 goat 18_49625434 18 49625434 Ancestral_priority_1043 ancestry 0.432 neutral IMAGE 10K 10K ancestral 38452805 Affx-122920228 AX-123323138 18 49659222 GGAAGACCATGAAGACAGGAGGAAAACGCCCTAGC[A/G]CCAGTCCCCATCACTCCAAGCTCCCCCTGATCTAG R 2 1 2 1 101000 r 74 goat snp46769-scaffold6523-30638 18 51884120 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394965 Affx-122964275 AX-123265320 18 49730493 ACAGACTTGCACACAGATCTGTGCCCAGGGTGTCA[C/T]GTGTGTGTTGCAGCCACATCAGACCAAATGTGTTG Y 2 1 2 1 101000 r 74 goat snp52311-scaffold777-37485 18 51958020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395527 Affx-122963866 AX-123265882 18 49760963 TGACCCTCTAGAAAACTCCTGTGGTGGGAAATGGG[A/G]TACCCCTGGCTGGGGTCCAGATGTCCAGGCTGACA R 2 1 2 1 101000 f 74 goat snp52312-scaffold777-67955 18 51988122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413894 Affx-122949838 AX-123284243 18 49821210 TGCAAGTCCTCACTGTGAGACCCACGCAAATTGCT[A/G]TGCATTTCCCCATCTTTTCCCTCTCCCTGCTGATT R 2 1 2 1 201000 f 74 goat snp52313-scaffold777-128202 18 52047376 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390159 Affx-122967978 AX-123260516 18 49855869 CCTGAGATAGGACAGGGAAGGAGGAGTTGAAGAGA[A/G]GGGGGAAGATGTGAGAAAACCTGAGGACAAAAAAG R 2 1 2 1 201000 f 74 goat snp52314-scaffold777-162861 18 52081916 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778924 Affx-122925716 AX-385266031 18 49895392 GAACAGATAGATAAACACAAGGAGGTCATATTTTA[C/T]GCCAGGAATGTATCCCAGTGATATTGTCTGATTCA Y 2 1 2 1 101000 r 74 goat snp52315-scaffold777-202384 18 52120989 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433133 Affx-122935689 AX-123303474 18 49926110 TTCAGTCAGACAGACAGGCACATGGACAACGGCAT[A/G]CACACCGATTCTCTGGCATAGGCTGAAAGACCCAC R 2 1 2 1 201000 r 74 goat snp52316-scaffold777-233102 18 52149556 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423457 Affx-122942589 AX-123293803 18 49956912 GGAGGATGGGACTCTGGCCAGAGGCCTAATCTGGC[A/G]GTGACTGACTCCAGGTCCCTAACTCTGATATTGAG R 2 1 2 1 101000 r 74 goat snp52317-scaffold777-263904 18 52179014 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784848 Affx-122947127 AX-385271895 18 50004024 CTGTTATGTGGCTGGTGGTTACCATGTTGGAAACT[A/G]CAGATATTTATTGCATGTTACCATCATTCCAGAAG R 2 1 2 1 101000 f 74 goat snp52318-scaffold777-311016 18 52228891 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442066 Affx-122928382 AX-123312403 18 50077535 CGTCTGGGAGAAGCACAGGCTTCCTCGGGGGTCGA[C/T]TGTGCAGCAGCGTTTAGTGGTGGACAGACCTGGGT Y 2 1 2 1 303000 f 74 goat snp52319-scaffold777-384527 18 52302779 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763492 Affx-986698021 AX-385251359 18 50123223 TGTTCCTCGAAACTTCACGTTGTCCTTTCACATTG[G/T]GGTCTGCATGCTGATCTCTCTAACTAGAAGTTCTG K 2 1 2 1 600010 f 74 goat 18_50123223 18 50123223 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 468277322 Affx-1111835791 AX-519550826 18 50126320 GGAGGAAAAGAGAGAGAGATAGCAAAGTGTGAAAG[A/G]TATAAATAGTTTGAGAAAGAGGGTATGGCGAAGGG R 2 1 2 1 101000 r 74 goat Random2.2K-1754 18 50126320 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800735 Affx-122974452 AX-385287652 18 50149669 GGAGTTTATTCCTTGGAGACGTGCCTCATATGAAA[C/T]GTATAGAGGATCCTTTAAGATGACTGTTCAAACAC Y 2 1 2 1 101000 f 74 goat snp52321-scaffold777-456661 18 52463102 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395929 Affx-122963589 AX-123266284 18 50226089 GGCCTGGGGCGTTTCATTTTCCTTCACAGGTACAG[C/T]GGCATTCCCAGATGCTGCTCCTGCCCCAGGCTGAC Y 2 1 2 1 102000 f 74 goat snp41227-scaffold534-1019044 18 52373925 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387783 Affx-122969707 AX-123258141 18 50308463 GAAGAATCAGATCTGTATTTGATCAAGATAATCAG[A/C]TCAATTAGCCCTTTAAAACTTGAGTCACTTCCCTG M 2 1 2 1 101000 r 74 goat snp41226-scaffold534-936670 18 52542162 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430976 Affx-122936700 AX-123301317 18 50347088 TCCTGGCACAATGCCCCATTGTCACAAGCTTCAAC[C/T]TTCTCTGAGGTCCAGTTGAACGTGTTTGCTGGATT Y 2 1 2 1 102000 r 74 goat snp41225-scaffold534-898045 18 52580874 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763494 Affx-986698023 AX-186253905 18 50360780 CCAGTTCTAACTGTTGCTTCCTGACCTGCATATAG[A/G]TTTCTCAAGAGGCAGGTCAGGTGGTCTGGTATTCC R 2 1 2 1 103000 f 74 goat 28_31344567_AF-PAKI 17 58915404 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38386573 Affx-122970702 AX-123256931 18 50382981 ACCTTTTTTGCATAGTTTTTCTGTGTATTCTTGCC[A/G]TCTCTGCTTAATCTTCTGCTTCTATTTTGTATATC R 2 1 2 1 303000 r 74 goat snp41224-scaffold534-862152 18 52615209 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391980 Affx-122966512 AX-123262337 18 50427566 TTCAACTATTACCATTTAACGCTACTTGCTTTATC[A/G]CATGTCCACTTACCTTCCTATCTCCCTGTTTATCT R 2 1 2 1 101000 f 74 goat snp41223-scaffold534-817567 18 52660493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463556503 Affx-1110044227 AX-515038552 18 50443243 GTAAGAGATACTGGTTCGATCCCTCCAGCATTCTT[A/G]CCTGGAAAACCTCATGGACAGAGAAGCCTGGTGGG R 2 1 2 1 102000 f 74 goat 18_50443243_AF-PAKI 18 50443243 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38386801 Affx-122970910 AX-123257159 18 50459759 ATCAGGTCCCCATATTTTCATTTTGCACTGGGCCC[A/G]GCAAATTATGTAGCTGGCCCTGGCTCTGACCCCTC R 2 1 2 1 103000 r 74 goat snp41222-scaffold534-785374 18 52692708 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420119 Affx-122945081 AX-123290467 18 50496271 TCTGGAAATGACTCTGGGATTCAAAGTAGCTGGAG[A/C]AAGGAGGATGTCAGGACATGGGGCTGGAAACGTGA M 2 1 2 1 101000 f 74 goat snp41221-scaffold534-748862 18 52729265 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786101 Affx-122935560 AX-385273137 18 50543406 TGCCTGGAGGCAGTATTCTCAACTGAGAGAGAGAT[A/G]CAGGTGGCTGACAAGTTAATCTCAGGTGGAATTCA R 2 1 2 1 202000 r 74 goat snp41220-scaffold534-701727 18 52827911 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428932 Affx-122938898 AX-123299274 18 50600844 GGTACCCTGAGGTATAGAGAGAGAGGCTTTAGTCC[A/C]AGTGGTGTGGTCTCTGGGCCACGACTTCTCAGTCC M 2 1 2 1 101000 f 74 goat snp41219-scaffold534-644289 18 52862107 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439781 Affx-122930506 AX-123310118 18 50630815 GTGACTGACCCCATTTTCTAGGTGCTGGGCAGTTA[C/T]GGGGCTCTCTGGGTACTCTGTCCCTCTCTCCCTTA Y 2 1 2 1 101000 f 74 goat snp41218-scaffold534-614318 18 52891089 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382809 Affx-122973564 AX-123253167 18 50662625 ACCCAAAACAGGAAGAGCAGCAAGCTTAACATCTA[C/T]AGGGATGAGAAGAATATCTCACCCATCTCTGCAGA Y 2 1 2 1 101000 r 74 goat snp41217-scaffold534-582508 18 52923287 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380377 Affx-122975339 AX-123250735 18 50693941 CTTTCCCATATAACCACGATCCTTCCTAACAAGAC[G/T]AAGGAAAGCCCTGTAATATCTAATAGTCACAAAAT K 2 1 2 1 101000 f 74 goat snp41216-scaffold534-551192 18 52954677 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412499 Affx-122951372 AX-123282848 18 50738160 TCTGCATTATCAGCATCACTGTTATCATTATTACT[A/G]TTCCTGGCTGTGTGACATCCCTGCCCTCTCTGAGC R 2 1 2 1 101000 f 74 goat snp41215-scaffold534-506973 18 52998678 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376387 Affx-122978102 AX-123246746 18 50773961 ATTCCCATCTTCAAAAAGCATCACTCTTCACCCAG[C/T]GGGTCAGGCCCAAACCTCCAGGACGACTTTTAAGT Y 2 1 2 1 101000 f 74 goat snp41214-scaffold534-471172 18 53033493 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394711 Affx-122964342 AX-123265066 18 50871079 CGAAGAGATAATGAAAAATTCAAATAGCCAACAGA[C/T]AATCAGAAAACTGGAAATGTGAGCCACAATCATTA Y 2 1 2 1 101000 r 74 goat snp41212-scaffold534-374054 18 53127069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277324 Affx-1111835792 AX-519550828 18 50872180 AGGGAGGGCAGTTTCCCCAACTCGGGGGCCAGGGT[A/G]GGGGTTCAGGGCGGTGATCTGAGTCCTGACATCAA R 2 1 2 1 103000 r 74 goat Random2.2K-1755 18 50872180 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320767069 Affx-122954293 AX-385254358 18 50908461 CAGTACAACTTATGTGGCAAAATGCACAGGCTAAC[A/G]TAACATTTCACCATGTGAATAGAACTTATACTTTT R 2 1 2 1 101000 f 74 goat snp41211-scaffold534-336672 18 53165004 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785515 Affx-122942302 AX-385272560 18 50952352 TAATACTGCAGACTGCAGTACTGAGTGGTTTACTC[A/G]TACTTTTAACTCTTTGTCTCTCTGAACTACTTTTA R 2 1 2 1 201000 r 74 goat snp41210-scaffold534-292781 18 53209195 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393562 Affx-122965402 AX-123263918 18 51009923 TCATCTACACAGCATTCTGTGTTCAAGGACTGAAC[A/G]TCTTAGTAAAAGTGAACATTCACTGGTTAATATAT R 2 1 2 1 201000 r 74 goat snp41209-scaffold534-235210 18 53266591 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382665 Affx-122973663 AX-123253023 18 51043893 ATGTAAAGTGACAGAGAAAGCTCATGCATATTGTT[C/T]AGTAAAAAATGCAGATTGTACCTTCATAATATCCA Y 2 1 2 1 101000 r 74 goat snp41208-scaffold534-201240 18 53300924 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463556853 Affx-1110044408 AX-515038896 18 51064883 GAGTGAATGGATGGTTAGATGGATGCGTGGTAGGA[A/C]GGAGGGATGGATGAATGTGTCAGAGGACAAAGGAT M 2 1 2 1 102000 f 74 goat Random2.2K-1756 18 51064883 A C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320780475 Affx-122939355 AX-385267566 18 51073340 TTCCATGTTCCTTAAGGTCGATGTCCAGTGCAGAA[C/T]AAAGCAAGTCTTCTTGTCATAGGCATAGCTTTCCT Y 2 1 2 1 101000 f 74 goat snp41207-scaffold534-171793 18 53330302 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425916 Affx-122941613 AX-123296262 18 51126379 TATATGATAAACACAGGCTACAGAGGACCCTGGTG[C/T]ACCTGGGGCTTGGTTTAAGACTTCTGCCCTCATCT Y 2 1 2 1 201000 r 74 goat snp41206-scaffold534-118754 18 53380969 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446889 Affx-122925226 AX-123317225 18 51183407 AGGGTTGGGCAGAAGCTCCACATCTGATTCTAATG[C/T]GGGAACAATTGAGTTTGTAAAGAGGTCAGTATAAA Y 2 1 2 1 101000 r 74 goat snp41205-scaffold534-61726 18 53438605 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398149 Affx-122961681 AX-123268504 18 51214875 TGATACGCTTTTACTGGGTCACACCGCTGACATTT[G/T]GGAGATATTTGTTACAGCAGTAATCCAGCCCTGAC K 2 1 2 1 101000 f 74 goat snp41204-scaffold534-30258 18 53470314 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766521 Affx-986698025 AX-385253882 18 51259081 AGAAACATCACTGGTTTCCTTTAGAGATCATCATA[C/T]GGAAACTAATGAGATTGGATGAAGGATTATATGAA Y 2 1 2 1 600010 r 74 goat 18_51259081 18 51259081 Ancestral_priority_1043 ancestry 0.764 recommended IMAGE 10K 10K ancestral 38443360 Affx-122927419 AX-123313697 18 51289453 CACCATCTCAGGTCTCTCGGCCTCACTAGGGCCCA[C/T]AGGAGGAAGCTGACACCTAATTTTTATGGGGAACC Y 2 1 2 1 101000 r 74 goat snp42159-scaffold550-44221 18 53894732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387950 Affx-122970014 AX-123258308 18 51323320 AAGGCATAGGCTCATTTTAGAAAATGCAAGGAGAA[C/T]CAGCCTGTGTATTCTGCCTCTGGTATTAGAGGAAG Y 2 1 2 1 101000 r 74 goat snp42160-scaffold550-78088 18 53928489 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446907 Affx-122924703 AX-123317243 18 51356024 TTCTGTGAGTCCTTGAGTCTGTGAGCTGAGGTCCT[A/G]TGACCAACTCTGTCTTGCTGTAAGATTTGAAGTGT R 2 1 2 1 101000 r 74 goat snp42161-scaffold550-110792 18 53961302 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420873 Affx-122944631 AX-123291220 18 51384609 AGCCATCTCTGCTCTGTCATTTCCTTGCTGAGTGA[C/T]CTTGAACAAGTCTCTTTCTGAACTTCTCCTTGTGG Y 2 1 2 1 101000 r 74 goat snp42162-scaffold550-139377 18 53990043 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405826 Affx-122955882 AX-123276178 18 51416854 GGGAAGCCACCCAAGTGAGGACAATTCTATAACCT[A/G]TTACCACAAAAATACAGTGAAACACATCACCCCAA R 2 1 2 1 101000 f 74 goat snp42163-scaffold550-171622 18 54022390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433685 Affx-122934549 AX-123304026 18 51476226 ACTTGCCCAAGATCACACAGCCGGGCTCCCCATAC[A/G]CCACTGTGCTACTTCCCACAGTTAAGAGAGAGCAA R 2 1 2 1 101000 r 74 goat snp42164-scaffold550-230994 18 54081637 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386045 Affx-122971476 AX-123256403 18 51516220 CCCACACTCATGGGACTGTTGTGGGGAGTAAATGA[A/G]TTCCTACAGAGAACGTTTAGAAAGTGCTCAGCACA R 2 1 2 1 201000 r 74 goat snp42165-scaffold550-270988 18 54119527 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795896 Affx-122950818 AX-385282848 18 51577991 CTACCCTTCTAAGAGTCAAAGAATAGTAGTCATTT[A/G]TTATTCCCATAGTTACTTTCTGAAGAGGTAAAGAC R 2 1 2 1 101000 f 74 goat snp42166-scaffold550-332759 18 54181481 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394365 Affx-122964643 AX-123264720 18 51629253 AAACATGGATTTGGGAGTCTTGGAGAGGTCAAGCT[A/G]CTTGCCCAAAGTCACACAGCTCGTTAGTGGCGCCA R 2 1 2 1 101000 f 74 goat snp42167-scaffold550-384021 18 54233113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437509 Affx-122932344 AX-123307847 18 51664949 CTTGGTAGCTGGGCTCTTTAAACTGGATGTGGGGT[A/C]GGGTTGTGGGAGGAGGGAGGCATGGGCGTCTGAGC M 2 1 2 1 101000 f 74 goat snp42168-scaffold550-419717 18 54269046 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414507 Affx-122949531 AX-123284856 18 51704958 GTTCTGACAGCAGGGAGGAGGCCCTACTTGCCAGC[A/G]ATGAGCGGGTTCCTCAGGACCACGATGACAGAGTC R 2 1 2 1 201000 r 74 goat snp42169-scaffold550-459726 18 54307340 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785036 Affx-122978163 AX-385272083 18 51737736 ATTCATGGACCTCAGTTTAGACTTTGGACATTTTC[A/G]TTTGTTCTATTGGCCTGTGTTTATGGGGACTCAGG R 2 1 2 1 102000 r 74 goat snp42170-scaffold550-492504 18 54339084 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402422 Affx-122958636 AX-123272775 18 51795858 TCAGCTCCACGCGGCACACCCTGACTAATACTCTA[C/T]AGGAGGAACACCATGATTTTGAAAGTGATTCCGGC Y 2 1 2 1 101000 r 74 goat snp42171-scaffold550-550626 18 54393778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389989 Affx-122968055 AX-123260346 18 51834127 CTCTGCACAGAAAAGGTCCGAAAGGAAACAATACT[C/T]TTAGCGGTATTCATCTCTGAGGAGCAGGACCGGGG Y 2 1 2 1 101000 f 74 goat snp42172-scaffold550-588895 18 54432875 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391164 Affx-122967442 AX-123261521 18 51869715 GTCTGGGTTCCATTCTTGTCTCTGACAGTCACTAC[A/C]CTTTTCTGAACCTCAGTCTCTGTAGATGTAAAATG M 2 1 2 1 201000 f 74 goat snp42173-scaffold550-624483 18 54468384 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380065 Affx-122975561 AX-123250423 18 51916419 GGACTCAAGAGAATAGCAGTAGGGAAATAATACAC[A/G]TAATGATCCTCACTCACTCACTCATTCATTCATTT R 2 1 2 1 101000 f 74 goat snp42174-scaffold550-671187 18 54514525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375843 Affx-122978529 AX-123246202 18 51956217 TTGCTGACCTTTCCCTGTCCATGATGTAGTGCCAG[C/T]CCAGGGGGCAGAGACTTTGATCACATACCCACCTG Y 2 1 2 1 201000 f 74 goat snp42175-scaffold550-710985 18 54554085 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433780 Affx-122934476 AX-123304121 18 51991994 TCCTCCTGGGTTGTAGGAAATTTTATCACCATCTG[A/G]CCTCAGGGATCCCCTACTAGGGAGCAGGCAGGAAC R 2 1 2 1 101000 f 74 goat snp42176-scaffold550-746762 18 54589831 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401635 Affx-122959592 AX-123271988 18 52029619 CTCCCTCTTCTCCTGTATTGCTTGTCTTGTCATCC[G/T]GTGCTCTGAATCCTGCTGTGACTCCCAACTGTCCC K 2 1 2 1 201000 f 74 goat snp42177-scaffold550-784387 18 54627698 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398223 Affx-122962213 AX-123268578 18 52085955 TCTGATTCCAAGCAATGTACAAACCAAACCTCCTC[A/G]CCAGCACTGCTCAGCTCTTCATCTGAAATAGCACA R 2 1 2 1 101000 f 74 goat snp42178-scaffold550-840723 18 54683102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413671 Affx-122950109 AX-123284020 18 52145967 GCCACAAGGGCCACAAACTCAGGATTGTCCACCCT[C/T]TCTTTTTCTTGATCCCCGTTTTCCTGGGACTCCTT Y 2 1 2 1 101000 r 74 goat snp42179-scaffold550-900735 18 54743077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422257 Affx-122943999 AX-123292603 18 52189886 CAGCTCCCAGTTAAGTCCCACAGCCATAGGCCAGC[A/C]CAGAGTAGCCCCTGGACCCCGGCCTTACTGTCAGG M 2 1 2 1 101000 f 74 goat snp42180-scaffold550-944654 18 54786445 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452830 Affx-122920735 AX-123323163 18 52221320 AGAGTCTCTGACCAGGGTGCTAAGGGGATATCCTA[A/C]GAGTTCAAGGATGTGGACGGGGGCACTTTGTGAAT M 2 1 2 1 101000 f 74 goat snp42181-scaffold550-976088 18 54817843 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384411 Affx-122972197 AX-123254769 18 52263758 TAGGGTCTGGGGGGAGACCAGGATGCAGATAAACA[C/T]CCAAGGGTTGTGAGACTCCAGGAGGGAGGTAAATC Y 2 1 2 1 201000 f 74 goat snp42182-scaffold550-1018526 18 54860016 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384661 Affx-122972140 AX-123255019 18 52293284 GATATACGACTGACCTTCTCAAAGTCTCCACTTCC[C/T]CTTTTATTTTTGAAAAGGAAGGGAAGCGGAATAAC Y 2 1 2 1 101000 f 74 goat snp42183-scaffold550-1048052 18 54889493 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445004 Affx-122926643 AX-123315341 18 52336584 AGCACATAAGCACGCACGGAAGTGTTAATACTTCC[A/G]TCACAGCTGATTGTAAGCTACCAACGTGGCCTCAT R 2 1 2 1 101000 r 74 goat snp42184-scaffold550-1091352 18 54932651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444138 Affx-122926800 AX-123314475 18 52379494 CTGTGAGAACCCTCCTCTTGCAGAGACCTGTTCCA[C/T]TGCTCCCCATTCATGTGTAGTATTCACTGCCTACT Y 2 1 2 1 101000 r 74 goat snp42185-scaffold550-1134262 18 54975788 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795823 Affx-122966213 AX-385282776 18 52412896 GTGAGACTCCTACCTTGAGGTTAGAGTTCTTGACT[A/G]TTAAGCAGTGCTGTGAAATTTCTAAGGTAGCTTTG R 2 1 2 1 101000 f 74 goat snp42186-scaffold550-1167664 18 55009204 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381192 Affx-122974539 AX-123251550 18 52465173 ATCATACATTAACTGTTGACATCTTTATGATGTTA[C/T]GGGTTTTTTTTTTGTCTCTCGGTAGTATTTTAAAC Y 2 1 2 1 202000 f 74 goat snp42187-scaffold550-1219941 18 55061635 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429406 Affx-122938527 AX-123299748 18 52500174 CAAAGCAGTTAGGCGCCACTGTATTTGTTAATGAA[C/T]GCCTTGTCCCCCCACCCACCTGCACCATCTCTTCA Y 2 1 2 1 101000 f 74 goat snp42188-scaffold550-1254942 18 55096219 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404230 Affx-122957649 AX-123274582 18 52534007 TGGGTCCTGGTTTCCATTCCTGCTGGGACATCCTG[C/T]GAGTCATTTCAGGGCGCAGTTGTTTGCTGTATGGG Y 2 1 2 1 101000 r 74 goat snp42189-scaffold550-1288775 18 55128967 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277326 Affx-1111835793 AX-519550830 18 52598466 GAAGCAACTTTGGGGCCAACCCAGTCACAGGGACC[A/G]TGTGGTCTCAGGGCAGGTCCAAAGAACAGTGAGTG R 2 1 2 1 102000 r 74 goat Random2.2K-1759 18 52598466 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443065 Affx-122928131 AX-123313402 18 52617391 CCTGCTGTTTTGGAGGTGTGGAGCCTTACTGGACC[A/G]CCAGGGAAGTCCTGAGAGGCATGTAACTTTATGAG R 2 1 2 1 201000 f 74 goat snp42191-scaffold550-1372159 18 55212039 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435644 Affx-122933763 AX-123305984 18 52671030 GAATATTAATGGGAAAGCTTGTTTGAAAAGGCAGA[C/T]TCCTGGGCCCCACCCCTGGGAAGCCTGACTCTTTG Y 2 1 2 1 101000 f 74 goat snp42192-scaffold550-1425798 18 55265330 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414313 Affx-122949577 AX-123284662 18 52716007 TTCTTCGCCCTGTCTGTCTCTCGGGCACTTATCTC[C/T]CTGTGGGTCAGGCACTTGGTTTCGGGGGCATCGGG Y 2 1 2 1 101000 f 74 goat snp42193-scaffold550-1470775 18 55310369 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387955 Affx-122969610 AX-123258313 18 52757163 CTTTGGCAGGTAGTGTTGCTTCATGCACTGTTCTT[A/C]CTTGTCCTGTTTCACCCTAGATCTTGGAGTTCTTT M 2 1 2 1 101000 r 74 goat snp42194-scaffold550-1511931 18 55351186 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446325 Affx-122925629 AX-123316661 18 52831303 GGCAAGGGCGACCCTGGAGAGGAGGCGTCTGTGAC[A/G]TGGTCGTCACCTGGGCAGAGCTGAGACACACAGCG R 2 1 2 1 101000 r 74 goat snp42195-scaffold550-1586071 18 55424320 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763502 Affx-986698031 AX-385251366 18 52858101 GGAGAGAGTGGCTCCAATGATCTGGGGGAGAAGGT[A/G]GCTGGGGCGTATGACCCTGGACTAGGAGGAGGGAG R 2 1 2 1 600010 f 74 goat 18_52858101 18 52858101 Ancestral_priority_1043 ancestry 0.49 neutral IMAGE 10K 10K ancestral 320766535 Affx-986698033 AX-385253895 18 52858155 GGACTAGGAGGAGGGAGGCTGGCGATCCTGACTGT[A/G]ATCTAAAATCCCTTGCAGCAGGTGTCAAATTTGCT R 2 1 2 1 600010 r 74 goat 18_52858155 18 52858155 Ancestral_priority_1043 ancestry 0.654 recommended IMAGE 10K 10K ancestral 38402770 Affx-122958312 AX-123273123 18 52861898 TCCTTCAAACTCACCTCAAATTCCATACTTAGCTT[C/T]GACCTCAGTCTGGCCCCAGTTCTAATCAGATCCCA Y 2 1 2 1 101000 f 74 goat snp42196-scaffold550-1616666 18 55454600 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416327 Affx-122947909 AX-123286676 18 52896691 TGGATAGATGGATGGGCTCTGGGTACCTTAATGAA[C/T]GTGATCCCCACAACCAGACCCCGCTTTGGGGGTGA Y 2 1 2 1 101000 f 74 goat snp42197-scaffold550-1651459 18 55489575 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402927 Affx-122958188 AX-123273280 18 52952544 GAACGCTTGCACCCTCAGCGTCTGAGTGTCACACT[A/G]CGTGTCCACCTGTGTGTCTGTGTAAGTAGCCTACT R 2 1 2 1 102000 r 74 goat snp18705-scaffold1890-45316 18 55544236 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272870 Affx-1111833121 AX-519546559 18 52957544 GGATGACAGAGTCGGAGAGACAGGGAGAGACAGAG[A/G]AAAGGAGTGGGACTTCCCTGGTGATCCAGTGGCTA R 2 1 2 1 103000 f 74 goat 18_52957544_AF-PAKI 18 52957544 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454157 Affx-122919326 AX-123324490 18 52992203 GGATCCCCCCAGTGGGAAAGAGAGAGGGTTTTCTA[A/G]GACATCTCTGGCTTGGCAACAATGAGTATTGTGTC R 2 1 2 1 101000 r 74 goat snp18706-scaffold1890-84975 18 55583445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788255 Affx-122976363 AX-385275274 18 53041330 GGCAGCTCCGACAGTTTATTAAGCAGCCACATGGC[A/G]TATTCTATTTGCACTCTGGAGAATGGAACACAGCG R 2 1 2 1 101000 f 74 goat snp18707-scaffold1890-134102 18 55633190 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436223 Affx-122932577 AX-123306562 18 53093920 AGAAACTGGTGGCGAGGGTCGCTGTTCGTCTCATA[A/G]GTGTCTGTTAGGCACCGATGTCACGAGCAAAGAGG R 2 1 2 1 201000 r 74 goat snp18708-scaffold1890-186692 18 55684910 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433266 Affx-122935227 AX-123303607 18 53154618 AATAATAACCGCCACAGGTTTGTAGCATTTGCTGC[A/G]TGTCAGGTGCTATTTTAAGTATCAGATGCACAATA R 2 1 2 1 201000 r 74 goat snp18709-scaffold1890-247390 18 55746179 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384790 Affx-122972004 AX-123255148 18 53248283 GGAAGAAACTGTCCTGGAGGCCAAGTATCATGACA[A/G]CGTCAGGAAGGGAGGCACTTAACGCTCATCCTGCA R 2 1 2 1 101000 f 74 goat snp18711-scaffold1890-341055 18 55839537 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445304 Affx-122925442 AX-123315641 18 53296071 ACCCTCTGAGCAACTATGACCATTGTCCCTCACCA[C/T]AGCCAGACATTAGCAGTAGATTTCAGCCGTTCAGC Y 2 1 2 1 101000 f 74 goat snp18712-scaffold1890-388843 18 55887324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436684 Affx-122932455 AX-123307022 18 53326845 AGTTCTCAGGCTACGTTCTAGGCCTCTACATCATC[A/G]TGCCTCGGGAAATGCCTCACACCCACCCCGTTAGA R 2 1 2 1 101000 f 74 goat snp18713-scaffold1890-419617 18 55917661 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442645 Affx-122928448 AX-123312982 18 53368328 GCGCTGATATACAGGGTGAATTGGGATGTTAAAGG[C/T]AACTGGAGTTTCCTGACTCCTAACTGTCCGGACAT Y 2 1 2 1 101000 f 74 goat snp18714-scaffold1890-461100 18 55959623 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791710 Affx-122960171 AX-385278701 18 53398875 AGGCCACAGCACACAATTCAATGGAATTTTTGAGC[A/G]TCATGGTGATTTGAGGTTTCCTCTTTGTGTTCCTC R 2 1 2 1 101000 f 74 goat snp18283-scaffold1857-26269 18 55991746 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377356 Affx-122977654 AX-123247715 18 53442060 CTACATTGAATTTAGACTCGAGTTTACTGTGCTCC[A/G]TGATGCCATTTCTGTTCATTAATTTGACTGCATTA R 2 1 2 1 101000 f 74 goat snp18284-scaffold1857-69454 18 56035017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378936 Affx-122976435 AX-123249295 18 53487685 GATGAGCTCTCTGGGCGAGAGGTCGGAAGAGGGCC[A/G]TGTATCCTGCTGTAAAATCAGCCTCCCAGGTGTCT R 2 1 2 1 101000 r 74 goat snp18285-scaffold1857-115079 18 56079181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773826 Affx-122975194 AX-385260966 18 53520671 TAGCTCCTACCAAAATACCAGGCAATAAAAACCAC[A/G]ACAGCTAGCCTTTAGGAGTAGAAAGCCAAAGCACT R 2 1 2 1 101000 f 74 goat snp18286-scaffold1857-148065 18 56112058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393137 Affx-122965553 AX-123263494 18 53576363 TGGTGTAAACCACGGCTTAGGTTTACGGTCCCCAG[A/C]CAGTGTTGTGGTACAGAGAGGCCTGTGACGGAGGT M 2 1 2 1 101000 f 74 goat snp18287-scaffold1857-203757 18 56165541 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404769 Affx-122957212 AX-123275121 18 53610384 CCGGTGCCTAGACTAAGTAGGTGCTCAATAAAATC[A/G]TGTGGAATGAAGGATTTAACCCTGCTACATGACCC R 2 1 2 1 101000 r 74 goat snp18288-scaffold1857-237778 18 56199590 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387781 Affx-122969708 AX-123258139 18 53681273 AGGCAGATAGAGAGCCTGGCTGGACCCTGCGGAAC[A/G]TCCTTGGGGCAGGCACCTGGGAGAGAAAGGCCTTC R 2 1 2 1 101000 f 74 goat snp18289-scaffold1857-308667 18 56270790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430958 Affx-122936824 AX-123301299 18 53713532 AGGCCTTGGGGAAACAGAATGTGCTACCTGAGGGC[A/G]TATTTATTTGGGGAAGGGGGTTCCCCAGAGGCTAG R 2 1 2 1 102000 r 74 goat snp18290-scaffold1857-340926 18 56303034 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421772 Affx-122944351 AX-123292119 18 53744572 AATGGGAGACCTTGGAGGAGGGCGTGAGAGTGTTC[A/G]TATTTCCCAAAGGGATCAGATTAATAAAGTGAGGG R 2 1 2 1 101000 r 74 goat snp18291-scaffold1857-371966 18 56334205 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772009 Affx-122978325 AX-385259165 18 53836690 TATTAATGGATATTCCTACATAGAACATAAGTGAT[A/G]TTTATAAGTTTCTCTGATCTTTTCATCCCTTAGAA R 2 1 2 1 101000 r 74 goat snp18293-scaffold1857-464084 18 56424733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393613 Affx-122965361 AX-123263969 18 53907613 GCAAGGACTAGGACTTTGTCCTCAAGAGAAGTAAG[C/T]AGAGGACCTGCGTTTTGGCTTCCTGGGACCAGGAC Y 2 1 2 1 101000 f 74 goat snp18294-scaffold1857-535007 18 56490049 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451847 Affx-122921079 AX-123322180 18 53940492 CTATAAATGAATCTTTCATGCATCCCCTGCACTCC[A/G]AGCTCTCAGTTCTAACTGGATTCAGCTTTTTTCCT R 2 1 2 1 201000 r 74 goat snp18295-scaffold1857-567886 18 56522928 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452436 Affx-122920575 AX-123322769 18 53969478 AAAGAGACCGCAGTAGGGCAGGAGGGAGACAGAGC[A/G]TGACAAGGGAGGCTGGGGGCCAGTGGCCCCAGGCA R 2 1 2 1 101000 f 74 goat snp18296-scaffold1857-596872 18 56552499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412446 Affx-122951411 AX-123282795 18 54119128 CGACATGTATTTCTGCCTCGACAGAGCAAGTAGAA[C/T]TGGGTGGATTTGGTTCATTTCGGGATCTTTTGCCT Y 2 1 2 1 101000 f 74 goat snp18299-scaffold1857-746522 18 56698383 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380461 Affx-122975733 AX-123250819 18 54152265 CTGAGCCACCAGAGAAGCCCATTCAGGAGGCAGGG[A/C]GGTGTTATCTAGCTCCCACAGAAAACCCTAATAAA M 2 1 2 1 101000 r 74 goat snp18300-scaffold1857-779659 18 56731923 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408484 Affx-122954417 AX-123278835 18 54182109 TCCTCTCCTCTAGAAAACTATCTGTAGCCCTGATC[A/G]TGGATATTATTATACTCATCTGGCCTTGAGGCATG R 2 1 2 1 201000 r 74 goat snp18301-scaffold1857-809503 18 56762181 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793473 Affx-122953252 AX-385280450 18 54212344 CAAAATACTGCTATCGCTCATCAACCTAGATTCAA[C/T]GTCCTGAACAAAAGTCAACAGACCTAATCCGGCAA Y 2 1 2 1 101000 r 74 goat snp18302-scaffold1857-839738 18 56792517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428605 Affx-122938693 AX-123298947 18 54265729 TGAGGCGCCATGGCAAGCCAGACCCTGTGCAAGCA[C/T]GTTATGGGCACCACTTCCTTGAAGACTCACAGCCT Y 2 1 2 1 101000 r 74 goat snp18303-scaffold1857-893123 18 56845251 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379724 Affx-122975881 AX-123250082 18 54355414 TAAAGCAAACTGCAAACACACACACAAAAACAATT[A/C]TACTCCAAAAAATAAAAAATAAAATACAGTGGCTT M 2 1 2 1 103000 f 74 goat snp18305-scaffold1857-982808 18 56934600 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379738 Affx-122975871 AX-123250096 18 54400919 TTATCCTCTGGCACCTGAACCCTCACCCCAGCCCC[A/G]CTCCAGACTTCTTCACATACCCTCAGGGGGATCGT R 2 1 2 1 101000 r 74 goat snp18306-scaffold1857-1028313 18 56980502 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414565 Affx-122949384 AX-123284914 18 54432837 GCGCCACCTTCTGAGTGCAGCTTTTTGCGAAGAGG[A/G]CTAAAAGCCTGGGGTTTACTGTTTGAGGAAAGTTC R 2 1 2 1 202000 f 74 goat snp18307-scaffold1857-1060231 18 57012777 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381920 Affx-122974139 AX-123252278 18 54491641 TATAGAGTGGTGAACGTCTGCTTCCTTCAGTGAAG[G/T]TGATCAGATCTGGGGGCCAAGGAACAGAGAGTCAG K 2 1 2 1 102000 f 74 goat snp18308-scaffold1857-1119035 18 57070636 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412414 Affx-122951434 AX-123282763 18 54524733 GTCTCAGTACTGATGCCCAAGAGTTGTGAATTACA[C/T]GCAGAGGGTCACTTGGGCCAGGGATGTGGCTTTGG Y 2 1 2 1 101000 f 74 goat snp18309-scaffold1857-1152127 18 57103150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384513 Affx-122973048 AX-123254871 18 54583682 ACTGAAGAAAGCAAAACAGGTGGCAGGACGTGGGG[A/C]TGGCTACTTAGATCAGACTCATCGGGGGGGTGTCT M 2 1 2 1 201000 r 74 goat snp18310-scaffold1857-1211076 18 57162007 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414284 Affx-122949598 AX-123284633 18 54599078 TCGTGGGACTTGAAGAGCTGACCAATATCCGCAAC[A/G]TAGAGAGACTGAAGAAGGAGCTGAGGGTGAGGATG R 2 1 2 1 101000 f 74 goat snp15035-scaffold16067-36343 18 57178169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401472 Affx-122958963 AX-123271825 18 54630011 TTGTCACCTTGACTTTCATTCCACTCATCAAAAGA[C/T]GCCAGTGAGACTTACTTGGTGGCACAGTGGATGAG Y 2 1 2 1 101000 f 74 goat snp15034-scaffold16067-5410 18 57209401 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434923 Affx-122934312 AX-123305263 18 54712504 GACTTTTTGTTCTGTAAGTGAAATCTCATGAGATA[A/C]GGAGCACGCACCTGGGGAACGAGAAGCTTGGATCA M 2 1 2 1 202000 f 74 goat snp50894-scaffold7383-5153 18 57289997 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391131 Affx-122966795 AX-123261488 18 54727121 GAGCCTATGTGGAGGAAGTGCTCACACAATTTACG[C/T]GGTCCTGAGGCTGGCACAGCCCTTTTATGCCATCA Y 2 1 2 1 101000 f 74 goat snp29471-scaffold3193-206680 18 57305018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452064 Affx-122920875 AX-123322397 18 54761218 TAATTCTTAAGCTTCTGGGCCAAGTATGCTTTAAA[C/T]TCAGCAATTTTCAGATTATAAAAAGGTAATCCACC Y 2 1 2 1 101000 r 74 goat snp29470-scaffold3193-172583 18 57338671 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386391 Affx-122970835 AX-123256749 18 54800707 CCGCAGAAGAAAAAAGACAATCCAGCAAGACTAAA[C/T]AAGAGTTTAGTATTTAAGCATGGTTAAGGAACTTT Y 2 1 2 1 101000 f 74 goat snp29469-scaffold3193-133094 18 57379127 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409198 Affx-122953177 AX-123279549 18 54835750 GAGAGAGAGACCAGGACTGAAATTACGATGCAATT[A/C]TCTGCATTTAACTCCATCCTCCATCTCAGGAGGTC M 2 1 2 1 101000 f 74 goat snp29468-scaffold3193-98051 18 57414623 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446841 Affx-122925268 AX-123317177 18 54888822 AGGGAGCCCTCCCTGATTTCACTGTATCCCTACTA[C/T]CTGGCACTTGGTAAAAAGCTAAACACTACAGAAAT Y 2 1 2 1 101000 r 74 goat snp29467-scaffold3193-44979 18 57467987 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379489 Affx-122976472 AX-123249847 18 54946233 TATGCTGAAGATGGGGTTCTTAAATTCAGTATTTG[A/G]TGGGGTAGAGCATGAAATTTCCTGGTTTGAGTTTT R 2 1 2 1 201000 f 74 goat snp26860-scaffold283-12333 18 57525671 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799615 Affx-122953063 AX-385286545 18 55002323 GAACAAATCGAAGACAGTTGGATGGTAGATTTAAG[C/T]GCAGATATAATCAGTAATTACACTAAACATAAATG Y 2 1 2 1 101000 f 74 goat snp26861-scaffold283-68423 18 57581681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434639 Affx-122933993 AX-123304980 18 55048519 GAGGTGGAAGAGAATGTCTCAGTACAGGGTTCTGG[C/T]ATCAGAATACTGTTTTGTGAAATGTTTTCAACTTA Y 2 1 2 1 101000 f 74 goat snp26862-scaffold283-114619 18 57625693 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438495 Affx-122931222 AX-123308833 18 55111919 GTGTGTTTGGGGAGGTCACAGCCTCTGACCTGACC[A/G]TCTCGCTTCTCGGGATTTATCCCCAAGGCAGAATC R 2 1 2 1 101000 r 74 goat snp26863-scaffold283-178019 18 57763143 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425789 Affx-122940709 AX-123296135 18 55149246 TTCATTCATTTATCTCCTATGTGGACTAAGGTCTG[C/T]GCTGCCAACTGGGGATACAGTGATGAACCAAAGAT Y 2 1 2 1 201000 f 74 goat snp26864-scaffold283-215346 18 57799394 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389678 Affx-122968708 AX-123260036 18 55186121 GGGGAGAGATGTGGGGAGAAAGAGGGCAGAGAAAA[C/T]GAGGGAAAGAGTAGAGGGGAGATGGGGAGAGCGAC Y 2 1 2 1 101000 f 74 goat snp26865-scaffold283-252221 18 57835998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380830 Affx-122975070 AX-123251188 18 55230253 GAAAAACCCTGGCCCTCATTCTCGGACACACGGAT[G/T]CGGGGAAAGAGAGGTGCAGAGAGAGCCAGCTGCAC K 2 1 2 1 101000 f 74 goat snp26866-scaffold283-296353 18 57874557 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771717 Affx-122932034 AX-385258874 18 55267001 TGCGTCTCCTTGAGTCTGGGACATTTCCATATTTA[C/T]GATATTGACAATTTGGAAGAAGAACTCTCCCCCTT Y 2 1 2 1 101000 f 74 goat snp26867-scaffold283-333101 18 57911677 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419041 Affx-122946026 AX-123289389 18 55301321 CCCCATCCCCAGGCATTGTAGTTTAAGTGGTCCAG[A/C]ATAGAGCTGGGCTCTGGGAGTTTCAAAAGCTCCCC M 2 1 2 1 201000 r 74 goat snp26868-scaffold283-367421 18 57945776 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376557 Affx-122977979 AX-123246916 18 55338579 AGGAGGCTCAGGTTGAATCCCGGATTTGGGAAGTC[C/T]TCACTGACACTGGCGAACTGGGCCGTGTCTTCGTC Y 2 1 2 1 101000 f 74 goat snp26869-scaffold283-404679 18 57982851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428785 Affx-122938411 AX-123299127 18 55373263 TGCAGGTAAATGATACAGCCCCAACGCTTCCCTGG[C/T]ATATTTCTTAAGGTACATTGTTTTTAAAAGCTATA Y 2 1 2 1 201000 r 74 goat snp26870-scaffold283-439363 18 58017577 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440405 Affx-122929614 AX-123310742 18 55401892 TTTGACACTTGGCCCACTTCCTGATTGATATCTCC[A/G]CACCGACCTTCCCTCCTCACTGACCCTTCATGGCA R 2 1 2 1 103000 f 74 goat snp26871-scaffold283-467992 18 58046210 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781576 Affx-122975389 AX-385268660 18 55449969 CTATTGTATTGACCTGCACAGGTCCTGATGAACTA[C/T]CTATTATGAAGGTTGGAAAGAAAACAATGATCCCT Y 2 1 2 1 101000 f 74 goat snp26872-scaffold283-516069 18 58093104 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383038 Affx-122973299 AX-123253396 18 55483399 ATGTAAGGCAAGGCAGGTCGCTCCTCTTCTCAACC[A/G]TCTGCAGTGCCTCCCGCCTCATTCAGAGTGAAGGT R 2 1 2 1 101000 f 74 goat snp26873-scaffold283-549499 18 58126576 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773917 Affx-122933051 AX-385261056 18 55536085 ACCCATATCCACTTGCTAATCTATACTTTTCATAA[C/T]GTGGTCTGTATTGTGCGTTTCTAACTCGGCATCAA Y 2 1 2 1 101000 r 74 goat snp26874-scaffold283-602185 NW_017190593.1 13350 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434642 Affx-122933992 AX-123304983 18 55571479 ATTTCACCCCGAGCTGGGTTGGTCCTGTCCCTGGG[C/T]ACCACATCGGTTACATTTGCCAGCCTCTCTCTTAC Y 2 1 2 1 101000 r 74 goat snp26875-scaffold283-637579 18 58277630 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802750 Affx-122959622 AX-385289649 18 55644467 GGCCAGCCTGAAGAAGCTACAAAAGACAGACCTTC[A/G]CCCTTCAGCCTCCCAATAAAGATTTTTGGGGTTCA R 2 1 2 1 102000 r 74 goat snp26877-scaffold283-710567 18 58202796 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378836 Affx-122976539 AX-123249195 18 55660877 GGTTCTACTTCACAGGCCCACCTCTTCAATGACAA[C/T]CTCAGAGAGCTCACCAGAATCCTGCTCATCTTGGT Y 2 1 2 1 101000 f 74 goat snp39963-scaffold510-201671 18 62056779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272872 Affx-1111833122 AX-519546562 18 55661414 AGAAAAAGACGGAGGAATCCTTTTCTTCGGATCAG[A/C]TTCTGCCTCCTTCCCCTTGTTTATCTCTTGGGCTT M 2 1 2 1 101000 f 74 goat 18_55661414_AF-PAKI 18 55661414 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38408879 Affx-122953985 AX-123279230 18 55714101 GCATCACAGTAGCAGGGCTGGGCTGGGGTGATGGT[C/T]GCCCAGAGGGGTGAGAGACTGAACCTCCCTGGAGA Y 2 1 2 1 101000 r 74 goat snp24719-scaffold2523-63156 18 58390391 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375877 Affx-122978503 AX-123246236 18 55745086 CTCTGGGCCGTTTGTTCCCTACCAGGGACTTCAAC[A/C]AGAGGGACAGAGGGCAGAGTGGCTGGCAGGTGAGC M 2 1 2 1 101000 f 74 goat snp24720-scaffold2523-94141 18 58421496 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394663 Affx-122964374 AX-123265018 18 55776973 CTAGGCACACGCCATGTGATGGGACCTCTGTTCGT[C/T]GGTTATAATATGTTCTTCCCTTTCTTCCTTTGAGG Y 2 1 2 1 201000 f 74 goat snp29453-scaffold3189-19092 18 58595562 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763508 Affx-986698037 AX-385251372 18 55805976 CAGCATACAGAAAGCCCTCCATCTGTCTACTGAAG[A/G]ATGAGGGCCACAGCCACAGCCTGTCAGTACCTGAT R 2 1 2 1 600010 f 74 goat 18_55805976 18 55805976 Ancestral_priority_1043 ancestry 0.512 neutral IMAGE 10K 10K ancestral 38384733 Affx-122972046 AX-123255091 18 55816487 AACCAGCAGATCAGGTGTACATGTGACAACCTGGA[C/T]GTGAAACAGGCATCTGAAACTGGAGGGGCAGTCTG Y 2 1 2 1 102000 f 74 goat snp46077-scaffold632-882794 18 58663435 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765353 Affx-122956997 AX-385252870 18 55845276 TTGTTGGATGAGTCAGTGTATCTATTTTTCCAGGA[A/G]ATGCAAAATTAAGTCCCCACGGTAGCAAAGCAGGT R 2 1 2 1 101000 f 74 goat snp46076-scaffold632-854005 18 58692348 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380406 Affx-122975317 AX-123250764 18 55875843 GTCTGTGACTCAGACACGAGGCTGGACCCCATGGC[A/G]CTGCTGGAGCTGGTGCGGGTGCTGGACGAGGACCC R 2 1 2 1 101000 f 74 goat snp46075-scaffold632-823438 18 58723099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412194 Affx-122951053 AX-123282544 18 55972514 ACACATAGTAAACGAGCAGAAAAGGCAAAATCCTC[A/G]TTTTTAGCAGAAACCTTACCACTTTAGATGTGCTT R 2 1 2 1 201000 r 74 goat snp46073-scaffold632-726767 18 58820481 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273864 Affx-1111833892 AX-519547473 18 56105320 TCATGTACAGACTGGGCAAAGGGATGTGAGTTGTG[A/G]GGAGACCAACATGGGCTC R 2 1 2 1 102000 f 74 goat GoatD01.009617 18 56105320 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320774509 Affx-122972947 AX-385261643 18 56111082 GTGGTTTCTCTTTGGGGTACAAAGTTCAATCTATA[C/T]AGACCCATTAGGTCAAAATAGTTATTTTATTTTTA Y 2 1 2 1 202000 r 74 goat snp46071-scaffold632-588199 18 58960722 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411703 Affx-122951539 AX-123282053 18 56182030 AAATAAACCAGATCTAAGTTTTGTTTTACAACTAG[C/T]CAATTCAATTGAGGTTGGTAGTATTTTATTTGAAA Y 2 1 2 1 101000 f 74 goat snp46070-scaffold632-517251 18 59026824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397445 Affx-122962111 AX-123267800 18 56238640 GAATTCCTTGACAGTCTTGTGATTAGGACTCCGAG[A/C]GTCTGCTGAAGGAGGTTCCATCCCTGCTTCCATCC M 2 1 2 1 101000 f 74 goat snp46069-scaffold632-460641 18 59084534 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375971 Affx-122978435 AX-123246330 18 56400259 CCTTGAGTTGACCTTTCTCCATAATTTAGGGTTCA[C/T]ACCTCAACTCCATTTTCTCCTCAGGACATAACCTG Y 2 1 2 1 101000 f 74 goat snp46066-scaffold632-299022 18 59247577 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431015 Affx-122936672 AX-123301356 18 56514202 ACTTTTCGAAGGGGAATCTCTGGTCAGGGCACAAA[C/T]GTATTTGTAAAATGCCTCATGGATGTAATGTGTAG Y 2 1 2 1 101000 r 74 goat snp46064-scaffold632-185079 18 59362773 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434560 Affx-122934130 AX-123304901 18 56548382 GATAATCCCTTCATGCCCCACTCCCCTGCTGGGGC[A/G]GGACATTTTAGCTAAGCTTAGGGCCACCATTCACC R 2 1 2 1 303000 f 74 goat snp46063-scaffold632-150899 18 59395279 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403154 Affx-122958094 AX-123273507 18 56603349 ACTCCATATATATGCTTTCTCCCTGGAGCCTTAAA[C/T]GGCCCTCACACCCTGAAGAAGACAGGAAACTAATA Y 2 1 2 1 201000 f 74 goat snp46062-scaffold632-95932 18 59465016 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428940 Affx-122938893 AX-123299282 18 56678709 TTCCAAGGTGTGAATATTGATTAAAGCATTAAAGA[C/T]GGAAAGAACAGTACTTCACGTATTCATTCCCTCTC Y 2 1 2 1 201000 f 74 goat snp46060-scaffold632-20572 18 60467072 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776851 Affx-122956308 AX-385263975 18 56721950 TCCCCAATATGAATTTCTTAGTGAATCTTGAAGAC[A/G]TACTGGCTTTCTTAGAAGTGTTTTCATATTCAGTA R 2 1 2 1 101000 f 74 goat snp17782-scaffold1848-22570 18 61725228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774197 Affx-122957816 AX-385261334 18 56773043 TTCTTAGTCATACAAAAGTCATGTTACTGCAAGAA[A/G]CGTGAAGACTAAGTGCTCATGCTCACAGAGGTAGA R 2 1 2 1 101000 r 74 goat snp17783-scaffold1848-73663 18 61776542 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402547 Affx-122958464 AX-123272900 18 56809849 GTAACAGATAAATTTGATGGAAAATACTATCCCTC[A/G]TGCATTGTAATATTTTTGTGCTATATAGAAATTCA R 2 1 2 1 101000 f 74 goat snp17784-scaffold1848-110469 18 61813628 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786240 Affx-122933926 AX-385273275 18 56842736 CTTGCCTACCAACTTCTGTCCCTCACAAGTGTCCT[A/G]TATTAATAAGTCTACTTCTTGCCTGTCACTTTGCT R 2 1 2 1 102000 f 74 goat snp17785-scaffold1848-143356 18 61846514 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451386 Affx-122921208 AX-123321719 18 56911389 AGAACTCATACTGGAGAGAAACTTTACAAATGTGA[C/T]GAGTGTGGAAAAGCCCTTACAAGACATTCATATCT Y 2 1 2 1 101000 r 74 goat snp17787-scaffold1848-212009 18 61915126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438332 Affx-122931343 AX-123308670 18 56950476 TCAGTAGCATCTCTGTTCTCCTGTTTTGACAGATG[G/T]TTACTGATGCAACTTTCATGAAAATTTTGGGTTTC K 2 1 2 1 101000 r 74 goat snp17788-scaffold1848-251096 18 61954192 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771765 Affx-122936630 AX-385258922 18 56984644 CCAGTGACCTACACTGGTATACACATTTATTAGAG[C/T]TGTCTCTGTATTTGTCTGTGCTCCTTTTTTAATTT Y 2 1 2 1 201000 r 74 goat snp17789-scaffold1848-285264 18 61988574 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422217 Affx-122944030 AX-123292563 18 57069260 TAATGCACAAAATGGCCGAGTGTCCCAACAGTCAC[A/G]TCCGACGGTGAGAGGAGACCTCTGAGAACCCTGCA R 2 1 2 1 101000 f 74 goat snp14392-scaffold1571-66697 18 62326897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403230 Affx-122957894 AX-123273583 18 57102558 TTGTTCAGTTTGCATCTACACAGAGGCTGGTATGC[C/T]AGAGAAACTCATATCATGTGTCAGGCCGTCTTCCC Y 2 1 2 1 101000 f 74 goat snp14393-scaffold1571-99995 18 62360918 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435058 Affx-122933740 AX-123305398 18 57188609 AGCATCAGCATCAGCAGGTAGATTCTCATTCACTT[A/G]CACCACCAGGGAAGTCCAAAAAACTAAGAATTGTA R 2 1 2 1 101000 f 74 goat snp20945-scaffold2053-135877 18 62456243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463561103 Affx-1110046555 AX-515043105 18 57189024 TTGGTTTCTTGGTCTGCAGAGGGATAACGGTAGTC[C/T]GTATCAGCACTCAGAGAAGGGTCACAGAAGCTAAT Y 2 1 2 1 201000 f 74 goat GoatD01.009517 18 57189024 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38417927 Affx-122946720 AX-123288275 18 57237807 GCTGAAGGGGAGGAGGAATCCAAGCCGACTCAGAA[C/T]GCCCTGGCTGAGGGATTAATCAGATGGATGGAGGT Y 2 1 2 1 101000 r 74 goat snp20944-scaffold2053-86679 18 62505611 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404452 Affx-122956745 AX-123274804 18 57275368 TTCTTTCTGAAACGTAGCAAGGTGAAAGGAGTGTC[A/G]TAAGGGTAAGCAAAGGGTAATAAGTGTTAAGTGCA R 2 1 2 1 101000 r 74 goat snp20943-scaffold2053-49118 18 62766852 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406508 Affx-122955146 AX-123276860 18 57322274 AGTCATACCTGCATACAGTGGAATATAACTTAGCC[A/G]TGAAAATGAAACAATGATACTTGCAGCAGTATGGA R 2 1 2 1 303000 r 74 goat snp20942-scaffold2053-2212 18 62815202 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438558 Affx-122931173 AX-123308896 18 57331379 AGTGAATGTGTATATTTTCTCAGTGCAGCAGTCTT[A/G]CAGATATGATGGCCCTTCCTGATGTTGGTGGTCTC R 2 1 2 1 102000 f 74 goat snp52184-scaffold773-6794 NW_017190779.1 4266 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392705 Affx-122966403 AX-123263062 18 57369592 GATATCCTTGTAGCATAGCAACTGAAAGTGAAAGT[A/G]TTAGTCACTTAGTCTTGTCTGACTCTTTGCGACCC R 2 1 2 1 103000 f 74 goat snp52185-scaffold773-45007 18 63006165 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402550 Affx-122958462 AX-123272903 18 57435962 ATGCAAATATATTTCACACGACTAGACACTTAAAG[A/G]TGGTTAAAATGGTCAATTTTATGTTATAGGTATTT R 2 1 2 1 103000 f 74 goat snp52187-scaffold773-111377 18 63064709 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383909 Affx-122973108 AX-123254267 18 57505055 GTAATTTAGGTTTAAAGTCTCCTCTGTGTTGGAAA[C/T]AATTAAATCATACTAAGGATAATCCTAACACTGGA Y 2 1 2 1 303000 r 74 goat snp52188-scaffold773-180470 18 63134591 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448039 Affx-122923708 AX-123318375 18 57550728 ATGTTATCAAGGGGAATTAATTTTGGGAAAAAATA[C/T]TTGTGAAACTAACTGAAATGGAAAATGGGACTTTA Y 2 1 2 1 103000 r 74 goat snp52189-scaffold773-226143 18 63180780 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799270 Affx-122928739 AX-385286200 18 57604654 GTAGATTTGGATTTAACATGACAATTCGGTAGAGG[C/T]ATATGTTGTGAGATGATTGTCACAGTAAGAAATTA Y 2 1 2 1 101000 f 74 goat snp52190-scaffold773-280069 18 63236575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768658 Affx-122945012 AX-385255836 18 57648702 TATGGCCATGAAGGTGTTTCTGGGGGAGATGAACA[C/T]TTGAACCAGTAGCTTGAGAAAAGCGGATTGCCCTC Y 2 1 2 1 101000 f 74 goat snp52191-scaffold773-324117 18 63279811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410107 Affx-122952829 AX-123280457 18 57689397 GGTTTGACAAGGAGAGTGGCTGGGGTCCAGAATTA[C/T]GGACCTCCTCTCCGTCCAGGGGGCAGAATCTGAAC Y 2 1 2 1 101000 f 74 goat snp52192-scaffold773-364812 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402984 Affx-122958147 AX-123273337 18 57775119 AAGAAGCCAGGAAGCATCCCCCTCCCCCACAGACA[C/T]AGGACGACCTCAGCTCCCCTTCCTGAGAACCCCAA Y 2 1 2 1 201000 r 74 goat snp52194-scaffold773-450534 18 63395168 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398696 Affx-122961858 AX-123269051 18 57814669 GACGCTTTTTGTTAATTCACGAGTGTCTCCCTTCA[C/T]GGCCTATAATTTTTCTGCTCCTTTTGTGAAATCCC Y 2 1 2 1 101000 f 74 goat snp52195-scaffold773-490084 18 63433720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453598 Affx-122920142 AX-123323931 18 57846938 TTCCCGAACCTACCAAGGACATTTGTTGAGGACTG[A/G]TTTGTTTTCCTTACAGCCCCTCGGGCCTGGTGAAG R 2 1 2 1 101000 f 74 goat snp52196-scaffold773-522353 18 63466474 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390409 Affx-122967653 AX-123260766 18 57882172 GTTCAATCCCTGGTTAGGGAACTAAGACCTCTGGT[G/T]CTGCATGCGCACTCAAAAGAAAAAATATATATGGT K 2 1 2 1 101000 r 74 goat snp52197-scaffold773-557587 18 63502602 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795387 Affx-122921360 AX-385282343 18 57929731 ACGTCTGTTTCAAGGGTACAAAATAATTGTATTTC[C/T]ATACATTGCCAGTTGATCACAGACAGTCTAGTTTA Y 2 1 2 1 101000 r 74 goat snp52198-scaffold773-605146 18 63551103 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414141 Affx-122949700 AX-123284490 18 57965645 GGGATTAAACCATAGTGGACTTTTTCTCTTTGAAA[C/T]AAGGAATGTTTTCTGAGATTACCAAATGATGATAT Y 2 1 2 1 101000 f 74 goat snp52199-scaffold773-641060 18 63587450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415822 Affx-122948885 AX-123286171 18 58042342 ACAGGAAGCCAACTAACAAACAGGCAGCTACAAAG[C/T]AGGGTCACAAGGGCAATGATGAGGCACTCCAGGTG Y 2 1 2 1 101000 f 74 goat snp52200-scaffold773-717757 18 63666023 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423518 Affx-122942454 AX-123293864 18 58159979 AGACAGATCCCTCCCCAAAACCTACAGTCTTCCCA[C/T]GGCCTGTGCCCTCCTCCCCTCCCTGACTCTCTGCC Y 2 1 2 1 303000 r 74 goat snp52202-scaffold773-835394 18 63783589 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766552 Affx-986698043 AX-385253911 18 58202396 GGATTGAATTCTTCTCCTCCGGGGGCCAAGGATCC[C/T]GGCATCGTAATTCTAAAACAACCTTTCACTGGTCC Y 2 1 2 1 600010 r 74 goat 18_58202396 18 58202396 Ancestral_priority_1043 ancestry 0.672 recommended IMAGE 10K 10K ancestral 468272874 Affx-1111833123 AX-519546564 18 58204152 AGATTGGCTTTAGATATTCTGACAGCTGCGCAAGG[A/G]GGAACGTGTGCCATTATTCATACCCAATGCTGTAC R 2 1 2 1 103000 f 74 goat 18_58204152_AF-PAKI 18 58204152 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406699 Affx-122955772 AX-123277051 18 58213899 GAGTCGTTACTGTGTCTCTCGAGACTTGAACAGCT[C/T]CTCAGTATCTTTCATGAGTTTTGGAGTCCAAGGAG Y 2 1 2 1 101000 f 74 goat snp17186-scaffold1794-29814 18 63846042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437349 Affx-122931941 AX-123307687 18 58274244 TGAGCATTTGTTTTCTAATCTGTCAAAAAGGCCAC[C/T]GTAGCTTAGTGAGAATCTGGAATTACTGCCTGGCC Y 2 1 2 1 101000 f 74 goat snp17187-scaffold1794-90159 18 63906131 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444959 Affx-122926677 AX-123315296 18 58314437 GAGCAGACCCATTGCTGGGGTGTCCAGTCATAACA[C/T]CCAGAGTTATGCTGCGGGAAGAAGGGAGTCTCCAG Y 2 1 2 1 101000 f 74 goat snp17188-scaffold1794-130352 18 63945638 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427749 Affx-122939252 AX-123298092 18 58371985 TAGAGCATTTTCTTCACCCCAAAAAGAGACCCCAT[A/G]CCTTAAACCCATCGCCTCTAGCCCAAGGCAATCAC R 2 1 2 1 201000 r 74 goat snp17189-scaffold1794-187900 18 63994313 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425063 Affx-122941260 AX-123295409 18 58424773 GAGAGAGAAGCACACTGAAGTCACTGGGGAGGAGC[A/G]GAGATCTTAGGTACAGGTCTGGAAAATCTGGAAAC R 2 1 2 1 101000 r 74 goat snp17190-scaffold1794-240688 18 64046388 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771015 Affx-122967011 AX-385258177 18 58471332 TCAGAATATGATCTTATTCCGAAATAGGGTTGTTG[C/T]AGATGTATGGAATTAGGGTGACCTCAGTTTGAATT Y 2 1 2 1 101000 r 74 goat snp17191-scaffold1794-287247 18 64093124 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431327 Affx-122937068 AX-123301668 18 58533559 CGGTGATGGTGCTGCTGCTGGTGGTCTGGAGATGA[C/T]GCACCAAGAACTACTTATTTAGAAACCCAGCCACC Y 2 1 2 1 101000 r 74 goat snp17192-scaffold1794-349474 18 64155819 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452554 Affx-122920527 AX-123322887 18 58580637 TAGCCTTTCTGTGATTCTGTTGTTTTAGTCTCATG[A/C]TTTGAAAGCTGTTTCTTCTCAGAAACAAAAAGACA M 2 1 2 1 103000 f 74 goat snp17193-scaffold1794-396552 18 64203145 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441019 Affx-122928948 AX-123311356 18 58615299 AGGCTGTCAAAACTTCAAATTTTAGATTTTGCTTC[A/G]GCTCCTCTCCCCAAGCTCCCCAGGTTCAAGTGTGA R 2 1 2 1 101000 r 74 goat snp17194-scaffold1794-431214 18 64234860 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396388 Affx-122963024 AX-123266743 18 58644339 TTAACCCAGAGCCCCAAACCGCAGGATCTGACGTT[A/G]CTGCCAGGTAGAGAGTGTCAGAATTGAGGTGGCTT R 2 1 2 1 201000 r 74 goat snp17195-scaffold1794-460254 18 64264306 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440890 Affx-122929228 AX-123311227 18 58688214 GAGCCATCGTTGGCTGCCTGAGCAGGGAACTGCCC[G/T]CATCCCTGCTCTGGTACAGTTTTCTCCGTGGGTCG K 2 1 2 1 202000 f 74 goat snp17196-scaffold1794-504129 18 64309040 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399267 Affx-122960558 AX-123269622 18 58710532 GCCAGTGGGAAGTCTCTGATGTTGAGCAAGATAGG[C/T]GCCATTACTGAAGGCCTTCCCACATTGAAAACATT Y 2 1 2 1 201000 f 74 goat snp18670-scaffold1886-453917 18 65317339 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453707 Affx-122919686 AX-123324040 18 58759954 ACTGGGAAGAAACCTCTTTTTAAATAGACCTTGTC[A/G]CTGAGTTTCCAATCACTCTTTAGAAACCCTGCAAT R 2 1 2 1 201000 r 74 goat snp18669-scaffold1886-404495 18 65268657 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802156 Affx-122921550 AX-385289060 18 58792601 AGGAGTGTTTGTCAGTCCACAAACACCACCAACTT[A/G]TACAAAATCCCGATTTGGTAGGAGAAACAGTAGAT R 2 1 2 1 101000 f 74 goat snp18668-scaffold1886-371848 18 65239659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450146 Affx-122922747 AX-123320481 18 58821195 GAAAAAACGTTTCAAGAAGGCAGATGCAAGAGGAC[A/G]TGTTCTAAGACAACTCAAGAGACAAGGGCGCTGGA R 2 1 2 1 101000 f 74 goat snp18667-scaffold1886-343254 18 65210923 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435479 Affx-122933445 AX-123305819 18 58864062 CCAAACGTGATCAGCTTATTGGAGAAAGGGAAAGC[A/G]CCCTGGATGGTGGACCCAGTGAAAAGACGCCGGGG R 2 1 2 1 101000 f 74 goat snp18666-scaffold1886-300387 18 65168625 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389001 Affx-122968650 AX-123259359 18 58903297 TGGAGGGGTGGGCAAGTCCTGGGTATCACGGCTCC[C/T]GCCCTTGAAGACACACAGACTTGAGTCTGAACCCT Y 2 1 2 1 101000 r 74 goat snp18665-scaffold1886-261152 18 65129439 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388902 Affx-122968851 AX-123259260 18 58955430 TGAGAATCCGCTGCGCAGCCTGATAACATCATGCC[A/G]CAGTGTAGACGAACAAGACATCCAACCCCGGGCTC R 2 1 2 1 201000 f 74 goat snp18664-scaffold1886-209019 18 65063484 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793371 Affx-122977118 AX-385280349 18 58984699 CACCTGAGCGACAGATGACTTATTGATGTTATTTA[G/T]AATTATTTTCTTACCAGGTGGCGATAATGGTAAAG K 2 1 2 1 201000 r 74 goat snp18663-scaffold1886-179750 18 65038336 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425615 Affx-122940909 AX-123295961 18 59015966 GTGTTTCTTTCCAACACAAGAGAGGTATAACTGAG[A/C]AAAATTGCACGTATGTAAGGTGTATGATTTGGTGT M 2 1 2 1 101000 f 74 goat snp18662-scaffold1886-148483 18 65008574 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390702 Affx-122967940 AX-123261059 18 59045288 TGAGCAAAAGGATGCTCCCTGACGCCACGCTCATC[A/G]TCTTCCTGAGGTCCAGCTTGTGGAAGACCGTGAGC R 2 1 2 1 101000 f 74 goat snp18661-scaffold1886-119161 18 64980463 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773063 Affx-122932343 AX-385260206 18 59076618 AATACAATTTGTCAAACAAAAAAGAATCCGTCAAG[C/T]TGTCCATCAGGCAAATTTCATCACAGTATTAAAAT Y 2 1 2 1 101000 f 74 goat snp18660-scaffold1886-87831 18 64948745 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411465 Affx-122951805 AX-123281815 18 59140968 GGAACCACGGCAGTGCTTATTGTTCCCATGATTGA[A/G]ACTTCAGTGTCGGTGCAGCTGACCACCGGCCAGGA R 2 1 2 1 101000 f 74 goat snp18659-scaffold1886-23481 18 64882286 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431023 Affx-122936666 AX-123301364 18 59171587 CAGGAAGTCAGAGACACTGGGGATTCTTCCCAGAG[C/T]ATGTCTCTGTCCCCATTCTTGTGCTGATCCAGACC Y 2 1 2 1 201000 r 74 goat snp16235-scaffold1707-506278 18 65364128 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429554 Affx-122937822 AX-123299896 18 59207364 GATACTTTAGTTTTCATTTATTGATTTTGGCCACA[A/C]CGAGAAGCATGAGGGATCTTAGTCCCCAGACCAGG M 2 1 2 1 103000 r 74 goat snp16234-scaffold1707-470501 18 65400302 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399384 Affx-122961327 AX-123269739 18 59262931 CATTCTGCTGCCTCCAGTCACCCCAGGTATGAGAT[A/G]CAACCCACTCAGAAACTTGGAGCAGCCTGACCTAC R 2 1 2 1 201000 r 74 goat snp16233-scaffold1707-414934 18 65456582 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394584 Affx-122964437 AX-123264939 18 59293417 GTGCCGAATGTGTAGTATATTTATTATATCAATAA[G/T]AGTCACGTGTGTGTATAATGCACATATGTATATAC K 2 1 2 1 101000 r 74 goat snp16232-scaffold1707-384448 18 65486894 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378536 Affx-122976622 AX-123248895 18 59407740 GTTGAATAAATGAGTGTCTGCCATTTTGCCAGTTC[A/C]GGATTAGAGCTTTCTGCCTGGCAAACCAATAGGAG M 2 1 2 1 101000 r 74 goat snp16230-scaffold1707-270125 18 65593668 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420149 Affx-122945589 AX-123290497 18 59489672 GCTCTGAATGCACGACAGCGTTCCCTTCAGCTGGG[C/T]GTAGGCTGGCATTAGGTGCCACAAGGTGAGATATC Y 2 1 2 1 101000 r 74 goat snp16228-scaffold1707-188193 18 65668465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377843 Affx-122977288 AX-123248202 18 59522202 ATTTTCACCCATTCGGTTTACTACAAAGCAGACAC[A/G]CCGTGTGAGTCCAGAGCTCAGAGAGCCCCCGCCTC R 2 1 2 1 101000 f 74 goat snp16227-scaffold1707-155663 18 65700985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430888 Affx-122936874 AX-123301229 18 59583380 CATGAAACACGCGTGAGATAAATGTAGGACAGATC[A/G]TAGAACATATTCTTTATCATTGTGATGAGGGTTAC R 2 1 2 1 101000 f 74 goat snp16226-scaffold1707-94485 18 65762671 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395762 Affx-122963679 AX-123266117 18 59614413 TTCTTTTCTTTCCTTTCCCCGAGTTTTATTGAGGT[A/G]TAATTATGAGATATTTTGATATATGTATATGTTGG R 2 1 2 1 103000 f 74 goat snp16225-scaffold1707-63452 18 65794263 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377215 Affx-122978175 AX-123247574 18 59655759 GTACATGTATTGGTTGGGGTTTTACTTTAACAGAT[G/T]TACAATGGAAAGGTATGCATGCGTGTGAGGAACTT K 2 1 2 1 101000 f 74 goat snp16224-scaffold1707-22106 18 65833504 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452868 Affx-122920708 AX-123323201 18 59692571 CCTGATTCACACCCAAGTGTCAAAGCCATGAGATC[C/T]CTAGTTTTGCCTGTTTATGTCTGTGTGTGTACATA Y 2 1 2 1 102000 f 74 goat snp17424-scaffold1804-14607 18 65875053 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781645 Affx-122974782 AX-385268729 18 59725078 CCTGTTTTTGCCTCCACTGATTTCCGTCCCAGTCT[G/T]TATGATAGCCTATCTTGTGCTTTGCTCTGGTTGTA K 2 1 2 1 101000 f 74 goat snp17425-scaffold1804-47114 18 65907712 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772487 Affx-122937690 AX-385259638 18 59772421 GTGGGAAACCATATCCAGTCATCAGTGCTTACATC[A/G]TCTCATAACTTTGTCAAAGATATAGATAATCTCTT R 2 1 2 1 101000 f 74 goat snp17426-scaffold1804-94457 18 65956025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776163 Affx-122974143 AX-385263291 18 59808160 TCATATTTATCTGATACATTTACACTGTAGTATGA[G/T]TGCCATCGTAGCATCAGTTAGCCTCTGTTATGCCA K 2 1 2 1 101000 r 74 goat snp17427-scaffold1804-130196 18 65991853 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430311 Affx-122938236 AX-123300652 18 59956113 CAAGAACCAGGAAGGTTAGCCTGGAGTTTGAGGAG[C/T]GGATAAAATGGAGGCTGGAAAAATCTGTCAAGACT Y 2 1 2 1 201000 r 74 goat snp17430-scaffold1804-278149 18 66141152 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766559 Affx-986698047 AX-385253918 18 59977059 CACACTTATTATGGGATGGGGCCCCCTCCCTTTTC[A/G]GCCATCAAGGAGGCTTCCTGCCCTTGTACAGAGAA R 2 1 2 1 600010 r 74 goat 18_59977059 18 59977059 Ancestral_priority_1043 ancestry 0.506 neutral IMAGE 10K 10K ancestral 38444605 Affx-122926950 AX-123314942 18 60023664 GAGTTATGGGCACCGCTGAGTAGCACAGCTGAGAA[C/T]GGTGGCCCAAGTGACGGAGATCTCATCACTGCTCT Y 2 1 2 1 201000 r 74 goat snp17431-scaffold1804-345700 18 66210792 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377085 Affx-122978274 AX-123247444 18 60052242 AAGGGGTTTTATTGCTAGCTCGAGCTAGGGCTCCC[A/G]TCTCATCCAGCACAGTGGAGTCTTGACGAGAGCCC R 2 1 2 1 103000 f 74 goat snp17432-scaffold1804-374278 18 66247185 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765670 Affx-122940412 AX-385253136 18 60088216 TTCCATGTGTTGATTTCCAACCACATATCATTCTT[A/G]ACATTTCTGTTCATATAACTTGTTCTAATTAGTGA R 2 1 2 1 101000 f 74 goat snp17433-scaffold1804-410252 18 66283753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767718 Affx-122957128 AX-385254952 18 60127871 TATCCTCATAGTGTTGCCTGGACAAAGTATTACTA[C/T]GCATGTACCAAACCTGAGGATTTAAAATATTTTTC Y 2 1 2 1 101000 f 74 goat snp17434-scaffold1804-449907 18 66321625 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426073 Affx-122941086 AX-123296419 18 60187729 TATGGTTTTCCTGGGTAAGGAACGCCCAGTGTTAC[A/G]TGTTCTCCCCTTCCCCCTTTTCCCCTAGAAGTTGT R 2 1 2 1 101000 f 74 goat snp17435-scaffold1804-509765 NW_017212008.1 19831 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424102 Affx-122942030 AX-123294448 18 60232869 CAGGGAAACTAAGATCCCACAGCCACATGGCACAG[G/T]GAAGGGGGAAAAAGTCCTGAGGAAAAAAGGCAATT K 2 1 2 1 303000 r 74 goat snp17436-scaffold1804-554905 18 66427684 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395190 Affx-122964510 AX-123265545 18 60276629 GCACCGCGAGGAGCGCTGGGAAATCACGTGTCGGG[A/G]GCCTCCGTCCTCATTAAAGAGATGGGGAGTCGATG R 2 1 2 1 101000 r 74 goat snp17437-scaffold1804-598665 18 66471647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385087 Affx-122971802 AX-123255445 18 60307085 TGGATGGAGCTAAGAAGTTTACTGTGCTGGCAAGA[C/T]GCTGAAATGTGTGGGGCCGTAGCCCATCTGTTGTC Y 2 1 2 1 201000 f 74 goat snp17438-scaffold1804-629121 18 66502472 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789487 Affx-122967720 AX-385276497 18 60366510 TGGGATTACTAATAATGTTGCCATTTTCTCCATTC[A/G]TTTATTCACTAAATGTCCAGTAGAATTGGTCCATG R 2 1 2 1 202000 f 74 goat snp17439-scaffold1804-688546 18 66561978 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800508 Affx-122967955 AX-385287428 18 60430648 GATCAACCGTTCATTAGTGTATAAGCTAGGCTACC[A/G]TGGACCAATCATATTGCTGCTTCATTACTGACATA R 2 1 2 1 101000 f 74 goat snp17440-scaffold1804-752684 18 66626134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427655 Affx-122939325 AX-123297998 18 60482071 ATTGTGTCCTATCCACTGAGAAACACTTTCATCCG[C/T]ATATTATCTCTTATTCCACTTCCTAGCATAAACTC Y 2 1 2 1 201000 r 74 goat snp17441-scaffold1804-804107 18 66677348 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399961 Affx-122960835 AX-123270316 18 60513604 AGAACATACCCCTAATGCAACTGGCTACCTGAAAT[C/T]GATGACATCATTCTGTATGTGTGATTATTTTTTTC Y 2 1 2 1 201000 r 74 goat snp17442-scaffold1804-835640 18 66709000 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800389 Affx-122950596 AX-385287311 18 60545571 GCACAAAAAGACAATAAAAGCTTAAGCCCATAGTC[A/G]TAATTTTTTGACAGAAACTTAAGTATCTTTCCTGC R 2 1 2 1 101000 f 74 goat snp17443-scaffold1804-867607 18 66741350 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434897 Affx-122934333 AX-123305237 18 60606668 TTTTGTGACTTTTTAATTTATGGAGTATTTTAATA[A/G]TGGAACAATGTGTTCTATTTTTTTCAGTTTTTTTT R 2 1 2 1 303000 f 74 goat snp17444-scaffold1804-928704 18 66803125 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384802 Affx-122971995 AX-123255160 18 60640232 TTTTTAGCCCATGGGCATAATTCTGGGATGCCCTT[C/T]ATATTCCAGTGATCTCAGAAAGGTACATCCTCATG Y 2 1 2 1 101000 r 74 goat snp17445-scaffold1804-962268 18 66837325 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804010 Affx-986696339 AX-385290699 18 60650315 GCTGCCCTCTGATTTTTTGGAGCCATCCTCCCCGA[C/T]GTCACAGGACTTTATGACTCTTCTCAGGTTGGGCC Y 2 1 2 1 600010 r 74 goat 18_60650315 18 60650315 Ancestral_priority_1043 ancestry 0.568 neutral IMAGE 10K 10K ancestral 320769691 Affx-122952120 AX-385256861 18 60675742 TATAGGCCATATTCTGAAAAACACAGAAAATTTAT[A/C]GTGACTATAATTATTCAGTGATTATAAGAATTATC M 2 1 2 1 101000 f 74 goat snp17446-scaffold1804-997778 18 66873855 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794632 Affx-122957500 AX-385281593 18 60708541 CTGTCTCTTTGGTGCAGGGGCCAACAGAAAACGAG[A/C]TTTGGAGGCCAGACCAACCCAACCCCTTAAATTCT M 2 1 2 1 101000 f 74 goat snp17447-scaffold1804-1030577 18 66906659 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272877 Affx-1111833124 AX-519546566 18 60731273 GAATGGGAGAAAATATTAGCAAATGAAGCAACTGA[A/C]AAACAACCAATCTCAAAAATATACAAGCAATTCCT M 2 1 2 1 303000 f 74 goat 18_60731273_AF-PAKI 18 60731273 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320797521 Affx-122959293 AX-385284460 18 60746513 GACACATTAGAATAGAAAGTATAAAACAGGACATC[A/G]CCAATAACAATAAATGACTCTGATGGGTAAGATAA R 2 1 2 1 101000 r 74 goat snp17448-scaffold1804-1068549 18 66945528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386370 Affx-122970850 AX-123256728 18 60783479 ATCACCAACTCCTAGAGCTTACTCAAACTCATGTT[C/T]ATCGAGGCGGGAATAAGCCTCCAGAAATCCTGAGG Y 2 1 2 1 201000 r 74 goat snp17449-scaffold1804-1105515 18 66982534 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767310 Affx-122935561 AX-385254591 18 60813747 CAGAGAACAGCAAAGATGGTAAGAACTATGGAAAC[A/G]TTAATCATAGCTTGTCTCTTAATGAACACAAGCCA R 2 1 2 1 201000 f 74 goat snp17450-scaffold1804-1135783 18 67011455 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771567 Affx-122923802 AX-385258725 18 60851101 GGACTCTGGTTCTCCTTTCTCGGTTGAGTTTTCCT[A/G]TGTTAGCTTCATTCTTAAGTAGCTTCTTAAGCTAC R 2 1 2 1 101000 f 74 goat snp17451-scaffold1804-1173137 18 67049619 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387229 Affx-122970580 AX-123257587 18 60891845 AAACAGTGGTTCTCTGGGATGGATCCCCCATCAGC[C/T]CTTAGGGAACACTAGGCAATGTCTGGGCACATGTT Y 2 1 2 1 201000 r 74 goat snp17452-scaffold1804-1213881 18 67089921 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407987 Affx-122954326 AX-123278338 18 60989742 AAAGAGACGTGACTGAGTGACTTTCACTTAACTGT[A/G]GATAGGCTGGATTCATTTTGTGTCAGCAGTGACAG R 2 1 2 1 201000 r 74 goat snp17453-scaffold1804-1311778 18 67182216 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766563 Affx-986698049 AX-385253922 18 61304234 ACTCCAAGGTCTCTTTTGTTGTCCTTCCAAATGAA[C/G]CGGAAACCTTCTTCATTACAACTCAAAATAACAGA S 4 1 2 1 600010 r 74 goat 18_61304234 18 61304234 Ancestral_priority_1043 ancestry 0.672 recommended IMAGE 10K 10K ancestral 350603685 Affx-1002479626 AX-413837820 18 63021986 AGGTTCCAGGAAGGGGCTGCTGACAAGATTAGGGT[A/G]TGTGCAGGGTCTCATGCTGTTGGCCCCTAATCTTA R 2 1 2 1 202000 r 74 goat 18_63021986_RH-map 18 63021986 A G 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603686 Affx-1002479627 AX-413837821 18 63043884 TCCCATCACAGAAAAGGAAAGAGCTCAGGGAGTGT[C/T]CAGTTAGCCTAGTTCTGCAGAACACCGCTGCAGAA Y 2 1 2 1 201000 r 74 goat 18_63043884_RH-map 18 63043884 T C 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603687 Affx-1002479628 AX-413837822 18 63143082 CAGTTTGGTCAGAAGCTCATCCGCAAGCAGCCGCC[A/G]AAACCCATAGATGAGTCTAAGAGACCCGTGGCTCT R 2 1 2 1 101000 r 74 goat 18_63143082_RH-map 18 63143082 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350603651 Affx-1002479629 AX-413837789 18 63204849 CCATCTTACTCTCTCCATACATCTCACCCTCTCCT[C/T]CCCTCTCCCCATGTCCATAAGTCTATTCTCTATGT Y 2 1 2 1 103000 f 74 goat 18_63204849_RH-map 18 63204849 C T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601343 Affx-1002478906 AX-413835773 18 63221934 AGCTTCTAGATCTGGGTGGCCAGAGGGTTTGCTAG[A/G]TGGAAGAATTACATTTACTGCAGCCCACGGCCACC R 2 1 2 1 201000 r 74 goat 18_63221934_RH-map 18 63221934 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601279 Affx-1002478907 AX-413835712 18 63299806 ACAAAAAGAAAGGCCATTTTGCCATTTGCAACAAC[A/G]TGAAAGCATTGGAGGGTATTATGCTAAGTGAAATA R 2 1 2 1 103000 f 74 goat 18_63299806_RH-map 18 63299806 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468272879 Affx-1111833125 AX-519546569 18 63323042 CGGAAGTTTAAAATCCTGCTTGGTTTATTCGCTAA[A/G]TCATGTTGGGCTCTTTGCGACCCCCTTGTACTGTA R 2 1 2 1 101000 f 74 goat 18_63323042_AF-PAKI 18 63323042 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 350601280 Affx-1002478908 AX-413835713 18 63353437 CTTAAATAAATCAGCATCAGATATCTCCTAAGGAC[A/G]AATATATTTCCTTTCCTAAGCATAGCTGCTGCTGT R 2 1 2 1 101000 f 74 goat 18_63353437_RH-map 18 63353437 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601281 Affx-1002478909 AX-311283995 18 63418802 GAGCGATTTCACTTTCACTTTTCACTTTCATGCAC[C/T]GGAGAAGGAAATGGCAACCCACTCCAGTGTTCTTG Y 2 1 2 1 103000 f 74 goat 18_63418802_RH-map 18 63418802 C T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320804012 Affx-986696340 AX-385290701 18 63494312 AAGTTCCACAGCCCTTTCTATTTATGGCCTCAGGT[C/T]TGTTTAATCTGGAAAACGCCCCCTTTAAAGCCAGA Y 2 1 2 1 600010 r 74 goat 18_63494312 18 63494312 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 350601282 Affx-1002478910 AX-413835714 18 63525967 CTCCCCAAGCAAGTTTTATGTCACAGTTAAAACAT[C/G]TGTGACAGAGAAACTGAAATGGGGACCTCAGTGCA S 4 1 2 1 101000 f 74 goat 18_63525967_RH-map 18 63525967 C G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601283 Affx-1002478911 AX-413835715 18 63601587 AGTTCTGTCCATGTTGTTCCTACCTTTTAAAGGCC[A/G]CATCATATTCCATTGGGCTTTTACACTGTATTTTG R 2 1 2 1 101000 f 74 goat 18_63601587_RH-map 18 63601587 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601356 Affx-1002478912 AX-413835783 18 63688665 TGTTCATTAAACAGTTGTTGAACAAAGGAAAAGAA[A/G]GAGCAAATGAAGAATGCTCTGGGCTCCGCAGAGCT R 2 1 2 1 202000 r 74 goat 18_63688665_RH-map 18 63688665 G A 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601462 Affx-1002479658 AX-413835879 18 63709313 GTGTGTGTGTGTGTGTGTGTGTGTGTTGTGAGAGG[G/T]GGGGGCTGACCTCCTGGAGGCAGAGGACGGGCCCC K 2 1 2 1 400000 r 74 goat 18_63709313_RH-map 18 63709313 T G Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601330 Affx-1002479659 AX-413835760 18 63735422 GAAGGTGTTGGGAGATGTGTCAGAGACACTCCTGG[C/T]AGCCCGTGGTCCTGGGACTGGGATTCCTGAACCCC Y 2 1 2 1 101000 f 74 goat 18_63735422_RH-map 18 63735422 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601331 Affx-1002479660 AX-413835761 18 63801319 CCAGGTCTTCTGGGATGTGATGGAAAGTTCTGGAA[C/T]TAACTAGAGGGGGTGTTTGCACGACATCATGAGTG Y 2 1 2 1 202000 f 74 goat 18_63801319_RH-map 18 63801319 C T 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601333 Affx-1002479661 AX-413835763 18 63821982 TGGGTGTGCCAGGACGGGTTGCTGAGGGCAGTCCA[C/G]AGGCTTCCTAGAAGAAGGGGACTTTAGAGCGAGGT S 4 1 2 1 202000 f 74 goat 18_63821982_RH-map 18 63821982 C G 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601334 Affx-1002479662 AX-413835764 18 63869331 CTGATGATTGGGTGGGTGGGTGGATGAATGGATGG[A/G]TAGATGAGTGATGGATGGATGGATGGATGAATTGG R 2 1 2 1 303000 f 74 goat 18_63869331_RH-map 18 63869331 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601336 Affx-1002479663 AX-413835766 18 63927615 TGTCCGGATCTGCTAAGCCACCCCAACCAGCCCCC[A/G]TCCCTCCCCCACCCCACCCCGCAGAGAGATTGATC R 2 1 2 1 303000 f 74 goat 18_63927615_RH-map 18 63927615 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601338 Affx-1002479664 AX-413835768 18 63973319 GACCGCCTGGTTTCTGAAGTCCCTGGAGTCCATAC[C/T]CCACTCGCCCCCCAGCCCAAGTCAGCTTTGGGAGG Y 2 1 2 1 400000 f 74 goat 18_63973319_RH-map 18 63973319 T C Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601340 Affx-1002479665 AX-413835770 18 64012491 GAGACAAGGGTTTGATCCCTGGGTTGAGAAGATCC[A/C]CTGGAGGAGGGCACAGCAACCCACTCCAGTATTCT M 2 1 2 1 103000 f 74 goat 18_64012491_RH-map 18 64012491 A C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601342 Affx-1002479666 AX-192098959 18 64124776 AGACCAGTCCTGGGTATTCATTGGAAGGACTGATG[G/T]TGAAGCTGAAACTCCAAATACTTTGGCCACCTGAT K 2 1 2 1 303000 f 74 goat 18_64124776_RH-map 18 64124776 G T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601344 Affx-1002479667 AX-413835772 18 64176089 CATTAACAAATTGAAAGATAAAACTGTTTGACTAT[C/T]TCAATAGATGCAGAGAAAGCCTTTGACAAAATTCA Y 2 1 2 1 303000 f 74 goat 18_64176089_RH-map 18 64176089 C T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468277205 Affx-1111835794 AX-519550711 18 64386555 GCTGAGACTTGATGCAGCTAAGAATAAATTAACAC[A/G]TATTTTCATAAAAAGAACAGGGTTCCATGGTTCTC R 2 1 2 1 101000 f 74 goat Random2.2K-1767 18 64386555 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 539476338 Affx-1251763847 AX-586011755 18 64440590 AATAGAAATATGAATACAATGCTAGATTTCTAATT[-/TTTAAAAAGATATGCTGGGAGAGGGAAAGATGGAGGAGGAAATAAATAAAATATCAGTATCAAAAAAAAATAAAATAAAA]TAAAAAGATATGCTGCTGCTGCTGCTAAGTCACTT - 8 1 4 1 20000 f 74 goat SV_301 18 64440590 - deletion junction SV-TF-chip 539476593 Affx-1251763847 AX-586011979 18 64440590 AATAGAAATATGAATACAATGCTAGATTTCTAATT[-/TTTAAAAAGATATGCTGGGAGAGGGAAAGATGGAGGAGGAAATAAATAAAATATCAGTATCAAAAAAAAATAAAATAAAA]TAAAAAGATATGCTGCTGCTGCTGCTAAGTCACTT - 8 1 4 1 20000 r 74 goat SV_301 18 64440590 - deletion junction SV-TF-chip 562165263 Affx-1251763847 AX-606940675 18 64440590 AATAGAAATATGAATACAATGCTAGATTTCTAATT[-/TTTAAAAAGATATGCTGGGAGAGGGAAAGATGGAGGAGGAAATAAATAAAATATCAGTATCAAAAAAAAATAAAATAAAA]TAAAAAGATATGCTGCTGCTGCTGCTAAGTCACTT - 8 1 4 1 20100 r 74 goat SV_301 18 64440590 - deletion junction SV-TF-chip 562165667 Affx-1251763847 AX-606941076 18 64440590 AATAGAAATATGAATACAATGCTAGATTTCTAATT[-/TTTAAAAAGATATGCTGGGAGAGGGAAAGATGGAGGAGGAAATAAATAAAATATCAGTATCAAAAAAAAATAAAATAAAA]TAAAAAGATATGCTGCTGCTGCTGCTAAGTCACTT - 8 1 4 1 20100 f 74 goat SV_301 18 64440590 - deletion junction SV-TF-chip 562165848 Affx-1251763847 AX-606941257 18 64440590 AATAGAAATATGAATACAATGCTAGATTTCTAATT[-/TTTAAAAAGATATGCTGGGAGAGGGAAAGATGGAGGAGGAAATAAATAAAATATCAGTATCAAAAAAAAATAAAATAAAA]TAAAAAGATATGCTGCTGCTGCTGCTAAGTCACTT - 8 1 4 1 20100 r 74 goat SV_301 18 64440590 - deletion junction SV-TF-chip 562165928 Affx-1251763847 AX-606941338 18 64440590 AATAGAAATATGAATACAATGCTAGATTTCTAATT[-/TTTAAAAAGATATGCTGGGAGAGGGAAAGATGGAGGAGGAAATAAATAAAATATCAGTATCAAAAAAAAATAAAATAAAA]TAAAAAGATATGCTGCTGCTGCTGCTAAGTCACTT - 8 1 4 1 20100 r 74 goat SV_301 18 64440590 - deletion junction SV-TF-chip 562166458 Affx-1251763847 AX-606941866 18 64440590 AATAGAAATATGAATACAATGCTAGATTTCTAATT[-/TTTAAAAAGATATGCTGGGAGAGGGAAAGATGGAGGAGGAAATAAATAAAATATCAGTATCAAAAAAAAATAAAATAAAA]TAAAAAGATATGCTGCTGCTGCTGCTAAGTCACTT - 8 1 4 1 20100 r 74 goat SV_301 18 64440590 - deletion junction SV-TF-chip 562166572 Affx-1251763847 AX-606941980 18 64440590 AATAGAAATATGAATACAATGCTAGATTTCTAATT[-/TTTAAAAAGATATGCTGGGAGAGGGAAAGATGGAGGAGGAAATAAATAAAATATCAGTATCAAAAAAAAATAAAATAAAA]TAAAAAGATATGCTGCTGCTGCTGCTAAGTCACTT - 8 1 4 1 20100 r 74 goat SV_301 18 64440590 - deletion junction SV-TF-chip 350601346 Affx-1002479668 AX-413835775 18 64492412 TTTCCAATTTGGATTCCTTTTATTTCCTTTTCTGC[C/T]CTGGTTGCTGTGGCCAAAACTTCCAGAACTATGTT Y 2 1 2 1 303000 f 74 goat 18_64492412_RH-map 18 64492412 T C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468277207 Affx-1111835795 AX-519550713 18 64510598 AGCTTGGAAGTCTCTACTTGACATATTTTGTGTTC[A/C]TCTGAGTATCTAGGAAGCAAGGTGGTCTACTTGTT M 2 1 2 1 201000 f 74 goat Random2.2K-1768 18 64510598 T G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 350601348 Affx-1002479669 AX-413835776 18 64570004 CGTTCGAACTATGGCAAACCACAGTCAAATTCAGA[C/G]AACAAATGAGAGGAATATTACTTAACAGAGAAAAA S 4 1 2 1 101000 f 74 goat 18_64570004_RH-map 18 64570004 G C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320763528 Affx-986698057 AX-385251389 18 64580545 ATGTTACATTCCCTGGAGGTGTCAAGTGCATTAAA[A/G]ATACCTTATCCCATGGGTTCTCTGCCCCTTTCCCC R 2 1 2 1 600010 f 74 goat 18_64580545 18 64580545 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 350601350 Affx-1002479670 AX-413835778 18 64606017 AGGGCTCCCTTCTCTCCACAGCCTCTCCAGCATTT[A/C]TTGTTTACAGACTTTTTGACGATGGCCATTCTGGC M 2 1 2 1 303000 f 74 goat 18_64606017_RH-map 18 64606017 A C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601351 Affx-1002479671 AX-413835779 18 64719681 TGGGGGAGAAGGTGCCCTGACTCCTCAGGTTTGAT[C/T]CCTTCCCAGAGGTTCTCCCCAAACCCTCCATCCAG Y 2 1 2 1 102000 f 74 goat 18_64719681_RH-map 18 64719681 C T 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601353 Affx-1002479672 AX-413835781 18 64911433 AGACCCCTTTACATTTCCTTTATACCCTTCAAAAA[C/T]ATCTCCCAAAAAGAAAAGAAAAAAAAAGATATAAA Y 2 1 2 1 101000 f 74 goat 18_64911433_RH-map 18 64911433 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601355 Affx-1002479673 AX-186527206 18 64928552 CAGTGCTCAGCCTTCTTTATGGTCCAACTCTCACA[C/T]CCATACATGACTACTGGAAAAACATAGCTTTGACT Y 2 1 2 1 103000 f 74 goat 18_64928552_RH-map 18 64928552 T C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 463565205 Affx-1110048647 AX-515047143 18 65139482 GCGCAGCCAAAAATAAAACAAGCTGCAGTGGAAAA[A/C]AAACAGTGGAGGGAAGTGTTGGTGTGGGCCCTGGC M 2 1 2 1 202000 f 74 goat GoatD01.054936 18 65139482 C A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 350601357 Affx-1002479674 AX-413835784 18 65290743 AAGAATACTGGAGTGGGTAGCCATTCCCTTCTCCC[A/G]GAGATCTTCCCAACCCGGGGATCGAACCCAGGTCT R 2 1 2 1 103000 f 74 goat 18_65290743_RH-map 18 65290743 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601494 Affx-1002479675 AX-413835909 18 65511096 CACTAAATCCCCCAGATGAAACAGAAACTCTCACA[C/T]TGTGCATTTTCACCTCAGTGAACACCTTCTATGGA Y 2 1 2 1 101000 r 74 goat 18_65511096_RH-map 18 65511096 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601361 Affx-1002479676 AX-185365509 18 65608875 AGAGTCTTCTCCAACACCACAGTTCAAAAACATCA[A/G]TTCTTTGGTGCTCAGCCTCCTTAATGAGCAATTCA R 2 1 2 1 103000 f 74 goat 18_65608875_RH-map 18 65608875 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601498 Affx-1002479677 AX-413835913 18 65730727 TTTCAGTTGGAGTTTCAATATCAAATTCTCAAAGA[G/T]TAATAGAATGAATATGCGTGGAAGTAGAAGGATAT K 2 1 2 1 101000 r 74 goat 18_65730727_RH-map 18 65730727 T G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601366 Affx-1002479678 AX-413835790 18 65778835 TATCCCATTGCACTCATCATTTCAGTACTTTTCTC[C/T]ACAGCAGAAACTAACACGATGTTATAAAGCCAATA Y 2 1 2 1 101000 f 74 goat 18_65778835_RH-map 18 65778835 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468272881 Affx-1111833126 AX-519546571 18 65849556 ATTTCTAATTTTAAAAACATAGATACACAGCAAGC[A/G]ACAGAGGTTTACTGTATACCACAGGGAACGATAGT R 2 1 2 1 201000 f 74 goat 18_65849556_AF-PAKI 18 65849556 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 350601502 Affx-1002479679 AX-413835917 18 65935852 CGTCATCTACAGTCAATAACCCGGGAGTCCTGCCC[G/T]GTCTAAGTCAGACTTGCCTGAAGTCAAATTCCTAT K 2 1 2 1 101000 r 74 goat 18_65935852_RH-map 18 65935852 G T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 539476339 Affx-1251763848 AX-185269453 18 66235306 CTCCCGGAGTTCACTCAAACTCATGTCCATTGAGT[-/TGGTGATTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]GGTGATGCCATCCAGCCATCTCATCCTCTGTCATC - 4 1 4 1 20000 f 74 goat SV_305 18 66235306 - deletion junction SV-TF-chip 539476594 Affx-1251763848 AX-586011980 18 66235306 CTCCCGGAGTTCACTCAAACTCATGTCCATTGAGT[-/TGGTGATTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]GGTGATGCCATCCAGCCATCTCATCCTCTGTCATC - 8 1 4 1 20000 r 74 goat SV_305 18 66235306 - deletion junction SV-TF-chip 562165070 Affx-1251763848 AX-606940482 18 66235306 CTCCCGGAGTTCACTCAAACTCATGTCCATTGAGT[-/TGGTGATTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]GGTGATGCCATCCAGCCATCTCATCCTCTGTCATC - 8 1 4 1 20100 f 74 goat SV_305 18 66235306 - deletion junction SV-TF-chip 562165230 Affx-1251763848 AX-606940642 18 66235306 CTCCCGGAGTTCACTCAAACTCATGTCCATTGAGT[-/TGGTGATTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]GGTGATGCCATCCAGCCATCTCATCCTCTGTCATC - 8 1 4 1 20100 r 74 goat SV_305 18 66235306 - deletion junction SV-TF-chip 562165595 Affx-1251763848 AX-606941006 18 66235306 CTCCCGGAGTTCACTCAAACTCATGTCCATTGAGT[-/TGGTGATTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]GGTGATGCCATCCAGCCATCTCATCCTCTGTCATC - 8 1 4 1 20100 r 74 goat SV_305 18 66235306 - deletion junction SV-TF-chip 562165980 Affx-1251763848 AX-606941389 18 66235306 CTCCCGGAGTTCACTCAAACTCATGTCCATTGAGT[-/TGGTGATTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]GGTGATGCCATCCAGCCATCTCATCCTCTGTCATC - 8 1 4 1 20100 f 74 goat SV_305 18 66235306 - deletion junction SV-TF-chip 38411733 Affx-122951518 AX-123282083 19 50878 TCTGGAGTTTCCACAAGGGAGTCAGGCCTCGTCTC[A/G]TGTGGAGACATGCAAGTCCATTCTCCTCTCGAGCT R 2 1 2 1 303000 f 74 goat snp16336-scaffold1721-50878 19 56308 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277334 Affx-1111835797 AX-519550838 19 68709 GAGGACAATCTCCTGGTTTTTCATGAGGTGCAGCA[A/G]CATATTAAGGTTTCTTTCGAGTATAGAGGGTACCT R 2 1 2 1 101000 r 74 goat Random2.2K-1770 19 68709 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320766530 Affx-986698030 AX-385253890 19 101321 GCAGCAATATCATTGACTCAAGAGGTGCATACTGC[A/C]CAATGTGTTGATACTATGTCTAAAAATGTCTCTCT M 2 1 2 1 600010 r 74 goat 19_101321 19 101321 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 38407402 Affx-122955247 AX-123277753 19 113494 TGCAACATCGAGGCCCTCCTCCACACTTGCACATC[A/G]CAGGCCTTTTCTGAGATGCCCAGGGACCCTCCCTC R 2 1 2 1 102000 f 74 goat snp16337-scaffold1721-113494 19 119463 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804016 Affx-986696342 AX-385290703 19 164703 AGATTAATTCAAGTATATTGATATATATGTATTAT[A/T]TGTCAATAAGTTTATACTTGTTGTCATATATAAAT W 4 1 2 1 600010 r 74 goat 19_164703 19 164703 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 38435279 Affx-122934046 AX-123305619 19 229096 ATATTCGCTGGCAGTGACTCAAGAAGAATCCCGGC[A/G]TGCCCTTCGCAACTCGAAAAGAGACCTGACTTCCC R 2 1 2 1 201000 r 74 goat snp16339-scaffold1721-229096 19 235152 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432766 Affx-122935436 AX-123303107 19 271080 ATGTTTCAGCTGGCCGCAAGTTGGCACTGTGCTGG[A/C]GGTAGTTGCTTGAGTACAATGATGGTGAGGAGATG M 2 1 2 1 101000 r 74 goat snp16340-scaffold1721-271080 19 277879 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780229 Affx-122974612 AX-180660637 19 317358 AACAATTGCAACCCTTTTATGACTCAGATTTAGGT[A/C]GGTTGACATCTCAAGGGTTCAGCTGACCTAGATAT M 2 1 2 1 101000 r 74 goat snp16341-scaffold1721-317358 19 324186 A C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394140 Affx-122965320 AX-123264495 19 381600 TGCCATGATCTTAGTTTTTTGAATGTTGAGCAAAA[C/T]TCAACATTTTTTAAAGCAAGCCTGCTTTTAACATT Y 2 1 2 1 103000 r 74 goat snp16342-scaffold1721-381600 19 388746 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786447 Affx-122976691 AX-385273481 19 412478 GACAATTGGTGTAAGGCAGTGTTTCCTTATCTTAG[C/T]ACTATTAACTTTAGTTAACTTAGTACTATTAATTT Y 2 1 2 1 102000 f 74 goat snp16343-scaffold1721-412478 19 420010 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798266 Affx-122949445 AX-385285201 19 472289 TGGATGAGAAGAATGATTCAAACTGTAAAAAAGCA[C/T]GGCTTGTATCCTTGAGTTCTTACTGTAATAGTTAG Y 2 1 2 1 101000 r 74 goat snp16344-scaffold1721-472289 19 479878 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432124 Affx-122936445 AX-123302465 19 511250 GGAGAGACAGGATACAAAATTCACTTTGCACTCTT[A/G]TGCTTTTTGGTATTGTTTTAAATTTATAAGTAAAA R 2 1 2 1 101000 f 74 goat snp16345-scaffold1721-511250 19 518727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377641 Affx-122977868 AX-123248000 19 540694 AGAGCAAGGCAATAAAAATTTTAGACTTTGTGGGT[C/T]ATAGGTTTTCTGCTGCAACTGCCCTAATCTGTCAG Y 2 1 2 1 101000 r 74 goat snp16346-scaffold1721-540694 19 548914 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443819 Affx-122927070 AX-123314156 19 593759 TCACATAATAGAATAAAGCAATGAAAAAGAGTGAG[A/C]TACCGTTTCACAAAACAGCATCAGAAAATCTTAAC M 2 1 2 1 201000 r 74 goat snp16347-scaffold1721-593759 19 601956 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410314 Affx-122952485 AX-123280664 19 698261 GCTTAGACACAGCTTGCTCCAAAGAACCCTCTACC[A/G]CCTTTCAGAAAATTTTCTCTAACTAAAGTGAAAGT R 2 1 2 1 201000 r 74 goat snp16349-scaffold1721-698261 19 706999 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377468 Affx-122977512 AX-123247827 19 732422 ATTTTGCTTGAGCAGGTGTAGAGAAATAGCAATTA[C/T]CCAAGATGGCCTGGTCAGGCTCTCTTATCACATGT Y 2 1 2 1 101000 f 74 goat snp16350-scaffold1721-732422 19 741163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782021 Affx-122929340 AX-385269100 19 783801 ACAGCATTAATTGTGATGCTGCAAATACATTGTTT[C/T]GAATGACAATGATATTGGGTCATTTAAAAACCTGC Y 2 1 2 1 101000 f 74 goat snp16351-scaffold1721-783801 19 793405 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775880 Affx-122964600 AX-385263011 19 822137 CTGAAAACGTTTGATCTCAGCCAAAAGAACAGACT[A/G]TAGGTAGTTGCTGTCACTTCAGCTTGGGTCATAGA R 2 1 2 1 101000 r 74 goat snp16352-scaffold1721-822137 19 830841 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771869 Affx-122959105 AX-385259025 19 844467 ATATGTACTGGGACTCAAGGCAAAGCAGTGATGCC[A/G]TAGGAAACTGTGCCAGATCTACCTGTGGTCTTGGT R 2 1 2 1 101000 f 74 goat snp1354-scaffold1038-4862 19 853209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776059 Affx-122919734 AX-385263189 19 881555 CCAGGGAAATTTGCTAGAATTAGTGACTCTAGAAA[C/T]TTAACTATTCTAAATTCTGAAAAATTTACCAACAT Y 2 1 2 1 201000 r 74 goat snp1355-scaffold1038-41950 19 890512 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773540 Affx-122978139 AX-385260681 19 953779 CCAATAGGAGTGAGGCGACTCTCCCATCTTATTCA[C/T]GGTGTCATTATCCAGCCTGCACCTTGAAGTCATAT Y 2 1 2 1 101000 r 74 goat snp1356-scaffold1038-114174 19 961240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384746 Affx-122972038 AX-123255104 19 995915 CACAACAGTCTGCAGGTTCCAGCACTGGAAATCCT[C/T]AGGCCAAACAACCAGCAAGGTAACACAATCCCATA Y 2 1 2 1 101000 r 74 goat snp1357-scaffold1038-156310 19 1003743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272935 Affx-1111833129 AX-519546621 19 1036553 AACATGGTGATGCTGAAACCCACCAAAAGAGATAC[A/G]TCATATCTGAAGACAAATAAGAAGCTGCAGCAAGA R 2 1 2 1 201000 r 74 goat 19_1036553_AF-PAKI 19 1036553 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320776976 Affx-122958571 AX-385264100 19 1098952 ACCTCTTATCAGACACTTTGTTATCTCAATACTTT[A/G]CTCTTAACATCATTGTAACCCTGAACTTTTTAACT R 2 1 2 1 101000 r 74 goat snp1359-scaffold1038-259347 19 1107366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782316 Affx-122924112 AX-385269393 19 1131644 AATTGAGACATTCTTCACTGTGTATCTTACTCATT[C/T]CTATTCATCTTCTTTTGATGATATACTTCCCTCTA Y 2 1 2 1 101000 f 74 goat snp1360-scaffold1038-292039 19 1139515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449392 Affx-122922709 AX-123319727 19 1167476 TTATGAAAAGATTTAAATAATATGAAAGTTATTTA[A/C]TTCTACCTGGACAAGAATGAAAGCAATGAGAACAG M 2 1 2 1 303000 f 74 goat snp1361-scaffold1038-327871 19 1175334 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766098 Affx-122960839 AX-385253513 19 1233866 GACCTTGTAGAGTCAGAAATGAACAGCACAGACAT[G/T]TTCTTGCCCTTATTGAACATAGAGTTTCCTTGGAA K 2 1 2 1 101000 f 74 goat snp1362-scaffold1038-394261 19 1242451 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774064 Affx-122972090 AX-385261202 19 1307850 ATTTCATGATTACACATTATTAGATTCTTCTCAGA[A/G]CAAGTTCTCTTCACCATAGGTAACACTCAGTGGAC R 2 1 2 1 101000 r 74 goat snp1363-scaffold1038-468245 19 1315612 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320794365 Affx-122933133 AX-385281329 19 1353954 AGATAAGATTAAGAAAATCTGTATCACAGGTCAAG[C/T]ACAGGTCAATTTTGCACAGATGCAATATGATGCAA Y 2 1 2 1 101000 r 74 goat snp1364-scaffold1038-514349 19 1362406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798087 Affx-122949767 AX-385285022 19 1396249 TCCTAGTCAGAATCAAGAAAAGGGACTGCTAGTGA[C/T]GTCATAATTGTAACATGGCTCCAAGGGAGCCCAGA Y 2 1 2 1 101000 f 74 goat snp1365-scaffold1038-556644 19 1405303 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798732 Affx-122938577 AX-385285663 19 1443187 CACAAAACGATGGCTATATGGAAATGTCTTCCAAG[C/T]ATGACCAATGCTGCATAGAACTTTCTATTCTTCCT Y 2 1 2 1 101000 r 74 goat snp1366-scaffold1038-603582 19 1448851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408713 Affx-122953427 AX-123279064 19 1492153 ACAACTCTTAGCTAGAATCTTCTTTTTAATTTTTT[A/C]AAGTCCTCAACTCCCAAAACATGGCAGCATGTATT M 2 1 2 1 102000 r 74 goat snp1367-scaffold1038-652548 19 1498340 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796144 Affx-122932911 AX-385283095 19 1564089 CACTAATGCAATCATTGATCACATACAGAATTATA[C/T]ACCTGATCGACTGCTACAAGTTACCTAGTCACCAT Y 2 1 2 1 101000 r 74 goat snp1369-scaffold1038-724484 19 1546129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434036 Affx-122934210 AX-123304377 19 1694694 GCCTTAAACTCTTTCTCTTTTCAATGGTCCTACTT[A/G]TTAATTTCCCTATATTTTAGATCATTTTTATTGTC R 2 1 2 1 201000 r 74 goat snp1371-scaffold1038-855089 19 1750132 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794399 Affx-122943503 AX-385281362 19 1731151 TTTGACGGTTTATATTTAGAAGGGCTTTTAAACAC[G/T]AATTGACACTACAAGTAAATCCCTTCTATTCCATC K 2 1 2 1 101000 r 74 goat snp1372-scaffold1038-891546 19 1788166 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389087 Affx-122968586 AX-123259445 19 1760833 AATCACATTACTTGGCCCAAACTACCAGTGGGCTA[G/T]CATTAGACCTGGAACTCCCTCAGTTGTGATCCAGC K 2 1 2 1 101000 f 74 goat snp1373-scaffold1038-921228 19 1819429 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784197 Affx-122925320 AX-385271248 19 1790163 TGCAACAATTCTCACAGAACTCTTACTGATCACTA[G/T]CAGAAGTCCTCAAACATCTAAAAGGACAAGAAAAA K 2 1 2 1 101000 r 74 goat snp1374-scaffold1038-950558 19 1848855 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390524 Affx-122967237 AX-123260881 19 1828583 CCAAAGGCCCAGACCCAGTTTCACCCACCAGTGGA[C/T]AGACTTCAGAAGCAACAAAGTTACCAACCCACAGC Y 2 1 2 1 101000 r 74 goat snp1375-scaffold1038-988978 19 1889015 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415392 Affx-122948749 AX-123285741 19 1871763 GATCAGAGGGATCATGAGAAGTTGGAGGGAATTCC[A/G]CAGTAACAGTAACTGCACATTAGATCACAAAAACT R 2 1 2 1 102000 r 74 goat snp1376-scaffold1038-1032158 19 1933070 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398653 Affx-122961894 AX-123269008 19 1916508 CTTTAAGGGTGCTGAACTTCTCATTGTTAGTGCTG[C/T]AATTTCAAGAGCAAGAAGGAATATCAGTCAACAAA Y 2 1 2 1 201000 r 74 goat snp1377-scaffold1038-1076903 19 1982771 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426178 Affx-122940585 AX-123296524 19 1949441 TCAATTCATTTATTTCTCTATATGAGAGACAGTGC[A/G]TTGTTTTTCTCATTTTTACAAGTGTCATGAGCTGA R 2 1 2 1 201000 f 74 goat snp1378-scaffold1038-1109836 19 2015701 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417951 Affx-122946704 AX-123288299 19 1996383 CCAGTGGACTACGTTTTGTCAGAAGTCTCCACCTT[A/G]TCCAATCCATCTTTCATTGAGTAAGACAAGTATGT R 2 1 2 1 201000 r 74 goat snp1379-scaffold1038-1156778 19 2063345 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784445 Affx-122936605 AX-385271494 19 2077775 AATGACTAACTGAATTTTCTCACTTTTCCCTAGTC[A/G]TTACTTATTATGTTACTCAATCTCAGATAAAATTT R 2 1 2 1 101000 f 74 goat snp1381-scaffold1038-1238170 19 2145555 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410154 Affx-122952794 AX-123280504 19 2107135 TCCTTACCAAAATAGAATATAATTACCACTATTCC[A/G]TAACCTCTACCCAAATCACATTGCCTCACTCTATG R 2 1 2 1 101000 r 74 goat snp1382-scaffold1038-1267530 19 2175348 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395023 Affx-122964218 AX-123265378 19 2141759 CCTGGTTTAAGAAAAAATCACCCCTGGAAAAATAC[A/G]TTTTCTGGTTGACTGACTGATATCAGAAAGGGCCA R 2 1 2 1 303000 r 74 goat snp1383-scaffold1038-1302154 19 2209961 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780765 Affx-122960123 AX-385267854 19 2212308 TGCACTGCAGTATTTAAACAAATCAATGTCCACTC[C/T]ACTTTCAAAGTCACCAAACAAACAATTGATATCCA Y 2 1 2 1 101000 f 74 goat snp1384-scaffold1038-1372703 19 2281451 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452598 Affx-122920494 AX-123322931 19 2288257 AATGACCCTGAAATCTAGGAGCCCCCAACCATTTG[A/G]CAAAAGCAATTGAAGTGCTCCCTGAACTAATGGGC R 2 1 2 1 101000 r 74 goat snp1385-scaffold1038-1448652 19 2360082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781307 Affx-122937347 AX-385268392 19 2329082 TGGCATAAAGATGTCATAAACACTGACAGAAAGAT[A/G]CATAAATGCTTGTCATGGAATTCATTTTAATTAAT R 2 1 2 1 101000 f 74 goat snp1386-scaffold1038-1489477 19 2401017 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803478 Affx-122965925 AX-385290302 19 2363948 TCTCTTGATTTACAAGGTTTAAGGAAATATAGAAA[C/T]GTATCATTCTTGGATTTGCTTGGCTTTTCCGATGT Y 2 1 2 1 101000 r 74 goat snp1387-scaffold1038-1524343 19 2436189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382481 Affx-122974200 AX-123252839 19 2394629 AAGTTACAAAAGATGGAAATATATTTTGCTAAAGG[C/T]AAAAGGGGAATTTTGTCCTAATGTTAGTTATTTCT Y 2 1 2 1 101000 f 74 goat snp1388-scaffold1038-1555024 19 2466987 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785619 Affx-122963763 AX-385272662 19 2430146 ACTGGAGAATCCACCATGGTTGAGGATAGGGGGAG[C/T]ATTGAAACTTAGAAAAGAATGCAGCTACAGGTACT Y 2 1 2 1 101000 f 74 goat snp1389-scaffold1038-1590541 19 2503166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798303 Affx-122971436 AX-385285238 19 2466710 TGCCAATGGCAATTGGACTTCAAATTTAATATTCT[A/G]TTACTCCATGGCACATATCACAGGAGACAGGAATC R 2 1 2 1 101000 r 74 goat snp1390-scaffold1038-1627105 19 2542868 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399920 Affx-122961318 AX-123270275 19 2507055 ATATCACTTTGATTCTTTTCATGTAGAAATGTGAG[C/T]ACACTATAACTGTAACCAATTTCTCACCAAGAGCC Y 2 1 2 1 101000 r 74 goat snp1391-scaffold1038-1667450 19 2583475 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378863 Affx-122976518 AX-123249222 19 2539309 TTAAACAATTCCAGGATGAGCGTTGCTGTTGAGTG[C/T]AGAAACATGGATGAAGGCGACATGAGGGAGAAGAT Y 2 1 2 1 101000 f 74 goat snp1392-scaffold1038-1699704 19 2615975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404181 Affx-122957686 AX-123274533 19 2600991 GTTAGTGACACAGAATGGAGAGTTCCAAAGATGAC[C/T]CATGGATATATGGTTACTTGATTTAAATCAAAGTG Y 2 1 2 1 303000 r 74 goat snp1393-scaffold1038-1761386 19 2679487 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388695 Affx-122968993 AX-123259053 19 2649275 AGAAATCATTTAAAGATTTATAAAGTCTTTTAGAG[C/T]ATTTTACCCTCTGATTAGATTTGTACATATTCACA Y 2 1 2 1 101000 r 74 goat snp1394-scaffold1038-1809670 19 2728456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387724 Affx-122969753 AX-123258082 19 2702238 ATGGAACTATGGAGAAAGACTAGCCAAAGAGGCCT[C/T]CTGATCTCCAGCTACCAGGGGCTTGAGAAAGGACT Y 2 1 2 1 103000 r 74 goat snp1395-scaffold1038-1862633 19 2782179 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378475 Affx-122976671 AX-123248834 19 2749452 GAGATGGTAGCCCTGCCATCACTCTACTGCTTTTG[C/T]GGCATGAGTTTGGCTATGGTTCTGAGAGGCTTCCA Y 2 1 2 1 101000 r 74 goat snp1396-scaffold1038-1909847 19 2830650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443766 Affx-122927110 AX-123314103 19 2795204 GGCTGTAGGAGAAACTCCCTACTGGCTGATACCTC[G/T]ATTCTGTAGTACGTTTATGTGAGAACCAGCCAGTG K 2 1 2 1 101000 r 74 goat snp1397-scaffold1038-1955599 19 2877507 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401221 Affx-122959320 AX-123271574 19 2843167 TCATTTCTATTAATTTCTACTAATTCTACCTGAAT[A/G]TATGTTTTCATTTTTCCCTGTCTAAAGTACCATAA R 2 1 2 1 201000 f 74 goat snp1398-scaffold1038-2003562 19 2925881 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770417 Affx-122922648 AX-385257583 19 2893208 ACTATGCTAAAAAGTTTTCTCACACACACCCAAAA[C/T]TACAAGATCTTGTGTGTAAAACTAAACTGTGTCCT Y 2 1 2 1 101000 f 74 goat snp1399-scaffold1038-2053603 19 2978189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782097 Affx-122971473 AX-385269176 19 2928198 TTTTCTTTATAACTCTCTACAAGAAAATTTTAAGA[G/T]AATTTCCTGCCTCTTGTTCAATGAATTCTTCAATT K 2 1 2 1 201000 f 74 goat snp1400-scaffold1038-2088593 19 3014521 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773641 Affx-122964301 AX-385260781 19 2999106 GGACTCTCTTGAAGGTAAGAACATTCATGGTGATT[A/C]AATTCTTAACTCATTTCCATGTATTACTAAGAGTA M 2 1 2 1 101000 f 74 goat snp1401-scaffold1038-2159501 19 3083636 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436410 Affx-122933021 AX-123306748 19 3030787 TAAGAGTTTAGGTATATATTTCTTCATCTTGGCTT[A/G]TTCTCCCAGACCCTTATTCATTTTTATTCATCCTT R 2 1 2 1 101000 f 74 goat snp1402-scaffold1038-2191182 19 3115880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420102 Affx-122945092 AX-123290450 19 3060809 CTGATGGAAATGAGAGAACAAGCCATGGGACTGAT[A/G]TTCAGGAGAAAAACATTTCAAGAAGAAGAACTAGC R 2 1 2 1 101000 f 74 goat snp1403-scaffold1038-2221204 19 3146228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390346 Affx-122967690 AX-123260703 19 3120124 TCAGAATTTGGCAACTATCTTGACAAATGGGTCAA[C/T]AATTTTCTTGAGAATGTTCTAAGTTAATGAAGTAC Y 2 1 2 1 101000 r 74 goat snp1404-scaffold1038-2280519 19 3206012 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768107 Affx-122965071 AX-385255309 19 3152956 ATATAAAGAGATACTGCTGAGCTCACTAGCTGTTA[C/T]ATAATTGAACTTATCAACTGTCTTGCAAGCTTTTA Y 2 1 2 1 101000 f 74 goat snp1405-scaffold1038-2313351 19 3239503 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768456 Affx-122969984 AX-385255636 19 3182036 AAATGTCCATTTAGCCCAATAACCTTCATTTTGCT[A/G]TTTGTTCTCTTTATGTATTATGGCTTTTTTTCACC R 2 1 2 1 101000 f 74 goat snp1406-scaffold1038-2342431 19 3268744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417559 Affx-122946913 AX-123287907 19 3222042 TAGTCACTCTCCTTCCCCTGGGGTACCCAGGAAGA[C/T]GCCCACACAAATGGAGATTTTCCTTATAAATGTAA Y 2 1 2 1 303000 r 74 goat snp1407-scaffold1038-2382437 19 3308671 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787567 Affx-122931789 AX-385274591 19 3266976 GAATAAAATATCTGTTTTTCCAATTGTGCACCTTT[A/G]TCATCTACTAAGGACATCACTCTAACATTTCTCTC R 2 1 2 1 101000 r 74 goat snp1408-scaffold1038-2427371 19 3353674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775274 Affx-122943126 AX-385262405 19 3298270 AAGCAAGACAATGAAACAATAGGCAAATATGATAT[A/C]CTGGTGAATGAAAGGACCCTAAGGCTTATGATCTT M 2 1 2 1 101000 r 74 goat snp1409-scaffold1038-2458665 19 3385441 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397892 Affx-122961957 AX-123268247 19 3350371 TTCTTGGTCCTTTTCTCTACACAGTGACAGTTTAA[C/T]AGCATAAAAAGAAAAATAAGCAATAAATAAGCAAA Y 2 1 2 1 101000 f 74 goat snp1410-scaffold1038-2510766 19 3431903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775798 Affx-122930877 AX-385262929 19 3418092 AGGTATTAAGTCTATATGCACTGTCTTCATTTTCA[C/T]ATCACCCACTCATATTTCAGCTAAGATATGGCTTC Y 2 1 2 1 101000 r 74 goat snp1411-scaffold1038-2578487 19 3499710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394212 Affx-122964900 AX-123264567 19 3509870 TGTGTGGTTAGACCTTCACCATGGAGGAACAGGCA[C/T]GTTCTCAGGAGTCTAAGCAGCTGGAGGTGGATCCA Y 2 1 2 1 101000 f 74 goat snp1413-scaffold1038-2670265 19 3591978 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403808 Affx-122957963 AX-123274160 19 3563975 AAGTAAGGAAGGGGAAACCTTCCCAGAAATTATAG[A/C]TGCAGTGGTTTAAATTCCAGCATTTAGCCTGAAGC M 2 1 2 1 101000 f 74 goat snp1414-scaffold1038-2724370 19 3647312 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272957 Affx-1111833139 AX-519546643 19 3596904 GTACATGTTCAGCTACCTCATCTCTTCCCATTCAC[A/G]TTCCAGAAATTATATCTTCGTGCTTTTCATTATTA R 2 1 2 1 201000 r 74 goat 19_3596904_AF-PAKI 19 3596904 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396790 Affx-122962756 AX-123267145 19 3602327 TTTATTACCTTGATGGTGATGGAATCATGGGTGTA[C/T]GCACATATCCAAACTCACAAAAATGTACACATTAA Y 2 1 2 1 101000 f 74 goat snp1415-scaffold1038-2762722 19 3685823 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422160 Affx-122943531 AX-115111674 19 3643873 CTCATCACTTCATCTCTCTGTATATTGGCCTGCAT[A/G]CAGTGAGCAGTGCAAGCTTGGGCTTAGTAACACAT R 2 1 2 1 101000 f 74 goat snp1416-scaffold1038-2804268 19 3727443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801301 Affx-122953647 AX-385288213 19 3692462 TGTTTGACCATAGGCTCTTCCTGATGATCTGATAT[A/G]CTCCTAAGAGGACATTTGTAATGCTTTTCTAAGGA R 2 1 2 1 101000 f 74 goat snp1417-scaffold1038-2852857 19 3776147 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421784 Affx-122944342 AX-123292131 19 3726458 TGACAGGTGGTTCTGAAAGTCCCTTCCTCTACAGA[C/T]GCACCAGACGTTCAGCTATGCAAGTCCCTCTGAAA Y 2 1 2 1 201000 f 74 goat snp1418-scaffold1038-2886853 19 3811227 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767949 Affx-122923516 AX-385255164 19 3769668 TTACAAGTTTATAGCATTTTGTCTTTTTACAAACT[A/G]TTTTCACATACTTTATTCTATAAAGACTCTCAACT R 2 1 2 1 202000 f 74 goat snp1419-scaffold1038-2930063 19 3854385 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399166 Affx-122960639 AX-123269521 19 3905742 TCAGCCCATTTAGTCAGTTATATATGTCATATATT[C/T]AATGAATGTTTACTATATTTGACATTATAGTATAT Y 2 1 2 1 103000 f 74 goat snp45211-scaffold616-1294250 19 3993645 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421797 Affx-122944331 AX-123292144 19 3942277 TCTCTGAAAAGCCTCTTCAAACACTCAGAATGGAC[A/C]ATACTTTGTTTACATGTATTTTCCATTAGAGTTTG M 2 1 2 1 101000 f 74 goat snp45210-scaffold616-1257715 19 4030505 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786918 Affx-122920882 AX-385273947 19 3987039 AGGACTGTATAGTCATACAGCCTAGGAAAAATGTC[A/G]TTTAAGTGAAAGAATCAGACTAGCTAAAAATGCTG R 2 1 2 1 101000 f 74 goat snp45209-scaffold616-1212953 19 4076041 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787878 Affx-122977481 AX-385274900 19 4037974 GAGATGGTCAACAAAACCCAAGCTAGTAACTTAAA[A/G]TAATTAATCAATTAGAAAAACTTCAGAAATATGAT R 2 1 2 1 303000 r 74 goat snp45208-scaffold616-1162018 19 4127758 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403674 Affx-122957505 AX-123274026 19 4067567 AACTCATAAACTGATTTTCAGTCTAACCAGGCAAC[G/T]ATTGCACTGTTTTTTACTGAGCCCATCAAAATTAT K 2 1 2 1 101000 f 74 goat snp45207-scaffold616-1132425 19 4157813 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771692 Affx-122938620 AX-385258849 19 4105760 TGTAATTAAAGCAAAAACATAAAGGATTGCATAAA[C/T]AATTCTAAAATCTCTAGATATCCTTCTTCCATTTT Y 2 1 2 1 101000 f 74 goat snp45206-scaffold616-1094232 19 4194203 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404825 Affx-122956641 AX-123275177 19 4137613 GGCTGGAGGAGACAAGGAGAGATTTGTCTTTACAC[A/G]TCTGCTACGGTAGGCTGCAGCAAACAGCTTCCTGA R 2 1 2 1 101000 f 74 goat snp45205-scaffold616-1062379 19 4225527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777381 Affx-122921521 AX-385264503 19 4210095 ACAAGACAATGCAATTGATAATACTCCTTTTTTTC[A/G]CTTGCTTTTTTCCTTCCATGATGAGATGAACATAG R 2 1 2 1 101000 r 74 goat snp45203-scaffold616-989897 19 4298930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794720 Affx-122951958 AX-385281680 19 4268956 ATTATTTCAATTTAAACTCTCCATTCTTCAACTAG[C/T]ATCTGCTGTTTCCTAGCTCACTTCCTCTAGCTCCC Y 2 1 2 1 101000 r 74 goat snp45202-scaffold616-931036 19 4359985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390974 Affx-122966920 AX-123261331 19 4319236 AGTTTATTTTTTCTGATGAGAAAGCCAAAGGTAGG[C/T]ATGCTTGGTTGGTAAGAGTCTTGACTTTCTTGCTG Y 2 1 2 1 101000 r 74 goat snp45201-scaffold616-880756 19 4411409 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786558 Affx-122924008 AX-385273591 19 4355100 ATTACTGCTTCGTTTTACAGATAAACAGATACAGA[G/T]AGTATGACCACAGATTTCTTGCTCTTGATTTTAGT K 2 1 2 1 101000 f 74 goat snp45200-scaffold616-844892 19 4447852 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417962 Affx-122946696 AX-123288310 19 4402403 CTCTTGAGTTGACCTTATCTGAAATGTAAACATAA[C/T]GTTAAGGTTTCTGGGAGAAAGCAGATAATCCTGGC Y 2 1 2 1 201000 f 74 goat snp45199-scaffold616-797589 19 4495129 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797123 Affx-122964765 AX-385284063 19 4451418 AACAAGGAGAAAAAAAGTCCCTAGTATCTCAGATG[C/T]AGGATTGTATGGCATTTTCTCTTCAACAGTGGCAC Y 2 1 2 1 101000 f 74 goat snp45198-scaffold616-748574 19 4544177 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417428 Affx-122947214 AX-123287776 19 4481114 AGTCTGGTTACCACTTCTCCAGGTCTTGCAACTAG[C/T]AACTGAGGAGGGCCAGCCAACAGAGTTGGCCGTCT Y 2 1 2 1 101000 f 74 goat snp45197-scaffold616-718878 19 4573896 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441293 Affx-122929462 AX-123311630 19 4521918 AGTCTTACAATTGCACACAGCCAGGGCTGCCAGGG[C/T]GTAATGAGGAGAGAGGAAAACCCAACAAGGACATT Y 2 1 2 1 101000 r 74 goat snp45196-scaffold616-678074 19 4615353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383008 Affx-122973325 AX-123253366 19 4574978 GCCATCCTGAGCCTGCGACTGCAGCAGGTCTTCAA[C/T]GAGTCCGCCTCTGAAAGAGTGATTTTTCTTTCAAT Y 2 1 2 1 101000 r 74 goat snp45195-scaffold616-625014 19 4667687 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399999 Affx-122960807 AX-123270354 19 4606920 GTCTCAAAAAAAAGTGAAAGTCAGGCACTTAGTGA[C/T]GTCCGACTGTTTGTGACCCCATGGACTATAGCCTG Y 2 1 2 1 101000 f 74 goat snp45194-scaffold616-593072 19 4699799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381776 Affx-122974300 AX-123252134 19 4664978 TAAAAAGTACTTTAGATCTTAATGCTGCTATTCCC[A/G]TGCATCTTACAAATATGTATCTTATATAACCGTCT R 2 1 2 1 101000 f 74 goat snp45193-scaffold616-535014 19 4758200 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422892 Affx-122943064 AX-123293238 19 4704734 CAGAGATGGGTACCTACTTTTTCTTTAAACTATTT[A/G]TTAAATTCTTAGACCTAGATAATTCAAAATACTCA R 2 1 2 1 201000 r 74 goat snp45192-scaffold616-495258 19 4798225 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426119 Affx-122940629 AX-123296465 19 4777760 CAGATGAAACGCAATACTATATGATACTACTTACA[C/T]GTGAAATCTAAAAGATAATACAAATGAATATATAT Y 2 1 2 1 102000 f 74 goat snp45191-scaffold616-422232 19 4872490 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417796 Affx-122947378 AX-123288144 19 4814524 GTCCAAGCCCCAGGAGCCAAATCTTATTCCTAGAC[A/G]TCAGTCTAAGAGCTACCTCCCCATTTTGATTTAAG R 2 1 2 1 101000 r 74 goat snp45190-scaffold616-385468 19 4909470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453699 Affx-122919691 AX-123324032 19 4851221 ATTGCTCTCTACATGGTTCCAGTAAGGCTGTCTCC[C/T]GTCCCCACTCAACATACAGTGTGGGTTCTCAATCA Y 2 1 2 1 101000 f 74 goat snp45189-scaffold616-348771 19 4945925 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379675 Affx-122975923 AX-123250033 19 4902403 TGCAAACGCTTTATGAAAGTATCATTTGACTCCTT[A/G]TTTTTATAGCTGCTTAGCATTTATTATTGGAGAGG R 2 1 2 1 101000 r 74 goat snp45188-scaffold616-297589 19 4997250 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416508 Affx-122947779 AX-123286856 19 4975477 GCAGATGAAGCCAGAAATAGATTAACCCTAGCTCT[A/C]GCAAAGACTGAAACTCAGCTGTAAGAGATTAAGGT M 2 1 2 1 101000 f 74 goat snp45186-scaffold616-224515 19 5071869 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802193 Affx-122929178 AX-385289097 19 5008745 TCGTCCCAAGGAACCACAGTCTTCTCAACGGAAAT[C/T]GTGATGAGAATGCCTTTCTCCATGTTGGCTCAAGG Y 2 1 2 1 101000 f 74 goat snp45185-scaffold616-191247 19 5105126 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416481 Affx-122947800 AX-123286829 19 5072810 GCCACGAGGGCCAGATCTCTAATCCGGCTGAAAGA[C/T]GGTCATATCAGGTTAATCCTGAGTCTTAAATTAAT Y 2 1 2 1 101000 r 74 goat snp45183-scaffold616-127182 19 5169887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427409 Affx-122940067 AX-123297752 19 5105760 CACAGTACAGAAGACATCCAGAGAGGAAGCAACCA[A/G]CCTTGTCACATGCTGAAAAATGGGGCCGAAAGTTA R 2 1 2 1 101000 f 74 goat snp45182-scaffold616-94232 19 5202750 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427386 Affx-122940084 AX-123297729 19 5135825 CACCATTTAATATATTGGTGCCCCCATTCCTCAGC[A/G]ACACATCTGATCTTTCATTATCTTCAGAAAATTCC R 2 1 2 1 201000 r 74 goat snp45181-scaffold616-64167 19 5232746 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390977 Affx-122966917 AX-123261334 19 5184211 AGGACTGTGCTTTATTACATGAATGACCGTTCACT[G/T]TAGATGCGATTCGTCTGCTTAAACAAGCTATAGAT K 2 1 2 1 101000 f 74 goat snp45180-scaffold616-15781 19 5281441 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401016 Affx-122959681 AX-123271369 19 5245446 GAAGCTATAAAATTGGCAATTAAGAACATCTGATT[A/G]CAGGCTGGAAATTAGTTATTTGGGAACTACTATCA R 2 1 2 1 101000 f 74 goat snp24063-scaffold245-400927 19 5340218 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452088 Affx-122920858 AX-123322421 19 5286869 GACTAATGGCACAAAACACAGTGGCTCAAACATAA[C/T]GAAGACTGTTACCTCTCCTGCATCTTGAAGTTGGG Y 2 1 2 1 101000 f 74 goat snp24062-scaffold245-359504 19 5382206 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783206 Affx-122954691 AX-385270273 19 5322058 AGTTTCTCCAAGATAAGGGTGATCACTGTCAATCT[A/G]TTGAAATCTCCCTGATAGCTTCTTGTGGCAATTAG R 2 1 2 1 201000 r 74 goat snp24061-scaffold245-324315 19 5424440 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380509 Affx-122975695 AX-123250867 19 5366747 CAAGAGGCCATTGGGCAAGAAAGTCTGACCACACC[A/G]TCTTGGCTAATGTGCTCTTTCTCTAGACAGGGTGT R 2 1 2 1 202000 f 74 goat snp24060-scaffold245-279626 19 5469446 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273937 Affx-1111833939 AX-519547543 19 5398327 AGCACTTTTGTCTTTGTATCTACCAGTGCCCGAAA[A/G]A R 2 1 2 1 102000 f 74 goat GoatD01.011105 19 5398327 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 539476340 Affx-1251763849 AX-586011756 19 5407474 ATGGAGTTTTCTTTTCTTTCTCTTTTTTTAAATTT[-/TAGGTTTTAATTTTTTATTTTATTTTATTTTTAAAATTTACTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTCTCC]AGGTTTTAATTTTTTAAAACGTATTATTTTTTTCT - 8 1 4 1 20000 f 74 goat SV_140 19 5407474 - deletion junction SV-TF-chip 539476595 Affx-1251763849 AX-586011981 19 5407474 ATGGAGTTTTCTTTTCTTTCTCTTTTTTTAAATTT[-/TAGGTTTTAATTTTTTATTTTATTTTATTTTTAAAATTTACTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTCTCC]AGGTTTTAATTTTTTAAAACGTATTATTTTTTTCT - 4 1 4 1 20000 r 74 goat SV_140 19 5407474 - deletion junction SV-TF-chip 562165061 Affx-1251763849 AX-606940473 19 5407474 ATGGAGTTTTCTTTTCTTTCTCTTTTTTTAAATTT[-/TAGGTTTTAATTTTTTATTTTATTTTATTTTTAAAATTTACTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTCTCC]AGGTTTTAATTTTTTAAAACGTATTATTTTTTTCT - 8 1 4 1 20100 f 74 goat SV_140 19 5407474 - deletion junction SV-TF-chip 562165598 Affx-1251763849 AX-606941009 19 5407474 ATGGAGTTTTCTTTTCTTTCTCTTTTTTTAAATTT[-/TAGGTTTTAATTTTTTATTTTATTTTATTTTTAAAATTTACTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTCTCC]AGGTTTTAATTTTTTAAAACGTATTATTTTTTTCT - 8 1 4 1 20100 r 74 goat SV_140 19 5407474 - deletion junction SV-TF-chip 562165650 Affx-1251763849 AX-606941060 19 5407474 ATGGAGTTTTCTTTTCTTTCTCTTTTTTTAAATTT[-/TAGGTTTTAATTTTTTATTTTATTTTATTTTTAAAATTTACTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCTCTCC]AGGTTTTAATTTTTTAAAACGTATTATTTTTTTCT - 8 1 4 1 20100 r 74 goat SV_140 19 5407474 - deletion junction SV-TF-chip 38385918 Affx-122971570 AX-123256276 19 5424750 AATGAGGCCCTGACCAGTCAGAAATAACTGATGGG[A/C]GTCCCATGCCTGGCTTTCTCCTCCACAGCACTCCA M 2 1 2 1 101000 f 74 goat snp24059-scaffold245-221623 19 5527335 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388987 Affx-122968658 AX-123259345 19 5455718 CGTGTCTCTGACTTCTCATTCTGCTGCCATCATTA[A/G]CTTGGATTTTCAGCATAACATACCTGGACTACTAC R 2 1 2 1 101000 f 74 goat snp24058-scaffold245-190655 19 5557902 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424336 Affx-122941945 AX-123294682 19 5494570 CCTGATGAGAAACGTACTTGGCAATGAACTACAAG[C/T]GCTCGTTTTCTGTGGATGGCGGAAGCGCACTGAAC Y 2 1 2 1 101000 f 74 goat snp24057-scaffold245-151803 19 5595191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390691 Affx-122967949 AX-123261048 19 5531324 CAATTCGCCCTCTGGCTCCTCAGTACACAGGGCTC[A/G]TGGGCAGGGAGTCTAGCTTGAGACTCTGACCACCT R 2 1 2 1 102000 r 74 goat snp24056-scaffold245-115049 19 5635416 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421260 Affx-122944753 AX-123291607 19 5565061 TTGGTCTCCTTATGGAGTGCCATTAACTTGGAAAT[A/G]CTGCCAGTTTTTTTCTGCAATCTACAACCACACGT R 2 1 2 1 101000 r 74 goat snp24055-scaffold245-81312 19 5669690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771906 Affx-122936002 AX-385259062 19 5611241 TTGTAAAGTTTCATGAACATTCTATACTTACTCTC[A/G]TATGTGAGTAGTACTTTGGAGAGTGATCATTGGGA R 2 1 2 1 101000 f 74 goat snp24054-scaffold245-35132 19 5715349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277213 Affx-1111835798 AX-519550719 19 5708018 ACTTCCTAGCACTCCCTTCCTAGCAATCATGTTTA[A/G]ATCAGAATGACTGGTTTTCACCCTTAACCACAAAC R 2 1 2 1 101000 f 74 goat Random2.2K-1776 19 5708018 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38421431 Affx-122943957 AX-123291778 19 5718895 TCCCTGTGGATCTCTGCTTCCTCACTCCAGCAATG[C/T]AGACCTACCACCATTTTGTGCCATTCTTGCCTGCA Y 2 1 2 1 101000 r 74 goat snp57815-scaffold931-2375302 19 5915782 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383700 Affx-122972484 AX-123254058 19 5757356 TAGCTACAACTTGCGGAGGTGGTGATCTGATGGCT[A/G]TGGGGTAACCAAGACCTTTACTGTGAGAATGTTGA R 2 1 2 1 201000 f 74 goat snp57814-scaffold931-2336841 19 5955243 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763509 Affx-986698038 AX-385251373 19 5794850 TCCAAAAGTTATGAACTTAAGGAACAAAAGTCCTT[A/G]GTGCAACTTCCATTCTTTCTTTGTGTCTTTGAGAA R 2 1 2 1 600010 f 74 goat 19_5794850 19 5794850 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 38400060 Affx-122960767 AX-123270415 19 5795362 CCTTGCTACATATCAATACACAATGGAAAAAATAC[A/G]CAGTACAAAGCCAGACACTCTGTCTCAGTTCAGGG R 2 1 2 1 201000 r 74 goat snp57813-scaffold931-2298835 19 5993595 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442580 Affx-122928498 AX-123312917 19 5834482 GAAGGAGACAACTTGCTCGGGTCAGTCACTCTTAC[A/G]CAGTGTTACCACTCCTCCACCAACCATCCCCTGAG R 2 1 2 1 101000 f 74 goat snp57812-scaffold931-2259715 19 6033268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390447 Affx-122967623 AX-123260804 19 5866112 TCGAGTAAAGTGGATAGGAGAAAATGGGCTTAATC[A/G]CTGCCTCCACCCTCACCAACCTCCCTATCTGTCCA R 2 1 2 1 101000 f 74 goat snp57811-scaffold931-2228085 19 6065322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394874 Affx-122964756 AX-123265229 19 5908851 GGACTTGCGGCTTACATCAAAGTTTCATGACTGCC[A/G]TCATGCCCAGAACAGGCAGAAATAAGATGTATTTT R 2 1 2 1 101000 f 74 goat snp57810-scaffold931-2185346 19 6108179 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381291 Affx-122974462 AX-123251649 19 5937539 TCCAGTCATGACCACCCTAGAGTGTCTCAGTGGAA[G/T]GACCATGTTCCCTACTGAGGACTCCCCTTTTTAGA K 2 1 2 1 102000 r 74 goat snp57809-scaffold931-2156658 19 6136882 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380688 Affx-122975171 AX-123251046 19 6022614 GACTGAGACATAGGCCTTGTCCTCAAAGATCTCAC[A/G]TCCTCACTGGAGAGAGACATTTAGAGACAGCGCTC R 2 1 2 1 101000 f 74 goat snp57807-scaffold931-2071583 19 6217289 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766561 Affx-986698048 AX-385253920 19 6023752 CAGGATTGGTTCTTCTCACCTCAGCCTGGATCATA[C/T]ATTATTTCCTTTGGCATGTTTGTCATGGTTTAGGG Y 2 1 2 1 600010 r 74 goat 19_6023752 19 6023752 Ancestral_priority_1043 ancestry 0.724 recommended IMAGE 10K 10K ancestral 38433839 Affx-122934447 AX-123304180 19 6075622 ATTCAGACTTCCAAACTGCCCTAGAAGTGCACAGA[C/T]ACTCCAATCACATTGGTGATTCAAAACTGTTCCTT Y 2 1 2 1 101000 r 74 goat snp57806-scaffold931-2018575 19 6276454 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416043 Affx-122948358 AX-123286392 19 6109118 TGTCTACTTTGGGGGAATTATATTAGATAAAAGTG[C/T]AAACTCCCTTGCATAGTGTAGCTGTTTGTATATAG Y 2 1 2 1 101000 r 74 goat snp57805-scaffold931-1985079 19 6309507 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274449 Affx-1111834294 AX-519548040 19 6120662 ATGGTATGAAAAGTAAGCATTTTTCACCAACAAGA[A/G]TCACACCCAATAGCAGGTGTCAAAGCTGCAGCTGC R 2 1 2 1 201000 f 74 goat GoatD01.029238 19 6120662 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38375367 Affx-122979231 AX-123245726 19 6146887 ACAAGCTGTAGCTCTGCCAATGACTGGTCTGACAT[C/T]GGCACCAGTTTTTCTGACTTCTTCAAACCTCTGTT Y 2 1 2 1 201000 r 74 goat snp57804-scaffold931-1947310 19 6344827 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418117 Affx-122947125 AX-123288465 19 6176445 CATCAAGATCTTTACTGTCCTGGGCCTTTCACACA[C/T]ACTCTTCTCTGCCCGGGATAGCATCCTCACACTCT Y 2 1 2 1 101000 f 74 goat snp57803-scaffold931-1917752 19 6374141 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463574313 Affx-1110050952 AX-515056138 19 6201448 CTAAAAAATAAGACAGCTGTCAGAAAGATGATTAT[A/C]GAAGGGAAAGAAGGGTGAAAACAGTTTACTAAAAC M 2 1 2 1 101000 r 74 goat 19_6201448_AF-PAKI 19 6201448 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38429346 Affx-122938574 AX-123299688 19 6207360 CTACTCCACAAGCGCGAGACGTGAGGTGCTGGAGA[C/T]GACTGTGTTTACACTCTGTGCTGGATTTAATCCTC Y 2 1 2 1 101000 r 74 goat snp57802-scaffold931-1886837 19 6404910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776627 Affx-122970518 AX-385263754 19 6237557 ATCCCTGACTCTAACCATCCTGCTGAGTAAGTTAC[A/G]CCAGTGTATACAACCATTCATAATGTGTTAACGTT R 2 1 2 1 101000 r 74 goat snp57801-scaffold931-1856640 19 6435096 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424907 Affx-122941305 AX-123295253 19 6298453 AACAGTTCGCTGAGGAGGCTAACATTAGTATTCCC[A/G]TTTCACAGATGAAAATGTTGAGATACAGAAAGTGG R 2 1 2 1 101000 f 74 goat snp57799-scaffold931-1795744 19 6495023 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793951 Affx-122931932 AX-385280920 19 6330456 AAAAGTAGGAAACATTGTAAAGGGAGATGGTGGAA[C/T]GACTTAGTCAACACCTGGTATAGATCTCAGTTATG Y 2 1 2 1 101000 f 74 goat snp57798-scaffold931-1763741 19 6527094 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377742 Affx-122977378 AX-123248101 19 6364956 CCGAGCAGATTCCGGATGCCCTCAGTGCCTCGTTT[A/C]TGGAGGCCACTCTCTCTTGGCATTTCTTTCCTCCT M 2 1 2 1 101000 r 74 goat snp57797-scaffold931-1729241 19 6561265 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408951 Affx-122953929 AX-123279302 19 6400149 CCACCATCGCAATTTCTTTATTTTGCATTTGTCTC[A/G]TGCCAGTCTGTGAGGGAGGAAACGGGATGCATGAA R 2 1 2 1 201000 r 74 goat snp57796-scaffold931-1694048 19 6596342 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450064 Affx-122922811 AX-123320399 19 6446052 TCCAAAGTGTCATATAGTTGGAATAGCAGAATATG[C/T]AACCTTTCAGATTTTAGATTGTTTTTATCGGATGC Y 2 1 2 1 101000 r 74 goat snp57795-scaffold931-1648145 19 6642995 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798458 Affx-122947404 AX-385285391 19 6498073 CATCCCCCGAATTTTCACAAAAATCTAGGGTTCTC[A/G]TCCTCGTTGATGGTCTCATCATCTCACACAGTCCC R 2 1 2 1 101000 f 74 goat snp57794-scaffold931-1596124 19 6695022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453360 Affx-122919945 AX-123323693 19 6576604 TTTGTGGTCCATGGGAATGGCAGTGACCTGAACAC[A/G]GAAATTCTGCCTTGTGGCCTGGCATTTCAGAATAC R 2 1 2 1 201000 r 74 goat snp57792-scaffold931-1517593 19 6774183 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766586 Affx-122974860 AX-385253942 19 6617438 CCCCCCACATCTCCCTCTGAAAAGTTATACATCAC[A/G]ATGTAGAATGTATTCCCTAGAATCCTAGGTGGAGC R 2 1 2 1 101000 f 74 goat snp57791-scaffold931-1476759 19 6815368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420876 Affx-122944628 AX-123291223 19 6647959 AATAACTTGAAAAGAAGGGACCTCATTGATGGAAA[A/G]TGAACTTCCTGAATGGTGTATATGGAAACATTACA R 2 1 2 1 101000 f 74 goat snp57790-scaffold931-1446238 19 6843069 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396327 Affx-122963072 AX-123266682 19 6754321 CTTGAAGAGACAAAGGACTGATGTTTAAGTCCTTA[C/T]GAAATTCTGGTTGAGGAGGCATAGTGTCCATATTG Y 2 1 2 1 101000 r 74 goat snp57787-scaffold931-1339876 19 6950023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436979 Affx-122933154 AX-123307317 19 6817390 CCGGGTAACTGCAGAGGATGGCCCTGAGCAACCTA[C/T]CTCACTTGATAGGGTGTCACAAGAGCCGTGGGGTC Y 2 1 2 1 101000 r 74 goat snp57785-scaffold931-1276807 19 7013082 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789602 Affx-122935696 AX-385276611 19 6865387 AGAGGCTTAAAGATGCATAGTTTGCTTAAAAAATT[A/G]CTGGTTCCTTTTAACCTTTGATTGTACCTTGAACA R 2 1 2 1 101000 r 74 goat snp57784-scaffold931-1228810 19 7060805 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439570 Affx-122930084 AX-123309907 19 6996572 AGGGTGCCTCTGGAAGAGCTGACCATTTAAATGCA[C/T]GAGCCAGCCCTTGCGTTTATGCTTTCTCTTATTCT Y 2 1 2 1 101000 r 74 goat snp57781-scaffold931-1097625 19 7191713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422448 Affx-122943346 AX-123292794 19 7029871 GTTATAATGGGCAGATTGACACAGATACCCAGGAA[C/T]CTCCCAAGGAGGAGTTAGTGAGATTATGGAGAAAG Y 2 1 2 1 201000 f 74 goat snp57780-scaffold931-1064326 19 7224994 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601369 Affx-1002479680 AX-413835792 19 7043663 CACAGCCCTGACATACTGAACAGGCTGAGCGTTTT[A/T]CCAGGGGCCACCTGCAGCCCTGCCTGCTGATCTTC W 4 1 2 1 102000 f 74 goat 19_7043663_RH-map 19 7043663 A T 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601506 Affx-1002479681 AX-413835920 19 7097018 AAGTTGAGTAGTTCTCAAATTCTAGTGAGACTAGA[C/T]TGCCTGAGAGTTTGATATTATACAGTCCCAGGCCC Y 2 1 2 1 101000 r 74 goat 19_7097018_RH-map 19 7097018 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601372 Affx-1002479682 AX-186315728 19 7119766 TATGATTTCATGCATATTATTGTTGAGAACAGGAG[C/T]AATGTTTTTCAAAAGTAAGTTAATTTAAAGGCTCA Y 2 1 2 1 101000 f 74 goat 19_7119766_RH-map 19 7119766 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38390349 Affx-122967687 AX-123260706 19 7132483 TGAAGGCTCTCATCGATGCCTCCGAGGCCAGCGCC[A/G]CAAGGAAGATAAAGGAAGAGGAGAAGAGGGTCACC R 2 1 2 1 201000 f 74 goat snp57777-scaffold931-961714 19 7328649 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601374 Affx-1002479683 AX-413835795 19 7149425 TTACATTCAGTGAAGACGGAATGTCAAAACCAGAA[C/T]AGGCCACAACCGAGGCCTCTTGTACCAGTTAGCCA Y 2 1 2 1 101000 f 74 goat 19_7149425_RH-map 19 7149425 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601376 Affx-1002479684 AX-413835797 19 7173408 CAGACACTCTGTCTATCAGAGCAACCAGACCAGGG[A/G]TCAAACCCATGTCCCCTGCATTGACAGGTGGATTC R 2 1 2 1 202000 f 74 goat 19_7173408_RH-map 19 7173408 A G 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38387469 Affx-122970358 AX-123257827 19 7180785 ATTTATAAAAACTCTTCCTGAGTCATATCTTTCAT[A/G]TTCTCTTGCCATGTGGTAGGTGCCCAGGAATTATT R 2 1 2 1 201000 f 74 goat snp57776-scaffold931-913412 19 7377161 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423624 Affx-122942370 AX-123293970 19 7249659 GTTTTCTCCCAGAGCCTGGTGGCCTTTTGGTAGAG[C/T]CCCTTGTTCAGGGCGTCCAGGACTTCCTCTGCAGC Y 2 1 2 1 101000 f 74 goat snp57775-scaffold931-844538 19 7447928 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601513 Affx-1002479685 AX-413835928 19 7270989 TTGTACAGCGGAAACTAAGGTAACATTGTAAAGCA[A/G]CTAAACTCCAATTTAAAATTAATAGTATATGAAAA R 2 1 2 1 201000 r 74 goat 19_7270989_RH-map 19 7270989 A G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601380 Affx-1002479686 AX-413835801 19 7305016 TACTGCTGAAGCCTAGCTTGAAGGATTTTGAGCAT[A/T]ACCTTGCTAGCATGTGAAATGAGTGCAATTGTGCA W 4 1 2 1 103000 f 74 goat 19_7305016_RH-map 19 7305016 T A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38405213 Affx-122956903 AX-123275565 19 7318394 GACAGAATTGGCCCAACTATACAGGGACAAGCAGA[C/T]GTCCCTTCCCTATCCAGGGGAGGAACTGATGATGG Y 2 1 2 1 101000 f 74 goat snp57773-scaffold931-775803 19 7506313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437937 Affx-122931631 AX-123308275 19 7350575 TGACATTCCTGCAGTTGGAAGGCAGCCCTCTCAGA[A/G]AGAGTGCTGTCCACTATGACACAGGCATCTAACCA R 2 1 2 1 101000 r 74 goat snp57772-scaffold931-743622 19 7539523 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601382 Affx-1002479687 AX-413835803 19 7408776 GCGAGATTACTGGCTTGACCACTCTCTCCTTCTTT[C/G]GACTCTCCTTTTTCTCCACCAGGTGGCCTCTGTCT S 4 1 2 1 103000 f 74 goat 19_7408776_RH-map 19 7408776 C G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601384 Affx-1002479688 AX-413835805 19 7473475 GGTGATGCTGGCCTTGTTGATTGGGTTCAGAAACA[C/T]CTCTTCTTCTGCAATTGTTTGGAATTATTTGAGGA Y 2 1 2 1 101000 f 74 goat 19_7473475_RH-map 19 7473475 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601386 Affx-1002479689 AX-413835807 19 7488901 GCTGAGCACCGAAGAATTGATGCTTTTGAATGGTG[C/T]TGGAGAAGACTCTTGAGAGTCCCCTGGACTGCAAG Y 2 1 2 1 103000 f 74 goat 19_7488901_RH-map 19 7488901 C T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320797107 Affx-122948553 AX-385284047 19 7530933 TCATCAAGGAAACCAATCACAACTCCACAAGGCCC[A/G]TAGCGTGATGGACTTGGATGTGTAAGCTGCCACTC R 2 1 2 1 101000 f 74 goat snp57768-scaffold931-563264 19 7719283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601388 Affx-1002479690 AX-413835809 19 7557879 GAGGAGCTGGTGGGCTGCCGGCTATGGGGTCGCAC[A/G]GGGTCGGACACCACTGAAGCGACTTAGCAGCAGCA R 2 1 2 1 303000 f 74 goat 19_7557879_RH-map 19 7557879 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38439923 Affx-122930012 AX-123310260 19 7561196 AGATATGTACGACATGAGAGAGAGACAGACAGAGA[C/T]GAAGGAAGAGGTATTTATTTCAAGAAACTGGCTCA Y 2 1 2 1 201000 r 74 goat snp57767-scaffold931-533001 19 7751605 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601389 Affx-1002479691 AX-413835810 19 7579885 TTATTTCTCCAGATAAACTCTAGAATGATTTTTTT[G/T]GGGGGAAGGGGACTGTGGAAAATGTTGTGCCACCC K 2 1 2 1 201000 f 74 goat 19_7579885_RH-map 19 7579885 G T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38383093 Affx-122973283 AX-123253451 19 7603570 TCTTCTCTTAGAATTTGAAAAGAGCTACTATAATG[C/T]GACATTCATTATTTAAAAATAGGAACAGTTAAGAT Y 2 1 2 1 101000 f 74 goat snp57766-scaffold931-490627 19 7793951 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601526 Affx-1002479692 AX-413835940 19 7615945 TCCAATTCCTAGCAACATTTCTTGATAAGACTATT[C/T]TTTTACTAATGAATGGCCTTGGCTTCCTTGCCACA Y 2 1 2 1 102000 r 74 goat 19_7615945_RH-map 19 7615945 T C 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601394 Affx-1002479693 AX-413835814 19 7634909 CCAGTATGTGTTCCTTGCACAGGCATACCATAGCA[C/T]TGAGAGGCTCAGGTTGAGTTAGGCCTCCCAGCATC Y 2 1 2 1 400000 f 74 goat 19_7634909_RH-map 19 7634909 T C Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38381671 Affx-122974737 AX-123252029 19 7636438 TCACAGCAACTGGTACTGAAGAGTTGCCCATGAAC[A/G]TGGTTTCTCATTCAAGGCACGCTGCCATACACTTG R 2 1 2 1 101000 f 74 goat snp57765-scaffold931-457759 19 7826399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601530 Affx-1002479694 AX-413835944 19 7658960 AAAATTTTATAAAAGTACTGTTTACAACAGCATCC[A/G]TAAGTTCAAAATATTTAGGTACAAACCTAGTAAAA R 2 1 2 1 101000 r 74 goat 19_7658960_RH-map 19 7658960 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601531 Affx-1002479695 AX-413835946 19 7692023 GTATGGTCCAGGAACCCCAAAGGTGAAAAATAAAG[A/G]TGAAAATACTGACCCAACACTAATCTACAAAACAT R 2 1 2 1 101000 r 74 goat 19_7692023_RH-map 19 7692023 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320778284 Affx-122940427 AX-385265399 19 7749210 GTCCTGCACCCAAACGGCTCAGGAAGACAAAAAAC[A/G]TGCAAAGTCAGCACTTCCTATAGAGCTGAAAAGAG R 2 1 2 1 101000 r 74 goat snp57763-scaffold931-344987 19 7937845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379346 Affx-122976165 AX-123249705 19 7801903 TGTGAGCAGTGCCATAAAGACACAGTCCAGGGGCT[A/G]AAAGCCCAGGCTTTACAGGCTCCCCAGAGCTCAGT R 2 1 2 1 101000 f 74 goat snp57762-scaffold931-292294 19 7990807 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378452 Affx-122976692 AX-123248811 19 7844268 ATGCTGCCCCATCTGTGACCCCACTGGGTAAGCTG[C/T]GCTTTGACATACAGACCCACTCACGGGATGGCACC Y 2 1 2 1 101000 r 74 goat snp57761-scaffold931-249929 19 8030734 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277215 Affx-1111835799 AX-519550721 19 7869943 AACGGGGGTATAGAATCTGGAACACCAAAGCTCAG[A/C]ATCTCACTTGACGCTGTTCACTGGGAGAAAGGCAG M 2 1 2 1 101000 f 74 goat Random2.2K-1777 19 7869943 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451030 Affx-122921451 AX-123321364 19 7904006 TCATGATCTCTGTCCTTAGAGGAGCCTGGGGTGAA[C/T]CGTCTGTCTTGTGGCTCTGCTGATCTGTTTCTGAA Y 2 1 2 1 101000 r 74 goat snp57760-scaffold931-190191 19 8090149 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601533 Affx-1002479696 AX-413835947 19 7914278 TATATGTGAATGTGTGAGTATGTGTATGTAGGTCC[C/G]TCCGCATGGATGTATATATAACTCATTCCCCAAAG S 4 1 2 1 201000 r 74 goat 19_7914278_RH-map 19 7914278 C G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38378734 Affx-122977035 AX-123249093 19 8020855 AAGGCCTGGTCCCTTGGAGCCCTCCTGAAAGCCTG[C/T]ATAGACTGAGGACTCAGCTTTGGTATTGTTTTCCT Y 2 1 2 1 101000 r 74 goat snp57757-scaffold931-73342 19 8204882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277341 Affx-1111835800 AX-519550845 19 8066144 TGCTGGCCTGACCCTCCTGACTGTCCCTGAGTCTG[A/G]GGCCTCTTCAGTAGCCAAAACTGTGGCTGAGACTC R 2 1 2 1 102000 r 74 goat Random2.2K-1778 19 8066144 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320783905 Affx-122922141 AX-385270960 19 8075652 GGTTCCCACTCCTGGGTTGTCATAAAGCTCTGTAT[C/T]ATGGTTTGGAGAAGCAGTTATGTGAAGTTTTATGT Y 2 1 2 1 101000 f 74 goat snp57756-scaffold931-18545 19 8259791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435254 Affx-122934065 AX-123305594 19 8277492 TGTCTGAGATGATCTCGCCAATGCTCTGCATTTCC[A/G]TGGATCAACCTCCTCCCACCTGAGTCTCCCGCTTC R 2 1 2 1 101000 f 74 goat snp55433-scaffold859-183196 19 8460090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440736 Affx-122929879 AX-123311073 19 8540886 CATCTACACCAGTGAAGGAAGGCATTCCCTATAGA[C/T]ATTCACTCACACAGCAGTCAAAAGATTTTGCGTAT Y 2 1 2 1 101000 f 74 goat snp55437-scaffold859-446590 19 8727764 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419601 Affx-122945995 AX-123289949 19 8597199 AAAGTGAGCTGTAGCAACTGGGAGACCAAGGAGGG[C/T]GAAGGCAGACACGTCCCCACAGGATTCCACATCTT Y 2 1 2 1 101000 r 74 goat snp55438-scaffold859-502903 19 8785735 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453761 Affx-122919601 AX-123324094 19 8632136 TTATGCTGTCTGTTGTGTTCTGGAATAAGGCTTCC[A/G]TCGGCTGGCAAATTTTGTTTTGTTTTCAGTCCACT R 2 1 2 1 201000 f 74 goat snp55439-scaffold859-537840 19 8820625 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277343 Affx-1111835801 AX-519550847 19 8684892 GAAGACAGCATGGATTCAGGGAACCTCACGTGGGT[A/G]TCAGAATTTGTCTTCCTAGGGTTCTCCCAGAATCA R 2 1 2 1 102000 r 74 goat Random2.2K-1779 19 8684892 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320763527 Affx-986698056 AX-385251388 19 8724794 GAGAAAAGACTTGCTCAGTGATGAACAGCAAGTGA[A/G]GGGCAGAGCTTGGCCAGGAGATGGCTCCTCTGACT R 2 1 2 1 600010 f 74 goat 19_8724794 19 8724794 Ancestral_priority_1043 ancestry 0.684 recommended IMAGE 10K 10K ancestral 38412549 Affx-122951331 AX-123282898 19 8754366 CAACCACAGACACCAGGACTACGAGGCTGAGGTGG[C/T]TGCCTAGACTCAGGACGGCAGACCTTCCGAGACCC Y 2 1 2 1 101000 r 74 goat snp55442-scaffold859-660070 19 8942862 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272973 Affx-1111833147 AX-519546656 19 8765032 GCTAAAACATAAGGAAGGAAAAAGCCCACGAAAAT[A/G]GAACAAAAGATGGTCGGGGACCAGAGTGAGGACCT R 2 1 2 1 202000 r 74 goat 19_8765032_AF-PAKI 19 8765032 A G 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450846 Affx-122922239 AX-123321180 19 8784128 CAGTTCTGGCTGCTCTGTGAGGGGGATGCTCAGTC[G/T]CTTCAGTCGTGTCCGACTCTTTGCGACTCCATGGA K 2 1 2 1 103000 f 74 goat snp55443-scaffold859-689832 19 8972898 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415334 Affx-122948795 AX-123285683 19 8882091 GTTGAAAATAATTTTAAAAGTCAAAGTAATTTTCT[A/C]TCACAGAGAGTTTTTAAAGTTTGAGTAAACATAGA M 2 1 2 1 101000 r 74 goat snp55445-scaffold859-787795 19 9069843 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435722 Affx-122933299 AX-123306061 19 8956076 TTTAACATTTCCACCTGTCAAGATCATTTTGAACA[C/T]ACAGTCTATCACCCATCACATTAGCATTCATCCTT Y 2 1 2 1 101000 f 74 goat snp55447-scaffold859-861780 19 9142547 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416403 Affx-122947854 AX-123286752 19 9007320 AACTTGACACACAAAGGACAATCCAGCCCCTGCTG[C/T]GGCCAGAGGACCTAGAAAGTTCACTCCAGGAGGAC Y 2 1 2 1 101000 r 74 goat snp55448-scaffold859-913024 19 9193648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783282 Affx-122952163 AX-385270347 19 9063965 GGGGCCTGAGGTGAAACCTTTAGGGGCCTAAAGAA[C/T]GGAAGACTTCATGGTTTCTTAGCACAAAACAAAAC Y 2 1 2 1 101000 r 74 goat snp55449-scaffold859-969669 19 9250588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766590 Affx-986698064 AX-385253946 19 9242819 GAACACACCTTACCCAAGATGCTGTGGAACTGTCA[C/G]TTAACTTCCTGCTGTATAGACGTTTCTGCCCCAGG S 4 1 2 1 600010 r 74 goat 19_9242819 19 9242819 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 320779962 Affx-122938600 AX-385267061 19 9287823 TCATTGTAATTCTTGTATCAATAAATGGAATCATG[A/G]CTTAAATTGTTTTGTCATTTGACACTGAAAAGCAT R 2 1 2 1 101000 r 74 goat snp55453-scaffold859-1193527 19 9476642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797785 Affx-122928416 AX-385284724 19 9371268 AGTCTTATGTAGGAAATGATAGCAGTGATATGCTT[A/G]TAAGATGTATAGTACATATCCATTTAAAATAATGT R 2 1 2 1 101000 f 74 goat snp55454-scaffold859-1276972 19 9561171 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447626 Affx-122923986 AX-123317962 19 9400045 ATTAGGCTGTACATCTAAACTAAAACTAGTAACAA[C/T]GGATTTCTCTCTGTTTTTTCCTAAGACATTTTTAT Y 2 1 2 1 101000 f 74 goat snp55455-scaffold859-1305749 19 9589461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795471 Affx-122925505 AX-385282427 19 9551609 TTTAGCTCTGCTTAAATTTAACTGGCATAATCCCA[C/T]AGTCCATTTTACAAAGTCTTCTCCTCAAGAGTGGT Y 2 1 2 1 101000 r 74 goat snp55458-scaffold859-1457313 19 9740541 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442559 Affx-122928517 AX-123312896 19 9589225 CCCTACTCCCAGAATTTGTACCTGAAAGTGATCTA[G/T]CCTAAAGAGAAAAGGCAAATCACCCCACAACCTGG K 2 1 2 1 101000 f 74 goat snp55459-scaffold859-1494929 19 9778357 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776873 Affx-122979152 AX-385263997 19 9624938 GAGTAAACTCTTAGGCCTGGAACTGATGCATCAAG[G/T]GATATACACATTTTACATTTTGATGTATATTGCTA K 2 1 2 1 201000 r 74 goat snp55460-scaffold859-1530642 19 9814589 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450309 Affx-122922144 AX-123320644 19 9654003 ATGTTTGTTCTCTTAACCACTGTGGTATACTTTCT[A/G]TATCAGTCATAAGATCTTAAGGGGAAAGAAACCTT R 2 1 2 1 102000 r 74 goat snp55461-scaffold859-1559707 19 9843693 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387382 Affx-122970429 AX-123257740 19 9857822 AAAGATGTTCCTGCAGGCTGAGAAGGCACCTAACC[A/G]TTTGTCTCGAACAGCAATGACAGCGTCTGACTCAT R 2 1 2 1 101000 r 74 goat snp55465-scaffold859-1763526 19 10049273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428962 Affx-122938877 AX-123299304 19 9930504 AGGATATGAACTCATGAAATAATAAAGAACCCTTG[A/G]AAACTGAAAATATTATAGCAGAAACAAAAACTTTA R 2 1 2 1 101000 f 74 goat snp55467-scaffold859-1836208 19 10121540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798341 Affx-122965142 AX-385285276 19 9984999 AGTTAGGCAATATTTGATTGGAGATCTTATCTATT[A/G]CCTGATTTGAAAGATGAAGAGTTAAGTACTTACAT R 2 1 2 1 101000 r 74 goat snp55468-scaffold859-1890703 19 10176153 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381638 Affx-122974762 AX-123251996 19 10033436 GGGTGGGACCTAAAGCGCCCACGGAAATGACGTTG[A/G]TCGCCCCTAGTCGCATGATGTGGCAAAATGCAAAA R 2 1 2 1 101000 r 74 goat snp55469-scaffold859-1939140 19 10224380 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793560 Affx-122974639 AX-385280535 19 10069595 CCTACATTGGCGCTTAGTGTGTACTTAAGGGCTAA[C/T]GTTCCAAATAAAGTCATTCAGTGCTTTGCAGAAAC Y 2 1 2 1 202000 r 74 goat snp55470-scaffold859-1975299 19 10260644 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414270 Affx-122949608 AX-123284619 19 10130565 TGGACAGATTGCCTCCAAATTTTAATCTGGAAAAG[C/T]ACTGGGATAGCTGTTTGGAAAAGGATTGCCACAAC Y 2 1 2 1 101000 r 74 goat snp55472-scaffold859-2036269 19 10321740 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449770 Affx-122922442 AX-123320105 19 10170483 AACAGAAACTCTGTATCCATTAAACAATAATTCCT[C/T]GTTCCCTACTCTCCCCTGCCCCTGGTAATTTTGAC Y 2 1 2 1 103000 r 74 goat snp55473-scaffold859-2076187 NW_017202903.1 5393 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444342 Affx-122926723 AX-123314679 19 10256269 TACTGCAATGAATATCTTTGAAAGAACACCTCTAT[A/G]TACCTGCATCATTTCCTGTGGGCAAATTTTTAAAA R 2 1 2 1 101000 f 74 goat snp55475-scaffold859-2161973 19 10447742 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405898 Affx-122955590 AX-123276250 19 10447698 GAGAAAGATGTCTCAGAAGCCCAGGCAAGGCAAGA[C/T]GATACCTCAGTCCAGAGTGGCAATAGAGAGGAAGG Y 2 1 2 1 201000 r 74 goat snp55480-scaffold859-2353402 19 10640444 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409634 Affx-122953532 AX-123279985 19 10498427 ATGTGAAGTAGTTATCTCATTGTCATTTTAATTTG[C/T]ATTTTCTAAATGACTAGTGATGTTGAGCCTCTTTA Y 2 1 2 1 303000 f 74 goat snp55481-scaffold859-2404131 19 10691574 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409901 Affx-122952894 AX-123280252 19 10563621 CAGGTTTCTTTTTAGTTCTTATTTTCCAGTTATCT[C/T]GTAATGGGTTTTTATTTTCAGTAAAAAGTTTTTCT Y 2 1 2 1 303000 f 74 goat snp55482-scaffold859-2469325 19 10757886 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414615 Affx-122949346 AX-123284964 19 10681717 CTTTTGCCTAGTGTGTAGAGAAGAGTTGGGTCCAG[C/T]AGAGTGCGCTGTTGGCCTTCAGATAAAGTGTTGAT Y 2 1 2 1 101000 r 74 goat snp55485-scaffold859-2587421 19 10876942 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393344 Affx-122965935 AX-123263700 19 10812321 TTACCAGGTCGTCAATGGTATGAAATTCAAGCATA[C/T]AGGGCCTTAAACCAGGCCCTTGGTAGGTAAGTGGA Y 2 1 2 1 101000 f 74 goat snp55488-scaffold859-2718025 19 11008182 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443721 Affx-122927146 AX-123314058 19 10846149 TATGTTTGTACAGATTAAGACCGTGTTTGTCTTTG[C/T]ACTCTTGCAGGTGGTACATGCTTTAAAATAGGAAG Y 2 1 2 1 101000 r 74 goat snp55489-scaffold859-2751853 19 11043686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420030 Affx-122945148 AX-123290378 19 10897386 ATCATAGAGAGGTTTATTAAAGTGACATTTTAGGG[C/T]AAAGCAAAATTTTCGCAAGTATTATGGAGTTTATT Y 2 1 2 1 101000 r 74 goat snp39537-scaffold502-1088128 19 11093687 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378717 Affx-122977049 AX-123249076 19 11007257 AGCAAATTCCCTGAAGCTGTTCTAGGAGTTAGTTT[A/G]GAATCACCTGACTTTCTCAGCGGTTCAGGCCCATC R 2 1 2 1 101000 f 74 goat snp39535-scaffold502-978257 19 11204341 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424068 Affx-122942053 AX-123294414 19 11106810 GACCACATTTTGAGAACCACTGATGTATGGGGGGA[C/T]AAGGGCAAATGTTCTAGAGTCAGGTAGACCTTAAC Y 2 1 2 1 101000 r 74 goat snp39533-scaffold502-878704 19 11302677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449498 Affx-122922627 AX-123319833 19 11177418 AGCTGGGCCTCCATCCACCTCAAGCCAGCCCAGGA[C/T]GCAGAGAAGTCTCATGTGAGGAAATACAGATCCTC Y 2 1 2 1 101000 r 74 goat snp39532-scaffold502-808096 19 11370986 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799683 Affx-122953838 AX-385286611 19 11211347 AAGAATATTAGAAATGAGAGCTGGTTCAGCTAAGG[C/T]GATGGACTTAAGATCATTTATAAGATGAAAAGTAG Y 2 1 2 1 101000 f 74 goat snp39531-scaffold502-774167 19 11404967 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768810 Affx-122951451 AX-385255987 19 11247420 AAAATAAAATGTGTCTCTAGGAAAAAGCAAACCTC[A/G]TAAATCTGAAATTTCTTTTATTGCTTCTTTGGGAA R 2 1 2 1 201000 r 74 goat snp39530-scaffold502-738094 19 11441018 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272889 Affx-1111833130 AX-519546577 19 11267834 TGTCCTTTGACGCATCATTCCCTAAGCAGCTCGGC[A/G]GAAGTTCTCTAAAAAGGAGAAGAAAAACGCTGAGT R 2 1 2 1 201000 f 74 goat 19_11267834_AF-PAKI 19 11267834 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395100 Affx-122964164 AX-123265455 19 11287052 ACTCTTTAACCAAAGAAGCTGCCTTTGATAAGAAA[C/T]GATAATTAATAGTGTATTTTTAAAGGATTTCATCA Y 2 1 2 1 101000 f 74 goat snp39529-scaffold502-698462 19 11480469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420807 Affx-122944681 AX-123291154 19 11317160 CTGAAGCCAACTTAGAAGCTCTGAGTCATTTTTAA[C/T]GGGGCAAATGTTTCTTTGATCCTTAGAGAGTATCC Y 2 1 2 1 201000 f 74 goat snp39528-scaffold502-668354 19 11510585 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452580 Affx-122920508 AX-123322913 19 11390838 TCACAAACACACAAATGCTCTCTCTTCCTTTAATG[A/C]ATTATTATACAAAATTTCACATTTATGCAAACACA M 2 1 2 1 201000 r 74 goat snp39526-scaffold502-594676 19 11583811 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800623 Affx-122926838 AX-385287542 19 11431262 TAATCTTTACATTTCCCTCTTTTGCACTGTATCAT[A/G]TTGCAGAACACACGCACTGTAGCTTGCGATTCATT R 2 1 2 1 101000 r 74 goat snp39525-scaffold502-554252 19 11624369 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772296 Affx-122930322 AX-385259451 19 11506002 GCCTTCAACTTTAAGTAGTAAGTGGCATAGAAAGA[A/C]AGCCACACGTGAGAAATCCTAGAGGCCAAAGGAAG M 2 1 2 1 101000 r 74 goat snp39523-scaffold502-479512 19 11699095 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388197 Affx-122969426 AX-123258555 19 11539433 AGAAGCAGCTTGAAGAATTTATTGCCTCCTCCCCG[A/G]CCCTTTCGTGGGGATGTTTCCATTAGAAGTCTGTA R 2 1 2 1 101000 r 74 goat snp39522-scaffold502-446081 19 11732492 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794920 Affx-122969696 AX-385281880 19 11572522 TTTAAGGTTTGCGTTTATCTAGTTTAAAATATTTA[C/T]GTCTGTTTGCTAGGTCAAAGTCTATAATTACTTTG Y 2 1 2 1 201000 f 74 goat snp39521-scaffold502-412992 19 11765321 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777444 Affx-122949266 AX-385264564 19 11622146 CATACTTATGCTGTAGTGTGATTTCAGGGTGATTC[A/G]TTTGCCTTATTTGTTGATAGGTGGTGTTTTTCAAA R 2 1 2 1 101000 f 74 goat snp39520-scaffold502-363368 19 11815054 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442508 Affx-122928554 AX-123312845 19 11686982 AGCAGAGTGCAGTGGAACCCTGGGCACTGTTGGGG[C/T]GCTTTGGGGAATTTTGATGCTTGTGCTGCACAGTG Y 2 1 2 1 202000 f 74 goat snp39519-scaffold502-298532 19 11880348 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384437 Affx-122973105 AX-123254795 19 11718162 TTAGTTGACTTATTAAACTTTTAAATTTATACATC[G/T]TCCTGTTAAATATTGTAGCACACTCCTTTCTATAT K 2 1 2 1 101000 r 74 goat snp39518-scaffold502-267352 19 11912131 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416143 Affx-122948285 AX-123286492 19 11824023 ACATAAATCAATAAAGTCTAAGTGTATAAAGACCA[C/T]AATTTGAATTAGTTCATAAGCAAAAACTAGGATCT Y 2 1 2 1 101000 f 74 goat snp39516-scaffold502-161491 19 12018471 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406920 Affx-122955611 AX-123277271 19 11870846 GCCCAAACCAGCCCTAGAAGCAATCAAGATGGTCT[A/G]TTTGTAAATAGCCTCCAAAATGACCTTCAGGGATC R 2 1 2 1 101000 r 74 goat snp39515-scaffold502-114668 19 12062791 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376819 Affx-122977926 AX-123247178 19 11908444 GCAGCATTTTCAGTGGTTGTTATGATAAAACGAAC[A/G]TGCAAAACTCATGTAACAGAAAATAAGAATGGTAG R 2 1 2 1 101000 f 74 goat snp39514-scaffold502-77070 19 12100737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277345 Affx-1111835802 AX-519550849 19 11969918 TTTTGTATTGATTAATATATCCTGCAAAAAAGCCC[A/C]TCTATTATTCAGCCTCCACCTTCCCATCCTTGTTG M 2 1 2 1 101000 r 74 goat Random2.2K-1780 19 11969918 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436695 Affx-122932330 AX-123307033 19 11996374 TTGGTGGTGACTCAGACCCTGGTAGCCTTGGAGTA[C/T]GGATGCTGTGGTCCTCAGCTGGGAACTGTCTCAAG Y 2 1 2 1 101000 f 74 goat snp8412-scaffold1302-1003425 19 12187464 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453851 Affx-122919536 AX-123324184 19 12040192 CTGGGCCCATGGGTAAATCGCAGACATATGCATTA[C/T]AAAAGCAGATTTGTAGAAAAAGAAGTTGCACTCTA Y 2 1 2 1 101000 f 74 goat snp8411-scaffold1302-959607 19 12231243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787251 Affx-122952167 AX-385274277 19 12094225 ATTTACTGACCAGTCAAGCAATGAGCAATAGGAGC[C/T]TGGACTTGGTAACAGGACAACTAAAAAGCTATTTC Y 2 1 2 1 101000 f 74 goat snp8410-scaffold1302-905574 19 12284334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793750 Affx-122971883 AX-385280722 19 12157261 TCTAAAATCTTGTAAAATCAAATCAGTTAATTATT[C/T]GAAACTCTGTACTGAATATACAGTATTCAGTGTGT Y 2 1 2 1 101000 r 74 goat snp8409-scaffold1302-842538 19 12347475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416994 Affx-122947991 AX-123287342 19 12222208 ATGAGGCTTGGGATCCTCACCTTTAGGACTACTGA[C/T]GATGTTGGCACTCAGTGAGGACGGGCTCTTACTCA Y 2 1 2 1 101000 f 74 goat snp8408-scaffold1302-777591 19 12412981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436625 Affx-122932501 AX-123306963 19 12277328 CTGCCAGACAACTCCAGTTTAAGGCTCTCTGGGGC[A/G]TATAGTACATTTTGGCTGGATGTGGCTTGAAGAGC R 2 1 2 1 101000 r 74 goat snp8407-scaffold1302-722471 19 12468746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783034 Affx-122930173 AX-385270102 19 12315194 GTCTTCTGGGAGATATTCTCTAATTTATCCTTCAG[C/T]TCTTTTTAATTTTGGATTTTTATTAAGCAGTTTAC Y 2 1 2 1 303000 r 74 goat snp8406-scaffold1302-684605 19 12506579 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798959 Affx-122961768 AX-385285889 19 12355060 TAGACACAGAAATAAAATTACTTCCACATTTTGAC[A/G]CTATAAATGGTAAGTCTACATTTTTTTAGTAAATA R 2 1 2 1 101000 f 74 goat snp8405-scaffold1302-644739 19 12546395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398934 Affx-122960995 AX-123269289 19 12387999 AGCATCTACAACGTGTAAGGCCCTGAATTCTCCTG[C/T]CTCTCTCCTCCCTGCCACCCAGGGAGGCAGGATTA Y 2 1 2 1 101000 f 74 goat snp8404-scaffold1302-611800 19 12579102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449625 Affx-122923194 AX-123319960 19 12416670 GTCCCCTGGACAAGGTTTGAAGTAGATTTATTCTC[C/T]GGGTCACTTCAGCTCTTGGTTTTTGATGTGATGGT Y 2 1 2 1 101000 f 74 goat snp8403-scaffold1302-583129 19 12607644 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414342 Affx-122950028 AX-123284691 19 12448814 CATCCGTCCCTCTGGGGCCCCAGACTCTGATCCAC[A/G]GCTTCTCTCCTCACCAAACCCCCTGCCCTTGAACT R 2 1 2 1 101000 r 74 goat snp8402-scaffold1302-550985 19 12640183 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441442 Affx-122928811 AX-123311779 19 12481205 TTTTAAAAACCTCTCCCAGTTATTTTAATGTGATT[G/T]CATGGGTGTATAGAACCCAGGTGCATTGAAGAACT K 2 1 2 1 101000 r 74 goat snp8401-scaffold1302-518594 19 12672585 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426003 Affx-122941139 AX-123296349 19 12540615 CTAATTCTGCTTCAGCAGGAGGAGGAAGGCTTGAG[C/T]CCAATCCCAGAAAACAGTATCTTCAGGCTCCAGGA Y 2 1 2 1 201000 r 74 goat snp8400-scaffold1302-459184 19 12732255 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451111 Affx-122921390 AX-123321445 19 12585543 CTCGAATAAGACCAACATAAGAACAACCTATAAAA[C/T]AAATAGATTTATTTAACTTTATGAAAGTTATATCT Y 2 1 2 1 102000 f 74 goat snp8399-scaffold1302-414256 19 12777466 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387853 Affx-122969647 AX-123258211 19 12640511 AGTCATTCCATCCCGCATCTTCATTTCTGAACCCC[G/T]AATGGCATCTCAATCCTGCTGGCCCCCCAAGAGCA K 2 1 2 1 201000 r 74 goat snp8398-scaffold1302-359288 19 12832339 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393570 Affx-122965396 AX-123263926 19 12672982 AGCTTTGCAAAGAGTAAAAGTAAAGCTGTTAGTTG[C/T]GTCAACTCTTTGTGACCCCGTGGACTGCAGCCTGC Y 2 1 2 1 101000 f 74 goat snp8397-scaffold1302-326817 19 12864852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783932 Affx-122945499 AX-385270986 19 12705008 TCCATCTGCCTGGGGACTAGAAAGCTTTTAGGTCT[A/G]CTTTTAGTTGTTTTACTAGCTAGTTATGGGACCCT R 2 1 2 1 101000 f 74 goat snp8396-scaffold1302-294791 19 12896622 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766717 Affx-122958074 AX-385254059 19 12742994 AAAATCTAAATATGGAAGGCCTTCTTTGTCACTCC[A/G]TTTCAGGGTGAACCATTAGTGTAAACATTAGGAAT R 2 1 2 1 101000 f 74 goat snp8395-scaffold1302-256805 19 12934519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442551 Affx-122928523 AX-123312888 19 12794147 CTAACTTCAGAGCAACAGGTTCTATGCTAGATCTA[C/T]AATACACATGATTTTTAAAGCTGTTTTTTAACTCC Y 2 1 2 1 201000 f 74 goat snp8394-scaffold1302-205652 19 12985698 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441648 Affx-122929199 AX-123311985 19 12872126 GACTCAGTAAGAAGCCTGAGAAGCAGGGGTATGAA[C/T]GCCTTCATACCCGCTCCAGTTTTGAGCCTTAACCT Y 2 1 2 1 201000 f 74 goat snp8393-scaffold1302-127673 19 13064317 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408007 Affx-122954313 AX-123278358 19 12939147 TACAAGAGAGTCAGTGCTCTCAACTCTGTCCATTG[C/T]GAACATGTGGAAGATGAAGGAGAATCCAGGTAGGT Y 2 1 2 1 201000 f 74 goat snp8391-scaffold1302-60652 19 13131153 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422302 Affx-122943477 AX-123292648 19 12992740 CCGCTCTGTGATACAGGTTTGATGCAAAGAGCATC[A/G]CTACTCACAAATCACGCGAGGTATACAGTTTGTGT R 2 1 2 1 201000 r 74 goat snp8390-scaffold1302-7059 19 13185271 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385088 Affx-122971801 AX-123255446 19 13025160 ACAATTTCCCATGAACTCCTAATTTTTCTTCTGGC[A/G]TCAGGCCCTCTTTGACGTTTACTCTTATTAGCTCA R 2 1 2 1 101000 r 74 goat snp27907-scaffold2992-122037 19 13217805 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424668 Affx-122942149 AX-123295014 19 13054002 TGGTACTTCTTTTCTCATCTAATACCATATCTTCA[C/T]GATCTTTCTATTTTAATGTGTATATTAATAGACCT Y 2 1 2 1 101000 f 74 goat snp27906-scaffold2992-93195 19 13246556 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452229 Affx-122920794 AX-123322562 19 13092842 ACTGCATATATAGAGGGCACCCTCCAAGTGATACC[C/T]GACTGTTTGACTGTGCGGAGGATTGGCACCCCTAA Y 2 1 2 1 101000 f 74 goat snp27905-scaffold2992-54355 19 13285074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426394 Affx-122940849 AX-123296740 19 13133400 GGATCTCTGCCCTTGTACCCTAACATACATACCAC[A/G]TGGAATTAGCAAGTCAACTTTTCTATGTTCCTTTC R 2 1 2 1 101000 r 74 goat snp27904-scaffold2992-13797 19 13325797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376686 Affx-122978991 AX-123247045 19 13149570 GTAACTATTACTATTTTAGACACAACACTCGACCT[A/G]TAGGATTTTAGTTTCCCAACCAGGGATCAAACTTG R 2 1 2 1 201000 f 74 goat snp12035-scaffold1444-2274 19 13342899 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277223 Affx-1111835803 AX-519550729 19 13177462 ACCACTGGACCATCAGTGATGTCCGATAGATTTTT[A/T]AAAATCCAACAGTGTAAATAATTAGTGCCATAGGT W 4 1 2 1 103000 f 74 goat Random2.2K-1781 19 13177462 A T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415532 Affx-122948667 AX-123285881 19 13191417 TAATCAACCTTAGGAAGTTTCAATGTAAGTATCAG[C/T]GTTTTTCTTTAATTTAAAATTTTTCCCATCTTTAT Y 2 1 2 1 101000 f 74 goat snp12036-scaffold1444-44121 19 13384499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393514 Affx-122965804 AX-123263870 19 13227508 CTTTTCTCCCTGCTCTCATCAGGTGGGCTACTCCT[A/G]CCTTCCTTTGGACTGTGGTCTGTTCTCCACCCAGC R 2 1 2 1 202000 f 74 goat snp12037-scaffold1444-80212 19 13420894 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396920 Affx-122963203 AX-123267275 19 13261207 AGAGGCTTCCATTTTTATTATGTTTTATTCCTATC[A/G]TTAATATATGAGAATGTGGTGAAGTTTTGCCAAAC R 2 1 2 1 101000 r 74 goat snp12038-scaffold1444-113911 19 13454877 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794338 Affx-122948951 AX-385281302 19 13308750 CCAAATCAAAACTTGTTCTTAGTTATGTTCAGTAA[C/T]ATAGAACACAGAAGAAATCACTCAAATCAAACAGG Y 2 1 2 1 102000 r 74 goat snp12039-scaffold1444-161454 19 13502492 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404680 Affx-122957280 AX-123275032 19 13361551 TAAAAAAATATTTATCCAAATCTTATGCCAGGCAC[G/T]CACTATTCTATACTTTAGGGATAGTTTGGTAAACA K 2 1 2 1 101000 r 74 goat snp12040-scaffold1444-214255 19 13555481 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454183 Affx-122919305 AX-123324516 19 13390901 GGATGTAGCATAAATGTAACTGCATTAAAAAGGGG[A/G]TTGGATAAGACAAGAAACTCTGAAATTTGAGTTTT R 2 1 2 1 101000 f 74 goat snp12041-scaffold1444-243605 19 13584861 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410685 Affx-122952745 AX-123281035 19 13420692 TCCCTGAGCCTAGATTTCAATAAAAGCTCCAGAAG[C/T]GTGTGGTTTTCGCTTTTTGTTTTCCCAGTATGTGT Y 2 1 2 1 101000 r 74 goat snp12042-scaffold1444-273396 19 13614648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413534 Affx-122950615 AX-123283883 19 13479018 GTTCACTGACAAACACAACCAAGTGTCTACTACCT[A/G]TGAAGTCCTCCGGGGACAGCTGCAAGCTTGGGACA R 2 1 2 1 303000 r 74 goat snp12043-scaffold1444-331722 19 13673203 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381000 Affx-122974668 AX-123251358 19 13510916 GAGCAGTCTGGGTCTCCAGGGAGCTAAGAGAAAGA[C/T]GGCTCTTGAGATGAGAAGGGACTCAAGTTTCTTTT Y 2 1 2 1 101000 r 74 goat snp12044-scaffold1444-363620 19 13704983 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412203 Affx-122950937 AX-123282553 19 13540466 TGAGTTTGGAGCAGGGGGATGACCACCGAGGTGAC[A/G]TAAATTGCTGAAAAGCCCCAGAACTAAGAAAAGAG R 2 1 2 1 101000 r 74 goat snp12045-scaffold1444-393170 19 13734148 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446943 Affx-122924676 AX-123317279 19 13573033 GTTCTTGCATGACGTCACAACTGATGTCAGGGCGT[C/T]GTAGGCCTGGGAGGTCCACGGGGCTGTTTCTAGAA Y 2 1 2 1 101000 f 74 goat snp12046-scaffold1444-425737 19 13766841 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432092 Affx-122936483 AX-123302433 19 13619904 CATGCCTTTCTATTTCCTATATTAGGGCACCTGCA[A/G]ACAACTCAGGCCAAAGTGTATCAGTTCATTAAGGA R 2 1 2 1 101000 f 74 goat snp12047-scaffold1444-472608 19 13813550 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377515 Affx-122977480 AX-123247874 19 13659434 CTGGATGACCACACAACTGTGCCAGATCAGATCAC[A/G]TCATGCACTTAACTCTTCCAGGACAGAGCAGGGTG R 2 1 2 1 102000 f 74 goat snp12048-scaffold1444-512138 19 13853335 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378507 Affx-122976647 AX-123248866 19 13696337 CTCTTGTAGGTGGTGATGTGCTTGTTGGTTGAGAT[A/G]CTCTTTTGCCCAAGACTTTGAAGCAGCTTTGAGGG R 2 1 2 1 101000 f 74 goat snp12049-scaffold1444-549041 19 13890549 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381122 Affx-122974576 AX-123251480 19 13757363 ACTCAGCAATATTTCCAATTCAGTGTCAATTCTCC[A/G]AACTGGGGAAGAACTCTGCCCCATTTTAGCAGAAG R 2 1 2 1 101000 f 74 goat snp12050-scaffold1444-610067 19 13952785 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272940 Affx-1111833131 AX-519546626 19 13784900 AGTGTCCTCTCTGAACTACACTGAAGCAGCTGTGC[A/G]TCCGTTTCTTTTATGAAAGTGTTGCCATGGTGTTT R 2 1 2 1 201000 r 74 goat 19_13784900_AF-PAKI 19 13784900 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449787 Affx-122922428 AX-123320122 19 13787328 TATTTCAGCCCATGATCTCTCTGACTCATGTCATA[A/G]GAATGCTTGATTGAAGGACTGTCAAGGAGAAATGG R 2 1 2 1 101000 r 74 goat snp12051-scaffold1444-640032 19 13982914 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419234 Affx-122945678 AX-123289582 19 13840393 GCTACACCCCCAAAGACGGATGTTCTCTTTGTTCT[A/G]GGAACTGATCGCACACTGGAAGACCCATTCCCTCC R 2 1 2 1 201000 r 74 goat snp16825-scaffold1762-4997 19 14140266 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398953 Affx-122960981 AX-123269308 19 13898134 CACCTTAACCAGAATATGTTAATAATTATGATATT[C/T]TCAACATAAGCCAACTTCTTACTCACCTTGATGAT Y 2 1 2 1 101000 r 74 goat snp16826-scaffold1762-62738 19 14197990 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413595 Affx-122950571 AX-123283944 19 13982772 GAAGCAACAGCTGAGGCTCAGGCCCTAGAAACGCC[A/G]CCCTCCTAGGCTGGTTCTCATCTGGCATTGCGGAA R 2 1 2 1 101000 r 74 goat snp16828-scaffold1762-147376 19 14281227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423394 Affx-122943123 AX-123293740 19 14011501 TACTTACCCATTTTGCCATCTTCTACAAAAAGCAC[A/G]TTGAGTGGGATGAGGCAGCTGAAGTAGAAGACATC R 2 1 2 1 101000 f 74 goat snp16829-scaffold1762-176105 19 14309924 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377238 Affx-122978156 AX-123247597 19 14046967 TATCACATTCACCAGCACATGTTGTATCTCTATAG[A/C]GTGTATGCAAGGCTTACACACATGGGTGCCAGGTC M 2 1 2 1 201000 f 74 goat snp16830-scaffold1762-211571 19 14345085 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377084 Affx-122978275 AX-123247443 19 14104250 CTAACATTTACTCTCAAGAGCTTCCCCCTCTCTCA[C/T]ATCGGGTCAATTCTCTGGGTTTTTTTTCCCTAAAA Y 2 1 2 1 201000 r 74 goat snp16831-scaffold1762-268854 19 14402172 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437739 Affx-122931728 AX-123308077 19 14134630 TTTGGGCAAAGGACACAGCAAATAGAAAGGCATGG[A/C]GATGAATCAGAATGGTAGGTCTGCCTGGAGCAGTG M 2 1 2 1 101000 f 74 goat snp16832-scaffold1762-299234 19 14432918 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376136 Affx-122978862 AX-123246495 19 14164571 CCAGCTAGGAAAAATATTTGCAACTGATATTACAG[A/G]GGGCCAGTGTCTCTCATATATAAAGAGCTTCCAAA R 2 1 2 1 101000 r 74 goat snp16833-scaffold1762-329175 19 14462907 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417656 Affx-122946841 AX-123288004 19 14211483 TGAGTTGAAGGAAATATGTATGTGGAGTTTGGCTG[A/C]TTTTCTGCAGTTTCATCTTAGATCTTCCCTCTCGA M 2 1 2 1 201000 r 74 goat snp16834-scaffold1762-376087 19 14510673 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449318 Affx-122922997 AX-123319653 19 14260011 GCTGGCGATCCTCCTATATTATCGCTGGAGAGTAT[A/C]TTTCTCTCTCCTGCTGGAGATAAAACCATGATGTG M 2 1 2 1 101000 f 74 goat snp16835-scaffold1762-424615 19 14560019 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386654 Affx-122970205 AX-123257012 19 14305157 CACTGGGGAGCCTGTGGATGCCTACTGCCTGCATC[C/T]TTAGCTCTAGTGCATGGGTTAGGAGAGAGGGCGTG Y 2 1 2 1 101000 r 74 goat snp1636-scaffold1046-1612947 19 14606685 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775361 Affx-122927730 AX-385262492 19 14338038 GCATTCTCCTTAAACTCTAAATTATAACTCAATTC[C/T]GTATTGCAGAGGTTATGAGATTTTAAGGTGCAGAG Y 2 1 2 1 101000 r 74 goat snp1635-scaffold1046-1580066 19 14640015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411961 Affx-122951137 AX-123282311 19 14367537 AGTAAGGTAACACACCATCCTCCCTGCAGTGGGAC[A/G]AGGTTCTTTCATGAAGCTTAATGGAAACATCATAT R 2 1 2 1 101000 r 74 goat snp1634-scaffold1046-1550567 19 14669456 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415949 Affx-122948434 AX-123286298 19 14408369 TTTGCCTAAGTCTCTGTGTCTTCAAGTGAAACCAT[A/G]TTTAAAACCTCCATGGGCAAGAGGGACCTCGTGCT R 2 1 2 1 201000 r 74 goat snp1633-scaffold1046-1509735 19 14710327 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398491 Affx-122961569 AX-123268846 19 14456418 CATCATCTCTAATCTGGACTACTTAGCATCCTACT[A/G]TTTCTGAATTGGAATCTACCCTCCACACTTCATTT R 2 1 2 1 101000 f 74 goat snp1632-scaffold1046-1461686 19 14758243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396488 Affx-122963541 AX-123266843 19 14487081 TCTTCATATATATTAGAATATCAGATAAAACATAA[A/G]GCACTGCTTTCCAGTCTTGTGAAAACACACCCATA R 2 1 2 1 101000 r 74 goat snp1631-scaffold1046-1431023 19 14789054 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379652 Affx-122975941 AX-123250010 19 14517365 TACAGATGAGAGCTCTCCTAAGAGGGGCCATGGGA[C/T]TGTCCAAAGCCATGCGGATAGTAAGGCATTTTAAA Y 2 1 2 1 201000 r 74 goat snp1630-scaffold1046-1400739 19 14819267 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398205 Affx-122962225 AX-123268560 19 14546063 CGCTCTACAGACGTTAACCCTAGCACTGCCACTGA[C/T]GCAGGGGTGACTGTGTCCAGGTCACATCGCCTTCC Y 2 1 2 1 101000 f 74 goat snp1629-scaffold1046-1372041 19 14847939 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447406 Affx-122924404 AX-123317742 19 14577961 GGCAAGCCGGGCCCTAGCCTACCCCTTCCCTGTGC[A/G]CAAGCTTCATGCCCAGGCAGTGCAGTGAGCGGTGA R 2 1 2 1 101000 r 74 goat snp1628-scaffold1046-1340143 19 14879682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427927 Affx-122939220 AX-123298270 19 14616894 TCCTTGAAATGTGTTGAAAGAATTCTAACCTCTGC[A/G]GACACAGGAAAATCCTCCATGTCAAATGACCTGTT R 2 1 2 1 101000 r 74 goat snp1627-scaffold1046-1301210 19 14919165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440860 Affx-122929250 AX-123311197 19 14655526 CAGGCCATGGGCCGCTGGAAAACCAAGCAAGGGCT[C/T]TCCTCAGAGGTGGCCAGCCCGGGAAGGCCCTCCCT Y 2 1 2 1 101000 f 74 goat snp1626-scaffold1046-1262578 19 14957080 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395718 Affx-122963714 AX-123266073 19 14695781 TGCCAAGCACTGTGCAGGTGATTGATGCCAGTTGT[C/T]TCATTCTAGCTTCAAAAGACGACACTAAAGAAGCT Y 2 1 2 1 101000 r 74 goat snp1625-scaffold1046-1222323 19 14997340 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277350 Affx-1111835804 AX-519550854 19 14714232 TTTTCTTTTTTTAAAAAAAGCTTTTCAAAGGAAAA[A/C]AAAGGTCAAAACCAGCACCCAGATCTGAAAGACCT M 2 1 2 1 103000 r 74 goat Random2.2K-1782 19 14714232 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413696 Affx-122950091 AX-123284045 19 14736176 CTACATTGGAGTGCAGAGTCTTAGCCACTAGATCA[C/T]CAGGGAAATCCCCCAGAACCAACCTCTTAATTGCT Y 2 1 2 1 101000 r 74 goat snp1624-scaffold1046-1181928 19 15037976 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800118 Affx-122930316 AX-385287041 19 14782955 TGAATGAAGAGGAGCCATTCCTTATGCCTAGGATC[A/G]TCTTGAATGCTAAAAGGAGATGACATTCCAACAAA R 2 1 2 1 101000 f 74 goat snp1623-scaffold1046-1135149 19 15082589 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385382 Affx-122971624 AX-123255740 19 14871911 CCCTGCCCAATTTTGCTTGCTTATCTTACACAGGA[C/T]GCCTAGGGAGTTTGGAGGGGGTCCATCAAGAACAC Y 2 1 2 1 101000 f 74 goat snp1621-scaffold1046-1046193 19 15171846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403839 Affx-122957942 AX-123274191 19 14904515 CTCCGGACCCAGGGAACAGGAGGAAAGGGAAGACA[C/T]GGCAAACTCAGCCTCCAGGGGAGAATGCCTAGATC Y 2 1 2 1 102000 f 74 goat snp1620-scaffold1046-1013589 19 15204855 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448955 Affx-122923136 AX-123319290 19 14944573 GTCTGGGGCCATTTACATATCTTCAGCATCTCAGG[C/T]AGCACCTAAGGTCTACAGTGGAAGGAGTCTGGGGC Y 2 1 2 1 101000 r 74 goat snp1619-scaffold1046-973531 19 15244835 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408953 Affx-122953927 AX-123279304 19 15030557 TGTTTTCCACCATTATCTGGATTACTATTAATATG[C/T]ATGGTCAGTGTACCTTCCATGGGGGTGGAACACAG Y 2 1 2 1 201000 f 74 goat snp1617-scaffold1046-887547 19 15326928 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783502 Affx-122971121 AX-385270565 19 15060421 GATGTATTGAAGGGGATGGATAGAGCATGCATATC[A/G]TCACGAGGATGTGAAATGAGATATTTACTCAGCAA R 2 1 2 1 201000 r 74 goat snp1616-scaffold1046-857683 19 15357110 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399003 Affx-122960944 AX-123269358 19 15097422 AGGATTCCTGTCTTTCCCTCTGCTTCGGAACCAAG[C/T]ATCACACAGGACAGTGTGTTTTGTGTTTTAAAAAA Y 2 1 2 1 102000 f 74 goat snp1615-scaffold1046-820682 19 15394183 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384081 Affx-122972856 AX-123254439 19 15140368 AACAATTTGCTACAAACCACATAACAGGTAAATAG[C/T]GAATACAGGATTTAAGTCCCTGTCTGGCTGACTCC Y 2 1 2 1 101000 f 74 goat snp1614-scaffold1046-777736 19 15437181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777361 Affx-122936122 AX-385264483 19 15195470 TTCTTCTAATTCAAGGACAAATTGTAAAGAACATA[C/T]GAGATCAGGTTCAAACTGGTCAGGAAATTCTAAGG Y 2 1 2 1 101000 r 74 goat snp1613-scaffold1046-722634 19 15493669 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448052 Affx-122923698 AX-123318388 19 15227126 AACTAGAAACCCAGGCCACTGAACTGGTCTTCCTG[C/T]TCCTTCCTGACATGAATATTGAGAGCAATGTTGTG Y 2 1 2 1 101000 r 74 goat snp1612-scaffold1046-690978 19 15525859 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435912 Affx-122932765 AX-123306251 19 15273749 GTGTCTCCTGAGAGCGCTGAGGTTGCGGCAAGAGA[C/T]GTCAGAGAATGGTGAAGATTTGAAAGCCATCGTGG Y 2 1 2 1 101000 r 74 goat snp1611-scaffold1046-644355 19 15571794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377077 Affx-122978280 AX-123247436 19 15309590 GGACAATGTGCTATAACTCCCATCCCCCACAGAGA[C/T]AGAAGGGTAACTGCCTCCAAGGATTACAATGCCCA Y 2 1 2 1 101000 r 74 goat snp1610-scaffold1046-608514 19 15607571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397778 Affx-122962512 AX-123268133 19 15361404 GAGAATGTCCCTGATGGGGGGTTTCATCACAGAGC[A/G]CTTGGGTCTATACTTGACACTGTGTGGATATTATC R 2 1 2 1 101000 r 74 goat snp1609-scaffold1046-556700 19 15659938 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391899 Affx-122966957 AX-123262256 19 15393171 ATGTACTTCCTGGGGAGGCAGAATCGGGGAGTGAA[C/T]GGACCATCAGGCTGGAGACTTTGGCAGTTCCTTTA Y 2 1 2 1 101000 r 74 goat snp1608-scaffold1046-524933 19 15691770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409593 Affx-122953565 AX-123279944 19 15464886 GAATCATTAAACTACCTTGGGAGAACATGTCAAAG[A/G]GTGGATTAGACAGATAATCAATGTGTAATTGTTGG R 2 1 2 1 101000 r 74 goat snp1607-scaffold1046-453218 19 15762962 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426373 Affx-122940245 AX-123296719 19 15508924 CTGTTTCCTTGCTATGAAGTAGGCATACTGGTGCA[C/T]ACATCAGAAAAAAAAATTAATATAACATGCCTGGC Y 2 1 2 1 101000 f 74 goat snp1606-scaffold1046-409180 19 15807327 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776302 Affx-122952751 AX-385263430 19 15545827 GTGTACACGTTATTCAAAAACACAATATGCAGACA[C/T]GATGGTAATTGGTTTCTAGTTGCCTGGAGATTCCA Y 2 1 2 1 101000 r 74 goat snp1605-scaffold1046-372277 19 15844214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414690 Affx-122949287 AX-123285039 19 15574426 AACAAAACTATGTACAGTATCATCTATATAAAATG[A/C]TTCCAAAATTGGAAGAAAATATAACTTCTTAAGAG M 2 1 2 1 303000 r 74 goat snp1604-scaffold1046-343678 19 15872838 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443396 Affx-122927391 AX-123313733 19 15704843 CAGCACGATGTTTAAATAGCTATCAGTGAACACGG[C/T]GTTGTACCCATGAGAGTGCTGAACTTCCTGCTCCG Y 2 1 2 1 101000 f 74 goat snp1601-scaffold1046-213261 19 16001289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277227 Affx-1111835805 AX-519550733 19 15732554 TTAATAGCAACTGCTTCGGAGAATTATGATGCCAG[A/G]AGCCTTACCACACCACGGAGCCGAGTATAAATGAT R 2 1 2 1 201000 f 74 goat Random2.2K-1783 19 15732554 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406600 Affx-122956253 AX-123276952 19 15736340 GTTGATGAGGTGGTCACCTAATTTTACTCCTAGAA[A/G]ATGAAATCATTGAAATAAGGACATGAAAGCCCTGG R 2 1 2 1 101000 f 74 goat snp1600-scaffold1046-181764 19 16033149 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439864 Affx-122930053 AX-123310201 19 15765862 ACAGCAAGTTCAGGGCAGAACCGGGGAAGAAGTCC[A/G]TCTTCGGACTCCCAGGGAGCATAGCAGCACACTGC R 2 1 2 1 101000 f 74 goat snp1599-scaffold1046-152242 19 16062548 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773986 Affx-122921116 AX-385261124 19 15802163 CCTCAGTGAAGTAAACTTCTGAAATAAAATGAGAC[A/G]TTCTTATCCATGCCAAGAATGGCTAAAAAGACTGA R 2 1 2 1 101000 f 74 goat snp1598-scaffold1046-115941 19 16100638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434769 Affx-122933893 AX-123305110 19 15866656 TGCTTCCTACAACCCACCAATCCATCTTTCTGAAA[C/T]GTGAACTTAAGCACACCTTTCTCCCTCTTCAAATC Y 2 1 2 1 101000 r 74 goat snp1597-scaffold1046-51448 19 16165281 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277354 Affx-1111835806 AX-519550858 19 15888221 AGGCGCCAGGGAATAGGAGGAGTCGGATCTGGTCC[A/C]AGCCTTTCTCAGCTGACGTGCTGTGTGACCTTAAA M 2 1 2 1 102000 r 74 goat Random2.2K-1784 19 15888221 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38379755 Affx-122975858 AX-123250113 19 15917359 CACAGCGGAGTTAAGCCTTGAAGGATGGAATGAGA[C/T]GCTCCTAAATGGAGAAGTGGGGGCAAAGGAGAGCA Y 2 1 2 1 101000 f 74 goat snp1596-scaffold1046-745 19 16216207 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443907 Affx-122927052 AX-123314244 19 15945080 TGTCAAATGAAGCCAGGGCACCTGTCCTGGCCCCA[C/T]GCAGGGCTGTTGTGTGAATCCATTGAGACCAGGCA Y 2 1 2 1 201000 r 74 goat snp4865-scaffold1163-26877 19 16243486 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273714 Affx-1111833758 AX-519547326 19 15975543 ACTGGGCTGCAGACAGAACTAGGAATCAAAGCCAC[A/G]GTTTCTAGACGTGGAGAACCTCCTTTGTACCTTTT R 2 1 2 1 201000 r 74 goat GoatD01.003727 19 15975543 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320788425 Affx-122977734 AX-385275442 19 15994089 GGAATGAAACATGATAATTAGTAACCAATTAATGC[A/G]CATTTCAACAAACTATATTTTAATTATTCTGTCAT R 2 1 2 1 101000 r 74 goat snp4866-scaffold1163-75886 19 16292457 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413553 Affx-122950602 AX-123283902 19 16029304 AGAGTAAGACCCCAAGGGGGTAAAGGGCTTCTCCA[C/T]GGCCACACAGTCACACCATCAAATAGATGACAGAG Y 2 1 2 1 101000 r 74 goat snp4867-scaffold1163-111101 19 16327676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417200 Affx-122947312 AX-123287548 19 16080877 TCAGACACAACTGAAGCAACTTAGCACGCACACAC[A/G]CACAGGTTAAGCTGCTCTTATAAAGGGGTGCCTTC R 2 1 2 1 101000 r 74 goat snp4868-scaffold1163-162674 19 16379273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397573 Affx-122962008 AX-123267928 19 16116943 TCTGTCAGATGAATCCCAGGACCCTGCCAGGATAA[C/T]ACATAGGCTGGGGTTCCAATCCAAATGGCTACCAA Y 2 1 2 1 201000 f 74 goat snp4869-scaffold1163-198740 19 16415124 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785922 Affx-122942473 AX-385272959 19 16158606 GGGAAACTTCTCAGTCTAAGATTTCTTTTTTCACC[A/G]TCATCTTCATTGACAAGGTCATTATTCAACAGATA R 2 1 2 1 101000 f 74 goat snp4870-scaffold1163-240403 19 16458062 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428169 Affx-122939035 AX-123298512 19 16188145 TGGGGGGAAAGGGAATAGAGGGAGGGCATTGCCTT[A/G]CTTTCAGTAGGCCAGATTGGCTGCCCAGGGCCTTT R 2 1 2 1 101000 f 74 goat snp4871-scaffold1163-269942 19 16487535 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380487 Affx-122975712 AX-123250845 19 16217489 TAGAGACGCTAACCCAGGGAGTGGAAAGAGGAGAG[A/G]TGAGACACAGGAAGAAGCCTAGGGGAGAGGGCCAC R 2 1 2 1 201000 f 74 goat snp4872-scaffold1163-299286 19 16517300 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426600 Affx-122939977 AX-123296946 19 16249572 AACAAGGCTAAACAGCTGGTCCAAGGTCAAAGGAC[A/G]ACTGTTACGGACTCAGCCAAGGCTTGAACTCAAGT R 2 1 2 1 101000 r 74 goat snp4873-scaffold1163-331369 19 16549290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780158 Affx-122922595 AX-385267255 19 16281856 TCATGATTTGGTGGGAAAACAGATATGGGAGCATG[C/T]ATTGACACCGTGAAATGGTTTGTGTCATGGTGTAA Y 2 1 2 1 101000 f 74 goat snp4874-scaffold1163-363653 19 16581611 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272942 Affx-1111833132 AX-519546628 19 16290246 GTCTCAGGGCCTCTAGGGTGAGCAGTTCACATAAG[A/G]CAGGAAGATACTGGATCCCATTATCATCCAAGTTG R 2 1 2 1 101000 r 74 goat 19_16290246_AF-PAKI 19 16290246 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38391984 Affx-122966509 AX-123262341 19 16330906 TCTTTTATTGATTTTTTTTCCACTCATATTACCTC[A/G]TTCAATCATTGCAGGAACACTGTGGCTTTTGCAGA R 2 1 2 1 101000 r 74 goat snp4875-scaffold1163-412703 19 16630496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376248 Affx-122978776 AX-123246607 19 16369220 AATATACTTAAACCACAAATATAAAATAAATTACA[C/T]TTAGACGCTGCTTAAAAACGTTTGCATGGTTAAGA Y 2 1 2 1 102000 r 74 goat snp4876-scaffold1163-451017 19 16668595 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404970 Affx-122956410 AX-123275322 19 16397956 CATTTCAGCCCTGGGAACGTCTCATTTTCCACCCA[A/G]TCAAAACTGTCTTTGTTCTTCAAACCTGGACCCAT R 2 1 2 1 101000 r 74 goat snp4877-scaffold1163-479753 19 16697058 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795130 Affx-122978240 AX-385282088 19 16478978 ATGCTGGTTTTGAGTTTCTATGAAAGAAGCTGACC[A/G]TAGAAAGCCCAGTATAGACCTGCTGGGTCTAAGAG R 2 1 2 1 101000 f 74 goat snp4879-scaffold1163-560775 19 16778261 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422392 Affx-122943391 AX-123292738 19 16518853 TAATTAAAATTCAATTGGCTAAAAAGTAAATAGAT[A/G]AATAAACCAGCCCAGGAAAAGGTAAATATGTGCAG R 2 1 2 1 201000 f 74 goat snp4880-scaffold1163-600650 19 16817630 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389458 Affx-122968341 AX-123259816 19 16552043 TTATTTTTTTTAAGCCAACATCATGCGATATAAGC[A/G]TGTATCCTTACTTAATAGTCTGTTGAAAGCATGTT R 2 1 2 1 101000 r 74 goat snp4881-scaffold1163-633840 19 16851224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421028 Affx-122944540 AX-123291375 19 16574994 AGGAAGTATTGCAAGCGAAGCTTTTCCCACCTATT[G/T]TCTCATTTTACCCTCAGGGCAGCCCTGCTCCTCAC K 2 1 2 1 101000 f 74 goat snp16481-scaffold1738-740 19 16873893 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770664 Affx-122965072 AX-385257828 19 16605393 AGAACCTTGGAAATGGGATTTCATCAGATTATCCT[A/G]TACATGTGGAGATCACAAGGGCCTAGGAGACCTGC R 2 1 2 1 101000 r 74 goat snp16482-scaffold1738-31139 19 16904197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394100 Affx-122964946 AX-123264455 19 16636797 CACAGTTGTTTGTTATGCAGCAACATCACTGACTA[C/T]GCGGTGTCTTTTGAGGGGCCTTTTCAAAAAGTGCC Y 2 1 2 1 101000 r 74 goat snp16483-scaffold1738-62543 19 16935472 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380671 Affx-122975185 AX-123251029 19 16681741 GTCCTTTACCTTTTTCTACATTCTTCTGAGTTAAT[A/G]TCTCCCTCTATATTGGAGAAGTCCCATCAGTCAAT R 2 1 2 1 101000 f 74 goat snp16484-scaffold1738-107487 19 16979792 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389244 Affx-122969037 AX-123259602 19 16761890 GGACTCAGAGCAGCAGAAGCCAGGAGACTTTCCTC[A/G]TTCTCAGTCCTGCAGTTTCTCCCTGCCCCCACCCC R 2 1 2 1 101000 f 74 goat snp16486-scaffold1738-187636 19 17059401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436209 Affx-122932586 AX-123306548 19 16815911 CCCTTGGCAAGGGGTGAACAAATCAGTTTCATCAG[C/T]AGGAAAGAAGTAGGGCTGGAAAATGCCCCTTAGGT Y 2 1 2 1 201000 f 74 goat snp16487-scaffold1738-241657 19 17113547 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788635 Affx-122967197 AX-385275652 19 16857903 TTTTTCAGTGCTGAAATGTGATAAAACCTACTATA[A/C]TTCTGAATTTGCCTACTTCTTAATATGCCTTCCAT M 2 1 2 1 101000 r 74 goat snp16488-scaffold1738-283649 19 17155640 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407265 Affx-122955346 AX-123277616 19 16887268 TTCACCCCACCAAACCACCCTAAACCTTAGTGGCT[A/G]CAGCAGTCAATATTTATTTATTCTTCATGCATCCA R 2 1 2 1 303000 f 74 goat snp16489-scaffold1738-313014 19 17184784 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422462 Affx-122943336 AX-123292808 19 16952599 TGCTTTATTGACCACAGTAGATCTAGTGATCAAAA[C/T]AATCCAGGAGCTATATCTTCTAAATTTGCATATAA Y 2 1 2 1 101000 f 74 goat snp16490-scaffold1738-378345 19 17249946 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446219 Affx-122925708 AX-123316555 19 16981838 AGATTCCTAAATGCACTGTCCTTTGTTCAGTTTCC[A/G]TCTTGGATAGAAGAGTCAGAAGGTCAGGAGGTCCA R 2 1 2 1 201000 r 74 goat snp16491-scaffold1738-407584 19 17279151 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421101 Affx-122944219 AX-123291448 19 17014798 GGCAGAGCTTGGAGCGGAGGGATGGTTTCCATGGC[A/G]ATAGCATCAGCATCTGAATGACTTCCTGTCACAAC R 2 1 2 1 101000 r 74 goat snp16492-scaffold1738-440544 19 17310840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378553 Affx-122976610 AX-123248912 19 17045087 AGATATTCCGCACTGTGGATTACGGTTGCCTGGAT[A/G]GGCTGCGAGGCTTAGTGAGAGTGAGGTGGAAAATG R 2 1 2 1 101000 f 74 goat snp16493-scaffold1738-470833 19 17341304 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425486 Affx-122941488 AX-123295832 19 17075612 TCCCATCCGTCCCATTTCTAAGAGGTAAATAAAGA[C/T]GCTCCCTGGGAGGGGGACATGAGGTTGCTCAAAAA Y 2 1 2 1 101000 f 74 goat snp16494-scaffold1738-501358 19 17371808 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765713 Affx-122937110 AX-385253175 19 17111714 TGTTGGTTATCCAGTTTGAATATAGCATTGTGTGC[A/G]TGCATTTTGAGTGATATTGAATTGCTACTCTAGAT R 2 1 2 1 101000 f 74 goat snp16495-scaffold1738-537460 19 17408123 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781673 Affx-122973210 AX-385268757 19 17144998 TCTAGCTTCCAAGTGGTATGTCAAGGTGACAAAGT[A/G]CACTATTACTTATGCAAGAAAGCTTTACTTTAAAA R 2 1 2 1 101000 f 74 goat snp16496-scaffold1738-570744 19 17441258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384229 Affx-122972375 AX-123254587 19 17214591 ATTTTAACTATTTCTCCCTGGAACTCTTTCTACAA[C/T]GCATAATTCACGTCCCTAGGTTCTTAATTTTAAGG Y 2 1 2 1 101000 r 74 goat snp16497-scaffold1738-640337 19 17510648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784466 Affx-122927346 AX-385271515 19 17274951 TTTTCTCTTTTGATTGAAAGGGCTATAAAATTCAA[C/T]GTACTGACAAAGGAAGCAACATAATCACACGAGTG Y 2 1 2 1 101000 r 74 goat snp16498-scaffold1738-700697 19 17571087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390641 Affx-122967148 AX-123260998 19 17386027 CCCCTGGTCCCCGCCTGGTTCCTCTCCCAGATCTC[A/G]CTCTGCCTTAACTTCTGCTCTGTCCCAACCAGAAG R 2 1 2 1 101000 r 74 goat snp16500-scaffold1738-811773 19 17683289 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797277 Affx-122947134 AX-385284216 19 17425282 CATTATTTCTACATAAATTAAGTGGGGGTGGGATG[C/T]GGGGTAAGCTTACAAACAATCCAACTGAAGAAAGT Y 2 1 2 1 102000 r 74 goat snp16501-scaffold1738-851028 19 17722582 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409093 Affx-122953327 AX-123279444 19 17499009 TCATTGCCTGGCTGGGAAGTAAGATCCTGCAAGCC[A/G]TGTGGTATGCCCCCCACACCCTGAAAAAATATTCA R 2 1 2 1 103000 r 74 goat snp16502-scaffold1738-924755 19 17796436 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423809 Affx-122942806 AX-123294155 19 17540289 AATCCATGAAAGTGTATGCTAAAAAAATACAGGGT[A/G]GGAGTCCTGAAGGGCATTTCTAGAACGGTACTAAG R 2 1 2 1 201000 f 74 goat snp16503-scaffold1738-966035 19 17837581 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391257 Affx-122967370 AX-123261614 19 17587081 AGATCTTGCCTCATTGGGTTTTACAGGGGATTACA[A/G]TACAGTACAGATCACTTAGAGGTTCATATCAATGC R 2 1 2 1 101000 f 74 goat snp16504-scaffold1738-1012827 19 17884341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379591 Affx-122976029 AX-123249949 19 17631830 TCTTTGATGCTGGTCTGTCCACTTAGCTGTCTCCA[C/T]GTCTCAGAGTCCCCTTGGCCTTACTCAGGCCTCGT Y 2 1 2 1 101000 f 74 goat snp16505-scaffold1738-1057576 19 17928782 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443846 Affx-122927528 AX-123314183 19 17672515 GAGGAGGGCTGCCAACCAGTTTCAGCCTGTGACAC[A/G]GATGAGACATAAACCTTTGTGTGTTAAGCCGCTGA R 2 1 2 1 101000 r 74 goat snp16506-scaffold1738-1098261 19 17969465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382927 Affx-122973388 AX-123253285 19 17734527 TTACTCTCAGTTTTGTTGAGCATGTTCTCATATTT[A/G]TTTCACATTTGTCTTTTCAGTGGGATTCCTGTTTT R 2 1 2 1 101000 r 74 goat snp16507-scaffold1738-1160273 19 18030277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431642 Affx-122936134 AX-123301983 19 17770416 CTGATTGGAAAACTGCCCACTATGTGGAGCTCCTT[C/T]TGGGCTCCAGACAGTGAGAAATGACCCCTCCTTCT Y 2 1 2 1 101000 f 74 goat snp16508-scaffold1738-1196162 19 18066245 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397758 Affx-122962526 AX-123268113 19 17814265 GACAGAAGGAAGGAGGGGTGCTTCTCAAAAGAAAG[C/T]AGGACTGCTGTTGGACAGGTAGCTTCCACGATGCC Y 2 1 2 1 101000 f 74 goat snp16509-scaffold1738-1240011 19 18110358 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381043 Affx-122974634 AX-123251401 19 17851774 TGTTCCCCAAGATGGCTCCTGTTTGGGTGGATATC[A/G]TATGGGGGAAAGATTGATCTCCTGAAAAGAAGCCT R 2 1 2 1 201000 f 74 goat snp16510-scaffold1738-1277520 19 18147730 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386842 Affx-122970084 AX-123257200 19 17901963 GATTTTAGGCATTCATCAAAGGTGTGCTGCCTGAA[C/T]GAGTCATGCACCCTGGGCCTGCTCTGCCTTTTCAG Y 2 1 2 1 101000 f 74 goat snp16511-scaffold1738-1327709 19 18196923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408725 Affx-122953418 AX-123279076 19 17962847 CACTTCCAATGGCTCTATTATTCAATTGCAGGCGC[A/G]TCTCTTCTGCTTGGCCCTAGCTCCAGTCTCCAGCA R 2 1 2 1 102000 f 74 goat snp16512-scaffold1738-1388593 19 18256215 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375857 Affx-122978518 AX-123246216 19 18003126 TGCCACTTGTCCACTTCTCTTCTTGATCTCCAGAT[A/G]TGTGTTTTCATTTATCTCTTAGATATACATTCCGA R 2 1 2 1 101000 f 74 goat snp16513-scaffold1738-1428872 19 18296615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273689 Affx-1111833781 AX-519547301 19 18041412 CTACCAGGAAGCCTAGCACGGGCCTCACAGTCCTG[A/C]CTGGCCTTGACACACACCTCCCACACCCCCACAGG M 2 1 2 1 202000 f 74 goat GoatD01.004687 19 18041412 G T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320785701 Affx-122960472 AX-385272742 19 18070992 ATTAAATAGACAAAAGGATAAACTATAGTGCTCTA[C/T]AAAACAATACACCTGTCACCATATTCCATAAATGT Y 2 1 2 1 101000 r 74 goat snp16515-scaffold1738-1496738 19 18364584 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427500 Affx-122939999 AX-123297843 19 18103863 TACTTATTAGGCAACTCTAATCCCAGTGAGCCCCA[C/T]GTGCCAAGTCACTTTAAAAATGTGTAACGTGCATA Y 2 1 2 1 101000 f 74 goat snp16516-scaffold1738-1529609 19 18397225 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444147 Affx-122926794 AX-123314484 19 18233882 ACAAAGCCAATAGCAGTATACAGAGAGATACATCT[A/G]TGAGAGAAGTTTCCAATCTCTGCCGGCTGGTGACT R 2 1 2 1 201000 f 74 goat snp16518-scaffold1738-1659628 19 18527831 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453858 Affx-122919531 AX-123324191 19 18305633 CAGCTTGGGTTTCAGATTTCTTGTGCATGCATGCG[C/T]GCTAAGTTGCTTCAGCTGTGTCTGATTCTTTGCAA Y 2 1 2 1 103000 f 74 goat snp16519-scaffold1738-1731379 19 18599591 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435202 Affx-122933636 AX-123305542 19 18357354 GACCCTTTTGCTTTTCTCATTCTTAGTTTCAGCAT[A/G]TATATGTTGCTTCAGTAGAGCCGCAATATATATCT R 2 1 2 1 201000 r 74 goat snp16520-scaffold1738-1783100 19 18650848 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377470 Affx-122977511 AX-123247829 19 18401091 AGGGGCACAGGTATATAGAGAGACACCCCAGGTCA[C/T]GCTGCTGGTTCCTGGCAGAGTTAAGACTTGAATCC Y 2 1 2 1 201000 r 74 goat snp16521-scaffold1738-1826837 19 18694955 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410470 Affx-122952210 AX-123280820 19 18435325 CAGGGAGTGGTTGCTCTGCTGAGTTTGGTCAGAGA[C/T]AGCCTCTCTGGGAAGGCAGCATCTGAGCTGAGAAC Y 2 1 2 1 201000 f 74 goat snp16522-scaffold1738-1861071 19 18728303 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776953 Affx-122924237 AX-385264077 19 18465930 CTAATAGAAATCATAATGTAAGTTCATAGCACGTA[C/T]GTACCTCACTGTAGCCAATGAAAGCATGCTGCACT Y 2 1 2 1 101000 r 74 goat snp16523-scaffold1738-1891676 19 18758922 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414481 Affx-122949551 AX-123284830 19 18517509 TTTGGAAAACAGAGAGGTAGAAGAAAAGATTCCCT[A/G]CAGCCCTCCCTCCCCACCCCCCATACTCAACTCAC R 2 1 2 1 101000 f 74 goat snp16524-scaffold1738-1943255 19 18810389 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442999 Affx-122928183 AX-123313336 19 18559124 CTATGGGGTTGCAGAGACACGACTGAGTGACTAAT[A/G]CTACTTTCTGAATAAACTCATAGGAGTTGGAAGGC R 2 1 2 1 101000 r 74 goat snp16525-scaffold1738-1984870 19 18849522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378671 Affx-122977082 AX-123249030 19 18612769 GTGTTTGCAAAGATTTACATGTTTTCCCTTAAGCT[A/G]CAGTGGAGGGTGGGCTCCCCGCTGGTGCTAGTGGT R 2 1 2 1 103000 f 74 goat snp37158-scaffold452-23542 19 18901574 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382047 Affx-122974938 AX-123252405 19 18655606 TTCCATTCCACACGATTTTACACTATCTGCTTTTC[A/G]TCACCTGTCACAATTTGTTTTAAAACTGGAATATT R 2 1 2 1 103000 f 74 goat snp37159-scaffold452-66379 19 19139852 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383114 Affx-122973267 AX-123253472 19 18689318 CATTTGTAACGGAACAGGGCCAATGGAGGCTTCCC[A/G]TGACAGACCCACCCCTACCTCCCTGTCTGTAGTAA R 2 1 2 1 10000 f 74 goat "snp37160-scaffold452-100091;SV_184:SV_185" 19 19174515 G A SV_184:SV_185 1 preexisting CNV preexisting neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437238 Affx-122932023 AX-123307576 19 18820151 GCAATGTTTGACATTCCCACCAGCAGTATATCAAC[A/G]TTCCAAGCTCCACAAGCAGTGGTTTCTAACACAGC R 2 1 2 1 201000 r 74 goat snp37162-scaffold452-230924 19 19306820 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396435 Affx-122962988 AX-123266790 19 18849004 TCCCACCTCTGTATTTTCTTCCTGCTGTTGCCCTC[A/C]TCTGGAAACCACTCCCAATACACTCAGTCTGCTTT M 2 1 2 1 201000 r 74 goat snp37163-scaffold452-259777 19 19335818 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799903 Affx-122937288 AX-385286829 19 18890770 CTACCTCTCAGCATATGTTAGCTTGCATAATATAA[G/T]CACAAACTTACCTAAATCAAAGATGAAAAAAGGTG K 2 1 2 1 101000 r 74 goat snp37164-scaffold452-301543 19 19377725 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766610 Affx-986698076 AX-385253962 19 18917496 CCGAAAGACCCTGGGGGAGGTGTGGTGGGGAAACC[C/T]GGCAGGACCTAGAGATCAGAGTCCACTCTGAGCCC Y 2 1 2 1 600010 r 74 goat 19_18917496 19 18917496 Ancestral_priority_1043 ancestry 0.436 neutral IMAGE 10K 10K ancestral 38436912 Affx-122933206 AX-123307250 19 18923226 TGACTCTGGGTTTGTTCCACCCAAGGAAACAGCAG[A/G]AGTCCCTGAACTCCCACCAGAATAAGACCCAGAGA R 2 1 2 1 101000 r 74 goat snp37165-scaffold452-333999 19 19410441 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795051 Affx-122949818 AX-385282010 19 18979083 AAAATGTACTGACATGAGGAGGCAACTGTTACATT[C/T]GAGTTGTCACATTTTTTACTGAAAGATAGTCCTAT Y 2 1 2 1 101000 r 74 goat snp37166-scaffold452-389856 19 19466337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766617 Affx-986698080 AX-385253968 19 18998180 GCTCACGGTGGGTGCCTCCACTGTTCTAAGTAAGA[A/C]CTGGGAAAATGATGATTGTTTTGCATGAAGGGAGC M 2 1 2 1 600010 r 74 goat 19_18998180 19 18998180 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 320784144 Affx-122963388 AX-385271196 19 19012032 CTTAGAGCATTGTATTGTGAATGGTAGCTTGTGTC[A/G]TTATGCAGAGCATTTTTTGTAGTACGCCTAATTAG R 2 1 2 1 101000 f 74 goat snp37167-scaffold452-422805 19 19499620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387829 Affx-122969667 AX-123258187 19 19064933 TTGGTAGGGGAAGAAGGCCTATTTGTTACATTTCT[A/G]TGGCAGAAGTCACATTGGTAGTGTGCAGCTTTTAT R 2 1 2 1 101000 f 74 goat snp37168-scaffold452-475706 19 19552387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409350 Affx-122954175 AX-123279701 19 19098636 TGGCGTGAAGACACACAGCAGGCACATGCAGACTT[A/G]AAAATTACTGTCACCTTGGAATGCCACGGTGGCCA R 2 1 2 1 201000 r 74 goat snp37169-scaffold452-509409 19 19586159 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272944 Affx-1111833133 AX-519546630 19 19135538 TCACGAGGGTCCCTGCCATGTGCAGGAGACAGGGA[A/G]CCCACGAACATAGAGTCAGCAGCCCAAGAAAATAG R 2 1 2 1 102000 r 74 goat 19_19135538_AF-PAKI 19 19135538 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320804024 Affx-986696346 AX-385290708 19 19137101 CCAGGGAGAAGAAGCTAACTGTGTGCTGCCCACAA[A/G]GACATAGAACCTGGAAGCTTGATGATACTGATTCC R 2 1 2 1 600010 r 74 goat 19_19137101 19 19137101 Ancestral_priority_1043 ancestry 0.614 recommended IMAGE 10K 10K ancestral 468277356 Affx-1111835807 AX-519550860 19 19146589 GCTGCCAAACAATCCAGGAGTGGAAAGGGAAGGAG[A/G]GTTGGATAGAAGTGAAGCAGATAGGTCAAGAGTTG R 2 1 2 1 101000 r 74 goat Random2.2K-1785 19 19146589 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320763553 Affx-986698082 AX-385251410 19 19146597 GACCTATCTGCTTCACTTCTATCCAACCCTCCTTC[C/T]CTTTCCACTCCTGGATTGTTTGGCAGCAAATCTAG Y 2 1 2 1 600010 f 74 goat 19_19146597 19 19146597 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 320766625 Affx-986698084 AX-385253976 19 19146639 ACTCCTGGATTGTTTGGCAGCAAATCTAGATATAT[G/T]ATCTCATTGCAAATATTCATAACGCTCTATCACAA K 2 1 2 1 600010 r 74 goat 19_19146639 19 19146639 Ancestral_priority_1043 ancestry 0.73 recommended IMAGE 10K 10K ancestral 320803453 Affx-986696347 AX-385290280 19 19146673 TTATCTCATTGCAAATATTCATAACGCTCTATCAC[A/T]AAGAAACTCTTCTACAATCCTTTATAAAGGCTTAC W 4 1 2 1 600010 f 74 goat 19_19146673 19 19146673 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 320766628 Affx-986698086 AX-385253979 19 19146683 GCAAATATTCATAACGCTCTATCACAAAGAAACTC[G/T]TCTACAATCCTTTATAAAGGCTTACTGCTGCTGCT K 2 1 2 1 600010 r 74 goat 19_19146683 19 19146683 Ancestral_priority_1043 ancestry 0.746 recommended IMAGE 10K 10K ancestral 38413100 Affx-122950944 AX-123283449 19 19152256 GGGGTAGGGGTGGGGGGCTGGCCATGACAGGTCCA[A/G]TGTGTGCAGATAAGGGCTCTTTATTTGGTATCCTA R 2 1 2 1 101000 r 74 goat snp37170-scaffold452-563029 19 19639977 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763559 Affx-986698088 AX-385251416 19 19153520 GCCTTCCTTGTGCTTTGAGAGGCTGTAAAACCTTT[G/T]GACATTCTGAATTTGCATTATCATAAGCAAGCATC K 2 1 2 1 600010 f 74 goat 19_19153520 19 19153520 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 320763567 Affx-986698096 AX-385251423 19 19153570 GCATTATCATAAGCAAGCATCGGTAATAACATATC[A/C]CTTAATTCAGTTTGAGCAATAGTTCTCACCAGATT M 2 1 2 1 600010 f 74 goat 19_19153570 19 19153570 Ancestral_priority_1043 ancestry 0.738 neutral IMAGE 10K 10K ancestral 320766599 Affx-986698069 AX-385253954 19 19153604 CCCTTAATTCAGTTTGAGCAATAGTTCTCACCAGA[A/T]TTTGTTTTAATTGGGCAATAAAATCAGTATAAGTT W 4 1 2 1 600010 r 74 goat 19_19153604 19 19153604 Ancestral_priority_1043 ancestry 0.748 recommended IMAGE 10K 10K ancestral 320763542 Affx-986698071 AX-385251401 19 19153647 TAATTGGGCAATAAAATCAGTATAAGTTTCTCCAT[G/T]AGATTGTTTTACATTAACAAAAGAAGAATAAGACT K 2 1 2 1 600010 f 74 goat 19_19153647 19 19153647 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320769632 Affx-122950164 AX-385256802 19 19185036 TTAGAATTCAGGTAGATATCATCTCTTTTCAAGTG[C/T]CTGAGTCTTGCAAGTGGAAAGAGTTTTAACCTTCA Y 2 1 2 1 101000 r 74 goat snp37171-scaffold452-595809 19 19672620 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427182 Affx-122939608 AX-123297525 19 19306026 CATCAAGCACTCATTGACTGTGCCAAGCTCTGTAA[C/T]GGGTGTTGAGTGCTAAGTGGGTGATGGTGTATAAA Y 2 1 2 1 102000 f 74 goat snp37174-scaffold452-716799 19 19793999 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400977 Affx-122960102 AX-123271330 19 19356317 GAAGTTATTAGCCCAAGGTCACACAGCCAATAGGA[C/T]GGCAAAGCTGGAACTTCAGTTTGGCAATCCAGCTC Y 2 1 2 1 201000 r 74 goat snp37175-scaffold452-767090 19 19843503 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786930 Affx-122946191 AX-385273959 19 19424857 CCTAGCTGAATGGAAACATTGACGTTGGAGATGGA[A/G]GTGCTAAAGATGATCGGTGCCAGGATTTGAGGAAA R 2 1 2 1 101000 f 74 goat snp37176-scaffold452-835630 19 19912076 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788838 Affx-122969622 AX-385275853 19 19469134 CTTCAGTAACTTGGTACAAAAGTAACTTGTTACAA[A/G]ACCATATAGGTGGTGAGTTGGCAGAGCCGAAACTG R 2 1 2 1 102000 r 74 goat snp37177-scaffold452-879907 19 19956256 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446948 Affx-122924674 AX-123317284 19 19515619 TCTGGCTTCTTAGTCCCAGAAAGAGAGACAGACAG[G/T]GAGAGGCCTAGCTTAGACGGCTGGATGCTGACTAC K 2 1 2 1 201000 r 74 goat snp37178-scaffold452-926392 19 20002842 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412092 Affx-122951123 AX-123282442 19 19580134 CCGTGTCATGGCTTCCTGCTGGAGCCTTCCTCCTT[C/T]AACCTGCCTTAGCTGGGTTCCCAGGTGGTTCCTCT Y 2 1 2 1 101000 f 74 goat snp37179-scaffold452-990907 19 20067437 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404048 Affx-122957161 AX-123274400 19 19701906 ATGGCTGGACCCAGAAGATCAAGGCTAGAACTCTG[C/T]CAGAAGGTGGGAAGAGCGGAGTGGGCAGTGAAGGA Y 2 1 2 1 101000 f 74 goat snp37181-scaffold452-1112679 19 20187140 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376119 Affx-122978875 AX-123246478 19 19745293 TGTCTGCTTTCGGAGGAGTCGTTTGAAATTCTTAA[C/T]GAGAAGCAGAATGCTTGAGTCCAGGAATCCAGGGC Y 2 1 2 1 101000 f 74 goat snp37182-scaffold452-1156066 19 20230379 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453460 Affx-122919854 AX-123323793 19 19785356 CAGGAAGTTCGATCAACATTTGTTGAATGAATGAG[C/T]GAGGATGAAGTTAAACCTACACCAAACCAAAGCCC Y 2 1 2 1 101000 r 74 goat snp37183-scaffold452-1196129 19 20270366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428754 Affx-122938433 AX-123299096 19 19832466 GAGCCATTCCCAGCTCAAACAGGAGGTGGTCTGAA[C/T]AAGAGCCCCCTGACCCTGGGACTGAGGCGGGGGAA Y 2 1 2 1 101000 f 74 goat snp37184-scaffold452-1243239 19 20317138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435194 Affx-122933641 AX-123305534 19 19912362 ACCGAGCAACTGAACAACAAATTCACACTATGGAA[C/T]ATTATACAGTCCATAAAGTGAGTGAATGTATCAGC Y 2 1 2 1 303000 r 74 goat snp37185-scaffold452-1323135 19 20397349 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414830 Affx-122949197 AX-123285179 19 19985433 TAAGAGAAATATCTCTCTGCCTTAACAGATTTACA[C/T]GTACCCTATTTCCACAAATTTGGGTGGAATTTGAG Y 2 1 2 1 101000 f 74 goat snp37187-scaffold452-1396206 19 20470105 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452379 Affx-122920621 AX-123322712 19 20035874 CCCTCCAAGCTGATCTGAACTGTCACTTTCAACCA[A/G]AGTCTTCTTGCTAGTATTGTACTACTGCCCAGCAA R 2 1 2 1 101000 r 74 goat snp37188-scaffold452-1446647 19 20521362 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394326 Affx-122964676 AX-123264681 19 20093053 TTTTAAGGCCACTCTTGAGATATAATTTACAGATG[C/T]GCTGTCTTTTTTAAAGTATAAATTATATACCATAA Y 2 1 2 1 101000 f 74 goat snp37189-scaffold452-1503826 19 20578933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794012 Affx-122965060 AX-385280981 19 20130285 AAGGGGTATAGTTTATTCTTGGTACAAGTATTACT[A/G]TTCTTATAGGAAAAGCACATTTTTCAAGGGTTTTA R 2 1 2 1 201000 r 74 goat snp37190-scaffold452-1541058 19 20616752 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405592 Affx-122955933 AX-123275944 19 20237107 TGGGCAGCCCTGCAGGAGGCATGTGATGAGAAGCA[C/T]GTCTGAATAACCCTTAACAGTGCGTTTTATACATT Y 2 1 2 1 201000 r 74 goat snp6956-scaffold1256-28098 19 20717808 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407307 Affx-122955315 AX-123277658 19 20279299 ATTGTGGACCTGGCCAAGGGAGCTCCCAGCTTATG[C/T]GAAGGTCTGGCTCTATGAGCTGCATTTATACTCAC Y 2 1 2 1 101000 r 74 goat snp6957-scaffold1256-70290 19 20760027 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse365 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38422349 Affx-122943443 AX-123292695 19 20311272 AAGAATAAGGGTAATGCTTTTTGGGGAGAGGAGGA[C/T]TTCTGGTTTTTCTATCATAAGCATGAATTATCTGC Y 2 1 2 1 201000 r 74 goat snp6958-scaffold1256-102263 19 20792072 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790945 Affx-122945244 AX-385277942 19 20342804 CATATTTTTGACATCTGAAGAGGCTTGCCTTCTGC[C/T]ATATCGCACTGAAAGTTTAATATACCCCCAAATAA Y 2 1 2 1 101000 f 74 goat snp6959-scaffold1256-133795 19 20823945 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797392 Affx-122968049 AX-385284331 19 20383708 ATTTCTTCCTTTAGGATACCCCTTCTGGAAACTTC[A/G]TACAGTGTCATGGTATGAATGCTGGTCAGACCAGA R 2 1 2 1 202000 f 74 goat snp6960-scaffold1256-174699 19 20865428 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787125 Affx-122973124 AX-385274151 19 20422980 GTGGACAAGGGGTGTTTAAACGGGAGCCTGACACA[G/T]AGAAGATGTGGACATATGGAAATGTGAGGAGAGTG K 2 1 2 1 101000 r 74 goat snp6961-scaffold1256-213971 19 20905041 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398960 Affx-122960976 AX-123269315 19 20461403 GAAATTCAGGAAACTATGTTGAAATCACAAACCAG[C/T]ATGTTTTCAAGATGTCAAAGCGCACACCTCAGTTA Y 2 1 2 1 101000 f 74 goat snp6962-scaffold1256-252394 19 20943719 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447810 Affx-122923924 AX-123318146 19 20515332 GGTTGCACAGAGTCAGACACAACTGAAGCAACTTC[A/G]CGGGCAGGCAAGCAATAGCTTATTTTATCAATTCT R 2 1 2 1 201000 r 74 goat snp6963-scaffold1256-306323 19 20997877 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777582 Affx-122948846 AX-385264701 19 20543577 ATTAAAATAACTGAAAATTCTATGTACCTAAAATA[G/T]TATAACAATATTCTGTGTTAACACATATGCCAAGT K 2 1 2 1 201000 f 74 goat snp6457-scaffold1229-2752749 19 21026018 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375963 Affx-122978440 AX-123246322 19 20606469 ATTCAGGACGCCAAAACACAGGAAAATGGAGGATG[C/T]ATACGTTTGAATCCTTCACAAGCAATGGCAGCTGT Y 2 1 2 1 201000 r 74 goat snp6456-scaffold1229-2689857 19 21088848 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425657 Affx-122940879 AX-123296003 19 20642903 AAACCTGTCCCAGGGTCCCAAGCTCTGGTCCATGT[A/G]CTGGCTGCATCAGAATCACTTGGGGAGTTTAAAAA R 2 1 2 1 201000 f 74 goat snp6455-scaffold1229-2653423 19 21125175 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463580257 Affx-1110056361 AX-515062003 19 20653676 GTGGATCTGAGAGTGAGAAGGGCGTCAGAAACTCC[A/G]GGCAGCACCGCCGCCTCCAGGAGTGTGCCCCTTCC R 2 1 2 1 102000 f 74 goat GoatD01.029099 19 20653676 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38427060 Affx-122939809 AX-123297405 19 20672590 TAGTAGCCTGGTCTCCTGCCCACTGAAAACTCCTC[A/G]TGGGCAAGGCAGATGCTGAAACTTTTTCTCAGGAA R 2 1 2 1 101000 r 74 goat snp6454-scaffold1229-2623736 19 21154503 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443408 Affx-122927382 AX-123313745 19 20702141 TTTGCCCTGGGTCTTGACTGAGTTATACTTCAAAA[C/T]GGAGCTAGTGTTGGTCTGTTAGTCTCCTTTACAGT Y 2 1 2 1 101000 f 74 goat snp6453-scaffold1229-2594185 19 21184082 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419133 Affx-122945757 AX-123289481 19 20754879 CTGGTGTAAAATACCAATGTAATTTATTTTGATCA[A/G]TGTAGCCCTCAGCCATTTCAGGTTCTTAAGGGAAG R 2 1 2 1 101000 r 74 goat snp6452-scaffold1229-2541447 19 21237066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417723 Affx-122947438 AX-123288071 19 20801340 AATGCCTGAGTCCAGTTCCAGCTACTTCCGTAATA[C/T]GTAAATGATTTTCATACTATGTAAATTATTTGCAA Y 2 1 2 1 101000 f 74 goat snp6451-scaffold1229-2494986 19 21283311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393482 Affx-122965828 AX-123263838 19 20835128 TGGTGGGTAGACTGTGTTCCAAGAGGACTATTAAG[C/T]GTAGCAACTGTGCTAGCTGTTACTACAGCCTCAGT Y 2 1 2 1 101000 f 74 goat snp6450-scaffold1229-2461198 19 21317431 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392491 Affx-122966136 AX-123262848 19 20943837 GAATGTATAACGTGCCTGACACCACAAAGCAGCCA[C/T]GATTAGGTCTGCTCTGATCCATCTGGCCATTCCCA Y 2 1 2 1 101000 f 74 goat snp6448-scaffold1229-2352489 19 21426895 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439278 Affx-122930980 AX-123309615 19 20998218 CTACAAGTTCATATAAGCATCAATTTCTGAATTTG[C/T]AATTTCCCTGGGAGGATAGTTTCAACTCTGTCCTT Y 2 1 2 1 101000 r 74 goat snp6447-scaffold1229-2298108 19 21481570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450689 Affx-122921899 AX-123321023 19 21043934 TGTCCAATCCTCTTCTAAACCTTCTAGTGCAGAAC[A/G]CAATATAGGGGGAGGGGAGTGGGACCTTAGAGGCC R 2 1 2 1 101000 f 74 goat snp6446-scaffold1229-2252392 19 21527238 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437540 Affx-122931905 AX-123307878 19 21111513 TCTAGGCACTGGGTCCATGCCGAGCATCAGCCTCA[A/G]CATAGCCGGCCCCTCCCTGAGTTGAGTCGATACAG R 2 1 2 1 201000 f 74 goat snp6445-scaffold1229-2184813 19 21593437 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451946 Affx-122920964 AX-123322279 19 21142938 TGGAAGAGCCTTTTCTGCTTGTGACAGAGACACTA[A/G]TCACTGGGTACAGAGATGGAGCTCAAAAGAAGCTT R 2 1 2 1 101000 f 74 goat snp6444-scaffold1229-2153388 19 21624772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442336 Affx-122928047 AX-123312673 19 21234819 GTATATATGAAATATAATTTTTCCTTTTATTGAAG[C/T]ATAGTTGCTGTGCCATATTACATAATTACAAGCAT Y 2 1 2 1 101000 r 74 goat snp6442-scaffold1229-2061507 19 21714120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384857 Affx-122971951 AX-123255215 19 21275755 CTCAGTAATGTTCCTAAAGGACAAATTGACTTTAT[C/T]TGGTGAACGGCTGCAGCTATTTAGCCTTAAAGAGA Y 2 1 2 1 101000 f 74 goat snp6441-scaffold1229-2020571 19 21755463 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454120 Affx-122919349 AX-123324453 19 21334990 TCCACCTGGATGCCAGTGCTTGTCCTGCTCACCCC[A/G]CCACCGTCCTCACAGCAGGGACCCCTGGGACATGT R 2 1 2 1 303000 r 74 goat snp6440-scaffold1229-1961336 19 21814460 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404506 Affx-122956705 AX-123274858 19 21389155 CAGTGTCTCTACATTAAGCCTTACTCTTGCACACT[A/G]TAAACAATGTTGCCTGCAATTCCATTTCAACAAAG R 2 1 2 1 201000 f 74 goat snp6439-scaffold1229-1907171 19 21868240 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse366 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38410674 Affx-122952753 AX-123281024 19 21467587 GAAGACAAGGGTCAGTAACTAGGTCAGAGATGGGA[C/T]AAAGACTCCCTCAGTTTACCTCTTCTGTTTTATAG Y 2 1 2 1 101000 f 74 goat snp6437-scaffold1229-1828739 19 21946664 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801354 Affx-122972977 AX-385288266 19 21518460 TGACCATATTCAACTGGCTGTGGTTGCAGTGGGCT[A/G]CTTGGTAAGCATTTTCTGGAGCCCCTGCATTTGTA R 2 1 2 1 101000 r 74 goat snp6436-scaffold1229-1777866 19 21997506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437570 Affx-122931881 AX-123307908 19 21553573 ACTGCTTAAGTCAGTTTGAGTCAGGCCTTCTATGA[C/T]GAGTAGCTGAAAACATCCTAATGGATGTGACAACC Y 2 1 2 1 201000 f 74 goat snp6435-scaffold1229-1742753 19 22032623 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390053 Affx-122968420 AX-123260410 19 21612505 ATGATCCTTATAGAGGCAGAAACCTTAGCTCCTAT[A/C]TGCTCATAACAGCCACAGAAACCACAAAGAGCAAG M 2 1 2 1 101000 f 74 goat snp6434-scaffold1229-1683821 19 22091379 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426283 Affx-122940311 AX-123296629 19 21643243 TTCAGGTGGCTGTGTGCCCACGTGCCAAGGCCTCT[A/G]CTGGTCTTCCACGGGACGTGTTACACATTCTGTCC R 2 1 2 1 101000 r 74 goat snp6433-scaffold1229-1653083 19 22122166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440821 Affx-122929279 AX-123311158 19 21675119 GGACCTTTGCACTTGCTGTTCCTTCTGCCTAGATG[C/T]GCTTCCCCCATATTTTCAGCTAGTATTTACCCTTC Y 2 1 2 1 101000 r 74 goat snp6432-scaffold1229-1621207 19 22154041 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272946 Affx-1111833134 AX-519546632 19 21694651 AGAGGGGTGTTCTTTTCTTTCACTGGGTTGTTGGT[A/G]GTTGAGCTGGCACGTTCTTGTTCCTCCGTTGCTAG R 2 1 2 1 101000 r 74 goat 19_21694651_AF-PAKI 19 21694651 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38440667 Affx-122929931 AX-123311004 19 21710718 AAGCCCTCCACTAAATTATTACATTTGCTGAATTC[A/G]TCTTATCTTTCACTCCTCCTCCCTTCCCTTGACAA R 2 1 2 1 101000 r 74 goat snp6431-scaffold1229-1585608 19 22188604 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767112 Affx-122947676 AX-385254399 19 21756075 TCAGCCCACATGGTCTTTCATGTCTAAACTGCATC[G/T]ATACTGCATTGCCTGTGATTCCCAGATTCCATTTC K 2 1 2 1 101000 f 74 goat snp6430-scaffold1229-1540251 19 22234559 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385085 Affx-122971804 AX-123255443 19 21811453 CCCAGAGTCGCTTACTTTCCCTCCACTGGTTTTAA[A/G]AGCCTGTCTTCTGAGCGAGGACAGCATGTCCTCTC R 2 1 2 1 101000 f 74 goat snp6429-scaffold1229-1484873 19 22290256 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442596 Affx-122928485 AX-123312933 19 21881355 TATCTGTAGCATCTCACCTGATTAGGACATGGAAC[A/G]CACTCAGCAAATATATGTTGAATGGGTAAGAGTAA R 2 1 2 1 101000 f 74 goat snp6427-scaffold1229-1414971 19 22360195 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417990 Affx-122946675 AX-123288338 19 21934480 GGACATGGCCCTCCCACCTTAGTGACCCTCTGATC[G/T]GCACCTCTGAAGGACTTCCCAGCCCTACCCATGAG K 2 1 2 1 102000 r 74 goat snp6426-scaffold1229-1361846 19 22412145 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401358 Affx-122959246 AX-123271711 19 21976849 AGGAGAGGTTTTCTGAAGTCAACTTTGTCTCCTCT[A/G]TTGAATTGAAGACATTCTTAAGCACTGCTTGTTCT R 2 1 2 1 101000 r 74 goat snp6425-scaffold1229-1319477 19 22453825 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424755 Affx-122941647 AX-123295101 19 22123350 GAATGTAATCAGGCTAAAACCAGAGATGCAACGGT[A/G]TAGAAATTGAGACAGAGATTTCTTTTTCTTTTTTT R 2 1 2 1 101000 f 74 goat snp6422-scaffold1229-1172976 19 22601487 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse367 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38382061 Affx-122974926 AX-123252419 19 22161031 TCATTGTGCTTTTGTTGTTGTTCCATCGCTATGTC[A/G]TGTCCAGCTCATTACGCTTCAGCATACTATGCATG R 2 1 2 1 201000 r 74 goat snp6421-scaffold1229-1135295 19 22639220 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446660 Affx-122924767 AX-123316996 19 22222679 AATCCTCAGCTCGCACACAAACTAATTCTCTGTAT[C/T]TTAATTTCTTCGTCTGTAAGATGGGGTTAATGATA Y 2 1 2 1 101000 f 74 goat snp6420-scaffold1229-1073647 19 22699087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390744 Affx-122967908 AX-123261101 19 22260351 ATACTAATTTGTGTGGCCCAGAAACTATAGCTTTT[A/G]TTGGTCTTTGTATGTTTTATCTGAGCAAACATCTT R 2 1 2 1 101000 f 74 goat snp6419-scaffold1229-1035975 19 22736624 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439128 Affx-122931090 AX-123309465 19 22345567 AAAAAACAATTCATCAATAATCCATTATCTTGTGT[A/G]CTCCGTACTTCTCACTGTAATCCTGTTAGAACAAG R 2 1 2 1 101000 r 74 goat snp6418-scaffold1229-950759 19 22822412 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439388 Affx-122930261 AX-123309725 19 22382741 GCCTGGTCCAATGCAGTTGCCAACCACCCCTCAAA[C/T]TCATCTCACACAGAACAACTATGATGTAGCCGTTG Y 2 1 2 1 201000 r 74 goat snp6417-scaffold1229-913585 19 22859640 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442989 Affx-122928189 AX-123313326 19 22476943 TCCTATTAAAAAAAAAAAAAAGCAGTGCTCAGACA[C/T]GGTCTGACCTGCAGTGATTCTACCTGAAGAAAGTT Y 2 1 2 1 103000 r 74 goat snp6415-scaffold1229-819383 19 22943889 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451253 Affx-122921937 AX-123321586 19 22537497 TTCTGTTACAAATGAGCGTGTCAGAGTTGACTGCT[C/T]GTTTCTAGTCAGACTGCTCTACACCAGCCCTGGAC Y 2 1 2 1 101000 f 74 goat snp6414-scaffold1229-758829 19 23004323 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383573 Affx-122972594 AX-123253931 19 22544832 AGCCCAACCGGTTCATGAATGTAGTTCACTTAAAC[G/T]AATGCAGATGGGAATAGAGTGACTGGGAGAGTGGA K 2 1 2 1 101000 f 74 goat snp4302-scaffold1134-99380 25 36503377 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438840 Affx-122930773 AX-123309177 19 22586615 TGTTTCCACTTGCCCAAGAATATCTTGTCTTAGTA[C/T]GTCCTTAGTATGGCTGTGTGATATTTTATTATAAA Y 2 1 2 1 101000 f 74 goat snp6413-scaffold1229-709711 19 23053214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602804 Affx-1002479177 AX-413837151 19 22604345 GCAGCTTTGGCCTCCGGCTGTCTGCCTCCCACCAT[C/T]TGCATTCCTGTGCTTTCACACCCCATCCCCACTCC Y 2 1 2 1 202000 r 74 goat miRNA-var1 19 22604345 T C 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602807 Affx-1002479178 AX-413837153 19 22604516 CAGCTGTGGCCAGCAGTAATCCCCTCCCCCCAGTT[C/T]AGCCCAAGGTTGGGAGGATCAAGTGCCAGCAGGGG Y 2 1 2 1 202000 r 74 goat miRNA-var2 19 22604516 C T 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350603624 Affx-1002479179 AX-413837771 19 22604637 AACCCCCAGGCTGGGCACGCCTCCTTCCCTGTCTC[G/T]CGGCTTGCCAAGTCTCACCACCGCATGGTGACAAA K 2 1 2 1 303000 r 74 goat miRNA-var3 19 22604637 G T 3 not_recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602809 Affx-1002479180 AX-413837156 19 22604713 TCCCAGGCCTGGCCCAAGGTCTGGTTCCACAACAA[A/G]TCAGTTCCATCTGCCAGGAAATAACCTGTGGGCAA R 2 1 2 1 201000 r 74 goat miRNA-var4 19 22604713 A G 2 recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602811 Affx-1002479181 AX-413837157 19 22604817 CAGTGTCCAGTCTGGAGAAGAATCTCCACCTTTCC[C/G]GCCTCTTTAGTTTCCTCTCAGTGAATCTGCCAGAA S 4 1 2 1 202000 r 74 goat miRNA-var5 19 22604817 G C 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602814 Affx-1002479182 AX-413837158 19 22605015 AAGCCCAGGGAGGGTGGCCATGAATCGGGTCGGCG[A/G]CCATCTGAGGGTACAGCGACAGCCTGGAGGAGACG R 2 1 2 1 202000 r 74 goat miRNA-var6 19 22605015 G A 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602816 Affx-1002479183 AX-413837159 19 22605155 ACTCATCCACAAACCCACCCCAGCCTCAGACACTT[C/G]GAGATCTCGCATGGATTCTGAAGATGCCTCCGGGT S 4 1 2 1 202000 r 74 goat miRNA-var7 19 22605155 C G 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602715 Affx-1002479184 AX-413837076 19 22605316 CCCGTAAGCAGGCTGTGCACCAGGGAGACACAAAT[A/G]TTCCGCCACTTCCAACGGTTCTGGGCGGCAGATTC R 2 1 2 1 201000 f 74 goat miRNA-var8 19 22605316 G A 2 recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602820 Affx-1002479185 AX-413837161 19 22606064 TCAGTTGTGGAGCGGGGCGGGGCGGGGGGCGGACA[C/T]GGGGGCACATCACTTCCTTCCAGCCACCTTCCTTC Y 2 1 2 1 303000 r 74 goat miRNA-var9 19 22606064 C T 3 not_recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602719 Affx-1002479186 AX-413837080 19 22606134 CCCGATGTTTCCAGACCTTGAACACATTTCAGCAA[C/T]CCCATGTAAACTCCAGGAGTCCTGCGCCTTGACAT Y 2 1 2 1 201000 f 74 goat miRNA-var10 19 22606134 C T 2 recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602721 Affx-1002479187 AX-413837082 19 22606276 TTGATCATCAGCCCCAATCTTGAAAAGCACCACGC[C/T]GCCCCCCGCCCCCGCCAGGGCTTGGTACCCATTAG Y 2 1 2 1 202000 f 74 goat miRNA-var11 19 22606276 T C 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 532567212 Affx-1207771858 AX-579205705 19 22606288 CCCAATCTTGAAAAGCACCACGCTGCCCCCCGCCC[A/C/G]CGCCAGGGCTTGGTACCCATTAGGGGAGGAGTGAG V 6 1 2 1 303000 r 74 goat miRNA-var12 19 22606288 C G 3 not_recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602828 Affx-1002479189 AX-413837166 19 22606306 CCCAATCTTGAAAAGCACCACGCTGCCCCCCGCCC[A/C]CGCCAGGGCTTGGTACCCATTAGGGGAGGAGTGAG M 2 1 2 1 400000 r 74 goat miRNA-var13 19 22606306 C A Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602830 Affx-1002479190 AX-413837168 19 22606362 CTGTGCCAATTTGAGGAGGCAAGGAGAGGTGGCAC[A/C]GGGTCATCTCAAGATTGGGGAAGAGTCAAAGGGAA M 2 1 2 1 102000 r 74 goat miRNA-var14 19 22606362 A C 1 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602729 Affx-1002479191 AX-413837090 19 22606688 CAACTCCCCTCCTCCACCAAAACCCCATTATATGA[A/G]TGGGGCTGCAGGGAACCCTTCATTCTTCCACACCC R 2 1 2 1 202000 f 74 goat miRNA-var15 19 22606688 A G 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602834 Affx-1002479192 AX-413837172 19 22607335 ACTGACATCAGTAAGACTACCCACTTGTATACCCA[A/T]GTGCAATGTACGAGAGTGTGATTTTAGTACTTCTT W 4 1 2 1 202000 r 74 goat miRNA-var16 19 22607335 T A 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602837 Affx-1002479193 AX-413837173 19 22607438 AGTTTGCTACAGGAAAAAAATGCTTCCAGCTATAG[C/T]TGCCTTTCTTTAATTACTAATGAAGCACACCTTTT Y 2 1 2 1 201000 r 74 goat miRNA-var17 19 22607438 C T 2 recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602735 Affx-1002479194 AX-413837096 19 22607576 TGCTCCTCAAGGGTGCTTAAAGACAAATTACACGG[C/T]GAGGAGAGGTGGAAGCGGGAGGATGAAGTCAAGGA Y 2 1 2 1 201000 f 74 goat miRNA-var18 19 22607576 T C 2 recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602841 Affx-1002479195 AX-413837175 19 22608461 CAGGGCTGTGGTCCTGCTCTAGGAGGCAGGGGAAG[A/C]CTGAGCCACCTTTGCTTGGTGGGAAGTCAATGCCA M 2 1 2 1 201000 r 74 goat miRNA-var19 19 22608461 C A 2 recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602739 Affx-1002479196 AX-413837100 19 22608502 CCACCTTTGCTTGGTGGGAAGTCAATGCCAAGACT[C/G]AGTTCCCAGCAGCTCCTTGGCATTGGTCTAACCCT S 4 1 2 1 201000 f 74 goat miRNA-var20 19 22608502 G C 2 recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602741 Affx-1002479197 AX-413837102 19 22608716 GATTCCTTCATGTATGCTCAATTGTGTGATTCCCC[A/T]TTTCACAGGTGGAGAAACCGACAGGGGGCCTAAGA W 4 1 2 1 202000 f 74 goat miRNA-var21 19 22608716 A T 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602847 Affx-1002479198 AX-413837178 19 22608986 TTTGCATAAAGGGGAAGGCAGGATTTTCTTTGCTC[C/T]ACTTCTTCCCACTGTCAAAGACCAACTAAGCTTGG Y 2 1 2 1 201000 r 74 goat miRNA-var22 19 22608986 C T 2 recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602849 Affx-1002479199 AX-413837179 19 22609422 AAATGGGAAAGACGTGAGCAAGGCCATGTCACAGG[A/G]ACACTGTCCCACTGGCCATCAAAGTCCAGCTCCAG R 2 1 2 1 202000 r 74 goat miRNA-var23 19 22609422 G A 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602852 Affx-1002479200 AX-413837180 19 22609921 CAGAGGCTGGAGGAAAGGGACGTAGGGCAGGCTGG[C/T]TGGGCAGCTTCCCCAGGACTCTTAAATGCCAGGCA Y 2 1 2 1 202000 r 74 goat miRNA-var24 19 22609921 T C 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602748 Affx-1002479201 AX-413837109 19 22610179 CGAGCTTGGGAGGGTGGGTCTGTGCTGACACTCTG[A/T]GAAGGGCATGGTCCATGCCAGTGTGAGGGGCCAAG W 4 1 2 1 303000 f 74 goat miRNA-var25 19 22610179 T A 3 not_recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602750 Affx-1002479202 AX-413837111 19 22610262 TTAGATATCTATACCCAGAGGGTAAAGAGAGATTA[A/G]GGTGGGAGGTTTTCAAATTACAAAACCCTCTTGGG R 2 1 2 1 201000 f 74 goat miRNA-var26 19 22610262 G A 2 recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602858 Affx-1002479203 AX-413837184 19 22610652 GCCAAGAGTTGGCCGAGAGGTGGGGAGAGAGGGAG[C/G]CCAGTGATGACTAACCCAGGCGCCCCACCCAGCCA S 4 1 2 1 103000 r 74 goat miRNA-var27 19 22610652 C G 1 not_recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602754 Affx-1002479204 AX-413837115 19 22610782 TGGGGGGAGGTGCAGAGGTGACCTTCTCTCGGCTC[A/G]AGACGGCCAGTTAGGCTGGGGAAGGGGGGAAGGTT R 2 1 2 1 202000 f 74 goat miRNA-var28 19 22610782 A G 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602862 Affx-1002479205 AX-413837188 19 22611104 CAAATCCTCAAGCTGGGAGGCCGGCTCCCGTATTC[C/T]CAGACCAGAGGGCGCCGAGGTTAGCCGCCCCCAGC Y 2 1 2 1 102000 r 74 goat miRNA-var29 19 22611104 T C 1 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602758 Affx-1002479206 AX-413837118 19 22611442 GGGGGGGTGCTGAGGATAGGGGAGCAAATCCGTGC[A/G]TCCGATCCCCACGGCCGGCGGCGCTGTCTCTTCCC R 2 1 2 1 202000 f 74 goat miRNA-var30 19 22611442 A G 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602866 Affx-1002479207 AX-413837191 19 22612075 TCTCAGGAAGAGCAGGAGAGGGTGCAGGAGTGAGA[A/C]CTGAAGGTGAAAATCAGCCCCAGGGCACACAGACT M 2 1 2 1 202000 r 74 goat miRNA-var31 19 22612075 A C 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602761 Affx-1002479208 AX-413837122 19 22612338 ACGAAAGATTTATAGCACAGTCTTCACCTGACGGT[A/G]GAAGGAAGACTTGTGGTCAGAAACTAGGGGACGGG R 2 1 2 1 201000 f 74 goat miRNA-var32 19 22612338 A G 2 recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602870 Affx-1002479209 AX-413837193 19 22612398 TAGGGGACGGGCCGGGCCAACGTGCAACTGGCCAG[C/T]AACCCCGTCCTCAGCACGTAGATACCCCCATTCTG Y 2 1 2 1 202000 r 74 goat miRNA-var33 19 22612398 C T 2 neutral Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 350602872 Affx-1002479210 AX-413837194 19 22613794 CAAGCTTGGAAGAAAGAGAAATACCAGCTGCCCCC[A/G]TTTACCATTATGCTTAGCACAGAAGTCCTGTTCCC R 2 1 2 1 101000 r 74 goat miRNA-var34 19 22613794 G A 1 recommended Goat_IGGC_65K_v2 miRNA miRNA-SNP SNP in a miRNA multi-breed 320801004 Affx-122942921 AX-385287918 19 22716712 GGTTTCAAAATCAAATCTCAAAAAGGATACTGTTA[A/G]AGGTCTAGCTCTATTCTCTTGTCTCTTTCACCCCG R 2 1 2 1 101000 r 74 goat snp6411-scaffold1229-579614 19 23182377 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767324 Affx-122975981 AX-385254601 19 22750414 GGCACTCTACCTCTAGGCAATTTCATCCATGTCTA[C/T]GACTTTATTTTCTACCTCCATGCAGATAACCTACA Y 2 1 2 1 101000 f 74 goat snp6410-scaffold1229-545912 19 23216231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393602 Affx-122965371 AX-123263958 19 22786614 CTGATTTTTCAGCAAAAAGGAGGAGGGTTTCACCA[C/T]GCATATGCTAACAGTAACAACAAAAAACTTGCTGA Y 2 1 2 1 101000 f 74 goat snp6409-scaffold1229-509712 19 23252267 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791031 Affx-122935784 AX-385278026 19 22887141 CTGTTTGTTTTTATACCACTGCTGCAAAATCAAAC[A/G]TTAAGACTGAGCTTTCCATCTATTTGACAAGCCGA R 2 1 2 1 201000 r 74 goat snp6407-scaffold1229-409185 19 23352777 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400830 Affx-122959795 AX-123271185 19 22962346 GGAAGGTATTGGTAGACCCAGAAATAGAAGCCAAG[C/T]AGTTCAGAAGCCTCCCAAGCATAGTGAGAACGGAT Y 2 1 2 1 101000 r 74 goat snp6406-scaffold1229-333980 19 23428138 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794411 Affx-122932643 AX-385281374 19 23002090 ATCTATCCTTATCAGCACTCATATGTACCATGTGT[A/G]CTGTCTGTCAGTGTATTCTAGGGAAGACACGGCTG R 2 1 2 1 101000 r 74 goat snp6405-scaffold1229-294236 19 23468021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766605 Affx-986698073 AX-385253958 19 23057948 AAATTTCTATATTATACCACATATTCCCTGGGAGA[A/G]AATAATGCTTTCATCCTCTTTACATCTCCGAAGCC R 2 1 2 1 600010 r 74 goat 19_23057948 19 23057948 Ancestral_priority_1043 ancestry 0.672 recommended IMAGE 10K 10K ancestral 38448271 Affx-122924185 AX-123318607 19 23088087 TAGGCTAACTGGCCTTAAAACAATGAACAAAATCA[C/T]GTACAATACACACACGTGCACACATGAGGAGCGGG Y 2 1 2 1 101000 f 74 goat snp6403-scaffold1229-208239 19 23553648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse368 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38404182 Affx-122957685 AX-123274534 19 23122275 AGAGGGAGAGAGTAGGGAAGGGAGTTCTGCTTTAT[A/G]CACGGGATGCTTCACAAACATGCAGACCTACATTA R 2 1 2 1 101000 f 74 goat snp6402-scaffold1229-174051 19 23587864 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382256 Affx-122973946 AX-123252614 19 23165103 GTAATACCAGCTAACACCTCCACTGAGCGCTTCTC[G/T]TATTCCAGGCCACATGCACTTTTCCAGGCATTATT K 2 1 2 1 201000 r 74 goat snp6401-scaffold1229-131223 19 23629973 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441642 Affx-122929204 AX-123311979 19 23195873 TCACAAACTGTATGATACTCCAGAAGCGTTCCTGC[G/T]AAAGTCTGCTATTGCTGCAGCTAAGTCACTTCAGT K 2 1 2 1 101000 f 74 goat snp6400-scaffold1229-100453 19 23660647 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449220 Affx-122923496 AX-123319555 19 23225611 AGCTACAGACCTGGGTGTTCAACCCCCTGATGACC[A/G]TCTTATTTGCATGTTTCACCTTCACTCCAAGACAA R 2 1 2 1 101000 r 74 goat snp6399-scaffold1229-70715 19 23691709 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399938 Affx-122961258 AX-123270293 19 23256245 TGCTCATATCTCCAAGGAGAGCTGTCAAATAATCC[A/G]CCTGGAGAGATTAAGACAGTTTCTGGATTGTCCTG R 2 1 2 1 201000 f 74 goat snp6398-scaffold1229-40081 19 23722423 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424830 Affx-122941363 AX-123295176 19 23306430 GTAAGGGTGTAGAAATTGGAGGTAATGAAAGACAG[C/T]AAAGCCAGAGAGATGCTTTCCAAGGACTGGTGGGG Y 2 1 2 1 101000 f 74 goat snp16332-scaffold1720-10005 19 23793093 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405712 Affx-122956533 AX-123276064 19 23366409 GTTAAGGTATTTCTTATTACTTTCATTTCCCTGGC[A/G]TTGGTCTGTCTTTGCCATACTCATTCTTGCAACTA R 2 1 2 1 101000 r 74 goat snp16333-scaffold1720-69984 19 23853488 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442126 Affx-122928338 AX-123312463 19 23411243 TCTATACCTAACCAATTTGTCCTTCAGATATAAGC[A/G]TACATACAAAAGGAAAATCTGAAATACGTGAAAAT R 2 1 2 1 101000 f 74 goat snp16334-scaffold1720-114818 19 23897975 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380917 Affx-122975022 AX-123251275 19 23477504 CTGGATTTGTTCTTGGATTTGCTCTTTAAAACCCT[G/T]TGTAATTGATTTGTTTTGTGCTTATTTGAAATATT K 2 1 2 1 101000 f 74 goat snp10648-scaffold1377-2234692 19 24011305 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439067 Affx-122930315 AX-123309404 19 23529035 ACTGGTTAAGTCCCTGAAGTTCTAACCTCTTATCC[C/T]GAGTTAGGAGGCTTTGAGTTGGCCCCACCCAGCCT Y 2 1 2 1 101000 f 74 goat snp10647-scaffold1377-2183161 19 24064034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380521 Affx-122975688 AX-123250879 19 23562142 CCCCAAACATGCATATTCCTAGGCCATTCTTCTAA[C/T]ATATGTGGGACCTCTGTTTCATGCACAAAGGATTC Y 2 1 2 1 101000 r 74 goat snp10646-scaffold1377-2150054 19 24097083 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788298 Affx-122971854 AX-385275316 19 23605701 CTTTGTAGAAAGGAATTTCCACAGAGATACAAAAC[A/G]TAGTGAAACAAGTACGTTGTTTGCTAGGAGGAGAA R 2 1 2 1 101000 f 74 goat snp10645-scaffold1377-2106495 19 24141089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401404 Affx-122959210 AX-123271757 19 23638007 AACAAGAGTAGATGGTACAAGGTACAATGCCTGGC[A/G]TATTTGTTGTTGCTAAGTCGATTCTTCTGCGACCC R 2 1 2 1 101000 f 74 goat snp10644-scaffold1377-2074189 19 24173302 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424615 Affx-122942191 AX-123294961 19 23682857 CACCTACACTTCTCAGAGTCAGCGGAAGGGACACA[C/T]ATGTGCTGGGGAGAAGACCACGAAGCAAGGCCGTG Y 2 1 2 1 101000 f 74 goat snp10643-scaffold1377-2029339 19 24216337 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426965 Affx-122940403 AX-123297310 19 23723910 CCTTCCCAGCATGGAAGAGGTGACTGAGGCCCAGA[C/T]AGGGGTAGTGACTGGCCTTAGTTACAAGCAAGTGC Y 2 1 2 1 101000 r 74 goat snp10642-scaffold1377-1988286 19 24257350 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804027 Affx-986696348 AX-385290711 19 23770727 GTTGGAACTTATGATTTTTATTTCTACAGCATAAA[A/G]TTCACAAGTCCAGATGAAGACCAAGAGTGAATGCA R 2 1 2 1 600010 r 74 goat 19_23770727 19 23770727 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 38435054 Affx-122933744 AX-123305394 19 23808043 TCTCCTGCACTGCAGGCAGATTCTTTACCACATGA[A/G]CTCCCAAGAAGCTTGGCCTCCAACAAACCCTACTC R 2 1 2 1 201000 r 74 goat snp10640-scaffold1377-1904153 19 24341402 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277359 Affx-1111835809 AX-519550864 19 23832455 TCTGCCTCTAGTTCCCTCATGACTTTGGGAAAGCC[A/G]ATAGCTCCCTACGTCCCCATCTGTTAAATAGAGTT R 2 1 2 1 101000 r 74 goat Random2.2K-1790 19 23832455 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415297 Affx-122948823 AX-123285646 19 23852460 AGCCGACAATGACTCCCAGCCCAACAGTCAGGACA[C/T]GGGAGATTATGATCCTTCAGGTGATCTTGACTGGG Y 2 1 2 1 101000 r 74 goat snp10639-scaffold1377-1859736 19 24386266 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602169 Affx-1002480058 AX-413836543 19 23859592 CCTATGCCCACGTGGCAGCTGCAGTCCTGCGGATC[C/T]CGCTCGGCAGAGGGCAGGAAGAAAGCCTTCTCCAC Y 2 1 2 1 303000 r 74 goat QTLSaanen19.116 19 23859592 C T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602110 Affx-1002480059 AX-413836486 19 23859596 TGCCCACGTGGCAGCTGCAGTCCTGCGGATCCGCT[C/T]CGGCAGAGGGCAGGAAGAAAGCCTTCTCCACGTGT Y 2 1 2 1 303000 f 74 goat QTLSaanen19.117 19 23859596 C T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38417822 Affx-122946803 AX-123288170 19 23891690 GGCTTTCCTGCCAGGCATGGGGCAGTCTTGGTTTC[C/T]CCGGTGAAGCCCAAACGCAAAGCTATCTGCACCCT Y 2 1 2 1 201000 r 74 goat snp10638-scaffold1377-1820506 19 24402548 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384349 Affx-122972247 AX-123254707 19 23939481 TTTCTAAACAGGCAGTCCTCTTGTATCTTTTGTCC[C/T]GTGTTGTTAATAAAGCACAGGTGTCCCCTGCTATC Y 2 1 2 1 101000 r 74 goat snp10637-scaffold1377-1772715 19 24450209 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435091 Affx-122933717 AX-123305431 19 23996088 CTTTCTGGGTCCCTCTGTCTAACCTAAACTGACAC[A/G]TACTCCTTTCGTATCTCTTTGTATGAGTGCTGAAT R 2 1 2 1 101000 r 74 goat snp10636-scaffold1377-1716108 19 24506369 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400501 Affx-122961280 AX-123270856 19 24048300 GAGTTGGATCGTAACGGAGACCTTGCATTAGATCT[A/G]GCCCTTTCCCGACGTCTGGAGAGTATCGCCACCAC R 2 1 2 1 201000 f 74 goat snp10635-scaffold1377-1663896 19 24558773 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418042 Affx-122946632 AX-123288390 19 24096937 AAAAGGCCCATCAGAATTAATCAGTTAATCAGTTA[C/T]AATATTGTTAATCAATGAAAATACATAATGTAGAC Y 2 1 2 1 101000 f 74 goat snp10634-scaffold1377-1615259 19 24607373 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443811 Affx-122927075 AX-123314148 19 24126321 TCCTCTACCTCCTGGGGCGGTCATACCCTACCAGC[C/T]CTGCTGAGAATGTTGTAGCCTCTGTGTAATGTGGT Y 2 1 2 1 101000 r 74 goat snp10633-scaffold1377-1585875 19 24636536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430833 Affx-122937439 AX-123301174 19 24174233 AGAGAGTTTAAATTACTTATCCAAGGTCACACAGG[C/T]AGTAAGTGGTGCTGCTCTATTCATATTCAGGACCT Y 2 1 2 1 101000 r 74 goat snp10632-scaffold1377-1537963 19 24684904 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272901 Affx-1111833135 AX-519546589 19 24205849 ATCACTGCCAGGTTACAAAAGGCCAAAAGATGGAA[A/G]ACGGTTCATGTGTCACCCAGGACCTGACTCGTTTA R 2 1 2 1 101000 f 74 goat 19_24205849_AF-PAKI 19 24205849 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38382083 Affx-122974908 AX-123252441 19 24251863 GCGTCTGGATCCCAATTAACAGCCGAGAAGTCAAG[C/T]TTCCCTGCCAAGGGGACTGGAAGGAGGGAAGAAAA Y 2 1 2 1 101000 f 74 goat snp10631-scaffold1377-1460333 19 24762354 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377277 Affx-122978127 AX-123247636 19 24285600 CCTGGCTATCTTGGGAAAGGGAGATATAGGCAGAG[C/T]TGAAGTCTAGCAGGCGAGAGTCCCTGAGACCAAGT Y 2 1 2 1 101000 f 74 goat snp10630-scaffold1377-1426596 19 24796910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419315 Affx-122945664 AX-123289663 19 24325658 TCCTGTCAACTATATTTCTCATGTCATGGGTACCT[C/T]TTCTCATAACCGGTTCTCTAAAACCCACTCCGTCT Y 2 1 2 1 101000 r 74 goat snp10629-scaffold1377-1386538 19 24836694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790198 Affx-122935015 AX-385277202 19 24368806 AGCAGTTTGTTTCCTAACATTAATTTAGGCAATAA[C/T]GCATTCTCAGACATCCCCTTCCCACTTAACAGAAT Y 2 1 2 1 101000 r 74 goat snp10628-scaffold1377-1343390 19 24879824 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782813 Affx-122922299 AX-385269885 19 24443851 TTTCTTTCTTGTCAAAGAAAAGGTTTGGATCTTAA[C/T]TATTTTCCTCCTTTTGAACAGAGATGGTTGGTCTG Y 2 1 2 1 101000 r 74 goat snp10627-scaffold1377-1268345 19 24955343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402853 Affx-122958247 AX-123273206 19 24511985 AAGCCTGCTGCTCTAATACTGCCAGCAGTGGGAGG[C/T]CTGTGTCTCTGAGAGTGGAAGTTGGCATGTGCACA Y 2 1 2 1 101000 r 74 goat snp10626-scaffold1377-1200211 19 25023762 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse369 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38428636 Affx-122938669 AX-123298978 19 24576282 TAGATATCATTCAAACTGCACACAAAAGAAATACT[G/T]CCTAGAAAAAATACTGTGCAAAATACATGCAGACA K 2 1 2 1 101000 r 74 goat snp10625-scaffold1377-1135914 19 25087981 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399962 Affx-122960834 AX-123270317 19 24636551 TTACAGTGTCATCATAGCCTGGAGAACAGACAGGC[A/G]TGAACGCGTGGATCTCTACATCCACTGAGGGATGA R 2 1 2 1 101000 r 74 goat snp10624-scaffold1377-1075645 19 25147677 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse370 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38399014 Affx-122960935 AX-123269369 19 24718386 CCAGCCTGCCCCCAGATCAGGGGGAACACGAGCAA[C/T]GGGAAAGGTCTCTCGGCTTAGTTCAGAGCAAAGTA Y 2 1 2 1 101000 r 74 goat snp10623-scaffold1377-993810 19 25228631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602112 Affx-1002480060 AX-413836489 19 24748582 CTCCACTGTTGGGCTGGTGCTCAGAGAGCACTCCT[C/T]TAGTCACCCAAGGCTGCACAGTGAGCTAGCCGCAG Y 2 1 2 1 202000 f 74 goat QTLSaanen19.118 19 24748582 T C 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601883 Affx-1002479943 AX-413836266 19 24753146 CTGCAGTGAAAGTGCAGAATTTTAACCACTGGACC[A/G]GCCTGGGAAGTCCCAGGATATTATGATGTTTATCC R 2 1 2 1 303000 f 74 goat QTLSaanen19.1 19 24753146 G A 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602175 Affx-1002480061 AX-413836549 19 24753686 TTCAGTCTCATATCTCCCTCTGCTTCCCTCTTATA[A/G]AGGACATTTGTAGCTGCACTAAGAGACCCACCTAA R 2 1 2 1 201000 r 74 goat QTLSaanen19.119 19 24753686 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38411823 Affx-122951243 AX-123282173 19 24755283 AGCCAGCTGGTAGCTTCTGGATTACCTCCAGTGAC[A/G]GGGAGCTCGTTCCACCACTAGCTGGATATGCCCTT R 2 1 2 1 101000 f 74 goat snp10622-scaffold1377-956913 19 25265701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601301 Affx-1002480062 AX-413835731 19 24755992 AAGTAAGGAAGGGCTACTTGAGGGATGTTCAGAGA[-/CAG]CAGAGAGTGAAGGATGGAATCAAGAAGTGTAAAAT - 2 1 2 1 201000 f 74 goat QTLSaanen19.120 19 24755992 - CAG 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602116 Affx-1002480063 AX-413836493 19 24759251 GGCTCAGTAGTTGTGGCCTGTGGGCTGAGTTGCTC[C/T]CGCGGCACCTGGAATCTTCCTGGATCAGGGACTGA Y 2 1 2 1 303000 f 74 goat QTLSaanen19.121 19 24759251 C T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602179 Affx-1002480064 AX-413836552 19 24763419 AAGCCCCATGGGTGTACCCCCACCCCTGCCCAGGT[C/T]CGTCTCTGGTTCTGTGCTGCCCTTCTCGTCTCACA Y 2 1 2 1 202000 r 74 goat QTLSaanen19.122 19 24763419 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602181 Affx-1002480065 AX-413836554 19 24763828 CTCACATGCTGTGCATGTGGCCAAAAAAAAAATTT[A/T]AAAAAGATGTAAAATAAATGGTGAGTTAGATGGGG W 4 1 2 1 103000 r 74 goat QTLSaanen19.123 19 24763828 A T 1 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601884 Affx-1002479944 AX-413836268 19 24764366 CTTCAGTTAATGATTTATTCTCATGATTCTGTGAG[C/T]TTGGCTGGATGGGTTCATGGCTGGGAACCAGCCCA Y 2 1 2 1 201000 f 74 goat QTLSaanen19.2 19 24764366 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602123 Affx-1002480066 AX-413836500 19 24766717 ATGTAGGGTCTAGTTCCCTGACGAGGGATGAAACC[C/T]CGGGGCCCCTGCGTTGGGAGCACAGAGTCTTAGCC Y 2 1 2 1 303000 f 74 goat QTLSaanen19.124 19 24766717 C T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601965 Affx-1002479945 AX-413836346 19 24777785 TTCTGTGGGCCCTTGATTGGTGCTGGTTATGCCCC[A/G]GGGCTATAAAGGGAACAGCTCTTCTAAGAAGGGCA R 2 1 2 1 201000 r 74 goat QTLSaanen19.3 19 24777785 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602184 Affx-1002480067 AX-413836557 19 24778897 CAAGTTACTCACCCTCTCTGTGGAGAGTTTCATCA[A/G]ATTGTAGTAGTGGATAGGAATTGTGTCTCCCTCAT R 2 1 2 1 201000 r 74 goat QTLSaanen19.125 19 24778897 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602186 Affx-1002480068 AX-413836559 19 24779764 AGAGTCAGACAGCTAGTGAGTGGGGGGTGTGGGAT[G/T]TGGAACCCAGACAGTCTGACTGCAGAATTCATATC K 2 1 2 1 202000 r 74 goat QTLSaanen19.126 19 24779764 T G 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602130 Affx-1002480069 AX-413836506 19 24782968 TGAGGGTCCTCGTTTAGGGTTCTGCTCCCAAGTAC[A/T]AACATGGGCATGGGAGGGAGAGGGTCATTCCCACA W 4 1 2 1 202000 f 74 goat QTLSaanen19.127 19 24782968 A T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601398 Affx-1002479946 AX-413835819 19 24788694 AGAAGGCCCTTTAGCCATCATTGACTTCAGCCTCC[-/CCAGA]CATTATGATGAGGAAGCTCTGTCCTGGAGAAGCTA - 2 1 2 1 201000 r 74 goat QTLSaanen19.4 19 24788694 - CCAGA 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601967 Affx-1002479947 AX-413836347 19 24790067 TCTCCACAGGGGATGGGGCTCCCTGCTCCCCCAAG[A/G]AGAGAACCTGGGGGACTTCCAGACCATCTAAAGCC R 2 1 2 1 202000 r 74 goat QTLSaanen19.5 19 24790067 A G 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38406843 Affx-122955668 AX-123277194 19 24791136 CAAGGGTATCATTCAACATGATTTTACAAACACAT[A/G]TACCTCTATAACCCAAACTTTTACCAAGATACAGA R 2 1 2 1 101000 r 74 goat snp10621-scaffold1377-921060 19 25301384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426726 Affx-122939880 AX-123297072 19 24873919 GTAGACTGTAAAGACTTACGCACCAGGGAGGGGAG[C/T]ACCGTGTCCTTGGGTGCTCGAAACCTCTCTCCACT Y 2 1 2 1 201000 r 74 goat snp10620-scaffold1377-838277 19 25384478 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784250 Affx-122966534 AX-385271301 19 24903099 ACAAGCTGTGGACCAGAACCTTCACATTCCTTATC[C/T]TATTTCCTCTTTGCGGTTCACGACATAAGCGCTAT Y 2 1 2 1 101000 f 74 goat snp10619-scaffold1377-809097 19 25413768 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441963 Affx-122928564 AX-123312300 19 24938871 CGTATCCTTGCATTTGCAGGTGCATTCTTTACCAC[C/T]GAGCCACCTGTGAAACCCCCTCAAAGGAGATTACA Y 2 1 2 1 303000 f 74 goat snp10618-scaffold1377-773325 19 25449532 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798966 Affx-122921867 AX-385285896 19 25033929 CCATACATGTAGGTGGGCCATTTTGTGTGATCTCT[A/G]TTTACTTATTTTTGTGCCATACCTGTCCCTTTATT R 2 1 2 1 102000 f 74 goat snp10616-scaffold1377-678267 19 25544601 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375936 Affx-122978460 AX-123246295 19 25106937 GTGTATCTCTGAGTCCTCAGCACTTGTCAAGTGTG[C/T]GGTGTGCAGTAAAGGGTTAATGCGTGATGCTTTTA Y 2 1 2 1 101000 r 74 goat snp10615-scaffold1377-605259 19 25617449 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407969 Affx-122954340 AX-123278320 19 25180864 GAAGGGGGCTGGGAGCAGTGCTAACTTAGAACCCA[G/T]CTTATTGGAGAAAACTTCTATGGCTCTGGATCCAT K 2 1 2 1 101000 r 74 goat snp10614-scaffold1377-531332 19 25691754 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398661 Affx-122961886 AX-123269016 19 25233291 CCTTGGATGCAGCTTTTTAGGTTAGAAAATAAAGA[C/T]GTCCCAGGCAGGTGGGAACCGTGACACCCTCGACA Y 2 1 2 1 101000 f 74 goat snp10613-scaffold1377-478905 19 25743935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382689 Affx-122973644 AX-123253047 19 25271275 ATGTATTCATTCTCTCTTTAACTTTATCCCCTAAC[A/G]TTGATCACTTCTATTGAAAAAAAGTTAAATGCCTA R 2 1 2 1 201000 r 74 goat snp10612-scaffold1377-440921 19 25782297 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382894 Affx-122973413 AX-123253252 19 25312056 CTCTCTTTCGCCCTCACAGCAAACCTGTAAAGAAG[C/T]AGCAGTTAGGAGTTTGCAGGTGAGAAGAGGAGGCT Y 2 1 2 1 101000 r 74 goat snp10611-scaffold1377-400140 19 25823025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444201 Affx-122927257 AX-123314538 19 25346843 CTCCTTGCTCAGCTGAGTCTGGTCCAGCCTGCAAG[C/T]GCAAAGGAAGCCTGGTTCTCCCGGGACCCCTGTGT Y 2 1 2 1 101000 r 74 goat snp10610-scaffold1377-365353 19 25858121 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446860 Affx-122925251 AX-123317196 19 25463013 TTGAACCCTCTCTGCTAATTAGATGCCCTTTGTCC[G/T]TTTATCACTGCGGTACCCTTGTCTGTTACAGCACC K 2 1 2 1 201000 r 74 goat snp10608-scaffold1377-249183 19 25974602 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380119 Affx-122976001 AX-123250477 19 25517617 TTCTTATATGCCAGGCTAAGTGGTTTTTACATGAA[C/T]TGTTAATTAGTTATTGTGAACTGCTGGTCGCCATG Y 2 1 2 1 101000 r 74 goat snp10607-scaffold1377-194579 19 26029220 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381863 Affx-122974182 AX-123252221 19 25560808 GAGGACAAGAGGCTTTTTGTTTTTGTTTAATCTTA[C/T]AGTAATCTAACCTTTAACCACAAGGCTTGAGATAA Y 2 1 2 1 101000 r 74 goat snp10606-scaffold1377-151388 19 26072328 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428543 Affx-122938735 AX-123298885 19 25603916 GACTTTCTTCCTCAATAGCTCTGCCTCTTCCTTCC[A/G]TCCTTCCACAAATACTTACTGAGCACCCACCATGC R 2 1 2 1 201000 f 74 goat snp10605-scaffold1377-108280 19 26115456 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441593 Affx-122928666 AX-123311930 19 25636558 TACATACCATAAAATTCTCCTGTTCTAAGTGTTCA[A/G]TTGAATGTGCTTTAGTTTATAGAGTTGTATAACCA R 2 1 2 1 101000 r 74 goat snp10604-scaffold1377-75638 19 26148755 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446088 Affx-122925809 AX-123316425 19 25679946 CCTCAGATCTCAGACTCCAGGCTGGTACTGTTTCT[A/G]TTGTTCATAATAGCCAAATGTGGTTCAGGCTTTAA R 2 1 2 1 101000 f 74 goat snp10603-scaffold1377-32250 19 26192128 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449595 Affx-122923214 AX-123319930 19 25774860 AGTGGGACATTCCCAGGGGCGAAGAGAAAGATTCC[A/G]CTTGGTTCCTAAAAATCAACAAAAGCCCTGCCCCA R 2 1 2 1 101000 f 74 goat snp23988-scaffold244-62565 19 26287227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404169 Affx-122957694 AX-123274521 19 25805397 CTTTAAAATTCTGTGAAAGGGTGAATTTTGTGGTA[C/T]GTGAATTGCACATCAATAGAACTGTTGTTAAAAAT Y 2 1 2 1 201000 r 74 goat snp23989-scaffold244-93102 19 26317344 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse371 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 350602132 Affx-1002480070 AX-413836509 19 25816244 GACATGCTCCTAGCTGGTGAGTCATTTGTAATTAA[C/T]CTCAACCTGGGATGAAAAATGTTGTGTATATGAAA Y 2 1 2 1 201000 f 74 goat QTLSaanen19.128 19 25816244 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38417542 Affx-122946926 AX-123287890 19 25858606 ACAAGTACCTGTGGAAACCAAGCTGATAAGTGACC[A/G]CATCAGCTACTGCTTGGGTATCAGCTGCTGAGCCT R 2 1 2 1 202000 r 74 goat snp23990-scaffold244-146311 19 26370999 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277237 Affx-1111835810 AX-519550743 19 25889433 TCAAGATACCAAAGGAAATTACAGGATCTAACAGC[A/C]ATTGTTTCTATATCAGCCATCAGAAACATCCAGAG M 2 1 2 1 101000 f 74 goat Random2.2K-1791 19 25889433 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468277363 Affx-1111835811 AX-519550867 19 25907644 ACCTCCCTGACTTTTTTATTTTTCTAAACAAGACT[A/G]TTACAAGACTTATACATCTCAAGCTTCTTTCTTTC R 2 1 2 1 201000 r 74 goat Random2.2K-1792 19 25907644 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396643 Affx-122962866 AX-123266998 19 25908361 CTGTCTGCTGTCCATCTGTCCTGCAGCTGCCCATA[C/T]GTCACTCAGTCTATGTGTACTCTCTTTGCCTATAA Y 2 1 2 1 101000 r 74 goat snp23991-scaffold244-196066 19 26420506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784413 Affx-122924428 AX-385271462 19 25958287 ATTATTTGTTCTGGAATGAGTGGGAAAACTCACCC[C/T]CGTCTTGAGGGACACCATGTACGCACACATGCTTT Y 2 1 2 1 101000 f 74 goat snp23992-scaffold244-245992 19 26470696 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396636 Affx-122962870 AX-123266991 19 26000942 ATCGAGATCCGGAATGCCCAGCTGGACTGGCCCTA[C/T]GAATACCTGCGGCCCAGCCTGGTGGAAAACAGCGT Y 2 1 2 1 201000 r 74 goat snp23993-scaffold244-288647 19 26513448 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416374 Affx-122947873 AX-123286723 19 26029589 CTTTGACAGGGGCCAGTGAAATACTTAGGGACATG[C/T]AGGATTTAGAATAGAATCCATCTGAATTCTCCTTC Y 2 1 2 1 201000 r 74 goat snp23994-scaffold244-317294 19 26542254 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424219 Affx-122942490 AX-123294565 19 26066457 CTTGGCTACACTGAGCCACCAATTCTTCAAAAAAA[C/T]GACTGCACACTTTCTTCCTGATTAACCCCTTTCTT Y 2 1 2 1 202000 r 74 goat snp23995-scaffold244-354162 19 26578775 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432349 Affx-122936277 AX-123302690 19 26098302 AACTGTTTCATCGCGGCGGGCCTTTACCTCCTCCT[C/T]GGAGGCTTCTCTTTCTGTCAAGTTCGGCTCAATAA Y 2 1 2 1 201000 r 74 goat snp23996-scaffold244-386007 19 26610610 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse372 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38438161 Affx-122931846 AX-123308499 19 26150581 CCTTTCAGGCACACTTATCTGCTCCTACTTCTACA[C/T]ACAGGTTTCCCTGGTGGCTCAGATAGTAAAGAATC Y 2 1 2 1 101000 f 74 goat snp23997-scaffold244-438286 19 26662281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601890 Affx-1002479948 AX-413836273 19 26153814 AATGTTTGAGAGAACAAATCCTCTAAGACTTGGAG[C/T]CATGATTGAATACACGCATGAGGTAGGTATAATTA Y 2 1 2 1 201000 f 74 goat QTLSaanen19.6 19 26153814 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602192 Affx-1002480071 AX-413836565 19 26154829 ATGACAGCAGCAGAAACTAGGTGCCAGTGGACTGA[C/T]TTAGTAAATTTGCTGCTTCTTTCAGAAATTTTAGA Y 2 1 2 1 201000 r 74 goat QTLSaanen19.129 19 26154829 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601892 Affx-1002479949 AX-413836275 19 26164860 AAGTGTATTTGCGTTACCACCTGGCTTCCATACTT[C/T]CAAGACCTGGTTCCAAAAAATCACATCCACAAAGC Y 2 1 2 1 201000 f 74 goat QTLSaanen19.7 19 26164860 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601973 Affx-1002479950 AX-413836353 19 26173578 AGAAAGAAAGAAAAGAAAAATCAAATTTGAAAAAA[A/T]TAAGTTAGCAAAGAGAAAAGGTGCATAGGGTGGAA W 4 1 2 1 303000 r 74 goat QTLSaanen19.8 19 26173578 T A 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601975 Affx-1002479951 AX-413836355 19 26175539 TTCTCTTTTTTCAGAAGCAGATTCTCAGGCACATG[C/T]CCTAGTGAGGGTATCACCACATTCATTACATTCAT Y 2 1 2 1 201000 r 74 goat QTLSaanen19.9 19 26175539 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601897 Affx-1002479952 AX-413836280 19 26182159 GCTTAGATATATCCATAGCAGTACGGTTGTACTTT[A/T]TTTGCTTGGTTCATAGGTTGTTAGTTTTTCTTCAG W 4 1 2 1 201000 f 74 goat QTLSaanen19.10 19 26182159 T A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601899 Affx-1002479953 AX-413836282 19 26184176 AGACGCAGGGACTGTGAAAAGAAGCACCACCTTAC[A/G]GACCAACCCAGGCCTTACAAAAGGAAAAGATTCTG R 2 1 2 1 201000 f 74 goat QTLSaanen19.11 19 26184176 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38404275 Affx-122957045 AX-123274627 19 26212116 CCCACCAGCCTTCCCAAGGACTCAAGAGAAGCCCA[G/T]GGCCCCTCTCCCCGCAGGTCTCCCCAACCTGACCC K 2 1 2 1 101000 f 74 goat snp23998-scaffold244-499821 19 26724454 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602136 Affx-1002480072 AX-413836513 19 26256117 CCTGCGGGCAAGGCAGAGCCAGTTGAGTCATCCTC[A/C]ATGTGTGGGTGGGGCTCTCCCTCTCTGAGTCACAA M 2 1 2 1 202000 f 74 goat QTLSaanen19.130 19 26256117 A C 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601901 Affx-1002479954 AX-413836284 19 26265396 AGGAAACTTCTGATTCTTGACTTGGAACTTGCTCG[C/T]CGGTGGCCTGGTTGTTGGTGACCCCTGGAGGAGAG Y 2 1 2 1 202000 f 74 goat QTLSaanen19.12 19 26265396 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320768271 Affx-122945496 AX-385255452 19 26268239 GCAGCTTCCAGTGAGAAGTGGGCTGGAGGCATAAG[A/G]GAAAGTGACAGGATAGGAACACCACCTCCCCCCAA R 2 1 2 1 101000 r 74 goat snp23999-scaffold244-555944 19 26780952 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602195 Affx-1002480073 AX-413836568 19 26277161 TTACTGTATATGAATTCCAGACAATCCTGCCAAAG[C/G]GTATGGTGATACTTTGTTTCAGTGTTTGTCTACCC S 4 1 2 1 201000 r 74 goat QTLSaanen19.131 19 26277161 G C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601903 Affx-1002479955 AX-413836286 19 26284437 GCTTAAACTGAAGAGTTAGTCCATGGTTTGGAAAA[C/T]CGGACAGAAACCACACCCGGAGGAAGTTGAATGTA Y 2 1 2 1 201000 f 74 goat QTLSaanen19.13 19 26284437 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601984 Affx-1002479956 AX-413836364 19 26304193 CCTAAGCTCACCAGCAGACCAGCAGTGGGACCAGG[A/G]ATCTGGTCAGGTCAGGCCCTTCCAGGAGGACCCGC R 2 1 2 1 202000 r 74 goat QTLSaanen19.14 19 26304193 A G 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38434766 Affx-122933896 AX-123305107 19 26333072 TCATTATAGTGGGTGGGGCCCCGTGTCCCTCCCAT[A/G]CTCCTGAGTCTTGACAAAAATCAAGCTCTCCTTGC R 2 1 2 1 101000 r 74 goat snp24000-scaffold244-620777 19 26844931 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449379 Affx-122922718 AX-123319714 19 26396591 ACCGACCTCTTCCCCTGCAACTTCTCTAAGAATGA[C/T]GTCATGCTCAGCGCCGTGGTCATGACCTACTGGAC Y 2 1 2 1 202000 r 74 goat snp24001-scaffold244-684296 19 26907844 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602140 Affx-1002480074 AX-186337485 19 26440498 CTCATGATGTATTCTGCATAGAAGTTAAATAAGCA[C/G]GGGTGACAATATATAGCCTTGACATACTCCTTTTC S 4 1 2 1 303000 f 74 goat QTLSaanen19.132 19 26440498 G C 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601907 Affx-1002479957 AX-413836290 19 26444054 TACTTTATGAAGCTGTTGCCCCTAGAGGGCCTGCC[G/T]TCAGACACCTGGGTGGTCCACCTCAGGGTCTTTGT K 2 1 2 1 303000 f 74 goat QTLSaanen19.15 19 26444054 T G 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38445997 Affx-122925874 AX-123316334 19 26446791 CAACATTTTGTGCCCATGTGGCCAGCACCCAGCAG[C/T]GAACGCTAAGTTCTCCCTCCCAGGCAGGGACTCCC Y 2 1 2 1 201000 r 74 goat snp24002-scaffold244-734496 19 26956209 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601988 Affx-1002479958 AX-413836368 19 26463270 GGTGGCCTCCTGACGGAAGGCCCCGGTCCTGCGCC[A/G]ACATGAAGTGCCGTCTGCCTACCCTGCTCCAGGCT R 2 1 2 1 202000 r 74 goat QTLSaanen19.16 19 26463270 A G 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602142 Affx-1002480075 AX-413836518 19 26543297 TATGATAAACCATAATGGAAAAGCTTATTACAAAA[A/G]GAAGGTATATATGGACTTCCATGGTGGCTCAGTGG R 2 1 2 1 303000 f 74 goat QTLSaanen19.133 19 26543297 G A 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601399 Affx-1002479959 AX-413835821 19 26545857 TGTTATTGAGAGAAAGGTCTATAATTTTCTTTTCT[-/TAAGC]TAAGCAATCCTTCTCTGATTTTTATCAAGGTTTTA - 2 1 2 1 103000 r 74 goat QTLSaanen19.17 19 26545857 - TAAGC 1 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601990 Affx-1002479960 AX-413836369 19 26546159 AAATATATTTAGGTTTTCTATTCTTGAGGAAGATT[C/T]CAGTTCTACTTTGGGAACTTGTCAACACTTCATCA Y 2 1 2 1 201000 r 74 goat QTLSaanen19.18 19 26546159 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38441876 Affx-122928631 AX-123312213 19 26564853 ATAAGATGAAAGTGGAGTGAGTCTTTCAGAGCCAG[C/T]AGGCAGAGGCCTCTCCGAGGAAGATGAAAGGATCT Y 2 1 2 1 101000 f 74 goat snp24004-scaffold244-852558 19 27074257 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601991 Affx-1002479961 AX-413836370 19 26567100 GCTTCCAGCAGCTTCTTCAGAAAGCATGCATGGGA[A/G]GGGAAATGCATCCTTGAAATCTTGCCTATCTGAAA R 2 1 2 1 201000 r 74 goat QTLSaanen19.19 19 26567100 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601914 Affx-1002479962 AX-413836297 19 26571966 GGAGATTAGTATGGTTTAAGAAGATACACATGAGC[A/G]GTCAGCTTAACAGGGGGTGGACGTGTGATGGTTCA R 2 1 2 1 201000 f 74 goat QTLSaanen19.20 19 26571966 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601299 Affx-1002479963 AX-413835729 19 26579117 GTATAAATCACTGGAATAGAGTACAGATATAGACC[-/CAT]CATATATATACAGTCAATTGATCATGAACAAAGAT - 2 1 2 1 201000 f 74 goat QTLSaanen19.21 19 26579117 - CAT 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601916 Affx-1002479964 AX-413836299 19 26586364 AGGTCCCCAGAAAGGCTCAGAAATTAGAGTTCCAA[C/T]TGATCCCTGAAGACAGGGGTGCAGGTTAAGACTGA Y 2 1 2 1 202000 f 74 goat QTLSaanen19.22 19 26586364 T C 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601918 Affx-1002479965 AX-413836301 19 26592292 CCAACATGGTGGGTCATTTTTGAGGGTCTGGCTCA[C/T]TGAAAGCAGGTTTACCTTGCCCTGGCCTAGCCCAG Y 2 1 2 1 201000 f 74 goat QTLSaanen19.23 19 26592292 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601999 Affx-1002479966 AX-413836378 19 26601886 GTGACTTTGGAAATGAGCAGAGAGACTAATTTAAA[C/T]CTGTGAGGATGACAGAGTATAAAGGCAAATCAGCT Y 2 1 2 1 202000 r 74 goat QTLSaanen19.24 19 26601886 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602002 Affx-1002479967 AX-413836381 19 26605584 CCCCCTACCCTTCTAAAATAACAATAATTGCTTAT[C/T]CGGAAGACTTATTCCATACCAGGTGATTAACTCAT Y 2 1 2 1 201000 r 74 goat QTLSaanen19.25 19 26605584 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602200 Affx-1002480076 AX-413836573 19 26607601 GGAGTGGGGGGATGGTAAGGGAGGGAGGGAGGGGA[A/T]AGATTTCTTGGAGAAACCGACAACCTCAATTCATC W 4 1 2 1 102000 r 74 goat QTLSaanen19.134 19 26607601 A T 1 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602146 Affx-1002480077 AX-413836522 19 26609728 TTCCCGAAATGGATAGCTAGGCCTTATTTCCTCAG[A/G]GACTCTACCCGCTCTACTAAAGGGAGAAATAATAT R 2 1 2 1 201000 f 74 goat QTLSaanen19.135 19 26609728 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602204 Affx-1002480078 AX-413836577 19 26610610 AACTGTTTCATCGCGGCGGGCCTTTACCTCCTCCT[C/T]CGGAGGCTTCTCTTTCTGTCAAGTTCGGCTCAATA Y 2 1 2 1 201000 r 74 goat QTLSaanen19.136 19 26610610 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602205 Affx-1002480079 AX-413836578 19 26611568 CCCGCGGGGTACGTGAGCCCGGGCTGGGGACCTGG[A/C]ACGCTGAGATCAGACGCTGGGACTCGATCACAGAC M 2 1 2 1 202000 r 74 goat QTLSaanen19.137 19 26611568 A C 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602153 Affx-1002480080 AX-413836528 19 26612688 GTAGTCTTCCACATCCATACATCTCTCCCAAAAGA[A/G]GAATTAGGGGGTGGGCCTTTCCCACTCCTCAGTTG R 2 1 2 1 202000 f 74 goat QTLSaanen19.138 19 26612688 G A 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602004 Affx-1002479968 AX-413836383 19 26612957 CTCTCTCGTCTCTTTAGGGCTCAAATAAAGGCCAC[C/T]TGTGAAACGAAAGGTATATGAAGATTCTGGTATCC Y 2 1 2 1 201000 r 74 goat QTLSaanen19.26 19 26612957 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602155 Affx-1002480081 AX-413836530 19 26613670 GCTCCATCTCGGCCCATTTTACTTCCTGTTCCAGA[C/T]CAGCCTGACTCTGGATTCTGGCCTTCTCTTGACCT Y 2 1 2 1 400000 f 74 goat QTLSaanen19.139 19 26613670 C T Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601404 Affx-1002479969 AX-413835825 19 26614373 AGCCTCAGCGGCGCCTCCCCCACCCTCGCTCTAAC[-/ACCACAGTGTGGTTTGGACGTGG]ACCACAGTGTGGTTTGGACGTGGCCACAGTGCCGT - 4 1 2 1 303000 r 74 goat "QTLSaanen19.140;QTLSaanen19.27" 19 26614373 "-;A" ";ACCACAGTGTGGTTTGGACGTGG" 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38424558 Affx-122942233 AX-123294904 19 26615494 CGATCTCCTAAACAGGTCAAAGCAATCACTGAAAA[G/T]AAAAATCAATCTTCTGTTCCTTGTAAGAGTTGTTA K 2 1 2 1 101000 f 74 goat snp24005-scaffold244-903199 19 27124885 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602006 Affx-1002479970 AX-413836385 19 26619327 ATCGCGCCCGGTCAGAGCCCCTCTTTTGCAGGCCC[C/T]CGCTAGAGGAGCCTGTTGAATGACCACACCCTCCC Y 2 1 2 1 202000 r 74 goat QTLSaanen19.28 19 26619327 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602008 Affx-1002479971 AX-413836387 19 26629614 CACAAGGTCATACAGCTAGAAAGTATCGAACCAGG[A/G]GTTGTGATTTAGGCCTGTGCTCCACTTTGTTGCTG R 2 1 2 1 201000 r 74 goat QTLSaanen19.29 19 26629614 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602211 Affx-1002480082 AX-413836584 19 26631155 TCTTTTTCTCTTTTGAACCTAGGCTACCTCCGGGA[C/T]TGTGACAGGCAACTACACAGCTTCTTTTGTGGTAG Y 2 1 2 1 201000 r 74 goat QTLSaanen19.141 19 26631155 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601929 Affx-1002479972 AX-413836312 19 26631468 GCCTTAAGCATCTTGATCTGCACCCCCTCCCTGCC[C/T]CCTCAGAGCAGGCGTGGGGCTCCTGCAATGTGTGT Y 2 1 2 1 303000 f 74 goat QTLSaanen19.30 19 26631468 C T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602160 Affx-1002480083 AX-413836534 19 26632026 TCTGAGATGCTTGTATTTTCCTCAGGCCAGTAAAG[A/G]GGGGACTGAAATGCAGAAAGACTTATCTGGGAAAT R 2 1 2 1 201000 f 74 goat QTLSaanen19.142 19 26632026 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602162 Affx-1002480084 AX-413836537 19 26639037 GCCATGGAGGAAATTCAGGGTGTTGATCCCAATGC[C/T]CGGAACAAGTGGAATCTCAGACTCTGGCTTAGATT Y 2 1 2 1 201000 f 74 goat QTLSaanen19.143 19 26639037 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601931 Affx-1002479973 AX-413836314 19 26640864 ACTCAAGGGCGAAAACACATTAGAAAGACAGTTTA[C/T]CGCTTTTGCCCTTCCTCAGCACACAGGAAGTCAGG Y 2 1 2 1 201000 f 74 goat QTLSaanen19.31 19 26640864 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601933 Affx-1002479974 AX-413836316 19 26647834 CTAACGGACTGACAAACCAGTCAATCATAAAGGAA[A/G]ATCAGTCCTGACTATTCATTGGAAGTACTGATGCT R 2 1 2 1 303000 f 74 goat QTLSaanen19.32 19 26647834 A G 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602164 Affx-1002480085 AX-166915875 19 26653215 TGAAAAAGTTGGCTTAAAGCTCAACATTCAGAAAA[C/T]CGAAGATCATGGCATCCGGTCCCATCACTTCTTGG Y 2 1 2 1 303000 f 74 goat QTLSaanen19.144 19 26653215 C T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601935 Affx-1002479975 AX-413836318 19 26653421 ATATTCAAAAGCAGAGACATTACTTTGCCGACTAA[G/T]GGTCCATCTAGTCAAGGCTATGGTTATTCCAGTGA K 2 1 2 1 303000 f 74 goat QTLSaanen19.33 19 26653421 G T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602017 Affx-1002479976 AX-413836397 19 26658374 ACTGACAAAATAGAGGCACGGCCCTAAACCCCTCC[C/T]CTTTGTTCCGTAGGCATGGACCTGGAATGAAGGAG Y 2 1 2 1 303000 r 74 goat QTLSaanen19.34 19 26658374 C T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 468273723 Affx-1111833802 AX-519547335 19 26659230 CTCAAGACCCAGGAAGAATCAATGTCTCCACCTGA[A/G]TCTGCAGGTAGGAAAACAACCGATGTTGC R 2 1 2 1 101000 f 74 goat GoatD01.005522 19 26659230 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38408855 Affx-122954005 AX-123279206 19 26661082 TTTGGACCACTGGGAAAATTTGAATGTGAACGATG[C/T]ATTATGTAAAGTATTAAATGAAGTTCAATTTTCTG Y 2 1 2 1 101000 f 74 goat snp24006-scaffold244-948787 19 27170279 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602019 Affx-1002479977 AX-413836398 19 26666496 CTGAAAAGCAGCTAAACCTGTGCAGAGAAACTATC[G/T]TAATCTGTGCACTTACACAGAGAGAATCCGGACAC K 2 1 2 1 201000 r 74 goat QTLSaanen19.35 19 26666496 T G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602021 Affx-1002479978 AX-413836400 19 26676013 TAAATAAAATTTTATTAAACTCTTTCTGTATTTCT[G/T]GTCTACAAGTTGACTTTTTGTCTTAGAATGCTAAC K 2 1 2 1 201000 r 74 goat QTLSaanen19.36 19 26676013 G T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602023 Affx-1002479979 AX-413836402 19 26677719 TCAGGTGGTCTGGTATTCCCATCTCTTTCAGAATT[G/T]TTCCACAGTTTAACTTCTTACCTCTGTCCAAATAG K 2 1 2 1 201000 r 74 goat QTLSaanen19.37 19 26677719 T G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601945 Affx-1002479980 AX-413836327 19 26686759 AATGAAATAAGCCAATCTCCAGAATTCCTTGGTGG[C/T]TCCACTGGTTAGGACTCTGTACTTCCAAGGCAAGG Y 2 1 2 1 303000 f 74 goat QTLSaanen19.38 19 26686759 T C 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601947 Affx-1002479981 AX-413836329 19 26700292 ACTCAATAACTGTGGTGCACAGGCTTAGTTGCTCT[A/G]ACGGCATGTGGGATCTTGCCGGGCATTGGCAGAAA R 2 1 2 1 303000 f 74 goat QTLSaanen19.39 19 26700292 A G 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602029 Affx-1002479982 AX-413836408 19 26704024 ATCTAGAAAGATGGTGAGAAATGTGTATGTTGATA[A/G]GATCTTTTTTGGCTATACTTTCATATTTAAATCTA R 2 1 2 1 201000 r 74 goat QTLSaanen19.40 19 26704024 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602032 Affx-1002479983 AX-413836411 19 26712860 CTGGTTCTACCCTAAAGCCATGTGCCCAAAGCCAT[G/T]TGCTTAGGGAGCAGTCTGTGAACCAGTAACGAAAA K 2 1 2 1 201000 r 74 goat QTLSaanen19.41 19 26712860 T G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38416306 Affx-122947927 AX-123286655 19 26722475 AAGCACAGAGTCCTAACCACTGAACCACTGGGAAA[G/T]TCCCAGGAGCTTGGTGTCTTTTGAGGGGTATTGGT K 2 1 2 1 103000 r 74 goat snp24008-scaffold244-1010180 19 27232227 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601302 Affx-1002480086 AX-413835732 19 26728937 AGCTCTTCTTCCAAATGTAATTTTCCAGTTGGGGG[-/TG]TGGGGGGGGTGAACATTAACATTCTGATGAGGATT - 2 1 2 1 202000 f 74 goat QTLSaanen19.145 19 26728937 - TG 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601953 Affx-1002479984 AX-413836334 19 26730536 GTTCCCTGACCAGGGACTGAATCCAGGCCACAGCA[A/G]ATGAAAGCCCAGAATCCTAACCACTAGGTCACCAT R 2 1 2 1 303000 f 74 goat QTLSaanen19.42 19 26730536 A G 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38411897 Affx-122951186 AX-123282247 19 26777010 AAGCTGCTGTATCTGCCAAGGGAAGCACTCTAACC[C/T]GGGCTCTGTCGCCTTTTGGGCTTCTGGCCTTTGCT Y 2 1 2 1 101000 f 74 goat snp24009-scaffold244-1064715 19 27284922 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602036 Affx-1002479985 AX-413836415 19 26785585 TAAGTTCCAAGAGATGTGTCTGGATTTTATCCCCA[A/G]ATAAATAGCTGATGAATAAATGACTAAATTGCAAA R 2 1 2 1 201000 r 74 goat QTLSaanen19.43 19 26785585 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601958 Affx-1002479986 AX-413836338 19 26801130 CACCCCCTTCCCAAGATTTAATCTCACTTCTCACA[A/C]CGGCAGGCTCAGTCCTCTTGCTCAGCCTTCCAGGG M 2 1 2 1 202000 f 74 goat QTLSaanen19.44 19 26801130 C A 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602165 Affx-1002480087 AX-413836540 19 26804190 CATGAGGCTTAGCCTGGAGGTGTGGTGGGGATGGA[A/G]GAAACAGGGCTGGCAGCAGGGGAGCATCTCGTGGA R 2 1 2 1 303000 f 74 goat QTLSaanen19.147 19 26804190 G A 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602167 Affx-1002480088 AX-413836541 19 26815877 AAATGTGGACCACTTTTAAAGTCTTTATTGAATTT[C/G]GTTACAATACTGCTTCTGTTTTATGTGTTTGGGTT S 4 1 2 1 303000 f 74 goat QTLSaanen19.148 19 26815877 G C 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602040 Affx-1002479987 AX-413836419 19 26818809 GTCAGGGAAATAGCTCCCATGTGCCACAACTAAAT[A/C]ATAAAGACCAAAGGTCTCATATGTCACAACTGAGA M 2 1 2 1 201000 r 74 goat QTLSaanen19.45 19 26818809 A C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602042 Affx-1002479988 AX-413836421 19 26824298 TGCTTGTCTTGTTCCACAATACTGTCCACCAGTCT[A/G]GCGGAAGCAAACAAGGTAGCCACGAAGGTAGTGCT R 2 1 2 1 201000 r 74 goat QTLSaanen19.46 19 26824298 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602170 Affx-1002480089 AX-413836544 19 26836450 AGTGAGCCTGAGGCTGTCCAGGTAATGGCACTCAT[A/G]ACCTCTGCCCACCTGCTACAGGGCCGCTATACACC R 2 1 2 1 202000 f 74 goat QTLSaanen19.149 19 26836450 A G 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602225 Affx-1002480090 AX-413836597 19 26841732 GATGGCCTCATTGTGTATGGGATGAGGGGAGAAGA[A/C]ATCAATAAAGGGAGAATGACACAGACCCCCCTCAG M 2 1 2 1 202000 r 74 goat QTLSaanen19.150 19 26841732 A C 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38380301 Affx-122975399 AX-123250659 19 26852765 CCAGTTTCTGCCTCTCCCAGTCCCCCTTATTTCTG[A/C]TGCAGCAATTCCTTCTGGAACTTTGGAGACCAGCT M 2 1 2 1 201000 r 74 goat snp24010-scaffold244-1140470 19 27360768 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377013 Affx-122977722 AX-123247372 19 26892646 GCCCAAGTGAGACCCCTAGAAGTCACTTGATTCCT[A/C]TAACCCTTCCTTGGATGTCCAGACATCCAGTCCTG M 2 1 2 1 201000 r 74 goat snp24011-scaffold244-1180351 19 27401023 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444737 Affx-122926402 AX-123315074 19 26972244 GAATGGAGCAATTCATGAATAATTCCTATGACACT[A/G]TGGTGCCCTTTTCCTTTCCCTGTGTTTCTCCTCAA R 2 1 2 1 201000 f 74 goat snp24012-scaffold244-1259949 19 27480793 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429531 Affx-122937839 AX-123299873 19 27021882 GAAGCGCGAATAGGCCCTGAGCACTATCTCAAAAA[C/T]AGTTAAGCCCTTGACAAGTGAACATTATGATGACT Y 2 1 2 1 101000 f 74 goat snp24013-scaffold244-1309587 19 27529983 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377854 Affx-122977280 AX-123248213 19 27050475 AGGATGGCCATGTGTAGAGGCCAGAGCTGAGCCTG[C/T]CCTGTTGGGAAACCAAGCTACCTCCATCCCATATC Y 2 1 2 1 101000 r 74 goat snp24014-scaffold244-1338180 19 27558520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601964 Affx-1002479989 AX-413836345 19 27087979 TGCTCTTGGGACGCCAGAAAACCCTTCTTGGCTCA[G/T]GCATCCACCTCCAAGATCAAGTAAGGCGGGGCATG K 2 1 2 1 201000 f 74 goat QTLSaanen19.47 19 27087979 G T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38405849 Affx-122955863 AX-123276201 19 27097065 TCTGATTCTAGTTCTTTTTTTCTCCCCTCTGGCCA[C/T]GCTGAATGGCTTGTAAGATACCAGGCCTGGGGAAC Y 2 1 2 1 101000 r 74 goat snp24015-scaffold244-1384770 19 27605322 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446393 Affx-122925579 AX-123316729 19 27138696 TTTGTTTCTGATTTGATTTGGCTTAGAGGGTAAAG[C/T]GTCCGCCTGCAATGCGGGAGACCCGGGTTCAGTCC Y 2 1 2 1 103000 f 74 goat snp24016-scaffold244-1426401 19 27646998 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406100 Affx-122956221 AX-123276452 19 27172738 AGCCTATTGCCTACTGGTGTATGTACCAGTGTAAC[C/T]CTCTCTGTCCCATTTCCCTGCCCCCCCCTGAGAAA Y 2 1 2 1 101000 f 74 goat snp24017-scaffold244-1460443 19 27681683 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602045 Affx-1002479990 AX-413836424 19 27179146 CTATGCCCTGCTTCATTTTGTACTCCAAGGCCAAA[C/T]TTTTTTTCATATTTCATTGTGCAGCTAAAATTCAC Y 2 1 2 1 303000 r 74 goat QTLSaanen19.48 19 27179146 T C 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602047 Affx-1002479991 AX-413836426 19 27190171 TCCTCTTTGCCTTTCATCTTTATGTCTGTTTCTCT[A/G]ATTTTATGAGGGATCTCTGTCAAATTTATCTTGTA R 2 1 2 1 201000 r 74 goat QTLSaanen19.49 19 27190171 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602049 Affx-1002479992 AX-413836428 19 27198133 AAAAGTTAATATGGAATCCATTTCTCACTTACTAT[A/G]ATTTGAGAGCATCATTAGAGTTTATGGCTTTTAGA R 2 1 2 1 201000 r 74 goat QTLSaanen19.50 19 27198133 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38402823 Affx-122958268 AX-123273176 19 27201608 GTTTCTCTGTGCCTGCTACAGAAATCACATCATAT[C/T]TTGCTGCACGGCGATAATCACGTGATGACTTCTTC Y 2 1 2 1 101000 f 74 goat snp24018-scaffold244-1489313 19 27711134 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602050 Affx-1002479993 AX-413836430 19 27203573 GCGATCATCCATCTGAACTCCTCTTCTAGAGTCAG[C/T]CAGCTCAATCTCTGTATTCCCCACAGTGCCTAAAA Y 2 1 2 1 201000 r 74 goat QTLSaanen19.51 19 27203573 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602052 Affx-1002479994 AX-413836431 19 27207748 AGGGCCGCGACCAATGTCACTCACTGTTCTCCTCC[C/T]CCAGGCCTCCTGGACACGTTGATAGAAATGAACAC Y 2 1 2 1 202000 r 74 goat QTLSaanen19.52 19 27207748 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602054 Affx-1002479995 AX-413836433 19 27214437 AGAGTCTCCTTTGAGACTTCCTAACCTTGAGTCAG[C/T]CCTCACATGGTTTCTGGTCATCGTTTATTTTACTG Y 2 1 2 1 201000 r 74 goat QTLSaanen19.53 19 27214437 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601978 Affx-1002479996 AX-413836358 19 27220123 AAAGTAGGTGCTTGTTTATTTTATATATAGCAGCT[A/G]ATATCTGCTAATCTCAAACTCTTAATTTATCCCTG R 2 1 2 1 303000 f 74 goat QTLSaanen19.54 19 27220123 A G 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602058 Affx-1002479997 AX-413836437 19 27228780 GACCGACTGGTTGACGCCACAGACATGGAAGCCTT[C/T]CGTGAGCATCCTAAGTGACAAACTCGGCTCCTTCT Y 2 1 2 1 201000 r 74 goat QTLSaanen19.55 19 27228780 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38376163 Affx-122978843 AX-123246522 19 27234478 ATGGGATGTATGTGAAGCCAATTACACATATTATC[G/T]CATTTAAGCCCAAACAACGCCATGAGGTCAGTACT K 2 1 2 1 101000 f 74 goat snp24019-scaffold244-1522183 19 27744036 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse373 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468274442 Affx-1111834289 AX-519548033 19 27255363 GAACGCAAAAAGTTCCTGCAGCTTGGCTGGAACAT[A/C]ATCTACGGCTTCAATGACTCTGACTTTGAGGTTTG M 2 1 2 1 101000 f 74 goat GoatD01.029040 19 27255363 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 350602060 Affx-1002479998 AX-413836439 19 27309430 GGAGAGGGGGACATCTGGGAAGAACCAGCCCCAGA[C/T]CTGTCTGACAGGGACATCTGGAGAGAAAGCCAGGG Y 2 1 2 1 202000 r 74 goat QTLSaanen19.56 19 27309430 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601985 Affx-1002479999 AX-413836365 19 27342006 TTCTTTTAGTCTCTGCAAAGTCCCACCCAGGTCTT[C/T]CTCCCGCATTGCAGGTGGATCCTTCACCAAGTGAA Y 2 1 2 1 201000 f 74 goat QTLSaanen19.57 19 27342006 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38442717 Affx-122927861 AX-123313054 19 27344876 ATAAAATCAGTGTTCATCAGCCTACCTGTATTTTC[C/T]GGCATGGAGGCTTGATCAGTGTTTCGCTCCTTTTT Y 2 1 2 1 201000 f 74 goat snp24021-scaffold244-1632581 19 27854624 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391315 Affx-122967325 AX-123261672 19 27397899 GTTGTGTTTCAATAAATGTCACTGGACTAATTGAA[C/T]AGACATGTGGGGGAAAAAAATGAACCTTGCCCATA Y 2 1 2 1 201000 f 74 goat snp24022-scaffold244-1685604 19 27907653 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601987 Affx-1002480000 AX-413836367 19 27423959 TTTTCCAGTGAGTTGGAGACTTCCGTACTAAGGAA[A/G]GATTCTTCTTTAAAAAAATTTTTTTTGGTTGCCTC R 2 1 2 1 201000 f 74 goat QTLSaanen19.58 19 27423959 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602174 Affx-1002480091 AX-413836548 19 27425808 TCTCCATCTCCAGGGCAGGCAATTACAAAGCTTGC[C/T]CGGCCTGCCAGGCTCAGCCCAACAATGTTCCATCC Y 2 1 2 1 101000 f 74 goat QTLSaanen19.151 19 27425808 C T 1 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602176 Affx-1002480092 AX-311004123 19 27428830 CCGGGAGTTGGTGATGGACATGGAGGCCTGGCATG[C/T]CTGCAGTCCATGGGGTCACAAAGAGTTGGACACGA Y 2 1 2 1 303000 f 74 goat QTLSaanen19.152 19 27428830 C T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602065 Affx-1002480001 AX-413836443 19 27430284 CTTTTCCTATTTGGAACCAGTCTGTTGTTCCATGT[A/C]CCAGTTCTAACTGTTGCTCCTGACCTGCATATAGG M 2 1 2 1 303000 r 74 goat QTLSaanen19.59 19 27430284 C A 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602067 Affx-1002480002 AX-413836445 19 27440307 TTTACCGTCACACACCCCACGGAGCCTTCCCAGGG[A/G]AGACACATGGGCACTGGACATCTCACAAGGAGGGC R 2 1 2 1 202000 r 74 goat QTLSaanen19.60 19 27440307 A G 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602178 Affx-1002480093 AX-413836551 19 27446546 GGCCCCACAGAGGAAGGGCATGAAAACGGTCAGCA[C/T]CGCCCTTCTCTCCAGCTCTGCTCTTTGCCCCCTCC Y 2 1 2 1 202000 f 74 goat QTLSaanen19.153 19 27446546 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601994 Affx-1002480003 AX-413836373 19 27448500 CATCTTGAAATGATGGTGCTGGAAGCTGGAGATCT[C/G]GGGTCCTGGGAGCGGTGGCAGTGCTGGAGGAAGGG S 4 1 2 1 201000 f 74 goat QTLSaanen19.61 19 27448500 G C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38440448 Affx-122929401 AX-123310785 19 27455014 GGGGGAATGGAGGACACCAGAACCTAGACGCTTCT[A/G]CAGACAGGCTCACTGTTCACTCAGTCACTCTCCCC R 2 1 2 1 201000 f 74 goat snp24023-scaffold244-1742719 19 27964861 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601406 Affx-1002480004 AX-413835827 19 27464430 GTGTGCATAGGGCATCCGATCAGAGTCCTGAGGCC[-/TGA]TGAGAGTAGCCCGGCTTCCTGTGGGCATTGAGGGG - 2 1 2 1 202000 r 74 goat QTLSaanen19.62 19 27464430 - TGA 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 468272903 Affx-1111833136 AX-519546591 19 27482976 AACTGCAGATTTATACCCACTGTCAAGTCCAGCAT[A/G]CAGGGGCAATATGAACTTGGGAATCATCAGCCAGT R 2 1 2 1 101000 f 74 goat 19_27482976_AF-PAKI 19 27482976 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38386507 Affx-122970750 AX-123256865 19 27484184 AAATTCTTATAACATTTAATGTCTTCAGGGATGGG[A/C]TGGGCTGAGGCCTGATGTGAAAAACAGGGATTTCA M 2 1 2 1 201000 f 74 goat snp24024-scaffold244-1771889 19 27994714 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602071 Affx-1002480005 AX-413836449 19 27502643 GGGGCCGGTGCGGCACCGGCTGGTTTAAGGACCAT[A/T]TAGGCTGTATAATGAGGCGGGAACCTAGCTGAAGG W 4 1 2 1 201000 r 74 goat QTLSaanen19.63 19 27502643 T A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601998 Affx-1002480006 AX-413836377 19 27508512 GGTTGCAAGTCCATTTGAGATGTGCCATCAAAAAT[G/T]GACAATTTCAAAGGTGAATTCACCATGAAGCCAAT K 2 1 2 1 201000 f 74 goat QTLSaanen19.64 19 27508512 G T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602000 Affx-1002480007 AX-413836379 19 27520458 AAGGGCTGGCCAGCCAGCTGCAGGACTGAAGACCA[C/T]CGGGAAACAAGGTGCAAGTCAGTGGGAGGGAGAGC Y 2 1 2 1 202000 f 74 goat QTLSaanen19.65 19 27520458 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38433767 Affx-122934487 AX-123304108 19 27528015 TCACTCCGTTCCCTTGCCATCAACCAATCATAGAA[C/T]TGTATACCAGCTGATCACATACCCTAGGATGCGCC Y 2 1 2 1 101000 f 74 goat snp24025-scaffold244-1815720 19 28038645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602001 Affx-1002480008 AX-413836380 19 27538275 GCTTTGTATTGTAAAAAGGTTGCACATCGCTGGAA[A/G]AACAGAAGAGCAGAGTGTGGGGAGGCGAGTGATGA R 2 1 2 1 201000 f 74 goat QTLSaanen19.66 19 27538275 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602079 Affx-1002480009 AX-413836457 19 27540053 TTTTCCTTCTGCAGTAAGGAGTCCTCTTTCCTGTT[A/G]ATAAGGCTCCGTGAAAATGTAGAGTAGCAAAAGCA R 2 1 2 1 201000 r 74 goat QTLSaanen19.67 19 27540053 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602081 Affx-1002480010 AX-413836459 19 27550708 AGCAAGGTGCTTTCTCCTCGGGCCTCATCTTCCTC[A/G]ATTTATTAAATGAGGGCTCTTTCACTCTACTATGC R 2 1 2 1 201000 r 74 goat QTLSaanen19.68 19 27550708 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602007 Affx-1002480011 AX-413836386 19 27554393 CATTAGATGAGTCTAAGAAGGAGCAGCCAGAATAG[C/T]TTGGAGGTAAGCCAGGGGAACTAATTTTCGGAAAG Y 2 1 2 1 201000 f 74 goat QTLSaanen19.69 19 27554393 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602084 Affx-1002480012 AX-413836462 19 27560591 CCTGTAGAACGGAAAGTTCTCGCCGGAGTTCACGG[C/T]TTAACAGTCAAGTCACAACTTCCAGGGGCCCCCCC Y 2 1 2 1 202000 r 74 goat QTLSaanen19.70 19 27560591 T C 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602011 Affx-1002480013 AX-413836390 19 27565254 AGAAACTCCAAATTTGGGGCCTGTGAGTAGCTATC[C/T]TGGAAGGCTCCGCAGGCGGCTGTTAACTGCAGCCC Y 2 1 2 1 201000 f 74 goat QTLSaanen19.71 19 27565254 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38381018 Affx-122974656 AX-123251376 19 27565601 CATTCACTCGCTCACTCATCAAACATTTATCCAGC[A/G]TCCATATATATTTGTGTGGGACCTGGGGATTCTCT R 2 1 2 1 101000 f 74 goat snp24026-scaffold244-1853306 19 28079607 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602088 Affx-1002480014 AX-413836466 19 27570894 TAGTTTTTCAAACATTATCTTTTTAGTGAGGCCTC[A/C]CCCTTACAATCTGTTTACAATTGCAACCACTTTTT M 2 1 2 1 201000 r 74 goat QTLSaanen19.72 19 27570894 C A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602015 Affx-1002480015 AX-413836394 19 27581001 TCTTCTGCTTCTGTAAGGTCCATATCATTTCTGTC[C/G]GTTTATCAAGCCCATCTTTGCATGAAATGTTCCCT S 4 1 2 1 303000 f 74 goat QTLSaanen19.73 19 27581001 G C 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602018 Affx-1002480016 AX-413836396 19 27586204 GGTGCCACTTCTTTTCTCCACCTTATCCCAGTGCC[A/C]AAGTCACTGCCCTTGGGGCGCTGTGCTGTGAATTC M 2 1 2 1 202000 f 74 goat QTLSaanen19.74 19 27586204 A C 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602094 Affx-1002480017 AX-413836471 19 27587636 TCAGAGCGCTCTTCAGATTTAAAAGCAGTGATTAA[C/T]CTCATTAGGATAAGAAAATAAACTCATTGTCACTT Y 2 1 2 1 101000 r 74 goat QTLSaanen19.75 19 27587636 C T 1 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602095 Affx-1002480018 AX-413836472 19 27587996 TCAATCAATCCCCGTAGAGGCCTAGGACAGAAGGC[A/C]CGGTAATTGTAGAGCGCGTCCGAGAAGAAAAATTA M 2 1 2 1 201000 r 74 goat QTLSaanen19.76 19 27587996 C A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602097 Affx-1002480019 AX-413836474 19 27593851 AGACGAGAGCTGGGGCTCAGGAGGGCAGGTCAGAG[A/G]ATCCCAGGCCCTAGTTTACCTTCTGATCTGAGTTT R 2 1 2 1 201000 r 74 goat QTLSaanen19.77 19 27593851 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38450239 Affx-122922262 AX-123320574 19 27596856 TATGGCATCATTAGCTGGGAGCTGCTGTTGGCTGA[C/T]GATGTTCTGTTAGTGGGTGCTGTTTCCAGAGTGAT Y 2 1 2 1 201000 r 74 goat snp24027-scaffold244-1884561 19 28110630 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602099 Affx-1002480020 AX-413836476 19 27597256 ATTCCTGCCCCCTCTGGCTCAGGAACCTCTCCCTC[A/G]ATGCGCACCGTGTAAGATAAGAGTATGGAGTCCCG R 2 1 2 1 201000 r 74 goat QTLSaanen19.78 19 27597256 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602028 Affx-1002480021 AX-413836407 19 27618017 CAAAATCCAATTTCTTAGAAAATGTTAAGAGCTCT[A/G]AATCCCAAGAGTCAGACTCTTCCTAAAGGGTCCTG R 2 1 2 1 202000 f 74 goat QTLSaanen19.79 19 27618017 A G 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602030 Affx-1002480022 AX-413836409 19 27623534 CGAGAGTGGCCTACGGGCACAGATGGACAGGTGGA[G/T]GGCACCCCCCACTCCTCCCCCAACCCCTGTGGACC K 2 1 2 1 202000 f 74 goat QTLSaanen19.80 19 27623534 G T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38420663 Affx-122944819 AX-123291010 19 27626789 AAGTCTCAGCAAAGAAATGTAACAGGAAAATTAAG[C/T]ACCAAATGGAACTGAAAATATATAATAACTGAAAT Y 2 1 2 1 101000 f 74 goat snp24028-scaffold244-1914494 19 28140299 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602104 Affx-1002480023 AX-413836481 19 27627930 AGCTGCTAAATAGGCCGGAGGCTCCCCTGGGCCCC[A/G]GTGGTTCTTACCTAGGGTATCTTTAGAAGTACCTC R 2 1 2 1 201000 r 74 goat QTLSaanen19.81 19 27627930 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602033 Affx-1002480024 AX-413836412 19 27630850 AAAACAAAGGAAGAATTAAGGTTAAATAAATTGCA[A/T]TCATCTGCTTCCTACTGTCCTAAAGTCACATTTCC W 4 1 2 1 201000 f 74 goat QTLSaanen19.82 19 27630850 T A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38402570 Affx-122958446 AX-123272923 19 27656331 TTAAAAGGTAGAGCTGGTGGAAAAAGTGATACGTG[C/T]AATTTCACTGATGAGAATGATGTAGTTCTGTGCGT Y 2 1 2 1 101000 f 74 goat snp24029-scaffold244-1944036 19 28169892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443505 Affx-122927797 AX-123313842 19 27689196 CTGTGTGTCCTGACCTAGTGGAATTTGGTGAGCAA[C/T]GGTTCAAGGGTGGGGTTGCTAGTACGATCAGGCTG Y 2 1 2 1 101000 f 74 goat snp24030-scaffold244-1976901 19 28202268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389021 Affx-122968636 AX-123259379 19 27731088 CAGAAGTCCCAGCTCTAAGCCCAAGAGACCACACC[A/G]CCTACAAGAACAACATTGCCAATGTGCTCTGGCCA R 2 1 2 1 101000 r 74 goat snp9038-scaffold1328-1791149 19 28245491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777050 Affx-122965238 AX-385264173 19 27783737 CAGGGTGGTGCTCAGTCATTAAACTATGATCTGCA[A/C]ACAGGAGGCATCTACAGGATGTCCTCTTCAGCATC M 2 1 2 1 101000 f 74 goat snp9037-scaffold1328-1738500 19 28298525 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384801 Affx-122971996 AX-123255159 19 27833831 CAAGCTTTTCTCAGGCAGCCCAGCATGGAGGCCTT[C/T]GCTATTCAAACACTGCAAGAATCGACAGGCTCGGA Y 2 1 2 1 201000 r 74 goat snp9036-scaffold1328-1688406 19 28348471 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409818 Affx-122952953 AX-123280169 19 27892936 TACCCAGCCTGAATTACATCGAACCCTGGGCGCCT[A/G]TGCATAGAATTCAGGGAGTCCATGAACTTGGATGA R 2 1 2 1 201000 r 74 goat snp9035-scaffold1328-1629301 19 28404892 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789075 Affx-122968201 AX-385276089 19 27955432 TTTGGTTTGGTTTCTGAGGCTGCATCTGGAAGAAT[A/C]AAATCTTCAGTTTCCTTGAAACGGAGCAGAAACAT M 2 1 2 1 101000 r 74 goat snp9034-scaffold1328-1566805 19 28467161 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602035 Affx-1002480025 AX-413836414 19 27997213 GAAAATTTTCAGCTAGAGGTTAGGTGCTGGGAAAG[A/G]GATCTCTCTCTCTAAGGAAACCTTATGTTTTCTTA R 2 1 2 1 101000 f 74 goat QTLSaanen19.83 19 27997213 G A 1 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602180 Affx-1002480094 AX-413836553 19 28002831 ACAGGGAGGCCTGGCATGCTGTGGTCCGTGAGGTC[A/G]GCGAAGAGTCGGGCACGACTGAACGACTGAACTGA R 2 1 2 1 303000 f 74 goat QTLSaanen19.154 19 28002831 G A 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602182 Affx-1002480095 AX-413836556 19 28003739 TGCCAAAAAAAATAACAAGCTTGATGGGAATTCCC[A/G]AGGTGGTCCAGTGGTTAGGACTTGGTGCTTTCCCT R 2 1 2 1 201000 f 74 goat QTLSaanen19.155 19 28003739 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602037 Affx-1002480026 AX-413836416 19 28003901 CAAATAGGAGAAAATAATTCCAATTTGATAGAGCT[A/G]GTGGTGAATACTTGGGTGTTTTTTATATATGTTGT R 2 1 2 1 101000 f 74 goat QTLSaanen19.84 19 28003901 G A 1 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38442085 Affx-122928368 AX-123312422 19 28008240 TAGTGACCAAGTGTGAGATGAAAAGATGAGATGAC[A/G]TTGACTTTTGTGACCCTGTTTTTTTTTCCCCCAAC R 2 1 2 1 101000 f 74 goat snp9033-scaffold1328-1513997 19 28519694 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602039 Affx-1002480027 AX-413836418 19 28011418 GACTCAATATTGTAAAGAGGTAAATTCCATCCAAA[C/T]CGGAGTTAGGAATTTGATGTGATTGCAATCAAAGC Y 2 1 2 1 201000 f 74 goat QTLSaanen19.85 19 28011418 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602113 Affx-1002480028 AX-413836490 19 28023392 AGCTCTCTTAGTGCGACAGGAGCAGAGTTGAGAAC[C/T]CTACTGTTCATCTCAGAAACCTCAACTCCCAGAGC Y 2 1 2 1 201000 r 74 goat QTLSaanen19.86 19 28023392 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602044 Affx-1002480029 AX-413836422 19 28027977 TGGAAGACAGCCTCTAAATTTTTGAAATTTCCTAA[A/G]GGTATGAGTGTCCTTGGTATTCTTGGTGGGTCTCT R 2 1 2 1 201000 f 74 goat QTLSaanen19.87 19 28027977 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602046 Affx-1002480030 AX-413836425 19 28030933 GCCCAGCGAGAGGATGAAAGTCCACTGCAGCCCTT[C/T]CCAAGGAGAGGCCGAGGGCCCTGCCGTCCCCCTCG Y 2 1 2 1 102000 f 74 goat QTLSaanen19.88 19 28030933 C T 1 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602119 Affx-1002480031 AX-413836496 19 28035134 GGAAGCTGCCCCAGGGAACCTTGTTCTAGCCACTG[C/T]TGGCAGGACGGGTGGTGTATCCTTTCTCTCAAGCC Y 2 1 2 1 202000 r 74 goat QTLSaanen19.89 19 28035134 T C 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602051 Affx-1002480032 AX-413836429 19 28043376 CAAAAGGTGGGGAGGGGGACTTCCCCGGTGGTCCA[C/G]GGGGTTAAGAGTCCACCTTGCAGTGCAGGGGACAT S 4 1 2 1 303000 f 74 goat QTLSaanen19.90 19 28043376 G C 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602238 Affx-1002480096 AX-413836609 19 28062802 GCTCTCCACCTCAGCGTTGTGCCCCAGTGACCCCG[C/T]CTATCCTCCAGGAGGGACTGTATATCCTTCTCACT Y 2 1 2 1 201000 r 74 goat QTLSaanen19.156 19 28062802 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602053 Affx-1002480033 AX-413836432 19 28066971 TCCCCCAGCCCTGAGGTCCGTTCGTAGTGGTTTTC[C/T]CGCCACCGACCTCTCCCTCTCTTTGTCGACTGCAA Y 2 1 2 1 202000 f 74 goat QTLSaanen19.91 19 28066971 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38415108 Affx-122949442 AX-123285457 19 28067010 ATTTCAGTAGGAATTTTCTGATTTATAGTCTGTTA[C/T]GTGGTTCTCTCTGGTTTCGAGTATTAACATCTTGC Y 2 1 2 1 101000 r 74 goat snp9032-scaffold1328-1455227 19 28578424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602187 Affx-1002480097 AX-413836560 19 28083368 TTCCGGACCCAGGGATTGAACCCGTTTCTCCTGCA[C/T]TTGGCAGGTGGATTCTTTACCGTTGAGCCACCCGG Y 2 1 2 1 303000 f 74 goat QTLSaanen19.157 19 28083368 T C 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602055 Affx-1002480034 AX-413836434 19 28083843 CGCCATGAAGTTTACAGCTGATGCCCTGCTTACCC[C/T]TGGCCTCCCACCCCCGCTGCTGGTTCCTGGGCCAG Y 2 1 2 1 201000 f 74 goat QTLSaanen19.92 19 28083843 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602242 Affx-1002480098 AX-413836613 19 28084756 ACAGGACAGGCCCCTACTGGTTGGTCCTCCCCAAA[C/T]CGCATGCATTAGCAGCCAAACCAAACCTCTAGCTG Y 2 1 2 1 201000 r 74 goat QTLSaanen19.158 19 28084756 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602244 Affx-1002480099 AX-413836615 19 28085301 ATGGGCAGTATTAATACATATCCAGCCTTCCTCCA[A/G]ATCGCCTGTAGGAATCCAACAGGCTAATGAATGTA R 2 1 2 1 201000 r 74 goat QTLSaanen19.159 19 28085301 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602246 Affx-1002480100 AX-413836617 19 28090132 AACCCCAAAATCAAATGGTTCTCTGGTTGGTAGGA[C/T]CCTATTCTTAGAAAGCTGAGAGAAGTAATAAACCA Y 2 1 2 1 201000 r 74 goat QTLSaanen19.160 19 28090132 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602196 Affx-1002480101 AX-413836569 19 28090944 TTTTTTTTAATCTAGTGACTTATCCTTTCAGGCAT[C/T]TCTTATGTGGGAAGAGAAGGAATTTTTATTTTATT Y 2 1 2 1 201000 f 74 goat QTLSaanen19.161 19 28090944 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602198 Affx-1002480102 AX-413836571 19 28092450 ACGAGGACATCAGGAAGAAAGCTGAGTCCAGTCCT[A/G]GTTACCTGTGCGAGGCATCTGGCCTGTGCACGTGT R 2 1 2 1 202000 f 74 goat QTLSaanen19.162 19 28092450 G A 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602126 Affx-1002480035 AX-413836503 19 28093948 TTCCCTGAATGGGCCGTCTCTTCCCCCTCACCCTG[C/T]TGCAGAAAGGGGCACACATGTGTGGCTGCTGTAAC Y 2 1 2 1 202000 r 74 goat QTLSaanen19.93 19 28093948 T C 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38388282 Affx-122969758 AX-123258640 19 28095691 TAGATGGGTACCAAACCAGAAATCTTATTGAAGAG[C/T]GATAACTTTTTCTTCCTGGGTTAGGAAGATCCCCT Y 2 1 2 1 10000 f 74 goat "snp9031-scaffold1328-1426546;SV_204" 19 28608779 G A SV_204 2 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602201 Affx-1002480103 AX-413836574 19 28098178 CCAGTCTAATTAAGTAGTGTTTTCCATTATAAAAA[C/T]TTATATTACCCCATTTGGGATATCCATTTCCATTG Y 2 1 2 1 201000 f 74 goat QTLSaanen19.163 19 28098178 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602255 Affx-1002480104 AX-413836626 19 28100152 AAGGCTGCCCCCGGGCTTCCTGTCCAGGCTGGTGC[C/T]CGCACGGCTAGGGCAGAGCTCCGCTGAAGGTCATG Y 2 1 2 1 303000 r 74 goat QTLSaanen19.164 19 28100152 C T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602128 Affx-1002480036 AX-413836505 19 28103222 GGCCCTGCCCTGCCACCCTCGCTGCGGGACCTGCA[C/T]CGGCACCCACTGTCCCATCCCAAGCTTCTCCCTTG Y 2 1 2 1 202000 r 74 goat QTLSaanen19.94 19 28103222 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602206 Affx-1002480105 AX-413836579 19 28104534 CCTGCAGGATGTCTGCCGGGAGTAACGGGGTACAC[A/C]CGTCTGGGCATCAGGCCCTGGGACCCCTCCTGCAC M 2 1 2 1 202000 f 74 goat QTLSaanen19.165 19 28104534 C A 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602129 Affx-1002480037 AX-413836507 19 28114503 AGATAATGTCAAAGGGTTTTCTCCCCACTGTATGA[C/T]TGTTCATTCTCCTATATGATGTTGACTAATTTTGT Y 2 1 2 1 201000 r 74 goat QTLSaanen19.95 19 28114503 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602064 Affx-1002480038 AX-185188418 19 28123341 CATTCTAAGTCGCTTCAGTCGTGTCCGACTCTGTG[A/C]CGACCCTGTGGACTGTAGCCTGCCAGACTCCTCTG M 2 1 2 1 303000 f 74 goat QTLSaanen19.96 19 28123341 C A 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38428435 Affx-122938820 AX-123298778 19 28125840 CCGTGTGAGCTGCAGCCAGAATACACAAAAATCTA[C/T]GGAGCTGAATTTCAAGCTTCAGTTTGGAGGAGTTG Y 2 1 2 1 10000 f 74 goat "snp9030-scaffold1328-1396397;SV_204" 19 28638929 G A SV_204 2 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602066 Affx-1002480039 AX-413836444 19 28154063 CCACATGACAAGAAGGCATTGGACTATGTGGTCAG[A/T]AAGAGCACAGCTGGAACAACTAGAAAGAACGCTAC W 4 1 2 1 201000 f 74 goat QTLSaanen19.97 19 28154063 A T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602135 Affx-1002480040 AX-413836512 19 28163875 AGTAGAGAAGCCTGGGTGGAGGGGGGCAGGGCACC[A/G]GCTGTGGTCAGAAGGACTTCAGCCTCTGTGAGCCC R 2 1 2 1 202000 r 74 goat QTLSaanen19.98 19 28163875 G A 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602137 Affx-1002480041 AX-413836514 19 28171577 CAGGGTCACACAGCTGGGTACAGCTGGAACCCCGG[C/T]TCTCCTTTCCACAGCATCCAGGGTTCCCAAGAAAT Y 2 1 2 1 202000 r 74 goat QTLSaanen19.99 19 28171577 T C 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602139 Affx-1002480042 AX-413836516 19 28180514 AGAATAATAGTCATCAGTTTGCTTATAAGTATAAG[C/T]TAGTGATAAATTATAAGCAAAACTAGTGTTTAAAA Y 2 1 2 1 201000 r 74 goat QTLSaanen19.100 19 28180514 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602074 Affx-1002480043 AX-413836452 19 28199246 AGAGCTTCTCCTGCCCCAAGTACTTTGTCTAAAAC[C/T]TCACCTCCTCTCCTGGCACTGTGCCCCCTTATTCT Y 2 1 2 1 102000 f 74 goat QTLSaanen19.101 19 28199246 T C 1 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602143 Affx-1002480044 AX-413836519 19 28205161 GACAGAAACAACATAGCAGAAGGAAGGCTTCAGAG[C/T]TGCTAGCCAATCTGGTCTTAAAGATATTTCAAACT Y 2 1 2 1 201000 r 74 goat QTLSaanen19.102 19 28205161 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 468273861 Affx-1111833890 AX-515071778 19 28211162 TGGATGGAGTGCAAAAATGGAGATCTGGCCACGCA[A/G]CAGGAGAACTGCCCTCTGCAGACCAGGAC R 2 1 2 1 102000 f 74 goat GoatD01.009563 19 28211162 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 350602145 Affx-1002480045 AX-413836521 19 28217289 AAATGTACACTGCCTCTGCCTCTGTCAGGGTCATT[C/T]CCTAGAGATCCTGAGCCTTTTGCCATTAGGGTCAG Y 2 1 2 1 201000 r 74 goat QTLSaanen19.103 19 28217289 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320770328 Affx-122925750 AX-385257494 19 28219086 TGCCAGGCTACGCTCCAAGCTATTTGCATGTGGAC[A/G]TACTTAAGGGCATCCTTACTCCTTGCAACCACTTA R 2 1 2 1 101000 f 74 goat snp9029-scaffold1328-1303151 19 28730193 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602080 Affx-1002480046 AX-413836458 19 28225129 TCTGAGCCACCAGGGAATTCCATTTCATTGCAACA[A/G]GATACATTTTTGTTTTGTTTTTAAATAATCTCATA R 2 1 2 1 303000 f 74 goat QTLSaanen19.104 19 28225129 G A 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38446979 Affx-122924650 AX-123317315 19 28263271 CCTTCACCTGCAAACTGAAGGTGTTATTCTAGAAC[A/G]TCCTCCCAGGCCTCCTCCAGCTGCTGCATTCTGTC R 2 1 2 1 101000 f 74 goat snp9028-scaffold1328-1258966 19 28774563 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775810 Affx-122957311 AX-385262941 19 28294020 TATTCTGTAAACCTCAGAGAGTCCGCAGGGCAAAA[C/T]GGAAACTCCAGCCAGAATGTAGGTAACCTAGAGGG Y 2 1 2 1 202000 r 74 goat snp9027-scaffold1328-1228217 19 28805325 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384160 Affx-122972796 AX-123254518 19 28322961 GCCCAGTTGGCAGTTGAGGTTCCAGGATAAGATGC[A/G]TGAGGGGGGAAGGGAGGGGCATTGGGGACTGTTTC R 2 1 2 1 101000 f 74 goat snp9026-scaffold1328-1199276 19 28832418 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse374 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38384478 Affx-122973073 AX-123254836 19 28356438 CCTTATCAGGCGGTTTCTGCCATCTCTCTTGTTTA[C/T]GTGGTGGAGGCTTTTGCAAGTTCGCGCCAGTCATT Y 2 1 2 1 201000 f 74 goat snp9025-scaffold1328-1165799 19 28865790 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438419 Affx-122931276 AX-123308757 19 28443540 AGACCAGAGCAGCCTCACTGAGCTCTGAGACTGCA[G/T]CTCAGGGTCCTTGAGACTTGGGGCTCTCAATTAGG K 2 1 2 1 201000 f 74 goat snp9023-scaffold1328-1078697 19 28953102 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398254 Affx-122962187 AX-123268609 19 28475094 GGGGAAGAGCATCCTTGTTGAATGAATGAGGACTT[C/T]ATGCATTTCTGTGTGTTTTTTGGCTTATGTTAGCA Y 2 1 2 1 101000 f 74 goat snp9022-scaffold1328-1047143 19 28985154 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787253 Affx-122938547 AX-385274279 19 28503888 ACCTTAGAAGTTATTGCCAAGCAGTTCTCCAGCAT[C/T]TGCTCAAACACCTCCAGCGACAGGGAACTTCCTAC Y 2 1 2 1 101000 f 74 goat snp9021-scaffold1328-1018349 19 29014132 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602148 Affx-1002480047 AX-413836524 19 28514270 TTGATGTGAGGCTCTTAGGGCAGAGAAGCTGACCA[C/T]TGGAGCACACGAGGATGCTATGCAGGTTGCAAGTG Y 2 1 2 1 202000 r 74 goat QTLSaanen19.105 19 28514270 T C 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601303 Affx-1002480106 AX-413835733 19 28515894 CAAAATCCACACCGAGAACGGCCGAATAGCCATTT[-/TC]TCCCCCCGTTTTCCCACTGAGAGTGAGATAGAAGA - 2 1 2 1 201000 f 74 goat QTLSaanen19.166 19 28515894 - TC 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38412685 Affx-122950765 AX-123283034 19 28539128 TAAGACAGGGGATCAGAGGGGGCTGGGATTTGGCT[A/G]TGTCTCCATGGGGATTCCTCTGGTTTAAGGAGCTA R 2 1 2 1 101000 r 74 goat snp9020-scaffold1328-983109 19 29049160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602085 Affx-1002480048 AX-413836463 19 28545732 AAATACTGCTTCCTCTGCGGCTTTTCAACTTAATG[C/T]CTTCTTAGCTCCAAGTTCTCCCTTATTATGATTGC Y 2 1 2 1 201000 f 74 goat QTLSaanen19.106 19 28545732 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602152 Affx-1002480049 AX-413836527 19 28555196 GATAAAGAAGCCAGACCACCCCACCCCTGAACTCA[C/T]CAAAGAACCCATATTGTATGAGTCCATTTATACAG Y 2 1 2 1 202000 r 74 goat QTLSaanen19.107 19 28555196 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38450048 Affx-122922824 AX-123320383 19 28595132 CTGTCTCATTTGACAGAAGGGAACCAAAGCCCAAA[G/T]AAATTACAACAGCTACTTTACAGAACTGGCATTAG K 2 1 2 1 201000 r 74 goat snp9019-scaffold1328-927105 19 29105144 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436316 Affx-122933260 AX-123306655 19 28634718 CCCAAGAAGGAGTAACTAACATACTTCTAATTAAA[C/T]GTGGAAGAACAGATGCAAAAATATCAGTACACTTG Y 2 1 2 1 201000 f 74 goat snp9018-scaffold1328-887519 19 29144916 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795588 Affx-122969372 AX-385282543 19 28665441 TGCAGCACTTCACATTTTTTCCTGGGGCAGTGGTC[A/G]TGCTTTATACTTACAGCAGCCACTGATAATAGTTG R 2 1 2 1 202000 f 74 goat snp9017-scaffold1328-856796 19 29175678 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387301 Affx-122970522 AX-123257659 19 28694326 AAATAAGGGTGAAATAAGGAAGGATCAATGAAAGA[C/T]GATTCAATGAAATGTGAAGAATGAACAGAAACCAA Y 2 1 2 1 101000 f 74 goat snp9016-scaffold1328-827911 19 29205155 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774223 Affx-122932423 AX-385261360 19 28743439 CTGTGTCCTTCGGAAGGATATGTGGAACAGGAAAG[C/T]GAGCGTTCAGTGCAGAAGAATGAGGATAATGTTTT Y 2 1 2 1 101000 r 74 goat snp9015-scaffold1328-778798 19 29253893 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399729 Affx-122960457 AX-123270084 19 28785821 TTTATCATTTGTGTTCATATCTGTCTTTCCCATCA[G/T]ACTCAGCAGAGGCTATGGTTGTCCTCTCTTGCTTT K 2 1 2 1 101000 r 74 goat snp9014-scaffold1328-736416 19 29296342 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432754 Affx-122935443 AX-123303095 19 28823911 AAACTGGCATTTTTGTGGGCCCAAAACAAAGGCTG[A/G]TAGTTTCATATGGTTCAACCTAATATGATGGGCAG R 2 1 2 1 101000 f 74 goat snp9013-scaffold1328-698326 19 29334255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602259 Affx-1002480107 AX-413836630 19 28845332 TTTTCAAAAGGAGACAAGCATCTGGGTGCTTATGA[A/G]AAAACCTCCCAATTGTTCAACGTTGGCAGTTCATT R 2 1 2 1 201000 r 74 goat QTLSaanen19.167 19 28845332 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38450423 Affx-122922055 AX-123320757 19 28855575 TGTTCTGGGCTGAAATGTATCCCCTGGATTCGTAT[A/G]TTCGTTGAAGTTCTAACCCCAGTGCCTCAGAATGA R 2 1 2 1 201000 f 74 goat snp9012-scaffold1328-666662 19 29365785 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602210 Affx-1002480108 AX-413836583 19 28860540 ATCACCTATAAGGACTTCCACTGCTTACCAAATGT[G/T]GTACCGTGCACCAAGGACTGGGCCAGGTGCCTCAC K 2 1 2 1 201000 f 74 goat QTLSaanen19.168 19 28860540 G T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601414 Affx-1002480109 AX-413835835 19 28861312 AAAGAGAGTCTGCAGCTTTCCTGAGAGGGAGTGAT[-/GGA]GGAGAAACGATCACTTCTGAAATCAAAACTGGGAA - 4 1 2 1 201000 r 74 goat QTLSaanen19.169 19 28861312 - GGA 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602212 Affx-1002480110 AX-413836585 19 28861620 CACAGATGTGAGCAGATGGTCCTTGCTGGTGCTAA[C/T]TGGGTGGTCGTCAGACACTTGATTTCGCAGTCGGA Y 2 1 2 1 400000 f 74 goat QTLSaanen19.170 19 28861620 T C Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602214 Affx-1002480111 AX-413836587 19 28861923 GGCTTCTCCACAAAGAACTCTCCAGCAAGTTCTCC[C/T]CTTCTCAACCACACGGCCAGCTGGGACACCTGGGG Y 2 1 2 1 202000 f 74 goat QTLSaanen19.171 19 28861923 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602216 Affx-1002480112 AX-413836589 19 28875531 TTCTTTTCTGAATCCCAGAAAACCAAACTGGAATT[C/T]CTTTAGTGACCACAGAACCACAACTGCAGGAATGA Y 2 1 2 1 201000 f 74 goat QTLSaanen19.172 19 28875531 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602089 Affx-1002480050 AX-413836467 19 28882373 AGAAGCCAAGTGATCAGCTACGATGACAGCAGCCT[A/G]GAGTTACCAAGGAGAGAACTGAAATATACATCTGT R 2 1 2 1 201000 f 74 goat QTLSaanen19.108 19 28882373 G A 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38443071 Affx-122928126 AX-123313408 19 28884220 GAAAGAAAAAAAGAAATTATACAGTGATCTCATTC[A/G]CGACCACAGACGGAAAAACCCTAAACAAATTAGCA R 2 1 2 1 102000 r 74 goat snp9011-scaffold1328-638017 19 29394386 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350602218 Affx-1002480113 AX-413836590 19 28888928 TACTGTACAAGGATGGATGACCCATGAAGGGTTAG[C/G]GTCAGAGAGGGTATGAATGCAAAAGGAGGGTGAGA S 4 1 2 1 201000 f 74 goat QTLSaanen19.173 19 28888928 G C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602091 Affx-1002480051 AX-413836469 19 28893803 ACCTAACACACTCATAGGTTCCAGGAACTGGGGCT[G/T]GTGGACATCTGGTGGGTGACATGATTGTGTAGACC K 2 1 2 1 202000 f 74 goat QTLSaanen19.109 19 28893803 G T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602271 Affx-1002480114 AX-413836642 19 28898846 GCCGGGCCACCCGCCCAAGCAGCACCAAGCCAGAA[C/G]GGTCTGTCACTCTCCAGTTGGTGACAGTTCTTTGA S 4 1 2 1 102000 r 74 goat QTLSaanen19.174 19 28898846 G C 1 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602093 Affx-1002480052 AX-185373751 19 28904028 GACAGAGGAGCCTGGCAGGCTACAGTCCATGGGGT[C/T]CGCAAACAGCTGGACATGACTTTCACTTCTTTTCC Y 2 1 2 1 303000 f 74 goat QTLSaanen19.110 19 28904028 C T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602222 Affx-1002480115 AX-413836594 19 28908034 CCTGAAATGCTGTGCTTAGCCGCTCAGTCGTCTGA[C/T]CTCTTTGTGACCCTGATGGACTATAGCCCGCCAGG Y 2 1 2 1 303000 f 74 goat QTLSaanen19.175 19 28908034 C T 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601272 Affx-1002480116 AX-413835705 19 28910602 GACTCTTTGTGACCCCGTGGCCTGCAGCCTGCCAG[C/G]CCTCCTCTGTCCATGGAATTCTCCAGGCAAGAACA S 4 1 2 1 303000 f 74 goat QTLSaanen19.176 19 28910602 C G 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602096 Affx-1002480053 AX-413836473 19 28913537 CCGGACCCAATGGAGGGCCTGTCTACTCTTCGCCC[G/T]GCGCGTTCTCCTCCCCATCCCACAGACACACACTT K 2 1 2 1 202000 f 74 goat QTLSaanen19.111 19 28913537 G T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601332 Affx-1002480117 AX-413835762 19 28918314 GTCTCCTCCAGCACTTCCTGTCTGCAGCCCGGCTT[C/T]TGGTGCTTACTCACGGAAGACAGGACGTTTCACCT Y 2 1 2 1 201000 r 74 goat QTLSaanen19.177 19 28918314 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38387069 Affx-122969892 AX-123257427 19 28919599 AATTTTTAATTGTCAGTTATATCCCAATAGAGCTC[A/G]TGAGGGAAACAACAGCAGACAGCTTTCCAGGTGAT R 2 1 2 1 101000 r 74 goat snp9010-scaffold1328-602638 19 29429865 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601335 Affx-1002480118 AX-413835765 19 28920263 GGAAGGCGTTTTAAAAAACAAACAAACAAACGAAC[A/G]AAAAGATGCTCTTTCCATTGATTTATTGTTACAGG R 2 1 2 1 201000 r 74 goat QTLSaanen19.178 19 28920263 A G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601275 Affx-1002480119 AX-413835708 19 28921981 CCCGCCAGCAGGGGGAGGACCACGCAGGGAGGAGG[A/G]GAGGGGAGCCCTATGGGATGGGCGCGTGGATGGAT R 2 1 2 1 303000 f 74 goat QTLSaanen19.179 19 28921981 G A 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602161 Affx-1002480054 AX-413836536 19 28923604 TCGAGGCCCCTTCCCCACACCCTCAATCTCTAACT[C/T]CCTGCCGTCACATCCACTCCAGACCTGACCCTCCC Y 2 1 2 1 202000 r 74 goat QTLSaanen19.112 19 28923604 C T 2 neutral Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601276 Affx-1002480120 AX-413835709 19 28931287 AAAAAGAAAGAAACGGATATTTACTCATCGCCCAC[G/T]TATGTGCCAAGTATATAAATCTGTGAGTTAAGTAT K 2 1 2 1 201000 f 74 goat QTLSaanen19.180 19 28931287 T G 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602163 Affx-1002480055 AX-413836538 19 28934219 TGGAACCAACAGATCCTGACCCCCTTTCCCAGTGA[C/G]GAGCAGAGTGGCCAGAGCCCCACTTCTGGGTTCAA S 4 1 2 1 303000 r 74 goat QTLSaanen19.113 19 28934219 G C 3 not_recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602103 Affx-1002480056 AX-413836480 19 28947496 CCTATTACTTGGTGGAGTTCAGGGATGACTTGCTC[C/T]CAGGGGCTCACACAGTGTCAACAGGGCGCCATTTC Y 2 1 2 1 201000 f 74 goat QTLSaanen19.114 19 28947496 C T 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350602168 Affx-1002480057 AX-413836542 19 28948260 AGAAGAAAGATAGTCCCTGCCTTCAAGGACCTCTC[C/T]TCTCTTAACATATGAGCTTTAACAGTGCCAGTTCA Y 2 1 2 1 201000 r 74 goat QTLSaanen19.115 19 28948260 T C 2 recommended Goat_IGGC_65K_v2 QTLs QTL-region SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38412914 Affx-122950402 AX-123283263 19 28960929 CAACTTGCATAGCTGGACCATGTTGGGGGGGCTCG[C/T]GTCAAGCTTTCAGTCAAATGAAACCCTCTGGGGTT Y 2 1 2 1 101000 r 74 goat snp9009-scaffold1328-561308 19 29471647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423474 Affx-122942578 AX-123293820 19 29013102 TGATGAGGCAAAAGCTCTCATCACCAAGAGCCTTG[C/T]GGAAGCTCAAGGCTGTTAAGACCATGGGGAACGAT Y 2 1 2 1 101000 f 74 goat snp9008-scaffold1328-509135 19 29524765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442405 Affx-122927993 AX-123312742 19 29055773 TCTTTGAGTAAAAAGCAATGGGAAAAGAGTGTGAG[C/T]GGATTTGATGAATTACAACTTGTCTTGGGTGTAGG Y 2 1 2 1 201000 r 74 goat snp9007-scaffold1328-466464 19 29567262 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419340 Affx-122945649 AX-123289688 19 29089818 ATTTAGGAAGAGAAGCTGACGGCAGAGGTCAGTTT[A/G]CAAGGAAGCTCCAATTATTCTCTAACATATTAAGA R 2 1 2 1 101000 f 74 goat snp9006-scaffold1328-432419 19 29601259 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388160 Affx-122969453 AX-123258518 19 29136125 TTTCTGCCAGGCACTGCTCTAAACACTTCTGGTGC[A/G]TTGCTTCATCTAGTCCTTACTGTTGTACAGTATAA R 2 1 2 1 201000 r 74 goat snp9005-scaffold1328-386112 19 29648777 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409917 Affx-122952883 AX-123280268 19 29181149 AGACGGGGAGTCCCAGGAGTGCTGCTAAATTAGGA[G/T]CCTGGCTTCATTATTATGCATCCCCAGTAAATCCG K 2 1 2 1 101000 r 74 goat snp9004-scaffold1328-341088 19 29693373 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780125 Affx-122934216 AX-385267222 19 29227623 CAATCCAGCAATACCAGACAATCGATAAATGTTTC[A/G]TTGAGTGGATAAACCCGATTATCATCGGTGTTGAC R 2 1 2 1 101000 f 74 goat snp9003-scaffold1328-294614 19 29740213 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277365 Affx-1111835812 AX-519550869 19 29255383 GCCAAAGCAAAGCAGCGAGAGAGGAAGGGTGCACC[A/C]CAAACAAGAAGACTGGAAAAGAGGACTTTCTTTTT M 2 1 2 1 102000 r 74 goat Random2.2K-1795 19 29255383 G T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433820 Affx-122935165 AX-123304161 19 29270846 TCAAAACAACACACATGGGCTCTGAAAGCACTTCC[A/G]AGAGAGGAACCGTGGCGAAAATTTCTAGGGAAGAA R 2 1 2 1 201000 r 74 goat snp9002-scaffold1328-251391 19 29783387 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406675 Affx-122955788 AX-123277027 19 29323463 CAGGAGCCCCAGAGGCTCTACCAGTTAGTATGTGG[C/T]ACTTATATGAATATGAATTCATGGTTAATAGGGCT Y 2 1 2 1 201000 r 74 goat snp9001-scaffold1328-198774 19 29835994 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse375 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 463586069 Affx-1110059358 AX-515067749 19 29371279 GTGGGCTGTAGAGGCAGCACTGCAGTGAGATGCTC[C/T]CTCTGCACATCCTCCTGGAAGCCGGCCATGGCGCT Y 2 1 2 1 202000 f 74 goat GoatD01.052614 19 29371279 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38381213 Affx-122974522 AX-123251571 19 29379671 CATCTCTCTGCTCAGCTATTCCTATAGCATCAGCC[A/G]TTGTTGTAATGGACAGAGCTTCGCCCTTCCTTCTC R 2 1 2 1 101000 f 74 goat snp9000-scaffold1328-142566 19 29891998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434422 Affx-122934671 AX-123304763 19 29430602 CGTTGACATAGGTTTATTTCTTAAAAAAAAATTCT[A/G]TTTTGAAAATATTGCAAACACAAAAAGTACAGAAG R 2 1 2 1 201000 r 74 goat snp8999-scaffold1328-91635 19 29942901 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452187 Affx-122921226 AX-123322520 19 29479661 TAACCGGTGAGAACACGGAGGCACAGAGCAGGAGG[A/C]AACACGTCTAGAAGATGACACAACTGCGGTGTGAA M 2 1 2 1 101000 r 74 goat snp8998-scaffold1328-42576 19 29992868 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387839 Affx-122969658 AX-123258197 19 29515248 AGTCCAACATGAGAGGTGTAGATCTCTGTGCCAGG[C/T]GAGCTGCAGAATTTATCTTTGTTTTGAGTTTCTCT Y 2 1 2 1 101000 f 74 goat snp8997-scaffold1328-6989 19 30028796 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443697 Affx-122927164 AX-123314034 19 29525106 TAAAGGATGGGAACTACTCTCTCAGAGGCATCATA[A/G]GCAAAGACTGGCTTTGGTTCCTGCAGCTGGCACAT R 2 1 2 1 101000 f 74 goat snp28360-scaffold303-2770 19 30038406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409859 Affx-122952923 AX-123280210 19 29568559 GTTTTCCTGGCTTTGAAGACCAGCAGAGCCTTGCC[A/G]CAATCAGCCTGAGCCATTTCTCCATTCCCTGTGAC R 2 1 2 1 101000 r 74 goat snp28361-scaffold303-46223 19 30081880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422682 Affx-122943667 AX-123293028 19 29600934 AGGCCGTGGGGCAGTTCTCATGGGTTGATCTCACA[C/T]GGAGTCAGTAGTGAATCAGTTGTTATCTTTGGTTT Y 2 1 2 1 101000 r 74 goat snp28362-scaffold303-78598 19 30114093 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787600 Affx-122946995 AX-385274624 19 29630185 AAGCTTGCCAGCCAAAACTATTTAGATGGAACAAG[C/T]GGGAATCAAACATAGCAAGCATCAAAGTTAATCTG Y 2 1 2 1 101000 f 74 goat snp28363-scaffold303-107849 19 30143389 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381434 Affx-122974349 AX-123251792 19 29730286 CTTGTGTGTTTCCCTGGCACTCAGCGGTTGCGCAC[A/G]CCACCGTTGTATTGCAGCAACAGTGCAAACTTTTG R 2 1 2 1 101000 r 74 goat snp28365-scaffold303-207950 19 30243829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379796 Affx-122975828 AX-123250154 19 29767990 CTTGGAGCCCTCGTGTTCAAGATGGAGTTAGTGCC[A/C]TCGCCTTTAGCTCATCTCCCCAGCCCTTACCTCCC M 2 1 2 1 201000 f 74 goat snp28366-scaffold303-245654 19 30281541 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410508 Affx-122952182 AX-123280858 19 29846038 CAAACAGGTGTTGTTAGTTCAGGGAGGGGCACTGC[G/T]ACTGGGTCGGGACGGTCTGTCAGGGCTGAGCTGCT K 2 1 2 1 101000 f 74 goat snp28368-scaffold303-323702 19 30359301 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446520 Affx-122925026 AX-123316856 19 29874657 AGAGCTTGAAGTATTCTAGAAACTCAGGGAAAGGC[A/G]TCATGGTTAGGGGTTACCCTGATGCCCTCCATCCT R 2 1 2 1 101000 f 74 goat snp28369-scaffold303-352321 19 30388441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378781 Affx-122977000 AX-123249140 19 29906282 GCCTTCCCTTGGAATTTGTTAGTTTTGCTTTGTCT[A/G]CATATTTCGGTGTGCTTCAAGGTATTCAGTAATCT R 2 1 2 1 201000 r 74 goat snp28370-scaffold303-383946 19 30419922 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416062 Affx-122948341 AX-123286411 19 29934922 TTTCTTTAACTATTTTTAAATAGGTTATATTATTA[C/T]AGTTCCCCTTAAATTAATTAGAATTGCAGCAGTTT Y 2 1 2 1 201000 f 74 goat snp28371-scaffold303-412586 19 30448591 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801378 Affx-122946223 AX-385288289 19 30020223 TAAAGATGAAAATCTCCTGTTCTTTGGAAGTGAAA[C/T]AAATATACTTACAAGAAGTAGTTAAAGATGAAATT Y 2 1 2 1 101000 f 74 goat snp28372-scaffold303-497887 19 30534624 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463586598 Affx-1110059630 AX-515068272 19 30025931 ACAAAAAACAGTGAAGCTGGTTTTCTCCTTGCCTC[C/T]GGAGGACAAGCAGAACAAACTACCCTTTATCTCTC Y 2 1 2 1 201000 f 74 goat 19_30025931_AF-PAKI 19 30025931 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395274 Affx-122964083 AX-123265629 19 30084694 TGAGGGGGAGGACATTATAATTTGGCTACTTCTCC[A/G]AGTCCAAAAACAGGGAGCTAAATGTAGTTACATAG R 2 1 2 1 101000 r 74 goat snp28373-scaffold303-562358 19 30599661 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772151 Affx-122955298 AX-385259306 19 30124020 AAATGGCAAGCAGAGCATTGTTCAGAGAAAAATTC[A/G]TAATCATAAATACTTTAATACCCAAAATGGAATAA R 2 1 2 1 101000 f 74 goat snp28374-scaffold303-601684 19 30640289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398733 Affx-122961829 AX-123269088 19 30175753 AGTCCGAGGCCACATGTGTGGGATGTCTGAGTCCA[A/G]ATCATTTCAGGTAGACTTGGTTTCATAAAGCAAAG R 2 1 2 1 101000 r 74 goat snp28375-scaffold303-653417 19 30692034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274280 Affx-1111834109 AX-519547877 19 30177198 CGCACACATATTCAGACACACTTCCCTGCAGCCCA[A/G]CCTCCACGGAACCCTTGACTGTTCTAAACACCTGA R 2 1 2 1 202000 r 74 goat GoatD01.018952 19 30177198 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38432018 Affx-122935920 AX-123302359 19 30236671 TGTTACCATGGCATTCCATTTTAGAAGATTTAGAG[C/T]GAGATATAAAAATACAAGTTCCTAGATACAAGTAA Y 2 1 2 1 101000 f 74 goat snp28376-scaffold303-714335 19 30753392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse376 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38401068 Affx-122959642 AX-123271421 19 30266065 GCTTGTGACTTCATTGCTTAAGATGGTCCCCAAGC[A/G]TATGCTGAAGTGCCGTCTGGTGTCCCTGAGCACAG R 2 1 2 1 101000 r 74 goat snp28377-scaffold303-743729 19 30782774 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785235 Affx-122930851 AX-385272280 19 30300499 AAACCCATCAACATCGCTTCAATCACAGGCTGTAT[C/T]AGTGATGAGCAGCTTAAAGGCTGATGTCATAATAC Y 2 1 2 1 201000 r 74 goat snp28378-scaffold303-778163 19 30817573 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse377 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38420183 Affx-122945563 AX-123290531 19 30350776 AACGTCTCACCACTACATGGAGTAGGTTTCTGGGA[G/T]ACCTGAAGGAAAGAAATGACTTTCTCTCTCCTTCT K 2 1 2 1 101000 f 74 goat snp28379-scaffold303-828440 19 30867891 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405400 Affx-122956292 AX-123275752 19 30437452 ATTTTTTACTGAAGTATAGTTGATTTACAGTGTTG[C/T]GCCAGTCTCTGATGTACAGCTAAGTACACACTGTT Y 2 1 2 1 101000 r 74 goat snp28381-scaffold303-915116 19 30954662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453289 Affx-122920377 AX-123323622 19 30544429 CTTCCAGATACTTCTCCTAAGAAAGAAAAACAAGG[A/G]GGACGAAACACATGTCCAAGCGCCAATACATGAGA R 2 1 2 1 201000 r 74 goat snp28383-scaffold303-1022093 19 31062000 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403054 Affx-122958529 AX-123273407 19 30608087 GCCTTCCAACAATGTGTGTTTATGGCTGCAGCGCC[A/G]CAGCTGGGAACCATAAGGCATGAATGAACGTGTGT R 2 1 2 1 101000 f 74 goat snp28384-scaffold303-1085751 19 31127012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415726 Affx-122948511 AX-123286075 19 30639314 GAGACAGACATGACTGAAGCAACTTAGCACACACG[C/T]ACGCATCTTTGCGGGACATTATTCAGCCTATTAGG Y 2 1 2 1 101000 r 74 goat snp28385-scaffold303-1116978 19 31157654 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392672 Affx-122966427 AX-123263029 19 30670421 AATATTTCTACAGTCATCAAAACTTTCTACTGTTC[A/G]TTTTGCAACAAGGCTCAATATCTTGGCATCACATC R 2 1 2 1 101000 r 74 goat snp28386-scaffold303-1148085 19 31188005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432401 Affx-122935844 AX-123302742 19 30702105 CAGGGATAAGGAAGAATGAGGACAGACATCCGAGA[A/G]AGAGTGATCCTTGAGCTGAGATCTGAGGCTGAGTA R 2 1 2 1 201000 f 74 goat snp28387-scaffold303-1179769 19 31220004 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440395 Affx-122929622 AX-123310732 19 30768292 CCTAACTATCCCTTTCTCCTGGCAACCATAATTTC[A/G]TTTTCTAAGTCTCACCCAAATTCTTCATACGCTTG R 2 1 2 1 201000 r 74 goat snp28389-scaffold303-1245956 19 31286341 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787183 Affx-122920173 AX-385274209 19 30826909 CAGGGGAAGAAGTAGCTGAGTTAACAGAAGAGCAT[C/T]GTGTATATTTATCTCCAAAGGTTATCATTTCTATA Y 2 1 2 1 101000 f 74 goat snp28390-scaffold303-1304573 19 31345705 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377292 Affx-122978116 AX-123247651 19 30859021 GCAGCAATTGCATTTTTTTTTCTTTTCTCTCGGCT[A/G]ATAGATCACCTGCTTTGGGGAAGCCTTGCCTAAAT R 2 1 2 1 201000 r 74 goat snp28391-scaffold303-1336685 19 31376483 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438014 Affx-122931572 AX-123308352 19 30895701 AAAGCTGGGAGCCTTGTAAAATTTTATTTCATAGC[A/G]CATAAGTCCTATTTCATGGTAAATATCTTCATTTT R 2 1 2 1 201000 r 74 goat snp28392-scaffold303-1373365 19 31413587 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390576 Affx-122967201 AX-123260933 19 30933712 TAAAGCTGGAAAACACAGGATCCGAGATACACCAC[C/T]GTCACAGAAACCCTATAGGTACAGTCCTGTTAAAA Y 2 1 2 1 101000 r 74 goat snp28393-scaffold303-1411376 19 31451030 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393696 Affx-122965253 AX-123264051 19 30965293 GAAGTCAGCATATGTTGTGGGAACACACGGCAGAC[A/G]CACACAGCACAGAAGTCCCCCAAAGCAGACTCCTT R 2 1 2 1 102000 f 74 goat snp28394-scaffold303-1442957 19 31482472 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424171 Affx-122942528 AX-123294517 19 31000654 TTACAAAATTTACCAGAGGGAAAGAAAGGAAAGAA[A/G]AAGAGGAAAACGAATTGGAATAGAGCTGGGCAATA R 2 1 2 1 103000 r 74 goat snp28395-scaffold303-1478318 19 31517814 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776438 Affx-122957426 AX-385263565 19 31030283 GTGGCTGGAGATGAGAAAGACTCAAGGAAGCAGAA[G/T]AGTTTAAGAAAAGTCAGCCTTAACATACAGCTCTC K 2 1 2 1 101000 f 74 goat snp28396-scaffold303-1507947 19 31546590 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386961 Affx-122969973 AX-123257319 19 31059310 AGATCTCTGATGCAATTAGACAAAGATCAACCAAC[C/T]GGGTGTAGAAATCTGAATATTTAACCAGCACCTCT Y 2 1 2 1 101000 f 74 goat snp28397-scaffold303-1536974 19 31573117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400563 Affx-122960419 AX-123270918 19 31089216 ATTACATCATTGCAGTCTGTGAAATCACAGAGCCA[C/T]GGGATTTTAAAGCTAAAAGGAACATGAAAATTATT Y 2 1 2 1 101000 f 74 goat snp28398-scaffold303-1566880 19 31603082 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401732 Affx-122959520 AX-123272085 19 31143385 TGCCACTCATGGAAGGCACTCATCCCCTGAAAATC[A/G]TCCTCACCATCAGTTATTTCAGGATGCTCCAGGAG R 2 1 2 1 101000 r 74 goat snp28399-scaffold303-1621049 19 31658122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387027 Affx-122969925 AX-123257385 19 31174109 TCACCTGACCTCCTTACCCACTCCAACCTCCAGCA[C/T]ACAAACATACCCTAACCAGCCAGTAGTCATCCCAT Y 2 1 2 1 101000 r 74 goat snp28400-scaffold303-1651773 19 31688903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse378 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38415728 Affx-122948510 AX-123286077 19 31221060 ATATTCTTTACCACTGAGCTGCCAGGAAAAGCCCC[A/G]TTGTAGCAATTGTTAATTCCCCCAGTCATCTTGGC R 2 1 2 1 103000 r 74 goat snp28401-scaffold303-1698724 19 31735983 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429025 Affx-122938323 AX-123299367 19 31266326 TGTATTTTCAGCTTCCTATAGGACAGATCTACCTC[A/G]CTACTCAGAATTCCCCAGTTCAGGAAGTGGGCTGC R 2 1 2 1 101000 f 74 goat snp28402-scaffold303-1743990 19 31781419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379548 Affx-122976057 AX-123249906 19 31295168 GACCTACTGTCATGACAGTTGTTCTGGGTGTGAGC[A/G]CCTACAAATCAGACAGAGTATTTCCCTCTGTTACT R 2 1 2 1 101000 r 74 goat snp28403-scaffold303-1772832 19 31810128 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769290 Affx-122964494 AX-385256462 19 31351368 GAGAAATAAATCATAGGAGCAAACACCTTTATTAA[C/T]ACCTGGAATCATTTGGTCTAACCTCCTGTCACTTC Y 2 1 2 1 101000 r 74 goat snp28404-scaffold303-1829032 19 31866314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422727 Affx-122943258 AX-123293073 19 31395031 AGATCTGGCAACACCGACTTACCAGCCCAGAGGGC[A/G]CCTGCTGCTTTTCTGCTTTCTCAGCCTCCCCTCCT R 2 1 2 1 101000 f 74 goat snp28405-scaffold303-1872695 19 31907848 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410968 Affx-122952020 AX-123281318 19 31444748 TTTGGCTTTTGATTTTGAAGGCTGCCCCCTTGCCT[C/T]CTCTTCTGCCCCATCCCCAGTTCATCAACCAGCTT Y 2 1 2 1 103000 f 74 goat snp28406-scaffold303-1922412 19 31956886 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277243 Affx-1111835813 AX-519550749 19 31481637 ACATGAGAGCTGGTCTCAGGACTGTTGAAACCCCT[C/G]GTGCCTTGAGCAGGGTGGGATGGGGGCAGAAACTG S 4 1 2 1 102000 f 74 goat Random2.2K-1797 19 31481637 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38428218 Affx-122939442 AX-123298561 19 31488419 GAAAATTCAGTCTTCAGATGGTTGTTTTATGTTAA[C/T]AAATTTGATCACAAAACAGAATGGAAGTGTAAAGA Y 2 1 2 1 101000 f 74 goat snp28407-scaffold303-1966083 19 32000583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383860 Affx-122973143 AX-123254218 19 31534024 GGCATTTCTTTTTTAAGGTATTTTTTGATGTATCA[C/T]GCACTGTGTTTTAAAATCTTTTATTTATCTCTTTA Y 2 1 2 1 101000 f 74 goat snp28408-scaffold303-2011688 19 32046232 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790295 Affx-122969802 AX-385277298 19 31587789 AACAAGAGTAGAAACTTCAGAAGTTGAGGATGACA[C/T]GCCATGGAAAACATTCAAAGGGAGTCTGTTTAGAG Y 2 1 2 1 101000 r 74 goat snp28409-scaffold303-2065453 19 32099694 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38382814 Affx-122973561 AX-123253172 19 31616800 TTAGCTGGATAATTTTTCTCCCCAAATTTGGAGGA[C/T]GGGTAGGTAGAGTAGGGAAGAGTATAGAGTGCTTT Y 2 1 2 1 101000 r 74 goat snp28410-scaffold303-2094464 19 32128595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403438 Affx-122957738 AX-123273791 19 31648394 GTTTCCTGTTATTGCAAAAGGATACTTGGAGAGCA[A/G]CACATGTATGCTAAGGAAGAAGGGATTACTTCAAC R 2 1 2 1 101000 f 74 goat snp28411-scaffold303-2126058 19 32160797 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411456 Affx-122951811 AX-123281806 19 31681378 GCTGATAAGTAGTCCTCTGTACCCCTACATGCTTC[A/G]TATTTTGATTTTGTTTATTTATCTCATCTTCCAGA R 2 1 2 1 103000 f 74 goat snp28412-scaffold303-2159042 19 32193746 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771870 Affx-122957785 AX-385259026 19 31732588 TGGAAAGTCAGCTAAAGAATGATTAGACAGTACAG[C/T]AAATGCTGCTGAAGGCACTGAACCCTAGAATGTGG Y 2 1 2 1 101000 r 74 goat snp28413-scaffold303-2210252 19 32244653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784299 Affx-122970649 AX-385271350 19 31767519 CATGAAAATACATCTCTGATTGGCATTCCGCTGCC[A/G]TTCCTTTCGAGTGCTGGTCACAAGTCAGAGCCTGG R 2 1 2 1 101000 f 74 goat snp28414-scaffold303-2245183 19 32279534 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399256 Affx-122960569 AX-123269611 19 31806169 GACAACAAATTCTGATACAGAATATATTTTCAAGT[C/T]ATTTTCCTCGGATAATTAGGCTCATGGTTCATCTG Y 2 1 2 1 101000 r 74 goat snp28415-scaffold303-2283833 19 32318110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443493 Affx-122927805 AX-123313830 19 31834891 TTGAAAACTTACCCTCCACCCCAGCCCCAAATCCC[A/G]CCCTTTACCAAACCCAAACTTTGTCTCATAGAATT R 2 1 2 1 303000 r 74 goat snp28416-scaffold303-2312555 19 32346734 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376646 Affx-122979020 AX-123247005 19 31874441 CCTTCATCATCTTAACCATCCTCATCTTTATTATC[A/G]TCCAACCGGTCCATCCCTTATAAGCCCATTTGACT R 2 1 2 1 101000 f 74 goat snp28417-scaffold303-2352105 19 32386101 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422655 Affx-122943688 AX-123293001 19 31907940 TCTGGAACACATGAAACAATGCAAGAATCTTCTAG[C/T]CTTGGAAGGTCAAAGAGCTTGTCTTTAGTGCCCCC Y 2 1 2 1 201000 f 74 goat snp28418-scaffold303-2385604 19 32419717 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422433 Affx-122943358 AX-123292779 19 31965142 CAATACATGCTTAACATTTTTAAGGTAAGATTTAC[A/G]TATAGTAAAATGTGCATATCTCAAGGGCACCACTG R 2 1 2 1 101000 r 74 goat snp28419-scaffold303-2442806 19 32475700 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395964 Affx-122963561 AX-123266319 19 32080038 TCCAGGCAGGCTAGAGCGGCCATCTGGAAGGAGAA[C/T]GTGGAGAAGAGGCACAGAAAGGAGGCCAGAAGAGC Y 2 1 2 1 201000 f 74 goat snp28422-scaffold303-2557702 19 32590902 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394273 Affx-122964716 AX-123264628 19 32115956 TAAAGGGCTGGCGATGTACCTGGCACACTCCTGCT[A/G]TACATTACTGAACTACTATTTCTTAGAACCCTGGA R 2 1 2 1 101000 r 74 goat snp28423-scaffold303-2593620 19 32627059 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449894 Affx-122922341 AX-123320229 19 32155834 ACCTTCCGGGACTCAAACACCCAATGGCTTTTTCC[A/G]TCTTCATCAATATGATTCCACCAGCGCAGGCCAAC R 2 1 2 1 101000 r 74 goat snp28424-scaffold303-2633498 19 32666467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407461 Affx-122954779 AX-123277812 19 32210686 TGACTTCCCACACCTGAGACCTGATGTCCTGGAGT[A/G]GGGGAAGTGGGGGAGAAGGAAGGGATCTGACCTGT R 2 1 2 1 102000 f 74 goat snp28425-scaffold303-2688350 19 32720688 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403481 Affx-122957705 AX-123273834 19 32261349 GAAAAAGTAGCCTGTGTCACATACTTCACTTCTTG[A/C]TCAATCATCTGATTCCATTTTATTGCTGTGCAAAC M 2 1 2 1 101000 f 74 goat snp28426-scaffold303-2739013 19 32771728 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse379 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38403489 Affx-122957699 AX-123273842 19 32305347 CTTCCGCTGAAAACACTGAGGCAGTTGATGCCCTT[A/G]TAATAATAATCGTGGAGAATCCTAGATCTTCGTTT R 2 1 2 1 201000 r 74 goat snp28427-scaffold303-2783011 19 32815676 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405392 Affx-122956296 AX-123275744 19 32334935 TTTGCACAAACTGTTAGGTCTTTCTGGAATGCCAT[C/T]CCTCCTGCCTCCATTCTCCTCACAACTCAAGACGA Y 2 1 2 1 101000 f 74 goat snp28428-scaffold303-2812599 19 32845627 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401818 Affx-122959454 AX-123272171 19 32364223 TAACACTTAAGGTCTTATCTCTTAGCAAGCTTGAT[A/G]TTTATAACACTTCTGGTGTCTTTCATGGCTGACCT R 2 1 2 1 101000 r 74 goat snp28429-scaffold303-2841887 19 32874914 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410780 Affx-122952672 AX-123281130 19 32402812 CGTGGGAAAGAGAAGTACAGAGTGGGAAGGCAAGA[G/T]CTGCTCTGGCCTTGGAGAGAAGGAAAGGTGGAACT K 2 1 2 1 101000 f 74 goat snp28430-scaffold303-2880476 19 32913654 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378137 Affx-122977123 AX-123248496 19 32458221 CAGATTCTTTACCACTGAGCTGCCAGGGAAGCCCT[A/C]AATGCAGATGCATGTCAGTAAAATGCAGTGACTGC M 2 1 2 1 101000 r 74 goat snp28431-scaffold303-2935885 19 32969177 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790097 Affx-122953035 AX-385277103 19 32517568 TTTTTTTAAGAAAGGGCTAAAAATGCACCCTGCAC[A/G]TAAAGAAGGAAAGGATACAGCCACTGCCATCAACT R 2 1 2 1 101000 r 74 goat snp28432-scaffold303-2995232 19 33028874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390055 Affx-122968419 AX-123260412 19 32567331 AGACCAGTATTACAAAAAATTAAGTGACAGAACCT[A/G]TGTAATATTGTCCTAGAGCTTTGCTGTCCAGTGAA R 2 1 2 1 101000 r 74 goat snp28433-scaffold303-3044995 19 33078682 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272905 Affx-1111833137 AX-519546593 19 32583907 AGCTGGCATCCACTCAGAGGCACCTACTCTATAGA[A/G]CCAGCGTCCATTCTGGGGTGTGCAAGGAGGAATGC R 2 1 2 1 202000 f 74 goat 19_32583907_AF-PAKI 19 32583907 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38429893 Affx-122938122 AX-123300234 19 32604085 AGCAGGGCTCTGAGATGTTGGTTTGCCTCCAGCAC[G/T]GTAGAACTGCCTTTCCCTACCTCCGAGGAACGATC K 2 1 2 1 101000 r 74 goat snp28434-scaffold303-3081749 19 33115422 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412832 Affx-122950463 AX-123283181 19 32652258 ACCTTAGTAAAATTTTCACTTTGGGGTCCAGCATC[A/G]TGGCCAAACTTGAACTTGGGAGAGACATAAAAATC R 2 1 2 1 201000 r 74 goat snp28435-scaffold303-3129922 19 33163484 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449064 Affx-122923050 AX-123319399 19 32692459 GACCCCACACCACGATGCCCAGGGCCAGAACTGCC[A/G]TACACCGCCTGGTCCCTCGGGCAGGACACAGGCAC R 2 1 2 1 201000 r 74 goat snp28436-scaffold303-3170123 19 33202781 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436100 Affx-122932675 AX-123306439 19 32766317 GCAACACTGAATATCCAGGGCTGACTGTCATGGCA[C/T]CTGCATTCCTGACAACGCCACTAACGCCAGGCTCC Y 2 1 2 1 201000 r 74 goat snp28437-scaffold303-3243981 19 33274919 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449254 Affx-122923043 AX-123319589 19 32798956 CAGGATATCGGGGTTATCTCTCTAGTGGCCTGGAA[C/T]GCGGAAAACTCTGTGAAACAAGCTTTTCTGAATTT Y 2 1 2 1 101000 r 74 goat snp28438-scaffold303-3276620 19 33307801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799052 Affx-122962746 AX-385285982 19 32839473 TGACTGAGCTATAAGAGAAACGTTATGACATTACT[C/T]TTCAGCAATGTGGAAATACATGTATCTCCCCACAT Y 2 1 2 1 101000 r 74 goat snp28439-scaffold303-3317137 19 33348609 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430281 Affx-122937289 AX-123300622 19 32885552 GAAAATGACAGTCTGCGGGGCAAGTCTGGACCAAA[C/T]GAATGGATCACACTCACTGACATACTGTCAATGCC Y 2 1 2 1 101000 r 74 goat snp28440-scaffold303-3363216 19 33392988 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442374 Affx-122928017 AX-123312711 19 32926692 GCTTATTATAGCTCATAGTTGATATGAATAGCATC[A/G]TGAACATGGTTGTCTCACATGCTGCTGGGGAATTA R 2 1 2 1 201000 f 74 goat snp28441-scaffold303-3404356 19 33434357 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438097 Affx-122931511 AX-123308435 19 32991546 TCACTTTAGTCGTCTTGGTGGTACTGTGTTAGTAA[C/T]AGGCATTTGGAGAATTCACAGCCATTATTTTTAAA Y 2 1 2 1 101000 f 74 goat snp28443-scaffold303-3469210 19 33499456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444589 Affx-122926958 AX-123314926 19 33039033 GGGGTTGCTTTGGCTGCATATCTCTTCCAGGGAGA[C/T]GGCTTGGACTGAGTGAGTCAGCCTGGGCTTTGGTG Y 2 1 2 1 101000 f 74 goat snp28444-scaffold303-3516697 19 33546716 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418248 Affx-122947029 AX-123288596 19 33133743 ACTCAGAGCAAGTGCATCAAACAGATGAAAAGCAA[C/T]GAAGATCAGCATTACCTGGCTCACTAGGGAAATAA Y 2 1 2 1 101000 f 74 goat snp28446-scaffold303-3611407 19 33640949 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440654 Affx-122929939 AX-123310991 19 33175798 GCAGTGGCCAGTGACTGCATCCTGGTAGAGGCAAA[C/T]GGCCAGTGCCAAGTGTTTGTTGGCAAGGGGACCAA Y 2 1 2 1 101000 f 74 goat snp28447-scaffold303-3653462 19 33682795 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277369 Affx-1111835814 AX-519550873 19 33198502 CCACCAGGGAAGCCCACCTAGCTTCAGTGGAGACC[A/G]TGAGATGTAGTCTTTTTAGGTGAACACCAGTGGAG R 2 1 2 1 101000 r 74 goat Random2.2K-1798 19 33198502 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447651 Affx-122923968 AX-123317987 19 33235623 TCACCCAGTATGAGCTGCACCCCTGCCTGCACCAT[C/T]GCTGACCTCGATAAAGGGAAAACCATTAACATCAC Y 2 1 2 1 101000 r 74 goat snp28448-scaffold303-3713287 19 33742891 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse380 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38430206 Affx-122937340 AX-123300547 19 33280741 CTTGTGCACACGCACTTGTATGTGTGCATGTCTGC[A/G]TGCACATGTGCGCACGTGTATATGTGTGTCTGTGT R 2 1 2 1 103000 f 74 goat snp28449-scaffold303-3758405 19 33787752 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427529 Affx-122939513 AX-123297872 19 33351681 AGGAGCCTGGGATGTGTCATCAGAGAGATGTGAGG[C/T]GCTCAGAAAACCACGGGGATTTGTCAAAAGGACAA Y 2 1 2 1 201000 f 74 goat snp28450-scaffold303-3829345 19 33857551 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411918 Affx-122951168 AX-123282268 19 33400429 ATGACCCACTCCTTGCAGCATGTCTGAGGACTGGA[C/T]GAGGTAGCGATTGTCAGGCAGAACTTGCTTCGGGT Y 2 1 2 1 201000 r 74 goat snp28451-scaffold303-3878093 19 33906279 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393981 Affx-122965039 AX-123264336 19 33432699 CTCGTTGTTTTAACTTGTAGTTTCTTGATGGCATA[C/T]GATTGAAGGCATCTCTTCATATGCTTCTTTACCAT Y 2 1 2 1 101000 f 74 goat snp28452-scaffold303-3910363 19 33937908 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382903 Affx-122973406 AX-123253261 19 33481687 TCCACACACCCAACCAGGGAAGATCCCACTTTTCC[C/T]GGAGTGTCCAAACCCCCAACCCCTGATTGTTCAGT Y 2 1 2 1 201000 r 74 goat snp28453-scaffold303-3959351 19 33986828 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406860 Affx-122955653 AX-123277211 19 33550524 CGTGTGTATGGGAAGAAGAACATCAAGCTGGAGCC[C/T]GTGCCTCTCAAGGGGGCCTCCCTGGACCCAAGGTG Y 2 1 2 1 101000 f 74 goat snp28454-scaffold303-4028188 19 34056065 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447049 Affx-122924524 AX-123317385 19 33605591 CCTACCTGTCTAGGCCTCCCCTGACCACATGCTGG[C/T]GGCCCTAAGGCAGCTCTGGCCTCAGGACATCTGAA Y 2 1 2 1 102000 r 74 goat snp28455-scaffold303-4083255 19 34111005 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394315 Affx-122964684 AX-123264670 19 33639009 AAGAGCAGAGCCACCAGGGCGTAGTGAATTACAGC[A/G]CCCACTTAGTAAGCAGCTACTGCATGCCAGACCCT R 2 1 2 1 201000 r 74 goat snp28456-scaffold303-4116673 19 34143960 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442646 Affx-122928447 AX-123312983 19 33672243 TCACTGGCCTGGGGCTTCCAGGAAGGCCACGACCA[A/C]TTTACTGCACATGCCAAAGTAGCCTGCCCTTGTAG M 2 1 2 1 101000 r 74 goat snp28457-scaffold303-4149907 19 34177306 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397383 Affx-122962271 AX-123267738 19 33707481 CCCAAGGTCAACAACACATAAGGAAAGTGAGGTGC[A/G]GGAGCTGAGCTCACATATCCAGAATTCGTTAGCAG R 2 1 2 1 101000 f 74 goat snp28458-scaffold303-4185145 19 34212274 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399485 Affx-122961182 AX-123269840 19 33738901 GTGCACACCCGGTCCCCTAGAGGGGCTCTCCGGGC[A/G]AGGTGGTTGCCCAGGTTGTAATAGTGTGATCTGCG R 2 1 2 1 101000 r 74 goat snp28459-scaffold303-4216565 19 34243770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383959 Affx-122972948 AX-123254317 19 33767692 TTCTTGCATCTTGTTTCAATAGAAACCAAGATGGC[C/T]GGGACCGTTTTCTCCAGAGAAACCTAGTTGACTAT Y 2 1 2 1 202000 r 74 goat snp28460-scaffold303-4245356 19 34272744 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416579 Affx-122947657 AX-123286927 19 33841974 TCACTGACCACGTGACCTTCACCTTCCAATCCCAC[A/G]GGAGATGAGACTACACTGGGGACATCTCTCCATTC R 2 1 2 1 201000 r 74 goat snp28461-scaffold303-4319638 19 34331801 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416167 Affx-122948268 AX-123286516 19 33924359 AATGGCCCAGTGAGCCTGGGGACTGGTGTGGAAGA[C/T]GAACGGCAAGGCGGGGTGGGCAAGAGGTGAGTGAC Y 2 1 2 1 101000 f 74 goat snp28462-scaffold303-4402023 19 34412960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432061 Affx-122935891 AX-123302402 19 33971073 GGAGGCATGAGTCCAGAGTCTCCTTGCCTCTGCAG[C/T]GCTAGTCACCCTCAGACTGAAAACCTTGCTGTCCT Y 2 1 2 1 101000 r 74 goat snp28463-scaffold303-4448737 19 34458581 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445436 Affx-122925360 AX-123315773 19 34001258 GACCAATCTGCTTCTAGCCATGCATTGTTCTAGGT[A/G]CGAGGGGTACAGCAAGCAGCAGGAAGATGCTCAAG R 2 1 2 1 101000 f 74 goat snp28464-scaffold303-4478922 19 34488631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427470 Affx-122940021 AX-123297813 19 34034058 TCTTTGGAGAAATGCCAAACTCAGCGCCCGAGCCC[A/G]TGGTTTTAAAACCTAAGTGAGATGACACCCTTCTC R 2 1 2 1 101000 r 74 goat snp28465-scaffold303-4511722 19 34521390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378822 Affx-122976549 AX-123249181 19 34104834 TCCGTATCTTGGCGGTTTAAACAGTGCTGCTGTGC[A/G]CACTGGGGTGTGTTATCTTTCTGCATCAGCATTTT R 2 1 2 1 101000 r 74 goat snp28466-scaffold303-4582498 19 34592060 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277371 Affx-1111835815 AX-519550875 19 34171609 GGGCCAGGTGGCGTGGGCTCCCTTTCCCTGCCCCC[A/C]ATTTCTCAGCGAGTAACCAGCGCCTGCATTTTGCC M 2 1 2 1 101000 r 74 goat Random2.2K-1799 19 34171609 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380977 Affx-122974686 AX-123251335 19 34176230 GAAGTCATCCAGTGAACTCCGAGGCCCCTTCCCCA[C/T]GGTCAGTCTTTGCAGGACTTCAGAGCAGTTAGCCA Y 2 1 2 1 101000 r 74 goat snp28467-scaffold303-4653894 19 34662967 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434028 Affx-122934217 AX-123304369 19 34257962 AATGAACCTGCTTTTCCCTCTCCTCCATCTGTTGA[A/G]AATCAATTGACTGTACGCAGACGGAGAGCTTACTT R 2 1 2 1 101000 r 74 goat snp28469-scaffold303-4735626 19 34755555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421591 Affx-122944496 AX-123291938 19 34291156 ACACAATTCTCAAGGAGAGAAAAACTTAGTGACAG[C/T]AGTCAGAAAATAAAGACTAGAGCAAAACTCAGCTT Y 2 1 2 1 201000 f 74 goat snp28470-scaffold303-4768820 19 34788831 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440559 Affx-122929311 AX-123310896 19 34343132 GCAGAGAGCAAATCTGCTCGCGTGTCAAGGACACA[A/G]CAGGTGCGCTTGAACTGCCCTCCCCAGTGCCCGCT R 2 1 2 1 101000 f 74 goat snp15849-scaffold1667-5473 19 34840821 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393635 Affx-122965302 AX-123263990 19 34395952 ATGCCAGTGACCCTCAGGAAACAGTGGGATCCTAC[A/G]GAGTCACCTTTTAGGTCCGGTGCCTTGGACTCAAC R 2 1 2 1 101000 f 74 goat snp15850-scaffold1667-58293 19 34892621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405661 Affx-122956571 AX-123276013 19 34464163 GTCTCTGGTGGCCATCTGGCCAGTGATGAATGTGA[C/T]GCCCACTTCCCCATGCCCTTCTGGGGACTTTGAAA Y 2 1 2 1 201000 f 74 goat snp15851-scaffold1667-126504 19 34959380 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389556 Affx-122968266 AX-123259914 19 34517841 TTAGGAGGCCTGTGTGCATCTGTCCACAAACACAC[A/G]TACACGCATGTGCCAGGCTCCGGCAGCAGAGCTGC R 2 1 2 1 101000 f 74 goat snp15852-scaffold1667-180182 19 35012166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse381 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38409830 Affx-122952945 AX-123280181 19 34557533 GCCCCTACCTCAAACATACAGTTAAATCTACAGCA[C/T]GGGTTGTTATAACACTGCTGGAAGAAGCCACAGTC Y 2 1 2 1 101000 f 74 goat snp15853-scaffold1667-219874 19 35053835 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387798 Affx-122969694 AX-123258156 19 34586744 AAACACATGTCCCCCATCAAGATAATGGATGCATC[A/G]TCAATGAGAAATTACTCACGGGCCAATCTAATAGG R 2 1 2 1 101000 r 74 goat snp15854-scaffold1667-249085 19 35082968 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765440 Affx-122933052 AX-385252941 19 34641462 TCCTCAGACCATCTATGAGTGATTTACTCCAACTG[A/G]CTTATCTGGTTTTCAATAACTGGGATATGGCCAAA R 2 1 2 1 101000 f 74 goat snp15855-scaffold1667-303803 19 35137777 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410753 Affx-122952694 AX-123281103 19 34691035 CTCTCCAGAACTCTTAGTGATTTTTAAAAGCATCT[A/G]TGTATTTCCTGGATGCTCTAAATTATAATAAAAAT R 2 1 2 1 303000 r 74 goat snp15856-scaffold1667-353376 19 35187473 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778515 Affx-122948533 AX-385265628 19 34785012 GTTATGTACTTCTCTAAGGAGTAGAGGTTGATGTT[A/G]ACATTTGCAACTATTCTTTACAGTATACAAAGTGA R 2 1 2 1 101000 f 74 goat snp15858-scaffold1667-447353 19 35281455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787972 Affx-122973001 AX-385274992 19 34832129 TGAACATTGCAAATCTAGAATTCAGATCTGGGCTA[G/T]AGACTGAGTTAGAAATTTGAAGGTGGTTAGCATTC K 2 1 2 1 101000 f 74 goat snp15859-scaffold1667-494470 19 35328365 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800806 Affx-122966740 AX-385287722 19 34913265 ATAATATCATTATTGAGGTTGGTGGCCCTAAACTT[A/G]CTTTCTTGTAAAGATGTAAGAAGCCACATAATGCT R 2 1 2 1 201000 r 74 goat snp15860-scaffold1667-575606 19 35409989 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427043 Affx-122939823 AX-123297388 19 34944056 CTCTTCTTCCTGGCTTCTCGTGGCCGCGTGAGGCC[G/T]TTCTCACGTCTCTAGATACCCTCTCGAATGTTCCT K 2 1 2 1 101000 r 74 goat snp15861-scaffold1667-606397 19 35440796 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415999 Affx-122948393 AX-123286348 19 34987027 GGAGGAGTTCTCCTCTGTGCCTCGATTGTTCTGTG[C/T]TCTCTGCTTGGGCTGGGGGTCTCCAGGGCCCTGTG Y 2 1 2 1 101000 f 74 goat snp15862-scaffold1667-649368 19 35483845 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421065 Affx-122944245 AX-123291412 19 35071678 AGGGCTTGGCGCCCACACAGCACTTCCACCTCCAT[C/T]GTCATGCTGACCCTCACGCCAGTCCCAGAGGGAAC Y 2 1 2 1 201000 r 74 goat snp15864-scaffold1667-734019 19 35567369 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422603 Affx-122943731 AX-123292949 19 35106782 AGGGAGCAAAGGACCAGGGACCTCTGTTCCTTGCA[A/G]TCATTCAGTGACTTAGACAGATTAAGTAAGGCTGT R 2 1 2 1 101000 r 74 goat snp15865-scaffold1667-769123 19 35602401 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse382 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468277252 Affx-1111835818 AX-519550757 19 35110759 TGTCTTGTTTATGCATTGTGCCTGTTTCACTGTAG[A/G]CAGTAAGTCTAAGTGAAGCAGTGAGGATGTTGAGT R 2 1 2 1 201000 f 74 goat Random2.2K-1801 19 35110759 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443510 Affx-122927792 AX-123313847 19 35192014 CCTTTTTTTCCCCCTCTACCTTTGAAAAAAGTTAC[A/C]ATTTACTGATACAATTAAGGCTAGTTTTATCTTGG M 2 1 2 1 201000 r 74 goat snp15867-scaffold1667-854355 19 35687377 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse383 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38423385 Affx-122943132 AX-123293731 19 35245149 CCTCATGCCTTCCTTGAACCTCCCCCGCCCCAGTC[C/T]TGAGTAGGGATCCTTTCTCTGCACAGCCCTCCCTC Y 2 1 2 1 101000 r 74 goat snp15868-scaffold1667-907490 19 35740201 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421282 Affx-122944737 AX-123291629 19 35280883 CTCAGTTTAACAAGGTGTCTGCTGGAAGGACTAGG[A/G]ATGGGGAGGGGTGCCTGTACCAGGCATCTCCAGGA R 2 1 2 1 101000 f 74 goat snp15869-scaffold1667-943224 19 35775875 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272955 Affx-1111833138 AX-519546641 19 35293100 CAACCAGAGACCCACAAAAGCAGTAAGGAGGTGCA[A/G]AACTTAGCCTTACAAGGACACACGTGATTGAATTT R 2 1 2 1 101000 r 74 goat 19_35293100_AF-PAKI 19 35293100 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38386202 Affx-122971356 AX-123256560 19 35320366 CTCTTCTGCCTGAAAAAAAGCAGCCTTACAGACAT[C/T]CCCTCGGAGACACACATCACACAGGGCTACACACT Y 2 1 2 1 102000 f 74 goat snp15870-scaffold1667-982707 19 35815117 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414679 Affx-122949296 AX-123285028 19 35385368 CTCTAGTTGGGATATGTGTATGGGGGATTCATGAG[A/G]ATCACACAGCATGGGACAGGGTGGCGGAAGGGCAA R 2 1 2 1 101000 f 74 goat snp15872-scaffold1667-1047709 19 35880260 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441510 Affx-122928724 AX-123311847 19 35428965 AAAAAGGAGAGACTACTGGCAGCTACATAAAGAGG[A/G]AAGAGGAGGATGAGGAAGGAGTTTTAATCTTGAAA R 2 1 2 1 101000 f 74 goat snp15873-scaffold1667-1091306 19 35923795 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446048 Affx-122925838 AX-123316385 19 35457976 CAAGTGCCTAGCCCTGTACTCTCCATGTTGCTTAC[C/T]AGAACATTTAGTTCCAAATTAAAGAAGCAGATAAG Y 2 1 2 1 101000 r 74 goat snp15874-scaffold1667-1120317 19 35952132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789567 Affx-122932341 AX-385276576 19 35491729 TCATTTATTAAACCATTAACTTGTTATTGGACATA[G/T]AGGCCATTGCTAATTATTTTGCCGCTATACTTATT K 2 1 2 1 101000 r 74 goat snp15875-scaffold1667-1154070 19 35985602 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446749 Affx-122925332 AX-123317085 19 35531159 GCACAGAGAGGGGAAACAGACTGTAAACACAGAAG[C/T]ACATAAATAAGGCAATTTCCAGCACAGGTCCAAAG Y 2 1 2 1 101000 f 74 goat snp15876-scaffold1667-1193500 19 36025018 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396896 Affx-122963222 AX-123267251 19 35586960 ACCTATATAGTCCAATGGTATAATGTGGTAACCAA[C/T]AAATTTAATTAGGAAATTTTTACCCCTGTGGGAAA Y 2 1 2 1 101000 f 74 goat snp15877-scaffold1667-1249301 19 36080680 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381377 Affx-122974392 AX-123251735 19 35628025 AAGAGGCACGTCTGGTACGGCGAGAGCATGACCGG[C/T]GGATTCCAGGTGCGTGAGCTGGACCTTGTAGCCAG Y 2 1 2 1 101000 r 74 goat snp15878-scaffold1667-1290366 19 36121482 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse384 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38380173 Affx-122975518 AX-123250531 19 35684435 TCCCTAAATGTGTCAAATGTATGGTCCAATCCAGT[A/G]CTCTCTCCTTCTCGTGGGGACCTGAGAGTTAGAAA R 2 1 2 1 201000 f 74 goat snp15879-scaffold1667-1346776 19 36178188 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384505 Affx-122973053 AX-123254863 19 35723474 CAGCCATGTGTCTACCCCCTTAGGCCCTGAGCTCA[C/T]CCTTCCTGTTTCAGCTGGACCCAGAACCCTGCTGT Y 2 1 2 1 101000 r 74 goat snp15880-scaffold1667-1385815 19 36216528 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771248 Affx-122927809 AX-385258406 19 35796304 GGGCTTGTATCATAAGGGGAGTAATAGGATTGTTA[G/T]CTAGCCGTATGTGAGAATTTAGCAATCCTGGAAGC K 2 1 2 1 101000 r 74 goat snp15881-scaffold1667-1458645 5 97180971 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446080 Affx-122925814 AX-123316417 19 35824947 AAGATCAGGCAGTGAAGATGCTAATGAAGCACCTA[C/T]TGTGCACGAGGCTTGTGCCAGAAGCTTTCACAGGC Y 2 1 2 1 101000 f 74 goat snp15882-scaffold1667-1487288 19 36317560 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377046 Affx-122978304 AX-123247405 19 35853962 ACACGCTGACACCCAGCGCTCCAGAGCCAGCCTCC[A/G]AGAGGCACACGCAGTATCACACAGGCAATGCCCAT R 2 1 2 1 101000 r 74 goat snp56698-scaffold896-2936911 19 36344277 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799292 Affx-122966022 AX-385286222 19 35971377 GCTTTTCCTTTGCTCTCACTGTTAGACTTGTTTCC[A/G]ACTGTACCCTTATCAGAAGCTTCTGGTAAACTCCT R 2 1 2 1 101000 f 74 goat snp56696-scaffold896-2819496 19 36461239 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414659 Affx-122949311 AX-123285008 19 36034592 CCTTGACATGGGTCAAAGCTCAGCAACCATAACCA[C/T]GACTCCACAGAGGTAGGAAAACTCTGCCTCTTGGT Y 2 1 2 1 101000 f 74 goat snp56695-scaffold896-2756281 19 36524557 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394522 Affx-122964533 AX-123264877 19 36079130 AACTCTACTAATGTTATCGTATAGCTCATGGAATT[A/C]TGCTAACAGCCCGGATGGGAGGGGGCTTTGGGGGA M 2 1 2 1 101000 f 74 goat snp56694-scaffold896-2711743 19 36568776 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435483 Affx-122933441 AX-123305823 19 36164879 GGTGGAGATTAAAGGAGAGTGGTAAAGGTCTGAAG[C/T]GTCTATTGTTGAGAAAAAGAAAGGGAGCTGACTAA Y 2 1 2 1 101000 f 74 goat snp56692-scaffold896-2625994 19 36655027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424995 Affx-122941900 AX-123295341 19 36202911 GAGGCAAGACCATGGTCCAGCGTGTGAGGAGTATG[A/G]TTCTGTATACGTGGAGTTGGCAGTCTGTGAAATCC R 2 1 2 1 101000 r 74 goat snp56691-scaffold896-2587962 19 36693037 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390528 Affx-122967233 AX-123260885 19 36259236 TCTGCTCGATGCCTAGGAAGAGAAACACAGGAGTT[A/G]CTCTGCCAGAAGTGAGTTGAAACTGAAGGCTCCCT R 2 1 2 1 101000 f 74 goat snp56690-scaffold896-2531637 19 36747881 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390297 Affx-122967724 AX-123260654 19 36338194 GAAAGAAGAGATTGGAGAACCAATTCAGGTCTGAC[A/G]TCTACTAATAAGATTTGCAGAAAATAAGAACAGAG R 2 1 2 1 101000 f 74 goat snp56689-scaffold896-2452679 19 36827493 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396893 Affx-122963225 AX-123267248 19 36367467 GGCAGAGAGTAAATACTTTAGGCTTTGCAGGCCAT[A/G]TAATCTCAGCTCTAAGTATGCAAGTCTGCTACTCC R 2 1 2 1 201000 r 74 goat snp56688-scaffold896-2423406 19 36857188 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419452 Affx-122945492 AX-123289800 19 36398845 CACTAACTCCAACACCAACTCACTTTTATTAAAAT[A/C]AATTCTGCTTATCAAAATCATTTTATCAAAATGCT M 2 1 2 1 101000 f 74 goat snp56687-scaffold896-2392028 19 36888688 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse385 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38392892 Affx-122965734 AX-123263249 19 36492457 ACTCATAATCCAGGGCTAGGATCCCCCAGAGATGC[C/T]CCATCCTGACCACTCTCCTTCCCTGGCCCACCCCA Y 2 1 2 1 101000 f 74 goat snp56686-scaffold896-2298416 19 36981616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410803 Affx-122952653 AX-123281153 19 36521051 GGAATCACTCAGCTTGATGTTAGCTGACCTGGAAA[C/T]CAGGAGTTCAAGGGCATCCCTCCTGCCCCTTTTCC Y 2 1 2 1 101000 f 74 goat snp56685-scaffold896-2269822 19 37010239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766038 Affx-122974727 AX-385253455 19 36588745 GAATTTCCACGTGGTGAAATTTATTAATAAATTGT[A/G]TAATTATTGGAAGGCAGAGATATGGAATAATATCT R 2 1 2 1 101000 f 74 goat snp56684-scaffold896-2202128 19 37075734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393176 Affx-122965523 AX-123263533 19 36634449 CCTCCCTTCCCAAGGGTGAATTGGCTTCTGCCACT[A/G]CTGAGTGCCCAACCTGCCAAAGCAGACTATACTAA R 2 1 2 1 101000 f 74 goat snp56683-scaffold896-2156424 19 37122148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433430 Affx-122935079 AX-123303771 19 36674941 TTATTAATATCATCTCCGGAATCACCTTGAGTCCC[A/G]TCACATCCACAATTTCTGGCTCTCTAGCCATTTGG R 2 1 2 1 101000 f 74 goat snp56682-scaffold896-2115932 19 37161165 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788688 Affx-122925146 AX-385275704 19 36711541 CCTGGGAAGCCTGTACTGATAGCTAGAATATTTAA[C/T]AAACATCTGCTATCGTTGGGTGACTATACCAGACA Y 2 1 2 1 101000 f 74 goat snp56681-scaffold896-2079332 19 37198025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403210 Affx-122957909 AX-123273563 19 36763561 TATCTTCTAGCATATTCTGGATTGGTCTTTTTAGT[A/G]TGATCTGAATTTCCCTGAGTCGGAGAACAAGTTAA R 2 1 2 1 101000 r 74 goat snp56680-scaffold896-2027312 19 37250481 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794833 Affx-122925480 AX-385281793 19 36793592 AAATTAGATTTCCCCGATGTAACTAGAAAGTAAGC[G/T]CTGTGTTGTGACTTTGGCACTACACAATGTCCACT K 2 1 2 1 201000 f 74 goat snp56679-scaffold896-1997281 19 37280489 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395837 Affx-122964024 AX-123266192 19 36850843 AGAATCTGTGCCCTCATGGAACAGTCCTAGGAGAC[A/G]TGTATTAATCTTGAGATGCTCATTAGATGAAAATG R 2 1 2 1 201000 r 74 goat snp56678-scaffold896-1940030 19 37338170 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794890 Affx-122970589 AX-385281850 19 36905299 CTTTTCATGGTTAACATGGTTCTACTTCCAGGGCC[A/G]GCATTCGTGACTGTCTCAATTTCAGCCAGAAGTGG R 2 1 2 1 101000 f 74 goat snp56677-scaffold896-1885574 19 37392673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427669 Affx-122939314 AX-123298012 19 37047830 ATGGGTAGGGAAGAGGGGATAGGTCTGACCCAGAC[G/T]ATCCCCATATTTACAAGCTTTGGGCCCTCTATGCC K 2 1 2 1 101000 r 74 goat snp56674-scaffold896-1743043 19 37535101 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783100 Affx-122978206 AX-385270167 19 37079511 TTGGAGGGAAGACTTTGAGGTCTGGAAAAGGAGGA[G/T]AGAGGGATTTATCATCCCTGATAGTGAAGTCATAA K 2 1 2 1 101000 r 74 goat snp56673-scaffold896-1711362 19 37566785 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439791 Affx-122930499 AX-123310128 19 37113741 TGTAGTTTGGAGGCACAAGTAACAATGCTTGTTTA[C/T]AGATAGGTCTGCGAATGTGTGAGAGAAGTTGGCAT Y 2 1 2 1 101000 f 74 goat snp56672-scaffold896-1677132 19 37601082 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445511 Affx-122925183 AX-123315848 19 37146562 AAGAAAGCTATCTGCCTCCCAACAATGCTGTGAAA[C/T]AAACAAAGCAGTAAATTAAAGGCAGGAGGCATGGA Y 2 1 2 1 101000 f 74 goat snp56671-scaffold896-1644311 19 37634643 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 532577593 Affx-1248697228 AX-579216009 19 37147312 TTTCACACGGGGTCTCCTCTGCCAATCGTGAGGCA[-/TAACT]TAACAGAACAGCCCCCACCCGTCCCAGGAGTGGAG - 8 1 4 1 20100 r 74 goat "ins-del_018;rs662236553" 19 37147312 TAACT - 5 "indels;junction" growth traits 0.462 neutral SV-TF-chip candidate gene ou candidate region IGF2BP1 562165491 Affx-1248697228 AX-606940902 19 37147312 TTTCACACGGGGTCTCCTCTGCCAATCGTGAGGCA[-/TAACT]TAACAGAACAGCCCCCACCCGTCCCAGGAGTGGAG - 8 1 4 1 20100 r 74 goat "ins-del_018;rs662236553" 19 37147312 TAACT - junction SV-TF-chip candidate gene ou candidate region IGF2BP1 562165587 Affx-1248697228 AX-606940998 19 37147312 TTTCACACGGGGTCTCCTCTGCCAATCGTGAGGCA[-/TAACT]TAACAGAACAGCCCCCACCCGTCCCAGGAGTGGAG - 8 1 4 1 20100 f 74 goat "ins-del_018;rs662236553" 19 37147312 TAACT - junction SV-TF-chip candidate gene ou candidate region IGF2BP1 562165863 Affx-1248697228 AX-606941272 19 37147312 TTTCACACGGGGTCTCCTCTGCCAATCGTGAGGCA[-/TAACT]TAACAGAACAGCCCCCACCCGTCCCAGGAGTGGAG - 8 1 4 1 20100 f 74 goat "ins-del_018;rs662236553" 19 37147312 TAACT - junction SV-TF-chip candidate gene ou candidate region IGF2BP1 532577594 Affx-1248697229 AX-579216010 19 37168307 AAGCCCCATTCCAGGGCCTCGGGTCCCACACCTCG[-/CCAGCTTCTCGGGAT]CCAATTCATGGCCAAGAGTGAGCTTCACGGTATCT - 2 1 2 1 500000 r 74 goat "ins-del_019;rs647937245" 19 37168307 CCAGCTTCTCGGGAT - 5 indels growth traits 0.582 neutral SV-TF-chip candidate gene ou candidate region IGF2BP1 562165218 Affx-1248697229 AX-606940630 19 37168307 AAGCCCCATTCCAGGGCCTCGGGTCCCACACCTCG[-/CCAGCTTCTCGGGAT]CCAATTCATGGCCAAGAGTGAGCTTCACGGTATCT - 8 1 4 1 20100 f 74 goat "ins-del_019;rs647937245" 19 37168307 CCAGCTTCTCGGGAT - junction SV-TF-chip candidate gene ou candidate region IGF2BP1 562166076 Affx-1248697229 AX-606941485 19 37168307 AAGCCCCATTCCAGGGCCTCGGGTCCCACACCTCG[-/CCAGCTTCTCGGGAT]CCAATTCATGGCCAAGAGTGAGCTTCACGGTATCT - 8 1 4 1 20100 r 74 goat "ins-del_019;rs647937245" 19 37168307 CCAGCTTCTCGGGAT - junction SV-TF-chip candidate gene ou candidate region IGF2BP1 562166461 Affx-1248697229 AX-606941869 19 37168307 AAGCCCCATTCCAGGGCCTCGGGTCCCACACCTCG[-/CCAGCTTCTCGGGAT]CCAATTCATGGCCAAGAGTGAGCTTCACGGTATCT - 8 1 4 1 20100 r 74 goat "ins-del_019;rs647937245" 19 37168307 CCAGCTTCTCGGGAT - junction SV-TF-chip candidate gene ou candidate region IGF2BP1 562166467 Affx-1248697229 AX-606941875 19 37168307 AAGCCCCATTCCAGGGCCTCGGGTCCCACACCTCG[-/CCAGCTTCTCGGGAT]CCAATTCATGGCCAAGAGTGAGCTTCACGGTATCT - 8 1 4 1 20100 r 74 goat "ins-del_019;rs647937245" 19 37168307 CCAGCTTCTCGGGAT - junction SV-TF-chip candidate gene ou candidate region IGF2BP1 320770294 Affx-122951277 AX-385257460 19 37183209 ACTGCAATTGGTTGGGTAGATTCTCTAAATAGCTT[A/G]CTCAATACTCACACTTCTTTATTTCTAGCAGAATT R 2 1 2 1 101000 r 74 goat snp56670-scaffold896-1607664 19 37671229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422412 Affx-122943374 AX-123292758 19 37213047 TAATAGCATTAGAATTCCTCTTAGGAAGAGAATCA[C/T]CATTGTTTGGCAAAGTAACCTGTTTCTCTCTCTGT Y 2 1 2 1 101000 r 74 goat snp56669-scaffold896-1577826 19 37701298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439295 Affx-122930969 AX-123309632 19 37255231 ACTTCGTTTCCTTGGAATTATGCAAAGTGCCATCC[A/G]TTTTTTATTTTGTCTTATATGGAAAACATTATCCT R 2 1 2 1 303000 r 74 goat snp56668-scaffold896-1535642 19 37744367 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789559 Affx-122975182 AX-385276568 19 37369023 AAATCATATAAAGTCTTTTTGGATGTGTTAGTGAT[A/G]TTGAATCCAATTCTAAGGGAAACAGAAATCTTCGA R 2 1 2 1 101000 r 74 goat snp56666-scaffold896-1421850 19 37858057 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395250 Affx-122964099 AX-123265605 19 37404037 TTTATTTTAGTTATAGCTCTAATCCCTTGAAGGGA[C/T]ATTGCCACCAGAATATTTCCACTCTGTGAATTGAC Y 2 1 2 1 202000 f 74 goat snp56665-scaffold896-1386836 19 37893688 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421297 Affx-122944102 AX-123291644 19 37433833 TTGTTTTCCCATCAGATCTCCCTATATCACCTGAT[A/C]GACTTGTTCCCTTTCTCTGTGTTTCTCACTCGTCT M 2 1 2 1 101000 r 74 goat snp56664-scaffold896-1357040 19 37923399 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799366 Affx-122977644 AX-385286296 19 37490829 GTTTTGAATCCAATTATTTTGGGTGGTTTAAAGTA[C/T]CGCACTCTTGTTGGACGGAAATTAGCAGCTATTGA Y 2 1 2 1 101000 r 74 goat snp56663-scaffold896-1300044 19 37980537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403678 Affx-122957501 AX-123274030 19 37525671 TTTGAAGTTGGAAAAAGCCAGTCTCCAGAGAGAAG[A/G]AAAGATCTGTCCTTTTACTGAAAACTTCGGTGTGA R 2 1 2 1 101000 f 74 goat snp56662-scaffold896-1265202 19 38015002 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437337 Affx-122931950 AX-123307675 19 37576005 AACTGAGGAGTTTCTGAAAAGCAAAACTAACCTAC[A/G]TGGGAAGTTAGGCGGGGGTGGAGCAGACAGAGGAG R 2 1 2 1 101000 f 74 goat snp56661-scaffold896-1214868 19 38063762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383085 Affx-122973734 AX-123253443 19 37647173 CCACCTGCCATGATGGGGATGAAGAAACCATGGAA[C/T]GCAGGGGCAATCCTCAGAAGATGACACCTTGAACC Y 2 1 2 1 201000 f 74 goat snp56660-scaffold896-1143700 19 38132778 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393976 Affx-122965042 AX-123264331 19 37728567 CAGTATTAATATGTGAAGCAGCCTGTGGACCACTA[C/T]GAACTCAGGGGCATTTCTCGATCCACAACAGAGAA Y 2 1 2 1 101000 f 74 goat snp56658-scaffold896-1062306 19 38214659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408696 Affx-122953439 AX-123279047 19 37775801 GCCTGAATCCCCAGACCTTTTCTTCTCTTTAATGG[A/G]TGACCGTAGCTCAGGTGTTTCATCCTGGAGGAGCC R 2 1 2 1 201000 r 74 goat snp56657-scaffold896-1015072 19 38261883 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448689 Affx-122923868 AX-123319025 19 37839736 GTGTATCTCAAGGGTCCTGGAGCTGGTGCCAGTCC[A/G]CTGGTGGGTGGGTTCATGTCCTAGGGTGATGAGCT R 2 1 2 1 202000 f 74 goat snp56655-scaffold896-951137 19 38325658 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402086 Affx-122958700 AX-123272439 19 37876489 TTGGAAGCAGAATGGCAAAATGAGAGTGGGCCTGA[A/G]AGTGGGATGCATGGACTCCAGGGGGGCCCAGCATC R 2 1 2 1 101000 f 74 goat snp56654-scaffold896-914384 19 38362152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse386 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38413492 Affx-122950647 AX-123283841 19 37962696 TTCTGTGAAGTAGGCACAACTGAACATCACAGAAA[C/T]GGTGCAAAACCGGGAGCTCTCCTCTCCTATCTGAT Y 2 1 2 1 101000 f 74 goat snp56652-scaffold896-828177 19 38448777 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450295 Affx-122922156 AX-123320630 19 38023216 CAAATTTTAGAATTTTCAGGGGGTAAAGTGAGGTT[A/C]TCAAAGAGTTTCTGCCCGAGGCGAGGGAGTTAGGA M 2 1 2 1 101000 f 74 goat snp56651-scaffold896-767657 19 38509810 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447294 Affx-122924922 AX-123317630 19 38052703 GGTACACTGGAAAGGAGAGGCTCACAGAAGGGTGA[A/G]TCTCTTATTGCTCAGGATCTGCTGGCTGACCCAAA R 2 1 2 1 201000 r 74 goat snp56650-scaffold896-738170 19 38538780 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799277 Affx-122924418 AX-385286207 19 38127861 TTATTAAAGCTGAACTGATTTGGGGGTTAATTAAA[C/T]GCTATCATTCACAGTCCAAATCATTCCACTTTTCA Y 2 1 2 1 101000 r 74 goat snp56648-scaffold896-663012 19 38614863 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272912 Affx-1111833140 AX-519546599 19 38161171 CCCCTTCTAACTCAGGCATCCCATAGGAGGCAGAG[A/G]TGATCAGGTATGTGTCTCACTGGAGAAGGGAAACC R 2 1 2 1 102000 f 74 goat 19_38161171_AF-PAKI 19 38161171 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423758 Affx-122942847 AX-123294104 19 38165193 TTAAAGTCTGTCTTCCCTACTAAACCTTCAGCTCC[A/G]TGAGAGCAGGGGTCTAGTTTGCATTTTGTCCATCA R 2 1 2 1 201000 r 74 goat snp56647-scaffold896-625680 19 38652042 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272381 Affx-1111834250 AX-519546110 19 38253276 TGAAGAGAACAAGACAACCCTTGTGGAGGAGACAG[A/G]TAAACCGATCACACGAATAAACGAGAGCCGGCAGC R 2 1 2 1 101000 f 74 goat GoatD01.027419 19 38253276 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38436846 Affx-122932212 AX-123307184 19 38266521 ACGATCTGGGGATTAGCATTCACTCCACTTACAGA[C/T]GAGGAAACTGGGTCATAGGTCAGCGAGCAGCCTGA Y 2 1 2 1 101000 f 74 goat snp56644-scaffold896-524352 19 38746963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse387 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38419126 Affx-122945761 AX-123289474 19 38305020 GGACATATAAAGCCCTTGGGGGCTGGTGTGAGCCC[A/G]CAGTAACACTAGCTCTTAGCCCATGTGCCAATCAA R 2 1 2 1 101000 r 74 goat snp56643-scaffold896-485853 19 38780731 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433078 Affx-122935736 AX-123303419 19 38348810 GTTTCTCTTCCATAAAATGGAGCAGTATCTACGTC[A/G]TAGAGTTAATATAAAGTGAAGGGACAAGAGACTGC R 2 1 2 1 201000 r 74 goat snp56642-scaffold896-442063 19 38824189 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417110 Affx-122947473 AX-123287458 19 38400042 TTCGATGTCTGATCGACACAGGAGCTGATCGGACC[A/G]TCCTCAGGGCAGAGGAGGTCCCACCTAGTTGGAAA R 2 1 2 1 102000 f 74 goat snp56641-scaffold896-390831 19 38875196 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401560 Affx-122958897 AX-123271913 19 38440131 CTCCATTATGGTTAAAATACAAAAATATGGAACAA[C/T]GTGGATCCTTGAAGGTGAGTCCTGAGCTCAGTGAG Y 2 1 2 1 101000 r 74 goat snp56640-scaffold896-350742 19 38916043 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397299 Affx-122962323 AX-123267654 19 38480579 GTAATCCCAGGGCTGAGCTGTCAAGCTCATTCTCC[A/G]TCTTCCAACATCTTCCAGAGCACCTACTATGTGCC R 2 1 2 1 101000 r 74 goat snp56639-scaffold896-310294 19 38955878 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389973 Affx-122968067 AX-123260330 19 38598753 TCCTCTCCCATGCAGTCAGCAGGTGGGGCTCAAAT[A/G]TCCAACCCTCTAGTCTCAAGGTCGTTTCCCCTGGC R 2 1 2 1 201000 r 74 goat snp56637-scaffold896-192120 19 39074299 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408584 Affx-122953659 AX-123278935 19 38649092 ATGAACGCTAACACACCCAGAACACGAAGCACTCC[A/G]TATACCAGCTACTAATACAGTTATTACCGCTACTG R 2 1 2 1 201000 r 74 goat snp56636-scaffold896-141781 19 39125152 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407329 Affx-122955300 AX-123277680 19 38733690 GATATGAAAAGTTCACTACATGATGATGAAAAATA[C/T]ACAAAAACTGGCAAACTGAAAGATGGGACTGAACA Y 2 1 2 1 201000 f 74 goat snp56635-scaffold896-57183 19 39210181 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404177 Affx-122957688 AX-123274529 19 38776255 CCCCCACCGTGCTGGGGCTTGACTTTCCACTCCTG[C/T]GATGTCCAGGGGGTAGAGGGTAATGCAGGACAGCT Y 2 1 2 1 201000 f 74 goat snp56634-scaffold896-14618 19 39252784 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431541 Affx-122936213 AX-123301882 19 38791334 ATGGAGGAAGCTGGACCAATGGATAAGTAGGATTG[C/T]GCCAAGCGGTAAAAGGACGAGGGCAGGGGGTGGCA Y 2 1 2 1 101000 f 74 goat snp4621-scaffold1149-362 19 39267714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449477 Affx-122922642 AX-123319812 19 38854372 CCAACAACCCTGCAACCTAGGTATTACCATCGCAC[A/G]TTGCCAATGACAAATCTGAAGCTCAGAGAAGTGGA R 2 1 2 1 201000 f 74 goat snp4622-scaffold1149-63400 19 39330266 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382432 Affx-122974239 AX-123252790 19 38973801 CCCAAGAGGAGAAAGTTCCAATCCTTTTATCATGG[C/T]TGGCTCCCCTAGCAACTGGCCTGCATCATTCGGTT Y 2 1 2 1 101000 f 74 goat snp4624-scaffold1149-182829 19 39448920 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391013 Affx-122966886 AX-123261370 19 39023820 ATCAGTTCATAAACTGGTACAGTCTCCTATTCTAC[A/G]TTAGAACCAGAAATACTGGTTTCCTGGACTATTCT R 2 1 2 1 101000 f 74 goat snp4625-scaffold1149-232848 19 39498954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402403 Affx-122959013 AX-123272756 19 39080051 AATGAGAAGATGTACAAGGGCTGTTGGAGTACACT[A/G]ACCTTCAATTTTTAGGGTGTTGCATTCACATTTCA R 2 1 2 1 101000 f 74 goat snp4626-scaffold1149-289079 19 39555291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382282 Affx-122973924 AX-123252640 19 39166224 TTGCCTTTTGTCCAGGACCCCACATAATGGGAGCC[A/G]GTGTCCCTGCCTGGGTCTCTGCAGTTCTATTCATG R 2 1 2 1 101000 f 74 goat snp4627-scaffold1149-375252 19 39638806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440198 Affx-122930702 AX-123310535 19 39199671 AAAGGAGGCGGATCCCAGAGGGCTCTCGTGGAGCT[A/C]TCAGAGCCTTTGTCTTCTTTCTGCTCTACATTGCT M 2 1 2 1 101000 r 74 goat snp4628-scaffold1149-408699 19 39670511 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420515 Affx-122944843 AX-123290862 19 39232992 TCTAGGAGTAATAACACCTGGAGGGAATATAACAT[A/G]TGGTGGTCTCTGTTCCCAGGCAAGATTGTGGGGGG R 2 1 2 1 101000 f 74 goat snp4629-scaffold1149-442020 19 39703472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423651 Affx-122942349 AX-123293997 19 39304193 TATGTGTAAACACGAAGAAGAATAGCTACTATCTA[C/T]TGAGTCCTACTATATACCCTAGGTACTTAGCCTAT Y 2 1 2 1 101000 f 74 goat snp4631-scaffold1149-513221 19 39774346 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447887 Affx-122923820 AX-123318223 19 39343181 ACTTTTGACAGTACAATATCTCAATGACATTTTCG[A/G]TCCAATAGGAAAGTCCCAATATCCTCTGTATTCAG R 2 1 2 1 201000 f 74 goat snp4632-scaffold1149-552209 19 39813390 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432068 Affx-122935885 AX-123302409 19 39381715 GCTTAAAGACCAGTGAGGGAATAAACACTTAAATC[A/G]GTGAATAATTTCAATATAATTGGGAGAAGTATGCA R 2 1 2 1 101000 f 74 goat snp4633-scaffold1149-590743 19 39851974 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415553 Affx-122948649 AX-123285902 19 39450109 CTTGGGAGCTCAAGGCCCCAGCAAACTAAGAGAAC[A/G]TGAGTCAGCTCCAATCCAGAATGGAAAACCAGTGA R 2 1 2 1 101000 r 74 goat snp4635-scaffold1149-659137 19 39920786 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441892 Affx-122928618 AX-123312229 19 39497215 GACCCGGTTTCCCAGGCAACCCTGTCCCTCATACC[C/T]AGCTCATTCACCGAGGCTCTGCAGGCCCTTTCCTG Y 2 1 2 1 201000 f 74 goat snp4636-scaffold1149-706243 19 39968127 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769795 Affx-122952489 AX-385256965 19 39533719 CCATATCACGTTATTTTCAATTCCTAAATATCATG[C/T]GATGTTTGTCTCCCAACCATTGCATATTCTTTTCT Y 2 1 2 1 101000 r 74 goat snp4637-scaffold1149-742747 19 40004704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse388 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468277379 Affx-1111835819 AX-519550883 19 39656875 CTTGAAGGACTCCTCTACCCCACCCTCTTTCAGCC[A/G]TCCTTAGCGGGATCTAGAACTCCTAAGATCTTTCC R 2 1 2 1 101000 r 74 goat Random2.2K-1803 19 39656875 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38385091 Affx-122971799 AX-123255449 19 39658677 AGGAGTTCCTTGGTTCTGTCCTAAGCCCTCTTCTC[A/G]TCCTTCTATCCATCTGGGCTTAGACTTCATCAGTC R 2 1 2 1 101000 r 74 goat snp4639-scaffold1149-867705 19 40129443 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387227 Affx-122970581 AX-123257585 19 39705880 TTGCTTTCCCTGTTGAATCTCAGTCCCCAGCTCCA[C/T]GTGGTCATGGTGGTTCTCTGGGCGCCACCCTAACT Y 2 1 2 1 201000 r 74 goat snp4640-scaffold1149-914908 19 40176621 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434415 Affx-122934675 AX-123304756 19 39765323 CTTGTAGGTGTACCCTTCTCCCCGTCTTATCTGGC[C/T]TTCTCGGGTAGGGGATGGCCAAAGGCTTGGGGACA Y 2 1 2 1 101000 f 74 goat snp4641-scaffold1149-974351 19 40235189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274218 Affx-1111834073 AX-519547818 19 39795556 CACTGGATGTTTCCTGCAGCCCTCCATCTCTTCTA[A/C]TCAAAGAGTAAAAGGTTATGAACCATGAACC M 2 1 2 1 202000 r 74 goat GoatD01.017147 19 39795556 T G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38423927 Affx-122942265 AX-123294273 19 39810131 CAAGATACTTAAAACACTGAAAATAAATCAGGCTC[A/G]TAAGGAAGGGAAGTTATGATGAGTTGATAAATTCC R 2 1 2 1 101000 r 74 goat snp4642-scaffold1149-1019159 19 40281315 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378261 Affx-122976887 AX-123248620 19 39897683 AGGATGCCTAGGGGCAGGAGACCCTTCCCACAGGC[C/T]CCTTCTGTGCTCTCTGAGCTGGGTCATACTGCGAC Y 2 1 2 1 101000 r 74 goat snp4643-scaffold1149-1106711 19 40368809 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433645 Affx-122934577 AX-123303986 19 39956920 ATCTGGTAGAAAGAACTTTGCAAGGGAGGAGGCCT[A/G]CAAACATACCCCAGCTTTGGAGGGAAAACCCACTT R 2 1 2 1 101000 r 74 goat snp4644-scaffold1149-1165948 19 40427407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420700 Affx-122944791 AX-123291047 19 40011488 GCACCCAAGTGAGCTGTAGGAAGGCATTTGTACAA[A/G]TAGATTCTGCAGCATCAAAGGAGAATTCTCTAAAA R 2 1 2 1 101000 r 74 goat snp4645-scaffold1149-1220516 19 40481910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse389 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38438635 Affx-122930911 AX-123308972 19 40068383 TGGCAGGCAGATTCTTTACTACTGAGCCACCTGGG[A/C]AACCCGTGCTATGATTGTGATAGAAATCGCAAGCA M 2 1 2 1 101000 r 74 goat snp4646-scaffold1149-1277411 19 40538932 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448390 Affx-122923689 AX-123318726 19 40106340 ACCCTTTTCCATTTCACTGACGCCCCCTGTCACTT[A/C]GCTACTTCTCCCAACAGTATTGTTATTTTCTAGTT M 2 1 2 1 201000 r 74 goat snp4647-scaffold1149-1315368 19 40577007 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802237 Affx-122940565 AX-385289141 19 40145352 GTTGTCAGTGTAATAGTTGATAAGTCTTGAGTTTC[A/G]TGGATAAGAGGTATTATGAGACTGCAAAGTGTTAT R 2 1 2 1 101000 f 74 goat snp30073-scaffold33-27577 19 40617505 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381543 Affx-122974836 AX-123251901 19 40189470 GTGACAAACCATGCTGTTTTTCCCTGAATGACACA[C/T]GCTCTCATTTTTAACTTCATTCTTTTCTTTATCTC Y 2 1 2 1 101000 f 74 goat snp30074-scaffold33-71695 19 40661499 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797346 Affx-122972893 AX-385284285 19 40224821 TTGGCACTTCATGAGTCAATAGCAAATGTCAGATA[C/T]GGTAATCCACAGCCCTGGGTTTAAGCAACTTATAA Y 2 1 2 1 101000 r 74 goat snp30075-scaffold33-107046 19 40696836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426888 Affx-122940466 AX-123297233 19 40271920 CTGGAATTGTGAACTTTTAATCTTTTTATTCATCA[C/T]GTCATTTAATCCATATTTTAAAAGAAAGAAGCCAC Y 2 1 2 1 101000 f 74 goat snp30076-scaffold33-154145 19 40744072 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433114 Affx-122935704 AX-123303455 19 40311841 CCTTTTGAATTCCCTTTGGCATGACACCAGGCCTG[C/T]TGGGTGATTTTGTGCGTTTAAGGCCACAGAAGAAA Y 2 1 2 1 101000 r 74 goat snp30077-scaffold33-194066 19 40784437 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441629 Affx-122928638 AX-123311966 19 40399603 TCTGGCTGTTCGTAGCCTTCACTATGATTTTGTAA[C/T]AAGTAGCAACTCTGCCACCTCAAAGGAAGGACTAG Y 2 1 2 1 201000 f 74 goat snp30079-scaffold33-281828 19 40881224 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430807 Affx-122937459 AX-123301148 19 40460468 AGTGGTCTGTGATGGTCCTGTTCCTGAAAGCACTA[C/T]GTCTATCAGGGACTAGTGGGGGTTACCATGAACTG Y 2 1 2 1 101000 f 74 goat snp30080-scaffold33-342693 19 40955737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380974 Affx-122974687 AX-123251332 19 40516323 TCTCTTTTTATACTCTGCTTTTAGCTGGTCTTACC[A/G]TGAGCAATGCTTTTTCCTTGTTATTTTTCCTACTA R 2 1 2 1 101000 f 74 goat snp30081-scaffold33-398548 19 41012528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392054 Affx-122966393 AX-123262411 19 40546370 GGATGGCTTATCTTATTTTGAAAAATACATAAAGT[A/C]TTTTCTATAACACAAGCATTATGCAATATTTGAAA M 2 1 2 1 201000 r 74 goat snp30082-scaffold33-428595 19 41043352 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449366 Affx-122922727 AX-123319701 19 40589413 GCCATGCTAAAACCAGTATGAACTGATATCTCATT[A/G]TGGTTTTGACTTGCATTCCTGTTGATTAGTGATAT R 2 1 2 1 103000 f 74 goat snp30083-scaffold33-471638 19 41097647 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785249 Affx-122965691 AX-385272294 19 40618892 CTGGGAATATGCGTGCTTTGGATTGCCTGTGTACC[A/G]TTGAATATAAGCCTTTCCCTATGCAGATAAATTTC R 2 1 2 1 101000 f 74 goat snp30084-scaffold33-501117 19 41131314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788075 Affx-122945868 AX-385275095 19 40669219 CCTTGGAAGTTAGGCATGACTAAAGGACTTGCTTT[A/G]TGTAACGTAAATGTGTTTATGACGCAGTATGCAAT R 2 1 2 1 101000 f 74 goat snp30085-scaffold33-551444 19 41182609 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272961 Affx-1111833141 AX-519546647 19 40704510 TGACCTACCATATTATTCCCATTTTACACATAAGG[A/G]CAAATGAGAATTATATATGAAGACACAAAAAAGTA R 2 1 2 1 201000 r 74 goat 19_40704510_AF-PAKI 19 40704510 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396801 Affx-122962747 AX-123267156 19 40709927 CTTACTATAACCATAAGAGAAAAAAATTAGTCATG[C/T]AGTTTCTAGTGCTTGGTTGGCATTTAATAAATGTT Y 2 1 2 1 101000 r 74 goat snp30086-scaffold33-592152 19 41222668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422461 Affx-122943337 AX-123292807 19 40750999 GAATACTGATCCTGTCGACCTCGTGGTAACTCTAG[C/T]GGCAGATGAGGTAACATGTGGAAATGCACCCTCTG Y 2 1 2 1 101000 f 74 goat snp30087-scaffold33-633224 19 41263739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409925 Affx-122952877 AX-123280276 19 40809012 GCCTCTTGGAGTCGTCTCTCCAGCTCCACATTCTC[A/G]CGCTCCAGCTGCCTCACCCTCTCCAGGTAGGCAGC R 2 1 2 1 101000 f 74 goat snp30088-scaffold33-691237 19 41321580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450457 Affx-122922952 AX-123320791 19 40838453 CCCTGTGACTTGTCACCATGACTGGCTGGTCTCAG[A/G]AACAGGCATATCCAGCTTCCCCTGGAAAATCGTGA R 2 1 2 1 201000 f 74 goat snp30089-scaffold33-720678 19 41349172 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449525 Affx-122922605 AX-123319860 19 40859322 CTACTAGCCCAACTGTATCATTTACAGAAGGCACA[C/T]AGGACCAGAGAGGTGACATGACCTGCCCAAGATAA Y 2 1 2 1 101000 f 74 goat snp38526-scaffold488-10203 19 41369930 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415035 Affx-122949499 AX-123285384 19 40899186 GGGGGCACAGTGCTCGTGGAAATTTGCTAACTGCA[C/T]GGGCGTCCTGGGGAGGGGATTGAGGGCCCAGTGCG Y 2 1 2 1 101000 f 74 goat snp38527-scaffold488-50067 19 41409045 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435900 Affx-122932773 AX-123306239 19 40950400 AGCAGGCAGGGAGGAGGCGTTTGCTCCAGGTCAGC[A/G]TTAGAAGTCAGTACACAGTGCCTGCCCCAGCCTTG R 2 1 2 1 101000 r 74 goat snp38528-scaffold488-101281 19 41459486 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433473 Affx-122935047 AX-123303814 19 40989605 TTCCAGCAGCCACACCAAACTCGTTCCCACTTCTG[C/T]GCCTTTGTCCACACTGATCTCTATACCTGGAACAT Y 2 1 2 1 101000 r 74 goat snp38529-scaffold488-140486 19 41496242 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416487 Affx-122947797 AX-123286835 19 41042405 GCCAAGGAACCCTCTCTTCAGTCTGGAATCACCTA[A/G]AGCAGTACTTTCCAGGAGCTATATAATGCAAGCCA R 2 1 2 1 101000 r 74 goat snp38530-scaffold488-193286 19 41543058 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401794 Affx-122959474 AX-123272147 19 41099457 CGTTTCCTCTCTGAGTCTCAGGGGCTGCAGCTTGT[A/C]TGATTTACCTTCATTTTTATACACCTCGCAGGGCT M 2 1 2 1 101000 r 74 goat snp38531-scaffold488-250338 19 41600612 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394293 Affx-122964702 AX-123264648 19 41167364 TCTAGGTTTTCGGGCAGGTGGGCTCTCCTTCAAGG[A/C]GAAACAGGCTTGCCCTCAAGTCCTTGGCTATTTCT M 2 1 2 1 201000 r 74 goat snp38532-scaffold488-318245 19 41668626 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391071 Affx-122966842 AX-123261428 19 41225024 GCAGAAGCCCTGCACCCCAGGGCGTCAAACACTTC[A/G]TCATGCCAACCGTTTGGAGAAGGGGCAGATGACTG R 2 1 2 1 101000 r 74 goat snp38533-scaffold488-375905 19 41724507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382641 Affx-122973683 AX-123252999 19 41257616 CCGATAGGAGTCTGTTCTCACACCAGTCCCAGAGG[C/T]GCTGTACTTGACCCAGGACGTGTGGTGCTGAGAGC Y 2 1 2 1 101000 f 74 goat snp38534-scaffold488-408497 19 41756571 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779264 Affx-122959211 AX-385266368 19 41290459 AGGTCACCAAAGCCAGTAAGTGATAAGAATAGAAT[C/T]TGATCTCAGACATGAAGACCCAGAGCCTATAACCC Y 2 1 2 1 101000 r 74 goat snp38535-scaffold488-441340 19 41789369 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378220 Affx-122976920 AX-123248579 19 41336254 TCTGCACTTGGTTCCTGAAAGGCCAAAATCACGTT[G/T]ATTCATATATTATTTCTATACCTCTAGGTTCTTGT K 2 1 2 1 101000 f 74 goat snp38536-scaffold488-487135 19 41835052 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432761 Affx-122935439 AX-123303102 19 41390226 CCGACTGGAAAGGAGGTGGGGACAGCCAGGGGATC[C/T]GAGTCAGGTAGGAGGAAAGGCGACCGGCAGAGGAA Y 2 1 2 1 101000 r 74 goat snp38537-scaffold488-541107 19 41889214 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436830 Affx-122932225 AX-123307168 19 41440542 CCTCAGTGTCCCCATCTGTAAAAAGCAGGGTTACA[C/T]TAGACCTTGGATGTTAGCAGTGACCTCTTGGGGGC Y 2 1 2 1 101000 r 74 goat snp38538-scaffold488-591423 19 41928950 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse390 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38418565 Affx-122946386 AX-123288913 19 41471456 GTGTGTGTGTCTGGGAGTGAGCGAGGGGCCGAGGC[A/G]GTCGAGACTTGCCGTCGCCTCTCCTTGTGGTTTGC R 2 1 2 1 303000 f 74 goat snp38539-scaffold488-622337 19 41959767 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418749 Affx-122946210 AX-123289097 19 41500635 CAGTAAACAAATACATACCAAATATTTGCTAAATA[C/T]GTCACAGGTTCTGCTGCCTGAGCATAATTCCAGGA Y 2 1 2 1 101000 r 74 goat snp38540-scaffold488-651516 19 41989550 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394610 Affx-122964417 AX-123264965 19 41539214 GTCCATGCAGACCTTGCCACCTGGAGATTCTTACA[C/T]GCTCCCTGTCTTGCTCCTGTTTGCCTCACCTGTCT Y 2 1 2 1 101000 f 74 goat snp38541-scaffold488-690095 19 42028026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385686 Affx-122971131 AX-123256044 19 41568293 TTTGCTAATATCAAGGTTAAAACCAGATACTCACA[C/T]GACCTAAGAGCCACGGATTTTACGATTTCTGCTCC Y 2 1 2 1 101000 f 74 goat snp38542-scaffold488-719174 19 42057636 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384783 Affx-122972009 AX-123255141 19 41602291 GAGGAAGCGCCTGCTACTGCTGAAGCATTGTGACC[A/G]TGCTGAATTTTACTCTCAATAGGAAATCAAAGGCC R 2 1 2 1 101000 r 74 goat snp38543-scaffold488-753172 19 42091591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406759 Affx-122955728 AX-123277110 19 41642613 TGAAATACTTGAAATTGCGTGCCTTTACCTTTTTC[A/G]CCTCATCTACTTCGAATGAAAGTTTTACTGCATTA R 2 1 2 1 201000 r 74 goat snp38544-scaffold488-793494 19 42132423 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383177 Affx-122973220 AX-123253535 19 41675040 GTTTTTCTCCCTAGACTCATAGGCACAATTCTTGA[C/T]CCTCTGACGTATATGAAAAGTGCCTGTAATATTTA Y 2 1 2 1 101000 f 74 goat snp38545-scaffold488-825921 19 42164865 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770628 Affx-122943243 AX-385257792 19 41705765 TTGAATGCCAGGCACTAAGTTAAGCAATGGCCATA[C/T]AACAGTTTAGGGTGAATCTATCCCTTGACCATTAA Y 2 1 2 1 101000 f 74 goat snp38546-scaffold488-856646 19 42196339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401643 Affx-122959587 AX-123271996 19 41763468 TTTAACACTCCCCACTCTTAGATTAGCAGCGAGGC[A/G]TCCAAGGAGGTGGTGTTTTTGTCCTCCACTCACTC R 2 1 2 1 101000 r 74 goat snp38547-scaffold488-914349 19 42254093 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402201 Affx-122959166 AX-123272554 19 41872236 GGCTGATTAATTTGATGGCTCAGCAGCAGCATCAG[A/G]GACCCAGGTGCCTTCCATTTTTCTGCTCTACCATC R 2 1 2 1 600000 f 74 goat snp38549-scaffold488-1023117 19 41872236 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402202 Affx-122959166 AX-123272555 19 41872236 GGCTGATTAATTTGATGGCTCAGCAGCAGCATCAG[A/G]GACCCAGGTGCCTTCCATTTTTCTGCTCTACCATC R 2 1 2 1 101000 r 74 goat snp38549-scaffold488-1023117 19 42361789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273665 Affx-1111833759 AX-519547278 19 41925072 CAGCTTCCTGGCTAGGCATGGGCCCTGCAGACAGA[A/G]TGGGGAGAAGGGATTTGGGTTAATGCAGGGAGCTT R 2 1 2 1 303000 f 74 goat GoatD01.003741 19 41925072 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38418948 Affx-122946494 AX-123289296 19 41926009 AGCCTCAGTGGGGGCGGGCAGGCAAGGGTAAGAAG[A/C]GAGAGAAAAGCACTCTTGAGTCTCTGTCCCACCCT M 2 1 2 1 101000 r 74 goat snp38550-scaffold488-1076890 19 42408435 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443295 Affx-122927467 AX-123313632 19 41955680 CTCTGATCTCCAAAACCCAGCTTTCCGCCTCAGGT[A/G]CTTAGCCTCTGACCCCTAGTTGCTTCGGAATCATA R 2 1 2 1 101000 r 74 goat snp38551-scaffold488-1106561 19 42438103 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447183 Affx-122925004 AX-123317519 19 41986625 ACTCAGGTTTTGGCTTTAGAAAGTTCTGGGTGCAA[A/G]TCCTGTAATCTTGGGAAAACTGAACTGCACCTCGT R 2 1 2 1 101000 f 74 goat snp38552-scaffold488-1137506 19 42468977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse391 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38445874 Affx-122925987 AX-123316211 19 42140022 AGGTCTCGTCCCCTTGAGTCAATTCAGAGCTCCTA[C/T]GGGGTTAGCTGAGACTGAATGGCAATTAGACTTCT Y 2 1 2 1 101000 f 74 goat snp30168-scaffold3312-295719 19 42626562 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774688 Affx-122922076 AX-385261822 19 42262928 TATATCCAGGGACTGCTAATTAATTAAGAATTTTA[C/T]AGCAATTCTAGGAAGCATGTACTATAATTATGCCT Y 2 1 2 1 201000 r 74 goat snp30165-scaffold3312-172813 19 42749643 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401167 Affx-122959360 AX-123271520 19 42301698 AGATGCATGACAAACCTGAGGTGGTTCCTACTATT[A/G]CACTATTTTATAGATGAGGGAATTTAAGGCACAGA R 2 1 2 1 101000 f 74 goat snp30164-scaffold3312-134043 19 42788805 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443121 Affx-122928088 AX-123313458 19 42351352 CCTTCCGGCTGGGGGGGGGGTCAGATTTCTTTTTC[G/T]GCAAGCAATTTTTATGACTAAAATCTTTAGTGATT K 2 1 2 1 201000 r 74 goat snp30163-scaffold3312-84389 19 42838363 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397708 Affx-122962562 AX-123268063 19 42383924 TACTTAAAGTAAGAATGTTCAAATATTCTCTGTAA[C/T]GTATCCTCCAATGCACTCTGTCCTGGGCTGTAATC Y 2 1 2 1 201000 f 74 goat snp30162-scaffold3312-51817 19 42871566 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434427 Affx-122934667 AX-123304768 19 42424756 AATCTTCCTCTAGGTCTTCTTCTTCTTCTCCCTCA[A/G]CATCTACGTCGTCCAGCCGGGGGATACTTTCCCGG R 2 1 2 1 201000 r 74 goat snp30161-scaffold3312-10985 19 42889756 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436403 Affx-122933027 AX-123306742 19 42443837 CCTAGTGCATTGGAGGATTTCCTAGAGAGAACATT[C/T]AAATGTTCTTTGAGCATTCATGGGTGGAGTGCCTG Y 2 1 2 1 101000 f 74 goat snp14765-scaffold1594-1737688 19 42952101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387639 Affx-122969854 AX-123257997 19 42525047 GAATGAGTACGGTGTTTAGCACAGAACCTGGCATA[A/G]GGCACTCAACCAATATTAGAGAAACACCACCTTCA R 2 1 2 1 201000 r 74 goat snp14763-scaffold1594-1656478 19 43033884 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453618 Affx-122919754 AX-123323951 19 42558208 GCATCCCCATTTTTCTTACTCAACACAATACTCTG[C/T]CCACTTGTAATTGCTCCAGGGATCCCCAGTTCAAA Y 2 1 2 1 101000 f 74 goat snp14762-scaffold1594-1623317 19 43067083 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766619 Affx-986698081 AX-385253970 19 42571036 TATTCATTTATTATTATTCAAAAAATAAATGGGGC[C/T]AAGTAGTTTCTGACTTCATTCTTTAAAATAACTTT Y 2 1 2 1 600010 r 74 goat 19_42571036 19 42571036 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 320763554 Affx-986698083 AX-385251411 19 42575103 TTCCTTCACCAGCCTCTTTATCAATTCAATTGATG[C/T]AAGAGTCCGAGGATCCAGGTTGGTCACAAAATGAA Y 2 1 2 1 600010 f 74 goat 19_42575103 19 42575103 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38429535 Affx-122937835 AX-123299877 19 42589549 GTGTGTGTTAGGGTTTTGGGGCGGGGGAATGAGTG[G/T]AAGAAACAGGAGAAAGAGAAGGAGCAATTCGTTTG K 2 1 2 1 303000 f 74 goat snp14761-scaffold1594-1591976 19 43098427 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427380 Affx-122940088 AX-123297723 19 42636205 TTTGATCTGTTTTTAGAAAGAGAATGCTGGCACCC[A/G]TGGAGAGGGGGGACTGAAGCTGGAAGTATGTGGAG R 2 1 2 1 103000 f 74 goat snp14760-scaffold1594-1545320 19 43145425 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422717 Affx-122943639 AX-123293063 19 42670325 GAGTTTCTTTTGAGGGAATTAGAAAATGGATGTCC[C/T]GTGCCCTGCTGGACAGCATTCTCCTGGGAAACCTC Y 2 1 2 1 101000 f 74 goat snp14759-scaffold1594-1511200 19 43179948 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421990 Affx-122943789 AX-123292337 19 42700031 CAAAAACCTCAGGTGTTTCCATCGTCGTCATCCAG[A/G]CTTTACCACTAAACACGGTACACTAAGCTATGGCA R 2 1 2 1 101000 r 74 goat snp14758-scaffold1594-1481494 19 43209731 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400137 Affx-122960707 AX-123270492 19 42730678 GCACGTGGGACTCCACAGTAATTTGGGCATGAGCT[A/G]TGGTGCAAACAACCAAACCAAATCCTTTTCTGGGA R 2 1 2 1 101000 r 74 goat snp14757-scaffold1594-1450847 19 43240283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386887 Affx-122970048 AX-123257245 19 42762578 TAGGGAACATGGAGTCTTAGCCACTGGACCACCAG[C/T]AAAGTCCCAATGCATAGTCTTCATAACCATTACTC Y 2 1 2 1 101000 r 74 goat snp14756-scaffold1594-1418947 19 43271950 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380366 Affx-122975347 AX-123250724 19 42792325 GCTCTGCCCCCTGGCCCTTAGCACATAGATGTTTG[A/C]TAAAAGTTTGTGGAATTAAACTTTTTTTTTCTTTT M 2 1 2 1 103000 f 74 goat snp14755-scaffold1594-1389200 19 43301461 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448875 Affx-122923269 AX-123319210 19 42885923 CAGGGGAGCCTTATGCTTTTAAACAATGAGATCCA[A/G]TATGAAACAATTTTCATTGCATTGCTGGGACTTGT R 2 1 2 1 101000 r 74 goat snp14753-scaffold1594-1295602 19 43396199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766626 Affx-986698085 AX-385253977 19 42923379 AAACAAAACAAAAACCCGTTGTGTGTGTTTCTCAC[A/C]TATTTCTTGAAAGCACTGTTACAGATGGAAGTGCT M 2 1 2 1 600010 r 74 goat 19_42923379 19 42923379 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 38444210 Affx-122927250 AX-123314547 19 42937174 ATGTAGTCACCCCCACATAGATTCAGAACATTTCC[G/T]CCACCCCAGCAAGTTCCCTCTTGCTCCTTTTCAGT K 2 1 2 1 303000 r 74 goat snp14752-scaffold1594-1244351 19 43447204 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763560 Affx-986698089 AX-385251417 19 42958566 TGTCAGGACAGGACTCATGATGACTCTCAGCCCAG[A/G]GTTCAGCCCACCAGGCCTTAAGGGAGGGCTTCTCT R 2 1 2 1 600010 f 74 goat 19_42958566 19 42958566 Ancestral_priority_1043 ancestry 0.484 neutral IMAGE 10K 10K ancestral 320766636 Affx-986698091 AX-385253987 19 42967396 GCTGTACTTTCACCTTGATGGTAAACCTTTTGTTT[C/G]CTGGTCTATTCTGAGCACCTAGTGCTCTGAATGTA S 4 1 2 1 600010 r 74 goat 19_42967396 19 42967396 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 320766640 Affx-986698093 AX-385253991 19 42967429 TTCCTGGTCTATTCTGAGCACCTAGTGCTCTGAAT[A/G]TACTTGATTTTTGATGAATATGTGTTGAATGTGAT R 2 1 2 1 600010 r 74 goat 19_42967429 19 42967429 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320777082 Affx-122955473 AX-385264205 19 43000740 ATCTCTGGGGTATGCTTGTATGTGCTGAACACTCT[A/G]CTAGAACCTGAGGTTTGTAATCTGATTTTATTCTC R 2 1 2 1 101000 f 74 goat snp14751-scaffold1594-1180785 19 43507424 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439987 Affx-122929800 AX-123310324 19 43056938 CACAGCTCCCCTCAATGGCATCATGGATTTTTTCC[A/G]CATTCTACAGATGCCAGCCAGGCACTGTACCTCTA R 2 1 2 1 201000 r 74 goat snp14750-scaffold1594-1124587 19 43563475 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391777 Affx-122967459 AX-123262134 19 43100785 GAGCAACCGACTATGACTTTTCACTTTTGTGAGCC[A/G]GCACTTGGCACAGGACCTAGCACACAGAAGACTAG R 2 1 2 1 201000 r 74 goat snp14749-scaffold1594-1080740 19 43604975 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405946 Affx-122955555 AX-123276298 19 43156178 ATATCTTCCGCTTTGCCTGATCTCTGATTCAGTTC[A/G]GGTGTACTGAAGCCACTCTGGTGCTTCCTCTGCTG R 2 1 2 1 101000 f 74 goat snp14748-scaffold1594-1025347 19 43660238 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428624 Affx-122938680 AX-123298966 19 43202057 CTCGCTGTATCTAACCCCACAGAGCGAGACTGGCT[C/T]ATCCACCCACTAGGCATACATGTCGAATTTCCCAT Y 2 1 2 1 201000 r 74 goat snp14747-scaffold1594-979468 19 43706075 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385821 Affx-122971022 AX-123256179 19 43237761 GTGTCCAGGTCTTTCATTAACATTTTAATTGACCT[A/C]TTTGCCTCTTTTTATAATTGAATTGCGGGGGTTCT M 2 1 2 1 202000 f 74 goat snp14746-scaffold1594-943764 19 43742276 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429043 Affx-122938309 AX-123299385 19 43272384 AAACCTTTTAAAACTTCAGAAAAACTTTGAGAACT[A/G]TACAGTGAGCAGCACATACCCTTCCCTTTGAGCCA R 2 1 2 1 101000 r 74 goat snp14745-scaffold1594-909141 19 43772357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463595066 Affx-1110064000 AX-515076661 19 43283469 CGACTATGCAACCATGATGCATATGAGGCACCTAC[C/T]GCATGCTGGGTACTGGGGGTGCCCTGGGGAGCAGC Y 2 1 2 1 101000 f 74 goat 19_43283469_AF-PAKI 19 43283469 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38393585 Affx-122965384 AX-123263941 19 43350043 AACATTTTTTATCCCTTCTGCCAAGACCCAGAGAT[A/G]CTGAAATTTCCAGCCCACTTCCAGGTTCTTTTCCT R 2 1 2 1 201000 r 74 goat snp14743-scaffold1594-831482 19 43849890 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412461 Affx-122951400 AX-123282810 19 43385721 GGAAATAGTCTACCATATTTCCTTGATCCTAAGAC[A/G]TTTTTTCATATTTTAATAAAGGTAAAATTCGATGT R 2 1 2 1 103000 f 74 goat snp14742-scaffold1594-795804 19 43885484 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773170 Affx-122950148 AX-385260313 19 43418810 TTGGTAACTAAACAGGTAAAGCAGTGAAGGCAACA[A/G]TGTAACAATCTAGTACCTAGACCTCTGAAGAGAAG R 2 1 2 1 101000 f 74 goat snp14741-scaffold1594-762715 19 43918504 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440426 Affx-122929420 AX-123310763 19 43451127 AAAGTTTCCTCTCAGAGGCTCCCAGGGTGGAGGGG[G/T]AACGAACAACCCTTCCTACCCATAGATGGCCCCCT K 2 1 2 1 101000 r 74 goat snp14740-scaffold1594-730398 19 43951108 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391060 Affx-122966850 AX-123261417 19 43483223 TTAAAACAAAATAAACAACAAGCGTGTATTCTCTT[A/G]CAGTTTCTGTGGGTCACAAAGTTGGGCACAGCTTA R 2 1 2 1 201000 f 74 goat snp14739-scaffold1594-698302 19 43983274 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391648 Affx-122966564 AX-123262005 19 43528615 TCTCCTCCTCCTTCAGTCTTCTTCCATCTCAGAAA[C/T]GACATTTCCTGTCAACCTTGATGACATGTTCTCCT Y 2 1 2 1 101000 r 74 goat snp14738-scaffold1594-652910 19 44028391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801452 Affx-122963503 AX-385288361 19 43582478 ATAACAATCCTCTGAGGTAGGTAGTAACTAAACCC[A/G]TTTCATATTGAGGTTAAAAATTGGCTTGAGGTCTC R 2 1 2 1 101000 f 74 goat snp14737-scaffold1594-599047 19 44082208 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435826 Affx-122932829 AX-123306165 19 43624725 TCTGTCTTCAGGGAGCACTAAGCTGAAGGAGTACC[C/T]GCTTTTCATTCCTCCCTGGCCCCCCAGCTTTCCCT Y 2 1 2 1 101000 f 74 goat snp14736-scaffold1594-556800 19 44124945 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771367 Affx-122952405 AX-385258525 19 43659280 AGTCTTACCACCTAAAAATAATAAAGCCCCTGCAC[C/T]TATACAGTGCCGAGTTTGGAAATAAAATTTCAACT Y 2 1 2 1 102000 f 74 goat snp14735-scaffold1594-522245 19 44159767 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375652 Affx-122978686 AX-123246011 19 43788773 GAGCAACTGAACTGAACTGAACTGAACCATCTTCA[C/T]AGTAGACCTGCTAGCGAACTATGACTGTTGCTTTC Y 2 1 2 1 101000 r 74 goat snp14733-scaffold1594-392752 19 44289058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800567 Affx-122970368 AX-385287486 19 43883101 GAAACGTTTTATTATATTATTCGTTTACTGCTAAT[C/T]TCGTTGTTCACACACCACGACTGTAAGTAACATTC Y 2 1 2 1 101000 r 74 goat snp14731-scaffold1594-298424 19 44382090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414332 Affx-122950035 AX-123284681 19 43945012 CTCTCCCTTCCAGGTTGGAAGCACTGTAGACCCCC[A/C]GACTTCCTGGCCTGACCCATAAGCCACACCATTCT M 2 1 2 1 101000 r 74 goat snp14730-scaffold1594-236513 19 44443902 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453625 Affx-122919750 AX-123323958 19 43981525 CTCACCTGACTGCAAACCTCCAATCCCCCTGCAAG[A/C]TTCAGCTCCAGATGATAAGCCCTAAAAGCAGGTGG M 2 1 2 1 101000 r 74 goat snp14729-scaffold1594-200000 19 44479946 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436241 Affx-122932561 AX-123306580 19 44023061 GGAGCACAGTTTCCTCCTCTACCCTCTGACCAGCA[C/T]TGGTATGAAACTTGATGGATTATGTCCCATAGCTG Y 2 1 2 1 101000 r 74 goat snp14728-scaffold1594-158464 19 44521437 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402946 Affx-122958174 AX-123273299 19 44066213 GCCAGGAATCAGTGTGACATGGGAGCTAGGACAGT[A/G]CCAGGGAGGGACACGCAGGGAGGGAGGCGTTGCCC R 2 1 2 1 101000 f 74 goat snp14727-scaffold1594-115312 19 44564695 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432054 Affx-122935895 AX-123302395 19 44101735 CTTTAAGAGCATTATTGAGCAAGTCTCAACCAGAT[G/T]AAGAAAATCTGACTAAGGGTGCTGCCTGAATGCCC K 2 1 2 1 101000 r 74 goat snp14726-scaffold1594-79790 19 44600222 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376406 Affx-122978089 AX-123246765 19 44138735 TCCTCCAGCTTCAGTTCCTGCTCCTCTCTGTGCTT[A/G]CCTCCAGGTTTCTGCTCACATTGTTCCCTGTATTC R 2 1 2 1 101000 r 74 goat snp14725-scaffold1594-42790 19 44637107 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402902 Affx-122958207 AX-123273255 19 44170711 ACCCTTCCTCAGGCAGCTCCTCTGAATGCCCAGCT[C/T]AGTCAGTTTTCTTGGTTATATACCATTGGAGACCC Y 2 1 2 1 101000 r 74 goat snp14724-scaffold1594-10814 19 44669300 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439478 Affx-122930162 AX-123309815 19 44201336 GATAGTATGCAGGATATCTTGTTTTTTATTTTTTC[A/G]CCTTTTTGATTTAACCATGTGCCTTGGAGCTTGTA R 2 1 2 1 101000 r 74 goat snp9210-scaffold1335-824136 19 44699817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415547 Affx-122948654 AX-123285896 19 44254274 TTAATGTGGGTCCTAGAGCATCTAAGATGACCTAT[A/G]TGGCTTGCATTGTGTTTCTTTGGGACGACACTGTT R 2 1 2 1 201000 f 74 goat snp9209-scaffold1335-771198 19 44750153 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450758 Affx-122921847 AX-123321092 19 44293362 AGGGAAGGGCATTCTCGATGGAGGACAGTACAGAG[A/G]TCAGAAGCATGAGATCTAGGGTGGGCCTGAAGCAT R 2 1 2 1 201000 f 74 goat snp9208-scaffold1335-732110 19 44789867 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395530 Affx-122963864 AX-123265885 19 44338514 GGCAGCCCCTCTTCCAGGTTTTCCTGGGTCTTTCT[C/T]ATCTCCCCAACCCATATTGACTGACTTGCCATTTT Y 2 1 2 1 101000 r 74 goat snp9207-scaffold1335-686958 19 44835332 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277380 Affx-1111835820 AX-519550884 19 44361553 CTTAGGGACTAAGATCCACACCGTGACTGTGGGTC[A/G]CCAAGCAGATGTAAACCATGGTCAGAGTTGGTGCT R 2 1 2 1 202000 r 74 goat Random2.2K-1805 19 44361553 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795172 Affx-122951854 AX-385282130 19 44367390 GAGCCACTAGGGAATCCCTCAATTAAATATATTAT[A/G]CTTTTATTCTTATGCTTTGCTTCCTTCTGTTTTCC R 2 1 2 1 101000 r 74 goat snp9206-scaffold1335-658082 19 44864098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439788 Affx-122930502 AX-123310125 19 44445600 CCGCTGAACGGATCACACGGAACACATGAGGTTAG[A/G]TGTCATTTTTCCTTTGCTTTAGATCAAGCCCAGTC R 2 1 2 1 103000 r 74 goat snp9204-scaffold1335-579872 19 44942157 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406227 Affx-122956118 AX-123276579 19 44488149 CGCGCTGATCCAAAAGGGATGGAGGAACCTTCAGA[C/T]CGTGCGGAGAGTAGGAGGGAACCGTCTATGGGGGA Y 2 1 2 1 201000 f 74 goat snp9203-scaffold1335-537323 19 44984724 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388232 Affx-122969397 AX-123258590 19 44542028 TACAAAAGTGTTTCTTCCAGGGGAAAAACACTTTA[C/T]AGACAGAAAAGATAAAATCAACACTGCTCTTTCTC Y 2 1 2 1 102000 r 74 goat snp9202-scaffold1335-483444 19 45038229 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425885 Affx-122941635 AX-123296231 19 44587826 ATGAATCAAGCATGGCCCTGCCCCCAGGGAGTCAA[C/T]AGGCTAGAAACAAGATTCAGGCTTGCAGATAAATG Y 2 1 2 1 101000 r 74 goat snp9201-scaffold1335-437646 19 45085087 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413232 Affx-122950245 AX-123283581 19 44627187 CTAGGCTTAGAATTCCAAGATTATCTTTGATTTCT[A/G]CCACTCTGCTGTGCCCTACCTCAAGTTATTTGCCA R 2 1 2 1 101000 r 74 goat snp9200-scaffold1335-398285 19 45124745 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442624 Affx-122928466 AX-123312961 19 44656775 TGTAGAGATTTTTCACATGATTTATTTCCTAATGC[A/G]CTTAAACCAGTCATTCTTCACCTATCTGGTGCCTG R 2 1 2 1 101000 r 74 goat snp9199-scaffold1335-368697 19 45154311 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788899 Affx-122942399 AX-385275914 19 44705537 AATCTAATTTTTAAAGCTAATCTTTGGACAAAAGT[A/G]TGTCATTTAAATTTGAAAAACTGCAGTGTTGTCTG R 2 1 2 1 101000 r 74 goat snp9198-scaffold1335-319935 19 45203119 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777706 Affx-122933937 AX-385264825 19 44744814 CGGCTTAAAGGAGTTTACAGAATTCAAATTCTTTA[A/G]AAATTGGTACTTCATCTAAGGCACTTTCAATTAAC R 2 1 2 1 202000 f 74 goat snp9197-scaffold1335-280658 19 45241842 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407384 Affx-122955260 AX-123277735 19 44795597 CCTTATGGTTGCAGGATGTCTGCCACAGCTCCAAG[C/T]ATCATGTCAGCACTCAACCTCATTCATGGCAGGAA Y 2 1 2 1 201000 r 74 goat snp9196-scaffold1335-229875 19 45293235 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433253 Affx-122935237 AX-123303594 19 44828234 AGACCATTTAGTCGCATTGAGAGGTGAGACCCCCT[A/G]TGTCTGCAGCTGTGGCATCATCTTAGGTGGAAGAC R 2 1 2 1 102000 r 74 goat snp9195-scaffold1335-197238 19 45325107 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451859 Affx-122921070 AX-123322192 19 44901836 ACACATGGCAAGGGCTCCCCAAGTGTTAGCTGGCT[A/G]CAGTGGCCCTGGCTATAGAAAACGTGTACCTGTCC R 2 1 2 1 101000 r 74 goat snp9193-scaffold1335-123636 19 45398360 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792986 Affx-122959934 AX-385279964 19 44934946 TTCCTCTATTCCTCTCAGACCTTCCAGTTTCTTAA[C/T]GTTGTGGAAGCCAACACCAATTACTTTCAAAAGAA Y 2 1 2 1 101000 f 74 goat snp9192-scaffold1335-90526 19 45431717 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396412 Affx-122963006 AX-123266767 19 44986612 CTGCCTTCTGTTTGGGGACTTAGGTGGTGCCTGGA[A/G]TTATTTTGAAATGATCATTGGTGTTTCTAGTACAC R 2 1 2 1 101000 r 74 goat snp9191-scaffold1335-38860 19 45483077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389659 Affx-122968723 AX-123260017 19 45018619 ACCTCTCCTTTTAAATATTAAATGAAACTTCGGTC[A/G]CATGTCTAGCATTTCAAGTAAATCCTTGCCCCAGA R 2 1 2 1 101000 r 74 goat snp9190-scaffold1335-6853 19 45515515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409890 Affx-122952902 AX-123280241 19 45028675 CACATGCTCTTTGAGAGCTGTGGCAGCCTGGAGAT[A/G]TTACAGAATTGGGGTGCCCTTTGTTTAAGCTGAAT R 2 1 2 1 201000 f 74 goat snp32141-scaffold364-3104 19 45524272 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425169 Affx-122941057 AX-123295515 19 45059070 CTTCAATCCCCCACCCCCAAGACTAACAAGTGCCC[A/G]TCTTAGACTCATATGACCTGCCGTCCTTTTCTTGT R 2 1 2 1 101000 r 74 goat snp32142-scaffold364-33499 19 45554381 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393306 Affx-122965963 AX-123263662 19 45100062 CCTTCTTTAATGGCTGAATTATTGCCTCACGGTTA[C/T]AGAATGACTGCTGCACCTCCAGGCATCACATCTAC Y 2 1 2 1 201000 f 74 goat snp32143-scaffold364-74491 19 45595430 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450682 Affx-122921905 AX-123321016 19 45131645 GACAACTCAGGCAAACTGTTGTTACATAGGTATCC[A/G]TGGCCGCAGAAACACCCAGCTCTAGATTCCTGTGT R 2 1 2 1 101000 f 74 goat snp32144-scaffold364-106074 19 45626480 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777120 Affx-122958924 AX-385264243 19 45163495 CCACCACTCAGTACTAAAGGGTTATCACACCCTAA[C/T]GTCTCCACCTTCCAGCCAGGGAGCAGTTCCTAAAA Y 2 1 2 1 102000 r 74 goat snp32145-scaffold364-137924 19 45658395 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779312 Affx-122942249 AX-385266416 19 45206734 CTAACATGAACCACATAATACTATTCTTAAATAAA[A/C]TCTCAACTCTCATTTCTTCCTGTCACTCTTATGTG M 2 1 2 1 101000 r 74 goat snp32146-scaffold364-181163 19 45701497 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444615 Affx-122926943 AX-123314952 19 45261927 CCTTACTAAACAAAAAGAAACATTTTTCAAAAAGG[C/T]ATAATGGAGATTTTACATGTGAGGAATTTAAGCCA Y 2 1 2 1 101000 f 74 goat snp32147-scaffold364-236356 19 45756758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770705 Affx-122954103 AX-385257869 19 45309749 AAAATCACACAATTGCATTAGATGCTCAAAAAGCC[A/G]TCACTTTTCACGTATTTTATCCATAGAATACTTGG R 2 1 2 1 101000 f 74 goat snp32148-scaffold364-284178 19 45804584 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440793 Affx-122929837 AX-123311130 19 45339527 GGAGGGATATTGATTCCTACATATGAGTCCCTATA[C/T]GCTGATTACATTTGTTTATGGGAGACACTGAAGTT Y 2 1 2 1 101000 f 74 goat snp32149-scaffold364-313956 19 45834220 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783151 Affx-122965269 AX-385270218 19 45371808 ACACATTTCATCTTGATCATCTTCTAAGCTCTCAC[A/G]TCACCTACAGACAGTACAGCACGTGGATCAGAGCA R 2 1 2 1 101000 r 74 goat snp32150-scaffold364-346237 19 45866417 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393065 Affx-122965613 AX-123263422 19 45408983 TTCAGGTGACTCATTGCTTCTTTTCTCTTTCCTTG[A/G]TGGCAAGGAATCTATACAGAGGACTGGGTTAATCA R 2 1 2 1 201000 r 74 goat snp32151-scaffold364-383412 19 45904006 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394795 Affx-122964817 AX-123265150 19 45445428 GGGCTAGACTCTAGGGTTCCCCTGTCCCAGAGTGA[G/T]AGTTCTTAACACATGGGTCACAGACCATTTAAGAA K 2 1 2 1 101000 r 74 goat snp32152-scaffold364-419857 19 45940813 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435068 Affx-122933733 AX-123305408 19 45485169 TAGGGGCGGGAGACCTTCAGAGGGGGTAAGGATTA[A/G]GCTAAGAGACAGGCTTTTCAAAGCACTGATACTGA R 2 1 2 1 101000 r 74 goat snp32153-scaffold364-459598 19 45980720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797009 Affx-122973337 AX-385283950 19 45527186 TGCAAGTTCACATATCTGTCATAAGATTCAAAGAG[C/T]TGAGAAACAATTGTGTTGTCACGGTTATGGGGAAG Y 2 1 2 1 101000 r 74 goat snp32154-scaffold364-501615 19 46022692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794671 Affx-122965022 AX-385281632 19 45565309 ATATAGTGGTCTAAGTTACACTTAAATATCTTAAA[C/T]GTAGTATTTTGATACAGATATCTGTTTAGGATCAA Y 2 1 2 1 101000 r 74 goat snp32155-scaffold364-539738 19 46060689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785224 Affx-122975520 AX-385272270 19 45597165 TAAAAAAGAAACAGTTCTATAGAGGTAAAATTTAC[A/G]TACATAAAATCTCCCATGCTCTGATTTACAAATTT R 2 1 2 1 101000 r 74 goat snp32156-scaffold364-571594 19 46093184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785152 Affx-122920981 AX-385272198 19 45635557 CAACATTGCCTAATTACTATAACTTTCTAATAAAC[A/G]TTGAACTCTGTTAGGTTGAATCAGTTCTCCAACTT R 2 1 2 1 101000 r 74 goat snp32157-scaffold364-609986 19 46132406 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795223 Affx-122973955 AX-385282181 19 45702438 AAGGGGATGATTGTATCAACAAGTTATATACTTTT[A/C]TGTAAAACATGAAGTTGAATGTCATAGGCAAAAAA M 2 1 2 1 101000 f 74 goat snp32158-scaffold364-676867 19 46197794 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404449 Affx-122956747 AX-123274801 19 45759787 TCACTTATGCATTTTTCAGTATCATTTATTCTGCT[A/G]TTCAACCCTTCTAGTGTCTTTTACTTCAACTACTT R 2 1 2 1 101000 r 74 goat snp32159-scaffold364-734216 19 46256446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272916 Affx-1111833142 AX-519546603 19 45798771 AGAGATTGAACCCACATCCCTTGCATTGCAAGGTG[A/G]ATTTTTTTCTTTCTTTTTTTTTTTATTGTTTTAAA R 2 1 2 1 103000 f 74 goat 19_45798771_AF-PAKI 19 45798771 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38414465 Affx-122949565 AX-123284814 19 45803359 ATTCAGATTGAAAGAAAGGACACATGCTGACTCTT[A/G]CTAGTGTCATGTGCAAATTAGGGAAAGATTTCAAG R 2 1 2 1 101000 r 74 goat snp32160-scaffold364-777788 19 46300614 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774721 Affx-122975287 AX-385261855 19 45862564 TATCTGGAAAATATAGGTATTGAATTAACAAAGAG[C/T]GAAAGTCAGGAGCTATTGGACACACTGCCATTGGA Y 2 1 2 1 101000 r 74 goat snp32161-scaffold364-836993 19 46360002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401388 Affx-122959223 AX-123271741 19 45925483 TTCTAAGGCAAAAATTAATAAGACTAAGAACATTT[A/C]GTTATGGTGAGAGTAAGGGGAAAGGGACTTACTGA M 2 1 2 1 201000 f 74 goat snp32163-scaffold364-899912 19 46424613 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383880 Affx-122973129 AX-123254238 19 46008159 GAGAAGGTCTTTTAGGTTTGGTGAAGAAGTCACCC[C/T]GACTGTGGACAGTCTGAGTGGAGTGGTAGAAATGG Y 2 1 2 1 101000 f 74 goat snp32164-scaffold364-982588 19 46507982 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404604 Affx-122957345 AX-123274956 19 46087410 CTTCTCCTGCCCTTAACAATGACCACTCAAATCTC[A/G]TCTCCCACTGAGATCATGGTGGCAGCCTCCTACCT R 2 1 2 1 101000 f 74 goat snp32166-scaffold364-1061839 19 46587831 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382935 Affx-122973383 AX-123253293 19 46119338 TTTTCTGCTCTGAGAATTATTGTAATTAGTATATT[A/G]AAAGTACAGATTCATTACCAAAAACAGCTCTATCA R 2 1 2 1 101000 r 74 goat snp32167-scaffold364-1093767 19 46620009 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403732 Affx-122958020 AX-123274084 19 46167469 ACGCCCATCAACAATGGAACAGTTAGGTTGTGGTG[G/T]CTCCACACAGGTCAGTAGCACACAGCACTGAGAAT K 2 1 2 1 101000 f 74 goat snp32168-scaffold364-1141898 19 46668153 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410819 Affx-122952640 AX-123281169 19 46262971 AAACCTGGTTCTATGACCTTGTAACCACGTGGGCT[G/T]GGACAGATCACTTCCGGGAGCCTGTTTTCCCCACC K 2 1 2 1 101000 f 74 goat snp32170-scaffold364-1237400 19 46763013 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416065 Affx-122948340 AX-123286414 19 46307126 ATCTATTCCCAAATGCAAAAATAAATAAAACAACC[A/G]AAGAATTGTTCCATTTTTTAAAACAAAATTTAGTA R 2 1 2 1 201000 r 74 goat snp32171-scaffold364-1281555 19 46807169 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425589 Affx-122941413 AX-123295935 19 46339194 TAATGAGAGAACATTCTTGAAACATGACTTAACCA[C/T]GCTTGGTCCTCAAACAAATTCCTGGTTGTGTGTGG Y 2 1 2 1 101000 f 74 goat snp32172-scaffold364-1313623 19 46839375 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396296 Affx-122963093 AX-123266651 19 46374718 ACTCAGCAGTGGGATGAACATCAGACTCTCCTGAG[C/T]AATGACACCGGGGCCATAGGACATGACTTGGGGGA Y 2 1 2 1 201000 f 74 goat snp32173-scaffold364-1349147 19 46874711 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800470 Affx-122946859 AX-385287390 19 46423096 TCTCAGAAAATTGGCAAACCATGTGCCATAATGGA[A/G]TAGAGAGGGAGGATCTCAAGCTTAGAAGCCAGACA R 2 1 2 1 101000 r 74 goat snp32174-scaffold364-1397525 19 46923687 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797321 Affx-122977916 AX-385284260 19 46455344 ACATTAGATAAACTTTATGGAAAAGGTTTTACAGC[A/G]TGTGAACTAACTAACCAGTTAGTACTGTCAAACTG R 2 1 2 1 101000 r 74 goat snp32175-scaffold364-1429773 19 46955355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799680 Affx-122931676 AX-385286608 19 46524449 TTCCAATTTCTTACAGCTGTCTCAGGTTCATAGAG[A/C]TTCCATAGCATCTAGGATTTGCACATTGTGGTGTG M 2 1 2 1 101000 r 74 goat snp32176-scaffold364-1498878 19 47024784 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798439 Affx-122926978 AX-284886843 19 46554620 AGAAGTTCCCAGTATCCAGTAAAAAGACAAGACAA[C/T]GCCATTTTTATTTTTAGGCAAGGTAAAAACCCCAG Y 2 1 2 1 101000 r 74 goat snp32177-scaffold364-1529049 19 47055364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786590 Affx-122962064 AX-385273622 19 46609076 ATAAGGTAGAGCAGCCTGGAGAAGACAAATCTTTT[A/G]CAGAGGAAAATATTAGAACCATTATTAACATCCTC R 2 1 2 1 101000 f 74 goat snp32178-scaffold364-1583505 19 47110302 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411751 Affx-122951505 AX-123282101 19 46649080 ATTATGTAAAAATATTTTTTTCCTAAGAGAATCTT[A/G]CAATCTATATTTGCTGCAGTATTCTGAAAGGATAA R 2 1 2 1 101000 r 74 goat snp32179-scaffold364-1623509 19 47150400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379887 Affx-122975776 AX-123250245 19 46680991 TAACTTTTACCCATAGATGTTAATACTTTCAGAGA[C/T]GAGGCCTTGATTTCTGTTTTGTTTCAACATTTTTT Y 2 1 2 1 201000 f 74 goat snp32180-scaffold364-1655420 19 47182318 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386910 Affx-122970030 AX-123257268 19 46774144 CATATTGATCTGACAAAAGCCTTAGGTTCTGAGGT[A/G]CAGAAATCGTTTCTGGGCTGTTCTTGGTGTCTACA R 2 1 2 1 101000 f 74 goat snp32182-scaffold364-1748573 19 47274428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403710 Affx-122958036 AX-123274062 19 46833947 AATGTGCAGAGGCAGAGAGAAGGGTTTTCTGTTTC[A/G]TGAACAGATTGGAGATTTGTTGGCAAGCAGATGGG R 2 1 2 1 201000 r 74 goat snp32183-scaffold364-1808376 19 47334349 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444904 Affx-122926254 AX-123315241 19 46879087 CTGGGGTCCAGAGCGAGGACCATTTCAGAGCCTGT[A/C]GTGCTCTGAAGTGATAAACAGGATGAGTCACTTGA M 2 1 2 1 101000 r 74 goat snp32184-scaffold364-1853516 19 47379357 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444667 Affx-122926454 AX-123315004 19 46915454 CTGCTGTTCAGAGGGGGCTTAGGATGCGCAAGGGA[C/T]GTGGCACAGGGCAGAGAGCTAGTAAAATGCAGAGC Y 2 1 2 1 102000 f 74 goat snp32185-scaffold364-1889883 19 47415777 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453803 Affx-122919571 AX-123324136 19 46947209 CATACCACAGGGATGGTGCTGTGTTTTCTTCTCAG[C/T]ACTTCTTACCAGATGAAACCACTTGGTTGGTTGGT Y 2 1 2 1 201000 r 74 goat snp32186-scaffold364-1921638 19 47447746 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277258 Affx-1111835821 AX-519550763 19 47006605 TAATGATGTGTGTCAACACTAATTTGATTGAGAGG[A/G]CAATACAGTAGACTTATGAAGAGCACGGGGTGTGC R 2 1 2 1 101000 f 74 goat Random2.2K-1806 19 47006605 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38414138 Affx-122949703 AX-123284487 19 47011720 ATCCCAAAGAAAAAGCCTCTTTTTCCTTTTCAGTC[A/G]GGGTATTTCCCCTTCTACCTTTATTCTTGCTTCTG R 2 1 2 1 201000 r 74 goat snp32187-scaffold364-1986149 19 47511501 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779155 Affx-122926802 AX-385266259 19 47057089 TTATCTCCACCCAACACTAGCCCTTATTTATCCTT[A/G]CTTTATATGTTACTCAGAAATGAATTCTTTAAAGT R 2 1 2 1 101000 f 74 goat snp32188-scaffold364-2031518 19 47556874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447808 Affx-122923925 AX-123318144 19 47107218 CCAGTCAAGCAAAGTTGAGCCTTGTCAGCAAAGTG[C/T]AGTCTTCATTTAACCGACTTTACATGTCTAAGGTT Y 2 1 2 1 201000 r 74 goat snp32189-scaffold364-2081647 19 47606179 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801582 Affx-122949470 AX-385288491 19 47143093 AGGATTCAATAACCAATGAAGGCTAACCAGTTCCT[A/G]TAGAATAACATAAAAACCCCTCTGGCTTTCACTGC R 2 1 2 1 101000 f 74 goat snp32190-scaffold364-2117522 19 47642181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413117 Affx-122950381 AX-123283466 19 47259231 TGTGAAGATTTAAACTGAGGTAAAATATACATAAC[A/G]TTTACTGCACACTCATACTGTTGTGTAACCTGTCC R 2 1 2 1 101000 r 74 goat snp32191-scaffold364-2233660 19 47723320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394198 Affx-122964911 AX-123264553 19 47291725 ACTCAGTTTCCTCATCTGTAAGATGGAGGTGACAA[C/T]GGTCCCAGTCTCAGGACATTTGTTAGGAACAATTA Y 2 1 2 1 201000 r 74 goat snp32192-scaffold364-2266154 19 47760744 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381054 Affx-122974625 AX-123251412 19 47332997 ATTTACCCCAGGTATGCAGCACAGATTCCACACTA[G/T]AAAATCAGTTAATTTTTATAATTATTTATTTATTT K 2 1 2 1 101000 f 74 goat snp32193-scaffold364-2307426 19 47801382 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277260 Affx-1111835822 AX-519550765 19 47347091 GTAACAAATGGACAGCTCTAGTTGGGGTGTGTACA[A/G]ATGTGGGGGCAGAGGTGTGAGCCCGTTAAACTGCT R 2 1 2 1 202000 f 74 goat Random2.2K-1808 19 47347091 A G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320770108 Affx-122974028 AX-385257275 19 47363176 ACAAAAGATGATTCTAAACCTTATTATGGAAAGAA[C/T]AAAAGGACCAAAACACCCCTAAAGAAGAATAAAAT Y 2 1 2 1 102000 r 74 goat snp32194-scaffold364-2337605 19 47831920 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408660 Affx-122953466 AX-123279011 19 47431087 GTAAGGGGTGGGAATGATGTCTCCCTGGGGAGAGC[C/T]GACAAGGACTACTGCACTGAGAAAGGGGGAGACGG Y 2 1 2 1 201000 r 74 goat snp21725-scaffold2131-42724 19 47883570 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422935 Affx-122943032 AX-123293281 19 47477343 AAGAGAAAATAGATTAGAACTACTAACGAAACATC[A/G]CCCCCTTTCCCGACCTCCCTTCTCTTGAGTGTCAC R 2 1 2 1 201000 f 74 goat snp21726-scaffold2131-88980 19 47929900 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392558 Affx-122966084 AX-123262915 19 47508738 GATACATTAGGCTTTTCTCCCCATATCATCTCTTT[A/C]GGGAAAACATTTGATCATGATAAAACACACACAGT M 2 1 2 1 201000 r 74 goat snp21727-scaffold2131-120375 19 47961491 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417753 Affx-122947412 AX-123288101 19 47562231 TGAAGCAAGGCCTTTAGAACGGTCTGATTAGCTCT[A/C]GGGAGATATTTTATTAAAAACTAACCCGTAGAAAG M 2 1 2 1 101000 f 74 goat snp21728-scaffold2131-173868 19 48015438 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400676 Affx-122960337 AX-123271031 19 47611634 GGGAAGGTCTATACATCATAATGCAAAATGAAAAA[G/T]CAGAATTTGGTATGATGTGTATACATCAAACACAT K 2 1 2 1 102000 f 74 goat snp21729-scaffold2131-223271 19 48064596 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445939 Affx-122925914 AX-123316276 19 47641591 TTTTTGACACTGCACTTCTGTCTTGGCAGGAGAAA[C/T]GGTTATGAAGTACACAAAAACAAAAAAGTTGATCC Y 2 1 2 1 101000 f 74 goat snp21730-scaffold2131-253228 19 48095078 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434098 Affx-122934944 AX-123304439 19 47672814 TTCTACTCCAAACCAACTCTGGGCTTTTGCCTGAA[C/T]GGCCTGGAATCCTCTGCTTCCACTACACAGATTAG Y 2 1 2 1 101000 f 74 goat snp21731-scaffold2131-284451 19 48126036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415689 Affx-122948539 AX-123286038 19 47722269 CACATTCCATCCCTCCTTCCTTCCATATAATGAAC[A/G]TCGACTTACCTCTTTTCAGATCACCATCAAAAGCT R 2 1 2 1 201000 r 74 goat snp21732-scaffold2131-333906 19 48175376 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384318 Affx-122972271 AX-123254676 19 47753101 TCACTAATTTTTTTCCTTGAAAAGATAATCATGCC[A/G]CTTAGTTTTCATTTGTAAAGTTTGACTGTCTTAAT R 2 1 2 1 101000 f 74 goat snp21733-scaffold2131-364738 19 48206595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447604 Affx-122924002 AX-123317940 19 47801770 GTATTACAGAAAACAGTAATAATTCTAAAGGTGGA[C/T]ATGTCTATTCTGAACTCGTCTTCTGAGATTTAAAA Y 2 1 2 1 101000 r 74 goat snp21734-scaffold2131-413407 19 48255994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763068 Affx-986697597 AX-385251034 19 47825370 GCTGATAAGAGGGACTTACCTAGTCCTCCTGGCAC[A/G]GTCCTGTGTGGGGTGGGGTGGGCACCTGGGGCTCG R 2 1 2 1 600010 f 74 goat 19_47825370 19 47825370 Ancestral_priority_1043 ancestry 0.592 neutral IMAGE 10K 10K ancestral 320763574 Affx-986698103 AX-385251429 19 47825418 GTGGGGTGGGCACCTGGGGCTCGTGTGTGTGATGT[G/T]TGCACATGGGGCCCCAAATCTGGGGAGCCCCGACT K 2 1 2 1 600010 f 74 goat 19_47825418 19 47825418 Ancestral_priority_1043 ancestry 0.474 neutral IMAGE 10K 10K ancestral 320763576 Affx-986698105 AX-385251431 19 47833613 TCTGAGCTCAGTCCAGATGACCTGGACACATGTGG[A/G]CCATGGCGGGAAGGCAGCCCACGCTTCTAAGAGGG R 2 1 2 1 600010 f 74 goat 19_47833613 19 47833613 Ancestral_priority_1043 ancestry 0.486 neutral IMAGE 10K 10K ancestral 320804036 Affx-986696353 AX-385290718 19 47833621 CAGTCCAGATGACCTGGACACATGTGGGCCATGGC[A/G]GGAAGGCAGCCCACGCTTCTAAGAGGGTGGTGTGG R 2 1 2 1 600010 r 74 goat 19_47833621 19 47833621 Ancestral_priority_1043 ancestry 0.514 neutral IMAGE 10K 10K ancestral 320791577 Affx-122967400 AX-385278568 19 47834872 AGGAAAAGGCAATTTATGAAGAGGATGGTCTAGCA[A/C]CTGAGTTAAGAGAACACAGGTTCATCACGTTAATG M 2 1 2 1 101000 r 74 goat snp21735-scaffold2131-446509 19 48288770 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377031 Affx-122977711 AX-123247390 19 47867232 TTACAAATACTGGATAAATTACTTCTTACAACACA[A/G]CTCTGAAGTAGATACTATTTTTATTTCTTATGGGG R 2 1 2 1 201000 f 74 goat snp21736-scaffold2131-478869 19 48321109 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440203 Affx-122930697 AX-123310540 19 47898253 GGTAAATGCTCAACAAACGTGAGCTATCATTACCA[C/T]GGTGAATGAGCTGGTCAAGCAGAATCTTCACCTAA Y 2 1 2 1 101000 f 74 goat snp21737-scaffold2131-509890 19 48352157 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410386 Affx-122952434 AX-123280736 19 47931062 CAAAAATAAATGCATCTGTCACAGAGGGGGGACTG[C/T]GCCAGCGTGAACCTGGGGTGCTCATCGTCAGCTGA Y 2 1 2 1 103000 f 74 goat snp21738-scaffold2131-542699 19 48384916 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379455 Affx-122976089 AX-123249813 19 47980910 ATGTCTCATTATTGATTTATTTATTGTGACTAATG[C/T]AACATACTATCCTAAGATTACTTAGTAATACAAGA Y 2 1 2 1 103000 r 74 goat snp21739-scaffold2131-592547 19 48434660 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396592 Affx-122962904 AX-123266947 19 48018904 CTATCTGAGAGTGTCAAATTCCACGAGTTAGGGCT[C/T]AGTCCTACAAGACTGCCTGCTACCTCCCCACCCCC Y 2 1 2 1 101000 f 74 goat snp21740-scaffold2131-630541 19 48472836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450730 Affx-122921869 AX-123321064 19 48076097 ATTACTGGTATAAAAACACCCCAGATAATCCCAAG[A/G]TGTATGGAAATCAAGCAAGAGAACCATTGTTCAAG R 2 1 2 1 101000 r 74 goat snp21741-scaffold2131-687734 19 48530383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401660 Affx-122959575 AX-123272013 19 48153219 TATCAGGCATCTGGAATCTAATACTAGGTGAAACC[A/G]GGCTAAATGTCACAAAAGTATAAAATTGTCTCAAT R 2 1 2 1 101000 f 74 goat snp21743-scaffold2131-764856 19 48607177 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416566 Affx-122947667 AX-123286914 19 48202531 ACTATTAAATAAAAGCAATAATAGGAAAACTTTAA[C/T]GTCTATAAAATATTAGCATTACAATGAAAAAGTGT Y 2 1 2 1 101000 r 74 goat snp21744-scaffold2131-814168 19 48656503 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448581 Affx-122923405 AX-123318917 19 48296218 TAAAATAAATTAATAACTGAAATAGAGATGAAAGT[A/G]TCTGATGGCTGGGATGAGAAGGGGAAGTAACTGGA R 2 1 2 1 201000 f 74 goat snp21746-scaffold2131-907855 19 48749705 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441380 Affx-122928855 AX-123311717 19 48349566 TGAGGGCAGAGAAATGATGCCCACTGCTCCTGGTG[A/G]GATCTGGGGGCAATGCTCACACAGAGATGTATTTT R 2 1 2 1 202000 f 74 goat snp21747-scaffold2131-961203 19 48803816 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421890 Affx-122944264 AX-123292237 19 48386037 GTGTTACAGCTCAAGGACGAGAAGAGGGCCACGAG[C/T]CCAAACATACTGTGATTGGTTACATGTTGCTAAAC Y 2 1 2 1 102000 r 74 goat snp21748-scaffold2131-997674 19 48841043 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394670 Affx-122964369 AX-123265025 19 48438413 ATGAGATGAGCCTGCTTATAGGCAGAGGGTTGGGG[C/T]AGTGACTGCAGAGCAGCACAATGAAGCAGAGAGAG Y 2 1 2 1 101000 r 74 goat snp21749-scaffold2131-1050050 19 48893402 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399284 Affx-122960545 AX-123269639 19 48482527 TGGGTGTAGAGTCCAGTTCCTTCTGGTTCGTGCAT[C/T]GAACTAACAGAGTACACTAGACCCTGTAGACACGG Y 2 1 2 1 101000 r 74 goat snp21750-scaffold2131-1094164 19 48937546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421041 Affx-122944528 AX-123291388 19 48534597 GAGTTCTCTGTGCAGGAACTGGAATGAATGCCATC[A/G]TCTTAGTCTTTCAAAAGCAACACTCAGGAACCCTG R 2 1 2 1 101000 r 74 goat snp21751-scaffold2131-1146234 19 48989947 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375619 Affx-122978710 AX-123245978 19 48574180 ATGAGAATTTCGATTCGGCTGTACACGCAGATGCA[C/T]GGGGAGCACCCTGCAGAAAGAGGTTCCCCTCTGCC Y 2 1 2 1 101000 f 74 goat snp21752-scaffold2131-1185817 19 49029406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463603754 Affx-1110065581 AX-515085251 19 48581821 ATAATCAATTTACAGACTATATAAAGCCATTAAAA[C/T]TGTTACTGAAGATTAATGAAGATATCGGAGAAGGC Y 2 1 2 1 101000 r 74 goat 19_48581821_AF-PAKI 19 48581821 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398563 Affx-122961513 AX-123268918 19 48644976 GCCAAGCAGAGTTGACAGTGCGATTTGGCCTGAGC[A/G]TTTAGAATAACATGGCCTCTTACTGAACGGGAAGC R 2 1 2 1 101000 r 74 goat snp21753-scaffold2131-1256613 19 49100230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428488 Affx-122938779 AX-123298831 19 48702095 CCTAGTAGGGGCTTTGGTGGGTAGGGTGTGGGCAC[A/G]CAGGGGTACAGGGACAGTGCAGGGTAGGAACTCAG R 2 1 2 1 103000 f 74 goat snp21754-scaffold2131-1313732 19 49156916 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445045 Affx-122926614 AX-123315382 19 48749589 CTCGTGTGTCAGGAGAAACTCTGGAAGAGTTTGGA[C/T]GGTAAAAGCACCCATTTCAAATTGCAGTCACAGCT Y 2 1 2 1 101000 r 74 goat snp21755-scaffold2131-1361226 19 49200496 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451987 Affx-122920932 AX-123322320 19 48792067 TAGCTTCCAGCCTACGTTTAGATGGCAGGAAAACC[A/G]TTTACTTATTTTCATGAATAAATGTCTGCTTTGAC R 2 1 2 1 201000 r 74 goat snp21756-scaffold2131-1403704 19 49242856 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425056 Affx-122941266 AX-123295402 19 48874549 AGCAGTGAGCACTAATTACACCTTCAGGCTTGTCA[A/G]TAACTGAATTCCTTCAAAGTCTTTCCCCAAAAGCC R 2 1 2 1 101000 r 74 goat snp21758-scaffold2131-1486186 19 49324957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777146 Affx-122958514 AX-385264270 19 48931628 AAAAGGCATTTTCAAAGTCTGATAACCATATGCAC[A/G]TGAGTTAGGTTTATAAACAAACTGAGAAGTGCTGG R 2 1 2 1 101000 r 74 goat snp21759-scaffold2131-1543265 19 49382191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449737 Affx-122922464 AX-123320072 19 48961677 AACAACTAGCTCCCCAATCGAATCAGCCAACCTGC[A/G]CTGGACTTCAAACACCAAACAGGCCTGCTGCTAGC R 2 1 2 1 101000 r 74 goat snp21760-scaffold2131-1573314 19 49411947 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770671 Affx-122937164 AX-385257835 19 49070256 CCTAAGTATGTCTTTACCACTTTATCTTCTAATTA[G/T]CTCTTATCCATGGAGAAGCATCTGTAAATAATCCT K 2 1 2 1 201000 r 74 goat snp21762-scaffold2131-1681893 19 49519814 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446243 Affx-122925691 AX-123316579 19 49172880 ATGCAATTGAAAACATGACTCACACTTTAGACCAA[C/T]ACCACAAATCACCTATTCCTAAACTTACACTCAAA Y 2 1 2 1 101000 f 74 goat snp21764-scaffold2131-1784517 19 49619321 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463604207 Affx-1110065809 AX-515085700 19 49196004 GGGGCAGGTGGGCAGCAGCCTGCAGACCCTCCTGC[C/T]GAAGCCTCAGTGAGCTGGCGCCACCCTGACAGCTG Y 2 1 2 1 102000 r 74 goat GoatD01.004749 19 49196004 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320771846 Affx-122959543 AX-385259002 19 49207321 CTAACAAATCAAACACCACAGTTGTTAAAAGTGGG[C/T]GAAGAAGATTTCTTATGTTGGATAGTGAGCTACAG Y 2 1 2 1 101000 f 74 goat snp21765-scaffold2131-1818958 19 49653789 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796707 Affx-122943356 AX-385283652 19 49257665 CATCTCACTATTTTTTGAGGTCATGTAACTAAAAA[A/G]TCTCTTTTCTGGGCACTTCTTCCTAGTGAAGAAAT R 2 1 2 1 101000 r 74 goat snp21766-scaffold2131-1869302 19 49704013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377080 Affx-122978277 AX-123247439 19 49291965 ACTGTCCTGTCCCCCTAGCCCCTAAAAAAATGCCT[C/T]GGAAAGAGAAAGGAGAGGGAGTAGGACTGGGGGTG Y 2 1 2 1 103000 f 74 goat snp21767-scaffold2131-1903602 19 49738362 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386860 Affx-122970068 AX-123257218 19 49341419 TAAGCCTCACCCTTCCTGGCACTGGTTCCCACTCA[G/T]CCCTGCAAAAATGTTTGTTGAATAAACAAGAGTTG K 2 1 2 1 303000 f 74 goat snp21768-scaffold2131-1953056 19 49784255 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407270 Affx-122955343 AX-123277621 19 49407872 TGCCCAGTAGGGATCCTTCCAGAGAAGGCAATGCA[A/G]CCCACTCCAGTAATCTTGCCTGGAAAATCCCATGG R 2 1 2 1 103000 f 74 goat snp21769-scaffold2131-2019509 19 49851241 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789408 Affx-122953167 AX-385276418 19 49471981 AGAAGTCACAAGTTGCTAACAAAAAGATAAGCATG[C/T]CACCACGTCTGGAATATGAAGAATGTGCTGAATGT Y 2 1 2 1 101000 r 74 goat snp21770-scaffold2131-2083618 19 49914364 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382410 Affx-122974255 AX-123252768 19 49596388 GGCCCTGCAATGTTTTTATTATCCCACAGGCATTA[G/T]ACCCTCATAGGCTCCCACTGTATGCTTGGGGTGCA K 2 1 2 1 101000 f 74 goat snp21772-scaffold2131-2208025 19 50038667 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417730 Affx-122947434 AX-123288078 19 49629316 TGAAAGCGTGTGTGGACGTATGTATGAATGTGTGC[A/G]TCTGTTTATTTATGGTAAAACACACACAGCAGGAA R 2 1 2 1 201000 r 74 goat snp21773-scaffold2131-2240953 19 50071789 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448649 Affx-122923352 AX-123318985 19 49659369 GCCTCTTCTTGGATCAATTCTGGACATGTGCATTT[C/T]GCTGGAAATCTCTCCAAAGTCCCTAGTCTTTCAAA Y 2 1 2 1 101000 f 74 goat snp21774-scaffold2131-2271006 19 50099661 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274861 Affx-1111834538 AX-519548446 19 49758201 ATAAGACATGGCCTATTAGCATCATACAACAAAAT[A/C]ATTTACCTCATTCTGGTAAACCCTGGTGGCTCAGA M 2 1 2 1 101000 f 74 goat GoatD01.040561 19 49758201 T G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320777873 Affx-122974943 AX-385264989 19 49774627 ACTGAAATACTCATATACCTATGTTGGAGAGTTTT[A/G]CTTTTCCTCACTTATCTCCTTTTGGTAATCTACTT R 2 1 2 1 101000 r 74 goat snp21776-scaffold2131-2386264 19 50214915 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771237 Affx-122941630 AX-385258395 19 49794943 AGATTTGGTAATTCATACCGGAAAGAAGGTACCTC[A/G]TGAAAGAGAACGCAGTGCTAACCCTTTTTTTTGTT R 2 1 2 1 101000 r 74 goat snp32202-scaffold3643-393290 19 50235479 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763580 Affx-986698109 AX-385251434 19 49812001 AAGGCAAAAAGAAAAAGATACCTGCACGCTGTGTC[A/G]AAGTCTGTTTTGAGAAAAAGGTGTAGATCTGGGTT R 2 1 2 1 600010 f 74 goat 19_49812001 19 49812001 Ancestral_priority_1043 ancestry 0.552 neutral IMAGE 10K 10K ancestral 320766671 Affx-986698111 AX-385254017 19 49812004 GCAAAAAGAAAAAGATACCTGCACGCTGTGTCGAA[C/G]TCTGTTTTGAGAAAAAGGTGTAGATCTGGGTTGGA S 4 1 2 1 600010 r 74 goat 19_49812004 19 49812004 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 38425985 Affx-122941153 AX-123296331 19 49839018 GCTGAGGCCCAGGATGGTTTACAGACCCGGGCGGC[C/T]CCTGCCTTTGATGTCAGAACATTAATTATTAGAAG Y 2 1 2 1 101000 r 74 goat snp32201-scaffold3643-349215 19 50277981 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766675 Affx-986698113 AX-385254021 19 49856623 GTCCTGGGGCAGCCGTGACCAAGGACCCCAAACAA[A/G]GGATCGAAAGAAGCAAGTTTGCCCTCCTCCAGGTT R 2 1 2 1 600010 r 74 goat 19_49856623 19 49856623 Ancestral_priority_1043 ancestry 0.556 neutral IMAGE 10K 10K ancestral 320763586 Affx-986698115 AX-385251439 19 49856656 AAGGGATCGAAAGAAGCAAGTTTGCCCTCCTCCAG[G/T]TTGGAGGCCGGAAATCCAAAATCAAGGTGTCAGCA K 2 1 2 1 600010 f 74 goat 19_49856656 19 49856656 Ancestral_priority_1043 ancestry 0.566 neutral IMAGE 10K 10K ancestral 320763592 Affx-986698121 AX-385251443 19 49886473 CCTGGTCCAGCTTCTCCTAGCTGCTGCAGGAATGG[A/G]GATCCCTGCTGACCGAGAATCCCTGAGCCCCTGGT R 2 1 2 1 600010 f 74 goat 19_49886473 19 49886473 Ancestral_priority_1043 ancestry 0.534 neutral IMAGE 10K 10K ancestral 38377242 Affx-122978154 AX-123247601 19 49898103 ACCAGGACGCACTTGGGGGACCATGCAGGTTCCCA[A/C]TGGGAGGTGATGTGCCCCGTTCCTGGCTATGACTC M 2 1 2 1 201000 r 74 goat snp32200-scaffold3643-290130 19 50336487 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798713 Affx-122919948 AX-385285644 19 49971923 CGCCGTGTCTCTATTGGGACACAACCTTGGTCGAG[A/G]TAACGGTGCACATTACACTGTGTTCAGTGTCTCCT R 2 1 2 1 101000 r 74 goat snp32199-scaffold3643-216310 19 50410408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418045 Affx-122946630 AX-123288393 19 50003793 GGGGCGACAGCACCCAGCCTGACACATTCATCTGC[C/T]GAGCCTACACTTATCACTCTGATCCGCAGAGAGGG Y 2 1 2 1 101000 r 74 goat snp32198-scaffold3643-184440 19 50442184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444149 Affx-122926793 AX-123314486 19 50049647 TATCCACAAGGAGAAATAACGCAATTATTGATATG[C/T]ATTTCCCAGCGTCAGAAATCATAAAGGTTTTGCCA Y 2 1 2 1 101000 f 74 goat snp32197-scaffold3643-138586 19 50488381 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802643 Affx-122976640 AX-385289544 19 50123948 CTTGGAAAACCTGTACACAACTTCTACAGGGACAG[C/T]GCTTAGCTTCACGGGCAAGGCAGAATAAGAGAGCA Y 2 1 2 1 101000 f 74 goat snp32196-scaffold3643-64285 19 50562838 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431896 Affx-122936008 AX-123302237 19 50155089 ATGGACAGACGGGTCTCTTGGGTGTGTTGGTTTGA[C/T]TGGACAGTGGGGAAAAGGGGTAAGCCAGAGGAATT Y 2 1 2 1 101000 f 74 goat snp32195-scaffold3643-33144 19 50593980 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410406 Affx-122952422 AX-123280756 19 50245594 CCGTGGGCCAGGCCAGTTGGAATGGCACAAGTCCT[C/T]AGGACAGTGACCAAACGATTTTGTTAAGGTCTAGG Y 2 1 2 1 101000 r 74 goat snp43728-scaffold5871-57262 19 50684550 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452143 Affx-122921670 AX-123322476 19 50299173 CTTTAACACTAACAACAATCATGCAGTCACTAATA[A/C]AAAGTCAGGGAGGAGCCTGGCAATAGGATGCTCCT M 2 1 2 1 201000 f 74 goat snp26107-scaffold2716-831681 19 50738180 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445249 Affx-122925483 AX-123315586 19 50337038 ATTATCATCCATCCATCCATCATTCATTCATCCAA[C/T]AAAACATTTCTTGTGTGAAGAGCCCCCTGTCCCGC Y 2 1 2 1 201000 r 74 goat snp26106-scaffold2716-793816 19 50776387 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398343 Affx-122962121 AX-123268698 19 50373100 CAGCCATACAAGGCAAAGGAACAGCAGACAAAAAG[C/T]AGATAAAATTCACAGAACTGGGTCTACAAGCAGCA Y 2 1 2 1 101000 f 74 goat snp26105-scaffold2716-757754 19 50812485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387100 Affx-122970675 AX-123257458 19 50426614 ATTCAAGTCCAAATGGCCAGTCTCTGGCCAAGGAG[A/G]CAGCAGGGTGGGGCAGAGGAATGACTGAGGTGGCC R 2 1 2 1 103000 f 74 goat snp26104-scaffold2716-704240 19 50862319 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401944 Affx-122958806 AX-123272297 19 50469107 CAGTCTCCTCAGAGTGAAGTTTCACCTGTGTGGAG[A/C]TGAGTCTCAGAGAGGTTGAGTGACGCCCAAGGCCA M 2 1 2 1 101000 f 74 goat snp26103-scaffold2716-661747 19 50904853 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403718 Affx-122958029 AX-123274070 19 50519863 TCTTTTCCTCACCAGGGTCTGGATGATTATGGGGC[A/G]CGGGCCGTGAGCAGGTAAGAGATTTTCAGACTCGT R 2 1 2 1 101000 f 74 goat snp26102-scaffold2716-610991 19 50951178 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774454 Affx-122933754 AX-385261590 19 50568847 GTGGAACTTGCTAGGATTTCACAGGTGTCTGTGCT[A/G]TGAAAGAAGTCGACATCTTGACATCAGAATGGGGG R 2 1 2 1 101000 f 74 goat snp26101-scaffold2716-562007 19 51000194 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396365 Affx-122963041 AX-123266720 19 50622792 ACAGCAGCATCTGGCGGGCGTGTGCCAGGATCACC[A/G]TGCAGACCCATCGTCTGCCCATAAATCCATTCCTG R 2 1 2 1 101000 r 74 goat snp26100-scaffold2716-508062 19 51053625 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408813 Affx-122954036 AX-123279164 19 50657650 GTTCAATTTTCTTTTCTGATTCTAGTTTCTTACGA[C/T]GGAAGCTTAAGTCATTGATTTTAGTCCTTTCTTCT Y 2 1 2 1 101000 r 74 goat snp26099-scaffold2716-473204 19 51088435 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433836 Affx-122934449 AX-123304177 19 50694987 GCAGAGGTTCTGGATGCATCAAAGGGCAAGGCTAC[C/T]GTGACCTGAAGCCCAGTGTGGGAAGAGGGACAGAA Y 2 1 2 1 101000 f 74 goat snp26098-scaffold2716-435867 19 51126226 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438082 Affx-122931521 AX-123308420 19 50748963 CTTCTCCCACAAATTTCTTTTGTGTGCCTCGGGGT[A/G]GTTCACTGATCCTTCCATCACTCTCTCCAGCTTTA R 2 1 2 1 201000 r 74 goat snp26097-scaffold2716-381891 19 51180220 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437778 Affx-122931701 AX-123308116 19 50789767 TGAGGAGGGGAAAGGGCAGAACCCTCACATCTGTC[C/T]CTTTGTTACGAAAGCAAGTGAGACCTCTGCTGAAT Y 2 1 2 1 101000 r 74 goat snp26096-scaffold2716-341087 19 51221427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441053 Affx-122928923 AX-123311390 19 50829289 TTTGATTCAGATCAATATCTTTTTAGGAAAAAAAA[C/T]ACCTTTAAGTGTTGTCTCAAACTAAATTAAAAAGC Y 2 1 2 1 103000 r 74 goat snp26095-scaffold2716-301565 19 51261007 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440703 Affx-122929904 AX-123311040 19 50879085 GCTGATGCTCTTCAAGGTCTCCATTAGCAGAATCT[A/G]CACTACTCTCTGCTTGGAGCTGTGGGACCTTTGAG R 2 1 2 1 101000 f 74 goat snp26094-scaffold2716-251769 19 51310484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801845 Affx-122978431 AX-385288752 19 50942064 CTGCTATGTGCTAGGTGAGAATGATTTTGGATTGC[A/C]CTATTTACTCAGATGTTGAAAGGAACACAAATGCT M 2 1 2 1 101000 f 74 goat snp26093-scaffold2716-188790 19 51374468 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425479 Affx-122941492 AX-123295825 19 50976378 GTCTGTAAAGTCACCACTTCCTTCCCGTGACTGCC[A/G]TTTATAGCTGGCAGTAATGAAAGGCGCCTGTTTTA R 2 1 2 1 201000 r 74 goat snp26092-scaffold2716-154476 19 51410547 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408765 Affx-122953389 AX-123279116 19 51009893 CCACTGGGATATTTTCCTAAACCGAGTCAAGCCAG[C/T]GTGTGACAAGCACCAGTTCCACTGGTGCATGAAAG Y 2 1 2 1 101000 f 74 goat snp26091-scaffold2716-120961 19 51443021 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454176 Affx-122919309 AX-123324509 19 51052738 CAGGAACATGTGTATATTCAGAAACTTATCTCCTC[A/G]TATTCTGAATACCATTCATTGGGAGGTGAGAACTG R 2 1 2 1 101000 f 74 goat snp26090-scaffold2716-78116 19 51486084 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406948 Affx-122955067 AX-123277299 19 51105987 CGAATTCATGACCCAAAGAGATGTCCATTTACTCC[A/G]TAAATCAGCAAGCATCCCAAAATACTGAAAGATGT R 2 1 2 1 201000 r 74 goat snp26089-scaffold2716-24867 19 51539222 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408319 Affx-122953765 AX-123278670 19 51135583 CCTGCAATGCAGGCAGATTCTTTACCCTCTGAGCC[A/G]CCAGGGAAGCTCTGGTGAGGATGTGGGAGGAGTCA R 2 1 2 1 303000 r 74 goat snp23084-scaffold2300-4630 19 51569240 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277262 Affx-1111835823 AX-519550767 19 51141646 TCAACAGGACCAGAGAAGACGGTGTGGAGAGAAAA[A/T]GCCAATGACTCCAACCTGCAAGCCCCACCCTCCAT W 4 1 2 1 102000 f 74 goat Random2.2K-1809 19 51141646 A T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376640 Affx-122979025 AX-123246999 19 51184016 ACTTCACTCTATGGCATAGTCTGTTGGACCGTGCT[A/G]TCCTACATCACCATCATCTGTGTAGTCAGGGCCCC R 2 1 2 1 101000 f 74 goat snp23085-scaffold2300-53063 19 51618461 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797607 Affx-122960495 AX-385284546 19 51232238 ACAACTTCATATGATGAAGCTTTCCTGTTTTTGAA[C/T]GAATAAACACAGCTAGTCAGACAATCAGAATCAGC Y 2 1 2 1 101000 r 74 goat snp23086-scaffold2300-101285 19 51666721 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420874 Affx-122944630 AX-123291221 19 51294578 ACCTACTGACCATGAATTTTTGCACCACATGCTGG[C/T]CCAGTACTCCTTACTGCTGTCCTGTGGACATAGGT Y 2 1 2 1 101000 f 74 goat snp23087-scaffold2300-163625 19 51728852 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381101 Affx-122974589 AX-123251459 19 51324166 TTTACTGGACAGTGTTGCTCCAGAGACTGGACACC[C/T]GGATGCCCTTACGTGGAATGTTTCCAACTTGGGTT Y 2 1 2 1 201000 r 74 goat snp23088-scaffold2300-193213 19 51758533 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380816 Affx-122975082 AX-123251174 19 51363153 ATTCCAAAAAGACAGGTACCTGGTGGAGCCCTTGC[A/G]TGGGTCGATCTTGAAATCATATTGTTGACTGTCCT R 2 1 2 1 201000 r 74 goat snp23089-scaffold2300-232200 19 51797485 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415969 Affx-122948417 AX-123286318 19 51396486 CCTGCTTGAGCTTTTTCTGAAAACAGACACTTCCC[A/G]TATGTATCAGTTATCTATAGCCCTATAATGGAGGA R 2 1 2 1 101000 f 74 goat snp23090-scaffold2300-265533 19 51831094 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405796 Affx-122955906 AX-123276148 19 51454566 CAGGGAGACGCTGCTTTATGGAGTTGCCATCGCAA[C/T]GGCCCCTGACCCTGGGGGCGCAATGGAGCACAAAG Y 2 1 2 1 101000 f 74 goat snp23091-scaffold2300-323613 19 51889682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272918 Affx-1111833143 AX-519546605 19 51501768 GCTCATACCAGGGGTTATTTTTGGAGGCAAAATGG[A/G]TAGTATTTTATACCCTCCTATTTATTCTCTTTGAT R 2 1 2 1 101000 f 74 goat 19_51501768_AF-PAKI 19 51501768 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389995 Affx-122968050 AX-123260352 19 51527816 CATTGAAATACAATACAATGCAACAAGAAAAGTTA[C/T]AGACATACACATGCACACCCGCGGTTCTTTCTCTG Y 2 1 2 1 201000 f 74 goat snp23092-scaffold2300-396863 19 51963025 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424515 Affx-122941733 AX-123294861 19 51612128 AAAATAGGCTGTTTCGGTTGGGTGGTGGCCAATTC[A/G]TGATGGGCCTCGTCCCAGCCCACACCCTCGCCACA R 2 1 2 1 102000 f 74 goat snp23094-scaffold2300-481175 19 52046601 A G 1 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38377734 Affx-122977383 AX-123248093 19 51661669 CCTTGGTTTGTTGTGTTAGCCCTGAAGTCACAGAA[C/T]AGAATAGGTCTCACTGTCCAGGGGAGTTGGCGGGG Y 2 1 2 1 101000 f 74 goat snp23095-scaffold2300-530716 19 52096392 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785975 Affx-122927630 AX-385273011 19 51696687 TATTTGATTTTTATGTTTTGGGCCTTAATCCCTGA[C/T]AGGATCCCTTAGGAATGGAATCTTGACTGTCTCCT Y 2 1 2 1 101000 r 74 goat snp23096-scaffold2300-565734 19 52131195 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382998 Affx-122973333 AX-123253356 19 51766960 CTTTGAAGGATGGGCTCCAGGCGGGGTGTGTGCAC[A/G]CTCACGGAATGCAAATCAATAATTTATGAGGAGAA R 2 1 2 1 101000 r 74 goat snp23097-scaffold2300-636007 19 52200731 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423288 Affx-122942648 AX-123293634 19 51803445 CAGTCACATGGCTGGTAATTGGTGGAGCTGGGTTT[C/T]GGGCTCAGATGCCATCCCCTCATCTTTGATTACTG Y 2 1 2 1 101000 r 74 goat snp23098-scaffold2300-672492 19 52236410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434292 Affx-122934765 AX-123304633 19 51841260 GCCCCCAGCAGTGCGACCGGGCACAGAAGGCTTTA[C/T]GGCAAGCAGGGGAGGGGATGGGACCTTGCAATGTC Y 2 1 2 1 201000 f 74 goat snp23099-scaffold2300-710307 19 52273614 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394077 Affx-122964966 AX-123264432 19 51872217 ATGACGGAGTCGATCTGCAGAGGCTGGGAACAGTC[A/G]TCTGCGGCAGCTGTATTATTTAGAGAGGCTCGGGG R 2 1 2 1 101000 r 74 goat snp23100-scaffold2300-741264 19 52304662 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414061 Affx-122949768 AX-123284410 19 51916138 CATGGATGTCCTTCCCAGGCCCACAGAATGTGTGC[A/G]CAGGCGTGTCCACACACTAGCCGTGTACATGAATG R 2 1 2 1 101000 r 74 goat snp23101-scaffold2300-785185 19 52348205 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382051 Affx-122974934 AX-123252409 19 51949194 AGCTGAGCAACTGAGTGGATGGAGGGGCTGTTTCT[C/T]GGGATAAGGGTGTCTGAGGGATAAGCAGACTGGAG Y 2 1 2 1 201000 f 74 goat snp23102-scaffold2300-818241 19 52380178 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788599 Affx-122928042 AX-385275616 19 51959452 AGCTGGGGCTGATCTAGCACATTCTTAGCAAAATC[A/G]TACCAGCAGTAACCCTGACAGTGATGAGTAAGCTA R 2 1 2 1 101000 r 74 goat snp50633-scaffold7289-9179 19 52390678 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376938 Affx-122977778 AX-123247297 19 51996477 CAGGTCTCCCACAATCCCTGGCCTCGGGGTTGCCA[C/T]GGAGGTGGTTTGAAAATCTGAGTTCTGTGCTTTTG Y 2 1 2 1 101000 r 74 goat snp50634-scaffold7289-46204 19 52426443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392760 Affx-122966000 AX-123263117 19 52025007 GGGGCTCCCAGGAGCACGGCTGAGGAGCCCAGAGC[A/G]TTCTCCCCTTTCTCCTCCAGACCACAGACAAGGGA R 2 1 2 1 101000 r 74 goat snp50635-scaffold7289-74734 19 52454926 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452825 Affx-122920740 AX-123323158 19 52058567 CAGCTGAGGGGATTTGGAAATTCTTTCAATTCGGC[A/G]TGAGGTTCCTTCAACACATTCGAGAAGGGCCTGTC R 2 1 2 1 201000 r 74 goat snp50636-scaffold7289-108294 19 52488553 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429286 Affx-122938619 AX-123299628 19 52091005 CTCCCCTTGGCCTTCCCCAAGCAGCCTGGTGTTAG[A/G]ATCGGGAGGTACGGGATAGCAGGAAGTGTAGGCTC R 2 1 2 1 101000 r 74 goat snp50637-scaffold7289-140732 19 52521380 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382554 Affx-122973775 AX-123252912 19 52139389 CTTTTCCTGGATTGTCTGTGGTTTGAAAATAGGAG[C/T]GGAGTGAAACAAGGGGCTCACCCTTTGATGAGAGG Y 2 1 2 1 101000 f 74 goat snp29370-scaffold3175-373136 19 52569654 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377949 Affx-122977207 AX-123248308 19 52220915 TAAGCCTCATAGAGGTGAAGGCTTCTGCCTAAGAA[C/T]ATCAAGCTGAGAGGAGTCAAACCTGGATACGTGAT Y 2 1 2 1 101000 f 74 goat snp29368-scaffold3175-291610 19 52645519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427017 Affx-122939842 AX-123297362 19 52249510 AGGTCAGGGTGGGTGGGGACTGGTGGAGATTTTAC[C/T]GTCTGGATCCAGGGAGCTCCTGGATTTACCTGTGA Y 2 1 2 1 102000 r 74 goat snp29367-scaffold3175-263015 19 52672001 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391892 Affx-122966961 AX-123262249 19 52299184 TGCAAAGCCAATTCATGTCCCTCTACCTGGGTGCC[C/T]GAGGCCAGAAAGAGGAGGGTGCAAGAGGGGCCTTA Y 2 1 2 1 101000 f 74 goat snp29366-scaffold3175-213341 19 52721778 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435673 Affx-122933334 AX-123306012 19 52379355 ACAAGGCAGGGCTAGACTAGCTCACGACCTAGTTG[C/T]ATAATATACTGTCACAACAATATCACACATGGACC Y 2 1 2 1 201000 r 74 goat snp29365-scaffold3175-133170 19 52799872 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800163 Affx-122949421 AX-385287086 19 52412227 GTAGTCCCTATTCACTTCTTTTAAGAGTACCTTTT[A/G]TAAGAGCAGAAATGGTAAATTCTGACAAATACCAA R 2 1 2 1 201000 r 74 goat snp29364-scaffold3175-100298 19 52832799 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771435 Affx-122928825 AX-385258593 19 52499729 GGGAATCCAGGGGACATTAACAAAAGGAGATACAC[A/G]TCTGGACACACGCTGGTGATGTGTCTGAGCCCTGA R 2 1 2 1 202000 r 74 goat snp29362-scaffold3175-12796 19 52920494 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401411 Affx-122959206 AX-123271764 19 52624977 CAGTGCATGCAACATGCTAGAACAGTGCCTTGCAC[A/G]TAGTGAATGCTCGACAAATGTTAGTTGTAATTATT R 2 1 2 1 101000 r 74 goat snp37971-scaffold470-785220 19 53043251 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434183 Affx-122934878 AX-123304524 19 52803227 GGGAACTTGTATTTATATTTTTATCTCTGTCCTTT[A/G]AAGTTTTCTATTTTTGTTAAAGTTTTATAATATAC R 2 1 2 1 201000 r 74 goat snp37968-scaffold470-606970 19 53216257 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444392 Affx-122926594 AX-123314729 19 52840610 GAGCCGGGCGGAAGGAGCGGTCTGTGATCTGTTCT[C/T]TGTTCCCACGGATCCGCCTATGCACATTACCCTTG Y 2 1 2 1 101000 r 74 goat snp37967-scaffold470-569587 19 53252089 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274756 Affx-1111834477 AX-519548342 19 52862361 CATGGGGTCCTCTGCAGGGACCACGCCGTGCTCAC[A/G]GGGTGGGGGCAGGGCAGGCAGCCGAGAAAACTTCC R 2 1 2 1 303000 f 74 goat GoatD01.037546 19 52862361 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38418346 Affx-122946593 AX-123288694 19 52918223 CTAATTCATATAACTTTCAGAGAAATAAAATTAAG[C/T]AAAAATCATTTTTATTCCATCTTCTATAGAATACC Y 2 1 2 1 101000 f 74 goat snp37966-scaffold470-491974 19 53328982 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375799 Affx-122978569 AX-123246158 19 52948865 GGATGTGACATCACTATCTTATTTAATCCTCATAA[C/T]ACTCACAGAAGGTGGTTGCTTTAATTCTGTTTCAC Y 2 1 2 1 101000 r 74 goat snp37965-scaffold470-461332 19 53359640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381533 Affx-122974845 AX-123251891 19 52996432 ATTTAACTGAGGCAGGGTGGTGAAGGGGAAAAGGG[C/T]GGCATCAGCCCTGAGAATGCCCTTCATGAAGGACT Y 2 1 2 1 201000 r 74 goat snp37964-scaffold470-413765 19 53407244 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388697 Affx-122968991 AX-123259055 19 53040184 CCTTCTCCTGGATCGTGCAAGTCCAGTCTGTCTCC[A/G]TCAGCTGTCCTTGGGCCAAGTGCCGAGGCCACTGG R 2 1 2 1 101000 f 74 goat snp37963-scaffold470-370013 19 53449925 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393021 Affx-122965645 AX-123263378 19 53078941 GGGCAGGATCACCTGATCGCAGGCAGGACCACATC[A/C]CTGCCTGATGGAAAGAACCATCCAGTTTAGAGGAA M 2 1 2 1 101000 r 74 goat snp37962-scaffold470-331256 19 53488302 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437142 Affx-122932148 AX-123307480 19 53110430 ACGAACCAAGCAAGAGGGCAAAACGACATGGGAGG[C/T]GGAAGGGCCAGGGCCTCTGTGGGGAGCATGGAGAC Y 2 1 2 1 101000 f 74 goat snp37961-scaffold470-299767 19 53520279 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394173 Affx-122964929 AX-123264528 19 53144191 CAGTGAGCTGTTGGTTTTCTTCTTTGGACTCAGTC[A/G]CCTTCCAATGCCACAGGCTCTGGCTAACATCCAGC R 2 1 2 1 201000 r 74 goat snp37960-scaffold470-266006 19 53553957 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766705 Affx-986698129 AX-385254048 19 53146077 GTGTGCCCCGTCCAACGGATGACAGCTGGTCCATA[A/G]CGGGACTCCCCAGGAAGAATCCACTCTGTGTGCTC R 2 1 2 1 600010 r 74 goat 19_53146077 19 53146077 Ancestral_priority_1043 ancestry 0.534 neutral IMAGE 10K 10K ancestral 320763602 Affx-986698131 AX-385251452 19 53146208 CCTGTCTATTGTAGAAAAATGTTGCAACCTTGCCA[C/G]GAGCCACGGCAGAAGTATCTTCAAGCTGACCACAA S 4 1 2 1 600010 f 74 goat 19_53146208 19 53146208 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 320763604 Affx-986698133 AX-385251453 19 53146628 ACCATAAATGCAGAATATTATGCAAGTGGAACTTA[A/C]AATGGCATTCTTAATCCTGTTTGTCCAGTCATAAC M 2 1 2 1 600010 f 74 goat 19_53146628 19 53146628 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320766655 Affx-986698102 AX-385254003 19 53146634 AATGCAGAATATTATGCAAGTGGAACTTAAAATGG[C/T]ATTCTTAATCCTGTTTGTCCAGTCATAACGGACCT Y 2 1 2 1 600010 r 74 goat 19_53146634 19 53146634 Ancestral_priority_1043 ancestry 0.728 recommended IMAGE 10K 10K ancestral 320763575 Affx-986698104 AX-385251430 19 53146671 TTCTTAATCCTGTTTGTCCAGTCATAACGGACCTA[C/T]GATCACATTCACGCATCACATTTCAGCTGGACAGC Y 2 1 2 1 600010 f 74 goat 19_53146671 19 53146671 Ancestral_priority_1043 ancestry 0.724 recommended IMAGE 10K 10K ancestral 320766662 Affx-986698106 AX-385254010 19 53146721 ATCACATTTCAGCTGGACAGCCAGTCACCAGCTTC[A/G]TGAAGCCCAAACACGTTGCTGTAAAAGGGCTCTAC R 2 1 2 1 600010 r 74 goat 19_53146721 19 53146721 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 320787984 Affx-122957597 AX-385275005 19 53199189 AAGAGCGGGGACAGCTTTCGAGTCTCTCAAGAATT[A/G]TAATAAATGTTTGAAATTAGTCATTACGGTGTTTG R 2 1 2 1 201000 r 74 goat snp37959-scaffold470-211008 19 53608888 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434941 Affx-122933861 AX-123305281 19 53264847 CCTGGGTTTTGAAAGGCAAACTGCAGAGGATGTCA[A/C]TGCGATGGGAATGGAAAGATGCTGCTATGAAGGGC M 2 1 2 1 101000 f 74 goat snp37958-scaffold470-145350 19 53673742 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444156 Affx-122926788 AX-123314493 19 53293693 TCTTCCTTTCGGTTCAGAGAGGACGGCTGTGAATA[A/C]TGAGAATGAGAAGGGAGTGGATATGATTAAAGCTG M 2 1 2 1 101000 r 74 goat snp37957-scaffold470-116504 19 53702493 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399129 Affx-122960666 AX-123269484 19 53343126 CAATTCAGAAATAAAGTGATTAAATTCCAAGTTCT[C/T]GTTAGACCAAGTTAGTTTCATCAAGAAAGCTACGG Y 2 1 2 1 101000 r 74 goat snp37956-scaffold470-67071 19 53728122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443433 Affx-122927363 AX-123313770 19 53389065 GATTTCTATTTGAAACTGTTAGGAAACTCATGATG[A/C]CTTTAGACCAGACAGGGGATGTCAAATGGAAATTA M 2 1 2 1 101000 f 74 goat snp37955-scaffold470-21132 19 53772498 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417009 Affx-122947979 AX-123287357 19 53424418 CAAGAGGCCTCAGGTCTCGCTGAAAAGCAGGACTC[A/G]TCGCTCAATAAGCCCAGCGGTGTTAATTAGGGGCA R 2 1 2 1 101000 r 74 goat snp3302-scaffold1101-14122 19 53808199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415385 Affx-122948755 AX-123285734 19 53470011 GGTTCTTGCCCAGTCCTGATGGGGCTGAGCCCAGT[A/C]GGTGCGGGGCTACCAACTTGACCCTTTAACTCGAA M 2 1 2 1 101000 r 74 goat snp3303-scaffold1101-59715 19 53854322 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410716 Affx-122952719 AX-123281066 19 53557328 ATGTAAAGAGGGCCTGTATATGCAGCCCCATGCCA[A/G]GGTTCTAGAGAACACACAAGAGGGAGACACAGGAA R 2 1 2 1 201000 r 74 goat snp3305-scaffold1101-147032 19 53940913 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409843 Affx-122952935 AX-123280194 19 53593122 GCAATGCTGTGAAAGTTATGGACGCAGGAAAACCC[A/G]AGGTTACCACAAGTTGCTCATCATATCCCTGCCCT R 2 1 2 1 101000 r 74 goat snp3306-scaffold1101-182826 19 53976056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427990 Affx-122939174 AX-123298333 19 53629883 GAAGCATCGTTCCTCCTTCTGTCTTTGCCTGTTTC[A/G]TTGTCAGCACACTGATGGAGAAGCGATCCTTCATC R 2 1 2 1 201000 r 74 goat snp3307-scaffold1101-219587 19 54013178 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430871 Affx-122937413 AX-123301212 19 53667714 TTGGTCAGATGGGTTCAGAAAACGGATTGAAGAAA[C/T]GGCCCTTCTTCTTCTCCTCCAGTAAACATGTGAAG Y 2 1 2 1 101000 f 74 goat snp3308-scaffold1101-257418 19 54051031 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419783 Affx-122945857 AX-123290131 19 53699137 CTTCATGGTCTCTGTCACAGCCCCTAAGAGAGCCA[C/T]GAAATGTGTCTGCTACAGTTGAGAGAAGCCAGATA Y 2 1 2 1 201000 r 74 goat snp3309-scaffold1101-288841 19 54082476 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397440 Affx-122962114 AX-123267795 19 53749381 CTACCCGAGCGAGGGTGGGGGATGAAGCCGTTTGA[A/G]TTTGTTGCAAAGAGTGGGGGCAGGAAGGGGAGTGA R 2 1 2 1 101000 f 74 goat snp3310-scaffold1101-339085 19 54132632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430869 Affx-122937415 AX-123301210 19 53804425 AAAAAGTCAGACACGACTTAGCGACTGAACAGCAA[C/T]GAGGGCCGTGCAAAGAAGGGAAGAAAGCTGCATAG Y 2 1 2 1 201000 r 74 goat snp3311-scaffold1101-394129 19 54187504 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434199 Affx-122934862 AX-123304540 19 53877142 TTTCACTTTGGGGTTCTTCTGCATCAAAAAGTAAA[C/T]GGTAGTTAGAATGTCCTCAAAGTCTGGGAAGAAAA Y 2 1 2 1 201000 f 74 goat snp3312-scaffold1101-466846 19 54260496 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426920 Affx-122940440 AX-123297265 19 53993390 GCCGGGCACATTTATGGATTTATAAATACACCCAC[A/G]TGGTTCCCAGGAACCTCTCTCTTCTGCCTCATTGT R 2 1 2 1 101000 f 74 goat snp3314-scaffold1101-583094 19 54377341 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383956 Affx-122972950 AX-123254314 19 54041645 TTAGAAAGTGATCTGCAATGCAGTTCTGCCACATT[C/T]GGGAAGGTTTTCTAATTTTGAAAAACAGTAGCCTC Y 2 1 2 1 101000 f 74 goat snp3315-scaffold1101-631349 19 54423615 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272968 Affx-1111833144 AX-519546652 19 54050270 ACAACTTCACAGCACCGCCAAGCTAGAGGGACCTC[A/G]CCCTGTAATCCCTTGTGTTTACACGCCTTGGAAAT R 2 1 2 1 101000 r 74 goat 19_54050270_AF-PAKI 19 54050270 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38408595 Affx-122953650 AX-123278946 19 54082965 AACAATTATCTACAGCAGAAGTCTTCCTGCCTCAG[G/T]GGGTGGAGCCCAGCCACATTCTTTAAGAGTGCTAT K 2 1 2 1 201000 r 74 goat snp3316-scaffold1101-672669 19 54462339 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452052 Affx-122920883 AX-123322385 19 54127328 GTGGTCCTCATGCCTGGCTGCCCATTTGAATCCCA[C/T]GGGAGCTTTAAAAATATTCCAATACCTGTCTCACC Y 2 1 2 1 201000 f 74 goat snp3317-scaffold1101-717032 19 54506749 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387593 Affx-122970258 AX-123257951 19 54158561 AGGCTTAAAGAGGATGTCATGAAATATTTCCTTCC[G/T]AACATTTCTTCTCCCCAGAGACCATCACTATGACC K 2 1 2 1 101000 r 74 goat snp3318-scaffold1101-748265 19 54538398 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431073 Affx-122936631 AX-123301414 19 54256577 ATTTGAAGGTTCTATATTTGAAACCTAAGTAGTTG[C/T]TATTCTAATAGACCTAAACCGAACTTTTTCCCTGT Y 2 1 2 1 101000 r 74 goat snp3320-scaffold1101-846281 19 54635373 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420084 Affx-122945108 AX-123290432 19 54298562 CGACCTCTGTGAGGCCCTTCCACAGGTACCAGGCC[A/G]TCAGGCAGTGAGGATGGACTCATTTTCCCTTGCTT R 2 1 2 1 101000 r 74 goat snp3321-scaffold1101-888266 19 54677285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380595 Affx-122975257 AX-123250953 19 54409804 TTCCTAACGCCTCTTGGACCAGTAGGCTTTGGAAG[C/T]GGGGTAGAATATATATGAGTCTAGAGTCCCCTGTG Y 2 1 2 1 201000 f 74 goat snp3323-scaffold1101-999508 19 54788477 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763583 Affx-986698112 AX-385251436 19 54437895 TACATAGGGTGCTGAGAACTTCGTAGATGGAACGA[A/G]AAGGAAAAGTAGAAGAAGGTCTGAGAAGGTAAGCA R 2 1 2 1 600010 f 74 goat 19_54437895 19 54437895 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 38421279 Affx-122944739 AX-123291626 19 54465175 GCATAGATTTCTCGCCTTGAAACGGGCTAGTTTCT[A/C]TGTTTTGCTTTTTTTAATAGGGAAAATGTTTAAAT M 2 1 2 1 101000 f 74 goat snp3324-scaffold1101-1054879 19 54839623 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380600 Affx-122975254 AX-123250958 19 54504863 TGAGAGCCCGGAGCAACAGAGCAGAGGTGAGGCTG[C/T]GTCCTCACCCCTTAATCACTGGGCCAGAAGCCCTG Y 2 1 2 1 101000 f 74 goat snp3325-scaffold1101-1094567 19 54878345 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402794 Affx-122958290 AX-123273147 19 54552986 TTGTGTCCGAGGGGCTGCCCACAGAAGGCTTAGAA[A/G]TCCCCACAAAGCCAGTTTGTTCTTAAAACAGTACC R 2 1 2 1 202000 f 74 goat snp3326-scaffold1101-1142690 19 54926349 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410836 Affx-122952626 AX-123281186 19 54608744 CACACAAGCCCCCAAAACACACTTCAGGATCCCCA[C/T]TGACCACAATCTACCTCTTGGGATTGCTATGTGGG Y 2 1 2 1 201000 r 74 goat snp3327-scaffold1101-1198448 19 54979742 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793477 Affx-122961789 AX-385280454 19 54662967 GTAAGATATAACCAGGCTGACGAAGGCTGTAAGAA[C/T]TGTGACTGAAGTGAAATTCCAATGGATACAGAAGA Y 2 1 2 1 101000 r 74 goat snp3328-scaffold1101-1252671 19 55033071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428399 Affx-122938948 AX-123298742 19 54699838 AGGGGTCGCCAGCAGGAGCCAAGGTGTGACGCAGC[A/G]GCTGAAAAGGTTGTGCTTGGTAGGCCAGGTGAACA R 2 1 2 1 101000 r 74 goat snp3329-scaffold1101-1289542 19 55070138 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275153 Affx-1111834731 AX-519548732 19 54751570 CCCCATCACCTAGAAGTCAGAGGGAGCAGAGGGCC[A/G]TGGGGGGGACTGCAGGGAACTCACCTCGCAGGAAG R 2 1 2 1 103000 f 74 goat GoatD01.050259 19 54751570 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38401009 Affx-122959686 AX-123271362 19 54763563 GAAAATTCTATGCAAAGTAAATGCAGAAGAACACC[C/T]CAAAAACACACATCATGCAAATTTCCTGAAGAAAA Y 2 1 2 1 101000 f 74 goat snp3330-scaffold1101-1353267 19 55133864 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406878 Affx-122955641 AX-123277229 19 54801193 GACCCCATACAAGCCACAACCCCTTGAGCATGAGT[A/G]GAAGTGGGGAGGGCCATGCGGCGCAGGAGCCACCA R 2 1 2 1 103000 f 74 goat snp3331-scaffold1101-1390897 19 55170937 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397303 Affx-122962321 AX-123267658 19 54841709 GCTCAGCCCCAGTGCTCCTGCCCTCGGCACTTAGA[C/T]GTGTGGTTACTGCGCTCGGACTGTGAGGATGCCAG Y 2 1 2 1 101000 r 74 goat snp3332-scaffold1101-1431413 19 55211338 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400912 Affx-122959733 AX-123271265 19 54879906 CCGTGTGGCCCTGCATCCGTATATGAGCAATGTAC[A/G]CAGGTATGCCCCAGCTTGCTTGATCTCTCAGTAGC R 2 1 2 1 201000 f 74 goat snp3333-scaffold1101-1469610 19 55248736 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769348 Affx-122975950 AX-385256519 19 54941602 TGGGGGGGTGGCAGATACAGCAATGAACAAGTAGA[C/T]GAAAATCCTTCCTCTCTAGGAGCCCCCACTGTAGT Y 2 1 2 1 101000 f 74 goat snp3334-scaffold1101-1531306 19 55310023 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393046 Affx-122965626 AX-123263403 19 54994116 TTAAGACTGCTTACCCCGGTGTCCTGGTGAATTAC[A/G]TGAGCAAACTGAGTTTTTCCTAGGCTAAGGGTACA R 2 1 2 1 101000 r 74 goat snp3335-scaffold1101-1583820 19 55362719 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795230 Affx-122931567 AX-385282188 19 55035940 TTCTTCTTATAGGCTTTACTTTTCTAAAGAGCAGA[A/G]TTTATGTTCACTGCAAAGTTGAGTGGAAGGTGCAG R 2 1 2 1 101000 r 74 goat snp3336-scaffold1101-1625644 19 55404643 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452083 Affx-122920861 AX-123322416 19 55072212 CATTTCTCTCCTTTGTCCCCCCTCCATCCCACATC[G/T]CTGGTCCAGGGAACTTCAAAAACCTGCTTTGTGGC K 2 1 2 1 201000 r 74 goat snp3337-scaffold1101-1661916 19 55439691 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383638 Affx-122972535 AX-123253996 19 55117182 TGGAGGGTAAATGAAGTACGAATAGAAACAAAGAA[A/C]GCTCATCAAGCAGCCAGCAAGTCTACTGGCAGCCA M 2 1 2 1 201000 f 74 goat snp3338-scaffold1101-1706886 19 55484745 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417919 Affx-122946727 AX-123288267 19 55181290 TGACTGGTGGATGAACATGTTTTGGACAAACCAGG[A/C]AAGGCAGAGAGAAAGAGAACAAGGGGCAAAGAAAG M 2 1 2 1 101000 f 74 goat snp3339-scaffold1101-1770994 19 55549012 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394840 Affx-122964782 AX-123265195 19 55269747 AACGTAAGCTTCATGAGGTGGGAACTAGTTTATTG[A/C]GGCTGTATCTGCAATGCTTGAAACAGTTTCTGACA M 2 1 2 1 101000 f 74 goat snp3341-scaffold1101-1859451 19 55639007 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443628 Affx-122927294 AX-123313965 19 55336459 CCCTCTGGAGATGTGTTCTACATTGGGGTATACCC[A/G]TTTTCCCATCTATTTAAAGATGTTTTCTGTATTAG R 2 1 2 1 303000 f 74 goat snp3342-scaffold1101-1926163 19 55704393 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404064 Affx-122957150 AX-123274416 19 55355399 TCCAGGGGTCAGAGGTCAGGGATACATCATTCTGC[C/T]CCAAGTAGTCAGATGTGGAGCTAGAACTTGGCCGC Y 2 1 2 1 201000 r 74 goat snp43334-scaffold5775-11915 19 55728018 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394255 Affx-122964728 AX-123264610 19 55399362 TCTGTCTTGGGGGGAGAGAGTTCTAAACACACATT[C/T]ACCTGCAGTCGCAGCTGGGATCAGCGTCTGGAAGA Y 2 1 2 1 101000 f 74 goat snp43335-scaffold5775-55878 19 55772313 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410497 Affx-122952191 AX-123280847 19 55465558 AAGACAGCCGCTAGCTGAGAACCACTGCTGATAAA[C/T]GCATAGTGAAATAAACACACTCCCAAAAGAAGCTT Y 2 1 2 1 101000 r 74 goat snp43336-scaffold5775-122074 19 55836206 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445070 Affx-122926219 AX-123315407 19 55508588 CACAGACCGGACTCAACACCACTTCCCAACATGCA[C/T]GCTACATCACTGCACAGACACCCTCCTCACTGACC Y 2 1 2 1 101000 f 74 goat snp23340-scaffold2331-23392 19 55878514 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453957 Affx-122919468 AX-123324290 19 55552326 AATTTCACGCTTAGCAAACCATCCCCTGATTGTAA[C/T]ATGGCTTGACATCCAGGACAATACATCAGTTTTGT Y 2 1 2 1 201000 r 74 goat snp23341-scaffold2331-67130 19 55922261 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794324 Affx-122975108 AX-385281288 19 55591340 AAGTCTCTGTATTGACTCATCTACCATAGTGGGTG[C/T]GCTTTCTTATTGGATTTTAGTGAAATGTGACCACA Y 2 1 2 1 101000 f 74 goat snp23342-scaffold2331-106144 19 55961243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274390 Affx-1111834172 AX-519547983 19 55612977 TTTTTGCTGGGTGCCTGTGACCT[A/G]TTCCCCAACGTCAGCAAGGCAGGCGCAAGGGTCTG R 2 1 2 1 102000 r 74 goat GoatD01.023291 19 55612977 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38442460 Affx-122927947 AX-123312797 19 55630078 ACCCTAAGTCACTGCCCCATTAATATTTCCATTTT[A/C]TTCCCTCTCTTGAATGTATTCAGTCTGGCTGTGAA M 2 1 2 1 303000 f 74 goat snp23343-scaffold2331-144882 19 56001308 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779246 Affx-122955164 AX-385266350 19 55684856 TAGCCTTCAAGGATGCAAAGCCAAGGTCAAGAGTG[A/G]ACACCCTGGATGTCCTTAAGGTTTAAGTGAAGCTG R 2 1 2 1 101000 f 74 goat snp41275-scaffold537-53500 19 56065023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380410 Affx-122975315 AX-123250768 19 55721350 TGGCATAACATCAAATCAGGTAAGGTGTTATTGGT[A/G]CAGTTGTGAGGGGTGACTTCTGTCAGGCTCCGTGA R 2 1 2 1 201000 f 74 goat snp41276-scaffold537-89994 19 56101551 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405163 Affx-122956941 AX-123275515 19 55758384 AATATGTGATTCCAAATATGGCCACAAGGTGGAGA[C/T]AGACAGCTGTCCAGTCCTCCTTCCTCGCTCCAGTG Y 2 1 2 1 101000 f 74 goat snp41277-scaffold537-127028 19 56138340 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452814 Affx-122920749 AX-123323147 19 55863197 CCGCTCGGAACCTCAAAGCTAAAAGAAAACTCTCC[G/T]ATTGGCCAGACTGCCTGTTATCACTCACGCACTTG K 2 1 2 1 101000 f 74 goat snp41279-scaffold537-231841 19 56239410 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771259 Affx-122931551 AX-385258417 19 55923470 TTATTAATAATTGAACTTTACGAGCACGAAGATAG[C/T]AGAAAGCTCGCTGAATTCACCTGGCTTGTTTCATC Y 2 1 2 1 101000 r 74 goat snp41280-scaffold537-292114 19 56304699 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406824 Affx-122955681 AX-123277175 19 55979204 AAGATAGACGGTGGTGACTGTCCTGGGCTTGCAAA[C/T]AAGGACCACAAGGACTGGAAAGATGCTTCTCAACA Y 2 1 2 1 201000 r 74 goat snp41281-scaffold537-347848 19 56437211 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442685 Affx-122927886 AX-123313022 19 56040942 GCTTAGACAACATTGAGCTCTTCTTAAAGATTTTG[C/T]GGGTGACATCCACCGCCAGAATTTGAGGGTTTCCT Y 2 1 2 1 102000 r 74 goat snp41283-scaffold537-409586 19 56499136 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435048 Affx-122933748 AX-123305388 19 56072642 CATTTCTTGCAGCTGTGATGCTGAGTCTAATAAAA[C/T]GGGTCCTGCTTGAACATTTGAACACAGACTCTACC Y 2 1 2 1 102000 f 74 goat snp41284-scaffold537-441286 19 56530906 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446679 Affx-122924754 AX-123317015 19 56110593 CTGGGTCCTGGTAGCCTTCTATCTTAGGTTCTTTG[C/T]TCTTAGGTTAAGAAATAGGTTCTCCTCTTGTCCCC Y 2 1 2 1 101000 f 74 goat snp41285-scaffold537-479237 19 56568791 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388622 Affx-122969133 AX-123258980 19 56158296 GTGGAGTTCAGGCCAGGAGGAGTGCAGGACCAGGG[C/T]GCTGAGGGGCTAGGGCACCTCTAGGGTCTGTGACC Y 2 1 2 1 103000 f 74 goat snp41286-scaffold537-526940 19 56615373 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435856 Affx-122932806 AX-123306195 19 56192301 AGTCTCAGGGAGGCTCAGTGTTCTACCTAGCGTCA[C/T]GGCCAGAAGTCAGGATTTGTACCACATTCTAGCTA Y 2 1 2 1 202000 f 74 goat snp41287-scaffold537-560945 19 56649374 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767130 Affx-122974440 AX-385254416 19 56242886 ACGATATCGAGGTGGGAGGTTATCTAGCATTGCCC[A/G]TGGCTCAGTGTAATCCTTGTATGAGAGGGAGGCAG R 2 1 2 1 101000 f 74 goat snp41288-scaffold537-611530 19 56700180 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798945 Affx-122951245 AX-385285875 19 56273823 ATACGGCCATCAGGTTAAAACAATTTTCCGCTGGC[A/G]TGTCGCTGACTCTCCGTGTACCTCTGCTTATTGGA R 2 1 2 1 101000 f 74 goat snp41289-scaffold537-642467 19 56729410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413539 Affx-122950611 AX-123283888 19 56308125 AGGGCCAAACTTCCCGGGCACCTCTGCACTTCTGC[A/G]CTCCTCCCGAGAAAAGGGGTACATCCTCTGTAATT R 2 1 2 1 201000 f 74 goat snp41290-scaffold537-676769 19 56763774 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791114 Affx-122939501 AX-385278109 19 56363230 GGGTACTGTTATGTACCCAAGGTTTACATTTCTTG[C/T]AACTTTTTTCTAAAGCTCTGGATCTATTTAAGGAA Y 2 1 2 1 101000 f 74 goat snp41291-scaffold537-731874 19 56814424 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438640 Affx-122930906 AX-123308977 19 56434454 TCCAACAACATGTGGGATTAGAAACTGCTGTTGGA[C/T]ATAGCTGTGTGCGAGGTCAACAGGTTGGGAGCTAC Y 2 1 2 1 201000 f 74 goat snp41293-scaffold537-803098 19 56886222 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768475 Affx-122939107 AX-385255655 19 56483778 AATCACAATGAAAGCCCAACAGCACTCACGGGAAC[A/G]GGATGAAAGTTTAATTACATGGTGTGGCTAAGCTG R 2 1 2 1 101000 f 74 goat snp41294-scaffold537-852422 19 56935703 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453003 Affx-122920110 AX-123323336 19 56518860 TGTGCTGAGGGTGAGAAACTCTGCCTTAAACCAAC[A/G]TTCGTCTTTGAGAGCCATGCCCAGACCTGAACACA R 2 1 2 1 201000 r 74 goat snp41295-scaffold537-887504 19 56969648 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272922 Affx-1111833145 AX-519546609 19 56556815 CCCTTCTTAGCCGCCAGCTCAGAGCGGATGAAATC[A/G]AGGGCCCTGTTCTGGGGAGAGAACACTGAAAATCC R 2 1 2 1 102000 f 74 goat 19_56556815_AF-PAKI 19 56556815 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468277264 Affx-1111835824 AX-519550769 19 56576054 TTTTAAACTCAGCTCTGTGGTTTCCAACCTGGGAT[A/G]ATTATTCTGTCCCTTCCCTCCCACCCACCAAGGAC R 2 1 2 1 101000 f 74 goat Random2.2K-1812 19 56576054 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402211 Affx-122959161 AX-123272564 19 56597243 TATGGGGTAGGCACCGCTATTATCCCCTTTTTCCA[C/T]TGTAGACTCTGAGATGCTGAAGGGTTACAGAGAGA Y 2 1 2 1 101000 r 74 goat snp41297-scaffold537-965887 19 57048456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799527 Affx-122952885 AX-385286457 19 56631187 CTCACAAACTCAAAATTCTTTTTATGATCCTAAAC[A/G]TTAGACTAAGGATTTGGCAGGCTGTATCAATAAAT R 2 1 2 1 101000 f 74 goat snp41298-scaffold537-999831 19 57082258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423773 Affx-122942836 AX-123294119 19 56689369 GAGAGGAAACTAAAATGACTAGATAAAACCATAAC[G/T]CACCCTGGCTTCAACAGTTACCAGCACATGGCCCA K 2 1 2 1 101000 f 74 goat snp41299-scaffold537-1058013 19 57140422 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397342 Affx-122962301 AX-123267697 19 56779771 AGTGTCTAGAAGCATTTACTTTTTTTGGCCCTGTC[A/C]CATGGCAATGTGGGATCTTAGTTCCCCAACCAGGG M 2 1 2 1 101000 f 74 goat snp41300-scaffold537-1148415 19 57223233 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420593 Affx-122945256 AX-123290940 19 56808545 TATAAAAATGTTTATGGAGCCTTCTGGGAGGGAGA[C/T]GGACATACTTGCATCTTGTTACCTACTTTAATTCA Y 2 1 2 1 101000 r 74 goat snp41301-scaffold537-1177189 19 57251101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403460 Affx-122957720 AX-123273813 19 56915432 AAGCCTCAGTGATTGCAGGCTTGGCTGACACTAAT[G/T]ACTCCCTCATGAGAAACCCCCAGCCAGAACCAGCC K 2 1 2 1 201000 f 74 goat snp41303-scaffold537-1284076 19 57358857 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773658 Affx-122923741 AX-385260798 19 56974276 TTCTGGTCGACCTATTCCCCTACTCACCTATTTAA[C/T]GGTAAATTTAAACTTGCAATTGAATATCCTTTCAT Y 2 1 2 1 102000 f 74 goat snp41304-scaffold537-1342920 19 57417511 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436659 Affx-122932475 AX-123306997 19 57016176 GTGGAGTACCTAACAGAGTCTGGCCAGCATACAGT[A/C]GGCATTTAATAGATATGAGTTGCATCAACAAATGT M 2 1 2 1 201000 r 74 goat snp41305-scaffold537-1384820 19 57458272 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418912 Affx-122946091 AX-123289260 19 57067259 GAAACCGTGTTTTGCAAAATGAAACCGATGCAGAC[A/G]TAGCTTTAAGTGGGTTGTGAATTTGGAGAAATTTA R 2 1 2 1 101000 r 74 goat snp41306-scaffold537-1435903 19 57509233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424747 Affx-122941654 AX-123295093 19 57107505 CGCCTCTAGGAAGTGTTCCTTCTGCTCAGAGAACC[A/G]CTTATCCTTCAAGATGGTTCAGGCATCTCTTTTGA R 2 1 2 1 101000 r 74 goat snp41307-scaffold537-1476149 19 57546948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400151 Affx-122960696 AX-123270506 19 57154302 CTTCAGGAACTTTTCTCAACTCACAGAAATATCAG[C/T]AAGATGCTTCTGAAGGAGGCATGTGGGACTTTGAT Y 2 1 2 1 101000 f 74 goat snp41308-scaffold537-1522946 19 57594286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403057 Affx-122958528 AX-123273410 19 57194569 CTTGGAGGAAATCTCTGAAAGAGAAAGAAAAGGAC[A/C]AGAAGCTATCAAGACTGAGGAGCCTTGACCTCTGA M 2 1 2 1 201000 r 74 goat snp41309-scaffold537-1563213 19 57634395 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434850 Affx-122934374 AX-123305191 19 57294832 CTGAAGGAGGACCCCCAGGGCTCTGATTAGATGAG[A/G]TGGTGGTCTTCCGTGGGCCCAGCCTGGGAAGGGCC R 2 1 2 1 201000 r 74 goat snp41311-scaffold537-1663476 19 57733971 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416181 Affx-122948257 AX-123286530 19 57352569 ATCTGCAAAGAAGAGGAAAGGGTAAGAGCAGAAGA[C/T]GAGACCAGCAACCCACAATCATTAACCTGGAGCAG Y 2 1 2 1 101000 f 74 goat snp41312-scaffold537-1721213 19 57791511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405286 Affx-122956853 AX-123275638 19 57383703 ACTGACAGACTTGTCAGGCTGCGCTCGACCCTTTG[C/T]GTCTTCTCTGAGCACTCCCCTGTCTTCTGCTCTTC Y 2 1 2 1 101000 r 74 goat snp41313-scaffold537-1752347 19 57822906 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400641 Affx-122960366 AX-123270996 19 57420837 CTGCACTGGCTGGTAGATGTTTTACCATCTGAGCC[A/G]CCAAGGAAACTTGAACAGTGTAAATAGGCCTTTTC R 2 1 2 1 103000 r 74 goat snp41314-scaffold537-1789481 19 57860272 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433036 Affx-122935767 AX-123303377 19 57453571 AGTCACTGTGCCTGTTCTTGTTAAGTCACTAAGTC[A/G]TGTCCAACTCTGCAACCACACAGATTGCAGCACAC R 2 1 2 1 303000 r 74 goat snp41315-scaffold537-1822215 19 57893449 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793848 Affx-122942286 AX-385280817 19 57518487 ATTGGAAAATGATGTGCCGGTCTGGGAATGTCCTC[A/G]TCACTTCTAGGGTGTTGCTTCTCCCAGACCATCTC R 2 1 2 1 101000 r 74 goat snp41316-scaffold537-1887131 19 57958826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396366 Affx-122963040 AX-123266721 19 57547622 CCCCAAAGTAAAACCTAGCAGAAGAAACTCTGAAA[C/T]GGGCCTTTCGTGGTGCAGAGAATCAGAGTATTTCA Y 2 1 2 1 101000 f 74 goat snp41317-scaffold537-1916266 19 57987749 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452607 Affx-122920488 AX-123322940 19 57579008 CCTTTGCTCTTTCCACCAAAGCCACAAAATGATCA[C/T]GACAATCACATCTCGCTCAGGTCTGTTATCCACTT Y 2 1 2 1 101000 r 74 goat snp41318-scaffold537-1947652 19 58019146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799099 Affx-122968381 AX-385286029 19 57669271 TTGTCAGTGTCTTTTCTTGTGTTTTGCATAAAACA[C/T]GGCCGATTCGATAACCCACTGGTCGATTCAATAAC Y 2 1 2 1 201000 f 74 goat snp41320-scaffold537-2037915 19 58108423 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407671 Affx-122954596 AX-123278022 19 57704005 AGAGTCAGATCCCGTTTATCTTGTTAAGAAAGAAG[C/T]GTGTATATCATATATCACAACTTTGCTTTCTAAAT Y 2 1 2 1 101000 f 74 goat snp41321-scaffold537-2072649 19 58143180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411316 Affx-122952283 AX-123281666 19 57755588 AATATTCAGAAAAGGAGCCAAGGAAAAATATTAGA[C/T]AGCAGTTCTCAGATTTATTTATTAAGCAGAGGCTT Y 2 1 2 1 101000 r 74 goat snp41322-scaffold537-2124232 19 58194891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407143 Affx-122954857 AX-123277494 19 57847280 CAGCTACTATCCCGTCAGTCTGAGATGAGCACCAT[C/T]CAAGCTGATGGATAGTCAGCCGTCAGGCCCCTTGG Y 2 1 2 1 101000 f 74 goat snp41323-scaffold537-2215924 19 58286856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771557 Affx-122972563 AX-385258715 19 57899752 CATCAGTTCATCAGCGCTGATCCTTCTTGATGAGC[A/G]TTTCTCAATCACTTCTTCCACGTTACTCTTGCCAG R 2 1 2 1 101000 f 74 goat snp41324-scaffold537-2268396 19 58339616 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428428 Affx-122938825 AX-123298771 19 57947423 ACCCCTTCTCTCCTGATTCATGGGATGAAGTCTTC[C/T]TGGGAATCATTTCCTCCTGGTTCTAGGTAAAAGCC Y 2 1 2 1 101000 f 74 goat snp41325-scaffold537-2316067 19 58387981 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437544 Affx-122931903 AX-123307882 19 57993531 TTTGCCAGCCAGCTTTGTCAAGTCCATCTTCCCTT[A/G]TAATTTTCTTCAGATAAATTAGTAGCTCATGCTCT R 2 1 2 1 102000 f 74 goat snp41326-scaffold537-2362175 19 58434309 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421488 Affx-122943915 AX-123291835 19 58028131 AGTGTCTTTGACTGTTATATGGGGAGAAGGAAACT[C/T]GCCTCACATCAGTGGTAGGAAGGTTAAATTTTCTG Y 2 1 2 1 101000 f 74 goat snp41327-scaffold537-2396775 19 58468935 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400787 Affx-122959829 AX-123271142 19 58063060 AAGAGAACTGAAAAAAACTGAAGGAAAAACAAGTC[C/T]ACTCAATAAATGGTATTAGGAATATTGGGTAACTG Y 2 1 2 1 101000 r 74 goat snp41328-scaffold537-2431704 19 58503755 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447667 Affx-122923957 AX-123318003 19 58101666 GGGAAACTGCAAGCCGAAGAATGTGGATCCAGGGA[C/T]GTCATTAGCTAAGGCTGCAAGTGCAGTCAGCCTGC Y 2 1 2 1 101000 r 74 goat snp41329-scaffold537-2470310 19 58545033 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426664 Affx-122939927 AX-123297010 19 58141280 CCGGCTGCGTTGAGAAACTGGATGCATCAGGAATG[A/C]ATAGAAGGTGGCATCTCTTGCCTGGGCGAATACTT M 2 1 2 1 101000 r 74 goat snp41330-scaffold537-2509924 19 58584612 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386144 Affx-122971402 AX-123256502 19 58197554 CTCCTGGAGATTTAATCTAGTAAATGAGGCATATA[C/T]GAAACAATATAGCATAATGTAATTACAATATAGTG Y 2 1 2 1 101000 f 74 goat snp41331-scaffold537-2566198 19 58638122 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403311 Affx-122957835 AX-123273664 19 58233524 TGGAGGGTCTAATCATCAGAGGGTTCCCGGGCTAA[C/T]GGTAGTAAGCTCTTTGGAAAACAACGCTCGATGCT Y 2 1 2 1 101000 r 74 goat snp41332-scaffold537-2602168 19 58673854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440804 Affx-122929829 AX-123311141 19 58285564 CGTGAGCTCCAGTCAGGACCACTTCTTCCTTCATT[A/G]CATCTGAGTGTGAACAATGAGCAAAAACTTATACA R 2 1 2 1 201000 r 74 goat snp41333-scaffold537-2654208 19 58726142 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795547 Affx-122964502 AX-385282502 19 58321965 TCGTCCAACTTCTGACCTAAATTTCCAGAGAAATG[A/G]TGGGTTCAGTCCTTTGAGGAAGTGCAAAACTAAGA R 2 1 2 1 101000 r 74 goat snp41334-scaffold537-2690609 19 58763175 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395516 Affx-122963874 AX-123265871 19 58353000 GAATGGCTTTTAAATGCCCAAGGAGCTCAGTCCAA[C/T]GGCAGAGATATTTGAAATATACACAAACATACAAG Y 2 1 2 1 101000 f 74 goat snp41335-scaffold537-2721644 NW_017217853.1 3348 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440858 Affx-122929251 AX-123311195 19 58386266 CTTCTTGCTAATTTCTTCATCTATAGGTCAACAGA[A/G]TAAGACTTGGTATAAAACAAAAACTCCAAGAAGGT R 2 1 2 1 101000 f 74 goat snp41336-scaffold537-2754910 19 58845239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428166 Affx-122939038 AX-123298509 19 58443286 CTGTAGAACAGACGCCGTTTCTTCGCTAGCATAGA[G/T]CCGTGGGGTTCGTTTTCCTCCTGGCTCTGTTTACC K 2 1 2 1 101000 f 74 goat snp41337-scaffold537-2811930 19 58902325 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417883 Affx-122946756 AX-123288231 19 58481174 TGAAGAGCAGGTAAAGATAGAATTGGAGAAGGAAA[C/T]GGCCACCCACGTCAGTATTGTTGCCTGGGAAATCC Y 2 1 2 1 102000 f 74 goat snp41338-scaffold537-2849818 19 58939964 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443461 Affx-122927829 AX-123313798 19 58541347 ACAGTGGGGAGAATGTTTTCAAAATAAAAATTCAA[G/T]ATGATACTGTTTTGTTTCAGTAAAAGCAAAGATAG K 2 1 2 1 101000 r 74 goat snp41339-scaffold537-2909991 19 59000084 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410196 Affx-122952578 AX-123280546 19 58579482 TGTCAAAGTTCAGGGGCAAGGAGAGACACGTGGCC[A/G]TATGTGATGCTATGATACATGCTGGCCAGAATGGA R 2 1 2 1 201000 r 74 goat snp41340-scaffold537-2948126 19 59038076 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426418 Affx-122940831 AX-123296764 19 58609425 AAGACTGCTGGAACGAAGAAATTTAATTAAAATGC[A/G]TTACTAAAAACATAACGAAGTTTTGGCATCTTCTA R 2 1 2 1 101000 r 74 goat snp41341-scaffold537-2978069 19 59068028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389108 Affx-122968569 AX-123259466 19 58667334 TTCTAACCGTTGTCCATGTGATGTTTCAAAACACT[A/G]TTGGTCTTGGATATTCTGATTCCAGGTTCAGAGCA R 2 1 2 1 201000 f 74 goat snp41342-scaffold537-3035978 19 59125786 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427160 Affx-122939625 AX-123297503 19 58749182 GCCACAGAACAATTCTGTAGAAATAAAGGGTCCAA[G/T]CCAGTGACAACTCCGAGAAGTTGGCAACACAGAAG K 2 1 2 1 101000 f 74 goat snp41344-scaffold537-3117826 19 59207375 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793401 Affx-122926233 AX-385280378 19 58785617 GAGGCATCAGAAAGAATCAGGGTGATCATTAAATC[G/T]CTGTCTTTTTAAGAAACCCATGGATTAAAAAAGTA K 2 1 2 1 101000 f 74 goat snp41345-scaffold537-3154261 19 59243845 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775632 Affx-122954388 AX-385262763 19 58832685 TCCAATATCTTCATAAGGATTTGATGATATGGGGA[A/C]ATATTTCTAATCATGGAATTCTAGCTGCTAAGAGC M 2 1 2 1 101000 r 74 goat snp41346-scaffold537-3201329 19 59290863 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418480 Affx-122946451 AX-123288828 19 58887562 CTGGAAAGTCTTCTCTATTTGAATTGTGGTGCTGG[A/C]GAAGATTTGGAGAGTCCCGTGGACCTGCAAGATCA M 2 1 2 1 102000 r 74 goat snp41347-scaffold537-3256206 19 59345836 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448197 Affx-122924239 AX-123318533 19 58918151 TTTTTATAATAAAGATCACCCAGAATAAGGTGAAC[A/G]TTACTAACCTAGGTGTAAAGAAGTCAAAACATATT R 2 1 2 1 101000 r 74 goat snp41348-scaffold537-3286795 19 59376198 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423710 Affx-122942884 AX-123294056 19 58947281 TGAACCTAAAAGAATCATGGTTAAAATAAGGTTTT[A/G]TTTTCTCCAAAGAAACACAAAATGGATATTCTATG R 2 1 2 1 101000 r 74 goat snp41349-scaffold537-3315925 19 59405763 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445413 Affx-122925378 AX-123315750 19 58991102 CCAGTTTGTCAGAATACCTTGAGAGCCTATCTTTC[A/G]AAGTATTTCCAGACTGTGACCTCTTCTAACCACCT R 2 1 2 1 101000 f 74 goat snp41350-scaffold537-3359746 19 59449933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788750 Affx-122946440 AX-385275766 19 59049860 GTCAATAATCTTTCCTGGCTTCCAACTTTGTTCAC[A/G]CCATGATGGCTTCAGATCGCTTCCTGAATGAATGA R 2 1 2 1 101000 f 74 goat snp41351-scaffold537-3418504 19 59508543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443328 Affx-122927443 AX-123313665 19 59082345 AAGGCGGGGCTGGTCTCCAAACTCTATGACTTACA[C/T]GTTATAATATTGGGGTAAATGCCTTAGATTTTTTA Y 2 1 2 1 101000 f 74 goat snp41352-scaffold537-3450989 19 59540901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601401 Affx-1002479697 AX-413835822 19 59096334 CCCGTTGCTTTAGTTTTGGTTAGTGGAGACTTGAG[A/G]ACACTGTCCAGCGAAGGGTCAGCGCTGGCATTTTG R 2 1 2 1 400000 f 74 goat 19_59096334_RH-map 19 59096334 G A Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38398688 Affx-122961864 AX-123269043 19 59112685 CTGATCAAGAATTAAGAACGTCAGGGCTTTCCTGG[C/T]GGTTCCGTGGCCAAGAGCCTGCCTGCCAGTGTGGG Y 2 1 2 1 101000 f 74 goat snp41353-scaffold537-3481329 19 59571373 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463606662 Affx-1110069948 AX-515088132 19 59138035 TGGGGTAACAGTAACAACGGAAGAACAGTTTATTC[A/G]TCTGTTGCAAAATATAACTTTCTGATTTTGTTCAG R 2 1 2 1 101000 f 74 goat 19_59138035_AF-PAKI 19 59138035 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320785250 Affx-122969437 AX-385272295 19 59144812 CTTTCTATGTGGATAAATGACCCTGAGATACTACA[G/T]CATACACAACTCTGTGTACTATCTAGTGGATAAGT K 2 1 2 1 201000 r 74 goat snp41354-scaffold537-3513456 19 59603845 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601403 Affx-1002479698 AX-413835824 19 59165645 AACCCAGGGATGGAACCAACATACAGCACACACAT[A/G]ATTTTATTTACCCAAGCCAAAAAAAAAAAAACAAA R 2 1 2 1 101000 f 74 goat 19_59165645_RH-map 19 59165645 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601405 Affx-1002479699 AX-413835826 19 59189555 GAATCCATAGCAAAATGGTAGACAGCCCTCTCCCT[C/T]GCACACTGGACCCCACAGAGTGTAGAACTTGGTTT Y 2 1 2 1 102000 f 74 goat 19_59189555_RH-map 19 59189555 T C 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38444339 Affx-122926725 AX-123314676 19 59199709 TTTACATCAACAGTGTAATCGTCCCCTATGAAAAG[C/T]GCCCCCCTCTGCAAAGCTAGTTAATAAAGCACTTG Y 2 1 2 1 202000 f 74 goat snp41355-scaffold537-3568353 19 59659296 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601540 Affx-1002479700 AX-413835952 19 59226004 ATGTAAAACTATGTAATGTCTGTCATTTTAATAAA[A/G]TCTCTGTTACAGCCAATACATCTGTTAAGAACACT R 2 1 2 1 101000 r 74 goat 19_59226004_RH-map 19 59226004 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38410411 Affx-122952418 AX-123280761 19 59230017 AAGATTTCAACATAGTAACCCTCTCACCCTCATCC[A/G]TATTACTTAATTTTTATTCCTTTGAAGACAATCAG R 2 1 2 1 103000 f 74 goat snp41356-scaffold537-3598661 19 59687855 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389011 Affx-122968642 AX-123259369 19 59263950 AAAAACCTACTGCTAACTTTTGTTGAGTACTAATT[G/T]TTGACCAGGTACTACTTAAGTTCCTTACATGTATT K 2 1 2 1 201000 r 74 goat snp41357-scaffold537-3632594 19 59721095 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601542 Affx-1002479701 AX-413835953 19 59266699 TGACCATCTCGTTAAATAAACTATAGCTGTTCTGT[C/T]CCAAAAGTAATGCATCTGACGATGAGATTTCTATC Y 2 1 2 1 101000 r 74 goat 19_59266699_RH-map 19 59266699 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38446276 Affx-122925667 AX-123316612 19 59297708 GGCGCTTCTGCTGTGTCCACTCACTAGACCTAAGA[C/T]GTCTTTGCTGACACCTTGCCTCTTGTCTTCTACGC Y 2 1 2 1 101000 f 74 goat snp41358-scaffold537-3666352 19 59754860 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445226 Affx-122925502 AX-123315563 19 59333897 CCTGGGTCAAGTTGCAGCAGGAGCCGTGGCAATAC[A/G]CGGGAATGAGTCAACGCAGGATTAGAACAAAGAAT R 2 1 2 1 101000 r 74 goat snp41359-scaffold537-3702541 19 59792443 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277390 Affx-1111835825 AX-519550894 19 59335691 ATACATCATTTATTCCACATTCACTTTATACCAGC[A/G]GCTTTGCAAACATAGATTGCATTATTGAACAATTA R 2 1 2 1 101000 r 74 goat Random2.2K-1814 19 59335691 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418211 Affx-122947056 AX-123288559 19 59387709 GATTGGTTAGAGAGAAAGAAACGCTGGGTGGTAGG[C/T]AGCCGTCACAGTTAAGATTCAGGACTACATTTGGG Y 2 1 2 1 201000 r 74 goat snp41360-scaffold537-3756353 19 59846743 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601411 Affx-1002479702 AX-413835832 19 59391114 CAAAAGCATCAATCCTTCAGTGCTCAGCTTTCTTT[A/G]TAGCCCAACTCTCACATCCATACATGACTACTGGA R 2 1 2 1 103000 f 74 goat 19_59391114_RH-map 19 59391114 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601413 Affx-1002479703 AX-413835834 19 59428375 AAATTCAGGAATAGTGTGTCCCAAGCTCAGTGGAC[C/T]CAAAGCCCTGTGGGTTTATTGCATGCTTTAGGAAC Y 2 1 2 1 101000 f 74 goat 19_59428375_RH-map 19 59428375 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38440982 Affx-122928979 AX-123311319 19 59436632 GGAGGAGGAGGAGACTCGTGGTACTCAAGAGGGAC[A/G]TGGATATGGAGGTGATACCCTGGGATGTGGGTTGC R 2 1 2 1 201000 f 74 goat snp41361-scaffold537-3805276 19 59895859 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601415 Affx-1002479704 AX-413835836 19 59466905 ACTGCAAGGAGATCCAACCAGCCCATCCTAAAGGA[A/T]ATCAGTTCTGAATATTCATTGGAAGGACTGATGCT W 4 1 2 1 303000 f 74 goat 19_59466905_RH-map 19 59466905 A T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38449189 Affx-122923521 AX-123319524 19 59472869 CTCGTCATCAGCTCAGCATTACTAGGTCTTCTGCA[A/G]TATGAGGATGAAAATGCATCTGGACAAAAGATATT R 2 1 2 1 101000 r 74 goat snp41362-scaffold537-3841513 19 59932464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383892 Affx-122973120 AX-123254250 19 59504167 CTCAAGCATCTTTGTAACACATGGAAATGTCCATA[C/T]GAGACAAACAGATGTAGAGAACAGCAGATCATGCT Y 2 1 2 1 101000 f 74 goat snp41363-scaffold537-3872811 19 59963535 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796447 Affx-122936510 AX-385283397 19 59540780 GGATCTTAAATATTTGAAGTTTCATCAGCAGACAG[C/T]AGATTTAGTTGGAACTACAGGTACAGTGAGGATAG Y 2 1 2 1 101000 f 74 goat snp41364-scaffold537-3909424 19 60000449 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435371 Affx-122933582 AX-123305711 19 59572607 ATTATTACTGGAGTGAAATGACAGAAATCAGCTCA[C/T]TCAGATCTTTGTCATTTTTTAACTACGTGAGAGAA Y 2 1 2 1 101000 r 74 goat snp41365-scaffold537-3941251 19 60032282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430389 Affx-122937770 AX-123300730 19 59624096 GTCATTAGCACCTGATTCCCTGGTAAGGACACATC[A/G]GTGGGTCATCAGTAAGACCAGAAGCTCTACAGACA R 2 1 2 1 101000 r 74 goat snp41366-scaffold537-3992740 19 60081152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601549 Affx-1002479705 AX-413835958 19 59638387 CTGTGATCACCATCTGCAGTGATTTTGGAGCCCCC[A/C]AAAATAAAGTCTCTCACTGTTTCCAATTGTTTCCC M 2 1 2 1 303000 r 74 goat 19_59638387_RH-map 19 59638387 C A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38402800 Affx-122958286 AX-123273153 19 59666741 AACTCACTCAAGGGACTGGCATTTCACTCCTGCAC[A/G]TTTATCAACAGGAAAAGGTAGTGGGATTAGGAATA R 2 1 2 1 202000 r 74 goat snp41367-scaffold537-4035385 19 60124356 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408003 Affx-122954315 AX-123278354 19 59713513 ACTCCAATCAGGAAAAGTCAAATGAACAAGCCTTC[A/G]TGCTGGCCAGATTCACAGCCTGAGAAAAATACATC R 2 1 2 1 101000 f 74 goat snp41368-scaffold537-4082157 19 60171812 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435402 Affx-122933559 AX-123305742 19 59748722 GGCGGTGTCAAGGACACAGCAAAAAGAAGGTAAAA[C/T]GCATTGTTAAAAGAATGAGCCCCAACTTCATGATG Y 2 1 2 1 101000 f 74 goat snp41369-scaffold537-4117366 19 60207891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277392 Affx-1111835826 AX-519550896 19 59784398 ACAGACTTGAAGGTAGCAACTCTTTTCCTGAGCCA[C/G]CTGTGCTCTGTCATGAATACTCTATCTGACACCCT S 4 1 2 1 101000 r 74 goat Random2.2K-1815 19 59784398 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446111 Affx-122925791 AX-123316448 19 59816836 AACACTGTAATAGAAGGTCCATGGTTAAAAGTTTA[C/T]GTTGGTGACAGTTGGTTCACAGGCACCTCCAACAG Y 2 1 2 1 101000 f 74 goat snp41371-scaffold537-4185480 19 60276319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387439 Affx-122970384 AX-123257797 19 59855002 GCATTTTTCAGTAAAGATTTCCATCACAAACCTGC[A/G]ACCATAGCAAGCTCTGGAAATGGGGCATTCAACGC R 2 1 2 1 201000 f 74 goat snp41372-scaffold537-4223646 19 60314903 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277394 Affx-1111835827 AX-519550898 19 59875032 AATGGTGACTTCCAGAAAGCAAGAGTCCAGAAGAA[A/T]TAGCCTCCCTTCCTGCCCATCGATATCTTTGTCTT W 4 1 2 1 202000 r 74 goat Random2.2K-1816 19 59875032 A T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434249 Affx-122934824 AX-123304590 19 59909004 CTCTTCTGCCTGCTCCCTTCTGTGCCTATTAACCC[G/T]AAGGAAACATTTACAACTCCACAAACGAAAATCAA K 2 1 2 1 101000 r 74 goat snp41373-scaffold537-4277648 19 60368593 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453057 Affx-122920066 AX-123323390 19 59942351 AAGGGTCAAAGCGGTTCCCAGCTCAAGAACCGTCC[A/G]TGAGTCCCCAAGGTCGCATGTGCGTACCTGATATG R 2 1 2 1 201000 f 74 goat snp41374-scaffold537-4310995 19 60401520 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601419 Affx-1002479706 AX-413835839 19 59948346 CAATGGATGTTGGCAATTTGATGTTTGGTTCCTCT[C/G]CCTTTTCTAAATCCAGCTTGGACATCTGGAATTTC S 4 1 2 1 303000 f 74 goat 19_59948346_RH-map 19 59948346 C G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601552 Affx-1002479707 AX-413835961 19 59978893 GACCCAGCCCTTCTCTCTTCACTCCCACTGTGGCC[G/T]CCCATGGCTGAGCCCACAGGAAATTCAAAGGACCT K 2 1 2 1 102000 r 74 goat 19_59978893_RH-map 19 59978893 T G 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38401662 Affx-122959573 AX-123272015 19 59997602 CATCGAAAAGTTTTCCTTTGGGACAGGAACCCCAC[A/G]TTCACACCAGAGGCACCTTCCACGTGGGATCCAAT R 2 1 2 1 101000 f 74 goat snp41375-scaffold537-4366246 19 60455708 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800692 Affx-122960717 AX-385287610 19 60041249 GATGATAGACAAAGGGCTTCTCAAATAGGAAACCT[C/T]TGAAAATGTCACATAAGGGAGTTGACATCAAATTG Y 2 1 2 1 201000 r 74 goat snp41376-scaffold537-4409893 19 60496480 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777793 Affx-122950487 AX-385264912 19 60072653 CTTGAAATGGGAATAAAGGACTGCCAAAATATTTG[A/C]TTAATACAGTAAAGTCTTATTTTTTGGTTTACTTG M 2 1 2 1 101000 r 74 goat snp41377-scaffold537-4441297 19 60526847 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424874 Affx-122941331 AX-123295220 19 60105484 GACGTGCAGGAGGTCACGGATCGGTGAGGCCCTGC[A/G]TTCAGCTCCCTCTGTCACCTGGGGAAGGTCATGAC R 2 1 2 1 101000 r 74 goat snp41378-scaffold537-4474128 19 60560516 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798306 Affx-122922800 AX-385285241 19 60139797 AGTTTCTTCAAGGAATATCCTATATTATCTCTCTG[C/T]ATAGAGTAAATAGCCTGGTGTTAAAGACTTACATT Y 2 1 2 1 101000 f 74 goat snp41379-scaffold537-4508441 19 60594685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413318 Affx-122950184 AX-123283667 19 60191056 AGTAAAGCTAAAATCTGGAGTCCTTTGACCACATC[A/G]TAACTGCCAGAGTTACCTCTATTTTGGTACCCTGA R 2 1 2 1 101000 f 74 goat snp41380-scaffold537-4559700 19 60643629 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449643 Affx-122922587 AX-123319978 19 60228797 AAACTCTGGGGCTGCCTGATCCCAGCATTTCAGGT[A/G]CCTTTTAGCTGAACTCCTCAGCTGTTGGCTGAATG R 2 1 2 1 101000 r 74 goat snp41381-scaffold537-4597441 19 60681054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443978 Affx-122926994 AX-123314315 19 60263552 TGAAAAGCTGTTGAGAGCGGGTCTTAAGAACACTG[A/C]TAAAGCATGCCTGGTCTATTCTCCTTGGGCAAGCC M 2 1 2 1 101000 f 74 goat snp41382-scaffold537-4632196 19 60715949 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428919 Affx-122938910 AX-123299261 19 60292765 GATGAAGCATTTGACTTTGAACTACAAACTTTAAA[G/T]ATTGGGAAGAGGAGGACTCCACAAAGCAGTTTAAG K 2 1 2 1 201000 f 74 goat snp41383-scaffold537-4661409 19 60745390 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427856 Affx-122939720 AX-123298199 19 60320600 AAAACCTTAAGTGTCTGGGAGGGATTCTTCGAGTC[A/G]TCATGAGATGGAGTGGTGAAAACTGGACTTCTTTG R 2 1 2 1 101000 f 74 goat snp28353-scaffold3022-468031 19 60771539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385580 Affx-122971837 AX-123255938 19 60352085 CAGTTAGTTTCAAAGAAGATGGTTCAACCAGAAAC[A/C]GTTAAAGGCATTGAGATCAGATTCATTCAACCAGC M 2 1 2 1 101000 r 74 goat snp28352-scaffold3022-436546 19 60802394 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397034 Affx-122963113 AX-123267389 19 60382120 ACAGGTGAGGAAGAAGGAACCAGAACCATCATCCT[A/G]TATCACAAAAGATTCCCCTCCCCCCAGACCTCTTC R 2 1 2 1 201000 r 74 goat snp28351-scaffold3022-406511 19 60832312 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765426 Affx-122943843 AX-385252930 19 60528684 GAGAGGCTGGCAGCAAAGTTTAACAGCCTCATTTG[A/C]TGATGAAAATATTGGAGAGTGAGCAAGTGAGACCT M 2 1 2 1 101000 f 74 goat snp28347-scaffold3022-259947 19 60977207 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450779 Affx-122921830 AX-123321113 19 60571609 TCAGCAGGATCCAGGGGTCAAAGGCCATATAGCGC[A/G]AGCCTGCAGGAGATGGACCACCTTGTGGGCCGGAT R 2 1 2 1 101000 f 74 goat snp28346-scaffold3022-217022 19 61020253 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277396 Affx-1111835828 AX-519550900 19 60633555 AGGCTGGCTCTGAGGAGGGAGAAATGTAATATCAC[A/G]TCCCTAGGAGAATGAACATTCTTTTCCTAGGATCT R 2 1 2 1 101000 r 74 goat Random2.2K-1817 19 60633555 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403086 Affx-122958505 AX-123273439 19 60645134 AATCCTCCCTGAGTTTTTAAAAGCTTTGTTGGACC[C/T]AACAATGCATGCGGAGGTGTCAGTGAGAAACGAAC Y 2 1 2 1 101000 r 74 goat snp28344-scaffold3022-143497 19 61093179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409163 Affx-122953203 AX-123279514 19 60673681 TCCACTTGAAGGTCAGGAGCAGCTCTGATCCCTCG[A/C]ATCTCTGGGGGGCAGGGGTCATTGGAGGTCACCTG M 2 1 2 1 101000 f 74 goat snp28343-scaffold3022-114950 19 61121681 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451516 Affx-122921107 AX-123321849 19 60783205 AGTTTAAGGGAGCGAGGTTTTATTATTCTAATTTT[C/T]GGAAACCAAGGTTCTGACATCTCCTGGTTGGTAAC Y 2 1 2 1 101000 r 74 goat snp28341-scaffold3022-5426 19 56353450 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433618 Affx-122934596 AX-123303959 19 60791914 TAGTGTGTGTGCCTGTGTGTGGGGGGAGTGAGTCA[C/T]GGAACACCACTACGTAGGGAAATGTACCACCCCAT Y 2 1 2 1 101000 r 74 goat snp49537-scaffold7069-73267 19 56362969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443787 Affx-122927095 AX-123314124 19 60825740 AAACCACTGAAAGACAAAAGAGAGAAGCCCGGAGA[C/T]GCAGCGGATGACTTGAGGCTTGAAAGCCCTAACGG Y 2 1 2 1 101000 f 74 goat snp49536-scaffold7069-39441 19 61207376 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786068 Affx-122936396 AX-385273104 19 60877101 AATGAAAAAAGTCTTTAGAATGAAGGATAATGAAA[C/T]ATAACAGAATTTGTGTGATGCAGCTCAAGTGATGC Y 2 1 2 1 101000 r 74 goat snp4053-scaffold1128-11821 19 61259064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421415 Affx-122943969 AX-123291762 19 60951148 TTCAATGCGGTAAAACACATAATGTAAAATTGACC[A/G]TTTTAGCCCCTTTTTTTTAAACTGTTTTTTAAATT R 2 1 2 1 101000 f 74 goat snp4055-scaffold1128-85868 19 61330024 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428494 Affx-122938775 AX-123298837 19 60986361 AACGCCAACAGGAAGGTGTCTGCAGGAGGGTGCTC[A/G]GGCCAGTCTTCCCAAAGCTGTTTGCTTCTTTGCAG R 2 1 2 1 201000 r 74 goat snp4056-scaffold1128-121081 19 61365196 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386465 Affx-122970776 AX-123256823 19 61050368 AAACAGGATCTGGGTAATGTCAAAGGTCCACCCGC[A/G]TTTGTAATTTCATAACCCTTGAAATAAGGAAAAGA R 2 1 2 1 201000 r 74 goat snp4057-scaffold1128-185088 19 61427797 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277274 Affx-1111835829 AX-519550779 19 61075774 GGATACAGTCGTGTCTGGCTTCAGGGGAGGAGCCT[A/G]GATATGAAGCAAAGTTTGCAAAAAAAAAACCACAG R 2 1 2 1 202000 f 74 goat Random2.2K-1818 19 61075774 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38441821 Affx-122929065 AX-123312158 19 61116310 TAAATGTTTCCAAGTTGGCATCAATTCAGTTCATT[C/T]TCATAGCACTTCTACGAAACAGGGAAGGTTAAATT Y 2 1 2 1 101000 r 74 goat snp4059-scaffold1128-251030 19 61491977 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419582 Affx-122945392 AX-123289930 19 61165732 CTGAGACGGACCTTAAGAGAAAAGACAGTAGCAGC[C/T]GGAGACAGAGGTAGAAACAGGATGTTTCAGGCAGA Y 2 1 2 1 101000 f 74 goat snp4060-scaffold1128-300452 19 61543115 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274598 Affx-1111834315 AX-519548187 19 61195333 AGCTCCCTCCTCAGCCTGTGGATCATGGCCAAGAG[A/G]ATCCCTCACTTGGAAGGGCATCTCTGCGTGTCCAC R 2 1 2 1 202000 r 74 goat GoatD01.029860 19 61195333 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434328 Affx-122934739 AX-123304669 19 61213605 GAACCACCCGCCTATGCTGGTCCCATCGCTGCTAC[A/G]GTGACCGCCTCTTAGTTAACAAAGCCCACAAAGCA R 2 1 2 1 101000 r 74 goat snp4061-scaffold1128-348325 19 61591263 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381460 Affx-122974983 AX-123251818 19 61265495 GAGGTTCACTTGAACAGAAGTCTTCTGTTAACGAT[G/T]GTAGAAAAAAAAGCATTTCTTTTTTAGATTAGCCT K 2 1 2 1 103000 f 74 goat snp4062-scaffold1128-400215 19 61643011 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420583 Affx-122945265 AX-123290930 19 61294981 GACACTGCTATCATTTTTATATTTATAAGTTCTAA[C/T]ACATCGCTCTAAAAATCCAGGGTTTCCATGTTTAA Y 2 1 2 1 101000 r 74 goat snp4063-scaffold1128-429701 19 61673104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433661 Affx-122934565 AX-123304002 19 61329343 AACATCCTTCTCTTCATGAAGCTCACCAGCTCCAC[A/G]CTCAAACAATATCGATGCTGAGTCTACCATGCAAG R 2 1 2 1 101000 r 74 goat snp4064-scaffold1128-464063 19 61708649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388518 Affx-122969208 AX-123258876 19 61389936 TGAATAAACAGCTTCGCCTGTTCTCATCTGGGTGA[C/T]GGTGTTTTATGCCCAAGTCTGGAGTTCCTGCAGAC Y 2 1 2 1 101000 f 74 goat snp4065-scaffold1128-524656 19 61768638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430268 Affx-122937298 AX-123300609 19 61427362 GGTATAAAGCACAGCCACCTCTCCGAATTATTTCC[A/G]AGGTATAGTCAGCGCCTGAAGCGGTTGAGCTCCTA R 2 1 2 1 101000 f 74 goat snp4066-scaffold1128-562082 19 61806739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800502 Affx-122943401 AX-385287422 19 61508232 ACTGGAAAACATGGTCTAATCAAAATAGACGGTCA[C/T]AGGCAACTATAGGTCGATGATACATTACTTGCAGA Y 2 1 2 1 101000 f 74 goat snp4068-scaffold1128-642952 19 61886599 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404019 Affx-122957183 AX-123274371 19 61544495 GGCTGGGGAGAGTATAACTTCATCACTCACCTCCC[C/T]GACTCCACCCAGAAAAAGCTCCCAGGGGGCACAGT Y 2 1 2 1 201000 f 74 goat snp4069-scaffold1128-679215 19 61909056 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382917 Affx-122973395 AX-123253275 19 61577116 TTTCCACGGCTAGCGCATTTCGATTCAGCTATTAG[C/T]GGGTTTGTTTTGGTTGTGTGGTTAAGACTGAGAGG Y 2 1 2 1 101000 f 74 goat snp4070-scaffold1128-711836 19 61982000 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386542 Affx-122970724 AX-123256900 19 61615128 TGACGGTTTTGACCATTTTCACCTGTTCCCCGGTC[A/G]TTGCATGACTCCTGGAGAGACGTCTGTTCAGAGCC R 2 1 2 1 101000 r 74 goat snp4071-scaffold1128-749848 19 62018184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381166 Affx-122975213 AX-123251524 19 61649323 AGAGCTTGGCTATTTTGCCGGATTAAAAGTTTTCC[A/G]TCCAAGATCCTTGGCCCCTAGTCTTGCCTTTTTTT R 2 1 2 1 101000 f 74 goat snp4072-scaffold1128-784043 19 62051469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428236 Affx-122939429 AX-123298579 19 61680359 TTCCTCCGCTCCTGTAGACACACTCGTGTAAACAC[A/G]TGTGCTTACTGAAGCCTCACGAGAGTGCTGTTTGC R 2 1 2 1 202000 r 74 goat snp4073-scaffold1128-815079 19 62083453 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398140 Affx-122961688 AX-123268495 19 61730635 TGGTAAGAACCGAGGGAAAGCGGTCTTTCCTCCCC[C/T]CAGTGTGAGCAGCGTCTGCGGTCTTCCCTAGTGAC Y 2 1 2 1 202000 r 74 goat snp4074-scaffold1128-865355 19 62113689 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423299 Affx-122942639 AX-123293645 19 61751425 TGACAAAGCAGCAAACTAGTGGTGTTTTGTATCCC[A/G]CTTTTCTTTTTCTCATTTAACATTTCCCACAACGA R 2 1 2 1 102000 f 74 goat snp24034-scaffold2445-3015 19 62094642 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272924 Affx-1111833146 AX-519546611 19 61765007 ATGTGCACCTCATATGAGTAGCTAATCAGGTGCAG[A/G]AAAATTAGATGGAGCATCGGCTTTGTATTTCACTA R 2 1 2 1 101000 f 74 goat 19_61765007_AF-PAKI 19 61765007 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38379481 Affx-122976478 AX-123249839 19 61809657 AAACAGGATGATTTACCTCCTGCGAGCCTCTGTCA[C/T]GGCTTTGGTAAGATGAGAGCCACCACAACCTATTG Y 2 1 2 1 101000 r 74 goat snp24035-scaffold2445-61247 19 62212013 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384532 Affx-122973032 AX-123254890 19 61875611 CAGGGCTGCTTGTTGGAACAGGACACCTGATTTCT[C/T]GGCCTAGCTCCAGCAGATCGATGCCAGAAATGTAA Y 2 1 2 1 201000 f 74 goat snp24036-scaffold2445-127201 NW_017216058.1 11545 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421826 Affx-122944311 AX-123292173 19 61906754 CCCACCTTCCAGAGCCTTGGCTGGTTCACCCCATC[A/G]TCACACTAGTGTCCTCTCTCCTCAGGAATTAGCCC R 2 1 2 1 101000 r 74 goat snp24037-scaffold2445-158344 19 62288936 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426343 Affx-122940266 AX-123296689 19 61954950 GCTGTGATGACTCTGCTGATGGAGACGGGGCACGT[A/C]AAGTCTGAAAGGACCTAAATATCTGGGACTTTATC M 2 1 2 1 101000 r 74 goat snp24038-scaffold2445-206540 19 62337133 C A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449097 Affx-122923592 AX-123319432 19 62027584 TTGTAGCTGAATATATCCTAGGGATGGGGGAGGAG[C/T]ATATAAACAGACTCCAAATGGTGGAAGACTTAAGT Y 2 1 2 1 201000 r 74 goat snp24040-scaffold2445-279174 19 62411100 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277278 Affx-1111835831 AX-519550782 19 62034470 CTTTGTAGCTACAGAGAGGATGTCAAGGAGTGAGC[A/G]CAGCTGTGTTCTAGTAAAGCTTTATTCATAAAATC R 2 1 2 1 101000 f 74 goat Random2.2K-1821 19 62034470 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38453501 Affx-122919820 AX-123323834 19 62071915 AAATGTGTGAACTTGTACAGCAAAAGACATGTACA[C/T]GAGTGCTCATAGTGGCAATATTTGTAACAATCAGG Y 2 1 2 1 101000 r 74 goat snp24041-scaffold2445-323505 19 62455849 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383965 Affx-122972942 AX-123254323 19 62123909 GTTTGGAAAAGCCTCTACCTCATTTCTGAGAGAAC[A/G]CTTTACCAGGTAAAGTATTCTTTGCTGGCAGTTTT R 2 1 2 1 101000 f 74 goat snp24042-scaffold2445-375499 19 62508173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410300 Affx-122952495 AX-123280650 19 CACACATCTGATTGCAGAGCCCTATGAGGACTGTG[C/T]GAAAGTGGATTTTCATTCAGATATTTCAAGATGAG Y 2 1 2 1 101000 f 74 goat snp35520-scaffold428-768998 NW_017189517.1 20853302 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410076 Affx-122952849 AX-123280426 20 37167 TTACCTTCCTTGCCACTAGCTTTAATCCTTCAACC[A/C]CCTCACCTCCACTATTGTGTTCATTCATAATGCTG M 2 1 2 1 101000 f 74 goat snp33128-scaffold387-360163 20 93808 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766695 Affx-986698124 AX-385254039 20 81696 GGCATATTACAGGTGCTCAAGCTTGCTGGAAAGAA[C/T]GAATACGCTTGTGACAAATGAATATCCTTTGGATG Y 2 1 2 1 600010 r 74 goat 20_81696 20 81696 Ancestral_priority_1043 ancestry 0.692 recommended IMAGE 10K 10K ancestral 38380393 Affx-122975327 AX-123250751 20 99590 GGAGTCCAGGGTGAGAGATCATCCCCGTGTCATGG[C/T]GGGATTAGATGACTCTGTCCTGGAAGCCCCTCCTC Y 2 1 2 1 202000 f 74 goat snp33127-scaffold387-297740 20 156083 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408936 Affx-122953941 AX-123279287 20 131243 CCAAAATGAGGCCTCAGGTGGGTAGAGGGGAAGGT[A/G]TTCTTGCTGGAACTCTAAGTGTGTCAAGGTGGAGA R 2 1 2 1 101000 r 74 goat snp33126-scaffold387-266087 20 188491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386354 Affx-122970861 AX-123256712 20 168404 AGACATCTCAGCCCTCCAGGGTCCACTCGAGGCAG[A/C]GGGTGAATCACAGCAGCCAAAAATGGTTTTCTTTA M 2 1 2 1 101000 r 74 goat snp33125-scaffold387-228926 20 225335 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380277 Affx-122975419 AX-123250635 20 259910 AGCTTAGCCTCTTCTTTCTAGAGCTCCTTCTGCAG[C/T]GCATGCAATGAGGCAACTGTCACGACCTTTCTTAT Y 2 1 2 1 101000 r 74 goat snp33124-scaffold387-137420 20 318392 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784963 Affx-122956152 AX-385272010 20 299932 TTCAGGTTTTCAGTGACCACATTTGAGTAGTGCTT[A/G]CTGTACTAGTATAGTTTCTGGAACTAGCTCTTAAA R 2 1 2 1 101000 f 74 goat snp33123-scaffold387-97398 20 358318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425200 Affx-122941032 AX-123295546 20 330659 TTCTGAGCTGAGTGAGGAAGTCAGATGAAATATGA[C/T]GCAATGCTATGATGAATGCTATGAACAGAAGTCCT Y 2 1 2 1 101000 f 74 goat snp33122-scaffold387-66671 20 388472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446279 Affx-122925665 AX-123316615 20 376597 AAAGACTTGACACAACCAAACAGAGAAACAAATAT[C/T]TCTAAAAAGGAGTGAAAACCATAAAACAATAAGGG Y 2 1 2 1 201000 r 74 goat snp33121-scaffold387-20733 20 434960 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441094 Affx-122928895 AX-123311431 20 404555 ACTTGGAGAAGGGCCAGCGTCTTCAGCTATTCCTG[C/T]GCTATCCTTCCTAAGGTCTGCCTGTGAGACTCAGA Y 2 1 2 1 101000 r 74 goat snp31685-scaffold3511-7126 20 462415 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397873 Affx-122961972 AX-123268228 20 445371 GCCGTTTCTCTGATTATCAGTGTTCTAGCCACCAA[A/G]GGCCCCTATGGGTTCCTCTCACTGTGATATCTGGG R 2 1 2 1 101000 f 74 goat snp31686-scaffold3511-47942 20 502762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423965 Affx-122942135 AX-123294311 20 487142 GATTTAAATGAGATTTAGAGTTAAGTGCCTGGCAC[A/G]TATGAGCATGTAATCAACACAGGAAAGAATAGTGG R 2 1 2 1 101000 r 74 goat snp31687-scaffold3511-89713 20 544640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769780 Affx-122936147 AX-385256950 20 532332 CAGGTCTCCTCCCAAAGCTCTGAAGTTTATAATTA[C/T]GACCAATTATCTTTGTTATTTCAATCTCTGTTTCG Y 2 1 2 1 101000 r 74 goat snp31688-scaffold3511-134903 20 590733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382469 Affx-122974208 AX-123252827 20 558099 GCCCTGAGAAGTATCCTGCTCTGTGCCATTTCTGC[A/G]CAGACGAGGACAGAGAGGATGGCACTCTGTACTTT R 2 1 2 1 600000 f 74 goat snp10875-scaffold13895-1990 20 558099 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382470 Affx-122974208 AX-123252828 20 558099 GCCCTGAGAAGTATCCTGCTCTGTGCCATTTCTGC[A/G]CAGACGAGGACAGAGAGGATGGCACTCTGTACTTT R 2 1 2 1 101000 r 74 goat snp10875-scaffold13895-1990 20 616529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429615 Affx-122937700 AX-123299956 20 623258 ACAGGGCTAGGTTCTCTCCACCAGAGTCAGTTAAA[C/T]GGTAGCCTCCACCTAGCAAGCACATACTGTCTGCT Y 2 1 2 1 101000 f 74 goat snp21474-scaffold2094-267985 20 681308 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788221 Affx-122965575 AX-385275240 20 655132 AGTGGTTCATGCCTATGGGAGTTGTACATATGGAT[A/G]TCATTGTCCTGGTGAGAGAAAATTTTGTGTTGTCT R 2 1 2 1 101000 f 74 goat snp21473-scaffold2094-236111 20 713118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386470 Affx-122970771 AX-123256828 20 690190 GCCTGAGGCTTGACTCAGCTTCTCCCAAGCTCATT[A/G]CCTTCTATAAAACGGGGGTGATAGCCTGGTGGGGT R 2 1 2 1 201000 f 74 goat snp21472-scaffold2094-201053 20 748638 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763597 Affx-986698126 AX-385251448 20 739755 TTCTCTGAAGGTGAGCCCAGCCCACACCTCAACCT[C/T]AATATCCAAGTTCTGGGCATCAAGACCCCCTGTCA Y 2 1 2 1 600010 f 74 goat 20_739755 20 739755 Ancestral_priority_1043 ancestry 0.506 neutral IMAGE 10K 10K ancestral 320766703 Affx-986698128 AX-385254047 20 739765 GTGAGCCCAGCCCACACCTCAACCTCAATATCCAA[A/G]TTCTGGGCATCAAGACCCCCTGTCAATCTGACTCC R 2 1 2 1 600010 r 74 goat 20_739765 20 739765 Ancestral_priority_1043 ancestry 0.578 neutral IMAGE 10K 10K ancestral 38407210 Affx-122955392 AX-123277561 20 753831 TAGTGACCAATAGAGATGCTGAGACAACTTGCTTT[A/G]CAGAAGAAAAGTGCTTAAATCTGTCCAATTATGCT R 2 1 2 1 101000 r 74 goat snp21471-scaffold2094-137412 20 812305 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433678 Affx-122934553 AX-123304019 20 785178 CTTAGGAAAGGAGTCTGGGTTAACAGGGGAGGTTG[A/G]AGCTGCATCGCTACAGATGACTGAGCTCAGGTGTA R 2 1 2 1 201000 r 74 goat snp21470-scaffold2094-106065 20 843377 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766802 Affx-122971125 AX-385254131 20 820871 GGTCCCAAATTCAGGGGAAGGTGATTAGATGAAGG[C/T]GAGAGCCCCTGGTCTTTTATAGATACCAAAGATAA Y 2 1 2 1 101000 f 74 goat snp21469-scaffold2094-70372 20 878746 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407789 Affx-122954953 AX-123278140 20 853443 ATCCAGTTACTAACTGTGGGAGTTTGATGGGTCAT[A/G]TAACCCTTGGAAACCTCAGTGGCCCCCATCTGTAA R 2 1 2 1 101000 f 74 goat snp21468-scaffold2094-37800 20 911825 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427468 Affx-122940022 AX-123297811 20 886258 TTCCTTACCCGGAAAGTCAAAGGATGCCAGGAGTT[A/G]CAGATCTGCTCCTTCACCACCCCTCCAGGACAAAA R 2 1 2 1 101000 f 74 goat snp21467-scaffold2094-4985 20 944687 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412589 Affx-122951298 AX-123282938 20 916942 AAATGTAAGCCACCTTTTTTGTTTCCCCTTGGTAG[C/T]GTTAGAGCCCAAGAAAATAAAATCGGTCACCTCAA Y 2 1 2 1 201000 f 74 goat snp52570-scaffold782-5391310 20 975196 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435133 Affx-122933683 AX-123305473 20 947867 GTCTGTCTGTCTGTCTCTGTCTTTGTTCCTTTAGC[A/G]CTTGCAGACTGGGAGTTTATTTCTCATCACGGTAC R 2 1 2 1 101000 r 74 goat snp52569-scaffold782-5360385 20 1006270 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794860 Affx-122954491 AX-385281820 20 1013329 TTAAATGAAGCAATCCTTTATAAAGCATTTAGCAC[A/G]TGGCCTGATGCTCACTAAATGTCCATGGCTTTCTT R 2 1 2 1 101000 r 74 goat snp52567-scaffold782-5294923 20 1071118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376543 Affx-122977991 AX-123246902 20 1049735 AACGGTGAAGGGGTTCTGACACAGGCTTTCCTGCC[A/C]GAGAGACTTCTGTCCAAACCTTGTCAGCCGTGTGA M 2 1 2 1 101000 r 74 goat snp52566-scaffold782-5258517 20 1107165 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420498 Affx-122944855 AX-123290845 20 1088140 TTCCATGGAATCAGAATGGAAGTGCTCTGCTCTCC[A/G]TGACCCTCCATCCTGGCCCTCTTCCTCTATTTTGG R 2 1 2 1 201000 f 74 goat snp52565-scaffold782-5220112 20 1145906 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398843 Affx-122961380 AX-123269198 20 1157196 TGGCAATGACTTACTGACGCCGCCCACAGGAGCTT[G/T]ATCAGCTAAATCCTGCATCTAAAAGATGATCAGGG K 2 1 2 1 101000 r 74 goat snp52563-scaffold782-5151056 20 1215026 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781208 Affx-122967312 AX-385268293 20 1203545 GAAAAATATCGCTTTCCACACTCTATTCTGGAAAA[C/T]GATATCCATCTGTGGGAATGCTGAGCAGGCATGAT Y 2 1 2 1 202000 r 74 goat snp52562-scaffold782-5104707 20 1261904 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773487 Affx-122938945 AX-385260628 20 1250772 AGTCAAATCTTTCTTCTCGTATCTTTCATTATAGT[A/G]TCTCCCACAGGTTTTTTTTCCACCAGTGTAGACAG R 2 1 2 1 101000 r 74 goat snp52561-scaffold782-5057480 20 1310007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401637 Affx-122959590 AX-123271990 20 1281988 GATTAGACTTGCTTGTTGTACCTGCTATCCTACTT[A/G]CTCTGCTTTGTATGCATTTTCCTCGCCACGAAGCT R 2 1 2 1 101000 f 74 goat snp52560-scaffold782-5026264 20 1341482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438282 Affx-122931400 AX-123308620 20 1325530 CCCATTACTCCTGCATCTCGGCTGGCTGTCTGCTT[A/G]TCTTCTGCTGAAGCAGAGGTAAAATCTAGCCACTT R 2 1 2 1 201000 r 74 goat snp52559-scaffold782-4982722 20 1385746 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409114 Affx-122953313 AX-123279465 20 1396372 TACAGGGAGATTTAAATAAGAGTTGATAGGAGTAT[A/G]TAGGAGGGGGCTATTTATTTTGTATATGTTGAGCT R 2 1 2 1 201000 f 74 goat snp52558-scaffold782-4911880 20 1457069 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422881 Affx-122943073 AX-123293227 20 1475190 TCTGTTTTGTGCGAATGGAGTTCTTAATATTGTTA[C/T]AGATTATCTGAAACTTTGCTTGAGGAAAGAACTTG Y 2 1 2 1 101000 r 74 goat snp52556-scaffold782-4833062 20 1535908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801264 Affx-122959735 AX-385288176 20 1514964 TATTTTAATTCCACTATCATTCCACTGCATAAAGA[C/T]ATCCTTCATCTTTTATCATCCTTTTTTACCTTCTC Y 2 1 2 1 101000 r 74 goat snp52555-scaffold782-4793288 20 1575691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399781 Affx-122960297 AX-123270136 20 1559780 AAGAGATCCCATCTCAGCTCTGGAAGAGCCTGTCA[C/T]GGTTTGAGTTACACCACTCCCCACCAAACAAATGA Y 2 1 2 1 101000 r 74 goat snp52554-scaffold782-4748472 20 1620775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794435 Affx-122920822 AX-385281398 20 1629050 TTTGCAATTAGTATCATCGTTGTTATTGTTTATTA[G/T]TATTATTATTATTACCTTGACTGTTTCCATCCACC K 2 1 2 1 103000 r 74 goat snp52552-scaffold782-4679202 20 1690271 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381001 Affx-122974667 AX-123251359 20 1681799 TTCCTCTCAGGTAGAGTACAGACCTCACAGCAAAG[C/T]AGCTCCAGACTGGACTTCCTAGTGTTTCAGAGGTT Y 2 1 2 1 101000 f 74 goat snp52551-scaffold782-4626453 20 1742936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375530 Affx-122979109 AX-123245889 20 1746669 CATAGCTGATCAGTAGTTCATCTTGAACTAAAGGC[G/T]CGTGTCTTTTCTTGAAGTGCACTGAGCCTTTCCTG K 2 1 2 1 101000 f 74 goat snp52549-scaffold782-4561583 20 1807590 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424518 Affx-122941732 AX-123294864 20 1792118 TTGAGGGATGTTGTGGAAACTTCTCTGAGCCTTGA[C/T]AGCTTGGTCTCCCAGACATTTGCCATTAGCTCCCA Y 2 1 2 1 201000 r 74 goat snp52548-scaffold782-4516134 20 1852322 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802299 Affx-122934034 AX-385289203 20 1844217 TTCCTGGATAGCCTCTTGAAATGATTTTAAGAACA[C/T]GGAGAAAATAAAGACTATGTGGTGTTAAGGCAGGT Y 2 1 2 1 101000 f 74 goat snp52547-scaffold782-4464035 20 1903905 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423091 Affx-122942927 AX-123293437 20 1904402 CCTCAGGGATAGCATGCTTTCCCAGTCAGCAGGAC[G/T]AGCTGTGTAATTTGTGGGGCTCAGAACAAAATGAA K 2 1 2 1 102000 f 74 goat snp52545-scaffold782-4403850 20 1963505 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449078 Affx-122923608 AX-123319413 20 1937503 GCTCTTTTTTTATTGCTGTTGTTTTGCTTCATTTC[A/G]TTTTTCTGGAAAATGAATAACTCAGCCCAGCTGGG R 2 1 2 1 303000 f 74 goat snp52544-scaffold782-4370749 20 1996887 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448261 Affx-122924193 AX-123318597 20 1973195 AGACTCTAATCACGGTACAACTCCAAGGGCATGGG[A/C]AAGTCATAGTGCTGTAAAGGGGAAGTCCTACCCTC M 2 1 2 1 101000 r 74 goat snp52543-scaffold782-4335057 20 2032343 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418119 Affx-122947124 AX-123288467 20 2026016 CGCTCTGCCATTTCCAAGCTGGGTGACCCAGGGCA[A/G]GTCCTTGTGCCTCTCTGGGCCTGTTTCCTTGGCTT R 2 1 2 1 303000 f 74 goat snp52542-scaffold782-4282236 20 2080645 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794328 Affx-122936203 AX-385281292 20 2061155 ATGATTCTTCGAAGAGAGAGTCTACAGTGGTGAGC[A/G]TCATCAGCAAGTCCTCCTTTCTGCATGAAGTCAAA R 2 1 2 1 101000 r 74 goat snp52541-scaffold782-4247097 20 2115121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396026 Affx-122963476 AX-123266381 20 2113823 TGCTGCTGGTTATTATGAGTAGTGCTAACTTATTA[C/T]ATACTGGAACAACTCCTCATAAAATAAATTACCTT Y 2 1 2 1 101000 r 74 goat snp52540-scaffold782-4194429 20 2168072 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377609 Affx-122977893 AX-123247968 20 2142556 GGACGCACCAATTTCTCCCTGTTAAGTGGAGAGAG[C/T]GAGAGTTGGGCCGAGGAAGTGAGATTGGGCTTCCT Y 2 1 2 1 101000 f 74 goat snp52539-scaffold782-4165696 20 2196053 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419886 Affx-122945352 AX-123290234 20 2176346 AAAAATCACAGTGGTGGTGTCAGAAGGAAGGGACC[A/G]TTTCCCCCCAAGTCTGTTTTTGTCCTCTCGTCTTG R 2 1 2 1 201000 r 74 goat snp52538-scaffold782-4131906 20 2229288 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395328 Affx-122964045 AX-123265683 20 2212824 ACATTTTGGGGACAAATGGAAGAGGAATGCATATG[C/T]ACCTTGGAAGAGTTATGGATGTTTTGCTGTTGTTG Y 2 1 2 1 101000 r 74 goat snp52537-scaffold782-4095428 20 2265854 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780948 Affx-122977404 AX-385268035 20 2241372 ATAATTTTTGTTAATTTTCAGTTACGCAGATGATA[C/T]GTTCATACATTCATCCTTAAAAACCACAACACAGA Y 2 1 2 1 101000 r 74 goat snp52536-scaffold782-4066880 20 2294467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433393 Affx-122935108 AX-123303734 20 2289828 GCATAAGACACTGACACCACACAGGTAGGGAAGCA[A/G]CCATTTTAGAGAGAATGGGATTGGATGTATATATT R 2 1 2 1 201000 r 74 goat snp52535-scaffold782-4018424 20 2342789 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452237 Affx-122920788 AX-123322570 20 2329971 TCATTATGAAAAACTCTCATTTTCTATTAAATCCT[A/G]TATGACTAGAAAACAAGAGCAAACCATGGCCAAGA R 2 1 2 1 101000 r 74 goat snp52534-scaffold782-3978281 20 2383886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445833 Affx-122926018 AX-123316170 20 2365867 TAAACAATGACGGAACTATCTGCAGGGCAGCAGAC[A/G]CAGAGAACAGACGTGTGAACACGGTGAGGGGAGGG R 2 1 2 1 303000 r 74 goat snp52533-scaffold782-3942385 20 2419932 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410303 Affx-122952493 AX-123280653 20 2401830 GCATGAGGCGTGAGACTATGGAAGAGCTAATAAAG[C/T]ATGTCTCCGCCGTTGAGGAGCTCTGTCTAATGCCA Y 2 1 2 1 101000 f 74 goat snp52532-scaffold782-3906422 20 2455737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764943 Affx-122957537 AX-385252524 20 2454374 GAGGTAATTAGAGTCCAAACATTATAGAAGTATAA[C/T]GTCATTATTCCTAAGAGTAAAGATATTAATATCAG Y 2 1 2 1 201000 f 74 goat snp52531-scaffold782-3853878 20 2508440 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787913 Affx-122923934 AX-385274935 20 2489376 AATTGAGACAACTCTTCCAAACTGGGACATTATGC[A/C]TATAGTCTATTATTTCCAGCTTCTTTGGAAAAGTC M 2 1 2 1 101000 f 74 goat snp52530-scaffold782-3818876 20 2543078 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769909 Affx-122977950 AX-385257078 20 2544095 AATCAACAACAGGCGCTCTTTATTGCATGATTACT[A/G]TGTTCTGGTTGCTGTGCTAAGGACATTCCTCATAT R 2 1 2 1 101000 r 74 goat snp52529-scaffold782-3764157 20 2594097 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378087 Affx-122977163 AX-123248446 20 2598613 TATAGTTGCTAACTTGTCCATATCGAGCATGACTT[A/C]TTTTTTTTACTCATGAATAAAATGAAGCAAAACAA M 2 1 2 1 101000 f 74 goat snp52528-scaffold782-3709639 20 2647241 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272965 Affx-1111833194 AX-519546650 20 2606539 AATATTCACATGTTGACGGGTGTCTTAGCAGGACC[A/G]CCAGACCTGGAGTGAGATCATTAAATCATGGCTTT R 2 1 2 1 101000 f 74 goat 20_2606539_AF-PAKI 20 2606539 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38416414 Affx-122947845 AX-123286763 20 2629832 CCCAGGGATCAAACCCAAGTCTCCTGCATTCCAGA[C/T]GCTCTAACCTCCGAGCAACCAAGGACTCCATACAA Y 2 1 2 1 101000 r 74 goat snp52527-scaffold782-3678420 20 2678836 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416190 Affx-122948249 AX-123286539 20 2689291 ATAGAGAATTCTTCCAAAGTGTAAAAGGTGTTTCC[A/G]TCCCAAGAGTTAGTGTGTAAAATCAGCAGGAGGAC R 2 1 2 1 101000 f 74 goat snp52526-scaffold782-3618961 20 2739578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423857 Affx-122942318 AX-123294203 20 2727512 CCTCTTTGGGATCAACAGAGAGCCTTATCTGTGTG[C/T]AAGATTTGCAGAGCCCAGCACCTCATGCTTTCCAC Y 2 1 2 1 201000 f 74 goat snp52525-scaffold782-3580740 20 2777603 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418702 Affx-122946293 AX-123289050 20 2769152 TTCAGCAGCATCAGATGTTTCTTTGGATTATTGCC[A/G]AGGACGAAAATGAAGATATGCATTAGTCCTAAGTG R 2 1 2 1 201000 r 74 goat snp52524-scaffold782-3539100 20 2818949 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396199 Affx-122963364 AX-123266554 20 2821876 TGTTCAGTTATTCACTATATCCCCGGCAATCTCTT[A/G]TAAAGGCAGTGCTTTCTTTTTTATTCTCTAGATGA R 2 1 2 1 101000 f 74 goat snp52523-scaffold782-3486376 20 2871375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397447 Affx-122962110 AX-123267802 20 2854602 ACAGCACAGGTTGGTGCTGACCTGCTATTTGAGTT[A/G]TGTGAAGGTGTTGTTACTGCTACTACATATCAATC R 2 1 2 1 201000 r 74 goat snp52522-scaffold782-3453650 20 2904444 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396599 Affx-122962899 AX-123266954 20 2939243 ACTTTATGTCAGAGACCACAAAAGCCAGAAGACAA[C/T]GAAACATATCATTAAAATAATGTCAAACCAGAATT Y 2 1 2 1 101000 f 74 goat snp52520-scaffold782-3369009 20 2990437 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376763 Affx-122977969 AX-123247122 20 2969587 AATCTGCTACAGGAACCGGCCCACAGCCCCACCTG[C/T]ACTGAACTGTCACATTTCCTGGCTCTCTCCAGTGT Y 2 1 2 1 201000 r 74 goat snp52519-scaffold782-3338665 20 3021017 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408837 Affx-122954018 AX-123279188 20 2998703 AAGGCCATGGCCATGGCTGACCTTTTCTTGAGGGT[A/G]GCCAGGAGCTATGAGAAGCTCCCACCAAGGCTGGA R 2 1 2 1 101000 f 74 goat snp52518-scaffold782-3309549 20 3050142 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770014 Affx-122952514 AX-385257181 20 3039335 CCTGTTTTCAGTCTCCAGGGTAAGTTCCCATCTAA[C/T]GGGCTAAGTGATGATTTACATCCCTGTGCCCAATA Y 2 1 2 1 101000 f 74 goat snp52517-scaffold782-3268917 20 3090873 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421863 Affx-122944282 AX-123292210 20 3124917 CTTATTCATTTTCATCATTTATTTACTCAGACTGA[C/T]ATTTTCTGCTGATTGCAGGCGACTTATTTGCTGGC Y 2 1 2 1 101000 r 74 goat snp52515-scaffold782-3183335 20 3176988 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440122 Affx-122929699 AX-123310459 20 3160426 TACTCTTGCTGTAGTTTGAGAGGTTTGCTGTCATC[A/G]TAAACTTACACCTCAATAAAACATTAAAAAGTCTC R 2 1 2 1 101000 f 74 goat snp52514-scaffold782-3147826 20 3212817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442754 Affx-122927754 AX-123313091 20 3219831 ACTGGTGACACCTTGGTGTAAAAGGCAAATAGAAA[C/T]AATTCATTTGTTGAATAATTCAGAATGTTTCTGAC Y 2 1 2 1 101000 f 74 goat snp52513-scaffold782-3088421 20 3272754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416232 Affx-122948218 AX-123286581 20 3275477 TGGCTTCACTGCGTAATAACTGAGTGACTTTGAGC[A/G]TGCCACTTTGCCTCTTTGATCTGCTGTCTGTGGAT R 2 1 2 1 101000 r 74 goat snp52512-scaffold782-3032775 20 3328259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414096 Affx-122949744 AX-123284445 20 3318263 CTAAAAGGATCTAATTCCCCCTACTTCAGGCTGCT[C/T]AGCTGTGGCACAAACCGACTGCCTGTACAGCATTC Y 2 1 2 1 201000 r 74 goat snp52511-scaffold782-2989989 20 3370927 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441572 Affx-122928682 AX-123311909 20 3354676 CCAAGCAGGGCACAGAGCACACAGTGGTAGGGAGT[A/G]TGACCAAGTCTGGCATGCAGCAAGTCACATAGGAG R 2 1 2 1 101000 r 74 goat snp52510-scaffold782-2953576 20 3407431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777955 Affx-122922011 AX-385265071 20 3453520 TCAATATCCTAATTTTGGTATTGTGTAATTATTAC[A/G]TAACCATTGGGGAAACTGGGCATACATAGTCTTTG R 2 1 2 1 102000 r 74 goat snp52508-scaffold782-2854732 20 3505633 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412512 Affx-122951360 AX-123282861 20 3514425 GTGCTGGGTGATAAGAGGAGGAAGGCTCCCCAGAC[A/G]CCCACCAGGCCGAGGAGGGCAGTCTAGCTTAGTGC R 2 1 2 1 101000 f 74 goat snp52507-scaffold782-2793827 20 3566574 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801966 Affx-122936472 AX-385288870 20 3569374 GCTTTTAAGTTTGGCTTTTAATAATCCTTCAATAC[A/G]TAGTAAGAAAACACATTATTCATTGTCACTCAGTG R 2 1 2 1 101000 r 74 goat snp52506-scaffold782-2738878 20 3621362 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435539 Affx-122933396 AX-123305879 20 3622303 ACAGGTGCCTCACAGAACACTTAAAACAGAATGTG[C/T]ATACAGACCCACAGAATCATGTGTAATCACAGCCA Y 2 1 2 1 101000 f 74 goat snp52505-scaffold782-2685949 20 3674287 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801334 Affx-122949544 AX-385288246 20 3654653 TCTCTTTTTCCCTTTTGGGCTGAACATTTTGATAA[C/T]GCTCTCTTACAATACTGTCCATTCTCAAATGGATT Y 2 1 2 1 101000 r 74 goat snp52504-scaffold782-2653599 20 3706256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439765 Affx-122930517 AX-123310102 20 3693525 GTTATCATAAACTGAAGGGAGTAGCTTAGGCTGTG[C/T]GGAAATTCAGTTCTTTGTCCCAGCCCTAAATTAAA Y 2 1 2 1 101000 f 74 goat snp52503-scaffold782-2614727 20 3744772 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441912 Affx-122928603 AX-123312249 20 3723654 AATAACCCTTTTGCTTATCGAGTGAGGTAATGAGT[G/T]TGAAAATATTTTGTGAATTACAAAGCAGTACACAA K 2 1 2 1 101000 f 74 goat snp52502-scaffold782-2584598 20 3774508 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435277 Affx-122934047 AX-123305617 20 3768138 GTCACTAGTTCCAGTATGCAGTAGGGGGAGATAGC[A/G]TCCACACCCTACCATTGGTTGGCTGTTGAGGGAGT R 2 1 2 1 101000 f 74 goat snp52501-scaffold782-2540114 20 3818825 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428335 Affx-122938998 AX-123298678 20 3807811 TGATTTAAATTAATGTTAGGTTTTTTTTTCATCCT[A/G]TGAAACCTTTTTAACATTTCTGTTTGATAATTCTT R 2 1 2 1 101000 r 74 goat snp52500-scaffold782-2500441 20 3858360 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400412 Affx-122959987 AX-123270767 20 3855301 TACTGAGTAACCCATGTGTGCCTGACTTTGCAGAG[C/T]GTTTCAGAGCCTGAACTCTAAAGTTAGACCCATCT Y 2 1 2 1 201000 r 74 goat snp52499-scaffold782-2452951 20 3906267 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449775 Affx-122922437 AX-123320110 20 3928051 AACAGGCTATTTAGTAATATCCTAAGGCATTCAGA[C/T]GATTGTTTTCTTTTTATTTATTGTTATTATTACAT Y 2 1 2 1 101000 f 74 goat snp52498-scaffold782-2380201 20 3979131 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393628 Affx-122965308 AX-123263983 20 3958684 ACCGTGGTGACACGGAATGCAGTGTACTGACTGGA[C/T]GGCATAAATCATCTACCTGCTTCTAGATAAGGTGG Y 2 1 2 1 101000 r 74 goat snp52497-scaffold782-2349568 20 4010009 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274712 Affx-1111834454 AX-519548299 20 4012026 TTCTGGTCCCTGTGCTCCGATAGCAGTCCTTTCCC[A/G]GAGGAGGGGGAGGGCGGGACGCAGCGGTCAGCCTG R 2 1 2 1 102000 f 74 goat GoatD01.036601 20 4012026 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38395508 Affx-122963881 AX-123265863 20 4014006 GTGTTTCAAGGAAACAACAAAAAACCTTTTTCCTG[C/T]ATTTCCCCTTTCTTTTCTTTTTAGTACAGTGGTTC Y 2 1 2 1 101000 f 74 goat snp52496-scaffold782-2294246 20 4065178 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447256 Affx-122924950 AX-123317592 20 4072051 TGCACTTAAAATGACAGAGCATTATCGAGAGAAAC[G/T]AAAGACTAAAACAGATACAAACAAAAAATATATAT K 2 1 2 1 101000 f 74 goat snp52495-scaffold782-2236201 20 4123905 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448007 Affx-122923732 AX-123318343 20 4101805 ACCATTTGTGAAGCTGTTACGTAGGATTTGACTAC[A/C]TTTCAAAAGACGCAACTCTCAATTTTTTTTTCCCA M 2 1 2 1 101000 f 74 goat snp52494-scaffold782-2206447 20 4154083 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442594 Affx-122928487 AX-123312931 20 4136424 AGCAGAGTTGGGAAGAGATGTACAATCTCAGCTCC[A/G]TATGGGTGTATTTGGACACAGAATATAAACGGCTA R 2 1 2 1 101000 r 74 goat snp52493-scaffold782-2171828 20 4189375 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432931 Affx-122935303 AX-123303272 20 4174642 GCAAGGTGCTCCTAAATGACCCTGTTTCCTGAATA[C/T]GGGGAGCAATCCTTTTTAATTAACCGCTGTAGCAT Y 2 1 2 1 101000 f 74 goat snp52492-scaffold782-2133610 20 4225536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781783 Affx-122963734 AX-385268865 20 4218762 GTCCCGTGTACCTTTTAATGTTCTTACCTTTTCAG[C/T]ACTCCCCAGGATCTTATATGGAAAGTTTTATAAAC Y 2 1 2 1 101000 f 74 goat snp52491-scaffold782-2089490 20 4269406 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407073 Affx-122954911 AX-123277424 20 4260508 ACAGAGAGTAAACTCCAGATTCCTCTCCTGGCCTC[A/G]CAGGCCCCATGGGATCTGGCCTTGGCCCACCAGTG R 2 1 2 1 101000 f 74 goat snp52490-scaffold782-2047744 20 4311739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788512 Affx-122959381 AX-385275529 20 4292694 CGGAGGGCCACCATTCAACCTACTACAACCCCATT[C/T]CCATTTCTCCACAAGATGTGATGGTTCTTGTTACT Y 2 1 2 1 202000 f 74 goat snp52489-scaffold782-2015558 20 4344389 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394529 Affx-122964527 AX-123264884 20 4322529 TGTTATCTCACTTACTCCTCACAAGCTATCTAAGG[A/G]CAGGTGTATTATCTTTGTTTAGTGAACAAGGAAAC R 2 1 2 1 201000 r 74 goat snp52488-scaffold782-1985723 20 4374196 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402488 Affx-122958586 AX-123272841 20 4353507 TGTCCAGCGAGGGTTCCTTATCCCTCTGGTATCAG[A/C]TGCTGCCGCCTGGGCATAGATCTAGCCCCTTAAAA M 2 1 2 1 101000 f 74 goat snp52487-scaffold782-1954745 20 4405245 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381238 Affx-122974503 AX-123251596 20 4422684 CTCTGAGGCACAGGGTAACAGTACCTCGTGCTCTG[C/T]GGTGATATAACCAACCATGTGACTGTTTTACTAGA Y 2 1 2 1 101000 r 74 goat snp52486-scaffold782-1885568 20 4474328 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416625 Affx-122947622 AX-123286973 20 4470626 GGCATTCCCTGGAGGCATCTTGGGGAGACCAAAGT[A/G]CCCCAGCTTGTCGTTCTGAGTGTGGCCATGACCTC R 2 1 2 1 202000 r 74 goat snp52485-scaffold782-1837626 20 4521995 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411174 Affx-122951861 AX-123281524 20 4518032 GGCTTCGTGGCAGCCGGTGCGGAAGGCAAGGTTAC[A/G]CTCCCATTTTCACAGAGCACTGAGGCCAGGGCGAG R 2 1 2 1 201000 f 74 goat snp52484-scaffold782-1790220 20 4569586 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406789 Affx-122955704 AX-123277140 20 4576613 CTGTCTGATGTCACAGCTCCTGTCCTTGGGTCCAA[C/T]GCCATATGTCCCGCCCTGGTGGTCATGGAAAGATC Y 2 1 2 1 101000 f 74 goat snp52483-scaffold782-1731639 20 4628381 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430754 Affx-122937497 AX-123301095 20 4636549 ATCAAATAATTGGCCATTGAACCCCCGCATGGGCT[C/T]AGCATAAAAAAATAAAGAGATTCTTTCTGAGTTTC Y 2 1 2 1 103000 f 74 goat snp52481-scaffold782-1671703 20 4688301 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384943 Affx-122972320 AX-123255301 20 4697900 CTCCCTGCTCCAGGTGACACTTTTGAGCCCTCTGC[A/G]CTGACGCTGATGAGCCTCCAGCATCTCATGCACAG R 2 1 2 1 201000 f 74 goat snp52480-scaffold782-1610352 20 4751094 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450269 Affx-122922178 AX-123320604 20 4743026 GGGTGGACCTCATGCCATCAGATGATAAATTCACC[G/T]ACAGTTTTTACTTTTTAAACAAATTATGATTTACT K 2 1 2 1 101000 f 74 goat snp52479-scaffold782-1565226 20 4796080 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782602 Affx-122947534 AX-385269676 20 4773685 GGGGAAAAGATTATTAAATGCACCAGGATATTCCT[C/T]TACTGGATGCAGCATGGCTTATGTGAGCATCTCCT Y 2 1 2 1 101000 r 74 goat snp52478-scaffold782-1534567 20 4826701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779077 Affx-122970412 AX-385266182 20 4804680 CTCTGTAGTTAATACATTCTCTGGCCTAGAGCTTT[A/G]CAGTGGTAAATATCAACTGCAGAGACCTCTTGCTG R 2 1 2 1 101000 f 74 goat snp52477-scaffold782-1503572 20 4857774 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453706 Affx-122919687 AX-123324039 20 4863049 AGGGAAAAGGGAGTGGATGCAGCGGCCACTGAGGT[C/T]ATGGTGTGAGCGCTTGGCCTGAGTTTTGCCTTTTA Y 2 1 2 1 201000 r 74 goat snp52476-scaffold782-1445203 20 4916063 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422959 Affx-122943015 AX-123293305 20 4895308 CCGCAGATCCCTACCTTCTGCCCATGATGTTCCTC[A/G]TCTCACTCGTAGCCTGTATCTTCTTCCCCCAGGAC R 2 1 2 1 101000 r 74 goat snp52475-scaffold782-1412944 20 4948468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449157 Affx-122923547 AX-123319492 20 4989173 ACCCAAGACAGTGAATGAAAAACTCCCCAATAATA[C/T]GTATCCTTGAGAAAGTTCAAAATTCCTAAGGGTAA Y 2 1 2 1 201000 r 74 goat snp52473-scaffold782-1319079 20 5042797 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446705 Affx-122924733 AX-123317041 20 5054235 TATATCCGTCCAGGTTTAAGTCCAGCAGGAAAAAA[C/T]GTAGCTTATACCTCAGTAGAGCCTGCACAAACTTG Y 2 1 2 1 102000 f 74 goat snp52472-scaffold782-1254017 20 5107639 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410935 Affx-122952045 AX-123281285 20 5092795 ATAAATAATTGTCTGGGCTTCGTTTAGCTAACAAA[C/T]GGCTTTTTTTCTTCTCTCTCTCTCTCCTCTCTTTT Y 2 1 2 1 101000 f 74 goat snp52471-scaffold782-1215457 20 5146793 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432384 Affx-122935855 AX-123302725 20 5122696 CTTGGCTCAGGGATCCGTAAGGAGGACCACATGGA[A/G]CAGATCTGGATCCAGCCTGCCGCAGAAGCCCGACC R 2 1 2 1 101000 f 74 goat snp52470-scaffold782-1185556 20 5176743 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272061 Affx-1111833202 AX-519545825 20 5125285 TTGAGTAGGCAGGGAAGACAGGGAGTCTGTTTCAG[A/G]CATAGGAAACAGCAGAGCAAATCACAGAGCAGCGC R 2 1 2 1 102000 f 74 goat 20_5125285_AF-PAKI 20 5125285 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38427402 Affx-122940073 AX-123297745 20 5162570 CAGGAGTGGGAGGGGAAACTGACTGCCCAGCTACC[A/G]TTTCCTTCTTGGAGTGAAAAGCAGTGACGGAGCAG R 2 1 2 1 101000 r 74 goat snp52469-scaffold782-1145682 20 5214745 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396220 Affx-122963351 AX-123266575 20 5205817 ATTCCTACATTCTCTCCCCCAAGATGAAAATGCAC[A/C]AAGACTATTTTCCTGTCTTGACTTTCAAAAGGCTA M 2 1 2 1 201000 r 74 goat snp52468-scaffold782-1102435 20 5256793 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436862 Affx-122932199 AX-123307200 20 5286880 TTTGGACTGGACATACACTCCAGCTCACCCCAGAC[C/T]TCAGGAGGCCCTATTGTCTCACCACAGGGTAGACA Y 2 1 2 1 101000 r 74 goat snp52466-scaffold782-1021372 20 5337910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277405 Affx-1111835832 AX-519550909 20 5286929 GTTTATCGCAGATTTGCCAGTGCTGACAAGGAGCT[A/G]TAGATCACCTGAGTAGCTACCTGGGGGGAAAGCTG R 2 1 2 1 102000 r 74 goat Random2.2K-1826 20 5286929 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320796676 Affx-122949467 AX-385283622 20 5333821 TACACAGTACAAGCATTAGAGGTGTCTGGGTAAAG[A/C]GTTCATAGACCTCCCTATGTATTTCTTTGCAACTT M 2 1 2 1 101000 f 74 goat snp52465-scaffold782-974431 20 5384786 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398520 Affx-122961544 AX-123268875 20 5403469 AAATGTAGGCACTAACTATTACCCACGGAAGCAGA[C/T]GCAAAGACAGGAACACATGTACAGGGGTTTTGTTA Y 2 1 2 1 101000 f 74 goat snp52464-scaffold782-904783 20 5454800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451480 Affx-122921134 AX-123321813 20 5442044 CCACAAATATCTGTGCACATAATACACATCAACAT[A/G]CCTTCATGTGTGCACATATACACAGATTCATTTCA R 2 1 2 1 101000 f 74 goat snp52463-scaffold782-866208 20 5493420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452584 Affx-122920505 AX-123322917 20 5482277 TTGTTTTTGGAGGGCAGTGAAAATGCGGCACACAG[C/T]AAAGGAGGAAAAGTCACTCTCATAAAATAGTGCTA Y 2 1 2 1 101000 f 74 goat snp52462-scaffold782-825975 20 5533623 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384694 Affx-122972117 AX-123255052 20 5529988 AAGGCCTGAATTTGGGGTTATTGTCCTTCAGAGAA[G/T]CGAGAGCCAAGTGCCTTTGAGTGCAGTGAGATGGA K 2 1 2 1 101000 f 74 goat snp52461-scaffold782-778264 20 5580876 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419063 Affx-122945807 AX-123289411 20 5562288 GAGTCCCTGGGTTTCAAAACAGGAAGTAGCTCAAC[C/T]TGGGTTGCTGTTCCTGGCAGCTTCCCTTCCCGGCA Y 2 1 2 1 101000 f 74 goat snp52460-scaffold782-745964 20 5613172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438476 Affx-122931233 AX-123308814 20 5593779 AAAAAAACAAAAACACGAAAAAACAGAAGAGGAAG[C/T]GTCCTCCTTTAAAACACAAAAGCAGTGCCTGGCTC Y 2 1 2 1 101000 r 74 goat snp52459-scaffold782-714473 20 5644373 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786879 Affx-122924929 AX-385273908 20 5627653 ATAGCTATACTTACTTACAAGCCAAGATCTGAAAA[C/T]AGTCATCAAATGTCCACAAGACCACTAAGTAGCAA Y 2 1 2 1 101000 r 74 goat snp52458-scaffold782-680599 20 5678190 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277282 Affx-1111835833 AX-519550786 20 5651540 ACCACCTTCAGGAATCTGGCAGTGCTTTTCAGACA[A/G]TGGCTCCCATCCCACCGGCGCGCATGAGACGGTTG R 2 1 2 1 101000 f 74 goat Random2.2K-1828 20 5651540 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403558 Affx-122957590 AX-123273911 20 5665397 CATCTGGGAGCTTACTGGACGACATCGTGATGAAC[C/T]GTTTAGCCCCAGATGAACACTCTGAAGAGAAGATA Y 2 1 2 1 201000 f 74 goat snp52457-scaffold782-642855 20 5716305 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409924 Affx-122952878 AX-123280275 20 5737756 TCAATGGACCAAATTTCTGAATTCAACTTGGTATG[C/T]ATAAGACTGGAAAGATCATCACTCCCACTCTAACA Y 2 1 2 1 101000 r 74 goat snp52455-scaffold782-570496 20 5789419 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406304 Affx-122956064 AX-123276656 20 5798799 GCTTTCAAAGGCATCATGAGGTCACACAGATCACC[G/T]GCATGCCTTTGGTCTGAAGCAGTGTTCAGTAAGTG K 2 1 2 1 201000 r 74 goat snp52454-scaffold782-509453 20 5850686 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444732 Affx-122926407 AX-123315069 20 5843051 GCTGTTTCTCCATTTGTTCTCCAACTGGAAGCTGG[C/T]GCAGTGAGTGATCTCCTTGGCAGCGTCCCCCCACA Y 2 1 2 1 101000 f 74 goat snp52453-scaffold782-465201 20 5895366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380427 Affx-122975303 AX-123250785 20 5896503 TTACCTATGATATATTAACTATTTTAGAACATAGT[A/G]TAAGGGGGGATCATTTTTCTTTAGGCTCTGAGTAA R 2 1 2 1 102000 r 74 goat snp52452-scaffold782-411749 20 5948152 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277284 Affx-1111835834 AX-519550788 20 5909684 CCCTCCAGATCTTAGGCTCCACTCTAGGAAGAAGC[A/G]GGGGAATATTTGATCATGTCCTTTCTAGCTAGTGA R 2 1 2 1 201000 f 74 goat Random2.2K-1832 20 5909684 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800917 Affx-122956432 AX-385287832 20 5956788 CTCAGGTCTCTCACTCCTGAAAAGATAGGTTCGGT[A/G]TTGTCTGGTTGGGAAACTGCAATCCATATATGGTC R 2 1 2 1 101000 r 74 goat snp52450-scaffold782-351464 20 6008661 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376111 Affx-122978883 AX-123246470 20 5995560 AAGTATTTTGTGGGGGCATTTATTACCAAACAAGC[A/G]CGAGTGGAATTTTACAAGCAGAGCCCAGAGCAACT R 2 1 2 1 101000 f 74 goat snp52449-scaffold782-312692 20 6048311 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419716 Affx-122945908 AX-123290064 20 6032089 TCTCCTTTGTTTACCCCCCGAGAGTTCTGAGTACC[C/T]TCTTGTGCTTCTGAGAACTTGATGACCTCTCAGCC Y 2 1 2 1 101000 r 74 goat snp52448-scaffold782-276163 20 6085431 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434065 Affx-122934187 AX-123304406 20 6068019 CTTCCCCAGAGAGCTACTTCTGGTCTCTGCTGACC[C/T]CTCGTGTCAGACCTGCCTCTTCTTCTCACATTACA Y 2 1 2 1 201000 f 74 goat snp52447-scaffold782-240233 20 6121398 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774459 Affx-122942449 AX-385261595 20 6105245 ATCACTGTTGATGGGCTGACATGGGTTCTGGAAAC[A/G]CATCAGGACCATGTCAACTGTTGGCCCATTTCACT R 2 1 2 1 201000 r 74 goat snp52446-scaffold782-203007 20 6159513 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423383 Affx-122943133 AX-123293729 20 6135147 TTTGTAATGGAAGCCTGATTCTCTGAAGACCCATT[C/T]GAGAATTAATGAAACTGAAGCTTGGAGTGGGTATG Y 2 1 2 1 201000 f 74 goat snp52445-scaffold782-173105 20 6190246 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399881 Affx-122960221 AX-123270236 20 6211601 CTTGGCTGAGAAAATTAGTCTACAGAGAGAAATAA[C/T]GACATCTGCACTGAGAGAGCCTGAGAAAGAGTTTC Y 2 1 2 1 201000 f 74 goat snp52443-scaffold782-96651 20 6265585 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769922 Affx-122943648 AX-385257091 20 6246253 TCAGTCGTCCTCCTTCCTATCGGTCTCTTAACTGA[C/T]TTGTGTTTCATTAGTACATTTCTCTCTGGATCTTA Y 2 1 2 1 101000 r 74 goat snp52442-scaffold782-61999 20 6300217 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438721 Affx-122930845 AX-123309058 20 6300372 GAAGACCATACTTGGATATAGGTGGGAGGTCATGA[A/G]GCACAGGGGTTGAATCCTCAGTGCTGGGTCATTTC R 2 1 2 1 201000 f 74 goat snp52441-scaffold782-7880 20 6354140 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789061 Affx-122945093 AX-385276074 20 6310637 ATCCACTCGTGAGTTCCCACTGCACTTACAGTGAA[A/G]TCAGCCTCACAACTGAAAGCAACGTAATTTGCTCT R 2 1 2 1 101000 f 74 goat snp10065-scaffold1357-2286 20 6364199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410221 Affx-122952559 AX-123280571 20 6339411 CCAATAAGCTATAGATAAAATATCTGAAATATGCC[A/G]CAGAACATACCAAGTGTGTGATGGATGTTAACTGC R 2 1 2 1 101000 r 74 goat snp10066-scaffold1357-31060 20 6393350 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449410 Affx-122922696 AX-123319745 20 6371265 TGCCTGGGCAAATTGTTGTGCTAGGTCTAGGATGC[A/G]TCTCAGATGGGTTCTCTGCGGGTTGTGTGCATGTG R 2 1 2 1 201000 f 74 goat snp10067-scaffold1357-62914 20 6422939 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778203 Affx-122974158 AX-385265318 20 6415942 TGAGAAAGTATGATGAGAGTCTAGAGAATGAAAGC[A/G]GAACTCTGATAACTGCGCTAGAAACAGAAAGAAGA R 2 1 2 1 101000 r 74 goat snp10068-scaffold1357-107591 20 6467568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419679 Affx-122945936 AX-123290027 20 6450975 ATATCGCCAACATGGTATGGTCATCTGTTATCTCA[C/T]GAGTAGATTCTCCCTGCAAACCCAGAAGATCAGAA Y 2 1 2 1 101000 f 74 goat snp10069-scaffold1357-142624 20 6502521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789762 Affx-122935097 AX-385276770 20 6549046 TTCTAGGTTTAATTGGATAAGCAAATGTTAGACTC[A/G]CAGTCTTGTGGCCAGCTTCAAAGTTCTCTTTCCAA R 2 1 2 1 101000 r 74 goat snp10071-scaffold1357-240695 20 6599604 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438665 Affx-122930887 AX-123309002 20 6609130 GCTGTAAATTCTTTTTTTCACTTTCTTTTTCTTTT[A/G]CCTAGAAAGGACATCTTGAGTTATGGCCTTGCTCT R 2 1 2 1 101000 r 74 goat snp10072-scaffold1357-300779 20 6660435 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387898 Affx-122970464 AX-123258256 20 6624241 CTGGCTGAATTCTCGCAGGGTGTGATCCTTCTAGA[G/T]CTGTCCCTGTGGCTGCCAGCGGCATAATTCCTGAC K 2 1 2 1 201000 f 74 goat snp57334-scaffold913-4055 20 6673406 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442201 Affx-122928791 AX-123312538 20 6658713 GTCTACTGGACACTTCTCTTCACATGGTCTTACTG[G/T]GAACAAGGCAAGAAAATGAACTTTCTGTTAATTGA K 2 1 2 1 101000 f 74 goat snp57335-scaffold913-38527 20 6708261 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377161 Affx-122978216 AX-123247520 20 6687713 GAGAAAGGAAAGAAACTAATAAACTTGAGAGTATT[A/G]TCCAAGGAAAGAGAAACTTGACAGTAGTCAGTTGG R 2 1 2 1 201000 f 74 goat snp57336-scaffold913-67527 20 6737468 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789720 Affx-122923763 AX-385276728 20 6736508 TCATAATAAACTGAAGCTATAAGATAGCCTTTTTA[C/T]GTAAGTGAGTCTTCTTAATTGATGGATAATGAATA Y 2 1 2 1 201000 r 74 goat snp57337-scaffold913-116322 20 6786557 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419656 Affx-122945953 AX-123290004 20 6780678 AATGAAGCTCACAGTAATAAAATACCCTAAATACA[C/T]GTGTGACAGAATTATGATAGATTCTCAGTTACTTT Y 2 1 2 1 101000 r 74 goat snp57338-scaffold913-160492 20 6831484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425258 Affx-122940985 AX-123295604 20 6812537 AGGATTAAAAAATCAAGAAAAACGAAAATCAGACT[A/G]CATCATGCAAAACAGGAATAGCTAAATAGGAAAAG R 2 1 2 1 101000 r 74 goat snp57339-scaffold913-192351 20 6865815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414131 Affx-122949707 AX-123284480 20 6841209 ACCAACTTCCATTACCTTGTCCCAGTGCCCTGCCC[G/T]TCTGTTACCTGAACCCGCTGAGCTTTCTCTTCCCT K 2 1 2 1 101000 r 74 goat snp57340-scaffold913-221023 20 6894998 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437479 Affx-122932370 AX-123307817 20 6894937 TTTGGTCAATGACTCAAATTAAGTTTTCACCAAAA[C/T]ACCTAGAAAAAGAAAATTTGGAACTTCCTTGATCG Y 2 1 2 1 101000 f 74 goat snp57341-scaffold913-274751 20 6950066 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763609 Affx-986698138 AX-385251457 20 6918386 TTACATACATATTATCTTGTTTATTCCTCCAGAGT[A/G]TACATAAAATCAGTGTCAGTGTCCCCCAAAGTTCT R 2 1 2 1 600010 f 74 goat 20_6918386 20 6918386 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 38413077 Affx-122950961 AX-123283426 20 6926470 ACTGAAGTCAGCTTTGGGGTGTCGTGGGCTCTGGG[C/T]ATGCCAGTGGCTCCTGGGGCAAGGGAAGCCATCTT Y 2 1 2 1 101000 f 74 goat snp57342-scaffold913-306284 20 6981267 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431279 Affx-122937102 AX-123301620 20 7032473 TCGGAACACTACAGACTCCTTTCTTAGAAGAATGT[A/G]TATTTTCAAAAACATCTTTTGTTCAGCTTTAGGGA R 2 1 2 1 101000 f 74 goat snp57344-scaffold913-412287 20 7088655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398035 Affx-122961766 AX-123268390 20 7077888 GATCATCTGAAGCACTTAGAAAGCATATATAAGAT[A/G]CCTGGTTCTCACTCCAGAGATTCTATTAAGTTGGT R 2 1 2 1 201000 f 74 goat snp57345-scaffold913-457702 20 7133891 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396305 Affx-122963086 AX-123266660 20 7150767 TAGTCTGCCTCTAAGAATTTCAAGGTCTACAGGGA[C/T]GCAGACAACTACTAATAATTCCAGTGCAAAGTGAT Y 2 1 2 1 101000 r 74 goat snp57347-scaffold913-530581 20 7207362 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400246 Affx-122960146 AX-123270601 20 7200067 ACAGAGTTAGACACAGCTGAAGTGACTGAGCATGT[A/G]CTGCTAAGTCGCTGCATACGTGCAATTTCTATGTT R 2 1 2 1 201000 r 74 goat snp57348-scaffold913-579881 20 7256669 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793861 Affx-122931757 AX-385280830 20 7250798 GGACCTTAAGGCAGTATATGCATTTGTTATAAATG[C/T]TTCTTGAGAATCCCTCTGCTGAGTTCAGAGAGTCA Y 2 1 2 1 101000 r 74 goat snp57349-scaffold913-630612 20 7307141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422134 Affx-122943548 AX-123292481 20 7281741 CAGTCTGAGGCACCATTCAAGAGGGATGCTAAGAA[C/T]GTAGGGTGGGTTCTGAGGCATCTATAAAGATAATT Y 2 1 2 1 101000 f 74 goat snp57350-scaffold913-661555 20 7339359 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403790 Affx-122957977 AX-123274142 20 7319709 CTGAGATGTGAGACAAAACAGTCCCCTCTGTGGGA[A/G]CCAGTTATGTCTTCCTTCTTGCCTTTTAGAGTCAT R 2 1 2 1 202000 f 74 goat snp57351-scaffold913-699523 20 7377480 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446700 Affx-122924737 AX-123317036 20 7348854 CCCAGGTAGGCAAATCCAAATGAGCCATTTCCTTT[C/T]TCAAGCCGGAGCGTTGTAGGGACCTAACCCTGCAG Y 2 1 2 1 101000 f 74 goat snp57352-scaffold913-728668 20 7406634 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439021 Affx-122930350 AX-123309358 20 7382492 GCCTTTCTGCGTGAGCAGGAAGCTTTCTTTTGCTC[A/G]CTACATTGTCCCCAGTACCTATAACAATTTCTGGC R 2 1 2 1 101000 r 74 goat snp57353-scaffold913-762306 20 7440277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273950 Affx-1111833946 AX-519547556 20 7403572 GACAGAAAGATCTAGGTCAAAATTTTGTTCTGCAG[A/C]TATTGAGGATGTGTTTTAAAAAATTATTTTTCAAC M 2 1 2 1 201000 f 74 goat GoatD01.011248 20 7403572 C A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38410425 Affx-122952407 AX-123280775 20 7421048 CACCTCTCGCTTCATTTATGCTCTAGCTGTGTTCC[A/G]CCTTTCAACTCTGTGGAATCCATACACAACACATA R 2 1 2 1 101000 r 74 goat snp57354-scaffold913-800862 20 7478795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416526 Affx-122947766 AX-123286874 20 7457045 GATCCTGAAGCATGTATGTCTCTCCACCGCTAGCA[A/G]AAGGCTAAAGAGATATGAAACAGCAACGAAACAAA R 2 1 2 1 201000 f 74 goat snp57355-scaffold913-836859 20 7513902 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421620 Affx-122944474 AX-123291967 20 7503859 GAGTGAGACTTAGTGGGTCCCAGTCTGGCTGGGTC[A/G]TATACCAGCAGAGGGCCATGAGTATTCCACATCTG R 2 1 2 1 101000 r 74 goat snp57356-scaffold913-883673 20 7560512 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419951 Affx-122945209 AX-123290299 20 7542427 GAATTGTTCTGGAGCTGGGAGCCTGTTTACCCTTA[C/T]GCAGGGGCCAGGCTGGACCCTACCAAAGATAATTT Y 2 1 2 1 101000 f 74 goat snp57357-scaffold913-922241 20 7599086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414590 Affx-122949364 AX-123284939 20 7583449 TTCCATCCCCACTGTTGCCTGGAGATTTACAGTAC[A/G]CCTCAGAATTTAAAAGGCTTCGAGAAGCCAGGCAG R 2 1 2 1 101000 r 74 goat snp57358-scaffold913-963263 20 7640897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378329 Affx-122977340 AX-123248688 20 7642907 TTTCTTGGCTGCCAAGTCACTGATGACAGCACCCC[C/T]GGCAGGTTGGACAATTAATATAGCTCCAATCCACA Y 2 1 2 1 101000 r 74 goat snp57360-scaffold913-1022721 20 7701210 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272076 Affx-1111833209 AX-519545839 20 7645009 AGGGATGCCTGACATGCTGCGGTTCATGGGGTCAC[A/G]GAGTGGGACACGACTGAGCGACTGAACTGAACTGC R 2 1 2 1 303000 f 74 goat 20_7645009_AF-PAKI 20 7645009 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320781410 Affx-122972376 AX-385268495 20 7686638 CTCACTTCTTAAACACTATTAAATACTAACTAGAG[A/C]GTAGCTTTTATTTGGAAATTTTCTATTATATTTCC M 2 1 2 1 201000 r 74 goat snp57361-scaffold913-1066452 20 7745063 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378645 Affx-122977100 AX-123249004 20 7723299 GCACCTCGGCCGATACATAATGAGATTATTACCGG[C/T]GGAAAATAATTTTAAAATGCCAAACCCCAGACCCA Y 2 1 2 1 103000 f 74 goat snp57362-scaffold913-1103113 20 7781629 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423013 Affx-122942975 AX-123293359 20 7776186 AACAGGTTATACAAACTCCAGGACAGAAGTGAAAG[A/G]CCTCACAGAAAGTGGCAGAACATGGACAGGGCCAC R 2 1 2 1 201000 r 74 goat snp57363-scaffold913-1156000 20 7834136 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785506 Affx-122975437 AX-385272551 20 7834282 GCACCATCTTTTGGAAATAGATCATCAATTTCCTA[C/T]GGTGTTCTCTAAGGAGATGCTGCTACCCTAGCAGG Y 2 1 2 1 201000 r 74 goat snp57364-scaffold913-1214096 20 7892320 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400190 Affx-122960189 AX-123270545 20 7929102 GGCTACTCTGAGGTCAGAATCCACTCCTGGCTGGA[C/T]GGGGCAGGAGCCTATGGTAACAAGACAAATCTAGG Y 2 1 2 1 102000 f 74 goat snp57366-scaffold913-1308916 20 7987065 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794330 Affx-122935593 AX-385281294 20 7961341 GCTGCTGGAAGCATGACAGGACCTGGGAAAAAAAA[C/T]ATGGACTTTTGTCTAAGAGCCATAAAACTGAGCAC Y 2 1 2 1 101000 r 74 goat snp57367-scaffold913-1341155 20 8019344 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441389 Affx-122928849 AX-123311726 20 7996796 ACTGGAGTTGAGATGAACCAACACACTGGACAAAA[A/G]TGGTTTCCAATCCATAGTGAGCAAAAGCTTGGATG R 2 1 2 1 101000 f 74 goat snp57368-scaffold913-1376610 20 8054735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800356 Affx-122974160 AX-385287278 20 8030493 CATTTCACTGCTGAGCTAAGACTATCCTGATAATA[C/T]ACTATAAAAAACACTTTTGAGATTTAAAATCAACA Y 2 1 2 1 201000 r 74 goat snp57369-scaffold913-1410307 20 8088634 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417663 Affx-122946836 AX-123288011 20 8087133 CAGATGAAAGCCAAAAGAGGGAAATGAAGAAAATT[A/G]CATACAAATCCTTCATAACTTTTACACTTCTAGTT R 2 1 2 1 201000 r 74 goat snp57370-scaffold913-1466947 20 8145397 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413143 Affx-122950361 AX-123283492 20 8153762 CTTTAGCATTCGGCAGGCTCCAGATTTTCCCCTCC[A/G]TCCTCGGAAATTTTCACACTGCCTCTGTATAGGTC R 2 1 2 1 101000 r 74 goat snp57371-scaffold913-1533576 20 8212053 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774549 Affx-122965137 AX-385261683 20 8196183 AACGCTACTAGTTTATAGAGATGTAAATTATAGCA[C/T]GGGCAGTTGGAGAATAATAGCTTCATCTTTTTCTT Y 2 1 2 1 101000 r 74 goat snp57372-scaffold913-1575997 20 8254790 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444892 Affx-122926262 AX-123315229 20 8241988 ATTTATTTGTAATAACTTGGGGATTTTATGAGCCC[A/G]CAAGAGGATGTAATTTAAGAAAATATTAGCAAGCT R 2 1 2 1 101000 f 74 goat snp57373-scaffold913-1621802 20 8300882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425944 Affx-122941187 AX-123296290 20 8282423 ACAGCTGCTTTCAGCTCTGGGTGCCCCCTAGAATC[A/G]TGGCACCTTTAAAAAAAGTATACCCTTTGTATGAG R 2 1 2 1 101000 r 74 goat snp57374-scaffold913-1662237 20 8341184 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790965 Affx-122976761 AX-385277962 20 8312243 AGAGTATCTCAAGGTTGCAAGGAATGTTATCTCTT[A/C]TATAAAACTGTTACCATATGCAACTACTCTATCTG M 2 1 2 1 101000 f 74 goat snp57375-scaffold913-1692057 20 8370993 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415369 Affx-122948767 AX-123285718 20 8349245 ACAATTATCAGTTGTGCCAGCAGGCTTTATTAAAT[C/T]CTCCATTTCTTTGGTTATAACTTTCTTTATCACAT Y 2 1 2 1 101000 f 74 goat snp57376-scaffold913-1729059 20 8406693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428882 Affx-122938333 AX-123299224 20 8413296 AGCCACAAGGGAAGCCAAGATAAGAACTGGAAACA[C/T]GGAAGGGGTAGGCAAGAGAGATCAACTTCCTCCAA Y 2 1 2 1 101000 f 74 goat snp57377-scaffold913-1793110 20 8470991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778053 Affx-122947614 AX-385265169 20 8442350 GTTGCTTTTCAATCTAACTTGTGGTGTCTCCCGCT[A/G]TATGTGCACAGCCTAGTATTTAGCCACAGACTCAA R 2 1 2 1 101000 f 74 goat snp57378-scaffold913-1822164 20 8500725 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785354 Affx-122962548 AX-385272399 20 8481124 AATCCCACTAACATGTGAAAGCAAAGATCTCAGAC[A/G]TCTCAGATCAAATTCTACTAGACGTACAGATGCTT R 2 1 2 1 101000 f 74 goat snp57379-scaffold913-1860938 20 8540054 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790694 Affx-122920725 AX-385277695 20 8523515 TCATTTTGGTCAATCTAATGAGAACTAAACCTAGT[A/G]TCTCACTGTTGTCTTACAGTAATTGCTCTGATTGA R 2 1 2 1 101000 r 74 goat snp57380-scaffold913-1903329 20 8583663 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794958 Affx-122959453 AX-385281918 20 8579232 ACAAAATTTCCATTACTGAAATGAGCTCCCTCTAG[C/T]GCCCACAGATAGAACAAATATGTATGAAACAGCTT Y 2 1 2 1 101000 r 74 goat snp57381-scaffold913-1959046 20 8639476 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437841 Affx-122932093 AX-123308179 20 8651238 GATGAGGGGTGCGATTTCAGAAAGAATGTTCTCAA[C/T]AGAAGACCTATGTGAGGAGGTACAAGGAGTGGAGG Y 2 1 2 1 101000 f 74 goat snp57382-scaffold913-2031052 20 8711529 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453125 Affx-122920012 AX-123323458 20 8684696 AAGATTTTGCACAGGTATATCAGCTTTCCACATTG[C/T]GCAGGTTACACACGATACAATACCAATCTTATTCC Y 2 1 2 1 101000 f 74 goat snp57383-scaffold913-2064510 20 8745608 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405597 Affx-122955929 AX-123275949 20 8715626 GAGAGAGAAATGCAGGTTAGACATCATGTAACCTG[C/T]ATACAAGTGGGGGACCTGAATTTGGAAAATTATGG Y 2 1 2 1 102000 r 74 goat snp57384-scaffold913-2095440 20 8776463 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406468 Affx-122955177 AX-123276820 20 8772171 CTAAGGAATTTGCCTAATAGTTTGGAAATAGTTGA[A/G]TTGGAAAGAAGTAAAGTATTATTTAATGTATGTGA R 2 1 2 1 101000 f 74 goat snp57385-scaffold913-2151985 20 8833744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407763 Affx-122954973 AX-123278114 20 8820530 TTGTAGGATGTTCTGTTTCTGTTCACCTCTAGCTT[A/G]TTAGTCCTATCTTTCTTCCTTCAATAATCTTTTAG R 2 1 2 1 101000 f 74 goat snp57386-scaffold913-2200344 20 8882790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383984 Affx-122972929 AX-123254342 20 8863237 GAATTGCTGGAAATGTAGATTTGTAGTGAGTCTTT[A/G]CATATTTTACATATGAGGAAACTGAGGCTCAGGAA R 2 1 2 1 101000 f 74 goat snp57387-scaffold913-2243051 20 8925847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414889 Affx-122949129 AX-123285238 20 8913789 ATCATCAAAGGAGTTACCTCAGCTGCCCGTTCACC[A/G]TGTCACACCTAAAAGGATTAGAGCTGAGATAAATC R 2 1 2 1 201000 r 74 goat snp57388-scaffold913-2293603 20 8977044 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414464 Affx-122949566 AX-123284813 20 8946394 GACAGTCGAGTGGTTTCTAGGGTCTTCCGCTCCAC[A/G]ACCTGCATTTTATTCCTTCTGCGCTATTGAGATGC R 2 1 2 1 101000 r 74 goat snp57389-scaffold913-2326208 20 9009425 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793801 Affx-122968168 AX-385280773 20 8992095 TTTATGGACTAGTTACTATAAACAGGAAAGGAGGG[C/T]ATCAAGAGAGCCTATTTAGGAGTAATTAGGAAAAC Y 2 1 2 1 101000 f 74 goat snp57390-scaffold913-2371909 20 9055384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394082 Affx-122964962 AX-123264437 20 9020691 CCCCAGTCTTCCTGTGGAGCCTTATTACCCTGGAG[C/T]GTAAAAGACTTCTGAGCACCAAACAAATAAACAAT Y 2 1 2 1 101000 r 74 goat snp57391-scaffold913-2400505 20 9083809 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442765 Affx-122927744 AX-123313102 20 9086854 AGAGACATGCTGAAGCAATAACAAATCCTAAACTA[C/T]ATTACATTATATATTATTACAGATAAAAACAGACT Y 2 1 2 1 101000 f 74 goat snp57392-scaffold913-2466668 20 9150605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768119 Affx-122942343 AX-385255320 20 9129111 AAGGACTTGTATTTCCAAAAGCTGTGTGTGCCTCT[A/G]TGATGCTAATCCTTTTACCTTCCTGCAGGGACACT R 2 1 2 1 201000 f 74 goat snp57393-scaffold913-2508925 20 9189056 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416620 Affx-122947624 AX-123286968 20 9161890 TGAGTCGATGGCGTTCCTACCGTGCAGTGGGCACC[G/T]TCACAATCACTTTCCACCCAACACACACACACTTG K 2 1 2 1 201000 f 74 goat snp57394-scaffold913-2541704 20 9221723 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424473 Affx-122941765 AX-123294819 20 9206063 AGAACTGAAGAATACAGAGAGCGATATGAGGTTAT[A/G]TTGACTTTTATTTTGAAAAGCACCTAGATTGCCAA R 2 1 2 1 101000 f 74 goat snp57395-scaffold913-2585877 20 9265779 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774829 Affx-122977863 AX-385261963 20 9240615 ACTTGTCCAGATTTTCATAATATTTATGGAAGGCT[A/G]GGATTCACATTTAGATTTTGGGACTCTAAAGCCTA R 2 1 2 1 101000 f 74 goat snp57396-scaffold913-2620429 20 9300935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443614 Affx-122927304 AX-123313951 20 9295477 GAGAATCAAAGTTTAGATACCTTGTGGGATACCTC[A/G]TGGGTGATTCTGCTTCCTGTCAATGGGTATATAAA R 2 1 2 1 101000 r 74 goat snp57397-scaffold913-2675291 20 9356238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453376 Affx-122919932 AX-123323709 20 9345259 AGTCAGCAGAACCTGACACCACTGCCACCAGTTGC[A/G]TGGCTGAGAGGGGGATGAGTTTGGAAATGGGTTCA R 2 1 2 1 103000 f 74 goat snp57398-scaffold913-2725073 20 9405755 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453252 Affx-122920408 AX-123323585 20 9395136 GAGAACAGGCTGGATCTCACACTACTCATGAAAAA[C/T]GGTTTTCCTGAAAATTGGACTCAGGCTCAGACATG Y 2 1 2 1 101000 f 74 goat snp57399-scaffold913-2774950 20 9455389 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387944 Affx-122970019 AX-123258302 20 9425110 ACTTCTCCTTCTGGATAATCATGGCTTTCTGATCA[C/T]GATTACCTGTATGCAAGCCGTACACTGTCAGTAAC Y 2 1 2 1 101000 r 74 goat snp57400-scaffold913-2804924 20 9485276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429728 Affx-122937608 AX-123300069 20 9475988 TGAGTGTGTGTGTCATACATGTATGTTTCATGTAT[A/G]TATTGACAGATGGGATTTTTCTTATTTATGCAAAC R 2 1 2 1 101000 r 74 goat snp57401-scaffold913-2855802 20 9535712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447198 Affx-122924993 AX-123317534 20 9516560 AAAGAGTCAGACACAACTGAAGTGGCTTAGCACGT[A/C]TGCACGAGTTAAGAGACTGTGGAAGAAATCCCAAA M 2 1 2 1 101000 r 74 goat snp57402-scaffold913-2896374 20 9574120 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439196 Affx-122931041 AX-123309533 20 9573549 TCTTACAGTCACAGAAGAACAAAAGAGAAAGGAGG[C/T]GAATAGAAAACAAACAGCAAAAAGGCAAATCCAAA Y 2 1 2 1 101000 f 74 goat snp57403-scaffold913-2953363 20 9631270 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452834 Affx-122920733 AX-123323167 20 9616903 ATCACCAGCTTTCTAGCTCTTCAGAGGAGGGAGGT[C/T]AGGGGAGCCAGAGCAGGTATGCACACGGAACGCCA Y 2 1 2 1 101000 f 74 goat snp57404-scaffold913-2996717 20 9674817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419607 Affx-122945991 AX-123289955 20 9647196 AGTCCACATTTTATGTGACTGGCCTGAGGCCTTTG[C/T]CCCCTTTCTTCATTGCCCTTTTCTACATCCTGCTA Y 2 1 2 1 201000 r 74 goat snp57405-scaffold913-3027010 20 9704942 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452810 Affx-122920752 AX-123323143 20 9698422 AGTGGGAAAATCTAAATATCTATTCATTTCAAACC[A/G]CATGTGCTGAGTACTTATTATGGGCAAGGCACTTT R 2 1 2 1 101000 f 74 goat snp57406-scaffold913-3078236 20 9755603 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388560 Affx-122969178 AX-123258918 20 9739518 TTTTTATCAACCCAGCAACTGCTATTGTTTGGTTG[C/T]GAATTCTGAGAGTTTATGCATAGGCCATGAATAAA Y 2 1 2 1 201000 r 74 goat snp57407-scaffold913-3119332 20 9797031 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438661 Affx-122930890 AX-123308998 20 9816089 TCAAGTAAAATTGAAACCAATTTGGATTGAAGCTT[A/G]TTTGCTTTATTTCCCAGTTGCTCAAGCATAGAATA R 2 1 2 1 101000 r 74 goat snp17082-scaffold1785-26080 20 9873689 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409356 Affx-122954172 AX-123279707 20 9846205 TCAGAGGCCTGGAGGAGAGGAAATGAGGCAACCCA[C/T]GAACTTTCAAAAAAATTTTTTGACGCTGCTAAAAG Y 2 1 2 1 101000 r 74 goat snp17083-scaffold1785-56196 20 9903744 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445628 Affx-122925093 AX-123315965 20 9876725 GGGAAGCCCCTTTTGGCACCTACAGCTGAGTAATA[C/T]AGCAAGCACAATGATATCAAGGTTGGTCCAGGTAG Y 2 1 2 1 101000 r 74 goat snp17084-scaffold1785-86716 20 9934310 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778407 Affx-122940055 AX-385265522 20 9961419 TGTTTTTTCAGAAGTTTAATTTGAACCCTAAAGAT[G/T]TGCTTGGGTGGATAAAGGAATTATCTACGTAAATC K 2 1 2 1 101000 r 74 goat snp17086-scaffold1785-171410 20 10018553 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393471 Affx-122965836 AX-123263827 20 10039853 ATTTAGAAAATATTACCAATTCATTTTGCTCAACT[A/G]CATCTGTCATAATTCAAATGAATGTAACTCAATTG R 2 1 2 1 101000 f 74 goat snp17088-scaffold1785-249844 20 10097420 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763623 Affx-986698152 AX-385251466 20 10048771 ATGATACAGCAATTATATTCCCATGAATGTACCCA[A/T]GAGAAATGAAAACATGTCCATACAGAAACTTGGAT W 4 1 2 1 600010 f 74 goat 20_10048771 20 10048771 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 38433125 Affx-122935694 AX-123303466 20 10086943 CAGTATTTTGTGCCTGTGTGGGTGTATATATCTGC[A/G]CTTAACATCACATTTTTAATGTTTTGATACATTCT R 2 1 2 1 101000 f 74 goat snp17089-scaffold1785-296934 20 10144483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391891 Affx-122966962 AX-123262248 20 10116080 ACTTCTGTGAAAACACCTTCAAAACTATATCTCTT[A/G]AGAATCTTAGATAGAAGCGTTTAAGATCTATTTGT R 2 1 2 1 101000 f 74 goat snp17090-scaffold1785-326071 20 10173588 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397654 Affx-122962606 AX-123268009 20 10173828 TTAGCATTACTGATTCCCAGTGCCAGTTGGCGTCC[A/G]TCGTTGCCTTCCTCCACATCTTTGATTCCAAGGCT R 2 1 2 1 201000 r 74 goat snp17091-scaffold1785-383819 20 10230349 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410443 Affx-122952391 AX-123280793 20 10223006 TATTTACAGAGTTAGTGCTTTTGATCTAGGTATGA[C/T]ACAGTTATTAAAAAGAAACAAACCCCTGCAGAACC Y 2 1 2 1 101000 f 74 goat snp17092-scaffold1785-432997 20 10278614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408851 Affx-122954008 AX-123279202 20 10250412 TGTGCTGTGTATGCTGGAATTTTTCAATTTCATGA[C/T]GTAGGCATGCAGAGGGAGCTTTTGAAGGAAGTTAC Y 2 1 2 1 201000 f 74 goat snp14653-scaffold1591-11752 20 10306534 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272055 Affx-1111833188 AX-519545819 20 10404922 CTCACTCCCAGAGCCTGACTTTCCGTCTCTGGCCA[A/G]GGAATCGAAATCCTGCTTCAAGCTGCTGCAGTCCC R 2 1 2 1 202000 f 74 goat 20_10404922_AF-PAKI 20 10404922 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320800374 Affx-122936318 AX-385287296 20 10412318 AACGGTTACAGATACTTAAGTATTTAACTCCTAAA[C/T]GAATACACAGGCTGTAAAAGCTAAACCCAAATTCT Y 2 1 2 1 101000 r 74 goat snp14657-scaffold1591-173658 20 10467914 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399329 Affx-122961369 AX-123269684 20 10516151 TCCAAAATTATATAACGGGTAAGGCAAGACTCCCC[A/G]CTAACTGGGCAAAGTGCACCCTAGGGTCAGCTGTT R 2 1 2 1 101000 f 74 goat snp14659-scaffold1591-277491 20 10572866 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802685 Affx-122920009 AX-385289584 20 10545487 AAGACGTTGTTTCCTGGTTAGGTGACAAAATGGCT[A/G]TTAATAGCTCTAAGGTTTCACTCTCAGCTTTAAAT R 2 1 2 1 101000 f 74 goat snp14660-scaffold1591-306827 20 10602149 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446855 Affx-122925255 AX-123317191 20 10575541 GCCTTGTGTTGTCTTTCTTCCACTTTTCATGGCAA[C/T]GTCTCAGTGAGGCAACTTTGTGTCTATATTCCTTT Y 2 1 2 1 201000 r 74 goat snp14661-scaffold1591-336881 20 10632203 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384952 Affx-122971916 AX-123255310 20 10634427 CCTAGTTCTTTGGTTTCCTTTAGTCTTTGCTGCAA[C/T]GTCATGTTTCTTCTTCTCTTCCTCCTTTTCCTCCT Y 2 1 2 1 101000 f 74 goat snp14662-scaffold1591-395767 20 10690223 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381256 Affx-122974490 AX-123251614 20 10663254 TTAAGCCTTGAAGTGAAGGGGTGTGTTCAAGGACA[C/T]AAGGAATCTAGTGTAGGAGTCAGAAGTCTAACCTG Y 2 1 2 1 101000 f 74 goat snp14663-scaffold1591-424594 20 10719081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381299 Affx-122974455 AX-123251657 20 10719950 ATTTTAGAATCAATGTCCTGAAAATGAGAAATTCC[A/G]GTGAAGTGATGTACCACACAACATCGTTTCCAGCA R 2 1 2 1 101000 r 74 goat snp14664-scaffold1591-481290 20 10769616 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789783 Affx-122964913 AX-385276791 20 10755032 GTGTTTTACATATAAATAGAGTAACTATATAATTT[A/C]TTATCCATAAGAAACACTTTTGAGTGTAAAAAGAG M 2 1 2 1 202000 f 74 goat snp14665-scaffold1591-516372 20 10804683 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424286 Affx-122941982 AX-123294632 20 10784804 GCGACAGAAGGTTATATCAAAGGCTTGGCTTCTTA[C/T]ATGGGGCCTTGTGGAATTTCCTTGCCTTGGAATCC Y 2 1 2 1 101000 f 74 goat snp14666-scaffold1591-546144 20 10834480 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802617 Affx-122928899 AX-385289518 20 10839015 TTATTGGATTGAAGTTCTGGTCATTTAATATTTTA[C/T]AACTTAGAAGAAAATCAGCTTAATGTGTTGAAGGC Y 2 1 2 1 101000 r 74 goat snp14667-scaffold1591-600355 20 10888066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787925 Affx-122959899 AX-385274947 20 10871052 GGATAAAAGGTTGTTGGAGGCTGATGCTCAGCGGA[G/T]ATTAATCTGCAGAGAGGTTTTTAGGTTGAGCTCTT K 2 1 2 1 101000 f 74 goat snp14668-scaffold1591-632392 20 10920757 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383275 Affx-122972727 AX-123253633 20 10903382 TTTCTATATGAAAAGACACTATATAGAAACACAAA[C/T]GATTTATAACTTATTTTTTAAACCATTTTAAAAAA Y 2 1 2 1 103000 f 74 goat snp14669-scaffold1591-664722 20 10953312 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783680 Affx-122935977 AX-385270738 20 10951639 GAGAGTAAGTAATACTAATGTACACGAATCCAATG[A/C]TGGCAGTGGGAAATAGTTATTCATGGAGATACATC M 2 1 2 1 101000 r 74 goat snp14670-scaffold1591-712979 20 11002283 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409136 Affx-122953298 AX-123279487 20 10989496 TTTCAAGTTTCAATTTGGGGCCTAAATTACATTTT[A/G]TTTAGTTCTGTTACCCTAAGTTGACATTGACAGAC R 2 1 2 1 101000 r 74 goat snp14671-scaffold1591-750836 20 11041104 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802542 Affx-122959674 AX-385289446 20 11055140 GGATGTTATTAACAATAGTGTAAGGACTGGGAGCC[A/G]CAGACTTCTGATTATTAAATCCTAAAATATTGTCC R 2 1 2 1 101000 f 74 goat snp14672-scaffold1591-816480 20 11107379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416919 Affx-122948050 AX-123287267 20 11146777 GAGTGCCTTGGCTGAATAATATACTTCTATTAGAG[A/G]GACTTTTTTTCCTCCTCTGTCTTTTGAACTGTGAA R 2 1 2 1 201000 f 74 goat snp14674-scaffold1591-908117 20 11199195 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377509 Affx-122977484 AX-123247868 20 11198086 TCATAAATATATTTTTCCTTCAGTTTTATAAAAAT[A/G]CTCTTACTCTTTTTCTCTCCCTTCATTTTTGCCAT R 2 1 2 1 103000 r 74 goat snp14675-scaffold1591-959426 20 11250701 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387914 Affx-122970451 AX-123258272 20 11235402 ATCACTCTTTCTTCTCCGAGTATAAACCCCTTGAG[C/T]GCAGATATCAGATATAATGCTTTGGTAACTTCTCT Y 2 1 2 1 201000 r 74 goat snp14676-scaffold1591-996742 20 11288573 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446023 Affx-122925856 AX-123316360 20 11275264 CAGGAGTTACATATGCTATATACTTCTGGTGCAGC[A/G]CAATCAAATATTCTCCTGGCTGCAACTCTTCATGT R 2 1 2 1 201000 r 74 goat snp14677-scaffold1591-1036604 20 11328889 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393153 Affx-122965542 AX-123263510 20 11310057 CAACTCCAAAGAACTGTAACAAACGCAGTCAGGCA[G/T]CAGCACTTCCAGCTTCCTGACTCTCTAGTCCTTCT K 2 1 2 1 101000 f 74 goat snp14678-scaffold1591-1071397 20 11363968 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383728 Affx-122972460 AX-123254086 20 11346653 GATGACCATGTGAGGCTTTCTGATCTAAGTTGAAT[A/G]GAAAGCTAGGAAAATAGCAGATACCCGGATAAAAA R 2 1 2 1 101000 f 74 goat snp14679-scaffold1591-1107993 20 11400629 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413302 Affx-122950195 AX-123283651 20 11378243 AACAAATCCCACAAAAATAAAATAATCATGAGTTC[A/C]TTAACTTTGTAACTGTTTAATGAGCAGTAGAGAAA M 2 1 2 1 103000 r 74 goat snp14680-scaffold1591-1139583 20 11432220 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379172 Affx-122976707 AX-123249531 20 11409314 TAAATTACTGAAAATATTAAAGAGATGTAGTTATT[A/C]GGCTGAAATTCACCCAAAGCAGCTCAGGGGATGAA M 2 1 2 1 101000 r 74 goat snp14681-scaffold1591-1170654 20 11463127 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413737 Affx-122950057 AX-123284086 20 11464765 CCCACTCACGGGAGACAGCATCTTGACTCTGCAAG[C/T]GTGTGCCCTTCAAGCCCCGCCTGGAGACGAACCCC Y 2 1 2 1 101000 f 74 goat snp14682-scaffold1591-1226105 20 11519319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449845 Affx-122922382 AX-123320180 20 11501011 GAGTCATGTTGGATTTGGGTGGGCCCTAAACACAA[C/T]GATTGGTACCCTTCTAAGGGGAGAGAGGTTTAGAA Y 2 1 2 1 101000 f 74 goat snp14683-scaffold1591-1262351 20 11554581 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417409 Affx-122947228 AX-123287757 20 11533740 GACTGAGGGACTCAGGACCAAGCTTACTGGCTCTG[C/T]ATCCCCAGCAGCCAGCATCATTCCTGCAGACCCAT Y 2 1 2 1 201000 r 74 goat snp14684-scaffold1591-1295080 20 11586781 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391551 Affx-122966634 AX-123261908 20 11627847 ATACATTTTTTTGCCATTAGCCTGTTGTTTACCAC[A/G]TCCTGCCTGTGGCTAGTCAGAAGGAAGATCCTGTT R 2 1 2 1 201000 f 74 goat snp14686-scaffold1591-1389187 20 11681672 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393175 Affx-122965524 AX-123263532 20 11658088 GATACAATTCTTCTTTCCACTTCTCCAAGTCTCTA[C/T]GTTCATGCTATAGCTCTGCAGACCCCTTGGACTCC Y 2 1 2 1 101000 r 74 goat snp14687-scaffold1591-1419428 20 11711804 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444947 Affx-122926688 AX-123315284 20 11714020 CACAATAACGGAAGACCCCAAAGAGTCCCTCACAA[G/T]CCTGAGACCACCCACTGGGCTGCAGAACCTAGTCT K 2 1 2 1 202000 r 74 goat snp14688-scaffold1591-1475360 20 11767966 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452792 Affx-122920236 AX-123323125 20 11750813 GGGAGCTCACAGTTTAGTAGGGGAGTTCATGCTCC[A/G]TTGCATTTGACTCTTTGCGACCCTGTGGACTGTAA R 2 1 2 1 201000 f 74 goat snp14689-scaffold1591-1512153 20 11804670 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447487 Affx-122924089 AX-123317823 20 11784666 CATTCACAAAGGTGTCCGAAGGCCCCTTACCTCAC[G/T]CAGTTTTTCTTTCTGGGTGAAATTCTCTGTATTTT K 2 1 2 1 202000 r 74 goat snp14690-scaffold1591-1546006 20 11838407 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388146 Affx-122969464 AX-123258504 20 11826467 ATTTCCTTTGCTCAAATTCACAACCCTCAGTGTCT[A/G]TGAGCATAATAATGATTGTCTTTTTTAATGCCACT R 2 1 2 1 201000 r 74 goat snp14691-scaffold1591-1587807 20 11880364 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775805 Affx-122921981 AX-385262936 20 11858015 CCATTATAATCACTAAATCATGCCTAGGTTTTAAA[C/T]ATTCAGGAATTAGTGTAATATAAAGTAGTGAGGAA Y 2 1 2 1 101000 r 74 goat snp14692-scaffold1591-1619355 20 11911821 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436878 Affx-122933234 AX-123307216 20 11901498 TGTACTTCCCATTGATAACAAAGGCTCCTTTGTCC[A/G]TGGCAAGAATACTTCAGTGGGTTACCATTGAGTGG R 2 1 2 1 303000 f 74 goat snp14693-scaffold1591-1662838 20 11954853 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772173 Affx-122923472 AX-385259328 20 11941971 TTCATCTTTTCCTTTTGACTGAGCCTAGTTAACAC[A/G]TTACTTTGGTCATTCTTCTGAGTACTCTGGGTGTG R 2 1 2 1 101000 r 74 goat snp14694-scaffold1591-1703311 20 11995190 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778224 Affx-122965974 AX-385265339 20 11986563 AAATGAATTCATATTGCCTGCTCGATTTCTGAATA[C/T]GAAAGAAGCTTTTAAGGAGCTAAGCCTGGCACAGC Y 2 1 2 1 101000 r 74 goat snp14695-scaffold1591-1747903 20 12040337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405832 Affx-122955876 AX-123276184 20 12022763 ATAACAATATGAGGTTTAGGCTGTAATGAGGATAT[G/T]GCCACAGGGCCAAGTATAGGGCAGTGTCCTTGGCT K 2 1 2 1 101000 f 74 goat snp14696-scaffold1591-1784103 20 12076982 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385947 Affx-122971550 AX-123256305 20 12088569 ACCATTGTTTCTCCAACACAATGGTATATAACAGG[C/T]GCTCAATAAGCAGTAAATGAATAAATAAATGCATA Y 2 1 2 1 103000 f 74 goat snp14697-scaffold1591-1849909 20 12143840 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780014 Affx-122943223 AX-385267113 20 12122832 TAAAACTCTAAATGTTGAGGCTGTTCAATCAGAAA[C/T]AAAAAGTCCTAACAGAGTGGTAGCTTTCAAAGCAA Y 2 1 2 1 102000 r 74 goat snp14698-scaffold1591-1884172 20 12177936 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788122 Affx-122960175 AX-385275142 20 12175667 AAGAAGTAGAATGCGTAAACAACTTAAATACAACT[A/G]GCCACCTTGCAGTACTTCCTCAAGGAGGTACACTA R 2 1 2 1 101000 r 74 goat snp14699-scaffold1591-1937007 20 12231730 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440902 Affx-122929220 AX-123311239 20 12207602 CATTTATAGACTGCTGTTTTGAAATGGGAGAAAAA[C/T]AGGAGGAAATCTGTGTAGATAACTCATTCTGAAAG Y 2 1 2 1 101000 f 74 goat snp14700-scaffold1591-1968942 20 12263802 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444774 Affx-122926353 AX-123315111 20 12258976 TCTGTGAGAACTAGAAGGCGAGCGTGGCCAATGAA[A/C]TATTCTAAGAGGTAATCAGGGGAAAAAAGGAAGGG M 2 1 2 1 201000 f 74 goat snp14701-scaffold1591-2020316 20 12315285 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429057 Affx-122938299 AX-123299399 20 12300284 TGACAGGTCAAAAGGACACAGATTTGGTTGTATTC[A/G]TTTAATCTTCTATGACATGCAGTTTACATAGTCTG R 2 1 2 1 201000 r 74 goat snp14702-scaffold1591-2061624 20 12356612 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381547 Affx-122974833 AX-123251905 20 12372230 TAGTCTTGCAAGAGTCTTTTCAACCACAGACCAAA[A/C]CACGTGGGTGGATGTGTATATACATGAATATGGGT M 2 1 2 1 101000 f 74 goat snp14704-scaffold1591-2133570 20 12428732 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445590 Affx-122925125 AX-123315927 20 12395069 TTCCCCTTCTCTCTTTTCCTCTCAGTTCTGTTTCC[A/G]TGTGGGATAATTCCGCATGTCCTAACTTGGTGGAG R 2 1 2 1 201000 r 74 goat snp17221-scaffold1797-414522 20 12451612 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408366 Affx-122953732 AX-123278717 20 12427552 TAACTAATCACTGGTGATTAACTTTAAGTAAGGTG[C/T]AGTGTTCATAAATCTATTTTTACTTACCTGTCTCA Y 2 1 2 1 101000 f 74 goat snp17220-scaffold1797-382039 20 12484062 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777443 Affx-122953748 AX-385264563 20 12456421 TTTCACAAGATGTGTCTAAAGTTGGTAATGTACAC[A/G]TCTTCTATCAGGAGATTTCTAGTACTTTGGGTCTT R 2 1 2 1 201000 r 74 goat snp17219-scaffold1797-353170 20 12512815 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802950 Affx-122962243 AX-385289841 20 12506430 TACCTTTTCCTTTGTGGAATGTGTAATACATAAGA[C/T]GTAGTTAAATGTATTTCTGTGTCTAATGTAGATAT Y 2 1 2 1 201000 r 74 goat snp17218-scaffold1797-303161 20 12562409 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388448 Affx-122969257 AX-123258806 20 12542099 ACTTGAGTTTGAATCTTAATTCTGTGATATTGTCT[A/G]TTGAATTAGTTAACTTATTTGGAATTCTGTTGCTC R 2 1 2 1 201000 r 74 goat snp17217-scaffold1797-267492 20 12598084 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384879 Affx-122971934 AX-123255237 20 12597269 GCACTTATGATAACGTGTCTCTGCATGGAGGCAGA[G/T]TGGCTCCATTGTGTTTTCATGCCTATTTTAGGACC K 2 1 2 1 101000 r 74 goat snp17216-scaffold1797-212322 20 12653281 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405478 Affx-122956022 AX-123275830 20 12663796 AAATTTGCGAATATTGACTTGATTTCTTTATTGTG[C/T]GTTTCAACCTTTTCTTTTTAAGGCTAATAGTATAT Y 2 1 2 1 303000 f 74 goat snp17215-scaffold1797-145795 20 12719771 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452101 Affx-122920847 AX-123322434 20 12702371 CTTGTTGACACCTTGATCTTAGATTCCTAGCCTCT[A/C]GAACTATGAGGTGGTAGAGTCTTGTGGTTTAAGCC M 2 1 2 1 201000 r 74 goat snp17214-scaffold1797-107220 20 12758465 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437179 Affx-122932124 AX-123307517 20 12759440 CTAGCGGTTTGCTGGCATGAGCTGGTTCCCTGTTC[A/G]GCCTGTATTCTGAGTTATTCAGAACATCCTCCACC R 2 1 2 1 101000 r 74 goat snp17213-scaffold1797-50151 20 12815449 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383647 Affx-122972527 AX-123254005 20 12795675 CGTTCTCATGATGCTCTTGATTTGCACTCTTGGCC[A/G]TTGGCCAACAGGAAAAGGAACCCAGATAATTCATA R 2 1 2 1 101000 f 74 goat snp17212-scaffold1797-13916 20 12851526 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768881 Affx-122975805 AX-385256058 20 12863319 GGTAGCTGTTGCTAATGTCAATAACACAGGTCCTA[G/T]CCTCATAGTAAGTCTTCCATAAAGCATGCTACAAG K 2 1 2 1 101000 f 74 goat snp24962-scaffold2563-53629 20 12918746 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429987 Affx-122938047 AX-123300328 20 12892132 TGCTCTGCCACAGCCTCTCTTGTGACCAAAGGCAC[G/T]TGTCCTGTGACTGGGAGGTCAGAGGTGCAGGTGAC K 2 1 2 1 101000 f 74 goat snp24963-scaffold2563-82442 20 12950551 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426113 Affx-122940632 AX-123296459 20 12922422 AACCACCTCTGTTTGCCAACTGGTCACACTTAAGA[C/T]GAACTAAGCAAGGCTGATTCCAAGAATGAACCACT Y 2 1 2 1 101000 f 74 goat snp43190-scaffold575-26608 20 12980872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448865 Affx-122923278 AX-123319200 20 12960619 TCCTGATAGGAATGACACTTTTTAATTTCCTTGCT[A/G]TCTGAGGATCCACCCGAAGATAATCAGGATAAACA R 2 1 2 1 201000 r 74 goat snp43191-scaffold575-64805 20 13019059 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277286 Affx-1111835835 AX-519550790 20 12970889 TGTTTTATTCCCACGGACTTCCCAGGCGGTACATG[A/G]TAAGAATCCGCCTGTCAGTGCAGGAGATGCAAGAG R 2 1 2 1 102000 f 74 goat Random2.2K-1837 20 12970889 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378350 Affx-122976833 AX-123248709 20 13035756 CCTAAGATTCTCCATGATCATACCCCTGCTGACCC[A/G]TTCAGCACCATTCCTTTGTGGTCCTAGGCACCCCT R 2 1 2 1 201000 r 74 goat snp43193-scaffold575-139942 20 13094104 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445987 Affx-122925880 AX-123316324 20 13070673 GAAATCCACCGTTTGGAACTCAGATAGCCTGGAGC[C/T]GCACCCCTAAACTTCTCCCATCCCAGCAGTCAGGA Y 2 1 2 1 102000 f 74 goat snp43194-scaffold575-174859 20 13128920 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780395 Affx-122954620 AX-385267488 20 13103775 TCTCTCCTTGAATGCGTCAGTAATACACCTTCAGA[C/T]GCAGAAGATCTCAGAGAATACCAGCTAAGATTGGG Y 2 1 2 1 201000 r 74 goat snp43195-scaffold575-207961 20 13162184 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391574 Affx-122966616 AX-123261931 20 13148144 AATGGACTGACTGTTCTTAAGGAAGCAAAGCAACC[A/G]TTTGGGTTGCACTGTAGCCCATCTGCCTGTCTGTA R 2 1 2 1 101000 f 74 goat snp43196-scaffold575-252330 20 13206752 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431344 Affx-122937055 AX-123301685 20 13178467 AGTGGAGTGCTGACTAATAGCAAGGTAAAAGGGAA[C/T]GGGTGGAAGAAAAAGGAAGATATAAACATGAACTG Y 2 1 2 1 101000 f 74 goat snp43197-scaffold575-282653 20 13237871 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272057 Affx-1111833189 AX-519545821 20 13191574 AATGTCATTGCTAATAATAAGACTTTGTATAAGAC[A/G]AAACCCCAAATCTGAGGCAAATGCTACATAAGAAA R 2 1 2 1 201000 f 74 goat 20_13191574_AF-PAKI 20 13191574 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38376105 Affx-122978889 AX-123246464 20 13222639 CTAATAGCAAAACAATGAAGGCTTGGATAAAAAAT[A/G]TATGATACATTCATATCACAGAAAATTTGGCAATC R 2 1 2 1 101000 f 74 goat snp43198-scaffold575-326825 20 13282695 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399191 Affx-122960621 AX-123269546 20 13303976 GAAAAGCAGGTTGTCTCTGATGCAGTAGGGAGCAG[C/T]GGGGACTATGGAAGATGAAATATTGTGTTAGCCAA Y 2 1 2 1 201000 r 74 goat snp43200-scaffold575-408162 20 13364164 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404870 Affx-122956483 AX-123275222 20 13346946 CCCTAGAATAAAGTAAATAAAAGCAGAAACCTTTC[A/G]TAAGTAGACTCTTGAGAAGTGATTCTGACCTCATT R 2 1 2 1 101000 r 74 goat snp43201-scaffold575-451132 20 13403143 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440437 Affx-122929410 AX-123310774 20 13385650 AAAATAACGAGACAGCTGCAGAAGTTAAGAGTTTA[C/T]ACTTGCTTCCTCACATGAAACTGGCTAGCTTATAA Y 2 1 2 1 101000 r 74 goat snp43202-scaffold575-489836 20 13442512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774057 Affx-122969519 AX-385261195 20 13494692 ATCATTAGTTATAAGTTTATTTAGATTCATATTGA[C/T]ATGGTCTAATTTTTGAGATTCATCAGATGTGGCTG Y 2 1 2 1 101000 r 74 goat snp43203-scaffold575-598878 20 13552797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798939 Affx-122971894 AX-385285869 20 13549599 ATAAATGCTATTTAATGAGAACATTCTTCCAAAAA[C/T]GGAAAATTGCTAGGCATGATAAGTGATTCAGTTAT Y 2 1 2 1 202000 f 74 goat snp43204-scaffold575-653785 20 13607833 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441329 Affx-122929433 AX-123311666 20 13591978 TTTTATCTTCCATTTTATCTAAAGATACTTAGACA[C/T]GCACATATATGTACACTTACATGTTAGAATACATA Y 2 1 2 1 201000 f 74 goat snp43205-scaffold575-696164 20 13650638 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782114 Affx-122937952 AX-385269192 20 13626311 AAGTAGTAAAAGTCCTGTTCAAACCAGCTCAGCAC[A/G]TTTCATTTTTCTCTCCCTGACCAATGTCTTGGACA R 2 1 2 1 201000 r 74 goat snp43206-scaffold575-730497 20 13685037 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395694 Affx-122963735 AX-123266049 20 13655536 CTTTGAACATTCTCTGGAAGATGAAATGTACAAGT[C/T]AGAGCAGCTTTGGCCTGGCTGATATACAGAGAAGG Y 2 1 2 1 101000 r 74 goat snp43207-scaffold575-759722 20 13714576 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783106 Affx-122966261 AX-385270173 20 13698152 TTTCTCATTGAGTAGACGCCTAGAGGAAAAGTAAG[C/T]ATGTAAGTTTCCTGGTTTGCAAATTGGAATTTAGG Y 2 1 2 1 101000 r 74 goat snp43208-scaffold575-802338 20 13756837 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779111 Affx-122974211 AX-385266216 20 13743306 TGAGGGTTTTATTACCAGTGCCCAATCTCTGTAAG[C/T]ATAAAGGAATGACGGTACAAGTTGACTATTAAGAT Y 2 1 2 1 101000 f 74 goat snp43209-scaffold575-847492 20 13801992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398604 Affx-122961485 AX-123268959 20 13788829 GCATACTTTGGTAGAAATATTTTGGAGGAGAATAT[A/G]TAGCAAGCAACAAAAGTCTGAAGGATATGCATACC R 2 1 2 1 101000 r 74 goat snp43210-scaffold575-893015 20 13847556 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441789 Affx-122929090 AX-123312126 20 13835689 GCCTGGGATAATGTGTTATTTGAGGCATAAGGATT[A/G]CCAGTTTTATCTATTTAAAAACTAACATGTCTTAT R 2 1 2 1 101000 f 74 goat snp43211-scaffold575-939875 20 13893223 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400101 Affx-122960734 AX-123270456 20 13934677 TAAATAAGTTGTAAGAGGTCAGAGGCCATCCAGAA[C/T]ATCTCAGTTTATCTTGAAGGCAATGATCCTCTTTG Y 2 1 2 1 101000 r 74 goat snp43213-scaffold575-1038863 20 13992084 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783792 Affx-122944263 AX-385270848 20 13963563 TTAGAAAAGAGACCTACCTAATATGCCTGGTTACT[A/G]AAAATTTTCCACTGAATTGCCTTTCAGTATGAAAT R 2 1 2 1 202000 r 74 goat snp43214-scaffold575-1067749 20 14021135 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769361 Affx-122923525 AX-385256532 20 13999329 AAAGGTTAAAGATTCTAGTTGGCTTTTGGAAAATA[C/T]AGCTTTGAAATCTAGAAAAGAATTTTATTCTGGAA Y 2 1 2 1 201000 r 74 goat snp43215-scaffold575-1103515 20 14056898 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787501 Affx-122945107 AX-385274526 20 14045073 TCCCAGAATATATATCACATCATAATCATTTGTTA[A/G]ATTAAAGATTCCCTTGCTTTCCTGTGTGTCCTTGG R 2 1 2 1 102000 r 74 goat snp43216-scaffold575-1149259 20 14103294 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795461 Affx-122970507 AX-385282417 20 14074466 TAGAATATTTCATCTGGCTCTCCTGGCAGGATACT[A/G]TGAAGTTGAGAGAGCCAGTATGAGAAAGTTGTGGC R 2 1 2 1 101000 f 74 goat snp43217-scaffold575-1178652 20 14132628 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779771 Affx-122919487 AX-385266871 20 14146648 AACTGTATCCAGAAGCCACTTAGTAATTTTTATGA[C/T]GCTGATTTCTTGTCAGAGGTAAAGACCTACATCTC Y 2 1 2 1 101000 r 74 goat snp43218-scaffold575-1250834 20 14205009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420761 Affx-122944715 AX-123291108 20 14191994 TTAACTGTGTTTAAATTACTTCAGTTATTTCTTCC[A/G]TGGCTAAGATTACAATTCAGACACTTCAGTCAGAA R 2 1 2 1 101000 r 74 goat snp43219-scaffold575-1296180 20 14250543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381317 Affx-122974439 AX-123251675 20 14231883 ATGAAAAGTATTCTGTAAGTTAATATTTGATGGAA[C/T]ATGTATATATCTGTTTGACGATGGTGTGATCAACA Y 2 1 2 1 101000 r 74 goat snp43220-scaffold575-1336069 20 14290403 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406044 Affx-122955477 AX-123276396 20 14316924 CAAAGGGCAATTTACTTTTCATCATTTGTACTATT[A/G]TATGTTCCTACCATATTTGTCACTTTTATTTCTTT R 2 1 2 1 101000 r 74 goat snp43222-scaffold575-1421110 20 14375789 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376524 Affx-122978006 AX-123246883 20 14385361 TAAAATGGAGCAGGGACTTTCCAGAGGGCAGATCA[C/T]AGCAGGGCAGTAAATGCAAGTGGTGATTCTCTCCC Y 2 1 2 1 201000 r 74 goat snp43223-scaffold575-1489547 20 14446049 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779496 Affx-122958486 AX-385266599 20 14421702 TTTAGAGAAATACAAACAAGACTATGTACATTTTA[C/T]GTACAGTCTTTCCTTAAAGTTTGCCTGGAATCTTA Y 2 1 2 1 101000 r 74 goat snp43224-scaffold575-1525888 20 14482480 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398385 Affx-122961649 AX-123268740 20 14460123 TTTTTGATGCTGTCTTCTTGTAGCAGACTCAGTCC[A/G]TCTCCTTAAATCACAGAAAATACTACAACCAAGAT R 2 1 2 1 101000 f 74 goat snp43225-scaffold575-1564309 20 14520951 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444382 Affx-122926601 AX-123314719 20 14496626 CCAACTATTGCTCTACTTTATTGCCCTTCATTTTA[C/T]GGTGAAATCTTAGTTCTCTCTCAAAATCTGGCTCA Y 2 1 2 1 101000 f 74 goat snp43226-scaffold575-1600812 20 14557598 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452008 Affx-122920916 AX-123322341 20 14527692 AATTTTGTGAGAAGACAGACATCTCAAATGTAGCA[C/T]ACAGGATAAAAATTACTAAGAAAAAGACATCATTT Y 2 1 2 1 101000 f 74 goat snp43227-scaffold575-1631878 20 14588842 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407610 Affx-122954643 AX-123277961 20 14574431 TTTATCCACAGGCCAGCACATAAAACACCTTTATG[A/C]ATATTCTCTCTGGAAAATCTCCTACAAAATACACA M 2 1 2 1 101000 r 74 goat snp43228-scaffold575-1678617 20 14636391 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769353 Affx-122945197 AX-385256524 20 14629085 TTATGGCATGCATTTTGTGATTTCTTATTAAGGCA[C/T]GCAGTTTGTGCTACAAAGGTCTACTGTGTACAGTT Y 2 1 2 1 101000 r 74 goat snp43229-scaffold575-1733271 20 14692238 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424054 Affx-122942065 AX-123294400 20 14735669 AGTTATCACCCTACCCACAGCCTAGTGCTTGGACT[A/G]CAGCACAGATTCCTAGCCAACCTTCTTATTCCAGG R 2 1 2 1 101000 r 74 goat snp43231-scaffold575-1839855 20 14799978 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445301 Affx-122925445 AX-123315638 20 14831568 TCTCTTGCCTTTCTCCAAGGTAGCTTAGTGGGCAA[C/T]GGTTTGGTGTGGTAGCACAATCACAAACTTTGTGG Y 2 1 2 1 101000 r 74 goat snp43233-scaffold575-1935754 20 14893005 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772547 Affx-122926259 AX-385259697 20 14862304 ATGCATTCTACATGAAAGGCCAAATAGTCCAAAAA[C/T]GTCAGGAATATCGATAGCTAATATAGGCTTAAAAC Y 2 1 2 1 101000 f 74 goat snp43234-scaffold575-1966490 20 14923890 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799389 Affx-122920324 AX-385286319 20 14900628 CATACAAAAAGTATCCTATTTCATGGTCACAAATC[A/G]TACCCCAATATGAGCTGCAGTGTTGCAAATGATAA R 2 1 2 1 101000 r 74 goat snp43235-scaffold575-2004814 20 14962248 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792162 Affx-122931028 AX-385279147 20 14952601 GAAAACTTTTAAAATTTACTCATCTTAGCAACTTT[C/T]AAATATACCATACAGTGTAATTAGCTTGGTGTGGG Y 2 1 2 1 303000 f 74 goat snp43236-scaffold575-2056787 20 15013955 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785590 Affx-122958837 AX-385272634 20 14986294 ACTGTAACTGTGTCTAGTTACAGTTGTTACATGTC[G/T]ACTAGTTATCTGAAACGTTGAAAATGTGACAGCAT K 2 1 2 1 101000 f 74 goat snp43237-scaffold575-2090480 20 15048320 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422203 Affx-122943498 AX-123292549 20 15027803 TGATACATTTTTCAGTTTTGAATCCTCTTACCACC[G/T]GTTACATTTTTACATTTATTAACCCCTACAAAGAT K 2 1 2 1 101000 f 74 goat snp43238-scaffold575-2131989 20 15089807 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392887 Affx-122965737 AX-123263244 20 15080454 AGAGACAAGCATTCTTTTCCATGTGGATATTCCTT[C/T]ATTTATACTGAGCATGTTTAAACTTGCAGAATCAA Y 2 1 2 1 201000 r 74 goat snp43239-scaffold575-2184640 20 15142561 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775862 Affx-122971853 AX-385262993 20 15141208 AGTAATAAAAGTAAATTGATAGTTTTTATTATAAT[C/T]GTGTTTCTGTCCCTTTATTCTTGAGTTTCAAAGCT Y 2 1 2 1 202000 f 74 goat snp43240-scaffold575-2245394 20 15204231 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801382 Affx-122925076 AX-385288293 20 15186754 GTAGGGTAATCTAGTTGTCAAGCTGTATAAATACA[C/T]GAAGATAAAAAGAGCCAAGCTTTCAGGGTTCAAAT Y 2 1 2 1 101000 r 74 goat snp43241-scaffold575-2290940 20 15250074 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765004 Affx-122955946 AX-385252579 20 15219496 CTGTCATGACTGCATTTGATACAGCTCCAAAATTA[C/T]GTATTAGATGCTAAAAATACAACTGGGAGAAGCCT Y 2 1 2 1 101000 f 74 goat snp43242-scaffold575-2323682 20 15270316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412899 Affx-122950416 AX-123283248 20 15264408 AGCATTTATCCTTCAATTAAAAAATAAAGAAAAAA[G/T]AATCTCCCCCAAAGTGGAGAAGATTGAATAAATAG K 2 1 2 1 103000 r 74 goat snp43243-scaffold575-2368594 20 15315309 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771968 Affx-122974811 AX-385259124 20 15303706 TTTCTTCATCTGGCTATTACCACTTATTTATGGTA[A/C]AACATCAGCCAGTGGCACAGATCAAATTCTACACT M 2 1 2 1 101000 r 74 goat snp43244-scaffold575-2407892 20 15355772 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405155 Affx-122956946 AX-123275507 20 15338018 CTTCTCTAGGGGGTCTTCCTTGACCACCTCATTAT[A/G]CATATCCACTAGTGTAGTCAAAGATTGCAGTAGCT R 2 1 2 1 101000 r 74 goat snp43245-scaffold575-2442204 20 15390166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441570 Affx-122928683 AX-123311907 20 15383373 CCTTTGCAGCAACATGGATGGACCTGGAGATTTTC[A/G]TACTAAATGAACAGATGTTTCAGTGCATTTCCCAG R 2 1 2 1 202000 r 74 goat snp43246-scaffold575-2487559 20 15436308 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275492 Affx-1111834930 AX-519549064 20 15419568 CTGCAGTTGCTCAGAGTGGCCATTCTGGAGGCCTC[A/G]GAGCTTTGGGAGCTGCTGCAGAGAGTTCGCCACAG R 2 1 2 1 202000 f 74 goat GoatD01.059091 20 15419568 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38392366 Affx-122966244 AX-123262723 20 15428565 AAGAATTCAATTTCTACTTTCAAAAATGCTAGAAA[C/T]ATTTCCTGGGTATCTGGAGTTAAGAAATATTCTTC Y 2 1 2 1 201000 f 74 goat snp43247-scaffold575-2532751 20 15481649 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447963 Affx-122923767 AX-123318299 20 15467990 AAGATAAAACCAAAGTATAGAAGAAAAATAGCAAT[A/C]GTTTATTTGTTTTTAATAGAATTAGATTTTAAAGT M 2 1 2 1 101000 f 74 goat snp43248-scaffold575-2572176 20 15521081 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387116 Affx-122970664 AX-123257474 20 15518150 AAAGACATGAGCCTCGAGAGATTTTTCAACTTGAA[C/T]AAAGAAAAAGCTGTGCTGTAAAATATTAAAGCAGA Y 2 1 2 1 101000 r 74 goat snp43249-scaffold575-2622336 20 15571426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420191 Affx-122945557 AX-123290539 20 15572504 TGGACTCATGCCCTTCTCACTAACCTGCCTCTTTC[A/G]CTGGCTGTGGTTCTAATTTGTGCCAATTCATCATC R 2 1 2 1 101000 r 74 goat snp43250-scaffold575-2676690 20 15626732 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783042 Affx-122946406 AX-385270110 20 15619305 TAAAATTATATTTGTGTGGGGAAAATTGCTACTTC[A/G]CGGGTTCAGTAATTGCTGTACATTTACAGTGCTTT R 2 1 2 1 101000 r 74 goat snp11421-scaffold1413-501765 20 15672952 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797351 Affx-122952130 AX-385284290 20 15650930 AAAAGGGAGCAGCCAGGATAGGGTGCATAATCAAG[C/T]GAGTTTCCCCTGAGGATGAATGGCTCTTATTCCCA Y 2 1 2 1 101000 f 74 goat snp11420-scaffold1413-470140 20 15704357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395533 Affx-122963862 AX-123265888 20 15706563 CAATATCATGTGTTTGTGTGTGCTTGTGTTGGGCA[C/T]AAAAACAGAATAACCTACTTCAAAATGGTAAACCT Y 2 1 2 1 303000 r 74 goat snp11419-scaffold1413-414507 20 15759909 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779179 Affx-122966522 AX-385266283 20 15746726 AAATATACACACAGGACCCTGTGTATGGAAAAACT[A/G]CTTTAAGTAAATAAAGAAACTATATACTGGCCCCA R 2 1 2 1 201000 r 74 goat snp11418-scaffold1413-374344 20 15800120 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771961 Affx-122970154 AX-385259117 20 15792884 GACTATTTCATATGCCACACAACCTCTTTTGAAAT[A/G]TTTGCCAGACAAATAGAGTATATGGACCTATCATT R 2 1 2 1 101000 r 74 goat snp11417-scaffold1413-328186 20 15846158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400796 Affx-122959822 AX-123271151 20 15833445 CTTGCTTCACAGCTCTGTGTAGTGTCATAACTCAA[G/T]AGAAGGTGATGGCTAATGTTAGGGCATCATTTTCT K 2 1 2 1 101000 f 74 goat snp11416-scaffold1413-287625 20 15887767 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378943 Affx-122976429 AX-123249302 20 15887284 TCCTTAGAAACCTGGTTGGATTTAACAGACAAATG[A/C]GGATTCAGACATTACAACAGAAGGCAGAACCACAT M 2 1 2 1 101000 f 74 goat snp11415-scaffold1413-233786 20 15942071 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273008 Affx-1111833190 AX-519546688 20 15989455 TAAACCAGTGGTTACAAACTGAAAAAGAAAAACTG[A/G]AAGAGACTATATAGTTTCTGGTTCAATGAGTTATC R 2 1 2 1 101000 r 74 goat 20_15989455_AF-PAKI 20 15989455 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437775 Affx-122931703 AX-123308113 20 16022139 AATAGATGATCTCATTCAGTGATTTTTCCACAGGC[A/G]CCAGTGTTTGAAGGGCCCCATTAACCTGTTCGTGG R 2 1 2 1 101000 r 74 goat snp11412-scaffold1413-98931 20 16080161 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438459 Affx-122931244 AX-123308797 20 16052148 CTCATTCAGGGCGAAGAGAGAAGAGATTTGGTATG[C/T]AAGGCGGCCTACACCTGGATATCGCTGTCTGGAAT Y 2 1 2 1 101000 f 74 goat snp11411-scaffold1413-68922 20 16110618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392854 Affx-122965761 AX-123263211 20 16081857 CCTGTTGTATGCATGTGGAAACTGAGGGGTAGTCT[C/T]CCAACTTTGCAGTTAGATAGTTGGTGGTATTTGGC Y 2 1 2 1 101000 f 74 goat snp11410-scaffold1413-39213 20 16140314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794957 Affx-122944632 AX-385281917 20 16141935 CAGAAGTACCAAAGCTTAACAGAAACTCCTGACTC[A/G]TATACAGAAAGTTACTGCTTAAATCAGCACCATAT R 2 1 2 1 101000 f 74 goat snp50994-scaffold74-20766 20 16211255 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449190 Affx-122923520 AX-123319525 20 16182489 CTACATGAGTTTTAATGAACTCATAGGAGAAATAA[C/T]AGAAAAACATTGAGCTTGATCTATTCCCCAAGTGA Y 2 1 2 1 101000 f 74 goat snp50995-scaffold74-61320 20 16253213 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436505 Affx-122932953 AX-123306843 20 16224643 TGCTTGATTAGACAGTGTTGCAGCCAGCTTCAGGG[A/G]TTAAACAAGGCTTTCAAGAACATTGGAAAAATCCA R 2 1 2 1 201000 r 74 goat snp50996-scaffold74-103474 20 16295728 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420766 Affx-122944712 AX-123291113 20 16262897 ACACCACCATCCCTGCCCTCCTTTAATCTCCTCTT[A/G]TCCAAGACTAAATAATTCTAGTTTCTTAAATACAT R 2 1 2 1 201000 r 74 goat snp50997-scaffold74-141728 20 16334589 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397269 Affx-122962345 AX-123267624 20 16301244 GTTACACAGGCTCCAAACAAAAGGTTTTCAACTTC[C/T]AAGAGAACAGGGTATGTTATTTAAATGAGTCTTTC Y 2 1 2 1 101000 f 74 goat snp50998-scaffold74-180075 20 16374527 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421761 Affx-122944360 AX-123292108 20 16401569 GCAATTGCTTGTGTAACTTGGAGCACATATTCATT[A/G]CTCTTTTTGAGACTCTCATCCTCCAAGATCACTTC R 2 1 2 1 101000 f 74 goat snp51001-scaffold74-280400 20 16475670 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425721 Affx-122940761 AX-123296067 20 16470628 TTTCCAGAAAGCAGACATGATAGCTGAAGCTCCAG[C/T]AGCCATCTTGGGACCATGAGGGAAAGAACGAAAGA Y 2 1 2 1 101000 f 74 goat snp51003-scaffold74-349459 20 16544720 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385596 Affx-122971204 AX-123255954 20 16513624 CCCCAATCTGTTTCACTCTAAAGCATGTGATAACC[A/G]TTAAAAAAAAAAAAAAAAACACCCACAGGCAGGTG R 2 1 2 1 103000 f 74 goat snp51004-scaffold74-392455 20 16587631 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410663 Affx-122952763 AX-123281013 20 16551510 ACAAAAATTTTATATTAAAGAAAGTGAAGAAAAGA[C/T]GAGGGAAATAGACAGGGTCTCGAGGAGAGAAAGCT Y 2 1 2 1 103000 r 74 goat snp51005-scaffold74-430341 20 16626174 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447449 Affx-122924370 AX-123317785 20 16584039 GATCAGGTTTTCCTTTTCTGACTCGCATTTGCTGA[C/T]GGGGCAAATAACTTAATCTCTGTTTTGGTTTCCTC Y 2 1 2 1 101000 f 74 goat snp51006-scaffold74-462870 20 16667688 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397537 Affx-122962036 AX-123267892 20 16623789 GTTTCCAACGTGGGCTTCCAAGGTTGCTCTGGGCA[C/T]AGACATCCAGCAAACCAAAGGAGGAGGACAACACA Y 2 1 2 1 102000 f 74 goat snp51007-scaffold74-502620 20 16708023 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476347 Affx-1251763857 AX-586011762 20 16645696 AAGTTTTTAAAAATCTTTTTTTTTTTTTTGAACTG[-/CTAAAATTTAAGGAACCGAGGCTGGAGGGAAAGATGGCGGATATAAAAAATAAAATTAAGAAAACAAAAATAAAATAAAA]TAAAATTTAAGGAACCCTAGGACTGATGTTTGGAG - 4 1 4 1 20000 f 74 goat SV_174 20 16645696 - deletion junction SV-TF-chip 539476603 Affx-1251763857 AX-586011988 20 16645696 AAGTTTTTAAAAATCTTTTTTTTTTTTTTGAACTG[-/CTAAAATTTAAGGAACCGAGGCTGGAGGGAAAGATGGCGGATATAAAAAATAAAATTAAGAAAACAAAAATAAAATAAAA]TAAAATTTAAGGAACCCTAGGACTGATGTTTGGAG - 4 1 4 1 20000 r 74 goat SV_174 20 16645696 - deletion junction SV-TF-chip 562165233 Affx-1251763857 AX-606940645 20 16645696 AAGTTTTTAAAAATCTTTTTTTTTTTTTTGAACTG[-/CTAAAATTTAAGGAACCGAGGCTGGAGGGAAAGATGGCGGATATAAAAAATAAAATTAAGAAAACAAAAATAAAATAAAA]TAAAATTTAAGGAACCCTAGGACTGATGTTTGGAG - 8 1 4 1 20100 r 74 goat SV_174 20 16645696 - deletion junction SV-TF-chip 562165283 Affx-1251763857 AX-606940694 20 16645696 AAGTTTTTAAAAATCTTTTTTTTTTTTTTGAACTG[-/CTAAAATTTAAGGAACCGAGGCTGGAGGGAAAGATGGCGGATATAAAAAATAAAATTAAGAAAACAAAAATAAAATAAAA]TAAAATTTAAGGAACCCTAGGACTGATGTTTGGAG - 8 1 4 1 20100 f 74 goat SV_174 20 16645696 - deletion junction SV-TF-chip 562165314 Affx-1251763857 AX-606940725 20 16645696 AAGTTTTTAAAAATCTTTTTTTTTTTTTTGAACTG[-/CTAAAATTTAAGGAACCGAGGCTGGAGGGAAAGATGGCGGATATAAAAAATAAAATTAAGAAAACAAAAATAAAATAAAA]TAAAATTTAAGGAACCCTAGGACTGATGTTTGGAG - 8 1 4 1 20100 r 74 goat SV_174 20 16645696 - deletion junction SV-TF-chip 562165353 Affx-1251763857 AX-606940764 20 16645696 AAGTTTTTAAAAATCTTTTTTTTTTTTTTGAACTG[-/CTAAAATTTAAGGAACCGAGGCTGGAGGGAAAGATGGCGGATATAAAAAATAAAATTAAGAAAACAAAAATAAAATAAAA]TAAAATTTAAGGAACCCTAGGACTGATGTTTGGAG - 8 1 4 1 20100 r 74 goat SV_174 20 16645696 - deletion junction SV-TF-chip 562165608 Affx-1251763857 AX-606941019 20 16645696 AAGTTTTTAAAAATCTTTTTTTTTTTTTTGAACTG[-/CTAAAATTTAAGGAACCGAGGCTGGAGGGAAAGATGGCGGATATAAAAAATAAAATTAAGAAAACAAAAATAAAATAAAA]TAAAATTTAAGGAACCCTAGGACTGATGTTTGGAG - 8 1 4 1 20100 r 74 goat SV_174 20 16645696 - deletion junction SV-TF-chip 562165756 Affx-1251763857 AX-606941165 20 16645696 AAGTTTTTAAAAATCTTTTTTTTTTTTTTGAACTG[-/CTAAAATTTAAGGAACCGAGGCTGGAGGGAAAGATGGCGGATATAAAAAATAAAATTAAGAAAACAAAAATAAAATAAAA]TAAAATTTAAGGAACCCTAGGACTGATGTTTGGAG - 8 1 4 1 20100 r 74 goat SV_174 20 16645696 - deletion junction SV-TF-chip 562166290 Affx-1251763857 AX-606941698 20 16645696 AAGTTTTTAAAAATCTTTTTTTTTTTTTTGAACTG[-/CTAAAATTTAAGGAACCGAGGCTGGAGGGAAAGATGGCGGATATAAAAAATAAAATTAAGAAAACAAAAATAAAATAAAA]TAAAATTTAAGGAACCCTAGGACTGATGTTTGGAG - 8 1 4 1 20100 f 74 goat SV_174 20 16645696 - deletion junction SV-TF-chip 38385082 Affx-122971806 AX-123255440 20 16656205 ATGAGTGTCTATTTCCAGCAGAACCTCATCCAATC[A/G]TTTACCACAAAACTGCTGAGTGGAAAGGCCAGCAC R 2 1 2 1 201000 r 74 goat snp51008-scaffold74-535036 20 16740228 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432561 Affx-122935535 AX-123302902 20 16685236 TTTCCAGCTTGGATCCCAAGATTAGACTAAGTTTA[C/T]GAAGTCAATTGTTGAACATTTTCTCTTTTCTAGTC Y 2 1 2 1 101000 f 74 goat snp51009-scaffold74-564067 20 16769544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390154 Affx-122967982 AX-123260511 20 16729679 TAGCTCTCGAAGCCCTATAAATTCTTCCTTGGTTC[A/G]CTCACTGTGACACACCCCGTGTTCCCCATCGTGTT R 2 1 2 1 101000 f 74 goat snp51010-scaffold74-608510 20 16813954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275262 Affx-1111834688 AX-519548839 20 16734334 GAACACAAACATAAATGAATGCTTTTGTCTGCAGT[A/G]TCCCAAGTTCCAAAGTTACCCATCCAGCTTACTTT R 2 1 2 1 101000 r 74 goat GoatD01.045983 20 16734334 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38448661 Affx-122923342 AX-123318997 20 16762848 CAGCTTCTGTTACTGAAAGATTCACTGCACAATCT[A/G]ATCAAAAAATAAAAACATGAAAAGCTGCATCACAG R 2 1 2 1 201000 f 74 goat snp51011-scaffold74-641679 20 16846958 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796966 Affx-122936489 AX-385283907 20 16794165 AGAAATCCTAACATCTTATGTCGTACTCAAATTTA[C/T]AAAAAGTTCACCAGGTAATCTGAGATATCTCTAAT Y 2 1 2 1 101000 r 74 goat snp51012-scaffold74-672996 20 16877871 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802113 Affx-122940031 AX-385289017 20 16825854 AGGAACTTCCGAGGACTTGAGGTCCTTACTAGTCA[C/T]GTTCATCAAATTAGTTAAGTACGCTAGATTCTAAG Y 2 1 2 1 101000 f 74 goat snp51013-scaffold74-704685 20 16909378 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448048 Affx-122923701 AX-123318384 20 16875340 ATTTCCCAGCACACCAGCATGACTAAAATGAAACA[A/G]ACCAGACCAAGTATGGTGAGAATGTGGAGCAAATG R 2 1 2 1 201000 f 74 goat snp51014-scaffold74-754171 20 16958907 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414738 Affx-122949725 AX-123285087 20 16916768 GCCAGCAGTTTGTTATATAAGTGAATATTGAAACA[C/T]GCCAGTCAAAAACGTTTGTGTTACAAAAGACATAA Y 2 1 2 1 201000 r 74 goat snp51015-scaffold74-795599 20 16998439 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788264 Affx-122930933 AX-385275283 20 16968040 GTGCTGATTCCTGAAAAGCCCTTCCTTCTACTTAT[A/C]TGCAAAACTACCCATCAAATTCCAAGCATTCACAC M 2 1 2 1 101000 f 74 goat snp51016-scaffold74-846871 20 17049733 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795468 Affx-122968918 AX-385282424 20 17009620 GGAGGGAGATTGAAGAGACATAGCTGATAAGAAAC[A/G]TACACCTTGAAGGTGGATATTATTGTGATGGGCTT R 2 1 2 1 101000 f 74 goat snp51017-scaffold74-888451 20 17091074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445960 Affx-122925899 AX-123316297 20 17064278 TTTCTGTGAAAATAGTATCTGCTTTCCTTGCTTCA[C/T]AGGACTGTTGGGTCAAATGTAAATGAAAATCATAA Y 2 1 2 1 101000 r 74 goat snp51018-scaffold74-943109 20 17145694 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788843 Affx-122935107 AX-385275858 20 17097953 CTCTTGGGTATTCACTTTCAGCTCCAGAGTAGTCT[A/G]TAGAGTTCTTTTACATCTTCACAGTTACTTTCCTA R 2 1 2 1 101000 f 74 goat snp51019-scaffold74-976784 20 17179357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396186 Affx-122963373 AX-123266541 20 17161950 TTACTATACTTTTTAATTGGACTTTTAAATATTGC[A/G]ATTATTCTATTCCTTATAGCTTCTAAGAACGTAAC R 2 1 2 1 101000 r 74 goat snp25892-scaffold2676-138124 20 17244241 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430551 Affx-122937021 AX-123300892 20 17205129 ATAAGAGAATTAGCTAATGCTGATGAGTCAAAGAT[A/G]CTTTCATAAACTTCACCTCTATTATTTTCAGATTA R 2 1 2 1 101000 f 74 goat snp25891-scaffold2676-94945 20 17287848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766767 Affx-986698164 AX-385254102 20 17233709 AGAATGTAGCCAAGGGGTGAGTCTGAGAGAGGCTC[C/T]TGAGACATACCAGAACCCATCCTTAACCTATATGC Y 2 1 2 1 600010 r 74 goat 20_17233709 20 17233709 Ancestral_priority_1043 ancestry 0.624 recommended IMAGE 10K 10K ancestral 320792741 Affx-122951238 AX-385279721 20 17248865 TGGAAGGTATGAAGACCACTGAGTGCAATGCTTCA[A/G]TTTATCAATACCCAGAGCAAAGGGTAGTACCTGGA R 2 1 2 1 202000 f 74 goat snp25890-scaffold2676-51209 20 17331642 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383936 Affx-122972965 AX-123254294 20 17291977 TGGGAGTCCTTTTCTAGAACTGCTTTCTTCTTGTG[C/T]AGGGTGTTGGTAGGTTGGTAAACCCAGCTGTGCAT Y 2 1 2 1 201000 r 74 goat snp25889-scaffold2676-8097 20 17375331 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405644 Affx-122956584 AX-123275996 20 17311014 TCATGGCTATTGAGAGGAACCTTGACAGTGATTAT[A/G]GGATTGTGGTGAATGTGGGCCATTCCAGAAGAGAG R 2 1 2 1 101000 f 74 goat snp26652-scaffold28-10841 20 17394158 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449872 Affx-122922359 AX-123320207 20 17341873 AGCTGGCCACATTTCCACAGTAGTGTGGGAGGCTA[A/C]AGAGAGAGGGCCTCTTCAATGTGGGATGCAAATTT M 2 1 2 1 201000 f 74 goat snp26653-scaffold28-41700 20 17425300 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415995 Affx-122948396 AX-123286344 20 17384454 TGATGGAGCGGATTGAGGCTATGTATTAGGGACAA[C/T]GGAAAACCACTGAAGGAATTTGAATAGGGATATAA Y 2 1 2 1 101000 f 74 goat snp26654-scaffold28-84281 20 17468807 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793454 Affx-122934616 AX-385280431 20 17431230 GTAAGAATTTATCACTCTCTGCACTCCATTATAAA[G/T]AGTTGATTAATTCTATTCTCAGCCACCAGGGGAAA K 2 1 2 1 101000 r 74 goat snp26655-scaffold28-131057 20 17515443 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403504 Affx-122957635 AX-123273857 20 17472098 ACAAGATGCTTGGCACAGAGAAAATGCTCCATGCA[C/T]GCTAGCCCTGGAGATGTGGAGGAAGGGTGGGTATT Y 2 1 2 1 102000 f 74 goat snp26656-scaffold28-171925 20 17556375 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442190 Affx-122928798 AX-123312527 20 17509391 GCCAAACATTTCTCTTATTTCCAAAAGCTTCCTTG[C/T]GTCCTTCTTCAATCTTTCCCTCCCTCTGCCCTTGT Y 2 1 2 1 101000 f 74 goat snp26657-scaffold28-209218 20 17594083 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463725964 Affx-1110126439 AX-515205756 20 17590489 CAGTATTCCTGCAGCCAAGGAATTTTCACTTGCCA[C/T]GGGAAAAAATTCTCTGAATATTTGTGTCTCACCCA Y 2 1 2 1 101000 f 74 goat GoatD01.017563 20 17590489 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320775333 Affx-122960071 AX-385262464 20 17600989 CAGACAACCAACAATTTTTCTTTCACATATTTAAG[C/T]GAGATGTTCGATCTGGTAAGGAAATAATAGTAATT Y 2 1 2 1 101000 f 74 goat snp26658-scaffold28-300816 20 17685305 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402338 Affx-122959065 AX-123272691 20 17646860 GGGCAAGCCCAGGAAAGGAGCTGCTTTTGTATGTA[A/G]ACCTTAAGAAGCTGATGTGGAATCCTTTCCATTCC R 2 1 2 1 101000 r 74 goat snp26659-scaffold28-346687 20 17730955 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381032 Affx-122974645 AX-123251390 20 17706839 CTAGTTCTTTTTAGCAACTTCTGCTTTATTCTGAC[C/T]ACATAGGAACATCGGAAAAATAGTTTGCAGCCCCT Y 2 1 2 1 101000 r 74 goat snp26660-scaffold28-406666 20 17790897 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779585 Affx-122974476 AX-385266688 20 17766287 ATCTCCAGCCCACTTCAACTTTTGATAATTTTCAG[A/C]TATACGCTAGATATGTGTATAATTGCCCAAGGAAT M 2 1 2 1 101000 f 74 goat snp26661-scaffold28-466114 20 17850110 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38388937 Affx-122968822 AX-123259295 20 17813875 AGAACCGAAGGGCCAGACAGCACTGCCAAGGGAGG[A/C]GCTTGGCTTTTCTCCCTAAAAGTAACGAATGGAAA M 2 1 2 1 101000 r 74 goat snp26662-scaffold28-513702 20 17897902 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798663 Affx-122927941 AX-385285595 20 17852157 TTGATTTCCTGAATCTAACTAAAACATTCCTGCCA[C/T]GATGCCAGATTCCTAGTCAGGCTTTTTGAAAGGAC Y 2 1 2 1 101000 r 74 goat snp26663-scaffold28-551984 20 17936190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429231 Affx-122937920 AX-123299573 20 17910579 TGGTCTGTTCCAAATGAGTGCTACCAAGGCTTAGG[C/T]GGCAGCGTGTTCATCTGACAGACAAGCGTGGCTGC Y 2 1 2 1 101000 f 74 goat snp49856-scaffold711-3378166 20 17994445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787428 Affx-122940662 AX-385274453 20 17941368 AGCATATGTTTGTATTAATGGTATAATTCTATTTC[A/G]TACATTTTCTTACTTGTGTTCGATGTTTGCAGGTA R 2 1 2 1 101000 r 74 goat snp49855-scaffold711-3347377 20 18024941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438500 Affx-122931218 AX-123308838 20 17978071 AATTTTACACAGCATTTTACAGTGAATACTCATCT[A/G]CCCACCATTTAATTGTAAAGTCTACCATTAACATT R 2 1 2 1 101000 r 74 goat snp49854-scaffold711-3310674 20 18061941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424273 Affx-122941993 AX-123294619 20 18015006 TTTCTCCTATTGCTTAAAAGCCTAGTTTAAGCCTG[C/T]ATTTGAAATTTAGGAGACATCTTTACCTGTCCTAC Y 2 1 2 1 101000 r 74 goat snp49853-scaffold711-3273739 20 18098666 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447019 Affx-122924545 AX-123317355 20 18056661 TGGATTTCTCCTCCTGCCTGAAACAATGAAAAAAA[C/T]GAAAACAAAATGTATAAAAGAGTGGTTTTCAGATT Y 2 1 2 1 103000 f 74 goat snp49852-scaffold711-3232084 20 18140542 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783528 Affx-122961827 AX-385270591 20 18090783 GATTCATGTTTGCAAGTATGCTTCATCAAGAAAAT[A/G]AAATGTTTTCGTTTTTAAGCTATCTCTGGTATTAT R 2 1 2 1 101000 f 74 goat snp49851-scaffold711-3197962 20 18174564 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38423463 Affx-122942585 AX-123293809 20 18138212 AGCCTCCAGGGCTCAGCCCCTCTGTCATTTCTCTC[A/G]CACTCTCAAAGCCCATGCCTTGAAAGCCATGGGGA R 2 1 2 1 201000 r 74 goat snp49850-scaffold711-3150533 20 18222141 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453013 Affx-122920103 AX-123323346 20 18175709 GTTGTCAGGCTACCTTCAGAGTCTGTTTTCTGTAT[A/G]CAGTAACAAAGGAACAGTGTGTTGAGTACAAAAGA R 2 1 2 1 201000 r 74 goat snp49849-scaffold711-3113036 20 18260056 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765333 Affx-122966907 AX-385252851 20 18207792 CCCTTGGCAACCAATAGGTGGTGCTATTGTCATAC[C/T]GTAGTTAAGTTGCTCGTGGCCCTAAGTAAAAATGT Y 2 1 2 1 101000 f 74 goat snp49848-scaffold711-3080953 20 18292831 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443794 Affx-122927090 AX-123314131 20 18237159 TTTTTAGCATTGGATGAGCATGGAGGTCTTTGGAG[C/T]AGATTTTAGTAAGAGGGCATATAGGTATCTTAGGG Y 2 1 2 1 201000 r 74 goat snp49847-scaffold711-3051586 20 18322193 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426652 Affx-122939937 AX-123296998 20 18299660 ACAACACTGTAAAGCAACTATGCTCCCCCCAAAAG[C/T]AATTTAACAGAAGTAGGGGGAGATAAAACTAAACA Y 2 1 2 1 303000 r 74 goat snp49846-scaffold711-2989085 20 18385220 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769649 Affx-122922398 AX-385256819 20 18351307 GGAAAAGGTAGTATTGTGTCTCTCTGAAGTGAAGG[C/T]AAAGAGCAGTTAGAGGATGGTGAAACAGGCACTGA Y 2 1 2 1 101000 r 74 goat snp49845-scaffold711-2937438 20 18436730 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772490 Affx-122931144 AX-385259641 20 18427196 AGTTGAGAATGTGAACAGACTCAGTGAAAAATTAT[G/T]TCAAAGGATAGATTTTCAATTTTGCTAATTACCAT K 2 1 2 1 101000 r 74 goat snp49843-scaffold711-2861549 20 18513059 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431971 Affx-122935955 AX-123302312 20 18464802 GACGTGATGATGGTCCAGAAGTGGTCAAATTCTGG[C/T]GCTACTTCAAGAGAAAGCCTTTGTTGTTGAGTGAG Y 2 1 2 1 101000 r 74 goat snp49842-scaffold711-2823943 20 18550585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421410 Affx-122943973 AX-123291757 20 18498269 CTAGAGTCTCCACTGCCTGATACTAATAAGCACTA[C/T]GGTCTCAGAACAGGCTAATACCACCCAAGATTCTA Y 2 1 2 1 201000 f 74 goat snp49841-scaffold711-2790476 20 18584387 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775499 Affx-122964431 AX-385262630 20 18529511 TTGGAAAGTGAGTATCTCTAAATCATAGCTTTTTC[A/G]CTTTTAAATAAAGGAATTAAATTGGATTATCCATA R 2 1 2 1 201000 r 74 goat snp49840-scaffold711-2759234 20 18615148 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272960 Affx-1111833191 AX-519546646 20 18543073 TAAAGAATGATGGTATGCCACGCTCAGTCATGAGC[A/G]TGATATGTGCTCAGTCATGTCTGACTCTGCGACCC R 2 1 2 1 202000 f 74 goat 20_18543073_AF-PAKI 20 18543073 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433978 Affx-122934257 AX-123304319 20 18577910 TACTTTATCTTCACTCACATACATGCACAGAGGAA[A/G]AGACACACACAGACACTCTTTGTCTGGGGACTATA R 2 1 2 1 101000 f 74 goat snp49839-scaffold711-2710835 20 18663955 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397234 Affx-122962373 AX-123267589 20 18636912 AGCATTGTACTGAGTAGTATCTCCAGGCTAAGTCA[C/T]AGAGGATACAAATAAGGTATATATTGCAATTCTGT Y 2 1 2 1 101000 f 74 goat snp49838-scaffold711-2651833 20 18728634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389172 Affx-122969092 AX-123259530 20 18689828 ATAGGAGAAGTAAGTCCCCAATCTGATTGGCTGCC[A/G]TGCTTCCCTGGGCTTTGGCTAAGTTCCTCTGTGAT R 2 1 2 1 201000 r 74 goat snp49837-scaffold711-2598917 20 18780503 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476348 Affx-1251763858 AX-586011763 20 18723087 TAATTTAGAGATGAGCAATAAAAAGGCAAGAAGAA[-/CAGGCCCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTGTGCAGGTGCGACTCTTGTTTGTGCTGGCCGCGGCA]AGGCCCCATACAAGATAGTACAAGACAATAGAGGG - 4 1 4 1 20000 f 74 goat SV_182 20 18723087 - deletion junction SV-TF-chip 539476604 Affx-1251763858 AX-586011989 20 18723087 TAATTTAGAGATGAGCAATAAAAAGGCAAGAAGAA[-/CAGGCCCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTGTGCAGGTGCGACTCTTGTTTGTGCTGGCCGCGGCA]AGGCCCCATACAAGATAGTACAAGACAATAGAGGG - 4 1 4 1 20000 r 74 goat SV_182 20 18723087 - deletion junction SV-TF-chip 562165144 Affx-1251763858 AX-606940557 20 18723087 TAATTTAGAGATGAGCAATAAAAAGGCAAGAAGAA[-/CAGGCCCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTGTGCAGGTGCGACTCTTGTTTGTGCTGGCCGCGGCA]AGGCCCCATACAAGATAGTACAAGACAATAGAGGG - 8 1 4 1 20100 f 74 goat SV_182 20 18723087 - deletion junction SV-TF-chip 562165811 Affx-1251763858 AX-606941220 20 18723087 TAATTTAGAGATGAGCAATAAAAAGGCAAGAAGAA[-/CAGGCCCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTGTGCAGGTGCGACTCTTGTTTGTGCTGGCCGCGGCA]AGGCCCCATACAAGATAGTACAAGACAATAGAGGG - 8 1 4 1 20100 f 74 goat SV_182 20 18723087 - deletion junction SV-TF-chip 562165939 Affx-1251763858 AX-606941348 20 18723087 TAATTTAGAGATGAGCAATAAAAAGGCAAGAAGAA[-/CAGGCCCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTGTGCAGGTGCGACTCTTGTTTGTGCTGGCCGCGGCA]AGGCCCCATACAAGATAGTACAAGACAATAGAGGG - 8 1 4 1 20100 r 74 goat SV_182 20 18723087 - deletion junction SV-TF-chip 562166512 Affx-1251763858 AX-606941920 20 18723087 TAATTTAGAGATGAGCAATAAAAAGGCAAGAAGAA[-/CAGGCCCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTGTGCAGGTGCGACTCTTGTTTGTGCTGGCCGCGGCA]AGGCCCCATACAAGATAGTACAAGACAATAGAGGG - 8 1 4 1 20100 f 74 goat SV_182 20 18723087 - deletion junction SV-TF-chip 38390022 Affx-122968446 AX-123260379 20 18797416 CTAAATTGCTCTTGAATCCTTCCCTCTTCCCTTCA[C/T]GTTCATGAAAACCATGTAGAGTCTACCTGCATGAC Y 2 1 2 1 101000 r 74 goat snp49835-scaffold711-2491329 20 18887877 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384080 Affx-122972857 AX-123254438 20 18854929 CTGGAAGGCTGTCTCACCCAAGTCACCGAGAGACA[C/T]AGGCAATTTGACCCTTTCCTGCACAGTGACTGAGT Y 2 1 2 1 101000 r 74 goat snp49834-scaffold711-2433816 20 18945207 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790716 Affx-122979133 AX-385277717 20 18883436 TTTCTCAACAGGATCTAGATTTTCTCAAAGAGTCA[C/T]AACTCTTTGCTGCCTAGGAATAATAGTCATATTGC Y 2 1 2 1 101000 f 74 goat snp49833-scaffold711-2405309 20 18974443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446287 Affx-122925659 AX-123316623 20 18934543 TCTTGTCATAAAATTCATCATGGTGTCTTCACTGC[G/T]CCAACATACAGAGCTCAGGACGCCTTGTGACTCCA K 2 1 2 1 101000 f 74 goat snp49832-scaffold711-2354202 20 19026084 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395777 Affx-122963669 AX-123266132 20 18963051 CCCACCTGAGCTTGGCCCCAGCCCGCTGCTGGCCC[A/G]CCAGCTGAAGACAGCCACATGAGTGACCACCAGGG R 2 1 2 1 103000 r 74 goat snp49831-scaffold711-2325694 20 19054539 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799114 Affx-122963055 AX-385286044 20 19009631 ATTAAAGGTTATAAACAACAAAGTTAAGATCTATT[A/G]AGGCAGAGATGATAATACTCTTCTGCCAAGAGAGT R 2 1 2 1 101000 r 74 goat snp49830-scaffold711-2279114 20 19102822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420952 Affx-122944980 AX-123291299 20 19042017 GACTACAGAGGGGACAAAATACTAAATGTTAAAAA[C/T]GAAAACATGTTCACAAAATGATTTAGTCAACAGGG Y 2 1 2 1 202000 f 74 goat snp49829-scaffold711-2246728 20 19135032 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404791 Affx-122956671 AX-123275143 20 19074727 TTATAAACGAGACCAAGGAAGAGGTACTATGAGAA[C/T]ATAGAGGGAGGGTGAGACTGCATCCAACTAGTAAG Y 2 1 2 1 101000 f 74 goat snp49828-scaffold711-2214018 20 19168452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409756 Affx-122953005 AX-123280107 20 19131534 TTTTCCACCCAAGGCTCATTTTTTCTAACTGTAGC[A/G]TCATGCCACTTTACAGCAGGCCAATTCTTTACCTT R 2 1 2 1 201000 r 74 goat snp49827-scaffold711-2157211 20 19222665 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777039 Affx-122947928 AX-385264162 20 19194649 GATTTGAAATGATAAAAAGTTGCCATTTGGTAAAA[G/T]CTATATAATTTTCTCATTTGGCATTAAGCATTTGT K 2 1 2 1 202000 r 74 goat snp49825-scaffold711-2094096 20 19285514 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766226 Affx-122944021 AX-385253624 20 19249806 ACTTGCAGGAAGCCTGAGAGATAATAAAATATTAA[C/T]GTTTTAAATCACTAAATTTCGAGGTAGTTTGGTAT Y 2 1 2 1 101000 f 74 goat snp49824-scaffold711-2038939 20 19340669 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376002 Affx-122978415 AX-123246361 20 19298832 GTGCAGATTCAAAGGTATGGATGAACTGACCAATT[A/G]TAAACTACACATTGCATTTTCAACTCAGTTCTTTA R 2 1 2 1 101000 f 74 goat snp49823-scaffold711-1989913 20 19390236 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792518 Affx-122954878 AX-385279499 20 19367013 TGGTAAATACTCTGCTAATGCTGTTAAATGCAGAT[C/T]GCCAAACTACAACTACATACAGCCAATGATCCCAA Y 2 1 2 1 101000 r 74 goat snp49822-scaffold711-1921732 20 19458753 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432945 Affx-122935294 AX-123303286 20 19406514 TGCTGAAACATAAATTAAGATGATGGCTTAAAATA[G/T]CATCGGCTGTCTCATAAATTTACATCTGTTGCCTT K 2 1 2 1 101000 r 74 goat snp49821-scaffold711-1882231 20 19497839 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416251 Affx-122948204 AX-123286600 20 19437081 CTGCCCACCAGGGACTACAAGATTCAGACAAGCAC[A/G]TGGGCTGATGCCTTTAAGCAGCTGACACACAGTTA R 2 1 2 1 201000 f 74 goat snp49820-scaffold711-1851664 20 19528291 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406174 Affx-122956158 AX-123276526 20 19476609 CGTGGGGATAAAAAGCATTTTGTGATAAATATATA[C/T]GTGTGTGTGTGGCTGAGTTGAATATAATTAAATAG Y 2 1 2 1 303000 f 74 goat snp49819-scaffold711-1812136 20 19567689 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792813 Affx-122937664 AX-385279791 20 19536723 ATTATAGCCAACAATGACCTCTTCTCTCTTTTATA[C/T]GTTATTGGACTTAGAGTTTGAATTACACAATGTTT Y 2 1 2 1 101000 f 74 goat snp49818-scaffold711-1752022 20 19627597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800667 Affx-122948870 AX-385287585 20 19565513 TAGTCAGCTAACCAGAAAATCACTGTGTTATACTG[C/T]ATCATTTTATCAACATCCCAAGTTTGGGCAATTAT Y 2 1 2 1 101000 f 74 goat snp49817-scaffold711-1723232 20 19656733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379510 Affx-122976081 AX-123249868 20 19597454 ATATCTCTCTAAGAATTAATTCAGCTACTTAAAAA[C/T]AGGCTACTGAGGGTCATTGACTCTTTTGGAATGTA Y 2 1 2 1 201000 f 74 goat snp49816-scaffold711-1691291 20 19688618 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409958 Affx-122954114 AX-123280309 20 19629165 TCAATTCACCATATCCCCTTAAAAAAAAAGAGAGA[C/T]GGTTTTGAGGTTGTTGTTTTGTTTACTATCGATAC Y 2 1 2 1 303000 r 74 goat snp49815-scaffold711-1659580 20 19720040 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416459 Affx-122947816 AX-106735252 20 19663467 CTATTATTGAACTGAAACAGTTGTGATGACACCTG[A/C]GACAACCAATGCAAATAAAAGCAAACTAAGCTACG M 2 1 2 1 101000 f 74 goat snp49814-scaffold711-1625278 20 19754633 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408557 Affx-122953677 AX-123278908 20 19692854 ACTATTATAAACTCCATTTTACAGGCGAGGAAACC[G/T]AGGTACATGTAGGTTAAACAACTTGTCAGAGTCTC K 2 1 2 1 101000 r 74 goat snp49813-scaffold711-1595891 20 19783468 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775147 Affx-122966384 AX-385262279 20 19731313 CCTATTCTGGCAACTGTTCTAACGATACTGGGTTC[A/G]TGTTCATCCTTAAAGGTCCAAAAGAATCCATTTAG R 2 1 2 1 101000 f 74 goat snp49812-scaffold711-1557432 20 19822222 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795691 Affx-122975985 AX-385282644 20 19777164 ATGTATCTGGGCATAAAAACAGTGATCTTATCACA[C/T]GTGACCACATTACAAAATAGGTCTTTTCCCCCCAG Y 2 1 2 1 101000 f 74 goat snp49811-scaffold711-1511581 20 19868206 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414683 Affx-122949292 AX-123285032 20 19807123 GGGAGCCTGTACTGCCATTTAAAAAGATGTTCTAT[A/G]TGCCTATCTTGGCATAAAACATTCATTCTGTGTTG R 2 1 2 1 101000 r 74 goat snp49810-scaffold711-1481622 20 19898682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791639 Affx-122932074 AX-385278630 20 19836003 CAGAATCCCTGGCTAAAACTGATTGCACAGTCTCT[A/C]AAATATGCATATGACAATCTTATGAGTTCTCTTAC M 2 1 2 1 101000 f 74 goat snp49809-scaffold711-1452742 20 19927567 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445584 Affx-122925129 AX-123315921 20 19877052 CAAGTGAATGCATGCTGGGAAGCCCTTCCTTTGGA[A/C]AAAGCACACGAGTTTTCTGTCAAATCAGGGAGCCC M 2 1 2 1 101000 r 74 goat snp49808-scaffold711-1411693 20 19968851 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408357 Affx-122953739 AX-123278708 20 19922927 ACGTGTGTATGTGTGTGTGTGTATGTGTGTGTCTA[A/G]TGTATCTAGTATAGGTTCTTGGATCATATAAACTA R 2 1 2 1 201000 r 74 goat snp49807-scaffold711-1365818 20 20014467 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402551 Affx-122958461 AX-123272904 20 19952735 CCACATTTTATAGAAGGCTGAATAGTGAACCAGAG[C/T]ACACTCATTTGGGACCTTGGTAAAATTTGTGGCCA Y 2 1 2 1 101000 f 74 goat snp49806-scaffold711-1336010 20 20044142 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437414 Affx-122932418 AX-123307752 20 20010863 TACGCAGCATAACTTTCCATTGACCCACCGACCAG[C/T]AAAACCAACTCAGAGTTACTCAGAGTCACTCCTCA Y 2 1 2 1 101000 f 74 goat snp49805-scaffold711-1277882 20 20102207 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770155 Affx-122968004 AX-385257322 20 20065006 TGCTAGAGGCTACATCACCTCTACTCAATAGTCAT[A/G]GGAAAAGACCAAGAGCAGCTACAACTGAAAACTCG R 2 1 2 1 101000 r 74 goat snp49804-scaffold711-1223739 20 20156457 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378618 Affx-122976564 AX-123248977 20 20108732 CTAACTGGGTCCTGAGAGACCAAACACAGTTCTTC[A/G]CATCCAGGTGGACTGACGAGTGAAGGATCAGATCC R 2 1 2 1 101000 f 74 goat snp49803-scaffold711-1180013 20 20199998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412915 Affx-122950401 AX-123283264 20 20159331 AACCCTGATTTACCAAATTTACACAGCTGAGACCT[A/G]CTCAGACAGGTTTTGAAAATAATATTTGACAAGAA R 2 1 2 1 101000 f 74 goat snp49802-scaffold711-1129414 20 20250665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801742 Affx-122932309 AX-385288650 20 20189959 ATAACTCAGCTGTTTAGCATGGAGCTGGAATGTAA[G/T]CACCGATAATCTGTACTTTTTACAATTGTATTATG K 2 1 2 1 101000 f 74 goat snp49801-scaffold711-1098786 20 20281127 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384207 Affx-122972391 AX-123254565 20 20243209 AGACTCTGACAACAAAACTGAAGCAAATAAAGGAA[G/T]AATTTTTATCTTCTAAAGCTTTAGGGCTTAGATGG K 2 1 2 1 101000 f 74 goat snp49800-scaffold711-1045536 20 20334179 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422926 Affx-122943039 AX-123293272 20 20281115 CTCTCACTCCTCTAAATCATTTATAAAAGCTTAAC[A/G]CCTCTGCCAGGTAGAAATGATCGCTCTGTTTTCAC R 2 1 2 1 101000 r 74 goat snp49799-scaffold711-1007630 20 20371951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802905 Affx-122927231 AX-385289803 20 20320560 AGCTACAGAACAGAGTGAAGCTGGGAAGTCTAAGG[C/T]AGATTTTGCTTGCAAGCCTGGCATAATTAGACAGT Y 2 1 2 1 101000 f 74 goat snp49798-scaffold711-968185 20 20411157 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406577 Affx-122955089 AX-123276929 20 20349498 ATGCTAGCCTGGTGTAAGAGAGTATAGTATTGTGT[C/T]AACATCTAACTGTGTAGTCATGGACAAGTTAATAA Y 2 1 2 1 101000 f 74 goat snp49797-scaffold711-939247 20 20440735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375891 Affx-122978493 AX-123246250 20 20381561 CATTTTGCCATTGAACTTCATCGCAGCTGGCCCCA[C/T]GAGATAACTACAACATTCGAAGCCTACTTGTATTA Y 2 1 2 1 201000 r 74 goat snp49796-scaffold711-907184 20 20472220 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435097 Affx-122933712 AX-123305437 20 20410739 TAGGCAGCATAAAATACCAGAGTATCTTTGGGATC[A/G]TTAAGAAAAGGTGTTTCACTTGGTTCACTGGGAGT R 2 1 2 1 101000 f 74 goat snp49795-scaffold711-878006 20 20501280 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785469 Affx-122975861 AX-385272514 20 20441963 GTTGCATGAGATTTTGGTTCTAAGTACACTGGTGG[C/T]AATATGTGTCATAGTTACAAACCTCTTTGAGGCTC Y 2 1 2 1 101000 f 74 goat snp49794-scaffold711-846782 20 20533066 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403440 Affx-122957737 AX-123273793 20 20492822 ACACGCCAATGCTCAGCTGATGCTTGGTGAATAAA[C/T]GAATTTTTTTGTAATTATACCATAATGCAAATTAG Y 2 1 2 1 201000 r 74 goat snp49793-scaffold711-795923 20 20583848 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788973 Affx-122946304 AX-385275986 20 20530553 GAACTCATCCATAAAGTGTTTGACAGCTGGAATGA[A/G]AAGCCATATTTGCTTCATGTTTCTTCCACAGCTGC R 2 1 2 1 101000 r 74 goat snp49792-scaffold711-758192 20 20621746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277290 Affx-1111835837 AX-519550794 20 20541066 AAACAGTCCACAGAATGTGCCTCAGTAATCCAAAA[A/G]GCAGTTATCGTGTAGGGTCTGATCTGGGATATACA R 2 1 2 1 101000 f 74 goat Random2.2K-1841 20 20541066 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769193 Affx-122925818 AX-385256368 20 20560455 CTCTGCCTTTGTGTTACTCATCCTTAGATAACAAG[A/C]TCTTAAAATGAATGAAGATGTCTTTACATGGTTTT M 2 1 2 1 101000 f 74 goat snp49791-scaffold711-728290 20 20651713 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781137 Affx-122971758 AX-385268222 20 20596402 TTAGAAAATATGAAAGTATGTTAAAAACCTAAGAC[A/G]CCAAAAGAGGTAAAGATATGAAGTATTGATTTGAC R 2 1 2 1 101000 r 74 goat snp49790-scaffold711-692343 20 20687699 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791543 Affx-122956676 AX-385278534 20 20636895 CATCTAATAGAGAAAATATGCTTCAGATTTACAGA[C/T]GCATGAAACACAGCTACCTGGAAATAAGGAGGAAG Y 2 1 2 1 101000 r 74 goat snp49789-scaffold711-651850 20 20727649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444696 Affx-122926433 AX-123315033 20 20677859 GGCAGACTGCTTGTGTTGGGGGAAGTTTACCTTAG[C/T]ATGTAGGTTCCTGGGTCAGAAAGGAAAATGATGAT Y 2 1 2 1 101000 f 74 goat snp49788-scaffold711-610886 20 20769115 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412803 Affx-122950485 AX-123283152 20 20733317 AAGGATTATAGAGCACTGCCCCCCACTGCCTGTTA[A/G]TAGCTGTAGTATACACCTTCTGGGTCTCAGGAAGC R 2 1 2 1 201000 r 74 goat snp49787-scaffold711-555428 20 20824450 T C 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410043 Affx-122953238 AX-123280393 20 20816229 CACTGAAAGGAAGTGCTCAGTTGCTCTTTGGGGAT[A/G]CAGTCAGCTTCTGGCATGTTTTCTAGACATCCTCG R 2 1 2 1 101000 r 74 goat snp49785-scaffold711-472516 20 20907690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407663 Affx-122954601 AX-123278014 20 20863400 TTCCTGCCTTGAATGGTAATATAAAAGCTGAAACT[A/G]CAGCAAACAACTTGGGAACATTAGGAGAAAAGCCA R 2 1 2 1 101000 f 74 goat snp49784-scaffold711-425345 20 20954745 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277417 Affx-1111835838 AX-519550921 20 20905823 CGTAGCTTACCCAGAGAACTAAGTTTAAACAAGAG[A/G]AGAGTTCCTAGTGAAATCTTCGTATTTTGTTTTCC R 2 1 2 1 101000 r 74 goat Random2.2K-1842 20 20905823 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794416 Affx-122949404 AX-385281379 20 20907867 ACTACAACTCTCATGGGACATCTTTATCCTATGGT[A/G]TCTGTTCTTGGCACATTTGGACTTGATATATTTGA R 2 1 2 1 101000 f 74 goat snp49783-scaffold711-380878 20 20998556 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790006 Affx-122929055 AX-385277012 20 20938305 TATGGTTTTACCTCATAGTAACATGAAATAAGTTT[A/G]ACATAAAATGAAGATTCCTTTTGGTACAGGTAGAT R 2 1 2 1 101000 r 74 goat snp49782-scaffold711-350440 20 21029120 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798852 Affx-122946308 AX-385285782 20 20982351 GAGCTCACAAAGGAAGACAGGCACAACCCAAATAA[C/T]GAGAAAGGTATAATGAGCAATGTCTCCATGCACGC Y 2 1 2 1 101000 f 74 goat snp49781-scaffold711-306394 20 21073154 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778759 Affx-122938245 AX-385265869 20 21038969 TTCTTGAGAGACAGTGTGCTCTGAGCTTTATTGAT[A/G]TCAACTCATTCAATCCTATCTTCAGGTCTATGATT R 2 1 2 1 101000 f 74 goat snp49780-scaffold711-249776 20 21130452 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384992 Affx-122971886 AX-123255350 20 21090528 AATCCCTAGGCGAACCTGGAGTTTCCCAAATTTTC[G/T]ACAGTTGAAACTCCTTTCCTTTTATCTGTTGAGAC K 2 1 2 1 101000 r 74 goat snp49779-scaffold711-198217 20 21182096 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272962 Affx-1111833192 AX-190677264 20 21097914 CCCCGTCCCTGGGATTCTTCAGGCAAGAACACTGG[A/C]GTGGGTTGCCATTTCCTTCTCCAATGCATGAAAGT M 2 1 2 1 303000 f 74 goat 20_21097914_AF-PAKI 20 21097914 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38430333 Affx-122938218 AX-123300674 20 21128439 GTAGTTCCAGACACTCTTCTCAGTAGCTACCCAAC[A/G]TTGTAAATCAACAGCTATACACTAAGATAAAATAC R 2 1 2 1 201000 r 74 goat snp49778-scaffold711-160306 20 21219790 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38424433 Affx-122941797 AX-123294779 20 21168771 ACTATTAACCTCAGACCCCAAGCGCTACCCTCACA[A/G]ACTCCTTGCACATTTAAGTTCTCTTTCAGGTATGG R 2 1 2 1 101000 r 74 goat snp49777-scaffold711-119974 20 21260688 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431549 Affx-122936205 AX-123301890 20 21199311 TTTTCAGCTGGGAACAAACAGTAGGATTTAGTTAC[C/T]GCAGAGACTATTCAATGGGGCTTTCACAGAAGACA Y 2 1 2 1 201000 f 74 goat snp49776-scaffold711-89434 20 21291484 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449586 Affx-122923220 AX-123319921 20 21242464 AAGTGCCTGTTATATATTATTATTTAATAAAATCC[A/G]TCAGGACAAATGCATTTACCTGGAGACTATTTCAT R 2 1 2 1 101000 r 74 goat snp49775-scaffold711-46281 20 21334674 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778514 Affx-122971824 AX-385265627 20 21283075 ATAATTAGACCTGAAAATACTTGTAGTTTTAAAAT[A/G]AGAAGAACAATAGGACTGTTTCTGCCTTGAAGTGG R 2 1 2 1 101000 r 74 goat snp49774-scaffold711-5670 NW_017215912.1 7716 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801472 Affx-122956999 AX-385288381 20 21299823 TCCTTAACCATTCAATTCCATAATAACTCCTCTGA[C/T]GTAATAATGCATCCTAAAAGAATCCTGCAGTATAG Y 2 1 2 1 101000 f 74 goat snp16797-scaffold176-10979 NW_017215912.1 22690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798816 Affx-122932419 AX-385285747 20 21331094 TAGTGTTCATTCTACTCCATTGCCTCTTAATTATG[C/T]AGAAATATTAATATATTGCTGTGACAGTCTCAGCA Y 2 1 2 1 201000 r 74 goat snp16798-scaffold176-42250 20 21423493 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404902 Affx-122956456 AX-123275254 20 21409493 GCTTTACTCTCTGCTGCAGGAAGCTATCTGCAGTA[C/T]GGCAGAGATTGAGAGTTTTCAAACTCCAGGTGACT Y 2 1 2 1 102000 r 74 goat snp16799-scaffold176-120649 20 21501336 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792877 Affx-122974084 AX-385279855 20 21454266 CAAATATTGGGAATATTCACCTAGCCAAGTCCACA[G/T]AAGTCCTATCCCAGTTAAAAATAGTTCAAATGTAA K 2 1 2 1 101000 f 74 goat snp16800-scaffold176-165422 20 21546628 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419622 Affx-122945979 AX-123289970 20 21468331 GGACAAATTGGGTGAGGGTATGCTGTGGAAACTAA[G/T]AGTTCTTTTGAGAAAACATTAATATTAGAATATCT K 2 1 2 1 101000 f 74 goat snp20594-scaffold2028-11800 20 21560549 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443979 Affx-122926993 AX-123314316 20 21551450 GATATACATAGTATTTATTATATGCCTGCATCTCT[A/G]TCTATTATGTTTCCTCATTTAGAGGCCCAATTAGA R 2 1 2 1 101000 r 74 goat snp20596-scaffold2028-94919 20 21643325 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38423695 Affx-122942894 AX-123294041 20 21612139 TGAATCAGTTAAGTGTTTAATGCAACTTCCATTCC[A/G]TGGTGAATGACCTTCCTAATCTGACTTTCCATCTA R 2 1 2 1 101000 f 74 goat snp20597-scaffold2028-155608 20 21701206 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445566 Affx-122925142 AX-123315903 20 21671108 TTTGCTTAACTAACAGTATTAGTGGTTCCTTTGCT[C/T]ATATTGCTTCTTCCATTCACTTAACAAAGATCTGA Y 2 1 2 1 101000 f 74 goat snp20598-scaffold2028-214577 20 21759605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422791 Affx-122943212 AX-123293137 20 21766244 AAGCCCACATCAGCCTCAGTCTCAAGACAATTATG[C/T]GGTGTGGATTCATTACCAGCCAGCTCTCAGTTCAA Y 2 1 2 1 101000 f 74 goat snp20600-scaffold2028-309713 20 21851081 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788367 Affx-122927727 AX-385275385 20 21870227 AGGCAATTTTAACAAGTCGCAGAGTTCGGAGTGGC[A/G]TGGGAAGCAGCACTGTTATGCCTACGCTAACAGAT R 2 1 2 1 101000 r 74 goat snp20602-scaffold2028-413696 20 21955178 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402549 Affx-122958463 AX-123272902 20 21964471 TGGAGGTAGGCCCTAGAGCAGCAATAGAGGCACAC[A/G]CAAGAGAAAACGCAGATCAAGATAATGATTTCCAA R 2 1 2 1 201000 r 74 goat snp20604-scaffold2028-507940 20 22051377 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766634 Affx-122935709 AX-385253985 20 22045884 AAAGATTCAAAGCCAAAACCAAACTGAGAAAATCT[A/G]CAATACCATAAATAATTAAAGCTCTATGGACATAA R 2 1 2 1 101000 f 74 goat snp20606-scaffold2028-589353 20 22132955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798099 Affx-122949867 AX-385285034 20 22074513 AGTATATTCAGTAGCTGCAATCCCAGAAAATTCAA[C/T]GTACATTAGAGTCAAGCAAGAAAAACTTGGTATTT Y 2 1 2 1 201000 r 74 goat snp20607-scaffold2028-617982 20 22161537 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407351 Affx-122955281 AX-123277702 20 22122106 GCTGGCTAAATAGGTGACGAAAGACACATAATGGG[C/T]GGTGACAACAAGAGTGCTGTTTATTATTTGAAAAT Y 2 1 2 1 101000 f 74 goat snp20608-scaffold2028-665575 20 22209764 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409207 Affx-122953169 AX-123279558 20 22132935 TTACAACCGGAAGGATCCCACTGTCCAGGATGCAG[C/T]AGGGAGTGTTTTAATAATGTTGGTCACCTCTCTTT Y 2 1 2 1 101000 r 74 goat snp25368-scaffold262-5967 20 22219949 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416891 Affx-122948074 AX-123287239 20 22167076 AAAGCAGGCGGCCCTGCTGAGCATTTGAGGTGTGG[C/T]GCTGAATAAAACTGCACGCCACCCAGCCTGCCCAA Y 2 1 2 1 201000 r 74 goat snp25369-scaffold262-40108 20 22254261 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775258 Affx-122978189 AX-385262389 20 22211701 AGAGGTCTGCCTGGAAAGATGCAGTTAAATACTGC[A/G]TCTTCCATTAATGGAAGTGCAACACTTAACATTCT R 2 1 2 1 102000 f 74 goat snp25370-scaffold262-84733 20 22299737 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787349 Affx-122953648 AX-385274374 20 22247356 GTTAATAGCAGAGTCTGGATGGGCTCCCAAGTCTT[C/T]AGTTACCACATGTTGCCTTAGAGTGAACAGACCAT Y 2 1 2 1 101000 f 74 goat snp25371-scaffold262-120388 20 22335562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447978 Affx-122923754 AX-123318314 20 22330444 GTCTAATATATATCCCAAAGAGGGTGTAGGGGGAC[A/G]GGAGACACAATTCTTTATTTGTCGTGGACTTTCAT R 2 1 2 1 101000 f 74 goat snp25372-scaffold262-203476 20 22418835 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447072 Affx-122924504 AX-123317408 20 22366009 GGACCAGGAGATCTAAGCGGGAGGATGGAGATTCC[A/G]TTTGGGTGTGTGGTGGCTGCAGCGCCTGGCTGAGC R 2 1 2 1 101000 f 74 goat snp25373-scaffold262-239041 20 22454026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401387 Affx-122959224 AX-123271740 20 22398786 TTTCTTTATAGCCTTCAAGTCCATTTCCATACCAC[A/G]TAAAGATGCAGAAAATTCTCTTCTCTGGTATTTAC R 2 1 2 1 201000 f 74 goat snp25374-scaffold262-271818 20 22486845 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794076 Affx-122923300 AX-385281043 20 22496323 TGGTATGTTTCTGAGGGACTATGGCTTTTTCATTA[C/T]TGTTCATACAGGCAGGATGGGAGTCTTTATGATAT Y 2 1 2 1 101000 r 74 goat snp25376-scaffold262-369355 20 22584140 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773003 Affx-122972600 AX-385260147 20 22530463 GCCACCTTTTCAGTAATGAGTGTTATATTGTCATA[G/T]ACTAATGGTTACTCTTGTCTACAGTGTCTATGGAA K 2 1 2 1 101000 r 74 goat snp25377-scaffold262-403495 20 22618700 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452366 Affx-122920630 AX-123322699 20 22565895 CTTGAGAATATTATAGGAAGAAAATGAGAGATGCA[C/T]GGAAATTCATGATTCCTTTTAATTTTTTCCTCGCC Y 2 1 2 1 101000 r 74 goat snp25378-scaffold262-438927 20 22654363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384575 Affx-122972997 AX-123254933 20 22623938 TAGGGTATTCTGCATACATTCTTTTAAGGGTTTGT[A/G]CTGTAAGCTGATGGAAACGTGCATGTGTTTTCTCC R 2 1 2 1 101000 r 74 goat snp25379-scaffold262-496970 20 22713176 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439659 Affx-122930599 AX-123309996 20 22653045 ATGGGTTCAGGGGTCAATGCCAGCTTCACTGGGTG[C/T]ATTATGGCTCTTGCAACATGAATGGATTCATGCTG Y 2 1 2 1 101000 r 74 goat snp25380-scaffold262-526077 20 22742794 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439472 Affx-122930165 AX-123309809 20 22708010 AAGAATTGTTTCTAAAACAGTATTTTAGAAAAATA[C/T]TGTTCAGTGACTCTTCATCATCACAATACAGAAAG Y 2 1 2 1 201000 f 74 goat snp25381-scaffold262-581042 20 22797878 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452115 Affx-122920835 AX-123322448 20 22767686 GAAAGGTCAGTGCTGTTCTTATCCTCACATGCGGG[A/C]ATTTTTTCATCTCTCTACTTCAGTTTGACCATGGT M 2 1 2 1 201000 r 74 goat snp25382-scaffold262-640718 20 22857499 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401071 Affx-122959640 AX-123271424 20 22811848 AGATAAAAGCAATTAAACTTTGCCTCTTTGCAAAT[A/G]CAGATGGGTATTTAAGTACCTAATTAAGCCTGAGT R 2 1 2 1 101000 r 74 goat snp25383-scaffold262-684880 20 22901661 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404267 Affx-122957052 AX-123274619 20 22857278 CCTTCCTCTGCCCAAAGATGAGCCTATTCAACTGC[C/T]CCTCCCCCCTTCCCACATCTGTGGGTGACACATGA Y 2 1 2 1 101000 f 74 goat snp25384-scaffold262-730310 20 22947184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433099 Affx-122935717 AX-123303440 20 22912126 AAGAGCAGCGGGAGTTCTAAGCGGGGAGATCAATG[C/T]GGCCAGAGAAAGCCCTCTTGGAAGAGAGATTCCTG Y 2 1 2 1 101000 f 74 goat snp25385-scaffold262-785158 20 23002326 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432331 Affx-122936290 AX-123302672 20 22948497 TAGTACAAAGGAAAATAAAGGTGATGGTGGCTAAA[G/T]CTGCTCAAGTTTCCTCAGGGCTGGGCTTTCATTTG K 2 1 2 1 101000 f 74 goat snp25386-scaffold262-821529 20 23038635 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408821 Affx-122954029 AX-123279172 20 23008351 AGCACAAAGCAGCCCACTCAGACGGGATTAATTGA[A/G]CATAGATTCATAAAAAGGCTATTTACAGACAACCA R 2 1 2 1 101000 f 74 goat snp25388-scaffold262-881383 20 23098819 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422595 Affx-122943737 AX-123292941 20 23059139 TCTGACTTTATCCCTTCGATATCCCAGAAACTCCA[C/T]AAAATCTGATTCCCAATTACTGGCATTGCTGCTGC Y 2 1 2 1 101000 f 74 goat snp25389-scaffold262-932171 20 23149991 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380822 Affx-122975077 AX-123251180 20 23104785 AAGACTGTCTTTATCATCAATGGAACAGGTTACCT[A/G]TCATCAAAAAAAGGACAGAAGCTGCATAGAACTCC R 2 1 2 1 101000 f 74 goat snp25390-scaffold262-977817 20 23195567 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425019 Affx-122941881 AX-123295365 20 23193134 TTTTACTCTTCATTCAGTGTGTAGTAGTTTCCCTT[C/T]AGTAGTGAGTTCAAAGTAAGGTTGCCAGCCCCTTG Y 2 1 2 1 101000 f 74 goat snp25392-scaffold262-1066166 20 23284287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780651 Affx-122962544 AX-385267741 20 23250025 AGCCATTTCTCTGATGCTTGGGAATCTCCTTCCAC[A/G]TAATTGTGACTGTCCTCACACCAATGTTCTCCACC R 2 1 2 1 101000 f 74 goat snp25393-scaffold262-1123057 20 23341044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792040 Affx-122937098 AX-385279028 20 23295977 CAGCAGCAAGACTGGTAAAAACACAAGTGTGATGC[A/G]ATAGTAAGAGTCTACAAAGTCCTAATTGCATTACA R 2 1 2 1 101000 f 74 goat snp25394-scaffold262-1169009 20 23386840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777153 Affx-122952651 AX-385264276 20 23415367 GCTCTGTAGTCACAGCTGTATGGGAAGTAGGGATA[A/G]GCGGTGATTTCTTACTATACTCATTCCTTACTTTG R 2 1 2 1 101000 f 74 goat snp25396-scaffold262-1288399 20 23505908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786172 Affx-122932939 AX-385273208 20 23492868 TATATAATTTCCCTCTACCAAGAAGAGCGTCTCAC[A/G]TGGCCTAAATTAATCTTACACGTTTTCATCATTAT R 2 1 2 1 101000 f 74 goat snp25397-scaffold262-1365900 20 23584512 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376972 Affx-122977754 AX-123247331 20 23526656 AGAACCCAGGGTGTGGCTACCTTTGCCAGTTCTAT[C/T]GCACTGGCTTTGTGTTAACTCAACATCTTGGATCA Y 2 1 2 1 101000 r 74 goat snp25398-scaffold262-1399688 20 23618273 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273015 Affx-1111833193 AX-519546692 20 23600848 TCATAAAGAGTCAGACATGACTTAGTGACTGAACA[A/C]CACCACCACCTTATGGAGGGCGATCTGCTTTATTC M 2 1 2 1 202000 r 74 goat 20_23600848_AF-PAKI 20 23600848 A C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396856 Affx-122963251 AX-123267211 20 23609045 ACTGAGACCCTGATAGTTAGAGAGGTGGTATGATA[C/T]GAAAAGAAGAGGAACTTTTTGTTAAAATTCTGACT Y 2 1 2 1 101000 f 74 goat snp25399-scaffold262-1482077 20 23700352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419068 Affx-122945805 AX-123289416 20 23703144 ACCAAAGGCCATCATCACCCTTCCTCCCAGGCCAT[C/T]GGAAGCGGATAAGAAACAAAGACACACTAACAACC Y 2 1 2 1 101000 r 74 goat snp25401-scaffold262-1576176 20 23795829 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800128 Affx-122955420 AX-385287051 20 23755239 AACTGGGTTGGTATTCAGCATGCAGCAATTTTTGC[A/G]TAGGATATACTACTATCTAGCTGCATGACTTTTAA R 2 1 2 1 201000 r 74 goat snp25402-scaffold262-1628271 20 23847965 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767856 Affx-122965692 AX-385255076 20 23812452 ACTGTCTCATGACATGTAAGGGGACAAAGGGCACA[A/G]TTTCTGTCTTATAAGGAATTTAAATAAAGGGGATG R 2 1 2 1 101000 f 74 goat snp25403-scaffold262-1685484 20 23904969 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793243 Affx-122923607 AX-385280221 20 23865837 AAGTATCTGAATAGTTAAGATGAGGGTTTGGGAGA[C/T]GAGTAAGTTTAACCCAGAGGAATAAAAAAAATGAT Y 2 1 2 1 101000 f 74 goat snp25404-scaffold262-1738869 20 23958284 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788275 Affx-122964587 AX-385275293 20 23903090 TCAAAGATGTTAGTGATGAGGTAGGTAGAAGGAAC[A/G]TACTGCTGCTTAGAGTTTTTAAAGGTGGGGTATCC R 2 1 2 1 101000 r 74 goat snp25405-scaffold262-1776122 20 23995559 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439919 Affx-122930014 AX-123310256 20 23992202 TCTATGATTCATACTTTAAAAAATTGTGGAGATGT[A/C]TTAGTTTCATTGTTGCTGTAACAACAATCTTTAAA M 2 1 2 1 103000 r 74 goat snp25406-scaffold262-1865234 20 24084766 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441596 Affx-122928663 AX-123311933 20 24035013 TCGATGTATGTGTGGTCCCTCTGTACTCTGAGGGC[G/T]TCCTTTTTCTTGAATCTACTTTGGTGGTAGCCCAC K 2 1 2 1 101000 r 74 goat snp25407-scaffold262-1908045 20 24127844 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446859 Affx-122925252 AX-123317195 20 24076557 ACTTGTGAAGGAGAATGACGCCCGATCTCCTGTAA[C/T]GAAGCGGTTAAATCCACGCTGATCCTGGGTGGGAT Y 2 1 2 1 101000 f 74 goat snp25408-scaffold262-1949589 20 24169263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418921 Affx-122946518 AX-123289269 20 24114033 TTGGAAACAGTACCCAGATTAGATGACTTAATTAG[A/C]TTATGTAAATTCAACATAAGAAATTTCTGATAAGG M 2 1 2 1 101000 f 74 goat snp25409-scaffold262-1987065 20 24210076 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392916 Affx-122965715 AX-123263273 20 24152685 TGGAAAAGTTCAATTGTTCAAGGCATCATGGATTG[C/T]AAGAGCTGACAAGGGCTCAGAGATCCACCAGCCCA Y 2 1 2 1 101000 f 74 goat snp25410-scaffold262-2025717 20 24248702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424952 Affx-122941271 AX-123295298 20 24185748 GATGGAGGGAGGAGAGTGGTCCGCCATCAGGTTCC[A/G]TGGTAAGAGCTGACTGCTGGGCATAAGGACCCCCA R 2 1 2 1 101000 r 74 goat snp25411-scaffold262-2058780 20 24281617 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770525 Affx-122952678 AX-385257690 20 24249528 TTTTAAAATTCATCTGTAGGTTTTAAACATAAAAA[C/T]AAATTATACATGTGTGGATTTTAACTTAGACCCTA Y 2 1 2 1 101000 r 74 goat snp25412-scaffold262-2122560 20 24345386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420318 Affx-122945017 AX-123290665 20 24286050 GTAGGTAAAAGGGTGTTGGATGAATTGGGGCTAAA[A/C]AGTTCAAGAATGAGGCCAGGAAGGTGCTAGTAGAT M 2 1 2 1 101000 f 74 goat snp25413-scaffold262-2159082 20 24379064 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787079 Affx-122973551 AX-385274106 20 24326198 TTTTGTATCATTTTCTGTTTTGAACCTGCAAGAGG[A/C]TTCTGTGCAATGGACCCCATGAAACAGGAGACAAG M 2 1 2 1 101000 f 74 goat snp25414-scaffold262-2199230 20 24419870 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398746 Affx-122961819 AX-123269101 20 24406173 CATTGTCCTAGACTCTGTTCAGTGGTTTGTCCCAG[C/T]ATTAATTCCATAGTGACGTGTGCCTAAAGTGCTCC Y 2 1 2 1 201000 r 74 goat snp25416-scaffold262-2279205 20 24500985 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802139 Affx-122964983 AX-385289043 20 24439664 TCAGATTGTTCCTCTGACTCCTAGAGGTTTCTTCA[A/G]CTAGTGATGATTATCACAAGGTTTGTTCAGATATT R 2 1 2 1 101000 f 74 goat snp25417-scaffold262-2312696 20 24535224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425923 Affx-122941608 AX-123296269 20 24489740 AATGCTAGCTCTGCCATAAATTAGCTGTATGACTA[C/T]GGGCTAATTGCTTAAACTCTCTGGGCTCCGATTTT Y 2 1 2 1 201000 f 74 goat snp25418-scaffold262-2362772 20 24586264 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782770 Affx-122977504 AX-385269842 20 24527773 AATGGACTTTGGAAACTACCTTTAACCAAAGGTAA[A/C]ATCTTAAGTTTCTTTATTTCTAGGATGATAAAGGG M 2 1 2 1 101000 r 74 goat snp25419-scaffold262-2400805 20 24624256 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786566 Affx-122937941 AX-385273598 20 24574216 GGGAAAACATAATATCTGGATCTCAGGGTTGCTGT[A/G]TGGAGTGAGTGATTGGTATGTATAAAGTCCTTAGA R 2 1 2 1 101000 f 74 goat snp25420-scaffold262-2447248 20 24671315 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376094 Affx-122978899 AX-123246453 20 24613124 CATGCTTAGTGCTTTGATAGTAAGACCCAGTTGGT[A/G]TTAATTAAAATTCATAGCAACTCACTGCCCACAGC R 2 1 2 1 101000 f 74 goat snp25421-scaffold262-2486156 20 24710389 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402475 Affx-122958597 AX-123272828 20 24642174 TGATCCTCACCTACAGATACATTATCCACTTTCTG[C/T]GCTCTTAGCCCCAAGAAGCTGACTTGTACAGACTG Y 2 1 2 1 101000 f 74 goat snp25422-scaffold262-2515206 20 24738777 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396191 Affx-122963369 AX-123266546 20 24710758 GTAAGGCCTTGAAGTCATTGAAGATGTAGACTCTT[A/G]CCTTTGTGGCAGGAAAGAACTTTTTAATTTCAAAA R 2 1 2 1 101000 f 74 goat snp25423-scaffold262-2583790 20 24807166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786292 Affx-122964777 AX-385273328 20 24746373 GGATTCCAGGGATTTAGACTTTTTCTCGAGAACCA[C/T]GGAAGCCCCTGAAGGTTTAAGCAGAATAATGACAG Y 2 1 2 1 101000 r 74 goat snp25424-scaffold262-2619405 20 24843109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408874 Affx-122953988 AX-123279225 20 24829762 ACGTCCTCCTCTGGGCTTTCTCAGTTCTCCCATCC[A/G]TGCTTAACTCATTCTTCAAGTGACATTCTCTGTCA R 2 1 2 1 101000 r 74 goat snp25426-scaffold262-2702794 20 24926006 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433361 Affx-122935132 AX-123303702 20 24865252 ATCTGTTTCCCTCAAATATTAGCCCACCACCTGGA[A/G]CAGGTGTTTTTTCCTGCTCAAGAATCAGTGTATAT R 2 1 2 1 101000 f 74 goat snp25427-scaffold262-2738284 20 24961494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444273 Affx-122926774 AX-123314610 20 24916038 GGCAGGGCAAAGCTAAAGATCAGTTAGCTATCTTT[A/C]ACACTTGAGGGTTCATTGCTGTTAGTTGCCAATCG M 2 1 2 1 101000 r 74 goat snp25428-scaffold262-2789070 20 25012232 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781693 Affx-122922651 AX-385268775 20 24962096 TATTGTCCTAATAGCTTTCTGTTTAAATTAAACAA[A/G]GTTGCCCTGATCACTAAGTGGTTCTATTACTGATG R 2 1 2 1 101000 r 74 goat snp25429-scaffold262-2835128 20 25058398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793070 Affx-122922628 AX-385280048 20 24991748 CATCTCTCTAAAGCCCTTATAAGTAGGGTGAGGCT[A/G]TTTGCATTTACAGAATTTTAGGACTAAAGAGTCAT R 2 1 2 1 101000 f 74 goat snp25430-scaffold262-2864780 20 25088043 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771079 Affx-122928565 AX-385258239 20 25023004 CACTTTCTTGATATCTCTTAATACCATGAGGGTGT[C/T]TGAGATATTTTAAAGCATTATAATACATGCCTCAA Y 2 1 2 1 101000 r 74 goat snp25431-scaffold262-2896036 20 25119201 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802599 Affx-122924589 AX-385289501 20 25052107 AAATTCAGCATAATCCAGAGACTTAATAAAAATTA[C/T]GCAAAACTTATTTAACACAGGAAATTACGATAAAT Y 2 1 2 1 101000 r 74 goat snp25432-scaffold262-2925139 20 25148325 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436705 Affx-122932323 AX-123307043 20 25083468 CCATGTAGAATAAATGAGTTCCTGAAATTTGAACC[A/G]TAAAGTAAATTCAAGTAATTTTAATTAGATAATCC R 2 1 2 1 101000 f 74 goat snp25433-scaffold262-2956500 20 25179714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452497 Affx-122920982 AX-123322830 20 25133926 TGCCCTATTTATGTTGTTGCTCAATTATTTTTAAA[C/T]AGAAACTTTAGAAATAGCTACTTCATTCCATTCCC Y 2 1 2 1 101000 r 74 goat snp25434-scaffold262-3006958 20 25230048 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414238 Affx-122949632 AX-123284587 20 25165001 TCCATCTCATGTGAAGAACTTGCACCCACTGTGTG[A/G]TACACGTTTATCTGTCCAGGTTCCTTCTCTCTCTC R 2 1 2 1 201000 r 74 goat snp25435-scaffold262-3038033 20 25261304 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405515 Affx-122955994 AX-123275867 20 25197515 TCCATGGTTCCTGTTCTTTTCAGTTCTTTTTTACT[A/G]CTCATCAGTAGCAGAAGGTAGAGAATTGGTGGAAT R 2 1 2 1 101000 r 74 goat snp25436-scaffold262-3070547 20 25293712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382054 Affx-122974932 AX-123252412 20 25270775 GCACAAAAGTCATGCCCAGGTACTGACATATTTGC[G/T]CCAATGCTTGAAATGACCTTGTGCTCAGTCACTAA K 2 1 2 1 101000 f 74 goat snp25438-scaffold262-3143807 20 25367321 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424561 Affx-122942231 AX-123294907 20 25306436 TTTTCCGTGTTCATCTCCAAATAAAGTTAGCCCCT[A/G]AAGGAAGGGGCAAGCAGCTACCAGCCCAATGACGT R 2 1 2 1 201000 r 74 goat snp25439-scaffold262-3179468 20 25403095 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784201 Affx-122946816 AX-385271252 20 25340517 ACTCAATGTAATAACTGTACATTAACTTTTCTATC[A/G]TTTTAACATTAAGATAAAACAAGATTTATAAAATT R 2 1 2 1 201000 r 74 goat snp25440-scaffold262-3213549 20 25438559 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429588 Affx-122937721 AX-123299929 20 25443986 TGACTGAGCGACTGAACTGAACTGACTGATCCCTT[A/G]CCTAAACTTAATGTAACTGCAAACTTAGAAATGAG R 2 1 2 1 201000 r 74 goat snp25442-scaffold262-3317018 20 25542086 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780164 Affx-122958961 AX-385267261 20 25563966 TAGTTCTTTCATTTCCATCTTCTACCATATTACTA[A/C]TTACATTATTTGTATTTCCTTATCTTTCTCCAACT M 2 1 2 1 201000 r 74 goat snp25444-scaffold262-3436998 20 25662143 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437749 Affx-122931721 AX-123308087 20 25599973 GTTTGACAACACTGGTACACGTGAGCCCAGGCAGA[C/T]GACAGAGGAGCCAAGGTCTATTTCAGTTTCCATTG Y 2 1 2 1 101000 r 74 goat snp25445-scaffold262-3473005 20 25698519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450588 Affx-122922026 AX-123320922 20 25648329 AAACTTTTTACCATCTTCTTTGATTTGGTACTGTG[C/T]AGCTTCATGTAATAACGCAGATCCATTGTAACAAT Y 2 1 2 1 101000 r 74 goat snp25446-scaffold262-3521361 20 25746994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394521 Affx-122964534 AX-123264876 20 25695616 CCCTCAGTCTTCCATTGTCTTTCTCCAGTGCATCC[A/G]TGGTCCCGAGCAACAACCTTCCAATTTCATAGTCC R 2 1 2 1 201000 r 74 goat snp25447-scaffold262-3568648 20 25794348 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774837 Affx-122932013 AX-385261971 20 25734695 AACTTTGTGAGTTAGAGAACTGGAAGATTGAACAA[C/T]AGTCACTTAGTTTCCTTGTTTCAATAAGTATATTT Y 2 1 2 1 101000 f 74 goat snp25448-scaffold262-3607727 20 25833272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421093 Affx-122944225 AX-123291440 20 25788607 GACATGATGGAAAATGTCTCCACACCAGGGAGTTT[A/G]AGATCCCTGGAAACCTATTTACTTGGCATGTACCT R 2 1 2 1 101000 r 74 goat snp25449-scaffold262-3661639 20 25887234 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426085 Affx-122941077 AX-123296431 20 25823979 AGAGTCAAAAAAAATTAGTGTGAGATATTGCCTCA[C/T]GTAATCTCAGCATGTCTTATAGAGAAAGGATATAG Y 2 1 2 1 101000 f 74 goat snp25450-scaffold262-3697011 20 25922478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379170 Affx-122976708 AX-123249529 20 25878487 TGTTACATTATATATATTTAAAGTTATATTATCTG[C/T]GACAGTGCAAGGCACATAATAAATAACTCTGGATT Y 2 1 2 1 103000 r 74 goat snp25451-scaffold262-3751519 20 25976977 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445807 Affx-122926036 AX-123316144 20 25919541 TGTTTTTAAAACCTCAGTGATGATGCGCGCATGCT[C/T]AGTCGCTTCATTTATGTCCAGCTCTTTGAGACCCT Y 2 1 2 1 303000 f 74 goat snp25452-scaffold262-3792573 20 26017864 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770841 Affx-122968752 AX-385258005 20 25959356 TTGTTCCAAAGCAGCCACATAATTATGTCATCACA[G/T]CTTGTATTTTTCTAATGTTACTCTAAACTGATTTT K 2 1 2 1 101000 f 74 goat snp25453-scaffold262-3832388 20 26057570 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770463 Affx-122952277 AX-385257629 20 26022894 TAATATTGGGAAAAGTGGTGAAAAATCACACACTA[C/T]GGATGACCACAGTGTTCAGTATGCAAGAAGAGCTA Y 2 1 2 1 101000 r 74 goat snp25455-scaffold262-3895926 20 26121389 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277418 Affx-1111835839 AX-519550922 20 26044306 ATTGCTTCATCTCAGAAGTCTGTTACCTGCAATGT[A/G]GGCTACCCTGCTTTAAAGAGCAAACAACAGGTAGA R 2 1 2 1 101000 r 74 goat Random2.2K-1844 20 26044306 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320794637 Affx-122948001 AX-385281598 20 26071360 AATTTGAATTTACCAGAATGGTGCCTTGTTTGATA[G/T]CTTCAGATTTGGATATCATCATTTTCTTCCCAGTG K 2 1 2 1 101000 r 74 goat snp25456-scaffold262-3944392 20 26169937 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272967 Affx-1111833195 AX-519546651 20 26127342 CATTAGTTACCATAACAAAAGCATACACACACTCC[A/G]CATCTTGGAGTTACTGATTAGAGTAACTGCTTTCC R 2 1 2 1 101000 f 74 goat 20_26127342_AF-PAKI 20 26127342 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320772885 Affx-122970366 AX-385260030 20 26130904 CCAATGGTTTGCCACGGTAAACATTAGTTCTACTG[C/T]AGATATACAGTAAATGTACAGTAGCAGGTATCTTG Y 2 1 2 1 201000 r 74 goat snp25457-scaffold262-4003936 20 26230065 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784261 Affx-122949169 AX-385271312 20 26186480 CAAAACCGATAGCAACTCAAATAAAAATTATAGCA[C/T]AAAATTCTTAAGGCATGCTAAATTCCTAACAATTA Y 2 1 2 1 101000 f 74 goat snp25458-scaffold262-4059512 20 26285628 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775427 Affx-122965987 AX-385262558 20 26220410 TTTGTTTAGAGGGCAGGGGGTAGTAAGAAAGAAGG[A/G]TGGAATGCTTTTCTAGATGCGTAAAATAGTGTCAT R 2 1 2 1 101000 f 74 goat snp25459-scaffold262-4093442 20 26319727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778856 Affx-122927005 AX-385265964 20 26260076 TTGTCTAATATACAATCTGATCTATGAAAGTTCTC[A/G]GCAGACTTTAGGATAATGTTAGTTCTTTTCTATTC R 2 1 2 1 101000 r 74 goat snp25460-scaffold262-4133108 20 26360244 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447069 Affx-122924507 AX-123317405 20 26302556 TAAAATTAGTTTGTGACATTTCCTCCCCTTTCTTG[C/T]ATAAATAGCTATTCTCATCCACTCTTGACCAGAAC Y 2 1 2 1 101000 r 74 goat snp25461-scaffold262-4175588 20 26403009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399976 Affx-122960825 AX-123270331 20 26339115 CGAAGAGTTTCTGAGTTTATAATTTCTGTTGGCTC[A/G]TATTTTCAAGCTGCTTCATTGGTGTCTTCTTAGTT R 2 1 2 1 201000 r 74 goat snp25462-scaffold262-4212147 20 26440436 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399922 Affx-122961317 AX-123270277 20 26390063 GGATGCATGAGGATTTCCCAGGCAGTTGTGGCCCA[C/T]ACTACAGAGACAATCAGAAAGGGATCAACTTTAAT Y 2 1 2 1 201000 r 74 goat snp25463-scaffold262-4263095 20 26491688 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444438 Affx-122926559 AX-123314775 20 26450143 TTGGGTGGTTTAGTGAATGATGCTTATAATAAAAA[C/T]GCATATGAATATATAGGATACACTGGCAATTAGAT Y 2 1 2 1 201000 f 74 goat snp25464-scaffold262-4323175 20 26551988 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390221 Affx-122967781 AX-123260578 20 26484607 TTATCAAACTTCACATGGAGGACAATAAGGAATAA[C/T]ATTCTCTTTGCTAAGATTGATCATGTTGCAATTTT Y 2 1 2 1 101000 f 74 goat snp25465-scaffold262-4357639 20 26586873 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377872 Affx-122977266 AX-123248231 20 26537589 GCAATAGAGGAGTAGCGGAGTGGGAGGTACAAACC[A/G]TTGGGCATAATATAGTACGATATGGGAAATGTAGT R 2 1 2 1 201000 r 74 goat snp25466-scaffold262-4410621 20 26639894 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431639 Affx-122936137 AX-123301980 20 26605872 TGTTGCTATAGTAGCTCTTGTTTTCTTAGCTATAC[A/G]TACCTTACTTCTTAATCTCTTTGCACAATACCATG R 2 1 2 1 101000 f 74 goat snp25467-scaffold262-4478904 20 26706340 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777374 Affx-122960300 AX-385264496 20 26650765 AATTTGGATCAAGTCAACCAGGTTACCTAATGTAT[A/G]CATAAAAGACATGGTCCTTGTAAATATAATGAACC R 2 1 2 1 101000 f 74 goat snp25468-scaffold262-4523797 20 26754673 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781487 Affx-122974114 AX-385268572 20 26691234 CTATATTAAATAGTTAATACTATTATTCATAAATA[C/T]GTCTTATTAGCCAACTACCATTTACATTCTTTACA Y 2 1 2 1 202000 f 74 goat snp25469-scaffold262-4564266 20 26795081 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784375 Affx-122973970 AX-385271425 20 26766290 CAAACATTGTGATAATTATGTGCTTCATAATTAAA[C/T]GTCTTCTTAACTAAGCCTTGGCAGTTATAATAAAT Y 2 1 2 1 101000 r 74 goat snp25471-scaffold262-4639322 20 26870827 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405745 Affx-122956509 AX-123276097 20 26821900 CAGGTTCTTACTGCCAATATTCTGGTCTATGGAAA[C/T]TGATTCTTTCTTGAAAGTTCTGACTGCAGTTTATC Y 2 1 2 1 101000 f 74 goat snp25472-scaffold262-4694932 20 26926998 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780594 Affx-122975699 AX-385267684 20 26857826 CAGTGCATCTTTTGTATCTTTGTTTAGATTTTGTC[A/G]TAAAATTTTGAAACTCATAATACTTTTCTTTCCAA R 2 1 2 1 101000 f 74 goat snp25473-scaffold262-4730858 20 26963230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420859 Affx-122944641 AX-123291206 20 26929380 GAGGTATCCATCTCTTGACACTGGTTACAGCAGAT[A/G]CTAAGTAAAGAAAGGCTGTGGAAGCTTCCAGACAC R 2 1 2 1 101000 f 74 goat snp25474-scaffold262-4802412 20 27035021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795510 Affx-122959402 AX-385282465 20 26967565 TGTCTTTAAAGAAAGAGTGGATTTTGGAGAAGGAT[A/C]GTAAACTACATAGCAAGAAAGACAAAGAAAAATGG M 2 1 2 1 101000 r 74 goat snp25475-scaffold262-4840597 20 27073802 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390781 Affx-122967881 AX-123261138 20 27028039 CTCCATTTACAGGTGCAGAATTAAAGAACACGTTC[A/G]CTCACTATATTATTGATGCACTTAAGTGGAGTGTT R 2 1 2 1 101000 r 74 goat snp25476-scaffold262-4901071 20 27135278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414745 Affx-122949719 AX-123285094 20 27089052 AACTTAGAAAACAGTCACTGAGTTTTGATTTATAG[C/T]CTTTGGCTTTTTTTTCTTTATGAGTGATTTAGACA Y 2 1 2 1 103000 f 74 goat snp25477-scaffold262-4962084 20 27198225 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771359 Affx-122965561 AX-385258517 20 27122524 ATGATATGTCCCACTCAAATCCACATTCTTTGCCA[C/T]AAGTAATATTATCCAAGAACTTTCTCTTTCAGTTA Y 2 1 2 1 101000 f 74 goat snp25478-scaffold262-4995556 20 27232283 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420143 Affx-122945593 AX-123290491 20 27156904 ATAACAATTAACATTGTTATTGTTGTTGCTTAGTC[A/G]CCCAGGCATGTCTGATTCTTCTGCAAGCTGCATTA R 2 1 2 1 103000 r 74 goat snp25479-scaffold262-5029936 20 27266925 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438987 Affx-122930378 AX-123309324 20 27188436 CAGTTCGCCATTTCTGCTGCTGACAGGAAATGTCA[C/T]TGCTAGGAAATAAGGCAGCAAGCTGCAGTCTCCAA Y 2 1 2 1 101000 r 74 goat snp25480-scaffold262-5061468 20 27298495 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770795 Affx-122920884 AX-385257959 20 27217377 ACTGCAAAATGTTGCATTTCACTGGAACTTCTGCC[A/G]TGTAGAAAACATTGGAAAACTATCACAGCTATTTT R 2 1 2 1 101000 f 74 goat snp45336-scaffold62-6888 20 27331983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390632 Affx-122967155 AX-123260989 20 27270939 AGAGCATTCGGATATATTCTTAGTTTTCCTCTACA[A/G]CATGTGGTTGTTTTCGTTTTTTGAGATCGAACACA R 2 1 2 1 101000 r 74 goat snp45337-scaffold62-60450 20 27385534 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416988 Affx-122947997 AX-123287336 20 27309772 TCTTCACTGAAAGGTTATTAATTAAATAAGAGATT[A/G]TACATAATATTGAAGAACACAAATATGGAATAAGT R 2 1 2 1 101000 r 74 goat snp45338-scaffold62-99283 20 27423915 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420931 Affx-122944997 AX-123291278 20 27338983 AACTTTTTAACACATATTTTCTTCAGTGTTTCTCA[G/T]ATGTCTACTGTATCTATTTGTCTTAAGTTCGGTTT K 2 1 2 1 101000 r 74 goat snp45339-scaffold62-128494 20 27453171 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425560 Affx-122941436 AX-123295906 20 27420108 AATGCCTTGGATTCAGTGAAGTGTCCTTGCAAGGA[C/T]AGAGAGATTTGAAGGTGTAATGACATATGAAGTGA Y 2 1 2 1 101000 r 74 goat snp45341-scaffold62-209619 20 27534928 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433782 Affx-122934475 AX-123304123 20 27452626 ATGGAGTTAATTGTTGTCTGTGTTCTTCTCTGATT[A/G]CCAATGTAAGATATAATTTTTAAAAGTACTGGAAG R 2 1 2 1 101000 f 74 goat snp45342-scaffold62-242137 20 27567839 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778018 Affx-122933716 AX-385265133 20 27484930 AATTTTGATTTTTGTGACCAGGTAATATTTCAGTA[C/T]GAGTTGTCTCGTTAGCTTTTCATAAGTTGTTAAAA Y 2 1 2 1 101000 r 74 goat snp45343-scaffold62-274441 20 27600388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800260 Affx-122978893 AX-385287183 20 27538395 TAACATGCTATATTACTGATGCCTCAAGTCACTTA[G/T]AGAAGCAACTACAATTAAATGTTTTTATATATTGA K 2 1 2 1 201000 r 74 goat snp45344-scaffold62-327906 20 27654008 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800868 Affx-122926422 AX-385287783 20 27583394 CTGTGCACTAGTAGCTGTCTCACTGATGAATTGCT[A/G]CGCATACTGCTAAGTCTCATTTCTTTCCATATATA R 2 1 2 1 101000 f 74 goat snp45345-scaffold62-372905 20 27701187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427476 Affx-122940016 AX-123297819 20 27646961 AGATATCTATAGACACATAATATATAACTTGCATA[C/T]ACTTTGTTAAAGAAAGTATCGTTAACGATCACATC Y 2 1 2 1 202000 f 74 goat snp45347-scaffold62-436472 20 27765357 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798636 Affx-122933160 AX-385285568 20 27703925 TTATCTAAAACTAACCAGTCTCTTTTTTCTTTGGT[A/G]ATGTAATGGTCACATTCTTTAAAGCATGGTAATTT R 2 1 2 1 101000 f 74 goat snp45348-scaffold62-493436 20 27823301 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770272 Affx-122936699 AX-385257438 20 27748389 TATTTATATTTCAGAACATTGCAGACATAAGGCAT[A/G]CCTGTCATACTTTCCTAAATACTTTTGCATATTTC R 2 1 2 1 101000 r 74 goat snp45349-scaffold62-537900 NW_017191568.1 7009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775096 Affx-122973936 AX-385262228 20 27795523 GAATACATCATAAAAGTCTTTAATGCAAAGGCACA[C/T]GCACACAATTTCTCAGATGATACTATAGTTCATGG Y 2 1 2 1 101000 r 74 goat snp45350-scaffold62-585034 20 27914056 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782257 Affx-122925744 AX-385269335 20 27838910 CAACAAAGAGAGGAAACAATGTCTTCACAGAGCTT[A/G]CATACTGGTCATTCATGCAGTCTCATTCTGCTGTG R 2 1 2 1 101000 f 74 goat snp45351-scaffold62-628421 20 27958191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788427 Affx-122944832 AX-385275444 20 27877909 ACACCAGAAAAGCATTGTCACCAAACAATAAATAA[C/T]GCTTCCATCTACAGTATCACTCAAAGATGAATCCA Y 2 1 2 1 101000 r 74 goat snp45352-scaffold62-667420 20 27997190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437178 Affx-122932125 AX-123307516 20 27909626 GTTTGCTGCACTACTGGAATAAATTTTGCTGAAAT[A/G]TTTTTCTTCCTTAGCTAGAACATGATAAGCTCATT R 2 1 2 1 101000 r 74 goat snp45353-scaffold62-699137 20 28029237 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784593 Affx-122937020 AX-385271641 20 27988391 CATGTAAGAAGTGCAATATAATTAGTGAATGGTAC[A/G]TAAGAAGTGTACCATGAATAATATACTATTCATCA R 2 1 2 1 101000 f 74 goat snp45355-scaffold62-777902 20 28108949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790150 Affx-122928348 AX-385277155 20 28019106 AGAGAAATAAGATATGATCTCTACTCTCTGGGAAC[A/G]TACAGTCTCATTCTTGGACATGATGCTTGAACAAA R 2 1 2 1 201000 r 74 goat snp45356-scaffold62-808617 20 28139535 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426858 Affx-122940489 AX-123297203 20 28068776 TTTATTAAAATCCAGATTTCTGAAACCTTCTATGA[C/T]GGCTCTTGTAATGAGCACTAAGGGAAGCTGGAATT Y 2 1 2 1 101000 r 74 goat snp45357-scaffold62-858287 20 28189344 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435331 Affx-122933611 AX-123305671 20 28118726 ATGCAGGTGCTAATATCCCTTTTCTAGGTTTAAAC[C/T]CAGAAGTAATTTTGGGGGGAGGGGAAGGTGTCCAG Y 2 1 2 1 201000 f 74 goat snp45358-scaffold62-908237 20 28239220 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412071 Affx-122951701 AX-123282421 20 28163867 GTTTTGAGAAAAAGAGTCCAAAATACTTATTTAAA[C/T]GGTAGGATTTATGAAGCTTGTAGCAGGACTGAAGT Y 2 1 2 1 103000 r 74 goat snp45359-scaffold62-953378 20 28284683 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396118 Affx-122963410 AX-123266473 20 28197425 CAGCTCCTCTTGCAACGCAGAGCAGTGGAAGAGTG[A/C]AGAGTGGATCTCAAGGCTAAGATGCCCAGGACTGG M 2 1 2 1 201000 r 74 goat snp45360-scaffold62-986936 20 28317962 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392597 Affx-122966055 AX-123262954 20 28227978 TCAGATTTTTCATGGTATTATACATTCAGACACCA[A/C]CATAAAGAGGAAGGGGTACAGATGAACAACAGAGA M 2 1 2 1 201000 f 74 goat snp45361-scaffold62-1017489 20 28348606 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444968 Affx-122926671 AX-123315305 20 28258607 TGCCATGGATTAAGAAATAAATCAAGGTCCACAGA[C/T]GCACAATGACAAAATAAAGATGAGCCTTCTTAGTG Y 2 1 2 1 201000 f 74 goat snp45362-scaffold62-1048118 20 28379308 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795901 Affx-122953853 AX-385282853 20 28314284 TATTTCTAGTTATTTTCTTACATGAATTCTCAGAT[A/G]CAGTTACTAAAAACAAAGATATCATGAAACCCTCC R 2 1 2 1 101000 r 74 goat snp45363-scaffold62-1103795 20 28435222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411385 Affx-122952230 AX-123281735 20 28358704 ACTCAAAATACCCCAACTCACTAATAATCAGTAGA[C/T]GCAAATTAAAATAAAGATGGGACATGCTTTAACAC Y 2 1 2 1 101000 r 74 goat snp45364-scaffold62-1148215 20 28479853 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416990 Affx-122947995 AX-123287338 20 28390966 GAGAATGAAATAGGCAGATTATTTCCTTAATGTCT[A/G]TAAACGTACTTCAGAATGTTATCTTTGTATGTTGA R 2 1 2 1 201000 r 74 goat snp45365-scaffold62-1180477 20 28511939 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394808 Affx-122964806 AX-123265163 20 28422571 GGAATGTAGAGATTAATGCATCCCCTACCATACAG[C/T]AGATTTCTTGGAGAGAGAAATGAAAAATAAGTGTT Y 2 1 2 1 101000 f 74 goat snp45366-scaffold62-1212082 20 28543405 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379357 Affx-122976158 AX-123249716 20 28461624 CACATTCTAGAGGAAGGTGGGTTGCATGAGAACCC[A/G]TGGAGGCGGGGCGTGCCATGGAAATGCCACTGAGG R 2 1 2 1 101000 f 74 goat snp45367-scaffold62-1251135 20 28582396 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389476 Affx-122968327 AX-123259834 20 28518022 TTGAGAAGACAAAGGATGCTAATTAAAGTCATGTA[C/T]GATGGTTAATTTTATGTGTCAGTTTGTCACCCATG Y 2 1 2 1 201000 f 74 goat snp45368-scaffold62-1307533 20 28638901 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392654 Affx-122966442 AX-123263011 20 28581160 TGGAAGAATGTGACATATCAAAAACATGAGGTTAG[C/T]GTTTCATTTCAGGGGAGAATTAAAAATTGTGGGGC Y 2 1 2 1 201000 f 74 goat snp45369-scaffold62-1370671 20 28702250 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277420 Affx-1111835840 AX-519550924 20 28620342 GGCAGGTGATTTAGAAAGATCAGGAATGTGATATT[A/T]ACGAACCCTACTAGCCGTCTTAGGCAAGAAATGAA W 4 1 2 1 101000 r 74 goat Random2.2K-1846 20 28620342 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402659 Affx-122958375 AX-123273012 20 28622205 ATCAGCCGAAGAAAGCATACCAGAGCAGTGATTAA[C/T]GTCATTTGGCTTTTAGTTTAGGGTATCGTCAAGGA Y 2 1 2 1 101000 f 74 goat snp45370-scaffold62-1411716 20 28743353 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767658 Affx-122974116 AX-385254898 20 28684285 AAATAGCCATATCTGCAGAAAGTCAGCCCTACTAG[C/T]ATTCCTTTGACCACAATGTGACACAATTTTTTAAA Y 2 1 2 1 101000 f 74 goat snp45371-scaffold62-1473796 20 28805878 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421537 Affx-122943873 AX-123291884 20 28742182 TCATCATACAATTCACAATTTCCCCTTCAGGATAA[C/T]GGTTTAGCTTGTATATTCTCTCTCTCTCTGTTTTG Y 2 1 2 1 202000 f 74 goat snp45372-scaffold62-1531693 20 28863584 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403615 Affx-122957551 AX-123273967 20 28790549 ATCTAAGCACATAGGTCAATAAAATATTGAAAAAA[C/T]GTTTGGAACAACCACTTTTTTCTTGAACCTCCTTT Y 2 1 2 1 103000 r 74 goat snp45373-scaffold62-1580060 20 28912526 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447878 Affx-122923828 AX-123318214 20 28848228 CACTGATGCCACTGAACCATCTCATCCTCAAACAG[C/T]ACTTTCAGTACTATTCAAACAGATCAAAGAGTACT Y 2 1 2 1 201000 r 74 goat snp45374-scaffold62-1637739 20 28971091 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791453 Affx-122960282 AX-385278444 20 28901114 GCTTGTTTTGAAAAGATTCTACAGTCTCCTTCAAT[C/T]ATTTAACTTGGAGTGTCACATATCTATTTTTATTG Y 2 1 2 1 101000 f 74 goat snp45375-scaffold62-1690625 20 29024211 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380279 Affx-122975417 AX-123250637 20 28938349 CTCAAGTTTAAGACAACAACAACCACAGTAGCAAT[A/G]TCTTGGGGACATTTTAAATTCAAGAGGGTTAGTAA R 2 1 2 1 102000 f 74 goat snp45376-scaffold62-1727860 20 29057616 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272970 Affx-1111833196 AX-185321382 20 28944384 TCTCTATGCAGGTCAGGAAGCAACAGTTAGAACTG[A/G]ACATGGAACAACAGACTGGTTCCAAATAGGAAAAG R 2 1 2 1 303000 f 74 goat 20_28944384_AF-PAKI 20 28944384 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38415642 Affx-122948576 AX-123285991 20 28993348 GAGCAATATAACACCAGCTTACTCTGGGCTGGGCC[A/G]TATGCAATGTGCTTTACAGATATCTCTCTCACTTT R 2 1 2 1 201000 r 74 goat snp45377-scaffold62-1782859 20 29113002 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438054 Affx-122931542 AX-123308392 20 29033505 ATTTATGTAGCTCCTAATCCCTTCAGGAAGGTGTA[C/T]TGTTCCTTCTCATTCCTTAATTGTGGGCTGTTAGT Y 2 1 2 1 101000 r 74 goat snp45378-scaffold62-1823016 20 29146518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765351 Affx-122924566 AX-385252868 20 29093089 ACAAAATAACATGACACAAATCAACAGATTACGAA[G/T]TATACATACTTAGGTCTCTGAAAACAAATATTTAT K 2 1 2 1 101000 f 74 goat snp45379-scaffold62-1882600 20 29205804 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774643 Affx-122945388 AX-385261777 20 29131325 GATTAGAGATAATGTGTATAACAAACCTCATAAAA[C/T]GTGCCTGACATAATGTAAGTGTTCATAAACAATCC Y 2 1 2 1 101000 r 74 goat snp45380-scaffold62-1920836 20 29244244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428066 Affx-122939113 AX-123298409 20 29183332 ACTCAGATCCATTCTTTGTTGAATGGATAAATTAA[C/T]GGACTACAGTAGTTTTACAAATGAGTCTGCTGATA Y 2 1 2 1 303000 f 74 goat snp45381-scaffold62-1972843 20 29296773 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448240 Affx-122924208 AX-123318576 20 29212046 ATGTGACAGCTCTGTGGTCCTCAGGGACCCAGGCC[A/G]TTTCTTTCTCTCTGTTCCACCAGCCTACTCTGTGG R 2 1 2 1 101000 r 74 goat snp45382-scaffold62-2001557 20 29326101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789452 Affx-122956806 AX-385276462 20 29256449 GGAATACATATGAAAATATTCATGAAACTCATTGC[A/G]TTTTGTTTGTGTCTGTTGGTTTTTTAGGTTTATTG R 2 1 2 1 102000 f 74 goat snp45383-scaffold62-2045960 20 29370622 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277422 Affx-1111835841 AX-519550926 20 29258748 TGTTTATTGTGTTAACCTGGTTTTACGATCTGTAG[A/G]AGATAATCAATCTGGTAACCATGGACTGAGACCCT R 2 1 2 1 101000 r 74 goat Random2.2K-1847 20 29258748 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320768802 Affx-122942641 AX-385255979 20 29292987 ATTTATCAGCATCAGAATCTAACTGGAAACTTACC[A/G]CTATTTTCCTATGGACTTGCCAGCCTACACTCATA R 2 1 2 1 101000 r 74 goat snp45384-scaffold62-2082498 20 29406856 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411180 Affx-122951858 AX-123281530 20 29341127 TGTAATTCATTAATACTTTGTAATGGTTTGGGAGT[A/G]TATATTGGGGAAAATATTTGGGGATATAGGGTGAG R 2 1 2 1 202000 r 74 goat snp45385-scaffold62-2130638 20 29454834 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790635 Affx-122950582 AX-385277637 20 29372097 TCAGCGATTAAGATGGAATCAATAGGCAGATGGAT[A/G]CAATAAATCTAAGGATTTATTTGAAAGAAGCAGAA R 2 1 2 1 201000 r 74 goat snp45386-scaffold62-2161608 20 29486326 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785855 Affx-122967571 AX-385272891 20 29405635 GATAAAGGATTATATCCATATGTCTGAGACACTTA[C/T]GAAAATCAGGATGAACATTAACACATTTTACTTTG Y 2 1 2 1 101000 r 74 goat snp45387-scaffold62-2195146 20 29519876 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390596 Affx-122967184 AX-123260953 20 29451576 CCAGTCTCCTTTTAGGTGAAGTAGAATTATAAGCA[C/T]GCCTACCTCAAAGAGTTGAGGATTATATAAAATAA Y 2 1 2 1 101000 f 74 goat snp45388-scaffold62-2241087 20 29566051 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785012 Affx-122959800 AX-385272059 20 29487776 AGTAGATTATTAATTTAGATGTATTAAATGGATAA[C/T]AGTATCAAACAATATCAAGGAAGGAAAAGAAACAG Y 2 1 2 1 201000 f 74 goat snp45389-scaffold62-2277287 20 29602874 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427389 Affx-122940081 AX-123297732 20 29528402 CTTAGCTTCACCCATAGTAGGTGCTTAACAATGGA[C/T]GAGTGTGGGCTTCCCTGGTGGCTCAGATAGTAATG Y 2 1 2 1 102000 f 74 goat snp45390-scaffold62-2317913 20 29642883 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384911 Affx-122972342 AX-123255269 20 29557489 TCAGAGACTACACTAAGGGGGGACTGTAAGACAAA[C/T]GGAGAATTGGAGAGCAGATGCATTATTTATCTTTT Y 2 1 2 1 101000 f 74 goat snp45391-scaffold62-2347000 20 29671922 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800420 Affx-122970097 AX-385287341 20 29608654 TCTGGTGTCAAGCTCACTCTTTTGTGCATCCTTTC[A/G]TATCTTGGTGCCCAATTTGGACGGCAAATAGAAAG R 2 1 2 1 202000 f 74 goat snp45392-scaffold62-2398165 20 29721166 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773263 Affx-122970680 AX-385260406 20 29654345 GCTATTTCACGCGGATGGTACAAATACATTTGAAA[C/T]GGCTTTTAAAATGCTCTCTCAAGGCTTTTAGCTAC Y 2 1 2 1 101000 r 74 goat snp45393-scaffold62-2443856 20 29768027 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794151 Affx-122952477 AX-385281117 20 29682895 TTAGAAATTGAAGTTTATATGAAATCAATGAATTT[A/C]TAACTAAATCTTTCTAGATGCACACAGATTAGTTT M 2 1 2 1 201000 f 74 goat snp45394-scaffold62-2472406 20 29797815 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448575 Affx-122923409 AX-123318911 20 29714907 GTACTGAGTTTCCAGAGAAGAGTGAAAACTATTCC[A/G]CATCTTGAGACAGGAAAGCTGTAAGATGCTTCACA R 2 1 2 1 101000 f 74 goat snp45395-scaffold62-2504418 20 29829860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447392 Affx-122924414 AX-123317728 20 29748880 ATAGAGGAACTTTTCTCCATGTTCTTGTGCCTTCC[A/G]TACTGGTAAATTATGGTTATTTGTCATAGATATGT R 2 1 2 1 201000 r 74 goat snp45396-scaffold62-2538391 20 29864323 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771760 Affx-122970283 AX-385258917 20 29788440 TCTCCAGAAATCTGTACAGTCACACGTTAAGCAAA[C/T]AGCCTTAAAAATGAATGCTTCTATGGGTTTAAGAA Y 2 1 2 1 101000 r 74 goat snp45397-scaffold62-2577951 20 29896112 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802019 Affx-122924626 AX-385288923 20 29846542 GAAGAAGTCAACTGAGTAAAAATTGCAGTAACTGA[G/T]ATTTATCTAAGTTGTAGAATTTGCATTTATCATCA K 2 1 2 1 201000 r 74 goat snp45398-scaffold62-2636053 20 29957554 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439265 Affx-122930991 AX-123309602 20 29889696 GTCTCAAGAGTCAGACACAACTGAGCTACCAAACC[A/G]TACAGAACTGAATTGAATATTGCACAAACTTACCA R 2 1 2 1 201000 r 74 goat snp45399-scaffold62-2679207 20 30001019 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774787 Affx-122930539 AX-385261921 20 29919016 AAAAGTCTCTAAGCTCTAAAGAACATTACTATGTT[A/G]TCATTTGGAAATTGGAGTTTTAAAACAGAAATTCA R 2 1 2 1 101000 f 74 goat snp45400-scaffold62-2708527 20 30030538 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786151 Affx-122945364 AX-385273187 20 29952234 TTGTGTTATTAACCATGTGTATGTCATGAGGGTTG[C/T]GAAATTTTTTGTAATCTGTAATTCAGCTTTTGGCT Y 2 1 2 1 101000 f 74 goat snp45401-scaffold62-2741745 20 30063919 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434882 Affx-122934347 AX-123305222 20 29998647 CCTTTGATTTATTTTTCCTTAATGATCTTCATTCT[A/G]TTACAGCATTTCATAGATTATCAATCATTAGTTCA R 2 1 2 1 101000 r 74 goat snp45402-scaffold62-2788158 20 30110390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451451 Affx-122921155 AX-123321784 20 30052388 AGCAAGAAAAGCAAAGGCTTGAAAAAAAAATCTTC[G/T]AAGAGCCATTTGGTTAAAAAATCATATGCATACAT K 2 1 2 1 201000 r 74 goat snp45403-scaffold62-2841899 20 30165615 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795259 Affx-122945194 AX-385282217 20 30170613 TGAATCTTTCAGAGACTTTTCTAATTAAATTATAA[C/T]AACATCTTATCCAAGGGCAGTTATCATTCCTCTAC Y 2 1 2 1 201000 f 74 goat snp45405-scaffold62-2960124 20 30285509 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787014 Affx-122951962 AX-385274042 20 30201519 TTCAATTACTATAGTCAGTCACAGTACAACTATTT[A/C]TTAAGTACCCACAGGGTGCACAGCATTTTACTAGG M 2 1 2 1 101000 r 74 goat snp45406-scaffold62-2991030 20 30316509 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421407 Affx-122943976 AX-123291754 20 30233105 AAAAAATTATATTATCTTTACAACTTTTACAAGTC[A/G]TTCCAAATTTCTTGACCAATATAGTGAACATCTGT R 2 1 2 1 101000 r 74 goat snp45407-scaffold62-3022616 20 30348269 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416017 Affx-122948378 AX-123286366 20 30262233 ACACATGGGTTAAACCTAAGCCTATTGCATATAAG[C/T]ATTTTCATCAATTAAAATTGCCTTATTATAACTAT Y 2 1 2 1 101000 f 74 goat snp45408-scaffold62-3051744 20 30377739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773594 Affx-122957021 AX-385260734 20 30294286 AGAGACAAGCCCTCACGTTTAAAACCTTATGAACT[C/T]TTTGGGTAATCAAACTTGGTACACTAATAAGTCAG Y 2 1 2 1 101000 f 74 goat snp45409-scaffold62-3083797 20 30409903 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392674 Affx-122966426 AX-123263031 20 30338405 TCATGCTAATATTTTGTTAGTTATTTTTGTCTTTA[C/T]ATTCACAAGGAATATTTGTCTTTAGTTTCCTTTCC Y 2 1 2 1 103000 r 74 goat snp45410-scaffold62-3127916 20 30454067 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452955 Affx-122920169 AX-123323288 20 30376741 ACTGGGGATAAGATCTGACCCAGGACTTTCTTGAG[C/T]ACAGTGAGAATGCTAAAGGGGAGCATCAATCCCAT Y 2 1 2 1 101000 f 74 goat snp45411-scaffold62-3166252 20 30492338 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422237 Affx-122944014 AX-123292583 20 30443997 TGTTTGAGCTTGCGAAAAGAAATCTGTCTTGCTCT[A/G]TTAATAAGGAGGTGTGCTGTGTTAGGTCACAGGCT R 2 1 2 1 201000 r 74 goat snp45412-scaffold62-3233508 20 30559774 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784530 Affx-122930467 AX-385271579 20 30524983 CAACTGATGCTGCTCTGAGGTCTGTGACATACTTA[C/T]ATCCACTTGAAAACTTTAGTTCATTGAGTGAATTA Y 2 1 2 1 101000 f 74 goat snp45413-scaffold62-3314494 20 30641251 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379995 Affx-122975612 AX-123250353 20 30559142 GGACAAGACTGAGCAACTAACACACAAGAAAGATA[C/T]GGTAGAGGAGAAAGAAGAAAGGTTTGGTAGAATTT Y 2 1 2 1 303000 r 74 goat snp45414-scaffold62-3348653 20 30675616 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447575 Affx-122924025 AX-123317911 20 30596584 TCAGGAAAAAGAAATTAAACAATCAAATTCTCAGA[G/T]CAGACCTGTGTTTTGCCTTCATGATCTGTCTTTGC K 2 1 2 1 101000 r 74 goat snp45415-scaffold62-3386095 20 30713733 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793912 Affx-122942538 AX-385280881 20 30637700 AGTTAGCACCTGGGCCAGAAGGAGCAGCTAATAAC[A/G]TATTCCAGGATAACAATATTGGGCCAAAATGACTG R 2 1 2 1 101000 f 74 goat snp45416-scaffold62-3427211 20 30755325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797999 Affx-122948283 AX-385284935 20 30702988 GCAAGCAAATAAAACACCAAAACCAGTAAAAGGCC[A/G]CTTGAAATTCTAAACTCTAGTCAACATAAAGGTAT R 2 1 2 1 101000 f 74 goat snp45417-scaffold62-3492499 20 30820621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386149 Affx-122971399 AX-123256507 20 30737154 TGTTTTCTGGTTTATTTTTTAGTTATTTTGTGCCC[A/G]TGAAATTAGCCGGGGAATTATTTACCATCATTCAT R 2 1 2 1 101000 r 74 goat snp45418-scaffold62-3526665 20 30855707 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771068 Affx-122969634 AX-385258228 20 30797637 TGCTTCATAGACCTTGTGAAGACCTTTAGATTTTA[C/T]GTGAATTGCAATAGGAAGCAAGGATATAAGTAAGC Y 2 1 2 1 101000 r 74 goat snp45419-scaffold62-3587148 20 30916576 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382474 Affx-122974205 AX-123252832 20 30849440 AACTGTCCCCAGGAGCAATAAGCAACCAGGTATGA[G/T]CACCTGTTGAGCCCCTTGAGCTTGCTGGTTTCCTG K 2 1 2 1 201000 r 74 goat snp45420-scaffold62-3638951 20 30969235 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412459 Affx-122951402 AX-123282808 20 30879744 CAAGAGACTCCTATCAAAACTATTCTACCTGCATA[A/C]AACTTTATTTGCATAAAATAACTGTATTTAATCCT M 2 1 2 1 101000 f 74 goat snp45421-scaffold62-3669255 20 30999939 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421213 Affx-122944138 AX-123291560 20 30911131 TCAAGAGAACCTCAGCAACCAAAGAACAAGGCAAG[C/T]ATATTTTTATGAAATAAGTATATTTTATCTACTCA Y 2 1 2 1 101000 f 74 goat snp45422-scaffold62-3700642 20 31031619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774017 Affx-122957428 AX-385261155 20 30966329 TGTTCATAAATTCCTAGTTGTACTAAAGTTCAACT[A/C]TCTGCCAACTCTGCACATAGCCTGAGAAACTCAAT M 2 1 2 1 101000 r 74 goat snp45423-scaffold62-3755840 20 31089078 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771090 Affx-122973151 AX-385258250 20 31003081 AGTGTGAAAAACTGAAACCAATTTGATATGCTTAA[C/T]TCAGATTATGGTTAAATGGTTAAGAAGATAGCTCA Y 2 1 2 1 101000 r 74 goat snp45424-scaffold62-3792592 20 31126441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418137 Affx-122947111 AX-123288485 20 31036145 CACTAAGAGTATACTAGACAAACATGAAGTAATCC[A/G]TGAACGACACACAGCTAATACAGCAGCGCCATACA R 2 1 2 1 201000 f 74 goat snp45425-scaffold62-3825656 20 31159635 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429033 Affx-122938317 AX-123299375 20 31082908 AAAAAAGTTTTGTGTCTCCTGCAAAAAATACTAGG[C/T]AAGATCCTATCAAGTTATTCAGTTGACTATATGTA Y 2 1 2 1 101000 r 74 goat snp45426-scaffold62-3872419 20 31206425 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450603 Affx-122922015 AX-123320937 20 31125832 TTTGATTCCAACATTGGAGTGCTCATCTGTTCACA[A/C]TACTCCGTACCTCGCTTTTCCCTTTTGTGAAACAG M 2 1 2 1 101000 f 74 goat snp45427-scaffold62-3915343 20 31248516 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439973 Affx-122929810 AX-123310310 20 31154494 CTTGCTGGTAACTTGTCAAATTCAAGAAATACTCC[A/G]CGAGAAGCGTCGTAGGCAGGAGCACAAGCTGCTAC R 2 1 2 1 101000 f 74 goat snp45428-scaffold62-3944005 20 31277196 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430091 Affx-122937532 AX-123300432 20 31190908 ACTTAAAAGAGTAAACAGTTGCTACCTCACTGTAT[A/C]TTTGGGCCAGGACTTTTGGAAGAGACTTAGCTGGT M 2 1 2 1 101000 f 74 goat snp45429-scaffold62-3980419 20 31313418 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277302 Affx-1111835843 AX-519550806 20 31223585 GTTGTCAGCAGTCGCTGGTGTTCTTTGGCTTGTTG[A/G]CATATTACTCCAATCTCTGCTTCCTCTTCACATTT R 2 1 2 1 202000 f 74 goat Random2.2K-1854 20 31223585 A G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398969 Affx-122960967 AX-123269324 20 31254695 AGGGTTACATGCTGCAAGGTCGTAGCCTGGGAGAT[A/G]ACAATAACTAAACCCAGTGTGCTGGGCTCCATTGT R 2 1 2 1 101000 f 74 goat snp45430-scaffold62-4044206 20 31377379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763641 Affx-986698170 AX-385251481 20 31305814 AGGCTTAAGCTAGCCTATGGAGACTTTCACACTTA[C/T]ATAATTATGTTCTAACATTATAACTGAGAACTGCC Y 2 1 2 1 600010 f 74 goat 20_31305814 20 31305814 Ancestral_priority_1043 ancestry 0.68 recommended IMAGE 10K 10K ancestral 38451855 Affx-122921072 AX-123322188 20 31308356 TCTTCAGTGTATGGCTCCCTGGCTTCTGTTCTTGC[A/G]CAGTAAGTATGGATTTCCATTGCTTCAGTCCGCTT R 2 1 2 1 101000 f 74 goat snp45431-scaffold62-4097867 20 31431560 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410736 Affx-122952705 AX-123281086 20 31344447 GTAATTAAGCACAGAAGACCACTCTGCAGAAAGAC[A/G]TATGAAGTAGAATGAGAAAACATGTGGCCCCGGGG R 2 1 2 1 101000 f 74 goat snp45432-scaffold62-4133958 20 31467553 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766782 Affx-986698172 AX-185200869 20 31394996 CTGCAATCACCATCTGCAGTGATTTTGGAGCCCCC[A/C]AAAATAAAGTCTGACACTGTTTCCACTGTTTCCCC M 2 1 2 1 303000 r 74 goat 18_22622818_RH-map 18 22622818 C A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320786491 Affx-122973599 AX-385273525 20 31411655 ATGTGCTTAGAGTACAAGAAAAAGTGACTCAGGAA[G/T]TATACGATGAGGATAAGATGAAGTCAGAAACAGGG K 2 1 2 1 101000 f 74 goat snp45434-scaffold62-4201166 20 31534673 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391122 Affx-122966801 AX-123261479 20 31471751 CCCCAGGATCCCTGTGTTTAAAATATTAAGGCAAA[C/T]GAAAGACATTTAAATATCTTTATTAGAATGGTTTA Y 2 1 2 1 101000 f 74 goat snp45435-scaffold62-4261262 20 31591488 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383328 Affx-122972688 AX-123253686 20 31493637 GCCTGGTGTTAGAGACAGGCTCAGCCAGGTTGCCC[A/G]TTTGCAAAACCCACAGCTGGTTCATGCTGGAGCTG R 2 1 2 1 102000 f 74 goat snp45749-scaffold6277-16119 20 31619574 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422620 Affx-122943716 AX-123292966 20 31543570 TGCTACACGTACCTCCTTCTCCATAGGAGTTCAGG[C/T]AGCAGGTTCTCCAAACTTCTGTGGACGTTTCTTCC Y 2 1 2 1 101000 r 74 goat snp30120-scaffold330-1306870 20 31783785 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798203 Affx-122971294 AX-385285138 20 31575396 GGAAATATTTATAAGGAATGATTAGTTTTAGGACT[A/G]GAGGTTGAATAGTTGGAAAGAAGGGAGTTCAAATT R 2 1 2 1 101000 r 74 goat snp30119-scaffold330-1275044 20 31816536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763645 Affx-986698174 AX-385251484 20 31641417 TTTTCTAAATTTCATTCATAAATAATTTCTGAGCA[A/T]CAAGAATAGGAGAATTCCATTGATCCTGTAAGCCA W 4 1 2 1 600010 f 74 goat 20_31641417 20 31641417 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 38435011 Affx-122933811 AX-123305351 20 31647954 ATGAAAGCAGCCATAGATAATATGTAAACTATGCT[A/G]CATAGATAATATGTAAAATGAACTTGACTCCATGT R 2 1 2 1 201000 r 74 goat snp30118-scaffold330-1202486 20 31890174 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412815 Affx-122950476 AX-123283164 20 31689473 GAGGCTTTAGAGGTTGTCAGATGTGAAGTAAATCC[A/G]TAATAATCATCAGAGCGTCATGTTTAGTGACCGTG R 2 1 2 1 101000 f 74 goat snp30117-scaffold330-1160967 20 31932488 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790329 Affx-122934913 AX-385277332 20 31747463 ACTTGTACCCTGGCTCAAAGGACGTTTTCCTTACT[A/G]TCTGTAGTAAGCAATCAGTAAGCTGTATTTGGGAT R 2 1 2 1 101000 f 74 goat snp30116-scaffold330-1102977 20 31989879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407900 Affx-122954395 AX-123278251 20 31779654 ATAGACAAGTTTACTGTTATTTTGAAGGCTGCTTC[A/G]GGCTTATTTTATGTCAGTGAAATTAGTTTTCTGAG R 2 1 2 1 201000 r 74 goat snp30115-scaffold330-1070786 20 32022360 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320778869 Affx-122939456 AX-385265977 20 31809846 TGGACTCTATTTTCACAGACTTCAAAATCATAGCA[C/T]GTTTGACTTGCAATAGGTCATTGATTTTCAGTTTG Y 2 1 2 1 101000 f 74 goat snp30114-scaffold330-1040594 20 32052579 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418563 Affx-122946388 AX-123288911 20 31856397 GTTCAGTTAGGTAGAGATGAGTGTTATGGGGAAAA[C/T]AAAACACGATAAGTGGATAAGTGGAGCTGGATGGG Y 2 1 2 1 201000 f 74 goat snp30113-scaffold330-994043 20 32099090 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398949 Affx-122960983 AX-123269304 20 31892669 TCCTTGGTAAAGCTACTGTTCAGTTATGTGTGTCT[A/G]TACACACACGCACACACACACAAGCTGATGTGTCA R 2 1 2 1 103000 f 74 goat snp30112-scaffold330-957771 20 32135505 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777510 Affx-122943313 AX-385264629 20 31928690 AGTCCTAGACACTATGCTATCTGGCCCTAAATGAC[A/G]TGAAAGTACATTAGAGACACTTCCTCAGGCAACTG R 2 1 2 1 101000 r 74 goat snp30111-scaffold330-921750 20 32171432 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782730 Affx-122944413 AX-385269802 20 31973880 ATTTGCAGTTTTTACACATATAGCTTTCCTAAGAG[C/T]GTGATTGAAGGTAGAATATCTAAAAGAGAGGAAGA Y 2 1 2 1 101000 r 74 goat snp30110-scaffold330-876560 20 32216622 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418471 Affx-122946458 AX-123288819 20 32005965 TTATCGGTAACTTCTCCCGCCTGGTGAGGGTTTCT[A/G]CCCAACACCTCAAAGATGTTGTTCTTTATATCCCT R 2 1 2 1 101000 r 74 goat snp30109-scaffold330-844475 20 32248701 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438650 Affx-122930898 AX-123308987 20 32035267 TTCTGCTGCCATGCCAACCATCCAAATGCCCAGGG[C/T]GGTGTACCCTTTATAAATGTGCTTTCTCTATAGTA Y 2 1 2 1 101000 r 74 goat snp30108-scaffold330-815173 20 32277876 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414505 Affx-122949532 AX-123284854 20 32104602 GAGGACCTAACAGACTTTCAGGCTATCTTCATCCC[A/G]CTTTCTCCCTGTCATTAATTTGCTGAGAGGGCTTA R 2 1 2 1 101000 r 74 goat snp30106-scaffold330-745838 20 32347971 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428448 Affx-122938811 AX-123298791 20 32152256 ATGTTCAGGAAGTGTTTGATGAGTGAATCAATAAT[A/G]CAACAGAGAATCAATGTGTCACCTGAAGTGTTTGC R 2 1 2 1 101000 r 74 goat snp30105-scaffold330-698184 20 32396039 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443008 Affx-122928176 AX-123313345 20 32203942 GATAATAAATAGGAATGCAAGTTATTCTGGATGAA[A/G]ACTTTTTACTAATGATTGAAATGAAAGCTCATGTC R 2 1 2 1 101000 f 74 goat snp30104-scaffold330-646498 20 32448462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796127 Affx-122953537 AX-385283078 20 32258461 CATTGGAGTGAAAAGCTAGAAATACATTTATAAAA[C/T]GTTTTTAGATTTTCGAAGTTGTTTCAAATGAAGAT Y 2 1 2 1 101000 f 74 goat snp30103-scaffold330-591979 20 32504327 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408452 Affx-122954442 AX-123278803 20 32323265 ATAAGTAACACTTTTTATTTTGTCTTTTGTTTTTT[A/G]GGCAGGTTCATTCATCCTTCCTATTTTCATCAGTC R 2 1 2 1 103000 r 74 goat snp30102-scaffold330-527175 20 32570134 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417889 Affx-122946752 AX-123288237 20 32361099 AGTACTGAGAATATAGCTTTGTAAAACATCAGAGT[G/T]TATATTCTAGTGGAAGAAGTTAATGCATTTTAAGA K 2 1 2 1 101000 f 74 goat snp30101-scaffold330-489341 20 32607597 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779099 Affx-122943226 AX-385266204 20 32395690 GACTCTAATTAGTTTCAGGATACAGATACAGGAGA[C/T]GATCAAGGAAAAGTTGAGCAATCAAGACAGAAGTG Y 2 1 2 1 101000 r 74 goat snp30100-scaffold330-454750 20 32642854 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392486 Affx-122966141 AX-123262843 20 32437473 CCAGCAACATTTTTAATGATTGATTATATTCTTCA[C/T]GTATCTTCTATGGTAAGGGCATAACCAAAATAAAA Y 2 1 2 1 101000 r 74 goat snp30099-scaffold330-412967 20 32685627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783621 Affx-122962508 AX-385270680 20 32473244 AAATGTTACTTTCAGTGGAAACAATTCAAGAAGGA[C/T]ATTCAGCATAAGTATGTTTTATCAGAGAACAAACA Y 2 1 2 1 101000 f 74 goat snp30098-scaffold330-377196 20 32721354 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450284 Affx-122922166 AX-123320619 20 32544457 TTTTAAAGCATTTTAAACTAATGCTATGTGCCCCA[C/T]TGAAAAATGTGAATCAAGTGTAAGAAAAAGGGAAA Y 2 1 2 1 201000 r 74 goat snp30096-scaffold330-305983 20 32792831 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796276 Affx-122928345 AX-385283226 20 32577042 ACAGCCATTAGCTAAAAACTTGCAGAAATGCCTAT[A/G]TCTGGTATGAGAGGAATGATATATTGCACTATAAC R 2 1 2 1 201000 f 74 goat snp30095-scaffold330-273398 20 32825739 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771718 Affx-122931861 AX-385258875 20 32624759 TATCCTATACGAGATTAATTAACCAGGTAACTAAG[C/T]AGTGTCTGAAGTGTCTAGGTCCAAAATGTATCCTC Y 2 1 2 1 101000 r 74 goat snp30094-scaffold330-225681 20 32874016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773315 Affx-122955991 AX-189024577 20 32681943 TAGCAATATATAAGATTTGGATTTTGGAATCAGAC[A/G]TTGTCCCCAACCAGCAGTTATTTCAGAAATTTGCT R 2 1 2 1 101000 r 74 goat snp30093-scaffold330-168497 20 32931619 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414147 Affx-122949696 AX-123284496 20 32717552 CCTATGGTGTCTTCTTCTTCTCATAAAAAGCACAC[A/G]TCTTATTGGGTTATGGCCCATTCTAATGAGTTTGA R 2 1 2 1 101000 f 74 goat snp30092-scaffold330-132888 20 32968097 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273023 Affx-1111833197 AX-519546700 20 32764740 TCAACCTGAATAACATCTGTAAGACTCGAATTAAA[A/G]AAAATATCAAAGGATGTCATTCCAGCAGACAGACA R 2 1 2 1 101000 r 74 goat 20_32764740_AF-PAKI 20 32764740 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445652 Affx-122926154 AX-123315989 20 32813258 TGAAATTTCTAGATAGAAAAAACATATGCACAGAA[C/T]ATTTGCCATCTGATGGTCTTTGGGGAATGTTATAA Y 2 1 2 1 201000 f 74 goat snp30090-scaffold330-37182 20 33064194 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431659 Affx-122936806 AX-123302000 20 32864643 CCGCTTTCATCTCGTAGGCAAGTTGTGTGCATGAG[C/T]GTTCAGTTGCTGAGTCGTCTCCGACTCTTTGCGTC Y 2 1 2 1 101000 f 74 goat snp48782-scaffold694-14104 20 33114706 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451463 Affx-122921146 AX-123321796 20 32896416 TCTTTCTTAACAACTTTGACCCAAGAGTTTTTGAA[G/T]CAGGAATGCACATAAAAGCTTTTGCTCTCCTTCAT K 2 1 2 1 201000 f 74 goat snp48783-scaffold694-45877 20 33146474 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792262 Affx-122947564 AX-385279245 20 32930676 GCAGGTTAGGTGAGTAAACACAGAAAACTCAATGG[C/T]AGTCCAACCCATTTACAAGTGAAAAGTTCAGCTGA Y 2 1 2 1 101000 f 74 goat snp48784-scaffold694-80137 20 33180654 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436586 Affx-122932890 AX-123306924 20 33003928 GATATTATAACAAATAGCAGTTCTTAAATGGCTTG[C/T]GGATCCTCTCAAGACAACAGATGCTCCTCTACACT Y 2 1 2 1 101000 f 74 goat snp48786-scaffold694-153389 20 33254454 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399994 Affx-122960811 AX-123270349 20 33035393 ATTTATTTCTTTAAATACATAATTTATAGAGAGGT[A/C]TTTGAGAAATGACTTGTAAGGAAACATGCTCCTTA M 2 1 2 1 101000 r 74 goat snp48787-scaffold694-184854 20 33282710 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452293 Affx-122920687 AX-123322626 20 33072128 TCTTTATCACTGAGCCACCAGGGAAGCCCACCCTT[A/G]TTAATAGAGACTCTATAATATCCCTAAAATTGTTA R 2 1 2 1 202000 r 74 goat snp48788-scaffold694-221589 20 33317906 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379378 Affx-122923286 AX-123249737 20 33111624 TGGAATGCCAACGTGAGAACTGGGCAGACCCTCTA[C/T]GTGACTGCTAAAGAATGAAAGTGCCCAAAATAAAT Y 2 1 2 1 201000 r 74 goat snp48789-scaffold694-261085 20 33357035 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775903 Affx-122976018 AX-385263034 20 33143345 AATTATTATGGAAGAAACAAACAGTAAATTATTAA[C/T]GACTAGTAAGTAAGTTGCAGTATTATAAACTGCAA Y 2 1 2 1 201000 f 74 goat snp48790-scaffold694-292806 20 33388791 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437655 Affx-122931793 AX-123307993 20 33190919 CATATTTGGACTGAGTCACTGATTACACCAGTCCA[C/T]AGAAATTTGCTGTGTCTATGACGATCACAATGAGT Y 2 1 2 1 101000 r 74 goat snp48791-scaffold694-340380 20 33438481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794487 Affx-122920554 AX-385281450 20 33250319 AGATGTTCTTTTCTTCAATACACAGATAATTGAAA[C/T]AATCTTTAACAACCAAGAGCTGAAGTCAGCTCCAG Y 2 1 2 1 101000 r 74 goat snp48792-scaffold694-399780 20 33498388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379660 Affx-122975935 AX-123250018 20 33347880 ATGTCAGTTTATCCCATAATTTTGAACATTACATC[A/C]TTAAACTGTCTTTATTTTCTTAATATTTATTCATT M 2 1 2 1 101000 f 74 goat snp48794-scaffold694-497341 20 33596020 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803346 Affx-122921069 AX-385290182 20 33401231 TAATTTTATTTTGGCTTGACTATTGAATAATCTGA[C/T]GTGGTATTAAGATCTTCCTGAAATCTTGCAGTGTT Y 2 1 2 1 101000 r 74 goat snp48795-scaffold694-550692 20 33649511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800760 Affx-122967859 AX-385287677 20 33451738 AAGCAGTTTAACATTTGTTATCATTCTGATTAACC[A/G]TATAGTTCTGTGAATTAAATCATTTACCAATTTTG R 2 1 2 1 101000 f 74 goat snp48796-scaffold694-601199 20 33700125 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396126 Affx-122963405 AX-123266481 20 33496868 CATTTAACACCAGGACCTTAGGCTGTCTCACTTGC[A/G]TATTTCTAAAGAATTCATTCCCTTTTATTTATTTT R 2 1 2 1 201000 r 74 goat snp48797-scaffold694-646329 20 33745798 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398138 Affx-122961689 AX-123268493 20 33531420 AAAACAAAGAAGGGAGCTTAGATACAGCAAAGAAG[A/C]GTACATAAAGCAAAGAGAGGACCTATCATGCTTTA M 2 1 2 1 201000 f 74 goat snp48798-scaffold694-680881 20 33780440 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779896 Affx-122969806 AX-385266995 20 33580560 AAATGTCAGAGTGTTGAAATCATACCGATAGGCTT[A/G]TCTGATTGAGTAAAATTAGTAATATGCATTTAAGT R 2 1 2 1 101000 f 74 goat snp48799-scaffold694-730021 20 33829662 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410144 Affx-122952802 AX-123280494 20 33614270 GGTACCACAAAATTTTGGCTCAGCACCTGGAGCTG[C/T]AATTTTGTGCAGGTATATATTTGAAAAGAACACAG Y 2 1 2 1 201000 r 74 goat snp48800-scaffold694-763731 20 33863623 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429815 Affx-122938187 AX-123300156 20 33660486 TTGTCCAGTATATTTGAAATTACTGTCTAGAGCCC[A/G]TATGAACCCAGACTTCTGTTTCTAACAACTTTGGG R 2 1 2 1 101000 r 74 goat snp48801-scaffold694-809947 20 33909773 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422554 Affx-122943769 AX-123292900 20 33700526 CAGGTTGACAGGTTGATTTTAACTCTGAGAAAGAA[A/G]TCAGGAAACCTGGGCCTTTCCAGGTAACTGACAGG R 2 1 2 1 101000 f 74 goat snp48802-scaffold694-849987 20 33957932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400288 Affx-122960083 AX-123270643 20 33740638 ATCTCCAACTTTTGAATGAGCTAAGAGTGGGAACA[C/T]GCTCTAATGGAAAAAAGGTACTTAGTGGGCATCCC Y 2 1 2 1 201000 f 74 goat snp48803-scaffold694-890099 20 33997772 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426329 Affx-122940276 AX-123296675 20 33786889 CCTAAAAACACAATTCAAACTTTTACCCTGCTTTA[C/T]GAGACCCTTAATATCCAGGGCTCTGTGGACGTCTT Y 2 1 2 1 201000 f 74 goat snp48804-scaffold694-936350 20 34043852 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392457 Affx-122966161 AX-123262814 20 33876478 TTTCTATTGAGAAACTTGAATTGATAGCTACTTTT[A/C]TTTTAGTTTTCTAGTGGGAATTAACCTTTATTTGT M 2 1 2 1 202000 r 74 goat snp48806-scaffold694-1025939 20 34128933 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797632 Affx-122920434 AX-385284571 20 33930551 AGAAAGGTTTACCTGACTAAGGTAATTACACAAAA[C/T]GAAATAAGTGCAGATTACAAAGTCCATAGCTTTAA Y 2 1 2 1 101000 r 74 goat snp48807-scaffold694-1080012 20 34183898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775021 Affx-122933200 AX-385262153 20 33964192 TCTAATTAATCTCTGTGAATGCTGCTGATTTGTGA[A/G]CCAGTAACAATTCAGCGGTTGCACAGTTCTTGAGA R 2 1 2 1 201000 f 74 goat snp48808-scaffold694-1113653 20 34218259 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382457 Affx-122974218 AX-123252815 20 34009921 AGAGGGGCATAAACATGATGAATACCTTTCAAAGC[A/G]TAAATTTTAAATGCAAACTACTACATTATAGTATT R 2 1 2 1 101000 f 74 goat snp48809-scaffold694-1159382 20 34264449 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427300 Affx-122940151 AX-123297643 20 34055555 TTCTTCCTCTCCTACTCACTGCCTCTTTGTAAATG[C/T]AAGCCACAGATGCAATTTAGACACAGTGCATCTTT Y 2 1 2 1 101000 r 74 goat snp48810-scaffold694-1205016 20 34310034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432434 Affx-122935818 AX-123302775 20 34094801 GTGGGATAAACAAAATGTGTTACATCAACTAGTAG[C/T]ATCCATTTCATTGATAAGACACACAAAATGAGATT Y 2 1 2 1 101000 r 74 goat snp48811-scaffold694-1244262 20 34351186 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441431 Affx-122928817 AX-123311768 20 34127726 GGGGACACGGCGTGAGAATCAGAGTCTTCATTGTA[C/T]AAGTGATGCTCTGATGGAGAGGTCATTGAATTTCA Y 2 1 2 1 101000 f 74 goat snp48812-scaffold694-1277187 20 34384287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446595 Affx-122924814 AX-123316931 20 34161387 GTCAATGAAGCTGGTATAAGCCATGTTTTGAGAAG[C/T]AAGTGTCTAAGTAAGATGACAATGCTGTGCCTCAA Y 2 1 2 1 101000 f 74 goat snp48813-scaffold694-1310848 20 34418842 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797949 Affx-122935970 AX-385284885 20 34197186 GACCTTCACTTTATAAGTAAAGTTAGTAGATTTTT[A/G]CTCTTTAAAAATAAGTGCTAATGTTGAAGCAATAT R 2 1 2 1 101000 f 74 goat snp48814-scaffold694-1346647 20 34455098 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434544 Affx-122934142 AX-123304885 20 34234127 CTCTTTCTGCATATCTTTCAAGTCTAAATAGCTAC[A/G]CTTGCAATGAATGTGCACCAACGTCTTTTACCTTC R 2 1 2 1 101000 r 74 goat snp48815-scaffold694-1383588 20 34491283 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776864 Affx-122958969 AX-385263988 20 34292516 GACACAACTAAAAGGTTCAACAACTCCTTATGGCA[C/T]GTCTGTATGCAGAGGTTTCTTTTCAACTTGCTTCT Y 2 1 2 1 101000 r 74 goat snp48816-scaffold694-1441977 20 34550434 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801392 Affx-122930166 AX-385288302 20 34321406 AAATTTTCCTGGGAATTTAGACAGTCCTTCAAAAA[C/T]GCTTTGCCCCCATATCACTGCAACTATAACCACTA Y 2 1 2 1 101000 f 74 goat snp48817-scaffold694-1470867 20 34579504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419310 Affx-122945668 AX-123289658 20 34462359 TGTGGTAGATTAGAAATCAGAAATATTTATCTGTT[A/G]TTATAGATTTCCAACCTCAAGTCTGAGAACTTATA R 2 1 2 1 101000 r 74 goat snp48820-scaffold694-1611820 20 34721828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768973 Affx-122932901 AX-385256148 20 34496969 AACGTTCTTGGTAGGTGCAAGATTCATTTTATAGA[C/T]GTCAGTTATTTCAGTATACAAACAATTAGAAGATG Y 2 1 2 1 101000 f 74 goat snp48821-scaffold694-1646430 20 34757022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412047 Affx-122951719 AX-123282397 20 34545025 AATAAATATTATTTTATCAAGATATTCATGCATTG[A/G]TTACTTGGGCAAAGTACTGTCTTCTCAAATGATAG R 2 1 2 1 101000 r 74 goat snp48822-scaffold694-1694486 20 34804768 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432569 Affx-122935529 AX-123302910 20 34581051 AGATTATGTCAAGTAACTCCTTAGTTTTTCTTCTG[C/T]GGCACAATCCCAATTTCTTTTTCTTACTTGACACA Y 2 1 2 1 201000 f 74 goat snp43375-scaffold579-673621 20 35484552 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415953 Affx-122948431 AX-123286302 20 34685367 TTGTTGGGAGCCTGGTAATGCTGAACAGCCAACTC[A/G]TGGAAACACTAAAATACCTGTTATTTGAGGTGTGA R 2 1 2 1 201000 r 74 goat snp43373-scaffold579-569305 20 35380318 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386429 Affx-122970804 AX-123256787 20 34715136 ACTTACCCACTTTTCACTTTCTTGGTACTACCACC[A/G]TCCTTTGGTATTCAAGCTAGAGACCTATTGCTTGT R 2 1 2 1 201000 r 74 goat snp43372-scaffold579-539536 20 35350597 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444735 Affx-122926404 AX-123315072 20 34781317 GCAGAGGCAGCTTTCCAGTTGTTTCCAATCTTCTG[C/T]GTATAAAATGTCTTGTTTCAATTTCATATTTCAGC Y 2 1 2 1 201000 r 74 goat snp43371-scaffold579-473355 20 35284362 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393974 Affx-122965043 AX-123264329 20 34824282 AGTCAGCTTGTGTAGAATCAGAGAAAACTTCTGGA[C/T]GACATTTATTCTCCCATCATGCTAGAGATTTCAGC Y 2 1 2 1 101000 f 74 goat snp43370-scaffold579-430390 20 35240902 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390140 Affx-122967991 AX-123260497 20 34878424 AGGCTCAGACAAGGTTTGCCACTGCTAATTGCTCT[A/G]CACTAATCCATGTCCCTGGCCTTCCCTGGTGGCTC R 2 1 2 1 101000 f 74 goat snp43369-scaffold579-376248 20 35186401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426457 Affx-122940800 AX-123296803 20 34919239 ATTGGTGGATTATGAGTTATGGATGGGAGCTTTAG[C/T]CTGTTTCTTCTTAGCCAAAATACCTTTCTTAAATA Y 2 1 2 1 101000 f 74 goat snp43368-scaffold579-335433 20 35145984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379200 Affx-122976296 AX-123249559 20 34966555 AATCTTTTCCATTAGATGATAACTTTGAGTTTCTT[A/G]TCTTAGTCTTCTTGGGTTGCTGTAATGAAATACCA R 2 1 2 1 101000 r 74 goat snp43367-scaffold579-288117 20 35098602 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406036 Affx-122955483 AX-123276388 20 35047246 AAGTACTGAGTAGCACAGAATGTACTGAAATAATG[C/T]GAATTCTTTGATCTGTGAGTTGCATCTCAAGCCTA Y 2 1 2 1 101000 f 74 goat snp43365-scaffold579-207426 20 35018136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401256 Affx-122959295 AX-123271609 20 35083883 TTACTATCATGATTGGAGCTCTCTTTTATTTATTC[C/T]TCTTATTTCTCTCAAAAGAAACCTCAGTCTTGAAA Y 2 1 2 1 101000 r 74 goat snp43364-scaffold579-170789 20 34981595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411873 Affx-122951205 AX-123282223 20 35131683 GTAGTCAGGTTGTTGGCAGAACCCAGGATTCCAGG[A/G]CTCAGATGTAGTACAGAAGATACAAATACTCTAAT R 2 1 2 1 201000 r 74 goat snp43363-scaffold579-122989 20 34933602 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443606 Affx-122927310 AX-123313943 20 35160696 TGATGGATCCAGATGGGCAGCAGCTGAAAGCCCCC[A/G]TCAGTGAGGCTCCCTACAAGAGTTGAATCGAATAA R 2 1 2 1 101000 r 74 goat snp43362-scaffold579-93976 20 34904554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431390 Affx-122936549 AX-123301731 20 35195934 GGAAGGTGGTGGTGGGGGTAGGATGGAGGAAGGTC[A/G]CTGCATGACTCAGAGAGGTTTGGCTTCTATAATTA R 2 1 2 1 201000 r 74 goat snp43361-scaffold579-58738 20 34869313 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793964 Affx-122960709 AX-385280933 20 35225660 TGTAGATTTTTGCCTTCCTCACATTTTTTTCATTT[A/C]TTTGTTCCTCAGCACTTGCAAGTGAGGTATTAATT M 2 1 2 1 202000 f 74 goat snp43360-scaffold579-29012 20 34839514 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412027 Affx-122951735 AX-123282377 20 35267481 AACACACCCATGTTCTTGGGAAGCAAGTGACTGAT[C/T]AAACTGCTTCTCATGGGGATTATTTGCAGTGGGGA Y 2 1 2 1 101000 f 74 goat snp52309-scaffold776-1458652 20 35527555 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275036 Affx-1111834648 AX-519548619 20 35287361 GATAGTATGTGGAATAGAGGTGAAGGTACAAAGCT[A/G]AGTCTTGTCAAAATTCCTGGGTGTGTGAGACTGTT R 2 1 2 1 201000 f 74 goat GoatD01.044435 20 35287361 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38390650 Affx-122967141 AX-123261007 20 35300834 TTTTTTTCCCCTAGGGGGTTTATTTTTGTTTGTTG[C/T]AATTCTCACAGAGTAAAAGGTTCAAGAGAAGGAAC Y 2 1 2 1 101000 r 74 goat snp52308-scaffold776-1425299 20 35561352 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431092 Affx-122936617 AX-123301433 20 35343432 AGCCCTTTAGCAAGGTCCATTAAGATATATAAGGT[A/G]TTTGTTCACTATCATCATTAATATAATTATAATAA R 2 1 2 1 101000 f 74 goat snp52307-scaffold776-1382701 20 35603379 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770331 Affx-122932369 AX-385257497 20 35442526 TGGTTCTTGACTATAAATGTTTGCAGATCTGAATT[A/G]CATTTTTCTTAGTAAAAGTGGGTCTTCTCCTACAG R 2 1 2 1 201000 r 74 goat snp52305-scaffold776-1283607 20 35703003 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445459 Affx-122925220 AX-123315796 20 35501669 GTCTGGGGTTAACAGTGAAGAGCAGGGACTTCTCT[C/T]TGGTCTCATGGTTTCACTCTGTTGATTGAAGATTA Y 2 1 2 1 101000 f 74 goat snp52304-scaffold776-1224464 20 35762884 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381486 Affx-122974961 AX-123251844 20 35555114 AGGTTCTGAACTCTGTGCAGACATCTGGCCCTCAC[A/G]CGTCTGGGAGGAGATCTCAGTCTACCGATACAAAG R 2 1 2 1 101000 r 74 goat snp52303-scaffold776-1171019 20 35816093 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413156 Affx-122950352 AX-123283505 20 35603249 GGTTACTACTTGTCCCAGTGCTGGTTATTAAATAA[C/T]ACAATCCTTCCTCCACTGACCTGGGATGCAATTAG Y 2 1 2 1 201000 f 74 goat snp52302-scaffold776-1122884 20 35864539 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781063 Affx-122974773 AX-385268150 20 35634032 CTTGAATTCCAAAATGTTTACTGGGAAGGCAAGAA[G/T]CAATTAAGGTTAGAGCCATCAATCTGAGAAGGGCA K 2 1 2 1 101000 f 74 goat snp52301-scaffold776-1092101 20 35895338 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386277 Affx-122970942 AX-123256635 20 35703370 GACAGGTGAATGCCTGGGCTTTATAGACTGATAAA[C/T]ATTTTGACAAAATATTTTTGACTCCTACCTGTGAA Y 2 1 2 1 303000 r 74 goat snp52299-scaffold776-1022763 20 35964553 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414438 Affx-122949954 AX-123284787 20 35764924 GGCCAGCACAGAGCCCTGTGTTTATTGATTAGTTC[A/G]TCTGAATAAACTCCTCCCCTTTCCCCACACAACAC R 2 1 2 1 201000 f 74 goat snp52297-scaffold776-961209 20 36025679 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376087 Affx-122978904 AX-123246446 20 35822378 ATTCTTCATATGTAATAACTACTGTAGAATGATGC[A/G]CTCTGTGTCACTCCGTGTCAGAAAGCCTGGGAGCA R 2 1 2 1 201000 f 74 goat snp52296-scaffold776-903755 20 36083094 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277304 Affx-1111835844 AX-519550808 20 35902899 GTTCTTTATTGTTTGAACCATGGGGGAAGCAATAA[A/G]CAGAGAAACAGTAAGACAAAAACTGATAGGTATTA R 2 1 2 1 202000 f 74 goat Random2.2K-1857 20 35902899 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320773711 Affx-122944695 AX-385260851 20 35928984 GAATTTCCATGAGTGCATGGATTATCCTATTTGCA[C/T]AACTAAAAATAACTTTCACCGTAAGAGACTATGTT Y 2 1 2 1 101000 f 74 goat snp52294-scaffold776-797149 20 36189745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421762 Affx-122944359 AX-123292109 20 36007822 ACAAAATCATTAACTACAGGACATATGCTATGTAT[A/G]CTGGTCACCTGGCAACCCTCTTTCTTCATCCACTG R 2 1 2 1 101000 r 74 goat snp52292-scaffold776-718311 20 36266651 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451388 Affx-122921206 AX-123321721 20 36065408 AGCCAAGTTCATATGACTGATAAGTAAAATTGGTC[A/G]CGGGTTAATACATTTACAGTAAGAAATAACTGTCA R 2 1 2 1 101000 f 74 goat snp52291-scaffold776-660725 20 36325224 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416477 Affx-122947803 AX-123286825 20 36095762 CAGCCCATGGGCCATATTTAGCTTGCTGCCTGCCT[A/G]TTTTTGCATGGCCCTTGAGCTAAGAATTGTTTTCA R 2 1 2 1 201000 r 74 goat snp52290-scaffold776-630371 20 36355810 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394297 Affx-122964699 AX-123264652 20 36143213 TTTCCCCCTGGCCTCCCCTCATCACTCCTAACACC[A/G]CACACAGCATCCACAGCACACGTTAGTGACTGAAT R 2 1 2 1 103000 r 74 goat snp52289-scaffold776-582920 20 36403528 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774529 Affx-122955003 AX-385261663 20 36200755 CAATATTTAAGTATGGTTAACATAATAGTAATGCC[A/G]CATATTTATATATCATCCTATCTCCAAGGAGCTCT R 2 1 2 1 101000 r 74 goat snp52288-scaffold776-525378 20 36461063 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421569 Affx-122943848 AX-123291916 20 36230301 TGGCACATGTGCTTCTCAAGGTGCATGGTCTTCTC[G/T]CTAGTTGTGGTGCAGAGGCCCTGTTGCCCTGTGGC K 2 1 2 1 102000 f 74 goat snp52287-scaffold776-495832 20 36490946 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446257 Affx-122925680 AX-123316593 20 36267374 TGTGCCCTTATTTCCACTTCCTCAGCACACACTGC[A/G]CCCTAGCACTAGCCACCAACCTCTTGCACTCGGAC R 2 1 2 1 201000 r 74 goat snp52286-scaffold776-458759 20 36528187 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426729 Affx-122939877 AX-123297075 20 36301447 TAGCAGTTGTTTCAGTTGTCTGGAAAACTCACTTA[C/T]TGAAGAAGTGGGAAAATCACTTATCCTTCAATAAT Y 2 1 2 1 101000 f 74 goat snp52285-scaffold776-424686 20 36564632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388214 Affx-122969412 AX-123258572 20 36380203 TTAACAGGAGAAAAATGGTTTACTAATATGTGCAG[C/T]GCACGTCATATGGGAAAATCCTGTATAAAAATATA Y 2 1 2 1 101000 r 74 goat snp52284-scaffold776-345930 20 36643181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410800 Affx-122952655 AX-123281150 20 36434931 TTTCTGTTTCTAAGACCAAATAAAGGAAATAATTT[A/G]CTTTAACTCCTCTCAGGGGAGCGAAATTATGTGTA R 2 1 2 1 303000 f 74 goat snp52283-scaffold776-291202 20 36698503 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770952 Affx-122958006 AX-385258114 20 36492656 ACCAGAATTATGTATATGCATTTTTTAGGTTTGTT[G/T]GTTTGTTTTCTTGGTGAGCAATAAGTAAGTGATAT K 2 1 2 1 202000 f 74 goat snp52282-scaffold776-233477 20 36756244 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794527 Affx-122924927 AX-385281490 20 36560600 CCGTCAGACTCATCCTAAGACTTTTATTGTATAAC[A/C]CTTCAACATATGTGTGCAGTGAAAAGATGTTCTGA M 2 1 2 1 101000 f 74 goat snp52281-scaffold776-165533 20 36824495 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794244 Affx-122961940 AX-385281210 20 36591349 AAGTTGATCTAAAAGGAACTAAAAATTGAGACTAT[A/G]CAGAATACGGCTGAAACAGGATAGTATATTTGGTT R 2 1 2 1 101000 r 74 goat snp52280-scaffold776-134784 20 36855847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417807 Affx-122946813 AX-123288155 20 36675407 CTCTTTATCCTGTCCTTTTTCCCAGCTCTCTCTGT[A/G]TCCAGCACAATATCTTGCTTATGGCAGATGTTCCA R 2 1 2 1 201000 r 74 goat snp52279-scaffold776-50726 20 36937914 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797834 Affx-122920661 AX-385284773 20 36707071 AAATTATTCATTTTTTAGATGTGGTAATGATAATA[C/T]AGTATATAAGAGCTTAGGATATGGAAAGTGAAGGA Y 2 1 2 1 201000 f 74 goat snp52278-scaffold776-19062 20 36970030 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767660 Affx-122970328 AX-385254900 20 36782620 CAGCTCAGAGGTTTCCTTACTGTATTTAAACATCT[A/G]TTTAGCACTTTTACTTGTTAGTAGTACGCTCAAAG R 2 1 2 1 101000 f 74 goat snp44657-scaffold607-56388 20 37046106 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386016 Affx-122971498 AX-123256374 20 36820349 ATCTTTGAGAAAGCCTGGAAGCACTTTGCTGCTCT[A/G]TTGTCTCCTCAAGTCAGCAGCTATTTGCTGAAAGT R 2 1 2 1 101000 f 74 goat snp44658-scaffold607-94117 20 37083826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797931 Affx-122929001 AX-189075906 20 36850498 TCGTAACTTACGAACCTAGAGGAAATGCTACCCAA[C/T]GCAAACCTAGATGTAATCATATTACTTGTGTGTAA Y 2 1 2 1 101000 f 74 goat snp44659-scaffold607-124266 20 37114689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400444 Affx-122959960 AX-123270799 20 36891439 ATTAATCTTCCCTTAGATTTAGCTAAAAGTAAAAA[A/G]GCACTGGAGCATCAGCAGAAATTAAAAAAAAGGTG R 2 1 2 1 102000 r 74 goat snp44660-scaffold607-165207 20 37155261 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277430 Affx-1111835845 AX-519550934 20 36907980 ATATCTAACTTTTAAAATTTATGACAAATTTATTC[A/C]AGAGAGGTTATTAATGATTTTCAGTTCTTTTGAAA M 2 1 2 1 101000 r 74 goat Random2.2K-1858 20 36907980 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797744 Affx-122921437 AX-385284682 20 36929792 TGCTTGACAAGGATCTGAAAGCCCAGTCAAGAAAA[C/T]CTAATTAACACCTTCAGTTTTATAAGAATGGCAGA Y 2 1 2 1 201000 r 74 goat snp44661-scaffold607-203560 20 37193614 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392018 Affx-122966481 AX-123262375 20 36961908 CTTAATTATGTTACAGTATCAAGTAGGCATCTATT[A/G]TCTTAATATCTGTATCAGGCTCTTACAGGAGAGGA R 2 1 2 1 101000 r 74 goat snp44662-scaffold607-235676 20 37226270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802724 Affx-122966841 AX-385289623 20 37050483 AAATGAGATTCACATGGATTCACTCCAGAAGACTC[A/G]TGGCTAAGACTAATGAACCAGTCTTTCACAACCCA R 2 1 2 1 101000 f 74 goat snp44664-scaffold607-324251 20 37313779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425868 Affx-122940650 AX-123296214 20 37088019 CTAGAGAGGTGGACATATATTTGAAAGATAAAGTA[G/T]AACTCAGGAGTCCTGGAACCAATGAATGTGTAAAA K 2 1 2 1 201000 f 74 goat snp44665-scaffold607-361787 20 37351597 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783126 Affx-122941181 AX-385270193 20 37125734 ACTTTTCATAATCATCTGAAATATGATTTTCAAGA[C/T]CTGAAAGGTGAGTTAATTGAAATAACTATCTGATT Y 2 1 2 1 101000 f 74 goat snp44666-scaffold607-399502 20 37389346 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389012 Affx-122968641 AX-123259370 20 37159477 GCAAAGGAATACATGTATTTGATGAAAATAAAAAA[C/T]AAAAATTTAAAGAGCTACAGAGAGGACAATTTAAA Y 2 1 2 1 303000 f 74 goat snp44667-scaffold607-433245 20 37423087 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792735 Affx-122947791 AX-385279715 20 37189783 TTCAGTGAGGCCTCAGTTTGAAAATGTTTGGCTTG[C/T]AGATCAATAACTCATAAGTCTGAAACAACTCTGAA Y 2 1 2 1 101000 f 74 goat snp44668-scaffold607-463551 20 37453439 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791923 Affx-122963281 AX-385278913 20 37223576 GCTAATACTTTGGAAGTATAGATGGAGGTATCAAT[A/G]TTCTTGAATAACACATGTTCACACTTGATCGTGTT R 2 1 2 1 101000 f 74 goat snp44669-scaffold607-497344 20 37487197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800276 Affx-122948139 AX-385287199 20 37254218 TCATGCAAACTAAACAAGTCATCTGTGGACTAAAC[A/C]TGTAGACACCATCTATTCTCTATAGGGTGGCAGCT M 2 1 2 1 101000 r 74 goat snp44670-scaffold607-527986 20 37517821 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378252 Affx-122976895 AX-123248611 20 37301583 GCTGCCAAGCTCAGTTGCTCCCTATCCTGCGATTG[C/T]GCAATTGCCTTTTGAATCTAAAAGCAGAAGTGTGC Y 2 1 2 1 201000 r 74 goat snp44671-scaffold607-575351 20 37565094 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779745 Affx-122939253 AX-385266845 20 37342590 ATACTTTACTAAGGTAAAATAACTTTCATCCAAGA[G/T]AATTCATTATACCATTTGAAAAATGATTTAGAAGA K 2 1 2 1 102000 r 74 goat snp44672-scaffold607-616358 20 37606084 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387061 Affx-122969898 AX-123257419 20 37391507 TTCCTTTGATTGGTCTCCTTTTGTATTACCCTATA[C/T]AGGCACAGACTTGTATCCAGTCAAAGACTCAAGGA Y 2 1 2 1 201000 f 74 goat snp44673-scaffold607-665275 20 37655050 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791623 Affx-122962597 AX-385278614 20 37422992 GAGATGCTACTTAATTAATACTTGAAGGGAACATA[C/T]GCTAAGCACTAAATTTGTACTGTAAAATATCAAGA Y 2 1 2 1 101000 f 74 goat snp44674-scaffold607-696760 20 37686537 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401345 Affx-122959258 AX-123271698 20 37464741 AAACTATCGTTCATATTTTCTATATTATCTTTTTG[C/T]GTGTCATTCTAGATGATTTTCTCAGGTCAATCTAC Y 2 1 2 1 101000 r 74 goat snp44675-scaffold607-738509 20 37728422 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400531 Affx-122960446 AX-123270886 20 37529166 TTCATGCTCCAGGACTGAGTGCCCAAGCCTGCTAC[A/G]CTCATTCATGCCTCCTCGTCATTGCCTCTCCTGGT R 2 1 2 1 201000 r 74 goat snp44676-scaffold607-802934 20 37792864 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451198 Affx-122921326 AX-123321532 20 37560575 AGTGCACTTGTGAATATTCTTGCAGCAGCTCTCTA[A/C]ATTGAAAGATTTTTCAGAAATAATTTGCTGTTTCA M 2 1 2 1 101000 f 74 goat snp44677-scaffold607-834343 20 37824338 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787181 Affx-122976489 AX-385274207 20 37600923 CTTATTTTTCTAGTTTCTTGATGCTTTTTATTCTA[C/T]AGGAAAATGCTACTTGAGGTTATCTTATGCGTTTG Y 2 1 2 1 201000 f 74 goat snp44678-scaffold607-874691 20 37864710 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277308 Affx-1111835846 AX-519550812 20 37622227 TGACCCCTGAAGAAGTTTAAGAAGCAAGGGCAGAC[A/G]TCTAGGGAATTCCACTATAAGAGAAAAAGAACAAC R 2 1 2 1 101000 f 74 goat Random2.2K-1859 20 37622227 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448596 Affx-122923395 AX-123318932 20 37639290 CCATACTGCCAGTATCATGTCTACCATACAAAGAA[A/G]AGGCAGTAGCCACCTATTCAACAGTTTGCACACCT R 2 1 2 1 101000 f 74 goat snp44679-scaffold607-913058 20 37903517 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766127 Affx-122954438 AX-385253535 20 37673107 TTTGCAGCCACCTCAAGCTCAAGGGTATATAAAAG[C/T]GAGAAAATCATTTGGACACAATGTGTTGGAATCCT Y 2 1 2 1 101000 f 74 goat snp44680-scaffold607-946875 20 37937710 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379304 Affx-122976201 AX-123249663 20 37701802 TCCTAAAGTGTTTGATGGTAGCAGTTTATAGAAAA[C/T]ATTTGCATCATTTAAAGAGTAAATCAAACAGTTTG Y 2 1 2 1 201000 f 74 goat snp44681-scaffold607-975570 20 37966956 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451812 Affx-122921482 AX-123322145 20 37744331 AACACATCTCATTTGATTAGTATTTTTTTATAGTA[C/T]GTAAAGATCAAGATTTTTTTAAAAACTTTGATGGA Y 2 1 2 1 103000 f 74 goat snp44682-scaffold607-1018099 20 38009492 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424613 Affx-122942193 AX-123294959 20 37794996 GCTATAGGAATTCATAAGGAACCTTGGAAAGTACT[A/G]TCATTCTGCACTGTAAAAGATAAAACAGTTCCTCG R 2 1 2 1 101000 r 74 goat snp44683-scaffold607-1068764 20 38060092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800568 Affx-122934480 AX-385287487 20 37874559 TGGTGCTGGTAGAAAAAGACTTTCAGTAACTTGAA[A/G]TTTCCATTTTAATTCTATGCTCATATTTTCAGTAA R 2 1 2 1 101000 f 74 goat snp44685-scaffold607-1148327 20 38141167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452484 Affx-122920990 AX-123322817 20 37904380 AATTGTGAGGAATTGTTGCTCCTGGATCTTGTTGG[C/T]GATACATCACTTATAGACTTTGTGTGTACTCTCCC Y 2 1 2 1 201000 r 74 goat snp44686-scaffold607-1178148 20 38170993 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419459 Affx-122945487 AX-123289807 20 37956692 TATATTTTCTTTTTAGTTAAATTATACAGTTAAAA[C/T]GTTACTCCCTTTGCAATTAAAAGCAAATATAAACT Y 2 1 2 1 201000 f 74 goat snp44687-scaffold607-1230460 20 38223028 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393644 Affx-122965295 AX-123263999 20 37997861 CACTGGTTTTGGTAGAAGCTGGACATGGTGACATA[G/T]GCTTCTTCTTGACTTGATCCCAAGGAAGTGAGGAT K 2 1 2 1 101000 f 74 goat snp44688-scaffold607-1271629 20 38266014 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381196 Affx-122974536 AX-123251554 20 38033002 TTCACACATCTTCCATGAAGAGTGACAGAAATAAA[C/T]GGTGACAATTTCATGCATCAAATGATAATTTGTGT Y 2 1 2 1 201000 r 74 goat snp44689-scaffold607-1306770 20 38301104 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393530 Affx-122965426 AX-123263886 20 38115167 TTTGAGGCTGGATGCAAGAATGTTTTATGGCTATC[A/G]TCATAAATGTAAAGTCTCTTCTGAAAGGGACTATG R 2 1 2 1 201000 r 74 goat snp44691-scaffold607-1388935 20 38383647 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463739101 Affx-1110133088 AX-515218747 20 38151619 CCAGTTGCCTTCAAACTAGGCTACCTTCAGTATCA[C/T]GCATACATGAAAACTTCCCAAGGGCTTCATGACAC Y 2 1 2 1 101000 f 74 goat 20_38151619_AF-PAKI 20 38151619 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468277310 Affx-1111835847 AX-519550814 20 38173165 TTCTCAGCAATTAGAAATGAACATAAGTCAAAGGT[A/G]TCAACAAATATCAGGTCGAAGTTCTCATTCTTTAA R 2 1 2 1 101000 f 74 goat Random2.2K-1860 20 38173165 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378933 Affx-122976436 AX-123249292 20 38219868 TGCCAATAATGAGATCTCAGTCTGGTTTATCCCAG[C/T]GGTCTTTCAGGGGCTCTTTTAAGGTGCACAGCTGG Y 2 1 2 1 201000 f 74 goat snp44694-scaffold607-1493636 20 38488286 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783335 Affx-122949350 AX-385270399 20 38249278 TCAATTAAAAATAATAATCAAAGGACATTTAATGA[G/T]TATTTTCAATGTTCAAAGCATTGTACCAGGCAAAT K 2 1 2 1 201000 f 74 goat snp44695-scaffold607-1523046 20 38518439 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421251 Affx-122944106 AX-123291598 20 38315581 CAAGATTCACTGAAGTCCAGGACTAGATCAGAAAA[A/C]ACCATGCAACTTCTGCCTTGCCTCTGGGAACCCAG M 2 1 2 1 101000 f 74 goat snp44696-scaffold607-1589349 20 38586365 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384199 Affx-122972398 AX-123254557 20 38349857 AGCCTTAGCAGAAATCAACTTTTCTGGCACCTTGA[G/T]CTTGGACTGCTAGCCTCAAGAATTGTGAGAAAATA K 2 1 2 1 101000 r 74 goat snp44697-scaffold607-1623625 20 38621474 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792194 Affx-122976418 AX-385279179 20 38382954 AGGGAAAGATGCTTGTCATAACAACTTTGTTTTCA[C/T]CAACTTAGGAGACCACTGGGTTTTTAAAAATGACA Y 2 1 2 1 101000 r 74 goat snp44698-scaffold607-1656722 20 38654899 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392115 Affx-122966349 AX-123262472 20 38443328 ATATCAAAATCAGTCAAGGAATTTTTCCATCAGAC[A/G]TACACCTCCCACCTTTGCTGAGTATATGCCCACTT R 2 1 2 1 201000 f 74 goat snp44699-scaffold607-1717096 20 38717048 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781785 Affx-122932489 AX-385268867 20 38457446 CAAGTTATCTCCAAATTCATGGATTTACACAGATG[C/T]ACTATTTTTCTAAGTCCCACAACGGTCTTGAAGTG Y 2 1 2 1 101000 f 74 goat snp4445-scaffold114-867758 20 38731108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 532577590 Affx-1248697225 AX-310754868 20 38459086 GAACCATTCACTTTGAACACACCAATCTCCTCACT[-/GTTCAGTTCA]GTTCAGTTCAGTCGCTCAGTCGTGTCCAACTCTTT - 8 1 4 1 20100 r 74 goat "ins-del_020;rs644277083" 20 38459086 GTTCAGTTCA - 5 "indels;junction" litter size 0 not_recommended SV-TF-chip candidate gene ou candidate region SPEF2 562166532 Affx-1248697225 AX-606941940 20 38459086 GAACCATTCACTTTGAACACACCAATCTCCTCACT[-/GTTCAGTTCA]GTTCAGTTCAGTCGCTCAGTCGTGTCCAACTCTTT - 8 1 4 1 20100 f 74 goat "ins-del_020;rs644277083" 20 38459086 GTTCAGTTCA - junction SV-TF-chip candidate gene ou candidate region SPEF2 320792714 Affx-122940857 AX-385279694 20 38489773 TGAACTGAGAAAACATTTAAGTGTGGGACAGGAAG[C/T]ACTATCAATTATGTCTTTGGTAACATAATTCCACT Y 2 1 2 1 101000 f 74 goat snp4444-scaffold114-835431 20 38764112 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422350 Affx-122943442 AX-123292696 20 38521459 CCTTCTATGTGCCCATTAGTTTTAAGAAAGCAACA[C/T]AAATTCAACGATGTCACCATGTCCAGCCTTGGCTC Y 2 1 2 1 101000 f 74 goat snp4443-scaffold114-803745 20 38795933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442590 Affx-122928490 AX-123312927 20 38553357 TTGAGTAATTGTTGGTGCTATATAGCAGGGAGATA[G/T]AACACAGTTTTCCTTTTTAAATCTTTGTGTAGAAC K 2 1 2 1 201000 f 74 goat snp4442-scaffold114-771847 20 38827196 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403361 Affx-122957797 AX-123273714 20 38605451 ACCATCTCCACACATTTTGAAAAGTTAGCTCATTT[A/G]CTACAACTTGTCTTTGGTCTTCCCTCCATCCACTA R 2 1 2 1 101000 r 74 goat snp4441-scaffold114-719753 20 38879813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277435 Affx-1111835848 AX-519550939 20 38619225 TGAAGAGGATTTCTCTGAAAATATGATAGGTTCAA[C/G]TGGTTTTCAGATGAATTCTTTTTACCTCTTAAAAC S 4 1 2 1 101000 r 74 goat Random2.2K-1861 20 38619225 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401922 Affx-122958823 AX-123272275 20 38673028 GGTCTTTCAGGACTACCAAGTTCTTCACACTTGTT[A/G]TCCCCATTACTGGTGCACGTGCCTGTGTCACCAAC R 2 1 2 1 202000 r 74 goat snp4439-scaffold114-652176 20 38947614 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277314 Affx-1111835849 AX-519550818 20 38690240 CACTAGCTGATTAAGGAGATAGCATAGCCTGGTGG[A/G]GAGATCAGGGCTTCTCAGACTCAGCACTGTAGGTA R 2 1 2 1 102000 f 74 goat Random2.2K-1863 20 38690240 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397598 Affx-122961987 AX-123267953 20 38718458 GTCACTCTTCAGTGTCTGCTCCTCTGATAGATTCA[C/T]GCCAAGAAAAAGTGGACAATGCCTAATATATGACA Y 2 1 2 1 101000 f 74 goat snp4438-scaffold114-606746 20 38993710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779273 Affx-122966805 AX-385266377 20 38773043 TTGTAACTGAAGAAAGTAAAATGTGTCCAAATCAA[C/T]AGTCAATATCTGTAGAATAAGTGTATCACTGAAGC Y 2 1 2 1 101000 f 74 goat snp4437-scaffold114-552161 20 39050454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407428 Affx-122954806 AX-123277779 20 38812251 AGTGTTCTAAGCCAAATATTTTAGCATGTGTCTGC[A/G]TTTTTTATTTCCAGAGAGGCTTAGATTACTGATAT R 2 1 2 1 102000 f 74 goat snp4436-scaffold114-512953 20 39090463 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791371 Affx-122978500 AX-385278363 20 38902848 GCTCAGTCAGACTTTGGCAACCACTAATAAAATGC[A/G]TTTCCTCACTTAATAATGTGAGAAAAAGAATCAGA R 2 1 2 1 101000 f 74 goat snp4434-scaffold114-422356 20 39175179 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769286 Affx-122962239 AX-385256459 20 38936054 AAGTCCGGGAATGACTTCATTATAATGTTCTCAGA[A/G]GCCGTGAGCTGGTTTGTCCTTCTAAATGAATCAAG R 2 1 2 1 101000 r 74 goat snp4433-scaffold114-389150 20 39208146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399196 Affx-122960617 AX-123269551 20 38975148 TTAGCGACAAAATTATACTGGAAATCTCTATCTTC[C/T]ACTTAATTTTTCTGTGAATGTAAAACTGCTCTAAA Y 2 1 2 1 103000 f 74 goat snp4432-scaffold114-350056 20 39247529 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400287 Affx-122960084 AX-123270642 20 39008192 TAAACTGAAAATTGATGTTGGATCTTCCTGTTGCT[A/G]TGTCGTTCTTTTAATTAACAAACAGTTTTTTTTAT R 2 1 2 1 201000 r 74 goat snp4431-scaffold114-317012 20 39281136 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775539 Affx-122970343 AX-385262670 20 39043113 CTAGATTCTCTTGTGCAAAACAGATTTCAGTATTA[A/G]CCCCATTGGTCCTTAAACCGTTAATAAAACGTTTT R 2 1 2 1 101000 r 74 goat snp4430-scaffold114-282091 20 39315063 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426650 Affx-122939938 AX-123296996 20 39083614 ACAAGTAACACATTTGAGTTTTGCCTTGAATGGTT[A/G]CATTTGTTCCTGGTGTAACCAAAGATTTTGCCAGA R 2 1 2 1 201000 r 74 goat snp4429-scaffold114-241590 20 39355578 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417279 Affx-122947249 AX-123287627 20 39116136 AGTCTTTATGATTTTCAACCCATCAACTCAGTTCA[A/C]AACAAGCAGAGGACATAGCCAGTAAATGAACACGG M 2 1 2 1 201000 f 74 goat snp4428-scaffold114-209068 20 39388022 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386663 Affx-122970198 AX-123257021 20 39166595 CTTGTCACAGTGACTTTGTGCTTTCCACATTTTAT[A/G]TATTCACCTGTAACATTTGAGGAGTGGCCCTGTCT R 2 1 2 1 101000 f 74 goat snp4427-scaffold114-158609 20 39438562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392507 Affx-122966125 AX-123262864 20 39223322 AAAATGACAGTAGTCACAGCTAGATTTTACTGAGC[A/G]TTTACTTGGATGAAGATTTCAAAGAAGCAAATTAC R 2 1 2 1 201000 r 74 goat snp4426-scaffold114-101882 20 39493352 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449840 Affx-122922385 AX-123320175 20 39260276 CAGGGCCAGCCAAGGCAGATTTTTGAAGTCAAGGG[A/C]TATTTTTATTTCTAACTTCATCTCTTAACTTCTGA M 2 1 2 1 101000 f 74 goat snp4425-scaffold114-64928 20 39530285 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398719 Affx-122961840 AX-123269074 20 39305242 CTAGCCTGCAACCAACTAGGTTTGGAACTGCAGCT[A/G]CCTAGGACTCCAGGATATATGCCAATTGGTATTTC R 2 1 2 1 101000 f 74 goat snp4424-scaffold114-19962 20 39575231 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781120 Affx-122959215 AX-385268205 20 39358231 TTTATGGGTTATGTCATTTTTATAGCAGCTGAAAA[C/T]ATATAGCAGCTTTTTATAGTAGTTGAAACTATTTA Y 2 1 2 1 201000 f 74 goat snp17002-scaffold1774-166397 20 39629006 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277439 Affx-1111835850 AX-519550943 20 39361588 TCCACGCCTCATCAATTCACCAGGGTAAACCCAGT[A/G]TCTCCCAGTTATGGGAATGGTCTGGGAACTGGTTA R 2 1 2 1 101000 r 74 goat Random2.2K-1864 20 39361588 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38400379 Affx-122960015 AX-123270734 20 39420773 CACTGGACCACCAGGGAAGTCTCGCTAAGCTCTTT[A/G]TGATAATAAAGAGAACTCACATAGTTTTGCCGTTA R 2 1 2 1 201000 r 74 goat snp17000-scaffold1774-103855 20 39691817 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422340 Affx-122943450 AX-123292686 20 39480771 TTAATGGTCAGAAAATGTGTGCTATTTTTAAGTTT[A/C]ACAATTCTTTTTTTCAACACAATATATACTACCAC M 2 1 2 1 102000 f 74 goat snp16999-scaffold1774-43857 20 39751384 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388978 Affx-122968665 AX-123259336 20 39512724 TATTGGTTTTGCCATACATTGACATGAATCCACCA[C/T]GGGTGTACATATCTCATTTCATTCAATTTTCCAAC Y 2 1 2 1 103000 r 74 goat snp16998-scaffold1774-11904 20 39783417 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439679 Affx-122930584 AX-123310016 20 39529334 TAATTACAAAATATTGATGCTGAGTGCTGCCCTTA[C/T]ACCAATAAAATGGGAATCATTTGTTAAGAGCAAGA Y 2 1 2 1 101000 r 74 goat snp14038-scaffold1557-4607 20 39799082 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402515 Affx-122958488 AX-123272868 20 39566056 AGCTGTGCAGTACTCTGAGCTTATTGGTGATGCAT[A/C]GATATTTAGATTTAAAAAATAATTTCCGAAATTTT M 2 1 2 1 102000 f 74 goat snp14039-scaffold1557-41329 20 39835856 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402775 Affx-122958308 AX-123273128 20 39609464 GCTCTTGTCTTGGTAGTGCTGTCTCCTATGTGGTC[G/T]AGGGGGTGAGAAGTCATCCAGGTTGAGGACCAACT K 2 1 2 1 101000 f 74 goat snp14040-scaffold1557-84737 20 39879276 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439450 Affx-122930181 AX-123309787 20 39704186 GAAAAGGGGAAAGGAATCTCCTACTACCTTGCCAC[A/G]TTGGTTGATGCTATTTATATGGTATTAGTAATGCT R 2 1 2 1 201000 r 74 goat snp14042-scaffold1557-179459 20 39972132 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780525 Affx-122960705 AX-385267616 20 39750678 AATGAATATCCTGAGTTGAAGCTGGACTGATTCTA[G/T]AGTTAATGCTGGAAGTTGTATTATATAAATTATTA K 2 1 2 1 201000 r 74 goat snp14043-scaffold1557-225951 20 40018305 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426405 Affx-122940841 AX-123296751 20 39780397 TCCAGACGAGGAGGCGGGGAAGACTTCTTGGAAAT[G/T]TCCCAGTTGAGTCTTTAAAAATTAATGGATATTGG K 2 1 2 1 201000 r 74 goat snp14044-scaffold1557-255670 20 40047921 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388171 Affx-122969442 AX-123258529 20 39809255 AAAGAGCCCCAGTGACCAGTGACTGCTTGTATTAT[A/G]ACAAATGCTAGGTTTGTTAAACTTATGTCTCTTGC R 2 1 2 1 102000 f 74 goat snp14045-scaffold1557-284528 20 40077011 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379678 Affx-122975920 AX-123250036 20 39860004 ATACCTTGGGAAAGGTTGGAAGAACAAGTGCTACC[A/G]TTCATTACAAGAGGCTTCTTAAAGAAAATTTACCC R 2 1 2 1 101000 r 74 goat snp14046-scaffold1557-335277 20 40128762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277441 Affx-1111835851 AX-519550945 20 39886115 CATTGCCAAGCATTACAGGGCCACCAGGTTTCTTC[A/G]TAAAATACTGAATTAGAGTCTAAAATAAGCTCCAA R 2 1 2 1 101000 r 74 goat Random2.2K-1865 20 39886115 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447063 Affx-122924512 AX-123317399 20 39900858 TGAAAGTAGCAATTGAGATGAGTTCTAAGTGTGGC[G/T]CTGTGTCCTGCATTTATCTCATCTGAAGGGCTTGA K 2 1 2 1 101000 f 74 goat snp14047-scaffold1557-376131 20 40170696 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422209 Affx-122944443 AX-123292555 20 39927734 CATGGTAACAATAACAAAGCAGTCATGATTGCCAA[C/T]ATCATGCCTATCACATCAGGCACTGTGAAATGATA Y 2 1 2 1 101000 f 74 goat snp37290-scaffold454-1876657 20 40197897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378815 Affx-122976553 AX-123249174 20 39983898 CTAGTTGATTCGCAAGAGGAAAGGGACAGGGCTCG[A/C]GTGACCCAACTCTTACTTTATCAGATAACTATGCT M 2 1 2 1 101000 r 74 goat snp37289-scaffold454-1820493 20 40253302 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441521 Affx-122928716 AX-123311858 20 40034921 TTCCTCTAGCCCATGTTTCCTTTCCTGCTAAGACC[A/C]GGGAAATCTAAAAGAAGAGTTGTGAAGGGCACCAC M 2 1 2 1 101000 r 74 goat snp37288-scaffold454-1769470 20 40304154 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797293 Affx-122950323 AX-385284232 20 40069839 TTTACAAGATGAGGAAGATAGTAGCAACCTCTTTG[A/C]TTTATACAACAGCTCTGCAGCCAGGGATTTGAAAA M 2 1 2 1 101000 r 74 goat snp37287-scaffold454-1734552 20 40340043 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423818 Affx-122942800 AX-123294164 20 40131043 ACATAGGTAGAACTTTTACAAACTGAATGGTTCCC[A/G]TGAAATAGGATGTTACTGTTAGTAGAACTGTTCAA R 2 1 2 1 101000 r 74 goat snp37285-scaffold454-1673348 20 40401016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425139 Affx-122941206 AX-123295485 20 40171689 GTTAGGAAAGTATCTCTGGTATACAATAAATCATA[C/T]TCAGTTGTTTTGCTTTAGAACAAAAATCAATATTT Y 2 1 2 1 101000 f 74 goat snp37284-scaffold454-1632702 20 40443269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790539 Affx-122952325 AX-385277542 20 40222509 TGCCTTAACCTCACACCAGAGTGTTAATCTTTCAC[G/T]AGTCCTTCCATTTCCATCAAAGACCACAGACTTAT K 2 1 2 1 101000 r 74 goat snp37283-scaffold454-1581882 20 40493920 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386100 Affx-122971435 AX-123256458 20 40275675 TAATAAATAATTAATAAAGAAAGAAATGACTAGGT[A/G]CTCCACCAAACAGAGTATCATTTCTTGCACTGATA R 2 1 2 1 101000 r 74 goat snp37282-scaffold454-1528716 20 40547401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277321 Affx-1111835852 AX-519550825 20 40324534 ACTCTTGGAGGGACACGTGGTCTCTTTTTCCCTTA[A/G]CAACCAGGAAGAATCTAAATTAATGTATTGAATCT R 2 1 2 1 201000 f 74 goat Random2.2K-1866 20 40324534 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439797 Affx-122930495 AX-123310134 20 40345448 TGCATGAATTACAAAGCTAGGTTCAAAAAAGTTTA[C/T]GCTTGCCTGATTCTCACTTCCCCTGTTGGGCTGGT Y 2 1 2 1 201000 f 74 goat snp37280-scaffold454-1458943 20 40618117 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437712 Affx-122931748 AX-123308050 20 40394425 TCTGGAGGCATTTAAGGTAGAGGCAAACATCCTAA[C/T]GATCCCTTTGAGCAAATTCACAAAACTACAGTGAA Y 2 1 2 1 101000 f 74 goat snp37279-scaffold454-1409966 20 40667528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428292 Affx-122939386 AX-123298635 20 40434430 AAGCTACGCTGCCTGAGGGTGTTTCTTGAGGGGTC[A/G]GGAGAGAAGAGGGGATGAAAGGAAGCTAGTTCTTC R 2 1 2 1 101000 f 74 goat snp37278-scaffold454-1369961 20 40707595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765730 Affx-122948054 AX-385253190 20 40481019 GGCACTAATTATTAAGTATATCCTACTCTAGAAAG[C/T]GGTTCTAATAGTGTCAAAAATTCTTATGCTATAAT Y 2 1 2 1 101000 f 74 goat snp37277-scaffold454-1323372 20 40753890 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392154 Affx-122966317 AX-123262511 20 40512597 ACACAGAGTGGGGTGAAGAGAGAAAGGCAGGCACA[G/T]AGGGCAGTGACAGTGCTGGTGTGTGCGCTGGGCCT K 2 1 2 1 202000 r 74 goat snp37276-scaffold454-1291794 20 40785250 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449781 Affx-122922432 AX-123320116 20 40541994 TTGTAGACAAGATTGTTGAAAAGTAACCCCAAAAC[A/C]TGTTGTTCTAAATCTCTCAGCAATAATCAGCTTGG M 2 1 2 1 101000 r 74 goat snp37275-scaffold454-1262397 20 40815303 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381353 Affx-122974411 AX-123251711 20 40593138 TTTTGAAAAGTTGGAAAACCTTTTCTAAAGCTGTA[A/G]GTGTTTGGCTCAAGTTTACCCTGGTTTAAGACTTC R 2 1 2 1 101000 r 74 goat snp37274-scaffold454-1211253 20 40867117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434370 Affx-122934706 AX-123304711 20 40648909 TTGGCCTTTCCTGTCTGGCATCACCGGTGACGTGC[A/G]TCCTTCTCGGCTGTCGTTCACCCCCTCACTCTTGT R 2 1 2 1 201000 f 74 goat snp37273-scaffold454-1155482 20 40925472 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376184 Affx-122978827 AX-123246543 20 40701775 GTGATTTACCTTTGTTTATTATTCTCAACAATCCC[A/G]CTTCCACCCCTGCTCTTCCTTATCTAAATATGCCC R 2 1 2 1 201000 f 74 goat snp37272-scaffold454-1102616 20 40978305 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421800 Affx-122944329 AX-123292147 20 40739121 CTTTGGAATGTGAATTAGCCTTTGAGTGTTAAATC[A/G]TCTAAGGACCTCTGGGACTGGGTGATAAGGTCCTG R 2 1 2 1 201000 f 74 goat snp37271-scaffold454-1065270 20 41015665 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273026 Affx-1111833198 AX-519546703 20 40786591 AATCAAAAGGTAATTCTGGGATTTTAAGCTCAAGC[A/G]GTGAGACAGATGCTGATGATCTAAACACAAACAGG R 2 1 2 1 101000 r 74 goat 20_40786591_AF-PAKI 20 40786591 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38427978 Affx-122939183 AX-123298321 20 40797445 AGATGAGGGCCGGGTAGAGGTCGGGGCAATGTAAG[C/T]AGAAACATAAAGATGTTTGTATCCCACCAGGGAAA Y 2 1 2 1 101000 r 74 goat snp37270-scaffold454-1006946 20 41074121 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789433 Affx-122948793 AX-385276443 20 40833654 GGTGTGGGGAAAAGAAGCACTTGGACCTTCTTCAA[A/G]TTGCTTAAAATTATAGGTGAGATCTTCCTTCTTCT R 2 1 2 1 101000 f 74 goat snp37269-scaffold454-970737 20 41110639 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277323 Affx-1111835853 AX-519550827 20 40854044 TTTGCCAGTTTACAGAAACCAGGATTTGGGTTTTC[A/G]CCATACAGGAACAGAGAATGAAAGTTTCTGAGAAA R 2 1 2 1 102000 f 74 goat Random2.2K-1868 20 40854044 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390801 Affx-122967865 AX-123261158 20 40873041 TCCTTGATAAATACAGTGACAGCTGCTGGAGTGAA[C/T]GGAAATTTAGTGCAGAAGATGATGTTATTTATCTC Y 2 1 2 1 101000 f 74 goat snp37268-scaffold454-931350 20 41151280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794228 Affx-122954644 AX-385281194 20 40931836 GTCTGTACAAATCTGTTAACAGGTAAGTTAACAAA[C/T]GAATAGGCAATTCACCACAAAAGAAATGTAAGTGA Y 2 1 2 1 101000 f 74 goat snp37267-scaffold454-872555 20 41210544 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783841 Affx-122926861 AX-385270897 20 40987176 GGGAGAGGAATAGGAACAGCAGAATGACAGTCGTC[A/G]GAAGGACTTCTATTAAGCGAGCCAGCCGAAGTTCA R 2 1 2 1 101000 f 74 goat snp37266-scaffold454-817215 20 41265954 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385895 Affx-122971587 AX-123256253 20 41094060 GCATTATTTAAAAAAACGAAAATCAAGCTAATTTT[A/G]CCTCTCACAATTTCTTTAAAATTTTCCTTGTTTTG R 2 1 2 1 201000 f 74 goat snp37264-scaffold454-710331 20 41373071 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801474 Affx-122958244 AX-385288383 20 41133117 TTTTCTACCAGGTTTTTAGCTAATCGTTCCCGCAC[A/G]TTTCTTAACTGATAATGCAATTTTAATGGATTCCA R 2 1 2 1 101000 f 74 goat snp37263-scaffold454-671274 20 41412320 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389559 Affx-122968265 AX-123259917 20 41167889 GTGACTTCTAATCCAAGGCACAAGGCTAAACCCCC[A/G]TGTAATCTGCGGGGGACTGAGTTGACTGCAGAATC R 2 1 2 1 202000 r 74 goat snp37262-scaffold454-636502 20 41446791 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797941 Affx-122977831 AX-385284877 20 41206046 GGGCTTAGCAGAAGCCACAGCCCTTTGGGCTTGTC[A/G]TTTGTTTCTAACAGGAATATGGCGCATGGAGTATC R 2 1 2 1 202000 f 74 goat snp37261-scaffold454-598345 20 41484891 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449805 Affx-122922414 AX-123320140 20 41235626 CAGTCTGTTGGTTCTTGGCCATCTATCCAGAGCTA[C/T]GGCCCTAAGGCTGACCAGTCCTCAGAGCTTTCTCT Y 2 1 2 1 101000 f 74 goat snp37260-scaffold454-568765 20 41514553 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452654 Affx-122920335 AX-123322987 20 41306494 TCGGGAAAGTTTGTCCTGCTTGTGCCAGTCCATGA[C/T]GGCCCCTCCCTTGGAATTCCTGATCCTCATTACCT Y 2 1 2 1 201000 f 74 goat snp37259-scaffold454-497897 20 41585361 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435170 Affx-122933657 AX-123305510 20 41359201 GTCACTGAAATAGGTAACCTGTGGGGGCCCACTTA[C/T]GCTCCCAAGGTATTTAGGCCTTTCTTCAGAATGTT Y 2 1 2 1 101000 r 74 goat snp37258-scaffold454-445190 20 41638601 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414398 Affx-122949986 AX-123284747 20 41403936 TCAGACTCTAGGAGGGTCCCATGTCCTGTGTGTTA[G/T]GTGACATATCCTGAAGGAAGAGATTGTGACCCACA K 2 1 2 1 201000 f 74 goat snp37257-scaffold454-400455 20 41683107 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449484 Affx-122922637 AX-123319819 20 41453735 GGGAATGTGCAAGCAGCATGCTAAGTGCTTGAACA[A/G]TAGTGAACCAAACACAGTTGAAGGTGTGAACCAAC R 2 1 2 1 600000 r 74 goat snp37256-scaffold454-350656 20 41453735 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778979 Affx-122922637 AX-385266086 20 41453735 GGGAATGTGCAAGCAGCATGCTAAGTGCTTGAACA[A/G]TAGTGAACCAAACACAGTTGAAGGTGTGAACCAAC R 2 1 2 1 101000 f 74 goat snp37256-scaffold454-350656 20 41733229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397885 Affx-122961962 AX-123268240 20 41511357 CACACCCGAAGCGACTGAGCACACTCTCATGCAAG[A/C]CCAGGCTTGCTCTGCCCTAACCCCTCAGCCACCCT M 2 1 2 1 103000 f 74 goat snp37255-scaffold454-293034 20 41790498 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441627 Affx-122928639 AX-123311964 20 41543515 ACAACTGTGTGTGCTCTTTGGAGGTGGAATAGCGC[C/T]GCCCACCACAGCTCTCATTTGCTGGATCAAGAAGT Y 2 1 2 1 201000 f 74 goat snp37254-scaffold454-260876 20 41822568 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447228 Affx-122924971 AX-123317564 20 41589104 TATTCCTTGCCTTTTACTTAAACCTAATGGTATGC[C/T]AGGCAGCTTTCCCTTTTATTAATAATAAAGACTGA Y 2 1 2 1 101000 f 74 goat snp37253-scaffold454-215287 20 41867437 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420327 Affx-122945009 AX-123290674 20 41668212 TCACAAATATGTTAGAAGATATAGATATATAAACA[C/T]ACAAGTTTCTAAAAACAGGAACTCCGTAGCCTGTT Y 2 1 2 1 303000 f 74 goat snp37251-scaffold454-136179 20 41946760 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783520 Affx-122979066 AX-385270583 20 41698335 TTTTATAAGAGTTTTCACATAAACCACAACATTCT[A/C]CCACAAGCACTACACTTTTCTTTAAATCCTATTTA M 2 1 2 1 101000 r 74 goat snp37250-scaffold454-106056 20 41976825 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396713 Affx-122962812 AX-123267068 20 41748791 CACTGCATGAATGATGGACTAGAGCAGTGGGGAAC[G/T]ACAACAGCTTAATTATATCAGGTGAGAGACGAGGA K 2 1 2 1 101000 f 74 goat snp37249-scaffold454-55600 20 42027836 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418709 Affx-122946287 AX-123289057 20 41793560 GCTTGTTCAGAAACGCTGTGAACATTTTTGTGGCT[A/C]TCTGTAATAATACACTGGAGAAAGCCATCTCGCAC M 2 1 2 1 101000 r 74 goat snp37248-scaffold454-10831 20 42070399 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377443 Affx-122977531 AX-123247802 20 41806166 GTAAAATATGACATTTACATCAGAAATAGAACGGA[A/G]TTGGTCAAAAGGAGCTAATCCATTCATTCAGTCAT R 2 1 2 1 101000 f 74 goat snp46242-scaffold637-4293364 20 42083749 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440103 Affx-122929711 AX-123310440 20 41838173 GGAATGGCTATAGCAGCTGACTGTCTTGTCCCATG[A/C]GGAGTGCCTGGCTCCATGGTGCTTGCGAGGATGTC M 2 1 2 1 101000 f 74 goat snp46241-scaffold637-4261357 20 42116463 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389131 Affx-122968553 AX-123259489 20 41873845 TACTGCGGATACCAATGACAGAGCATACTTAGAGC[A/G]TTAAAATTACAAAACTATTTCCCACTTGAAAAGGA R 2 1 2 1 101000 f 74 goat snp46240-scaffold637-4225685 20 42152314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390179 Affx-122967965 AX-123260536 20 41903091 CAGATTCTTTACCATTGAGCCATCTGGGAAACCCT[A/C]GTTGCTAATTTATCTGGCAACTTCAGGAACATATA M 2 1 2 1 303000 r 74 goat snp46239-scaffold637-4196439 20 42181396 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380534 Affx-122975677 AX-123250892 20 41940315 TGTTTGCCAGAATGTTCCAGCTACTTCTGTCTGGT[A/G]GCATACTGTTTTTCTATCCTCCTGCTGACTGGAGA R 2 1 2 1 101000 r 74 goat snp46238-scaffold637-4159215 20 42218621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775705 Affx-122928297 AX-385262836 20 41974058 ATAGAAAGCTGGTTAAATATCTCATGAAAAAGTAG[C/T]AGCTCCCCTGTTAGTTTCCACACATAATTGTGGTA Y 2 1 2 1 101000 r 74 goat snp46237-scaffold637-4125472 20 42252405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423197 Affx-122942718 AX-123293543 20 42082023 GGGTAATATCAAGACCAACAGAAGACACTGTTCAG[A/C]GATTTATTTTTTCCTGGGAGATAAAATTGTTTTTC M 2 1 2 1 101000 f 74 goat snp46235-scaffold637-4017507 20 42361243 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393054 Affx-122965620 AX-123263411 20 42121718 TGGAATATACTCAGAGAAACTAGTCAGATGATTCT[A/G]CAGGTAAGCACATTTATGAAATCAGATATTATGCA R 2 1 2 1 101000 f 74 goat snp46234-scaffold637-3977812 20 42399767 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441597 Affx-122928662 AX-123311934 20 42164468 TAAATCTACCCCTGATCAATCAACCAAAGATTGCA[A/G]TGTTCCTGACTCATTGTACCTTCAAACATAGCTTT R 2 1 2 1 201000 r 74 goat snp46233-scaffold637-3935062 20 42443048 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391276 Affx-122967356 AX-123261633 20 42263647 GCGGGTTAATTTGGAAGAAACAAAGCTGGAGGCCA[C/T]AGACATTGACCAGGAGAGGGATGCTTTTCTAAAGT Y 2 1 2 1 101000 r 74 goat snp46231-scaffold637-3835883 20 42544490 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441464 Affx-122928758 AX-123311801 20 42322493 TGTGACAAGAATGTCAAATATATAATATTAAGTCA[C/T]ATATGCCTTTCATCTGAGAAGAACTAGGGAGTGTG Y 2 1 2 1 101000 r 74 goat snp46229-scaffold637-3777037 20 42604333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419173 Affx-122945727 AX-123289521 20 42401866 TCAAGTGGTGGAAGGTAATGTACCACAGTTTACAG[C/T]AAATCACTTAAATTTTTTGGAAAGCAAATCTTACT Y 2 1 2 1 101000 f 74 goat snp46228-scaffold637-3697664 NW_017214754.1 10416 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388104 Affx-122969494 AX-123258462 20 42435578 ATTGTTCTAGTTGTTGTAGCCCCTTCATATCAGAC[A/G]TCTACTCACCTTATACAATAGTTATATGCTCTTAA R 2 1 2 1 201000 r 74 goat snp46227-scaffold637-3663952 20 42724130 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781759 Affx-122950939 AX-385268841 20 42486445 AATTATTAAATGGGTCATTTTTATCACAATTGTCC[A/G]TCACATTCAGTCTAGAAATGTATCACCGAACATTT R 2 1 2 1 101000 r 74 goat snp46226-scaffold637-3613085 20 42775686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798587 Affx-122973433 AX-385285520 20 42547624 AATCAGAAGTATCTGGCAGGTACCTAGCATCATCC[A/G]TGTTTTCTGAATGAACGATAAATGGACATGCAGAA R 2 1 2 1 101000 f 74 goat snp46225-scaffold637-3551906 20 42838159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453902 Affx-122919498 AX-123324235 20 42576556 GCTATGTGACTTTGGACATATTTTAAATTCTAAGA[A/G]CATCATATATATTGTTTATAAAAGAGGACTTACAG R 2 1 2 1 303000 f 74 goat snp46224-scaffold637-3522974 20 42867642 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782117 Affx-122941367 AX-385269195 20 42654809 AGCCTCCTCAGTTCCTTCAGGGACAAAGTGATTAC[A/G]CTTATTGATCAGCTAATGATTTTTCTCTCCTTAAA R 2 1 2 1 101000 f 74 goat snp46222-scaffold637-3444721 20 42946916 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776480 Affx-122952564 AX-385263607 20 42696608 TTTACTCACAATAGATACTAATCAAGGTTTGAAAA[C/T]GGCAACATGTGATCTAATTTAGAAACTTAAGAATA Y 2 1 2 1 102000 r 74 goat snp46221-scaffold637-3402922 20 42985143 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277325 Affx-1111835854 AX-519550829 20 42707282 CTAACAAAATATTCAGTGATCTAAAACAAAACTAA[A/G]ATATAGAAAACAAAAAAGTTAAAATATATATATAA R 2 1 2 1 101000 f 74 goat Random2.2K-1869 20 42707282 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437233 Affx-122932027 AX-123307571 20 42760960 AACTACAAGGTATGAAAAAAGTAACTTACAATGAC[A/G]TAATGGAAAGCATAGAGAATACAGCCAATATTTCA R 2 1 2 1 101000 f 74 goat snp46219-scaffold637-3338570 20 43050436 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798257 Affx-122931022 AX-385285192 20 42789968 ACCATTTTCTCAATTATAATTTTTTGAGAATAAGA[C/T]ATAGATTAATGTCTCAACTGTCCTCCCATGTTTGG Y 2 1 2 1 201000 f 74 goat snp46218-scaffold637-3309562 20 43079566 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453212 Affx-122920440 AX-123323545 20 42856580 TGATCCATTAATTTATCTTAATTATGTTAATTGCC[A/G]CACAAGCAGTTCTATTAATGTGATCAGTATCTGTC R 2 1 2 1 101000 r 74 goat snp46217-scaffold637-3242950 20 43145949 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437433 Affx-122932405 AX-123307771 20 42915624 CCAGAACAAAGTTTATGCTCGAAGAAGCAAGATTT[A/G]CACAAATTTACACAACTGAGGATTGTGATATTAAC R 2 1 2 1 102000 f 74 goat snp46216-scaffold637-3183906 20 43204492 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449151 Affx-122923551 AX-123319486 20 42975553 CCAGCAACTGGAACTTTCACATTGCTGACAAAGAT[A/G]TAAATTCATTTAATCATTTGGAAAAACTGTTTGAC R 2 1 2 1 103000 f 74 goat snp46215-scaffold637-3123977 20 43265078 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790876 Affx-122938283 AX-385277874 20 43013827 TTCATGAAAAACCACAGGTCACTCTATTAAATCAC[A/G]TTATATAGAACAATCATTTTATTGTCAATAACACT R 2 1 2 1 201000 r 74 goat snp46214-scaffold637-3085703 20 43303806 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446248 Affx-122925687 AX-123316584 20 43217399 CCTTCAAAGGTCTACTGAGATATTTTTAGTTTTTG[C/T]ACCTCACTGCACACCTATATCTCACCTCACCTACA Y 2 1 2 1 101000 r 74 goat snp46210-scaffold637-2882131 20 43515795 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800933 Affx-122972704 AX-385287848 20 43255036 ATTCACCTTTGGTATAGTATTGACCTTCTTTGACT[A/G]TATTTTGAGTATTACATCTTGTTGCTTTAGAATTA R 2 1 2 1 101000 f 74 goat snp46209-scaffold637-2844494 20 43554947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787327 Affx-122952993 AX-385274352 20 43292739 AAGATTCTTCTATTTCAATCATCTTATATTGAGTA[A/G]CCAGTCATGTTACTCATGTACAATTGGCTTAAACG R 2 1 2 1 101000 r 74 goat snp46208-scaffold637-2806791 20 43593730 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409365 Affx-122954165 AX-123279716 20 43361342 CTGCTGGGGTCACTAAACTCTAAAACAGTGAGAGG[C/T]GCTCCTATTGCTGAAACAGACACAAAAACTCAGTA Y 2 1 2 1 101000 f 74 goat snp46206-scaffold637-2738188 20 43662122 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790958 Affx-122925194 AX-385277955 20 43401462 GTGTCTATTGGAGGCTAGGTACAGTGCTGTACACC[A/G]TACACCCTGAATAAACAGAAAAGTGGAAAGAGTTA R 2 1 2 1 201000 r 74 goat snp46205-scaffold637-2698068 20 43702596 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389626 Affx-122968748 AX-123259984 20 43498328 AACACTAATTATACACAGGCTGAGTGTATGAGGGA[C/T]CATTTTCCAGGCACTAGGATTTTCAAAACAAAGAG Y 2 1 2 1 101000 f 74 goat snp46203-scaffold637-2601202 20 43798601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410659 Affx-122952765 AX-123281009 20 43529564 TTGGGAGGACCCCAAAAAAGTTCATGTTGCCAAAT[A/C]TAAGGGTCACTTCACCATCAGTATATTACTGGAAA M 2 1 2 1 201000 r 74 goat snp46202-scaffold637-2569966 20 43829908 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400225 Affx-122960163 AX-123270580 20 43564674 CTCTTCTAGTAAAGTTACCACATCTGTCAAGGCAG[C/T]GTCAATCAGGACAACCACTGGGCTTGCAGGAGTTA Y 2 1 2 1 101000 f 74 goat snp46201-scaffold637-2534856 20 43864631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417451 Affx-122947197 AX-123287799 20 43683277 ACTTTTATGGCTACAGTGAAAAGCAATACTAAGTG[A/C]TGGTGAATGAGAGTAGATATTGGATTTCTTAGACT M 2 1 2 1 101000 r 74 goat snp46199-scaffold637-2416253 20 43981178 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436747 Affx-122932291 AX-123307085 20 43763921 AAAAATGGTCTCATTTGGTAGTAGCAGTAGAATTG[C/T]AATTCAGGATACACAAACTGTAGCAAGCTTCAGGA Y 2 1 2 1 101000 r 74 goat snp46197-scaffold637-2335609 20 44063000 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419642 Affx-122945964 AX-123289990 20 43796311 GTTAAATTAAAAAATGTAGGCAGTTTTGGATACAT[C/T]ATGTGCTGTGTAAGATATTAAGCTTCAATTCCTTT Y 2 1 2 1 101000 r 74 goat snp46196-scaffold637-2303219 20 44095046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272976 Affx-1111833199 AX-519546659 20 43855683 ATTCGATTTTATGTTCTAATTTTCTCTCTTCACAC[A/G]TTTCTATTATTTTCCTCTGAATTCTGAGAAAAATT R 2 1 2 1 102000 f 74 goat 20_43855683_AF-PAKI 20 43855683 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38378424 Affx-122976777 AX-123248783 20 43926095 ATTCAGTGCATTGTTGATAAATATTTGGTTTGCTT[C/T]CAGTTTAGAGCAAGTATAGTCAAAGCTTCCATGTT Y 2 1 2 1 101000 r 74 goat snp46193-scaffold637-2173435 20 44223928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402067 Affx-122958715 AX-123272420 20 43987405 AAGAGACTTTAGAACACATTCTACTGTATCAGGTA[C/T]GGCACAATTAATACATCTTAAAACTCTTTTATAAT Y 2 1 2 1 101000 f 74 goat snp46192-scaffold637-2112125 20 44286559 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784859 Affx-122921455 AX-385271906 20 44028742 GTTTTTCTTTTTTCTGACATCTAATATGTTTAATA[C/T]GCTTAAATCTCCAGAACCAGTTTGCAATAGCTATT Y 2 1 2 1 101000 r 74 goat snp46191-scaffold637-2070788 20 44327749 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380350 Affx-122975360 AX-123250708 20 44062183 ATTGATACTCTGCTTTTCTATGGTAACATAAAGTG[C/T]AGCATTAAAACTTACTTTTTACTGATCTTATTTAT Y 2 1 2 1 101000 f 74 goat snp46190-scaffold637-2037347 20 44362185 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797766 Affx-122970534 AX-385284705 20 44121159 TAACATTATAATTGATTTGAAATGAATATAAAACA[C/T]GAAATTAACTCTCCATTCTATCATAGTTTCTGTGA Y 2 1 2 1 303000 f 74 goat snp46189-scaffold637-1978371 20 44422039 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275338 Affx-1111834737 AX-519548913 20 44152257 GCCTCTCAGGGCTTGTTTTC[A/G]CAAGGCTACCAGTGCAAATCCACGAAATCAGGTCC R 2 1 2 1 101000 r 74 goat GoatD01.050756 20 44152257 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38441838 Affx-122929051 AX-123312175 20 44157865 AGACAAAGAGTTTCTTATTTGACTTAGTGCTAACA[C/T]GACTTGGAATTTTGCCAGGCATATAGTAAACCTTC Y 2 1 2 1 101000 r 74 goat snp46188-scaffold637-1941665 20 44459005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801120 Affx-122941487 AX-385288034 20 44239383 GCCCTCATGTCTTATGTGTAGTTTGCTTGAAGACA[A/G]AGGTGAGGCAAGGCTTAAGGGCATATGACTTTGTT R 2 1 2 1 101000 r 74 goat snp46186-scaffold637-1860147 20 44541145 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426649 Affx-122939939 AX-123296995 20 44282670 GAATATCTGATTTAAATATTTTCTATGAAACAAGT[A/G]TACATTATTTACTAGTCCCTCATCTCATCACTTAT R 2 1 2 1 101000 r 74 goat snp46185-scaffold637-1816860 20 44584909 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790244 Affx-122944266 AX-385277248 20 44355786 TTGAAAAGAAGAACACAGAAAAAGTTGAGAAATGT[A/G]TGTGCTTGTGTCTCTGTGAGCTTTTTCACTTTTCA R 2 1 2 1 201000 f 74 goat snp46184-scaffold637-1743744 20 44656966 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386885 Affx-122970050 AX-123257243 20 44395609 GTTAGTTACATTTGGAATAGCTAATAACTTTTTCT[A/G]TATCTGTAAAACATGCAAATACTTATTTTGTGTTC R 2 1 2 1 101000 f 74 goat snp46183-scaffold637-1703921 20 44697704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380821 Affx-122975078 AX-123251179 20 44426636 AATTAAAAAGCCTCTACTCCTTTAACCTCACGCAA[A/G]CAAATGTATATGTGTTAATAATCCATGAAGTCTAT R 2 1 2 1 101000 f 74 goat snp46182-scaffold637-1672894 20 44727518 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397684 Affx-122962582 AX-123268039 20 44459645 TTCAACAAGTACAGATCAAATATCTATGAAGAAGA[C/T]GCTTAACCCACTAGAAATTCATTTTCTCAAATTTA Y 2 1 2 1 101000 f 74 goat snp46181-scaffold637-1639885 20 44760420 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444567 Affx-122926974 AX-123314904 20 44586802 TAGTGTCACTAAGAAAAGGAAGAAAAGTTTATTGC[C/T]CTAGTTTCTCTGATGCACATATAACCAAAAGCAGT Y 2 1 2 1 201000 r 74 goat snp46178-scaffold637-1512728 20 44889006 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416538 Affx-122947755 AX-123286886 20 44660875 GCTCAATTAATATTATAGTTAGCAATAATTGATTA[C/T]AGACATTATCCACTTAGGAAAGAAAGAAATAATTT Y 2 1 2 1 202000 f 74 goat snp46176-scaffold637-1438655 20 44965868 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427665 Affx-122939317 AX-123298008 20 44738832 GCCATATCAGTAAACAAGGATGTCATTTTCATCAA[C/T]GATTGCAGCCCTAAATGTGAGCTGATGAGCTTTAA Y 2 1 2 1 101000 r 74 goat snp46174-scaffold637-1360698 20 45043556 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274183 Affx-1111834092 AX-519547784 20 44855007 GAGACTATACACCATCACCACCAAGGTAAATTTAA[A/G]CTTATTTAGCCACATGTGGCTGGTGGCTGCAGTAT R 2 1 2 1 201000 f 74 goat GoatD01.017782 20 44855007 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38413684 Affx-122950099 AX-123284033 20 44856908 CCATTATTTCTTCATTTTATCATGCATCCCACTGG[C/T]AGACTATTATTGTATAACATAATGTTAATAATGCA Y 2 1 2 1 101000 f 74 goat snp46171-scaffold637-1242622 20 45162294 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449521 Affx-122922608 AX-123319856 20 44910436 GTTGGGTGACTCTGAAGGAAATCTAAGGAGCTGGG[C/T]TGCAGAGTACACCACACATCTAATCCAGCAGACTA Y 2 1 2 1 101000 f 74 goat snp46170-scaffold637-1189094 20 45215079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793341 Affx-122942920 AX-385280319 20 44945400 CCTACTTGATCTGCATGTGTGACATCATTAATTTC[A/G]GTGGATAAACCAAATTTGGGGTGGGTAATCATCTT R 2 1 2 1 102000 r 74 goat snp46169-scaffold637-1154130 20 45250215 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792600 Affx-122958477 AX-385279581 20 45066417 TATTCTAAATGAGAACTATAAAAGTGAATATCTTT[A/G]CTTTGGTTCTGATCTTGAGAAGGGAAATAATTCAG R 2 1 2 1 201000 f 74 goat snp46167-scaffold637-1033113 20 45372161 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801792 Affx-122919941 AX-385288700 20 45106356 GTGAGTTATACAATCTTTAGACTTTGATTGGAAAA[G/T]ATATTTCAGTTGTTTGTGTGTGCTGTATATGTGAG K 2 1 2 1 101000 r 74 goat snp46166-scaffold637-993174 20 45412696 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403378 Affx-122957784 AX-123273731 20 45157399 ATGATGGAGAAATAATATCAAGAAGTCCACCCTAA[C/T]AATCCATCCTTGCTAAATAGTAATGTATGAGTCAG Y 2 1 2 1 101000 r 74 goat snp46165-scaffold637-942131 20 45463758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796438 Affx-122922020 AX-385283388 20 45205360 TTTACAGAACTGAGGACGTTTTCTATTAAAATAGT[A/C]TAATGGTGAGATGATTAAGATGACACTAACAAGGA M 2 1 2 1 201000 r 74 goat snp46164-scaffold637-894170 20 45511387 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797479 Affx-122944024 AX-385284418 20 45306051 ATGTTTCAAGGTGGAAGAGGAAGTGAGGAAAAGAA[A/G]AGAAAAGTAGTATTTACTCACTGAAACCTCACAAA R 2 1 2 1 103000 f 74 goat snp46162-scaffold637-793479 20 45613083 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443287 Affx-122927474 AX-123313624 20 45342998 AAATCATACTGCTCCCCTGATTTTTTGTTCAGGGG[C/T]ATATGATTGTTTTGAACCTACTATGAACCTTGAAA Y 2 1 2 1 101000 r 74 goat snp46161-scaffold637-756532 20 45650232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377144 Affx-122978227 AX-123247503 20 45393643 AATAATAATTCATTCTAACATCCTGATCAGTAACT[A/G]GAAAGGAGAGGGACAGAAATGAAGTACTCACTGAA R 2 1 2 1 201000 f 74 goat snp46160-scaffold637-705887 20 45701486 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380414 Affx-122975312 AX-123250772 20 45422895 ATAAATAATAATCTTATAAAGAATATTTAAAGGAG[C/T]GTACGGATGTTGCCTTTGAGGAAAGATAGTTTTCT Y 2 1 2 1 101000 r 74 goat snp46159-scaffold637-676635 20 45730674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413385 Affx-122950129 AX-123283734 20 45456957 GCAGCTGTTTTTCTGGAATTCTCTTGCTTTTTCTA[C/T]GATCTTTTTTTACAGTATGGAAAGGAAAGGCATAA Y 2 1 2 1 303000 r 74 goat snp46158-scaffold637-642573 20 45765245 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403604 Affx-122957557 AX-123273957 20 45489142 ATTTATCCCTAGGGAAACCTTCTTCCCTGAACATC[A/G]TCTATTATTTCAACTATTATTCTTCACTCTTTTTC R 2 1 2 1 101000 f 74 goat snp46157-scaffold637-610388 20 45797913 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432678 Affx-122936044 AX-123303019 20 45614035 CCTTATACTTCTTTTCTTGTAGGAATTTAGCTCTT[A/C]TTGATATTGAAATTTGAATCTTAATATTTATCCCT M 2 1 2 1 101000 f 74 goat snp46155-scaffold637-485495 20 45922503 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448905 Affx-122923178 AX-123319240 20 45653807 AAAGCACCATGGTGGCAGAGCTAAGGCTAATGCAC[A/G]TCTAACTCCAAACCTAAAAACCATTTTGGCTACTG R 2 1 2 1 101000 r 74 goat snp46154-scaffold637-445723 20 45963198 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407026 Affx-122954948 AX-123277377 20 45712128 CATGGTTTTACTAGCGATACAGGCATTCAAATATG[C/T]AATTAATTTTTGAATGATAATTCTAGCAGGAAGAA Y 2 1 2 1 101000 f 74 goat snp46153-scaffold637-387402 20 46021699 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409340 Affx-122954183 AX-123279691 20 45760158 CATGTTTGAGAGCTGGTGCAGTTATATTACTAGAA[A/G]AGCAAATAAAGAAACTCAGAGTCTTCATATATCGT R 2 1 2 1 101000 f 74 goat snp46152-scaffold637-339372 20 46069863 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424909 Affx-122941303 AX-123295255 20 45851032 AGGCAAATCTTTTATGATAAGGTGATTGGTGCTGG[C/T]AACATTTTTGACACAAAAACTTAGGACTGTAGGTA Y 2 1 2 1 101000 f 74 goat snp46150-scaffold637-248498 20 46160794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766231 Affx-122934007 AX-385253628 20 45897886 GGAGTAATTGTGGGTTGGGTTGAAGTAGTTCAGAT[A/G]TAGATGATCAGGAATGAGTTGAATAAAAAGCTACA R 2 1 2 1 101000 f 74 goat snp46149-scaffold637-201644 20 46207374 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437058 Affx-122933093 AX-123307396 20 45930231 TAGAGTTGACCTTCTCTTGTGGAAATTGAATAGTC[C/T]AGCCAGGATGTATGCCTGAATGAAAGGCTATCTGA Y 2 1 2 1 101000 f 74 goat snp46148-scaffold637-169299 20 46240522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415298 Affx-122948822 AX-123285647 20 45997597 ACCTGTGAAATCATTATTTTACAAACCCCATCAAT[G/T]AATTCAGATATTTTATCCCTCATAGTACCAGAACA K 2 1 2 1 201000 r 74 goat snp46147-scaffold637-101933 20 46308493 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419206 Affx-122945700 AX-123289554 20 46086728 AACTGTAGTAAGTCAGTCCACAGTGGAAAGCAAAA[G/T]AGATTGTGAGTAACACTGATAAGAATATAAATAGC K 2 1 2 1 101000 f 74 goat snp46145-scaffold637-12802 20 46398322 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390232 Affx-122967773 AX-123260589 20 46113437 AAGTAATGAATTACTAATATTAATACTAAATACCT[A/G]CACTGCTTCCTCTGAAGAAAGAGATATTATCATGA R 2 1 2 1 101000 r 74 goat snp51100-scaffold742-513116 20 46424861 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788517 Affx-122962491 AX-385275534 20 46149138 GGGACCAAAATATGCCTAAATGAGGAGAAAAAATA[C/T]GATCCTATATAAAGGCATACTTGTCATTTATAAAA Y 2 1 2 1 201000 r 74 goat snp51099-scaffold742-477415 20 46461047 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417570 Affx-122946904 AX-123287918 20 46183253 GAATTTAATTACAGAATAAAGTTCCAGTCTTATTT[A/G]TTCTTTTGAGGTACCTTTTAGACTTTCTGAATACA R 2 1 2 1 102000 r 74 goat snp51098-scaffold742-443300 20 46495230 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432537 Affx-122935552 AX-123302878 20 46230455 CTATTCAACAATTGCCATCATTTTTAATAAATTCA[G/T]CAATCACTTTGATTATCCGCACAACACAATGACTC K 2 1 2 1 101000 r 74 goat snp51097-scaffold742-396098 20 46542944 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391146 Affx-122966785 AX-123261503 20 46293664 CAGCAGAAAGAGGAGTGAGGTACTAACTCTCTTTC[A/G]TCAAAACTGGATACAAAAAGGCAGTTACATATTCC R 2 1 2 1 101000 r 74 goat snp51096-scaffold742-332889 20 46605795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427792 Affx-122939768 AX-123298135 20 46383149 AGTTATTTTAAATGTGCTGAAAAGGAGCAAGGAAA[G/T]CAAACTGACATGGCATATGATAATCAGGACTTAAC K 2 1 2 1 201000 f 74 goat snp51094-scaffold742-243404 20 46695831 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803135 Affx-122921992 AX-385289999 20 46422826 CAGCCAATTCTTGCAAGAACCATGACAAATTGTCA[C/T]GTTAATTCTCTGCATATGAAATCTGGAGTTTTTCA Y 2 1 2 1 101000 r 74 goat snp51093-scaffold742-203727 20 46736081 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796385 Affx-122966951 AX-385283335 20 46485227 AATGACTATAAGAGCATATTTAAATGAATAACAAG[C/T]AAATTAATGTAGTTTACTGGCCTAAACATATTTTT Y 2 1 2 1 201000 f 74 goat snp51092-scaffold742-141326 20 46796310 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776255 Affx-122942480 AX-385263383 20 46517335 TTTTTAAAATAAACCATATTGGGTTCTATTATCCA[C/T]AGAATTCAAATTAATTCTCCATACAGTAAATTTAA Y 2 1 2 1 202000 r 74 goat snp51091-scaffold742-109218 20 46828432 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800173 Affx-122957859 AX-385287096 20 46564669 TTATTATGAGCCATAATCTCAGTTCCACAGAAAAA[C/T]ATTATGTTCTATATTTTTAGACAGCAAATTTTAAT Y 2 1 2 1 201000 r 74 goat snp51090-scaffold742-61884 20 46875762 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409588 Affx-122953569 AX-123279939 20 46613760 TTCTTCTTCACAATTGCAGAAGCACCCAGGGCTGC[C/T]TTATTTCCTCCTAACCACACTAATTGTTTTGTCTA Y 2 1 2 1 201000 r 74 goat snp51089-scaffold742-12793 20 46925807 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787483 Affx-122966557 AX-385274508 20 46642677 TCATGTTTTTCTCAAGAATCAGTATAAGATTATTT[A/G]TGTTTCAGTTGTCACTTTTTTCCACATAAATTTGT R 2 1 2 1 101000 r 74 goat snp14428-scaffold1576-16025 20 46967569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450511 Affx-122922503 AX-123320845 20 46692441 CTTGTCATATTCCATTATCAGCAAAAACTAAAGAG[C/T]AACACCTGCTTTAAAAACAAGAACAAAAAGCCTTT Y 2 1 2 1 101000 f 74 goat snp14429-scaffold1576-65789 20 47015920 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381036 Affx-122974641 AX-123251394 20 46740045 TCTTAGTCAGTTCATAGTTCAGACTAGTTCATAGT[A/G]TTGTCAGTCAGTTCAACTTTCTTTGTATGTCCAAC R 2 1 2 1 101000 f 74 goat snp14430-scaffold1576-113393 20 47063802 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399915 Affx-122961323 AX-123270270 20 46769865 CATTAGAAAACAGGAAAATTTGAATTATAAAGATC[G/T]CATTAACTCGCTTAAGGGATCAAGCACATACCTGC K 2 1 2 1 101000 r 74 goat snp14431-scaffold1576-143213 20 47095219 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437370 Affx-122931924 AX-123307708 20 46806635 GCCAGGTATCTTTCTTTGATAACAGAGAAGTACCT[A/C]GGTTTTCTTATACTCATTTCCTTCAAGCTATGCCA M 2 1 2 1 101000 f 74 goat snp14432-scaffold1576-179983 20 47132953 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38423893 Affx-122942291 AX-123294239 20 46840884 CCAGGCCTCCCCTCTTTTCTTCTCAGACTGTCTTA[C/T]GACCCTTATCACTAAGAGACATAGCTTAGTTTCCA Y 2 1 2 1 201000 r 74 goat snp14433-scaffold1576-214232 20 47167447 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427732 Affx-122939266 AX-123298075 20 46870371 TTCAGAGTAGCTTAAATTCTCTACAGTATTCCACT[C/T]AAAAGTAAAATGACTGATTTATTTTTTATTCATCA Y 2 1 2 1 102000 f 74 goat snp14434-scaffold1576-243719 20 47196981 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779501 Affx-122948512 AX-385266604 20 46903630 GCAAAGAAAAATAGGGATTTCAAAATATAGTACCC[A/G]TTTTCCAAGAAAGATTTTAGACCTCTATCTTCTTC R 2 1 2 1 201000 f 74 goat snp14435-scaffold1576-276978 20 47231677 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785533 Affx-122948401 AX-385272577 20 46947265 AAAATGTATGCCTGCTAAAGCTTTTTGTAAATCAA[G/T]ACCCTGTAGTAACATTCCACTAGTAAATACCATTA K 2 1 2 1 101000 r 74 goat snp57431-scaffold916-32935 20 47279662 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797037 Affx-122932876 AX-385283978 20 46979566 GAGCATATGAGTTGAATAGCATTTTGACTTTGGAA[C/T]ATTTTTATGTCCACTCTATCATTAATATATTATTC Y 2 1 2 1 101000 f 74 goat snp57432-scaffold916-65236 20 47311551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790889 Affx-122978179 AX-385277886 20 47058236 TGGATATAAGGCAAATACAACTTTGATGTGAAACA[C/T]AGTCTTATCTAACTTCATTTCCACATGGCAAGAGA Y 2 1 2 1 101000 r 74 goat snp57434-scaffold916-143906 20 47393868 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790690 Affx-122933472 AX-385277691 20 47098943 ATGGTCAAATTATCAGATACTGATAGTAGCAGAAA[C/T]GACAGTCTGATGTTCTGTTGATTTCTAGATTGAGT Y 2 1 2 1 201000 r 74 goat snp57435-scaffold916-184613 20 47434796 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778247 Affx-122966817 AX-385265362 20 47144829 TGCATCAAAGATGCAATTAATTAATATAGCTCATT[A/G]CTTGTAGGTTGATACAATCAAGATATTTTGTTACA R 2 1 2 1 201000 r 74 goat snp57436-scaffold916-230499 20 47481797 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385680 Affx-122971135 AX-123256038 20 47179352 GTAATGGATAATGATGTTATTGAAGCAAATGGCTA[C/T]GACAACAAAAAATGTCAGAGGCTAGACTGAGGTCC Y 2 1 2 1 201000 f 74 goat snp57437-scaffold916-265022 20 47516462 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432084 Affx-122935874 AX-123302425 20 47209366 TCTGTAGTAGTAATATAAACATTTTTGGTGGTTAT[A/G]TGGTCATGACTTTCCTAGGAATAACATTAGCGTGT R 2 1 2 1 101000 r 74 goat snp57438-scaffold916-295036 20 47546441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391205 Affx-122967413 AX-123261562 20 47239249 ACTCCAGGACTCTGATTGTAGTCACTAGCTTTATG[C/T]CCATTTGAAAGAAGGCAGGCATGGAATGGAAAGAG Y 2 1 2 1 101000 f 74 goat snp57439-scaffold916-324919 20 47576667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799923 Affx-122959598 AX-385286849 20 47280349 GTATACTACTTCTTAAGAGCAATAATTTACAAAGT[A/G]TGTGATATGAAGGAAATGCAACAGACATCATGTTG R 2 1 2 1 201000 r 74 goat snp57440-scaffold916-366019 20 47618881 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792817 Affx-122925940 AX-385279795 20 47346749 AATGTTGAGCCATCCTGAAAGGCATTGGCAAGGGA[C/T]AAAATTCATGTCTAAACGATCAGTTCATGGTCACC Y 2 1 2 1 102000 f 74 goat snp57441-scaffold916-432419 20 47685858 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774783 Affx-122942060 AX-385261917 20 47423705 GGAAGAAGAAATTAACTTTCAGATTCCTAAACTTA[A/C]TCTTCAACCATTTTTTCCAGGACACAGGACTTAGA M 2 1 2 1 201000 f 74 goat snp57443-scaffold916-509375 20 47763369 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787056 Affx-122966901 AX-385274084 20 47479615 CTCACAAGAAAGGTAAGGTTAGTAGTACCTTTCCC[A/G]CAACTGTCATCAAGCTCTCCAGCACATCCCCACCC R 2 1 2 1 101000 r 74 goat snp57444-scaffold916-565285 20 47819934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421612 Affx-122944479 AX-123291959 20 47549152 ATTCACGGGGTTGCAAAGAGTCGGACACGACTGAG[C/T]GACTGAACTGACCTGAGTGTTAAAATTTTGATAGT Y 2 1 2 1 303000 f 74 goat snp57445-scaffold916-634822 20 47890978 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775659 Affx-122960447 AX-385262790 20 47594170 ATGGGCACCTGGAGTATCAGGAATTTATGTTCAAA[G/T]ATTTCTTTAGATATTTATGGTTAAGTCCACTGGTA K 2 1 2 1 101000 f 74 goat snp34080-scaffold40-5934922 20 47942250 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792723 Affx-122972771 AX-385279703 20 47625233 CATGTACTTTCAGTAACAATGTAGGATAGAAATGG[A/G]TTTACTTTAAGCTTTTTGTTCTTCTTAAAACTTTA R 2 1 2 1 201000 r 74 goat snp34079-scaffold40-5903859 20 47973503 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440240 Affx-122930669 AX-123310577 20 47701303 TGCTCAAATTTGAAGGAGATTTCAAATAGGTATGC[A/G]TAGTATTGAGAGCCCATTCCCTCAAAAAACCTACT R 2 1 2 1 101000 r 74 goat snp34077-scaffold40-5827789 20 48050011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771080 Affx-122930681 AX-385258240 20 47777531 ATCACCTCTTCTATAATTATGTCATTCTCTCCTCA[A/C]AGAAATTGCAGTATTGAGGTATTTTAATTGAACAG M 2 1 2 1 101000 f 74 goat snp34075-scaffold40-5751561 20 48127179 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801551 Affx-122930059 AX-385288460 20 47832950 CAGTACTTCTATCCTCCACTTTATTAGTATATTTA[C/T]AAGTGGCCATAAACTCTAAAAAATTTTACTTCTCT Y 2 1 2 1 201000 r 74 goat snp34074-scaffold40-5696142 20 48183468 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405966 Affx-122955537 AX-123276318 20 47880499 ATACAATTGACCCCTGGAGGGTAGAAACACATTCT[G/T]CTATTAATTGATTATGAACCATGGTAACTGGATAT K 2 1 2 1 201000 r 74 goat snp34073-scaffold40-5648593 20 48231310 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793651 Affx-122931817 AX-385280624 20 47930072 CTAATTGGTCTAATTCCTTACTTTCATAAAAACTT[A/G]CTCTTCAATTGCTCAGTGAAAAAGAACTTGCATAT R 2 1 2 1 102000 r 74 goat snp34072-scaffold40-5599020 20 48281816 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791386 Affx-122970038 AX-385278377 20 47966910 ATTTGGGGAATTACAAGTAGTAGAAAGTATAGGAT[A/G]GTGAAACCAGATTTTATGTTGCTTAACTGAATAAA R 2 1 2 1 201000 r 74 goat snp34071-scaffold40-5562182 20 48318637 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793602 Affx-122937708 AX-385280577 20 48025248 CTGGGAGATGTGAAGAGAAAGATATGAATCATCAC[A/G]TTAGATTAAGTCAAGGAGCTGAAAGCAATAGGCTT R 2 1 2 1 101000 r 74 goat snp34070-scaffold40-5503844 20 48377272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273030 Affx-1111833200 AX-519546705 20 48028061 TTAGTAACTCCTCAAAGTCTCAATATATCATGTAG[A/G]AAGCGTTTTATGATGACTAACACTCCATTATTTTA R 2 1 2 1 101000 r 74 goat 20_48028061_AF-PAKI 20 48028061 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425047 Affx-122941861 AX-123295393 20 48060696 ATAAACATACTGATAGAACACTGAGCATGATAATA[G/T]CAATTTGAATGTTTATATTTGTAATGCCAAGAGGA K 2 1 2 1 101000 f 74 goat snp34069-scaffold40-5468396 20 48412737 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416781 Affx-122948166 AX-123287129 20 48092885 TGAGATATTCTTGAATAGTGCACTGGTTTCCAATG[C/T]CATGATTATAAATACCAGATCCCCACTTACTTCTC Y 2 1 2 1 101000 f 74 goat snp34068-scaffold40-5436207 20 48445108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417775 Affx-122947394 AX-123288123 20 48122438 AATCTTCAGTTTTATCACCATTTCAATGACTATCA[C/T]ATTATTCTTTTAAGTAGCTGATTAAAAATATTCTT Y 2 1 2 1 101000 f 74 goat snp34067-scaffold40-5406654 20 48474689 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777948 Affx-122920758 AX-385265064 20 48189071 TAACAGGAGTTTTAGTTCAGAATTAACTGCTCTCC[A/G]TCACTGTGTAGGACAGTATTTGCAAAAACTTATAT R 2 1 2 1 101000 f 74 goat snp34065-scaffold40-5340021 20 48542230 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785158 Affx-122959028 AX-385272204 20 48264539 ATGTGCTCAGCATAATGGATAAAATAAAAGCCCTC[A/G]TTAAGGCATATAATTGTTAAATTGAAAGATGTCGT R 2 1 2 1 101000 f 74 goat snp34063-scaffold40-5264553 20 48620748 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779977 Affx-122949962 AX-385267076 20 48298484 TATCCCCAAACACATTTTGTTGTGTTATAATTACA[G/T]ACAATATGATGCATTATACATCATATAGCTATTTT K 2 1 2 1 101000 f 74 goat snp34062-scaffold40-5230608 20 48654727 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413847 Affx-122949871 AX-123284196 20 48338025 AATTTTTTATCCTCTCCTCATCCTCTGTGAAGAAC[A/G]GTACTGCCCTAGTCAGCTCTGGCTGCCATAACAAA R 2 1 2 1 201000 f 74 goat snp34061-scaffold40-5191067 20 48694352 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796931 Affx-122938801 AX-385283873 20 48401588 CAATGAAAGACTGATGATCTATTTGCACACTTCCA[C/T]TTATACTCTCTTACCTCATTCCCCAAATTTAAGAA Y 2 1 2 1 101000 f 74 goat snp34059-scaffold40-5127504 20 48758866 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795332 Affx-122920952 AX-385282290 20 48436764 CATTTTAATACTTAGATTTCACAGCCTGTGCTATG[C/T]TGTTTATCAATAACAATGCTTTTTACTTAGTCTAT Y 2 1 2 1 101000 f 74 goat snp34058-scaffold40-5092328 20 48794546 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410164 Affx-122952787 AX-123280514 20 48513459 TCTTTAGGAAAAGCAAAATAAAAAACAAAAAATTG[C/T]CCAGAATGGGGTGGAGAAATTATATATTCCTAGTA Y 2 1 2 1 103000 r 74 goat snp34056-scaffold40-5015633 20 48871202 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384383 Affx-122972220 AX-123254741 20 48584612 GGTTTTATTTAAGGGCAAAAAGTAGGTTTAGTTCT[C/T]AAAACGAAGAACATAATTGACTTAGCTTTTTACAG Y 2 1 2 1 101000 f 74 goat snp34054-scaffold40-4944480 20 48941355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437124 Affx-122932162 AX-123307462 20 48700949 CAGGATCATTATAATAAAAATCATAGTAAATTAAG[C/T]AAAGTCTATATCATTTTCATATACATTATTAAGTG Y 2 1 2 1 303000 f 74 goat snp34052-scaffold40-4828143 20 49058839 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802595 Affx-122944818 AX-385289497 20 48765998 TAGGAGCAAAAGAGTACACTATTTTTACATCATTG[C/T]ATCACCTAGGAATTGGAGTTGTTTTCAACAAAATG Y 2 1 2 1 101000 r 74 goat snp34051-scaffold40-4763094 20 49123997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380178 Affx-122975514 AX-123250536 20 48822840 ATTTTTTTAACCACCAAAATAAAAGGCAACTGAGT[A/G]CTGGGAGAAGATAATTGCAATAAATTAATTTTATA R 2 1 2 1 101000 f 74 goat snp34050-scaffold40-4706252 20 49181002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405841 Affx-122955868 AX-123276193 20 48862353 ACTGTTTTCAGTCAAAATAAACTAAAATCCAGATG[C/T]ATATGATATAAAAATATGCATTTAATTATGAAAAA Y 2 1 2 1 103000 f 74 goat snp34049-scaffold40-4666739 20 49220814 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767460 Affx-122952345 AX-385254728 20 48909208 ATTAGTGTTGTGCTTTCTCTTCTAGTATTTTTGCA[G/T]CTTATATGAGAATTAATAATTGATTGATAATAGTT K 2 1 2 1 101000 f 74 goat snp34048-scaffold40-4619884 20 49268237 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402955 Affx-122958167 AX-123273308 20 48976888 TGTACTATGGAAAGTTTTTCTTCTTACTTATTTTC[A/G]CTTGCCTCAAGCCTAGCACAGGCTATTCTACGTTG R 2 1 2 1 101000 r 74 goat snp34046-scaffold40-4552204 20 49335596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798068 Affx-122934225 AX-385285004 20 49007976 GTGACTGCATGACCTAATTCCTTACAATAAATAAA[G/T]ATATTTATCTATGTAAAGAAACCTTTGCCTCTGAA K 2 1 2 1 201000 r 74 goat snp34045-scaffold40-4521116 20 49367373 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416275 Affx-122947950 AX-123286624 20 49045393 TCAGGTGGACATCACTCATGCCTCTAGCTCCTAGG[C/T]ACTGGCAGAAAGTGTTAGAGAAGGCAGAGAAGGAT Y 2 1 2 1 101000 r 74 goat snp34044-scaffold40-4483699 20 49404920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433181 Affx-122935652 AX-123303522 20 49209268 TTTGCCCTGGTCCATCCCATGTGACTATAAGGCTG[A/C]TTTTAGGGAATGTGGTATGATTGATTGTACTTATT M 2 1 2 1 201000 r 74 goat snp34041-scaffold40-4319824 20 49568881 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396351 Affx-122963053 AX-123266706 20 49267107 TAATGTAAACCGAGCATCCACTGATTGGAAGAGAT[A/G]TTTCAGATCATCATAAGCTGTACTTCTAAAAAGCA R 2 1 2 1 101000 f 74 goat snp34040-scaffold40-4261985 20 49629992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801300 Affx-122923355 AX-385288212 20 49303836 TTAAACTATTTTCCTCCCTTACTGTCTTTGACCAC[A/G]TCTGTTACTTATTGGTTCTCTATTTCTTTTGCTAC R 2 1 2 1 201000 r 74 goat snp34039-scaffold40-4225256 20 49667624 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383840 Affx-122973158 AX-123254198 20 49380095 CTTCTCTCTGTTTCTCAATCTGTTTCCTTCTTTTT[A/G]TTTTTCTCTCTGTTTATCCAATTATAATTATGTGT R 2 1 2 1 303000 r 74 goat snp34037-scaffold40-4148997 20 49744015 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377317 Affx-122977682 AX-123247676 20 49433795 GACAGCCTCAAGGTACAAAGAGGATTGGAAGAGTG[C/T]CTTGTCAAAAAAACAAACGAACCAACAAACAACAA Y 2 1 2 1 101000 f 74 goat snp34036-scaffold40-4095297 20 49798074 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395405 Affx-122963955 AX-123265760 20 49487603 AAAATAAGCTTTATGGGGAAGACCTCTGCATGCGT[A/G]CCTGGGGTGCATCATCACATTTATTGGGCATTTTC R 2 1 2 1 101000 f 74 goat snp34035-scaffold40-4041489 20 49852366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774159 Affx-122974794 AX-385261297 20 49567236 AATAAATAGTACCCTTAATTGCTGATCATTCAATA[C/T]AGAATCTTATCCAATCTCAGATATATGCTATGTGA Y 2 1 2 1 101000 r 74 goat snp34033-scaffold40-3961856 20 49927533 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394961 Affx-122964278 AX-123265316 20 49596261 CAGAGAGCATATTTATGGTCAATACTTCAGACAGA[C/T]ATCAGGCTACTCTTTGCAGTACTGTTAGCAGTAAA Y 2 1 2 1 101000 f 74 goat snp34032-scaffold40-3932831 20 49956593 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788624 Affx-122956134 AX-385275641 20 49628116 GAATTAAAATATATCTTGGAAGATAGTATCCATTT[A/G]TTTCTGATTCTATCTCAATAGTCTCCTTGTTAGTG R 2 1 2 1 101000 r 74 goat snp34031-scaffold40-3900976 20 49988461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448034 Affx-122923711 AX-123318370 20 49703669 ACAGAAGATGCAAAAAGAAAAGTATCTTAGTGATT[A/G]TATCAGCTAAAGCACAACATCAGCATTTATTAAAT R 2 1 2 1 101000 r 74 goat snp34029-scaffold40-3825423 20 50063784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422383 Affx-122943399 AX-123292729 20 49764763 ACTGTCTCATTCACAACATTGGGTAGGAAATAGAA[C/T]AGTGAATTTCATTTTTCTCTTTTGAGAGGTAATCA Y 2 1 2 1 101000 f 74 goat snp34028-scaffold40-3764329 20 50125543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777630 Affx-122947509 AX-385264749 20 49837955 CTAAGATGATACTTGATAAAAAACACCCTGAAATT[A/C]CACCTAGCGATTAGCATCGAAATTCATACTGCCTA M 2 1 2 1 101000 r 74 goat snp34027-scaffold40-3691137 20 50199575 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777613 Affx-122937746 AX-385264732 20 49895109 ATGCTGTAACTGTCAACCTGTTGTCTGTTTCATGC[A/G]TTAACATAAGACCTTCCCCTATGATCTCACATATC R 2 1 2 1 101000 f 74 goat snp34026-scaffold40-3633983 20 50258558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771286 Affx-122932885 AX-385258444 20 49944380 ATTGTAAAATATCAAACATGTTAAATGTCAATGCT[A/G]TCAGAGATAATGCATTCTAGAAATTCAAGCCTATG R 2 1 2 1 101000 r 74 goat snp34025-scaffold40-3584712 20 50308512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796849 Affx-122923612 AX-385283792 20 49986635 AGGAATCAATCCTAATCAAAACTTTGACTTCATGT[A/G]TTTGTATGTTTTCAAATGTGGTGATTATTTCTCCT R 2 1 2 1 201000 r 74 goat snp34024-scaffold40-3542457 20 50351369 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392463 Affx-122966157 AX-123262820 20 50016224 TCACTGAAGAAAAATTTGAGAAGGAATTATCACCT[A/G]TATAGAAATAAAAGATTTTCAACATACTTATAATC R 2 1 2 1 201000 r 74 goat snp34023-scaffold40-3512868 20 50380573 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274294 Affx-1111834166 AX-519547891 20 50060115 GAACTGCAGCCTGAACAAGAGAAGAGAAGTGGAAC[A/C]GTGTGGGGCAAATGGTGGACTCCACAGCACCACAC M 2 1 2 1 202000 f 74 goat GoatD01.022821 20 50060115 C A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320799000 Affx-122949358 AX-385285930 20 50069693 CCTTCTAGATTTTTGACTACACAAGAAAATATTTT[C/T]TGTGTGTTCATCCTTCTAATCTAAGCATTAAGAAA Y 2 1 2 1 202000 f 74 goat snp34022-scaffold40-3459399 20 50433236 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418088 Affx-122946599 AX-123288436 20 50118101 TGCTTAGATAGTTTTTGTCATCTAGTAAGTGTTTA[C/T]GATTAACAGCTGTCACCTGCGTCGTCTGTGTTACT Y 2 1 2 1 201000 f 74 goat snp34021-scaffold40-3410991 20 50481254 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765783 Affx-122945019 AX-385253238 20 50158611 CACAAGCATGCCTTTTTCATGGATGACTGAAAGGA[C/T]GAAACTGTCTAAATGTGTCAATTACAGAAATTGTA Y 2 1 2 1 101000 f 74 goat snp34020-scaffold40-3370481 20 50521868 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413405 Affx-122950712 AX-123283754 20 50201847 TGGGGTAAAAACTAGAGAACAGGCATAGATCCAGA[C/T]GAATGGTACACCAATTAGAGAATGAAAGCCAAACT Y 2 1 2 1 101000 f 74 goat snp34019-scaffold40-3327245 20 50565366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771656 Affx-122951210 AX-385258814 20 50261954 TCTTGGAAGTCTTAGACTACAACAATATAAATTTC[A/G]TTTAAGAATATTAGATTCATCTTTGTGGAGGCATT R 2 1 2 1 101000 f 74 goat snp34018-scaffold40-3267138 20 50625665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788527 Affx-122975045 AX-385275544 20 50307676 TTAACTTGCACATGAAGTGTAAGATAAAGTGCTCA[G/T]CATTGGGCAAAATGATGTAAAGCTGTAGTATCTAA K 2 1 2 1 101000 f 74 goat snp34017-scaffold40-3221416 20 50671469 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794233 Affx-122938388 AX-385281199 20 50338515 CAAGTATGGGGTGTAGAAGAGAGTTCATCTAGGAC[A/G]GAAGTAGCCCAAATTGAAAGATCTGCTAGTTACAC R 2 1 2 1 101000 f 74 goat snp34016-scaffold40-3190577 20 50702246 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444675 Affx-122926450 AX-123315012 20 50374688 GCATCTCTTCTCCCTTTCTTACTGTCCTCCAGCCA[C/T]GATGACTGATGAGCTTTGAGCTCTCACATCTATGC Y 2 1 2 1 101000 r 74 goat snp34015-scaffold40-3154404 20 50736582 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434450 Affx-122934650 AX-123304791 20 50421663 ATCATGATCAAGACTGACTACTTTTCCATTTGCCT[C/T]TTATATATACCTGAACCGCTTTTACTACTTACAGA Y 2 1 2 1 101000 r 74 goat snp34014-scaffold40-3107429 20 50782727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769383 Affx-122948018 AX-385256554 20 50461942 TATGTAATATCTCCTTATAATGTAAGGGAGGAGAG[A/G]TGAATGGTACCTTAAATTCCTAATGCTAAGAGCTC R 2 1 2 1 101000 r 74 goat snp34013-scaffold40-3067150 20 50822597 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378761 Affx-122977015 AX-123249120 20 50528864 TACCAAACTAAATGATTGATTTCTGAATAGCAATC[G/T]AATATGTCATGACTGATTTCCTCTATTTACTTTTG K 2 1 2 1 201000 f 74 goat snp34012-scaffold40-3000228 20 50885633 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449039 Affx-122923072 AX-123319374 20 50591829 GTATAGCATGCAGGTGTTGAAAGAAGAGTTCTAGG[A/C]GGGAGGAAGCAGAAAGTGATGGCTTTCTTCCAAGC M 2 1 2 1 201000 f 74 goat snp34011-scaffold40-2937263 20 50948733 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403944 Affx-122957456 AX-123274296 20 50630781 AGTGGATGATCATTTCTAAATTATCATGATGGTTG[A/G]CTCATGTACAAGGTGACCACATCCTTGCTCACAAC R 2 1 2 1 101000 r 74 goat snp34010-scaffold40-2898311 20 50988286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422914 Affx-122943047 AX-123293260 20 50686630 AAAGCCACAAGAGCAAATAACTATTCTTTTAAGTT[A/G]TAATTATGGGGAAGAGTGGAGGAGAAGGAACAGTT R 2 1 2 1 102000 f 74 goat snp34009-scaffold40-2842462 20 51044179 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272059 Affx-1111833201 AX-519545823 20 50705491 AGTGGCTCAGGGGTAAAGTATCCACCCACATTGCT[A/G]AAGCTGCAGGAGATATGGGTTCAATCCCTGGGTGG R 2 1 2 1 201000 f 74 goat 20_50705491_AF-PAKI 20 50705491 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38454143 Affx-122919333 AX-123324476 20 50729168 TATTTAAGGACTGAATTGTCATACTCACAGATAAG[C/T]AGAGAAAGAGAAGATCTAAGAGTTGAAATTGAAAG Y 2 1 2 1 101000 f 74 goat snp34008-scaffold40-2799924 20 51086394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433227 Affx-122935615 AX-123303568 20 50769718 TTGTTCTTATTTTAAAAATCTTCCACTTCTCTTTG[C/T]TACTCTGTGGGCTTCTTCCCTGAGGAGAGGGGAGG Y 2 1 2 1 201000 r 74 goat snp34007-scaffold40-2759374 20 51127003 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411212 Affx-122952359 AX-123281562 20 50798616 CCAGACAACTAAAATAAAAATCAACTTGTTTAATC[A/G]CATGCCTATAAAACAGGGCATTTTGTCAGCCTTTC R 2 1 2 1 101000 r 74 goat snp34006-scaffold40-2730476 20 51156046 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451995 Affx-122920925 AX-123322328 20 50848470 CAGCTGACAGATTTCATTAGGATTATATGAGAATC[C/T]CATTTGAATCAACAGAAATCTATTGATCAATTCTG Y 2 1 2 1 101000 r 74 goat snp34005-scaffold40-2680622 20 51206312 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416072 Affx-122948334 AX-123286421 20 50877420 ATTGCCTGCATTTGGTGCAATAACCTTGAGCAAAA[C/T]AATTAATTTCTTTTATGTAGATGGGAATAATAGTG Y 2 1 2 1 102000 f 74 goat snp34004-scaffold40-2651672 20 51235281 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785538 Affx-122975221 AX-385272582 20 50910679 TGACGGCATTAGATTGGAGTTGAAGGTACTAGAGC[A/G]TAATCGTGATTTTCAACATCTGTACAGTGATGGAG R 2 1 2 1 101000 f 74 goat snp34003-scaffold40-2618413 20 51268676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386699 Affx-122970172 AX-123257057 20 50953956 TTTTGACAATGTGCCATGTATGATTATAACCTAAA[C/T]GCAATATGTTACATTTTAATAGAAGCTACTCTCAC Y 2 1 2 1 101000 f 74 goat snp34002-scaffold40-2575136 20 51312314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774606 Affx-122937764 AX-385261740 20 51009981 CAAATCACTTGATCTCAGTTTATTCATCTATGTAA[C/T]GGAAGGTTTGGAATAGATGTCTATAGATTCCAGGA Y 2 1 2 1 201000 f 74 goat snp34001-scaffold40-2519111 20 51368880 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771573 Affx-122957450 AX-385258732 20 51067164 ATCCCTTAACGTTTTTAAGGAAAAACTAAATAATT[A/C]TCCTGTGTATTTACTGTGATCACAATTATGGTTAT M 2 1 2 1 202000 f 74 goat snp34000-scaffold40-2461928 20 51426416 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380020 Affx-122975594 AX-123250378 20 51112614 CCAAAGTTTTTGCTTACTGGGCTTGCAGTCACAAG[C/T]GTTTTGGAAATTTCATAGTCTCCAGAAAATAACAG Y 2 1 2 1 101000 f 74 goat snp33999-scaffold40-2416478 20 51471549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386712 Affx-122970161 AX-123257070 20 51149620 AAAATGTGCAGAAATAATTCTAATCATTAATGTCA[A/G]TTTATAAGGTTTTATTTTGTAAACATGGGGACATA R 2 1 2 1 202000 r 74 goat snp33998-scaffold40-2379472 20 51509317 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791995 Affx-122940783 AX-385278983 20 51199616 CATCCATCTTGAGTGGTCCTTCATGGCATGGATCA[C/T]AGCTTCATTGATTTAAGCAAGCTTCTAGTCACAAC Y 2 1 2 1 102000 r 74 goat snp33997-scaffold40-2329476 20 51560899 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793093 Affx-122928619 AX-385280071 20 51271362 ATTCTGCTGCTCTTCCTGAAAAAACTCAATTTCTG[A/G]TCATTTCTGCTTGCCTCAGTTGACTTCCTCATTTA R 2 1 2 1 101000 f 74 goat snp33995-scaffold40-2257730 20 51633616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779384 Affx-122951038 AX-385266488 20 51346716 CTTTATAGTTCTAACAAGTTCTACCCAGAAGTAAA[C/T]TGAGCTTCAGGCAGCACACCTGATCATTTATTTAA Y 2 1 2 1 101000 r 74 goat snp33994-scaffold40-2182376 20 51710589 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764907 Affx-122943423 AX-385252497 20 51377842 TTGGGGGCATGGCTAACCACTGATTTCTAGCCTTG[C/T]ATCCCCAGGAAACAAATGCAACTTAGTTTTGCATT Y 2 1 2 1 101000 f 74 goat snp33993-scaffold40-2151250 20 51741931 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434952 Affx-122933854 AX-123305292 20 51425104 AATGGGAAAATAAAGAGAAAAACCTGATAGGTCAC[C/T]AGAGATTATAGCAACTTTGAGATTCTCTACTCACA Y 2 1 2 1 201000 r 74 goat snp33992-scaffold40-2103988 20 51789878 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391878 Affx-122966973 AX-123262235 20 51455109 TTCTTCCTTACACTCCAATATTTCAAAATATTGTA[C/T]GTTTGTTTGTGTGTGTGTTTACTGAAATCATTGTG Y 2 1 2 1 303000 f 74 goat snp33991-scaffold40-2073983 20 51821679 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798348 Affx-122971192 AX-385285283 20 51521093 GATTAGAGTTTGGACTTTTTCCTTGGGACATGCAA[C/T]ATTCAGCAGGTGTTTTTGATCATGTATTCTGTTCA Y 2 1 2 1 101000 f 74 goat snp33990-scaffold40-2007999 20 51886262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795500 Affx-122963252 AX-385282455 20 51562341 ATGGAAAAGACTAACAATGACTGGCACATAGGAAA[C/T]ATTCAAAGGATGTTATGTTCACTCTCTTTAACTTT Y 2 1 2 1 101000 f 74 goat snp33989-scaffold40-1966751 20 51927913 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431043 Affx-122936653 AX-123301384 20 51598741 CCCAGTTGGGATATTTTTCCAAGGTCACAAAGTTC[A/G]TAAGTGATAAGGACAGGATTTTAACCCAGGTACTC R 2 1 2 1 201000 r 74 goat snp33988-scaffold40-1930351 20 51961013 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787366 Affx-122919624 AX-385274391 20 51629940 CCTGTATGATTTCTTCTTTGCAGGTATAAATTATA[C/T]ATTCAAGATAAAGATGAAGAAGGGTTGACATGCCT Y 2 1 2 1 201000 f 74 goat snp33987-scaffold40-1899152 20 51992336 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793031 Affx-122936566 AX-385280009 20 51723009 GAATAAAAACAATAAAAATAGGGGCAGAAAATAGA[C/T]GGGTAGCAAAATCCGGGTTCACCATTGAGAGCAAA Y 2 1 2 1 101000 r 74 goat snp33985-scaffold40-1806083 20 52087505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802366 Affx-122920211 AX-385289270 20 51755127 ATCATTCGGATTTTAGCACTCAGAGACAATAATTG[C/T]TTCAATTTTTCAAGTCAGTATTTCTCAGTGAAGTA Y 2 1 2 1 201000 r 74 goat snp33984-scaffold40-1773965 20 52119655 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766493 Affx-122942489 AX-385253859 20 51795036 GCTCTTAGGAGATAACTTTCATCTTGTATATTCAC[A/G]CATTATCTGAACAGATAGAAGTGTAAATCTGCTAC R 2 1 2 1 101000 f 74 goat snp33983-scaffold40-1734056 20 52159873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424468 Affx-122941769 AX-123294814 20 51913411 GTCACTTCTACTGAAAGGATAAGTTGATAAGTGCT[A/G]CTCATGTGACTAATAAAATTTTATGAGCCCTTTGA R 2 1 2 1 101000 f 74 goat snp33981-scaffold40-1615681 20 52279518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770534 Affx-122971217 AX-385257698 20 51954495 TAGAACCTTTCTAACTCTCTCCTAGTGATCCTTCA[A/G]TGAGAGTATTGCTTTAATCAATACTCAGTATCTGG R 2 1 2 1 201000 f 74 goat snp33980-scaffold40-1574597 20 52322413 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277449 Affx-1111835855 AX-519550953 20 52005309 GAATTTATTTTTTTTAATTGGAGGTTAATTACTTT[A/G]CAATATTTTCTGTGTTTCATCATCAACATTTCTAG R 2 1 2 1 101000 r 74 goat Random2.2K-1874 20 52005309 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38389697 Affx-122968693 AX-123260055 20 52022541 TTTAATTATTTTTCTTAGTGTTTTACTACTCTCCA[C/T]GTGGTTACAAAGACATTCTATTCAGTTTATCTTTC Y 2 1 2 1 101000 r 74 goat snp33979-scaffold40-1506551 20 52391377 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391921 Affx-122966940 AX-123262278 20 52058881 CAGCGTTAGTCCTTCTAATGAATATTCATCCTTGC[A/G]GAAGGGGTGATGCATTTAGGAAAAAAAGATATGCA R 2 1 2 1 101000 r 74 goat snp33978-scaffold40-1470211 20 52428229 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447937 Affx-122923787 AX-123318273 20 52092734 GAGACCGAAGTTATTGAGTCTGTCTCCTCCCCTTC[A/G]TTGCCTTGTGATGGAGAGTGGCAACCTCGTGGGCC R 2 1 2 1 201000 r 74 goat snp33977-scaffold40-1436358 20 52462326 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769477 Affx-122971621 AX-385256647 20 52139257 TGCTATATTAAGGGATGTATCTCTTTGTTTTATAA[C/T]AATGCCTGACAAAGAGTAGTGATTTGTTGAATAAT Y 2 1 2 1 101000 r 74 goat snp33976-scaffold40-1389835 20 52509131 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775186 Affx-122935915 AX-385262317 20 52169862 AGTGAAATAGTTTCCAAGATAGTAAAATTTTCCTG[A/C]TCTTAGTGGAAATATAGTTTTACACTTATTCTCTT M 2 1 2 1 101000 f 74 goat snp33975-scaffold40-1359230 20 52539484 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779531 Affx-122965512 AX-385266634 20 52199733 AGAACTCCTTTGATGACATTCCTTTGATTGACTGA[A/G]CTCCATAGGACTTATTACTAGTTAAAATAAGTCTA R 2 1 2 1 101000 f 74 goat snp33974-scaffold40-1329359 20 52569122 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793210 Affx-122950292 AX-385280188 20 52240381 TCTTAAAATAGAGATATTAGTCTGGTTTTCTTACA[C/T]GGGACCAATGTCATCACAAGATCCTTAATACTAAG Y 2 1 2 1 101000 r 74 goat snp33973-scaffold40-1288711 20 52609289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448270 Affx-122924186 AX-123318606 20 52271219 TATGTGCAAAGTTCCCATATATTCACAGACACTTT[A/G]CCAGCACTTACCTTCACTGACACTTAAATTAACTG R 2 1 2 1 101000 r 74 goat snp33972-scaffold40-1257873 20 52640199 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777638 Affx-122948647 AX-385264757 20 52305376 TTGGCCTCCTTGCTCAGTAAATGCACAGTTTGTAA[G/T]ACTGGGTATCCATATGTCCTTTTGTTTTTATTTTC K 2 1 2 1 102000 f 74 goat snp33971-scaffold40-1223716 20 52674178 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385880 Affx-122971598 AX-123256238 20 52340119 AAACATGTTCTCAAGCACTTCTTTCCTTCTGGTAA[C/T]AGGCTGACCCTGAACAAGTTTGCATTTAGCTGAAT Y 2 1 2 1 101000 f 74 goat snp33970-scaffold40-1188973 20 52709231 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444349 Affx-122926717 AX-123314686 20 52373712 GTTTGTGTTGACAGGATATAGGTAACTGATGTGCT[A/G]TGTATTGATGCATGCATGTTTTAATGTACTTTATT R 2 1 2 1 101000 f 74 goat snp33969-scaffold40-1155380 20 52743240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401806 Affx-122959465 AX-123272159 20 52406367 ATACCCTCATTAGGTCTCCCAAGTTACAGGCAGTC[A/G]CTTTACCATCCGAGGCACCAGGGAAGCTATAATAC R 2 1 2 1 103000 f 74 goat snp33968-scaffold40-1122725 20 52775606 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416051 Affx-122948351 AX-123286400 20 52438896 TATGTAAATTTATTACACACCAATGAGGAGGGGTT[A/C]AGGAAACCAGTTAAACAGTAGAGACTAGGAGTTTT M 2 1 2 1 101000 r 74 goat snp33967-scaffold40-1090196 20 52808961 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421815 Affx-122944318 AX-123292162 20 52472734 GAGTCTCTTTAGAAAGTAATTTGATCACAAAGGTC[A/G]CAGAATGAGAAAACTGAAAGACAATTTAGAGGTAT R 2 1 2 1 101000 f 74 goat snp33966-scaffold40-1056358 20 52842946 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777800 Affx-122936855 AX-385264918 20 52520357 AATTGCTACACAAAAGACATAAACATTTACATTAA[C/T]GTGAATGTTCTTGTTTGGTCTATAGACACAACTTA Y 2 1 2 1 201000 f 74 goat snp33965-scaffold40-1008735 20 52890909 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414805 Affx-122949216 AX-123285154 20 52549659 ATTTTTGCATTTCTCTGTGAATAAATGAAAGCTAC[C/T]GTACTGTTTGCTTCAGACATATTTGCATTTTTAGG Y 2 1 2 1 101000 r 74 goat snp33964-scaffold40-979433 20 52919872 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404174 Affx-122957691 AX-123274526 20 52612527 CTGAGAGGGACACCTGCCTACAGTCAGCAAGAAGA[C/T]AGGGATTTCATTTCTAGAACTGCATGGAACCAATT Y 2 1 2 1 201000 r 74 goat snp33963-scaffold40-916565 20 52982287 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380798 Affx-122975093 AX-123251156 20 52645626 AGGAAAGAGAAGTGGAAAAAATATGGATGTTAAAA[C/T]ATTGTCACTCATGTGAAATGATGGTTCAATGTACA Y 2 1 2 1 303000 f 74 goat snp33962-scaffold40-883466 20 53015868 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429291 Affx-122938614 AX-123299633 20 52693125 AAAGTGTATCTCTTTCAAACTGGTTTATCAGTGGT[A/G]TCAAGGTTGGCTAGGGACACCAGGACTTACAGCTA R 2 1 2 1 101000 r 74 goat snp33961-scaffold40-835967 20 53063353 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389594 Affx-122968773 AX-123259952 20 52728044 TGAGATTTTTTGATGTCTCTTTCTGTTCTTGGCCA[C/T]AGCAAACACCATCTTCCAGTAACACAAGAGAATAT Y 2 1 2 1 303000 f 74 goat snp33960-scaffold40-801048 20 53098345 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772799 Affx-122937293 AX-385259944 20 52770719 CACTTGAGATTCCTATTAGACTTCCTATTAGAGTT[A/G]CTGGCTAGGATATTACACATAAGTCTAGCTTTGTA R 2 1 2 1 101000 r 74 goat snp33959-scaffold40-758373 20 53140952 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774747 Affx-122972901 AX-385261881 20 52830716 AATACTGAGATCAAACCCTTTAAACTATAAAATAA[C/T]AGTTAAGCACATTTTGTGGAAGATAATGCGCAACT Y 2 1 2 1 101000 r 74 goat snp33958-scaffold40-698376 20 53201426 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788220 Affx-122961692 AX-385275239 20 52897453 ATACATTAAGTGCTACATTAAGTACTTTATTTCTT[A/G]TCTATGCCACTGAAGCTACACCCCAAGAGAAAAAT R 2 1 2 1 101000 r 74 goat snp33956-scaffold40-631639 20 53269029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440638 Affx-122929950 AX-123310975 20 52951039 AGAATGAATTAATAATAAATATGCATTTGGAAATT[A/G]CAGTTAAATTTACCAGTAAGATAGGATGTTCTTCT R 2 1 2 1 101000 r 74 goat snp33955-scaffold40-578053 20 53318803 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438641 Affx-122930905 AX-123308978 20 52981793 TATTTTATAAGTGCCTGTCAGATTGTGTTATAACT[A/C]TTTTCATGGATGGACTTTCAGTTAGAAAAAAAAAA M 2 1 2 1 101000 f 74 goat snp33954-scaffold40-547299 20 53349626 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438505 Affx-122931213 AX-123308843 20 53022102 CTTAATACAGTTGTTTCATGGCCCGAGATCCAGTT[A/G]TTCTGTGCTGACATTTCCCATTACCGAACAAACTT R 2 1 2 1 101000 f 74 goat snp33953-scaffold40-506990 20 53389414 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774663 Affx-122955679 AX-385261797 20 53091506 AAAATGGATAAGAGCATGCAGCATAGGTCTCCATA[C/T]AGGGTGTTCAATATTTAGAGTAAATATCGGAAGAT Y 2 1 2 1 101000 f 74 goat snp33951-scaffold40-437586 20 53458589 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792479 Affx-122961473 AX-385279460 20 53132501 AAGGAACATGACAGCACAAGTAATACATATTTTCC[C/T]TTATGTAAGGTTTCCTAAAATATTTCTTCTTAAGA Y 2 1 2 1 201000 r 74 goat snp33950-scaffold40-396591 20 53499513 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383589 Affx-122972582 AX-123253947 20 53164323 AATACTCTCATGAAATGTATGACTCCCTCTCCACC[A/G]TCAGGTCTCTGTACCAAGGTCATGTACTAGAGAAT R 2 1 2 1 101000 f 74 goat snp33949-scaffold40-364769 20 53531117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782166 Affx-122955813 AX-385269244 20 53243376 AAACAGCAGTGAAAGATTTAATGAGACCATTTAGT[A/C]AGACTTACACTAATGAACACATCAGTGAGAATGGG M 2 1 2 1 101000 f 74 goat snp33948-scaffold40-285716 20 53610174 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451876 Affx-122921057 AX-123322209 20 53333653 GCCAACATAGGGGATAGATTCCAGCACTGAATAAA[C/T]GGCAACAAAGTCATTAAAATGATAAAATATAACAC Y 2 1 2 1 101000 f 74 goat snp33947-scaffold40-195439 20 53700618 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271898 Affx-1111833203 AX-519545680 20 53353547 TAAACAACCACCACCACCACATATTACTGTTGTTT[A/G]CTATATTTGCTTCATGTTTAATTTGATTGGCTGTC R 2 1 2 1 101000 r 74 goat 20_53353547_AF-PAKI 20 53353547 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320800749 Affx-122933430 AX-385287666 20 53367833 ACTCATCCTAAGTGTCAGCTCAGATGATTTGAGCA[A/G]AGGTTAATTTTTCTCCTTACACAACAATTTACATA R 2 1 2 1 101000 f 74 goat snp33946-scaffold40-161259 20 53735292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421834 Affx-122944305 AX-123292181 20 53452124 AAAAAAGTACAGCCTTTTAAAAAGTTCTGTTGAAA[A/C]AGTATCCAAAATGAAATATACCAGAAAATAGTTTT M 2 1 2 1 101000 r 74 goat snp33945-scaffold40-76968 20 53819542 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385133 Affx-122971769 AX-123255491 20 53527918 TTTAAAAGGGATCTGAAAAGTTAATCCTGACAAAA[C/T]ATAGCTCACAAGGTGTACATTTGGCACTTAAAGTT Y 2 1 2 1 101000 r 74 goat snp33944-scaffold40-1174 20 53897012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416301 Affx-122947930 AX-123286650 20 53531793 GTATAAGCTTGAGGTTTTCTACAGGACATGGAGAA[C/T]GATACAAGTGCAGAGTGAGCCACTTAAATGATTGT Y 2 1 2 1 101000 f 74 goat snp25964-scaffold269-2602 20 53909004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777004 Affx-122975400 AX-385264128 20 53562661 ATACTTCCAGATTTCAAATATGCGAGATCATTTCT[A/G]ATGTGTAAACCACCTCCTTTGTGGTGGTCCTGGCA R 2 1 2 1 101000 r 74 goat snp25965-scaffold269-33470 20 53940102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795219 Affx-122932534 AX-385282177 20 53619704 GTATATGTGTAGTGAATACTTACATATATACACAG[C/T]AAAAGGTACAGCCAATCAGCACTGGTGGAGCACTG Y 2 1 2 1 201000 f 74 goat snp25966-scaffold269-90513 20 53996914 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390142 Affx-122967989 AX-123260499 20 53654085 GAATGAAATTTGTCTGATCATGGGTACTACTAATC[C/T]TATAAAGAAAAAAGTGGGACTTAATTTCTCATAAT Y 2 1 2 1 101000 f 74 goat snp25967-scaffold269-124894 20 54030898 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787533 Affx-122923306 AX-385274557 20 53740876 GAAAGCATTTTAAATGGCTCAGGAAGTAAAACCCT[C/T]TAACTGTCCTATTTAAGCTATCCCTTCTACAGTTA Y 2 1 2 1 101000 f 74 goat snp25969-scaffold269-211685 20 54118448 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375778 Affx-122978586 AX-123246137 20 53775304 GACATGACTGATAGATTCATTGAGTTATGAAGCCC[A/G]CAAGACTTTGATCCTTGAAGGGGTTATGTTTCTTA R 2 1 2 1 101000 f 74 goat snp25970-scaffold269-246113 20 54153643 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782785 Affx-122959757 AX-385269857 20 53822141 GCAAAGAGTTTGTGGAAAATGCCCTGCTGTAGTAG[C/T]AAGCTTAAAGCTTAGGAGCTTTAGTTCACAGAGCC Y 2 1 2 1 101000 f 74 goat snp25971-scaffold269-292950 20 54200542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381473 Affx-122974970 AX-123251831 20 53862191 TCTTGGAGCATTTTCCAATTATAATATTTTGAGAA[G/T]AAATATTATGTTGATTTTCACTGTTGAATAGTTTG K 2 1 2 1 303000 f 74 goat snp25972-scaffold269-333000 20 54241311 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794421 Affx-122946682 AX-385281384 20 53897721 ACAGACATTTATGATGTAAGCATTATAAGTTTAGC[A/G]TCAGGTATATTAATTTACTTAAAGCTGTCAAAGTC R 2 1 2 1 101000 r 74 goat snp25973-scaffold269-368530 20 54278309 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381080 Affx-122974606 AX-123251438 20 53957701 GTTTTAAATAAAACTTTCTGAAATCTAATTATAGT[A/G]TACAACTTTGTCATATCATCTTCCCTAAGAAATTA R 2 1 2 1 102000 r 74 goat snp25974-scaffold269-428510 20 54340433 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789760 Affx-122922083 AX-385276768 20 54015131 AATGTAATGTACATTCTAATCCAAATGAAGAGAAA[G/T]AAGAGAATAAGATAGGAAGAAATTTGAAATAAGCT K 2 1 2 1 201000 r 74 goat snp25975-scaffold269-485940 20 54398309 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384021 Affx-122972898 AX-123254379 20 54073165 GAGTGAAATGATAGATTCCAACATTTAGTGCAGGA[A/G]TAGTAAGATTATAATGACCAAGAGCATCATGAATT R 2 1 2 1 101000 r 74 goat snp25976-scaffold269-543974 20 54456433 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441241 Affx-122929501 AX-123311578 20 54117508 CCTTTAAAATAATATTTTGAAACATTGTCACCTGA[A/G]TTACATGGGGTTCTTGCTAAATAATAAAAGTGTGC R 2 1 2 1 101000 r 74 goat snp25977-scaffold269-588317 20 54501982 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476350 Affx-1251763860 AX-586011765 20 54127186 AGGGCAGGGGCCAACCTTATTTTCCATAAAAAAAA[-/TTAATAATTTTTTTTTTTTTAACCGGGACAGTGTTTTTATTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TAATAAAAATTTTAAATAGCATACTTATAGCCTCA - 8 1 4 1 20000 f 74 goat SV_275 20 54127186 - deletion junction SV-TF-chip 539476606 Affx-1251763860 AX-586011991 20 54127186 AGGGCAGGGGCCAACCTTATTTTCCATAAAAAAAA[-/TTAATAATTTTTTTTTTTTTAACCGGGACAGTGTTTTTATTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TAATAAAAATTTTAAATAGCATACTTATAGCCTCA - 4 1 4 1 20000 r 74 goat SV_275 20 54127186 - deletion junction SV-TF-chip 562165248 Affx-1251763860 AX-606940660 20 54127186 AGGGCAGGGGCCAACCTTATTTTCCATAAAAAAAA[-/TTAATAATTTTTTTTTTTTTAACCGGGACAGTGTTTTTATTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TAATAAAAATTTTAAATAGCATACTTATAGCCTCA - 8 1 4 1 20100 r 74 goat SV_275 20 54127186 - deletion junction SV-TF-chip 562165647 Affx-1251763860 AX-606941057 20 54127186 AGGGCAGGGGCCAACCTTATTTTCCATAAAAAAAA[-/TTAATAATTTTTTTTTTTTTAACCGGGACAGTGTTTTTATTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TAATAAAAATTTTAAATAGCATACTTATAGCCTCA - 8 1 4 1 20100 r 74 goat SV_275 20 54127186 - deletion junction SV-TF-chip 562166054 Affx-1251763860 AX-606941463 20 54127186 AGGGCAGGGGCCAACCTTATTTTCCATAAAAAAAA[-/TTAATAATTTTTTTTTTTTTAACCGGGACAGTGTTTTTATTCTTCCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCC]TAATAAAAATTTTAAATAGCATACTTATAGCCTCA - 8 1 4 1 20100 f 74 goat SV_275 20 54127186 - deletion junction SV-TF-chip 38386828 Affx-122970094 AX-123257186 20 54153407 CAGCCCGAGCAAAATGGAATTGACAAAGAATCTCA[A/C]GTTTTGCCTCAGTGATTAATTGAGATCACTTCCCC M 2 1 2 1 101000 f 74 goat snp25978-scaffold269-624216 20 54536349 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398239 Affx-122962201 AX-123268594 20 54186898 CAGTGCTTATTTCTAATAGTCTCAAGTCCATTATC[A/G]TTCTGGTTTCTATTCTCAGGTTGAATTCTAAATAG R 2 1 2 1 101000 f 74 goat snp25979-scaffold269-657707 20 54569907 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383101 Affx-122973277 AX-123253459 20 54243716 GGAAGTTCAAAGTTTCTTCCTGAGTCTTTTGTGCT[A/C]TATTTTAAAACAATCATATACAGCACCACCTTATC M 2 1 2 1 201000 r 74 goat snp25980-scaffold269-714525 20 54627803 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418468 Affx-122946460 AX-123288816 20 54272225 TTGCTTTCAGCCTAGTAGTTTTGAGATTCATAAGA[C/T]AGTAGATATTAATCAGTCCAGACTTGATTTCCAAG Y 2 1 2 1 101000 f 74 goat snp25981-scaffold269-743034 20 54655980 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382717 Affx-122973621 AX-123253075 20 54312397 ATCAATCAAGATCCCTCTAATCATCCACAAGAACT[A/G]TCTCAATAATGGTCATAAGTATTTCCCCAATGTTT R 2 1 2 1 101000 f 74 goat snp25982-scaffold269-783206 20 54695997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437051 Affx-122933098 AX-123307389 20 54373468 AACATTGGGTGGGGGAAGAAAAGAAGCATTTTACA[C/T]GAGCTGATATTGCTATTGGCTGAGTATTAGCATCT Y 2 1 2 1 101000 r 74 goat snp25983-scaffold269-844277 20 54758052 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418477 Affx-122946453 AX-123288825 20 54416855 GTGACTCAGCATTACTTCTCAGCTCTATCATGCAT[C/T]CATTTTATAGTTGATCTCTCAAAAATCAATAATGC Y 2 1 2 1 101000 r 74 goat snp25984-scaffold269-887664 20 54801158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384668 Affx-122972136 AX-123255026 20 54467456 GGAAATTTGGCATCAATAGTAATCAATATAAAATG[C/T]ATATTTATATTAATATATTAATTTATATGGAGCTT Y 2 1 2 1 103000 f 74 goat snp25985-scaffold269-938265 20 54852491 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782640 Affx-122943671 AX-385269713 20 54498183 TTGAGGCAGAATGCTGAGAGCTGGTTCAAGCCTCT[A/G]CAGCTCTTAGCAAAGGTGCAGAATTCTTCAATTAC R 2 1 2 1 201000 f 74 goat snp25986-scaffold269-968992 20 54882769 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800443 Affx-122953857 AX-385287364 20 54549074 AAAACAGAGCTCACAGTGAGTTGTTTCTGTAAGGA[C/T]TGACTAGGCAAAATTACAATTTAGAAATATTATTT Y 2 1 2 1 101000 f 74 goat snp25987-scaffold269-1019883 20 54934025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439024 Affx-122930348 AX-123309361 20 54590485 ATCAAGTAACACATAGAATTTAAAATTACATTATT[G/T]ACGTGGCTATCAAGCTGATAATTTAATGTAAATGA K 2 1 2 1 103000 r 74 goat snp25988-scaffold269-1061294 20 54975822 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409425 Affx-122954121 AX-123279776 20 54634895 AAGCTGAGTCATTTTTCTAGAACGCATTTCAAAAA[C/T]GATAAGAGAAGGAAAGGCAAAAAGGAAGATTGAGA Y 2 1 2 1 102000 r 74 goat snp25989-scaffold269-1105704 20 55020192 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396693 Affx-122962828 AX-123267048 20 54710006 TTTTTCATGTATAAGTAAAATTGCAGTCCATAGCT[A/G]TTATTTTATTATACTTTTCTATGTGTTTTGAGCTC R 2 1 2 1 103000 f 74 goat snp25990-scaffold269-1180815 20 55096366 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426630 Affx-122939954 AX-123296976 20 54763578 AACACTGGTAACATGTCAATGTCCTTTTACTGTTT[A/G]ATGTTTTATCATGCATTAGGATTTTTTGATTTTGT R 2 1 2 1 201000 r 74 goat snp25991-scaffold269-1234387 20 55150495 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384306 Affx-122972281 AX-123254664 20 54802271 AACTTGCAAACCATTTGAACTATATCTCAGAACAT[A/G]CTGATATTTTCATTTTTCGTCATGTCAGTAAAAGA R 2 1 2 1 101000 f 74 goat snp25992-scaffold269-1273080 20 55189337 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382331 Affx-122973891 AX-123252689 20 54897509 AGAATTACCCAAGGAAACTTTCCAGGATCTACATC[C/T]GTAGCATTCAGGAAGAATCAGTGACTTCTCTTAGC Y 2 1 2 1 101000 r 74 goat snp25994-scaffold269-1368318 NW_017219146.1 8903 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444388 Affx-122926597 AX-123314725 20 54934876 CTGGAAGGTATTGATGAAATGATAAATCATAGTCC[A/G]TTAGAACCAAACAGACACTGCAGAAATAAATTCAC R 2 1 2 1 101000 f 74 goat snp25995-scaffold269-1405685 20 55321681 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443031 Affx-122928158 AX-123313368 20 54971506 CTCAGCTCTGCCTTCTGCATCATAGCATGTGTCTC[A/G]CTGATGCTGGTCCAAAGGATCAGTGCTCCTGAGAA R 2 1 2 1 101000 f 74 goat snp14391-scaffold1570-3600781 20 55356615 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785991 Affx-122926192 AX-385273027 20 55016258 AACTGATTTCTTCCATCCTTACTTTTGTTCCATTC[A/G]CCCTGTTTCAATATACTTGGTAGTAAACAGTTAAC R 2 1 2 1 101000 f 74 goat snp14390-scaffold1570-3556029 20 55402354 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407501 Affx-122954748 AX-123277852 20 55061121 ATTCAATTCCTTCAAAAACTCATGCAGAACTCTTC[C/T]ATTCTTCCCAAAAGTCTATTTATTTTTGTGACTAT Y 2 1 2 1 101000 f 74 goat snp14389-scaffold1570-3511166 20 55447646 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385988 Affx-122971518 AX-123256346 20 55093751 GGTTTCCAAGTAGCTTCAGCACCTACTCACTCCTC[A/G]TCCTGAGTCATCCTCAGTGTCTTGTACTGCTGACC R 2 1 2 1 101000 f 74 goat snp14388-scaffold1570-3478536 20 55480353 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415448 Affx-122949179 AX-123285797 20 55134969 TGTGGGAATTATTAAAATGAAAGTCATGCCAAAAG[C/T]AAGGAATTAATGCTGGCACATCATCTTAGCACTAT Y 2 1 2 1 101000 r 74 goat snp14387-scaffold1570-3437318 20 55521453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414876 Affx-122949140 AX-123285225 20 55166377 TGCGCTCATGCCTATCACTGCCGCTGTGTGGACCC[A/G]TGGCTCACTCAGACCAAGAAGACGTGCCCTATTTG R 2 1 2 1 101000 r 74 goat snp14386-scaffold1570-3405910 20 55552797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422666 Affx-122943679 AX-123293012 20 55236998 CCCTAGAATGTTACGTCTGTTGTATCAGGTTCACC[A/G]CCTGGAAACAGACTTACTGAGTACTTGTTCTTTGG R 2 1 2 1 101000 f 74 goat snp14385-scaffold1570-3335289 20 55624367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417571 Affx-122946903 AX-123287919 20 55307078 ACCTGGTTGGTATTTGTGTGCCTTGGAAACCAGCC[A/G]CTATTCAAAGCTTTCTAGGCAATTTGAATCAGGTT R 2 1 2 1 101000 r 74 goat snp14383-scaffold1570-3265209 20 55694457 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437042 Affx-122933107 AX-123307380 20 55338336 GATCTCCTTTGAAGTTCTCCAGAGTTTTGCCCACC[G/T]AGCAGCTATATCGGGTGCAGAGAGGGATAAAACCA K 2 1 2 1 201000 r 74 goat snp14382-scaffold1570-3233951 20 55725357 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418434 Affx-122946523 AX-123288782 20 55389396 GTCACTTCAGGGAGGAAACCTGTTGGTATATGTAT[A/G]TTTTTGTTAGCACCATCTTGTGAGATAAAAAATAC R 2 1 2 1 201000 r 74 goat snp14381-scaffold1570-3182891 20 55776416 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416881 Affx-122948080 AX-123287229 20 55425315 GAAAGCGAACACACTGAAGAAACAGATAATAATCA[C/T]GGAACACCAGTGATCATTTCAAAGCGCTATTGACA Y 2 1 2 1 101000 f 74 goat snp14380-scaffold1570-3146972 20 55812308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400776 Affx-122959873 AX-123271131 20 55484220 CCAGTTTGGATTTCCCCTCCCCTTTTACCCCCGTG[C/T]GTGAAATCCTTTTAACTGGTAACCACTGCAGAGTG Y 2 1 2 1 101000 r 74 goat snp14379-scaffold1570-3088067 20 55871034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405201 Affx-122956912 AX-123275553 20 55525356 TTATTTCCAAATGCTCTCATAAAACTAACGTGCTT[A/G]TCAGTATTATTTTCCAAATTCTCAAATGCAACATA R 2 1 2 1 101000 f 74 goat snp14378-scaffold1570-3046931 20 55912229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384167 Affx-122972424 AX-123254525 20 55576978 TCTCAAAAGCATTGGTCTTTATGCAAGTCCCTACA[C/T]GATTATATCTTCAGTTTCACCTCCAGCTGTCCCTG Y 2 1 2 1 101000 f 74 goat snp14377-scaffold1570-2995309 20 55963837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770433 Affx-122966011 AX-385257599 20 55610966 ATAATGGCAATTTCTAGCTTACTCGGGTATCTATC[A/G]TTTGAACCCAATAGCTGTCATCAGTAGTCAAATAA R 2 1 2 1 101000 f 74 goat snp14376-scaffold1570-2961321 20 55996790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436809 Affx-122932242 AX-123307147 20 55639698 TCAGTAACATTCCTTGGATGTGCCTTGGCAGGTAA[C/T]ACTACTCAGTAAATGTTGCTTCTCCTCTAGGCTGT Y 2 1 2 1 101000 f 74 goat snp14375-scaffold1570-2932589 20 56025700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395105 Affx-122964159 AX-123265460 20 55740500 TGAGCTTTCTTTCATATGAGACTAAACAGTCAGTA[C/T]GCTATCACTTACCTAATTCAATGTGTTTCAGAAAC Y 2 1 2 1 101000 r 74 goat snp14373-scaffold1570-2831787 20 56126590 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448742 Affx-122923326 AX-123319078 20 55780483 CCAATTTAAGTAAATGAAGCTGATAAACCCAAAAA[G/T]CAACAGTAGCCACACTCATAAGCATGCAAGCTACT K 2 1 2 1 202000 f 74 goat snp14372-scaffold1570-2791804 20 56166369 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376829 Affx-122977918 AX-123247188 20 55821533 TAAACAGTGTCTTCCCCAGATAGGAAGGGAAATGC[A/G]TTCAAAACACCTGCTTTGTTCTCTGAAAAAGTGTT R 2 1 2 1 101000 f 74 goat snp14371-scaffold1570-2750754 20 56207452 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408438 Affx-122954452 AX-123278789 20 55856915 TTGATTCAACAGGATTTGGATGAAGTTTCCCCCAC[A/G]CCAAGCTTTTCCCAACTGTGAAAGCCACCTTGAAA R 2 1 2 1 101000 r 74 goat snp14370-scaffold1570-2715372 20 56242667 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778997 Affx-122946489 AX-385266104 20 55895865 ACTGAGTAGCCTCAGATACATTCTGCTGGTAGATA[C/T]GGAGCATCCATGTTACTGTTCGAAAGTCATTTTTA Y 2 1 2 1 101000 f 74 goat snp14369-scaffold1570-2676422 20 56281889 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273739 Affx-1111833782 AX-515234790 20 55903056 CAGAGATGGAGGGGC[A/G]AGGGGCAGAGCCCTGAGGGCTGAGAAAAACAGGAT R 2 1 2 1 103000 r 74 goat GoatD01.004732 20 55903056 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38448535 Affx-122923438 AX-123318871 20 55929698 CACGCACACACACGTGCAGAACAGAGGACGGAACT[A/G]CTGGCAATATGGATGAAAATAACCTACAAAGAGAA R 2 1 2 1 101000 r 74 goat snp14368-scaffold1570-2642589 20 56316404 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440639 Affx-122929949 AX-123310976 20 55972715 TGAAATATGTTGATCTCATTTTCCTAATGAATTTA[C/T]GTTTTGTTTCCAAAATCACTCCAGAATACTTCAAG Y 2 1 2 1 201000 f 74 goat snp14367-scaffold1570-2599572 20 56359512 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271900 Affx-1111833204 AX-519545681 20 56002050 CGTCCCGTGATACCAAACATTCATCTGTGCAACGC[A/C]TCTGAAATCTTTTGTCCCCTAGTAGCTAGCAGTTA M 2 1 2 1 101000 r 74 goat 20_56002050_AF-PAKI 20 56002050 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38419764 Affx-122945872 AX-123290112 20 56002458 CTGTACACAGAGTCCCGCCGGTACGAAAGCTCGTC[A/G]TCTGTATCAAACCGAGAATCGAAGTCCTCTTCACT R 2 1 2 1 101000 r 74 goat snp14366-scaffold1570-2569829 20 56389112 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431069 Affx-122936634 AX-123301410 20 56031412 GTCAGGGTCCTTTAAAGATTTGCTCAAGTTGCTTT[C/T]AAGGAAGATGACAGCTTTCCCTCGTATTCAAACAG Y 2 1 2 1 101000 f 74 goat snp14365-scaffold1570-2540875 20 56418045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447556 Affx-122924038 AX-123317892 20 56068989 GCTGTTCCCTTAGAATGTGTGTGTTTTTATTGACA[A/G]TATACTGCAAGAAGTTATTTCTTTAAAAACAAAGG R 2 1 2 1 101000 r 74 goat snp14364-scaffold1570-2503298 20 56455941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384517 Affx-122973044 AX-123254875 20 56104342 TTCCTCTCCAGAAGAAAACAAAGAATTCTTTATGA[C/T]GAACAGCACACAAACCCTACAGTACTTTTTTGGCT Y 2 1 2 1 201000 r 74 goat snp14363-scaffold1570-2467945 20 56491287 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422108 Affx-122943567 AX-123292455 20 56192356 GATTTTTAACAATGAGCTACTGTGTGGATATTGCA[C/T]GTTTTAATGGTGAATGAGTACAAGGCCATATCCAA Y 2 1 2 1 101000 r 74 goat snp14361-scaffold1570-2379931 20 56579682 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427080 Affx-122939796 AX-123297423 20 56229402 GAACCAACCACTCAGGCAAAACTGAACTTCGGACC[A/G]TTGACACCACAACAAACAAAAACAAGTTTTCAAAC R 2 1 2 1 101000 f 74 goat snp14360-scaffold1570-2342885 20 56616620 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425696 Affx-122940781 AX-123296042 20 56268318 CTGGTAAATAATGGCTCCAAATTCCAGAGCTGGAG[C/T]GATAAGGCCTCCCCCAAGCTAAGCACTGAAGACTC Y 2 1 2 1 101000 r 74 goat snp14359-scaffold1570-2303969 20 56655380 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402143 Affx-122958661 AX-123272496 20 56298823 AATTAAAAGACAAAAAATAAACACAAAAATATTTT[A/C]TCCCCTCTGAGTTAGTTGACCTAATATGAAATTGC M 2 1 2 1 103000 r 74 goat snp14358-scaffold1570-2273464 20 56685177 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451900 Affx-122921036 AX-123322233 20 56354021 TTAAAGAATCCATCGATATGTGACCAGAACTAAAA[G/T]CCCCAGAACTAGGAGTCTCATGATAAAACTTCTTT K 2 1 2 1 201000 f 74 goat snp14357-scaffold1570-2218266 20 56740926 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379355 Affx-122976160 AX-123249714 20 56406073 AACAATGTGCCTCTGAGGAGTCTCTAAGCAAGTCT[C/T]GGAGCAAGGCGGAGCAATCAAGACTGATTAAAAGG Y 2 1 2 1 101000 r 74 goat snp14356-scaffold1570-2166214 20 56793384 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391577 Affx-122966615 AX-123261934 20 56442542 CACTTCTTAAACACAAATGAACAATTTGAAAAAAT[A/G]CATTCTTGAGGAAATTTCCCCAAAGGATGAACAGT R 2 1 2 1 101000 r 74 goat snp14355-scaffold1570-2129745 20 56830588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412705 Affx-122950749 AX-123283054 20 56490276 GATGGCTCTCAGACTCTAGGCTCAATGACCACAGC[A/G]TAAACAAAACTAATCTGTTGGCTTTACAAGGCTTA R 2 1 2 1 101000 r 74 goat snp14354-scaffold1570-2082011 20 56878783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443316 Affx-122927452 AX-123313653 20 56536295 TCACTCTGCCGAAAACCTGAAACTATCACAATGTC[A/G]TTAACGGCTATACTCCAATATAAAATATAAAGTTT R 2 1 2 1 103000 f 74 goat snp14353-scaffold1570-2035992 20 56924715 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802952 Affx-122945978 AX-385289842 20 56594014 TATTCGTCTAATTCTTTCTGAACCATCCATATCTC[A/G]TCCCTCAAGGTAATCTCTTGTTCAACTGTTTTGAT R 2 1 2 1 101000 r 74 goat snp14352-scaffold1570-1978273 20 56982407 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379281 Affx-122976218 AX-123249640 20 56623794 ATGATATCAGCTCTGACACTGAAGCACAAATTTGT[C/T]TAGTTGCAAACCTTGAGTGCTCCAAGCCTATTCAC Y 2 1 2 1 101000 r 74 goat snp14351-scaffold1570-1948493 20 57012090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784080 Affx-122945817 AX-385271132 20 56663920 CCTGCTGAATACACTAATGACCTCAACTTTTACTA[C/T]GTAGCTAGAAGGTAACTGAAATGACTTTTTATGGA Y 2 1 2 1 101000 f 74 goat snp14350-scaffold1570-1908367 20 57052328 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376047 Affx-122978934 AX-123246406 20 56728089 TGAGAACCACTAAAGGATATTAGGTAAAAGGAGAA[G/T]AAAGACCCTGAATCTCTTGACTCATTTAGGTGTTA K 2 1 2 1 101000 f 74 goat snp14349-scaffold1570-1844198 20 57116839 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400175 Affx-122960676 AX-123270530 20 56770260 AAATGTATTAGAAGACACTGTCTCTTTCAAGATCC[G/T]CTATCCCTTATTCAACATCTAACACTCAATTCATT K 2 1 2 1 101000 r 74 goat snp14348-scaffold1570-1802027 20 57159504 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799641 Affx-122969054 AX-385286570 20 56801612 AAGAATCTGCAGCAGCCCAGACTACTGCATTTGAA[C/T]ACCCAATGTCTATCGCTATGTATGCCTTGCAGTTT Y 2 1 2 1 101000 f 74 goat snp14347-scaffold1570-1770675 20 57190940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778545 Affx-122920868 AX-385265657 20 56894146 TTTATTACTCATGTGCAAATCAGTTTACTGATTTA[C/T]TATAACTTCCTGAAGACAATCATAGAAAGCCAATT Y 2 1 2 1 201000 f 74 goat snp14345-scaffold1570-1678141 20 57283921 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388666 Affx-122969100 AX-123259024 20 56947750 AACTTATGAGCAGAGCCCTAGAAAATTACAGTGTT[A/G]CCAGCACTGAGACAATAAACCAATCAGCAGCTACC R 2 1 2 1 101000 f 74 goat snp14344-scaffold1570-1624537 20 57338711 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430140 Affx-122937392 AX-123300481 20 56993093 TGTTAATAGATAATGCAAATAAGCATTCTTTGAAC[A/G]CTTACTGTATGCCAAGCACTCCACTAAGTGCTTGA R 2 1 2 1 201000 f 74 goat snp14343-scaffold1570-1579194 20 57384156 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439369 Affx-122930273 AX-123309706 20 57028266 CAGAATATGAAGCTCAATATTTTTTAAACATGAAA[C/T]GATCCCCCTTTAAAGTTGTAGTTGTCTTTCTAAAT Y 2 1 2 1 101000 r 74 goat snp14342-scaffold1570-1544021 20 57418684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775148 Affx-122937047 AX-385262280 20 57063056 AAACGTTTAGCTCACTTCTTCAAAGTCCCATTTAA[G/T]TATAATAACACAAGCATAGTATCATTTCTTTTTAT K 2 1 2 1 201000 r 74 goat snp14341-scaffold1570-1509231 20 57453431 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422119 Affx-122943558 AX-123292466 20 57124987 TTTGGTACCAGTGTCTACTCAGACGCATACCTCTA[C/T]GGTCTTACTCTGCCTGTCTCCTCTGGGAGAAGAGG Y 2 1 2 1 101000 f 74 goat snp14340-scaffold1570-1447300 20 57516343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277451 Affx-1111835856 AX-519550955 20 57139876 TGTAGGAGATAGACTGAGGCAGTGTCAAGAACATG[A/G]CTCTTGGTGAACCCTCTACACATCTCTCTGTCTTA R 2 1 2 1 101000 r 74 goat Random2.2K-1879 20 57139876 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38375553 Affx-122979091 AX-123245912 20 57166642 GGACTATAGGTTTAAAAATATGTAAATCAGGTGAC[G/T]ACTGGAGACCAGTTCCCTCAGCCACTGTCAAAAGA K 2 1 2 1 201000 r 74 goat snp14339-scaffold1570-1405645 20 57558090 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407119 Affx-122954873 AX-123277470 20 57199457 TTCCTGGAGGGCTTACAGTGCTTGGGTTCTCAACC[G/T]CATTCCTGGATTTATTTCAGAATGAATCTCTATTC K 2 1 2 1 201000 r 74 goat snp14338-scaffold1570-1372830 20 57591469 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396823 Affx-122963276 AX-123267178 20 57233439 CCATTCAGGTATCATAAATGCTTATATATTATATG[C/T]ATCATTATGTAAGTTTAATTTAAAACATCCAACAC Y 2 1 2 1 201000 r 74 goat snp14337-scaffold1570-1338848 20 57625205 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414001 Affx-122950274 AX-123284350 20 57276932 GGGAGAAGGACATTGGGAGGGAGAGGAGGTCTCCC[A/G]GAAACTCCCACCACACGACATTTCCCTCCCTCGGT R 2 1 2 1 101000 r 74 goat snp14336-scaffold1570-1295355 20 57668631 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418308 Affx-122946980 AX-123288656 20 57325343 GAGCAAATGGCATGACACTGTTCCAATACAACTGT[A/C]GGCTTTTTTCTTTTTTGCAAACACTGGCATCAGAC M 2 1 2 1 101000 f 74 goat snp14335-scaffold1570-1246944 20 57718931 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405905 Affx-122955584 AX-123276257 20 57361530 TGTATTTTTCACTGTATCCATGGATCAGCCTTCTA[C/T]GAAACAACCTGTGGTTTAGCTAGATATTTCTCAAG Y 2 1 2 1 101000 f 74 goat snp14334-scaffold1570-1210757 20 57755714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443253 Affx-122927547 AX-123313590 20 57423726 GCAGTTACCAATAAATGGCTAATATATGAAATGAG[C/T]GGATGGAGGAATAAATCATAGAATTTTAGATTTGG Y 2 1 2 1 101000 f 74 goat snp14333-scaffold1570-1148561 20 57818532 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432278 Affx-122936329 AX-123302619 20 57460745 AAAGCCAAGTCTCCAAGTATTTGGAAATAGCCTTC[A/G]CTTGAACGGATGTGACAGCAGCTAAGAAGTGGATG R 2 1 2 1 101000 r 74 goat snp14332-scaffold1570-1111542 20 57856129 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399911 Affx-122960196 AX-123270266 20 57497803 GACCCCATGGAAAAATTCTTCGTGTTTTAGAGTGA[C/T]ATTGAGAAAAATGATTCAATCAATTGAATTTAATA Y 2 1 2 1 101000 f 74 goat snp14331-scaffold1570-1074484 20 57892877 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377273 Affx-122978129 AX-123247632 20 57558556 CATCAAGAGAAGCCACATCTTCATCTCTGATGAAA[C/T]GTATTAACTAAAGTAATATTACTAAATATTATATT Y 2 1 2 1 102000 f 74 goat snp14330-scaffold1570-1013731 20 57954150 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789637 Affx-122943656 AX-385276646 20 57594691 ATATACCCTAATCCCAGAATTGGTAAGGAGAAAGC[A/G]TTATGAGCAATAGTGTGGCATTATCCCTAGGTGAC R 2 1 2 1 101000 f 74 goat snp14329-scaffold1570-977596 20 57990570 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795463 Affx-122967076 AX-385282419 20 57642281 AATGATGAAACTAATATTACAAAGTGATAATAACA[C/T]GCTGCCACACGCTAATCCAATGTTTGTAATTTCTA Y 2 1 2 1 101000 r 74 goat snp14328-scaffold1570-930006 20 58038308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401780 Affx-122959485 AX-123272133 20 57677110 TCCCTATGACTGGGTTCAGTTCAAGTCTCTCCCCA[G/T]CATGATGGTTTTTCACACCTACTTTGCCTCTTTGC K 2 1 2 1 101000 r 74 goat snp14327-scaffold1570-895177 20 58073830 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787092 Affx-122936251 AX-385274119 20 57725442 TAAACTCCTCTTTGAACTGTCCCAGTTGGAAGGAC[A/G]CAGACCATGTCATGGTCTCGGAGTCAGAGAGCTCT R 2 1 2 1 101000 r 74 goat snp14326-scaffold1570-846845 20 58122724 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434650 Affx-122933985 AX-123304991 20 57754746 GATAGCAGATTCTCCCTTATGAGCAGAGTTAGGTG[C/T]GGGAGAGATAGGCTATGACAGAGAGAAAGAGGCCA Y 2 1 2 1 101000 f 74 goat snp14325-scaffold1570-817541 20 58152055 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786187 Affx-122971816 AX-385273222 20 57785069 TCTATGGGGTTGTCATATGATAATTTATTCATCCA[G/T]CTGTGAGACTTCAGAACATTTCTTTTTGCTTGATT K 2 1 2 1 101000 r 74 goat snp14324-scaffold1570-787218 20 58182526 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400494 Affx-122961286 AX-123270849 20 57817254 GATGCTAGAAGTTCAAAATCAACGTGTCAGCAGGG[C/T]GAGGCTTCCTTAAAAGACTCTAAGAAAAAATACTT Y 2 1 2 1 103000 f 74 goat snp14323-scaffold1570-755033 20 58215014 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382433 Affx-122974238 AX-123252791 20 57846006 TCAGTATCCTTTCGTTCTTGAGACTTCAAAGTGAG[C/T]GAGATGCTTTATTTTTTAATTTTGGGTTTCTTCAT Y 2 1 2 1 201000 f 74 goat snp14322-scaffold1570-726281 20 58243683 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390465 Affx-122967607 AX-123260822 20 57881050 TGGAGGTCTTTCATAAAAGCGAAGTGGCCCAAAGC[A/G]AACTTTCAAAAAGTGGGGTACCCACTTAGATGGAT R 2 1 2 1 101000 f 74 goat snp14321-scaffold1570-691237 20 58278803 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401568 Affx-122958891 AX-123271921 20 57915104 AGCGGGAAGGCAACATTGGTAGGTGCTTTGTGATC[G/T]CCATAAAAATGCAAAGATACAGATTCAATGCAGGA K 2 1 2 1 201000 f 74 goat snp14320-scaffold1570-657183 20 58312734 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798605 Affx-122950613 AX-385285538 20 57959469 ACTGGGAAAGCATTTTTCAGGGATATGATTTATTT[A/C]TTTTACTCTTGGATGCTTGCTGTATTTATCTAAGG M 2 1 2 1 102000 f 74 goat snp14319-scaffold1570-612818 20 58357052 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382555 Affx-122973774 AX-123252913 20 58027354 CAGGGAATTTTACTTGTACTCATACACAAAAATAC[A/G]TGGATGCCTTTTTAAAAAATGATCTGTATCTAGTT R 2 1 2 1 101000 f 74 goat snp14318-scaffold1570-544933 20 58424822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445992 Affx-122925877 AX-123316329 20 58081679 GAAATAACCACTCTGCTCCCTAAATACAGAACACA[C/T]ACAAACACACACATGTGCATGACAAGTCACGTGAT Y 2 1 2 1 201000 f 74 goat snp14317-scaffold1570-490608 20 58479707 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779989 Affx-122946732 AX-385267088 20 58162986 CTTAATGAGGGCACCAGCTTCAGATTTTTATATTT[A/G]TATGTATGGGACTGCATGCTTCTATGATTAACCTA R 2 1 2 1 101000 f 74 goat snp14316-scaffold1570-409301 20 58559998 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410649 Affx-122952774 AX-123280999 20 58195937 CCTGTAAGTTCGCTCTGACATCGCGGACGGGTGAC[A/G]TGGTGGAGACCTTCATCTTGCACTCATCCAGTCCA R 2 1 2 1 201000 r 74 goat snp14315-scaffold1570-376350 20 58592973 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448448 Affx-122923646 AX-123318784 20 58230781 CCGTGTCTCAACCCCCGGTACATCTTTATTGTGCC[A/G]AGGGGCAAATCAAGAACCACAGACTCATGTAGACA R 2 1 2 1 101000 r 74 goat snp14314-scaffold1570-341506 20 58627600 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788128 Affx-122944216 AX-385275148 20 58266755 TCCCTAAAGCCTTTGAAAAAGAATTTTGACTCAGT[A/G]TGCAGTTCTTTGTCAGAACAGGCTTGATTTTCATT R 2 1 2 1 201000 f 74 goat snp14313-scaffold1570-305532 20 58662696 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387401 Affx-122970414 AX-123257759 20 58304765 TAAATAATTCCCTTGACAAAGAGAAATAATGGAAC[A/G]CGCTGCTGCTGTTTCCTAAAGTCAGCTCATTTGCC R 2 1 2 1 201000 f 74 goat snp14312-scaffold1570-267522 20 58701120 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795350 Affx-122919467 AX-385282306 20 58374378 GTGCTTGCACAAAAGTCCCATGAAACCATGGGACC[A/G]TGTAAACCATGGTTTACAAAGAAACCATGGTCAGG R 2 1 2 1 201000 r 74 goat snp14310-scaffold1570-197909 20 58770701 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405673 Affx-122956562 AX-123276025 20 58407718 TTTCAGTGGATTTTTAACTGCTTTATTCTTGTAGC[A/G]TTGGCCTAAGAATTTGGTGCCCAAAGCATTTTCTT R 2 1 2 1 101000 r 74 goat snp14309-scaffold1570-164569 20 58803426 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404249 Affx-122957064 AX-123274601 20 58455079 GATGTCTTCCTTGAAAAAACTAACTGACTGAGTCC[A/G]TGCCTTTGCCCTGCTGTGTTCTGGGCACCACGGGG R 2 1 2 1 101000 f 74 goat snp14308-scaffold1570-117208 20 58850502 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454252 Affx-122919652 AX-123324585 20 58520578 TTGCTGCCCTTCATTGATTAAATGTTTCTTCCCAG[A/G]AACCACCTCTGGAGTGTCCGCATTAGCACGGGATT R 2 1 2 1 101000 f 74 goat snp14307-scaffold1570-51709 20 58913901 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272068 Affx-1111833205 AX-519545831 20 58532687 GGTGGCTTAGACAGTAAAGAATCCACCTGCAATGT[A/G]GGAGACCTGGGTTCGATCACTGGGTTGAGAAGACC R 2 1 2 1 103000 f 74 goat 20_58532687_AF-PAKI 20 58532687 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426482 Affx-122940232 AX-123296828 20 58550538 TAGAAGGCTCCTGTAATAGTCCAAACATATGATAA[C/T]GAGTACACAGAGAGGGAAGCATTAAAGAAGATGAA Y 2 1 2 1 201000 f 74 goat snp14306-scaffold1570-21749 20 58944158 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274972 Affx-1111834520 AX-519548553 20 58577223 GGACTGGACAGGCCCCAGGCCTGAGCTGGGAGCCC[A/G]AAGTGGCAGACAGGAGCAGGTCTGAGTCAGCCCAG R 2 1 2 1 102000 r 74 goat GoatD01.039487 20 58577223 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320788198 Affx-122967815 AX-385275217 20 58592077 GAACTAATGTTACACAGACTAATTTCTGAGTCCTT[C/T]GACATCAAAGAAATCACACAGACAAGTCTATGAAG Y 2 1 2 1 101000 r 74 goat snp42538-scaffold563-676242 20 58985896 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445149 Affx-122926162 AX-123315486 20 58641642 TCAGAATACAGAGCAAGTGGGCTTCACCAGGACTG[C/T]GATTTAGCCAACTGTGACAGGGAGTTATATATGTC Y 2 1 2 1 101000 r 74 goat snp42537-scaffold563-626677 20 59035563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779514 Affx-122928723 AX-385266617 20 58677335 TTTGGAAAACAGAAATAACCATAGAATTACATTCC[A/G]TCACAGGATTATACTGGGAGAGGAATATCAGGAAG R 2 1 2 1 101000 r 74 goat snp42536-scaffold563-590984 20 59070583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417548 Affx-122946921 AX-123287896 20 58712642 AGAGTTGCTGATAGATTCGAACATACTTTATGACT[A/G]TGTTCCTATGCATTTTGCAGACAATTACATAAAAC R 2 1 2 1 101000 r 74 goat snp42535-scaffold563-555677 20 59105832 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784685 Affx-122923885 AX-385271732 20 58754284 TTCCAATTAATCTTAAGTATGTGCATTATCTTTAA[C/T]GCTAACCAATAGCTCTCGATCCTTCTTGCTTTTAA Y 2 1 2 1 102000 r 74 goat snp42534-scaffold563-514035 20 59147500 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799526 Affx-122919904 AX-385286456 20 58793294 ATGGAGCCCAATAATTTCTCAGAGTGGGAGTACAG[C/T]AAATGAGCAAGAAGGAAGAGGTACAGTTTAGTGTC Y 2 1 2 1 101000 r 74 goat snp42533-scaffold563-475025 20 59186124 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765315 Affx-122972235 AX-385252838 20 58868438 GATAAAAAGACAACATCCTGCCCATCACAGAGGTT[A/G]CTTTCTAAGAGGTAGAGATGACAATGCAATATGCA R 2 1 2 1 101000 f 74 goat snp42531-scaffold563-399881 20 59261809 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396618 Affx-122962883 AX-123266973 20 58908259 CCTTGTTTATGCCAAAAATAAAACAAAAAATTTGC[A/G]TAAGCCACTACTGCTCTGGTTTTCTCTTACAGACA R 2 1 2 1 101000 r 74 goat snp42530-scaffold563-360060 20 59301665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778576 Affx-122944820 AX-385265688 20 58963535 ATTTGTATACAAATTCATCACAGCCATTAAGCAGT[A/G]CACTTGGTGATCAGAAATGACTTCATAGCCTGGAT R 2 1 2 1 101000 r 74 goat snp42529-scaffold563-304784 20 59357285 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780056 Affx-122935837 AX-385267154 20 59003997 GCATCACAGAGGGTCTTCCATTACAGACTCTCTAA[C/T]TGTGGTGTGCAGGCTGTCACTGCAGTGTGAGGGCT Y 2 1 2 1 202000 r 74 goat snp42528-scaffold563-264322 20 59398740 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386023 Affx-122971492 AX-123256381 20 59036730 TGCATAAGTTTTCTTTTGCTGCACAGGAAATTACC[G/T]CACAATTAGCAGCGCAAAGCAACAGCTGTTTGTTA K 2 1 2 1 201000 f 74 goat snp42527-scaffold563-231589 20 59431316 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788541 Affx-122942304 AX-385275558 20 59114553 GCAACTTACCATTGTTCATACAGTGTTTCAAACTT[A/G]TTTATAATGAAATCCATCTTCTTAATGTCAAACTG R 2 1 2 1 101000 f 74 goat snp42525-scaffold563-153766 20 59509268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425641 Affx-122940891 AX-123295987 20 59161857 ACACCCCATCAGCAAATCCTCTTTGGCATTACCTG[C/T]AGATTATATCCAGACTTGGATCATTTCACTATCTC Y 2 1 2 1 101000 r 74 goat snp42524-scaffold563-106462 20 59556584 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435015 Affx-122933808 AX-123305355 20 59197423 TAGTTTTCTTTCTTCAGAGATTAGTTTGGGATCCA[C/T]GTCACTAACATAGGAGTTGACATCACTTTTCTGGA Y 2 1 2 1 101000 f 74 goat snp42523-scaffold563-70896 20 59592063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431633 Affx-122936142 AX-123301974 20 59237007 ACAAAACAAGAACTCTATCACAAACAAGGGACACC[A/G]TGCTTCTTTCTTTTAGTTTTAAGTCTTCAACAATT R 2 1 2 1 101000 f 74 goat snp42522-scaffold563-31312 20 59632110 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429598 Affx-122937714 AX-123299939 20 59268121 ATCAAATTTTTTTTCAATTGGTAAATATTTCTGAG[C/T]ACCTATTGTGTGTAGGCACAGAACTAACTGTGATG Y 2 1 2 1 101000 r 74 goat snp42521-scaffold563-198 20 59662881 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399855 Affx-122960242 AX-123270210 20 59273574 TGGAGTGCTCAAGGACACTGCTGCTTTCAAGAGTC[A/G]TGTTACAATGCATTTCCAACTGTCTTCCTGCTATT R 2 1 2 1 101000 r 74 goat snp16100-scaffold1695-4174 20 59677475 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427599 Affx-122939368 AX-123297942 20 59337285 ACAGCTGGGAGAAAATATAAAATCAATACATACTT[A/G]TACCACAACTAATAAGATTTCCCACCAAACGTACA R 2 1 2 1 101000 r 74 goat snp16101-scaffold1695-67885 20 59741091 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439492 Affx-122930150 AX-123309829 20 59383201 ATTTATTGGACAAAATATAATGAAATATAAAGAGG[A/G]TACTAAACAATCTTGGCGCTTTTAATCTAGAATTC R 2 1 2 1 101000 r 74 goat snp16102-scaffold1695-113801 20 59787503 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779694 Affx-122926235 AX-385266794 20 59424135 TCAAAGTCTATTAGGAGTCAGCTGGTGAAAGAAAA[C/T]ATGGTCTGCAGAATTTGGATATAATATAGAAAGAT Y 2 1 2 1 101000 f 74 goat snp16103-scaffold1695-154735 20 59828365 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450535 Affx-122922486 AX-123320869 20 59464048 TGAGTCTCCTGCTTCTCCTGCATTGGCAGACAAAG[C/T]GAGGACAGAAATAAAATGTGTTCAAGATGGGTCAA Y 2 1 2 1 101000 r 74 goat snp16104-scaffold1695-194648 20 59868624 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789170 Affx-122950008 AX-385276182 20 59501009 GGAGATGTTCAAGTGGTAGAAATCCATTATATTTT[A/G]ATCAGCTAATATTTTTCATTGGAGCTTTCATAGGC R 2 1 2 1 101000 f 74 goat snp16105-scaffold1695-231609 20 59906994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771807 Affx-122948343 AX-385258964 20 59503403 CTCCAGTGAGCCATTAAAAAATGGTATATTTTTCT[A/G]TTAGTACTAATGGAAATACATTAATCATGAATAAA R 2 1 2 1 103000 f 74 goat snp58499-scaffold952-1712 20 59912979 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798833 Affx-122952077 AX-385285763 20 59531905 TGAATACAGATACTGTTATTTATATACTAGTTGAA[A/G]TGGTGTTTTCTATTTCATGATCATATGTTAAATTT R 2 1 2 1 101000 r 74 goat snp58500-scaffold952-30214 20 59941293 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801892 Affx-122972943 AX-385288799 20 59579255 TTAGCCATGACAGCTGAGCTTAGTCCATTAGGATA[C/T]GTGCCCCTGTGAGGCCTATATTCTATTGGTGTATT Y 2 1 2 1 201000 r 74 goat snp58501-scaffold952-77564 20 59989153 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412076 Affx-122951697 AX-123282426 20 59643773 ACTCACCCAACATGACACAATCACTGTAAAAGTCC[A/G]TTTGGCCAACTAAGGCTGGCAGTACCAGTTCTATC R 2 1 2 1 101000 f 74 goat snp58503-scaffold952-142082 20 60054166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382771 Affx-122973974 AX-123253129 20 59692834 TTCCTTTTCTGCCTGACTCTGTGGATCTTTCTTTA[C/T]AGCCTTGGTTGTAAATGTGTTATTCTGTGGGCCTT Y 2 1 2 1 201000 r 74 goat snp58504-scaffold952-191143 20 60102747 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446573 Affx-122924831 AX-123316909 20 59744025 AAATTGTGAAATTGGCTTTGACACCAAGTAGCATG[C/T]GGTCCTTAAAAACTGATGAATGAATTATTAGCAAA Y 2 1 2 1 101000 f 74 goat snp58505-scaffold952-242334 20 60154831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378317 Affx-122977349 AX-123248676 20 59790304 GAATGAGCTCTACTCATCTTTAAGAATTTTTTTAA[C/T]GACAAGTTACATTTGTTATTCTGCTTTGGCTTCAA Y 2 1 2 1 103000 r 74 goat snp58506-scaffold952-288613 20 60201241 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393291 Affx-122965439 AX-123263647 20 59879802 CTGATATTGTATTCTCTCTTCCTCTTGGAATATCT[A/G]TTTCTGTAGTGCACACTGTGGAACACTTTACTGTT R 2 1 2 1 101000 r 74 goat snp58508-scaffold952-378111 20 60290829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770876 Affx-122920344 AX-385258039 20 59961739 ATTTTAAGTTTCAAGGATGAGTAAAGCCTAGATAC[A/G]CTTGTCAGAGGCTTGTTACTATCTGGTTATCAGAA R 2 1 2 1 101000 r 74 goat snp58509-scaffold952-460048 20 60503532 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780925 Affx-122921871 AX-385268012 20 59991899 GACCTGAAATTCTTGGGACCAGAAGTGGTACCAAC[A/G]TACATGCTAGGCAGAAGGATCTTCAGGATCCGTGA R 2 1 2 1 101000 f 74 goat snp58510-scaffold952-490208 20 60534417 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431427 Affx-122936518 AX-123301768 20 60023145 CAAAGTTGATGAGGGAAAAAAAAAAAAAAAAAGAT[C/T]AGGGTAGATCCTGAAGATAGGATTAGATTTCAAGT Y 2 1 2 1 103000 r 74 goat snp58511-scaffold952-521454 20 60566178 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452204 Affx-122920814 AX-123322537 20 60052807 CCAGTTAGGACACAGAGAATAAACCTTTTTATCCT[A/G]TGCGTTAGTCACCTATGTACCTCTTACACATAATG R 2 1 2 1 101000 r 74 goat snp58512-scaffold952-551116 20 60595995 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423666 Affx-122942336 AX-123294012 20 60093658 TAGAAATACACGAAGCCCTCTCCTCCACTCTCATG[A/C]ACAGCTCTAATAAGTGCTGTAGTGGAGAAACTGGA M 2 1 2 1 102000 f 74 goat snp58513-scaffold952-591967 20 60637579 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381579 Affx-122974807 AX-123251937 20 60145650 CACTAGAAATAGCAACCAAGCTAAAGGCAAAATCA[C/T]GTCATCTCTCACATATCAGAAACTGTGCCAAGTGT Y 2 1 2 1 101000 f 74 goat snp58514-scaffold952-643959 20 60688250 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782934 Affx-122965862 AX-385270004 20 60188571 ATATCCCTTTCATCTGGAGAGTTTTAGGTATTTTA[C/T]AATGCCATGTAAACCTCAGGTCAGAGACTCCCACT Y 2 1 2 1 101000 r 74 goat snp58515-scaffold952-686880 20 60730842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407253 Affx-122955357 AX-123277604 20 60223634 GACTGAATGAAGTGAATCTGACCAATAGCTGTTGG[C/T]AATGTGGAATACTATGTTTAGAAGGAAACTGGGGA Y 2 1 2 1 101000 r 74 goat snp58516-scaffold952-721943 20 60766814 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407104 Affx-122954886 AX-123277455 20 60258067 TGAAACACAAAATGCTTTAATGCTCCTTTTGCTAA[C/T]GCAGTGAATGATGCTTTCTAATCTGGGCTTTCTCT Y 2 1 2 1 101000 f 74 goat snp58517-scaffold952-756376 20 60799393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378301 Affx-122976854 AX-123248660 20 60312816 TTGTACAGACAATGGACCAAAGATCACTAAGTCAA[C/T]GAAATGTCCTAAAGTGAGTATAGGTAAAGTTGAAA Y 2 1 2 1 101000 f 74 goat snp58518-scaffold952-811125 20 60854352 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776377 Affx-122947239 AX-385263504 20 60393376 CCTGTTGAGTGGTGAAGGGAAGATAATGAAGATGC[A/G]TTTGTGTAAAGGACCACAACTGAAGAATTATTTTG R 2 1 2 1 101000 f 74 goat snp58519-scaffold952-891685 20 60936000 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804055 Affx-986696363 AX-385290730 20 60401493 TGGAGCAGCCGTGAATAGATACCCCATGACCAAGG[A/T]AATCGAAACTCAACTAAGACGGTTGGTGTTGTGAG W 4 1 2 1 600010 r 74 goat 20_60401493 20 60401493 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 320763673 Affx-986698202 AX-385251502 20 60401525 AGGTAATCGAAACTCAACTAAGACGGTTGGTGTTG[A/T]GAGACAGCATCAGAGGGCAGACACATTTAGACCAT W 4 1 2 1 600010 f 74 goat 20_60401525 20 60401525 Ancestral_priority_1043 ancestry 0.612 recommended IMAGE 10K 10K ancestral 320766776 Affx-986698169 AX-385254109 20 60401910 ACAATACCCAGTTGTGGATGTGACTGGTGAAACAA[A/G]CAAGGTCTGGTGCTGTAACCAGCAATATTGCATAG R 2 1 2 1 600010 r 74 goat 20_60401910 20 60401910 Ancestral_priority_1043 ancestry 0.606 recommended IMAGE 10K 10K ancestral 320766780 Affx-986698171 AX-385254113 20 60401949 GGTCTGGTGCTGTAACCAGCAATATTGCATAGGAA[A/C]CTGGTATGTTAGGTTCAGGAATCAAGGCAAAGTGG M 2 1 2 1 600010 r 74 goat 20_60401949 20 60401949 Ancestral_priority_1043 ancestry 0.592 neutral IMAGE 10K 10K ancestral 320766824 Affx-986698195 AX-385254147 20 60402925 AAGAGAAGAGAAAAGCAAAGGAGAAAATGAAAGAT[A/G]TAAGCCGCTGAAAGCATCGTTCCAAAGAATAGCAA R 2 1 2 1 600010 r 74 goat 20_60402925 20 60402925 Ancestral_priority_1043 ancestry 0.528 neutral IMAGE 10K 10K ancestral 320763668 Affx-986698197 AX-385251497 20 60402952 TGAAAGATATAAGCCGCTGAAAGCATCGTTCCAAA[A/G]AATAGCAAGGAGTGATAAGAAAGCCTTCAGGAGCG R 2 1 2 1 600010 f 74 goat 20_60402952 20 60402952 Ancestral_priority_1043 ancestry 0.526 neutral IMAGE 10K 10K ancestral 320766835 Affx-986698201 AX-385254158 20 60403154 CAGAAGCAGAAGATATTAAGAAGTGGCAAGAATTC[A/G]CAGAAAAGCTGTACCAGAAAAATCTTCACGACCCA R 2 1 2 1 600010 r 74 goat 20_60403154 20 60403154 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 38405241 Affx-122956883 AX-123275593 20 60427163 GGTAAAGTTAGCCCAAGAAGTAGGAAAGCCCCACC[A/G]TGAGTGTAGGTAATCTGAGAACCGTCTGAGACCTG R 2 1 2 1 101000 r 74 goat snp58520-scaffold952-925472 20 60967107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395645 Affx-122963784 AX-123266000 20 60456485 GAGATCCTCTTCTGTATGTTGTCTATACACTTATT[C/T]AAATTATACAAATAAAAATAACCTAACAAAACATT Y 2 1 2 1 103000 f 74 goat snp58521-scaffold952-954794 20 60996742 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438456 Affx-122931247 AX-123308794 20 60486220 TTTACATTTGCATGATGCTTCAGAGATCATAAAAC[A/G]CTTGCTATATTTTTTTCATTTATATTCTGTAGAAC R 2 1 2 1 201000 f 74 goat snp58522-scaffold952-984529 20 61026654 C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392549 Affx-122966091 AX-123262906 20 60523935 TCATAACACTGTTTCTTTTTAAGGCTGTAAAACTC[A/G]CCTTGGCCTATCTGACTGCAGTTGCATTTTCACAT R 2 1 2 1 101000 r 74 goat snp58523-scaffold952-1022244 20 61064861 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442170 Affx-122928307 AX-123312507 20 60554379 GAAGAATGCGCAAATTGAGTGGAGAGTGTGATATC[C/T]ACATATTATGGATTGCATGGGTTTTTGTAACTCCA Y 2 1 2 1 101000 r 74 goat snp58524-scaffold952-1052688 20 61095136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419285 Affx-122946244 AX-123289633 20 60608543 CTTAAAGTAGGGATGCGTTTCATACATTTAAATCC[A/G]TAAGTTCATAGTGATGGGGGAAACTGCATTGGATA R 2 1 2 1 101000 f 74 goat snp58525-scaffold952-1106852 20 61149926 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781948 Affx-122975954 AX-385269029 20 60657765 TTTCATATCAAGTCCAAATATATGAATGAAAAGTA[C/T]GATCTTTCAGACTATTTGGAATGTATAGTTTGGAT Y 2 1 2 1 303000 f 74 goat snp58526-scaffold952-1156074 20 61197512 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435700 Affx-122933315 AX-123306039 20 60716370 GTCAATTTGAGACCTCCAGGCCAGTCTGCGCTTCC[A/G]CGGAGCTCCCCGGAGGCGGCCCCCTCTCTCCTCGC R 2 1 2 1 101000 f 74 goat snp58527-scaffold952-1214679 20 61256370 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801215 Affx-122969024 AX-385288127 20 60763580 GATCATAAAGAGCTAAGCAGTTTCTACAGGCTCTC[G/T]TTCCATCTTTGTCTTTGCCTCAATCTCTGTCTTTG K 2 1 2 1 101000 f 74 goat snp58528-scaffold952-1261889 20 61304254 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391355 Affx-122967292 AX-123261712 20 60813718 ATACACAAAAAAATCAATAGCTTTCCTATGTGCCA[G/T]CCATAAATAACTAGAAAATGTAAAACGGTATGAAG K 2 1 2 1 201000 r 74 goat snp58529-scaffold952-1312027 20 61354984 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395958 Affx-122963567 AX-123266313 20 60852951 CAGCAATATGTTTTCTGGGAAGGCACTGTGTGTGA[C/T]GTAGCTTGAGCACTGGATTAGGAGCTGCACTCAGC Y 2 1 2 1 101000 r 74 goat snp58530-scaffold952-1351260 20 61394312 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380396 Affx-122975325 AX-123250754 20 60904604 GTCCATCAGGACAGGAAAATAAACTGGGAGATACA[G/T]TCAGATACCAGGAGACCAGTTGATTTATCAGTCAA K 2 1 2 1 101000 f 74 goat snp58531-scaffold952-1402913 20 61446157 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400959 Affx-122960114 AX-123271312 20 60938696 GTTAGGCAAATATGGAGAGAAAAGTTAGTTAAGAA[C/T]AAAGCAAAGACACCACTTCATCAAATAGATGAGAG Y 2 1 2 1 101000 f 74 goat snp58532-scaffold952-1437005 20 61480406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386380 Affx-122970842 AX-123256738 20 60993394 GTCAGTTTGGAAGAAGGCAGATGATCTCAAGTGGT[A/G]CTGAGAACTGGGGAAACAGAATCCACTTTCAGTCC R 2 1 2 1 101000 f 74 goat snp58533-scaffold952-1491703 20 61535050 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390568 Affx-122967206 AX-123260925 20 61029857 TTCTTCCCCTCACAGCTCCCATGTCCTGTGAACTC[C/T]ACTTCAGGTCTCTTTTGCTTTTATCCCTTTATCTC Y 2 1 2 1 101000 r 74 goat snp58534-scaffold952-1528166 20 61571369 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446638 Affx-122924784 AX-123316974 20 61060801 CCATTAACCATATTTCATTTCATTTTCTGCTCCCT[A/G]TCATGTCTCCAAAGGGTGCTGAGGCTCTCAATCCT R 2 1 2 1 201000 r 74 goat snp58535-scaffold952-1559110 20 61602257 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388150 Affx-122969461 AX-123258508 20 61090141 GTGTCCTGTGTCTTAATTTCCAACTGCTGATTGGA[C/T]CAGAAATGGGTATCCAACCCAAGGGTGGCTCATCC Y 2 1 2 1 201000 f 74 goat snp58536-scaffold952-1588450 20 61631602 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389352 Affx-122968470 AX-123259710 20 61122131 TGCCTTTATCCCAGTGTTTCCAAACTTAAAAGTGC[A/G]TAGGAATGACCAGGAGGCTTATTGAACACTAATTG R 2 1 2 1 101000 r 74 goat snp58537-scaffold952-1620440 20 61667246 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440332 Affx-122929675 AX-123310669 20 61162524 AAATACATGGTTTATGACAGTGTTGAGGAAATAGC[A/G]CAGAAAGAAGGAGAAGGTAGGATAAAGAATAGAGA R 2 1 2 1 201000 f 74 goat snp58538-scaffold952-1660833 20 61707512 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272070 Affx-1111833206 AX-519545834 20 61174985 TGGCTCAGTGAGAAATATGGTAATCCTCCCTGTGT[A/G]TGTGTCCTTTTATTAAATAATTGAATATGTATCCC R 2 1 2 1 101000 f 74 goat 20_61174985_AF-PAKI 20 61174985 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38385119 Affx-122971778 AX-123255477 20 61262625 GTGGATGAAGAATCCAGGCAAGGTGCATCTGGGTA[G/T]TTCTTTTCTTGCATGTGCCCTTTAAGTGAGGCTGG K 2 1 2 1 101000 r 74 goat snp58540-scaffold952-1760934 20 61807703 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383312 Affx-122972699 AX-123253670 20 61319727 TCTAGATCAGAGGCTTACACACTTTAAACAAGCAT[C/T]GTGATCACCCTGAGAACGTGACAAAAGGCAGATCC Y 2 1 2 1 101000 f 74 goat snp58541-scaffold952-1818036 20 61864640 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407711 Affx-122955013 AX-123278062 20 61326232 GACAACTATGAGAACTCAGGAGCGTTGGAGCTTTG[A/G]GATTCTGTACCTGAATGTGTGCGCTTGATACTGTT R 2 1 2 1 101000 r 74 goat snp25352-scaffold2613-1277 20 61870962 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408404 Affx-122954479 AX-123278755 20 61365126 GTAGAGTAATCCTCTAAGGTGGGTGATTTGGCCAA[C/T]GGAGCTCTAACTCAAATGAGAAAAAACATATACCA Y 2 1 2 1 101000 r 74 goat snp25353-scaffold2613-40171 20 61909553 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421122 Affx-122944203 AX-123291469 20 61401829 AGCCAAAGAAAGAGGAAGTAATCCCAATTGTCCCA[C/T]GAGGCTGGCAGGACTAGTATAAGGAAAGCTGAGAA Y 2 1 2 1 101000 f 74 goat snp25354-scaffold2613-76874 20 61946705 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772333 Affx-122963218 AX-385259486 20 61446743 GGATCACTGAAGCCTAGTATTTGCTCTTCATTTGA[A/G]TATGAGATATTTCCTAAGGATGGTAGGGCCCACCT R 2 1 2 1 101000 f 74 goat snp25355-scaffold2613-121788 20 61991642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277333 Affx-1111835858 AX-519550837 20 61494100 CTGTGAGCCTAACATGAGCACTGGCTTCCCAGGTC[A/G]TGCTAGCAGTGAAGAACCCACTTGCCAGTGCAGGA R 2 1 2 1 102000 f 74 goat Random2.2K-1881 20 61494100 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432485 Affx-122935592 AX-123302826 20 61507548 CTGTTGAGTCTAACAAGAGACCTGGGAGAAAGAGG[A/G]CAGTCATGTTAGGGAGAGAATGGTCATACAGATAA R 2 1 2 1 101000 f 74 goat snp25356-scaffold2613-182593 20 62054554 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423573 Affx-122942407 AX-123293919 20 61549609 CAGGAGATGCCTTATTTCAGCATCAGCTCCCACTC[A/G]CCTTCCTGTTTAGGGATGTGAACCCTAGCATGTAC R 2 1 2 1 201000 r 74 goat snp25357-scaffold2613-224654 20 62097472 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775774 Affx-122977548 AX-385262905 20 61600762 TTAATTCTTTCAACAAAACCAAGATCTTTATTTAC[A/G]TGAGAGAAGTGGCTTTGTATGCTGTTCCTGCCTTC R 2 1 2 1 101000 r 74 goat snp25358-scaffold2613-275807 20 62149913 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409086 Affx-122953332 AX-123279437 20 61640500 ATCTCACCTAAAACTGGCATGCTTTCCTCTTAAGA[C/T]ATCTTGGTAAACCCACGGTTTTTAATGCCAATTCT Y 2 1 2 1 101000 r 74 goat snp25359-scaffold2613-315545 20 62189451 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450468 Affx-122922942 AX-123320802 20 61693027 GAAGCGGAGCACACACAAATTCTGAATATTTCTCT[A/G]TGCATCACAGCCCAGCCGTGTGTTTCTCAGTCAGA R 2 1 2 1 101000 f 74 goat snp25360-scaffold2613-368072 20 62241867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384441 Affx-122973102 AX-123254799 20 61735944 ACCTCTTTTAAGTGCTGTCATTGGAAAATAAATAT[A/G]CTGCATTTGGGGGTTTTCAGGCAGAGTTTCTGTCA R 2 1 2 1 201000 f 74 goat snp25361-scaffold2613-410989 20 62284755 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433630 Affx-122934588 AX-123303971 20 61782213 CCAGCAGCTGCACAGCCTGACTTCAGAATTCACCT[A/G]CAGATTTTGCCCTCCCACCTGAGCTCCCCAAATAC R 2 1 2 1 201000 f 74 goat snp25362-scaffold2613-457258 20 62331036 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773153 Affx-122967858 AX-385260296 20 61818538 TGTGGATTTTCCAATACTAATGTTAGCTTGAGGCA[G/T]GCAATGAGAGTTTGAGTCCATATTCTCGCATCAGC K 2 1 2 1 101000 r 74 goat snp25363-scaffold2613-493583 20 62367303 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388453 Affx-122969254 AX-123258811 20 61835205 TGGGTCCTCTCCTCCTCTCTTTTCAGATCTTCATC[A/G]TTGGTCCTGATTTTCACCTTGACTTTCTAGACTCT R 2 1 2 1 201000 r 74 goat snp30988-scaffold342-1108583 20 62383786 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379640 Affx-122975951 AX-123249998 20 61903687 GCGGCTTTGCATTTCATTCACTTGCTTGAATTGCA[C/T]GCGTGTAGCTGAGCCAGTTCTCAGCTGGGGAAATG Y 2 1 2 1 101000 f 74 goat snp30986-scaffold342-1040101 20 62451190 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406239 Affx-122956110 AX-123276591 20 61980510 ATCTGATGTCCATAAGATCCTGAGATACCAGAGCT[G/T]CTCTGCCCTCAGGGATGAAGGAGCCGAACCTATGA K 2 1 2 1 201000 f 74 goat snp30984-scaffold342-963278 20 62528411 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447277 Affx-122924935 AX-123317613 20 62014356 AGCGAAGTTCAGCAGCAAAGGTCCAGCTATTCCTT[A/C]GGAAGGAATGTTGTTAAAGAAAAGGGAACCAGTTA M 2 1 2 1 101000 f 74 goat snp30983-scaffold342-929432 20 62562410 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412991 Affx-122951022 AX-123283340 20 62049769 AACAACTGCTTTTCAGAAAAGCAGGGCACCCGACT[G/T]CTGTGAGGCAGTAAGCAGTCTAGGGCAGCTCTGGG K 2 1 2 1 101000 f 74 goat snp30982-scaffold342-894019 20 62597769 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428242 Affx-122939424 AX-123298585 20 62102347 TCAAAGGACCGGCACATTTTCAACCTGTCCATTTA[C/T]GGAGCCCCTGCCAAGTGGCTTTCTGTTGTTGTTGG Y 2 1 2 1 101000 f 74 goat snp30981-scaffold342-841441 20 62650113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435078 Affx-122933725 AX-123305418 20 62137065 GTGTATTTGGAGTATTTGATCAACTTTCTGGCTGC[C/T]GATTTTGGAAGGACCCCAGGCACGTGTCACTCTTA Y 2 1 2 1 101000 f 74 goat snp30980-scaffold342-806723 20 62685105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410594 Affx-122952116 AX-123280944 20 62177945 GCCAAAATGTTGTGGTGAATTCTTGAGACAATCTA[C/T]ACCCTCACAGCCAAAGAGTAAGAATGAGCTGATAA Y 2 1 2 1 201000 f 74 goat snp30979-scaffold342-765843 20 62726733 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377044 Affx-122977700 AX-123247403 20 62228451 CTCAGATTGTGGAGCCTTGGGCTAAAGGCTTGACA[C/T]GACCTCTCTCAGCTAGTGCTCACCACCTATGAAAA Y 2 1 2 1 101000 r 74 goat snp30978-scaffold342-715337 20 62777776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400703 Affx-122959932 AX-123271058 20 62286132 TGTTTGTTTTATGAATGATAACTTAGAAGTTCTCA[A/G]AGAAAATGGTCAGCAAAGGTCTTAAAAAACCATAA R 2 1 2 1 101000 f 74 goat snp30977-scaffold342-657656 20 62835994 C T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380346 Affx-122975363 AX-123250704 20 62331021 AGCCAGGTATTCTTCAAGATGAAACACTTTAAATG[A/C]GGAAAAGCATTTTATTTTATATTAATAAAAGAAAA M 2 1 2 1 101000 f 74 goat snp30976-scaffold342-612767 20 62880892 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434490 Affx-122934621 AX-123304831 20 62385308 GATACTGGGCAGCTGGACTTCTGAGTGCTTGCAGA[C/T]GAACAGGCGAGCAGAGAGGAGAGGCACAGAAACAG Y 2 1 2 1 201000 f 74 goat snp30975-scaffold342-558480 20 62935257 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375581 Affx-122978738 AX-123245940 20 62431083 CTCCTCGCCTCGTCAATGTACGGCTTGTCTTCAGG[C/T]GAACAGTCTTCTCTCTTGCGATGCACAAAGCCATG Y 2 1 2 1 101000 r 74 goat snp30974-scaffold342-512705 20 62980567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416697 Affx-122947569 AX-123287045 20 62487116 CAACAGGAAGAATTAGACCTTGCAGAGTGATTGAC[A/G]ATTCATCTCACTACAGATTTTTCACTTTGAGACTC R 2 1 2 1 101000 f 74 goat snp30973-scaffold342-456672 20 63035190 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804067 Affx-986696369 AX-385290738 20 62516832 TTTCCTACTCTTACTCTCTCTTTCAGGCTAGTTCC[C/T]ATCTGGAGTACAGAGATCCGCCATGTCTACTTATT Y 2 1 2 1 600010 r 74 goat 20_62516832 20 62516832 Ancestral_priority_1043 ancestry 0.608 neutral IMAGE 10K 10K ancestral 320763682 Affx-986698211 AX-385251509 20 62516855 CAGGCTAGTTCCTATCTGGAGTACAGAGATCCGCC[A/G]TGTCTACTTATTTGCCTGGGTTTCTAAGACCTGAA R 2 1 2 1 600010 f 74 goat 20_62516855 20 62516855 Ancestral_priority_1043 ancestry 0.642 neutral IMAGE 10K 10K ancestral 38391016 Affx-122966884 AX-123261373 20 62542338 AGTGGAATTTAAGAGGGGATAAGTCAAATTGATCC[A/G]TGGACTATTAATTATACAAGAATAAGGCATGTATA R 2 1 2 1 101000 f 74 goat snp30972-scaffold342-401450 20 63089330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418794 Affx-122946178 AX-123289142 20 62582197 GTGTAGGGAAGCAATGGTGAGAAAATCAGACATGG[C/T]CCCAGCCTCTCAGATCTTTTGATCTGGTACAATGG Y 2 1 2 1 101000 f 74 goat snp30971-scaffold342-361591 20 63128883 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785489 Affx-122936550 AX-385272534 20 62618669 TTATACTTTGCAATAATAAGTGCCCAGATACCTTA[C/T]AGCTGCTCACTTGGCACTGCATGATCAAGCAATAA Y 2 1 2 1 101000 r 74 goat snp30970-scaffold342-325119 20 63166013 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444000 Affx-122926906 AX-123314337 20 62728890 ATCTTACAGGGCTTTTGTTTGGAGAGTAATCAAAG[C/T]TGAGATGTTCCCGGGGAGCCCAGGTGATCAGGACA Y 2 1 2 1 101000 f 74 goat snp30968-scaffold342-214898 20 63276488 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401046 Affx-122959658 AX-123271399 20 62760752 AGCTGGATTTTTCCAAGAACTCACACTTTTTGTTT[A/C]ATTGAAGTATATATTTTGATTTACAATATTATGTT M 2 1 2 1 103000 f 74 goat snp30967-scaffold342-183036 20 63308453 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452841 Affx-122920728 AX-123323174 20 62817584 TCCTCTCTTAAATATCCTTGAAGCACAAAAACTCA[C/T]AGCCCTGAAAACTAGGAAATAACCAGAGGTAGCAC Y 2 1 2 1 101000 f 74 goat snp30966-scaffold342-126204 20 63365956 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396836 Affx-122963268 AX-123267191 20 62855814 CCACAAAACCTAAATAAATAAATTACTTGACCCTC[A/G]TGCAGAAGCTGATGCTGCAGTTTTGAGGCAGAATA R 2 1 2 1 101000 r 74 goat snp30965-scaffold342-87974 20 63404154 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393979 Affx-122965041 AX-123264334 20 62901776 TAGCTGAGCATCACTGTGCCACACAGGCACTGCCA[C/T]CTCCCTTATCTCCCAGGCCTGGCCTTCACACCCTG Y 2 1 2 1 102000 r 74 goat snp30964-scaffold342-42012 20 63450721 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430095 Affx-122937529 AX-123300436 20 62932852 AATATTCTTCAAATGAAATTAACTGACCAACAGGT[A/G]CTTTGAGGCTTTCAGGCTACTACTCAACTCAAATG R 2 1 2 1 101000 r 74 goat snp30963-scaffold342-10936 20 63482205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434009 Affx-122934233 AX-123304350 20 62959708 TTGACACACCTACACCCCAGGCTCGTCTCATATTT[A/G]TTTAGTCAAAATCTCTGAGGGATATTTGAGAATCT R 2 1 2 1 303000 r 74 goat snp6996-scaffold1258-15821 20 63509323 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448665 Affx-122923339 AX-123319001 20 63051625 GATTACCAGCATCTCATGTCCTTGGTTCCTCCAAA[G/T]ATCCCCGGTGGGAGAATGGGTCAACACCCACGCTT K 2 1 2 1 201000 f 74 goat snp6999-scaffold1258-107738 20 63601792 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431417 Affx-122936527 AX-123301758 20 63097195 AATTTTAAAAAAATCACAAAAGAACAATCTATAAT[A/G]CCATGTGCACAAGTCAGCAGAAAATATAGATTCAG R 2 1 2 1 101000 r 74 goat snp7000-scaffold1258-153308 20 63639967 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398900 Affx-122961020 AX-123269255 20 63128551 GCATCTCTTTGATCCCCAGGCACTTCCTGGGAAGT[A/G]TATCAGAGCTGTGATCTCTGTCCTGAAAACAAGTA R 2 1 2 1 101000 r 74 goat snp7001-scaffold1258-184664 20 63671078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443621 Affx-122927299 AX-123313958 20 63186182 AAGTGTTATGCAAATATTGGGTTGGTGGAGGCCAG[C/T]AGAGAAGGGGAATTGGCGGAAGCTGACTCATGAGA Y 2 1 2 1 101000 f 74 goat snp7002-scaffold1258-242295 20 63729003 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801379 Affx-122920688 AX-385288290 20 63237467 AAGGGTCTTCTGAAAGTTTTAGTCCAATATTGACC[A/G]TTTCTCTGCTTTTCAGCTCTGAATTTTGGTGGTGC R 2 1 2 1 101000 r 74 goat snp7003-scaffold1258-293580 20 63778115 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803032 Affx-122949212 AX-385289908 20 63267655 TCTCATTTCTCCTAGTAACTGAAAATAACATTCAG[A/C]GCTGGCCATTAAGATTCCCTGAGACAGTTGTATTC M 2 1 2 1 101000 r 74 goat snp7004-scaffold1258-323768 20 63807970 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765433 Affx-122969788 AX-385252936 20 63319007 ATGGTCACAGATAGAAAATCCCATTGTTGAGGCCA[C/T]GTTTATTTGACAGGTGCTGTCAGTCCCCTAGGCAT Y 2 1 2 1 101000 f 74 goat snp7005-scaffold1258-375120 20 63859238 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391009 Affx-122966890 AX-123261366 20 63367511 TTGAAGCTGGCTGCTTTAAAAAATTGAATCAGTAC[A/G]CTTCTGCTAGACTGTTTTTTGAACTATATGTGGGT R 2 1 2 1 101000 r 74 goat snp7006-scaffold1258-423624 20 63906508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769950 Affx-122943113 AX-385257119 20 63397121 GTCTCAGATTGAAATTATCTCTGTGTTCTGTGGAG[C/T]GTTTGATTTCTTTGTGTCTTCAGGATTCTATGAAA Y 2 1 2 1 101000 f 74 goat snp7007-scaffold1258-453234 20 63935778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428128 Affx-122939065 AX-123298471 20 63405813 AGTATCACAGATGTGTACTCACACACATTCACAGA[C/T]GTGCCCTAGAATAAGAGATACTTCTCAAGACTATT Y 2 1 2 1 201000 r 74 goat snp6218-scaffold1219-594498 20 63944255 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405656 Affx-122956574 AX-123276008 20 63456074 ACTCTGAATTTGTTCCTGCCTGCCTTTTGAATCAG[C/T]GTAGTGAGTTCAACCAGACCCAACAGACGAACATA Y 2 1 2 1 101000 f 74 goat snp6217-scaffold1219-544237 20 63994123 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378736 Affx-122977034 AX-123249095 20 63487315 CCGGGACTGGAGGCCTCCTGGTGGGGCGGGGCATC[A/G]CTCTCTGAGGAAGGCAGGCCATTCAGTGCCATGGG R 2 1 2 1 101000 r 74 goat snp6216-scaffold1219-512996 20 64025587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408393 Affx-122954487 AX-123278744 20 63518735 CTGCTGTGAGGCCAACTGAGACCATCAGTGGAGAG[C/T]ATTTGTACGTTAACCGAAAGCACTTGTACACGCCA Y 2 1 2 1 101000 r 74 goat snp6215-scaffold1219-481576 20 64056698 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384261 Affx-122972316 AX-123254619 20 63570583 AGTCTACGCTTTGGTATCCTATCCTCTCTACTCTG[C/T]ACAAGAGAGGTAACTACAGGTTCCAGCCCCCTCTC Y 2 1 2 1 101000 f 74 goat snp6214-scaffold1219-429728 20 64108001 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392412 Affx-122966204 AX-123262769 20 63643304 GTTGCCAAAGAGTGGAACATGACTTACCAACTAAG[C/T]AACGATACACAATTGAATCTGGTTCACAGAACAGA Y 2 1 2 1 201000 r 74 goat snp6213-scaffold1219-357007 20 64180705 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416078 Affx-122948330 AX-123286427 20 63699591 GTCCCAATCAAAGCAAGCACTCAGCCTTTCCTTTA[C/T]GCAGGATTGGGGTTTTACCCTCTTTCCTACACTGA Y 2 1 2 1 101000 f 74 goat snp6212-scaffold1219-300720 20 64236987 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420079 Affx-122945111 AX-123290427 20 63747102 CTTTGAGGGATTTGCATTTTATCTGATTTCCTTTT[A/G]CTATCTATTTCTTATTGATTTGCAAACACCCTAAA R 2 1 2 1 201000 r 74 goat snp6211-scaffold1219-253209 20 64283595 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272072 Affx-1111833207 AX-519545836 20 63758411 AGAGGAGCCTGGGGGGCTAGTCCATAGGGCTGCAA[A/G]GAGTTGGACGCGACTGAAGAGACTTCGCTAAACAA R 2 1 2 1 303000 f 74 goat 20_63758411_AF-PAKI 20 63758411 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395223 Affx-122964484 AX-123265578 20 63779957 TATTTTTTCAACATGAGTGCCTTGAAGTGGATGCC[G/T]CAGCAATCCACCTCCCCTTCAAAGCATTGCTTCTT K 2 1 2 1 101000 f 74 goat snp6210-scaffold1219-220354 20 64316075 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783364 Affx-122935823 AX-385270428 20 63815131 AAGCAATCAACTCTGGATTTCCTTATGAATCCATC[A/G]TAGAGATATTTTAATGCATGAAAGCTATACTATAG R 2 1 2 1 201000 r 74 goat snp6209-scaffold1219-185180 20 64351661 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790319 Affx-122934450 AX-385277322 20 63866352 GGGTAATACTAGCTATCAGCTTGTACTCAAATTGG[A/G]CTGACAGAACAATTCCATATGACTTCTACACATGG R 2 1 2 1 101000 r 74 goat snp6208-scaffold1219-133959 20 64402591 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431181 Affx-122937181 AX-123301522 20 63919897 CTGGATGGCAAGAACTATATGAGGTTTTTGGCACC[A/G]TCATCATCAACACCTGGTTATTCCTTGCATAGAAC R 2 1 2 1 101000 f 74 goat snp6207-scaffold1219-80414 20 64457161 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778659 Affx-122936095 AX-385265770 20 63954830 CCTGGTCTAAGGCAAAAGCACAAAATTTGATGACG[C/T]ACAGATAATTTAATGTAAACTGTAGCTAAAATATG Y 2 1 2 1 101000 f 74 goat snp6206-scaffold1219-45481 20 64493273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375503 Affx-122979128 AX-123245862 20 63987714 AAGATCCAAATACAACAATTGGCCAGAGCTAGCTA[C/T]ATAATTTGTAGGACAAAATAGAAAATAAAAAGGTA Y 2 1 2 1 102000 f 74 goat snp6205-scaffold1219-12597 20 64526974 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801614 Affx-122947647 AX-385288522 20 64055487 AAAATGAGTAAATCCTCTGATTTCTAAGGATTATC[C/T]AAAGAATATCTAAGGATTAATATTTCAGTCAATTT Y 2 1 2 1 201000 r 74 goat snp29475-scaffold3195-55077 20 64607772 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424899 Affx-122941312 AX-123295245 20 64084246 ATGAGATGACCAGACTAGCAAAGTGTGCATAAGCT[C/T]AAGTTAAAAAAAAAAAAATGGCAGGAGGAGATAGA Y 2 1 2 1 101000 f 74 goat snp29476-scaffold3195-83836 20 64636880 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446509 Affx-122925035 AX-123316845 20 64144032 AGCTAAAGTGATTTAGCTTGATGGTGATTTTCAGG[A/C]GCTCTCTTAAATGACAAAATTAATCACATCCACTT M 2 1 2 1 101000 f 74 goat snp11367-scaffold1412-31953 20 64697469 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801811 Affx-122961721 AX-385288719 20 64187922 GTGCCAGGGAATCCCAAACATGTACAAACACATCT[A/G]TAATTTAAACTCAAAATCATGGAACAGAACCCAGT R 2 1 2 1 101000 f 74 goat snp11368-scaffold1412-75843 20 64741632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381387 Affx-122974384 AX-123251745 20 64221510 TATGAGGTGAATTCTATTGATCTGTCTGCAAATTC[A/G]TCCTCTGTCATCTCCAGTCTGCTATTGACCCAATC R 2 1 2 1 101000 r 74 goat snp11369-scaffold1412-109431 20 64775742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399265 Affx-122960560 AX-123269620 20 64250831 AATGGGTCAGAATTTTAAAATTTATCCGAACAAAC[A/G]AATTCAGGATTTCTGGTGCATGGATAGATTTGGCC R 2 1 2 1 201000 r 74 goat snp11370-scaffold1412-138752 20 64805369 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433629 Affx-122934589 AX-123303970 20 64302421 TTTCATCTGCAGGTAACAGGAAGCCCAGCTGGCAG[C/T]GGCTTCAACCATAGAAACATCCGTTCACATGTTGA Y 2 1 2 1 101000 r 74 goat snp11371-scaffold1412-190342 20 64859386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788249 Affx-122949105 AX-385275268 20 64344441 CCTTTAGCACAATATCCTTGTTTTTGCCAGCAGAC[A/G]TAAGTAATTTGATCGTGCTAGGAAATTGGCTAAAG R 2 1 2 1 101000 f 74 goat snp11372-scaffold1412-232362 20 64902194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406935 Affx-122955077 AX-123277286 20 64375032 GAGTGGGGAAAAGGAAGTGGTGGTTACTATAGGGA[C/T]AAGATGGCCTGGTGGATTTGATGGAGACAAAGATG Y 2 1 2 1 101000 f 74 goat snp11373-scaffold1412-262953 20 64933508 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381504 Affx-122974867 AX-123251862 20 64417463 TCATTCCTTCCTTTCATTGAAAACTGTAGCCTCTG[C/T]GTCACTGGTTTCTTCCACACCTTATCTACGTTCTA Y 2 1 2 1 101000 f 74 goat snp11374-scaffold1412-305384 20 64975908 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453782 Affx-122919585 AX-123324115 20 64446898 ATTTGTGGCTTCTTTGCTTCTCTGCTCCATAAGCA[C/T]GTGCTCTTTCCTCACCATCTCCTCCCTTCTGGCTG Y 2 1 2 1 101000 f 74 goat snp11375-scaffold1412-334819 20 65005619 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796718 Affx-122923716 AX-385283663 20 64482317 CCCACCACTGTGCCTTCCGTGAAAAGTAGGTCCTG[C/T]GAGAATCAATGATAGAAGTTAAAAAGGAACATTCC Y 2 1 2 1 101000 f 74 goat snp11376-scaffold1412-370238 20 65041642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796503 Affx-122959344 AX-385283452 20 64515757 CACCTAGAAAAATATTGCTCTCGTTATTATTTGAA[A/C]GGGCCTTCAACGAAAGTAAGACATCACCTTAGTTT M 2 1 2 1 101000 r 74 goat snp11377-scaffold1412-403678 20 65074592 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404787 Affx-122956673 AX-123275139 20 64566312 TCTGAAGGTCATGTGTGACCTCTGTTGCAGGATTT[A/G]TTTTCCACAATTTAAAAATGTAAAAATTATTCTTA R 2 1 2 1 101000 f 74 goat snp11378-scaffold1412-454233 20 65125963 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381097 Affx-122974592 AX-123251455 20 64613811 TTATAAAGCTATCAAAGTCATGTGTTTGCATGGGC[A/G]TTAGAATAGATTATTTCTAGGCCCCCTGGGTCTTT R 2 1 2 1 201000 r 74 goat snp11379-scaffold1412-501732 20 65173695 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431993 Affx-122935937 AX-123302334 20 64651676 TTTGGTGTTTTGATATGGCAACCTGAGCAGACTAA[C/T]GTAAGCTGTCTCTCTTAATTCAAGCTTATTACACA Y 2 1 2 1 201000 r 74 goat snp11380-scaffold1412-539597 20 65211095 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378027 Affx-122977580 AX-123248386 20 64692694 AAAAGTCAGACACAACTGAGTGACAAAGCACAGCA[C/T]GTAGCACAGTACACATCCCTATTAGTGTTATAAAC Y 2 1 2 1 201000 r 74 goat snp11381-scaffold1412-580615 20 65251916 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786448 Affx-122928179 AX-385273482 20 64726741 AAAAATAACCATGCTAAGTATAAGTAAATCATATG[C/T]CAGAGTGGAATTTCAAAATATAGGTTGTATTTCCA Y 2 1 2 1 101000 r 74 goat snp11382-scaffold1412-614662 20 65286242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425386 Affx-122941560 AX-123295732 20 64762825 CTTTGCTACCCTAGCTGAGAAACTGAATCTTCTTG[C/T]AGAGATCTGGTGATGACAATGGCAGTATCATAACA Y 2 1 2 1 101000 f 74 goat snp11383-scaffold1412-650746 20 65322382 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442271 Affx-122928269 AX-123312608 20 64805620 GACAGGTGAGGAAGCGCTTGGTGCCCACGTGGACA[C/T]GACCCTCTCAGGGAGGTGTTTGACTACAAGGATGA Y 2 1 2 1 101000 r 74 goat snp11384-scaffold1412-693541 20 65364614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391400 Affx-122966779 AX-123261757 20 64863159 GACTAAACACACTGGATTTAGAAAAGAATTCCTCA[C/T]GGCACGGCTTGCTCACCCAGTGTGGCGTGTTTAAT Y 2 1 2 1 201000 r 74 goat snp11385-scaffold1412-751080 20 65424370 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377971 Affx-122977621 AX-123248330 20 64931937 AATCATGTTGGTGAAGGGTTTCTTTGCTGAGTTAA[C/T]GATTGCCACCAGGCCTCCATATCCTTAAGCACCTG Y 2 1 2 1 303000 f 74 goat snp11387-scaffold1412-819858 20 65492802 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772094 Affx-122921184 AX-385259249 20 64973108 ATTGATCATATGTGCAGATAATCAAGCAGAAACCA[C/T]GCCCATCCTTGATAACTCTTCCCTCTTATGACCCC Y 2 1 2 1 101000 r 74 goat snp11388-scaffold1412-861029 20 65534106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774596 Affx-122971928 AX-385261730 20 65042942 ACAGCCCATGCTCTATTTAGAGAACCAGAGATGTG[C/T]ATTTTAAAGCACGCTATTGATGATAAGTACCATAC Y 2 1 2 1 101000 f 74 goat snp11390-scaffold1412-930863 20 65604840 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422563 Affx-122943762 AX-123292909 20 65071902 ACAAAGGCACCGTCACGTTATTGTGAAATGTCTGG[C/T]AATCCTCTGGCTCTTGCATGTGATACTAAAATGGT Y 2 1 2 1 101000 f 74 goat snp11391-scaffold1412-959823 20 65633922 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395534 Affx-122963861 AX-123265889 20 65109150 AGATGAGCACATGTCAGCCTAACCAGCGATGTTTC[A/C]CTTCAGCTGCGTGTGGATCCCAGAGGGAGGGTCCA M 2 1 2 1 101000 f 74 goat snp11392-scaffold1412-997071 20 65670883 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375703 Affx-122978647 AX-123246062 20 65148293 TATTTTTTTATTGTGAATATATTTTTAGTGTAAAA[C/T]GGTCTTTAATTGGGAAATCCTTAGTCACCGATTTT Y 2 1 2 1 101000 r 74 goat snp11393-scaffold1412-1036214 20 65709287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436038 Affx-122932726 AX-123306377 20 65184037 ATACATTAACCCACTTGACATTCGAAGGATGTCAA[C/T]GATACCATCATAAATTTAACCATGGTTTCTGCTAA Y 2 1 2 1 102000 r 74 goat snp11394-scaffold1412-1071958 20 65745399 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427681 Affx-122939307 AX-123298024 20 65213893 AAAGAGTACAACTTCTGTCAAAGGCAAATCATTAA[C/T]ATCCCTGATAAGAAAAGAACTCCTCAAAATGGAGA Y 2 1 2 1 101000 f 74 goat snp11395-scaffold1412-1101814 20 65776116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446996 Affx-122924636 AX-123317332 20 65277753 CTTCTCTTCCACCCAGTTGAGAAATCTGGCCGCTA[C/T]ATACAGAGCAGAGTTCTCCTGACATCCATCGGCCA Y 2 1 2 1 201000 r 74 goat snp11396-scaffold1412-1165674 20 65840444 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399768 Affx-122960308 AX-123270123 20 65319045 ATTCCTGGCACAAGGTGAACAGTGTATAGGAGACA[C/T]GGCTGTTATCTGCATTGTCCTAAAAGTGATCAAGT Y 2 1 2 1 101000 r 74 goat snp11397-scaffold1412-1206966 20 65881351 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396960 Affx-122963171 AX-123267315 20 65352501 TGAGGACCTCTGTCTTATTAGCTGCTGTCTTCCTC[A/G]CAGCATATCAATCACTCAGCCTCCCTTGCTCACAT R 2 1 2 1 101000 f 74 goat snp11398-scaffold1412-1240422 20 65914734 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382965 Affx-122973359 AX-123253323 20 65390699 AGACAATCATGTTTGTTCTCTCTTATCCTTTGAAG[C/T]AGCGAATCGAATGCCTCTGGTAGATTCCATCCTTT Y 2 1 2 1 101000 r 74 goat snp11399-scaffold1412-1278620 20 65953498 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433171 Affx-122935660 AX-123303512 20 65423706 TAGTGTAACGTGGGGGAGAAGTCACATGTAGTCAC[C/T]GACAACTCAGTTATCACCACTCTTCCCAGCACACA Y 2 1 2 1 101000 f 74 goat snp11400-scaffold1412-1311627 20 65986583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437603 Affx-122931858 AX-123307941 20 65470723 ATTACATCACTGAAACGCTATACTCTCTGATTACC[C/T]GCTATGTAGCACAGTCCTATAGATCTCAGTACTGT Y 2 1 2 1 101000 r 74 goat snp11401-scaffold1412-1358644 20 66032502 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377361 Affx-122977650 AX-123247720 20 65527718 AAAAATATGAATTTAAACATTTGGGATTTTGTGAG[A/C]TGTTTTCTTATGATTCTTCACTTACTAAAAGCTCT M 2 1 2 1 101000 r 74 goat snp11402-scaffold1412-1415639 20 66089895 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375650 Affx-122978688 AX-123246009 20 65582322 GTTAACTATACCCTTGAGGGCAATGCTTATTTAAA[C/T]AAACAAGGCAATGCAAACTCAAAAGCCCATTTCCA Y 2 1 2 1 201000 f 74 goat snp11403-scaffold1412-1470243 20 66144153 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382870 Affx-122973518 AX-123253228 20 65627633 CAATAGAGAATGCAAAGAATGTGATCAAAACAGAG[A/C]TGAAAGTGTAGACAGTTCTTCTTGGGAGCTTGACT M 2 1 2 1 101000 r 74 goat snp11404-scaffold1412-1515554 20 66190247 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376749 Affx-122978537 AX-123247108 20 65656174 TTCTCTGTGGATAACAAGTGCTAAATATTGTGACA[A/G]TGCTCATCTGGAAACACCAAAAACTGACCATAGAC R 2 1 2 1 101000 f 74 goat snp11405-scaffold1412-1544095 20 66218934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274961 Affx-1111834515 AX-519548543 20 65685331 CAAGGCTGTCACACCTGTTTTGTCCTGTCTGGAGC[A/G]CCCTGCAGTTATCACCCAGTCAGTCCTTGAGAATG R 2 1 2 1 202000 r 74 goat GoatD01.039219 20 65685331 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38401674 Affx-122959565 AX-123272027 20 65688715 AACAAAGACCTTTTTAAAGATGATCACATGTATCA[C/T]GGGTGCTAGGTGCAGGAGTTAAGAGGGAGTCAGAG Y 2 1 2 1 201000 f 74 goat snp11406-scaffold1412-1576636 20 66251804 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433811 Affx-122935173 AX-123304152 20 65726831 ATAGGTTACATCATTGCACCTTGTTCCGACAAAAC[A/G]GATTCAGATCTGATGTCTGACGGCCTTCTTGACCT R 2 1 2 1 101000 f 74 goat snp11407-scaffold1412-1614752 20 66291002 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410307 Affx-122952490 AX-123280657 20 65773600 CACAGCACGACAGCACCCAGAAAGTTCAGGGCTGA[A/C]GAAGCAGAGGAACGAACCAGGGGCACCCTGGCTCC M 2 1 2 1 101000 f 74 goat snp11408-scaffold1412-1661521 20 66337910 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450699 Affx-122921892 AX-123321033 20 65823335 AAGAGATGGCCGAGAGGCAAAGACACACTGTCTCA[C/T]GCACCTCTCATTTTCCAGGGAGTGAGGATGAGCCG Y 2 1 2 1 101000 f 74 goat snp16752-scaffold1753-385059 20 66387958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404919 Affx-122956445 AX-123275271 20 65888078 GAGGGTGAGCAAGGACTTAGAAATCTCTTCGAGCC[C/T]GGATTTTTCTTCAACTAGGAAATGAGAATAACAAC Y 2 1 2 1 101000 r 74 goat snp16751-scaffold1753-320316 20 66453073 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788780 Affx-122931610 AX-385275795 20 65960884 TGTCTTCATATATTTCTGCCATCTTTATAACAGGT[A/G]TATTTCATATATTTCTGCCATGTCTGAAAATAATA R 2 1 2 1 201000 r 74 goat snp16750-scaffold1753-247510 20 66524578 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448616 Affx-122923380 AX-123318952 20 66027032 TTTCTGTTTACTTGCGTCTTCAGTTTCTCTCATCC[A/G]CGTCTTAACAGGTTTCAATGCACAGAATTTTCATG R 2 1 2 1 201000 r 74 goat snp16749-scaffold1753-181362 20 66590942 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412035 Affx-122951729 AX-123282385 20 66058468 ACTGAAGTCACTGAGCATGCATGCTAGGAAGCCTC[A/G]GAGACACAACGCTACTTCTAGTACCAGAAGGACCA R 2 1 2 1 101000 r 74 goat snp16748-scaffold1753-149926 20 66622313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395661 Affx-122963760 AX-123266016 20 66106553 ATGCAGACGTGCCTAGAAGCAGAGGTGCCCCGCGC[A/G]TGATGCGTTCCTGGTGACGCTTGTCTGACTCGCTT R 2 1 2 1 101000 r 74 goat snp16747-scaffold1753-101841 20 66669629 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445994 Affx-122925876 AX-123316331 20 66139666 AGAACAGTCAGACTGAAACACCTTCAGTTCTCAGT[A/G]TTTGAACTAGAAATAGGTAAGCGATTCTGGGGCAG R 2 1 2 1 101000 r 74 goat snp16746-scaffold1753-68728 20 66703129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454098 Affx-122919365 AX-123324431 20 66174065 CAGGGAAGCTCACGTTCAGAGGCCCTGCTTGCGTC[A/G]GTTTCTTCCTTGAGAAATGTGCTCTGGGTGCCATG R 2 1 2 1 101000 r 74 goat snp16745-scaffold1753-34329 20 66737512 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443372 Affx-122927410 AX-123313709 20 66205148 ACATAACTGAGTGACTGAACACTCAGTGCTGCACG[C/T]GCCTGCACAGTTCACAAGTGACGAGATGTGAGAGC Y 2 1 2 1 201000 r 74 goat snp16744-scaffold1753-3246 20 66768682 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430405 Affx-122937758 AX-123300746 20 66236765 GGTTGAGTGAGACTTCTGGGCCATCAGATGGGGAA[G/T]AGATTGCCCTTAAAATCTCACTGGGTCATCCTCAG K 2 1 2 1 101000 f 74 goat snp22699-scaffold2254-167105 20 66811746 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396749 Affx-122962785 AX-123267104 20 66296275 AGCTGCCTGCTCGCCCGCAGCAGATTCTGAAAGGA[A/C]GACATTTGCCTTGTAATTTAGACTTCAGTCCCACA M 2 1 2 1 101000 r 74 goat snp22698-scaffold2254-107595 20 66870514 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421816 Affx-122944317 AX-123292163 20 66348720 GAGGTTACCATGGTAACCAGGTGAGAGATGCCGGT[A/G]TCCTGTGGGAGAAGACGGGTAGGAGGAGCAAGACG R 2 1 2 1 101000 f 74 goat snp22697-scaffold2254-55150 20 66921766 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272432 Affx-1111835859 AX-519546158 20 66369516 TCAAAGTTTACTCTTGTGTTGTACATGCCACGAGG[A/G]AGTTAAGTGAAACCTGCCCTGCTGTGTCCAGCTCT R 2 1 2 1 101000 f 74 goat Random2.2K-1885 20 66369516 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272074 Affx-1111833208 AX-519545838 20 66399939 GACTTCCTGCCTAAACAACAACAATACGTTCACAC[A/G]TAGCCGATTCACTTCGCTGTACAGCAGAAACCAAC R 2 1 2 1 103000 f 74 goat 20_66399939_AF-PAKI 20 66399939 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320797970 Affx-122928688 AX-385284906 20 66419189 AATCAGGCAAAGAGCAAAAGACAACAGAAGAAGGA[A/C]TTTTGTTGACAACAATCGTATTATGACCTTGATTA M 2 1 2 1 101000 f 74 goat snp15550-scaffold1642-405740 20 66992459 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405753 Affx-122956503 AX-123276105 20 66459172 AACGAAGACAGGTCTCTGAGGACAACAGCAGTGTC[G/T]GGACGGTTTTCCTCTGGGCCTGGCGAGTGGGGACA K 2 1 2 1 101000 f 74 goat snp15549-scaffold1642-365757 20 67031960 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397108 Affx-122962695 AX-123267463 20 66499370 TGGGCCCCTCAGCATCTCCAATCCATGTCAGGTTG[C/T]CATTTCCCTACCTGTCATCATGCTTCCTTTAATAG Y 2 1 2 1 101000 r 74 goat snp15548-scaffold1642-325559 20 67071742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463756937 Affx-1110142159 AX-515236331 20 66519118 ATCAAAGTAGAGTTAAGGCACAGAGAAGGCAACTT[C/T]ACTTTCACTTTTAACTTTCATACACTGGAGAAGGA Y 2 1 2 1 101000 f 74 goat Random2.2K-1886 20 66519118 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38452712 Affx-122920297 AX-123323045 20 66534153 CTCACTGCAGGAATAAGTCTAAATCTTTGTTTTTA[C/T]ATTTAGACAAGAAAAAATATTTTTTAAATAATCAT Y 2 1 2 1 102000 f 74 goat snp15547-scaffold1642-290776 20 67106969 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433987 Affx-122934250 AX-123304328 20 66572650 ACTAACATAATATTCTACCTTATTTTTATTACATG[A/C]GTCCTTTATTCTGCTTAGTAGCTTCAGGAATAACT M 2 1 2 1 201000 f 74 goat snp15546-scaffold1642-252279 20 67147359 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404417 Affx-122956773 AX-123274769 20 66623300 TTGCGCTGGGAGTTCACACCCACGCTTACTTTGGA[C/T]GGGGTTAAATATTCTGAAGAAGGAAGTTTCCCAAG Y 2 1 2 1 201000 f 74 goat snp15545-scaffold1642-201629 20 67198288 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774134 Affx-122975101 AX-385261272 20 66683178 CAATTCTTTTCTTGAAGTAGGTTCCTTACTTGGGT[A/C]GGATGTGGACTTAACTTCCTCAGAAGTTGAAGACA M 2 1 2 1 101000 f 74 goat snp15544-scaffold1642-141751 20 67258097 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277335 Affx-1111835860 AX-519550839 20 66704387 ACTGAGAAGAGATTGGTCTTCTTAATCAACGGGTC[A/G]TATAAAGAAGAGATCTGCTTCACCATTTTGTGTCG R 2 1 2 1 101000 f 74 goat Random2.2K-1887 20 66704387 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382912 Affx-122973399 AX-123253270 20 66713588 AGACATTAACAAGCAACACTTAGCAGAGGCAGCAG[C/T]TCCCGGTGGAATTGCAGTGCCCGAAGATACAGAAT Y 2 1 2 1 201000 r 74 goat snp15543-scaffold1642-111341 20 67289113 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402705 Affx-122959201 AX-123273058 20 66804789 TGTTTCCCTGTTGCGATTTCCCCCTGCTGTTAAAA[C/T]GCTCATCTCTGTTACTCAAATGCTAGCAGGCAGGC Y 2 1 2 1 202000 r 74 goat snp15541-scaffold1642-20140 20 67380298 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409755 Affx-122953006 AX-123280106 20 66837576 GATGATGTCAGGAGAGTGACCTTCCGGGAGGGTGT[A/G]AGTGGCCATTGAGAAAGGCATCAGGACTCTTTCCA R 2 1 2 1 101000 r 74 goat snp23360-scaffold2336-477045 20 67413477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397462 Affx-122962098 AX-123267817 20 66866830 GCGTTCTCCTTGTGAAGGTAAGCTTCAGCGCTGGG[C/T]GCGGCTTATGAAGAAACACCTCGTGTAACACAGCG Y 2 1 2 1 201000 r 74 goat snp23359-scaffold2336-447791 20 67442916 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423763 Affx-122942844 AX-123294109 20 66897202 TACCACCTGGGACGATCGTGGATTTTCAGAGACCT[C/T]GACCAGGCTTATCCTGAGAGTCTGTGAACTTGCCT Y 2 1 2 1 101000 f 74 goat snp23358-scaffold2336-417419 20 67473326 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400742 Affx-122959900 AX-123271097 20 66927738 GCAAGACTAAGTGAGGATCCTTCGTTGTGCAGACC[A/G]CAAACTTGCTTCTTCAAGAAACTTACACTCTAATA R 2 1 2 1 101000 r 74 goat snp23357-scaffold2336-386883 20 67499562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431099 Affx-122936611 AX-123301440 20 66980126 ATGAAGCAATGGTCAGAGTTGTCTCACCCCTCGTG[C/T]GAAATTCCTCCCAGCCCACTTCAACCTTCTTTTGT Y 2 1 2 1 202000 f 74 goat snp23356-scaffold2336-334495 20 67552185 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409558 Affx-122953594 AX-123279909 20 67010685 TGATCTCCCATTGCATCTTCTTTGTGTCTCTCCGA[C/T]GGCAAGTCTCATATCCTGTCTTGGATTTTAGTTAT Y 2 1 2 1 201000 r 74 goat snp23355-scaffold2336-303936 20 67583226 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430210 Affx-122937338 AX-123300551 20 67141406 GGAGTTTCATCAAACCTAGTGTGAAAAAGGAATTC[A/G]CCTCAAAAAGAACGAGAGAAACTTTTCGATAAGGG R 2 1 2 1 101000 r 74 goat snp23352-scaffold2336-173215 20 67713557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426565 Affx-122940168 AX-123296911 20 67184026 GTAAATTGCTTCATCTGATTGCTGTCATTTAGTTA[C/T]AGTGTCGGTGGCACTGATTTGGCTGGGCAATCCTT Y 2 1 2 1 201000 f 74 goat snp23351-scaffold2336-130595 20 67756448 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788590 Affx-122956026 AX-385275607 20 67231676 TCTCCAGACTTTATTTTTCTCTGAGCCACACCTAA[G/T]CTGAGAGCAGTTCCATTTAAAGACTGAGTCATTCC K 2 1 2 1 101000 f 74 goat snp23350-scaffold2336-82945 20 67805132 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412661 Affx-122950781 AX-123283010 20 67266588 AAAAATGTCTGGAGACTACAGCAGACTTCACATCC[A/G]CCAGAGCCCGCATTTTAAATCCCTGCTGCCAGGGA R 2 1 2 1 101000 f 74 goat snp23349-scaffold2336-48033 20 67840164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404508 Affx-122956703 AX-123274860 20 67295343 ATGTGGAAGGAAGCTCGGGGAAAATAATTCTGTAC[A/G]TCCCGTATTACTGCAAAAGAATTCCAAGGCAGAAA R 2 1 2 1 101000 f 74 goat snp23348-scaffold2336-19278 20 67869813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402126 Affx-122958673 AX-123272479 20 67327345 ACAAGCAGTTGTGCTCTGGGCCCTGGCAGTCCTGG[C/T]AGCCACAGCTGGTGAATTTAACTCAATTCAACTCT Y 2 1 2 1 101000 r 74 goat snp54680-scaffold836-754970 20 67901473 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452019 Affx-122920908 AX-123322352 20 67369999 TAAGACATTAGAAATTTGGAGTAAGACATGTAAAG[G/T]AACACGTAGTTTAAGTAATTGGTGATTTCTTTCAG K 2 1 2 1 101000 f 74 goat snp54679-scaffold836-712316 20 67943922 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380294 Affx-122975404 AX-123250652 20 67406644 CTGAGTGACTAACACTTTCACTTTAGGGGCCAACC[A/G]GTCGATTCCAGATGATTACTTTGTGGGTTTACCAA R 2 1 2 1 101000 r 74 goat snp54678-scaffold836-675671 20 67980852 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435503 Affx-122933423 AX-123305843 20 67463004 ATGAAAACTTTTAATAAAATGTAAAAGTATGAAAT[C/T]AGTCTCCTCACCTCACTTAAAAGTTCTGGGAACTT Y 2 1 2 1 101000 r 74 goat snp54677-scaffold836-619311 20 68037647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412488 Affx-122951380 AX-123282837 20 67497459 CAGTGCTGCTGGGGATTTGTGGAAGAAGACCCGGG[A/C]TGAGAAGTGCCTTCTTGTTCCCTGGTCGACTTAGG M 2 1 2 1 101000 r 74 goat snp54676-scaffold836-584856 20 68072225 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476352 Affx-1251763862 AX-586011767 20 67561703 ATATTAAAAACAAAGAAAGAAAACAGACAGAGGAA[-/AGACAAATTACTTTCTTTTTTTTTTTTTTTCCTCTTTTTTCTTCCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCCTC]GACAAATTACTTTCAAAGTGATGTCATGAGAGTTA - 4 1 4 1 20000 f 74 goat SV_310 20 67561703 - deletion junction SV-TF-chip 539476608 Affx-1251763862 AX-586011993 20 67561703 ATATTAAAAACAAAGAAAGAAAACAGACAGAGGAA[-/AGACAAATTACTTTCTTTTTTTTTTTTTTTCCTCTTTTTTCTTCCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCCTC]GACAAATTACTTTCAAAGTGATGTCATGAGAGTTA - 4 1 4 1 20000 r 74 goat SV_310 20 67561703 - deletion junction SV-TF-chip 562165311 Affx-1251763862 AX-606940722 20 67561703 ATATTAAAAACAAAGAAAGAAAACAGACAGAGGAA[-/AGACAAATTACTTTCTTTTTTTTTTTTTTTCCTCTTTTTTCTTCCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCCTC]GACAAATTACTTTCAAAGTGATGTCATGAGAGTTA - 8 1 4 1 20100 r 74 goat SV_310 20 67561703 - deletion junction SV-TF-chip 562165450 Affx-1251763862 AX-606940861 20 67561703 ATATTAAAAACAAAGAAAGAAAACAGACAGAGGAA[-/AGACAAATTACTTTCTTTTTTTTTTTTTTTCCTCTTTTTTCTTCCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCCTC]GACAAATTACTTTCAAAGTGATGTCATGAGAGTTA - 8 1 4 1 20100 r 74 goat SV_310 20 67561703 - deletion junction SV-TF-chip 562165468 Affx-1251763862 AX-606940879 20 67561703 ATATTAAAAACAAAGAAAGAAAACAGACAGAGGAA[-/AGACAAATTACTTTCTTTTTTTTTTTTTTTCCTCTTTTTTCTTCCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCCTC]GACAAATTACTTTCAAAGTGATGTCATGAGAGTTA - 8 1 4 1 20100 f 74 goat SV_310 20 67561703 - deletion junction SV-TF-chip 562165561 Affx-1251763862 AX-606940972 20 67561703 ATATTAAAAACAAAGAAAGAAAACAGACAGAGGAA[-/AGACAAATTACTTTCTTTTTTTTTTTTTTTCCTCTTTTTTCTTCCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCCTC]GACAAATTACTTTCAAAGTGATGTCATGAGAGTTA - 8 1 4 1 20100 r 74 goat SV_310 20 67561703 - deletion junction SV-TF-chip 562165640 Affx-1251763862 AX-606941050 20 67561703 ATATTAAAAACAAAGAAAGAAAACAGACAGAGGAA[-/AGACAAATTACTTTCTTTTTTTTTTTTTTTCCTCTTTTTTCTTCCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCCTC]GACAAATTACTTTCAAAGTGATGTCATGAGAGTTA - 8 1 4 1 20100 f 74 goat SV_310 20 67561703 - deletion junction SV-TF-chip 562166578 Affx-1251763862 AX-606941987 20 67561703 ATATTAAAAACAAAGAAAGAAAACAGACAGAGGAA[-/AGACAAATTACTTTCTTTTTTTTTTTTTTTCCTCTTTTTTCTTCCCATCCTATTCCTCCGCCATCTTTCCCTCTCCCCTC]GACAAATTACTTTCAAAGTGATGTCATGAGAGTTA - 8 1 4 1 20100 r 74 goat SV_310 20 67561703 - deletion junction SV-TF-chip 38397477 Affx-122962085 AX-123267832 20 67592020 CGTTGACATTTAAGTCTACTTAATTTATCAAATCT[C/T]GTTTATGTCCTGATTTTGTACACTAGTATCTATCA Y 2 1 2 1 101000 r 74 goat snp54674-scaffold836-490295 20 68166809 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416325 Affx-122947911 AX-123286674 20 67626691 CCCAGCTGAGGAAGGTAACAATAGGCAGGTAGAAA[C/T]CAATTAGTGTGTACCAAAAGTTCAGGATCTTTGAA Y 2 1 2 1 101000 f 74 goat snp54673-scaffold836-455624 20 68201387 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382644 Affx-122973681 AX-123253002 20 67662551 AAAATTGAAGGGTTCTCGTTAGTTACCTATTTTAC[A/G]TATAGTAAATGTCAATATGTCCTTGTCAATCTCCC R 2 1 2 1 103000 r 74 goat snp54672-scaffold836-419764 20 68237290 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428628 Affx-122938677 AX-123298970 20 67702508 TGTCTATTCTATCCACTTCAGGTTGAGTAGTTTCT[A/G]TTTATTTAATCATTATACAATTTTCTTCTAGTATC R 2 1 2 1 201000 r 74 goat snp54671-scaffold836-379807 20 68276942 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38390618 Affx-122967166 AX-123260975 20 67733843 GGTATACAAAATAAAGCTGTTATAAATGCAGTAAG[C/T]TGTCTACATAGGAACGTTCCAGGTGAAAATTTCAA Y 2 1 2 1 201000 r 74 goat snp54670-scaffold836-348472 20 68306629 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797287 Affx-122939494 AX-385284226 20 67784465 TTCTAACAGTAATTCAAGCCCATGACACAACTCAC[A/G]TAAACTAAAGAGGCCACTGACCCAGTAAAAATGTT R 2 1 2 1 101000 f 74 goat snp54669-scaffold836-297850 20 68362768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436515 Affx-122932945 AX-123306853 20 67826483 CAAATAGGATACTGTGGATTCAGATTTACAGCCTG[C/T]AGCCAAAATATTCCTGTGAGCATTATTGAAAAATG Y 2 1 2 1 101000 f 74 goat snp54668-scaffold836-255832 20 68404419 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452939 Affx-122920183 AX-123323272 20 67860319 CAAACTGGGTCTGGTTGAACCACTGTATTGCATTG[C/T]AACCCTGTGATTCAAAGTAATATTTAGGAATCCAT Y 2 1 2 1 101000 f 74 goat snp54667-scaffold836-221996 20 68438400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277459 Affx-1111835861 AX-519550963 20 67920251 TGGACGTCATTGACTCTAGAGAACCCACAGGAGCC[A/G]TTCGTATTTTCAGGGTGATTTGAAAAGTAAGATAT R 2 1 2 1 201000 r 74 goat Random2.2K-1888 20 67920251 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784810 Affx-122951256 AX-385271857 20 67945182 ATTCAATTATTTAACAGGAAATGCCCCATTTATCT[A/G]TTATTTTTAGTGTTTCCTAATTGAGCTCAAATAGC R 2 1 2 1 102000 f 74 goat snp54665-scaffold836-137133 20 68525143 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445720 Affx-122926104 AX-123316057 20 67984133 GAGATGGAGAGAAAGAGACTGAAGCATCTTATAGC[A/G]CCAGAAAGTGAGACTGTGCTCATAACAGAGCAAAA R 2 1 2 1 201000 r 74 goat snp54664-scaffold836-98182 20 68564444 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394105 Affx-122965350 AX-123264460 20 68065807 AAAATGATACTCCAGGAGCTGAAGCCTGGAGAACA[C/T]GCCCAAGAAACTTGCTTTGAGATGAACTGTGGAGG Y 2 1 2 1 102000 r 74 goat snp54662-scaffold836-16508 20 68646023 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451018 Affx-122921459 AX-123321352 20 68103972 AAAAGAAATTAATTCCAAGGACCCTCAGAATTCAG[C/T]GTAGAACAGACCCTGTGTTTGACATTATTCCTCCT Y 2 1 2 1 101000 f 74 goat snp9942-scaffold1355-21558 20 68684712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443368 Affx-122927412 AX-123313705 20 68145017 CAGCCTGGCACATAGCTTATTTTCTGCCTCTCTGC[A/G]TTCACAGTCCATCAGCAGTGATGGCCAAGCACTGG R 2 1 2 1 101000 f 74 goat snp9943-scaffold1355-62603 20 68725818 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447621 Affx-122923990 AX-123317957 20 68199641 GGGCCAGGTTAACATATCTCCAAGCTGGGCCACAC[G/T]TTGAGCAACGGAACAGAAGCAGCAGCTCTCAGGCC K 2 1 2 1 202000 r 74 goat snp9944-scaffold1355-117227 20 68779233 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383508 Affx-122972643 AX-123253866 20 68228900 GCTGGAGCTGTCACCTGCCTCGCCTTCAAGCTACA[C/T]GGGAAAGCTACAGTGGGAGGCAGTGCACCACTGAG Y 2 1 2 1 101000 f 74 goat snp9945-scaffold1355-146486 20 68807657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432886 Affx-122935338 AX-123303227 20 68262226 TGGGCCATCCTGAAATGCACTCATTGTGTGATCTT[G/T]AAAACATTTGATGACCTTCCAGTTTCCTCACTGGG K 2 1 2 1 101000 f 74 goat snp9946-scaffold1355-179812 20 68841125 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376384 Affx-122978104 AX-123246743 20 68308106 CAGCATTGAGTCAGAGCAGGAAAATGTGAGCTTTC[A/G]CTCTGACAGATTTCAGAAGCAGGCAGAGGATTAGA R 2 1 2 1 101000 f 74 goat snp9947-scaffold1355-225692 20 68887360 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410061 Affx-122953223 AX-123280411 20 68344922 CCACTCCTGATTCAGGCTGATACGGTGGCTTGGAC[C/T]TGGTATTTGACAATATCCTCTAATGGGTCACTCTG Y 2 1 2 1 101000 r 74 goat snp9948-scaffold1355-262508 20 68922850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432090 Affx-122936484 AX-123302431 20 68384336 TTTTGTGGATATTTGCTCCCCTAAAACTCTGAGTA[A/C]ACAGAAAGAATCAAGGTTCCTAAAATAAGATTCAC M 2 1 2 1 101000 f 74 goat snp9949-scaffold1355-301922 20 68961438 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780200 Affx-122957145 AX-385267296 20 68448626 GCCCCCAACAAGACTTCTCGTTAGGAAGTCTTCAC[A/G]CTGTGGATCTTTCCCTTGAAACATTTCATTCTCTT R 2 1 2 1 201000 r 74 goat snp9951-scaffold1355-366212 20 69025350 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375968 Affx-122978437 AX-123246327 20 68486286 AGCCATGTCCTGACCCAGGGGGTCACAGGGCAGGA[C/T]GGCTCCGGTGGCTCAGGTCATGTTAACAGGAAACC Y 2 1 2 1 101000 r 74 goat snp9952-scaffold1355-403872 20 69063188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379639 Affx-122975952 AX-123249997 20 68576983 TAGCAAAACCAAACAACAAAAAGATTAGAAGGGCC[A/G]CTGCTTGTAAAGTAGAAATGTAGCTGGGAATTCCT R 2 1 2 1 101000 r 74 goat snp9954-scaffold1355-494569 20 69155034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438379 Affx-122931309 AX-123308717 20 68605838 AAGACGAGCCTCCAGAATATCCTTGGCAGAAACGA[C/T]GAAGAACCTCAGTGGAGGGCCTGGTTAAATTCTCC Y 2 1 2 1 101000 f 74 goat snp9955-scaffold1355-523424 20 69183879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377027 Affx-122977713 AX-123247386 20 68654183 CCCTATGACCTACAGTTCCACTGGTGGGTATTTAC[G/T]CAAGAGAAATGAAAACATGTGACCACAAAACAGAC K 2 1 2 1 101000 f 74 goat snp9956-scaffold1355-571769 20 69232082 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453394 Affx-122919918 AX-123323727 20 68685671 TTTCAAAAAGTGCCTTGCCCATCCGTTCCATGGAA[C/T]GTTACTCAGAAATAGCCAGGAGCGGAGCTATTGCC Y 2 1 2 1 101000 r 74 goat snp9957-scaffold1355-603257 20 69263614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768709 Affx-122940435 AX-385255887 20 68747396 AGGGGTCATAAAGTGGAATGACGATCCTTCCATGT[A/G]TGTGTTGTGTCACGAAACTGCTGATTGACACGAGG R 2 1 2 1 101000 f 74 goat snp9959-scaffold1355-664982 20 69320071 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443727 Affx-122927142 AX-123314064 20 68852535 GTCCGGCATATTGACAACTGTCAGAATACATTAAA[C/T]GCGTCACCTTATTCCGATGCAAAACATTCCTTTTG Y 2 1 2 1 101000 f 74 goat snp9961-scaffold1355-770121 20 69423073 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277340 Affx-1111835863 AX-519550844 20 68870974 CTTTCCTCTGTGTTCTTGGCTATTACGAGAGTTCT[A/G]ACAATGGCCATCCTTGCCACTATATCAGTACTGTT R 2 1 2 1 101000 f 74 goat Random2.2K-1892 20 68870974 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402451 Affx-122958613 AX-123272804 20 68908614 ATCTGAGCAAACTGGTTTAAGGAGAGGCAAGGGGG[C/T]ACAGGTAAGCCACCCCCTTTGGCCCTAGAAAGCAC Y 2 1 2 1 101000 f 74 goat snp9962-scaffold1355-826200 20 69479024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463759311 Affx-1110143369 AX-515238677 20 68916181 AAAATACTGTGGACAGAAGAGCCTGGCGGGCTGCA[A/G]TCCACGTGATCACAAGAGGCAGACACGACAAAACC R 2 1 2 1 303000 f 74 goat 20_68916181_AF-PAKI 20 68916181 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38441707 Affx-122929155 AX-123312044 20 68995296 CTCCTAAGATGACATTCATGCATTGGGGAGAGCAG[C/T]AGATTTGATATCTAAGCTGATGGTTTCTCGCAGTG Y 2 1 2 1 101000 r 74 goat snp9963-scaffold1355-912882 20 69564895 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389934 Affx-122968096 AX-123260291 20 69045152 AGAGGCCGACCCCAGGATCTTTACACGCTGCTCTC[C/T]GTGCCCTCGCTGGTGTGGCATCAATAATAAATATG Y 2 1 2 1 101000 r 74 goat snp9964-scaffold1355-962738 20 69616211 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601424 Affx-1002479708 AX-413835843 20 69079563 TAAAGACCCAGGTTCTATTCAAATGGGAGGTTTTC[A/G]CTGCACACACAGCCTTAATCAAAAGTAGAGCAGCA R 2 1 2 1 101000 f 74 goat 20_69079563_RH-map 20 69079563 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38431672 Affx-122936795 AX-123302013 20 69082625 TGATCACTTCTGTTTGAAGTGTGTATATTTTAATG[C/T]GTATATTATGCACACGTTTATCATATAGTAGATGT Y 2 1 2 1 201000 r 74 goat snp9965-scaffold1355-1000211 20 69653888 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601426 Affx-1002479709 AX-413835844 20 69103221 ACTTGTGAGCAGTGAGGGGACACTCTTCTGTGCTC[C/T]GTGGGGAACAGTGACTGTGCTTTTCCAAAAGTAAT Y 2 1 2 1 400000 f 74 goat 20_69103221_RH-map 20 69103221 C T Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38401215 Affx-122959324 AX-123271568 20 69123245 TCCTTCGGCCAAGTCTACCACCTAAGATCCACCCC[A/G]CAACCCACCCAGCGCTTCTCCAACCATAAAGCTGC R 2 1 2 1 103000 r 74 goat snp9966-scaffold1355-1040831 20 69694339 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277342 Affx-1111835864 AX-519550846 20 69134589 CCACCAAGCAGTCAGGAGCTCCATCTTTGCAAGAC[A/G]TTTCTCAGCCAAAGGATTCTGGCCAAGTCACACCC R 2 1 2 1 101000 f 74 goat Random2.2K-1893 20 69134589 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38393463 Affx-122965843 AX-123263819 20 69162573 AGCGTTGGTGAGAGGCGATAGAACAGAGGTGTGGC[A/G]TGAGAGAAAGCTATGTCGAGGCGGTGGAGTTGACT R 2 1 2 1 101000 r 74 goat snp9967-scaffold1355-1080159 20 69733798 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377851 Affx-122977281 AX-123248210 20 69195791 GCCCACCTAGGGCCCACCTGGATGCTGGCGGTTCC[A/C]CCTGGACAGCCTGTCACTCAGTCTTCATCTGCAAA M 2 1 2 1 202000 f 74 goat snp9968-scaffold1355-1113377 20 69767109 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601557 Affx-1002479710 AX-413835966 20 69211280 TAAAATGCTCTTCTCCTGAAGGAATTCCTCCTAGT[A/G]AGGTTAAGAGAGAAAAACATCCAATAAAAGAAAAC R 2 1 2 1 201000 r 74 goat 20_69211280_RH-map 20 69211280 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38391268 Affx-122967362 AX-123261625 20 69252353 AGGAGGTGTGGCCAGGCCAACAATCTCTATCAGAT[G/T]GCTAGGGTCCCCAGAACCGAGAGAGAAGAAAGTTT K 2 1 2 1 202000 f 74 goat snp9969-scaffold1355-1169939 20 69824102 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463759646 Affx-1110143537 AX-515239007 20 69264089 CAGGCGCCGGCATCCTGCAGTTGCCTCCAAAGGAA[A/G]CACTGGAAGACAGAAGGGTGCTGGGCACCAGGACA R 2 1 2 1 202000 f 74 goat GoatD01.059074 20 69264089 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 350601429 Affx-1002479711 AX-413835848 20 69305568 GATTTCGTTTTCTGCCTAATCTTTGCAAAACGTCC[A/T]TTGCACGTTTCTAATTATTTTGGTTGTAACTGTAA W 4 1 2 1 101000 f 74 goat 20_69305568_RH-map 20 69305568 T A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38452748 Affx-122920271 AX-123323081 20 69318200 TGCTGGAATAACCCAAAGCATGATGAGACAGAGAG[G/T]ACTGCAACCAGCCCTGAGAGTCCTCTGAGCAGTAG K 2 1 2 1 101000 f 74 goat snp9971-scaffold1355-1235786 20 69890095 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412990 Affx-122951023 AX-123283339 20 69368072 CCACACACGTATACTTTCCCCAAAACTATGCAGGC[A/G]TTCCTTATATACGTGTATGTTTAACAAAATCATTT R 2 1 2 1 201000 r 74 goat snp9972-scaffold1355-1285658 20 69938423 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601432 Affx-1002479712 AX-185310451 20 69369043 TTTTCACTCTCCTCTTTCACTTTCATCAAGAGGCT[C/T]TTCAGTTCCTCTTCACTTTCTGCCATAAGGGTGGT Y 2 1 2 1 103000 f 74 goat 20_69369043_RH-map 20 69369043 C T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320775835 Affx-122925193 AX-385262966 20 69430896 TCATATGGTATTTAACCATACGGGATGAATCTTAA[C/T]GAAAGATTTCAGTGTGTATATCAACTGTACGGACA Y 2 1 2 1 101000 r 74 goat snp9973-scaffold1355-1348482 20 70001254 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601433 Affx-1002479713 AX-413835851 20 69439726 GGTTTTTTTTCTGGGCATGTTTGGAAGGATGTTGC[A/C]TGTGAAGTTGTTTGTACCAGGAGGCAAAGAAAATC M 2 1 2 1 101000 f 74 goat 20_69439726_RH-map 20 69439726 A C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38427316 Affx-122940137 AX-123297659 20 69459671 TTTAAATATGTGTTTTTACACTGCTTTTTAAAAAC[A/G]TTGTAAACACTTAAAAAATGTGTTAACTCAAGAGG R 2 1 2 1 103000 r 74 goat snp9974-scaffold1355-1377257 20 70030093 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408889 Affx-122953978 AX-123279240 20 69503660 CCATTCCGTCTGCTCTTTTGTTTCCTAAACTGAGC[G/T]CGTGCTTCAAAGCGAGGGGGAAGCGTGCTCCGCTG K 2 1 2 1 101000 f 74 goat snp9975-scaffold1355-1421246 20 70076248 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601435 Affx-1002479714 AX-413835853 20 69505550 CATAGGGCTTTTCTCATTGTTGAGTCAATGACTGC[C/T]GCCAGGCCTCCATATCCTTAGGCACCTGGGAGTAT Y 2 1 2 1 303000 f 74 goat 20_69505550_RH-map 20 69505550 C T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601437 Affx-1002479715 AX-413835855 20 69539636 TGATGTCTTTCAAAGCTCAGCACAATAACATGCGC[A/G]GACTGTGGACACTTCAGAACTCTCTTTCTCAACAA R 2 1 2 1 101000 f 74 goat 20_69539636_RH-map 20 69539636 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38452403 Affx-122920602 AX-123322736 20 69548022 TTGAGATCTGTGTAAGTTGGGTCTCTAATGGGACA[A/G]TCATTAAAAATAATTTCAATTATTCACGTTTGAAT R 2 1 2 1 101000 f 74 goat snp9976-scaffold1355-1465608 20 70120835 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411503 Affx-122951684 AX-123281853 20 69579604 TTTGCCCTTGTGAATTTGGAGCTGATCCTTTTGGT[A/G]TGTAATACAACAGCTCCAGTTCTTCCTGGTTTCTC R 2 1 2 1 101000 r 74 goat snp9977-scaffold1355-1497190 20 70151995 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796200 Affx-122920305 AX-385283151 20 69615632 GAAAAAGAAAATTCACCAGAATATTCACAGTGAGC[A/G]TTTACTTCTAATGGAATTGAAGTGATTTTTATTTT R 2 1 2 1 101000 f 74 goat snp9978-scaffold1355-1533218 20 70177402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601439 Affx-1002479716 AX-413835857 20 69635680 ATCCTGAAGTTGATAAGCATTTTCATCTGATTCAG[A/G]GACTGTGTAGGGAGCCAAGGCGTGGCTTCAGGCAG R 2 1 2 1 101000 f 74 goat 20_69635680_RH-map 20 69635680 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38377458 Affx-122977519 AX-123247817 20 69675603 GTTATAAATGGCCAAGGGACTGACCCTGCTAACAG[A/G]GCTTTACAAAGTCCCTCGGAAAAGTATGAATGATC R 2 1 2 1 201000 r 74 goat snp9979-scaffold1355-1593189 20 70237203 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601570 Affx-1002479717 AX-413835975 20 69677132 GCCGTTAAGCCCTTCCCCTGAGGTGACTGGTGGTG[G/T]TGTGTCTACGCGGATGTGGTTTCCCTGTTTCCCCA K 2 1 2 1 101000 r 74 goat 20_69677132_RH-map 20 69677132 T G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320779505 Affx-122947594 AX-385266608 20 69730261 TTTGTCTCATCTCAGTGCGTTTCTCGCCGTTAAGT[A/G]TTCTGTTAGCTGTAGTTTTCTTCTGGTTAATGAAT R 2 1 2 1 101000 f 74 goat snp9980-scaffold1355-1647847 20 70292076 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419424 Affx-122945515 AX-123289772 20 69766671 GGTGACGATGTGAGCAGTGGGGCTCTGGGTTCACG[C/T]AGAATCCGAAAGCACTTTCCACTTTCAAACATCAG Y 2 1 2 1 101000 r 74 goat snp9981-scaffold1355-1684257 20 70327988 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601571 Affx-1002479718 AX-413835977 20 69797720 CAACTGAACAACAAAAAGACAAATGACCTAATTTA[A/G]AAAACAGAAAAATTGGCTCAAGAAAAAAGTGAAAA R 2 1 2 1 201000 r 74 goat 20_69797720_RH-map 20 69797720 A G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38416925 Affx-122948046 AX-123287273 20 69823710 TGAGTTCAGTGAAGCTGAAGAAGGCCAGCCCAGTC[A/G]TCACAGAACCGAGAACCCGAAGACCCCAGAGGGTC R 2 1 2 1 201000 r 74 goat snp9982-scaffold1355-1741296 20 70385670 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601573 Affx-1002479719 AX-413835978 20 69851550 ATAAATGGGTTAATTTTGGTTACAAATGGTAGATC[A/G]GCTGTTAGACCTTCCTCCACAAATTTCTGAGATTG R 2 1 2 1 101000 r 74 goat 20_69851550_RH-map 20 69851550 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38382725 Affx-122973615 AX-123253083 20 69870074 TTGACGGCAACTGGAATGGATCTCAGGACCGTCAC[A/G]TCGAGTGAAAAAATCCCACTTCAGTGCATCCTGCA R 2 1 2 1 101000 r 74 goat snp9983-scaffold1355-1787660 20 70434076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420150 Affx-122945588 AX-123290498 20 69884330 TCCCTCGGAGTCTGATGAACTCAGCATTGCTTTCC[A/G]CGTTCCCAGCATCCTGGCTTCTTTGAGATCAGGGC R 2 1 2 1 101000 f 74 goat snp22017-scaffold2165-7330 20 70449632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601447 Affx-1002479720 AX-413835865 20 69920169 GGATTTGATTCAGGTCATATCTGAATGGTCTACTG[G/T]CTTTCCATGCTTTCTTCAGTTTAAGTCTGAATTTG K 2 1 2 1 303000 f 74 goat 20_69920169_RH-map 20 69920169 T G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38438268 Affx-122931410 AX-123308606 20 69921382 TCAGCTCGCTCTTCATGCAGCTCTGGGGCATCTAC[A/G]GAAGCTGGGGTCTCAGAGAGGCAAACGGGCATCGG R 2 1 2 1 103000 f 74 goat snp22018-scaffold2165-44382 20 70487048 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440592 Affx-122922951 AX-123310929 20 69953236 CAGAAATCAGACAAAAAGATATTCCAAGACAACTA[C/T]GAACCACTGTCTCTTATAAATGCAGATTCTTAACA Y 2 1 2 1 101000 f 74 goat snp22019-scaffold2165-76236 20 70519763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601577 Affx-1002479721 AX-413835981 20 69956390 GAGAATTGAAATAGTAAGAGGCATTCAAAGTTAAA[A/G]GAATTTATATGTCAGGACTCACTCTACAGAAACAT R 2 1 2 1 101000 r 74 goat 20_69956390_RH-map 20 69956390 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601579 Affx-1002479722 AX-413835983 20 69979163 AGACAGACGCCGCGTTATGGCCCTTCGCTCCCCTC[C/T]CCACCCTAGCTGTCAAATTTACTGTTGAAGCTTTT Y 2 1 2 1 101000 r 74 goat 20_69979163_RH-map 20 69979163 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38437254 Affx-122932011 AX-123307592 20 69986472 TCCCTAAGATGTCTTGATCTACTCAGCATGGTGTC[C/T]GGGTAAATATAGTGTATAGTGGAGAAATATGTTTT Y 2 1 2 1 101000 r 74 goat snp22020-scaffold2165-109472 20 70553403 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421993 Affx-122943787 AX-123292340 20 70041427 CTGTACCTTTCCTTCGCTCCTGTCGCCTCTGTGCT[C/T]GCGCTATCACTGATCTGCTTTGTCTCTAGAGAGCT Y 2 1 2 1 201000 f 74 goat snp22021-scaffold2165-164427 20 70606905 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399814 Affx-122960273 AX-123270169 20 70078199 TGCTCAAACAACCTTCCAAGTTTCACAGTGAAAAT[A/G]GTAAGCGTGTGTCCTGCTGGGGGTGTGCTGTTCAG R 2 1 2 1 103000 f 74 goat snp22022-scaffold2165-201199 20 70643476 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412026 Affx-122951736 AX-123282376 20 70115045 TTCACGAGGCACTAGGTCCACCTCAGTGGACACCC[A/G]CGCCAGATGCCAGGCTGAACTTAAAGCGGCTTTTT R 2 1 2 1 101000 r 74 goat snp22023-scaffold2165-238045 20 70680454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397995 Affx-122961798 AX-123268350 20 70172521 GCCGAACTATAACTACCTCCCGGAACGTGGGCAGA[C/T]TCCGGGAGATGGTGAAGGACAGGGAAGCCTGGCAC Y 2 1 2 1 103000 f 74 goat snp22024-scaffold2165-295521 20 70738358 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801627 Affx-122941218 AX-385288535 20 70174641 TACCTTGACTCATTGTGCAAACAATTTTAATAGCA[C/T]GTATAGTTGTTTATACACTGAAGAAACCCAGGAAA Y 2 1 2 1 201000 r 74 goat snp49476-scaffold705-582004 20 71781355 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400167 Affx-122960683 AX-123270522 20 70351681 GGTCCGTCAGTCTCTCCTCACGGTCAGGCTTTACG[G/T]CTTCTGTCCTCTCTGTGTGCTTGTTCCTCAGATAC K 2 1 2 1 101000 r 74 goat snp49474-scaffold705-404964 20 71615682 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430855 Affx-122937424 AX-123301196 20 70420130 CTGGCTTGAACGCTCATGGCGGGCTGTCCCATGTG[C/T]AGTATCACCTTCTGTGGCATCTGCTGTCAGAAGTA Y 2 1 2 1 101000 r 74 goat snp49473-scaffold705-336515 20 71549443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380636 Affx-122975230 AX-123250994 20 70473748 CCCTCCTCAATCATCACAGGGACAGAAGAGACACT[A/C]CCAGGACCACAGCACAGCTCACTTCGGGAAGGACC M 2 1 2 1 101000 f 74 goat snp49472-scaffold705-282897 20 71496295 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416711 Affx-122947558 AX-123287059 20 70573001 TCCGCTGTCGCCCTGACCTCGGTGTAGTCGGTCAG[C/T]GTGTCCTGTGTCCTCAGGCTCACGCGTCAAGTGTG Y 2 1 2 1 201000 f 74 goat snp49470-scaffold705-183644 20 71397347 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425068 Affx-122941256 AX-123295414 20 70609585 TGATCCTCTTAGAGCCAGTCAGAGCCGGTGGGATC[G/T]AGTTCACAGCGATCAGAGGAAGTTTCTAAGCCTCG K 2 1 2 1 101000 r 74 goat snp49469-scaffold705-147060 20 71362641 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379298 Affx-122976205 AX-123249657 20 70683440 CACATAAAACAGGTGACTGACGAGAATCGGTCACC[A/G]TGGGGCATAGGGAACCCTACCCGGTACTCTGTCAA R 2 1 2 1 202000 f 74 goat snp49468-scaffold705-73205 20 71210271 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452163 Affx-122921651 AX-123322496 20 70776906 GCTGAGCCCTGGGCCAGTACTGGGGTCTTGTGAGC[A/C]GCCCTTGCCCCCGCAGACAACCTGTGGAGCGCGTA M 2 1 2 1 101000 f 74 goat snp41244-scaffold5353-35648 20 71117115 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411977 Affx-122951777 AX-123282327 20 70810470 GGGGAGGGATTCTTCCTTCCTGTAGGTTCACAAAG[C/T]GGAGGAAACACCCCCCGGATGCATGTGCCTTTTGC Y 2 1 2 1 101000 f 74 goat snp41243-scaffold5353-2084 20 71084690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451588 Affx-122921647 AX-123321921 20 70816623 TAGCTTAAACAAAGCAGAACAGAGATTTGCCCAGC[A/G]TCCAAGGGGGCTGGAGGTGGGCAGTGCCTGGCCGT R 2 1 2 1 101000 f 74 goat snp24774-scaffold2533-75423 20 70744976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381634 Affx-122974764 AX-123251992 20 70857380 TAGCTAAACGGTACTATTAGTGCAGAGGAAATAAA[C/T]GGCCATTTCACTCTGCAGACTACACGTAATTGTGC Y 2 1 2 1 101000 f 74 goat snp24773-scaffold2533-34666 20 70785792 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406900 Affx-122955628 AX-123277251 20 70906454 CGTGATACATGCTTAAGGCATTTATTGGATTGATG[C/T]GGAGATGGCCTGAGTGTCCAGGCTCAGCAAATATT Y 2 1 2 1 101000 f 74 goat snp25945-scaffold2687-14309 20 70856206 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420738 Affx-122944762 AX-123291085 20 70949432 AGCAGAAAGAATTTCAGGGAGAAGTGGGAAATCTG[C/T]GCCCCTTCTTTGTCATCTAAAATGACAGAATCAAT Y 2 1 2 1 101000 f 74 goat snp25946-scaffold2687-57287 20 70899124 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444764 Affx-122926361 AX-123315101 20 70998759 CTAGAAACTTCCTTTACTGCTGAGCTAAAAGAGCT[A/G]TTTAAGCATTAAGAAAGAGATTTAGGTTGGAGCCT R 2 1 2 1 201000 r 74 goat snp25947-scaffold2687-106614 20 70948280 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428439 Affx-122938818 AX-123298782 20 71038358 TCCCTTTCTCACAGCTTCTTAGGGGGCTTCCCAGC[A/G]CTTCCGTCACTTTGTGTCCCTTGTATGACCTTTTA R 2 1 2 1 101000 r 74 goat snp25948-scaffold2687-146213 20 70988434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425927 Affx-122941606 AX-123296273 20 71106127 TTGCCATGCCCTCCTCCAGGAGACCTTCCCGACCC[A/G]GGGACCAAACTCCTGCCTCATTGTTTCCTGCTTTG R 2 1 2 1 101000 r 74 goat snp25949-scaffold2687-213982 20 71051846 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430961 Affx-122936822 AX-123301302 20 71142431 TATGTTTCTATTTTAAAATAAATTTCTCTGGCTGT[A/G]CACTCTTCGTGGCCTGACATGACGTAGGTTTCAGA R 2 1 2 1 101000 r 74 goat snp25950-scaffold2687-250286 NW_017189686.1 25711 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410988 Affx-122952007 AX-123281338 20 71198426 GGACGCACGGCATATAGTCACAGTTGTTGAAATCA[C/T]GCCAAATGTAAAAAGTACCGGACTTATCCAAGCCC Y 2 1 2 1 101000 r 74 goat snp25951-scaffold2687-306281 20 71286275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277467 Affx-1111835865 AX-519550971 20 71345308 TGGGGTGGGGCTAACTTTTCCATTTCTCTTTCTCC[A/G]AAAACTGACAAACATGGGAACAGATGGTTTATAAT R 2 1 2 1 101000 r 74 goat Random2.2K-1895 20 71345308 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468274537 Affx-1111834353 AX-519548128 20 71483465 GACTTGCCTGTTTGGGGCATCTCGTGAGAAGAACC[A/G]CAGCCGGGCGGCCTGGCGCCTCATCCTCTCCTGCA R 2 1 2 1 202000 f 74 goat GoatD01.031424 20 71483465 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38406778 Affx-122955714 AX-123277129 21 11488 GTCCTGCCCTGTGGAGGTGGGCAGTGAGCCAGCAC[A/G]TGCTCGGATCGATGATGACACCCTCACATGCATTC R 2 1 2 1 303000 f 74 goat snp57409-scaffold914-11488 21 1207439 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422678 Affx-122943670 AX-123293024 21 53361 AGCTGGTGCATCAAACCTGTGGTCCCTGAAATGCC[C/T]GGCCTCAGGCCATAGAAGTCATGTTGGATTCAGAG Y 2 1 2 1 101000 r 74 goat snp57410-scaffold914-53361 21 1249372 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438133 Affx-122931481 AX-123308471 21 83744 CTGTAGATTCCATGAGGAATGCTATTGTTTTTCTC[A/G]TTTTGTTTTCCTGAGGGCTGGTGGATATAGAGGAA R 2 1 2 1 202000 f 74 goat snp57411-scaffold914-83744 21 1280863 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771748 Affx-122956704 AX-385258905 21 120204 ATCAGAATAGACATTGAGCCTCTCCATTTTTATGA[C/T]ACTTTCATTGCTAGGAATTCAAATACAAGTAGGAA Y 2 1 2 1 101000 r 74 goat snp57412-scaffold914-120204 21 1317744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767537 Affx-122956621 AX-385254793 21 155190 CCTTCATGGACATACTAGGTGTTCTCACACCAGTC[A/G]TGCTTCTCTCTAGACAGACAATATCAGAGAGGAAG R 2 1 2 1 101000 f 74 goat snp57413-scaffold914-155190 21 1353019 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397095 Affx-122962706 AX-123267450 21 198568 AAACTGAGACAAGTGTTTTCTCCTTCAAATGCACA[C/T]ACCAATGCAGGCTGCACAATAAAGACTCAAACAAG Y 2 1 2 1 101000 r 74 goat snp57414-scaffold914-198568 21 1396387 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799146 Affx-122951608 AX-385286076 21 265698 TAGGACTTAAAAGACAGTTCCATTCATTTCCAAGT[C/T]TCTGCTTACTGTATGATTAAGTAAAACAAGGCACA Y 2 1 2 1 101000 f 74 goat snp57415-scaffold914-265698 21 1463590 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420065 Affx-122945121 AX-123290413 21 304538 AAACTAACCAGCTAACCAGAACTGAGTCAGCAGGA[C/T]AGAGAAAAAGGAAGCACCAGACAGATTAGTAGTTT Y 2 1 2 1 201000 f 74 goat snp57416-scaffold914-304538 21 1502438 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275327 Affx-1111834730 AX-519548902 21 335142 TAAAT[A/G]GACTGCAGATATTTCTCCAGGATATATGGGATTAT R 2 1 2 1 103000 r 74 goat GoatD01.050155 21 335142 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38426986 Affx-122940386 AX-123297331 21 361040 AAGAAACACTGTTGTAGCAAAATTCTGTGAAGACC[A/G]TTGCCTGACAGGACAAGTGCTCAGCAAATTGTAGT R 2 1 2 1 101000 r 74 goat snp57417-scaffold914-361040 21 1559071 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397472 Affx-122962089 AX-123267827 21 398124 GAAACTTCTGCTCTTCAGGAAAGGTGTCTCACCAG[A/C]GGCACAGCCTAATGGAGAGCGATGCTGATGTTAGT M 2 1 2 1 101000 f 74 goat snp57418-scaffold914-398124 21 1595462 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378034 Affx-122977574 AX-123248393 21 432931 TGACTGATAGTCGTAAGCAGGCATCTGCTCCACTT[A/G]TAAAGAAAAGTCCTTGGTGGGGATGGCTCCAAATT R 2 1 2 1 201000 f 74 goat snp57419-scaffold914-432931 21 1630675 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772916 Affx-122956715 AX-385260060 21 466757 CCTGGTCTTTTTATGATAATGCAGATATACTTTCC[A/G]TCAAATTGTGACAAAAGAAACACATCTTTTTACAA R 2 1 2 1 101000 r 74 goat snp57420-scaffold914-466757 21 1664486 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789750 Affx-122923037 AX-385276758 21 556527 GGTTGCAGATGTTTTTGTTGAAGCTTTACTCAATA[C/T]TCTTCTATTGAATAGTAACCTCTTTTCTTTATTTG Y 2 1 2 1 201000 r 74 goat snp57422-scaffold914-556527 21 1755816 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377790 Affx-122977326 AX-123248149 21 651816 AGTGTTTCCTTTGCTGGAAGCTCCTTGTCTCCCTC[A/G]TCTACCTGAGGAATGCTCATCTTCCTCTGTAGCAT R 2 1 2 1 101000 r 74 goat snp57424-scaffold914-651816 21 1852172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419104 Affx-122945776 AX-123289452 21 693626 TTCACTAAAATCTGTTCATTTTACTGTATGAAAAG[C/T]ATACCTCAGTAAAAGCAAAAGTTGGGAGTGACCAC Y 2 1 2 1 101000 r 74 goat snp57425-scaffold914-693626 21 1894026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421214 Affx-122944137 AX-123291561 21 754611 AGTAGCAAGGGGATCTGACGAGGTCAGGGACAGCA[C/T]AGCACAGCCCTGCATGGACTGAGTCCCAGGGAGAA Y 2 1 2 1 201000 f 74 goat snp57426-scaffold914-754611 21 1950819 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411451 Affx-122951814 AX-123281801 21 806925 GACTCTTGTCAAGCAGCTCCATAAGCTCAGGGACA[C/T]GGCAACAGTCCTGAAAGGCTGCACTCACACATAGA Y 2 1 2 1 201000 f 74 goat snp57427-scaffold914-806925 21 2002964 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272106 Affx-1111833231 AX-519545864 21 827171 TCCTATGGCCACTAGTGAGTTTTCCAAATTTGCTG[A/G]CATATTGAGTGCAGCACTTTCACAGCATCATCTTT R 2 1 2 1 103000 f 74 goat 21_827171_AF-PAKI 21 827171 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468275340 Affx-1111834738 AX-519548915 21 832526 TTGCCTTTTCCAGAACACTTTAATATCTATCTACA[A/G]TTTTTCTTTGACAGCTACAGGACTGCAGCTTGGAT R 2 1 2 1 101000 r 74 goat GoatD01.050771 21 832526 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320797644 Affx-122962259 AX-385284583 21 861003 ATAAGGAAATATTAAAGTGACTAGTGACAAATTTT[A/G]TTTAAAGACAAGCAGTAAACAAAATTCTAAGCTCA R 2 1 2 1 102000 f 74 goat snp57428-scaffold914-861003 21 2056033 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385573 Affx-122971842 AX-123255931 21 910292 CCAGTGGGCCACGCCTTTGCAGACATCTATTTCAG[A/C]ACAGAAAACTGGAGAAAGAAGGAAACTCTCTTCCA M 2 1 2 1 201000 f 74 goat snp57429-scaffold914-910292 21 2105067 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786691 Affx-122952633 AX-385273723 21 927573 TTCCTCACCTGTGAAACGAAGGTACGAAAACAGGA[C/T]ATCAGGAGGTTATGGTGCAACTGCACACTAAAGCA Y 2 1 2 1 101000 r 74 goat snp46624-scaffold648-16555 21 2122186 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793254 Affx-122932542 AX-385280232 21 959412 TTTAAAATGTCACCAATAATTCAGAGTCCTTTGAG[A/C]CTCACACTCAAAGTTCTCATGGTACATGCCCAAAG M 2 1 2 1 201000 f 74 goat snp46625-scaffold648-48394 21 2154068 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435284 Affx-122934042 AX-123305624 21 1013529 CTTTTCTTTTCCCCTACCCTGTGGTCCATCGCGTC[A/G]CAAAGAGCTGGACACAACTGAGTGACTGAACTGAA R 2 1 2 1 201000 f 74 goat snp46626-scaffold648-102511 21 2226477 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402785 Affx-122958299 AX-123273138 21 1048149 GACATAGAAGGGGGGAGGGGAGGTGGGAGGTAGCA[A/G]AGGTAACTCTGCCGAAGTATAGCTGCTGCCCAGGG R 2 1 2 1 101000 r 74 goat snp46627-scaffold648-137131 21 2261233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454160 Affx-122919323 AX-123324493 21 1109261 TGAATATGCAAATACTTTGGCACTACTGGCAGAAA[C/T]GAATCTTCTTTCCCCATTGAATTGTCTTAGTATTT Y 2 1 2 1 201000 f 74 goat snp46628-scaffold648-198243 21 2321296 C T 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416576 Affx-122947659 AX-123286924 21 1161793 AAAACAGGAATAGACATCAGCTCTAACATTTGCCA[C/T]GAAAGCTCTGGGGTGACATAAACTGTATTGAAATC Y 2 1 2 1 201000 f 74 goat snp46629-scaffold648-250775 21 2374004 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417258 Affx-122947266 AX-123287606 21 1219912 GCACAAACTCAGCTTGTTTAACCAGGGCAAGATGA[A/G]TTCACAGTACTGCCTTCCTGCCCAGCCACGGACCT R 2 1 2 1 101000 f 74 goat snp46630-scaffold648-308894 21 2427341 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763696 Affx-986698225 AX-385251520 21 1236772 TACTAGGACAACCTGATATGGTCCTGTCCATTTCT[C/T]GGACAGCTGGCTTGGACTCCCTTTTTCTTGCCAGG Y 2 1 2 1 600010 f 74 goat 21_1236772 21 1236772 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 320763698 Affx-986698227 AX-385251522 21 1237212 TTTATGCCTAAGCATGCGGCCAGGTTCTGAGATAT[C/T]GTGGCTGTAAATGAGGGCCCATTGTCACTCTGAAG Y 2 1 2 1 600010 f 74 goat 21_1237212 21 1237212 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320763700 Affx-986698229 AX-385251524 21 1237234 GGTTCTGAGATATCGTGGCTGTAAATGAGGGCCCA[A/T]TGTCACTCTGAAGTGATCAAGGCAACCCAAACCTA W 4 1 2 1 600010 f 74 goat 21_1237234 21 1237234 Ancestral_priority_1043 ancestry 0.536 neutral IMAGE 10K 10K ancestral 320766890 Affx-986698231 AX-385254208 21 1237253 TGTAAATGAGGGCCCATTGTCACTCTGAAGTGATC[A/G]AGGCAACCCAAACCTAGGTACTGTCTCCTTCAGCA R 2 1 2 1 600010 r 74 goat 21_1237253 21 1237253 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 320803501 Affx-986696371 AX-385290321 21 1239330 TACTTGGGTTAAGCTAATCTGAGCTTTCTTGGGGG[A/T]TACTCAATAGCCCTTTTCATACAGGAAATTTAGAG W 4 1 2 1 600010 f 74 goat 21_1239330 21 1239330 Ancestral_priority_1043 ancestry 0.542 neutral IMAGE 10K 10K ancestral 320804073 Affx-986696372 AX-385290743 21 1239340 AAGCTAATCTGAGCTTTCTTGGGGGTTACTCAATA[A/G]CCCTTTTCATACAGGAAATTTAGAGTTTTAATAGT R 2 1 2 1 600010 r 74 goat 21_1239340 21 1239340 Ancestral_priority_1043 ancestry 0.672 neutral IMAGE 10K 10K ancestral 320763677 Affx-986698206 AX-385251506 21 1239361 GGGGTTACTCAATAGCCCTTTTCATACAGGAAATT[A/T]AGAGTTTTAATAGTGTCCATTTGAGAGCTGGTAAA W 4 1 2 1 600010 f 74 goat 21_1239361 21 1239361 Ancestral_priority_1043 ancestry 0.602 neutral IMAGE 10K 10K ancestral 320765882 Affx-122977375 AX-385253319 21 1288299 GATCCCAGGAAGCTATGATACCTTCAGGTGCTTCA[A/G]CTGAGCAGTTGCCCATCTTAGCAACAATCACTTGC R 2 1 2 1 101000 f 74 goat snp46631-scaffold648-377281 21 2496545 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387456 Affx-122970369 AX-123257814 21 1334388 TCCTCTCTTGGCTGTCTCTAGTGACCCTGTTACTG[C/T]AACAAAGTGAAAGTCATTAAAAGCCCTTTTCTCTC Y 2 1 2 1 101000 f 74 goat snp46632-scaffold648-423370 21 2543002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384470 Affx-122973080 AX-123254828 21 1386516 ACAGAAGGGTGGGAAGGATCAGCAGATCCCTCTGA[C/T]TGCATGGTCCTGGGAGTCCAGTGTGCAAGGTAAGC Y 2 1 2 1 201000 f 74 goat snp46633-scaffold648-475498 21 2595533 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447403 Affx-122924405 AX-123317739 21 1415496 ATCTATCCCAGAAGCCCAGAAAGGGGCTGCAAAGG[C/T]CTAGTCATGCCAAGGTGCCTGGCATGATAAGTAGA Y 2 1 2 1 102000 f 74 goat snp46634-scaffold648-504478 21 2624353 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436336 Affx-122933243 AX-123306675 21 1459600 GTCATTTCAAGATATTTCAGACAGAAATCTGCTTA[A/G]TACTAACAGTTTGGGGTCCTCTTTGGATTTCCAGG R 2 1 2 1 201000 f 74 goat snp13938-scaffold1545-96431 21 2668134 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442350 Affx-122928034 AX-123312687 21 1506924 ACTTACACCCTGAAGTTGTAGCTGATGGACAAGAA[C/T]GTCTGGGTAGCACTAGAATCAGCTCAAATAATGGA Y 2 1 2 1 101000 f 74 goat snp13937-scaffold1545-49107 21 2715820 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388322 Affx-122969368 AX-123258680 21 1550121 CCCACTGTCTGCCACATGCCCTCACCCTCACCTGG[C/T]TCTCACTGTCTCCCTGAAAGTTTGTGGTATGGTCA Y 2 1 2 1 101000 r 74 goat snp13936-scaffold1545-5910 21 2760594 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409587 Affx-122953570 AX-123279938 21 1566235 CTCCTCCTTCTTGTTCCTCCATCAGCATCCTCTAC[A/G]TTTTAAACCACACACAAGGTCATTTTACCCAGTAG R 2 1 2 1 201000 r 74 goat snp57177-scaffold91-2960182 21 2776570 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437859 Affx-122932076 AX-123308197 21 1608652 AGATAGGTAGTGTCATGAGTGTTTAGACTAGGCAT[A/G]AAGTGGAAATTATTTCTGATAAAATAGCCAACTGA R 2 1 2 1 101000 f 74 goat snp57176-scaffold91-2917765 21 2819431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769205 Affx-122922374 AX-385256380 21 1643655 TTTCTTATAGATAAAAATTTGCAGACATTTGTAGC[G/T]CCTTTGACATCTGTGTTATCATCAAAAAGATGACT K 2 1 2 1 101000 r 74 goat snp57175-scaffold91-2882762 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421875 Affx-122944274 AX-123292222 21 1713542 AGTTGGCACAAGTGTCCAGGCCTCTTTGCAAGGAG[C/T]TATCAATAACAAAAACAAACAGGACCTATGAAAAC Y 2 1 2 1 101000 f 74 goat snp57174-scaffold91-2812875 21 2909449 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431037 Affx-122936656 AX-123301378 21 1770992 GTGAAGAAGTGATTCTCCTTTTTCTCCTAAAACAT[A/C]TTTCTCATATTGTTTTAGTCTTTAATCTTAGATGA M 2 1 2 1 103000 f 74 goat snp57173-scaffold91-2755425 21 2967779 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275080 Affx-1111834585 AX-519548660 21 1829641 TGCAGGTATTTTTAAAGAAAGTCTTCCAGTACATC[A/C]AAATCTCATTATCCAGAGCTGAGAGAGACTGCAGA M 2 1 2 1 201000 r 74 goat GoatD01.042286 21 1829641 C A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320786824 Affx-122949731 AX-385273852 21 1848830 GCCCAAATTTGACAGGCAAAAACATTTTCCAGAAT[A/G]TTGCAATTTTCCTTCAGTGGTCAAAGTACAGATGT R 2 1 2 1 101000 r 74 goat snp57172-scaffold91-2677587 21 3046047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454260 Affx-122919647 AX-123324593 21 1923283 AGTGTTCGAGTTTTTCCACTTTCTGGTCACTGCTG[A/C]AGTCCAGCCTTGCCCACCACTCTATCCTTTCCCCC M 2 1 2 1 101000 f 74 goat snp57170-scaffold91-2603134 21 3119523 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792916 Affx-122921265 AX-385279894 21 1963765 CATCCTTGCACTTAACTTTGAAATACACTGACCTA[C/T]TATAGCAAGAGACCTATCCCTCTTGCTTTGAGAAA Y 2 1 2 1 101000 f 74 goat snp57169-scaffold91-2562652 21 3160440 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802816 Affx-122971048 AX-385289715 21 2019420 TATTATGGATGTTGTGTTTGAGAAGTTAATTGAAT[A/G]TAAATGTCCTAATCCTGGGCCCACAATGTTTTCAA R 2 1 2 1 101000 r 74 goat snp57168-scaffold91-2506997 21 3215791 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440207 Affx-122930694 AX-123310544 21 2061071 TTTAGTTTTTGAGATTTATTCATAGTAAAGTGTGT[A/G]TCAATAGTTTCTTCTGTTTATTAGTGAATAGTATT R 2 1 2 1 101000 r 74 goat snp57167-scaffold91-2465346 21 3257511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393556 Affx-122965407 AX-123263912 21 2116399 TTTTTGTCTTTCCCCTCAGGGAGGCTGTAAAGCTT[A/C]TGTTGCTACAGCTCTTAGAAAAGGAATCTTCCACA M 2 1 2 1 101000 r 74 goat snp57166-scaffold91-2410018 21 3312185 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441930 Affx-122928589 AX-123312267 21 2171453 ATTTTACAGAAAAATAAAACTCCAAGTAAATATTT[C/T]TGAGTCAAAAATTGAAAAAGTGAACATAAATAAAC Y 2 1 2 1 103000 r 74 goat snp57165-scaffold91-2354964 21 3367325 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770572 Affx-122949883 AX-385257736 21 2202068 AAGATACCAGTGAGTTAGAATAGGTCAGAATGTCT[A/G]TGTAGAGACTGTGACCACTAATCTCTATTCCCTGA R 2 1 2 1 101000 f 74 goat snp57164-scaffold91-2324349 21 3398052 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408352 Affx-122953742 AX-123278703 21 2312545 TCTGCCCCTTGCTTGGAGCTGGTTCTCTGCTTCAG[C/T]ATCCATGGCCACAGGGGGCACCTACATTCCTGCTG Y 2 1 2 1 102000 f 74 goat snp57162-scaffold91-2213872 21 3499190 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406008 Affx-122955505 AX-123276360 21 2348842 GCTCAGATTTAAGGCTGAGCAGCATATAAATGCAG[C/T]AGTATCCTCAAACTGGAATTCCCCTAGCAGGGCTC Y 2 1 2 1 101000 r 74 goat snp57161-scaffold91-2177575 21 3535243 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405449 Affx-122956045 AX-123275801 21 2381975 AAGGACATGGATTGCTGGGAGCCAACCACCGCCCA[C/T]AGGCCTGGCAGCTCAGTCCACAGCAAAGGCACTCG Y 2 1 2 1 201000 r 74 goat snp57160-scaffold91-2144442 21 3566403 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794013 Affx-122933407 AX-385280982 21 2426642 GACACCAGAACAAAACTGGTAAAGTCATTACCAGA[C/T]GATTTAGTTCAATCCAAACCTACTATGGTCTGACT Y 2 1 2 1 101000 f 74 goat snp57159-scaffold91-2099775 21 3632674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405367 Affx-122956313 AX-123275719 21 2470754 CACAGTAAAATAGGAACCTGCTACAGACGGGTTCA[C/T]AAGATCGCTGGTTTAAAAAAGCCTTTACTAGTTTT Y 2 1 2 1 101000 f 74 goat snp57158-scaffold91-2055663 21 3676591 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389270 Affx-122969017 AX-123259628 21 2509853 GTGGCACAGCGCAGGGCAAAGGCCCTCCTGGTACT[A/G]CAACGGAAGCTGGAGGTAATAATCTTCTATCTGGA R 2 1 2 1 101000 r 74 goat snp57157-scaffold91-2016564 21 3716061 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436658 Affx-122932476 AX-123306996 21 2549318 GTATTCCACACATGGTGTGTGTTCCACTTTCACTA[C/T]GGTAGTTTTATTTTACTTCTACAGATTTCATAATG Y 2 1 2 1 201000 r 74 goat snp57156-scaffold91-1977099 21 3753213 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396631 Affx-122962872 AX-123266986 21 2578070 GAAGATGTCTGCCGCCGTCACCAGTGCTAACTGTG[C/T]ATGTCTGCTATGTGCCAGGTACTTTGTTATGTGAT Y 2 1 2 1 201000 f 74 goat snp57155-scaffold91-1948347 21 3783014 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440274 Affx-122930641 AX-123310611 21 2643760 TGGAAAGCCCCTACATCTTATTTTTATTTGCCTTG[A/G]ATTCCATTAAGGGGCATTCAACACAACATTAGATC R 2 1 2 1 102000 f 74 goat snp57154-scaffold91-1882657 21 3849977 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451039 Affx-122921444 AX-123321373 21 2688351 ATGTGCTGCATGCATTCACTAGATGAGGCAATCCT[A/G]CAAGAGGTCAATACTCAGGTCTGGCTTTCCTTCTG R 2 1 2 1 101000 f 74 goat snp57153-scaffold91-1838066 21 3893847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396009 Affx-122963488 AX-123266364 21 2717083 GTTCCCACTTTGCTCCCCTCTGTGCCCCTAGTGGC[A/G]TCTGTAGGATCTGCTGGGTTCTGGAGACAGGAGTG R 2 1 2 1 101000 r 74 goat snp57152-scaffold91-1809334 21 3923319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774211 Affx-122926703 AX-385261348 21 2760393 GAATTATGACATACGTGGTTTCCTGTAACAAAATT[A/C]GATTTTAACTTCATTTAACACAGTAACAATTATTA M 2 1 2 1 201000 r 74 goat snp57151-scaffold91-1766024 21 3967273 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441181 Affx-122929546 AX-123311518 21 2798072 AAGCTTACCAACTTGCAGGCATCCAAGTGTGTGCT[A/G]CTCCCAGAGAGCCTGATGCTCTGAGATGTGGGGCT R 2 1 2 1 101000 f 74 goat snp57150-scaffold91-1728345 21 4005253 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277346 Affx-1111835866 AX-519550850 21 2798745 CTTATTTACACATAGTGCTGTACCCCAAACTGTTT[A/G]TTTACATTTTTTAAATAGTTTAAACTAGTTCTAAC R 2 1 2 1 102000 f 74 goat Random2.2K-1897 21 2798745 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451486 Affx-122921130 AX-123321819 21 2873782 CTCCTTGGAAATGCTTTCTCAGAGCTACTGAGATG[C/T]GGTCTCCTGGGCTCAGAATCCTAAACATTCCCACC Y 2 1 2 1 101000 r 74 goat snp57149-scaffold91-1652635 21 4080233 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379564 Affx-122976047 AX-123249922 21 2902434 GGTATCATTACATGGGTATTACATGGTGGGTATTA[C/T]AAGATATGTTAACAGTGATCACCTACATTGTTTGA Y 2 1 2 1 101000 f 74 goat snp57148-scaffold91-1623983 21 4109140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378615 Affx-122976567 AX-123248974 21 2957368 GGAGTAAAGAAGCCTAGGGTTATCAGCTGGCTGAC[G/T]GCCAACTGAGAAAAGGGGCACTTTAGGAACCCCTT K 2 1 2 1 201000 f 74 goat snp57147-scaffold91-1569049 21 4161680 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786039 Affx-122971369 AX-385273075 21 3000201 CACAAGAGAAACCAATGTTTGCTATATTAAATACA[G/T]CAGGAAAGTAATGTGCCAGAGTGGTTGCTTCATTT K 2 1 2 1 101000 r 74 goat snp57146-scaffold91-1526216 21 4203164 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403937 Affx-122957462 AX-123274289 21 3049999 ACTGGCAGAGCACAGGGGTTCTCTTTTCCCCACAT[A/G]CTTTCCAACATTGGTTATCTCTTGTTTTTTTTTGA R 2 1 2 1 201000 r 74 goat snp57145-scaffold91-1476418 21 4253685 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400879 Affx-122959758 AX-123271232 21 3079993 TAACTGCTCCTCAGTATCACTAATTCAAGATTACA[G/T]CAATATGCCTGTATATTCCTATTGCTGTTGTTTAA K 2 1 2 1 101000 f 74 goat snp57144-scaffold91-1446424 21 4283951 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421934 Affx-122943830 AX-123292281 21 3131868 ACAGTTATTACTTTGAACTCTTTATTGGGTAGATT[A/G]CCTAGTTCTAATTTACTTAATTCTACTTTTGGTAT R 2 1 2 1 201000 r 74 goat snp57143-scaffold91-1394549 21 4335575 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422120 Affx-122943557 AX-123292467 21 3206921 GTCTGGGGATGGTGAAAGTTTAGAGAGGAACCTAA[C/T]GCTCTTCACTTATCACCTGGAAGAAGAGTTAGAGA Y 2 1 2 1 101000 f 74 goat snp57141-scaffold91-1319496 21 4412204 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782412 Affx-122957580 AX-385269488 21 3241350 TTTTTGTGAGTGTGAGTTTGTGAGTTTCTTTTTAG[A/G]TTCCCATCAGATTAAAGTTGCTTTTACCATTAGTC R 2 1 2 1 101000 f 74 goat snp57140-scaffold91-1285067 21 4447224 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795187 Affx-122949259 AX-385282145 21 3270817 TGCGTAAGACAATTGAGTTGAGGGTTAAGGATTCA[C/T]CTTGCTAATGTCAAAAGTGACACTAACAAGATTCC Y 2 1 2 1 101000 f 74 goat snp57139-scaffold91-1255600 21 4477040 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463763420 Affx-1110145438 AX-515242727 21 3331073 GCCTGGAAAGAGGAGAAGAGGACGAAGGGGATGAG[A/G]TAGTTGGATGGCATTGCTGACTTGATGGACATGAA R 2 1 2 1 303000 f 74 goat 21_3331073_AF-PAKI 21 3331073 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423718 Affx-122942877 AX-123294064 21 3342505 ATTCAGCTGCTGTGTCTCCTTTGTCCCTTCCATTC[C/T]GGGACAGTGCCTCAGTCTTTCGTCGCTTTTCATGA Y 2 1 2 1 201000 r 74 goat snp57138-scaffold91-1183912 21 4548712 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417563 Affx-122946910 AX-123287911 21 3387339 TGGTTCCCTATTACGATAAACAGGAGAGAACTTAA[A/C]TGACTTTGTCATCAGGATGTATACTAGCTCTTCCT M 2 1 2 1 101000 f 74 goat snp57137-scaffold91-1139078 21 4593359 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379553 Affx-122976054 AX-123249911 21 3428092 CCTCACCTGCAGAGGATCTTGGTTCAAGCTGCCTC[A/G]GCAACTCTGGCTTCTCTTCAGAGGAGTTGGAAAAG R 2 1 2 1 101000 f 74 goat snp57136-scaffold91-1098325 21 4633808 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780467 Affx-122964586 AX-385267558 21 3480049 TTTGTCACAAAAATAATCATCACTGCATCATTAAA[C/T]GTCTTTAAAAGTTAAGCCTGATGTTCAATGGCCTC Y 2 1 2 1 101000 r 74 goat snp57135-scaffold91-1046368 21 4686897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792942 Affx-122974283 AX-385279920 21 3523781 AAAATACTAAAATCTCAGTCATAAAATAGGCAAGG[A/C]ATATTTTTTAACAGTAGAACTTTCTAATAATTAAA M 2 1 2 1 101000 f 74 goat snp57134-scaffold91-1002636 21 4730561 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434612 Affx-122934090 AX-123304953 21 3552534 CTTTGTCTGAACGACAACCACCTGGATGCAGTCCC[A/G]CCCTCAGTTTGCCTACTGAAGAGCTTATCAGAACT R 2 1 2 1 101000 r 74 goat snp57133-scaffold91-973883 21 4759246 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476353 Affx-1251763863 AX-586011768 21 3580480 TCTTCATATATGGGAAGAGCTCTGTGGTGTTTGCA[-/TGAAAAAGGTTTATTTTTTTTTTGTTTGTTTTTTTTTTTTATGGATACAAAAACAAGACCCCTCTATATGCTGCTTACAA]GAAAAAGGTTTAAAAAACAACTAAATATAAAACTA - 4 1 4 1 20000 f 74 goat SV_130 21 3580480 - deletion junction SV-TF-chip 539476609 Affx-1251763863 AX-586011994 21 3580480 TCTTCATATATGGGAAGAGCTCTGTGGTGTTTGCA[-/TGAAAAAGGTTTATTTTTTTTTTGTTTGTTTTTTTTTTTTATGGATACAAAAACAAGACCCCTCTATATGCTGCTTACAA]GAAAAAGGTTTAAAAAACAACTAAATATAAAACTA - 4 1 4 1 20000 r 74 goat SV_130 21 3580480 - deletion junction SV-TF-chip 562165113 Affx-1251763863 AX-606940525 21 3580480 TCTTCATATATGGGAAGAGCTCTGTGGTGTTTGCA[-/TGAAAAAGGTTTATTTTTTTTTTGTTTGTTTTTTTTTTTTATGGATACAAAAACAAGACCCCTCTATATGCTGCTTACAA]GAAAAAGGTTTAAAAAACAACTAAATATAAAACTA - 8 1 4 1 20100 f 74 goat SV_130 21 3580480 - deletion junction SV-TF-chip 562165602 Affx-1251763863 AX-606941013 21 3580480 TCTTCATATATGGGAAGAGCTCTGTGGTGTTTGCA[-/TGAAAAAGGTTTATTTTTTTTTTGTTTGTTTTTTTTTTTTATGGATACAAAAACAAGACCCCTCTATATGCTGCTTACAA]GAAAAAGGTTTAAAAAACAACTAAATATAAAACTA - 8 1 4 1 20100 f 74 goat SV_130 21 3580480 - deletion junction SV-TF-chip 562166253 Affx-1251763863 AX-606941661 21 3580480 TCTTCATATATGGGAAGAGCTCTGTGGTGTTTGCA[-/TGAAAAAGGTTTATTTTTTTTTTGTTTGTTTTTTTTTTTTATGGATACAAAAACAAGACCCCTCTATATGCTGCTTACAA]GAAAAAGGTTTAAAAAACAACTAAATATAAAACTA - 8 1 4 1 20100 f 74 goat SV_130 21 3580480 - deletion junction SV-TF-chip 562166322 Affx-1251763863 AX-606941730 21 3580480 TCTTCATATATGGGAAGAGCTCTGTGGTGTTTGCA[-/TGAAAAAGGTTTATTTTTTTTTTGTTTGTTTTTTTTTTTTATGGATACAAAAACAAGACCCCTCTATATGCTGCTTACAA]GAAAAAGGTTTAAAAAACAACTAAATATAAAACTA - 8 1 4 1 20100 r 74 goat SV_130 21 3580480 - deletion junction SV-TF-chip 562166412 Affx-1251763863 AX-606941820 21 3580480 TCTTCATATATGGGAAGAGCTCTGTGGTGTTTGCA[-/TGAAAAAGGTTTATTTTTTTTTTGTTTGTTTTTTTTTTTTATGGATACAAAAACAAGACCCCTCTATATGCTGCTTACAA]GAAAAAGGTTTAAAAAACAACTAAATATAAAACTA - 8 1 4 1 20100 f 74 goat SV_130 21 3580480 - deletion junction SV-TF-chip 320779873 Affx-122932505 AX-385266972 21 3593264 ATTAGCAGCTGTGGATATACTCACATAGTTTTTCT[A/G]CTTTCATCTGCCGTTCTAATGAATGATAGTAGGTG R 2 1 2 1 101000 r 74 goat snp57132-scaffold91-933153 21 4800254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432266 Affx-122936338 AX-123302607 21 3670488 GACTAGAAGTCTCTTAGTAGCTGTCCATCATGGGC[A/G]TCCTTGGAGTGGTGGAAATCAGGGTAACTCCCGTA R 2 1 2 1 201000 f 74 goat snp57130-scaffold91-855929 21 4873797 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779176 Affx-122937237 AX-385266280 21 3708487 ACAGCTAAAGTCTGGGGCACTCTCGTCTCAGCACC[A/G]TTTCTTCCTAAGTTGGGGAAGTCCTGTTTCTCACA R 2 1 2 1 102000 f 74 goat snp57129-scaffold91-817930 21 4912286 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765369 Affx-122927618 AX-385252882 21 3771692 ACTTCACTTTTTCAGAGAGGCTCCCATCTTCTTTA[C/T]GACTGGATACAAATCTCACCTTCATAAAGTCTTCA Y 2 1 2 1 101000 f 74 goat snp57128-scaffold91-754725 21 4977161 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402458 Affx-122958609 AX-123272811 21 3806847 TGTGGTGCTTGTAGAGACACTGAGGAGAAGGGCAG[C/T]GGAATATACTGGAGAAGTCACAAAGAGCGTGGGCA Y 2 1 2 1 201000 r 74 goat snp57127-scaffold91-719570 21 5012984 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428651 Affx-122938659 AX-123298993 21 3885522 GAGCGCCTCCACAGCACCTCCTTCTCTCTGCTTTC[G/T]CACACAGGTCACAGGTCTTCATGGACAGGCCTTGC K 2 1 2 1 101000 r 74 goat snp57126-scaffold91-640895 21 5093056 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394410 Affx-122964610 AX-123264765 21 3924156 ATGTGTTTTTGCCAGGAGCACTCTTCCCTCAGATA[C/T]GCCAACAGTGTCTTCTTCACCTCCTCAAAGTCTTC Y 2 1 2 1 201000 f 74 goat snp57125-scaffold91-602261 21 5131772 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449291 Affx-122923016 AX-123319626 21 3953744 AAATGGTGAACTTTATGTTATGTGTATATACCACC[A/G]TAAACTATTTTAAAGAAGGAAATGCTGGTGACATG R 2 1 2 1 202000 r 74 goat snp57124-scaffold91-572673 21 5161899 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783150 Affx-122948970 AX-385270217 21 3999194 ACGGAGATGCGATTTAGTCTCATTTCTATTTATTA[C/T]ATTTTTATACAGGTGTGTGTTTACCCATTCTTTTA Y 2 1 2 1 201000 f 74 goat snp57123-scaffold91-527223 21 5208484 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386560 Affx-122970710 AX-123256918 21 4049239 CATTTCCATATAAAATTTTAAAACAACAAAATTAC[A/G]TACTTTGCAGAAATCCCTCACTCATTCTTGTATAG R 2 1 2 1 101000 r 74 goat snp57122-scaffold91-477178 21 5258529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440309 Affx-122930213 AX-123310646 21 4106367 ACAAGACACAAGTACAAATTACTAACAATCCATTT[A/G]CAAGCCACAAGAAAACAGGAAATATTAAGGAAGAA R 2 1 2 1 201000 f 74 goat snp57121-scaffold91-420050 21 5315884 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432487 Affx-122935591 AX-123302828 21 4147701 TTCAGGTCTGCTCTTTACCTACTAACCAGGTGACC[A/G]TGGCCAGCTCACTTAGCTCTCATTTTCTTGACTGA R 2 1 2 1 101000 f 74 goat snp57120-scaffold91-378716 21 5357415 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441603 Affx-122928657 AX-123311940 21 4250209 ATTATTCCATGATGGATGCTCTACAGGAGACAAAC[A/G]CACTGATCCACTGTAACACTGGCTTCCCTGGTAGC R 2 1 2 1 101000 f 74 goat snp57118-scaffold91-276208 21 5461796 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390878 Affx-122967806 AX-123261235 21 4338385 ATACAAAGCTTGACAGAGAAGCTACAATCAGATCT[A/G]TTCATCAAAAACCTTTGGTTGGTAATATCACATAT R 2 1 2 1 101000 r 74 goat snp57116-scaffold91-188032 21 5550248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436569 Affx-122932902 AX-123306907 21 4414198 CATACAGCACGACCATCACTTAAGGGGGCGGTTGT[A/C]GTTCAGTGGCTCAGTCGTGTCCGAATGTTTGTGAC M 2 1 2 1 101000 f 74 goat snp57114-scaffold91-112219 21 5629172 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397853 Affx-122962457 AX-123268208 21 4443503 GGGAGAAAATTCAAGTCACAGAGGGTTTCAAAGCG[C/T]AGTCGAAACATTGCCTGTAACAGTAACACCAGCCA Y 2 1 2 1 101000 r 74 goat snp57113-scaffold91-82914 21 5658525 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378715 Affx-122977050 AX-123249074 21 4500972 CAAGACCTCTGCTTCCGTTAGCAGGGCCACTGTTC[A/G]CTTCTGTTTGTGCTCAGGGCTGGCCCAGCCAAGAG R 2 1 2 1 101000 f 74 goat snp57112-scaffold91-25445 21 5716427 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385622 Affx-122971185 AX-123255980 21 4527085 TTTTGAACTACAATAACTGAAATAAACTATGCATA[C/T]AAGACAGAGATAAAAACGCCAGCACTACAATGAGT Y 2 1 2 1 101000 r 74 goat snp25061-scaffold258-1932790 21 5742005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407293 Affx-122955326 AX-123277644 21 4558775 GATGCTAGGTTTGTGACCCGGGCTGCCTCCCTTTA[C/T]GGTACTCTTGGCTGGGTTTGTGAAATAAGTGCTCA Y 2 1 2 1 101000 r 74 goat snp25060-scaffold258-1901100 21 5773100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421336 Affx-122944072 AX-123291683 21 4597405 AGGCATAGGCCAGTGTTCTCCCCGTCTGCCTTGGT[C/T]TCCCCTGCAGGACAATGTCTGCATGACCTGCTGCC Y 2 1 2 1 303000 r 74 goat snp25059-scaffold258-1862470 21 5811618 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433717 Affx-122934526 AX-123304058 21 4639278 ACACTCACTCGCCCTCCGGGTGACTTGCCCGCCTC[A/G]TGCTCCTCTCGCTGAGTGGGTGGGTGTCAGCTACT R 2 1 2 1 101000 r 74 goat snp25058-scaffold258-1820597 21 5854327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408156 Affx-122954219 AX-123278507 21 4677179 CCTTTCTTTCTCCAATGTTTCCTACTTTAGACAAA[C/T]AAGTAAAAGCTTCAAAACAATACTATTTAATTTAA Y 2 1 2 1 101000 f 74 goat snp25057-scaffold258-1782696 21 5891949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378945 Affx-122976427 AX-123249304 21 4721546 GTTTCATGTGAACGCCAAGAATGGTAACAGGGTCA[C/T]GCTCCTTGTGCTATTTCACTTCCTGGGAAACAGGA Y 2 1 2 1 201000 f 74 goat snp25056-scaffold258-1738329 21 5936386 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442956 Affx-122928217 AX-123313293 21 4752325 GTTCCTCTGCTATTTCTTCTGTTCTTTACTCTGGA[G/T]TCCCTGTTAGACAAAAAATGGACACCTTTCAAGGT K 2 1 2 1 201000 r 74 goat snp25055-scaffold258-1707550 21 5967168 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393203 Affx-122965504 AX-123263560 21 4805911 GGGGGAGTAAGGGCCCCCACTGTTCTACCTGTTGA[C/T]AAATGTTTAGAGGCTGAGCAGTGAGGGGTAGGAGA Y 2 1 2 1 102000 r 74 goat snp25054-scaffold258-1653964 21 6020976 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776158 Affx-122968408 AX-385263286 21 4886061 CCACTTTGTAAACCATTTATAGCTTTGAAAGTGTT[C/T]AGTGCTTCTTTGGTTGTTATTTATGCATGTTCATG Y 2 1 2 1 101000 r 74 goat snp25052-scaffold258-1573814 21 6102134 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787151 Affx-122934399 AX-385274177 21 4953842 CTCAATAAATGCCCAAGATGACTTTGTAATGACAT[A/G]TCTTTCACTTTGCAGTATTTGCAGTAATATTTGAA R 2 1 2 1 101000 f 74 goat snp25051-scaffold258-1506033 21 6170750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423142 Affx-122942761 AX-123293488 21 5062310 TTATTTTTTTCAATTCCTTTTTAATTTTATTTTAG[C/T]TGTCATATATCCTTTAACCTGAGACAGTCCTTGAA Y 2 1 2 1 101000 r 74 goat snp25049-scaffold258-1397565 21 6278694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401101 Affx-122959411 AX-123271454 21 5123701 AAGTTGATTGCAATCTCCAAAGGTTAGATATAGCC[A/G]CCTTAGAGAAAATCCATTCATCAGTTTTGAGGTGA R 2 1 2 1 101000 f 74 goat snp25048-scaffold258-1336174 21 6341147 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444681 Affx-122926446 AX-123315018 21 5163541 GTGCAGGAAAAGGGGTGTTTTGGTTGAGGAAGTTC[A/G]TCCCCCCTCCCTGGGGACACTGAGCCCAGATGCTT R 2 1 2 1 101000 f 74 goat snp25047-scaffold258-1296334 21 6380853 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420504 Affx-122944851 AX-123290851 21 5225351 TTCCCTCTTCTTACCACGTGGGTTTCTTCCTCTGA[C/T]GAAACTCTGCTCCCTGGAAGGACCAGAGAGGAATC Y 2 1 2 1 102000 r 74 goat snp25046-scaffold258-1234524 21 6441780 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773853 Affx-122954120 AX-385260993 21 5352087 TACCATATACCATTGAATTATATGAGATATTTACT[A/G]TAATCATTTGAGGGATGTGCTGTTCTGTCTCCTTT R 2 1 2 1 101000 r 74 goat snp25044-scaffold258-1107788 21 6567435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382540 Affx-122973786 AX-123252898 21 5405141 TTCAGCCTAAAGTACTTTTTAAAATATTTCTTATA[A/G]TGCAATTCTCCTGGCAATGAACTATGATCATTTCT R 2 1 2 1 101000 r 74 goat snp25043-scaffold258-1054734 21 6621103 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795225 Affx-122937262 AX-385282183 21 5457102 GGAAATAATAGAATATAACCAAAAAGTTACAAGAC[A/G]TTGCTTATTGAAAGCTTATGTTACTACATTTGTAC R 2 1 2 1 201000 f 74 goat snp25042-scaffold258-1002773 21 6670167 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769553 Affx-122970309 AX-385256723 21 5600048 GTTGTGGAAAGGAGAGAAGTAAACACCTGGGAGAT[A/G]TGTCTATAGAATCCAGGCAACCTAAAGAACACTTA R 2 1 2 1 101000 f 74 goat snp25039-scaffold258-859827 21 6812158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430077 Affx-122937543 AX-123300418 21 5702700 TCCCAGAGACTGTCCTTCTTGCTGAAGAGGGCCAG[C/T]GTTCCCGTCTGGCATTCGCTCCCAGGAGCCCTCAT Y 2 1 2 1 201000 f 74 goat snp25037-scaffold258-757175 21 6914761 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771035 Affx-122943351 AX-385258197 21 5751513 GTCTTGGATTTTTTCTCAGTTTACTGTAATAGCGG[C/T]TGAATGGGTTGGGTACTTGTGGTGAAACCTATTTG Y 2 1 2 1 101000 f 74 goat snp25036-scaffold258-708362 21 6962193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405450 Affx-122956044 AX-123275802 21 5810065 ATTCTAAAACTGTTAGGCTAATGATACTATTGGTA[C/T]AGAAAAGAAAAGAAGGAAGTAATCAATAGAGGTCT Y 2 1 2 1 101000 f 74 goat snp25035-scaffold258-649810 21 7020528 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463765544 Affx-1110146507 AX-515244824 21 5835022 AATCTCGTTGAAGTGGAAGCCTTCAAGAGGTTAGT[C/T]CTCCCTGCCCAGACCAGCAGGCCACATGCCCACTG Y 2 1 2 1 101000 f 74 goat 21_5835022_AF-PAKI 21 5835022 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320779881 Affx-122948073 AX-385266980 21 5892765 CTGTCAAAGGATCAGATGAGGACCTCTGTGTTCCT[A/G]TCATAATAGGAAGCTTGAGGCAATATTACTACATA R 2 1 2 1 102000 f 74 goat snp25034-scaffold258-567110 21 7081867 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778184 Affx-122962444 AX-385265299 21 5950966 TACCTAAATCTACAGCTTTCGCTGATTCCAACTAC[G/T]GCCAAGATTTTGTTCGGATTTCTTTTCAGTGTTAC K 2 1 2 1 101000 r 74 goat snp25033-scaffold258-508909 21 7141244 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417587 Affx-122946891 AX-123287935 21 6014494 GGCTCAAGCAGCGGACTCTGGTTTATTCAGCATCA[C/T]GCTGACTTCACTTATCTCTCGACTGACAAAAACAC Y 2 1 2 1 101000 r 74 goat snp25031-scaffold258-445381 21 7204328 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387514 Affx-122970322 AX-123257872 21 6043629 GCACATTCTCTAACAGAAGGAAGGAAAGATTGGCA[G/T]TTAGAAGCTTCATTAAACTTTTGGCCTTTTCAAGG K 2 1 2 1 201000 r 74 goat snp25030-scaffold258-416246 21 7233421 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802128 Affx-122919859 AX-385289032 21 6091656 ATACAACATTATGGGATGTGTGTGTAATAGGATGG[C/T]GAACTGGAGAGCCACTATAGTTACATGATTATTCT Y 2 1 2 1 101000 f 74 goat snp25029-scaffold258-368219 21 7281647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414779 Affx-122949237 AX-123285128 21 6203034 TTTACTTGACCTTCCTGGGGTCCTAATAGTCTTTA[C/T]GGTAGATACAGTATTATTATTGTTCCCATGATAGA Y 2 1 2 1 201000 f 74 goat snp25027-scaffold258-256841 21 7393046 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405819 Affx-122955888 AX-123276171 21 6237162 CCAACTGGGCAAAGTCGCCTCCATTTTGCAGGTGA[G/T]AAAGGTGATATCAAAGGAACAAGACACATTCTCTT K 2 1 2 1 101000 r 74 goat snp25026-scaffold258-222713 21 7427199 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411202 Affx-122952366 AX-123281552 21 6282280 AGATCCGGCCCTCAGACCCAGGACTCCAAGCTTAA[C/T]GCTCTTTCCAAGATGGGTCAGTTGCAGATGGGGCA Y 2 1 2 1 101000 r 74 goat snp25025-scaffold258-177595 21 7472854 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790861 Affx-122940258 AX-385277859 21 6314172 GATGGTAATTCTAAAGTATACTTTACCCTCAATGT[A/G]CCTGAAATGACAGCACCAACTTGGTTGGAATTATA R 2 1 2 1 201000 r 74 goat snp25024-scaffold258-145703 21 7504143 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390700 Affx-122967941 AX-123261057 21 6377307 TGGTTGCATTGCTCCAGCCCAGAGCGAAAACACAC[A/G]TGCTCCATGAAGGACTTCATTCAAGGGGTAAAGCC R 2 1 2 1 201000 f 74 goat snp25023-scaffold258-82568 21 7566505 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800928 Affx-122934600 AX-385287843 21 6407801 AAAACTAGGGGTGAATAGTGCATCACTGGAAAGAC[A/G]TTTGTGAAGGCCCAGAGACATAGGCACACCAAAAT R 2 1 2 1 101000 r 74 goat snp25022-scaffold258-52074 21 7596830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421594 Affx-122944495 AX-123291941 21 6446345 GTCTGGGGGGTGATTCTGACTCAGTTGGCTTGCAC[A/G]TGAAATATGCACTCACAGGGAAGTCCTCCACTGTC R 2 1 2 1 101000 r 74 goat snp25021-scaffold258-13530 21 7635083 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381848 Affx-122974192 AX-123252206 21 6467465 CGGGTTGGGAGGGCTGGGAACCAGGGAAGAGCCTC[A/G]TCCTAAGTCGTGTCCCAGACCTTGGATTTCCCTGC R 2 1 2 1 101000 r 74 goat snp14993-scaffold1603-7491 21 7655901 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420334 Affx-122945003 AX-123290681 21 6497018 CAACAAAGAAGTTAAAAAGTGGAAAAAGAATGCAA[C/T]GGTTACTATAGAGTTAAATTTAGCGAAGGTATATG Y 2 1 2 1 101000 r 74 goat snp14994-scaffold1603-37044 21 7685472 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769113 Affx-122962853 AX-385256288 21 6526291 GAGTTGACTTCTCTCATAAATTCAAGAACAAAAAG[C/T]AATAAATTGAACATATGAAGGACGTTGCTTTTTTT Y 2 1 2 1 101000 f 74 goat snp14995-scaffold1603-66317 21 7715005 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436045 Affx-122932720 AX-123306384 21 6565092 AGACAAAAGCAAAAAACCCCTAAATCAAACCAAAA[C/T]AAAATGCTGGGTGCACAGCAGCTCAGGTAGAGTAA Y 2 1 2 1 102000 r 74 goat snp14996-scaffold1603-105118 21 7753869 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391930 Affx-122966933 AX-123262287 21 6597979 TCTGTAGACCTTCTCTCTCTCACAGTTATTTAATG[A/G]AGAAACCAGGTTGTTTGTTCTACAGAATTTTTCAT R 2 1 2 1 101000 r 74 goat snp14997-scaffold1603-138005 21 7786727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430320 Affx-122938229 AX-123300661 21 6640124 CGTTTTAGTCTGTCAGTACCTGTGGGGGATCTGTC[C/T]GCAGTTATCCACAGCCCACCCTCCAAATTCCTTCC Y 2 1 2 1 101000 r 74 goat snp14998-scaffold1603-180150 21 7829389 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389631 Affx-122968745 AX-123259989 21 6670824 CTGTAAAGAACAGAAATTTGGAAACTACACATCAC[C/T]ACATAAATGTAAAAGATTTGTTTGACTTTAAGAAT Y 2 1 2 1 101000 f 74 goat snp14999-scaffold1603-210850 21 7860690 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424748 Affx-122941653 AX-123295094 21 6709034 TGGTATTCTGCCAAATATCTCTCTATTTGATGTAG[C/T]AGAGGATACCACACAATGGGGGGTATAAACAACAG Y 2 1 2 1 201000 f 74 goat snp15000-scaffold1603-249060 21 7898621 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382703 Affx-122973631 AX-123253061 21 6746340 TCTGCAACTTAATTTCCATCTGCCAATGAAATAAA[C/T]CTGAAACCTTTCATCTGGGTTAATAGCCTAACTGA Y 2 1 2 1 201000 f 74 goat snp15001-scaffold1603-286366 21 7935864 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450782 Affx-122921828 AX-123321116 21 6784589 TTTCATGGGTGGCAATTTAGTTATGGAAGGTAGAA[C/T]GGCAGAGGTGTATGTTCAACAGTTTTGTCCCTTTT Y 2 1 2 1 101000 f 74 goat snp15002-scaffold1603-324615 21 7973922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446904 Affx-122924705 AX-123317240 21 6819714 AAGCAAGAGAAGACCCAGAGACCCCCAGAGAACCA[C/T]GGAGACATGATGACAATGAAATGTGGTGTCCTAGA Y 2 1 2 1 101000 r 74 goat snp15003-scaffold1603-359740 21 8009279 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450980 Affx-122921735 AX-123321314 21 6872392 GTTTCCATTCAGTGCAGTTTGTCCCTAATCATCCC[A/G]GTGGACAATTAATGCCAGGTCGTCCACGCATTTGG R 2 1 2 1 101000 f 74 goat snp15004-scaffold1603-412418 21 8062060 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412988 Affx-122951025 AX-123283337 21 6923912 CTGTTGAGAGACTGATATCTGTCTAGAAGTCTAAA[C/T]GATACCTTTTCTTAAAATTAGTTTTTATAGGAGTA Y 2 1 2 1 101000 f 74 goat snp15005-scaffold1603-463938 21 8112659 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277349 Affx-1111835868 AX-519550853 21 6954275 TTAGGGTGATGAAAAAAATTGTTTTGCATTAGAAG[A/T]CAGAGGTCTTGGGTTTGAGTCCTAGTGTGTTAATC W 4 1 2 1 201000 f 74 goat Random2.2K-1902 21 6954275 A T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427575 Affx-122939476 AX-123297918 21 6964722 TCAGCACTGAATGCAGGTAGCTGCTTGAATTCCTG[C/T]AGGACTGGCTGCCCCCTTAAATCACCTCACAAGCA Y 2 1 2 1 201000 f 74 goat snp15006-scaffold1603-504748 21 8154294 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767326 Affx-122956768 AX-385254603 21 6994147 AGCACAGCAACCAAATTGGACTTGCCCTATTTATC[A/G]TTGAAATTAGCATATCATCATGCATGCTTTCAGGT R 2 1 2 1 101000 f 74 goat snp15007-scaffold1603-534173 21 8183995 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400610 Affx-122960385 AX-123270965 21 7037016 GCCGTGTGTCTCTGCAGCATCTGTGTCACAGCTAC[A/G]CTGGCTTTCTTAAAATTTAAAATAAGCACCGTTAA R 2 1 2 1 101000 f 74 goat snp15008-scaffold1603-577042 21 8226903 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401175 Affx-122959353 AX-123271528 21 7087411 TTATTTGCTTTTATGAGTGATTCAAAAAAAGAAGG[C/T]GATCTCTTCTGGTCTTTGCTTAGTGAGAAGATGAT Y 2 1 2 1 101000 r 74 goat snp15009-scaffold1603-627437 21 8277503 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429070 Affx-122938289 AX-123299412 21 7138601 TGAAAAAGAGCAAACTTATTTTGGGCTCCAAAACC[G/T]CTGGGATGTAGCCGTGAAGCTAATACTCATGTTGC K 2 1 2 1 101000 r 74 goat snp15010-scaffold1603-678627 21 8328923 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436463 Affx-122932983 AX-123306801 21 7186574 ATGGTGGTCATCCCCAGAAGGGAATCTCTCTCTTA[C/T]ACTTCTGTGTTGAAAAACAAACAAAGATTCCCTAT Y 2 1 2 1 103000 f 74 goat snp15011-scaffold1603-726600 21 8376431 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439319 Affx-122930951 AX-123309656 21 7234603 TATAGAGAGACATAAGATAAATATAGAAGAAAATG[C/T]AAGAAATCTTTGGACATTGTCACTTCTTTAACATG Y 2 1 2 1 101000 r 74 goat snp15012-scaffold1603-774629 21 8424938 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788768 Affx-122966266 AX-385275783 21 7265296 TTCTATTTTGTCCCATTGGACTGTCTGTCTATGCA[C/T]AGGGAAGTACTTGTTGATGTGGTTAAAGTGGCTTT Y 2 1 2 1 101000 r 74 goat snp15013-scaffold1603-805322 21 8456005 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391393 Affx-122967264 AX-123261750 21 7314906 TTTTATATTTAGAATGTTTCTGAACATGTGGATGC[A/G]TCTTTCTGGTTGATAGAAACATTCTATTCTGTTTT R 2 1 2 1 101000 r 74 goat snp15014-scaffold1603-854932 21 8506105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436406 Affx-122933025 AX-123203649 21 7343636 CTGGATCACAACTAGGAGCTGGCTAATTAGATTGG[C/T]GGTAGTAAGAAATAGATGGGCAGAGGAATTAGTGG Y 2 1 2 1 101000 f 74 goat snp2907-scaffold1089-423120 21 8534563 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395935 Affx-122963585 AX-123266290 21 7375146 GAGGAAATGTGTGAAAAGGTGAGGTTTGTTTATTA[C/T]AATCTCAACTCATTCTTCCAAAAATAAAGCTTTTT Y 2 1 2 1 101000 f 74 goat snp2906-scaffold1089-391610 21 8566511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765842 Affx-122927461 AX-385253289 21 7493344 ATACTAATCTGTGAGAATTAAAGTTCTGAAGGGAG[C/T]GTTAGTCACATAGTAGTTATTCCATAAATATCACA Y 2 1 2 1 101000 f 74 goat snp2904-scaffold1089-273412 21 8686494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396398 Affx-122963016 AX-123266753 21 7537175 AAAGCAAGGGATGAGCTTTCTTGGGTGATTCCCCC[C/T]CTAGGGTTGCTGTCCCTGGGTCAGTGAGAAGCCAT Y 2 1 2 1 201000 f 74 goat snp2903-scaffold1089-229581 21 8730158 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411103 Affx-122951916 AX-123281453 21 7569364 GGGCAAACCAAGCCTCCTCCCCTTCTAGTTCTCTT[A/C]GCCACTGAATCTTCCGATGGAAGATCTACTAAGAA M 2 1 2 1 103000 r 74 goat snp2902-scaffold1089-197392 21 8762413 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788936 Affx-122922052 AX-385275949 21 7632250 GTAATAGCATTCTCAACAGTATGTCCGGGCTTCCT[A/G]CTCTTTTTGATGCCTCTGATATACTAACAGTCACT R 2 1 2 1 101000 f 74 goat snp2901-scaffold1089-134506 21 8825224 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426414 Affx-122940834 AX-123296760 21 7674302 GACAATTTCAGTATCTCCTGCTCATCAAAGGGCTA[C/T]AGAAAATACATGCACTTTCCTCTTTGGTACTGAAA Y 2 1 2 1 101000 f 74 goat snp2900-scaffold1089-92454 21 8866994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440083 Affx-122929726 AX-123310420 21 7721410 GTGATTTCCTTGGAGCCCCTCTGTTGAAGCTAGTC[A/G]CTGACAATTGCCTTAGCATCACCTCAGCTGGAACC R 2 1 2 1 201000 r 74 goat snp2899-scaffold1089-45346 21 8915189 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773097 Affx-122970036 AX-385260240 21 7752366 CATACATAAGTTATAGAGTAGTCAGATTCTCTGAC[A/G]TGGTACAGAGTCGTTGTGGAGTGCTGGGAGGAGAA R 2 1 2 1 102000 r 74 goat snp2898-scaffold1089-14390 21 8946035 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772780 Affx-122973538 AX-385259925 21 7771104 TCATGCTTAAGTTATCTGTTGCAGACATTATGTTC[C/T]AGTGAAATTCAGTCAGGAGTCAGTTCTTAAGTCCA Y 2 1 2 1 101000 r 74 goat snp50302-scaffold72-4249 21 8978488 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412877 Affx-122950430 AX-123283226 21 7808696 AGATTTTCAGGGATTACTTGCATAGGGGATAGTAT[C/T]TTCTGTTCAGAATGTTCCTACCCATTTTGAGATTT Y 2 1 2 1 101000 f 74 goat snp50303-scaffold72-41841 21 9015777 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784524 Affx-122964709 AX-385271573 21 7841859 AAAGGGCAAGTAATTTATGCTGCTCACTCTAGAAC[C/T]GTTAATGGTATTATAAGACCTGACATGTTGCCAGC Y 2 1 2 1 101000 r 74 goat snp50304-scaffold72-75004 21 9048444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784127 Affx-122968812 AX-385271179 21 7880045 AATTTTTTACCCTGTTTTTGTCAATCAGTTCATTG[C/T]GCAAACTAATCAAAATGTGTTTCATTTCTAGATAC Y 2 1 2 1 101000 r 74 goat snp50305-scaffold72-113190 21 9086717 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392026 Affx-122966476 AX-123262383 21 7926986 AGAAAGCCTTGAAGACATCCCACTGCTGGAACACC[A/G]TGTTTGAAATAGGGACTTTTTACGTTCAGATGATT R 2 1 2 1 201000 r 74 goat snp50306-scaffold72-160131 21 9133580 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425768 Affx-122940725 AX-123296114 21 7963519 CTGCAAGAGGTAAGCAAGACTGGAGATGTCATCAA[C/T]ATTGATCAGTGGAAATTTGCAGATTCCCAAAAGAG Y 2 1 2 1 101000 f 74 goat snp50307-scaffold72-196664 21 9170661 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453736 Affx-122919619 AX-123324069 21 8003594 GAATGAGAAGTGCCCGCAGACATTCTGTTGTTGGG[C/T]AGCTAGAGCGGAAACTGTCTCATGGGTTGACCCTG Y 2 1 2 1 101000 f 74 goat snp50308-scaffold72-236739 21 9210863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423369 Affx-122943142 AX-123293715 21 8036874 GGGAAAAAAAAAATACTAGTGGGCGCCAGAACTTA[C/T]GAAGCAACTCTCATCAAGGGCATCTGAGCTTTTGC Y 2 1 2 1 101000 f 74 goat snp50309-scaffold72-270019 21 9243857 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416984 Affx-122947999 AX-123287332 21 8068763 GTCATATTCTCCCCAAGAAAATCCCTGACTTTATC[C/T]AGCTTCTTACCCTCCACTTCCAGAAGGTTTATTTC Y 2 1 2 1 102000 f 74 goat snp50310-scaffold72-301908 21 9275846 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424285 Affx-122941983 AX-123294631 21 8099662 AGGTGAAGTGATGAAAAGAGGCAGAATATTCTAGT[A/G]CAGTTTGAGAAAGATGGGTGTACTACTTACCTGCA R 2 1 2 1 101000 r 74 goat snp50311-scaffold72-332807 21 9306505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799523 Affx-122955284 AX-385286453 21 8185937 CTGATTTCAAAACCTACCATAAAGCTGTCGTAATC[A/G]TGATAGTATGATCTGGGTATAAAGACAGATATGTT R 2 1 2 1 101000 f 74 goat snp50313-scaffold72-419082 21 9393479 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768511 Affx-122973402 AX-385255691 21 8221130 TCAGGCCAGTGGCAATAAGGATATTAGGGAAATGA[C/T]GGAATTCTCCCCCAGCTGGACATGTTAATTGAGAA Y 2 1 2 1 101000 r 74 goat snp50314-scaffold72-454275 21 9428776 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394888 Affx-122964745 AX-123265243 21 8262061 TATTCTTCTTCCAGAGCTTTAACTAATTCCATCCC[A/G]TCACCCAGAAAATTGTTAGTGTCACATTCCCAGAG R 2 1 2 1 101000 f 74 goat snp50315-scaffold72-495206 21 9469742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383480 Affx-122973438 AX-123253838 21 8307453 CTGTGGTTCCAAGGAAATAATGATTGAAATACTCC[A/G]CAATGGAACAACATGATAACCAGACAGTAGTTGCT R 2 1 2 1 101000 f 74 goat snp50316-scaffold72-540598 21 9515031 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401396 Affx-122959216 AX-123271749 21 8338293 GCATCCTCCCCTGAAGGCATCACATTTATAGTTGA[C/T]AAACAAAATGATTTAAAATTGTATTTTTGCTGAAA Y 2 1 2 1 101000 f 74 goat snp50317-scaffold72-571438 21 9545678 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271940 Affx-1111833232 AX-519545716 21 8344469 TTCTAACCCACATGGTTGGGTCTCAAACTCAGCCA[A/G]AACCTTGCTTAGGACTTGAACCAGTTTGGAACTTT R 2 1 2 1 101000 r 74 goat 21_8344469_AF-PAKI 21 8344469 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38376911 Affx-122977798 AX-123247270 21 8367591 TTTAGAAAGCAAAAGTTTATAAGCAAAATGTGCTG[C/T]GCTGCTCTGTGCCAAGACACTTCAGGCTTGTCTGA Y 2 1 2 1 201000 f 74 goat snp50318-scaffold72-600736 21 9574639 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782830 Affx-122958339 AX-385269901 21 8413556 TTGATGCCAAGTACTTTCCTTCTGGAATTTTAAAC[A/G]TCCCCCCACTGAGCAGGAAATCATATACCATCCAG R 2 1 2 1 101000 f 74 goat snp50319-scaffold72-646701 21 9620106 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783426 Affx-122966298 AX-385270489 21 8447668 ACTAAATATATAGCCCACTTTATTTAAGAAAGATA[C/T]CTATATTCCAGAAATGGAACATTATGGTAATAATC Y 2 1 2 1 101000 r 74 goat snp50320-scaffold72-680813 21 9653418 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794429 Affx-122952636 AX-385281392 21 8634785 ATCTTTACTGGGGTTCTTTGGGATTCTCAAAGACG[C/T]TGTAAACTTTATTTTTATGACCAGTCATTTGGGGA Y 2 1 2 1 201000 r 74 goat snp50324-scaffold72-867930 21 9842634 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767393 Affx-122974276 AX-385254666 21 8670195 TTCCAAAATTATCTCTTTCAGATCATTTCTCCTTA[C/T]GTATGCAGTTTAGAAGTTTATGGCGAGTTAAACAC Y 2 1 2 1 101000 f 74 goat snp50325-scaffold72-903340 21 9878022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408009 Affx-122954311 AX-123278360 21 8700968 TAAGTATATTCACCTTTTAATTCTCACCATCCCCT[A/G]TCTGACCCACCTCCTACACCTGCTGTAAGGATTAA R 2 1 2 1 201000 f 74 goat snp50326-scaffold72-934113 21 9908834 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793859 Affx-122957374 AX-385280828 21 8777584 AACACAGGGTCCGGAGTTTTATGCTCAGATTCCAG[C/T]GGCATGAGATGAGAAGCAACTCAAAGTCAAGGTTG Y 2 1 2 1 101000 r 74 goat snp50328-scaffold72-1010729 21 9986096 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378239 Affx-122976905 AX-123248598 21 8815082 CTTTTCTAGCAAGTAGGATATGATGGTTACCTTCC[A/G]TCATTGCTGTCCTTGATTCTGATCATCTTTCTAAT R 2 1 2 1 201000 r 74 goat snp50329-scaffold72-1048227 21 10024223 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438267 Affx-122931411 AX-123308605 21 8865812 AACTCAAACTATTCTACAAAATTAAAATCCTGACA[C/T]GTTGTTGGTTAAACTATTCTGTGCCTTGTGAACAT Y 2 1 2 1 101000 r 74 goat snp50330-scaffold72-1098957 21 10075064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447011 Affx-122924550 AX-123317347 21 8906959 GATTTTTAAGCTGGGGAGTGACATGGTCTGATTTA[C/T]GTTGTTTAGAGGTCGATGACCACCATGTGGGGAAT Y 2 1 2 1 102000 f 74 goat snp50331-scaffold72-1140104 21 10116813 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406799 Affx-122955697 AX-123277150 21 8937706 AGCAGTTAAACTGAAAGTGAATAAAGGAGTTCAGG[C/T]TCAATTATCTATTCCCAATTGTATGTTCCAAAAAC Y 2 1 2 1 101000 r 74 goat snp50332-scaffold72-1170851 21 10147981 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428025 Affx-122939145 AX-123298368 21 8968590 TCAACTAGTAAGATAAATAAGCTAGATCACATTTA[C/T]GTCTCAAAATTAGCCTGGCCATACAAAATTATACC Y 2 1 2 1 101000 r 74 goat snp50333-scaffold72-1201735 21 10179465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428693 Affx-122938631 AX-123299035 21 9010677 CGCAACTCCATTTAATACAAAGAGGAGTGTGATGT[A/G]TGATGTGGAGTATTTTATTAGATGTGATCACTTTT R 2 1 2 1 101000 r 74 goat snp50334-scaffold72-1243822 21 10222082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447109 Affx-122924476 AX-123317445 21 9048894 ACCAAAGCCAAAACAGTGATCATTTATAACCATTT[C/T]GTTAGCTCCAAGGACAAAAGACCCAGAATTCCCTT Y 2 1 2 1 101000 f 74 goat snp50335-scaffold72-1282039 21 10260323 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429961 Affx-122938069 AX-123300302 21 9090067 GCCTGAGGTTGCTACAGCCCAGGATATAACCAGGA[C/T]GTAATCAGCAATCGTAGTAAATCAGTGGGTTCCCA Y 2 1 2 1 101000 r 74 goat snp50336-scaffold72-1323212 21 10300570 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440598 Affx-122929284 AX-123310935 21 9122820 ATTTGCATACTAGCTTGGCCAATTACTAGATGTAT[C/T]GTCTTGGGTTGGATGAGATCAGAAAACATATAAAA Y 2 1 2 1 101000 f 74 goat snp50337-scaffold72-1355965 21 10333331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395531 Affx-122963863 AX-123265886 21 9176191 TTGTCTGTAAGATGGACAAACTACACATATCTGTA[C/T]GATTTTCTTTCTTTCTTTCTTGTCCCTTATGTTCT Y 2 1 2 1 101000 f 74 goat snp50338-scaffold72-1409336 21 10386483 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447969 Affx-122923762 AX-123318305 21 9248469 ACAAAAAAGTATCTCCAATAAACATGCAACTAAAG[C/T]ACAATTCTAGCAGAAGAATTAGCAAACTAATGTCA Y 2 1 2 1 101000 f 74 goat snp50339-scaffold72-1481614 21 10459455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436681 Affx-122932458 AX-123307019 21 9290124 ATTAAATATAAATCCTTCAGAGGTTTCTAAGTGTT[A/C]TCTCTCTAAAAGACCTCTTCTGTTTGTCCCATAGA M 2 1 2 1 101000 r 74 goat snp50340-scaffold72-1523269 21 10501768 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794006 Affx-122973458 AX-385280975 21 9319247 TGAAGTATTTTACTGGGAAGGGACCATCTCTAGAA[C/T]GAATTAATTAATATGGTGATATCATGCTGGTATAA Y 2 1 2 1 101000 f 74 goat snp50341-scaffold72-1552392 21 10530972 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376265 Affx-122978762 AX-123246624 21 9355055 ATTTTCCTCACTTTTCCTGAGCTTCTTGTCAAGAA[C/T]GGATGAATAAAAACTTACCAGACTCTCATCTACTT Y 2 1 2 1 101000 r 74 goat snp50342-scaffold72-1588200 21 10567476 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400356 Affx-122960033 AX-123270711 21 9390480 GGATCAACTAAAAGTCACATTTTAAAAACATTTAA[G/T]AGCATGATGCATGAAAAAATACATGAGAGCATACA K 2 1 2 1 103000 r 74 goat snp50343-scaffold72-1623625 21 10602882 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442790 Affx-122927726 AX-123313127 21 9430643 GCCATAATTGTGCAAACTTGGAAAGGAAGCTGGGT[A/C]TAACACAGAACCTGCCTGCATACTCACCAGAATAC M 2 1 2 1 201000 r 74 goat snp50344-scaffold72-1663788 21 10643068 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773523 Affx-122936087 AX-385260664 21 9466012 CTTGCGTTACATTTTTTTGCACAATTTGTCTTTTG[A/G]TTTCTTAAATTCAGAATAGCCATATAGAATCTCTA R 2 1 2 1 101000 f 74 goat snp50345-scaffold72-1699157 21 10678323 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785586 Affx-122961383 AX-385272630 21 9494680 GACTCTTACCAAATCCAGGCCATGAATATTTTCTG[C/T]ATGGCATATTATTGAACAGTCAAATGAATTTCGTA Y 2 1 2 1 101000 f 74 goat snp50346-scaffold72-1727825 21 10706807 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412809 Affx-122950480 AX-123283158 21 9538892 TAAGGTTTACTTGATCCATATAGAAGTGGAATGCT[C/T]ATTGTATAATTATTATACAGATGAATAGTTTTGAA Y 2 1 2 1 101000 f 74 goat snp50347-scaffold72-1772037 21 10751263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779459 Affx-122923669 AX-385266562 21 9568946 GGTCCCAAAGCTCATCTTCTCTCAATGAACAAGAA[C/T]AGTCAAATATGTTTTAGCTCCAAATCACAATGTAA Y 2 1 2 1 101000 f 74 goat snp50348-scaffold72-1802091 21 10781259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770769 Affx-122920583 AX-385257933 21 9610901 TGGCATGAAGGAAAGTTAACTAAATTAGTGGCCAA[C/T]TGGGACACTTGGTGACCTACTAAGGAACTAAGGAA Y 2 1 2 1 101000 r 74 goat snp50349-scaffold72-1844046 21 10824959 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785045 Affx-122974430 AX-385272092 21 9668849 TGGTATAGAAAGTTTAAATCTAAATATCAATCTTG[G/T]AACATTCTAGAACCTGAAACCCAGAGCAGATCCTT K 2 1 2 1 101000 r 74 goat snp50350-scaffold72-1901994 21 10883094 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426109 Affx-122940635 AX-123296455 21 9704221 ATACTTCTTCCCTCAAGCCCACTAATTTACACCAC[A/G]TATGGAAAGAAGATATAAAAATGTCCTGGTTTTGA R 2 1 2 1 103000 f 74 goat snp50351-scaffold72-1937366 NW_017211125.1 16181 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391386 Affx-122967269 AX-123261743 21 9745193 ACATTACTTGATAATGTCAAAACATTGTCCAAAAT[A/G]GTGACATCGATATTTTCTCCATGCAACAATGAATG R 2 1 2 1 101000 r 74 goat snp50352-scaffold72-1978338 21 10959478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399708 Affx-122960475 AX-123270063 21 9776968 TCTCCATGATGTTCACGATATATTTTTTCCTGTTA[A/G]CCCGTCTGTCTGTTTCAACTCTCGTTCTCAACCTA R 2 1 2 1 101000 r 74 goat snp50353-scaffold72-2010113 21 10991370 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772023 Affx-122977105 AX-385259179 21 9839029 GGACACAATATGGTTGGCACTGTATAAATTCAGCT[A/G]TTTTGACAGGAAGGCAGAAGACTTTTTTACTCCAT R 2 1 2 1 101000 f 74 goat snp50354-scaffold72-2072174 21 11050256 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409747 Affx-122953013 AX-123280098 21 9892272 TGGAGGAATCAGTCAAAAGACAGATTCACTGAAGC[G/T]ACCTTCCAACTCCCTATTTCTTCTCTCTCTTATTG K 2 1 2 1 201000 r 74 goat snp50355-scaffold72-2125417 21 11104557 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772532 Affx-122944100 AX-385259683 21 9924915 AATGTGTAACTTCCTGTAAGTCACTTTTGGTTCAA[C/T]GGCAAATAGCAGCTAATTGCACAATTGAGTGCTGA Y 2 1 2 1 101000 r 74 goat snp50356-scaffold72-2158060 21 11137195 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394453 Affx-122964584 AX-123264808 21 9983393 GACTCCTACCCAAAATGGGCAGGTTCAGAAACCAG[C/T]AAAGGGGAGAGTTGACATGACTGGGAAGTGAAACA Y 2 1 2 1 201000 f 74 goat snp50357-scaffold72-2216538 21 11196169 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397806 Affx-122962493 AX-123268161 21 10034287 TGAGAAATAAATAAAACATGGAAGATGCTGATGGC[A/G]CTCTTCTTTCCTCCCCTTCTGGGAGGAATCAGTCT R 2 1 2 1 103000 f 74 goat snp50358-scaffold72-2267432 21 11247073 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777875 Affx-122968235 AX-385264991 21 10087489 ATGCTCCTTTCGTTAGTTTGTTTAATGAATTATTC[A/G]TTCAATTAATGCTTATATAGCTTTTGCTTTGTTCC R 2 1 2 1 201000 f 74 goat snp50359-scaffold72-2320634 21 11300578 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424510 Affx-122941737 AX-123294856 21 10132338 TTTTGCAAGCCTGAAAAAGGTAAGTGCTATGTTTT[A/G]CTATCGCTAAGCTTCAGAAAACCCCAAGGCCAACA R 2 1 2 1 101000 r 74 goat snp50360-scaffold72-2365483 21 11346583 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386303 Affx-122970923 AX-123256661 21 10167058 ATGGAATATTTCCTCAATAGGAGAAATCCATGGAG[A/G]TCAAGCTGCTGAATGAGAAGGTATAAACAAAGTCA R 2 1 2 1 101000 f 74 goat snp50361-scaffold72-2400203 21 11380697 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786122 Affx-122966243 AX-385273158 21 10225232 AACTTTGTCAAATACAACCACTCTTTACAAGTAAC[A/G]ATGACTAGAGACACAGCTGATTAGACCAAAGGTGT R 2 1 2 1 101000 r 74 goat snp50362-scaffold72-2458377 21 11437221 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404954 Affx-122956421 AX-123275306 21 10255148 ATGAAGGGAACAAACAGAAAGTGTACAGAGAATTC[A/G]TTTTCTCTATTTGCAGCTGAGAAATATGTAAGGGT R 2 1 2 1 102000 r 74 goat snp50363-scaffold72-2488293 21 11466324 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447510 Affx-122924072 AX-123317846 21 10291289 CAGTGGTGTGGGCAAGAAAAGAAACACAAGAGGAC[A/G]TTGGAAATGGATCTTGGACATTATTCTAAGCTTGA R 2 1 2 1 101000 r 74 goat snp50364-scaffold72-2524434 21 11502724 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439324 Affx-122930306 AX-123309661 21 10353311 GAAAGAAGGAAAAGGTCAGTTCCTTGCTCTCAAAG[C/T]AACAATTACGTAGGAGGAGAATCAAAATGGAAGCG Y 2 1 2 1 201000 r 74 goat snp50366-scaffold72-2586456 21 11564807 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391222 Affx-122967401 AX-123261579 21 10396630 TGAGTGAAACAGAAAGCAGCCTTCAACTGTTGCCA[C/T]GTTAGCTGACTTATTTCACTGGTGGTTTCCTCCCT Y 2 1 2 1 101000 f 74 goat snp50367-scaffold72-2629775 21 11607025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800978 Affx-122959423 AX-385287892 21 10443772 AAGAAACACCTTATGGAAATGTGCCTGGCACACAA[C/T]AGTCAATCAAGAAGCATGAGCTCCACGTGCCCTTT Y 2 1 2 1 101000 f 74 goat snp50368-scaffold72-2676917 21 11654668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378540 Affx-122976619 AX-123248899 21 10479318 CTCTCAACTCAGTCATCATTTTTGATGCCTTTAAC[A/G]TGAACATACAACCTGGAGGCTTCCCGATTTTTAGA R 2 1 2 1 101000 r 74 goat snp50369-scaffold72-2712463 21 11689759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791444 Affx-122936934 AX-385278435 21 10518966 GAAAGACACCTTGTGATCTGACACCACCAATTTCT[A/C]CGGATTCATGTCTCACTTTGTCTCCACTGAACTGT M 2 1 2 1 101000 f 74 goat snp50370-scaffold72-2752111 21 11729873 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412837 Affx-122950459 AX-123283186 21 10554632 TATAAAAAGTCTTAAATTTATATTACATTTTTGTA[C/T]GAGCAATGAGGGGTTTGAGAGATAGATGGAAAGAG Y 2 1 2 1 303000 f 74 goat snp50371-scaffold72-2787777 21 11765353 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413348 Affx-122950157 AX-123283697 21 10585314 GGGAAAAATACCTAATGAAGTGACAGTGTTTGAAG[C/T]AGGAACTGAATGAGTAGAAGGGGTCAACTACGTGA Y 2 1 2 1 101000 f 74 goat snp50372-scaffold72-2818459 21 11795675 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404440 Affx-122956754 AX-123274792 21 10626462 GAACTCCTTTATCTGACTAAAAGCAGAGACTCCTA[A/C]AAAGAACTGAATTGTTTTAAATTCCCTGTCCAAGA M 2 1 2 1 101000 f 74 goat snp50373-scaffold72-2859607 21 11837099 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388376 Affx-122969326 AX-123258734 21 10678835 ATTTCTTCCCTGTACCGTGAACACATGAGCAGTGT[C/T]GCTCCTCCAGTCTCAAATGTGGTGGATCGGGTCAT Y 2 1 2 1 101000 f 74 goat snp50374-scaffold72-2911980 21 11889058 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375953 Affx-122978448 AX-123246312 21 10714188 AAAATGTATGGCTTGCTTTCATAAAGTCTTAAAAT[G/T]AACAGCCAGAATATCCTCAACATGATCCTATAGCA K 2 1 2 1 101000 r 74 goat snp50375-scaffold72-2947333 21 11924893 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387435 Affx-122970387 AX-123257793 21 10752589 TCACAAGCTTCTCACACGTCTTGGAAAAGCCCTGC[A/G]GGCTTGGAATGTGTTGTTCCCTCATTTGAAAACTT R 2 1 2 1 101000 r 74 goat snp50376-scaffold72-2985734 21 11963855 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786401 Affx-122952100 AX-385273435 21 10790427 CAGATGGCAACTGGGCAACCATGTGGGAAACACAA[C/T]GCTCATCTACACGGCATGTCATTTTAACCTGGCAT Y 2 1 2 1 101000 f 74 goat snp50377-scaffold72-3023572 21 12001064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277475 Affx-1111835869 AX-519550978 21 10817512 CACATAATGCCCAAGCAAGCAAACCAAAGCTTTGA[A/C]TTTGGTTTACACTAATAGTAAGACTATCTCGCGGG M 2 1 2 1 101000 r 74 goat Random2.2K-1904 21 10817512 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38406977 Affx-122955049 AX-123277328 21 10831629 TTGCGATTGCCACATACTGGGCTATGAGCTAATTC[G/T]ATTTTTCTAGCGTCATAAACAACAACCTTAACTAC K 2 1 2 1 101000 r 74 goat snp50378-scaffold72-3064774 21 12042181 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272980 Affx-1111833210 AX-519546662 21 10861787 AAAAAGAACAAAACACTTTCTATCCTCAAGCTGGT[A/G]GGAAAATTGATATAATTTTAAAACACAGTGTTGTT R 2 1 2 1 101000 f 74 goat 21_10861787_AF-PAKI 21 10861787 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320777136 Affx-122937220 AX-385264259 21 10871268 TCACAAGATTGGGCAACAGTACAAACACCTCATGG[C/T]TGGGTGGAAGAGAATAAACAACAGTTCCTGGATGG Y 2 1 2 1 202000 r 74 goat snp50379-scaffold72-3104413 21 12081286 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388825 Affx-122968894 AX-123259183 21 10906494 AGATTCCTGCCCGCTGGGAGGTCGGGAATTCACAA[C/T]ACACCCCACCACCCACAGGAAAATAGCTTTGAAAT Y 2 1 2 1 202000 f 74 goat snp50380-scaffold72-3139639 21 12116181 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418726 Affx-122946276 AX-123289074 21 10937787 TTAGTTGACTCCTTAATAAGAAGGTAATACCTCTT[A/C]ACCAGAAAGAACATGAGAAGAGCTGTTACTGGATT M 2 1 2 1 201000 f 74 goat snp52035-scaffold765-754333 21 12151240 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428384 Affx-122938958 AX-123298727 21 10982277 AAGTCTCCTGCACACTGAGCCTGAGAGCGTATCAG[A/G]TGAAAGTAACCTTCCACACAGCAGTCCCTGTGATG R 2 1 2 1 201000 r 74 goat snp52034-scaffold765-709843 21 12196199 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388671 Affx-122969097 AX-123259029 21 11026968 TCTATATTGTGAGCACCAAATGAAGGGAAATGGCC[A/G]TTTTCCACTGTAAGAAAAATAACTCAAGTTAAACA R 2 1 2 1 101000 f 74 goat snp52033-scaffold765-665152 21 12241334 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428135 Affx-122939059 AX-123298478 21 11087889 TTTCAAGAGGAGGGCAGATGATGATACTGTCTGCC[A/G]CTGGAGGAAAAGTAGGGTGAAAACAGAAAAGTGAT R 2 1 2 1 101000 r 74 goat snp52032-scaffold765-604231 21 12302183 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427003 Affx-122939851 AX-123297348 21 11125801 CCGTGAAAGCATAGACACACACTACTCCCATTTCT[C/T]CTCTGCTACTCCCTGCCCTCCACTCTGCTCTGCAC Y 2 1 2 1 101000 f 74 goat snp52031-scaffold765-566319 21 12340083 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397339 Affx-122962303 AX-123267694 21 11186778 GATAACGTATTTATCATCTCCCACTGGCTTGGCAA[A/C]TTCTGTGTCTTATTCAGTTCTAATAGACATGCAAG M 2 1 2 1 201000 r 74 goat snp52029-scaffold765-505342 21 12401132 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378064 Affx-122977182 AX-123248423 21 11234735 AAGAGATAATGCCTGCTCTTGCAGCTATTCATGAA[A/G]CTCTGGGCTTGGCAGAGCAGCCTCCCTGGAGAACC R 2 1 2 1 103000 r 74 goat snp52028-scaffold765-457385 21 12449399 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779674 Affx-122951356 AX-189281005 21 11272306 TTCATCTTTAATCTACACACTTAGGCCTGCATATA[C/T]GCACATTCTATCTTCCTTATCCCTTATTAAACTGG Y 2 1 2 1 101000 r 74 goat snp52027-scaffold765-419814 21 12486788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413944 Affx-122950722 AX-123284293 21 11344456 GATGAAACCTCTCAGTGGTCAAGTACTTAAAGGGG[C/T]GCTTTTAAAGCTGTAACTGTATGGTGGTGGAGAAG Y 2 1 2 1 101000 f 74 goat snp52026-scaffold765-347664 21 12559054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378770 Affx-122977008 AX-123249129 21 11424008 TATTAACCTGAATTTTCTGAGAACTGAGTGAAAAT[A/G]AAAGATTAGCTATGGTGATGGTTGGCAATGGGATG R 2 1 2 1 101000 r 74 goat snp52024-scaffold765-268112 21 12641269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430907 Affx-122936861 AX-123301248 21 11501660 GCTCAGAAGTCACCACAGCCCTGGCTGTAGAGTGC[A/G]GATTGAGCTGTCCTGGGATTCCTTGCTCTTCTGCA R 2 1 2 1 101000 r 74 goat snp52023-scaffold765-190460 21 12719467 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409942 Affx-122952866 AX-123280293 21 11541965 TTCCACAGATGGTGACCAGCACAGCCTGTCTCATC[A/G]CAGAACAATAGCCAACATCCTTTATTGACCCCAGT R 2 1 2 1 101000 r 74 goat snp52022-scaffold765-150155 21 12760066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433240 Affx-122935247 AX-123303581 21 11582601 GCTGTAGAATTAACTTTTCAAAGAGCATAATGTGC[A/G]TTAGCTGAGATGATGATGCATGCTAAATGCTGAAT R 2 1 2 1 201000 f 74 goat snp52021-scaffold765-109519 21 12800622 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400315 Affx-122960061 AX-123270670 21 11611125 ACCCCTGGCACTCAAGGGGTTTTATGTAACTATGT[A/G]CTGCCTTTGTCCTTATACCAAAATAGATCCTGGAT R 2 1 2 1 101000 r 74 goat snp52020-scaffold765-80995 21 12829046 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791964 Affx-122946237 AX-385278953 21 11642288 TGGTGAATAAATTCCTCACAAGTCATTTAAAAATA[C/T]GATTGCTGCATTCTTAAGACAAAGAATCTCCCACG Y 2 1 2 1 201000 f 74 goat snp52019-scaffold765-49832 21 12860217 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443079 Affx-122928120 AX-123313416 21 11681691 GGAGGAGAAGAATGCCCTCCTTCCATCTGTAGCCC[A/G]CCCCCTTGGGACGAACAAGAGCACATGCATTGGGA R 2 1 2 1 101000 f 74 goat snp52018-scaffold765-10429 21 12899207 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413720 Affx-122950071 AX-123284069 21 11710597 TCTGTCCTCCCACCTCCTCCCTTTCACACAGGCCC[A/G]TCTCTCACCCTCTCAGCTAAAGGTCGCCTGAAAGC R 2 1 2 1 101000 r 74 goat snp30989-scaffold3422-18378 21 12930469 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378555 Affx-122976609 AX-123248914 21 11743689 GCCAATGTGAAGAAACAAAGTGTCCTCCTGTAGCC[C/T]GAGGGCAGTTCTCCAAGAAAGAGCCTCAGGTCTCA Y 2 1 2 1 101000 f 74 goat snp30990-scaffold3422-51470 21 12963430 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439840 Affx-122930460 AX-123310177 21 11787347 CCGCACTTTGGAAAGCAAGGCCTTAAGAAGGAACA[C/T]GAGTTCTCCAGGTAAAGAGAGCGTGGTCCTGCACC Y 2 1 2 1 101000 f 74 goat snp30991-scaffold3422-95128 21 13006876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380757 Affx-122975123 AX-123251115 21 11825426 TATCTGAAACCTATAGTGCCTCTCAAAACTGGCAC[A/G]TGGGGATCTGTCTCCTCCTTTTGGGTCCCCTCACA R 2 1 2 1 101000 f 74 goat snp30992-scaffold3422-133207 21 13044619 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415357 Affx-122948776 AX-123285706 21 11860105 GAAAGCATTTTTAAAGACTGTGTTTGGGGTGAGGG[C/T]GACAGGATGCATGCCTTTCTTCTGATCGGTTGGTG Y 2 1 2 1 101000 f 74 goat snp30993-scaffold3422-167886 21 13079641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400915 Affx-122959731 AX-123271268 21 11927888 AAACAGCGAGAGCACATACTCATGAGTAGACAGCC[A/G]TGTCAACAGCACCTTCTTCATCGGTGACAGTCACT R 2 1 2 1 101000 f 74 goat snp30994-scaffold3422-235669 21 13147521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776952 Affx-122962685 AX-385264076 21 11974367 GATCCAGCGATATACTAAACAACCCAGGAAAGACT[A/C]GAATTATGATATGCATCAATTTCTATGATCTTTCC M 2 1 2 1 101000 f 74 goat snp30995-scaffold3422-282148 21 13193841 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425152 Affx-122941196 AX-123295498 21 12001558 TTATGGTGCCCATTTGGTCAAACATTTGTGTAGAC[A/G]TTGCTGTGAAGGCCTGTCCAGACATGATTAACATT R 2 1 2 1 101000 r 74 goat snp23851-scaffold240-2753244 21 13221252 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412114 Affx-122951109 AX-123282464 21 12052314 AAAGACATAAATCTGACTTGGGAAAATTTGCACCA[C/T]GAGAGCTCTGCCAAAGTGGCATCTGCTTTGAAATG Y 2 1 2 1 201000 f 74 goat snp23850-scaffold240-2702488 21 13272638 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771903 Affx-122969734 AX-385259059 21 12100306 AAACTAACTCATAGTCTTTAAAACTTTGGATTTCT[C/T]ACCCCTCTCCTTAATAGTCAGTACTTCCCAACCAG Y 2 1 2 1 101000 r 74 goat snp23849-scaffold240-2654496 21 13318994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405929 Affx-122955567 AX-123276281 21 12135382 TCATTCATCCCAGAGGAAACCCTTAATTTGTTTCT[A/G]TGTTTGCCCCAGTTGGAATCAGGCTGCATATAGTC R 2 1 2 1 201000 r 74 goat snp23848-scaffold240-2619420 21 13353967 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406519 Affx-122955137 AX-123276871 21 12176148 TGGTTAACCTTAGTTAGCTTTCTTTTCCCATGTTT[A/G]TTATAACCAAGCACATGGTGCGTATACCTTTTCAC R 2 1 2 1 201000 r 74 goat snp23847-scaffold240-2578654 21 13394835 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774828 Affx-122961996 AX-385261962 21 12206072 TAGGGATAATGGGGAAGATCTGATAATAAAACTTT[C/T]AATTTTCTTAGCCCTCATAGTTGAACAGCATAGTT Y 2 1 2 1 101000 r 74 goat snp23846-scaffold240-2548730 21 13424771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769224 Affx-122951985 AX-385256398 21 12237080 TGATGTTTAATTGCCCTGTTACATATGGGAACAGC[A/G]ACGTGAGTCAGTTATCTGTATATTCTTCTTCATCT R 2 1 2 1 101000 f 74 goat snp23845-scaffold240-2517722 21 13455801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416604 Affx-122947636 AX-123286952 21 12304112 GCTCTCCCTGTTGACGGGAGAGCAGCAAAGAATGC[A/G]CGTCCATCTTCTCAAGCCATCTCACCGCTGCTTGG R 2 1 2 1 101000 f 74 goat snp23843-scaffold240-2450690 21 13520674 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451954 Affx-122920957 AX-123322287 21 12333031 ACATCAAAGGGTGTACAGAGAAAGTTCCTTTCCAC[C/T]GGACTCCAGCTTCCTAGAGGCAATCCGTGGTGGGT Y 2 1 2 1 101000 f 74 goat snp23842-scaffold240-2421771 21 13549357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412466 Affx-122951397 AX-123282815 21 12373920 ATCCCCTTCTTAATATAACTCTGAGGGAAAGGTCT[A/G]CAAAGGTGACCAAAGATCAGACATCAGAGTGTGAG R 2 1 2 1 101000 r 74 goat snp23841-scaffold240-2380882 21 13590870 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443886 Affx-122927497 AX-123314223 21 12407819 CGAATCTAACTCATTTACAGCCAAGTACACCCAAC[A/G]TCGTGCTAGAAAAGGACAATTCAGGAGAGATATGG R 2 1 2 1 101000 f 74 goat snp23840-scaffold240-2346983 21 13625016 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277353 Affx-1111835870 AX-519550857 21 12413169 GATAGTTTTTGAGGGCTGAAAAGGATAGTCCATCC[A/G]TTTATGTGCTAGTCACAATCTGATGGCTGTGAACA R 2 1 2 1 101000 f 74 goat Random2.2K-1906 21 12413169 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391653 Affx-122966560 AX-123262010 21 12471991 GCTCCCCCACAACTCAACCATTTACTTCCTCGTGA[C/T]AGAGGACAAAATCACCTCTCTCTGTATGTGCCTCA Y 2 1 2 1 101000 f 74 goat snp23839-scaffold240-2282811 21 13689233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417930 Affx-122946718 AX-123288278 21 12519765 ACCAACTAAACGTCGGCCCTGATGCCCCAGACTCC[A/G]CAATGAGGCGTTAGTGGATAAGAAGCCCTGCGTGA R 2 1 2 1 101000 r 74 goat snp23838-scaffold240-2235037 21 13737657 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463777483 Affx-1110149042 AX-515256617 21 12523667 TCCTCTCAACCCCTCTGTCCAGAATCATGGGAGGG[A/G]CAAGCCTAGCGTCTGCCTGAGTAAGTCCTAGTACT R 2 1 2 1 101000 r 74 goat Random2.2K-1907 21 12523667 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38393664 Affx-122965278 AX-123264019 21 12576315 CACAACAGAAGTTCCTCATCCTTGCAAAATGTGAT[A/G]TAGGTTGGTGGGGGCTCTCTTCCAACCAGCGATTC R 2 1 2 1 101000 f 74 goat snp23837-scaffold240-2178487 21 13794317 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406255 Affx-122956102 AX-123276607 21 12650236 GATTGAAACATGAAGCAGCATAGCAGTTGCCTCCC[A/G]TCCTGCCTGCTCCTCTTCCAACATCCGAACCATTT R 2 1 2 1 102000 r 74 goat snp23836-scaffold240-2104566 21 13865701 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406876 Affx-122955643 AX-123277227 21 12683605 TTTCTCTTAAGGAGCTGTACAGTGGGTTAAAAAGT[A/G]TATGATCATAACTTTTGCATTCATTAGCATCGTTT R 2 1 2 1 101000 f 74 goat snp23835-scaffold240-2071197 21 13901993 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392306 Affx-122967520 AX-123262663 21 12714433 CTCCCAGGCATCAGGTTCCATATTAGGGGTTAATA[G/T]CCAAAGATGGATGAGTCAGAGGCTCTGCCCTTAAA K 2 1 2 1 201000 f 74 goat snp23834-scaffold240-2040369 21 13932634 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399296 Affx-122960537 AX-123269651 21 12756217 CATTACATAAAAATATGCCTTTTAAGAATAAGAGG[A/C]TAAGAGACAAGTAGAATAGAGTCAACCCAACTAAC M 2 1 2 1 101000 r 74 goat snp23833-scaffold240-1998585 21 13974419 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792771 Affx-122945308 AX-385279750 21 12813679 CAGTGCCTGTGACAATGGCTAATTTGATGATGGAT[C/T]CCCTAGAAATTAAATAAATGGACAGCCTATCAGGT Y 2 1 2 1 101000 r 74 goat snp23832-scaffold240-1941123 21 14032519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463770757 Affx-1110149137 AX-515249970 21 12819906 ATTCAAAGAGACAGTCGTGGAGAGGAGCTGCAGGG[A/C]GCTGCTGTGGCAGTTTCCATGCAGTGTCCCATGGG M 2 1 2 1 102000 f 74 goat GoatD01.037976 21 12819906 A C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407993 Affx-122954321 AX-123278344 21 12848125 AATCAGCGTGATGTTAGGATAAGAACCCACACATA[C/T]AGATCAATGGGACAAAACAGAGAGCCCAGAAATAA Y 2 1 2 1 201000 f 74 goat snp23831-scaffold240-1906677 21 14067194 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404536 Affx-122957397 AX-123274888 21 12879826 CAAAAAGAGCCTGGCCTAGAATGCACTGACAAATA[C/T]GCACTTGAACACCAAACAGGATTTTTCTCTCTCAT Y 2 1 2 1 101000 f 74 goat snp23830-scaffold240-1874976 21 14099521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427291 Affx-122940157 AX-123297634 21 12914485 GAAGTCGCCCACCTTTTCATGCAAACAGCTGCCTC[A/G]CACCTGAGCCCTCTGCACCTCCTAGACTTCAGGTA R 2 1 2 1 101000 f 74 goat snp23829-scaffold240-1840317 21 14132211 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397766 Affx-122962520 AX-123268121 21 12943171 TGTGTGTCACACACCACACTGATGATGAATGAGAC[A/G]CAAATAGTCCTTGGCCTCAAGGAGGAAGACAAGCA R 2 1 2 1 101000 f 74 goat snp23828-scaffold240-1811631 21 14160890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454300 Affx-122919260 AX-123324633 21 12981383 GGTTCTAGAGAAGGCTAACATGAAGTTATAAAAGT[A/G]TCTTGTTTGCTTACCAAGAACTCTTGATTTCTATA R 2 1 2 1 101000 f 74 goat snp23827-scaffold240-1773419 21 14199268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449423 Affx-122922688 AX-123319758 21 13020506 TGTGCTGGGAGAAACCCCTGGGCTTCTGGATTGCC[A/G]TTTTTGCTTTTGCTTCCAGCAATATACAGAGTTTG R 2 1 2 1 101000 r 74 goat snp23826-scaffold240-1734296 21 14238706 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780935 Affx-122971416 AX-385268022 21 13064799 GGTGTGACTGATCTCTAACCAGCACACTTTGTGAC[A/G]ATCGCATGCAAATAAGCACCCTCTGCTTCTGAGAT R 2 1 2 1 101000 f 74 goat snp23825-scaffold240-1690003 21 14282654 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395357 Affx-122963990 AX-123265712 21 13106985 GCTTGATGAGGCTGGCCCGCCCTGGGTCATCTCTC[A/G]TTTATGACTCCGGCAGGACTTACCAAGGTTGATAA R 2 1 2 1 101000 r 74 goat snp23824-scaffold240-1647817 21 14321837 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382392 Affx-122973842 AX-123252750 21 13142790 GAGTATAAATCGATATTTCAAATTATTTTCTCCAC[A/G]ATTTCACATTTGTTGCTGATCTTTTTTGCCATTGC R 2 1 2 1 101000 r 74 goat snp23823-scaffold240-1612012 21 14356725 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388242 Affx-122969790 AX-123258600 21 13173639 GGCTCCTGAACTCATTGGTTTCAAATTATGATTGT[A/C]TTTTTAGAGAGCTGTGTTACTTATCCCAGCAGGCA M 2 1 2 1 201000 r 74 goat snp23822-scaffold240-1581163 21 14387013 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429496 Affx-122937867 AX-123299838 21 13233653 TTCTGAAAGTACATATATATTTTCTCAAGGAATCC[A/G]CAGTATTTGAAAAAAGGCCTCCACAGTCAGCAGTT R 2 1 2 1 101000 r 74 goat snp23821-scaffold240-1521149 21 14443259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421492 Affx-122943911 AX-123291839 21 13287193 CAGGGTAGATCTAAGGGAATGAGCAGTCAGGGTTA[A/G]TGTTGAAAGAGTCTGGCTAGAGAGAGCCCTTGGAT R 2 1 2 1 101000 f 74 goat snp23820-scaffold240-1467609 21 14496216 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799591 Affx-122968351 AX-385286521 21 13317398 TCTCCAAAAATCTGATAATTGTTTACTTATATCTT[C/T]GTTTATGTATAGTTCTTTAATCCATCTGTTTCAGT Y 2 1 2 1 101000 r 74 goat snp23819-scaffold240-1437404 21 14526719 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385959 Affx-122971539 AX-123256317 21 13352302 ATACAGTCTAACCTTCTGTATGATCAGGCCACTCA[A/G]GATGGTTGCCCTCTTGCTCTGTTGCTCTCTGCATA R 2 1 2 1 201000 r 74 goat snp23818-scaffold240-1402500 21 14561594 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272982 Affx-1111833211 AX-519546665 21 13369585 TAATTCATGTTAACATATAACAAAAATCAAACCAA[A/C]ACTGTAAACCAATCATCAATCAATTAAAAACAATA M 2 1 2 1 101000 f 74 goat 21_13369585_AF-PAKI 21 13369585 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320801727 Affx-122974999 AX-385288635 21 13383000 GTTTGTCTTAACATATGATGGTGCAGGAGGCATGA[C/T]TCAAGCAGTGGGCTACACCCTGGAGATATAAGCAT Y 2 1 2 1 101000 f 74 goat snp23817-scaffold240-1371802 21 14592504 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375917 Affx-122978473 AX-123246276 21 13432589 AGAAGCAAACGCCCACCTCTCCTTTAGCTCAGCCT[C/T]TGTGTGACTTGTGCTACTCAGACTCTTGCTTCATC Y 2 1 2 1 201000 r 74 goat snp23816-scaffold240-1322213 21 14642631 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401058 Affx-122959649 AX-123271411 21 13470518 CTATCAGTAGAAACTAACAACATTGTAAAGCAACT[A/G]TACTCCAATTAGAAAAAAATACTTCCCCCCCCAAA R 2 1 2 1 103000 r 74 goat snp23815-scaffold240-1284284 21 14680484 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776124 Affx-122952958 AX-385263254 21 13503520 AATGGAACCATTCTTTCTCGGGGAGTTCTTTCTCT[A/G]ACAGAGTTTTGAGAGATCCCCCTCCATATACTTCT R 2 1 2 1 101000 f 74 goat snp23814-scaffold240-1251282 21 14713637 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801196 Affx-122951592 AX-385288109 21 13534366 TGGTCTGCTTGCTTCGTCTTAATCATATCCATTAA[C/T]AGATTGGTAAGGCTGTTTCTACTGGTTGGTGAGGT Y 2 1 2 1 101000 r 74 goat snp23813-scaffold240-1220436 21 14744038 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274173 Affx-1111834085 AX-519547774 21 13554166 CTGGGCTATACTACAGCCACCACTGCAGCCAACCA[A/G]TCGCCTGTCCTGAGAGCGCTGGGACCTCCCCGTTT R 2 1 2 1 102000 f 74 goat GoatD01.017501 21 13554166 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38419669 Affx-122945943 AX-123290017 21 13579376 TTGCACAGCCCCTTTAAAATCATTGTCTTCTAGCC[A/G]TGTGGCTGCTATGCTGATCTCCACTCCCCGCACCC R 2 1 2 1 101000 f 74 goat snp23812-scaffold240-1175426 21 14789906 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425096 Affx-122941236 AX-123295442 21 13612976 AGGTAAATGGCAACCATACTTCTTATTCATCTGGC[A/G]TGTTTTCAAATCCTAAATGAAATCATGCAGGATGC R 2 1 2 1 101000 f 74 goat snp23811-scaffold240-1141826 21 14823495 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394502 Affx-122964548 AX-123264857 21 13655973 TTCTAAATTCAGCCTATAGATGGGGAAAGGCTGCT[A/G]GGAAAAGAGAAAGAAAGTGGAGAAGGCACATCAGT R 2 1 2 1 101000 f 74 goat snp23810-scaffold240-1098829 21 14866509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438638 Affx-122930908 AX-123308975 21 13762995 CCTACTAAATTGTTTTTGTTAGACCTATTTAGAGA[C/T]GAAGGAAATGGAGGGATAGAGATTGCTAGATTGCT Y 2 1 2 1 101000 f 74 goat snp23808-scaffold240-991807 21 14973579 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777860 Affx-122964353 AX-385264977 21 13805421 TCAAGAGTGAAATACCAGACAATTTCCTGGGCAAA[G/T]AATTCTGATTAGCTGAGTTCCTGCCTAAAAGCAAG K 2 1 2 1 101000 f 74 goat snp23807-scaffold240-949381 21 15017405 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383837 Affx-122973160 AX-123254195 21 13839670 TCCCGGGTGGGATGTGTTCCCTCTCAGCACTGCAC[C/T]GTGCCTGGGATGCAGGCTCCTCCTCATCGCAGCAA Y 2 1 2 1 201000 f 74 goat snp23806-scaffold240-915132 21 15051084 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407742 Affx-122954989 AX-123278093 21 13884080 TTGGGAAAATGAAAAATACCCATGGAAATCAGCAG[C/T]ATGTCCTCTTTATGAGCAAACACTGAGCTCATTAG Y 2 1 2 1 101000 f 74 goat snp23805-scaffold240-870722 21 15096670 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390282 Affx-122967734 AX-123260639 21 13956946 AAGGCACAGCCTGATTACCCTTCCAGGATGGGCTG[C/T]GACAGAAGCTTGTCCCGGTTTTTCATAAGCTGCAG Y 2 1 2 1 101000 r 74 goat snp23804-scaffold240-797856 21 15168522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400551 Affx-122960428 AX-123270906 21 13991914 GAGAAATATTATATCTTATGGAGCATTTATCATGA[C/T]ACTGCTGGCCAGGAGTGACTGCCATACAGCTGTAA Y 2 1 2 1 201000 f 74 goat snp23803-scaffold240-762888 21 15203963 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401061 Affx-122959646 AX-123271414 21 14050950 TCTACTGACTCCTTCACTCTTCTTTCTGGCTGTAA[C/T]GCTTCAGCTGTCTTTGCTGCCTTTGGAGTTGAGCT Y 2 1 2 1 101000 f 74 goat snp23802-scaffold240-703852 21 15263332 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387866 Affx-122969638 AX-123258224 21 14105689 CAGAGTTAGCTATGAATAGAAATATAAACTATCAC[A/G]TTTTGAAAACTTTGTAAATATCCCTGAGAGGTCTG R 2 1 2 1 101000 r 74 goat snp23801-scaffold240-649113 21 15318468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385061 Affx-122971823 AX-123255419 21 14144710 TAAGCTCGTCTGACAGTAGAGAGCAAGAGAGACCA[C/T]GATCACAGCAGCGCTATTTACAAGGTATGGAAGCA Y 2 1 2 1 201000 f 74 goat snp23800-scaffold240-610092 21 15357616 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388969 Affx-122968798 AX-123259327 21 14196096 TCTGAACAATGCCTGGAGCTAAGGGACTGCTACCC[A/G]GTGTACTGGAGGCAGAATTTATGTGAGAAAGGATG R 2 1 2 1 201000 r 74 goat snp23799-scaffold240-558706 21 15409836 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795995 Affx-122944189 AX-385282947 21 14228468 CTCATGACTTTAGTTCAGAGGTTTTGTACATTTAG[C/T]CTTCTTACTGAAGACATTTCTGATACAGTACCTGG Y 2 1 2 1 101000 r 74 goat snp23798-scaffold240-526334 21 15442541 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442761 Affx-122927747 AX-123313098 21 14257041 GGCGCCGCTGCAGGCGGAAAGACTCCACACTGGCC[A/G]TATCGCTCACTAAATTTGTGACTTGGAGAAAGTTA R 2 1 2 1 101000 r 74 goat snp23797-scaffold240-497761 21 15471287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783609 Affx-122967946 AX-385270668 21 14287650 TTTTTTTAAATCATGCTGAGTCTTCAAAAGAAAAC[A/G]ATATGTGTTTTATACTTACAACACATCTCAGTTCA R 2 1 2 1 101000 r 74 goat snp23796-scaffold240-467152 21 15501896 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766722 Affx-122948780 AX-385254064 21 14334498 ACTGTGTGACCTGTCACTGTATTTCAATATTTCTA[C/T]GTCTGAAAAATACCCTTCAACCATACTGATTAACT Y 2 1 2 1 101000 f 74 goat snp23795-scaffold240-420304 21 15546523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772028 Affx-122936803 AX-385259184 21 14372582 CAAAATCTTACAAACCGTAAGTACTAGTAAGAACC[A/G]TACCATCCTATACCATCCGTACCTGGCACATACAC R 2 1 2 1 101000 r 74 goat snp23794-scaffold240-382220 21 15584540 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408145 Affx-122954228 AX-123278496 21 14452470 AAACGGTGCATAAAGTGTGTATGGACAATAAAACC[A/G]TTGAGCAAAACCTTGCCAAAGTGACTTTTCTAGTG R 2 1 2 1 101000 f 74 goat snp23792-scaffold240-302332 21 15664184 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416922 Affx-122948047 AX-123287270 21 14513673 ATACACACATTCACGAAATAAAAGTGTTGGCCAAC[G/T]CAAAGAAGACGTCTAGGGGACTAAGAAAGAACATG K 2 1 2 1 201000 f 74 goat snp23791-scaffold240-241129 21 15723415 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422368 Affx-122943427 AX-123292714 21 14558001 AGGCAACATTGGTGGTGTACAAGACAAAAACTTTA[C/T]TCGTTTATCCAAATTCATTTTCAAAGCTAAGCATG Y 2 1 2 1 101000 f 74 goat snp23790-scaffold240-196801 21 15767552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430566 Affx-122937011 AX-123300907 21 14593232 GGTCAGAAATAAGAGCATGTCTCTATACCTCAAAC[A/C]TTTTAAAGAAAATCTTGGAGATGGCTATAATACAT M 2 1 2 1 201000 r 74 goat snp23789-scaffold240-161570 21 15802894 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376435 Affx-122978067 AX-123246794 21 14636141 GGAGTCAGGGCAGCGGGGGCCCAGGTTGCAGCCCC[C/T]CTTGTCTGTGGGTACCCTTATCCAGAAGTTTCCTT Y 2 1 2 1 101000 r 74 goat snp23788-scaffold240-118661 21 15843905 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417880 Affx-122946759 AX-123288228 21 14673569 AGGTGAGCTCGAGTCCTTCTGCTGTGCCATCTTTT[A/C]CAGTCGAGAGCCTTCTTTCATCGAATGCGTGCTGC M 2 1 2 1 201000 r 74 goat snp23787-scaffold240-81233 21 15881494 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389460 Affx-122968340 AX-123259818 21 14718810 GCGGATTTTTTTACCCACTGAGCCATCAGTGAAGG[A/C]TGGAGTCTTATATATGGGCCTCCACAATTTCCAAG M 2 1 2 1 201000 r 74 goat snp23786-scaffold240-35992 21 15926472 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382285 Affx-122973922 AX-123252643 21 14776542 CAATACTGGAACAAGGATATGTAGTGTGGAGTGGC[A/G]TGAGGTGTCAGGCAGACATTTCATTGCCTGTCAGC R 2 1 2 1 101000 f 74 goat snp57207-scaffold911-21641 21 15983138 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436567 Affx-122932904 AX-123306905 21 14808263 GACTCTGATAGCAGCAGCTGACCACGGGCAGTGTC[A/G]TATCAGAGGGCCAGTCTTTTTATTACCCCACGCCC R 2 1 2 1 101000 r 74 goat snp57208-scaffold911-53362 21 16015468 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378310 Affx-122976846 AX-123248669 21 14854555 CAGAAAAAGCAACACATCAGAATCTCAGTTCTGAA[C/T]GTCGCAGTCTCCAACGCTTCCACTTGCTCAGGGCC Y 2 1 2 1 101000 f 74 goat snp57209-scaffold911-99654 21 16062071 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453286 Affx-122920380 AX-123323619 21 14967586 GGACCAGTGTGTCTATCAGGGTTCTCACCATAACT[A/G]CATATATTCCTGAATATAATAGCTTATACCAAATC R 2 1 2 1 101000 f 74 goat snp57212-scaffold911-212685 21 16173605 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411787 Affx-122951476 AX-123282137 21 15036197 TACAAATGCTTCCATGTGATGAATTTATCTCTTAC[A/G]TTTTATAGCTCAAGTGCGATTGAACAAACTAGTAC R 2 1 2 1 101000 r 74 goat snp57214-scaffold911-281296 21 16241258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431213 Affx-122937156 AX-123301554 21 15096168 CCATAATGTTTTCCCTTGGGAGCTACTCATTTTAG[C/T]ACTCTACATCTCTCTGTCAGTACTACAAGGTGAAA Y 2 1 2 1 101000 f 74 goat snp57215-scaffold911-341267 21 16301192 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415256 Affx-122948851 AX-123285605 21 15131093 AAATCTACCTGTAGACTCTCTCCCACAGGTCTTTG[G/T]CTGGATTGGTTCTTAGCCTTATTCCTAAACTAATT K 2 1 2 1 201000 r 74 goat snp57216-scaffold911-376192 21 16336115 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390313 Affx-122967712 AX-123260670 21 15187493 GAACATTGGGGTGCAGTCAAGGATTTGAATTCAGA[C/T]GGCCTTGCTCTGATCTGAGCTGTGTGCTATCCTCT Y 2 1 2 1 101000 f 74 goat snp57217-scaffold911-432592 21 16392486 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402836 Affx-122958259 AX-123273189 21 15216881 TTGTACGCCCGAATGCATGCTTAGTCCCTTCAGTC[A/G]TGTCCGACTCTTTGTGACTCTATGGACTGTGGAGC R 2 1 2 1 303000 r 74 goat snp57218-scaffold911-461980 21 16421830 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399819 Affx-122960268 AX-123270174 21 15307508 TTTCCCACGTTGGCTGCTTCACCTTGTGAAACTCC[A/G]TTCCTCTGAGCTTTATTCCCTCCTCTATGTGTTTA R 2 1 2 1 201000 r 74 goat snp57220-scaffold911-552607 21 16513915 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431025 Affx-122936664 AX-123301366 21 15376714 CCCATTATGCAATTGCATTGGGCTTATTACTGTTT[A/G]TATGTGACTTCTCTGTTTTCAAAAAATAAAGTGGT R 2 1 2 1 101000 f 74 goat snp57222-scaffold911-621813 21 16583131 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453918 Affx-122919903 AX-123324251 21 15413803 CCCGACTTCTGAAATTTCTGGCCTGGCTGGACACA[G/T]AGCTAACCCCTCTGAGGCTCAGATTCCTTACCAGT K 2 1 2 1 201000 f 74 goat snp57223-scaffold911-658902 21 16620642 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403450 Affx-122957728 AX-123273803 21 15452736 TTCTCTGCACCCCTACACCTCTTTTAGAACCAGTG[C/T]GCCTATGTGTTTCCTCCTGCTTATGGCTTGTAAGC Y 2 1 2 1 201000 r 74 goat snp57224-scaffold911-697835 21 16659504 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414959 Affx-122949075 AX-123285308 21 15514780 TTTCTTTCCCCCTCTGTAAGTCTGCAATTTTTCAG[C/T]GGGGAAAAAAAGATAGCAATGCTGACCATTTTCTA Y 2 1 2 1 102000 r 74 goat snp57225-scaffold911-759879 21 16721259 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438106 Affx-122931502 AX-123308444 21 15590760 GACCTGTGCACCAGGCCCTGATAAAAGGAGGATTA[C/T]AAAGGGAGCAGGATGGAGGAGAGACTCAGAACAGA Y 2 1 2 1 101000 f 74 goat snp57227-scaffold911-835859 21 16797157 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418405 Affx-122946547 AX-123288753 21 15645994 CTAGTATCGTCCCATGGCTCACGTGTGGGCACTCC[A/G]TGTGATCCTATTTTGAGAATTTTGTAGAAGTCTTC R 2 1 2 1 201000 r 74 goat snp57228-scaffold911-891093 21 16849859 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446713 Affx-122924727 AX-123317049 21 15732024 AATTAGTGGCAGAGCCCTATGCCCCTGTTATTGTT[A/G]CTGTTCACTGTGCCTATAATGGTCATCAGCCTTAT R 2 1 2 1 101000 r 74 goat snp57230-scaffold911-977123 21 16936192 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426828 Affx-122940512 AX-123297173 21 15822341 TCCCACTGTTCTCTGAAATTCTTACCCCATTCTAC[A/G]CCACCCTGTGGCCTCAACATGCACAGTGTTTCAAA R 2 1 2 1 101000 f 74 goat snp57232-scaffold911-1067440 21 17026821 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378032 Affx-122977576 AX-123248391 21 15865297 ATGGGGCCACAAAGGATTCTGATGGGGGCAAACAG[C/T]GAAGGCAGGTCCATCACTTGGTCAAGGATGGGACA Y 2 1 2 1 101000 r 74 goat snp57233-scaffold911-1110396 21 17069444 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272983 Affx-1111833212 AX-519546666 21 15906463 ATGTTTGAAGGGGCTTGATTGAGCCCACACCTTCC[A/G]GGAGCCCCCTTGGACCAGGATGTGCTGCCACATGG R 2 1 2 1 102000 f 74 goat 21_15906463_AF-PAKI 21 15906463 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38397693 Affx-122962574 AX-123268048 21 15959450 TCAAGTCATGCATAGCTAAAAAAGTATTTGTTGAG[C/T]GCTACTATGTTTTATCTATGTGTTATGGGGTCAGT Y 2 1 2 1 101000 f 74 goat snp57235-scaffold911-1204549 21 17164113 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385403 Affx-122971342 AX-123255761 21 15996649 AAAAAAAATTTAATTTCTATGTTACAGATAATGGA[G/T]AAGTCAATGCTATTTTACTTCCTGTTTATTAATGA K 2 1 2 1 101000 r 74 goat snp57236-scaffold911-1241748 21 17195733 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385813 Affx-122971028 AX-123256171 21 16041268 TAAGTCATTGTTCATTATAGTTCATCATGTAGCAA[C/T]AGACAATTTACATAGGAAGATCTTATCTATGGAGT Y 2 1 2 1 101000 r 74 goat snp57237-scaffold911-1286367 21 17240860 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800230 Affx-122926405 AX-385287153 21 16089211 CAGAATTAAGTTCCTTAGCTTCTTATTTCCAAATA[C/T]GTAGGAACCCTTCACTTATCTTTCTTCCCACTTCT Y 2 1 2 1 101000 r 74 goat snp57238-scaffold911-1334310 21 17288890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422207 Affx-122944444 AX-123292553 21 16128941 ACCTCCACTCAAAATAACATGGTGTGAACTTCTTG[C/T]GGTGTCTTTTCTCTCCTCCTATGTAGCCCATGTGT Y 2 1 2 1 101000 f 74 goat snp57239-scaffold911-1374040 21 17328104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407261 Affx-122955350 AX-123277612 21 16198025 TGCATTTGCAACAAACATTATGAAAATGAAAGAAA[C/T]GCCTTGAGAAACAGTTGCAATCTTGCTCTTTGGTG Y 2 1 2 1 101000 r 74 goat snp57240-scaffold911-1443124 21 17397493 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396981 Affx-122963157 AX-123267336 21 16253590 GAGAGCTTACTATGTTTCAGGCATTGCCTGAGGGG[A/C]GGAGGATATAGTAATTAGTTCATGGTCAGCCTGAA M 2 1 2 1 201000 r 74 goat snp57241-scaffold911-1498689 21 17453262 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447689 Affx-122924624 AX-123318025 21 16309834 CTCTCCCTGACCATTTTTTTGGGATAAACTAAAGG[A/C]TCTCAAAGTCTGGCTCCAGGCTAGCATTAGCACCT M 2 1 2 1 101000 f 74 goat snp57242-scaffold911-1554933 21 17511418 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450477 Affx-122922937 AX-123320811 21 16378414 CCTCCTTGCGTCAACACTTCGGACCAATTCATTCT[A/G]CTTAAAGATAAATAAATTAGTGTAAGAATCAACTG R 2 1 2 1 101000 f 74 goat snp57244-scaffold911-1623513 21 17580022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408401 Affx-122954480 AX-123278752 21 16412275 GATGGCCAATTTACAAATGTATTTCTCTTGTGTCC[A/G]TCACCTCCATTTGGGGGCCAAGCATATTTCCATAT R 2 1 2 1 202000 f 74 goat snp57245-scaffold911-1657374 21 17613733 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795657 Affx-122925180 AX-385282612 21 16445859 CATCTAACACTCTTTCTCAGTCCCAGGAAAAAAAC[A/G]AAACAGAGAGAATGCAAGTTGAAAAGATCTTCAGT R 2 1 2 1 202000 r 74 goat snp57246-scaffold911-1690958 21 17645551 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440328 Affx-122929678 AX-123310665 21 16479526 AAGTGAGTGAAAATGAATCAATTTATGACATCTCT[A/G]CTATGTCCAAGAAATCTTTAGATGGGTACAGTTCA R 2 1 2 1 101000 r 74 goat snp57247-scaffold911-1724625 21 17679284 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277357 Affx-1111835872 AX-519550861 21 16518216 ATGGGGTTGCAAGAGTCAGACATGACTTAGTGGCT[A/G]AACAATAACAGCAACAAGTGGATGAAGGATGTGAT R 2 1 2 1 103000 f 74 goat Random2.2K-1913 21 16518216 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451637 Affx-122921611 AX-123321970 21 16537291 AAAGTGCAATTCGCAAGGCCTTTGTATTCATGAAA[C/T]GTTTATTAGAGTAACTGGCTGTTTCCTTTTCATCT Y 2 1 2 1 101000 f 74 goat snp57248-scaffold911-1782390 21 17739095 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399402 Affx-122961246 AX-123269757 21 16581714 TCCACAGAATGAATGGGATTTCCCAGATAGTCCAG[C/T]GATGAAGAATCTACCTTTTAATGCAGGCGACTCAG Y 2 1 2 1 101000 r 74 goat snp57249-scaffold911-1826813 21 17783560 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782404 Affx-122968132 AX-385269480 21 16639626 TTTAAGGAAAGACTAAAAGAGAAGGAAAGCTACTT[C/T]TGATAAATGGTGGTAAAGGGTCTATTATTCAAATT Y 2 1 2 1 101000 f 74 goat snp57250-scaffold911-1884725 21 17842044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387442 Affx-122970382 AX-123257800 21 16682842 CCTAATTCATGGGATTCCATCGAAAACAGCTCACT[C/T]AGCTTCTGCCTACATCCCTTTGCACAAGGCTCCAG Y 2 1 2 1 101000 f 74 goat snp57251-scaffold911-1927941 21 17884557 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416907 Affx-122948061 AX-123287255 21 16718054 TATGTGTTTTAGATAGATAATTGTTTTGAGGGACA[A/G]AACTCCTCCAAGGGTTAATTTGCAGAAAATCAAGG R 2 1 2 1 101000 r 74 goat snp57252-scaffold911-1963153 21 17919838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381924 Affx-122974137 AX-123252282 21 16766305 GTCTTGAAATGCATGAGATCCACAGTCAAGAGTTA[C/T]TAAAGGCCATATACTGGAAATCTAATATTTCTCCC Y 2 1 2 1 101000 f 74 goat snp57253-scaffold911-2011404 21 17968000 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412853 Affx-122950449 AX-123283202 21 16807964 TCTCCCCCCAGGTCATTACTTGGTTTTAAAAGGAA[C/T]GAAAACAGCAGGCTTTTCCACTTACCATGCATAAA Y 2 1 2 1 202000 r 74 goat snp57254-scaffold911-2053063 21 18010069 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428654 Affx-122938657 AX-123298996 21 16837668 TCACTCTGCTCTGCAAGAAATGTGCTATAGTTCTG[C/T]GACTGCCTAGCTGGCCCTGTGATTTTAACTACAAA Y 2 1 2 1 101000 r 74 goat snp57255-scaffold911-2082767 21 18039733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433192 Affx-122935642 AX-123303533 21 16884706 GCTGCAGAGTCACATGCTGCCAAGACTCACCACCA[C/T]AGCTAGTCCCCATCTCTGGGTCAGTGCTTGTCAAT Y 2 1 2 1 101000 f 74 goat snp24630-scaffold2508-359612 21 18087194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775232 Affx-122957573 AX-385262363 21 16921383 CCACTTTGCCTCCTATATTTAATGAGTAGCAGGAA[G/T]CTTTTTGTATTCCCTTAGACATTCTTTAGGAGAAA K 2 1 2 1 101000 f 74 goat snp24629-scaffold2508-322935 21 18123967 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434787 Affx-122933880 AX-123305128 21 16978764 AGACCTGTGAACCATGATAGTTTCTAAAACAAACA[G/T]CATCTTTTCTCAGTACTTGAGATCTTCCTCTTCCT K 2 1 2 1 101000 r 74 goat snp24628-scaffold2508-265554 21 18181367 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441998 Affx-122928428 AX-123312335 21 17020489 TCAAGTCAGGTGTTCTTCCTACTGGACCATCTCCA[C/T]GCTGCGGCAGAACTCATATAGTGTCATGCCCTTGT Y 2 1 2 1 101000 r 74 goat snp24627-scaffold2508-223829 21 18220066 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798177 Affx-122930754 AX-385285112 21 17064671 CCCCTTTTCTTGCCCATGTGAAAGTTTATCTGCCC[A/G]TTTTCTGGGCTACATTCCTCCTATTGCCCAAGGCA R 2 1 2 1 101000 f 74 goat snp24626-scaffold2508-179647 21 18263901 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405584 Affx-122955940 AX-123275936 21 17116601 GCCAGATTGTCATTCTTCCCATCAGGAGAGCAAAA[G/T]CCGTCTCTTTTGTTAGAATCGTTTGCTCGGATTCT K 2 1 2 1 201000 r 74 goat snp24625-scaffold2508-127717 21 18315875 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434472 Affx-122934635 AX-123304813 21 17172399 TTAGAGTCTCTTTCTCTTTCAAGAGAAAATGAGAT[A/G]CTTCCATCCTTTCTTCTTGCAGTGCTTTAATGTCA R 2 1 2 1 201000 r 74 goat snp24624-scaffold2508-71919 21 18371444 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434282 Affx-122934773 AX-123304623 21 17203356 TTGGCTTTCATTATTAGGTGATCATTTCTAAAGGC[C/T]GAAGACTCAATAGCACATTTTCATCTGGGAAATAG Y 2 1 2 1 201000 f 74 goat snp24623-scaffold2508-40962 21 18401386 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438235 Affx-122931435 AX-123308573 21 17236051 TCCAACTGGATATGCTCAATGCTCCTGAGGGCTCC[A/G]TAGCATAGGGATAGCTAGGCACCTGTGGCCAACAG R 2 1 2 1 201000 r 74 goat snp24622-scaffold2508-8267 21 18433968 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428118 Affx-122939072 AX-123298461 21 17273130 GTTCCCTGATGTAGGAAAATTCAGACTCAAAAGAA[A/G]ATACAAGGGGCTCTATGATATAGACGAGAGAGCCT R 2 1 2 1 101000 f 74 goat snp7156-scaffold1265-491962 21 18470726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443421 Affx-122927373 AX-123313758 21 17301758 ATCATGGAAATTAATTCATCTTGGAGTCCTGATAA[C/T]ATACACTGTTTTGTTCTCTTTTAAGAGTATGTTTT Y 2 1 2 1 101000 f 74 goat snp7155-scaffold1265-463334 21 18499390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436383 Affx-122933044 AX-123306722 21 17352201 CTTGCACTTGTAGTGATACTTCACAGGTCTGTTTT[C/T]TGACAAGGCCCCTGTATCTGAAACACCCAGTTTTT Y 2 1 2 1 101000 r 74 goat snp7154-scaffold1265-412891 21 18549589 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389838 Affx-122968169 AX-123260195 21 17396198 CTTACAAAATGAAGTCACTTCAGGTCTCATTTTTC[A/G]TACCGTGAAGCAGAGTCAAGATTAGATTGGGGATG R 2 1 2 1 201000 f 74 goat snp7153-scaffold1265-368894 21 18593733 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429938 Affx-122938088 AX-123300279 21 17443606 TCATCTCTTACACTGCTTTAATTTTTCTCCATAGC[A/G]CTTGTTATGACCTGACATGGTGTTCTGAGTCTGTG R 2 1 2 1 101000 r 74 goat snp7152-scaffold1265-321486 21 18641207 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445784 Affx-122926055 AX-123316121 21 17525641 AGGACTCCACGAATGGGGGGTGGTCCTGACACTTA[C/T]AGGGTACTATCTCCCATGACACTCTACACCTGGGA Y 2 1 2 1 101000 r 74 goat snp7150-scaffold1265-239451 21 18722756 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425000 Affx-122941897 AX-123295346 21 17572976 CTGCAATTAAATAAAACACGGTCTTCCCTGGTAAC[G/T]CAGTCCTGAAGAATCTGCCTGCCGATGCAGGAGAC K 2 1 2 1 101000 f 74 goat snp7149-scaffold1265-192116 21 18769807 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422039 Affx-122943617 AX-123292386 21 17622214 CAGTTTGCTCCTCGAACAACACAGATTTTAACTAT[A/G]CAGGTCCACTTACACATGGATTATTTTTTAAGCCA R 2 1 2 1 101000 f 74 goat snp7148-scaffold1265-142878 21 18818991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772176 Affx-122926242 AX-385259331 21 17657375 TTCAATTATGCAGCTTTTGGTAACATTTAAAAAAC[A/G]TTTTTCATTGATCACCTAGAGATTTGTTTACATAA R 2 1 2 1 101000 f 74 goat snp7147-scaffold1265-107717 21 18854277 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439848 Affx-122930455 AX-123310185 21 17693088 GGTTACTCACTGGGAAGGGCAGGAGAAGGTTGGGA[C/T]GCAAGGAGGGCTAGCCCCCACCGCTGACCCAGTAG Y 2 1 2 1 101000 f 74 goat snp7146-scaffold1265-72004 21 18887929 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419128 Affx-122945760 AX-123289476 21 17760579 GAGTGGCACCTCGTCCCAGACAAAGCCCGACACTC[A/G]TCTCTCAGTGTTTAGCTTCTTGAGGATTGAGTAGA R 2 1 2 1 101000 r 74 goat snp7144-scaffold1265-4513 21 18964532 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377581 Affx-122977433 AX-123247940 21 17775348 TACATGGTCACAGGACTCGGATGACCCAGCGGGAC[G/T]GAGGGGAGCCGAGGACTGGGATACAAGTCCAGTTT K 2 1 2 1 101000 r 74 goat snp22920-scaffold2287-10157 21 19192457 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383876 Affx-122973132 AX-123254234 21 17833204 TTCAGCCTCTTTGGACACCATATGGTTCTACCTGC[A/G]CCTGCCACAGCTCTTCTCCACTTGTGTGGCCTTCT R 2 1 2 1 101000 f 74 goat snp41029-scaffold530-11784 21 19225290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447181 Affx-122925005 AX-123317517 21 17888509 TAAAAGAAAAGTAGCTTTATTTTAAGGAAATTACA[A/G]CTGGGGGAGAAGGCAGACCACTGTGCAAAAGAACC R 2 1 2 1 201000 f 74 goat snp41030-scaffold530-67089 21 19278649 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421191 Affx-122944153 AX-123291538 21 17983765 GCACAGACAAGAGAATAAAAAGTTGTCCTCAAGGC[A/G]TAAGAGACCTTGGCAGCTGCAAAGGGCAACCTCTC R 2 1 2 1 101000 f 74 goat snp41031-scaffold530-162345 21 19371748 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434951 Affx-122933855 AX-123305291 21 18012444 TTTGTTTCCTCCTCTGCAAAATGGAGTTAACAGTA[C/T]AATCCAGCACCTCATTCCTGAAACATTTGGGGTCA Y 2 1 2 1 101000 r 74 goat snp41032-scaffold530-191024 21 19407041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408801 Affx-122954045 AX-123279152 21 18053378 TTCCTTTAATTATCAATTAAGCAGATCCTTGTAAG[C/T]ATAAACTCTGTATGAACATAATAAACTATTCCCAG Y 2 1 2 1 101000 f 74 goat snp41033-scaffold530-231958 21 19448210 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441045 Affx-122928931 AX-123311382 21 18089423 GACTGAGTGACAAGTTCTGTGGCTTCTCTTTCTTA[C/T]GTTAGATGTCAGGGTCTGGTCTGAGAAATTCATCT Y 2 1 2 1 201000 r 74 goat snp41034-scaffold530-268003 21 19483347 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801816 Affx-122926510 AX-385288723 21 18119461 TCTATTGTTTCCCTCTAGTTCTTGAGAATATGACT[A/G]TCCCAGAAATACACATGCACGTACCCTCAGATGTT R 2 1 2 1 101000 r 74 goat snp41035-scaffold530-298041 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379388 Affx-122976138 AX-123249746 21 18174212 TTCTCAATGTGCTGAGCAAGGAGCACTCTAGAAAC[A/C]TCTCTGTCCCCATTGCCTAGCCCCTGGGCTCCTTT M 2 1 2 1 101000 f 74 goat snp41036-scaffold530-352792 21 19531004 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391660 Affx-122966555 AX-123262017 21 18205343 CTTGGTAATGAACTTCAGGTGAGACAAGGGAGGAA[C/T]TGGGAGCCCTTGGGCAAAGCCTCAGCCTCTGTTAA Y 2 1 2 1 101000 f 74 goat snp41037-scaffold530-383923 21 19565629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419640 Affx-122945966 AX-123289988 21 18255885 AACATATTTATCCTATGTTTGGGGCTGGGTAGAAT[A/G]TCCCAAATAAGACATAAAAGATATGAAAAAAACCA R 2 1 2 1 101000 f 74 goat snp41038-scaffold530-434465 21 19616089 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439367 Affx-122930275 AX-123309704 21 18286926 GTGAGAAATCTAATGTCAATATGATTCTTATATTT[A/G]TACATGATCTGCTCTTTCTTTTGTTTTTTCTGAAA R 2 1 2 1 102000 f 74 goat snp41039-scaffold530-465506 21 19646964 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442991 Affx-122928188 AX-123313328 21 18324586 CTTGGAAGATGGAAGTTGGAGGTGGGAATGAAGGG[A/C]AAGTTCAAGGAAGAGGACAGGCCTGCTTACAAGTG M 2 1 2 1 101000 r 74 goat snp41040-scaffold530-503166 21 19680603 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447966 Affx-122923765 AX-123318302 21 18358699 ATCCAGACGTTTATTAAGCATCTGAAACAACACCA[G/T]CCCAGAACCGAGGTGGCAAACGTTTTCTGGAAAAA K 2 1 2 1 101000 f 74 goat snp51502-scaffold754-2958016 21 19714478 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774515 Affx-122975466 AX-385261649 21 18389487 GGCCAGAAGTCTGACTTGAGTTACTCTCTGACAGC[A/G]TGCCAACTCAAAGATCCATACACAGCACTTCTTGG R 2 1 2 1 101000 f 74 goat snp51501-scaffold754-2927228 21 19745386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272985 Affx-1111833213 AX-519546667 21 18421853 TGCTGAAGCGTCAGTGGCTCCGGCTCACAGGCTTA[A/G]TAGTCGTGGCACACGGGCTTAGTTGCTCCAAGGCA R 2 1 2 1 202000 f 74 goat 21_18421853_AF-PAKI 21 18421853 A G 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320768413 Affx-122979015 AX-385255593 21 18436361 GACAAACACATAATCATAAACCAGCATCTTAGAGA[C/T]AGTGAAGATCTGAGAGATCACCTGTCCTCATTGTG Y 2 1 2 1 101000 r 74 goat snp51500-scaffold754-2880354 21 19791571 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388789 Affx-122968924 AX-123259147 21 18478027 CCAAGCAGGTTGGCAGAGAAGGGGCAGGGGAGGGA[A/G]TCAGGTCCTTATCTCCACTCTGGGGTCCAAGTTGA R 2 1 2 1 101000 r 74 goat snp51499-scaffold754-2838688 21 19832970 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386319 Affx-122970888 AX-123256677 21 18525783 GACCATATTTAGCAAATCCATAATGCTTATTGTGT[A/G]CCAGGCACTGCTCTAACTGCTTCTGATATCAAAAC R 2 1 2 1 201000 f 74 goat snp51498-scaffold754-2790932 21 19880302 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399274 Affx-122960553 AX-123269629 21 18559078 CAGCAGAAACCCTGCAGGCATGATGACCAACGTAG[C/T]AGTGATGTATATCCCCAAGGAGGAGACTCACAGAT Y 2 1 2 1 101000 r 74 goat snp51497-scaffold754-2757637 21 19913499 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418604 Affx-122946356 AX-123288952 21 18604775 CACAATTTCGAAAGGCCAGAAGGGGATCTCTGTGA[C/T]AGGAGGGCCTGCCATCTGCTCCAGAGTGACATGGT Y 2 1 2 1 101000 f 74 goat snp51496-scaffold754-2711940 21 19959081 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789174 Affx-122939437 AX-385276186 21 18635897 GACCAGTGTGAATTAGAGACAGGAGAAGAATCCAA[A/G]TGTCAGGACCCTGGTTACATTAACACCAAGTCAGG R 2 1 2 1 101000 f 74 goat snp51495-scaffold754-2680818 21 19990256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789907 Affx-122976225 AX-385276913 21 18676224 CATCCCTAAACAAGTCAACTACGATATTCCATTTT[A/G]TTAACTTAGAGCTCCCTAGCCTCTTATTAAACACA R 2 1 2 1 101000 f 74 goat snp51494-scaffold754-2640491 21 20030534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449817 Affx-122922405 AX-123320152 21 18726172 TGACTTGGGATTCTTGGGATGATGAGCCCACTCTG[C/T]ACTGGCTCTGTTTCCGCTCTAGTCTACAGAGGCAT Y 2 1 2 1 101000 r 74 goat snp51493-scaffold754-2590543 21 20082400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451864 Affx-122921066 AX-123322197 21 18771359 CATCCCAGTGTTAGAGGAGAAGCACAGAAGGGCAC[A/G]TCAGCTCTGTCCTGTGCCCACCAGGTGCCCTGTGT R 2 1 2 1 101000 f 74 goat snp51492-scaffold754-2545356 21 20127551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389036 Affx-122968625 AX-123259394 21 18800007 CATATGACACTCACTCCAACTCCCTGTAGGAGAGC[C/T]ATGCCCAGGAAACTAGAAGGGTGCAAGGCCACCCA Y 2 1 2 1 201000 r 74 goat snp51491-scaffold754-2516708 21 20156105 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402652 Affx-122958380 AX-123273005 21 18832548 TAGGTAGCTATCGAGGTTTGGTGGCAAGATGATAA[C/T]GGTGTGCATTACCTTCCTTAGATGAAGAATCCCCC Y 2 1 2 1 101000 f 74 goat snp51490-scaffold754-2484167 21 20188528 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799262 Affx-122929123 AX-385286192 21 18893413 CTAGAACATTCCTGTGTAGGTACAGCACCTAGCAC[A/G]TGTCTGTCCTATAACAGACGTTCACAAGGGCAGCC R 2 1 2 1 101000 f 74 goat snp51489-scaffold754-2423302 21 20248401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766868 Affx-986698218 AX-385254187 21 18928294 GGTCCAGTCCCCTCACTGTGGCACCCAAAAGAAAG[C/T]GTAATCATCCTGTATTTAGTTCAAGCTTCTCATCA Y 2 1 2 1 600010 r 74 goat 21_18928294 21 18928294 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 320766871 Affx-986698220 AX-385254189 21 18934094 TCTGCAATGTTCTTTCCCCCAAATAAAGTAACTTT[C/G]GTAAGGTACAGGAATTTGACATGGAAATCTCTCTG S 4 1 2 1 600010 r 74 goat 21_18934094 21 18934094 Ancestral_priority_1043 ancestry 0.696 recommended IMAGE 10K 10K ancestral 320763693 Affx-986698222 AX-385251517 21 18934260 AAGAAATCAACCAGAGCAGGAAAGAAATCGCTGAA[C/T]AAATCTGAAAGTGAAACTGACTTGAATCAATAAGC Y 2 1 2 1 600010 f 74 goat 21_18934260 21 18934260 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 320803506 Affx-986696374 AX-385290326 21 18934314 GACTTGAATCAATAAGCATGAATTTCTTAGTGGAC[A/T]TGTTCAACAAAGTTGATAGGCTCCATTTTGTGTGA W 4 1 2 1 600010 f 74 goat 21_18934314 21 18934314 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 320766881 Affx-986698226 AX-385254199 21 18934326 TAAGCATGAATTTCTTAGTGGACTTGTTCAACAAA[A/G]TTGATAGGCTCCATTTTGTGTGAATAAACCCCTCC R 2 1 2 1 600010 r 74 goat 21_18934326 21 18934326 Ancestral_priority_1043 ancestry 0.618 neutral IMAGE 10K 10K ancestral 320804081 Affx-986696376 AX-385290749 21 18934346 GACTTGTTCAACAAAGTTGATAGGCTCCATTTTGT[C/G]TGAATAAACCCCTCCTTTTCTGTGGTTCTGTTATC S 4 1 2 1 600010 r 74 goat 21_18934346 21 18934346 Ancestral_priority_1043 ancestry 0.61 recommended IMAGE 10K 10K ancestral 320766885 Affx-986698228 AX-385254203 21 18934463 TTCCGATGTGGCAGGGAATAAACCAATGCAGAGAC[A/G]ATTCTTTGGGTAAATGTACATCGACTAAAGCCTGG R 2 1 2 1 600010 r 74 goat 21_18934463 21 18934463 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 38453008 Affx-122920107 AX-123323341 21 18949885 GACCTAGAGTGGAGGGAGACAACCTCTCTCTATAG[C/T]AAGACAATATGGCAGCAAGAGAAGCCGGCGTATTT Y 2 1 2 1 201000 f 74 goat snp51488-scaffold754-2366830 21 20305321 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380206 Affx-122975491 AX-123250564 21 18986884 CCATCTTCTCCTTTCTCTGGGGACTCTTCAACGAC[A/G]TCAATATCAGGACCAGGATCAGAGGACCTTGAGGA R 2 1 2 1 201000 r 74 goat snp51487-scaffold754-2329831 21 20342326 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382746 Affx-122973601 AX-123253104 21 19058737 GCCTGGCACACCACACTGCCCTGCAGATGTTGGCT[A/G]CTACTACATGACCAGGGAGAACTCTCCATGTCTGG R 2 1 2 1 201000 r 74 goat snp51486-scaffold754-2257978 21 20414027 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277484 Affx-1111835873 AX-519550987 21 19094650 CGGATTCATTTGTTCCTCCCAGAATCCCATGAACT[A/C]TGCACAAAGTGTCCCCGTTTTTACAAGCACACAGA M 2 1 2 1 101000 r 74 goat Random2.2K-1917 21 19094650 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397870 Affx-122961974 AX-123268225 21 19106105 AACCCTGACACCAGAGATCATCCCATCACACGCCA[C/T]GCATGGTGTCCCACTCTTGCTCCATAGCTTTCGGT Y 2 1 2 1 101000 f 74 goat snp51485-scaffold754-2210610 21 20461445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766888 Affx-986698230 AX-385254206 21 19109858 AGGAGATTAAATGAGATAACACAAAACCCAGTGAT[C/T]CTGTAACATTTCCACTAAAGACAGAAAGAACAGAA Y 2 1 2 1 600010 r 74 goat 21_19109858 21 19109858 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 38451117 Affx-122921387 AX-123321451 21 19135706 ATGAGAGGGAGGTAGGACCAAGGAGGCTTCAGCCC[A/G]CAGCATTCTGAAGGGATGTTGAGAAGGTGCAGGAG R 2 1 2 1 101000 r 74 goat snp51484-scaffold754-2181009 21 20490596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413565 Affx-122950593 AX-123283914 21 19184096 GGAGAGGGCAGAGAGGAAACGAACATCCACCCCAG[A/C]GAGAGGGTGGTTGGAGCCTTGGGAGCAAGTCATGT M 2 1 2 1 101000 r 74 goat snp51483-scaffold754-2132619 21 20539026 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401483 Affx-122958954 AX-123271836 21 19251967 GGGGAAAAAGTACTTATCAGATGACCATATAGAAT[A/G]CAATATACATTTTATAAGACTTTAAAACAAAGAAA R 2 1 2 1 101000 f 74 goat snp51482-scaffold754-2064748 21 20606718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392819 Affx-122965787 AX-123263176 21 19282276 CCAAAACTGTCTTGCAAAGTTTCTAAGGTTTACAA[C/T]AACCTTGTATGCCATAAAAAGGACCTGAAAGCCAG Y 2 1 2 1 101000 r 74 goat snp51481-scaffold754-2034439 21 20637719 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782783 Affx-122975118 AX-385269855 21 19338874 CAATAGCAACCACTTTTACTTGATAATATGTCACC[A/G]ATATCTCCCCCTGTCTGTAAACATCCATTGTCATT R 2 1 2 1 101000 r 74 goat snp51480-scaffold754-1977841 21 20695838 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476354 Affx-1251763864 AX-586011769 21 19397205 AGCAGGTACGAAAATCTCAAGAATTTTTGAGACCT[-/TGAAAAGGGAAGAATTCGAGGGGAGAGGGAAAGATGGCGGAAAAAAAAATAAATAAATAAAAAATAAAAAAAAAAAAAAA]GAAAAGGGAAGAATTCACTTAGATTTATTAGGCGA - 4 1 4 1 20000 f 74 goat SV_187 21 19397205 - deletion junction SV-TF-chip 539476610 Affx-1251763864 AX-586011995 21 19397205 AGCAGGTACGAAAATCTCAAGAATTTTTGAGACCT[-/TGAAAAGGGAAGAATTCGAGGGGAGAGGGAAAGATGGCGGAAAAAAAAATAAATAAATAAAAAATAAAAAAAAAAAAAAA]GAAAAGGGAAGAATTCACTTAGATTTATTAGGCGA - 8 1 4 1 20000 r 74 goat SV_187 21 19397205 - deletion junction SV-TF-chip 562165109 Affx-1251763864 AX-606940521 21 19397205 AGCAGGTACGAAAATCTCAAGAATTTTTGAGACCT[-/TGAAAAGGGAAGAATTCGAGGGGAGAGGGAAAGATGGCGGAAAAAAAAATAAATAAATAAAAAATAAAAAAAAAAAAAAA]GAAAAGGGAAGAATTCACTTAGATTTATTAGGCGA - 8 1 4 1 20100 r 74 goat SV_187 21 19397205 - deletion junction SV-TF-chip 562165742 Affx-1251763864 AX-606941151 21 19397205 AGCAGGTACGAAAATCTCAAGAATTTTTGAGACCT[-/TGAAAAGGGAAGAATTCGAGGGGAGAGGGAAAGATGGCGGAAAAAAAAATAAATAAATAAAAAATAAAAAAAAAAAAAAA]GAAAAGGGAAGAATTCACTTAGATTTATTAGGCGA - 8 1 4 1 20100 f 74 goat SV_187 21 19397205 - deletion junction SV-TF-chip 562165844 Affx-1251763864 AX-606941253 21 19397205 AGCAGGTACGAAAATCTCAAGAATTTTTGAGACCT[-/TGAAAAGGGAAGAATTCGAGGGGAGAGGGAAAGATGGCGGAAAAAAAAATAAATAAATAAAAAATAAAAAAAAAAAAAAA]GAAAAGGGAAGAATTCACTTAGATTTATTAGGCGA - 8 1 4 1 20100 r 74 goat SV_187 21 19397205 - deletion junction SV-TF-chip 562165915 Affx-1251763864 AX-606941324 21 19397205 AGCAGGTACGAAAATCTCAAGAATTTTTGAGACCT[-/TGAAAAGGGAAGAATTCGAGGGGAGAGGGAAAGATGGCGGAAAAAAAAATAAATAAATAAAAAATAAAAAAAAAAAAAAA]GAAAAGGGAAGAATTCACTTAGATTTATTAGGCGA - 8 1 4 1 20100 f 74 goat SV_187 21 19397205 - deletion junction SV-TF-chip 562166097 Affx-1251763864 AX-606941506 21 19397205 AGCAGGTACGAAAATCTCAAGAATTTTTGAGACCT[-/TGAAAAGGGAAGAATTCGAGGGGAGAGGGAAAGATGGCGGAAAAAAAAATAAATAAATAAAAAATAAAAAAAAAAAAAAA]GAAAAGGGAAGAATTCACTTAGATTTATTAGGCGA - 8 1 4 1 20100 f 74 goat SV_187 21 19397205 - deletion junction SV-TF-chip 562166266 Affx-1251763864 AX-606941674 21 19397205 AGCAGGTACGAAAATCTCAAGAATTTTTGAGACCT[-/TGAAAAGGGAAGAATTCGAGGGGAGAGGGAAAGATGGCGGAAAAAAAAATAAATAAATAAAAAATAAAAAAAAAAAAAAA]GAAAAGGGAAGAATTCACTTAGATTTATTAGGCGA - 8 1 4 1 20100 f 74 goat SV_187 21 19397205 - deletion junction SV-TF-chip 562166542 Affx-1251763864 AX-606941950 21 19397205 AGCAGGTACGAAAATCTCAAGAATTTTTGAGACCT[-/TGAAAAGGGAAGAATTCGAGGGGAGAGGGAAAGATGGCGGAAAAAAAAATAAATAAATAAAAAATAAAAAAAAAAAAAAA]GAAAAGGGAAGAATTCACTTAGATTTATTAGGCGA - 8 1 4 1 20100 r 74 goat SV_187 21 19397205 - deletion junction SV-TF-chip 38441334 Affx-122929429 AX-123311671 21 19470225 TGAGCAAAAGTAAGAGAAAGATGCCTAGGCATAAA[C/T]GGGGCAGGGGTTGTGTCTTCCCCTTCCAATATTCA Y 2 1 2 1 201000 f 74 goat snp51477-scaffold754-1846490 21 20827199 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277362 Affx-1111835874 AX-519550866 21 19542491 ATATAGGAGGTGAGTTTATCATGGCAGCTCACGTC[A/G]CTGGACCTCCGGGGCTGCCCGCCGAACTCCCCGTT R 2 1 2 1 101000 f 74 goat Random2.2K-1919 21 19542491 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320763703 Affx-986698232 AX-385251527 21 19560793 GCGTCCCATTATCTATGGAGACACAAGGTAGGATG[A/G]TCCTTATCTGCAACCCCAAACCTTCAATCCTCTGA R 2 1 2 1 600010 f 74 goat 21_19560793 21 19560793 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 38379276 Affx-122976240 AX-123249635 21 19613769 TATACTTATTTCTAAGACATTTTTCTAGCCAAGAA[A/G]TTCCAATGTAAAGGTTTCCTGTCCTAGTTGCAGAA R 2 1 2 1 101000 r 74 goat snp51474-scaffold754-1702946 21 20968060 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790308 Affx-122919705 AX-385277311 21 19696516 CTTTTCAGTGCTGTCACAGGTCTACCTGAATTCCC[C/T]TGTGATTTGCCACCAGTGGATAGACCAAGACACGG Y 2 1 2 1 101000 f 74 goat snp51472-scaffold754-1620199 21 21050634 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385703 Affx-122971115 AX-123256061 21 19740399 GATGGCAAGAAAGTGAAAAAGTGAGTGAAAGTGTT[A/C]GTCGCTTCAGTCATGTCTGACTCTCTGCAACTCTG M 2 1 2 1 101000 f 74 goat snp51471-scaffold754-1576316 21 21094536 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401233 Affx-122959311 AX-123271586 21 19779157 CTCAGTAAGCTTGGGCAGGCTATCATGTTTTCCTC[A/G]TGTAGTTTTTCTACCTCTTTTCCTTCCGGGTTAAT R 2 1 2 1 101000 f 74 goat snp51470-scaffold754-1537558 21 21131076 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776295 Affx-122935279 AX-385263423 21 19888216 GGCCTTACCCTCATCCCTACCCACTTCTTCCTTGA[C/T]GTTGTCTCCCAGCCTTATAGACTACCACTCCCAAC Y 2 1 2 1 202000 f 74 goat snp51468-scaffold754-1428499 21 21240080 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405569 Affx-122955949 AX-123275921 21 19920965 CAGGTTTCCTTCAGAGGGCAGCTCCCTCGGCATCC[C/T]GGCTGCCCCCACACCATCCTTTCTCCTGGAAAACT Y 2 1 2 1 201000 f 74 goat snp51467-scaffold754-1395750 21 21272761 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376660 Affx-122979010 AX-123247019 21 20053275 GAGCTGCTGGACGACCTCGGCGAGGTGCCCACCAT[C/T]GAGTCCCTGATAGGTAAGGTTCCGACTTAACTGCC Y 2 1 2 1 101000 r 74 goat snp51464-scaffold754-1263440 21 21405090 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788177 Affx-122973780 AX-385275196 21 20097725 TGCAATAGGCAGTTCGTGCTTAGAAAGTATATACA[C/T]AGCAGTGTGTCCTGGTTGGTGATTTACAATTTCTT Y 2 1 2 1 101000 r 74 goat snp51463-scaffold754-1218990 21 21449425 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787071 Affx-122929602 AX-385274098 21 20218372 TTGCCAAAGGACCCTTATTGGTTAGCAGACAATTA[C/T]AACACATCCTAAACCAATGGTTCTTGCATTTTCCT Y 2 1 2 1 101000 r 74 goat snp51461-scaffold754-1098343 21 21570388 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391832 Affx-122967009 AX-123262189 21 20273963 CCCTGTTGCTTTTTGAAGATCATTGTAAACATTTT[A/C]GCTTAGAAGAGTTCTTTCTTCATTGATGAAATAAA M 2 1 2 1 101000 f 74 goat snp51460-scaffold754-1042752 21 21626336 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437082 Affx-122932666 AX-123307420 21 20333686 TAGTATTCATAGAGCCTGAGAAAAACAAGCGGGAA[C/T]TGAGGAGCAAGAGTTTGTTAGTGCATCTGAGCCCT Y 2 1 2 1 101000 f 74 goat snp51459-scaffold754-983029 21 21686673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778071 Affx-122977472 AX-385265187 21 20401749 AGAAGTCAAGATCAAAATACTCTCAAATTTCTCAG[A/C]ACTAAAGGCTGTCAAGTTTCCATACTAAAAGCATC M 2 1 2 1 101000 r 74 goat snp51458-scaffold754-914966 21 21753861 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422249 Affx-122944005 AX-123292595 21 20444454 GCTAATGTTTGCCACAGGCAGGACCACTAAGGAAC[C/T]GGACTTTGGGACTGAAGATCCAAAAAAATCCCTAG Y 2 1 2 1 201000 r 74 goat snp51457-scaffold754-872261 21 21796495 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390339 Affx-122967696 AX-123260696 21 20482121 CCTGAGTCATCACTTGGTTGTGAGGCAGCCTCCTC[A/G]CTGGTCCCCTATTCCAAGCATCCCAGCTACAACCC R 2 1 2 1 101000 r 74 goat snp51456-scaffold754-834594 21 21834583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384316 Affx-122972273 AX-123254674 21 20511592 AGGAGGCAGATCTGAATAGAGATGTGTTACAAATA[C/T]ACACACCAGGTTTCAGAGATTTAGTACCAGAAAAT Y 2 1 2 1 101000 f 74 goat snp51455-scaffold754-805123 21 21863987 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388604 Affx-122969147 AX-123258962 21 20579542 CCTCCTTATACCTGCACCCTTGTGTGATCCCTCTC[A/G]TGTTAAGTACTGCTGTGATGTGAAGACGACAGGAC R 2 1 2 1 101000 r 74 goat snp51454-scaffold754-737173 21 21932207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444762 Affx-122926363 AX-123315099 21 20616843 GCATCACTAAGTATCTTTGAGGCAGAATGCACAAG[C/T]AAGGAGCAGGTCAACCGGGAAGCCCTTTCTATGTC Y 2 1 2 1 101000 f 74 goat snp51453-scaffold754-699872 21 21969186 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411252 Affx-122952329 AX-123281602 21 20668291 ATGTTGCTCTCTCTAATCAGTGCCACAGATGAAAG[C/T]GAAATTTCTACTCTAGAGAAAAATTACAGAAATAC Y 2 1 2 1 101000 f 74 goat snp51452-scaffold754-648424 21 22020683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435933 Affx-122932750 AX-123306272 21 20718411 TGTTTTCCACAGAGCTGGAGGCCTCTATCCTAGAC[G/T]GCACCTAGAGCCCGTGGTCCAAAGCCTCCAGCTAA K 2 1 2 1 101000 f 74 goat snp51451-scaffold754-598304 21 22071315 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785261 Affx-122974549 AX-385272306 21 20752911 TTATTCAAGATTTCTGTTATGTGTAGAAAATTCCC[A/G]TTTCTAGTTTTGTGTTTGCCCTCTAAAACCTGAGC R 2 1 2 1 101000 r 74 goat snp51450-scaffold754-563804 21 22102554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442502 Affx-122927915 AX-123312839 21 20804185 CTGTTTTTCCCTCGACAACTCTTGGAGCGCTCTGC[A/G]TTGCCACCCTTTTCTGGGATCAACAAACCGCCCTT R 2 1 2 1 101000 r 74 goat snp51449-scaffold754-512530 21 22153516 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785891 Affx-122919524 AX-385272928 21 20834768 GCTGATTGCGAGGGAGAATCAGCTTTTTTCTGGCA[C/T]ACTTAGTGAATCATTTCATGAGCTAGAAATTATAG Y 2 1 2 1 101000 f 74 goat snp51448-scaffold754-481947 21 22183815 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437471 Affx-122932376 AX-123307809 21 20922893 TGGTCCCAGGAGACGTTTCTATGAGTCAAGTGTAA[C/T]GTGCCAGAGCTCTTCAAGGTGCTAGGAAACCAGGC Y 2 1 2 1 101000 f 74 goat snp51446-scaffold754-393822 21 22271773 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449530 Affx-122922602 AX-123319865 21 20954655 AAGTATCTACAGAGAGGGGAATCCCCTAAACCTGC[A/G]TATAAAATCCCTACAAATCCGTGGATAACTCTTTA R 2 1 2 1 201000 r 74 goat snp51445-scaffold754-362060 21 22303502 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428745 Affx-122938440 AX-123299087 21 20988614 TTCACTGGGGGTCATCAGAAGGCTGGGCAGTGCTT[A/G]CTCTCCTAGTATAGATCTAATCATGGCATCCCTGA R 2 1 2 1 201000 r 74 goat snp51444-scaffold754-328101 21 22337271 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419474 Affx-122945477 AX-123289822 21 21018305 CTAAGTTTGACTTTTTAATTAACATATTGGACTGT[A/G]CCTTCCGTTACTGAATGGAGACTATGCTTTCAAAT R 2 1 2 1 101000 r 74 goat snp51443-scaffold754-298410 21 22366837 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451528 Affx-122921098 AX-123321861 21 21050886 CTACCTCATTTTTCTCAACTCTTCATAGAGAGTTC[C/T]GTGGTTGTTTATTTGTTTATCTAATGTGATAATTG Y 2 1 2 1 101000 f 74 goat snp51442-scaffold754-265829 21 22399557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402417 Affx-122958641 AX-123272770 21 21113592 GAGTGAACTCACTGTGGCTTAAGAACAATGGATTT[A/G]TTATTGTTTACTAGGTTTCCTTCTCTTAAGACACA R 2 1 2 1 101000 f 74 goat snp51440-scaffold754-203123 21 22462082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394546 Affx-122964465 AX-123264901 21 21159023 CTGATTTAAAGCATCTATTTCCACTTTCTCTGTCC[C/T]GGGGTGTCAGAATTCTGCCCATTCTCCAACTCTCC Y 2 1 2 1 101000 f 74 goat snp51439-scaffold754-157692 21 22507357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783219 Affx-122977579 AX-385270285 21 21193242 TATTTGAAGCGTTTATTTTCTGAAGGATACGTTTT[A/G]TTCTTTTGCTAATCTGTATAGTAGTACACCTAAGA R 2 1 2 1 101000 f 74 goat snp51438-scaffold754-123473 21 22541476 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800715 Affx-122945904 AX-385287632 21 21346669 CTGAAGGATCAAGTCCAAAGCTTACCCATGTTCCC[A/G]TGATAGGAATTTGAGAGACATCTACAACTCCAATC R 2 1 2 1 101000 f 74 goat snp32586-scaffold374-29855 21 22935559 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273040 Affx-1111833214 AX-519546713 21 21375598 AGAGCACCGAGCTGAGCTCCTTGTGCTTTCTAGTC[A/G]GTTCCTGCCAGCCGGCTGTTTTACACAGGCCGTAT R 2 1 2 1 103000 r 74 goat 21_21375598_AF-PAKI 21 21375598 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320763705 Affx-986698234 AX-385251529 21 21375961 TCTCTCTGTTTTCAGACAACACCTCACTGGTGTTG[C/T]CTTTGCCTCACCCTAAGTCCAAAACATCTCTGCCT Y 2 1 2 1 600010 f 74 goat 21_21375961 21 21375961 Ancestral_priority_1043 ancestry 0.564 neutral IMAGE 10K 10K ancestral 320804083 Affx-986696377 AX-385290751 21 21375962 CTCTCTGTTTTCAGACAACACCTCACTGGTGTTGT[C/T]TTTGCCTCACCCTAAGTCCAAAACATCTCTGCCTC Y 2 1 2 1 600010 r 74 goat 21_21375962 21 21375962 Ancestral_priority_1043 ancestry 0.744 recommended IMAGE 10K 10K ancestral 38409638 Affx-122953530 AX-123279989 21 21382659 TAAGAATAAAGTATTTTCATAAAACCTCAAAGCAA[C/T]GATTGGGGAAATAGTATAAGAGGGCAGTGAAGTTA Y 2 1 2 1 201000 f 74 goat snp32587-scaffold374-65845 21 22971560 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377808 Affx-122977315 AX-123248167 21 21440517 GCAAAATGGGAACAAGAATAACTCCTGCTTATGAG[G/T]TTCTCTGAGGATTAGATAGATCGCATATCATATAC K 2 1 2 1 101000 f 74 goat snp32588-scaffold374-123703 21 23030023 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277488 Affx-1111835875 AX-519550990 21 21441060 GTGGCATAGAATCATTATACGCGTGATGAGATAAT[A/G]TATGTTAATTGGCTCGTATTTAGTAAACACTCAAT R 2 1 2 1 201000 r 74 goat Random2.2K-1920 21 21441060 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320772370 Affx-122944424 AX-385259523 21 21497217 TTATTTTAGGCCAACCCATAGAGAAATAGCATGTC[A/G]TTTGAATCACTATTAACATGTATCCAATTTTCACT R 2 1 2 1 101000 f 74 goat snp32589-scaffold374-180403 21 23087903 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405189 Affx-122956921 AX-123275541 21 21526960 TCCTCACCTGATGTTCCTGTGATCTGAAGATCTTA[A/C]AGACATTCAGGGAAGAAACTTTAACACAGAGTGGA M 2 1 2 1 102000 r 74 goat snp32590-scaffold374-210146 21 23117931 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406602 Affx-122955846 AX-123276954 21 21620254 ACATCTGGGAGATGGAAAGTTAAGCATAATGTTCT[A/G]TAGGAATTATTAAGGCCTCTCTAGGGGAAACCATC R 2 1 2 1 201000 f 74 goat snp32592-scaffold374-303440 21 23211386 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436901 Affx-122933214 AX-123307239 21 21656080 ATGGATTATCATTTTTAACTTCTGAACAAAATAGA[C/T]GCCATACATTACTCATGTTCCTAAGAATTTAAGAA Y 2 1 2 1 101000 r 74 goat snp32593-scaffold374-339266 21 23247220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411838 Affx-122951231 AX-123282188 21 21735813 TTACGCAGCAGGTGACCAGGGTGGGCCACCTCACA[C/T]GGGATGCTCACAGACTTGAGGACCACTGGACCAGG Y 2 1 2 1 201000 r 74 goat snp32595-scaffold374-418999 21 23327153 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766899 Affx-986698236 AX-385254217 21 21770097 CAGACCTGGGTTCCCTCCTAGCTCAGGATCCAACA[C/T]GGACAGGTCTGGAGAAAAGACTCTTCTCATAGAAT Y 2 1 2 1 600010 r 74 goat 21_21770097 21 21770097 Ancestral_priority_1043 ancestry 0.606 recommended IMAGE 10K 10K ancestral 38443560 Affx-122927349 AX-123313897 21 21777890 GGCTTCCTCTCCCTGGTGATTAGTCACCTTCTTAA[C/T]GGCCTCTCTACCTCCAATCTCATTCTTTTTTGTTT Y 2 1 2 1 201000 r 74 goat snp32596-scaffold374-461076 21 23369942 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442982 Affx-122928195 AX-123313319 21 21812171 AGTAAAGGTCATTTTCTTGGTATTATTTCCCCAGA[C/T]GAAACAATTTTAAGATGACTATTTTTTCTGTAATA Y 2 1 2 1 201000 r 74 goat snp32597-scaffold374-495357 21 23403848 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383727 Affx-122972461 AX-123254085 21 21843121 ATCAAGTTACTATTCTATAGTAAGAAAATGACTTG[C/T]GGTATTTGGCTCAGGAGCAGTAGAGAAGGGAGCAG Y 2 1 2 1 201000 f 74 goat snp32598-scaffold374-526307 21 23434563 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401690 Affx-122959553 AX-123272043 21 21884883 TAGAAGCCTAACTTTGAGAGCCCACCTGCATTACC[A/G]CTTGCAGAAATGGATTTATAGATGTCTAGTTAAAC R 2 1 2 1 101000 r 74 goat snp32599-scaffold374-568069 21 23476532 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793044 Affx-122968258 AX-385280022 21 21918386 TAAATCTCCAAGGCTTAGGAGAAAACTTCTCTTCT[A/G]TCAAAATAATATTGTATAGTGAGGAAAAAAGACCA R 2 1 2 1 101000 f 74 goat snp32600-scaffold374-601572 21 23510043 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781632 Affx-122975424 AX-385268716 21 21961471 AGAATCTCTATTTGCAGAGTTACATTCTACATGAC[A/C]TAACCTGAAAATGAAAGACACTGGCTAAAGATTTA M 2 1 2 1 201000 r 74 goat snp32601-scaffold374-644657 21 23555034 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780128 Affx-122970652 AX-385267225 21 21998677 TTTCCATTTCATTCTCATAGCCATCTTGTGATTTA[G/T]ATTATTTTTACTTGCAGAGGTAGAAATGGAAAGAA K 2 1 2 1 101000 r 74 goat snp32602-scaffold374-681863 21 23593045 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431762 Affx-122936722 AX-123302103 21 22041505 AGGGCCGCAAGGCTGTGAATCTTCAGTGAGCCTGA[C/T]TTTGTGAAGCCAAGTCGCTTGGAGTTCTGCAGACA Y 2 1 2 1 201000 r 74 goat snp32603-scaffold374-724691 21 23636085 C T 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439242 Affx-122931008 AX-123309579 21 22079496 TGAAATATGCAAATATATTCAGTTTCATGCAAGAA[C/T]GCGTGTTCCACATTGTGGTTCTTTTTCCAAATGCC Y 2 1 2 1 101000 r 74 goat snp32604-scaffold374-762682 21 23674455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404909 Affx-122956451 AX-123275261 21 22160546 TAAACAATGTTCATAACAGCAGGTCCACGACTGGG[A/C]AATCTAGATTTGGTGGTGGTACTGGGAACTGGTTC M 2 1 2 1 102000 f 74 goat snp32606-scaffold374-843732 21 23753731 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774088 Affx-122969914 AX-385261226 21 22215269 TTCACTTCTGGTTCCAAATTACCCATCATTAGACT[A/G]CTAATATCTGTGATAGTTTTATTATATCCAAAGCA R 2 1 2 1 101000 f 74 goat snp32607-scaffold374-898455 21 23808798 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426186 Affx-122940579 AX-123296532 21 22289569 AAGAGCCAAATGGTTTTAAGGTGAGCGCTACAAAA[C/T]ATTCAAAGTGTAAAGAATTTCAATCTTAAGAAAAA Y 2 1 2 1 101000 f 74 goat snp32609-scaffold374-972755 21 23883088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411913 Affx-122951173 AX-123282263 21 22373754 CCGATCAAGAATCTTGGAAAGAAATCTTTCCTGAT[A/G]CTCTTGAACGTTTGCTGACATTCCCCAGTATTATT R 2 1 2 1 201000 r 74 goat snp32611-scaffold374-1056940 21 23966130 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439494 Affx-122930148 AX-123309831 21 22440329 CCTCAAGGAGACCCAAATCTACTCAAGGAAACATG[A/C]GTCATTCACTAAACAAACATTTACTGAGTGCCTAG M 2 1 2 1 101000 f 74 goat snp32612-scaffold374-1123515 21 24032289 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423285 Affx-122942650 AX-123293631 21 22472563 AGAATCTCCCACTTGTTCTGAATGTGCGTTTTGTA[A/G]CCCTACAAGTTTACACAGTGTCTGTGCTGGTGTGT R 2 1 2 1 101000 f 74 goat snp32613-scaffold374-1155749 21 24064522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799616 Affx-122932783 AX-385286546 21 22513878 ATGGGTCATTTTCTGTAACTCTGGAATCAGCGACC[A/G]GGACACACCCAGCATAGAAACTTCCTTTTGGAGAC R 2 1 2 1 101000 r 74 goat snp32614-scaffold374-1197064 21 24102813 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385388 Affx-122971354 AX-123255746 21 22546404 CATGTCTTGTCCATATAACTAGACCAGAAGCATGG[C/T]AAAAATCTATATTAGCTTCACGTTGAATGTCAGCT Y 2 1 2 1 101000 r 74 goat snp32615-scaffold374-1229590 21 24135427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411657 Affx-122951564 AX-123282007 21 22580131 GCAATGACATGGCTTTTCTCAGGTCCTGGATGCTA[C/T]GTAGAGTTTCTCTCATCTCCTTAAGAATGTGGCTA Y 2 1 2 1 101000 f 74 goat snp32616-scaffold374-1263317 21 24169003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440734 Affx-122929881 AX-123311071 21 22687681 CGGCAAATTAGAAAACCTTCGGTGACTTCGGTTAA[A/G]CGGCTTGCCCTGGGTGGGTCACACCGCACTGTGAA R 2 1 2 1 101000 f 74 goat snp32618-scaffold374-1370867 21 24277317 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780225 Affx-122963433 AX-385267321 21 22732811 GTTTGTATTTTGATCACTTCCTATTCAATCTATTG[A/C]TGAGAGACAGTCCCCCACATGTTTTTGGTAATGGC M 2 1 2 1 101000 r 74 goat snp32619-scaffold374-1415997 21 24322925 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785265 Affx-122971004 AX-385272310 21 22771736 AAAACTTGAGTAGTTGCTCCTCCAGCAGAGCATAC[A/G]ACCTGCCTTTGCACAAGTAGGTGAGTAGAACACAG R 2 1 2 1 101000 f 74 goat snp32620-scaffold374-1454922 21 24361878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783195 Affx-122957344 AX-385270262 21 22809823 AGGAAATAAGTATCTGAGGCAGATGGAAAGACCTA[C/T]TTATCACCAGGTTGATCCAGTTGCTGTTGAAATGA Y 2 1 2 1 101000 f 74 goat snp32621-scaffold374-1493009 21 24400077 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436896 Affx-122933219 AX-123307234 21 22856788 TGTACCTCCAACACTGAAAGCAGTAGAACATAATA[C/T]GTGTTCAGTTAATATTTGTTAGACTGATTGGCTGC Y 2 1 2 1 201000 f 74 goat snp32622-scaffold374-1539974 21 24447566 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380879 Affx-122975051 AX-123251237 21 22892204 CTTAGTTGTTCCGTGGCATGTGGGATCTTCCCTGC[A/G]TTTTTTATTCTTTAACTCTGGAGATTTCTTGAGAT R 2 1 2 1 101000 r 74 goat snp32623-scaffold374-1575390 21 24483139 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802501 Affx-122972652 AX-385289405 21 22927077 GGACATGGGGTTACACCATGAGCCTAAGGAGTTTC[A/G]CATCAAAATTAGTTTCTTGATGGAATCTCTATTTT R 2 1 2 1 101000 f 74 goat snp12378-scaffold1468-196454 21 24671090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453051 Affx-122920071 AX-123323384 21 22998069 ATATAAGCAGTCCTCTAGCGGTCAGCAGTGAAGCC[A/G]GCTGATGCAGGCAATTCTGAACTACTGCCAGGAGA R 2 1 2 1 102000 f 74 goat snp12377-scaffold1468-125462 21 24741914 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412274 Affx-122950886 AX-123282623 21 23028157 CCCAAAATAACAAGAAACATTTTAACTATGCTAAA[C/T]ATATATTGTTTTACTTTATTTCTATTATAGTATCT Y 2 1 2 1 101000 f 74 goat snp12376-scaffold1468-95374 21 24772666 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394456 Affx-122964582 AX-123264811 21 23059278 TATGACTCTCTCGACAGAAAGACTAAAACTCCTTG[A/G]GGGAGGTGCTTGCAAGGATGGAACAACGTCATAAA R 2 1 2 1 101000 f 74 goat snp12375-scaffold1468-64253 21 24803774 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393919 Affx-122965086 AX-123264274 21 23093186 TCTCCTCAGACTTTGATTTCGCAGCCCTTCTGGCC[C/T]CCAGAGAGTTAACTTGTCCCTGTTACCATTAGACA Y 2 1 2 1 101000 r 74 goat snp12374-scaffold1468-30345 21 24837862 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434654 Affx-122933982 AX-123304995 21 23154133 AGAGTCAGACACGACTTTTTGAAAGTAAAAGTGAG[C/T]GACTTTCACTTTCACCACTTAGCCATCTTTCATTT Y 2 1 2 1 103000 f 74 goat snp15094-scaffold1612-30503 21 24898567 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767287 Affx-122977633 AX-385254569 21 23182788 TTCTTCTTTTCTATTTAATGTCCTTGACTTTCCTC[A/G]TTGCTAACATATTTACCAAAATGGGATTCTGAAAC R 2 1 2 1 101000 f 74 goat snp15095-scaffold1612-59158 21 24927149 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406924 Affx-122955086 AX-123277275 21 23242877 TGCTACTCTCCCAGTTTGTCCTCCGCTCCCCTGTT[A/G]TAGTTATACTCTGAAGCTTTAGAATATGTTTTGTT R 2 1 2 1 201000 r 74 goat snp15096-scaffold1612-119247 21 24986262 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379216 Affx-122976283 AX-123249575 21 23284045 GCTAGATCAGGGCATTTTGACAACCTCTGCCTTTG[C/T]GACTGGTCTTCTGTCTGCCCCTCTTTCCCATCCTC Y 2 1 2 1 101000 f 74 goat snp15097-scaffold1612-160415 21 25026356 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399354 Affx-122961351 AX-123269709 21 23319871 GTACTGCTGGGGAAGGTGTGTTCTGATAAAAGGGA[C/T]GCATGTGTCTGGCTCTACGACATTGCAGTTTTCTG Y 2 1 2 1 101000 f 74 goat snp15098-scaffold1612-196241 21 25062284 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446446 Affx-122925080 AX-123316782 21 23362856 GAATTTCCTGACAGTTACAGAGTGAAGACCTGGGC[A/G]CCAGCAGGTGGTGGAGATAAGATGGGAGTGGGCAT R 2 1 2 1 101000 f 74 goat snp15099-scaffold1612-239226 21 25105267 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419510 Affx-122945450 AX-123289858 21 23513897 TGTCCCTCTCTGGGACTCAGTGCTCCCTTCTCCAA[G/T]ATAGGAGTGGGTGGACCAGACCATATCTAGGTGTC K 2 1 2 1 101000 r 74 goat snp46081-scaffold633-139399 21 25267416 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795360 Affx-122965893 AX-385282316 21 23545135 GTTTTGAAGATGAAGTTAAAGGTGACAGTATTTGC[G/T]AAAAGACTTCACAATGCAAAGCATGCAGGAGACCT K 2 1 2 1 101000 r 74 goat snp46082-scaffold633-170637 21 25298472 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422152 Affx-122943536 AX-123292499 21 23651818 TCCATGGGGTCACAAAAGAGTCAGACATGACTTTG[C/T]GAGTAACCAACAGCAACAAAGCACATAGCTGCTAG Y 2 1 2 1 303000 r 74 goat snp46084-scaffold633-277320 21 25406760 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429416 Affx-122938519 AX-123299758 21 23729607 CAACAGAGGAAGAAAATAGCAGATGTCCTGGAGGG[C/T]GAAACTGAAAAAAGGAGAGACAGAGGAAATCATTT Y 2 1 2 1 201000 r 74 goat snp46086-scaffold633-355109 21 25480975 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449509 Affx-122922618 AX-123319844 21 23758128 AAAAAAAAATTTTTAAGTACAAATATGCTGTAAGT[A/G]TATGTCATAACTGAATCAGTGTCTTTTACACTGAG R 2 1 2 1 101000 r 74 goat snp46087-scaffold633-383630 21 25509561 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399633 Affx-122961074 AX-123269988 21 23826009 AAAGTGACTGCAAAGGTGGCTTATAAATATGAGTG[C/T]CAGAAAGACACAGGCACAGAATACCCAGTTATTCC Y 2 1 2 1 101000 f 74 goat snp46088-scaffold633-451511 21 25579380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406691 Affx-122955778 AX-123277043 21 23860638 TCATGCATTTAGCTTTGGCACCAGTTCTGGGAAGC[A/G]GTTGGTGGAAATGGTGGAAGTGTTGGCTAAGAAGA R 2 1 2 1 101000 f 74 goat snp46089-scaffold633-486140 21 25613988 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277366 Affx-1111835876 AX-519550870 21 23863093 GAGTATGTGCTGTATGAGCCCATCAAAACTGGGTC[A/G]TTTGTAAAGACGTGGATGGACCTAGAGTCTCTTAT R 2 1 2 1 101000 f 74 goat Random2.2K-1922 21 23863093 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417201 Affx-122947311 AX-123287549 21 23910064 ACAATAGGAGCTACAAATGGGAACCACATAAGTAG[C/T]TAAACATTTTCTAATAGCCACATTTACAAAGAGAA Y 2 1 2 1 101000 f 74 goat snp46090-scaffold633-535566 21 25663319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441935 Affx-122928584 AX-123312272 21 23952809 GAGTCTTCAGATCAGATACTTTTGTCTAGTTTATA[A/G]CATTGTTTGAGCCAGTACAATCCGCCTTTTGTACA R 2 1 2 1 101000 r 74 goat snp46091-scaffold633-578311 21 25706268 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800655 Affx-122939622 AX-385287574 21 23988370 GAGGATGAAAGGCAGTTGAGATGCTGTGCTCAGAA[G/T]CTCATAGCTCAAACCTGCGTGTAGTGAGAATGGAA K 2 1 2 1 101000 f 74 goat snp46092-scaffold633-613872 21 25742280 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438329 Affx-122931345 AX-123308667 21 24028150 TCTGTGCTGTGCAACCCTGGGGCTAGTACCTGTGC[G/T]ACTTGGCATGATCAGGGCAAGGGTCTGTCTCCTCA K 2 1 2 1 101000 r 74 goat snp46093-scaffold633-653652 21 25780988 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381641 Affx-122974760 AX-123251999 21 24058246 GGAGACCAGCCCTACGGGGGAAAGTGCTGGAATTC[A/G]GCCAGTACCAGCTGCTATATCAGAAAGACTTAGTG R 2 1 2 1 101000 r 74 goat snp46094-scaffold633-683748 21 25811086 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382801 Affx-122973570 AX-123253159 21 24093268 TGAAGGTTTAGTTTGATGTAATAGGACCAGATCTA[C/T]GGGGTGCCACAAGTCAAAATTCTTGGGGTGGGGGG Y 2 1 2 1 101000 f 74 goat snp46095-scaffold633-718770 21 25846191 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273042 Affx-1111833215 AX-519546715 21 24117826 TCCATTCTGTGAGTCTTTCTTCTATCGACAAGCAT[A/C]AATGGGTCCTACCAAAAGTTAGGTTTTTTGATAGT M 2 1 2 1 101000 r 74 goat 21_24117826_AF-PAKI 21 24117826 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320788195 Affx-122957225 AX-385275214 21 24130162 CAGAGAATCTGGTTATGCTGAAAAAGAAAATTGTC[A/G]TTTGTGAGGTGGTTTCCTAAATGGATTAACACAAA R 2 1 2 1 101000 f 74 goat snp46096-scaffold633-755664 21 25883212 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413425 Affx-122950697 AX-123283774 21 24170920 TTCAAATCATATGGAGAAGTTGCCAGGTTTAGGGA[G/T]CAGGTAGTCGCTTATCCAAAGAAGGCTAACCGCGG K 2 1 2 1 101000 r 74 goat snp46097-scaffold633-796422 21 25923939 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394767 Affx-122964839 AX-123265122 21 24234090 GTCTCTAACCACATCTGGTTACTGAGCACCCAAAA[C/T]GGGGCTAGTCGGAATTGAAATGTGCTGCTCTTGTA Y 2 1 2 1 201000 f 74 goat snp46099-scaffold633-859592 21 25987116 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790741 Affx-122946965 AX-385277742 21 24262837 CAGGTGCTAAATACAACATTAGCATATCAAACTAT[A/G]TATTTATTAATTACAAGACTACTTGAATGGTTTAA R 2 1 2 1 201000 r 74 goat snp46100-scaffold633-888339 21 26016888 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451816 Affx-122921479 AX-123322149 21 24292850 GTGTCACCTTCTGCACCTGCACCCTGCCATCCAGT[C/T]TCAGCATCTTGGGGTTTCTGCATGTGATAGATTGT Y 2 1 2 1 201000 f 74 goat snp46101-scaffold633-918352 21 26047561 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413727 Affx-122950065 AX-123284076 21 24353466 AGCTTCAGATTGATCTAGTGTTCATTATGCAACAT[A/G]TGATTGTCATAATCACTCACATTTTATTACATTAG R 2 1 2 1 101000 f 74 goat snp46102-scaffold633-978968 21 26108144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397879 Affx-122961967 AX-123268234 21 24395940 CCCTCTTGGAGGTTCCAGGCTAGTGGGGCTGAAGG[C/T]AGAGAGGGTAGCGTATTTAAGGAATTGAAAGTAGA Y 2 1 2 1 101000 r 74 goat snp46103-scaffold633-1021442 21 26150922 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421973 Affx-122943801 AX-123292320 21 24438936 CTGGAGTCACGTCCCCTGCTCTCCCCCAAGGATAT[A/C]GGGTGTTTATCACAACCAGCTGCTCAAGAGCCTAC M 2 1 2 1 101000 r 74 goat snp46104-scaffold633-1064438 21 26193998 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803396 Affx-122949560 AX-385290227 21 24527059 TGTAAAATACAAGATATATTTTCATGTAGTCCAAT[A/C]TGTTGACCATTTCCTTCAGATTTCTTCCTCTTGGT M 2 1 2 1 101000 r 74 goat snp46106-scaffold633-1152561 21 26282471 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415026 Affx-122949021 AX-123285375 21 24578366 TCCCAAAGATGAGCGATTTATGAAATGATTTCAAA[C/T]ATGGACAGACTTTAAAACATTTTTGTAGTAACGAG Y 2 1 2 1 101000 f 74 goat snp46107-scaffold633-1203868 21 26333691 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763711 Affx-986698240 AX-385251534 21 24606101 ATTTCTAAAAAGTGTTTTAAATAAACTGTAATCCT[G/T]GGGGAGCAGCTAAAAATATAGTCTGTTCTGCTTTG K 2 1 2 1 600010 f 74 goat 21_24606101 21 24606101 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 38402097 Affx-122958694 AX-123272450 21 24693588 GCGTCCTGACTGTGTATGTAGGTGTGGAGCACTGA[A/G]TGGTGCTCCTGTGGCCTGTTCTTAATTTCACAGTA R 2 1 2 1 101000 r 74 goat snp46110-scaffold633-1319090 21 26449038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781580 Affx-122967576 AX-385268664 21 24744968 CAGCTCCAACCTCTACCAACGGATTCCATGATCCA[C/T]GAAAGTCAAAGTCCCTCCCTAGGATTGCTGCTAAT Y 2 1 2 1 101000 f 74 goat snp46111-scaffold633-1370470 21 26499931 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397118 Affx-122962687 AX-123267473 21 24818347 GAGTCTCAGTTCCTTGATTTATCAAGTGCAGTTAG[C/T]GGTATGATGTCTGACCTACCTTCTTTGTCCCATTT Y 2 1 2 1 101000 f 74 goat snp39052-scaffold496-53807 21 26573655 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403856 Affx-122957931 AX-123274208 21 24819434 ATTCGATCAGCATCAGGTCCCAGGGAGTCTGGCAG[C/T]AATTGTTTCCCCCTCCTACTTACAAAAATTATATT Y 2 1 2 1 201000 r 74 goat snp14912-scaffold160-819 21 26574778 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419878 Affx-122945356 AX-123290226 21 24869195 ACAGCCAATTTTCTATCTGTCAATCTACAGAGAGT[A/G]CAGTTGCTTTCTTACACACTTGGAATTCATTCTCA R 2 1 2 1 101000 f 74 goat snp14913-scaffold160-50580 21 26624823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420969 Affx-122944580 AX-123291316 21 24924603 TTTGCAAGGTAATTATAGATATATGCTTACACATG[C/T]TTCTTGGATCATATTTGATTACAGATTTAGGAGAG Y 2 1 2 1 101000 r 74 goat snp14914-scaffold160-105988 21 26680802 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277368 Affx-1111835877 AX-519550872 21 24954161 CTTCCCTGAGAGATCAGCAAAGTCAAATCATCAAC[A/C]TCTCATGAGGACATCACCTTGGGCTCCCTTCTGCT M 2 1 2 1 101000 f 74 goat Random2.2K-1923 21 24954161 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416738 Affx-122948201 AX-123287086 21 24965954 CTTCTCATCTCTCATTGACTCTTTGGGCTGGGAAC[G/T]CTCCTTTGCTGAGCAAGCTGGTTAACTCTTCAAGT K 2 1 2 1 101000 r 74 goat snp14915-scaffold160-147339 21 26721816 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442288 Affx-122928257 AX-123312625 21 25001083 CATGTCAGGTGAGGGTTTTGCAATTAGACGAGCTG[C/T]CTGGCTTGCTTATGATTTGGAGTCACACTGAATGG Y 2 1 2 1 101000 f 74 goat snp14916-scaffold160-182468 21 26756909 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274055 Affx-1111833978 AX-519547659 21 25012648 ATTTAGTTATTT[A/G]AAGAATGTGCTAAGTTTAAAATTAAAGGGCACCAT R 2 1 2 1 101000 r 74 goat GoatD01.012543 21 25012648 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38387345 Affx-122970488 AX-123257703 21 25037435 TAAAATGCTTTTTATCAGATTTACATTTCACCTAC[A/G]TTCAAAAATATCAGCCTCTTTTGAGGATTTAAAAG R 2 1 2 1 101000 f 74 goat snp14917-scaffold160-218820 21 26792944 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801659 Affx-122924192 AX-385288567 21 25080757 GGAAGGAGTTAGAAGGGAGGGGGAGAACAAGAAAA[C/T]AAATTAAGAAAGTCATGGGAAAAGTGTACAAAATA Y 2 1 2 1 202000 r 74 goat snp14918-scaffold160-262142 21 26838119 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449638 Affx-122922592 AX-123319973 21 25124547 GAAAGTCGGCTTCTGGGCTGTGAAATATAGTAGAA[C/T]GTGCCTGAGCAAAACCCCAAGGGCTTGTGTCTCAC Y 2 1 2 1 101000 f 74 goat snp14919-scaffold160-305932 21 26882048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428700 Affx-122938625 AX-123299042 21 25170001 TACCCACACCTGGGCCTACATTACAAAAAACCGTC[A/G]TTCAAAATGACACATCATTCAAAATGACCCAACCT R 2 1 2 1 101000 f 74 goat snp14920-scaffold160-351386 21 26928321 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383245 Affx-122972750 AX-123253603 21 25221238 ATAGATTTGACCAGTATTGCCTTAGAAGATATAAC[G/T]CCAGAGAGGTCATCACCATCAACGATAAATTTAAC K 2 1 2 1 101000 f 74 goat snp14921-scaffold160-402623 21 26980318 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429799 Affx-122938199 AX-123300140 21 25257276 ACTCCAGCCCTACAGAGTTTCCATGTAACCAGCCC[C/T]TCCATAGTCAGAATGGCCTCAAGCAACAGTAAAGA Y 2 1 2 1 101000 r 74 goat snp14922-scaffold160-438661 21 27016052 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38434665 Affx-122933975 AX-123305006 21 25294196 GACCTCTGATATAATCGTGGCCTTTTCTTCTTATT[A/G]TGTAATTTTAAAACATGAAAACATAAAACAAAAAC R 2 1 2 1 102000 f 74 goat snp14923-scaffold160-475581 21 27053417 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412396 Affx-122951449 AX-123282745 21 25333717 AGAATCTTTACAATACTCAGTCTTAATGTTGTGTT[A/G]TGGTACTTCTTCTACTCGTTTATGTATTTTCATGT R 2 1 2 1 101000 r 74 goat snp14924-scaffold160-515102 21 27092940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376160 Affx-122978845 AX-123246519 21 25389425 ATTGTTGTTGTTGTTGTTGTTAATGGCATAAAACA[C/T]ATAGAAAGTAAGAAATTTTCTAGAAAAGTCCCATG Y 2 1 2 1 101000 r 74 goat snp14925-scaffold160-570810 21 27148546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792608 Affx-122929179 AX-385279589 21 25435744 CACAGAACAAAAGAGGGCCCAACCCTCTCATTTAT[G/T]CTCCAGCTAATATTAGCTTGAGAGACAGGCAAATA K 2 1 2 1 201000 r 74 goat snp14926-scaffold160-617129 21 27196534 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763713 Affx-986698242 AX-385251535 21 25461065 CCTGGAGCACAGAGATCCTTAGGAAAAACTGGCTT[C/T]CTGGGCTGTGGATTATAGTGGAAAGTGTGAGCAAA Y 2 1 2 1 600010 f 74 goat 21_25461065 21 25461065 Ancestral_priority_1043 ancestry 0.69 recommended IMAGE 10K 10K ancestral 468275391 Affx-1111834770 AX-519548965 21 25477348 TTTT[A/G]AATAACGGCTTTTTGTAATGTAGGCCCAGGTGTGG R 2 1 2 1 101000 r 74 goat GoatD01.052196 21 25477348 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38399500 Affx-122961171 AX-123269855 21 25482791 AGCCTGGGACACCTTGCCCTCTTGCCCTTTTTGCT[A/G]CTACCAGGGACGTCTCTCCTAGGCCAAGCATCACC R 2 1 2 1 101000 f 74 goat snp14927-scaffold160-664176 21 27243495 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420563 Affx-122945279 AX-123290910 21 25534731 TAACCAAAGAATACTATATGCTTTCACTGCATCCT[A/G]AAATTCATTCAGCCTCTTAACTATACTCTCTGGTG R 2 1 2 1 101000 r 74 goat snp14928-scaffold160-716116 21 27291273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418356 Affx-122946586 AX-123288704 21 25578264 AACACATGGTATCAAAAAATCTAACTGATGGCATC[A/G]ATCATTTTTAAATAAAAAGTTGTTTTTGAAGTGCA R 2 1 2 1 101000 f 74 goat snp14929-scaffold160-759649 21 27335153 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378755 Affx-122977019 AX-123249114 21 25638141 GGGGGCCCTGTGAGGGCTGCTCCCCAGAGGGCACT[A/G]CACTAAGTCCTGGAGCTGTACTGTCCTGGGTCCTA R 2 1 2 1 101000 r 74 goat snp14930-scaffold160-819526 21 27395231 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793784 Affx-122944522 AX-385280756 21 25674262 TTGTGTTACACAGTAGATCCTGGTGACTTTATGAG[C/T]AGTAGTATACCTAGATTAGTCTGAAGAAGCTCGTT Y 2 1 2 1 101000 r 74 goat snp14931-scaffold160-855647 21 27431299 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390189 Affx-122967802 AX-123260546 21 25711815 CTTTCTTGGTGACTGGAAGTTTCCCTTCTAAGTCT[C/T]TGAGGCTGTGTCTCTTTTTGAAAGACGTTCATTTG Y 2 1 2 1 102000 f 74 goat snp14932-scaffold160-893200 21 27469002 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454013 Affx-122919427 AX-123324346 21 25746081 CGATGGCAACAGTCTGGAAAATGGACAGTCTCAAA[C/T]GCCTGGAAAGAACTCTCCAAAGAGGTGAAGTGTAG Y 2 1 2 1 102000 f 74 goat snp14933-scaffold160-927466 21 27503343 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427746 Affx-122939254 AX-123298089 21 25806668 ACTATAAAAATTGTGTTGACTGGTACTTAATATTC[A/G]CAAGGTCCAGGAGGGGGAGGAAGGTGTAAGTAAAC R 2 1 2 1 201000 f 74 goat snp14934-scaffold160-988053 21 27564040 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406068 Affx-122956244 AX-123276420 21 25842048 TCATCAGGCACTTCTGTGTGTTGCCTTCTCTTTCC[C/T]TGTATGTGCTGTTTAAATATTTCCTTGCCAAGCAT Y 2 1 2 1 101000 r 74 goat snp14935-scaffold160-1023433 21 27600122 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401608 Affx-122959619 AX-123271961 21 25888333 GAATGTTTGTTGCATTGACCAGAACATAGACTTGT[A/C]GGTCTTCCTCAGACCTTTTAATTTTATTATTTTTA M 2 1 2 1 101000 f 74 goat snp14936-scaffold160-1069718 21 27646157 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446022 Affx-122925857 AX-123316359 21 25933091 TACTGAGATGGCACTCTAGAGCCCCTGCTCTGAAA[C/T]AAGAGAAACCATTGCTGTGAGAAGCCCGAATACCT Y 2 1 2 1 303000 r 74 goat snp14937-scaffold160-1114476 21 27691053 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438152 Affx-122931466 AX-123308490 21 25993461 ACCCCTCTCTTGGTTTTCTCCATGGCAGCATCTTA[C/T]AAAACTACAGTGTGATATCACAGCCAGGAAGGACA Y 2 1 2 1 201000 f 74 goat snp14938-scaffold160-1174846 21 27750803 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417673 Affx-122946826 AX-123288021 21 26045814 TTCTGTAAAGAATGTCTTCAGCTCTTGTGTCCCAG[C/T]GCCTGCTCATATGTTGTGGGGCTGTCATTATCACC Y 2 1 2 1 101000 f 74 goat snp14939-scaffold160-1227199 21 27803563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425664 Affx-122940876 AX-123296010 21 26096183 GGTACTAACTGAAGTATTATTTTTCATTCTGAAAA[C/T]GGGAACCAATCTGAGTTTTCGGCAAGAGGGCACTG Y 2 1 2 1 103000 r 74 goat snp14940-scaffold160-1277568 21 27854418 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443174 Affx-122927608 AX-123313511 21 26158109 CTTGCCAAACCCAGAGGATGCCAGGTGGTCCTTAC[A/G]TGTCCTGGCGTCTCTGCCATGTGGGATCTGCTGTC R 2 1 2 1 101000 f 74 goat snp14941-scaffold160-1339494 21 27916504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415467 Affx-122949162 AX-123285816 21 26226074 ACCAGCCTAAAAGTAAAATGCAACTCAAATTTACA[G/T]CTCACCAAAGTGATCAGATACCATACACCATACAG K 2 1 2 1 101000 r 74 goat snp14943-scaffold160-1407459 21 27984968 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425215 Affx-122941020 AX-123295561 21 26307918 CCACGCCCCATGACTCATCTGGGTGTCAGCTCTAT[C/T]GCTGTGTATGAGCTGCGGGCAGCCGTCCCTTTCCA Y 2 1 2 1 101000 f 74 goat snp14945-scaffold160-1489303 21 28065399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436961 Affx-122933167 AX-123307299 21 26357379 GGAGAAGGTTTAGAACACTAGATAAATGGTGCATA[C/T]GAGTGCCACAGCAGGTGGAGAGGACAAGGCCTGCT Y 2 1 2 1 101000 f 74 goat snp14946-scaffold160-1538764 21 28115228 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417752 Affx-122947413 AX-123288100 21 26409753 ACAAGACCTGCTGGACACTAGACATGATATAAAGG[C/T]ATAACTAATAAAACATAAGGAAGAAGCTAAATGGA Y 2 1 2 1 101000 f 74 goat snp14947-scaffold160-1591138 21 28167835 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397625 Affx-122962628 AX-123267980 21 26441743 TCCCTTAGTAGAAATGGAGTAGCCATCCTGGTCAA[C/T]AAGAGTCTGAAAACACTTTCACAGGCCATCATAAA Y 2 1 2 1 101000 r 74 goat snp14948-scaffold160-1623128 21 28199883 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448202 Affx-122924235 AX-123318538 21 26520555 TCAGGAGGGAAGCCCTGTCCACGGTGCTCCTAATG[C/T]GGAGAAGACAGCACCTCTGCCGCCCAAGGCACCCC Y 2 1 2 1 101000 f 74 goat snp14949-scaffold160-1701940 21 28279495 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375950 Affx-122978450 AX-123246309 21 26553842 GTTTGCCCATAAGACACAATGTATTTTATATGTAC[A/G]TACACAAATATGCCAAATAACAGCTCTGCCTAAAT R 2 1 2 1 101000 r 74 goat snp14950-scaffold160-1735227 21 28312730 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429642 Affx-122937679 AX-123299983 21 26593930 GATATTTGTATTTCCTTGCCGTCCTTCACTTAGTA[C/T]GATAATCTCTGGATCCATCCATGTTGCTGCAGATG Y 2 1 2 1 303000 f 74 goat snp14951-scaffold160-1775315 21 28353317 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273044 Affx-1111833216 AX-519546717 21 26633319 TAAGTGCCAGACCTGGGCACCCAGGGTCATAGCCC[A/G]TTACTAGTTCAGCAAAATCCAGTGACTTCCCAGAG R 2 1 2 1 101000 r 74 goat 21_26633319_AF-PAKI 21 26633319 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425414 Affx-122941540 AX-123295760 21 26652882 ACTTTGTGTGTCTGTGTGTCTCTGTGTGTTTGTGT[A/G]TATGTGTATAGTTGTGTAAGTTTTATCATTGTGTG R 2 1 2 1 101000 r 74 goat snp14952-scaffold160-1834267 21 28411814 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768663 Affx-122957917 AX-385255841 21 26683421 CCTTCTTTGTCCCTTGTGGCAGTCTTTATTTTAAA[G/T]CCTGTTTTATGTGATAAAGACTCTTAGCTATTTCT K 2 1 2 1 201000 f 74 goat snp14953-scaffold160-1864806 21 28442293 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429839 Affx-122938165 AX-123300180 21 26718069 CAATAAATTTGACTTCATCAAAATTTAAGCCTTTT[A/G]TTCTATGAAAGACCTTGTTAAGAGATGAAAGCTTC R 2 1 2 1 101000 r 74 goat snp14954-scaffold160-1899454 21 28477226 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419793 Affx-122945850 AX-123290141 21 26770429 CAGGGTTCATCTGAGACCTGTGACTCCTCTACTGA[A/G]GGCTCACTGCGAAGATCAGGAAAAAGGATTAGGAG R 2 1 2 1 101000 r 74 goat snp14955-scaffold160-1951814 21 28529863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386506 Affx-122970751 AX-123256864 21 26822431 GATATACACATGCACATTCGTATGCATATACATGT[A/G]TCCACATACACCTACGTTCATGCACACACAGATGT R 2 1 2 1 101000 r 74 goat snp14956-scaffold160-2003816 21 28581825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404060 Affx-122957153 AX-123274412 21 26860755 CATACTCAGTGGATTGTTCATTTTCTGGCGGGTGC[A/G]GTAGGCTAAGAGAACAGCTCTGATTAACCCATCAT R 2 1 2 1 101000 r 74 goat snp14957-scaffold160-2042140 21 28620061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796537 Affx-122921344 AX-385283484 21 26896632 ACATTGGAAATTTCATCCTTTCATTCTTGTGATGC[A/G]TTTTATTTGATTATGACTATTAGTCTTTTGGGCTT R 2 1 2 1 202000 f 74 goat snp14958-scaffold160-2078017 21 28655943 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399844 Affx-122960251 AX-123270199 21 26928350 CGTGGGCTCCCTCTCTCGGGGTGATGGTCGGCCTC[A/G]CTGGGCCCTGACAAAGGAGAGACACTCTTGTTGTA R 2 1 2 1 101000 r 74 goat snp14959-scaffold160-2109735 21 28688247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393360 Affx-122965922 AX-123263716 21 26979214 CCTGGCACTTAGGGCTTTGTGGGTGGATGTTGCAG[C/T]GTTGAGTCCGGGAGGAGGGAGAGTGATTAACAGGC Y 2 1 2 1 201000 f 74 goat snp14960-scaffold160-2160599 21 28738147 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791095 Affx-122931626 AX-385278090 21 27015417 TGGACAGCCTTGAAGTCCAGTTTCTTCATAAGAGT[A/G]TTTATCCAAGGATAGCATTAACTTCACTATAAAGC R 2 1 2 1 101000 f 74 goat snp14961-scaffold160-2196802 21 28774805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800457 Affx-122935720 AX-385287378 21 27096939 TATGTTAATATCTTTCCTCTTCCAAGAGATTTAAC[A/G]CAGTGACTGAATCATTATGAGCTTAGTATTAAAAA R 2 1 2 1 101000 r 74 goat snp14963-scaffold160-2278324 21 28855945 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275145 Affx-1111834620 AX-519548724 21 27131012 GGGAGGCTGCAGGTGGCTGTAGGTCTGACTGCATG[A/G]CTTGAGGGAAAATTATGGGTGCTGGGTGCTTCTGG R 2 1 2 1 102000 r 74 goat GoatD01.043602 21 27131012 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320764783 Affx-122954370 AX-385252395 21 27138785 CAGCACCCTTCTTCCAACTCATTATCCATTTCCTC[A/G]TTTTATCCTGAGTTTGGATATTGAGCTATTTGTTT R 2 1 2 1 102000 f 74 goat snp14964-scaffold160-2320170 21 28899374 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778842 Affx-122934358 AX-385265950 21 27176894 GCTTTTCAGAGAAACACGAGTGTAATACTTGGTGA[C/T]GGTTGTCACTGATGTACTCATTTCATAGAACCTTA Y 2 1 2 1 101000 f 74 goat snp14965-scaffold160-2358279 21 28937289 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399516 Affx-122961159 AX-123269871 21 27220878 AGAAGCTCTCCTCTGGTCCCTTTGGTTCTATGTGA[C/T]AGTAACTGTTTTTCACAGCTGTCGTGGTAATGCCG Y 2 1 2 1 201000 f 74 goat snp14966-scaffold160-2402263 21 28981398 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781047 Affx-122962336 AX-385268134 21 27259376 AGTTTCTAGACTCCTTTGATCAATTTCCCTGATTC[A/G]CTCAACCTCAGAACCATATATGGCTGCCACCAGAG R 2 1 2 1 101000 f 74 goat snp14967-scaffold160-2440761 21 29019829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801258 Affx-122933990 AX-385288171 21 27289093 GTCAAGAGACATATCCAGGGGAAGCCTCATAGTTA[G/T]ATTTCACCCAAATGTCCCCATGATCAGGATATAAA K 2 1 2 1 201000 r 74 goat snp14968-scaffold160-2470478 21 29049480 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415168 Affx-122949012 AX-123285517 21 27348188 CCATTTGTCACTAATAGACTCATCAGATGAATGAA[C/T]GGAAAAGATACAATCTCCAGTTTTAAGAAGTTACT Y 2 1 2 1 101000 f 74 goat snp14969-scaffold160-2529573 21 29109080 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375524 Affx-122979113 AX-123245883 21 27393050 TTAGCAACTGGAGGACCTCTGCTGTGGGCTGCCCA[C/T]GTCTCCAGAGCCCCTGCAGTCTTTTCTGTCTCCAG Y 2 1 2 1 202000 f 74 goat snp14970-scaffold160-2574435 21 29154258 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766919 Affx-986698246 AX-385254231 21 27425263 GACCTGTGCCTGCCGGGAGACCAGCCCTAGACTAG[C/T]CTGAACCTGACCAAGTTCTGTCTACATGGTAGGTT Y 2 1 2 1 600010 r 74 goat 21_27425263 21 27425263 Ancestral_priority_1043 ancestry 0.458 neutral IMAGE 10K 10K ancestral 38386298 Affx-122970927 AX-123256656 21 27427484 GCAATTAGACTTTGTAATGGTTATTGATACTAGTC[A/G]AACCATGAAGACTTTTTTTCACTTGCCCTTAGTCT R 2 1 2 1 101000 f 74 goat snp14971-scaffold160-2608869 21 29188628 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408284 Affx-122953793 AX-123278635 21 27461852 TTTCCACAAGCAGTGTAGATTAATTGGCTTAATAA[A/G]TTAAGAAAAAGTAAAAATCACATAAAAGGAAAGAG R 2 1 2 1 103000 f 74 goat snp14972-scaffold160-2643237 21 29222874 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766923 Affx-986698248 AX-385254234 21 27469223 TTGTGTACGTGTACCCCACCCCCTGTCTCCATTCA[G/T]GTTGCTCCTGTAATTAGCCTGCTTCCCTGTCTTGG K 2 1 2 1 600010 r 74 goat 21_27469223 21 27469223 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 38384430 Affx-122972181 AX-123254788 21 27507688 ACTTCTCAAATGAAATCTGTCTAAGAGCTAGCCAG[C/T]GTATTAAAGGTTACTTCAAATGTCAATAAGACATC Y 2 1 2 1 201000 r 74 goat snp14973-scaffold160-2689073 21 29268897 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395806 Affx-122963647 AX-123266161 21 27545932 TTAGAAGGGTAGGGACAATATATGCTAGGGGAAGC[A/G]CCCCTCCTACAGAGATTTAGCTCTTGCAGTTCTCC R 2 1 2 1 101000 f 74 goat snp14974-scaffold160-2727317 21 29307705 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396897 Affx-122963221 AX-123267252 21 27585777 TCTGTTCTTTGTTTTTGTTTTTCTCTTTTTCTATC[A/G]TCTGTCTTGTTAATTCAGAGCATTATATGATTTCA R 2 1 2 1 201000 r 74 goat snp14975-scaffold160-2767162 21 29344991 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439191 Affx-122931046 AX-123309528 21 27621635 TAGACTTTTTCATGAAGGGCATATTCCAGTCTATT[A/G]CCCACTTCTCTAAAATTAGGCTTTCTGTCTTTTAC R 2 1 2 1 101000 f 74 goat snp14976-scaffold160-2803020 21 29379867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796630 Affx-122920227 AX-385283576 21 27669280 CAATAAAGCTTTCATCCAACTATACTGATTTTTAC[A/G]TGCTTAAATTTTGCTCTAGAGAATAAATAAAATGG R 2 1 2 1 101000 f 74 goat snp14977-scaffold160-2850665 21 29427803 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784135 Affx-122922002 AX-385271187 21 27724496 TACAAATCATATCACTCCCAGAGAAGCAATTTAGC[A/G]TGTAAGGATTCCAGCCCTGATGTGAGAGTTTACGT R 2 1 2 1 101000 r 74 goat snp14978-scaffold160-2905881 21 29482898 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801962 Affx-122947273 AX-385288866 21 27761716 CAGTGTATCAAAAGTCTGTTCAGGTATAAATAACA[G/T]AAAACTGACCAGTGGATTGCCTCCACACATAAGGA K 2 1 2 1 101000 r 74 goat snp14979-scaffold160-2943101 21 29520154 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396912 Affx-122963210 AX-123267267 21 27793906 TCAAATATCCTGGCTCCAGTGCAAGGGTCTTCTTG[A/G]GTTAATTTCGCTTTGGTTTGCTTTACTCTTGTTTT R 2 1 2 1 201000 r 74 goat snp14980-scaffold160-2975291 21 29552465 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411754 Affx-122951502 AX-123282104 21 27834330 ATCACATGCCATAGGCAGGCAGCAGTCAGCCTCTG[C/T]GTCCTGTCTCAGGAAGCACCATCTTGCTGGGGTTA Y 2 1 2 1 201000 f 74 goat snp14981-scaffold160-3015715 21 29592663 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785966 Affx-122946606 AX-385273002 21 27877301 CATCCTTCCTTTTGGTTGATAACCTTTCTTTCCCC[C/T]CACTGTATTGTTGATCTAAACTTGTTTTTAAATCA Y 2 1 2 1 101000 f 74 goat snp14982-scaffold160-3058686 21 29635612 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796437 Affx-122922393 AX-385283387 21 27906547 AAATTTGGATGGCACTGCTTCTAAAGTTTGTATTA[C/T]TAGATAGGATAATTGTTATAAGTTTGGAATACCCT Y 2 1 2 1 101000 f 74 goat snp14983-scaffold160-3087932 21 29664542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452339 Affx-122920652 AX-123322672 21 27928462 CCTACTACTCCCTTTAATACAGGTTTCTCAGTAGC[A/G]CTAATGTCTAAAATGCCATCTAACTCATTTATGCT R 2 1 2 1 201000 r 74 goat snp28586-scaffold3064-79107 21 29686453 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445949 Affx-122925907 AX-123316286 21 27957544 CCTCTTTGATAACATCTGAGAATACAAGGGCAGTG[C/T]GGAATTTTAAGGCTAAGATCTGGGAGGAGATCGAC Y 2 1 2 1 201000 r 74 goat snp28585-scaffold3064-50025 21 29716117 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430461 Affx-122937261 AX-123300802 21 28003803 GCTATAAATTGATAAGAAAAATGCAAACGAAACAA[C/T]AGAAAAGTGGGCAAAGTACGTGAATAAGTATATCA Y 2 1 2 1 101000 r 74 goat snp28584-scaffold3064-3766 21 29760621 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401918 Affx-122958825 AX-123272271 21 28023249 TCAACTGACCCTCTCCTGCTATTCTGTCTAGAGAA[C/T]GCATGATTTGATTTCCATTATTTCCAGACTGTCAC Y 2 1 2 1 101000 r 74 goat snp24405-scaffold2471-15581 21 29787220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399893 Affx-122960212 AX-123270248 21 28052171 AGGCCATATCAGGGCATGTATTTCTAGTATTTACT[A/G]TATCTCAGTAAGAATTTAGGCCTTTTCCCCCTTTT R 2 1 2 1 101000 r 74 goat snp24406-scaffold2471-44503 21 29816346 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435102 Affx-122933707 AX-123305442 21 28098619 ACAAGTCATTAATTGCATAATGCTATTTTACTCTC[A/G]TAAATAGCCAATCTTCTATCTTCCCCTTCAAATGC R 2 1 2 1 101000 r 74 goat snp24407-scaffold2471-90951 21 29862206 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375819 Affx-122978555 AX-123246178 21 28137789 CGCTTCTGTGCGAGGCTCCACCTGCACTAGCCTCC[A/G]CTGTCCCTCCAGGGTACCAAATTTTCTCCTGTCTC R 2 1 2 1 101000 r 74 goat snp24408-scaffold2471-130121 21 29901340 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277370 Affx-1111835878 AX-519550874 21 28149944 GCTTTTCCTAGCCCTTTGTGTGGCCCTTTCCAGAA[C/G]AGAAGGCAGAGCTGCCAGGAGCTCAAAGCCTCTCC S 4 1 2 1 102000 f 74 goat Random2.2K-1926 21 28149944 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38442871 Affx-122927667 AX-123313208 21 28196861 GCACAGAAGGCAGGGCTGCCGTGGGGCTTTGAATG[C/T]GCGGCCAAGAAGCTTAGATTTATCCCCAGAGATGC Y 2 1 2 1 101000 r 74 goat snp24409-scaffold2471-189193 21 29960281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450177 Affx-122922311 AX-123320512 21 28210705 TGGGGTAAGAAGTGGGCCCACGTGTACACAGGGGA[A/G]GTCAGTGATGGTCAAGACTGGAAGTCAGAGAGGGT R 2 1 2 1 101000 r 74 goat snp8911-scaffold1320-6290 21 29973859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424320 Affx-122941956 AX-123294666 21 28242659 TTTTTAAAAAATGGCAAGACAAAATGTGATGTCAC[A/G]TACGGACATGAATTTGAACAAACTCCGGGAGATAC R 2 1 2 1 201000 f 74 goat snp8912-scaffold1320-38244 21 30005468 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414441 Affx-122949953 AX-123284790 21 28312048 AGAGCATCCCATAGCTCACTCCATCGACAGGTGAG[G/T]CAAGTAGATGCCTTGCAGCCCTGTTCACAGATGTG K 2 1 2 1 101000 r 74 goat snp8913-scaffold1320-107633 21 30074920 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445042 Affx-122926616 AX-123315379 21 28342508 GTCTGGGCAGAATGGTCATGGCAGTGACAGACCAC[A/G]TCTCCCCTGGGTGGTGTAACAGGATCGAGCCCTAG R 2 1 2 1 201000 r 74 goat snp8914-scaffold1320-138093 21 30105721 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277372 Affx-1111835879 AX-519550876 21 28393808 TAAACTCTGCTCAATGATACATCTGTAGGCATTAG[A/C]AGATGCAAGTTTGTCTTTGAGTGGGAGGCCTGATT M 2 1 2 1 201000 f 74 goat Random2.2K-1927 21 28393808 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409981 Affx-122953282 AX-123280331 21 28395727 TGAACCCTTTGGTCTAACACCAAAGGCAACTCATG[C/T]CCTCCTTGGCCCTTGTGTAACATCTCTAACCTGCG Y 2 1 2 1 101000 r 74 goat snp8915-scaffold1320-191312 21 30158856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426080 Affx-122941081 AX-123296426 21 28452211 GGGTTATTTTGCCCCAGGGACTCTGATTTCTGGGA[C/T]GTGCTCTGCCCTTTATCCTAAGACTCCTGACCTTG Y 2 1 2 1 201000 r 74 goat snp8916-scaffold1320-247796 21 30215839 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421204 Affx-122944145 AX-123291551 21 28510045 AAACTTAACAAAAAGTTGTGAAAATAAAAGTAGCA[C/T]GAGGCCCACCAATACATGATTTGCCTATTGTTAAA Y 2 1 2 1 101000 r 74 goat snp8917-scaffold1320-305630 21 30273649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429758 Affx-122938257 AX-123300099 21 28560493 GGCTCTAAGAGAGCTACAGGGGCAGCTTGAGATAG[C/T]CCTCCACTCCAGACCCCAAGACTGAGGATATGCCC Y 2 1 2 1 101000 f 74 goat snp8918-scaffold1320-356078 21 30324183 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393035 Affx-122965634 AX-123263392 21 28600876 TTCCTGGAGCCCGTCTTTGGCCAGGTGAGGAGATA[C/T]GGATAAGGAAACACAACTGTTCAACTGTATGACCC Y 2 1 2 1 101000 r 74 goat snp8919-scaffold1320-396461 21 30365152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406628 Affx-122955827 AX-123276980 21 28637044 GAAGACAAAGCTGCTGAGACAGGAGGCTGGATCCG[C/T]GACCTGTCATCCCATCTGCCCAGGGTGACCTGGGC Y 2 1 2 1 201000 r 74 goat snp8920-scaffold1320-432629 21 30401004 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410419 Affx-122952412 AX-123280769 21 28671031 ACAGATCTTTAAGAGGGCAGAGCCAGTGACGCCTA[A/C]GCCACCGCCTCCCCAGCCTTTTGCCCCAAACGGCG M 2 1 2 1 101000 f 74 goat snp8921-scaffold1320-466616 21 30435185 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428685 Affx-122938635 AX-123299027 21 28718627 ACTTGGCAGTTACATGTTCCAGCTTCCTCTTCCTT[A/G]CTAGCAGCTCTCTGTGGTAATGTAATGTTTAGTCC R 2 1 2 1 201000 r 74 goat snp8922-scaffold1320-514212 21 30482720 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766086 Affx-122930390 AX-385253502 21 28751956 GCACACACTAAAATGCCTCAGGAGAAAACAGATGC[A/G]GTACTCATAAGAGAAAGCTTTAACTTGTTTGAGCG R 2 1 2 1 101000 f 74 goat snp8923-scaffold1320-547541 21 30516039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426560 Affx-122940172 AX-123296906 21 28798623 GAAGTTTCCTCAGATCCCTATTCCATTGTGTTCTC[A/G]CTCTCTTTTTAAAACCTCAGTGTTGGCTTGTCTGT R 2 1 2 1 101000 f 74 goat snp8924-scaffold1320-594208 21 30562808 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401908 Affx-122958831 AX-123272261 21 28816660 ACTGCCCTGGGGTCCAGATTTCTGCATTCTCTGGA[A/G]AAACAATGGGACCATATCGCCAGATGACCAGAGGT R 2 1 2 1 101000 r 74 goat snp8717-scaffold1311-9746 21 30580692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399476 Affx-122961190 AX-123269831 21 28881370 GCCTGGAGTCACATCACCGGAGGAAGGGGCTCCCC[A/G]ATCTCCCGTGTCCCAGAAGCCATCTGAATTGTTCC R 2 1 2 1 101000 r 74 goat snp8718-scaffold1311-74456 21 30645916 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387499 Affx-122970334 AX-123257857 21 28947683 GGGCTACAGTCCATGGGGTCACAAAGAGTCAGGCA[C/T]GACTGTGTGATTGCCACTTTCTACTGATATGCTTA Y 2 1 2 1 101000 r 74 goat snp8719-scaffold1311-140769 21 30712398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784822 Affx-122936322 AX-385271869 21 29006372 CAAAACTTGTGGTGGACACAGTTTTCACATAGACC[G/T]AATCAGTGGTCCTACCTTATGTGTTTTCAAGATTG K 2 1 2 1 101000 f 74 goat snp8720-scaffold1311-199458 21 30769420 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382574 Affx-122973760 AX-123252932 21 29029795 GATGCAAGTCTGTATACTTCTCCTCTGTTGCCGAG[A/C]TGTTTCTATTGCTGTGATACCTGTTCACATAAAGC M 2 1 2 1 201000 r 74 goat snp28608-scaffold307-4689 21 30792336 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393025 Affx-122965641 AX-123263382 21 29124588 GAAATCTTTAGAAAAGGCAAATCAAGAGACAGGAA[C/T]AGATTAATAATTGCTTGGGACTGGGGGTGGGAAAA Y 2 1 2 1 201000 f 74 goat snp28610-scaffold307-99482 21 30888124 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442730 Affx-122927852 AX-123313067 21 29165739 TTAATCCATCCCCTTTCCAAACTGAACCAGAGTTC[A/G]CAAATGCTGGCCAGCACATCCACCATAGGACTTTC R 2 1 2 1 201000 r 74 goat snp28611-scaffold307-140633 21 30929694 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271911 Affx-1111833217 AX-519545691 21 29182118 ATAATCTCAATAGATGCAGAACAGAATCTGACACA[A/G]TTCAACAACTATTGATGATAAAAATTCTCAACAAA R 2 1 2 1 201000 r 74 goat 21_29182118_AF-PAKI 21 29182118 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38441574 Affx-122928681 AX-123311911 21 29209464 CTGCCCCTGCAGATACCCCTGAGTAGGTCCATGTC[A/G]TTTACACTTCTAAGCTGGCAGAGAGTGTGGGTGGA R 2 1 2 1 101000 r 74 goat snp28612-scaffold307-184358 21 30973541 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397667 Affx-122962595 AX-123268022 21 29272384 CCCAGTGTGTGATCAGGTTGGGCTCTCAGTTCGTG[A/G]CTTGGGTCAGGGCTCAGTGTGTGAGCAGACTTGGG R 2 1 2 1 101000 f 74 goat snp28613-scaffold307-247278 21 31035189 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400901 Affx-122959740 AX-123271254 21 29310621 AGACACACGTAACAGACACACACATACGCTCTCAT[A/G]TTAAACCTAGGAGCTGCCCCTGATGCAAGAGGCAC R 2 1 2 1 201000 r 74 goat snp28614-scaffold307-285515 21 31073331 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381428 Affx-122974354 AX-123251786 21 29352488 ATACTTTTTACTGAGGCCAAGAAATCCATAGGCCT[A/G]TGAGGACACATTCACCAGGATAAAGGGTAACTGCT R 2 1 2 1 101000 r 74 goat snp28615-scaffold307-327382 21 31114727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417382 Affx-122947700 AX-123287730 21 29399372 ACCTCGAACATTTACGGGTTATGCAAACAGCTTCC[A/G]TCGGTATATTTTTAATAATCACCACTCTTATTATT R 2 1 2 1 101000 f 74 goat snp28616-scaffold307-374266 21 31161626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779556 Affx-122967892 AX-385266659 21 29432600 GGTTAACTTTGAGGAAGTCTTTAAGATACTTCCGG[A/C]GTTGGAATTAGTTTTTCTTTCAAATCTGCATTGCC M 2 1 2 1 201000 r 74 goat snp28617-scaffold307-407494 21 31195099 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446464 Affx-122925068 AX-123316800 21 29477324 TGGTTCCTGGCCCTTTCTTCCATTTTCAAAGTCAG[C/T]AGCACAGCATATTCAAATCCCTCTCTTAACACTGA Y 2 1 2 1 201000 r 74 goat snp28618-scaffold307-452218 21 31239859 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382274 Affx-122973931 AX-123252632 21 29506088 AGAACTGCCAACTGAATTCCCTGACCAGATGGGGC[C/T]ACAGCTCAACTTTATATATGGGCAGAGCTGCTGCC Y 2 1 2 1 101000 r 74 goat snp28619-scaffold307-480982 21 31269064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405934 Affx-122955563 AX-123276286 21 29540201 TCCGTGATTATAGGTGACACTAATAATAATGATGA[C/T]GATATGAATTCATATGACTGCAGTAGAATGGCACA Y 2 1 2 1 101000 f 74 goat snp28620-scaffold307-515095 21 31303247 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427916 Affx-122939227 AX-123298259 21 29587530 AGCTCCAGTCCCAACTGGCCTTCAGTATTTTTTTA[C/T]GGCAGAGGGCTGGCTTTCAAAACCCTTTCCTTTCT Y 2 1 2 1 201000 f 74 goat snp28621-scaffold307-562424 21 31350612 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420737 Affx-122944763 AX-123291084 21 29662168 ATGGGGTGACTTATATTTTTTATTAGGTGTCAAAA[C/T]AGAAAAACAGGGTAGAATAGGAGAGTCCAGAAATA Y 2 1 2 1 201000 f 74 goat snp28622-scaffold307-637062 21 31425576 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796371 Affx-122978932 AX-385283321 21 29726667 TTTTCAGTACTCAGAGTAATGAACTCCAAGGAGAA[C/T]GAAAATCTAAAGTTGTGAATTTAAAACTCACTCAC Y 2 1 2 1 101000 f 74 goat snp28623-scaffold307-701561 21 31490029 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397590 Affx-122961995 AX-123267945 21 29765520 TAATTTTTCCATTTAATCAGCTAGAGTCTAATTCT[A/G]TTGCTAGCTACTTGCTAACCACTAAGCCATGATAA R 2 1 2 1 101000 r 74 goat snp28624-scaffold307-740414 21 31529856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452980 Affx-122920126 AX-123323313 21 29840862 CCAAAGGGATATGAAGAGAAGCATCTCCCTCATCT[G/T]CTATACCCCCAAGGGAGGCATGCTTTCATGACGGG K 2 1 2 1 201000 f 74 goat snp28626-scaffold307-815756 21 31606042 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787739 Affx-122973634 AX-385274762 21 29872985 ATCATATTATGATTGAATGTACACCTGACACATTT[A/C]AGTTGCTAGTATAGCAAATGTGGTCTTGCTCTCTC M 2 1 2 1 101000 r 74 goat snp28627-scaffold307-847879 21 31638238 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406942 Affx-122955071 AX-123277293 21 29908528 ATTCACCTTACTTTCCAGTATAGAACCAGCACTTC[A/G]CTTTGGTTCTCATGCCCTTGGTCCTGCCTTTTCCT R 2 1 2 1 101000 f 74 goat snp6520-scaffold1230-1732217 21 31673511 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452928 Affx-122920190 AX-123323261 21 29954232 TTGGCATGAGACACCTCAGTGGGAAGAGCCCCAGA[C/T]GGGCCTTCAGGCTGGAGAGCCAGGCCCTGGTCCCA Y 2 1 2 1 101000 f 74 goat snp6519-scaffold1230-1686513 21 31719232 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401749 Affx-122959509 AX-123272102 21 30008698 GTTCCCCTTTGGAATAGTCTACCCAGGAATAGACT[A/C]GATGTGTTATCTTGTCCCCAACCACACACATACAC M 2 1 2 1 101000 r 74 goat snp6518-scaffold1230-1632047 21 31774262 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433068 Affx-122935744 AX-123303409 21 30048591 GACTCGGGCTGCTCTGAGATCGGTGGCTGGATTAA[C/T]AGTTCTCTGAGTGAGGGCCAAAGGACGTAAGGTGG Y 2 1 2 1 101000 r 74 goat snp6517-scaffold1230-1592154 21 31812636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441748 Affx-122929125 AX-123312085 21 30089888 TCTTCTTTAAAAAAAAAAAAAATGAATCAGAGAAC[A/G]TATGATCTGATGTAAGAAACTGACAGAGGGAAGTT R 2 1 2 1 101000 r 74 goat snp6516-scaffold1230-1550857 21 31852681 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799252 Affx-122948612 AX-385286182 21 30119765 TGAAGCCAATGCATTAGATAATATTGAACCACAGA[A/G]TAGTAAAGCTAGGTAATATGGTGATCATATTAGCA R 2 1 2 1 101000 f 74 goat snp6515-scaffold1230-1520980 21 31882828 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423989 Affx-122942117 AX-123294335 21 30150934 AGGTTCAGGTCATAATAAGTTAAGCTTTGCCACCC[A/G]CATAGTCTCTTTGCAACTGCTCAGCTCTGCCTTGG R 2 1 2 1 201000 f 74 goat snp6514-scaffold1230-1489811 21 31913916 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775505 Affx-122935974 AX-385262636 21 30192632 AGAATGAAGTTTGCTGTGTGTTATGGGGAAAATGT[G/T]TATGCAGTTGCCATGGAAATAACATGTAGGCATTT K 2 1 2 1 101000 r 74 goat snp6513-scaffold1230-1448113 21 31955631 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801338 Affx-122958967 AX-385288250 21 30243451 AATCGATACTATTGGTGTGCTGGATGGTGTATCAC[A/G]CTGCATATATTACATAAGAATTGTAAGTTTCCTCT R 2 1 2 1 101000 f 74 goat snp6512-scaffold1230-1397294 21 32006987 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415711 Affx-122948522 AX-123286060 21 30311931 GAGTTTTCTACCACTCTGTTCTCTTGGAGCTGATT[A/G]TTTTCTTTAGTTCCCACTGTTTGGGGGGCTTATAA R 2 1 2 1 202000 f 74 goat snp6511-scaffold1230-1328814 21 32075693 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408908 Affx-122953962 AX-123279259 21 30374560 AACAACAGCATGAACCAAGACAGAAAAGGGTGGGT[A/G]CAAGATACTTTTTATTTTACCCCCAGAGACCAATT R 2 1 2 1 101000 f 74 goat snp6509-scaffold1230-1266185 21 32139845 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803446 Affx-122959164 AX-385290275 21 30414666 AAATAAAATGATTCCCAAAAATTGGCTGAGATCCT[A/G]TAAGAATCTGCTTTTATATGGTCCATGAGGGGGTG R 2 1 2 1 101000 r 74 goat snp6508-scaffold1230-1226079 21 32180205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450530 Affx-122922489 AX-123320864 21 30444261 GAAGGCTTCCTTTCTGCTGCAGAAGGTGCCTGTCT[C/T]GGGGGTGTCTAGTCAGCGGAGTATACGCAGGCCCG Y 2 1 2 1 101000 f 74 goat snp6507-scaffold1230-1196484 21 32209768 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440162 Affx-122930729 AX-123310499 21 30476079 TAGACTTATACAAGTAATTTCTAATTAGGATCCAT[C/T]ACAAACAAAACTACTTACATATTGTTCTACATGTA Y 2 1 2 1 101000 f 74 goat snp6506-scaffold1230-1164666 21 32241611 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393597 Affx-122965375 AX-123263953 21 30505654 CTTCTCAGGACATCCCCTGGCTCCTGGGGTCTCAG[C/T]ACCCAGTCCCTCAAGCAGACAGAGAGTACTGCCTG Y 2 1 2 1 101000 r 74 goat snp6505-scaffold1230-1135091 21 32270984 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451531 Affx-122921096 AX-123321864 21 30608974 AAGGATTCAGTGAGTGACTTAGATCCACTGTGCTC[A/G]TGGTAAATGGTCAGCATGGGGTTCAGGCCAACTCT R 2 1 2 1 101000 f 74 goat snp6503-scaffold1230-1031771 21 32370281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394990 Affx-122964255 AX-123265345 21 30640029 GATGGACTGAGAGGAGAAGGGGAAAGATGAGGGAG[G/T]GAGATAAGCCAGACAGTTTTAAGCCCCTACAGAGA K 2 1 2 1 201000 r 74 goat snp6502-scaffold1230-1000716 21 32401358 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433918 Affx-122934385 AX-123304259 21 30679520 CCAGGACCCCACCTCCACTGTCAATATCCCTAGGC[A/G]TTTCTGCTTTCAGGCTCAAAGCCACTGTGGCAATT R 2 1 2 1 101000 r 74 goat snp6501-scaffold1230-961225 21 32440835 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432281 Affx-122936326 AX-123302622 21 30714510 CAATTTGGCGGTGTATCCAAATTTAAAATGTGTAT[A/G]CCCTGAGATCTCACCCCTGTGGTCCGGGGGTTAGG R 2 1 2 1 101000 f 74 goat snp6500-scaffold1230-926235 21 32475844 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416194 Affx-122948245 AX-123286543 21 30767400 CCACACCCTGGTGCCTTCTACGGGAATCCTCTGTC[A/G]TCATCTCTCAGGCCAGGATGGAACTGGGAGGAGGC R 2 1 2 1 201000 f 74 goat snp6499-scaffold1230-873345 21 32528859 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438320 Affx-122931351 AX-123308658 21 30796606 CCCTACCCCCTCTGCCCCCAGTGCCAGCCCTGCCT[C/T]TTCAGTAGAAGATCAGATGGTCGGGTAGTCCAGGA Y 2 1 2 1 101000 r 74 goat snp6498-scaffold1230-844139 21 32556788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398438 Affx-122961614 AX-123268793 21 30840897 AGACCGAGCTGGTGAGAGCCAGACAGGTGCAGAGA[C/T]ACAGTGGAATCTAGAGAGAGAATCAGAGCCAGGAT Y 2 1 2 1 101000 r 74 goat snp6497-scaffold1230-799848 21 32601062 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387059 Affx-122969900 AX-123257417 21 30907336 AGAAAGTGGGCAGCCTGCTCCTCCCAGCTGGCTCT[A/G]TCCTCTCCAGTGTCAATGATCCCATCATGAGTTAC R 2 1 2 1 101000 r 74 goat snp6496-scaffold1230-733409 21 32667646 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412805 Affx-122950484 AX-123283154 21 30939998 GAGTGGGATTCTTTCTTCTTCCTTTCTTAAAGGAA[C/T]GGCACTGAAAAGAAAACAGCCTTTGGAGCTGCATG Y 2 1 2 1 102000 r 74 goat snp6495-scaffold1230-700747 21 32700122 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777634 Affx-122978682 AX-385264753 21 30970545 AAGTGGAAAGCAGTATGGGAAGCAGATTGAGGCCA[C/T]GGGAAATGGGACACATTTCCTGAACAAAGAGCAGA Y 2 1 2 1 202000 r 74 goat snp6494-scaffold1230-670200 21 32730646 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766971 Affx-122954428 AX-385254270 21 31013801 GAATTTGTATACATAATCCTTGTATATATATGATA[A/C]AAGTGATATGTCAATTAACAGGAAAAGTGTATTAT M 2 1 2 1 201000 f 74 goat snp6493-scaffold1230-626944 21 32774281 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769079 Affx-122977450 AX-385256254 21 31111985 GCAGGAGTCAAAGCTATGCTGAGCATACAGACTGG[A/C]GACTTCTCACAAATGTTGAGACCCTCGACTCACCT M 2 1 2 1 101000 f 74 goat snp6492-scaffold1230-528760 21 32872699 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778916 Affx-122928143 AX-385266023 21 31140923 CATCATGGCAGCAACTGTCTCTGCCTATTTTGTGA[C/T]CATCAATCTCAATAATCCTACCCGTTCCCCCAATA Y 2 1 2 1 101000 f 74 goat snp6491-scaffold1230-499822 21 32901646 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769044 Affx-122952525 AX-385256219 21 31175763 AGAATATGGTATACTGTTTTATAAAGGTTATGTTT[A/G]TAAAGACTAAAAGGAAAAACTATTCCTCCATACAA R 2 1 2 1 102000 r 74 goat snp6490-scaffold1230-464982 21 32935367 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451309 Affx-122921285 AX-123321642 21 31206857 AGGTCCTCGCACATCCGTTTCCTCTGTCTAGGAAA[C/T]GCTTGCTCACTTCATCTGGCTTAGCCTTCTGTCCA Y 2 1 2 1 101000 r 74 goat snp6489-scaffold1230-433888 21 32966680 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384652 Affx-122972147 AX-123255010 21 31257040 TACAGGTGCTGAGCATATCCTGGCTTGGAGGTTTG[A/G]GACATGGATGGGACTGTAGTCCTGTGGAAAGGTTA R 2 1 2 1 101000 r 74 goat snp6488-scaffold1230-383705 21 33016405 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421367 Affx-122944048 AX-123291714 21 31288495 CATTTTTTTTCTTGAAAAACAAAATTATTGAAGAA[G/T]AGTTGACTTACAATGTTTCAGGTGCACAGCTAGGT K 2 1 2 1 303000 f 74 goat snp6487-scaffold1230-352250 21 33048161 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440417 Affx-122929608 AX-123310754 21 31320371 GGGCAATGATTTAGTGAGAGAAAAATGGTAGGCCT[A/G]TAGAAGAAAAAGGCAGAGAGGAATCAAGATTTTTC R 2 1 2 1 101000 r 74 goat snp6486-scaffold1230-320374 21 33080110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417758 Affx-122947409 AX-123288106 21 31366086 AAGCCTGGAGTGCTGCAGTTCATGACTTAGCGACT[A/G]AATAGCAACATCAAGACAGTATAGCACCTCTGGCC R 2 1 2 1 101000 r 74 goat snp6485-scaffold1230-274659 21 33125592 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429716 Affx-122937616 AX-123300057 21 31400589 CTATGCAGTTTCTCTGTCCCCTAGGAACCACAATT[A/G]TTTTTTTATTGATGTCCTACTAGAGATTCTTGATT R 2 1 2 1 102000 f 74 goat snp6484-scaffold1230-240156 21 33159659 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446871 Affx-122925241 AX-123317207 21 31432173 CACACGTATCTGCAGGTCATAGTGGCCTGTAGATG[C/T]AACTTCTACTTGAAACTTTTAAGAAATTCACCTGG Y 2 1 2 1 101000 f 74 goat snp6483-scaffold1230-208572 21 33191422 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421239 Affx-122944116 AX-123291586 21 31496466 CGTTATCAATAGCTAGGCAGAACACTGCAGAGAAA[A/G]CAGTGGCCTCTCTTTCCCCTGGACATGTATGGTAG R 2 1 2 1 101000 f 74 goat snp6482-scaffold1230-144279 21 33256086 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442102 Affx-122928355 AX-123312439 21 31534546 GATCACCTTCGCCTTAATTGCCTCCTTCCGCTGGG[C/T]GTCCACTTCGTCTGCAGAAAGTGGGGGTTTAAATG Y 2 1 2 1 202000 f 74 goat snp6481-scaffold1230-106199 21 33294470 T C 2 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38395087 Affx-122964173 AX-123265442 21 31572407 GTGTAACCCCAGAGGTTGAGTGGAAGTTCCTTGGG[C/T]AGAGAATGGGGAGGGGCGGAGAGGGAATGGCAAGG Y 2 1 2 1 101000 f 74 goat snp6480-scaffold1230-68338 21 33331586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437979 Affx-122931595 AX-123308317 21 31634546 CACACTATGTAGGGACTCTCCTGGTCGTCCAGGGG[C/T]GGAGACTCCATTCTTTCAATTCAGGGGGACCAGGT Y 2 1 2 1 202000 r 74 goat snp6479-scaffold1230-6199 21 33388524 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415371 Affx-122948766 AX-123285720 21 31642746 ACCATGTCCCATCCCTTCTCTCAGGTGATGTGACT[A/G]AAGCCCAGAAGCGTAAAATGAACTGTCCAATCCAA R 2 1 2 1 101000 r 74 goat snp18311-scaffold1858-1902 21 33397037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376353 Affx-122978329 AX-123246712 21 31682140 GTACATCAGCTCAGATGTCATATCTAGGAAACCCC[A/G]TGCTCCCCTGTCTGTATCTGCTTCTCCCACTTCCT R 2 1 2 1 201000 r 74 goat snp18312-scaffold1858-41296 21 33437000 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443722 Affx-122927145 AX-123314059 21 31712406 ATTTATTTGATCTTTAACAAGTCACTCTGATCTGG[C/T]AAAAAGTGGGGTCACTCTCAGAAGTATGCTCTGGT Y 2 1 2 1 201000 f 74 goat snp18313-scaffold1858-71562 21 33467549 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802279 Affx-122948935 AX-385289183 21 31751840 GGGACAGCTCTCCTTGAATGAGCAGGTCACCAAAG[C/T]ATATCTGATAAACACCTGGGAGCTTTCCTGGGATC Y 2 1 2 1 201000 f 74 goat snp18314-scaffold1858-110996 21 33507023 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389361 Affx-122968462 AX-123259719 21 31785968 AGGTGGCTGGGTTTGAGATATACACAGAACAGGCA[C/T]GGCTGAGTCAGTGACCACCAAGCTGGGCTTGCCCA Y 2 1 2 1 101000 f 74 goat snp18315-scaffold1858-145124 21 33540132 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451896 Affx-122921040 AX-123322229 21 31832012 ATGACTCATGGGGTGTATATCAGTTAATGCAGGCT[A/G]AACAACTGCAGCAAATAGACCCAAAACACAACTCA R 2 1 2 1 101000 f 74 goat snp18316-scaffold1858-191168 21 33586193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429491 Affx-122937872 AX-123299833 21 31864419 CAACTACTTCTTATCACCACCCTCTACCCCTCTTG[C/T]GCTGGCCAGCATTATCTCTCACGTGATTAGCGCAG Y 2 1 2 1 201000 r 74 goat snp18317-scaffold1858-223575 21 33618556 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411693 Affx-122951546 AX-123282043 21 31910873 TTTGCCATGTGTACCTCCACATTCCCTCAAACAGG[C/T]AGCTGCCTCTGCCGGGACACCACATCCCCTCAACC Y 2 1 2 1 101000 f 74 goat snp24909-scaffold2547-519358 21 33665407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420218 Affx-122945538 AX-123290566 21 31963948 TGGGCTAGTCCTCTAAACTCTATGAGTTCCATGCC[A/G]TCATTTGTAAAATAAGGATGACGACTACACTTCCT R 2 1 2 1 201000 f 74 goat snp24908-scaffold2547-466283 21 33718582 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378786 Affx-122976997 AX-123249145 21 31994301 CAGGGAAGTCCCAGTATTGGCATTTTTCACTTCTC[G/T]AATGTCTGTGCCTTTGGTTTCCTGACACTGGACAG K 2 1 2 1 101000 r 74 goat snp24907-scaffold2547-435930 21 33748864 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428160 Affx-122939043 AX-123298503 21 32023226 GATGTCCCCTGCAAACTTTCCGGAGCCCTGCTGCT[G/T]GATGCGCTTGCGCAGGAGGCTGACGAAGTCCTGAG K 2 1 2 1 201000 r 74 goat snp24906-scaffold2547-407005 21 33778340 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381321 Affx-122974436 AX-123251679 21 32059067 GATAGAGAGGAAGAAACCCCATGAGGAATGAGTGA[A/C]TTCTACAGGGTCTCAGAGTAAATTCAATGAGAAAT M 2 1 2 1 101000 r 74 goat snp24905-scaffold2547-371164 21 33814174 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271913 Affx-1111833218 AX-519545693 21 32084606 CTGCCTTGCAAGGTGGTTGTGAGAATTAACAATCT[A/G]TGTAAATCACATTGTATTCTGTCTCATATATTATT R 2 1 2 1 201000 r 74 goat 21_32084606_AF-PAKI 21 32084606 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38402039 Affx-122958734 AX-123272392 21 32124486 CATTCTTTTTCCCCCATTCAATCCACTGCCAAGTC[A/G]TGTCAATTCTCCTGTGATCTTGATTTTGGCTGCTC R 2 1 2 1 201000 r 74 goat snp24904-scaffold2547-305745 21 33878674 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452428 Affx-122920582 AX-123322761 21 32156240 TCTTTTCCCTCCCTCAACCCCATCTAGCTTCCACC[A/G]TAACCAGGCAGGACTCAGCCCTGAACTGGGACCCT R 2 1 2 1 201000 r 74 goat snp24903-scaffold2547-273991 21 33910867 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442801 Affx-122927719 AX-123313138 21 32207221 TTCACTGGAACACACCCACCACCCACACAGACACA[G/T]GGTCACAGAGATGCACATTCATTTCTACACATAAA K 2 1 2 1 101000 r 74 goat snp24902-scaffold2547-223010 21 33956209 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277498 Affx-1111835880 AX-519551000 21 32223310 TTGTTGTGAGGGGTTTGTTTGGTGGTTGGGTTTTT[A/C]TTCTCCCAACAGGGAGGAGATCCGTTTACCAAAAA M 2 1 2 1 201000 r 74 goat Random2.2K-1930 21 32223310 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427771 Affx-122939233 AX-123298114 21 32269905 CCATTTGCAGACCTCACTGGAAGATTCGGGACCAT[A/G]CTCTGAATGGAGTGGATTGGGCAAATGTGCTTTCT R 2 1 2 1 101000 r 74 goat snp24901-scaffold2547-160326 21 34019095 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432780 Affx-122935425 AX-123303121 21 32314473 TGCTCTCTTCTCACGCAACTACAATAGATAGCTGT[A/G]TAAGATTCTTGGGGAATCAGCTTACAAAGTGAAGG R 2 1 2 1 201000 f 74 goat snp24900-scaffold2547-115758 21 34063812 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770431 Affx-122939666 AX-385257597 21 32350052 GATGATAACCACAGACAAGTTTTACTTCGGCAGTG[C/T]ATACAAAATCCTGGATAAAAGGCCAGCAAATGAAA Y 2 1 2 1 101000 f 74 goat snp24899-scaffold2547-80179 21 34099352 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395183 Affx-122964515 AX-123265538 21 32395326 GGTGCCCAGGAAGCTTCTCACGCCCTGGTTGTGAT[A/G]CCTGAAGGCCTACACGACAGAACGATATCCCAGGC R 2 1 2 1 201000 f 74 goat snp24898-scaffold2547-34905 21 34144276 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437903 Affx-122931658 AX-123308241 21 32426660 TTCTCTTATCAAGGTGGACAGTGAGGAGGGCCCAG[G/T]GTGAACCAAATGCTGAAGGTGATTCCTGCCCAGCT K 2 1 2 1 201000 r 74 goat snp24897-scaffold2547-3571 21 34175193 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766860 Affx-122959024 AX-385254180 21 32436159 GTTTACAGTTTTGTTTTCCCTCTTCTTTATCTTTT[A/C]TTGGATAGATTACTCTTTACCTTTCCTTTTTTCCC M 2 1 2 1 303000 f 74 goat snp19114-scaffold1921-268207 21 69392691 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778703 Affx-122954129 AX-385265814 21 32474471 TAATGTTTTAATTAGATTTAGGGCAGAGAAAGAAA[C/T]GTCAAGGCTATATGATAACTGATTAAGTCAAGTTG Y 2 1 2 1 101000 r 74 goat snp19113-scaffold1921-229895 21 34349483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793989 Affx-122969720 AX-385280958 21 32505756 TACGCTTCTTTTGTGACTTGTATTTCACATTCCGT[A/G]CATGTGTGTAGAAAGATCCACATGAAATAGCTATA R 2 1 2 1 101000 f 74 goat snp19112-scaffold1921-198610 21 34381112 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448056 Affx-122923695 AX-123318392 21 32559299 TCATATGTGCTCAGGGTTGGGAAAAAAATCACATA[C/T]GCTTTAGCTGAACTTTATCATTAAAGATTCGGATG Y 2 1 2 1 101000 r 74 goat snp19111-scaffold1921-145067 21 34434388 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798733 Affx-122977934 AX-385285664 21 32652580 AAACAGTAGTGATCATGAATACAGGAAAAATACAT[A/C]CCCAAACTTAATTGTCTAATGATGATTTTTAAATT M 2 1 2 1 101000 f 74 goat snp19109-scaffold1921-51786 21 34527608 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404841 Affx-122956630 AX-123275193 21 32702309 TATCTTGAACAATACAGTGAGTTAGTAAGTCTGAT[A/G]TTTTGTTTTTTAGTGTTTTCCCAGTGCCCTTTAGC R 2 1 2 1 201000 f 74 goat snp19108-scaffold1921-2057 21 34577232 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796531 Affx-122942165 AX-385283477 21 32704913 TCTGGAAATGGTATTACAGGCTCAAAGAATAGGCA[C/T]GTTTCAAAAACTATCAGTAGCTTTTTGGAATATAA Y 2 1 2 1 101000 f 74 goat snp11038-scaffold1395-2293678 21 34579810 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770760 Affx-122943941 AX-385257924 21 32736378 GTCTTAAGCATTTACTTGTTGGAGTAAGTGAAAAC[A/C]AGCATTCTAGAAACAACAGATTCAAGCTGGGAGAG M 2 1 2 1 101000 r 74 goat snp11037-scaffold1395-2262213 21 34611084 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777436 Affx-122929747 AX-385264557 21 32781128 TTCCCTTCACATACGGAGCTCTGTGTAATTAATAA[C/T]GCTCTCCCCCTTTACTTTCTACTTGAGAAGACCTG Y 2 1 2 1 101000 r 74 goat snp11036-scaffold1395-2217463 21 34655701 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377767 Affx-122977357 AX-123248126 21 32836155 CCTAAAGGGCTTCTCTACTTTATGCCCTTGTGCTT[A/G]CCATTTTTCTTCTCTTATATCTCTTGTTTCTTATC R 2 1 2 1 101000 f 74 goat snp11035-scaffold1395-2162436 21 34710377 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450657 Affx-122921924 AX-123320991 21 32868093 CTGTCCACTTGGAGGAGATTGTATCTGTGTTGAAA[C/T]GCACAGCCCTTTCTCTGTCATCTTGGTCTTCGTGA Y 2 1 2 1 101000 f 74 goat snp11034-scaffold1395-2130498 21 34742008 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784975 Affx-122922505 AX-385272022 21 32897879 CCCTACTGTATCCCAGTTCTAGAACAGTGCCTGAG[C/T]AAATTTTTAATGTTAGGTGTGTGATTAGTTGAAAT Y 2 1 2 1 102000 f 74 goat snp11033-scaffold1395-2100712 21 34772102 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414197 Affx-122949659 AX-123284546 21 32951494 TGCCTCCCTCTGTCACACTTACAATCCCAATTCCA[C/T]GTACCCCCACCGATTATGCTCAGACATTCCCCACA Y 2 1 2 1 101000 r 74 goat snp11032-scaffold1395-2047097 21 34825691 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448684 Affx-122923872 AX-123319020 21 33013643 CATTAGATCCAGAAAGTCCAACAAATATGAAACAC[A/G]CTAAAGGAAAAAAGACATAAATATTTGTATATATT R 2 1 2 1 101000 f 74 goat snp11031-scaffold1395-1984948 21 34888153 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414458 Affx-122949570 AX-123284807 21 33047001 ATATTTAAGGACCATCAAATCAGATGACGATTGAG[A/G]TTTGTTGCATGGAGCTTTTAAAGACAAATTCTCTG R 2 1 2 1 101000 f 74 goat snp11030-scaffold1395-1951590 21 34921716 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384642 Affx-122972153 AX-123255000 21 33090023 TAAGTAAGAAAACTGACAGTGGAAGAAACTGGAAA[A/C]AAAGTCCAGTTAAAAAGTCCAATTTAATTAGACTG M 2 1 2 1 101000 f 74 goat snp11029-scaffold1395-1908568 21 34964772 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451889 Affx-122921046 AX-123322222 21 33133572 CGTCTCTCTCTATAATTGGGGCTAACTCTCCCAGT[C/T]TATTGGTAACTCTACCCTGCGTATAACAGGGTATG Y 2 1 2 1 101000 r 74 goat snp11028-scaffold1395-1865019 21 35008430 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409913 Affx-122952886 AX-123280264 21 33184434 TATGTTGAAGTCAATAGTATATGGGTCTTTCCCAC[A/G]TCCAGATGTGGACCATATGGAGAGTCAGCCTGGAA R 2 1 2 1 201000 r 74 goat snp11027-scaffold1395-1814157 21 35059677 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783337 Affx-122954542 AX-385270401 21 33214673 GCTCTTCTAATTTCAGAGACCTTAAATAAAGGGCA[C/T]GTGGATGACACACATTACGACAAGAAGTGTGTTCT Y 2 1 2 1 101000 r 74 goat snp11026-scaffold1395-1783918 21 35089854 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434731 Affx-122933922 AX-123305072 21 33267798 GTGGGTGGCTGAAGATAAGCAGAATGTTTGACTTG[C/T]CTGGCGATGAGCAGAATTGCGGAAGAAATAAACAT Y 2 1 2 1 101000 f 74 goat snp11025-scaffold1395-1730793 21 35143017 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423704 Affx-122942888 AX-123294050 21 33326515 TCTTTCTATCTCTCTGTAACTGCTATACCTATTCA[C/T]TGATAATGAAAGCAAGGACCATGGTTTTTAATCTT Y 2 1 2 1 101000 f 74 goat snp11024-scaffold1395-1672076 21 35201833 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381934 Affx-122974129 AX-123252292 21 33370596 TGAAAAGCAAATGTGCAAAATTAAAGTTGTGAGTC[A/G]TTTATTCTGTGTCTTAATGAACTATATATGGCCCA R 2 1 2 1 101000 r 74 goat snp11023-scaffold1395-1627995 21 35245753 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782075 Affx-122967338 AX-385269153 21 33414633 TGGAAATGGACTATTGTAAGTATCTTATACTGTAC[A/G]TGAAGTGGCATAACACCACTTGAAGGTAAACTGTA R 2 1 2 1 101000 f 74 goat snp11022-scaffold1395-1583958 21 35289836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414917 Affx-122949108 AX-123285266 21 33472764 AACAGAAGCACAGTTTACTTTTTAGGATTGGCCTC[C/T]CCTCTGATTTGAATAAATTATTTTTTCACCTAGAC Y 2 1 2 1 101000 f 74 goat snp11021-scaffold1395-1525827 21 35348142 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277500 Affx-1111835881 AX-519551002 21 33480534 TAGACTGTAAGCGCCACGCAGGCAGGAGCTCTGTC[A/T]GCCTTGCTCACTGCCATATCCCCTTTCCCACCGCG W 4 1 2 1 303000 r 74 goat Random2.2K-1932 21 33480534 A T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444784 Affx-122926347 AX-123315121 21 33524925 CAGCTTTCTTTGTATATCTCTTTGGATTCATGTGT[A/G]CCTATGTTATGCTTTGGGGTTAGATAGCAATATTC R 2 1 2 1 201000 f 74 goat snp11020-scaffold1395-1473666 21 35400613 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429912 Affx-122938108 AX-123300253 21 33583602 GTGCTTTCCCATATACTTCCCAAATCTCTAAAAGC[A/G]CAAAGGCAGAAGGCCTAGAGGAAGTGAAAATCAAG R 2 1 2 1 201000 f 74 goat snp11019-scaffold1395-1414989 21 35460034 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449982 Affx-122922876 AX-123320317 21 33641051 ACCCAAATGAGTTTTTCATGTAATTTACCTATATC[A/G]TTGTGGTTTCTGTAAACAAAAAAAGATTAAATAGA R 2 1 2 1 101000 f 74 goat snp11018-scaffold1395-1357540 21 35517469 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781912 Affx-122929459 AX-385268993 21 33674276 AGTTCTTGCCAAATGCCTACCTGGCGAAATCCCTA[C/T]ATTTACAACTTTTTCATCTTCAGAAACATGAAAAT Y 2 1 2 1 201000 r 74 goat snp11017-scaffold1395-1324315 21 35550744 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794628 Affx-122958997 AX-385281589 21 33722008 CAATATGGTTGGTCTGCAGGGTGATTCAAATGGCC[A/G]CATATTTTAAGTTCCCTGATGGCATCATTTCTGTC R 2 1 2 1 101000 f 74 goat snp11016-scaffold1395-1276583 21 35596028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779724 Affx-122967829 AX-385266824 21 33767104 TATATTGACTCAAAGAAGTAGCTTGAATATTTATG[G/T]GTCAACCAGCTATTTTAAAACTGCACAGGATCAGT K 2 1 2 1 101000 r 74 goat snp11015-scaffold1395-1231487 21 35641193 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376018 Affx-122978404 AX-123246377 21 33867901 AATTGGCCGCTCTATTTCTCTATTTATTTTTGTCT[A/G]TCCATCCACTTCTTTCTTGCTAGTTTAGAAGCTTT R 2 1 2 1 103000 r 74 goat snp11013-scaffold1395-1130690 21 35742140 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776222 Affx-122928996 AX-385263350 21 33923812 TTATAGACAAATGCTCTGAAATTACTTTTGTGTTC[C/T]ACTCACAAACCACATAGATGCATTTTTCTTCTTAA Y 2 1 2 1 101000 f 74 goat snp11012-scaffold1395-1074779 21 35799090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376908 Affx-122977801 AX-123247267 21 33970626 CAATGACAGGGAGTGAAACATGACAGGGAGTGTAC[A/C]TTTTGTCTGAAGAATTAGCCACAGAAGCCTTGTGG M 2 1 2 1 101000 r 74 goat snp11011-scaffold1395-1027965 21 35845424 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376833 Affx-122977915 AX-123247192 21 34024222 AATCCCAGCCCTAATGCTTTCCAATAAATAACTTG[C/T]AGAGAGAGAACAACCCAAGTCCAATTTCTATTTAT Y 2 1 2 1 101000 f 74 goat snp11010-scaffold1395-974369 21 35899094 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391297 Affx-122967339 AX-123261654 21 34057574 GTGCAACCAGTGTGGAGAGAAGTGGATGGATTCTT[G/T]ATATTTTTATGTATAATCTACAATATTCTGTGATT K 2 1 2 1 201000 r 74 goat snp11009-scaffold1395-941017 21 35931142 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774461 Affx-122929958 AX-385261597 21 34101531 CTGCACCATGGGTGAACTGACAATGGAATAATCTG[C/T]AGCTATAAGAATGAAAAATTTCCCTACATCTTGAT Y 2 1 2 1 201000 r 74 goat snp11008-scaffold1395-897060 21 35975116 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788521 Affx-122952085 AX-385275538 21 34135044 TGTGTATTTCTGATTTTCCTACCTGGTCTGACAAG[C/T]ACCAATTTTCTAACCTTTAAATACATCTTTAAATA Y 2 1 2 1 101000 f 74 goat snp11007-scaffold1395-863547 21 36008899 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385851 Affx-122970998 AX-123256209 21 34211360 GTTGGCTCCTCTGAAAGCCTCCTCCTGGTCACAAT[C/T]GCTCACATGGAGTACCCACTCTGTTCCACACACTC Y 2 1 2 1 101000 r 74 goat snp11005-scaffold1395-787231 21 36085192 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421518 Affx-122943888 AX-123291865 21 34248429 TTCAGGCTTATTACTGTTCTGTGCGCATTTGCACC[A/G]TCTCTGCCCTCAAGGAGCATTTAACCCAGTTGAAT R 2 1 2 1 101000 f 74 goat snp11004-scaffold1395-750162 21 36122262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392424 Affx-122966196 AX-123262781 21 34294735 AGTACTTTTTAGAAAGGCAGTTATTTATATAAAAT[A/C]TATAATCAAAAGAAAAATACACTTTTTGCAAGTTA M 2 1 2 1 303000 f 74 goat snp11003-scaffold1395-703856 21 36168946 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763729 Affx-986698257 AX-385251543 21 34310554 AAGAGTCGGATACAGATGAGTGACAAATTCAGCAA[C/T]TAAAGTTAAATGAAGTCATAAGCATGGGGCCCTAA Y 2 1 2 1 600010 f 74 goat 21_34310554 21 34310554 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320789587 Affx-122951783 AX-385276596 21 34324208 TTTGTAAAGACTCCCTAGAGTATCCCTAATAAACT[A/G]CATCCTTTTACCCAAGAATAGATACAGAGATACAT R 2 1 2 1 101000 r 74 goat snp11002-scaffold1395-674383 21 36198775 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763731 Affx-986698259 AX-385251545 21 34334097 ACTTTAACCTCTCATAATTAGCGCCTACTGGAAGT[C/T]GGCCTGGCCATTTCTCGCAGGCAGTGACAATGATA Y 2 1 2 1 600010 f 74 goat 21_34334097 21 34334097 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 320766948 Affx-986698261 AX-385254252 21 34334113 ATTAGCGCCTACTGGAAGTTGGCCTGGCCATTTCT[C/T]GCAGGCAGTGACAATGATATGATATTGCCACATTA Y 2 1 2 1 600010 r 74 goat 21_34334113 21 34334113 Ancestral_priority_1043 ancestry 0.546 neutral IMAGE 10K 10K ancestral 320763735 Affx-986698263 AX-385251547 21 34341506 TAAAAATACATGTATCTTATTGCTAGGCCCTTTTA[C/T]AGGGAACTAAGAAGCAAGGTTGTAGGCAAACTATA Y 2 1 2 1 600010 f 74 goat 21_34341506 21 34341506 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 320800217 Affx-122943341 AX-385287140 21 34388475 ATTACTTATTGCCTGTTCTTTTCAATGAGAATGAA[A/C]GAACAATGAGGGCAGGTACCTACTCTGATTTGCTT M 2 1 2 1 101000 r 74 goat snp11001-scaffold1395-610116 21 36263608 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377251 Affx-122978147 AX-123247610 21 34424136 TCATGGACTTCTTTAACAAAGTTTCCAAACTTCCA[C/T]AGATTTCCGTAGCTCTTAAGTTTTATTTCTTCATG Y 2 1 2 1 101000 r 74 goat snp11000-scaffold1395-574455 21 36299436 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802462 Affx-122925565 AX-385289366 21 34486518 GAAAAGGGGGAAAGAGAATGCATTCATAATATGTA[C/T]GCAATGGCTCTACCAGAAGCGCCACACATCTCTTC Y 2 1 2 1 102000 r 74 goat snp10999-scaffold1395-512073 21 36362581 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787252 Affx-122959982 AX-385274278 21 34551122 TTTTCAAATTTACCATTGCATTTTTAGTGAAGAAA[A/G]CCTGCTCACAGCACTAACATAAAACTCATATATTC R 2 1 2 1 101000 r 74 goat snp10998-scaffold1395-447469 21 36427404 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782657 Affx-122948374 AX-385269730 21 34625377 AACTGGACAACAACAATGACCAATGTCATACTGCT[A/G]TCTTCTCATCATAGCAATACTGATCACCTCTTAAG R 2 1 2 1 101000 f 74 goat snp10997-scaffold1395-373214 21 36501714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378728 Affx-122977040 AX-123249087 21 34686545 AAATATGATCAAAGTAAAAATAACCTGTTCCCTAT[A/G]CAAACACAAAGGCGCTAGCAAGTACCTTTCCAATT R 2 1 2 1 101000 r 74 goat snp10996-scaffold1395-312046 21 36563154 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429352 Affx-122938569 AX-123299694 21 34722051 TATGTACATCCCATGTAAGGTTCCAACAACTAAGT[A/C]TGAGAAAAAAATCTAATTTGACTTGACTGCTGATT M 2 1 2 1 101000 f 74 goat snp10995-scaffold1395-276540 21 36598320 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784864 Affx-122920888 AX-385271911 21 34788349 ATCCTGAAGAACTAGATCAGTCAAAGAAAAAATGA[A/G]TTCAAAAGCTCTAGGGCTTCCAAAGGGAACTCAAG R 2 1 2 1 101000 r 74 goat snp10993-scaffold1395-210242 21 36665037 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382820 Affx-122973556 AX-123253178 21 34829021 GCTTATGAGCTTAATGTTAGAATGAAGCCAAAACC[A/G]TAACAGCAAACTTCAGTTTCAGGTAGGTGATCTTT R 2 1 2 1 101000 f 74 goat snp10992-scaffold1395-169570 21 36704386 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785778 Affx-122937741 AX-385272818 21 34862766 CTGTCCCAATGTAGTGAACTAAAGAAGAGTCAAGG[C/T]ACAGTGCAATAAGATTTACCTTAGAGTAAATATTT Y 2 1 2 1 101000 f 74 goat snp10991-scaffold1395-135825 21 36736182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271915 Affx-1111833219 AX-519545695 21 34880642 GAATGAGGGATGGGGGAGGGATTCATGCTGTGCTC[A/G]CTTCTTCAAAAAGGACGTTCTATGACATCCTGTGA R 2 1 2 1 101000 r 74 goat 21_34880642_AF-PAKI 21 34880642 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320787265 Affx-122950409 AX-385274290 21 34925171 TCTCAGTTATCCATTACATTTAATCTCCACTGGTA[A/G]CAATTAGATTGGTGAATCATTCATTGTTACCTTGG R 2 1 2 1 201000 f 74 goat snp10989-scaffold1395-73420 21 36798975 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778321 Affx-122936850 AX-385265436 21 34967731 GGAAGTCACGCAGGAAGCATCAGTCCTGATTCAGT[A/G]CATAGTTTGGATTAGAAATCACAGAACAGGTCTAG R 2 1 2 1 101000 f 74 goat snp10988-scaffold1395-30860 21 36841766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791443 Affx-122966188 AX-385278434 21 35039353 ATATTGAGAGGAAAAACTTACCAGGGTCCATTTAA[C/T]GGTTAGCATAGAAATTGCCCAATATATGTCTCCAG Y 2 1 2 1 101000 r 74 goat snp4190-scaffold1130-40663 21 36912676 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442096 Affx-122928360 AX-123312433 21 35090829 ACAGCCACCTGCATAGAATCTGAGGCTTGGGGCAC[A/G]TCCTCTAAAGGAGCTACAAACTCTGGCCTGAATTC R 2 1 2 1 101000 r 74 goat snp4191-scaffold1130-92139 21 36964203 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426169 Affx-122940592 AX-123296515 21 35149939 GGATGTGCTGTGATGACCACAGTGAAGTAAAGTAA[C/T]ACTGCCTTACTGCCTTGAGAGGAAATCACTGACTT Y 2 1 2 1 102000 f 74 goat snp4192-scaffold1130-151249 21 37023642 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405016 Affx-122956377 AX-123275368 21 35221745 AATGCAGATACAAGCTTTAGTATGGAGTGATCTAA[C/T]GATATTTTAATTGAGGATGCACTATCAAGTTCCTT Y 2 1 2 1 101000 f 74 goat snp4193-scaffold1130-223055 21 37096731 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770788 Affx-122970353 AX-385257952 21 35276457 TTGGCAATAAGTGGCAAATGTATTCAAGTACAGTA[C/T]GGGGCATAAGAGAACAGGCATATTTTGATATCTAA Y 2 1 2 1 102000 r 74 goat snp4194-scaffold1130-277767 21 37151722 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394947 Affx-122964290 AX-123265302 21 35314928 GTTAACCTCATCAACCTTTAATCCTTAACTGTACT[A/G]TAGGAGGTTATTGAGATTTCTTTTTATAACCTCAT R 2 1 2 1 101000 f 74 goat snp4195-scaffold1130-316238 21 37191359 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803026 Affx-122975155 AX-385289903 21 35374270 ATAATTTGCAGAAATATTAGAGCCTTTCTCCAATA[C/T]TCAATGCCCTCACTTTGCAGATGTGGAGACTTACA Y 2 1 2 1 102000 r 74 goat snp4196-scaffold1130-375580 21 37251654 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787325 Affx-122979144 AX-385274350 21 35420937 AAGAAACCTACCCATGATCAAGATAAAGCAATAGA[A/C]TGTGTGAGGTCCATTGACTGGAGTATTTCAAAAGG M 2 1 2 1 101000 r 74 goat snp4197-scaffold1130-422247 21 37298695 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766959 Affx-986698267 AX-385254259 21 35432492 ATGGAGGCATCTCTTGTGTGGCATTTGGAGTATGG[C/G]GCACCTATTTACCTTGGCTATGGTTTCACTCATAC S 4 1 2 1 600010 r 74 goat 21_35432492 21 35432492 Ancestral_priority_1043 ancestry 0.73 recommended IMAGE 10K 10K ancestral 320804093 Affx-986696382 AX-385290757 21 35432520 AGTATGGGGCACCTATTTACCTTGGCTATGGTTTC[A/T]CTCATACCTCTTTCATTTAAGACTGCAACAAGGAT W 4 1 2 1 600010 r 74 goat 21_35432520 21 35432520 Ancestral_priority_1043 ancestry 0.776 recommended IMAGE 10K 10K ancestral 320766963 Affx-986698269 AX-385254263 21 35432571 TTTAAGACTGCAACAAGGATAACTGCCCTTCTCAG[C/T]GGTTTTATACTTAGTCATTGGATGTGCAGAACAGT Y 2 1 2 1 600010 r 74 goat 21_35432571 21 35432571 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320777966 Affx-122936935 AX-385265082 21 35483017 TCTGAAACATTTTTATGGCATAACCTTGTCTCCTT[A/G]TTAGATGGTAACATCTAGATTATTCAAAAACAAGA R 2 1 2 1 101000 f 74 goat snp4199-scaffold1130-484327 21 37361073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412737 Affx-122950531 AX-123283086 21 35587758 GGGTCTGCATTTTATTTGTTACATATTAAATTATT[A/C]AGTGTAAAACTTTTGTTTCTAGCTCACAGATATCT M 2 1 2 1 101000 r 74 goat snp4201-scaffold1130-589068 21 37468045 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787617 Affx-122952362 AX-385274640 21 35635242 GAAAGAGGATGAAAGAACTGTTAAGTAAACAGATA[C/T]AAGAAACAGGATTGCTTGATCTCTGCGATGCTTTC Y 2 1 2 1 101000 r 74 goat snp4202-scaffold1130-636552 21 37516563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416103 Affx-122948314 AX-123286452 21 35665207 TGCTACTCAACAAGGTGAAGGCTTAAGAGAAAGAT[A/C]GAATTATTGGGAAAAAACTAATATTTAAAATTATA M 2 1 2 1 101000 f 74 goat snp4203-scaffold1130-666517 21 37546006 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791876 Affx-122926165 AX-385278866 21 35693758 TCTTGGAAAGTTTTATGATCCATATCAAACTTTGA[A/G]TTTTAATACTACTGACAACAACAAATAAGAAAACG R 2 1 2 1 102000 f 74 goat snp4204-scaffold1130-695068 21 37574732 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421098 Affx-122944221 AX-123291445 21 35737969 TGTGAATGTTTTTGCAGATTGATTATTTTCTTTAA[C/T]AGATTAAATCATATTCAAACCATTTCAAGGATGCT Y 2 1 2 1 303000 r 74 goat snp4205-scaffold1130-739279 21 37618975 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802829 Affx-122959172 AX-385289728 21 35772049 AATTCACAAAGTAAAATTCCAATAATAGTTATATT[A/C]TAAAATATATTGTGGAGTTAATGCAAACTCAGTTA M 2 1 2 1 202000 f 74 goat snp4206-scaffold1130-773359 21 37654358 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400419 Affx-122959980 AX-123270774 21 35823356 TGTGGGGGGAAAAAGTCTCTAGAAGTACAAAAGAA[C/T]AAAAGGAAATGTTTTATTGGCAGTGAAATATAACT Y 2 1 2 1 101000 f 74 goat snp4207-scaffold1130-824666 21 37705814 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792580 Affx-122920287 AX-385279561 21 35872061 AGTCTGTCAGTCTGTACTATAAACTTTGGATTTAA[C/T]GCTAAATTTCCACCCTGCCAACCTGACATTCAGGT Y 2 1 2 1 101000 r 74 goat snp4208-scaffold1130-873371 21 37754414 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380203 Affx-122975493 AX-123250561 21 35902626 TGACACTGTGGGTGTGTCAGAGGGAGAAAGAGAGA[A/G]GGTGAGTTTGAAACTGCATGAGACTGCATTCATAC R 2 1 2 1 201000 r 74 goat snp4209-scaffold1130-903936 21 37785081 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411667 Affx-122951557 AX-123282017 21 35933291 CTAAATCAGTCATCCTTTATTGACTGATATGGGAC[A/G]CATTCTTTTGTTCAAAAGGTAAAGGAACAGGTTAA R 2 1 2 1 101000 f 74 goat snp4210-scaffold1130-934601 21 37816085 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375737 Affx-122978620 AX-123246096 21 35966767 GATGGCAGACTTAAATCATATTAAATGTGACCTCC[A/G]CTTCTGGGCAACATGACACAATAGGACCTGGAATT R 2 1 2 1 101000 r 74 goat snp4211-scaffold1130-968077 21 37849810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787803 Affx-122934424 AX-385274826 21 36008889 CTGATTGTCTACTTTACATACCTTATAGTAAATAT[A/G]TCATTAGTTAGCAACTTTGTAAGTTTCAGTTTGAC R 2 1 2 1 101000 r 74 goat snp4212-scaffold1130-1010199 21 37893378 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778579 Affx-122950655 AX-189595986 21 36065497 CACGTAGATTCAAAATTCACCAAGTGTTCATTTGC[A/G]CCTTAAGTAAGATAACAGTCAAGATGCTTTTATAA R 2 1 2 1 101000 f 74 goat snp4213-scaffold1130-1066807 21 37948797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398699 Affx-122961856 AX-123269054 21 36097264 TTTATGAAAAAATTATTTTTTCTCCCACTTTTTAT[A/G]TGTGGCTCTCTGTAATTTCCAGACAAAGTAGTCAA R 2 1 2 1 101000 r 74 goat snp4214-scaffold1130-1098574 21 37979222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802707 Affx-122924408 AX-385289606 21 36141053 AGTGTAAAGCTTGTTTTGACAATAATTACTTTCTC[A/G]TGTTTCTTCCCTCTAATTTCTGTGCTTTCCAGTTT R 2 1 2 1 101000 r 74 goat snp4215-scaffold1130-1142363 21 38024190 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792522 Affx-122956602 AX-385279503 21 36183454 TTATTAAAGAGTCTGGGTTCCAGTTGACAACTGAC[A/G]TCCATTATTATGGTACAATTAGTCCAAGTTCATGT R 2 1 2 1 101000 f 74 goat snp4216-scaffold1130-1184764 21 38067221 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381870 Affx-122974178 AX-123252228 21 36231251 CAACTTATACTGAATGCATTAACACCATGATACCA[A/G]GGAATAATATCATACTTTGCATCTGAAAAAGAGAT R 2 1 2 1 101000 r 74 goat snp4217-scaffold1130-1232561 21 38115540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452996 Affx-122920114 AX-123323329 21 36283962 CTCAGAAAGAGCTGTGTTACATCTGGAAGAGCACT[A/G]TGATGACATTTCAAATATTTGCTTTAATTCTGTTA R 2 1 2 1 101000 f 74 goat snp4218-scaffold1130-1285272 21 38165973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774334 Affx-122957436 AX-385261470 21 36369106 GGTAAAAAATAAAATGCTGTTTACAAGTTTTCTCT[A/G]GTTTGTTATATAAAATGTGTTGTGCATGTGATATC R 2 1 2 1 101000 f 74 goat snp4220-scaffold1130-1370416 21 38248581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782693 Affx-122965261 AX-385269765 21 36411415 AAAAATCCAAGGGTTTGTCTTTAGGTAATAGAAGA[C/T]AATGCCAGTGCAAGGGCAGTCTCATAATGTTCAGT Y 2 1 2 1 101000 r 74 goat snp4221-scaffold1130-1412725 21 38290942 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775203 Affx-122967465 AX-385262334 21 36450561 CTGCTTTTCAAAGTGGAGGAACTAGAACCTCAGGG[C/T]AGCTAGCAGTTCCTAGAGAGACTTTCAGGTGCTTC Y 2 1 2 1 101000 f 74 goat snp4222-scaffold1130-1451871 21 38330811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426505 Affx-122940213 AX-123296851 21 36497512 TTCTCACCAAAATTAAAACTTTTACTCTGTAAAAT[A/C]TCACATGAAGAGAATGAATTGAAAAGCATCTTAGT M 2 1 2 1 202000 f 74 goat snp4223-scaffold1130-1498822 21 38378338 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434926 Affx-122934309 AX-123305266 21 36530449 GAGTATATTCTGAATGAACACGAAACCCTGTTTTA[C/T]AATGAAAATGAAAATTCTGCAAAGTTTTTTCTAGC Y 2 1 2 1 101000 f 74 goat snp4224-scaffold1130-1531759 21 38411642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447655 Affx-122923966 AX-123317991 21 36564244 GTTACAAAGACTCAGACATGACTTAGAGACTAAAC[A/G]TCAACAACAATCAAAACTAAGTTTCTGTTTCTTTG R 2 1 2 1 303000 r 74 goat snp4225-scaffold1130-1565554 21 38445604 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772294 Affx-122958880 AX-385259449 21 36593845 AAGAAAAAGATTGTCATTGGGTTTTAATACCTAAA[C/T]GACCTTTCACTAATTTTCTGTTCTAAGCACTGTAA Y 2 1 2 1 101000 r 74 goat snp4226-scaffold1130-1595155 21 38475254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432625 Affx-122935487 AX-123302966 21 36653230 TTATATTCATATATCATAAAAGCAAATATCCAAAA[C/T]GAAGCAATAATTCTACATATTTATGGGCCTAACAA Y 2 1 2 1 101000 r 74 goat snp4227-scaffold1130-1654540 21 38534586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393221 Affx-122965490 AX-123263578 21 36669654 CAATGGCAGTAGACAGCTGTAATATGAGAAAGTTG[C/T]GTTCGGCAGAAAAAGCAAGTAGGAGATGAGAAAGT Y 2 1 2 1 101000 f 74 goat snp36666-scaffold444-7877 21 38557865 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778450 Affx-122955467 AX-385265564 21 36710447 ATGATTCTCTACAAAAGCCAATAGATAAGGCTAAG[C/T]AAGAGCAGTACCTGTATGTCCCAGTTTCAAGGTAT Y 2 1 2 1 101000 r 74 goat snp36667-scaffold444-48670 21 38598882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784936 Affx-122978898 AX-385271983 21 36780873 AGTTGGACTCATATTGAGGTAAAGGGACATATATA[G/T]AGAAGACAGATTTCCCCCATAAATATTTTTTTCTG K 2 1 2 1 101000 r 74 goat snp36668-scaffold444-119096 21 38669490 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774511 Affx-122929550 AX-385261645 21 36813109 TAGAATAGTCTTTGGCCATTAACTTTTATTTCACA[C/T]ACAGTATCTAAGCTGTCAGTAATTTATGTTAGTGC Y 2 1 2 1 101000 f 74 goat snp36669-scaffold444-151332 21 38701625 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797957 Affx-122963785 AX-385284893 21 36873538 TCAAGTAGGAATGATCTTAATGTGTTCTACAGAAC[A/G]TTTACAGAGTGTAAGTATATGAAATATAAGAAAAT R 2 1 2 1 202000 f 74 goat snp36670-scaffold444-211761 21 38762331 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800744 Affx-122957192 AX-385287661 21 36912310 TTCTCTGCTTTTGTTTAACTGGAATCTTTATTATT[A/G]CCAACTATTGAGCAAAATTTTTGGCACTATAGAAT R 2 1 2 1 101000 r 74 goat snp36671-scaffold444-250533 21 38801114 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435605 Affx-122933791 AX-123305945 21 36967596 GATGAACTATTCTAGTGAGTGTGGAATGGATCCAA[C/T]TAGTCTGAAAAATTACAGTTTGAAAATTTTAAGTG Y 2 1 2 1 101000 f 74 goat snp36672-scaffold444-305819 21 38857595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394646 Affx-122964387 AX-123265001 21 37008313 TAGATTTCATTATAAAAAGAACTCATTGTAAGATG[C/T]AAAGGAAATAAGATGTTTTTTGTGAACTAAAATTC Y 2 1 2 1 201000 f 74 goat snp36673-scaffold444-346536 21 38898387 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801968 Affx-122940135 AX-385288872 21 37089637 ACAGAGCAAGGAGAAAAGACTCACATGTCAATAAA[C/T]GAAGCTGGAAAATTACACATTTAGGAAGATTAAAA Y 2 1 2 1 201000 r 74 goat snp36675-scaffold444-427860 21 38979801 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396510 Affx-122963523 AX-123266865 21 37120837 TTCCAAGCTCTTTCTGACTTTTCAGAAACATACAT[A/G]TTCCTCCCAGCCTGTGGGTACACTGCTCCTCTCCC R 2 1 2 1 101000 f 74 goat snp36676-scaffold444-459060 21 39010897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782931 Affx-122932436 AX-385270001 21 37152005 GAAACGAAAAAATGAATGATTATTTTCAAGCAGCT[A/G]TGTAATTTGAAGTTCATTTACTCATTACAGACTTT R 2 1 2 1 101000 f 74 goat snp36677-scaffold444-490228 21 39042372 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793154 Affx-122973207 AX-385280132 21 37185369 AAATGGAATGATTTTCACACCTATGATAACAGAGG[C/T]AATCTCCTGAACTCCACTCCACCTGGACTTCTAAC Y 2 1 2 1 101000 r 74 goat snp36678-scaffold444-523592 21 39075953 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394535 Affx-122964523 AX-123264890 21 37222892 AATACATCTTTTCCATTCACCAGGCAAGTGAGACT[A/G]CTTTGCTCTCTGTCTCCGGTTACTAAGCTAGCATT R 2 1 2 1 101000 f 74 goat snp36679-scaffold444-561115 21 39113267 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769363 Affx-122953996 AX-385256534 21 37259387 TTAGGAAACTGATATATGGAGATATCAATTGACTT[A/G]TACAAGGTGACCCAATTAGGAAATGTGGAAGCCAC R 2 1 2 1 101000 r 74 goat snp36680-scaffold444-597610 21 39150454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401350 Affx-122959253 AX-123271703 21 37301417 GTTATAACCTATGGCAATTTGGTAAACTACACCTG[A/C]GGGTAGAACTGAAACACTTCTGTCTGCCTTGTCCC M 2 1 2 1 101000 f 74 goat snp36681-scaffold444-639640 21 39192561 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789394 Affx-122955889 AX-385276404 21 37365822 TACTTCCCAATCTTTTATTTTGACTCATGTATGTA[C/T]GCACTGAAAAAGCCTTCTGTGTTTCAATGTGTTAA Y 2 1 2 1 102000 r 74 goat snp36682-scaffold444-704045 21 39258164 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271917 Affx-1111833220 AX-519545697 21 37410868 CAAAGATAATAAAAGTCAATACTGTATCCCATAAC[A/G]GTGAAAACAGACAATGTCTCCTTGGTAATAATACA R 2 1 2 1 101000 r 74 goat 21_37410868_AF-PAKI 21 37410868 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38409961 Affx-122954111 AX-123280312 21 37423879 ATTTTGTTAGTCAATTAAATTAAATGTTAGTTCAC[A/G]TAAAGAAAAAACTAGTCATCCAGGATTAGCAGTAA R 2 1 2 1 101000 r 74 goat snp36683-scaffold444-762102 21 39316366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450135 Affx-122922756 AX-123320470 21 37468701 ACACAGTTAAAGCCATTTGGATTTTTCCTAAAAGA[C/T]GGGGACTGATTCAATACTTGTTTTGAGACCTACCT Y 2 1 2 1 201000 f 74 goat snp36684-scaffold444-806924 21 39361040 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801637 Affx-122978813 AX-385288545 21 37507098 AGAAAAAGAAAACATATTGGGATGCTGGGATGCAC[A/G]TGTCTTGTTTGCAGGCATTTTGGACACTTGAAGGC R 2 1 2 1 101000 r 74 goat snp36685-scaffold444-845321 21 39399242 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786200 Affx-122928691 AX-385273235 21 37525047 TGTGACACAGTGGTGGGATAACTGCTAAAACAGTG[C/T]TATAAAATTGATGTAGGCATTTTCATTCCCTGGTA Y 2 1 2 1 101000 f 74 goat snp38857-scaffold492-3852859 21 39417117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448912 Affx-122923171 AX-123319247 21 37554768 CATTAAATACTCATCTCATTTCGACCCCATTTGTC[G/T]ATTTTTAATTGGCAATAAAGTGAATTCACTATTTA K 2 1 2 1 201000 r 74 goat snp38856-scaffold492-3823138 21 39446832 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777801 Affx-122974599 AX-385264919 21 37586251 AGCAGACTCCAACATGAAATCTAGAAATTGAGTAC[A/G]TATACATATTTTCATAAGTGTGCATTTAAAAAATC R 2 1 2 1 101000 f 74 goat snp38855-scaffold492-3791655 21 39477864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389407 Affx-122968375 AX-123259765 21 37624840 CATTGTGCCTGCATTTTATACCATGGCTTAGAGAA[C/T]AAGCCCAGTGAATGGGTAAATTAAGATTTTATCTG Y 2 1 2 1 102000 f 74 goat snp38854-scaffold492-3753066 21 39516890 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798079 Affx-122963022 AX-189617147 21 37735664 TAGATAGTAGACTACATTAGACTTTCAGCCTGTTA[C/T]CAGATTGTTGATTCCTCTGAGAAGAAAACTGGTGG Y 2 1 2 1 101000 r 74 goat snp38851-scaffold492-3642242 21 39628567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798226 Affx-122936614 AX-385285161 21 37786090 GACACTCACTAAGTAATGAAGCTGGGTTTCAAAAC[C/T]GAGGCATTCATGCGCCAGAATTGGCATTCTTAACC Y 2 1 2 1 101000 f 74 goat snp38850-scaffold492-3591816 21 39680034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277378 Affx-1111835882 AX-519550882 21 37799084 GGCAATGTCTCCAGGTGTTTGCCTAGTTAATAACA[A/G]AAGGCTCCCTAGAGGGCCTAGACTAAGCATAAAAG R 2 1 2 1 201000 f 74 goat Random2.2K-1936 21 37799084 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434230 Affx-122934837 AX-123304571 21 37818969 ACTGTGTCAGTTGTTACATTTCTTCCAGTCTCATA[C/T]GGTCTGTTCCGGTGTCTCAGACGTCCCTTGTTTTT Y 2 1 2 1 201000 f 74 goat snp38849-scaffold492-3558937 21 39712855 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383646 Affx-122972528 AX-123254004 21 37910842 CTTCATCTCAGAGCCCTACTAATAGAGGTCCCTCA[C/T]AAATACCAGGCATCAGTGCTCCTGGGGGAGGCGAT Y 2 1 2 1 101000 f 74 goat snp38847-scaffold492-3467064 21 39804244 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781702 Affx-122958373 AX-385268784 21 37942711 GTCTCTGCTCAGATTTCTTCTCTTCAATGAAGCCT[A/G]TCCTGGAGCTATATTTAACTTGTAAACAACCCTTA R 2 1 2 1 101000 f 74 goat snp38846-scaffold492-3435195 21 39835951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441771 Affx-122929105 AX-123312108 21 37991178 CCAGCATCCCTTGACCATTTGTGATGGGAGGTGTG[C/T]ACTGGTGCTTCTTCCTTGGTAAGTCTCCAGTGTCT Y 2 1 2 1 201000 f 74 goat snp38845-scaffold492-3386728 21 39884577 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38452505 Affx-122920975 AX-123322838 21 38021608 TTTGAAACATAATTTGCAAGCCTAAATCCCAGGGA[C/T]GGGGGAGCCTGGTGGGCTGACGTCTATGGGGTCAC Y 2 1 2 1 103000 f 74 goat snp38844-scaffold492-3356298 21 39915014 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383145 Affx-122973243 AX-123253503 21 38057108 AACGGGCTAACCTCACCAGAATGTTACCCATAGTC[G/T]ATTACCAACTTCTGAACTCCTTTAAAAACAGGCAC K 2 1 2 1 101000 r 74 goat snp38843-scaffold492-3320798 21 39950959 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420022 Affx-122945155 AX-123290370 21 38092599 TTTGCTGGAGCCCACATGGATTTCTCTGTTGTTTA[C/T]GGCACATAATTATGCCACCTAATGTTCATTATGTA Y 2 1 2 1 201000 r 74 goat snp38842-scaffold492-3285307 21 39986823 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375885 Affx-122978496 AX-123246244 21 38123295 TAAAAGGGATGGATTGAGCAAAGATGTTTTTCTGG[C/T]AATTATTTGCCTTTGTTTCTTTTCTTCTCTGTTCT Y 2 1 2 1 101000 f 74 goat snp38841-scaffold492-3254611 21 40017732 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420892 Affx-122944615 AX-123291239 21 38152855 AGCGGCAATATGCCTTTTGCTAAAGCAGTAACTTC[A/C]CTGGTATTGAAAAGAATATGAGGAAGTCCTTGGGA M 2 1 2 1 101000 f 74 goat snp38840-scaffold492-3225051 21 40047559 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779056 Affx-122978884 AX-385266161 21 38207636 GATTCTAAAGCTTCTTTTGCCCTTACCCACACTTA[A/G]TACTAACCATGTTTTAAGCTGTAAATATGAAGTGA R 2 1 2 1 101000 f 74 goat snp38839-scaffold492-3170270 21 40103127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442636 Affx-122928455 AX-123312973 21 38266520 TGTTCCTGTAAAAGGGACAGCCATTGCCTCCAGAA[A/G]TGATTTAAATGATCCAGATCCTCACAGCCCAAGCA R 2 1 2 1 101000 r 74 goat snp38838-scaffold492-3111386 21 40162065 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446097 Affx-122925802 AX-123316434 21 38319550 TGGTATGATCCATCATAGACTGCAGTCAGGGACAC[A/G]TGTATTTTGAGAGGTTAGTAAGACCTAGATTTTGG R 2 1 2 1 201000 r 74 goat snp38837-scaffold492-3058356 21 40215074 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802185 Affx-122957298 AX-385289089 21 38350145 AACTGGATCAGTCCAGGGCCAAAGAGGAGACATGA[C/T]ATTCATGCCTAGGTTCTCCAGAAATTAGCCTAATG Y 2 1 2 1 101000 f 74 goat snp38836-scaffold492-3027761 21 40245597 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786159 Affx-122936644 AX-385273195 21 38386151 TTGGTTTTCATTTGGCCCCTATCCTATTCTTTTAA[C/T]TGGTATATACGTTAGATTCCAAGTTATAGACTATT Y 2 1 2 1 101000 f 74 goat snp38835-scaffold492-2991755 21 40281281 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387619 Affx-122969868 AX-123257977 21 38418503 GGTCAGACATGTCTAAGTAACCAAACCACCATGAA[C/T]AGATGAGAGAACCTGTCTTTTCCATTCTATGGCTA Y 2 1 2 1 101000 f 74 goat snp38834-scaffold492-2959403 21 40314468 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441398 Affx-122928843 AX-123311735 21 38453781 AAGAGCTAATTTTTTTTCTAGGTGCTAGTAATGAC[A/G]TTTAGCCATGTATCATATACTAACACAATTAACTA R 2 1 2 1 101000 f 74 goat snp38833-scaffold492-2924125 21 40349770 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408262 Affx-122953811 AX-123278613 21 38500065 ATTCCATTTTACAGATGAGGAAATTGAAATCCAAA[G/T]AAATGAAATAATCTGCCCCAAATCATGCAATCATA K 2 1 2 1 201000 r 74 goat snp38832-scaffold492-2877841 21 40396591 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435917 Affx-122932762 AX-123306256 21 38532217 GGGTGTTGTTGTAAGCACTAGTTTTGATTGTGGCA[A/G]GATGGGCTCTGTGACTCTCCTCTTGTTCCGTTGAG R 2 1 2 1 101000 f 74 goat snp38831-scaffold492-2845689 21 40428824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406867 Affx-122955650 AX-123277218 21 38567085 TGAAGAGGAAGAAGCTGTAAAGAAGCTTGGAAATT[C/T]TAACCAGGTATGCTGCAGGCAGGCTGTGAATTGCG Y 2 1 2 1 101000 f 74 goat snp38830-scaffold492-2810821 21 40464402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453997 Affx-122919439 AX-123324330 21 38605509 TGATGTTGCTTAGATAATGCTTCAAATAATCCCCA[C/T]ATCTCTTAGAGTTTCTTCTTTCCCATTCTTGTCTC Y 2 1 2 1 101000 f 74 goat snp38829-scaffold492-2772397 21 40503519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771778 Affx-122928960 AX-385258935 21 38665981 CCCCTAACTCAACATGTCTAAATTCAAATTCACCA[G/T]CCCCCTATCCAAACCTCTTGTTCTAATTTTCTTAC K 2 1 2 1 101000 r 74 goat snp38828-scaffold492-2711925 21 40563977 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404670 Affx-122957289 AX-123275022 21 38739517 TGAGTCACCGGGGAATCTGCCTATTTTCTCCTTTC[C/T]TTTCAAGGAAAGAGCTAACCAAGCGAGTCCGCATG Y 2 1 2 1 201000 r 74 goat snp38826-scaffold492-2638389 21 40636230 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768615 Affx-122920400 AX-385255795 21 38770074 TAAACACATCATTACAGCACCTCACCTAAAATAAA[C/T]ATAAAAATTCTAACTTATAAACAATATTTAGTCAG Y 2 1 2 1 202000 r 74 goat snp38825-scaffold492-2607832 21 40667515 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411195 Affx-122952371 AX-123281545 21 38824663 ACATACATACATCATTTTTAAAAAGATCAGTATTG[C/T]GAGAAACAAAAATCATCTATATGTAATTGGTTCAA Y 2 1 2 1 101000 r 74 goat snp38824-scaffold492-2553243 21 40722153 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796566 Affx-122931360 AX-385283512 21 38871829 CCTAGAATGATCCAACAAGGAACATGGTGCCTTAT[A/G]CAAGAAATTTTCCCTCTGCAAGTAAATGACCTTAT R 2 1 2 1 201000 r 74 goat snp38823-scaffold492-2506077 21 40769994 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397375 Affx-122962278 AX-123267730 21 38911593 GTACAAATATATATTTGGGCTTTTTACTTTGTTGG[A/C]TATCTGCTTTTTTAATACTAGTAAGTTTTTAAGAA M 2 1 2 1 101000 r 74 goat snp38822-scaffold492-2466313 21 40809520 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445911 Affx-122925936 AX-123316248 21 38954619 CAGCCTAAAGCACTGGGGTTTGGGCCAAGGTTAAC[C/T]AGATCTCTGGCACCTCTGATGGAGACCGGAAGAGA Y 2 1 2 1 101000 f 74 goat snp38821-scaffold492-2423287 21 40852475 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441620 Affx-122928644 AX-123311957 21 38994132 CAAAAAGTTCAGAAGGGATGAATGAGATGAAAAGG[G/T]TTCTAAATTTGGAGAATAATAGTAATAATACTGAT K 2 1 2 1 101000 f 74 goat snp38820-scaffold492-2383774 21 40892391 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797959 Affx-122921723 AX-385284895 21 39023001 TCAATTGGCAAATTAGTAATTTCTGTATAAAAGTG[C/T]CACAGGTACAGTTCATTAAATGAAATGATTCCACC Y 2 1 2 1 101000 r 74 goat snp38819-scaffold492-2354905 21 40921262 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789111 Affx-122947024 AX-385276124 21 39055579 TCTCCATTTGATTTCAGATTTGTAGGAATTGGAGG[A/G]TTACAGTCTGGGATTTCTGTTGGGCAGATCAGAGT R 2 1 2 1 101000 r 74 goat snp38818-scaffold492-2322327 21 40953479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449123 Affx-122923573 AX-123319458 21 39092774 ACTTGAGCATAGTGCTGTCCATCCCCATTAAAGAC[A/G]TACTAGCTTATATATTTTTTGAGAAATTGTGTCTT R 2 1 2 1 201000 r 74 goat snp38817-scaffold492-2285132 21 40990396 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435408 Affx-122933555 AX-123305748 21 39123187 CAGTAATGTGGGGAAAATTCCAGTTTTCCTCAAAT[A/G]CCTCCAGTCTGTAAAAGCAGTTTTCAGCCTTTCTG R 2 1 2 1 101000 r 74 goat snp38816-scaffold492-2254719 21 41020593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795053 Affx-122968344 AX-385282012 21 39183385 ATTTTTGTGAAGCCTTTATGGGGATATGGACACTT[C/T]TAGATCTCAAGTATGAGTACCTAACTATAGGTATT Y 2 1 2 1 101000 f 74 goat snp38815-scaffold492-2194521 21 41081324 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414161 Affx-122949684 AX-123284510 21 39231124 TTTTAATGCCACTCTGGTGGTCTAGTTCTCCTTTA[A/G]GAAGAGAAAACTGAGGCACATGCATTCAAAGAGGA R 2 1 2 1 101000 f 74 goat snp38814-scaffold492-2146782 21 41129117 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417206 Affx-122947307 AX-123287554 21 39261673 TTCCCAAAGTTGTTGCTTTTCAGCCTTTTAATAAT[C/T]AGTGTTTCATGACTGCATTCTTTTTTCTAAATATA Y 2 1 2 1 101000 f 74 goat snp38813-scaffold492-2116233 21 41159993 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394254 Affx-122964729 AX-123264609 21 39297737 GCCCTGAAATCTTTCCTCTTTGAATATGGAAGAAT[A/G]ACTATAGTGCCTTTTGTGATATCTGTAGATCATTT R 2 1 2 1 101000 f 74 goat snp38812-scaffold492-2080169 21 41195647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453990 Affx-122919444 AX-123324323 21 39358859 ACACAGGGTGGTGGCTACAATGAGAAGAATCTGCA[C/T]GGCTTCCTGCCTCTTGGGTTGTGACTCACCAGGGA Y 2 1 2 1 101000 f 74 goat snp38811-scaffold492-2019047 21 41257466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803036 Affx-122947906 AX-385289912 21 39391413 GTAACAGATAAAAGGGAAAATGGAGTGTGAACATA[C/T]CTCTTCATTTATTCCTCCTGAAACTGTTTGCTTTC Y 2 1 2 1 101000 r 74 goat snp38810-scaffold492-1986493 21 41286181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449229 Affx-122923489 AX-123319564 21 39423627 TTGTCCTGAAATTAGAAATAGGTTTTTATTACTTT[A/C]TTTATGCACTTAGAAATTAAATTATCTCTAAATCA M 2 1 2 1 202000 r 74 goat snp38809-scaffold492-1954279 21 41318327 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376289 Affx-122978378 AX-123246648 21 39453567 TACCTTTGATATACACCCATAGTGATAGACAGTGT[C/T]TGAAACTGGCAGTATTTGAAAAAAAAGTTAAGTTT Y 2 1 2 1 101000 f 74 goat snp38808-scaffold492-1924339 21 41348375 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798116 Affx-122948805 AX-385285051 21 39484734 CAATGAAAACACTAAATTTTGGCTTCATATTGTGT[A/C]GGAGAGATGAAGCAAAATGAAGATGATCTGAAAGT M 2 1 2 1 101000 r 74 goat snp38807-scaffold492-1893172 21 41379489 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408616 Affx-122953496 AX-123278967 21 39532306 AGGCTTCATAATAACTCTGATAGCCCTTGCCCCAA[C/T]AGAAGAACATTTAGATTTTTTCAGAAATCCCTAGT Y 2 1 2 1 101000 f 74 goat snp38806-scaffold492-1845600 21 41423908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277381 Affx-1111835883 AX-519550885 21 39545976 GGAAGCCAGAGCTTCTGCTGTAGATTTGAGAGTCT[A/G]TATTATATATTAGGTCACTGAAAATTGGTTGATCA R 2 1 2 1 101000 f 74 goat Random2.2K-1938 21 39545976 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795067 Affx-122949120 AX-385282026 21 39574204 ATGGGGTTTGCAGTATATTGAAGCAGGAAATACTC[A/G]CCTTTCCCAAAGTTAATTCCTGTGAATCTATCTTA R 2 1 2 1 101000 r 74 goat snp38805-scaffold492-1803702 21 41465745 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418584 Affx-122946370 AX-123288932 21 39619473 TAGCACAGACGTAAATAAACAACTTGAACTGTCTT[A/G]TTCACCACTCTATTCAAAATACCTACCATAGTGTC R 2 1 2 1 101000 r 74 goat snp38804-scaffold492-1758433 21 41511008 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797641 Affx-122939172 AX-385284580 21 39675871 CTAATACACCTATTAATCAACATTACAATTTCACT[C/T]ATCTTCAGTGTACTTTTCATTTTTGTACCATCTTA Y 2 1 2 1 201000 r 74 goat snp38803-scaffold492-1702035 21 41565712 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451344 Affx-122921263 AX-123321677 21 39723101 ATGAAGAAAATAATAAAGCCTACCTCACAGGGCTA[C/T]TGGAATACTATGACAGGTCCTGAATGGGTCTCCCT Y 2 1 2 1 201000 r 74 goat snp38802-scaffold492-1654805 21 41613238 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442019 Affx-122928411 AX-123312356 21 39753695 GATTTAAATGGCTTTTTGCAAATTAAAGGAAATTT[C/T]CTCACCAGTAAAATTAAGCATGAAACCATTGTGTC Y 2 1 2 1 101000 r 74 goat snp38801-scaffold492-1624211 21 41642414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430488 Affx-122937238 AX-123300829 21 39785999 TACATGAATAGGAAAGATAAGGAAATGTCTGTTTC[A/G]TTCTTGCCAATTTTTGACTCCTCACTCCTAAAATT R 2 1 2 1 101000 r 74 goat snp38800-scaffold492-1591907 21 41674658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796716 Affx-122977403 AX-385283661 21 39839119 ACTAGTTATAGGTGCTGCAATATGTTCTCAGCTTA[C/T]GATTTATCTCAATTTCTACATGATGTCCTTTACCG Y 2 1 2 1 101000 f 74 goat snp38799-scaffold492-1538787 21 41728053 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777621 Affx-122953431 AX-385264740 21 39890229 TTGTCATTTAGTGCAGAGCTGCTAGATGGAATAAC[G/T]AATAACAATAGCTGTAAAGGTCACTGCAAATAATA K 2 1 2 1 101000 f 74 goat snp38798-scaffold492-1487677 21 41775111 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412331 Affx-122950844 AX-123282680 21 39949908 TGGAGTTCTAGTCTAGAATTCAGTTGAAACCTCAG[A/G]AAGACTTTGTTTTAGGACTTGAGAAATAAGAATTT R 2 1 2 1 101000 f 74 goat snp38797-scaffold492-1427998 21 41835720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425894 Affx-122941628 AX-123296240 21 39986679 TGGCCCTTCTTTGCAATGCATTTAATTTAATAAAA[C/T]ACCAGATTAAAGGTAGGACAGTCTCATCCTTATTA Y 2 1 2 1 303000 f 74 goat snp38796-scaffold492-1391227 21 41872837 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437004 Affx-122933135 AX-123307342 21 40019414 TACTGTATGACACTGCTAAAATAAAGACAACCAAA[A/G]AACTGTGGGAGCCAGAAAGGTATAAAAGGGAGTGA R 2 1 2 1 102000 r 74 goat snp38795-scaffold492-1358492 21 41904830 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272086 Affx-1111833221 AX-519545847 21 40042565 AGCCCCAGTTTGAGTTCCCTGAGTCATACAGCTCT[A/G]TAACAACCTAGAGGGATAGGATGGAGAGAGAGGTA R 2 1 2 1 103000 f 74 goat 21_40042565_AF-PAKI 21 40042565 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38434883 Affx-122934346 AX-123305223 21 40059328 CCCTATAAAGGCAATGATATTGCACAATACCTTCA[A/G]CTGGGACAGTTTCCTATTGTATCTTAACTTGCCTA R 2 1 2 1 101000 f 74 goat snp38794-scaffold492-1318578 21 41944739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798569 Affx-122931350 AX-385285502 21 40101506 TACATTACAGATACATTCATTTGAAGAATTAACTT[A/C]TTTTTCCTAAACCTCAAACTTCCAGCACTATGATC M 2 1 2 1 202000 f 74 goat snp38793-scaffold492-1276400 21 41987093 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791750 Affx-122919641 AX-385278741 21 40132190 ATTCCACTTTTTGCCAACTGAACATCCATTAGCTG[C/T]AATTTACAGTACAGCTGACTATATGTATGCATGAT Y 2 1 2 1 101000 f 74 goat snp38792-scaffold492-1245716 21 42018113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395155 Affx-122964119 AX-123265510 21 40184767 ACATTGCCACATAAAGCTCTAAAGACAAGGATAAA[C/T]ATACCATACTTAATAGAGTGATGAGGAAACTTCTA Y 2 1 2 1 101000 f 74 goat snp38791-scaffold492-1193139 21 42070435 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795078 Affx-122939441 AX-385282037 21 40233309 CAAACTCACTTTTTATTATTCCTATGCATGTTTCC[A/G]TAAGTTTACTAGATACTGATGCATCCATATACATT R 2 1 2 1 101000 f 74 goat snp38790-scaffold492-1144597 21 42118935 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454167 Affx-122919317 AX-123324500 21 40271750 GCTTGAAAAGCCCACCAAGTAAGGATTAGTGATTA[A/C]ACAGGCTGTATTTTCAATGGTGACCAGGGGTGGTT M 2 1 2 1 101000 f 74 goat snp38789-scaffold492-1106156 21 42157306 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773756 Affx-122950155 AX-385260896 21 40307503 AGGTAGGTACTGGAGATCAATACGAGAATGATGCT[A/G]CATGGTATCTGCCATTCACTTTAGATTAACAGTTA R 2 1 2 1 101000 f 74 goat snp38788-scaffold492-1070403 21 42193105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384423 Affx-122972186 AX-123254781 21 40372429 GTACGGAATTTTAGGGTAACCACATTAAACAGATA[C/T]GAAATATTTATTCTTATTTATGATCCTGTGGCAGA Y 2 1 2 1 101000 f 74 goat snp38787-scaffold492-1005477 21 42258021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436385 Affx-122933042 AX-123306724 21 40429591 TGACTGGGTACTGACCAATGGAATGTAGGTAGCAG[C/T]AACACTTTGCTACCGGGTCTAATCCCCAAAACTTC Y 2 1 2 1 101000 f 74 goat snp38786-scaffold492-948315 21 42316018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422487 Affx-122943315 AX-123292833 21 40461625 TTCATGCCAGAGAGAGGCATGCACAGTTCCTCGTC[A/G]GAAAGAAGGTCACTCAAGGGGCCAGATTCCACACT R 2 1 2 1 201000 r 74 goat snp38785-scaffold492-916281 21 42348080 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428091 Affx-122939095 AX-123298434 21 40510434 TAGATGATGTCCTCATAACTGTAAATTTAGCCCAG[C/T]GCTCTCTTTGATTCTATTTACCTAAAACAGACAAG Y 2 1 2 1 101000 f 74 goat snp38784-scaffold492-867472 21 42397311 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769947 Affx-122951166 AX-385257116 21 40547010 AAAAGGTCACGGTTTAACTGGTCCAAAGGCTGATT[A/C]TTTGATCCCCTTCCCAGCTCCATATCAAGGTTTCC M 2 1 2 1 201000 r 74 goat snp38783-scaffold492-830896 21 42434160 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409967 Affx-122954105 AX-123280317 21 40579502 GAACAGAATTTTGACCAGAAGATAAGAAATAAATA[C/T]GGCTAGGCTGAAAGGAGCCTTTAGAAATGAACCTA Y 2 1 2 1 202000 f 74 goat snp38782-scaffold492-798404 21 42466633 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419333 Affx-122945653 AX-123289681 21 40614106 GGTGAGGTCCTGGACAAGCCAGTCACCAGCCTTTT[C/T]GCCTCTCAATTCTATCATTTATAAGCTAAACAAAA Y 2 1 2 1 101000 r 74 goat snp38781-scaffold492-763800 21 42501302 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400554 Affx-122960426 AX-123270909 21 40646041 TGTGGGCATACCATACTACAAGCAGAAGGTAAGAA[C/T]GGGTCGTTCATATGATGTGAAGTGACCCATTTTCA Y 2 1 2 1 101000 f 74 goat snp38780-scaffold492-731865 21 42533234 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768850 Affx-122967872 AX-385256027 21 40677795 TATTAATAATACTAGCTGCACCAGTACTTTACTGA[C/T]ATATTTCTTTCTACATTTAAATCAACAAGACATGT Y 2 1 2 1 101000 r 74 goat snp38779-scaffold492-700111 21 42564969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428583 Affx-122938708 AX-123298925 21 40711278 CCTTGGGTGTTTTACCCTGGGGCCATCCCATTTAT[A/C]GTGGCCTTATTATTTTCAATTATGTGGCTAGATGT M 2 1 2 1 101000 f 74 goat snp38778-scaffold492-666628 21 42598544 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774149 Affx-122963807 AX-385261287 21 40751088 TGTAACCAATAATAAAGTACCAATGTGTGGAAATC[A/G]CTTTCTGTGTAAGTATGAAATAGATTGTCTTAAAA R 2 1 2 1 101000 r 74 goat snp38777-scaffold492-626818 21 42638542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395221 Affx-122964486 AX-123265576 21 40817810 TATGACCACCAGAAGCTAGCATATATTCATAGAAG[C/T]CTTAAGAGTTTTATTAGCTTTTATTACCAAATTAA Y 2 1 2 1 101000 f 74 goat snp38775-scaffold492-560096 21 42705571 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378697 Affx-122977064 AX-123249056 21 40893252 ATGTCAGAATTTTTCTTACTCTTCTGAACTAGTAA[A/G]GAACTCTATCTGTATAAAGTCTCAGCATGTTTTTA R 2 1 2 1 101000 r 74 goat snp38773-scaffold492-484654 21 42781018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781365 Affx-122945712 AX-385268449 21 40937642 TGCCTTTATTTCACAATGGAGGAAAATGAGTCAGG[A/G]GGTACTTAGTGTCAGAAACAGCAGTAAAATGACGG R 2 1 2 1 101000 f 74 goat snp38772-scaffold492-440264 21 42825487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426899 Affx-122940459 AX-123297244 21 40966514 AATGGTACTCCAATATGTACTTGAACTCACAAATA[C/T]ATTGCTTACATTCTTTAACCAATTTTTTTATTGAT Y 2 1 2 1 101000 f 74 goat snp38771-scaffold492-411392 21 42854419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791320 Affx-122947982 AX-385278313 21 41010286 TTTACTCATCTGCAAAATTATCAGATTGAACTATA[C/T]GCCCAAGTTAAAAACTGGTTATCCCATATCTCGCT Y 2 1 2 1 101000 r 74 goat snp38770-scaffold492-367620 21 42898193 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779894 Affx-122960771 AX-385266993 21 41040115 AGCATTTTCTGTGAATTTTACAGGTAAAATATGTA[C/T]AGTCCCTTCCTTCCTGAATGACAGTGGGGGCTATA Y 2 1 2 1 102000 r 74 goat snp38769-scaffold492-337791 21 42928016 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386342 Affx-122970870 AX-123256700 21 41084057 TTTGCTTTAGAAACAGCTCTAGTGGCTTACAACCA[C/T]GGCTCTGGGAGCCAGAGTAGAAATCCAAACTAGGA Y 2 1 2 1 101000 f 74 goat snp38768-scaffold492-293849 21 42972032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789991 Affx-122936731 AX-385276997 21 41129302 ATATATTTTTCAGTCTGTTCGTGTCACTAACTCCA[C/T]GGTTCTTCCAAAATATAGGCCTGAATCACACAGGA Y 2 1 2 1 101000 r 74 goat snp38767-scaffold492-248604 21 43015240 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405711 Affx-122956534 AX-123276063 21 41187123 AATTAAAATGTGCTTAAAGTTTAAACATCTTCAAG[C/T]GGAGAAGAAGGCAGGAGACTGCAGAAAACAGATTT Y 2 1 2 1 201000 f 74 goat snp38766-scaffold492-190783 21 43073677 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788106 Affx-122975472 AX-385275126 21 41221697 AATTTAACTCCTGAGTGTCTTACTCACACTTTGTC[A/G]TTAATGACTAAAAATTCCATCTCTACCGAGCAGAA R 2 1 2 1 101000 f 74 goat snp38765-scaffold492-156209 21 43107024 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431514 Affx-122936233 AX-123301855 21 41266876 ATGTTTCAGCTTTCCACAGGCTACCCTTTTAAAAA[C/T]GTCACTTAACATCTCTCAACTCCATCAAGGGTGAG Y 2 1 2 1 101000 f 74 goat snp38764-scaffold492-111030 21 43152627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800718 Affx-122973222 AX-385287635 21 41304580 AAATGCACTCTAAAGTAAAAGATACATATAAGGAT[A/C]TCTTGACCTAGTATACCTTTTAGCTTTAAGTGGAA M 2 1 2 1 101000 r 74 goat snp38763-scaffold492-73326 21 43190015 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768447 Affx-122927048 AX-385255627 21 41341901 ATAAATTCTCCAAATGGATCAGTAATCTTCTAGTA[C/T]GGAGAATAGTTTGATCTACAACAATCCAATTCCAT Y 2 1 2 1 101000 f 74 goat snp38762-scaffold492-36005 21 43227657 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398202 Affx-122962228 AX-123268557 21 41376867 CCGAGGATGAACTCTAGCTAACAGAGAGTAATAAC[C/T]TGAAGCACTAAGAAGGACTGATTCTAAGTCTAGGC Y 2 1 2 1 101000 f 74 goat snp38761-scaffold492-1039 21 43262615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438000 Affx-122931581 AX-123308338 21 41398785 AGATGCCCTTCAGGTCTGAATCAAGACCCTGAGGG[C/T]GCAGTGAAGCTCAGGATTCTTCGCAAGGCAGCGCC Y 2 1 2 1 201000 r 74 goat snp39895-scaffold51-20780 21 43286721 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408149 Affx-122954225 AX-123278500 21 41478871 CATGTCCTATTTTGTACAGTCTAATATGACAGGCA[C/T]TAGCCATGTGTGGCTGTGGAGCACTAAGAATATGG Y 2 1 2 1 101000 f 74 goat snp39897-scaffold51-100866 21 43367609 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398994 Affx-122960949 AX-123269349 21 41559880 AATGATGTAATATTGACATAAGGCCCCAAGAGTAC[A/G]TCACTGTGGGCTCTTGGGCTTTGGACTGGCATGGC R 2 1 2 1 102000 f 74 goat snp39898-scaffold51-181875 21 43448368 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419911 Affx-122945333 AX-123290259 21 41594951 CATGTTTTACAAATATTGGAATGTTTGCCTCAAAT[A/C]TCATCCCATCACCTCTTCTAGTAAATTCCTATGTA M 2 1 2 1 101000 f 74 goat snp39899-scaffold51-216946 21 43483911 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421878 Affx-122944272 AX-123292225 21 41630907 TTTAAGGAACAGATTTCTAATTCAAGATCCAGGAA[C/T]TGGATTTGGGGGCCTTCTGAATCCCTGAAATAGGT Y 2 1 2 1 201000 f 74 goat snp39900-scaffold51-252902 21 43519729 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379218 Affx-122976282 AX-123249577 21 41664589 CTGAAAAGATGAGAGTCGGTTTGACCCTGGATTCT[A/C]GAAATCATGAGCCAAGTCACTCACAGGGATGGAGA M 2 1 2 1 101000 f 74 goat snp39901-scaffold51-286584 21 43553412 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438315 Affx-122931355 AX-123308653 21 41703127 ACCTGGAGGTTCTGCAGGGAAGACCTCCCAAAACC[A/G]CATGACCTGACTTTAGGGAACTTACGTAGTAGCTC R 2 1 2 1 101000 r 74 goat snp39902-scaffold51-325122 21 43591397 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771816 Affx-122946008 AX-385258973 21 41733590 TGAAGATGTCAAAAATAGATATTCATTAGCAAAAT[A/G]ACAGATATAGATAATTATCAGGTTATCTCCTATTT R 2 1 2 1 101000 r 74 goat snp39903-scaffold51-355585 21 43621810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391063 Affx-122966848 AX-123261420 21 41762130 AAAATTTTTATGCATTGAAATCTTGGGTTGCAAAA[C/T]GAATCAGAAAAGGAAGACTCACACAGACCTCAGTC Y 2 1 2 1 201000 f 74 goat snp2-scaffold51-384125 21 43650260 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776712 Affx-122957587 AX-385263838 21 41791631 TTCATTTAAAGCAAAGGTCTCCAACAAATACATTT[A/G]AAGCCATCCTTTCCGATCTACTTTTATCTCATTTT R 2 1 2 1 101000 f 74 goat snp39904-scaffold51-413626 21 43679666 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412431 Affx-122951422 AX-123282780 21 41829184 TTGAACATGATGAATAAACTTGACCTCATATGTAC[A/G]TTCTTGCCTGGAGAATCCCAGGGACGGGGGAGCCT R 2 1 2 1 101000 f 74 goat snp39905-scaffold51-451179 21 43717222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425737 Affx-122940750 AX-123296083 21 41861252 GACTGGTGAAGAATTGAAGGGGAACAGTTGTGTAA[C/T]GAGAATATATTTCTCACATATTTACTGAGAATATG Y 2 1 2 1 101000 f 74 goat snp39906-scaffold51-483247 21 43749660 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379930 Affx-122975660 AX-123250288 21 41890153 GACAAAGTCTGGTAGCAAATCAACTCTTTCCACTA[C/T]AGTAACACCAAACCCTGCCCTGAGCCACCTTGGAA Y 2 1 2 1 201000 f 74 goat snp39907-scaffold51-512148 21 43778514 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403338 Affx-122957814 AX-123273691 21 41927979 AAGATAACACAACAAAGGATTCTCAGAGGATACTC[A/G]TGACTTACCAAATATGGGCTCACACCGCATTACTG R 2 1 2 1 101000 r 74 goat snp39908-scaffold51-549974 21 43816366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405555 Affx-122955962 AX-123275907 21 41978207 CATCAATGCATTACAAGTTACCCTGCCTCCTTAAA[C/T]AGGATACATTGAACATAATTTAGCCTTTTAAAATC Y 2 1 2 1 101000 f 74 goat snp39909-scaffold51-600202 21 43866821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798332 Affx-122957107 AX-385285267 21 42013890 GTTTTGTTCCCTTTCTTTGTATTGCTTTTACTACC[A/G]TTAGTAGGCCAAAATCAAAGCTCAAAATCAGAAGT R 2 1 2 1 101000 f 74 goat snp39910-scaffold51-635885 21 43901317 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407986 Affx-122954327 AX-123278337 21 42045788 GAGGTACGGTTCTGAGTTGCCTTGTCTCACAGTTC[A/G]CCTCCCAAAGATTCCAGACAGTCCTAACTTGAGAC R 2 1 2 1 101000 r 74 goat snp39911-scaffold51-667783 21 43933315 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412980 Affx-122951031 AX-123283329 21 42091158 TTATCAGTCAAAAATACAGCAACAGAGTGACTGCT[A/G]TTCACAGGTCTCTCGGCTACTAGAGAGCCCTGTTC R 2 1 2 1 201000 f 74 goat snp39912-scaffold51-713153 21 43978861 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430715 Affx-122936901 AX-123301056 21 42122877 GGCCCACCACAGTGAGGAGAGACAGCTGTTGTTGA[A/C]TTTAGTCTTGCTTTTTTTCCCTGGGTTTGAATTTT M 2 1 2 1 101000 f 74 goat snp39913-scaffold51-744872 21 44010956 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408036 Affx-122954289 AX-123278387 21 42179712 TTACAGCGGAAACATGGCTCAGGTGTCTTCCCCTG[A/C]TGCTATTGGTATCTTGAGACTATCCAGAAATGTAA M 2 1 2 1 201000 r 74 goat snp39914-scaffold51-801707 21 44067744 C A 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438053 Affx-122931543 AX-123308391 21 42240122 GAAATCTCTCTCCAAATCCTGCTTTGACTCTTCTG[C/T]ATATCCACTTCATCCTCCATCCTCTTCAGATCAGA Y 2 1 2 1 201000 r 74 goat snp39915-scaffold51-862117 21 44129530 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385748 Affx-122971079 AX-123256106 21 42270014 GAGACTAGAAGTTACCAGGGGCTGTGGGAAGCAGG[A/G]TATAGGGAGTTATTGTTTAATAACCAGAGAGTTTC R 2 1 2 1 303000 r 74 goat snp39916-scaffold51-892009 21 44160046 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394123 Affx-122965335 AX-123264478 21 42445125 TGATATCATCTCCTGATTTTAAAGATATTTAAAAC[A/G]TGTTATACTTAAATACCTCACGTGCTCAGTTGTGC R 2 1 2 1 101000 r 74 goat snp39920-scaffold51-1067120 21 44335773 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435057 Affx-122933741 AX-123305397 21 42476078 CAAAATATATATTGTCATAGTACTTTGTCGGAGCT[A/G]TTCCAACTAACCCATCTCCTGAAGACCCTAGTCAA R 2 1 2 1 101000 r 74 goat snp39921-scaffold51-1098073 21 44366804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446329 Affx-122925626 AX-123316665 21 42505055 GAAATGTACGGTGACTGATTTGGGGGCATATCAAG[C/T]GCATAGGAGCCAGTTTCAAAGGAGTCCCACTGCCA Y 2 1 2 1 101000 f 74 goat snp39922-scaffold51-1127050 21 44404118 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795605 Affx-122923954 AX-385282560 21 42535503 GACCATAGTTTGAAAATCACTGCCCTATATCAAGA[A/C]TTTTACAACTGTAAATAACATAACAACTTGATAAT M 2 1 2 1 102000 f 74 goat snp39923-scaffold51-1157498 21 44435112 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782181 Affx-122937073 AX-385269259 21 42565641 TAAGAATACTTTATCATCTGCCAAAAACCGACTAA[A/C]AGATGTGTCTCTCGCATTATCAAAGTTATTAAGTA M 2 1 2 1 101000 r 74 goat snp39924-scaffold51-1187636 21 44465501 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802145 Affx-122961675 AX-385289049 21 42618118 TATCTTTAGTGTTGCAACACTTACATGGTAAACAT[A/G]AAACTACATGTATTCAGTAGTGTACACTCAATGGG R 2 1 2 1 101000 r 74 goat snp39925-scaffold51-1240113 21 44517297 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273711 Affx-1111833796 AX-519547323 21 42660316 CAGACTACAAAAACCATCCAGACAAGAAGAGGCTG[A/C]CAGAGAAAAAGCAGAAAAGCCCAAACCATGTGCTC M 2 1 2 1 201000 f 74 goat GoatD01.005411 21 42660316 C A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38448947 Affx-122923141 AX-123319282 21 42684920 GATGCATGCTATAGTATGGATGAACCTTTAGAACA[C/T]TATGGTAAATTAAGAAAACAAGACTGAAAAGGTCC Y 2 1 2 1 101000 f 74 goat snp39926-scaffold51-1306915 21 44584273 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271920 Affx-1111833222 AX-519545700 21 42686840 TGAAAGCATTGAATACATTTACCTTTGCTTTTCCA[A/G]GCCTCTATGTAGTGTCCGGCATACAATAAATGCTC R 2 1 2 1 101000 r 74 goat 21_42686840_AF-PAKI 21 42686840 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450861 Affx-122922228 AX-123321195 21 42715864 CCTATAGACAGAAAGAGCTGCAAGAGGAAAATAAC[A/G]TTTGTTTTGGTGAGGGGGAGTTCAATTAAAAATAT R 2 1 2 1 101000 f 74 goat snp39927-scaffold51-1337859 21 44615173 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421971 Affx-122943802 AX-123292318 21 42761026 TGATGTCTGAGTCTGAGTGGTAAAGTCTGTGGATT[A/G]CAATGTCAATTTCCTGGTTTTGATATTATACTATA R 2 1 2 1 101000 f 74 goat snp39928-scaffold51-1383021 21 44660581 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392172 Affx-122966305 AX-123262529 21 42792132 TGCTTCTCATCTCTTTCTCTTCCACCCTCTAGGGC[A/G]TCCTAGGCCGTCCTAGGCCTTTCCCTTCCTCGTCT R 2 1 2 1 101000 f 74 goat snp39929-scaffold51-1414127 21 44691632 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408134 Affx-122954238 AX-123278485 21 42840600 GTCTCATCCTCATTCAGCCTAAAGGAATATATGCT[A/G]CAAGGTTCTGTTCTCAGCCAGTATTTCTTATTATT R 2 1 2 1 101000 f 74 goat snp39930-scaffold51-1462595 21 44740285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766336 Affx-122945558 AX-385253717 21 42874240 TTCATCAACAGAAAAGAAGCACTTTCTAGTGTCTA[C/T]GGTTTTCAGTCTTACAGATATTCTTGTATTTGGTT Y 2 1 2 1 101000 f 74 goat snp39931-scaffold51-1496235 21 44774048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448021 Affx-122923722 AX-123318357 21 42931672 GGAAGAGTGGAATGTGTGTGGATTGAGCTAGTTAC[A/G]CAGATGATTTAAACACTTTTTTAAAAACTTGACTC R 2 1 2 1 101000 f 74 goat snp39932-scaffold51-1553667 21 44831874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783367 Affx-122966676 AX-385270431 21 42973918 TATTCACTGCCCTCTGAAGTGGAGATTATTTATTT[A/G]TAGATTATTTTCTGCTCAACTTTGTTCTATAAGAG R 2 1 2 1 101000 f 74 goat snp39933-scaffold51-1595913 21 44874375 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453045 Affx-122920076 AX-123323378 21 43017950 CATGTGTGTGTAATCACAGCCATTTCTAAGGCGAC[C/T]GATTGTGTTTTGAGATGGCAGATAATCTAAGGGAC Y 2 1 2 1 101000 r 74 goat snp39934-scaffold51-1639945 21 44918965 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445333 Affx-122925419 AX-123315670 21 43069572 TCTGAAATTCATCCAAAAAGCAAAATTTCTAGTGA[C/T]GGAAATTAAGTGTTTAATTACTGTTTTTGACATTT Y 2 1 2 1 101000 f 74 goat snp39935-scaffold51-1691567 21 44970361 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386895 Affx-122970042 AX-123257253 21 43108103 ATGATTCCAGACTCCGCTGAAACTCTGGAAGGCAC[A/G]CAGAGCCAGGGGTTACTCTGAAGTCCAAGCCTCCA R 2 1 2 1 201000 f 74 goat snp39936-scaffold51-1730098 21 45006375 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393641 Affx-122965297 AX-123263996 21 43145395 GGAAAGGAAGGGTTGTCATAATAAAAGTCACTTTC[A/G]TCTCAGTGAGGCAGGGTGGGGACTGGGACAGCCTG R 2 1 2 1 101000 f 74 goat snp39937-scaffold51-1767390 21 45043372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431083 Affx-122936624 AX-123301424 21 43175440 TAGCGTAAAGGGTGAGTTTCCCCACCTCTCTGGAA[C/T]AGCAACTCTGTCCCATCCAGAAAAATATACCACAT Y 2 1 2 1 101000 r 74 goat snp39938-scaffold51-1797435 21 45069269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788293 Affx-122944667 AX-385275311 21 43233789 CTGCACATCATACCTACCTATAGGATTTTTAAAAT[A/G]CAGAGATGCTCAGAATCCTCCTCTGACTTGAAAAA R 2 1 2 1 102000 r 74 goat snp39939-scaffold51-1855784 21 45127862 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779779 Affx-122973889 AX-385266879 21 43296044 TAATATAAGCTTTTGGGAAATACAGAACTCATTTC[C/T]TGAAGTTTCAGTTTTAGTAGGGTTTCATCCAACTT Y 2 1 2 1 101000 r 74 goat snp39940-scaffold51-1918039 21 45190094 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764570 Affx-122940757 AX-385252225 21 43345347 TATTTCTTCTTTTGGTTCTATTAGCTCTGCTTCAC[A/G]TATTTTGCAGTTCTGTTGTTTGCTGCACATATGTT R 2 1 2 1 201000 f 74 goat snp39941-scaffold51-1967342 21 45239408 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774566 Affx-122927537 AX-385261700 21 43403620 AGTCTGAGAAGCAGGCTTAGTGTTCCATGTCATTG[C/T]ATTGTTTTTAGTGCCTGAAGTGCTAATTATATGAT Y 2 1 2 1 101000 f 74 goat snp39942-scaffold51-2025615 21 45298426 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801541 Affx-122975527 AX-385288450 21 43464109 CTAAGAGGGGAAATATTTTGCTTTCACAAAAATCC[G/T]ATCAAATATTTGTACTAATCACATGAACCCGAAGA K 2 1 2 1 101000 f 74 goat snp39943-scaffold51-2086104 21 45353994 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379453 Affx-122976091 AX-123249811 21 43506873 AGCATTTGGATCCAACTTGCCTGAAGTACCATGGT[C/T]TTTTCTATTTCCCAGGTCAACAAAGTCCTTATTTC Y 2 1 2 1 101000 r 74 goat snp39944-scaffold51-2128868 21 45396720 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407876 Affx-122954502 AX-123278227 21 43535767 ATATTGGAAATAGGACGCAAAGAATCGTACAAAAG[A/G]ACTAAGTGATATAATTTTAGAAGTTTTGCAGCTGT R 2 1 2 1 101000 f 74 goat snp39945-scaffold51-2157762 21 45425743 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790317 Affx-122959584 AX-385277320 21 43596524 AGAAAGTATTAACTTCAAATCCCTTACAAAGTTAG[C/T]ATAAGAAAAGGACAGTAAGAAGTAGAATAACATCC Y 2 1 2 1 101000 r 74 goat snp39946-scaffold51-2218519 21 45488809 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404035 Affx-122957172 AX-123274387 21 43629432 TAATTCAATCTCATTTACAATAATTGATTCATAAA[C/T]AAATGTGTCATGTCCATGAAATGACCAGATAGGTT Y 2 1 2 1 201000 f 74 goat snp39947-scaffold51-2251427 21 45521139 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381531 Affx-122974846 AX-123251889 21 43684664 ATTTCGGTGATTGTATACTATTTACTTATTTCCAT[A/G]TGCTCTGTGGTTAAAGTGAAGGGGCTCATATTTTC R 2 1 2 1 201000 f 74 goat snp39948-scaffold51-2306659 21 45577809 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449870 Affx-122922361 AX-123320205 21 43763648 CCCTTCTGTCTTCTGACTGGGAATTGCATGAAAGA[G/T]CAAAGCCATAGCCATCCAGTTGAACCTAGTCAAAC K 2 1 2 1 201000 f 74 goat snp39949-scaffold51-2385643 21 45658331 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422530 Affx-122943278 AX-123292876 21 43795595 AGAAGGCAGTTAATTATCTCTCTGTCTCTCTGTGT[A/G]TTTAAATTTTGTTCCCTCTCCCTAAAAGAGAGGTG R 2 1 2 1 201000 r 74 goat snp39950-scaffold51-2417590 21 45690285 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432513 Affx-122935570 AX-123302854 21 43827405 TAAAATGTTTTACCTGCTGTTTGCTGAAAGACATT[A/G]TAAAATTAGAAATGAGAAAGACATCTTATGTCACC R 2 1 2 1 303000 f 74 goat snp39951-scaffold51-2449400 21 45720469 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446495 Affx-122925046 AX-123316831 21 43862920 CACCAGCACCTGTTTGTTCTCCCCAGTTTCTGTAC[A/G]AAATAAATAAGCCAGAAGAGCCAGAGCCTCCTCCT R 2 1 2 1 201000 r 74 goat snp39952-scaffold51-2484915 21 45756268 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404687 Affx-122957275 AX-123275039 21 43898307 TTCTGCTTTTTATTGAAAGGCCAAGTGTTTTTAGC[A/G]ACACTGGTGATTTTTCAGTGACAGCTAAAAATACA R 2 1 2 1 201000 f 74 goat snp39953-scaffold51-2520302 21 45792447 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414029 Affx-122949794 AX-123284378 21 43943144 CATAACTATGGAAGGTTCTCAAACAACCTACACCA[C/T]GAAGACCCAGGGTCAGTAATTTTACACATAAAGTC Y 2 1 2 1 101000 f 74 goat snp39954-scaffold51-2565139 21 45836434 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380986 Affx-122974679 AX-123251344 21 43975393 AATTCTGATAAGGTTTCTGTGAGTTTAGTGATATG[C/T]GCTTTAAACATAATTTGAAGCTTTTAAAATACTGT Y 2 1 2 1 101000 f 74 goat snp39955-scaffold51-2597388 21 45868644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420801 Affx-122944686 AX-123291148 21 44022082 AACTAGGCCAAGTACTCTTACAGCTTCAGCACTTG[C/T]GGTTCTCTCTACCTCTGTATTCACAAGGCTAGCTC Y 2 1 2 1 101000 r 74 goat snp39956-scaffold51-2644077 21 45915575 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421880 Affx-122944271 AX-123292227 21 44110789 TCCCCAGCTTCTCTCTCCAAACTTCCACGCTCACA[C/T]CTATCAGAGCCCACAGTAGACGCAAGCCTTTCAAA Y 2 1 2 1 201000 r 74 goat snp39958-scaffold51-2732784 21 46004536 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431578 Affx-122936184 AX-123301919 21 44141837 CGTCTTTACTCACAAAGCCTCTTCCTTTCACCACA[C/T]AGAGTATAGCAGGAAGTGTCCCTGCTGTATATTTT Y 2 1 2 1 201000 r 74 goat snp39959-scaffold51-2763832 21 46035837 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378958 Affx-122976417 AX-123249317 21 44176440 AACAGAAAGCTTCATGGAGGAGACAGCATTTAACC[C/T]AGGACTTGCACGAGGAAAAGGAATTAGACAACCGG Y 2 1 2 1 101000 r 74 goat snp39960-scaffold51-2798435 21 46070409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789882 Affx-122961186 AX-385276889 21 44214249 ATTAAATTAGCGACAATTTCTCTGGTAAAACAAAC[A/G]TGAAAAGCCAGAGGTTTGTTCTACGGACAGCAAAT R 2 1 2 1 101000 r 74 goat snp18956-scaffold191-11926 21 46108099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379719 Affx-122975886 AX-123250077 21 44271507 AGAAAAACATGAGCTTCTTTTCAGGCTTAATGTTG[C/T]CACTTCTCTCAAACTTGAGATGAAAATATTAATAT Y 2 1 2 1 101000 r 74 goat snp18957-scaffold191-69184 21 46165721 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437229 Affx-122932029 AX-123307567 21 44301633 TGTTTAGGTGGTTTGTGGTGGAAGAAAGCAATGGA[C/T]GGCTACACACTGGATTTTAGTTGCTCTTTGGCTTT Y 2 1 2 1 101000 f 74 goat snp18958-scaffold191-99310 21 46195254 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410503 Affx-122952185 AX-123280853 21 44398728 GAGCCAAACAAAACTGGAGTGTGGGGGAAAGCTGA[C/T]AAAGGCAGACAGGGAGCTGAACGGATTCTAAGAGT Y 2 1 2 1 101000 f 74 goat snp18960-scaffold191-196405 21 46293283 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400637 Affx-122960368 AX-123270992 21 44430151 ATTCCCCTGCTTAAAATCTTTTGTTGGCTTCCCAG[C/T]GTTCTTCAGATAAACAGAAAAATCCTTAGTGTGGC Y 2 1 2 1 101000 f 74 goat snp18961-scaffold191-227828 21 46324744 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398479 Affx-122961579 AX-123268834 21 44473341 GGGGCCATTTTCATTTAGGCAAAGGAGAGAGGGAA[A/G]ACTAGGTAGCCTTCAAAGGAGAAGGAAAACAGCTT R 2 1 2 1 201000 r 74 goat snp18962-scaffold191-271018 21 46367897 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401597 Affx-122958868 AX-123271950 21 44518722 TGAATGTGTCACTCTCCTGACCTAAATCCCTCAGA[C/T]GCTGCCCAGGACTTTCAGGATTAGAGTGTGAGCTA Y 2 1 2 1 201000 f 74 goat snp18963-scaffold191-316399 21 46413514 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422092 Affx-122943581 AX-123292439 21 44554758 CCCCAGGAATTAAGCTGAAAACTAACACATATATC[A/G]CAGAAAAGAGAGACTATTTTGCTTTGTTTGAAGTG R 2 1 2 1 101000 f 74 goat snp18964-scaffold191-352435 21 46449545 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277506 Affx-1111835884 AX-519551008 21 44597522 TTGTAGCCAGTCACTAATTTTCTTACATCATAGTC[A/G]CTGTTCTTCAGAGTTCACTATATGACATTTTAGGG R 2 1 2 1 101000 r 74 goat Random2.2K-1943 21 44597522 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38414321 Affx-122950043 AX-123284670 21 44615249 GAGGCCTTTCCATGCTCAGATTAATTCACTGTACC[A/G]TTCTTCAAGCAATAACATCCTATGAGAGTCAAAAA R 2 1 2 1 101000 f 74 goat snp18965-scaffold191-412926 21 46510036 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392376 Affx-122966235 AX-123262733 21 44645142 AAAGAATGGGAGATAGTGGTGCCATGATTTGGAGA[C/T]GAATCCAGGTAGAGACACATTGGGTGAGGGGTCTG Y 2 1 2 1 201000 f 74 goat snp18966-scaffold191-442819 21 46539582 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402907 Affx-122958203 AX-123273260 21 44707626 AGTTAGGGATATGGAACACCAAGGAAAAATCAAGA[C/T]GGAACAAAATAGGATATAAAAGTTTGTAAGTGGTT Y 2 1 2 1 101000 f 74 goat snp18967-scaffold191-505303 21 46602299 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277508 Affx-1111835885 AX-519551010 21 44733531 GCCTGTAAGATTCCAAGTAATTTATTTCTATTTTG[A/G]GCTCCTTTATCTACATGATAAGGACTTAATCTTCT R 2 1 2 1 101000 r 74 goat Random2.2K-1944 21 44733531 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384529 Affx-122973034 AX-123254887 21 44739626 GTCTGTATTGCCGGTTTCACTTTCATAATTTTGCA[C/T]CTTTCCCTTATTTTTAATCTAAAATTAGACATTGG Y 2 1 2 1 101000 f 74 goat snp18968-scaffold191-537303 21 46634504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429029 Affx-122938320 AX-123299371 21 44802635 TGCCTTAAACTTTTTAGTAACTCAGGCGCCTGTGA[C/T]AAAGGAGTTCAGAACTCATTATTTGCATACTTACA Y 2 1 2 1 101000 f 74 goat snp18969-scaffold191-600312 21 46698135 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379001 Affx-122976382 AX-123249360 21 44860383 TTGTAGGAATCTCTTTTTTTAAAGTTGAGGAATAA[C/T]GCCATTAATGAAATATAGATACTTAATAAACCATT Y 2 1 2 1 201000 r 74 goat snp18970-scaffold191-658060 21 46756142 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393443 Affx-122965858 AX-123263799 21 44892775 TTAAACATCCATTATGTGTACATGGTCTATCACAG[C/T]GAGGAGTCAACTGGGACATACAGTATTTCTGTTAC Y 2 1 2 1 101000 r 74 goat snp18971-scaffold191-690452 21 46788703 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408663 Affx-122953464 AX-123279014 21 44947154 TTGCCATTTCCTTGGCTGCTTTTTGTATGCTGTGT[A/C]GTTTTTCTTCCTATTCTTTTCTTTATTGTTGTCAT M 2 1 2 1 103000 f 74 goat snp18972-scaffold191-744831 21 46838611 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408076 Affx-122954730 AX-123278427 21 45022591 TGAGTGTGTTTTCTATGCTGATACTTTTCCAAGAG[A/C]TTGTATAATTTAACTAATTTAATTCTCATAATAAC M 2 1 2 1 101000 f 74 goat snp18974-scaffold191-820268 21 46913905 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392895 Affx-122965732 AX-123263252 21 45053680 AGTATTATTAGCTTCAACTTATCAACCATTCACAG[C/T]ACTACACTTCACATATAATTTATGACCATAAATCT Y 2 1 2 1 101000 f 74 goat snp18975-scaffold191-851357 21 46945018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793139 Affx-122920545 AX-385280117 21 45095805 ATTTACATCAATTCATGTGGGTTTGTGAAAAAAAT[A/G]CCGTGACTCCTTTACTTAATGGGATTCTTTCCCTG R 2 1 2 1 101000 r 74 goat snp18976-scaffold191-893482 21 46987403 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411428 Affx-122951831 AX-123281778 21 45152508 AGTGGTCCCTGAAGAAACCTGAATAAGAAAGATGT[C/T]ATAGCTAAGAAGAAAGGAAAGTGGGTTAAGGATTA Y 2 1 2 1 101000 f 74 goat snp18977-scaffold191-950185 21 47044109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787137 Affx-122948424 AX-385274163 21 45193322 AATGAATTTATTTAAACTTCATAGCTGAGAGCAGC[A/G]TCAGTGCTTATCCTAGGCTTTCTATAATGTGAAAT R 2 1 2 1 101000 f 74 goat snp18978-scaffold191-990999 21 47085255 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787244 Affx-122946919 AX-385274270 21 45246288 GTCTTCTCTTCTATCGTCTATAAACATATTCACAT[A/G]CCATCTATTTCTTTAAGGACTTCCTCAGCCATACA R 2 1 2 1 101000 r 74 goat snp18979-scaffold191-1043965 21 47138855 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415745 Affx-122948495 AX-123286094 21 45295267 AATATGTCCCCAGGAAGATGTGTAATCGCCTTACA[C/T]GCCGGGCTTAGGGGCCGGCTTCTGGGGCCCCTCCA Y 2 1 2 1 103000 f 74 goat snp18980-scaffold191-1092944 21 47187705 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445640 Affx-122925084 AX-123315977 21 45326788 GCTCAGAGAAATTGAAAAGCATGCTTGCAAGTAGG[A/C]TCCAGGCTACTGCTGACCTCTGATCTCTCTTCTTG M 2 1 2 1 201000 f 74 goat snp18981-scaffold191-1124465 21 47219058 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407427 Affx-122954807 AX-123277778 21 45355855 AAGAGCCTGACAGGACTGAATCGAGTTAGCACACA[C/T]ACTTGCCTCCAATTCCTAAATCTTTCTGAGGGTAT Y 2 1 2 1 201000 r 74 goat snp18982-scaffold191-1153532 21 47248076 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775560 Affx-122942777 AX-385262691 21 45387794 GGGGAAGAGCCCAGCACATCAGAAAGCTCAATAAA[C/T]GTTAGTTATTGTTACTATCCTTTGGATTTCAACAA Y 2 1 2 1 201000 f 74 goat snp18983-scaffold191-1185471 21 47279862 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454022 Affx-122919421 AX-123324355 21 45429675 TTGGAATCCATGGACTATTGTAGTAGCATTACTTG[C/T]ACCTAACCTGCCAGGTATTCCTGTTTTTAATAGCT Y 2 1 2 1 101000 f 74 goat snp18984-scaffold191-1227352 21 47321773 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410360 Affx-122952453 AX-123280710 21 45463729 CTTAAGAGTAAGGTTGCTATAAGCCTTCTTTTTCA[C/T]GTCTTTGTTAACATTGCTGGAACATAGAGAATGTA Y 2 1 2 1 101000 r 74 goat snp18985-scaffold191-1261406 21 47355991 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400954 Affx-122959698 AX-123271307 21 45528028 TTTGCTCCACTCAGTTTATTTTCCTTCTGTGTCTC[A/G]TTCTTCCAGTACGTCTCCAGCTCCTCAGAGACTTG R 2 1 2 1 201000 r 74 goat snp18986-scaffold191-1325705 21 47421968 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271922 Affx-1111833223 AX-519545702 21 45586712 CATTGTATTACTTTGACCTTCTGTGGGTCTGCAGA[A/C]TGAGTAGCTCAGGTCAGGTGTTCATGCCTATATGA M 2 1 2 1 101000 r 74 goat 21_45586712_AF-PAKI 21 45586712 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38408727 Affx-122953416 AX-123279078 21 45592724 TAATCAGGTATGATATGCCCATAAGTTTGAGTTTT[A/G]TATAAGGAGCTTCAGTTATCCCTTGTGTATTCCAT R 2 1 2 1 101000 r 74 goat snp18987-scaffold191-1390401 21 47487098 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378103 Affx-122977150 AX-123248462 21 45736881 AAGCTGAGCATGAGATTCATGCCTAGTCTCAATCC[A/G]CACCAGTTTAATCAGAATCTCTGGGGACTATGTGT R 2 1 2 1 101000 f 74 goat snp18990-scaffold191-1534558 21 47631763 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797313 Affx-122919740 AX-385284252 21 45777835 ACATTTTGCAAAGGACAACTGGTAAAAACAGAGTC[A/G]GGTGATGGTGACCAGCAGTGCTAATATGACCATAT R 2 1 2 1 201000 r 74 goat snp18991-scaffold191-1575512 21 47673145 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277510 Affx-1111835886 AX-519551012 21 45808026 TTTCTTTTTGGTCTAATTGTACTGGGTAGTAACCT[A/C]TTTTAGGATGCAATCGCCTTTTATGTCTTTTTGAA M 2 1 2 1 101000 r 74 goat Random2.2K-1947 21 45808026 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417134 Affx-122947362 AX-123287482 21 45831531 AGAATTTAGGAGTGACCTGTGTTTCTCCAGTGTGT[A/G]CTAGTCATATTCCTAATCCCGACAGTGAATAGCAC R 2 1 2 1 201000 r 74 goat snp18992-scaffold191-1629208 21 47726967 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390527 Affx-122967234 AX-123260884 21 45905777 ATGAAGTGATAGTAGAGAAATATTCTGAGGAAGGA[C/T]GCTGACCTTAACCTAACAGAGCTTTTAAGAGATCA Y 2 1 2 1 101000 r 74 goat snp18994-scaffold191-1703454 21 47801146 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418149 Affx-122947101 AX-123288497 21 45970969 TTATGCATTTTGAGTCATCATAGGGCTTATGGATT[A/G]TGCAGAAAATTTCTGTACATTTGCAATGATTCTGA R 2 1 2 1 101000 f 74 goat snp18995-scaffold191-1768646 21 47867193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798190 Affx-122978173 AX-385285125 21 46003908 ACATATAAAATGTAAATACGCCCAGCACCATACAG[C/T]GGTATCAACAGGAAATTTACCCACCTTTCCAAAAC Y 2 1 2 1 101000 r 74 goat snp18996-scaffold191-1801585 21 47900548 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770340 Affx-122923150 AX-385257506 21 46038919 GAATTTATTTTTACATTGGGATAGATTAGTCACTA[C/T]AGTAAAACTACTTCTAGTTTCTTACCTAATTTAAA Y 2 1 2 1 201000 r 74 goat snp18997-scaffold191-1836596 21 47935606 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446704 Affx-122924734 AX-123317040 21 46072616 ATACTACACACGTGTATTCCTATATTCATTGAGGT[A/G]TTATGACTACACCACATGAGAGCTTGCATACTGTA R 2 1 2 1 101000 r 74 goat snp18998-scaffold191-1870293 21 47969900 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416638 Affx-122947613 AX-123286986 21 46130508 GCTGTCTGGAAAGTAAGCTGACTGCAAAGCAGGAC[A/G]CAGACAATGACAGGCTGGTACCCACTCAACCCCTC R 2 1 2 1 101000 f 74 goat snp18999-scaffold191-1928185 21 48028524 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443593 Affx-122927321 AX-123313930 21 46193924 CCTAGTTCTGTGTGCCGTGTCCTGCCCAGGAAATG[C/T]GAGCCCAACAAACTACAAAGCCCCTTCTGGCTTCT Y 2 1 2 1 201000 r 74 goat snp19000-scaffold191-1991601 21 48093735 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436777 Affx-122932267 AX-123307115 21 46232700 CAGAGTAGCTAATGAGCAACCCTCATCATAGGACT[A/G]TATTACCTAGCTAAATGAAAAAAAGGACCTTAAGC R 2 1 2 1 101000 f 74 goat snp19001-scaffold191-2030377 21 48131103 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443992 Affx-122926913 AX-123314329 21 46277180 AAGTTCAGGAGATGGTGATCTAGCTGGAGTCAGAA[C/T]GCCTTAACTTTCAGCTCTGCCATTCGCTGCTGTGC Y 2 1 2 1 101000 f 74 goat snp19002-scaffold191-2074857 21 48175384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452126 Affx-122921683 AX-123322459 21 46306991 AACAGGAACAATTAACAATTAACAAGCAAGTAAGA[C/T]GAAAGAAAACTTTTAGAATTTTCTGAAACTTTCAG Y 2 1 2 1 101000 f 74 goat snp19003-scaffold191-2104668 21 48205178 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784469 Affx-122964276 AX-385271518 21 46349076 ATCTTGAAGGGCCATGTATTCTCTTCCACTCCAAA[C/T]GGTAGCATAATGTTCTTAGCAACATTAACCTCAAC Y 2 1 2 1 101000 f 74 goat snp19004-scaffold191-2146753 21 48247512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394414 Affx-122964607 AX-123264769 21 46378415 AATTCTTATTTATTGTTGTAATCCCATACTGAATC[A/G]TGCCTAACAAAGTAATTCATAAAAGAAATAAAGAA R 2 1 2 1 101000 f 74 goat snp19005-scaffold191-2176092 21 48277644 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388082 Affx-122969511 AX-123258440 21 46432689 CTGTTAGAAGGACCAGTCAGGAGTTAGCGTGAGAG[C/T]ATGTACGGGGGAGAGCGATGAAGCTCTATGAATAA Y 2 1 2 1 201000 f 74 goat snp19006-scaffold191-2230366 21 48332428 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434128 Affx-122934922 AX-123304469 21 46467445 TCTTCTCCTTTTGGTGATGGCAATTCTAACAGACA[C/T]GAGGTGATATTTCATTGTGGTTTTAATTTGCATTA Y 2 1 2 1 101000 f 74 goat snp19007-scaffold191-2265122 21 48367258 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405910 Affx-122955580 AX-123276262 21 46551049 TTGGACACAACTGAGCGACTAAACAGCAACAACGA[C/T]GACACATTTGGGAGTAAGGGTAAAGGATTCCATAA Y 2 1 2 1 101000 r 74 goat snp19009-scaffold191-2348726 21 48451687 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415154 Affx-122949407 AX-123285503 21 46566132 AGTTGATTGATCTCTATTGTTCAACTGTACCCTTT[G/T]TCTCTTTAAAAATATATCCATGATGGTTTTCCACC K 2 1 2 1 303000 f 74 goat snp58166-scaffold942-9053 21 48466495 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378276 Affx-122976874 AX-123248635 21 46607278 GAATCTGGTTAAAAGATATAAAGGAATTCTTTGAA[C/T]GATTTTTGTGACTTTTCCATATGTGTGGAATTATG Y 2 1 2 1 201000 f 74 goat snp58167-scaffold942-50199 21 48507415 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766804 Affx-122950173 AX-385254132 21 46693106 TGAGAACAGAGAGTGTTTGTCTCTCAAGTTAAGCC[G/T]AAACACCGATAGAGAAAAGTAGTTATGAAGGGGTT K 2 1 2 1 101000 f 74 goat snp58169-scaffold942-136027 21 48594463 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791708 Affx-122927407 AX-385278699 21 46737876 TCCTCCTGTTACTTTTTGAGATAGTTTCTGAATCT[A/G]TTTCAGTTCACTAGTTGTTCCTCATGTAACTAATT R 2 1 2 1 101000 f 74 goat snp58170-scaffold942-180797 21 48639461 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800848 Affx-122974141 AX-385287763 21 46782133 TCAGAGTCTGTGCCTAAATTTGTGTCTGCCCAAAT[A/G]TCCTTAATTTGGGCATTGTGAACCTTCCATTCATC R 2 1 2 1 202000 f 74 goat snp58171-scaffold942-225054 21 48683922 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388143 Affx-122969466 AX-123258501 21 46821782 CAGGGGAAGAATTGGGTTCTCAGCAACATAATAGG[C/T]AGTGCGGAGGACTGGCTTACCAAAGGATGCTTTTC Y 2 1 2 1 101000 f 74 goat snp58172-scaffold942-264703 21 48723368 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394726 Affx-122964331 AX-123265081 21 46872456 CTACGTGTGGTCTCACAATAACCTAATTTACTGGA[C/T]AGGGGTTATTGGTTTTAATACCAATATTTAAATTT Y 2 1 2 1 101000 f 74 goat snp58173-scaffold942-315377 21 48773802 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777176 Affx-122940690 AX-385264299 21 46902014 TGGTTATATGCAGGGAGACTGGACCTTCTACAAGC[A/G]TGGTTGTGAAGGTGATGAATTTTTGCAGAGTAGCT R 2 1 2 1 101000 r 74 goat snp58174-scaffold942-344935 21 48803469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430991 Affx-122936689 AX-123301332 21 47006152 ACTTCTATAATTTTTATAATGAATTTCTAAAATCT[A/G]TTCATAAAAATGGATTTAATGAGGACACCTACATG R 2 1 2 1 103000 r 74 goat snp58176-scaffold942-449073 21 48915706 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804097 Affx-986696384 AX-385290760 21 47068265 TAATACTACTGAAGATGTTGCCTGTGTTCATAATC[A/G]TAAGAAATACTGTATTTACATGAAGAGTGAAAATT R 2 1 2 1 600010 r 74 goat 21_47068265 21 47068265 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 320763720 Affx-986698249 AX-385251539 21 47068299 CATAAGAAATACTGTATTTACATGAAGAGTGAAAA[A/T]TAAAGATAAAAAATTTTTCCTATCCTCATGTTAAG W 4 1 2 1 600010 f 74 goat 21_47068299 21 47068299 Ancestral_priority_1043 ancestry 0.72 recommended IMAGE 10K 10K ancestral 320766928 Affx-986698251 AX-385254240 21 47068320 ATGAAGAGTGAAAATTAAAGATAAAAAATTTTTCC[C/T]ATCCTCATGTTAAGAATCTATGCTTTGAAACAGTG Y 2 1 2 1 600010 r 74 goat 21_47068320 21 47068320 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 320790682 Affx-122961069 AX-385277684 21 47089495 TCAATAATTGCTTCCACATAAAAATAATCACTCAA[G/T]CTTGCCTGACCAAGTCTTCTCACATTCACAGAACT K 2 1 2 1 101000 r 74 goat snp58178-scaffold942-532416 21 49000972 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785497 Affx-122945031 AX-385272542 21 47121139 ATTGATGTTACTGAGATACTTTGAAACTATTTGTG[C/T]ACCTTCATTTACTTCTGATATTGTTTAACACTAAT Y 2 1 2 1 101000 f 74 goat snp58179-scaffold942-564060 21 49032632 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788279 Affx-122956267 AX-385275297 21 47150841 TTTTATGTATTGTGTATTTTCCTTATCAGATGTGC[A/G]TCTCAACTTTGCATTCCTTTAGTATTCCAGATATA R 2 1 2 1 101000 f 74 goat snp58180-scaffold942-593762 21 49061699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433957 Affx-122934272 AX-123304298 21 47182929 GCAACTGTTGAAGCTGTGTGAAGCCACAGAGAATA[C/T]GGAGAGTAGGCCAACATTTGAGTTTTATGAAATTT Y 2 1 2 1 101000 f 74 goat snp58181-scaffold942-625850 21 49097847 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397315 Affx-122962312 AX-123267670 21 47224193 AAAAAAATCACACTTAAGGAAGAACAAGTGGTATT[A/G]CCAGGTATACTAAGCTGAAGATGGAACTTAAAGAT R 2 1 2 1 101000 r 74 goat snp58182-scaffold942-667114 21 49139740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803291 Affx-122940377 AX-385290134 21 47257130 TCTTTATTAAATTAGGTGTATGCAAAAGAAGCGAA[A/C]TTCAAATTTGGCTAAGAAAGAGCCTAAGAAGGTGG M 2 1 2 1 101000 r 74 goat snp58183-scaffold942-700051 21 49172699 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422524 Affx-122943283 AX-123292870 21 47293175 TAGTATAACTTCCTTGTTCCTGCTCCTTTCTGCTC[A/G]TAAAAGTCTTTCATTTTGTGTCGTTTCTCAGGCCC R 2 1 2 1 303000 r 74 goat snp58184-scaffold942-736096 21 49208988 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383357 Affx-122972667 AX-123253715 21 47333798 TCAGATACTTTAAAATTTATCAAATTGATCTTGTA[A/C]AGAAGAGCAGAGTCTTCCATATTGGAAAAAAGTTA M 2 1 2 1 201000 f 74 goat snp58185-scaffold942-776719 21 49249417 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422706 Affx-122943649 AX-123293052 21 47367092 AATAGTTTTACAGGAGGCAGGGGAAATAGACTGTG[C/T]GATACAGAATTGAAAATGCCTGCTCAGTGAGAGTG Y 2 1 2 1 101000 r 74 goat snp58186-scaffold942-810013 21 49282558 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789231 Affx-122933724 AX-385276242 21 47410041 TACTCTCTTCGTCCTTTTCAGTCCAAGTTGGTGGC[A/G]TTTCTTCTTACATAAAGTACTTGAAACCTTGTGAA R 2 1 2 1 101000 f 74 goat snp58187-scaffold942-852962 21 49325125 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795224 Affx-122926699 AX-385282182 21 47446280 GAATATATAACACCAGTTAAAATCCAGTGTAGGAG[A/G]TATGTATCACTTTGGGCAGGGAATGAACTGGAAAG R 2 1 2 1 101000 r 74 goat snp58188-scaffold942-889201 21 49361403 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776076 Affx-122924745 AX-385263206 21 47475107 TATTTTTCAGTATGTTTTGAAAAGACTGGAACTTT[A/G]CTAGTGTTTGTACAGTCTGGCCTCAGAAGTTAGGC R 2 1 2 1 101000 r 74 goat snp58189-scaffold942-918028 21 49390197 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789017 Affx-122924527 AX-385276030 21 47565255 AGCTGTGACCTTTGTAGACTCTCTAGATCCTCACA[A/G]TAAAGGAATAAATATTCTTCTAGACACATCTTACT R 2 1 2 1 101000 f 74 goat snp58191-scaffold942-1008176 21 49480251 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779057 Affx-122936015 AX-385266162 21 47596908 AACTAATTTTTACTGGCATATCTGATATTTTTTCA[C/T]AGAATTCCTAATACTGTATGGGAAAACTGTAGAGG Y 2 1 2 1 101000 r 74 goat snp58192-scaffold942-1039829 21 49511875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418525 Affx-122946418 AX-123288873 21 47638341 ATCCCACCCTTTCTGGAGCATCATGATCAGTTGCA[C/T]GTATACCAGTTACTTCCTCCAGGTGCTGTGTGTTT Y 2 1 2 1 101000 f 74 goat snp58193-scaffold942-1081262 21 49552332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407111 Affx-122954880 AX-123277462 21 47692896 TCTGGAGGGATCTTTGATCTTTCCCTTGACATCTG[C/T]AGTACTAAAGTAAAAACAGAAAACTCTACATTCCT Y 2 1 2 1 101000 f 74 goat snp58194-scaffold942-1135817 21 49607661 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432315 Affx-122936303 AX-123302656 21 47722004 GAGAGACTCATTTGCTACACAATATTGCTGAGCCC[A/G]GGCTTGGTCAATGTCAGTACCATAAAGAAGTGTGC R 2 1 2 1 101000 f 74 goat snp58195-scaffold942-1164925 21 49634325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386758 Affx-122970127 AX-123257116 21 47752413 AGTGGTCTTCGGAATTTCTAGTCTATTAAGAATGT[A/G]CATATAACCCTGTCTTCAGGTGACAGCCTGAGGCA R 2 1 2 1 101000 f 74 goat snp58196-scaffold942-1195334 21 49664702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376483 Affx-122978034 AX-123246842 21 47795672 GGCCAAACTCTGGGGAATGGATACAGAGTTTCCAT[A/G]CCCTTTCTTAGGAGCATTAACCTCCAGCATCTACT R 2 1 2 1 101000 r 74 goat snp58197-scaffold942-1238593 21 49707977 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396225 Affx-122963347 AX-123266580 21 47831753 TTAGGGTAGAAAGTCTTGTTAGAGATATCTTTTAA[C/T]GAGGTGGGTCAGAGGGGACGATGACCTAAGGATGG Y 2 1 2 1 101000 f 74 goat snp58198-scaffold942-1274674 21 49738264 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392064 Affx-122966387 AX-123262421 21 47867803 GAGGTGTTATAAATATTGAGCGTATTCCCTGTGCC[A/G]TCCATTCTGTTTCTTTGACTTGTTTTATAACCGGT R 2 1 2 1 101000 f 74 goat snp58199-scaffold942-1310724 21 49775281 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782970 Affx-122933599 AX-385270039 21 47916423 CTTGCATTTCAGGAAGATGCTTTATGATTTGAACT[A/G]CTAGGGATAGCATTCAATTCTACAGTCAAGGTAAG R 2 1 2 1 101000 f 74 goat snp58200-scaffold942-1359344 21 49823829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411523 Affx-122951668 AX-123281873 21 47990469 ACAAGGTAACTGTTTCTTTTTGAGGGGTGGGTGCT[A/G]TGCTGGGTCTTCATTGCTCTGCATGGACTTTCTCT R 2 1 2 1 103000 f 74 goat snp58202-scaffold942-1433390 21 49898627 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797552 Affx-122929778 AX-385284491 21 48043810 AGCCAGCACTGAGAACCCTATCAACATCTTCTGAT[A/G]CAATGTGGAAATTTGTTGTTAAAACATTTGTTGCT R 2 1 2 1 101000 f 74 goat snp58203-scaffold942-1486731 21 49950579 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384330 Affx-122972261 AX-123254688 21 48083809 ATGTTCCCACAACCTTTTTCATTCTTCTCTTGAGA[C/T]GTGCCACTGGGAAATTTGATTTACTTCTTCCATAA Y 2 1 2 1 201000 r 74 goat snp58204-scaffold942-1526730 21 49991204 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443968 Affx-122927002 AX-123314305 21 48126366 CTATAGTCTTTTTTTCCCGCTATATGTCAAAGTTT[A/C]TAATGAGGGGAGTTGCCTAATATTTTGTAATGCTG M 2 1 2 1 201000 f 74 goat snp58205-scaffold942-1569287 21 50033284 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413257 Affx-122950227 AX-123283606 21 48166693 TTACAACATAAGCTTATACTCATCCATTGATTGGT[A/C]GTTAGTTGTAGGAGCAAGGCCTATTCACCATGATA M 2 1 2 1 101000 r 74 goat snp58206-scaffold942-1609614 21 50074590 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767177 Affx-122961199 AX-385254460 21 48261705 CTGGCCTTGAAGAGTAGAAGATTGGTAGCTTTAGG[G/T]ACTTGATCTAGTCCTGTACATCATGCTTGTGCAAG K 2 1 2 1 101000 f 74 goat snp58208-scaffold942-1704626 21 50169977 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272091 Affx-1111833224 AX-508408074 21 48307956 GGAAAATACTCTGATGCTGGGAGGGATTGAGGGCA[A/G]GAGGAGAAGGGGATGACAGAAGATGAGATGGCTGG R 2 1 2 1 103000 f 74 goat 21_48307956_AF-PAKI 21 48307956 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320771667 Affx-122951353 AX-385258825 21 48349135 TGATATGAACCAGACATTTCCCTTTCAGTTCTACT[A/G]TAACTGTAATTGTTTATCACCAGTAGAACATCTGA R 2 1 2 1 101000 f 74 goat snp58210-scaffold942-1792056 21 50256248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800341 Affx-122927611 AX-385287264 21 48411336 AATTTCAAAGAATACTGCTCCTCTATAGTGAGGAC[C/T]ACTGTTTCAGCATCTGAGAATAACCTGTCTTGTTA Y 2 1 2 1 201000 f 74 goat snp58211-scaffold942-1854257 21 50318522 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376771 Affx-122977964 AX-123247130 21 48447543 CCTAGTGAAGGGTGACGTTTGTTAAGCAGTGTATA[C/T]GCTCCATAAGATCGATTGAGAAGGAGGTGAAATCA Y 2 1 2 1 101000 f 74 goat snp58212-scaffold942-1890464 21 50355513 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441626 Affx-122928640 AX-123311963 21 48499071 TACACATATTCACACCCACATACATGAATGTAACC[A/G]TACACATACATTACCCCCCAGCATTTCCATTTGAG R 2 1 2 1 101000 r 74 goat snp58213-scaffold942-1941992 21 50407631 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798867 Affx-122956546 AX-385285797 21 48543631 GGTGCAGATTGATGACAGAATTAACATCCCTGGGG[C/T]AGTCTTTGACCAAAGGAAGAAGAGGGTCAGACAAT Y 2 1 2 1 101000 r 74 goat snp58214-scaffold942-1986552 21 50452262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418890 Affx-122946105 AX-123289238 21 48601925 CTCTACTCCTGCTAGCATGCTCTGTAGTTTGCCTT[A/G]CTACCTAAAGGCAAAAGAAGGCAAGTAAAATACGT R 2 1 2 1 101000 f 74 goat snp18605-scaffold188-632282 21 50510498 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778815 Affx-122948337 AX-385265924 21 48658113 AACTGGTAGTAGTGAGCTAATAAGACAACCAACAG[C/T]AGAGTAGTTCAGAAGCAATGTGCAGAGCTTCCAAG Y 2 1 2 1 101000 r 74 goat snp18604-scaffold188-576094 21 50567652 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384067 Affx-122972866 AX-123254425 21 48699123 AACAAAAGAGGGACAGTAACAGAAGGATCACGTTT[A/G]TTTTTTTTTCTTTTTTCTTTTGTCTGGATTAGCAC R 2 1 2 1 103000 f 74 goat snp18603-scaffold188-535084 21 50608813 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404967 Affx-122956411 AX-123275319 21 48730063 CTGGGAGTCCTGATCACTGCTGAGCCAACTTTCTA[G/T]ACGCACCACCAGCTCCCCACTTTCTGAGGATGAGA K 2 1 2 1 201000 f 74 goat snp18602-scaffold188-504144 21 50640124 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799050 Affx-122935399 AX-385285980 21 48767205 GTCTTTGTTAAAGTTTGATAATGAAATAACAATAA[C/T]GACCAAAATGTAAGCAGAGGTTTATTGAGTGCCAG Y 2 1 2 1 101000 r 74 goat snp18601-scaffold188-467002 21 50678241 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420671 Affx-122944813 AX-123291018 21 48802791 TGGTATTGTGAGGAGCTTTTGATTCTTTTCCCTGA[C/T]ATAAAGTTCTTTTAACTCAAGAGCAGGAAATGATG Y 2 1 2 1 201000 r 74 goat snp18600-scaffold188-431416 21 50713613 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382489 Affx-122973823 AX-123252847 21 48862797 CCCAGTCACCCAGCATTAAACACTAACACTTGTGT[C/T]CCAGAGCCCTTCAGCCCTTCCCTCACAAGCTTTAT Y 2 1 2 1 202000 f 74 goat snp18599-scaffold188-371410 21 50773286 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422937 Affx-122943031 AX-123293283 21 48904011 TGTAAGTGTGGTCCCCATACCAGCACCATTTCATC[A/G]CCTGGAAGTTTATTTGAAAAGCAGAATTTTTTAGG R 2 1 2 1 101000 r 74 goat snp18598-scaffold188-330196 21 50818260 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381246 Affx-122974497 AX-123251604 21 48952606 TAAAGAGGCAGGTAGCACTGTTATTTGATGGTTTC[C/T]GAGGCCCAGATATAAGTCATTTGCACAAGGCCATG Y 2 1 2 1 101000 r 74 goat snp18597-scaffold188-281601 21 50867634 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410146 Affx-122952800 AX-123280496 21 48982066 AATAATCATAACAACAACCAGTCAATGGGAGTAAA[C/T]AGCAGTACAGAGGGCAATGATGATCAAAGAAATAG Y 2 1 2 1 201000 f 74 goat snp18596-scaffold188-252141 21 50897610 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396594 Affx-122962902 AX-123266949 21 49019844 GGAAAGAAGTAGAGAAGCCAGGCCACAGTAAACCA[C/T]GATGAGAAATCAATAGATGACATGAAAAACAGTGA Y 2 1 2 1 101000 f 74 goat snp18595-scaffold188-214363 21 50936414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420411 Affx-122944918 AX-123290758 21 49049768 CTCAGAGTCTGCTCCTACAAATCAAAAATCATAAT[A/G]CCAACTAATTAAATCATCAGCAAAGAATTCTGTCT R 2 1 2 1 101000 f 74 goat snp18594-scaffold188-184439 21 50966648 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419618 Affx-122945983 AX-123289966 21 49103666 TTCATCATTTCCTAGGAGTAATAGTAGTCTAATCA[C/T]GAGTGAAATTATATGAAAAGGTAAAAATGTATATT Y 2 1 2 1 101000 f 74 goat snp18593-scaffold188-130541 21 51020950 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406329 Affx-122955450 AX-123276681 21 49159165 GTTCCCAATGACTCCATCTTGGATATCATAACCAT[A/G]TATACTTTATGAAAAAGAATAAACCTTCTTACTGT R 2 1 2 1 101000 f 74 goat snp18592-scaffold188-75042 21 51076966 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782353 Affx-122942794 AX-385269429 21 49221199 AATTTTTAAATGACTCTTCCTTACAGATCATTTAG[A/G]TCTGAGTCTATAAAACTGGCAGGTACTGAATGGTT R 2 1 2 1 101000 r 74 goat snp18591-scaffold188-13008 21 51138248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440464 Affx-122929387 AX-123310801 21 49238755 TCTTTCACTGTAGTCTCTAACCTGAAGTCTTACAT[A/G]TCATGTAATCAAGGAAGTGACATCCCTATATCCCC R 2 1 2 1 101000 r 74 goat snp20930-scaffold2051-4449 21 51452209 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423540 Affx-122942435 AX-123293886 21 49270247 TGCTAATCAGAATTCACTCTTACCTACTATGATGG[C/T]ATGGTTTGGTTGATTGAATATTCTATTCTCTGTGG Y 2 1 2 1 101000 r 74 goat snp20931-scaffold2051-35941 21 51482793 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401150 Affx-122959372 AX-123271503 21 49313198 TAGCATTTTCTATCAGACAAATTATCTGATGTGTG[C/T]TCACTAGATGATTCCTGATTGACTGGTAGAAGATT Y 2 1 2 1 201000 f 74 goat snp20932-scaffold2051-78892 21 51525997 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405703 Affx-122956540 AX-123276055 21 49359540 TAAATTTCATTCCATAAATTTCTTCCTTTCTACTT[A/G]TGCACATCAGCTTATATGTTTTCTACAATTTTCTG R 2 1 2 1 101000 r 74 goat snp28477-scaffold3034-19496 21 51578120 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414100 Affx-122949741 AX-123284449 21 49397444 TTGAAACATGCAAGTAACTTGTGAGAATAACAGCC[A/G]TTTTTACTCTTTGTAAAAGGATAGTCAATACTGGA R 2 1 2 1 102000 f 74 goat snp28478-scaffold3034-57400 21 51616631 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773478 Affx-122956175 AX-385260620 21 49426232 ATAGACCTGGGTCTAAGTCATAGCACTACTACATG[C/T]ATTTGTGCTATTCTTGGAAGTGAGTCACCTACTCT Y 2 1 2 1 201000 r 74 goat snp28479-scaffold3034-86188 21 51645631 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801938 Affx-122929763 AX-385288843 21 49466852 AGACAATTAAATAGCTATATTCTAAATGTATGTGT[A/G]TGTGTGTACTTGTTAGATACATATTATGATATATT R 2 1 2 1 101000 f 74 goat snp14984-scaffold1600-8027 21 51689960 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770810 Affx-122954004 AX-385257974 21 49499329 GGCTTACTTGCTTTTCTTTAAGACATTTGTCTGCA[G/T]AAATGAACTTTCTCCCTATTAAAATAGCCTGAATA K 2 1 2 1 101000 f 74 goat snp14985-scaffold1600-40504 21 51722424 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798620 Affx-122934221 AX-385285553 21 49547423 CCTTATTTGATATAATTTAAGGAGTTTGTTTCTTA[C/T]ACTCAAATATGGCTCATTAAGTTATGCAAGGAGTC Y 2 1 2 1 101000 r 74 goat snp14986-scaffold1600-88598 21 51771340 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803204 Affx-122975462 AX-385290063 21 49577692 TTTGCAAAACTTATTTTTGAGTGCATGTACAAATG[A/C]TTCATAGCTATAATTATGTTTGATGATTATTTTGT M 2 1 2 1 201000 r 74 goat snp14987-scaffold1600-118867 21 51801839 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380996 Affx-122974671 AX-123251354 21 49626253 GGGAAAAGTGACAAAGAAGAAAGGAAATAAATAAA[G/T]CAACTGAAGAAAGTTGACACAAATGTGGTACCACA K 2 1 2 1 303000 r 74 goat snp14988-scaffold1600-167428 21 51850016 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784209 Affx-122926631 AX-385271260 21 49676573 TAATATACCTTTTTGTATCCAGATTACAAAAGGTC[C/T]ATATTATTATATTATCTAGATCAATAAGGCATTTT Y 2 1 2 1 201000 r 74 goat snp14989-scaffold1600-217748 21 51904908 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796778 Affx-122934209 AX-385283721 21 49730224 ACACATCACATACTGTTTATTTGGATTCCTACAGA[C/T]AAAAATCATGTGCATTATCATCCACGATACAACCT Y 2 1 2 1 101000 f 74 goat snp14990-scaffold1600-271399 21 51959567 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800842 Affx-122922173 AX-385287757 21 49777115 GTCATAAATAAAGTAGAGCAGGCATTTGAATGAAT[A/G]TAACTGTAATTCCAAATAACATGCCTTTTCCAACA R 2 1 2 1 101000 f 74 goat snp17003-scaffold1775-29222 21 52124152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394096 Affx-122964948 AX-123264451 21 49857424 CTGGAAGGAAGAAATTAACACATCCCCTCCAGAGG[C/T]TGACTGGAACAAAAACCACTTGAATTACTCCCTCC Y 2 1 2 1 201000 r 74 goat snp17005-scaffold1775-109531 21 52205914 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397933 Affx-122961926 AX-123268288 21 49888684 TTTCTACTGAAAATTTAAAAGTGATTGCTATAAGG[G/T]TAAAAATTGCTAACAAATTGATTTTCTTTTATTTA K 2 1 2 1 101000 f 74 goat snp17006-scaffold1775-140791 21 52237298 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415293 Affx-122948826 AX-123285642 21 49921046 ACCCAGGGATCCAACCCAGTTCTCATTGGCAGGCG[G/T]GTCCTTTACTACTAGCTCCACCTGAGCAAGAGGGA K 2 1 2 1 102000 r 74 goat snp17007-scaffold1775-173153 21 52270169 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394751 Affx-122964852 AX-123265106 21 49970014 TTTCTAAAGATGTGAAGATGTAAAGATGAAGACAT[A/G]GCATTTGGTCCCATCACTTCATGACAAATAGATGA R 2 1 2 1 201000 f 74 goat snp17008-scaffold1775-222121 21 52318881 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448047 Affx-122923702 AX-123318383 21 50016155 TGTTGCCCCCCAATTTTTTCTCTCTCAGAGCTTAT[A/G]TCATTCTTTAATAGTAGGGAAAATAGTGTCCACAA R 2 1 2 1 201000 r 74 goat snp17009-scaffold1775-268262 21 52365872 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378740 Affx-122977031 AX-123249099 21 50051819 CCCACTTTACCCCTCTTTTGCACATCCAGTGCATC[A/G]CAGTCCTGTCATTATTTGTGATAATTGGTTTTAGC R 2 1 2 1 201000 r 74 goat snp17010-scaffold1775-303926 21 52402012 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794247 Affx-122973851 AX-385281213 21 50091234 TAAATTCTTTCTTGTATATTTCAGTCTTTATTATA[C/T]ATGATTTGAGGCCACAGGTTTAGTTGTAACTACTG Y 2 1 2 1 201000 f 74 goat snp17011-scaffold1775-343341 21 52441245 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775967 Affx-122971070 AX-385263098 21 50123395 CTCTTCTTAACTTGATATCTTAATATCAAGGGCCA[C/T]CTGCTACTGCAGATGCCAAGTTATGGGCTACTGGC Y 2 1 2 1 101000 r 74 goat snp17012-scaffold1775-375502 21 52471736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385079 Affx-122971808 AX-123255437 21 50171110 GCACTTTCTATAAGCAAAGATGGAATTATGTTATT[C/T]ATGTCAGAATGGTCTAATGTGAAAACTTACAGTCT Y 2 1 2 1 101000 r 74 goat snp17013-scaffold1775-423217 21 52520704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414765 Affx-122949246 AX-123285114 21 50239734 AACCCACATTAAAAGATAGAGTAATCCCAGAACAA[C/T]AAGAGTAGAGAATTGGAGAAAGAGATGAAAAGGTT Y 2 1 2 1 101000 f 74 goat snp15691-scaffold165-4247195 21 52764313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399965 Affx-122960832 AX-123270320 21 50273631 CTTACTATCCTCAAAATAGACCACATGGTCCAAGA[C/T]GTTGTTTGTCCTAGAATTCGAGTTCCAAGGCTACA Y 2 1 2 1 101000 r 74 goat snp15690-scaffold165-4213298 21 52798984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432518 Affx-122935566 AX-123302859 21 50324845 ATCATACTTTTTTAGTCTCAGATTTATGTTTTTCT[A/G]CAAAAGTGTATATCTTCATAACAAGTTACTCTTTA R 2 1 2 1 101000 r 74 goat snp15689-scaffold165-4162084 NW_017195157.1 29618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446034 Affx-122925848 AX-123316371 21 50381469 AGGGAACAACAGATGCAAAGGCTTTGAACCAGCAA[C/T]GAAATACTGCAAGGAATCCACTGTGATGGGAATAG Y 2 1 2 1 101000 f 74 goat snp15688-scaffold165-4105460 21 52902743 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783216 Affx-122933239 AX-385270282 21 50410127 AACAGAAAAAAAAGACAACTGACTTGGTCAAATAC[A/C]TCTTGAAAGATGTATTTAAAAAGCCACTTGAGTGG M 2 1 2 1 201000 r 74 goat snp15687-scaffold165-4076802 21 52930723 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771312 Affx-122954782 AX-385258470 21 50446297 TGTGTGCATGGGTACACATTTCTCTTAAGGAATCT[A/G]CTGAATAGTGAGTATCTTGGAAGGATCTCAGGAAA R 2 1 2 1 101000 f 74 goat snp15686-scaffold165-4040632 21 52967162 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451939 Affx-122920969 AX-123322272 21 50481977 GATTGTGACTCAGAGCAACAAAATGGACCAGCAGA[C/T]GCAAATCCATTGATTTTTGGCAGCTGGAAGTTGAA Y 2 1 2 1 101000 f 74 goat snp15685-scaffold165-4004952 21 53003168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376555 Affx-122977981 AX-123246914 21 50514650 ACATTCAAATTGCAAAAACAAAAAACAAAAAACAG[C/T]GAAAATCTTGGCAGCAGCCAGAAAGGGGAAAAAAT Y 2 1 2 1 103000 r 74 goat snp15684-scaffold165-3972279 21 53033967 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378971 Affx-122976407 AX-123249330 21 50543243 TTCGTGAAGTCAAAATATTGAAATAGATACATGAA[C/T]GCCTCTGTCCCAAATTTTACATTTTATTTGCGATC Y 2 1 2 1 101000 r 74 goat snp15683-scaffold165-3943686 21 53062509 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378497 Affx-122976655 AX-123248856 21 50580043 AAGTGTTCGGTGAGATCTTTAGGAAAGACAAAAAC[A/G]TCAATGGTGCTGGGGTTGAAAAATCTTGGTCTGTT R 2 1 2 1 201000 f 74 goat snp15682-scaffold165-3906886 21 53100046 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436347 Affx-122933071 AX-123306686 21 50618549 GAAATGCATATCCTCCCTTTCTGTGATGTTTTCTC[A/G]TATCATTTAAAGAATTCTTACCTTTCATCTTTTTT R 2 1 2 1 202000 r 74 goat snp15681-scaffold165-3868380 21 53139077 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785124 Affx-122923235 AX-385272170 21 50689076 CAGCCTTTTTTATTCAGTTCACAATTCTTTAACCG[C/T]AAACTTGCAAACCATTAGAAGTAGTATAGTCAATT Y 2 1 2 1 201000 r 74 goat snp15680-scaffold165-3797853 21 53209425 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406551 Affx-122955111 AX-123276903 21 50728500 TGACTTTGCAATTGGCCAGTTGGAAATATGAATAT[A/G]TTGAAATATGATTCCAGATATATGTCTATAGACCA R 2 1 2 1 101000 f 74 goat snp15679-scaffold165-3758429 21 53248657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445012 Affx-122926636 AX-123315349 21 50779953 TTATAATGGTCTATAAGAATGTGAATTGTGGCATT[A/C]GTACCTGGGTGGTTTTAAAAGGTAAAAAAATCAAA M 2 1 2 1 101000 f 74 goat snp15678-scaffold165-3706976 NW_017189601.1 35465 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376545 Affx-122977989 AX-123246904 21 50819201 AAGTAGATTTTGTGAGATTATCTTTCATTGTCTTC[A/G]GATCTAGTACAAAAATCCTAAACTTCTTTGATCAT R 2 1 2 1 201000 r 74 goat snp15677-scaffold165-3667728 21 53310704 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271927 Affx-1111833225 AX-519545706 21 50845814 AGAATATTCTCCACCTGCAAATTAAGACCAAAAGT[A/G]AGATATGATGTGAGGTGTTTTTGTTAAAGGAGGAA R 2 1 2 1 101000 r 74 goat 21_50845814_AF-PAKI 21 50845814 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320770688 Affx-122965926 AX-385257852 21 50866904 AGAACAGTTAATTTCCATTCCAGGGAAGAGCAGCT[A/C]TATGATTCTGGGCAACACCTGTTAACAGAAATAGG M 2 1 2 1 101000 f 74 goat snp15676-scaffold165-3620025 21 53356853 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386763 Affx-122970122 AX-123257121 21 50895923 GGAACCTTTGAGATGAAGTCCTTGAGTGTCCTGTT[A/G]CAGAGAGAACTCACAGAGTGCCAGGAGGAGGAACA R 2 1 2 1 101000 f 74 goat snp15675-scaffold165-3591006 21 53384997 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392904 Affx-122965725 AX-123263261 21 50978702 TAATGCTTCTCTCACTGATATTCTCTGAGACCTTG[C/T]ATCACTATGATTCCATTGCACTAGCCTGGAAAACA Y 2 1 2 1 101000 r 74 goat snp15673-scaffold165-3508227 21 53467600 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770649 Affx-122964049 AX-385257813 21 51019397 ATCCATCTTCTAACATATTGTAAAGGAAATTGTCA[C/T]GATTACCCTTGTCTTGTCAAAAGCATGTCAATGGA Y 2 1 2 1 101000 r 74 goat snp15672-scaffold165-3467532 21 53508666 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377518 Affx-122977479 AX-123247877 21 51058071 TCATAAATTTCAGAAGGGTCAGAAAAGATCCCATC[A/G]TCTGTCCTTCAGTATCAGTTGTTTGGTGGTCGAGC R 2 1 2 1 101000 r 74 goat snp15671-scaffold165-3428858 21 53548663 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427923 Affx-122939222 AX-123298266 21 51103353 GTCCCTCAGAGCATCATGTGGCATTCTGCAAATAA[G/T]GAATTTTAAATGAAAAGTGGTCAGCTGTCTCAGTG K 2 1 2 1 102000 f 74 goat snp15670-scaffold165-3383576 21 53596158 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410041 Affx-122953239 AX-123280391 21 51132425 GCCAGAACATCATTTAAAGCGAAGGAGGAAAGGAA[C/T]AGGCCAAACTGACTCCATCTTGAGAAGGAAACTCC Y 2 1 2 1 201000 f 74 goat snp15669-scaffold165-3354504 21 53625948 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451621 Affx-122921623 AX-123321954 21 51208019 GAAACCCAACCGGAGACAGTCATTTTAGTCTCTCC[A/G]TAGAGCTCCTCTCTAAGCAATCCTGTGACTTCAAT R 2 1 2 1 101000 r 74 goat snp15667-scaffold165-3278910 21 53702688 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389073 Affx-122968596 AX-123259431 21 51255432 TTCAAAAACATCAACTCCAACTAAAACAAAGCAGC[A/G]TTACCAGAGTTTACTTCATATTCCTCTGCTAGACA R 2 1 2 1 101000 r 74 goat snp15666-scaffold165-3231497 21 53748490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415743 Affx-122948497 AX-123286092 21 51294842 GTGTGCTGGTGTTTCTCCACTCGACTATTAGACCT[C/T]TTCAAAGACTCTCTCATCCATGAGTAACTGTCAAA Y 2 1 2 1 101000 f 74 goat snp15665-scaffold165-3192087 21 53788282 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788827 Affx-122939537 AX-385275842 21 51327121 ACTATTGAATGGATGTTTGTTAAATAAACCACAAC[C/T]AGAACCATACCATTATACCATTTGTAATTTGGTGT Y 2 1 2 1 101000 f 74 goat snp15664-scaffold165-3159808 21 53822488 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441331 Affx-122929432 AX-123311668 21 51369433 GAACAAGGAACTAAATCTTTATTTAGAGAGCTTTT[A/G]CATGACTGCTTTTCAAATGGATTCTCAATATAAAC R 2 1 2 1 101000 r 74 goat snp15663-scaffold165-3117496 21 53879893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443858 Affx-122927519 AX-123314195 21 51424350 CTCCTAAATGATTATCTTTTCAGTGTAGGATAATA[C/T]GTAAACTTTTAGGAAATATTTCCCACTTAAAAATT Y 2 1 2 1 101000 f 74 goat snp15662-scaffold165-3062579 21 53935974 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414808 Affx-122949214 AX-123285157 21 51461952 GGATGAAGACAGGAAGATTAGTTAGGAGACAGTTG[C/T]AATTATGCATACAAGATATAATGGAAGCTTAGATA Y 2 1 2 1 101000 f 74 goat snp15661-scaffold165-3024977 21 53979134 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405585 Affx-122955939 AX-123275937 21 51498803 ATCATCTGGGAAAAACTGTCTGAAAAGGGAAGATA[C/T]AACATTAGCTGGTGACAAACACCATCATCCAAGAT Y 2 1 2 1 101000 f 74 goat snp15660-scaffold165-2988126 21 54016388 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425197 Affx-122941034 AX-123295543 21 51530645 TAGGGATGGGGGTACTTGTGTGGTGTGAACATAAA[C/T]GGGTAGCTTGAAGGAGTTCTTTGGCAGTGGTAGAA Y 2 1 2 1 101000 f 74 goat snp15659-scaffold165-2956284 21 54048290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385301 Affx-122971683 AX-123255659 21 51572686 CTTGAGATCAGATTCTGTTCGTTTGGAGTGTCATC[A/G]TCAGGTTGTGTACTGAATGTGTCCTCAGTCCTAAT R 2 1 2 1 101000 f 74 goat snp15658-scaffold165-2914243 21 54093287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403096 Affx-122958498 AX-123273449 21 51615483 ATCTCCATTGCAATTGGTATGTCATGTTATGTGAG[C/T]ACATATCCTGCTATCCACCTTGACTTCCAGTGGAG Y 2 1 2 1 101000 f 74 goat snp15657-scaffold165-2871446 21 54136708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438593 Affx-122930945 AX-123308930 21 51678821 ATAAATGTCCGTTAATCTTGAATATGTTACTTTGC[A/G]TTAGAGTGTTGGTACTTGCATTTTTGGTACTGTAG R 2 1 2 1 101000 r 74 goat snp15656-scaffold165-2808108 21 54200151 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779732 Affx-122929768 AX-385266832 21 51724822 CTTTACACTGCTGTCAGAAATCTCAAGCCCATTCC[G/T]AATGTGAGCCTTTGCTCTCCTCATACCTCCCCTTA K 2 1 2 1 101000 f 74 goat snp15655-scaffold165-2762107 21 54246384 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436026 Affx-122932735 AX-123306365 21 51758481 GTGTTAATGGACTAGATGGAGAAATCTTTTTACAA[C/T]GTATATAGGTATTTAATCATCACATTGTACACTTT Y 2 1 2 1 101000 f 74 goat snp15654-scaffold165-2728448 21 54280005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399813 Affx-122960274 AX-123270168 21 51795289 CCAGTTTTTTGCTGGCTATACTAGATGGAGAAGGA[A/C]AATTCAGCTGTGAACAAAACAAAATCCCAAGGAGC M 2 1 2 1 201000 f 74 goat snp15653-scaffold165-2691640 21 54316775 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415290 Affx-122948828 AX-123285639 21 51899542 TGGCCAATGGTTTAAAAGGTACAGTGTTCATAAGC[A/G]TGCATTATATACTTGAAGCTTGTCATATATGTTGA R 2 1 2 1 101000 f 74 goat snp15651-scaffold165-2587387 21 54422525 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423281 Affx-122942654 AX-123293627 21 51932302 TAGCTTCCTTGCTTTTCCAAGAAATTTGTTAACTC[A/G]TATTATTTTTAAAATAGGGACAGCTCAGATTTGTA R 2 1 2 1 103000 f 74 goat snp15650-scaffold165-2554627 21 54455375 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418276 Affx-122947007 AX-123288624 21 51962562 AACAGAGAGAAATGTATTTGTGTGAAGAATAGAGT[A/G]GACAATGGTTCCCAGGACGTTCTATCTTTCAGCAT R 2 1 2 1 101000 r 74 goat snp15649-scaffold165-2524367 21 54485725 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788823 Affx-122942047 AX-385275838 21 51992531 TGACCACCCCTCTTTGGCATGTGCTCTTATTACCA[C/T]AAGTGTTATCCACCCTCCTGACTATAATCTTAGCA Y 2 1 2 1 202000 f 74 goat snp15648-scaffold165-2494398 21 54516095 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768950 Affx-122945116 AX-385256125 21 52027710 TAATTACACATATGTGCAGAAAAAGAAAGTGCAGA[C/T]AGGTTACACCAAAATATAACGACGAGTGTCTCAGT Y 2 1 2 1 201000 f 74 goat snp15647-scaffold165-2459219 21 54551029 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402941 Affx-122958178 AX-123273294 21 52086295 CTTCAATGCAAGAAGAACACAGTTGAAAACGAATG[C/T]AGATTGTAAAGATGAAAAAGACAACTCTGGGGAAG Y 2 1 2 1 201000 f 74 goat snp15646-scaffold165-2400634 21 54609827 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785838 Affx-122952425 AX-385272875 21 52123651 TGCAGTTTCTAGAGTGATCTATCATAAAGTCATAA[C/T]ATACAGAGGTGTGTTAACCTGTTGCCTAAAATTCT Y 2 1 2 1 101000 r 74 goat snp15645-scaffold165-2363278 21 54648138 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795968 Affx-122966238 AX-385282920 21 52171908 CTAATTTGCTAATGTCCTCTATTTCTGGACACTAG[A/C]TCAACTCTTTAGTTACAGTCTATTATTTGAAATAC M 2 1 2 1 101000 f 74 goat snp15644-scaffold165-2315021 21 54696675 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432012 Affx-122935924 AX-123302353 21 52208708 TTGTGCATTTATATCTTAGGCTTCTTATAAATTCC[C/T]TGTATTTTATGAAGATGATTCTTTTGTTATATTGT Y 2 1 2 1 101000 f 74 goat snp15643-scaffold165-2278221 21 54733837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376529 Affx-122978001 AX-123246888 21 52284471 GGTTTAGAATTTAAAAACCTGTGACCTTTGCAGCC[A/G]TGCCCTAGGTGATCATCCTCTCCGGCCCTACAACT R 2 1 2 1 101000 f 74 goat snp15641-scaffold165-2202458 21 54809696 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413106 Affx-122950387 AX-123283455 21 52313243 CCGCTCCACCTGCGTGCACAAAGCCGTTAGTGACA[C/T]GTTAGAGCTGTGCAAACCCTCCCTTAGCTGGACCC Y 2 1 2 1 101000 r 74 goat snp15640-scaffold165-2173686 21 54838541 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385077 Affx-122971810 AX-123255435 21 52376005 TTCTAGATTTTTCTATCCCAGTAAACCCAGTTTAC[A/G]TAACTTTCCCTTGCTGGTAATACTTTGCCTCTCTC R 2 1 2 1 101000 r 74 goat snp15639-scaffold165-2110924 21 54896182 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375597 Affx-122978725 AX-123245956 21 52450407 GACAAGTCACAATGGCTTCTCCATCTCCATTAATC[A/G]TCCTTTAGGCATTTTTCATGTCTTTGTTCTACTTT R 2 1 2 1 201000 f 74 goat snp15638-scaffold165-2036522 21 54970982 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406747 Affx-122955737 AX-123277098 21 52506765 CTAACGCACACACAGCGTTCCCTGTGGAATGCTCC[A/G]TGTGGAGAAGGCTGGGTTCTGACCTGGAGACACAC R 2 1 2 1 102000 r 74 goat snp15637-scaffold165-1980164 21 55027108 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392885 Affx-122965739 AX-123263242 21 52560556 CATATTCAAATTATTAAATGAAATAGTGAGTGTGT[A/G]CCCTCTGTTCTTATCTAAAACTTGAGTGAGTGTAG R 2 1 2 1 101000 r 74 goat snp15636-scaffold165-1926373 21 55080402 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418952 Affx-122946490 AX-123289300 21 52594565 CAAAAAATTCAGTTTCTCAGTTCCATTAGCCACAT[G/T]TCAAGTTGCATCAAGCCACAAAGTGGTTAGTGGTT K 2 1 2 1 101000 r 74 goat snp15635-scaffold165-1892364 21 55114301 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791784 Affx-122923447 AX-385278775 21 52651808 AATTAATAGAGCCAGTTATAGCAAGATTAGAACCT[A/G]TGTATCTCAGTTACTAATCCAAGGTTCTTTCTTTT R 2 1 2 1 101000 f 74 goat snp15634-scaffold165-1835121 21 55171674 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453784 Affx-122919584 AX-123324117 21 52689258 ACAGCAAAGGATTCAAAACTTCTAACCCTGATAGC[A/C]GGAAAAAACAGTGAAGCATTCAAGAGCAATGAAAT M 2 1 2 1 101000 f 74 goat snp15633-scaffold165-1797671 21 55209229 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796027 Affx-122958230 AX-385282979 21 52737033 TGTGACATACAGTCTCAGATGGCATGCTACGATAC[A/C]ATCACAGACAGACTTAGGTTATTTCAAGGATTTAT M 2 1 2 1 101000 f 74 goat snp15632-scaffold165-1749896 21 55257059 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437567 Affx-122931884 AX-123307905 21 52766904 CAAAGTATTGTTACATTTTATTTTATTAGAAAACT[A/G]TACTTAACCTTCATAGTTAGGCATGTTGCCCAGTT R 2 1 2 1 101000 r 74 goat snp15631-scaffold165-1720025 21 55287616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428662 Affx-122938651 AX-123299004 21 52820046 GTATACAGTCATGCATGTATATGCTGCCTGATCTC[A/G]AAGATCAGGCTTCGTACTTTCTTATGAGTACACAT R 2 1 2 1 101000 r 74 goat snp15630-scaffold165-1666883 21 55340665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418857 Affx-122946129 AX-123289205 21 52896690 TGGTTCTGACTGCAGGTAGCAGATTGACTGCAGGG[C/T]GGGCAAAGCTGGAAGCATGCAGATGAGGGAGGGTG Y 2 1 2 1 101000 f 74 goat snp15628-scaffold165-1590239 21 55418330 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412977 Affx-122951034 AX-123283326 21 52936823 AGAATCGATGTATCCCTTTATCTCCAAGCTGGGAA[G/T]CAATGACTCAGCTTTCTTCTTTAAACATTTCCCAG K 2 1 2 1 101000 f 74 goat snp15627-scaffold165-1550106 21 55459923 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380567 Affx-122975276 AX-123250925 21 52969325 TATTTAAGCTCAGTAGGACGACTGTTATTTCAAGC[A/G]CTGTCTAGGTTATACTGTCCTAAGGTTTACTCTTT R 2 1 2 1 101000 f 74 goat snp15626-scaffold165-1517604 21 55492988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450979 Affx-122921736 AX-123321313 21 53026302 TTCCAAGAGAGTAGTGTGGATTTCTGCACCCATAC[A/G]TGGTTCTGCCATCCCTGAGCTGTACCTGATTGAGA R 2 1 2 1 101000 f 74 goat snp15625-scaffold165-1460627 21 55549766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417528 Affx-122946934 AX-123287876 21 53081522 GTGTTCCCTGATGATATCTGGGCTTTGTGGTTTGC[A/G]CCTGGTGCATGGTGGGGGGACCCTTTCTCTGATCG R 2 1 2 1 101000 f 74 goat snp15624-scaffold165-1405407 21 55603199 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791914 Affx-122945390 AX-385278904 21 53118085 CACCTGTTACTGGAAAAGTTTACACACAGAGAAAC[A/G]TGTTTGCCTCGCCATGGGGAAAATGGGCCTTGTGC R 2 1 2 1 102000 r 74 goat snp15623-scaffold165-1368844 21 55640136 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277515 Affx-1111835888 AX-519551017 21 53144613 TAATAATTTACTTATTGCTGTTTGAAGCTAAAGTG[A/T]GACTTACATTAGAAAACTCTTACACACAATAAACT W 4 1 2 1 101000 r 74 goat Random2.2K-1951 21 53144613 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415063 Affx-122949476 AX-123285412 21 53152658 GGTTACAGGAAGTGTCGGGTGGGACCAGAGCATCC[A/G]TGAGTGACTATAAAGTTTCATTCGAGGTCAGGACG R 2 1 2 1 101000 r 74 goat snp15622-scaffold165-1334271 21 55674628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453916 Affx-122919905 AX-123324249 21 53199697 CCTTAGTGGTTCTAGTACCTCAGTCTAGTGGTAAC[A/G]TCTCCGCAATCTTTTGTGAATGGTCATTGATAATG R 2 1 2 1 101000 f 74 goat snp15621-scaffold165-1287232 21 55721628 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446925 Affx-122924689 AX-123317261 21 53258598 ACTGTAACACCTAAAGAGGAGGAAATGTGACCCCA[G/T]CATGGGGCTGAGTCTGGGGGAGGAACTGGTTTACA K 2 1 2 1 101000 f 74 goat snp15620-scaffold165-1228331 21 55781592 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438202 Affx-122931819 AX-123308540 21 53301532 ACTCAATATTATCACCTCCCTCTCCCAAAACAAAC[G/T]ATATCTGTGTCCTCTCTGAATACACATGATCCGTA K 2 1 2 1 101000 r 74 goat snp15619-scaffold165-1185397 21 55824373 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434825 Affx-122934799 AX-123305166 21 53333110 TGCAAGCAAAATTTAAATTCCTTCTTTTCTTTCTT[C/T]TAGCTTTCAAGGGTAGACTTCTGCGGTTTCGAAAG Y 2 1 2 1 101000 r 74 goat snp15618-scaffold165-1153819 21 55856592 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272096 Affx-1111833226 AX-519545855 21 53350312 ATCAGCGTCTTTTCTAATAAGTTGACTCTGCATCA[A/G]GAGGCCAAAGTATTGGCGCTTCAGCTTCAGCATCA R 2 1 2 1 103000 f 74 goat 21_53350312_AF-PAKI 21 53350312 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38424117 Affx-122942019 AX-123294463 21 53369391 GGTTGCTTAGCCTAATATTGACATTAGTTTGACAA[C/T]TGAAGAAATGAAGATCACTTGTTATTTTCACTTCT Y 2 1 2 1 101000 f 74 goat snp15617-scaffold165-1117538 21 55893333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790238 Affx-122978734 AX-385277242 21 53416874 TTAGGTATCATCTCAAAGAGGCATTCCTTCAATAG[C/T]ACATACCCCTTACCCCCATATTCTCTATCATAGCA Y 2 1 2 1 101000 r 74 goat snp15616-scaffold165-1070055 21 55940830 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772509 Affx-122973948 AX-385259660 21 53468576 CAGATGACTTACATCCTCTTAGATTATTCTTCTGG[A/G]TGAAGAATCAGATGATGTAAGCAAAAAGAAGGAAT R 2 1 2 1 101000 f 74 goat snp15615-scaffold165-1018353 21 55992484 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419183 Affx-122945719 AX-123289531 21 53501615 CAAGGATGTTTTTCAGGAATGGAAGGGCATGCCTC[A/G]CTGTCCTTCACAGACCCCATCCTGTCCCCTGAGTG R 2 1 2 1 103000 f 74 goat snp15614-scaffold165-985314 21 56025910 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445134 Affx-122926174 AX-123315471 21 53535134 ATGACATGGACAGTGACCTGGGAGGAAGTTAGAGA[A/G]ACTAACAGAGACCAGACCCCATGAGGATTTAGAGG R 2 1 2 1 201000 f 74 goat snp15613-scaffold165-951795 21 56059477 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410870 Affx-122952603 AX-123281220 21 53581417 GGTTATTATTACTATAATTGAATTATAGATGATAT[A/G]CAAAAATATATGTTTTTACGTGTACCACATAGTGA R 2 1 2 1 101000 r 74 goat snp15612-scaffold165-905512 21 56105219 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377688 Affx-122977418 AX-123248047 21 53620729 TGTCTCAGTCCACACGCAGATCCACTGCCATGGAC[A/G]GAAAGAATTTGGGCTCGAGGAGTTTAACGAGCACA R 2 1 2 1 101000 r 74 goat snp15611-scaffold165-866200 21 56144631 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448276 Affx-122924182 AX-123318612 21 53652455 AAGAGAAAGGCAGAAAATCTGGAAGGAAAACTTGT[A/G]TCATTACAGGTCGGTTGGAATAATTTACTCTTGTG R 2 1 2 1 201000 r 74 goat snp15610-scaffold165-834474 21 56176354 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801146 Affx-122962847 AX-385288060 21 53693407 GAATTCATTTTGTTTTTCCCACCAAATGTGCTCCC[A/G]TATTCTTTCTTTTAATGGTTTCACCATCTACCCGT R 2 1 2 1 303000 r 74 goat snp15609-scaffold165-793522 21 56217345 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422398 Affx-122943387 AX-123292744 21 53739709 TGCCGCGATTCATGGGGTTGCAAAGAGTCGAACAC[G/T]AGACTGAACTGAACTGTGTTTAACACTGATTGAGT K 2 1 2 1 103000 r 74 goat snp15608-scaffold165-747220 21 56263576 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416462 Affx-122947813 AX-123286810 21 53828147 CCTTCAGGGGCTGCTCTCTCACTCCTTAGCTCAGC[A/G]CCAGGAAGGCCTCCGGGTATGCACTTAGCCCTCTT R 2 1 2 1 101000 f 74 goat snp15606-scaffold165-658782 21 56347623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450621 Affx-122922000 AX-123320955 21 53887496 AGTTGAGGTGTGCGTGAGCTTTAGTTGTGGCATTC[A/G]GTCTCTTAGTTGCAGCATGTGGGATCTAATTCTCT R 2 1 2 1 101000 f 74 goat snp15605-scaffold165-599433 21 56407366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445499 Affx-122925190 AX-123315836 21 53926465 TGCAAAGCAGACATTTTGGAGCAAGTTCACAATGA[A/C]TGTGGATTAAAACAGATATTCTCTGAGCAAAGAAA M 2 1 2 1 101000 f 74 goat snp15604-scaffold165-560464 21 56446353 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428141 Affx-122939055 AX-123298484 21 53972419 GAGGGGGGCAAGCCGGAATCACACTGAAGCGCAAA[C/T]AGCAAGAGAGAAACACTCCCGAGATAGGAAGACAT Y 2 1 2 1 201000 f 74 goat snp15603-scaffold165-514510 21 56492316 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451468 Affx-122921142 AX-123321801 21 54015578 GAGTACGAAGAAGGAAGACCGTGGGTCCTAGGATC[A/G]AGGTTATCCATCACCCTGATAAATGACTCATGGAG R 2 1 2 1 101000 r 74 goat snp15602-scaffold165-471351 21 56535586 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439572 Affx-122930082 AX-123309909 21 54073855 GGTGTTGCACATCATAGATGCTTAACTAAACAGTC[A/G]CTGAATGACAGACAGTTGTAATTTAGACACACAAC R 2 1 2 1 101000 f 74 goat snp15601-scaffold165-413074 21 56594266 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383433 Affx-122973473 AX-123253791 21 54112247 TTTGCCTCTGTGTGGACAGGAGGTAAGACAGACAC[A/C]CAGGCGCGTGACAAAGCTGAATCCTGTTGCTTGGC M 2 1 2 1 202000 r 74 goat snp15600-scaffold165-374682 21 56632610 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450025 Affx-122922842 AX-123320360 21 54145916 GTTCGTAAATCTTTTTAATATGTATTTGAGAGCTA[C/T]GAAGCAGTCAAAATTGTTTAATGTTTCTATCTATT Y 2 1 2 1 201000 r 74 goat snp15599-scaffold165-341013 21 56666367 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391333 Affx-122967311 AX-123261690 21 54175101 AAACTTTATTATTGCAAAATCACTCAGTATCCTTC[A/G]GGTCAGCCAGGAACACAGTGTCTGCGGTGACTGGG R 2 1 2 1 101000 f 74 goat snp15598-scaffold165-311828 21 56695383 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426656 Affx-122939934 AX-123297002 21 54208144 AGATCGACTTCGCTGCACGTGGGTGAGTGGACCCA[C/T]GTTCTGCTGAGTAACAAGCACTCCAAAAGACCTGT Y 2 1 2 1 101000 r 74 goat snp15597-scaffold165-278785 21 56728750 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386576 Affx-122970700 AX-123256934 21 54239144 CAGCTAAAGGGCCTGTGACTCTGAAGTCTTCCCCT[A/G]TCATAGCCACAGCCGCCCTGGGGCTGTGCCTCCAA R 2 1 2 1 102000 f 74 goat snp15596-scaffold165-247785 21 56759669 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406581 Affx-122956268 AX-123276933 21 54276599 TTGATGCCTCCTGGAGGATTCATTCCAGACCAGGG[G/T]CTCTGCTAAGCTCCTTGCAAAGGTCTGATCCTTGG K 2 1 2 1 201000 r 74 goat snp15595-scaffold165-210330 21 56797232 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390369 Affx-122967672 AX-123260726 21 54348217 GTGTTACCACAGTTCAGTTTTAGGACACGCCCATC[A/G]TTCTAGAAAGTTCCCCGGTGCCTGTACTCGTCCCA R 2 1 2 1 101000 f 74 goat snp15594-scaffold165-138712 21 56867544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418597 Affx-122946361 AX-123288945 21 54392463 TCTTTCTTCCTCCCTACCCTCACGTCACCACCCAG[C/T]GAGGATACGGTGAGCTGGTTGCAAGCCAGAAGGAA Y 2 1 2 1 101000 r 74 goat snp15593-scaffold165-94466 21 56911998 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398544 Affx-122961527 AX-123268899 21 54459031 TCTGGCGTGTAAGTCAACAGAACAATCATGACCCA[G/T]AGGTGAAGCAAAGCCTAAAGAAAGAAAAAACAACC K 2 1 2 1 101000 f 74 goat snp15592-scaffold165-27898 21 56979723 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427408 Affx-122940068 AX-123297751 21 54514196 CTGAGACAATATTTCCTCCTAGATTTGATGGACTC[C/T]AAAGTCCAAGCTCTTCACCAGTTTGGAATTGAACT Y 2 1 2 1 101000 f 74 goat snp12088-scaffold1446-1104756 21 57030759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428044 Affx-122939132 AX-123298387 21 54560021 ATGCTGGAATTGCTGTCTCTGCCTGGAGCTTCTAA[C/T]TCTGGCTCCTTCCCATCTTTGCGTTTCAGACCGCG Y 2 1 2 1 102000 r 74 goat snp12087-scaffold1446-1058931 21 57076401 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426963 Affx-122940404 AX-123297308 21 54608000 TGAACAGTGGCGATCACCTCTAAGACCCCAGCTCC[A/G]TTCTCCTCTGGCCCCTGTGGCTCTGAAATGATTCA R 2 1 2 1 101000 r 74 goat snp12086-scaffold1446-1010952 21 57123940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393387 Affx-122965902 AX-123263743 21 54642125 CTCAGGCAAGCCCTGGGGGTTTCTTTTTGTACTTC[C/T]ACCAGGATAGATGGGACCCCCACCCAGAGTAAGGA Y 2 1 2 1 101000 f 74 goat snp12085-scaffold1446-976827 21 57158094 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406462 Affx-122955181 AX-123276814 21 54673664 ACCTCCTGCTGGGAGGGACTGGGTCAAGGTCAGAG[C/T]CAGGCTTTGGCTCCCTACCCTTAGTCGCAGACCCA Y 2 1 2 1 101000 r 74 goat snp12084-scaffold1446-945288 21 57189593 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791958 Affx-122929439 AX-385278947 21 54712669 ACTCTCTATTATGTAATTTAGTTGAAAGCTTTTAA[C/T]GAGTCTTATCAAGACTTTAGATCTAACTTCTGGTT Y 2 1 2 1 101000 r 74 goat snp12083-scaffold1446-906283 21 57228599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428462 Affx-122938799 AX-123298805 21 54753707 AATACTGGAGTGGGTTGCCGTTTCCTTCTCCAGTT[A/G]TATGATCCCTTATAACTCTAAAACTGTGTGACTCA R 2 1 2 1 303000 r 74 goat snp12082-scaffold1446-865245 21 57269638 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421868 Affx-122944279 AX-123292215 21 54788196 AAGGGCAAGAAATTATGAGGCCAGAACAGATACTA[C/T]GAATTACTACCATTTAAAAAATGAACACATATAAC Y 2 1 2 1 101000 f 74 goat snp12081-scaffold1446-830756 21 57304032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378973 Affx-122976405 AX-123249332 21 54849382 TAGACAGTGTGTTCAGTAACTCATCGATTAACCAT[A/G]TTTTCATCTACTACCACTCCTTTCCCCAAATGCGT R 2 1 2 1 101000 r 74 goat snp12080-scaffold1446-769570 21 57366397 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442210 Affx-122928786 AX-123312547 21 54898056 GGCGCACATGGGCATAAGTTTCTCTATATAACCAA[C/T]AGTGGATTTTTGCTGGATGCAGGACAAGCCAATTT Y 2 1 2 1 101000 f 74 goat snp12079-scaffold1446-720896 21 57415217 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386836 Affx-122970088 AX-123257194 21 54942572 GGGCAACCAGGCCAGAGCACTGTGGTCCAACACAG[A/C]GTGTTGAAGGCTGTCATCACAAAGAGCCCCCCACC M 2 1 2 1 102000 r 74 goat snp12078-scaffold1446-676380 21 57459790 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402478 Affx-122958595 AX-123272831 21 54978656 TCATGGATCACCTCATTTAATCTTCACAACAACTA[C/T]GACTATCCCCATTTTATGAATAATGCAGTTGAGGT Y 2 1 2 1 201000 r 74 goat snp12077-scaffold1446-640296 21 57496699 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393121 Affx-122965565 AX-123263478 21 55026340 GCTTTCATAATTTGTGATAAAGGAAAGTGTTTCCC[A/G]TTGAGAACCCTGACCTCAAAGACAAAAGGAGAATT R 2 1 2 1 101000 f 74 goat snp12076-scaffold1446-592612 21 57544682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375721 Affx-122978632 AX-123246080 21 55108713 AAGGTTATCCAGGTGAGAAAGAGGAAAGTGAAGGG[C/T]AGAAATATGACTGAAAATAGAAAATTGTATAGGAT Y 2 1 2 1 101000 f 74 goat snp12075-scaffold1446-510239 21 57627117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425622 Affx-122940905 AX-123295968 21 55141370 CAAACACATGCAGTTAGACCATGGGAATCTTTGAA[C/T]GTCAGTTTAAGGACTCTGAACTTTATTCTCTAGGC Y 2 1 2 1 101000 f 74 goat snp12074-scaffold1446-477582 21 57660195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388767 Affx-122968939 AX-123259125 21 55179468 TACTGGCTTGAGGAAGTAGTACGTGTGCAGAACGT[A/G]GTAACAAAGTTTAGAAAATGCAGGGTGATCATGTT R 2 1 2 1 101000 f 74 goat snp12073-scaffold1446-439484 21 57698287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405183 Affx-122956925 AX-123275535 21 55266468 CCAAGTCACACCTATTTTCCCTGCTTTGTTATTCA[C/T]GATCCCCATATGCCTGACACAGCATCTGGTTACCT Y 2 1 2 1 101000 f 74 goat snp12071-scaffold1446-352484 21 57785363 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797665 Affx-122957038 AX-385284604 21 55298713 TTACTAAGCTTCTGAAATTGGGGACTAGCTGAGGA[C/T]AGTGACACTCATGTGCCTTGATGGATCAAGAGACC Y 2 1 2 1 101000 r 74 goat snp12070-scaffold1446-320239 21 57818025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419476 Affx-122945475 AX-123289824 21 55356676 CTTCTCTTCTGAAAGAACAGGGTTTCGAGATTGGA[C/T]GTGTTAATTGGCCTTCACTGGTCACCTAAGCAAGC Y 2 1 2 1 101000 f 74 goat snp12069-scaffold1446-262276 21 57875937 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434447 Affx-122934652 AX-123304788 21 55387589 CTGCAGGCTCACCCTTTAGGGTTCTCTGATGCTGA[C/T]GGCCCTGGTGGGTGTACACAGGGTCTTGTATTAGA Y 2 1 2 1 101000 f 74 goat snp12068-scaffold1446-231363 21 57906414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411411 Affx-122951842 AX-123281761 21 55429434 TCAAGTGAAGGTTAACTCAGATGTTGATGAACAGT[A/G]CCCGGGAGGACACAGGTGAATGATGTTAGAGGGTC R 2 1 2 1 101000 f 74 goat snp12067-scaffold1446-189518 21 57946365 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420974 Affx-122944577 AX-123291321 21 55484860 AAGGTGTTGTGGATAACTGGAAGGAAGGAATGTGA[A/G]CACAGTTGTGTAAGTGCCTTGACGGCAGGGATTCT R 2 1 2 1 101000 f 74 goat snp12066-scaffold1446-134092 21 58001781 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446316 Affx-122925637 AX-123316652 21 55532230 CCAGGGCTCCTCACTCGGGGCAGCTCCAGAGTCCC[A/G]CACTTCAAGTCTTCAGAGTCATCAGCTGAGGCTTC R 2 1 2 1 101000 r 74 goat snp12065-scaffold1446-86722 21 58048867 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409189 Affx-122953183 AX-123279540 21 55585790 AAGGAGGCTACGGTAGAGACGCTGACAGAGACCAA[A/G]ATCCATTGTGAGACTGAGGAGAAAGACTTGTATCT R 2 1 2 1 101000 r 74 goat snp12064-scaffold1446-33162 21 58102259 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377231 Affx-122978161 AX-123247590 21 55618260 CTGAAGCAGAATGTGTTTTTCCACAAGGAATTCCA[C/T]GCCTATAAAAGCACCCCAGGACTGGAGAAGAAGGT Y 2 1 2 1 101000 f 74 goat snp12063-scaffold1446-692 21 58133744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784358 Affx-122956003 AX-385271409 21 55623431 CTGGTTTGCATGATTGCCCTCAAGAGCCTTGACCC[A/G]TGGCTTTGTAAAGGGTAGCGTTTCCCAGATCTTGG R 2 1 2 1 101000 f 74 goat snp25268-scaffold2598-2826 21 58210908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425133 Affx-122941211 AX-123295479 21 55663129 CAATGACAATGTGTGTGGGGGAATTCTCTCACACA[C/T]CCACCAAGTGATTCTCCTCGACTTCAGCTGTGTGT Y 2 1 2 1 102000 r 74 goat snp25269-scaffold2598-42524 21 58250934 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445348 Affx-122926386 AX-123315685 21 55700321 CTACGATAGCTGTTTATCATCCTTTCTTTCTGCAG[A/G]TGCCAGAGATTTGGCCTTATTTTCTCCATCTATCT R 2 1 2 1 101000 r 74 goat snp25270-scaffold2598-79716 21 58288379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378126 Affx-122977133 AX-123248485 21 55736636 ATTGTCTCTAGCTATTTTGTGCCAAAGTGACAGAG[C/T]TGAGTACTTGTGACAGATAAACTACAAAGCCTAGA Y 2 1 2 1 101000 f 74 goat snp25271-scaffold2598-116031 21 58324767 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277517 Affx-1111835889 AX-519551018 21 55761515 TGTTAGTCTTCTTCATTTATATTTTATAATATTAT[A/G]TAGTTTTCAAAGCCTTATCATGTGTATTCTAATCT R 2 1 2 1 101000 r 74 goat Random2.2K-1954 21 55761515 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435635 Affx-122933770 AX-123305975 21 55767281 AAGCAAATTGTGTTATTCAGCAGTCTAAAACAAAG[A/G]TTAGAGCTCAGGATTGCCAGTGGTAGATGTTCTAA R 2 1 2 1 101000 f 74 goat snp25272-scaffold2598-146676 21 58356005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766972 Affx-986698274 AX-385254271 21 55779593 CAGCAGCCAGGAGGTGCTGTCCGAATTGAGGGCAC[C/T]GTCTCAGAAACTCATCACGGAGAACCATCAGTCAG Y 2 1 2 1 600010 r 74 goat 21_55779593 21 55779593 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 38389682 Affx-122968706 AX-123260040 21 55804375 CTGCACTGTGTCCTGGGAATATGAGGTTTTGAGTC[A/G]TATGTTAGCCTGTTTACTGCCTCTGTGACCTTGGT R 2 1 2 1 101000 r 74 goat snp25273-scaffold2598-183770 21 58393109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383610 Affx-122972557 AX-123253968 21 55839266 CGCTGCCCTGCAAGTCCAAGGAGGATTTCCTCATC[A/G]GGAGTGCTGGTGCTGGGTCATCCTTTGCAGGGGCA R 2 1 2 1 101000 f 74 goat snp25274-scaffold2598-218661 21 58428724 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394672 Affx-122964367 AX-123265027 21 55896876 TGGAACTGAGTTGCACTGACTGATAAAGGCTATGT[A/G]CTCAGTTAGGTCCAGTTCTTTGCGACCTTGTAGAC R 2 1 2 1 101000 f 74 goat snp25275-scaffold2598-276271 21 58486751 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380556 Affx-122975284 AX-123250914 21 55935213 GATCATAGCTCAGGCTTCTCTTTGTAAGCATTTGG[A/C]TTCTGACTATGAGAGAGAGGCTAAAATCACACTAA M 2 1 2 1 201000 f 74 goat snp25276-scaffold2598-314608 21 58525348 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408644 Affx-122953477 AX-123278995 21 55965725 GGCCTTCTTGGCTTTTTCTGTGTCTGAAAAGTCAA[C/T]CATCTGGATGTCCATTTTCTGCAGCTTGCTTATCT Y 2 1 2 1 101000 r 74 goat snp25277-scaffold2598-345120 21 58555732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396066 Affx-122963444 AX-123266421 21 55996745 TTTAAATGACATACCCAAGTCACCCAGTTACTAAA[C/T]GGCTTACCCTCTTGTCCCCTGTCCCCAGTGGCACA Y 2 1 2 1 101000 f 74 goat snp25278-scaffold2598-376140 21 58585520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378297 Affx-122976857 AX-123248656 21 56055225 GACAGCAGCTTCAGTTCCATGATTAGAGAGGAAGT[A/G]TGAGACTGGATTCCTGGGCCAAGGAGGTGTCTGTT R 2 1 2 1 101000 f 74 goat snp25279-scaffold2598-434620 21 58644282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403696 Affx-122958045 AX-123274048 21 56101065 GAAGGCTGAGACACAGCAGAACCCCAGACAGATAG[C/T]ACCAGAGAACAGAGGCCCCAGGCCCTCTCACGGCC Y 2 1 2 1 101000 f 74 goat snp25280-scaffold2598-480460 21 58690352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767438 Affx-122974941 AX-385254710 21 56140572 ATCACACGTGCTGGGGGCTTTGTTGAGGAGCCTCA[C/T]GATACAGCACTTGTTAGTGTGAGAGGAAGGCCCTG Y 2 1 2 1 202000 f 74 goat snp15073-scaffold1611-8472 21 58838503 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801227 Affx-122939162 AX-385288140 21 56177693 GCAGTACAGTAATTTCAGAGAGGAAAGATGTCAGC[A/G]TTCTTGTAGTCATGTTATCTGAGGAAGCAGAAAGA R 2 1 2 1 101000 f 74 goat snp15074-scaffold1611-45593 21 58876061 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463804925 Affx-1110162987 AX-515283707 21 56200359 CCGACGAGTTATTTCTGTCAATTTCTGCTGATGTG[C/T]GTTCTGTAATACTGACATTTCATGTTGATGGTTAT Y 2 1 2 1 201000 r 74 goat 21_56200359_AF-PAKI 21 56200359 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320793786 Affx-122960140 AX-385280758 21 56208023 CAAAGAGTTAACCCTCTAATTGGTATATAAAAAGC[A/G]TACAAGAAATTATACCTGTGGCTATTTTAATGAGC R 2 1 2 1 101000 r 74 goat snp15075-scaffold1611-75923 21 58906453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463804966 Affx-1110163007 AX-515283748 21 56242608 CACGGCAGAGGAGGTACCGTCATCTTCCTGCAGCT[G/T]TGGTGGGTCTCTGCTGGCAAGTAACGCCACGGAGA K 2 1 2 1 202000 r 74 goat GoatD01.028463 21 56242608 G T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38377805 Affx-122977317 AX-123248164 21 56247717 GCAGGGCACTTTACACCTTCTCACTTGATCACAGG[C/T]CAGTCCTGCCAGGCACAGCCTGTTACAGTCATCAT Y 2 1 2 1 201000 f 74 goat snp15076-scaffold1611-115617 21 58946490 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388499 Affx-122969221 AX-123258857 21 56283092 CCCTCTGTTTTAAGGGCCCTGCCCGTATTTATCCT[A/G]CAAGTCGGCTTTGTCATGTACAGACTTTCCCAGAG R 2 1 2 1 101000 f 74 goat snp15077-scaffold1611-150992 21 58979859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802912 Affx-122963501 AX-385289809 21 56332572 CCTCTTTCTGAGATACGATGGGTAAGTTTACGTTA[A/G]CATTGAGGTTTGCTAAGGATAATCAAAGATGAAAT R 2 1 2 1 101000 f 74 goat snp15078-scaffold1611-200472 21 59029709 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770278 Affx-122947588 AX-385257444 21 56364662 AGGGAAGACTTTAGCTTTGAAGGCCTACTGTGCGC[A/G]TGAAGGTCCCAGATATGTTAATTTTCTGGTCGACC R 2 1 2 1 101000 f 74 goat snp15079-scaffold1611-232562 21 59061430 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412677 Affx-122950769 AX-123283026 21 56395259 TGAAGTGGTTCAGAGCTTTGTAGCCTCCAAACCCA[C/T]GTGACCTCTGAGCCTCAGCTTTCTAATATGTAAAA Y 2 1 2 1 201000 f 74 goat snp15080-scaffold1611-263159 21 59092021 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445728 Affx-122926098 AX-123316065 21 56429049 CAGATCGAAAACCCAGGCTAATGGGGATGAAACAA[C/T]CTGCCTAAAGTCACTCCCTAGCAGAAAGTGCTAGG Y 2 1 2 1 101000 f 74 goat snp15081-scaffold1611-296949 21 59125693 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802667 Affx-122951403 AX-385289566 21 56499475 ACAAGCAAGAAGATAAATTAAGCTTAGCAGTTGGC[A/G]TGTCAGGAATTCTCAGTAAATGAGCACTAATATTT R 2 1 2 1 101000 f 74 goat snp15082-scaffold1611-367375 21 59196469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791342 Affx-122931171 AX-385278335 21 56540040 TGCCCTGATAGCTAAATTTTCATTGCTGCTGCAAA[C/T]GATAACCTTTTACTACATTTTCTATTGGCTCGTTG Y 2 1 2 1 101000 f 74 goat snp15083-scaffold1611-407940 21 59237182 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399511 Affx-122961163 AX-123269866 21 56598551 TTCAGTTCCGCAGCGAACACAAACTGGTTCAGGGC[A/G]CTAACGGAACTTCAGATGCTGTGTGAAATGAAGAT R 2 1 2 1 101000 r 74 goat snp15084-scaffold1611-466451 21 59296032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792175 Affx-122939422 AX-385279160 21 56645730 AACCAGAAACTACACACAGAAATAGAGAGAACGGA[C/T]GTGACTGATAGACCAAATGGAGCAAACAGGTAGAG Y 2 1 2 1 101000 r 74 goat snp15085-scaffold1611-513630 21 59343363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391346 Affx-122967298 AX-123261703 21 56681741 GTTTTTCAGTGAGATGATAGAAGCTGCACGTTGAC[A/G]GTGACAGAGCTTCAAGATGGAAAAAACCTGGAATC R 2 1 2 1 101000 f 74 goat snp15086-scaffold1611-549641 21 59379526 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381417 Affx-122974362 AX-123251775 21 56712025 GCTAGGCCTAGAGAAACTTCAGTCTTTGTCCTCAA[C/T]CCAAAGTCTGTGTTAGTTTTTCCTGGCTGGTATCA Y 2 1 2 1 101000 r 74 goat snp15087-scaffold1611-579925 21 59408565 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423790 Affx-122942823 AX-123294136 21 56761999 GGCCTGGTGGTTTTCCGAGACATTCCTTTCGTTTT[A/G]CTTATTCTCAAAAGCTGCAGGCCACGTTCTAAATG R 2 1 2 1 101000 r 74 goat snp15088-scaffold1611-629899 21 59457536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433447 Affx-122935065 AX-123303788 21 56806315 GCTAGACAACTCACTTAGTGCTTGCCTACTGCCCC[A/G]TGGTCTCCACAATGTAATCACCTAGTACAGACACC R 2 1 2 1 101000 r 74 goat snp15089-scaffold1611-674215 21 59501532 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449720 Affx-122922527 AX-123320055 21 56912083 AGAAGTGTCCTGAGTATGGAGGGAAAAGCTATGAC[A/G]CCTTGCAAAGGGGGAGGGACTCGAAGGACTCAGGG R 2 1 2 1 101000 f 74 goat snp15091-scaffold1611-779983 21 59606793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791375 Affx-122959460 AX-385278367 21 56979012 AGCAGCAATTCAATCTGTTGCCTTCTATCAGTCCA[C/T]GGACTTGGGTAAGAATCCTGCTGTAAACCTCACGG Y 2 1 2 1 101000 f 74 goat snp15092-scaffold1611-846912 21 59675089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447755 Affx-122924577 AX-123318091 21 57020422 GTGTTTTCCTCTTTTGGTTCCTTAGTGAGGTTGAT[A/C]GGCTCTCTATCAATGTTTGTTGAATAAATCAGTGT M 2 1 2 1 101000 f 74 goat snp15093-scaffold1611-888322 21 59716374 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438819 Affx-122930787 AX-123309156 21 57043352 ATTTCTTCATCTGTAGAATAAGGACAGTTGTACAT[A/G]CCTCTGTGAAGATGAAATGAGATTCGATGTGTGAA R 2 1 2 1 201000 f 74 goat snp4824-scaffold1160-5709 21 59739082 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429066 Affx-122938292 AX-123299408 21 57074168 ATATGATGTATTAAACTCCAGACTGAAGTATTATT[A/G]CTGTATAAAATCACCTGTAAAATCTGTATTCCTTT R 2 1 2 1 101000 r 74 goat snp4825-scaffold1160-36525 21 59769537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451738 Affx-122921535 AX-123322071 21 57103679 CTGGGAACCTGGGTTCGGTACCACTGGCAATGTGG[C/T]AAAACCAGGGTATCTGGCTCTTAGGATCAGCTCTG Y 2 1 2 1 102000 r 74 goat snp4826-scaffold1160-66036 21 59798865 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432339 Affx-122936285 AX-123302680 21 57133457 ACATTCAAACCAGATGTTGGGCTGGCTTGATCCTG[C/T]AATTACATCTTTCCTCCTCTTTTCTAACGCTGGGT Y 2 1 2 1 201000 r 74 goat snp4827-scaffold1160-95814 21 59825667 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395321 Affx-122964050 AX-123265676 21 57167473 TCCTCTTACAGGATGGCAGCCTGGCTGCTGAGGAT[A/G]CTGTCCTGCTGCAGAGTCCAACTGCAACTCAAAAG R 2 1 2 1 201000 f 74 goat snp4828-scaffold1160-129830 21 59858873 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400181 Affx-122960671 AX-123270536 21 57203440 CCCCTCACACTCCCCATATTGAAAGAATAATGTAC[A/G]TCTTCAGTCTCACACGAGGGCTTTTTAACATTGAA R 2 1 2 1 201000 r 74 goat snp4829-scaffold1160-165797 21 59895364 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386476 Affx-122970767 AX-123256834 21 57257621 TTTTCATTAGCTTAGCGGGCTCTTCCTCAGCATCT[A/C]CTGCCTTGAGAGTCCTAGTGGAATGTGATCTTCTT M 2 1 2 1 101000 r 74 goat snp4830-scaffold1160-219978 21 59947493 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437900 Affx-122931661 AX-123308238 21 57315321 ACCTCTTTTCTTGATCAGATTGCAACCCAAAGCTC[A/G]TATTTCAATGGACCAGCCTTGGGATAAGACCACCA R 2 1 2 1 201000 r 74 goat snp4831-scaffold1160-277678 21 60004107 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400724 Affx-122959915 AX-123271079 21 57359433 TTTTTGCACCAAGAAGCACAACAATGAGACTCAAA[C/T]GAGTGTTTCCATAGTCCTGGGCACACTTCTCCATG Y 2 1 2 1 101000 f 74 goat snp4832-scaffold1160-321790 21 60048328 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407447 Affx-122954791 AX-123277798 21 57472654 ACACGAGGGCTCCAGTTTCTCTACATCCTGATGCA[C/T]GTCAAACAACAAACTCACTTCTAATCAATTTTGCC Y 2 1 2 1 201000 r 74 goat snp4835-scaffold1160-435011 21 60160873 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427685 Affx-122939303 AX-123298028 21 57510026 CTTGGCAAGTGCCAATTTGTAGTTGACACTCATCT[A/G]GTCTATGGAAGGGATTCTTATCCGTGTCCCAATGC R 2 1 2 1 201000 r 74 goat snp4836-scaffold1160-472383 21 60198141 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435334 Affx-122933609 AX-123305674 21 57548868 TTCATCTTGCAAATGTTTATTTAGGCAAGTAGGGC[C/T]CCCCCCTCCCCTCCCCACCTGGTGGTCTCAGGGTC Y 2 1 2 1 101000 f 74 goat snp4837-scaffold1160-511225 21 60236928 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443569 Affx-122927341 AX-123313906 21 57587926 ACTTTCAAGTCTTTCTCTCTTCTTAATGTCAGGGC[C/T]AGAGATGATCAGGAGTTTCAGGGACCTTCTTGTCC Y 2 1 2 1 101000 r 74 goat snp4838-scaffold1160-550283 21 60275967 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398627 Affx-122961468 AX-123268982 21 57618470 TCCTGATCAAAAGAGCTGAACTTCCCGATGGTCTT[C/T]AGGGAAGAGTGTTTAAAGGCAACATTTGGGATGAG Y 2 1 2 1 201000 f 74 goat snp4839-scaffold1160-580827 21 60306760 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390488 Affx-122967592 AX-123260845 21 57701724 ATAAAATGGAAGATTCCTTTCTGTCTGTATTGCCA[C/T]CAAATCCTTGAAAATGGCAGCCATGGGCTTGAAAG Y 2 1 2 1 101000 r 74 goat snp39663-scaffold5046-18798 21 60391071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438137 Affx-122931478 AX-123308475 21 57737668 ACTGTATAATTCTCATCCAATGGGTCCTCCCTGAG[C/T]GAAACATCTACAGCTCCTCAATCAAAACACACTTT Y 2 1 2 1 201000 r 74 goat snp39664-scaffold5046-54742 21 60427014 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385554 Affx-122971227 AX-123255912 21 57773979 TCCTTGAGGTCTGGTGGGGAAGTCTGGGTGGGCAC[A/G]TCTGGCCAGCAAGTCACCTCGAAAGGGTTTAAATC R 2 1 2 1 202000 f 74 goat snp12297-scaffold1460-1039186 21 60462774 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398530 Affx-122961535 AX-123268885 21 57802640 GCCACAAGGTGCGGGTCAGGAGTGAGGGATTCATT[A/G]TTCAGCCCCGGGGAGTGATGCCAGAATCAGTGGTG R 2 1 2 1 201000 f 74 goat snp12296-scaffold1460-1010525 21 60490319 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417527 Affx-122946935 AX-123287875 21 57833966 TGAGGGTTCTTTGGTTCTATCCTGCCCCCTCCCCT[A/G]TATGATCTTGGAGCCTAAGTGGAAAAGTGCAGCAG R 2 1 2 1 101000 r 74 goat snp12295-scaffold1460-979199 21 60521649 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375363 Affx-122979233 AX-123245722 21 57864084 CAGGTTTCCTTTCTGCAAATTTTAATTGAAATAGA[C/T]ACAGGATTAAAGGAAAATTTGATGAGCAGCTTCTA Y 2 1 2 1 303000 f 74 goat snp12294-scaffold1460-949081 21 60551736 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416045 Affx-122948356 AX-123286394 21 57911100 GGAGGAGAGAACAGTGTAGCATTGTGATGAAAGAC[A/G]GGAATGAAGGCTCAGAACTCCAGTAACTGCTGCTG R 2 1 2 1 101000 f 74 goat snp12293-scaffold1460-902065 21 60597405 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423278 Affx-122942656 AX-123293624 21 57941889 GGAAGTCCCCTGCCATTTCATTTTTTAAATCTAAA[C/T]TGGGAAGCTTTTTTCTTCTTCTTCTTTTCCCCACT Y 2 1 2 1 103000 f 74 goat snp12292-scaffold1460-871276 21 60628553 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783277 Affx-122948713 AX-385270342 21 57988620 TCCATGATCATGTTGACCATGCTCTCTTTCATCTC[C/T]AGAGATAATTTATAACCAGTGTCTCAAAACTGCAA Y 2 1 2 1 101000 f 74 goat snp12291-scaffold1460-824545 21 60674966 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430340 Affx-122938213 AX-123300681 21 58036270 GATTTACAGAAGTTAAAACATAAATATGGCTTTTT[C/T]GTTCTAATTTTTGCCACCACAGCCATGTTTTTTCT Y 2 1 2 1 101000 r 74 goat snp12290-scaffold1460-776895 21 60722627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376216 Affx-122978803 AX-123246575 21 58071574 TCTGACTATGGGATCTTGGTTTTGGAAGACAGTCT[A/G]TTGAGTAGGCGCTTTAGTCAAGACTCTTCAAATGG R 2 1 2 1 101000 r 74 goat snp12289-scaffold1460-741591 21 60757795 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408939 Affx-122953938 AX-123279290 21 58111810 TGTCACTGCCTACAGAAAACCTGGTGCTACATGTT[A/G]CCTTTTCTTTCTCTATCCCAGTTGATAGCACCTTC R 2 1 2 1 101000 f 74 goat snp12288-scaffold1460-701355 21 60798009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379672 Affx-122975926 AX-123250030 21 58147157 TTCCTCATGCCAGCTTCACTGGGCTGTTGGAAGGC[A/G]CTCTCTGGCCTCCAAGCATATAGATAGATTTTAGG R 2 1 2 1 101000 r 74 goat snp12287-scaffold1460-666008 21 60833450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804107 Affx-986696389 AX-385290765 21 58171879 CTGGTTTGGGGCAGGAGCATGACTTTCCCTCTCAG[A/G]ATCCTCTTCTTGCATATGTTTGAAATCCACAGTCC R 2 1 2 1 600010 r 74 goat 21_58171879 21 58171879 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 38389553 Affx-122968268 AX-123259911 21 58178037 GGGAGACACAGCGAGCCTTCAGCCAGGCAGTGGAC[A/G]TGGGTCTTCTCTACCTCCCCTCACCATCGCAAACC R 2 1 2 1 201000 f 74 goat snp12286-scaffold1460-635128 NW_017212929.1 9053 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388554 Affx-122969182 AX-123258912 21 58256328 ATTCAAATTTGCTGTGCTGGAGGGTTGCTATCAGC[A/G]GAAGCTAGTATAAACAGCAAAGCCCGAACCAGACC R 2 1 2 1 101000 f 74 goat snp12284-scaffold1460-556837 21 60942075 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416344 Affx-122947893 AX-123286693 21 58314366 AAGAAGAGAGGGAGCTAAAGTTCTAAAAAGCACTC[A/G]TTTGGGATAAAGATAGATCAATGGTTCAGGATATT R 2 1 2 1 101000 f 74 goat snp12283-scaffold1460-498799 21 61000439 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388227 Affx-122969400 AX-123258585 21 58360490 ACAGTAGTTATTTTATTTGTAAAATAACAACCAAG[C/T]GGTATGAGTTGCCTAAACCATCTGGGCAACAATAT Y 2 1 2 1 101000 r 74 goat snp12282-scaffold1460-452675 21 61046593 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402153 Affx-122958652 AX-123272506 21 58395370 CTTTAATCCCATTGGCAATAGCTGTTTCAATTCAC[A/G]TCATGAATAACTGAATAGATCCCCTTGTGTTGGGC R 2 1 2 1 101000 f 74 goat snp12281-scaffold1460-417795 21 61081491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410290 Affx-122952504 AX-123280640 21 58453111 TACTTAAGGTCCTCAAAACTCTTTAATAATAACAA[C/T]AACCAGCAACAAAAGAATAATCATTTACTAAGCTC Y 2 1 2 1 201000 f 74 goat snp12280-scaffold1460-360054 21 61139358 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391562 Affx-122966626 AX-123261919 21 58511612 AGACTGTCCAGCAAACAATGTTTTCAGCAGACAGA[C/T]GTGGAGTCCCAGCTTCAGGGCTAACTAGGAAACTA Y 2 1 2 1 102000 r 74 goat snp12279-scaffold1460-301553 21 61197890 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439310 Affx-122930957 AX-123309647 21 58542301 GTGATCTGGGGCTGACACTCACAATGTCAGTATGC[A/G]CTGAGACCCTTCATACAAAACATGGTTGGAATTTA R 2 1 2 1 201000 r 74 goat snp12278-scaffold1460-270864 21 61228299 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423472 Affx-122942579 AX-123293818 21 58577806 CAGGCTCTACCGCTACGCTCTTTCCGTCTCACCAG[A/C]GGGCACCTCATGTAGCTCAATAGCAGAATAGCAAA M 2 1 2 1 201000 f 74 goat snp12277-scaffold1460-235359 21 61263517 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784921 Affx-122931617 AX-385271968 21 58617157 AAAGATCATGATCGACTTTCCACACACATGAAAAG[C/T]GAGGCAATGACATGAACAGGCAGTTTACAAAAGGA Y 2 1 2 1 101000 r 74 goat snp12276-scaffold1460-196008 21 61303264 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395186 Affx-122964513 AX-123265541 21 58682111 TCCAACTGTCCTTGAGCATTTTGTCTAGAAGGGAT[A/G]CAAGACGAATTACTGAAGTGACATAAAAATCCCGC R 2 1 2 1 101000 f 74 goat snp12274-scaffold1460-131054 21 61366479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271930 Affx-1111833227 AX-519545709 21 58707942 TTAGAGGAGCTGGGGATAGACAGCAGATCACCAGG[A/G]CCGTTGGCACAGAAGCTTGTCCCTGTCGGGGGAAA R 2 1 2 1 202000 r 74 goat 21_58707942_AF-PAKI 21 58707942 G A 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320763752 Affx-986698280 AX-385251561 21 58725030 CTTTGTAATATATTTTGGGATAGACATCAGTCTTG[A/G]GAATGTGCCTGAGGTGGAATCAGCTGTAAACCCCC R 2 1 2 1 600010 f 74 goat 21_58725030 21 58725030 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320766986 Affx-986698282 AX-385254284 21 58725197 TCCTGTGCGGTGCTCAGCAGAGCAGGTAAGAGGTA[A/T]TAGGTATTAACAATGGCTCAGGGCCATCATGATCA W 4 1 2 1 600010 r 74 goat 21_58725197 21 58725197 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 320779978 Affx-122951765 AX-385267077 21 58752020 CACGATCTGACTCTAACGTCACATCGTCCAGGATG[C/T]TCCTCCGACGCTTTGACTCTGAAAGTCACTCTCAC Y 2 1 2 1 101000 r 74 goat snp12273-scaffold1460-61145 21 61436426 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766990 Affx-986698284 AX-385254288 21 58755782 AGGAATTGGTTCTAGAAAATGAATCCAACTTCTCC[C/T]CATGTTGCCAGACTCTTGAATAAAGCAAGCTTTCC Y 2 1 2 1 600010 r 74 goat 21_58755782 21 58755782 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 38435950 Affx-122933535 AX-123306289 21 58780624 CATTTGCAGTTGTTGCTTTCCCCAGGCGTTTTTAC[A/G]CTACTGGCCATCACAGCTGTCATCATCTGAATTAC R 2 1 2 1 201000 r 74 goat snp12272-scaffold1460-32541 21 61464923 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389909 Affx-122968113 AX-123260266 21 58812385 AACTACTGGAAACTCAGAGAGAGACATGGAATAGA[C/T]GCTCCTTCATATCTTATCACAGAATTCCCAGTGGC Y 2 1 2 1 101000 r 74 goat snp12271-scaffold1460-780 21 61496251 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388613 Affx-122969140 AX-123258971 21 58835602 CAGGCCTTCCAGGCTTCTGACGTCGTTGGTCCTTT[A/C]GGGGCTTCCTTAGCCCTCCATCCGTCCTTTGCAGA M 2 1 2 1 101000 f 74 goat snp33621-scaffold3947-257645 24 58948257 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391658 Affx-122966556 AX-123262015 21 58869293 ATCTCGGCTATGAATCAGTGTAAGGAAAGAACCCT[A/G]TTTTGCCATTCTGTCTTATTTCACTATGTTGAGAC R 2 1 2 1 101000 f 74 goat snp33620-scaffold3947-223954 24 58982054 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380706 Affx-122975158 AX-123251064 21 58914313 GCACTTTCCAAAAATATTCATACAAAACCCCCAAG[C/T]ACTGTTCAATTATGTAAAAAACTGGGAAGTGTTGA Y 2 1 2 1 201000 r 74 goat snp33619-scaffold3947-178934 24 59024494 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394387 Affx-122964628 AX-123264742 21 58949632 GTGTTAAGTTGTGGGTCTCAGACAGACATTATCAA[C/T]ATAACTTGAGAATTTGTTTGAAATGCAAATTCCCA Y 2 1 2 1 101000 f 74 goat snp33618-scaffold3947-143615 24 59066234 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774472 Affx-122954783 AX-385261608 21 58987056 GATGCTAGATGTGGAACCATACAGAGAGACTGAAC[C/T]TAGAGATGGGACACCAGTTAAAAAGCAGTTGGAAA Y 2 1 2 1 101000 f 74 goat snp33617-scaffold3947-106191 24 59103728 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444362 Affx-122926708 AX-123314699 21 59030393 CGCGTTGGGAACAGTTGTTAAAGAAGTTGAGGCCA[C/T]GTGCTAGGACTCATCCATCTCCTTCCAGGCTCAGC Y 2 1 2 1 101000 f 74 goat snp33616-scaffold3947-62854 24 59148175 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418882 Affx-122946111 AX-123289230 21 59081990 ACTGCTGTCTCCTGTGCAGAGCCTCGTCCTTGTCC[C/T]GGGAGACCTGCGGTTACTGTTGTACTTTATGAATC Y 2 1 2 1 101000 r 74 goat snp33615-scaffold3947-11257 24 59199414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384460 Affx-122973089 AX-123254818 21 59107962 TGACAAATCACCTTGATGGTAGGAGGTGGGCACCA[A/G]CGTGACAGGAAGGAAATCTATAGCCCATCCAGTTA R 2 1 2 1 101000 r 74 goat snp58807-scaffold960-458048 21 61513473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423050 Affx-122942962 AX-123293396 21 59154760 AGCTCATCACTTACGAAAAAACTGAAATAAGATAT[A/G]CCAGCATACAGTGGGTCTTTGCAGAGAGCCTTTTC R 2 1 2 1 201000 f 74 goat snp58806-scaffold960-411250 21 61560092 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437253 Affx-122932012 AX-123307591 21 59194076 CAGATCCTGGACAGAGAAGCACGAGGGCTCCTCCA[C/T]GAGTATCGCAGCAACAAACAGGGCTTCTGCTAAAA Y 2 1 2 1 101000 r 74 goat snp58805-scaffold960-371934 21 61599023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390698 Affx-122967942 AX-123261055 21 59225893 CCACCAGGAGATTCTATGATCTTCTGCTCCCCTTC[A/G]GAGCTGTGTATCCCAGAGGGGAGAAGTTGCAGGGT R 2 1 2 1 103000 f 74 goat snp58804-scaffold960-340117 21 61630736 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404475 Affx-122956727 AX-123274827 21 59270834 TTTCTTTCCAAATACCACCTACCCTTCGTCCTATG[A/G]CAATTGTAAGGAATCCCACCCCAGCCCACCCGCTC R 2 1 2 1 101000 f 74 goat snp58803-scaffold960-295176 21 61675664 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792042 Affx-122963039 AX-385279030 21 59300759 TTTAGGGGCAAAGATAAGGCAGAGAACAAGATAAC[A/G]CCTTTGCCTCCTCACAGCTTCTTCCCATAATTTCC R 2 1 2 1 101000 f 74 goat snp58802-scaffold960-265251 21 61704765 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408605 Affx-122953642 AX-123278956 21 59351270 AGGTTGCTGGAGTATTAGATGAACTTAAGCAAGAA[C/T]AGTGCCTGCCACGAGTTAAGAGCTGTGTCCTTGAT Y 2 1 2 1 201000 f 74 goat snp58801-scaffold960-214740 21 61755110 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449751 Affx-122922455 AX-123320086 21 59431697 TCCAGGTCCCTTCCAGCCCGTTGATTCTGTATTCC[A/G]TCAGCAGAGCTGGATGTCGCTCAGGATTCCAGAGC R 2 1 2 1 102000 r 74 goat snp58799-scaffold960-134313 21 61834559 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409596 Affx-122953562 AX-123279947 21 59483067 TACCTTTTGGGAAAATCCAAACTTTAAAATCCTTC[A/G]TAAGTCCTTTCATGATACAGCCCTGGGTACTACAC R 2 1 2 1 101000 r 74 goat snp58798-scaffold960-82943 21 61886121 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380372 Affx-122975343 AX-123250730 21 59511694 TTCGCAACCAGGAAAATGAACAGAAGGGTCAAGAT[C/T]CTTCAGAATTTGGCTCTGAGTGTCCCCTCTGTTGG Y 2 1 2 1 101000 f 74 goat snp58797-scaffold960-54316 21 61914700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440183 Affx-122930712 AX-123310520 21 59555389 ATACAACTACTACAAGACAGGCTCCAAGTTACACT[G/T]CTCTGTGCATACTACAAGAACAAAGCCATGCCTGC K 2 1 2 1 101000 f 74 goat snp58796-scaffold960-10621 21 61959371 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389217 Affx-122969057 AX-123259575 21 59566492 GGTTTCATAGGCAAGGGCTGTCTGTGATGACTGCA[C/T]GTGGCACTCGTGGGTTCACAAGAACAATCCACGCA Y 2 1 2 1 101000 f 74 goat snp11721-scaffold1431-697775 21 61964187 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779650 Affx-122929902 AX-385266752 21 59600643 GATCCTATTCAACTCTGTCTGCTCAAAGCTTTCAT[A/G]TTTGTCTAATTTCACCAAGTTCCAGCTGATCTATA R 2 1 2 1 101000 r 74 goat snp11720-scaffold1431-663624 21 61998554 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394461 Affx-122964578 AX-123264816 21 59644688 GGTTTTACAATTTGAGAAAATACTATAACAAAAGC[A/G]TAAAAAAGAGTATATACAAATGGCTCTCTACTAAA R 2 1 2 1 201000 f 74 goat snp11719-scaffold1431-619579 21 62029526 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450195 Affx-122922296 AX-123320530 21 59680628 AAACTGGGTCACCACCAAGAATGCCATCTTCTCAG[C/T]GCCATCCGAGATTTGCCAATTAACTTTTTTTTTAA Y 2 1 2 1 201000 r 74 goat snp11718-scaffold1431-583639 21 62066402 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426471 Affx-122940791 AX-123296817 21 59715258 CATCTCACTAGGAACTGAGGACTGTTCTCCACTGC[A/G]TCCTGGGCAGGTGCATTTTTATCTCTTCGATCTGA R 2 1 2 1 201000 r 74 goat snp11717-scaffold1431-549009 21 62100979 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277395 Affx-1111835890 AX-519550899 21 59744817 CAGTGGGTGTAGATTTCGCACAGTTGTGGAAGGCA[A/G]AAGTCCAAGATCAAGTCTGTAGCGGATACGCTCTG R 2 1 2 1 101000 f 74 goat Random2.2K-1955 21 59744817 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398619 Affx-122961475 AX-123268974 21 59761517 AGCAGAAAAAACCTCGTGATAGCTGGAAACTTCCC[A/G]TCATTAGGAGCTGGGCTGGCTTCCAGCTGGTACCC R 2 1 2 1 101000 f 74 goat snp11716-scaffold1431-502750 21 62147470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446765 Affx-122925321 AX-123317101 21 59807208 AGCCTCTCCCCAGTGGTGCTATGCCCAGGGTATCA[C/T]ACAGATCCAAGATCTCCTGGACCATCTCTGTTTCG Y 2 1 2 1 201000 r 74 goat snp11715-scaffold1431-457059 21 62193065 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422385 Affx-122943397 AX-123292731 21 59837108 GAGAGAGTGATGATGACAATGGTGTCTGAAAAGAA[C/T]TTGGGGTGTCACCTGGTCATCCCACAAGGATGGCT Y 2 1 2 1 101000 f 74 goat snp11714-scaffold1431-427159 21 62222948 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797882 Affx-122973312 AX-385284820 21 59868091 GAACTTGCTATATATTTACCAAATAAAGACACAAG[C/T]GTCCCAGTGAAATCTGCATTTGAGATACACAGCAA Y 2 1 2 1 101000 r 74 goat snp11713-scaffold1431-396176 21 62253715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432305 Affx-122936308 AX-123302646 21 59901064 ACAGGCTGCAATTTGCCTGGAAAGAGGGCGCATTC[A/G]GGGGCTTCCCCAGTGGCTCAGCAGTAAAGAATCCA R 2 1 2 1 101000 f 74 goat snp11712-scaffold1431-363203 21 62286672 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791207 Affx-122924759 AX-385278201 21 59939293 ACCAAGAGATAATCATAAGCATTCACCACCTGTAT[A/G]TTCAATAAGTATTTATCAAGTGATTGTATACATAG R 2 1 2 1 303000 r 74 goat snp11711-scaffold1431-324974 21 62324751 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775838 Affx-122978015 AX-385262969 21 59977358 AATTACTTATGAAGACCAGTGGCATTTGCATAACA[C/T]ACTCTGTAGCAAATCAAATTCCAGATAGATTAAAC Y 2 1 2 1 101000 f 74 goat snp11710-scaffold1431-286909 21 62362918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277521 Affx-1111835891 AX-519551022 21 60004143 TATTTCAATGGACCAGCCTTGGGATAAGACCACCA[A/G]TATTTGTAAAAACCATTCAAGGCACTTTTCTTTTT R 2 1 2 1 201000 r 74 goat Random2.2K-1957 21 60004143 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779583 Affx-122923057 AX-385266686 21 60015263 GATTTGATATTTGCACTGCCTCTCCAAATTCCTGA[C/T]GAGATTTTTTAAGTTGTAAGTCTATTGTACAAAAG Y 2 1 2 1 101000 f 74 goat snp11709-scaffold1431-249004 21 62400885 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426605 Affx-122939973 AX-123296951 21 60051609 CGAGTAAGTGGTGCTGGAGAGAAAGGTCTATGCTC[A/G]TCAATGGTGGAAGAAAACCTTTTACTTTTAAAATG R 2 1 2 1 201000 r 74 goat snp11708-scaffold1431-212658 21 62437185 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391304 Affx-122967334 AX-123261661 21 60113995 TACTTACTGAAGCCCATGGAGACCTTCAGGAGACA[C/T]GGGCCAGGCAGGAAACACTGTTTCCATTTGGCAGA Y 2 1 2 1 202000 f 74 goat snp11707-scaffold1431-150272 21 62499038 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391356 Affx-122967291 AX-123261713 21 60142844 TTCTCCTCAATCGTGTCTGGATCACCCCCTCACCA[C/T]GGAAAACCCTTCCAAGATACAATTGTTTCTTGGAA Y 2 1 2 1 101000 r 74 goat snp11706-scaffold1431-121423 21 62527877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802813 Affx-122927913 AX-385289712 21 60191001 ACACTTTGGTTACAGGTGCTCAAGGAGAAGCTCCC[A/G]TTTGAATAGATTTTTGAGCTAAAGATAATGCTTTG R 2 1 2 1 101000 f 74 goat snp11705-scaffold1431-73266 21 62575041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388131 Affx-122969477 AX-123258489 21 60221339 TTTTAAGGCGATTCTGATGGATGTTAACTTCAAGA[A/G]CCGCTGTTCTGGAGAATAAATACCATTTCTGACTT R 2 1 2 1 101000 f 74 goat snp11704-scaffold1431-42928 21 62603336 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774187 Affx-122946015 AX-385261324 21 60252056 CTCACCAATTCACCATCCCTAGATGGTGCAATTTC[G/T]GATGCCTGTGACATGCTTTGTTTATTGACAAGACA K 2 1 2 1 201000 r 74 goat snp11703-scaffold1431-12211 21 62634444 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435154 Affx-122933667 AX-123305494 21 60283340 CTTACTTTCTGCTAAAGGCTTGCTAGAAGCAATTG[A/G]CTACAGTTTGGTGTAATAGCCTTAAATCATGGGAT R 2 1 2 1 101000 r 74 goat snp31754-scaffold355-18974 21 62665136 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435675 Affx-122933332 AX-123306014 21 60333809 ACTGAAGCTCTGTACTTGTCTTACAAGTTGAATAA[C/T]AACTCAAATGGTGACATGGTGAGAGGTGCCTTTGA Y 2 1 2 1 101000 f 74 goat snp31755-scaffold355-69443 21 62715582 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398756 Affx-122961448 AX-123269111 21 60384968 AATGAGTCTAGGATCTGGAATTTGAACCCTGGACT[A/G]TGATTTCAGGGAACTTGCTCTTTACCACTACATCA R 2 1 2 1 201000 r 74 goat snp31756-scaffold355-120602 21 62767469 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448137 Affx-122924289 AX-123318473 21 60414435 TTTCTTGGCAGAACCCACACCTTCCTGAGATCCTC[A/G]CATAGCAGAGGTGAACAGTTTCCATAACCTGCCCT R 2 1 2 1 201000 r 74 goat snp31757-scaffold355-150069 21 62796962 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277524 Affx-1111835892 AX-519551025 21 60466768 CAGGACAGCACTTGGAAGGGGCCTGGCCGGAGAGC[A/G]CTGGCTATGCTTCTGTGTGTTGGAAAGCCGAAGTC R 2 1 2 1 102000 r 74 goat Random2.2K-1958 21 60466768 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38410377 Affx-122952441 AX-123280727 21 60468306 ACCCAACCTGATAGAGGATAAACACCTGGAGCAGC[A/G]TTGTACCATCTGTCCTGGGTGAAGCTGTCCATGAC R 2 1 2 1 101000 f 74 goat snp31758-scaffold355-203940 21 62850851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445714 Affx-122926108 AX-123316051 21 60501165 CCAGGCCTGATGACAGGCCACCCTGTGGCCCTGTC[C/T]TGTCTCATGTCCTGAAAGTTAATGCACCTTGAAGG Y 2 1 2 1 101000 r 74 goat snp31759-scaffold355-236799 21 62883464 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392051 Affx-122966395 AX-123262408 21 60547589 CATCTGAAATGGAATAGTTAGCAAAGGTTCCTGGC[C/T]CTATGAAACTGAAATTTTGGTGGAGAGAGACAGAG Y 2 1 2 1 101000 f 74 goat snp31760-scaffold355-283223 21 62930277 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409695 Affx-122953054 AX-123280046 21 60588847 CGCTCCTTGCTGCATCAGACACTGATTCAGAAGTC[A/G]CCTTTGCAAGCCTGCTGACACATTTCATAGAGGCA R 2 1 2 1 101000 f 74 goat snp31761-scaffold355-324481 21 62971402 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396439 Affx-122962985 AX-123266794 21 60628438 CAGAAAAGTAGAAACTTACACCAGGCACTTCAACT[A/G]GAGGGAGTCCAATCCTGGGAATTGGTTATATGGCC R 2 1 2 1 101000 f 74 goat snp31762-scaffold355-364072 21 63010786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380378 Affx-122975338 AX-123250736 21 60664766 CCAGGTTCAGATGTGGGGAAACTAGAGAAAGTCAA[G/T]CCCCAGAAAGATGGGGAGGTTGTCTTGAAGCAATG K 2 1 2 1 101000 f 74 goat snp31763-scaffold355-400400 21 63047166 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779460 Affx-122941024 AX-385266563 21 60716175 TTTTTATGGGTAAAAACAACATCTCATTCTTTCCC[A/G]TATCCCTTCACTCCCACGGAAGAGAGATGGCTTGT R 2 1 2 1 101000 r 74 goat snp31764-scaffold355-451809 21 63097868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450703 Affx-122921890 AX-123321037 21 60756369 TCTTTGCAGACATTATATTAATATGTTTTGCAAGT[A/G]TTTTTTTTCCCAGTTGGCAGCTTGCCTGTTCATTT R 2 1 2 1 202000 f 74 goat snp31765-scaffold355-492003 21 63138196 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797550 Affx-122951419 AX-385284489 21 60789093 CTCTCTGACATGATTTCTCCATCCATAAAGTGAGG[A/G]TAATATTAATCGTGCCTACAGGGTTGTCCTGAGGA R 2 1 2 1 101000 f 74 goat snp31766-scaffold355-524727 21 63170473 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416851 Affx-122948101 AX-123287199 21 60883558 AGTTGGACATGACTGAGGGACTGAACTGAACTGAT[A/G]CACTTAACCCACCTGGCCTTTATTCCCCACCCAGT R 2 1 2 1 201000 r 74 goat snp31768-scaffold355-619192 21 63265537 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406851 Affx-122955660 AX-123277202 21 60945451 ATCAGCATTATCAGCAGTGCTCCCATTCACCACTG[C/T]GGCTTAACAAGAACCTGAAAACTAGTCATTTAAAT Y 2 1 2 1 201000 r 74 goat snp31770-scaffold355-681085 21 63328617 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409499 Affx-122953639 AX-123279850 21 60994766 CCTGGAGGCAGGAGGCAGTTCAATGCCCCCATCAG[A/C]GGGGATGCCAGGAGTCAGAGTCCACCAGAGCCAGT M 2 1 2 1 101000 f 74 goat snp31771-scaffold355-730400 21 63377759 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406145 Affx-122956184 AX-123276497 21 61025191 GTGACTATCTGGCCAAGAGGATTCTGACTTACCTC[G/T]AGAGTGAGAACTTAATAGCCACAGGCAAGTAGAAA K 2 1 2 1 201000 r 74 goat snp31772-scaffold355-760825 21 63409058 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418673 Affx-122946314 AX-123289021 21 61055664 GTGCCCAGGCTCTGTGCTGGGTGCTGAACATTCCA[C/T]GGAGATTAAAAGCCATGTTTGTGGTGCTTACAGGC Y 2 1 2 1 101000 r 74 goat snp31773-scaffold355-791298 21 63439854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770314 Affx-122946676 AX-385257480 21 61089012 TGGGGCCTGGACACGGATTTTGAAAAACTCTCACG[C/T]GATTCCAGTGTGTAACCAGGAGTGAGAACCACTTT Y 2 1 2 1 101000 r 74 goat snp31774-scaffold355-824646 21 63473195 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428290 Affx-122939387 AX-123298633 21 61120019 GGCCACCCCTGCACTGAAAGGCGAACTCTTAACCA[C/T]GGGACCACCAGGAAATCCCTGAAAGCTTTCCATCT Y 2 1 2 1 303000 f 74 goat snp31775-scaffold355-855653 21 63504051 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277526 Affx-1111835893 AX-519551027 21 61130744 TCCCCACAGAATTTTTAATTATAAACCATAATCTA[A/G]TATAAGCATTCTTGCATTTATAATAGACTATACCC R 2 1 2 1 101000 r 74 goat Random2.2K-1959 21 61130744 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38428072 Affx-122939109 AX-123298415 21 61159364 TGCAGATGGAGTTGCGGATTTGAAGAAGGTAGGCA[G/T]CATGAACCACCCAGCTGGCTCAATAGTAAAGAATC K 2 1 2 1 201000 f 74 goat snp31776-scaffold355-894998 21 63542605 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447721 Affx-122924602 AX-123318057 21 61207944 AAGCCACAGGACTTTGTCTCCTGTAAGCCTGACAA[C/T]AGCTTAGGAAAGCTCACAAACCTCAGCCACCTCGG Y 2 1 2 1 101000 f 74 goat snp31777-scaffold355-943578 21 63590310 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381850 Affx-122974191 AX-123252208 21 61244774 AACTCCCATCCGCTACAGCCCTGACCCTGGCCCCA[G/T]CCTCCAAAACCACCCTGCTGGAGTGAAGAAAGCAG K 2 1 2 1 101000 r 74 goat snp31778-scaffold355-980408 21 63627189 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445634 Affx-122925089 AX-123315971 21 61283378 GGTGACTTCATGTCTGGGTTTCTCTGCCTTCCTGC[A/G]GCAGAGCCAACTGGGAAAGAGCGGGAGAAAATGTC R 2 1 2 1 101000 r 74 goat snp31779-scaffold355-1019012 21 63665882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407971 Affx-122954339 AX-123278322 21 61312795 CCGGTGACCTAGCTGCCTGATGGCTGTGTTTGCTC[A/G]TCGCTTGTGGGTCATTACAGGGATTCAGGGTGACA R 2 1 2 1 101000 r 74 goat snp31780-scaffold355-1048429 21 63695454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272100 Affx-1111833228 AX-519545859 21 61313667 ATTTTATTAGGGGCTTCTCTGGAAAGGTGGCATTT[A/G]GGTGGAGCTCAGAAGGAAATGAGGCAACACGTATG R 2 1 2 1 102000 f 74 goat 21_61313667_AF-PAKI 21 61313667 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38396097 Affx-122963424 AX-123266452 21 61348941 AGATAGGGGCAGAAGGGACCGGAAGCCACACTCAT[C/T]ATGGTCGTAAGCTGACCAGATGCCCCTCGTTCTGA Y 2 1 2 1 201000 r 74 goat snp36897-scaffold4473-121792 21 63731709 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793855 Affx-122920431 AX-385280824 21 61395995 TTTGTACAATTGAAGAAGTGTTTTATCTTGGCTAT[C/T]AGTTCATTCTGAATCATATTTAACTGCTTACAGGT Y 2 1 2 1 101000 f 74 goat snp36896-scaffold4473-74738 21 63777865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385760 Affx-122971067 AX-123256118 21 61437383 CCCGATGACTCTGTGTGTGCAGAAGGCAGGGATCT[A/G]TAGAGGCAGAGAGTGCGGGAGTGGTTGCCAGGGGC R 2 1 2 1 101000 f 74 goat snp36895-scaffold4473-33350 21 63819271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386455 Affx-122970783 AX-123256813 21 61509102 GCCAGGTGACCTGAGAGGGGCTCCAGGGGCCAGTG[A/C]CATCGGTGATTCCTTAAGCTGGGCAGTAGGGTTCC M 2 1 2 1 101000 r 74 goat snp19578-scaffold1973-453669 21 63895613 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398014 Affx-122961782 AX-123268369 21 61541768 TCCCCTCGCTTCTCACAAGAACTCATCTCTAGGGA[C/T]CTTGACCCTCTCCTTTTCCTTCTCCAGCCCTCCCA Y 2 1 2 1 101000 f 74 goat snp19577-scaffold1973-421003 21 63927824 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412158 Affx-122951079 AX-123282508 21 61635580 CACCCAGCTGCCGGCCATCTCCTCTTGGAGGAAGC[A/G]TCTAAGGCCCTCGGTTGACCCGTGATGTTGGCACA R 2 1 2 1 101000 r 74 goat snp19576-scaffold1973-327191 21 64020766 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775758 Affx-122964887 AX-385262889 21 61675039 GGCTAATGGTCAAATCTGTCCCTTCACAGAGAGGA[C/T]AGTTTATTAAAGACGGCGAGTTTCAATCTTTTCCA Y 2 1 2 1 101000 f 74 goat snp19575-scaffold1973-287732 21 64060014 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412744 Affx-122950525 AX-123283093 21 61739785 CACACAAGAGGGATGGTTTCCAAAGAATAATTATA[C/T]GGAGCACTTTTTTTTACAAGGAGATGCAAGCGCTG Y 2 1 2 1 101000 f 74 goat snp19574-scaffold1973-222986 21 64124672 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274412 Affx-1111834239 AX-519548004 21 61780956 CCACTGCAGCTGAAGAACAATCCTATAAAGCGGTC[A/G]CTAGAAATGCCTTTTGAAGTTTAGGCAACAGAAGC R 2 1 2 1 101000 f 74 goat GoatD01.027034 21 61780956 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38379223 Affx-122976278 AX-123249582 21 61786909 AGTACTTAGGATGAACTGAAAAAAGAGATTAATCA[C/T]AGGAAGACCAAGAAAGCAGTAACCCTGGACGTGGA Y 2 1 2 1 101000 f 74 goat snp19573-scaffold1973-175862 21 64171883 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379268 Affx-122976246 AX-123249627 21 61866405 CTGCACCGGAGGGTGGATTCTTAACCACTGGACCA[A/C]TGGGGAAGTCCCTGCTATCCTTATTATTACTAAGT M 2 1 2 1 103000 r 74 goat snp19572-scaffold1973-96366 21 64246025 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800178 Affx-122960523 AX-385287101 21 61930554 TCATGAGATGAGACTGGAAAAGGAGAATAACGTCT[C/T]AGTATTATTACAAACACAGTTTTGACTCAGAGCCC Y 2 1 2 1 101000 f 74 goat snp19571-scaffold1973-32217 21 64309426 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435570 Affx-122933373 AX-123305910 21 61961439 CGAGAGCATCGCTTGTCTGGGCTGTGGATCTTCAA[C/T]GCGGCCTAGAGTCTGACACAGCGCAACTCAGCCCT Y 2 1 2 1 101000 f 74 goat snp19570-scaffold1973-1332 21 64340120 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797011 Affx-122933658 AX-385283952 21 61963129 CTCGGGACAATTACTGCCCGAGTAAGACATTTTTT[C/T]CCTCCTTTTCTTAATAAGCTCCATTCAGGACTTAA Y 2 1 2 1 101000 r 74 goat snp1637-scaffold10461-29557 21 64342224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277528 Affx-1111835894 AX-519551029 21 61991578 AGTCTTATGAAAGGTGACAGAAGCAGAGATAAGAT[A/G]TTTTTACACACCATGTGATTCCCAGGTGTTCATCC R 2 1 2 1 101000 r 74 goat Random2.2K-1960 21 61991578 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38405324 Affx-122956344 AX-123275676 21 62003067 CCGAATAAACTACCACCACGTCCTCCTCCAAACAC[A/G]GGAATAAAGGACTGACCCAGGCGACTTACAACATG R 2 1 2 1 102000 r 74 goat snp15989-scaffold16810-10282 21 64376367 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377353 Affx-122977657 AX-123247712 21 62033066 GAAAATTCCTGGAGCTGTACTCCGAAAATGTTTGC[A/G]TTTAATATATGTCACATTTGAATTAAAAAGTGAAC R 2 1 2 1 202000 r 74 goat snp21331-scaffold2084-25976 21 64403560 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414344 Affx-122950026 AX-123284693 21 62063432 CACTGTTTTTACTTGCTTCCATGTATGGAAATTCA[C/T]AGTACTCAAAAAATCTCAAGGACAAGCAAGCTAAC Y 2 1 2 1 101000 f 74 goat snp21332-scaffold2084-56342 21 64433809 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435668 Affx-122933337 AX-123306007 21 62101899 AGAGAACGAGGATCGCTCCCTGTACCTTGTTTCCT[C/T]TTATCTCGGGGTCAGCATGCTTAGCAAGGCCACAT Y 2 1 2 1 201000 f 74 goat snp21333-scaffold2084-94809 21 64472317 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450673 Affx-122921912 AX-123321007 21 62139292 AGTGAACTTGGGAATCGGTGCCAGCCAGAGGGGAG[C/T]GAAAGAGAAAGGGCAGTGGCCACGCTGCTCATTTG Y 2 1 2 1 202000 f 74 goat snp21334-scaffold2084-132202 21 64509654 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393672 Affx-122965272 AX-123264027 21 62169861 ACTTGCAGGGCTGGTCACGGATTAAGTGGGATAAC[A/G]CAGGTAAGTAAACAGCCTAGCACAGCATCAGTCGC R 2 1 2 1 101000 f 74 goat snp21335-scaffold2084-162771 21 64539988 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385701 Affx-122971117 AX-123256059 21 62255432 TCACTTGGGAGGGAAGTTGTTGGGCAGTTTAGGGA[C/T]GGATGGATTTCCTGAAATGTGTTTCCACGACTGGT Y 2 1 2 1 201000 r 74 goat snp21336-scaffold2084-248342 21 64625683 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378913 Affx-122976451 AX-123249272 21 62295760 TATGAGGTAAGATTTGTTGAGCTTTGTCACGCAGT[A/G]TATGCTCAGCTGTTTTAGCACCGTTTGTTGAAAAG R 2 1 2 1 101000 r 74 goat snp21337-scaffold2084-288670 21 64666140 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463803459 Affx-1110165613 AX-515282265 21 62347164 TTCTGATCAGAGGCTGTTTTACTGCAGACAGAGTC[A/G]TAGGTGTTCTCTCACTCAGTTTAGGTCCCTGCAGT R 2 1 2 1 101000 f 74 goat GoatD01.003807 21 62347164 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38438011 Affx-122931574 AX-123308349 21 62364297 TGGGCGAGATCTCCATTGCCCTGGCCCCGTGGCCC[A/G]ACCTCAGTCCTGTGCCCAGAGTTGTCAGGAGGGGA R 2 1 2 1 101000 r 74 goat snp21338-scaffold2084-357207 21 64729507 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400202 Affx-122960181 AX-123270557 21 62397916 CATTCATGGTGCCTCTATGATGTCCTCAAAGCTTC[A/G]GAGTAGCTGAGCTGAATGCCTTTGCTGCAGGGATG R 2 1 2 1 101000 f 74 goat snp21339-scaffold2084-390826 21 64763548 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430178 Affx-122937361 AX-123300519 21 62426780 TTGAGGCAACTTTGGATCGATCAAGTCTGTTGGCA[A/C]CATTTTTCACACAGTATTTTCTCAGTGTCTCTGTG M 2 1 2 1 101000 f 74 goat snp21340-scaffold2084-419690 21 64792423 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421459 Affx-122943934 AX-123291806 21 62466660 TCCGGGCCCAGATCCCTGCACATCTACTTTATGGC[C/T]GTGTGACTCCAGAGAAACTACTTTACTTCTTGGAG Y 2 1 2 1 101000 r 74 goat snp21341-scaffold2084-459570 21 64833025 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449183 Affx-122923526 AX-123319518 21 62504249 ATTCCCCATCATCCCCATTCTGTAGATGAGAAGAC[C/T]GAGGCAGGTCCTAAGAGGTCCCGTGACTCTCCCTA Y 2 1 2 1 201000 r 74 goat snp21342-scaffold2084-497159 21 64867196 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393430 Affx-122965868 AX-123263786 21 62553567 AATGCGTTCCCAGGCTCTGCCATTTCAGGATGGAG[C/T]GTCTCTGCTTACCTCCTTGTCCACTCACTCACCAA Y 2 1 2 1 201000 r 74 goat snp21343-scaffold2084-546477 21 64915611 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441391 Affx-122928847 AX-123311728 21 62585141 TTGAGGCTGCCTTCCATCTGTTTTAATTTGGTTGA[C/T]GGACATCAGACCTGAAACAGATCTGCCGCTGGAAG Y 2 1 2 1 101000 f 74 goat snp21344-scaffold2084-578051 21 64947104 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402660 Affx-122958374 AX-123273013 21 62616930 ACCCTCACCTTCTAGATTCCCCCAAATCTGATACA[C/T]GGAATGGAGTGTAGGAAGGAAAATGACACTAGCTT Y 2 1 2 1 101000 r 74 goat snp21345-scaffold2084-609840 21 64978203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382524 Affx-122973798 AX-123252882 21 62697696 AGCAAAAAATCTCCCCATTGTATTTCTTCAAACCC[A/G]TGGGCAAGAATCCAAACTCCTTAGCGTAATTATAA R 2 1 2 1 102000 f 74 goat snp21347-scaffold2084-690606 21 65058599 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800733 Affx-122943596 AX-385287650 21 62753313 GTTCTTGACCTTTTGTTGTTCATGAATATGGATGG[C/T]ATTATTATAAGTAAATCGATGCATGAATAAATGAA Y 2 1 2 1 101000 f 74 goat snp21348-scaffold2084-746223 21 65113952 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452701 Affx-122920303 AX-123323034 21 62838136 AAGCGGCCCCCTTCCCGAAATAATATAACTAAATA[G/T]CGGCAGTGCCAACTACAAAAACTCAGAGCCAATGA K 2 1 2 1 201000 r 74 goat snp21350-scaffold2084-831046 21 65198707 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392022 Affx-122966478 AX-123262379 21 62902309 GATTGGCAAACTGAGGCTCCAGCTATGAAGAAGCC[C/T]GAGATCTCAGGGGCAAGTGTGGAGCTGGAGTTCCA Y 2 1 2 1 101000 f 74 goat snp21351-scaffold2084-895219 21 65263030 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402584 Affx-122958436 AX-123272937 21 62936459 TGATAGAATGACAAGCTGCGTCAGCCGCTCCCAGC[A/C]TGGGTGGAAGCAAAAAGCCCCAGCGGTGATGAGCA M 2 1 2 1 101000 r 74 goat snp21352-scaffold2084-929369 21 65297363 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380880 Affx-122975050 AX-123251238 21 63014390 ACCCAGCCCGTGCCCTTTGCAGACACATTTATCCA[C/T]GTGCATTGTGAGTACATGTGAATAAATTCCCCCCA Y 2 1 2 1 101000 r 74 goat snp21354-scaffold2084-1007300 21 65372420 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432216 Affx-122936374 AX-123302557 21 63063947 AGGTGGGAATTTGGGGAGGGGGTATAGGATACAGA[C/T]AGTCAAAAGATACAAACTTCTAGTTATAAAATAAA Y 2 1 2 1 103000 f 74 goat snp21355-scaffold2084-1056857 21 65422520 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445716 Affx-122926106 AX-123316053 21 63117099 GTAAGATACACACGTATAGTGTGAAGCATCATGAC[A/G]CCAGGTAACAAACAGCTAAGGGAGCTGAACAATTC R 2 1 2 1 201000 f 74 goat snp21356-scaffold2084-1110009 21 65476543 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772222 Affx-122964617 AX-385259377 21 63172691 GGTATGCAGGATATACTCTTAACAAAAGGACAAGC[A/G]TCAACAAGGGTCTCTATGAGGAATGACTGTGCAGA R 2 1 2 1 101000 f 74 goat snp21357-scaffold2084-1165601 21 65531140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425465 Affx-122941503 AX-123295811 21 63227594 CTAGGACGGGATCTGGGTTTCCAGCAGTGGAGTCA[C/T]GGCGGCTTCTGTGGCCGGCCCGACGGGGCGCTGAG Y 2 1 2 1 101000 f 74 goat snp21358-scaffold2084-1220504 21 65585997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397611 Affx-122961977 AX-123267966 21 63327568 ACCCTGGTCTCTCCGGGGCAGTTTGACACAATGAA[C/T]GCTCCTGATGGAGCTCCCTTCCTCCCTTTGTCTTC Y 2 1 2 1 101000 f 74 goat snp21360-scaffold2084-1320478 21 65686140 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376260 Affx-122978766 AX-123246619 21 63376203 TCACTTCTTATTTCTATTATTATTGCATCAGGTCC[A/G]TCTCAGATCCCTAGGGATTCGATCTCAGAGATTAC R 2 1 2 1 102000 r 74 goat snp21361-scaffold2084-1369113 21 65734491 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446752 Affx-122925330 AX-123317088 21 63452468 ACACGGCATGCAGGGCGGACAAGGCAGGTGATAAG[A/C]GCAGTTTCCCGGGCCATTCAGGCGAAGGCGTCCCT M 2 1 2 1 101000 f 74 goat snp21363-scaffold2084-1445378 21 65788500 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784567 Affx-122928381 AX-385271615 21 63502305 GCTGCAAAGGCCTTGGGTCTCCTTAAGCATTTCAT[A/G]TCTACATGGTTGTACTTTTGCAGGTATTTATATTC R 2 1 2 1 101000 f 74 goat snp21364-scaffold2084-1495215 21 65838247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430775 Affx-122937483 AX-123301116 21 63536543 GTGTTTTTAATATAGGGCCTTAAGGCCATCCACAG[C/T]TAGAGAGAAATTTACAGGGGTGAAGTTCACAGTGT Y 2 1 2 1 101000 f 74 goat snp21365-scaffold2084-1529453 21 65872747 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417560 Affx-122946912 AX-123287908 21 63585724 TTCCAATGACCACGCACCTCTTCCAAAACCAGAAG[C/T]GATCCTGGGCCCATTCTTTCCAAGGTGATGGCAGA Y 2 1 2 1 101000 f 74 goat snp21366-scaffold2084-1578634 21 65921439 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419313 Affx-122945666 AX-123289661 21 63615090 TAAGACTTACACCGTTAAGTGTGAGTGCAGGCCTG[A/G]CCTCGATCAGGAAACTCTCTTCTGTTCTTCCTGTC R 2 1 2 1 101000 r 74 goat snp21367-scaffold2084-1608000 21 65950808 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394753 Affx-122964850 AX-123265108 21 63652562 CTTCTTGATCTGAACGACACAAGAGCTGCATGACT[A/G]CACACCAACATATTCAGAGATGCTGCAAACATTCG R 2 1 2 1 101000 f 74 goat snp21368-scaffold2084-1645472 21 65988426 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416054 Affx-122948348 AX-123286403 21 63693334 CTTTTGACCCATGTGTATCTTTATATTAAAGTGGA[C/T]GTATCATAGACAGTATATGGTTGAGTCTTATACTT Y 2 1 2 1 101000 r 74 goat snp21369-scaffold2084-1686244 21 66029567 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766980 Affx-122936339 AX-385254278 21 63722225 AACGAATTGGAAGAGATTCTGGACGTCATTGAGCC[A/G]TCAGAGTTCGTGAAGATCATGGAGCCTCTTTTCCG R 2 1 2 1 101000 f 74 goat snp21370-scaffold2084-1715135 21 66057435 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442124 Affx-122928340 AX-123312461 21 63763500 TGCTTTCAAAGTCTTGCCCACTGCACACCTGCTAC[G/T]CAGTTCCTGCAGAGCCAGCAAAGTGTGCAGTTGTG K 2 1 2 1 101000 r 74 goat snp21371-scaffold2084-1756410 21 66098119 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388370 Affx-122969331 AX-123258728 21 63803127 GGCACGTATCAGCAGCGTGCACTTGGGAATGTTTA[C/T]ACACAGACACACTCAAGGGAGCGCAGAGTCCCCTC Y 2 1 2 1 101000 f 74 goat snp21372-scaffold2084-1796037 21 66137713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431947 Affx-122935972 AX-123302288 21 63827328 ATGTTGAAGCGCGTGGAGCCGCTGCGCAACGAGCT[A/G]CAGAAGCTGGAGGACGACGCCAAGGACAACCAGCA R 2 1 2 1 101000 r 74 goat snp15956-scaffold16776-22879 21 66161443 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396192 Affx-122963368 AX-123266547 21 63866057 AAAGGTATTGACGAGGATGACCCCACTGCTGACGA[C/T]AGCAGCGCTGCAGTCACTGAGGAAATGCCGCCCCT Y 2 1 2 1 101000 f 74 goat snp57700-scaffold926-851694 21 66200850 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271934 Affx-1111833229 AX-519545713 21 63879001 GTTGGCCCATTGGCTTCTCCTCATCCTGACCTCCC[A/G]GTGGTGTTTGATGCCCACCATGGGCTCGTTTGCTA R 2 1 2 1 102000 r 74 goat 21_63879001_AF-PAKI 21 63879001 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38393883 Affx-122965124 AX-123264238 21 63959991 ACAAGCTCACCTCTTAGGAACAAAAAACTACAAAC[A/G]TGATAAAGAGACCAGTGAGCACTGGGATTCACACG R 2 1 2 1 201000 f 74 goat snp57698-scaffold926-757760 21 66294894 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386816 Affx-122970104 AX-123257174 21 63990111 ACCTGAGGGGCTCCTGGAACCAGTACCCTGCAGAC[A/G]CCCAGGGATGATTGTATTTCCTCAATGCTAAGGCA R 2 1 2 1 101000 r 74 goat snp57697-scaffold926-727640 21 66325143 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425635 Affx-122940895 AX-123295981 21 64053986 CCTTTGCTATTTTTTTTACTTATTTTCTTCAAGAT[A/G]CAGGCAAATAAATACATCCTCACCAAAGACAACGT R 2 1 2 1 101000 r 74 goat snp57696-scaffold926-663765 21 66389153 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277530 Affx-1111835895 AX-519551031 21 64067550 GCTTTTCAGTATCAGGAAGTTCTCCCTCTGCCTTT[A/C]GTGATAATTTAAAGATAGCCAGGCCCCTTGTCTAA M 2 1 2 1 201000 r 74 goat Random2.2K-1962 21 64067550 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468274423 Affx-1111834277 AX-515283683 21 64069650 ATCTGCTGAGTATCTGCAGCTTACCACGTGTTGTC[A/G]TTCTCAGCCCATCCCTG R 2 1 2 1 101000 f 74 goat GoatD01.028580 21 64069650 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38442313 Affx-122928240 AX-123312650 21 64090320 CGCAGGCGTGTTACACACCAGCCAGGGCCCACACG[C/T]TCAGTGGGAGACAAGCGGCACCCACCTCGAAGTTG Y 2 1 2 1 101000 r 74 goat snp57695-scaffold926-627431 21 66425702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786822 Affx-122926739 AX-385273851 21 64122472 GCTGTGTTCTCTAGACCCGGGAAAGAATACAGAAG[C/T]GTCTTTCAAACGTTCTTTAAGAAGAGAAACTCAGG Y 2 1 2 1 101000 r 74 goat snp57694-scaffold926-595279 21 66457848 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446052 Affx-122925835 AX-123316389 21 64167196 CTTCTGAGCCTCGATAACATGTACTAGAAGCGTGA[C/T]GGGTTCTGTGTTCCCTGGCATCCAGTTACATACAG Y 2 1 2 1 101000 f 74 goat snp57693-scaffold926-550555 21 66501446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391514 Affx-122966665 AX-123261871 21 64235488 CAGAGGCTCCCCCCACCCACTGCAAAGCCTGAACT[A/G]CTTGCTATCCGATGCTTCCCAAAACGTCTGCCCAT R 2 1 2 1 101000 r 74 goat snp57692-scaffold926-482263 21 66568824 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375948 Affx-122978451 AX-123246307 21 64272865 GGCTGAGTATGCTCAGGAGAGATATGAAACCTAAC[A/G]TTTTCAAACAAGGGTAACCCTTCACATTGCTGATG R 2 1 2 1 201000 r 74 goat snp57691-scaffold926-444886 21 66601758 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405964 Affx-122955539 AX-123276316 21 64375279 GGTAAGTCTACGTAATGGAATACCATCTGCTCCAG[C/T]ACAGACTCGAGTTCCGGAGAAGGGCTGTAAACACT Y 2 1 2 1 101000 f 74 goat snp57689-scaffold926-342472 21 66705801 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778283 Affx-122978759 AX-385265398 21 64411959 GATTTTTCATAACTACCAAGTGTGAATTTCCCTCT[A/G]TTTTTCAACGTGGACCCAAATAAGCTCATTTCACA R 2 1 2 1 101000 f 74 goat snp57688-scaffold926-305792 21 66742407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773691 Affx-122934657 AX-385260831 21 64483333 AAGGGAAGCCCATATTACAGTAGATAAATAAAAAA[C/T]GTTAAAAATGTCACCTGTGGAAGACAGAAGAAACA Y 2 1 2 1 101000 r 74 goat snp57686-scaffold926-234418 21 66813739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418386 Affx-122946560 AX-123288734 21 64521124 ACTTTAAGAAAACACAAACATCTCCCCCTGTCGTC[C/T]GGGTTGGCTCTTGGGCCCAGAGAAGAGATGCCAGC Y 2 1 2 1 101000 f 74 goat snp57685-scaffold926-196627 21 66851406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379239 Affx-122976267 AX-123249598 21 64588831 AGCCCAGGCCCTCGTGCAGGAGGCCTTCTTCTTTC[A/C]GCTCCTGGTTAGGTGTGCACGGTGACTTAGAGATT M 2 1 2 1 101000 r 74 goat snp57684-scaffold926-128920 21 66919353 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786598 Affx-122951087 AX-385273630 21 64646591 GAAAACCAGGCCTTTCTGAAATGCCAGCAATAGTA[C/T]ACAGAATTTTGATAAAATACTACCTACTCAATGAT Y 2 1 2 1 101000 f 74 goat snp57683-scaffold926-71160 21 66963401 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434881 Affx-122934348 AX-123305221 21 64695102 ATCTATTAATACCATCTAGCCATCCATTCTCTGTG[G/T]CTCAGAGCCTTCACAAGCATCCCCTATTTATCCTC K 2 1 2 1 101000 r 74 goat snp57682-scaffold926-22649 21 67011277 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445543 Affx-122925159 AX-123315880 21 64737637 TGCTTGTAAACAGGATACAGTGTTCCCAGCATAAA[G/T]AAGGCATAAGGACTGACCCATCTTGAGGCAATGGG K 2 1 2 1 102000 f 74 goat snp30345-scaffold3337-12823 21 67072194 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403917 Affx-122957477 AX-123274269 21 64762993 CTTCTTTACCAAGTACAGGCTTCCCTCCTCAGAGA[C/T]GAGTTGTTTCGTGTTTCGATATTCAAGCATGTAAT Y 2 1 2 1 201000 r 74 goat snp7651-scaffold1276-972500 21 67148132 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277532 Affx-1111835896 AX-519551033 21 64787154 CCGCACTGGCAGGCGGGTTCTCTATCGCTAGTGCC[A/G]CCTGGGAAACCCCCTCTCCTTTCAGTAGCTGTATT R 2 1 2 1 102000 r 74 goat Random2.2K-1963 21 64787154 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388547 Affx-122969187 AX-123258905 21 64793194 ATTGGATTTTCCAGAGATATGAGCACCTGGCTCAG[C/T]GAGACACGGAAAGATCCAGGGCACCAAGGCTGACG Y 2 1 2 1 101000 f 74 goat snp7650-scaffold1276-942299 21 67177807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381443 Affx-122974342 AX-123251801 21 64855698 GCCAAAAGCATGATCAAGATCAAGTTCTCTAGGAC[A/G]CTCACTCTGCAGGTGATGGCCAGGGGTAAAAGCAG R 2 1 2 1 101000 f 74 goat snp7649-scaffold1276-879795 21 67239191 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790354 Affx-122953980 AX-385277357 21 64897809 TTAATTGCATCTTTTCCTATTTCCCTCAAATAAAA[C/T]CATAGCTTATTAGTATTTAATCACTCCCCCATATT Y 2 1 2 1 101000 r 74 goat snp7648-scaffold1276-837684 21 67274478 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452450 Affx-122920567 AX-123322783 21 64934262 TGAATTCATTGGAACTACATACAGAAAGAAGAGGC[C/T]GAAGACACAGGACACGAGAAATGAAAGAAATGACA Y 2 1 2 1 101000 r 74 goat snp7647-scaffold1276-801231 21 67310680 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421308 Affx-122944093 AX-123291655 21 64972437 GGGAGATTTAATCACAGGAGGGTAGCGTAAGGAAA[C/T]GCAGTGAGTCCATGCTGTGGAGCTGGACTGAGATC Y 2 1 2 1 201000 f 74 goat snp7646-scaffold1276-763056 21 67349176 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449108 Affx-122923583 AX-123319443 21 65039350 CTCCCAGCAAAACCCATTTTCCACATGCCCCCCTC[A/G]CCCGCTGAGCTCCCTCCCCTGGGGACACAAGGGAG R 2 1 2 1 103000 f 74 goat snp7645-scaffold1276-696143 21 67416523 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454181 Affx-122919307 AX-123324514 21 65179600 TGCCAAGCCAGGTGACCGAGCCAGGACACAGTGAA[A/G]TGACCACCCCACTGTCGTGTCAGGACAGCACAGGG R 2 1 2 1 201000 r 74 goat snp7643-scaffold1276-555893 21 67518302 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398175 Affx-122962654 AX-123268530 21 65245223 CCACCCTTCCATCCGACGGTCACGTGGCTTGTTCA[C/T]GCCTTCTGTTAGCACGTGGCTCCGGGTGGATGCCT Y 2 1 2 1 101000 f 74 goat snp7642-scaffold1276-490270 21 67585736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769966 Affx-122947736 AX-385257134 21 65289305 AGAATTTAAAATTATTCCTGTGGGGTTTAGTTTAC[A/G]TGGAGAGAATACATGCTGTTAGGCCTGTCATAAAA R 2 1 2 1 101000 r 74 goat snp7641-scaffold1276-446188 21 67626161 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425986 Affx-122941152 AX-123296332 21 65333662 TGAAACACAGTGGTTTACTTATTGCATCATAAGTC[A/G]TTCTGAATCAGTAGTCATTGCCTGGGGGACCTCGC R 2 1 2 1 101000 f 74 goat snp7640-scaffold1276-401831 21 67669946 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394406 Affx-122964612 AX-123264761 21 65399866 CTGCATCGTGCTTCTCTTTGGAAAGCTTCCAGTGC[C/T]GCTCCGGCTCATGGTCATCATTAACCAGCCTTCCA Y 2 1 2 1 101000 f 74 goat snp7639-scaffold1276-335627 21 67735134 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423571 Affx-122942409 AX-123293917 21 65441791 ACGGCTTGGACTTTAATTAGAGCAGCCTTGCTTTG[C/T]GGCCTGTCACACAGGCATCAAGTATCTTCTCTGTC Y 2 1 2 1 101000 f 74 goat snp7638-scaffold1276-293702 21 67776197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427680 Affx-122939308 AX-123298023 21 65560975 CAGAAGCACGCATCTAAGGAGGCACTAGGCAGAAA[C/T]GGCACATGTCCTAAGAAAAGCCTAAGAAGCCCCAG Y 2 1 2 1 101000 r 74 goat snp7636-scaffold1276-174518 21 67895005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407068 Affx-122954915 AX-123277419 21 65668664 TTTCCACACCATGGCAGGGATTGGGACGTGACTCC[A/G]TTCCACATTATTCAGTGACAAATATGCTTCACAGA R 2 1 2 1 201000 r 74 goat snp7634-scaffold1276-66829 NW_017218283.1 47871 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438951 Affx-122930404 AX-123309288 21 65725504 CTTATAGACAAAGTATAGTTGGATCTCGCTTTCCT[A/G]CCCGATCTGTCCATCTGTCTCTCATTTTGGCTATT R 2 1 2 1 201000 f 74 goat snp7633-scaffold1276-9989 21 67993759 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376250 Affx-122978774 AX-123246609 21 65738141 GTGTTCTCCAGCAATACCAGGGATCCCTGGAGAAA[C/T]GACTGATCCTAGGGCTGGAGCAGAAAAAATTCCAG Y 2 1 2 1 202000 f 74 goat snp25962-scaffold2688-441741 21 68006246 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414116 Affx-122949730 AX-123284465 21 65785557 ATGTCATACCTCAAAGAAACTTGGCCAGGGAAATA[C/T]GGTTCTTTGGGGCCACTAACTGTGACAGCCTCGTA Y 2 1 2 1 101000 f 74 goat snp25961-scaffold2688-394325 21 68054143 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402977 Affx-122958152 AX-123273330 21 65815006 AACATCTTCTTCTCTGCTTACTCACCCATTTTTGC[A/G]TATTGTCCTTTCTCGTTAGAGCCTTTAATGCATTA R 2 1 2 1 201000 r 74 goat snp25960-scaffold2688-364876 21 68083757 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437069 Affx-122933082 AX-123307407 21 65918966 ATTTTAATGTGCCCGGTTCACCAAACGTCTGCTTA[C/T]GCTTTGCGAGAGTGGTGTGAGAGCTCGCGTTGTCC Y 2 1 2 1 101000 f 74 goat snp25958-scaffold2688-260916 21 68185828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376442 Affx-122978063 AX-123246801 21 65952666 GAGCACAGCTCCCTCCTCTGCAGATTTATGGGGCC[A/G]CAGGGAGGCACCCGGGGTGTCTGTGCGTTCTTTTT R 2 1 2 1 303000 f 74 goat snp25957-scaffold2688-227216 21 68219557 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774952 Affx-122962138 AX-385262085 21 65987348 TGAAGAAAATACTTAGGAAATATGGGTCATTTATT[A/G]TGGAAAATGAAGAAGATTCAAAGAATGGAGCCTAG R 2 1 2 1 101000 r 74 goat snp25956-scaffold2688-192534 21 68253844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399493 Affx-122961176 AX-123269848 21 66032890 AATATTCCGCAGGGCTGACCCTGTGATTGACGACC[A/G]TGCTCCTTCATTAGTGGGGATGTTCGGGAGGTTTG R 2 1 2 1 201000 f 74 goat snp25955-scaffold2688-146992 21 68293382 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376325 Affx-122978351 AX-123246684 21 66080698 CCCCGTGGGGTCATCTGTGTTTTCAGGGAGCCAGC[A/G]CTGTCTTCCTGCTCTTTTCTGGTCTGTGTCCCCAT R 2 1 2 1 102000 r 74 goat snp25954-scaffold2688-99184 21 68339042 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427648 Affx-122939329 AX-123297991 21 66161285 CCGCCCGCCTGGGGGCCAAACAAATGGTATCACAG[C/T]AACCAGGGAACCCTCTGCTGCAGCAGAGATGTGTG Y 2 1 2 1 201000 f 74 goat snp25952-scaffold2688-18597 21 68592516 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411388 Affx-122952228 AX-123281738 21 66228854 GGTAGAGGCAGGGCTCTCAGCAAGACTCCGAGAGG[C/T]AGTCCCCTCTGGGTTCACTCTGACCTGACTTGAAA Y 2 1 2 1 101000 r 74 goat snp27046-scaffold2877-48873 21 68659049 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442411 Affx-122927987 AX-123312748 21 66264182 TTGAACCACCAGGGAAGCCCCAACATTTCTTCTTC[A/G]TGACAGCCATCTTGCCAGTTATTCTTAATGCTCGT R 2 1 2 1 201000 r 74 goat snp27047-scaffold2877-84201 21 68694660 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453468 Affx-122919848 AX-123323801 21 66317017 AATCACCCATGTTGTCCCTTCATTCTACCCCTGTC[A/G]TAACCAGGTTTTACAGCTCACTTCTCAATCCAGGA R 2 1 2 1 201000 r 74 goat snp27048-scaffold2877-137036 21 68748285 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431199 Affx-122937167 AX-123301540 21 66387989 ATCTAGCGACCTGGGGAAGCCCCCTTGGCTCTCTC[C/T]GGGGACGGCCCTGTCCCAGGGGCCTCCCGGCATGG Y 2 1 2 1 103000 f 74 goat snp5092-scaffold1174-66161 21 68812847 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391685 Affx-122967587 AX-123262042 21 66419674 TTAGGGTCTTTCACAGTAAAGCTCATCCACGACGC[A/G]GCCTTAGAGAAGCGGGAGCGGAATTTGACCCTGAC R 2 1 2 1 101000 f 74 goat snp5093-scaffold1174-97846 21 68844495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272105 Affx-1111833230 AX-519545863 21 66451286 CTCCGGGAGGCAGCTGTCACTGGGGTCCTTTTCTA[A/G]CCACGATCTAACACAGCACACAACAGAGGCGAGCT R 2 1 2 1 202000 f 74 goat 21_66451286_AF-PAKI 21 66451286 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38377481 Affx-122977503 AX-123247840 21 66460031 AACCAACTGTGAGGCCCGACAACAGAGAAAGGGGA[A/G]GGACAAACGCCAAGAACGAGGGCGGCCTGCGTCAT R 2 1 2 1 201000 r 74 goat snp40976-scaffold5271-82192 21 68885309 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386394 Affx-122970832 AX-123256752 21 66564166 TGTTCTGGAGATATGCGGGCTTCTTGTTGCTCTTT[A/C]CTCGCTCAGTCGTGTCCGACTCGTTGCGACCCCAC M 2 1 2 1 101000 f 74 goat snp37055-scaffold4491-185111 21 68414726 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438204 Affx-122931458 AX-123308542 21 66599858 TTGGCTTCCTTTTCAGAGTTGCTTACTTACAGTAT[A/G]TAGTTCCTTTCCCTTTTCATTCATTCGATTTTAGA R 2 1 2 1 101000 f 74 goat snp37054-scaffold4491-149419 21 69232517 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418598 Affx-122946360 AX-123288946 21 66656252 CACCGCAAAGAAAAGTCTACACAAAGCCCAGAAGC[C/T]GCCATGGGACTGGGGCAGGGAGGCGGCCTGGGGGC Y 2 1 2 1 101000 f 74 goat snp37053-scaffold4491-93025 21 68499653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438885 Affx-122930737 AX-123309222 21 66714483 GCCTGTAGGCAGACTCTTCACAGAGCCAGGCTCCT[A/G]ACCCCAGGGCTCCGGGCCCTCAGCCTGGGAAGCCG R 2 1 2 1 101000 f 74 goat snp37052-scaffold4491-34794 21 68558183 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277535 Affx-1111835897 AX-519551036 21 66736628 TCAAGGGTATATATCTTTCTTCGAGGACTCAGCCT[A/C]TGGCAAATTTCAGATTTAAAAAGACCCAGCGATGG M 2 1 2 1 101000 r 74 goat Random2.2K-1965 21 66736628 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320763765 Affx-986698293 AX-385251570 21 67027446 TTCACCATTGCCCGGGGTTTGCTCAGATTTAGGTC[C/T]GTTGAGTCGGCAATGCCATCCAACTATCTCATCCT Y 2 1 2 1 600010 f 74 goat 21_67027446 21 67027446 Ancestral_priority_1043 ancestry 0.58 neutral IMAGE 10K 10K ancestral 320767013 Affx-986698297 AX-385254306 21 67143586 ACTAACGCACAAAGAAAGTAAAAAGAGAGACTAAT[C/T]GAGCCTCAAACTAGTGGTTACTTCTCTGCAAATTT Y 2 1 2 1 600010 r 74 goat 21_67143586 21 67143586 Ancestral_priority_1043 ancestry 0.508 neutral IMAGE 10K 10K ancestral 468277410 Affx-1111835898 AX-519550914 21 67185169 TTATCAGCATCCTGCCAGGACAGGGTGGTTAACCC[A/G]GCATCCAGGAGGGAGTCCTCCAGAGCTGGGAGCAG R 2 1 2 1 102000 f 74 goat Random2.2K-1967 21 67185169 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468277412 Affx-1111835899 AX-519550916 21 67420174 CCCATCAACTGTCCAACATTTCAAAGAGAATCACA[A/G]TTTCAGAAGAGTATAGTAAAGGTGGTCCACACTCA R 2 1 2 1 101000 f 74 goat Random2.2K-1968 21 67420174 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320803545 Affx-986696393 AX-385290351 21 68939117 TTCCTGGCGCCTGTGCTTCTGTGGCACAGCTCAGC[C/T]GGTGCTCCTCAGACGTCGGAGGGCCTGCCCCAAGG Y 2 1 2 1 600010 f 74 goat 21_68939117 21 68939117 Ancestral_priority_1043 ancestry 0.406 neutral IMAGE 10K 10K ancestral 468277541 Affx-1111835900 AX-519551042 21 68980733 CTAACCACCTACAATAACCCCTTAGGATACAGCCT[A/C]ACTGGTGTCCAGACATTTTCAAGTGTCCTCTGGGG M 2 1 2 1 201000 r 74 goat Random2.2K-1971 21 68980733 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392975 Affx-122965672 AX-123263332 22 7792 CTGTGCCATGGGCCACCGCGGTTTGAGTCAATTCA[C/T]GGCGTGAAAGTCGAGGCAGTGCAGGAAATACAGGT Y 2 1 2 1 201000 f 74 goat snp6908-scaffold1251-1645032 NW_017192837.1 4217 G A 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382143 Affx-122974047 AX-123252501 22 36695 TGACACTGCTGCTTAAGCTCAGGACGAAAGTGGAC[G/T]TGCATGTCTCCACTTGAGACGAGGCCTGACACCCC K 2 1 2 1 101000 f 74 goat snp6907-scaffold1251-1616129 22 31266 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414646 Affx-122949322 AX-123284995 22 70141 CCCAATGAATTGAAAGCAAATGAACGAACCACAAC[A/G]CCACACCCACAGCCATCTTTAGCAATGTATTCTAT R 2 1 2 1 101000 f 74 goat snp6906-scaffold1251-1582683 22 65141 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780041 Affx-122930232 AX-385267140 22 106196 TTCCACTTTAAACCTGTATATCTGTAGAGCTGATA[G/T]GAGTTCCCTGTAGGTAGCTTATAGTTGGGTCTTGT K 2 1 2 1 101000 r 74 goat snp6905-scaffold1251-1546628 22 102104 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272115 Affx-1111833235 AX-519545873 22 149511 CTGTTAAAATGGCTAAAACAGCTGTGAACACCATA[A/G]CCACTGGGGTTACAAGAACTCTTTTCAGAGAAGGC R 2 1 2 1 101000 f 74 goat 22_149511_AF-PAKI 22 149511 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38376546 Affx-122977988 AX-123246905 22 163025 AGACACTGAGGAACTCACATGAGGTATATATATCT[A/G]CTCCTGGGTGAAGTCCAAAAGAGCCCTGAGCCTCT R 2 1 2 1 101000 f 74 goat snp6904-scaffold1251-1489799 22 159101 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404299 Affx-122957029 AX-123274651 22 197994 CCGCGATCAATTGTGTGTCCTCAAATTGGATAACT[A/C]TAGGTAAAACAGACAAATTCGAAGAGACATAAAAT M 2 1 2 1 101000 f 74 goat snp6903-scaffold1251-1454830 22 194935 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425582 Affx-122941419 AX-123295928 22 266369 AGATGATGACTATGTGGGCATCCATTATATGATTA[G/T]CTACAGTACTTTACATGCCTTGAAACAGTTTATAA K 2 1 2 1 101000 f 74 goat snp6902-scaffold1251-1386455 22 263485 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380507 Affx-122975697 AX-123250865 22 357457 ACTCAGAGTGCCTCAAGGGCTGGTCAGGTGGAGCA[A/G]TTCTGCCCACAGAAAGTGCAAGTTTGCAATTGTGA R 2 1 2 1 101000 r 74 goat snp6900-scaffold1251-1295367 22 353494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418470 Affx-122946459 AX-123288818 22 420534 GCCATTCAAAGGCTCCCCTTCTCACTTACTGCTGA[C/T]GAGCCAGGCTCCAAAACTTGCAATCAGTTAATCCT Y 2 1 2 1 201000 r 74 goat snp6899-scaffold1251-1232290 22 416832 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402671 Affx-122958365 AX-123273024 22 465899 AAGAACAGGCCCCAAAGAACAAATCCTTGCTAATC[G/T]CAAATGATAATCCTCACATTGACATAAATTATTCT K 2 1 2 1 201000 r 74 goat snp6898-scaffold1251-1186925 22 462795 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412713 Affx-122950742 AX-123283062 22 505483 CTGCTAAAAGACCAACCATGAGCCTTTAGGGTGGG[A/C]GGAGGTACCCTGAGTCATTCCTCCAATGACACATC M 2 1 2 1 201000 f 74 goat snp6897-scaffold1251-1147341 22 498611 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436069 Affx-122932700 AX-123306408 22 572475 ATACATTGTCCAGCATGGTAACCACTAGCTACAGA[C/T]GATTATTTGAATGTAAATTAGTTTAATGAAGATTA Y 2 1 2 1 101000 f 74 goat snp6895-scaffold1251-1080349 22 565375 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449875 Affx-122922357 AX-123320210 22 618464 CAGATGACTGTGTCCCCCTGTCTGTATCTCTGAGG[C/T]GATATGTCTCACTAAAACTTGGAGCCCTGTTACCA Y 2 1 2 1 101000 r 74 goat snp6894-scaffold1251-1034360 22 611923 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434189 Affx-122934872 AX-123304530 22 687814 ACATCACTCAATCTCTGCTTCCTGGATCACACTAC[A/G]TTTTCTTTGTGTGTGAAATCTCCTTCTGTTTCCCT R 2 1 2 1 201000 r 74 goat snp6893-scaffold1251-965010 22 676773 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407654 Affx-122954608 AX-123278005 22 736907 CATCCAGGTGAGAAACCTGGGCACCCTCCATCCCG[C/T]AGAGGTGACAATAATAATGACGGCTACTTTTATAA Y 2 1 2 1 101000 r 74 goat snp6892-scaffold1251-915917 22 726571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425632 Affx-122940897 AX-123295978 22 780884 CAAAAGCCAACAAGAGGATTCCTGCTAAATGCTTT[A/G]TATATATGACTGTGAAGAAAGCTGAGCACTGAAGA R 2 1 2 1 103000 f 74 goat snp6891-scaffold1251-871940 22 770498 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426378 Affx-122940241 AX-123296724 22 912136 TATATCATGTGGGATATGTTAATATAATCAAGTTT[A/C]TAAACCTTGTTCACCAGTTTACAACAGACTGTCCT M 2 1 2 1 201000 f 74 goat snp6888-scaffold1251-740688 22 902083 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434525 Affx-122934158 AX-123304866 22 945922 GATCATGTTGTAAACATGTTAACTCCAGCTGGAGA[A/G]AGGTCTGCAAATAAAACCAGAGATAACATGAGGCA R 2 1 2 1 101000 f 74 goat snp6887-scaffold1251-706902 22 935947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375647 Affx-122978690 AX-123246006 22 976804 GGACACAGAGGGAAGCAGTCAGCACTCAAGCAAAC[A/G]TTTATTTTCTTGGAATATTAACTTATGGATAGCAT R 2 1 2 1 201000 r 74 goat snp6886-scaffold1251-676020 22 966160 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394989 Affx-122964256 AX-123265344 22 1007603 GTTGGTGATGCCATTCAGCCATCTCATCCTCTGTC[A/G]TCCCCTTCTAGTGGTTACAAACACAGAATTATTCA R 2 1 2 1 101000 r 74 goat snp6885-scaffold1251-645221 22 996856 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400231 Affx-122960158 AX-123270586 22 1036275 CTCTTGAGCCAAATGACCACTGTCAGGAGCCAATG[C/T]AACCTGAAGGCAGAAGCACAAATGATACTAGGTCA Y 2 1 2 1 101000 f 74 goat snp6884-scaffold1251-616549 22 1025419 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439658 Affx-122930600 AX-123309995 22 1123649 TATATAATTTAAATTTTCCCCTTCCATAATAAAGG[A/G]TTAAATAGATAGAAATTCACTGTGGAACAAAGAGG R 2 1 2 1 101000 r 74 goat snp6883-scaffold1251-529175 22 1112083 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415759 Affx-122948931 AX-123286108 22 1163379 TCTTCAGAATCCTTTCATCACCTCAAGCTAGAATT[A/C]TGTACCCCATTAAACAATAATTCTCCACTCATTCC M 2 1 2 1 201000 f 74 goat snp6882-scaffold1251-489445 22 1151127 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382565 Affx-122973767 AX-123252923 22 1192588 ACATCATGCAGACTGAAAAACTCCATCATACACTC[A/G]TGAGAAAATGAGAGCAAGAAACACCAACAATGTCT R 2 1 2 1 101000 f 74 goat snp6881-scaffold1251-460236 22 1180459 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405906 Affx-122955583 AX-123276258 22 1242308 ACTTGGTGACTGAACAAATTCTCCCATACTCAAGG[C/T]GAAAAGGTGAGGTGAAGTCCTTCGTATCAACAGTG Y 2 1 2 1 201000 f 74 goat snp6880-scaffold1251-410516 22 1230950 C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441618 Affx-122928646 AX-123311955 22 1281665 CCTCAGGCCCAGGGCCACTCCTTTCCTGAAATTAA[C/T]GGCTCACATATATAAGTACCGTTTAGCCACAAATT Y 2 1 2 1 101000 r 74 goat snp6879-scaffold1251-371159 22 1271312 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382367 Affx-122973863 AX-123252725 22 1319592 TCTTCACTTGCTATCATCTCAAAAAGATTTTAATA[C/T]GCTCTTTCAACAGGAAAAATATTTCTTTCAGTTTT Y 2 1 2 1 201000 f 74 goat snp6878-scaffold1251-333232 22 1309832 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447246 Affx-122924956 AX-123317582 22 1371920 ACTTAAGACTGTCAGTCAAACCTATACACATGTCT[A/G]CAAAGCATCAAGACAGCAATTAGAGCACTAAGCCA R 2 1 2 1 201000 f 74 goat snp6877-scaffold1251-280904 22 1364032 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391190 Affx-122967423 AX-123261547 22 1403153 TGCAGGTCAGGAACTGAATATGATCATGTTAGAGT[A/G]TCTTTACTCTATTTACAGATTAAATAGCAAGGATG R 2 1 2 1 101000 f 74 goat snp6876-scaffold1251-249671 22 1395942 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387822 Affx-122969674 AX-123258180 22 1461469 CATAAGAAATTATTTTGTTTTAAAAGCTTCAATGA[A/G]GTATAATTCACACATTACTTTGTGTGATATAGGGC R 2 1 2 1 103000 r 74 goat snp6875-scaffold1251-191355 22 1453348 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787672 Affx-122970432 AX-385274695 22 1518830 GCATAGTATAATCCCATTCATGTTATTACATTAGA[C/T]AATTAAAAGCTGGCAAATTTTTCACTGGATGGATC Y 2 1 2 1 101000 r 74 goat snp6874-scaffold1251-133994 22 1512058 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797867 Affx-122974042 AX-385284805 22 1553203 CAAGTCCATTTAACATCCACCACATGTAGCTACAC[A/G]TTTCCCTCATGATAAGAACTGTTTTCCCCAGACTT R 2 1 2 1 101000 f 74 goat snp6873-scaffold1251-99621 22 1544199 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445426 Affx-122925368 AX-123315763 22 1601141 AGCTTGGGTCTTTTATTGCCAACTCAAGCCATTGA[C/T]GCTGGTTTTACTGGAGATGTGGAGACTGAGAGTCT Y 2 1 2 1 201000 f 74 goat snp6872-scaffold1251-51683 22 1592729 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438508 Affx-122931211 AX-123308846 22 1649544 CTCAGTGTCTGCCATATAAAAAGAGATCAAAAATT[A/G]TTTCCTGAAGGAATGAATGAATATCATTGTCACCT R 2 1 2 1 202000 f 74 goat snp6871-scaffold1251-3280 22 1640928 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400363 Affx-122960028 AX-123270718 22 1653069 CATTTTCATGGTTTTTTTTAATCACACATGTCAGG[A/C]GGATATATGAGTATAGGTAGAGTTCACTTTCCTGT M 2 1 2 1 101000 r 74 goat snp24413-scaffold2476-146 22 1644317 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396591 Affx-122962905 AX-123266946 22 1712706 TACCAGATATTAAAATATACTAAAAACTCCCAGAA[A/G]TTAAAGTGTGTAAGTGGTCCATGCCTAGACCAATC R 2 1 2 1 101000 r 74 goat snp24414-scaffold2476-59783 22 1704290 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773285 Affx-122944488 AX-385260428 22 1776349 CTATGAAAACTGTCTTTAAAATAGATCCGAAGTAG[C/T]TTGGAAAATATAGGTAAGGAAACATCAATCTCAGC Y 2 1 2 1 101000 r 74 goat snp24415-scaffold2476-123426 22 1767384 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388379 Affx-122969323 AX-123258737 22 1801507 CTTGTCCTCTGTTACAGAAGTGGTCCCTCTTAACA[G/T]GTTATGAATATCATAATACTGCATTCACATGGTTT K 2 1 2 1 201000 r 74 goat snp6782-scaffold1248-208536 22 1792541 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463809759 Affx-1110168705 AX-515288498 22 1804587 GGTCACTGCAGGAAACCACTAGCCCTTGAGTCTTC[A/G]TCTGGTGTCCATTTCTGCAGAAACCTTTACCAGGA R 2 1 2 1 201000 f 74 goat GoatD01.029474 22 1804587 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38442424 Affx-122927977 AX-123312761 22 1865659 GATACGGATACGGATGACAGACGCAAGAACTGACA[A/G]GAGGGCACAGAGTGTGAGAAGGCAAGGGTCACTGT R 2 1 2 1 102000 f 74 goat snp6781-scaffold1248-144384 22 1855546 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397740 Affx-122962538 AX-123268095 22 1897578 TGGGTTAGCCCGTGAGCCATAGTGACCAGAGTACC[A/G]TGGAAACTCTTGAATTGGTAGAGATGTTTATATTT R 2 1 2 1 101000 r 74 goat snp6780-scaffold1248-112465 22 1887707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418827 Affx-122946153 AX-123289175 22 1937318 CACACCTGACCTGTCTTAGCGCCCTCCTCATATGC[A/G]TGCACATCTTTTTGCTAAGACGGATTCCAGGGCCA R 2 1 2 1 101000 r 74 goat snp6779-scaffold1248-72725 22 1927766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803461 Affx-122961285 AX-385290288 22 1977852 TCTTTGCATTTCCTATAAGAACGGCTGTGGAGAAG[A/C]TTCTTTACAATAAGCAACAGTTTGCTGGTAAATTC M 2 1 2 1 101000 r 74 goat snp6778-scaffold1248-32191 22 1968636 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380913 Affx-122975025 AX-123251271 22 2006582 ATGTAGAAGCTGCTGGTAGAGGCCACATAGCTGCT[A/G]CTGAACATCATGGAGGAGCTGGGTTGAGTTAGTAT R 2 1 2 1 201000 r 74 goat snp6777-scaffold1248-3461 NW_017195002.1 18342 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404287 Affx-122957036 AX-123274639 22 2012852 CAGATTCCTCTCGCCTTTCCCAGTGGGTGGTTCCC[C/T]ACTCCACCACCAGGATAGCTACCCTGCGCCCCACC Y 2 1 2 1 101000 f 74 goat snp22226-scaffold22-2710 22 2003792 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430203 Affx-122937343 AX-123300544 22 2052087 AGAGTGAGATTTCCCAAGAATTAGATGTGGGAAGA[G/T]AAGAGAAGAGGAGGAAAGTGTTGGGGAAGAGGAGA K 2 1 2 1 201000 f 74 goat snp22227-scaffold22-41945 22 2042056 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800542 Affx-122935148 AX-385287462 22 2155975 TAGACTTTAAATGAGAATTATAACTTGGAGAAAAC[C/T]CAGTCCTGGGAATTTTTCATGATGAGATCATTAGC Y 2 1 2 1 101000 r 74 goat snp22229-scaffold22-145833 22 2147767 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277543 Affx-1111835901 AX-519551044 22 2211005 AGAGGTATTGACGGGCCAGTGGGGAGCTGGGGCGC[A/G]GGGAGGAGGAGCAAACCCTGCCTGGAAGGCACAGG R 2 1 2 1 202000 r 74 goat Random2.2K-1974 22 2211005 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430217 Affx-122937333 AX-123300558 22 2229379 GAACTAAGACCTGTTTTTCATCCCTGTTGAATGGA[A/G]CTCTCTCGGGACTTTGACAAGTAGAACGTGGTTGA R 2 1 2 1 101000 f 74 goat snp22231-scaffold22-219237 22 2218429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426956 Affx-122940410 AX-123297301 22 2259135 AGTATATACTTATATTAGATTTTAAGACAAAATTA[C/T]CACGTAAATTCAGCCAGTCCATTGTGCCAAACTAT Y 2 1 2 1 101000 r 74 goat snp22232-scaffold22-248993 22 2248145 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420785 Affx-122944698 AX-123291132 22 2338712 TCTGAGAATAAATGAAAATATAATCTATAATAAAG[C/T]AGGTTTTGCAAACCAACAGGCAATGAACATATTAT Y 2 1 2 1 103000 r 74 goat snp22233-scaffold22-328570 22 2328560 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426156 Affx-122940601 AX-123296502 22 2441197 CCAAGTTTGAAATGTGTCATCTGTACTCGAGAAAC[A/G]CATCAGGAATAAGAGAAAGAAATGGACTCGGGTAG R 2 1 2 1 201000 f 74 goat snp22235-scaffold22-431055 22 2431147 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783306 Affx-122978820 AX-385270371 22 2528219 TTTTTAAAAACTGAGTCTGTGAAAAAGTTCTTATA[A/G]CTACTTGTCATTCCTGTTTAAAAAGATATTTCGTT R 2 1 2 1 101000 r 74 goat snp22237-scaffold22-518077 22 2519556 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388900 Affx-122968852 AX-123259258 22 2579189 CAGGCTCCCACATCATCTTCTCTCATGTTGGACTG[C/T]AATAATTTGTTTATGTGTTTGTCTCTCTCCCTCTG Y 2 1 2 1 101000 f 74 goat snp22238-scaffold22-569047 22 2573100 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274660 Affx-1111834426 AX-519548246 22 2581239 ACGGAAGACCTGCTGAGCTGAGACCCACTTTCCCA[A/G]CCCTGTTCCACCGCGTCAGCTTCTCTGCCAACTGA R 2 1 2 1 102000 f 74 goat GoatD01.035297 22 2581239 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38428841 Affx-122938365 AX-123299183 22 2651688 TGGTGGCACTGTCGGAAAGTGCAGAGAACATCTCT[A/G]TCGCTGCAGAAAGTCTCACTGGACCAGAGAAAATA R 2 1 2 1 101000 r 74 goat snp22240-scaffold22-641546 22 2644389 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375894 Affx-122978490 AX-123246253 22 2691617 GACAGCTGTTTAAAAATAAAGACATAAAATAGAAA[C/T]GTCTCACTGAATAAATAAGCAGAAAAAAGTATATT Y 2 1 2 1 101000 f 74 goat snp22241-scaffold22-681475 22 2684964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383565 Affx-122972601 AX-123253923 22 2720500 GTGTTTTTGTAGGTTAAGGGGAATTTTCTTGAACT[C/T]GGAATATTGCTTGACTCTTCTTACATACATTATAA Y 2 1 2 1 101000 f 74 goat snp22242-scaffold22-710358 22 2714025 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801116 Affx-122946581 AX-385288030 22 2750180 TTCATAAGAATTCATATTGGCTATACTCCATATCT[A/G]AGACCTTTGTTCTGTTGAACAATGAAACTGTGTAA R 2 1 2 1 202000 f 74 goat snp22243-scaffold22-740038 22 2743714 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771210 Affx-122952536 AX-385258368 22 2784887 GGTACTTGCTGATGGACTTTACTGAATCTCTGACC[A/G]TACTGTATCATTGTTCCATTCAGCTTGAAAGCAGT R 2 1 2 1 101000 f 74 goat snp22244-scaffold22-774745 22 2779273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277419 Affx-1111835902 AX-519550923 22 2844509 ATCCAGGGTTATATGTCAATATAGGAGAAGGGAAC[A/G]ACAGAGGATGAGATGGTTGGATGGTATCACCAACT R 2 1 2 1 201000 f 74 goat Random2.2K-1975 22 2844509 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320771911 Affx-122942638 AX-385259067 22 2857142 TGTTGAGGGGTAGAGATAGGACTAAGTATTCAGTT[A/G]CTTTTACACTGACACTTACTGTACGTTATATTTTA R 2 1 2 1 101000 f 74 goat snp22245-scaffold22-847000 22 2852331 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401182 Affx-122959349 AX-123271535 22 2902520 CCCAGGGGAGTGGTATAAATGATCCTTTCTTGTCT[A/G]CTTTGGCTTCATGCATTCCTCTCTCACCTCACTTC R 2 1 2 1 201000 r 74 goat snp22246-scaffold22-892378 22 2897560 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272558 Affx-1111833241 AX-519546274 22 2904217 CTGCTGTAGATGCTGTAATAGCAGCCCTCGGGTGA[A/G]ATGACAGTCACCACTGACATGCAAATCAGGACGTT R 2 1 2 1 101000 r 74 goat 22_2904217_AF-PAKI 22 2904217 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38384289 Affx-122972295 AX-123254647 22 2933527 GGGAGAAACAAAGATGGTTTTAAGGCTTGACGTAT[A/G]CCATGCTGACTCCACTGGTTGAAGAATGAAAAATT R 2 1 2 1 101000 f 74 goat snp22247-scaffold22-923385 22 2928494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412923 Affx-122950394 AX-123283272 22 3036913 ACATAGGCCCAGATATTAATTTACATCTGGGTTAT[A/G]CATTTCAGAACATTTAAAATTTTGTTTTCTTTCCA R 2 1 2 1 103000 f 74 goat snp22249-scaffold22-1026771 22 3032860 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386424 Affx-122970808 AX-123256782 22 3085346 GTGAAGCATATTGCATTTAGAAGGTAGGTTAGCAC[C/T]AGGTGACCATATAATTTATAGACCAAACCAGACAG Y 2 1 2 1 201000 f 74 goat snp22250-scaffold22-1075204 22 3081820 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407371 Affx-122955269 AX-123277722 22 3151348 CCAAGTCCTAGCCTTTGGACCATCAGGGAATTTCC[A/G]CAAAATGGATCTCAAGAGATGTCTTGAACCACATG R 2 1 2 1 101000 r 74 goat snp22252-scaffold22-1141206 22 3148110 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384600 Affx-122972575 AX-123254958 22 3182219 TGGTGCCTATGGGGCATCCCCTGGTGACATGTAGT[A/G]TTCAGCTGGATCTAGAGCTCAGAGAAGACATGGAT R 2 1 2 1 101000 r 74 goat snp22253-scaffold22-1172077 22 3179012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274989 Affx-1111834528 AX-519548571 22 3229381 CCAGAGATGCTTTTCTTCTTCCTAAGCCAGCGCAA[A/C]GGACCAGACGCAAGCCCACACAACGTCACTCTTTA M 2 1 2 1 202000 r 74 goat GoatD01.040033 22 3229381 T G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38389164 Affx-122968528 AX-123259522 22 3272200 AGAAGCCAGGCAGGGCAGTTTAATGTCATGGGTTC[A/G]CAGCACTGGTCTTTGGTGACATATGGCTGGGATTC R 2 1 2 1 101000 f 74 goat snp22255-scaffold22-1262058 22 3268988 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415107 Affx-122949443 AX-123285456 22 3302385 GTTCCTCCCCTAAGGAGCTTGGAGTCAGCAGGCAC[A/G]TTACCTAATCCAGAATGCAGAATAAAGAACAAGCA R 2 1 2 1 101000 r 74 goat snp22256-scaffold22-1292243 22 3299074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773672 Affx-122975825 AX-385260812 22 3340311 AACATCTAGGCATTCAGATTTGTTTCTATCCATTA[C/T]GGCAAACTTAGACATTAGCAACTCCTACACAAATC Y 2 1 2 1 101000 r 74 goat snp22257-scaffold22-1330169 22 3337025 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449266 Affx-122923034 AX-123319601 22 3370483 TGCAAGGAGAAGAGAGGCTGGGGGATGTGAAGCAT[A/G]TTTTAAAATAATTTCCTCTCCCACCTATGTATCAT R 2 1 2 1 303000 r 74 goat snp22258-scaffold22-1360341 22 3367236 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769582 Affx-122953834 AX-385256752 22 3406477 AGTCACAATAATGGATTTTTTGGATAAAGAATGCT[A/G]CTTTAATGCTTTTTGTGAATATCCACCTCAGTTTC R 2 1 2 1 201000 r 74 goat snp22259-scaffold22-1396335 22 3402683 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797889 Affx-122929260 AX-385284827 22 3462188 TTTACAGAAGATAGTGAATTGAATCTAAGCAAGTC[A/G]GAGCACTTGGGTCATTTCATAATTGTTCCCCTGTC R 2 1 2 1 101000 r 74 goat snp22260-scaffold22-1452046 22 3459302 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777826 Affx-122958596 AX-385264943 22 3523392 TCCATAGATAGGAAAGATATGTTAATTGGGAAAAC[A/G]TAGGTTTAATAACATGTCATCCTATTGATAAACAA R 2 1 2 1 101000 f 74 goat snp22261-scaffold22-1513250 22 3521626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402304 Affx-122959091 AX-123272657 22 3554646 TCTGAAAAACTCTGTTTTCAGTTGATGGGTTTGCA[C/T]GGACCTCAAAGAAGCTAACTTGTAATCCATGCCTG Y 2 1 2 1 201000 r 74 goat snp22262-scaffold22-1544504 22 3553327 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421366 Affx-122944049 AX-123291713 22 3584074 AGGAAGAAGAAGGTGCTGACTGGTGGATGGGCAGC[G/T]TGGACAGTCTGTCATAGAATGTGGTTATTTAATTT K 2 1 2 1 101000 r 74 goat snp22263-scaffold22-1573932 22 3582753 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385688 Affx-122971129 AX-123256046 22 3613331 CACTTTATAATATGCATCCCAGCAACACACATTCA[C/T]GCAGATTTTTTATTCTCATTTTCTGCCTCAATCTC Y 2 1 2 1 101000 f 74 goat snp22264-scaffold22-1603189 22 3612152 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449256 Affx-122923042 AX-123319591 22 3643563 GTGTTTCCAAGTTGGTACAGCAGTCAGTCAGTACC[A/G]TTAAGGACATAGGCTTTTTCTGTCTTTCTTCTCTG R 2 1 2 1 201000 f 74 goat snp22265-scaffold22-1633421 22 3642865 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763775 Affx-986698303 AX-385251578 22 3645215 TAACCATGAGGGCTTACTTTTTTTGCAATTTCTAG[G/T]ACATCTATATAAGTAACATCAGCCATATACTATAA K 2 1 2 1 600010 f 74 goat 22_3645215 22 3645215 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 320763777 Affx-986698305 AX-385251580 22 3645243 TTTCTAGGACATCTATATAAGTAACATCAGCCATA[C/T]ACTATAACCTGAGAAGATTCATCGCTCCTCCAACA Y 2 1 2 1 600010 f 74 goat 22_3645243 22 3645243 Ancestral_priority_1043 ancestry 0.69 recommended IMAGE 10K 10K ancestral 320763747 Affx-986698275 AX-385251556 22 3645285 ACCTGAGAAGATTCATCGCTCCTCCAACAATACTT[C/T]CCATGTAATTTAACATGTCAAATGAACTCAGGTAG Y 2 1 2 1 600010 f 74 goat 22_3645285 22 3645285 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320799940 Affx-122944395 AX-385286866 22 3704317 AATCATAGTTATCATATTATTAAAGAAATGTAACG[C/T]ATTTTAAATCCTGTGTTTCCTGACTTGTTGGGTAC Y 2 1 2 1 202000 f 74 goat snp22267-scaffold22-1694175 22 3705150 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788207 Affx-122938783 AX-385275226 22 3833379 GCCTCTATGACAGATGCTTTTGTTTTGTCAAGGAA[C/T]CATTAAAAATAGAAGTGTTTTTGAGAGGCAGTGAG Y 2 1 2 1 101000 f 74 goat snp6383-scaffold1224-2432279 22 3835578 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453104 Affx-122920030 AX-123323437 22 3884367 AGGAATGGCATTTCATCCTGAATTTGGAAATCCCC[A/G]ATGTATCTAAAATGGCAGGAGAAATAGGGGCAGAG R 2 1 2 1 101000 r 74 goat snp6382-scaffold1224-2381291 22 3887005 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798023 Affx-122975540 AX-385284959 22 3927023 ACTACTATGAACAATGGAACAGCCATTTATAAAGA[C/T]TGCTGAATTCTCCAAATGCCAATGACATCTGGTCT Y 2 1 2 1 101000 r 74 goat snp6381-scaffold1224-2338635 22 3929321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786071 Affx-122948041 AX-385273107 22 3956878 ACACATTCATGGTTCACAGAATTAGCATGAAGTTG[C/T]AGCTTCATAAATACTACCTTTCCAGTTTAGAATGA Y 2 1 2 1 101000 f 74 goat snp6380-scaffold1224-2308780 22 3959195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399450 Affx-122961209 AX-123269805 22 4002159 TTGATTATTCCACATATGAGCCTAATTTAAACTAA[C/T]GGCATCTTTTATTTTTCAAAATTGAAGAGAAAATA Y 2 1 2 1 101000 f 74 goat snp6379-scaffold1224-2263499 22 4004416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447815 Affx-122923919 AX-123318151 22 4083966 GAGATCCATATGCTAATCAAAGGGTGATCAGGACA[A/G]TGATGTCAACTTCATCTCCTCTGTGCCCTTTCTTG R 2 1 2 1 101000 f 74 goat snp6377-scaffold1224-2181692 22 4086397 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277421 Affx-1111835903 AX-519550925 22 4095221 TTTAGGATTTGTCCATAGCAAAATTCAGAACCTCT[A/G]TTACTGTTCTCAAGAATAAATGGTTCATATAATGG R 2 1 2 1 101000 f 74 goat Random2.2K-1977 22 4095221 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38411367 Affx-122952244 AX-123281717 22 4126127 TTAGGAAGGACCAGGAAGTTCAAGTGGAGGGAAAC[A/G]CGCAAGAAAGGAAAGCTAGTGGTATGCTAGTATTA R 2 1 2 1 101000 f 74 goat snp6376-scaffold1224-2139531 22 4128373 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386627 Affx-122970227 AX-123256985 22 4186960 GCATCCCCAAGGTCATTGCATAGTTCATCCCAGGA[C/T]GCAGTCATGAAGAAGCATTTCGTCTCTTCCTCCCT Y 2 1 2 1 101000 r 74 goat snp6375-scaffold1224-2078698 22 4187987 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785017 Affx-122970725 AX-385272064 22 4276262 GCATATAATCTGTAAGTATATGACTATAATTCGTA[C/T]ATATATTACACGTAATGGACTGTGTCAGCATAAGT Y 2 1 2 1 201000 r 74 goat snp6373-scaffold1224-1989396 22 4276092 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770521 Affx-122975874 AX-385257686 22 4334812 TCCCCTTCAACAGAAGAGCCTCAGCTGGAATATGA[C/T]ATTCATCTGGGGATGCCTGTCCTAGAAACTAAAGT Y 2 1 2 1 101000 r 74 goat snp6372-scaffold1224-1930846 22 4334630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439514 Affx-122930131 AX-123309851 22 4374381 GGAGCGTCATACAAACACACACTGAAGTCTGACCA[C/T]GGATTTAGGTGTTTAGACACAGAATATATTGTAGG Y 2 1 2 1 201000 r 74 goat snp6371-scaffold1224-1891277 22 4373960 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795912 Affx-122964825 AX-385282864 22 4408584 AAGATTCAAGGAACCGAAACTGTGACAATCAAGAG[C/T]GCTTTCATGTTGCTTGAATCACTTACGGATTCATA Y 2 1 2 1 101000 f 74 goat snp6370-scaffold1224-1857074 22 4408942 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783201 Affx-122964212 AX-385270268 22 4439145 CCAGCCTTTCTTGACTTGTAAATTGTCATCAATGG[C/T]CTCTTTTTATGCCATGTATATTTGTTTTGACAATG Y 2 1 2 1 101000 f 74 goat snp6369-scaffold1224-1826513 22 4439478 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415736 Affx-122948503 AX-123286085 22 4487260 GTTTGTTTTCTTCTGGCCCTTTATTGCACCTACCC[A/C]TGACTTCCTGGAAGAGACTGCCATTTTCTTGCAAA M 2 1 2 1 101000 f 74 goat snp6368-scaffold1224-1778398 22 4488654 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793919 Affx-122964792 AX-385280888 22 4517842 CACCTAGAAACTCGTTTATCACTCTGTTGCTCTCT[C/T]GCCAGTAATGTCAGCACACGCTGCCCTTTTTTTCC Y 2 1 2 1 201000 r 74 goat snp6367-scaffold1224-1747816 22 4518795 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441006 Affx-122928958 AX-123311343 22 4549572 AGTGAACCATTCTCGAGGGCCTATAGGTCTGGAAC[A/G]CATAAAAGATTAACACGCTGTTCCTCCTTGGTTTC R 2 1 2 1 201000 r 74 goat snp6366-scaffold1224-1716086 22 4550572 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787095 Affx-122970782 AX-190917680 22 4624208 CTCAATCGTCTAGTTTCTGCCTAATCAAAAATTAC[A/G]ACAAATATGCTCTCCTACAAGGTATTACTATTACT R 2 1 2 1 201000 r 74 goat snp6364-scaffold1224-1641450 22 4622322 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448454 Affx-122923641 AX-123318790 22 4697379 TCAGCTTGTGACAGAGTGGGTCACAAGGCCTCTGT[C/T]GAGATTTATAACTCAGAACCTTACCCTTAGGAGAG Y 2 1 2 1 101000 r 74 goat snp6362-scaffold1224-1568279 22 4695474 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38385023 Affx-122971863 AX-123255381 22 4758200 TTTCAACAGTCCATATAACTAATGGAAATAGGGCC[A/G]TACTTCATTCTGAGTTTCCAGGTAACATTTTTACA R 2 1 2 1 101000 f 74 goat snp6361-scaffold1224-1507458 22 4756363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428540 Affx-122938738 AX-123298882 22 4814201 AGCAAAATCAGGCCTATCGTATCATTAGTGTGAGC[A/G]TGTACGGTCTCACCTGGCCCACTGTGAGCCTTTAT R 2 1 2 1 101000 f 74 goat snp6360-scaffold1224-1451457 22 4812493 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763753 Affx-986698281 AX-385251562 22 4852086 CAGAGAGAAGTCTTAAAATGACCTCAATCAGTCAT[C/T]CAAATGTATACCCATTTTACCTGAAAACCTTTCCT Y 2 1 2 1 600010 f 74 goat 22_4852086 22 4852086 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 320763755 Affx-986698283 AX-385251564 22 4852109 TCAATCAGTCATCCAAATGTATACCCATTTTACCT[A/G]AAAACCTTTCCTCTTTGACAAATGAAGAAATATTT R 2 1 2 1 600010 f 74 goat 22_4852109 22 4852109 Ancestral_priority_1043 ancestry 0.704 neutral IMAGE 10K 10K ancestral 320799688 Affx-122961804 AX-385286616 22 4878169 GCTGTTTTTCAGAGATAAGGCTCTGCAGTGCTGTG[C/T]ACAGTTATGATTATGTAACATTTGCTGCTTTTGGA Y 2 1 2 1 101000 f 74 goat snp6359-scaffold1224-1387489 22 4876877 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398075 Affx-122961733 AX-123268430 22 4924953 AGGGTGTCTCATCTCTCCCGCTGCTTAAGAGGAAA[C/T]GGGGTGATCAGGATCTGAGTAGAAAGAGCTTCATG Y 2 1 2 1 101000 f 74 goat snp6358-scaffold1224-1340705 22 4923672 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386025 Affx-122971490 AX-123256383 22 4960660 AACAAAAGAAAATAATTTCATGAGTGAGTCAGAAT[A/G]CTCATTGACAAGATTCTGTTTTGGTGGCCAATTTG R 2 1 2 1 101000 r 74 goat snp6357-scaffold1224-1304998 22 4959676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781519 Affx-122932439 AX-385268605 22 5005562 TTGATCTCCAGGAGATCCTGTTTTCCATGTCAGAC[G/T]AAGAGTGTATTTTATACTCAAGACGATGATAGACA K 2 1 2 1 101000 f 74 goat snp6356-scaffold1224-1260096 22 5004791 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775360 Affx-122946467 AX-385262491 22 5064042 GATTTCTTGAATTGTACAATGAGAAACTGCCTTCA[C/T]GCTGATTATCTCACCTCACAAGGAAACAAACAGTC Y 2 1 2 1 101000 f 74 goat snp6355-scaffold1224-1201616 22 5063234 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438089 Affx-122931516 AX-123308427 22 5139606 CTTGTAGGAAATAACAAGAATGAAGTCCAGGGTTA[C/T]ACGACATTCCCTTTCTCAAGCTTTAAAATGGCAGT Y 2 1 2 1 101000 f 74 goat snp6353-scaffold1224-1126052 22 5138633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789455 Affx-122947630 AX-385276465 22 5196719 TATGTCACAGTTTATAAAACCATTCCCATAATCTG[C/T]GATGTTCAGGTGGTTTACAGCATTTCCCCCTTGTG Y 2 1 2 1 101000 r 74 goat snp6352-scaffold1224-1068939 22 5194539 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399940 Affx-122961256 AX-123270295 22 5255586 AAGTAGCTGTCTTTTTGCTTTTATTTTTGCTTTAC[G/T]ATTATCTCACTGCACCAAGGCTTTCTCTTCTATTT K 2 1 2 1 101000 r 74 goat snp6351-scaffold1224-1010072 22 5253297 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392606 Affx-122966049 AX-123262963 22 5287472 GTGTTAAGCAGTCTTATATAAATACTGTGCTCCTC[A/G]GCAATCCCCATCCTCCATTTATAACCAAGACCAGA R 2 1 2 1 101000 r 74 goat snp6350-scaffold1224-978186 22 5284744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378457 Affx-122976687 AX-123248816 22 5331478 CACAAACAGGCATTAGAACAGGCTGCCTCATCTTA[C/T]AGTGAGCGAGCCCTCGTGTTCTTGGGGGTGGGGAC Y 2 1 2 1 101000 f 74 goat snp6349-scaffold1224-934180 22 5329067 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792007 Affx-122961330 AX-385278995 22 5366205 TTTTATATCAATTTGGTGGCAAATTGTGCATATGA[C/T]GCTATTTCATTCTTCCTTCTTTCCCGCTCCCCTCC Y 2 1 2 1 101000 r 74 goat snp6348-scaffold1224-899453 22 5363634 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425830 Affx-122940678 AX-123296176 22 5428828 ATGTTGTTAGAACTTTCTTTGGAAAATAGTCTGAC[A/G]CTTGCCATACTTGAATGCATGCCCACCTCTTTTGC R 2 1 2 1 102000 r 74 goat snp6347-scaffold1224-836830 22 5427039 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272134 Affx-1111833249 AX-519545891 22 5443388 TCCCTCAGCTTCCCTGGTGGCTCAAGTAGAAGAGA[A/G]CAGGTCTGCAAGGCAGGAGACATGGGAGATGCGGG R 2 1 2 1 103000 f 74 goat 22_5443388_AF-PAKI 22 5443388 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320771966 Affx-122935240 AX-385259122 22 5501312 TAAATTTCCCATACATTTCGTTAATTCAGAGCTGA[A/C]ATTTCCTGAAATTTCAGGCTGCTCTCCCTTCTTAG M 2 1 2 1 101000 r 74 goat snp6345-scaffold1224-764346 22 5493801 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388099 Affx-122969499 AX-123258457 22 5576654 GACTGTTCAGTGAAGGTGGTGAAGATGATTCTGCA[C/T]GGCTCCAGGAAGTTGTTTCTGGTTTTTGTTACTTG Y 2 1 2 1 101000 f 74 goat snp6343-scaffold1224-689004 22 5568958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450205 Affx-122922290 AX-123320540 22 5617564 TTTACGTTGGTTGTCTCTGCCTCTGGATGCTCCCA[C/T]GTGATTATCTGTGAGAGGGTGGAGAGAAAAAAATG Y 2 1 2 1 201000 r 74 goat snp6342-scaffold1224-648094 22 5609869 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412401 Affx-122951444 AX-123282750 22 5718841 TACAATTGACATATAACATTATGTAAGTTTAATGT[A/G]TATAGTGTGCTGCTTTAATGCCCATATATATTGAG R 2 1 2 1 103000 r 74 goat snp6340-scaffold1224-546817 22 5708887 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375724 Affx-122978630 AX-123246083 22 5752956 ATGTCACTTGTTGAGTGAACACCGTGAGATGGGCA[C/T]GATGCTAGACTCTTTAATTTCATTTCAAGAACTCT Y 2 1 2 1 101000 f 74 goat snp6339-scaffold1224-512702 22 5742780 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394158 Affx-122964940 AX-123264513 22 5784516 AAATGCTAAAAAACGTCTATCAGACTTGACTTTCT[A/G]AATTGAATTGGAACACCTAACAGCAGGGAAGGATC R 2 1 2 1 101000 r 74 goat snp6338-scaffold1224-481142 22 5774293 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782702 Affx-122940723 AX-385269774 22 5826400 CCAGTAAAGACAGACCTGTGTTTGGGGGTGATAGC[A/G]ACAATGGAAAGCTTATCAGGCTCTGTGTATTTGAA R 2 1 2 1 101000 f 74 goat snp6337-scaffold1224-439258 22 5816170 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382887 Affx-122973417 AX-123253245 22 5857588 CTGCCTGTTGGCAGTGGTGGTGGTAACTGTTTTCT[C/T]GTCAGACTGTTTCTGCAGTGTGGATTTGAGAACTG Y 2 1 2 1 201000 r 74 goat snp6336-scaffold1224-408070 22 5847615 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423214 Affx-122942706 AX-123293560 22 5894127 TACAGAACGCTAGCTTTGACTTACGTAGAAAAAAA[C/T]CTGAATGTTGGAGCGTGTGTAGCTTTCGGTTGAGT Y 2 1 2 1 102000 f 74 goat snp6335-scaffold1224-371531 22 5883917 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792128 Affx-122931020 AX-385279113 22 5947171 CAGTTTACACAGTAAACACTGACCAGATTTTGTTG[A/C]GAGTAAGATCTACACAGGATAGAGAGTGAAGTAAG M 2 1 2 1 101000 f 74 goat snp6334-scaffold1224-318487 22 5937119 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441301 Affx-122929454 AX-123311638 22 5988927 GAAACACACACCCGTGAAATATGGTTACCAACTTA[C/T]GAATAAATTACAGTTGACAAACAACTTTTCCCTCA Y 2 1 2 1 101000 r 74 goat snp6333-scaffold1224-276731 22 5978828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385557 Affx-122971225 AX-123255915 22 6037706 AAATATAATGACTAACAGATACCCAAGAGAAAAAA[C/T]AATTTTTCTTTCTCAAGGATGTGGTTCATTATAAA Y 2 1 2 1 103000 f 74 goat snp6332-scaffold1224-227952 22 6027598 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444018 Affx-122926891 AX-123314355 22 6084903 TGCTTTCTTAAGACCAATTGTTCACACTTTGTAGA[C/T]ATTAGACAAATATATTTCGATTAAATACTATACTT Y 2 1 2 1 101000 f 74 goat snp6331-scaffold1224-180755 22 6075643 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439130 Affx-122931089 AX-123309467 22 6126560 CTTGACAGGACAGTGGGACCCACATGGGTCTAACA[C/T]GAGTTGTGGTGTTGCTTCTGGCTTTGGACCCCAAA Y 2 1 2 1 201000 r 74 goat snp6330-scaffold1224-139098 22 6117807 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443020 Affx-122928167 AX-123313357 22 6175180 AAAAAAATTGCCCTAAGGTGGTCAAGGACTGATCC[A/G]TGACCCAAATGTGAGACTTAGCAGGGGCTCTGGGG R 2 1 2 1 101000 f 74 goat snp6329-scaffold1224-90478 22 6165731 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450992 Affx-122921727 AX-123321326 22 6221913 TAAACATGAGAGCTACCCAGAGAAAGATGAGTTTA[A/G]GAAGTGGCTTAGAATTCTGGTTTATTTAGCATCTT R 2 1 2 1 101000 r 74 goat snp6328-scaffold1224-43745 22 6212346 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463819596 Affx-1110170502 AX-515298221 22 6235497 CCAAAGACACCCAGCGCAGCCAAAGTTGAAAACAC[A/G]TAAATAAAAACAACACGAACCAGACAAAACTTGGA R 2 1 2 1 201000 r 74 goat Random2.2K-1978 22 6235497 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417773 Affx-122947395 AX-123288121 22 6285890 GCTGGTTCTAACTCCACCCAGGGACTTTTTTCCTC[C/T]GTTCTTTAAAAAAAAAAAAAAAAAAAAGAACAACT Y 2 1 2 1 101000 f 74 goat snp4725-scaffold1155-20133 22 6276229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443454 Affx-122927833 AX-123313791 22 6331098 TCCACAGTGAGGATGAGGTTAAGGAAAGGACCGGC[A/G]TTGACTTTGGTTTCTATTATTTGAAGATGTTTGCT R 2 1 2 1 101000 r 74 goat snp4726-scaffold1155-65341 22 6321698 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799076 Affx-122919420 AX-385286006 22 6376297 GGCAGTTTCTTGTTCTAACTGTCACAAAGCCAGAG[C/T]ATAACTTTGAACTAAATGTCATCTCTTTGGGGTTG Y 2 1 2 1 101000 f 74 goat snp4727-scaffold1155-110540 22 6366377 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435869 Affx-122932796 AX-123306208 22 6415254 GTGTTTGAGCAATGGCTGAATGGTCTAGGTTGGCC[A/G]TGGCTGGGACAGCTGGCTTCTCTGTCTTCACCAGG R 2 1 2 1 101000 f 74 goat snp4728-scaffold1155-149497 22 6405780 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409633 Affx-122953533 AX-123279984 22 6458242 TTATAGGAATGCCTAAAGGGACAGCTGAAGGAAGT[A/C]TGTGTGTCTGAAAGGTCCCTTAATGACAGGTACCC M 2 1 2 1 101000 f 74 goat snp4729-scaffold1155-192485 22 6449247 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400578 Affx-122960409 AX-123270933 22 6500172 GGTAGTCTCAAACACACATATCTACAATGTACACC[A/G]TAGGCATGGTGCCCACTGGCCTTGTGCAGTGTGTT R 2 1 2 1 101000 f 74 goat snp4730-scaffold1155-234415 22 6490892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416661 Affx-122947595 AX-123287009 22 6548591 CAGATTTGAATGTACAGCGGATAATGATAAATTTC[A/G]CCGCTGAGCGATCTCAGAGGACATCTGCTTGGGTG R 2 1 2 1 201000 f 74 goat snp4731-scaffold1155-282834 22 6538856 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375898 Affx-122978488 AX-123246257 22 6580097 TTGCTCCTACCTGCAGGAGGGCCTATGCTCTTGGC[A/G]GTTCAGATAGCTGTTTTCTTTGTTGGTTTCTGCTA R 2 1 2 1 101000 r 74 goat snp4732-scaffold1155-314340 22 6569835 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430451 Affx-122937269 AX-123300792 22 6633530 GCCCTGTGCTATGGCTTGTGGTTTTCCTGCACCCT[A/G]CCTTCTAAATAAGACCTTTATTAAACTCTGCTCAG R 2 1 2 1 101000 r 74 goat snp4733-scaffold1155-367773 22 6622212 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790096 Affx-122959866 AX-385277102 22 6655466 TAGGGTCCAGCTCCCTAGAGGGATGGCGTTGGACA[C/T]AGGAACTTCGTCTTCTCTAGCGTGGTTCACCTTTG Y 2 1 2 1 202000 f 74 goat snp2908-scaffold109-5291 22 6644298 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777951 Affx-122960199 AX-385265067 22 6701441 AAAAAAGTGTATAAACCTTCATCAAAAATGGAAAA[C/T]AGAATTAACGTTTAGGTGCCAGTCTCTCCTTAGGC Y 2 1 2 1 101000 r 74 goat snp2909-scaffold109-51266 22 6690130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453823 Affx-122919555 AX-123324156 22 6737173 CCAGTCCAACAACAAGAAACTGCTGTCCATCAGTG[A/G]TCAAACAAAAATAATAAGACGTAACTTACAGGCTT R 2 1 2 1 101000 f 74 goat snp2910-scaffold109-86998 22 6725794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434508 Affx-122934608 AX-123304849 22 6767175 CAGCTCCTTAGTTCCCTGTGGTTGGTTGTGTTCCT[A/G]TTGTCTTGTTTTATAAATCTGTCTTATCCCTGTAT R 2 1 2 1 201000 r 74 goat snp2911-scaffold109-117000 22 6755702 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443450 Affx-122927836 AX-123313787 22 6803345 AGAACCACTCGGTCATCTCCTTCTAAGCAGTCGCA[A/G]TTCTCCAGGCTTTAGGTCTGATGTAGGGGTCATAG R 2 1 2 1 201000 r 74 goat snp2912-scaffold109-153170 22 6792530 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411857 Affx-122951218 AX-123282207 22 6835722 ACTGCCGTCCTGCCTTGCTCTCCAAAAATCAGCGG[C/T]TTAACAAGGACCCAGGGTCTACAGGAGCTGCCCCA Y 2 1 2 1 201000 r 74 goat snp2913-scaffold109-185547 22 6824930 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448966 Affx-122923128 AX-123319301 22 6896840 ATCCATACATTACATCTTGTTTGATCTGCAAAAGA[C/T]GAAGAAGGTTACCAAGGCAACAAGATAAAGTCATT Y 2 1 2 1 101000 f 74 goat snp2914-scaffold109-246665 22 6885107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416257 Affx-122947964 AX-123286606 22 6931522 TTTTAAAATAAAGATATTTTCTAATCCACTTAAGA[G/T]ATTCACAAAGAGTCATTGGGCTGTTATCAGTTCAC K 2 1 2 1 101000 r 74 goat snp2915-scaffold109-281347 22 6920127 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388298 Affx-122969387 AX-123258656 22 6972152 TCACCTCTGCTTCACGTGACATCTGTTGGGACATA[A/C]TGTCCACCACGTCCGATGTCTCAGCTCAGATTGCT M 2 1 2 1 101000 f 74 goat snp2916-scaffold109-321977 22 6960377 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449753 Affx-122922454 AX-123320088 22 7028703 TCTCTGGTGACCTACGTGGGAAGGCAATCCCAAGA[C/T]GAGGGGATGTAAGAACACGTGTAACTGGCTCACTT Y 2 1 2 1 101000 r 74 goat snp2917-scaffold109-378528 22 7016858 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450935 Affx-122921770 AX-123321269 22 7057567 GTTAAAAGAAACAGAGCCGTCTTTTGTGTCTAACT[A/G]CATTAGTACCATTTCCTGATGATTCTGATTTTTAC R 2 1 2 1 101000 r 74 goat snp2918-scaffold109-407392 22 7045451 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403657 Affx-122957518 AX-123274009 22 7121769 GTTAGAAACCTGGAATCAGGTGCTGCCACTGAAAC[A/G]ACTCGTGACTTTGGATTAGAGAAGTCTGTTGAAGG R 2 1 2 1 101000 r 74 goat snp2919-scaffold109-471594 22 7109752 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441762 Affx-122929113 AX-123312099 22 7161290 TAGGATTTTAGTAAGTTTCTCCGCAACTGTCAACA[G/T]TTCTGTACGTGATACTGAAGTAATCTTTCTGCCGA K 2 1 2 1 101000 f 74 goat snp2920-scaffold109-511115 22 7148005 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396001 Affx-122963494 AX-123266356 22 7227610 AGAGCCTAAAATATATATGAAAGGCCTACTAAAAG[C/T]GCTCTATGCCAGGACGGCAGTGACAGAGCTCCCAG Y 2 1 2 1 101000 f 74 goat snp2921-scaffold109-577435 22 7214691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800153 Affx-122926440 AX-385287076 22 7276822 ACAGAAAACAAGTTCACAAAAATATAAGGAAGCGA[C/T]TGCCAGGCGTAACACTTTGACTCATGACTACTGAA Y 2 1 2 1 101000 f 74 goat snp2922-scaffold109-626647 22 7263889 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402222 Affx-122959154 AX-123272575 22 7312794 ATACACGGTATCTGGCACCTTGTGAGGGCTCAAAA[C/T]GCTGGCAACAAAGTGTATATTCAAGTTCTCTATCA Y 2 1 2 1 101000 r 74 goat snp2923-scaffold109-662619 22 7299789 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795404 Affx-122932634 AX-385282360 22 7377141 AAATTTGTGGCCACCATGTATCATTATTTGCAGTT[C/T]GCTTACTATAAACGTAAGTACTCATCTTCTAGGCA Y 2 1 2 1 101000 f 74 goat snp2925-scaffold109-726966 22 7363510 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420979 Affx-122944574 AX-123291326 22 7413334 CGCTGGGCTCTCCAAGTGCTGCTGCTTCCATGCTT[C/T]TTCTTGTTGCATTTCTGGAAGCCCACACATGCCTT Y 2 1 2 1 101000 r 74 goat snp2926-scaffold109-763159 22 7399683 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775574 Affx-122942150 AX-385262705 22 7454410 GCAAGCGCCCTAAACACTCTAGAGTGTTAGCTCAG[C/T]TAGTACCCTGTGACCTTACCTTTTGATCAAGCCAT Y 2 1 2 1 101000 f 74 goat snp2927-scaffold109-804235 22 7441269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410941 Affx-122952041 AX-123281291 22 7506686 TAAATCATTTCTGTCATTTTACTCTCAGATTTTCT[A/G]TTCCCAATAGTAAGAGCTTTCCCTTTCCCAGCTAC R 2 1 2 1 101000 r 74 goat snp2928-scaffold109-856511 22 7494555 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397389 Affx-122962266 AX-123267744 22 7548837 CGAGAGGTTTGCCTCAATCCACCAGCAGACTTCTG[C/T]AGCAACAAGAACCTCAGCTGTTTCCTGTGACCATC Y 2 1 2 1 201000 f 74 goat snp2929-scaffold109-898662 22 7536852 A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407552 Affx-122954684 AX-123277903 22 7584266 TGTTTCAACTGTCATCAACTTGACAGCTAAATGAC[A/G]TCAAAGCTGGCTGCAATGCCATGCTGAACTGCTGG R 2 1 2 1 101000 r 74 goat snp2930-scaffold109-934091 22 7560841 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768901 Affx-122937359 AX-385256078 22 7619238 CAATAAGAAGTAGAATATCCAAATGAATAACTACT[A/G]TAACAAGGACCTCAAAGACTTGTCTGAACTGCTTA R 2 1 2 1 101000 r 74 goat snp2931-scaffold109-969063 22 7595812 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442302 Affx-122928249 AX-123312639 22 7648228 CAAATTTAATATTATGCTTCTCCAAATTACCTTAA[A/G]TCATTCTTATTTTTTCTCTATGTATTTAAAATTTT R 2 1 2 1 103000 f 74 goat snp2932-scaffold109-998053 22 7625101 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414384 Affx-122949996 AX-123284733 22 7726922 TGAAAGTCTGTGCCTCGACGCCTCCAGAACATCCA[A/G]TGGGTTGTTTTCCCTTGCTGATCCTGCTGGGTGTC R 2 1 2 1 101000 r 74 goat snp2933-scaffold109-1076747 22 7703052 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781139 Affx-122953058 AX-385268224 22 7789778 ATTGCATCAGTAAAGCACGGAGTATCACAGTGCTC[A/G]TTACTGTGCATAATTAACTCTGTAATCTTACAATC R 2 1 2 1 101000 f 74 goat snp2934-scaffold109-1139603 22 7763366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418292 Affx-122946993 AX-123288640 22 7822233 AAAACTGTCAACACATGATCCAACGGAGCAAAATG[C/T]TCAACCAATGGCACTCTTAAACCTAGCCAACCTAT Y 2 1 2 1 101000 f 74 goat snp2935-scaffold109-1172058 22 7795049 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320771025 Affx-122951458 AX-385258187 22 7908419 GGTACCTGCTATTTTTGGTAGCAGATGTGATCTTT[C/T]GACGCTTGGTAATCCATGCACAAGGAAACCTCAGA Y 2 1 2 1 101000 f 74 goat snp2937-scaffold109-1258244 22 7882109 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408760 Affx-122953393 AX-123279111 22 7993639 GCTGTGCCCCAGTTCCACGCTTGATTGAACTTGGG[C/T]GATTTGCTGCTGTTGCAGTGTAAACACTAAGTATA Y 2 1 2 1 201000 r 74 goat snp2939-scaffold109-1343464 22 7967795 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272140 Affx-1111833252 AX-519545897 22 7994788 AAGATCCCTGGAGCAGGAAATGGCAACCCGCTCCA[A/G]TATTCTTGCCTGGAGAATCTCATGGACAGAGGAGC R 2 1 2 1 303000 f 74 goat 22_7994788_AF-PAKI 22 7994788 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320794885 Affx-122945143 AX-385281845 22 8038106 GACCTTTTCCTCTGTGAGAAGAGAGCAGGACCTTA[C/T]AATAAATATTTTTGTGAAAGAGGATAGAACCAGAT Y 2 1 2 1 103000 r 74 goat snp2940-scaffold109-1387931 22 8012234 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407538 Affx-122954693 AX-123277889 22 8068003 GTATCAAGTGACATTTGTCCCTCTCTCTCTGACTC[A/G]CTTCACTTCGTGCGATCATCTCTAGGTCCATCCAT R 2 1 2 1 103000 f 74 goat snp2941-scaffold109-1417828 22 8042863 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385689 Affx-122971128 AX-123256047 22 8098185 ATTTCATCTGAAACTCTCAATTTTACTTAGTTTCT[A/G]CCTCATCTTTCTCCTCTTGCTCCCTTGTAGGTTTC R 2 1 2 1 201000 f 74 goat snp2942-scaffold109-1448010 22 8071784 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435022 Affx-122933802 AX-123305362 22 8140305 AACATTCCTGTGGTGCCTGGTATTTGACAGTCCTT[A/G]TGTTTGGTGTTGGGCCAATGGGGCTGAACAAGAGA R 2 1 2 1 101000 f 74 goat snp2943-scaffold109-1490130 22 8114063 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438706 Affx-122930856 AX-123309043 22 8221777 GGAAAGAAGAGGCTTGAGCTGGGCTTGACAGGAGG[C/T]GGAGAGGATGCTCTCAGAAGGTATCTTTGGAGGGG Y 2 1 2 1 201000 r 74 goat snp2945-scaffold109-1571602 22 8195632 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436679 Affx-122932460 AX-123307017 22 8273419 ACACTCTAATTTGCATTTCGAAGATGTGCTGACAA[C/T]GGTAAGCTCAGTTTTGTTTCAATTACTAGAAATTC Y 2 1 2 1 101000 f 74 goat snp2946-scaffold109-1623244 22 8247693 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433162 Affx-122935667 AX-123303503 22 8314839 GGTTGGACTATTAAAGATTTCACTTTCCTTGTGGA[A/G]TGACCTCCTAGCTGGCCTAAGGCAGTTGGGCATGG R 2 1 2 1 101000 f 74 goat snp2947-scaffold109-1664664 22 8289000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777648 Affx-122950321 AX-385264767 22 8351924 GCTTTACAAAAGGCAGAGGCAATGTTTCTAATTGT[A/G]TTGTCTTCTAATGATATGGCTGTCACAAGCCCTCT R 2 1 2 1 101000 f 74 goat snp2948-scaffold109-1701749 22 8326777 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450489 Affx-122922927 AX-123320823 22 8404395 TGGTTTGGAAAATCAAATAAAATTGACTTGATACC[A/G]TCTCACATCCTGTATATAATGGAATACTACTCAGC R 2 1 2 1 101000 r 74 goat snp2949-scaffold109-1754220 22 8379033 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444846 Affx-122926299 AX-123315183 22 8438816 CTTCATTGCTTCCTGCATCTCCAAGAAAACATGTG[C/T]GATCATTTTCTTCCTGCCTGAAGAACACTCATTGT Y 2 1 2 1 201000 f 74 goat snp2950-scaffold109-1788641 22 8413252 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425847 Affx-122940665 AX-123296193 22 8485761 GGTGAAGGTGATAAATAGGTTTACTCTAGCCCTCA[C/T]GGAGTCCAAGGACACTCCTGTGCAAAGAAACCCCT Y 2 1 2 1 101000 f 74 goat snp2951-scaffold109-1835586 22 8458892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450160 Affx-122922323 AX-123320495 22 8532819 GGTCTAATAAACAAGGAGTATCAGAATGAGATCTG[C/T]GCATTGGAAGATCCCTCAGGTTGCCATGTGGAAGA Y 2 1 2 1 101000 f 74 goat snp2952-scaffold109-1882644 22 8507478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769298 Affx-122963002 AX-385256470 22 8598710 TGAAAATTCCTTGAAATCTTTTAACCCCCAAGAAC[A/G]TCTAAGCTTAACTCCCCCTCCATTTCTTCCTCTTC R 2 1 2 1 201000 f 74 goat snp2954-scaffold109-1948535 22 8573427 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773509 Affx-122977655 AX-385260650 22 8643732 TGCTTTAATGCCAGTGGAGAACTAGATTTTGGAGA[C/T]ATCTGAGCACACTCAAAACCAACTAGGAGAACCAG Y 2 1 2 1 101000 r 74 goat snp2955-scaffold109-1993557 22 8618040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787798 Affx-122968829 AX-385274821 22 8691120 AGCTTTGGATGAGTGGCTAACACCCTTCACTAGTT[A/C]TGTAGTCATGTACCATTAGATTGAATTTATTTCAC M 2 1 2 1 101000 f 74 goat snp2956-scaffold109-2040945 22 8665290 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446244 Affx-122925690 AX-123316580 22 8731382 AGCAAAACTGAATGAGAAGTCCCATTTACCCTCTT[A/G]CCTCAAATACACACAATCTCCTCCCCCCATCATCA R 2 1 2 1 201000 f 74 goat snp2957-scaffold109-2081207 22 8706556 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795819 Affx-122973257 AX-385282772 22 8763824 TCATTTTTCTATAGCCTAAGGCACAGCCTACGGTC[A/G]TGAAACTATTACTGGTTATGGAGTTGCCCAAGCCT R 2 1 2 1 101000 f 74 goat snp2958-scaffold109-2113649 22 8739778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773784 Affx-122944211 AX-385260924 22 8800727 CTTATAGATAATCAGGATCCTGCATTTGGTAATTT[A/G]TTTGTTTTCTGGTTATTGAATTTTAGTAGAGGCAA R 2 1 2 1 101000 f 74 goat snp2959-scaffold109-2150552 22 8775731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430771 Affx-122937486 AX-123301112 22 8850551 ATTGGGATTGTTAACATGGGGTACTTGTTGACAAA[C/T]GAAACATGAAAGCCAAGAAATAGAGCTGCCCTGGC Y 2 1 2 1 101000 f 74 goat snp2960-scaffold109-2200376 22 8825301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415192 Affx-122948994 AX-123285541 22 8890347 TGTATTTACTAGCCACCTAAGATGTCCCAGGCACT[A/G]TGTTAGGTGCATAGAATGACAGAATGGCAGTAAGG R 2 1 2 1 201000 r 74 goat snp2961-scaffold109-2240172 22 8865401 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429259 Affx-122937897 AX-123299601 22 8958129 ACAAAGGAGGTCCTCTTTGGGACCCCTATTTCCTG[C/T]CGGCCTGTAAGAATAGAGGAAGCTGGAATGTGGAG Y 2 1 2 1 101000 r 74 goat snp2962-scaffold109-2307954 22 8934559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799206 Affx-122963207 AX-385286136 22 8992938 AAACTCAGTTTGATTCATAGATCAACACTGATTCA[G/T]CAGTTCAATTCAAAATCCATTACACTGTTGATGTG K 2 1 2 1 201000 r 74 goat snp2963-scaffold109-2342763 22 8968458 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399216 Affx-122960601 AX-123269571 22 9031870 TTTATGAAGTCCCAGGTTGCTCCTTGCTGTGTCTT[A/G]TCTCCAAAAGAAATTCTCTGAGGACTTTAAGAATC R 2 1 2 1 201000 r 74 goat snp2964-scaffold109-2381695 22 9007504 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419668 Affx-122945944 AX-123290016 22 9081149 CTTCTGCTTTCCTGACCTTGACACACACCAAGTTT[A/C]TTGTATTTTAAAGCTCAGGCAAATTTTTAATTCTT M 2 1 2 1 201000 r 74 goat snp2965-scaffold109-2430974 22 9057585 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786977 Affx-122929637 AX-191159109 22 9144681 CAGTTATAGTGGTTGTCTTAGTAAAAAATATGCCC[A/G]TTACATTGACCTTAATTAATAAAATGAGTGTTTGT R 2 1 2 1 101000 f 74 goat snp2966-scaffold109-2494506 22 9121817 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780873 Affx-122928933 AX-385267960 22 9188923 CTCTGTAGGTCCAGTCTTTTAAGAAACTCTACAAT[C/T]GAATAGTAGTGACTGTTTATAAAATCCAGACAGTA Y 2 1 2 1 101000 f 74 goat snp2967-scaffold109-2538748 22 9166169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394668 Affx-122964370 AX-123265023 22 9242391 TACAGTGGTTGTATTTTGCTTACACTAATATACTT[C/T]GCATATGCAGAACCAGATAATGAAACCACATATCT Y 2 1 2 1 101000 f 74 goat snp2968-scaffold109-2592216 22 9220439 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783309 Affx-122958762 AX-385270374 22 9265899 ACGCTTTAGAGAACTGGAAAAGAGAAGAAGTGATA[C/T]AGAAATTTGTCAACATTTAAGTAGAGACAAGCAGA Y 2 1 2 1 101000 f 74 goat snp15813-scaffold1658-14664 22 9311943 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447704 Affx-122924611 AX-123318040 22 9305973 CCACAAATGCATACATCATAATCCTCCCAAGTCCA[C/T]AGTTTCCTATGGTTCCCTCATGAGGTTGTACATTC Y 2 1 2 1 101000 f 74 goat snp15814-scaffold1658-54738 22 9351884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411536 Affx-122951658 AX-123281886 22 9334730 TCCTTCCTCAGCACTTCAAACATTTTGCCTCTTGC[A/G]TTTCCCTTCTTTTTGCCTCTGCCTTGTTGCATTCT R 2 1 2 1 201000 r 74 goat snp15815-scaffold1658-83495 22 9380580 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375452 Affx-122979167 AX-123245811 22 9364734 AAGTCAAGAAAGGCATTAGGGTAAAAAATAAATCC[A/G]ACAGAGTCTGTATCTATTTATTCCTTGTATAAAGG R 2 1 2 1 101000 f 74 goat snp15816-scaffold1658-113499 22 9410920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784213 Affx-122948398 AX-385271264 22 9456288 AATGCTGAAAAACTCCAATTTAACAGTCTGCAGAA[G/T]CACAATGTGTACTTAGTTAACACACACTCTCCTAT K 2 1 2 1 201000 r 74 goat snp15818-scaffold1658-205053 22 9503027 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426463 Affx-122940796 AX-123296809 22 9496634 AGCACAAGCCATTCACCAAGTTCTCTGATGTGCAG[A/G]GATGCTGGTGGGAAATGAACAGGGTAGTGGAGCCC R 2 1 2 1 101000 f 74 goat snp15819-scaffold1658-245399 22 9543357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416196 Affx-122948244 AX-123286545 22 9531759 GTCTGTCCTATCCACGAGCTGTGCAGAGTCTTATG[G/T]GGCTCAGAAAGGAAGTTGGATGAAGCGGACCTGTG K 2 1 2 1 101000 f 74 goat snp15820-scaffold1658-280524 22 9578297 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452611 Affx-122920485 AX-123322944 22 9562619 CACAGCAGTTGACATGGAGACAGCAGGGGAGTAAG[A/C]GGCATTGCTTAAAAAAGCAGGTGGTAATTTGGCTT M 2 1 2 1 101000 r 74 goat snp15821-scaffold1658-311384 22 9607853 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426247 Affx-122940338 AX-123296593 22 9595609 AGCTGCATCACAAGGCACAGCTCCTGCAACCTTTT[A/C]AGATAAATGAGACTGAAGAGAAAACTGAAACAGCA M 2 1 2 1 101000 r 74 goat snp16137-scaffold17-18858 22 9640503 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795685 Affx-122948966 AX-385282639 22 9625677 GAAACTGATTTGAGTTGATCATTTCTGGGCCAGAG[C/T]AAGTTGGGTGTAAAAAGTCCATGACTGAGGAGTAA Y 2 1 2 1 101000 r 74 goat snp16138-scaffold17-48926 22 9670798 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384896 Affx-122971923 AX-123255254 22 9686644 CAGAGGGGTTTCTTGGCAGGGATCCCTAATAAAAA[C/T]GTATTATTTTTTCCATTCTTCATTTTGGCCTTCAT Y 2 1 2 1 102000 f 74 goat snp16139-scaffold17-109893 22 9727124 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802277 Affx-122972658 AX-385289181 22 9783159 GTCTGAATACTTTATTCATGGGTCAATGTTTTACA[A/G]TTGTATATAAAAGATCGTGTAACATTTTAGTATCT R 2 1 2 1 101000 f 74 goat snp16141-scaffold17-206408 22 9823746 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419592 Affx-122945385 AX-123289940 22 9812902 TTGGGTAACAGAAACTGACCTATAGTCTTCAAATC[A/G]TTTCTATTGCTTTTGAGCCTGTGCTTGTGTGCATT R 2 1 2 1 101000 f 74 goat snp16142-scaffold17-236151 22 9854924 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777410 Affx-122929012 AX-385264531 22 9874451 CTCTTCTTTATAAAACAAAGAGCAACATGTCCTAC[C/T]TTAGAAGTCATTGCAAAGGATTGTGTAATGCATAT Y 2 1 2 1 101000 f 74 goat snp16144-scaffold17-297700 22 9916729 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439396 Affx-122930254 AX-123309733 22 9918337 CTGTTTCTCCTAACCCTCCACCTGCTTTCTGTCCA[G/T]CTGTTCTTCCCATTGCTGGTCCTACAAACCAACAG K 2 1 2 1 201000 r 74 goat snp16145-scaffold17-341586 22 9960570 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384718 Affx-122972058 AX-123255076 22 9948672 CCCATATACCTGCCTCTGAGTGTGCATGGAGTGTG[A/C]AGGGAACATTCCTCTGAGTGCACTAGAGTATACAG M 2 1 2 1 101000 r 74 goat snp16146-scaffold17-371921 22 9991182 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793004 Affx-122938499 AX-385279982 22 9981252 TTTATATCTATATACATAAGAAAGATTGTTCTTTA[A/G]CTGACATTTTGTGTCCTCTGGTCAGATTTTTATTT R 2 1 2 1 102000 r 74 goat snp16147-scaffold17-404501 22 10023540 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444740 Affx-122926400 AX-123315077 22 10014934 ATAGCCATGTTTTTTGTGCACCCTAAAGATTGTCT[A/G]TGATTCTGCATTGCCTATTTTGTGAGGGATGTGAA R 2 1 2 1 101000 f 74 goat snp16148-scaffold17-438183 22 10057166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399531 Affx-122961148 AX-123269886 22 10066764 TACGTGCCTGCTCAGATCAACTGCCCAGAGCCCAG[A/C]GTGGGAAAGGATCTAAGGGGGGCTCAGTGGGAAAG M 2 1 2 1 101000 f 74 goat snp16149-scaffold17-490013 22 10109574 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788304 Affx-122931495 AX-385275322 22 10112371 CTCCATTCCATAATGGGACAAAAGAACTGGGATTC[A/G]TAAATCACATTTGTCAAGAATAAGTAAAAGGAGAA R 2 1 2 1 101000 f 74 goat snp16150-scaffold17-535620 22 10154998 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390351 Affx-122967686 AX-123260708 22 10148874 AGTCTTACCTGGATGCCACCTAGGGCTACAGCACA[G/T]CCTCACCCTTCAAGTGTGACCCCTGAGGGCTGTCC K 2 1 2 1 101000 f 74 goat snp16151-scaffold17-572123 22 10191804 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798388 Affx-122924919 AX-385285322 22 10210861 GACACACTGATATTCTGTTCTCATAAAAGTGAACT[A/G]TATCATGATTGAAATGCACTTAATGTGGCAAAACG R 2 1 2 1 201000 f 74 goat snp16152-scaffold17-634110 22 10254054 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437673 Affx-122931778 AX-123308011 22 10247758 GTCACCCAGCTGACACATACTCATTGCCCTGGAAG[A/G]CATGTTTCCAGCGGTGTTTTGAGATGTACTGAACT R 2 1 2 1 201000 r 74 goat snp16153-scaffold17-671007 22 10290821 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377334 Affx-122977670 AX-123247693 22 10351677 TTCCTCACGCTGAACTTCTTTCCTTCAAAAGCTGC[A/G]CTGCGATGGATGTTGAGGGAAAGGCTCACACCCAC R 2 1 2 1 101000 f 74 goat snp16155-scaffold17-774926 22 10394668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277549 Affx-1111835904 AX-519551050 22 10372942 TGGTGGTTCAATTTCATTCGGCCGTCCTCCCCTGT[A/C]AGGCACCCTTCCCATCAGCACCTTATTAATGGCAC M 2 1 2 1 101000 r 74 goat Random2.2K-1980 22 10372942 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439907 Affx-122930022 AX-123310244 22 10455272 GCTGTTGAGACAGCATCAAGGGCAACACACGTCCC[A/G]ATTCTAGAGATGGTAGAATGTGAGCAATGGCATAT R 2 1 2 1 201000 r 74 goat snp16157-scaffold17-878521 22 10496197 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408305 Affx-122953775 AX-123278656 22 10504602 TTGGCTCTGCACAAAGGCTTTGGGACTCAGGAGGC[A/G]TACTGATTTTGGCTGCATGTCAGTGAGTGTCCCAG R 2 1 2 1 101000 r 74 goat snp16158-scaffold17-927851 22 10545696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787712 Affx-122936582 AX-385274734 22 10536289 TTTTTAAAACAAATAAGCAAACGACTTTTCTGACT[A/G]TGTGAAATGACATCCTAGTCACTTGTTCCAGCACA R 2 1 2 1 101000 f 74 goat snp16159-scaffold17-959538 22 10577566 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444811 Affx-122926329 AX-123315148 22 10575757 GGATCCAGACAGAAGCAAGACCTCTTCATCATGAC[A/G]TCCAAATCCAGATAAGAACAGGATAGTCCAGACCA R 2 1 2 1 101000 r 74 goat snp16160-scaffold17-999006 22 10616954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272110 Affx-1111833233 AX-519545868 22 10588981 AGGTCACCAGGAAGTCTCAGACCTCTGGGAATGGG[A/C]CTGAACTCCCTGACTCCCAGGACAGATGTCTGCTT M 2 1 2 1 202000 f 74 goat 22_10588981_AF-PAKI 22 10588981 G T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38375606 Affx-122978718 AX-123245965 22 10609714 ACAATGAGCAGAAAGACATGGCACTCGTCTTCGCT[A/G]TTGGGGTGGTGGGGAGTAGAGGGAGGTTACCAGTC R 2 1 2 1 101000 f 74 goat snp16161-scaffold17-1032963 22 10650635 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385389 Affx-122971353 AX-123255747 22 10653910 GTGTGGTTTCCCTAAGATACATGTTGGTGAAATTA[C/T]AGGCAGACCTTATTTTATTGTACTTTATTGTGCTT Y 2 1 2 1 201000 f 74 goat snp16162-scaffold17-1077159 22 10694829 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420493 Affx-122944859 AX-123290840 22 10709963 TTTTCTAAGAAAGACTAGTCCTACCCATTGCTACA[C/T]GGTGGCTAAGGAACCATCTCCACTAGCCCCACCAT Y 2 1 2 1 102000 f 74 goat snp9496-scaffold1342-1364790 22 10750438 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390145 Affx-122967987 AX-123260502 22 10769305 CTTAGGACCCCAGAAACGACCTCTCTGAGATTGAA[C/T]GGGATGACAAGGCCACTGGATGAAGGGAGTGGGGC Y 2 1 2 1 101000 f 74 goat snp9495-scaffold1342-1305448 22 10810143 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406265 Affx-122956094 AX-123276617 22 10799948 AAACAGGCCCATATATTCCCACTCTACCTTCTGGG[C/T]TGAACCAATCTTGTTCTAAAACATTGGAGAAAAAC Y 2 1 2 1 201000 r 74 goat snp9494-scaffold1342-1274805 22 10841130 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427630 Affx-122939343 AX-123297973 22 10834171 GAACAGCGCATTTGAACCATCTCGTTAGCAATGAA[C/T]GGCCAAGCCCAGAGAAAATCGGGTGGAAATGAGCA Y 2 1 2 1 101000 f 74 goat snp9493-scaffold1342-1240582 22 10875393 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440102 Affx-122929712 AX-123310439 22 10884082 CTTCAATTGTTTCTTCCTCAGCCCCTGTTTTGAGA[C/T]GGCTTTGGCCATGAAAAAATAAAGTATCATAGGCA Y 2 1 2 1 201000 r 74 goat snp9492-scaffold1342-1190671 22 10925409 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390965 Affx-122967050 AX-123261322 22 10914002 CTGGAGGTAAGGAGGCCAGCAAGGAGGCTATGCTA[C/T]TGAAAGATCCCTCAGGGTGTAGCATGGAAGTGGAC Y 2 1 2 1 101000 r 74 goat snp9491-scaffold1342-1160751 22 10955225 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38408271 Affx-122953804 AX-123278622 22 11001872 AGAATGACATGTGGGAAAAGAATTCTGGCTTTAAA[G/T]CTTATGACCAAGCAGCTCTGAAGAGTGAAAGGGAA K 2 1 2 1 101000 r 74 goat snp9489-scaffold1342-1072881 22 11043577 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783992 Affx-122925947 AX-385271046 22 11045923 TCTTGAAATCATTCAAGTCTCCGATCCACTACTTT[A/G]TTCTTTTATACCCATTCTACTACACAGCTCATATA R 2 1 2 1 101000 f 74 goat snp9488-scaffold1342-1028830 22 11087648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443126 Affx-122928085 AX-123313463 22 11084821 CTGCGATAGCACCCCCATTTGTAAAACAGAAAAAA[C/T]GTGGAGATTTTCTGTATCTAAAGAAGGTAGGCAGT Y 2 1 2 1 103000 r 74 goat snp9487-scaffold1342-989932 22 11126640 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448908 Affx-122923175 AX-123319243 22 11137290 TCCGAGAAGCCTCCCTGGAAGAGGAAACCCTAGCC[A/G]CTTCCCCTCTACTTCCGAAATTCTAGATCCACCCT R 2 1 2 1 101000 r 74 goat snp9486-scaffold1342-937463 22 11179227 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428676 Affx-122938641 AX-123299018 22 11177286 TCCCCAGAGGGCACTGGAAGTGTGACCCTTGCCTG[C/T]ACATCTGCTCCGGCTTTTATGAGTTCCCTTCATAT Y 2 1 2 1 101000 r 74 goat snp9485-scaffold1342-897467 22 11219335 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415439 Affx-122948714 AX-123285788 22 11207883 AGTGGGAAGAGCCTAGATTGTCCAGATGGGCCCCT[A/G]TGTGTAATCCAATCCCAGGGCTGTTGGAGGATGCC R 2 1 2 1 201000 r 74 goat snp9484-scaffold1342-866870 22 11250090 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408281 Affx-122953795 AX-123278632 22 11292723 AAGAACAAAATCTGAAGTCAGCACCAGCAAGGAAA[C/T]AGTGAAGATCAGAGAGGAAATAAATAGAGATCAAA Y 2 1 2 1 201000 f 74 goat snp9483-scaffold1342-782030 22 11334176 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453374 Affx-122919933 AX-123323707 22 11347335 AGTTTCATCCCTGTAAGTGATTCATGGAAAATAAA[C/T]ACATTCAAGCCATCAAAGAGATTGGCAACACATCA Y 2 1 2 1 101000 f 74 goat snp9482-scaffold1342-727418 22 11389155 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445030 Affx-122926624 AX-123315367 22 11388896 GCTGAAACCCTTCAGGAGTTCCGGGCTTTCTGAGC[A/G]TGAGCCTCACGTTCTCCTTGTCTGGCGCCTTTCAA R 2 1 2 1 101000 f 74 goat snp9481-scaffold1342-685857 22 11429044 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400781 Affx-122959834 AX-123271136 22 11466878 TTTTGGGGGAGGTGACTTGTTCTCACTTAGTTGTA[A/G]CTCACTCAAATCTGAGAGAAAAAAAAAAATTAAAG R 2 1 2 1 101000 f 74 goat snp9479-scaffold1342-607875 22 11505916 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385687 Affx-122971130 AX-123256045 22 11521031 AGAATGGTATAAGAACCCACAGAAGATGACTCTAA[C/T]GGGAGTTAGGAATAGATAACCATAATAAGTAGTGG Y 2 1 2 1 101000 r 74 goat snp9478-scaffold1342-553722 22 11560574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382010 Affx-122974068 AX-123252368 22 11563299 CATATATGCCTTTCCCTTCAGCAGCACAGCTAACA[C/T]GTGCATCTTCATCTCTACCTAATCAAGGAAGAAAC Y 2 1 2 1 101000 r 74 goat snp9477-scaffold1342-511454 22 11603136 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421427 Affx-122943959 AX-123291774 22 11603232 TCTTAGTAATGACTTAAAGTTTGTTTTAAAGAAGA[C/T]TGGGACTTCCCTGGCAGTCCAGTGGTTAGAATTCC Y 2 1 2 1 201000 f 74 goat snp9476-scaffold1342-471521 22 11643235 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412417 Affx-122951431 AX-123282766 22 11640147 CTAGTAAAAGACATATAGTCCCACTTCAGGTTACA[A/G]TGGAGATGGTCAAGAAAGAACATGCCTTGTACTGT R 2 1 2 1 201000 f 74 goat snp9475-scaffold1342-434606 22 11679975 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378237 Affx-122976907 AX-123248596 22 11685228 AAGAGCTCAGAGAAATATAGCAATTTGCCAGATGT[C/T]ACCCAGCTACTGACGGACAGATCCAGGATTTCAGG Y 2 1 2 1 101000 f 74 goat snp9474-scaffold1342-389525 22 11725481 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408646 Affx-122953475 AX-123278997 22 11774382 CGCGCACATTCATCATCCTGACACGAATTATGTGG[C/T]GAAGAGCGGACAGGTCTGTTTTGAAACTCTCTTCA Y 2 1 2 1 101000 f 74 goat snp9472-scaffold1342-300371 22 11811729 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763762 Affx-986698290 AX-385251567 22 11798758 CTGCTGGAACTGAAAAGAGGTAGGTTCAGATTAAC[G/T]CTTGAAAACCTGAAATGGGCAGAAATTAGTATTCT K 2 1 2 1 600010 f 74 goat 22_11798758 22 11798758 Ancestral_priority_1043 ancestry 0.692 recommended IMAGE 10K 10K ancestral 320767007 Affx-986698294 AX-385254301 22 11798763 GGAACTGAAAAGAGGTAGGTTCAGATTAACTCTTG[A/G]AAACCTGAAATGGGCAGAAATTAGTATTCTAACAC R 2 1 2 1 600010 r 74 goat 22_11798763 22 11798763 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 320767029 Affx-986698306 AX-385254321 22 11799183 CACCCAGGATCAGTCCCATCTCACAAGCAGCCCAT[C/T]TAATGCCCCAGATTCCTGTTTCTCATTTGATGCTT Y 2 1 2 1 600010 r 74 goat 22_11799183 22 11799183 Ancestral_priority_1043 ancestry 0.598 neutral IMAGE 10K 10K ancestral 320763182 Affx-986697711 AX-190467010 22 11799214 CCATTTAATGCCCCAGATTCCTGTTTCTCATTTGA[G/T]GCTTAACATTGCGGCCACAGCTCTGCTGCTCCAGA K 2 1 2 1 600010 f 74 goat 22_11799214 22 11799214 Ancestral_priority_1043 ancestry 0.474 neutral IMAGE 10K 10K ancestral 320767032 Affx-986698308 AX-385254324 22 11799229 GATTCCTGTTTCTCATTTGATGCTTAACATTGCGG[C/G]CACAGCTCTGCTGCTCCAGAGTTTTCATCCAGAAT S 4 1 2 1 600010 r 74 goat 22_11799229 22 11799229 Ancestral_priority_1043 ancestry 0.51 neutral IMAGE 10K 10K ancestral 320767036 Affx-986698310 AX-385254328 22 11799254 AACATTGCGGCCACAGCTCTGCTGCTCCAGAGTTT[C/T]CATCCAGAATATAGTCCCTCTTCCAAAATCAGACT Y 2 1 2 1 600010 r 74 goat 22_11799254 22 11799254 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 38429219 Affx-122937929 AX-123299561 22 11811242 AAAGCCATTTGTTGTTAGTCATTTGCCAACACACC[A/G]CTAGCAAAAGGACCCCCTTAAGTATGAGGGAACAT R 2 1 2 1 101000 f 74 goat snp9471-scaffold1342-263511 22 11848616 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767040 Affx-986698312 AX-385254332 22 11817783 TTAAAAATGAGCTGCAGTCTAGGTGACACTGGAGA[C/T]AGCAATTCTGATGTGGTCTGTCTGGCTGCTTCTTG Y 2 1 2 1 600010 r 74 goat 22_11817783 22 11817783 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 38416572 Affx-122947662 AX-123286920 22 11899928 AGGCAGAAACTTGGAATCATCCGCAGAGGCTGGTC[A/G]TTGGGGCCGTGGCAGTATTAATTAGATTTTGTTCA R 2 1 2 1 201000 f 74 goat snp9469-scaffold1342-174825 22 11937558 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380541 Affx-122975670 AX-123250899 22 11961347 TTTCCTCACCAAATGGTGACTTCTTTAGTAGAGGA[C/T]AGATGTTAGACTTACTTTGCATTCTGTTCCAAAAG Y 2 1 2 1 101000 r 74 goat snp9468-scaffold1342-113406 22 11998179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430980 Affx-122936696 AX-123301321 22 11992102 GACCTGGAAACCTCATGTCCTGATTCTTAGCCAGC[A/G]CTCTGTCCAGAGTAACTCATGGTGTCCATAAAGGA R 2 1 2 1 102000 f 74 goat snp9467-scaffold1342-82651 22 12028660 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410628 Affx-122952090 AX-123280978 22 12026137 TGTTATCCACCTGAGTCTCAGAGTCTTCACCTGTC[A/G]ACTAGAGATAGTTGTCCTTCGGGGAGATTGTTCAG R 2 1 2 1 201000 f 74 goat snp9466-scaffold1342-48616 22 12062667 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439155 Affx-122931072 AX-123309492 22 12066593 TTTGCCCGGATTACCCTAACAGATGCCTGGGACTA[C/T]AAAGATGAATTGGTAGGGGTCTGTGCATTTTCTAA Y 2 1 2 1 101000 f 74 goat snp9465-scaffold1342-8160 22 12103974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376091 Affx-122978901 AX-123246450 22 12102068 GTGGTACTGTAGTGGAGGCCGTGGTGGGGTGGGGT[A/C]GTGGGGAGAGAGGAAAAGGTAAAGTGAAGTCCATG M 2 1 2 1 303000 f 74 goat snp11275-scaffold1404-906561 22 12142898 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409245 Affx-122953142 AX-123279596 22 12135712 ACTGAGGTACAGATATCCTGGAATAGTTTTATTGC[A/G]CTCTTGGGTTGGATACAGTATACCTTGGAGCCCAT R 2 1 2 1 101000 r 74 goat snp11274-scaffold1404-872917 22 12176550 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399400 Affx-122961247 AX-123269755 22 12211431 CTAAAGGTTAAAATCATCAGCTGTTTAGTAGCTAG[C/T]CAGCACAAACTGCAAGTTTAATTATTTGATTTAGA Y 2 1 2 1 101000 f 74 goat snp11273-scaffold1404-797198 22 12251225 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422629 Affx-122943709 AX-123292975 22 12262686 CGGATTAGGGAATGGTCCTTCTGCTTAACAATTCC[C/T]CTAATTAACATATCAACTTTCAACACAACTAGGCA Y 2 1 2 1 101000 r 74 goat snp11272-scaffold1404-745943 22 12302490 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776727 Affx-122935386 AX-385263853 22 12350350 CAATCCTACATGTCCCATTTCTGCAAGAGCAGACC[A/G]TACAAGCCTGGTCGGACGGAAGGATTATTTTTATG R 2 1 2 1 101000 f 74 goat snp11271-scaffold1404-658279 22 12389483 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392768 Affx-122965994 AX-123263125 22 12432352 ACTTTTCATCCCCTGGTTCAGGATCCAATCCAGGG[C/T]GGTGCGTGGATTGCACTGTCGAGTCCTTTTACTCA Y 2 1 2 1 101000 r 74 goat snp11269-scaffold1404-576277 22 12471005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772188 Affx-122958416 AX-385259343 22 12465389 GCCGATGCACTGAGAAATGTAAGTGCCACTTCCTG[C/T]AAAAGTTTCTTTAATCTAAAACTTTCCCCTCTGTT Y 2 1 2 1 101000 f 74 goat snp11268-scaffold1404-543240 22 12504444 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415084 Affx-122949458 AX-123285433 22 12499689 GGTTGCACTTGGAATCGCTTGGAGAGGTTTTAAAC[A/G]TATGCCCAACGCTAAACAGAAAGAATTTAGATAAT R 2 1 2 1 101000 f 74 goat snp11267-scaffold1404-508940 22 12539033 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439260 Affx-122930995 AX-123309597 22 12548224 GGTAAATCGGTAATATACATTTTCTCCAAAGCTTC[A/G]TTCCTCAACATTAAATAGCACCACGTGCAGAACCC R 2 1 2 1 101000 r 74 goat snp11266-scaffold1404-460405 22 12586254 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444742 Affx-122926399 AX-123315079 22 12581145 TCCCCCAGTTATCTCCTCCTCCTCACACCCACTCC[A/G]CTGCCTCCTTCCCAGCAACATTCAACATGCCAGGT R 2 1 2 1 101000 r 74 goat snp11265-scaffold1404-427484 22 12618466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781462 Affx-122952766 AX-385268547 22 12651384 ATAAACAAGACTAAAATCTGTTAACAATTAACAAA[G/T]AAAAATAGTTAACACTTATCACACACCAACACAAC K 2 1 2 1 101000 r 74 goat snp11263-scaffold1404-357245 22 12689017 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384265 Affx-122972312 AX-123254623 22 12700302 AGGCCCTGCTCTGCTGAACTTGTGTGTGTGAGTTG[C/T]GTGGTCATGTCCGACTCCATGCGACCCCATGGACT Y 2 1 2 1 101000 f 74 goat snp11262-scaffold1404-308327 22 12737958 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777262 Affx-122922368 AX-385264384 22 12730115 TTTCCAGTTGCACACATTTGTGTGAACAGCATGCA[G/T]ATCAAAACCCAGAATGTTACCACTATCCCTATGGT K 2 1 2 1 101000 f 74 goat snp11261-scaffold1404-278514 22 12768115 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429895 Affx-122938120 AX-123300236 22 12786902 GCTGTAACAAATAAACCCCAAGGCCTCAGTGACTT[A/G]TCTCACCAAAAGTTTCTTTCCAGCACAAAGTTCCC R 2 1 2 1 201000 r 74 goat snp11260-scaffold1404-221727 22 12824643 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424478 Affx-122941762 AX-123294824 22 12817803 CTTTATTTACAAAACCAAAGTCTTGCTACATATGC[A/C]TTTGATTATCTTTACTTTCAAAATTTCAAGACAGT M 2 1 2 1 101000 f 74 goat snp11259-scaffold1404-190826 22 12855644 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442893 Affx-122927650 AX-123313230 22 12848584 GGAAGCCTGGAGGGCAGTGCAGTCTTCTAGGTAGA[C/T]GGGTGAGGTCTGGGCCAGGATAGGAGACAGAGAGG Y 2 1 2 1 201000 r 74 goat snp11258-scaffold1404-160045 22 12886809 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375493 Affx-122979135 AX-123245852 22 12877241 AAGATGATCTATCTGCTTACTGTTTGTATTAACCA[A/G]TTCTGGACTTAGCTATAATGAACATGCAACGTACT R 2 1 2 1 101000 f 74 goat snp11257-scaffold1404-131388 22 12915541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423584 Affx-122942398 AX-123293930 22 12909828 GTCATCCTCACTTATATCAGGGAGGGCGAGGTCTT[A/G]CTTGGAGGAGAGCCAGGCTAACACTCATCAAGTGG R 2 1 2 1 101000 f 74 goat snp11256-scaffold1404-98801 22 12948064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417118 Affx-122947468 AX-123287466 22 12953653 AAAGGAGAAAGGCAGCAGAGGATGAGAGCAGGAGC[A/G]CTCTTTAGAACACAGACAGACAGAAGCCCGGGCTT R 2 1 2 1 101000 r 74 goat snp11255-scaffold1404-54976 22 12991047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419748 Affx-122945884 AX-123290096 22 12986368 GTATGTAATCCTAGAACAACCATGTCCTTATGTCA[C/T]GGGGCTCCCTAAAGCTCTGGTAACAGCTACATTGA Y 2 1 2 1 201000 f 74 goat snp11254-scaffold1404-22261 22 13023774 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435148 Affx-122933672 AX-123305488 22 13011499 TTGCCTTTGCCCCTTGGAGTCAGAGCTAAAGTCCC[A/G]TTGCAGTGGGGCTGGTGTTCTCCCTTCCACAGTGA R 2 1 2 1 101000 f 74 goat snp43628-scaffold5848-2771 22 13048951 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445125 Affx-122926180 AX-123315462 22 13043598 TGACTGGGCTGCCCACGCCTGCCCAGTCCCTGGCA[C/T]AGACAGGGCCCGAGTCTAAGGGAGATTTAGTATGT Y 2 1 2 1 103000 r 74 goat snp43629-scaffold5848-34870 22 13081759 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409833 Affx-122952942 AX-123280184 22 13062387 ATGCAGTAGCAGCCAAGGGGCACAGGAATGAGTTA[C/T]GCTGACCTAGGTCAGTACCTGGTTGGGCTGGAGTC Y 2 1 2 1 101000 f 74 goat snp31681-scaffold351-4750197 22 13100330 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769315 Affx-122967928 AX-385256486 22 13091188 CTAACAAAAGCAATTTCTCGTGAAATTGAAATTGT[A/G]TGTATCAGTGTATCTCCTACTTGTTCTATTTCATG R 2 1 2 1 101000 r 74 goat snp31680-scaffold351-4721396 22 13129412 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427589 Affx-122939465 AX-123297932 22 13128066 GAGAAAGACTATCCACCTAATCTGTGGATAGTTCT[C/T]TACATTTAACTTCAATTCCCTGGCAGCCCAGTGGT Y 2 1 2 1 103000 f 74 goat snp31679-scaffold351-4684518 22 13167018 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444028 Affx-122926884 AX-123314365 22 13199627 TGGTGTACATGTACTAAAGAAACCAAAGTTAAAAA[A/G]AAACAACCAGGGACTTTCCAAAGTGATCCAGTGGC R 2 1 2 1 202000 f 74 goat snp31678-scaffold351-4612957 22 13238724 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389705 Affx-122968686 AX-123260063 22 13234047 ACGCTCCAAGGAAGGGCCATGTGAGGAGGACATAG[C/T]GAGACAGTAGCCTCCAAGCCAACAGGATAGGCCTC Y 2 1 2 1 201000 f 74 goat snp31677-scaffold351-4578537 22 13273833 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426597 Affx-122939980 AX-123296943 22 13280689 ACTAGTGATGAAGAATGATAGAGATGGAAGCAGAT[A/G]CTTCCCACTCTGGCGGAAGAGTACTGGTGTACAGT R 2 1 2 1 101000 f 74 goat snp31676-scaffold351-4531895 22 13320229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272112 Affx-1111833234 AX-519545870 22 13320813 TGATTCTTTCCAAAGAGTTTTGAGGTGGTTTGAAG[A/G]TGAAAACAGACTAGGAAATGAATCATTGGCTAATA R 2 1 2 1 101000 f 74 goat 22_13320813_AF-PAKI 22 13320813 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320768674 Affx-122928702 AX-385255852 22 13321456 CTACTTATTACCCATTAACACTCCAGCATGAACCA[A/G]TATATCAGATCAATGCTAGCCCTGGGATGTGATTG R 2 1 2 1 101000 f 74 goat snp31675-scaffold351-4491128 22 13361060 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432529 Affx-122935557 AX-123302870 22 13373718 AGGAGACTGCTGGGAACGAAACAGAATAACCAGCG[C/T]GAAGGCTAAGAGTGCTGCACAGATGTCCGAGGTGT Y 2 1 2 1 201000 f 74 goat snp31674-scaffold351-4438866 22 13412965 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438752 Affx-122930821 AX-123309089 22 13413181 GAGCTCAGAAATTCTGTTCTGTTCTCTGGGTGTAC[A/G]TGGTCAGTGTGCTTGATTCTCTCTCCTGCTTCTAC R 2 1 2 1 201000 r 74 goat snp31673-scaffold351-4399403 22 13452301 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442887 Affx-122927654 AX-123313224 22 13479225 TATCCTCAAAATGTTATCTTGAGTTCTAAGTGTAA[C/T]GGGAAGTCACTGAAGGATTCTCAGCAAGGAGCAGG Y 2 1 2 1 201000 f 74 goat snp31672-scaffold351-4333359 22 13518452 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426743 Affx-122939866 AX-123297089 22 13543389 GGGTCTTCCAGATGCACCTTTATGCCCTGGCTCTG[C/T]GCTCTGTGTGGTTTGGGGCCACAGATACATCCCTT Y 2 1 2 1 201000 f 74 goat snp31670-scaffold351-4269195 22 13582797 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791759 Affx-122949683 AX-385278750 22 13577964 GGCGGGAGCTGGGTGATCAAAGAATAGAAGAGAGA[C/T]GACTGGTTTGTATCCCAAGTTGGGTGAATGGGACG Y 2 1 2 1 101000 r 74 goat snp31669-scaffold351-4234620 22 13617268 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793204 Affx-122978755 AX-385280182 22 13617171 ATGAACTTGATTAAATTTTGTTGTCTTGGCCAAAG[C/T]AGACAAACTAGAAGAATTCGACCTTTTTTGATTTG Y 2 1 2 1 101000 f 74 goat snp31668-scaffold351-4195413 22 13656509 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431053 Affx-122936646 AX-123301394 22 13662445 TTATATGTTCCACACTGAGCTCCTCCTCTGGCCAA[C/T]GCCACAGGGCTCAGAAACCAACTACTCAAATCTAC Y 2 1 2 1 101000 r 74 goat snp31667-scaffold351-4150139 22 13701795 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388139 Affx-122969470 AX-123258497 22 13701706 GTAGGAAGGGCTTCTTGGGTTCTCTTGGGGTTGGT[C/T]AAGCATTCCAAGCCTGCTCCACGTTTATCATCACC Y 2 1 2 1 101000 r 74 goat snp31666-scaffold351-4110878 22 13741017 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 532577592 Affx-1248697227 AX-579216008 22 13711074 ATCTAGATTCTATACCTGCATTAATCTACGATGTT[-/TTTCTC]TTTCTGACTTCTTTCACTCTGTATGACAGACCCTA - 2 1 2 1 500000 r 74 goat "ins-del_012;rs654123328" 22 13711074 TTTCTC - 5 indels litter size 0 not_recommended SV-TF-chip candidate gene ou candidate region CTNNB1 562165415 Affx-1248697227 AX-606940826 22 13711074 ATCTAGATTCTATACCTGCATTAATCTACGATGTT[-/TTTCTC]TTTCTGACTTCTTTCACTCTGTATGACAGACCCTA - 8 1 4 1 20100 f 74 goat "ins-del_012;rs654123328" 22 13711074 TTTCTC - junction SV-TF-chip candidate gene ou candidate region CTNNB1 562165989 Affx-1248697227 AX-606941398 22 13711074 ATCTAGATTCTATACCTGCATTAATCTACGATGTT[-/TTTCTC]TTTCTGACTTCTTTCACTCTGTATGACAGACCCTA - 8 1 4 1 20100 r 74 goat "ins-del_012;rs654123328" 22 13711074 TTTCTC - junction SV-TF-chip candidate gene ou candidate region CTNNB1 562166056 Affx-1248697227 AX-606941465 22 13711074 ATCTAGATTCTATACCTGCATTAATCTACGATGTT[-/TTTCTC]TTTCTGACTTCTTTCACTCTGTATGACAGACCCTA - 8 1 4 1 20100 r 74 goat "ins-del_012;rs654123328" 22 13711074 TTTCTC - junction SV-TF-chip candidate gene ou candidate region CTNNB1 532577595 Affx-1248697231 AX-579216011 22 13712297 AGTGATCTTTGGGAGTCAGAGGTACCTTGAAGCTG[-/TACTTGGCTGTGCACAGT]TTTGGAGGTGCTGTTTGGAATTAGTGCTGACAAGA - 2 1 2 1 500000 r 74 goat "ins-del_013;rs646881456" 22 13712297 TACTTGGCTGTGCACAGT - 5 indels litter size 0.616 recommended SV-TF-chip candidate gene ou candidate region CTNNB1 562165189 Affx-1248697231 AX-606940601 22 13712297 AGTGATCTTTGGGAGTCAGAGGTACCTTGAAGCTG[-/TACTTGGCTGTGCACAGT]TTTGGAGGTGCTGTTTGGAATTAGTGCTGACAAGA - 8 1 4 1 20100 r 74 goat "ins-del_013;rs646881456" 22 13712297 TACTTGGCTGTGCACAGT - junction SV-TF-chip candidate gene ou candidate region CTNNB1 562165545 Affx-1248697231 AX-606940956 22 13712297 AGTGATCTTTGGGAGTCAGAGGTACCTTGAAGCTG[-/TACTTGGCTGTGCACAGT]TTTGGAGGTGCTGTTTGGAATTAGTGCTGACAAGA - 8 1 4 1 20100 f 74 goat "ins-del_013;rs646881456" 22 13712297 TACTTGGCTGTGCACAGT - junction SV-TF-chip candidate gene ou candidate region CTNNB1 562165688 Affx-1248697231 AX-606941097 22 13712297 AGTGATCTTTGGGAGTCAGAGGTACCTTGAAGCTG[-/TACTTGGCTGTGCACAGT]TTTGGAGGTGCTGTTTGGAATTAGTGCTGACAAGA - 8 1 4 1 20100 r 74 goat "ins-del_013;rs646881456" 22 13712297 TACTTGGCTGTGCACAGT - junction SV-TF-chip candidate gene ou candidate region CTNNB1 562165839 Affx-1248697231 AX-606941248 22 13712297 AGTGATCTTTGGGAGTCAGAGGTACCTTGAAGCTG[-/TACTTGGCTGTGCACAGT]TTTGGAGGTGCTGTTTGGAATTAGTGCTGACAAGA - 8 1 4 1 20100 f 74 goat "ins-del_013;rs646881456" 22 13712297 TACTTGGCTGTGCACAGT - junction SV-TF-chip candidate gene ou candidate region CTNNB1 562166474 Affx-1248697231 AX-606941882 22 13712297 AGTGATCTTTGGGAGTCAGAGGTACCTTGAAGCTG[-/TACTTGGCTGTGCACAGT]TTTGGAGGTGCTGTTTGGAATTAGTGCTGACAAGA - 8 1 4 1 20100 r 74 goat "ins-del_013;rs646881456" 22 13712297 TACTTGGCTGTGCACAGT - junction SV-TF-chip candidate gene ou candidate region CTNNB1 538942833 Affx-1251531510 AX-585489962 22 13718297 GTTCTGTTCGCTTTTTGTTCCAACTTTGTGTGTAT[-/TATAAA]TATAAAATTTTCAAAATTTTGAGCAACATATATAC - 4 1 2 1 400000 r 74 goat ins-del_014 22 13718297 TATAAA - SV-TF-chip candidate gene ou candidate region CTNNB1 562165054 Affx-1251531510 AX-606940466 22 13718297 GTTCTGTTCGCTTTTTGTTCCAACTTTGTGTGTAT[-/TATAAA]TATAAAATTTTCAAAATTTTGAGCAACATATATAC - 32 1 4 1 20100 r 74 goat ins-del_014 22 13718297 TATAAA - junction SV-TF-chip candidate gene ou candidate region CTNNB1 562165497 Affx-1251531510 AX-606940908 22 13718297 GTTCTGTTCGCTTTTTGTTCCAACTTTGTGTGTAT[-/TATAAA]TATAAAATTTTCAAAATTTTGAGCAACATATATAC - 16 1 4 1 20100 f 74 goat ins-del_014 22 13718297 TATAAA - junction SV-TF-chip candidate gene ou candidate region CTNNB1 562166066 Affx-1251531510 AX-606941475 22 13718297 GTTCTGTTCGCTTTTTGTTCCAACTTTGTGTGTAT[-/TATAAA]TATAAAATTTTCAAAATTTTGAGCAACATATATAC - 16 1 4 1 20100 r 74 goat ins-del_014 22 13718297 TATAAA - junction SV-TF-chip candidate gene ou candidate region CTNNB1 562166251 Affx-1251531510 AX-606941659 22 13718297 GTTCTGTTCGCTTTTTGTTCCAACTTTGTGTGTAT[-/TATAAA]TATAAAATTTTCAAAATTTTGAGCAACATATATAC - 32 1 4 1 20100 f 74 goat ins-del_014 22 13718297 TATAAA - junction SV-TF-chip candidate gene ou candidate region CTNNB1 38418568 Affx-122946384 AX-123288916 22 13752601 ACTTCCCAGCACTAATTTTTCCGTGATTCATACTG[C/T]GTCTCAGCTGAAAAGGATGTGAAAGCTGTCACAGT Y 2 1 2 1 101000 f 74 goat snp31665-scaffold351-4059983 22 13792732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428673 Affx-122938644 AX-123299015 22 13786484 CAGCAGGGAGGATCACGGAGCCATCTCCAGGCTGG[C/T]GGTCAAGAGATGCCTGCAAGGAAAGTACTGTCATG Y 2 1 2 1 101000 r 74 goat snp31664-scaffold351-4026100 22 13827557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413830 Affx-122949884 AX-123284179 22 13840504 GCCACATATTGCTTTTGACCTTGACAACTGACTTT[A/G]ATCTCTGTGATACCTGGTATCTGTCTGAAAGCGGT R 2 1 2 1 101000 f 74 goat snp31663-scaffold351-3972080 22 13883312 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446425 Affx-122925982 AX-123316761 22 13874339 TGTTAATAAATAAGAAAAAGGAAGGTACATGGACT[A/G]TGTATCCAACTCAGGGAGTTCAAATGAAAGCAGCA R 2 1 2 1 101000 r 74 goat snp31662-scaffold351-3938245 22 13917365 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398163 Affx-122962662 AX-123268518 22 13910490 CCCAGCCTAGTGCAAAGAATGAAGGGAGGTTGGCC[A/G]TGTGACCATTTGTCTTTTTTATGATGTAATGATGT R 2 1 2 1 101000 f 74 goat snp31661-scaffold351-3902094 22 13953517 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388845 Affx-122968881 AX-123259203 22 13959463 CTACCCAGTACACACATAAGTGAAATAAAAATGTC[A/G]CAGAAACAATAGTATATGTGACACCTTTAGATATC R 2 1 2 1 303000 r 74 goat snp31660-scaffold351-3853121 22 14002450 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395110 Affx-122964155 AX-123265465 22 13995383 CTCTTCCTCATTGCATCCCTTAAAGTCCCTTGGAT[A/G]TTCTGGAACCACTGTTTTCTCCCAAATTCTCCACT R 2 1 2 1 201000 r 74 goat snp31659-scaffold351-3817201 22 14038509 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792315 Affx-122945374 AX-385279297 22 14033187 ACCATGATCAGTAAATTCAGGAATTTGGAAAATGG[A/G]GAATTTCAGTAGAGAATTAGAACTATAAAAACAGG R 2 1 2 1 101000 f 74 goat snp31658-scaffold351-3779397 22 14076859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395496 Affx-122963890 AX-123265851 22 14067784 TTCGTCTTCCTTATTTCCTTCCCCTTTGCTGTTTA[C/T]ATCCAGCTAGTCAACCTGTCCTTTGACTGTGATTC Y 2 1 2 1 201000 r 74 goat snp31657-scaffold351-3744800 22 14110704 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796421 Affx-122956282 AX-385283371 22 14149226 AACATTTCTCAGTCTCTTATCTTGAGAAATCAGAA[C/T]GCTACCCTGATAAGTTCAAGCGTTTAAGCTCGGTT Y 2 1 2 1 201000 f 74 goat snp31655-scaffold351-3663358 22 14191876 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431997 Affx-122935934 AX-123302338 22 14221897 TGGGCAACCTCTAACTGGTTTCCATAGTATACCTC[C/T]GCTGGTATACTATATACTAGACTAGACTAGACTAG Y 2 1 2 1 101000 r 74 goat snp31653-scaffold351-3590687 22 14272601 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425714 Affx-122940767 AX-123296060 22 14252448 GGGGTGGGGTCCTCTATGCTTAACTGGTGAGAAAA[C/T]GGGGAAAACCAACTGGAAGCAAATCTGCATATCTG Y 2 1 2 1 201000 f 74 goat snp31652-scaffold351-3560136 22 14303159 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409159 Affx-122953207 AX-123279510 22 14556144 TGGTTTTCCCATAGCATTTTCACAGATCTTCAAAC[G/T]ATGTGAATTATATAGTGGAAAAAAATTCAAAAGTA K 2 1 2 1 201000 r 74 goat snp31645-scaffold351-3256440 22 14604683 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783476 Affx-122951060 AX-385270539 22 14600999 GAATCCCTCCCTGCCTTGCTGATTCCAAAGAAAAT[A/G]TCTGTTAATTGTCGTCTCACTTTCCAAAGACCAGG R 2 1 2 1 101000 f 74 goat snp31644-scaffold351-3211585 22 14649054 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400009 Affx-122960801 AX-123270364 22 14641928 TAAACAGACCCATCTGGTAAGGGGGATTGCTGGCT[G/T]CCTGCAGGTCCCTGCACAGAGGCCCTTGTGGTGCC K 2 1 2 1 101000 f 74 goat snp31643-scaffold351-3170656 22 14689440 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427108 Affx-122939669 AX-123297451 22 14682880 GGGAACAGCAATGTAAAGGAGACACAACACAACTA[C/T]GTTCACAGGGATGAGAAGAGATTTGAGACTGGGAT Y 2 1 2 1 101000 f 74 goat snp31642-scaffold351-3129704 22 14730151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804119 Affx-986696395 AX-385290773 22 14815056 TCCTCAGCCCCGGCAGGGTCCAGCCTTGCCATCCA[A/G]GAGGGCTCAGGCTCCAGAAATGTGACACCAGCCAG R 2 1 2 1 600010 r 74 goat 22_14815056 22 14815056 Ancestral_priority_1043 ancestry 0.444 neutral IMAGE 10K 10K ancestral 320763792 Affx-986698320 AX-385251591 22 14815131 CGGAGGCCTCAGGGGAATATAGTAGGCGTTTCTTT[C/T]TTTCCTTTCCTCATGTAACCATTTATTTTGTGGTG Y 2 1 2 1 600010 f 74 goat 22_14815131 22 14815131 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 320763794 Affx-986698322 AX-385251593 22 14815161 TCTTTCTTTCCTTTCCTCATGTAACCATTTATTTT[G/T]TGGTGGCATCTAGGTGATTTAATCGTTGCTTTGGT K 2 1 2 1 600010 f 74 goat 22_14815161 22 14815161 Ancestral_priority_1043 ancestry 0.606 recommended IMAGE 10K 10K ancestral 320767063 Affx-986698326 AX-385254352 22 14815185 CCATTTATTTTGTGGTGGCATCTAGGTGATTTAAT[C/T]GTTGCTTTGGTTTGAGGTGAACAGCAACTTGATTT Y 2 1 2 1 600010 r 74 goat 22_14815185 22 14815185 Ancestral_priority_1043 ancestry 0.652 recommended IMAGE 10K 10K ancestral 320767080 Affx-986698336 AX-385254369 22 14815254 TTTTTTTCTTCGTGTGAAAGTGTGGATTCATTGTT[A/G]GATTCTTCTTCCATTGGGAATATTCTGGAGCGCCC R 2 1 2 1 600010 r 74 goat 22_14815254 22 14815254 Ancestral_priority_1043 ancestry 0.66 recommended IMAGE 10K 10K ancestral 320763810 Affx-986698338 AX-385251609 22 14818293 TTACTAGTTTTATAGATTTATCATGTTTCTGGCTG[C/T]GCCGGGTCTCCATTGCTGCTGCCCCTTGGCTTCTA Y 2 1 2 1 600010 f 74 goat 22_14818293 22 14818293 Ancestral_priority_1043 ancestry 0.606 recommended IMAGE 10K 10K ancestral 320803553 Affx-986696397 AX-385290357 22 14818390 CAGTGGCTTCTCCTGTCCTGGAGCACCGGATCGAG[A/G]GCGCAGACAGGGTAGTTGTGGCCCACGGGCTTAGT R 2 1 2 1 600010 f 74 goat 22_14818390 22 14818390 Ancestral_priority_1043 ancestry 0.488 neutral IMAGE 10K 10K ancestral 320767058 Affx-986698323 AX-385254348 22 14818533 TAACCATTGGACCACCGAGAATGTCCTACCTCTCG[C/T]TTTAGACTTTAAAGTCAATTCCATCCTGTTCTTTT Y 2 1 2 1 600010 r 74 goat 22_14818533 22 14818533 Ancestral_priority_1043 ancestry 0.702 recommended IMAGE 10K 10K ancestral 320767078 Affx-986698335 AX-385254367 22 14818711 CTGACTGGTGAGATATTATATGTCTCTCTCTCTCT[A/C]TCTTTTCTTTCCCAAAATAATACCTTTCTTTCATT M 2 1 2 1 600010 r 74 goat 22_14818711 22 14818711 Ancestral_priority_1043 ancestry 0.668 recommended IMAGE 10K 10K ancestral 320763809 Affx-986698337 AX-385251608 22 14818784 GTTGAATTTTTCTGTGTGTATTTATGTAGTCCGTT[A/G]ACGCCTTTCGGCAGTGCTGGGTGTTTTTTGCTGCC R 2 1 2 1 600010 f 74 goat 22_14818784 22 14818784 Ancestral_priority_1043 ancestry 0.486 neutral IMAGE 10K 10K ancestral 320767088 Affx-986698341 AX-385254377 22 14818793 TTCTGTGTGTATTTATGTAGTCCGTTGACGCCTTT[C/T]GGCAGTGCTGGGTGTTTTTTGCTGCCCAGGTTCTC Y 2 1 2 1 600010 r 74 goat 22_14818793 22 14818793 Ancestral_priority_1043 ancestry 0.474 neutral IMAGE 10K 10K ancestral 320763218 Affx-986697747 AX-385251146 22 14818837 TGGGTGTTTTTTGCTGCCCAGGTTCTCTCTAGCGG[C/T]AGCAGGCGGGGGCTCTGTAGTTGGGGTGGGCGGGC Y 2 1 2 1 600010 f 74 goat 22_14818837 22 14818837 Ancestral_priority_1043 ancestry 0.618 recommended IMAGE 10K 10K ancestral 320803561 Affx-986696401 AX-385290363 22 14818909 GACTCTGTTTGTGGTGGCCTCTGTTGTTAGGGAGC[C/T]CTATCTCTTAGGCGAGGGGCTGGAGTAGTTGTGGG Y 2 1 2 1 600010 f 74 goat 22_14818909 22 14818909 Ancestral_priority_1043 ancestry 0.572 neutral IMAGE 10K 10K ancestral 320763819 Affx-986698347 AX-385251617 22 14819005 TATGGGATCTGCCTGGATGAGGAATCAATACGGTG[A/T]CCCCTGCGTGGCAGGTGGATTTTTTACCAGTGAAC W 4 1 2 1 600010 f 74 goat 22_14819005 22 14819005 Ancestral_priority_1043 ancestry 0.534 neutral IMAGE 10K 10K ancestral 320767102 Affx-986698349 AX-385254389 22 14819243 CACAAGGTGGCAGCACGTTGCCCGCCCACCTCGGC[C/T]TGCTCAGGCAACCAGAGCCTTAGCGAAAGGCCTGT Y 2 1 2 1 600010 r 74 goat 22_14819243 22 14819243 Ancestral_priority_1043 ancestry 0.472 neutral IMAGE 10K 10K ancestral 320763827 Affx-986698355 AX-385251624 22 14819377 CTCTCAGCCTGTCCCCTTCAGCCCGGAAGACATAT[C/T]CCAACTGTTGCAAAACCTGTGCTGAGGATGCTGCC Y 2 1 2 1 600010 f 74 goat 22_14819377 22 14819377 Ancestral_priority_1043 ancestry 0.448 neutral IMAGE 10K 10K ancestral 38452592 Affx-122920499 AX-123322925 22 14861027 GGGGACTTGCACCAACACCTGATGGGGCCAGTCGC[A/G]TAAACCCCCCAATCCCATCCTACCCAGATGAGACG R 2 1 2 1 101000 r 74 goat snp31637-scaffold351-2951557 22 14909216 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277551 Affx-1111835905 AX-519551051 22 14946874 ACGCTGGTGGGTAGTTTGACCCTGAAGAGAGGGCT[A/G]TTCTCAGCAGTGTAACCAACAGTATTGGATCTCTG R 2 1 2 1 201000 r 74 goat Random2.2K-1983 22 14946874 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320768816 Affx-122977109 AX-385255993 22 14965649 CTTATAAAAAAGTAATTTTTACACCCAAACACACA[C/T]GATATGGATACCTTTTGTATAGCTCAACCTGACAA Y 2 1 2 1 101000 f 74 goat snp31635-scaffold351-2846935 22 15012224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435396 Affx-122933564 AX-123305736 22 15001448 GACAGCAGTGTACGTGCTGGAAGGGCCTCGGAGCA[C/T]GTCTTTGCCAGATGCATAAAGGAAGGGGTGCTTAG Y 2 1 2 1 201000 f 74 goat snp31634-scaffold351-2811136 22 15048220 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400519 Affx-122961266 AX-123270874 22 15036390 CTTTGCCAGGAAAATAGAATGTAAGGTGGAATCTA[C/T]GGAGCATTTAAAAATTTAATCTAAATCTCTCTTCC Y 2 1 2 1 101000 f 74 goat snp31633-scaffold351-2776194 22 15083516 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407448 Affx-122954790 AX-123277799 22 15097064 CCTGAGCAATGCAAGGTTTGCAAGGATGAGTGCTC[A/G]TTAAACGCTAACGTGGGACTGGAACTCACCACTGA R 2 1 2 1 101000 r 74 goat snp31632-scaffold351-2715520 22 15144251 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442664 Affx-122927902 AX-123313001 22 15133551 ACGTGTTATACGAGAACTGAACATTTTTACTTTTA[C/T]GGAAAGGACTCCATTCTGTAATTAGAACAAACAAA Y 2 1 2 1 101000 f 74 goat snp31631-scaffold351-2679033 22 15180673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409993 Affx-122953274 AX-123280343 22 15218107 CACTCATCAGTGCCCAGAGCACAGGAAGCTTAGAG[C/T]GTGCAATCATTTGTTCCTAAGAGGAGATATAATTA Y 2 1 2 1 201000 r 74 goat snp31629-scaffold351-2594477 22 15264999 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390108 Affx-122968015 AX-123260465 22 15248220 TCATTTTAAAAATAGGAATGAATTTCAAATAGATC[A/G]TTGTGCAACTATGAGAAAAGAATCAGTATAATTCA R 2 1 2 1 101000 r 74 goat snp31628-scaffold351-2564364 22 15294915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385259 Affx-122972081 AX-123255617 22 15281376 ACAGGATAGTCAGAAAAGAAATCTACAAAGCTGTA[C/T]ACATACAGATGTTTCTACTTTTGTTTTTACATATC Y 2 1 2 1 101000 f 74 goat snp31627-scaffold351-2531208 22 15328104 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429819 Affx-122938184 AX-123300160 22 15311434 CTTAGGAGTAAAGCAAAATATTGCATATGTCATTT[C/T]GGAAGTATCTTTTGGTCTTTATTGCAGTGTATATT Y 2 1 2 1 101000 r 74 goat snp31626-scaffold351-2501150 22 15358200 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406576 Affx-122955090 AX-123276928 22 15345209 TTTAAGTTTGATTTCCTGTTGCTTCTTTTTCTAAC[C/T]ACCCCAAAAGGACACCAGGCGATATCCTTGATGAT Y 2 1 2 1 101000 r 74 goat snp31625-scaffold351-2467375 22 15392193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443144 Affx-122928069 AX-123313481 22 15383293 TAAGGATCACCACACCCACTTCCTCTTACAGGCAA[A/C]AGCTAGGAGACAGAGAAGGGGCTTGCCCAAGATCC M 2 1 2 1 102000 f 74 goat snp31624-scaffold351-2429291 22 15430080 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399932 Affx-122961310 AX-123270287 22 15470475 GCAAGACCTGCTCTGAAGCAGAGTCTCCTGCAGGA[C/T]AAGGCAAAGCTACCCTTGCCAGGACTCTGCTTGTT Y 2 1 2 1 101000 r 74 goat snp31622-scaffold351-2342109 22 15517549 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277427 Affx-1111835906 AX-519550931 22 15546145 AGTGTGTGGCCAAAGCCAGCTGACCTGTAAAACTA[A/C]AAAAGAAAAACACAAACTTGTTTTAAGAACTGACC M 2 1 2 1 101000 f 74 goat Random2.2K-1984 22 15546145 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432350 Affx-122936276 AX-123302691 22 15548840 TCATCTCTGGTAACTGATGACAAATCTGATCCTCA[C/T]AGCCTTCTCTTCTCTCTTGGGAATGCTCGCATCCC Y 2 1 2 1 101000 f 74 goat snp31620-scaffold351-2263744 22 15596220 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407747 Affx-122954984 AX-123278098 22 15585928 GCAAGAAAATATTTTTTGTGATGGAAACAGAGTTG[A/C]TTAAAAACCAAAAAATGACTTGTCCTATTCCTTTT M 2 1 2 1 101000 f 74 goat snp31619-scaffold351-2226656 22 15633196 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427580 Affx-122939473 AX-123297923 22 15621106 CTGACCCACAGAAGATGTTAAATTTATATTGTTTA[C/T]GCCACGAGTTTGTTGTAATTCGTTAAACAAGGGAA Y 2 1 2 1 101000 r 74 goat snp31618-scaffold351-2191478 22 15668608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390934 Affx-122967074 AX-123261291 22 15669424 AGCGTCCACCGACAGAGAAACGGACAGAGAAGATG[C/T]GGTCCCCATGTCCAATGACACAGTACTGTCATAAA Y 2 1 2 1 101000 r 74 goat snp31617-scaffold351-2143160 22 15717058 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770946 Affx-122942799 AX-385258109 22 15706756 TATGGGAGGAGGATCGAAAGGTCAAATAGAGGTTG[A/G]ACTGTGGATACAGTTTCCTTTCCTCCCTCCATCTG R 2 1 2 1 202000 r 74 goat snp31616-scaffold351-2105828 22 15754376 A G 2 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38382340 Affx-122973884 AX-123252698 22 15748875 GAACCCCTATCTCCCACACTGCAGGCAGATGCTTT[A/G]CCATCTGAGCCACCCCAGGAAGCTCCACTAGTCAT R 2 1 2 1 101000 r 74 goat snp31615-scaffold351-2063709 22 15798572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376559 Affx-122977977 AX-123246918 22 15782781 CACATGGGTCTGTCTTGGGTTCAAAACACGGCTCT[C/T]TTCCCCATGTGCCTTAGGCAGATGCTGAGAAGAGT Y 2 1 2 1 201000 f 74 goat snp31614-scaffold351-2029803 22 15832474 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790414 Affx-122966304 AX-385277417 22 15816051 AAAGATGAACTATGGGGATTGAAGAAAAAAATCAA[C/T]GGTGGTTAGGGACTATACGGGAAAGAGAGTGACTA Y 2 1 2 1 202000 f 74 goat snp31613-scaffold351-1996533 22 15866218 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792787 Affx-122967236 AX-385279766 22 15869191 GTGTGGCTAATGGCACGAATGTCCAACTGTCCTAA[C/T]AATCACATCTGACAGAGGTGATCCCTGCTGTGTGA Y 2 1 2 1 101000 r 74 goat snp31612-scaffold351-1943393 22 15919691 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272117 Affx-1111833236 AX-519545875 22 15876795 ATGAAAGTCGAAAGTGAAAGTGAAGTCGTTCAGTC[A/G]TGTCCGACTCTTAGCGACCCCATGGACCGCAGCCT R 2 1 2 1 103000 f 74 goat 22_15876795_AF-PAKI 22 15876795 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38399914 Affx-122960193 AX-123270269 22 15903585 GGTGAACTACAAAAAGGGGTTAACAGCTGCTTCTG[C/T]GGTCTTTCCTCTAGCCTCAGGGTATCTGAGGATTT Y 2 1 2 1 101000 f 74 goat snp31611-scaffold351-1908999 22 15953776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386179 Affx-122971375 AX-123256537 22 15935624 AGATAACCTGTGTAGTAAGCTCCAGGTGTGACCCA[C/T]GAAGGATGTGGCCTGAGAACCGCCTACTTAACCCC Y 2 1 2 1 201000 r 74 goat snp31610-scaffold351-1876960 22 15986452 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787314 Affx-122946234 AX-385274339 22 15986262 TACATAAAAGCAGAAAAAATGGCAGTCTAGACCTA[C/T]GCCCTATAAATCAACTTATTTACCCTCTGAAATTC Y 2 1 2 1 101000 r 74 goat snp31609-scaffold351-1826322 22 16036728 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388300 Affx-122969386 AX-123258658 22 16037428 GCAAAGTATGTTCTTAAAATTAAAAACAAAAACAA[C/T]GCTGCTGGCATACAAAATTAAACAACAAAAATGAC Y 2 1 2 1 103000 r 74 goat snp31608-scaffold351-1775156 22 16088362 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434949 Affx-122933856 AX-123305289 22 16086292 AGCAATCCAAGAGAAATGTGCTTTCAGATTCACGC[A/G]GACATTTCCACATAATAGTTGGACACGTGAATCTT R 2 1 2 1 201000 r 74 goat snp31607-scaffold351-1726292 22 16136824 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775067 Affx-122932626 AX-385262199 22 16135213 TGATCTGACCAACAAGCTGGCCTTAACCAGTCTCT[A/G]CATGAGGTCATAGATCTTATGACACGCAAGAAGGG R 2 1 2 1 101000 f 74 goat snp31606-scaffold351-1677371 22 16186408 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450870 Affx-122922222 AX-123321204 22 16186243 TTACTCCTGCAGCTTAAGACAGGTATCAGCCTAGA[A/C]GATTAGAAGCTACTGAGGGCCTCCTCCCGGATCCA M 2 1 2 1 101000 f 74 goat snp31605-scaffold351-1626341 22 16237602 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394397 Affx-122964619 AX-123264752 22 16229897 TTCACAGCCAGTCAAACTACCAAGCCAAGTGTGAG[A/G]GCAGAGAAAGTTGTTTTACATACATAGGCACCCAA R 2 1 2 1 101000 f 74 goat snp31604-scaffold351-1582687 22 16281425 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402094 Affx-122958696 AX-123272447 22 16259115 GCTCAGACAGGCAAGGTCAGATACCCATTAAGTGG[C/T]AGAGAAGCCCTCAAACTCAAGACTCTCTAGGTCTA Y 2 1 2 1 201000 r 74 goat snp31603-scaffold351-1553469 22 16310654 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439600 Affx-122930061 AX-123309937 22 16297779 CTACAAACATCAGCAGGAAATCTGTAGAGGGTGGT[G/T]TGAGACTACTGGTCTACTGAGGAACATATGCAAGT K 2 1 2 1 201000 r 74 goat snp31602-scaffold351-1514805 22 16349608 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436597 Affx-122932520 AX-123306935 22 16484074 TCTTGTGGTGATAGCTTTTTGAAACTTGCTATCGG[C/T]ACAGGAGATAGGAGAAAGTAGCCATTACCTTGTTT Y 2 1 2 1 101000 f 74 goat snp31598-scaffold351-1328510 22 16541846 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463821622 Affx-1110174665 AX-515300229 22 16506781 CCCTGAGCAGGTTAAGTGGTTTGTCCGAGATCACA[C/T]GGCCTGAGAAGGCAGGACCGGCTCAAGGAGCCTGG Y 2 1 2 1 201000 f 74 goat GoatD01.054105 22 16506781 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38385226 Affx-122971697 AX-123255584 22 16522696 TAGCTTCTAAGGACTTTTATTATCTGACTCTTGCT[A/G]TTCTACTCACTGTGGTGCACTCTGCCCTCCAGTTA R 2 1 2 1 201000 f 74 goat snp31597-scaffold351-1289888 22 16580272 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430500 Affx-122937228 AX-123300841 22 16572297 CCACAATACACATTCATAACTGTTGGCAGAAGGCT[A/G]TGAGTGACCCACAGAGGTAATGTTTTTACAGGCAA R 2 1 2 1 101000 r 74 goat snp31596-scaffold351-1240287 22 16629901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427429 Affx-122940053 AX-123297772 22 16610736 GGGAGACGTCATATTTTTAAAAGTTGATTTCCAGC[A/G]TTTCTTGAAAACTCAGAAAACCTGGTGCTTTGTGT R 2 1 2 1 201000 r 74 goat snp31595-scaffold351-1201848 22 16668213 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378980 Affx-122976399 AX-123249339 22 16650489 TGTATTTGTAAAACAGTCAACTTGAATTTGCAGAC[A/G]TAAACAACACAATCAATGGGTAGGTTAAACTAGCA R 2 1 2 1 101000 r 74 goat snp31594-scaffold351-1162095 22 16708146 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398523 Affx-122961541 AX-123268878 22 16690592 TTACCTGGATATCTTGAAGACACCTTGAAATTAGA[C/T]GTCTGGATTAAAACTCACCTCTCCCTAAATTTGCT Y 2 1 2 1 101000 f 74 goat snp31593-scaffold351-1121992 22 16748348 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403982 Affx-122957427 AX-123274334 22 16719981 TGTGAAGCCCTGAAGAATTTTTGAGCACCTACTGT[A/G]TGCCAGATCCTGTGCTGTGCTTCATTTCAGTTCAT R 2 1 2 1 201000 r 74 goat snp31592-scaffold351-1092603 22 16777814 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774742 Affx-122937028 AX-385261876 22 16752522 AGGCCATTGTCAGTGTAAGTCTGTGGAGGGTTTGG[C/T]AGGAAGAGGTCACTGTTAATAACTGTCCAGGGATT Y 2 1 2 1 101000 r 74 goat snp31591-scaffold351-1060062 22 16810327 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436165 Affx-122932620 AX-123306504 22 16842463 TTGTTCATTCAATAACAAAATGCTTTCACAGCTGT[A/G]CTGTGTCTCTCCTGGGAAGTACGTGTCTTCTTCAG R 2 1 2 1 101000 r 74 goat snp31589-scaffold351-970121 22 16900729 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799327 Affx-122926735 AX-385286257 22 16895528 CATTTTCTTGGGCAATAGCATTCTTAAGGTCTAGC[A/G]TTGCTTGCTCTCTGTCTGCTCTTTTTTCCCAAAGG R 2 1 2 1 101000 f 74 goat snp31588-scaffold351-917056 22 16953950 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377381 Affx-122977635 AX-123247740 22 16990528 GGCTATGGGAAGGAGCCCCGAGTTTTGGGTTACAT[C/T]GCTTATATAGGGTATATTCATGTAAAGGGGAATTT Y 2 1 2 1 103000 r 74 goat snp31586-scaffold351-822056 22 17045472 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451287 Affx-122921303 AX-123321620 22 17078112 CTATCCACCCAGACATGGCCTTATTCTGCCCTAGA[A/G]CCACTGCTTCAGTTCTGTCCTGAATGCTGGATGCT R 2 1 2 1 101000 r 74 goat snp31585-scaffold351-734472 22 17133333 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420249 Affx-122945066 AX-123290597 22 17116368 GGAGCTGTCCCCTCCCACTGGGGACAACTCCTCCA[C/T]GGGAACTCTATCCACCGACAGGGATCCAGGACTTT Y 2 1 2 1 101000 r 74 goat snp31584-scaffold351-696216 22 17171645 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411299 Affx-122952293 AX-123281649 22 17163558 GTCATTTCACCACCCTCCTAATCCCAAATCCAGTG[A/G]GCTGTCTCAGCCCTGGTCCTCCTCACCCTCTCTCT R 2 1 2 1 303000 r 74 goat snp31583-scaffold351-649026 22 17218732 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429851 Affx-122938156 AX-123300192 22 17219762 CAAAAGAGATTTTCTTTTCCCCTCCAAAGTTCATG[C/T]AGAGGGTAGGCAAGCAAAAAAGTTTTAAAACCAGT Y 2 1 2 1 101000 r 74 goat snp31582-scaffold351-592822 22 17275130 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768258 Affx-122960470 AX-385255439 22 17293848 GAGTGGAGGAGAAGTAGATGAGGTTAGGGTAGCAC[A/G]TGGAGGTCAAATGATTTCAGGTCTCATGTGCCACT R 2 1 2 1 101000 r 74 goat snp31581-scaffold351-518736 22 17349207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379391 Affx-122976136 AX-123249749 22 17347017 AAAAAAAAATTGCCCGTTATCAATGAACTGATCAG[C/T]ACAGCTTCCAGTAATGGTGATGGACAGGTAGGTAA Y 2 1 2 1 201000 f 74 goat snp31580-scaffold351-465567 22 17402391 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447845 Affx-122923899 AX-123318181 22 17386572 TCACGTCTTCCCTTCAGCATCAGACTCATCTAATT[C/T]GTGGCTTCAGCTGCCTTATTATCTTCATTATCACA Y 2 1 2 1 101000 f 74 goat snp31579-scaffold351-426012 22 17442078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404782 Affx-122956677 AX-123275134 22 17424906 TCTCTCTCTCTCACACTCCCCACTCCTCCCAGACA[C/T]ACGCATCCACACACAGCAATCTATCGGCAGTGCTC Y 2 1 2 1 102000 r 74 goat snp31578-scaffold351-387678 22 17480398 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426188 Affx-122940577 AX-123296534 22 17466365 AGCCAGAGAGTCTTAACAAAATCATAACTTATCTC[A/G]TCAGAAAGCTGAGGTTGTAAGGGGACCAAGAAAAC R 2 1 2 1 201000 f 74 goat snp31577-scaffold351-346219 22 17522762 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794704 Affx-122925551 AX-385281664 22 17495414 TAACAGAGTCCAAAAACTGACTCACACATAAAGAT[A/G]TCTAATATATGCCAAAAATGGCACTGCTGAGTGGT R 2 1 2 1 101000 r 74 goat snp31576-scaffold351-317170 22 17551947 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792595 Affx-122971194 AX-385279576 22 17557983 GGCAATATGCTGAGTATTTACATGTCTTAACTTAT[G/T]CAATGGTCTGATAAACCTAATGAGATCCATCTAGG K 2 1 2 1 101000 r 74 goat snp31575-scaffold351-254601 22 17614379 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410381 Affx-122952438 AX-123280731 22 17593181 CTGCTGATCAGGACGTCCAGCTGCAGGTCCTTAGC[A/G]GGTCATGTAGCCCCATGGCTGCTGCTAACCAGAAT R 2 1 2 1 101000 r 74 goat snp31574-scaffold351-219403 22 17648734 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416575 Affx-122947660 AX-123286923 22 17638661 TGCACGAGCTCCCACTCGCCAGCCACCCGGAGAGG[A/C]ACTATGACAAGCATTCAAGCACTGACTGCCCCCAC M 2 1 2 1 101000 r 74 goat snp31573-scaffold351-173923 22 17694533 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383040 Affx-122973298 AX-123253398 22 17668884 AGTTTCCACACGTTCGATTTGCTTAACCAGCCAAG[C/T]GGTTGGAGCTGCACTGTGGCCCCAGAGCAGCTGGT Y 2 1 2 1 101000 f 74 goat snp31572-scaffold351-143700 22 17725148 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782746 Affx-122979166 AX-385269818 22 17716090 GTGGTTTCATAAGGGAAATCGCTCTGTGGGCTGTC[G/T]AGCTGTTTTTATTTGGAGGTTGTTGAGGGTAGTCG K 2 1 2 1 101000 r 74 goat snp31571-scaffold351-96494 22 17772328 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416153 Affx-122948277 AX-123286502 22 17744610 CCCCCCCGGGGAACAGCAGCTGTGTGAGGGCAGGA[C/T]GCTTTCTGGCCTTACTCAGCCAGTGTTGGATCTTC Y 2 1 2 1 101000 r 74 goat snp31570-scaffold351-67974 22 17800642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422517 Affx-122943289 AX-123292863 22 17787106 GAAGGGGGCCAGGAACAGTCTCTTCATGACACCAC[A/G]TTCTTGATTAATCAATGCCAAACATGTATGCTTTG R 2 1 2 1 101000 r 74 goat snp31569-scaffold351-25478 22 17842626 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428076 Affx-122939105 AX-123298419 22 17815038 TTATCTTACTTAGCATAGTAGTGGACCCACCTCTT[A/G]CTGGAAGGAGTAGTAAAGAATTTGTAGCCATTAAA R 2 1 2 1 101000 f 74 goat snp40941-scaffold5261-2355 22 17870370 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443986 Affx-122926918 AX-123314323 22 17848247 CAAACTTCTTTCCCACCTTGTCACTCTCTAAATGA[C/T]GTTTTTGTATGTCCATTTGTATATTTCTTTTTCTG Y 2 1 2 1 101000 f 74 goat snp40942-scaffold5261-35564 22 17901235 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447234 Affx-122924966 AX-123317570 22 17854971 TCTTACAACAGATTTTGAGCTCTTGTTCTGTGACC[A/G]TCTGAGTGGAGGCCCAGTGGATCACATCCACACCT R 2 1 2 1 101000 f 74 goat snp15950-scaffold1677-4999 22 17909309 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419940 Affx-122945309 AX-123290288 22 17883989 GAATTCTCTGTGTGATGAGCCTGTACACCATCTGG[C/T]GACCAGCATCTCAGAAAGAAGGCTGTCTTCAGTCA Y 2 1 2 1 201000 f 74 goat snp15951-scaffold1677-34017 22 17938019 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801936 Affx-122955369 AX-385288841 22 17942578 CCAACTCCCTGGCCAGTGTGTCAACCTGTCAAATA[G/T]AAGAGGTGTTCATGTCCCCATTCACATCTTCCCTC K 2 1 2 1 101000 f 74 goat snp15952-scaffold1677-92606 22 17996998 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419913 Affx-122945331 AX-123290261 22 17979966 AGTGCTCAGCATGCTCTCTGCCCAAATGTTCTTTC[A/G]TCAGTGGAGGTCAGTTTTCCCAGGTCACCATCCTT R 2 1 2 1 101000 f 74 goat snp15953-scaffold1677-129994 22 18034659 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386888 Affx-122970047 AX-123257246 22 18078060 GGAGCTTCAGCTTCAGTGACTTCAGCTTCAGTTGA[C/T]ATAATGACTCTACCAGCTTTCATTTCCATGAGCAG Y 2 1 2 1 101000 r 74 goat snp15955-scaffold1677-228088 22 18135154 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406662 Affx-122955798 AX-123277014 22 18131036 GAGAAATAGTGGTGTGTGAGTTGATACAGTGTGGA[C/T]TGAAAACAGGATAAGCAGGGAAATAGTACCATGCT Y 2 1 2 1 101000 f 74 goat snp17671-scaffold1830-30819 22 18188686 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382671 Affx-122973658 AX-123253029 22 18163209 CAACCCCTCTGTCTTGTACTCGACTTTGCACCTGC[A/G]CAAATAACTATTTCACTTCGTTTCTTTGTCTATTC R 2 1 2 1 201000 r 74 goat snp17672-scaffold1830-62992 22 18220966 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442176 Affx-122928807 AX-123312513 22 18234124 CTTGTTGCTTTATCTTGGCTCCAGTTTGGATGCAG[C/T]GATGTTGTTGTTATTGTTTTCTGAACATCACAAGA Y 2 1 2 1 101000 f 74 goat snp17674-scaffold1830-133907 22 18292086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431959 Affx-122935963 AX-123302300 22 18283692 CCAGATCAAATCAGTTCATCTCTCTGGACAAAACT[A/G]TAATTTGAAAAGATACATGCACTCCTCCGTTCACA R 2 1 2 1 303000 f 74 goat snp17675-scaffold1830-183475 22 18343179 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775928 Affx-122926365 AX-385263059 22 18326347 GGCTATTGATCATATCAGTCAATAAGGACCAAGGA[C/T]ACCAAGGATTAGAGATACTAGATAGACTTTAGTAA Y 2 1 2 1 101000 r 74 goat snp17676-scaffold1830-226130 22 18387107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391622 Affx-122966583 AX-123261979 22 18416354 CTGTCCAGCTACCACCTGCCAGAGACAGTGCTCAG[C/T]GGTGAACATGCAGCAACAAGAAGGAAGAGAACAGC Y 2 1 2 1 201000 r 74 goat snp17678-scaffold1830-316137 22 18477087 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463829287 Affx-1110175392 AX-515307809 22 18433292 TGGACACACTGAACATGTGTTTCCCCCCACAAATC[C/T]ATATGTTAAAGCCTCACCCTTGGTATGGCCTTGTT Y 2 1 2 1 201000 r 74 goat 22_18433292_AF-PAKI 22 18433292 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403198 Affx-122958062 AX-123273551 22 18474059 GCTGGTGTTCTAGTGACTGTCCTTTCAGAGAGTGT[A/G]CGGTGAAGTGTCATTTTAGATTGTTCAGCATCAGG R 2 1 2 1 101000 r 74 goat snp17679-scaffold1830-373842 22 18534541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446493 Affx-122925047 AX-123316829 22 18530851 CTCTATGGCAGGATCGTAACACGTACCCAGACACA[C/T]GCTCCACGCACACACACACACAATCGATGAAAGCC Y 2 1 2 1 101000 f 74 goat snp17680-scaffold1830-430634 22 18591701 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430324 Affx-122938226 AX-123300665 22 18567526 CCTGTCAAATGACCTTTTCTGGATAAAGGAAAGGA[C/T]GAAGATGGTGAAGGCACCAACTGCCCTAAGTTTCT Y 2 1 2 1 101000 f 74 goat snp17681-scaffold1830-467309 22 18629015 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277429 Affx-1111835907 AX-519550933 22 18568569 TTGCTATTGGTGAACTGACACTTTGAGGAAGTTGC[A/G]ACTCGGCTACATACTATCACTGGGGTCTGTCTTTG R 2 1 2 1 101000 f 74 goat Random2.2K-1985 22 18568569 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388959 Affx-122968805 AX-123259317 22 18597942 CTTAACATTCTAATGCCTTCAGGTTTTGCCTTACC[A/G]TTACTAATGATGACCACAATAATAATTTGACTGTA R 2 1 2 1 101000 f 74 goat snp17682-scaffold1830-497725 22 18659423 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414349 Affx-122950022 AX-123284698 22 18679815 CTTCCCACCGTCTCTACTGAGCATTCACAGAGCAT[A/C]GTGATGACTTGTCCAGGAGTTTCAGGGAGCATGTT M 2 1 2 1 101000 f 74 goat snp50710-scaffold730-2005808 22 18740893 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437784 Affx-122931696 AX-123308122 22 18716977 TCCTGAAGGTGCTCAGCTCGCTGCCCCTTTCAAGT[A/G]CTGAAACAGAATCTCTCACTGGAGAATCATCCTGG R 2 1 2 1 101000 r 74 goat snp50709-scaffold730-1968646 22 18778092 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447495 Affx-122924083 AX-123317831 22 18754169 GTAGGAGTTGGAGACCAGGCTCCTTATGACTGATT[A/C]TCATGATTGATTGGTGATGTCTGCTATGGTTATAG M 2 1 2 1 101000 f 74 goat snp50708-scaffold730-1931454 22 18815225 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435559 Affx-122933381 AX-123305899 22 18783990 TCTGTCACTAATTGTCCCTCTCTGTTTCCATCTCT[A/G]TTTCTCTCTCTGCCTCATCCCACGTTCAGTGTGTA R 2 1 2 1 303000 r 74 goat snp50707-scaffold730-1901633 22 18844075 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398971 Affx-122960966 AX-123269326 22 18826531 AGATGTGAGCAGCACACCCCTCTGTACCTTGAGCT[A/G]CCTCCATGCCTTACACAGGGACATGATGCCTAGTC R 2 1 2 1 201000 r 74 goat snp50706-scaffold730-1859092 22 18875740 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794127 Affx-122921215 AX-385281093 22 18880575 TACAAACGATCTGTGCATTCATTCGATTCTAATTC[A/G]CAACACTGTCAAAAAAGTAGCAATCTAGATCTGAC R 2 1 2 1 101000 r 74 goat snp50705-scaffold730-1805048 22 18929438 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799762 Affx-122952478 AX-385286689 22 18923255 GACAATATATCTCACTCAGCTCTCAAACCTGAAAT[A/G]CCTAAGTCTCCCACTTCTGGTATTGATACAGGATG R 2 1 2 1 201000 r 74 goat snp50704-scaffold730-1762368 22 18972281 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429355 Affx-122938567 AX-123299697 22 18952531 CCCGAGAAGGTTTCAGAGTTTGTAACATTAAATTT[A/C]TTATACATCCCAGGATTTGTCAGTGTTCAGAAAGA M 2 1 2 1 101000 r 74 goat snp50703-scaffold730-1733092 22 19001394 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387735 Affx-122969744 AX-123258093 22 18982338 GACCTTGAGAACAGAAGATGGTTCTTCCATATGAT[A/C]ACACCAGCCTTGAAGTTGAATATCTTGATATTCAA M 2 1 2 1 101000 r 74 goat snp50702-scaffold730-1703285 22 19031501 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785048 Affx-122960086 AX-385272095 22 19014471 ACTCATTAATCACTGGGATATGGTGTTTGAATGAC[A/G]TTCAGTATGAATCAGAGGTGTTTGTTGTATGCAGC R 2 1 2 1 101000 f 74 goat snp50701-scaffold730-1671152 22 19063417 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797216 Affx-122964107 AX-385284155 22 19070954 GAAAATCCTGATATACACATGATATCATGATATTC[A/G]TATATCAGAAAGCCTATCACAAGGAAAAAACAAAA R 2 1 2 1 202000 f 74 goat snp50700-scaffold730-1614669 22 19121165 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385180 Affx-122971732 AX-123255538 22 19104990 TTTTCAGTGAGACAACTAAGGCCCAGTTTGGTTGA[C/T]TGACTTTCTAAAGTCATATAGTCAAACAGAGATAG Y 2 1 2 1 102000 f 74 goat snp50699-scaffold730-1580633 22 19155321 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803188 Affx-122978921 AX-385290049 22 19134289 AAGGGTGGAAGGATACGGCATTGTAGGGACAAGAT[A/G]TGAGAAACAATGTGTGTTTCTCTCTTCCCTTCCTT R 2 1 2 1 101000 r 74 goat snp50698-scaffold730-1551334 22 19184561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428526 Affx-122938750 AX-123298868 22 19170014 CATTTGGCAAATCCTACTCTGCATGGGGATCTACC[A/G]TTTAGTTACAAGCAGCAGGAGTCTCTAGCACCAGG R 2 1 2 1 201000 r 74 goat snp50697-scaffold730-1515609 22 19220566 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423941 Affx-122942251 AX-123294287 22 19202345 TTATCTTGAATTCCTTGGAAACTGAAGGCAGGTGG[C/T]GAGATTCAGGATTTGATCTTTATTTTGCCAAAATC Y 2 1 2 1 201000 r 74 goat snp50696-scaffold730-1483278 22 19252246 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406832 Affx-122955675 AX-123277183 22 19250855 CAATACGTTGGCTGGGGCAGGAAATGGACCCTACA[C/T]CTGGTCCTGTTTACAACAAGTGGCTTGTTAAAATA Y 2 1 2 1 101000 r 74 goat snp50695-scaffold730-1434768 22 19300699 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418304 Affx-122946983 AX-123288652 22 19305616 GCAGTCTGAGGGTCAGTTTTCTGCTCAGTGTTTCC[A/G]CCTTCATCATGTAGCTCTACATTTGTCCTAAAAGG R 2 1 2 1 101000 r 74 goat snp50694-scaffold730-1380007 22 19355824 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766957 Affx-122932532 AX-385254258 22 19356568 GTGAATTTTCCAGTTCCTAAAGAAGCAATCACCCA[C/T]GGAGATTTCACCCACCCTTTCGACAAATGAAAGGG Y 2 1 2 1 101000 f 74 goat snp50693-scaffold730-1329055 22 19406087 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400472 Affx-122961301 AX-123270827 22 19401160 ATTTTCCAAGAACCACGTAGTCATTCTGAGTCTTT[A/G]TTTTCCCAGTTGCAAACTGAGAGAACAGAGTAGAA R 2 1 2 1 202000 f 74 goat snp50692-scaffold730-1284463 22 19450612 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771302 Affx-122965670 AX-385258460 22 19447477 CTGTTTCTTTCTCAAAATATTGTCTTGGTGTAAGT[A/G]CATGGAGGCAACTTATGTATCCTCAATCAAAATGT R 2 1 2 1 101000 f 74 goat snp50691-scaffold730-1238146 22 19497469 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774287 Affx-122971372 AX-385261423 22 19511347 GGGAGAGGTACAATAAACATGATATTCACATGTAT[A/G]TTAATTTCTTGTAGTATGTGAAGGTGATATATGCT R 2 1 2 1 101000 f 74 goat snp50690-scaffold730-1174276 22 19561647 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454174 Affx-122919311 AX-123324507 22 19560169 TAAATACAATAAAAATAAGAATATAACACTGTTAT[A/C]TCCCTATAAGAAATAGGAAGATTGATGTTTCTCCA M 2 1 2 1 103000 r 74 goat snp50689-scaffold730-1125454 22 19611229 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780082 Affx-122943975 AX-385267180 22 19600414 TTTAGAAGTCCTAGGGAGACATTTTATTCCAACTT[C/T]CTATGTTACATTTATCTTCTGTGCTTCTGAGTTTA Y 2 1 2 1 101000 f 74 goat snp50688-scaffold730-1085209 22 19651968 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411696 Affx-122951545 AX-123282046 22 19654374 AGTCCCCAAACTTCCCCTCATTGTGTTCACTTTTT[A/C]TTCTATCACCAGTTACAACCCCCTTAGAAGACTTT M 2 1 2 1 201000 r 74 goat snp50687-scaffold730-1031249 22 19706843 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771602 Affx-122930623 AX-385258760 22 19683585 CATCAACATGCTCTCTTCCAGACCCTCAGAACTTA[C/T]TAACTTTAAAAGTCGTTCCAAGGGTAGAAACCTTT Y 2 1 2 1 101000 f 74 goat snp50686-scaffold730-1002038 22 19735829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448333 Affx-122924138 AX-123318669 22 19721238 GTTGTTGTTCACTGTGAATTAATTTTACCAGAGAC[C/T]GCATTGTTAGGTAAGTCTTCTCCCTTAAACCAGTC Y 2 1 2 1 101000 r 74 goat snp50685-scaffold730-964385 22 19774073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403658 Affx-122957517 AX-123274010 22 19801653 GAAGAAGAAAGACCCCTCTTACTTCTTGGCAAGGA[C/T]TCAGCCGATGAAAGGCCTAGAATCTCTGTTTACTG Y 2 1 2 1 101000 r 74 goat snp50684-scaffold730-883970 22 19856681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781176 Affx-122977702 AX-385268261 22 19871031 TTTGGATATTAGATTTTTGTCTGATAGAAGTTACA[C/T]ATCACAATAAAATTGACTGTACAATTTTATTCATT Y 2 1 2 1 101000 r 74 goat snp50683-scaffold730-814592 22 19927046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795304 Affx-122928212 AX-385282262 22 19918516 TTTTATTATCTTTTACTTTTCTTCAGTACTTGCTT[A/G]CATTTCTTCTCTCCTCATTTTTCGTGTCCTTTGAA R 2 1 2 1 202000 f 74 goat snp50682-scaffold730-767107 22 19975294 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796451 Affx-122954017 AX-385283401 22 19949840 TCCAAGGAAATAGCAGTTGTGCGTTTCATGGGCAG[C/T]TTTAGTCATTTCCCTCAATAAAACATGACCATAAC Y 2 1 2 1 101000 f 74 goat snp50681-scaffold730-735783 22 20007446 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771315 Affx-122943138 AX-385258473 22 19983941 AAATCACAATTGTGATGGAGTATAATGATTCGTAA[A/G]TTCAACAGCTACTTTTAAGAAACCCAAAGTCAGTG R 2 1 2 1 101000 r 74 goat snp50680-scaffold730-701682 22 20042176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437990 Affx-122931587 AX-123308328 22 20037285 GCTGTAAAAATGCCGTGGGAGAGTGCAGTGGAAGC[C/T]AAGGTCCATTTGAGAGGTGGACATCATAGTCACAT Y 2 1 2 1 201000 r 74 goat snp50679-scaffold730-648338 22 20094945 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420453 Affx-122944888 AX-123290800 22 20081119 ACAGGGAATCCATACTGGTTCAGAAAGTCAATCCT[A/G]TTTAAGTTTTCACTTGACTCTAACAGCCTCCCACA R 2 1 2 1 201000 r 74 goat snp50678-scaffold730-604504 22 20130676 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378869 Affx-122976514 AX-123249228 22 20122628 TAGGGTGTTTCACCCATAAGACAAACAGAACGTTC[C/T]CTGGTCATGATGATGTTGTAGGCCAGGAAAGAGGG Y 2 1 2 1 101000 r 74 goat snp50677-scaffold730-562995 22 20172871 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417124 Affx-122947464 AX-123287472 22 20153868 AACTTGAGAGAGAGAGAAACATATGAATGCAAAAG[A/G]GATCAATACTGAATTTCTAGGATCATCTCCAGTGA R 2 1 2 1 101000 r 74 goat snp50676-scaffold730-531755 22 20204138 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776814 Affx-122960109 AX-385263938 22 20198534 GTTTGTAAAATATAACTATTATAAGCTGAAATGCA[G/T]CTCTTTCTGAAGTGTCTGTGATTGAAGTTGGCTTC K 2 1 2 1 101000 r 74 goat snp50675-scaffold730-487089 22 20248744 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439335 Affx-122930297 AX-123309672 22 20237635 TCTCATATATGTATAACATATATGGATATCTAAAC[C/T]AAAAAATACAGAAGGAAATTTTTAGATGATGATAT Y 2 1 2 1 103000 f 74 goat snp50674-scaffold730-447988 22 20287905 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770629 Affx-122950736 AX-385257793 22 20271768 AACATTTCCAGAGAAAAGACTTTTCCTATATTATC[G/T]CCTTATGCTCAAAAACCAGCAAGGAAAGCCATTGT K 2 1 2 1 101000 r 74 goat snp50673-scaffold730-413855 22 20322317 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399950 Affx-122960843 AX-123270305 22 20306605 ACTATTAACAATGAAAAGGAATTAACTATGCACAA[C/T]AGTCAATTACAAACAGCAACAAAGAGTAATTTTAC Y 2 1 2 1 202000 f 74 goat snp50672-scaffold730-379018 22 20357174 G A 2 parentage parentage neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441413 Affx-122928831 AX-123311750 22 20364369 AGTCACCTTTTAATCCTCCACACTGATCTGTGGCC[A/G]TGTCTCTTTATGCTTCAGAATTATGTTTTTATGCT R 2 1 2 1 201000 r 74 goat snp50671-scaffold730-321254 22 20417474 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375430 Affx-122979184 AX-123245789 22 20394132 CTTTGGTGTTTAAGGCACTGGCGATAAAAGATGAA[C/T]GAGACACAGCTCTGCCCAGTTTAGTGGAAGGACCC Y 2 1 2 1 101000 f 74 goat snp50670-scaffold730-291491 22 20447278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394775 Affx-122964832 AX-123265130 22 20427543 AATGAACTGTGGCTTACATTCAAAGCTGTGTCAAC[A/G]GATCTTGGTTCTGAATGACCCAGGCTGTCCAATGT R 2 1 2 1 101000 f 74 goat snp50669-scaffold730-258080 22 20480424 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376061 Affx-122978925 AX-123246420 22 20474232 AATTTGATAGTGGGATTGTCAGGGGAATTGCAGCT[A/G]TAGGAGACTTTGGGGTAGAAGGTCTGGGTGTGCAG R 2 1 2 1 101000 f 74 goat snp50668-scaffold730-211391 22 20526719 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437514 Affx-122932339 AX-123307852 22 20532632 CCCCTCTGTGGCTCCTTCTGGCTCATTTGTAGACT[A/G]TGTTTTCTCTCTTGTGACCTCCTTCTGTGTTTCTT R 2 1 2 1 101000 r 74 goat snp50667-scaffold730-152991 22 20585037 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429652 Affx-122937670 AX-123299993 22 20574778 TTGTTTTATCTCTTTATCCAAGCAGTAAATGAATA[A/G]TAGTAATGCAGAGAGATTTGGATAATCAGTGTAAG R 2 1 2 1 101000 r 74 goat snp50666-scaffold730-110845 22 20627256 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447450 Affx-122924369 AX-123317786 22 20619690 GAAGGAAGAAGGCTCAGCACACTTGATGTTCACAG[A/G]AAAAGAAATCAAGAATAAACTTTGTAAAAAAGTAA R 2 1 2 1 101000 f 74 goat snp50665-scaffold730-65933 22 20672918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453465 Affx-122919850 AX-123323798 22 20671576 TCTCTGTGCTTTTCATGGGCCTTCTGATAAGTTCT[A/C]GCCAGTGGGTTGTGAGCTAAAATGATGCACATAAT M 2 1 2 1 101000 f 74 goat snp50664-scaffold730-14047 22 20724342 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409517 Affx-122953627 AX-123279868 22 20704916 AAGTGGCAACTGAGTCTCTGTTTTATTTAAAGATA[C/T]GGGACTTCTCTATTCTCTCCTATTCTGGGCCAAAG Y 2 1 2 1 101000 r 74 goat snp616-scaffold1018-218959 22 20756551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451806 Affx-122921488 AX-123322139 22 20734520 ATGCATCTGCATGCAGGCCCTTTGAGAGGTGTTCC[A/G]TTGTTGTTCCCTGCAGTTTTTTAGCTTCCCTGAGC R 2 1 2 1 101000 r 74 goat snp615-scaffold1018-189355 22 20786215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407625 Affx-122954630 AX-123277976 22 20772760 TACCCCCAAGTCATTGCCACAAAGGGTAGCCCTCC[A/G]CGATGACTGAATGATGGAGGCATAGAATATACTAG R 2 1 2 1 101000 r 74 goat snp614-scaffold1018-151115 22 20824349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445909 Affx-122925938 AX-123316246 22 20801502 GTTGAATATGGACTGTACTTATGGGATTCTAAATT[A/G]TGAGACTTCCACCTCCTTCCTCCCCCTCCCCAGTT R 2 1 2 1 201000 f 74 goat snp613-scaffold1018-122373 22 20853380 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772964 Affx-122960230 AX-385260108 22 20840085 TGATGTTTGATGGTTAATAAAATGGAAAGATTTAC[A/G]TGAATAGCTGAGTGCATCTTTCACTGTGGTGCCAG R 2 1 2 1 201000 f 74 goat snp612-scaffold1018-83790 22 20888269 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779557 Affx-122953852 AX-385266660 22 20869134 TCCTAGAATCAATTCCACACAGTAGAAAGGTGGTA[C/T]GATGTGATTTCTTAAAGTGTACCGCTTGATGATTT Y 2 1 2 1 101000 f 74 goat snp611-scaffold1018-54741 22 20917051 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450736 Affx-122921864 AX-123321070 22 20898995 TGCTATCTTGAAAATTCCTGTGTAGGGGAAAGCTC[A/G]TTTATTGATACTTGGTTGGTGGGCAGTATGATAGA R 2 1 2 1 101000 f 74 goat snp610-scaffold1018-24880 22 20946630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411699 Affx-122951543 AX-123282049 22 20967592 GTGTCCAGGGAGTTTCCCAGACCGCCACTTCCTCC[A/G]TCTGTCCCCCTTCACAGTCTCTCAACAGTCTTCAC R 2 1 2 1 101000 r 74 goat snp53540-scaffold813-2476065 22 21021180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272119 Affx-1111833237 AX-519545877 22 21016120 GGTGATGATGTTTGCTTGCTAATTCATGTCTGACT[A/G]CAACCCCATGGACTGCAGATCTCTAGGCTTCTGTC R 2 1 2 1 103000 f 74 goat 22_21016120_AF-PAKI 22 21016120 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418545 Affx-122946403 AX-123288893 22 21030462 TTCTTCTCTTTCCTTTTCTTTTTGCCTTACTCCTG[C/T]GATGCACAGTAATAAATTGAGGTAAGCTCTGTGTA Y 2 1 2 1 101000 r 74 goat snp53539-scaffold813-2413195 22 21083874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378582 Affx-122976590 AX-123248941 22 21060612 ATGAAATGACAGATGTTAAGTGATTAGCATCATGC[C/T]TGCCCATAGAAGGGGCTAGATAAATGGTAAGTGTT Y 2 1 2 1 201000 f 74 goat snp53538-scaffold813-2383045 22 21114195 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404264 Affx-122957054 AX-123274616 22 21090206 AAACAGTGACTATATTTTAAAATCAATGTTTGATG[A/C]CAATCATCTTTATTTGGCCTTGGAGTACAGAATGA M 2 1 2 1 101000 r 74 goat snp53537-scaffold813-2353451 22 21144241 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792188 Affx-122924116 AX-385279173 22 21119212 ATGAATATTCAATTGGGGAATGTCAGTAGTTGAGT[A/G]TGTCTGTGGATCTGATTATTTTTCAGGAGAAACCC R 2 1 2 1 101000 r 74 goat snp53536-scaffold813-2324445 22 21173394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437285 Affx-122931988 AX-123307623 22 21156731 GCCACTATGAATTTAGAAGAAGAGAACAAGATGAC[A/C]GAAAGTCTAAAGGAAAAAAAAAAAAGAAGGCCAAA M 2 1 2 1 101000 f 74 goat snp53535-scaffold813-2286926 22 21210887 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389573 Affx-122968790 AX-123259931 22 21188000 GTTTCCTCAAGAGGGCACATTATATATTCCTGGGC[A/G]TTGTTCAGTGCCCAGCACATTGTTGTTCTCATTAA R 2 1 2 1 101000 f 74 goat snp53534-scaffold813-2255657 22 21241607 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429200 Affx-122937945 AX-123299542 22 21230924 CCTAATCTATTGCATGCTTGCCTCTAGATTTCTAT[C/T]CGTAACTAAAAGCTATCTAAACCACTGTTTAGAAC Y 2 1 2 1 101000 r 74 goat snp53533-scaffold813-2212733 22 21284595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414042 Affx-122949785 AX-123284391 22 21283284 CAAGCAGCCACTGTGTAAGCAGGCCATTGACTTTC[A/G]CAAACATTTGTCAGTCATTTAAGGGGGTTAGGATC R 2 1 2 1 101000 f 74 goat snp53532-scaffold813-2160373 22 21337916 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782324 Affx-122920987 AX-385269401 22 21323222 GGGGGGAAAAAAAACAGTAGTGCTCATGTTACAAT[A/G]CTGAAGTTTGTCATCTGAACGAAAAAGGAAATGGG R 2 1 2 1 101000 f 74 goat snp53531-scaffold813-2120435 22 21378189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381493 Affx-122974874 AX-123251851 22 21363189 TTATGCTTAAGAAAATGAAAGGTAAGCCACAAGCT[A/G]GGCAAAAACACTTAAAAAACATGTCAGACAAAAGG R 2 1 2 1 201000 f 74 goat snp53530-scaffold813-2080468 22 21418224 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390968 Affx-122967048 AX-123261325 22 21397615 TTTGATATCACTTTTCTGTGCTTACTTGTGTCACC[A/G]TACTCCACTGTCCACTTTACCATTTCACTGACCAC R 2 1 2 1 101000 f 74 goat snp53529-scaffold813-2046042 22 21452683 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448313 Affx-122924153 AX-123318649 22 21450722 TAGATGTTGTCTTTTGTACTATGTCTGGCTTAAAA[C/T]AGCATTTTTTAGATGGTTGAAAGAATACAAAACCA Y 2 1 2 1 101000 f 74 goat snp53528-scaffold813-1992935 22 21505494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428495 Affx-122938774 AX-123298838 22 21488924 TACAGTGTCTCCTGCCTGCCAGGCTTAAAGAATCT[A/G]TCTGGGAATAAACAAGAAAAGCATGTTGGACTTAG R 2 1 2 1 201000 r 74 goat snp53527-scaffold813-1954733 22 21543650 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422567 Affx-122943758 AX-123292913 22 21587869 AATATTTTTAAACTGTGGGCTGACCATGGACTAGT[A/G]TTTACTGGTATTCTTGACTCCAGGAGTCCCAAGGA R 2 1 2 1 101000 r 74 goat snp53525-scaffold813-1855788 22 21640013 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412422 Affx-122951427 AX-123282771 22 21643252 ACGAGAGAGTGTTCATGTGTTCAGAGGTCTTGGAG[C/T]ATCAGAGGACAGATCAGCAGCAGAAATTCTGGGAG Y 2 1 2 1 101000 f 74 goat snp53524-scaffold813-1800405 22 21695334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785274 Affx-122959004 AX-385272319 22 21703138 GCAAATGTGAAGTGCTGTTCCATTGAAACCCGGAG[C/T]ATCAGGTCTCACTGTCGTAAGCCAAATACAAAGAA Y 2 1 2 1 101000 f 74 goat snp53523-scaffold813-1740519 22 21756218 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796088 Affx-122937447 AX-385283040 22 21743678 TTAAATCGTAATGGCAGATACACAGGTCTCTGTTA[C/T]GCTATTTTCTGAACTTTTGTAACGTTTCAAAATGA Y 2 1 2 1 101000 f 74 goat snp53522-scaffold813-1699979 22 21796767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441610 Affx-122928653 AX-123311947 22 21778268 ATTCACCAAAGCAGAGATGAAAGCATTTATAACTG[C/T]GCTGTTATCCGACAGAATGGCCACTCTCTCCTACA Y 2 1 2 1 101000 r 74 goat snp53521-scaffold813-1665389 22 21831658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376211 Affx-122978807 AX-123246570 22 21832722 AAAAGATAAAGACAGTGGAACTAGAAATTGCTCCT[A/G]TGGCCCTTCATAAATTGGTTTTCCCTACACTCTGA R 2 1 2 1 101000 r 74 goat snp53520-scaffold813-1610935 22 21886742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429561 Affx-122937816 AX-123299903 22 21872987 TATCTAATCTTCCTATTTTGTTGCTGGTGGTGGTG[G/T]TGTTGCTCCTTTGAGAGAAGCTGGAAATTTGTGTT K 2 1 2 1 103000 f 74 goat snp53519-scaffold813-1570670 22 21927090 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438439 Affx-122931260 AX-123308777 22 21943608 TAGGAATGGGTTTCATAGCACACTTTCTTAAACTC[C/T]AAGATATCTAGCCAAACCTTCACTCTACAAATGAG Y 2 1 2 1 101000 f 74 goat snp53518-scaffold813-1500049 22 21998973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405012 Affx-122956380 AX-123275364 22 21981634 GACAGAGATGATCCTTATTTTCATGAAATTTAAAT[A/G]ATATTGAGGAAGATGCACAAAAGATGAGGAAAGAA R 2 1 2 1 101000 r 74 goat snp53517-scaffold813-1462023 22 22037533 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785810 Affx-122929672 AX-385272848 22 22064438 GCATTAAATCACCCTCTGAGTACCTCAGGAGAAAC[A/G]TATTCTATTCAAATCATGCATTTCTTTCAACTCCA R 2 1 2 1 101000 f 74 goat snp53515-scaffold813-1379219 22 22120643 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384482 Affx-122973071 AX-123254840 22 22126733 GATGGAACCACACCATCGACTCCCCCCCGACTTGT[G/T]CCCAGAGCCCACAGTCTGTATGTCTGCCCCATGAT K 2 1 2 1 201000 r 74 goat snp53514-scaffold813-1316924 22 22183708 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776770 Affx-122933825 AX-385263894 22 22155745 TGTTCAGAAAGATTATTTGTGAATAATGAAAGACC[A/G]TTTCAAAGTCAGGAAGAAAACTACATATTACCTCA R 2 1 2 1 101000 r 74 goat snp53513-scaffold813-1287912 22 22213299 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389665 Affx-122968718 AX-123260023 22 22191774 CCTATTCAAGCTCATAGAGCCAACTGTCTACAGAG[C/T]AGAAGCAAAGGTTCTGTCTCCTGACTCCCAGCTCT Y 2 1 2 1 101000 f 74 goat snp53512-scaffold813-1251883 22 22249733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432287 Affx-122936323 AX-123302628 22 22227407 GTATAAATATTTTATTTCATATGATTTTAAAAACC[A/G]TCTTTCCAGGAAGAGTCCTGTTTAAAATATGAGGT R 2 1 2 1 101000 r 74 goat snp53511-scaffold813-1216250 22 22285234 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767206 Affx-122922791 AX-385254488 22 22465161 TTAACTCACACCCCTTGTGTGGCAGTAAAAAAGAA[C/T]GATAGCTTATCCTATTTTCCGCCCACAATTCCCAT Y 2 1 2 1 102000 f 74 goat snp53507-scaffold813-978496 22 22527882 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447938 Affx-122923786 AX-123318274 22 22523128 TGTCTTAGTTCAAAGTACAAATCTGGGCACACTGA[G/T]CACAGAGCTGTACAGTCTTTTCTGGTTGCTCCTAG K 2 1 2 1 201000 r 74 goat snp53506-scaffold813-920529 22 22586245 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393045 Affx-122965627 AX-123263402 22 22555903 AGGCATCCTTGGCCAGACTAGCGTCAATAAATCCA[A/G]TATTTCTAATATTTTCCTTATGGAAAGTAACATTT R 2 1 2 1 101000 f 74 goat snp53505-scaffold813-887754 22 22619034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796527 Affx-122973054 AX-385283473 22 22605089 GGAGGTTACAAAAGAGCATGAAATACAAGCCATAT[A/G]TTTTTAAAAGATGGATATGTTATATTCAATGGTGC R 2 1 2 1 101000 f 74 goat snp53504-scaffold813-838568 22 22668393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769086 Affx-122964668 AX-385256261 22 22634602 CCAGAAACACACTGTTGAATCAAGAAGCAACTGTA[C/T]ACAGTATGATTCAATTTTTAGTATTCAAAACAAAA Y 2 1 2 1 101000 f 74 goat snp53503-scaffold813-809055 22 22698330 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395233 Affx-122964477 AX-123265588 22 22681226 CTTTGTGCTATGTGCAGGGATGTAAAAATGAACAC[C/T]GCAAACAAATTGTTTGCTCAGTCTCACAAAAAGAA Y 2 1 2 1 101000 f 74 goat snp53502-scaffold813-762431 22 22744925 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394130 Affx-122965329 AX-123264485 22 22726226 ATCAGTTGAAAATAGGGTGACCCAAAGATCCCTTA[C/T]AAGTCCTGACTTGGGGAAAGAGACCATAAAGTGGA Y 2 1 2 1 101000 f 74 goat snp53501-scaffold813-717431 22 22790055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277556 Affx-1111835908 AX-519551056 22 22768601 CTAGATCACCTAACGTGATAGCCAATGGGGCTTGA[A/G]TTCAGTAGTCTCACAGGACTACAGCAAACAGAGAA R 2 1 2 1 101000 r 74 goat Random2.2K-1986 22 22768601 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429677 Affx-122937649 AX-123300018 22 22775475 ACTTTCAGTTAGCCACCACTGCCTGCAGAAGCAGC[A/G]TTTCTTGATAAAGTGCAGGATGCTCAGTTACAGTT R 2 1 2 1 201000 r 74 goat snp53500-scaffold813-668182 22 22839744 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779465 Affx-122974755 AX-385266568 22 22807785 TGTGGAGGTATGGTAGGTGGGTAAAGGCTAAACTC[A/G]CCCTTAGTTACATACAACTATATGTGAAACAGATC R 2 1 2 1 101000 f 74 goat snp53499-scaffold813-635872 22 22872222 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438468 Affx-122931237 AX-123308806 22 22841709 CATTTCATACAGACTGTATAAACTATAAACTTCTG[C/T]ATTAGAGTGTGTTTTGATGAACTATAGGTTGACCT Y 2 1 2 1 101000 r 74 goat snp53498-scaffold813-601948 22 22906152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772927 Affx-122920264 AX-385260071 22 22875702 CCTGTCTTCTGAATGAGGGGATGAACAAACTCTCA[A/C]TTGTGAAGATGTCACACTTAGGAATGGCCCTTTAA M 2 1 2 1 101000 f 74 goat snp53497-scaffold813-567955 22 22939647 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382661 Affx-122973667 AX-123253019 22 22906428 AGAGGTGGGAGAACGAAGGACATAAGCAACGTGAC[A/G]AAGTGTCCAGTGCAGCGGTCACGGTCCACATTCTT R 2 1 2 1 201000 f 74 goat snp53496-scaffold813-537229 22 22969700 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427772 Affx-122939232 AX-123298115 22 23000230 CAGTGTTGGTCTTATGTCCAGCTGCCTGAATTACT[A/G]CAGCTTGGCTGAAGGAACCATGTTCTCTCAAGCCT R 2 1 2 1 101000 f 74 goat snp53494-scaffold813-443427 22 23063968 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430047 Affx-122937564 AX-123300388 22 23053135 TTCTTTGGTGAGAGCTGCTTTATTGAGTATCTGTG[C/T]GACGCTGGAGGAAGAATCATGTTGGATGGTACATG Y 2 1 2 1 201000 r 74 goat snp53493-scaffold813-390522 22 23116859 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450355 Affx-122922106 AX-123320690 22 23107154 TCTAGCAGCCCTCTTTTAGTCTCTGAATGTTCCTC[A/G]TTTGTGATGTTGGATAGGGGATATGTCTGTGCGTA R 2 1 2 1 101000 f 74 goat snp53492-scaffold813-336503 22 23171000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444311 Affx-122926745 AX-123314648 22 23197632 CATGGACCAAGTTTACTCCATGGGCTGCTGAAGTA[C/T]GAGAAAGATAAACTCAACTGAATTTCCTATAATTT Y 2 1 2 1 202000 r 74 goat snp53490-scaffold813-246025 22 23261676 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798917 Affx-122968797 AX-385285847 22 23258863 TCCATGGTTCCTGCAACTTCCTAGTTACCGAACTA[C/T]GCATCTTCTACAAAATTCAGAAAGTTTTGTGGCAC Y 2 1 2 1 201000 f 74 goat snp53489-scaffold813-184794 22 23323210 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403518 Affx-122957625 AX-123273871 22 23292594 TCTGTATTTAGAAACTCCTCTGACCCCACTACCCC[A/G]TTTCTATGCTGTCCTTTGCACCAAAACCGCACTGA R 2 1 2 1 101000 r 74 goat snp53488-scaffold813-151063 22 23357202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433912 Affx-122934390 AX-123304253 22 23324201 GGCAGCGTAGGTGGCTCGGTGCCATTGATTAAAGA[C/T]CTTTTCTCAAAGTTATCTTTAGAACATCCCTGGTC Y 2 1 2 1 101000 f 74 goat snp53487-scaffold813-119456 22 23388731 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277434 Affx-1111835909 AX-519550938 22 23379121 CCAAGTGGCTACCTTACAGTCTAGCTATAAAATCT[A/G]TAAAATCTAGGTGGATGAGACAATAACTCAGAAAA R 2 1 2 1 101000 f 74 goat Random2.2K-1987 22 23379121 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38426771 Affx-122940557 AX-123297117 22 23433987 TGTAATAAGAGATCCCAAATTTTTCAGAGGAGCTC[G/T]AAGTCTGAACTTTTACTTTAATTGTTGGAAACTAA K 2 1 2 1 201000 r 74 goat snp53485-scaffold813-9670 22 23499072 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782610 Affx-122941446 AX-385269683 22 23448440 TAGAGTTAGAAGTGACCACAGAGAGAGTATTTAAC[A/G]CTTTGTATTTTATAGATAGGAAGCTGTTCTCTGTG R 2 1 2 1 101000 f 74 goat snp55377-scaffold857-1256070 22 23513867 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410197 Affx-122952577 AX-123280547 22 23486724 GTTATTGCTTCTCATGTGCACTCAAGGCACAAAAA[C/T]ATCCCCAAGTTAGGCAAACCCAAGTGAAGAGAGCC Y 2 1 2 1 201000 f 74 goat snp55376-scaffold857-1217786 22 23552346 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782634 Affx-122950565 AX-385269707 22 23530783 TGATACCAGGAGATGCTTAGCTGCAGTTACTGTGA[C/T]GTTACCCTGTTAAAAATATCACACAAGTTACCAGA Y 2 1 2 1 101000 f 74 goat snp55375-scaffold857-1173727 22 23597394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396094 Affx-122963426 AX-123266449 22 23565180 GGAGCCCTCAAACAGCCTACCTGGCACATGATAGT[A/G]TTATGACTAGAGGCCCTTTAAGCACATGATGTTTT R 2 1 2 1 101000 r 74 goat snp55374-scaffold857-1139330 22 23632112 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415253 Affx-122948942 AX-123285602 22 23595958 GTTCACATACTTCCGTATGGACTTCTAATATAGGC[A/G]ACAGTGTCTCTGTCATATAGATGAAAAACTTGGAC R 2 1 2 1 101000 r 74 goat snp55373-scaffold857-1108552 22 23662543 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399263 Affx-122960562 AX-123269618 22 23745325 TTTTCCAAACTTCTCCATAGAAGAAAGTGATAACC[C/T]GGGGCTCTTGGTTTTAGTTCTGCCCATTCTACAGC Y 2 1 2 1 201000 f 74 goat snp55370-scaffold857-959185 22 23810333 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277560 Affx-1111835910 AX-519551060 22 23848562 GCATTCAGTGACTTATGGGAGCAGAACTCCAATCA[A/G]TCTCTGTATTCACTAGACCATATTCCCTCTGTATG R 2 1 2 1 101000 r 74 goat Random2.2K-1988 22 23848562 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272121 Affx-1111833238 AX-519545879 22 23870601 ATTAGATGTTTAGAAATGTGCTTAAGTCACCAGGT[A/G]AAATACACACGATATATAAACTACCATAACCTCTT R 2 1 2 1 101000 f 74 goat 22_23870601_AF-PAKI 22 23870601 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38410913 Affx-122952061 AX-123281263 22 23909589 CGGAGGGAAATCAGGAAAACAGAATCTTTGACCTC[A/G]AAAGTCAGAGTGGGAAAAACTGTCCCATCGTAGTA R 2 1 2 1 201000 r 74 goat snp55367-scaffold857-794921 22 23975169 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782127 Affx-122922282 AX-385269204 22 24003563 TCAGATGAACTGCTTAAGTCAACTAAATTCATCAC[A/G]TATTAGTAGAACTCTAGAAGAGTGTGTGGCTTTCC R 2 1 2 1 101000 r 74 goat snp55365-scaffold857-700947 22 24069562 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791884 Affx-122955084 AX-385278874 22 24041369 CAGTGAAGATTCATTTAAGTTTTTGTTAGGTAGTG[C/T]GGGTTTATCAGAAGGATAAAAGCAGAAATGAAGAA Y 2 1 2 1 101000 f 74 goat snp55364-scaffold857-663141 22 24109109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796203 Affx-122939017 AX-385283154 22 24098861 TTCTTCTTCCTCACCTTAAGACCATTATTTAATAC[A/G]GCTTTTAAATTCAGCATAACAGCCTGAAACCTGGC R 2 1 2 1 101000 r 74 goat snp55363-scaffold857-605649 22 24167097 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782882 Affx-122957066 AX-385269952 22 24137909 ACCAACACCTGACTTTCACCCTGGTGAAATCAATA[C/T]GCCAGCTTTTGCTAAAGTCACCAATAATCTAATAG Y 2 1 2 1 201000 r 74 goat snp55362-scaffold857-566601 22 24212150 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802939 Affx-122948845 AX-385289832 22 24209568 ATACATTACTGATATTGTTTCCGATCAAATAGTTG[C/T]GATGATTACACAGGGCAGTTGGAACAATCCCATAG Y 2 1 2 1 101000 r 74 goat snp55360-scaffold857-494942 22 24284379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277562 Affx-1111835911 AX-519551062 22 24224550 GTACAGTATTAAATGTTTTGTATGTAAACTTACTC[A/G]TAAAGAAGTTAGAGGTGTACTTAGAGAAGCTGTGA R 2 1 2 1 101000 r 74 goat Random2.2K-1989 22 24224550 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320771704 Affx-122932889 AX-385258861 22 24381582 CTGCTTCTCACCTCATGATACCAAAGTCCTTGACC[A/G]TTTGTTTACTTCACAGTAAGATTAGAACAGAATGG R 2 1 2 1 101000 f 74 goat snp55356-scaffold857-322928 22 24453118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388645 Affx-122969115 AX-123259003 22 24531025 CAAATACATGTTTTAATTACAAGGTATAATACAAA[G/T]AATGGGGTTTTGCAAAGGAAATATACTAAAATAGA K 2 1 2 1 201000 f 74 goat snp55353-scaffold857-173485 22 24604820 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442409 Affx-122927989 AX-123312746 22 24707232 CAGGATTTGATGCTAAAATGACGATGAAGGTAAAA[C/T]GAAATTGAGGATTGGAAAGGCAGCTGTGTATTAAC Y 2 1 2 1 101000 f 74 goat snp24948-scaffold2559-2623 NW_017189835.1 21262 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413431 Affx-122950693 AX-123283780 22 24805515 ATTTCACTGTGTCAGGCCTTTTCTCATTTAGGTTA[C/T]GGACTACTGTTATGGTGAACGCTGGAGCTTAAGTC Y 2 1 2 1 101000 r 74 goat snp24950-scaffold2559-100906 22 24879727 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402113 Affx-122958681 AX-123272466 22 24852899 TAATGGTGAGTTAGTGAATGGGGCCTAGTACTCAG[C/T]GATGCTTAAGTCTAGATACCAGGGACCTCTATAAT Y 2 1 2 1 101000 r 74 goat snp24951-scaffold2559-148290 22 24930682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407573 Affx-122954669 AX-123277924 22 24912816 TACACATACATATAAATATGATTTGCATGTTGTAA[C/T]AATTGTTGTAGAGACTGCTAGTTGTCTACCAAAAT Y 2 1 2 1 201000 f 74 goat snp24953-scaffold2559-208207 22 24990437 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38387321 Affx-122970505 AX-123257679 22 24957648 AACAAAGCTGCATGGTTAGATGTTAATTTTCATGC[A/G]TTTCATGGTCTTTAAAAGAATAGAAAGTAAACCTT R 2 1 2 1 101000 r 74 goat snp24954-scaffold2559-253039 22 25034915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407725 Affx-122955002 AX-123278076 22 25078691 GATATTATTCCCTGTCATTACTTCCATTCTTATTG[C/T]TCCTCCTTCCTGCCACACACAGAAACTCAACTTTG Y 2 1 2 1 101000 f 74 goat snp21229-scaffold2073-18228 22 25157360 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277440 Affx-1111835912 AX-519550944 22 25085927 ACCTTTACCTTCTTTACACTGATTTTTATTTTACT[A/G]TATTGTTTTTTCTGATAATAATCGATATTAGAATG R 2 1 2 1 101000 f 74 goat Random2.2K-1990 22 25085927 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444930 Affx-122926702 AX-123315267 22 25112319 GCTTTACTGGCACCTGAGATTTGGAAAGATTAAAT[A/G]CTATGCCAAGATCATACAAACTGTAAAAGGTCAGA R 2 1 2 1 101000 r 74 goat snp21230-scaffold2073-51856 22 25190761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800541 Affx-122973371 AX-385287461 22 25147317 AGCACAGTTTGTGATCCTGGTTGACTGGGTAGTTG[A/G]TATTGTGTAGACTTGGTCTGTGTTTGCTTCATAGA R 2 1 2 1 101000 f 74 goat snp21231-scaffold2073-86854 22 25226165 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793804 Affx-122941934 AX-190650350 22 25186697 GGTAAAATTGTAGAGAGTATCTGTGGCTTAAAACC[A/G]TTTTCATTGTTCATTCACTGGTTAAACAAATGTTT R 2 1 2 1 101000 f 74 goat snp21232-scaffold2073-126234 22 25265456 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438378 Affx-122931310 AX-123308716 22 25220938 GCTGGTGTACTTATCATGTTCCAGAGTCACGTTTT[A/G]CACAGATTATCTCCTTTAATCTAGTTTAAGTTATA R 2 1 2 1 101000 f 74 goat snp21233-scaffold2073-160475 22 25299928 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320769157 Affx-122970327 AX-385256332 22 25259319 TTATATTATATGTTGTATTATACTCTAATCTTTAG[A/G]AAGTGCTTTATAGATCTTTGATGGCTGATTACTTA R 2 1 2 1 101000 r 74 goat snp21234-scaffold2073-198856 22 25338630 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792960 Affx-122959845 AX-385279938 22 25294679 GATGTAAACAAAGTACTTGCCACAGAAATAGAATT[A/G]TAGCAAAGCTGGTGCGAAATGATGAAAGTAGAGAG R 2 1 2 1 101000 r 74 goat snp21235-scaffold2073-234216 22 25374125 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381332 Affx-122974428 AX-123251690 22 25326343 AAACAGCAACCACCACCACAGCAGTCTATTAATTG[C/T]GAAAACACATATATGAGTGGTCTTTTTCCCTCTCT Y 2 1 2 1 201000 r 74 goat snp21236-scaffold2073-265880 22 25407127 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427252 Affx-122939555 AX-123297595 22 25371119 CAGTACACTTTATAAATGAGTGGGATTCTTTAATA[C/T]GACCTTCAATTTCTAAGAAATGTCATTATTATTTA Y 2 1 2 1 101000 f 74 goat snp21237-scaffold2073-310656 22 25452349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379003 Affx-122976380 AX-123249362 22 25403020 GACATAATCTTGATATTTTCATTTTTAATAATTAT[A/G]TCACCTCTACAGTCTTAGTTTCAGTTATTCAGTTT R 2 1 2 1 101000 r 74 goat snp21238-scaffold2073-342557 22 25484459 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790671 Affx-122920909 AX-385277673 22 25441600 TTTTGTCCTTGGAAGATCCCTGATTTCTTTACATT[A/G]TATACTTATGTCACCTTCTACCAAAAAGCACTAAA R 2 1 2 1 101000 f 74 goat snp21239-scaffold2073-381137 22 25523892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432246 Affx-122936353 AX-123302587 22 25482065 TCAGGCAGTGCGTTCCAGTGAACAAGGAATAGATG[C/T]ATAGCCTTTCATTAGGTAGCACTGAAGGTACACAG Y 2 1 2 1 101000 r 74 goat snp21240-scaffold2073-421602 22 25564784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416979 Affx-122948003 AX-123287327 22 25580290 TGGTGTTTGGGAAGTTCTTAGATAAGCCTGTATCC[A/G]TATGAACACCATGCTTGACAGAGATAAATAATACA R 2 1 2 1 101000 f 74 goat snp37-scaffold1-1644633 22 25660617 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784371 Affx-122954157 AX-385271421 22 25644453 TGCAACAGTACATCACACTAAACCATTTTATTAAC[A/G]CAAACAGGCTCCAAACTTCAACCTTCGATAAAGTA R 2 1 2 1 101000 r 74 goat snp36-scaffold1-1580470 22 25724214 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452232 Affx-122920792 AX-123322565 22 25736374 TAACTTAATATGTCTATGAGACTGTGCATGGCCCT[A/G]CCTTTGCCTGATTTACAAGTTTGATTCATTTTTCT R 2 1 2 1 201000 r 74 goat snp34-scaffold1-1488549 22 25816480 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378772 Affx-122977007 AX-123249131 22 25768406 GAAGCCTGAATAAAGGTAACTTTCTTTAATTTTTC[A/G]TATCTACATGTCCTCTCATTTTGTTTTCACTTATA R 2 1 2 1 201000 r 74 goat snp33-scaffold1-1456517 22 25848392 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414374 Affx-122950002 AX-123284723 22 25859107 CCAATGTGCTTAAGCAAAAACATGTATTTTACTCT[A/G]TTCTCTGTATCTGTGATATTTATTCTTTATTAATA R 2 1 2 1 101000 f 74 goat snp31-scaffold1-1365816 22 25939115 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775164 Affx-122956651 AX-385262296 22 25934953 ATTACCATTTAAAGCCAAAATGACCATACAGTCTC[A/G]CCCCAAATTCATGAGTAGCTTTCTATTCAGTCCAG R 2 1 2 1 101000 f 74 goat snp30-scaffold1-1289970 22 26015367 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448764 Affx-122935618 AX-123319100 22 26003308 TCTGTGTTTCAGAGTACTGCTATTTCTAGGACCTC[A/G]TTCTTAGTTAGGCAAGCTCAGATTCTGCAGGTATG R 2 1 2 1 101000 f 74 goat snp29-scaffold1-1221615 22 26083891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774443 Affx-122951758 AX-385261579 22 26039240 GATAAATCTGGCATTCTTCCCTTCATCATTAAATA[C/T]AGGATGAACTACTGTGCTTACACTCTTGAGGGTTA Y 2 1 2 1 201000 f 74 goat snp28-scaffold1-1185683 22 26119806 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783788 Affx-122976600 AX-385270844 22 26079153 CTCAGGTTTTAATGCACTATAAAAGCTGACGTAAT[A/G]CTTGTTTGATTTGCTTAGCAGGAGCACATCATGAA R 2 1 2 1 101000 r 74 goat snp27-scaffold1-1145770 22 26159742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413334 Affx-122950169 AX-123283683 22 26122496 AAGAGCTGGTCTTGGGGCTTCTTCCGGCTTCAGCT[A/G]TATTGTGCACTCTGGGATCATAAGGACACAAAGCG R 2 1 2 1 101000 r 74 goat snp26-scaffold1-1102427 22 26203643 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450691 Affx-122921898 AX-123321025 22 26155227 GATCAATAATGCTGAAGCAGCTTTCCTTTAACTCA[C/T]GGACACTCAGCATAAACTGAACTGAATGACATGGA Y 2 1 2 1 101000 f 74 goat snp25-scaffold1-1069696 22 26236345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414606 Affx-122949352 AX-123284955 22 26209100 GGTTAGCTGGAACCAGCTTAGTCAAGCTGATGAGG[C/T]GGGGCAGTGGCAGACGAGAACTGAACTGACTGCTT Y 2 1 2 1 201000 f 74 goat snp24-scaffold1-1015823 22 26288997 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392804 Affx-122965968 AX-123263161 22 26258432 TTGTGTAGCCATGTGTGGGGTTCCTGGGAACTAAG[A/G]TGTGTGACTTCTCTGAGAACATTGGGGCTTCCCAA R 2 1 2 1 101000 f 74 goat snp23-scaffold1-966491 22 26341086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448758 Affx-122951259 AX-123319094 22 26301918 GTCTGAGCATCAGCATGCTTTCTAGGACCTAATTG[C/T]AAGGGCAGCAGTGAGGATTATAATGAAGGGGAGAG Y 2 1 2 1 201000 f 74 goat snp22-scaffold1-923005 22 26384210 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447980 Affx-122923753 AX-123318316 22 26358541 CATAGTGTACGACAACCCATCAGCCCAGTGTTTCC[A/G]TGGTTGCTCAGGCAAATAAAATGCAGCTCTAGGTA R 2 1 2 1 101000 r 74 goat snp21-scaffold1-866382 22 26441215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272993 Affx-1111833239 AX-519546674 22 26373311 TGTCTAAGACCTGCGCTTTTATTATTATTGCTAAT[A/G]TTAAATCAAGATTAATGGGAGAAATATCAATAACC R 2 1 2 1 101000 f 74 goat 22_26373311_AF-PAKI 22 26373311 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450569 Affx-122922041 AX-123320903 22 26404225 CTGAGCTACTTGAGAATACTACTCTTACTTTATGC[A/G]TCAATATGTCTCCTCCTACTGACAAAGTTCCTGGC R 2 1 2 1 101000 r 74 goat snp20-scaffold1-820698 22 26487410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428879 Affx-122938336 AX-123299221 22 26516257 GTTTATGAACAAAATAGCAAGCTTTTCAACAGTTA[C/T]AATGATGCTTGTAAACAAGCTTTTTAGTAAAAACC Y 2 1 2 1 101000 f 74 goat snp18-scaffold1-708666 22 26601209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277442 Affx-1111835913 AX-519550946 22 26566109 GTACCTGTGAAGTTTCATACTTGCAGCTTAATAAC[A/G]TATATCAAGACCAAAAGCCTATAATTCCCATTAGA R 2 1 2 1 101000 f 74 goat Random2.2K-1992 22 26566109 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789855 Affx-122973694 AX-385276862 22 26581647 AATGTTTAAAAAGCAGTTACTAACTCTAATGCAAG[A/C]CAATAAAGACTGGTGTCAAAGAAATACATATGAAG M 2 1 2 1 101000 r 74 goat snp16-scaffold1-643276 22 26667213 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448762 Affx-122942253 AX-123319098 22 26615872 TCAGACTATCCAATGCCCTTGTCAATAGCCATGTG[C/T]AGCTGTTGAGCACTTGAAATGTGGCCAGTGCCACA Y 2 1 2 1 101000 f 74 goat snp15-scaffold1-609051 22 26699231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425081 Affx-122941248 AX-123295427 22 26658805 CTAGAAACGGAGAATCTTAAGAGAAAAACCTTAGC[G/T]TGGTTCACAATGGAGAAACATCAACTTTGAATGGT K 2 1 2 1 101000 r 74 goat snp14-scaffold1-566118 22 26742675 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446537 Affx-122925013 AX-123316873 22 26703035 TCTCACAATCTGCTCCCTCTGCCCTGTTGTTACCA[C/T]ACCCTGGGCTTTGTGCATTCATCCTTTTCTCTTCA Y 2 1 2 1 101000 r 74 goat snp13-scaffold1-521888 22 26785537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451580 Affx-122921686 AX-123321913 22 26776748 GTAGGTAGATATCTGGAATGCTGCTAAACAACTTA[C/T]GATGTACAGGACAATCTCCACAACAAAGAGTTATC Y 2 1 2 1 101000 f 74 goat snp12-scaffold1-448175 22 26859944 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411916 Affx-122951170 AX-123282266 22 26810272 GCATCTGACCCAGTTTATAGTCTCTGACACCTCCC[A/G]TTTTCTCCAAAGGGTTGATTTATGATTGTACAACA R 2 1 2 1 201000 r 74 goat snp11-scaffold1-414651 22 26893862 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384765 Affx-122972023 AX-123255123 22 26872268 TGTGCCAGGTATTCGTTGCTTATACCCAGTACCTT[A/G]CAACTCTTAAAACAACCCCAGGAGGTAACTGTTGT R 2 1 2 1 101000 f 74 goat snp10-scaffold1-352655 22 26957685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792066 Affx-122939945 AX-385279053 22 26903350 TGTTACCTTTAATCACTTCATAAAAGGAGGAACCA[C/T]TGAGTGGCTAGTAGATTTCAGGCATAGATAGAGCT Y 2 1 2 1 101000 r 74 goat snp9-scaffold1-321573 22 26988796 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448757 Affx-122954820 AX-123319093 22 26938335 TAATATTTCTTTTGGTATCTAAAGGGAAAGCTCAC[A/G]CATCATTGTTATTTCTTCTCTGTTTGCCAAAGAAT R 2 1 2 1 101000 f 74 goat snp8-scaffold1-286588 22 27023830 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774781 Affx-122944066 AX-385261915 22 26984990 CGGCTGATTTCCACACTGGTGGGCATTTCCAGTCA[A/G]GCTCATATACGGATTAGCAAGACGGTACAGGCACA R 2 1 2 1 101000 f 74 goat snp7-scaffold1-239933 22 27070381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773495 Affx-122921041 AX-385260636 22 27028623 TATGATTTGAACACAATTGCCAACTTTAATTCAAA[A/G]AACATAAGGAAGACACCTCTCTTGTCAATAGGCCA R 2 1 2 1 102000 r 74 goat snp6-scaffold1-196300 22 27114233 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451109 Affx-122921392 AX-123321443 22 27074754 AAGAGCACCTATCCAGCACAAATGGCTTCCCACTC[A/C]AGCAGTATGATTTACTCTCCCCTAAGAAAGATACT M 2 1 2 1 101000 r 74 goat snp5-scaffold1-150169 22 27160634 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448761 Affx-122946587 AX-123319097 22 27104485 CGCTCCATGGTGGGAAGATGCAAACTTCAAGCTCA[C/T]GTACTTCAAAGGAAATTAATTTCCCACTGGTCTTG Y 2 1 2 1 101000 f 74 goat snp4-scaffold1-120438 22 27190249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420781 Affx-122944702 AX-123291128 22 27147215 TCTTTCAGGAATTAATCAGCCTAGGTGGGATGAGA[C/T]GACAATAGACTCACATATGATCCCTTGACTGAGGC Y 2 1 2 1 101000 f 74 goat snp3-scaffold1-77708 22 27232616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448760 Affx-122949096 AX-123319096 22 27194084 AGCTTATGAGAAACAAGAAACTCCCTGGCCTTTAA[C/T]GATGAACTTGGGAAAGTCATATCTAACTCAGTATA Y 2 1 2 1 102000 f 74 goat snp2-scaffold1-30839 22 27275292 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791299 Affx-122925500 AX-385278293 22 27222753 CGTCCATCACAATAAAGCAGCTTAATAAGCAGTGA[A/C]ATATTCATTTAACGAAATACTAATAGACCATGAAA M 2 1 2 1 101000 f 74 goat snp1-scaffold1-2170 22 27303588 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410224 Affx-122952557 AX-123280574 22 27311311 AGGTGGGTGGGTAGTGGTTGTGTGTGTATGTGTGT[A/G]GTAGGATGGGGTGTGGAGATAGTGTAGCCTGTCAT R 2 1 2 1 103000 r 74 goat snp22773-scaffold2271-212444 22 27397254 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401484 Affx-122958953 AX-123271837 22 27343214 AAGATTCCAGACTCTTTTACAGCAAGACTAATGGG[A/G]CTTCAGTTCCCAAAGATTTAGAATTTCTACGCTAG R 2 1 2 1 101000 f 74 goat snp22772-scaffold2271-180541 22 27429230 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400117 Affx-122960723 AX-123270472 22 27380056 AATTTATTTTATCTTATAAAATAAAGAACTAATTT[A/G]TTATTGACATACAGGGTCAGGCGTGAGGCCCAGGT R 2 1 2 1 103000 r 74 goat snp22771-scaffold2271-143699 22 27466029 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422952 Affx-122943018 AX-123293298 22 27414770 AAAATTTAATAAACAGTCCTTTCTCCTTTTCTGTG[A/G]AAGTTCAAAAAATATTTGGATATAAAATATCCTTC R 2 1 2 1 101000 f 74 goat snp22770-scaffold2271-108985 22 27501519 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778339 Affx-122967106 AX-385265454 22 27449831 ATCCTGCACATCATTCCATCATAACACAAAATTGG[A/G]TCTATTTTCCTGGCGCAATATGCTGCTCACAACGT R 2 1 2 1 201000 r 74 goat snp22769-scaffold2271-73924 22 27537069 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320782665 Affx-122937817 AX-385269738 22 27507953 CAGGTATAAATTCAGTGATGAGCTAGCACTGGTTT[A/G]TACTGATTCACAAGGGTAAATTGTTAAATTAGGAG R 2 1 2 1 101000 f 74 goat snp22768-scaffold2271-15802 22 27595725 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414292 Affx-122949593 AX-123284641 22 27535564 GTATGAATCACAAGATTTATCATTTTGGACCTGCT[A/G]TTCTCCACATGTGCATTTTTGGCACTGTAGTAGGC R 2 1 2 1 101000 f 74 goat snp1333-scaffold1036-11710 22 27623323 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401490 Affx-122958948 AX-123271843 22 27566574 AAAAGTCAAATAAGAAAAAGTCAGGAGTGATACCA[C/T]GATGAAAATACACCATTGCAGGAGGAGAATCATAA Y 2 1 2 1 101000 f 74 goat snp1334-scaffold1036-42720 22 27654736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773681 Affx-122972764 AX-385260821 22 27619794 GATAGTTCACGCTGGTGATTAAATCAAGCTTGAAT[A/G]TTGCAATTCAACAGAGATTCTGGGCAACCTTACAT R 2 1 2 1 202000 r 74 goat snp1335-scaffold1036-95940 22 27708973 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428687 Affx-122938634 AX-123299029 22 27676024 GTCAAGCGTCTTCCTCTGTCGCCCAGTATTCTCTG[C/T]GCTAGGACTCATACTGTCTTCCCAGCTCTATCTCC Y 2 1 2 1 201000 r 74 goat snp1336-scaffold1036-152170 22 27765587 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414980 Affx-122949057 AX-123285329 22 27704921 TTCCTTTTACATAGCCTTTTGACCAGTCTTAACTG[C/T]ATGACTGCATATTTTCTCCAGATGAGCAGTGTTGT Y 2 1 2 1 101000 f 74 goat snp1337-scaffold1036-181067 22 27795303 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770878 Affx-122967379 AX-385258041 22 27756432 AATGAGAAAGATATATTAGGCAAAAAATAAGTAGG[A/C]TGGAAAGCTGACAGATACTGAAATGAGCTCCCAGT M 2 1 2 1 101000 r 74 goat snp1338-scaffold1036-232578 22 27847273 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797299 Affx-122944241 AX-385284238 22 27790617 AGTAGTGATAATAGTAACAGTAGTGACAACAACAA[C/T]GGGATTCCTACTTTGCTTCAGGCATAGCACTTAAT Y 2 1 2 1 101000 r 74 goat snp1339-scaffold1036-266763 22 27881379 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449731 Affx-122922521 AX-123320066 22 27849072 CCCCAGTCTATACCCCAGTTCAGTTGAATCAGTCA[C/T]GTCCAACTCTTTGCGACCCCATGAATCACAGCACA Y 2 1 2 1 103000 f 74 goat snp1340-scaffold1036-325218 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406333 Affx-122955446 AX-123276685 22 27907097 TCATTTACCGCGTATCCCTTCCCAGTTGCCTTGTC[A/G]TTGATTAAAAATGTTTTCTTCCTTTGGGCATTGCT R 2 1 2 1 101000 f 74 goat snp1341-scaffold1036-383243 22 27998296 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407134 Affx-122954864 AX-123277485 22 27917899 GTTGCATTCTGCACAGTCCTTGGGGTCACCTTTCA[C/T]GGAGACCACAGTGGGACTCAACAGCTCTGCTCATA Y 2 1 2 1 201000 r 74 goat snp3002-scaffold1091-6468 22 28009120 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793273 Affx-122944258 AX-385280251 22 27953705 TGGAAAACTCGAAGTTAAATACAGCTTTCCATTCC[A/G]CTAGTTCTAGAAAAATGTGTGGATTTCTTCTGATT R 2 1 2 1 201000 r 74 goat snp3003-scaffold1091-42274 22 28045066 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420282 Affx-122945042 AX-123290630 22 28002947 TATACTTCTTGAGTGTATTTCTGGCCTATTTCAGA[C/T]GTTTGACTGGAAGCTCTGGCCATGGGATAAGCCAC Y 2 1 2 1 201000 f 74 goat snp3004-scaffold1091-91516 22 28093820 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434742 Affx-122933913 AX-123305083 22 28074871 CCAAAGTTTCTTTGATAGAAAACATTTCAAACTAA[C/T]GTATCTTCCCTGAAGATACGTTGTTTTGTGGCCCA Y 2 1 2 1 101000 f 74 goat snp3006-scaffold1091-163440 22 28165364 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428065 Affx-122939114 AX-123298408 22 28118324 GAACTCTGACTTAGCTCTTAATTAACCTGCAGTTC[C/T]GTGATTTCATACTCATCTATTCTGAACTGCCTTTC Y 2 1 2 1 101000 r 74 goat snp3007-scaffold1091-206893 22 28208308 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419652 Affx-122945956 AX-123290000 22 28150658 CCTGAGAGCAGGGGATTCAAGAAAGAGAGCGCACT[A/G]CAGACGGAAGCCTTGGTTTCTTTTCTACTTGAATC R 2 1 2 1 101000 f 74 goat snp3008-scaffold1091-239227 22 28240616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407095 Affx-122954893 AX-123277446 22 28198070 AATCGGGTCAGAGAGGATCATCATGTTGGATTGTC[A/G]TCTCCAGAGGAATGCATGCAGTTCTGGGAGTGGAC R 2 1 2 1 101000 f 74 goat snp3009-scaffold1091-286639 22 28287973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799783 Affx-122966373 AX-385286710 22 28248383 CCAGTGTACTTGGCAGAATGATGGGTAGTAAGAGT[A/C]GGGAGACAGGAGCCAAACAGTTGAGAATACTCTGG M 2 1 2 1 101000 r 74 goat snp3010-scaffold1091-336952 22 28338597 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407430 Affx-122954805 AX-123277781 22 28277787 AACTACTGACAGCATGTATGGTTTTCACAGGAATA[C/T]GGCATGGGTGTGTACTGCCTACATTCTGCTAGTGA Y 2 1 2 1 101000 f 74 goat snp3011-scaffold1091-366356 22 28367961 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442354 Affx-122928031 AX-123312691 22 28333565 AGCTAGAAGGACAACACAGAAAGGTATTCACCAAG[C/T]GAAAAATAAAGCTGTAGAATACCAGGGATTCTATA Y 2 1 2 1 101000 f 74 goat snp3012-scaffold1091-422134 22 28425018 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423495 Affx-122942564 AX-123293841 22 28362619 TTTAGACTCTCAACATCTCCCAGCTGTATTTGTTT[A/G]TTCAACAAATATTTAAGGAGCTATAACTATGTTAC R 2 1 2 1 103000 f 74 goat snp3013-scaffold1091-451188 22 28454119 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450882 Affx-122922212 AX-123321216 22 28405425 TGGTCATGCTTGCGGTTAGGAAGCTGGTGTTTAAA[C/T]GCCACTCCTTCTCCACTTTTGTATACACATCTAAT Y 2 1 2 1 201000 f 74 goat snp3014-scaffold1091-493994 22 28496980 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277568 Affx-1111835914 AX-519551067 22 28432657 TTCAGAGAAATTTGGGTGGAGGAAAAGCCCAACCG[A/G]TGGTATGAATTCCCTTCCTTTGTATTCTAGGCTTC R 2 1 2 1 201000 r 74 goat Random2.2K-1994 22 28432657 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320787930 Affx-122930888 AX-385274952 22 28444207 TGAAAAATGAAGCAATAAAATTTACACACGTATTA[G/T]CACATTCTCTTTCTAAATTTTACTCCAAAAAAAGA K 2 1 2 1 201000 r 74 goat snp3015-scaffold1091-532776 NW_017195047.1 4274 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428252 Affx-122939416 AX-123298595 22 28487416 TTCATCCTAAGAAGAGTGAGCACCACTGAATTTTT[A/C]TCAAGAGAATGCAAATATAAAGCCACCTGAATCCC M 2 1 2 1 101000 f 74 goat snp3016-scaffold1091-575985 22 28576081 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395422 Affx-122963943 AX-123265777 22 28574255 AGAAGAGGAGATGGAAGATGGAGACAAAAGAAGAA[C/T]GGGAAAGAGAAAACAGCTGAGACTGTGTCAGAAAA Y 2 1 2 1 101000 f 74 goat snp3018-scaffold1091-662824 22 28663187 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412357 Affx-122950825 AX-123282706 22 28611472 GTAAATACTCTGTCTCTGGATCCACTTCTCTCACT[A/G]TTGCTGGGTATGGCTCTGCATCTTTTTGAAATAAT R 2 1 2 1 101000 f 74 goat snp3019-scaffold1091-700041 22 28700447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775542 Affx-122957875 AX-385262673 22 28668707 ATGTTTCATAAGTATTTCAATGGCCTTATTGTATA[C/T]GTGTCAGTTACTGTTAGTCGTCTCAAATTTGTTTG Y 2 1 2 1 101000 r 74 goat snp3020-scaffold1091-757276 22 28758394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771009 Affx-122932205 AX-385258171 22 28726420 TAAACTTAAGGCTCCTAAGATTATAGACATGAAAA[C/T]GATATGTGAAAAGGGACCATTATGAGGGAGTAATC Y 2 1 2 1 101000 r 74 goat snp3021-scaffold1091-814989 22 28816319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445868 Affx-122925991 AX-123316205 22 28777482 CTTCTCTCCAAGAATCTGATATTTAAAAATTTAAG[A/C]TAAGCATTGAAGTAGTCAATGGTAAGTCAACTTTC M 2 1 2 1 103000 r 74 goat snp3022-scaffold1091-866051 22 28867455 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772346 Affx-122939620 AX-385259499 22 28831156 TGTCCCTATCTGGCAGAATCTTAGTGAAGATTAAA[C/T]GAAGTGACTCTGGCAAAGTGTTTAGGGCAGTGCCT Y 2 1 2 1 102000 r 74 goat snp3023-scaffold1091-919725 22 28921380 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442260 Affx-122928277 AX-123312597 22 28864635 AGGATGGATTATGCTCAGAAGTCATGTTGTGGAAT[A/G]CTTTACGGGGAAGGAGATTTTACTCATTGGTCAAA R 2 1 2 1 101000 f 74 goat snp3024-scaffold1091-953204 22 28955210 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272123 Affx-1111833240 AX-519545881 22 28878478 ATGGACTTCTGGCCTCTAGAGCTATGAGAGGATAA[A/G]TTTCTGTTGTTTTAAGCCAGCCAGTAATAGTTTGT R 2 1 2 1 103000 f 74 goat 22_28878478_AF-PAKI 22 28878478 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438521 Affx-122931201 AX-123308859 22 28913230 TACTCCTAACCTAGTACTGACCCAAGTCCCTGGGA[C/T]GCCAGACTGGAATATAAAACATAGGAACAGACCCC Y 2 1 2 1 101000 r 74 goat snp3025-scaffold1091-1001799 22 29004587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396526 Affx-122962954 AX-123266881 22 28958980 CGTGAGTCTTAAAGTCAAGCAAGTTAGAAAAGCTA[C/T]ACCTCCTGGCCTTAAAATATAACCCCAGAAAGAGT Y 2 1 2 1 101000 f 74 goat snp3026-scaffold1091-1047549 22 29050358 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431773 Affx-122936713 AX-123302114 22 28988346 TTTGTCCATGCATGGAGAATAGGATCAGAAAGATA[C/T]ATACCCCAACTCTTCACAGTTAATACTCTGGGATG Y 2 1 2 1 101000 r 74 goat snp3027-scaffold1091-1076915 22 29079762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375474 Affx-122979150 AX-123245833 22 29018417 CTTCTAGGAGTGTCTATCTTTTTCCAAGAGCTTTC[A/G]CAACCATTAACTCATTGGACCCCACCACAGAGTGT R 2 1 2 1 101000 r 74 goat snp3028-scaffold1091-1106986 22 29109938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437341 Affx-122931947 AX-123307679 22 29050509 TCCCTTTAGCTTTCTCATTTCACTGCAATCTCACC[C/T]CAAACTATAGTTTGCACTCAGACTAAAGGAAGGTA Y 2 1 2 1 101000 f 74 goat snp3029-scaffold1091-1139078 22 29141876 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377615 Affx-122977888 AX-123247974 22 29090282 ACGGTTTTGCAGCAGTGTATCTGGGTAGCAAACAG[C/T]AGAGTGATTTGGTCCATATGCATATAGAAATGCAA Y 2 1 2 1 101000 f 74 goat snp3030-scaffold1091-1178851 22 29181915 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274267 Affx-1111834152 AX-515314388 22 29094974 GTTGGCTTTTGTTTTAGACTTGTCCTCTCTTGATC[A/G]TTAAGACGGCTG R 2 1 2 1 101000 f 74 goat GoatD01.021852 22 29094974 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802232 Affx-122958724 AX-385289136 22 29123819 ATGAAGTATGTTCCAACCCACGTGGGAACTTGACT[C/T]TCATCTGTCTAAAGAGTACTGGATGATACGAAAAT Y 2 1 2 1 202000 r 74 goat snp3031-scaffold1091-1212388 22 29215499 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768159 Affx-122926277 AX-385255358 22 29160277 TGGTCTTGCCTCTTTACTCTACCCATTGCATGGAC[C/T]AGTCTCAACATTGGAGGCTTGAAGAGGATTCAGTT Y 2 1 2 1 101000 f 74 goat snp3032-scaffold1091-1248846 22 29252101 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431117 Affx-122936598 AX-123301458 22 29197840 CAAGCATGGTAACAGCGAACCTAATAGTTAAGAGT[A/G]TGCTGGCTCTGTGACCTTGGACAGGTCCCTAACCT R 2 1 2 1 101000 f 74 goat snp3033-scaffold1091-1286409 22 29290045 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380063 Affx-122975563 AX-123250421 22 29231313 TGGTGGTGGCATGTGTGTTTTCTGGAATAAAGGAG[C/T]CTTAGCTGTCACCCGAAGAGGAGCTATTGCCAAAC Y 2 1 2 1 101000 r 74 goat snp3034-scaffold1091-1319882 22 29323507 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439713 Affx-122930558 AX-123310050 22 29272323 GAGGGCCCCAAAAAGCCCTGCAAGACCAGGCTGAT[A/C]GCTGAGCCTGTACTGTCTCGTAAGCTGAGCAGCCA M 2 1 2 1 101000 r 74 goat snp3035-scaffold1091-1360892 22 29364720 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422313 Affx-122943470 AX-123292659 22 29309948 AGCAATGGGAGGTCATGCCCATAGCATTAATGAAC[A/G]TGTTCCAAATCTCACTCTTGCAGTGAGCCTAATAG R 2 1 2 1 101000 f 74 goat snp3036-scaffold1091-1398517 22 29402427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449001 Affx-122923102 AX-123319336 22 29385494 AGACCCTTTACCTGGACACTGTCCTCTCCACCCAC[C/T]CATGGGAAACTCTTCTCGGTCTCTACATCCTGGAG Y 2 1 2 1 101000 r 74 goat snp3037-scaffold1091-1474063 22 29477837 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437295 Affx-122931982 AX-123307633 22 29434268 ACTGCGAGGCTGGGTTCAAGGGCTGCCCAGGATTG[C/T]AAGTTCGATCCATTCTGGGCACCAGTCTGCCTCCA Y 2 1 2 1 101000 r 74 goat snp3038-scaffold1091-1522837 22 29526839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378922 Affx-122976445 AX-123249281 22 29490048 CTCAGTTTCCAGCCTAAAGTGGAAAAGAAAGAAGC[C/T]ATATTTATTTAACCTCAAAGTTAATCAACAGGGAC Y 2 1 2 1 201000 r 74 goat snp3039-scaffold1091-1578617 22 29582504 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277570 Affx-1111835915 AX-519551069 22 29509669 GGAGTCTGATACATTATTATCCTAATCTTACAGAC[A/G]AAGTTCTGAGATGACTGTCCATACACAGCTCATTT R 2 1 2 1 101000 r 74 goat Random2.2K-1996 22 29509669 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320774647 Affx-122966677 AX-385261781 22 29521835 TTGTGTCTTACCTTAGACCAAACTTGTAATTACAC[A/G]TTTTAGTCTTAAAACATTTGATTGGCTTTTTCAGG R 2 1 2 1 201000 r 74 goat snp3040-scaffold1091-1610404 22 29616308 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436697 Affx-122932329 AX-123307035 22 29588745 AGATGCAGCTTCAGATTCACATCTCCCACACTTAG[C/T]AACCCCAGAGGAACAAGAGATGCTATTTCCCAAGA Y 2 1 2 1 101000 f 74 goat snp13898-scaffold154-4423866 22 29683081 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428854 Affx-122938354 AX-123299196 22 29627230 ATGACCAACCTCCCTACCCTGGCCAGGAGACAGTC[A/C]AGTTCTGTCTCCACTTTTAGAATATCTGGGGTCTC M 2 1 2 1 101000 r 74 goat snp13897-scaffold154-4385381 22 29722160 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400120 Affx-122960721 AX-123270475 22 29712699 TTCTTTACTTTTCCTTCCTTCTGCCTGGAATGCTG[A/G]GGGAATGGCTGGGGTGTCAACAGCCTATTGATCAC R 2 1 2 1 303000 r 74 goat snp13895-scaffold154-4299912 22 29807504 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408775 Affx-122953381 AX-123279126 22 29752198 GGTAAGGACTGGTAAGTTTTCTGAGTGAGGATGTC[A/G]AAGGTTCTCAGGCCTGTCCGCTTCCTGCAGATACT R 2 1 2 1 101000 f 74 goat snp13894-scaffold154-4260413 22 29847016 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437634 Affx-122931807 AX-123307972 22 29796752 TCAAACCCAGTGTCATAAATGAGAGATGGTCCCAC[A/G]TGACCCCACTTTCCTCTGCCCACATGTATCAGCCA R 2 1 2 1 101000 f 74 goat snp13893-scaffold154-4215859 22 29891487 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773399 Affx-122929776 AX-385260541 22 29834378 GATATTTACAATCCCTACATTGTACAAAATCACAT[A/G]CTCTTGAATTTATATCCCACTCAAAGCAGGAAGAA R 2 1 2 1 101000 r 74 goat snp13892-scaffold154-4178233 22 29928984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431858 Affx-122936073 AX-123302199 22 29868106 CTCCAGGGGAACAAACTGTGCATTTTCTGGGTCAG[C/T]ATTCAGAAGTTAGAATTCTGAAGAAGAGACGATAA Y 2 1 2 1 101000 f 74 goat snp13891-scaffold154-4144505 22 29962665 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387721 Affx-122969754 AX-123258079 22 29910780 CTTCCTCTGGGTATTATGGCAGTCAGGACTTGCTA[C/T]AGCCACTTTGTCTCCAAGATAATAAGAGGTAATCA Y 2 1 2 1 101000 f 74 goat snp13890-scaffold154-4101831 22 30003389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444834 Affx-122926310 AX-123315171 22 29943297 ACACGTTTCCAGTCCGCCCCACTGTGAACAGGGGT[A/G]CTCTGCTTGAGGAACAACGTGGCCAGAAAGAGTGG R 2 1 2 1 101000 r 74 goat snp13889-scaffold154-4069314 22 30034894 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412528 Affx-122951347 AX-123282877 22 29977137 CTCTAACCAAAACTCTGACCTCTAGAAATGAAATA[C/T]ATAGCAACTGAAATTTAAAAGGAAAAGAAGAGAAA Y 2 1 2 1 201000 f 74 goat snp13888-scaffold154-4035474 22 30068594 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448064 Affx-122924344 AX-123318400 22 30010520 TTCAAAGAAGAAAAAAGGAGGGGGAGACTTCGGAA[C/T]GGATAGCAATCAAATAAAATAGCCAGCATCAACAA Y 2 1 2 1 201000 r 74 goat snp13887-scaffold154-4002091 22 30102001 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431771 Affx-122936715 AX-123302112 22 30039480 CTATTCAAAGCGGAGTTACTAATAAGACCAAAAGG[C/T]AGAAGCAAACCAAGTGTCCACTGACAGATGAATAA Y 2 1 2 1 101000 f 74 goat snp13886-scaffold154-3973131 22 30131012 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442052 Affx-122928392 AX-123312389 22 30083341 TTCTCCTGACCAACCAATTTCTTCTCTCCCTCTTA[C/T]ACACCTCACTCCAGCCACACTAGTCTTCTTTCTCT Y 2 1 2 1 202000 r 74 goat snp13885-scaffold154-3929270 22 30175309 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783873 Affx-122958046 AX-385270929 22 30118895 GCCTTATGGCTTCCTTATTGACGCATGACTTTTAC[A/G]TTCAGTATATAAGTGAGTATCTGCATATATAAACA R 2 1 2 1 101000 f 74 goat snp13884-scaffold154-3893716 22 30210180 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783828 Affx-122932230 AX-385270884 22 30153106 CAATGACAACAATTCTATGGTTCCTTCATAAAATC[A/G]CCTCTTCTCTTTAATTCCTCTCCACACTGAAATTG R 2 1 2 1 101000 r 74 goat snp13883-scaffold154-3859505 22 30244686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277572 Affx-1111835916 AX-519551071 22 30174083 ATCTTCTTTTTGTAAATGAGGAAGCTGAACCTGGA[A/G]AGCTTAAGTAACCAGCCCACGGCAGAGCCAGGATT R 2 1 2 1 202000 r 74 goat Random2.2K-1997 22 30174083 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382062 Affx-122974925 AX-123252420 22 30243492 CGAGTGGATTCCTAGCCACTGCCCCACCAGCGAAG[C/T]CCTAAGGCCAGTCTTTGAAACCTCTCCCATACCCT Y 2 1 2 1 101000 r 74 goat snp13881-scaffold154-3769119 22 30334824 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383945 Affx-122972958 AX-123254303 22 30284836 CTAGCAAACCTAATTAATATGCAGTGTGGGCTGTA[C/T]AGTGTTTTAATTTGGGGGTGGGGGGTTGGCGTGTG Y 2 1 2 1 101000 f 74 goat snp13880-scaffold154-3727775 22 30376177 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403781 Affx-122957984 AX-123274133 22 30424353 TTACAGGATGTACAATGTATCTTAAAATGACTAAC[G/T]AAAGCCTTCAAGAAAATGTATTTGCGATTCCAAAC K 2 1 2 1 201000 f 74 goat snp13877-scaffold154-3588258 22 30515596 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799189 Affx-122919839 AX-385286119 22 30470560 AACAATTTATTCTAGCTGATCATTAAGAATTTCAT[C/T]AATTAAATACATAAATGCAAGAACCTGGACCACTT Y 2 1 2 1 101000 r 74 goat snp13876-scaffold154-3542051 22 30561888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389319 Affx-122968495 AX-123259677 22 30519365 TCAAGGAGCTCACAGCTTCCCTGGGCATTTTGCCA[A/G]GGACACTGGATCTCAGCTAAGGTGGACATTCTGGA R 2 1 2 1 101000 r 74 goat snp13875-scaffold154-3493246 22 30610639 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385940 Affx-122971556 AX-123256298 22 30551560 AGAAAGAGAAGATGGGAGAAGAAGAAAAATAAGTC[A/G]TGGGCGAGGGCTGGATAGGTTTTCTCCAGGAGGTG R 2 1 2 1 201000 r 74 goat snp13874-scaffold154-3461051 22 30643851 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797977 Affx-122954710 AX-385284913 22 30585653 AGTATCATTATGTACCAATCATACCAAAATGAGCC[A/G]CCGAAGGCCATATTTCCAAAATTGGGTTGAGCAAG R 2 1 2 1 101000 r 74 goat snp13873-scaffold154-3426958 22 30677933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402841 Affx-122958255 AX-123273194 22 30630210 TTTAGAAGTACATGCCCCGTGGATCTGGACAGTTC[A/G]CTTGTCCCTGGAGGAGAAGGTGGGCCCTGTGGTGG R 2 1 2 1 101000 f 74 goat snp13872-scaffold154-3382401 22 30722539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377262 Affx-122978138 AX-123247621 22 30687399 ATAATCCAGTTTTTAAAAGGGTTTCAAAGTCTGCA[C/T]GTAAAGACACCATGTAGTACTGTGCTGTCCAGTGC Y 2 1 2 1 101000 r 74 goat snp13871-scaffold154-3325212 22 30780422 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395443 Affx-122963928 AX-123265798 22 30754943 TAGGTCCTTAAAAGTTGTCTATCTTATATGGGTGA[C/T]GGGTTTAGAGGCAAATATTTGAGTCCTAGGCCACA Y 2 1 2 1 201000 f 74 goat snp13869-scaffold154-3257668 22 30848167 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437248 Affx-122932016 AX-123307586 22 30784630 ACTGTCAGGATGGGAGGGGTGGGTAGTGATGTCAC[A/G]TGATTCTATTAGTTATTCAGACTGATCTTGGTTCC R 2 1 2 1 101000 r 74 goat snp13868-scaffold154-3227981 22 30877984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440956 Affx-122928998 AX-123311293 22 30833000 CTGTTCTAGTCACTCCCTGCTGTTGTCACCCCTGA[C/T]ATAGAATATAGGAAGCAGATTATTAGGCCTTCTCA Y 2 1 2 1 201000 r 74 goat snp13867-scaffold154-3179611 22 30926697 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384938 Affx-122972323 AX-123255296 22 30868475 CTAAAGCATTACACCTGTTGGCTGTCTTTTTCTCC[A/G]TGTCTCCTCCCTGTGAATACATAGAAAATCCCCAA R 2 1 2 1 201000 r 74 goat snp13866-scaffold154-3144136 22 30962005 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450464 Affx-122922945 AX-123320798 22 30899087 TAGATTATGGAATGACAGCTGCAGAACACCTTTCT[A/G]TGAAATGTCTCAGTGTGCTAAATTCTCTCTCTCTT R 2 1 2 1 101000 f 74 goat snp13865-scaffold154-3113524 22 30993250 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782803 Affx-122974660 AX-385269875 22 30956750 TGGCTGCTAATTTTAACAAATATCATCTCATGATC[G/T]ATGAATATTGCCGCAAATTACTTCTTTTTAATTTA K 2 1 2 1 101000 f 74 goat snp13864-scaffold154-3055861 22 31051295 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395821 Affx-122963635 AX-123266176 22 30993812 TTTTTAATAGCAGAATCACTTCCATGCCACTCTCA[C/T]GATTAAAGTTTTTATAAGATAGGGGGTTATTTGTA Y 2 1 2 1 101000 f 74 goat snp13863-scaffold154-3018799 22 31088608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801385 Affx-122969953 AX-385288296 22 31082703 CATTATTCAGTTACCCCACAAATGTATTTTATGTA[C/T]GTGTAGTTTATGTCATGATGACAATACAGTTATGG Y 2 1 2 1 202000 f 74 goat snp13862-scaffold154-2929908 22 31177813 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440362 Affx-122929649 AX-123310699 22 31114617 ATCGATTTGTGTGTGTATTTCAAGCAGGCATCTTA[C/T]GCACACAGTGCTTGTGGCCGACAGCACTCTCCCCT Y 2 1 2 1 101000 f 74 goat snp13861-scaffold154-2897994 22 31209998 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444366 Affx-122926705 AX-123314703 22 31160055 AATTTTATCTAGTAGTTTCCCCATGTTTCCTAACT[A/G]TTTGAAATGGGTCCTTGTAATTAAGAAATGTTAAA R 2 1 2 1 201000 r 74 goat snp13860-scaffold154-2852556 22 31255480 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414870 Affx-122949143 AX-123285219 22 31200417 ACAGGAGGCAATAAGTGGAGGAGCAAAGCACATGT[A/G]CATTTCCAGCTCCTTTGGCCCGCTGTGTGTGCACA R 2 1 2 1 201000 f 74 goat snp13859-scaffold154-2812194 22 31296055 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395003 Affx-122964234 AX-123265358 22 31255441 TCTCAGAGAGGTGAAATCACTCAAGTCACACAGCT[A/G]GTAAGTAGTAGAGTGAGATTTGAAGCCAGATCTCT R 2 1 2 1 202000 r 74 goat snp13858-scaffold154-2757170 22 31351228 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451653 Affx-122921599 AX-123321986 22 31291648 TATTAGGCTCATCATTGTAAACAGTCAAAACTTAA[C/T]GGACCCCTAGTTCAGGATAAAGGTCCATCTAGTCA Y 2 1 2 1 101000 f 74 goat snp13857-scaffold154-2720963 22 31388413 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443880 Affx-122927501 AX-123314217 22 31326736 CTGTCATTGAATGGAACGGTCTGGCAATACCATCA[C/T]TTGAGGCAGTGTGCAAATATTTGGTGATGTCATTG Y 2 1 2 1 101000 f 74 goat snp13856-scaffold154-2685875 22 31423635 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407063 Affx-122954919 AX-123277414 22 31360934 CAGTTGTGTCCAAAAGCCAGATCAGTGATATAGGT[A/G]TGTGGAGTGTGCAGTGGGCAAGACAGTAGGGGTGG R 2 1 2 1 101000 f 74 goat snp13855-scaffold154-2651677 22 31457886 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463837318 Affx-1110179472 AX-515315754 22 31405752 ACCGCACAAAACAGGATCCAATACTTAGAGAAGTT[G/T]CTCTATCTGCAGCTCAGGCTACATAAGTGAGTTGT K 2 1 2 1 101000 r 74 goat 22_31405752_AF-PAKI 22 31405752 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38430000 Affx-122938038 AX-123300341 22 31414258 GTGGAGGTATGGCTCTCTTTTCACTTTTGTTCTTC[A/G]TGTAGATGTAATGGCTGGAACCCAAGCAGTCATCT R 2 1 2 1 201000 r 74 goat snp13854-scaffold154-2598353 22 31511130 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419001 Affx-122946054 AX-123289349 22 31452643 TTTTCAGAGAGGGACATCTCACCTCACAGAGTTGA[A/G]TATCATTTGGCACGTCAGGGACAGGCAGCTTCTAA R 2 1 2 1 101000 f 74 goat snp13853-scaffold154-2559968 22 31549493 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383677 Affx-122972502 AX-123254035 22 31482759 ATATGTAATTTCATCTTTATATGTTTTCTTGTTAG[A/G]CCTCTTCTAGAAAAATCGTAGCCAAAAGTTTTCAT R 2 1 2 1 101000 r 74 goat snp13852-scaffold154-2529852 22 31579603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772587 Affx-122951015 AX-385259736 22 31522450 TCAACTTGATAATTGATAATATTAGATAATATTGA[C/T]ATTGATAATATTAGAGGATTGTGGTATTATATTCC Y 2 1 2 1 201000 f 74 goat snp13851-scaffold154-2490161 22 31619578 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276005 Affx-1111835115 AX-519549560 22 31528037 TCGGAGCTGGGACCGAGAGCAGCCAGGCCTACAGC[A/G]TCCCTGCAAAAATGGGGTCGAAACTGGAAGACATC R 2 1 2 1 102000 r 74 goat ilmnseq_rs654112183 22 31528037 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468276108 Affx-1111835171 AX-519549659 22 31528224 ATCCGACTCACCAGCTCTGGAGAGCAGAGACCCGT[A/G]GATGGGATAAGGGAAAGTCCGTGAGCTCGAGCCTG R 2 1 2 1 102000 r 74 goat ilmnseq_rs659116091 22 31528224 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468277450 Affx-1111835917 AX-519550954 22 31545283 CTTTTGTTTTTGTTCTTTCAAAGACACACTTGAAT[A/G]GAAGAGGAATTTTTTTTTGCACCAAATCTATATTC R 2 1 2 1 201000 f 74 goat Random2.2K-1998 22 31545283 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275916 Affx-1111835149 AX-519549474 22 31559847 GCCAACCAAGTCCTGAGCTTGCCATGTCCAAACCA[A/G]CCTGGCGACCATGTCATGCCACCAGTGCCGGGGAG R 2 1 2 1 102000 f 74 goat ilmnseq_rs656908213 22 31559847 C T 1 neutral Goat_IGGC_65K_v2 Illumina 320794840 Affx-122932241 AX-385281801 22 31584741 GTACTGTTACCTTTCCTAATATATTTGGGCATGAA[C/T]ATCATTCCTTTCTTGGAGCCACTTATAAATTCAGT Y 2 1 2 1 101000 f 74 goat snp13850-scaffold154-2427870 22 31679893 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276157 Affx-1111835268 AX-519549707 22 31617860 AAACAGAAAAACACACATTGAGTTCCTAATGAGAC[A/C]TTTCATTTGCATTTTGGGGTATCCTAAATCGCACC M 2 1 2 1 101000 f 74 goat ilmnseq_rs669339542 22 31617860 C A 1 recommended Goat_IGGC_65K_v2 Illumina 38389841 Affx-122968167 AX-123260198 22 31621314 GCCTCTGTGACCCCTGCCATTCTTTTAGTGGTTCC[A/G]TGATGTCAGAACCATCCTTGTAGTGATTTATCTTG R 2 1 2 1 201000 r 74 goat snp13849-scaffold154-2391297 22 31717360 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391259 Affx-122967368 AX-123261616 22 31652405 AGAAGTAGCCATGCTTAATTAATCACAGTGCCCGC[A/G]GCTTTGCCACTTAACTGATGTGTCTGTGTTCACAG R 2 1 2 1 101000 f 74 goat snp13848-scaffold154-2360206 22 31748556 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400450 Affx-122959956 AX-123270805 22 31688795 CACGCTGACCCTGCATGCCTTGGCCACGGTCCTCC[C/T]ATTAGCGCTGATGAACATCTGAGGGACCTGCCTGG Y 2 1 2 1 101000 r 74 goat snp13847-scaffold154-2323816 22 31785158 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377771 Affx-122977354 AX-123248130 22 31724256 GAGCAGCTCCTACAGAGTCAGAGGTGGGCTAAAGC[G/T]CAAAGAGGAAGGGGAGACTGGGAGCCTGGGGCACA K 2 1 2 1 101000 f 74 goat snp13846-scaffold154-2288355 22 31820575 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441580 Affx-122928677 AX-123311917 22 31777075 AATACAAAACTATGCTAAAATATTTAAATCTTAAA[G/T]AAGTTTTTGGATTTCATGGTTTAGTCCTGGAACAA K 2 1 2 1 103000 r 74 goat snp13845-scaffold154-2235536 22 31873327 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452661 Affx-122920331 AX-123322994 22 31826927 ATGAACTGTCCTATGAGCTGGAGATAAATATGAAG[C/T]GGGTACAGCAAACAGGCAACTGTTTACATGGTGCA Y 2 1 2 1 101000 r 74 goat snp13844-scaffold154-2185684 22 31923650 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418464 Affx-122946464 AX-123288812 22 31871967 GATAATGACTTCAGCCAGTCACTTAAGAATCGTAA[G/T]GAGCATCTGAGACTGAAAACACAGAAGTGATCACT K 2 1 2 1 101000 f 74 goat snp13843-scaffold154-2140644 22 31968423 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400418 Affx-122959981 AX-123270773 22 31902530 CACTCATGGTGGAGTAACCAGAAGAAGTAGGATTT[A/G]TACTGAGTCTTGAAAGAAAGAGAGTTGTATCAATA R 2 1 2 1 101000 f 74 goat snp13842-scaffold154-2110081 22 31999092 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431880 Affx-122936059 AX-123302221 22 31972736 GGAGATCTAAAGTAGACTTTTTAAAGTGTGTATGC[A/G]TGTGTTTGGGTAGAGGATTTTTCTTTTCTTTAAAG R 2 1 2 1 101000 r 74 goat snp13841-scaffold154-2039875 22 32080046 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410717 Affx-122952718 AX-123281067 22 32028707 ATCCCCCTACCCTAGAGCTTGTTTCCCCACTGAAA[C/T]GGCCTGAAATGCCTGCCCATCTGCCTTTCTCCACC Y 2 1 2 1 101000 f 74 goat snp13840-scaffold154-1983904 22 32134165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792365 Affx-122946288 AX-385279346 22 32124997 ACAAACGCACAAGGCAGCATAGATCTCGATATTCA[C/T]GATATAAGACACGTAATTTAAATGTTAGGAAAACA Y 2 1 2 1 101000 f 74 goat snp13838-scaffold154-1887614 22 32230786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413951 Affx-122950311 AX-123284300 22 32196394 TCATTAACATTAAAAAGTCATGAGTGCACACACAC[A/G]CAATGCCTAAAAGTTGGCAAATCTTACAACTTTCA R 2 1 2 1 101000 r 74 goat snp13836-scaffold154-1816217 22 32302815 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768805 Affx-122920204 AX-385255982 22 32238031 TTGCTTTATTAATGCCACTAAATTGATTGAAAGAA[C/T]AGGCATAGATTTAGGCCACTCTTCTGCTTGTTAAA Y 2 1 2 1 101000 r 74 goat snp13835-scaffold154-1774580 22 32344232 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783104 Affx-122931111 AX-385270171 22 32278302 ATCACATCAATTCGCTTTGAATTTTAGGGTATTTA[A/C]GTAGCATCTGAAAGGCAGTGATAACAATGTGTGAA M 2 1 2 1 101000 r 74 goat snp13834-scaffold154-1734309 22 32384466 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796013 Affx-122974424 AX-385282965 22 32314180 TCCTTCCACTAAAACAAAAGCCCTCAACATACAAA[C/T]ACCTGTTTTGTTCAAGGCTGTATCTTTAGCATATA Y 2 1 2 1 201000 r 74 goat snp13833-scaffold154-1698431 22 32416128 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780588 Affx-122966909 AX-385267679 22 32343741 AAAAAAGTAAGATAATTTGAGGAGAAAAGTAATCT[C/T]TAAGGGTAGAATTGAAATGCTATTCAATTTTCAGT Y 2 1 2 1 101000 f 74 goat snp13832-scaffold154-1668870 22 32445943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769346 Affx-122965589 AX-385256517 22 32446845 AGAGGTCCCAAAACATAGTCAAGGCCATGAGACTG[C/T]GGATGACTGAATCTACCACTTTCCATGCAAAATTT Y 2 1 2 1 101000 f 74 goat snp13830-scaffold154-1565766 22 32549893 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431729 Affx-122936749 AX-123302070 22 32477351 GTTACCAGCTGGTGACCCTGGCCAAATGCTTCATC[A/G]CTCTGTTCCTTAGCTTCCTGTAAAACGCAGACAAC R 2 1 2 1 201000 r 74 goat snp13829-scaffold154-1535260 22 32580356 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428769 Affx-122938422 AX-123299111 22 32508127 GCACAATAACCAACTAGCCCTGGGCACTTTCACAG[C/T]AGTCAAATGGTATCGATTGTACACTGATTTATTAA Y 2 1 2 1 201000 r 74 goat snp13828-scaffold154-1504484 22 32611191 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38417130 Affx-122947365 AX-123287478 22 32537984 AGCGTCTTCCTAATGCTGGACTTTCCCTGTCACCC[A/G]CTCCCCACATCTATTGTCAAGATAAACACTGCAGT R 2 1 2 1 101000 r 74 goat snp13827-scaffold154-1474627 22 32639836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378044 Affx-122977568 AX-123248403 22 32588210 GTTTTCAACAAGTAACTTCATTCCTGTTTGCCTCC[A/G]TTTCCATGTCTGCAAAATAATAAACCTTCAGAGGG R 2 1 2 1 101000 r 74 goat snp13826-scaffold154-1424401 22 32689633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798712 Affx-122950812 AX-385285643 22 32624935 TTTGTGTAATACACATTCATTCCAAGATCTACCAC[A/G]TTTTCTACAGACCTGTTTTAAATACACCAGTATAT R 2 1 2 1 101000 f 74 goat snp13825-scaffold154-1387676 22 32726720 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386839 Affx-122970086 AX-123257197 22 32657986 ACCCCCTCACATTTCTGTAAGTAGAAACCTTGAGA[C/T]GAGAAGGTTGACTGCTAAGACTCTTGGTGCGGTTT Y 2 1 2 1 101000 f 74 goat snp13824-scaffold154-1354625 22 32759589 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418143 Affx-122947107 AX-123288491 22 32751231 GTCTTAGCTACTGTAAGTAACACTGGAGTGAATAG[C/T]GGAGTGCACCTTTCTTATTTGAATTACTGTTTTTG Y 2 1 2 1 201000 r 74 goat snp13822-scaffold154-1261380 22 32853143 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443143 Affx-122928070 AX-123313480 22 32832012 ATGGGTTCATCTGGGATTATCAACATGGTGTCTAT[A/G]CCCTTTTCCAAGATGGTAGTTTCAGGATAGCTGAA R 2 1 2 1 101000 f 74 goat snp13820-scaffold154-1180599 22 32934943 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451333 Affx-122921271 AX-123321666 22 32868864 TGAGTCTCATTGCTTTGTAATTTTATTCCAGAAAG[C/T]GAACATGCCATGTTTTGTGACTTAGTCTACTTTTC Y 2 1 2 1 101000 r 74 goat snp13819-scaffold154-1143747 22 32971877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398087 Affx-122961723 AX-123268442 22 32899841 TAAGCGAGGCCGCTTATCATTCAGGTTCACTGCAC[A/G]TTTTTCTTATAGCAAAGAAATGTTTCTCCACACTC R 2 1 2 1 303000 r 74 goat snp13818-scaffold154-1112770 22 33002872 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790136 Affx-122967510 AX-385277141 22 32981979 ACTGCAGTTAAGAAGAAATTTATTTGTACTCAGTG[A/G]TTAATTGGCTTTGTTTGATAGAGCATTGCTTCAGA R 2 1 2 1 101000 f 74 goat snp13816-scaffold154-1030632 22 33085641 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442911 Affx-122927636 AX-123313248 22 33013068 CTTATATTAAAAGATGTTTTGAAAAATTAATTGTA[C/T]GGAAAATCCTAACACAATTTTGCCAAATTTCATCT Y 2 1 2 1 103000 r 74 goat snp13815-scaffold154-999543 22 33117391 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381153 Affx-122974553 AX-123251511 22 33103670 ATTCTAGAAATCCAGACTTAGAGGGGTATCAAATA[C/T]GAGGTGTGTGTTGTTTCCTGACAAACTTTGTGGCC Y 2 1 2 1 101000 f 74 goat snp13813-scaffold154-908941 22 33208128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405873 Affx-122955608 AX-123276225 22 33183816 CCTATGTCCTATGTGACTGGCGCCCCCTGGAGTTG[C/T]AGAGCCACAGCCTAGGGTTTTCCTGCCTTTCAGGG Y 2 1 2 1 101000 r 74 goat snp13811-scaffold154-828795 22 33287818 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437080 Affx-122932667 AX-123307418 22 33212527 TATTATTAAATGCCCTTCATTTCCCTTGGAGCTAG[C/T]GTGGGGTTTTTGTTATGCTAAAGTACAATGAGATA Y 2 1 2 1 101000 f 74 goat snp13810-scaffold154-800084 22 33316548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419527 Affx-122945436 AX-123289875 22 33248698 CTTCAGTAGAATTATAATTAATTGCTTTCCTTTTA[C/T]ACCATTTTAAGTCCCAAGAATTTTAACAAGGGGGT Y 2 1 2 1 101000 r 74 goat snp13809-scaffold154-763913 22 33353296 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432831 Affx-122935382 AX-123303172 22 33294636 GATTGTCATATGAAATAGTGCGGCCGTGAGCTAAC[A/G]CAGGACTATTGCCTGTGGAACCCCAATTTTTATTT R 2 1 2 1 101000 f 74 goat snp13808-scaffold154-717975 22 33399309 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394020 Affx-122965010 AX-123264375 22 33324980 TATGGGAGATAGTGACTATGAATCTGGCTATGGAT[A/C]TGAGCATTTTATAAGCCAAAGAAATCATGTTACTG M 2 1 2 1 101000 f 74 goat snp13807-scaffold154-687631 22 33429768 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391452 Affx-122966738 AX-123261809 22 33355332 CTTTGCTTGCCTTTGCCAACTTCTAGGTCCTGCCT[A/G]CATGTCTTTGCTTTTGGCCCCATTCTTCCATCTTG R 2 1 2 1 201000 r 74 goat snp13806-scaffold154-657279 22 33460194 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406197 Affx-122956139 AX-123276549 22 33411456 AAGCCCCGCATGCCCCAACTGTGATTCAACACAGT[A/G]CCTAAGCAGCACTTAGATAAATAGATATCCCAAGG R 2 1 2 1 101000 r 74 goat snp13805-scaffold154-601155 22 33517449 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402360 Affx-122959046 AX-123272713 22 33444656 GGAAAGAAATGGGTGACAGGAAGTGATCTATAAGA[C/T]AAGAAGGCATTGTGGGGTTTGTGGGAACTAAAGAG Y 2 1 2 1 101000 f 74 goat snp13804-scaffold154-567955 22 33551365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424441 Affx-122941791 AX-123294787 22 33486595 TATTATTTTATACACTGGGAATACAGTGATGAACC[A/G]GAGTGGCACACAGAATGCAGCAACAATGGTCTAGG R 2 1 2 1 101000 f 74 goat snp13803-scaffold154-526016 22 33594530 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397830 Affx-122962476 AX-123268185 22 33522166 AAATTAGAAACACACTATTATTGACATTGTTTGCT[A/G]TTGTTTAGTCACTAACTCATGTCTGACTCTTTTGT R 2 1 2 1 303000 f 74 goat snp13802-scaffold154-490445 22 33625245 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413390 Affx-122950125 AX-123283739 22 33557118 TGTTTCCCTTACTCTACTCCCTGATCTTAATGACA[A/G]CCATAGCCCTGTTGTTTATGTCACACTTAAAACAC R 2 1 2 1 101000 f 74 goat snp13801-scaffold154-455493 22 33660548 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410713 Affx-122952721 AX-123281063 22 33605054 TTGAGCACTGAATTTACGGATGACTTAAAATAAGA[C/T]GTCACTCTATTGCCCAATGAATCAGTGTTTTGCAA Y 2 1 2 1 101000 r 74 goat snp13800-scaffold154-407557 22 33709683 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416191 Affx-122948248 AX-123286540 22 33665056 TTTATACCTACCTATTTACAAAAACTTGGGAACAC[A/G]TTCCCCATCAGGCTGGGCTAGTGGTTTTCAACCAC R 2 1 2 1 201000 f 74 goat snp13799-scaffold154-347555 22 33769707 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429940 Affx-122938086 AX-123300281 22 33712526 CCTAGAAATGGAAATGGGATAAGCTCATGGAGAAA[C/T]GAGGGTAGAAAAAGATCCAGCCCCTCTTATTCCAC Y 2 1 2 1 101000 f 74 goat snp13798-scaffold154-300085 22 33818697 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385841 Affx-122971005 AX-123256199 22 33769136 GAGCTGGGCGCCCCCATCCCCAAAGAGAGAACACA[C/T]GAGCCACATCTGCCCATGGGCTCTCCACACGCCCT Y 2 1 2 1 201000 r 74 goat snp13797-scaffold154-243475 22 33876261 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277576 Affx-1111835918 AX-519551075 22 33796430 CTCTCACTTAAAAGTCTTGCCTCCAGCTTTGATGC[A/G]TTCTTTATGCTGCAATTGGGAAATAGCCCATTTCC R 2 1 2 1 101000 r 74 goat Random2.2K-1999 22 33796430 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436750 Affx-122932289 AX-123307088 22 33798669 CCACCAGCATCATTATCCTCATCCCCACTATCAGA[C/T]AGCCGTATTATAGACAATAATCTAAACTGTTTTGT Y 2 1 2 1 201000 r 74 goat snp13796-scaffold154-213942 22 33905239 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381739 Affx-122974327 AX-123252097 22 33829725 CTGCTGTTGCAAGAAAACCATCTCTGGATCCCAGA[C/T]AGAATTTCCCTGCCACAAATGCACACTGTGTTTTT Y 2 1 2 1 101000 r 74 goat snp13795-scaffold154-182886 22 33936610 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423795 Affx-122942819 AX-123294141 22 33872675 ATCCTAGACTTCTGTTCAGAGTAAATCTAAACTAA[C/T]GCCTACTGAAGTTTACACATGTACAGATTAACTTT Y 2 1 2 1 101000 f 74 goat snp13794-scaffold154-139936 22 33979549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434194 Affx-122934867 AX-123304535 22 33914327 CTTCCAAATAAGCCTAAAATGCATGTCAAGGAACA[A/G]CGTACATTTGTCTTTGCACTTCCTATGGAAGTTTT R 2 1 2 1 101000 r 74 goat snp13793-scaffold154-98284 22 34020973 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396775 Affx-122962766 AX-123267130 22 33956438 TGGCATGTAAATTGAGACTCAAGGAGCTTAAATAA[A/G]TTGTCCAAGGGCACACAGCTATTAAGCAGTGGAGT R 2 1 2 1 201000 f 74 goat snp13792-scaffold154-56173 22 34062979 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788628 Affx-122940667 AX-385275645 22 33991570 TCAATATTAAGGCAAATGGTAGAATACATGTATGT[A/G]GTATTAATTATGAATCTTCCATTGTAAAATACATT R 2 1 2 1 101000 f 74 goat snp13791-scaffold154-21041 22 34098446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397959 Affx-122961907 AX-123268314 22 34021493 GTAAAGCACCTGTCAACTCAAATACCAGTGCTTTG[C/T]ATTCCCCAGTGTACACTGCATATGTTATACAATGG Y 2 1 2 1 101000 r 74 goat snp53648-scaffold816-2958695 22 34141466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773913 Affx-122969165 AX-385261052 22 34065314 ATTTGGTAATGTCATGATCAGGGATACATTTTCAA[C/T]GGTCACTCTGGTCTCTTAGTGGATAATATATCTGA Y 2 1 2 1 101000 r 74 goat snp53647-scaffold816-2914874 22 34186166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416698 Affx-122947568 AX-123287046 22 34121030 AAGTTTTCTCTGTCTAGACCCAATAGCCCTTTTTC[A/G]CCAACCCTTCCTAAAGTATTAGGGTTTTCTTTGCT R 2 1 2 1 101000 f 74 goat snp53646-scaffold816-2859158 22 34241538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385276 Affx-122972070 AX-123255634 22 34163897 GCTATGCATTAAAATTTAGTCCCTAGAGAGACTAC[A/G]CATTTTTACGAGGCCACAAAGAAGAACATCTCAAC R 2 1 2 1 101000 r 74 goat snp53645-scaffold816-2816291 22 34283732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272560 Affx-1111833242 AX-519546276 22 34172193 CATCATTTATTTCAAGCTCTGTTTCTATTTTGGCC[A/G]CTCAGTACGCAGTTACTAAAAAATGCTACATAGCA R 2 1 2 1 101000 r 74 goat 22_34172193_AF-PAKI 22 34172193 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320768758 Affx-122924401 AX-385255935 22 34193606 TCTACTTGACTTGACTTGTGAGTTAAAATAAATCA[C/T]ACTTGCAGATTTGCTCCCCATCTTCCTGTAATAAT Y 2 1 2 1 101000 r 74 goat snp53644-scaffold816-2786582 22 34313320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412868 Affx-122950438 AX-123283217 22 34252880 AACCAGGGTGACTGAACCAACCTGACTCAGCTTGT[A/G]CTTGCCTCTCCCAACCTTGACAACAAGTGGGTTCC R 2 1 2 1 201000 r 74 goat snp53643-scaffold816-2727308 22 34372641 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424136 Affx-122942006 AX-123294482 22 34337963 GAAAATGATAGAACACAGGGGAACTTGCATGTTAT[A/G]CTGCTGTGTGTGAGGCCAGCTTATTCAAGTCAGTA R 2 1 2 1 101000 f 74 goat snp53642-scaffold816-2642225 22 34458569 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429289 Affx-122938616 AX-123299631 22 34384246 TTGTTTGCCTTCTACTTTAAATATTTCAGTGTGTC[A/G]AGTTATTTTCCACTGCATGAGTGCTTAGTTGTGCC R 2 1 2 1 101000 r 74 goat snp53641-scaffold816-2595942 22 34505774 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277458 Affx-1111835921 AX-519550962 22 34407928 AAAAAGCTAAGAAGATATAATGGAAAAAACATCTC[A/G]TTTACAGTATTAAATGAAAAAGTAAAAGGGAATAA R 2 1 2 1 101000 f 74 goat Random2.2K-2000 22 34407928 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416674 Affx-122947585 AX-123287022 22 34454107 GTTGGTGTACTGTCAACTCTGATTACATCGGTCAA[C/T]ACCCAACCCCGATAATGGCAACATAGTGGGTTTGA Y 2 1 2 1 101000 f 74 goat snp53640-scaffold816-2526081 22 34577395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775248 Affx-122977209 AX-385262379 22 34493367 AGTAATCACCCAGGATATAATTTTTCTAACCAAGA[C/T]GCTCATCAGATTTTAAAATTATCAACCAGTCTGTT Y 2 1 2 1 101000 r 74 goat snp53639-scaffold816-2486821 22 34617105 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397777 Affx-122962513 AX-123268132 22 34528995 AAAACCAACAAAAATCAACTCAGTTTTGAAATTTC[A/G]TTTCCCAAATATATGTTTCAAATACATCTGCATAC R 2 1 2 1 101000 r 74 goat snp53638-scaffold816-2451193 22 34652651 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400545 Affx-122960434 AX-123270900 22 34590737 AGGTGATTCATTCACTCAACATTAACAGGGGTGAC[C/T]ATCAGGCCAACAGGTTCAAATAATTACTGACAGGG Y 2 1 2 1 201000 r 74 goat snp53637-scaffold816-2389451 22 34714591 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404179 Affx-122957687 AX-123274531 22 34625699 CTCACTGGGAAAACTTGTCAAAACTGTAGAAAAGT[A/G]CAAAGAAGCAGGCAGAAATCACCTAGCATCCTTCT R 2 1 2 1 201000 f 74 goat snp53636-scaffold816-2354489 22 34750090 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380543 Affx-122975668 AX-123250901 22 34668357 ACAGCCCATGGAATTCCAAATCATTCATCTAGAAG[A/C]GACAAGAGGAAAAAAAATACTAAAAACGTTAACTT M 2 1 2 1 101000 f 74 goat snp53635-scaffold816-2311831 22 34793397 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382270 Affx-122973934 AX-123252628 22 34729437 AGCCAAGGGGAAAAAAGTCACCTCTCTGTTCCCTA[C/T]AATGGTCTAGTCAAGTTCAGGTCTTGCACTGCTAG Y 2 1 2 1 101000 r 74 goat snp53634-scaffold816-2250751 22 34854494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793420 Affx-122962825 AX-385280397 22 34762466 ATAGGATGTCTCTGGTCATTGCTTTCAGTGCAAAA[C/T]ATTTCCACTGTTTGTAATTATTCTGAGAGATGCTT Y 2 1 2 1 101000 f 74 goat snp53633-scaffold816-2217722 22 34887539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798405 Affx-122933525 AX-385285339 22 34812276 TAGAGACTAGACAAACGCATGTTACTTGTAATGCA[C/T]AGAAGTGTATGGTCAGATGACAAATACACAGTGTC Y 2 1 2 1 101000 r 74 goat snp53632-scaffold816-2167912 22 34937046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418241 Affx-122947034 AX-123288589 22 34850081 CCGGTTGTTCATTAATATATAATAGGAACATTAAA[C/T]GCATTGTTTCGCCTTCTAGAGAAGCTGTGGCCAAT Y 2 1 2 1 201000 f 74 goat snp53631-scaffold816-2130107 22 34974991 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421351 Affx-122944061 AX-123291698 22 34887358 TTTGAGAACCACACAGGTGATGGCGAAGCCACAGT[C/T]TCCCAAGGTAATGGGTGTGTGTGACATTTTATCCA Y 2 1 2 1 101000 r 74 goat snp53630-scaffold816-2092830 22 35012087 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384603 Affx-122972573 AX-123254961 22 34924142 TCTGCCTAACATTCCAGGCATTAGAAAACAAACTC[A/G]TGCTTGCCTGTACACATGGCTATGTTTAAAATGGA R 2 1 2 1 201000 f 74 goat snp53629-scaffold816-2056046 22 35049024 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453041 Affx-122920079 AX-123323374 22 34997182 TGGCTCACTATTCTGTTTTGTTAATAGTTCTATTT[A/G]CATTTAGGCTACAAATGTAGTGATTTGATTAAAGT R 2 1 2 1 103000 f 74 goat snp53627-scaffold816-1983006 22 35122017 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432693 Affx-122936033 AX-123303034 22 35043953 AATGTAACATTGATACATTCATATTATCTGATACA[C/T]GGTCAGTTTTATAATTTTCTTCTATTGTCCCAGTA Y 2 1 2 1 201000 f 74 goat snp53626-scaffold816-1936235 22 35168655 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791904 Affx-122971278 AX-385278894 22 35087229 GTGTAGTTACAGAGAGTAAAATTAGGATTGATTGG[C/T]AGAAGTTTCAAGGAAAGTTTTGCTCTGTCTGAATT Y 2 1 2 1 101000 r 74 goat snp53625-scaffold816-1892959 22 35211922 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382573 Affx-122973761 AX-123252931 22 35127921 TGTTGATGTTCAAACCACGGTCTGTATTGAAACCT[A/G]CCTGAACCCCACCGTTCTTCTTTGGCAACCAGAAA R 2 1 2 1 101000 f 74 goat snp53624-scaffold816-1852267 22 35253441 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402369 Affx-122959039 AX-123272722 22 35185593 CTTGTCCACGGAAGCTTCCTGATGCTCTGGCTCAA[C/T]AGGACCTCACCTAACATCCAAATTCCACTCTTTAT Y 2 1 2 1 101000 r 74 goat snp53623-scaffold816-1794595 22 35311648 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440181 Affx-122930713 AX-123310518 22 35219861 CCCTGTCTTTAGTGTAACCCATCTTCCCTTTCTGC[C/T]ACCTGTGAGCAGTGGTTCCCCAACACAGATCTGTT Y 2 1 2 1 101000 f 74 goat snp53622-scaffold816-1760327 22 35345734 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428110 Affx-122939079 AX-123298453 22 35250704 AGGGACCCTTTTAAGGGAATCCATTCCTTCTCTAC[G/T]TCTCTACTCAGGGACAGCCCTGAGCCTATACCAAA K 2 1 2 1 101000 f 74 goat snp53621-scaffold816-1729484 22 35376404 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765097 Affx-122925364 AX-385252660 22 35326199 ATAAAGTCTTAATGGATAAATGAAAAATCTCTCTC[A/G]TAGTAACAACAAAGGCAAATATCTTCGTGTTCTAT R 2 1 2 1 101000 f 74 goat snp53619-scaffold816-1653989 22 35451472 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420779 Affx-122944703 AX-123291126 22 35364777 ACATCTGCTCAAGCCAATGTGCAATCATAAAAAAA[C/T]TGACTTGAAAAGACAATTTTTTAAAGTATGTATTT Y 2 1 2 1 103000 f 74 goat snp53618-scaffold816-1615411 22 35488577 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389227 Affx-122969051 AX-123259585 22 35420861 GTGGGGCTGGTGACCATGTCCTCAGGCTTCCAGAA[C/T]AGCTGGCACAGACTAGGTTCAATCCTTTACTACAT Y 2 1 2 1 101000 r 74 goat snp53617-scaffold816-1559327 22 35540998 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426629 Affx-122939955 AX-123296975 22 35472293 ATACAAGCAAGGCAGAAAGTTCCAAAGAATTCATC[A/G]TGCTGCAAAACAGAGCATTTTTTCAGATGGCTTAG R 2 1 2 1 201000 r 74 goat snp53616-scaffold816-1507895 22 35592463 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430258 Affx-122937304 AX-123300599 22 35501279 CCTCAAGTGTTTTTCAAAGCGTGGTGCACTTTGCA[C/T]GGAGGAGTGGGAAAGGGTTATGAAATATGCTTTTT Y 2 1 2 1 101000 f 74 goat snp53615-scaffold816-1478909 22 35621273 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377623 Affx-122977882 AX-123247982 22 35544862 GTGCTCCCTCATTAATCTCAGGAAATCAGCAACAA[C/T]AACAACAAAAGATGATAAAGTCAGTCATTCTGACA Y 2 1 2 1 101000 f 74 goat snp53614-scaffold816-1435326 22 35665433 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427624 Affx-122939349 AX-123297967 22 35592223 ACCTGACTATAAATTAGAAATACCTACAAGACACT[G/T]TAAAAAATAAGATTAGAATTGCAGTTTCCAATCTC K 2 1 2 1 101000 f 74 goat snp53613-scaffold816-1387965 22 35712738 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800112 Affx-122928494 AX-385287035 22 35622540 CTCTGTTTTTACCAGAAAATCAACTCTAAACAAGA[C/T]GTAAACAGTTGTGCCTGGCTATGTTCTAATAAAAC Y 2 1 2 1 201000 r 74 goat snp53612-scaffold816-1357648 22 35743008 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782612 Affx-122964637 AX-385269685 22 35670277 CCCCGACCTGAATTCTGGACAAAATTCAGGCCAGC[A/G]TCTTTATTCCCCAAGAACTTTTACATAATTCTTTT R 2 1 2 1 101000 f 74 goat snp53611-scaffold816-1309911 22 35791741 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410055 Affx-122953228 AX-123280405 22 35705179 GATTTATTTGCTTAGCATTTTGATGGTCTAACAGT[A/G]TTCTAACTTGTAGCCAGGGTCTTTAGCAGAGAGAC R 2 1 2 1 101000 r 74 goat snp53610-scaffold816-1275009 22 35826825 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784570 Affx-122946528 AX-385271618 22 35738802 TCCACTACTATCTAAGATTGCTTGTGAAAGCTTTT[A/C]TCACTTGTGTAAATGTTACCTTGGGATAGTTTTTC M 2 1 2 1 101000 f 74 goat snp53609-scaffold816-1241386 22 35859830 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800759 Affx-122926376 AX-385287676 22 35780163 TGAAGAGATATGCAACCCATAACTCCAATTGGATA[C/T]GTCACATTGAGACCACACTTCCATGCTGAGGGAAA Y 2 1 2 1 101000 r 74 goat snp53608-scaffold816-1200025 22 35901388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446173 Affx-122925742 AX-123316509 22 35817489 TTCCAGCTAAGCTAACAAATTCAATTGTGTACATA[C/T]AGTTAATTTTACACTCATTTTTCAATTGTACATTC Y 2 1 2 1 101000 f 74 goat snp53607-scaffold816-1162699 22 35938494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790828 Affx-122949505 AX-385277828 22 35865731 GGCATCTCCAGCTCGTGTTATAGATTCTGTGTAGC[C/T]TATCAAGTAGTTTACAAGGTCTCTGACCTAGTCAT Y 2 1 2 1 101000 f 74 goat snp53606-scaffold816-1114457 22 35986625 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441132 Affx-122929584 AX-123311469 22 35938515 CTGCTATGGGGCTATTCTGTGTGCTAGCGAATGAG[C/T]AATAGTATCCCCAGCCTCTGCTCACTAGATGCCAA Y 2 1 2 1 201000 f 74 goat snp53605-scaffold816-1041673 22 36059920 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391971 Affx-122966520 AX-123262328 22 35977553 GACATGGAGAGAGAGGGGTAGTAACAGAGAGAGAT[A/G]CAGAGATGAGAGAGAGAGCAAGAGATCACATACAA R 2 1 2 1 201000 f 74 goat snp53604-scaffold816-1002635 22 36098789 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440893 Affx-122929227 AX-123311230 22 36021978 GCGCGCAGCACTGACCAATGGGGACGTGAGGCTCC[A/G]CAGGACAGAGAGTCACTTTGATGTAGGAGGAAACA R 2 1 2 1 101000 r 74 goat snp53603-scaffold816-958210 22 36143088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802582 Affx-122919242 AX-385289484 22 36057768 TGAATGCTTTCAACTTGAGTTCAAGGCGATATGTA[C/T]GACAAATGTGAGCCATGTCATCAACAGCTGATAAC Y 2 1 2 1 101000 r 74 goat snp53602-scaffold816-922420 22 36179963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774843 Affx-122921789 AX-385261977 22 36088239 CTGCCATAGAGGTCAAGCAAAAGCCCTCCTTTTCA[C/T]TGCCCAATAACAAAGACTTGCTGAAGAAATTAATA Y 2 1 2 1 101000 r 74 goat snp53601-scaffold816-891949 22 36209442 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399068 Affx-122960894 AX-123269423 22 36144242 AATCAACTCTACTTCAATTAAAAAACAGAAAAGAA[C/T]GCTTGCTTTTTAGCTGTGCACAAAGCAACCTTAAA Y 2 1 2 1 103000 r 74 goat snp53600-scaffold816-835946 22 36266587 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776167 Affx-122926682 AX-385263296 22 36180285 AATTAACACCTATAATCTTCATAGTAGCTCTAAGT[A/G]TCAGATACCATCAATGTGCACATTTTACAGAAGGG R 2 1 2 1 101000 r 74 goat snp53599-scaffold816-799903 22 36304101 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433704 Affx-122934535 AX-123304045 22 36243219 CCACCTCTCCATGCAGGCCTGCCCCATCTAATTGA[C/T]ATGGGAGCTTTCTGCAAATTAATCACTCTGAATAT Y 2 1 2 1 101000 r 74 goat snp53598-scaffold816-736969 22 36367600 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376718 Affx-122978966 AX-123247077 22 36276311 CTTGGCACTTGAGCAACACCTTTCTCTGAAAGCCC[A/G]CCGAGAACTCTACAGTTTAATTAAGTCTGCGAATT R 2 1 2 1 101000 f 74 goat snp53597-scaffold816-703877 22 36401215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408074 Affx-122954732 AX-123278425 22 36367791 TGTTCTATTACCTATGATGTTGAAGAAGAATGACT[A/G]CATGAGGAATAAGCCTGGTAGGAAATACGCCAGCA R 2 1 2 1 101000 r 74 goat snp53595-scaffold816-612397 22 36493267 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781059 Affx-122931909 AX-385268146 22 36400333 GAAAATGCATCATTTAAGGCTGGCTCCCATGTGAT[A/G]TTGAAATTCATGTGAAGTCTACATTTTTATCCATG R 2 1 2 1 101000 f 74 goat snp53594-scaffold816-579855 22 36525859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801059 Affx-122947765 AX-385287973 22 36492763 GAGAACCCAGATTCAAATTCTGAGCTAGATGATTC[C/T]AGAGCCCAGGTTATTTGTACTACACTGGGCTTGGC Y 2 1 2 1 101000 f 74 goat snp53592-scaffold816-487425 22 36619011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789358 Affx-122977283 AX-385276368 22 36527131 CATTTCACACGTGGTTCATCTGGGCATAGAGTACC[A/G]CATCTGGGAAATACACTTCTCACTAATTGGAGGTA R 2 1 2 1 101000 f 74 goat snp53591-scaffold816-453057 22 36653355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421013 Affx-122944552 AX-123291360 22 36556377 GTACCTATACTGAGCGACTAAGCAGAGCAGAAAAC[A/G]CAATAAAACCCCAGCCATCAGCAAAGAAGAATTGA R 2 1 2 1 201000 r 74 goat snp53590-scaffold816-423811 22 36682662 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418374 Affx-122946571 AX-123288722 22 36608383 CAAATGGGTACCTTAGAGCTACCTGTGTTGACAAA[C/T]GTCATTGTGTCTCTGGGAAGCAATGACTTTTAAAT Y 2 1 2 1 101000 f 74 goat snp53589-scaffold816-371805 22 36734498 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398055 Affx-122961749 AX-123268410 22 36646211 AGGACGTGACAGCCAGAAGGAAGTGGACAGGAGTC[C/T]GCAGAGGTTCCACACCTGCATTCTGGAGCCAGACC Y 2 1 2 1 101000 f 74 goat snp53588-scaffold816-333977 22 36771069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450727 Affx-122921872 AX-123321061 22 36704694 AAGAACCAAAGTCAATTCAATGCACCATAGCAAAC[A/C]GATCATAAAGGAAATATGTCCACTAAGGCTAACTG M 2 1 2 1 101000 f 74 goat snp53587-scaffold816-275494 22 36829326 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383493 Affx-122973429 AX-123253851 22 36760875 TCCACAGGCCTTGTGCTCATGCCACAGTGCACGCC[A/G]TGAACCTCACCACCTCTTTCCTCGTCCACACATAC R 2 1 2 1 101000 r 74 goat snp53586-scaffold816-219313 22 36885456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774791 Affx-122930483 AX-385261925 22 36803183 CAGAATGGAATTTAGGATCCATATCCTGGTCTGGT[C/T]CATAAGGCACTGTATCAACTGTCCCCATCTCCCCA Y 2 1 2 1 101000 f 74 goat snp53585-scaffold816-177005 22 36927556 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449296 Affx-122923012 AX-123319631 22 36842915 ACAGTGAACCTTCCCTCCTAGCATATAACCAGGTC[C/T]GTATACAGCCAAGGTGCTAAGTGAAATCACTTGCT Y 2 1 2 1 101000 f 74 goat snp53584-scaffold816-137273 22 36967309 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786744 Affx-122973213 AX-385273775 22 36871529 CTGGACAGTACTTTGAAGGTAATGTTTCTAAGGAG[C/T]AGAAATGTACATGAGGACAAGTAGCAGTGTCTATA Y 2 1 2 1 101000 r 74 goat snp53583-scaffold816-108659 22 36995668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272514 Affx-1111833243 AX-519546232 22 36900463 ATGAGACTGAATGCATGTAAACTGTCCAGTAAACA[A/G]AGGCGCTTTCAGTAACAGAGGCTATTTCAATAACA R 2 1 2 1 101000 f 74 goat 22_36900463_AF-PAKI 22 36900463 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38390363 Affx-122967678 AX-123260720 22 36935363 ATATCACTGACTTTTGTTCTTTTCAGTATGTTGCT[A/G]TTCAAATAGGTTCTTTAGGTATTTAAAGTAATCCT R 2 1 2 1 201000 r 74 goat snp53581-scaffold816-44825 22 37059567 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378416 Affx-122976782 AX-123248775 22 36968458 CACACAATTTAGAGGCAGAGAAAAATATAAAAATG[C/T]ACATACAAGGATGTACCTTAGAATCTCATAGAATC Y 2 1 2 1 103000 r 74 goat snp53580-scaffold816-11730 22 37092662 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400031 Affx-122960786 AX-123270386 22 37064561 AACACCATCTCCTAGCCAGCAGAGGACCAAGCCAA[C/T]GCTAAGTTGAAACTACAAACAAAATACACCTGAAC Y 2 1 2 1 101000 r 74 goat snp15372-scaffold163-3977207 22 37189256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781266 Affx-122948233 AX-385268351 22 37127962 ATGAAAGCCACAGGAACCAGGTGGAATTCCAAAGA[C/T]GATAGAAATCATCAGTGTTACTGGGTAATGTGTCT Y 2 1 2 1 101000 f 74 goat snp15371-scaffold163-3913806 22 37252785 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769096 Affx-122953152 AX-385256271 22 37184424 AATAAGAACAGACCCTCACACAGTGAGTTAATGCA[C/T]AGGCATAGCCCTCACCCCATAGCAGCTATTCAGTA Y 2 1 2 1 101000 r 74 goat snp15370-scaffold163-3857344 22 37309056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767785 Affx-122927709 AX-385255010 22 37283649 CTCATTTTCAGATACCACCAAGTTGATCATCTATG[C/T]GCATATGTTTTCACATTTAGTTTGTTATTCCTTAT Y 2 1 2 1 101000 f 74 goat snp15369-scaffold163-3758119 22 37408023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784373 Affx-122967207 AX-385271423 22 37325350 CATGAAAGAAATCATAGCTCTGTCTGACAGAGGCA[G/T]GAGCACCCCATCTTCTATGTTCCTTTTCCATAAGA K 2 1 2 1 201000 r 74 goat snp15368-scaffold163-3716418 22 37449706 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429020 Affx-122938327 AX-123299362 22 37396709 CATGTCGTTGCCTGCTGGTTAGGGACTGTGCTCTG[A/G]AGTCAACTAGATTTAACCTTTAACCCCAGCCCTAC R 2 1 2 1 101000 r 74 goat snp15367-scaffold163-3645059 22 37521117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383651 Affx-122972525 AX-123254009 22 37461408 AGCACAAAAATATGTTTAATGTGTAATTTTTAAGG[C/T]GGACGCAAGCCCTGTGTATAGAAACCTAAAAGGAT Y 2 1 2 1 101000 r 74 goat snp15366-scaffold163-3580360 22 37586075 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774753 Affx-122948611 AX-385261887 22 37498306 CATCATTGATGACCTCTGTAAAGTGGTAAACAGGG[C/T]TGGTCCCACAAATGATGTCTGTAACACCTGGAAGG Y 2 1 2 1 101000 r 74 goat snp15365-scaffold163-3543462 22 37622862 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403254 Affx-122957878 AX-123273607 22 37532247 GGTTATATATTAAAAATATATACGATTTTTTAAAA[A/G]ACACCTACATTTATGTGCCTAACCACTCAAGAATT R 2 1 2 1 102000 r 74 goat snp15364-scaffold163-3509521 22 37656795 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401442 Affx-122958986 AX-123271795 22 37560787 ATGTCAAAGAGGTTTATCAACTTGACACACGCTCA[C/T]GATCAAAAGAAAGAATAAAATGATTCACCAGAAAC Y 2 1 2 1 201000 f 74 goat snp15363-scaffold163-3480981 22 37686206 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787635 Affx-122955282 AX-385274658 22 37611968 AGAAACCTCCTCTCTTGGTTGTAGTACCAGGACCA[C/T]GATCTCTACTCTTCGAACAAAGGTTCCATCTTGAA Y 2 1 2 1 101000 f 74 goat snp15362-scaffold163-3429800 22 37737112 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376336 Affx-122978342 AX-123246695 22 37648828 TTCAAAGCATAATTTACAGATCAGTGTCCAGTACC[A/G]TCTAGCTGCTTTACACATGCCCTGTTTGATCCTCA R 2 1 2 1 101000 r 74 goat snp15361-scaffold163-3392940 22 37773776 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432817 Affx-122935394 AX-123303158 22 37680400 AAATATTGGACCCTAGCTCGTCTCAGATTCTACCT[A/G]CAACATGCATACTACAATGTACAGGAAGGCTGCCC R 2 1 2 1 101000 f 74 goat snp15360-scaffold163-3361368 22 37804189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390266 Affx-122967748 AX-123260623 22 37777871 GGTACTTAATAAAGCCAACAACAGATAATTCCTCC[G/T]AACCTTTTCATGTACAAGTGTTGATTACACACTTA K 2 1 2 1 101000 f 74 goat snp15358-scaffold163-3263897 22 37901975 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795733 Affx-122922854 AX-385282686 22 37832477 AAAGCAAAAACACAGTAAGGAGAGCCAAAGTGAAA[A/G]TAAGATAAACCATTTGTTATTCACTATACTGAGAG R 2 1 2 1 201000 r 74 goat snp15357-scaffold163-3209291 22 37956487 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415047 Affx-122949489 AX-123285396 22 37865722 TGTGAATGGTCTAGGGGAGAGAGGCAGCTTGGAGA[G/T]ATACTGTTGTGTGTGAAAGGTTAGGTTTCCTAGAA K 2 1 2 1 101000 r 74 goat snp15356-scaffold163-3176046 22 37990096 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385875 Affx-122971602 AX-123256233 22 37899543 GGCAGGAACAGGGGTCAGAGGCAATCCATATGCTT[A/G]TAAGACCTCACCGGGAATTGGCTTTGACTCTTAAA R 2 1 2 1 101000 r 74 goat snp15355-scaffold163-3142225 22 38023890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445935 Affx-122925918 AX-123316272 22 37944439 CTGAATATAGAGGTTCTAGCCCAAAATTTACAAAG[C/T]ATTTAACATTGTAAATAGGATATGGAACTCAGGGT Y 2 1 2 1 101000 f 74 goat snp15354-scaffold163-3097329 22 38067515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779036 Affx-122963965 AX-385266143 22 37987490 ATCAGGTCATCAGAGTAAGTATGTCTCTTCTGTGT[A/G]GAGATATTTTAGGTCAGGTAAAAGATCAAGAGAGG R 2 1 2 1 101000 f 74 goat snp15353-scaffold163-3054278 22 38111082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416171 Affx-122948265 AX-123286520 22 38016883 AATTCCTGTTTTGGAGTCAAAGTCAGGTTGAGTAC[A/G]TTGATCTAGGGTTTTAGTTTTCCCAAGATGAAATC R 2 1 2 1 101000 f 74 goat snp15352-scaffold163-3024885 22 38140702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423373 Affx-122943139 AX-123293719 22 38090112 CTCATTTTGCATTTCTGCTTCCTCAAGGCATCAAA[C/T]GGGGAATTATTGCTGGAATTTACCTCTCAAAAATG Y 2 1 2 1 101000 f 74 goat snp15351-scaffold163-2951656 22 38213920 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382075 Affx-122974914 AX-123252433 22 38172493 ATCAGTGGCCCCAACTTCCCTCTCAGACTGAATAG[A/C]TTTGTGTTATGCTAGGGAACCTGAAGACACTCTTC M 2 1 2 1 201000 r 74 goat snp15349-scaffold163-2869275 22 38295690 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385852 Affx-122970997 AX-123256210 22 38203241 TGATAGGCTACATTATGCAAATCTCCTAAACTGGT[A/G]CTTCTCAAATGTTACTGAACATATGAATCCTTAGG R 2 1 2 1 101000 f 74 goat snp15348-scaffold163-2838527 22 38326471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382693 Affx-122973640 AX-123253051 22 38233489 ACTCAATAGTTCCTCTTGGGTCAGATGTTTACCCT[G/T]GTTTGAGCTAAGGATCACACAGAACACTGATCGGT K 2 1 2 1 101000 f 74 goat snp15347-scaffold163-2808279 22 38356836 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781649 Affx-122962149 AX-385268733 22 38293677 AGTGCTCTTCCAAGTGTAATGTGTAGATCTGTGCC[A/G]TTTGTGAACTACTCATTATTGGCCTGCACCAAGAC R 2 1 2 1 101000 f 74 goat snp15346-scaffold163-2748091 22 38417436 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449632 Affx-122923188 AX-123319967 22 38330777 TCTCCAGATGGCAATTACAGTGCCCTATCTATGCT[C/T]TCACAGTGTCAGGCCAGCCAATGTGTAGTGACATA Y 2 1 2 1 101000 f 74 goat snp15345-scaffold163-2710991 22 38454643 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428537 Affx-122938741 AX-123298879 22 38384515 AAAAGGAAGAAAACTAGTCATTATGTGACTACTGA[C/T]AGAAATTCAAATACTGCCTTTGAGGGATTCCTGTA Y 2 1 2 1 101000 f 74 goat snp15344-scaffold163-2657253 22 38509155 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794405 Affx-122956949 AX-385281368 22 38429911 CTACACGCTTTCCCACTAAGGAAAGGTTCTATAAG[C/T]GATAATACTAACACAACTTTGAGTGAGCACACCAT Y 2 1 2 1 101000 f 74 goat snp15343-scaffold163-2611857 22 38554952 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765778 Affx-122941171 AX-385253233 22 38471605 TCTCTTGACCTCTGACCAGTGAAGAAGGAAAGAAA[C/T]GGTGGACACAGTTTTTGTTGTCTGACAAACCCACA Y 2 1 2 1 202000 f 74 goat snp15342-scaffold163-2570163 22 38596654 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452698 Affx-122920304 AX-123323031 22 38591869 TACCTTGGTGATGGTAAGGCTGTCGTATCATCTCT[A/G]TAGGCCATAGAAGGTGTTAAGGGAAGCATTGGGTT R 2 1 2 1 201000 f 74 goat snp15340-scaffold163-2449899 22 38715342 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775484 Affx-122934373 AX-385262615 22 38632958 AGAGATTTTCTCTAAGAAGTACACAGTCCACTTAA[C/T]GAAGCTAGCAACCCCTTCCAAAAATGGCATTTGCA Y 2 1 2 1 101000 r 74 goat snp15339-scaffold163-2408810 22 38756243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418367 Affx-122946577 AX-123288715 22 38731604 AGAAAGTCTATCCAAAGTAGAGGCTGAAAGAGAAA[C/T]GGTTTTCTAATAAATCTTCAAAATAACTGAAAAGC Y 2 1 2 1 101000 f 74 goat snp15338-scaffold163-2310164 22 38854918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390075 Affx-122968401 AX-123260432 22 38802029 TGTAAGAGCTGCACATGAGGCTGGGTTCCCTGCAG[C/T]ATCTTTCTACCAGCCTCAAAGAGAACTTCACATAG Y 2 1 2 1 101000 r 74 goat snp15337-scaffold163-2239739 22 38925322 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432247 Affx-122936352 AX-123302588 22 38833181 ATTTGCCTATGTATAAAATTCAAATATGGAGTCCC[A/G]CATAAATGAAAGGTGTGTCATTAATATACCATGTG R 2 1 2 1 101000 r 74 goat snp15336-scaffold163-2208587 22 38957132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776098 Affx-122963867 AX-385263228 22 38890618 TTTTGAAAGTAGTCCTAATATTCCTATTACTCATA[C/T]AGCAATCTAATAAAAACTACCTATAGAGTTAACAT Y 2 1 2 1 101000 f 74 goat snp15335-scaffold163-2151150 NW_017213846.1 8341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434728 Affx-122933925 AX-123305069 22 38957280 GTGAATGTGTGGTGGAACTCTTTATTGTGGTACTT[A/G]CTTCCTAGGGGTGGGTTTTAGAAAGCCCTCTAACT R 2 1 2 1 101000 f 74 goat snp15334-scaffold163-2084488 22 39081008 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375653 Affx-122978685 AX-123246012 22 38993514 GTAGCTAGTCAGCTGCACCTCTGCCCCTTAACCTC[C/T]CTGTGCCCCATTTTCCTCACCTCTAAAGTAGGGTG Y 2 1 2 1 303000 f 74 goat snp15333-scaffold163-2048254 22 39117083 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451254 Affx-122921936 AX-123321587 22 39029939 GGAAATGCTGACGTTATGACAGTTACAAAGTTCTT[C/T]CCTAATAAATGGGCTTGACCATCTGATATACCAGC Y 2 1 2 1 101000 f 74 goat snp15332-scaffold163-2011829 22 39152603 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388663 Affx-122969103 AX-123259021 22 39071499 CGAATGCAGACACACGCAGTCTGGCAGGGCCTGTC[G/T]ACTTCCATGTCATTTTGCTTCCAGCAGGAATAAAT K 2 1 2 1 101000 r 74 goat snp15331-scaffold163-1970269 22 39194121 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379457 Affx-122976088 AX-123249815 22 39120628 GAATCTTTGCATCAGACACAAAGAAAATTTTTACC[A/G]TGTCTGCATCCAGGGGCCCAATCAATAGCATGTTT R 2 1 2 1 101000 r 74 goat snp15330-scaffold163-1921140 22 39241801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408138 Affx-122954235 AX-123278489 22 39160995 AATTTTTCCTTTTACACAATCTCTACAGAACCCTT[C/T]GCATGAGAGAATAAAGACAATAGAGAAGGAAAATG Y 2 1 2 1 101000 f 74 goat snp15329-scaffold163-1880773 22 39281949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378985 Affx-122976396 AX-123249344 22 39189577 ACAAATCCTACCCTCCCCTGTCAGGCTACCTCTTG[C/T]GTTAAGGATGTGAAAGACCCAAATGAACTCCCCAA Y 2 1 2 1 101000 r 74 goat snp15328-scaffold163-1852191 22 39310383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409143 Affx-122953293 AX-123279494 22 39236050 CTGCTATATTTACAGTGGATAATCCTAATATACCA[C/T]AGGGTTTTCCTATGGGTTAATGACATATAATTTGG Y 2 1 2 1 101000 f 74 goat snp15327-scaffold163-1805718 22 39356860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445477 Affx-122925207 AX-123315814 22 39289359 CAGGCCCCGGGCTGCATTGCTTCTGGATACAGTGA[A/G]TCCGGATTTGGCAGCCCCATTCTGTCCTGCCTGTA R 2 1 2 1 101000 f 74 goat snp15326-scaffold163-1752409 22 39410538 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445873 Affx-122925988 AX-123316210 22 39335483 ATACCCCAGACTGAGGGACATGCTGTGGATCAAGA[C/T]TCTTCTGTTGAAATGGTGCGAGATCAGGGAAGACG Y 2 1 2 1 201000 r 74 goat snp15325-scaffold163-1706285 22 39456618 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444034 Affx-122926879 AX-123314371 22 39395710 GGTTTAGGAATTCAGATGATGGGGCCTCATTGTTT[C/T]ACTGAGCAAAAAGGAGTTTATCAGTTCCATATTGC Y 2 1 2 1 201000 r 74 goat snp15324-scaffold163-1646058 22 39516771 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432408 Affx-122935839 AX-123302749 22 39442203 ATATAATCTCATTCCATTCAGAACATCTCTAATTT[C/T]GGTGGAAATGGCTTCATAAAGAATTTAAAATGAGC Y 2 1 2 1 101000 f 74 goat snp15323-scaffold163-1599565 22 39563572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392107 Affx-122966356 AX-123262464 22 39480701 TCTTATCTTCAAACTGCAGCCAAGTTTCATTACTG[C/T]GGCTTATGTGTCGTGGCTTTGTCTTCTGGGCATCT Y 2 1 2 1 101000 f 74 goat snp15322-scaffold163-1561067 22 39601771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277584 Affx-1111835922 AX-519551083 22 39485428 AACAGTCTCCGCAGCTTGCCTTGTGAGGCCACCCC[A/G]CAGTTTAATCGTCCTCACTGTTAGGTTTTCTGTTC R 2 1 2 1 101000 r 74 goat Random2.2K-2002 22 39485428 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320764722 Affx-122972096 AX-385252340 22 39522539 CCATTAAATGGCTGAATTAGAGTGCTAATGAACCC[C/T]AAAAGAAAGTTGATCCTTGTCCTGGAAAGGTGGGC Y 2 1 2 1 101000 f 74 goat snp15321-scaffold163-1519229 22 39643340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397733 Affx-122962543 AX-123268088 22 39613408 AAGGAAGAAAGCTGTGAAATCATAATGAAGTGGAC[A/G]TTGTTCATGATCAGGGGAAATAGTCGCATAGATTG R 2 1 2 1 201000 f 74 goat snp15319-scaffold163-1428360 22 39734003 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424609 Affx-122942196 AX-123294955 22 39708039 TGCTCTATAATCATCCTCCTTCATTTGTAGAGGCA[C/T]GTGGGTACTTCTCTGCTCCTTAACCTCTCTGGACC Y 2 1 2 1 101000 f 74 goat snp15318-scaffold163-1333729 22 39826487 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272565 Affx-1111833244 AX-519546281 22 39739092 AAATGGACTAAGGCCCTCTCCCTGGTCAACTTCTC[A/G]GCCTGACCGGCACTGATTTAACAATGAAGAATTTA R 2 1 2 1 101000 r 74 goat 22_39739092_AF-PAKI 22 39739092 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38408257 Affx-122953813 AX-123278608 22 39739978 TTGAAAAGTAGCTTAACATAAAAAATGACTGAACT[A/G]TTTTCCTAACTCTCTTTTTTACTTTTTTTTTTACC R 2 1 2 1 101000 f 74 goat snp15317-scaffold163-1301790 22 39858513 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781484 Affx-122925766 AX-385268569 22 39829867 TCCACTACAGCACATGGGCAAGGCAGTCAAAAAGT[C/T]ACTGGACACTCAATAAACTTCTCTTTGTTTCTCAG Y 2 1 2 1 101000 r 74 goat snp15315-scaffold163-1211901 22 39948542 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445934 Affx-122925919 AX-123316271 22 39865585 GCAAGTCCCCAGAAAGAAACCTGTTTTGGAGCCTC[A/G]CTTACCTGATTAAAGGCAGACACTCCTGGAAATGA R 2 1 2 1 101000 r 74 goat snp15314-scaffold163-1176183 22 39984346 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376664 Affx-122979007 AX-123247023 22 39901348 CACAGTACACGTATATCATATTTCTTGATTGACTA[C/T]GGTTACTCTTTCCATTTAAACTCAATTAATGATCA Y 2 1 2 1 101000 f 74 goat snp15313-scaffold163-1140420 22 40019989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394697 Affx-122964351 AX-123265052 22 39950926 TCCCAACCATCCTCTTGTTGATTTACCCCTTCCAT[C/T]CCCTCCGCATTTGTTTCTCTTTCTCTCTCTGTATC Y 2 1 2 1 101000 f 74 goat snp15312-scaffold163-1090842 22 40070061 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444813 Affx-122926327 AX-123315150 22 39987834 TGCTTCTTAAGACTATATTAGTTAGTAGCTGCCCA[C/T]GCACAGTCAAAGACAGTGTTTACCCTCATGTCTAC Y 2 1 2 1 101000 f 74 goat snp15311-scaffold163-1053934 22 40106834 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385112 Affx-122971784 AX-123255470 22 40030778 AAAATTCAGTGCTCTTTTCCCTCTAGTCCTCACAG[A/C]CTACCCTTCTGTCTGTGCTCATTTCCTTTCCCAAG M 2 1 2 1 201000 r 74 goat snp15310-scaffold163-1010990 22 40149074 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434130 Affx-122934920 AX-123304471 22 40098212 TGAGCACACACATAGTCCATATGTAATTTTATATG[C/T]ATGTATGTTAGGATTCTTTGTCCTAATGAACATTA Y 2 1 2 1 101000 r 74 goat snp15308-scaffold163-943556 22 40216791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422835 Affx-122943108 AX-123293181 22 40153514 GTAGTTACAGCTTGGCTCTGGTGTCAGAGTATGGC[A/G]TTCTAATCCACTCAGGGAACGTTGCTTGGCCTCAC R 2 1 2 1 201000 r 74 goat snp15307-scaffold163-888254 22 40272400 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434595 Affx-122934104 AX-123304936 22 40192304 AGGAAAAAAATAACAGCAAACTTACAGAAAAGAGG[A/G]CTTTTTAAGGCATGTTGGATTCCCCAAGAAACGGA R 2 1 2 1 101000 r 74 goat snp15306-scaffold163-849464 22 40308951 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795875 Affx-122958598 AX-385282827 22 40267252 TTTATAATACATATAATGAATGTATAATATAATGA[A/G]CTTTTAATTATATATGGTATTCTACAAGTACAGGT R 2 1 2 1 202000 f 74 goat snp15305-scaffold163-774516 22 40384126 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787644 Affx-122978204 AX-385274667 22 40300753 CATATCTCATCTTCTTTTACCAGCAACCCAATTTT[A/C]CTTTGAGAAACTATTCACCCCTATTGTTGGCGTAT M 2 1 2 1 101000 f 74 goat snp15304-scaffold163-741015 22 40417676 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408777 Affx-122953380 AX-123279128 22 40329588 AAAGAAACACATGTAAAATCTGGCAGGTTGTTTTC[A/G]GTTCTGTCAGGAAAATATTTAGTAACAGCCTTGTA R 2 1 2 1 101000 f 74 goat snp15303-scaffold163-712180 22 40446596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790942 Affx-122930627 AX-385277939 22 40369419 TCTTACATCCTCTGTATTACCACCACTAAGCTGCT[A/C]GGAAATCCTAGAGAGCAGTTCCCAGGACTTCCAGG M 2 1 2 1 101000 r 74 goat snp15302-scaffold163-672349 22 40485771 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423849 Affx-122942775 AX-123294195 22 40460628 GAACTAGATTGTCAGGGACCCTGCATGCCCAGCTA[C/T]GGAACTTGCATCAGGTTATGGTCACCAAGAACCAT Y 2 1 2 1 101000 r 74 goat snp15301-scaffold163-581140 22 40575470 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383789 Affx-122973197 AX-123254147 22 40503505 CTTTTCTCATCTTGTCCAAGAATTAATTGCATTGC[C/T]GAAATTAGACATCCAACCTGCTCCATGCAAACAGG Y 2 1 2 1 101000 f 74 goat snp15300-scaffold163-538263 22 40618561 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380780 Affx-122975105 AX-123251138 22 40534151 TATCTGATTGACAGTCAATGTCTCTGCCTCAGGAA[C/T]GGAGGAAGCCCAATAAAGGGAGAAGGGAAGCTCAA Y 2 1 2 1 101000 f 74 goat snp15299-scaffold163-507617 22 40649572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447106 Affx-122924479 AX-123317442 22 40564895 CTGTCCTTTGGCGACTGCACAAAGAGCCAAAAAAG[G/T]GACTCCTTCACAGCATGAGGACACTTTCAGCTGAG K 2 1 2 1 101000 f 74 goat snp15298-scaffold163-476873 22 40680240 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377267 Affx-122978134 AX-123247626 22 40602002 ATGGTGGTGGGTGAGAAGGGGATAAATCACCCCCC[A/G]GCTGAGAACCACTGTTTTAAGAGAACACCCCTCCT R 2 1 2 1 101000 r 74 goat snp15297-scaffold163-439766 22 40717238 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799340 Affx-122974638 AX-385286270 22 40668960 AGGATGCCATAAGAAAATGGAGGACTGGTTTATAA[C/T]GCATACCAATAAACGTCCAGTTGCTTCATGCCCCT Y 2 1 2 1 101000 r 74 goat snp15296-scaffold163-372808 22 40784136 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795551 Affx-122923969 AX-385282506 22 40699613 TAAAAACTATTTAACATATGCAACAAACAGCAAAA[C/T]ATTTCCCTACTCTGCTTCTGGATACAAACTTTACA Y 2 1 2 1 101000 r 74 goat snp15295-scaffold163-342155 22 40814685 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409052 Affx-122953356 AX-123279403 22 40756959 ACATCATTTGTAACAATGTTTTTCTCATCTGTAAC[A/G]TCTATCAGAGGTTTTCTTTTCCAGTTTATTTTATA R 2 1 2 1 101000 f 74 goat snp15294-scaffold163-284809 22 40872301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393237 Affx-122965478 AX-123263594 22 40811668 ACGTAGATTAGGGTTAACAGTAGAATTAGAATTAG[C/T]ATAGTGCAGTATTAGAAATAGTATATTTAGAATAC Y 2 1 2 1 101000 f 74 goat snp15293-scaffold163-230100 22 40927637 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390670 Affx-122967125 AX-123261027 22 40849354 TAAAATCATGTATCACTTCCTCCTGTGACCTGTCA[C/T]AAAATGTGACATAACTTAACGTGACAGCTCCAATT Y 2 1 2 1 201000 r 74 goat snp15292-scaffold163-192414 22 40964837 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392863 Affx-122965754 AX-123263220 22 40888872 TGTCATTTGACCTTTGACTTCTGTCCCTTTGATAC[G/T]CCCTAATTCCAAAAGACAGGATTGATAGTGATGGT K 2 1 2 1 101000 f 74 goat snp15291-scaffold163-152896 22 41003932 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378429 Affx-122976774 AX-123248788 22 40950564 CAAATGAAAGGTGGTTAAAAGGGCTCATGAAGTGT[A/G]TGGCCTCTGAGTATTACAAAATACAAAAAACTTGT R 2 1 2 1 101000 f 74 goat snp15290-scaffold163-91204 22 41064606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426923 Affx-122940438 AX-123297268 22 40993931 GGGGCTGATGATACAGAAATATTTTACACATATGC[A/G]TGCATATATTTACATGTGTGCACATGTATACATAA R 2 1 2 1 101000 f 74 goat snp15289-scaffold163-47837 22 41107456 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410444 Affx-122952390 AX-123280794 22 41035347 GAGGACAGTGGTTAATTTGCAGGTAACAATATTGC[A/G]TTATTTATAAATAAAATGTTCGATTGTCATGGACT R 2 1 2 1 101000 f 74 goat snp15288-scaffold163-6421 22 41149585 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779839 Affx-122952393 AX-385266938 22 41062319 CATTAACCTTTGTCATTAACCATAGTGAACTAAAT[A/G]TGATTCTTATATTGGACTATTTGATTGTCTCTCAT R 2 1 2 1 101000 f 74 goat snp54151-scaffold827-20452 22 41176340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454210 Affx-122919284 AX-123324543 22 41106098 AAGAATGGGAAAAGCGCAGCATGACTAACCGTCCT[A/G]TATAGTGACTTGGTGATACTCTGGACTAAGTCAGT R 2 1 2 1 101000 r 74 goat snp54152-scaffold827-64231 22 41220418 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38432568 Affx-122935530 AX-123302909 22 41141960 CATTGAGTATATTTGCATTGTCATGCAACCATCAT[C/T]GTTATCCATTGCCACAACGTTTTTTAAATCCAAAA Y 2 1 2 1 101000 r 74 goat snp54153-scaffold827-100093 22 41256009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792632 Affx-122931973 AX-190860038 22 41199143 TATGAGGCAGTATTTGACAACCTGCCATGGAAACC[A/G]CAGTGACTGTTTTGTTCATCTTGGCTTCTGTCTCT R 2 1 2 1 101000 f 74 goat snp54154-scaffold827-157276 22 41313185 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397851 Affx-122962459 AX-123268206 22 41243275 CGTGTTCCCTTGTGGTCTCCTTTCCCAGTCTGGCC[A/G]TTGGTTCTCTGGGTTATCAGTTTGATTTCCTTTTT R 2 1 2 1 101000 r 74 goat snp54155-scaffold827-201408 22 41357200 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774732 Affx-122940061 AX-385261866 22 41285461 GCCCTTGACCTCTCTGAGTATAGATGCCCTCATCT[A/G]TAAAATGGAGTTCAAAGTAGAACTTTGTAGAGGGT R 2 1 2 1 201000 f 74 goat snp54156-scaffold827-243594 22 41399467 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375772 Affx-122978591 AX-123246131 22 41320554 CCATTTCACGTCTATAGCTTTGGTACTGCTCACCA[C/T]GCTGCTTTCTCATTTGTCATCTTCCATCTAGAAAA Y 2 1 2 1 101000 f 74 goat snp54157-scaffold827-278687 22 41434945 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790399 Affx-122963741 AX-385277402 22 41363046 GACCCGACCAGAGCCATCTGGTCCTGAATCAGAAC[A/G]TTGTAACTTCATCCTGCTCCAGGATGGAGAAGACC R 2 1 2 1 202000 f 74 goat snp54158-scaffold827-321179 22 41478523 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392647 Affx-122966448 AX-123263004 22 41393826 GAGGTCTAGTTGGCCCCCGTCCCCATTCACCAAGC[A/G]TCTCTCATTTTGACGTTTGATGCAACTTCATATAC R 2 1 2 1 101000 r 74 goat snp54159-scaffold827-351959 22 41509762 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785660 Affx-122948151 AX-385272702 22 41447014 AATGGGACCAAAACTAGCAGAATAAGAATACAGTT[A/G]TGCCATCTTTATTGTGGGCTCCCATCGTTTGCTGT R 2 1 2 1 101000 f 74 goat snp54160-scaffold827-405147 22 41563421 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425003 Affx-122941894 AX-123295349 22 41486221 GCAGGGCTATATGCTCCACCCTGCCCCCTTCAACC[C/T]CATATCCTCAGCCTGCCTTTTGTCTGTGAAGAAAA Y 2 1 2 1 303000 f 74 goat snp54161-scaffold827-444354 22 41603109 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439516 Affx-122930129 AX-123309853 22 41516647 GCTTCTCAGAGGAGCTCTGGCTGGCTCATAGTCTG[C/T]GGCAGGGAAGTGGGGCAACTCAGCCAGTGAAAGGA Y 2 1 2 1 101000 f 74 goat snp54162-scaffold827-474780 22 41632859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769779 Affx-122933503 AX-385256949 22 41557301 GAGGAAACCTTTGCTTTCACAGATAAAAGAGGATC[A/G]TGATGGCATGATACCTTCTCGCCTATTTCTGACTT R 2 1 2 1 101000 f 74 goat snp54163-scaffold827-515434 22 41673500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769422 Affx-122942064 AX-385256593 22 41598938 TCCTGCACCTGATTGAAGATTTGGTAAAATAAAAC[A/G]TTATTTACCAAAGCAGGCCATGCCCTGGGGCTTAC R 2 1 2 1 102000 r 74 goat snp54164-scaffold827-557071 22 41715494 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378787 Affx-122976996 AX-123249146 22 41631130 ATGTTATAACTGTCTGTGCCCCTTACACTGGAAGA[C/T]TATTTTTGGTAGACATTAACTCTCCCCTATGTCTA Y 2 1 2 1 201000 r 74 goat snp54165-scaffold827-589263 22 41747621 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787272 Affx-122940336 AX-385274297 22 41667895 CTGTTTAGACATACAAAATTACAATCTGTTTGTGG[C/T]GTTATCTTACATACAATTCATTAAAGATCACTTGC Y 2 1 2 1 101000 f 74 goat snp54166-scaffold827-626028 22 41784406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436924 Affx-122933196 AX-123307262 22 41725668 TAAGTAAAATGCACAGGAAGGAATTTGCTGTTACA[G/T]AATTTATTGGAGTTTGATATGCCCTTTGTCAAATC K 2 1 2 1 101000 r 74 goat snp54167-scaffold827-683801 22 41842227 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407317 Affx-122955308 AX-123277668 22 41756302 TCAACCAGCAGTGAAGTAAAGGCAGGCTTGTGAGA[C/T]TGAGCCCTTAACTTGTGGGATAGTGCTAACCCTAG Y 2 1 2 1 101000 f 74 goat snp54168-scaffold827-714435 22 41873025 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443795 Affx-122927089 AX-123314132 22 41818384 TCTGGGAACTTCTGTCCTAAAATAGGCAATGATGA[C/T]GACGATGATGATGATAGAAAGCAGCTCTTGAGCAC Y 2 1 2 1 101000 f 74 goat snp54169-scaffold827-776517 22 41934138 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775043 Affx-122953930 AX-385262175 22 41861064 AACTTGCCTTGCTGTCCAATCTGCCTTTGTATCTC[A/G]TAACTTAAGGATTATCTTCTTGTTTGTCTCTGATT R 2 1 2 1 101000 f 74 goat snp54170-scaffold827-819197 22 41976839 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392795 Affx-122965975 AX-123263152 22 41919939 TGTTCTGGGACTTCAAGGGGAAGAAGCGAGTACAG[C/T]GAGGGATGTCTCTGAGAACCGCATGCATATGGAAT Y 2 1 2 1 101000 r 74 goat snp54171-scaffold827-878072 22 42036570 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423605 Affx-122942383 AX-123293951 22 41961634 TGGCTCTGCAGTCAGGAAGGAGACAGCAGGCCTCT[A/G]CCACTCATCCTCCACCCTTGAGGGAGCTCCTAATG R 2 1 2 1 202000 f 74 goat snp54172-scaffold827-919767 22 42078941 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446663 Affx-122924765 AX-123316999 22 41995897 CTGGCCAGGACCCTCGAAAGGCAACACACAAACAA[C/T]AGGGCTATCACAGCCTCAGAGGTTCTCCCTGAGGA Y 2 1 2 1 201000 f 74 goat snp54173-scaffold827-954030 22 42113240 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444956 Affx-122926679 AX-123315293 22 42043933 ACAGTAGAAGTCAAAGTCATTAAAATGGCCTAGAA[C/T]ATTCCACATGATCTGCCCTCATCCCCTTATCGCTA Y 2 1 2 1 101000 r 74 goat snp54174-scaffold827-1002066 22 42161791 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426192 Affx-122940574 AX-123296538 22 42098946 ATCTCCATTTTAGAGGTTCTTTATACTTGGTCTGT[A/G]ATAAAATTTGCAATTTTTTTCAATTTTTCTTTTGT R 2 1 2 1 103000 f 74 goat snp54175-scaffold827-1057079 22 42217545 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277586 Affx-1111835923 AX-519551085 22 42151478 CCCTATTGTTCTTTCTGCTGAAATTCTTTCTTCCC[A/G]TTGAGAGACCATGAGAAAAATACAGCTTTATATTC R 2 1 2 1 101000 r 74 goat Random2.2K-2004 22 42151478 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38442040 Affx-122928398 AX-123312377 22 42156805 AGTTTTTTGGTTATCAGAAAGAAAGGATCATAAAA[C/T]GTCAGCAGGCCTCATGGCCATAAGATGACGTAAAA Y 2 1 2 1 303000 f 74 goat snp54176-scaffold827-1114938 22 42276503 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409231 Affx-122953153 AX-123279582 22 42188957 AATTAAACTAATTTAATAGTATTTCTGGATATACT[A/G]TAGTCTGGCATTTCCCTAAGGGGAGAAAACAAATT R 2 1 2 1 102000 r 74 goat snp54177-scaffold827-1147090 22 42308675 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799152 Affx-122950691 AX-385286082 22 42222640 TACAGTAAGGTCTCAAAGAAGTGTCAGTTGTTGTT[A/G]CTTGAATTGTAAGTTTTTGCTAGGTTTCTGTGCTA R 2 1 2 1 101000 f 74 goat snp54178-scaffold827-1180773 22 42343596 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432170 Affx-122936410 AX-123302511 22 42283777 TGGACTGGAGTTTCACATAGGGGTAAAGTGATTAG[A/G]GATCAAGAAAAATGTCAGAAAAAGGGGATTTTAAG R 2 1 2 1 101000 f 74 goat snp54179-scaffold827-1241910 22 42404850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445595 Affx-122925120 AX-123315932 22 42320556 TCTTCTGTTTTATGTCACATCATATTTATCCTTCC[A/G]TTTCTTTCTGATTTTCTACCATAATTTCCCTCTCC R 2 1 2 1 101000 f 74 goat snp54180-scaffold827-1278689 22 42440596 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421646 Affx-122944454 AX-123291993 22 42356339 AGCCTCGCCTGGGAAAAGTAGGGCCGAATGAGAAC[A/G]CTTCCCATGAAAACTGTTCTGAAATAGTGTTGTAA R 2 1 2 1 101000 r 74 goat snp54181-scaffold827-1314472 22 42476384 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425981 Affx-122941156 AX-123296327 22 42407849 GTTTTATTCCCAGAACCCAGACTTTACGCTTCTTC[A/G]TTCTCTCTTCAGACGGGCTTCTACCACATGACAGG R 2 1 2 1 201000 r 74 goat snp54182-scaffold827-1365982 22 42528009 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413572 Affx-122950587 AX-123283921 22 42466509 GTCACTTGTCACTGTCACTGGTCTGCTTCCTTTGT[A/G]CCAGACCTGCTTCTGACCAGGTTTCCCAATTGCTT R 2 1 2 1 201000 f 74 goat snp54183-scaffold827-1424642 22 42587527 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421461 Affx-122943932 AX-123291808 22 42502335 CCCTATGCACCCACAGGCCAGGCAAGTTCTTGGAG[A/G]GACCACTTGGTCAGAAGTGGGGAGAAGGGTGGGGA R 2 1 2 1 101000 f 74 goat snp54184-scaffold827-1460468 22 42623766 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789467 Affx-122921266 AX-385276477 22 42533012 GGTAAGATTTATATTGCATGCTCATAATTTAAATA[C/T]ATCTCATTTAGTTCCCACATCCCATAGTACCGATG Y 2 1 2 1 201000 f 74 goat snp54185-scaffold827-1491145 22 42653786 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381075 Affx-122974610 AX-123251433 22 42575937 GTGCGTCAGTAAGGACCTACAAAAAAAAAAAGTTA[C/T]GAATGACATTAACCGGGAAACATTGTTTAAAGAGT Y 2 1 2 1 201000 r 74 goat snp54186-scaffold827-1534070 22 42694871 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385150 Affx-122971756 AX-123255508 22 42631378 GCCCTCTGCTAGCTGACTCCCAGGTCAGTAAATCA[A/G]AATCCAGGGGTAGGACTCAGGCACTGATATTTATT R 2 1 2 1 201000 f 74 goat snp54187-scaffold827-1589511 22 42750279 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376501 Affx-122978022 AX-123246860 22 42660498 ACACAGGTTCTCAGCACAGTCCAAGGCTCAGAGCA[G/T]CTGGGCTGGAAGTATCTCTTCTCGGACGCCAGGCA K 2 1 2 1 202000 r 74 goat snp54188-scaffold827-1618631 22 42779235 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271955 Affx-1111833245 AX-519545729 22 42732260 TTGAGAGTCTGGGAACCACTATTCTGCAGCATAAA[A/G]TTATAGGCCTTTCTCTTTTGTCCCAGTATTTCTGT R 2 1 2 1 101000 r 74 goat 22_42732260_AF-PAKI 22 42732260 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433127 Affx-122935693 AX-123303468 22 42751283 TAGAATTCCCTGACAGTCCAGGGATTAAGACTTGA[C/T]ACTTTCACTGCCAGGGGACTAAAGATCAAGCAAGC Y 2 1 2 1 103000 f 74 goat snp54190-scaffold827-1709416 22 42870206 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777670 Affx-122940705 AX-385264789 22 42798543 TTTCTAATGTTTATTGATGATTCTCAAATATTAGC[A/G]TGCAGAACTACTTGGAGATCATTGAGGACCCTACC R 2 1 2 1 101000 r 74 goat snp54191-scaffold827-1756676 22 42917283 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385256 Affx-122972083 AX-123255614 22 42829367 TGGAGATACTCAAATGCAGCCCCAGAGTAATTTCA[C/T]GGCACTTGCATAGAGTCAGTTAATAAATTATGCCA Y 2 1 2 1 201000 r 74 goat snp54192-scaffold827-1787500 22 42948504 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426840 Affx-122940504 AX-123297185 22 42859391 AAAGAAGGTAATGGATATGAGTCATACAAAAGAGG[C/T]AGTGAATATGAAAGGACTTCTCCAAAAGCCACAGC Y 2 1 2 1 101000 f 74 goat snp54193-scaffold827-1817524 22 42978560 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421359 Affx-122944054 AX-123291706 22 42919343 TACATATTCTAAAGTGCTTTCCAGAAAGATCTGAC[A/G]GTGGTTAAGTGACTAAATCAGGAGGCTGGCTGGGA R 2 1 2 1 101000 f 74 goat snp54194-scaffold827-1877476 22 43039050 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786712 Affx-122934986 AX-385273743 22 42989064 AATTCCCCAAGACACTTAAACGTAAGTCCTGAGTA[C/T]TGAGGAAAAACCTAGGTCCTCTAATGGGTTTCTCT Y 2 1 2 1 101000 r 74 goat snp54196-scaffold827-1947197 22 43107741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410469 Affx-122952211 AX-123280819 22 43023458 CCACTGGCCTCCACTCTAGTCAACTGGCCTTCTCC[A/G]CATTCAGGCTTTGATGCTGACAGAGCCTCTGGAGC R 2 1 2 1 101000 r 74 goat snp54197-scaffold827-1981591 22 43142139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415830 Affx-122948880 AX-123286179 22 43069413 GGCTGTGAAGGAGAGCATGCTGTCAGGGTAAGGCG[C/T]TCGGGCCAGCTGATGTGAAAACTGAGGCCATCACC Y 2 1 2 1 102000 f 74 goat snp54198-scaffold827-2027546 22 43188095 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273767 Affx-1111833828 AX-519547378 22 43081967 AGCAGACCCACGCCTGCAGAGAAACCCACCCTGGC[A/G]CCTTGCATGATAGTGATGCACTGGGCGTGGCCGAC R 2 1 2 1 202000 f 74 goat GoatD01.006091 22 43081967 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320775568 Affx-122920476 AX-385262699 22 43201624 TGCAATCATTTTTCAAAGATACATTTGTACATGAA[C/T]GAAATTATACTTACCTATACTTTTGTATCCTGCTT Y 2 1 2 1 101000 f 74 goat snp54201-scaffold827-2159757 5 90526162 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776497 Affx-122945595 AX-385263624 22 43250220 TAAATAAACATTTTAAGAGTGTTTTATTTACAGCC[A/G]CTGGGACTCATTCCATTATTTACCCACCATTTCCT R 2 1 2 1 101000 r 74 goat snp54202-scaffold827-2208353 22 43370120 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422526 Affx-122943281 AX-123292872 22 43297286 ACAACTACTACTAGTACTTACTACTTGGTAAACTA[C/T]AGTGAGACTGGAAATAGACTGCTGTGTCAACCACT Y 2 1 2 1 101000 f 74 goat snp54203-scaffold827-2255419 22 43417811 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433843 Affx-122934444 AX-123304184 22 43369238 ATGGAGAAAATGGAATAGGAAAAACAGTAGAGGGA[C/T]ATAAGATGTTTGTTGTACCAATGACTTTGCCTCTA Y 2 1 2 1 101000 r 74 goat snp54204-scaffold827-2327371 22 43489612 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800243 Affx-122966105 AX-385287166 22 43510684 CTTTTATTTATTTATATTACCTCAGTGGCTGCAGA[C/T]TCAATACAGTGTTGATTAAAAATATCATGGATGTG Y 2 1 2 1 101000 f 74 goat snp54206-scaffold827-2468817 22 43632275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444508 Affx-122926507 AX-123314845 22 43556070 AAAGCTAAAATCAGATACAGTTTCAAAGGAGCTCT[A/G]CTTTTCAGTCCATCTTGTTGGCTTTATTACTGACT R 2 1 2 1 101000 f 74 goat snp54207-scaffold827-2514203 22 43677943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770389 Affx-122954158 AX-385257555 22 43593325 AACTTTTAAACAATTGTGTGCAAAATAACTTTCTC[A/G]TTTCCAAAACACTTTTCATCTGTTTGCTGTGAGAG R 2 1 2 1 303000 r 74 goat snp54208-scaffold827-2551458 22 43715223 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431836 Affx-122936092 AX-123302177 22 43646549 GCATGCATGTATGCATTTTTCCCAATGTTAAGAGT[C/T]AAGAGACATTTTCTTGTTCAACACCTTCGTTTGTA Y 2 1 2 1 101000 f 74 goat snp54209-scaffold827-2604682 22 43768608 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798414 Affx-122972047 AX-385285348 22 43689843 ATTTGCTTTAAGTCAATTCCACTAATATCTGAGTT[A/G]CTAGATTGTGGAAATGTTATTTCCAGTTATCTTCC R 2 1 2 1 201000 f 74 goat snp54210-scaffold827-2647976 22 43812148 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788538 Affx-122958747 AX-385275555 22 43734452 GAGGGATGTCATTCTAACCACATTTTAGAGTAGAC[A/G]CTTAGGCCTTTTCTTTCTTGTGTCCTCTGTTCTCC R 2 1 2 1 101000 r 74 goat snp54211-scaffold827-2692585 22 43857221 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790084 Affx-122955218 AX-385277090 22 43801767 AACATTTGGCTGTGGATGTGATTCTGGCTTTTCAG[C/T]GAAGGAGCTTCTGTAACCTACTCTGCTGATCAGAT Y 2 1 2 1 101000 r 74 goat snp54212-scaffold827-2759900 22 43924453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277464 Affx-1111835924 AX-519550968 22 44012341 AGCTGTGAGTGATGCTGAAGGGGCAGTGAAGTGCC[A/G]CCAGGTGGGCTCTGGTGCTCTGAATGCACACTCAA R 2 1 2 1 102000 f 74 goat Random2.2K-2005 22 44012341 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38440976 Affx-122928984 AX-123311313 22 44025773 ATGTCCACTGAGTCACTGAATGATAGATGAAGACT[A/G]CAGGCTTCTTCCCTGATGGTTTAGTGCAGGTATCT R 2 1 2 1 101000 f 74 goat snp54217-scaffold827-2983906 22 44148698 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410089 Affx-122952841 AX-123280439 22 44066277 AAGCTCACAGAGTGACTGAACTAACTCAGTAGGTC[A/G]CTCAGGGTCCTGGCAGCATGTAGTTTACATAGCTG R 2 1 2 1 201000 r 74 goat snp54218-scaffold827-3024410 22 44189260 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435309 Affx-122934020 AX-123305649 22 44101665 TAATCACTCTGTGTGTGGGAAGGGAGAGGAAATTC[A/G]TGCCTTGTAGTCTGTATAATCTTGACAGCCATCCT R 2 1 2 1 201000 r 74 goat snp54219-scaffold827-3059798 22 44224977 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451107 Affx-122921393 AX-123321441 22 44137662 TCTGTCTCTCCACAAATCCTCTAGAAATTGTTCAG[C/T]GCCAAAAGAAAAAGTAAAAATGAAAAGACTTGTGT Y 2 1 2 1 101000 f 74 goat snp54220-scaffold827-3095795 22 44261869 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421364 Affx-122944051 AX-123291711 22 44195252 AAAAGATCATGAGTCTCCCTTAACATCCAGTGTAT[A/G]TGCTGACTGCATTAACCTTAGTGGCTAGCACAAGG R 2 1 2 1 101000 r 74 goat snp54221-scaffold827-3153385 22 44319715 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437665 Affx-122931784 AX-123308003 22 44267880 GGAGCTGTCCCTGGCTCAAGGAATGCTGACTGTGA[C/T]TACCAAGAGGATGATGGGACCAGAAGAGATAGACA Y 2 1 2 1 201000 r 74 goat snp54222-scaffold827-3226013 22 44392494 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433897 Affx-122934402 AX-123304238 22 44325536 GTAGGAAGCAGTGTGCGTGGCATCCATACAGACGG[C/T]GAGTGAGGGAAGCAGCAATGGTCAGATGCAGAAAA Y 2 1 2 1 101000 r 74 goat snp54223-scaffold827-3283669 22 44449992 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798777 Affx-122943853 AX-385285708 22 44373831 TTTTTATTTTAGTGTTTGAAGCTTAAATGGAACCT[A/G]CCTTTGGGCTTCAGATTTTATTTATAAGGTGGTTT R 2 1 2 1 101000 r 74 goat snp54224-scaffold827-3331964 22 44498133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380617 Affx-122975242 AX-123250975 22 44409702 TGCTTTTCTGATGACTTGGATTTCTACAGCTGCTC[A/G]TAGTTCTTGAACTTCCTCAAAAAAGTACAGGCGGA R 2 1 2 1 101000 f 74 goat snp54225-scaffold827-3367835 22 44534141 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419821 Affx-122945828 AX-123290169 22 44461912 AAACTTCAGCGTTGCACACAGTGTTTGTGAAAGAG[C/T]GTACTCCTTGGCCCCACCTCAGAAGTCCTCCTCAG Y 2 1 2 1 101000 f 74 goat snp54226-scaffold827-3420045 22 44586253 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416032 Affx-122948367 AX-123286381 22 44492044 GAAACCAAATCAGCTTAAGGAAAATGGGAATTTAT[C/T]GTCTCATGGTTTCTGGAAAGGACAGAATTGAGGCC Y 2 1 2 1 102000 r 74 goat snp54227-scaffold827-3450177 22 44616296 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775174 Affx-122932304 AX-385262306 22 44534959 AATTGTACACTAAGATGTTTGAAGGGAAGGGATAT[A/G]TGTTCTGCTGCCATGCTTGTTGATTTCCTATACTA R 2 1 2 1 101000 r 74 goat snp54228-scaffold827-3493092 22 44659495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430402 Affx-122937760 AX-123300743 22 44652391 ACAGAGTAATGTAATTTAGTAAATTATGATTTGAT[A/G]GCTGGGCAACAGCCCCAGTGTTGAACAGTATTTGG R 2 1 2 1 201000 f 74 goat snp54230-scaffold827-3610524 22 44776373 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445156 Affx-122925555 AX-123315493 22 44684968 TCTCCCACAGTTCTTTTTAGTGAACTTTTCAGCAT[A/C]CTCAGACTTCTTCTCAAGATTGCCTTCCGGGCAGC M 2 1 2 1 201000 f 74 goat snp54231-scaffold827-3643101 22 44808968 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273831 Affx-1111833870 AX-519547442 22 44691807 AGCTTCCCAGTTGCTGTGCATGTTGGTCCTGGACT[A/G]CACTGAGAGGGGATCTGCACCTGCAGAGCACTCTC R 2 1 2 1 202000 f 74 goat GoatD01.008619 22 44691807 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320786792 Affx-122919523 AX-385273822 22 44722990 ACAGAGCTTCATGGACACACCAGGGGCATGTTCTT[C/T]GAGCATGAGCTCCGGGTTGCAATTCATGTATATAA Y 2 1 2 1 101000 f 74 goat snp54232-scaffold827-3681123 22 44846248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797268 Affx-122945216 AX-385284207 22 44754245 AATTCTTTTCAAGTGATGGTCCTCAGTCAATATGC[A/G]TATGATGAATAAATTATGTCAGTAAATTCTGAATG R 2 1 2 1 101000 f 74 goat snp54233-scaffold827-3712378 22 44877396 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776102 Affx-122960377 AX-385263232 22 44813068 TAGGAAGCCATTTGGAAGTCTTAGTTCTGACTGAT[A/G]TTTAAAAGGATTACTTTGACCAAAAGAATGAAGAA R 2 1 2 1 101000 f 74 goat snp54234-scaffold827-3771201 22 44936700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770200 Affx-122949982 AX-385257367 22 44852743 ACCTCTTTACCCACAAACCAGTGGGAAGCTAGAGA[A/G]GTTTAGTAAGATCCTGCTTTGTACTGAGGGGTGGG R 2 1 2 1 101000 f 74 goat snp54235-scaffold827-3810876 22 44976875 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408245 Affx-122953821 AX-123278596 22 44884249 ACTGCAGCTGCTCCTCATTCATTTAACTCAGAAAG[C/T]ATCTTCCATTGTGGTTGTACCATTTTACACTTCAA Y 2 1 2 1 101000 f 74 goat snp54236-scaffold827-3842382 22 45009082 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416808 Affx-122948136 AX-123287156 22 44953203 TTTAAACTTCAGCGAGGAGAAAACAAGTCCCAAAT[A/G]CAATCTTGAGAGTAGCCAGGTCCAAGCTGAAAACA R 2 1 2 1 101000 f 74 goat snp54237-scaffold827-3911336 22 45075519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781729 Affx-122961892 AX-385268811 22 44986545 TGTCATCACTTTATCAAAATATTGAGGCCCTGGCA[C/T]TGAGCAAGTAGAGATATTCAAGATACATAAATGCC Y 2 1 2 1 101000 f 74 goat snp54238-scaffold827-3944678 22 45108900 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401447 Affx-122958982 AX-123271800 22 45047284 TCTAACATTTGTAAAGCTCTCTCACTTACTTTATC[A/G]CCAATAAGTTATCACATTTCAAGTGGAAGACTTCT R 2 1 2 1 101000 f 74 goat snp54239-scaffold827-4005417 22 45170082 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427097 Affx-122939784 AX-123297440 22 45089271 AAGATCCTTGAAGGCGAGAACAGGGTCTCATTGGT[G/T]TATCTGTTACAGTTGATCTGATGTTGGAACGTGAA K 2 1 2 1 201000 r 74 goat snp54240-scaffold827-4047404 22 45212005 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417417 Affx-122947222 AX-123287765 22 45120088 GATGCTAGTTCTAAAAATATTGTTAAAATTTACCA[G/T]CTTTCCTTCCTTTGTGTCTTGGATCCAATCCCCCC K 2 1 2 1 101000 r 74 goat snp54241-scaffold827-4078221 22 45242798 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388899 Affx-122968853 AX-123259257 22 45170292 AATCTGAGACGCAGATATCAGTGGGTGGGAGGGGT[A/G]TGAAAACTGAACACTAAAAGCAAAATAATAAGCTG R 2 1 2 1 201000 r 74 goat snp54242-scaffold827-4128425 22 45292925 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392335 Affx-122966687 AX-123262692 22 45216702 ATTGACTAACCCTTGCTCTCTTTCAGTCTGTCTCC[A/G]TTTCCCCAATATTTAGGAACCTTAGCCAAAACAAA R 2 1 2 1 201000 r 74 goat snp54243-scaffold827-4174835 22 45339258 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271957 Affx-1111833246 AX-519545731 22 45238645 TCCAGGAGTTAGGGGCCACTTCCATCGGCCACTTC[A/G]TTTGGGGCTGTGCACATTTTATACTAGTTTTTCCA R 2 1 2 1 102000 r 74 goat 22_45238645_AF-PAKI 22 45238645 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38384596 Affx-122972577 AX-123254954 22 45252138 CTTGATTTCTGCTTCCGGGACATACTCACTGTGTC[A/G]TCAGGGGTGAATTCATGAACCTTTCTGAGTTTGAT R 2 1 2 1 101000 f 74 goat snp54244-scaffold827-4210271 22 45374750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431411 Affx-122936532 AX-123301752 22 45281427 TTGTTTCTATGGCATTTATAGCTGTATGAAAGGAT[A/C]TTATTTATTGATATATACATTTGCCTGCCTTCTCC M 2 1 2 1 102000 f 74 goat snp54245-scaffold827-4239560 22 45404082 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383540 Affx-122972619 AX-123253898 22 45323486 GAAAGCCCAGTGGGGCTTTTACAAATATTGGTTTA[C/T]GAAGAATCTTTTTCATCTTGTGTTTTGCAGATAGG Y 2 1 2 1 101000 f 74 goat snp54246-scaffold827-4281619 22 45445887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796255 Affx-122976468 AX-385283205 22 45354879 TGATGTTGGTTTGGACATTGGTATTAAAACAATCC[A/G]TACAAGTTCGGGCAAACACAACTGCAGAAATCTTT R 2 1 2 1 101000 r 74 goat snp54247-scaffold827-4313012 22 45477200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406243 Affx-122956108 AX-123276595 22 45388101 TTTTATCCTTGAAGAGAATCTTAGTGCAGAACCAG[C/T]GCATTTGGGTTCAGCACTGCAGCTAGTGTGCCACT Y 2 1 2 1 101000 f 74 goat snp54248-scaffold827-4346234 22 45509037 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383022 Affx-122973313 AX-123253380 22 45418440 GTCATGTATTTACAGAGTGCTGTATCTAGATCTCA[C/T]GGTAACTGCAAACCAAAAATCTATAATAGATACAT Y 2 1 2 1 101000 f 74 goat snp54249-scaffold827-4376573 22 45540892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387821 Affx-122969675 AX-123258179 22 45449376 CAAACTGTAACTTCCAGTCCTCTGCATCTCAGCAA[G/T]GATGCCATCAACTGTGCAGTTTAAGCCAGCTATCC K 2 1 2 1 201000 r 74 goat snp54250-scaffold827-4407509 22 45571892 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379520 Affx-122976074 AX-123249878 22 45478536 TTTTTGAGGTTTTGGTCAAACCACTTTAGGCAAAA[G/T]AGAACTTCTTTGTTTAAAGGAAATAGACTTTTAAA K 2 1 2 1 101000 f 74 goat snp54251-scaffold827-4436669 22 45601027 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274177 Affx-1111834087 AX-519547778 22 45497723 GTATATATCATAGGAGCGCAGCCTCTCTGCAGCCA[A/G]CTGGCAGGACTTTCCCAAGGACAGAAGAAACTCTG R 2 1 2 1 202000 f 74 goat GoatD01.017528 22 45497723 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38421693 Affx-122944410 AX-123292040 22 45511843 AACGGGGCACTGCCCCTTAGCCCCTCTTGCCTCTC[A/G]AGGGGTGTCATGAGAACACATCTGAGATCAGGACC R 2 1 2 1 101000 r 74 goat snp54252-scaffold827-4469976 22 45634745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780471 Affx-122965928 AX-385267562 22 45551244 AACAATACTAATTAGGAGCATTGGGATAGGAGACA[A/G]AATCTTGGCCCTGGGCCTCTATGTTAACGCTTAAC R 2 1 2 1 101000 r 74 goat snp54253-scaffold827-4509377 22 45674624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796378 Affx-122959317 AX-385283328 22 45590015 CAGGTCTTAGGCATGAGGATCATGGGCAGCAGACT[A/G]ACAGGTCTACAACAAAACAAATGTGAAGGCCTTCA R 2 1 2 1 101000 r 74 goat snp54254-scaffold827-4548148 22 45713484 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802855 Affx-122956171 AX-385289753 22 45623413 AGGGATTAACATATTACAAACTCTAAGCAAAAAAA[C/T]CTCTCAGATTTCAAGAGACCTCAAGGTGGGAGACA Y 2 1 2 1 102000 r 74 goat snp54255-scaffold827-4581546 22 45746901 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409443 Affx-122954090 AX-123279794 22 45653672 TCTGAACTAAGTGGATTTTCTTCTTCCTCATAATC[A/C]TTTTAAAATTTAAAATACTCTCCGCATTGCCTTTA M 2 1 2 1 303000 r 74 goat snp54256-scaffold827-4611805 22 45776373 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788226 Affx-122967013 AX-385275245 22 45704752 GTAGGAAACTTGTGATATATATTGAAGTAATTAGG[C/T]AAGAGGTAATGTAATGGTCACATTTATAAAGCAGG Y 2 1 2 1 101000 r 74 goat snp54257-scaffold827-4662885 22 45827292 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421398 Affx-122943983 AX-123291745 22 45749595 GCCGATGGTGATCTTTTACCCCCAGCACCTAGTTA[C/T]GCCTGGGACAGAGCAGGTGCTCAGTAAATATTCAC Y 2 1 2 1 303000 f 74 goat snp54258-scaffold827-4707728 22 45872080 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778139 Affx-122933852 AX-385265254 22 45802050 TCATGTCAAAAAACAGTGAAGCTCTCCCTTAAAGA[C/T]GAAAATGGTTGGATATTATATCCCAAAACTAACAT Y 2 1 2 1 101000 f 74 goat snp54259-scaffold827-4760183 22 45925377 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393250 Affx-122965468 AX-123263607 22 45832204 CTGCTTTGCCTTAAGTGACCACCATCTTCTGGACC[A/G]TAAGCTCTCCAGGGACAGGGACACGTTCTTGTTCC R 2 1 2 1 101000 f 74 goat snp54260-scaffold827-4790337 22 45955535 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384205 Affx-122972393 AX-123254563 22 45866270 ACAGAAACTAGGAAGTTCTTGAAATTGCAGTGTGA[C/T]AGTAACCACCATATTCCTCTGAGAGTGTGTCTGAA Y 2 1 2 1 101000 f 74 goat snp54261-scaffold827-4824403 22 45989559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407629 Affx-122954627 AX-123277980 22 45906475 CTAGGGTTAAGGCCATGGGGAGAGGGGGTTAAGAG[C/T]AGACATCAATCCCAAAGACATCTGCCTGGGAAAAG Y 2 1 2 1 201000 r 74 goat snp54262-scaffold827-4864608 22 46029826 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403817 Affx-122957958 AX-123274169 22 45936636 ATGATTGCGGCTCACATGACATTCTTCCTGGACAG[C/T]ACTAGTCTAGGCAGAATCTCACTGTAATTGCCTTG Y 2 1 2 1 101000 f 74 goat snp54263-scaffold827-4894769 22 46059987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394258 Affx-122964725 AX-123264613 22 45984235 ATATATTTCCTGCTTGGAAACCACATTGTTCCACA[C/T]GGCAGGCCAGGGATCAGTGTAGATTAAGGAGGATC Y 2 1 2 1 201000 f 74 goat snp13224-scaffold1509-31328 22 46107776 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799434 Affx-122952173 AX-385286364 22 46071697 CTGGAAGAACTAGACCTAAATGTGCAAATGAGGAT[A/C]TAGTTGATATGGCTTTACAGTGTGTAATTAGCATG M 2 1 2 1 101000 f 74 goat snp13226-scaffold1509-118790 22 46195447 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412894 Affx-122950420 AX-123283243 22 46125730 TATTTTCCTACTGCCCTCCCAGAGTAAAAAGGACA[C/T]AGAAGTCACATGATGCTTTAGCTTGACACAACTGC Y 2 1 2 1 101000 r 74 goat snp13227-scaffold1509-172823 22 46249626 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446604 Affx-122924808 AX-123316940 22 46155263 TATTAGGGGAATGGGGATTGTTACCAACATCTCTC[A/G]TGAACTTACTGTGAGGATGAAATGAGATGGTTCAG R 2 1 2 1 101000 f 74 goat snp13228-scaffold1509-202356 22 46279013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416188 Affx-122948251 AX-123286537 22 46199864 GGGCGGGAACAAAGTTGATCTGGCTACCTTCAGTA[C/T]ACCCACTCCAAATCTCCTTTGAAAGGAGAATAAAC Y 2 1 2 1 201000 f 74 goat snp13229-scaffold1509-246957 22 46323412 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800862 Affx-122944465 AX-385287777 22 46253695 AAAAAATAAAAATTAATAGGAGTATTAGTTTCAAA[C/T]GAGCCAAGGAAATACCAAACTCCCCATGCATGTGT Y 2 1 2 1 101000 r 74 goat snp13230-scaffold1509-300788 22 46378588 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408645 Affx-122953476 AX-123278996 22 46336919 CTGTTCAATTTAGTTTAACAAGTATTTGTTGAGAA[A/C]CTATTAAGTAATCAGAATAGCAATAAGAACTGAGT M 2 1 2 1 101000 r 74 goat snp13232-scaffold1509-384012 22 46461830 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432399 Affx-122935846 AX-123302740 22 46369997 CTCTTTCCTCCAACCATACACTCTTCCCAGTCACA[A/C]GACTTAATATACACCTATATGCCAATCAGCCCAAG M 2 1 2 1 201000 r 74 goat snp13233-scaffold1509-417090 22 46495472 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402004 Affx-122958760 AX-123272357 22 46477239 CCTCACAGATCCTATTTTCTGTCCCTGTATTTGAC[A/C]ATGACCTTCTCTTCCCAACTCTGCTTCTGCATTTT M 2 1 2 1 201000 f 74 goat snp13236-scaffold1509-524332 22 46603601 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412751 Affx-122950522 AX-123283100 22 46512617 TTGTCTCTCAGTTAACTGGCCTGTCATGAGGCAAA[C/T]AGAGCGAGCATAAACTGGGTAACAAAAGGATTATC Y 2 1 2 1 101000 r 74 goat snp13237-scaffold1509-559710 22 46639138 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437009 Affx-122933131 AX-123307347 22 46561287 AAATGATGTAAAATCTCTCATCAGTCAAATGTAAA[C/T]AAAGACATCAGAATTTTTCAGACCATTAAATCAGC Y 2 1 2 1 201000 f 74 goat snp13238-scaffold1509-608380 22 46687915 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376578 Affx-122979075 AX-123246937 22 46648584 AACTGTTGGTCTCCAAAGCCCACCCCCTCGACCTC[A/G]TCTGAACGCCTGGCCCCTCCCACTTGAGTCAGGAC R 2 1 2 1 101000 r 74 goat snp13240-scaffold1509-695677 22 46775329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396405 Affx-122963011 AX-123266760 22 46707486 GAATCCTTCCCTCTCTCGCTGTGCGCTGGGGGTGA[A/G]CACCCCCACCTCACAGACATGCAGGGAAGATTCAG R 2 1 2 1 202000 f 74 goat snp13241-scaffold1509-754579 22 46834874 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406657 Affx-122955807 AX-123277009 22 46737352 TGAGTCTATTGCCTTTGAAGAGATGAACAGCTAGC[A/G]TCCAAGATTAGTGATAACTTGTACCCAGAGGTATA R 2 1 2 1 101000 r 74 goat snp13242-scaffold1509-784445 22 46864684 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785044 Affx-122966700 AX-385272091 22 46775019 TTTGCTGGGCTTTACTTTCCACCAAGCATCCTGAC[A/G]TCCTAAATTAGGTCTGAGATCAAGCTGATAATCAT R 2 1 2 1 101000 f 74 goat snp13243-scaffold1509-822112 22 46902120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386776 Affx-122970112 AX-123257134 22 46865185 TCTTGTCCCCTTGACTGGGAGGTGGAGTGGGTAGA[A/C]GTGTCCTCTCCCTTCATCTTCCACTCGGAGCTGTA M 2 1 2 1 101000 r 74 goat snp13245-scaffold1509-912278 22 46991657 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393454 Affx-122965850 AX-123263810 22 46899665 GTGTTCACAATAGCATATGCCTGCCCTCCTGTCTC[C/T]GTCTTTAAGGGAACTACTGACATCAGTAACCATTC Y 2 1 2 1 201000 r 74 goat snp13246-scaffold1509-946758 22 47026852 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793103 Affx-122957127 AX-385280081 22 46937485 ATCTTCCCACCCCATAGGTTACATCTTGTTCTAAC[A/G]TTTTTATGTATGATAATTAGGCTTAATTTTATTCC R 2 1 2 1 102000 f 74 goat snp13247-scaffold1509-984578 22 47065347 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449784 Affx-122922430 AX-123320119 22 47004685 AACTCACAGGCTTATCCATCCATTCTTTTCTTTCT[A/G]CCATCACTTTTCTGAGTAACATGAGTGTAGCAGGC R 2 1 2 1 201000 r 74 goat snp13248-scaffold1509-1051778 22 47132599 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438959 Affx-122930398 AX-123309296 22 47033790 GCATCCTCCCCAAGCTGGGGGCAATGCTGGCCATC[A/G]GGGATCTGAGGCTGAGAAGGCTTACAGACAAAGCT R 2 1 2 1 103000 r 74 goat snp13249-scaffold1509-1080883 22 47161655 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452441 Affx-122920572 AX-123322774 22 47070031 TACATGGGCCACTGAAAATCATATTGATTTAGAGA[C/T]GAGAGTTGTTTTTTTTTCTTGGGTTGTAATACTAT Y 2 1 2 1 101000 f 74 goat snp13250-scaffold1509-1117124 22 47197130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396557 Affx-122962932 AX-123266912 22 47125869 CAGAATCACGCTGCTTCTCTGAAAGTTAAAGAATC[G/T]AAGAGACTCTTCAACAGCTCCTCACTTCTCAAGAG K 2 1 2 1 101000 f 74 goat snp13251-scaffold1509-1172962 22 47253253 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787326 Affx-122961976 AX-385274351 22 47156617 GGACTTTTTTTGGGCTTAAAAGAGGAGCCAGACCT[A/G]GATGCAAATGGTAGAAATTAGAGATCTTGATACCT R 2 1 2 1 101000 f 74 goat snp13252-scaffold1509-1203710 22 47284667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443383 Affx-122927401 AX-123313720 22 47186342 GAATCTCAACCACAGCCGGACCTGCTTAAACCAAG[C/T]GCAGGGGAGAACAAAGGATCTGGAAGGAGTAGAAG Y 2 1 2 1 101000 f 74 goat snp13253-scaffold1509-1233435 22 47314128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407808 Affx-122954556 AX-123278159 22 47262435 AGGAGCAGACATTTGCAGTGATCTGACCCAGTGCT[A/G]ACAGCCAGGTCTCTTACAAATACATGCACGGAGTG R 2 1 2 1 101000 r 74 goat snp13254-scaffold1509-1309528 22 47389801 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428706 Affx-122938470 AX-123299048 22 47294913 CACAGTATAAATATATACTAACAGTCAGTCTTTAT[C/T]TGTATATCCAACTCCCATTTCCAGTTGTACTTGCG Y 2 1 2 1 101000 r 74 goat snp13255-scaffold1509-1342006 22 47422830 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397880 Affx-122961966 AX-123268235 22 47337829 TCCAATTGTCCTATCGTTAAGCCCATCAGACAACA[C/T]GTCTTGCACATACACACTCATTTATTTAATACATA Y 2 1 2 1 101000 f 74 goat snp13256-scaffold1509-1384922 22 47465524 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402109 Affx-122958685 AX-123272462 22 47400214 CTCTCAACAGTGTTATTTTAATGACCACAGGGCAC[A/G]TTTTTTAAAGTGCTTTGTGGTTTATCACACCTTAG R 2 1 2 1 202000 r 74 goat snp13257-scaffold1509-1447307 22 47526955 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384291 Affx-122972293 AX-123254649 22 47432645 TCCATGGAAACGGCCACAAAGTCAGTGTACCATTC[A/G]TCTTCCAGGGTTTCTCAGGACGCAATTACAAACTG R 2 1 2 1 101000 f 74 goat snp13258-scaffold1509-1479738 22 47559842 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277466 Affx-1111835925 AX-519550970 22 47448799 GATTATAGGGGACCTTGAAGCCACCATCAGAGTCT[A/G]ACACGGAACTCTAGGGCCCAACCTCCTATGAAGGC R 2 1 2 1 102000 f 74 goat Random2.2K-2006 22 47448799 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38453325 Affx-122919973 AX-123323658 22 47516825 TCTTCTTCTCCCCTCACAGAAAAGATCAACATTCG[C/T]GTGTTGGACCCTTTCACCATCAAGCCCCTGGATAA Y 2 1 2 1 201000 r 74 goat snp13260-scaffold1509-1563918 22 47643606 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379470 Affx-122976484 AX-123249828 22 47549745 GCAGCCTGGGATGGGACCTTGTCTGGATTTCCCTA[C/T]CACAGGATTCACTGTCTGGCTCCCCCACCTGACTG Y 2 1 2 1 101000 f 74 goat snp13261-scaffold1509-1596838 22 47676406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435410 Affx-122933553 AX-123305750 22 47621638 GAGAGATGCAGTGGGCTTGCCCTTATGAATCACCC[A/G]TTTCCTCCTGAAGAGCCCCCTGAAATCCCGCCTTT R 2 1 2 1 101000 f 74 goat snp13262-scaffold1509-1668731 22 47744274 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429153 Affx-122937987 AX-123299495 22 47657859 TTAGTTGCGGCACATGGGATCTTTGATATTCCTTG[C/T]GGTGTGCGAGATTTTTAGTCATGATATGCGAACTC Y 2 1 2 1 101000 r 74 goat snp13263-scaffold1509-1704952 22 47780316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788788 Affx-122946787 AX-385275803 22 47700707 TTCTGAAACCTTATTATTTCTAAGCACCCATTTCT[A/G]TAGTAGAGAACCCACTTACCCCATGTTTATATTAT R 2 1 2 1 101000 r 74 goat snp13264-scaffold1509-1747800 22 47823093 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389746 Affx-122968250 AX-123260103 22 47729453 ATGCTTTGCTAGGTTTGAAACCTGGTTTTCCTTCT[C/T]ACTAGCTGTAGGACACTGGCAGGTACTGCTTGTTC Y 2 1 2 1 201000 r 74 goat snp13265-scaffold1509-1776546 22 47852196 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785449 Affx-122949905 AX-385272494 22 47779595 CAGGTATCACAGAGACCTTTAGTTTTTAGTAATGC[A/G]TCTCTTTAGCAAAAGACTATGGATATAATAGCAAT R 2 1 2 1 101000 f 74 goat snp13266-scaffold1509-1826688 22 47901366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421288 Affx-122944732 AX-123291635 22 47811893 CTAGTTGGGAGAGAAAACAACAATAGTCAGGAGAA[C/T]ACCGAAGAATTTCTGAGATGAGAGCTATTAGTGCT Y 2 1 2 1 101000 f 74 goat snp13267-scaffold1509-1858986 22 47933543 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432961 Affx-122935280 AX-123303302 22 47851977 ACACATCCTGGGCCCAGCCTCTGCTTGTACAAAAA[G/T]GTGAGCAGGAGATTCACTCACACCCCCTCCCCTAT K 2 1 2 1 101000 f 74 goat snp13268-scaffold1509-1899070 22 47973775 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406369 Affx-122955416 AX-123276721 22 47896189 AGTCCCAAACCCAGTCTCTGGGGGCAAAGCCAGTT[C/T]GGGGTGGGCGATGGGGTTGAAGAAGCTCCCGCTGG Y 2 1 2 1 101000 f 74 goat snp13269-scaffold1509-1943282 22 48018365 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272582 Affx-1111833775 AX-519546296 22 47922319 GCTGTAGTCCAGGCCAAGGA[A/G]CACAGCCATGATACCAAACACTGGGCTGCAGCAAG R 2 1 2 1 102000 r 74 goat GoatD01.004237 22 47922319 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38415132 Affx-122949424 AX-123285481 22 47942533 GTTGATAAATTATTTTTATATAATTCTGGGAGTAC[A/G]TTTAAAGATATGAAGTTATACATAGTACCTGAGCA R 2 1 2 1 202000 r 74 goat snp13270-scaffold1509-1989626 22 48063477 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770503 Affx-122920201 AX-385257668 22 48024910 GTAAATGAAGACTCAGGGTGTTGGCTCTTACCAAA[C/T]GGACATGGTAAGCTGGAAGTGTTTTTGTCAGTATT Y 2 1 2 1 101000 f 74 goat snp13271-scaffold1509-2072003 22 48146089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418014 Affx-122946655 AX-123288362 22 48057955 GTACTAAGGGCGCTTATTCATTAGTAGTGCATGTG[G/T]GGGGGGGTTGTTATTACTTAGTTCATGTTGCATGT K 2 1 2 1 201000 f 74 goat snp13272-scaffold1509-2105048 22 48179117 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385078 Affx-122971809 AX-123255436 22 48088544 CGTAGTATCATGTCCACCAATGTGTCCACAAGTCC[A/G]TCTTCTACACCTGGTTTCCTGTTCTTGCTCTGATA R 2 1 2 1 101000 r 74 goat snp13273-scaffold1509-2135637 22 48209734 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38421667 Affx-122944431 AX-123292014 22 48164926 CGGCTGACGGGTGAGTGCCCACTCTGCTTTGTCCT[A/G]TTTTGGGTGAAGGCCAGTGTCCCCAGCGGGCTTCC R 2 1 2 1 201000 r 74 goat snp13331-scaffold1513-1669682 22 48474861 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 468271958 Affx-1111833247 AX-519545732 22 48206613 TGAAAACTGAAAAGAAAAAAAAAAAAAAGAGGGGT[A/G]GACTATGTGGAAACGAAGCAACGGAAAAAGAATCA R 2 1 2 1 101000 r 74 goat 22_48206613_AF-PAKI 22 48206613 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38389132 Affx-122968552 AX-123259490 22 48346959 GAGCATTTCCTCAGAATTCTGGCCTGGAGAGGATG[C/T]GTACACAGTATGACTTCAGGCTCTGTGAGATACGC Y 2 1 2 1 101000 r 74 goat snp13328-scaffold1513-1487649 22 48655315 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376280 Affx-122978385 AX-123246639 22 48385884 GTGGCCCAAGGATGTGCCTGGACCTGCTTGTCAGT[A/G]TCCCGACAAATCTACAGCCTCCCTGCACAGACTTA R 2 1 2 1 201000 r 74 goat snp13327-scaffold1513-1448724 22 48690738 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423743 Affx-122942857 AX-123294089 22 48416086 AGTAAACAAAAAGAGCAGTTTGAATGCTACCTTGT[C/T]GAGTCCACCATCCTGGGTTCTGCCATGTAGTCACT Y 2 1 2 1 201000 f 74 goat snp13326-scaffold1513-1418522 22 48721565 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432188 Affx-122936397 AX-123302529 22 48464177 TGACAGCAGAACTTTCCCCTGCAAATTGAACTGAG[C/T]ACCATGGACGCCTCTAGATTGACTTAAGTGGAGCC Y 2 1 2 1 201000 r 74 goat snp13325-scaffold1513-1370431 22 48769977 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415367 Affx-122948769 AX-123285716 22 48556154 GAGGGGACAAGGTGAATTTTAAGCCCTCAGGGAAA[C/T]TCTGATACATACCAAAGTTTGAGAACCACCACAAG Y 2 1 2 1 201000 f 74 goat snp13323-scaffold1513-1278454 22 48862241 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440060 Affx-122929742 AX-123310397 22 48586075 TGGGAAAGACAGCCATCACTGAACTGGTGATTCAA[C/T]GGCTAAGACTCTGCGCTCCCAGTGCACGGGGCCTG Y 2 1 2 1 103000 f 74 goat snp13322-scaffold1513-1248533 22 48892031 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378263 Affx-122976886 AX-123248622 22 48615157 TCGACACGCACGCCTGCCCCCCCGCCTGAGTGCAG[A/G]AGCTCTTACCAATGAAGCTGATGGCCTCGGGGAAG R 2 1 2 1 101000 r 74 goat snp13321-scaffold1513-1219451 22 48918247 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402909 Affx-122958201 AX-123273262 22 48661525 AGGAAAGTACATGTGGACAGAGGCAGAAAGGAAAA[G/T]AGAACATTGCTTCAAATCTTGAAGGTATTAAAAAC K 2 1 2 1 101000 f 74 goat snp13320-scaffold1513-1173083 22 48964641 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273501 Affx-1111833655 AX-519547117 22 48667381 AGATCTAGCTCACAAAGTCACTCACCCTCTACTAC[A/G]CAATG R 2 1 2 1 101000 f 74 goat GoatD01.000734 22 48667381 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38424859 Affx-122941341 AX-123295205 22 48727163 GGGATGGAGGGTTGGAAAATATAGCTCTCAAGTTC[A/C]GTTTCCTCCAAAAGTCTCGGGTCCTAAGCTCCTGG M 2 1 2 1 101000 f 74 goat snp13319-scaffold1513-1107445 22 49030082 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426301 Affx-122940295 AX-123296647 22 48782879 TTCAGCCTCCCTGCCACCTGGTCCTCCTCAAATTC[A/G]CGGGCCTCAGCCTTCTCCTCCTCTGTGGAGGACAG R 2 1 2 1 101000 f 74 goat snp13318-scaffold1513-1051729 22 49085064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405261 Affx-122956870 AX-123275613 22 48901087 TTTTTTCTGACGTACCTTGCAACCGTGAGAAGTGC[A/C]GGAGCGAGCGGCGAGGTTGAAACGTATCTGACAGA M 2 1 2 1 101000 f 74 goat snp13316-scaffold1513-933521 22 49204949 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377960 Affx-122977200 AX-123248319 22 48983067 GGCAAGGTGAATTAGTTGTCCTTTCCTCAGATGTT[A/G]TTGCTGAAAAGCACTCCACCGTATAGGTGTGTACA R 2 1 2 1 201000 r 74 goat snp13315-scaffold1513-851541 22 49286157 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450770 Affx-122921836 AX-123321104 22 49035878 AGACCCAGTGACTCAAATTGGGATCTTCCTCCTAA[C/T]GGGGTGATGTGTAGAAACTGGAAGAAGAATGAACG Y 2 1 2 1 101000 f 74 goat snp13314-scaffold1513-798730 22 49339099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773361 Affx-122943728 AX-385260503 22 49095876 AAGCTCTTATCTTGCTGACTAATTATTCTCAGCAC[A/G]TAACATAAACAGCACAGTACACCCTTCAAATGTGA R 2 1 2 1 101000 r 74 goat snp13313-scaffold1513-738732 22 49398985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418283 Affx-122947001 AX-123288631 22 49143519 TCAGTCAACTGCCTTCAGTCCTAAGAGCCAGGTGC[A/G]TAAGATCCCACAGAAAACAGATTCCGGTCATTGTG R 2 1 2 1 101000 r 74 goat snp13312-scaffold1513-691089 22 49446494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434123 Affx-122934925 AX-123304464 22 49192783 GGGATGTGGTTGCAGGCTTGGAGCAGGAAGGCTAC[A/G]AATGAGGACAGAGGTGCCAGCGAGGCAGATAAGCA R 2 1 2 1 201000 f 74 goat snp13311-scaffold1513-641825 22 49495704 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792016 Affx-122923511 AX-385279004 22 49230814 AAGAGGTGGCCAGAGCTCCATATTTCATCCTTGGA[G/T]AAGTTTCTCCTCAATGCTCCATGACTCTGCCTTTC K 2 1 2 1 101000 f 74 goat snp13310-scaffold1513-603794 22 49533786 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396728 Affx-122962801 AX-123267083 22 49259828 TGTCCATAGATAGTACATTTGATCAACGCAAGACA[C/T]CTCTGAATATGTGATGACCACTCTCCAACTTCACA Y 2 1 2 1 101000 f 74 goat snp13309-scaffold1513-574780 22 49562803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435458 Affx-122933461 AX-123305798 22 49295664 AGGTAACCCGAGAGAGAAATTTTCTTTTGAAATGA[C/T]GGCTGAGAACTTTGTTAATTAAATCAAACAGTTTT Y 2 1 2 1 201000 r 74 goat snp13308-scaffold1513-538944 22 49598634 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771351 Affx-122923379 AX-385258509 22 49356947 TCACTTCAGGAAGGATGCTCAGGAAGAGGAAGTAC[A/G]TTTGAAAAATAAGAAGATTGCAAGAAAGTAGGAGC R 2 1 2 1 101000 f 74 goat snp13306-scaffold1513-477661 22 49660691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441419 Affx-122928827 AX-123311756 22 49399824 TAATCATAAGGAGTCTGAGAAATCAAGTGTCCATC[A/G]TTTTCCACTTGTATCCTGTAAGGCAGCTCTACGTT R 2 1 2 1 201000 r 74 goat snp13305-scaffold1513-434784 22 49704953 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438704 Affx-122930857 AX-123309041 22 49496260 TTTGTCTGCCAGGCCCTGGCCCTGTGCACAATACA[C/T]GTATCTTACCTAACTCTTTTCATTCCCATTTTATG Y 2 1 2 1 101000 r 74 goat snp13303-scaffold1513-338348 22 49812140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439187 Affx-122931048 AX-123309524 22 49526331 TTCAAAGACAACCCCAGGAGACTTTCATGGGAAGC[A/G]TGGGGTGTGTGTGTGTGTGTGGTATGTGTGTGTGT R 2 1 2 1 101000 f 74 goat snp13302-scaffold1513-308277 22 49842888 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791664 Affx-122964282 AX-385278655 22 49587306 GAATATAATTCATTTGTAAAGGAGACTCCAGTCCT[A/G]CCATCCATCTTAAGCTAAAATTCAATACTTCCCGG R 2 1 2 1 101000 f 74 goat snp13301-scaffold1513-247302 22 49903957 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387762 Affx-122969724 AX-123258120 22 49628770 TTAAAGCTCATTTATGATGGGCCTGCCCAGGCCTG[C/T]GGCTTCTGTGCATAATTCATGGGTCTCCCAGAAAG Y 2 1 2 1 101000 r 74 goat snp13300-scaffold1513-205838 22 49945211 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401519 Affx-122958927 AX-123271872 22 49660005 GGAACTGTCCCCTGACTACAGGGAGACACCTCATG[C/T]GTGGTCATGTCCCTTCCCTAGCAGTACCCTGCATG Y 2 1 2 1 201000 r 74 goat snp13299-scaffold1513-174603 22 49976426 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376440 Affx-122978064 AX-123246799 22 49694866 ATGGGCAGGTGTGGCTGAGGTCTTGAGTGATTCTG[C/T]GGGACATGGTGGGAGTGCACACAGGGAGCTGCTGG Y 2 1 2 1 101000 f 74 goat snp13298-scaffold1513-139742 22 50009264 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390122 Affx-122968005 AX-123260479 22 49788954 ATGAAGGTAGCGTGACGTTCCCTCATTCGTCCGTA[A/G]GGAGGTGCTGTGGGACCTTGAGGCCTTGGCTAGGG R 2 1 2 1 101000 f 74 goat snp13297-scaffold1513-45654 22 50103364 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432548 Affx-122935544 AX-123302889 22 49821433 ATACAAAATGGAAATTAAAGCAGATCCGGACTGCC[G/T]ACTCTGTTCCAGGAGGCCCGGGCCACTTGCGCTGG K 2 1 2 1 101000 f 74 goat snp13296-scaffold1513-13175 22 50135725 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433679 Affx-122934552 AX-123304020 22 49868126 ATTCTGTGGAGGGCAGGGTCGGGGTGCCACCCGCA[C/T]AGGGGGCAACCAGCAGAAGGATGGGTGTAAACACG Y 2 1 2 1 201000 f 74 goat snp12818-scaffold1497-33419 22 50181260 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431813 Affx-122936110 AX-123302154 22 49897307 ACTGTGCCCCTACATGGGCTGAGACACCTGACATG[C/T]GTGTCTGGAACACCTGTAACAGCCCTTGTGTGACT Y 2 1 2 1 101000 r 74 goat snp12819-scaffold1497-62600 22 50210686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427890 Affx-122939693 AX-123298233 22 49960018 CCATGCGCTTTGCCAAGGTCCCAATGGGCATGGGC[C/T]TCTTTGTCCTCTCCCTTGCCCCTCTTCTCCTATTC Y 2 1 2 1 101000 r 74 goat snp12820-scaffold1497-125311 22 50272108 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381729 Affx-122974691 AX-123252087 22 49990549 CTGGAGCTGCCATGCTCCTTTCTACTCACAATCTG[C/T]AACAGACTATACTGAGGAGCTGCCTTCTAGGAACA Y 2 1 2 1 101000 f 74 goat snp12821-scaffold1497-155842 22 50302758 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444830 Affx-122926314 AX-123315167 22 50097302 GAAAAGTCTATTCCAAGCAAGCTGACTCCATGATT[C/T]ATGATCTTTAAAAATTTCAGAATTTTCCAAGTTTT Y 2 1 2 1 101000 f 74 goat snp12823-scaffold1497-262595 22 50409361 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38385941 Affx-122971555 AX-123256299 22 50125937 GTGGGAGTCAGCAGGTCTTAACCATGATCTTCCTC[A/G]GGTCTGGGATGGCCTAAGTAGCTACAAAGAGGGCA R 2 1 2 1 101000 r 74 goat snp12824-scaffold1497-291230 22 50437256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398685 Affx-122961867 AX-123269040 22 50164279 GGCATTAAGTACATTCACAACGTTGTGTAACCATC[A/G]CCACTATTTCCAGAGCGTTTCCATCAGTCCAAACT R 2 1 2 1 101000 r 74 goat snp12825-scaffold1497-329572 22 50475711 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436894 Affx-122933221 AX-123307232 22 50205446 TCCCAAGGCTCGTAAGTTGTGCTTGGTGGCAGACC[A/G]TGACAGTCCAGGACAAAAGATGTTGTTATAAGAGT R 2 1 2 1 101000 r 74 goat snp12826-scaffold1497-370739 22 50517713 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415721 Affx-122948515 AX-123286070 22 50241498 CAGAGGGTTGGGTGTCCATCTCTTGGGGGACTTTG[C/T]AGCCTGTGCTGTGGGTATCACCCATCTCTTTGACA Y 2 1 2 1 201000 r 74 goat snp12827-scaffold1497-406791 22 50553910 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394717 Affx-122964337 AX-123265072 22 50278130 AACTTGGTTCCTGCCTGCAGACCCTCTCCTTCTCA[C/T]TCCCTTCGCTGTAGGTACAGGGGACGACACAGTCC Y 2 1 2 1 201000 f 74 goat snp12828-scaffold1497-443423 22 50589900 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440212 Affx-122930690 AX-123310549 22 50338094 CTCCCCTCCCAGGCTCAGCTTTCTGAGGACACACA[C/T]GGCAGACAGGCAAATTCTTCACCCCTCCTACAGCC Y 2 1 2 1 201000 f 74 goat snp12829-scaffold1497-503387 22 50649625 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403979 Affx-122957429 AX-123274331 22 50408201 ATCCTGGATATAGAATTGCTGGGTCAAAGGTTATG[C/T]ACCTTAGAACTGCTAGAGACTGGCAAAATACCCTT Y 2 1 2 1 101000 r 74 goat snp12830-scaffold1497-573494 22 50719528 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393475 Affx-122965834 AX-123263831 22 50444311 TAGGGGTATTTCGCCTGTCTCTGTGATGCTGGGGG[C/T]GCCAGATCCTGGACAAGCATTTCACTTTGGGAGGC Y 2 1 2 1 201000 r 74 goat snp12831-scaffold1497-609604 22 50755644 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406488 Affx-122955161 AX-123276840 22 50504854 TTGGAAAAAATTCATCACCCTATAAAAAGCCTCAC[C/T]ATTCTTTTGGTAGTCATTCCCTATCCCTCCCTCCT Y 2 1 2 1 201000 f 74 goat snp12832-scaffold1497-670147 22 50815010 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444052 Affx-122926862 AX-123314389 22 50543590 AAATTGAGGGAATGTGAAAAGTACGTCAAGTGAAT[A/G]TATCATCCAGGGAATGTCAGTGATTGGCTTACTCC R 2 1 2 1 101000 f 74 goat snp12833-scaffold1497-708883 22 50853791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277592 Affx-1111835926 AX-519551091 22 50546864 GTGGAGTGTTCTCCAGGCCTGCCACGGAGCTCCGT[A/G]CTGGAGCTGACCAGAGTCAGAGCTGTTCCTTCTAC R 2 1 2 1 102000 r 74 goat Random2.2K-2009 22 50546864 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429830 Affx-122938173 AX-123300171 22 50588143 TAGTCTTGTACAATGACAGCTGTGCCAGTTGCTTA[C/T]AGTCATCATCTCTTCTGAGTGGTCAGGACTCAGTT Y 2 1 2 1 101000 f 74 goat snp12834-scaffold1497-753436 22 50898046 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391785 Affx-122967452 AX-123262142 22 50633906 ACAACCAACACGGAGATTCAGGGTAACTATCCCAC[G/T]GTCAGTCCTGGATTCCTTGTGTGTCAGGAAAACCA K 2 1 2 1 101000 f 74 goat snp12835-scaffold1497-799199 22 50943494 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443242 Affx-122927556 AX-123313579 22 50664628 AGTGGTGGGAGGGGAGAGGCAGGGATCCCCAGTGT[A/C]GTTGACAGAGCCTGACTGCTATATCTCTGGCAGAA M 2 1 2 1 101000 r 74 goat snp12836-scaffold1497-829921 22 50973318 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768385 Affx-122950881 AX-385255565 22 50699010 CTGAGCTAGGTAAAAATGGTTTATTTGGAACTTCA[C/T]GTTCAAGAACCCTCTTGAGTTGGGTACTTCCTGAA Y 2 1 2 1 101000 f 74 goat snp12837-scaffold1497-864303 22 51007712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403079 Affx-122958510 AX-123273432 22 50730246 GTAGCTCCCGGGGTTTGTGGTGCTGACGGGTGGGC[A/C]AGGCAAACTGAATGACAGACCATGGTTTTGGGAGC M 2 1 2 1 101000 r 74 goat snp12838-scaffold1497-895539 22 51038886 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463849554 Affx-1110185677 AX-515327858 22 50736983 TATTCAAACTATGCCTCCCATGCTGAATTCTTTTT[C/T]TAGAAAAAAGGACATCCCCAAATTATCTCTCTCAA Y 2 1 2 1 101000 r 74 goat 22_50736983_AF-PAKI 22 50736983 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418883 Affx-122946110 AX-123289231 22 50758933 GTGAGGCTTCCTTCTTTGGGTTCATTCAACACTGC[A/G]TTCAGGTACTGCCTCTCCTTGGACACCCTCTCCAC R 2 1 2 1 101000 f 74 goat snp12839-scaffold1497-924226 22 51067806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397157 Affx-122962434 AX-123267512 22 50789246 ACACATCCACCAGGTGGATCTATATTTGAAAGTCA[G/T]CTGGCTTCATGGAAGCCCTTAAACAAGCATATCGT K 2 1 2 1 101000 f 74 goat snp12840-scaffold1497-954539 22 51098309 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423872 Affx-122942309 AX-123294218 22 50867126 CTTTACCCATGTATTTACTATACCAGTATCAAGCT[A/G]CCACACAATTTCACTGAACAAGAAGTTAGATAAAG R 2 1 2 1 101000 f 74 goat snp12841-scaffold1497-1032419 22 51176442 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447831 Affx-122923909 AX-123318167 22 50901306 AACTGAAAGAAAAGAACTGTCAACTGAAAATTCTA[C/T]ACCTCGAGAGAATATCCTTCAGAAATTAAGTTTCC Y 2 1 2 1 101000 r 74 goat snp12842-scaffold1497-1066599 22 51211244 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787223 Affx-122972781 AX-385274249 22 50940245 TTTTATCACACTTGTAACCAGTTTAAAAGTCTCTT[A/G]TAAGAAATGAACAGGCTGTCTTTTGGCACTCTGTT R 2 1 2 1 101000 r 74 goat snp12843-scaffold1497-1105538 22 51250185 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388133 Affx-122969476 AX-123258491 22 50973479 TTTCCTTGTGGGCTGCTGAGTTAACAAGGGCTTGT[C/T]GCTGTAAGTCGGGGAGGAGAGTCAGAACCCATAGG Y 2 1 2 1 101000 f 74 goat snp12844-scaffold1497-1138772 22 51283682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377255 Affx-122978144 AX-123247614 22 51026471 CCAGATGGGGAAAGAGACTTTGACCTGTTGCAGGA[A/G]CTGTAAGGTGGTCAGGATTTCAGGGGAGAGAAGGA R 2 1 2 1 101000 f 74 goat snp12845-scaffold1497-1191764 22 51333698 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417178 Affx-122947326 AX-123287526 22 51062168 TCACACACAGACACATCTGGAAACACATGTCCACG[C/T]GCACACAGAGGCAGCCTCACAGACACGGTCAGTTA Y 2 1 2 1 101000 f 74 goat snp12846-scaffold1497-1227461 22 51369439 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376460 Affx-122978050 AX-123246819 22 51092669 TTAAACTGGAGGCCGGCGATACTGTCTCTGTTCTC[C/T]CACTGCCAGCTTCCCCGCCCAACACACACACAAGG Y 2 1 2 1 101000 f 74 goat snp12847-scaffold1497-1257962 22 51400401 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404904 Affx-122956455 AX-123275256 22 51122873 ACTGGCCCCTGGCCTTCTGTTCAGTTGCTATGAGC[C/T]GCATTACAGAGGGGTCTCTTCAATCAGTCCCTCCC Y 2 1 2 1 101000 r 74 goat snp12848-scaffold1497-1288166 22 51430685 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788369 Affx-122968501 AX-385275387 22 51156737 AGGTCTGGAATCCCAAGCTAGGAATTTATTATAAT[A/G]GTGTTTCGCAACAAACTTTAAGAGGAACAAGTAAC R 2 1 2 1 101000 r 74 goat snp12849-scaffold1497-1322030 22 51464719 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800264 Affx-122953584 AX-385287187 22 51248980 ATCTTCATAGATCTTTGTGGAAGCATGATCTTCGG[C/T]GTCATGCTTTCTTTAGCGTCAATTCTGCAAAAGCA Y 2 1 2 1 101000 f 74 goat snp12850-scaffold1497-1414273 22 51552953 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378845 Affx-122976531 AX-123249204 22 51299114 GGTCTATTGCTCCGTATTCCATCCTTCTCCCCTGC[A/G]CCCAGCAATCAAGGCTAGAGGAGCCGGATAAAGGG R 2 1 2 1 103000 f 74 goat snp12851-scaffold1497-1464407 22 51603619 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416560 Affx-122947671 AX-123286908 22 51336840 TGGCTGCCTCTCATCTGGCCTGAGAAACGGTCATC[C/T]GCACAGTTCTTTGCTCTGTTTCACACTCAGGCCAT Y 2 1 2 1 101000 r 74 goat snp12852-scaffold1497-1502133 22 51641427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400347 Affx-122960038 AX-123270702 22 51433715 TGGGAAGCCAGACCTTAGGCACATCACTTAACCTA[C/T]AGGCCTAGTTGCCTCATCTGTAAAATGCGGATGAT Y 2 1 2 1 101000 f 74 goat snp12853-scaffold1497-1599008 22 51738471 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377162 Affx-122978215 AX-123247521 22 51464318 CAGCCCACTGTTCCCTCCTGTGAAACACCTTTCTT[C/T]CCCTGCTTTGCATAGCAAACTTCTGCCAGTCCTTC Y 2 1 2 1 101000 f 74 goat snp12854-scaffold1497-1629611 22 51769133 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274789 Affx-1111834494 AX-519548375 22 51515529 AACCTCATCCAACTTCTTGGAAGAGCAGAAACAGG[A/G]GCCCCTACCAGGCACTAGGTCATCCCTGCAGAGAT R 2 1 2 1 202000 f 74 goat GoatD01.038265 22 51515529 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38405106 Affx-122956981 AX-123275458 22 51551660 ACTTCTGTGCATTTAAATTATATATGAACACTATT[C/T]AATCTGTATAGACCTAGAAAATATTTAGTCCAGTG Y 2 1 2 1 101000 r 74 goat snp12856-scaffold1497-1716953 22 51858019 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391608 Affx-122966594 AX-123261965 22 51585557 TGCCGAGCAGCAGAGGTGCAGTGTGCTCTCCTGCA[C/T]GTGGCAGCCCTTTTAGAGATGAGCAGGTGCCTTGT Y 2 1 2 1 102000 r 74 goat snp12857-scaffold1497-1750850 22 51892117 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392741 Affx-122966015 AX-123263098 22 51648992 TGTGTCCAGCACGTGTGTGGATAGTGGGGAATCAA[G/T]GTTGGAAATTTAGAAACAAGGACATGCAGTGGGCC K 2 1 2 1 101000 r 74 goat snp12859-scaffold1497-1814285 22 51955056 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450724 Affx-122921875 AX-123321058 22 51684918 TAAAGAAAAAGCATGGTAAACAGAAAAATAAACAT[A/G]TACACCAAAACAGCAATAATCACAATGACTGTAAA R 2 1 2 1 101000 r 74 goat snp12860-scaffold1497-1850211 22 51991005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376411 Affx-122978085 AX-123246770 22 51759718 TTCTACTTTCCTTATTCTCTCTTCTCAGTCTCTTT[C/T]TCTCTGTGTCTGTCTATATTCAAAAAGATTGGTTC Y 2 1 2 1 201000 r 74 goat snp12861-scaffold1497-1925011 22 52065720 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782240 Affx-122935231 AX-385269318 22 51808922 ATAGTAAGGCATCATAACAAACCATTTCCCTGATC[A/G]TACAGAGAACTGGATGTTAGAGTACAGCATGTATT R 2 1 2 1 101000 f 74 goat snp12862-scaffold1497-1974215 22 52114912 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416563 Affx-122947669 AX-123286911 22 51880372 GGTTGCACGTCTGGACAGTGTCACCATCACGGGGT[A/G]TTTGTTGAAATGCAGATTCCCAGGCCCTGCCCCCA R 2 1 2 1 201000 f 74 goat snp12864-scaffold1497-2045665 22 52186260 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793156 Affx-122970396 AX-385280134 22 51909369 GACATACAGACAGTGTATGTTGCATATAAAGTAAT[A/G]TAGCGATTTCCTTCCAAATTCCTTAATACATTACA R 2 1 2 1 101000 r 74 goat snp12865-scaffold1497-2074662 22 52215230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789797 Affx-122969761 AX-385276804 22 51953525 CTCGATTCAACTGCTTACCTGTATTCTACGTGGAA[C/T]GAGAAACTTGTTCAGCCTGATGAAGGGACTGCTGC Y 2 1 2 1 101000 f 74 goat snp12866-scaffold1497-2118818 22 52259185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404041 Affx-122957168 AX-123274393 22 51984853 CTCAAACTCGTGTCCATTGAGTCAGTGATGCCATC[C/T]GACCATGTATTTATATATTTTAAATACATGTGCAC Y 2 1 2 1 303000 r 74 goat snp12867-scaffold1497-2150146 22 52290213 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446581 Affx-122924825 AX-123316917 22 52015477 TTGGGCGAGCACTGCATTATTCTTTCAACTCTTCT[A/G]TACGTCTGAAATCTGGAAAATGAATGTCTTAAGAG R 2 1 2 1 201000 r 74 goat snp12868-scaffold1497-2180770 22 52318319 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421284 Affx-122944736 AX-123291631 22 52058077 ATTTACCCCAGGAAAACAATCTCCCCTTTCTCCTA[C/T]ATTTCCAATTCTTCCCTCTTCTGGAAAATTCCCAT Y 2 1 2 1 201000 r 74 goat snp12869-scaffold1497-2223370 22 52360868 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381450 Affx-122974337 AX-123251808 22 52091909 CACAATCCTTACTCACCTGAATACCTTTCACATTC[A/G]TTTTCTAAAAATAGAAAGATTTTTAGCTTTCCTTA R 2 1 2 1 103000 f 74 goat snp12870-scaffold1497-2257202 22 52394675 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401185 Affx-122959347 AX-123271538 22 52123375 AGAAGGTAACTTGGGGGATCCGGGTCTCCAGGAAG[A/G]CAAGGCCTCAGGGACCTCAGTACTGGGACACCCAG R 2 1 2 1 102000 f 74 goat snp12871-scaffold1497-2288668 22 52425669 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438854 Affx-122930763 AX-123309191 22 52173520 GTTTTTTATTATGAAAAACTTCAAATGTTTGTACA[C/T]GAGAGAATGGTATGATGAATACGCTTTGCTCTGCC Y 2 1 2 1 101000 r 74 goat snp12872-scaffold1497-2338813 22 52476740 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771132 Affx-122919586 AX-385258292 22 52215008 CATGCCGATGAGGTTGTAGTTTAACTTTAAGCGAC[A/G]TAGTTGAAAATTAATTCAGGTCTTCTGATTTAAAT R 2 1 2 1 101000 f 74 goat snp12873-scaffold1497-2380301 22 52518237 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438586 Affx-122931153 AX-23353629 22 52310398 CGCTGCCCTTTAGGGAACTCAGGCTGCGGAACTAC[A/G]TCCCAGAGGACGAGGACCTGAAGAAGAGGAGGGTG R 2 1 2 1 101000 f 74 goat snp12874-scaffold1497-2475691 22 52614002 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398047 Affx-122961757 AX-123268402 22 52346033 CTGGTCCCCTGTTGGCCTCTGCTCTCAGGAGGGTA[C/T]AACGTGGGTCCCCTCACACACCGGATCAAGTTTCT Y 2 1 2 1 101000 r 74 goat snp12875-scaffold1497-2511326 22 52649718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412345 Affx-122950834 AX-123282694 22 52395286 TAGAGACACTGTAATGACTTCATGTGAGTAAATTA[C/T]GTAATGAGGGCACACCAGTTCTCTGCCTATGCCAC Y 2 1 2 1 101000 f 74 goat snp12876-scaffold1497-2560579 22 52699435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426078 Affx-122941082 AX-123296424 22 52427609 AAAGGCTTGTCGTTGCACCCCCTTCTTCATGTCTT[A/G]TTCTTACTGTAATTCCTGTTGTCCCTTATACAACC R 2 1 2 1 201000 r 74 goat snp12877-scaffold1497-2592902 22 52732254 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393823 Affx-122965170 AX-123264178 22 52478251 TCTAGACCTGGGCATGAAGGTGACTTTTAGGGGTC[A/G]TGCATTCTTTCTCACATGACACTGGGGGATTAAAA R 2 1 2 1 201000 f 74 goat snp12878-scaffold1497-2643544 22 52783007 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384850 Affx-122971957 AX-123255208 22 52529369 CTAGGGATGATGACACAAACCCCAGGGCTACTGGG[A/C]GGATCCCACGAGACCACGCTGGGAGGCCTAGCCCA M 2 1 2 1 101000 f 74 goat snp7888-scaffold1283-702014 22 52834182 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449205 Affx-122923508 AX-123319540 22 52575497 AGAGGCTACCCCTCACAAATCTGCAGTAGTCTCGC[A/G]TTGAAATAAAAAATGGTAATAACAGATTATAATCC R 2 1 2 1 201000 r 74 goat snp7887-scaffold1283-655886 22 52880557 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376857 Affx-122977839 AX-123247216 22 52629702 TTACCTGATCTGGTTGGTGGAGCCCTTTGCTCCAG[C/T]ACATTAAGGACACATTTATACCAACCGTACATGCA Y 2 1 2 1 201000 r 74 goat snp7886-scaffold1283-601681 22 52933996 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431169 Affx-122937191 AX-123301510 22 52660202 AGGAAGTACCTTTTGCTTATGGAATCTATTGCGGG[C/T]AATTCTCACCAGTCTGGGTCAGCTAGTTTGCTCAG Y 2 1 2 1 101000 r 74 goat snp7885-scaffold1283-571181 22 52964800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452130 Affx-122921679 AX-123322463 22 52689271 TTCTCCTTGGGAAAAGGTCTCATCACCCCCACTTC[A/G]TGTGATGGATAATTTGAATGTAAGTGTTGTTCTAT R 2 1 2 1 201000 r 74 goat snp7884-scaffold1283-542112 22 52993887 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795979 Affx-122958406 AX-385282931 22 52745763 TGGGACCTAAATAGACCAGGCAAGTTAGTGGGTTG[C/T]GAAGGAACAAAGCTAATACAGGATGTATGCTAGGA Y 2 1 2 1 101000 r 74 goat snp7883-scaffold1283-485620 22 53051489 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804136 Affx-986696403 AX-385290787 22 52750976 GAGGTGGAGCTGAGGCTGCCTGGGAGTGACTGCAG[C/T]GCAGTAGGGATTCCTCCTGTTGCGTTAGACCTGGG Y 2 1 2 1 600010 r 74 goat 22_52750976 22 52750976 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 38397085 Affx-122962713 AX-123267440 22 52780719 TAACCTGCATTCTTCTTTATTTTAGTTGTCTAGCG[C/T]GGGTCGGGGGTTCCTCTTAAACTCTCTGTGAAAGT Y 2 1 2 1 201000 f 74 goat snp7882-scaffold1283-450664 22 53086563 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399063 Affx-122960897 AX-123269418 22 52825017 CAGCTGGGCTGAAGTGAAAGTCCAAAAGAAACTAA[C/T]GTTACTGGGAGAGCATGGGCTTGGATGACTGAGCT Y 2 1 2 1 101000 f 74 goat snp7881-scaffold1283-406366 22 53131010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406672 Affx-122955791 AX-123277024 22 52861300 ATAACTGACATATGTGTGTACATACATGTACGTTA[C/T]ATTTGTACATATACATATAAATTTTTATATTTCAA Y 2 1 2 1 303000 r 74 goat snp7880-scaffold1283-370083 22 53167306 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423145 Affx-122942759 AX-123293491 22 52921053 GAACACCTTGGAGCTCCCTCAACCCCATGTGGCTA[C/T]AGTTCCAGGTCAGGTGTCAGAATCTGGCTGGGAGA Y 2 1 2 1 201000 r 74 goat snp7879-scaffold1283-310330 22 53228064 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383788 Affx-122973198 AX-123254146 22 52950786 ACTACCAAGTCATTATAACTTATAACTATTATAAG[A/C]TACTCTTTTTGGTTAATAGGAAAAGCAAGGCTCAG M 2 1 2 1 101000 r 74 goat snp7878-scaffold1283-280597 22 53257858 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398331 Affx-122962129 AX-123268686 22 52986942 ATCTAAATGTCCATCGACAGATAAAGGAATAAAGA[C/T]GTGCCTCAGGGGAATACTACCTAGTCATAGAGAAG Y 2 1 2 1 101000 r 74 goat snp7877-scaffold1283-244441 22 53294035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774833 Affx-122936978 AX-385261967 22 53021696 CAAAGCATGGTCTACTGACATGCTTTGCAGCATTG[C/T]AGATTTTTAGGAAAACTCAGATTCAGGGAATCAGA Y 2 1 2 1 101000 f 74 goat snp7876-scaffold1283-209687 22 53329351 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775162 Affx-122968331 AX-385262294 22 53094317 TCTTCACATGGCAACCAGAGTGACTCTGTTTCTAA[C/T]GTAAGTTAGGTCAAGTCATGCTTCTAACCCAAATC Y 2 1 2 1 101000 f 74 goat snp7875-scaffold1283-137066 22 53399886 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783488 Affx-122922152 AX-385270551 22 53145827 AACCTGGCAGCCACGCAATGAACTCTTGACCTCCT[C/T]CAGGTTCCAGAGACCTTCATTTCAACACCTGAACC Y 2 1 2 1 101000 f 74 goat snp7874-scaffold1283-85556 22 53451515 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397628 Affx-122962625 AX-123267983 22 53186425 CTCTTGCTTTTAAACCAGATGAGAGCTTGACAACT[A/G]TAAGCTAGAGACTGATTTTTTTTCATGTTATAGCT R 2 1 2 1 101000 f 74 goat snp7873-scaffold1283-44958 22 53491433 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416090 Affx-122948323 AX-123286439 22 53217827 GGTAGACTTGCCCCGGCTGGTGGCAGAAAAGAAAG[C/T]GGGGTGTCGTGAGGAAGGTAGGGGCTCCTTAGACA Y 2 1 2 1 201000 f 74 goat snp7872-scaffold1283-13556 22 53522629 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429388 Affx-122938542 AX-123299730 22 53285035 TTTTGCTGGGCTTGTTGACGCCTATCTTAGGGCCT[A/G]TAGAAAAACATGTAAAGATACAAGTGTGTATTTTT R 2 1 2 1 201000 r 74 goat snp23954-scaffold2419-376561 22 53592624 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272131 Affx-1111833248 AX-519545889 22 53295632 GCAGGCAACTGAAAATAATAGTTGCAAGAAACGCC[A/G]CGGGAAGAAAGAGCCACCTCTATGGACCGTTGGTG R 2 1 2 1 101000 f 74 goat 22_53295632_AF-PAKI 22 53295632 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468277594 Affx-1111835927 AX-519551093 22 53300933 AGAAGGGAGCTGAAGGTGATGTCGGCTGTGGAAAG[A/G]AGGAGGCTACAGAGGCGGAGAACTTGGCCAAGCCT R 2 1 2 1 202000 r 74 goat Random2.2K-2013 22 53300933 A G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789636 Affx-122926547 AX-385276645 22 53322221 AACGGGGAGGCTTCTACTTCACAGTATCATTATTA[C/T]AAGGATTGACAGAATGGAGACAAAACCAGCATGCG Y 2 1 2 1 101000 r 74 goat snp23953-scaffold2419-339375 22 53629607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427720 Affx-122939276 AX-123298063 22 53356024 CTCTGATGTTCGTCCCACTGGGCCGGCGTGAGCCT[A/G]TGGAATCCAGGTGGACTGTTCATCGGAACCCAGCC R 2 1 2 1 101000 r 74 goat snp23952-scaffold2419-305572 22 53663949 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404694 Affx-122957270 AX-123275046 22 53392288 TTGCTTGAGATATGCGGTTTAAGTCCAGCCTTGAA[C/T]GAACAATTGAGAGTGATTTTTCAGTGATTGTCATA Y 2 1 2 1 101000 f 74 goat snp23951-scaffold2419-269308 22 53700150 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382434 Affx-122974237 AX-123252792 22 53442180 CCCTCACTCTGCAAAATGTATTTCAGGAAGGCTAC[A/G]TGAAATCTCTTTTTTGGTAAAGTTGATCATTTTAA R 2 1 2 1 201000 r 74 goat snp23950-scaffold2419-219416 22 53748039 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376649 Affx-122979018 AX-123247008 22 53511702 TGAAGAAGGCCCCTGACCTAGACACGAAGTGAACG[A/G]TACAGCTACTCCCTGGGATAGGGAGTCCTGGAAGA R 2 1 2 1 102000 f 74 goat snp23949-scaffold2419-149894 22 53817969 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424142 Affx-122942550 AX-123294488 22 53544323 TCAGAGTCTTTTCTTGGATCCCTTGTGGATTTTTC[C/T]GCCTGTTTCCTGAGTGAGGTGAACTTGTGTATCAG Y 2 1 2 1 101000 f 74 goat snp23948-scaffold2419-117273 22 53850533 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396112 Affx-122963414 AX-123266467 22 53660098 TTGTAAAATTTTATGTTGCTTTGACTCTTTCCTTG[A/C]CTCATTTCCTTTTTTATTTTATTTCCTTTTTCATT M 2 1 2 1 103000 f 74 goat snp23945-scaffold2419-1498 22 53966852 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777298 Affx-122963596 AX-385264420 22 53676460 CTGCTGCGATGACCTGGATAAAGTACAAAGCAGGA[A/G]GAGGAGGTAAATTATATTGTTGAAATCTCAGCCTG R 2 1 2 1 101000 f 74 goat snp19032-scaffold1912-14765 22 53982078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432927 Affx-122935307 AX-123303268 22 53708409 GACATCTTCTTTGCTTTTGCGGGTTAACACTGGGT[A/G]TCAGACTCTAAGGCAGGGTCTGGATGAGACAAGGA R 2 1 2 1 101000 f 74 goat snp19033-scaffold1912-46714 22 54014102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406225 Affx-122956119 AX-123276577 22 53739839 CACTACAAAGAATGGGTCACACAAAGACTCACGGG[C/T]GCAGAGGTTCTGGGACATAGGGAGACATTCTGTTC Y 2 1 2 1 201000 f 74 goat snp19034-scaffold1912-78144 22 54045466 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277472 Affx-1111835928 AX-519550976 22 53759043 CTCTCCACAGCCCCGAGTTCGAGGATGCTCTGTGT[A/G]CCCTGATGGTGATGGCCGCCCCCATGGCCCCTCAC R 2 1 2 1 103000 f 74 goat Random2.2K-2014 22 53759043 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38427198 Affx-122939596 AX-123297541 22 53823578 TTTGTTTTTATTTTGGTGACTGCTCTGAGGCACCA[A/G]TGTAACGTTACTCTTTTACTCCTGGGAGACACCAT R 2 1 2 1 101000 r 74 goat snp19036-scaffold1912-161883 22 54129141 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790243 Affx-122932468 AX-385277247 22 53868174 TTTCCGTTGTATGAGATTTGTTAAGGTGCATTTTA[C/T]GGTTCAGAACGTGGTCTGTCTGCATGAATGTTTCC Y 2 1 2 1 101000 r 74 goat snp19037-scaffold1912-206479 22 54174158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775170 Affx-122961088 AX-385262302 22 53906543 ACCATGCCTTGTGATTCCAGTGATAGGAAAATTGA[C/T]GGGAATACACGGGTAAAGCTTGTTCCACTGTAGAG Y 2 1 2 1 101000 f 74 goat snp19038-scaffold1912-244848 22 54212351 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375441 Affx-122979176 AX-123245800 22 53935827 CCAAAAAAAAAAATAAACTTGTAGGTAAATATTGC[A/G]CTTCATCCTGACAAGAGAACTTTAATGCTAAATTA R 2 1 2 1 101000 r 74 goat snp19039-scaffold1912-274132 22 54241649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790299 Affx-122973190 AX-385277302 22 53993659 GCTGAAGATCATGAAAAAATGGGTGCCTCCAGACT[A/G]CAAGATTCACAGGTGAGAGCCTAGAACTTCAGTAG R 2 1 2 1 101000 r 74 goat snp19040-scaffold1912-331964 22 54299887 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433838 Affx-122934448 AX-123304179 22 54031843 GAAGAGGTCTTGCTGGAGGGCTTCCCATCTCTAGC[A/G]TCTGTCCAGAGACTCAAGTCCACCCACGTCGGTCA R 2 1 2 1 101000 r 74 goat snp19041-scaffold1912-370148 22 54336948 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390609 Affx-122967174 AX-123260966 22 54088638 GTTTCACTTGATCTTTAGAATGCTGAATCTTACAA[C/T]ACAGAGGCCAGGAGCTTGGAACTCAGCTGGGGATT Y 2 1 2 1 101000 f 74 goat snp19042-scaffold1912-426943 22 54392184 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414753 Affx-122949254 AX-123285102 22 54120634 GTAAAAGCTCTTAGGAGCAGACCGGGTGACTTTAC[A/G]TCACCTGACTTGGGGACGGGGATAGCCAGAGAAGA R 2 1 2 1 103000 f 74 goat snp19043-scaffold1912-458939 22 54423226 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423024 Affx-122943413 AX-123293370 22 54149449 AACTTGGCTGAACCTGTCTCTCTGTCCCCTTCAGA[C/T]TGAACTCGTTTTTGAATGTTCTCATAGCTCGCTGA Y 2 1 2 1 201000 r 74 goat snp19044-scaffold1912-487754 22 54452166 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443108 Affx-122928099 AX-123313445 22 54205338 CTTTGAACTTATGCGTGACACACACATGCAGGCCC[A/G]TTCTCAGCCTCAGTTTCCTCATCCATAGAGTGGGG R 2 1 2 1 201000 f 74 goat snp19045-scaffold1912-543643 22 54508135 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441343 Affx-122928884 AX-123311680 22 54241041 TAGTAGGTGCTCAGCAAAGCCTGGCTTGCTTCTCC[A/G]TCTCTTCCCTGCGAGGTGACGCCAATTTTAGACCA R 2 1 2 1 201000 r 74 goat snp19046-scaffold1912-579346 22 54543721 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434575 Affx-122934117 AX-123304916 22 54275042 GCAGGAGTGAAAAAGACACGCATGAGTAAAACACC[A/G]TGCACGAGTTACCAAACCACGCATGAGTAGAAAAG R 2 1 2 1 101000 f 74 goat snp19047-scaffold1912-613347 22 54577909 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430432 Affx-122937739 AX-123300773 22 54366999 AAGACTGAGCGTGCACGCACGCAGTGATGCCCTTC[A/G]CAGGATCCTCACAAAGGAGGGCGGTACTTCAGGGC R 2 1 2 1 202000 f 74 goat snp19049-scaffold1912-705304 22 54668518 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419915 Affx-122945330 AX-123290263 22 54404717 GATAGAGAAGGATTAGCAGAGAATATACAAAATGG[C/T]GGTGTTGGAGGGGAGTTTGGGTGCTCTTTGTCCTG Y 2 1 2 1 101000 f 74 goat snp19050-scaffold1912-743022 22 54705760 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434102 Affx-122934941 AX-123304443 22 54453320 CTGCCTTGGAGCTGGGATTCACACCATCTCCCTGT[C/T]GGGTAAATAACCTGAGGGGGAAAAAATAGAGGAAA Y 2 1 2 1 201000 f 74 goat snp19051-scaffold1912-791625 22 54754332 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378381 Affx-122976809 AX-123248740 22 54499344 TGTACTCTGGGTGAAATGTCTGGAGACAGGCAGGG[A/C]TTCTAAAGCCCTAAAAACCTAAAGAGTATCCAAAA M 2 1 2 1 201000 r 74 goat snp19052-scaffold1912-837649 22 54800345 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421145 Affx-122944188 AX-123291492 22 54529330 AAAGCACATAAAAGTTATTGCAAAGGAAAGCCACA[C/T]AGTGGGAGAAGATATTTATGATACGTGCATCTGAC Y 2 1 2 1 201000 f 74 goat snp19053-scaffold1912-867635 22 54830348 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792068 Affx-122927876 AX-385279055 22 54608531 GACCGCCCTTCTGAACTTTCACGGCATTCTCAGTG[A/G]TTACACAGTTCCCTCCCCATCCTGAAATAAATAGC R 2 1 2 1 101000 r 74 goat snp19055-scaffold1912-946836 22 54907504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800368 Affx-122963071 AX-385287290 22 54646582 TTAATCATCCTGAGAATAGAACTTCTAAAAAGCAC[A/G]TTCCTGAGATGAGGACATTTGATTGTCCCTTTTTG R 2 1 2 1 101000 r 74 goat snp18450-scaffold1869-27856 22 54944121 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427397 Affx-122940076 AX-123297740 22 54720309 AAAAATAAGCAAGCGACAGAATGACAACTAGAGTA[C/T]GACGCTATTTTTATAATGTAAACGACACACACCAA Y 2 1 2 1 101000 f 74 goat snp18451-scaffold1869-101583 22 55017227 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386677 Affx-122970186 AX-123257035 22 54779192 CCAATGAACAAGGAATACTTCTACAGTACTAACGA[C/T]GAACTTAATGCCCAGAAATCGGAGGTGCTCATTCC Y 2 1 2 1 101000 f 74 goat snp18452-scaffold1869-160466 22 55075333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422838 Affx-122943105 AX-123293184 22 54814325 AAATGACTGCCGTGGGGAGCAGAAGGGTAAATGAC[C/T]GTAGTAGCCTCTCAGCAAGCTGGGGGACAAGCCCC Y 2 1 2 1 101000 f 74 goat snp18453-scaffold1869-195599 22 55110999 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433472 Affx-122935048 AX-123303813 22 54847029 TATTTCTTTAAAGAAAAAGCTGCGTTGCTTTTCCT[A/G]TAGTTTTCTAGAAACCCAGAGTGTCTGGAGTCTGT R 2 1 2 1 101000 r 74 goat snp18454-scaffold1869-228303 22 55143797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426322 Affx-122940281 AX-123296668 22 54894310 CAGTTTTGGAGCTGCCAGCTGGAATCCCAGCCACT[A/G]ATGGGAACCCCTCCTTATTCTCCCATTGGCCCCTG R 2 1 2 1 201000 r 74 goat snp18455-scaffold1869-275584 22 55191102 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425053 Affx-122941268 AX-123295399 22 54937301 TCATAACCAGGAAGTGATCTGAGCACACTCCTTAG[A/C]GACACTGGGCACAGCAGAGCCAAAAGGTGGCAAAG M 2 1 2 1 101000 f 74 goat snp18456-scaffold1869-318575 22 55234708 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797135 Affx-122956792 AX-385284075 22 54977153 ACACTAATACACCAACCACCCAGGTCATAAATTAA[C/T]GTTTAGCTCTTTTTGATTTATCATACATCTACTCA Y 2 1 2 1 101000 f 74 goat snp18457-scaffold1869-358427 22 55275038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396087 Affx-122963430 AX-123266442 22 55033224 ATTCGGTGGCCTTTATGGTGCCTTAATCGTACCTC[A/C]GTGAGAAGTCATCAAGCATCCGTCCCCTCCTGATT M 2 1 2 1 101000 f 74 goat snp18458-scaffold1869-414498 22 55331630 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448010 Affx-122923730 AX-123318346 22 55067186 CAAGGCATGGGTGTATAATTATTTCATCTTTTAAA[C/T]GAAGTTGACATTCTATCTGTCAAACATGGACTCTG Y 2 1 2 1 103000 r 74 goat snp18459-scaffold1869-448460 22 55365937 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410576 Affx-122952129 AX-123280926 22 55100261 TTTTTTTTTTTAAGTTTTCAGAGCCAAATAGTTTT[A/G]TGGAACTGCTACCAGAGGGGAAAGTATAATTTTGA R 2 1 2 1 202000 f 74 goat snp18460-scaffold1869-481535 22 55399062 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432826 Affx-122935387 AX-123303167 22 55157183 CCAGCTAAGCCATCAAGTTGTTCCCCCACCACCAT[C/T]GCCACCCTCCGAATTCTGTCGTCTCCCAGTGGAAT Y 2 1 2 1 201000 r 74 goat snp18461-scaffold1869-538457 22 55456209 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277474 Affx-1111835929 AX-502702060 22 55160189 TTGGACACGACTGAGCGACTGAACTGAACTGAAAC[A/G]CCCAAATGTCTATCAACAGGAGCTTGCAAAAACAC R 2 1 2 1 303000 f 74 goat Random2.2K-2015 22 55160189 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38433550 Affx-122934990 AX-123303891 22 55210206 TTGCTTCTGTGTTCTCCTGTTGATTTCTGCTCCTA[C/T]ATTTATATTTACCTTCCTTTTTCAGTTTGACTCTT Y 2 1 2 1 201000 r 74 goat snp18462-scaffold1869-591480 22 55509322 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438399 Affx-122931292 AX-123308737 22 55243524 AACGAAGAAAATGATCTCTGGCGGTTATTTATATT[A/G]TCAGCCTCCTCTGGAGTGCTTTTTTTTTTTTTTTT R 2 1 2 1 201000 f 74 goat snp18463-scaffold1869-624798 22 55540866 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378906 Affx-122976487 AX-123249265 22 55260974 CTCCAGCGTCCAACCACTGACTTAACCACTTAACT[G/T]AACCACTGGGGGCTAGGTATCCAACTGCCTGCCTC K 2 1 2 1 101000 f 74 goat snp12244-scaffold1458-16655 22 57755271 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411224 Affx-122952350 AX-123281574 22 55356236 GAAGGGGACACCCAGATTCGGGATTTCAAAGGAGC[A/G]TGTCAAAAAGGGACTTCTGGAACCGAGCTCGGAGG R 2 1 2 1 101000 r 74 goat snp12246-scaffold1458-111917 22 57848140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395782 Affx-122963666 AX-123266137 22 55470778 ATTTTTTACACCCCAGAGATGATGATTTAATTGGT[A/G]CAGAATGTAGCTTGGGCATTGAGAATGCTGTGAGT R 2 1 2 1 101000 r 74 goat snp12249-scaffold1458-226459 22 57958151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418281 Affx-122947002 AX-123288629 22 55505305 CCGGTGCTCCAGCAGGACTTAGGCCTGTTAGATGG[C/T]AGAATCTTTATCGTATCATTAGCTAAAGATAAAAA Y 2 1 2 1 101000 r 74 goat snp12250-scaffold1458-260986 22 57992321 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385950 Affx-122971544 AX-123256308 22 55559663 GGAGTTTCTGACGTTGAGGGTGATGGCCTGGAAGA[C/T]GCTCAGCAGGCAGGTGGCACAAATGGAGAGGCCCC Y 2 1 2 1 101000 f 74 goat snp12251-scaffold1458-315344 22 58039467 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383595 Affx-122972578 AX-123253953 22 55595147 CTTCTGGGGAGGCCAGAGGGGGCTGGACAAGACAT[A/G]CGGCTAATTCTGCCCCAAGGCTCAGTGTCAGAGCT R 2 1 2 1 201000 r 74 goat snp12252-scaffold1458-350828 22 58075260 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392275 Affx-122967544 AX-123262632 22 55628468 TCTCTTTCCCACCTTTGGGGCAGTGAGGGGATGAG[A/C]TCACCACTCCTTTTGCCCTCAAGGTGCTCGTTCTG M 2 1 2 1 101000 f 74 goat snp12253-scaffold1458-384149 22 58108276 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435937 Affx-122932747 AX-123306276 22 55659787 CCCCCCAGCCCGTCAGCAGCAGAATCAACCAAGTC[C/T]GGACTCCAGGGACTCTCCCTGCGTACAGCCTCTCG Y 2 1 2 1 201000 f 74 goat snp37321-scaffold4552-10955 22 58138559 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380482 Affx-122975716 AX-123250840 22 55704170 TACTGCTCACACTCTGATCTCTTCCGGCGCAGTCT[A/G]GGTTTGACCTCAGCCTCTCCTGTTGCAGTTTAAAC R 2 1 2 1 201000 f 74 goat snp37322-scaffold4552-55338 22 58183350 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272136 Affx-1111833250 AX-519545893 22 55802336 GGATTTCAGTGTTGTAAATTGCATATTAAAAGGCA[A/G]AGACATTACTTTGCCAACAAAGGTCCGTCTAGTCA R 2 1 2 1 303000 f 74 goat 22_55802336_AF-PAKI 22 55802336 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320774475 Affx-122937857 AX-385261611 22 55817612 GCTGACAAACTGAACGGGACCAGCCTTGTTTTCTG[A/G]GAAGGTAACTTTCCCAGAAACAAGGAAGCAACAAC R 2 1 2 1 101000 r 74 goat snp30452-scaffold3358-23451 22 58293928 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440964 Affx-122928992 AX-123311301 22 55861784 TCCCTTTCCCAGGGCTGGGCCAGAGGCTTTCTACA[C/T]GGTCCAAAGAGAATTTTCACCTCCCACATTCCAAC Y 2 1 2 1 101000 r 74 goat snp30453-scaffold3358-67623 22 58392651 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782016 Affx-122920695 AX-385269095 22 55899700 GGTCCCTATGAAGGGGAAGGGCACGGTCATTTGAA[C/T]GGTGTCCTCCACGTTCCTATCACCTGATTGCGTGT Y 2 1 2 1 101000 r 74 goat snp30454-scaffold3358-105539 22 58352619 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784803 Affx-122957294 AX-385271850 22 55934371 AGTAAATAGACCCGTACACCCTGATGTTATTTATT[A/G]CTGCAATGGGCAGATATGTAAGCATGTTTTTAAGA R 2 1 2 1 101000 r 74 goat snp30455-scaffold3358-140210 22 58437267 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601453 Affx-1002479723 AX-413835871 22 56001035 CTTCCTGCAAGAGAGAAATATCATTCAAGGGGCCT[A/G]AACTGCCATAGGAAATGCAGCAACTGAAGATGTTA R 2 1 2 1 101000 f 74 goat 22_56001035_RH-map 22 56001035 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38447965 Affx-122923766 AX-123318301 22 56028048 AACCACGACATAATCCTTGCTGACAGAGCAAATAC[A/G]TGACCTCTTGAATATTAATATTTAGACTCTGCTTG R 2 1 2 1 101000 f 74 goat snp55992-scaffold870-69484 22 58520439 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601455 Affx-1002479724 AX-413835873 22 56052662 ACCAAGTGAGAAGCAATGAATAGACAAATCTTTTT[C/T]CTCTTTTTGAATTGTCAGCTTAACTGTGTAGTTTC Y 2 1 2 1 101000 f 74 goat 22_56052662_RH-map 22 56052662 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601585 Affx-1002479725 AX-413835989 22 56074665 GCCAGCCCAGCCCAGCCCTTCCCCTAAATCCCAAG[A/G]AACTGACACAGTGGAACACCCCATTTTTAAAAAGC R 2 1 2 1 101000 r 74 goat 22_56074665_RH-map 22 56074665 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601460 Affx-1002479726 AX-413835878 22 56105703 AAGGATGGGCACCTCCCAGGTTCTGCCTTCAGTGC[C/T]ACGTGCGACGCAGTGGAGGCCTGGGCTGGGTCCAG Y 2 1 2 1 102000 f 74 goat 22_56105703_RH-map 22 56105703 C T 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38404833 Affx-122956635 AX-123275185 22 56117030 ATGGGGCAGAATTACAGAGGTCCTCTGTGGGGGAT[A/G]AGCGGAAATTGTTCGAATCAGGGAGACAGGCAGGC R 2 1 2 1 101000 f 74 goat snp55994-scaffold870-158466 22 58606512 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601461 Affx-1002479727 AX-413835880 22 56121709 ACCTTGAAGACAATGAAGAGGTGGGGAACCTTGGC[C/T]CCCAGGCTTCAGAGGCCCTCAGCTTTGTCACTGAT Y 2 1 2 1 202000 f 74 goat 22_56121709_RH-map 22 56121709 T C 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38382496 Affx-122973819 AX-123252854 22 56160903 CAGCGGAGCTGTCTCGGAGCTGGCCAAGTGTTTGC[A/G]TTTTGACATCCAGAAACGGGCAGCGGCCCCAGCAG R 2 1 2 1 101000 r 74 goat snp55995-scaffold870-202339 22 58646390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601463 Affx-1002479728 AX-413835881 22 56179586 ACAAGGAAGCTGACTCTAAACACTATTATTCAACA[C/T]AGTTTTGGAAGTCCTAGCTACAGCAATTAGAGAAG Y 2 1 2 1 101000 f 74 goat 22_56179586_RH-map 22 56179586 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601592 Affx-1002479729 AX-413835995 22 56199289 ACAGCACTGAGCCGCCCTGCCCTGTGCTTCCCAGG[C/G]ACTTGGACCCATTCTGTCTCCAAAGACGTCTTCAC S 4 1 2 1 101000 r 74 goat 22_56199289_RH-map 22 56199289 C G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601467 Affx-1002479730 AX-413835885 22 56237998 ACAGGCATCCTGAGAGAACAGAAATGTCCTTCAGA[G/T]TGAGTGCTCATGGACTGCGGTATATCTGTGGTGAG K 2 1 2 1 101000 f 74 goat 22_56237998_RH-map 22 56237998 T G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38394648 Affx-122964385 AX-123265003 22 56259246 CTCCTGTGGTTTCCGGGGACAGGCACTCGGGAAAA[C/T]TCAGGGCTTGTTTACAGGATGCGGTGGGCCCAGGC Y 2 1 2 1 101000 f 74 goat snp55996-scaffold870-300682 22 58740418 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601595 Affx-1002479731 AX-413835997 22 56263447 GTCCATTCAGATCCCTTTTCCATTTTTTAATTAAG[C/T]TGTCTCTTTATTATTGACTTGTAAGAGTTTTTTAC Y 2 1 2 1 101000 r 74 goat 22_56263447_RH-map 22 56263447 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38382752 Affx-122973595 AX-123253110 22 56320457 TTAGAAAGCACTTTTCACGAGCCGAGGGCTTTCTG[A/G]AGGCTGCCTCCGTGTACTGACGTCAGTCCGTCAGT R 2 1 2 1 101000 f 74 goat snp55997-scaffold870-361893 22 58798676 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601597 Affx-1002479732 AX-413835999 22 56360705 CACGAGGTATTGACTGGGTCTTATGGGCACTACTA[C/T]GTGCCAGTCACTGAAACCTTTCAGTGGTAGGAAGT Y 2 1 2 1 101000 r 74 goat 22_56360705_RH-map 22 56360705 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38421202 Affx-122944146 AX-123291549 22 56366411 TTGCTTTTGGCATTGTTAATGCTGTCACTGTTTCA[A/G]CTCTCCTGAGATTTGGAAAGACTCATCACTGAGAC R 2 1 2 1 101000 r 74 goat snp55998-scaffold870-407847 22 58842443 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601599 Affx-1002479733 AX-413836001 22 56409097 TAGGATTTGCTGAGCTGGGGAGGCTGTGCCTTCGC[C/G]TCGCTGTGCTTTTTTCTGCTACAGTCAAGGTGGCC S 4 1 2 1 101000 r 74 goat 22_56409097_RH-map 22 56409097 G C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38430032 Affx-122937577 AX-123300373 22 56421131 GACATGACCTTGGCAGCTTAAGCGAGGTGTTACAC[A/G]CGCGCACACATACACACACACACACTTCTCTATGG R 2 1 2 1 101000 f 74 goat snp55999-scaffold870-462567 22 58892843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601601 Affx-1002479734 AX-413836003 22 56425294 CAGACCTTTTGATTTATCAGGTGTACCTTGGGGAT[A/G]CTAATCCCCTCATCACAGGGTAACACCCAGGAGTT R 2 1 2 1 101000 r 74 goat 22_56425294_RH-map 22 56425294 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38425822 Affx-122940685 AX-123296168 22 56477323 CTTAGACCTCAGGCCTCTCCCTTAAGCACTAGGCC[A/G]CGTGGCCCTGTTGGTCAAAGTTCAGGGCAGCGCAA R 2 1 2 1 102000 r 74 goat snp56000-scaffold870-518759 22 58949910 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601478 Affx-1002479735 AX-413835894 22 56483644 TGCTTATCTCAGCATGCCTTACAGTTAGGATTCAT[A/C]ATTGTCTGTGAGTGGCATGAAAAAGGCACTGCTTT M 2 1 2 1 101000 f 74 goat 22_56483644_RH-map 22 56483644 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38451576 Affx-122921689 AX-123321909 22 56524290 ACGTGGGCACTTTCTCCTTAAAAAAGAAGAAAATC[A/G]ATGCCTGGAACACGTAAGAACATGAGAGTAAATTT R 2 1 2 1 201000 r 74 goat snp56001-scaffold870-565726 22 58995442 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601481 Affx-1002479736 AX-413835895 22 56553880 TTGGGGTGGGGTGGGAAGAAAGTACAATCTGTTTG[C/T]AGAACATACATTAACTTAACCTTAAAAATGCATCC Y 2 1 2 1 101000 f 74 goat 22_56553880_RH-map 22 56553880 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38423036 Affx-122942974 AX-123293382 22 56592167 AAAGTCATACACGTGTGCACACAGCGATGGTTACA[C/T]GGAAGAGTGCTCAAGCTGACCTGCAGACTTAATTC Y 2 1 2 1 101000 f 74 goat snp56002-scaffold870-633603 22 59063261 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277600 Affx-1111835930 AX-519551099 22 56598337 TCTAAGAGCCCCTCCACCTGTTGGTTTCCTGTGAC[A/G]GGGACTCGTGCGAAGTCCTGTAGGATGTCCCACAG R 2 1 2 1 202000 r 74 goat Random2.2K-2016 22 56598337 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431412 Affx-122936531 AX-123301753 22 56622506 TTGCTGTTCGAAGTGACTTTGCGAAAGCTGACTGC[A/G]TGTGGGACAAGCATGGCCTCTGTGGTGTGTAGGGG R 2 1 2 1 101000 f 74 goat snp56003-scaffold870-663942 22 59093624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601606 Affx-1002479737 AX-413836008 22 56623173 TCAAAGAAAAATTAAATCAAAACAGATGAAAGACC[C/T]AAACTCAAGAGCTGAAACTATCAACCTCTTAGAAG Y 2 1 2 1 101000 r 74 goat 22_56623173_RH-map 22 56623173 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601608 Affx-1002479738 AX-413836010 22 56641824 ATTTATGCAACATGACTTTTATTATATACATTATA[C/T]AATCATTGTAACACGTTTATTTCCAGAAGAGTGCC Y 2 1 2 1 101000 r 74 goat 22_56641824_RH-map 22 56641824 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38411941 Affx-122951151 AX-123282291 22 56665194 CTGCTTTCTATCTTAATGGAGGCCTCAGCGAGATC[A/G]GACCTGTGGCCCCGAAACCGACAGGAAATAAGTGT R 2 1 2 1 101000 f 74 goat snp56004-scaffold870-706630 22 59106364 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601487 Affx-1002479739 AX-413835902 22 56684251 TGCTTCAGCCACAGTAAGCTCTTTCTAAACCGAGT[C/T]CTTCAAGTATCCTGTGTTCTGTCATAACTCTGTGC Y 2 1 2 1 101000 f 74 goat 22_56684251_RH-map 22 56684251 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601611 Affx-1002479740 AX-413836013 22 56725995 ACCACTGAGCCACCTGGGAAGTGAAAGTGTCAGTC[C/T]GACACTTTTCCCCAAGAACTTTAGCCTGCCAGGCT Y 2 1 2 1 201000 r 74 goat 22_56725995_RH-map 22 56725995 T C 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601491 Affx-1002479741 AX-413835906 22 56746046 TTTACATCTCTGGGTTATGAAATACTAGCTAAACT[C/T]ACTTGGATAATTTTTTTTTTCCTGTCTGCCCACCC Y 2 1 2 1 201000 f 74 goat 22_56746046_RH-map 22 56746046 C T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38375739 Affx-122978618 AX-123246098 22 56761786 TCTTGCCTCGTTCAGGTGAGTGAAATGCAGAGACT[A/G]GACGCGCAGGTCAAGGAGCTGGTCCTGAAGGCGGC R 2 1 2 1 101000 f 74 goat snp56006-scaffold870-803222 22 59203770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601493 Affx-1002479742 AX-413835908 22 56770432 AGTAACAAGAGTTAGCTACAGTTAGTAACACAGAC[A/T]TTTTAGTAACTGTTAATAAGGGAGAAAAGAGAGAC W 4 1 2 1 101000 f 74 goat 22_56770432_RH-map 22 56770432 A T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601495 Affx-1002479743 AX-413835910 22 56793210 AAAACTTACTGTGTGGGGCAAAAACAAAATCTTTG[C/T]GTGTATGTGCTGTGCTTCGTCAGGATCAGAGATGG Y 2 1 2 1 201000 f 74 goat 22_56793210_RH-map 22 56793210 C T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38444677 Affx-122926448 AX-123315014 22 56805760 TGCATTTGTAAACTCGATAGTGCCACATTCCCCAT[A/G]CCAACCTGACGGCGCATCAGTGGGCACTCCTGCCA R 2 1 2 1 101000 f 74 goat snp56007-scaffold870-847196 22 59245290 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601497 Affx-1002479744 AX-413835912 22 56813482 TCAAGGCTATGGTTTATTCCAGTGGTCATGTATGG[A/G]TGTGAGAGTTGGACTGTGAAGAAAGCTGAGCGCCG R 2 1 2 1 103000 f 74 goat 22_56813482_RH-map 22 56813482 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38409033 Affx-122953864 AX-123279384 22 56851130 TGCCTGGAATCCTCTCCCAGGAGCCATTCCCTGGC[C/T]GCCTCATTCTTGTTGCCAAGGTAGGTTTCAGTCCA Y 2 1 2 1 101000 r 74 goat snp56008-scaffold870-892566 NW_017204235.1 1300 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277478 Affx-1111835931 AX-519550981 22 56855648 TGATATGTGTGCTTTTCTATCTTGTTCTAATAGGA[A/G]GCACTGATGCTATTTTTTTGCAGGGGGTCTCCAGA R 2 1 2 1 201000 f 74 goat Random2.2K-2018 22 56855648 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 350601499 Affx-1002479745 AX-413835914 22 56893968 CACCAAAGTTTAGCAAATGGAGAAAAAGAGAGACG[C/T]CTTCAGATTCAACGGATGAAGTGATGGAAATGAGA Y 2 1 2 1 101000 f 74 goat 22_56893968_RH-map 22 56893968 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601501 Affx-1002479746 AX-413835916 22 56913188 CATTACTTTGCTGACAAAGGTCCATACATCAAGGC[A/G]TGTATGTATGGATGTAGTCATGTATGGATGTGAGA R 2 1 2 1 103000 f 74 goat 22_56913188_RH-map 22 56913188 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601624 Affx-1002479747 AX-413836023 22 56931723 AGTGCCATGACCCTTGGCAAGCCAGTGTGTGAGAG[A/C]TGAAATAACCCTTGAAAAACAAGAAGAGAAGGATG M 2 1 2 1 101000 r 74 goat 22_56931723_RH-map 22 56931723 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601626 Affx-1002479748 AX-413836025 22 56959833 AGGATAAAATATGGACCCCTAAACTTCCTCACACT[C/G]TACCAAAACACACTTTACTTGGTGCCAACAGCATA S 4 1 2 1 400000 r 74 goat 22_56959833_RH-map 22 56959833 G C Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601508 Affx-1002479749 AX-413835923 22 56979767 CGCTAGGTCAGATGGTAAAGAATCTGCCTGCAATG[C/T]AGGAGATGCAAGTTTAATCCCTGGGTTAGAAGATC Y 2 1 2 1 303000 f 74 goat 22_56979767_RH-map 22 56979767 T C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38438396 Affx-122931294 AX-123308734 22 56982908 AGAAAGGAGGTCTGCGAGCTGCTCGGTAGAGGAGC[A/G]GGAGGCCAGTCTCGCTCGGCTCGGGTCCTGGGCTT R 2 1 2 1 101000 f 74 goat snp52635-scaffold787-47010 22 59381190 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601510 Affx-1002479750 AX-413835925 22 57009122 CTATACCTGGCAAGACTAGCCATATAAAATAGAAA[C/G]TAACCTATAAGGTTGAATACTTGGGGAATCAAAAG S 4 1 2 1 201000 f 74 goat 22_57009122_RH-map 22 57009122 C G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320789016 Affx-122938039 AX-385276029 22 57011496 CCAGTATATCTTACATTGATGTCTTAAAGTTGAGG[A/G]AAAAGTGCTGTATTTGTGAACAAGTAAGCTTTAAA R 2 1 2 1 101000 r 74 goat snp52636-scaffold787-75598 22 59410016 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 350601512 Affx-1002479751 AX-413835927 22 57051759 AGATCTAACCAGTCCATCCTAAAGGACATCAATCC[C/T]GGATATTCATTGGAAGGACTGGTGCTGAAGCTGAA Y 2 1 2 1 303000 f 74 goat 22_57051759_RH-map 22 57051759 C T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38425352 Affx-122941585 AX-123295698 22 57061837 GTGGTTTGTGCCGACAGTTTTAGGACGTTAGTACC[A/G]TAGAAGATGAATCTGCTGTTGTAACCACATCTGAG R 2 1 2 1 101000 f 74 goat snp52637-scaffold787-125939 22 59458050 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601632 Affx-1002479752 AX-413836031 22 57087217 CAGCTTCTTCTCTAAGTACCCTTTTAGCAAATATT[G/T]GAGGAATAATGGTTTGTAAGAATGCCAAATTATTA K 2 1 2 1 101000 r 74 goat 22_57087217_RH-map 22 57087217 T G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38444278 Affx-122926770 AX-123314615 22 57091133 CTGTGTCTGCTTGGAAATCTGCCTTAAAGACCTCA[C/T]GTCGATCGTTTGATGGCCTGGGAAGACTTGCCTGG Y 2 1 2 1 201000 r 74 goat snp52638-scaffold787-155235 22 59487565 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601516 Affx-1002479753 AX-413835931 22 57114098 CAGAGGATGAGATGGATAGACTGCATTACCGACTC[A/G]ATGGACATGAGTTTGACTCTGGAGTCAAATTTCAG R 2 1 2 1 201000 f 74 goat 22_57114098_RH-map 22 57114098 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601636 Affx-1002479754 AX-413836035 22 57143638 GGCTTTCCTGGGTGGGAGAAGAGGGTGGACAGGGC[A/G]AGAAGAAACAGCCGAGGGCTTGTCCTCCTTGCTGT R 2 1 2 1 400000 r 74 goat 22_57143638_RH-map 22 57143638 A G Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38398715 Affx-122961844 AX-123269070 22 57145371 AAGCAGTAGGTACGAAGGGACTCCTGTGTCTTTAG[C/T]GCTGTGCCAGGCGGGGGTGTTTATTAGAGTCTGGG Y 2 1 2 1 101000 f 74 goat snp52639-scaffold787-209473 22 59545669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426621 Affx-122939960 AX-123296967 22 57178731 GTCTCCAGTTCAGTGGCATCGCATACGTTCACAGC[A/G]TGGTCCAGTCATCAGCTCCATCACCTCCAGAAGCT R 2 1 2 1 101000 f 74 goat snp52640-scaffold787-242833 22 59579327 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601520 Affx-1002479755 AX-413835935 22 57179672 TTAGCTTTAGGCTTTATCGATTGACTTGCTACTTT[A/G]GAAGGCAAGGATTTAGCTCCCCCTGCAGCACTGCC R 2 1 2 1 101000 f 74 goat 22_57179672_RH-map 22 57179672 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601640 Affx-1002479756 AX-413836039 22 57203145 TGTTTTTACATCAGGTTCTCCATCCTCAGTTTGGT[C/T]TGGATTACTGAATACCCGAAGGGCCACCTCTAGGA Y 2 1 2 1 201000 r 74 goat 22_57203145_RH-map 22 57203145 C T 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38406182 Affx-122956151 AX-123276534 22 57208925 TCTTGCCTCTCACACAGCAAAACCCTTTACAACGA[C/T]GATCATGAAATAATAGTAATGAAGAAGGAGAGCGT Y 2 1 2 1 201000 r 74 goat snp52641-scaffold787-273027 22 59609044 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601525 Affx-1002479757 AX-413835939 22 57241001 AGCACCGAGAAAACCACAGTGAGAGAGTACACGAG[C/T]GGCTGGCAGGGCTGAGAGTGGGAGAAGGGGCAGTG Y 2 1 2 1 102000 f 74 goat 22_57241001_RH-map 22 57241001 T C 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38452788 Affx-122920239 AX-123323121 22 57255006 CCAAGTCTCTGCTTGGGTCAAGTTTGCAAGTGCTC[C/T]GCGGGCAGAGTGAGTCAGCCCAGAGGCGGTGGAGG Y 2 1 2 1 101000 f 74 goat snp52642-scaffold787-319108 22 59654946 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601643 Affx-1002479758 AX-413836042 22 57272527 ATAAACCAGTACACCGATTAAAAATTTTTAAAACA[A/G]TTGTGTGAAAGTGATAATAGCTGCAACAAACAAGA R 2 1 2 1 101000 r 74 goat 22_57272527_RH-map 22 57272527 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601529 Affx-1002479759 AX-413835943 22 57292939 TCAACAGGTCTGATCTTCTCATCAAAAATTTTGTT[C/T]ATGTTCTGTGGACTGGTAATTCTACTTCCAGGAAT Y 2 1 2 1 101000 f 74 goat 22_57292939_RH-map 22 57292939 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601532 Affx-1002479760 AX-413835945 22 57325047 CAGCACACACGGGATTAAGAGAATCAAATGTGCAA[A/G]AGACTAAGAGCCTGGGACTGGGAATCACACATTCA R 2 1 2 1 101000 f 74 goat 22_57325047_RH-map 22 57325047 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320781443 Affx-122973009 AX-385268528 22 57377331 GCTGGGCAGAATAGATGTAAATGGATATTTATTTA[C/T]TAAGATACAGAGACTCTCAAATTGGATTAAGACAC Y 2 1 2 1 201000 f 74 goat snp25681-scaffold2640-112045 22 59772052 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601534 Affx-1002479761 AX-413835948 22 57399187 TGGATGGATGGATGGGTGTATGGCTGGCTGGCTGG[A/C]TGAAGGGATGGATGGATGGATGGATGGATGGGTAG M 2 1 2 1 202000 f 74 goat 22_57399187_RH-map 22 57399187 C A 2 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38453419 Affx-122919886 AX-123323752 22 57414570 TTTATGTCTGGTATGTTTTTATCTTTTGTGACTGT[A/G]CTTTGCGAATGTCTGCCAGGAACAGCATTTAGCCT R 2 1 2 1 101000 r 74 goat snp25680-scaffold2640-74806 22 59806042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601536 Affx-1002479762 AX-185319174 22 57434765 TGAGATGGTTGGATGGCATCACTGACTCAATGGAC[A/G]TGGGTTTGGGTAAACTCTGGGAGTTGGTGATGGAC R 2 1 2 1 103000 f 74 goat 22_57434765_RH-map 22 57434765 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38417792 Affx-122947382 AX-123288140 22 57479905 CTGCTGATGTAAAACACACAGGATGTGAAATAGCT[C/T]ATGAAAATCGTGTATGTGGACATGTTTGAAGTGAT Y 2 1 2 1 101000 r 74 goat snp25679-scaffold2640-9471 22 59870818 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601539 Affx-1002479763 AX-186346407 22 57485311 ATGCCAAAGAATGCTCAAACTACCGCACAATTGCA[C/G]TCATCTCACACGCTAGCAAAGTAATGCTCAAAATT S 4 1 2 1 103000 f 74 goat 22_57485311_RH-map 22 57485311 C G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601541 Affx-1002479764 AX-314281011 22 57506891 CAGATGGTGACTACAGACATGAAATTAAAAGACAC[A/G]TGCTCCATGGAAGAAAAGCTATGACCAACCTAGAC R 2 1 2 1 103000 f 74 goat 22_57506891_RH-map 22 57506891 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601659 Affx-1002479765 AX-413836056 22 57525104 ATCCTGTCTGCCCTTTCAGTTCAAAATGTGAAACC[A/G]CACCCAGGATTCTAACTATCAGAGCAGAGGAACAT R 2 1 2 1 101000 r 74 goat 22_57525104_RH-map 22 57525104 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601661 Affx-1002479766 AX-413836058 22 57597634 CAGAGTTAGACACTGCTGAGTGGCTAACACACGCA[C/G]GTATTTCAGCTGGTAAGAACAGGAACCCCAGATAC S 4 1 2 1 201000 r 74 goat 22_57597634_RH-map 22 57597634 C G 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601663 Affx-1002479767 AX-413836060 22 57616381 AAGCTTACTAGTAAAACAGAATCCAAGCCCCACTC[C/T]GCCCACCAGAACTTCTTAAGTCAAAATCTGCATTT Y 2 1 2 1 101000 r 74 goat 22_57616381_RH-map 22 57616381 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601664 Affx-1002479768 AX-413836062 22 57637828 CTTTTTCTTTCACTTTGTGGGCAAAAGGACAACAG[A/G]TCTGCACATTAATTTTGCTTATAAAGGGAGTGGGG R 2 1 2 1 101000 r 74 goat 22_57637828_RH-map 22 57637828 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38432055 Affx-122935894 AX-123302396 22 57673240 GAGCAGATCTGCGGTTTTTTCTTACCCTGGCAGGG[C/T]CGTTCTCCAACATCTCCTCCTGGCTCTCTGCTGAC Y 2 1 2 1 201000 f 74 goat snp17685-scaffold1833-172589 22 60024624 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601666 Affx-1002479769 AX-413836063 22 57682531 CCGGCCAGGAGCGGGGCCTTGCATGCTGGAGACCA[C/T]ATCCTGTCCATCGACGGTACCAGCACTGAACACTG Y 2 1 2 1 101000 r 74 goat 22_57682531_RH-map 22 57682531 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601555 Affx-1002479770 AX-189203196 22 57697365 ATGCCCACTGGAAAAACCATAGCCTTGACTAGACA[G/T]ACCTTTCTTGATAAAGTAATGTCGCTGCTTTTGAA K 2 1 2 1 103000 f 74 goat 22_57697365_RH-map 22 57697365 G T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601670 Affx-1002479771 AX-413836067 22 57718009 TCCACCACAGAACAAGATCTCAGCATCCCTAATAC[C/T]GTAGGAATGTCAATCAAAAGAGCAAAGAGAATTCA Y 2 1 2 1 400000 r 74 goat 22_57718009_RH-map 22 57718009 T C Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38403848 Affx-122957936 AX-123274200 22 57771698 CGACGTGCCTTGAAGCACGCGTTGGCGTGCCAGGT[A/G]TGTCCGCTCGGGTGTGAGATGAAGTCAGACCCCAC R 2 1 2 1 101000 r 74 goat snp17686-scaffold1833-271047 22 60121167 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409540 Affx-122953608 AX-123279891 22 57818560 AGCAGGATCTGACTCCCTGCCTTGGTCACCGGCTT[A/G]TCGGCTCCCAGAGAGAAGTAAGTGGCCATCTCGTC R 2 1 2 1 101000 f 74 goat snp17687-scaffold1833-317909 22 60151175 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803568 Affx-986696404 AX-385290368 22 57829586 TTGTGAAAAATTTATTCATCAGATTCCCTTTGAGA[C/T]TGGGGTCTGTTGCACATTACTGTTGCTGTTCAAGT Y 2 1 2 1 600010 f 74 goat 22_57829586 22 57829586 Ancestral_priority_1043 ancestry 0.722 recommended IMAGE 10K 10K ancestral 350601560 Affx-1002479772 AX-185546808 22 57830577 GCAGATGGTGACTGCAGCCATGAAATTAAAAGACA[C/T]TTGCTTCTTGGAAGAAAAGTTATAACCAACCTAGA Y 2 1 2 1 103000 f 74 goat 22_57830577_RH-map 22 57830577 T C 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38409059 Affx-122953352 AX-123279410 22 57862564 CATTCATCCAGGCAGCAACTTTCCATCTCCAGCCG[C/T]GAAAACAGACAGACAGAAGGCCCCTGCCCCAGCGG Y 2 1 2 1 101000 f 74 goat snp17688-scaffold1833-361913 22 60193727 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601562 Affx-1002479773 AX-413835968 22 57879226 CCTAGAGAAGATAGGGGACACTTTCAAGGCCAACC[A/G]GGCTAATTCAGGGTCAGGCTTGGGATGGGGTTGAC R 2 1 2 1 101000 f 74 goat 22_57879226_RH-map 22 57879226 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601675 Affx-1002479774 AX-413836072 22 57917430 CACGGCTGCCATTCAGCAGGCTCCCTGCACATCCC[C/T]GAGGGTCCCTTTTGACTCTGCCATTTCCCGAGGCA Y 2 1 2 1 102000 r 74 goat 22_57917430_RH-map 22 57917430 T C 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601677 Affx-1002479775 AX-413836074 22 57942182 AATTTCGGATGATGATAGGTGCTTTGAAAAAAAAA[A/T]AATAAAGCAGATTAAAGGCACAGAAAGTTCGGAGG W 4 1 2 1 400000 r 74 goat 22_57942182_RH-map 22 57942182 A T Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468271966 Affx-1111833251 AX-519545738 22 58331321 GGACCTGATACCGCAAGGGGGCCCGCCTGGGTGAA[A/G]TTGTGTGCCAAGTGCAGCGAGGCTCCACTTCCTCG R 2 1 2 1 102000 r 74 goat 22_58331321_AF-PAKI 22 58331321 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468277482 Affx-1111835933 AX-519550985 22 59574735 AAGCTTGAGTGTCAGGCCTCCGTAAGCATCATGGC[A/G]GTGATGACTGCGGCTAATCAGGGAAAGCGGCCTCC R 2 1 2 1 102000 f 74 goat Random2.2K-2022 22 59574735 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390785 Affx-122967878 AX-123261142 23 24084 GCCATCGTGTTTTGAATCGGTCCTCGGGGTGTACC[A/G]TTGAATCAGTGCAGGGGAGTCAGGTGTGTCTGGAG R 2 1 2 1 303000 f 74 goat snp37292-scaffold455-24084 23 48834655 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439089 Affx-122931124 AX-123309426 23 70883 CTTTGACAAGGTCATGAGGGAAGAAGTTGACATAC[G/T]CAAGAACGTGATCAGACTTCAGGAGTTCCCCCTGG K 2 1 2 1 101000 f 74 goat snp37293-scaffold455-70883 23 48787355 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417060 Affx-122947514 AX-123287408 23 107778 CAACAAATGAAACAAAAAGCCCAAAACAGTATTAA[A/G]AATGCTAACTGAATTAGGGGAAATGTAGATGAATA R 2 1 2 1 303000 f 74 goat snp37294-scaffold455-107778 23 48750219 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397116 Affx-122962688 AX-123267471 23 165591 AATTCTTGAGTGGGTTGGAATTTTCCAGCCAAGAA[C/T]ATTGCAATTGGTTGCTATTTCCTAGCAGCACCTTA Y 2 1 2 1 101000 f 74 goat snp37295-scaffold455-165591 23 48690977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410235 Affx-122952549 AX-123280585 23 225596 TCAGTAACTGCAGCTTGAATTGCTACACATCTAGT[C/T]TTTTTTTCCCCTTACAACTTCACAGATATTAAAAG Y 2 1 2 1 303000 r 74 goat snp37296-scaffold455-225596 23 48630155 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402152 Affx-122958653 AX-123272505 23 265473 GGTTTTTGCTTGTTGTTGATATCTAATCTCATAGC[A/G]TTGTATTTGAAAAAGTGCCCAGTATAATTTCAGTT R 2 1 2 1 201000 r 74 goat snp37297-scaffold455-265473 23 48589087 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451448 Affx-122921158 AX-123321781 23 296340 TTTCTATTTTTAAGTTTTTCCCAAATCTCCATATC[A/G]TTTCCCATAGAGGCTAAACTAACCTACATTTCCAC R 2 1 2 1 101000 r 74 goat snp37298-scaffold455-296340 23 48557356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765978 Affx-122969650 AX-385253402 23 363472 CACTTTTTAAGGTGTCAGTTAAAGTAATGCTTGTG[C/T]AAATTCTGAGTTGGGAACCTGTTTGAGTAGAACTT Y 2 1 2 1 101000 f 74 goat snp37299-scaffold455-363472 23 48489792 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428367 Affx-122938971 AX-123298710 23 423994 GAGAAGCTTCATAGCAGTCAGAGACTGGGTCAAAG[G/T]CAAAGAGACTAGCTTGGTCCTGCACCAATGTGGAA K 2 1 2 1 101000 r 74 goat snp37300-scaffold455-423994 23 48430241 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452791 Affx-122920237 AX-123323124 23 537596 TTATTTACCAAAGTGATTATTTTCTTTGTGTATAT[A/G]CAGTGCCATAGTCCTGGTGGTTGAGTAACCAAAAC R 2 1 2 1 101000 r 74 goat snp37302-scaffold455-537596 23 48324920 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385589 Affx-122971210 AX-123255947 23 588159 CTTCTCCACACTTAGATGTGGCGCCAGCCATTGTT[A/G]CCCCATAGGTTTGTTTGCTTAAGTTCAACTGCTAA R 2 1 2 1 101000 r 74 goat snp37303-scaffold455-588159 23 48272930 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781186 Affx-122926736 AX-385268271 23 626569 GCCCTAAGAGTGATTATCAGTAGATCTTCTGATCA[A/G]TCCTGAAGAGTTTGGTACACTGATGGGAGCATCTT R 2 1 2 1 101000 r 74 goat snp37304-scaffold455-626569 23 48233893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802294 Affx-122939126 AX-385289198 23 664274 CTCAGTCAGGCTGATGAGAGGGAGGGGTATGGCAC[C/T]TTTAGTTATGGTGTTTAGGGAGTGCCTATTGTGTC Y 2 1 2 1 202000 f 74 goat snp37305-scaffold455-664274 23 48195567 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385942 Affx-122971554 AX-123256300 23 729229 ACTCTTTTTTAAAAGATCAGTTTGACTACTGTGTT[A/G]TGAAGAGATGTAGACATACAGGAAAAGAGCAAGGA R 2 1 2 1 101000 r 74 goat snp37307-scaffold455-729229 23 48129603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277608 Affx-1111835934 AX-519551107 23 794101 CTGATCAGCAGTTTAACACAGGGCTACATGGAGCC[A/G]GAAATAAATGCGGGAAAACGAGTGAATTTATTTTT R 2 1 2 1 101000 r 74 goat Random2.2K-2023 23 794101 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38398780 Affx-122961428 AX-123269135 23 808285 ACCCTCTGAGGAGCTGTTCCTCATGCTGGAGACCT[A/G]TACAAGGACAAACTTCCACGCTTCCAGCCCCTACA R 2 1 2 1 201000 r 74 goat snp37308-scaffold455-808285 23 48052343 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273059 Affx-1111833267 AX-519546730 23 833685 AACCCCACGGGGGTCAGATACGCAGAAGTTGAGAG[A/G]GAAGGCTGCGGTTGAAATGGCACCTTGGGCTCCAT R 2 1 2 1 202000 r 74 goat 23_833685_AF-PAKI 23 833685 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38444477 Affx-122926531 AX-123314814 23 854383 ACAGTTCACAGGATCACACCACACTACATGTGCTA[C/T]GGCTTAAAGAACACAGCAAATACAGTTCAGGCTGA Y 2 1 2 1 101000 f 74 goat snp37309-scaffold455-854383 23 48006179 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388382 Affx-122969309 AX-123258740 23 916941 TTGTGCATGTGGCTCTTCCTTGCCAAATTCAGGAC[A/G]ATTTTAATAGGAAGAGAACAATGGAAGGAACAGAG R 2 1 2 1 201000 r 74 goat snp37310-scaffold455-916941 23 47942175 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799374 Affx-122939302 AX-385286304 23 946505 AACAGTAAATGTAGTTTTAAAGGGAAGAGAATAAA[C/T]ATTTTAAGTTGTGAAACTAGTAAGATTTCTATGGA Y 2 1 2 1 201000 f 74 goat snp37311-scaffold455-946505 23 47911847 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425021 Affx-122941880 AX-123295367 23 996497 AATGTACTGAATTCTGAAATATGGCTTGTAGAAAG[C/T]AAAATAAAGATAAATTTAAGTTTCCTGCAAGGCAA Y 2 1 2 1 201000 f 74 goat snp37312-scaffold455-996497 23 47861705 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398872 Affx-122961042 AX-123269227 23 1032389 GATTTGACAGAGAAACCAAAAGCTACACAGATAAG[C/T]AGAATTTAAAAGAACTCAGCACCACCACAAAGGAA Y 2 1 2 1 101000 f 74 goat snp37313-scaffold455-1032389 23 47825621 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784563 Affx-122943082 AX-385271612 23 1068702 TTCCTCATCTGGAAAAGAGAAACCACACCAATTCC[G/T]CCCTTATGGATTACTTGATGAATGATGATGATAAA K 2 1 2 1 101000 f 74 goat snp37314-scaffold455-1068702 23 47788434 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601569 Affx-1002479776 AX-413835974 23 1079767 TGATGCTTCCTAGGGCGCATTTGACTTCACATTCC[A/C]GGATGTCTGACTCTAGATGAGTGACCCAGGTCATT M 2 1 2 1 303000 f 74 goat 23_1079767_RH-map 23 1079767 A C 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38419382 Affx-122945618 AX-123289730 23 1111365 AAGAGCTGTCATTTATGAAGCAGTTATGTGTCACT[C/T]TCTGTGGAAGACAGTTTTCCTGTATTATTTCATAT Y 2 1 2 1 103000 f 74 goat snp37315-scaffold455-1111365 23 47742603 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793545 Affx-122944259 AX-180660642 23 1220426 TACTCTGTAACTAAAGCACACTAACCAAGATATTT[A/C]TTAATTAAGAAGTACTCCCTGTATTTATGTATTTA M 2 1 2 1 101000 f 74 goat snp37317-scaffold455-1220426 23 47630909 G T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273743 Affx-1111833784 AX-519547354 23 1236732 GCCCCACGCTTCAGGCTGTCCCAGCGAGAGGCCCC[A/G]GGTGGGACGGCCCGGGAGGGCAGGGCCCAGGGTCT R 2 1 2 1 202000 r 74 goat GoatD01.004793 23 1236732 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802987 Affx-122958928 AX-385289870 23 1291363 ACTGTCAGTTTGATGACTTTGTACTATTTACAATA[A/G]ACTCAGCATCATTCTGGCTTATGGGACAATTGACT R 2 1 2 1 101000 r 74 goat snp37318-scaffold455-1291363 23 47559221 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601681 Affx-1002479777 AX-413836078 23 1321870 TAGTCCCTGCTTTCAGTTCTTCTGGGTGGAACTGC[C/T]GAGTCATACGGTGCTCATGGTTGTGGGGAAAACAC Y 2 1 2 1 102000 r 74 goat 23_1321870_RH-map 23 1321870 C T 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38423451 Affx-122942592 AX-123293797 23 1323791 TAGAGATTCCCACTATTTCAACTGTTTCAGTGCTC[C/T]AAAGCAGGGTTGCTGGGGGACTGAGCACTGAATGT Y 2 1 2 1 101000 f 74 goat snp37319-scaffold455-1323791 23 47526079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774550 Affx-122935013 AX-385261684 23 1389800 ATGGAGGAAGATGCTATTGCCTAGAGAAGCCAATT[A/C]TGACTCCATATTCGAATTGTTTCTTTGACTTTGCT M 2 1 2 1 101000 f 74 goat snp23987-scaffold2438-303016 23 47445239 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601574 Affx-1002479778 AX-185342247 23 1396984 GAATACACAGAAGAACTGTACAAAAAAGATCTTCA[C/T]GACCCAGATAATCATGATGATGTGATCACTGATCT Y 2 1 2 1 303000 f 74 goat 23_1396984_RH-map 23 1396984 C T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601684 Affx-1002479779 AX-413836080 23 1417518 GAAAGATTCCTACAGTGGATTTTTATAAAGCTCTT[C/T]GAGCTTCTTTCAAGGGAACAGCCTCGTAAAAGTAA Y 2 1 2 1 101000 r 74 goat 23_1417518_RH-map 23 1417518 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38444643 Affx-122926922 AX-123314980 23 1420752 CTTTGAGGTGGTTGCTTCCTTCTTCACAAAGTCAA[G/T]CACAGGGGTTCCTCTGGACTGAAGGCCATTTCCCA K 2 1 2 1 201000 f 74 goat snp23986-scaffold2438-272064 23 47412666 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376456 Affx-122978054 AX-123246815 23 1450974 TCAGTGTCAGGGCACAGAGACTGGATTTGGCATCA[A/G]TTTCTGAATTTTCTTCAAAGGGAATTGCTCTGTGC R 2 1 2 1 201000 r 74 goat snp23985-scaffold2438-241842 23 47377508 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773676 Affx-122922706 AX-385260816 23 1488992 TTGGGGAGTGCAGGGTGATGATATTGATCCTCTGT[A/G]AAGTTTAATCTCTGCTATGCCTTACACAAACTATT R 2 1 2 1 101000 f 74 goat snp23984-scaffold2438-203824 23 47338497 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784187 Affx-122934843 AX-385271238 23 1530908 GGGTTTTTAAAAAGCTTCAGTGTCCAAGTTTGTCA[C/T]GCATATAAAGAAACAAAAGTCATGTTTGTAAGTTA Y 2 1 2 1 202000 r 74 goat snp23983-scaffold2438-161908 23 47294924 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433980 Affx-122934256 AX-123304321 23 1560629 ACTTTTCTTCAAAAGTATTCCTATTGAGGAATTCA[G/T]ACCTTTGATAATGGTTGATAAAAATTGTTTCTCTA K 2 1 2 1 101000 r 74 goat snp23982-scaffold2438-132187 23 47265209 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601578 Affx-1002479780 AX-413835982 23 1588332 ACATGTGTTCTGATGTGTTTCACATGTGATGAGAA[C/T]ACCAGAAGTGCTCAGAGGTATTTCCTAGGTGTTTT Y 2 1 2 1 400000 f 74 goat 23_1588332_RH-map 23 1588332 T C Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320787817 Affx-122925606 AX-385274840 23 1589950 ATTTATTATTGCAACAGCTATTGTACATGTTTAAG[A/G]CGCAGATTTCTGTAGCTGCTATACTGAGGTCAATG R 2 1 2 1 101000 r 74 goat snp23981-scaffold2438-102866 23 47234899 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767144 Affx-986698372 AX-385254429 23 1608115 GAATTGTTTATTGTGTATGACAAGTGGTTCTTTTG[C/T]TGATGAATCCTTCGAACCTGAAACGAAAGTAAAAC Y 2 1 2 1 600010 r 74 goat 23_1608115 23 1608115 Ancestral_priority_1043 ancestry 0.622 recommended IMAGE 10K 10K ancestral 320763846 Affx-986698374 AX-385251640 23 1615102 GCCTCAGAAACAAGAAGGGAGGCAGACATAATTCA[C/G]AAGCAATATTCAAATTCAAAATCAGAGTTTCACAC S 4 1 2 1 600010 f 74 goat 23_1615102 23 1615102 Ancestral_priority_1043 ancestry 0.532 neutral IMAGE 10K 10K ancestral 320767151 Affx-986698376 AX-385254436 23 1615477 GACGTGAAAGGGGCCCAATTTCGTGTCCAGCCAGC[A/G]TTGCTCACAGGCAGCACCGCTGACAAGTGGGGTCC R 2 1 2 1 600010 r 74 goat 23_1615477 23 1615477 Ancestral_priority_1043 ancestry 0.454 neutral IMAGE 10K 10K ancestral 320767158 Affx-986698380 AX-385254443 23 1616962 TCTCTGACGCTGTTTTTTTTATAATCCAACTCTCA[C/T]ATCCATACGTGATTCTGCAGTTTTGAGACTGCTCC Y 2 1 2 1 600010 r 74 goat 23_1616962 23 1616962 Ancestral_priority_1043 ancestry 0.552 neutral IMAGE 10K 10K ancestral 320797700 Affx-122943093 AX-385284639 23 1628357 ATCTTGTTGTCTGGAGTAGATCTGTTTTAAGGCCA[A/G]TCTGGATTATATCTTTCTTAGTGGCTGCCTGCTTC R 2 1 2 1 101000 f 74 goat snp23980-scaffold2438-64459 23 47197009 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448987 Affx-122923111 AX-123319322 23 1685425 CAAATATATGAGCTTTGTTGTAACTTCATTTTTGA[C/T]ATTGTTCTTTTAGGATTTTTATTTGTTCTTCAAAA Y 2 1 2 1 101000 f 74 goat snp23979-scaffold2438-7391 23 47139319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426370 Affx-122940248 AX-123296716 23 1707323 TTTTACTCAATAGAAATCAGCAAATGCCACAAATC[A/G]TGGCTCTACAGTCCCTCAAAGCCAGGCAAAGATCA R 2 1 2 1 202000 r 74 goat snp29279-scaffold3157-14408 23 46715707 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435626 Affx-122933776 AX-123305966 23 1737585 CAGAAATAGCTCTCCATTATCTCCATTGTATTACT[C/T]GGTAAATTTAGCAGAAAGAAGGGGATGGAAAAATA Y 2 1 2 1 101000 f 74 goat snp29280-scaffold3157-44670 23 46685190 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793921 Affx-122959897 AX-385280890 23 1774036 TCTGTTTTGTGTTTACTAAAATTCTCTCTCCCAAA[C/T]GAGTCAAACTGCTTTGCATGTAGACATGGAATATG Y 2 1 2 1 101000 r 74 goat snp29281-scaffold3157-81121 23 46651056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403251 Affx-122957880 AX-123273604 23 1807092 GAGTTGGACACAACTTAGCAACTGAGTGATAACAA[C/T]AAGACCTAGGATTTCAGCTCTGTGAGGCCCATCAA Y 2 1 2 1 201000 r 74 goat snp29282-scaffold3157-114177 23 46618179 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601688 Affx-1002479781 AX-413836085 23 1883320 TTGAGGGACCGTCCCTCATCCCTAAGTGCTCTCAT[A/G]ACAAAGCTCAACTCTTTCCAGCTCCTGGGAGCCCA R 2 1 2 1 102000 r 74 goat 23_1883320_RH-map 23 1883320 A G 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38419250 Affx-122946269 AX-123289598 23 1894250 TGTTTCCCAAAATTTGCTTGGCTGATGTCATTGTG[C/T]CATTAGGCCTGAGGTTGACCCTCATCACTTTAGGC Y 2 1 2 1 201000 r 74 goat snp48759-scaffold692-1142193 23 46515146 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601690 Affx-1002479782 AX-413836086 23 1897836 ATTGATAACAATTGAAACAGAAAACATAAATGCTG[C/T]CATATTTCACGGACTGTGAGTCTCCACCAGCGTAA Y 2 1 2 1 101000 r 74 goat 23_1897836_RH-map 23 1897836 T C 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38376230 Affx-122978791 AX-123246589 23 1930295 GATCTGGATTTGAGTTTGAGGTCACTACTTCCTAG[C/T]GGCTTACCTAGTGGCTCAGATGGTAAAGAATCTGT Y 2 1 2 1 101000 f 74 goat snp48758-scaffold692-1106148 23 46479498 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601692 Affx-1002479783 AX-413836088 23 1932745 TGCTTTCCTCTTTTAGCTTCTTTCCACCACCTCTG[C/G]AGACAAGCTTGCCAGCTACCAAAACAAAATGTTTC S 4 1 2 1 201000 r 74 goat 23_1932745_RH-map 23 1932745 G C 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38445649 Affx-122926157 AX-123315986 23 1968464 TGGAGGCTCCATTGGAGGACCTGGGTGGTGTGAGC[C/T]GTATGCATTCTAATGCTTTGCTGCAGATGCAGGCA Y 2 1 2 1 101000 r 74 goat snp48757-scaffold692-1067979 23 46439847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431217 Affx-122937153 AX-123301558 23 2024900 CTTGAGCGTTTGGAAGCCTCCTCTTTCTCTCAGGC[A/G]TCAGCATCATATGCTCGTGGGTGAGGGCTGGGAGG R 2 1 2 1 102000 f 74 goat snp48756-scaffold692-1011543 23 46382579 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434944 Affx-122933859 AX-123305284 23 2060615 TTGTTCCTGTTCTTCATTCTCTGATCATCCTCCAC[A/G]CTAATCAGTGGGCAAGGCTGAGAGATTATCAGGTG R 2 1 2 1 201000 r 74 goat snp48755-scaffold692-975828 23 46351526 C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453032 Affx-122920087 AX-123323365 23 2116603 AAATGCACAAGGAATTGTGTGTTAGATTCCCAACT[A/G]CTCCTCCCCTGCCCCCTTGAAACACTTCCATAGAT R 2 1 2 1 101000 f 74 goat snp48754-scaffold692-919840 23 46295253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435906 Affx-122932768 AX-123306245 23 2207452 AGGAAGTACCAGGGGGAAAACCTGAGATCTGACTC[A/G]CCTTGCCCATCAGATCTCTGCCGCATGACCTTGTC R 2 1 2 1 103000 f 74 goat snp48753-scaffold692-828991 23 46202465 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423804 Affx-122942811 AX-123294150 23 2237488 AGTTAATCCTGCTTTACCTGAATGTACAGAACTTG[A/G]TAGCTGTTGAGGGCATATCCCTGAGCTTTGTTTCT R 2 1 2 1 101000 r 74 goat snp48752-scaffold692-798955 23 46171402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790438 Affx-122926461 AX-385277441 23 2283162 CTCAGGAAGGCAGGCTTGCAGGTAAAAACAAAGAC[A/G]TCCAGTGTATTGTGCTTTGTCAAAAGAGAAGAGGA R 2 1 2 1 101000 f 74 goat snp48751-scaffold692-753281 23 46124838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436662 Affx-122932472 AX-123307000 23 2338506 TTGAGTAATTTAGTAACTAAGCATTTAATGGGGGC[A/G]CTGTGTATTAAATGCTTATTGGCATGCGTTCTGGT R 2 1 2 1 101000 r 74 goat snp48750-scaffold692-697937 23 46069366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425778 Affx-122940717 AX-123296124 23 2393549 TTCATGGCAGCACTATTTGTTCCTTTTTCTTTTAC[C/T]TTAATTGCCTTCCTTTCTCTGTCTGTTGCTGCTAC Y 2 1 2 1 101000 r 74 goat snp48749-scaffold692-642894 23 46013863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778296 Affx-122923302 AX-385265411 23 2455555 TCTGTGATTTCATAGGCCACAATGGCTTGTGGAAA[C/T]GACCGCGGTATTATTCTGTAATGCTTCTTAAGTTT Y 2 1 2 1 201000 r 74 goat snp48747-scaffold692-580888 23 45951779 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434368 Affx-122934708 AX-123304709 23 2514510 GCTATAATCCCAAAGAAAGGGAGTAGCAATTTGCA[C/T]TTATAGGCTTTTCTAACAGTTGTGATAAGTACATT Y 2 1 2 1 201000 r 74 goat snp48746-scaffold692-521933 23 45892911 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388637 Affx-122969121 AX-123258995 23 2549701 CTAAATGTTACAGGTTGTGCTTATCTCTAACTTGT[A/G]CTGCCTTACTTTCCATAAGCCTGGTTTTCTATGCC R 2 1 2 1 101000 r 74 goat snp48745-scaffold692-486742 23 45858037 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375591 Affx-122978730 AX-123245950 23 2585007 CTGGTGCAGGAGGGCCGACAGGTATTGTACTCATC[A/G]TAGGAAATCCCAGGATAACATCAGAAACCAGTGGT R 2 1 2 1 101000 r 74 goat snp48744-scaffold692-451436 23 45822079 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414756 Affx-122949252 AX-123285105 23 2668144 ACATCTCTGAAGGGCCATGAGCTCCAGAGCTCCCC[A/G]TGGGACTGGCTGAAGCCTCAGTTGCATCTAACCGA R 2 1 2 1 201000 r 74 goat snp48742-scaffold692-368299 23 45740359 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791240 Affx-122936837 AX-385278234 23 2701424 GTTTTGTCAGTTCTCTCCAAAAATGTGTAAAACTC[A/G]TTTATAAAAAGGCAAACAGCACAAGTAGATTTATG R 2 1 2 1 102000 f 74 goat snp48741-scaffold692-335019 23 45707395 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408680 Affx-122953450 AX-123279031 23 2796836 TTCCTCCTGAGAGGTTACTGTCCACATTGCAACCA[G/T]GTCTTTGTGGATGAAACCAGTACCTGGAATCACAA K 2 1 2 1 101000 r 74 goat snp48739-scaffold692-239607 23 45611823 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414480 Affx-122949552 AX-123284829 23 2842127 AGACCTGTTCTGGAATACATTGACCTGGTCAGCAG[C/T]GATGATGATGAGCCCAGCACCTCTCAACGTGAGGT Y 2 1 2 1 101000 r 74 goat snp48738-scaffold692-194316 23 45566326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422252 Affx-122944003 AX-123292598 23 2878129 CATCCTCTCTGTATATTGCCATATATGTAAACACC[A/G]AACTAAACACAATATTGTTTATTGATGCTTTTGAA R 2 1 2 1 101000 f 74 goat snp48737-scaffold692-158314 23 45530320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439464 Affx-122930171 AX-123309801 23 2911090 GGGTACAGACCCTGGGGAGGTCCCTGAGGTCCATC[A/G]CTGGGGCCGCACTTACAACACTTAATAGAGAACAA R 2 1 2 1 101000 r 74 goat snp48736-scaffold692-125353 23 45498165 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396447 Affx-122962981 AX-123266802 23 2950224 CAAGGCTTCTGCAGCATCAAATCATTCTCTCCTCC[A/G]TCAGCATCACATCACGTCAGTGACCACCCGCATCC R 2 1 2 1 201000 r 74 goat snp48735-scaffold692-86219 23 45459002 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277610 Affx-1111835935 AX-519551109 23 2970435 CTATGTTTTTCTTACTCTCTGTTTGTTTATTGCCT[A/G]TTGCCCTTCATGAGAATGCAGACAGTTAACCGTTC R 2 1 2 1 101000 r 74 goat Random2.2K-2024 23 2970435 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434433 Affx-122934662 AX-123304774 23 2986741 GTGACCCTGGAAACTAAAGTGCTGAGACACAGAGC[A/G]CTGCCCAGAGGCACTCAGTCCAGAGAGGACACAAA R 2 1 2 1 103000 f 74 goat snp48734-scaffold692-49702 23 45422367 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440551 Affx-122929317 AX-123310888 23 3030940 TCAGCTGTACAAGCACACGTCCTTCAATTAGTAAG[C/T]CAGGGCGTTCTCAGCATCTGCAACTTGTAATTACC Y 2 1 2 1 101000 f 74 goat snp48733-scaffold692-5503 23 45378164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791836 Affx-122944436 AX-385278826 23 3057244 AGTCATTGCCCAGAGATATCTGCTGTTTACACTCT[A/G]GTAGATAGTTACCTATCTGCCTATTTATCTATAAA R 2 1 2 1 101000 f 74 goat snp23620-scaffold2385-20702 23 45352364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391993 Affx-122966501 AX-123262350 23 3138702 CTCGCTGGAATATTCCTCGCTTTATGTGTAAGTCA[G/T]TGCCCCATGCGCTTGCCGGCCAGAGCGGGAGCCTC K 2 1 2 1 101000 f 74 goat snp23622-scaffold2385-102160 23 45271069 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424805 Affx-122941382 AX-123295151 23 3173757 GTCAAAGAGGCAGGTTCCCTGTTGCCAAATGTTTG[C/T]TGTTTGGAATTACTGTTTGCAGTTTCTATTCAAGC Y 2 1 2 1 101000 r 74 goat snp23623-scaffold2385-137215 23 45235765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277611 Affx-1111835936 AX-519551110 23 3179662 AATATATACCATTAGTGAAGTTCAGGTCCACTTCA[A/G]CACATGTCCTTTCATGCAAGGGGTTTCAACACAGA R 2 1 2 1 102000 r 74 goat Random2.2K-2025 23 3179662 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447023 Affx-122924542 AX-123317359 23 3204120 GGCGCTGGTGGTCAGATCGTGTTTTGACACAGCAC[A/G]TGTGCACAGTCCCTCACGTGTGAGTGGGGCTGTTT R 2 1 2 1 101000 f 74 goat snp23624-scaffold2385-167578 23 45204587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785327 Affx-122974394 AX-385272372 23 3246845 TTTTCTTGCATTGAAAAGACATTTCAAGACTATAT[C/T]CTGGGTTAAGTTTATGACACTGTTTTACAGAAACG Y 2 1 2 1 101000 r 74 goat snp23625-scaffold2385-210303 23 45161791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409165 Affx-122953202 AX-123279516 23 3281515 AGTATATGACTCTTCCAGGTGCCAGATTAATTGTC[A/G]CAGGCTCAGGAGCAGGACTTCTGGCATCTCAGATG R 2 1 2 1 101000 f 74 goat snp23626-scaffold2385-244973 23 45126749 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392878 Affx-122965744 AX-123263235 23 3323563 GAACAAGTTTCATCTTGAATCATGACACATTACTT[A/G]TCCCTTTTCCATGTTGGAACTAACAACGGGATCTC R 2 1 2 1 101000 f 74 goat snp23627-scaffold2385-287021 23 45085138 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790047 Affx-122968397 AX-385277053 23 3354205 TTTTTATAAAACCATGATCACTTTTTCATAAATTC[A/G]TTCATTAAGAGACATTTATATGCTAGGTCAGCTAT R 2 1 2 1 101000 r 74 goat snp23628-scaffold2385-317663 23 45053563 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400794 Affx-122959824 AX-123271149 23 3396787 GTAAACAGTCTGGTCTGCTCAGCGGCTTCCCCATC[G/T]CGGAGCCCGTCACAACAAACACTGCAGCTCTTGAC K 2 1 2 1 101000 r 74 goat snp6313-scaffold1222-497357 23 45010508 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273000 Affx-1111833261 AX-519546681 23 3405353 ACAAGTTTTTGTAAGGAATTTCCATACTGCTTGCC[A/G]TACTGACGGTATCAATCTACATTCCCACCAACACC R 2 1 2 1 303000 f 74 goat 23_3405353_AF-PAKI 23 3405353 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320770499 Affx-122924558 AX-385257664 23 3454995 TGTGTGTTTTCTTTTAACAGTTAATCCTGGAATCA[C/T]AATGGAATGATTCTTGGAGAGTAAAGATGCTACGA Y 2 1 2 1 101000 r 74 goat snp6312-scaffold1222-439149 23 44953187 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776810 Affx-122941948 AX-385263934 23 3512124 CCCAGCTCTGAACTCACAGGAGATGTCTATGAAGA[G/T]GAAATTCGGACCCCACTCTTCATACAGTCCCTACT K 2 1 2 1 101000 r 74 goat snp6311-scaffold1222-382020 23 44894440 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423978 Affx-122942126 AX-123294324 23 3543009 TAACACTGTGAGTCTCCAAGAGGAAACTCTAACTT[A/G]CAGTATATTTTCCAAATTTATCTTACAATGGAGGG R 2 1 2 1 101000 f 74 goat snp6310-scaffold1222-351135 23 44863054 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411287 Affx-122952303 AX-123281637 23 3577407 GCAGCCACTCATAAGGGAGGACTGCTGAGGTTTGC[A/G]TGGGAAAGGCAGGCTTTTCAAAAGACATACAGGAA R 2 1 2 1 101000 r 74 goat snp6309-scaffold1222-316737 23 44827914 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402851 Affx-122958248 AX-123273204 23 3680715 CATATTTCTTGCATAAAGCTCCTAAATCCTTGAGA[C/T]GAGAGTGACATAAATGTTTTTGTTATGTGACTTTG Y 2 1 2 1 101000 f 74 goat snp6306-scaffold1222-213429 23 44723283 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779327 Affx-122975649 AX-385266431 23 3736587 TAGAAAATATTTGTCAATCATTCCCTTTATTACTA[C/T]ACAAAATAAGAATATGCTGTATCCACTTACTAGGC Y 2 1 2 1 101000 r 74 goat snp6305-scaffold1222-157557 23 44667216 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434877 Affx-122934352 AX-123305218 23 3779602 TGATTGACAGATTTGTGCTCAGCCGGAAACACTAC[A/G]CACCCTCTCTGCTTCAGTGACCATTTCTACAGAAG R 2 1 2 1 101000 f 74 goat snp6304-scaffold1222-114542 23 44624452 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277614 Affx-1111835937 AX-519551112 23 3799569 CTCAGACCCTTGATATTCTTGCCAGGATAGGAGCA[A/G]TCATTTTAATTTACAGAAATGCTGTTTACCACTTT R 2 1 2 1 201000 r 74 goat Random2.2K-2026 23 3799569 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422831 Affx-122943112 AX-123293177 23 3834696 GGGTCTGTGGCCGGAGAGGCATGGGAATTCGCATG[A/C]GGAGCACCAGGAATGCAACAAAGCTTTGAAAACAA M 2 1 2 1 101000 r 74 goat snp6303-scaffold1222-59448 23 44568162 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275205 Affx-1111834652 AX-519548784 23 3857555 GATTTTTTGC[A/G]CAATATACTAGCTGTAAATGCATAAAAAACCTGCA R 2 1 2 1 101000 r 74 goat GoatD01.044487 23 3857555 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320802268 Affx-122944458 AX-385289172 23 3886535 CAGCATCAAAAGGATCTGAGAAGATTTAACTTCTA[C/T]GATGATGAGGCTGAAATAAAACTTTGGCATGAGAA Y 2 1 2 1 101000 r 74 goat snp6302-scaffold1222-7609 23 44515611 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393820 Affx-122965570 AX-123264175 23 3910807 TCATAATGTGACCTCAGGCACACTCATCACATCCT[C/T]AAGTCCTGGGAGGCAACACAGTGAAGTGGAAAGAC Y 2 1 2 1 201000 f 74 goat snp15848-scaffold1666-170824 23 44484815 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801628 Affx-122954653 AX-385288536 23 3996980 TCTAATTTTCTGGTATAATTCTCCTTCTTTTTATT[A/C]GTTTGAATATGTTTCATATGTACAGTGAATAGTGT M 2 1 2 1 101000 f 74 goat snp15846-scaffold1666-84651 23 44397824 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787766 Affx-122965421 AX-385274789 23 4048762 CCTGTGGTAGACAAGATGCTGTATTGGAGAGATCC[A/G]CATGGTGAGGAATTGTGACTTATCCACATGGTAAG R 2 1 2 1 101000 f 74 goat snp15845-scaffold1666-32869 23 44345297 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38411417 Affx-122951838 AX-123281767 23 4078501 CTGTCTCTAGACTTGGAGTTGAGGTGCCCTTTGTC[A/G]TTCGTCTTTTTATTTTGACCTTTTTAAAATTGCTA R 2 1 2 1 101000 f 74 goat snp15844-scaffold1666-3130 23 44315437 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782529 Affx-122936930 AX-385269604 23 4088693 TTTTCATACAGCATTATTTCTATGATCCAAACCTG[C/T]AATTATTGCTAGTATTAATCAATATAGATGTGTTT Y 2 1 2 1 101000 f 74 goat snp50401-scaffold721-6963 23 44296440 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424597 Affx-122942204 AX-123294943 23 4146660 GATCTTCTGAGTTAAGAGTATCACGTTCTAAATGG[A/G]AACCTACAAGAAATTCAGTTTATGTGGTAAGTTTT R 2 1 2 1 101000 f 74 goat snp50402-scaffold721-64930 23 44237528 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434297 Affx-122934762 AX-123304638 23 4180738 TGGTGAATTTCAGCACAGTAATTTAACTTTTTAAA[C/T]AGAAACTTCACTGCTTAATATTTTGGCCAGGCTTG Y 2 1 2 1 303000 f 74 goat snp50403-scaffold721-99008 23 44203257 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764851 Affx-122934121 AX-385252450 23 4230514 GTATATACTTTTTCTAAAATTTAGTGGACTGCGTA[C/T]ATAAATCACTAATTGGATAGCACGTACATTCAAAA Y 2 1 2 1 101000 f 74 goat snp50404-scaffold721-148784 23 44153972 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786484 Affx-122937537 AX-385273518 23 4281559 GCAGAGTCTGGATCAGTGCCACCCACTCAAACAAA[C/T]AGAACATTTCTGCAGCAAAGCAATAAATATAAAGT Y 2 1 2 1 101000 f 74 goat snp50405-scaffold721-199829 23 44101809 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431395 Affx-122936545 AX-123301736 23 4322920 ACAGCAATTTTGGAATGAAAGCAAGATGGTCAAAA[C/T]AGGAATAGTTCTAAAAAAATTCTCATGGAAAGATT Y 2 1 2 1 201000 f 74 goat snp50406-scaffold721-241190 23 44060387 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408570 Affx-122953669 AX-123278921 23 4360501 CTTGAATATGTGCTGGTAGCTTTTATTTCAGTTTT[A/G]CTAGCTTTAAATAGCAATGCTTCAGCTTTTGTATT R 2 1 2 1 101000 r 74 goat snp50407-scaffold721-278771 23 44022904 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787775 Affx-122974305 AX-385274798 23 4402170 CAGGTTGACTTGAGAAAGAGGTCAAGGCAATTAGA[A/G]AATCATTTGAATTTTTTCACAAACTATTTGTAATT R 2 1 2 1 201000 r 74 goat snp50408-scaffold721-320440 23 43981144 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435074 Affx-122933727 AX-123305414 23 4433964 GCAGGGAAGGATATGGGCTTCTCCTTCTCAGGACC[A/G]TGGCGGGGATAGCTGTGTGCAGTGTGTGGGGAGGC R 2 1 2 1 101000 f 74 goat snp50409-scaffold721-352234 23 43948219 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419960 Affx-122945202 AX-123290308 23 4475496 ACCCAACTGACACAGCTGTGATACAACAATAACAA[C/T]GCCACTCATTTAGGTGGAGCTCACCTCTGCCCCAT Y 2 1 2 1 101000 f 74 goat snp50410-scaffold721-393766 23 43909928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435436 Affx-122933480 AX-123305776 23 4537422 AGGAATTCTGATCAGTAGCAGCTCTCGCTGTTCTT[C/T]GCTTCAGCTGTCTTTGGGGACACGCTGGGCTGGGT Y 2 1 2 1 101000 f 74 goat snp50411-scaffold721-455692 23 43847961 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449136 Affx-122923563 AX-123319471 23 4619681 GTGAGGAAGGGCAATCTAGGCATGGTGCTAGAGAT[A/G]TATTGATAGAAAGACTTAAGAATCCGACTGGAAAT R 2 1 2 1 101000 r 74 goat snp50413-scaffold721-537951 23 43765473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773194 Affx-122958126 AX-385260337 23 4652764 TCCATCTGTTTATTATTCTCTTTTAGAAAAACCAA[A/G]TCATTTACCTAATTTTTACAATAAAGCATTCTTTT R 2 1 2 1 101000 f 74 goat snp50414-scaffold721-571034 23 43732371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779007 Affx-122961828 AX-385266114 23 4693222 TTAAATTAGATGGTATTGAACAAGCTACATTCAAC[A/G]TGCATTTATAGGAAGCCTTAAGAGTGGATAAAACC R 2 1 2 1 101000 r 74 goat snp50415-scaffold721-611492 23 43691943 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777337 Affx-122940354 AX-385264459 23 4725481 ACCATAGTGGAGAGTTACAATGGGAAAGCAAGAAT[A/G]ATTTTGTACGCAAAAAGAAATGGCTTCCAGAAAGC R 2 1 2 1 101000 r 74 goat snp50416-scaffold721-643751 23 43659843 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422022 Affx-122943630 AX-123292369 23 4754572 AAATTCACAATAGAAGACATAAAATCTAATAAAAT[A/G]TCTCATATATAGCTGTAGGATTTTTCAATGTCTTG R 2 1 2 1 101000 r 74 goat snp50417-scaffold721-672842 23 43630507 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788290 Affx-122966140 AX-385275308 23 4796157 TATTGAAATATATGCAGACTCTGCTACCTTCTCAC[A/C]CTTCTACTTCTCTAGTCCAAGACACCACGCATTTC M 2 1 2 1 101000 r 74 goat snp50418-scaffold721-714427 23 43588972 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768054 Affx-122924901 AX-385255262 23 4845056 TTACAGGTTAGAAGAATGTGATTATGTTGTATCTT[A/G]TTCTTCAATGTTAAAATCTTTCCTTAGAGATGGAA R 2 1 2 1 101000 f 74 goat snp50419-scaffold721-763326 23 43539898 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404778 Affx-122956680 AX-123275130 23 4877098 CACTGCGGACTTGTTGGAAGAAGAGTCAGTCCACG[C/T]GTGAAATGCCTAATCTGGGCCCGGTGTATAAATGG Y 2 1 2 1 101000 r 74 goat snp50420-scaffold721-795368 23 43507645 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785951 Affx-122932477 AX-385272988 23 4957146 TCACAGTGAAGTAGGAATAACACATAGTTAAAGAA[C/T]AGTTACCATGTCAGATCTATTTTATGATTTGAAAT Y 2 1 2 1 101000 f 74 goat snp50422-scaffold721-875416 23 43427943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414539 Affx-122949506 AX-123284888 23 5008146 TGCAACCGAGGCTTTAAAGAGTATAGAACTTGTCA[A/G]CTTCCTGAAGGAGTATTAAATAAGTAACCAGAGTC R 2 1 2 1 101000 r 74 goat snp50423-scaffold721-926416 23 43376616 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797004 Affx-122927933 AX-385283945 23 5046247 GACAGAAGAATATTCCTAACCACTTCCAGTTCATT[A/G]CTACCCAATTCCCAATGATTTTTGCTCAAATAAAC R 2 1 2 1 101000 f 74 goat snp50424-scaffold721-964517 23 43336499 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775757 Affx-122961407 AX-385262888 23 5083270 TGATCTTCCGTCTCACTTGTTTCCATATTCAAATC[A/G]TTAATAAATTCCTTGGACTCCACCTGCAAAATAGG R 2 1 2 1 201000 r 74 goat snp50425-scaffold721-1001540 23 43299299 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425180 Affx-122941049 AX-123295526 23 5142500 TACAGCCCAGCAAGTCAAATCTCAAGACAGAAAAG[C/T]ACATATGGGCAGGAAAATACCTTGCTAGTCATTTG Y 2 1 2 1 101000 f 74 goat snp50426-scaffold721-1060770 23 43245100 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401111 Affx-122959403 AX-123271464 23 5179955 GCCAATACTTTGCAAATACTTCAGATATACAATGT[A/G]CTGAGCTATATAGTTTAAATTGTACTATTATTGCC R 2 1 2 1 101000 r 74 goat snp50427-scaffold721-1098225 23 43209572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394062 Affx-122964976 AX-123264417 23 5209302 GGGATGGCAAGGACTCTGATTTCTTACCCCACTGA[C/T]TCACCGAGATTATCTCCTGTTTTTCCCTTTAAGAA Y 2 1 2 1 101000 r 74 goat snp50428-scaffold721-1127572 23 43180210 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787264 Affx-122974246 AX-385274289 23 5242946 CTTCCATTGAAATAGTCTCTCAGTCTGGAAAGTGA[A/G]AGTTTTAAGCTGAGATGATTAATTAGGGTAAGTCT R 2 1 2 1 201000 r 74 goat snp50429-scaffold721-1161216 23 43146269 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425973 Affx-122941163 AX-123296319 23 5273997 ACTTGATAAAACACTGCACAGTGAAGCTTCAGTTT[A/G]TCCCACAAGTTACCCTGATACAAACCCAGATTATG R 2 1 2 1 101000 r 74 goat snp50430-scaffold721-1192267 23 43116389 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440053 Affx-122929748 AX-123310390 23 5323147 TTCTTCTCAGTCATTTTCACTGAGTCATTTTGTGA[C/T]GTTTGCAAGGTCCTAAGTTAAAGAATTGGCTACTA Y 2 1 2 1 101000 r 74 goat snp13289-scaffold1511-39359 23 43066579 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443024 Affx-122928164 AX-123313361 23 5364430 GTGGTGCTTAAAATATAGCTTCAGGAAACAACCAG[C/T]TGTGTTTCCAGGGGAGAATGAAGTTTGAATTCTAA Y 2 1 2 1 101000 f 74 goat snp13290-scaffold1511-80642 23 43024540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399226 Affx-122960593 AX-123269581 23 5398739 CAGGATGTTCAGAGAGGAAATTAAAAGAAAATATC[C/T]CAACAGAAATATGTTTGCTATTGTTAACATTAAAC Y 2 1 2 1 201000 r 74 goat snp13291-scaffold1511-114951 23 42991223 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391781 Affx-122967456 AX-123262138 23 5447068 TGACAGCATTTATCCTGATTTATTCTAATTAACCT[A/G]CTTATATTTTCCACTTCTACTCATGTTCCATACAA R 2 1 2 1 101000 r 74 goat snp13292-scaffold1511-163280 23 42943557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391684 Affx-122967588 AX-123262041 23 5483315 CTATACAAATTTCATTCATACATTCAATTATAAAA[C/T]AGTTTGCAAACATACTGTGTGCATGACATCAATCT Y 2 1 2 1 101000 r 74 goat snp13293-scaffold1511-199527 23 42906664 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429599 Affx-122937713 AX-123299940 23 5514762 CTCTTAATCAGTTTCATCTCCTTGACCCTGAGCCC[A/G]CAGCTTGATCCCTGCTTTTTTATCTGGGACCTATT R 2 1 2 1 101000 r 74 goat snp13294-scaffold1511-230974 23 42875193 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446480 Affx-122925057 AX-123316816 23 5569385 ACTGAGTGACTTTGTAAATGTGCTTGTGGTGGATG[C/T]TCCTGGAAGCCTGGTGATTTGCCTTAAGAGTCTCT Y 2 1 2 1 101000 f 74 goat snp13295-scaffold1511-285597 23 42822352 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774709 Affx-122928232 AX-385261843 23 5618176 TAAAACTTGTAAGCATTCACTACTTCATTTCAATA[C/T]AACCAAGTAATAATTGAGGCTCATCTCTGAGTCTG Y 2 1 2 1 201000 f 74 goat snp38859-scaffold493-35116 23 42756286 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449670 Affx-122922567 AX-123320005 23 5669531 GAACACAGACTACCTTATAGATTTCAGCTAGTGCC[A/G]TGAACTTGAGAACATTGCTCACTGCTCCATGACAA R 2 1 2 1 101000 f 74 goat snp38860-scaffold493-86471 23 42704763 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430624 Affx-122936966 AX-123300965 23 5710373 AATCAATAAATGTTCTATCTCATCCAAATTTGAAG[C/T]GGCTTTCTGTTTTGTGAAAACAAAAATGTCATGTG Y 2 1 2 1 201000 f 74 goat snp38861-scaffold493-127313 23 42663036 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781252 Affx-122936289 AX-385268337 23 5748163 TCTCTTCCTAGTGTTTTGGATTTTCCATTATATTT[C/T]CCTCTGTGTACTGCAACCTGGATATATTTTATTGC Y 2 1 2 1 101000 f 74 goat snp38862-scaffold493-165103 23 42624546 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398431 Affx-122961619 AX-123268786 23 5776783 TCTCTCTCCACCTGCTTGAAAACAGGAGCAGAGCA[C/T]GATATTTTTGCTATTTGTATTCTTTATGCCTAGCA Y 2 1 2 1 201000 r 74 goat snp38863-scaffold493-193723 23 42595574 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797787 Affx-122946333 AX-385284726 23 5825614 TCATTCCACTAACTTGCTGGTTATCACTTGTGCTA[C/T]GAATTTGGGATTTATAACAGTCCTATCATTAGAAA Y 2 1 2 1 101000 f 74 goat snp38864-scaffold493-242554 23 42546710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790450 Affx-122956752 AX-385277453 23 5883913 ATGGAATCTGTAAGATATGCTTGGTAACTAGCACC[A/G]TTACCAATGGTTCAGGATTCTCCCTGATCATTGCC R 2 1 2 1 101000 f 74 goat snp38865-scaffold493-300853 23 42488946 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272154 Affx-1111833266 AX-519545911 23 5918277 ACTTAGTGGTTCTGCCACATTCAAGAGAAAAAACC[A/G]AAAGGCACAAAGCCTTTTGAAGCTTTGGCTTGGAG R 2 1 2 1 101000 f 74 goat 23_5918277_AF-PAKI 23 5918277 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38432226 Affx-122936367 AX-123302567 23 5938398 GACGGTCATGGACCGACAGGACTGCGGACACCCTG[C/T]GGATTCCAGCATCCACATTCAGGTGCGGATGATCA Y 2 1 2 1 202000 r 74 goat snp38866-scaffold493-355338 23 42434340 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420287 Affx-122945039 AX-123290635 23 5982279 CCATTTTTTTTTATGGATGTGCAGGAGTGCAGGGT[A/C]CCCAGGAGTGCAGGGTAAAGATGTTGGAAGGATGT M 2 1 2 1 101000 f 74 goat snp38867-scaffold493-399219 23 42390598 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380074 Affx-122975554 AX-123250432 23 6064441 TACAACTAGTCCTGTGGACACCCCTCCAAAGCCTT[A/G]CCTTCTCTCACGTCATCATCCCCTTTGGGTAAATC R 2 1 2 1 201000 r 74 goat snp38869-scaffold493-481381 23 42307818 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380485 Affx-122975714 AX-123250843 23 6093748 TCAGCATGGCTACAAGTGTAGAGAATCTCTGAAAA[C/T]ACATAGACATCTTCTAAATTGTGAGTCAATTTAAT Y 2 1 2 1 101000 f 74 goat snp38870-scaffold493-510688 23 42278707 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448302 Affx-122924161 AX-123318638 23 6135629 TCAGGAACGCTGCAAAAAGTTTCCGAAGTTCTAAT[A/G]TTGAAAGTAATTTGTTCTCTGCTCTGGTCCATTGG R 2 1 2 1 201000 f 74 goat snp38871-scaffold493-552569 23 42236354 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795372 Affx-122976988 AX-385282328 23 6187669 TCCTGAGCATCTCATTAATCATAACTGCCAGTGGT[A/C]GAGTTTCCAGGTATCTGAAAATGCCTAATTAATTG M 2 1 2 1 101000 f 74 goat snp38872-scaffold493-604609 23 42183721 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376535 Affx-122977997 AX-123246894 23 6271552 GGAAACACTTCAGGGTTTCAACACCAGATGCTGAA[C/T]ACGTACAGCATGTCCAGCAGGGCCTTGGCACCTGC Y 2 1 2 1 101000 f 74 goat snp38873-scaffold493-688492 23 42101367 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414791 Affx-122949228 AX-123285140 23 6306653 TTCTGGGGTTCTTTCTTCTATGAAATGGTACCTCT[A/G]TCTCCACTTAACATACATAGAAGAGCTGCCTAACA R 2 1 2 1 201000 r 74 goat snp38874-scaffold493-723593 23 42065647 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784242 Affx-122936049 AX-385271293 23 6339115 CCATCCATGTTGCTACCACTAATCTCAAGAAAAAT[A/G]TTTTCACTATCAACAAGCTCTTTTGAGAGGAAAGT R 2 1 2 1 101000 f 74 goat snp38875-scaffold493-756055 23 42033249 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787725 Affx-122930656 AX-385274748 23 6368061 GAAGGAACACTGTCTGTGGTCCTCAAGACCTAATA[C/T]GGAATAACCAGGCTTAACATGCCCAGAATCCACTT Y 2 1 2 1 101000 f 74 goat snp38876-scaffold493-785001 23 42003902 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403225 Affx-122957898 AX-123273578 23 6413699 GACAAGAAGGGGTTCGAGCCCTAAAACACACCTAG[A/C]TACTGTGCCAGGCAGTGAACACAGAAGCATTGCTA M 2 1 2 1 201000 f 74 goat snp38877-scaffold493-830639 23 41957224 A C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38376961 Affx-122977762 AX-123247320 23 6473246 CAATCCAGGTCATCCTGCTGAGCTCCAAAACTACC[A/G]TCTGCTAGTGGGTACCTATCTTCCAGTCGATCCAC R 2 1 2 1 201000 r 74 goat snp38878-scaffold493-890186 23 41897704 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375775 Affx-122978589 AX-123246134 23 6524810 TGTAAAAAAGTCTATTCTTCTCACATTAGTGGATT[A/C]AAATGCAATTTCAGTAAAAATTCCAATGAGACTGC M 2 1 2 1 101000 f 74 goat snp38879-scaffold493-941750 23 41845420 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781590 Affx-122920827 AX-385268674 23 6559756 ATAAAGCAAATCAGCCTGACTCATAACTGATCTTC[C/T]ATCTGGACTTTGCCTTGATATTCAGAGGTGATCGC Y 2 1 2 1 101000 f 74 goat snp38880-scaffold493-976696 23 41810387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414754 Affx-122949253 AX-123285103 23 6610110 ATCCTTCCTACTTGCAGGCAAAAGGTAAGCTAAAG[C/T]ACTCCTCAAATTTCCTCTCATTTTGTTGTTATAAA Y 2 1 2 1 101000 f 74 goat snp38881-scaffold493-1027050 23 41760321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401962 Affx-122958794 AX-123272315 23 6672265 GGTGCATTAGCATGGGGGCCATTGCTGGGAGTGGG[A/G]ATAAAAGGAAATAAAAATGAATGAATGAAGCACAG R 2 1 2 1 103000 f 74 goat snp38882-scaffold493-1089205 23 41697337 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447584 Affx-122924017 AX-123317920 23 6715660 CCTGAATCTGTAGGTGTTACCTGAAAACTTGTAAA[C/T]GTTGGGAGCAATTCCAGATTCTGCAGCCTGCAGCT Y 2 1 2 1 101000 f 74 goat snp38883-scaffold493-1132600 23 41654195 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277615 Affx-1111835938 AX-519551114 23 6734418 AGAATTAGGGAAGGGGAGGGTCTGAGAGCGTATCC[A/G]GAGGTGACGATAAGGATGAATGGGAATCACCTGAA R 2 1 2 1 101000 r 74 goat Random2.2K-2029 23 6734418 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320788133 Affx-122949687 AX-385275153 23 6750400 CATTTAGCATAAAGTCAAAATCCTAAGATTACCTA[C/T]AAGTGCCTGGTTCCATGTAATTTCTCCAGTCTCAT Y 2 1 2 1 101000 r 74 goat snp38884-scaffold493-1167340 23 41619231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438836 Affx-122930777 AX-123309173 23 6796825 ATAAGAATTTAAGAAGATTGTTGACTTTAAGATCT[C/T]GTATGATGAAGCAATTCTGTTCCTGTAGAGAACAC Y 2 1 2 1 101000 r 74 goat snp38885-scaffold493-1213765 23 41572216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800277 Affx-122957692 AX-385287200 23 6845340 AAAATATAGGGAAGGGCAAACTCATGAATATTTAT[A/G]TATCTCAAAGAACAATCTAAAGACTGATCAGACAG R 2 1 2 1 101000 f 74 goat snp38886-scaffold493-1262280 23 41522806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435648 Affx-122933760 AX-123305988 23 6893353 GGTTGTCTCTTCCATGGAAGATCTAACAGAGAAAC[G/T]ATAGAGGTTCAGAGACATGGGTTTTTTTAATCTGT K 2 1 2 1 101000 f 74 goat snp38887-scaffold493-1310293 23 41474311 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390480 Affx-122967597 AX-123260837 23 6922519 GAAATGATAGAGATAAGGCTAGAGATTAGTGAAAC[A/G]GAGAACAGAAAGCAATTAAGTAATTAATGAAAACA R 2 1 2 1 101000 f 74 goat snp38888-scaffold493-1339459 23 41448675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434137 Affx-122934915 AX-123304478 23 6961079 AGCATTGGCTCACCAGAAGTCTCCCCCTATATGCT[C/T]GCAGTTTCAATAATTTAAACATGCTAGAAGTCTTC Y 2 1 2 1 101000 r 74 goat snp38889-scaffold493-1378019 23 41409991 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443293 Affx-122927468 AX-123313630 23 6989948 TCCCCAAATGTGTCTCTGTGAGTTACCCATTTATG[C/T]AACAAGCACTTTGTACAGAAGCCCCTTGTTAATGT Y 2 1 2 1 101000 f 74 goat snp17154-scaffold1790-18314 23 41382373 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781455 Affx-122937821 AX-385268540 23 7021471 ATTTCTGTTCAAAGAATATTACTTACCAGCCTAAA[C/T]GTTTCTGGCAAAAGTGTTATAAAGTGTTACAGGGC Y 2 1 2 1 101000 r 74 goat snp17155-scaffold1790-49837 23 41351170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444978 Affx-122926663 AX-123315315 23 7114166 CGGTGGCTGAGCTGAAGTGGAGACGGTCCAGGTCA[C/T]GAAGTCACCAACGTGCTGAGGAGCTAGGTGGGGAA Y 2 1 2 1 201000 r 74 goat snp17156-scaffold1790-142532 23 41261053 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439237 Affx-122931012 AX-123309574 23 7168075 ACCGCTGCTCTAGAGTCCTAAGGAGGTAAATGCCT[A/G]GTGTCTTTTCAGGAGGCATTCCAGTGGCTCAGTGG R 2 1 2 1 101000 f 74 goat snp17157-scaffold1790-196441 23 41208047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782784 Affx-122952741 AX-385269856 23 7220319 TGGTGGTAACTGCTTCCCTCAAGAAAAAATACCCA[C/T]AGATACAGACGTTTGAATGTGATTCAAAGCAAAAT Y 2 1 2 1 101000 f 74 goat snp17158-scaffold1790-248685 23 41154629 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404719 Affx-122957249 AX-123275071 23 7281115 TCAGTCGTGTCCGACTCTTTTGCAACCCCATGAAT[C/T]GCAGCACGTCAGGCCTCCGTGATTTTCTAATTTTC Y 2 1 2 1 303000 f 74 goat snp17159-scaffold1790-309481 23 41093533 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419900 Affx-122945342 AX-123290248 23 7311862 CCCGGGAGTCCCCGGCTGTGCCCTAAGAGCCCACA[C/T]GTCTGTCCCAGATACACTCCTGGGTCCGTGTGCCT Y 2 1 2 1 101000 r 74 goat snp17160-scaffold1790-340228 23 41062880 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389754 Affx-122968245 AX-123260111 23 7384108 ACGGAGGTAGTCAAGTGCCAAGGAGGCGGGTATCC[C/T]GGGGACACATCTGAGAGCAGAAAAGACTGTAGTTG Y 2 1 2 1 201000 f 74 goat snp17161-scaffold1790-412474 23 40991729 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444672 Affx-122926452 AX-123315009 23 7429068 GCTGTCACCCTGCTCCATGTGCCAGAGGATACACG[C/T]GGGGTGACACTATTTATTCAAAGTGTAAAGCCCTG Y 2 1 2 1 101000 r 74 goat snp17162-scaffold1790-457434 23 40946642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450735 Affx-122921865 AX-123321069 23 7488105 CTGGACAAGGAGGGGGCCACCAAGCTGGTGTGTGA[C/T]CTCATCACCAGCACCAAGAACGAGAAGATCTTCCA Y 2 1 2 1 101000 r 74 goat snp17164-scaffold1790-516471 23 40887946 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395765 Affx-122963677 AX-123266120 23 7530883 AAGAAGCCTGGACTCTAACTCGGGCAAGATGATTT[A/C]TTTGGGACACTAGTTCACCATCTTCTTGGTCTGCT M 2 1 2 1 101000 f 74 goat snp17165-scaffold1790-559249 23 40845236 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436875 Affx-122933236 AX-123307213 23 7570940 TGTGATGTTTTGATGATGTTGTACAAATAAAAAAC[A/G]TTTAGCACAGTGTTTGACACAAGGTACCCCAGATG R 2 1 2 1 103000 r 74 goat snp17166-scaffold1790-599306 23 40805222 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406154 Affx-122956176 AX-123276506 23 7601011 ATACAGTGGGTCCCCCGGGCCAAAGAAGAGGAGGA[C/T]GTGGCCTTTTTGGTGCTGCAAAGCTGGGACCCCAA Y 2 1 2 1 101000 r 74 goat snp17167-scaffold1790-629377 23 40775408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418925 Affx-122946514 AX-123289273 23 7639000 TGGCCCGTAAATTCAACTCTTTGGAGAGAATGGGA[C/T]GTAACAAACATTTCTTTAGCACCTATTATGTGCCA Y 2 1 2 1 101000 f 74 goat snp17168-scaffold1790-667366 23 40738199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419177 Affx-122945724 AX-123289525 23 7679832 TTCTGTCGTGAAGAACCACCTTCCCAGTGATGGCC[A/G]CAAAGTAGCTTTTCCTCTCTTCCTCGCTTGCCACC R 2 1 2 1 101000 r 74 goat snp17169-scaffold1790-708198 23 40697316 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423931 Affx-122942261 AX-123294277 23 7708948 TGCTGAGACATATCCTTAGAGATTAGAAGACACCA[C/T]GCACAGCCTAGTTAAGCCCTCTTTCTTGAGCCCCT Y 2 1 2 1 101000 f 74 goat snp17170-scaffold1790-737314 23 40668357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385767 Affx-122971062 AX-123256125 23 7747403 TGGATGCTGAGCCCTGTAAGCAGCAGGCTTCATAC[C/T]GGACACAGGGCAGGGGAGGGGAATCAGTTTTGATT Y 2 1 2 1 201000 f 74 goat snp17171-scaffold1790-775769 23 40629733 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401837 Affx-122959439 AX-123272190 23 7777480 AAAATAAAACAGCATATTTTCCTGTGGTAGCTTGC[A/G]CTTCTCTGAGATGTCTAAAAAATGAGAATCTAGAC R 2 1 2 1 201000 r 74 goat snp17172-scaffold1790-805846 23 40599492 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451393 Affx-122921202 AX-123321726 23 7811590 GTGTCCACATTGGTGGCATAGGTCTTCCTTTGAGG[A/G]CAGAAACAAACACCAATATGATTTCTCAAGCACCT R 2 1 2 1 201000 f 74 goat snp17173-scaffold1790-839956 23 40565221 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446929 Affx-122924686 AX-123317265 23 7860588 GACAGGCAGAGGCCAACTATCCAAACTGCTAGCAT[A/C]GAGGGGACCAGAGGGGACCCACCCAACGCTACCAG M 2 1 2 1 101000 f 74 goat snp17174-scaffold1790-888954 23 40516154 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418780 Affx-122946187 AX-123289128 23 7898033 CATGCTCTGCCTTTTTCCCGTGTTGTTGGTCGGTC[A/G]CTCAGTTGTATCCAACTCTTTGTGACCCCTGTGCA R 2 1 2 1 103000 f 74 goat snp17175-scaffold1790-926399 23 40480667 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394295 Affx-122964700 AX-123264650 23 7971510 ATATGTCTTTTGATTTAATGATATGTGGCCCAAAC[A/G]TGCTGCAGAAAGTATACAATGCCATCTCAGTAGTA R 2 1 2 1 101000 f 74 goat snp17176-scaffold1790-999876 23 40416542 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384670 Affx-122972135 AX-123255028 23 8019967 CTGCCTGGTTCTGTAAAAGCCCAGAAGGTTTACAA[C/T]GTTGGGGAGTTGGTGGCAGAGTGACTCAGAGCCCT Y 2 1 2 1 101000 f 74 goat snp17177-scaffold1790-1048333 23 40367697 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446718 Affx-122924724 AX-123317054 23 8054785 AAAGAGAAGAAAAAGCCCCATCACTTAACACCAAA[C/T]AGCAACATTATCGATAAACCCTTTCTCTGCTGCCC Y 2 1 2 1 201000 r 74 goat snp17178-scaffold1790-1083151 23 40332685 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395472 Affx-122963907 AX-123265827 23 8088111 GCTGCATAAGGAGAAATCTACTTCTACAACAAACT[A/G]TCAATTATTACCTGATCAAACATTTTATCATTAAT R 2 1 2 1 101000 r 74 goat snp17179-scaffold1790-1116477 23 40299752 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423089 Affx-122942928 AX-123293435 23 8121717 GGAAGGCAGAACACCTGGCCAGTAAGAGTGGGAAG[C/T]GGTAAACTCACTGCCACCACCGCCCCCCAAGAAAA Y 2 1 2 1 101000 f 74 goat snp17180-scaffold1790-1150083 23 40266089 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377375 Affx-122977639 AX-123247734 23 8157928 ATACCCAATTTAGTGAAATAAAGTCTTAAGAAATA[C/T]GTTTCAGTCTTCTGTAGTGTTTATGATATTAACTG Y 2 1 2 1 101000 r 74 goat snp17181-scaffold1790-1186294 23 40229626 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447731 Affx-122924596 AX-123318067 23 8201308 TGAGATACCACCTGACACCCATTAGGATGGTTACT[A/G]TTTTAAGAAAAATAACAACAATGTGTGTGGAGTAA R 2 1 2 1 303000 r 74 goat snp17182-scaffold1790-1229674 23 40186286 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414227 Affx-122949640 AX-123284576 23 8240350 TCACACCCTGGTGTAACCCTCACCAACCTCCCTGC[A/G]TGGACTCTGGGCTTGGCCATTGAGTTGCTTTGGCC R 2 1 2 1 201000 r 74 goat snp17183-scaffold1790-1268716 23 40147441 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395494 Affx-122963891 AX-123265849 23 8261929 GGGTTGGAAAGAATTGAAGCAACTGAGCAACTAAG[C/T]ATGACAAACCCTAGTTACTTCACTATTTCTTTTGA Y 2 1 2 1 201000 r 74 goat snp41917-scaffold5468-15230 23 40125197 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277619 Affx-1111835940 AX-519551118 23 8302123 GAGGCCGGGGGTATGTAAAGGGGGGATTGGTCATT[A/C]GTACTGACTTCATGACAGTGGATATAGAGGAGTTG M 2 1 2 1 101000 r 74 goat Random2.2K-2030 23 8302123 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38430096 Affx-122937528 AX-123300437 23 8329930 GGAGACCACGTTTTGCTGGGAATGAAAGGACCCCC[A/G]CCCCAAGCAGGATGCTTAGTGACTGGGAGGAGGCG R 2 1 2 1 102000 f 74 goat snp23563-scaffold2376-384575 23 40059644 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449706 Affx-122922539 AX-123320041 23 8401975 AATTAAGTCACAGTCTCAAAAAAGAAAAAGCAATT[A/G]TATCTGTAAAGCACAACAAACGGAGATGTGCCGAT R 2 1 2 1 201000 r 74 goat snp23562-scaffold2376-312530 23 39987667 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790937 Affx-122930720 AX-385277934 23 8460742 TTAACTGCTCAATGAAGTTGTCAGGCTTTCACCGC[C/T]CCTAGTACAGTGCTTCATTTTACCGTCATTAGTGT Y 2 1 2 1 101000 f 74 goat snp23561-scaffold2376-253763 23 39928872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434587 Affx-122934110 AX-123304928 23 8496871 GAAACCACCTGTTGCTTCTCAGCCTCTGCCTGGCA[G/T]CACCCTTCTGCCCCTGACTGACTGTGCCCTGCTGG K 2 1 2 1 202000 r 74 goat snp23560-scaffold2376-217634 23 39892763 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444270 Affx-122926776 AX-123314607 23 8533507 TATGTGTGATGATGAACACTTGTCCTGTTCTGCAC[A/G]TCCATCCTATCCCTTCCTCCCTATTTCCAGGAAAG R 2 1 2 1 101000 f 74 goat snp23559-scaffold2376-180998 23 39855627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446489 Affx-122925050 AX-123316825 23 8564237 TGATCTCTCCCTTTTCAAAGCTCTAAACTGACCAC[A/G]TAGTTAATACATTTTTCTTGGCCTTAAAATTTACT R 2 1 2 1 101000 f 74 goat snp23558-scaffold2376-150268 23 39824645 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464688079 Affx-1110192671 AX-516158659 23 8587196 CTGGGGCAAAGGTCTTAACCACACTTCTTGAAATA[C/T]CTTCTAGCATTAATATTCTGTTAAAAAATTAAAGC Y 2 1 2 1 101000 f 74 goat 23_8587196_AF-PAKI 23 8587196 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38390229 Affx-122967775 AX-123260586 23 8601352 ACTGAAAGGCATGGCTGGTCAAGGGAGGCAATGGG[C/T]AGTGCTCAAAGAAGTTTCCCAAGTACCACAGGTAA Y 2 1 2 1 101000 r 74 goat snp23557-scaffold2376-113153 23 39787726 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429525 Affx-122937842 AX-123299867 23 8645529 AGAGTCACCCATGCCCTTTGGCCACACCTTCACCA[C/T]GAGCTACGGAGAATCAGGTTCCATCTCAAAAGAAA Y 2 1 2 1 102000 f 74 goat snp23556-scaffold2376-68976 23 39743458 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398760 Affx-122961445 AX-123269115 23 8691603 GTCCTGCAGATTTCACAGGTGTCAATCATATTCTT[A/G]GCTCCAGCTTCATTTCTTTGGACAGGGAACCCTCA R 2 1 2 1 101000 f 74 goat snp23555-scaffold2376-22902 23 39697354 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439292 Affx-122930970 AX-123309629 23 8716351 TGAGCAAGACACTCCACTGCTCTGGATCTGGAAAA[C/T]GAAGACAGATGTGAGTGCACATCTCAGGGCTGCTG Y 2 1 2 1 101000 f 74 goat snp49956-scaffold714-2351436 23 39672711 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434482 Affx-122934627 AX-123304823 23 8755342 GACCCTGTTCGGTTACTGAGGTGTGAAGCTTGACC[A/G]TCGGGCCGGGCACAGCTGGGCAGGACACTGGCTCA R 2 1 2 1 101000 f 74 goat snp49955-scaffold714-2312445 23 39634874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377901 Affx-122977242 AX-123248260 23 8789010 CTCTGAGCCTGAGCTCTGAGGGATCTCAGGATCTA[A/G]CTCTGTAGCTGACAGGCACTGAACGTGGGCCACAT R 2 1 2 1 202000 r 74 goat snp49954-scaffold714-2278777 23 39601094 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426010 Affx-122941133 AX-123296356 23 8824579 TCTGGGAGTGGGGACAAAATCTCCCCTGTTGAGAA[C/T]GCCTGACTCATTGACTACATTTCCCAGCCTCCCTT Y 2 1 2 1 101000 f 74 goat snp49953-scaffold714-2243208 23 39564455 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435698 Affx-122933317 AX-123306037 23 8854362 TCTTTAAAGAATTCCCAGGGGAGATGCTTCAATTA[C/T]GATAAGCGGACACAAGAAAGAGGAAGACGTGGGAT Y 2 1 2 1 101000 f 74 goat snp49952-scaffold714-2213425 23 39534590 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277623 Affx-1111835942 AX-519551122 23 8899604 AGAAAACTAACAGAATATTTTGAGTTCTAAAACGA[A/G]CTACTAACTTTTGAGATTTATAGATTTATTCTCTC R 2 1 2 1 101000 r 74 goat Random2.2K-2031 23 8899604 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396411 Affx-122963007 AX-123266766 23 8906264 GCTGTATTGCTGAAGTCATAAGTGCCTTTCTGATA[C/T]GCACCACTTGGTGCTTGGAGCCCTTGCAGGAATGG Y 2 1 2 1 101000 f 74 goat snp49951-scaffold714-2161523 23 39482237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448503 Affx-122923458 AX-123318839 23 8936731 GTGGTCCCATCCTCGAGCTGGATCACTTGCCCCTC[A/G]AGAAGCTTGTCTCCTGTGGGGGCAGAAATGGAGAG R 2 1 2 1 103000 f 74 goat snp49950-scaffold714-2131056 23 39451659 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375485 Affx-122979141 AX-123245844 23 8978075 GAAGCCCAGAACACACTCAGTGGGTTAAGAGATGC[A/G]TGAGGGAAAAATCAGCAGGTGGTTTGAGCCACCAA R 2 1 2 1 101000 f 74 goat snp49949-scaffold714-2089712 23 39411825 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426730 Affx-122939876 AX-123297076 23 9010377 TGGGGCATGCATTCTTAAGGCTGGAAACTAATTTG[C/T]AGGATTTAGTGGCTTTTCTGGCCACTGGCTTTAAG Y 2 1 2 1 101000 f 74 goat snp49948-scaffold714-2057410 23 39379802 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435217 Affx-122933625 AX-123305557 23 9051413 AGTCATCCATTTATTGATACACAAACTCTACTAAA[C/T]GCCACATCGTACACAGCACTGTGAGACTGGCTGGG Y 2 1 2 1 101000 f 74 goat snp49947-scaffold714-2016374 23 39339947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453818 Affx-122919559 AX-123324151 23 9106572 GAGACAGAGTGGTTGCGGGGGAGGGGTGCGAGGGT[A/G]CGACTGATTCTGAAGGCACCTTGTTCTCCCCACGC R 2 1 2 1 101000 r 74 goat snp49946-scaffold714-1961215 23 39286347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387337 Affx-122970493 AX-123257695 23 9159904 GTGGACACACATGATCCAGTCTCAGAAGGATACAG[C/T]TGGCACCAGAAACACAACCCAACAGCCAAAGTAAT Y 2 1 2 1 101000 f 74 goat snp49945-scaffold714-1907883 23 39232586 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427308 Affx-122940143 AX-123297651 23 9190014 GAAGGCTACCAATGCCCAAGCAGTAAGAATTAGCC[A/G]TAAGCCAGAAGTCACTTATCCTAACAAGAGAGAGT R 2 1 2 1 201000 f 74 goat snp49944-scaffold714-1877773 23 39202383 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801345 Affx-122945562 AX-385288257 23 9305097 ATTACAAAGTCCTTTTAGCTTTATCAGTCACAGAT[A/G]GAGCAGATTTTAGTTTGTTCCCAGGTCAAGTGTAG R 2 1 2 1 101000 r 74 goat snp49942-scaffold714-1762690 23 39084492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449964 Affx-122922889 AX-123320299 23 9345877 ATTTATTATAAGATAATATTGATGATGGCGTGGTT[A/G]CCCTGATTCTCTCATAGAGTTACTGCTGCCAAAAA R 2 1 2 1 101000 r 74 goat snp49941-scaffold714-1721910 23 39043712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431638 Affx-122936138 AX-123301979 23 9382277 GGTCTGCAGGGAACCACCTGGGAGCTTGTTAATGA[C/T]GCCCCACCCAAATAAGAATCCCCTGGGAGTCTGTT Y 2 1 2 1 303000 r 74 goat snp49940-scaffold714-1685510 23 39007953 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446510 Affx-122925034 AX-123316846 23 9435795 AAGACAGGGGTTGGTAAAGGCAGGGTTTAAATTCA[A/G]ATCCAATCCCAAAACCGTCGACCTGCCTGGGCAGC R 2 1 2 1 101000 f 74 goat snp49939-scaffold714-1631992 23 38955911 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801748 Affx-122934302 AX-385288656 23 9521876 TTATTCAGTAGAATCTAATCAATTGCACTCATTAT[G/T]ATGATGCTCACATTCTTTCATATTTAGCCATTGGG K 2 1 2 1 101000 r 74 goat snp49937-scaffold714-1545911 23 38870024 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387143 Affx-122970644 AX-123257501 23 9623400 TGGAATGAGAGACCTGAACTCTTGTAGCTTGACCT[A/G]TGAGTCTACTACTGAACCCCACTTATCAAAGATCC R 2 1 2 1 101000 r 74 goat snp49934-scaffold714-1444387 23 38768298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788719 Affx-122957588 AX-385275735 23 9667483 TTACTTTGCTCCTATTAGCTTATTTGTATCCTGAC[G/T]ACAGCAATCCATTGCCTGTTTCTATCCTTCAGCCC K 2 1 2 1 101000 r 74 goat snp49933-scaffold714-1400304 23 38724759 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441535 Affx-122928708 AX-123311872 23 9704763 GTGTGTTGACACGCAAGGCCAAGCTTCAAGGACAG[C/T]AGTTAGTGATACTTTTAAAATACATGCCACAAACA Y 2 1 2 1 101000 f 74 goat snp49932-scaffold714-1363024 23 38687477 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444783 Affx-122926348 AX-123315120 23 9733685 CCTACCTCTGGTCAGGCGGCCTCAGCTCTCTGCCT[A/G]CACATTCTCGTGTAGCTTCTCTTTCATGTTGGTAT R 2 1 2 1 101000 r 74 goat snp49931-scaffold714-1334102 23 38658429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277501 Affx-1111835943 AX-519551003 23 9763415 CTGCAAGTTCTTGTTAAAGGAAATGACTCTGTAAC[A/G]TGACATATGCATGCAGTTGGTGACAGGATATCCAG R 2 1 2 1 101000 f 74 goat Random2.2K-2033 23 9763415 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449037 Affx-122923073 AX-123319372 23 9787704 GTCACGTGGAAGGCTGTGTAGCAGTTCACCTTATG[A/G]CACTGGATGGCTGCACCTAGCCCCTTCTGCTTGCA R 2 1 2 1 201000 f 74 goat snp49930-scaffold714-1280083 23 38604321 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423349 Affx-122943158 AX-123293695 23 9819438 GAGGGTTTGAAAGAAAAGTGCTGCGTTCCTTGCAG[C/T]TTAGAGCAGCAGAGGCTGGGCAGGGCAAGCACAGC Y 2 1 2 1 101000 f 74 goat snp49929-scaffold714-1248349 23 38574131 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432328 Affx-122936292 AX-123302669 23 9852385 CATTGTTCCTGGTGTTGAGCTCAAAGCCCTGAGAA[C/T]TCCAAGTGGATGCTGTCAGCAAAGGATCACCTCCT Y 2 1 2 1 101000 f 74 goat snp49928-scaffold714-1215402 23 38541257 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443385 Affx-122927400 AX-123313722 23 9881324 GACTTCTTCACCTCGGCCACACCCACATTGAGGAC[G/T]CGAAGGTATTCATCTGCGGAGGAAGCAGAGAGGAG K 2 1 2 1 201000 r 74 goat snp49927-scaffold714-1186463 23 38512519 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406648 Affx-122955814 AX-123277000 23 9913850 CCTGGGGCTGTTGGGTTCTGAAAGGCTTCTCAGAG[A/G]ACATTCTTCGAGGACCTTGCCTTGACTGATTATGA R 2 1 2 1 101000 r 74 goat snp49926-scaffold714-1153937 23 38480010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445509 Affx-122925184 AX-123315846 23 9998005 TCGTTGCTGCTTTTGTCTGGTTTGTTGAAGAACTG[C/T]GGACCCACTGGCCATTTGTCTGTTTATTGGTCAAC Y 2 1 2 1 101000 f 74 goat snp49924-scaffold714-1069782 23 38395567 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387864 Affx-122969639 AX-123258222 23 10066387 TCCAAGCCAGGAGAATCAAAGTGGCCTGATCTGGA[A/G]AGCTTCTTCAACTTGGGTTGTGAATTTCATTCCAA R 2 1 2 1 201000 r 74 goat snp49923-scaffold714-1001400 23 38327002 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793673 Affx-122971608 AX-385280645 23 10102897 TCCTGTATAAAAGTAGAATATGAGAACATTGGGCT[A/G]TTTCATAGAAACACTTCAGTGATCCTACATATTGG R 2 1 2 1 101000 f 74 goat snp49922-scaffold714-964890 23 38290560 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780198 Affx-122968930 AX-385267294 23 10221276 TTCCCAGAGGAAGAAACCAAGACACAAAGAGACTG[C/T]GTAACTTGTATAAAGTCACACACCAGGACCCAATT Y 2 1 2 1 101000 f 74 goat snp49920-scaffold714-846511 23 38171661 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398643 Affx-122961456 AX-123268998 23 10268357 CTTGGTGGAGCCGACATTCTATGAATACTGAAAAC[A/G]ACACATTTAATAAATAAATAAAATTTCCAAGTGAC R 2 1 2 1 101000 f 74 goat snp49919-scaffold714-799430 23 38124061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441420 Affx-122928826 AX-123311757 23 10309477 GATGCCAAAGCTGCCAGGGGCATAGGTCAAGCAGC[A/G]TCTGCTTAGGCAAGAGGGCCTCAGGTGCTTAGTTA R 2 1 2 1 201000 f 74 goat snp49918-scaffold714-758310 23 38083154 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419828 Affx-122945822 AX-123290176 23 10343294 GAGTGATATCAGAGAGGCAAACGTGTGGGTGAATG[C/T]GGGGGCCAGATGGTGCGGGGCTTTGTGCACGGGGA Y 2 1 2 1 101000 f 74 goat snp49917-scaffold714-724493 23 38049244 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377679 Affx-122977426 AX-123248038 23 10391927 CAACTTTTGTAACCTTGCAACCACCCTGCGAACTA[A/C]ATAGTAGTATTTTCCCTTTTCACTGATTAGAAGAT M 2 1 2 1 101000 f 74 goat snp49916-scaffold714-675860 23 38000582 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400428 Affx-122959972 AX-123270783 23 10436957 ACAGCTGCGGTACTTCGAGCAAGTTATCTCTGCAA[A/G]TCTCAGTTTCCTCAAAATAAAAGGGGGAATAGTGA R 2 1 2 1 201000 f 74 goat snp49915-scaffold714-630830 23 37955679 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769699 Affx-122947961 AX-385256869 23 10470806 TCTGTAGCTGTCTGAACTGTCAGGCATTTGTAGAA[C/T]ATAAGACAGAAACTTTTTCAAGTACAGCTACACAT Y 2 1 2 1 101000 f 74 goat snp49914-scaffold714-596981 23 37921997 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38384477 Affx-122973074 AX-123254835 23 10502880 GTCTTTTAATCCTGAGCATCCTGTCCCCTAAGCCT[A/G]CATCAAATAACTCCCCCTCTGACAGTGGTAACCAC R 2 1 2 1 201000 r 74 goat snp49913-scaffold714-564907 23 37891037 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450257 Affx-122922187 AX-123320592 23 10553375 CCTCCCCGAAACTCTGATGTTAATAATAACAAACA[C/T]ACACTCTTTCTTAGTGCTGCACAAGTATTTTCTCA Y 2 1 2 1 201000 r 74 goat snp49912-scaffold714-514412 23 37841886 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422081 Affx-122943590 AX-123292428 23 10581892 AACTCCATGAAGGCAGAAATTTTGTCTCCTTCATC[A/G]CTGTACCCTGGTATAGGAACTGCATTTGGCCCAAA R 2 1 2 1 101000 r 74 goat snp49911-scaffold714-485895 23 37813352 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386166 Affx-122971385 AX-123256524 23 10620398 GAGCCTGTCTCCAGAGTTCACGCTGTTGGCTACTA[C/T]ACTACGTACAACTTGGAGAGCTGGTCCCTGTCAAT Y 2 1 2 1 101000 f 74 goat snp49910-scaffold714-447389 23 37775012 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444472 Affx-122926535 AX-123314809 23 10674224 TAGCTGGAGTGGACTTCTGCACTCTTCTTTGAATG[C/T]GGCTTTGGGTTGGGAGAGGGAGAAGGGAGAGGCCA Y 2 1 2 1 101000 f 74 goat snp49909-scaffold714-393563 23 37720975 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384807 Affx-122971992 AX-123255165 23 10708800 CCAGGGTTGACTTCCAAGTCAGCTTTAACCATTGC[G/T]CCCCTCTATATTCCTGGGGCTACACTGGATCCCCC K 2 1 2 1 101000 f 74 goat snp49908-scaffold714-358987 23 37686102 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414136 Affx-122949704 AX-123284485 23 10787432 GTTCTCCACAGGGAATAAGGTGAATTCACACACAC[A/G]TGGTTCCGCTGTTGCTGTTTAGTCTCTAAGTTGTA R 2 1 2 1 201000 f 74 goat snp49907-scaffold714-280355 23 37607353 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406198 Affx-122956138 AX-123276550 23 10830016 AGAGTTTGCGCTTATAACCACTATGCCAAATACTG[C/T]GTGCCTGAAACAAGAAGAGAAGTGCGGCACGATGC Y 2 1 2 1 101000 f 74 goat snp49906-scaffold714-237771 23 37564857 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397863 Affx-122962450 AX-123268218 23 10872447 GTAACTTAGTCTAGTTTCTGGAACAGGAGGACCTA[C/T]TGCCCCAACCCAGGTGTTCCTTTGCTGTTCAGTTG Y 2 1 2 1 101000 f 74 goat snp49905-scaffold714-195340 23 37521896 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396516 Affx-122963519 AX-123266871 23 10908079 CAAGCGCTCACGACCACTGGACCAGACAGCTATGT[A/G]CCCCGGGCAATAATGGTAGTAATAGCAATAGCTAA R 2 1 2 1 101000 r 74 goat snp49904-scaffold714-159708 23 37486332 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391202 Affx-122967415 AX-123261559 23 10945745 AGAGATAACTGCTTACTAGGGCACTCCTGGGACCA[C/T]AGGAAGCACTATGGAACCCTAGCTGAAGAGCTCAA Y 2 1 2 1 101000 r 74 goat snp49903-scaffold714-122042 23 37448160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389480 Affx-122968323 AX-123259838 23 10978508 ACTCTTCCTTGGGCCCCTCTTTGGCAGCAAGCAGC[A/G]GCCCCGGGAGCCCTGAGCTCGGACACGGCGCTAAT R 2 1 2 1 101000 f 74 goat snp49902-scaffold714-89279 23 37415463 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385775 Affx-122971056 AX-123256133 23 11008720 ACCATCATTGCTGTATAATTTTTCATTGTATGACT[A/G]CACTGCAATTTATTGATCTTTTTTTTCTGCTGATT R 2 1 2 1 101000 f 74 goat snp49901-scaffold714-59067 23 37385616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416129 Affx-122948295 AX-123286478 23 11037749 GTTCTACTTTGGAGAGGAGAAAGGAAAGGCCAGAC[A/G]CCTACTGATCCTTTTATTTGGGGGCCAATGAATCC R 2 1 2 1 303000 r 74 goat snp49900-scaffold714-30038 23 37356677 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424618 Affx-122942189 AX-123294964 23 11087626 AGGTGAATCAGCCTGATCCTGCGGGAACTCCAGAG[C/T]GTAACTCACACTCAGGGTTAGTCCTGCTTCAAGGC Y 2 1 2 1 101000 r 74 goat snp59290-scaffold975-19740 23 37308702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451609 Affx-122921632 AX-123321942 23 11127089 TCTTTGTGAGACACTGCAGTTCCTGTTCCAGGCAA[C/T]GACTTGCTAGGTCTTTTAGATCAAGCTTCCTTTTA Y 2 1 2 1 101000 r 74 goat snp59291-scaffold975-59203 23 37269117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428370 Affx-122938968 AX-123298713 23 11161169 TCCCAGGGCCTTCCTGTATCCAACATGCTCTTCTT[A/G]CCAGCTGGGTTCCCCGTGCTCCTCCTGAACTGAGG R 2 1 2 1 101000 f 74 goat snp59292-scaffold975-93283 23 37236001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272142 Affx-1111833253 AX-519545899 23 11183656 TCTGTACATTGGACATGGTAGCTAATTACAGCTGA[A/G]CACAGACGATAGGAAGGAGAGAGGAGGAACACAGA R 2 1 2 1 101000 f 74 goat 23_11183656_AF-PAKI 23 11183656 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38377012 Affx-122977723 AX-123247371 23 11211967 CTAATGGGGGGAGTCTGGAGCTTCAGAAGGCCCTA[C/T]GGAGGCTAAGTAATTAGAATAACTCTCATCCTACT Y 2 1 2 1 101000 r 74 goat snp59293-scaffold975-144081 23 37185569 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435991 Affx-122933504 AX-123306330 23 11258708 CTCCTGTATTGTAGGCAGACACCTTACCGTCTGAG[C/T]GACCAGGGAAGTCCTTCCCTAGAGTTCAGGTGATT Y 2 1 2 1 103000 f 74 goat snp59294-scaffold975-190822 23 37138706 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394203 Affx-122964907 AX-123264558 23 11291322 GTCCATGGAATCCCAAAGAGTTGGACACGACTGAG[A/C]AACTTCACTGGTTGCAAGAAAGTGAGTGAGACTGG M 2 1 2 1 103000 r 74 goat snp59295-scaffold975-223436 23 37101768 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791602 Affx-122954863 AX-385278593 23 11327885 GGATACCACCAAGGTGTGATTTTATCAAGTTTTTG[C/T]AGGACTAGTCATTAGTCACTGGGAGAGCTCTGGCC Y 2 1 2 1 101000 f 74 goat snp59296-scaffold975-259999 23 37064886 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764822 Affx-122924509 AX-385252426 23 11369376 AATTACTCTCTGCTAAGCTCTTTCTGGCTTTGGTT[A/G]GAAATATTTTTCTGGTAAGTTTTTAATTAGGAAAT R 2 1 2 1 101000 f 74 goat snp59297-scaffold975-301490 23 37023441 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445058 Affx-122926228 AX-123315395 23 11399459 GGAATTTTTTGAGGGAGTTGTATAACAGGCTATGC[A/G]TGGGTACAGACCATTAGTGCTGGCTCCTGACTGTA R 2 1 2 1 101000 f 74 goat snp59298-scaffold975-331573 23 36993457 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421641 Affx-122944457 AX-123291988 23 11430272 TCTGTGTTTAAAACTATGTTTTGCTTCCTTTGGAA[A/G]CTTGTTTGCTGCAGTAACTTTGGCAAAGCATCCAG R 2 1 2 1 201000 f 74 goat snp59299-scaffold975-362386 23 36962617 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396726 Affx-122962802 AX-123267081 23 11462823 ATTATGGGGATATACGATATCCCCAAAGAGCCTGG[C/T]GGACTACAGTTCATGGGGTTGAAGGTGGTCGGACA Y 2 1 2 1 103000 f 74 goat snp59300-scaffold975-394937 23 36929842 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801342 Affx-122919434 AX-385288254 23 11559168 AACGTGTGGTCTGTTACTTTTTGAGAAAGACTGCC[A/G]TTCTCTAAATACAGCGTTTTACATTGTTTGAAAAA R 2 1 2 1 101000 f 74 goat snp59302-scaffold975-491282 23 36833016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416431 Affx-122947833 AX-123286780 23 11607818 CTTATGGTAGGAAACCAGAGCCTGGTCGGGAGGTC[A/G]TTAAAGAGACTTTTGATAACACGGAAATAAAAGCA R 2 1 2 1 201000 r 74 goat snp59303-scaffold975-539932 23 36783988 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435974 Affx-122933515 AX-123306313 23 11645703 TTGAACGTTCATGACACTTGAGTGGAAACAGGTCT[A/G]TGGGTACCGAGAAAAGAGGATAAAGATTCAGCCCG R 2 1 2 1 101000 r 74 goat snp59304-scaffold975-577817 23 36745870 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386610 Affx-122970240 AX-123256968 23 11681229 GGGTGTTTGGCCAGGGCCAGACTGGCAGTTAAACA[C/T]GGCAAATTGAATAAGTGGGTTAACCTTTGCTTTCT Y 2 1 2 1 101000 r 74 goat snp59305-scaffold975-613343 23 36710817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396358 Affx-122963047 AX-123266713 23 11718003 TCCCAAGAAATGGTAACATTTCAACACAGGACCTA[C/T]GCCACAGCCAAAAGCTGCAATCCCATCCTGGAAAC Y 2 1 2 1 101000 f 74 goat snp59306-scaffold975-650117 23 36674209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795002 Affx-122951010 AX-385281961 23 11750143 CTCCTGGAGGTGGCTGGGAAATCTGATTTGAGAGT[A/C]CCTGAGGACTGAAGGTTTTCAAAGATAGATTACTG M 2 1 2 1 101000 f 74 goat snp59307-scaffold975-682257 23 36642119 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449021 Affx-122923086 AX-123319356 23 11803214 TTTAGAAAACTCTCTGAATTAAGGACCCCTCTGCT[A/G]TTCCAACAAGTTTGCTTCTTTGCCACATTCTAACA R 2 1 2 1 101000 r 74 goat snp59308-scaffold975-735328 23 36594161 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404638 Affx-122957316 AX-123274990 23 11832943 AGTTAAGTGTTTGCTTTTTGGCCTTCCCTATTGAA[C/T]TCTGATATTCCTGAAAACAGAGACCTTTTCTTGCT Y 2 1 2 1 101000 f 74 goat snp59309-scaffold975-765057 23 36564086 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417907 Affx-122946737 AX-123288255 23 11862623 CCTAAAATAACCCAAATTCCTAACCCATTAAAACT[A/G]TAAGGTAATAAATATTTATTGTTAAGTCACAACGT R 2 1 2 1 101000 f 74 goat snp59310-scaffold975-794737 23 36534442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430712 Affx-122936904 AX-123301053 23 11906593 TGTTAATGATATGTTTATTGAATATTATAGCTAAC[A/G]TATCACTATTAGGTTGTGTCAAATTTATGGCATAG R 2 1 2 1 101000 r 74 goat snp59311-scaffold975-838707 23 36491601 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383390 Affx-122973504 AX-123253748 23 11936981 CTTCTTGGCTAAAAGCTGCCACCATACTTTCTCCT[A/G]TAAATCACACATGTCTAGGGCAGAGAAGAGACCTA R 2 1 2 1 101000 r 74 goat snp59312-scaffold975-869095 23 36461259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796197 Affx-122945899 AX-385283148 23 11966978 TGCACAAACAGGGTAGAAACATCTTTATATCTCCC[C/T]TGTTGCTCTGAGTGCAGCAGCCTCAGTATATATTT Y 2 1 2 1 201000 r 74 goat snp59313-scaffold975-899092 23 36431353 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419485 Affx-122945468 AX-123289833 23 12021151 GCTTATGTGCTCAGTTTCAGTTTGTTGTTGTTCAG[C/T]TGCCCAGTCGTGTCTGACTCTCTGTGACCCCATGG Y 2 1 2 1 103000 f 74 goat snp59314-scaffold975-953265 23 36377277 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432737 Affx-122935457 AX-123303078 23 12078527 ACCCTTCCATGCTGATAAGAATATTTTGTTTATAA[C/T]GTGTCCAGGGTTTTACACTAACTAAACAACCAGAA Y 2 1 2 1 101000 r 74 goat snp59315-scaffold975-1010641 23 36319500 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428930 Affx-122938900 AX-123299272 23 12118079 AGGGCGGGCGCTGCTGACTTCCAGCCAATCGCTTG[A/C]TGGAAAGGAAGTTGGCTTTCTGCTGATTGGGTCCC M 2 1 2 1 101000 r 74 goat snp59316-scaffold975-1050193 23 36279293 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410976 Affx-122952015 AX-123281326 23 12164905 CATGAGCACAGGAGAGTGGAACTGGAGAAGAAAAT[A/C]TTTAATTGAGTGAGGACTAGGGTAGAAAAGTCTTG M 2 1 2 1 201000 r 74 goat snp59317-scaffold975-1097019 23 36232091 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423539 Affx-122942436 AX-123293885 23 12195448 TATTGCTAGTGTTACATATCAGAACTGTCGGGAGT[A/G]CCAAGAAGGACAGTAATGCTTTTGAATCCAGTGAA R 2 1 2 1 101000 f 74 goat snp59318-scaffold975-1127562 23 36201159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437913 Affx-122931650 AX-123308251 23 12241407 GGTGCTTAGAAAATCTGGTCATATGTGCTTTGTAC[A/G]TAAAGTTTATTTAAGCTATTCCCTTAAATAACTAA R 2 1 2 1 101000 f 74 goat snp59319-scaffold975-1173521 23 36155216 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403892 Affx-122957493 AX-123274244 23 12281623 CCCATCTCTTACGAGAAAGCATTAGTAGCTCAGTC[A/G]TGTCTGACTCTTTGTCATCCAATGGACGGTAGCCT R 2 1 2 1 103000 f 74 goat snp59320-scaffold975-1213737 23 36114720 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377595 Affx-122978310 AX-123247954 23 12328214 GCCTATGTTTCCTTCCAAATGTTACATAGTTTTGT[A/C]TTCCATATTTGAGTCCTTAATCCGTCTGTAGTTGA M 2 1 2 1 101000 r 74 goat snp59321-scaffold975-1260328 23 36079165 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798438 Affx-122955021 AX-385285372 23 12365053 TAACTCAGAAAGAAAGTACGTATTTTCTTCCAGAG[A/C]TTACAGGCTGTAATACTATTTTTCAGTTGATGAGT M 2 1 2 1 101000 f 74 goat snp59322-scaffold975-1297167 23 36042284 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391833 Affx-122967008 AX-123262190 23 12402523 CAATATGATAGTGAATATGAACTTCAAACAGCTTC[A/G]TGCTTTCTGGTGAACAACTAGAGACGTGATGCCCA R 2 1 2 1 101000 r 74 goat snp59323-scaffold975-1334637 23 36004798 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442746 Affx-122927842 AX-123313083 23 12530559 CATTCATTCACTCCATTCTCACTGGGCGTCTTCTA[C/T]GTGACAGGCTCTGTGCTATGTGCTGGAGCCTTGGG Y 2 1 2 1 101000 f 74 goat snp59326-scaffold975-1462673 23 35877480 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388818 Affx-122968901 AX-123259176 23 12577217 TCTGTCCTCCTGGGACTTTGGAGACTATTCAGTCC[A/G]TAAATGTTGATTGAACACCTGCTACAAGCCATGTT R 2 1 2 1 101000 r 74 goat snp59327-scaffold975-1509331 23 35830218 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801881 Affx-122967839 AX-385288788 23 12607455 TCATTTTTCAAGCTGATTACCCTCTGCCTGCCATT[A/G]GACTATGAAATATTTCCATCTAGACAATAACTGTT R 2 1 2 1 101000 f 74 goat snp59328-scaffold975-1539569 23 35800253 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417928 Affx-122946719 AX-123288276 23 12650252 GATCGGGGCTTTTTCAGGAAGATTAAGAATCAAGA[C/T]GCTGTGCAGCCCACGGGCACAAGGACATAAGTGGC Y 2 1 2 1 101000 f 74 goat snp59329-scaffold975-1582366 23 35757103 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453522 Affx-122919803 AX-123323855 23 12695551 ATACAATCACAGCACAAAATGAAATCTTGAGCAAT[A/G]TAGTTGTAGCACACACACACACAAAAAAGTAGTGA R 2 1 2 1 201000 f 74 goat snp59330-scaffold975-1627665 23 35711759 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416877 Affx-122948082 AX-123287225 23 12755228 CGGAATGACTAGAAATGTGGCTTACAGCCTGAGGC[A/G]CTGGGTTCAAACTCCAGCTGTCACTTTTAGCTGGG R 2 1 2 1 102000 f 74 goat snp59331-scaffold975-1687342 23 35652878 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428570 Affx-122938717 AX-123298912 23 12788055 AATCAATCCATACAGCTCCTAACTATAAACTCTAG[A/C]TTTCTCCTCTGCAAACCTCCTTCCATACGTTTTTC M 2 1 2 1 101000 f 74 goat snp47839-scaffold673-2048684 23 35619716 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425713 Affx-122940768 AX-123296059 23 12820367 AAGGAGGAGATGAAGGTGCCTGATTTTAAGGCTTC[A/G]AATGATTTATGTACTCATTTATTGGAAATTCATCT R 2 1 2 1 101000 f 74 goat snp47838-scaffold673-2016372 23 35587247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443184 Affx-122927601 AX-123313521 23 12853673 AGAATCCTGGCGTTGGCTTCTCTGCATCAGCGAGC[C/T]ACCTCTGGCAGCATTGTCTTTGGCATCAGAGAACA Y 2 1 2 1 201000 r 74 goat snp47837-scaffold673-1983066 23 35554561 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424955 Affx-122941928 AX-123295301 23 12902172 TTGTGTGCACTCTTTAAAAATGGAGTCTGTTTCCT[A/G]TGGCCCTCTGGCTCTCCCAAGAGAGCTGGCCTTCA R 2 1 2 1 101000 f 74 goat snp47836-scaffold673-1934567 23 35506287 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434778 Affx-122933887 AX-123305119 23 12948320 CAAGGTAAAGGCGGGGATTTGCTCCTCTTTTGAGC[A/G]TTTTGACTTCCCAAAGGAAACAGAAAAACAACAAA R 2 1 2 1 101000 f 74 goat snp47835-scaffold673-1888419 23 35460387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403597 Affx-122957562 AX-123273950 23 12980702 CCAGGCTTAGTGTCCAGGCACATAGATTATCTACC[A/G]TCTTTCTTGTCTGTATGAACTAAAACTGAATGGCA R 2 1 2 1 101000 f 74 goat snp47834-scaffold673-1856037 23 35428109 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406753 Affx-122955732 AX-123277104 23 13020715 ACCTCTATCGTGATGTAGTCCTTTATTGAAATGCC[A/G]TATATCCGTGAAAATTCATGAACTAGAACCACACG R 2 1 2 1 101000 f 74 goat snp47833-scaffold673-1816024 23 35388151 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779541 Affx-122949368 AX-385266644 23 13093199 TTAGAGTCTAAGTATGTCTCATGAAGTAAAACAGT[A/G]TAACTGCTGGTCTTAACCATAGGGAAAATAGTCAC R 2 1 2 1 101000 r 74 goat snp47832-scaffold673-1743540 23 35315440 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394826 Affx-122964793 AX-123265181 23 13142106 CAAGGCTAAATTTCATGTCTTTTCTCTCTATAATC[A/G]TTCATGAATAAATTCATTTTGGTATTTTATACGTC R 2 1 2 1 101000 f 74 goat snp47831-scaffold673-1694633 23 35266644 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425773 Affx-122940720 AX-123296119 23 13185358 ACGAGGGGATATTTGAAGCTGCAGACTGAACACGG[C/T]GCATCATTCTGGAGTGTGAATTTCACTTAAAGACT Y 2 1 2 1 101000 f 74 goat snp47830-scaffold673-1651381 23 35222192 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790191 Affx-122951374 AX-385277195 23 13224952 GAATCCTGGCCTTGCCCTTTATTAATTGTATGACC[A/G]TAGAAAGTTATTTAACCCTCTTGGGCCTCAACTTT R 2 1 2 1 101000 f 74 goat snp47829-scaffold673-1611787 23 35182287 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419513 Affx-122945447 AX-123289861 23 13280719 TATATCCCAGGAATATGGCTCTGTGTGGCACACCG[A/C]TCATCTAGAAAATTCCACCTGCTTCCTAAAGGACC M 2 1 2 1 101000 r 74 goat snp47828-scaffold673-1556020 23 35126076 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436964 Affx-122933165 AX-123307302 23 13316841 CTCCTCCACCAACCAGGAAGGGGGATGGTGCTTCC[A/G]AGCTGGGCTGAAGAAGGGATTCTCTCTGGGCTCAT R 2 1 2 1 101000 r 74 goat snp47827-scaffold673-1519898 23 35089882 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376761 Affx-122977970 AX-123247120 23 13346505 AGGTCTCAGCTGATTTTGTTTGGTCTTCCAGGAGG[C/T]GGGACTGTTTCTTGTAAAGAGTGTATGCTCTCATA Y 2 1 2 1 101000 r 74 goat snp47826-scaffold673-1490234 23 35061475 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414204 Affx-122949654 AX-123284553 23 13377997 GTCGCAAAGAGTTGGACATCACTTAACAACTGAAC[A/C]ACCACCAAGCTCTAAAATCCTAACCACCTCACAAG M 2 1 2 1 101000 r 74 goat snp47825-scaffold673-1458742 23 35030189 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415671 Affx-122948551 AX-123286020 23 13408853 GAAAATGATAAGAATTCAAAGGGCATCAGTATAAA[C/T]GGAAAAATCGCCATTTGCCATGGACACATTTTAGA Y 2 1 2 1 201000 f 74 goat snp47824-scaffold673-1427886 23 35000216 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390307 Affx-122967717 AX-123260664 23 13449235 GCATATGGTTGGCTGCCTTGTGCCCAGTTAATCAC[A/G]CTGGTGTCCATGGTCCCTGGGTGGCTCAGACCCTG R 2 1 2 1 101000 f 74 goat snp47823-scaffold673-1387504 23 34959802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396465 Affx-122962968 AX-123266820 23 13492805 CAGGTCCTGTTCTAGTCTTACCAGCTGACCTGGGC[A/G]TCTCATAGTCCCAAACCAACCACTACCGAAAACAA R 2 1 2 1 101000 r 74 goat snp47822-scaffold673-1343934 23 34915088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432187 Affx-122936398 AX-123302528 23 13546239 TGGGAGGTCTTTGTTTAGCCAGTCCTACTCCCGCT[A/G]TCTCTACCCAGGCCAGAGGGTATTTCTGAATCCAC R 2 1 2 1 202000 r 74 goat snp47821-scaffold673-1290500 23 34861464 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382451 Affx-122974223 AX-123252809 23 13621318 AAACAGTTTATTTCCTGAACTTTTAACAGAGACAA[C/T]GTAAGATATAGAAAACTGACAATATACTGAAGATA Y 2 1 2 1 101000 f 74 goat snp47819-scaffold673-1215421 23 34785695 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390273 Affx-122967742 AX-123260630 23 13671316 AGGCTCCTATCACCCCCTCCAGCTGTGTTTGCAAA[C/T]GGTCCCTGCTAACTTGACCAATTACTTACATCTTA Y 2 1 2 1 101000 r 74 goat snp47818-scaffold673-1165423 23 34735864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383483 Affx-122973437 AX-123253841 23 13711053 TGTAGAAGGAAGCAGGACGAAAGGAAAAAACAAAA[C/T]AGGAAAGATAGAGACCATGAATGAAGTTTACATTG Y 2 1 2 1 102000 r 74 goat snp47817-scaffold673-1125686 23 34696336 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439569 Affx-122930085 AX-123309906 23 13755808 GGCCCGGCACAGGGTGTCGTGGTCCAAAGATTGAC[A/G]TCTGTGATGCTTCATTAGGCAGGGCTGTCTCAGCA R 2 1 2 1 101000 r 74 goat snp47816-scaffold673-1080931 23 34651998 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272144 Affx-1111833254 AX-519545901 23 13795713 CTTAGGGCTCGGCTTCACAAACCCAAAGTATTTCA[A/G]ATTGGCAGTAACCTAAAAGTGTGGCTGTCTCAAAT R 2 1 2 1 101000 f 74 goat 23_13795713_AF-PAKI 23 13795713 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418789 Affx-122946181 AX-123289137 23 13801429 TCCTCATCTCAGACTCATTCCTGCTGATCTGTTCC[A/G]TCCCTACCCCCAGTCCCAGCCAAGGACCCTGCCTT R 2 1 2 1 101000 f 74 goat snp47815-scaffold673-1035310 23 34606736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377061 Affx-122978292 AX-123247420 23 13850429 TTGGCTCCGCACCCCCTCCGCCCACCCACGAGCAC[C/T]CGGCTTTAGAAAGCTCCAGCCACCTGGCCCATTTC Y 2 1 2 1 101000 r 74 goat snp47814-scaffold673-986310 23 34560326 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378056 Affx-122977187 AX-123248415 23 13949843 CAAGTGCAAACCTAGGGAAGCAGAGAGGAGACGCC[A/G]TTCCTACCCTGGGTAAACTCCTAGAGGCGTGCTGA R 2 1 2 1 201000 r 74 goat snp47812-scaffold673-886896 23 34462203 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409182 Affx-122953188 AX-123279533 23 13998641 GGTGGGTGGGTGGGTGTCAGAGGTAAGATTCCTTC[C/T]GAAGAGAGGATGTGAGTCGCCCCCTATGGAAGCCT Y 2 1 2 1 201000 f 74 goat snp47811-scaffold673-838098 23 34413727 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386345 Affx-122970868 AX-123256703 23 14096587 GACTGGGTTGCGAGTTAGGGGTCTTGACTCTACCA[C/T]GTATGTGACTTGGGTGGGACACCCCCGAGGCCTGG Y 2 1 2 1 201000 f 74 goat snp47809-scaffold673-740152 23 34316513 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426437 Affx-122940815 AX-123296783 23 14127531 CCCCAACCTCAGTGTGCCTTCCCTTTGTCTCTGCA[A/C]TCCTGCTGAGGGCCATCTACTGCCTGATGGTCTGG M 2 1 2 1 201000 f 74 goat snp47808-scaffold673-709208 23 34286050 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797240 Affx-122950283 AX-385284179 23 14179265 CAAGACCCAGGGACACACTGTGTAATGTACCTCTT[C/T]ATCGTGCTTATAGTTATATCTTTTTCCTGCTGGAG Y 2 1 2 1 101000 f 74 goat snp47807-scaffold673-657474 23 34234562 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411691 Affx-122951548 AX-123282041 23 14213831 ATGCAATTTACTGGTTCATTCATTTGCTCACTCAC[A/G]TGTTAATTAGGTAGTCACTGTGTCTGAGCATTGTT R 2 1 2 1 201000 r 74 goat snp47806-scaffold673-622908 23 34202755 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453341 Affx-122919959 AX-123323674 23 14261164 ATCTTCATCACGTGTAACCTTGGATCTGACCATGC[A/G]TAGTATTCTTTTTTTCACACACTCAGTTTTTCAAA R 2 1 2 1 101000 f 74 goat snp47805-scaffold673-575575 23 34155212 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405388 Affx-122956298 AX-123275740 23 14311146 AGTCCAGGTGCAGGGAAAGAGCTGAGGGAATGCAG[C/T]TGACTTGGCCAAGGTTCCCACCTCCCTGAGAACTG Y 2 1 2 1 201000 f 74 goat snp47804-scaffold673-525593 23 34104828 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392712 Affx-122966036 AX-123263069 23 14344600 CTTTCGCAAGGGGGTGAAGAATTAAACATTTCTTT[A/G]CATCTTTGGGGATCAAGGAAGTTTTATATTTTTGT R 2 1 2 1 101000 f 74 goat snp47803-scaffold673-492139 23 34080348 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794547 Affx-122946013 AX-385281510 23 14380559 TACCCTTTCTGACCTCAACATTTTGTGAGATTGGG[C/T]AACTTCAGCACTTGTATATGAAACACACTCCGGAA Y 2 1 2 1 101000 f 74 goat snp47802-scaffold673-456180 23 34043459 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763866 Affx-986698394 AX-385251656 23 14385642 AAACTCTTGGAGGAAGTAGACACATGTTTAAGGAG[A/G]GCATTACTTACGTTTTGTTTAGGATTTGGGTCAGT R 2 1 2 1 600010 f 74 goat 23_14385642 23 14385642 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 320804143 Affx-986696407 AX-385290792 23 14385643 AACTCTTGGAGGAAGTAGACACATGTTTAAGGAGG[A/G]CATTACTTACGTTTTGTTTAGGATTTGGGTCAGTT R 2 1 2 1 600010 r 74 goat 23_14385643 23 14385643 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 320763868 Affx-986698396 AX-385251658 23 14390913 GGGAGAGAGAAGGAACCTTGCAGAAATGGACACAT[A/C]CGCATTTCCTGGTCGGTCCCCTGGGCCTCAGCAGG M 2 1 2 1 600010 f 74 goat 23_14390913 23 14390913 Ancestral_priority_1043 ancestry 0.592 neutral IMAGE 10K 10K ancestral 320804145 Affx-986696408 AX-385290794 23 14391035 TGACCGGGACTTGGGAAACCCAGAGTGATGGAATG[C/T]GTGGAATGGCTGCAAGGTGATGCAGGAGATGAGGA Y 2 1 2 1 600010 r 74 goat 23_14391035 23 14391035 Ancestral_priority_1043 ancestry 0.468 neutral IMAGE 10K 10K ancestral 320763874 Affx-986698402 AX-385251664 23 14391135 TGGGGAGGATGAGCCAGTTCACCTTTGTATCTGCT[A/G]TGGTCTCAGCCTTTGTGTCCCCCAGAAATTTCATA R 2 1 2 1 600010 f 74 goat 23_14391135 23 14391135 Ancestral_priority_1043 ancestry 0.556 neutral IMAGE 10K 10K ancestral 320763876 Affx-986698404 AX-385251666 23 14391179 GCCTTTGTGTCCCCCAGAAATTTCATATGATGAAA[C/T]CCTGATTCCCATGGTTATGGTAACCCTAGGTGGGG Y 2 1 2 1 600010 f 74 goat 23_14391179 23 14391179 Ancestral_priority_1043 ancestry 0.524 neutral IMAGE 10K 10K ancestral 320767153 Affx-986698377 AX-385254438 23 14391213 ACCCTGATTCCCATGGTTATGGTAACCCTAGGTGG[G/T]GCCTTTGTGAGGTGATGGAGTTACAAGGATGGAGC K 2 1 2 1 600010 r 74 goat 23_14391213 23 14391213 Ancestral_priority_1043 ancestry 0.54 neutral IMAGE 10K 10K ancestral 38407094 Affx-122954894 AX-123277445 23 14416954 ATGAGAACCACCTAAGTAAAGAATAATGTATCAGG[G/T]ATACAGAAGTGTGTGGGGATGATAAACACCTGATT K 2 1 2 1 201000 f 74 goat snp47801-scaffold673-419785 23 34011212 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452240 Affx-122920786 AX-123322573 23 14446363 AAGCAGGGCTGTCCAGCATTTCAGCAACCTTGCCA[A/C]GATCCATATGCTGCTCATGCATTTAAGACAACATA M 2 1 2 1 201000 r 74 goat snp47800-scaffold673-390376 23 33981893 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277627 Affx-1111835944 AX-519551126 23 14452862 TGAGAGCTATTACAGTGCCACACAATTTGCAAAGC[A/G]CTTGATGTGAAATACTATATTCAATCCTGAGATAA R 2 1 2 1 101000 r 74 goat Random2.2K-2036 23 14452862 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320767156 Affx-986698379 AX-385254441 23 14471879 TTCTTGCTTATTTTCTCTGCCTTTATCCTGAGCAG[A/C]CAGATTTCTAAGGTTAAGACCAAAGGCTTTGTGAA M 2 1 2 1 600010 r 74 goat 23_14471879 23 14471879 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 38426197 Affx-122940375 AX-123296543 23 14482478 CGCCTGGAAGAAAAGGAATATATAACAAGAGCTGA[C/T]GAAGAAACAGTCCCTGAATGTGTGGGATTGCTGAG Y 2 1 2 1 101000 f 74 goat snp47799-scaffold673-354261 23 33945678 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408756 Affx-122953396 AX-123279107 23 14513261 TGGAAAGTCCAGGAAAGAACAAAGAAGAAAACACA[C/T]GTTACTGGGCCGGTCTAGGAACTACTACTGTCAGC Y 2 1 2 1 101000 r 74 goat snp47798-scaffold673-323478 23 33915041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378353 Affx-122976831 AX-123248712 23 14561996 AAGATGCCATCTGAAAATTACAATAATCTGTAGGA[A/G]ATGCTGAAGTGAGTATCGATGGGATTGTAAGAAAA R 2 1 2 1 101000 r 74 goat snp47797-scaffold673-274743 23 33866285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400704 Affx-122959931 AX-123271059 23 14595018 CTCCCTGAAGACATGATCCCTCACCCCTGCCAACT[C/T]TATACACTGGGGAGGGTGCCCTGGACCTCCCTGGA Y 2 1 2 1 101000 f 74 goat snp47796-scaffold673-241721 23 33832989 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383088 Affx-122973732 AX-123253446 23 14670637 TGATTTCATCTTTTGAATGAAGAGTTCCAAGTACA[C/T]GAATAAAGAGAAGTGACACACACATAGCTTCTTTC Y 2 1 2 1 101000 r 74 goat snp47794-scaffold673-166102 23 33757855 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382186 Affx-122974015 AX-123252544 23 14728771 GTTCTTTACAGAGGAGTGGTCAAGGATAAGGGAAG[A/G]GGTCATGATGCATTGAAAGAGAGGGAGCTGTTAAC R 2 1 2 1 201000 f 74 goat snp47793-scaffold673-107968 23 33698024 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451932 Affx-122921013 AX-123322265 23 14759916 CAAAAGGGCCAAGCAGCAACATGGGGGCAAAATTA[C/T]GGTGGAAGCCCCCCTAGCAAGGCGGAGAGGGGGTG Y 2 1 2 1 101000 f 74 goat snp47792-scaffold673-76823 23 33666862 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420804 Affx-122944684 AX-123291151 23 14819117 ATGAAACTTGCTCCCCCTGCATTGGAAGCACGGAG[A/G]CTTAACCCCTGGACTGTCAAGATCCCGTCACTTTT R 2 1 2 1 103000 r 74 goat snp47791-scaffold673-17622 23 33607729 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404517 Affx-122956697 AX-123274869 23 14837860 CCCAGTCCTCACCTAGGTACCTAAGAGCTTCCCCA[C/T]TAGAGTTCCCTGCTGCTTCTTCACACCTTCTATTG Y 2 1 2 1 101000 r 74 goat snp32140-scaffold3636-36009 23 33588975 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413958 Affx-122950305 AX-123284307 23 14870131 TATTATTGTTATTATTGTCACCCTTGTTACGCTGC[A/G]TGTTAACCCCCTCCCTCTCTTCTTTCAGCTGCTCC R 2 1 2 1 201000 f 74 goat snp32139-scaffold3636-3738 23 33557865 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376988 Affx-122977742 AX-123247347 23 14881525 CCTACATGCTGTGGCCCATGTACCACAAGATCCCA[C/T]ATGCTGAACTAGGATTCCATGCAGCTGAATACACA Y 2 1 2 1 101000 r 74 goat snp31006-scaffold3423-428862 23 33547896 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448216 Affx-122924226 AX-123318552 23 14924176 TGCAGTTCATGGGTCACAAAGAGTTAGCGACTAAA[C/T]GACAACACAGGGCAGTCTAGGGGACCAGATGCCCG Y 2 1 2 1 103000 f 74 goat snp31005-scaffold3423-386211 23 33505214 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453624 Affx-122919751 AX-123323957 23 14952692 ACTCCAGCCATATTTGGAGCTCCTGTGACACTCCC[A/G]TGGAATAGCGTTTAGACCTGCTGGAGACAAGGCCC R 2 1 2 1 101000 r 74 goat snp31004-scaffold3423-357695 23 33476665 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767160 Affx-986698381 AX-385254445 23 14966494 AGACGTGTCATGGGGTTAAGTGAATTTGCAGGGAG[C/T]AAGTCTCTAATTTTACCTGCACGGAAGATTTAAAG Y 2 1 2 1 600010 r 74 goat 23_14966494 23 14966494 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 320763855 Affx-986698383 AX-385251648 23 14966546 CTGCACGGAAGATTTAAAGGACCAGTTAGCTAACA[C/G]GGTTTCCTGGTGGAGGTGCTGGGCAGGGTAGTTAC S 4 1 2 1 600010 f 74 goat 23_14966546 23 14966546 Ancestral_priority_1043 ancestry 0.702 recommended IMAGE 10K 10K ancestral 320803580 Affx-986696410 AX-385290375 23 15022730 CAGAGTATCCTGAGCAAACCTCTGGGCCTCACCTC[G/T]TCATTCCTTCCTTTTCAGTTTAGTGATTTTACAGG K 2 1 2 1 600010 f 74 goat 23_15022730 23 15022730 Ancestral_priority_1043 ancestry 0.47 neutral IMAGE 10K 10K ancestral 38427617 Affx-122939356 AX-123297960 23 15024091 CTGCAGCAATCTGGACGATTACCTTGTGTGTACTC[A/G]TCTCTAAGGTGGCCCAGCAGGGTCAAGAAAGGTCA R 2 1 2 1 101000 f 74 goat snp31003-scaffold3423-286296 23 33405199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441814 Affx-122929071 AX-123312151 23 15060026 ATCCGAGTGGTCAAACTGAACTTCCCCCACCTGCC[A/G]CTGACTGTTACGTGCTGGTACCCTGTCTCCAAAGA R 2 1 2 1 101000 r 74 goat snp31002-scaffold3423-250361 23 33371062 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412999 Affx-122951017 AX-123283348 23 15097308 GTTCTCTCGGCACTCTGGCCCCAGAAACCTGCTCC[A/G]CTCAATCTATCTCTCCTCCTTCAAATGTCTCCCCT R 2 1 2 1 101000 r 74 goat snp31001-scaffold3423-213079 23 33333538 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428533 Affx-122938744 AX-123298875 23 15136679 GCACAATGATGATCAGATTTTATACATAACTTTGC[A/G]TACTACTTTTTGTCACTTGACATATCCCTGTGTTA R 2 1 2 1 101000 r 74 goat snp31000-scaffold3423-173708 23 33293583 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437835 Affx-122932097 AX-123308173 23 15178508 AGGAATGTCAGTTGGCTACCACCTGACTCCTTGGG[C/T]GGCAGGGGGAGGTGTGTGCATGTGTGTGTGTGTAT Y 2 1 2 1 101000 f 74 goat snp30999-scaffold3423-131879 23 33251806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448917 Affx-122923167 AX-123319252 23 15211394 TTGGGGGAGGGGGTGGAGGCCTTTATATTTGTTCC[A/G]CTTGAATTTGACTCTCCCAGGGTCTTACGATTTTA R 2 1 2 1 101000 r 74 goat snp30998-scaffold3423-98993 23 33219047 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799108 Affx-122929375 AX-385286038 23 15257043 GTAGTGGAAGGATTTCAACAGAGAGCATAATCCTC[A/G]TTATAATCCTCCCTTCGCTGGCGGTGCCTGTTTGT R 2 1 2 1 202000 r 74 goat snp30997-scaffold3423-53344 23 33173545 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777954 Affx-122922148 AX-385265070 23 15301716 CATGATGTGTTCCTGAAAATAAACAGAAATCGAAC[A/G]TGGTAAATATGACTCTAGATTTATGCATTATAAGG R 2 1 2 1 101000 f 74 goat snp30996-scaffold3423-8671 23 33129011 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441860 Affx-122929035 AX-123312197 23 15320865 TGAATGAATGAGAGAGGGGGGAACGCAGGAAGAAA[A/G]TAGGTTGGGGCAGAGACATTTGGACACACTCTGAG R 2 1 2 1 101000 f 74 goat snp11436-scaffold1417-10379 23 33109704 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414013 Affx-122950266 AX-123284362 23 15375300 ATGGCCTTCAATCTTCCCAACTTCCCAGCTGGAAC[A/G]CTGTTCCATCTTTCCTTCCCACAGACCAGGACACA R 2 1 2 1 101000 f 74 goat snp11437-scaffold1417-64814 23 33057466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394919 Affx-122964314 AX-123265274 23 15408492 CCTAAGTCTTCAGTGGCTTCCCATTACCTCCTAAA[C/T]GAGTCCTAACTCCCCAACCCAACATTGTTTATTTG Y 2 1 2 1 201000 r 74 goat snp11438-scaffold1417-98006 23 33024517 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426023 Affx-122941125 AX-123296369 23 15454936 TTTTTGAGTGGCTCAGAAAGCAAATGACAGTGACA[C/T]GAAGTGGCAGAACACAGAACTCTCCTGGGAGGAAG Y 2 1 2 1 101000 f 74 goat snp11439-scaffold1417-144450 23 32978042 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413358 Affx-122950149 AX-123283707 23 15492654 AAGAGCAGGGGCTGAGGCTGTGACATCCTCTGGGG[G/T]TCCCCACACTGTGGCCATAAAGGTCAGTGAAGGTA K 2 1 2 1 101000 r 74 goat snp11440-scaffold1417-182168 23 32940337 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416879 Affx-122948081 AX-123287227 23 15585121 TGTCAGATCAGATTTCTGAAAGAAACACCTTCTCC[A/G]TGGGACTCCTTGAGGGGTCCTTAAGCCAAGACTCC R 2 1 2 1 101000 f 74 goat snp11442-scaffold1417-274635 23 32847444 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428094 Affx-122939092 AX-123298437 23 15616511 TCACCTGAGAGCCTGCTGTGGACATTCGTGTGCAA[C/T]AGTGGGAGGATCACAGAGCCTGGCTTCCGTCTACC Y 2 1 2 1 201000 f 74 goat snp11443-scaffold1417-306025 23 32815994 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793422 Affx-122957924 AX-385280399 23 15665494 TCCTTACATACATCTAAAGATGGTGAACTATCTCT[C/T]AAAGCAACTCGTCCTATCACCAACAGTTTTGGCTG Y 2 1 2 1 101000 f 74 goat snp11444-scaffold1417-355008 23 32767349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436027 Affx-122932734 AX-123306366 23 15696714 AAATCTCCATACTCAAGTTTTCAATGTAAATGATA[C/T]TTCAGTTCAGTTCAGTTCCGTCACTCAGTCGTGTC Y 2 1 2 1 103000 f 74 goat snp11445-scaffold1417-386228 23 32736234 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274677 Affx-1111834436 AX-519548263 23 15704657 CCTCACCTGCAGGCGAGGCTGTCTCCGGGGGGAGC[A/G]TGAGCTCCCTGCCCTGGCTCCTGTGGCCCCAGGCC R 2 1 2 1 303000 f 74 goat GoatD01.035774 23 15704657 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38383570 Affx-122972597 AX-123253928 23 15733736 AATGATCTGTTCCCATGTTTTGGTTATTTTAGCAA[C/T]ACAATCTGAATATTCACCCTAAAGAGCCTGCTCAG Y 2 1 2 1 101000 r 74 goat snp11446-scaffold1417-423250 23 32699207 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433929 Affx-122934297 AX-123304270 23 15767670 CTTTAATATGCCACAGCACCCTAGCTGAAAAACAC[A/G]CCAATATCTCCAGTTGCTCTAGTCTCCCCCTCCCC R 2 1 2 1 101000 r 74 goat snp11447-scaffold1417-457184 23 32665301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769775 Affx-122929870 AX-385256945 23 15803434 ACCCAGCTTTCTTCGGCTGACTGATACTGCTAACC[A/G]TCTTCACTGAGAAGTTAGGGATTCCACTTCTCCTT R 2 1 2 1 101000 r 74 goat snp11448-scaffold1417-492948 23 32629253 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452200 Affx-122920818 AX-123322533 23 15837366 GAACATCTCTCTCTCTCTCTCCATGGTCTCTCTAG[C/T]ATGAGAGTAGTTGGATTCATATACAGCAGTACAAA Y 2 1 2 1 101000 r 74 goat snp11449-scaffold1417-526880 23 32595415 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791648 Affx-122970515 AX-385278639 23 15885209 AAATTGTAGTAGGGCACTATGGGGCTGTTGGTTAG[C/T]GAGTTATTTTGGGCGAATTGATGAGGACACTAGAG Y 2 1 2 1 101000 f 74 goat snp11450-scaffold1417-574723 23 32547390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793440 Affx-122957431 AX-385280417 23 15916445 TGAAATATTTTCAGACCTAGAATTAGGTTGTAATA[C/T]AGAATTGTATAAGTAAAATAGTCCTCTCACAATAA Y 2 1 2 1 103000 r 74 goat snp11451-scaffold1417-605959 23 32516151 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421901 Affx-122944254 AX-123292248 23 15986377 TAGCCGCTTAGTAAAATAGTTCATAACCACGCCAT[A/G]CCACCCACCACTCTCGCGTGATCATGTGTGCTGAA R 2 1 2 1 101000 f 74 goat snp11452-scaffold1417-675891 23 32446123 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409536 Affx-122953611 AX-123279887 23 16057207 CAGAATGGTGGGAACGAAATAAAAATTGTTTTTTG[C/T]GATAGAAGTCAGCAGGGACTTGTACATTCTGGTGG Y 2 1 2 1 101000 r 74 goat snp11453-scaffold1417-746721 23 32375287 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774650 Affx-122964336 AX-385261784 23 16104718 TCGTGTATTTTCTTTCATAGTTAGTGTTTCAATCT[A/G]TTGCTTTCCTTATTCTTTTGATGCTTAAATCCTCC R 2 1 2 1 101000 r 74 goat snp11454-scaffold1417-794232 23 32327702 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397994 Affx-122961799 AX-123268349 23 16136345 CCTGGCAGCAACTACAGGACAGAGTGCGACTCAGA[C/T]GGCTAAAAGTGAAACCGCATGGCTTGGAAGTGCCA Y 2 1 2 1 101000 r 74 goat snp11455-scaffold1417-825859 26 47178432 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277629 Affx-1111835945 AX-519551128 23 16158772 TCTGTTACCGTAGACTGAGAGAATATGAGGGGTGC[A/G]TTGAAAATAGGTACGAGGATAACTGCAGAGATGAC R 2 1 2 1 201000 r 74 goat Random2.2K-2038 23 16158772 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399660 Affx-122960514 AX-123270015 23 16172284 TGATGGAAGAGAAACCCAGACGGAAGGATATGAGA[C/T]GCGGACCTGGGGGGGCATGGACAGTTCTAGGCCCC Y 2 1 2 1 101000 f 74 goat snp11456-scaffold1417-861798 23 32260306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396717 Affx-122962809 AX-123267072 23 16220358 CCACCCTACTCCCCCAGGTTTAAGGTACATGCTCA[C/T]GGGTCCTGACTGATTGATTCAATTGGGTAATTGGA Y 2 1 2 1 101000 r 74 goat snp11457-scaffold1417-909872 23 32212505 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785346 Affx-122955588 AX-385272391 23 16256899 TAAGCACTTGGAATAATAGGAACGGTGGAGGAAAT[C/T]ACAGTACATCCATTTGATGGGCCCTATGCAAAAAT Y 2 1 2 1 101000 f 74 goat snp11458-scaffold1417-946413 23 32175855 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437477 Affx-122932372 AX-123307815 23 16294145 CACTTAAGAATGACCTCCCTTTGGGTTGAGTTTGA[A/G]TTAGGTTTTGCCAGGACATTTGTCCATTAAAGGTG R 2 1 2 1 101000 r 74 goat snp11459-scaffold1417-983659 23 32138787 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271974 Affx-1111833255 AX-519545744 23 16297430 CCTCGGGTCAGGGAACTAGGATCCTACAAAGCCAC[A/G]GGGTCCAACGCACCCCCCGCCACCAAAAAAATTAT R 2 1 2 1 102000 r 74 goat 23_16297430_AF-PAKI 23 16297430 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468277630 Affx-1111835946 AX-519551129 23 16311480 TTCTCGGTGGTGGGGAGGCCCTTCTGTGTAGGTTC[A/G]GTTGAAAATCACCTTATCCAGGGGTCAGCTGCCTT R 2 1 2 1 101000 r 74 goat Random2.2K-2039 23 16311480 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38410170 Affx-122952783 AX-123280520 23 16377947 ATACTCTAGAAAACGGACCCTCCTTTTCCAGGGAC[A/G]CTGAAGGAAGGCAGCAGTGACAGACTGTACATGAT R 2 1 2 1 101000 f 74 goat snp51826-scaffold761-5189653 23 32054939 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277632 Affx-1111835947 AX-519551131 23 16424550 TTGGCTTACTTTGAACCAAGGCAGTCAACCAATAT[A/G]CTCTGATGATATGCCAAACACTCTGCTAAGGGTAC R 2 1 2 1 101000 r 74 goat Random2.2K-2040 23 16424550 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436539 Affx-122932926 AX-123306877 23 16442519 GTTTTTCCCCAGCACCAAGATCCAAGATGTCACAA[A/C]ATTAGCTACTTGGAATCTCTTCCCAAACCCTAGCC M 2 1 2 1 201000 r 74 goat snp51825-scaffold761-5125081 23 31986083 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449174 Affx-122923533 AX-123319509 23 16557665 CCTTTTTATTGCCAAATAACATTTTATTGTATGTG[C/T]ATGCTACATCTTGTTTAATCATTCATGGGTTAATG Y 2 1 2 1 101000 r 74 goat snp51823-scaffold761-5009935 23 31870289 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784797 Affx-122926489 AX-385271844 23 16614270 AACTTATACTCAATGAATCAATTATATTGGTTCTT[A/G]CAGAGCTTTTCAAATAAGGGTTCCCAATCATTGTA R 2 1 2 1 101000 r 74 goat snp51822-scaffold761-4953330 23 31813412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376625 Affx-122979036 AX-123246984 23 16684329 ACTTTGATTTCTTAAACATGTTAGAATTAAGTACC[A/G]TGTTACTTTGTAAGTCTTTTTTACTGAAGGAGAGA R 2 1 2 1 101000 f 74 goat snp51820-scaffold761-4883271 23 31743139 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417620 Affx-122946865 AX-123287968 23 16729470 TGTCTTCTTACTGTTTGTGTTCAGAGTACCTGACT[A/G]CCACATTCTATAGGTGGAGAAATATGGCTCAAGGT R 2 1 2 1 101000 f 74 goat snp51819-scaffold761-4838130 23 31697889 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791462 Affx-122934001 AX-385278453 23 16799884 CAGAACCGAAAATCTTCTCAGGGGTCCAAAGGAAA[C/T]GGAGCCAAAGGAAAAGGTGGCCTTTTTCCAAACTT Y 2 1 2 1 202000 r 74 goat snp51818-scaffold761-4767716 23 31628309 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447744 Affx-122924585 AX-123318080 23 16828986 GCTATCCCCCAGCAGAGCCTGAGCAGTGACTGTGC[A/G]TTCACTTTCTACTTGTACAAATTTTACATTTACTA R 2 1 2 1 101000 r 74 goat snp51817-scaffold761-4738614 23 31599098 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767167 Affx-986698385 AX-385254451 23 16849476 ACATTTTCAGAGCGCCTATCCTAGTCTCTCATTCT[A/G]GAAATTTCCAAGGACTAATATAGATCATCCTTGAT R 2 1 2 1 600010 r 74 goat 23_16849476 23 16849476 Ancestral_priority_1043 ancestry 0.592 neutral IMAGE 10K 10K ancestral 320763861 Affx-986698389 AX-385251652 23 16879918 CCACATGTATTTGAGTCATGTCATATCTGTAATTA[C/T]AGAAAAATACCAAAACCATAAGTACAATTTCCCAG Y 2 1 2 1 600010 f 74 goat 23_16879918 23 16879918 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 320772341 Affx-122947939 AX-385259494 23 16897386 ATTCCCTTCAGGCAGAACTGCCTAACTAGAGGATA[C/T]TCAGTCACTGTGAATTTCAGACTCACTATGAAAAT Y 2 1 2 1 101000 f 74 goat snp51816-scaffold761-4670214 23 31531927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378813 Affx-122976555 AX-123249172 23 16967762 CTCCAGGTGGGAGGGGGATAAAGTAGAGGCTGCAG[C/T]GAGAGCTGTTGACTCCCTGTGATCCCCGTGCTGTT Y 2 1 2 1 101000 r 74 goat snp51815-scaffold761-4599838 23 31461542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426930 Affx-122940433 AX-123297275 23 17000098 CCAGGCATACATTGAAGCCCCTCCACCTGTTGGGG[C/T]ACCTCCTTAAGGAATGAACACTCATTGCAACAGCC Y 2 1 2 1 101000 r 74 goat snp51814-scaffold761-4567502 23 31431389 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781119 Affx-122948278 AX-385268204 23 17032041 TCTGTGAGACTGCACATGTAGTGTACGTCTACATA[G/T]AGGATGGACTCATTTACAGAGGGTGCAGGTATAGA K 2 1 2 1 101000 r 74 goat snp51813-scaffold761-4535559 23 31399381 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388800 Affx-122968915 AX-123259158 23 17098708 CTCCTCAGAGCCAGCTCTGCCATCCCTTCCATCGT[A/C]AGATTCTCCTGTAGAGTACAGAGAGCTCAGCCTGG M 2 1 2 1 101000 r 74 goat snp51812-scaffold761-4468892 23 31332817 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429783 Affx-122938210 AX-123300124 23 17136773 ACAGCTCCCAAGTCCATGTCTCTGTTCTACAAGAT[C/T]GCCTGGTTAGAACCCCACTTCTGGCCACTGTAGAG Y 2 1 2 1 101000 f 74 goat snp51811-scaffold761-4430827 23 31294686 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435129 Affx-122933686 AX-123305469 23 17172494 AGGGTCAGTTTTGGCGCCAGGTCATTGCACCTGGT[A/G]AGAACTCTCATAGATCAGCCTGGGGATGGTTGGTG R 2 1 2 1 101000 r 74 goat snp51810-scaffold761-4395106 23 31259191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388783 Affx-122968927 AX-123259141 23 17217864 GCTTTGTGTTTCCTAAGCGTCACTGCTGGTTGATA[C/T]GTAGTTTGTTTTGGGGAAGGCGCAGGGTACCTCTC Y 2 1 2 1 102000 f 74 goat snp51809-scaffold761-4349736 23 31213605 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375977 Affx-122978432 AX-123246336 23 17277675 AGCATGTACTAATTCTCACGCAGCCTCCACACACA[C/T]GTGCACATGCCTCAAACACAAATCAACTCTGGCTT Y 2 1 2 1 202000 r 74 goat snp51808-scaffold761-4289925 23 31156286 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411644 Affx-122951573 AX-123281994 23 17337574 CCATATTCCTCCTGGGTGATGTCATCAGGGTTCCT[A/G]GTCCAAATGGGCTTGGTTTTGTTCAGTTCTTCCTG R 2 1 2 1 101000 r 74 goat snp51807-scaffold761-4230026 23 31097309 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38429770 Affx-122938249 AX-123300111 23 17372018 ATCCTTGGTTTGTCCTGTACGTTAGTCTCTGTTAA[C/T]GTTCATCCTTTTCAAAGATGAGTCACCAACCTCTC Y 2 1 2 1 101000 f 74 goat snp51806-scaffold761-4195582 23 31063006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383707 Affx-122972479 AX-123254065 23 17420442 CCATGAGCTGGGTCTGAATGAGCTGGGGGAGGGAG[A/G]AGGGGTCCCAAATGAGTGGGATCGCAGGGCCATCA R 2 1 2 1 303000 f 74 goat snp51805-scaffold761-4147158 23 31014530 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405401 Affx-122956291 AX-123275753 23 17456383 AGGTCAGGAAATACTTCCCAGCTTAAGGACCAAAA[C/T]GGCAGTTATGGAGGCTGGGGAGATTACTTTAATGC Y 2 1 2 1 101000 f 74 goat snp51804-scaffold761-4111217 23 30978564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414751 Affx-122949255 AX-123285100 23 17545848 GAATGGGATGATGCAGCTGGCAGGCAACCAGGGAA[C/T]GGAAGCTGTTTCCACATTCAGCACCCAGAAAGGTG Y 2 1 2 1 101000 r 74 goat snp51802-scaffold761-4021752 23 30891696 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391799 Affx-122967035 AX-123262156 23 17582153 AGCTACTTGAAACGTCAGCCACAGTTTGTCTCTGC[A/G]TCAAGCAAAATCCACTGCAGATGCAGCTGGCTTTC R 2 1 2 1 201000 f 74 goat snp51801-scaffold761-3985447 23 30855419 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404812 Affx-122956652 AX-123275164 23 17634756 TCTCAGCATCTCCCAAACCCAAGACCCAGGGCACC[A/G]CAACACACAACTGTAGGAGGCACCCTTCACACCAC R 2 1 2 1 101000 r 74 goat snp51800-scaffold761-3932844 23 30802853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393648 Affx-122965291 AX-123264003 23 17711674 TTGCTTTGATGTGTAAGTTTTCCAAAAAGCAGTTA[C/T]GTATTTTAGTAGGCAAATGTTTTATAACAAGCATG Y 2 1 2 1 101000 r 74 goat snp51798-scaffold761-3855926 23 30725825 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448020 Affx-122923723 AX-123318356 23 17749822 CATGGACAAGAATTTATAGGGTTCACACACTCCGC[A/G]CTCTGCTGTCCCTTGTTCCCCACCCCCTTCTGTGA R 2 1 2 1 101000 f 74 goat snp51797-scaffold761-3817778 23 30687896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799935 Affx-122938661 AX-385286861 23 17788158 GTCTATTCAGTAGAATACAGAACATAAGACAGTCT[A/G]CTTGAAAGGGTGTCTGTTGGCCTAAGGATAATATG R 2 1 2 1 101000 r 74 goat snp51796-scaffold761-3779442 23 30649405 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396962 Affx-122963170 AX-123267317 23 17820152 GTGGGGGTGCTTGGTAGCAAACACTGCAAACGTCC[A/G]CAGCACTGGGGAAGGGAAGTTTGCCGGGAATCTCC R 2 1 2 1 101000 f 74 goat snp51795-scaffold761-3747448 23 30617408 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794319 Affx-122974859 AX-385281283 23 17866033 CATCTTAGTAATTTTGTATTTGATCTCAGAGCCAC[C/T]CTATGGAATAAGAGCTCTCTTTGGGCAGTTTACTT Y 2 1 2 1 101000 r 74 goat snp51794-scaffold761-3701567 23 30570854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799990 Affx-122948616 AX-385286914 23 17935441 TTATTATCCTCTGTTTGCAAATGAGGACCCTAAAG[C/T]ACTTGCTGAAGATCACAGTTAAAAGGTAAAAATGC Y 2 1 2 1 101000 f 74 goat snp51793-scaffold761-3632159 23 30501311 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450324 Affx-122922132 AX-123320659 23 17981471 GATCTGAATGTTTAAATAACGCTGCTTGTGGACTC[C/T]CCACACATCTTCTATGTAGATAATGAAGAGTGTCT Y 2 1 2 1 101000 f 74 goat snp51792-scaffold761-3586129 23 30454943 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449034 Affx-122923076 AX-123319369 23 18020724 GAATTACAGAATCTGCTGCCCAAGTCCAGCTGCCC[A/G]CTGAGACACTGTATTCTGGGATTGAATAAAAACCA R 2 1 2 1 101000 r 74 goat snp51791-scaffold761-3546876 23 30414533 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399365 Affx-122961343 AX-123269720 23 18054779 GATATATGTTTGTTAAAAATGAAGCACTTTCCTAT[A/G]TCCTCTGCAGAAATTGTCCTGAGGAAAGTGAAAAT R 2 1 2 1 101000 r 74 goat snp51790-scaffold761-3512821 23 30380585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441239 Affx-122929502 AX-123311576 23 18112584 TTACGTGGCAAACAGAATTGTTTCTCTTTCTGACT[A/C]TTCTGTTTTACAGTATTGAGGAGAGTGGCATTTGT M 2 1 2 1 303000 r 74 goat snp51789-scaffold761-3455016 23 30322879 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379424 Affx-122976109 AX-123249782 23 18180963 CCAGTTCACCTTTCATGTGCAGTTTTCTTTTCTCT[A/G]ATTCTTTCTAGCCAAGAGTAAAATGCTGAATCTTA R 2 1 2 1 201000 r 74 goat snp51788-scaffold761-3386637 23 30254440 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782213 Affx-122926492 AX-385269291 23 18214259 AACCTGCAGTGAGAGTTTCCTAAGAGGATGGATCA[C/T]GATTACAGTTCTACTAGCTGCTTTTAGTATTTCTT Y 2 1 2 1 101000 f 74 goat snp51787-scaffold761-3353341 23 30221088 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436203 Affx-122932592 AX-123306542 23 18252434 CATACAATTGTGTAGTTATGGAAAGGACTACGTGG[C/T]CTGCAAAGCCTAAAATATTTAATATCTGTTTTGTT Y 2 1 2 1 101000 f 74 goat snp51786-scaffold761-3315166 23 30182746 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391179 Affx-122967431 AX-123261536 23 18303622 ATTACACAGAGAAAAAACAAAGAACAAAAGTAAAA[C/T]GAGAAAAAAATTAGTGTTTTAAAAAAAGCACTGGG Y 2 1 2 1 303000 f 74 goat snp51785-scaffold761-3263978 23 30132455 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425898 Affx-122941625 AX-123296244 23 18341466 AAAAACTTCGTTTTTCTTGGAACATTACCCTTCTC[A/G]TCTTTTTGTAGAAACATAATAAGGCCAGAGCATCT R 2 1 2 1 101000 f 74 goat snp51784-scaffold761-3226134 23 30094702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393110 Affx-122965580 AX-123263467 23 18395246 AGCTCTTTTAGAAAACAGAGCCAAAGAGGCAAGAA[C/T]GAGCAGATCTAAAAGGCAGCCTCTAATTCATAGCT Y 2 1 2 1 101000 f 74 goat snp51783-scaffold761-3172354 23 30040909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275092 Affx-1111834683 AX-519548671 23 18446241 AAAACAATAAAAGCAGTCTGCAGTAGTCACCGGAA[A/C]GCCGGGGCAGCCGGATCAATACCCATATATTGATT M 2 1 2 1 101000 f 74 goat GoatD01.045795 23 18446241 A C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38439793 Affx-122930498 AX-123310130 23 18446538 TATTCAAGGCCGAGAGTCTGCACCAAAGACCTAAG[C/T]GCTGTGCAACTTTGATTGTACCTCTCTCAGCCAGC Y 2 1 2 1 101000 r 74 goat snp51782-scaffold761-3121062 23 29989272 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450740 Affx-122921862 AX-123321074 23 18500989 CCATTTTACTGTGGAGGAGACTGAGGCTTTACTAC[A/G]TTCAGTACCCTGCTCACGGTCATCACATGTGAAGG R 2 1 2 1 201000 r 74 goat snp51781-scaffold761-3066611 23 29934235 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763863 Affx-986698391 AX-385251654 23 18508980 TAAAAACTGAAAGTAAAGCAATCATTCAGTGGTTC[A/C]GATAAAAGAAAAGCATCTTTACCTGAGTTACCCAT M 2 1 2 1 600010 f 74 goat 23_18508980 23 18508980 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 320767182 Affx-986698393 AX-385254464 23 18508981 AAAAACTGAAAGTAAAGCAATCATTCAGTGGTTCA[A/G]ATAAAAGAAAAGCATCTTTACCTGAGTTACCCATC R 2 1 2 1 600010 r 74 goat 23_18508981 23 18508981 Ancestral_priority_1043 ancestry 0.61 recommended IMAGE 10K 10K ancestral 320763867 Affx-986698395 AX-385251657 23 18523293 TGCGATTTAAGGGCCAACAAGGCCAGCTAGCTTCC[C/T]GAGCCCTTTCAGCCTGGCTGGGAAGCGGCCGGCGC Y 2 1 2 1 600010 f 74 goat 23_18523293 23 18523293 Ancestral_priority_1043 ancestry 0.51 neutral IMAGE 10K 10K ancestral 320787699 Affx-122978166 AX-385274722 23 18541816 GCAGATCTTTTCACAACATATTATACCTGACAGAA[C/T]GCACTTGAATTTGATAAAATGCAGCTCCTTCATTT Y 2 1 2 1 101000 r 74 goat snp51780-scaffold761-3025784 23 29893709 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797589 Affx-122945493 AX-385284528 23 18617282 TCTTTAAAAAACCCTTAATCACTCCAATGTATACT[A/G]TGATAAGTTTAAAGGAATCAAAACCAAATGAAGAA R 2 1 2 1 201000 r 74 goat snp51779-scaffold761-2950318 23 29818002 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38426151 Affx-122940605 AX-123296497 23 18673412 ATTGACGCCAGGTATTTTTTAAAGGTCCAGCAATA[C/T]AGAAGCAGGACGCAGGGCTCCACCTTCCAGGCCAT Y 2 1 2 1 101000 f 74 goat snp51778-scaffold761-2894188 23 29761657 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390876 Affx-122967807 AX-123261233 23 18740444 CTAATTCAAATAAAGTTGGTTTATTTTCAAATAGT[A/G]CAAAATCGATCATCAGACATCTTATTGAAGGTGGG R 2 1 2 1 101000 r 74 goat snp51777-scaffold761-2827156 23 29694620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394791 Affx-122964820 AX-123265146 23 18791438 TGGGCACTGGGTATCGTGACTGAGTGTCTGGCACA[A/G]AGATGGGCATGGACATCTGAAAATCCAGAGTGAGC R 2 1 2 1 201000 f 74 goat snp51776-scaffold761-2776162 23 29643384 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394170 Affx-122964931 AX-123264525 23 18899718 TAGAATCCTGTAATTAGGATAAAAAGTGTTAAGCC[A/G]TATTTCTATTGCAGGTAACCTAGTTTTCTTCAATG R 2 1 2 1 101000 f 74 goat snp51773-scaffold761-2667882 23 29534913 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447997 Affx-122923739 AX-123318333 23 18954154 TATCAGTAGTACAGATTAAGAAGCTGAGACATGAG[A/G]TGGTAGATAGCAAACTCCTCAGGAGGTCTGAACTC R 2 1 2 1 101000 r 74 goat snp51772-scaffold761-2613446 23 29480555 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425223 Affx-122941014 AX-123295569 23 18985422 ATTTGTCTTCCCGAATGCATCTAAAGCCCCAACTC[G/T]GAGAATAACGGGAGAGATATAGCCCTACATTCTAA K 2 1 2 1 201000 r 74 goat snp51771-scaffold761-2582178 23 29449358 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277511 Affx-1111835948 AX-519551013 23 18992878 TATGAAGACAACTTGATTTGCTCAGCGTGGTGTAG[A/G]GAAAGGGAGGTGGGGGGTGGGGTGGGGGGTTGCTG R 2 1 2 1 101000 f 74 goat Random2.2K-2042 23 18992878 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797488 Affx-122935204 AX-385284427 23 19031295 TTATCCAAAAGCTTGTTTTTATACCTAGAAGTGAT[A/G]CTGTCCTCAGTTTCAGCTGATGGTGCCACCTTGTA R 2 1 2 1 102000 r 74 goat snp51770-scaffold761-2536305 23 29402698 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271976 Affx-1111833256 AX-519545745 23 19034215 TGAACTTAGAATTAGTGAAGAAAAATTCCTAGAAA[A/G]TTCATATGTGCTTTGATAGTGCCAAATGCCACAAT R 2 1 2 1 101000 r 74 goat 23_19034215_AF-PAKI 23 19034215 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448235 Affx-122924212 AX-123318571 23 19077787 AGTAATAATAATAAATAATAATAACTGAGTATTTA[C/T]GGTGTACTGGACACTAGAACTCGTGTATTTCTTGA Y 2 1 2 1 103000 r 74 goat snp51769-scaffold761-2489813 23 29356117 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388430 Affx-122969272 AX-123258788 23 19124079 AAAACTTTTGAAATTTCCAAAGGTATTGCCTTGCA[C/T]GACAGACACACCCCACCCAAAGCCCAATCTAGGTG Y 2 1 2 1 201000 f 74 goat snp51768-scaffold761-2443521 23 29309340 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771706 Affx-122943127 AX-385258863 23 19174377 CCATAGCGAGTAATTTCATTCTGGACCTCAAGGAG[A/G]AAGATTTCTTTTACAAAGGCTTTTTTCATAACATG R 2 1 2 1 101000 f 74 goat snp51767-scaffold761-2393223 23 29258910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417695 Affx-122947459 AX-123288043 23 19209971 TAACTCAGCTCTGTCTATGATCCACAGAGGGTCAG[A/C]TGCCTATTTTCCCATATAGATTAATTAAAGTGGTT M 2 1 2 1 101000 f 74 goat snp51766-scaffold761-2357629 23 29223364 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439489 Affx-122930153 AX-123309826 23 19260712 AAATGGGCACAGAGATTCCTGTCTGGGGTTCTGTA[C/T]ATGCCTACCATGTCCTATCCTTGACTTCTGTCGTA Y 2 1 2 1 201000 r 74 goat snp51765-scaffold761-2306888 23 29172576 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405223 Affx-122956895 AX-123275575 23 19290943 GCCAAAAAGTGTCCCTGTTTTTGTTGCTACTTCTA[G/T]TTTGGAGGGCAAATAGGAGGCTGACTATCCTAGGA K 2 1 2 1 102000 r 74 goat snp51764-scaffold761-2276657 23 29142270 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423935 Affx-122942257 AX-123294281 23 19321108 GGAAAAACATCCAAGGGAGAGGAACTTTCCTGAAG[C/T]AAGACGGAAAGGAAATTCACACAGGGATGTACAAT Y 2 1 2 1 101000 f 74 goat snp51763-scaffold761-2246492 23 29112200 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387245 Affx-122970568 AX-123257603 23 19429107 TGCTAACTTTTTTCTTTATTAACAGTCTCGTGTGT[A/G]TGTTCCCGTGTGTTTGCACTGTTTGTAGTTTTTGC R 2 1 2 1 101000 r 74 goat snp51761-scaffold761-2138493 23 29002454 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395549 Affx-122964250 AX-123265904 23 19486239 CAGGAAAAAAAAAAAAATACTGGTAGAATTGTCAA[C/T]TATGATTACCCATGACTGAGAAAAAAAGGAGACTG Y 2 1 2 1 101000 r 74 goat snp51760-scaffold761-2081361 23 28945611 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776926 Affx-122953463 AX-385264050 23 19609871 GATCCCAGCTGACCACCTGCTGATTACATTTTTAT[C/T]ATTAATAGTTTAGCAGAACAGCCTTAGGTTTTGGT Y 2 1 2 1 201000 r 74 goat snp51757-scaffold761-1957729 23 28822354 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412594 Affx-122951294 AX-123282943 23 19661506 ATTCTCATAAAAAGCTGTGAATCCTCACTGAACAA[C/T]GGAGCCAGTAGGTGACAGCTATGTGGAAGCAGCAC Y 2 1 2 1 201000 f 74 goat snp51756-scaffold761-1906094 23 28770760 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397201 Affx-122962398 AX-123267556 23 19700117 TAAACTTTGGGTTTGCCAACCTGATCGCCAAGCAC[A/G]CTGGCAGGTCAGACAGACTCTCAGAGTTTGCCATC R 2 1 2 1 201000 f 74 goat snp51755-scaffold761-1867483 23 28731439 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799315 Affx-122947298 AX-385286245 23 19740675 CAACCACAACTCCCTAACTTCACCGGAGCTTTACT[A/G]TTTCCCTCTGTACTAAGTTGTCAAAGATTTTTAAA R 2 1 2 1 101000 f 74 goat snp51754-scaffold761-1826925 23 28691099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794508 Affx-122934178 AX-385281471 23 19771444 AAAGAAAAGGATGCCAGTTCCCAGTTACTAGCATC[A/G]CTGGAAAACATCAGCGCTCTAGTACCTTCGACAGC R 2 1 2 1 202000 f 74 goat snp51753-scaffold761-1796156 23 28660519 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438740 Affx-122930831 AX-123309077 23 19862845 TCCTTTGGGTAGATATAGAAGCAAGTTAGTGCAGC[G/T]TGAAGACAGATCTTCCCACATGGAAAGTCAATATG K 2 1 2 1 101000 f 74 goat snp51751-scaffold761-1704755 23 28569641 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273823 Affx-1111833839 AX-519547434 23 19900368 TGGATGAGGGAACGCTAGGGGGAAAAGACAACCCG[A/G]CGAAAGGAGCAGAGAGCCCAGTTCTCAGGACTAAC R 2 1 2 1 202000 r 74 goat GoatD01.006562 23 19900368 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38379142 Affx-122976729 AX-123249501 23 19947974 CAACTAGTCACTTTGTGCTCATCCTGTCTCTTCAG[C/T]GCCATGGATGCCTTGCTTTAGGAAAAATGAAATGT Y 2 1 2 1 201000 r 74 goat snp51749-scaffold761-1619626 23 28484293 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420606 Affx-122945246 AX-123290953 23 20013536 GCAGCGTGGAGGCATAACCACTGGACCACCAGGGA[A/G]GTCCTGTGATCTCACTCTCCTTGAGAGATGCTGAA R 2 1 2 1 101000 r 74 goat snp51748-scaffold761-1554064 23 28418758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434229 Affx-122934838 AX-123304570 23 20043733 GGCTGAGCTCTGCAGTTTCCGAGGGTACAGAGTCT[A/G]CTTTGAACGTGGGAGGCTCTACACCAGGACCTACT R 2 1 2 1 101000 f 74 goat snp51747-scaffold761-1523867 23 28388570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378133 Affx-122977126 AX-123248492 23 20076613 GCCTCCTCCTCACTTTCACCTGGCTGACTTCTATT[A/G]AATTTTGAGGGTTGAATTCTTTTAATATTTCTTTT R 2 1 2 1 101000 f 74 goat snp51746-scaffold761-1490987 23 28355753 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410248 Affx-122952538 AX-123280598 23 20161971 AAGACAGATCAACAGAAACTTCTTGAACTAAAACA[G/T]AAAAATAATATTCTTTTACAAAACAGAACATCCAA K 2 1 2 1 303000 f 74 goat snp51744-scaffold761-1405629 23 28270396 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419311 Affx-122945667 AX-123289659 23 20192925 CAATCTCAATGCATCTTTTGTATTTCAAAATAACT[A/G]GATGGAAAATCACTTCTGTAGCATGAATTCCCACT R 2 1 2 1 101000 r 74 goat snp51743-scaffold761-1374675 23 28238585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277513 Affx-1111835949 AX-519551015 23 20232886 ACTCCACCATTTATCTACTGCTAATGTCTTTTCAA[A/G]AGTTGTACTTATAAAAATGTGAGCAATTAAAAGAC R 2 1 2 1 101000 f 74 goat Random2.2K-2043 23 20232886 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429718 Affx-122937615 AX-123300059 23 20307366 CGTGTTTTAGGTAAGGAAATTAAGACCCAGAGAAG[C/T]GAAGCAACTCGTACGGCTAACAGACAAACCTAAGG Y 2 1 2 1 201000 r 74 goat snp51740-scaffold761-1260234 23 28126858 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431131 Affx-122936585 AX-123301472 23 20337657 TAAATTAAACATAAACAAGGTGCTCGTGCTTTCCT[C/T]ACTGCTTCATTCCAACGTGTGATAAATATTGAAAA Y 2 1 2 1 101000 f 74 goat snp51739-scaffold761-1229943 23 28096579 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384114 Affx-122972829 AX-123254472 23 20372412 CTGCTTACAGATTTCAAGGAGGGTGAAATGCACCA[C/T]GCCAGGTCTCCTTTGCAAACTATGAAGGACTACGT Y 2 1 2 1 101000 r 74 goat snp51738-scaffold761-1195188 23 28061254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401595 Affx-122958870 AX-123271948 23 20433961 TTACATGTGACTACTCCACTCTACCCAGACTCTTC[A/G]TTCCTTTTTTTGACACAGAACTACTCTTTTATCTC R 2 1 2 1 101000 r 74 goat snp51737-scaffold761-1133639 23 28000110 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450495 Affx-122922516 AX-123320829 23 20472157 TTGTAAAATCTTTAATTCCCCAGTTTTCACAATAG[G/T]AAGTGGGAGATAAGAGTTCAGCTAAGGAAATAAGA K 2 1 2 1 101000 r 74 goat snp51736-scaffold761-1095443 23 27961499 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378566 Affx-122976602 AX-123248925 23 20501453 GGACTGAGGTGACACTGATCCCCTGAGCTGATTCC[A/G]TGGAAGCTCTTTACCTTTGCAATCAAATTTTCTTA R 2 1 2 1 101000 r 74 goat snp51735-scaffold761-1066147 23 27932154 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402388 Affx-122959025 AX-123272741 23 20537500 GAAAGCTCAATACAAAGCAAGGGAAGAAAGAGTAA[C/T]GAAAAGGAAGCATAAAAATCAATATAAATAAGAGG Y 2 1 2 1 101000 f 74 goat snp51734-scaffold761-1030100 23 27895879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766200 Affx-122965081 AX-385253600 23 20569401 CCAAGGCAAACCTTGAAAGAGTTGGAGAAATGTCC[A/G]GTAGGAACTCAGCCTGACACTGTAAAGTGTTATGG R 2 1 2 1 101000 f 74 goat snp51733-scaffold761-998199 23 27865689 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427195 Affx-122939598 AX-123297538 23 20608053 TACAAGGGAAACTGTATTGAACTACCAAGGTCCTC[A/G]TGGTCTTTTCTCTGAAAACATCCTTCAGCCAAGGG R 2 1 2 1 101000 f 74 goat snp51732-scaffold761-959547 23 27827948 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768371 Affx-122959047 AX-385255551 23 20644107 CTTCTTATCATTCAGTTAGCTAAGTAAGTGTATGA[C/T]GCTTAAAGAAGGGCTTCTCAAATTCTGATTGTCAT Y 2 1 2 1 101000 r 74 goat snp51731-scaffold761-923493 23 27792308 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767197 Affx-986698401 AX-385254479 23 20646449 TGGTTGGAATCTCGCTGGGGCCTCCAGAAACGTAG[A/G]AGCCAGAAATCAAGCACCACACACGGAGAGCTGGA R 2 1 2 1 600010 r 74 goat 23_20646449 23 20646449 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 38431701 Affx-122936772 AX-123302042 23 20771365 TTATTTCTTTTATCTTCCTCAATACTTATAAATAG[C/T]AACCTTTTTCTCCTCCTTTTCACTTTCTTCTCCCT Y 2 1 2 1 303000 f 74 goat snp51728-scaffold761-796235 23 27664633 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385889 Affx-122971592 AX-123256247 23 20825397 TCTGAATTTCTTCTTCAAAGAAGAATTTCTGTGGC[A/G]CATATTATCTATTTTACTGTTTTGATGTTGTTATA R 2 1 2 1 201000 r 74 goat snp51727-scaffold761-742203 23 27609988 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378365 Affx-122976822 AX-123248724 23 20889676 TACTATACTGAGCTTTCCAGGCATTATTATGAAAA[C/T]AAGCCTTGAGGAAAGCAGTTGAGCAAGGAAGATGA Y 2 1 2 1 102000 r 74 goat snp51725-scaffold761-677924 23 27545546 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410711 Affx-122952723 AX-123281061 23 20933777 CAAGGCTGATCTTTCCACCTGCATCTTTAATATCA[C/T]CTTCCCTCCTCATCTTTGGGACAACCTGATATTGC Y 2 1 2 1 101000 f 74 goat snp51724-scaffold761-633823 23 27501733 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790869 Affx-122977321 AX-385277867 23 21027323 CATTCTTGTCATAGCCAACAGAAATGGGCATGGAT[A/G]CTCAATACACATGCCAGGTTACCTCTTCCAGTATT R 2 1 2 1 101000 f 74 goat snp51721-scaffold761-540277 23 27407073 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390739 Affx-122967913 AX-123261096 23 21102001 GCAACTTCTTGAACCAGGGAGTATATCAAACATTA[G/T]AAACAACTCTCCATCAACATGTATCTGCATTTGAG K 2 1 2 1 101000 f 74 goat snp51719-scaffold761-465599 23 27331707 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389568 Affx-122968793 AX-123259926 23 21133953 AAAGATAAAGATGATTCTGTGTTATACTATCCTTT[A/G]TTCTTCCTTTTCAATCTTTAGCTTTCATGATGCAT R 2 1 2 1 303000 r 74 goat snp51718-scaffold761-433647 23 27298851 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768629 Affx-122934254 AX-385255808 23 21214424 AGGGAAGATGTAAATTTGACAAATCCTAGAAGATA[C/T]GTAGGGAGGAGAATATATACTGGGAGAATTAAATG Y 2 1 2 1 101000 r 74 goat snp51716-scaffold761-353176 23 27217263 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786486 Affx-122955128 AX-385273520 23 21324103 AAGGATTATCTCCCAAATTTCCATGTAATTAGTGC[A/G]TGTGTTTGAATAAGTTTATGTTGCCAAGTAAGCAA R 2 1 2 1 101000 f 74 goat snp51714-scaffold761-243497 23 27108249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390987 Affx-122966908 AX-123261344 23 21367124 TACTATAGGAATACAGAGAAAGCAGTGGTGAATCA[C/T]GCCTGAGCCAGAAAGCCTTGGAAAATTTCTATGCA Y 2 1 2 1 201000 f 74 goat snp51713-scaffold761-200476 23 27065555 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779576 Affx-122923053 AX-385266679 23 21440391 CACCCATGGGGTAAGAAAAAGAATGGTGAAATTGA[G/T]TCAATAAAACCTCAGGAAGCTTCAATATCAGGTAT K 2 1 2 1 101000 f 74 goat snp51711-scaffold761-127209 23 26992666 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793634 Affx-122977116 AX-385280608 23 21470058 CGTACATTTATTGACTTAAGCAAGAAACTATTTTG[A/C]TTATACATTATCATAAGATATCACATTGAGGCCAC M 2 1 2 1 201000 f 74 goat snp51710-scaffold761-97542 23 26963095 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803584 Affx-986696412 AX-385290378 23 21489601 TTCCGTCTCCTGAAGGCCTGGTCTCCACAAGCTCC[A/G]TGTCCTGGGTCTGGTCCTCCCCATTGCGCTGCCAG R 2 1 2 1 600010 f 74 goat 23_21489601 23 21489601 Ancestral_priority_1043 ancestry 0.432 neutral IMAGE 10K 10K ancestral 38449127 Affx-122923570 AX-123319462 23 21502678 GGGTTCTTCCTTGTATATTTCATGGATTTGACTAG[C/T]AATTTTTTTATTGTATTTTACAAAAGTAGCAGTTG Y 2 1 2 1 101000 f 74 goat snp51709-scaffold761-64922 23 26930119 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776867 Affx-122928926 AX-385263991 23 21539149 TCTTTCCTTATAAAATCATTTCAGTTTATCCTATG[C/T]AGACCAGTTGATTATCTTTTTCAAGAATCATTTGC Y 2 1 2 1 101000 f 74 goat snp51708-scaffold761-28451 23 26893345 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410418 Affx-122952413 AX-123280768 23 21585506 TTATTACATTTTGCATTCTCAAATATTTTCCACTT[A/C]TTTTCATATCACTCTCTGAACAAAACAAGATATAT M 2 1 2 1 101000 r 74 goat snp47460-scaffold668-3143519 23 26847388 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412759 Affx-122950516 AX-123283108 23 21619562 GGTGCGATTTTAAAGATACCTTTCTGGGCACAACC[A/G]CCTGATGAGGACTGCTATGATGATTCTGTTTATTG R 2 1 2 1 101000 r 74 goat snp47459-scaffold668-3109463 23 26813403 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784552 Affx-122941962 AX-385271601 23 21671990 TAAAGGATAGTAAAGTGTGTCAGCCCTTTCTGCTA[A/G]AATATTCCAACTCCTACCTATCTTAAAAGCCATGC R 2 1 2 1 101000 f 74 goat snp47458-scaffold668-3057035 23 26762231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388353 Affx-122969344 AX-123258711 23 21704139 GCCAAGGCTTCCCACTTCTCCTCCATCTCTCAAAT[C/T]CTGGCTTGGGGCCCTTGGCTTGAGGGTAACCCCAT Y 2 1 2 1 303000 r 74 goat snp47457-scaffold668-3024886 23 26730173 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394368 Affx-122964641 AX-123264723 23 21748885 GTGACACAAAGAAAAGAAATGAGCACTGGGGCCCA[C/T]GCAGGTACTGGGCTGGCTTGAGCACCCTTCCTGGT Y 2 1 2 1 102000 f 74 goat snp47456-scaffold668-2980140 23 26685123 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424752 Affx-122941650 AX-123295098 23 21812453 ATTATTCTAGGTTTCTTTATGTCTAGAGGAAGGCA[C/T]GGCACATATTAACATCTTAGTAAATACTTAAATAT Y 2 1 2 1 201000 r 74 goat snp47455-scaffold668-2916572 23 26621283 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433886 Affx-122934410 AX-123304227 23 21862082 GACTTGTAAAGTCAAAAAATGTAAATATTTAATTT[A/C]TTTTGAATTAGAGGAAAAAGTAATCAGGTGGGTAG M 2 1 2 1 103000 r 74 goat snp47454-scaffold668-2866943 23 26571267 A C 1 parentage parentage not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396564 Affx-122962927 AX-123266919 23 21913543 ACACAAGTAGGTTTTACTTTTATGAAAAAATTTAA[G/T]AATGATTTTTGTGACCCTGTTCTTTGAACATAGCA K 2 1 2 1 103000 r 74 goat snp47453-scaffold668-2815482 23 26519512 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773354 Affx-122933639 AX-385260496 23 21951494 AAGACTGACCTTGATTGGTGTCAGATTCTCTAAAC[C/T]CAGATATCAGCAAGCTATTTCCTCTTATATCATTC Y 2 1 2 1 101000 f 74 goat snp47452-scaffold668-2777531 23 26481089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772210 Affx-122942159 AX-385259365 23 21981040 TTCTGGCTATGTACATGAGTTCATATTTAACTTAG[A/G]ATTTGCCTATGAAACTGTTTTCCTGACAAGGAGTC R 2 1 2 1 101000 r 74 goat snp47451-scaffold668-2747985 23 26451211 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277514 Affx-1111835950 AX-519551016 23 22013252 TGGACAATTAAGGAATCCAGTGCCTTTGGGGAAGA[A/G]GCAGGAAACCATCCCTGAAATAACTGGTCAGCGGT R 2 1 2 1 101000 f 74 goat Random2.2K-2045 23 22013252 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320799850 Affx-122923614 AX-385286776 23 22019451 TTGGGAAATTTTATAGATACCACATCCGACAGCCA[C/T]TTTCCCACTATGCAGTCTTAGAGGTCTGATCTCCA Y 2 1 2 1 101000 r 74 goat snp47450-scaffold668-2709574 23 26412844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425509 Affx-122941472 AX-123295855 23 22059833 CGAATTTCTTTGAACAAAGGAGGTAAATTTTCTTT[A/G]TATATTTTAGTTCATTTTCCCCATTCAGATATAGT R 2 1 2 1 201000 r 74 goat snp47449-scaffold668-2669192 23 26372739 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763877 Affx-986698405 AX-385251667 23 22093757 TTCGCCTCTCTTTCTGTGCATATGCAGCTGATTCA[A/T]TATCCCCAGTCTCACCACCCATTCAAAGTCTTCCT W 4 1 2 1 600010 f 74 goat 23_22093757 23 22093757 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 38446176 Affx-122925740 AX-123316512 23 22118527 ACTGAAAGTATTGCTAAATAAAAGCAAGTTAACAG[C/T]AGATGTAATGAGAATGACAGTAAGTTAATTTACTC Y 2 1 2 1 101000 r 74 goat snp47448-scaffold668-2610498 23 26313678 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768809 Affx-122931452 AX-385255986 23 22172172 GCATGAGGATAAGAACTGCACATATATTAAATAAT[C/T]GAATCGTTAAAGCAACCTTATGATTTAGATGGTTG Y 2 1 2 1 101000 r 74 goat snp47447-scaffold668-2556853 23 26259090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787875 Affx-122968995 AX-385274897 23 22218032 TACTCAGCACTTCAAGTCCTTGTCTTTATGGAAGC[C/T]CTTCTCTAGGAGCAAGAAACTATTTAAAGAAATCA Y 2 1 2 1 101000 f 74 goat snp47446-scaffold668-2510993 23 26212940 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801283 Affx-122973004 AX-385288195 23 22258295 AACAGGAATTAGATGAAGTTATTTTCTTAAAAGAG[A/C]TCAAGGTTCAGTGGAGTAGATTTGTAAGGAAGATG M 2 1 2 1 201000 f 74 goat snp47445-scaffold668-2470730 23 26170854 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794067 Affx-122921207 AX-385281036 23 22287223 AAACCTGTTACAAATGTGTCTTTAATTTGTGTATG[C/T]ATTGAAAGAATGCAGAGTAACTAAGACAGTATCTG Y 2 1 2 1 101000 r 74 goat snp47444-scaffold668-2441802 23 26141650 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771812 Affx-122943096 AX-385258969 23 22318735 AAAGTTTACAAGATAGTTTTTAACCAAAATTATAC[A/C]CACAGCATAAAACTGGATTATTAACACACTTCCCT M 2 1 2 1 101000 r 74 goat snp47443-scaffold668-2410290 23 26103857 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406749 Affx-122955735 AX-123277100 23 22367790 AATCTTTGCCTTTATCCTTAATATTCATTCTATTC[A/G]GAATAAACCTTGGAAGTGCTATGTGGGGACAAAGA R 2 1 2 1 201000 f 74 goat snp47442-scaffold668-2361235 23 26054235 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381413 Affx-122974365 AX-123251771 23 22430353 GACCAACTCCCTACTAGGCAAAGTTTCTCTCCTGG[A/C]TTCCCTTACTCTTTCATGCTGCCAAGTATCTCTCC M 2 1 2 1 201000 r 74 goat snp47441-scaffold668-2298672 23 25991526 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409416 Affx-122954128 AX-123279767 23 22472702 ACATTTATATCCAGCTGTACTTTGACCTGAAGCAG[A/G]TCTGCCTTGGGAGTCTGGAGAATTTTAAGTTCTGA R 2 1 2 1 101000 f 74 goat snp47440-scaffold668-2256323 23 25948188 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376975 Affx-122977751 AX-123247334 23 22504796 CTTTCCAACATACAAATCTTCTAGTTTATGCCAGT[A/G]CTTGATGAAATCTGTATCATAGATTTACTGCTCAC R 2 1 2 1 101000 r 74 goat snp47439-scaffold668-2224229 23 25916109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400644 Affx-122960363 AX-123270999 23 22558522 TTTCCAAAAGCTGGTACAAGCAAAGTTACAGAATA[C/T]GGGAAGAACATAAAGAGAGAATTTGCTCCCTGGTT Y 2 1 2 1 101000 f 74 goat snp47438-scaffold668-2170503 23 25862281 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418791 Affx-122946180 AX-123289139 23 22610001 TCAGAAGTTCACTAGGTCTGGAAAGGGAAGGCTTC[C/T]GATCCCTGGGAGAGGCTGACAATGTCAGGACATGC Y 2 1 2 1 101000 f 74 goat snp47437-scaffold668-2119024 23 25811150 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433214 Affx-122935625 AX-123303555 23 22657195 CTTCAAAGAACATCATGCCAGAATGCCATCTCACT[A/C]GCAACAAGAGGGGAGCACCTTCTTTGACTTGGACC M 2 1 2 1 101000 f 74 goat snp47436-scaffold668-2071830 23 25763558 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790181 Affx-122967506 AX-385277185 23 22697266 ATACATTTGCAAATCTGTCTTCTAAATGTTCTGCT[A/G]CAGATCAGATGCCTTGTTATTGAGAAATCAAACAG R 2 1 2 1 101000 f 74 goat snp47435-scaffold668-2031759 23 25723823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776148 Affx-122951929 AX-385263277 23 22752605 CAGAACAAAGCAAAGACATAAACAATCACAACTAA[G/T]ATATCAAACCATATACTGAGTACTTACTCTACATG K 2 1 2 1 101000 r 74 goat snp47434-scaffold668-1976420 23 25667335 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434866 Affx-122934361 AX-123305207 23 22792959 GTCCCTATGATACATTTCTGCTGTAACAGTTTATT[A/G]TTTTATAAAGATGAATCTAAATTCCACTCCTGGAA R 2 1 2 1 201000 r 74 goat snp47433-scaffold668-1936066 23 25627039 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444412 Affx-122926579 AX-123314749 23 22825197 TTCTGTTAAAACTATATGCCCTGTCTCCAGATAAC[A/G]TAGATTTAGGCAGCTGCAGTTGACATCCCTGGAAA R 2 1 2 1 101000 f 74 goat snp47432-scaffold668-1903828 23 25593920 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420912 Affx-122944601 AX-123291259 23 22860850 TATTTCCAATTCTATGTTCCTGCTCATTTGGAATA[A/G]AGTCAATTCCTCAAATAGGAAAGTCTTTTCAATTT R 2 1 2 1 101000 f 74 goat snp47431-scaffold668-1868175 23 25558304 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419003 Affx-122946053 AX-123289351 23 22890979 GATACAATTTGACAGCGATGAAATGTTGACAACAA[C/T]GATAGTTGTCAACAAGGAGGATATAAAATCTATTG Y 2 1 2 1 101000 f 74 goat snp47430-scaffold668-1838046 23 25528150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389070 Affx-122968599 AX-123259428 23 22937420 ATATCCCATTCCTACCTAATGCACCCCAAACTGAG[A/C]GCATCAGGCAAGCTTACTGCAGAGATTACATCTGA M 2 1 2 1 201000 r 74 goat snp47429-scaffold668-1791605 23 25478577 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788983 Affx-122941231 AX-385275996 23 23022528 TTGTAATGCAAACCATGCTAATACACAAATTCAGC[A/G]TTAATACTGTCATGGCTACTATTATGGAGTGTGAT R 2 1 2 1 101000 r 74 goat snp47427-scaffold668-1706497 23 25392638 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767210 Affx-986698409 AX-385254491 23 23033171 TTTTCTCTTAGAGTAAGATGGGTTTCTGGGGAGGT[A/G]AGGGCCCAATACTTTCCCTCATAGAACCTAATGGC R 2 1 2 1 600010 r 74 goat 23_23033171 23 23033171 Ancestral_priority_1043 ancestry 0.69 recommended IMAGE 10K 10K ancestral 38379215 Affx-122976284 AX-123249574 23 23072676 TTAGATGTAAGTTTATCAAGATGCAGTGACTTCTG[C/T]ATCAAAGCAAATTAAAGTGACCAGGCTGAGTGCAT Y 2 1 2 1 101000 f 74 goat snp47426-scaffold668-1656349 23 25342444 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447122 Affx-122924466 AX-123317458 23 23119459 AAGGGCAATCTTAAGATCCTAAGAGAGTTTCAAAC[A/G]TGCTTCTGAATTAAGCATGCTAAACCTCACCAGTC R 2 1 2 1 101000 f 74 goat snp47425-scaffold668-1609566 23 25295705 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277516 Affx-1111835951 AX-185223827 23 23177564 TCAAAGACACTTGCTCCTTGGAAGAAAAGCTATGA[A/C]AAACCTAAATAGCATATTAAAATATGCTGTTTAGA M 2 1 2 1 103000 f 74 goat Random2.2K-2047 23 23177564 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436211 Affx-122932585 AX-123306550 23 23182922 TGAGGAATCTATTCCAGAATCAATTGATCTATTAA[C/T]GACCCTTGACTTTTATTTTTTCAGCTATACACATT Y 2 1 2 1 101000 f 74 goat snp47423-scaffold668-1546103 23 25232218 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795694 Affx-122922429 AX-385282647 23 23239912 CCCCACTTGGACACAAGCCCTCTAAAATGACATTA[A/G]CGATGGCTAATGGTCTGTAAATGTGTCGGGTGATG R 2 1 2 1 101000 r 74 goat snp47422-scaffold668-1489113 23 25174992 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277642 Affx-1111835952 AX-519551141 23 23244204 TGTACATCATGGCATTTCCTCATCTGCCCCTGTAA[A/G]AGTTGTGCCAGGCTCAATTCCCATTCTGACACCAA R 2 1 2 1 201000 r 74 goat Random2.2K-2048 23 23244204 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320763883 Affx-986698411 AX-385251672 23 23253260 AAACTAATTGTGAAATAGTGCTCCTCTGTTCACAA[A/G]AGAAAAATCTGAGAATCAAAGGGGTCAGTAGCATG R 2 1 2 1 600010 f 74 goat 23_23253260 23 23253260 Ancestral_priority_1043 ancestry 0.644 recommended IMAGE 10K 10K ancestral 320763290 Affx-986697819 AX-385251205 23 23253337 TTTCTGTTGGTTAATGGACAGATCAATAATTTGAA[C/T]TCAGCTCTGTTTAAATGCGAAGTGAAGTCTCTGTA Y 2 1 2 1 600010 f 74 goat 23_23253337 23 23253337 Ancestral_priority_1043 ancestry 0.74 recommended IMAGE 10K 10K ancestral 320804155 Affx-986696413 AX-385290804 23 23253367 TTGAATTCAGCTCTGTTTAAATGCGAAGTGAAGTC[G/T]CTGTATCCCTATGTCTCCCTATCCCTATCCCTTTT K 2 1 2 1 600010 r 74 goat 23_23253367 23 23253367 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 320767233 Affx-986698421 AX-385254514 23 23253437 TTTATCCCTATAAACTGCCACTCGTGGTCCAGCCT[G/T]CTGAGTCTTCAATCACAAGATAGAGAACAGTGGCA K 2 1 2 1 600010 r 74 goat 23_23253437 23 23253437 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 320763895 Affx-986698423 AX-385251683 23 23253503 TGGCACTCTCTGCAAGGAAGTTATTGTACTTTTTC[A/T]ACAGGGTCCTGCATAGAAGAGGTTTTGAATTTTTC W 4 1 2 1 600010 f 74 goat 23_23253503 23 23253503 Ancestral_priority_1043 ancestry 0.612 recommended IMAGE 10K 10K ancestral 320767240 Affx-986698425 AX-385254521 23 23253513 TGCAAGGAAGTTATTGTACTTTTTCTACAGGGTCC[C/T]GCATAGAAGAGGTTTTGAATTTTTCTTAGAATCAG Y 2 1 2 1 600010 r 74 goat 23_23253513 23 23253513 Ancestral_priority_1043 ancestry 0.708 recommended IMAGE 10K 10K ancestral 320763899 Affx-986698427 AX-385251687 23 23253607 GAGAGCTTTTTCAAATATATTCTCATTAGAATTTC[A/G]TTCATTTCAGAGTCATGGGAAGGAGTTACTGTTAG R 2 1 2 1 600010 f 74 goat 23_23253607 23 23253607 Ancestral_priority_1043 ancestry 0.626 recommended IMAGE 10K 10K ancestral 320763903 Affx-986698431 AX-385251691 23 23253713 GATAAAAAGAAGAGTGAGCAGGAAAAGTGAGTTAG[C/G]TGATGAAAGCAGAACAAAGAGAAACAGGTAATAGA S 4 1 2 1 600010 f 74 goat 23_23253713 23 23253713 Ancestral_priority_1043 ancestry 0.644 recommended IMAGE 10K 10K ancestral 320763905 Affx-986698433 AX-385251693 23 23253820 AAGAGAAAATTATACATAGGAAGTAGGAGGATTGA[A/G]AAAAGAGAAGATGTGAGAAAAATCACTATAGAAAG R 2 1 2 1 600010 f 74 goat 23_23253820 23 23253820 Ancestral_priority_1043 ancestry 0.758 recommended IMAGE 10K 10K ancestral 320767261 Affx-986698437 AX-385254543 23 23253835 ATAGGAAGTAGGAGGATTGAAAAAAGAGAAGATGT[A/G]AGAAAAATCACTATAGAAAGATCATATCTTACAAA R 2 1 2 1 600010 r 74 goat 23_23253835 23 23253835 Ancestral_priority_1043 ancestry 0.754 recommended IMAGE 10K 10K ancestral 320763911 Affx-986698439 AX-385251698 23 23253863 AAGATGTGAGAAAAATCACTATAGAAAGATCATAT[C/T]TTACAAATTGTCACTAAAGTTTACCATTTTCTCTC Y 2 1 2 1 600010 f 74 goat 23_23253863 23 23253863 Ancestral_priority_1043 ancestry 0.762 recommended IMAGE 10K 10K ancestral 320767268 Affx-986698441 AX-385254549 23 23253866 ATGTGAGAAAAATCACTATAGAAAGATCATATCTT[A/G]CAAATTGTCACTAAAGTTTACCATTTTCTCTCCTG R 2 1 2 1 600010 r 74 goat 23_23253866 23 23253866 Ancestral_priority_1043 ancestry 0.706 recommended IMAGE 10K 10K ancestral 320763917 Affx-986698445 AX-385251704 23 23254032 AATTCTTATGAAAGAGCTAATAGGAAGATCATATT[C/T]TGTAAAGAGTCATTGAAGTTTACCATTTTCTTTCC Y 2 1 2 1 600010 f 74 goat 23_23254032 23 23254032 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 320763886 Affx-986698414 AX-385251675 23 23254439 TTTAGAGTGAAGAAACTTATATTTATTTTCTAGGT[A/G]TTGTTCTGTAAAATATACAGGGGTCACATTGCTCT R 2 1 2 1 600010 f 74 goat 23_23254439 23 23254439 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 320803590 Affx-986696415 AX-385290383 23 23254491 ACAGGGGTCACATTGCTCTTTACCAAATGATGAAG[C/T]AGAAAAAGAAATTTTAATTTATCATGACTGAACTT Y 2 1 2 1 600010 f 74 goat 23_23254491 23 23254491 Ancestral_priority_1043 ancestry 0.654 recommended IMAGE 10K 10K ancestral 320791028 Affx-122978609 AX-385278023 23 23299428 AGCTTAGAGAACTGTAAGTAACTTAAGAGTTCTCC[A/G]CTTAATTCCATTGTATTAGAGATAAAAATAAAATC R 2 1 2 1 101000 f 74 goat snp47421-scaffold668-1429597 23 25115230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788426 Affx-122943234 AX-385275443 23 23344715 CTGTGCTCCTAATCTATTGGCCTCACTCTGCCACC[A/G]CATAAACTACAGATCCCTTGACTAGAAGAGAGGCA R 2 1 2 1 202000 f 74 goat snp47420-scaffold668-1384310 23 25070023 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445999 Affx-122925873 AX-123316336 23 23395023 TTTTTGTGTGTATGTGTACATAAACACCTCATGAG[C/T]ACAGAAGCCCAATCAGTTATATTCATGACTATTCC Y 2 1 2 1 101000 r 74 goat snp47419-scaffold668-1334002 23 25019611 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435052 Affx-122933745 AX-123305392 23 23427176 AGTGAATGGATCATGGTGGGAGTGAGGTTGGGAGC[A/C]GGTGGTGCAGTTAGAAAGCTGGAGGTTAGGGCTCC M 2 1 2 1 201000 r 74 goat snp47418-scaffold668-1301849 23 24987387 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799406 Affx-122942626 AX-385286336 23 23475926 AGAAAGCACAGAAGAGAGGACTGTGCTAAATATAT[A/G]TATTTGAGGGTCATCAGCCAAACATGAAATCAAAG R 2 1 2 1 202000 f 74 goat snp47417-scaffold668-1253099 23 24937663 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410141 Affx-122952803 AX-123280491 23 23529920 TTGAACAATGTGAGTTGGTCAAGGAACAGGAAGCC[A/G]CAGGGGGTTGATGGAATGTTTACTAAAGTTAGAGA R 2 1 2 1 101000 f 74 goat snp47416-scaffold668-1199105 23 24884708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772221 Affx-122958483 AX-385259376 23 23565756 CAAAAATTCCAGATCAAAGTGGCATTCTCACTTTT[A/G]CCAATGGGCAAAATTTTATATTCTTTGAAAGGAAA R 2 1 2 1 201000 r 74 goat snp47415-scaffold668-1163269 23 24848602 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393300 Affx-122965433 AX-123263656 23 23602150 TCAATTTGGTCAATATTAAAAAGAAGTAGTAGAAT[A/G]TCTGAGGGATGGGCATTCATATGTACTGCTAGTGT R 2 1 2 1 101000 r 74 goat snp47414-scaffold668-1126875 23 24811860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780226 Affx-122922399 AX-385267322 23 23656338 GTGATTTTAGCCAAAGACAGCTTGTAAGGAGCTGC[A/G]CAAACTTAACTTCCTCAAATAAAAGGAGAAGAAAG R 2 1 2 1 101000 f 74 goat snp47413-scaffold668-1072687 23 24757593 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380257 Affx-122975450 AX-123250615 23 23707272 TTTTAGAATTGAATACGTGATTGAAGCACCAATCC[A/G]CTTCACAGGGGCTAATGGATTTTCTTCAACACAGG R 2 1 2 1 201000 f 74 goat snp47412-scaffold668-1021753 23 24707212 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414351 Affx-122950021 AX-123284700 23 23749739 CACTCTGGGCACAGTGTGAGTTGTACTGTAATTGC[A/G]TCTGTGGATTTTCTTTCTTGATTCTTCCCCTTCTC R 2 1 2 1 101000 f 74 goat snp47411-scaffold668-979286 23 24664476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387527 Affx-122970311 AX-123257885 23 23784483 TTGAAATCTATGATGAGAATTTTCCTTCTTCTTTC[A/G]TCATAGAGAAATTTCTCTATGATGAGAAAGGCAGT R 2 1 2 1 201000 r 74 goat snp47410-scaffold668-944542 23 24629975 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420127 Affx-122946010 AX-123290475 23 23825219 TCAACGCCAGTTTGTCCTTTACATGTTTCCCTTCC[A/G]TTGACTGCAAGTATTTTCATTTTGTCTCTGAAGTT R 2 1 2 1 101000 f 74 goat snp47409-scaffold668-903806 23 24589242 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802519 Affx-122946707 AX-385289423 23 23872050 TTTATCACATTAGGTGACTTTTAAATCATCTAATC[A/C]AAGCCAAGAATGGAGTGATAGCTTTTGACTTCAGT M 2 1 2 1 101000 r 74 goat snp47408-scaffold668-856975 23 24542632 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425940 Affx-122941191 AX-123296286 23 23901488 AACATTAGAGGGTATGTTTCTTTTCAAATTAGAGT[A/G]TTAAATATTAATACTAGTGATGTGATTATTTTTGC R 2 1 2 1 303000 r 74 goat snp47407-scaffold668-827537 23 24513114 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774890 Affx-122972641 AX-385262024 23 23964073 TGAACTACAGAACCTCTCCAAAGATGTTATGAGTC[G/T]ATTTTCCCCTCTGATTCTCGAAATTCACTTCTCCC K 2 1 2 1 101000 f 74 goat snp47406-scaffold668-764952 23 24452273 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788360 Affx-122963781 AX-385275378 23 23999143 CCATCATTCAAAATGATCACTATAGACTTTGTTGG[C/T]AGTATCATTAATGTAAAACAGTACCTCATTATCAT Y 2 1 2 1 101000 f 74 goat snp47405-scaffold668-729882 23 24416237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804161 Affx-986696416 AX-385290810 23 24020094 TATCCCTCCAATGCTATGGACAGACCTTGCTCTGA[A/T]CCTAATGCAAATAAACCAACTGCACATAAGTCTTT W 4 1 2 1 600010 r 74 goat 23_24020094 23 24020094 Ancestral_priority_1043 ancestry 0.62 recommended IMAGE 10K 10K ancestral 320804164 Affx-986696418 AX-385290813 23 24020911 TAGGGTAGCAAAGAGTCGGACACGACTAAGCATGA[A/G]CCCATGTCATACAATGTTTCGGACGTACTTATATG R 2 1 2 1 600010 r 74 goat 23_24020911 23 24020911 Ancestral_priority_1043 ancestry 0.634 recommended IMAGE 10K 10K ancestral 320763923 Affx-986698451 AX-385251710 23 24020943 TGAGCCCATGTCATACAATGTTTCGGACGTACTTA[C/T]ATGAAGAAATTACTTATTAAGTGTCTGAAGTTCAT Y 2 1 2 1 600010 f 74 goat 23_24020943 23 24020943 Ancestral_priority_1043 ancestry 0.624 recommended IMAGE 10K 10K ancestral 320767291 Affx-986698453 AX-385254572 23 24020949 CATGTCATACAATGTTTCGGACGTACTTATATGAA[A/G]AAATTACTTATTAAGTGTCTGAAGTTCATATCTAA R 2 1 2 1 600010 r 74 goat 23_24020949 23 24020949 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 320767295 Affx-986698455 AX-385254576 23 24021766 GCCTGCTCCGTAGACACAGTCAACACACAGCAGAT[A/G]TGAATTGCAATACGGTAATACTATGTGGACTTGGA R 2 1 2 1 600010 r 74 goat 23_24021766 23 24021766 Ancestral_priority_1043 ancestry 0.646 recommended IMAGE 10K 10K ancestral 320767299 Affx-986698457 AX-385254580 23 24021938 CCCCTCTGTCTGTGTTGGATCTCAAGCAATTCATG[A/G]GAAACCTAGAAATTGGCTGAAACAGGGTTTATCAA R 2 1 2 1 600010 r 74 goat 23_24021938 23 24021938 Ancestral_priority_1043 ancestry 0.672 recommended IMAGE 10K 10K ancestral 38448183 Affx-122924250 AX-123318519 23 24042967 TATGCCAAGAGAACTAGAGCTATGCCATTAAAATA[A/C]TATTTCATTGGATCAGGGAGAAAATTATAGGAGAA M 2 1 2 1 101000 f 74 goat snp47404-scaffold668-686058 23 24372252 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763933 Affx-986698461 AX-385251720 23 24079425 AGAGAAGCATGATGTCAGCAATACATCAGAAAGTA[C/T]TCTGATACCATGTGTAGGGAGACATGAGACCAGCT Y 2 1 2 1 600010 f 74 goat 23_24079425 23 24079425 Ancestral_priority_1043 ancestry 0.734 recommended IMAGE 10K 10K ancestral 38392143 Affx-122966325 AX-123262500 23 24110349 TTACTAACCTAACCCTGTAAAGGCTCTCCTGTAAA[G/T]GCTTCCTCGGTCTTTCTAGCTCACACCCGTTGTTC K 2 1 2 1 101000 f 74 goat snp47402-scaffold668-618676 23 24305226 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785174 Affx-122972637 AX-385272220 23 24153180 AGCTTTGCATCCGAAAGAACACTTGTTAGATTTCA[C/T]GCAGCATGTCTAGGTGTCTTCTGATCGGAAGGTGT Y 2 1 2 1 101000 f 74 goat snp47401-scaffold668-575845 23 24262292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400774 Affx-122959874 AX-123271129 23 24184821 TACAGTTGCCCAGTTTCGCCCCTGGCCCTTGCTCC[A/G]AGGCCTGGATTCACCAGCAGGTGGTCGGGGGTTTG R 2 1 2 1 101000 f 74 goat snp47400-scaffold668-544204 23 24230609 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789397 Affx-122945184 AX-385276407 23 24225460 GAGGGGTCCTGGTAGGAAGGGGGCCCCCAGTTTCC[G/T]AAATCAAATTTACAACTTTGTTTCAGATCAGAGCG K 2 1 2 1 303000 f 74 goat snp47399-scaffold668-503565 23 24189877 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277643 Affx-1111835953 AX-519551142 23 24247004 CCAGCACCCCCTCTGTCCCTACTGGTGTATCCTTC[A/G]GAACTTCCATCATCTCTCTTCCTTGTTGTAAAAGG R 2 1 2 1 102000 r 74 goat Random2.2K-2049 23 24247004 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392783 Affx-122965983 AX-123263140 23 24285870 ACTTCAGAGAGGAAAAAGGAAGCATTGATGGGACA[C/T]CTGAGGCATAACACTGTGAATAACGGGTTATTCAA Y 2 1 2 1 101000 r 74 goat snp47398-scaffold668-443155 23 24128909 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765164 Affx-122938180 AX-385252715 23 24325514 TCATCTGATAAGTTATAGTTTATAGTTTAAACTTA[C/T]TCCAGACATGAGTATTTGGAACCACCATCTATAAA Y 2 1 2 1 202000 f 74 goat snp47397-scaffold668-403511 23 24089720 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379532 Affx-122976067 AX-123249890 23 24354486 GACATATGTATTCATATCACTCTAATGACAGCATT[A/G]CTTGGGCCCTATTACAAAGAAACCAAGTACCAAAA R 2 1 2 1 101000 f 74 goat snp47396-scaffold668-374539 23 24063512 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277645 Affx-1111835954 AX-519551144 23 24355619 TGAAGGAAAAACATCAAAACACAGGTAAATTAGGT[A/C]CTGTTAGAACTTCTATTTAAGAATAACCTCCCGGT M 2 1 2 1 101000 r 74 goat Random2.2K-2050 23 24355619 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320787514 Affx-122959208 AX-385274539 23 24404159 TGGACCATTGTTTGCACTGTCTTTCCTGCCTGTTT[A/C]TTAGTTACCCACAATAAACTTCATAGTGAAAAAAA M 2 1 2 1 102000 f 74 goat snp47395-scaffold668-324866 23 24013138 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434986 Affx-122933830 AX-123305326 23 24438516 GCCTTGTGAGTCCCTGTCCTCTCCCCCAGGGAATG[A/C]TGGTTGGAGATCCTGGTACCAACCTCGCTCTCCCG M 2 1 2 1 103000 r 74 goat snp47394-scaffold668-290509 23 23978767 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387006 Affx-122969940 AX-123257364 23 24469597 TACATTTGAGGTACTTCTCATGTCTTTTTTGTGCT[G/T]CTTCTTTTTCTCTTTAAGCAAGTATAATCCCATTC K 2 1 2 1 202000 r 74 goat snp47393-scaffold668-259428 23 23947947 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798481 Affx-122967848 AX-385285414 23 24503839 CAGATGACATATGTCAACTGACAAATACAGTTTTC[A/G]TTAGTCATTTTTAAGAGTCTGTTTGCAATTAAACT R 2 1 2 1 201000 r 74 goat snp47392-scaffold668-225186 23 23914132 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398954 Affx-122960980 AX-123269309 23 24560477 CCAATAAGCCCACTCCTCCTGATGGTCATGCAGAG[C/T]AGGGGTGCATAGACGGGAACAAAGGGAGAAGAAGG Y 2 1 2 1 103000 f 74 goat snp47391-scaffold668-168548 23 23857654 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272150 Affx-1111833257 AX-519545907 23 24571617 TAACCAGGGAGGCCCATATTCTGATAACCAGGAAT[A/G]CTACAGATAAACCGTGCCTCTCAGGCCTGGCAGTC R 2 1 2 1 101000 f 74 goat 23_24571617_AF-PAKI 23 24571617 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320800335 Affx-122923299 AX-385287258 23 24592053 CCAAGAGCTTCCTTTACACATTCAGGTCAACAGTC[A/G]TCTATATCTATGCACTTTACTTCAGTACATCTCAG R 2 1 2 1 101000 f 74 goat snp47390-scaffold668-136972 23 23826079 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394425 Affx-122964597 AX-123264780 23 24655037 CCTAGTAATTAGCCTTAAAAGAACCATCGGTAGCC[A/G]TGCCTCTTGCCCAGATGCCCACCTCCTCTTCTCCC R 2 1 2 1 101000 f 74 goat snp47388-scaffold668-73988 23 23763035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389454 Affx-122968343 AX-123259812 23 24686021 GTGGGGAGCTGGTGGCTTCTTGGCTGAAAGGAGTC[C/T]GCCAGGTGACCTCCTGAGTCACCCCCAGGGAAGGA Y 2 1 2 1 101000 f 74 goat snp47387-scaffold668-43004 23 23732398 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383743 Affx-122972449 AX-123254101 23 24722915 GTGAGAAGAAAGGTTAGTATGACAAGTTGTTGATC[A/G]TAAAGGTTAACTTTTATTAAACCATTACTACGTGT R 2 1 2 1 101000 f 74 goat snp47386-scaffold668-6110 23 23697772 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388372 Affx-122969329 AX-123258730 23 24737465 GGTGTGTGCGAAAAATTGAGATAATAAAACTACAA[C/T]ACTTGGTTAAAAATAAAAGGTGATGTACCTTAAGA Y 2 1 2 1 101000 f 74 goat snp17772-scaffold1843-8341 23 23683338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797745 Affx-122927963 AX-385284684 23 24835686 CTCAAGCCAAGTTCTAGAAAGGGATCTACCTGAAG[C/T]ACATTAGTGAGAACAGAATCAATGGGAATATCCTA Y 2 1 2 1 101000 f 74 goat snp16395-scaffold1729-11200 23 23345288 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439639 Affx-122930614 AX-123309976 23 24870606 TTTCCTTGTGACAAATCATTGCTGCCCACATCAAG[C/T]ACTTCCCCAAAGGTAACACTAGAGGAAATCCCCCA Y 2 1 2 1 101000 f 74 goat snp16396-scaffold1729-46120 23 23310335 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417443 Affx-122947204 AX-123287791 23 24905833 TACCAAAAATGTATTCCACTGGGGACCTTGTCATT[A/G]TTTCATCTGTTTCTTGTACCCTTGCCTCAACAAGC R 2 1 2 1 101000 r 74 goat snp16397-scaffold1729-81347 23 23275521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408658 Affx-122953467 AX-123279009 23 24942097 ATTTTGAATCTTTCTACATGATTAGTTTCTCCTCT[A/C]TCTCCCCATTCTCTGGACTGAGAACATGCAAAGGG M 2 1 2 1 101000 r 74 goat snp46421-scaffold6429-26032 23 23393164 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395903 Affx-122963609 AX-123266258 23 24951416 TACTTGAGAATGCTTTGTACTATGATCAATGGCAG[C/T]GGAAAACTGAGATTCAAGCTTTCCTTTCACCAAAG Y 2 1 2 1 101000 f 74 goat snp10153-scaffold1362-827355 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277647 Affx-1111835955 AX-519551146 23 25065264 GTCCAGAATATGAGTATGGATAAGAGTAGAATTCA[A/G]ATACTTTTTCACTCCAAACAAATTCTTACAGTAGG R 2 1 2 1 101000 r 74 goat Random2.2K-2051 23 25065264 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418532 Affx-122946413 AX-123288880 23 25112277 CATAATGGACCAGTTCCAGTAAAGGGAGTGAAAAC[G/T]ATGGGCCTGTTAATCTTATTACTTTTTCTCAAAAT K 2 1 2 1 101000 f 74 goat snp10151-scaffold1362-666494 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786548 Affx-122921084 AX-385273581 23 25176216 AATGTTTTTCACTATATCTATAGCAACATCATTTA[C/T]GATAGTCATGCCATGTAAGCAACCTAAGTATCCTT Y 2 1 2 1 102000 r 74 goat snp10150-scaffold1362-602555 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777565 Affx-122953478 AX-385264683 23 25206580 GTTCCACAAGTTATCAAAAACCTAAGCCATTGTAT[A/C]TTATCTGCCATCCATGACTTTTACATGGTCACAGA M 2 1 2 1 101000 f 74 goat snp10149-scaffold1362-572191 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450191 Affx-122922300 AX-123320526 23 25252971 AGAAAGGGTAGTTTAGTGAGGGTTTGGAATAGCAG[C/T]GGTAAGAAAAATTTACCAATTTTTTTCTGAAGGTC Y 2 1 2 1 101000 f 74 goat snp10148-scaffold1362-525800 23 23122362 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430351 Affx-122937799 AX-123300692 23 25283587 ATCCAGAGTCAGCTTTACTGCAAAGACAAGAGATC[A/G]TCAGGTTTCTGGGAGGGTCTCAGTAGGCTTAGGCC R 2 1 2 1 101000 f 74 goat snp10147-scaffold1362-495184 23 23091492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415781 Affx-122948915 AX-123286130 23 25326839 GAAATTATTGAATTATAGTTTGTTCAAATTTCACA[C/T]GGCCATTTTCTTTCTACAGGGAAACCTTCATTCAA Y 2 1 2 1 103000 r 74 goat snp10146-scaffold1362-451932 23 23047811 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432822 Affx-122935390 AX-123303163 23 25364648 CCCTCACAATAAAGGGTTTTTCTCTTAGAGTAAGA[C/T]GGGTTTCTGGGGAGGTGAGGGCCCAATACTCCCCC Y 2 1 2 1 303000 f 74 goat snp10145-scaffold1362-414123 23 23033154 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795992 Affx-122933676 AX-385282944 23 25403920 ACACTTTGTTCACCTAACATTGATAATCAAAGATT[A/G]CATCTTAAAGGCATACTTGTCCTTTACTTTAGGCA R 2 1 2 1 101000 f 74 goat snp10144-scaffold1362-374851 23 23000857 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772931 Affx-122927429 AX-385260075 23 25446904 GATACTAGGATTGCTAACCAAACAATTGTTGGTGC[A/G]TTTGGAAAAGAACTCTACTCACCTAACACAAAACT R 2 1 2 1 101000 f 74 goat snp10143-scaffold1362-331867 23 22957626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394320 Affx-122964680 AX-123264675 23 25482261 ACTCAGTTGGGTGGCATCAGGGAAGGTGAATATCT[A/G]TGGGGCAAAACCTCATGAAACTTCAAGGTTCTGTG R 2 1 2 1 201000 f 74 goat snp10142-scaffold1362-296510 23 22922277 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387986 Affx-122969587 AX-123258344 23 25514759 AATGAATTTCAAATCATTTTCTCTCACTTCTTGCA[C/T]AGTGTCAGAAAGTGAAATAAAAGAGTGGAGTCCAC Y 2 1 2 1 303000 f 74 goat snp10141-scaffold1362-264012 23 22889148 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788933 Affx-122960607 AX-191364671 23 25570237 TTCAACAGGGAGAATGAGCCTGTTATTTTTAATTC[A/G]TATTTGTCATTACAGTCAGCTGAGGAGGTCACATA R 2 1 2 1 101000 r 74 goat snp10140-scaffold1362-208534 23 22832382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779703 Affx-122952791 AX-385266803 23 25603408 GTAAGACTTTCCTCTGAGGATTATAATAAAGTATG[C/T]GCTGTTCAGAGTAAAATTGGCACTGGGTGAACAGT Y 2 1 2 1 101000 r 74 goat snp10139-scaffold1362-175363 23 22799224 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401886 Affx-122958849 AX-123272239 23 25672909 CCGAGGCAACGAGTCTGTGGGGGGGGCGGCAGGGA[C/T]GGGGGCAGGGAGCGGTGCTGTGACCACATTCACTT Y 2 1 2 1 303000 f 74 goat snp10138-scaffold1362-105862 23 22731447 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788857 Affx-122938222 AX-385275872 23 25764133 TGAAATAAATTGCAAGAATGATGAGCGGAAAAGAT[A/G]GAAGGAATACAAAAGAGGAGACGATGTATTGAAAA R 2 1 2 1 101000 r 74 goat snp10137-scaffold1362-14638 23 22639752 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424741 Affx-122941659 AX-123295087 23 25820452 CCTGGGGTGGTACACTGCAGCTGTCTTGCCTCTCA[C/T]ATATAGTCCCTCAGATCACATACACCAGCCACACC Y 2 1 2 1 201000 r 74 goat snp17102-scaffold1786-435508 23 22563545 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770813 Affx-122947208 AX-385257977 23 25864207 ATATATTCATATTCTTTTGACAAATTGATTGTTAA[C/T]GATGATCATAAGTACTTAATCCAGAAGAAAGTTTA Y 2 1 2 1 101000 r 74 goat snp17101-scaffold1786-391753 23 22519808 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381175 Affx-122975205 AX-123251533 23 25930490 GGTCAATTAATTTCATGAGTCCTCACTAGGGAAAT[A/G]GTTCATTAGAAAGCAACGTCAGGGCATCATTTCCT R 2 1 2 1 101000 r 74 goat snp17100-scaffold1786-325470 23 22456619 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441632 Affx-122928636 AX-123311969 23 25966007 CGGAGCGCATCGGTGCCACACTCGGGGATCCCCGT[A/C]GGGAAATCTGCCTTCTGTGGGGGAAGGAAGAGTCA M 2 1 2 1 201000 f 74 goat snp17099-scaffold1786-289953 23 22420550 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446782 Affx-122925309 AX-123317118 23 26001211 CAGTCAGCCAGAGTGAGCTCATTGCCATCCAGAAA[C/T]TTCCTCTGAGAGATGCCCTCATCCTCAGCACTGGT Y 2 1 2 1 102000 f 74 goat snp17098-scaffold1786-254749 23 22385285 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405254 Affx-122956875 AX-123275606 23 26066141 GACGGTGTGCATAGTTTCTCCAATGAACAACTTGA[A/G]AGAGAAAGCCTCCCATCCACATACTTCAGCACCTG R 2 1 2 1 101000 f 74 goat snp17097-scaffold1786-189819 23 22320924 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409449 Affx-122954085 AX-123279800 23 26130119 CTCCAGAGAGAAAGACCTGACAGCTTGTGGTAGAA[C/T]GTCCCCACTGTACCCCCACCCCCAGAGGGTTCCCA Y 2 1 2 1 101000 f 74 goat snp17096-scaffold1786-125841 23 22259693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792495 Affx-122963297 AX-385279476 23 26181338 TCCCCATTAGGAAGGTGGAAGATCAGAATACTTCA[A/G]TGGACTTAAGGTCAAAATGCCATGAAAAGAGAGGC R 2 1 2 1 101000 f 74 goat snp17095-scaffold1786-74622 23 22208531 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772544 Affx-122943092 AX-385259694 23 26236163 TCTTTCATGATTTTATTTCAGGTTAACGTCATTCA[C/T]GCAGTTGTGCAGGCATGTTTCGAGTATTGCATTTT Y 2 1 2 1 101000 r 74 goat snp17094-scaffold1786-19797 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437216 Affx-122932040 AX-123307554 23 26257507 GACTCATGCATGAGCCAAGCACATGTGAAGGCTTC[A/G]TTCCTGTTTTCCTTTTGTCAGCCATCTTTCAGAAC R 2 1 2 1 201000 r 74 goat snp25254-scaffold2590-1448 23 21949305 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393426 Affx-122965871 AX-123263782 23 26301201 GTGATGAAGGTTGATCTGGATTCCAGGAAGCAGAA[A/G]AGAGGACTCAACCCTTATGGTTCCCCACTGGCTCC R 2 1 2 1 101000 f 74 goat snp25255-scaffold2590-45142 23 21865487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776330 Affx-122921807 AX-385263458 23 26351995 GCGGCCTTAAAAAGGAGCAAGCAGCAGCAGAAGAG[C/T]ACTATGGACATAAAAGCTTCCTCCGTGGGAGCTCA Y 2 1 2 1 303000 f 74 goat snp25256-scaffold2590-95936 23 21814558 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430395 Affx-122937765 AX-123300736 23 26397406 TGCTGTACAGTAGAACCTTGTTTATACTCGGTAAC[A/G]CACTTGATTTCCTCCAATTGTCTTTGGTAAGATCT R 2 1 2 1 201000 r 74 goat snp25257-scaffold2590-141347 23 21770666 G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769882 Affx-122927753 AX-385257051 23 26435243 TCCGAAGGACAGACATGAGACAAACAGAAATGAGG[C/T]GGTGACTCTTCTAAAAGGTGAAAATAAGTCGCCAT Y 2 1 2 1 101000 r 74 goat snp25258-scaffold2590-179184 23 21732516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414486 Affx-122949548 AX-123284835 23 26474990 AATACTGTCAACAGCTCTGCAGAAGCTGAGAGGAG[C/T]GGGGAGATACCTGGCACCTAGGACTTCAGTACCCT Y 2 1 2 1 101000 f 74 goat snp25259-scaffold2590-218931 23 21692615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442996 Affx-122928184 AX-123313333 23 26593286 AGCCAACCGGGTGGGTGTCACAGGGCCGCTGACCA[C/T]GCTGGGGCAGGGGTGTCACACGAAAAGGACTTAAA Y 2 1 2 1 201000 f 74 goat snp25261-scaffold2590-337227 23 21575257 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406287 Affx-122956078 AX-123276639 23 26629950 TGGCACCCAGCAAAGAAGTCAGTCTGATATTCTGT[C/T]CTCAAGTAAACTGTCCAGGGATATCAAATAAAACA Y 2 1 2 1 201000 r 74 goat snp25262-scaffold2590-373891 23 21538662 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802575 Affx-122930090 AX-385289477 23 26671447 CTTTATCTTGTGCACCATGTCTCCTATTAGACACA[C/T]GCTCATTCCCTAGATCTTCACGCAGTAAATTCTAG Y 2 1 2 1 101000 r 74 goat snp25263-scaffold2590-415388 23 21493150 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414818 Affx-122949206 AX-123285167 23 26747561 AGGTTGGGTAGTATTCCAGTGTCTGCATGTGCCGC[A/G]TTCTGTTTCTCCATCATCCATCGCTGGGCGTGTGG R 2 1 2 1 102000 f 74 goat snp25265-scaffold2590-491502 NW_017218284.1 25287 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766481 Affx-122967476 AX-385253847 23 26800882 AGAAAACAGACATCTAGGCTTAAAGCCCTGTTTAG[C/T]TGACATAACTTTTAGCTTTTCCTTTAGTTACATCA Y 2 1 2 1 101000 f 74 goat snp15229-scaffold1623-8812 23 21304880 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38424571 Affx-122942223 AX-123294917 23 26855080 TAAAATGCAAGTGAAAGTAGCACTTTGCAAAGCAT[C/T]AAGCACTATGCAAACAAATGTCAGGTGCTATTTTC Y 2 1 2 1 101000 f 74 goat snp15230-scaffold1623-63010 23 21251371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771604 Affx-122977842 AX-385258762 23 26903868 AACTGTCATCTCTTCCCTCTGGGTTTGTACCCATT[A/G]CCCCTATCTTTGCACCTGAGTAGAAAATTTGTAGT R 2 1 2 1 202000 f 74 goat snp15231-scaffold1623-111798 23 21203326 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405150 Affx-122956951 AX-123275502 23 26934351 GATACTTATCATACTTTTCACTTATTTATTTGGTA[C/T]GTATCTGTTTTCCCCATTAGAATGTAATTCCCATA Y 2 1 2 1 102000 r 74 goat snp15232-scaffold1623-142281 23 21172359 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782006 Affx-122933837 AX-385269085 23 26981907 CCACCATTTGCAAAGCTGATGTGTTGTAATTTGCA[A/G]CAAGGAGGTTCATGGCAGAGACCCACTTGTCTGTG R 2 1 2 1 101000 r 74 goat snp15233-scaffold1623-189837 23 21124355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463875572 Affx-1110198703 AX-515353563 23 27012825 TATACCAACTCTCTATCTATAGGCTACAAAGAAGA[C/G]ATTGTAGTCCCAAATTTTACAGTAATTTGACTGGG S 4 1 2 1 101000 r 74 goat Random2.2K-2056 23 27012825 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384300 Affx-122972286 AX-123254658 23 27015863 GCAATCTTCTCTCCTGGGATGCAGGCATACCTTCC[A/G]CTTCCTCTACCTTTGTAGACCTTCTGCCTTTTGAG R 2 1 2 1 101000 r 74 goat snp15234-scaffold1623-223793 23 21090968 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430633 Affx-122936960 AX-123300974 23 27047591 CGAACTTGGCCCCAACTCAGTTGTGTGCATGCTAA[G/T]CCACTTCAGTCTTGTTCAGTTCTTTGCGACCCTAT K 2 1 2 1 202000 r 74 goat snp15235-scaffold1623-255521 23 21058723 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405126 Affx-122956968 AX-123275478 23 27072138 CCCCTGCATTGGTGGGTGACCATCCTGCAGATGGA[A/G]TGATAGGAGAAGCAAAAGATTTGGGAAGGACTGGG R 2 1 2 1 102000 r 74 goat snp24702-scaffold2521-66113 23 21032377 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437639 Affx-122931805 AX-123307977 23 27172027 AGAAAGAGAAAGGGGAAGAAGGGAGTCATTGAACA[C/T]GAATCCATATTTGCAGCATGGGAAAGCTGATGGGT Y 2 1 2 1 101000 r 74 goat snp18718-scaffold1893-93177 23 20842894 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421502 Affx-122943902 AX-123291849 23 27200650 CACCTCGAGGTCAAAACCAAATGAGCTTTCTAGAC[A/G]TGACAAGGTATTTTTCATAACAGCAATGGTTCTCT R 2 1 2 1 101000 f 74 goat snp18717-scaffold1893-64554 23 20813755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381917 Affx-122974142 AX-123252275 23 27257452 ACACTTGTCTTGAGACCTAAGGCAACCCATATATT[A/C]TCTAGAGTTTTAAATATATATACATATATATAATA M 2 1 2 1 101000 f 74 goat snp18716-scaffold1893-7752 23 20757039 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271980 Affx-1111833258 AX-519545749 23 27295488 ATAAAATTATTTTTCAAGTCCCCTGAAATGCCACT[A/G]CTTAATCAGTCTATGTTTTCCTATTTTGGAAAATA R 2 1 2 1 201000 r 74 goat 23_27295488_AF-PAKI 23 27295488 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38410455 Affx-122952380 AX-123280805 23 27329740 TTTGTAATGTCATGAAAAGCAATTAAGTCACCTGG[C/T]GTCATATATTTTAAGTTATCACCTCTACCCAATTT Y 2 1 2 1 101000 f 74 goat snp41919-scaffold547-64437 23 20081299 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430748 Affx-122937501 AX-123301089 23 27380911 TATACACAATGGAATATTATTTAGCCATTAAAAAA[G/T]AAGATTCTGTCACTTGCAAAAAAAAATGGATGGAA K 2 1 2 1 103000 r 74 goat snp41920-scaffold547-115608 23 20029352 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782902 Affx-122929576 AX-385269972 23 27449259 TGGTCAGCCTCTTTTATGGCAGTGTCATCTACATG[C/T]ACTTGCAACCAAAGAAAGGTTCCATGCACAAAGCT Y 2 1 2 1 101000 r 74 goat snp41921-scaffold547-183956 23 19960764 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799012 Affx-122959510 AX-385285942 23 27506970 TGAGATGAAAACATTTAGGCTCTAACTCTAAAATT[A/G]TTTCTATAGAAGATGAAATTCTGTATATGTGGCTT R 2 1 2 1 101000 r 74 goat snp41922-scaffold547-241667 23 19902836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776973 Affx-122953963 AX-385264097 23 27548942 GGTAGAAGTCATTTGAAAAGTAAACTGAATCTTAA[C/T]GTGGAGAAGGAGAACATTCCCACTAAGGTCAGGAA Y 2 1 2 1 101000 f 74 goat snp41923-scaffold547-283639 23 19861028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388682 Affx-122969002 AX-123259040 23 27607749 AGGTTGCGCGCAGCTTCCCTTGCACTCTCCTCTGC[A/G]CAAATAACTTGATCTGAGAGATGCTACAACAGGAG R 2 1 2 1 101000 r 74 goat snp41924-scaffold547-342446 23 19802229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431636 Affx-122936139 AX-123301977 23 27654944 ATGAGGCCCCGGGTTCGATCCCCGGCATCTCCATG[C/T]AGTTCTACTTTTGTTGTGGCTGTCTAATTCAGACT Y 2 1 2 1 101000 r 74 goat snp41925-scaffold547-389641 23 19754672 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771782 Affx-122925871 AX-385258939 23 27691266 CATATATTTGCTTTTTATGACAGTAATTTTAGAAT[A/G]TTATGGGTATTGCCAAACATTCCCATTTCTGTAAG R 2 1 2 1 201000 f 74 goat snp41926-scaffold547-425963 23 19718266 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405864 Affx-122955851 AX-123276216 23 27739285 TTTAAAGTTATATTGCTCACGTTTACATGGAATTC[A/G]TAGTTGACAAATCTCTTTTACATCAAGGATTTCAT R 2 1 2 1 201000 f 74 goat snp41927-scaffold547-473982 23 19672016 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769024 Affx-122967656 AX-385256199 23 27769082 TAAATTCTTAGGAGATGACAATTCAAATGCAAACC[A/G]CCTAATACTGCATGTGACTTTATATCTCAATCACT R 2 1 2 1 101000 r 74 goat snp41928-scaffold547-503779 23 19641763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799858 Affx-122940868 AX-385286784 23 27799394 TGCAGTGCTCTTTCTGCTAAGCCATCGGAAGCATT[A/G]TATTGCCATATGCAACTTAGAGCACTTACGAGGCA R 2 1 2 1 101000 f 74 goat snp41929-scaffold547-534091 23 19611474 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413238 Affx-122950240 AX-123283587 23 27849491 TTTCTTTAAATATTTCAATATAAATTACAAGCATC[A/G]TGACTTGTCACCCTTTCGTATGTGCATCTCTGAAA R 2 1 2 1 101000 r 74 goat snp41930-scaffold547-584188 23 19561055 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274401 Affx-1111834177 AX-515354125 23 27914970 A[A/G]TAGTTTCTTCTTTTATCAGCCATATAGAATTTCTG R 2 1 2 1 101000 r 74 goat GoatD01.023494 23 27914970 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38408593 Affx-122953651 AX-123278944 23 27915463 CCTGGGGTTCTTCAGAGCAGGAATCCAGCAAGGGA[C/T]TGGAGAACAGAAAACGTTCTGCTTGTGACTGAACA Y 2 1 2 1 101000 r 74 goat snp41932-scaffold547-650160 23 19495028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404339 Affx-122956998 AX-123274691 23 27950707 CATGGGTCTTATCTCTGCTCAGTAGTTGAGGTCCA[C/T]GGAGTCTTTGCTCTTTGGCATGTGGAATCTTTCCA Y 2 1 2 1 101000 f 74 goat snp41933-scaffold547-685404 23 19459623 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423161 Affx-122942746 AX-123293507 23 27999160 CCGAGATGCAGGGTCAATTCAAAAATTATGAAATA[C/T]AAGGACAAGAACTGAGGCTTTCCTGGCAATCCAAT Y 2 1 2 1 201000 f 74 goat snp41934-scaffold547-733857 23 19410933 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790202 Affx-122934336 AX-385277205 23 28042905 AAATGCATGCACAGGCTAAATAGAACCCATTGGCC[C/T]GTTTGCTTTCTCTGATTTAAGATGCAAAAGGTCAC Y 2 1 2 1 101000 f 74 goat snp41935-scaffold547-777602 23 19367055 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767992 Affx-122922513 AX-385255206 23 28073935 GATTGAACATTTTAAAAAACCAGCTTTGAGGAAAT[A/G]TTTTGGATGGTTTGACTTAAAATATGGGACTTATG R 2 1 2 1 201000 f 74 goat snp41936-scaffold547-808632 23 19335839 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422787 Affx-122943215 AX-123293133 23 28110235 GAGAAAAGAATTTAAAGAAGACAAATATGACATTG[A/C]TATCCTAATTACCTTCCAGTGTAATATACACTTGG M 2 1 2 1 101000 r 74 goat snp41937-scaffold547-844932 23 19299191 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400241 Affx-122960150 AX-123270596 23 28162529 ATTTCTCTGGGACCAGGCTTATGCTATTCCATTTG[C/T]GATCACATCCTTGCATAGCAGCATTGTCCGCTCTA Y 2 1 2 1 201000 r 74 goat snp41938-scaffold547-897226 23 19245576 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789943 Affx-122949147 AX-385276949 23 28193960 TTCACAAATATAATGCATTAGGAGTAGAGATAACT[A/C]TTTTGCCAGAATGTATCTATGAGAAGTATCTTAGG M 2 1 2 1 101000 f 74 goat snp41939-scaffold547-928657 23 19213912 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765133 Affx-122973377 AX-385252689 23 28224632 AATGTTAAATTAATTTGGAATTAAAAGTTCTAAAA[C/T]GCAATTAAATTGGAACAGGATACTTGGTGTCTAAG Y 2 1 2 1 202000 f 74 goat snp41940-scaffold547-959329 23 19182126 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785834 Affx-122938418 AX-385272871 23 28274344 TAAAGCAAAACTTCACGCCATGACCCTTGTAGCAA[C/T]GACTGTGCAGGCCTTTAAGTTCTTCAGAATGACTG Y 2 1 2 1 101000 r 74 goat snp41941-scaffold547-1009041 23 19132363 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793670 Affx-122924155 AX-385280643 23 28306391 TATTATGCCAATACTTCACAGCCTAAATGCTTATG[C/T]ACTTTATTTACATAAGCTTGATCAAATCCTCATTC Y 2 1 2 1 101000 f 74 goat snp41942-scaffold547-1041088 23 19100299 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388725 Affx-122968970 AX-123259083 23 28350876 CACTTCCCAACATGAAAATGTTTTCTTGATGATTC[G/T]ACACAAATTGACCACCTCTGGGTAACCAGCGGTCG K 2 1 2 1 101000 r 74 goat snp27811-scaffold2989-221933 23 18922018 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436419 Affx-122933015 AX-123306757 23 28381065 TTTGGAAGTTTGAAGAGTCAAGGATACACCGAAAA[C/T]GAGAACGCTGTGAGCAGGATTTGAACCTGCGCGGG Y 2 1 2 1 101000 f 74 goat snp27810-scaffold2989-191744 23 18891686 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393131 Affx-122965557 AX-123263488 23 28421359 GGCTACTTCATGTATGGACAATGGTAGAAGAGGAG[C/T]TGGTTTTACTTGTGTTGTTGTTATACTTGTCTGTA Y 2 1 2 1 101000 f 74 goat snp27809-scaffold2989-151450 23 18851527 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416483 Affx-122947799 AX-123286831 23 28498975 AAATAGAGTGTATCAAAAAATAAAGTGTCTCTATA[C/T]GCACTGATTAGGAAATGTATGTCACACTAAAAATG Y 2 1 2 1 101000 r 74 goat snp27808-scaffold2989-73834 23 18774303 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381007 Affx-122974663 AX-123251365 23 28554796 AGGTGAATGGGCTGCACTGATTACCTCTCCAGTGG[A/G]TTGTGGGAAGGCCGGTGGACCTGGAGACTTCTGTA R 2 1 2 1 201000 f 74 goat snp27807-scaffold2989-18013 23 18717492 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452934 Affx-122920186 AX-123323267 23 28604939 TACATGGTGTCAACCGCCATTCTCTGCCTCTTCCT[A/G]CTCATGTCTTTGGTTCAAAACACTGCCCTAATCCA R 2 1 2 1 201000 r 74 goat snp4530-scaffold1146-32031 23 18647313 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786314 Affx-122941554 AX-385273347 23 28641381 TTCCACCCTTAACACGTCCAGATATTTCGAGACCC[G/T]AGAACAGTAAAGTACCTTCAGTTTGTTGCAGCCCC K 2 1 2 1 101000 r 74 goat snp4531-scaffold1146-68473 23 18611049 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442337 Affx-122928046 AX-123312674 23 28670200 CGCTGAGGAGACAGATGGTACAGACTGAAAGACCA[C/T]GCGCCACTCTCACCAGATACACCACAGCTTTACAA Y 2 1 2 1 101000 f 74 goat snp4532-scaffold1146-97292 23 18581976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784331 Affx-122968632 AX-385271382 23 28726683 GCAGCTCCTCTGGGGCAGAATTCCAGAATTAGGAA[C/T]ATAATTAGTTTATCTTAAATGTAAGAGTGTTAAGG Y 2 1 2 1 102000 f 74 goat snp4533-scaffold1146-153775 23 18525459 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798922 Affx-122962578 AX-385285852 23 28787370 TTGCCCTAGAATACAGAACGTACCAGAGAACAGTC[C/T]CTCTAGTGACAGAATCTAACAGAAAACCAGCCAGC Y 2 1 2 1 101000 r 74 goat snp4534-scaffold1146-214462 23 18463128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390973 Affx-122967045 AX-123261330 23 28859913 CTCCCTAGAGAATTTGGCCTCTGGGATGGGAGACC[A/G]CAAGAAGCAATCTGAGTCACTTCCCTGCCCCTTGA R 2 1 2 1 101000 r 74 goat snp4536-scaffold1146-287005 23 18390343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420673 Affx-122944811 AX-123291020 23 28891202 GTAGAGGGTGGGTAGGTGGGGGAGAGGAGCCCCAA[C/T]AGCACTGACTATTTGATGAATTATGAATTATATAA Y 2 1 2 1 101000 r 74 goat snp4537-scaffold1146-318294 23 18359113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784370 Affx-122922616 AX-385271420 23 28936437 AAAGGCATACCGTGAGTCAGTGTATATATTTACCT[G/T]CTTACCTTTAGCCAATTTCAGGGCCCCCATGAGCG K 2 1 2 1 101000 f 74 goat snp4538-scaffold1146-363529 23 18313706 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382598 Affx-122973716 AX-123252956 23 28983595 CGCTGATTGGATCAATTCAGCCAGTAGAAACGTTG[C/T]ATGCAAATAAGGAGATTTAGATTCTATTTCTTGAT Y 2 1 2 1 101000 f 74 goat snp4539-scaffold1146-410687 23 18266513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771337 Affx-122933034 AX-385258495 23 29012556 ACTTTAAGACCAGAAATCGTGTGGGCCACCTTAAA[A/G]GAGCATCACAGGACCCAGTATGACCAAAAAGCAGT R 2 1 2 1 101000 r 74 goat snp4540-scaffold1146-439648 23 18237629 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783378 Affx-122940920 AX-385270442 23 29059323 TTTTATGAGTAATCCATCAATTCTAAAAAATTACG[A/G]CCCTGATCATTTAAATCTCACATCTGCATCATTTT R 2 1 2 1 101000 r 74 goat snp4541-scaffold1146-486415 23 18190180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399620 Affx-122961083 AX-123269975 23 29090838 GCAGTGTGGAATGTTCTCTGGTTGGGGAGTGGTCT[C/T]TTAGCAGTGTCTCTTAGGTAACAGCTTGTCAAACG Y 2 1 2 1 101000 r 74 goat snp4542-scaffold1146-517930 23 18158616 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396757 Affx-122962779 AX-123267112 23 29122834 AGAGACCACAGGGCTTGGTGACAAGTGAGTTCTCA[A/G]TAACAGAGGAAGGGTTAAAAGGAAACTTGAATGGG R 2 1 2 1 101000 r 74 goat snp4543-scaffold1146-549926 23 18126578 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450529 Affx-122922490 AX-123320863 23 29166112 GTAAAATAAAGTCTTTTCTGATACTCCAGGTGCAC[A/G]TTGCTTTCTCTTGCCGTGAGCCAAATATCTACTGT R 2 1 2 1 101000 r 74 goat snp4544-scaffold1146-593204 23 18083573 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790565 Affx-122926171 AX-385277568 23 29206396 AAAGCAAGGATTCAACTAAAGTTACTGGATAGGCT[A/C]TGTCCCTCTAATAACCAGGACCAGTCTCTTGGATC M 2 1 2 1 101000 f 74 goat snp4545-scaffold1146-633488 23 18043019 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434770 Affx-122933892 AX-123305111 23 29258168 GCTCAGGGCAGTCAAAAAGACACAGAGATTTGGAA[C/T]ACATATAGTAGCCTGTGAAGTGAAGTGAAGTGGCT Y 2 1 2 1 201000 f 74 goat snp4546-scaffold1146-685260 23 17987144 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789789 Affx-122949925 AX-191419710 23 29287292 AACAGAAAATATATGAGGACCCTAGAAAATATTGC[A/G]TGCTAGAAAACAAGCTATCCAAGATCACTAGGGTC R 2 1 2 1 101000 f 74 goat snp4547-scaffold1146-714384 23 17958031 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386467 Affx-122970774 AX-123256825 23 29381055 ATTTTTGTTCTTTGTCCCAAATCTCTGTAGCTTTT[A/G]TTTATGTAGAGGTTTAGATTACATTGTTTTACTTT R 2 1 2 1 201000 r 74 goat snp4549-scaffold1146-808147 23 17863289 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383582 Affx-122972587 AX-123253940 23 29410335 AAATAGTTATGTCTCGTTTTTTGGCTTGACATGTC[A/C]ACAGCTTTCAGGATATAGAATCATCCTAGAACTCT M 2 1 2 1 101000 r 74 goat snp4550-scaffold1146-837427 23 17833837 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420405 Affx-122944922 AX-123290752 23 29446120 TTCAAACAAAGACCCTCCAGTCCCCCTCCTTGCCT[A/G]AGAATGCCACACCATTTGTTAGAAAGTTTGCCTAC R 2 1 2 1 101000 r 74 goat snp4551-scaffold1146-873212 23 17798015 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406031 Affx-122955488 AX-123276383 23 29485950 AAAGTAGCCCTAGTCAGGCCTCTGATGAACTGCCC[A/G]CCATGTCTAAACACCAGAGTGAGTGGCTGCCCGGT R 2 1 2 1 201000 r 74 goat snp4552-scaffold1146-913042 23 17758238 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379440 Affx-122976099 AX-123249798 23 29524406 TACATCAAGAATAAATTGCTCTATCAAGTGCAGGT[C/T]TGACACAGGTACAGTCAGCTGGGTGGTGTTACTCA Y 2 1 2 1 101000 f 74 goat snp4553-scaffold1146-951498 23 17719845 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421820 Affx-122944315 AX-123292167 23 29570487 ATGGTGTTCCAAAAGAGTCAGACATGACTAAACAA[C/T]GGCAAAGAGCTTTCTAGAATAATTACCCTATGATA Y 2 1 2 1 303000 r 74 goat snp4554-scaffold1146-997579 23 17675511 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778956 Affx-122921654 AX-385266063 23 29614918 CTAAGAAACAAATATTTGGGAATGATTATTAAACA[C/T]GATTCTGTAGATTCTGCAATACTGGCTTCTCCAAT Y 2 1 2 1 101000 r 74 goat snp4555-scaffold1146-1042010 23 17631120 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404775 Affx-122956683 AX-123275127 23 29652782 CAATATTTATTGATTGCATATAAGGTCTTGGGCTA[C/T]GTGCCCTGTGTCTTAGGAGATTACAATGATTATCC Y 2 1 2 1 101000 r 74 goat snp4556-scaffold1146-1079874 23 17593328 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802770 Affx-122932709 AX-385289669 23 29795823 ACATTTATGTCACCTGAACAGTATGTGTATATATG[A/C]GTGTTTAATCCAGAGCACTTTAACAATTATCCTAT M 2 1 2 1 101000 f 74 goat snp4559-scaffold1146-1222915 23 17451189 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449175 Affx-122923532 AX-123319510 23 29836487 TTCAGAAATAGCCCTGAAGGTTCCATACCATGTGG[C/T]ATCTGTGAAAAGAAAGACAAAACTTTTCCCTCTTT Y 2 1 2 1 101000 f 74 goat snp4560-scaffold1146-1263579 23 17410916 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781423 Affx-122927161 AX-385268508 23 29898563 GTCAAAAAATATTGATCTTATGTTCTTTCCTTAAA[C/T]ATTATTTATCCCTCACTCTCTGGTTCCCTGGACCC Y 2 1 2 1 102000 r 74 goat snp4561-scaffold1146-1325655 23 17349104 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273047 Affx-1111833259 AX-519546720 23 29909287 GAGCACATTAGTGTGTGACCCAGGAAATGAACTAT[A/G]TCACAGCTACTCACACATTCGTTGTCCTCTGAAGG R 2 1 2 1 201000 r 74 goat 23_29909287_AF-PAKI 23 29909287 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445986 Affx-122925881 AX-123316323 23 29942481 TTAATTTAAGCATCACTTGAGTACTTTTTTTCCCC[A/G]GTAATGAAAACAATCATTTATTATGCTCACAGAGC R 2 1 2 1 101000 r 74 goat snp4562-scaffold1146-1369573 23 17303718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449818 Affx-122922404 AX-123320153 23 29972732 GATAAAAGATTTCTGTATGAAGCTTGCAGTCTGAC[A/G]TTCTTCTGCTAGGTCCTTGGTTCCCAGAGTATTTT R 2 1 2 1 201000 f 74 goat snp4563-scaffold1146-1399824 23 17275180 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766749 Affx-122965677 AX-385254085 23 30019026 ACATGGTGGTCCCTATTTTGACTCAAGTGCTTTTA[C/T]ATCTCAGGATATTAGTGATATTTCGGTATGTTGAG Y 2 1 2 1 101000 f 74 goat snp4564-scaffold1146-1446118 23 17233248 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417424 Affx-122947217 AX-123287772 23 30052240 ATGTCCAAGTGGCTTGATTACTGCTCTCTATAGAC[A/G]CAGGATAGGGAAAGAATGGAAACAGAGAGAACTTT R 2 1 2 1 201000 f 74 goat snp4565-scaffold1146-1479332 23 17199681 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277525 Affx-1111835956 AX-519551026 23 30053708 AAGGAAGAAGAACCATGTATCCTCCTTTGAGATCC[A/G]CCCTATTTCCACAGTATGGTGTTGAGAAAGGATGG R 2 1 2 1 101000 f 74 goat Random2.2K-2057 23 30053708 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38426410 Affx-122940837 AX-123296756 23 30091622 CCTATTTTGGTTTGTCAAATTTGTGTGTAGGTGCT[A/G]TACCAAGAGAGAAAAAACAAAAACCCAGGTAACAA R 2 1 2 1 201000 f 74 goat snp4566-scaffold1146-1518714 23 17162685 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 532577588 Affx-1248697230 AX-579216005 23 30101631 GGAACACATACTGGGCCATACTTGGGGCAGAGACA[-/GAGACA]AACACACTTGTCAAAGGGACATTTCCGTGATGACC - 2 1 2 1 500000 f 74 goat "ins-del_017;rs648686495" 23 30101631 - GAGACA 5 indels litter size and body height 0.584 neutral SV-TF-chip candidate gene ou candidate region Runx2 562165326 Affx-1248697230 AX-606940737 23 30101631 GGAACACATACTGGGCCATACTTGGGGCAGAGACA[-/GAGACA]AACACACTTGTCAAAGGGACATTTCCGTGATGACC - 8 1 4 1 20100 r 74 goat "ins-del_017;rs648686495" 23 30101631 - GAGACA junction SV-TF-chip candidate gene ou candidate region Runx2 562166090 Affx-1248697230 AX-606941499 23 30101631 GGAACACATACTGGGCCATACTTGGGGCAGAGACA[-/GAGACA]AACACACTTGTCAAAGGGACATTTCCGTGATGACC - 8 1 4 1 20100 f 74 goat "ins-del_017;rs648686495" 23 30101631 - GAGACA junction SV-TF-chip candidate gene ou candidate region Runx2 320792652 Affx-122941364 AX-385279632 23 30163319 GCTTCATCCTCACTTTCATTCTCTTCCTCAAATCC[A/G]ATTATCAGAGCTGTTTGCCTCAGTCACTGAAATAC R 2 1 2 1 101000 f 74 goat snp4568-scaffold1146-1590411 23 17090693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418352 Affx-122946590 AX-123288700 23 30196415 TCATTGTAGTAGCTATCAAGAGGCCAGGAAATGCT[A/G]TAGGAGTTGTGGGGCTGTTTGGACCTTTGTGACTC R 2 1 2 1 201000 f 74 goat snp4569-scaffold1146-1623507 23 17057750 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778853 Affx-122959846 AX-385265961 23 30227802 TCCAACTCTAATGTTTAATCCATTTAACATTTAAA[C/T]GTTCCAAAGAGAGGCTTAAGACTCTTTTTTAAAAG Y 2 1 2 1 303000 f 74 goat snp4570-scaffold1146-1654894 23 17026184 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404743 Affx-122957235 AX-123275095 23 30268497 GAATGGGTTAGCATTGCTTTTTCAATAATACACCC[A/G]TGACGAGATATAGAAAAATCTGTTTCTCCATGAAT R 2 1 2 1 201000 r 74 goat snp4571-scaffold1146-1695589 23 16985434 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776558 Affx-122945548 AX-385263685 23 30354784 ACCCTTTGCATTTTAGTCTTGTGATTTGCTTATTG[C/T]ATGCTCATTTCCATAGTAAAGACAGACTAAATGTT Y 2 1 2 1 201000 f 74 goat snp4573-scaffold1146-1781876 23 16898480 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394176 Affx-122964926 AX-123264531 23 30396743 TTTAAGACTTTCATTAAAATATTAAGTATCACAGG[C/T]TAACCGTGTTCTTTTCCCCCACCACTAAGTATTAA Y 2 1 2 1 101000 r 74 goat snp4883-scaffold1164-40780 18 47818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429133 Affx-122938002 AX-123299475 23 30426514 TCCTTAAAACTTCCTGCTGAGGAAATCCACCTCAG[C/T]AGAGCAGATGTAGCCAATCATTGCTGAGAAGGTCG Y 2 1 2 1 101000 r 74 goat snp4884-scaffold1164-70551 18 77717 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426707 Affx-122939892 AX-123297053 23 30466115 ATGTATGGGGCTTATCTATCAAATCTTGCACTCAG[A/G]GTCAAGGTAGTGTCCAGGCAGGTTAGAAGCAAGGT R 2 1 2 1 101000 f 74 goat snp4885-scaffold1164-110152 18 117251 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783573 Affx-122943846 AX-385270635 23 30508218 ATGCTTAAGTAATGGGGAAGATGCCACATTATGGC[A/G]TGCACTAGAGATGGGAATCTTGTAGCCATCATTCT R 2 1 2 1 101000 r 74 goat snp4886-scaffold1164-152255 18 159275 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442649 Affx-122927912 AX-123312986 23 30566896 AAGAAATTTGGCCACAAGAGGGAGCACTATTCCTA[C/T]GCTTGCTTATTTATTAACTATTGTAACACATGTTT Y 2 1 2 1 201000 r 74 goat snp4887-scaffold1164-210933 18 217788 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407330 Affx-122955299 AX-123277681 23 30604779 ATCATGTTCGCTGGCAGAAGACCAAGCAAAGGTCA[C/T]GTTCTGATGGCTTAGCTACAATAGGGCTGATGAAG Y 2 1 2 1 101000 f 74 goat snp4888-scaffold1164-248816 18 252989 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403991 Affx-122957205 AX-123274343 23 30637581 CTCTTTCTGCTCTTTTGGTTGAATTTCCTGACCTG[C/T]AGAGGTCAGAATTGATCTGATATTCTCCCTTTCTG Y 2 1 2 1 101000 f 74 goat snp4889-scaffold1164-281618 18 285515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801077 Affx-122969646 AX-385287991 23 30681762 TTTATCATCTCACTTAAAAATGTGCAGCCTAAAAT[A/G]TACTTAAGAACAACATGTAACACATTTAAATGTCA R 2 1 2 1 101000 f 74 goat snp4890-scaffold1164-325799 18 329294 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393057 Affx-122965618 AX-123263414 23 30724301 CTGTTGCCAATCTGAACAGAAATAGACCACATAGA[C/T]ACACATAGACACATAACAGACAGTGACACAGATGC Y 2 1 2 1 101000 f 74 goat snp4891-scaffold1164-368338 18 372276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277527 Affx-1111835957 AX-519551028 23 30768115 GTGCTTGGGCGCATCTTCCCGTTTCCATGGCACTT[A/C]CTTGGTGGGGTTTCTGGGAGCCCTCCGGTGGACAG M 2 1 2 1 202000 f 74 goat Random2.2K-2058 23 30768115 T G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409126 Affx-122953305 AX-123279477 23 30778667 TGTCTTGCTACTAAGATGTGTTTGTAGACTGTTTT[A/G]TAAGGAGAGCAGATGAGGAAGGGCTGCTACCACCA R 2 1 2 1 101000 r 74 goat snp4892-scaffold1164-422704 18 426908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792843 Affx-122963787 AX-385279821 23 30827174 GAATTTTCAGTCAATATGTATATTCGCAAACATAC[A/G]CAAGAATAGAATCTATAATTTCCCAATTACCCATC R 2 1 2 1 101000 r 74 goat snp4893-scaffold1164-471211 18 475748 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801899 Affx-122928161 AX-191440129 23 30876927 TCTATGAATTTTGTCTTAGACACTACCCAAGAGCA[C/T]GTTTATAAACCGTACTTAAACTCAAATGGTTTTTT Y 2 1 2 1 101000 f 74 goat snp4894-scaffold1164-520964 18 525489 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450754 Affx-122921850 AX-123321088 23 30909638 GAAGCTGTCCTCATTTTTAAGCAGAAGTGTCCGTG[C/T]GGAGTTGTTTATAAGCACTCCGGCACCCACATATT Y 2 1 2 1 102000 f 74 goat snp4895-scaffold1164-553675 18 559157 T C 1 neutral GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38406903 Affx-122955625 AX-123277254 23 30941945 CACAAGAAAATAAACCATCTTTATCTGCACATGAC[A/G]TTATGATTGTCTATGTAGAAAAATCTAGAATAATC R 2 1 2 1 101000 f 74 goat snp4896-scaffold1164-585982 18 594381 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797319 Affx-122921108 AX-385284258 23 30973767 TCTCTTTATTTAGAGCACAAGCAGTTTTGCATAAT[A/G]TAAACTATCTCTGCTATGGAGTGAACGCATTCAGG R 2 1 2 1 101000 r 74 goat snp4897-scaffold1164-617804 18 626051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439377 Affx-122930268 AX-123309714 23 31003047 ATGGATTGACACGGCATTCCATAATATTACATACT[A/G]CTGATGTCCTTACCAGAGCATACTCTTTTAGTTCA R 2 1 2 1 101000 r 74 goat snp4898-scaffold1164-647084 18 655120 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438024 Affx-122931564 AX-123308362 23 31054062 ACTGCTCCAATTCTTGAGCTTAATATTTGAGCATG[C/T]ACTGAGTGCAAGACACTGCACTAGTGGGTGTGAGT Y 2 1 2 1 201000 f 74 goat snp4899-scaffold1164-698099 18 705906 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277529 Affx-1111835958 AX-519551030 23 31082497 AGAGTGGAGGGGGGCTGGGGTCCTGGATCTGGGCT[A/G]CTGGAATGAATGGGGAGGAGGAAGCAGGAGCTATC R 2 1 2 1 303000 f 74 goat Random2.2K-2059 23 31082497 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418966 Affx-122946078 AX-123289314 23 31106625 AGTACAATCACTGGTTTCTTTAAACCATAGTCAAG[A/C]TTTGTAACTTTCCTTTATTCCTGTCTCTCGCTTGA M 2 1 2 1 101000 r 74 goat snp4900-scaffold1164-750662 18 756624 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396913 Affx-122963209 AX-123267268 23 31161963 AACCCAAGGCAGGCAGTACTGTAAATGGCCAGATA[C/T]GTTAGCAATGAAGGTTTATTTAGGTCTTCCCACCC Y 2 1 2 1 101000 f 74 goat snp4901-scaffold1164-806000 18 810322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796959 Affx-122934566 AX-385283900 23 31200483 GCATGTCAAGATCAAGATGTATCTTTAAAGATAGA[C/T]GGTTTCATGGTCAGAGGCCTTTTGCTGTGAGGCTT Y 2 1 2 1 101000 r 74 goat snp4902-scaffold1164-844520 18 849020 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453348 Affx-122919954 AX-123323681 23 31242358 TTGAGGCAGCAAGAAACAGAGCTCAGCATTCTGTT[A/G]TAAGTGTACACATCAAAATCTCTGAGATACAAGAT R 2 1 2 1 102000 r 74 goat snp4903-scaffold1164-886395 NW_017216503.1 5861 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409399 Affx-122954140 AX-123279750 23 31302711 TTTATTTTGTTTCTCAAATTATTCCAGGTTTGTCT[A/G]TTGAGAGTTCCTGCAGATTGCTCCTTTTCCTTAAA R 2 1 2 1 101000 r 74 goat snp4904-scaffold1164-946748 18 960279 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417085 Affx-122947495 AX-123287433 23 31337355 AGTCCTTCATGTCAAGCAGATCCTTCCTTCTCCCC[A/G]TCTCCTCTTGAAGGATGCTGAAAAAGAAAAATGTC R 2 1 2 1 201000 r 74 goat snp4905-scaffold1164-981392 18 995136 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778605 Affx-122966547 AX-385265716 23 31367933 GTGATCCTCATTAAGTAAAACCCAAAATATAGTAT[A/G]TAGTTTACTTCTATATTGTCTTTCTCATTTACCTT R 2 1 2 1 201000 r 74 goat snp4906-scaffold1164-1011970 18 1025645 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779262 Affx-122937076 AX-385266366 23 31422051 ACTTCAGTCAGAAACAAGGCATAAGCTTTGACTTA[C/T]GAGATTAGTGATGAATTAATTCAAAATTATCTCAT Y 2 1 2 1 201000 r 74 goat snp4907-scaffold1164-1066088 18 1080016 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275285 Affx-1111834702 AX-519548860 23 31423857 CTGGCAGGCCTGCAGTCACGCCGGCTCCAGGGAGC[A/G]ATGAAAGTTCAGCTCCATTGTCCCCACCTACCTAC R 2 1 2 1 201000 r 74 goat GoatD01.046807 23 31423857 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38445432 Affx-122925363 AX-123315769 23 31481035 TATTTCCTTGTGTGCTTCCTTGTGTGCTTAATCGT[A/G]TCTGACTCTGCGACCCCTTGGACTGTAGCCTGCCA R 2 1 2 1 102000 f 74 goat snp4908-scaffold1164-1125072 18 1139343 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386305 Affx-122970922 AX-123256663 23 31572563 TTTTATAAGACCTATTGGATTTTAATGATACCTGT[A/G]TAGATTCAAACTGCAGAAACAGCCACCATACATAG R 2 1 2 1 101000 r 74 goat snp4910-scaffold1164-1216600 18 1231403 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443265 Affx-122927490 AX-123313602 23 31603305 TTGCTCACTTACTAAGAAATACTAGATACAATTAG[C/T]CCCCAGTAATAATCCTTTTTTTTTGGCTAAATTGG Y 2 1 2 1 201000 f 74 goat snp4911-scaffold1164-1247342 18 1262149 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445978 Affx-122925887 AX-123316315 23 31699150 TAAGATTGGAGAAAGAGACTTGAAAGTCTCCAGAC[A/G]TGGGTTTTGGAGCCAGCATATCAGATATCTGTTAT R 2 1 2 1 201000 f 74 goat snp4913-scaffold1164-1343187 18 1357706 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381167 Affx-122975212 AX-123251525 23 31731417 AACTGTATGTCTTGCAGGTACCTACAATTAACTCC[A/G]CAATTAACATGCTTATTATCACAAATGGCTAAACA R 2 1 2 1 101000 f 74 goat snp4914-scaffold1164-1375454 18 1390783 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803381 Affx-122966821 AX-385290214 23 31776204 GTATTCAGATTATTATACCACAGAACACAATGCTA[C/T]AGAAATAATCCATTAAAATTGTTGGAAAAGTTGAA Y 2 1 2 1 101000 r 74 goat snp4915-scaffold1164-1420241 18 1435287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783094 Affx-122948292 AX-385270161 23 31818225 TGCCTGAATAATGGACAGTTTTAGAGCAGTAGGCA[C/T]GTCATGTCAAAAGCATGGCTTTGAATGAGTGAGCT Y 2 1 2 1 101000 r 74 goat snp4916-scaffold1164-1462262 18 1479067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803338 Affx-122951314 AX-385290174 23 31872430 GTAACAAAATAGAACTAGGTGTTTTAGGCAGTAAA[C/T]GACTTAGAAAGTGCTTATAGGGTTTTTTCATGGTC Y 2 1 2 1 101000 r 74 goat snp4917-scaffold1164-1516467 18 1533125 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378117 Affx-122977141 AX-123248476 23 31967333 ATTGAAATAATACTGAGAAGATCAGCATGGCCCCT[A/G]CCCGAGGATGACACACATTTGTAAAGTCTTCCGTA R 2 1 2 1 101000 r 74 goat snp4918-scaffold1164-1611370 18 1629128 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402244 Affx-122959139 AX-123272597 23 32021906 AATATGTATCTGTCAAAGGCCTTTTTCTTCAGATG[C/T]ATAGTCGTGATGTTTCCATGTTGGTCAACAGGTAC Y 2 1 2 1 101000 r 74 goat snp4919-scaffold1164-1665943 18 1685702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432489 Affx-122935589 AX-123302830 23 32049104 GAGATACCTTAGAGTACCTATTTCTATCATTTGCT[A/G]CAGACCCTTAACATTTTTTGGTGATTTCTGCTACT R 2 1 2 1 101000 f 74 goat snp37057-scaffold45-17628 18 1815236 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434185 Affx-122934876 AX-123304526 23 32104142 CAGCCTAAAGATGTATCAGCTGGACCCTAAAGCCC[A/G]TGACTGCGCTCTCATCAGAAACCTAACTTAAATGC R 2 1 2 1 101000 r 74 goat snp37058-scaffold45-72666 18 1871294 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426076 Affx-122941084 AX-123296422 23 32142985 CTTATTTAAGTGTTGAGAGTGACTAGTGACTTACT[A/G]CTTGTTATCACTGGGTAGTCCTTCTTTGGTTCTGG R 2 1 2 1 101000 r 74 goat snp37059-scaffold45-111509 18 1910733 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426975 Affx-122940396 AX-123297320 23 32192177 AAGGACAGTGTTAAAGAATGTTAAAGCCACTGAAC[A/G]GATGCAGTCATCTCCAGTGCTAGTAAGGTTATGAT R 2 1 2 1 201000 f 74 goat snp37060-scaffold45-160701 18 1960114 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434151 Affx-122934903 AX-123304492 23 32244914 TCTTAGGAATCCTTGAGATTTTGCAAAACTGATCC[A/G]TTCTTCGTATTCCACATCTTATGAGCTGATGGCTT R 2 1 2 1 101000 r 74 goat snp37061-scaffold45-213438 NW_017215769.1 20243 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428210 Affx-122939448 AX-123298553 23 32276705 TCATCTACACTGATGATTGTCCCAAGAAAATAAAA[C/T]TTGTGAGGCCTATCAAATACCTAACTCAAACTTTC Y 2 1 2 1 101000 f 74 goat snp37062-scaffold45-245229 18 1484917 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407524 Affx-122954703 AX-123277875 23 32311311 GTCCCGCTGAAGAACGGAGCCATTATTAGAGGGAG[C/T]AGAATGGGATTTCAGGGATCTTGGTCAGGGGCTGG Y 2 1 2 1 101000 f 74 goat snp37063-scaffold45-279835 23 14428466 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769469 Affx-122974173 AX-385256639 23 32343388 TTGGTTGCTATTAAATGAGTTGCTTTCAGGCTAGA[G/T]CCAAAGAAATGGAAGAAGGAGGCATCTGTGGAACT K 2 1 2 1 102000 r 74 goat snp37064-scaffold45-311912 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380053 Affx-122975570 AX-123250411 23 32375275 CTTCAATGAGATGAGTGCTTTTATATATAAGAGAC[A/G]CACAGAGCTCCCAAGCCCTCCCCTGTGTGAGGATA R 2 1 2 1 303000 r 74 goat snp37065-scaffold45-343799 18 1972659 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783975 Affx-122952295 AX-385271028 23 32459467 TTTGATATTTGTTTTATGATATTACAACAAAGAGA[C/T]GAGGAAGAAAACATGACATTCCTAACACACACTCT Y 2 1 2 1 201000 f 74 goat snp37066-scaffold45-427991 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439461 Affx-122930172 AX-123309798 23 32508896 GTCATTACGATAGTTACATTACATAATTATAATAG[C/T]AAGCACCATGGGCATTAACAGGTAGGAAGACCAAC Y 2 1 2 1 201000 f 74 goat snp37067-scaffold45-477420 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272998 Affx-1111833260 AX-519546679 23 32550325 AGGGAGAAGGGAGGGGAGCTCAGGATGGGGAACAG[A/G]TGTATACCTGTGGCGGATTCATGTTGATGTATGGC R 2 1 2 1 303000 f 74 goat 23_32550325_AF-PAKI 23 32550325 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38452760 Affx-122920261 AX-123323093 23 32591647 CTATGGTTTAAAATTGATGCCATCACTGGGCAAAT[A/G]TTTGCCATACAAAGGGGATTGAGAGGGGAAGTAAA R 2 1 2 1 201000 f 74 goat snp37069-scaffold45-560171 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770244 Affx-122969498 AX-385257410 23 32631720 AAGCTGCCCTTGTACATACTGAACCCTTGTTCACT[C/T]AATAGAAGACCTTTTTAAGCAAATTGAAATTAATA Y 2 1 2 1 101000 f 74 goat snp37070-scaffold45-600244 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784421 Affx-122922936 AX-385271470 23 32667917 CATGCAGCTTCAGCTGTTCATTTCACAGTATTCCA[C/T]GAAATTTTCAGCTTCCCTGAATATATTGGGGAAGT Y 2 1 2 1 101000 f 74 goat snp37071-scaffold45-636441 23 14902679 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438193 Affx-122931825 AX-123308531 23 32718530 ATAAACATGTGAGAAGTGATCATTTTTATTAAACA[C/T]AAACAAACAAAACCTGCAGAAATAAGAGTGGCTTG Y 2 1 2 1 201000 f 74 goat snp37072-scaffold45-687054 23 14852085 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399751 Affx-122960321 AX-123270106 23 32759458 TTGGCTAATTCCTACAGAGAAGAAGCAAGCAGCCA[A/G]AGGAAAGTAGTGTCTGAGTGTCTTTACCATTTTAT R 2 1 2 1 101000 r 74 goat snp37073-scaffold45-727982 23 14814621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425445 Affx-122941520 AX-123295791 23 32806343 TGTCTCAAAAAATCTGGTACTCAATTCACCGTGTA[C/T]ACTTTGCACACCATACTGTAGCTTCTTAGTTACTG Y 2 1 2 1 101000 f 74 goat snp37074-scaffold45-774867 23 14767663 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273822 Affx-1111833865 AX-519547433 23 32810577 AGATCTCTACAGGTCAGCACGACTCAGTGGTGCCC[A/G]AGAGGGACTCAGTGTGGCCGAGGGTCAGGCGGAGC R 2 1 2 1 202000 f 74 goat GoatD01.008419 23 32810577 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38420541 Affx-122945298 AX-123290888 23 32839200 ATCTGAGCCCAATTAGAATCATCCTTTCAATCTCA[C/T]GTCACAGGAGGTCATTATGTTTACAATCTCAATCA Y 2 1 2 1 201000 f 74 goat snp37075-scaffold45-807724 23 14734785 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387599 Affx-122970253 AX-123257957 23 32876779 TTGAACTCTGCAGTTAGTGATAAGGCCCAAATTCA[C/T]GCGTTCATCCACTCATCCATTCAACATAACAACAA Y 2 1 2 1 101000 f 74 goat snp37076-scaffold45-845303 23 14697183 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447646 Affx-122923972 AX-123317982 23 32933985 AATGTGTTTTGTTTTAAACTCTCCAACCTCAGTTA[C/T]GCTTTTCCTAATACAAGACCCACTATTAGTTTTCA Y 2 1 2 1 101000 r 74 goat snp37077-scaffold45-902509 23 14639392 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381946 Affx-122974120 AX-123252304 23 32976144 TCTAGCACATACACATCTGCTAAACTTCTGGCCTA[C/T]GAGAGTCAGGAAAACAATCAAAGAAGGAGAAAGAG Y 2 1 2 1 101000 f 74 goat snp37078-scaffold45-944668 23 14596759 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789052 Affx-122946031 AX-385276065 23 33024835 CAAGAATTTCTAAAGAAAATGGAATGCATGTAATA[C/T]GAATGTGATTCAACTTAGGCACGATTGGTGTCTCC Y 2 1 2 1 101000 r 74 goat snp37079-scaffold45-993359 23 14548114 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785086 Affx-122956277 AX-385272133 23 33077362 GAAGACAAAGACCAACTCAAGTCAGTAAGCAAATA[C/T]AAAAGGCAAGACTAACAGCAGATTGCGATCAGCGC Y 2 1 2 1 101000 r 74 goat snp37080-scaffold45-1045886 23 14495436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453450 Affx-122919861 AX-123323783 23 33127596 ACATCAGTAAACAAAGCAGGCAGACACTTGTCCTC[A/G]TGGAACTTATATTCTAGGTGGGGGGAGACAGATAA R 2 1 2 1 102000 f 74 goat snp37081-scaffold45-1096120 23 14445022 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796564 Affx-122945267 AX-385283510 23 33196253 ATTCCTAGTTTAGAAATCCAAGAAACTCTTCTCCC[A/G]TGGGTCCTCATAAAGATGGCACTGGGTGATGAAAC R 2 1 2 1 101000 r 74 goat snp37082-scaffold45-1164777 23 14375728 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436357 Affx-122933064 AX-123306696 23 33214787 GTGTTCTCCAATGTATGGTGGCCTGAAGGCTTTCA[C/T]GAGTTTCATTTTGCTTTTAGAAGACTAGCTCATTT Y 2 1 2 1 101000 f 74 goat snp49974-scaffold715-704333 23 14357181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396704 Affx-122962821 AX-123267059 23 33248222 TTACGCCTATACCCACAGTTCTTTTTGAGATACTC[A/G]TCTTTGTAGATCTATTTTGAGTTTACTGGCTTCAT R 2 1 2 1 101000 f 74 goat snp49973-scaffold715-670898 23 14324823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435532 Affx-122933402 AX-123305872 23 33306712 GGGAACCTCTGAATGTCTTTCAGAGTTAGCACAGT[A/G]TAGTAAAGAGGGCATTGAGTCAGGTGTTCATTGGA R 2 1 2 1 101000 f 74 goat snp49972-scaffold715-612408 23 14266714 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393950 Affx-122965062 AX-123264305 23 33364135 AAGCATGTGCAGTTCACTCTTCTCAGATACTGCTC[A/G]CCATCTGTTTCCAAAGTGAGAAACGAGCATCACTT R 2 1 2 1 102000 f 74 goat snp49971-scaffold715-554985 23 14209361 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440959 Affx-122928995 AX-123311296 23 33407833 TCCTCCTGTTGTACCAGTCTCCAAGGTCTAGTTCA[A/G]AGGAGACTAGCAAGAAAAAGAAAAACCATGTTGCC R 2 1 2 1 201000 f 74 goat snp49970-scaffold715-511287 23 14165597 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388504 Affx-122969217 AX-123258862 23 33449761 ATGCCCACAGAGGAGCAGGGAGTTTATGCTTCTTC[G/T]CTGGTCTTTCCGAGTTTTTGTGGATATACTTAGTG K 2 1 2 1 101000 r 74 goat snp49969-scaffold715-469359 23 14123483 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277533 Affx-1111835960 AX-519551034 23 33496326 CTCTGCCTGAAACACTCTTACCCGGATATCCACCT[A/G]GCTCCTTCCCTCATCTGAGGTCTGTCCAAACATCA R 2 1 2 1 102000 f 74 goat Random2.2K-2061 23 33496326 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417254 Affx-122947268 AX-123287602 23 33502350 ACAGAGTGTGGCTCAGGCCAGAGTAGCTTTATTGA[C/T]GAGACGCAAGGCGGAGAAGAGAGAAGTCAAGGATG Y 2 1 2 1 101000 f 74 goat snp49968-scaffold715-416770 23 14070226 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403425 Affx-122957747 AX-123273778 23 33570101 AGAAGGTCTTGGGGGGTTTAAAAGTATTTGTAGCT[A/G]CTTTCATTTAAATATATCTGTGTGCCATTATTTAC R 2 1 2 1 101000 f 74 goat snp49966-scaffold715-349019 23 14002359 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377192 Affx-122978193 AX-123247551 23 33613290 CAAACGGGCCCAGAGAAGAATCTGTTGCCTGGTGT[A/G]CTCCTGTACTGAGCGCTCATGCTGTGGTTGACAGT R 2 1 2 1 201000 r 74 goat snp49965-scaffold715-305830 23 13959319 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424939 Affx-122941280 AX-123295285 23 33645137 TACTTATACACCAAAAAATTAGGCATATGTTGTCA[A/G]TCTGGGGATTATGACAATTTTTTTACTGTCTGTCA R 2 1 2 1 101000 f 74 goat snp49964-scaffold715-273983 23 13927624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452546 Affx-122920532 AX-123322879 23 33680550 ATGGCACTGGGGCTTATACTTATGTGGATACTTAA[A/G]GACTTATTCATAAGGATGGCAAAGAGGAGAATAAG R 2 1 2 1 101000 f 74 goat snp49963-scaffold715-238570 23 13892094 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420047 Affx-122945136 AX-123290395 23 33721633 GACCCATTGACTTACATTGATCCTACCAATCCCCC[A/G]CCTCCCAAATAACCCTGGAAAGCAGTCCATGCTCC R 2 1 2 1 101000 r 74 goat snp49962-scaffold715-197487 23 13851166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452038 Affx-122920895 AX-123322371 23 33761096 GAGGAAAAGAAAAGTGCAAATTTGAAAGCTAACTT[A/G]TTTATGAAAAGGCATTTCCAATTCCATTTTAATTT R 2 1 2 1 101000 r 74 goat snp49961-scaffold715-158024 23 13813575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413023 Affx-122951000 AX-123283372 23 33835679 TCTCCTCTCTCTCCAGAAATTTGGCCACTCAATTC[C/T]TGTTTGCCTTCATTGTTCTTCTATGGCTTTCAGTA Y 2 1 2 1 201000 r 74 goat snp49959-scaffold715-83441 23 13738771 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431611 Affx-122936159 AX-123301952 23 33876213 CCTTCCTTCCCTTGTTACCGCCTCCAGTCTTTCTT[A/C]TTCCTCCCTCTTTCCCTCGCTTCCACATTTATGCT M 2 1 2 1 102000 r 74 goat snp49958-scaffold715-42907 23 13698191 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387812 Affx-122969682 AX-123258170 23 33917587 ATGAAATAAAATGATGAAAGCCGCTCATTGCATGC[A/G]AAGGGGTTTGGAGCTTACCTTGATGACCCATGGAA R 2 1 2 1 201000 f 74 goat snp49957-scaffold715-1533 23 13656601 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399643 Affx-122961066 AX-123269998 23 33928525 AGTTTCATCTTAGAAGTTCCTTTGGCTGTAAAGGC[A/G]TGGGTTTTCCCTGCAGTGAGGTCACGGCACTGGGC R 2 1 2 1 101000 f 74 goat snp19224-scaffold1933-605546 23 13645736 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790346 Affx-122950331 AX-385277349 23 33960112 AGAAGCATGAGATCATGCATTGTTTATGAAGAGAG[A/G]TGATTTTTATTCTAGACTTGTATTGTTCTTGCAGA R 2 1 2 1 101000 f 74 goat snp19223-scaffold1933-573959 23 13614170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767495 Affx-122966236 AX-385254759 23 33989199 ATCTGGAGTTTGTTCTGGCATCAACCCTGAACACC[A/G]CAGTAAGTGGTACAGTTGGCTAAGTTTCCAAAAGT R 2 1 2 1 101000 f 74 goat snp19222-scaffold1933-544872 23 13584988 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404420 Affx-122956771 AX-123274772 23 34062921 TTGGGGTCAGGAGTCTAAGGTGTGATCCTTGCCCT[C/T]AAGGAGATGGAAGTGTAGTTGGGAAAGGAAGCAGG Y 2 1 2 1 101000 r 74 goat snp19220-scaffold1933-471150 23 13511045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430014 Affx-122938025 AX-123300355 23 34110825 GTGGTATAGGGCGCTTTCCATGTGAAGATTCCTCA[C/T]GAGCGTTTATTTTTCTTTCTGGCTTAACGCTCATT Y 2 1 2 1 101000 f 74 goat snp19219-scaffold1933-423246 23 13463199 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409173 Affx-122953196 AX-123279524 23 34139573 TGTTTTGTTTTTATTTTTTGGCTTTATCTAAAGCC[C/T]CAGGGTGGCTTATATAAAAAGTACATAATACATTT Y 2 1 2 1 103000 r 74 goat snp19218-scaffold1933-394498 23 13434370 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430645 Affx-122936950 AX-123300986 23 34176133 GGACTGGAAGAGAAAATAGGTCAAAAAGCCCAGCC[A/G]CCCCTGAAATGAATTTTAGACTCTTATTATTGATG R 2 1 2 1 101000 f 74 goat snp19217-scaffold1933-357938 23 13397811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432263 Affx-122936341 AX-123302604 23 34207425 GTGCGCAGCCCTCCAGTGGACTCTGATTCTATTTG[C/T]TCAGCCCTTTGGTCTGTAGGTGAAATTCAGTTATC Y 2 1 2 1 101000 r 74 goat snp19216-scaffold1933-326646 23 13366763 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398928 Affx-122961000 AX-123269283 23 34256960 TTAGCAAATGGTACCCCCTGGCACCTAAGGAGGCT[A/G]TCTGTCATCATTGTTGTTATTACTATGACAGCTAC R 2 1 2 1 102000 r 74 goat snp19215-scaffold1933-277111 23 13317288 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412421 Affx-122951428 AX-123282770 23 34311333 GAGGAGACAGTATGGAAATGAAGATTTTCAGTTTT[A/G]CATAATAATCTAGTAACATCTAGTCGTGTGTGTGT R 2 1 2 1 101000 r 74 goat snp19214-scaffold1933-222738 23 13262910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435717 Affx-122933303 AX-123306056 23 34370393 ACTGATGTCTGTGTCCCCTTGCTGACAACTGCATC[A/G]TCATTTCTGTGGATTGGGAGACCCTGCATTTTCTA R 2 1 2 1 201000 r 74 goat snp19213-scaffold1933-163678 23 13203785 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774805 Affx-122970720 AX-385261939 23 34425609 GGTTTTACTGTGTCAGATACCTCTTAAGACACATT[A/G]AGTTTATCCAGTGGGACAGAATCTGAGATTCCTAT R 2 1 2 1 101000 r 74 goat snp19212-scaffold1933-108462 23 13147908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780723 Affx-122933062 AX-385267813 23 34482058 GAACTTCCACCCATATCAGCCTTTAGAAATGGGAC[A/G]TTTAATTTGTTTCCAGAATCAGAGATAACAGTGTG R 2 1 2 1 101000 f 74 goat snp19211-scaffold1933-52013 23 13091393 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801015 Affx-122947994 AX-385287929 23 34524764 TCAGCCCAAGAAGGTAATGAAACATGTCATCACTC[A/G]TGTACCGAAATACATAAAAAACATACTGAAGACCT R 2 1 2 1 101000 f 74 goat snp19210-scaffold1933-9307 23 13048056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450009 Affx-122922853 AX-123320344 23 34556299 ACTTAAATTAAGACTTGTGTAGTCCATGAAATAGT[A/G]CCTCTTCAAGCCTTTATGCGCAGAGGATTGATACT R 2 1 2 1 101000 f 74 goat snp39719-scaffold505-2190443 23 12954473 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418833 Affx-122946149 AX-123289181 23 34598429 TAGAAGTATGGCACTCTGACCCCTAGTGGTTAGAT[C/T]ACACCAAGAAAATTCAACGTTAGCCCAAAGACAAT Y 2 1 2 1 201000 r 74 goat snp39718-scaffold505-2148313 23 12913083 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400670 Affx-122960342 AX-123271025 23 34693644 TTTCTGCTTCTCGTAAAGCGGTAGAATTCCTTTTC[A/G]GTGCTGAAGGGCCCGTTACATCAAATGGAACAGGT R 2 1 2 1 101000 r 74 goat snp39716-scaffold505-2053098 23 12817318 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393144 Affx-122965548 AX-123263501 23 34725278 TGGTCACTCTATTTATAGGATCTTTAAAGTAAGTA[C/T]ATTTTCAGTGAGCTAAGGTGAATAAGGAGACAACT Y 2 1 2 1 101000 f 74 goat snp39715-scaffold505-2021464 23 12785857 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767309 Affx-986698463 AX-385254590 23 34801187 GGTTATTAATCTGTTTAAAATACATGGGCTGAAGG[G/T]AAGAATCAGTAGGAGTATAACGAGCAGTCTGAGCA K 2 1 2 1 600010 r 74 goat 23_34801187 23 34801187 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 38382373 Affx-122973858 AX-123252731 23 34813051 ACAGCCTCTAGATATCTGGTCCCTCATCACCTCCG[C/T]GGCCTCCTTTCCTCCACTTACCAAAGGCTGACTCC Y 2 1 2 1 201000 r 74 goat snp39713-scaffold505-1933691 23 12699482 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378677 Affx-122977077 AX-123249036 23 34844541 TCCTCCAGTAGCCAGATAATCTCAGAAGGAACCTA[A/C]CCAATGCCTACTGCCAAGGGAAGGGGACTCACAGA M 2 1 2 1 101000 f 74 goat snp39712-scaffold505-1902201 23 12668066 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434418 Affx-122934673 AX-123304759 23 34877041 TTAAAAAAAAAAGTCTTGGCACTCAGTTCGCCAAA[C/T]TGCAAAGTCCTTAAAGCCAGGAATTCCTCCTCTTG Y 2 1 2 1 101000 f 74 goat snp39711-scaffold505-1869701 23 12635395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778287 Affx-122963121 AX-385265402 23 34926807 TACAAAGGGGGAAATACTTAAGCCACCTCTTTAGC[C/T]ATGGCAAAGAAAAACCTTAATATAGGTGGGTAGTA Y 2 1 2 1 101000 f 74 goat snp39710-scaffold505-1819935 23 12586239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770139 Affx-122951775 AX-385257307 23 34970009 CACTCAAAAAGAGACCCGATGAAATCAACACACTT[A/G]TATTACGATGGCCAAGATTATTTTCTTTCAAGTTC R 2 1 2 1 101000 f 74 goat snp39709-scaffold505-1776733 23 12543232 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449491 Affx-122922632 AX-123319826 23 35007340 GCCATTTAAAACAACTTTTAAGAAGTTTCTGTAAT[A/G]ACATGGAGATATGTGAGATATGTTCAGATGTTTCT R 2 1 2 1 101000 r 74 goat snp39708-scaffold505-1739402 23 12506118 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445438 Affx-122925359 AX-123315775 23 35038498 TCCCTGTAGTCTCAAGTATGTGCCACCAAATTGCC[A/G]TCCTCCTTTTTATGTGAAGGCGTTCCTTTTAGATC R 2 1 2 1 101000 r 74 goat snp39707-scaffold505-1708244 23 12475057 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273002 Affx-1111833262 AX-519546683 23 35074687 CTAGGAGAGGGACCGCACGCCTGGGGAAATACCAC[A/G]CCCCTTGGAGAAGCCCCATCTTCAGCTGGGCTCAG R 2 1 2 1 102000 f 74 goat 23_35074687_AF-PAKI 23 35074687 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38432900 Affx-122935326 AX-123303241 23 35085604 TCTTTCTGAAGGGGGTGTTCTGCCTTCAGCCTGCA[C/T]GGAAACTGTTTTTACCACCTAATCGCTCCAGTATG Y 2 1 2 1 101000 r 74 goat snp39706-scaffold505-1661138 23 12427991 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413984 Affx-122950288 AX-123284333 23 35118363 TTATAATCAAGGAATGAAGGCAACCAGAAAAGTCC[A/G]TTTTAATCTGCATGCATGTATTTTCTTTTCTTTTT R 2 1 2 1 201000 r 74 goat snp39705-scaffold505-1628379 23 12395099 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769685 Affx-122920829 AX-385256855 23 35151107 AATTTAGTGCTTTTCTTCTCTCCACAAAAATAGCA[G/T]AACATTAGGAATACAGATCTGTACATTTTGATAAT K 2 1 2 1 101000 f 74 goat snp39704-scaffold505-1595635 23 12362138 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776509 Affx-122934934 AX-385263636 23 35190449 CACTGCTTCTCAAATGTTGACTCAGGCATTGACTG[C/T]GTAACTGCTTCTTCACGTGGTCTTTAAAATAGCCT Y 2 1 2 1 101000 f 74 goat snp39703-scaffold505-1556293 23 12322714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391352 Affx-122967294 AX-123261709 23 35302963 CTTGCCTGCCTCAAAATACTATGTGATAAGTAAAC[A/G]AAAAGACTCACAAAACCGTATTTTGGAAATATGAG R 2 1 2 1 101000 f 74 goat snp39701-scaffold505-1443779 23 12210356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421581 Affx-122944504 AX-123291928 23 35332963 CACCGTAGCTGCCTTCAAAAGTGGGAAGGGCCATC[A/G]TGGGGAGGAGGGTTACGTTTTTCTGTGTAGACCCA R 2 1 2 1 201000 f 74 goat snp39700-scaffold505-1413779 23 12180493 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794847 Affx-122959894 AX-385281807 23 35392076 ATATGTGTGTGTTATATCTAATTCTCTGCAGATAC[A/G]TATCGGGATAGAAACCAGGATAGTCCAAACATTGC R 2 1 2 1 101000 r 74 goat snp39699-scaffold505-1354666 23 12121651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403132 Affx-122958111 AX-123273485 23 35438774 AACCTAATTAGAAAACATAAAGCAAAAGCCCAAAG[C/T]ATATCTTACTCCCCAGCAGTACCTCTTGATCCGTA Y 2 1 2 1 101000 r 74 goat snp39698-scaffold505-1307968 23 12074765 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392350 Affx-122966256 AX-123262707 23 35475846 ACAGCTTGACATCTGTTTAAAAGTTTCTCATTTTC[A/G]TGGGACTTCCTTGGTGGTCCAGTGATTAAGAATCT R 2 1 2 1 101000 f 74 goat snp39697-scaffold505-1270896 23 12037088 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798397 Affx-122965913 AX-385285331 23 35527998 GAGTAACAAATCAATCTGTCCTGCATGATAATAAC[A/G]TTTGTTGACTCATACAGGTAGAAGTCCAGGGTAGG R 2 1 2 1 101000 r 74 goat snp39696-scaffold505-1218744 23 11984792 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771549 Affx-122930657 AX-385258707 23 35573068 GGACATTGCAGGACTTGAGATGCAGGGGATTGATC[A/G]TCTTTTATACTGTCCATTTTCCTTTAGTTCTGATT R 2 1 2 1 101000 f 74 goat snp39695-scaffold505-1173674 23 11939770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381535 Affx-122974843 AX-123251893 23 35659731 GCCTAAAACCCAAGCACATAGGACACCAAAAGTGG[C/T]GCTCTTAACACAGGGTGTCATTACCCTGCCTTGTA Y 2 1 2 1 201000 f 74 goat snp39693-scaffold505-1087011 23 11852774 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376416 Affx-122978080 AX-123246775 23 35689620 TGAACTTGCCCTATGATTCCGGTCCCTCCTTCCTT[A/G]TCAGAATTGGGAAATATCTGGAACCAGTTATTCAT R 2 1 2 1 201000 r 74 goat snp39692-scaffold505-1057122 23 11822870 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449057 Affx-122923056 AX-123319392 23 35740757 CTATGTCATCGGCAGACTCCACAATTTACCCTTTA[A/C]TCTCAACCAGGATCTGTTTGGTTGTGTGTATTTAT M 2 1 2 1 101000 r 74 goat snp39691-scaffold505-1005985 23 11771124 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384472 Affx-122973079 AX-123254830 23 35777138 AAAATAAATCAGCACGTCTTATATCAGGACTTGCA[C/T]GCATTATTTTTCAAAACACAAATGAAAAATCACTG Y 2 1 2 1 102000 f 74 goat snp39690-scaffold505-969604 23 11734315 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396414 Affx-122963004 AX-123266769 23 35810900 TAAGTAGATGGGGAAGAAGAGGTACCTTCTCCATG[C/T]GGAAGAATTTCAAAGAAATTATTTAAATACTCTAC Y 2 1 2 1 101000 f 74 goat snp39689-scaffold505-935842 23 11700549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463875738 Affx-1110202011 AX-515353723 23 35835691 CCCAAATCACCACTGCCTTTACTACGCTTACTAAA[A/G]TATGGTCTTTAGACCAGTTATTCTCAACCAAGGGC R 2 1 2 1 101000 f 74 goat Random2.2K-2064 23 35835691 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38411927 Affx-122951160 AX-123282277 23 35850610 TGTATACAACAGCCTTTCATCACAAGGAGTCTGGT[A/C]GTGGTCTGAAGAAACCATTCTCTAGACTTCTGTTT M 2 1 2 1 101000 f 74 goat snp39688-scaffold505-896132 23 11661129 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446652 Affx-122924774 AX-123316988 23 35883283 ATTTTATTGCCCTAAATGCATTAGTAATGCATTTC[A/G]TATCACTATGTGCCACCACTACCTAGTACAATTCT R 2 1 2 1 101000 r 74 goat snp39687-scaffold505-863459 23 11628236 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452872 Affx-122920705 AX-123323205 23 35949244 TCCTTTGGTGCTTCAGGCTGAAAACCACATCTCTT[A/C]ATAGTTTCTAAATGCCTGTTTCCATCTACTTTTAA M 2 1 2 1 101000 f 74 goat snp39686-scaffold505-797498 23 11562540 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376492 Affx-122978028 AX-123246851 23 35980068 TCCAAAATAGACTCTTTAAGGAGATCTACCGACAG[C/T]GTTCTGAAATATAGAAATGCTGCCCTAACTATATA Y 2 1 2 1 101000 f 74 goat snp39685-scaffold505-766674 23 11531038 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428643 Affx-122938665 AX-123298985 23 36067467 CATTTCTTTGTTTATGCATTTGGAGTCCTTTTCCT[A/G]TCTAGTCCAGTGAAACAAATGGTTTTTTAAAATTT R 2 1 2 1 201000 r 74 goat snp39683-scaffold505-679275 23 11443675 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412443 Affx-122951414 AX-123282792 23 36099057 CATAATCACATAGGAATTATACACTTGCTCCGTCA[A/G]TGTTTGCCTGCTTGGCATATTTCTAAAACATCTCT R 2 1 2 1 101000 f 74 goat snp39682-scaffold505-647685 23 11411882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405635 Affx-122956591 AX-123275987 23 36232417 ATTCTACTCACCAGTGAGAGGCACCAGAGGATGTT[A/G]TTGGTGGGTGGTGGGGAAACATTCAGTAATTTATT R 2 1 2 1 101000 f 74 goat snp39679-scaffold505-514325 23 11278215 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435709 Affx-122933309 AX-123306048 23 36272066 AGCCTTGTCTTCTTCTCCCCACCCTCTTCCTCTTC[G/T]CCTTCCCTTTCCTCCTTCACTTTGTCTTTCTTATT K 2 1 2 1 303000 r 74 goat snp39678-scaffold505-474676 23 11238516 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381468 Affx-122974975 AX-123251826 23 36316106 TGTGGGCTTCAAGACATCCCATGAGCTATGTCATA[C/T]ACTAAAGCCCAGGCATTGCTATTTTAAAAATATCC Y 2 1 2 1 101000 f 74 goat snp39677-scaffold505-430636 23 11194999 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418132 Affx-122947115 AX-123288480 23 36345471 CATCTTTAGGGGAGATCCACTGAGTAGGAAATAGT[A/G]ACCCACTCCAGTGTTCTTGCCTGGAAAATTCCATG R 2 1 2 1 101000 f 74 goat snp39676-scaffold505-401271 23 11165803 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796889 Affx-122973250 AX-385283831 23 36378172 GGCAAATTTTGAGAGAGAGGACCACTGGGTCAAAA[C/T]GGAGTTAGGAAGTCACATGAGTTTTTTTTTTTTTT Y 2 1 2 1 101000 r 74 goat snp39675-scaffold505-368570 23 11134807 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403643 Affx-122957529 AX-123273995 23 36411729 AGTCCCTGAATGGCCAGAGAGTGGGTCAAAGATGC[G/T]AGAAGGGAGGAGAATCACAAGACTGGGCAGTACAG K 2 1 2 1 201000 f 74 goat snp39674-scaffold505-335013 23 11101389 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378701 Affx-122977060 AX-123249060 23 36544974 GCCAGAATAGAGCATCTTTGCAATTAGGATCTGTT[C/T]GTCTTGCTAAAATAAATTTAAAATTGCCTAGGTCA Y 2 1 2 1 101000 f 74 goat snp39671-scaffold505-201768 23 10967135 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779587 Affx-122972709 AX-385266690 23 36580923 GTCCCCAGTGCCTAAAAATGAAAAATGTCTGTAAT[A/G]CTGTCATTTAAGGGCATTTCAATTCTATGATAAAT R 2 1 2 1 101000 f 74 goat snp39670-scaffold505-165819 23 10931371 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797258 Affx-122966526 AX-385284197 23 36615298 TACAGAACCTCTTTTTCCACATTACCACCTAGTAA[C/T]ATCCTGTAGGGCTAGAATTATACATTATATGTTTA Y 2 1 2 1 101000 f 74 goat snp39669-scaffold505-131444 23 10897337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385432 Affx-122971322 AX-123255790 23 36662937 CAGAACAGAAATGCAATAAAGAGTGAAATACAAAC[C/T]AAAATATAATATGTATAATAAGGGTTTTTATAGAT Y 2 1 2 1 101000 f 74 goat snp39668-scaffold505-83805 23 10849104 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454073 Affx-122919382 AX-123324406 23 36708447 AAATAATTAAGAAGGTAAAGATAAATATAAAATGA[C/T]GCTCATTGGAATAAATTTGCCCCGTTTTGTACTTT Y 2 1 2 1 101000 r 74 goat snp39667-scaffold505-38295 23 10803720 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423971 Affx-122942131 AX-123294317 23 36742442 AGCGGAAGGAAGGAGAAGGCCCTTAGGAAGCCAAG[C/T]GCAGGAAGAAGAAAGCCTCAGTACCTTCCTGTACC Y 2 1 2 1 201000 f 74 goat snp39666-scaffold505-4300 23 10769726 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424490 Affx-122941753 AX-123294836 23 36780879 ACAAATGGAATGAAGTGCCCTTGTCTAGGAGAATG[C/T]GTATCAGCCCAGAAAGGAAAGCCAGAAGTCCCGAT Y 2 1 2 1 101000 f 74 goat snp51385-scaffold751-2159316 23 10731207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786490 Affx-122963105 AX-385273524 23 36810499 AGGCCTGCATAAATTCTGAACTCTCTTCTAGCAAA[C/T]ACAGGGACCAAGCAGTAATTGATACAAGACAATGA Y 2 1 2 1 101000 f 74 goat snp51384-scaffold751-2129696 23 10701536 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399590 Affx-122961106 AX-123269945 23 36839700 CCTGCTTTGTAAGGCAGATTCTTAACCAGTCAACC[A/G]CCAGGGAAGTCCTAGAATTCAAGGTTTAAATGACT R 2 1 2 1 101000 r 74 goat snp51383-scaffold751-2100495 23 10672541 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386234 Affx-122970973 AX-123256592 23 36871249 GTATTAAAGAGCAGAACTTGCCTCCTGACATTTTC[A/G]TGGTATCTTCCACATTCCAGGTTCCCCCGCCAGCA R 2 1 2 1 101000 f 74 goat snp51382-scaffold751-2068946 23 10641156 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783890 Affx-122960008 AX-385270945 23 36906754 AGGAATTCCCCAGGAAGCACTTATAACCTAAAAGT[G/T]ACATCCAACTTTTATCTCTATAAAACAGTACATAA K 2 1 2 1 102000 f 74 goat snp51381-scaffold751-2033441 23 10605638 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785625 Affx-122928720 AX-385272667 23 36948868 TAGCATCGCTGGATATCAGGTAGGGCAAACCTGAC[A/G]GTATGTCAGCCTTTCTCTCCACAATTCAAGTTTTC R 2 1 2 1 101000 f 74 goat snp51380-scaffold751-1991327 23 10563546 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790868 Affx-122970622 AX-385277866 23 37039214 GTGCAGGTTTAGACTTCATGTGTTAAGCTTTTTAA[C/T]AGAAGTATATGGAATGTGCAATCTGCTTTTTCTAG Y 2 1 2 1 101000 r 74 goat snp51378-scaffold751-1900981 23 10472351 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410751 Affx-122952695 AX-123281101 23 37120515 AAAAAAGAAACCCCAATAATTCAAACCTCACTTGC[A/G]CAAAGAGGTACTAGACTGCTCTTTGTACTTTCTTC R 2 1 2 1 102000 f 74 goat snp51377-scaffold751-1819680 23 10390130 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376096 Affx-122978897 AX-123246455 23 37159462 TCTGTTCCCTGAGCTCCCCAGGAAACAGTATGTTC[A/G]TAAGAATAAATAGACCCAAGAAAGCTACTTACATT R 2 1 2 1 201000 r 74 goat snp51376-scaffold751-1780733 23 10350848 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375744 Affx-122978615 AX-123246103 23 37222200 ATTATACTTTCCCACATGCCTTTAGACCCCTTCCT[A/G]TGCAGCAGCAGAACATATTTCCCTGTTATTTGATT R 2 1 2 1 201000 r 74 goat snp51375-scaffold751-1717995 23 10288034 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773789 Affx-122919769 AX-385260929 23 37265223 TATTGATCCAGCTTACTTTATATGTTAATTTGGAA[C/T]CACCCTTTTCAGAGTTGTACCAGATAAAACACTGT Y 2 1 2 1 101000 r 74 goat snp51374-scaffold751-1674972 23 10244833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766205 Affx-122971911 AX-385253605 23 37319761 GGGTTACCATAATAACATCCACAGCTGTTTACTGC[A/G]TACAGAAAGCTTTCCATAAATGATCCCACTTAATC R 2 1 2 1 101000 f 74 goat snp51373-scaffold751-1620434 23 10190343 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428188 Affx-122939019 AX-123298531 23 37373253 GGTGGAAAGCAAACCAGCAGGAAGAGGAACCTTGA[C/T]GACGCAGGGCAGAGATTTCCAATGACAGGATCTGT Y 2 1 2 1 201000 f 74 goat snp51372-scaffold751-1566942 23 10136700 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415208 Affx-122948981 AX-123285557 23 37421524 AAAATGTGACCACCCTTTCAGCTAATCTCTACCTA[C/T]TTGATTCTGGCAGTTTATTGTTGGCACAAGCCTGG Y 2 1 2 1 101000 r 74 goat snp51371-scaffold751-1518671 23 10088518 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447648 Affx-122923970 AX-123317984 23 37456435 GACTGGGCATTCCCATCTTCACATCTTAACCCCTC[A/G]CAGGCTGTGGGTGGAGTAAAAGAAAAAGTGTGAGA R 2 1 2 1 102000 f 74 goat snp51370-scaffold751-1483760 23 10053824 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375651 Affx-122978687 AX-123246010 23 37487890 TCTCTTCACTGGAGTAGAGTTCTCTTGCTACTGCT[A/G]CTAATAAACTTACACAATGAATTTCCTGGAATGTA R 2 1 2 1 201000 r 74 goat snp51369-scaffold751-1452305 23 10022337 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441281 Affx-122929471 AX-123311618 23 37550633 CTAAAGAAAAAAGGAAGAAAAATTACATTTACTAC[A/G]TATTCACATGCAGCCTTTCAGAGACTTACCATCTG R 2 1 2 1 101000 r 74 goat snp51368-scaffold751-1389562 23 9959202 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402814 Affx-122958275 AX-123273167 23 37612216 TCTTCCTGGAAAGGAGTGTCCTTCGGTCCTACCCC[A/G]TCTCTAGGCTGACAAAGCTCACCTTTGTAGATCTG R 2 1 2 1 101000 r 74 goat snp51367-scaffold751-1327979 23 9896554 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389906 Affx-122968116 AX-123260263 23 37651418 GGTAATGTCCCCCAAAGCCTTGAGGGACTGCAGCC[A/G]CCAGAGGCCCAGAACTCCTGAGTCCTGACCTCACT R 2 1 2 1 201000 r 74 goat snp51366-scaffold751-1288777 23 9856948 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463876934 Affx-1110202612 AX-515354903 23 37673648 CCAATCCCTAATATACAGGCATGTGTATATGTATG[C/T]ATCAATATGTACATATGTGTGTGCTCATATATAAA Y 2 1 2 1 102000 f 74 goat 23_37673648_AF-PAKI 23 37673648 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403646 Affx-122957527 AX-123273998 23 37693133 GTATGTATGCAGACATACACACTTAGAGCATGCAA[C/T]GTGCTTAGCACAGTACTTTGGGTGCATGGTAAGCA Y 2 1 2 1 101000 f 74 goat snp51365-scaffold751-1247062 23 9815646 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422594 Affx-122943738 AX-123292940 23 37763373 GGCCTGTCCTCGTATTTACTACTATTAGAATAATG[C/T]CAGGTTCGGGGTTAGCACATAAAATAGATGTTTCT Y 2 1 2 1 101000 f 74 goat snp51363-scaffold751-1176822 23 9746648 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378118 Affx-122977140 AX-123248477 23 37795506 AACACAAAAGTCAGCACTTGCTCCCACTAAGTAAG[C/T]AGACATTTCTTTTTCAGGTTATAAAATAGATGGGG Y 2 1 2 1 101000 f 74 goat snp51362-scaffold751-1144689 23 9714508 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422548 Affx-122943264 AX-123292894 23 37844909 TCAGTAAACAAGCAGCATAGAGCAACACAGACTTA[C/T]AAACCAACACTTCGCAGGGGTCGGTGACTTGCCCA Y 2 1 2 1 101000 f 74 goat snp51361-scaffold751-1095286 23 9664951 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448976 Affx-122923119 AX-123319311 23 37894200 ATACTCAGAGGTGTCCCACGGGCCCTTAGATTTCC[A/G]CAGCTCAGACAATCTCACTCGCAACTATCATTTAT R 2 1 2 1 101000 r 74 goat snp51360-scaffold751-1045995 23 9615770 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791606 Affx-122935348 AX-385278597 23 37938527 GCCTTGTTGATCTATGGAAAGGGGACCTTTGTGGT[A/G]AGTTTTCATAACATGTCTGTCTGTAAAAGACAACA R 2 1 2 1 101000 f 74 goat snp51359-scaffold751-1001668 23 9571032 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423774 Affx-122942835 AX-123294120 23 37981557 GACTAATTTCTTGGTGATTGTGTTCCACTGTAAAC[A/G]CAAAAGGCCTGCTGTTACTAGTTTAAAAATGGAAA R 2 1 2 1 101000 f 74 goat snp51358-scaffold751-958638 23 9527842 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277534 Affx-1111835961 AX-519551035 23 38012921 AGTCTCTTCTTGGATCAGCAGGGATAAGACTCTGC[A/G]TGTCTTACTACCCTCGGGAGCTGAGATGCTGGAGT R 2 1 2 1 201000 f 74 goat Random2.2K-2068 23 38012921 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388420 Affx-122969279 AX-123258778 23 38027931 GCAAACATTTGGTGTTAAACACAAACTCTGTGCAG[C/T]GATGACTGGGATGGTAGGAAGAGCAGGACAAATAT Y 2 1 2 1 201000 f 74 goat snp51357-scaffold751-912264 23 9481432 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273826 Affx-1111833867 AX-519547437 23 38037600 GCCACGTGAGAAACCCCATGTGGTTTCCCATGCTA[A/G]CGCTTAAGGACTCAGCTCCCCAGAAGTCCAGCTCT R 2 1 2 1 102000 f 74 goat GoatD01.008534 23 38037600 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38381367 Affx-122974401 AX-123251725 23 38057913 AAACTACTTTTAAAAAAACAAAACATGGTTTACTG[C/T]ATTTACATTTTGGTGACTTTTTACTGTGATAAACA Y 2 1 2 1 101000 r 74 goat snp51356-scaffold751-882282 23 9451149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389390 Affx-122968388 AX-123259748 23 38111795 TTAGTAGGCAGCCTAACCAGGAGTCCAACTCCAGC[A/G]TGCCAGTTCCAAAGTCCATGCTCGTTTTGTTGCAG R 2 1 2 1 101000 r 74 goat snp51355-scaffold751-828400 23 9396760 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442812 Affx-122927713 AX-123313149 23 38155046 TAATCAATTTGAAGTGAGGAATTTCTCTCACCTGT[A/G]CCCTCCTTACCATTTAACTGCTTTAGAGCCTGAGG R 2 1 2 1 101000 r 74 goat snp51354-scaffold751-785149 23 9353652 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788928 Affx-122927091 AX-385275942 23 38185426 ATTGTTTTTTATGTGAATTATCTCCAAGCTTCGCT[C/T]ATCAGCTGTAATGCTTCAAGTATATAGAAACCTTC Y 2 1 2 1 201000 f 74 goat snp51353-scaffold751-754769 23 9323125 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441342 Affx-122928885 AX-123311679 23 38240419 GAACATCCTGTTAAGAGGCAGAAATTTTTCTAACT[A/G]TCTGCTTGGGCTTTTTAACATGAGATTTCCAATCA R 2 1 2 1 101000 f 74 goat snp51352-scaffold751-699776 23 9267777 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792214 Affx-122923854 AX-385279199 23 38293885 ATAAGAACCAGAATAATCACTTATTGTAAAACCAG[C/T]GAGGGTGACTGGACCCACAGGAAAAATGAAGATAG Y 2 1 2 1 101000 r 74 goat snp51351-scaffold751-646310 23 9213831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402387 Affx-122959026 AX-123272740 23 38329530 CATCTCTCTGTTAGAAACTGACTAATAAATCAGCC[A/G]TGTGTACTCTAAAGCTCATGGGAGAATGTCTCTTC R 2 1 2 1 101000 r 74 goat snp51350-scaffold751-610665 23 9178030 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404446 Affx-122956750 AX-123274798 23 38362059 CAATCAGACATGACTGAGTGACTAACACATACACA[C/T]GCACAGTATGTCTAATTAGTCACAGGGCAAAGACT Y 2 1 2 1 201000 r 74 goat snp51349-scaffold751-578136 23 9145471 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774780 Affx-122923338 AX-385261914 23 38425238 CCTTCGGCATAGAAGAGAGTTGTGGTTAGAACAGG[C/T]GCCTTAGAACCAGAGGGAGCTGGATTTATTTTTGA Y 2 1 2 1 101000 r 74 goat snp51347-scaffold751-514957 23 9082132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790677 Affx-122945470 AX-385277679 23 38454538 TGTCATCTACGTGATTCTTATTTTTAGTTGCATCA[C/T]TGATTTTGCTGCATGGACAAAGACCTTAAATAAGG Y 2 1 2 1 101000 r 74 goat snp51346-scaffold751-485657 23 9052699 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415672 Affx-122948550 AX-123286021 23 38486633 GTAGTTTTGACTCCTCCAAGTGAACTTCGCAAAGC[A/G]TTCTGCAGTGAAGGGTTCAGAAGGAGAGGACTGCA R 2 1 2 1 101000 f 74 goat snp51345-scaffold751-453562 23 9020482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768491 Affx-122954379 AX-385255671 23 38533747 AGTAGGAAATGACAACTATGACACGAGTTGTTTTA[C/T]AGGAATGATTAAGGACCTGAGTTGAAGCATGTGAC Y 2 1 2 1 101000 r 74 goat snp51344-scaffold751-406448 23 8973510 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419217 Affx-122945691 AX-123289565 23 38588832 CTCCTTTTTTTTTTTTCCCCTAAAAATACTAACTC[A/G]TGATAACATTACTCCAGCGCCAGAGTTCATTAACT R 2 1 2 1 101000 r 74 goat snp51343-scaffold751-351363 23 8918972 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378313 Affx-122976844 AX-123248672 23 38636122 TGACCATATATGCAATGAATGCGAACCAGTACTAA[C/T]AGGAAGGTGAATCTTCCCGACTGTACTCACAGGGA Y 2 1 2 1 101000 f 74 goat snp51342-scaffold751-304073 23 8878746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777362 Affx-122960660 AX-385264484 23 38703201 TCTTTCTTCCCTTTGTGTCATGATTTTATTGCTGC[A/G]CGTAGATCTATATCTTCTGATCTCCGCTTAATTTC R 2 1 2 1 102000 f 74 goat snp51341-scaffold751-236994 23 8812508 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390810 Affx-122967857 AX-123261167 23 38738680 AGCTCTGGAAGGACCAGGCTTTTACTCAGCTACCC[A/G]TTAGCGTGACCTGGCTGCCAAACAGCTTCCATATC R 2 1 2 1 101000 f 74 goat snp51340-scaffold751-201515 23 8777182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772821 Affx-122932106 AX-385259966 23 38816313 TACACAAATGTGATTTGGAGGTTGTTTGGAGCCCT[A/G]CTGTACTTTAAACGCATCTGGTATTCATTACAATG R 2 1 2 1 101000 f 74 goat snp51338-scaffold751-123882 23 8699537 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778058 Affx-122978514 AX-385265174 23 38865632 CCTCTTAACAAGCCAAATGAAGAGCAACAACAGAG[A/G]CTCTAAAGTCCGTTTTGGAATATAGAACAAAGCTT R 2 1 2 1 101000 f 74 goat snp51337-scaffold751-74563 23 8650119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437788 Affx-122931693 AX-123308126 23 38906577 TTAAATAGTTTTAAAACATTAAGTTTCAGGGCCTC[C/T]TAAGCCCATTTCTTCCCCAAACCATACAGCATGGT Y 2 1 2 1 101000 r 74 goat snp51336-scaffold751-33618 23 8608944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401852 Affx-122959427 AX-123272205 23 38936735 TTATCTCTTAGTCTGCTAGCACCACCTGGGAAGGA[C/T]GCATACACCAGCAAGGTGGGGTAAACAGTTTCAAC Y 2 1 2 1 103000 r 74 goat snp51335-scaffold751-3460 23 8578488 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385691 Affx-122971126 AX-123256049 23 38944228 TTCTCGAAATGCTCAGGAGCTCTGCGAAGAAAGTA[C/T]ATGAGCATATTGGCTCTCCCTTCCATTCCTGCCCA Y 2 1 2 1 101000 f 74 goat snp10313-scaffold1368-4371075 23 8571029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398184 Affx-122962648 AX-123268539 23 38972877 ACTTGCAGATTCCCATTGAGTCAAGTCACCTTCCT[C/T]ATTTCTAAAGAATAATATTCGCAACACTGTGAAAA Y 2 1 2 1 101000 f 74 goat snp10312-scaffold1368-4342426 23 8541809 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431224 Affx-122937148 AX-123301565 23 39013319 CTGTAAACCCAGTCATAGAATAATGACTGGTACAT[G/T]TTAGGCACTCATTAAGTACTTGTAAGATGGGTGTC K 2 1 2 1 101000 r 74 goat snp10311-scaffold1368-4301984 23 8501602 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414893 Affx-122949125 AX-123285242 23 39046303 TGACTTTGGGTTAGCACCTCAGAGCAATGGTAAAA[C/T]GTAGTCTGAAGTGCTTCCCCCTCCTTCCTGAAGGG Y 2 1 2 1 201000 f 74 goat snp10310-scaffold1368-4269000 23 8468853 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785008 Affx-122942697 AX-385272055 23 39077482 ATCCCTTAAAACCCTTCCTTAATTCTCCTTCACCG[A/G]AAGGAATCATGTCCAAAATTCTTAGTGCAGCTCTC R 2 1 2 1 101000 f 74 goat snp10309-scaffold1368-4237821 23 8437673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435107 Affx-122933703 AX-123305447 23 39108419 GTTTATATAACCTGTGTGATGCCATCTTGTCACTA[C/T]ATACCCCATAACAAGACAATAGGACCACAGGACAG Y 2 1 2 1 101000 f 74 goat snp10308-scaffold1368-4206884 23 8406731 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784572 Affx-122926027 AX-385271620 23 39140265 CTGTTCACAATCAGCTGTAGATACAGCACACACTC[A/G]TCTGTATTATCATCAGTGTCTCATTACTTTCTTAA R 2 1 2 1 101000 f 74 goat snp10307-scaffold1368-4175038 23 8374873 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787011 Affx-122941339 AX-385274039 23 39172196 CTGTATTCACCTGTGGTATTTCACCAGAACTTGTC[A/G]TCATTACACATTTCTAACCATTAGACAAATTTCAG R 2 1 2 1 101000 f 74 goat snp10306-scaffold1368-4143107 23 8342793 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393214 Affx-122965495 AX-123263571 23 39208438 AAGGCACACACATTTACAGGACAGGCTGGGGGTCA[C/T]GGGAAGGTCGACCTTACACACAGGGCAGCCTGGGC Y 2 1 2 1 101000 f 74 goat snp10305-scaffold1368-4106865 23 8306566 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439799 Affx-122930493 AX-123310136 23 39264627 TTAGATGGTAATCTATAATGGACGAGAAAGCAGAC[C/T]TCTCATCTTGGAGAGAATTATTGAGTCTCCACCAT Y 2 1 2 1 101000 f 74 goat snp10304-scaffold1368-4050676 23 8250179 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431113 Affx-122936601 AX-123301454 23 39298787 AGGCCCGGGGGGTTTACTCACTGGCAGCACATTCC[C/T]CTGGAAACAAGAGGAGTGGAGAATAAACATTCCTA Y 2 1 2 1 101000 r 74 goat snp10303-scaffold1368-4016516 23 8216280 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435863 Affx-122932801 AX-123306202 23 39330127 CACCCAGCCCAGGTTCTCCACGTCCTGCTCCTTCT[C/T]CCACAGCTGCTGCTCCAAAAAGCAAAGCAGATGAA Y 2 1 2 1 101000 r 74 goat snp10302-scaffold1368-3985176 23 8184782 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427972 Affx-122939187 AX-123298315 23 39367857 TGTTTCACATGGTTTGATGAAGGAAGAAGGAAAGA[C/T]ATTTTCTCCTTCCCTCTGCAAAGTCTCAGCAGTTC Y 2 1 2 1 201000 f 74 goat snp10301-scaffold1368-3947446 23 8146771 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410835 Affx-122952627 AX-123281185 23 39398373 TTTAAAAATCTGGGTCATTGGGAGAGAGGGTGGGC[A/C]GAGAAAAAAGGAGGTCCTCACTCTACAAGCGAGTG M 2 1 2 1 201000 r 74 goat snp10300-scaffold1368-3916930 23 8116417 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426894 Affx-122940462 AX-123297239 23 39488968 CGGTGCAGCAGTGTTTGAAAATGAATGCTTCCAGT[A/G]CATACGCGCTTATCAATTTTTTTCTCACATTATGT R 2 1 2 1 101000 f 74 goat snp10298-scaffold1368-3826335 23 8025687 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412711 Affx-122950744 AX-123283060 23 39528933 CTCGGTGATGGAGGGAAACAGTTTCTTGGCCTTGC[A/G]TCCAGGATGTGCTTTAAGGAAGCCAAGAAGGATTG R 2 1 2 1 101000 r 74 goat snp10297-scaffold1368-3786370 23 7985445 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783093 Affx-122949943 AX-385270160 23 39569879 GAAACTAGACTCATTTGACCTGCATGTGGTTTTGC[A/G]CTTGACCAAAATGAGACAGTAGCAAATGTCCAATT R 2 1 2 1 101000 f 74 goat snp10296-scaffold1368-3745424 23 7944532 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387019 Affx-122969930 AX-123257377 23 39630104 CCACAAAGTAGAGAGTAAACCGTGTCAGGCAGCAC[C/T]GTCCTCTTTTAATATCGAGCATTGAATTATTCAAA Y 2 1 2 1 101000 r 74 goat snp10295-scaffold1368-3685199 23 7883718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444374 Affx-122926607 AX-123314711 23 39752417 CCAGGTACGATTGGCTTTATTAGGAAAAAGGGTTT[A/G]GTGCTTAAACGGTGAATTTCTGCTCTTTCACTTTC R 2 1 2 1 101000 r 74 goat snp10293-scaffold1368-3562886 23 7760156 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429376 Affx-122938552 AX-123299718 23 39783319 TTCCATAAAGGGAAAAAAATATCTCTCTGGGGTAG[C/T]GGATATGGAAATTCCAGAAACACAATGGGATGCAT Y 2 1 2 1 101000 r 74 goat snp10292-scaffold1368-3531984 23 7729359 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432426 Affx-122935826 AX-123302767 23 39829915 AACTTGGCCCTCTCCCCACTTACTTTCCAAAGAGA[A/G]TATTGCCCACGCTATTATTAGAGAGTTAAAAGAAT R 2 1 2 1 201000 r 74 goat snp10291-scaffold1368-3485388 23 7682706 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439481 Affx-122930160 AX-123309818 23 39904964 AGCTGAACTGGAGAGATCCCTGGAGTCGAAGAAGC[A/G]TCTCTCTACTGTGACTTGCCCAAAATAGTCTTCTC R 2 1 2 1 101000 r 74 goat snp10289-scaffold1368-3410339 23 7607606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387580 Affx-122970269 AX-123257938 23 39955927 TGCTTGTCATAACTTAGGAATGTTAACTTATGCTC[A/G]TCTGCTGAGAGACTCACTGAGAGTCATCAACAGTT R 2 1 2 1 101000 f 74 goat snp10288-scaffold1368-3359376 23 7556653 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775587 Affx-122969139 AX-385262718 23 40017660 GTAAGAACTCATAGCTTACCAGTGGCCAATAAGCA[C/T]ATGCAAAAATGCTAAACTTCATTAGTTATTCAGTT Y 2 1 2 1 101000 f 74 goat snp10287-scaffold1368-3297643 23 7495128 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409675 Affx-122953072 AX-123280026 23 40060779 GGAGGGCTGAGACCAGCAAGGAAGTCAGAATTCAC[A/G]TTTTCTCTAAAGAACCATGCACACAAACAGGCTTG R 2 1 2 1 101000 r 74 goat snp10286-scaffold1368-3254524 23 7451824 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400727 Affx-122959912 AX-123271082 23 40095445 AGTAACTGTGTAGGGGGTGAACATTAGTCATCACC[A/G]CAGAAATGTTAACTGGTTTGACCCAAGTCACTGAA R 2 1 2 1 101000 r 74 goat snp10285-scaffold1368-3219858 23 7417276 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392718 Affx-122966033 AX-123263075 23 40148134 AATTGTCAAGAAATACATAAATACTATAATAAATA[C/T]GGCACCTTACACTGAGAAAGACCTAAAGGTTACTT Y 2 1 2 1 103000 r 74 goat snp10284-scaffold1368-3167169 23 7364462 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463885015 Affx-1110203450 AX-515362890 23 40173834 CAAGCCCGGGGAGGGCAGCGGGGCCACAGGAGGGA[G/T]ACTGCGCTCTGTCCTCAAAGAAACAGGGAGCCATC K 2 1 2 1 102000 r 74 goat 23_40173834_AF-PAKI 23 40173834 G T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320772482 Affx-122976881 AX-385259633 23 40178428 TTCTCTAGGGCTCATGAGTCTAGGATCCAATATCT[A/G]TCTAGCTTGGAGTTGAAAGTCAGGTGACAAGCTTT R 2 1 2 1 101000 f 74 goat snp10283-scaffold1368-3136875 23 7334508 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410008 Affx-122953263 AX-123280358 23 40216569 GCCTAAGTTACCTTCCCACGTGTTGCTCTATGTTC[A/G]TAGCTCACCTGAGTAGAAGATGGGACAGGTTACGA R 2 1 2 1 101000 f 74 goat snp10282-scaffold1368-3098734 23 7300505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409048 Affx-122953359 AX-123279399 23 40249912 TCTAAAGCAACTGAGCACGCACGCACAATAGGAAT[A/C]TGCTTATGTCATTTTATTGGTTAAAATGCTCCTGT M 2 1 2 1 201000 r 74 goat snp10281-scaffold1368-3065391 23 7266792 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385155 Affx-122971753 AX-123255513 23 40292266 AGGGGAAGTGAAAACTGGAAATATTTCCACCGCAC[A/C]ACCTCTGTGTTTCTCTGGAAGGCTGAAGCCAACAG M 2 1 2 1 201000 r 74 goat snp10280-scaffold1368-3023037 23 7224477 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437250 Affx-122932014 AX-123307588 23 40408117 CTGTATTTTGTCAATGAGAAATAAGATTTAAAGAC[A/G]TTCAAGGGTTCCAACTATTTCCTGGGATGTTCTCT R 2 1 2 1 103000 r 74 goat snp10278-scaffold1368-2907186 23 7108792 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434973 Affx-122933839 AX-123305313 23 40456098 CCATGGTTCCCTTTCATTCTCTGGCCTCTTCCGTC[A/G]TGTCCTGTGTGAATAGCTGCAAATTGAAGGACCAT R 2 1 2 1 101000 r 74 goat snp10277-scaffold1368-2859205 23 7061636 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405748 Affx-122956506 AX-123276100 23 40487229 CAGCACTGACCGAGTGCTCATTTACTGTCAGCCAC[A/G]GTGCCAGGCACCTGCTGCAGATGTGAAGAGGGCAC R 2 1 2 1 101000 f 74 goat snp10276-scaffold1368-2828074 23 7030615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784674 Affx-122943287 AX-385271722 23 40526975 TTCTCCAAGCAGGAAAACATATACCATTCCATTCC[A/G]TGTTTAAAGTCATCCAATCTCAGTATCACAGAATC R 2 1 2 1 101000 f 74 goat snp10275-scaffold1368-2788328 23 6990856 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408424 Affx-122954462 AX-123278775 23 40579755 TTACATGTTCTCCATCAGTTACACTCAAGCATTGC[A/G]GCTCCTTTCCATTCTTCTGGAAGGCCGGAACTCAG R 2 1 2 1 101000 f 74 goat snp10274-scaffold1368-2735548 23 6938087 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768268 Affx-122963548 AX-385255449 23 40613469 TTTTTAATGGCTTGCTTCCCGGACTAATAGAAAAC[C/T]AGAGGAGTTTTCAAGCTGAGCTAAAAATGAGAATA Y 2 1 2 1 101000 f 74 goat snp10273-scaffold1368-2701834 23 6904785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396424 Affx-122962997 AX-123266779 23 40681796 GGCAGATTTCTGCTACCAACCCCAGGCAGGGTTCG[C/T]TTGTTCCCTTTGTAAGAACACTTACTGCTTAGGGC Y 2 1 2 1 101000 r 74 goat snp10271-scaffold1368-2633507 23 6836419 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768877 Affx-122968339 AX-385256054 23 40720506 TTTTGAGAAAAGAAAAGCTGATGTGGAATTTTGAC[A/G]TGATGGTCAGTAAGCTCATGGGTGTCTATTTGTTA R 2 1 2 1 101000 f 74 goat snp10270-scaffold1368-2594797 23 6798775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409816 Affx-122952955 AX-123280167 23 40753956 CTTTGCGGGACCCTCAGGATGTACAAAACCCATCC[A/G]TACCTCACCAGGTTACCTACCCCTCTTGTCCCCCA R 2 1 2 1 101000 r 74 goat snp10269-scaffold1368-2561347 23 6765273 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772144 Affx-122946634 AX-385259299 23 40785604 TGTCTTCATTTTTCTGACACCTCTTTGACCCAGGG[A/G]AGGATAAATAGCTCATTACCTATAGGGTGAACCAA R 2 1 2 1 101000 f 74 goat snp10268-scaffold1368-2529699 23 6733488 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777327 Affx-122966755 AX-385264449 23 40837166 TTTTCAGATAGACCTAGGAGCCAACTGAGAAAAGT[A/C]TGCTTCTGAAACACAGAACCTGACAACCGTCTCCT M 2 1 2 1 101000 r 74 goat snp10267-scaffold1368-2478137 23 6687495 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424038 Affx-122942078 AX-123294384 23 40871296 GGTTTAAGTGAGAAAAAGATATGTTTGCTTTGTTT[A/G]TTACCTCTGTGGAGGTAGATGAGCATGAATCCACA R 2 1 2 1 202000 f 74 goat snp10266-scaffold1368-2444007 23 6653253 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794284 Affx-122962663 AX-385281248 23 40915189 TTTTAATCTTCTGTGGTGGAGAAAATATGCAGGTT[A/C]GTGTGAGATGCAAAGCGGGATGGAATGTAGTTTGT M 2 1 2 1 101000 r 74 goat snp10265-scaffold1368-2400114 23 6609672 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393397 Affx-122965895 AX-123263753 23 40947078 GCTGAGGTGACAGTGAAATGCCCAGTGGTACTCAT[G/T]GCAGAAGTGGTCGGACTGGGAGCAACACCCACCAC K 2 1 2 1 101000 f 74 goat snp10264-scaffold1368-2368225 23 6578004 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422409 Affx-122943377 AX-123292755 23 40976333 TATAAGTAATACTCTGGAGGTGGGGGGCGGGGGTA[C/T]GTACTATTTTCGACACTAATCTAAACCATTTTAGA Y 2 1 2 1 201000 r 74 goat snp10263-scaffold1368-2338970 23 6549282 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388758 Affx-122968946 AX-123259116 23 41060251 CTCTGAAAGTCTCCGTCTGTCCCACCACCACTCTG[C/T]GAATAAATTCTTTCACCGTTGCTTCGCCACAGAAT Y 2 1 2 1 101000 r 74 goat snp10261-scaffold1368-2255052 23 6465866 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771046 Affx-122926830 AX-385258206 23 41097660 CCAGATTTAACACAGTGCCAAGCATACAGTAGGCA[C/T]ATGATACTTATTGAATGATAGATCTATGGATTCCT Y 2 1 2 1 101000 f 74 goat snp10260-scaffold1368-2217643 23 6428430 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407320 Affx-122955307 AX-123277671 23 41127485 TGGGGCTTCCCAGGTGGTTTAGTGGTACAGAATCT[A/G]CCTGCAAACACAGAAGAGGTAGGTTCGAGCCTTGG R 2 1 2 1 103000 r 74 goat snp10259-scaffold1368-2187818 23 6397852 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406297 Affx-122956069 AX-123276649 23 41158040 AATGATCAGAAACCTGAAAAAAAGATCAACAGCTA[G/T]TCCTCTCCTGTTTTGCATCACTTTCTCAAGCTTGA K 2 1 2 1 101000 r 74 goat snp10258-scaffold1368-2157263 23 6367339 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390064 Affx-122968411 AX-123260421 23 41216285 GTAGATACTGTAAGCACCTAGTTCATAGGCTTTTT[A/G]CAAAGATATATGTGTATCCACTTAGAACAGAGCTC R 2 1 2 1 101000 f 74 goat snp10257-scaffold1368-2099018 23 6307814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411476 Affx-122951798 AX-123281826 23 41249870 TTAGAGAACTTTTCTCGGAGGGGGTTTCCGTGTCC[G/T]GCTGCCTTTAAAGATGGCCGCCTTCCCCCGCCCCT K 2 1 2 1 202000 r 74 goat snp10256-scaffold1368-2065433 23 6274311 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438949 Affx-122930405 AX-123309286 23 41304513 TCATCACATCTCACCGGTCGATCCTGGGCCTGCGA[C/T]AGCTCAGTAGACAAGAGCTATCAGGGATTTTGAGT Y 2 1 2 1 202000 f 74 goat snp10255-scaffold1368-2010790 23 6220033 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405707 Affx-122956537 AX-123276059 23 41435667 ATAGGGAGCAAGGTATCACTCTAAAGCAATTTAAG[A/G]TGCTGGTTAAAGTATGTATTTAGAAATTTGTTGTA R 2 1 2 1 101000 f 74 goat snp10252-scaffold1368-1879636 23 6088288 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383715 Affx-122972472 AX-123254073 23 41538424 CTTGAAAGCTGTGCTGTGCTTAATCTGACTCTTGG[C/T]GACCCCATGGAGTGTAGCCCACCAGGCTCCTCTGT Y 2 1 2 1 103000 f 74 goat snp10250-scaffold1368-1776879 23 5985905 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410632 Affx-122952087 AX-123280982 23 41567072 AGTTTATATTGCTCTGTCAAACCACAGTACAATAC[A/G]TAAGTTTACAGATTTGCAAAGATACAATTTACGTG R 2 1 2 1 101000 f 74 goat snp10249-scaffold1368-1748231 23 5957220 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797524 Affx-122944128 AX-385284463 23 41599655 TATGTACTTCTCTTTAGATAATGCTATTACTGCAC[A/G]TGGCAGAGTAAACATAGCTTTTTGATGTACAGGGA R 2 1 2 1 101000 r 74 goat snp10248-scaffold1368-1715648 23 5924376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439046 Affx-122930331 AX-123309383 23 41630302 ACGTAATGCAGAAACGTGCTGTCTGTGACATGATG[C/T]GATGCTGTAGAAAGCTGGCTGCCTTTACAGGACCA Y 2 1 2 1 101000 f 74 goat snp10247-scaffold1368-1685001 23 5893844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792493 Affx-122966146 AX-385279474 23 41664666 TTGGGCAGTTAACTCAGTGGATACAGAGATTTTTC[A/G]CACAGTTAACTCATCGGGTGCACTTTGAGTATTGT R 2 1 2 1 101000 f 74 goat snp10246-scaffold1368-1650637 23 5859382 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448140 Affx-122924286 AX-123318476 23 41707417 TAAGGCAATCACTCCTCTCAACAAAAATAGAATTT[A/C]GGGAGTGCCAGTCAGAGCATCCTGCTGACTGAATC M 2 1 2 1 201000 f 74 goat snp10245-scaffold1368-1607886 23 5816606 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394286 Affx-122964706 AX-123264641 23 41736133 CAATGTGAAGATCAAGCAAACTCCAAGCTGAAAGC[A/G]CTGAGGAGTGTCCTGCCTGCTTAGCTCCAGGCCGT R 2 1 2 1 101000 f 74 goat snp10244-scaffold1368-1579170 23 5787842 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403978 Affx-122957430 AX-123274330 23 41766328 CCATATATTAGTATCATTTTGTAATTCAAAAATTT[A/G]TTAGATTGATCTGAACTACCAAGATTGTGAAGGAA R 2 1 2 1 101000 r 74 goat snp10243-scaffold1368-1548975 23 5757575 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382628 Affx-122973692 AX-123252986 23 41824224 GTCAGGGCGGAGGGGTAGGAATGTGGAAAAGAGGA[C/T]GATTGTATTCTGTGAGCTTTCTAAATATTGAGCTA Y 2 1 2 1 101000 r 74 goat snp10242-scaffold1368-1491079 23 5700019 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403396 Affx-122958273 AX-123273749 23 41855075 GGTGACGCAAGTGGGGAGCTTCCGGGGAGCCAGGC[C/T]GAGGGAGCCAGGTGCTTCTTCCTTCCTTTTCTGGA Y 2 1 2 1 103000 r 74 goat snp10241-scaffold1368-1460228 23 5669982 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389089 Affx-122968585 AX-123259447 23 41894433 GGCACGTTCATTTAGAGGAAAAAGAACTGCTTCTG[G/T]CCCCACCCCTGAGCTATAAAATCAGTTCTTAGTGC K 2 1 2 1 201000 r 74 goat snp10240-scaffold1368-1420870 23 5631529 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398000 Affx-122961794 AX-123268355 23 41928474 ACTGATGCTAAGAAATCTCCTGTAATCATATTTTT[A/G]TGTCAGAATTGGGTTTACGCAATTTATCTCACTGG R 2 1 2 1 101000 r 74 goat snp10239-scaffold1368-1386829 23 5597452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380538 Affx-122975673 AX-123250896 23 42003135 GATTCTTGAATAGTTAACTATCAGAATATAAATGC[A/G]TTTCTCTTTTCTTGCATAGTGATTGGAAGGAATGA R 2 1 2 1 101000 f 74 goat snp10238-scaffold1368-1312168 23 5523140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384817 Affx-122971984 AX-123255175 23 42043110 GTAACTTAAAAACATCAATCGTTTATTATCTCGTA[C/T]GGTTTCTGTGAGCCAGGAATTCCTGAGCAGCTCTC Y 2 1 2 1 101000 f 74 goat snp10237-scaffold1368-1272193 23 5482734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417287 Affx-122947243 AX-123287635 23 42071773 ACAGAAGACTGGGCAGTTAGCTATGGCTGCGTAAA[C/T]GGTGCCTCTTCAGAAGTCCACAGAAGGACAGCCAT Y 2 1 2 1 101000 f 74 goat snp10236-scaffold1368-1243530 23 5454074 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427241 Affx-122939563 AX-123297584 23 42119183 ACTGGAGCCCCGTGCCCTCACTTCTGGTCACTAAC[A/G]TGGGGACTAGCCTGCTCACCAACCTCCTGGCAGCT R 2 1 2 1 101000 r 74 goat snp10235-scaffold1368-1196120 23 5406432 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454027 Affx-122919416 AX-123324360 23 42218028 TTTTTGGCCAACCCCAAACATTTGAATAGCACTGC[A/G]CTGTGCATGAATCATTTTCACAGGCAGGCTATTTT R 2 1 2 1 102000 f 74 goat snp10233-scaffold1368-1097275 23 5307180 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401523 Affx-122958923 AX-123271876 23 42251057 AATCACAAACATTATTTCACTCAATATTCACCTAA[C/T]GAGCCCTAATGAGGTGGGTCACAATATTCTAGGTT Y 2 1 2 1 101000 f 74 goat snp10232-scaffold1368-1064246 23 5274086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798933 Affx-122946196 AX-385285863 23 42305109 CATCTTCTGCTCTTGAGCTCTCCCATTAGGGCTTT[A/G]CTATAAAACCCACTTGCTTGGGCCAGTTTGAGTGG R 2 1 2 1 101000 f 74 goat snp10231-scaffold1368-1010194 23 5220073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388474 Affx-122969239 AX-123258832 23 42342217 TCAGGTAGGGGAAAACCTCATGCTTCTTGGTGCTG[A/G]GAGGATATTTGAATTGGATTTTTTGCAGGCTGATA R 2 1 2 1 101000 f 74 goat snp10230-scaffold1368-973086 23 5183087 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414360 Affx-122950013 AX-123284709 23 42392011 AAAAGAGATGACATTTTTGGAGTCAGAAGGCTTGT[G/T]CCTGGTTTTGTTACCTATAGTATGTGATCCTGAGT K 2 1 2 1 101000 f 74 goat snp10229-scaffold1368-923292 23 5132769 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422826 Affx-122943188 AX-123293172 23 42443074 AAGTACATGATTGGATAACTGCAGTTAAAGACTAC[A/G]CTGAAGGCCAGATTATACATTATATAATTGTTATA R 2 1 2 1 101000 f 74 goat snp10228-scaffold1368-872229 23 5081478 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784129 Affx-122973659 AX-385271181 23 42508061 AAAATGGTACAGGTATTAGTTTTAGCTTTCACACT[A/G]CCCACAGACAATAGGCACAATATTATCCCTATTTA R 2 1 2 1 101000 r 74 goat snp10227-scaffold1368-807242 23 5017478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443436 Affx-122927360 AX-123313773 23 42542561 GCTACCCCTTGGACCTATATATTGCAAAGTGTGAT[A/G]TATTGAAGGGCTCCTAAGGGACTGATGGAGGAGAC R 2 1 2 1 201000 f 74 goat snp10226-scaffold1368-772742 23 4982980 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405490 Affx-122956012 AX-123275842 23 42588072 TTTCTCTCTCCGCGAAAGCTTGCTCGTGTGTATCC[A/G]CTTTCCTGTGTGGAAATTTCCAGGTGTGTCCAGGC R 2 1 2 1 201000 r 74 goat snp10225-scaffold1368-727231 23 4937807 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393001 Affx-122965654 AX-123263358 23 42678288 GACTTTCATAGACTTCCTGTGATTCATTTTTGACT[A/G]TTCGGCAACTAAGGTACAGTGATCCCAAGAAACTT R 2 1 2 1 101000 r 74 goat snp10223-scaffold1368-637015 23 4846647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273004 Affx-1111833263 AX-519546685 23 42684598 AAATAATCATATTTCAAGACATGAGCACACTTACT[A/G]GAACCAAAACCCCAAAAGGAAACTTCTAATGCTGT R 2 1 2 1 201000 f 74 goat 23_42684598_AF-PAKI 23 42684598 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38448068 Affx-122924341 AX-123318404 23 42708466 AGGGCTTTTGGTTTGTCCCCAGCCTGCTCCCTGTC[A/G]TGGCAACCTCTTTCCTTGTCGTACCGTGTAGACAC R 2 1 2 1 101000 r 74 goat snp10222-scaffold1368-606837 23 4816235 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410785 Affx-122952668 AX-123281135 23 42753103 AATATGATTTGGGAAGTGTCTGTCTCCTCAACTCA[C/T]GCGGACCAGCGCTTGCATGCTAAGTTGCTTCAGTC Y 2 1 2 1 101000 f 74 goat snp10221-scaffold1368-562200 23 4771797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797232 Affx-122967063 AX-385284171 23 42785186 TTTGTCTCTTCCATTGGAGAATTACTAGTTAAAAT[A/G]CCCAAGTTACAGGTGGCCTTCGGTTTAAATACTTT R 2 1 2 1 101000 r 74 goat snp10220-scaffold1368-530117 23 4739376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796734 Affx-122976101 AX-180660635 23 42825446 GAACCTCGTGGTTTAAATTTTGAAAGATTTCCACC[A/G]TCCTTTAGTGTTTCGTATTAATAACAAAGTAATTT R 2 1 2 1 101000 f 74 goat snp10219-scaffold1368-489857 23 4699270 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379278 Affx-122976221 AX-123249637 23 42855638 GTGCCCTTATCCCTTAAAGCTTTTATGGTTTCAGA[G/T]CCCTACTAAAATTCCATCAGAATAAGTATTTTAGG K 2 1 2 1 101000 f 74 goat snp10218-scaffold1368-459665 23 4668978 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402057 Affx-122958722 AX-123272410 23 42911082 CGCAGTTATGGAATAAACAAGGAAATGAATCACAA[C/T]GGCTTGGATGAAGTCAGAGCTCTGGAGCCAAGGCA Y 2 1 2 1 101000 f 74 goat snp10217-scaffold1368-404221 23 4614248 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800035 Affx-122975658 AX-385286958 23 42975796 TAATTCCTCATTTCCAAACAGGTGGTCTGGAGGTA[A/G]TTCAGCATGTCCAATAATGATTTACCAAAAAAATG R 2 1 2 1 102000 f 74 goat snp10216-scaffold1368-339507 23 4549846 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379261 Affx-122976252 AX-123249620 23 43010366 ATAACCAGAAACAGTCTCTAAAAATGACAACATAC[A/G]TAATTCTGCATACGCTACATGGTTGTTGCCACATA R 2 1 2 1 101000 r 74 goat snp10215-scaffold1368-304937 23 4515226 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420538 Affx-122945300 AX-123290885 23 43044669 AATTTATAGAAATTCTAACATTTCACATACAAAGA[C/T]GACTAAGAGAGAGGTTTGTGTAAGCTTTTAGTTTT Y 2 1 2 1 101000 r 74 goat snp10214-scaffold1368-270634 23 4480896 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448625 Affx-122923373 AX-123318961 23 43093294 AAAAATCTAGCCTCCTGAGGTTCTTTTTCCTCTCT[A/C]GAGTGACATTCTCCACCCTTCTTGATTTGAGCATC M 2 1 2 1 201000 r 74 goat snp10213-scaffold1368-222009 23 4432135 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437914 Affx-122931649 AX-123308252 23 43132359 ATGTTGGAAGGATTGTGTGAACTCAGCTAAACGAA[C/T]TAACATTTATAAGTGCTTAGCAGAGTAACTGGGAA Y 2 1 2 1 101000 f 74 goat snp10212-scaffold1368-182944 23 4393156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411178 Affx-122951859 AX-123281528 23 43162374 GCTGACTTTGTTATTCCTGGAACATAACCATGCAC[A/G]TCCCTTCTCAGCCTCAGGGCTTTGCTTACACATCA R 2 1 2 1 101000 f 74 goat snp10211-scaffold1368-152929 23 4363119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441470 Affx-122928754 AX-123311807 23 43220002 TTTTAAAATATTGAAAATTGAGGTGAGGTTGTCAG[C/T]GTGGAATGTTCGAGCAAGGAGTCCGAAACAACATG Y 2 1 2 1 101000 r 74 goat snp10210-scaffold1368-95301 23 4305385 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421530 Affx-122943878 AX-123291877 23 43264883 TCCATATCCACTTCTGCAATATCATTTTGCAAGGA[C/T]GTCTGCCTAATAATGAGACGCTGAGTATCTGCAGA Y 2 1 2 1 101000 r 74 goat snp10209-scaffold1368-50420 23 4260097 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392041 Affx-122966401 AX-123262398 23 43329068 AGACTCTGGCACCCTCTTTCCAAGCAAAGTGAGCC[A/G]TCCTTGACTCTCATTTTCCCCTCCCCTGTGTTTCA R 2 1 2 1 101000 f 74 goat snp46515-scaffold643-4056499 23 4198932 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776768 Affx-122962308 AX-385263892 23 43370916 ATTAATACATGGGATAAAAAGCTATGGGAGCTCTC[A/G]CTTCCACAGTGTGTATGATAGATATCTTATTCCAG R 2 1 2 1 101000 f 74 goat snp46514-scaffold643-4014651 23 4157100 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795774 Affx-122943984 AX-385282727 23 43423690 AGTGCTCAAACTGGGGTGGTGGTAGAGAATTAGCT[A/G]ATGATGAGCCAGATTCTGGGTTGATTTTCAAAGTA R 2 1 2 1 101000 f 74 goat snp46513-scaffold643-3961877 23 4104330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463880957 Affx-1110204665 AX-515358881 23 43428922 CTGCAGCATAGGGATCTGTAATAGATACCTGTTGC[C/T]TTTCCCTCAGCACTATCTTTACCTTTAGGAAACCA Y 2 1 2 1 201000 f 74 goat GoatD01.016537 23 43428922 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38452535 Affx-122920540 AX-123322868 23 43462152 TCATACCATCAGTAGAGAAAAGGCAAGCCGATTTT[C/T]AATGAAGCCCCATAGTATGCAATCATTTTAATTAA Y 2 1 2 1 101000 f 74 goat snp46512-scaffold643-3923415 23 4065920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388423 Affx-122969277 AX-123258781 23 43492695 CTCAAATCTACATCCCTTTTAAGTAAAGGGATGTG[C/T]ATGACCCATAAGGAAAATAAGATTTTAAAAAGAAT Y 2 1 2 1 103000 f 74 goat snp46511-scaffold643-3892872 23 4035394 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773128 Affx-122939533 AX-385260271 23 43542921 CAGGCTTGGCAGAGAGTTTTTCTAGCCAAATGATT[A/G]TCAATATACACCTGCACTGTTAAAAGATGGTGTTG R 2 1 2 1 101000 f 74 goat snp46510-scaffold643-3842646 23 3985193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442186 Affx-122928801 AX-123312523 23 43606147 AGACACCTAACTGTGTACCTGGCCCAGTCGATGGG[C/T]ACATGAATCTGGGAAAGTGAAAAAGCAGACCCTCA Y 2 1 2 1 101000 r 74 goat snp46508-scaffold643-3779420 23 3922642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451755 Affx-122921523 AX-123322088 23 43668550 CTCAAGATGCTGTTAGTTGGGGGCAGGCTTGTAAG[C/T]GACAATTAGAGTGTCTAGCCAATGCCTGATAGATG Y 2 1 2 1 101000 r 74 goat snp46507-scaffold643-3717017 23 3860542 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453959 Affx-122919466 AX-123324292 23 43767593 GGACTCCTTATGTTCACTCCCATTTGTGCAAATGC[A/G]CCCCCTTTTACAGGCTAAATAGCCATGCCCATGTC R 2 1 2 1 101000 f 74 goat snp46505-scaffold643-3617974 23 3759469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771211 Affx-122934405 AX-385258369 23 43828315 GATAATATTTGCTGATTTAAAGCACTTTAAATTCC[A/G]CTACAAGTAGGGGAAGAGGCAAGGGGTAATTACTC R 2 1 2 1 102000 r 74 goat snp46504-scaffold643-3557252 23 3698033 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403409 Affx-122957761 AX-123273762 23 43862442 ATTTTACCAAAGAGATTATGGACAGTTGCTGTCAC[A/G]TCTTTAAGTGTTTGATAGAATTCTCAATTGAAACC R 2 1 2 1 101000 f 74 goat snp46503-scaffold643-3523125 23 3663973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769770 Affx-122967841 AX-385256940 23 43896747 TAATATTTATTATACTGTGGCATTTGCGAACTGGC[A/G]TAATAGAATATATATATCCTAATTTACCCCAAAGT R 2 1 2 1 201000 r 74 goat snp46502-scaffold643-3488820 23 3629545 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376438 Affx-122978065 AX-123246797 23 43936152 TTAGAAGTACTCATTTAACTTGGATTTCACTTGCT[A/G]CTTAAGTACACACCTCCCTCCCCCACACCTGTAAT R 2 1 2 1 101000 f 74 goat snp46501-scaffold643-3449415 23 3589931 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601587 Affx-1002479784 AX-186246341 23 44006912 CATGTCTACTGGAAAAACCATAGCCTTGGCTAGAC[A/G]GACCTTTGTTGGCAAAGTAATGTCTCTGCTTTTGA R 2 1 2 1 303000 f 74 goat 23_44006912_RH-map 23 44006912 G A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38395333 Affx-122964042 AX-123265688 23 44010460 AAGAATCTGAAAAGAAAGAAGAACGGAAGAGAGTT[A/G]CAGGAAGGTGAGGGAGAGGATCTTGACAATTTTGC R 2 1 2 1 101000 r 74 goat snp46499-scaffold643-3375107 23 3515344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408392 Affx-122954488 AX-123278743 23 44042366 CAGCCCTAAGAAGCTGGAGCGGAGTGTGGCAACAG[A/C]TACTACCTGGGTTTTGACAGTCTGCCTGGGAATGT M 2 1 2 1 101000 r 74 goat snp46498-scaffold643-3343201 23 3483182 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789744 Affx-122925488 AX-385276752 23 44074688 AGGGAAGGGAGAGTAGCTCCAGAATGAAGTAGGAT[C/T]AAGAAGAAACTTTTTACGAGGTTATAGGAGAGTTG Y 2 1 2 1 101000 f 74 goat snp46497-scaffold643-3310879 23 3450831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445776 Affx-122926062 AX-123316113 23 44104608 TGCTTTCTGTTTCCAAATCCCTAATTCCTCTTTGG[C/T]AGTAAATAGTCACTCAGGCACACACCTCTCTTTTG Y 2 1 2 1 101000 r 74 goat snp46496-scaffold643-3280959 23 3420409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601589 Affx-1002479785 AX-413835992 23 44130403 CTCAAAATCCTGCATGAATAATATCCTGCAAGAAG[C/G]TTGAATTATCTGAATAGTTTTAAAATTCAGATTAT S 4 1 2 1 101000 f 74 goat 23_44130403_RH-map 23 44130403 C G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38375594 Affx-122978728 AX-123245953 23 44189316 TTCTGTTCTGCCCCGTCTTCTCACTTCCTCAACTG[C/T]GTCATCTTCTACCACCTGAATGCTCTGGACCTCTC Y 2 1 2 1 101000 r 74 goat snp46494-scaffold643-3196251 23 3337891 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399019 Affx-122960930 AX-123269374 23 44223843 TATAAAGCTTGTTTAAATACTCAGCTGTGGGTATG[C/T]TCACCTCCCTGAGCCTCCTAGGTTTGTTATGAGGT Y 2 1 2 1 201000 f 74 goat snp46493-scaffold643-3161724 23 3302716 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415907 Affx-122948463 AX-123286256 23 44252467 CTGCTGGGAACTCTTCCTTAGTTAATTCACCAACC[A/G]GTTTCTGAAACATCCTGGCTGCGATTTTCCTTAGA R 2 1 2 1 101000 f 74 goat snp46492-scaffold643-3133100 23 3273745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393191 Affx-122965513 AX-123263548 23 44283221 ATTTCGGGTTGTGGGCGTGGCTGGCACACGCTTCT[A/G]CATACAGTGGACCTGCAGGAGCGCGATTCACCTCC R 2 1 2 1 202000 r 74 goat snp46491-scaffold643-3102346 23 3243082 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777757 Affx-122973019 AX-385264875 23 44371628 TGTTCCTTCAGGACTTATTGCTACTCCAGTGATCA[C/T]GGCTCAGCTAATGACCCCACCATTTACCCAGTTTC Y 2 1 2 1 101000 r 74 goat snp46489-scaffold643-3013939 23 3154496 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383982 Affx-122972931 AX-123254340 23 44416152 CATGTCATGAGATGACTAGTGTGTAAGAAAATGCA[C/T]GAAACAATGTTGGGCTATCTGCCTCAGTGAAGATG Y 2 1 2 1 101000 f 74 goat snp46488-scaffold643-2969415 23 3109647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601591 Affx-1002479786 AX-413835994 23 44428064 GACCACCTTACCTGCCTCCTGAGAAACTTGTATGT[C/T]AGTCAAGAAGCAACAGTTAGAACTAGATATGAAAC Y 2 1 2 1 103000 f 74 goat 23_44428064_RH-map 23 44428064 C T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38441449 Affx-122928769 AX-123311786 23 44449798 CAAAAGTAGATAAAATCATAGGTTTACAAGTAAAA[C/T]GGAGCCTTAGAAAAATATTCTACTTCTTAGAAAAA Y 2 1 2 1 201000 f 74 goat snp46487-scaffold643-2935769 23 3075962 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430728 Affx-122936891 AX-123301069 23 44494480 CCTCCTGATAGTCCACGACTTTCCACTGTGTGAAC[A/G]CGCACATCATCTACTGTCCAAAGGGTGAGTGACTT R 2 1 2 1 101000 f 74 goat snp46486-scaffold643-2891087 23 3031137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774803 Affx-122929017 AX-385261937 23 44539662 TTTACTCTAGCTGTTAATCAACAAACTACTAGAAA[C/T]ACGCAGAAGGGGGAAATGAATTTTACAAGATGAAA Y 2 1 2 1 102000 r 74 goat snp46485-scaffold643-2845905 23 2985882 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393741 Affx-122965224 AX-123264096 23 44569466 ATTTTCAGTACTTAAAACACTATGTACGGTCACCC[G/T]GAGGGATCTGTGGGGTGCTGATTCCAGGACCCTCA K 2 1 2 1 101000 f 74 goat snp46484-scaffold643-2816101 23 2957999 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772711 Affx-122925616 AX-385259858 23 44618745 GACTAGAACCTAATTATAAGCAGCTTTCCCGGCAA[A/C]TCCTAAATGTGCTGGACCAAGCCCTGAAAGTGAGT M 2 1 2 1 101000 r 74 goat snp39144-scaffold499-30539 23 2909371 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 350601593 Affx-1002479787 AX-185149506 23 44651974 TCCAAGGGACTCTCAAGAGTCTTCTCCAACACCAC[A/G]GTTCAAAAGCATCAATTCTTCAGCACTCAGCTTTC R 2 1 2 1 303000 f 74 goat 23_44651974_RH-map 23 44651974 G A 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38436076 Affx-122932694 AX-123306415 23 44660414 TTCAGCATCAGTCAATCCTCGTGGTAACACCCTTC[A/G]CCCCACCGCCCTTGCTCAGGCGACGTGGCCGCTTA R 2 1 2 1 101000 f 74 goat snp39145-scaffold499-72208 23 2868529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446674 Affx-122924758 AX-123317010 23 44742332 GGCAGGAGAACTCTAGAAGGGAAATGCCAGGATCC[C/T]GTGATTTATGGGATTCCGGGTAAGCACTCTCGTTA Y 2 1 2 1 101000 r 74 goat snp39147-scaffold499-154126 23 2786718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277538 Affx-1111835963 AX-519551039 23 44743539 TCACTGCTCCATGGTCAGCTGATGTTCTGCCAGCC[A/G]AGCGCTCTTGCCGGCTGACGGCCCTTACTCCATCT R 2 1 2 1 102000 f 74 goat Random2.2K-2070 23 44743539 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320780363 Affx-122931134 AX-385267458 23 44772701 TTTCCTGACACCAAATGCAAGGTAAGACTCTGCCC[A/G]TATCCTCAAAGAGGTGATGGACAGACCAGAAGGGG R 2 1 2 1 101000 f 74 goat snp39148-scaffold499-184495 23 2756329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601596 Affx-1002479788 AX-413835998 23 44790117 CATATGAACGCTTCTTCAAAGCTGTAAATGAATCA[C/T]TAGAAAATTGTTCTTTATATCATCTTCTCTTCACA Y 2 1 2 1 101000 f 74 goat 23_44790117_RH-map 23 44790117 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38444578 Affx-122926966 AX-123314915 23 44808484 GATGCGCTCTCCTCACATCTCCACCACCCCCTACA[C/T]GTGCATATGTTTGTCAGAAAACACTCCAACATGGC Y 2 1 2 1 101000 r 74 goat snp39149-scaffold499-220278 23 2720277 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440239 Affx-122930670 AX-123310576 23 44841575 CAAGCTGTGTGCTCACAACTTGTGCATTTTTACAC[A/G]TATGTTACACATCAACCTAGAAGACGTTTATTTCA R 2 1 2 1 101000 f 74 goat snp39150-scaffold499-253369 23 2687248 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601598 Affx-1002479789 AX-413836000 23 44845226 GATATCTGTTTCCTTCTTTAGGTTTGGGAATTCTT[C/T]AGCCATAATTTCTTTAAATACATTTTTGATCCACT Y 2 1 2 1 103000 f 74 goat 23_44845226_RH-map 23 44845226 C T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601705 Affx-1002479790 AX-413836099 23 44911536 AGGCTGCCAAAAGTCACCCTTGGACAATGCCCCCA[A/G]TGTAAGCCCCTCTTGATCATACATCCATACATCTC R 2 1 2 1 201000 r 74 goat 23_44911536_RH-map 23 44911536 G A 2 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38453224 Affx-122920429 AX-123323557 23 44919288 CTCTGTGCCTCCCGAGAAGGGTCTTTTTGTTTTTT[A/G]CTACGGTAGGCACTCTTAGTTGTGGCATGTGGGAT R 2 1 2 1 103000 f 74 goat snp39152-scaffold499-331082 23 2610035 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601707 Affx-1002479791 AX-413836101 23 44931364 ATTTTATAGGGATGATAGTTCAATTTATTTCCATC[A/G]TACTAAATATGAGTAAGTCTAAATTTTGAGATGGC R 2 1 2 1 101000 r 74 goat 23_44931364_RH-map 23 44931364 A G 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38420666 Affx-122944817 AX-123291013 23 44965669 ATAGGGATACTCAGCAGAGTTTCCAGTCCTGAGGT[A/G]TATGATGCCAGCTGCAGTTCATAATCCTGCAGAAT R 2 1 2 1 101000 f 74 goat snp39153-scaffold499-377463 23 2563136 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601605 Affx-1002479792 AX-413836007 23 44981500 CTTAAAATGTGCTGAATCCATAACATGGTAATGAT[A/T]TGAGGACAGCTCACACTGCTGCCTCCTCCCTGGTG W 4 1 2 1 400000 f 74 goat 23_44981500_RH-map 23 44981500 A T Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320792776 Affx-122926053 AX-385279755 23 45039036 GCAAGTAAGGCTTTACTAAATCTACACGCTTTACT[A/G]TTTTTGATGCTTTCGAAATTAATCTTGAGTTTTAC R 2 1 2 1 101000 r 74 goat snp39154-scaffold499-450830 23 2490316 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403571 Affx-122957581 AX-123273924 23 45069455 GCTTATGAACTGGGAGGTACCAGCTGAGAGAAGAA[C/T]AGTAAAGATGAAGAGTAAGTACACTATAAATAATT Y 2 1 2 1 101000 f 74 goat snp39155-scaffold499-481249 23 2460001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407559 Affx-122954679 AX-123277910 23 45114815 TGCTGCCCTGGGAAGTGACAAACCCTACATTTTAA[C/T]GAGAGCACATTTGAAGGGCATGATGTTTGGAACAG Y 2 1 2 1 101000 f 74 goat snp39156-scaffold499-526609 23 2418885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789967 Affx-122945126 AX-385276973 23 45155951 TGCTTAAGTATTTAAACATCTGAGCCAAAGCTGAC[G/T]TCAAGGAAACGAGTGACTGTATAGCTGTGAACCGC K 2 1 2 1 101000 f 74 goat snp39157-scaffold499-567745 23 2378287 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419224 Affx-122945686 AX-123289572 23 45197424 TGTGCTGCACAACTCTTCTGGTTCAGGTCTGATCA[A/G]TTTATATCTGGGTGGTCATCTCCAAAAGGTTAAGA R 2 1 2 1 101000 r 74 goat snp39158-scaffold499-609218 23 2336840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382459 Affx-122974217 AX-123252817 23 45236735 AAAAGAATTTTTTTTTAAGAGATTCACTGAAGGAC[A/G]TAAATAAATGTAAAAAGCCAGGCCCTCCAAGCAGC R 2 1 2 1 101000 r 74 goat snp39159-scaffold499-648529 23 2297378 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273006 Affx-1111833264 AX-519546687 23 45237525 GCCCCAGAGTTTTCATGCTGTCATTTCTTGCAGAC[A/G]AGGAAGAATTCTGTTTAAGCAAAGAATTGAGCTTG R 2 1 2 1 101000 f 74 goat 23_45237525_AF-PAKI 23 45237525 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320792463 Affx-122922221 AX-385279444 23 45305851 CTATCTACTTGCTATGACCTTCGACCCTGTTCCAC[G/T]CGAGTTCCTCTGAATACACTTGCTCACCATCCAAA K 2 1 2 1 101000 f 74 goat snp39160-scaffold499-717645 23 2228673 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433790 Affx-122934470 AX-123304131 23 45349634 GTAAGGATTTGAGTGATCTTATGATATCACACTCT[C/T]TCCTGTAATAGATATGCTCTCATCCTTGCAAACAC Y 2 1 2 1 201000 f 74 goat snp39161-scaffold499-761428 23 2185443 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444808 Affx-122926332 AX-123315145 23 45463337 CTGCTTCTTGCATTTAGGAAAGCAATGATGCCTCG[A/C]GAATTACTGCAAGGATTCCCTGGTGGTCCAGTGGC M 2 1 2 1 101000 f 74 goat snp39163-scaffold499-875131 23 2071862 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392633 Affx-122966457 AX-123262990 23 45500102 GTTAAGCAAAGAAAGAAAGCAAGGAACAGTGAGCA[C/T]GCACAGTGGTGTACATCTCGTGTAAGGAAGTTGGG Y 2 1 2 1 101000 r 74 goat snp39164-scaffold499-911896 23 2036680 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277540 Affx-1111835964 AX-519551041 23 45512947 AGCAACCCTATGTTATGTAAAAAAACTATCAGCCT[A/G]GAAAATTATATTCTCCCTGGATTTTTCACATTAAT R 2 1 2 1 101000 f 74 goat Random2.2K-2071 23 45512947 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38445191 Affx-122925528 AX-123315528 23 45533518 AGCAGACACAGCTCAGCCTTTGTGCAGAAAGCCAC[A/G]CAAGTGTGCAACATTCAGGTGAGGGACACACAAGC R 2 1 2 1 101000 r 74 goat snp39165-scaffold499-945312 23 2003052 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427935 Affx-122939215 AX-123298278 23 45574296 TATCTGAAAATCAGATTTAATCGGGCATCCTTTAC[C/T]TCTTAGTTTGCTAAATGAGGTTGGTCAGTCGGGTT Y 2 1 2 1 101000 r 74 goat snp39166-scaffold499-986090 23 1962883 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425965 Affx-122941168 AX-123296311 23 45623906 TACTTGGAGTTTTCCCTGGTCTATTTGGAAGGTGG[C/T]AGGCCTCCCCAGGTGACACTAAAGGTAAAGATCCC Y 2 1 2 1 101000 f 74 goat snp39167-scaffold499-1035700 23 1913571 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394981 Affx-122964262 AX-123265336 23 45680592 TCATTAATTCCATGCATTTTAGGTTAGACGTTTCT[A/C]TGCTGTCATGCGGCACGCCTGCAATGCTCTTTGGT M 2 1 2 1 101000 f 74 goat snp39168-scaffold499-1092386 23 1856879 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390010 Affx-122968039 AX-123260367 23 45712796 AGAGTGTGGGCTGAAAGAGGGTTTGAAGAAACAAC[A/G]CCTGAAAACTCCCTTCATTTGGCATAAGACACAAA R 2 1 2 1 101000 f 74 goat snp19939-scaffold1995-20950 23 1822593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777722 Affx-122930732 AX-385264840 23 45759385 ATAGACTTTTTATCTTGGTTCCTAAAGGACAATGA[C/T]AAGTATTTCAGAAACAATCCTTCCATTCATGCAGA Y 2 1 2 1 101000 r 74 goat snp19940-scaffold1995-67539 23 1775797 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794390 Affx-122975298 AX-385281353 23 45815015 TTGGTAAATTGAAACATAGTCCTTTACTGACATAA[C/T]ATTGTCAAGATTTGTTCTCCTCCCTGAGTGATCGT Y 2 1 2 1 101000 r 74 goat snp19941-scaffold1995-123169 23 1720699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441089 Affx-122928898 AX-123311426 23 45844966 TCCGCCACTGTCCATCTCAAAGTGCTCGCCCAGGA[C/T]GGGTCCGTGGAGCTGTGGCTCTGGTCTGGCCAGTG Y 2 1 2 1 101000 f 74 goat snp19942-scaffold1995-153120 23 1690688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447165 Affx-122924433 AX-123317501 23 45880305 CCACGGAGCCGTGTTTCCGCCTTTTAGGTGTCAGC[A/G]TGCTGAGTCCTGTGTATGAGCTTCTTTGGCAATTT R 2 1 2 1 101000 r 74 goat snp19943-scaffold1995-188459 23 1654651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385799 Affx-122971038 AX-123256157 23 45939229 TGGGTCATGTCCAGGCTTCCCAGAGGCTGAGCCCC[A/G]TGTATTCCCAATAATACCACCTAGACAACTGTCAT R 2 1 2 1 101000 r 74 goat snp19944-scaffold1995-247383 23 16807137 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766909 Affx-122979102 AX-385254225 23 46003116 CCTCCCCAGCTGCCATCTGATCGTTTCCGATGCCA[C/T]GAGGACTTCTTAACGGGAAGTCACTCTAGAACTCA Y 2 1 2 1 202000 f 74 goat snp19945-scaffold1995-311270 23 16742778 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433840 Affx-122934446 AX-123304181 23 46095778 CCTTCCTTTGAAACACTGCAATGGCTTCCCAGGAC[A/G]TCTGGAATAAAATCCAAATTCCTTATGGTGGCCTA R 2 1 2 1 201000 f 74 goat snp19947-scaffold1995-403932 23 16651445 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793617 Affx-122959282 AX-385280591 23 46142201 GGTGTTCGTTACACAGTGAACTCCTGTTGATGGCT[A/G]CATGATACAGTGCACATATCATGAAGAAAGAAAAA R 2 1 2 1 101000 f 74 goat snp19948-scaffold1995-450355 23 16606143 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438724 Affx-122930843 AX-123309061 23 46177638 CTTAGAGACAAAAACTCTACTATCTGGCCCCAGTT[A/C]TCTTTCGGAGTTACCTGTTTGTCCTCGGATTTTGC M 2 1 2 1 201000 r 74 goat snp19949-scaffold1995-485792 23 16570557 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765180 Affx-122957997 AX-385252730 23 46207923 CACAGGGAATAGCAAGTGTTGATGGAGACACAGAG[C/T]GACTGAGATCCCCATTCACTGCTCGTGAGATGGGG Y 2 1 2 1 101000 f 74 goat snp19950-scaffold1995-516077 23 16540062 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404625 Affx-122957326 AX-123274977 23 46240533 TTGGTAGGTAGGCTACATTTTCAGCTCAGTCAGTC[G/T]ACCTGCGATGATGTATTCTGCGTTGAGGCAGAAAC K 2 1 2 1 201000 r 74 goat snp19951-scaffold1995-548687 23 16506873 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392458 Affx-122966160 AX-123262815 23 46279221 CGGAAACTTCTAGATCCCTGATGAAAGAGTATCAC[A/G]CCCAGCTTTGCACAGTAGACAGCACTCAACACACA R 2 1 2 1 101000 f 74 goat snp19952-scaffold1995-587375 23 16470842 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396419 Affx-122963000 AX-123266774 23 46333267 TTCTTGGACTAACGAAGCCCAGGTTCAACTACTGC[A/G]CGGGCTAAGTCTGCACCTAGCAGTCCGTGCTGAAA R 2 1 2 1 101000 f 74 goat snp19953-scaffold1995-641421 23 16419759 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415796 Affx-122948904 AX-123286145 23 46362817 TTCTTATTTCTTTTCCCCATAAGTATTTACACTTC[A/G]TTTTTTGCCTTTTATTCAGAATTTCCTCTTCTTCA R 2 1 2 1 102000 r 74 goat snp19954-scaffold1995-670971 23 16401821 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773811 Affx-122927969 AX-385260951 23 46419394 AGGGAAATAGAGTTTGGTGAAACATGTCAGCTTCT[A/G]CTATTAAGAAAAGAGTACAATGTTCCTCTCACTCC R 2 1 2 1 101000 f 74 goat snp19955-scaffold1995-727548 23 16345368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425480 Affx-122941491 AX-123295826 23 46456912 TGGGGGACCATAGTCCATGGGTCACAGAGTCGGAC[A/G]TGACTGAGCTACTGAGCCCAAGACACTGGGCTGAG R 2 1 2 1 303000 f 74 goat snp19956-scaffold1995-765066 23 16307726 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431330 Affx-122937066 AX-123301671 23 46486086 CCCGCTGCTTATTAATTCTTGGCTCACGGATGGAA[A/G]AATATGTAAGAATCACTTCTAAAAATAAGCACGTT R 2 1 2 1 101000 r 74 goat snp19957-scaffold1995-794240 23 16279470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442408 Affx-122927990 AX-123312745 23 46519327 TATATGATATTTAGAACTAAGATATGTTTTCCTCC[A/C]CTATGAGCTTTCTTACTAAGAACTACCTTATTTTG M 2 1 2 1 101000 r 74 goat snp19958-scaffold1995-827481 23 16246033 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791193 Affx-122970046 AX-385278188 23 46570722 AGTAGGTAAAGAAGCTTTGAGTTAGTCTGGCCCAC[A/G]TTAAAATGACTGTTTCCACTGAGAATGTGCCCTTT R 2 1 2 1 101000 r 74 goat snp19959-scaffold1995-878876 23 16194819 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476366 Affx-1251763877 AX-586011777 23 46597367 TGATTCTGATCTTCAGTACTTCTAAGACCTTCAAT[-/TTAAATTCAATGACTAGGGGAGAGGGAAAGATGGCGGAGGATGCATGTAAGAATTAAAGATTTTAAAATTAAAAAAAAAA]TAAATTCAATGACTATGGTTTTATGTCTTTAAAAT - 8 1 4 1 20000 f 74 goat SV_262 23 46597367 - deletion junction SV-TF-chip 539476622 Affx-1251763877 AX-586012005 23 46597367 TGATTCTGATCTTCAGTACTTCTAAGACCTTCAAT[-/TTAAATTCAATGACTAGGGGAGAGGGAAAGATGGCGGAGGATGCATGTAAGAATTAAAGATTTTAAAATTAAAAAAAAAA]TAAATTCAATGACTATGGTTTTATGTCTTTAAAAT - 8 1 4 1 20000 r 74 goat SV_262 23 46597367 - deletion junction SV-TF-chip 562165436 Affx-1251763877 AX-606940848 23 46597367 TGATTCTGATCTTCAGTACTTCTAAGACCTTCAAT[-/TTAAATTCAATGACTAGGGGAGAGGGAAAGATGGCGGAGGATGCATGTAAGAATTAAAGATTTTAAAATTAAAAAAAAAA]TAAATTCAATGACTATGGTTTTATGTCTTTAAAAT - 8 1 4 1 20100 r 74 goat SV_262 23 46597367 - deletion junction SV-TF-chip 562165518 Affx-1251763877 AX-606940929 23 46597367 TGATTCTGATCTTCAGTACTTCTAAGACCTTCAAT[-/TTAAATTCAATGACTAGGGGAGAGGGAAAGATGGCGGAGGATGCATGTAAGAATTAAAGATTTTAAAATTAAAAAAAAAA]TAAATTCAATGACTATGGTTTTATGTCTTTAAAAT - 8 1 4 1 20100 f 74 goat SV_262 23 46597367 - deletion junction SV-TF-chip 562165871 Affx-1251763877 AX-606941280 23 46597367 TGATTCTGATCTTCAGTACTTCTAAGACCTTCAAT[-/TTAAATTCAATGACTAGGGGAGAGGGAAAGATGGCGGAGGATGCATGTAAGAATTAAAGATTTTAAAATTAAAAAAAAAA]TAAATTCAATGACTATGGTTTTATGTCTTTAAAAT - 8 1 4 1 20100 f 74 goat SV_262 23 46597367 - deletion junction SV-TF-chip 562166181 Affx-1251763877 AX-606941589 23 46597367 TGATTCTGATCTTCAGTACTTCTAAGACCTTCAAT[-/TTAAATTCAATGACTAGGGGAGAGGGAAAGATGGCGGAGGATGCATGTAAGAATTAAAGATTTTAAAATTAAAAAAAAAA]TAAATTCAATGACTATGGTTTTATGTCTTTAAAAT - 8 1 4 1 20100 f 74 goat SV_262 23 46597367 - deletion junction SV-TF-chip 38410045 Affx-122953236 AX-123280395 23 46609266 CAAAGACGTTATACAGAAGAGCCCTGAGCTAACTC[A/G]TTCAGTAAACACTGAGTGCCTGTTGTTGCCAAATG R 2 1 2 1 101000 f 74 goat snp19960-scaffold1995-917420 23 16156483 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773934 Affx-122932922 AX-385261073 23 46649860 TTTGGGATTATTAACTTGGCAGATTTTAGCATGTA[C/T]TTTTACTTCTAAAAACACAGCCTTTCACTTCCTCG Y 2 1 2 1 201000 r 74 goat snp19961-scaffold1995-958014 23 16117108 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395620 Affx-122963805 AX-123265975 23 46686247 CCAAATGGTAAGCACACTCGTTTTTCCTTCATTCT[C/T]AAGGAAATGCATACTGTAAAAAAGAAAAAGTCAAC Y 2 1 2 1 101000 f 74 goat snp19962-scaffold1995-994401 23 16080875 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378639 Affx-122977104 AX-123248998 23 46726984 ACAAACGGTAAGCCTCAGAAATGCTTCGGGGAAAC[A/G]GGAACTGAGCTATCCAGGGCCGGTTTCCTGCCTCT R 2 1 2 1 101000 f 74 goat snp19963-scaffold1995-1035138 NW_017217773.1 20139 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411062 Affx-122951947 AX-123281412 23 46812878 TGTACACGAGACACCGCAGCCGGGAGAGTTCACTG[C/T]GGCGCTGGGCGTCTCAGAAAAACAAAGGGCTTGCA Y 2 1 2 1 101000 r 74 goat snp19965-scaffold1995-1121032 23 15978677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780102 Affx-122931802 AX-385267199 23 46876299 TATTTCAGTAAAAATGATTAATGTGCTTCAAAAAA[C/T]GTATATGAAAATTTAATAGCAATTCTCCTATATTT Y 2 1 2 1 102000 r 74 goat snp19966-scaffold1995-1184453 23 15914429 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397176 Affx-122962417 AX-123267531 23 46909387 CAGGAGTCATTCCGCCTGGACGGGTCTCAGCTACA[C/T]AGGAAAGGGGGGATTACAGTCTTCGGGATGTTGAG Y 2 1 2 1 201000 f 74 goat snp19967-scaffold1995-1217541 23 15881267 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404152 Affx-122957082 AX-123274504 23 46942088 CAAAGTGCTTTTCAAAGACCTTGCTCCACTCACGC[C/T]GCCACCGAAAACAAGAAAATGCCTATTTCTCTGTG Y 2 1 2 1 101000 r 74 goat snp19968-scaffold1995-1250242 23 15849802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441010 Affx-122928954 AX-123311347 23 47024246 AGAGTGATCCACGGTCTTGGCTCTAATGGAGGAAC[A/G]TGCACCAAGGATAGGTCCCGGGGGGAAGAAGCAGC R 2 1 2 1 202000 f 74 goat snp19969-scaffold1995-1332400 23 15766928 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429272 Affx-122937886 AX-123299614 23 47053767 CAACTCGCTGCAGTAGATTCTTCATTTTCGTCCTC[A/G]TGTTTTTTGCATCTTCATTTTGCTGATAAGTCCAG R 2 1 2 1 101000 f 74 goat snp19970-scaffold1995-1361921 23 15737432 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387672 Affx-122969831 AX-123258030 23 47112249 GCCCCCAAACCGGAGTCTATCTCCTGTACTGTTCC[A/G]TGCTCTCGCCTACACCTCTGACTTTACGGGGGGCT R 2 1 2 1 101000 f 74 goat snp19971-scaffold1995-1420403 23 15677989 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421245 Affx-122944111 AX-123291592 23 47166925 CCTCTCCTTTCATAGGCCACTGAAGGACCTTGTAA[C/T]GTGCCCAAACCAGGTATGCTGGACTTTATCAATAA Y 2 1 2 1 101000 r 74 goat snp19972-scaffold1995-1475079 23 15622830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429918 Affx-122938103 AX-123300259 23 47199361 GTAAGTGTTTAAAACGTGTAACTGTGAATTCAGTA[G/T]CCTATGGCCTGGCTTTTTTGCAGTTTTCATTTGAA K 2 1 2 1 101000 f 74 goat snp19973-scaffold1995-1507515 23 15590476 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766088 Affx-122919505 AX-385253504 23 47249616 CTTGTAGTCACATTTCCTAAAACTATCGCTCCAAC[A/G]TTTAATGAATGTGGTAACATTTGTATACCTAGATT R 2 1 2 1 101000 f 74 goat snp19974-scaffold1995-1557770 23 15541390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412902 Affx-122950413 AX-123283251 23 47282882 ATGTTTAGAAATGAATACAAAGATGACGTATTGCA[C/T]GCTTTCTAATCGGAGTTTTAAAATGTCTTCCAGCG Y 2 1 2 1 101000 r 74 goat snp19975-scaffold1995-1591036 23 15508844 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445370 Affx-122925411 AX-123315707 23 47329676 GTCTCTCTGACTGTCAGAGCAGGACCTGCTGACGG[G/T]GAACTTGGAGGAGCTTTAGGAGTATAATCAGAATC K 2 1 2 1 101000 r 74 goat snp19976-scaffold1995-1637830 23 15463505 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410031 Affx-122953246 AX-123280381 23 47367517 GGAGTCCAGATGAAAGGGGAGTTTGCCTCAGACTC[A/G]TTGGAGGGGCACAGGTTTGGTGAAAAAGATCTGAG R 2 1 2 1 201000 f 74 goat snp19977-scaffold1995-1675671 23 15425541 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438110 Affx-122931500 AX-123308448 23 47451444 TAGGCGTTCTTCCTGGCAGACCGCAGCCATCCCCC[A/G]CTGGCTCTGGAAACTGACTAAAGCTGAGGGAAGAG R 2 1 2 1 101000 r 74 goat snp19979-scaffold1995-1759598 23 15342983 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383021 Affx-122973314 AX-123253379 23 47494646 TATCCCTCCCACTGGCAGGTTTCTATCTCACTTCG[C/T]GCATCTGCTGGAAAGGTCTGAACTTTCTCAGAAGA Y 2 1 2 1 101000 r 74 goat snp19980-scaffold1995-1802800 23 15299809 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385864 Affx-122971611 AX-123256222 23 47556913 TGACAAAGGCAAACACAGACACAAAAGCGGTAGCC[A/G]GAGGTCAGTCGTAAGTACCTGATGAACAAATCAGA R 2 1 2 1 201000 r 74 goat snp19981-scaffold1995-1865067 23 15241301 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436608 Affx-122932512 AX-123306946 23 47606433 TCACAAACACTCCGTGGACTTGTGTGCCTCTGTCT[A/G]TCTGAACACACAGGTTTTAATTTTATTTAAGTGGC R 2 1 2 1 201000 f 74 goat snp19982-scaffold1995-1914587 23 15192538 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436525 Affx-122932938 AX-123306863 23 47665455 GGGAAGGAAACACATCAACACTGGCTGCCCTTGGG[A/G]AGGGGAACTGAGTGCTGGGGGACAGCAGTTCAGGG R 2 1 2 1 101000 f 74 goat snp19983-scaffold1995-1973609 23 15134505 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450420 Affx-122922058 AX-123320754 23 47740055 CGCTCCTGGGGGGCAGAACGCGCTGGGAGGCTCCG[A/G]CACAGCTCTCTAATCTCTGCTGCTGAGTCACACAC R 2 1 2 1 101000 r 74 goat snp19984-scaffold1995-2048209 23 15058762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440415 Affx-122929609 AX-123310752 23 47770359 TCATACCCTGGGTGTTTTCAACAGCTTTTAAACAC[A/G]TCTGAAAACAAGTGCCTGCTTCTTTAATTACTATT R 2 1 2 1 101000 r 74 goat snp19985-scaffold1995-2078513 23 15028200 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273009 Affx-1111833265 AX-311460106 23 47834794 ATATACCATGTTCATGGATCAGAAGAATCAATATA[A/G]TGAAAATGAGTATATTACTCAAAGCAATTTATAGA R 2 1 2 1 103000 f 74 goat 23_47834794_AF-PAKI 23 47834794 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38379030 Affx-122976359 AX-123249389 23 47846432 GAGGAACTGGCCTCTGATCTTCCACGATTTCAACA[C/T]GCTCACAGTTTCCTACCCCAGGAGCAGGGAGGCAG Y 2 1 2 1 101000 f 74 goat snp27806-scaffold2987-52627 23 1535927 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767235 Affx-986698422 AX-385254516 23 47857867 CCTGGCTGGAATTGGCAGCGCCCTTTTATTTACTT[C/T]TCTTGCTTCTCATTTTAATATCTTATACTAGACTA Y 2 1 2 1 600010 r 74 goat 23_47857867 23 47857867 Ancestral_priority_1043 ancestry 0.724 recommended IMAGE 10K 10K ancestral 38433719 Affx-122934525 AX-123304060 23 47883524 CATCTCGAGCACATTCCCAGATGGAGGGTTCAAGC[A/G]TGGGAAGCCCACCTTTTTTGCCCACCTTACACTTT R 2 1 2 1 201000 r 74 goat snp23883-scaffold2405-552851 23 1498941 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769094 Affx-122934760 AX-385256269 23 47941296 CTTCGCAGACGGACCAAATACAAAAGACTGAGACA[A/C]ACTCTTACAAATTGTGGATTAATGTCTTAAAATTT M 2 1 2 1 101000 f 74 goat snp23882-scaffold2405-495079 23 1440963 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415151 Affx-122949409 AX-123285500 23 48004021 AAATGTACAGACCATGGGTGGCGGGTCGTTTTCAA[C/T]GCCGGGCTCGTTTTCTGGGCTGGGAGTTGTTGTTT Y 2 1 2 1 101000 f 74 goat snp23880-scaffold2405-432354 23 1380505 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413697 Affx-122950090 AX-123284046 23 48036979 CATCTGCGTGGCTGAGTCTTGTGTTTATTTCCAAC[A/G]TGCACTGAGTTGTGAAGGCACCTCCACACGTAGGA R 2 1 2 1 201000 f 74 goat snp23879-scaffold2405-399396 23 1347478 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409271 Affx-122953122 AX-123279622 23 48077365 TGGAAATCTTTCCTTATTCTAAGAAACATTTCACA[C/T]GCTTATTTCTGGCTCGCTTTATACTTTCCCAAAAC Y 2 1 2 1 101000 r 74 goat snp23878-scaffold2405-359010 23 1306534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421482 Affx-122943918 AX-123291829 23 48109565 GCGACATGAAGGAGATGAGTCACCAGAGGAGTGTC[A/G]TGATGATATTTCTCTTTGATAAAGAAAAATTCTGA R 2 1 2 1 101000 f 74 goat snp23877-scaffold2405-326810 23 1275771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430857 Affx-122937423 AX-123301198 23 48149987 CCCCAGGGCTCCTGGAGGACCATTCTCAGGAGCGG[A/G]TCTTGGAGTTAGAGGAGGTAAGTAAAGGGTTATTC R 2 1 2 1 101000 r 74 goat snp23876-scaffold2405-286388 23 1235208 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770523 Affx-122925061 AX-385257688 23 48186494 TCTGTCAGGTAAGCTTTTGTAAGCCATAATACATA[A/G]GCAACTTTTCTATCACTTAGCCCAGTTCAATCACC R 2 1 2 1 201000 r 74 goat snp23875-scaffold2405-249881 23 1198090 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783275 Affx-122977127 AX-385270340 23 48256710 AGAACGCATACCTGTCCGACACTGAAGAAAAGGCT[A/G]TTTGTGTCAGACACATTAGAGAAACTGTTCAAGAC R 2 1 2 1 101000 f 74 goat snp23874-scaffold2405-179665 23 1128829 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277667 Affx-1111835965 AX-519551165 23 48259616 AAAACATTTTTTGGCATAACTGTGATCTATCCTGG[A/G]TAATCTTACATGTCATTTGGAAGACTGTATATTCT R 2 1 2 1 101000 r 74 goat Random2.2K-2075 23 48259616 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388087 Affx-122969508 AX-123258445 23 48291257 GGCCACGGACCCCCAGCCAACGGCAAGACACGCCC[A/G]CCTTCGGGAAGTGAAGAACGCAGAAGTGACTACAC R 2 1 2 1 101000 r 74 goat snp23873-scaffold2405-145118 23 1095035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443654 Affx-122927199 AX-123313991 23 48333125 GTGCACCGCGAATATTTTGCCCTTGAGCGTAGAAA[C/T]GGTTTGAGTAATACCCCGAGTGTAAGCTCTTCCTA Y 2 1 2 1 101000 r 74 goat snp23872-scaffold2405-103250 23 1052089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450167 Affx-122922318 AX-123320502 23 48366667 CTGGCCTGTGCCCGTGCTTGACCCTCGCGTACGTG[C/T]GTGTGGGCTTCCAAGCCCTTGTTCTATTAAACTTT Y 2 1 2 1 101000 r 74 goat snp23871-scaffold2405-69708 23 1018737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386726 Affx-122970151 AX-123257084 23 48404291 TTTTCCACCTGTGGAACAATTACTGAGCCAAGTCC[A/G]CGTATCGGTTGAGGATTGGAGGAAAACGGTCGTGT R 2 1 2 1 101000 f 74 goat snp23870-scaffold2405-32084 23 980977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436865 Affx-122932196 AX-123307203 23 48434850 AATCACTGACAGATAATCTTCATTATCAGAAGAAA[G/T]CTTTCAAAACTTTGCAGCAAGAAATACAACAAAGC K 2 1 2 1 101000 r 74 goat snp23869-scaffold2405-1525 23 950631 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428776 Affx-122938416 AX-123299118 23 48440896 GATGGGGCACCAGGGAATCGAAAGCATGTTTTAAA[A/C]AACAGAGGGAGCGAGAGGAATTCCCTAAGGGCCCT M 2 1 2 1 201000 f 74 goat snp20296-scaffold2009-4422 23 944426 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381679 Affx-122974730 AX-123252037 23 48476011 GGTGTGGCCGCATAAATGTCCTTTAAAAATAAAGA[C/T]GTAGAGAGGACCGTGCTCTGTGACCTGGACACTAA Y 2 1 2 1 101000 f 74 goat snp20297-scaffold2009-39537 23 908690 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785751 Affx-122937360 AX-385272791 23 48513436 GGATTTTTATACTCTTTCTAAACTTAAATAGCCAA[C/T]CTGCCTTAGTCAAGGACTCAGAAATTCTTAAGGAT Y 2 1 2 1 101000 r 74 goat snp20298-scaffold2009-76962 23 876260 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422870 Affx-122943081 AX-123293216 23 48564571 TGTTTTTGATCCCCTTACACTTGGTGGTCTGTGTC[A/G]CAGACCCTACAGTGATGGTCTGTTTTAAACCTGAG R 2 1 2 1 202000 r 74 goat snp20299-scaffold2009-128097 23 833919 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379066 Affx-122976331 AX-123249425 23 48594217 AACCTTAGTGATGCTGAGCGTCTTTGCATTTGCTC[A/G]TTGCCTGTCTCTGTGTCTTCTTTGAAGAGTCGTCT R 2 1 2 1 102000 f 74 goat snp20300-scaffold2009-157743 23 806825 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791132 Affx-122950044 AX-385278127 23 48682204 AATAATAAAGGAAGCCTTATCTTACGTGAGTGAAA[G/T]GCGCCCTCACGGTAATAGCACAGCTACAGTAATGA K 2 1 2 1 202000 r 74 goat snp20301-scaffold2009-245730 23 719991 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784038 Affx-122957886 AX-385271091 23 48729420 TCTTTCTCTAACAGTTACAACAATTTATAGCCTCA[C/T]CTGCTATGATGAAGAGGACCTACCTCATTACATGT Y 2 1 2 1 101000 r 74 goat snp20302-scaffold2009-292946 23 672642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767242 Affx-986698426 AX-385254523 23 48782472 ATGGAACACTCCCGATTGGATTTTACTGCCTCAGG[A/G]GCAGCTAATGACTTATTCCACACCTTCTCTAACTT R 2 1 2 1 600010 r 74 goat 23_48782472 23 48782472 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 320804172 Affx-986696422 AX-385290821 23 48782516 TGACTTATTCCACACCTTCTCTAACTTTATTTCGG[G/T]GAAGAACATTCTGTCTACTATTTTTGGCTATGCCA K 2 1 2 1 600010 r 74 goat 23_48782516 23 48782516 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 38393595 Affx-122965376 AX-123263951 23 48802045 GCTGGGTATCTGTGTTGAGTCGTCCCAGTGAGAGT[A/G]GACACTGTGATTCTCCCTGCCTTTGATGCAGGTGG R 2 1 2 1 201000 f 74 goat snp20303-scaffold2009-365571 23 600560 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437226 Affx-122932031 AX-123307564 23 48840904 GGTGGGTTTTCCTTTGAGCACAGGGTTGGGCTGAC[A/G]GAAACTCCAGACACAGTCCCCCGGAGCACTTCCCT R 2 1 2 1 101000 f 74 goat snp20304-scaffold2009-404430 23 561955 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776397 Affx-122924294 AX-385263524 23 48886424 TTGATGTAAACCTTAAAGGAGTTGGAAAGACAGCT[A/G]TCAAGAAAGCCCCGGTTAACGAGCTGTCCTAACTT R 2 1 2 1 101000 f 74 goat snp20305-scaffold2009-449950 23 517619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449369 Affx-122922725 AX-123319704 23 48918935 AGAAGCTGGCTCTGTAATTCTTACTTATTATAAGA[A/C]TGTATAGGCTAATTAAAAAAGCAAGGTGTGATGGT M 2 1 2 1 101000 r 74 goat snp20306-scaffold2009-482461 23 485318 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410168 Affx-122952784 AX-123280518 23 48954960 GTGCCGCAAGCTTAAACACCGGGCTGCGTTCTGAC[A/G]TGGCCGATGGAGGGCGGCTGGGACGCCCTCAGCAG R 2 1 2 1 101000 f 74 goat snp20307-scaffold2009-518486 23 449240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399944 Affx-122960847 AX-123270299 23 49002427 GCTTTACTTGGAAGCACCACTTCTCCTTGTAAAAG[A/G]CAAAACCAAGAGTTTCATGGCTGCACAAATGCGTC R 2 1 2 1 101000 r 74 goat snp20308-scaffold2009-565953 23 403404 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423594 Affx-122942391 AX-123293940 23 49074222 ACGACCAAGTCGGGTGGCAGAGGAACCTCCACGGT[A/G]TCTTTCAAGCTGCTCAGACCTGAGAAGATAGGTAT R 2 1 2 1 101000 r 74 goat snp20310-scaffold2009-637748 23 331872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399362 Affx-122961345 AX-123269717 23 49126379 TCTTGGGTGTCCCTTCCCCTGCAGTTCTGTGTATC[C/T]GGTCACTTGTGGGTTAGTAACCAATTTCCTGACTC Y 2 1 2 1 101000 r 74 goat snp20311-scaffold2009-689905 23 280161 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399762 Affx-122960313 AX-123270117 23 49182224 CTAAAGCTGAGGCAGTTCGTTTCCGGCAAACAAAG[A/C]CCTATTTTATAAGAAATGTTCAAGGAAGATTTTCA M 2 1 2 1 101000 f 74 goat snp20312-scaffold2009-745750 23 223669 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402576 Affx-122958442 AX-123272929 23 49220595 GTCTCCACTTCATTCTTCTCCATACAGCTCCTTCC[A/G]CACTCAGAGCATCCTGCTCGCGAATATTTCATCCT R 2 1 2 1 101000 r 74 goat snp20313-scaffold2009-784121 23 185773 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380935 Affx-122975010 AX-123251293 23 49273591 CTCCGAACAGGACTTCCTGACCAGGGTCCAACCTG[A/C]GTCACCAGGGGATCCGTGAGCTCCAAAAGGGCATC M 2 1 2 1 201000 f 74 goat snp20314-scaffold2009-837117 23 131880 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413545 Affx-122950607 AX-123283894 23 49319968 CCTTCAAAACACAGCCCATGTCCTCAAATTTTGTA[C/T]GGAGTCCCAGATACACTTCAGTTGCATATGTGTAT Y 2 1 2 1 101000 f 74 goat snp20315-scaffold2009-883494 23 85339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779090 Affx-122920309 AX-385266195 23 49384692 CCTGATGGGATGTTCATGTCCAAATAAACTTCTTT[A/G]TATCATTAAAAAGATTAAGAAATTACAAACTTCTG R 2 1 2 1 201000 r 74 goat snp20317-scaffold2009-948218 23 20496 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403102 Affx-122958493 AX-123273455 24 19632 AAGGATAGCAGGGGGAACATGAAAAGAGAGGAGGT[A/G]CCCGGTGTGGTTATGTACATCATGGGAGGATGTCA R 2 1 2 1 102000 r 74 goat snp20278-scaffold2008-19632 NW_017199929.1 13821 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273029 Affx-1111833277 AX-519546704 24 30385 AGACCATTGTACAACCTCATGGTTGTAGGCTGTGT[A/G]ATACAATTCTTTTTCTTTTGTACCTTTGTGATGAC R 2 1 2 1 101000 f 74 goat 24_30385_AF-PAKI 24 30385 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38415851 Affx-122948864 AX-123286200 24 65783 TTGGTATCCAGGCCCCTCCTATCAGTGGACTTGTT[C/T]GCACTTGCATTGCCCAGTAGCCAATAAGCTATAGC Y 2 1 2 1 201000 r 74 goat snp20279-scaffold2008-65783 NW_017204678.1 8126 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399722 Affx-122960463 AX-123270077 24 130142 CAGCCAGATATTTGTTGAGTGTCTTCTTTTTGCTG[A/G]GTGTGGGATTTACAGGGTAAGTAAAACAGATGTGG R 2 1 2 1 303000 r 74 goat snp20280-scaffold2008-130142 NW_017219161.1 10877 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446612 Affx-122924804 AX-123316948 24 195980 AAAATTCACTTAAAAATCACTTTAGATTTGAAAAA[C/T]AGCAATGGAAAAAATATGAGTTTTAGATCAGGAGA Y 2 1 2 1 103000 r 74 goat snp20281-scaffold2008-195980 24 56021 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776105 Affx-122977360 AX-385263235 24 235356 TAGTTCTCCCTAAATCTGTAACATGGATAGCAGTA[C/T]GCTACTGACAATTGAATAACATAAATTGCTTCCCC Y 2 1 2 1 201000 r 74 goat snp20282-scaffold2008-235356 24 96322 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431302 Affx-122937087 AX-123301643 24 357581 AAAGTCCTAAAATAGGTGTGTTTTATCTCATTCAC[A/G]TTTACAGGCATGCAGATTATATATACTCTCAGTTC R 2 1 2 1 101000 r 74 goat snp20284-scaffold2008-357581 24 220649 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424045 Affx-122942073 AX-123294391 24 402805 AACAGATAAACGAAATGCGAGGTATCTGCCCACTA[A/G]GGTATTATTCAGCCATCAGAAGGAGTAAAGCGCTC R 2 1 2 1 101000 f 74 goat snp20285-scaffold2008-402805 24 265939 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394073 Affx-122964968 AX-123264428 24 467922 TGTGAAATCACACAACTACTTTGGATAATACCAAA[C/T]CTAGGTATTTATCCAAGAAATATCAAAATAGCTGT Y 2 1 2 1 303000 f 74 goat snp20287-scaffold2008-467922 24 331188 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431800 Affx-122936120 AX-123302141 24 502780 AGCAGGTTCAGCGAAGCTCCTGGTTAGACAGAGCT[G/T]AGTCTTCTAGGGAAAGTGGAGTCCAGGCTGCTGCT K 2 1 2 1 101000 r 74 goat snp20288-scaffold2008-502780 24 365881 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767253 Affx-986698432 AX-385254534 24 589618 TACGACATGGTTTACTGAATATTTTAAGCCCACTG[G/T]TGAGAACTACTGCTTAGAAAAAAAGATTCCTTTCA K 2 1 2 1 600010 r 74 goat 24_589618 24 589618 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 38445273 Affx-122925466 AX-123315610 24 666420 GAGTCTATGAACTTTTCGCATGTGTATGCTCAGTC[A/G]CTCAGTTATGTCCTACTCTTCATGACCTCTTGGAG R 2 1 2 1 101000 f 74 goat snp20290-scaffold2008-666420 24 530727 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434994 Affx-122933823 AX-123305334 24 727687 GGGGTCGTTTCTGTGCAGTCAGAGTAACAGAACAA[C/T]GTGGAACAGATGTCTTTCCCTCAGGGGTTTTCTAC Y 2 1 2 1 201000 f 74 goat snp20291-scaffold2008-727687 24 585572 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413251 Affx-122950231 AX-123283600 24 760935 TGACTAGAACTTGTCCCCAAACTCTTCAGCCCAGC[A/G]TCATCGCAAGGAAAGCAACAGCCAGGTCCCAAGAG R 2 1 2 1 201000 r 74 goat snp20292-scaffold2008-760935 24 619165 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427265 Affx-122939546 AX-123297608 24 813351 AACTAAAATGCCTTAAAGCTGCCTGCACATCTCCC[C/T]TCCAACACGGCCGGGACGCTGCGTTTCCAGCATGG Y 2 1 2 1 202000 r 74 goat snp20293-scaffold2008-813351 24 670563 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381283 Affx-122974467 AX-123251641 24 844955 GCTTCATGGCTCTTTTTGAGGGGTCCTCTTACCAC[A/G]GGAGAAGCCTCGCTCCCATGTCCTGAGGGCCATCC R 2 1 2 1 101000 f 74 goat snp20294-scaffold2008-844955 24 701474 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421625 Affx-122944470 AX-123291972 24 873494 GAGATCTATTTCCATTCTCGCTTATTTCAGAAGGA[A/G]CCTGCGACCACCCTCTGGTAACCCAGGCCCTTACC R 2 1 2 1 101000 f 74 goat snp20295-scaffold2008-873494 24 730044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397336 Affx-122963293 AX-123267691 24 909161 CCCCTAGTTTGCTCTCTGGTCCAGCGAGACACAAG[C/T]GTTTCTTTTCAGTAAAATTCTCAAAAGTGGAGGGC Y 2 1 2 1 101000 r 74 goat snp24999-scaffold2570-5047 24 765324 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773845 Affx-122941291 AX-385260985 24 948041 ATGTTTGGACTTAGTCCTAAGTTAGGCCTTAGTCA[C/T]GTTAGGCCTTAGTCCTAAGTGTCTGCCCTGCGTGC Y 2 1 2 1 201000 r 74 goat snp25000-scaffold2570-43927 24 803505 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379500 Affx-122976464 AX-123249858 24 977275 TCCTTACTGTCTTTCTTGCCATGAGCTCCTGAGGA[C/T]AGGATCTGTAAGGACTCTGGCACACACACTGGTCT Y 2 1 2 1 101000 f 74 goat snp25001-scaffold2570-73161 24 832694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396014 Affx-122963484 AX-123266369 24 1008445 TGCAAGAATATATGTACCAGGATGTTCACTACAGC[A/G]CTCTTCAATAGCAGAAAAGAAAACCATCCAAAATC R 2 1 2 1 101000 f 74 goat snp25002-scaffold2570-104331 24 863962 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419744 Affx-122945887 AX-123290092 24 1126457 CTCTGCCTCTGTGCGCGTCCAAACATGCCCATCAC[A/G]TTTGCTTTGTGAAGGGCGGCTGTCAGCATGGTGAC R 2 1 2 1 101000 r 74 goat snp25004-scaffold2570-222343 24 982181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802844 Affx-122970185 AX-385289742 24 1188581 AATATCAGACTCTGGTGATGATGGAAATAGGCCAC[A/G]CTAATGACAAGGCAGCAAGGATTATAGGTAAGAGA R 2 1 2 1 101000 f 74 goat snp25006-scaffold2570-284467 24 1040325 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405506 Affx-122956000 AX-123275858 24 1214908 CGCCCGCTTCCCAGGTAGCTGAATGGTTCTACTTC[A/G]CAGCAAGTTCGTCCCACTCGGCTCCCAGCAGAATA R 2 1 2 1 201000 f 74 goat snp34813-scaffold4144-194441 24 1065924 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422445 Affx-122943348 AX-123292791 24 1251905 TGGTCAAGTGCCTATGAAATTCCTCAGTGTGTTTT[C/T]AATGTATCAAAGGGCCAAAAATTAGAAGACATAAA Y 2 1 2 1 201000 r 74 goat snp34812-scaffold4144-157444 24 1103121 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395467 Affx-122963910 AX-123265822 24 1284195 GTGAGCACAGAGGTGTGAAGGTTCTCTTCCGCTCT[A/G]CAGCCATCAGAAATTTAAAGAGAAGATAGCCAGAG R 2 1 2 1 101000 r 74 goat snp34811-scaffold4144-125154 24 1135329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397448 Affx-122962109 AX-123267803 24 1331431 TTGATGGTAACAGGCAAATGGCACTCTTGAAGTCA[A/G]CAGACACCTGTTCCACCCAATGCCTTGCAGAGGAA R 2 1 2 1 101000 f 74 goat snp34810-scaffold4144-77918 24 1183397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781662 Affx-122970203 AX-385268746 24 1360820 CTATGATGAGTCAAAGCTTTCAGGCATCAAACAAA[C/T]ATCACCATGACTATTTGAGGACCTCGGAGAAAGTG Y 2 1 2 1 101000 f 74 goat snp34809-scaffold4144-48529 24 1212854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406957 Affx-122955061 AX-123277308 24 1408368 GAATCTAGCTTCTGTCTTCTGCCCTCAAACCCAAA[C/T]GTCTGCTATGGCCTCTCACACTGCTTCCTCCACTT Y 2 1 2 1 201000 r 74 goat snp34808-scaffold4144-981 24 1259059 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795483 Affx-122969269 AX-385282438 24 1431162 GCCTTCCAGACATATGTCATTAACAGAGTTTACAT[A/G]TTTTATTCAAAAAGGTGAATAGCTAACCTCACATA R 2 1 2 1 101000 f 74 goat snp24614-scaffold2503-428373 24 1375069 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429669 Affx-122937656 AX-123300010 24 1461214 TAAAAGAAAAAAAATTGGTGATTAGAATCCTGAAA[C/T]GGAAGCATTAGTGAGGATGTGTGTAGTAGAAGAGC Y 2 1 2 1 201000 f 74 goat snp24613-scaffold2503-398321 24 1405534 A G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381490 Affx-122974877 AX-123251848 24 1506449 CAGGGCAGAGCTAGGCAGAAGAAGGCTATTCTGTC[A/G]CAGACTAAAATCAATTCTGATGGTTCAAACCCTTC R 2 1 2 1 101000 r 74 goat snp24612-scaffold2503-353086 24 1451232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407090 Affx-122954898 AX-123277441 24 1550878 GTAACCATGCAGGAATTACTCATGAATGGTTAAAC[A/G]GCTCAAACAGAAAAGTGAACTCCAAATTATCTCAG R 2 1 2 1 101000 f 74 goat snp24611-scaffold2503-308657 24 1494988 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429269 Affx-122937888 AX-123299611 24 1613760 TTGAAATGTTATTTTTCCTTAGGGTAAAAGAAATG[C/T]GTGTACTTCAAAAATATTGAATTATAAACCTTATT Y 2 1 2 1 101000 f 74 goat snp24610-scaffold2503-245775 24 1558401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376484 Affx-122978033 AX-123246843 24 1652825 TCGTGTTAGGAGACTGTGCCGGGTAATTATACAGA[C/T]GTACTCGGTGAAGTCATTTAAATGACAATTTTTAT Y 2 1 2 1 101000 f 74 goat snp24609-scaffold2503-206710 24 1597781 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800974 Affx-122944435 AX-385287889 24 1683744 CATTTTCAATGCATGTTGAAGAGTGCGTCTCGGTT[A/G]TGACTTTATTAAACATCTACATAAAAGCTTTCCAG R 2 1 2 1 101000 f 74 goat snp24608-scaffold2503-175791 24 1627803 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765644 Affx-122928451 AX-385253113 24 1722421 AGGGGCTTTTAATTTCACAGAATCCCGTTCATTGC[A/G]TGAGAACTTAGCAGAAGGCAACAATATTTTTAAAC R 2 1 2 1 101000 f 74 goat snp24607-scaffold2503-137114 24 1674743 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432738 Affx-122935456 AX-123303079 24 1756571 CTGAAAATCCTAGAGCACATGGGACAACTCCCACC[A/G]CAGGGAATTCCTGAGCCCAGACTGTTATCAGAGCC R 2 1 2 1 201000 f 74 goat snp24606-scaffold2503-102964 24 1704832 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780358 Affx-122935889 AX-385267453 24 1790611 GTATACATACATACACATAATATTTGGAATGTCTA[C/T]GGGAAACTTTCACACACTGTAGGTCACAATTTTAC Y 2 1 2 1 101000 r 74 goat snp24605-scaffold2503-68924 24 1739052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441986 Affx-122928437 AX-123312323 24 1831895 CCTGGTTTAGAAATGAAATAATATTGTTTCAAATG[C/T]GGCAATTTTCTTTTTATTCTTGAAACAAGCAAACT Y 2 1 2 1 101000 f 74 goat snp24604-scaffold2503-27640 24 1780694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417079 Affx-122947501 AX-123287427 24 1878915 CTCTTCCTGTCCCCCGTTTTTGAGAGGATCAGGAC[A/G]TGAGCTATCTTGAGTAAGGTGTGGGCAGAGAAATG R 2 1 2 1 102000 r 74 goat snp23181-scaffold2314-19281 24 1825195 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380791 Affx-122975098 AX-123251149 24 1916842 ATTCACAGGGGCTTCTCCTTGTGACCGGATCACCC[G/T]CCAGAAGCACAAGCTCCAGCACCATCCCGCTGGGA K 2 1 2 1 201000 r 74 goat snp23182-scaffold2314-57208 24 1863542 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476367 Affx-1251763878 AX-586011778 24 1940735 ACTTGCCATCTGCATCTACAGAGATTAAGTCATAG[-/CCACTGCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]CACTGCAACTGCTGACTTTCAATGCCCCTGAAAGG - 4 1 4 1 20000 f 74 goat SV_124 24 1940735 - deletion junction SV-TF-chip candidate gene ou candidate region 539476623 Affx-1251763878 AX-586012006 24 1940735 ACTTGCCATCTGCATCTACAGAGATTAAGTCATAG[-/CCACTGCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]CACTGCAACTGCTGACTTTCAATGCCCCTGAAAGG - 4 1 4 1 20000 r 74 goat SV_124 24 1940735 - deletion junction SV-TF-chip 562165067 Affx-1251763878 AX-606940479 24 1940735 ACTTGCCATCTGCATCTACAGAGATTAAGTCATAG[-/CCACTGCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]CACTGCAACTGCTGACTTTCAATGCCCCTGAAAGG - 8 1 4 1 20100 f 74 goat SV_124 24 1940735 - deletion junction SV-TF-chip 562165930 Affx-1251763878 AX-606941339 24 1940735 ACTTGCCATCTGCATCTACAGAGATTAAGTCATAG[-/CCACTGCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]CACTGCAACTGCTGACTTTCAATGCCCCTGAAAGG - 8 1 4 1 20100 f 74 goat SV_124 24 1940735 - deletion junction SV-TF-chip 562165973 Affx-1251763878 AX-606941382 24 1940735 ACTTGCCATCTGCATCTACAGAGATTAAGTCATAG[-/CCACTGCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]CACTGCAACTGCTGACTTTCAATGCCCCTGAAAGG - 8 1 4 1 20100 r 74 goat SV_124 24 1940735 - deletion junction SV-TF-chip 562166561 Affx-1251763878 AX-606941969 24 1940735 ACTTGCCATCTGCATCTACAGAGATTAAGTCATAG[-/CCACTGCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]CACTGCAACTGCTGACTTTCAATGCCCCTGAAAGG - 8 1 4 1 20100 r 74 goat SV_124 24 1940735 - deletion junction SV-TF-chip 562166569 Affx-1251763878 AX-606941977 24 1940735 ACTTGCCATCTGCATCTACAGAGATTAAGTCATAG[-/CCACTGCTGCGGGGGACTGCCCGTGAAGGGTTAAGTCTTGCCCTATGCAGGTGTGACTCTTGCTTGTGCTGGCCGCGGCA]CACTGCAACTGCTGACTTTCAATGCCCCTGAAAGG - 8 1 4 1 20100 f 74 goat SV_124 24 1940735 - deletion junction SV-TF-chip 38383858 Affx-122973144 AX-123254216 24 1949542 GCTTCCACGAGCACATGAGAAGCAGGTGCCTCTGT[C/T]GATCGGTGTCATTTTCCTTTCCATATGTGTGAGCC Y 2 1 2 1 201000 f 74 goat snp23183-scaffold2314-89908 24 1897392 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770427 Affx-122925324 AX-385257593 24 1981244 AAACTGCTTTCCAAAGATCCACCCAGGAGTTCTCA[C/T]GCCAAGCATACGTTTCTCTCCAATTTGCCTCCTTT Y 2 1 2 1 101000 f 74 goat snp23184-scaffold2314-121610 24 1929313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380439 Affx-122975296 AX-123250797 24 2009857 TAAAAAGTTTATCATTTCCTTGTATTTTCCAATTA[C/T]GACCCAAAGCTGATAAAATGGACAAAAGTAACTCG Y 2 1 2 1 101000 r 74 goat snp23185-scaffold2314-150223 24 1966717 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382502 Affx-122973814 AX-123252860 24 2080841 GGAGACTTGGCAAATTAATGACTGAATGAGTAACC[A/G]TTGCACAGTGTTTGCAGAGGCACAAAAAATTTGCA R 2 1 2 1 101000 r 74 goat snp23187-scaffold2314-221207 24 2033973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463886101 Affx-1110207275 AX-515363969 24 2092303 TGCTGCTTAAAAACACCAGGAACACGTCCCTGCAG[A/G]AACCATCTTTCCCTCGAGGCCTGCCTTTGTGAGGC R 2 1 2 1 202000 f 74 goat GoatD01.000398 24 2092303 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38419518 Affx-122945442 AX-123289866 24 2125794 CAGCTTCAGCCTCATCGTGATACCCACACACCTGC[A/G]TTTATCATGCTGTTTCATGCTGGTCTGCAGAGATT R 2 1 2 1 101000 r 74 goat snp23188-scaffold2314-266160 24 2079363 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430962 Affx-122936821 AX-123301303 24 2176214 CACATTCAGTTTTGGGTTTTCCAGCTTATTTGTAA[A/G]TAACCTTCTCATTTATCTGATTCTTTCTTTCTTCA R 2 1 2 1 101000 f 74 goat snp23189-scaffold2314-316580 24 2128904 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410834 Affx-122952628 AX-123281184 24 2208596 AGCCACCGAGGTGGGGAGCCAGAAATGGGTACAGC[G/T]GAAACGAATAAACCTCCAAGATCTTCTCACATCAC K 2 1 2 1 101000 r 74 goat snp23190-scaffold2314-348962 24 2161371 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434336 Affx-122934732 AX-123304677 24 2240935 ATAGTTAACCTATGGGGCAGTTAGGGACACAGCAA[C/T]GTCCAAATTGGCTGTTTGTTACCAAGGCGGCTTCC Y 2 1 2 1 201000 r 74 goat snp23191-scaffold2314-381301 24 2193461 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421229 Affx-122944125 AX-123291576 24 2277125 TAGCAACAAGCAGAAGCACACACAGTTTGTTTAGA[C/T]GAGACAGTGGCAAGGCAGAGAGGACACTGGAGAGG Y 2 1 2 1 101000 f 74 goat snp23192-scaffold2314-417491 24 2229480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765829 Affx-122969680 AX-385253276 24 2332494 GTTTTAAAAAAAATCCTTTCCTTTTCTATAATCCC[A/G]TCGTTGTTGAGTGGCACACAAGAAGGATGGAACTA R 2 1 2 1 201000 f 74 goat snp23193-scaffold2314-472860 24 2284665 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425038 Affx-122941867 AX-123295384 24 2411428 ATAGACATACTGGTCCTGGAAGCCTCAAACTAATG[C/T]GAAGAGACCAAAAAGTCATTCGCTTTGGTCTAATC Y 2 1 2 1 101000 f 74 goat snp29445-scaffold3182-62097 24 2415144 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434683 Affx-122933961 AX-123305024 24 2450627 TCTGAGTTGAGAAGGATGGTATTATCATACAGCAG[C/T]ATTTCCTGCAGGATGTTAAGGCACTTTATAAATAT Y 2 1 2 1 101000 f 74 goat snp29444-scaffold3182-22898 24 2454347 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434356 Affx-122934716 AX-123304697 24 2477414 TGCTAGCCATGGGCAATTCATTCTCTCCTAAATGC[A/G]GTTCCCTGATCTCTGAAAGAAGCAACCCTAGCAGG R 2 1 2 1 101000 f 74 goat snp54935-scaffold84-2444622 24 2480955 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375774 Affx-122978590 AX-123246133 24 2506117 CAAGCACTCCCTGACTGAGATGCACAGAGTCCATA[A/C]GCTGCACTGTAATTCCAGTGATTCATGTTGAACCT M 2 1 2 1 101000 r 74 goat snp54934-scaffold84-2415919 24 2509605 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430629 Affx-122936962 AX-123300970 24 2554073 ATGGAGTCATAAAAACCTCATGACTGCTCTCTTTC[A/G]TGTGGGGAGATACCTACCTTCGAACTCAAGAGTTA R 2 1 2 1 101000 f 74 goat snp54933-scaffold84-2367963 24 2557529 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273024 Affx-1111833274 AX-519546701 24 2561360 ACTCCTCCAGGGAACCTTCTATCAGTGGATCCCAC[A/G]CCATCTGACCTTCCGTGTCAGGCTCAGCTCCCTGA R 2 1 2 1 102000 f 74 goat 24_2561360_AF-PAKI 24 2561360 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38390519 Affx-122967241 AX-123260876 24 2598781 CTCATCGATGCTGTAAGAGGGTCAGAATTATAAAA[C/T]GACAAGTGAGTGAGTGATAGTTGCCCAGCTGCGCC Y 2 1 2 1 101000 f 74 goat snp54932-scaffold84-2323255 24 2602150 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422989 Affx-122942992 AX-123293335 24 2644827 AAAGTTCTCAGCTTCCCACAGACTCCTTCAGGGAC[A/G]TTAGGAAAATGACGGCTCATGTTTTAACCCATCTG R 2 1 2 1 101000 r 74 goat snp54931-scaffold84-2277209 24 2648594 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386307 Affx-122970897 AX-123256665 24 2691597 GTTACCCTCTTCTACCCAAATGCTCCCTGTTCCTC[A/G]ACGTTTATCTTCTTCCTCAATCTCTAGAAAACACT R 2 1 2 1 101000 r 74 goat snp54930-scaffold84-2230439 24 2691026 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407982 Affx-122954329 AX-123278333 24 2762201 GCCTGTTGTGGATGATTCACATTTGTTATACAGTT[C/T]GTGTGTCTCTTCCTCTTTGTTTTACCCGTAACGTG Y 2 1 2 1 101000 f 74 goat snp54928-scaffold84-2159835 24 2761387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795776 Affx-122942576 AX-385282729 24 2812726 TAACGTTGTGACAGAGTTTTAAGGGTCACAGAGTC[A/G]TCATAACCACCAAGGTGGTCTGCAAGTTCTAGCCA R 2 1 2 1 101000 f 74 goat snp54927-scaffold84-2109310 24 2812042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767256 Affx-986698434 AX-385254537 24 2831976 ACTTCAGGGTTATGTTCACCTTTCTGTAGCTATAG[A/G]TATTTTTAAATGGGAATTTCCCCCAAAGAAGGATT R 2 1 2 1 600010 r 74 goat 24_2831976 24 2831976 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 38415205 Affx-122948983 AX-123285554 24 2852963 CCCCACTGTTATTAAATAAACTCAGTAAGGACAAG[A/C]TACCTGATCAAAAAGATACACAGAACTGAATAGAC M 2 1 2 1 101000 f 74 goat snp54926-scaffold84-2069073 24 2852348 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423440 Affx-122942602 AX-123293786 24 2899821 GTCTCAAAGAGTCGGCCAGGACTGAGCAACTAACA[C/T]GAAACACTTCTTCTGATGAAATCTGCCTCATCCTT Y 2 1 2 1 101000 r 74 goat snp54925-scaffold84-2022215 24 2899037 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376481 Affx-122978036 AX-123246840 24 2929514 AAAGTTTATTGAACAAGTACAGGGTGTGAGGCCCC[A/G]CATCACTGCTGTAGGGGACACAAAGATGAGAATGA R 2 1 2 1 202000 r 74 goat snp54924-scaffold84-1992522 24 2928463 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431386 Affx-122936552 AX-123301727 24 2972308 ACAGTAATTAAAAGTATGTCATTCTGGCACAGTAT[A/G]CTTTAGCATGTTATTGGGAAGCTTCTTTGAAACCT R 2 1 2 1 101000 r 74 goat snp54923-scaffold84-1949728 24 2969569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799682 Affx-122920044 AX-385286610 24 3028952 TTACTTGAATAGCCTATATACAAACATTTGCACAG[C/T]GTCTTACCATTTCCTTTCACACAGGGAACCTGCTT Y 2 1 2 1 101000 r 74 goat snp54922-scaffold84-1893084 24 3026926 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786219 Affx-122944658 AX-385273254 24 3061259 ACCACTGACCTCTACTCTGGGATGCTCTCATTTCA[A/C]ATGTAACATAGGGTCACAAGGTGCCTAGCCTCTGA M 2 1 2 1 101000 f 74 goat snp54921-scaffold84-1860777 24 3059023 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382314 Affx-122973904 AX-123252672 24 3151596 GAATCCATCACTAAGACACCTTCAGATGCCAGCCA[C/T]GGCAGAGGCATCCCTGATGGTTCAGATGGTAAGGA Y 2 1 2 1 201000 f 74 goat snp54919-scaffold84-1770440 24 3150791 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446868 Affx-122925244 AX-123317204 24 3197528 AAGTCTATTAGCATACAGGAGGTGTTAAATAAGTT[G/T]ATGTGTTTTTTTGAAATTGCAGGTATTTGTGAGTT K 2 1 2 1 101000 f 74 goat snp54918-scaffold84-1724508 24 3196686 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774018 Affx-122966717 AX-385261156 24 3230290 CAATTGCCTTTCCAGGGGCCAAGCTTTTGTTCTCT[A/G]AGATAGTTTAGACCTAAGTCTAAATTAACTTTTTA R 2 1 2 1 102000 f 74 goat snp54917-scaffold84-1691746 24 3229772 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443351 Affx-122927425 AX-123313688 24 3258805 TAGCATATTTCCACCTCAGGAAAAAAATGTTTTTC[A/G]TTGTAACAATTTCTGACAGGTCTAGCATTCTCTAG R 2 1 2 1 101000 r 74 goat snp54916-scaffold84-1663231 24 3258337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437209 Affx-122932043 AX-123307547 24 3316185 GGACTCACCGTCCACTCTGGATCAGGGAGCCCCTC[A/G]TCTGCACACACGCCCTCAGACCCCCTTCCTTTCCA R 2 1 2 1 101000 f 74 goat snp54915-scaffold84-1605851 24 3315408 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415420 Affx-122948727 AX-123285769 24 3374189 TTTATACAGTTGTTTACATTTTTGAAAAAGAAATA[C/T]AAGATGAGCTGATGGTCAGTTTTGTTTTTTCCTCT Y 2 1 2 1 101000 r 74 goat snp54914-scaffold84-1547847 24 3373599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427900 Affx-122939684 AX-123298243 24 3417117 TTCAGACCCGTCATTTCATGATGTGTGTGCTGAAA[C/T]GCTTATTCAGATGATAAGTACTCCTTTTTTTAAAT Y 2 1 2 1 201000 r 74 goat snp54913-scaffold84-1504919 24 3416552 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776024 Affx-122966640 AX-385263154 24 3459513 CTTTGGTACATATTGCAAAGCTCTTCTCAAAATGA[A/G]TCAATGGAATCTCCATTTGCAGTGCAGGAATATTC R 2 1 2 1 101000 r 74 goat snp54912-scaffold84-1462523 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453573 Affx-122919765 AX-123323906 24 3492162 GATATATAGGAGGGAGTGATGAGCTGGGACTGCAT[C/T]GAGGTTTAGAAAATTTGGTTGTAAAAAATAGCCTC Y 2 1 2 1 201000 r 74 goat snp54911-scaffold84-1429874 24 3489570 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407964 Affx-122954345 AX-123278315 24 3549756 GCCCACGCCCGTGTCACTCGACGTCTTCTCAAAGG[C/T]GAGACAATGAGTTAAACGCTAGCAGCTCTGCTACA Y 2 1 2 1 101000 r 74 goat snp54910-scaffold84-1372280 24 3546789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439213 Affx-122931029 AX-123309550 24 3578699 GATGATCTAGTAAACTGATGACCGTGGCAGTATTG[C/T]AAATGCTACCACCTTGCAGTTCCATCTTGTGTTTG Y 2 1 2 1 101000 r 74 goat snp54909-scaffold84-1343337 24 3575944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769098 Affx-122927004 AX-385256273 24 3618457 TAGCCTCGTCAGTAGAATGTATTAGTTATTTTTTA[C/T]AGACACAGTTTCATTTAACAACAAAACCAAAATTC Y 2 1 2 1 101000 r 74 goat snp54908-scaffold84-1303579 24 3614523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451494 Affx-122921123 AX-123321827 24 3647181 TTACAGCTGCAAAGAGTGAGGTTGTTCCAGGCTCA[C/T]AGTATGCCCTGTTGTTACCAGGGGCTGAAGTGAAG Y 2 1 2 1 101000 f 74 goat snp54907-scaffold84-1274855 24 3643374 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273701 Affx-1111833749 AX-519547313 24 3677246 CTACCTGTCTGTCTGCACGGGGCTTCCTCTCGGCG[A/G]TGGGCTGGGTACCACCCAGCAAGATGCAGCCCTGC R 2 1 2 1 202000 r 74 goat GoatD01.003527 24 3677246 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320781659 Affx-122928922 AX-385268743 24 3691448 CTTTCCACAGACATGGTGAGGTCATTCCCAAGCAT[A/G]ACGCTTTCAGCACAAATAGGTTACTTCTGTGAAGA R 2 1 2 1 101000 f 74 goat snp54906-scaffold84-1230588 24 3687754 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411750 Affx-122951506 AX-123282100 24 3755592 CGAGGTTCTTAGCTCTGAAATAACGTCTTTATAGC[A/G]TCCATAGGTGCACAACCTGAAACATAGCTGTTGCT R 2 1 2 1 101000 f 74 goat snp54905-scaffold84-1166444 24 3751817 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442151 Affx-122928319 AX-123312488 24 3805150 TATATGTTCACATACACACACACATATACTCATAT[A/C]TGCATATATGTGTTACTGTGATGGGAGGAACCCTA M 2 1 2 1 103000 r 74 goat snp54904-scaffold84-1116886 24 3801454 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801681 Affx-122978874 AX-385288589 24 3847151 CATTCTTGCCCAAGTGCCGCAGCTCTTTAGTGTTA[C/T]GGGGTATTTACTTTGTCAATGATGATAAAATGAGC Y 2 1 2 1 101000 f 74 goat snp54903-scaffold84-1074885 24 3843695 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798688 Affx-122962058 AX-385285620 24 3879023 AAATGAAGAAATGCTGTAAACTTTCCTAGTGGCAG[C/T]GTGAGGCTTCTAATTGTTTTTCTCTCTTGTAGGAA Y 2 1 2 1 101000 r 74 goat snp54902-scaffold84-1043013 24 3875973 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398910 Affx-122961012 AX-123269265 24 3940855 CTTTCACAAGCCCCTTTATAGAATTCCCTGTCGAG[A/G]TGAAATGTTTCCAAGTAGTGATAGGCTTAGTTTCT R 2 1 2 1 201000 r 74 goat snp54901-scaffold84-981181 24 3934998 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791062 Affx-122971008 AX-385278057 24 3999324 TCTCAGTAAGGAGGTGATAATTAGCTTGTTGTGAG[C/T]GGTGTCACAGACGTACAGAAACTGGTGACACAAGC Y 2 1 2 1 101000 f 74 goat snp54900-scaffold84-922712 24 3988298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432585 Affx-122935516 AX-123302926 24 4035083 GTGAACATGCTGATTGCTATTCCAGGCAAACTGTA[C/T]GGGAGGGGAGCCACCGATGACAAGGGGCCGGTGGC Y 2 1 2 1 101000 f 74 goat snp54899-scaffold84-886953 24 4019194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427122 Affx-122939659 AX-123297465 24 4075909 AGTAGGCTATTTAATTTCCATTAGGCCTTCTCTCA[C/T]TTAACCAAACATAAAGAAATGAAAAGACTGTTTGC Y 2 1 2 1 101000 f 74 goat snp54898-scaffold84-846127 24 4054518 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443720 Affx-122927147 AX-123314057 24 4138943 GCCCCATAACAATTGCATTCTGAGAGTTCTCTGAA[C/T]GATGGTGGGCGCCCAGGGCTCCCAAAATGTAACAG Y 2 1 2 1 202000 r 74 goat snp54896-scaffold84-783093 24 4118125 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801686 Affx-122965686 AX-385288594 24 4182947 AGCAATGGTATTTACTTCCAAAAAGAACGACACAA[C/T]GGATTACACATGTAGGTCATCCTCCAGGAAACAGC Y 2 1 2 1 101000 r 74 goat snp54895-scaffold84-739089 24 4162140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766064 Affx-122971098 AX-385253480 24 4217806 GTGGTATGTTTTAAAAGATCATGTCCACAATAAGC[A/G]AATGATGTAGTGACGGAACAGCAAAATAAAGTTGG R 2 1 2 1 101000 f 74 goat snp54894-scaffold84-704230 24 4197315 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395726 Affx-122963708 AX-123266081 24 4261871 ATATGTCCCAAGGTCAAACACAACAAAGGATGTGG[C/T]TGAATTTACTACCATCTACTTCCTGTCCATTTTGC Y 2 1 2 1 101000 f 74 goat snp54893-scaffold84-660165 24 4241655 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394931 Affx-122964304 AX-123265286 24 4290792 CCATCAGGTTGGTCAGGAAATGGGGCCAATTTAAC[A/G]TTCTGATAAACAGTGTTTCCCAGAGGACTGGAGAG R 2 1 2 1 101000 f 74 goat snp54892-scaffold84-631244 24 4270846 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383467 Affx-122973447 AX-123253825 24 4321650 TCTACACATCCTCGGGGCAGGCATGCATCCTGCGC[A/G]TCCTTTTCCAGAGCAGAGCATCGTGCTACGTGGAC R 2 1 2 1 101000 r 74 goat snp54891-scaffold84-600386 24 4301279 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277671 Affx-1111835967 AX-519551170 24 4380952 AATCTATTTCTTCCTATCACATCACCCCTTTAAGC[A/G]TTCCCACACCATCTTTGGAAACTGTATATACCTTA R 2 1 2 1 101000 r 74 goat Random2.2K-2081 24 4380952 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392990 Affx-122965662 AX-123263347 24 4381701 GTGCTGATGGTCCAGAAAGGCATATCTTTGTATCT[G/T]CTGAATAATCCTCACAATAACCATGCAATGAGTGT K 2 1 2 1 201000 f 74 goat snp54890-scaffold84-540335 24 4361407 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377501 Affx-122977488 AX-123247860 24 4417593 AATCATCTGATGTGTGCTTTGTGGTTCTACTTATG[C/T]GTCTGATCTCAGAGCTCTTCAAGAATTCCTTGATG Y 2 1 2 1 101000 f 74 goat snp54889-scaffold84-504443 24 4397904 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447768 Affx-122924567 AX-123318104 24 4455823 AGGGACTCTCGCTGTCACGATTTCTTTAAAGAAAG[C/T]GTCTCAGAAAAAGAACCCGTTTTGAGTCTTGGTCT Y 2 1 2 1 201000 r 74 goat snp54888-scaffold84-466213 24 4436926 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782521 Affx-122941142 AX-385269597 24 4487306 CAACTTTAAAATAACTATCTCCTCTCCCCTTTCAA[G/T]CTTGAAACCCAGTGACATAACAGCCTCTTGAAACA K 2 1 2 1 101000 f 74 goat snp54887-scaffold84-434730 24 4468238 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275187 Affx-1111834754 AX-519548766 24 4510416 TGATCCCCTGCAGTCTGAACTTGTGAAATGTGCAA[A/G]CAGACACTAGCTTTCCTTTCTCTTTTCATCCC R 2 1 2 1 101000 f 74 goat GoatD01.051507 24 4510416 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38395126 Affx-122964142 AX-123265481 24 4547250 TAACAATCATACAATATGGTGTTCATACAAGTCTG[C/T]AACAATCACACAATATGGTGTTCACGCAAGTCCAT Y 2 1 2 1 101000 f 74 goat snp54886-scaffold84-374786 24 4527899 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781304 Affx-122954178 AX-385268389 24 4604301 TTGATCAACACATTTTTAGACCACTCAGTTTATTT[A/C]GTGTGTAGTTAAATGATGCATAGGTATAGGAGCTT M 2 1 2 1 101000 r 74 goat snp54885-scaffold84-317735 24 4585111 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376658 Affx-122979012 AX-123247017 24 4656929 GTCTTGTTCCCATTTTACGGATTGAAGACCGAGGT[A/G]TATGGAGGCTAGTGATTGTCCCAAACTCATAAAGT R 2 1 2 1 101000 r 74 goat snp54884-scaffold84-265107 24 4638652 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406950 Affx-122955066 AX-123277301 24 4699093 CCATCTCCACCTCACCACAATGCAGTGTCTAACAC[A/G]TATGAGCAACTCTTCAGGTATCAGGCATCACCCTG R 2 1 2 1 101000 r 74 goat snp54883-scaffold84-222943 24 4681378 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419446 Affx-122945498 AX-123289794 24 4727758 AAGCAGGTTGTTAATTAAACCTGATATTAGTGCCA[C/T]GTTGTAAGGTTGAGAAGAGGGACAGAAACTTCACT Y 2 1 2 1 201000 f 74 goat snp54882-scaffold84-194278 24 4710890 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421906 Affx-122944250 AX-123292253 24 4772083 TTATTATATGTCATGAAAAAATAAAAGGCCATCAT[C/T]AACAATAAAGTCCTCCTTGGTGGTGTTTTTTAACA Y 2 1 2 1 101000 r 74 goat snp54881-scaffold84-149953 24 4756127 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800976 Affx-122919674 AX-385287890 24 4809296 TCTTGTTCATCATCATCATAGAAATACCTTAATAA[C/T]AAGAATTAGTGTCAAATCATACCAAAAATTCATTT Y 2 1 2 1 101000 f 74 goat snp54880-scaffold84-112740 24 4793369 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394821 Affx-122964797 AX-123265176 24 4840003 AAGGAACCAAAGAATCATTCAGAAGTCTAGGCAGA[C/T]AGAGAAACTGTTGAATAAAAAGGGCATACTTCTTA Y 2 1 2 1 201000 r 74 goat snp54879-scaffold84-82033 24 4824131 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415303 Affx-122948817 AX-123285652 24 4935255 ACCAAGGAAGTCATGGGCAATATGTAAAGGAATAA[A/C]GTTTTCCAGTGAAACTTTATTTACAAAAATAACCT M 2 1 2 1 101000 f 74 goat snp59813-scaffold994-13120 24 4916823 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408248 Affx-122953819 AX-123278599 24 4988477 AACATCTGACAATGATTCTTTGAAGACCTAGTAGG[C/T]AAGGACAAGATGAAAAAGTATACATTTGCTTTGGT Y 2 1 2 1 101000 f 74 goat snp59814-scaffold994-66342 24 4971323 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392082 Affx-122966375 AX-123262439 24 5030823 TGAAAACATGCAAAATATATGTAAAATTTACAAAC[A/G]TCTCTGTGATAGAGAAGCACAGTTCTTATTGAACT R 2 1 2 1 103000 r 74 goat snp59815-scaffold994-108688 24 5013863 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417189 Affx-122947318 AX-123287537 24 5062715 GCCTTATCAGCTCTAAAGTTAAATTCTGTATTAGT[A/G]TGTTGAATTAGCTCTTCAACACGGCTTCCAGGTGG R 2 1 2 1 101000 f 74 goat snp59816-scaffold994-140580 24 5045739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778995 Affx-122963331 AX-385266102 24 5092002 CTTTACAACAATGTGCATATAAATTACACTGTACT[A/G]TACACCTATAAATTTGTTGATAGGGTAAATTTTGT R 2 1 2 1 101000 f 74 goat snp59817-scaffold994-169867 24 5075700 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273095 Affx-1111833285 AX-519546761 24 5094488 GGGAAACCCTGAACTACAGAAGTGACATTGATGGG[A/G]AAACAATGAAGGGTATTTGCGAAATTGAACCTTGA R 2 1 2 1 101000 r 74 goat 24_5094488_AF-PAKI 24 5094488 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449524 Affx-122922606 AX-123319859 24 5122809 GACACCTCACTTCACCCAGACGACCGCAAGGATTA[C/T]AGAGTGATTATGATACAGAAGGACTATTCGCAATC Y 2 1 2 1 101000 r 74 goat snp59818-scaffold994-200674 24 5106700 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409054 Affx-122953355 AX-123279405 24 5156302 TTTGTACCGTCAAGAATGCACGGGGGTGAATTATG[C/T]AACAGAATCTAACAGCTAAGGTTTGGTGCCATGGT Y 2 1 2 1 101000 f 74 goat snp59819-scaffold994-234167 24 5140230 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422066 Affx-122943601 AX-123292413 24 5202428 ACTTGATCATTTAAAGAAAGTTTTCCTCTGGGAAC[A/G]TTCAAATATTTTAACTTACCTTATGTAAAGCATTT R 2 1 2 1 201000 r 74 goat snp59820-scaffold994-280293 24 5186568 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384125 Affx-122972820 AX-123254483 24 5239320 TAAGTGTTTCTCATAACTTCTAATTTTTGCAAAAA[C/T]GGAAATGCCAAATTCATCCTGAAATTCTTATATTT Y 2 1 2 1 102000 r 74 goat snp59821-scaffold994-317185 24 5223638 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763910 Affx-986698438 AX-385251697 24 5256952 AGAAATAGACATGAAGTTGTGTCAGGAGAAATGGG[A/C]AGTACAGGGTGTCTCACCTATGGAGGAGGAGTGCC M 2 1 2 1 600010 f 74 goat 24_5256952 24 5256952 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 320767267 Affx-986698440 AX-385254548 24 5257091 AGTACCCAACTATACGAGATTCAGTGGATGAACTT[C/T]ATGGTATATAAATAACTTCTCAATAAAGATATTAA Y 2 1 2 1 600010 r 74 goat 24_5257091 24 5257091 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 320763914 Affx-986698442 AX-385251701 24 5264037 TGTAACTCTTCAGTTTACGTTAGTGACTGTTATCA[A/G]TACTGCTTTTACCCTGACTGACACCAACAGGGAAG R 2 1 2 1 600010 f 74 goat 24_5264037 24 5264037 Ancestral_priority_1043 ancestry 0.738 recommended IMAGE 10K 10K ancestral 320763920 Affx-986698448 AX-385251707 24 5289009 TAGGTCTCTAGTACATAACCATTAATTAACTCAAG[C/T]TAGTGTCAATCTAAGGTGGGGTGATTTCTTAATCT Y 2 1 2 1 600010 f 74 goat 24_5289009 24 5289009 Ancestral_priority_1043 ancestry 0.75 recommended IMAGE 10K 10K ancestral 320763922 Affx-986698450 AX-385251709 24 5289085 ATTTTCTTGGAATACAGAACTCAGGTAAAGTTCAA[C/T]ATGATCAGTAAAAAGTTAATTTTTCTAGAAATATT Y 2 1 2 1 600010 f 74 goat 24_5289085 24 5289085 Ancestral_priority_1043 ancestry 0.69 recommended IMAGE 10K 10K ancestral 320763924 Affx-986698452 AX-385251711 24 5289141 TTTTCTAGAAATATTCTCAGCCATTTTCACTGTTG[A/G]TAGTCATCAGGGGGTCTTTGGATTGAAAAACAGGT R 2 1 2 1 600010 f 74 goat 24_5289141 24 5289141 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 320763926 Affx-986698454 AX-385251713 24 5289248 ATTCTCTCAGAAAAGTTAGAAACTGGTAAGACTGA[A/G]TCCTACATTTCAGATAACAATTTGGGGGAATTCTC R 2 1 2 1 600010 f 74 goat 24_5289248 24 5289248 Ancestral_priority_1043 ancestry 0.714 recommended IMAGE 10K 10K ancestral 320767300 Affx-986698458 AX-385254581 24 5289371 GATTTTTTTAATTCATTTGTTACATTGTAGAAATT[A/C]ATTTGATCCTGAAATAAGTCAATTTATTTTACTGG M 2 1 2 1 600010 r 74 goat 24_5289371 24 5289371 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 320796049 Affx-122937776 AX-385283001 24 5290505 TTTTGGAGCCTAGAGGAGAAGCAATACAGTAGTAT[A/G]TTAAAAAGTAGTTTGTGTTATTTTGCACGGCAAGC R 2 1 2 1 101000 f 74 goat snp35504-scaffold4277-17619 24 5276644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408033 Affx-122954291 AX-123278384 24 5319271 GAGAGCTTGCCTGCCAATGCAGGAGACATAAGAAA[C/T]GTGGATTTGATCCTTGGGTTGGTACTTAGCATGCA Y 2 1 2 1 303000 f 74 goat snp9688-scaffold1349-11048 24 5288912 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784792 Affx-122947164 AX-385271839 24 5365574 TCACTTTTCAGCCTTCAGAAGCAGTGTCTAGTTTA[A/G]AGACTAGCACACTTTCACGCTTTTGACATCCCTCA R 2 1 2 1 101000 f 74 goat snp9689-scaffold1349-57351 24 5336347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396271 Affx-122963310 AX-123266626 24 5401933 ATCATTTTCTGGAGGCTATTGCAGAGAAAAACCAG[A/C]TCACAGAGCTTAGTCAGCTTGTTACTGGTTCCACT M 2 1 2 1 101000 f 74 goat snp9690-scaffold1349-93710 24 5372751 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438536 Affx-122931192 AX-123308874 24 5434046 CTGATCCTGCAGTTATATTCACCTTGTGAGGTGCC[A/G]TGAAATAAGGAAATTTCTTAATATGCTCTGCTCGC R 2 1 2 1 101000 f 74 goat snp9691-scaffold1349-125823 24 5406202 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771612 Affx-122936604 AX-385258770 24 5487916 ACAGGGAAAAACCTGTAAAAACCACAAATACATGG[C/T]GGCTAACCATGTTCATTTTCAAAAGCAGTTAGGAA Y 2 1 2 1 201000 r 74 goat snp9692-scaffold1349-179693 24 5460141 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783894 Affx-122949774 AX-385270949 24 5524563 TTAGAAACTGTACTACAGACCCTACAAAATAATGA[C/T]GCTAAACTCACAAATACCCTCACCAATACCTACAT Y 2 1 2 1 101000 r 74 goat snp9693-scaffold1349-216340 24 5497541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385103 Affx-122971789 AX-123255461 24 5587685 TGACTCTGGCTTGGCAGGCAGATTCTTTACCACTG[C/T]GCCACCTGGGAAGGTGTGAGGTCATGAATGCTAAT Y 2 1 2 1 103000 r 74 goat snp9694-scaffold1349-279462 24 5558357 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430120 Affx-122937409 AX-123300461 24 5627595 TTGGAAAAAATTCATGTCTACCCTCTGAAATAAAT[A/G]CAATAAAAAATAAATGTGTTAACTGTATTTCATAT R 2 1 2 1 103000 f 74 goat snp9695-scaffold1349-319372 24 5598275 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423787 Affx-122942825 AX-123294133 24 5681552 GCCTTCTGGCTACTGTGAATAATGCTGATATGAAT[A/C]TGGGCGTAGAAATACATGTTCCCGTCCCAAGAGCT M 2 1 2 1 101000 r 74 goat snp9696-scaffold1349-373329 24 5652392 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393839 Affx-122965158 AX-123264194 24 5720767 CTGAAGCGATTTAGCACAACACACACATACATATA[C/T]ACCCAGAAAAGACATAAGAAAATACTTATCCTCAA Y 2 1 2 1 103000 f 74 goat snp9697-scaffold1349-412544 24 5692220 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447342 Affx-122924885 AX-123317678 24 5749814 GGTTTACAGTTCCCATAATTCTGGAATGATCTGTC[A/G]TCATCTACCCAAAATTCTGCCCCACCATCACCTCT R 2 1 2 1 101000 r 74 goat snp9698-scaffold1349-441591 24 5721635 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443455 Affx-122927832 AX-123313792 24 5803577 TAAACCCTTCATAGTTCTTGACAGTTAGAAATGGA[C/T]GTAAAACCAAATCTACCACTTCAGTGAATTTTGCA Y 2 1 2 1 101000 r 74 goat snp9699-scaffold1349-495354 24 5776083 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766372 Affx-122923399 AX-385253751 24 5835473 TAAATGAAGAGTGTTGGAAACCAAAGTCAGGGAGA[A/C]TCACTGAAGAACGGAAAGATGACAACTTAACTCGG M 2 1 2 1 101000 f 74 goat snp9700-scaffold1349-527250 24 5808247 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411943 Affx-122951149 AX-123282293 24 5875268 TAACTGGCTGTCACTGGAAAGAAACTCTTATTAAA[C/T]GATCCCTTTAAAACATTAAATTGAAGACATGCTGA Y 2 1 2 1 101000 f 74 goat snp9701-scaffold1349-567045 24 5848012 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400503 Affx-122961279 AX-123270858 24 5905754 CAAAAAAAGGCTAAAATGCATTCTCCCATCTTTTC[A/G]TTTGTTTCATTTTACTTCTCAATCTTGAGAAACTT R 2 1 2 1 101000 f 74 goat snp9702-scaffold1349-597531 24 5878180 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414260 Affx-122949616 AX-123284609 24 5952658 CTTCCTAAGGAAAGCAAGTAAATGAAAATTCAATT[A/G]CATTCTTTCAACAAGGCATTTCTCCTGCTACTTCC R 2 1 2 1 101000 r 74 goat snp9703-scaffold1349-644435 24 5925349 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432510 Affx-122935573 AX-123302851 24 5982173 ATAGACTGTCCCCCTGGCCTAACCCAGGCAGCCTC[A/G]TCTTGGACCATTTCCCCATGCTCAGGCAGGTGTGT R 2 1 2 1 101000 r 74 goat snp9704-scaffold1349-673950 24 5954644 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400717 Affx-122959920 AX-123271072 24 6065161 CCTAAAAGAAGCCACGTACTAACTAGACTCTTGGC[A/G]CTTGGTCATCACATCTGGAGAAGTGGCTTAAGTCA R 2 1 2 1 101000 f 74 goat snp852-scaffold1022-992922 24 6097962 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775815 Affx-122951446 AX-385262946 24 6113982 GCCATTGGGTATTAGACAAGATTTTTGAAACATTT[A/G]TTCAAGTTTCCTAATGATGTGTGCAGTGTTATCTA R 2 1 2 1 101000 f 74 goat snp851-scaffold1022-944101 24 6147821 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384069 Affx-122972865 AX-123254427 24 6183170 CACCATAATGACTTATGTAAATTCATTGTATTTCT[A/G]TTTCACAGTATTTAAATTTTTTCAGGTGCAACCAC R 2 1 2 1 303000 f 74 goat snp850-scaffold1022-874913 24 6218061 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411112 Affx-122951910 AX-123281462 24 6226786 TTATTCACTAGATTATTTTGAAAGTCAAGTAAATC[A/G]TTTCACAATTTAGAAATGTTTTCTTTTGCATTGCC R 2 1 2 1 103000 r 74 goat snp849-scaffold1022-831297 24 6262672 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393496 Affx-122965818 AX-123263852 24 6280747 TAACATATGAAAATATTTGCTAATAGAGCCTATTG[C/T]GTTCAACAAAATTAGCATAATTATTCTCTAAAAGA Y 2 1 2 1 101000 r 74 goat snp848-scaffold1022-777336 24 6317251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410961 Affx-122952026 AX-123281311 24 6323375 CCATACATATGTAGTACAAACATGTCATTTATGCC[A/G]TCAGCTTGCTCTGTTATTAAGAAAATATGTTATTA R 2 1 2 1 101000 f 74 goat snp847-scaffold1022-734708 24 6359488 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796485 Affx-122964535 AX-385283435 24 6370319 GGAAATGCAACTGACCCAATTAGGAACAACACACC[A/G]TAACATCACATTGTTTAATACCAGTAAAAACATAT R 2 1 2 1 101000 f 74 goat snp846-scaffold1022-687764 24 6407033 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798720 Affx-122977944 AX-385285651 24 6401255 TGTGGAAAAACAGATTTTCTTTTAAGTACTGCCAA[C/T]AATCACTCTAAAGGACCATTAACATTCCTCTGACA Y 2 1 2 1 102000 f 74 goat snp845-scaffold1022-656828 24 6438098 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273551 Affx-1111833685 AX-519547166 24 6424296 CAGCCTTCCACCGGCAGCTTTGTGGGTGGGTGCCT[A/G]ACCCAACCCGAATGCTGGCTTCCCGTTCTTCTTAC R 2 1 2 1 202000 f 74 goat GoatD01.001456 24 6424296 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38447576 Affx-122924024 AX-123317912 24 6432860 GTGCACAGAAAGCCTCCAGCACATCATTTGCCTCA[C/T]AAATAGACTTGCTCAATAAGATACATTATTTTTTT Y 2 1 2 1 201000 r 74 goat snp844-scaffold1022-625223 24 6470011 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395294 Affx-122964071 AX-123265649 24 6466680 TTGTCCCACATGGAGACCACTTGAAGGCCATTATA[C/T]GAAGAAACAGTGGAATGAGAAGCTAAAACCTCAAG Y 2 1 2 1 201000 f 74 goat snp843-scaffold1022-591403 24 6504213 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770156 Affx-122961120 AX-385257323 24 6497229 GCCTCCCCAACTAATAAGGTTGATAACATGTTCAG[A/C]TGTCATTAACCATGTAGAGTCCCTCTTCCTGATTG M 2 1 2 1 101000 f 74 goat snp842-scaffold1022-560854 24 6535081 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790702 Affx-122930258 AX-385277703 24 6531365 AATACTGCATTTCCAGGATGTATGTTTAAGTCTTA[A/G]GAATGTGCACTAGCCTCATGAATTTTTGTGCATGG R 2 1 2 1 101000 r 74 goat snp841-scaffold1022-526718 24 6569009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440776 Affx-122929850 AX-123311113 24 6566787 ATTCTCCGACCCCTAGATTACAATCTATTCTGATA[A/G]AAATGGGCAAAGAGTCCTTGGATGTGTTTCCATGT R 2 1 2 1 102000 f 74 goat snp840-scaffold1022-491296 24 6602974 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408805 Affx-122954042 AX-123279156 24 6598893 ACTCTTAAGTTTCCCCAAATGTAAGCACCATGGGT[A/G]TTTTAGCATACTGGGCTTTGGCTAGGAACCGTGAC R 2 1 2 1 101000 r 74 goat snp839-scaffold1022-459190 24 6637532 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394612 Affx-122964416 AX-123264967 24 6641530 GTTTATGTCTTCATTTATATCTGACTTGATTATTT[C/T]TTTATCACTTTTTCAGTGAATAAACATATTGGTTC Y 2 1 2 1 201000 r 74 goat snp838-scaffold1022-416553 24 6680447 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400525 Affx-122960450 AX-123270880 24 6672995 TGGTGCTCATCATGGTCAATAGAGCCCCTTCACTC[A/G]CAGAAGCGGTCCTGCTTGGACCGTGTATCATACGT R 2 1 2 1 101000 f 74 goat snp837-scaffold1022-385088 24 6712082 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451781 Affx-122921505 AX-123322114 24 6719050 TGTCCTGGGTTGAATTTTCCTGAAGCCTCATGCCT[A/G]TTGAGTAACCACCTCAACCAGCCTTGGAGAAGTGA R 2 1 2 1 101000 f 74 goat snp836-scaffold1022-339033 24 6758676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385792 Affx-122971043 AX-123256150 24 6755556 GTGTACCAGGTGGAGCATTTCTGGGACTCTCGAAG[C/T]AGGAGAGTCTCTGACTCACAACCTGGGAGTGTCAC Y 2 1 2 1 102000 f 74 goat snp835-scaffold1022-302527 24 6795021 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776915 Affx-122926092 AX-385264039 24 6796728 TGTAGAAAAATATGGCTATCTAGCAAACTTTGAAA[G/T]AGCCCAAAGTGTAGGGCAGCACAGAAATACTTACT K 2 1 2 1 101000 r 74 goat snp834-scaffold1022-261355 24 6836509 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380080 Affx-122975549 AX-123250438 24 6898705 CCTGTAAGTTGATCTCTGAAGAGATGTGTGAGTCA[C/T]GTGCACACTCTCTAGCTTTCCATCTTACTTGCCAA Y 2 1 2 1 101000 f 74 goat snp831-scaffold1022-159378 24 6939548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417941 Affx-122946710 AX-123288289 24 6932924 TTAAATGAAAAAATTAAATTCTGTCCTGATGATTT[A/G]CCAGTGAGCTTCCCCACAATGTCAAGTTAGCCAGG R 2 1 2 1 101000 r 74 goat snp830-scaffold1022-125159 24 6973643 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416247 Affx-122948207 AX-123286596 24 6979067 AAGGCATCTTCTTCCCCCAGTTTAAGTCCCAGCCG[A/G]AAGACACAGATGGGGTTGGCGTGACTCCAGCTGTA R 2 1 2 1 101000 r 74 goat snp829-scaffold1022-79016 24 7019621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447329 Affx-122924893 AX-123317665 24 7010352 ATTGATCAAAGAACTGGAATAATTGAGTAAATGCA[C/T]AGGACAACACAAAAAACAGGCTGCTGGGTATTGCT Y 2 1 2 1 201000 f 74 goat snp828-scaffold1022-47731 24 7049317 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384648 Affx-122972149 AX-123255006 24 7056817 TCTCCTTCTGTCTCTTATACATACGCACACACACA[C/T]ACCCCTCCTTCTTTTGTTTAAGAAGGAAATGGCAA Y 2 1 2 1 103000 r 74 goat snp827-scaffold1022-1266 24 7097229 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767303 Affx-122921337 AX-385254584 24 7063423 TTGATTTTAACCATTTATAAATATTCTATAATTTT[A/G]CTTAGTGTTTTTACATCAAGCAAATACAAATATCT R 2 1 2 1 303000 f 74 goat snp27537-scaffold294-67724 24 7103955 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450922 Affx-122921779 AX-123321256 24 7129041 CCTAAAGTTGTTGTTGTATTATTCATACTGTTATC[A/G]CTATTATTTTAGTGGTTAAGAGCTCATATTTTGGA R 2 1 2 1 101000 f 74 goat snp27536-scaffold294-2106 24 7169392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381668 Affx-122974739 AX-123252026 24 7132730 TTTCAATCAGTAGCTAGATTCTGCTCAGTGGGAAT[A/G]TGCTGACTGTGAAGGAATGGTGCCTACCTCCCAAA R 2 1 2 1 101000 f 74 goat snp19300-scaffold1948-1484 24 7172688 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389922 Affx-122968104 AX-123260279 24 7172464 TCGGCCTCACTGCAAAGCTCAAAGGATCATAGTTC[A/C]CCGACCAGGGATCGAACCCGTGCCCCCTGCAGTGG M 2 1 2 1 103000 f 74 goat snp19301-scaffold1948-41218 24 7212997 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377590 Affx-122978314 AX-123247949 24 7228140 CTGCCCACTGTATGCCAGGCATCATGTCCCTTTTC[A/G]TTGAGAATATATGCTGGAAAGGCAAATTCATTTGA R 2 1 2 1 201000 r 74 goat snp19302-scaffold1948-96894 24 7268820 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409968 Affx-122954104 AX-123280318 24 7262980 AACAATGGTACTTCCAAAGAACACATAAGTGCTGC[A/G]TTTTGAATTTCTGCAAAAATTTGCATTTACATAGT R 2 1 2 1 201000 r 74 goat snp19303-scaffold1948-131734 24 7303822 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790415 Affx-122939717 AX-385277418 24 7303855 GTTCAGTTTATATTGATTTACTTAAATTGAATGGA[C/T]GGATGGATATGGAAAATACTTTATTAGTAAAAGCT Y 2 1 2 1 201000 r 74 goat snp19304-scaffold1948-172609 24 7344407 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391272 Affx-122967358 AX-123261629 24 7378751 AAGGCTGAGAAATCTCACTCCTTAATGAAATAAAA[C/T]AGCAGATAGAGAGACAGACGATAAAGAGCATCTTA Y 2 1 2 1 201000 f 74 goat snp19306-scaffold1948-247505 24 7420647 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433753 Affx-122934499 AX-123304094 24 7444675 CTTAGGACTCATGCACTGAGGCCACATCCTTTAAA[C/T]GCTGGTCTTAAAGGTAGAGGAGGAGCAGGGGCTGT Y 2 1 2 1 201000 f 74 goat snp19307-scaffold1948-313429 24 7487167 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424071 Affx-122942051 AX-123294417 24 7485815 CGATATTGCAGTGATTTCTCTAGTTGCTTTGAAAA[C/T]AGCCAGATAAATAGAGAATAGGAGATCTGTGATTC Y 2 1 2 1 201000 r 74 goat snp19308-scaffold1948-354569 24 7528483 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770473 Affx-122966828 AX-385257639 24 7506820 TGCTATTATTAAACATATGCACTCTATCTGTATAC[A/G]TATCTAATAGGCTTGCCTTAACACAAAAAGTTTTG R 2 1 2 1 101000 r 74 goat snp6572-scaffold1232-1400614 24 7557806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780452 Affx-122953028 AX-385267543 24 7551127 GTTGCTTAAATGTGTGATTTATGATGGCAAATGGT[A/G]TGTTACAACCAAAATATAGGAATATCTGCTTGTGA R 2 1 2 1 101000 f 74 goat snp6571-scaffold1232-1356307 24 7602731 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399095 Affx-122960872 AX-123269450 24 7590442 TTGGTGGTATTTATGTACTTTATCATCTGACTTGC[A/G]TTTTTAAGCATAGTAGCTACTGGCTTCACAAGATG R 2 1 2 1 101000 r 74 goat snp6570-scaffold1232-1316992 24 7642477 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382576 Affx-122973758 AX-123252934 24 7626050 GTAAACCCTTTAGGATGCAACTTGAATGTGGGCTA[C/T]ACCCCTTAAATAGATCAGGTTCCTTAGTCACTTCT Y 2 1 2 1 101000 r 74 goat snp6569-scaffold1232-1281384 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781610 Affx-122943526 AX-385268694 24 7658391 ATTAAGAAGCTAAATCTTAGTTCCTTCATAGTTAA[C/T]GATATTGTTATATGAATGTACAAACAGAGAAATGA Y 2 1 2 1 101000 r 74 goat snp6568-scaffold1232-1249043 24 7704068 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273050 Affx-1111833287 AX-519546721 24 7681209 TAACTGTACTTTCCCCAGAATTCTAAAAAGAAGTG[A/G]TGGGAAGACACTCAGGAGTGGCCATCCGTCTATGA R 2 1 2 1 202000 f 74 goat 24_7681209_AF-PAKI 24 7681209 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38386414 Affx-122970817 AX-123256772 24 7733051 TGAATGAAGATAGACCTATTCGAAGTTCTACGTGA[C/T]GCAAGAAAAGCAATGCTCGTTTTGGGACCAGTCTT Y 2 1 2 1 101000 f 74 goat snp6567-scaffold1232-1174383 24 7779427 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790195 Affx-122927210 AX-385277199 24 7764478 TGTCTTGAATCTGAATCTAGCAAAACTGAAGAGGC[A/G]CTAAGTAAGACAGTAAGAACTAGTTTGCAAGTTCT R 2 1 2 1 101000 f 74 goat snp6566-scaffold1232-1142956 24 7811889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799009 Affx-122952143 AX-385285939 24 7818015 ATCTTGCTTCCCAAGTTTAAGAGTTTGAACTTGCC[A/G]TTTAATTACAAATATACTTGTCAAATAGAGTGGAG R 2 1 2 1 102000 f 74 goat snp6565-scaffold1232-1089419 24 7866586 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404380 Affx-122956801 AX-123274732 24 7868614 TACACATTCAACAAATGGTTAAATAATTATGCAGC[A/G]TCTACTGTTTGTCAGCTTGTGTACACTGGTTGTGT R 2 1 2 1 101000 r 74 goat snp6564-scaffold1232-1038820 24 7918282 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426108 Affx-122940636 AX-123296454 24 7911275 ATGTGTGATCCTATACATCATAATTTAAACTCAGC[A/G]TTTCTATTCCTTCTTTAAAATAGGAATAATAGTAT R 2 1 2 1 303000 f 74 goat snp6563-scaffold1232-996159 24 7961198 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405894 Affx-122955593 AX-123276246 24 7963664 GTAGTGGAACAAAGAGATGATTAGGGAAGTAACTG[C/T]AATATTAAGCAACATTTCCTCCATATAATCACCAG Y 2 1 2 1 101000 f 74 goat snp6562-scaffold1232-943770 24 8013729 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774396 Affx-122962445 AX-385261532 24 8026402 AGAATCTCAAATGCAAAAAGAGGAAAATTATAGGC[A/G]TACTCTAGAAAGTTTAATATCAAAAGTACTTTACT R 2 1 2 1 103000 f 74 goat snp6561-scaffold1232-881032 24 8076579 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384759 Affx-122972028 AX-123255117 24 8078420 AACTTGACAATTGTGTGCTGGCACCGCAGCATCTC[A/G]TCTTGGTAGCCATGACTGTGGCAATATTTCATTGT R 2 1 2 1 201000 r 74 goat snp6560-scaffold1232-829014 24 8130089 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449587 Affx-122923219 AX-123319922 24 8117696 TTAAAAATGCAGGATGTGAGTTCTGCGTGAACCCT[C/T]GGGTTGTGTGCTTAGTCGATCAGTCGAGTCCGACT Y 2 1 2 1 101000 f 74 goat snp6559-scaffold1232-789738 24 8170856 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780214 Affx-122944127 AX-385267310 24 8169179 AGTCTGTGCCTGACTGTCCCATGTTTGAAATAAAT[A/G]CTAAATATGGCCTATCTCAAACAGTTGGAAACATG R 2 1 2 1 101000 f 74 goat snp6558-scaffold1232-738255 24 8222966 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780006 Affx-122952809 AX-385267106 24 8255666 AACAAAAAAAGGCAAAATTTCACTTGGAGAAAACC[A/G]CTTTTATCTTGGTTCCTTTACTTCCTGTTTGCTTC R 2 1 2 1 101000 f 74 goat snp6556-scaffold1232-651768 24 8309168 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401869 Affx-122958862 AX-123272222 24 8316530 ATGAATATAAAAGTTAGCCACCTAGTTTATTTGAC[A/C]TGACTTTGTTTTGCGGCCTGGCAAAGTATTTTATA M 2 1 2 1 101000 r 74 goat snp6554-scaffold1232-590904 24 8370780 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771665 Affx-122969774 AX-385258823 24 8357878 CTACGACAACAGTAATAAGACTTAAGAGTAAATGC[A/G]CTGAGAAATTCTATTGGCAAGTGAATCGGTGAGTG R 2 1 2 1 101000 r 74 goat snp6553-scaffold1232-549556 24 8411791 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787945 Affx-122966225 AX-385274966 24 8389911 GTTTATACAAAAGCCACAAAATCCCAAAGAACAAA[A/G]CTGATTTTGTCAGCTCTTTCATCGTGGGAAAGACT R 2 1 2 1 101000 r 74 goat snp6552-scaffold1232-517523 24 8443642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277547 Affx-1111835968 AX-519551047 24 8428927 GAACTTTCTATTACACCAAACTACAAAAGTCGCGC[A/G]TCAGAGATCCTGTATTGCTATGGTTCCCAAAATAT R 2 1 2 1 101000 f 74 goat Random2.2K-2083 24 8428927 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380043 Affx-122975577 AX-123250401 24 8430799 CATTTACAGCTTTCTGTTACAAGTAATGCAGAAAG[C/T]GATATTGGCTGCTAAGTTCTGTAACCTTGTGGATG Y 2 1 2 1 101000 r 74 goat snp6551-scaffold1232-476635 24 8484920 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801272 Affx-122954496 AX-385288184 24 8491053 AGATAGTCTCATAGAATTCGTCATACTCCAAGGGC[A/G]TGTGCTCAAAGTAGCCGAGAAGTTCCTAAGCCCCA R 2 1 2 1 101000 f 74 goat snp6550-scaffold1232-416381 24 8545841 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453812 Affx-122919563 AX-123324145 24 8525038 AGTCACATTTAAAACAGGGAAGGGATGGTCGATCT[A/G]TACAAAAAATTTAAATACTCACATCTACAAGCCAA R 2 1 2 1 101000 f 74 goat snp6549-scaffold1232-382396 24 8580058 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793290 Affx-122921179 AX-385280268 24 8558595 ATATTCCCCCTACTAACATGATCACAGTAAGATTC[A/G]TCACTGAACTAGGATGTCCAGTGTATCTATGTTCT R 2 1 2 1 102000 f 74 goat snp6548-scaffold1232-348839 24 8612840 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389431 Affx-122968359 AX-123259789 24 8588156 AGAGGATAAGACCAGTTATGCGCTTCCCAGATGGC[A/G]CTATTGGTAAAGAATCTGCCTGCCAGCACAGGAGA R 2 1 2 1 101000 f 74 goat snp6547-scaffold1232-319278 24 8643365 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774930 Affx-122969548 AX-385262063 24 8626877 AGAAAGCAGGGGGTTAGAGACAAATACTGTGCACT[A/G]TATGGTAGTCAGTTTGAAAATTGAGGAAAAAATAT R 2 1 2 1 102000 f 74 goat snp6546-scaffold1232-280557 24 8682457 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786774 Affx-122927377 AX-385273805 24 8663609 AAAGCAAGCCAAGAAATATGTATAATTGATATTAG[C/T]GAGAAAGTTTCTAATTAACTTCGCAGCAAGGCACA Y 2 1 2 1 201000 f 74 goat snp6545-scaffold1232-243825 24 8719120 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422843 Affx-122943102 AX-123293189 24 8700694 CCGACAGTGTCAAACCATCCTCCAGTTCTCCAAGA[C/T]ACATAGAAGTCGGACGGGAAGCCCTTGCCAGACAA Y 2 1 2 1 101000 f 74 goat snp6544-scaffold1232-206740 24 8756625 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451382 Affx-122921212 AX-123321715 24 8742289 ATAATGGCCAACCAGAAGCTAGGAGCATGGAACAT[C/T]CTTCCCTAAGCCTTCGGAGTAACAGGGCCCTACCC Y 2 1 2 1 101000 f 74 goat snp6543-scaffold1232-165145 24 8798910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780575 Affx-122968313 AX-385267666 24 8823189 ATGAATTCACCCAATAGTCATTAGTTTTATTATCC[A/G]TTCAAAGGAGGAGGTACCCAAGTGATCCCTAAGAT R 2 1 2 1 101000 r 74 goat snp6541-scaffold1232-84245 24 8881105 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802471 Affx-122953411 AX-385289375 24 8869437 AGTCCTGGGTTAACTTATAAATTTTTATGGACTGG[C/T]ATTACATTGTCTTAAACTGCACATCAGAAAGGTTC Y 2 1 2 1 101000 f 74 goat snp6540-scaffold1232-37997 24 8927260 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792681 Affx-122924962 AX-385279661 24 8906705 AATTTAATTTTGCATGTTGGTCTGGTATATTTAGA[A/C]GCACAACTTAATTTGCTTAATATTTCAAGAGCTTG M 2 1 2 1 101000 r 74 goat snp6539-scaffold1232-729 24 8964225 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454130 Affx-122919341 AX-123324463 24 8913378 AGAAAGGGCCACAGATGCTAGCACAGCCAAGCAGT[C/T]AGAGTGGAGGCAAAGGGTGTTCATGTGTGAGCAGA Y 2 1 2 1 201000 r 74 goat snp22740-scaffold2267-5845 24 8987876 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773456 Affx-122962029 AX-385260598 24 8948418 AATGAAGAACATGGGCAACCCTAAATTAAAAGAGA[A/C]ATGAGCCCATCCCTCTATTCCGTTATTCTTCCTGT M 2 1 2 1 101000 r 74 goat snp22741-scaffold2267-40885 24 9023452 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789070 Affx-122930244 AX-385276083 24 9001508 TACAGCATTTTTTATGCAATAGTTTCTTTGCTCAT[A/G]CATTCAAAACAAACCCCCTCAAACTACAGAATGTG R 2 1 2 1 101000 r 74 goat snp22742-scaffold2267-93975 24 9077232 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423262 Affx-122942667 AX-123293608 24 9078000 CAATTGAATTCGTGTATTTGGTTAAGGAATTTGGA[C/T]GGGATTTTTCAGGAACAACTTTCAATTTAAATACA Y 2 1 2 1 101000 r 74 goat snp22744-scaffold2267-170467 24 9154406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454083 Affx-122919374 AX-123324416 24 9115929 ATTTGAGAATCTTCATGTTTGGGTTTGTTTTGTTC[A/G]CCTGCTTTCCTAGTAATAGGGTCCCTTGGCTTCGA R 2 1 2 1 101000 r 74 goat snp22745-scaffold2267-208396 24 9193289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793146 Affx-122954365 AX-385280124 24 9175615 CATTTGATAGGAATACTCCCAATATTTCTACAGAG[C/T]TGTACTCCAGAAAATATTTTTCCACTGAAAATCAG Y 2 1 2 1 201000 r 74 goat snp22746-scaffold2267-268082 24 9254059 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392202 Affx-122966283 AX-123262559 24 9214436 ACCTCCTGCATTGCAGACAGATTCTTTGCCACTGT[A/G]CCACCAGGGAAGCCTTTTCTTACAGGAAAAGACAT R 2 1 2 1 103000 f 74 goat snp22747-scaffold2267-306903 24 9291586 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793115 Affx-122962751 AX-385280093 24 9247694 CAAGGAAAACTGGCCCACATTCTGGGTCATTACCT[A/G]TCGATTCAGTAACTCGAGTCAATATTTTATATCTG R 2 1 2 1 101000 f 74 goat snp27765-scaffold2969-28258 24 9324591 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793484 Affx-122923078 AX-385280461 24 9278550 GGGGTGTTATAAAAATGAACTCAAATGAAGACTGG[A/C]TACACTGAGTAATAGTCATTTCTTTTCATTGAACT M 2 1 2 1 101000 f 74 goat snp27766-scaffold2969-59114 24 9354691 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400068 Affx-122960760 AX-123270423 24 9307516 TTGTCCCTGGCTGACCCACAGGAAGTCATGAGTTG[C/T]AAGTCGTAAGGTGCTAATATTCTGTCAACATCAGA Y 2 1 2 1 101000 r 74 goat snp27767-scaffold2969-88080 24 9383327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432587 Affx-122935514 AX-123302928 24 9337594 AATAAGGCAGTGAGCTTTCACAATGTAGAGGAAAA[C/T]GAGGTGCATATTAATCAAACTTTTAGAAAGTCCCA Y 2 1 2 1 101000 f 74 goat snp27768-scaffold2969-118158 24 9412967 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786166 Affx-122941918 AX-385273202 24 9372590 TTCATTTTAAATAAATCAATGTCCAATTAACTAAA[C/T]ATGCCAGGTATATTTATGCATCAATATTGCTTTCC Y 2 1 2 1 101000 r 74 goat snp27769-scaffold2969-153154 24 9448596 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453725 Affx-122919627 AX-123324058 24 9418172 GAATATTCACATCTAATCTTCACTCAGAGGTAACG[C/T]GGCCTTAGATTCTGGAAAGAGGTTTATTTCTCTTC Y 2 1 2 1 101000 f 74 goat snp27770-scaffold2969-198736 24 9494284 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782090 Affx-122960192 AX-385269168 24 9472669 CAAGTATTTCTTGAGCCATGACAAACTGGCAGGCC[G/T]TATGCAGTGCACATGTACATGGTCCTAACCTGAAT K 2 1 2 1 101000 f 74 goat snp27771-scaffold2969-253233 24 9548824 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399782 Affx-122960296 AX-123270137 24 9521884 CCCCCTGTCCTGATGATTAATTTTGTGTCAAAGCC[C/T]GAGACCACCTTAGAATCAGATTTATCCTTGTGGAA Y 2 1 2 1 101000 f 74 goat snp27772-scaffold2969-302448 24 9598233 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395852 Affx-122964014 AX-123266207 24 9578464 TTACAGGCAAGAACGTGTATAAGGGACTATGAGGA[C/T]GATCGTGATTGTCTGGAAGAACTGTGATGTCCGTC Y 2 1 2 1 101000 f 74 goat snp27773-scaffold2969-359028 24 9655259 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449898 Affx-122922337 AX-123320233 24 9613481 GTATCATTTATTAACAATTATATAGAGAGTATACA[G/T]ATTTCCCCTAGTCTGACCATATGCAACCTTTCTAA K 2 1 2 1 101000 r 74 goat snp27774-scaffold2969-394045 24 9689503 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397458 Affx-122962101 AX-123267813 24 9645508 AAGTGTGGTCAGGGTTTAAACTCCTGAAGGATAAA[A/G]CATTTCCTCCATCTTGCAGTCCTGGCAGTTTCAGA R 2 1 2 1 201000 f 74 goat snp46745-scaffold651-318660 24 9722114 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426658 Affx-122939932 AX-123297004 24 9688897 TCTTAATCCCTGTATGGATATCAGATAATAATACC[A/G]CTTAAGTACCCTACATTTATATTTAAAATATGATG R 2 1 2 1 101000 f 74 goat snp46744-scaffold651-275271 24 9766245 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410244 Affx-122952542 AX-123280594 24 9726770 CTCATGGCTGTCCTGTTGCTTGGAGCTCACCTTCT[A/G]TGGTTAGGCTCCCAGTTAGACAGCTACACAGGAAC R 2 1 2 1 101000 r 74 goat snp46743-scaffold651-237398 24 9804779 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798214 Affx-122940329 AX-385285149 24 9817104 AATAAAAATGAAACAGTTGACAACATCAGAAAATA[G/T]CACCTGCTTTCTCAGCTGTGTTTTAACACTGGCAT K 2 1 2 1 101000 r 74 goat snp46741-scaffold651-147064 24 9900092 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441003 Affx-122928961 AX-123311340 24 9851374 ATATGTATTCTTCAATATAAAACCAGCCCACCATG[C/T]AGGAGAAATTGACCATGGAAAGCTCAATTATGATC Y 2 1 2 1 101000 f 74 goat snp46740-scaffold651-112794 24 9932884 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378366 Affx-122976821 AX-123248725 24 9883500 TAACACTAGGTGATAGATAAATATTAATTTTTCAA[G/T]AATGTTAGCAGAAGTACATCCAAATACTGCTGCTT K 2 1 2 1 101000 r 74 goat snp46739-scaffold651-80668 24 9963639 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780858 Affx-122942456 AX-385267946 24 9912177 ATCCTTATGGTTGCTATATTTATCTAACAAAATAG[C/T]ATGCCTGCAGCCATACCAGGAAATAATGAATATCA Y 2 1 2 1 101000 r 74 goat snp46738-scaffold651-51991 24 9992624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784695 Affx-122939130 AX-385271743 24 9991966 TGCTGTTATCAAATGTCAGATTTAACAAAGGAAAC[A/G]TAGATGCTTGGGAGGATTTTCCCGATTTCTGTCTT R 2 1 2 1 101000 r 74 goat snp48323-scaffold685-771019 24 10079062 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791357 Affx-122937619 AX-385278350 24 10032078 GATAAGGGGCACTCATCCAAGGGCAAAATCTCACA[A/G]TAAAATGTTGCTAAACTTTGAGATTTGACTGACAC R 2 1 2 1 101000 f 74 goat snp48322-scaffold685-730907 24 10119186 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396538 Affx-122962946 AX-123266893 24 10105861 GGAGATATCCTTCTGAGTATTTTGATGGTTAATTC[A/G]TGTTTCTTCCACTCCTCAAGTCATTAACTAAGACA R 2 1 2 1 101000 r 74 goat snp48320-scaffold685-657124 24 10191949 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435942 Affx-122933541 AX-123306281 24 10136396 TACCAAAATTATTCTAATTTTTTATTTTGTTCTCT[A/G]TGAGTTATTCATTTTTCCACTTTGACTGCAATTTC R 2 1 2 1 101000 r 74 goat snp48319-scaffold685-626589 24 10222566 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774346 Affx-122937471 AX-385261482 24 10182646 TGATACTCTGTAAATGTCCTCACTTGAGAGTGATA[C/T]GACTCATAGGTATGGTTATAAATACAAAGACTGCC Y 2 1 2 1 101000 f 74 goat snp48318-scaffold685-580339 24 10268683 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784752 Affx-122921681 AX-385271800 24 10234688 TCCAGTCTCAGAGACCATTGTAATTGTTCACAAGG[C/T]ATCTTCCCTTTCACCCTGTTTCTAAGAAAAGCCTG Y 2 1 2 1 101000 f 74 goat snp48317-scaffold685-528297 24 10321643 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383434 Affx-122973472 AX-123253792 24 10269608 TCTCGATCAAGTGGGTTCGTTGTGAAGATTGTGCC[A/G]TTGTCATCAACACTGAACACTTCACTTCTGGTAAT R 2 1 2 1 101000 f 74 goat snp48316-scaffold685-493377 24 10356803 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421082 Affx-122944233 AX-123291429 24 10298663 AAATGTTTGGAGAAAGGTTGCTTCAGGCCTTGAGC[A/G]TGACATTGGAAGAGTGGAGAGCATACAGAAACAAG R 2 1 2 1 201000 r 74 goat snp48315-scaffold685-464322 24 10384716 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273061 Affx-1111833268 AX-519546732 24 10313270 TCTACAGAAAAATGCAATTTAGGTTCCCCCGCCCT[A/C]ATACTGCAATGCAACCAATCTATCAAGATCAAAAG M 2 1 2 1 201000 r 74 goat 24_10313270_AF-PAKI 24 10313270 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38432545 Affx-122935546 AX-123302886 24 10335755 ATTTTTATTATGAGATCCTAGCCCCACAATAAGTT[A/G]TAATTAATTCATGATTATATTTAGTGGAATATCCA R 2 1 2 1 202000 r 74 goat snp48314-scaffold685-427230 24 10422566 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430894 Affx-122936871 AX-123301235 24 10378183 TGTTTGCTTCCAGATGGTTCCATGTGCCACATCTT[A/G]TTTTCTGGCATCTCCAGATTGTTGAATGCTGTCTT R 2 1 2 1 201000 r 74 goat snp48313-scaffold685-384802 24 10464481 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797633 Affx-122932412 AX-385284572 24 10423645 CATGTTATTCCTCGTACTGAATTTTAGATATTTTT[A/C]TTTGTATTAAATGCTAGTGATTGCTCTAAACAAGC M 2 1 2 1 303000 f 74 goat snp48312-scaffold685-339340 24 10510797 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386247 Affx-122970963 AX-123256605 24 10463277 GACAAGGATAAAAATATTTCCGCTTATACCTCCAC[C/T]CAGTATATCTGATTCCGAGCATCTTTACTATCAAT Y 2 1 2 1 101000 f 74 goat snp48311-scaffold685-299708 24 10549257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425810 Affx-122940694 AX-123296156 24 10514837 CACCCATCCAAGAGCTATTAGTACCCCACTTAGCA[C/T]GATAAGAGATGGGTCCTTATTGTCACCAACCAGAA Y 2 1 2 1 101000 r 74 goat snp48310-scaffold685-248148 24 10602675 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387779 Affx-122969709 AX-123258137 24 10557732 AGTAACAGCAGAGGCGGAGGTAAATTAAGGAAGAG[C/T]GGGGTCAAAGCCAAAGGAACAAAGTGTTTCCATGA Y 2 1 2 1 101000 f 74 goat snp48309-scaffold685-205253 24 10645281 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794941 Affx-122964891 AX-385281900 24 10587404 GAGCCCACTGAAATATCTTACAGACTCACACAAGG[C/T]GTGAATGATAAGAGCGTGGGTTATGCTCACAGCTC Y 2 1 2 1 101000 f 74 goat snp48308-scaffold685-175581 24 10675216 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601607 Affx-1002479793 AX-413836009 24 10628764 CACCCATATAAATGCCATCTCCTTCAAGTATGTCT[A/T]GAAACAGACAGTTTATATGAACATTTTCAGTGACA W 4 1 2 1 400000 f 74 goat 24_10628764_RH-map 24 10628764 T A Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320775637 Affx-122928320 AX-385262768 24 10637848 CCACATTATATCATCAAAATGATAAAGAGAAGGTA[C/T]GTAATTTAGTATTGCAAAATTATATACCATATTGG Y 2 1 2 1 101000 f 74 goat snp48307-scaffold685-125137 24 10725839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785149 Affx-122963799 AX-385272195 24 10686611 ATGTATCCATGTGACTCCATACAGAAACTACTTTG[C/T]AACTAATTGAATAAAGTACATTCAGATAAAACTGG Y 2 1 2 1 101000 f 74 goat snp48306-scaffold685-76374 24 10775058 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421812 Affx-122944320 AX-123292159 24 10752457 TTTTCTACTTTACATTTCACCCACCTGTTTAAGTC[A/G]CTTCTTGATAGAATGTTCATGGTTATTTTCCCTTT R 2 1 2 1 101000 f 74 goat snp48305-scaffold685-10528 24 10842103 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450574 Affx-122922037 AX-123320908 24 10765472 TCCTGAGGCACCTAAGCTAGGTATTGCATTTCTCA[A/G]TGAGTTTATTTCTCTACCTTTTAAAACAGACCTCA R 2 1 2 1 101000 f 74 goat snp27760-scaffold296-1512837 24 10860821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395757 Affx-122963683 AX-123266112 24 10826970 AGCTTGGACTTACTCTAAACTGTTTCTGGTCAGGG[A/G]TGTCTGGGGACAAATGGAACGTATGTGATGGTTAA R 2 1 2 1 101000 f 74 goat snp27759-scaffold296-1451339 24 10923633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376477 Affx-122978038 AX-123246836 24 10856662 CTGCAAAAATATGGAAGCGATCTCTTTAATTGGTC[A/G]CTCCAACCTACAGTGAAGGAGGTCAAGTATTTTAG R 2 1 2 1 101000 f 74 goat snp27758-scaffold296-1421647 24 10953166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780837 Affx-122960172 AX-385267925 24 10889580 TATTCTTTAGAACACTCAAGAAAGCAAGAAGAATC[A/G]TGTAGACTACAGTATCTTTAAATGCTTTTCTGAGG R 2 1 2 1 101000 f 74 goat snp27757-scaffold296-1388729 24 10986036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802513 Affx-122954084 AX-385289417 24 10922438 TTATTGTGGGCTATTTATCAGCTCAAAATGTTCCC[A/G]CATAATTACAAATCATCACATAATGTAATGAGTCA R 2 1 2 1 101000 f 74 goat snp27756-scaffold296-1355871 24 11019073 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388882 Affx-122968864 AX-123259240 24 10964406 CGCTTTTGCATTCCCCAAAATATATTCAGTGGATC[G/T]ATCGTAAAAACAAGTGAACTTCACTGTGAACAGTA K 2 1 2 1 201000 r 74 goat snp27755-scaffold296-1313903 24 11061063 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409088 Affx-122953331 AX-123279439 24 11013466 TTGCTTAGTTTTATGAAGTCATAAAATCTGTTTTC[A/G]TCTATGATCACACAGTCTGGTTACTCCAATGTTAT R 2 1 2 1 101000 r 74 goat snp27754-scaffold296-1264843 24 11110283 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408932 Affx-122953944 AX-123279283 24 11054853 GACTGGTATGGTTGGCACTCAGTACACATTTGTTG[G/T]GTCAATTGTGAATAGACAGTTGAGGGCTTGAGTTC K 2 1 2 1 101000 r 74 goat snp27753-scaffold296-1223456 24 11151436 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429021 Affx-122938326 AX-123299363 24 11100851 TTAGCAAACATTCCTTATGGTTCAAGCTGCATGAC[A/G]TGAACTTTTTTACCTTATCGTAACATAAGCTGAAG R 2 1 2 1 101000 r 74 goat snp27752-scaffold296-1177458 24 11197605 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427280 Affx-122939534 AX-123297623 24 11132073 GTAACTGAATAGAGAAGCAGTGGAGTGGATATTAT[A/G]TACAGGAGAATAAAAATGAAATGGACAGCAGACTT R 2 1 2 1 101000 f 74 goat snp27751-scaffold296-1146236 24 11228775 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277676 Affx-1111835969 AX-519551175 24 11185448 CACTGCCAGGCTTCTGTCCCTTGTGATCAGTTGCT[A/G]CTAAGTTTTACACCAAGAGCATCATGTGCCACACT R 2 1 2 1 101000 r 74 goat Random2.2K-2086 24 11185448 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38408755 Affx-122953397 AX-123279106 24 11219368 CACAGTTACTGACACATTGTAGAAAATATTTGCCT[A/G]CTTAGCCAATGAAAAAGGAATGTGTGTTCTGGTAA R 2 1 2 1 101000 r 74 goat snp27749-scaffold296-1058941 24 11317192 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768224 Affx-122958787 AX-385255408 24 11273215 TCATCAGGTGTTTAAAATATCAGTATCCTACAAAC[A/G]CATCTGCTTTTGATTTGTAATCTAGGTATATTACA R 2 1 2 1 101000 f 74 goat snp27748-scaffold296-1005094 24 11371537 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399634 Affx-122961073 AX-123269989 24 11337170 ACTTGACAGATATTTTCTTATATTTTCAAACTTTT[A/G]CCTTAAAATTGATTTTCCTCAAGGACATATTCATA R 2 1 2 1 101000 r 74 goat snp27747-scaffold296-941139 24 11435933 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420373 Affx-122944945 AX-123290720 24 11373641 CACACAGATATTTTAGCAAATTATCTGAAAACAGA[C/T]ACAGAACATAGAAAAACTGATGTAAGATCATATTG Y 2 1 2 1 201000 f 74 goat snp27746-scaffold296-904668 24 11472402 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387732 Affx-122969746 AX-123258090 24 11408048 GTGAAAATATTTAAAACCTGACTGGAGTATTTGTC[A/G]TTTTTTCACAAACATCTCACTCTAGAGACAAAAAT R 2 1 2 1 101000 r 74 goat snp27745-scaffold296-870261 24 11506909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277678 Affx-1111835970 AX-519551177 24 11500546 TGAACAAGACTTTAGGTTAATGTCACTTTTTAAAT[A/G]AAGTTTAATTTCACATGCAAGCTGAATTGATATTA R 2 1 2 1 101000 r 74 goat Random2.2K-2087 24 11500546 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396977 Affx-122963160 AX-123267332 24 11519171 ATGGATACTTTCAATTTTTCAGTTAAGGCCTCTAC[A/G]TCATTGAAAATTACTTAAATATATCAGATTCAGAC R 2 1 2 1 101000 f 74 goat snp27743-scaffold296-759138 24 11619643 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395106 Affx-122964158 AX-123265461 24 11570721 TTACATTGTTATACATCTAGTATAATTATATTTGC[A/G]TACTTTTCTTTCCTGACAATTGATTAGGAACAGTC R 2 1 2 1 101000 r 74 goat snp27742-scaffold296-707588 24 11670813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778119 Affx-122943303 AX-385265234 24 11600126 TGTATAAATTATGGTTTACTTTTTTAAGAAGAACA[A/G]TATCCTATATTCCATCTTCTACCTTGATTCAACCA R 2 1 2 1 201000 f 74 goat snp27741-scaffold296-678183 24 11700155 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796347 Affx-122957369 AX-385283297 24 11657337 CTTATATTTCCAGTTCCATGAAATTATAGCTATAC[A/G]TTTACTCAGTTTTCAGCTGGTTTGCTTGCCCTATT R 2 1 2 1 201000 f 74 goat snp27740-scaffold296-620972 24 11757364 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797072 Affx-122966300 AX-385284012 24 11733481 CATTGTCTCCTCCATTCTACTTCAAAGTATCCATC[G/T]TAGTGGATAGTGACACTATGGCTAAAGACTACTTA K 2 1 2 1 101000 f 74 goat snp27739-scaffold296-544828 24 11823708 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795426 Affx-122952138 AX-385282382 24 11766508 GTTGGGTCAGTAGTCCCCATTATTAAGAAAAGGAA[C/T]GTAAGATTCTTAATGGTTACATAACATGAGTGTTT Y 2 1 2 1 102000 f 74 goat snp27738-scaffold296-511801 24 11857235 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376169 Affx-122978838 AX-123246528 24 11807515 AAAAGAGACTTTAATTTAAAGTATATTAATAAATG[C/T]ACCATGAACTCCCAAGACAGAAAATGTACCAGGCA Y 2 1 2 1 101000 r 74 goat snp27737-scaffold296-470794 24 11898076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779901 Affx-122949864 AX-385267000 24 11837030 ACATATTCTGGTTTCTGTTAATACTACATAGTCAG[A/G]CTTAAATAAGCTTGCATATTCCTTTCCAAAAATGT R 2 1 2 1 101000 r 74 goat snp27736-scaffold296-441279 24 11926479 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402536 Affx-122958472 AX-123272889 24 11876543 ATGCACGTTTGACACTTCAGCACCATCGCTGGTTC[A/G]TTTTTCTCTTTTGTTTCTCATTTCTAACCAGTCTT R 2 1 2 1 202000 f 74 goat snp27735-scaffold296-401766 24 11966018 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447470 Affx-122924353 AX-123317806 24 11905262 CAAACACTGTGTTATTTGCAATGAATGCATTATTT[A/C]GTCCTCACAAGTGATATATGAGATTCGTATCATTA M 2 1 2 1 101000 f 74 goat snp27734-scaffold296-373047 24 11994854 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413842 Affx-122949875 AX-123284191 24 11953317 AATGCTGAGGACTTAATAGTAGAAACCCCCAATGG[A/C]TACGAGAAGCTACTGTATAAAGGAGAAACAGGGAA M 2 1 2 1 201000 r 74 goat snp27733-scaffold296-324992 24 12042558 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407502 Affx-122954747 AX-123277853 24 12011022 AATAGTATTTTAAAAGAAAGAAAACCAGTGATTAT[A/G]TAAGTGTTCCTCAGACCATTTAAATGAAATTCTCA R 2 1 2 1 101000 r 74 goat snp27732-scaffold296-267287 24 12100197 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402679 Affx-122958359 AX-123273032 24 12048741 GTGTTCATAATCCAAAAAAGGATGTGAATGGCTCC[G/T]AAGAGCCTGTCTGCACCCTGGCCTCTTCTCCCACA K 2 1 2 1 101000 f 74 goat snp27731-scaffold296-229568 24 12138106 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403192 Affx-122958068 AX-123273545 24 12087085 AGTAGAGCCTGACAGATTATTTCTTCCTTTATTAG[A/C]GTGTATGCTGGACCTCATTTGTCTACTAAGTAACG M 2 1 2 1 101000 r 74 goat snp27730-scaffold296-191224 24 12176494 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771167 Affx-122953426 AX-385258327 24 12115613 TATGTTTTTACATAGGCAGGTGACTTAATTGGAAT[C/T]ATTCCTCAGGAAGATAAATTTAACAGTTAATGAGC Y 2 1 2 1 101000 r 74 goat snp27729-scaffold296-162696 24 12206641 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791097 Affx-122932628 AX-385278092 24 12173852 GCTCTGAAAACTCTACTGCCTTTCCTCCCATCCTC[A/G]TTGAAAATGTGCTTTCTACCTATTACGTCATCTGT R 2 1 2 1 102000 f 74 goat snp27728-scaffold296-104457 24 12264913 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391261 Affx-122967367 AX-123261618 24 12203750 AGTTGGCAACAAAAACATTTTGTTTTGAGAAAAGA[C/T]TTGATATTATTTGTAGACAAAAATAACAGTAATTG Y 2 1 2 1 303000 r 74 goat snp27727-scaffold296-74559 24 12294395 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410853 Affx-122952612 AX-123281203 24 12233340 CTTTTCTTTTGCACAGTCCAAACAGACAGTGGCAC[A/G]CATTATATTTCTTTGTGTCTTCAGGATACCAGCAT R 2 1 2 1 101000 f 74 goat snp27726-scaffold296-44969 24 12323834 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379503 Affx-122976462 AX-123249861 24 12271273 ATGTAAACAAGTCCAAGTCTCCGTCTTTGGGAACC[A/G]AAACTGACATCTTGGAATCATCTTGATTATAGAAG R 2 1 2 1 101000 f 74 goat snp27725-scaffold296-7036 24 12361845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791831 Affx-122921470 AX-385278821 24 12281311 AAAAAGAAAGTTTACTAAGATGTAGACGTTATCCA[G/T]AGAGCTTAAAATCTAGCATATTCAGTATATTTTCC K 2 1 2 1 101000 r 74 goat snp32942-scaffold3820-112377 24 12370934 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400751 Affx-122959892 AX-123271106 24 12339515 CTGTTTCCTCTCTCCCTTTCCACACCAATCTCCAG[C/T]CACAGACCCTGACTTTTCTCAATGGGCATCTTTTG Y 2 1 2 1 101000 r 74 goat snp32941-scaffold3820-54173 24 12429598 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409497 Affx-122954047 AX-123279848 24 12369216 AGGAAAACGGGGTATTTAGGAAGAGAGAAAATGGA[C/T]GACTGATATTCACATTGATAAGCAGAAAAGATATT Y 2 1 2 1 201000 r 74 goat snp32940-scaffold3820-24472 24 12459247 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786032 Affx-122919428 AX-385273068 24 12465828 TAATGAGATCCTTAACCCTGCTGACATGTCATTTT[A/G]CAGATTAATAGTTCTCAGGATATAGGTTTAGTAGA R 2 1 2 1 201000 r 74 goat snp10672-scaffold1379-72041 24 12576471 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401435 Affx-122958990 AX-123271788 24 12512666 CACCTCTTATATATACTTAGAAATTATATCAAAGT[A/G]CTATCTTTGCATATTTGTTTCCCCCTAAGTCTCTT R 2 1 2 1 201000 f 74 goat snp10673-scaffold1379-118879 24 12623505 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790600 Affx-122928918 AX-385277602 24 12543398 GTACATTAGCAAAGCAAATCTCAGTTATCTGCATG[A/C]GTATATAACTGCTGTTATTTATGTAAATCTCACCT M 2 1 2 1 101000 f 74 goat snp10674-scaffold1379-149611 24 12654595 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779145 Affx-122940023 AX-385266249 24 12624935 CAATGATCTGGATTTTCAGAGTCAGGCCATAAAGC[A/G]TCATCTTGATGAGTACTTACATTACATTTTGGTGT R 2 1 2 1 101000 f 74 goat snp10675-scaffold1379-231148 24 12735916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386612 Affx-122970238 AX-123256970 24 12664577 GCATTTAGAATGTATGTTTTAGTGCAGAATGTACC[A/G]TAAGGTGTTTTTTTCTCTGCTGTTTTTTTTGTATT R 2 1 2 1 101000 f 74 goat snp10676-scaffold1379-270790 24 12776490 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787322 Affx-122978666 AX-385274347 24 12707725 TTCTCTAAATTTTCTGCTCTCCTCTCTAACTGAAT[A/C]TTTTATCACTTTTAAGAAGCACTCCTTACAGCATA M 2 1 2 1 201000 r 74 goat snp10677-scaffold1379-313938 24 12819731 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801994 Affx-122966223 AX-385288898 24 12786488 AGCCTTTTCTAAGCCTTCACAAAATGTAATGTAAA[C/T]ACATTGAGTGAATTACATATTGACACTGAATATTC Y 2 1 2 1 201000 r 74 goat snp10678-scaffold1379-392701 24 12900540 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451512 Affx-122921110 AX-123321845 24 12815624 ACTCTATACACAGTGCACACATACATATATGATAT[A/G]TAGGCTACAAAAAGTTTCAAGAAACAATTTGTCCT R 2 1 2 1 103000 r 74 goat snp3499-scaffold1109-248 24 12935668 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774162 Affx-122945085 AX-385261299 24 12858841 TATATCAACTTAATAATTAATATTCCCCAGGTCAT[A/G]TGAACATGAAAGTCATTTGTCCAGTTTCTTTAAAT R 2 1 2 1 202000 f 74 goat snp3500-scaffold1109-43465 24 12979557 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774636 Affx-122957146 AX-385261770 24 12913617 GTGGAGTAAAATATTGGAGTGTAATAAATATTGAA[C/T]AGTTGAAAGATTTGGTTTATGCAGTAAGGGGAAAT Y 2 1 2 1 101000 r 74 goat snp3501-scaffold1109-98241 24 13034984 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769884 Affx-122978608 AX-385257053 24 12981530 TAAACAGAAACTTTTGATGCTTTAATTTAGGGAAA[C/T]AAGTAATTCTAATGGGTAGAGGAGGTCATTGAGAA Y 2 1 2 1 101000 r 74 goat snp3502-scaffold1109-166154 24 13102641 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444012 Affx-122926896 AX-123314349 24 13042246 AGTATTTCCTTGTGTTCTCAAAGTTATGACCTTAG[A/C]TGAGACATTAGAGAAAAGGGAGAGGGTGATTTCCT M 2 1 2 1 201000 f 74 goat snp3503-scaffold1109-226870 24 13163265 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390981 Affx-122966914 AX-123261338 24 13070940 GGGAGGTCAGGGTCTAGATGCCATGCTTTTGTTAG[C/T]ATACTCTTTTAAGTCTTCTATGTCTGAGCTGTGGT Y 2 1 2 1 101000 r 74 goat snp3504-scaffold1109-255564 24 13192567 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783025 Affx-122942314 AX-385270093 24 13119273 TTCTTCCATCTTGTGAAGCTATCATCTTCACACAA[G/T]ATATGTACAGATGCCATAAAAGGATAAGAAAACAT K 2 1 2 1 101000 f 74 goat snp3505-scaffold1109-303897 24 13241488 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444259 Affx-122927212 AX-123314596 24 13131438 AAAAGGGCTGCATAATATCATATGCCCCCATATGC[A/G]GGGAACAAATAAAGCCATCCCCAGAAGTTAGCTGA R 2 1 2 1 202000 f 74 goat snp37157-scaffold451-1880027 24 13254062 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273014 Affx-1111833269 AX-519546693 24 13154211 ATCTCTAGTTTTCTTGAAGAGATCTCTAATCTTTC[A/G]CATTCTATTGTTTTCCTCTATTTCTTTCAATTGAT R 2 1 2 1 303000 f 74 goat 24_13154211_AF-PAKI 24 13154211 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38410336 Affx-122952468 AX-123280686 24 13189959 TACAGTGTTCCAGTGTGATGCCAGCTTTCATTAGT[A/G]TTCAAATTCACTTTGGCAGGGAGCTCAGTTTATAA R 2 1 2 1 101000 f 74 goat snp37156-scaffold451-1821506 24 13313129 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440073 Affx-122929734 AX-123310410 24 13223869 AAGAAAAAAGAGCAGAGATAAAGTGGGCACTGTGA[A/G]AGAAGCAGGCTGAAAACTTTTGATGGATCAGGGAG R 2 1 2 1 101000 r 74 goat snp37155-scaffold451-1787596 24 13347221 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773619 Affx-122924147 AX-385260759 24 13275962 GTTCTATAATTACACTAATGGTTCTACAAGTAACT[A/G]TTTATACAAAAAGAGCACTAATTGTCCACTTATTC R 2 1 2 1 101000 f 74 goat snp37154-scaffold451-1735503 24 13399658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392531 Affx-122966107 AX-123262888 24 13315828 CCTGGGTTCTATAAAATGGGAACTCTCAGTGTGGA[A/G]TATCCTCAGTTTTTACTCACATTCAAAGTCTAAGA R 2 1 2 1 201000 r 74 goat snp37153-scaffold451-1695637 24 13440083 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393579 Affx-122965389 AX-123263935 24 13363311 CACGGGGTACAATTAGGACAATAGATGAGCATATA[A/C]CAATTGAATGAGCAAGAGCATGGAACGGAGAGCTG M 2 1 2 1 101000 f 74 goat snp37152-scaffold451-1648154 24 13487995 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394873 Affx-122964757 AX-123265228 24 13396680 GGTTAGGGAGTGGTGGCTTCTTTGTCAGTGTCAGT[A/G]CCATAATCAGGCAGAGAAATATTTAAGGAGAAACT R 2 1 2 1 201000 r 74 goat snp37151-scaffold451-1614785 24 13521446 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781228 Affx-122972654 AX-385268313 24 13435829 CTATCTATCCATCTGACATACATAGATATATCTTA[C/T]AATTCTTACTTGTTGATAAAAGAAAATCAACATTT Y 2 1 2 1 201000 r 74 goat snp37150-scaffold451-1575636 24 13561090 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399237 Affx-122960583 AX-123269592 24 13509908 GCATATTAAATAATTACATTTTTAGAAAAACTGAC[A/G]TAATATCCTGAGACTGCATTTAAGGGCAGAGTCTA R 2 1 2 1 101000 r 74 goat snp37149-scaffold451-1501557 24 13636319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423568 Affx-122942412 AX-123293914 24 13565015 CATGAAGCAGTTTCTGATTTATGTGGTGAGCTTCC[A/G]ACTTTTGGTATTTTCTTTCTCAACCTCAATCCATC R 2 1 2 1 101000 f 74 goat snp37148-scaffold451-1446450 24 13692829 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387038 Affx-122969917 AX-123257396 24 13617522 GTTGGAGGGGCAGAAGCACAGGATAGTCAAGAGTG[A/C]CACCTCTGGGCAAGTGAAACACAAACAAGAGAATA M 2 1 2 1 101000 r 74 goat snp37147-scaffold451-1393943 24 13746595 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772608 Affx-122944303 AX-385259756 24 13653061 GACCCAGGAATTCAGTGCTGGATACTGCCTTTCCC[A/G]TAAACTTCATTAGATATATGATGAGAGAAGTGACG R 2 1 2 1 101000 f 74 goat snp37146-scaffold451-1358404 24 13782343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392088 Affx-122966370 AX-123262445 24 13699110 GACAGTATCTTACATAGGTGAATGAGATAAGAATT[C/T]TTTATTTTTTATTTTCTTTCCTGAGAGTTTTTCTG Y 2 1 2 1 303000 f 74 goat snp37145-scaffold451-1312355 24 13831880 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781108 Affx-122937951 AX-385268193 24 13730566 ATTTTTATATAAGGGCAACAAATTATAGGAATATA[C/T]AATATGCTTGTAGTATCAAAGGGACATGTAGGATG Y 2 1 2 1 101000 r 74 goat snp37144-scaffold451-1280899 24 13863784 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440920 Affx-122929026 AX-123311257 24 13762067 CCATTCTGGTGACAGAATGTAATGAGAATGGGAAA[C/T]AGTAGAAATCCAAAGCAATTACTTTACAATGGTGA Y 2 1 2 1 101000 f 74 goat snp37143-scaffold451-1249398 24 13895343 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420273 Affx-122945050 AX-123290621 24 13804760 TAGTAATTCTTGTGGAAAATTTTTATTTCGTGTTT[A/C]TGAAAGAAATATATATTAAAGTACTATGTGTAAAA M 2 1 2 1 101000 r 74 goat snp37142-scaffold451-1206705 24 13939608 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418103 Affx-122947135 AX-123288451 24 13848679 GTGACTTTAGCTGGCACCTTCAACTGTTGATGAAG[C/T]ACTTTTGATTTCTCCATTGCAATACAGTTCCTAGC Y 2 1 2 1 201000 f 74 goat snp37141-scaffold451-1162786 24 13983250 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414247 Affx-122949626 AX-123284596 24 13877681 GATATCCTTGGCTTTTTCCAGGGGGTCAGTGGAAA[C/T]AAATCAAGTTTTCTTTCATTTTCACTAAATCTAAC Y 2 1 2 1 202000 f 74 goat snp37140-scaffold451-1133784 24 14013764 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435921 Affx-122932759 AX-123306260 24 13924845 CCCAATACCATTTTTTTTTTAATCATGTAGTCTGT[A/G]TTTTCCTTTATTATCATTGCCATTCAGATTTTTGG R 2 1 2 1 201000 r 74 goat snp37139-scaffold451-1086620 24 14056093 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777625 Affx-122976623 AX-385264744 24 13956598 ACTAACTGCTAATATAATAACTGTATTATTTATGT[A/G]ATCTGCAATTTCATATATTCAACTTTAAATCTTTA R 2 1 2 1 101000 f 74 goat snp37138-scaffold451-1054867 24 14087918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424633 Affx-122942176 AX-123294979 24 13988028 TGAAGGTAACCATTTAATGTATGGATTGGCATATA[C/T]AGTCCATGGGCCCTATCTGGCCCATTGCCTGTTTT Y 2 1 2 1 201000 f 74 goat snp37137-scaffold451-1023437 24 14119355 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771225 Affx-122931373 AX-385258383 24 14018703 CAAAGACAGTGTGTTCAAAGCTTATGATTTTGGCC[A/G]TAGATAAAACAGTGAAGCGTTTTGGTCATTGTCAC R 2 1 2 1 101000 f 74 goat snp37136-scaffold451-992762 24 14149833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423536 Affx-122942438 AX-123293882 24 14052344 CAGAATCCAGACTCAGGTTTGTAATCACAGAAACT[A/G]CATTTATTTTAGTTCATCCAGAAAAAGTTAGTATT R 2 1 2 1 101000 f 74 goat snp37135-scaffold451-959121 24 14183500 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388707 Affx-122968984 AX-123259065 24 14097592 CACATCACATCAGTTGCCCTGCCAGTCTCCTTAGG[C/T]ATAAAATTGGGCAAGGCAGAGAACAGGAGTATGTG Y 2 1 2 1 202000 r 74 goat snp37134-scaffold451-913873 24 14229426 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769082 Affx-122924710 AX-385256257 24 14154041 CTACTTCAGGGCACCTGTAGGTGCTACATTTCATG[C/T]AGCTTGTGGGGCTTAGGTTTCCCAATCGGGGATTG Y 2 1 2 1 303000 r 74 goat snp37133-scaffold451-857424 24 14285789 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780390 Affx-122953716 AX-385267484 24 14182989 CAGCCTGTTGGACAGTAACTGGCAAAAAAGTTAAA[A/G]CCATTTGAACCACTCAGAATGTTGGCTGGAGAAAA R 2 1 2 1 101000 r 74 goat snp37132-scaffold451-828476 24 14314731 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386696 Affx-122970174 AX-123257054 24 14216554 TTTCTGTGAAAATCAGGAAAATGGGCTAAAATCCA[C/T]GCTTCAATAGAAGCCCAGTGGAAATCAGCAAGAAG Y 2 1 2 1 201000 f 74 goat snp37131-scaffold451-794911 24 14347809 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778010 Affx-122951889 AX-385265126 24 14308198 AGAAACAGTAAAATGATTTCTGATTTGGATTAAAA[C/T]ATTTTATGTCCAGGTCTCTTGAAGTGCTATAATCA Y 2 1 2 1 101000 r 74 goat snp37129-scaffold451-703267 24 14440286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764710 Affx-122928246 AX-385252330 24 14337114 AAATCCAATCTAGGATTGAAAGCTGCAACTGTCAT[A/C]GATAAAAAGTACCCTTCTGAGCGTTGCTATTGAGT M 2 1 2 1 101000 f 74 goat snp37128-scaffold451-674351 24 14469009 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431576 Affx-122936185 AX-123301917 24 14371152 TAAGTCCTATCTTACTTCCATATGATAGCTCATTG[A/C]TGAACTAAGCTGGACGTCTACAATTCCAAATACAC M 2 1 2 1 101000 f 74 goat snp37127-scaffold451-640313 24 14502867 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447773 Affx-122924563 AX-123318109 24 14404086 AGCCCAGTTCCCTGCAGTTGGCATTCCCTTATATC[A/G]CATCATAGATTATCCAGGCATGACCATCCCACTGG R 2 1 2 1 101000 r 74 goat snp37126-scaffold451-607379 24 14535837 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776637 Affx-122954671 AX-385263764 24 14454225 CACATACAGCTTGTTTTGCTACAGAAAAATGCTGA[A/G]CAATGACCATTTTGATCCAATAAATATCTAAGCCC R 2 1 2 1 101000 f 74 goat snp37125-scaffold451-557240 24 14586023 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771139 Affx-122935070 AX-385258299 24 14505970 GTCAAGCTTTTTCCAGTTCTGCATCTTTAGAATGA[G/T]CCTAAAATGAAGATTACTGGAACCACAGAATGAGA K 2 1 2 1 101000 r 74 goat snp37124-scaffold451-505495 24 14639002 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448185 Affx-122924248 AX-123318521 24 14547325 AACGTCCTACTCTGAAGGAGTGGTTGGAGGGGGAC[A/G]TTTAGGTTCTAACTGAGAGCCTCCCTAGCCTGTTC R 2 1 2 1 103000 r 74 goat snp37123-scaffold451-464140 24 14680453 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791306 Affx-122932203 AX-385278299 24 14602117 ATGATATATGTGATTTATAGGGTTAAAAATTTTGC[A/G]CTTAAAGGATAATTAGCACACAGCATATTAATATC R 2 1 2 1 102000 r 74 goat snp37122-scaffold451-409348 24 14737693 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778147 Affx-122924867 AX-385265262 24 14678163 GGCTGACATATACGTTTGTGCAGATTGTGTGGTCT[A/G]CTAGGGTATATCCAATAAAGTGAGTGGTGACTTAC R 2 1 2 1 101000 r 74 goat snp37120-scaffold451-333302 24 14813389 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787441 Affx-122925639 AX-385274466 24 14727933 TAATATATATCTTCCCACTTAGTTTGCAAGTTCAA[C/T]CAGTTTCACTATATTTCTCATTTTACTCTCATCTC Y 2 1 2 1 201000 r 74 goat snp37119-scaffold451-283532 24 14863056 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787734 Affx-122971460 AX-385274757 24 14762274 GCCCCTGTGTAGTTGAATTAAATACATAGCTGTCA[C/T]GATACAAGGGAAATTTGCAGTTTGAGTACAGTTAT Y 2 1 2 1 101000 f 74 goat snp37118-scaffold451-249191 24 14897357 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386505 Affx-122970752 AX-123256863 24 14792979 ATACAGAGCCCAGACACTTAACTGATATGAGAAAT[A/C]TTTCAGACAACATACATTTGTCTTTTACTTCATTG M 2 1 2 1 101000 f 74 goat snp37117-scaffold451-218486 24 14927741 C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382915 Affx-122973397 AX-123253273 24 14827431 ATTATAAGCAATTCTATTTACAAGTGATGCTACCA[C/T]ATTGGCTCAACCAAATAGTATATCACCAACACAAG Y 2 1 2 1 101000 r 74 goat snp37116-scaffold451-184034 24 14961985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772957 Affx-122961463 AX-385260101 24 14857341 AAAGCACAAAAATTGGTATTATAAATGCTTCATGA[C/T]ATCTATAAAACATAGCATAACTTCCACTCATCAGC Y 2 1 2 1 101000 r 74 goat snp37115-scaffold451-154124 24 14992465 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778446 Affx-122920513 AX-385265560 24 14886389 GTTATTATTTTATTACAATATGAGTTTTGTACACC[C/T]GAGGCAACTGTCTATAGAAATAAATAAGAACTATG Y 2 1 2 1 101000 r 74 goat snp37114-scaffold451-125076 24 15021269 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794447 Affx-122930296 AX-385281410 24 14918443 CTTGCTTTCTGTTGGAGTAATCAAAAATATATCTT[A/G]ACATTGTTCTACAAAGTAAAACAGATTGAATACTA R 2 1 2 1 201000 f 74 goat snp37113-scaffold451-93022 24 15054058 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786636 Affx-122934749 AX-385273668 24 14973654 GCTCATATAAGCAAAATTGGAGTTAGGACATGGTT[A/C]TTCTCAAAAACCATGGATATTCCACTAGAACTGCC M 2 1 2 1 101000 f 74 goat snp37112-scaffold451-37811 24 15108870 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787562 Affx-122958233 AX-385274586 24 15007828 CCCTTCACACAGAAAAATGCAACTAAATGAAAATT[C/T]AACTTTCAAGTACACCTAACAGTTTATTCAAAGCA Y 2 1 2 1 101000 f 74 goat snp37111-scaffold451-3637 24 15142859 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790762 Affx-122937427 AX-385277763 24 15033588 ATTGGACAGCTAACTTAACCTCTTTATTTACCACA[C/T]CCTCTTCGTAAAAAGGAAAAGACAAATGTCTATGC Y 2 1 2 1 101000 r 74 goat snp8255-scaffold13-3859745 24 15171840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770690 Affx-122930303 AX-385257854 24 15067571 ACTTTTGGTAATTAATACATGAGTATTTGAGATGC[A/G]TCAAAGTACTCTCATTCGTGAAAATATATGTTACA R 2 1 2 1 101000 f 74 goat snp8254-scaffold13-3825762 24 15204736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441111 Affx-122929599 AX-123311448 24 15113893 TCTCCCTAGATGAAGTCATCTAAATTAAAAAATGT[A/G]CATATTCCTAATGAATTAAATAAATGTAAATACTA R 2 1 2 1 103000 f 74 goat snp8253-scaffold13-3779440 24 15252126 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793024 Affx-122977364 AX-385280002 24 15186171 TTGTCCATTTTGGTTTGATTTCGAAATTTCATCAT[A/C]ATTATAGTGCTACCAAGGAAAAAGTCAAAGATCCT M 2 1 2 1 201000 r 74 goat snp8252-scaffold13-3707162 24 15325799 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395226 Affx-122964482 AX-123265581 24 15225779 CCATTGCGGGTATTTTGCTAATGGTAAAGCAGTGG[A/C]AGTGAAGATAATAACAACAATATATATTAGTGATA M 2 1 2 1 101000 f 74 goat snp8251-scaffold13-3667554 24 15366157 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448090 Affx-122924325 AX-123318426 24 15267889 TCTAACATTCTTTCCATCCCTTTCTTTTAGTAAGT[A/G]CTATCCATTCTCAATTCAGAGGTTTTTCTAGTCTG R 2 1 2 1 101000 r 74 goat snp8250-scaffold13-3625444 24 15409312 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772682 Affx-122963154 AX-385259829 24 15337745 CATCTTAAAACACATGATAATTAGAATCCGTTGAT[A/G]TTAGCAGAATAGATAACAAAGAAAGATATTAGAAC R 2 1 2 1 101000 f 74 goat snp8249-scaffold13-3555588 24 15479454 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397036 Affx-122963111 AX-123267391 24 15366841 AGGCTCTATGCGCCGTCGCAGCCACCCACGCTCTG[C/T]GCTGTAAAGAATGTGTTAGCAGCTTCTTTTGGATG Y 2 1 2 1 103000 r 74 goat snp8248-scaffold13-3526492 24 15509186 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399812 Affx-122960275 AX-123270167 24 15408235 ATCTCAGATACTTTTTGTATTTCTGCAAGGATGTG[A/C]TTGGTGTTACACACATTAGTCTTCATTCTCAATAG M 2 1 2 1 201000 r 74 goat snp8247-scaffold13-3485098 24 15550496 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429757 Affx-122937586 AX-123300098 24 15439641 AAATTCTAAAATGTGGTAAACCGTATAAGGGAAAA[G/T]ATATTTTCTTCATTATATTCTTTTCATATTTCCAA K 2 1 2 1 103000 f 74 goat snp8246-scaffold13-3453692 24 15581368 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422087 Affx-122943586 AX-123292434 24 15476502 CTGATTCACCCTTGTTCTGCTTTCTCTCTAGTCCC[A/G]TTGAATCCGAGTCCACAAAATTTAAAGACCAAGGC R 2 1 2 1 201000 r 74 goat snp8245-scaffold13-3416831 24 15619546 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408014 Affx-122954308 AX-123278365 24 15520916 TCTTTAGTCTTTAGGTTCATCTTCCCCAACAAGTC[A/G]CATGTATGCTAATTGACTGAGCATGAAATTAAGTG R 2 1 2 1 201000 r 74 goat snp8244-scaffold13-3372417 24 15664369 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430316 Affx-122938232 AX-123300657 24 15568733 GAGAGTCATTTGTTGGGTAGAAAAGTAATTGGCCT[C/T]CTCGGGTATAATCCATCAATTCTCCCAAAGAACGG Y 2 1 2 1 101000 f 74 goat snp8243-scaffold13-3324600 24 15712897 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768484 Affx-122937534 AX-385255664 24 15606126 TTTACTATAGCCATTTTTGGAGTAACAAATCCAGC[C/T]GAAATTCATGCTTGGAATGCCTTAAAGGGATGCAA Y 2 1 2 1 101000 r 74 goat snp8242-scaffold13-3287207 24 15750854 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799961 Affx-122924223 AX-385286887 24 15665442 GTGCTTGTTTCTCAGATTCTGAGGTAAATGAGCTA[C/T]GGTAGGAGAAAGGGATAATTGGAAGAACATATTTC Y 2 1 2 1 101000 r 74 goat snp8241-scaffold13-3227891 24 15810592 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453427 Affx-122919878 AX-123323760 24 15726346 GCATTACGGGTGATTAATCAATTGCCTAGGAACAT[A/G]CAGACAAGGTGGGATTTTATTAATAATATGGCTCT R 2 1 2 1 101000 f 74 goat snp8240-scaffold13-3166987 24 15870618 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449196 Affx-122923515 AX-123319531 24 15769792 AAGGGAAAATATATTTAAAGTGGAAAAACGTTGAC[A/G]TTCATTTTGGCAGAGTAGATTTAGTTTAACCTGAG R 2 1 2 1 101000 r 74 goat snp8239-scaffold13-3123541 24 15915213 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448255 Affx-122924197 AX-123318591 24 15811882 AAGCCTCAATTTCTCTAATCTCATTGCTTTGTGGA[C/T]GGTTGATTCATTTCCTTGAAAACTCTAACAGTGTG Y 2 1 2 1 201000 r 74 goat snp8238-scaffold13-3081451 24 15958383 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388912 Affx-122968843 AX-123259270 24 15871255 GGACAGTTGTAACTCAGTATTGCCTGGATTAGATC[A/G]TCTTTGACTACTTAGTGAAGTTATGCTACAATTTT R 2 1 2 1 101000 f 74 goat snp8237-scaffold13-3022078 24 16018568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767325 Affx-986698472 AX-385254602 24 15927490 TCCTCTCGGCTGTGCTTAGTGCACTGGTCCCCATC[A/G]CCTGCACTTAAATACCTAGAAAACGAAAGAACAAA R 2 1 2 1 600010 r 74 goat 24_15927490 24 15927490 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 468273016 Affx-1111833270 AX-519546694 24 15928222 AATAGTTCTGGCAAGAGAAGGCAAATGCAAGAGAA[A/G]GGTAAGACCTACAGAAAATAAATCCCAAACAATTA R 2 1 2 1 101000 f 74 goat 24_15928222_AF-PAKI 24 15928222 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320763949 Affx-986698477 AX-385251731 24 15928225 AGTTCTGGCAAGAGAAGGCAAATGCAAGAGAAGGG[A/T]AAGACCTACAGAAAATAAATCCCAAACAATTAAAA W 4 1 2 1 600010 f 74 goat 24_15928225 24 15928225 Ancestral_priority_1043 ancestry 0.576 neutral IMAGE 10K 10K ancestral 320777866 Affx-122928283 AX-385264983 24 15967268 AAACCACTTGAAGTCATTTACTATCTCTTGAAGCC[A/G]CTGACATATAACTCTGGAGATTTTATTCATCTTCT R 2 1 2 1 101000 f 74 goat snp8235-scaffold13-2926065 24 16115584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422710 Affx-122943645 AX-123293056 24 16030186 TTGCATGAAATTTTGCCAAATTCTGAAGACATACT[A/G]CAGTCTTATTTATGAAACTTCGTGTTCCTAAATAT R 2 1 2 1 101000 r 74 goat snp8234-scaffold13-2863147 24 16178917 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437516 Affx-122932337 AX-123307854 24 16065507 TTCTCTTTCTCTTTATCTTACACTAGTCTCCTTAG[C/T]AATTACACCATTTTTTTTCTTTATGAATATCTACA Y 2 1 2 1 103000 f 74 goat snp8233-scaffold13-2827826 24 16214622 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791466 Affx-122947430 AX-385278457 24 16103398 GGACTATTGAGAAATAACTTTGCCTCAGAGAAATG[C/T]GGCCATTCTGGTGTTTCCAATCTTGGGTCTCTAGC Y 2 1 2 1 101000 r 74 goat snp8232-scaffold13-2789935 24 16252899 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427033 Affx-122939829 AX-123297378 24 16182326 CAGTTCTAGTTGGCAAAAATTATATAATCTTATGA[G/T]TTGAGTTTCACCTTTGATTTACTATATCTATATAA K 2 1 2 1 101000 r 74 goat snp8230-scaffold13-2711007 24 16333298 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413567 Affx-122950591 AX-123283916 24 16242883 GCAGGGAGGAAAACAGTTTCAATGCTTTTAATTCT[A/G]CAGAAGGGAAACAACTTATAGCCTCCTCAGGCCCT R 2 1 2 1 201000 f 74 goat snp8229-scaffold13-2650450 24 16393774 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394421 Affx-122964601 AX-123264776 24 16291784 TCAGTGCAGGATTTTGGTATTTTAGTGGCACCAGA[C/T]ACCTGGCAGAAGCAAACTAAATTTTCTGTAAATAA Y 2 1 2 1 101000 f 74 goat snp8228-scaffold13-2601549 24 16438980 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391919 Affx-122966941 AX-123262276 24 16333332 CCTCAGGTTTTCCACCTGGAATTTCCTGAGCATCC[A/G]CCCCCCAGACAACAAGAATCTGCCTGCTTTTCCAC R 2 1 2 1 303000 r 74 goat snp8227-scaffold13-2560001 24 16481059 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786695 Affx-122930666 AX-385273727 24 16367229 TTTTCAAGACACAATAATTGAGATTATACTCACTG[C/T]TTACTTCTAAGGAGCCAGCCATTGCCTCATTACCC Y 2 1 2 1 101000 r 74 goat snp8226-scaffold13-2526104 24 16516181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786922 Affx-122925132 AX-385273951 24 16498320 ATTTAATTATAAAATTTCCTAGGATAATGCACACC[A/G]TTATACTAAGATCCTAAGAAATATGCAATATTCAT R 2 1 2 1 201000 f 74 goat snp8223-scaffold13-2395013 24 16647863 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422228 Affx-122944022 AX-123292574 24 16530712 AAAACAATAGGACTAACCCAGGCAGAGCAGCAAAA[C/T]GAAAAAAAGAACTTACAAAATAAAGATACCTTTCC Y 2 1 2 1 102000 f 74 goat snp8222-scaffold13-2362621 24 16680811 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769717 Affx-122965558 AX-385256887 24 16608246 ATTAAATGTTAATGGAATTACCTTTTACCCAGTTT[A/G]CCACATCACGTGTTGTTTGCTTCAGAAAGAATAAT R 2 1 2 1 101000 r 74 goat snp8221-scaffold13-2285087 24 16759532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772358 Affx-122960476 AX-385259511 24 16641024 TCATAAAGTCATTATGAACATTATAATGGTTAATA[C/T]ATGTTGAATATATAGAACAAAATCTAGCATATGGT Y 2 1 2 1 101000 f 74 goat snp8220-scaffold13-2252309 24 16792611 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771031 Affx-122950816 AX-385258193 24 16675410 GTCCAATTCACTCTGCTAGATATTACAGTAGACTT[A/G]AAGATAGATAAAAGTACCCCCTAATTTAGGACGGT R 2 1 2 1 101000 f 74 goat snp8219-scaffold13-2217923 24 16827294 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441690 Affx-122929170 AX-123312027 24 16710192 GAAGGAAGAAGAGAGGGAGTTAGAGGATGAGAACA[A/G]CAAAGAAAGGAAGAAAACACTAAGAGAGAGCGGAG R 2 1 2 1 101000 f 74 goat snp8218-scaffold13-2183141 24 16862103 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420501 Affx-122944853 AX-123290848 24 16802205 CTTTTTTAAACTGCACCCCTAATTGATATTTCTTG[C/T]AGTCAATGTGAATTTTATAGTGTTGCTAATGGAGA Y 2 1 2 1 201000 r 74 goat snp8216-scaffold13-2091128 24 16955686 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379134 Affx-122976736 AX-123249493 24 16851600 TGTTTTTTCCAGAATGTCATATAGTTGGAGTCACA[C/T]GGCCTTTTCAGACTGACTCTTCCACTTAAAAATGT Y 2 1 2 1 101000 r 74 goat snp8215-scaffold13-2041733 24 17004371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437760 Affx-122931713 AX-123308098 24 16886086 AATGTTGTGCATTTTTGCTTCATGTATTTTGAAGT[A/G]CTGCTGCTTAGTGAACACACATATATAACTGCTAC R 2 1 2 1 101000 r 74 goat snp8214-scaffold13-2007247 24 17039373 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422014 Affx-122943636 AX-123292361 24 16921462 ATGTCCTGCCTATTTTGGAGTGTACGTCAACTTTG[C/T]AAGATACTTGATTTTTATTATTACCACCATTGGTA Y 2 1 2 1 101000 f 74 goat snp8213-scaffold13-1971871 24 17074810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435769 Affx-122932875 AX-123306108 24 16969450 GAAGTGAATCACTGCTCAACAATTGATGATAACCT[C/T]TAGCTGGCTGAGGCCTTCAGAATTTGACAATCATG Y 2 1 2 1 101000 f 74 goat snp8212-scaffold13-1923883 24 17123313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790446 Affx-122953321 AX-385277449 24 17024792 TTTAATCAACGGGAGAACAAGTAGGTGATTTTGGA[C/T]GTGTCACCCAACCTACACAGGTACCCTCATCAACA Y 2 1 2 1 201000 f 74 goat snp8211-scaffold13-1868541 24 17178490 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774578 Affx-122953014 AX-385261712 24 17058128 GACAGCTCAACAATCTTCTCTGTAAAACTTGTTAA[C/T]TTGAACCCCCACCAATGCAGACACTGTGATAATTC Y 2 1 2 1 101000 r 74 goat snp8210-scaffold13-1835205 24 17211911 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410369 Affx-122952447 AX-123280719 24 17093916 TTTCTTTTAATATTTCTGTGAGCATCATATGGACC[G/T]AAATTACTTTATATCATTTATTATGGCCAATGGTT K 2 1 2 1 101000 f 74 goat snp8209-scaffold13-1799417 24 17247648 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777962 Affx-122951666 AX-385265079 24 17149742 GCCACATGGACAGATGCTGATGTTTCAAAGAGCAA[G/T]CACTGTCTGGTTTCGTGAACACCCAATAAGAGTGG K 2 1 2 1 101000 f 74 goat snp8208-scaffold13-1743591 24 17304035 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377703 Affx-122977407 AX-123248062 24 17184428 CCCCACTGCAGACCTAATGCAGGTCTGCAACCGAG[C/T]AGTCACTAGCGTAAAGTTCTATTGTGGAAAAGACT Y 2 1 2 1 101000 r 74 goat snp8207-scaffold13-1708905 24 17339098 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416710 Affx-122947559 AX-123287058 24 17231566 AGGTGATTACCTCACTAGAACCTGCTTGTGAAATT[A/G]CAGTGGTCAGGAAAATGTGGGGTGGCTATAAGCTC R 2 1 2 1 101000 f 74 goat snp8206-scaffold13-1661767 24 17385789 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785378 Affx-122949500 AX-385272423 24 17307204 CCTCCTCTAAGATTACATATGGAAAAATGAGCCCT[G/T]ACCTCCTTCCTTATAGCATGTATAAATATAAATTC K 2 1 2 1 101000 f 74 goat snp8204-scaffold13-1586129 24 17462000 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434965 Affx-122933844 AX-123305305 24 17340512 TTGGGATAAACATGGAAATAGTAAAAGCAAAAAAG[A/G]GCAGGGTTGGAGGGCTAGGATATAACAGGGGATAC R 2 1 2 1 201000 f 74 goat snp8203-scaffold13-1552821 24 17495489 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430029 Affx-122937579 AX-123300370 24 17436937 TGAGAGGTCAGTTTCTGGATCTTTTATTTCAAATT[A/G]CTCAGGTGGAGGGACTGAGCTACAAATAAGCTTGC R 2 1 2 1 101000 f 74 goat snp8202-scaffold13-1456396 24 17593794 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433225 Affx-122935616 AX-123303566 24 17472509 AGCATGTTTGCAGTAATAAACAACAATGTTATTAG[C/T]GAATATAAAGCCCATGATAAACAATGCCATGATGT Y 2 1 2 1 101000 f 74 goat snp8201-scaffold13-1420824 24 17628941 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385712 Affx-122971108 AX-123256070 24 17530414 ATGGAAGACTAGACTTTCTGCCACTTACAGTTCAC[C/T]AGGTTACATCATAGGGCTTCCATGGCTACCTACTC Y 2 1 2 1 101000 f 74 goat snp8200-scaffold13-1362919 24 17687260 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436790 Affx-122932256 AX-123307128 24 17560250 CCTTGCCTGGATAAGGATTTGAATGCAGACTCAGC[A/G]TTTAAATATGATATGAGTCAACCGAATCCAAATGC R 2 1 2 1 201000 r 74 goat snp8199-scaffold13-1333083 24 17717497 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398195 Affx-122962639 AX-123268550 24 17634428 TCCCTGTGTACATCACGTGTATTTGAGGTTAACAC[C/T]GTGTGTGAGCTAACAGAGGCTTTTTGCCAGCTTTT Y 2 1 2 1 101000 f 74 goat snp8197-scaffold13-1258905 24 17792182 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277682 Affx-1111835972 AX-519551181 24 17662537 GCAAGAAACTGACCAAAAACAATCACTAGGGTTTT[A/G]AATTATATATTGTTAAGCCAAAGAGTTTTCCTTCG R 2 1 2 1 101000 r 74 goat Random2.2K-2093 24 17662537 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447908 Affx-122923807 AX-123318244 24 17669257 ATTCTTATGTTTATGCATTCCCTCTAATATCCTGC[G/T]AAGAGCTCTGCACAGAAGAAGGGTTTATAAATATT K 2 1 2 1 101000 f 74 goat snp8196-scaffold13-1224076 24 17827038 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415364 Affx-122948771 AX-123285713 24 17703847 TCCAGCTGTCACTAAGCTAATTATGGCCATTTCTC[C/T]TACACTGATTTGTATTTACAAATCACTCCTAGATG Y 2 1 2 1 101000 f 74 goat snp8195-scaffold13-1189486 24 17861838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769822 Affx-122965318 AX-385256992 24 17804149 GGGAACCCATATGTATTGGTGTATAATGGTCTTAG[A/C]TAAAATGCATCTTGAGTGGCAAAATTTTGAGTAGG M 2 1 2 1 101000 f 74 goat snp8193-scaffold13-1089184 24 17962447 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396946 Affx-122963181 AX-123267301 24 17861277 TCCTATCTTGGCCTTTCCCCATGTAGCCCAAATTT[A/G]TGTGTACTCATTCTCCAATACTCATCTCTATTCAA R 2 1 2 1 101000 r 74 goat snp8192-scaffold13-1032056 24 18019698 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434407 Affx-122934681 AX-123304748 24 17908770 AAAGAAGATATTTTTATTCATAATTCAGTTGCCTT[A/G]TACTTCTAGGAGAATTTAGTCTGTTGATTCATTAG R 2 1 2 1 101000 r 74 goat snp8191-scaffold13-984563 24 18068331 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398943 Affx-122960988 AX-123269298 24 17939348 TATTTCAGAATCTGCATGAAATGGTCCTGAACTGC[A/G]TTAAAATCTAGCACACTGTGTTGTTTAAAGAGTTC R 2 1 2 1 201000 r 74 goat snp8190-scaffold13-953985 24 18098965 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445679 Affx-122926134 AX-123316016 24 17978909 AGGTTGGGAGTTCTAGTCATCTCATAACATTTTCA[C/T]GATTTTTTTCAGCTGATATTTTGTGTTTTTATTTT Y 2 1 2 1 101000 f 74 goat snp8189-scaffold13-914424 24 18138881 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417556 Affx-122946915 AX-123287904 24 18092475 AAGCAGAAGTCAGAATTTGTTTTTGAAATGACTTT[A/G]CAACTGCCGCTGCATTTATAAAGGAACCTAGTAGA R 2 1 2 1 101000 r 74 goat snp8187-scaffold13-800858 24 18250559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428820 Affx-122938381 AX-123299162 24 18156050 TTTCAACCCTATATTACAAATCATTAAAAACTGTT[A/G]CTAACTGACATCTGTTACTATATTTCTGAGACAGG R 2 1 2 1 101000 r 74 goat snp8186-scaffold13-737283 24 18314693 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383418 Affx-122973483 AX-123253776 24 18197220 TCATAGAATCCCAAGGACAGTTAAAACTGCAGAGG[C/T]GACAACACTGACCACAGACTCTCAGGGAATCTAAA Y 2 1 2 1 101000 f 74 goat snp8185-scaffold13-696113 24 18356504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792808 Affx-122947603 AX-385279786 24 18250832 TTAAATAATAATAGAAGATATCCGTATATGATGCC[A/G]CAAGGCAAGATATGTTCTGTTGGTAAGGACAATGA R 2 1 2 1 101000 r 74 goat snp8184-scaffold13-642501 24 18409927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383850 Affx-122973150 AX-123254208 24 18287817 GTTGCCTTTGTCTTTGTCCTATGTCATTCATTGTT[A/G]CATATGAGAATCATACTCCCTGGTGTCACAGACAG R 2 1 2 1 102000 f 74 goat snp8183-scaffold13-605516 24 18447655 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385725 Affx-122971099 AX-123256083 24 18338227 TTTTGATTCTGGGCAATCTTGTGATGACAGGGAAT[A/G]TGAGGAGATGACATTTCTGGGTTTGCCCTTCCTAT R 2 1 2 1 101000 f 74 goat snp8182-scaffold13-555106 24 18498645 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420679 Affx-122944806 AX-123291026 24 18374592 AGTGTTCCAGCTTGCTTGTCACTGTGTCTGGAGCA[C/T]GTAAACTTGGGTTTGGCAACCCCATCCCATCCTTT Y 2 1 2 1 101000 r 74 goat snp8181-scaffold13-518741 24 18535902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786205 Affx-122949185 AX-385273240 24 18423053 TTATTCCAATGCTTAATTAAAGCTGTTAGTGATAT[A/G]CTTTTCCTGCAAATGAATGAAACAACTCGCACTCA R 2 1 2 1 101000 r 74 goat snp8180-scaffold13-470280 24 18584920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426038 Affx-122941114 AX-123296384 24 18459549 TAAGTAGCCACCTATAAATGTAAATCTTGGAGGGA[C/T]ACACTGAATATCCAAATTCCAATACTTTAGTTATA Y 2 1 2 1 101000 f 74 goat snp8179-scaffold13-433784 24 18624117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277685 Affx-1111835973 AX-519551184 24 18467441 GTAAAAAAAAAAAAAAAAAAAAGATAGAGGGATGA[A/C]TGTTGTTTCCAGTTCCATGTATAAGAAGCCTGGAA M 2 1 2 1 101000 r 74 goat Random2.2K-2094 24 18467441 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399473 Affx-122961192 AX-123269828 24 18489240 GATTTTGTAGATGAGGAATACAAATGGAGAACACC[A/G]GCACAAAGGATATGAGAGCAGTTTTTTCGGGAGGG R 2 1 2 1 101000 r 74 goat snp8178-scaffold13-404093 24 18653466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437929 Affx-122931637 AX-123308267 24 18559858 TTGTGTGGTTAACAATGTTGCCACAGCCCCAATAC[C/T]GCTTTCTTCTGAGCCACAGTAAGAAAAAATCATCC Y 2 1 2 1 101000 f 74 goat snp8176-scaffold13-333475 24 18723569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419749 Affx-122945883 AX-123290097 24 18606209 CCCTTTTGTTAATCTTCCAGAGAATTAACTCCATA[C/T]GCAAATCAATGTATCAATTATGCTTTTCCTTAAGA Y 2 1 2 1 101000 r 74 goat snp8175-scaffold13-287124 24 18768798 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273681 Affx-1111833777 AX-519547293 24 18608389 AAATCCTTAACTGCAGAAATGAATTTCCCTGGAAA[A/C]GAAGGAGAAATTTTGCCAGTGGTCTGCAGATTTA M 2 1 2 1 101000 f 74 goat GoatD01.004364 24 18608389 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320795072 Affx-122965480 AX-385282031 24 18639778 TTTTACTTTCATTTGAGATGATACCCATTCTCCCC[A/G]CTATTTTCTGTAACATTCAGAACAGTTTTGGAGAG R 2 1 2 1 101000 f 74 goat snp8174-scaffold13-253555 24 18802189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788970 Affx-122964505 AX-385275983 24 18680775 GACACGGAGTATGTAAGAAATGAAATTGACTATGG[C/T]AAGGTCTAAAGAGAAGATGTGGTCATAAAAGTTAT Y 2 1 2 1 101000 f 74 goat snp8173-scaffold13-212558 24 18842889 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394595 Affx-122964427 AX-123264950 24 18711977 TTTGGGGCCACTACTAGCTTCTGAGTTCTGATTAC[A/G]CTGGCATCAGCATTGTTTTTCCAAGTGATTGTTTA R 2 1 2 1 201000 f 74 goat snp8172-scaffold13-181356 24 18875185 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273066 Affx-1111833271 AX-519546737 24 18729308 AAATACAATGATGTCTTATTGATAAAATATTAAAC[A/C]TGTAATTTTTCATTGGATTCCCTTGGATTTTCTTG M 2 1 2 1 101000 r 74 goat 24_18729308_AF-PAKI 24 18729308 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438824 Affx-122930784 AX-123309161 24 18740709 AGAGTCATTGTGCAAAAAACTGAGAGTGCAGGGGG[A/C]GTATACTGATCAAATAAAGTCCAGGGGAATGAGAG M 2 1 2 1 201000 r 74 goat snp8171-scaffold13-152624 24 18904093 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430592 Affx-122936991 AX-123300933 24 18798551 GTGAGAATCTGTCGTAAGCTAGATTTGGACAAGTT[A/G]TTCCAAATGAGTCAATCAAGTCCTCAATCAGCTCC R 2 1 2 1 101000 r 74 goat snp8170-scaffold13-94782 24 18962156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386959 Affx-122969975 AX-123257317 24 18837026 TCCAAGGGTTCTATATATATGCTTTTATATGCTTT[A/G]CCTACCACTTGCAGAAACATGCAACATACATATCT R 2 1 2 1 101000 r 74 goat snp8169-scaffold13-56307 24 19000668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802137 Affx-122924540 AX-385289041 24 18867230 CTACCTAGAAATACTCACTTGGTTAGGCTCAGTTC[A/G]CTGTTCATCATTATCCACTAGTACATTGTTTTTTT R 2 1 2 1 101000 f 74 goat snp8168-scaffold13-26103 24 19031727 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781843 Affx-122966894 AX-385268925 24 18900280 AATGCATGTATTGTGTGTGCATGGATATTAGCTAG[A/C]TAGATAGATAATAGACAGACATAAATACAAGGATA M 2 1 2 1 101000 f 74 goat snp633-scaffold102-6848 24 19074365 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384357 Affx-122972242 AX-123254715 24 18928877 GGAAAAGAGAGGCTGATTTCTGACTCCGCTGGCAG[G/T]GGGAACTCAGTGGTATTTGAGGATTTGGTAATATG K 2 1 2 1 201000 r 74 goat snp634-scaffold102-35445 24 19103538 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387446 Affx-122970378 AX-123257804 24 18958851 TCTATGACGGTAGTAACTGAGAGTCAAAACGTTAA[C/T]AGAAGAATTAAAAGAAATTTTAAAAGTCTACCATA Y 2 1 2 1 101000 f 74 goat snp635-scaffold102-65419 24 19133836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398542 Affx-122961529 AX-123268897 24 19005840 TATTTAATTGTTTTGTTTTTCCTAAGAGCTTTGAG[A/C]GCCACCCCTTACAGTATTTATTGTAATAGCTCATA M 2 1 2 1 101000 r 74 goat snp636-scaffold102-112408 24 19181645 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430102 Affx-122937523 AX-123300443 24 19058356 TCAGGCAGCCCTTCCTCATGTTCTCTCCATTCTCC[A/G]TTCCATCCCCTGCTATCTCTTAATTTGATTTTCTC R 2 1 2 1 101000 r 74 goat snp637-scaffold102-164924 24 19234739 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802607 Affx-122954613 AX-385289509 24 19087583 GAAGTCCTGAATCCATCTCCCTACACATTACTTGT[A/G]CTCTTTATTCTCCTATGCTAACCTATTTTTTAGAG R 2 1 2 1 101000 f 74 goat snp638-scaffold102-194151 24 19263977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400065 Affx-122960763 AX-123270420 24 19201976 TCCTCTTCATGGACTTTCCTGACCTCTGTAAGTTT[A/G]TATCTAATATATCTCTGATGACTTTCCTCCATCAG R 2 1 2 1 101000 r 74 goat snp641-scaffold102-308544 24 19378192 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411829 Affx-122951239 AX-123282179 24 19251092 ATTCTTGCTTTGAGAACTCCATGAACAGTATGAAA[C/T]ACGTATACTCAATCCCCAAATATCTGATTGTTACA Y 2 1 2 1 303000 r 74 goat snp642-scaffold102-357660 24 19436046 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799461 Affx-122955621 AX-385286391 24 19320585 CCTGTGCCTTGCTGATCAGCACACTCTGCATAGTG[C/T]GTTTCTCCCTTCATTTTGTGTCTTGCAGACTCGAG Y 2 1 2 1 101000 f 74 goat snp643-scaffold102-427153 24 19505407 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800464 Affx-122957617 AX-385287384 24 19364812 AGAGTCTATTGTATTTACCAAAAATACTGACCTCC[A/G]TGCTTTCTGGGACCTCCTTCTATGGAACTGCTGGT R 2 1 2 1 101000 r 74 goat snp644-scaffold102-471380 24 19549688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429377 Affx-122938551 AX-123299719 24 19413195 GCATGCACAGGTGTGAGCACAGTGGTGAATTCACA[C/T]GGCCCCCTTACTCCCCCCTCTCAGGGACCCACTTC Y 2 1 2 1 102000 f 74 goat snp645-scaffold102-519763 24 19598177 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414281 Affx-122949600 AX-123284630 24 19454026 CTTCCTGCACCATTTCATCCTCACCTGAGTGCAGG[C/T]GGGCAACCATGGAAGAAAAGTCCATATACTAATAT Y 2 1 2 1 101000 r 74 goat snp646-scaffold102-560594 24 19639050 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404325 Affx-122957010 AX-123274677 24 19482909 AAAAGAGCTAATAAAACAAGAGGACCAATGAAGAA[A/G]CTGACAGCTCACCTTCCTTTTCTCAGGAAGAAGTC R 2 1 2 1 201000 f 74 goat snp647-scaffold102-589477 24 19668030 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803282 Affx-122964780 AX-385290127 24 19528727 GACAAGAAGGTTGGTGCACTTGTCGTCATCACAGC[A/G]TATGACAAAAACAGTTGTCCAGCCCTCAGGGCACC R 2 1 2 1 101000 r 74 goat snp648-scaffold102-635295 24 19713813 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424138 Affx-122942005 AX-123294484 24 19590379 CTTTGGGGGCACTAGGGGATCGAGTCCTCTAATGC[A/G]CGTGGCAGTGAAAAAGATGACCCCTAAGCCCCATG R 2 1 2 1 101000 r 74 goat snp649-scaffold102-696947 24 19775482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781758 Affx-122978317 AX-385268840 24 19628646 CCAAGCGCTCAGCACGAAACCAAGCATCTCGGCTG[C/T]GCTGTGTCATTTTGTACTCCCGTTTCTCCTAGGAG Y 2 1 2 1 202000 f 74 goat snp650-scaffold102-735214 24 19813462 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429418 Affx-122938518 AX-123299760 24 19665030 AGAAGATGAGCGAGGAGACAGTGGACAGGAGCTCA[A/C]AGGGAGAGATCTGAGATTTCTGTCCTTAGAAATAA M 2 1 2 1 101000 r 74 goat snp651-scaffold102-771598 24 19849906 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402073 Affx-122958710 AX-123272426 24 19708866 CAGCCTTGGGAGGCCCACTTCCCATGTGGAAGCAG[C/T]GAGAGGCTGTTACTTGGCTGTTACTTGACGTTGAC Y 2 1 2 1 102000 r 74 goat snp652-scaffold102-815434 24 19893983 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439656 Affx-122930602 AX-123309993 24 19767289 GAGCTGGGGCCAGGACAAGGAGGGTGTGTTCAGTG[C/T]GACAAATAGAAAAGATGTTTCCAAGGGTAGAGCAG Y 2 1 2 1 101000 r 74 goat snp653-scaffold102-873857 24 19951972 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399668 Affx-122960508 AX-123270023 24 19822696 TTTCCTGTGTGAGGCCACGGATGAAGCTTCGCTGC[A/G]TAGCCGCTGTTACCAACCCACGTGGCCAGCGGGGT R 2 1 2 1 201000 r 74 goat snp654-scaffold102-929264 24 20004865 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445182 Affx-122925535 AX-123315519 24 19858230 AGTGTTAGTGTCTCATCAGAGCAAGTCTGCCGGCC[C/T]GGCCTCACAGGCCAGCCTCCCATTCGGCTCTCTAA Y 2 1 2 1 101000 f 74 goat snp655-scaffold102-964798 24 20040919 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426474 Affx-122940788 AX-123296820 24 19909818 ACGGCCTCCAAAGTCAAATAAATCCCAGGAAATAC[A/G]AGGTTTGAAAAAAAAAGCCATAAAGAAGAGAGAAG R 2 1 2 1 101000 f 74 goat snp656-scaffold102-1016386 24 20092551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277687 Affx-1111835974 AX-519551186 24 19912365 GCACGCACGCACGCACACACACAGCACCGTAAGTG[C/G]CAGAGCTGGGATTCAAGGTCAGGCGTTACAGGTCA S 4 1 2 1 103000 r 74 goat Random2.2K-2095 24 19912365 G C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449340 Affx-122922980 AX-123319675 24 19948867 TGGTAAGAAAGCAGGGTGGAGATGTAAAAGGGTCT[A/C]TGTTTCGGAAACTGCTTATGTTACAAAGGGGCTAT M 2 1 2 1 101000 f 74 goat snp657-scaffold102-1055435 24 20131510 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772093 Affx-122925630 AX-385259248 24 19979212 ATCTTGCTTAGGGTTTAGTAACACTTTTGGAAATA[C/T]ACTTGGGATTTGCATTCTAGAGGTGCCAGAACATA Y 2 1 2 1 101000 r 74 goat snp658-scaffold102-1085780 24 20161826 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391238 Affx-122967388 AX-123261595 24 20030898 ATAGCAGGGCTGGCCTGATGACACCTTTCTCAAAG[C/T]GCCTTTTCAATTGCAGCTTTTTAATGTTGCTATGG Y 2 1 2 1 101000 r 74 goat snp659-scaffold102-1137466 24 20213520 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414345 Affx-122950025 AX-123284694 24 20076891 TCAGAGAGAACTCTTGGGACTTCTGAAAACAAGAA[C/T]AAATACATTGACCTAACAATCACTCGTCTTAATCT Y 2 1 2 1 101000 r 74 goat snp660-scaffold102-1183459 24 20260410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449067 Affx-122923047 AX-123319402 24 20116737 GCTGTACCCCAAGGAAATGAAAGAAAAGAAAAGGA[G/T]AGATGAGAAATTGTATCAATTAGTACATGTTCACT K 2 1 2 1 201000 r 74 goat snp661-scaffold102-1223305 24 20300652 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387452 Affx-122970373 AX-123257810 24 20154292 TTATTAAGAGTTAAATATAATTCCTATAAGGATAT[A/G]TTAATAAAGCTAAAGGACATGCCCAAAGTAACTGC R 2 1 2 1 101000 r 74 goat snp662-scaffold102-1260860 24 20337994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450379 Affx-122922089 AX-123320714 24 20196478 TTTTTTTGGAGTCAAAATTTATATGCACATTTTCA[A/G]CCTTGTGGGGGTTTAGCACAGTTTGCAACCAAACA R 2 1 2 1 201000 f 74 goat snp663-scaffold102-1303046 24 20380970 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390682 Affx-122967954 AX-123261039 24 20228133 TCACTTTCTATCATATACAAAAAATCTGTTAAAAA[C/T]GAAATGCTAGCTCCACTGGGTGGCACACGACTAAG Y 2 1 2 1 201000 f 74 goat snp664-scaffold102-1334701 24 20413253 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778002 Affx-122923222 AX-385265118 24 20259734 TTCTCACTAATACCAGGATAAAAGGAAGAATGTCT[A/G]TTCTATTCAATACTTCCTGCTTCCATTTGTAAACC R 2 1 2 1 201000 r 74 goat snp665-scaffold102-1366302 24 20444937 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441732 Affx-122929136 AX-123312069 24 20332642 AAAGAGGAAGCCTCAAATGAAATAATTTCTAAAAA[C/T]ACACAGAAGGGAATGAAAATGAATATGTGAGATGT Y 2 1 2 1 202000 f 74 goat snp667-scaffold102-1439210 24 20517694 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770288 Affx-122960309 AX-385257454 24 20401132 GAGCAGTGGCTTTACTGGTGTATCAGTAGTTGGTA[A/G]TTAAGGTTTCTCTCCATGACCTCTGCTGAGCAGTA R 2 1 2 1 101000 r 74 goat snp669-scaffold102-1507700 24 20587047 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766900 Affx-122929076 AX-385254218 24 20442965 CAGTTCATTTTTGTTAGAGAATATTGAACACTCTC[A/G]CAATTTGATGGGTTATAATGTTCCATGTAAAATCC R 2 1 2 1 101000 f 74 goat snp670-scaffold102-1549533 24 20628842 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800984 Affx-122943998 AX-385287898 24 20473348 CTGCATGTATCTGGGGATAGTCTGGGATTTAGATT[A/G]TAGCACAAAGGCTGACTGCTCTATTTATCCTCTGT R 2 1 2 1 101000 f 74 goat snp671-scaffold102-1579916 24 20659234 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775607 Affx-122960345 AX-385262738 24 20519251 TGTATGTATGTATATTACCTGCTGAAAGAGAAAAG[C/T]AGATCCAGTTCTAGAAGCTATTTGGAAAGGAAATC Y 2 1 2 1 101000 r 74 goat snp672-scaffold102-1625819 24 20705219 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786383 Affx-122956374 AX-385273417 24 20559312 ATACTCTTTTTGGCTGCTGGGAAAAGAAAACATTA[C/T]TGAACTTGTAAATCCTCCTTGACAATGCTTTACAT Y 2 1 2 1 101000 f 74 goat snp673-scaffold102-1665880 24 20745311 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377978 Affx-122977616 AX-123248337 24 20588489 TGGGGACTCACAATGCTACCCCACCACTCTCCCCC[A/G]TTAACACACCATCTTCATGGCACTTGGTTTCCGGG R 2 1 2 1 101000 r 74 goat snp674-scaffold102-1695057 24 20774418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274477 Affx-1111834218 AX-519548068 24 20598710 GTGTCCACAGAACATGCTCTGGAC[A/G]TGAGGCTGTGTGATAGCCTCCCACACCCAGCCTCT R 2 1 2 1 102000 r 74 goat GoatD01.025943 24 20598710 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38448373 Affx-122924105 AX-123318709 24 20632837 GTTAATTTTACTGTATGATAATTTAAAAAGCCATA[C/T]AGTCGAATCTAAAAACAAACACTCAGTGTGAATCC Y 2 1 2 1 101000 r 74 goat snp675-scaffold102-1739405 24 20818501 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401104 Affx-122959409 AX-123271457 24 20663797 AACCGAGCACTCCTTGCAGGGTCAGCTGAAACCTT[C/T]CTGTGACATCACAGAGTGGACACAGGCTCCAAGCA Y 2 1 2 1 202000 r 74 goat snp676-scaffold102-1770365 24 20850855 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430174 Affx-122937365 AX-123300515 24 20726171 ATGAAAACTAATACAGAACACATAAGAGGCAGAAT[C/T]GAGTGGCTCTGCATTCATCCCTTCTGCTTTTTCTG Y 2 1 2 1 101000 f 74 goat snp677-scaffold102-1832739 24 20913363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391521 Affx-122966659 AX-123261878 24 20759229 TTACTGTCAACACTGAGTGAGTCAAAGAAATTCTA[C/T]GCTGGAAATCCTTCCCCTGAATCCAAAAGTGCCGC Y 2 1 2 1 101000 f 74 goat snp678-scaffold102-1865797 24 20946756 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422046 Affx-122943613 AX-123292393 24 20818594 CTCAGCCTCAGCCAATCCTGTCAAGATAATCTCTG[C/T]ATTCCTGGTGGGGGGCGGGGGAACAGCACTGGTGG Y 2 1 2 1 101000 f 74 goat snp679-scaffold102-1925162 24 21006765 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412147 Affx-122951086 AX-123282497 24 20870575 AATATTCACTCTCCTATTCTTTCTTAGGAAAAGAA[C/T]CCCAGTTTTACTTAGGGTGGCCCTGCCATCAGCTA Y 2 1 2 1 202000 f 74 goat snp680-scaffold102-1977143 24 21058517 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418499 Affx-122946436 AX-123288847 24 20973663 CACTACGCAGATATAATGCTATATTTTAATTCTGG[C/T]AGAAAATGTTAAGAATAGCTCCCTTTGGGTGGTAA Y 2 1 2 1 101000 f 74 goat snp682-scaffold102-2080231 24 21161246 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381205 Affx-122974529 AX-123251563 24 21043643 GTGATTCTTTCACCATTCTGCCTGGAACTGATTCC[C/T]CACCCCAACCCAAGTACAAAGGCTCCTCTATGTCC Y 2 1 2 1 101000 f 74 goat snp684-scaffold102-2150211 24 21230816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770958 Affx-122976847 AX-385258121 24 21086154 TTGTATGAAAAAAACTAAAAGATCAAACGAAATAC[A/G]TGAAACAATGGCACTTCAAAATACTTAATGTCTGG R 2 1 2 1 101000 r 74 goat snp685-scaffold102-2192722 24 21273288 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802680 Affx-122976878 AX-385289579 24 21120357 TTTCTGCGGGTTTATGTCTAGATAGTTAGGTGAAA[C/T]AGCTGGCAGACTGAACACATTAGATTTGTACTCAA Y 2 1 2 1 101000 r 74 goat snp686-scaffold102-2226925 24 21308069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394644 Affx-122964389 AX-123264999 24 21151482 GCAGACCATGAGTAATCATCGTTAATTAACTGTTC[A/G]GAAATGCTGTGTGACATGATGAGCTAGATTCGTGT R 2 1 2 1 101000 f 74 goat snp687-scaffold102-2258050 24 21339899 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449028 Affx-122923081 AX-123319363 24 21199606 CTTCTCCAAGGGATCTTTGTGGCCTAGTGATCGAA[C/T]GCATGTCTCCTGCATCTCCATGAATTTTGACCACT Y 2 1 2 1 101000 f 74 goat snp688-scaffold102-2306174 24 21388595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799774 Affx-122956869 AX-385286701 24 21243065 TTTTAAGAGCTTGATGCAATTTGTGGTAAGTGATC[A/G]TACTCAACCTGAATCCTACCCCCAGTTTCGCCCTT R 2 1 2 1 101000 r 74 goat snp689-scaffold102-2349633 24 21431890 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766286 Affx-122977528 AX-385253676 24 21297582 CATTTAAGAAAATTTGGAACAGGGAGGAAAGGCTC[A/C]TGAATCAACCTCAATTATTGGCGAAGGGATTGTTT M 2 1 2 1 101000 f 74 goat snp690-scaffold102-2404150 24 21486952 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405007 Affx-122956384 AX-123275359 24 21330848 GAAACGAAATATTTTAGTGATTGTGAGGAAAAGGC[A/G]CAGAACTTCTGAGAAAATCACAGTCCGACTGCCCA R 2 1 2 1 101000 f 74 goat snp691-scaffold102-2437416 24 21520116 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273068 Affx-1111833272 AX-519546739 24 21342858 TGTCTGTGGATTGGGGCATGACATGAACTTCTGGA[A/G]CACAATGGACTTGTTCATAGCATATAGCAAGCAAA R 2 1 2 1 101000 r 74 goat 24_21342858_AF-PAKI 24 21342858 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38383440 Affx-122973467 AX-123253798 24 21403391 TCAAGTTTAGAAAAATTTGAATCTTGACTAAGGCC[A/G]TCAAGCTAGTAAATTTCAAGACTGAATCCATAACC R 2 1 2 1 101000 r 74 goat snp692-scaffold102-2509959 24 21592745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403120 Affx-122958120 AX-123273473 24 21456589 TTTCTCTTTTGTGTGTTTTTCTACAGTAGATTTTT[A/G]GTTTGAAGTTACCATGAGGTTTTAATATAGCAGTT R 2 1 2 1 103000 f 74 goat snp693-scaffold102-2563157 24 21645989 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422265 Affx-122943995 AX-123292611 24 21501398 AAACCACAATTACTTTTTCACCAACCTAATAACTA[C/T]AGAGAAGCACAAAATCACAGGGGTCAGAAACAATT Y 2 1 2 1 101000 r 74 goat snp694-scaffold102-2607966 24 21691530 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797948 Affx-122944860 AX-385284884 24 21559741 TCCTTTCTTCTAACTACTGTACTCTTTCTGTGTGT[A/C]GAAGCTCCTAAAAGGATAAGCTACACACCAGTAAA M 2 1 2 1 101000 r 74 goat snp695-scaffold102-2666309 24 21749579 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389079 Affx-122968592 AX-123259437 24 21595620 GACTATATGGGAATTCATTATACTATTCTACTTGC[A/G]CATATATTTGAAATATTCCACAGTAAATGTTAAAG R 2 1 2 1 101000 f 74 goat snp696-scaffold102-2702188 24 21785492 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400534 Affx-122960444 AX-123270889 24 21632174 GATGCTGTCGCCCCATTAACAGAGTCAGCCAGGAC[C/T]GCCTCAGTTTTGCCCTGTTGACTCATTTAGAGCCA Y 2 1 2 1 101000 r 74 goat snp697-scaffold102-2738742 24 21821986 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433446 Affx-122935066 AX-123303787 24 21661091 GGAGACCCTGGAAGGTGACTTTTTAAGAAGAAATC[A/G]AGAGAAACAGGTACATGAAGAGCAGATGAGTCCAG R 2 1 2 1 101000 f 74 goat snp698-scaffold102-2767659 24 21850974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424094 Affx-122942036 AX-123294440 24 21692216 TTGAAGAGGAGGGAATAACTTTAATCTATGAGACC[A/G]GTGTTATCCTAATACCAAAACCAGGCTCAGACAGG R 2 1 2 1 201000 f 74 goat snp699-scaffold102-2798784 24 21882577 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428321 Affx-122939007 AX-123298664 24 21723700 ATGGAAATAGTCTGTCTTCACAGGGACCTGGGTTA[A/C]GCAAATGGAAACATTTGGCAAAACTCACGAAACCT M 2 1 2 1 101000 f 74 goat snp700-scaffold102-2830268 24 21914228 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401038 Affx-122959665 AX-123271391 24 21762636 TAGGAATGCATTCATTTAACAGGAGGTTTTGAGGG[C/T]CTGATATGTGTGGTGACCAGTGCTCAGTATCAGAG Y 2 1 2 1 101000 f 74 goat snp701-scaffold102-2869204 24 21953107 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381937 Affx-122974127 AX-123252295 24 21810620 CTTCCTTTGACCCCAATAAGTCAAGTCCTTGGGAC[A/G]TCTTTGAAGGAAATAATTTGAAAATTAACATGTTT R 2 1 2 1 103000 f 74 goat snp702-scaffold102-2917188 24 22001230 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394604 Affx-122964421 AX-123264959 24 21840763 TCTGTCACATTTGTGTAAGTTGCAGGGAGGGTTCT[A/G]TGTACTGAAATAATCTGCATGCCAGTCATTGGGTT R 2 1 2 1 101000 f 74 goat snp703-scaffold102-2947331 24 22031066 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800839 Affx-122964421 AX-180660640 24 21840763 TCTGTCACATTTGTGTAAGTTGCAGGGAGGGTTCT[A/G]TGTACTGAAATAATCTGCATGCCAGTCATTGGGTT R 2 1 2 1 600000 r 74 goat snp703-scaffold102-2947331 24 21840763 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393323 Affx-122965950 AX-123263679 24 21899968 TTCATGCCTGCCAAGGAGACAGCTGTGAATGATAA[A/G]GTTACTGAGCAGCAGTGTCTGGTTCTGGCCAATCA R 2 1 2 1 101000 f 74 goat snp704-scaffold102-3006536 24 22090761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433239 Affx-122935248 AX-123303580 24 21947093 TTATATTACACTTCCTAGCATGGAGCTTGGTATAT[A/G]GTAGGCTTCACATGTATTTCTTCTCCTCTGCCTTT R 2 1 2 1 101000 r 74 goat snp705-scaffold102-3053661 24 22137873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442692 Affx-122927880 AX-123313029 24 21981142 TTTGACTCAGGACATTGGGTTTTCATTTTGCAGTA[C/T]GAAATTAAAGGCCAGAGGATTCCCAAGGAGACTGA Y 2 1 2 1 101000 f 74 goat snp706-scaffold102-3087710 24 22172713 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385041 Affx-122971848 AX-123255399 24 22010568 ATGAGCATCCGCGCTCTGCTCACACTCACGTGTTC[A/G]TCCGAAGCGTAGAGGACTTCCATTAGTCGCTGCAC R 2 1 2 1 101000 r 74 goat snp707-scaffold102-3117136 24 22202146 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446399 Affx-122925576 AX-123316735 24 22052682 GCATCATCCTCACCGTCCCAAGCCAGTGGCTTGAA[C/T]GAGGCTCTCTTTCTAGTTTCTTAGCATCTTTTGCT Y 2 1 2 1 101000 r 74 goat snp708-scaffold102-3159250 24 22245073 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398876 Affx-122961038 AX-123269231 24 22089024 ATTCTTGGCTGACAAATGTGGATTCCTAGTCTTTT[C/T]GAAGGACAATTCAAAATATTGATTTTTAAAATTTT Y 2 1 2 1 101000 f 74 goat snp709-scaffold102-3195592 24 22281875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406716 Affx-122955759 AX-123277067 24 22134638 TATCACCAAATAAAATGCTACATTTTCACTTTTCA[A/G]CTAGCCTGGAGACATACAACTGGGTAAGAAACAGC R 2 1 2 1 101000 r 74 goat snp710-scaffold102-3241206 24 22327501 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403665 Affx-122957511 AX-123274017 24 22179918 TAGGATGGGATTAAATACATTTACAATTTGTTTTC[A/G]TTTTTAGAAAAGATTTAGCTGATTTCAGATACTTC R 2 1 2 1 201000 r 74 goat snp711-scaffold102-3286486 24 22373205 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791478 Affx-122947342 AX-385278469 24 22222956 CATCAGAGCTTATGGTGTGGTTGTCGATAAGCTCT[A/C]TTCATCTGGCCTAATGACTGAGTTTCAGATTTCTC M 2 1 2 1 101000 r 74 goat snp712-scaffold102-3329524 24 22416152 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776644 Affx-122934993 AX-385263771 24 22275257 GTCAACAAGAATGAAAACCAGGAAGGACACAAATA[C/T]GAATGATTCACATTTCTGAAGTATATTTTCCAAAT Y 2 1 2 1 101000 f 74 goat snp713-scaffold102-3381825 24 22468045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277690 Affx-1111835975 AX-519551188 24 22288564 TCATGTTCATCTGTTAACACTCCCCCACTACCCCC[A/G]CATAAAACCAGGTGCATAAGGCCTAGAAGCAGAGT R 2 1 2 1 102000 r 74 goat Random2.2K-2098 24 22288564 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789226 Affx-122931589 AX-385276237 24 22307538 TGACATTCTCTACATTTATGAGTTTGTGGAAATAA[A/G]CCATTTATCTTATTTTGCTACAGTTCTTAGCATCT R 2 1 2 1 101000 r 74 goat snp714-scaffold102-3414106 24 22500148 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391156 Affx-122967448 AX-123261513 24 22337352 GTGATGGACTTAACTTGTGAGGCAGTTTTGTACCA[C/T]GAACATGAAACAATGTATATTTTACCTTGTTATCA Y 2 1 2 1 101000 f 74 goat snp715-scaffold102-3443920 24 22529988 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277692 Affx-1111835976 AX-519551191 24 22350015 GCCATACCTCACTGAGCATCTTCTATATCCCAGGA[A/G]TGTACCAGGCACTCTCCAGGAGTTTCAAATCAATG R 2 1 2 1 101000 r 74 goat Random2.2K-2099 24 22350015 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444173 Affx-122927277 AX-123314510 24 22391493 CCGAAGGAGAGGTTTCTGTGAGTGAGTGACACAGA[C/T]ATGTTCACTAGTAAGTGTCACACAAAGCAGAGTAA Y 2 1 2 1 101000 r 74 goat snp716-scaffold102-3498061 24 22584040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415093 Affx-122949452 AX-123285442 24 22502718 GGCAAATTCTTAATCTGATAGTAAGAAGAATAACT[A/G]CATTCTTTCATAACACATCTCCTGGTATCACTGTA R 2 1 2 1 101000 r 74 goat snp718-scaffold102-3609286 24 22696236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430427 Affx-122937744 AX-123300768 24 22545986 GAATTCTCCAGGCAAGAATACTGGAGTGGGTAGCC[A/G]TTCTTTTCTCCAGACTCTCAAAGACTTCCCTCAAA R 2 1 2 1 103000 r 74 goat snp719-scaffold102-3652554 24 22739746 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434237 Affx-122934833 AX-123304578 24 22578112 AACTAGACACCTTTGAAAATTTAAAGGCTATTTGT[A/G]TTTACCAAGTCCTTTTCTTCCCCCATAGTTTAAGA R 2 1 2 1 101000 f 74 goat snp720-scaffold102-3684680 24 22771834 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402042 Affx-122958732 AX-123272395 24 22617645 TTATAGCTGAAACACCATGCTTCTGCTGAGTATCC[C/T]CCAACCTTGGCTTCTTAGACTCTCCTCCTGGCTGG Y 2 1 2 1 101000 f 74 goat snp721-scaffold102-3724213 24 22811354 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446095 Affx-122925804 AX-123316432 24 22665430 ATGGTGGGAAAGGGACTGCTCATCCTAATTGCTCA[C/T]GACTCGAAAGCATCCTACCCAGACAGGCAGTGCTT Y 2 1 2 1 101000 f 74 goat snp722-scaffold102-3771998 24 22859943 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425587 Affx-122941415 AX-123295933 24 22705523 TAACCTAAACTGAGCAGGGATATGATTTTACAGAC[G/T]ACCAACGTACTGTGATTTGAATTTTAAATACAAAA K 2 1 2 1 101000 f 74 goat snp723-scaffold102-3812091 24 22900057 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384315 Affx-122972274 AX-123254673 24 22757121 AGGGGACACAGTATTGGGCCACTGCCTTGAGTCAC[A/G]CTAAGGTACACGCAGTTTTACTCACTATTGTTTTT R 2 1 2 1 101000 r 74 goat snp724-scaffold102-3863689 24 22952317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426960 Affx-122940406 AX-123297305 24 22793660 GCCACAATAAATGTGTACAATAAATAAAGGCCTGA[A/C]AAAGAAATGGAATTTTAGTCTTGCATTAATATCTG M 2 1 2 1 101000 f 74 goat snp725-scaffold102-3900228 24 22988820 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451643 Affx-122921606 AX-123321976 24 22827165 TTTGCCTCCACTGTGCCTTCACCTGAAGCACTGAC[C/T]AATGCTGAACAGAAACACATCCATGACAACTGGTA Y 2 1 2 1 101000 f 74 goat snp726-scaffold102-3933733 24 23022672 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776251 Affx-122973410 AX-385263379 24 22871547 AGATTCAGTGTTTTCAACTAGATCTCGAGTCTGCT[A/G]TTAGGCTCCAGTTTGCCCATTGTAACCCTACCTGC R 2 1 2 1 101000 f 74 goat snp727-scaffold102-3978115 24 23069037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400923 Affx-122959726 AX-123271276 24 22917920 TCTCCAGTTCATATTAAAAGAAATAGTCGTTAGAC[A/G]CTGGATGATCTGCTCCATGTAAATTGTTGCCCTGA R 2 1 2 1 101000 r 74 goat snp728-scaffold102-4024488 24 23108467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389937 Affx-122968094 AX-123260294 24 22997339 CAGGTAACTGCCTGGGTTTGATTTTCACCTCTGTC[A/G]CATATTGGCTGTGTGACTTTTGGCAAATTGCTTAA R 2 1 2 1 102000 f 74 goat snp730-scaffold102-4103907 24 23180662 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799058 Affx-122974289 AX-385285988 24 23041707 TTTGGATGACTGATAACTCGAGTATTTTCTATATT[A/G]TAAAATACTATAAAGCTCCATTCTTTTAATAAATC R 2 1 2 1 101000 f 74 goat snp731-scaffold102-4148275 24 23225223 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782020 Affx-122935127 AX-385269099 24 23086925 TGACCTCTATATCTTTGTATGGACTTCACATATCC[C/T]TGGGCAAGAGAAGCTAGAGAATAAATTAGGCTGCT Y 2 1 2 1 101000 r 74 goat snp732-scaffold102-4193493 24 23268004 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420446 Affx-122944894 AX-123290793 24 23138998 AATAAGAATTTATTGACCATCTACTGTGGTCATCT[A/G]CTATGGATGAGAACTACTATATAAAGTGTTAGAAA R 2 1 2 1 101000 r 74 goat snp733-scaffold102-4245566 24 23321032 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405017 Affx-122956376 AX-123275369 24 23180269 TAGGAATTATAGAGCAAAATGCGAAAGTTCAGGCG[C/T]TCATCAAAACAGTCTGGTGGGAATGACTGAAAAAT Y 2 1 2 1 101000 f 74 goat snp734-scaffold102-4286837 24 23363031 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393322 Affx-122965951 AX-123263678 24 23212441 TTGCTCCTGTGATTAGAGCCTGTCCTTGCAATGAC[A/G]TGGTCTGAATTCGGAGCTCCCAGACTGGGATAACA R 2 1 2 1 202000 f 74 goat snp735-scaffold102-4319009 24 23395288 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798846 Affx-122947042 AX-385285776 24 23243496 CAGTCCTTCAACACTTATTAAATGGAGATAGTGAA[A/C]CTCTGTGCAATTTTAGGTGATTCTCATCAATAAAA M 2 1 2 1 101000 f 74 goat snp736-scaffold102-4350064 24 23426212 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426709 Affx-122939890 AX-123297055 24 23290765 CAAAAATGACAAGTGAAATTGATAGACATTTTGAC[A/G]CTGAGAAGTAAGTGACTTGTAATAATATTTTTCAG R 2 1 2 1 101000 r 74 goat snp737-scaffold102-4397333 24 23474018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395869 Affx-122964003 AX-123266224 24 23323214 GTAGCCCTCAAGGTAAAAGATTCAGCCACATAGGC[A/G]TGGGGGCAGTGTTTCAGTTTGCTGTGAATGTATTT R 2 1 2 1 101000 f 74 goat snp738-scaffold102-4429782 24 23506485 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781554 Affx-122942494 AX-385268639 24 23412419 CAAAACTTCAAGTACAAGAAAATCTTCATTTTAGA[C/T]AAGCAGATCTAAAGGAGGGGAAAAGAAAAGAAATG Y 2 1 2 1 102000 r 74 goat snp740-scaffold102-4518987 24 23594195 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385365 Affx-122971638 AX-123255723 24 23447975 GGTATCAGAGGCAGGAGATTTAGACAGAAAAGAAA[C/T]ATAGGTTTGTAGAGGGCCAGCATGTCACCAGTGAG Y 2 1 2 1 101000 f 74 goat snp741-scaffold102-4554543 24 23629813 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448055 Affx-122923696 AX-123318391 24 23483828 AGATAGAAATACATTACCTTCTCAATAAATGCAAG[C/T]GGTACATAACTATGGGAGTTCCCTGATAATTAAGA Y 2 1 2 1 101000 r 74 goat snp742-scaffold102-4590396 24 23665944 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793904 Affx-122953026 AX-385280873 24 23541826 GAGGTAGGCCTTATTTGCTTTGATTTCTTCCTAAG[C/T]ATCTTTCACTATCAGCAATTTGTTAGTAAAAATGA Y 2 1 2 1 101000 f 74 goat snp743-scaffold102-4648394 24 23723623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801757 Affx-122950912 AX-385288665 24 23572495 GTCATAACTGGAGAGCTGCATACCAGGTAGATATT[A/G]TCTTAGTGTTTTCGCTTGTCACCTGAACTCTGCTG R 2 1 2 1 101000 f 74 goat snp744-scaffold102-4679063 24 23754128 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775734 Affx-122957154 AX-385262865 24 23601182 GTGTCAGTTCCATTAAAATAATTACATCTCAAGTA[A/C]GCACTTACTTTTACCTCAAGGCTTAAGATATGAGT M 2 1 2 1 101000 f 74 goat snp745-scaffold102-4707750 24 23783248 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399127 Affx-122960850 AX-123269482 24 23659776 CTAAAACCCTCCCACTCTTTCTTCTGAAATTCAGG[A/G]TTAGTCATTAGCAAAATCTGATTGACCTGGCCCTC R 2 1 2 1 201000 r 74 goat snp746-scaffold102-4766344 24 23842139 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426460 Affx-122940798 AX-123296806 24 23696314 GTGAGAAGCTGGCTGTCTGCAAGCCAGGAAGAGTG[C/T]CCTCACTAGAAACCTATCCTGATGGACCTGCATCT Y 2 1 2 1 101000 r 74 goat snp747-scaffold102-4802882 24 23878575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797543 Affx-122934372 AX-385284482 24 23726403 AGAAGCAGCTGTGGATGTAATAAGGAGAATAAGTC[C/T]GAGTGGAAGCAAGTCTGGAGTCAGTAAAACCACTT Y 2 1 2 1 101000 r 74 goat snp748-scaffold102-4832971 24 23908818 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454217 Affx-122919681 AX-123324550 24 23758646 AAACAACAATAACCCTTCACATTCATTTTGCAAGA[C/T]AAGTCACTCTATTTAAAAACAAATAAAAACAGCAA Y 2 1 2 1 201000 f 74 goat snp749-scaffold102-4865214 24 23941463 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401023 Affx-122959675 AX-123271376 24 23816823 TCAGTCTGGTTGAGATGGATTATTCTTTTTCTGTC[A/G]CTAAGTCGTGTACAACTCTGCAGTCCCATGGACGG R 2 1 2 1 103000 f 74 goat snp750-scaffold102-4923391 24 23999734 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437092 Affx-122932187 AX-123307430 24 23847394 ACGATTTTAAATTTCACATAGACAGGGCTTCCAGT[C/T]CAAGATGGCACAGTAGAAGGATGTTAGCACATCTC Y 2 1 2 1 201000 f 74 goat snp751-scaffold102-4953962 24 24030574 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388000 Affx-122969576 AX-123258358 24 23876758 TGCCTGAGGGTGAGCAGAACAGAATTACGGATATC[G/T]GAAATTTTATTTCTGTTCCCCCTAATCTAAACCTT K 2 1 2 1 101000 r 74 goat snp752-scaffold102-4983326 24 24060738 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273022 Affx-1111833273 AX-519546699 24 23891194 CTCTCGGCTAATAACTCTAGCTACAGATTTTCTTC[A/G]GGAAATGGCAGTTTTAGGGGCTTGTTTTTGAGGAA R 2 1 2 1 101000 f 74 goat 24_23891194_AF-PAKI 24 23891194 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398725 Affx-122961835 AX-123269080 24 23906573 CTGGTAAGTGTCTTCTCCTTTGCAAAATAGGGCCC[A/G]TATTGTACAAACCTCATAGGCTGTCGTGAAGAGTA R 2 1 2 1 101000 r 74 goat snp753-scaffold102-5013141 24 24090183 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434302 Affx-122934759 AX-123304643 24 24068028 TTATCTCTTTTCTGCATTTCCTCATTTGTCATGGA[A/C]GGTTCTTCACTTATTTGTTCTTTTAAGCAAGACTT M 2 1 2 1 101000 f 74 goat snp756-scaffold102-5174596 24 24254037 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777916 Affx-122922027 AX-385265032 24 24115975 TTACCGTACTGCGTAGAGTACCAGTAGTATACTAG[A/C]TTTATTTCAAGCCAGAGATGCCCAGAAACCTGTGT M 2 1 2 1 201000 r 74 goat snp757-scaffold102-5222543 24 24300506 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430484 Affx-122937241 AX-123300825 24 24261987 GAAACTTGCAAATAGTTTCAAAAAAATAATGTCAG[A/G]AACAATTATGTTTATTTGTGTGTAAATGAAATAAA R 2 1 2 1 303000 r 74 goat snp759-scaffold102-5368555 24 24448113 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277571 Affx-1111835979 AX-519551070 24 24294503 GTAAGGCACAAAATGGGAATCAGAAGAGAAACTGT[A/G]TAATTATGACATTTCTTGTTCAAGCCTAGGAGATA R 2 1 2 1 101000 f 74 goat Random2.2K-2100 24 24294503 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438369 Affx-122931316 AX-123308707 24 24298282 ACAGTCTTTTTGTGAAGAAGCAAAGAAAGCTGCAC[G/T]GCATCAGTGCAGATAGCATTGGGGGTAGAGAGTGA K 2 1 2 1 101000 f 74 goat snp760-scaffold102-5404850 24 24484801 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383226 Affx-122972765 AX-123253584 24 24341517 TCTGGGCAAGAACACCGGAGTGGGTTACCATTCCC[G/T]TCTCCATTCAGCTCTCATAGGCAAGGCCTATGTTT K 2 1 2 1 101000 r 74 goat snp761-scaffold102-5448085 24 24528715 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396619 Affx-122962882 AX-123266974 24 24377106 CACACAAAGTTGACATTAAACTATAACAGATGAAG[C/T]GGCCATGTTGGACACATCTCTCCTTTCCCCTCCTC Y 2 1 2 1 101000 f 74 goat snp762-scaffold102-5483674 24 24564952 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413034 Affx-122950992 AX-123283383 24 24411569 AGAGAGCTTTGAAAATATCTACACCAAAAAAATAA[C/T]ATACTACAGAAAATTATCATTCAAATTAAACAAAA Y 2 1 2 1 101000 f 74 goat snp763-scaffold102-5518137 24 24597995 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389223 Affx-122969053 AX-123259581 24 24459229 CTAATGCTACAGGAATCATTGCTGAAAATTGAAAT[A/C]GGTATTTCTGTGGTAATCCACTTCAGGCAGACCTT M 2 1 2 1 101000 f 74 goat snp764-scaffold102-5565797 24 24646193 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421077 Affx-122944237 AX-123291424 24 24490308 CAATTTAAGTAACAATACTTTGGCATTGTTTTTTC[A/G]TCAGTTTACAAGTTGCTTTCAGATGTGTTAGCTTT R 2 1 2 1 101000 r 74 goat snp765-scaffold102-5596876 24 24677275 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381660 Affx-122974747 AX-123252018 24 24524588 GACATTCTGAGATCAGTACGTGTCAGTAAAGATTT[A/G]AAGAAGAATTCGCTAGCGTGCTACAGGGGCAGGAG R 2 1 2 1 202000 f 74 goat snp766-scaffold102-5631156 24 24710996 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427527 Affx-122939514 AX-123297870 24 24559532 ATCAGCACTTGAAAGAACCAAGAGGGTCCCCAGAC[A/G]TGGAGAGAGCATCTGCAGGGCAGTCAGAAGATGCT R 2 1 2 1 201000 f 74 goat snp767-scaffold102-5666100 24 24746056 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375611 Affx-122978715 AX-123245970 24 24588806 CTCTCCAAGTTTACTTTATAGAATCACCTGCTTCC[C/T]ACTTTCTTAATCAAAAATATTAAATTCAAATGGTT Y 2 1 2 1 101000 f 74 goat snp768-scaffold102-5695374 24 24775798 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388281 Affx-122969759 AX-123258639 24 24647479 TGATTTAATTAACTATTGTCTGCCCACTGCTCACT[A/G]CTTGGCTATTGCTACGTGGGGTGCTCTCCTGCAGG R 2 1 2 1 101000 f 74 goat snp1776-scaffold1049-1495416 24 24833618 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419932 Affx-122945317 AX-123290280 24 24698445 ATTTAGCTCTGAGTAGAATGCACATTTTACTCTTT[A/C]TTTATTGTTGTTGTTTGTTGCTAAGTCGTGTCCAA M 2 1 2 1 202000 f 74 goat snp1775-scaffold1049-1444450 24 24885628 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771942 Affx-122964688 AX-385259098 24 24741587 CACTTCTCCAAATATCAATGAATAATTTCTACTGT[A/G]TATTTGTGGAGGAGCTAGAAATTCCTAGTGACCAA R 2 1 2 1 101000 r 74 goat snp1774-scaffold1049-1401308 24 24928886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414431 Affx-122949959 AX-123284780 24 24788066 GATCATGGCTAAAAGCAGCTAAGTGCTTTCTTTCT[C/T]GGTGCTTAGCAGTTTCTCTGGAAGTCAGCAGACAA Y 2 1 2 1 101000 f 74 goat snp1773-scaffold1049-1354829 24 24975959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794107 Affx-122937942 AX-385281074 24 24834138 CAAAGATAGTTCAATTTAGTAAGCCTACTTCTGAA[C/T]AAATGGACTGGCACAACAACAGTCTGGAAGAAAAT Y 2 1 2 1 101000 r 74 goat snp1772-scaffold1049-1308757 24 25021881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773039 Affx-122967555 AX-385260183 24 24885201 TTTTACCAATGTTAAAAGGAAAGCCAGTCAAGCGA[C/T]AATACTGTACATACACTTCCTCATTATTAACAGTG Y 2 1 2 1 101000 f 74 goat snp1771-scaffold1049-1257694 24 25073016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424593 Affx-122942207 AX-123294939 24 24943477 GTTCATGGGTCACAGAGGAGACCCTTTAAAAGAGC[G/T]CATCAGATGTGCATGCATCCCCAAACTGGTCTTGA K 2 1 2 1 101000 r 74 goat snp1770-scaffold1049-1199418 24 25131876 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774174 Affx-122919472 AX-385261311 24 24995558 TTCCTTTCTCACTACTCTAGTCTGCGTACAAACTT[C/T]CAGTATCCATGCTTTATCTACAGTTTTATACTCTT Y 2 1 2 1 101000 f 74 goat snp1769-scaffold1049-1147337 24 25184096 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797762 Affx-122922589 AX-385284701 24 25031880 CATTTTCATTTACATTTCTCTCACTCTGTGAATTT[A/G]GGAACAATAATCATCTACCACGGGCCTGGAGGGCT R 2 1 2 1 201000 f 74 goat snp1768-scaffold1049-1111015 24 25220303 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441070 Affx-122928911 AX-123311407 24 25089764 GATAAAATGATAAAACAAGTACCTGTTCCTCCTCA[C/T]GGGATATAACATCAATCTGATATGTATCTGAGTTC Y 2 1 2 1 101000 r 74 goat snp1767-scaffold1049-1053131 24 25277847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411268 Affx-122952316 AX-123281618 24 25141900 AAGATTTTTTTTACCCCCAGGCTTGTGCCTAAACT[C/T]AACAGCTGAGGCCCCATCTGCTCCCGATGTCATCT Y 2 1 2 1 202000 r 74 goat snp1766-scaffold1049-1000995 24 25330134 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439474 Affx-122930164 AX-123309811 24 25175177 AGATTCTTTACCGTCTGAGCCACCACAGAAGCTCA[A/G]TTCTCCTGTACCCAAAGTTTAAGAACCACTGGAAT R 2 1 2 1 101000 r 74 goat snp1765-scaffold1049-967718 24 25363329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391349 Affx-122967296 AX-123261706 24 25231757 ATAGTTCTAGTTATCTTGACTTGTACCTTTTTTCC[A/G]TCTCCCTTCTAGTTTATTTTGAAATAAACTTTGTC R 2 1 2 1 101000 f 74 goat snp1764-scaffold1049-911138 24 25420638 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277573 Affx-1111835980 AX-519551072 24 25300424 ACCAACAACACACCTCCTCCCAGGTGGTGCTAGTG[A/G]TAAAAAGCAAAACAAAACAAAACAAAAAAACCCGC R 2 1 2 1 303000 f 74 goat Random2.2K-2101 24 25300424 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424275 Affx-122941991 AX-123294621 24 25309165 TATGGTGCCATTTACTAAGAGAGGAATAAACAGCT[A/G]GAGGTGAGTGCGTTACTGTCCATGTTGAGCTGAAG R 2 1 2 1 101000 f 74 goat snp1763-scaffold1049-833730 24 25498214 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795278 Affx-122970532 AX-385282236 24 25343427 TTATGTCTAGTGCACAACTGAAGATGACAGGGCAC[A/G]GAGAAATTTATTGATCTACCCAAGAAATCTCATGT R 2 1 2 1 101000 f 74 goat snp1762-scaffold1049-799468 24 25532175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769724 Affx-122945266 AX-385256893 24 25374440 TTACTAAAATATTCAACTGATTGGACTTATTCTGA[A/G]TCGTATGTCAAAAATACAAGACAGAAAACTGCAAC R 2 1 2 1 101000 r 74 goat snp1761-scaffold1049-768455 24 25563524 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399497 Affx-122961174 AX-123269852 24 25411585 GTAGTGTTTCTAATTTATCCCCAAATATCTATTAC[A/G]TTTATGATAAACCTTACCAATCATGGTAACTTAGG R 2 1 2 1 101000 r 74 goat snp1760-scaffold1049-731310 24 25600569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428246 Affx-122939421 AX-123298589 24 25476511 GATGGTAATGCCATCTCTTGAGACAAGGAAGTTGA[C/T]AGAAGCATCACGTTGGGGAGGGTAGGGGAGCTCAG Y 2 1 2 1 101000 f 74 goat snp1759-scaffold1049-666384 24 25665416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394624 Affx-122964406 AX-123264979 24 25507539 AGTCTTTAGTATTTCAGTTGATGAAGCTCATCAAT[A/G]CTTCACTGCCTTCATCTGGGGAGGAAAAGAGTTCA R 2 1 2 1 201000 f 74 goat snp1758-scaffold1049-635356 24 25696336 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375706 Affx-122978645 AX-123246065 24 25538484 TCTGCACCTGAACTGACCCTTTGGGCTGCCTTGCC[A/G]TAAACAGGGTCAGAGAGGGGTTACTTACCACTGGG R 2 1 2 1 201000 f 74 goat snp1757-scaffold1049-604411 24 25727332 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376149 Affx-122978852 AX-123246508 24 25594404 TACACACATAGTCATGGCTGATTCACATTCATGTA[C/T]AGCAGAGACCTCCACAATACTGTAAAGCAACTATC Y 2 1 2 1 101000 f 74 goat snp1756-scaffold1049-548491 24 25783341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406473 Affx-122955173 AX-123276825 24 25663050 GAGGTCATGGGGCCAGTAACAGGAGGAACAGTAGT[A/G]TTTGCCACCAGGGCCAAGGCTGCGTTTAGCCTCAG R 2 1 2 1 101000 f 74 goat snp1754-scaffold1049-479845 24 25853564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797449 Affx-122919701 AX-385284388 24 25715234 TAGCTTTTGTCTTTGCGTTATAGACTTAGTAATTA[C/T]TGTGTGCCAGGTCTGCCACAAGACCATCATTACTG Y 2 1 2 1 101000 r 74 goat snp1753-scaffold1049-427661 24 25907224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776356 Affx-122938361 AX-385263483 24 25749650 TTTACGTAAAGTTACATATAATATCACACCTTTGC[C/T]AGCCCCAATAAGATTCTAGGGAAGAATAAAAGTGG Y 2 1 2 1 101000 r 74 goat snp1752-scaffold1049-393245 24 25941612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780603 Affx-122931128 AX-385267693 24 25778220 CAACAATAAAGGTTTTCATAATTACTTCCTATTTC[C/T]TTTAAAATGTGATCATAACTAGTTAATCAAGTTTT Y 2 1 2 1 101000 f 74 goat snp1751-scaffold1049-364675 24 25968896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435105 Affx-122933704 AX-123305445 24 25838557 GAGACAGATGAATAACATATTAATAAATTCTAAAA[C/T]GTTACAGAGAAGATGCATCTGGGGAATGTAGTTCC Y 2 1 2 1 202000 f 74 goat snp1750-scaffold1049-304338 24 26029912 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444786 Affx-122926346 AX-123315123 24 25872253 AATAGTACCTCAATTCTCCAAGAAAGCCTCACTCA[C/T]GTCACCAGAATCACGTGACTCTGCCTCTCTCTTGC Y 2 1 2 1 101000 f 74 goat snp1749-scaffold1049-270642 24 26063322 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801491 Affx-122933278 AX-385288400 24 25908535 ATGGAACAGTTTTTCTCAAGCACTAATATTTACTC[A/G]TAATGATTTGATTTAAAAACTGAGTCACAGACAAA R 2 1 2 1 101000 r 74 goat snp1748-scaffold1049-234360 24 26099464 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780087 Affx-122938539 AX-385267185 24 25942094 TAGATATATATATGACACCAGAGGCTCACATATAA[C/T]ATAAAAACATATTCCAAAGAGTTTTTCTGGAATGT Y 2 1 2 1 101000 r 74 goat snp1747-scaffold1049-200801 24 26132826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445190 Affx-122925529 AX-123315527 24 26029371 AACATTTGAGAGCACACTTGAAAGAATGGTCTAGC[A/G]CAACTTTTACTCTGCTTAAAAGGAGCCGTTTATCC R 2 1 2 1 101000 f 74 goat snp1745-scaffold1049-113524 24 26221038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468276220 Affx-1111835227 AX-519549770 24 26035051 GCCAAACTATTGGTTCCACATCCCCAGTGACCTCT[A/C]GACACAAAGTAACACGGTACAGTAACATACATTAC M 2 1 2 1 101000 r 74 goat ilmnseq_rs665821255 24 26035051 G T 1 recommended Goat_IGGC_65K_v2 Illumina 468275847 Affx-1111835040 AX-519549409 24 26035093 CACTGGGGATGTGGAACCAATAGTTTGGCTTATGC[A/G]AATGTCTGGACTCACCATTTGTGTCACTTGAATTT R 2 1 2 1 101000 r 74 goat ilmnseq_rs643647655 24 26035093 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275853 Affx-1111835116 AX-519549415 24 26035331 TAGACAGGTGCCATTACTGTTTCCGTTACTACAAC[A/G]TTGGGTGCAAGCGGAGGATCAAAGACAATCGTAGT R 2 1 2 1 101000 f 74 goat ilmnseq_rs654170858 24 26035331 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468275793 Affx-1111835012 AX-519549357 24 26035418 TCAGAAGTGTAAGTCTCGGTCACTACAATATCCCC[A/G]TGCATCACGGGTTCAGGTATTGCCATTTCTTCTTT R 2 1 2 1 101000 r 74 goat ilmnseq_rs640606090 24 26035418 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276172 Affx-1111835276 AX-519549722 24 26035490 AACTCAGCCTCTGAGAGAGTCATTCCTGAAGATTC[A/G]TTAACAAAGTAGTTCGGTCCAAGTAAAGGGAGGTC R 2 1 2 1 101000 f 74 goat ilmnseq_rs670607034 24 26035490 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468275942 Affx-1111835163 AX-519549500 24 26035491 TGACCTCCCTTTACTTGGACCGAACTACTTTGTTA[A/G]TGAATCTTCAGGAATGACTCTCTCAGAGGCTGAGT R 2 1 2 1 201000 f 74 goat ilmnseq_rs657954078 24 26035491 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275859 Affx-1111835119 AX-519549421 24 26035538 TTCGGTCCAAGTAAAGGGAGGTCAGTGCTGATGGG[A/G]ATACAGGACTGCTGTGAAGGAAATGGGTCAATTTC R 2 1 2 1 102000 f 74 goat ilmnseq_rs654310494 24 26035538 G A 1 neutral Goat_IGGC_65K_v2 Illumina 463907934 Affx-1110214992 AX-515385600 24 26035574 ATACAGGACTGCTGTGAAGGAAATGGGTCAATTTC[C/T]GTGTCTAAGCAGATTTCAGCAAGAGTCTTAAATTT Y 2 1 2 1 101000 r 74 goat ilmnseq_rs647312470 24 26035574 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275720 Affx-1111834973 AX-519549288 24 26035772 CCTTCATCTTCGCCTGCATAAGCATATGCTTTCTA[A/G]AGTTGGAAGAAAAACCGACAATTAGAAGTTTCTTT R 2 1 2 1 101000 r 74 goat ilmnseq_rs635516771 24 26035772 A G 1 recommended Goat_IGGC_65K_v2 Illumina 463907947 Affx-1110214998 AX-515385613 24 26038658 AGAAATAGCTGTCCAGGAAAGCCAGGTTCAGGCCG[C/G]TGTCCCCATAGTCCCGCTGGATGCCCACCGCCGAG S 4 1 2 1 202000 r 74 goat ilmnseq_rs662883683 24 26038658 G C 2 neutral Goat_IGGC_65K_v2 Illumina 468275745 Affx-1111835064 AX-519549311 24 26038755 TTGAAGGGGGTGTCTCGGGAGTGGAGCTCAGTACC[A/G]GTCTGGGGGCGGCCGCTGGCCTGGCAGCAGGAGGA R 2 1 2 1 103000 f 74 goat ilmnseq_rs646638321.2_F2BT 24 26038755 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 468272429 Affx-1111835005 AX-519546155 24 26038768 GGAGGAGGAACAGTTGAAGGGGGTGTCTCGGGAGT[A/G]GAGCTCAGTACCGGTCTGGGGGCGGCCGCTGGCCT R 2 1 2 1 103000 f 74 goat ilmnseq_rs639841415 24 26038768 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275614 Affx-1111834997 AX-519549184 24 26038774 TATGCAGGAGGAGGAACAGTTGAAGGGGGTGTCTC[A/G]GGAGTGGAGCTCAGTACCGGTCTGGGGGCGGCCGC R 2 1 2 1 102000 f 74 goat ilmnseq_rs638374939 24 26038774 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468276028 Affx-1111835208 AX-519549582 24 26038795 TCAGAAATCTACACTAACACCTATGCAGGAGGAGG[A/C]ACAGTTGAAGGGGGTGTCTCGGGAGTGGAGCTCAG M 2 1 2 1 103000 f 74 goat ilmnseq_rs663557093 24 26038795 T G 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275982 Affx-1111835104 AX-519549539 24 26038805 CTCCCGAGACACCCCCTTCAACTGTTCCTCCTCCT[A/G]CATAGGTGTTAGTGTAGATTTCTGAAAGGAGACGG R 2 1 2 1 101000 r 74 goat ilmnseq_rs651898969 24 26038805 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275950 Affx-1111835168 AX-519549509 24 26040984 AAGGGCTGGGGACGAGTTTTGCTCCTGTGCCTGAG[A/G]GGGGAGAAGGAGTGGTGCAGTCCTGGAGAATAGAA R 2 1 2 1 102000 f 74 goat ilmnseq_rs658801442 24 26040984 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468275741 Affx-1111835062 AX-371697197 24 26041006 TGCTGCAAACGAAAACAGCCAGAAGGGCTGGGGAC[A/G]AGTTTTGCTCCTGTGCCTGAGGGGGGAGAAGGAGT R 2 1 2 1 202000 f 74 goat ilmnseq_rs646230505 24 26041006 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276098 Affx-1111835240 AX-519549649 24 26042483 ATGGTAGCTCTGTTACCAGTGTGTCTGTCACTGAC[A/G]ACCAAACTGAGGCTTCAAATGTTGGTATGGGATCA R 2 1 2 1 201000 f 74 goat ilmnseq_rs667207355 24 26042483 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275649 Affx-1111835015 AX-519549219 24 26042539 CTGTGACATCAACCACATGTGCTTGTCCTCGGGCA[C/G]CACAGGCGTCAGCACCGGGGATGGTAGCTCTGTTA S 4 1 2 1 103000 f 74 goat ilmnseq_rs640859421 24 26042539 G C 1 not_recommended Goat_IGGC_65K_v2 Illumina 468275905 Affx-1111835143 AX-519549463 24 26042556 GAGTTAAGGGCCTGTGACTGTGACATCAACCACAT[A/G]TGCTTGTCCTCGGGCACCACAGGCGTCAGCACCGG R 2 1 2 1 101000 f 74 goat ilmnseq_rs656131357 24 26042556 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276265 Affx-1111835250 AX-284801403 24 26042601 GTAAGGGACAGTTTTAACAGAGCATGCGAATTGCC[A/G]CAGATCATAGAGTTAAGGGCCTGTGACTGTGACAT R 2 1 2 1 101000 r 74 goat ilmnseq_rs668073914 24 26042601 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275807 Affx-1111835095 AX-519549371 24 26044860 GCATTCTACTTACCATTTACTGATCTGATATCCCA[A/C]ATGTCCGCTGTCCCTGGGGGTTCATTAACAACACA M 2 1 2 1 201000 f 74 goat ilmnseq_rs650388637 24 26044860 A C 2 recommended Goat_IGGC_65K_v2 Illumina 468276061 Affx-1111835222 AX-519549613 24 26044929 CAGAAGGTAAAGGGAGACCCATAAGAGTGACTGTT[A/G]ACGCCTGCAGCAGAGATCAGGATGGAGGGAGAGGC R 2 1 2 1 101000 f 74 goat ilmnseq_rs665420347 24 26044929 A G 1 recommended Goat_IGGC_65K_v2 Illumina 468275843 Affx-1111835038 AX-519549406 24 26045011 CACGGGAACCATATGTATCGAAGTTCCTGACGTCA[A/G]CGATTACTGCCCAGTCATTGCTGCTGAGAGAGAAA R 2 1 2 1 101000 r 74 goat ilmnseq_rs643371902 24 26045011 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275872 Affx-1111835126 AX-519549433 24 26047827 TCAAAATATATTACCAATGGGATATACACAGCAGA[A/G]ATCCTGGCTATAGACGGTAAGAAAATTTGTTGTCA R 2 1 2 1 101000 f 74 goat ilmnseq_rs654962894 24 26047827 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275814 Affx-1111835098 AX-426427919 24 26047896 GACTTCTTATCAAATTCCCTAGAAAATTGTATCTC[A/G]CCAGTCCTTGAATCTATTTTTAACAAGTTGCCTGC R 2 1 2 1 201000 f 74 goat ilmnseq_rs650725832 24 26047896 G A 2 recommended Goat_IGGC_65K_v2 Illumina 463901419 Affx-1110215004 AX-515379145 24 26049414 ACCTGAATTCTCACAGGGGTTGAGTGCATTCGGAA[C/T]TGAGAAGCAACCGAGTGGTGAAACTCAGCTTGGTT Y 2 1 2 1 101000 f 74 goat ilmnseq_rs652105092 24 26049414 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468276163 Affx-1111835199 AX-519549713 24 26055044 AGAGAACTGTTTAAGTTCGGAACTGATCCGATTTC[A/G]AACAATTGATCTCGACGAAGAAGGCACTGACAACT R 2 1 2 1 101000 r 74 goat ilmnseq_rs662975292 24 26055044 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275816 Affx-1111835099 AX-519549379 24 26055061 TACTCAGCGAGTATCGAAGAGAACTGTTTAAGTTC[A/G]GAACTGATCCGATTTCAAACAATTGATCTCGACGA R 2 1 2 1 202000 f 74 goat ilmnseq_rs651326996 24 26055061 C T 2 neutral Goat_IGGC_65K_v2 Illumina 468276162 Affx-1111835271 AX-519549712 24 26056308 GATGGAGCTACGGATGGACTGTCTTCAGAGTGTGA[C/G]TGCAGAATCAAGGTTTTAGATGTCAATGATAATTT S 4 1 2 1 101000 f 74 goat ilmnseq_rs669472482 24 26056308 G C 1 recommended Goat_IGGC_65K_v2 Illumina 468276187 Affx-1111835284 AX-519549737 24 26056743 GAGAATCATCTGAATTCTAAAATTGCCTATAAGAT[A/C]GTGTCCCAGGAGCCGGCGGGCTCACCGATGTTCAT M 2 1 2 1 101000 f 74 goat ilmnseq_rs671963040 24 26056743 G T 1 recommended Goat_IGGC_65K_v2 Illumina 468275933 Affx-1111835158 AX-519549491 24 26056776 ACGATCTTATAGGCAATTTTAGAATTCAGATGATT[C/G]TCTTCATCTGCGTCTGTGGCACTTAACTTTACCAC S 4 1 2 1 101000 f 74 goat ilmnseq_rs657540481 24 26056776 C G 1 recommended Goat_IGGC_65K_v2 Illumina 468275678 Affx-1111835030 AX-519549248 24 26057428 AAAATGTGTACACAGCCAGCATTGAAGAAACCAGC[A/G]ATGCAAGTAAGCAGAGTGACACGCCTTCACTGCAT R 2 1 2 1 103000 f 74 goat ilmnseq_rs642582659 24 26057428 C T 1 not_recommended Goat_IGGC_65K_v2 Illumina 468276013 Affx-1111835201 AX-519549567 24 26057433 TACACAAAATGTGTACACAGCCAGCATTGAAGAAA[A/C]CAGCGATGCAAGTAAGCAGAGTGACACGCCTTCAC M 2 1 2 1 101000 f 74 goat ilmnseq_rs663179909 24 26057433 G T 1 recommended Goat_IGGC_65K_v2 Illumina 468276071 Affx-1111835226 AX-519549622 24 26057479 GCTGGCTGTGTACACATTTTGTGTAAAGACGGGGG[A/G]GTTGTCATTTATGTCCATAACTTTGACTCGAAGTT R 2 1 2 1 102000 f 74 goat ilmnseq_rs665773774 24 26057479 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468276344 Affx-1111835290 AX-519549877 24 26057483 GCTGTGTACACATTTTGTGTAAAGACGGGGGGGTT[A/G]TCATTTATGTCCATAACTTTGACTCGAAGTTCAAG R 2 1 2 1 201000 r 74 goat ilmnseq_rs672552458 24 26057483 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275940 Affx-1111835162 AX-519549498 24 26057543 AACTTTCCACAGATTTATTGCCGGGCTCTGAATTC[A/G]CGGGGTGAAGACTTAGAAAGGCCTCTTGAACTTCG R 2 1 2 1 202000 f 74 goat ilmnseq_rs657895731 24 26057543 T C 2 neutral Goat_IGGC_65K_v2 Illumina 468275794 Affx-1111835088 AX-519549358 24 26058171 CTGTGACTTACCAAGAAAAGTGGTGTTATCTCTCT[A/G]TCCACCACTGAAGTGATGTTAATTTCCCCCGTCCG R 2 1 2 1 101000 f 74 goat ilmnseq_rs649717956 24 26058171 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275575 Affx-1111834979 AX-519549145 24 26058291 GAGATGCGGTATGTAATCTTCTGATTCACTTCACA[A/G]TCTGATCGAATCTATGAAGAAAATGGCCAAAAGTG R 2 1 2 1 101000 f 74 goat ilmnseq_rs636342190 24 26058291 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275968 Affx-1111835097 AX-519549525 24 26060439 GAAGCGGGAGTGGGTCAAGTTTGCTGCGGCCTGTC[A/G]GGAAGGAGAGGATAACTCCAAGAGGAATCCGATTG R 2 1 2 1 101000 r 74 goat ilmnseq_rs650561819 24 26060439 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468275844 Affx-1111835112 AX-519549407 24 26060447 AGAAGACAGAAGCGGGAGTGGGTCAAGTTTGCTGC[A/G]GCCTGTCGGGAAGGAGAGGATAACTCCAAGAGGAA R 2 1 2 1 102000 f 74 goat ilmnseq_rs653657386 24 26060447 C T 1 neutral Goat_IGGC_65K_v2 Illumina 468275815 Affx-1111835023 AX-519549378 24 26060487 CAAACTTGACCCACTCCCGCTTCTGTCTTCTGACC[A/G]TTTGCCATTTTGCGGTGCCGTTTTCCGCATCCAAT R 2 1 2 1 101000 r 74 goat ilmnseq_rs642006881 24 26060487 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276247 Affx-1111835241 AX-174331086 24 26060514 TTCTGACCGTTTGCCATTTTGCGGTGCCGTTTTCC[A/G]CATCCAATTCCTTCACCTTAAGCAAAAAACGTCCC R 2 1 2 1 101000 r 74 goat ilmnseq_rs667234597 24 26060514 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275944 Affx-1111835164 AX-519549502 24 26074340 GTACTTCTTTCCCAGGTCTTTAGATTCTACTTACC[A/G]TTAAAATGATCAGAAGGCAAATGTTCCTGAAAAGG R 2 1 2 1 201000 f 74 goat ilmnseq_rs658493722 24 26074340 G A 2 recommended Goat_IGGC_65K_v2 Illumina 320801511 Affx-122927135 AX-385288420 24 26076473 TGTTTGCATAGAGTACTGACTAATTTTATGAAAAA[C/T]GACCACTTCCCATTATCATCAAAATTGTTGGCAGA Y 2 1 2 1 101000 r 74 goat snp1744-scaffold1049-66422 24 26268339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420312 Affx-122945021 AX-123290659 24 26141363 ACTTGGACTAAGGTAAAAATGATGGAAAAGGTGAG[A/G]ATGGCCAAATTAAGACAGCATCTCAGATAACAGTG R 2 1 2 1 101000 f 74 goat snp1743-scaffold1049-1532 24 26333972 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409835 Affx-122952940 AX-123280186 24 26147824 ACTCAAAAGGAAAATTTTCTCTAGGATTTCCCCAG[C/T]AGTCCAATGATTAAGACTGCCTTTGAATGCAGGGG Y 2 1 2 1 202000 f 74 goat snp53209-scaffold800-1273452 24 26340512 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406371 Affx-122955415 AX-123276723 24 26186012 AGACTACTGGAGACAGTTGAAGTCAAGAGTAAGCT[A/G]TAATATTTCACTGCTGCTCAGGACAAGAGCCATCC R 2 1 2 1 101000 f 74 goat snp53208-scaffold800-1235264 24 26378508 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450951 Affx-122921757 AX-123321285 24 26214668 CTGTTGACCTCTGAGATTGGAGTTTGCAGATAGTG[C/T]GCTGATGCTGAAATGGACTCACTGGTTTGTGGCAC Y 2 1 2 1 101000 f 74 goat snp53207-scaffold800-1206608 24 26407146 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773091 Affx-122967436 AX-385260234 24 26287536 TATAGCTGCAAAAGCAAACCAGTGAAGAGGAAAAA[C/T]ATAGATCTTAGCTTCAAGTTTCAAAAACTGTCTAA Y 2 1 2 1 101000 f 74 goat snp53205-scaffold800-1133740 24 26479671 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783746 Affx-122919802 AX-385270802 24 26431363 AAGGAGGCTAAGAAGGAACATTAGTGTATAAAGTA[C/T]GCGTGAGCAGTGTGGTAGATACTAGAAGAAAAAGA Y 2 1 2 1 101000 r 74 goat snp53202-scaffold800-989913 24 26624745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453547 Affx-122919784 AX-123323880 24 26469168 TTGGAACAAGTTATTTCTCTGTAGGTGGAATCACA[C/T]GGTCTCAGAACTGGATTATTAGAAATAAGAGAAAC Y 2 1 2 1 101000 f 74 goat snp53201-scaffold800-952108 24 26661475 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436129 Affx-122932646 AX-123306468 24 26567467 TCACATGGTCACATTCCCTCTCTCCTCTGTAGCTA[C/T]GTTTGTCCTTGTGACTAAGTTTGGTCAATAGCCTA Y 2 1 2 1 101000 r 74 goat snp53199-scaffold800-853809 24 26761710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273025 Affx-1111833275 AX-519546702 24 26649222 TCATGGAAAAAGCAAGAGAGTTCCAGAAAACATTT[A/C]TTTCTGCTTTCTTGACTATGCCAAAGCCTTTGACT M 2 1 2 1 103000 f 74 goat 24_26649222_AF-PAKI 24 26649222 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320801611 Affx-122970483 AX-385288519 24 26696523 TACAAGGTAGATCTGAGTGTTTCTTAAGGGCAGCC[A/G]CCTTTGGTGTGTCCACTAAGTGATCCATCCAACAA R 2 1 2 1 101000 f 74 goat snp53197-scaffold800-724753 24 26891290 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785055 Affx-122919504 AX-385272102 24 26738134 AGATTCATATGAAATATCTGGTTTGACCAATGTAG[C/T]ATTTAATCAGTCCTACCAGGAGTGAAAATGAAAGT Y 2 1 2 1 101000 r 74 goat snp53196-scaffold800-683142 24 26933148 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773754 Affx-122957043 AX-385260894 24 26781227 TTGAAAAAGAACAAAAATAAGTACTCACAAAAATA[C/T]AGGCCAAAATCTTGGAGAAGACGAAAGAGGATTTA Y 2 1 2 1 101000 r 74 goat snp53195-scaffold800-640049 24 26977533 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376244 Affx-122978780 AX-123246603 24 26914895 TGTTGTCCATTCTGTCAGTTTTGACAACCGTACAA[C/T]GACATGTATCTTCTATTGTGGTTTCATACAAAATA Y 2 1 2 1 201000 r 74 goat snp53192-scaffold800-506381 24 27113251 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413799 Affx-122949906 AX-123284148 24 26949572 GCTCATGAGACTGCTCACCCAAGAGCAGTGAGGTG[A/C]GAATCAATGACACGGGACCAAATAAATTGGTGAGG M 2 1 2 1 101000 r 74 goat snp53191-scaffold800-471704 24 27148299 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390582 Affx-122967196 AX-123260939 24 27064866 TAGTCCCTTGAGCCTCTTCCACATTCTTAACACTT[A/G]TCATTACTTCTCAGCAAAGTTATTTCACGGGGTCA R 2 1 2 1 201000 r 74 goat snp53189-scaffold800-356410 24 27265854 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441365 Affx-122928867 AX-123311702 24 27094746 CTAATTTAAAAATTCAGCTTCCTTGAGCAACTCTC[A/G]CTTGTTAAACAGCATTCTTGATATGGTGTGCACTG R 2 1 2 1 101000 r 74 goat snp53188-scaffold800-326530 24 27296008 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428857 Affx-122938352 AX-123299199 24 27140854 CCCTCAGGATAAAGTCCAATCTCCTCATATGTTTC[A/G]CCAGGCCCTTCATGATCTAGTACTTGATCTCTCTA R 2 1 2 1 101000 r 74 goat snp53187-scaffold800-280422 24 27341365 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380126 Affx-122975995 AX-123250484 24 27181425 AAATGTTTTTATCTGTTAAGTGGAGGAACATTAAG[C/T]GAGGCTATCTTCTAGAAAATTACTGACATGTTGAA Y 2 1 2 1 101000 f 74 goat snp53186-scaffold800-239851 24 27382129 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399032 Affx-122961598 AX-123269387 24 27211163 CCTAAATATGAAAATCCACAACATATAGTTAATCA[C/T]AGGGGATCATCTGTCAATTTTTCAGACTTTATCCC Y 2 1 2 1 201000 f 74 goat snp53185-scaffold800-210113 24 27412359 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388973 Affx-122968795 AX-123259331 24 27248515 ACTCAGCAGTTGGGCTTCAGTAAAATAAACTTGCC[A/G]TTTGAATGGAGATAGATGGAACAGCATGGAGTTTA R 2 1 2 1 101000 f 74 goat snp53184-scaffold800-172761 24 27450289 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277575 Affx-1111835981 AX-519551074 24 27301875 CTACCCCATGACTGCTTTTGGTTTTACCTGAATAA[A/G]ACATGGATTTCCGTGTGTTATCTTACAATTGCAGT R 2 1 2 1 101000 f 74 goat Random2.2K-2102 24 27301875 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407144 Affx-122954856 AX-123277495 24 27325049 ACCTTTCCTTGCTAATCATAGGCTACTTTTACCAT[A/G]CCTCCAGGGTTTATCTATTTCCTTTCACAATATTT R 2 1 2 1 101000 f 74 goat snp53182-scaffold800-96227 24 27528417 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408482 Affx-122954418 AX-123278833 24 27378073 CTGTGGCAAAATTTCCCTCCATCTGGGTAACTGCC[A/G]TCTCCCTGTGTTCAAATTTCCTTTTTCTTATAAGG R 2 1 2 1 101000 f 74 goat snp53181-scaffold800-43203 24 27580152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780870 Affx-122960129 AX-385267958 24 27420194 TTGTTTTAAAACTGTATGTCTAACAAAACTACTCT[A/C]TTCACATCCACTGACATTTTGTTAATACAATATAG M 2 1 2 1 101000 r 74 goat snp53180-scaffold800-1082 24 27624145 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277577 Affx-1111835982 AX-519551076 24 27496757 GAATGATCACTGAAAAGATAAAAGACTTAGAAACT[A/C]TAAATAAAGTAATTGATCTGACAATACTAAGCAAA M 2 1 2 1 101000 f 74 goat Random2.2K-2103 24 27496757 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800886 Affx-122932982 AX-385287801 24 27645022 GGACATAATATATAACAAGTGAAAAACATTCACTG[C/T]AGCTGTTCTGTAGTCAGAATATCATTGACTGAACA Y 2 1 2 1 101000 r 74 goat snp55496-scaffold86-223647 24 27853176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412978 Affx-122951033 AX-123283327 24 27748067 TCCAAATGCTGAAAACATATTTGGATGAAAATTTG[C/T]ACTTTGCAAGGTTAAAGTACCTTATACATAATAAC Y 2 1 2 1 101000 f 74 goat snp55499-scaffold86-326692 24 27953365 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432034 Affx-122935909 AX-123302375 24 27827639 AGGACCTGTCCTTTGAAATACTGTAACATGCAACT[A/G]TTTTAAGCCTTATATCCTATTTCCCGAGTTTTGAC R 2 1 2 1 101000 r 74 goat snp55501-scaffold86-406264 24 28034214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385378 Affx-122971627 AX-123255736 24 27863586 TCAACTGATAAATCCCCACTGATGATTTTCCATAG[A/C]GATGCATAAACACAATTTTCAAAAAAGATAAAGGA M 2 1 2 1 201000 r 74 goat snp55502-scaffold86-442211 24 28070506 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422905 Affx-122943054 AX-123293251 24 27990452 AAGGATGTTGCTTTGATTCAGACTATTGCAACAGG[G/T]CTTCCCAGTGGGCACTAGTGATAAAGAACCTGCCT K 2 1 2 1 101000 f 74 goat snp55505-scaffold86-569077 24 28198848 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389774 Affx-122968230 AX-123260131 24 28021775 ATAGGATGCTTATGCGCTTTACAATCAGGTAGGCA[A/C]GAGGGGCCACGCTGAGAACTTACTGGGCTACAGTT M 2 1 2 1 201000 f 74 goat snp55506-scaffold86-600400 24 28230701 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796861 Affx-122936620 AX-385283804 24 28125889 GGGAAAAGGAACAAGGAAGTTGTACGAGGCAAATA[C/T]GGGTGTATTGCCAGGCTACTTTCCTTTAGGGAATA Y 2 1 2 1 201000 r 74 goat snp55508-scaffold86-704514 24 28335862 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771741 Affx-122933389 AX-385258898 24 28156544 GGTTGTGGTGGAAAGATAGCAATCAATCAAGTTAT[A/G]TTTTGCCATTTGGGAAAAGGGACTCAAGAGGAACT R 2 1 2 1 101000 f 74 goat snp55509-scaffold86-735169 24 28366755 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768638 Affx-122924702 AX-385255817 24 28204542 CCTCACTCTGATATGCAGAGAACATGTAACTATTT[A/C]TTTTGATTACAGCTAATATGCTCCTGCTAAGCTAT M 2 1 2 1 102000 f 74 goat snp55510-scaffold86-783167 24 28414811 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786679 Affx-122977214 AX-385273711 24 28280177 TCCCTGAAAATGCCCTTGCTAATTTAACTGATAGC[A/G]TTTGACACTCCTCTTACACACTACAAGCTGTACGT R 2 1 2 1 101000 f 74 goat snp55511-scaffold86-858802 24 28469954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445119 Affx-122926185 AX-123315456 24 28340152 TCTTCCAGCTTCTAGAAACATCACAATAACAATAA[C/T]AAGGACAATAATAATATCTAACATTCATATCACTT Y 2 1 2 1 101000 f 74 goat snp55512-scaffold86-918777 24 28530306 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432966 Affx-122935276 AX-123303307 24 28379582 CCCAGCAAACCCATGACAACATCTCAATGATACAT[A/G]TTCAAAATATTTATGGCATAGAAATTATGTATATA R 2 1 2 1 101000 f 74 goat snp55513-scaffold86-958207 24 28569564 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797043 Affx-122954113 AX-385283984 24 28436527 AAATTTCTCAGTCATTCTGCCTACAACTGGGCCTA[C/T]GAGTTGTTATTGCAGTTGTAAATACCATAGGTCCA Y 2 1 2 1 101000 f 74 goat snp55514-scaffold86-1015152 24 28627009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778403 Affx-122939714 AX-385265518 24 28477250 CACAGTTTTCCTGAAGAAACTCTCTACTGTTCATG[C/T]GATAGACTAAGAGGAACCACTTACAACCCGTCCCA Y 2 1 2 1 101000 f 74 goat snp55515-scaffold86-1055875 24 28667427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763951 Affx-986698479 AX-385251733 24 28573851 GAATAGAAGTTGTGGGTAACCTGGGAACCTGTTAT[C/T]GAGATTAGCACCTGAAGTGGGGGAGAGCAGTCATA Y 2 1 2 1 600010 f 74 goat 24_28573851 24 28573851 Ancestral_priority_1043 ancestry 0.578 neutral IMAGE 10K 10K ancestral 38399923 Affx-122961316 AX-123270278 24 28620125 GGGCCCATTAATGTTAGAACAGTCTTGGAAGAGAT[A/C]TCTCTACAGTTAACTGGCATGGGATAGCTCTTGTT M 2 1 2 1 101000 r 74 goat snp55519-scaffold86-1198750 24 28811542 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422964 Affx-122943011 AX-123293310 24 28656402 TCATTCTCCTTCTTAGTCACCCTTCATATCCTCTT[C/T]TCCCTCTTCATCTGCAAAATGGTAAAGTAGTAACT Y 2 1 2 1 202000 f 74 goat snp35208-scaffold421-2048331 24 28846439 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432770 Affx-122935433 AX-123303111 24 28699987 TTCGTTCTGTGTGTGCATACAAGTATCATCAGTTA[C/T]GTGACTTCATACGGGAAAGCGTTAATGAAATGCAT Y 2 1 2 1 101000 r 74 goat snp35207-scaffold421-2004746 24 28890002 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438971 Affx-122930388 AX-123309308 24 28732863 GGTACTCTCTACCCTTCTAGGTTAGTTTCAGTTTG[C/T]CTTTTATAGCTGTTAAATTGCAGAAAAATTAATAA Y 2 1 2 1 201000 r 74 goat snp35206-scaffold421-1971870 10 28218397 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428898 Affx-122938927 AX-123299240 24 28768050 TCTGAGTAGGTACAGATGTAGAGGAGCAGAGCAGG[C/T]GAGTCTAAGGAGGAAGCAGAATGAACACAGAGGTG Y 2 1 2 1 201000 r 74 goat snp35205-scaffold421-1936683 24 28958108 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377905 Affx-122977239 AX-123248264 24 28796564 GAGAACACATAAATGTTTTATTCTTAAAATGACTG[C/T]GGTATCCTAGATTTTCCAGTCTAAAACAAAGCCTT Y 2 1 2 1 101000 r 74 goat snp35204-scaffold421-1908169 24 28987198 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451679 Affx-122921581 AX-123322012 24 28833425 AAAAAATAAAATAAAAATCTACTTACAGGTTTAAC[A/G]TGTGAGTTCGAAAATCATTTTTTAAAGGGCAAGAT R 2 1 2 1 101000 r 74 goat snp35203-scaffold421-1871308 24 29023996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400273 Affx-122960124 AX-123270628 24 28862420 CAGGAGCAGTCATTTGGAAAGAAATCAGATTCCAT[A/G]GCACTTGGTGGCATCATCTTCTACTCCAACAAATA R 2 1 2 1 101000 f 74 goat snp35202-scaffold421-1842313 24 29053327 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444399 Affx-122926588 AX-123314736 24 28895178 TCCTTTCCTGCCTAGACTGACTCACAAAGTCCCCA[C/T]CCTCCTGAAGCTTGATTTCAATATATTCTCTCATT Y 2 1 2 1 201000 r 74 goat snp35201-scaffold421-1809555 24 29086039 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387213 Affx-122970592 AX-123257571 24 28932081 TTCAGTTCCATAAGTGTCAATAAAGATAGAACCAA[A/G]TTTTCATCTGACTCTTTAAGTTCTCATCACAAAAG R 2 1 2 1 101000 f 74 goat snp35200-scaffold421-1772652 24 29122979 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434205 Affx-122934857 AX-123304546 24 28984042 CTGCGATGGCCACGGGAAAAGGAGAGCTAACATGC[A/G]CTGGACACTGTGCTGAAGGCTCTATGCTTCGGGTT R 2 1 2 1 201000 f 74 goat snp35199-scaffold421-1720691 24 29175025 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788371 Affx-122922598 AX-385275389 24 29034210 AAGGCAGTTCACAGGCGACAGAAATGAACCACCAA[C/T]GGCCTGCAGCTAGAAAGGGAGGATCTTAAATGAAG Y 2 1 2 1 101000 r 74 goat snp35198-scaffold421-1670523 24 29224386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403050 Affx-122958533 AX-123273403 24 29079893 GGTAGATGAAATCTTTCTCACTATGACTCAAAATA[C/T]GGATGCAATAAAAGATTAAGTTGGACCACATAAAA Y 2 1 2 1 101000 f 74 goat snp35197-scaffold421-1624840 24 29270499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776794 Affx-122942115 AX-385263918 24 29116864 GATAGAAGTCTAAAAACCAGAAATAGCCCTTTTCC[A/G]TCTTATTTTTCAAGGATCCTGTGGACAGAGTGTTT R 2 1 2 1 102000 r 74 goat snp35196-scaffold421-1587869 24 29307858 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801917 Affx-122972369 AX-385288822 24 29171861 ATGAACTATATTCCTGGAACTTCTGAAACAGGATA[C/T]GACTCAATTCAAAACATAAAATGATGATTGCTGAT Y 2 1 2 1 101000 r 74 goat snp35195-scaffold421-1532872 24 29362652 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405337 Affx-122956335 AX-123275689 24 29231130 TGCAGCTGCAAAACAAGTCTCTCCCCGTTTCAACA[C/T]AGTACAATTTCTTAGCCCCTCCAAGAAAGAAATAC Y 2 1 2 1 201000 r 74 goat snp35194-scaffold421-1473603 24 29422530 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440241 Affx-122930668 AX-123310578 24 29278494 TTTCTTCATTTCCTGGGGCAGTTAATCAGCATGAA[C/T]GTGGACGGCTCAAAACTGTGACCCTGCCAGAGCCA Y 2 1 2 1 101000 f 74 goat snp35193-scaffold421-1426239 24 29470369 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395296 Affx-122964069 AX-123265651 24 29327339 TGCTAAATATTTCCTTATCTGCTGACAGCTAGATC[A/G]TCTGTAACCACTTATCTCTGGTGGCCTTTTGGGAA R 2 1 2 1 101000 r 74 goat snp35192-scaffold421-1377394 24 29519361 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273027 Affx-1111833276 AX-189234815 24 29330842 GGCTACAGTCCATGGGGTTGCAAAGGGTCAGACAC[A/C]ACTGAGCAACTAACATTTTCACTTTCACACGTGTG M 2 1 2 1 303000 f 74 goat 24_29330842_AF-PAKI 24 29330842 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446247 Affx-122925688 AX-123316583 24 29417171 TGTGTGAGCCATGAGCAACATACTTGAGCTTCAAC[G/T]AAAAGCAAATTATTCATTACCTACCACTTGGTCTT K 2 1 2 1 101000 f 74 goat snp35190-scaffold421-1287562 24 29609134 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431190 Affx-122937174 AX-123301531 24 29507231 CCCTTGAACAGTGTGTGGGGGTGGGTATTAGCGGT[A/G]CCACCACTGGGGAATTAGGGGCATGGATTCTTGGC R 2 1 2 1 103000 f 74 goat snp35188-scaffold421-1197502 24 29699692 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414811 Affx-122949211 AX-123285160 24 29571871 TCATCACTGTTAAAATACCATTGCACCTGTGCTGC[A/G]CTGGACTTAGTCAGGCAGTCGTGTCCGACTCTGCA R 2 1 2 1 101000 f 74 goat snp35187-scaffold421-1132862 24 29764985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432638 Affx-122935476 AX-123302979 24 29620024 TACTTAGGCAGCTAGAAACTGGAAGTCAGTTTCAC[A/G]TTCAATGTCTGTCTGTATTATGGTCTGAATGTTTG R 2 1 2 1 201000 r 74 goat snp35186-scaffold421-1084709 24 29814041 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392015 Affx-122966484 AX-123262372 24 29679943 TAGCAAAATGGGAGCCTTCAACTGTGGGAATAGGA[C/T]TTGCCCTTATGGCCCTTACAAGGACAACAGTTAAA Y 2 1 2 1 101000 r 74 goat snp35184-scaffold421-1024790 24 29873723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798442 Affx-122968273 AX-385285375 24 29755960 GGGCTCTTTCAGGAAAGTTTCAGATAGCACAATGA[C/T]TAACATCTATAGATTCAAAATAGGTAGAAATCCTC Y 2 1 2 1 101000 f 74 goat snp35182-scaffold421-948773 24 29951055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438523 Affx-122931200 AX-123308861 24 29785267 GGAAATTTGGAGCAAGAAGCCTATATAAACAAACC[A/G]TTACTTCTTTATTTTACTACCCCAATCCAGACTTT R 2 1 2 1 201000 r 74 goat snp35181-scaffold421-919466 24 29981000 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398794 Affx-122961418 AX-123269149 24 29832592 CTCATTTCATAAGCAAACATAGCACTAGTGAAGTT[A/G]CCTCTGAATGAATCGCTGAGAGGAAAGAGAAACTG R 2 1 2 1 101000 f 74 goat snp35180-scaffold421-872141 24 30028205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417014 Affx-122947975 AX-123287362 24 29866451 TGTAGCTTGCTGATGACATTTCTTCCCAAATATGG[C/T]ATAAATATGCACTATATAATGATTTCCCAGGTGGC Y 2 1 2 1 201000 r 74 goat snp35179-scaffold421-838282 24 30062373 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383761 Affx-122972436 AX-123254119 24 29915198 CCATTCCTGGATTGATGGGGATTCAGTCACCACTG[A/C]GGCTCATTCACTTCTGTCCCCTCTGTGGTCCATCT M 2 1 2 1 201000 f 74 goat snp35178-scaffold421-789535 24 30111022 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453200 Affx-122920450 AX-123323533 24 29946539 TAACGATTTTTCACTGAGATCTCAAACAGTTCTCT[A/G]CCCTTATGTCATATGAAAGGGGTCTGTAAACTGTG R 2 1 2 1 101000 f 74 goat snp35177-scaffold421-758194 24 30140941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406012 Affx-122955502 AX-123276364 24 29975218 ATTTCATCAGCCTTGCCCCCGTAAGTGCTGTCATA[C/T]ACACTGCCTCCTCTGATGGTCACTGCTGTCACTTG Y 2 1 2 1 202000 r 74 goat snp35176-scaffold421-729515 24 30169929 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381564 Affx-122974819 AX-123251922 24 30014500 GAAAACAGTCCATCAGAAGGTGTCCTGAATTCTTA[C/T]GTCCCGAATCAGGTATTTTCTCCTCTCTTGAAAGG Y 2 1 2 1 101000 f 74 goat snp35175-scaffold421-690233 24 30208696 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777656 Affx-122948089 AX-385264775 24 30043955 TTCACGTACAGTAGTTCATTGTGGGACTTTCCTGG[C/T]GGTCCCATGGTTACGACTCTATGCTCCTATGTCTA Y 2 1 2 1 202000 f 74 goat snp35174-scaffold421-660778 24 30238078 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423146 Affx-122942758 AX-123293492 24 30124850 ATGTTTATGTTCTAAGAAGGTAACTCTAATGACAA[C/T]ACTGAGACACCCAGGGAAACCTGTCAGAAATCTAT Y 2 1 2 1 201000 f 74 goat snp35172-scaffold421-579883 24 30318760 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379371 Affx-122976148 AX-123249730 24 30159451 CGGCCACCAAAGGGACCTGGGATTTAGGCACCTGC[C/T]GAAAAGATGACAGTGGGACTTCTGGGGACTCCCCT Y 2 1 2 1 201000 f 74 goat snp35171-scaffold421-545282 24 30353289 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412208 Affx-122950933 AX-123282558 24 30216104 ATGCACTCAAACTAAAATTCTTTGATAGGATGTCT[A/G]TGTGCATTGGGGGCCCTCCATCCTTTTAAAAGGGA R 2 1 2 1 201000 f 74 goat snp35170-scaffold421-488629 24 30410006 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785294 Affx-122959857 AX-385272339 24 30277612 TGTTTAAATAAAGGTGATTGTAACCTACGAAAATG[C/T]AGAGTTTGATTAGGATTAAGGGACAAACTTGAGAT Y 2 1 2 1 101000 r 74 goat snp35169-scaffold421-427121 24 30471969 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391540 Affx-122966644 AX-123261897 24 30326550 CATGGTGCCCTGGAGCTCAGCCCGAATTAAAGCAC[A/G]CTCCCAGTCATAAGACCTCCTAGTCCCTGCCCTGC R 2 1 2 1 201000 r 74 goat snp35168-scaffold421-378183 24 30521754 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381264 Affx-122974483 AX-123251622 24 30381106 GTAGGCAAACTTATTAACTCAGTAAGTAGCAGACT[C/T]GGGTTTCAGACCAATAATGGGGCTCCAGCCTCTGA Y 2 1 2 1 101000 f 74 goat snp35167-scaffold421-323627 24 30575088 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416972 Affx-122948009 AX-123287320 24 30430170 CAAAGTTCTGCCCCCTTTCTGGTGGGGGAGAGGAC[A/C]AAGAAACACATGAATGTATAATGTATTGTCAGGTA M 2 1 2 1 101000 r 74 goat snp35166-scaffold421-274563 24 30624357 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781533 Affx-122926470 AX-385268618 24 30488008 GGTATCTTTAACATTAAATAGCCTGACCAGATACT[A/G]GAGTTCACACCAAGAAAAAATGAGGATTCCAAAAC R 2 1 2 1 101000 r 74 goat snp35165-scaffold421-216725 24 30682572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422873 Affx-122943079 AX-123293219 24 30517773 TGCTGCCCCACAGGCAAAGGTATCCTGGAAGCAAA[C/T]GAAGCAGAAGGAGGACATCGCATGATGGCACGAGG Y 2 1 2 1 101000 r 74 goat snp35164-scaffold421-186960 24 30712159 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421742 Affx-122944375 AX-123292089 24 30563481 AATGTAAGAACATTATTGAGAGTTAGTTACACAAG[C/T]GATAGAAGTGAGAACTTCTGCTACTGCTTTTTATT Y 2 1 2 1 101000 f 74 goat snp35163-scaffold421-141252 24 30755155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380863 Affx-122975434 AX-123251221 24 30609193 GGTTCAGCACACAGGTGCTTAAGTTCCCCAACAGG[A/G]ATCAAACCCGTGCCCCATGCAGTGGAAAGCGCAGA R 2 1 2 1 103000 f 74 goat snp35162-scaffold421-95540 24 30800988 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396747 Affx-122962787 AX-123267102 24 30644605 CCTGGGAGATGCCCCTCACCTCAGCCAGGGCTAAG[C/T]ATGTTTGTAACATTGGAAAAACACGTTACCTGAGT Y 2 1 2 1 101000 r 74 goat snp35161-scaffold421-60128 24 30835647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392522 Affx-122966113 AX-123262879 24 30673191 AAAACTGATCGCTGAGTTCCCTTCCCCAGATCTAG[C/T]GCAGTTTTGACCTCCTCCGAAAGTTGGAACTATTA Y 2 1 2 1 101000 r 74 goat snp35160-scaffold421-31542 24 30864270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403777 Affx-122957987 AX-123274129 24 30711124 TCATAGACCCCTGCAATGTTTAAAGTCCAAAGTGG[C/T]ATGGAAGGGTCCCTAAGCCCTTTGAAACAACAGCA Y 2 1 2 1 101000 r 74 goat snp59289-scaffold974-1217154 24 30902163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794367 Affx-122973704 AX-385281331 24 30742321 AAAGTATTTAAACGATCTGATGCAAAACACAGATA[C/T]TGGACTAGGCTCAAGGTACAGAACTTGAAGGTACA Y 2 1 2 1 101000 r 74 goat snp59288-scaffold974-1185957 24 30933874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421542 Affx-122943869 AX-123291889 24 30771311 CACTGTGTGCCAGCTAGGTCTTTAGCTGAGAGTGT[A/G]CAAAAGCACTTGCATGGAAAACTATATGAAAAATG R 2 1 2 1 101000 r 74 goat snp59287-scaffold974-1156967 24 30962899 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803038 Affx-122928078 AX-385289914 24 30823543 GACTTTCCTATAGGAACTCTATTTCAAGATAACCA[A/G]ATGTTTGCTGAAATTTTCCTTTTTAGAACAAGTAC R 2 1 2 1 101000 r 74 goat snp59286-scaffold974-1104735 24 31015383 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432183 Affx-122936400 AX-123302524 24 30859085 CTCTAAGGACCCATGACATCACTCAAGATCAAGCC[G/T]AAAACTGCAGAAGACAGAGCAGGAGAGCACGGCTA K 2 1 2 1 101000 f 74 goat snp59285-scaffold974-1069193 24 31051362 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772827 Affx-122952710 AX-385259972 24 30890263 ACCAAATGCATGAAGTTTATGATCAGGTTGGCTCT[A/G]CAGATCTTTTATAGTTCTAGCAAATATTTGGAATA R 2 1 2 1 101000 f 74 goat snp59284-scaffold974-1038015 24 31082540 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443250 Affx-122927550 AX-123313587 24 30927093 AGAGTCCACTTCTCAAGGCAAGAATGGCATTCATG[C/T]ACAGGAAGGGAAGAATTCATGCCAGCCGTCTCTGG Y 2 1 2 1 201000 r 74 goat snp59283-scaffold974-1001185 24 31119451 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400148 Affx-122960699 AX-123270503 24 30981410 TATAAGTGGTACAATGATAAACAATGCAGGATACA[C/T]AAGAGACTGGGATTCAATCCCTGGGTGGGGAAGAT Y 2 1 2 1 201000 f 74 goat snp59282-scaffold974-946868 24 31173278 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451668 Affx-122921588 AX-123322001 24 31012675 TCAATTTAATGATCCTGACATCTGTCTTATCCAAA[C/T]AGAAGAGAAAAAAATACACATGAAAAGGGAGTTTT Y 2 1 2 1 101000 f 74 goat snp59281-scaffold974-915603 24 31204394 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405658 Affx-122956573 AX-123276010 24 31065433 AACGGGAAGGAAAGATTTACTTCAAACAGCCTTCC[G/T]AGTGTCTTGCTCCTCACCAAGAAGTCTCCTTGAAA K 2 1 2 1 101000 r 74 goat snp59280-scaffold974-862845 24 31257681 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443472 Affx-122927822 AX-123313809 24 31114874 AATAGATAGCACACAGTAGAAACTCAGTAATAGTT[A/G]TTTAGTATTATTGCTATCATTCATGAACTAAGCAC R 2 1 2 1 201000 r 74 goat snp59279-scaffold974-813404 24 31307210 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452809 Affx-122920753 AX-123323142 24 31149961 GGAACAAGGCAGCAAAAAGAGCGACCATTGTTCTC[C/T]GTGAAAAGACATAAACAAAACCTAGTGTATTAATT Y 2 1 2 1 101000 f 74 goat snp59278-scaffold974-778317 24 31342626 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775452 Affx-122951751 AX-385262583 24 31194048 ATTTATGATCATACACCACAGCATAGGAGAGCTCA[A/C]GAATATTTTATACGAGTAATGAAGTTTTAGTAATA M 2 1 2 1 101000 f 74 goat snp59277-scaffold974-734230 24 31386758 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385475 Affx-122971290 AX-123255833 24 31230025 GAAGGGTTACAGACTCAAGGATACTGAAGCAGGGC[A/C]CCAAGGTTCCCATTTCTATTCGAATGAGATTAAAC M 2 1 2 1 201000 r 74 goat snp59276-scaffold974-698253 24 31422747 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422944 Affx-122943025 AX-123293290 24 31262308 GGCCTTAAACACCCTTTCCTGTCACTGTGCAGGGT[A/G]AGCATTGATACATTCAATTGTAATAGAACAGTACA R 2 1 2 1 201000 r 74 goat snp59275-scaffold974-665970 NW_017191992.1 8384 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412799 Affx-122950489 AX-123283148 24 31299251 ACCTCTGGCCATCAATGATCAGCAAATACCAAGAA[C/T]AGCACCTTCCTATGAAAAGATCAGTTAGCTTTTGC Y 2 1 2 1 101000 f 74 goat snp59274-scaffold974-629027 24 31492128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780326 Affx-122967898 AX-385267421 24 31361968 TTAGACAAGCTTATGAACTGTGAATCATGTCGATG[A/G]TGCCCCTTTATCAATGAGGACCAAACTGAGATTCT R 2 1 2 1 101000 r 74 goat snp59272-scaffold974-566310 24 31555619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389317 Affx-122968497 AX-123259675 24 31417742 GCATGCTATATAAGTAGAAAGGTTGGAGGACATTA[C/T]AGTGAAGCAAGATTGGAATGCAAGAGACATTTGGT Y 2 1 2 1 101000 f 74 goat snp59271-scaffold974-510536 24 31610954 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404316 Affx-122957016 AX-123274668 24 31453025 TTTGCCATCTTCTAATCTTTTCAGGACACAGAACT[A/G]ACTCAAAGTCCTCCCCATGCCAGTGTGGCTTAGCC R 2 1 2 1 201000 f 74 goat snp59270-scaffold974-475253 24 31645578 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771057 Affx-122973036 AX-385258217 24 31490221 CAGCTCCAAATAAAGAACAAGCAGAATTATCCATG[C/T]ATGGTTGTTGAACAACATTAGTTCAAAGAAGTCTG Y 2 1 2 1 101000 f 74 goat snp59269-scaffold974-438057 24 31682947 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442902 Affx-122927643 AX-123313239 24 31519905 GAGAACGAGAACCCTTATCACCTTCATTCTAGTCA[G/T]GTAAATAACTTTCCATCATAATGCACTGATGGGAC K 2 1 2 1 101000 f 74 goat snp59268-scaffold974-408373 24 31712544 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790786 Affx-122934904 AX-385277786 24 31549936 AATTAAGTGAACATGCTATTTTATACTGACGTGGT[A/G]TCCAATCATTGGTTCAGTGACTCTTCCTCAAAACT R 2 1 2 1 101000 r 74 goat snp59267-scaffold974-378342 24 31742563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277708 Affx-1111835983 AX-519551207 24 31609483 TGTCCCAGCAGCCCCCCAGGCACTGGGTGGGCTGG[A/G]CATCCGGGATCAGCAAGACTACCCACTGAGATGTA R 2 1 2 1 102000 r 74 goat Random2.2K-2104 24 31609483 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320773521 Affx-122958972 AX-385260662 24 31670144 TCTCCTAACAAATTTCCTCAGAGATTTGTTTTCTT[A/G]TGCTCTTGAACTTGATGTCTAACATTAAAAACTGA R 2 1 2 1 101000 f 74 goat snp59265-scaffold974-258134 24 31863621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378356 Affx-122976829 AX-123248715 24 31718870 GTCACATGCACGACACTCATTATGAAAGCTTGTGA[C/T]GGGAGGCCCTCAGACTGGAGTTATCCCAGGGTGTC Y 2 1 2 1 101000 f 74 goat snp59264-scaffold974-209408 24 31912121 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434501 Affx-122934612 AX-123304842 24 31787691 CTTTGAGAGGGCACTTATAGCAGTGATAATGACAA[C/T]AGCATCCAGCATTTTCAGAACTCTTTATAGTTTAA Y 2 1 2 1 101000 f 74 goat snp59262-scaffold974-140587 24 31981346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377973 Affx-122977620 AX-123248332 24 31823241 TACCTGTCACATTGCAAGGCTTACAAATATATATA[C/T]GGGCCTTACCCAGCTGTGGGGTTCTGTGAGAACAT Y 2 1 2 1 201000 f 74 goat snp59261-scaffold974-105037 24 32016877 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404168 Affx-122957695 AX-123274520 24 31859040 CAGAATAAAAGCCAGATTGGTTGCGATTTCCTATA[C/T]AAACCCAGAGATACATGGGCCACAGACAGACACTC Y 2 1 2 1 101000 f 74 goat snp59260-scaffold974-69238 24 32052838 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800578 Affx-122962128 AX-385287497 24 31925259 GACTGCTGTGCTTGAGTATCATCTATATGTTTTAG[C/T]TTCCTTCTTTCTCCAGTTTTCCAGCATTTGAAACT Y 2 1 2 1 303000 r 74 goat snp59258-scaffold974-3019 24 32119949 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384343 Affx-122972251 AX-123254701 24 31935979 TTCTCTGGATTTAGACTTTTCATTTGAAGAAATGC[A/G]CCTGGCAGATCTCAATCATGAGAAATAAAGGGAGT R 2 1 2 1 101000 r 74 goat snp1530-scaffold1042-7602 24 32129765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392068 Affx-122966385 AX-123262425 24 31966910 ACAGAGGCAATTTCCCAGTGGGAAAATGTGGGGGA[C/T]GGGAAATACAAGGACCCACCCCCAGAAGCTGGGAA Y 2 1 2 1 202000 r 74 goat snp1531-scaffold1042-38533 24 32160558 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398868 Affx-122961045 AX-123269223 24 31996845 ATGTGGGGAGATTGTACAGTCTCAGAACTTTATAA[G/T]ATTCTTACAGATCCCAGCCTTTTCCTGATTGTGTT K 2 1 2 1 101000 r 74 goat snp1532-scaffold1042-68468 24 32190359 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273031 Affx-1111833278 AX-519546706 24 32006434 GAACTAAAGAAATGGTTTCTAGCAGCATCTGTTCC[A/G]ACATCCCATTTCATAAATGATGAAATCAAGTCCCA R 2 1 2 1 101000 f 74 goat 24_32006434_AF-PAKI 24 32006434 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38380144 Affx-122975980 AX-123250502 24 32037106 AGGGACACAGAGCCGATGATACAGAAGGTGCCCTC[A/G]ACTTCCTTTAGGACTCTGCCTCTGCTTCCAGGCAT R 2 1 2 1 101000 r 74 goat snp1533-scaffold1042-108729 24 32229913 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450913 Affx-122922189 AX-123321247 24 32077515 GGAATTCATAATTCACCTTGGCTCACAGGTCCTAG[C/T]GCAACTTTTGTGTGGAAATTCATTTCTCCTATGGT Y 2 1 2 1 101000 f 74 goat snp1534-scaffold1042-149138 24 32269828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426632 Affx-122939952 AX-123296978 24 32109993 AGCACCGAACAAGAATGCTTACAGGAGGAGTGTGT[C/T]CCATTCCGCCACACTGAGCCCTCCTGTGTCTTCTT Y 2 1 2 1 201000 f 74 goat snp1535-scaffold1042-181616 24 32302651 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786326 Affx-122964149 AX-385273360 24 32150604 ACGTTGTTGCTGGGATATCTGTAATTCTAGAGACA[C/T]GGCGGCTTCTAAGCAGCATGTGTACATTTAAGAGA Y 2 1 2 1 101000 r 74 goat snp1536-scaffold1042-222227 24 32343297 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404384 Affx-122956798 AX-123274736 24 32202920 CAAAAAAGTATTATACATGTATAATTAAACTGTAG[C/T]CATCATAGTAATAATAGGGATCCTGAAGACAGAAC Y 2 1 2 1 101000 r 74 goat snp1537-scaffold1042-274543 24 32395806 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390175 Affx-122967968 AX-123260532 24 32257884 GGGAACCAGACAGGCAGCCTCTCTTGCAGAAGAGT[A/G]CTGCCATGTGACACTGGAATATAAGCAGAAGTAAT R 2 1 2 1 101000 r 74 goat snp1538-scaffold1042-329507 24 32450666 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410640 Affx-122952779 AX-123280990 24 32301474 TTAGTGTCCAAAAATAACTACAAGTGTGTAAAAAA[C/T]GCAAAACACAAAATCCTTTGGAAAGAGAAGTTCCT Y 2 1 2 1 201000 f 74 goat snp1539-scaffold1042-373097 24 32495017 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402114 Affx-122958680 AX-123272467 24 32330137 CTGCATGATTCAATATCTTTCTCCTTTTTATGGCC[A/G]TGTAGTATTTCCTTGTATAAATACACCACAGTGTA R 2 1 2 1 101000 f 74 goat snp1540-scaffold1042-401760 24 32523733 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443824 Affx-122927066 AX-123314161 24 32407452 ATTAGTAAAATAAGTAGGCACTGACCTCTAAGATT[C/T]ATTTCAGATCTCACAAATTATGATCCTGTTAGTCT Y 2 1 2 1 101000 f 74 goat snp1542-scaffold1042-479075 24 32601885 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777414 Affx-122965365 AX-385264535 24 32448094 TGTGATTTAGTGTAGGGTTTTGCCAGGGTCTGTTT[A/G]TCAGGTGACACTTGCTGAATATCTCCTTTTTCCTC R 2 1 2 1 101000 f 74 goat snp1543-scaffold1042-519717 24 32642341 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273778 Affx-1111833836 AX-519547389 24 32467186 GAGACAATCCTGAGCTGCTTGGTGCTGCCTGTATG[A/G]AGACAGGTGAGTGCACAGAGGCATCC R 2 1 2 1 102000 f 74 goat GoatD01.006454 24 32467186 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38403785 Affx-122957981 AX-123274137 24 32481166 ACTTAAGTTCCTCACCTGGAGGGCTTCTTAACCTA[C/T]AAGTTTCTGGGTCTTATCCCTGGCATTTCTGATTC Y 2 1 2 1 101000 r 74 goat snp1544-scaffold1042-552789 24 32675422 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777651 Affx-122977006 AX-385264770 24 32525868 AAATTGATTACTTTGTAAATTGAACAGTTATCGTG[C/T]GCCTTAGACTTGAGACTTTTAACAATTGCTTTAGA Y 2 1 2 1 101000 r 74 goat snp1545-scaffold1042-597491 24 32720908 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788374 Affx-122958153 AX-385275392 24 32555627 CCTGAAGTCATTCTGTTTTCATGGTTTAGAAGTCA[C/T]GGATTACAGCATTCACTTGTGAACCGACTGGATGT Y 2 1 2 1 101000 f 74 goat snp1546-scaffold1042-627250 24 32750786 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799799 Affx-122947014 AX-385286725 24 32606579 AAAGTAATGGTTACATCTAAACATAGTTTTTCTTC[A/G]TTAAGATTACAAAGGTGTGGCCGGTTGTAAGCTTA R 2 1 2 1 201000 f 74 goat snp1547-scaffold1042-678202 24 32801485 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802074 Affx-122961506 AX-385288978 24 32664645 TGAAAGTCTTAGGAAAAATGGGTAATTCTGCTATC[C/T]GGTCGTGCTTCTTTGGAATACTGTTTTATACAGAG Y 2 1 2 1 101000 f 74 goat snp1548-scaffold1042-736268 24 32860189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444045 Affx-122926869 AX-123314382 24 32702168 GAGGGCACTAACAATGCAAACGAAGATATGAACAC[G/T]ATTTAAAAGACGTGTTCAATGCTTTAAAGTTCTTT K 2 1 2 1 101000 f 74 goat snp1549-scaffold1042-773791 24 32897846 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445101 Affx-122926197 AX-123315438 24 32751268 GTGCTTCTCTAGAAGCCTCAAACCATCCTTCAGAG[A/C]CACAATGTTTGCTAACAGGACCTGTGATAGCCTCT M 2 1 2 1 101000 f 74 goat snp1550-scaffold1042-822891 24 32947649 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437392 Affx-122932433 AX-123307730 24 32802685 TCTCTGCCCTACCAGACATGCCTAGTGAACGAAAA[C/T]GATCTCATGTAAATTAAAAAACAACAACAACAACA Y 2 1 2 1 101000 f 74 goat snp1551-scaffold1042-874308 24 32994391 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389611 Affx-122968759 AX-123259969 24 32832756 TAGGGAGGAGGAAAGAGGATCTAAGTCAAAGGTCT[C/T]TGGGGAAGTGAGGTTATTTCCCTTCTGGGAGGGCG Y 2 1 2 1 101000 f 74 goat snp1552-scaffold1042-904379 24 33024334 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794237 Affx-122928245 AX-385281203 24 32887296 GTAAACCTGGTGATGATATGAAAAGATTCATTGAG[C/T]AAGACCAGTGTTGGTCCTTAGAAAAAAATACGGTT Y 2 1 2 1 201000 f 74 goat snp1553-scaffold1042-958919 24 33078939 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435185 Affx-122933646 AX-123305525 24 32938821 CATTTCTGCTGATGTTCCCTCGGGCATGGGCAAAA[C/T]GACCATACAGCGTGCCTCAGTTCCGAGTTAGGCAT Y 2 1 2 1 102000 f 74 goat snp1554-scaffold1042-1010444 24 33130503 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381867 Affx-122974180 AX-123252225 24 32996397 TTAAAGCCCCATGCCCTTTATATGATGTGAAGGAT[A/G]CAAGCTGATAACTGATTTTAAAAGCTGTGTTCAAG R 2 1 2 1 202000 r 74 goat snp1555-scaffold1042-1068020 24 33188152 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788127 Affx-122946150 AX-385275147 24 33033287 CAGGAACTTTCCTTCAAAAAAGTCTAAGTTATAAT[A/G]TGAAATAAATCTGGTATCACAGTTTTATAATTTGA R 2 1 2 1 201000 r 74 goat snp1556-scaffold1042-1104910 24 33224891 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783529 Affx-122974968 AX-173470632 24 33062094 AGGCCTGATTTAACAAAACTTTTGGGCAAAAGAAA[C/T]GGAGAACCCTTCTATCATGAAACTGAATATAATAC Y 2 1 2 1 101000 r 74 goat snp1557-scaffold1042-1133717 24 33253708 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771265 Affx-122922360 AX-385258423 24 33101352 GAGCAAACAGAGGTGGTGTAAGGTGTTGAGCTCAA[C/T]GTAAGGACAAAACCCATGACTCATTCCCTAGGAAG Y 2 1 2 1 101000 r 74 goat snp1558-scaffold1042-1172975 24 33294431 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796761 Affx-122921147 AX-385283705 24 33218491 ACCCAACAGAAAGTGCTACCAGTACAACACTTAAT[A/G]CTTTCTAAAGGCTTCAGTGCTTGTTCATTTGACTA R 2 1 2 1 201000 r 74 goat snp21086-scaffold2064-17345 NW_017189645.1 1930 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791088 Affx-122952742 AX-385278083 24 33284574 CATAGGTAAAGCCTCATGATTCTTTGAGAACATCA[C/T]GCCTCACCTGAAATGATGTAGAAAATGAAAAGAAA Y 2 1 2 1 201000 r 74 goat snp21088-scaffold2064-83428 24 33502319 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786714 Affx-122979009 AX-385273745 24 33329156 ACACTTTAAAAAAAAGTGGGTGAAATAATAGGACC[A/G]TCTACTTTATTTCAAACCAGTTTTTCCTCTCTTAG R 2 1 2 1 101000 r 74 goat snp21089-scaffold2064-128010 24 33547986 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274475 Affx-1111834314 AX-519548066 24 33350885 GGATCCAGTCTAGAAAGTGGGGACTGCAGGAACTT[A/C]ACCTGACATCCAGGTTTCAGATGAAGCAGCTGGGG M 2 1 2 1 201000 f 74 goat GoatD01.029836 24 33350885 A C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320779117 Affx-122921556 AX-385266222 24 33372583 GATGGGATACAACAGTGTTTGAAAAACTATAACCT[A/G]TTTATGTGGGAGGTGCCTGGCTGAAACTTGGGGCA R 2 1 2 1 101000 f 74 goat snp21090-scaffold2064-171437 24 33590472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763326 Affx-986697855 AX-385251231 24 33389280 TTTAGTTTGTGCAAGCTTATTTCTATCCATTTTAG[C/G]AACCATTTGGACTTTGGTTCTGTTGGACATGAAAT S 4 1 2 1 600010 f 74 goat 24_33389280 24 33389280 Ancestral_priority_1043 ancestry 0.75 recommended IMAGE 10K 10K ancestral 320767342 Affx-986698481 AX-385254618 24 33389685 AAAGATCGGGCCCCAAAACAGTAAAATGAGAGAAT[A/G]AGAATTCAGCAAAGTTGTTGACTATAAGAGCAACT R 2 1 2 1 600010 r 74 goat 24_33389685 24 33389685 Ancestral_priority_1043 ancestry 0.588 neutral IMAGE 10K 10K ancestral 320763959 Affx-986698487 AX-385251741 24 33390530 ATAGTTGCTTAGGGCTTAAGGGGATGGGGAGATAA[A/G]GGAGCATTAGTTAAAGGTTCTGGGTTTCCTTCTTA R 2 1 2 1 600010 f 74 goat 24_33390530 24 33390530 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 320767358 Affx-986698489 AX-385254634 24 33390549 GGGGATGGGGAGATAAAGGAGCATTAGTTAAAGGT[C/T]CTGGGTTTCCTTCTTAAGGTGATGAAGATGTTTTA Y 2 1 2 1 600010 r 74 goat 24_33390549 24 33390549 Ancestral_priority_1043 ancestry 0.644 neutral IMAGE 10K 10K ancestral 320763963 Affx-986698491 AX-385251745 24 33390570 CATTAGTTAAAGGTTCTGGGTTTCCTTCTTAAGGT[A/G]ATGAAGATGTTTTAAAATTGACTGGTGATGATTTC R 2 1 2 1 600010 f 74 goat 24_33390570 24 33390570 Ancestral_priority_1043 ancestry 0.604 neutral IMAGE 10K 10K ancestral 320767366 Affx-986698493 AX-385254642 24 33390590 TTTCCTTCTTAAGGTGATGAAGATGTTTTAAAATT[A/G]ACTGGTGATGATTTCTCATATCTATGAATATGCTA R 2 1 2 1 600010 r 74 goat 24_33390590 24 33390590 Ancestral_priority_1043 ancestry 0.742 recommended IMAGE 10K 10K ancestral 320763967 Affx-986698495 AX-385251749 24 33390643 ATATCTATGAATATGCTAAAAGGCATCAAGTTGTA[A/G]CTTTAAATTGGTGAATTGTATGTGAGTTATCTCAA R 2 1 2 1 600010 f 74 goat 24_33390643 24 33390643 Ancestral_priority_1043 ancestry 0.752 recommended IMAGE 10K 10K ancestral 320763969 Affx-986698497 AX-385251751 24 33390686 TTGGTGAATTGTATGTGAGTTATCTCAATAAAGGT[A/G]TATAAAAAGGAATTTGTAACTTAATATAGCTCATT R 2 1 2 1 600010 f 74 goat 24_33390686 24 33390686 Ancestral_priority_1043 ancestry 0.728 recommended IMAGE 10K 10K ancestral 320767375 Affx-986698499 AX-385254649 24 33390689 GTGAATTGTATGTGAGTTATCTCAATAAAGGTGTA[A/T]AAAAAGGAATTTGTAACTTAATATAGCTCATTTTA W 4 1 2 1 600010 r 74 goat 24_33390689 24 33390689 Ancestral_priority_1043 ancestry 0.462 neutral IMAGE 10K 10K ancestral 320763973 Affx-986698501 AX-385251754 24 33391022 GGCAATTGAATAAGACCCATTGAAGCCTAGTGTAC[C/T]ACAGTACGTGGAGCGCAGAGTCAGACAGGACTTGG Y 2 1 2 1 600010 f 74 goat 24_33391022 24 33391022 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 320767389 Affx-986698507 AX-385254662 24 33391137 TTCTTCTGTGCAGAAAGTCATTGACATTGCTATTT[G/T]CTGTGTCTTTATGCATACTAAAATCAAGCTCCGGA K 2 1 2 1 600010 r 74 goat 24_33391137 24 33391137 Ancestral_priority_1043 ancestry 0.714 recommended IMAGE 10K 10K ancestral 320763981 Affx-986698509 AX-385251762 24 33391317 CTGCACTGGCTGAAGAGGCCCTGAGGGTCTTGCTT[C/G]TCATTCCTTGGCCTTCAGTGTGCTCTTCCCTGCAC S 4 1 2 1 600010 f 74 goat 24_33391317 24 33391317 Ancestral_priority_1043 ancestry 0.482 neutral IMAGE 10K 10K ancestral 320767399 Affx-986698513 AX-385254672 24 33391321 ACTGGCTGAAGAGGCCCTGAGGGTCTTGCTTGTCA[C/T]TCCTTGGCCTTCAGTGTGCTCTTCCCTGCACGGGG Y 2 1 2 1 600010 r 74 goat 24_33391321 24 33391321 Ancestral_priority_1043 ancestry 0.49 neutral IMAGE 10K 10K ancestral 320763952 Affx-986698480 AX-385251734 24 33391441 GCCTTTGATTTTAAGTTGCTTGGAATCCGGCCTAG[C/T]CTGTCGCTTGCAGGGTGACGAGCCAGTGTCAGAGG Y 2 1 2 1 600010 f 74 goat 24_33391441 24 33391441 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 320767344 Affx-986698482 AX-385254620 24 33391455 GTTGCTTGGAATCCGGCCTAGTCTGTCGCTTGCAG[A/G]GTGACGAGCCAGTGTCAGAGGTGACCTCGGTTTCT R 2 1 2 1 600010 r 74 goat 24_33391455 24 33391455 Ancestral_priority_1043 ancestry 0.514 neutral IMAGE 10K 10K ancestral 320763956 Affx-986698484 AX-385251738 24 33391488 AGGGTGACGAGCCAGTGTCAGAGGTGACCTCGGTT[C/T]CTTCCCTCAGTGGTTGCTGTCCGGAGTCCCAGCCC Y 2 1 2 1 600010 f 74 goat 24_33391488 24 33391488 Ancestral_priority_1043 ancestry 0.478 neutral IMAGE 10K 10K ancestral 320767356 Affx-986698488 AX-385254632 24 33430374 ACTCTGGCTTGGCAGAAAGACATAAAATAATGCAA[A/C]CTGAGACTGATTTTCTCATCTGTTACATAAAGGGA M 2 1 2 1 600010 r 74 goat 24_33430374 24 33430374 Ancestral_priority_1043 ancestry 0.656 recommended IMAGE 10K 10K ancestral 320763962 Affx-986698490 AX-385251744 24 33430486 AAACAACAAATGAAGAGGAAGCCATTAAGTGACAG[C/T]CAGCCTCTGAGCTCAGGGGACACGGGACTCTAAGT Y 2 1 2 1 600010 f 74 goat 24_33430486 24 33430486 Ancestral_priority_1043 ancestry 0.61 recommended IMAGE 10K 10K ancestral 320763964 Affx-986698492 AX-385251746 24 33430550 TCTAAGTTTACGCTCCCTGTAAACATCCACCATGC[C/T]CTCTGGCACAGGGCAAACATCAGTGTTATCAATCT Y 2 1 2 1 600010 f 74 goat 24_33430550 24 33430550 Ancestral_priority_1043 ancestry 0.618 recommended IMAGE 10K 10K ancestral 320767367 Affx-986698494 AX-385254643 24 33430569 TAAACATCCACCATGCCCTCTGGCACAGGGCAAAC[A/C]TCAGTGTTATCAATCTATGAGAATCATCTTATAAT M 2 1 2 1 600010 r 74 goat 24_33430569 24 33430569 Ancestral_priority_1043 ancestry 0.748 recommended IMAGE 10K 10K ancestral 38378756 Affx-122977018 AX-123249115 24 33442980 GGCAGAGCCCACGGAAGGGGTGGGAGAGGAGTGAA[C/T]GGTCAGGGGCATAATGCCCTCAGAAGGGGCAACAG Y 2 1 2 1 201000 f 74 goat snp21092-scaffold2064-241834 24 33660914 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773936 Affx-122944186 AX-385261075 24 33494419 GATTCTCCAACACCTCGAATGGGAAAGTCAGCAAA[C/T]ATCCTTACACAGAGGCACCTTTAAGAAAGCACTCA Y 2 1 2 1 101000 r 74 goat snp21093-scaffold2064-293273 24 33712718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378927 Affx-122976441 AX-123249286 24 33528556 GATTCATCTCTGTTGCTTTTCTGCCCTGGTCTTTG[C/T]GCTATTCATGTGTGGTGTCTATTATACCGTGTGTG Y 2 1 2 1 201000 r 74 goat snp21094-scaffold2064-327410 24 33746826 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433137 Affx-122935686 AX-123303478 24 33569985 TCTGAAGATGCGGTATCATTTGGAGGGGCTAAAAT[A/G]TATACTCTCTAATGTGCTGGCTCAGGCTGTGAGCT R 2 1 2 1 101000 f 74 goat snp21095-scaffold2064-368839 24 33788721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800354 Affx-122927481 AX-385287276 24 33607954 TAATTGGTAATTTTAGTTCCAGTTATAACTAAAAA[C/T]GGGAAGTTCAGTTAGTATAGATCATATTCCTTAGT Y 2 1 2 1 102000 r 74 goat snp21096-scaffold2064-406808 24 33827315 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422766 Affx-122943231 AX-123293112 24 33645974 TGTTGTACATAGTTCAAGGTCCTAAATAGCACTTA[C/T]AGTTCAGACAAGGGAAAACAGCAAAATCTCAAAGT Y 2 1 2 1 101000 f 74 goat snp21097-scaffold2064-444828 24 33865341 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448696 Affx-122923863 AX-123319032 24 33673805 TCTCAGCACTTCCTTTGGTACCACAACAAACCACA[C/T]GTTAATACTAAACGTTAAAACCAGAAGTCAGATGA Y 2 1 2 1 101000 r 74 goat snp25018-scaffold2573-276309 24 33895390 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443075 Affx-122928122 AX-123313412 24 33703902 AGCAAAACACTGGAATTAGAGTAAAGAGGATAGCT[G/T]ATTATTTGCTATTTTTACATAGAGTTTCTAACATT K 2 1 2 1 101000 f 74 goat snp25017-scaffold2573-246212 24 33925575 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397409 Affx-122962252 AX-123267764 24 33741661 GTTCACTGGTAATTGCTCAATTGTATTGACGCCCT[A/G]CAGAGGGGTATTGAGAAATGAGGGCTATTGACAAG R 2 1 2 1 101000 f 74 goat snp25016-scaffold2573-208453 24 33963539 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777483 Affx-122977170 AX-385264603 24 33770558 TGAGGTGGGGAAGGCAAGGACAATATGGTCCTGCT[C/T]CATGTCAGTAAGAGCCTTCTCTACTGACATTTTCC Y 2 1 2 1 201000 f 74 goat snp25015-scaffold2573-179556 24 33992690 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446347 Affx-122925612 AX-123316683 24 33821443 CAACATATGGTTACGGCAGTGCCTAAGCCACCAGG[A/C]ATAGCATCATTCCTATGGCAGAAAACACTCAGAGG M 2 1 2 1 101000 r 74 goat snp25014-scaffold2573-128671 24 34042411 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767103 Affx-122920134 AX-385254390 24 33857983 GAGCTCCTACATGGTAACAAAACTCAAAATAACTC[A/G]GAGGGAAGTAAGCTATAGATTTATCTATCACTCTA R 2 1 2 1 101000 f 74 goat snp25013-scaffold2573-92131 24 34079409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378213 Affx-122976925 AX-123248572 24 33892510 AATAATTGGAAAGAGAGACTTCCTGCAGCAGGCAC[A/G]TTTGTTTTCAAAACCTATTTTTGTAGAATGGTTGT R 2 1 2 1 201000 r 74 goat snp25012-scaffold2573-57604 24 34113920 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781216 Affx-122964391 AX-385268301 24 33966685 AAGTGGGAGATTTATTTTTACAACAACCATTAAGG[C/T]GGCTATTTCTCTCCTTGTTTTCAAAGGTGGAAACA Y 2 1 2 1 101000 r 74 goat snp14474-scaffold1579-16472 24 34188996 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393634 Affx-122965303 AX-123263989 24 34012774 TGCAAAGAGTCAGACATGACTGAATGAGTGAACAA[C/T]AACAACAGGAAATCCAAACATCCCACTTGTAGTCC Y 2 1 2 1 201000 r 74 goat snp14475-scaffold1579-62561 24 34235685 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783817 Affx-122971713 AX-385270873 24 34042806 ATTTCAGAAGATCTTTATGTCACCAAACACCCTGA[C/T]TCCCTTGTTATTCAGAAATGGAAGGTGAACACAGA Y 2 1 2 1 101000 r 74 goat snp14476-scaffold1579-92593 24 34265729 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793618 Affx-122948215 AX-385280592 24 34094630 CCACAAAAATATTAGCCTGCTAATAATCAACACAT[C/T]TTTCTCAAGTGCACCTTTGGGAACTATGAGGAGGA Y 2 1 2 1 101000 r 74 goat snp14477-scaffold1579-144417 24 34318141 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433413 Affx-122935093 AX-123303754 24 34130184 TAGGAAAGATTCAATGACAGATCTCCATTGATCCA[C/T]AGAGAGAATTCTTGACTCACAGCCTTTAGTCATAT Y 2 1 2 1 101000 f 74 goat snp14478-scaffold1579-179971 24 34354058 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450932 Affx-122921772 AX-123321266 24 34171389 AAACCAGCAAATGTAAGTGGACCAAAAGTGATGAT[A/G]TTTCATAAGGAAATCCCAGACATAGTCTAAAGATG R 2 1 2 1 101000 f 74 goat snp14479-scaffold1579-221176 24 34394955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437317 Affx-122931964 AX-123307655 24 34222229 ACGGAAACAGAAAACTGCTTTTAACTCCAACAAGA[C/T]GACATGTGGAAAAGTTTGAAAAGACAAGCTATAAC Y 2 1 2 1 101000 f 74 goat snp14480-scaffold1579-272016 24 34445822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787920 Affx-122959308 AX-385274942 24 34251052 TCTTATTTGGATGACTATGATACTGACACTCATAC[A/G]TGCCTGAAACTAAAATCTTGGTGGCTCTTTAAACA R 2 1 2 1 101000 r 74 goat snp14481-scaffold1579-300839 24 34474602 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434514 Affx-122934604 AX-123304855 24 34295829 TACCATCTTATCAGTTCTAAAATGCACATTTCCCA[C/T]GTTTTTGTATTTCTACAATCTGGATGTCTGACTAT Y 2 1 2 1 101000 r 74 goat snp14482-scaffold1579-345616 24 34519373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402014 Affx-122958753 AX-123272367 24 34324572 AGTGGTTACATCTTCCATCTTCCTCTTCATTCCAC[G/T]TCATTGTAGAAGGGAAACTCAAGGGCCATAGGAAT K 2 1 2 1 101000 r 74 goat snp14483-scaffold1579-374359 24 34547365 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801549 Affx-122942339 AX-385288458 24 34396637 TAATGCTTTCATTAAACTCCCATCCATTTTACAGA[C/T]GAGCAAACTGAGGCCAGCTCAAAAGTTAACAGAGT Y 2 1 2 1 101000 r 74 goat snp14484-scaffold1579-446424 24 34619514 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397561 Affx-122962018 AX-123267916 24 34430154 TACCTTGAGACTTAGGACAACATCCTTCCCTTCTC[A/G]TAGGGTGTGATGTGTTCCTGGCATGTAGTAAGCAC R 2 1 2 1 201000 r 74 goat snp14485-scaffold1579-479941 24 34652845 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447489 Affx-122924087 AX-123317825 24 34444239 ACCTACAGGCATAATGTTTATTATGTGCTGACAAC[A/G]TGCAGGGCTCAAAAGTTTTCTCCTGCCATTTATGG R 2 1 2 1 101000 f 74 goat snp27336-scaffold290-4212631 24 34666851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384554 Affx-122973014 AX-123254912 24 34489959 TGCTCCTGGTTCTCTGCAGACGTTATTTCCTCTTT[C/T]ATAATACTGTTTTCTTTGCCTGAAAAGCAACCTTT Y 2 1 2 1 101000 f 74 goat snp27335-scaffold290-4166911 24 34713059 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451950 Affx-122920961 AX-123322283 24 34529323 AGGTGGTCTTTGGTGTGTGTTTATCGTCATACACA[C/T]ATTGATAAGTTGTATTTCTTAGCTCATGTAATAGT Y 2 1 2 1 101000 r 74 goat snp27334-scaffold290-4127547 24 34752089 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432340 Affx-122936284 AX-123302681 24 34581988 AGACAGTATCTTTTCTAAAAGTCTTCCATTCACCT[C/T]ATTACTTTTTTTTTTCCATTGAAACAGACTCTGAG Y 2 1 2 1 101000 f 74 goat snp27333-scaffold290-4074882 24 34804800 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787331 Affx-122972054 AX-385274356 24 34615168 TAGATAAGAGATTGTGAGTGTATCTCTTCAATTTC[A/G]AAGCACATTCTTCTGTATTTCCTGGGTCATGTACC R 2 1 2 1 101000 r 74 goat snp27332-scaffold290-4041702 24 34837851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273033 Affx-1111833279 AX-188001728 24 34645886 CCTGGTGTGCTGCGGTTCATGGGGTCACAAAGAGT[A/C]GGACACGACTGAGCAACTGAACTGAACTGAACTGA M 2 1 2 1 303000 f 74 goat 24_34645886_AF-PAKI 24 34645886 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38416240 Affx-122948211 AX-123286589 24 34651095 TCTCTGGTCCACAGCCCAGCCTGTACTGTTTATCA[C/T]TGTGATGGTTAAAGCTTCCTCAGGGTTAATTTGTG Y 2 1 2 1 101000 r 74 goat snp27331-scaffold290-4005775 24 34871998 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422660 Affx-122943684 AX-123293006 24 34691983 ATGCCCTGCAAGGTCAGCTCTGCCTGTTGAAATCA[C/T]GCCTTGAACTAATTCAAAAAACGTCAGACCAAAGG Y 2 1 2 1 101000 r 74 goat snp27330-scaffold290-3964887 24 34913010 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782249 Affx-122946869 AX-385269328 24 34722304 ACTGACTACTCTCAGCAGGATTTTGAAGTGGTTTG[A/G]TAGATAGTAATTGATTATATTCATCTTAGAGTAAG R 2 1 2 1 101000 f 74 goat snp27329-scaffold290-3934566 24 34943826 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402286 Affx-122959106 AX-123272639 24 34755790 CTAAGCACTCCTAAGTGAAAAGGTTAAATGACATA[C/T]GCGATGCAATCAATTATATGAACTCAATATTTAGG Y 2 1 2 1 101000 f 74 goat snp27328-scaffold290-3901080 24 34977460 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427625 Affx-122939348 AX-123297968 24 34805740 TGAGGGCATGACAGACCAGTAGAAGAACGGCAGCC[A/G]TCCATCATCATAAGTAACAACGGGACAGGAAAACA R 2 1 2 1 101000 r 74 goat snp27327-scaffold290-3851130 24 35026411 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386527 Affx-122970735 AX-123256885 24 34925768 CATTATATAGAAACTAACAAAACAAAGCCCTCAGC[A/G]CTGGGAATGACATCAGATGATTTCAACCCAGCCTC R 2 1 2 1 201000 r 74 goat snp27324-scaffold290-3731102 24 35146964 G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410690 Affx-122952740 AX-123281040 24 34962887 GTGGCCTGTATGCACAGTACAGTTTGAGATTCCCT[A/G]CTGTAGAGGAGAAAAGAGAGATATGGCTGAAGAGG R 2 1 2 1 201000 f 74 goat snp27323-scaffold290-3693983 24 35184043 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797006 Affx-122968933 AX-385283947 24 35028512 AAAAGTGTTCTTATGTGTTTTAAAAGACGGGACAA[C/T]GAGGATTCAATTATAAAGCAAGGCCAAAAACATAT Y 2 1 2 1 101000 f 74 goat snp27322-scaffold290-3628358 24 35249735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381475 Affx-122974969 AX-123251833 24 35077279 TAGACTGGGGTTTCCACAAAAATCTGAACCGTAAA[C/T]GAAATGTCAGATTTGGGAAGGCTGGAGCCCACAAA Y 2 1 2 1 201000 f 74 goat snp27321-scaffold290-3579591 24 35300555 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777190 Affx-122960928 AX-385264313 24 35183585 AAAAAAAATGCCCTCAATTAAATTAGTACATGCCA[C/T]TGATCTTAAGATGCACTCTAATTTTAGAGATTTTG Y 2 1 2 1 101000 f 74 goat snp27319-scaffold290-3473285 24 35406020 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385789 Affx-122971046 AX-123256147 24 35245790 AAATTTAAGATACTCACGGAGAACTGTTTCTAACA[G/T]ACATTAGCCAACTTTTCATTTCAATTGTAGCCACT K 2 1 2 1 101000 f 74 goat snp27318-scaffold290-3411080 24 35468247 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421978 Affx-122943798 AX-123292325 24 35281686 AAGGAATCACATAGAATACAGTGTGTTATATTGCC[A/G]CTTAGCCCACTCCTGTCCCCAAACCTACTGGACCG R 2 1 2 1 101000 f 74 goat snp27317-scaffold290-3375184 24 35504194 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771904 Affx-122955557 AX-385259060 24 35325403 CTTAGTCTGTGAAACCTAACTTGGTCATAGTTAGC[A/G]TAGGAGTTACATAATGAATAAGGGTTTTGATAGCA R 2 1 2 1 101000 f 74 goat snp27316-scaffold290-3331467 24 35547831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443798 Affx-122927087 AX-123314135 24 35381976 CAAACCTATGATGACAAGCTCACAGCAGTGGAAAG[C/T]GACCTGAAAAAACTAGGTAATCTGCAGTGAGAGTG Y 2 1 2 1 201000 r 74 goat snp27315-scaffold290-3274894 24 35604759 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446546 Affx-122925006 AX-123316882 24 35475876 AGTGAAAGGTTCCAGGAAATTCTTCAGGCTGACCC[A/G]TCAAGATAATAGTCCTTCTATTTCAACACTTTTTG R 2 1 2 1 201000 r 74 goat snp27314-scaffold290-3180994 24 35698904 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450291 Affx-122922159 AX-123320626 24 35508796 TGAGAAACAGCAATAAGTACAAGGAAGCATATACT[A/G]TGGAGAGGAACTCAAGTCTTTCCTAAAAACTAAGT R 2 1 2 1 101000 f 74 goat snp27313-scaffold290-3148074 24 35731742 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453557 Affx-122919777 AX-123323890 24 35546463 GCCGGCACCACCGTGTGGCAGCAGAGGTGTGACCA[C/T]GTCTGAAGACGGAACAGCTTCCAGATGTGGACACC Y 2 1 2 1 102000 r 74 goat snp27312-scaffold290-3110407 24 35769020 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385823 Affx-122971021 AX-123256181 24 35595978 CATTGAGCAAATTTGATTCCTTTCAAGAAAAGATG[A/C]TCTATGCTTATTTGGTGACTTTAAGCATACCCCCA M 2 1 2 1 101000 r 74 goat snp27311-scaffold290-3060892 24 35820670 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38442120 Affx-122928342 AX-123312457 24 35687906 TGTGGTGTTTGAGGTGGCAGAGAGCTGTGCTCACA[C/T]GGGCAGGGGTGTCTGCTGGGTTCCACCTCCCCCAC Y 2 1 2 1 103000 f 74 goat snp27309-scaffold290-2968964 24 35912973 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273577 Affx-1111833681 AX-519547191 24 35737303 TTTCATCAGCAGTTCAATGCCAAACTGCAGAACCC[A/G]GAAAGTGTGGTCAAAGAGAGAAGACCATCCGTGAA R 2 1 2 1 202000 r 74 goat GoatD01.001306 24 35737303 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38397241 Affx-122962368 AX-123267596 24 35738571 TACCTACTTTTCCCCCTCGTAACATTAGGATTATT[A/G]TGGGATCAAATTGAATAATAAAAAATATTCTTGAA R 2 1 2 1 103000 f 74 goat snp27308-scaffold290-2918299 24 35963886 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777508 Affx-122945656 AX-385264627 24 35774695 TAAAGAGGTTTTCAAAAACACAGATTTATTCTAAA[C/T]GTATTTTTAACCAGATTGCAAAGTTAGCTTGCAAA Y 2 1 2 1 101000 f 74 goat snp27307-scaffold290-2882175 24 35999960 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447778 Affx-122923951 AX-123318114 24 35871353 CTAACCATGGGCTTAGTGACCTAAAGAAAATATTG[C/T]ATTTTTCCAAGAACCTAATGTCCATCCTAGGAGAA Y 2 1 2 1 101000 r 74 goat snp27306-scaffold290-2785517 24 36096382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400654 Affx-122960356 AX-123271009 24 35916592 CTATAAACCATGATATTGTGTTGCCGCCTGAAAAA[G/T]ACCTAAACAAAGCCTAAGGAAAGCAGGCAGGCTTC K 2 1 2 1 101000 f 74 goat snp27305-scaffold290-2740278 24 36141352 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407362 Affx-122955273 AX-123277713 24 35994496 TGGGTACACATGATGCACCCATGTGGCTTTGGAAA[C/T]GGAGAGGACCATGTGAGAAGGTTTGTGGGTGGTTT Y 2 1 2 1 101000 f 74 goat snp27304-scaffold290-2662374 NW_017217508.1 18536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402463 Affx-122958605 AX-123272816 24 36036897 CTACTTGTTTCCTATCATCAAAAGCTGTCACACAG[C/T]ATCTTGAATAACTTTGGCTTTTTAGCTTTCTCTTA Y 2 1 2 1 101000 f 74 goat snp27303-scaffold290-2619973 24 36262440 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452882 Affx-122920225 AX-123323215 24 36065794 ATGAGGCAAAGAGAGAGAAGGTGAAGGATCACATG[C/T]GATGAAAAGACAATCCTGCGAGTGGCAATCACCAT Y 2 1 2 1 201000 f 74 goat snp27302-scaffold290-2591076 24 36292986 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387583 Affx-122970266 AX-123257941 24 36100957 AATGTAAAGAGATTTCAGTTATCGTAACTAGCTAT[A/G]TTGCTCCGTATGTTACCTGTTTGGGGGGAATTTGT R 2 1 2 1 201000 f 74 goat snp27301-scaffold290-2555913 24 36329484 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398480 Affx-122961578 AX-123268835 24 36131463 TATGCCAGAGACTGGTATAGGGACCCAAACATAAA[G/T]GCTGTATTGTATCTATCCTCCAAACTCACAATCCA K 2 1 2 1 101000 f 74 goat snp27300-scaffold290-2525407 24 36360378 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386568 Affx-122970704 AX-123256926 24 36160136 TTGTATTAGCAGTTTGTTCTGTTTAATTCTGAGTC[A/G]TATTCCACTGTATGACTATACCACAGTTTTCCTGT R 2 1 2 1 201000 f 74 goat snp27299-scaffold290-2496734 24 36388874 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426202 Affx-122940372 AX-123296548 24 36211877 GGGTGTCTAATAGGTCAAATTGATAAATAGATTAA[C/T]ACATGTAAATTTTTAATTTGGATAAGTGAAATTAA Y 2 1 2 1 101000 f 74 goat snp27298-scaffold290-2444993 24 36439718 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778187 Affx-122972199 AX-385265302 24 36266735 GAGAAAGAGAAAAATGAAGCCTACTTGGATTGATA[C/T]GAAAACTTAGGGTCATAGATTTGTTATTTATGAAG Y 2 1 2 1 101000 f 74 goat snp27297-scaffold290-2390135 24 36495332 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449472 Affx-122922646 AX-123319807 24 36296535 TCTCCATGACCCTTGTAAAGTGACTGAAAAAAATA[C/T]AAAGGAGCATATGGAATCTTTGGTATTGCTATTTC Y 2 1 2 1 101000 f 74 goat snp27296-scaffold290-2360335 24 36525204 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417135 Affx-122947361 AX-123287483 24 36357104 TTATTACATAGCATGGTTTTGAAAGCTCAGGAACA[C/T]AGAAACCACTGGCAGTTCTGGCCAGAGCCTTGCAG Y 2 1 2 1 101000 f 74 goat snp27294-scaffold290-2299766 24 36586817 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277710 Affx-1111835984 AX-519551209 24 36366687 TTTGTACTTAGATCAGATGTGATTTGTTCAAAATC[A/G]TATAGTGAATGAATGGCAGACCCATTTTTTAAATT R 2 1 2 1 101000 r 74 goat Random2.2K-2106 24 36366687 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320792673 Affx-122975248 AX-385279653 24 36425866 GTTACTCCTTGCACTCTACCCTGAAGCCATACTTT[A/G]CTTATTTACTTGCCCCATACTCTCCAACATCAGAG R 2 1 2 1 101000 f 74 goat snp27292-scaffold290-2231004 24 36657013 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782734 Affx-122950388 AX-385269806 24 36515322 ATTATTTTATGAACAAAGTTAATGAATTAGGCTAA[A/C]TGACCACTGAGTACATTTCAATGTTTGTATCAATA M 2 1 2 1 101000 r 74 goat snp27290-scaffold290-2141548 24 36747247 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274386 Affx-1111834169 AX-519547978 24 36556845 A[A/G]AGAGCCAGGCTGCAGCCAGGAGCTGGAGAACAAGA R 2 1 2 1 102000 r 74 goat GoatD01.023246 24 36556845 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38376218 Affx-122978801 AX-123246577 24 36596979 AATTAAACACTCAACAGTAGCAAACAGTGCTATTT[C/T]TGGGCTGTCAGGCGCTGAGGGGAAAACCACAGCGT Y 2 1 2 1 101000 f 74 goat snp27288-scaffold290-2059891 24 36829599 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380621 Affx-122975240 AX-123250979 24 36644135 AACATTAAAATACGTTTTCAATACATTATTAAGCA[C/T]GCAAGTTATTTTTAAAATTCGGGTATACAGGCTGT Y 2 1 2 1 201000 f 74 goat snp27287-scaffold290-2012735 24 36876890 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791988 Affx-122951918 AX-385278976 24 36709141 GCACCTACTCCTTAATAATAAAGGAATTTAATGTC[A/G]TTAATAGCTATGACCTTTAAATTTTGTTCCAGAGG R 2 1 2 1 201000 f 74 goat snp27286-scaffold290-1947729 24 36940996 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385503 Affx-122971266 AX-123255861 24 36745849 TAGCAATAAATAGGAAAAGGAGGCAGTTAAAAAAC[A/C]TATTGAAGCAAGAATGTATGAAATTAGGGTTCGAT M 2 1 2 1 303000 r 74 goat snp27285-scaffold290-1911021 24 36977916 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792898 Affx-122930929 AX-385279876 24 36802895 CTCTCCAGGGAGCTAAAATCAAATATCTACACACA[C/T]ACTTGAACAATACTGATGGAGAAATTTAAGCAAAG Y 2 1 2 1 101000 f 74 goat snp27284-scaffold290-1853975 24 37035330 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426897 Affx-122940461 AX-123297242 24 36847950 ACTGCTTACTTGTAATGTTTCTGTGAGGATCAGTG[A/G]CACAGCATAGCACCTAGTACAGCCCCTTGTTTGTG R 2 1 2 1 201000 r 74 goat snp27283-scaffold290-1808920 24 37080478 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769091 Affx-122944345 AX-385256266 24 36902079 ATGCAATATTGTTTCTGAGTTTTTACTCTTGGAGA[C/T]AGAATGATTGAGGTAGAAAGTATCAAGGGCATATA Y 2 1 2 1 101000 r 74 goat snp27282-scaffold290-1754791 24 37135401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399123 Affx-122960854 AX-123269478 24 36941694 ATGGAGGAGGCCCACAGCTAAGAAGGGGTTCAACT[A/G]TCTAGTAGCCAAAAGGAAGGACACTTGTCCAGGAC R 2 1 2 1 101000 r 74 goat snp27281-scaffold290-1715176 24 37175000 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445546 Affx-122925157 AX-123315883 24 37006889 ACATGGATTCTGTGTCCTCTTTTGGAGCCTCTGCT[A/G]CATTTGTTCCTTCCACCAGTAAGCCAGAGAATGGT R 2 1 2 1 201000 r 74 goat snp27279-scaffold290-1649981 24 37241073 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384854 Affx-122971954 AX-123255212 24 37040474 GAATAAAAATATTCGGCTTCTCAGTAAAATAAAGA[C/T]ACCAATATCTGTTTTTCTATTTTTCTGTAGCTGTG Y 2 1 2 1 103000 f 74 goat snp27278-scaffold290-1616396 24 37274589 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779006 Affx-122930385 AX-385266113 24 37093807 CTCTTGACTAGACTCTACTCCCTAACAGCTGTGAA[C/T]GTTTTGTAAAGCAGAGCCCTGAAAGAGCCACAGTG Y 2 1 2 1 101000 f 74 goat snp27277-scaffold290-1563063 24 37327192 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784291 Affx-122957288 AX-385271342 24 37134230 TACATCTCCAGCTAGCAAATGCCTGGAATACAGTA[C/T]ATACTCAAATGATTAAAAGAGCAAACAATTACACC Y 2 1 2 1 101000 f 74 goat snp27276-scaffold290-1522640 24 37367987 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783524 Affx-122946731 AX-385270587 24 37184678 ACACTGAGGCAGGTCTGGAAATACACAGAAAAGGG[C/T]AATGGAGAAGCAAATTATCTCAATTATGTATTCAG Y 2 1 2 1 101000 f 74 goat snp27275-scaffold290-1472192 24 37418398 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463914892 Affx-1110218495 AX-515392491 24 37204143 TTCCATCAGTACATTTAAAATCAAAATGTGATGTA[A/G]TAACAAAAATATTATATTTCTTAGTCTTCACCAGT R 2 1 2 1 101000 r 74 goat 24_37204143_AF-PAKI 24 37204143 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38423329 Affx-122943173 AX-123293675 24 37238223 TATTACACCATTTTACATAAAGGACCTGAGCATCT[A/G]TGGATTTTGGTTTCATGGGATGTCCTAGAACTAAT R 2 1 2 1 101000 r 74 goat snp27274-scaffold290-1418647 24 37472177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418047 Affx-122946629 AX-123288395 24 37290948 CTTGAAAAATATCATCAGCTTAGGGAATTCCCTGG[C/T]GATCCAGTGGTCAGAACTCAAGACTCATTGCCGGG Y 2 1 2 1 303000 r 74 goat snp27273-scaffold290-1365922 24 37524817 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413601 Affx-122950567 AX-123283950 24 37328040 GGGACAGGTAGATGAGAGCTGGCCATACTGCACCC[A/G]TGGCAGGAAGAGTGAGAACGAGTTGCCAGAAAGCT R 2 1 2 1 201000 f 74 goat snp27272-scaffold290-1328830 24 37561573 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772550 Affx-122952261 AX-385259700 24 37378363 TCTGATTTTCCTAACATTGGAAGACATTTGTCTAA[C/T]GTTAGCAAGCCATTTAGAGAAATATGAAGGAAAGA Y 2 1 2 1 201000 r 74 goat snp27271-scaffold290-1278507 24 37607630 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433599 Affx-122934956 AX-123303940 24 37409224 CATATCAGCATCAGTCTCCTGGTTGTGCTTTTATG[C/T]GGTAGTTTTGTAAAATGTTACTACTGGGGAAAATT Y 2 1 2 1 101000 f 74 goat snp27270-scaffold290-1247646 24 37638271 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395872 Affx-122964002 AX-123266227 24 37458795 CTCACCCATCCCCTATACCTCACCTCTAACTTCTG[C/T]AACCTCTGCTTTTTTGACACCTTTATTTACCCCTT Y 2 1 2 1 201000 r 74 goat snp27269-scaffold290-1198075 24 37687250 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390813 Affx-122967855 AX-123261170 24 37491405 GGCTTCAAGCAGAACCCTGAGACCCTGGGATTATC[A/G]CCAAGCAGGGACCCCTTCATAAAGACCCATCCATT R 2 1 2 1 101000 r 74 goat snp27268-scaffold290-1165465 24 37719927 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399403 Affx-122961245 AX-123269758 24 37553435 ATGCATGAGAAAAAGTGAATGAAAACAGTTCAAGC[A/G]CTGTTAAGGAGAATCAGTTTACAGACTCGAAGGAA R 2 1 2 1 101000 r 74 goat snp27267-scaffold290-1103435 24 37782079 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802682 Affx-122947831 AX-385289581 24 37606187 TGCTCTCAAAATGAGTATTAGGAATAATAGGCAAA[C/T]GCTGAAAAGTCACGTTTTCATAGTGAGTCTCCAAG Y 2 1 2 1 101000 r 74 goat snp27266-scaffold290-1050683 24 37834745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448401 Affx-122923680 AX-123318737 24 37652526 TGTCAGGGAAAAGTTCTTAAACCAGAGGAATCACT[A/G]CTTTGATTCACTGGCTGGCACATGGCACAAACCCA R 2 1 2 1 101000 f 74 goat snp27265-scaffold290-1004344 24 37881166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415157 Affx-122949405 AX-123285506 24 37702201 ATCTGCCCAAAGGTTCCCACAGCACCAGTTTCTCC[A/G]TCCTCCCAGGTCTCCTCCTAAATGGGTCTTTTCCT R 2 1 2 1 101000 r 74 goat snp27264-scaffold290-954669 24 37930308 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442429 Affx-122927973 AX-123312766 24 37735218 AAGAACACAGAACAGTTTTAAGCATGAGAACTGTA[C/T]GAAATAAGAACACCCTCTGGCTCCCTCAACAAAGC Y 2 1 2 1 101000 f 74 goat snp27263-scaffold290-921652 24 37963832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427474 Affx-122940018 AX-123297817 24 37874842 AATGCCTCATTCCTGCTCCCCCAAAGTTTATAGTT[G/T]AATGGAGATTATACCAAAAAATAAATGTTATTTAT K 2 1 2 1 201000 r 74 goat snp27260-scaffold290-782028 24 38102140 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430193 Affx-122937351 AX-123300534 24 37908860 CATAGGGTCGCAAAGAGCTGGACACACTGAATTAG[C/T]ACGCATGCACTCACATGCATATCGTTAGATACAGA Y 2 1 2 1 101000 r 74 goat snp27259-scaffold290-748010 24 38136165 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418257 Affx-122947022 AX-123288605 24 37948009 GAAAGACAGAAGGGGAAAACTCTTTAAGAGGTGGT[A/G]TATGTGTGGGTACGTGGGTGTGTAGAGGCCAAGAA R 2 1 2 1 101000 f 74 goat snp27258-scaffold290-708861 24 38174599 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432546 Affx-122935545 AX-123302887 24 37977831 GGGAGGTGGGGAGACCCTCTGAGTATAAGCTGTGC[A/G]CCTGAAATGTGGCCAGAGATGGTGCAGTGCCTGTG R 2 1 2 1 201000 f 74 goat snp27257-scaffold290-679039 24 38204381 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792458 Affx-122923565 AX-385279439 24 38010618 AAATGTTTTGAGTTTTCAAATCCTCAGCTGTTAAC[A/G]CCCTTCACTGCTTCTTCACCTGTTTCATGTACCAC R 2 1 2 1 101000 r 74 goat snp27256-scaffold290-646252 24 38236713 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435357 Affx-122933591 AX-123305697 24 38043879 TCCAATCCATCAATCAGAGCTTTTATCTCTGCCAT[A/C]TGTGGCTTTCCCAGTAAACAAACAAACAAACAAAA M 2 1 2 1 101000 f 74 goat snp27255-scaffold290-612991 24 38269834 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273911 Affx-1111833927 AX-515386515 24 38070258 AGCAACAGCTTCAGGGCAAGGACAGATAATGGGAA[A/C]CATGATACAGATTCTCTTGCTCAAAG M 2 1 2 1 101000 f 74 goat GoatD01.010706 24 38070258 A C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320786352 Affx-122922545 AX-385273386 24 38094861 TTTAAAGATTCTCCCTGTGTTAAATTATGTCTTAC[A/G]ATATTGAGACAAAAAAATGTTTCTGCCCCTTAAAA R 2 1 2 1 202000 r 74 goat snp27254-scaffold290-562009 24 38320523 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416313 Affx-122947922 AX-123286662 24 38133298 CCAAAAACTGAACCTTAATCTAGTGACATCCCTAC[G/T]CAATACTCACTCCATGGAAGTATCAAGCATTCTCA K 2 1 2 1 101000 f 74 goat snp27253-scaffold290-523572 24 38358973 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783308 Affx-122919955 AX-385270373 24 38192157 CTCCAAAATAGAATGATTGTTAGTGTCTAAATATC[G/T]CTTCCTCCCAGTGTCAACAGAGGTTTTTCTCTGTT K 2 1 2 1 101000 r 74 goat snp27252-scaffold290-464713 24 38417400 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783738 Affx-122944117 AX-385270794 24 38232696 CCTTAATAGGAATAGATCAATAAAGTTTTGGTGGA[C/T]GATTTCATCAATCTTAGCAGAGGGCTTAACCCTGT Y 2 1 2 1 101000 r 74 goat snp27251-scaffold290-424174 24 38458001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450137 Affx-122922754 AX-123320472 24 38276098 AAATAATAGAAGGTATCCCTACATATCAAAACTGG[C/T]GTAATATACTTAAATTTTTTAAAATATAAAGGCAG Y 2 1 2 1 102000 f 74 goat snp27250-scaffold290-380772 24 38501558 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765832 Affx-122935201 AX-385253279 24 38307139 ATGGTCCACCTATATTGTATAACTGAATCCTGCAA[C/T]AATTCTTGCAACCACAGTTACTGTGTTCATTCCTT Y 2 1 2 1 101000 f 74 goat snp27249-scaffold290-349731 24 38532467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436266 Affx-122932543 AX-123306605 24 38343582 GGAAGAAGCAATGTTATTGGATTAGGAGAGCCTCC[A/G]TTCTCCACGGTCCCAGATCAAAGCCTGTCTGTTTT R 2 1 2 1 101000 f 74 goat snp27248-scaffold290-313288 24 38568672 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772507 Affx-122955809 AX-385259658 24 38391361 TGAAGAGCATCAGACCTGGTTTAAGTGCCAGTGCT[A/G]CTACTTTTTTGTCTAACTTCAGCAAATTGCTAATT R 2 1 2 1 101000 f 74 goat snp27247-scaffold290-265509 24 38616215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775467 Affx-122968801 AX-385262598 24 38488326 CCTGTGGTTTTTAATCTCCTGCTAGATCATGAACT[A/G]TAACAACATAGGGCATGCTCCTTAAAAAATATCCC R 2 1 2 1 101000 f 74 goat snp27245-scaffold290-168544 24 38713719 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403329 Affx-122957820 AX-123273682 24 38535983 GACTCCTTTACGACAGCATTTAAACATATGTAAGT[A/G]TCTCTAATTGCTAAGGAGAGGCTTCCTAGAACCAA R 2 1 2 1 101000 f 74 goat snp27244-scaffold290-120887 24 38761188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801859 Affx-122978452 AX-385288766 24 38575180 TAGGTGCTGAGGATATCATAATGGACAAAAATGGG[C/T]GATACTACCCGCTATTATAGCCTTAAATTATAGTG Y 2 1 2 1 101000 f 74 goat snp27243-scaffold290-81690 24 38801272 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388216 Affx-122969410 AX-123258574 24 38605898 TTTTATTTACAGTAGTTTTATATGTTTTATGTTCC[A/G]TGTGTAGCTTACTAGCCTAACATTTCTGTTTGAGA R 2 1 2 1 101000 r 74 goat snp27242-scaffold290-50972 24 38831971 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792512 Affx-122964956 AX-385279493 24 38641860 AGAATCTGCCAGAAAGACATACTTTGTATTGACCA[A/G]TTCTGTACAAATTGGCTATTCATTCAGATATTGGC R 2 1 2 1 101000 r 74 goat snp27241-scaffold290-15010 24 38867382 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418825 Affx-122946154 AX-123289173 24 38688381 CACTGCATACATTTCAAACACTGATGTACACTTGA[C/T]GGTCTCTCTCCCTCTCTAAATATCTACAAGTGTTT Y 2 1 2 1 101000 f 74 goat snp27786-scaffold2970-58579 24 38914835 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401211 Affx-122959327 AX-123271564 24 38743860 TGTAATTGCCTTCTCTAAAAGAAATACTTTATATT[A/G]TATCATTTTAATTCCCTTGTTTCTTTTACTGAATT R 2 1 2 1 101000 f 74 goat snp27785-scaffold2970-3100 24 38970154 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402710 Affx-122959198 AX-123273063 24 38789435 TACAGAATGTGATTTTATTAAAGAATACTATTTTA[C/T]GGGACAGTTCATTTTAAATCAATTAAGCATTCAAC Y 2 1 2 1 101000 r 74 goat snp54528-scaffold833-42376 24 39013066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422898 Affx-122943059 AX-123293244 24 38872498 GTTGCACAGAGTTGGACACGACTGAGTGACCAAGC[G/T]CATAGAACCACTATCTTAAAAGTTTGGGTTTCTGA K 2 1 2 1 101000 r 74 goat snp54529-scaffold833-125439 24 39085223 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320795251 Affx-122957908 AX-385282209 24 38919827 GAGAGGTTTTTCCTGTCTAACTAACCTTGGTATGT[A/G]TAACCACCACCTACTACTACACAGACACAAATACA R 2 1 2 1 101000 f 74 goat snp54530-scaffold833-172768 24 39133006 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784123 Affx-122961712 AX-385271175 24 38962490 TTAACAACAGCATTGAAATGGAATGAGTGAAAATG[A/C]TGAATTAGCAGAGACACAAACACTGCTCTGTTTGT M 2 1 2 1 102000 r 74 goat snp54531-scaffold833-215431 24 39174640 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440118 Affx-122929702 AX-123310455 24 38995212 GACTTTGTCTCCGTTATGACCCTGGCACCATCTTG[C/T]TCTGACGGAGGTGGCTCTACTCTCAGTGCTGCTCC Y 2 1 2 1 101000 f 74 goat snp54532-scaffold833-248153 24 39207285 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433709 Affx-122934531 AX-123304050 24 39087914 CAGCACAGCCAGAGCAAGACGGGAGAGTTCACATG[A/C]GGAGAGCCCACCTAGGTTTGACTGAAATTCTCTGC M 2 1 2 1 101000 r 74 goat snp54534-scaffold833-340855 24 39299617 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788889 Affx-122928010 AX-385275904 24 39131031 AGCATTTCCCTCCATGTGTCTTGTGTATTAAATTA[C/T]AACTCTTAGTGACATTGCTGACATAAACCCTTATG Y 2 1 2 1 101000 r 74 goat snp54535-scaffold833-383972 24 39342719 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782423 Affx-122958655 AX-385269499 24 39162370 TCCCCACTTTAGGCAAACAGGCCATAGTTAACTCT[A/G]TACGTTAAGGAGTATGCACCTATAACTACTCCCAA R 2 1 2 1 101000 f 74 goat snp54536-scaffold833-415311 24 39374251 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398068 Affx-122961740 AX-123268423 24 39209323 AGCTTGAAATGGTTAAATAACACAGTGAGCCACTC[A/G]TGGCAGTCTCTGTCTTCTGGATATTTATTAAAGAC R 2 1 2 1 201000 r 74 goat snp54537-scaffold833-462264 24 39421171 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795772 Affx-122941968 AX-385282725 24 39254689 TTGGAGCTAATCATCTGAAAAGTGATTCTTTGCCA[C/T]GTTTTACAAAGCAAGAAGTTTTCTAAATACGATAT Y 2 1 2 1 101000 f 74 goat snp54538-scaffold833-507630 24 39466759 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382714 Affx-122973623 AX-123253072 24 39284965 CCTGCCAAAAACATTCTTTGAAGGAATTCCCTGGC[A/G]TCTCAGGGCTTAGGACTCTGCTTCCAATACTGCGG R 2 1 2 1 101000 f 74 goat snp54539-scaffold833-537906 24 39496654 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795761 Affx-122934902 AX-385282714 24 39316853 GCATAGTTCACTAGCTTTCTAATCTTAATTAATGA[C/T]AGTAGAAAGCTTCAAAATTTCTTATTTAGATTTCC Y 2 1 2 1 101000 r 74 goat snp54540-scaffold833-569794 24 39528052 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447855 Affx-122923890 AX-123318191 24 39378643 GGTGAGTTCTGGTCCTGCTGGGGACCAATCATAGA[C/T]GGGCAACTCATCTGCTTCCTCCCACCCAGACAGGA Y 2 1 2 1 201000 f 74 goat snp54541-scaffold833-631584 24 39589906 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391617 Affx-122966587 AX-123261974 24 39441244 ATGGGACATTTTGACCTAGTTACAAACACCAGTGT[A/G]TTCTCCCAGAAAGTAATTTTAAAAACATGGGTTTA R 2 1 2 1 101000 f 74 goat snp54542-scaffold833-694185 24 39652719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425978 Affx-122941159 AX-123296324 24 39477786 AGGACCCAGCATTTCACAGTAAACCACTAAGTCCT[A/G]CATGTCCAAATAGGCCCTGTGTGTTTAACACAGTT R 2 1 2 1 101000 r 74 goat snp54543-scaffold833-730727 24 39689225 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403413 Affx-122957759 AX-123273766 24 39520473 TGGTAAACAGGACAAAGAGATACACTCTAAAGGAT[A/G]CTCCCTGGTGAAGAAAAACACATTTCCGCCTCTCC R 2 1 2 1 101000 f 74 goat snp54544-scaffold833-773414 24 39732191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412592 Affx-122951296 AX-123282941 24 39590005 AACATGTCTAATCCTGGACCCTGGCTTAAAAGGAC[A/G]TTTACATCCTGTAGTCCCAATGTTGTCATCTTTAA R 2 1 2 1 201000 r 74 goat snp54545-scaffold833-842946 24 39802599 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387590 Affx-122970260 AX-123257948 24 39657370 CTGCCTATACCAGGTCTTGATCTTTAGTTTCCTTT[A/C]GTACATTTTTAAAAGGATTTTCATATCTCTGTAAC M 2 1 2 1 101000 f 74 goat snp54547-scaffold833-910311 24 39867510 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382732 Affx-122973610 AX-123253090 24 39695376 CATCAAGCCCCTCGTCCCGCCCCACAGTTTTTAGC[C/T]TGCTGGGACCTATTAAACACTACAGTTTACAAGCT Y 2 1 2 1 101000 r 74 goat snp54548-scaffold833-948317 24 39906575 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435247 Affx-122934071 AX-123305587 24 39731288 TTGTTGAAAACAGATCCTTTTTGTCCCAGAAAGCC[G/T]ATTCAATGAATTTGTGTTTGATGGAAGGCAGTTTA K 2 1 2 1 101000 f 74 goat snp54549-scaffold833-984229 24 39943086 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411587 Affx-122951617 AX-123281937 24 39760614 TGAGTCATGTAAAGACTAAGAAAAAAAGTTTTTGT[A/G]TCCCAAGTAAAAAGTTAATTACAAAATTAATTAGA R 2 1 2 1 303000 r 74 goat snp54550-scaffold833-1013555 24 39971739 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273035 Affx-1111833280 AX-519546709 24 39790120 AAGCTTCTGAATTCTCACAACATCCCTCAAGATAG[A/G]TTCTATTATTATCTGCAGTTTATAGATGAAGCAAT R 2 1 2 1 101000 f 74 goat 24_39790120_AF-PAKI 24 39790120 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38434139 Affx-122934914 AX-123304480 24 39799998 GAAATTGTCTAAAAAAACAAACAGGCAAAAAATAA[C/T]GGACCTGGAGAAAATGCACTTGACTTCAGAAGAAC Y 2 1 2 1 103000 r 74 goat snp54551-scaffold833-1052939 24 40011728 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439908 Affx-122930021 AX-123310245 24 39829828 AGGCAGGGAATGAGTCACTGCAGAGAGACAATGCC[A/G]CAGAAAGGCTTTCGACAGCATAATCCTCTGAAGCA R 2 1 2 1 101000 r 74 goat snp54552-scaffold833-1082769 24 40041527 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799505 Affx-122973664 AX-385286435 24 39861476 CAGGGTGAGAACACGATGGGGAATACCATCTGATG[C/T]ACAGAATCACTTAACAACGTATTCATTTCATCTCT Y 2 1 2 1 101000 r 74 goat snp54553-scaffold833-1114417 24 40073220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415750 Affx-122948938 AX-123286099 24 39897159 GTGTCATATAGTTCTTTCCCTGTCTAAGGATGTAG[A/C]TATACATCATTGGTCAAAGGATTACACAGCATTCA M 2 1 2 1 101000 f 74 goat snp54554-scaffold833-1150100 24 40108774 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275574 Affx-1111834885 AX-519549144 24 39967564 CTTCATGTTATTAATTCTCTGCAGTTAATTATGTA[A/G]TTCTTCATGAATTAACCTTCACTGTGCATTCCTCC R 2 1 2 1 201000 r 74 goat GoatD01.057483 24 39967564 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38422030 Affx-122943624 AX-123292377 24 40015343 GAAAGGCTTCATCAGCTTTCTCCTCACTCCTCTCA[A/G]AGAGCGGAGGAAGGTGGGAACAGAACAGAAAACGG R 2 1 2 1 202000 r 74 goat snp54556-scaffold833-1268284 24 40227599 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383632 Affx-122972540 AX-123253990 24 40050904 TAGGCACATTGCAAGCAGAATCGTTTCCACCTTGA[C/T]GACCACTGTGTCATTTAGAAACTACTCACTCAGGC Y 2 1 2 1 201000 f 74 goat snp54557-scaffold833-1303845 24 40263321 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435099 Affx-122933710 AX-123305439 24 40110670 CATAAGGTCAGGCAAATACCTTCCGCTCCTTATCA[C/T]GGAGATGGAATGCTCTTGACCATCACTGTAGGTGC Y 2 1 2 1 101000 r 74 goat snp54558-scaffold833-1363611 24 40323377 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376071 Affx-122978917 AX-123246430 24 40180825 TTCAATAATGCAAGAAAACGGGAGTCAAAGGCAAA[C/T]AGAGGGCACAGTAAGACTAACTGTCATTATTTGTA Y 2 1 2 1 101000 f 74 goat snp54560-scaffold833-1433766 24 40393255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408514 Affx-122953708 AX-123278865 24 40214400 TCAACTCTCTTAAAATTACGTATCTGGTTCTGGAT[A/G]TGCCTCCTGAATGCGTCAATCAAGGGCTGTCCTCG R 2 1 2 1 101000 f 74 goat snp54561-scaffold833-1467341 24 40426601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412467 Affx-122951396 AX-123282816 24 40310491 GTCTCCAACAGAGGAAGGTTCCCACACTGTCTACC[A/G]TGGTGACTGCTTTGAAGAGTCAGTGCATCATGTGC R 2 1 2 1 201000 f 74 goat snp54563-scaffold833-1563432 24 40523296 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777661 Affx-122928607 AX-385264780 24 40372580 CATTTCACTTTATGGTTAAAGAGTATTCAAAAAGA[A/G]GTAGGGAGAGAAAGCTCATTTTGTCATTTTCCAGC R 2 1 2 1 101000 r 74 goat snp54565-scaffold833-1625521 24 40580918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412640 Affx-122950796 AX-123282989 24 40404908 CATTTACTGTACAACATTTGGAAAACGAAGAAAAA[C/T]AAACACATTTGCACAAAATAAGTATAACGTCATGA Y 2 1 2 1 303000 r 74 goat snp54566-scaffold833-1657849 24 40613140 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408161 Affx-122954215 AX-123278512 24 40440836 GTAACTCTCAACCCTAGGATCAGACCCGTTCTCTT[A/G]CAAAGAATATCTTCCATCCCCTCCGTGGGCAAGTC R 2 1 2 1 101000 f 74 goat snp54567-scaffold833-1693777 24 40649112 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419221 Affx-122945688 AX-123289569 24 40483616 CTCCCTGCCTGGGATTTGTTTCAAGTTAAGATGCG[C/T]GAGAAAGCATTTGGATGGATTTTCAAGAAGTGGGT Y 2 1 2 1 101000 f 74 goat snp54568-scaffold833-1736557 24 40691958 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277585 Affx-1111835986 AX-519551084 24 40504966 AATGGGGCTCCACAGTATGGAGACTTTAGGACACA[A/G]GAGGAGCACCTGGGCCGTGGGCTTGGGAGGACTCT R 2 1 2 1 101000 f 74 goat Random2.2K-2112 24 40504966 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392340 Affx-122966683 AX-123262697 24 40515848 TAAAATACATATTTTAAATTGCTGCAGGGCCTTAT[G/T]CAAACTTGAAATAAAAAGTGGCTCCAGGGGGTGGG K 2 1 2 1 201000 f 74 goat snp54569-scaffold833-1768789 24 40724552 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434795 Affx-122933875 AX-123305136 24 40552886 GTATTCCTCATTTTTCCCAGGGAGGATGCTGAGAA[C/T]GAATGAGGAGTTTCCTAAATATTTGTTGTGTTTCT Y 2 1 2 1 201000 r 74 goat snp54570-scaffold833-1805827 24 40761692 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447070 Affx-122924506 AX-123317406 24 40581424 AAAATGTGTTAGGGTTTCTGCAAGAAACAGAAGGT[A/G]CCTTTGAAATGGGTCATTGAGGAAGATTTAATAGA R 2 1 2 1 101000 r 74 goat snp54571-scaffold833-1834365 24 40790361 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376717 Affx-122978967 AX-123247076 24 40630538 TGCAGAGATGACAAGAGATTCCCAGGCCCATAGAA[A/G]CTCACAATCCAGCAGAGAAGACACAGAGGCCACAG R 2 1 2 1 101000 f 74 goat snp54572-scaffold833-1883479 24 40839867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782368 Affx-122937752 AX-385269444 24 40669609 TTCCGAAGGTTGGTGATGAATGAGGATTTAGAAGC[A/G]TATTTATTAATCATTTCAGTAGGCTAAAAGAGACT R 2 1 2 1 101000 f 74 goat snp54573-scaffold833-1922550 24 40878439 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382099 Affx-122974896 AX-123252457 24 40702093 GTTGGACACGGCTTAGCAACTGAATAGCAACAACC[A/G]CTGTGTCATTGAGGACATGGAGGGGAGGGTTCAGG R 2 1 2 1 303000 r 74 goat snp54574-scaffold833-1955034 24 40911045 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434024 Affx-122934220 AX-123304365 24 40738807 CCTCAAAGAAGTTGATCAGAAGATATGTTGCATGC[A/G]TGCATACTGAGTCACTTCAGTTGTGTCTGACTCTT R 2 1 2 1 201000 f 74 goat snp54575-scaffold833-1991748 24 40947787 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275071 Affx-1111834669 AX-519548652 24 40773330 GACCCGTTTTGATAAGTTTCTCATATTGAGGACAC[A/G]AATGACACAGACCTGTGAGGTCCTCATTTTTCTTG R 2 1 2 1 201000 f 74 goat GoatD01.045071 24 40773330 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38407086 Affx-122954902 AX-123277437 24 40789086 AAACCACAAAAAACTCAAAACCCTTCCATGCCATG[C/T]TCTGTATGTCTTGGTCAGGTTCCTGGTGCAGTGCT Y 2 1 2 1 201000 r 74 goat snp54576-scaffold833-2042027 24 40997925 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442286 Affx-122928259 AX-123312623 24 40831196 CAGAACTTGATGAAAAATTGCATGCGAGGAAAGAG[G/T]AACACAAGTGAGGTGACTTCTGCTTATGGAGCACG K 2 1 2 1 101000 f 74 goat snp54577-scaffold833-2084137 24 41038705 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439491 Affx-122930151 AX-123309828 24 40892250 TATCACTAACTAGCAGAACAGTATGATGTGGGACC[A/G]CATGCACACACACACACGTGCACACACATTCGGTA R 2 1 2 1 201000 f 74 goat snp54579-scaffold833-2145191 24 41099152 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436491 Affx-122932962 AX-123306829 24 40941530 GCCCAAGAGGTCCACAGGGCCCTGCTGGCTTTCAC[A/G]CCTGGTCATAGTCAGGGTCATGATGTGGATGGGGT R 2 1 2 1 101000 r 74 goat snp54580-scaffold833-2194471 24 41148254 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380815 Affx-122975083 AX-123251173 24 40970306 GGGGAATTGCAGTCAGCATTGTGGGCTGTCTTGCC[A/G]TCTCTGCATTGGTGCCCTCATTGACACTCCTTACG R 2 1 2 1 101000 r 74 goat snp54581-scaffold833-2223247 24 41177025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413361 Affx-122950146 AX-123283710 24 41001328 ATCCATATGGTTTGATGTTGTCAATGCCTCACACT[A/G]CATTAGTAATCACCAAATATGGGGGTGATTTTGAT R 2 1 2 1 201000 f 74 goat snp54582-scaffold833-2254269 24 41208323 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388268 Affx-122969771 AX-123258626 24 41040039 CTTCAAAAATATTAAATTCATATACCCTTGTAATG[C/T]AGGAATCTTCTGATATATAAGTGTCACCTGTTTAT Y 2 1 2 1 101000 r 74 goat snp54583-scaffold833-2292980 24 41247011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414861 Affx-122949150 AX-123285210 24 41093420 TCAGTAAACATAGCCTGAATTGCTTTCATTTGTTG[C/T]GATAGCAACAGACAGCAAAGGCACTCAAGATTTAA Y 2 1 2 1 101000 r 74 goat snp54584-scaffold833-2346361 24 41300420 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390747 Affx-122967907 AX-123261104 24 41123055 ACATCCCAGTAGTGGGAGATCTGAGGCCCCAAGAG[A/G]GGCCTGGGGGGAAAATGCAAAGACCCATTAAGTCA R 2 1 2 1 103000 r 74 goat snp54585-scaffold833-2375996 24 41329985 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447237 Affx-122924964 AX-123317573 24 41158871 ACATGACTGATGGAAAGTGGGGCTAGAGTTCTGGT[C/T]CTCTCTGTCACAGGGAGCCTTGTCACAGTCCCCCC Y 2 1 2 1 202000 r 74 goat snp54586-scaffold833-2411812 24 41365838 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426336 Affx-122940270 AX-123296682 24 41188118 CAAAGTACTACCAAACCAAATTCAGCAGCATGCTA[G/T]CAAATGCACAGAAAACACTGTTAATTGTTACACAG K 2 1 2 1 101000 f 74 goat snp54587-scaffold833-2441059 24 41395169 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790997 Affx-122978953 AX-385277994 24 41230684 TCTAGAGATTCTTGTAGTTAACTTGAAGCAGAGCC[C/T]GCAAGAGAAGTATCTGCTAGTTCTTTTCAGTAAAA Y 2 1 2 1 101000 r 74 goat snp54588-scaffold833-2483625 24 41436662 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274165 Affx-1111834080 AX-519547766 24 41254800 TTTGGAGTCACGTTCTCTTGAGGTGGGCAACTGAA[A/G]TGTACCATTATATCCT R 2 1 2 1 101000 f 74 goat GoatD01.017418 24 41254800 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38401491 Affx-122958947 AX-123271844 24 41289055 GTGGCGGGACAGCATTTTAAGGACATTTGCGGGTG[C/T]GTTATAATTCCCGGGCAATTCACAGGGATGAACCC Y 2 1 2 1 101000 r 74 goat snp54589-scaffold833-2541996 24 41494946 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410329 Affx-122952473 AX-123280679 24 41346158 GGCTTCTGACCAGGGAAGAACTGTTCTTTAAAAGC[A/G]TCATCTTTGCATATCGTGGGGTGACAAGTGCAATG R 2 1 2 1 101000 f 74 goat snp54590-scaffold833-2599099 24 41551936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406406 Affx-122955221 AX-123276758 24 41396125 CCCCTGAGTCTGAGTTTTCTGTTCTACAACGTAAA[C/T]AATGATCACCTTATAGGTAAGGTATGAGGTTGGGC Y 2 1 2 1 101000 f 74 goat snp54591-scaffold833-2649066 24 41601731 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413372 Affx-122950138 AX-123283721 24 41431839 TTCGGGTAGCAAGACACTAGATGGCCACAGGCTCA[A/G]TGACCCCTCCCCAAGGTCTAACCCACACATCGCAC R 2 1 2 1 101000 f 74 goat snp54592-scaffold833-2684780 24 41637456 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277717 Affx-1111835987 AX-519551216 24 41444307 GAGGCTGACACTCTCTGGACACACATAAAGCGAGT[A/G]TTCACATGAACTTTCTGCAGAAATAATAAAATTGG R 2 1 2 1 101000 r 74 goat Random2.2K-2114 24 41444307 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425838 Affx-122940673 AX-123296184 24 41470158 AGAGTGTTTCTATTCTTAAAGCCCTATTCTGATTA[C/T]ATTACTCCCCTGATCACAATTCTCCTCTGCCTCCT Y 2 1 2 1 101000 r 74 goat snp54593-scaffold833-2723099 24 41675667 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424729 Affx-122941669 AX-123295075 24 41509416 ACAGCTGTGTTACTCATGCTCCAGATCCAAATATC[A/G]TTGCACAGCATCTCTGCACACGGCCCATTGTGGCC R 2 1 2 1 101000 f 74 goat snp54594-scaffold833-2762357 24 41715102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431658 Affx-122936807 AX-123301999 24 41591993 TGTACAGATAGTGTTCTTATTCATTAGTAGTCAGT[A/G]CAATGCCTTGGATCATAATTACCCACGTAATCTGA R 2 1 2 1 101000 r 74 goat snp54595-scaffold833-2844934 24 41798513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447317 Affx-122924904 AX-123317653 24 41651442 TTAAAGGCCTTTTTCTAGACTGTCCTCATTTCTTA[C/T]GGATCATAAGCTTCATTTCATACTAAAATCATCTA Y 2 1 2 1 201000 r 74 goat snp54596-scaffold833-2904383 24 41858643 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416646 Affx-122947607 AX-123286994 24 41687570 TCGGTATAGTATTTCCGTATAAACTCTCCAAAGAA[C/T]AGGTCCTAAAAAAAGGAATCAGTCCTGGGAGAAGC Y 2 1 2 1 101000 f 74 goat snp54597-scaffold833-2940511 24 41894814 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768319 Affx-122971896 AX-385255499 24 41718029 TGAGTTATGATTTCTTCATTGTACTACTCCTAGGA[C/T]GCTGAGTTTTTAGAGTTGTTTGCCATTTTCCACTG Y 2 1 2 1 101000 r 74 goat snp54598-scaffold833-2970970 24 41925428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430138 Affx-122937394 AX-123300479 24 41749535 ACCCCAGATGGGTCAGCGAACCAGAAAGTCTAATG[C/T]GCCATGAAACTACCTTGTGCAGTGTCAGCTATCCC Y 2 1 2 1 101000 f 74 goat snp54599-scaffold833-3002476 24 41950933 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428661 Affx-122938652 AX-123299003 24 41805543 GAATTTGTGGCATTCACAGGTCCTGACCTTGGTTC[A/G]CAGCCTTTAAGTTGGTGGTTCTTTCTGCTCCTTTT R 2 1 2 1 101000 r 74 goat snp54600-scaffold833-3058484 24 42007358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402118 Affx-122958677 AX-123272471 24 41837554 CTGAGAACAAGAACCAAGTCCTGTGTATCTGGCTA[C/T]AGTCACTGGTTCATAGTAGGTGTTCAATTAGGTTT Y 2 1 2 1 101000 f 74 goat snp54601-scaffold833-3090495 24 42039619 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389281 Affx-122968525 AX-123259639 24 41883844 GAAGAGCCACCCCACGACTGTGACCTCCCGCAGCA[C/T]GGCCCTCTGAACTTTAGGTGTTTGGGGAGCCCAAT Y 2 1 2 1 101000 r 74 goat snp54602-scaffold833-3136785 24 42086004 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401480 Affx-122958957 AX-123271833 24 41958311 GAATGATAAGCTGGAACACTGCATATATGGAATTC[A/G]TTCAGTGGTTAGTGGAAGATGCTTTAATGAGTGAA R 2 1 2 1 101000 r 74 goat snp54603-scaffold833-3211252 24 42161375 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408067 Affx-122954264 AX-123278418 24 41995376 CTCCAGAATGTTCAATTTTGTTAAGAAAAGGAAAA[C/T]TATTTTTCAGTTTTGCATCTTTGGTTATTGTTGTT Y 2 1 2 1 103000 f 74 goat snp54604-scaffold833-3248317 24 42198357 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775098 Affx-122922257 AX-385262229 24 42024575 ACTGAGTCTGCTGTCAAAAAAAGTGAGAGTCCTTA[C/T]GAGATCAGGGCCTCATTCACACTTCTTCACATGGG Y 2 1 2 1 101000 f 74 goat snp54605-scaffold833-3277516 24 42227589 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410812 Affx-122952645 AX-123281162 24 42055211 TAGTAATAGCATCAGTAAAGAAAACTAAGCGCTCT[A/G]AGCGACCAGGGACCAGTGATGTTCAGAGGAAGCAT R 2 1 2 1 101000 f 74 goat snp54606-scaffold833-3308152 24 42258109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393085 Affx-122965599 AX-123263442 24 42087108 TCGTGTCCTGAGGCGGGTGTCAGGGAGCACGCTGT[A/G]TGGCGATCTGGGTTATGAAATGCGTGACTTACCTC R 2 1 2 1 101000 r 74 goat snp54607-scaffold833-3340049 24 42290199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405523 Affx-122955988 AX-123275875 24 42118106 TCAAATAGTCATTGTTTCCCCAACCATGAATGGAA[C/T]GAATGTCATTAAAAAAAAAAAAATCCTACCAAGGA Y 2 1 2 1 103000 f 74 goat snp54608-scaffold833-3371047 24 42321360 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377938 Affx-122977216 AX-123248297 24 42155322 TACACTTGGCCTTGCCTACAAGGGTTCCAGGAGGG[C/T]GGAGGAAATCCTTGAGAAATTCTTTCCTCCTCCTC Y 2 1 2 1 201000 r 74 goat snp54609-scaffold833-3408263 24 42358596 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379334 Affx-122976176 AX-123249693 24 42250672 TGATTGCTCTAAATATTAATAAAACCGTGTGCTCT[A/G]TACAAAAAAAGCTCTGTGCTTACAAAGAATAAAGT R 2 1 2 1 201000 r 74 goat snp54611-scaffold833-3503613 24 42453727 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397452 Affx-122962107 AX-123267807 24 42297250 TAGTGGTTTTTTGGTTTTGTTTTTTGCTAACACAG[C/T]GCTAGTGGGTCCACAATAAAGACCCATAAGATCAT Y 2 1 2 1 101000 r 74 goat snp54612-scaffold833-3550191 24 42500467 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407181 Affx-122954826 AX-123277532 24 42333273 CGTAAGCCTCATTCTCAGCAGTTGTTTGTGCACAG[C/T]GCGTGTTAGCCTCTTGTTCTTTACAGCCTTGCTCA Y 2 1 2 1 201000 r 74 goat snp54613-scaffold833-3586214 24 42536581 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273037 Affx-1111833281 AX-519546711 24 42374379 GGCCTAGGAGGAGCGACCGTTCTGCAAACACTGAC[A/G]TGTGGAGGGTGGTTGAGGCCTGGGGACCAGCTGCT R 2 1 2 1 202000 f 74 goat 24_42374379_AF-PAKI 24 42374379 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320794224 Affx-122944409 AX-385281190 24 42517472 TGTGAAGAGTAACAGCAGAAAGCAATGCACATGAA[C/T]AGAATGATCCCTAGAATATACGGTGTGTGGAAGCC Y 2 1 2 1 101000 f 74 goat snp54616-scaffold833-3770413 24 42720565 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439689 Affx-122930577 AX-123310026 24 42571612 TGAAACGCTTGCTCCCAGAACAATGTCCAACACAG[C/T]GAGGAACTGGACTAATGCCTCAAAATCAGCTTCTC Y 2 1 2 1 201000 r 74 goat snp54617-scaffold833-3824553 24 42774950 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409886 Affx-122952905 AX-123280237 24 42623007 CCAGGCTCAGTGAGGACCATGGCCCCTGTCATTGA[C/T]AGCAAGGCTGTGGCCAAACATGTATTGGTGATGGA Y 2 1 2 1 101000 r 74 goat snp54618-scaffold833-3875948 24 42826231 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777727 Affx-122947661 AX-385264845 24 42656807 GATTCTGTGAACATGTTTGCACTGTATGTGTGGGA[A/G]GAACATACCGTGTGTCTTACACCCTATGAATGTGA R 2 1 2 1 101000 f 74 goat snp54619-scaffold833-3909748 24 42860098 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785568 Affx-122959524 AX-385272612 24 42735353 CTATTGACACTAGGTCATGGTCAAGGAAAGCACAG[C/T]GTTTCTTGCAGGCGTGAAGCAAGAGGTCCAGATAG Y 2 1 2 1 101000 f 74 goat snp54620-scaffold833-3988294 24 42940377 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763974 Affx-986698502 AX-385251755 24 42763732 AGATGTATTTTCTACATAATATCCACATGTCATCA[A/G]TCTGCACTGAAGCAAATTAAAATATCTCCTCTCAA R 2 1 2 1 600010 f 74 goat 24_42763732 24 42763732 Ancestral_priority_1043 ancestry 0.702 recommended IMAGE 10K 10K ancestral 320763976 Affx-986698504 AX-385251757 24 42763775 TGAAGCAAATTAAAATATCTCCTCTCAACAAACCC[A/G]TATCATCTCTCCAGACCCTTGTGCCCAGGGCCTGG R 2 1 2 1 600010 f 74 goat 24_42763775 24 42763775 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320767401 Affx-986698514 AX-385254674 24 42763807 CCCGTATCATCTCTCCAGACCCTTGTGCCCAGGGC[C/T]TGGTAATCTATCAGCCAACAAGTATTTATTCAATG Y 2 1 2 1 600010 r 74 goat 24_42763807 24 42763807 Ancestral_priority_1043 ancestry 0.648 recommended IMAGE 10K 10K ancestral 38425795 Affx-122940704 AX-123296141 24 42777144 ATGGCCTGGGGGTGGGGCCAGGGAGAGAGAAGCGA[C/T]GCTATAGGAAAGCAAAGCAAAGGACCAACTGACAC Y 2 1 2 1 101000 r 74 goat snp54621-scaffold833-4030085 24 42982240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418271 Affx-122947011 AX-123288619 24 42810854 AACAGGCTGAGGAAGCAGCCCATCAAGAGGGAAGC[A/G]GATGATGGGGGTGAGGATGCCAACATGTCTGAGTG R 2 1 2 1 201000 f 74 goat snp54622-scaffold833-4063795 24 43015749 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424245 Affx-122942468 AX-123294591 24 42844514 TTCAACATCACATCCATGTCCACTGCAGATAAAGC[A/G]TCTCTTGACCTGTGCATAAGAAACTGGATTCAGAA R 2 1 2 1 101000 f 74 goat snp54623-scaffold833-4097455 24 43049930 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376683 Affx-122978994 AX-123247042 24 42874383 TTTCTGTTTGCATGCCCGTTTCTAGAAGCCCAGGT[C/T]GTTAACCTCTTTACTGTAATAGTTTCTAAAAGGCA Y 2 1 2 1 101000 f 74 goat snp54624-scaffold833-4127324 24 43079471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770262 Affx-122939732 AX-385257428 24 42907342 AATTTTTTTTATTGGTGACCTACATAGATTTGTCA[A/G]TTTGTTCATTCATGTGGCCAAGTGAGAAGGAAAAA R 2 1 2 1 101000 r 74 goat snp54625-scaffold833-4160283 24 43112358 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452435 Affx-122920576 AX-123322768 24 42937854 GAAAGACATATGCTTAGTTCAGTGCTGTTTATACA[C/T]AAGAACAAAGGGAAAGGGCTCAATATTCGTCAAGG Y 2 1 2 1 101000 f 74 goat snp54626-scaffold833-4190795 24 43142765 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386004 Affx-122971507 AX-123256362 24 42953985 CATGGCTTTGTGTTGGTACACACCTTCTCTCAGGC[A/G]CCCTCCCGGCAAACTGGTCAGCAGAGAAAGCTGCC R 2 1 2 1 101000 f 74 goat snp40849-scaffold526-287 24 43158722 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439831 Affx-122930466 AX-123310168 24 43017079 AGAAATGACTGACACCATCTTGTACAGTGCTTTTC[A/G]TTTTCCTTTTCTTCACAACAGTGTGTTCCTGAGAT R 2 1 2 1 102000 r 74 goat snp40850-scaffold526-63381 24 43221945 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434381 Affx-122934699 AX-123304722 24 43064519 CAAGGCCAGAACTAGAACTGTCCTTGTGAACTAGA[C/T]GGAAGGGTTTGAGTGAGCAGAGGAAAGGAATGAGG Y 2 1 2 1 101000 f 74 goat snp40851-scaffold526-110821 24 43270643 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771952 Affx-122919758 AX-385259108 24 43120816 CTGAATCACTAAATCATCATAGCAATTCTATCAAG[C/T]AGGCATTATTCTTACCCTGCTTCCTTCTGATTAAG Y 2 1 2 1 101000 r 74 goat snp40852-scaffold526-167118 24 43327564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419106 Affx-122945774 AX-123289454 24 43185978 CCTTGCCTTGGTGATTTTTGTGCAAGGTTATGGAT[A/C]TAGCTGTATTTTCATGTCTATTCACTCACTGTCCT M 2 1 2 1 101000 r 74 goat snp40853-scaffold526-232280 24 43392713 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383988 Affx-122972925 AX-123254346 24 43219999 AGGATGGAAGCACACAATCCACAAATAACTTCCTA[C/T]ATATGATTTCTTGAGTTATTTCAGTTATACACTTG Y 2 1 2 1 101000 f 74 goat snp40854-scaffold526-266301 24 43426825 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781303 Affx-122943516 AX-385268388 24 43258897 TTGTTAAAGATGGACTAGAAATGAGGGACTGGTGG[C/T]GGAGAAATAAGTTGAAAAGCTACTATGTTGGTGTA Y 2 1 2 1 101000 f 74 goat snp40855-scaffold526-305199 24 43465560 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788457 Affx-122970216 AX-385275474 24 43293341 TGATGAGGCAGTGAACACAAGCAACTAAGAGTGAG[C/T]GCCAATCCAGTCATTCACTCCCAGAAACCTCCCAT Y 2 1 2 1 101000 r 74 goat snp40856-scaffold526-339643 24 43500031 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432857 Affx-122935361 AX-123303198 24 43339185 GAATATATTATAAATGTACTTGTCCTTCCTCAGAT[A/G]TTTAACATCGTGAAAGAATAATCTGTGGAACACTG R 2 1 2 1 101000 r 74 goat snp40857-scaffold526-385487 24 43546164 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396164 Affx-122963377 AX-123266519 24 43420281 CCTCCTCACACACAGATGCCTGCAGTGCTGTAGAT[A/G]TGACAGGGGTGATGCTTAAAGCATTCTTAACATGG R 2 1 2 1 201000 f 74 goat snp40859-scaffold526-466583 24 43627428 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399687 Affx-122960492 AX-123270042 24 43457542 ACACGCCGCTAAGGGTCTTCGGCCGGTGAATTAAA[C/T]GGTAAAGGGTGAGGTGGCCGGGTTCCTGTGGAAAA Y 2 1 2 1 201000 f 74 goat snp40860-scaffold526-503844 24 43664709 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447037 Affx-122924532 AX-123317373 24 43498720 GGGTCCCAATGAATGGTGTAGAAACAAAGGAAAGT[C/T]CAGTGCCTCTGGGTCCTAGGGGGTGGTGTTCCCCT Y 2 1 2 1 101000 f 74 goat snp40861-scaffold526-545022 24 43705812 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386512 Affx-122970746 AX-123256870 24 43537816 AGAGATGAAGAACAGTGAGAAAGACCTGTACTGTC[A/G]TGCAGACAGCCCTTTGTCTCAGACTTGGTTTCTAT R 2 1 2 1 101000 f 74 goat snp40862-scaffold526-584118 24 43744832 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436939 Affx-122933184 AX-123307277 24 43568684 GAGAAACTCTCACAGCAGGGAACCTAAGGAGATGC[A/G]TGACTGCATGTAATGTGGTGTCCTGGGTGGGGTAC R 2 1 2 1 101000 f 74 goat snp40863-scaffold526-614986 24 43775637 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320763988 Affx-986698516 AX-385251768 24 43637967 AAGTTCTCCAGGCACTCACAAGGCTTGTGGATTCT[A/G]GACTACACACTCAAGAACTGTGCCTCTGAGTTGGG R 2 1 2 1 600010 f 74 goat 24_43637967 24 43637967 Ancestral_priority_1043 ancestry 0.586 neutral IMAGE 10K 10K ancestral 320763990 Affx-986698518 AX-385251770 24 43638202 AGCTGCCCAGTCAGTCAGTTACACTCATCTTTTCT[A/G]TAAAATTTAGTAACGTTAGATCCATGATCTTTCTC R 2 1 2 1 600010 f 74 goat 24_43638202 24 43638202 Ancestral_priority_1043 ancestry 0.672 recommended IMAGE 10K 10K ancestral 320767425 Affx-986698528 AX-385254698 24 43638225 CTCATCTTTTCTATAAAATTTAGTAACGTTAGATC[A/C]ATGATCTTTCTCTATTTGAGCTCCAGTCTGTCATC M 2 1 2 1 600010 r 74 goat 24_43638225 24 43638225 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 320767443 Affx-986698538 AX-385254714 24 43638577 TGATTTTCCCTGTCAGGATACTTGGGTTCCAGGAC[A/G]GTCTTAGCTGCACTGTTTCTGTTGAAATTTTTTCC R 2 1 2 1 600010 r 74 goat 24_43638577 24 43638577 Ancestral_priority_1043 ancestry 0.586 neutral IMAGE 10K 10K ancestral 38388531 Affx-122969199 AX-123258889 24 43665081 CTGTTCTGGGAACCACCAGTGCAAGTTATGTGGGT[C/T]GTGTCAGGATCCCCGGCTCCAGGAACACGGGCTTC Y 2 1 2 1 101000 f 74 goat snp40865-scaffold526-711383 24 43872707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797056 Affx-122956544 AX-385283996 24 43703981 TAATCTCATTAAGAAGAGGGGAAGTAACCCATCAT[C/T]CGAGTTTCACAAGATTGAACAGTGAGCCGGGCTGT Y 2 1 2 1 101000 f 74 goat snp40866-scaffold526-750283 24 43910902 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448218 Affx-122924225 AX-123318554 24 43767975 TTGTGGGGTTCATTTCAGGCTGATGGGAGTCTGTT[C/T]TCCTCAGGACCTGCAGGGAGATGGTGCCCTTGAAG Y 2 1 2 1 101000 f 74 goat snp40867-scaffold526-814277 24 43974576 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381518 Affx-122974856 AX-123251876 24 43796505 ACTAGGGGTCAGAATGACACAGGACACTCACGGAA[C/T]ATAGTGCACCTGAACGGAGCGACCAGAAACCACCA Y 2 1 2 1 101000 r 74 goat snp40868-scaffold526-842807 24 44003532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379351 Affx-122976163 AX-123249710 24 43841334 AATTGGCAAAAGGTCCCAGGCAGTGCATCTGCTTC[A/G]TCAGTAAGACTTCAGAAACTGCAGTTCCCACCTAG R 2 1 2 1 101000 r 74 goat snp40869-scaffold526-887636 24 44049055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401511 Affx-122958932 AX-123271864 24 43893141 GAGACATTTTACAAGAAATAGTCTCTTCACTCAAA[C/T]GGATATTAGCACATTTTAATATCATACCTGGAAAT Y 2 1 2 1 101000 r 74 goat snp40870-scaffold526-939443 24 44101445 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776271 Affx-122920805 AX-385263399 24 43935870 ATTGATTTATGTGTATGTTTTTAGTCCAATATCAT[A/G]TTGGCTTGATTATCCTAGCTTTGTTTAATGGTTTG R 2 1 2 1 101000 r 74 goat snp40871-scaffold526-982172 24 44144941 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783603 Affx-122925571 AX-385270662 24 43987125 AATTTTGTTTAAAGTTTAATATATGTCCCTCAGAA[A/G]GGAGTTCAGCAACAGGTGTATGGAAGGCAAAGTGG R 2 1 2 1 101000 r 74 goat snp40872-scaffold526-1033427 24 44196868 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443698 Affx-122927163 AX-123314035 24 44016362 AAATATATGATTGAAAGGCTAAGAGGAATAAAGGG[A/G]TCAAATGCACATGAGTATGAGTAAGCTCTGGGAGA R 2 1 2 1 201000 f 74 goat snp40873-scaffold526-1062664 24 44227048 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434262 Affx-122934814 AX-123304603 24 44059732 ATAATCATAAAAAAAAAAAAGGAAACATGAGACAG[A/G]AGGGAGGAAATCACAACTGTTTCTAGCTATATTTG R 2 1 2 1 101000 r 74 goat snp40874-scaffold526-1106034 24 44272231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440030 Affx-122929765 AX-123310367 24 44139083 TTTTGTTGTTGTTTTTGTTAATGTGACAGAAACAG[C/T]GGAAGCAGGAGTTCAGATATGCTATTGTATAAAGG Y 2 1 2 1 201000 f 74 goat snp40875-scaffold526-1185385 24 44352540 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405791 Affx-122955910 AX-123276143 24 44184883 AGTGTGGCTAAAATAAAAGATTGTGGTATGAAACA[G/T]AAGGATTTTTCATAGAAATATACTTTCTTAAGCCA K 2 1 2 1 101000 f 74 goat snp40876-scaffold526-1231185 24 44398337 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431964 Affx-122935960 AX-123302305 24 44214011 GTCCCACCTAAGTCCTAAAACTATATTGAATACAT[A/G]TAATGAGGACTGTCTCTTTTGCTTCTAGCTTCGAG R 2 1 2 1 101000 r 74 goat snp40877-scaffold526-1260313 24 44428073 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434670 Affx-122933971 AX-123305011 24 44252536 ATAGTAATTGTGGGACTAGTGCCACATGATAGTAG[C/T]AATATCAGCTTTCAAAATCCTTTGAGTGTAAAAGT Y 2 1 2 1 101000 f 74 goat snp40878-scaffold526-1298838 24 44466657 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439163 Affx-122931066 AX-123309500 24 44314141 ATGTATTATGCTTGGAAGTTGATTCTGCTTGGATA[G/T]CAATGCACAGGTGTGTGTGTGAATTTTATGTGAAG K 2 1 2 1 201000 f 74 goat snp40879-scaffold526-1360443 24 44527159 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792699 Affx-122928302 AX-385279679 24 44378401 GGTGTCTTCTGTAATACACTTAAACAAAAGATACT[A/G]CAATCACAGTTACTTCTTACAGGTGAACCCTGTAT R 2 1 2 1 101000 r 74 goat snp40880-scaffold526-1424703 24 44587865 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433355 Affx-122935137 AX-123303696 24 44421653 CCAGAACTAGATGAGGAAAAAAGGTATAAGGATCA[C/T]TGAGCCCTTTAAGAGTACCGAGCAGCTTCCGTCTC Y 2 1 2 1 101000 f 74 goat snp40881-scaffold526-1467955 24 44631088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382106 Affx-122974890 AX-123252464 24 44461209 TGACAGTTGCCCCTGGTGGCTCAAGAAAATCCTGC[A/G]GAAATCCTTAGGAATAAGACAAAGACTTCTGGTTC R 2 1 2 1 101000 r 74 goat snp40882-scaffold526-1507511 24 44670656 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770608 Affx-122944350 AX-385257772 24 44517000 GGAAATTACAGTCTATATATACAGAATATATTGAC[A/G]TCTTCCAAGAATAGAAAGATTATTGTATATGACAT R 2 1 2 1 101000 f 74 goat snp40883-scaffold526-1563302 24 44726551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404243 Affx-122957068 AX-123274595 24 44551767 AAGAATAGCTGATGGCCCTGTTGTCAGTTTCTTTA[C/T]GCTCACTATCTATTACAAATTAAGCTGAAATTGTG Y 2 1 2 1 201000 r 74 goat snp40884-scaffold526-1598069 24 44761312 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424356 Affx-122941854 AX-123294702 24 44585224 GCTGACAGGGCACGTAGCTTGCTGATGGGAATGTG[A/C]GGTCTGTGCTCAGATGCTAGCCTTGTCTGCACTGT M 2 1 2 1 201000 r 74 goat snp40885-scaffold526-1631526 24 44794820 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788009 Affx-122935444 AX-385275030 24 44628618 ACCTCAGAGAAGTCGTGTGAACCATTTATGCTACA[C/T]GTTTTTCAAGCATAGAATGGGACCGATAATTCCTC Y 2 1 2 1 101000 r 74 goat snp40886-scaffold526-1674920 24 44838515 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38447260 Affx-122924947 AX-123317596 24 44666762 GTCCAATGAGGGTAAGCCACTGCCGTATTTTCAGT[A/G]CTGGTGAAACCAGGAAATTCTTCTGTTTGGCATTT R 2 1 2 1 101000 f 74 goat snp40887-scaffold526-1713064 24 44875232 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777326 Affx-122943776 AX-385264448 24 44705885 ATGGCAAACCCTCCATCGTAATAGAGGAAATGATA[A/G]TTATTAGTTTGCCTGCATTGCTAAAATTAGCTGAC R 2 1 2 1 101000 f 74 goat snp40888-scaffold526-1752187 24 44914288 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431489 Affx-122936249 AX-123301830 24 44739532 AGAAAATTTATCAATCGAGGTCAACAGATTACAGT[A/G]GAATGTTTTCGTATAAGTTTAACTTTTTTTATTTC R 2 1 2 1 101000 f 74 goat snp40889-scaffold526-1785834 24 44948094 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785589 Affx-122946671 AX-385272633 24 44773119 GCCCCGAGTAGGTGACTAAGGGCCGACAGGATTAG[C/T]ATGTTAACTTGGCTGCTGTCCGGAGTGGGAGGCCA Y 2 1 2 1 101000 r 74 goat snp40890-scaffold526-1819421 24 44981820 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452139 Affx-122921672 AX-123322472 24 44817411 ACACAAACAAGTAGAGTGGCAGCTCCCTGTGATGG[A/C]ACACTGAACAGTGGAGAGCTATTCTATCTGAGGAA M 2 1 2 1 202000 f 74 goat snp40891-scaffold526-1863713 24 45026095 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405907 Affx-122955582 AX-123276259 24 44857246 GAACTATACACACATTCTCACAAAATGAATGCACA[C/T]ATACTTTATGAAATCTTAATAAATTTCATGTTTAT Y 2 1 2 1 101000 f 74 goat snp40892-scaffold526-1903548 24 45066378 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421711 Affx-122944397 AX-123292058 24 44891762 CACCACCACCAAGATCTGTGCCAGCGTTTCCATGA[A/C]TCTATGCAATCACAGAAGAATGGGCTTTCAGGGAA M 2 1 2 1 101000 r 74 goat snp40893-scaffold526-1938064 24 45100804 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783446 Affx-122970971 AX-385270509 24 44929396 ATCAAGACTATATGGTTTTGGTTTTAAGAGACACA[C/T]AGGCCAACAGAACCAGATAGAGACCCACTTGTATA Y 2 1 2 1 101000 r 74 goat snp40894-scaffold526-1975698 24 45138519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384580 Affx-122972994 AX-123254938 24 44981525 CCATACACATCCAGACATCACATCTGTATTCAAGG[C/T]AGGAAGACAGAAAGAAGAAAGCTTGGTGCTATCAC Y 2 1 2 1 101000 f 74 goat snp40895-scaffold526-2027827 24 45190441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273039 Affx-1111833282 AX-319300635 24 44987153 ATTTCCTGGCATATTGAGTGAAGCACTTTCACAGC[A/G]TCATCTTTTAGGATTTGAAATAGCTCAGCTGGAAT R 2 1 2 1 103000 f 74 goat 24_44987153_AF-PAKI 24 44987153 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320769222 Affx-122930616 AX-385256396 24 45030281 TCATCAAAGATAGTGATAGACTCATTAATCCCTTT[A/G]TTACCGAGTGATTACTTATTATTTGTAGATTAAAA R 2 1 2 1 101000 f 74 goat snp40896-scaffold526-2076583 24 45238895 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401841 Affx-122959435 AX-123272194 24 45086931 TGGATCTGGTGCATATTTACCTAACTAGGCTGTGG[C/T]GTAGGGATGAGGGAAGAAAATGATGAGCATTGGTG Y 2 1 2 1 101000 f 74 goat snp40897-scaffold526-2133233 24 45295636 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432116 Affx-122936452 AX-123302457 24 45141357 GTGTACTTGTGTGGGTGCTGGGGCGAGATTGACCT[A/C]TGGGATTCAACCCAAATGGCCACTTATCCTCAATT M 2 1 2 1 101000 r 74 goat snp40898-scaffold526-2187659 24 45349636 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385770 Affx-122971060 AX-123256128 24 45182763 GATGGACATCTGTTGCTTTCCTGGGAGGAATCTAC[A/G]CTCTTTTCCCATAAGCACTGATGCTACCTTCTCAC R 2 1 2 1 201000 r 74 goat snp40899-scaffold526-2229065 24 45391074 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405427 Affx-122956271 AX-123275779 24 45212122 TGTCATCACAGCATATCTGCTGAGTGAGTGATTCT[A/G]TAAGAGTACTTGTCAAATCCAAACTTCCTCCAGCA R 2 1 2 1 201000 r 74 goat snp40900-scaffold526-2258424 24 45420454 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795068 Affx-122925086 AX-385282027 24 45246051 GGAGAAGGAGCAGACATGCGTATCTGTGAGCCTCA[C/T]GGTTTAGACACACGTTATCAAGGAGGATGCTTTTG Y 2 1 2 1 101000 f 74 goat snp40901-scaffold526-2292353 24 45453463 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391409 Affx-122966773 AX-123261766 24 45275040 GTGCTAGGCAAAGTCCGACAGACTTAAGTGGCTCA[C/T]TCCAACAGTATGGCTAAAGCATCCTTTTAGCCTCC Y 2 1 2 1 101000 r 74 goat snp40902-scaffold526-2321342 24 45482399 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429984 Affx-122938050 AX-123300325 24 45305169 CTTAAACCCCATAATGAGTTCATTGTTCCCTCCTC[C/T]GAAATCACATTAAAATGCTGGGATGTCCCCCATCT Y 2 1 2 1 201000 r 74 goat snp40903-scaffold526-2351471 24 45512467 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417968 Affx-122946691 AX-123288316 24 45337517 CCAGAAAGAGATGGAAAATTAGAGCCATTTTTGCA[A/G]TCAACCTCATGGAGGTTATGAAGATCAAGTGAGAT R 2 1 2 1 101000 f 74 goat snp40904-scaffold526-2383819 24 45544805 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784560 Affx-122921466 AX-385271609 24 45367481 ACAAGATAGTAAAGATTTGGTTATTAATTAAACCC[A/G]CCCAAGGTTAAACAACCAGTAGGCAGCAGAGCTAA R 2 1 2 1 101000 r 74 goat snp40905-scaffold526-2413783 24 45574239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449010 Affx-122923096 AX-123319345 24 45401789 TAGAAAGATACTAGCAGCAGGGTGACTACCCAATA[C/T]TCATCAAGTGAGCTGATCTTTTTCTGCGAGCACCA Y 2 1 2 1 101000 f 74 goat snp40906-scaffold526-2448091 24 45608771 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399434 Affx-122961222 AX-123269789 24 45437955 TAGAGAGAGGGTCTAGGCCTCCCAAGGATTTTGAG[G/T]CTCCGCAAGCTCCCCTGCTCTTTGGTGATGGGAGA K 2 1 2 1 101000 f 74 goat snp40907-scaffold526-2484257 24 45644678 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409908 Affx-122952889 AX-123280259 24 45481745 GTCAAACTCCAAAACCCATCTAATGCTAAAATGAC[A/G]TGCTTCCTTGTTTTGGTGGGTAAGGAATTAGGATT R 2 1 2 1 101000 f 74 goat snp40908-scaffold526-2528047 24 45688262 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780219 Affx-122974111 AX-385267315 24 45516917 GCGATAATGATCAAACCAAGGAAAGTTTAGGGTCC[A/G]TTCATGTTCTAATCAGCCCTCTTAATCTGACAGTT R 2 1 2 1 101000 f 74 goat snp40909-scaffold526-2563219 24 45722594 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376579 Affx-122979074 AX-123246938 24 45560152 AAAAATAGGCCACAAACAAACAATAGTAAACAATC[A/G]CCCAAGGAAAAATATTTATAATGTGGGTAATATAA R 2 1 2 1 101000 f 74 goat snp40910-scaffold526-2606454 24 45767916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417530 Affx-122946933 AX-123287878 24 45628644 TTCTAAAATGTGTAACAAGGAAAGCTCTGAGGTGC[A/G]TCCCTCGGAGACGGGTACTTGGTGGCCCACAGGAC R 2 1 2 1 101000 f 74 goat snp40912-scaffold526-2674946 24 45834936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376378 Affx-122978109 AX-123246737 24 45683789 ATCTCAATGATTCCACTTTTCCTTTTATTTCTGTC[G/T]GTCTGTCCTGGAAGACTCATCAGCACTTATGGAAG K 2 1 2 1 101000 r 74 goat snp40913-scaffold526-2730091 24 45891996 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389363 Affx-122968460 AX-123259721 24 45722088 AAAAGATTACTGAGATATGTTATTCTTCCGTTCAT[A/G]TTAAGTCTTAGAAACTCCGGGAGTATCTTACACTC R 2 1 2 1 101000 r 74 goat snp40914-scaffold526-2768390 24 45930269 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376681 Affx-122978995 AX-123247040 24 45754160 TATGTCACCTTTCTGACTTCATCTCAGCTACTCTC[C/T]CCTCACTCACTCTGCCTCTCATTTACCCTAACCAC Y 2 1 2 1 101000 f 74 goat snp40915-scaffold526-2800462 24 45962130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798499 Affx-122919771 AX-385285432 24 45785746 GGGCCCACCTTTGAACGCCAAGTCATTGATTTCCC[A/G]TGTCCCTACTCTACCTTTAAAATGCACTGGGCCTC R 2 1 2 1 101000 r 74 goat snp40916-scaffold526-2832048 24 45994239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447051 Affx-122924522 AX-123317387 24 45816205 TATAGCTCCGCTTGCCCGTGGTTTTAGTTCTTCCC[A/G]TCCTACACTTCCTTAACAAGCTTCCTTTTGAGGTG R 2 1 2 1 101000 r 74 goat snp40917-scaffold526-2862507 24 46024484 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440144 Affx-122929683 AX-123310481 24 45846526 AATTTCTGTAAGACAAAAAATTTGCCAGCACAAGT[A/G]TGCCATATTCAGGAGATGTGTGAGCTGAAGAATAA R 2 1 2 1 201000 f 74 goat snp40918-scaffold526-2892828 24 46054694 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797724 Affx-122944394 AX-385284663 24 45882067 AAACAAACTTCCGTTTGGGTAAGGAGGAAAAAGAA[C/T]AGACACACATGTTTTAAATGTTCCTCTTATGCTGG Y 2 1 2 1 201000 f 74 goat snp40919-scaffold526-2928369 24 46089965 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275395 Affx-1111834772 AX-519548969 24 45920538 ACCACTGTAAAAAGAAAGAAAAGGAAATTCATGAA[A/G]CTGTCACTGCAGCTATACCAGCAGGTGCTGAAACA R 2 1 2 1 102000 r 74 goat GoatD01.052303 24 45920538 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38403217 Affx-122957904 AX-123273570 24 45922629 GGCACAAATGTAGGGACCATTGCACGTAGAGGTCC[A/G]AGCCCTGCAGCATCACTACCCTTTGCCCGGAGTTC R 2 1 2 1 101000 f 74 goat snp40920-scaffold526-2968931 24 46130606 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429520 Affx-122937847 AX-123299862 24 45970951 TCCTGTGACTCAAAGTACTATCATATTCACTGATA[C/T]GGTTTTCTAAAACTGTCTGATTATTCAGGCATCAA Y 2 1 2 1 101000 r 74 goat snp40921-scaffold526-3017253 24 46179109 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376609 Affx-122979050 AX-123246968 24 46018551 AAAAAGGAAATATTTGCCCTGATAATTTAGTTACT[A/G]CCTTTTCTGGTCTACTTTCTGACTTACTTATGTGT R 2 1 2 1 201000 f 74 goat snp40922-scaffold526-3064853 24 46226772 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783998 Affx-122974441 AX-385271052 24 46077006 GATGGGGTTAGGGAAGGTTTCACAGAGAAGTTAAA[A/G]CTCAAGCAAGGTTTGAAGGGTGAGTAGAAACTGCA R 2 1 2 1 101000 f 74 goat snp40923-scaffold526-3123308 24 46285186 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415146 Affx-122949412 AX-123285495 24 46107634 GATGAGCCTAGAGGGCTTAGCTGGGGAGGAGTCCA[C/T]GGTGGACATCCAGGGGTGTTGGAAGTCCACACACC Y 2 1 2 1 101000 f 74 goat snp40924-scaffold526-3153936 24 46315980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451867 Affx-122921065 AX-123322200 24 46193281 AGGGGACCCCTCGCACCTTCTCAAACTTCTCGGTC[C/T]CCTGATTCTAACCCTGGAGGTCCCTAAGGGATGCC Y 2 1 2 1 201000 r 74 goat snp40925-scaffold526-3239583 24 46400648 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769959 Affx-122962199 AX-385257128 24 46239299 TGGAAATGCTGGATGGGATTAACAGGGATCCTACC[A/G]CGACTTTCTACACTAAGAACCTATCAAACACGGGA R 2 1 2 1 101000 f 74 goat snp40926-scaffold526-3285601 24 46446655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798728 Affx-122925972 AX-385285659 24 46268575 GGGGCGAGAGCAATAACTGCTACCCAAGTACAGGG[C/T]AGACGCCTGAGAAGCACACTATGGACGTAAAAATG Y 2 1 2 1 101000 r 74 goat snp40927-scaffold526-3314877 24 46476005 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431661 Affx-122936805 AX-123302002 24 46298355 ACTGGAGGTTGGGAAGAGCCACCATTCCCCAGGTC[A/G]TTACTGAGATAGAGTTACAGCTACCTCTGTATTTA R 2 1 2 1 101000 r 74 goat snp40928-scaffold526-3344657 24 46505833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390767 Affx-122967893 AX-123261124 24 46328063 TCAAATAATATTTCTGGCATGATACTGAAATAATC[A/G]CAATTGATTTCTCTGAACTATTACATATTAAGGTT R 2 1 2 1 101000 f 74 goat snp40929-scaffold526-3374365 24 46535390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434764 Affx-122933897 AX-123305105 24 46373250 AATCTTCTTTCCCAGAATGAAGGGACTGGGCTTCA[A/G]GGTGTCTCCCTGTGCCCCATTCTGGCTGAGGTCAT R 2 1 2 1 101000 f 74 goat snp40930-scaffold526-3419552 24 46580519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422199 Affx-122943501 AX-123292545 24 46433797 CATGCAGCCCAGCAAACGGCATCTCGGTTTCCCTT[G/T]CCTCCTTCAGTGGGAAAGGCTCTGTGGAGCGCAGT K 2 1 2 1 101000 f 74 goat snp40931-scaffold526-3480099 24 46640902 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406187 Affx-122956148 AX-123276539 24 46479621 ATTCCACACCCCAGGCATACACGCTCGCCTGGAAC[A/G]CAGACCTTGACCCAGAAAGAAAGGCTCTTTCTTTC R 2 1 2 1 101000 r 74 goat snp40932-scaffold526-3525923 24 46684710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452613 Affx-122920483 AX-123322946 24 46516142 AACTGCAGCGGCTAATGGCTGTATCCTTGTAGAAC[C/T]GAAAAGGCAGGCAACATTTTTTTGTTTACACAGGT Y 2 1 2 1 101000 f 74 goat snp40933-scaffold526-3562444 24 46721739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381260 Affx-122974486 AX-123251618 24 46552493 AAGAACCATGCAGTGTCAAGTCAAAGGACTGGCAG[G/T]TGACTGAGAAAGGGCTCTGAGGACATGCTGAAGGA K 2 1 2 1 201000 f 74 goat snp40934-scaffold526-3598795 24 46757757 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794137 Affx-122919503 AX-385281103 24 46612751 TGTTATCAATTGTTCAATCACAGAAATCACTCCTT[A/G]CCTTGCCTTTTGTCCTCCATCTTCACCCCTGCAAC R 2 1 2 1 101000 r 74 goat snp40935-scaffold526-3659053 24 46818549 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410626 Affx-122952091 AX-123280976 24 46651822 AATCAGATTTCTTCACACTGTTTGCACTTTGCCTT[A/C]GCCTTTACTAAACAGTATGAAAAGAAAATGAACAA M 2 1 2 1 101000 f 74 goat snp40936-scaffold526-3698124 24 46857679 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391441 Affx-122966746 AX-123261798 24 46690549 TGCATTTGAAGAGGGATTTCTCCATATTTTTTAGC[C/T]TCCAGTGGGGTAGCAACAAGTGTGATGTTATTCCT Y 2 1 2 1 201000 f 74 goat snp40937-scaffold526-3736851 24 46896675 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419083 Affx-122945793 AX-123289431 24 46730879 CCTAGTCCAAATAAATGTGTATATATTTGTTCCTT[G/T]AGTGATAAGCAATAAAATGCCAATTAGTTTGGCAG K 2 1 2 1 101000 r 74 goat snp40938-scaffold526-3777181 24 46937024 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411354 Affx-122952255 AX-123281704 24 46768297 TGTGCACGCTGATCATCTAGGCTCCCGAAGAAGTC[A/G]CTGGAGAGAGATAAGGACGTTCATGTGGAGTCTGT R 2 1 2 1 101000 f 74 goat snp40939-scaffold526-3814599 24 46974462 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396261 Affx-122963318 AX-123266616 24 46805482 GCCACTATGCTGGCCCTAAAGAACCACAGCTGATC[A/G]CAAGGAGAGAATAGTGAGTGATTTATCTATCTCCC R 2 1 2 1 101000 r 74 goat snp40940-scaffold526-3851784 24 47011516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440865 Affx-122929247 AX-123311202 24 46841549 TTTATTGTTAAGCATTTACCTCCCCAAATTATCAC[A/G]TTTCTTGGAGTAGCACATTAAGGGGTGTGATTGGT R 2 1 2 1 201000 f 74 goat snp24785-scaffold2537-184448 24 47049161 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404244 Affx-122957067 AX-123274596 24 46909695 CTCCAGAGAGAGGAAAGTGGGAAATAAAATAATAT[A/G]TAAACATATTTTAAATTATATACATTTAATTTTTT R 2 1 2 1 103000 f 74 goat snp24784-scaffold2537-116302 24 47116765 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406541 Affx-122955119 AX-123276893 24 46971036 ATTAGAAACAGCAGAGGAGAAACTGGCCATAGGAA[G/T]AAGTCATATCTCTGGACAGTGAGAATAATAATTTT K 2 1 2 1 101000 f 74 goat snp24783-scaffold2537-54961 24 47177154 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420003 Affx-122945169 AX-123290351 24 47008443 CCCCAGGGATGCAACAGTGAATGAGAGAGACAGTC[A/G]TGGTACAAGCCCTGACAGTCTAGAGTGAGAACCAG R 2 1 2 1 101000 r 74 goat snp24782-scaffold2537-17554 24 47215032 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443534 Affx-122927772 AX-123313871 24 47076110 ATTTCAGTGCCCAAATAAAATTCTGGGCAAATTGG[G/T]ACAAATCGCTTAGCCTAATTACCTCTGGGCCACTC K 2 1 2 1 101000 r 74 goat snp13155-scaffold1502-50014 24 47277131 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444809 Affx-122926331 AX-123315146 24 47108971 ATAAAAGGGAAGGGCTGTTCGGTGGAAGAAGAATC[A/G]GTCTTCAGAAACCAAGTTAACTGATGTCTTTCCCA R 2 1 2 1 101000 r 74 goat snp13156-scaffold1502-82875 24 47309661 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452124 Affx-122920830 AX-123322457 24 47139992 GGACTGAAAGCTTCTGCAGAACTGGAGAGGAAACC[A/G]TGGTGGGTTGAACTAAGGTGGTGGCAGATGGACAG R 2 1 2 1 201000 r 74 goat snp13157-scaffold1502-113896 24 47340680 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450410 Affx-122922064 AX-123320745 24 47190324 TATTCTGGAAAATGCAGAATTATAGGGACAGAAAA[C/T]AAGGATCAGTGTTTGCCAAAGGCTTCATGTAGAGG Y 2 1 2 1 201000 f 74 goat snp13158-scaffold1502-164228 24 47390902 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384654 Affx-122972145 AX-123255012 24 47261239 GGAAAGTTCTTGCGAGATTTGGTGAGTAAAATTTG[C/T]AAACCACTTAGGCTGGCGCCTGCTGCTGAACAGTG Y 2 1 2 1 101000 f 74 goat snp13160-scaffold1502-235143 24 47462020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404641 Affx-122957313 AX-123274993 24 47294569 TAAATTTTGGAGGTGTGAGGGACCTGGTCTGTATG[C/T]GGATTGTGGTTACCCAAACTCTAGGCATTTGTGAA Y 2 1 2 1 201000 r 74 goat snp13161-scaffold1502-268473 24 47495162 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425990 Affx-122941149 AX-123296336 24 47347699 ATTCATGTCTACATGAGGATGGCATGTAATTAACA[C/T]GTCATAATCAAAATGACTAAGTTTGACACATTATA Y 2 1 2 1 101000 f 74 goat snp13162-scaffold1502-321603 24 47548091 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410247 Affx-122952539 AX-123280597 24 47386834 TCTAATTCCAGATCTTACAAAGTGAATAGTCAAGA[C/T]TCTGATGAACATCAGAGAAACAAGAAACAGATGTT Y 2 1 2 1 101000 f 74 goat snp13163-scaffold1502-360738 24 47581004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440711 Affx-122929898 AX-123311048 24 47423608 ATTAGTGTAGAGCAGTAGTCCCAACTGGGCCTCTC[A/G]CAGGTGCTCACAGAAGCCTGGAGAGGGACACACTG R 2 1 2 1 101000 f 74 goat snp13164-scaffold1502-397512 24 47617814 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789873 Affx-122951651 AX-385276880 24 47453009 GAGAGAAATAGATGTATTCACAAAAGTTAGTGTAC[A/G]TACATACATTCCCAAATCTATTCACTGACTTAGAA R 2 1 2 1 201000 r 74 goat snp13165-scaffold1502-426913 24 47647264 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428944 Affx-122938889 AX-123299286 24 47579785 AACGAGGCCTCAGAAGTCCTAAAGTACAAAGCCAA[A/C]CAAGAATAAGCAGTGCTTTCGGACCTTTAAAAAAG M 2 1 2 1 101000 f 74 goat snp13168-scaffold1502-553689 24 47774344 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273041 Affx-1111833283 AX-519546714 24 47580435 AGCTGTTTCTCACTCCAGCGCCAGCTTTCAGTTAC[A/G]TGAAAGACTCAGTTGGATCTGCAGGGCAGGATGGA R 2 1 2 1 101000 f 74 goat 24_47580435_AF-PAKI 24 47580435 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320793568 Affx-122949043 AX-385280543 24 47617796 TACTTAATATTTCTTGACTGGTGTTCCATGTTAGC[A/G]TATATGTAGCAAGGCAGCTCTTTATTTCATGCCAA R 2 1 2 1 201000 f 74 goat snp13169-scaffold1502-591700 24 47812783 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427439 Affx-122940045 AX-123297782 24 47684770 TAAGTCATGAAGTTTTCTTTTCTGAGCTGTTGAAA[C/T]GTACATATTATCTCAGCAAGCTCACTGGTTGTTTC Y 2 1 2 1 101000 r 74 goat snp13171-scaffold1502-658674 24 47879655 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378941 Affx-122976431 AX-123249300 24 47732585 AATTATAACGGAGCCCATCCTCTCCCACAAGACCC[A/G]TTTTAACCAGTGTGTAATAAAGCCCCAGCTCATCC R 2 1 2 1 101000 r 74 goat snp13172-scaffold1502-706489 24 47926908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426827 Affx-122940513 AX-123297172 24 47791404 AAATCTTTATATAAGCAATTCTCGGGTACTCATAT[A/G]TCTGCATCTTTACAGTCAGCCAATATCCTGCCACT R 2 1 2 1 101000 f 74 goat snp13173-scaffold1502-765308 24 47985140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445176 Affx-122925539 AX-123315513 24 47821927 AGGCTCCTCAGGGGTCCTACAGACCCACACCCTCA[C/T]GTCACCCCAAGGAGACGGTGTGTCCAAGGTTACAA Y 2 1 2 1 202000 f 74 goat snp13174-scaffold1502-795831 24 48015245 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381724 Affx-122974694 AX-123252082 24 47878864 TCAGCCTCCACTCGTTTTCCTGTCTAAGGCCCTCC[A/G]TGCCACCTCCCTCCGGTCCCACCTTTCCAGCAAAG R 2 1 2 1 101000 f 74 goat snp13175-scaffold1502-852768 24 48072324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392266 Affx-122967552 AX-123262623 24 47923673 TCGTATGAGCAAGGGCAAAATGAAGGACAGCAAGT[A/G]AAACACTGAATTAAAAGCCACTTAAATTAAGAATT R 2 1 2 1 101000 f 74 goat snp13176-scaffold1502-897577 24 48117628 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780398 Affx-122939021 AX-385267492 24 47964894 CCCCGAGGAGAAACCATACGCTGTCAGAGCTGGAC[A/G]TCTAACTCAATCTCATTTTCCAGCTGACGCTACTG R 2 1 2 1 101000 r 74 goat snp13177-scaffold1502-938798 24 48159618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275498 Affx-1111834934 AX-519549070 24 48008035 ACTCCCTGACTTCTTCAAGCACACAGAGGTGATCC[A/G]GGGAAGCCCCTGGCCTTTGGTTGCCCAGTCCAGTG R 2 1 2 1 201000 f 74 goat GoatD01.059191 24 48008035 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320769126 Affx-122964999 AX-385256301 24 48067824 GGGCCTTGGAATGGGGCCCTTGAAGCTTTCCAGCA[C/T]ATCACACAGCCTAACCATTACCCAGGATTTACCAG Y 2 1 2 1 101000 f 74 goat snp13179-scaffold1502-1041728 24 48263026 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454117 Affx-122919351 AX-123324450 24 48116154 GGACCTCCCACCCATCTAGGTCATCACAGAGCACC[G/T]AACTGAGCTTCTGGTGCTTTGTAGCTGGCTATAAA K 2 1 2 1 103000 r 74 goat snp13180-scaffold1502-1090058 24 48311253 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413109 Affx-122950385 AX-123283458 24 48149132 GGCTGTCCCAGCCTATGGAGCTCCACAAAACCCAG[C/T]ACAGAGTTGCAAGCCAGGAGCCATCTCAAGAGAAA Y 2 1 2 1 101000 r 74 goat snp13181-scaffold1502-1123036 24 48357396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447693 Affx-122924621 AX-123318029 24 48155679 GTAGGTACAAGATTTCAGGTGTTGACACCTCTACC[A/G]TCTCTTTTGCCTGGGAGTTAGCTGGCCAGCCTCTC R 2 1 2 1 101000 f 74 goat snp7691-scaffold1277-1567031 24 48363872 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432987 Affx-122935262 AX-123303328 24 48189320 CTGGGGGGAAGCAAAGCTGGAAGAGTAGTTGGTAC[A/G]TTTCTGGTCCTTGACAACTAACTAATATGGTCGGA R 2 1 2 1 101000 r 74 goat snp7690-scaffold1277-1533390 24 48397870 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442863 Affx-122927673 AX-123313200 24 48226831 GTATTCTGAGGTTGGAGGATAGAACTGCTTCTCTC[A/G]TTGGAATCTAAAAAGCACTGAGCCAACCTCTCAAA R 2 1 2 1 101000 f 74 goat snp7689-scaffold1277-1495879 24 48435916 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427090 Affx-122939789 AX-123297433 24 48264051 CTGTGTGACCTGAACATGCCCCTTCTCTGGGCCTT[A/G]GTTTCTTTTCTGTAAAATGTAAAAAGCTAGGGCAG R 2 1 2 1 303000 f 74 goat snp7688-scaffold1277-1458659 24 48473393 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441747 Affx-122929126 AX-123312084 24 48301968 TTACATGTGCAGGAGGAGACACGTTCAGAAGTGTT[C/T]GCTGATGTATCCTGTATCTCCAGGGGAAATTCTGA Y 2 1 2 1 101000 f 74 goat snp7687-scaffold1277-1420742 24 48508471 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787342 Affx-122935285 AX-385274367 24 48344560 GATGAACTCCTTGCCGATGAATGTCCCAAAGTGTA[C/T]GTGCATCGCAGATCCTGCAGAGCCCATCATCCTGC Y 2 1 2 1 201000 r 74 goat snp7686-scaffold1277-1378150 24 48551002 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421345 Affx-122944065 AX-123291692 24 48391738 GAATGCCTGGGGCACCTGTGTAGAACTTTCAAACC[A/G]TCCTGCATAAAATGGGGTGCACTGAATTTATACAG R 2 1 2 1 201000 f 74 goat snp7685-scaffold1277-1330972 24 48598441 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398731 Affx-122961830 AX-123269086 24 48448651 ATGCCTGGCACCTAACAGACATTTGAGAAATGCCT[A/G]TTTAATAAGCAGGATTTTATTTACCAGAATACTAC R 2 1 2 1 201000 r 74 goat snp7684-scaffold1277-1274059 24 48654442 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433371 Affx-122935126 AX-123303712 24 48485071 TCAGGAACACAACTCCAGGTACCCCTTCCCAGGTA[C/T]GGGTGAAGAGTGAAAGTGTCAGTTGCAAAGTCGTG Y 2 1 2 1 101000 r 74 goat snp7683-scaffold1277-1237639 24 48690563 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380399 Affx-122975323 AX-123250757 24 48536347 GATCTTGACCCACTCTGTAATGTACCATCCCATTC[A/G]TCCCCGTGACATTCTTGCGGAAACACAGAAAGGCC R 2 1 2 1 101000 f 74 goat snp7682-scaffold1277-1186363 24 48739501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403757 Affx-122958003 AX-123274109 24 48591457 CCTCAGCCTTCTCTCTGTTGTCTCAAGCGCATCCT[A/G]CAAAGGGGCCCTGAAGGTGGAGTTTAGTCCTCAGA R 2 1 2 1 201000 f 74 goat snp7681-scaffold1277-1131253 24 48794249 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792528 Affx-122932841 AX-385279509 24 48640029 CTGATGCTGGCCGTGTTCCTTTGACAGTATCTCAA[C/T]TGATCCTAGTAAAACCCACAAAAAGTCCCAGACAC Y 2 1 2 1 101000 f 74 goat snp7680-scaffold1277-1082681 24 48842830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432014 Affx-122935923 AX-123302355 24 48674852 AAATCAGAGTCCCTGCTGTGAGTCTGTGCACCTGC[A/G]TTTGTTAAAGCTGTCCAGGAGATGCAAACCCTCCA R 2 1 2 1 101000 r 74 goat snp7679-scaffold1277-1047858 24 48876672 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386686 Affx-122970181 AX-123257044 24 48734090 GAGGAAGGAGGAGCTGGTACTAGAACTCGAGGGGC[A/G]TGAGCATGTACTGTCTGCAGTGTTTGGGTTTTGCT R 2 1 2 1 101000 r 74 goat snp7678-scaffold1277-988620 24 48936421 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780722 Affx-122930677 AX-385267812 24 48772354 AACAGTAAACATGATTGTAAATGGTTTCAGAAACT[A/G]CTGGGATAATGCTGGCTTTAGGACCATTCAGTCCC R 2 1 2 1 101000 r 74 goat snp7677-scaffold1277-950356 24 48974639 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776985 Affx-122959650 AX-385264109 24 48810517 GAAGGCTAATCCCTTTTCTTTGCTCCAAACACATA[A/G]AAGTAATAGATGAACCATAACTGGAAAAAAACCTT R 2 1 2 1 101000 f 74 goat snp7676-scaffold1277-912193 24 49013593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390924 Affx-122967083 AX-123261281 24 48847354 AGATTAAGTCCCAAGAAGTTTCTTCTTTAGAACAA[C/T]TGATTTTAAAAATCAAATAAATGAGGCCTCTAGCA Y 2 1 2 1 103000 f 74 goat snp7675-scaffold1277-875356 24 49050518 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416716 Affx-122947555 AX-123287064 24 48881713 TGAAAGATGGTAATAAAGAGCAGAGGGCAATGATA[C/T]AGAAAATAGAAACGCAGTAGAGAAACTCAGAATTC Y 2 1 2 1 303000 r 74 goat snp7674-scaffold1277-840997 24 49085045 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405811 Affx-122955894 AX-123276163 24 48917830 CATTGGGCTGGTGAGACGAAAATTGGGCTTTTCAT[A/C]TGCACCCACCTCCACCAGTGAGCTTTCTCAATTTC M 2 1 2 1 101000 f 74 goat snp7673-scaffold1277-804880 24 49121191 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443243 Affx-122927555 AX-123313580 24 48952900 TCTTTCTAGAGCTCTTAATAAGTATATTTTGGATC[A/G]CCACGTTTCTCTTATATTTTGTCTTTTTGCCTTTT R 2 1 2 1 101000 f 74 goat snp7672-scaffold1277-769810 24 49156326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780232 Affx-122929208 AX-385267327 24 48997720 GGTAGTAGACCTAAAACTGAATGCTGGTCTTGCCA[C/T]TTACTAACTAGATGTTCCTGGGCTATTTAACCTCT Y 2 1 2 1 101000 f 74 goat snp7671-scaffold1277-724990 24 49201148 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419257 Affx-122946262 AX-123289605 24 49068774 ACTGGTCAGTCATAGTGGTTGTTGGGTGAGCACAC[A/G]GTTAGGCTTTATTGTATGTATCTCTAGGAACACTA R 2 1 2 1 101000 f 74 goat snp7669-scaffold1277-653936 24 49272566 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383547 Affx-122972614 AX-123253905 24 49105079 TATGTGTCTAGCACTTTGAATAGGACCTGAGGATA[C/T]AGTAAATGCTATGTAAATCTTTGCACTTATTATTA Y 2 1 2 1 101000 f 74 goat snp7668-scaffold1277-617631 24 49308848 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405377 Affx-122956306 AX-123275729 24 49137566 TTTTTAACCACATCAGAAAGCAGGATTGGAAGAGT[A/G]TGATGGCATCAGGATAGTTATGGGGCAGTGATACT R 2 1 2 1 101000 f 74 goat snp7667-scaffold1277-585144 24 49341562 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397099 Affx-122962703 AX-123267454 24 49166332 TCACACTGGACCCACTCCACCCAATCTAAAGAGAA[C/T]GAAGCTTTCCAGTAGCCATGAGAGATTTAAGCATG Y 2 1 2 1 102000 r 74 goat snp7666-scaffold1277-556378 24 49370446 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777880 Affx-122956679 AX-385264996 24 49219837 TTTGGACTGTGTGGTGGGGAGAACATCCTATGAAT[A/G]TCACAGCAAAAACTAAGAGCCTGGCTTTAGGGAAC R 2 1 2 1 101000 r 74 goat snp7665-scaffold1277-502873 24 49423605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442856 Affx-122927678 AX-123313193 24 49249308 AGTAGGAAAAAAAAAGGTCAAAAGAATCAAATTCA[C/T]TCAGAAAGGGCGCAGTGGCTCTTACAGATGGGCCT Y 2 1 2 1 101000 r 74 goat snp7664-scaffold1277-473402 24 49452460 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449267 Affx-122923033 AX-123319602 24 49291001 AGAAGATTCCAATTTCCCTTGCTTCTTGCCCACAG[C/T]ACGCAGACCTTGCCTCTTCAGCTTGTGTAGTAAAT Y 2 1 2 1 101000 f 74 goat snp7663-scaffold1277-431709 24 49494633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785864 Affx-122958805 AX-385272901 24 49327216 CACAGATGCATTTCAGACAGCAAAAGGGAGGAAGA[A/G]ACTAGGAAGGGCTATCGCCAGAAAGACAAGAAGTA R 2 1 2 1 101000 f 74 goat snp7662-scaffold1277-395494 24 49530860 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795475 Affx-122959702 AX-385282430 24 49377720 CTTTTAGGAACCTGTTTCCCTTGTAGGGAAGAAAA[C/T]TATCTGAAGTAGTCAAGCTAAGCATTTGTTTCTAT Y 2 1 2 1 101000 f 74 goat snp7661-scaffold1277-344990 24 49583300 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411346 Affx-122952260 AX-123281696 24 49426128 TTATTTCCAAAGTTTTTAAAGGTGGATTTGCATTT[C/T]TTCAGTGTGAGTTATGTTTTATTTCGAATCTCTGC Y 2 1 2 1 201000 f 74 goat snp7660-scaffold1277-296582 24 49632497 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439044 Affx-122930333 AX-123309381 24 49457980 TTTTATTATGAGTAACTAGCTGTCAAACATAATCA[A/G]GTTCTAATGCTCTAAGGTATTCATTATATATATGC R 2 1 2 1 101000 r 74 goat snp7659-scaffold1277-264730 24 49664539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402099 Affx-122958693 AX-123272452 24 49500572 AGGAAAGTCACTGAATGATGTGAGGACTTCCCAGG[G/T]CTTTGATTCCCAGTCTTCTCATCTGGCTCCTCTTT K 2 1 2 1 201000 r 74 goat snp7658-scaffold1277-222138 24 49706843 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785276 Affx-122919270 AX-385272321 24 49616434 TTAGGCTAATAGCAACCATGAATAAGTTACAAGGT[A/G]TTTGAATGTCTACAAGTACCTGAATATATTTATAT R 2 1 2 1 101000 f 74 goat snp7655-scaffold1277-106276 24 49822326 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396233 Affx-122963339 AX-123266588 24 49651040 TCGAATGAAATTCATGGAGAGCACTTGGCTAGCTG[C/T]AAGATAATAAACAAAGAGAATGAGCTGGATGATGG Y 2 1 2 1 101000 f 74 goat snp7654-scaffold1277-71670 24 49856975 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401237 Affx-122959307 AX-123271590 24 49683872 GTGATTAAATTGATATAAATTATTCACCGGTCTGT[A/C]TTTTAATGTTTTTCTTCTGCCATCTGGAAACCCTC M 2 1 2 1 201000 f 74 goat snp7653-scaffold1277-38838 24 49889711 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403813 Affx-122957960 AX-123274165 24 49712537 TGACCCCTTAAGGCAGATAGGGTTTTTAGCAGTTT[A/G]CTGGTTCGAGTTTCTGTTGCAACTGACTTAACCCA R 2 1 2 1 101000 f 74 goat snp7652-scaffold1277-10173 24 49918134 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382057 Affx-122974930 AX-123252415 24 49724332 CTTGCCCTGCATGCGTCCTCAACCTCATCAGTCCA[C/T]GTAATTACAAAGTCTCAACAGAGTCCCCGAGATGT Y 2 1 2 1 201000 r 74 goat snp18378-scaffold1861-1523 24 49929775 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418127 Affx-122947119 AX-123288475 24 49756022 CCAGCAGCGACTTGACCCACTCTCATCACAGCTCC[C/T]GAAACTACACACACAAACTAAGGCTATAGAAATGT Y 2 1 2 1 101000 r 74 goat snp18379-scaffold1861-33213 24 49961197 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424764 Affx-122941642 AX-123295110 24 49800708 CTCCGTACTTGCAGCAATCCTTCCCTTCCTCTCTC[A/G]TCTCCTTATGACCAACATCCCTGCCAGATGGGTTG R 2 1 2 1 101000 r 74 goat snp18380-scaffold1861-77899 24 50006376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396272 Affx-122963309 AX-123266627 24 49835011 TTGAAGGAGGTGATCGTCCTGTTGTATTCTGCGCT[A/G]CACACCTCTTCTGGATGGCCTTTGTCTAATTCTGA R 2 1 2 1 101000 f 74 goat snp18381-scaffold1861-112202 24 50040742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381566 Affx-122974817 AX-123251924 24 49880417 TCATCACCTCAGACATTACACCTTTCACCACCTTC[C/T]CTTGAAGAAACTGTTTAGCATTCAAGTCCCATCTC Y 2 1 2 1 101000 f 74 goat snp18382-scaffold1861-157608 24 50086275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771654 Affx-122932084 AX-385258812 24 49914872 GGTTCCTCCTTGCCAAGTGGTTAAAATGCCAAGAC[A/G]TATTGGGTTTTGTAACTTTGCTTTCCTTAACATAA R 2 1 2 1 101000 f 74 goat snp18383-scaffold1861-192063 24 50121653 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433283 Affx-122935214 AX-123303624 24 49968824 TTTGATTTCCACGGTGGACATTGTGAATGGTGAAC[A/G]TAGCTTTTCATCTAAGAGTGCTAACAAATTTTTTA R 2 1 2 1 101000 f 74 goat snp18384-scaffold1861-246015 24 50177029 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765804 Affx-122973187 AX-385253257 24 50014457 CTGAGAGCAGCTCCATGCTGACTTTCTAGAGAGTC[C/T]CGTTATTATGGTAACTTAACAGTAATCAGTGCCAT Y 2 1 2 1 101000 f 74 goat snp18385-scaffold1861-291648 24 50222490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436449 Affx-122932995 AX-123306787 24 50044039 ACTGGGCGAACTGTCCTCCTTTCAGAAGAAGGGTC[A/G]TGCAAGGATTTCGAATCCTCCTGGCCACACTACAG R 2 1 2 1 101000 r 74 goat snp18386-scaffold1861-321230 24 50252840 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422850 Affx-122943098 AX-123293196 24 50081997 GTCTATAAATTTTGTCCAACTCCAATTCTGCCTTG[C/T]ACTGGTGACCTCTGTCCTCCCTCAGCTCACAGTCT Y 2 1 2 1 101000 f 74 goat snp18387-scaffold1861-359188 24 50291046 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768683 Affx-122969085 AX-385255861 24 50159746 GAATGGCAAAACATTAAAGATAATGAAATATAATT[A/C]TTATTTTGCATTCTTGGCTATTCAGCTGTTGGAAA M 2 1 2 1 303000 f 74 goat snp18389-scaffold1861-436937 24 50368805 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273043 Affx-1111833284 AX-519546716 24 50165765 GCAGAAGATATTAAGAAGAGGTGGCAAGAATACAG[A/G]GAAGAACTGTACAAAAAAGATCTTCACGACCCAGA R 2 1 2 1 103000 f 74 goat 24_50165765_AF-PAKI 24 50165765 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38393274 Affx-122965450 AX-123263631 24 50189303 CTAAACAACTCACCCACGGTGTCTTAGCTCCTAAG[C/T]AGCAGAGCCAATGCCCAAAGCCAGAGGAGGGAACC Y 2 1 2 1 101000 f 74 goat snp18390-scaffold1861-466494 24 50398282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434404 Affx-122934683 AX-123304745 24 50224779 CTCAATGAAGAAGGCTAAGAACTCCTCCCAGGTAA[C/T]GTAGGTGTGTTTGAAGTAGGTACCTTAACCAAAAG Y 2 1 2 1 101000 f 74 goat snp18391-scaffold1861-501970 24 50433496 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789208 Affx-122945870 AX-385276220 24 50279746 TTCTGTGTGCTTTTACTCAGAGCCGTGTCCTGTGA[A/C]TTCTGAAACTGGACATTGAGCCAGCTTCTTTCCCC M 2 1 2 1 101000 r 74 goat snp18392-scaffold1861-556937 24 50488709 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447413 Affx-122924398 AX-123317749 24 50312837 ATGTGTTATCTGGCAAAGCATCTTGATGTAAAACC[A/G]TGTACCATAGCTAATTTTACTGTTTTTAAGATTTG R 2 1 2 1 101000 f 74 goat snp18393-scaffold1861-590028 24 50521821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774395 Affx-122941099 AX-385261531 24 50372958 TGCTCAATGCGTTGACCTGCTACCAGAAAGAAGTT[A/C]GAGTTAGGCATGTATACGGGATAACTGCAGACAGG M 2 1 2 1 201000 r 74 goat snp18394-scaffold1861-650149 24 50580702 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403467 Affx-122957715 AX-123273820 24 50422018 AGATAACTAGAAACAGTGCTACAACTAATCTCTTC[A/G]TATGTACCTCTTTGTTTATGAATATTTCTCTAAAA R 2 1 2 1 101000 f 74 goat snp18395-scaffold1861-699209 24 50630270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394746 Affx-122964856 AX-123265101 24 50451004 AAAGCTAAATATTTCTTTGCCACAGGAACGAGTCC[A/G]TGATCTCCAAAACTAAAAGTCAATCAGAAGAAATA R 2 1 2 1 101000 f 74 goat snp18396-scaffold1861-728195 24 50658971 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376786 Affx-122977953 AX-123247145 24 50503084 ATCTGCTCGAAATTTATTACTAAATAAAAACAGTT[A/G]TGGGGTGGAGGAGATTTTAGACATCTCTGGTCCAA R 2 1 2 1 201000 f 74 goat snp18397-scaffold1861-780275 24 50710643 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408629 Affx-122953488 AX-123278980 24 50542320 TCCAGGGGATCGCAGAGTCGGCCACGACTGAGCAC[A/G]TCAGCACGCTGTGCAAGTAAAGGTTGTCAGACGAG R 2 1 2 1 101000 r 74 goat snp18398-scaffold1861-819511 24 50749951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409019 Affx-122953873 AX-123279370 24 50575649 TCCTCCCACTCTACTAGGACTCCCCATGGACGTTA[C/T]GTATCAAGTGTAGGGTTGGTTATTTTTTTCACTTT Y 2 1 2 1 201000 r 74 goat snp18399-scaffold1861-852840 24 50783269 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431046 Affx-122936651 AX-123301387 24 50612333 AACCCAGCCTTCTGCCCCGGCAGTGGGCAAAGGTC[C/T]GAGGCCTAGTGCTCCCCACGCTGAGCTATGAGACA Y 2 1 2 1 101000 r 74 goat snp18400-scaffold1861-889524 24 50819810 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385594 Affx-122971206 AX-123255952 24 50645427 TTAGGGCTGCAGGACAGCCCGCCCAGGGCAGGGCC[A/G]TTTTTGTTTCGAGATGCACGAATCATGGAGAAGTG R 2 1 2 1 201000 r 74 goat GoatD01.030483 24 50852850 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320801898 Affx-122930403 AX-385288804 24 50679723 GAATCTAGTCAGGATAGTCAAAAGTAAAAAATCTG[A/G]CAAGACAGTCAAAAGTTGAAACCTGCGTGGGCAGA R 2 1 2 1 101000 r 74 goat snp18402-scaffold1861-956914 24 50887329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426142 Affx-122940611 AX-123296488 24 50738897 TACCTCTCACTGGTCTCACAACACCCAGTGCAGTG[C/T]GGCTGGGGTGGGGGTGGGGACCAAGAATTTGCATT Y 2 1 2 1 201000 f 74 goat snp5519-scaffold1194-21961 24 50946587 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444679 Affx-122926447 AX-123315016 24 50773542 AGCTGCTGGATCTCAGGTCTGGGGCACTGCAATGG[C/T]GCTGGCTGAGGTGGCTTTCAGTGGGTGGGGTGAGA Y 2 1 2 1 101000 f 74 goat snp5520-scaffold1194-56606 24 50981196 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439981 Affx-122929804 AX-123310318 24 50818535 TGCTTTAATTTACCTACATGGGTCCATATGAGCTA[C/T]TTGAGTATTGCTCTTGGGGGATCCTATTCTGGGGA Y 2 1 2 1 201000 f 74 goat snp5521-scaffold1194-101599 24 51026254 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448840 Affx-122923296 AX-123319176 24 50858166 AAAATTGCTGTACCAGAGGTAGGGATGAATCATGC[G/T]GTAAATTGACCTGTGACTGCTTGCTGGCAGAAGGA K 2 1 2 1 101000 f 74 goat snp5522-scaffold1194-141230 24 51065860 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427086 Affx-122939792 AX-123297429 24 50893523 CTACCTTTTCCCTCGTGGTCACAAGAGGGCTGCTG[C/T]AGCTCCATTCAGCATATCTGCATTTAAGGGAGGAA Y 2 1 2 1 101000 r 74 goat snp5523-scaffold1194-176587 24 51101590 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803093 Affx-122977982 AX-385289964 24 50935240 TTTTGATAGGATTTGGCTTAGTGGAGAGAGTAAAG[A/G]CGGACTTGCTTTGACCTGGGTGCTATTCTTCACTC R 2 1 2 1 101000 r 74 goat snp5524-scaffold1194-218304 24 51142703 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451921 Affx-122921021 AX-123322254 24 50973228 AGGGCCGGTATGGAGGTCTTGTAATGCCTAATAAA[A/G]TCGTACAACTCCTAGATACTTGTAGCTATTATCTC R 2 1 2 1 101000 r 74 goat snp5525-scaffold1194-256292 24 51180106 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277719 Affx-1111835988 AX-519551218 24 51013690 GGACCATTCAAATTATAAACTCTTTTGGGTACTGA[A/C]CTGTTTTACATACAATCATCTCTTCCAAAATACCT M 2 1 2 1 101000 r 74 goat Random2.2K-2116 24 51013690 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320784856 Affx-122966423 AX-385271903 24 51023559 CATGTGTTGGATATTAGTAGGAAGAGTGAGCAGTC[A/G]TAGCTGGGCATCGTAGCATATTAACTGGATCCAGT R 2 1 2 1 101000 f 74 goat snp5526-scaffold1194-306623 24 51229181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434789 Affx-122933879 AX-123305130 24 51068388 AATAGCCCCAATATTGGTTTCAGTCATTTCAGTGA[C/T]GTTTTGGAGGGCTGCTCAAAGGTTTGTCCATGGTG Y 2 1 2 1 201000 r 74 goat snp5527-scaffold1194-351452 24 51274030 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411239 Affx-122952340 AX-123281589 24 51110779 TGAGAAAGGACATCAGAATGGTGTGTTTCTGGGAC[A/G]TTGTAACTGGATTTCATCCAGCTGTTCTCTTTGGG R 2 1 2 1 101000 r 74 goat snp5528-scaffold1194-393843 24 51315081 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406954 Affx-122955062 AX-123277305 24 51208761 CTTAGGTCCTTGGACAGCCTGAGGATTTACAGCCT[A/G]CCTCCTTGGCAAAATAAAGAATACCACTGTAATTT R 2 1 2 1 101000 f 74 goat snp5530-scaffold1194-491825 24 51413702 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799158 Affx-122929104 AX-385286088 24 51263602 GGAATAATTTCCATCTCCACTTGGATTTGAGCAGT[A/G]TTTTCTTATCATGTGTTCTTCCGTTTTCTTGAACC R 2 1 2 1 101000 f 74 goat snp5531-scaffold1194-546666 24 51468804 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421199 Affx-122944148 AX-123291546 24 51326899 TTTTCTTGTGGAATCATTTCTGTGGAAAATAATGG[C/T]ACATGGAAACTTGTTGAAAAAGGTGGAGGGAGAAG Y 2 1 2 1 101000 r 74 goat snp5532-scaffold1194-609963 24 51532057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408166 Affx-122954211 AX-123278517 24 51360520 TCAGCTGACTTCATCTGCATAGAGCAGTGCCAGGG[A/C]AGTGCTCTTAGAAAATGTTACACTCCTCTGGCATG M 2 1 2 1 101000 f 74 goat snp5533-scaffold1194-643584 24 51565554 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413053 Affx-122950979 AX-123283402 24 51442035 GTCCCCAGCAAGAAGAGCACATTCTGTCATCACCC[C/T]GAGATCAGTAATTAGAACTGCCCTCTAAGAAGCAC Y 2 1 2 1 201000 r 74 goat snp5535-scaffold1194-725099 24 51647332 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429808 Affx-122938191 AX-123300149 24 51450595 AGCAGCCCACAATAAGGAGATAAATAAAACTGTAC[A/G]TCCAGACACAGCAGAATGAAATTTAATAAATGGCT R 2 1 2 1 101000 f 74 goat snp10314-scaffold1369-2913 24 51655993 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405698 Affx-122956543 AX-123276050 24 51493004 GAGAGTCAGAACAAAACAAAGAAAACCACATGGGC[A/G]TCTTAGATTTTTTGTACAGGGAATCTAGTTTGGAC R 2 1 2 1 201000 r 74 goat snp10315-scaffold1369-45322 24 51698504 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423186 Affx-122942727 AX-123293532 24 51531184 ATATTCTTATAAAAATTATTGATTGGGCACCTATG[C/T]GCTCAGTAACATACCCAGCAGTGGAGATACAATGG Y 2 1 2 1 201000 f 74 goat snp10316-scaffold1369-83502 24 51736582 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432611 Affx-122935497 AX-123302952 24 51620800 ACCTTTTTTCCCACCCCAAGCAGGGTTTTGTGCTT[A/C]TTCTAATGGCAAAAATGGGCAAGCAGGTATAACCA M 2 1 2 1 101000 r 74 goat snp10318-scaffold1369-173118 24 51827282 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414462 Affx-122949567 AX-123284811 24 51654967 GCAGAGGAGGCTGGAAGTATCCTGTTCTGCTACTT[A/G]TTTACCTTCTCTGAGAATTAACAGTCACCAGCACT R 2 1 2 1 101000 r 74 goat snp10319-scaffold1369-207285 24 51860564 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771443 Affx-122962569 AX-385258601 24 51688897 TTGGGATATGGGATCATGTAATATTTATACCAACC[A/G]GCATGTTATCAGCAAGCCCAAAACAGCTGGAAAGC R 2 1 2 1 101000 r 74 goat snp10320-scaffold1369-241215 24 51893292 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448607 Affx-122923387 AX-123318943 24 51722774 AGCATCCTGACCACGTTGAAAGCAGCGTTTGGGGC[A/G]TCTGCTAAGACCTCCTTCAGACCTGCAGTCATAAC R 2 1 2 1 201000 r 74 goat snp10321-scaffold1369-275092 24 51927091 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390844 Affx-122967831 AX-123261201 24 51757317 TGGACCCAATAAAGAATCCTCGTTCTTGACCCTGA[A/G]CTTTTATCTCCGGATACCTCATCCTCAGCTAAGGA R 2 1 2 1 101000 r 74 goat snp10322-scaffold1369-309635 24 51962017 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435248 Affx-122934070 AX-123305588 24 51795269 GCTTAGACATATTGATTAGCAGCTGATTATATGGC[A/G]TTGCATATAGTTTATTCTTAGGTAGTGAGCCTGAA R 2 1 2 1 101000 f 74 goat snp10323-scaffold1369-347587 24 51997632 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436413 Affx-122933020 AX-123306751 24 51846861 GAGTGCATCCATCCAGACCTTTAAATCCACAGTGT[A/G]TGAACACAGAGATGAAACGGCTCAGATGAAGTGTG R 2 1 2 1 201000 r 74 goat snp10324-scaffold1369-399179 24 52048597 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423959 Affx-122942141 AX-123294305 24 51878695 AGCTTTGTTAAAATGAAAAGAAAAGTGGCTTCCTG[A/C]TGAGGGTGGTTTCCTGTAAAGAGCTGCTTATGCCA M 2 1 2 1 103000 r 74 goat snp10325-scaffold1369-431013 24 52080591 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771417 Affx-122973087 AX-385258575 24 51908206 GAGGAGGAAAACAACAAAGCCCTCTTGATTGGATA[C/T]GTTGTTCACCTCTAACCTTTGCCCCCTCCCCTGGA Y 2 1 2 1 202000 r 74 goat snp10326-scaffold1369-460524 24 52110018 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802201 Affx-122943643 AX-385289105 24 51949884 CAGGAGAATAACAGATACTGTATCTTAAAAGACAC[A/G]TTCAATAGTTTAATCATTTCCACTAAGCTTCACTG R 2 1 2 1 101000 r 74 goat snp10327-scaffold1369-502202 24 52151646 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792619 Affx-122919788 AX-385279600 24 51995834 TATTTGTGAACTTTGGTATAATAAGTTATTCAGTA[A/G]GTGATTGACACAAGTCTTGCAAGAAGCCAGAAGTG R 2 1 2 1 101000 r 74 goat snp10328-scaffold1369-548152 24 52197074 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430956 Affx-122936825 AX-123301297 24 52042467 TCCTAGCTTCTTAAAAAAGCAGTGGAAACAAAATT[C/T]AGCCATGAACAAATGCTTAAAATCATCATATACAT Y 2 1 2 1 101000 f 74 goat snp10329-scaffold1369-594785 24 52244616 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413866 Affx-122949857 AX-123284215 24 52080756 AATTTTTGTTCCCAAAGTGGTTTGGCTTTATCTTC[A/G]TTTTGCTTTTCTTTATGTGAACATTTTGAATTACA R 2 1 2 1 101000 f 74 goat snp10330-scaffold1369-633074 24 52283054 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277591 Affx-1111835989 AX-519551090 24 52104390 GACAAAATATCATATTCCCTGACAGCTTTAAAACA[A/G]TATAAAGCTAGAAATCGGCTGTTGATCCTTTTATC R 2 1 2 1 101000 f 74 goat Random2.2K-2117 24 52104390 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395488 Affx-122963895 AX-123265843 24 52118032 TTCGTTCTTACCCCAATAAGAGACAGATATACTCT[C/T]TGTCTTAGTTGTATTATAAGAAGGGGCTCCTACTT Y 2 1 2 1 102000 f 74 goat snp10331-scaffold1369-670350 24 52320338 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445570 Affx-122925139 AX-123315907 24 52160539 CTCATCCCTCTCCTAAGTCTACTGAGCTTTTGCAG[C/T]ACAGTGCACAAGCATTCTTATTATCTCAACTCTTC Y 2 1 2 1 101000 f 74 goat snp10332-scaffold1369-712857 24 52363370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780132 Affx-122944779 AX-385267229 24 52165424 CACTGGGTTATGGGACCCAGATTTTCATTCCTAGA[G/T]TTCAAAATTTCAATGAGTTTTTTTGAAACATTCGT K 2 1 2 1 201000 r 74 goat snp8739-scaffold1312-781568 24 52368114 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390729 Affx-122967921 AX-123261086 24 52194702 TCTGCAAAATGACTGTGAAAAATGACACGTGAATC[A/G]TGGCAGAAAGGACTGCAACCACTTAGACACTATTA R 2 1 2 1 101000 f 74 goat snp8738-scaffold1312-752290 24 52397508 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413079 Affx-122950960 AX-123283428 24 52239239 CTTTTTTCTATCATTGCCTGAGTGATGCTGGGGAG[A/G]CAAATATGCATATTTAGGGGAATAAATCATCTTAA R 2 1 2 1 101000 f 74 goat snp8737-scaffold1312-707753 24 52441767 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765001 Affx-122934906 AX-385252577 24 52272038 TTAACCATCCATAGGACACACTAGAAGAATGTCAG[C/T]ACAGGACAACTTCTGTTTAAGTTATATATGAATAT Y 2 1 2 1 101000 f 74 goat snp8736-scaffold1312-674954 24 52474642 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452413 Affx-122920593 AX-123322746 24 52319207 CTGCCAGATAAAAGTACTCTATGTACCTTCAGAGA[C/T]GAGAAGCATTAGAAAGGTCTCTTGCTTGGAAAAAC Y 2 1 2 1 101000 f 74 goat snp8735-scaffold1312-627785 24 52521754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425385 Affx-122941561 AX-123295731 24 52364883 AAAAGGCATCATGTTGCTTCCTACAAAATGTGTAA[C/T]GGGTCTGAACTGAAATAACAAAAAAATGGCTACAC Y 2 1 2 1 101000 f 74 goat snp8734-scaffold1312-582109 24 52567222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781088 Affx-122928056 AX-385268174 24 52466448 AAAAATGGCTAAATGTCTTCATAAATGAGAAAGTA[C/T]GAAGGAGAAAAGAAGATTCGTCTTGAAAATCCTAA Y 2 1 2 1 201000 f 74 goat snp8732-scaffold1312-480544 24 52668666 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783728 Affx-122974814 AX-385270784 24 52496525 TAATGAGTGAATATGACTTGTGGATGGTTGTGGAC[A/G]TGTTCTTTAGCATTTTTCTGATTATGAACCCCTGG R 2 1 2 1 101000 r 74 goat snp8731-scaffold1312-450467 24 52698078 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780434 Affx-122940037 AX-385267525 24 52536070 TCCATTCTAATCAGGGCATTAAACATGTATAGATA[C/T]GTTTTATACTTTAATTAGAAAACAGATAAATAAGC Y 2 1 2 1 201000 r 74 goat snp8730-scaffold1312-410922 24 52737666 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398959 Affx-122960977 AX-123269314 24 52583302 TGACTCGTCTCTTCAGAGCTAAGGTAGTTCTTATC[A/G]TCTGTATCACTTAACTGGCACTCAGCAACAGGAGA R 2 1 2 1 101000 r 74 goat snp8729-scaffold1312-363690 24 52784468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453050 Affx-122920072 AX-123323383 24 52617321 CAGTGATAACAACATTCTTGCCCACATAATGCTTA[C/T]ATTCTGGGGGTGAGAAAAGGGATTCAGGAAACAAT Y 2 1 2 1 101000 f 74 goat snp8728-scaffold1312-329671 24 52818378 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443961 Affx-122927008 AX-123314298 24 52679829 GAAGAAAACAACCCTTTTGTTTAATTCAAGTGTGG[C/T]GGAGGACATGGGATTAATGCCACTCACTGTGTTGT Y 2 1 2 1 101000 r 74 goat snp8727-scaffold1312-267163 24 52882713 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387277 Affx-122970543 AX-123257635 24 52718064 TGGTTTAATTGGCTCAGCGAGCTAGAAATGCTGAC[A/G]TAAGATAGAGAAACTTCACACATAATGGTAACCAA R 2 1 2 1 101000 f 74 goat snp8726-scaffold1312-228928 24 52921443 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770983 Affx-122967300 AX-385258145 24 52748176 TTCTCATGAAACTGCAGAAGTTCAAGATTCTGAAG[A/C]TCCCCTAAACAAGCGAACTGATTCCAAGAGAACTT M 2 1 2 1 101000 r 74 goat snp8725-scaffold1312-198816 24 52951357 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779538 Affx-122927762 AX-385266641 24 52787873 CATCTAAAGATACAGGAAGAAGAAACATCCTTAAT[A/G]TGGAATTTCATCAATTTTTTAGAGGTATTCTTTGA R 2 1 2 1 101000 f 74 goat snp8724-scaffold1312-159119 24 52990707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424457 Affx-122941778 AX-123294803 24 52840563 GCTCAGAAGGATAGAGTTTTTCCTTCTGGATAGAT[A/G]TCTCCCCAAAATGTAAACAGTTCAGTAAGAATCCA R 2 1 2 1 101000 f 74 goat snp8723-scaffold1312-106429 24 53047001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427674 Affx-122939311 AX-123298017 24 52872241 AAGTCAGATGTTGTTGTGTGTTTATGTTTATGATG[A/G]GGAAAAATGAATAAGGAAATTACTACTCCTTTTCT R 2 1 2 1 101000 r 74 goat snp8722-scaffold1312-74751 24 53078419 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794443 Affx-122956464 AX-385281406 24 52925788 AATAGCAGAATGATAATTTGCTTATATAAACAAGC[A/G]TGACTAATGAGCCTTTAAATGGCTTTTTTGTGCCT R 2 1 2 1 101000 r 74 goat snp8721-scaffold1312-21204 24 53132308 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402348 Affx-122959058 AX-123272701 24 52978125 ACTTGATGTTTTAATAAAATACTGGTTCCTTTAGC[A/G]TGGTGTTCCAGGATTTAGGGAAAACCTCTGCTAAC R 2 1 2 1 101000 r 74 goat snp6937-scaffold1253-31034 24 53183990 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429190 Affx-122937954 AX-123299532 24 53011041 AAGCAAGTGTGTCCGCTATCCATGGAAATCTATTC[A/G]TGGAAATCTTTGCTTTAAAACATTTGTTCCCCTTT R 2 1 2 1 101000 f 74 goat snp6938-scaffold1253-63950 24 53217239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426655 Affx-122939935 AX-123297001 24 53044553 TAATGAATTCTTTGAGAGTGTTTCTCAAACTTTAG[C/T]AATTATAAAATCCATCTGGAAATCTTGTTAAAATA Y 2 1 2 1 201000 r 74 goat snp6939-scaffold1253-97462 24 53250989 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463920132 Affx-1110224473 AX-515397690 24 53071537 AAAACAGAACACACTTGAGTCAGTTCTAATGAGGT[A/G]GATGAAACTGGAGCTTATTATACAGAATGAAGTTA R 2 1 2 1 103000 f 74 goat 24_53071537_AF-PAKI 24 53071537 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38429865 Affx-122938143 AX-123300206 24 53107135 TGTGCATCTCTTGATGGGTCTGGGAGACCACACTC[A/G]CAACCCAGAGCAAGCAGGGGAGGCCAGAGCTCATA R 2 1 2 1 101000 f 74 goat snp6940-scaffold1253-160044 24 53313286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408139 Affx-122954234 AX-123278490 24 53147947 CTCAGTAATCCATCGCTGATGTCGGCAATTCAACC[A/G]TTTTAACTCATTCTCTAATCTGTTTTAATTTTGCT R 2 1 2 1 201000 r 74 goat snp6941-scaffold1253-200856 24 53354103 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798278 Affx-122971678 AX-385285213 24 53202916 CCGATACTTTTCTCACTTAGGTTTCCTAAACAATA[C/T]ACTTTTTAGTGTTACAAATCTTTGACTATATCAAC Y 2 1 2 1 101000 f 74 goat snp6942-scaffold1253-255825 24 53409363 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801495 Affx-122975937 AX-385288404 24 53266613 TGAGAAGGAAAGAAGTTGAGACAGAATTGAGTAAC[A/G]TGGCTACTGAATAGTACATCTCACTAGCCTCTAAA R 2 1 2 1 101000 r 74 goat snp6943-scaffold1253-319522 24 53470610 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776841 Affx-122919983 AX-385263965 24 53328640 TTCACACGTGAATACGTATTTAAACACATAACTGT[A/G]ATAACAATTTAATGCTAGCTCCATGCACAGGGTCA R 2 1 2 1 201000 r 74 goat snp6944-scaffold1253-381549 24 53533058 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776779 Affx-122938507 AX-385263903 24 53373067 ATGCTCTCCCCATGCAATGAAAGACAATCACACTG[C/T]GATGAGCAGTATGATTAAACAAAGTTTCATGATCA Y 2 1 2 1 102000 f 74 goat snp6945-scaffold1253-425976 24 53577168 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435142 Affx-122933677 AX-123305482 24 53497074 ATGTTTCCCTCCTGCCCTGAATTTTTGTTGTTGTT[A/G]TTTTTGTTGTTCTCTTAAGCCATAGACTTTTGAAG R 2 1 2 1 303000 r 74 goat snp25888-scaffold2675-24035 24 53706924 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418274 Affx-122947009 AX-123288622 24 53523039 AACTTTCCTAATCAGCTTCTGATTCCACGTGATGG[C/T]ACGCTTCCGAGGGTTGCCTCAAATTAACACTCTTC Y 2 1 2 1 101000 r 74 goat snp19081-scaffold1919-1831 24 53736756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409460 Affx-122954075 AX-123279811 24 53577701 AAAGGAAATGAACAGAGTGCCAAGGCAGAAAATAA[A/G]GAGTATTGGGGGTATTTATAAAGTGGAGGGTAGTT R 2 1 2 1 201000 f 74 goat snp19082-scaffold1919-56493 24 53790881 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476370 Affx-1251763881 AX-586011781 24 53643578 ACAGTAAAACAGGACAAAAAAAAAAAAAAAAAAGC[-/AACTAATTAGAAATTTTAACCAGGGAGAGGGAAAGATGGCGAAGGGGAAAAAAAAAATTACTCTTCCACTTATAACTTTT]CAAATTTTGAGAAAAAGAAGGGTGTAATATAATTT - 4 1 4 1 20000 f 74 goat SV_274 24 53643578 - deletion junction SV-TF-chip 539476626 Affx-1251763881 AX-586012009 24 53643578 ACAGTAAAACAGGACAAAAAAAAAAAAAAAAAAGC[-/AACTAATTAGAAATTTTAACCAGGGAGAGGGAAAGATGGCGAAGGGGAAAAAAAAAATTACTCTTCCACTTATAACTTTT]CAAATTTTGAGAAAAAGAAGGGTGTAATATAATTT - 4 1 4 1 20000 r 74 goat SV_274 24 53643578 - deletion junction SV-TF-chip 562165155 Affx-1251763881 AX-606940567 24 53643578 ACAGTAAAACAGGACAAAAAAAAAAAAAAAAAAGC[-/AACTAATTAGAAATTTTAACCAGGGAGAGGGAAAGATGGCGAAGGGGAAAAAAAAAATTACTCTTCCACTTATAACTTTT]CAAATTTTGAGAAAAAGAAGGGTGTAATATAATTT - 8 1 4 1 20100 r 74 goat SV_274 24 53643578 - deletion junction SV-TF-chip 562165348 Affx-1251763881 AX-606940759 24 53643578 ACAGTAAAACAGGACAAAAAAAAAAAAAAAAAAGC[-/AACTAATTAGAAATTTTAACCAGGGAGAGGGAAAGATGGCGAAGGGGAAAAAAAAAATTACTCTTCCACTTATAACTTTT]CAAATTTTGAGAAAAAGAAGGGTGTAATATAATTT - 8 1 4 1 20100 r 74 goat SV_274 24 53643578 - deletion junction SV-TF-chip 562165412 Affx-1251763881 AX-606940823 24 53643578 ACAGTAAAACAGGACAAAAAAAAAAAAAAAAAAGC[-/AACTAATTAGAAATTTTAACCAGGGAGAGGGAAAGATGGCGAAGGGGAAAAAAAAAATTACTCTTCCACTTATAACTTTT]CAAATTTTGAGAAAAAGAAGGGTGTAATATAATTT - 8 1 4 1 20100 f 74 goat SV_274 24 53643578 - deletion junction SV-TF-chip 562165736 Affx-1251763881 AX-606941145 24 53643578 ACAGTAAAACAGGACAAAAAAAAAAAAAAAAAAGC[-/AACTAATTAGAAATTTTAACCAGGGAGAGGGAAAGATGGCGAAGGGGAAAAAAAAAATTACTCTTCCACTTATAACTTTT]CAAATTTTGAGAAAAAGAAGGGTGTAATATAATTT - 8 1 4 1 20100 r 74 goat SV_274 24 53643578 - deletion junction SV-TF-chip 562165769 Affx-1251763881 AX-606941178 24 53643578 ACAGTAAAACAGGACAAAAAAAAAAAAAAAAAAGC[-/AACTAATTAGAAATTTTAACCAGGGAGAGGGAAAGATGGCGAAGGGGAAAAAAAAAATTACTCTTCCACTTATAACTTTT]CAAATTTTGAGAAAAAGAAGGGTGTAATATAATTT - 8 1 4 1 20100 r 74 goat SV_274 24 53643578 - deletion junction SV-TF-chip 562165865 Affx-1251763881 AX-606941274 24 53643578 ACAGTAAAACAGGACAAAAAAAAAAAAAAAAAAGC[-/AACTAATTAGAAATTTTAACCAGGGAGAGGGAAAGATGGCGAAGGGGAAAAAAAAAATTACTCTTCCACTTATAACTTTT]CAAATTTTGAGAAAAAGAAGGGTGTAATATAATTT - 8 1 4 1 20100 r 74 goat SV_274 24 53643578 - deletion junction SV-TF-chip 562166238 Affx-1251763881 AX-606941646 24 53643578 ACAGTAAAACAGGACAAAAAAAAAAAAAAAAAAGC[-/AACTAATTAGAAATTTTAACCAGGGAGAGGGAAAGATGGCGAAGGGGAAAAAAAAAATTACTCTTCCACTTATAACTTTT]CAAATTTTGAGAAAAAGAAGGGTGTAATATAATTT - 8 1 4 1 20100 f 74 goat SV_274 24 53643578 - deletion junction SV-TF-chip 320780455 Affx-122922650 AX-385267546 24 53644180 CTGCCCCAGCACTACCAGTGATCCTGACAGAAGAC[A/G]TAACTATATTGCTTAACTGGCAACCAGAGGCACAC R 2 1 2 1 101000 f 74 goat snp19084-scaffold1919-122972 24 53857208 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423993 Affx-122942113 AX-123294339 24 53682676 AAGCCCTCACTTATGTCTACCCTACATTAAATATT[A/G]TAAGAGAAAGTCTGATGAAGTGTATCAATAGATGT R 2 1 2 1 101000 r 74 goat snp19085-scaffold1919-161468 24 53895758 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414523 Affx-122949520 AX-123284872 24 53817563 TAGACGATTTATTGGTGGTCCCCTCTGCATGGGTC[A/G]CTCTAGTCAGATGGCTAACTCCCTCACAACGTTAG R 2 1 2 1 101000 r 74 goat snp19088-scaffold1919-296355 24 54031195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389793 Affx-122968213 AX-123260150 24 53864022 TAGAGTCCCAGGAGGGATGGAAGAGACCAGAAAAT[A/G]AGGCCAGTGCATAAAGCAGACTCAGCCACAGGGGA R 2 1 2 1 101000 f 74 goat snp19089-scaffold1919-342814 24 54078226 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452397 Affx-122920607 AX-123322730 24 53934222 CTATCTGAGCTGAAGATTAGCAGAAGGATGTGCAA[C/T]GATTAAAGTTCACATTGCTGGAAGGTTTCCACAGA Y 2 1 2 1 101000 f 74 goat snp19090-scaffold1919-413014 24 54147886 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794017 Affx-122965833 AX-385280986 24 53967061 CATATGTCTGGCTAGCTGAAAATGTTTCATTTACC[A/G]TAGATATTTAAGGCATAGTAATAAAAATATTTTCT R 2 1 2 1 102000 f 74 goat snp19091-scaffold1919-445853 24 54180801 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416147 Affx-122948281 AX-123286496 24 53986341 GGACCCACAGGCATTTACTATAGGACTCTACTTGG[C/T]ACAAAGTTGATGTCAATAACTGTTGGTTAAATAAG Y 2 1 2 1 101000 f 74 goat snp34936-scaffold417-6636 24 54205617 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797601 Affx-122942116 AX-385284540 24 54034202 CTAATAGCTAATTCTGTGAATAGCCAGTGTTACAG[C/T]AACTCAGAAAGGGACGGTTCACAATGGAGCAAACA Y 2 1 2 1 101000 r 74 goat snp34937-scaffold417-54497 24 54253896 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407173 Affx-122954832 AX-123277524 24 54097819 ATTTGCCTTATCAGGAATTACATCTAAATGAAACC[A/G]TATGGTCTGTACCCTTTTGTATATGGCTTCTTTCA R 2 1 2 1 101000 r 74 goat snp34938-scaffold417-118114 24 54317623 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780748 Affx-122965374 AX-385267838 24 54131347 GAAGGCATTTGATTGCAATAGCTATTTAACTCCCT[A/G]TTTTTTCAAGAGAACCACCAGTAGATGGTGACTGA R 2 1 2 1 101000 f 74 goat snp34939-scaffold417-151642 24 54349892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791354 Affx-122964665 AX-385278347 24 54168936 ATTTGAGACGGCAGGACTTTTGTGCTATAGGAATA[C/T]ATGAAGAATTTGAACTAGTCAAGGTGGTGGGTTTG Y 2 1 2 1 101000 r 74 goat snp34940-scaffold417-189231 24 54387787 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778141 Affx-122952713 AX-385265256 24 54197997 TGAGCTTCCAAGAGTTCCCAACTCCGTGCAACATT[A/G]TCTCATTATCTGAAAGCTATTGAATCCGGTGGAAT R 2 1 2 1 101000 f 74 goat snp34941-scaffold417-218292 24 54417408 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445085 Affx-122926208 AX-123315422 24 54229265 AATGTCCTTGTGCTAATGATGACTTTTCTCTTCAC[A/G]TCAGTAGCAGCTGGAGGTGAAAGTTGTCTAAGACA R 2 1 2 1 101000 f 74 goat snp34942-scaffold417-249560 24 54448701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377660 Affx-122977853 AX-123248019 24 54266145 AATAATAAAAATATCACAGCCATACTTTCACAGCC[A/G]TATGTTCACAAGTGTTATAGCAGGCACAAAACACT R 2 1 2 1 101000 f 74 goat snp34943-scaffold417-286440 24 54485583 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388664 Affx-122969102 AX-123259022 24 54370773 CTGTGTGGATATAATGCAGGTGAAGGTTTATCCAT[C/T]CACCTTTTGACAGACATCTCCGTTGCTTGCAGTAT Y 2 1 2 1 101000 f 74 goat snp34946-scaffold417-391068 24 54590784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408917 Affx-122953956 AX-123279268 24 54408258 CCAGGCAAGAACACTGGAGGGGGTTGCAAGCAAAG[C/T]GGATTGCTTTTACAAAGATGGGAAAGCAAAACTCA Y 2 1 2 1 101000 r 74 goat snp34947-scaffold417-428553 24 54628570 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438062 Affx-122931535 AX-123308400 24 54438109 GGCAAAGTTGGCTGGTGTATTGTCTGTTAATTCTC[A/G]TTGCCAAATAATATTCTCTTGACTGAAGAAACCGT R 2 1 2 1 101000 f 74 goat snp34948-scaffold417-458404 24 54658336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769191 Affx-122947170 AX-385256366 24 54489704 AAAGGGATAGGATTTGGGAAAGTTGCATAACACTC[A/G]TCTATGTAAATACAAGATTTTAGTTCTTTAATTTC R 2 1 2 1 101000 f 74 goat snp34949-scaffold417-509999 24 54709930 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793582 Affx-122966797 AX-385280557 24 54530435 TCTCCACTAATAAAGGTAATGTACTAAGTCCTCTA[C/T]GAGGTGCAAAATTTGCAAGCTACATACTTAGGTAC Y 2 1 2 1 101000 f 74 goat snp34950-scaffold417-550730 24 54750946 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437050 Affx-122933099 AX-123307388 24 54582061 TTTGTGTTTAATAATGTTTTATCAATATTTGTGCC[A/G]TGTTTATGTTGCTTTGGCTTAGTTGTGCACTAATA R 2 1 2 1 101000 r 74 goat snp34951-scaffold417-602356 24 54802642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383387 Affx-122973507 AX-123253745 24 54612214 TTAATCCAGAAATTTCTTTTTTTTCCCTTCTAGAT[C/T]ATGTTTAGTTTTTAAAAGAACCAATGACCCTTCTA Y 2 1 2 1 101000 r 74 goat snp34952-scaffold417-632509 24 54832958 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422311 Affx-122943471 AX-123292657 24 54656489 GACATTACCAAATGTTTCCTGTGGGGCAAAATCAC[C/T]CCCTGGTGAGAATCACTAGAGTAAGGGTTTAGGTT Y 2 1 2 1 101000 f 74 goat snp34953-scaffold417-676784 24 54873011 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785708 Affx-122939600 AX-385272749 24 54723107 TTTAAAAAAGTTTTGTAACTTAACTGATATCATCA[C/T]AGACAGCTGGTAGCAATGCAACAGTTAACAATCTG Y 2 1 2 1 101000 r 74 goat snp34954-scaffold417-743402 24 54939498 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431086 Affx-122936621 AX-123301427 24 54791708 ACTATCCTGCAAACAACTTTACTTCCTCTCATTTC[A/G]TTTCTGTCAGACTTTCCATTATAAATTACATTTTC R 2 1 2 1 101000 f 74 goat snp34955-scaffold417-812003 24 55008145 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382003 Affx-122974075 AX-123252361 24 54886498 GGACTGTTAACCTTTCTCTGCACCCTCCCCCCAAA[C/T]AGTTTAGGTACAGTCTGATCTAGAAAGGCGTAAAA Y 2 1 2 1 201000 r 74 goat snp34957-scaffold417-906793 24 55103018 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419865 Affx-122945367 AX-123290213 24 54941636 CTAGCTGGGTTAACCTTGGGTAAGTAATCTAATTT[A/G]TCTGAGATTCAATTTCCTCAATTGTAAAATGATAA R 2 1 2 1 101000 f 74 goat snp34958-scaffold417-961931 24 55157056 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380793 Affx-122975096 AX-123251151 24 54983907 CTCTGCTCTTTCTTTTTCCTCAGGTTCAGTAAATC[A/G]CCAGAGCTAGGCAGTACTACATTTTAAACCACAGC R 2 1 2 1 201000 r 74 goat snp34959-scaffold417-1004202 24 55199304 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791134 Affx-122924388 AX-385278129 24 55023269 TCTGTTATGATGAGAAAAGTATTTTAGTCTCTTCC[C/T]TGTTAATATCTATCAAAAGCCTGCTTTACGCTCTT Y 2 1 2 1 101000 r 74 goat snp34960-scaffold417-1043564 24 55237430 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430787 Affx-122937475 AX-123301128 24 55081642 GTCCAGCCAAAAGCATTTCCAGGAGCCTGTAGTTT[C/T]CACCAACCCTGATGTTTTCAGACTTCTTGATACCC Y 2 1 2 1 101000 r 74 goat snp34961-scaffold417-1101937 24 55295805 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796293 Affx-122949998 AX-385283243 24 55115559 ACGGCTTTTTGCACATTTGTTATTCTCTTTGACAT[A/G]CACAATAAATCGTAATAGTTACCAAATTACTGTTC R 2 1 2 1 101000 f 74 goat snp34962-scaffold417-1135854 24 55330102 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382163 Affx-122974032 AX-123252521 24 55146348 CCTACCTCAGTGTTTAGGCGTTTTTCTGATACTTA[G/T]AGAAATGCGAGTTTTATAATATGTTAAAGTTTCAT K 2 1 2 1 101000 f 74 goat snp34963-scaffold417-1166643 24 55360558 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411748 Affx-122951508 AX-123282098 24 55192627 TTCCCTTCAGATTGAAGTTCGGAGTCCTGTCTCAA[C/T]TGATATTTTGAGCATTAATGTGTAGACTAATTTGA Y 2 1 2 1 101000 f 74 goat snp34964-scaffold417-1212922 24 55406899 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381098 Affx-122974591 AX-123251456 24 55224696 CAGAACCACCTCATCACAAGGATGGGAGAAAGAAA[G/T]AAATGTGAAAGAAAGATCATCTTTTATCTTGCTCA K 2 1 2 1 101000 f 74 goat snp34965-scaffold417-1244991 24 55438831 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451929 Affx-122921015 AX-123322262 24 55302143 ACGAACCAGGGACGCAAGCCCTCTTTCAGAAGTCT[C/T]TGGAAACCTGAGCTTTGAACATGCTAGGAGCAACG Y 2 1 2 1 101000 r 74 goat snp34966-scaffold417-1322438 24 55516809 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786185 Affx-122959664 AX-385273221 24 55340685 AAAGAAAGAGTTAGGATTAAGGTAGTGAGACGTTA[C/T]GAGTGACTTGAGTTGGCAAGTGCCTTAGTAATTGT Y 2 1 2 1 101000 r 74 goat snp34967-scaffold417-1360980 24 55556229 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277726 Affx-1111835991 AX-519551224 24 55357106 ACGAGCTTTCTAGAAAGCTGGTGTTGGCGGAGGAG[A/G]TAACCGTTAATTCTCAGCGGAAGCTCTGAGACTGA R 2 1 2 1 101000 r 74 goat Random2.2K-2121 24 55357106 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451278 Affx-122921310 AX-123321611 24 55369589 CATCCCGTGAGGGTGTGTGTGCTTGCTTGCTGGGC[A/G]TGTTGAGGATAACCTTTCCTCAGAGCCACACCCTG R 2 1 2 1 101000 r 74 goat snp34968-scaffold417-1389884 24 55585382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406890 Affx-122955634 AX-123277241 24 55408259 CTTCTCTAAAAATCATTTCCTCTCCCTTAAGAGGC[A/G]TCCATCCTCACTCCCTTTTCCTGATTAAGATGACA R 2 1 2 1 201000 r 74 goat snp34969-scaffold417-1428554 24 55624377 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799209 Affx-122953906 AX-385286139 24 55463927 ATCATTCCCTTCTAGCTCTCATGTACTCAGAAGAC[A/G]TACTCATTTGGTTTTGATGCAACTGGGCAACTCTA R 2 1 2 1 101000 f 74 goat snp34970-scaffold417-1484222 24 55680119 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391585 Affx-122966610 AX-123261942 24 55507505 AGGAGAGGAAACCAGATTGACTTAAGCTGATCACT[A/G]CTGAGGAATCATTAAAATACTCAGTCTTGCATAAT R 2 1 2 1 101000 f 74 goat snp34971-scaffold417-1527800 24 55723646 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396150 Affx-122963387 AX-123266505 24 55558562 CAAGTGATTTCCCCCCCTTTTTATTCAAGGTCCCC[G/T]AACTAATTTTACTAGCATTCATCTTCTAAGTGGAT K 2 1 2 1 201000 r 74 goat snp34972-scaffold417-1578857 24 55775091 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442691 Affx-122927881 AX-123313028 24 55596950 TCTTAGCGTCACTATTGGTGGATCCTGCTCGATGA[C/T]GTTCTGAGATGTACTATGCAGTACACAGCAACACC Y 2 1 2 1 101000 r 74 goat snp34973-scaffold417-1617245 24 55813517 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442885 Affx-122927656 AX-123313222 24 55630046 CTTGACAAAGTTTTCTAATAATATCAAGACTGGTA[C/T]AAAGATTTCCATTATCACCATTTCTGTTTAAGATT Y 2 1 2 1 101000 f 74 goat snp34974-scaffold417-1650341 24 55846586 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273048 Affx-1111833286 AX-186144626 24 55660550 GCGACCCCATAGACGGCAGCCCATCAGGCTCCCCC[A/G]TCCCTGAGATTCTCCAGGCAAGAACACTGGAGTGG R 2 1 2 1 303000 f 74 goat 24_55660550_AF-PAKI 24 55660550 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38410874 Affx-122952601 AX-123281224 24 55666240 TGATGAGCAATGAACAGCTTTTCCTTTCTCATTGG[A/C]GGAGGTCTATACATCAAGTTGAGCTTTCAAGCATA M 2 1 2 1 201000 r 74 goat snp34975-scaffold417-1686535 24 55882520 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784599 Affx-122970177 AX-385271647 24 55699419 TACGCAAAATTGGGAGGAACCCAAGCATTCAGCCC[A/G]TCATACTCTGCAAAACAGATCCCTTAGCTGAACTG R 2 1 2 1 101000 f 74 goat snp34976-scaffold417-1719714 24 55915698 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431151 Affx-122936571 AX-123301492 24 55754006 AAATTTAGGATTTAACAGGCTGTTTCTACAAACTC[A/G]TGGGTCATATTTGAGACCATCTCTGCCGCTTCCTC R 2 1 2 1 201000 f 74 goat snp34977-scaffold417-1774301 24 55969752 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428560 Affx-122938724 AX-123298902 24 55786080 CCAAAGAAAGAGAAGTTTCTTTAGGAAAATTGTCC[A/G]CATCAATCTAGGAACACATCTGATCCTTGACTAAA R 2 1 2 1 101000 r 74 goat snp34978-scaffold417-1806375 24 56001456 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440994 Affx-122928968 AX-123311331 24 55826371 TGAGAATACAGAAAACATATTTGTAGCTATTTCCA[C/T]GTTGATGTTAAGATATGCCGAGGGAGCCTTACAAA Y 2 1 2 1 101000 r 74 goat snp34979-scaffold417-1846666 24 56041452 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382492 Affx-122973822 AX-123252850 24 55863064 GCACCCACGTTCACAGGTAGGAGCTTTCAGCTGCC[A/G]TCTTTGGAGAAAATTCTACCACAGAAGAGCAGGAG R 2 1 2 1 101000 r 74 goat snp34980-scaffold417-1883359 24 56078111 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448300 Affx-122924163 AX-123318636 24 55894858 AAATATTGTCACATAATTTCTTTTTAAAGTCAAAT[A/G]TACTGGGATGCAACTTGTCAATGGGCCAGGTTATA R 2 1 2 1 101000 r 74 goat snp34981-scaffold417-1915153 24 56109867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782688 Affx-122962477 AX-385269760 24 55924490 TGGCCTTTCCAAGTCCACTTGTCAGAATCACATGC[A/G]GTGAGCACATGAGTGCACATACACTCCTCAGTTCC R 2 1 2 1 101000 r 74 goat snp34982-scaffold417-1944785 24 56139498 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413236 Affx-122950242 AX-123283585 24 56009317 AGCTTAATTTTAAACTACCGTGACAAAGTTGAACC[A/G]TGCTTTTAAAACTCAGATTTAAAGTCAGCGATTAT R 2 1 2 1 101000 f 74 goat snp34984-scaffold417-2029612 24 56224229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431206 Affx-122937162 AX-123301547 24 56042050 TCATTAGCCCCTGCTTTTAATTAACTTTTGATGTT[A/G]TTGGTGTCTTTTCCTTCTCGGAAAGAACTAATACA R 2 1 2 1 202000 f 74 goat snp34985-scaffold417-2062345 24 56257067 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438630 Affx-122930916 AX-123308967 24 56147811 TGCTACCGGGAGGGAAGATGGTGAAAGGTAACAAA[C/T]GCTAACTCTAACACTCTAAGTCATTTTTCTTAGAG Y 2 1 2 1 201000 r 74 goat snp34988-scaffold417-2168106 24 56363052 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452170 Affx-122921239 AX-123322503 24 56188812 ATGGGAACTAATCAGAGTGAATAAATAACATTTCT[A/G]TTACTCTCAGACCTAATTCTTTAGGTAGTTCAGCC R 2 1 2 1 101000 r 74 goat snp34989-scaffold417-2209107 24 56403966 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416178 Affx-122948259 AX-123286527 24 56240366 ATCCATTTCCTCATGGAAGTGAAAGTCGCTCAACC[A/G]TGTACTACTCTTTGCAACCCCATGGATACAGGCCA R 2 1 2 1 102000 f 74 goat snp34990-scaffold417-2260661 24 56455593 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437597 Affx-122931862 AX-123307935 24 56276242 AGATGAAGGCTCTCACCTTTATTGAACACAGGACC[A/G]TGGCTTGAGGAAGGCAACCAACATTTCCTCCCCAA R 2 1 2 1 101000 f 74 goat snp34991-scaffold417-2296537 24 56491525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787848 Affx-122929818 AX-385274871 24 56343044 GGACTCACATTTCCGAGTACTCCTTTTGTGCCAGA[C/T]ACTGTATTAGCTGCATTCATTATTCTGTTTAATTC Y 2 1 2 1 101000 f 74 goat snp34993-scaffold417-2363339 24 56558487 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381993 Affx-122974083 AX-123252351 24 56374740 AACAAAAGATGGGGAAGGAAGTGGTTGTGACCAAG[A/G]CACGAGAAAAGGGAAAACTGAGAACAGCCATCTGA R 2 1 2 1 101000 f 74 goat snp34994-scaffold417-2395035 24 56590158 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422966 Affx-122943010 AX-123293312 24 56431737 AAAGTGTTGGTTAATGTATTTGTGGATCTTCCCAA[C/T]GGGATGAATGATCTTCAGAGAGTTTATTGTGGAAA Y 2 1 2 1 101000 f 74 goat snp34995-scaffold417-2452032 24 56647573 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381305 Affx-122974450 AX-123251663 24 56482563 CCTCCCCTCCATGCTCAAGACCAGGGCCACTTTGC[A/G]TGTAGTTTCTGAATGGCTAGGGCATGAAAACAGCT R 2 1 2 1 101000 r 74 goat snp34996-scaffold417-2502858 24 56698976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390822 Affx-122967847 AX-123261179 24 56568488 TTACTAGCACCTTCTGTATGTCTACAGTTTCATTA[C/T]GCTCAGCATGTCATTAAGTCCTCACTTCAGCCGGA Y 2 1 2 1 101000 f 74 goat snp34998-scaffold417-2588783 24 56785857 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430081 Affx-122937540 AX-123300422 24 56610358 AGGGGATTTTTGTGGTCTTCAAGATAGATTCAGAG[C/T]AGTACTGGTTAAGTTACTTGGATAAATTCACTCCC Y 2 1 2 1 101000 f 74 goat snp34999-scaffold417-2630653 24 56826630 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422139 Affx-122943545 AX-123292486 24 56653957 ACGCTCATGCATTGGAGAATTAATACTGTTAAAAC[A/G]TCAACACTTTCCAAAGTGATCTGTGGATTCAACAC R 2 1 2 1 201000 r 74 goat snp35000-scaffold417-2674252 24 56870592 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382304 Affx-122973910 AX-123252662 24 56685362 CAGAATCTCAAGCCAGAAACCAGGAAGTTAACTCA[A/G]AATTCTTTCCTTTCCCCCCAGGTAGCCATACTGGC R 2 1 2 1 101000 f 74 goat snp35001-scaffold417-2705657 24 56902132 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387148 Affx-122970641 AX-123257506 24 56720278 TTGGTTTGGTTAGTGATTCTTTGGCATGCCAGGCT[A/C]AGCATTTGGGTCTCTGGTGTCCTCTGAAGATGTCT M 2 1 2 1 101000 r 74 goat snp35002-scaffold417-2740573 24 56937469 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388011 Affx-122969568 AX-123258369 24 56750115 GTATCAAGAACCTTGAAAATAGTCATGTTCTCTGA[C/T]GTGGTGATTCCTCTTTAAAAAAGGACTCAGGACTT Y 2 1 2 1 101000 f 74 goat snp35003-scaffold417-2770410 24 56967251 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378121 Affx-122977138 AX-123248480 24 56754016 GAGCTGAAAACCCATGCAATGACATGGATGAACCT[C/T]GGAAAATAATGATGAGTACAAGAAGCCAGATGCAA Y 2 1 2 1 201000 r 74 goat snp16324-scaffold172-2780 24 56971170 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274830 Affx-1111834443 AX-519548414 24 56783390 TGGCCTGGCCAGGGTCTGCAGGCGTTGGCTCGGTC[A/G]GGGGATGAGAGTTAATGGGCTTCACAAGTGAAGTC R 2 1 2 1 102000 r 74 goat GoatD01.036174 24 56783390 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38406916 Affx-122955614 AX-123277267 24 56791668 ACATGACTCTTTGAGAGAAGCGCATGAAGTCATTA[C/T]GATGCTTTTTAATGTGTAGCCGATCATGGTGAATA Y 2 1 2 1 101000 f 74 goat snp16325-scaffold172-40432 24 57009023 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419143 Affx-122945750 AX-123289491 24 56828470 GCTCACTGTATCTGGGGCGCTGGGCCACCTTCCCC[A/G]TCAAAGCCTTCTCTCCTGGTTTTACACTTTAACCA R 2 1 2 1 101000 r 74 goat snp16326-scaffold172-77234 24 57045711 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781478 Affx-122973306 AX-385268563 24 56886101 TGGATCAGCTCGATGAGATAATGGTCGTAAAATGC[A/G]AGCTTCCCATCGGCGAACGTATTCCAGCTAAAATC R 2 1 2 1 101000 r 74 goat snp16327-scaffold172-134865 24 57103216 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428206 Affx-122939451 AX-123298549 24 56930686 GGCCTACCTTACACATCCCTGTGAAGCTCCTTAGC[A/G]GAGTACACAGTAGCTCAGACTCAAGTAACCATTCG R 2 1 2 1 101000 r 74 goat snp16328-scaffold172-179450 24 57146289 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797136 Affx-122924477 AX-385284076 24 56964812 CCTGGTGCAAATACACACCTATGTTTGCTAAGTGA[A/C]CATGGAGTGATGCTCATTTCCCGAACTGTCTAGGA M 2 1 2 1 101000 f 74 goat snp16329-scaffold172-213576 24 57180352 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435296 Affx-122934031 AX-123305636 24 57041493 GAAGATCAAGTGGGGAAATTTGTAAGAAACTAGAA[C/T]AGTGCCTAGCCAGTTGTAAGCACTAAATAAATGAT Y 2 1 2 1 101000 f 74 goat snp16331-scaffold172-290257 24 57255218 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426508 Affx-122940211 AX-123296854 24 57054416 ACAGTTGGGCTTCCATCTCCAGAAGATTCTGATCT[A/G]CTGATCCTGGGGTTGGCTTGGACACTAGAACTTTG R 2 1 2 1 101000 f 74 goat snp15071-scaffold1610-275361 24 57269677 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417651 Affx-122946844 AX-123287999 24 57089543 TCTCTCCCGCCTTGGTATGTCTCCTTCCCACTGCA[C/T]GCGTGCAGCCAGAGAACTCTCATCTTGGGCTGTTG Y 2 1 2 1 101000 r 74 goat snp15070-scaffold1610-240234 24 57304845 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401254 Affx-122959296 AX-123271607 24 57134439 GAGCTGGTAATACATAGTAATGGCAACACTTGAAA[C/T]GATGAGGAATGAGGTCCTCACAAACGGAAATCAAC Y 2 1 2 1 101000 f 74 goat snp15069-scaffold1610-195338 24 57349358 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453530 Affx-122919797 AX-123323863 24 57163162 GAAACCACTTCCTGTGTTTGGGGATTCCCACAGCC[C/T]GAGTTCCGGGGCCAGCTGGGGCCATCCCCCAAGAC Y 2 1 2 1 101000 f 74 goat snp15068-scaffold1610-166615 24 57377968 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395177 Affx-122964104 AX-123265532 24 57202757 CTTGGACTCAACAACAACATGAACACCTCCAAATG[C/T]CTGTCACCCTCGTCTGGCACACTGTCCCAGGTCTG Y 2 1 2 1 101000 f 74 goat snp15067-scaffold1610-127020 24 57417651 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403038 Affx-122958545 AX-123273391 24 57239502 CGGTTGAGAGACAATAAAAGGTGCTTTGAAGACAC[A/G]TTGCGAAGTCCCCTGTAAGGTAACCGCCCTCATCA R 2 1 2 1 101000 f 74 goat snp15066-scaffold1610-90275 24 57454593 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776964 Affx-122934262 AX-385264088 24 57281963 TGGCATATTTTAAAAGGATGCTGTGTCTATTCATA[C/T]GTACAAAGACTGGGAGATCAGCACACATTTATAAT Y 2 1 2 1 101000 r 74 goat snp15065-scaffold1610-47814 24 57497143 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449062 Affx-122923051 AX-123319397 24 57313665 ACTAGAAATACTGAATCCAACAGTAGAAGGATCTT[A/G]CTTTTATTAAGACAATGGTTTCACCACTTGTAGTC R 2 1 2 1 101000 r 74 goat snp15064-scaffold1610-16112 24 57528734 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787731 Affx-122941616 AX-385274754 24 57331378 CTGTTGTAAAAAGTACTATACCAAAGGCAAACTCC[A/G]TGCCAACAGTGGATGCTACGCATTCACATAATAAA R 2 1 2 1 101000 r 74 goat snp58240-scaffold944-668778 24 57545935 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386186 Affx-122971370 AX-123256544 24 57363096 TGGCTTTAAATTTCTTTTCATAAACTAACAAGTCA[A/G]CAAGAACAAATCCATGTTTTGCTTTATTCTTTGCA R 2 1 2 1 201000 f 74 goat snp58239-scaffold944-637060 24 57577497 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773241 Affx-122937341 AX-385260384 24 57399631 GGGGTAAGAACACGTTCCTTATTTCTCAAAGCAAA[C/T]AGGTTTTAGAATCCCTAAACTAAATATCCTTTTCC Y 2 1 2 1 101000 f 74 goat snp58238-scaffold944-600525 24 57614275 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788825 Affx-122960923 AX-385275840 24 57455197 GCCTCCCAATCAGAACATTCATTTTAAGTCCGATA[C/T]AATTATTAACACCCTTTACACGTCCATATTTGCTG Y 2 1 2 1 101000 f 74 goat snp58237-scaffold944-544959 24 57669785 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382151 Affx-122974041 AX-123252509 24 57483801 AGTCCGACAGTCTTAAATGACAAGTTTCCCAAGGA[A/C]TGTATTTCAAAGTGTTGCCCCAGCCCATGGTACTC M 2 1 2 1 101000 f 74 goat snp58236-scaffold944-516355 24 57698418 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391011 Affx-122966888 AX-123261368 24 57560766 AGGTACCCACTGTTCTAAGGTGAAAGGATTCGCCT[C/T]GCAAAGTACAGGCCTATCTCCTGGGGGAAGAAGAC Y 2 1 2 1 101000 f 74 goat snp58234-scaffold944-439390 24 57775467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404486 Affx-122956720 AX-123274838 24 57615765 GATGTGTTTCAGAGAGCAGTGTTTGATAGGCAGCC[A/G]TTCCACATTGCCTGACAGGATTAACTACACCAAGA R 2 1 2 1 201000 r 74 goat snp58233-scaffold944-384391 24 57829818 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395358 Affx-122963989 AX-123265713 24 57694342 GACAGGGCCACGCCACTGGATGCTCAACCTTTCTT[A/G]TGTGCCAGCTCATTCTTTCCTGGGACAGGACTTGG R 2 1 2 1 101000 f 74 goat snp58231-scaffold944-305814 24 57908842 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445339 Affx-122926393 AX-123315676 24 57729942 GGCAATCGAAATCCTGCTTCTAAGACTGGCAGAAA[C/T]GTTGTCAGTGATAGGGTTCAGTGCCAAGAGAGACT Y 2 1 2 1 101000 f 74 goat snp58230-scaffold944-270214 24 57944475 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393039 Affx-122965631 AX-123263396 24 57813682 TGGAGATAACATTCTAGAATCATCACAATAATAAA[C/T]GGAATTCTAAATTCCTCACTGATACACTTAAAAAG Y 2 1 2 1 102000 f 74 goat snp58228-scaffold944-186474 24 58028980 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777506 Affx-122975156 AX-385264625 24 57869384 TTAAATCTGTCACAGATGGAACTCAACAAATACTT[A/G]CTGAGTAAATACCTGCTCTCAAAGAAGTTAAAATC R 2 1 2 1 101000 f 74 goat snp58227-scaffold944-130772 24 58085123 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400058 Affx-122960768 AX-123270413 24 57918299 GAAGTCTGTGGGGCAGTGGGTTCTGATTTCAGATG[C/T]GCTGTTAACTACCTGCTGAACCCCACCTCCACCCG Y 2 1 2 1 201000 r 74 goat snp58226-scaffold944-81857 24 58134109 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277728 Affx-1111835992 AX-519551227 24 57927401 AAATTAAAACCACAATGAGATCGCATTTCACACCC[A/G]CTAGGATGGCTATTACAAAGCAGAAAGTCAAATGT R 2 1 2 1 101000 r 74 goat Random2.2K-2124 24 57927401 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390357 Affx-122967682 AX-123260714 24 57951903 ATTTGTTCTTTGTGGAACATGATCTAGGCAGGTTT[C/T]CTGTGTTTTCAAAGAAATAAGCAGGGATTGGTTTC Y 2 1 2 1 101000 f 74 goat snp58225-scaffold944-48253 24 58167645 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772112 Affx-122965406 AX-385259268 24 57985571 CCTCTAAATAACTATGTCTGTAGAAAAACACTGTT[G/T]CTGGTCTCCTTTCTCTTAATTCCTTCCACATGAAA K 2 1 2 1 101000 f 74 goat snp58224-scaffold944-14585 24 58201355 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421424 Affx-122943961 AX-123291771 24 58015760 CTCATCGCTCCAAAAGCACTGCCAGCTTCAGGTCC[G/T]CGGAAGGAGGGGCCCTGTCTTCCTACCCCAGAGAC K 2 1 2 1 101000 f 74 goat snp6586-scaffold1234-449254 24 58230715 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396074 Affx-122963439 AX-123266429 24 58048567 CTTCAAATCTGATGCGTGTTCCCTGGCACTTACCC[A/G]TCTGAGACATGGCAGTCACGTCCTCTTCAGTGCAG R 2 1 2 1 101000 f 74 goat snp6585-scaffold1234-416447 24 58263534 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452106 Affx-122920842 AX-123322439 24 58080033 TTCTTAGCCTTTGACCTAATAATTCCACCAGGAAA[C/T]AGGTTCCCAAGGAAATAAATACAGAAGAGGAGAAA Y 2 1 2 1 201000 f 74 goat snp6584-scaffold1234-384981 24 58294335 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795155 Affx-122927103 AX-385282112 24 58119507 GGCTTTCTATTGGTCTCTTATGTTTTCTCAGTTTA[C/T]AGACATTAAAAGAAAGGACTTTCTGATCATGTTTG Y 2 1 2 1 102000 r 74 goat snp6583-scaffold1234-345507 24 58328796 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801204 Affx-122945930 AX-385288117 24 58148409 GGGCCATAACAGCAACAATGCACCGCTGTCTCAAA[C/T]GGCTTTATTAGTAAAAAGCAGCAGAGCTAACAGCC Y 2 1 2 1 101000 r 74 goat snp6582-scaffold1234-316605 24 58357128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400792 Affx-122959825 AX-123271147 24 58183857 GTCAACTCCTGTTTAAACCACATTTGTTTTAAGCC[A/G]CTGTGAATAAGGCTTTTCTTACAGCCAGATAAACC R 2 1 2 1 201000 f 74 goat snp6581-scaffold1234-281157 24 58393366 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417386 Affx-122947698 AX-123287734 24 58213164 AACCAGACGGTAACTGTCCCAGGAGGGGAATTACC[A/G]TTTTGACTCTGGAGCATTTGCAGGAGGCAGATGTG R 2 1 2 1 101000 r 74 goat snp6580-scaffold1234-251850 24 58422390 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438732 Affx-122930836 AX-123309069 24 58248051 AAGGATAAGACTTATTTTCAGGGACTTCCCTGATC[A/G]TCTGATGGTTAAGACTTCAAGCTTCCACTGCAGGG R 2 1 2 1 201000 f 74 goat snp6579-scaffold1234-216963 24 58457034 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399595 Affx-122961101 AX-123269950 24 58277182 TCTTCACCGAAACTCTTGGTTTATCAGCAGCTACA[A/G]ACTAAGCCCAGGTTGCTGCCTGGGGCTCTCAGTAC R 2 1 2 1 101000 f 74 goat snp6578-scaffold1234-187832 24 58485706 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394145 Affx-122965316 AX-123264500 24 58332462 ATTTATTAATATTTAGTATAATTCTATGCTTTTAA[C/T]ATGTTCACAATGTCTCTGCATTTTAAAGAAACCAA Y 2 1 2 1 201000 f 74 goat snp6577-scaffold1234-132552 24 58542712 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767513 Affx-122947453 AX-385254775 24 58364304 TTCCAGGGACTTCTAATTTCTGAATTAGGTACTCA[C/T]ATTATCTTAAAAATTGGCAAACTGTCAAAAAGGGG Y 2 1 2 1 101000 f 74 goat snp6576-scaffold1234-100710 24 58574805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781749 Affx-122921022 AX-385268831 24 58405084 AACTTGCTTTGGAATCTAGGTAATGCCTAATTTTC[C/T]GAATCAGTGGTTTGTGCCCCTGGTTCATACATACA Y 2 1 2 1 101000 r 74 goat snp6575-scaffold1234-59930 24 58622476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412254 Affx-122950899 AX-123282603 24 58449024 GACTCTCTGGAGGAGCCTGGAGTCCACTGCTAGTT[A/G]TCAGGGCCATACGCTGTTCCCAAAATCCTCCTGAA R 2 1 2 1 201000 r 74 goat snp6574-scaffold1234-15990 24 58666302 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422430 Affx-122943360 AX-123292776 24 58484081 GTGAAGGGGCGAGAGGCACTGGTCACTTCCAAGGC[A/G]TCTGTCTTGGTTATGGAAAAGTACTACGCCTTCAT R 2 1 2 1 101000 r 74 goat snp42033-scaffold5486-18968 24 58700965 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439685 Affx-122930579 AX-123310022 24 58487747 ACAGTGATGCCACGTAATCTGTTCCGCTCGTTTAC[A/G]TTTTGCCCCGGATACCACCTCTGCCAAGACAACCG R 2 1 2 1 101000 f 74 goat snp22065-scaffold2174-224728 24 58704670 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381370 Affx-122974398 AX-123251728 24 58544798 TTCTTCGTGGATTTATTATTATTACTGCTTTGTCC[A/G]TTTATGTGCTACAGAAACTTTGGATGAGAAGATAC R 2 1 2 1 201000 r 74 goat snp22064-scaffold2174-167677 24 58761858 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387453 Affx-122970372 AX-123257811 24 58598439 TCAGGGAAGCTGACAGGTCTATATGGAAACCATCA[C/T]GGACAGCGGTATGCTGAAAAGTTAACAATTGTACA Y 2 1 2 1 101000 f 74 goat snp22063-scaffold2174-114036 24 58815585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421033 Affx-122944535 AX-123291380 24 58631583 AGAAATTTGCCTGGTATAGGTCTTTTAATGTGTTC[G/T]TGATTCACTTTGCTGTTTTGACTGAATGTCCCTCT K 2 1 2 1 201000 f 74 goat snp22062-scaffold2174-80892 24 58848402 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410226 Affx-122952555 AX-123280576 24 58707800 TATATTCTTTACACATTTTAGAATCAGTTGCTAAC[A/G]TGTATTTACCTCATTAGATTTTAGGAAGAAACAAG R 2 1 2 1 101000 r 74 goat snp22061-scaffold2174-4675 24 58924145 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418420 Affx-122946535 AX-123288768 24 58719729 ACAGACTTGTCAGGTATAAAATGATGTCTCATCTT[A/G]CTATTCAAGTTATATTTTAAATTCTAGCTCCTCAT R 2 1 2 1 101000 f 74 goat snp58828-scaffold960-1339903 24 59218782 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399232 Affx-122960588 AX-123269587 24 58762821 ATTGTGATTTAGTTGGTCTAGGCTGTGGCCTGGAC[G/T]TTGGGATCTTATAAATATCCTCAGGCAATTCTAAT K 2 1 2 1 101000 r 74 goat snp58827-scaffold960-1296811 24 59262205 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780700 Affx-122973226 AX-385267790 24 58796552 TCTAGTAGACAGTATAATCTCAAACTTCTCAACTA[C/T]GTCTTTCACCAAAATGATGCTAGGCACAAGTGGAA Y 2 1 2 1 101000 r 74 goat snp58826-scaffold960-1263080 24 59296549 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417974 Affx-122946687 AX-123288322 24 58832432 CTAAGTGACTCAGTGCAGCCAGGCTCATGGGATGC[A/G]TCCATTGGCTTCCACCAAGCAGCACCAATCCACGA R 2 1 2 1 101000 r 74 goat snp58825-scaffold960-1227200 24 59332634 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791091 Affx-122944721 AX-385278086 24 58875291 GGTTTTGCCTACAGAAGTAGATGAGTGATACTAAC[A/G]ATAATCAAAACTCACACCTATATAATATTTACTAT R 2 1 2 1 101000 f 74 goat snp58824-scaffold960-1184341 24 59375743 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453117 Affx-122920018 AX-123323450 24 58907653 CTCTTCTTTTTCTTGAATTGCAAGATAAATCACCA[C/T]AACTCTCGTAGGAGACAGGTAACTCTCTAATACTT Y 2 1 2 1 101000 f 74 goat snp58823-scaffold960-1151979 24 59408238 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798416 Affx-122970730 AX-385285350 24 58946289 CCACTCATTCTCTCACTTACTTGATAAAAAATTAA[C/T]AACTAATTGATTACTAAGTGCTATTTACCATTCTA Y 2 1 2 1 101000 f 74 goat snp58822-scaffold960-1113343 24 59447267 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402643 Affx-122958387 AX-123272996 24 58989582 GCCAGTTGAAAAGAGGCTTTTCTCAAAAGACATGC[A/G]TTGCCACAGCATAACAAAGGCTAAACCTGTGTGCG R 2 1 2 1 101000 f 74 goat snp58821-scaffold960-1070050 24 59490376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796989 Affx-122961312 AX-385283930 24 59085437 AGTTGAACTGAGGATTGTTGAATTACTTTGGATTT[A/G]TAATTTCAGATGCTTCAAAATACGCGCGTCCCTTG R 2 1 2 1 201000 f 74 goat snp58819-scaffold960-974195 24 59587282 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453753 Affx-122919607 AX-123324086 24 59142798 TGAGTGCCTACACTTGCCTAGGCACTCTCATCGTG[A/C]GTAAAACACTCTGAACTCCTGAAATAGGTGGGACC M 2 1 2 1 101000 r 74 goat snp58818-scaffold960-916834 24 59645061 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414970 Affx-122949065 AX-123285319 24 59182403 ATCTGGTGGTTTTGTTTCTAAAACATAGTTTTACT[C/T]CACTGCTAAGAAAATTATCTTAGAAAGGTGCTTTC Y 2 1 2 1 101000 f 74 goat snp58817-scaffold960-877229 24 59685017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395703 Affx-122963727 AX-123266058 24 59231627 AAGAGTTGGACACAACTGAAGCAACTTAGCATGCA[C/T]GCACACAGACATACAGTGAAATTAATAGTCTCTCT Y 2 1 2 1 303000 r 74 goat snp58816-scaffold960-828005 24 59734069 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775504 Affx-122965768 AX-385262635 24 59271693 ATAGCGTGGGAGCTGATGGAATAATATCCAAAGAA[C/T]AAGACCTAAACATACGTCCTTTACTTAAACATTCC Y 2 1 2 1 101000 f 74 goat snp58815-scaffold960-787939 24 59774348 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798930 Affx-122955226 AX-385285860 24 59327106 CCCTTACTATGGGATAGAAATCTTTTTATGAGAAA[G/T]AAAATGAAAATTTGAAAAGGGTTAAATAATAACAC K 2 1 2 1 303000 r 74 goat snp58814-scaffold960-732526 24 59830666 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786925 Affx-122964814 AX-385273954 24 59372409 ATATTAGACGGGTTTAGAATAGTAATCTTATATCA[A/G]TCTTGCCTTAGTAAGTTTTATTTTCCATTTGTTAA R 2 1 2 1 101000 r 74 goat snp58813-scaffold960-687223 24 59876409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409025 Affx-122953869 AX-123279376 24 59401608 TCAGCTTGGGTTCCTTTATGATAGGAAGAAAATGA[C/T]GGGACAAGTGACAAAAATGACCCATCAGAGGCATG Y 2 1 2 1 101000 f 74 goat snp58812-scaffold960-658024 24 59905824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427981 Affx-122939181 AX-123298324 24 59436477 GCAGATGAGGGATCTCAATCTTTCCTGTTTTTAAA[C/T]GTGGCAATGGTAGTTGCTCATTAGCAGAGTTGAGG Y 2 1 2 1 201000 f 74 goat snp58811-scaffold960-623155 24 59940802 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771391 Affx-122937547 AX-385258549 24 59477591 GACCCATGTATACATTAAACTTGTAAAACTCTAAC[A/G]TTTATAGTTGACTTAATTGATAAAGGAACTAATAA R 2 1 2 1 201000 r 74 goat snp58810-scaffold960-582041 24 59982116 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409258 Affx-122953132 AX-123279609 24 59521603 TTTAGGCTAATAAATCTCAGTCACAAATTAATCTC[G/T]CACAGAATGAAAAAAGGAAGATCACAACAGGAAAA K 2 1 2 1 101000 f 74 goat snp58809-scaffold960-538029 24 60026051 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798356 Affx-122919609 AX-385285291 24 59563401 AAAAGGGCATACTTCTTTACACGGCAAAAACAGAA[C/T]GGATTTATTATAGAATCTGTAGGAAATGCTCATTA Y 2 1 2 1 101000 f 74 goat snp58808-scaffold960-496231 24 60067963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451587 Affx-122921648 AX-123321920 24 59597270 AGCATATCTCTGAATGACTCCACAGAGCAGTCCTG[A/C]TTCACTTTATAATTGTTATAAAAGAGAAATACACT M 2 1 2 1 201000 r 74 goat snp13599-scaffold1525-1942437 24 60104041 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452945 Affx-122920177 AX-123323278 24 59636380 TGGAGAAGTGATTAAATTTCTTTTTCTTTATAGTT[A/G]CAGAGGTGAAATAGGGTAAGTTCTATTAGAAAGCA R 2 1 2 1 101000 r 74 goat snp13598-scaffold1525-1903327 24 60143290 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381988 Affx-122974088 AX-123252346 24 59714349 GCCTACGGAGAGTGCTTAGTAAGTAACAGGAGGCT[A/G]GAGAGCTTTGCTGCTCAGGGGATGGTCCTGGTTCC R 2 1 2 1 101000 f 74 goat snp13596-scaffold1525-1825358 24 60220646 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405858 Affx-122955856 AX-123276210 24 59745394 GGGTTGGGTATGGTGTGGGCGCCAGCCTGACATGC[A/G]TTAATCACGTGGCCGTTCCAGGCACAGTTCAGATG R 2 1 2 1 101000 r 74 goat snp13595-scaffold1525-1794313 24 60251280 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448465 Affx-122923632 AX-123318801 24 59804159 CCATGAAGACAGTGAAAAAACTGAGCCTGGAGAAA[C/T]ATCACCCCTTAGAAATTAATTTTTATTTTCTTTAG Y 2 1 2 1 101000 r 74 goat snp13593-scaffold1525-1735548 24 60317600 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780297 Affx-122928668 AX-385267392 24 59839234 GAGGAAATTCGGGGTGAGAAAGGGTCTTCTTGTTA[C/T]GCGCTAAGAGTTGTTTCCTGAGTAGCTCTCTTCCT Y 2 1 2 1 101000 r 74 goat snp13592-scaffold1525-1700473 24 60352643 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386366 Affx-122970853 AX-123256724 24 59869519 GTAAGTGCATACACATTCCTTGGCCTTGGTGGAGA[C/T]TGTGGTTAACTGGAAAGCCTGCTTCTCGTAAGGGA Y 2 1 2 1 201000 r 74 goat snp13591-scaffold1525-1670188 24 60382918 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391030 Affx-122966873 AX-123261387 24 59950722 AACCTGGTGAAAAGTCTAGATAATTCTTTATTTTC[C/T]TACAATTTATAATTTGTTGCTTTTTCTAACACTTA Y 2 1 2 1 101000 r 74 goat snp13589-scaffold1525-1588985 24 60462712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391303 Affx-122967335 AX-123261660 24 59996787 GCAGATTTCGGTGGCTTGAAATTTATTTTCTCACC[A/G]TTCGGGAGGCCAGAAGTCCGAGGCAGGGTGTCCAC R 2 1 2 1 201000 r 74 goat snp13588-scaffold1525-1542920 24 60508090 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382529 Affx-122973795 AX-123252887 24 60032392 GCGGTCCTGGGTTAGTTTCCGCATTGAGGTGGGGC[C/T]CCATGACTGGTTCTCACCAAGAGGACGTGTGTGCG Y 2 1 2 1 201000 f 74 goat snp13587-scaffold1525-1507315 24 60543221 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799447 Affx-122929696 AX-385286377 24 60069365 AGAGGCTGGCTAACCACTGGGGACGCATGATTGAT[A/G]TGAGGCCTAAACTAAGTGACTTCGAAGGTCAGAGG R 2 1 2 1 101000 f 74 goat snp13586-scaffold1525-1470342 24 60580230 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395070 Affx-122964185 AX-123265425 24 60102154 GCTTCATGTAAATGGAATCTTGTCAGTATAGACTC[A/G]CTGTTTCACCCAGTGGTGGCCACTTGAGATTCGTC R 2 1 2 1 101000 f 74 goat snp13585-scaffold1525-1437553 24 60613779 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429800 Affx-122938198 AX-123300141 24 60137790 CAATCAGTTCAAGACAGAAAATCCATATGCGGTTT[A/G]TCAGTGTGAGATGCTGTTTGCATCTCTGTGCTGTC R 2 1 2 1 201000 f 74 goat snp13584-scaffold1525-1401917 24 60649760 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795511 Affx-122973509 AX-385282466 24 60166890 GGGAGAGAGTTCAGAAAGACAGGTGATGTCACTTA[C/T]GGTTTTGACTGAGGTTACTGTAAGGAATTAGGAAT Y 2 1 2 1 101000 f 74 goat snp13583-scaffold1525-1372817 24 60678782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433935 Affx-122934291 AX-123304276 24 60292201 AATCAGAAGATGTGTATATGACTATTTTTTTGGTC[A/G]TCAGCAATGCTGATCTGCAAACATTTCTGTGCAAC R 2 1 2 1 102000 f 74 goat snp13581-scaffold1525-1247506 24 60806226 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787403 Affx-122950030 AX-385274428 24 60337603 GGGGGAGTGGTCAGAAATACTACATAGGAATTATT[A/G]TGTCATAATTTCTACAAATGCTTTATCTTGAGTTC R 2 1 2 1 101000 f 74 goat snp13580-scaffold1525-1202104 24 60851737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796290 Affx-122933987 AX-385283240 24 60371709 TGGCTCTATGAAAAGAACACTAGGTCAGGGCTAGA[C/T]GAAAGGTAAACAGAGCATTCTTATGTAGCATGAAG Y 2 1 2 1 201000 r 74 goat snp13579-scaffold1525-1167998 24 60886235 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422163 Affx-122943530 AX-123292509 24 60438157 TCCCTGAAGAGCAGAAAGCGCATGACGGTGACTAG[C/T]GGGGCGCTGGTTTCAGTGGCTGCCCGAGTCCAGGA Y 2 1 2 1 101000 f 74 goat snp13578-scaffold1525-1101550 24 60953918 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450680 Affx-122921906 AX-123321014 24 60485944 TCTACATCTCAGGTGTGTAGCTTCTGTTTCAAACC[A/G]TGACGATGAACTTCCTGGCAATTCGTCAACCCTGG R 2 1 2 1 101000 f 74 goat snp13577-scaffold1525-1053763 24 61003049 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446624 Affx-122924793 AX-123316960 24 60518416 GATACAGGAATGACCTTTCTCTAGCCTTCCAAGCC[A/G]CCTTTTTCTCTCTTCTCTTTCTGCTCCAGCCATAA R 2 1 2 1 101000 f 74 goat snp13576-scaffold1525-1021291 24 61035970 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781279 Affx-122965752 AX-385268364 24 60591341 CTTTCTGCTCAGAAAAACAACTGCAGGTTCTTTAC[C/T]GTCTTCACGGGTGTTACTTTTCACCATTTGGGGGC Y 2 1 2 1 101000 f 74 goat snp13575-scaffold1525-948366 24 61109852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770854 Affx-122930892 AX-385258018 24 60652700 GGAGGAGGTCAATTTCTCGCTCATTTGGAGCCTTC[C/T]GTCTCTAATGAATTCGTCTCTCAAGCTCAGGTGAA Y 2 1 2 1 101000 f 74 goat snp13574-scaffold1525-887007 24 61170718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382029 Affx-122974952 AX-123252387 24 60684865 GGTCTGAGGTCAGGGTGCCAGCACCCTTGGGTTCT[A/G]CTCAGGGCCCTCTTTCAGGGGCAGATAGCCACGTT R 2 1 2 1 201000 f 74 goat snp13573-scaffold1525-854842 24 61203140 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793504 Affx-122965536 AX-385280481 24 60772871 GATTTTAAACTCGAGATTGGTGTTTTTAAACATAT[A/G]AGATATAGCAAGCTTTAACTACAATTTACGGTGAC R 2 1 2 1 101000 r 74 goat snp13571-scaffold1525-766836 24 61291762 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401556 Affx-122958899 AX-123271909 24 60814668 ACGGACCAAGATGCACTGAGATGAAGACAGAGAAC[C/T]GAGGCAGAGCTGAGGAGTCTCATTTCCCAGGGGGA Y 2 1 2 1 101000 f 74 goat snp13570-scaffold1525-725039 24 61334678 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440975 Affx-122928985 AX-123311312 24 60853806 TTATGTCATGAAAACATGCTTAGACGTGAAAAGCT[G/T]AAAAGCTCGTATCACAAACAGAGCAGGCATATCTG K 2 1 2 1 101000 f 74 goat snp13569-scaffold1525-685901 24 61374291 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416131 Affx-122948293 AX-123286480 24 60952047 CGAATTCCAAGAGGAATCAGTTCTTAGAGCATCAA[A/C]GATCTCTCACTGACAGGTGGTCTGGAGGTGGGAAG M 2 1 2 1 101000 f 74 goat snp13568-scaffold1525-587660 24 61472729 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413087 Affx-122950953 AX-123283436 24 60988901 TGAAAAATTTACGTATCAACCAAAACTGTGTGAGC[A/G]GTATCTAGCTTTAACTATTCTATGAGCTCCAGGAG R 2 1 2 1 101000 r 74 goat snp13567-scaffold1525-550806 24 61510393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792790 Affx-122970901 AX-385279769 24 61020458 GCCTCTGCCAGCAGAGCCGAGTCTTCAATTCAGCA[C/T]GTCCTTCATTTGAGCAGGTACTGTGACTGAAAGCG Y 2 1 2 1 101000 f 74 goat snp13566-scaffold1525-519249 24 61541989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801651 Affx-122941699 AX-385288559 24 61050539 AAAATGACGTGTTCCTGTTTTTCTCATGTAGTTGA[C/T]GCTGAGTTTCAGATTATTATCGTATGTAGATTCCA Y 2 1 2 1 101000 f 74 goat snp13565-scaffold1525-489168 24 61570354 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784668 Affx-122923726 AX-385271716 24 61120319 AAGTGATAACTGCCAGTTCTTGAAAAGGGACTGTT[A/G]GTATAATATCCTTTTTGCAAAAATCAGGAAACGTT R 2 1 2 1 101000 f 74 goat snp13564-scaffold1525-419388 24 61640598 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389619 Affx-122968753 AX-123259977 24 61152550 CCGAGGCGTCGACTTCTTTCTAAAGATCAGGCTTC[A/G]GTTTTTCTTCATTTCCGGAGCCCATGCTTTCCTCC R 2 1 2 1 101000 r 74 goat snp13563-scaffold1525-387157 24 61673090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411358 Affx-122952252 AX-123281708 24 61266038 GACAAGGCTTTATTTTTATCATTTTTTAGGAAGTA[G/T]TATTTTCACAGTAGATGTTTTGGCCCTTGTTTCAA K 2 1 2 1 101000 r 74 goat snp13560-scaffold1525-273669 24 61779243 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409947 Affx-122952862 AX-123280298 24 61337453 ACTGTCTGCCCAGCTCCGAGCTGCGACTCGGAACC[G/T]CACTTCAGGAATATGAATCTAGCAGTCTGAAAGCT K 2 1 2 1 101000 r 74 goat snp13558-scaffold1525-202254 24 61850461 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403972 Affx-122957435 AX-123274324 24 61371396 GCTGTTCTGTGTTTGTCCGAGAAAGAGGAAGCTGC[A/G]TCCAGCAGCACCCAGGGGTGGCGAAAATGCAGAAG R 2 1 2 1 101000 f 74 goat snp13557-scaffold1525-168311 24 61884440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432007 Affx-122935927 AX-123302348 24 61409017 CAGCGCTGCAAAGAACAGAGCAGTGTTTCTAATTA[C/T]AATGCTTCTTAAAAACGCAAAAGGCTAAATCCCAT Y 2 1 2 1 101000 r 74 goat snp13556-scaffold1525-130690 24 61922241 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446402 Affx-122925574 AX-123316738 24 61441248 GCGGCAGAAACCAACAGAACATTATAAAGCAATTA[G/T]CATCTAATTTTAACAAATGAAGGCTAAAAAGACCA K 2 1 2 1 201000 r 74 goat snp13555-scaffold1525-98459 24 61955175 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379005 Affx-122976378 AX-123249364 24 61476967 GTAACGTTCTGAAGTCTCACGGCGTGATGTATCCC[A/G]TCCTTATTTGGCACTACTTTTTTCTATAGCCCTGT R 2 1 2 1 101000 r 74 goat snp13554-scaffold1525-62740 24 61990887 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421508 Affx-122943897 AX-123291855 24 61568616 TTAGATGCAGAACCAATGAATTTTTAGTAGTTGAC[A/G]TTTTTACCTGAAATTAAAATATGGATAATTTTGCT R 2 1 2 1 101000 f 74 goat snp17701-scaffold1838-25056 24 62111118 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437696 Affx-122931761 AX-123308034 24 61641110 AGGGTCCTAAGGAGAGCCCAACTTGGGAGCAAGTC[G/T]ATAATGCAGGTGCCTCTGTGAGAACACAGAGGGGC K 2 1 2 1 101000 r 74 goat snp17703-scaffold1838-97550 24 62183245 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429969 Affx-122938062 AX-123300310 24 61693109 TCATCCAAAAAGCCAATGTCTGTTTAAATTTCTCC[A/G]CTCGACTCTCCATTTTCTCCTTTTATAACTGGCCA R 2 1 2 1 201000 f 74 goat snp17704-scaffold1838-149549 NW_017191228.1 7397 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274510 Affx-1111834235 AX-519548101 24 61736337 CTCGCTGCAGCGGAGCCTGAGGGGGCAGCCCCTCC[A/G]GCGTCCTGAGTCTGGAGCCAGAGCTGCAGGCGCCT R 2 1 2 1 303000 r 74 goat GoatD01.026848 24 61736337 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320763995 Affx-986698523 AX-385251775 24 62065794 GGATGTGGAATTACTGGCCTGGTAATCATCTGGTC[C/T]GGAGAAGGCAATGGCGCCCCACTCCAGCACTCTTG Y 2 1 2 1 600010 f 74 goat 24_62065794 24 62065794 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 320763997 Affx-986698525 AX-385251777 24 62066291 GTTCTTGAACAACACATCTCCCGAAAAAGAAACGA[C/T]AATACCGTGATGAGAGAGCAGCGCCGGTGCAAGCT Y 2 1 2 1 600010 f 74 goat 24_62066291 24 62066291 Ancestral_priority_1043 ancestry 0.652 recommended IMAGE 10K 10K ancestral 320803622 Affx-986696431 AX-385290408 24 62067161 TATCATCTGTCTCATCTCTTTAGAGACTCAGTTCG[G/T]GTCCCGTGTCTGACCTCTGGACGCTGATATTTAAG K 2 1 2 1 600010 f 74 goat 24_62067161 24 62067161 Ancestral_priority_1043 ancestry 0.672 recommended IMAGE 10K 10K ancestral 320767430 Affx-986698531 AX-385254703 24 62301444 AATGTCTGAATTGCAGGGTTTCGCTTTTGCTTACC[A/G]TTGGCTTTACTAACATTCCATAATGTCATGTGTCT R 2 1 2 1 600010 r 74 goat 24_62301444 24 62301444 Ancestral_priority_1043 ancestry 0.712 recommended IMAGE 10K 10K ancestral 320764005 Affx-986698533 AX-385251785 24 62302704 TTGGTAGAATCCAGCTTGCCATGATTCATAGAGGA[C/T]GCGCTAATACTGTGGAGAAAGAAACTCTCACATCA Y 2 1 2 1 600010 f 74 goat 24_62302704 24 62302704 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 38388347 Affx-122969348 AX-123258705 24 CTACTAACACAAATTATATGTATATCTAAATATAA[C/T]ATGTATCCTAAATGAGAGGAATTAACAAGGATACC Y 2 1 2 1 303000 f 74 goat snp35530-scaffold428-1260556 NW_017189517.1 48461606 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403806 Affx-122957965 AX-123274158 25 81587 TGGGTACAGTCCATGGGGTCGCAGAGAGTTGGGCA[C/T]GACTTCACTTTCATCGATGACTTACAATATTCTAT Y 2 1 2 1 101000 r 74 goat snp22157-scaffold2188-447543 25 82419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386757 Affx-122970128 AX-123257115 25 127928 TCCTCTCTGGTCTCCAGGCCCCGGCACGGCTTCCC[A/G]GGCAGAGCGAGCCATCGAGAGGTTTTGAAGAAAGG R 2 1 2 1 101000 r 74 goat snp22156-scaffold2188-401202 25 121322 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452679 Affx-122920318 AX-123323012 25 159625 TCTTTCTTCTCCTGGGTAGTCTGTGTCCTGACCCC[A/G]CAAACTTTTGTCTAGGGAGTTGATTTTAATGGAGG R 2 1 2 1 201000 r 74 goat snp22155-scaffold2188-369505 25 153084 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452289 Affx-122920690 AX-123322622 25 191207 TGGTGGCGGTATCAGGCCTTGGTTTTATACCGTAG[C/T]TTTACAGTGAGCTGCTCAGGTGTCATCATTGTGTT Y 2 1 2 1 201000 r 74 goat snp22154-scaffold2188-337923 25 184687 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430023 Affx-122937584 AX-123300364 25 224859 GATGCTGAAGGAAAGCACAGCCCGCGCTGGGCACA[C/T]GGACACCGAGGGAATGAAGCCGCCTTCACCTCAAA Y 2 1 2 1 101000 r 74 goat snp22153-scaffold2188-304271 25 218386 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427837 Affx-122939734 AX-123298180 25 280195 CCTGTCCAGGGATCCCTCCCCTGGGGAAAGTGCTC[G/T]CTTCTGACACCTTTCTCTGGTTCGCCAATGACTTC K 2 1 2 1 101000 r 74 goat snp22152-scaffold2188-248935 25 262122 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381748 Affx-122974320 AX-123252106 25 314122 CCTGAGGCCCTATTGTGTCCACTGCCTCCTTCTGA[C/T]GTCCCTGAGTCCCTGGAGAAGGGGATACCCTAGAT Y 2 1 2 1 101000 f 74 goat snp22151-scaffold2188-215008 25 294813 A G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405297 Affx-122956847 AX-123275649 25 366521 AAAGCTTCAGTTCAGTTCAGTCGCTAAGTCGTGTC[C/T]GACTCTTTGCCATACACACAAAAACCAGCCTTTCA Y 2 1 2 1 201000 r 74 goat snp22150-scaffold2188-162609 25 346785 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273078 Affx-1111833299 AX-185394132 25 378378 GTGGGTTGCCATTTCCTTCTCCAATGCATGAAAGT[A/G]AAAAGTGAAAGCGAAGTCGATCAGTTGCATCTGAC R 2 1 2 1 303000 f 74 goat 25_378378_AF-PAKI 25 378378 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38380748 Affx-122975130 AX-123251106 25 447002 GCTGACCAACGGGCAGAGCCCCAGCAGAAGCAACC[C/T]GACCAGGCAGCAGACAGGCAGAGCTCCTGGGAAAG Y 2 1 2 1 103000 r 74 goat snp22148-scaffold2188-82128 25 420011 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417131 Affx-122947364 AX-123287479 25 507499 GAAGGTGCAGAATCACAAGGCTGTCAGCCCCCGAG[C/T]AGGGAGAGGGAGCAGGGGAGGGATGTGGGGGAGTG Y 2 1 2 1 101000 f 74 goat snp22147-scaffold2188-21631 25 477261 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416916 Affx-122948052 AX-123287264 25 544718 TGCGTGGTGTATGACGTATCTGAAGAGGCCACTGT[C/T]GAGAAGGTGAGCGTTCCAGGTTCTCGTCCCTGGTG Y 2 1 2 1 101000 f 74 goat snp39436-scaffold5002-15489 25 513428 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769017 Affx-122973618 AX-385256192 25 670096 CTTTAACTTCCACGTGCTTTTGGCGTTAGCACATG[C/T]GCTAAAACGGGACGATACAAAGATTAGCATGGCCC Y 2 1 2 1 101000 f 74 goat snp25066-scaffold2586-41676 25 632551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453514 Affx-122919809 AX-123323847 25 709019 GAGACGCCAGTCTGCAAGGGCCAGTCTGTACTCTT[A/G]GCTTAGTTTTTCTGTAAATCTAAAATTGTTCTTAA R 2 1 2 1 101000 f 74 goat snp25067-scaffold2586-80599 25 671439 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411960 Affx-122951138 AX-123282310 25 742071 GTGTGTGAACCCCAGGTCACGGGAGGGAGCCCCAC[A/G]ATGTAACGTGAGTGGACCCAGGACACTCCTCACAC R 2 1 2 1 101000 r 74 goat snp25068-scaffold2586-113651 25 702894 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765038 Affx-122952654 AX-385252608 25 799619 TCGAAGTGCAGACTTTCAGTGGGTGAGCTGTATGG[C/T]ATGTGAGTTGTATCTCGGTAAAACTGGTTTGAACA Y 2 1 2 1 102000 f 74 goat snp25069-scaffold2586-171199 25 759161 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426237 Affx-122940344 AX-123296583 25 838347 AATTGAGTGTACCTGTGCGCGTACATGTGTGCTGG[C/T]ATGTACACGTGTGTGCCTCTGTGTGTACACACATG Y 2 1 2 1 103000 f 74 goat snp25070-scaffold2586-209927 25 796386 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784420 Affx-122969005 AX-385271469 25 890786 TCGGCTCCTTCTCGTGTGTTTTGAGCACTCTTCCA[C/T]ACCCTCTTCCTATTCCTTGCCTCTAATGTGTGTTA Y 2 1 2 1 101000 r 74 goat snp25071-scaffold2586-262366 25 846453 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410693 Affx-122952738 AX-123281043 25 945266 GGAGTGACAGCGCAGCCCCTTTCACAGCACAGATC[A/G]CTTTTTTAGGCCAAATGCTGCCTTCAGCCTGGTCT R 2 1 2 1 101000 r 74 goat snp25072-scaffold2586-316846 NW_017213010.1 6054 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422266 Affx-122943994 AX-123292612 25 976599 TGATGCGTGAGCACACACACGGGCTCTCACTCCCT[A/G]TATTTACTGAACTGTACAGTTCAGTGTCTACACTG R 2 1 2 1 303000 f 74 goat snp25073-scaffold2586-348179 25 914576 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411645 Affx-122951572 AX-123281995 25 1006939 CAGCCGTGGAGGGGACAGAGGCCCAGACAGGAGGA[C/T]GCGGCCACCACCAAGGATGCAGGTGACCCTGGATG Y 2 1 2 1 101000 f 74 goat snp2821-scaffold10821-27247 25 946007 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452590 Affx-122920500 AX-123322923 25 1158327 AGAACCAGGAGCTGCGTTAATTTATCTCGGGCCTC[A/G]GGCTATGAAGTGGGCTGAGTGGTAGGTCCCAGCCT R 2 1 2 1 101000 f 74 goat snp24069-scaffold2451-105853 25 1081481 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396779 Affx-122962763 AX-123267134 25 1233463 CTCCCATTTCGTAATCCCAAGCACTCAAGAACCAG[C/T]CAGGTAGTCCTTTTCACTGCAAAGGGCCACTGCCT Y 2 1 2 1 101000 f 74 goat snp39892-scaffold5099-40563 25 1134544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448942 Affx-122923146 AX-123319277 25 1271992 CACTCCCTGGTGAAGGACACAGGCAGTTTATGGAG[C/T]GTGAAGGACTGGCCATTGAGTCCAACATTTGTCGT Y 2 1 2 1 101000 r 74 goat snp39893-scaffold5099-79092 25 1173066 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378159 Affx-122976968 AX-123248518 25 1312347 GCAATCAGGCACTCAGAGTCTCTGCCTGTCGGTCA[C/T]GTGCACAGTGTGTGTGTCCGCGCGAGGCCGGGCAG Y 2 1 2 1 201000 r 74 goat snp39894-scaffold5099-119447 25 1213008 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385439 Affx-122971317 AX-123255797 25 1378654 AAGAGCCAGAACTCTCCTGATGGATGAGGTTGGGC[C/T]GCGGTCCTGAGGTTGAAGAACCGTACAGGGACTGT Y 2 1 2 1 101000 f 74 goat snp16896-scaffold1766-13800 25 1290207 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796755 Affx-122942731 AX-385283699 25 1416735 AAAAGTGAAGACATAAAAGAATACCGCAAATAGAA[C/T]ATTACAAAGCCATTAACAATGTGATGGTGTTCTCT Y 2 1 2 1 101000 r 74 goat snp16897-scaffold1766-51881 25 1328587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377915 Affx-122977232 AX-123248274 25 1448034 GGCTATCTAGTAGAATTCCAGGACTTTTTGGTTTT[A/C]TTCTTAGCATTCTTGAAATAAAAATTGACTATATT M 2 1 2 1 101000 f 74 goat snp16898-scaffold1766-83180 25 1359892 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412058 Affx-122951711 AX-123282408 25 1506133 AATTGCAGGAGGATTCTTTACTGTCTGAGCCACCA[A/G]GGAGCTCAGATAAAATGCACACAAATGAAAAATGG R 2 1 2 1 101000 r 74 goat snp16899-scaffold1766-141279 25 1415200 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414213 Affx-122949649 AX-123284562 25 1658209 CACAGCACCAGGCTCACAATGGGCTCCTGCACCGT[A/G]AGGTTGTGCATGGCCATAACCCAGCTGACCGCGTT R 2 1 2 1 101000 r 74 goat snp16901-scaffold1766-293355 25 1551123 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764009 Affx-986698537 AX-310479088 25 1690504 CCTCCGTCCATGTGCTTCAGCGCCTTCTCAGCCTC[A/G]TCTGGATTCTCAAACTCCACATAGGCGTAGCCTTT R 2 1 2 1 600010 f 74 goat 25_1690504 25 1690504 Ancestral_priority_1043 ancestry 0.518 neutral IMAGE 10K 10K ancestral 320767444 Affx-986698539 AX-385254715 25 1690509 GTCCATGTGCTTCAGCGCCTTCTCAGCCTCGTCTG[A/G]ATTCTCAAACTCCACATAGGCGTAGCCTTTAGACA R 2 1 2 1 600010 r 74 goat 25_1690509 25 1690509 Ancestral_priority_1043 ancestry 0.69 recommended IMAGE 10K 10K ancestral 320767448 Affx-986698541 AX-385254719 25 1690600 ACAGGCATGTCAATCATTTTAATTTTCCCATAGGT[A/G]GAGAATATCTCCATGATGTGATCCTAGGGAGGAAG R 2 1 2 1 600010 r 74 goat 25_1690600 25 1690600 Ancestral_priority_1043 ancestry 0.726 recommended IMAGE 10K 10K ancestral 38430076 Affx-122937544 AX-123300417 25 1748234 GGGTCCCTCCAGGGTTAAGCTCTGATCTTAACCCC[C/T]GTGCCCTTGGCTCCAAGATCCCTGGTCTTTACTGT Y 2 1 2 1 102000 r 74 goat snp16903-scaffold1766-383380 25 1629690 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411137 Affx-122951892 AX-123281487 25 1801767 GCCTGCTCTCATTGAATGTTTTCAAGGTTCATCCA[C/T]GAAGTAGCAGGTGTCAGTGGTTCATTGCTTCTCAA Y 2 1 2 1 201000 r 74 goat snp16904-scaffold1766-436913 25 1683490 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417040 Affx-122947529 AX-123287388 25 1886850 TAGGATGGGCATGTGTGAAGTTCTGTTGGTGATGG[A/G]GAAGGTAAAGTCAAACCTCTTAAGACTGTAAAGCC R 2 1 2 1 101000 f 74 goat snp16906-scaffold1766-521996 25 1766640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406727 Affx-122955750 AX-123277078 25 1947343 ATCGTAGGAATCTAGCTGCTCTGTGTAATCTGATC[A/G]TGTCCATTTGTCCCGTTGTAGCGGAGGGCTATGTG R 2 1 2 1 101000 f 74 goat snp16907-scaffold1766-582489 25 1827754 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378145 Affx-122976979 AX-123248504 25 1980994 TCAACTGAAAAATGACAATTTGATTCAAACTTCTC[A/G]GTGCTCTCATGACACTATGCAAAACCAGTTTTCCC R 2 1 2 1 101000 r 74 goat snp16908-scaffold1766-616140 25 1861790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448439 Affx-122923652 AX-123318775 25 2026816 TCTTGCTGGAAATGGAAATAACCCAAGGGGAAGCC[A/G]CTGGTGAAGTTGGGGGAGGTGAGCTCAGTTTGAGG R 2 1 2 1 101000 f 74 goat snp16909-scaffold1766-661962 25 1907730 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416627 Affx-122947621 AX-123286975 25 2055527 GCTGGTGGTGTGAGGAGAGCCTCCATGGGCCCTAC[A/G]CTTTACCCTTTCCTGAGGAGGAGCTTCTGTGGATG R 2 1 2 1 101000 r 74 goat snp16910-scaffold1766-690673 25 1936018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450954 Affx-122921755 AX-123321288 25 2105772 GTAAAACCAGTTGGTGTGTTTCTTTTCTGCTTTCC[A/G]TCTTGGTCCTGTTGAGAAGAGGTTCTCTGCCTGGA R 2 1 2 1 101000 r 74 goat snp16911-scaffold1766-740918 25 1984825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784511 Affx-122977943 AX-385271560 25 2164485 CTCAGAGATGGTCTTCAGAGATTTCTGAATAAGAT[A/C]GTTTTCTGAAGTGTTCTGTGCAACAGTAAAAAGAA M 2 1 2 1 101000 r 74 goat snp21915-scaffold2151-37915 25 2043129 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787461 Affx-122967080 AX-385274486 25 2204276 TCCACTCAAATACTCAACATCCCCTTGTACATATC[A/G]TATCATATAGCCATCTCAACCTTATTATGACTCCA R 2 1 2 1 101000 f 74 goat snp21916-scaffold2151-77706 25 2081791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449476 Affx-122922643 AX-123319811 25 2252292 AGGCGCAGTACTTATTCTGGGTCTGTTGTTCAGTC[A/G]CTCATTTGTATCTGATCCTTCTGCGACCCCATGGA R 2 1 2 1 101000 r 74 goat snp21917-scaffold2151-125722 25 2129209 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788607 Affx-122971483 AX-385275624 25 2319022 TGGTGTAGGAGCTGTAGCTTTGGCTTAAAGGTGCC[A/G]GGGCTGATGTAATCTTACCTTGAACTCCTGGCAAG R 2 1 2 1 101000 r 74 goat snp21918-scaffold2151-192452 25 2193957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420442 Affx-122944897 AX-123290789 25 2351235 CTATGCGATTTTTTAAAGTGCTGACTGGGGACTTG[C/T]CTGGTGGTCCAGTGGCTAAGATCTGCACTTCTTGT Y 2 1 2 1 101000 f 74 goat snp21919-scaffold2151-224665 25 2226142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425416 Affx-122941538 AX-123295762 25 2393394 GGAGGCTCTGACTGAGCTGACTCTGACATGACCTT[A/G]TGGTAAACGAAGCTCATCTGGCAGTCTGTCTGCTG R 2 1 2 1 201000 r 74 goat snp21920-scaffold2151-266824 25 2266512 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405497 Affx-122956007 AX-123275849 25 2432098 AGAACCAGTGTCCTTGAGTCTCTGTTCTGAGCTAT[A/G]CCTCCCCCAGTCTACACCTCTTGCAATCTGGTGAA R 2 1 2 1 201000 f 74 goat snp21921-scaffold2151-305528 25 2301933 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376190 Affx-122978822 AX-123246549 25 2470948 GTGTAGTCTCCCTTACCCCCAAAGAGGGGCAAGCG[G/T]AGATACCTTAATCCTTTTCTCAAACAGGCTTCTGT K 2 1 2 1 101000 r 74 goat snp21922-scaffold2151-344378 25 2339997 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432201 Affx-122936385 AX-123302542 25 2500608 ACTTCATGAAGTCTGCTTCACAAAAATGCCACATC[A/G]CATTGAATTATGTTTTTTAAAGAATGGGAAGTAAA R 2 1 2 1 101000 f 74 goat snp21923-scaffold2151-374038 25 2370128 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788992 Affx-122935598 AX-385276005 25 2521935 TTGTCTGGTATGAGAATTATATGTCAACCAAAATT[A/G]TGAAGAAAACAGCTCAGTCCACAATGAAACATAAA R 2 1 2 1 201000 r 74 goat snp28587-scaffold3066-12770 25 2379711 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435441 Affx-122933476 AX-123305781 25 2595071 TCCGCTCATTGCATTGGAAGTCCAGAGTTTTAGCC[A/G]TTGGACCAGAGGGAAGTCCCTGTCCTGATTTTTAA R 2 1 2 1 103000 r 74 goat snp28588-scaffold3066-85906 25 2451883 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422901 Affx-122943057 AX-123293247 25 2777551 AGACAGCGACACCCGAGCGTCAAGTCGCGCGCTGG[A/G]CCTTCTAGGCTGGACGGACTTGGAGACTCGGCGGT R 2 1 2 1 101000 r 74 goat snp28591-scaffold3066-268386 25 2640481 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434350 Affx-122934722 AX-123304691 25 2848506 AATCTCCAGTGTTTCTGCTGCTCACTGATGGAAAG[A/G]ACAGTTCTTCGGGTTTTGGCCAAGAGATGTGGCCA R 2 1 2 1 202000 r 74 goat snp28593-scaffold3066-339341 NW_017207976.1 93 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447981 Affx-122923752 AX-123318317 25 2885478 TTGGAGCTAGACATAAAGGGAGGTATTTGTAGTCA[C/T]GGAAGCAGGGAACCATGCACGCAGGTGATCCCAGG Y 2 1 2 1 101000 f 74 goat snp28594-scaffold3066-376313 25 2748954 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434879 Affx-122934350 AX-123305220 25 2930055 TGATTGCACCTACCCCTTACTTAAGATCACATAGA[C/T]ACTAGCTTCACCGCTTTCCTCTTTGGACCATCCTT Y 2 1 2 1 201000 r 74 goat snp28595-scaffold3066-420890 25 2794262 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418086 Affx-122946601 AX-123288434 25 2960318 AAGACTAAGTACTTTGTTCAGATGCCCAGTAATAA[C/T]AGTCAGGGGTGACTCTTCATCTCCCCAACAGCGTC Y 2 1 2 1 101000 f 74 goat snp28596-scaffold3066-451153 25 2819329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420146 Affx-122945590 AX-123290494 25 2981817 CCAGCTCTTCACCGCGCCTGTGCTCAGGGTCTGAA[C/T]GGGGGAGGGAGGAGAAGAGGGGCAGAGGTACGAGG Y 2 1 2 1 101000 f 74 goat snp24698-scaffold2518-585604 25 2840597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416386 Affx-122947865 AX-123286735 25 3017598 CTTGTCCTTCCTATCTCTTCCAAACACCTTTTATT[A/C]TTCTCTGTTTATTTGTTTAAAGCAACTTGCTCACC M 2 1 2 1 101000 f 74 goat snp24697-scaffold2518-549823 25 2875812 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383714 Affx-122972473 AX-123254072 25 3074379 TTTAATTACAGCTGTTTGGATTAACAGTCTTACTG[C/T]AGACACAGCAATACTTTTGGTGGCTATTACAGTTT Y 2 1 2 1 101000 r 74 goat snp24696-scaffold2518-493042 25 2929706 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273069 Affx-1111833295 AX-519546740 25 3101936 GGCAACCCACTCCAGGATTCTTGCCAGGAAAATCC[A/C]TCGGACAGCGGAACCTGGCGGGCTACAGTCCTTGA M 2 1 2 1 103000 f 74 goat 25_3101936_AF-PAKI 25 3101936 G T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38437658 Affx-122931790 AX-123307996 25 3126238 ATTTGAGCATGAATTAGCTTCATCTTTGCAAGCAT[A/C]TGTCAGTCACAAGAGAGAAGTTGCCTCCTGGGTAT M 2 1 2 1 101000 f 74 goat snp24695-scaffold2518-441183 25 2980287 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422465 Affx-122943333 AX-123292811 25 3192086 GAGAGGAAGAGCAGAATTCTGTGAAATGTCAGCTT[A/G]CTTTCTCTTTCACATTCTACTGGAAGTAATCATGG R 2 1 2 1 101000 f 74 goat snp24694-scaffold2518-375335 25 3046668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417333 Affx-122947739 AX-123287681 25 3231292 TGTGTTTGAAGACAAAATAGTTAAAAGTTATTAAC[A/G]TCTTCCCTTGTTAAGATGAAATGTTCCTTACTGTG R 2 1 2 1 101000 r 74 goat snp24693-scaffold2518-336129 25 3085763 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392618 Affx-122966041 AX-123262975 25 3282769 CCCTGATGGAGACTTAAGACACCCTGAAATGGGGA[C/T]AGCAGATATTCTGTATCTTTCAAAAATCTTTGTAA Y 2 1 2 1 101000 f 74 goat snp24692-scaffold2518-284652 25 3137280 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434461 Affx-122934642 AX-123304802 25 3315128 GAATGTTGACACATCCCATGTTGAGCTGGCTAGGA[C/T]GACCAGTGGTCTTTGTTTTCTGTTTCTCTCTATTT Y 2 1 2 1 101000 f 74 goat snp24691-scaffold2518-252293 25 3169824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401633 Affx-122959594 AX-123271986 25 3353128 ATATGGTATTGTCAGCTGTGGTCACCACAGTTTAC[A/G]TTAGCCCCTCAAACTGTATTTCTGTATTTTTAACA R 2 1 2 1 101000 f 74 goat snp24690-scaffold2518-214293 25 3208057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436430 Affx-122933008 AX-123306768 25 3392496 CAGTGTGTACCTCTCACCAGGACCTGGAACACTTA[C/T]GTCCACCAGATCGAATGTCTTCTCCGAACTATGTA Y 2 1 2 1 101000 r 74 goat snp24689-scaffold2518-174925 25 3247374 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404924 Affx-122956441 AX-123275276 25 3442467 ACAGTGAAATGAAAGGTGTCCCAGTGGTTAGGATG[C/T]GATGCTTCCACTTAGTCCTCGATTTGGAACTAAGA Y 2 1 2 1 201000 r 74 goat snp24688-scaffold2518-124954 25 3296724 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433455 Affx-122935059 AX-123303796 25 3491087 CTTTCTGTTACCTGCTTGAGGCAGAGATTGAGGGA[C/T]GACAGGAGGTCTGAGTCTGCTTCCTCCAGCCCAGC Y 2 1 2 1 101000 f 74 goat snp24687-scaffold2518-76334 25 3345166 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397135 Affx-122962673 AX-123267490 25 3524182 ACATGAAACAGAGCTCCTTGGAGTCACCAGTGAGA[A/G]CAGTTTTCATGGAGTTCTGGCTCCGGATGGAGTGA R 2 1 2 1 201000 r 74 goat snp24686-scaffold2518-43239 25 3375504 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454153 Affx-122919328 AX-123324486 25 3564391 CCTACATGCCTCAGAGCAACTAAGCCTGTGTGCCA[C/T]GACTACAGAGTCTGCACCGGCAACGAACGATCTCT Y 2 1 2 1 201000 r 74 goat snp24685-scaffold2518-3030 25 3415547 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275274 Affx-1111834808 AX-519548850 25 3581002 AGCATTTGCCCTGGCATTCCACAGCTGCAGTGCCC[A/G]GGGAAGGGTACTGGGCCTGGACCCTGGTGTCCACC R 2 1 2 1 102000 f 74 goat GoatD01.054263 25 3581002 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38434376 Affx-122934703 AX-123304717 25 3617274 CTAGATGGATCTTCTCTCTCCATTTGCCCCAGTTC[A/G]CGCCCAATTTTGATGGTAAATGGAACTCAGACTGC R 2 1 2 1 201000 r 74 goat snp57091-scaffold909-49754 25 3466876 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381234 Affx-122974505 AX-123251592 25 3665585 GTCTGGCCTTCAGGAGAAAAGTCCAAGGGGGAGCT[A/G]TGGACATCTGGAATGGGGCTTGCCGACTCCTCTCA R 2 1 2 1 101000 f 74 goat snp57092-scaffold909-98065 25 3514978 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438614 Affx-122930927 AX-123308951 25 3753620 CTCCCTCCATCCTCTCAAGGATCCTGTGCAAGTTT[A/G]CCTAAGTTGAGCAGAGAGGTGGTGTGCTCAGAGTT R 2 1 2 1 101000 f 74 goat snp57094-scaffold909-186100 25 3602867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386011 Affx-122971502 AX-123256369 25 3787490 TGTTGGGCCTGATGACTCCAAAAGGTCAGCTCCCC[A/G]CTAACATGGGGTTGGAGGGGAAAGCCTGACTCCAG R 2 1 2 1 103000 f 74 goat snp57095-scaffold909-219970 25 3637593 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412155 Affx-122951080 AX-123282505 25 3889542 CTGCTGAGCCCATTTCTAAATCAGCCTCTGAAATC[A/G]GTGTCAGTGAGGCCCTTTGGGAGAGAACTGGTCCC R 2 1 2 1 101000 f 74 goat snp57098-scaffold909-322022 25 3734200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387663 Affx-122969839 AX-123258021 25 4010873 GACCCTAAGGAAATTTGCGATAGAGCCGGGAACAT[A/G]GTAATAAGTAAATGTATTGTCTAATATTATCTTGG R 2 1 2 1 101000 f 74 goat snp57101-scaffold909-443353 25 3835526 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429751 Affx-122937590 AX-123300092 25 4069393 CAGTGGAGCACCCAGGAAGGCTCAGAGGAGGCGAC[C/T]GTGCAGGGAGGCTCTGGGTAAGGTGGGGTGAGGCT Y 2 1 2 1 101000 f 74 goat snp57102-scaffold909-501873 25 3893977 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447942 Affx-122923783 AX-123318278 25 4099978 CTTCATCGAGGTGTGCTAGGCATACAACAGAGTAC[A/G]TATATTTCAAGTGTATCATCTGATAAGTTCTGACG R 2 1 2 1 101000 r 74 goat snp57103-scaffold909-532458 25 3924959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380517 Affx-122975690 AX-123250875 25 4170518 GGGAGCCACCAGGGGCTGTGACATCTCATTTCTCC[A/G]TGGGACTCTCCAGTACCATCTTTCCCAGAATTGCC R 2 1 2 1 201000 f 74 goat snp57105-scaffold909-602998 25 3995403 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404749 Affx-122957229 AX-123275101 25 4204473 TGAGAAGGAACAGTGTGGGTTGCGGGTGAGACTTC[A/G]TCCTAAGTCTCCCATGGGCTTCAAGTGAATACAGG R 2 1 2 1 101000 r 74 goat snp57106-scaffold909-636953 25 4026742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415365 Affx-122948770 AX-123285714 25 4250002 GTGTCCCTGGATATCCTTGGTGGCAAAGAGCAACG[C/T]ATGCTGCTCTGGGAAAGCCAGGCCTGGGGGAGAGC Y 2 1 2 1 101000 f 74 goat snp57107-scaffold909-682482 25 4072199 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420540 Affx-122945299 AX-123290887 25 4282276 TCTCTGGGGTGGGTTGATGGGGAAGGGCAGGGAGA[C/T]TGAGCAGAGTGGGGCTAGGGGAACTGAGTCAACTT Y 2 1 2 1 103000 r 74 goat snp57108-scaffold909-714756 25 4104388 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390455 Affx-122967616 AX-123260812 25 4316071 GGTTTGCTTGCTGAAAGGGGTCAGGCTCTAGGGAG[G/T]CTTGTGTGTGTGTCTGTGTGTGATGTGAACCTCTG K 2 1 2 1 201000 f 74 goat snp57109-scaffold909-748551 25 4138138 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446285 Affx-122925660 AX-123316621 25 4349672 TTCTCTCTTCTCTTGGATCTGTTCCATATCCTGGC[A/G]CCATCCTTCCCACCACCCACTTAAAATAGAATCAC R 2 1 2 1 201000 f 74 goat snp57110-scaffold909-782152 25 4171209 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800994 Affx-122973192 AX-385287908 25 4379659 GCATGCATGCATAGATTAGTTTATAGACCCTTTAA[C/T]GGCTTTCTTTCCTTGCATAAGTGAGTGCAGAAATT Y 2 1 2 1 101000 r 74 goat snp57111-scaffold909-812139 25 4203222 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447806 Affx-122923927 AX-123318142 25 4461041 GCACGACTGAAGTGGCTTAGCACAGCACAAAGAAA[C/T]GCAAGTGGAACTTCAAGTTATACGGTAGAAAACCC Y 2 1 2 1 201000 r 74 goat snp12427-scaffold1472-1308556 25 4285825 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432396 Affx-122935848 AX-123302737 25 4517971 GGTCAAGAAGAAAGACACACAGCTGGGTGATAATC[A/G]AATCCTTGAGAGCTGAGAACATGTTTCCATGGCAG R 2 1 2 1 101000 f 74 goat snp12426-scaffold1472-1251626 25 4343152 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277731 Affx-1111835994 AX-519551230 25 4523850 AACTGCAGGGGCTGCTGGGAAGTACTTCTGGAGGG[A/G]TGTCTGATACAGTCCTAGACTCCCAGGCATCTCCA R 2 1 2 1 201000 r 74 goat Random2.2K-2131 25 4523850 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38442903 Affx-122927642 AX-123313240 25 4546566 GACAGACAGACAACAACAGGGAGACCAAGAGACTT[A/C]TCATAGCAGTTGGTTCATACAACTAAGGAGGTGGG M 2 1 2 1 101000 r 74 goat snp12425-scaffold1472-1223031 25 4371730 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275491 Affx-1111834837 AX-519549063 25 4575400 AATGACAGTAGCTATCCAAGGGGGACATGCCAATG[A/G]CAGAGGTTTCATGAGGGTAAACCCCACTGCAGAAG R 2 1 2 1 101000 r 74 goat GoatD01.055905 25 4575400 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320766955 Affx-122962133 AX-385254257 25 4580430 GATACAGATGGTCTCATGAGCCACAATTAGAGAAA[C/T]GCAACTCTCATACAATTACCAGATTTCCCAGGTTT Y 2 1 2 1 101000 f 74 goat snp12424-scaffold1472-1189167 25 4406024 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410759 Affx-122952689 AX-123281109 25 4635230 GACTCATCCTAGGACTCTCTATAGCACAGGGTCAG[A/C]GGAGGTCAGACCCCAGAGTGTTCCCGTTTATGCCG M 2 1 2 1 101000 f 74 goat snp12423-scaffold1472-1134367 25 4461382 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380592 Affx-122975259 AX-123250950 25 4703700 TTATTTCTGAAAAAGTTCACGATAAAGAAGGACCT[C/T]CTATTAATTATTAAAAACAAAAACCCGGAGACACA Y 2 1 2 1 101000 f 74 goat snp12422-scaffold1472-1065897 25 4530532 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277603 Affx-1111835995 AX-519551102 25 4748789 GGAAGAACAGAGCAATCAGGGGTGATTTCCAGAGG[A/G]GAAACAGCGATGTGGGGTCATGAACAAGGTGGAAG R 2 1 2 1 202000 f 74 goat Random2.2K-2132 25 4748789 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449042 Affx-122923070 AX-123319377 25 4751129 AGCATTGTCAGATGCAGTAATAAGAGCAAAAGCTA[C/T]GAAAGAGAAAGTATCAGGTACACAATAGTGTAATC Y 2 1 2 1 101000 f 74 goat snp12421-scaffold1472-1018468 25 4577991 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402546 Affx-122958465 AX-123272899 25 4781318 AAGAGAGGTGAACAAAGGCGACGAATACACATTTA[C/T]AACGTGTGTGGGTGCACTTTCAACCCTACGACACT Y 2 1 2 1 201000 f 74 goat snp12420-scaffold1472-988279 25 4608197 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445944 Affx-122925911 AX-123316281 25 4849520 CCAAGGAACCAGCCCAAGGTCACACAGCGAGCAAG[C/T]GGCAGAATAGCGTGCCCCTGTCTGTCCTAGCTTTC Y 2 1 2 1 101000 r 74 goat snp12418-scaffold1472-920077 25 4673607 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273622 Affx-1111833731 AX-519547235 25 4883764 ATTATTTGCCTGTATAGCCTGCAGAATCGTGTGTT[A/G]GAGGAAATGGTCCTTTGGCAGGGACTCTGTGTGAG R 2 1 2 1 201000 f 74 goat GoatD01.002898 25 4883764 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38438406 Affx-122931286 AX-123308744 25 4886662 TAAACATCTTTTTAAATTCTCTACCTACTGTCCGC[A/G]TCAGTCATAGTCCCCTTACTGCCCCAGAGGGTGAA R 2 1 2 1 101000 f 74 goat snp12417-scaffold1472-882935 25 4710596 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404373 Affx-122956805 AX-123274725 25 4934933 GCTCATTTCTAGATAAAGAAAGAGCAGCCAGCATG[C/T]AGCTACTAAATGTAGCTCAGAGATGCTGAGGGACT Y 2 1 2 1 101000 f 74 goat snp12416-scaffold1472-834664 25 4759023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448127 Affx-122924298 AX-123318463 25 4966960 AAACGAAGGAAGCATTTTAAATGCAGGCTGTGCAG[G/T]TTGGCCAAGTTCCGGCTTGCGGAGATTAAATAATA K 2 1 2 1 101000 f 74 goat snp12415-scaffold1472-802637 25 4791768 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397751 Affx-122962531 AX-123268106 25 5009215 GACTGAGGAAGGGAATGAGTGTCCAGATGGGCTTA[C/T]GAAACAGGATCCAAGAAACTGAATTCCTGGAAGGC Y 2 1 2 1 101000 r 74 goat snp12414-scaffold1472-760382 25 4833899 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385904 Affx-122971580 AX-123256262 25 5038222 ACAAAAACTGCAAGAGGTTGTCATTACAACTCCAA[C/T]GACAGATCATAAGACTTAGACCCCCCGTCTCTCTG Y 2 1 2 1 101000 f 74 goat snp12413-scaffold1472-731375 25 4862828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405724 Affx-122956524 AX-123276076 25 5073096 TCAACGGGGAATCTAGGCAGCTTCTGTGTTCTCAG[A/C]TATAACAATTTTTAATATATTTGTGGACTTTGTAT M 2 1 2 1 103000 f 74 goat snp12412-scaffold1472-696501 25 4897572 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446508 Affx-122925036 AX-123316844 25 5119776 CTGATCTGCAAGAATATCCTAGGGAGAACCGGCTG[C/T]GAACGGTAATTGCATTACTCCATTCCCTGCGAATT Y 2 1 2 1 101000 r 74 goat snp12411-scaffold1472-649821 25 4944733 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417143 Affx-122947355 AX-123287491 25 5181126 TCTCTGTTTTGTTTTCTTCACAGCTGAAGGTTTCT[G/T]GGATCATACACCTCTTTTCTTTGTCTGAAATAGAC K 2 1 2 1 101000 r 74 goat snp12410-scaffold1472-588471 25 5005976 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601609 Affx-1002479794 AX-413836011 25 5193781 TGGACCTAGAGTCTGTCATGCAGAATGAAGTAATT[C/G]AGAAAGAGAAAAACACATACTGTATATTAACACAT S 4 1 2 1 102000 f 74 goat 25_5193781_RH-map 25 5193781 C G 1 neutral Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38398581 Affx-122961500 AX-123268936 25 5243065 TTATCCACACTAATGGCAGGATTCAGAGGCAAGGG[A/C]GACCAATGAGACTGGATAATCCAAAAGCCACTTTC M 2 1 2 1 201000 r 74 goat snp12409-scaffold1472-526532 25 5068169 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390209 Affx-122967789 AX-123260566 25 5279935 TGTTTGTAGACACAAAAACTTAAGAGCACACCAAA[C/T]GCACCGATACCTAATACCACCTATTTTTAACAAGA Y 2 1 2 1 101000 f 74 goat snp12408-scaffold1472-489662 25 5105278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601612 Affx-1002479795 AX-413836014 25 5297231 AGTCCATGACGTCATGAAGAGTTGGACATGACTAA[A/G]TGACTTCACTTTCATTTATTGGAGAAGGAAATGGC R 2 1 2 1 303000 f 74 goat 25_5297231_RH-map 25 5297231 A G 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 320785400 Affx-122939300 AX-385272445 25 5309181 ATCGCAAACACAATCAAAGCCATGGATGGCATTAC[A/G]TAATGACCGCTCGAAAGCAGTTGCACTTACTGAAT R 2 1 2 1 101000 f 74 goat snp12407-scaffold1472-460416 25 5133446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450590 Affx-122922024 AX-123320924 25 5353726 CTGCAAAACCTCTCAATTATAGAAACAGCAGGCAA[C/T]AGGAATAGAAGTCAACAGGATGTGAGGCAGTGTGC Y 2 1 2 1 101000 f 74 goat snp12406-scaffold1472-415871 25 5177959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386419 Affx-122970813 AX-123256777 25 5394146 ATAGTGAGAGAAATGCCATGAGAACTGACCATTCT[A/G]CTGCCCAATTAATCATTCTAACAAGCTTGAGATTG R 2 1 2 1 101000 r 74 goat snp12405-scaffold1472-375451 25 5219398 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601614 Affx-1002479796 AX-188711166 25 5420276 TGTCCATCAGCAGATGAATGGATAAGAAAGCTGTG[A/G]TACATATACACAATGGAGTATTACTCAGCCATTAA R 2 1 2 1 103000 f 74 goat 25_5420276_RH-map 25 5420276 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38445140 Affx-122926169 AX-123315477 25 5422717 ACGACCACACAAGACCCACCTCTTGGACATTTCCA[A/G]TCCTTGGATCCCCAACCCCCAGCTCTACTGCCCTC R 2 1 2 1 101000 f 74 goat snp12404-scaffold1472-346880 25 5247801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384758 Affx-122972029 AX-123255116 25 5455667 ACTGTGATGGACGAGTCCTTTTCACTCTATGTTAA[A/G]TAACACTGAGGCGAACATCTCTGCCCATAGCTTCA R 2 1 2 1 101000 f 74 goat snp12403-scaffold1472-313930 25 5280333 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601616 Affx-1002479797 AX-413836017 25 5464210 AACTAGAAATAATTGTAATGTTCAGAACAGCAAGT[A/G]TCCAAGCTCTTGGGAAAATAATGCTATTTGGAAGG R 2 1 2 1 101000 f 74 goat 25_5464210_RH-map 25 5464210 G A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38414329 Affx-122950036 AX-123284678 25 5494521 TGTGGGAGGGATAGAGACCATTAAAATGCATTTGG[C/T]ACTACGTCTCTGGAGGAACCCGCGAGCTTTCATCC Y 2 1 2 1 101000 f 74 goat snp12402-scaffold1472-275076 25 5319482 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601618 Affx-1002479798 AX-189225918 25 5515712 GAAGTTAAACAAGCAGGGTGACAATATACAGCCTT[A/G]ACGTACTCCTTTTCCTATTTGGAACCAGTCTGTTG R 2 1 2 1 103000 f 74 goat 25_5515712_RH-map 25 5515712 G A 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38411494 Affx-122951781 AX-123281844 25 5536218 TTCACACCAAATCAATTTACACTGGATACGGAAGA[C/T]GCTTATGCAACTCCTGGGCTGCAGTTTGCAATGAG Y 2 1 2 1 101000 f 74 goat snp12401-scaffold1472-233379 25 5361560 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601621 Affx-1002479799 AX-413836020 25 5560118 TAGGGGCCCTAGACACACAGGCTTTAGCAGTTGTG[A/G]TGCACAAGCTTAGTTGCCCCGAGGCATGTGGAGTC R 2 1 2 1 103000 f 74 goat 25_5560118_RH-map 25 5560118 A G 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38409106 Affx-122953318 AX-123279457 25 5570005 ATCTGTTTTTGCTCCCTTTGAACTGCAGCAAACAG[A/G]TGCATGATTACAGCAGCAAATATTTATCATCCTGA R 2 1 2 1 101000 r 74 goat snp12400-scaffold1472-199592 25 5395330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273081 Affx-1111833301 AX-519546750 25 5614847 AAGTCAGACACGACTTTAGTGGCTCAACAAAAACA[A/G]CAACAGACTAACTGGTCGTTCTGTTCACTCTAGAA R 2 1 2 1 101000 f 74 goat 25_5614847_AF-PAKI 25 5614847 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 350601723 Affx-1002479800 AX-413836115 25 5617732 TATAATTCAGCAGCCCACTGCCTTTCTGGAAGTTG[C/T]GAAATTGGAGAGAGTTGCTTTTGTCCAAATGAATA Y 2 1 2 1 101000 r 74 goat 25_5617732_RH-map 25 5617732 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38408794 Affx-122953366 AX-123279145 25 5620549 ACTTAGCGAAAGAGCTGCTTTTTCTGAGTATCACA[C/T]GGGCACAGCATCATCAAAAGAGTATCTCAAGCAAA Y 2 1 2 1 101000 r 74 goat snp12399-scaffold1472-149048 25 5445780 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792039 Affx-122936482 AX-385279027 25 5660178 TGCAGCTATTTGGATGTTAACACATACATAGATTC[A/G]TTTAATCACCAGAAAATCAGAATTCAAAGCAGTTC R 2 1 2 1 201000 r 74 goat snp12398-scaffold1472-109419 25 5485528 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601725 Affx-1002479801 AX-186156499 25 5669208 CTTTGTTGTCCGGAGAAGGCAATGGCACCCCACTC[C/T]AGCACTCTTGCCTGGAAAATCCCATGGATGGAGGA Y 2 1 2 1 303000 r 74 goat 25_5669208_RH-map 25 5669208 C T 3 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601628 Affx-1002479802 AX-413836027 25 5687327 TTGTTTTCAAAAGGGATTAGGGCTCCAGGTCTCAT[C/T]GGGGTAGGAGGAACAGGAGAGAAAAATGGCAGTGT Y 2 1 2 1 101000 f 74 goat 25_5687327_RH-map 25 5687327 C T 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 350601630 Affx-1002479803 AX-413836029 25 5719293 AGATGACCTGACCTGCTTCTTGAGAAACCTATATG[C/T]AGGTCAGAAAGCAACAGTTAGAACTGCAGATGGAT Y 2 1 2 1 103000 f 74 goat 25_5719293_RH-map 25 5719293 C T 1 not_recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 38447724 Affx-122924600 AX-123318060 25 5752533 TGACCGTTCCTTCTAAAACCATTTGCATTTGTACA[C/T]GCCCCCTAGTCCAGCAGGACTGTCCCTATCACTGT Y 2 1 2 1 201000 f 74 goat snp12395-scaffold1472-17064 25 5577830 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769432 Affx-122933089 AX-385256602 25 5777951 ACTGCTTGTTTCTTTGCTTCGTTTAGAAGGAGGTG[A/G]TGTATTAAAGTCAAGGTCTTGTATAGCTGATGGGA R 2 1 2 1 101000 f 74 goat snp42993-scaffold570-8255 25 5603054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413374 Affx-122950137 AX-123283723 25 5816488 GAAATGCAGTCTTTGTCCCTGGAGGAAAAATAAAC[C/T]ACTCATGAGCAGCCAGCCAAGCTTTGCCACTGAAC Y 2 1 2 1 101000 f 74 goat snp42994-scaffold570-46792 25 5641536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428970 Affx-122938871 AX-123299312 25 5911717 AGAGAGATAGCATCGCATATCTGCCCAAGAATTAA[C/T]GCCCCTCACAATAGATAGAGAACTAAAATACTGCC Y 2 1 2 1 101000 f 74 goat snp42996-scaffold570-142021 25 5737852 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443765 Affx-122927111 AX-123314102 25 5940690 TAGGTTCAGAGACCCCATATTGTCCTCAAAGAGTC[A/G]CCAGGATCATTTCTGTCCAGAGATGTTCATTTTCT R 2 1 2 1 101000 r 74 goat snp42997-scaffold570-170994 25 5766850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350601633 Affx-1002479804 AX-413836032 25 5942000 TCATATTTGGATTGCTGTAATGTTATTCTCACTTT[A/C]CTTCTGTGGACTCTTTTTTTTAAAATAAACTTTCA M 2 1 2 1 101000 f 74 goat 25_5942000_RH-map 25 5942000 C A 1 recommended Goat_IGGC_65K_v2 High and low recombination areas RH-map-variant SNP in low or high recombination rate regions (Rachel Rupp, personal communication) muti-breed 468275369 Affx-1111834757 AX-519548943 25 5980183 CCGAGCACCTCTGGCCAGGGCTTCCTGAGCCTACC[A/C]TTTGCTGGATGGTTTATCCTGCATCCCAGACTGCA M 2 1 2 1 201000 r 74 goat GoatD01.051657 25 5980183 G T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38394941 Affx-122964295 AX-123265296 25 5994777 TTATTCTAACACCATCTGTTTTGGGGCATATCAGT[A/G]TCCATAGTATTAATTTTTAAGTGGTTACTCTAGAG R 2 1 2 1 101000 f 74 goat snp42998-scaffold570-225081 25 5820247 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378280 Affx-122976872 AX-123248639 25 6032086 AGTTGAAATTCAAAGACCAGAGCCCAGTCAGTTTC[C/T]GGGGCTCCCTTGCCTTAAGTTGAAATGAGATTTCT Y 2 1 2 1 201000 f 74 goat snp42999-scaffold570-262390 25 5857458 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792956 Affx-122937780 AX-385279935 25 6066279 AATTGAAACTTTTTGAGTTATTAACTCTTAACAGC[A/G]CCTAAGCTATGAGTTAGTTTGCAGAGGCAAAGCCT R 2 1 2 1 101000 r 74 goat snp43000-scaffold570-296583 25 5891291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453988 Affx-122919446 AX-123324321 25 6101521 AAAGAGCAATATGCCTGTGGCATGTAGCTTGTTCC[A/G]CTTTAGAAACTCTGAGATGGCAGTTGCAGGTGGCC R 2 1 2 1 101000 r 74 goat snp43001-scaffold570-331825 25 5926715 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447163 Affx-122924434 AX-123317499 25 6133490 CATGATTTTCTGTCTTTACATTCTGAGCTCTGGTG[C/T]CTTTCTCAATAACATGGAAACAGCCATTTCCGTCT Y 2 1 2 1 101000 r 74 goat snp43002-scaffold570-363794 25 5958439 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397019 Affx-122963125 AX-123267374 25 6164334 AAAATGCTCACAAGTGAAAGAAAGCGACCCGGCTT[A/G]TATCTCTTATCAATGGATTACTGAATGCAGCTTAG R 2 1 2 1 201000 r 74 goat snp43003-scaffold570-394638 25 5988958 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399208 Affx-122960608 AX-123269563 25 6201632 GAGTTGAGATATGGTTATCCCCTCTGGCAATGCGT[A/G]CTTTCTGGATTTCCACCTGGCCAGCTTCAGTCTTT R 2 1 2 1 101000 f 74 goat snp43004-scaffold570-431936 25 6026662 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438903 Affx-122930440 AX-123309240 25 6233659 TTATTGACTGGACATTTGAGATTCATGTCCAAATA[C/T]ACTCAGCTTGGGGAACCGGGAGATGCTATTTCACT Y 2 1 2 1 101000 f 74 goat snp43005-scaffold570-463963 25 6058595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769600 Affx-122966629 AX-385256770 25 6266122 AGTGAAACGCACACAGGAGCTTTCATCTCCATCTC[A/G]ACATTGCACAGCATACAAAGATGCATGTTTCATTC R 2 1 2 1 101000 f 74 goat snp43006-scaffold570-496426 25 6091154 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789824 Affx-122957471 AX-385276831 25 6295880 TTTTCACATTGAGGCTTACGAGAAAATGAAAAAAC[A/G]TTTTTTGAAACTGTCCAGGGTCTTAGTCAGCAGTC R 2 1 2 1 101000 r 74 goat snp43007-scaffold570-526184 25 6120491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800803 Affx-122978345 AX-385287719 25 6371943 AGAAACTTAGCGCGCCATAGTTTCAGTGCTCTTTG[C/T]AAACATATGTGGTAAACACATATGGTAAACATGTA Y 2 1 2 1 101000 f 74 goat snp43009-scaffold570-602247 25 6196721 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440007 Affx-122929784 AX-123310344 25 6401260 CATCCTTTAGGGGGGTACCATAATAACCCAGAAGC[A/G]TTCAGTAAATGCTTGCTTGATTGCAGGGAGGATCA R 2 1 2 1 101000 r 74 goat snp43010-scaffold570-631564 25 6225887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422024 Affx-122943629 AX-123292371 25 6441638 AATGTCCGTCATCTTCCTGTTCCCCTCCTCTGTCC[A/G]TCCCTGTTTGCCCACCTCTGTTTCACAATGAAATC R 2 1 2 1 101000 r 74 goat snp43011-scaffold570-671942 25 6266494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418750 Affx-122946209 AX-123289098 25 6515367 AGGTGCAATGCACTTAGGCCTCTTTCTCCTGACCT[A/C]TGAAAAACTAGTATTTGTGAAGAAGTGTATTGGTT M 2 1 2 1 201000 r 74 goat snp43013-scaffold570-745671 25 6339794 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447608 Affx-122923999 AX-123317944 25 6555659 GAGCCCAGAAAGATTGACCAACACATTCATGGTTG[C/T]ACAGCATGTAGTAGAAAAAAGATTCAAACCAAGAA Y 2 1 2 1 101000 f 74 goat snp43014-scaffold570-785963 25 6380136 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451093 Affx-122921403 AX-123321427 25 6600736 ACCATTTGCATGTGATTTGCATGCATTTACATAAG[C/T]CTGCAAGAGCCCTGTTAAGTCTGAGCAGAGGTGAT Y 2 1 2 1 101000 f 74 goat snp43015-scaffold570-831040 25 6425241 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450554 Affx-122922472 AX-123320888 25 6631806 TCATGCAGTCATCTCTGTGCACAAACTTTAAAGCT[A/G]TGTCTTTTCCAGCCTCTCTCTGAAGGCTGCAGCAC R 2 1 2 1 101000 f 74 goat snp43016-scaffold570-862110 25 6456340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422674 Affx-122943673 AX-123293020 25 6678557 TCTTTGGGGTCATGGAGTGGTTGATCTAGAGATCA[A/G]CTATTTAAAATTATATGGTGGTAGAGATAGATAGG R 2 1 2 1 101000 r 74 goat snp43017-scaffold570-908861 25 6502672 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393621 Affx-122965355 AX-123263976 25 6707569 TCTCAGTCGAATTGACAAAGCTCTTTCACAAACAC[A/G]GGTTCATATTTCCCATTCAGTATGCAACTTATGTG R 2 1 2 1 101000 r 74 goat snp43018-scaffold570-937873 25 6531682 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385722 Affx-122971101 AX-123256080 25 6750485 ATTTTTTGGTGATGATTTCTGTGATCAAATGTCTG[C/T]ATCAGGAAGAAATAATTCTTACCTGGTATTGAAAT Y 2 1 2 1 101000 r 74 goat snp43019-scaffold570-980789 25 6574732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453033 Affx-122920086 AX-123323366 25 6785212 AGCAGCCCAATTACCTGATGAGACAAAAAATAGCC[A/G]CAGATGGGATTTCCCTGCTGGTCCAGTGGTTAAGA R 2 1 2 1 201000 f 74 goat snp43020-scaffold570-1015516 25 6609195 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392545 Affx-122966095 AX-123262902 25 6841114 GCTCAGATGCTACAAGTTGTGTAATCTGGAGAAAA[C/T]GTTGAAAATTGGTGGAGGTCCTTTTTCTCATCCTT Y 2 1 2 1 101000 f 74 goat snp43021-scaffold570-1071418 25 6666200 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420210 Affx-122945543 AX-123290558 25 6883154 GGCCCTTTAATTGTGGTGAGTAAAACCTTGAGCAA[C/T]GGAATCAGACAAATTTGAGATCCAGTCCTAGGTTT Y 2 1 2 1 101000 f 74 goat snp43022-scaffold570-1113458 25 6708332 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432774 Affx-122935430 AX-123303115 25 6912416 TTGGGAAACTCTATCCCTTCTCTTTGGGATTCACA[A/G]GCACATCATCCTATTCAAGATTCTGAGACAGCCTG R 2 1 2 1 101000 f 74 goat snp43023-scaffold570-1142720 25 6737054 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444661 Affx-122926458 AX-123314998 25 6941744 TCTCTTCTCCCCTCACTTTCTGCCTCCCCTCAAAA[C/T]GCAGTAATGAGGAATCCAGTATAAAGTAATTAGAC Y 2 1 2 1 101000 r 74 goat snp43024-scaffold570-1172048 25 6766746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421670 Affx-122944428 AX-123292017 25 6975283 GTTAGTGTTAGCACCTGAATTGGAGCACGTGCCTA[A/G]GCCAGTCCTGTGGTTTCCCCTGGTGGCTCAAATGG R 2 1 2 1 101000 f 74 goat snp43025-scaffold570-1205587 25 6800279 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398450 Affx-122961605 AX-123268805 25 7035556 AAGAATGCCGTCTGGTCCCCTGGCAGGCTTCACAC[A/G]GCAGCCCTTCCTCTTCAGAGAGAACGCCTCCTTCC R 2 1 2 1 201000 r 74 goat snp43026-scaffold570-1265860 25 6861363 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411500 Affx-122951686 AX-123281850 25 7077685 TAAAAGGATACAGGACATACTGCGGTCTTAGCCCA[C/T]GGACATGAGAAAGATTTCCAAGAGGTGAGCGGTGG Y 2 1 2 1 101000 f 74 goat snp43027-scaffold570-1307989 25 6903396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377492 Affx-122977495 AX-123247851 25 7111309 GGCCTCTCCAAGGCAACCACCGTACCATCACCATC[A/G]CCAGCGATGCCTTCTCCTCACTGTCAACAAAAGCA R 2 1 2 1 101000 r 74 goat snp43028-scaffold570-1341613 25 6937501 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777058 Affx-122949354 AX-385264181 25 7140705 GAAATCCGCCTTGCCCTTCATCTGCGTATGATTCT[A/G]TACTTGCATAGTGGTTCAAATGTCGGTATTTAACT R 2 1 2 1 101000 f 74 goat snp43029-scaffold570-1371009 25 6966927 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770096 Affx-122977792 AX-385257263 25 7173413 GGAGGATAAACAAGATGGCTTCTGAAGTGATGTAG[C/T]GCTTCATGGCAGTAAGAGTCCAAATGAGTTCTACA Y 2 1 2 1 101000 r 74 goat snp43030-scaffold570-1403717 25 6999359 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422865 Affx-122943085 AX-123293211 25 7202609 TCTCTCTGAGGTCTGCTGCCCTCAATTTGGAATGG[A/G]CTAAAGATACGGTAGCCAGAAATGGACTTTAGTAT R 2 1 2 1 201000 r 74 goat snp43031-scaffold570-1432913 25 7029150 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434868 Affx-122934359 AX-123305209 25 7254230 AAAAAGTCTGCATAGTTCCTGTCCACTCTTTGATG[C/T]ATCTGGACTTAGGCGTGGAGGGTGAAATCATCACC Y 2 1 2 1 101000 r 74 goat snp43032-scaffold570-1484534 25 7080110 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418174 Affx-122947081 AX-123288522 25 7286620 CTCTGCTTGATGAGGAGGAGATCTTCATAATGAGA[C/T]ACAGTGTCCCAACTCGTCCGGCTGATAAATGCTAA Y 2 1 2 1 101000 f 74 goat snp43033-scaffold570-1516924 25 7112633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414222 Affx-122949644 AX-123284571 25 7317886 TACTGGACAAATCTGTACTGGACATCACACTCCTC[A/G]CTCCACCCTCAAGGTATCTAATGATCAGACCAGTG R 2 1 2 1 101000 r 74 goat snp43034-scaffold570-1548190 25 7144301 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388732 Affx-122968965 AX-123259090 25 7346586 CTACCTTATCCTGACTGATGCATTTCCTCCATAAG[C/T]ATTTTACTAGGATACCAATAGTTTCCACCTTGATT Y 2 1 2 1 101000 r 74 goat snp43035-scaffold570-1576890 25 7172967 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766392 Affx-122949000 AX-385253770 25 7384942 GGAATTTTAAGTCTGTGCTCCTCAGTTGCAGAGAA[C/T]AGTTATCTGGTCTACCTCACTGTGCAGATAAACAC Y 2 1 2 1 101000 f 74 goat snp43036-scaffold570-1615246 25 7211145 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425805 Affx-122940696 AX-123296151 25 7421351 AGACAAGGTACAACCTTGCCTTGTCCCACTAGCGA[C/T]TTGGAATCAGGCCTGTCTGAGGCCTGGCCGGCTCT Y 2 1 2 1 101000 f 74 goat snp43037-scaffold570-1651655 25 7247549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441109 Affx-122929600 AX-123311446 25 7503657 ATTAATAATTCACCATTGACATCCCCACAGCTATC[A/C]AAAAGTAGCAGTAAAAAGAACATGAAAGCTTTTTT M 2 1 2 1 101000 f 74 goat snp43039-scaffold570-1733961 25 7328072 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432398 Affx-122935847 AX-123302739 25 7539700 TCCAAATGAGGTCCCATTCCCGGGTACTAGGATCA[C/T]GTTTTTCTGGAGGGTGATACCCTTCAGTCCACTCC Y 2 1 2 1 101000 f 74 goat snp43040-scaffold570-1770004 25 7362696 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429166 Affx-122937974 AX-123299508 25 7559405 ATAAGGGCATACTCTTGATCCTGAAATTCCACTTT[A/G]AGAAACAGAGAAGCAATTGCTCCGAAAGGTACATT R 2 1 2 1 101000 f 74 goat snp30552-scaffold3385-18984 25 7382738 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378336 Affx-122976842 AX-123248695 25 7594311 TTAGTGATTATCTTCCCCTTGAGAGGGTGTGCATG[C/T]AGGCAGCATATTACAGTTAGTAAGGCCTTTTCATG Y 2 1 2 1 201000 r 74 goat snp30553-scaffold3385-53890 25 7417895 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453822 Affx-122919556 AX-123324155 25 7622898 CGCCCGGCTGGCTGAATCACCACCCGCTCCCCACT[A/G]CATCCCTGCAGAAGGCCCAGGAGGTGGTTCTGAGC R 2 1 2 1 102000 r 74 goat snp16182-scaffold1701-15096 25 7445513 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395579 Affx-122963840 AX-123265934 25 7668610 GATATTCCAAGCAATTATGAAACATTAAGAATTTA[C/T]GTTTTCTAATATCATGGCTTTTTATAGATTGGCAG Y 2 1 2 1 101000 r 74 goat snp16183-scaffold1701-60808 25 7491250 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436531 Affx-122932934 AX-123306869 25 7701960 TGAGGTTCAGGGGGTCTCTCCTGGAGGTGAGACAA[C/T]TTTGCAACTGATTGATTTGACTTCAGATGCTTCTA Y 2 1 2 1 101000 r 74 goat snp16184-scaffold1701-94158 25 7524603 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425288 Affx-122940961 AX-123295634 25 7746855 CACCCGGGATGAAGAGGTCCCCATCTTGATGCCCC[C/T]TTGGCTTTACCCACCACCCACCACCCCCCAGGAGG Y 2 1 2 1 303000 r 74 goat snp16185-scaffold1701-139053 25 7569990 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390730 Affx-122967920 AX-123261087 25 7796474 TGTCTTATGATAACATGGAGTGGATGTTTTATTAA[C/T]AATAACATCAGCAACATTAGAAACAGCCGAGAATG Y 2 1 2 1 201000 f 74 goat snp16186-scaffold1701-188672 25 7618869 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450990 Affx-122921729 AX-123321324 25 7841668 AAATGGCGAAAATGACCATGGGGGCGGCTAAGGAA[A/G]TCACGTGGCCAATATGCTTCTAGGCTGTGAAACAA R 2 1 2 1 101000 r 74 goat snp16187-scaffold1701-233866 25 7664498 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430440 Affx-122937734 AX-123300781 25 7913646 TACTTATTAGAGGAGGCTGGCTGCAGTATGGAAAG[A/C]AGACAGCAGGGGGCGAGAGAGAGACGCCCGAGGCC M 2 1 2 1 101000 f 74 goat snp16189-scaffold1701-305844 25 7735732 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427615 Affx-122939357 AX-123297958 25 7969699 GCCATTTTCTTTGGTAAGAGAAAGCAGGTCTTCAC[A/G]TCTGCCAGAACACAATTTATATATTGGCTCCATTA R 2 1 2 1 101000 f 74 goat snp30456-scaffold336-26262 25 7792023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439393 Affx-122930257 AX-123309730 25 8003278 ATAGATGGCTACGGCTCAGATGTGGGCACCTCTCT[A/C]TATATATAGATACAGATTTGGATCAAGACACAGAC M 2 1 2 1 201000 r 74 goat snp30457-scaffold336-59841 25 7825513 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774284 Affx-122937198 AX-385261420 25 8050510 AATATATCACTGGGGTTGCTAGGAGGATGTTAATA[C/T]GGGCCACATATAAGGTAACATTATTGTATAATGTT Y 2 1 2 1 101000 r 74 goat snp30458-scaffold336-107073 25 7873383 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423876 Affx-122942305 AX-123294222 25 8094386 CCTTGATTCACATCCTGGTTCTGTTTCTCCTTGCC[C/T]GTGTGATTTTGGATGACTTACTTGACTGCTCTGAG Y 2 1 2 1 201000 r 74 goat snp30459-scaffold336-150949 25 7916856 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765006 Affx-122961988 AX-385252580 25 8133351 TGAGGTGGTTTCCTACACCATACAACTCACTCCCT[A/G]TAAATCATTACCAGGCAGGCATCAACACCATCATA R 2 1 2 1 101000 f 74 goat snp30460-scaffold336-189914 25 7955522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273128 Affx-1111833302 AX-519546792 25 8152528 AATGATAGCATTTCCTTCTTTTAAGTGGGTTTCAC[A/G]GGGACAGAGACCAAATTTGTTCCATTAATTACTGA R 2 1 2 1 101000 r 74 goat 25_8152528_AF-PAKI 25 8152528 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38445078 Affx-122926213 AX-123315415 25 8190809 GGGATTGGGACTGTCTGGCCTGGGTTCAAGAGCCT[A/G]CCTTTGCATATGTGAGCTGAGTCTCTACCCCACCT R 2 1 2 1 101000 r 74 goat snp30461-scaffold336-247372 25 8012664 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423088 Affx-122942929 AX-123293434 25 8223566 AAACATGACCATATTCTAGAAAGAGTTTTGAATGA[C/T]GGGGAAAAGACTTTCCTAATTCTGTCAGGTGTCTC Y 2 1 2 1 201000 f 74 goat snp30462-scaffold336-280129 25 8045578 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440412 Affx-122929611 AX-123310749 25 8256976 TTTCCGGGGCTCAGCGCATGATCACATGCAAGGAG[C/T]CTTGGCTTTGAATGCTCAACAGAGTGTCAGGGGCT Y 2 1 2 1 101000 r 74 goat snp30463-scaffold336-313539 25 8078853 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385127 Affx-122971773 AX-123255485 25 8309849 CAAATTTGTAGAGCTGCCAAGAACCCAAACTCTGG[C/T]GTGGAGATTGTAATGCTTGGTGAAACAGCCAGGCC Y 2 1 2 1 101000 f 74 goat snp30464-scaffold336-366412 25 8132394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414820 Affx-122949205 AX-123285169 25 8353111 TGCTTTCCTGAAAAAAGAAGACAAGATGAAGTTCC[A/G]TTGTACTTCTCTCCCCACTCTTTTCAGCCTTGAAT R 2 1 2 1 101000 r 74 goat snp30465-scaffold336-409674 25 8175565 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418333 Affx-122946960 AX-123288681 25 8498417 GCTATTTTATTCTCTAAACATGCTGATGTAAAAGC[A/C]CTCCAACAGAGAGACTTCTGGTCCACAGCGCTGTC M 2 1 2 1 101000 f 74 goat snp30468-scaffold336-554980 25 8321854 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406549 Affx-122955112 AX-123276901 25 8527675 AGCTGAAAGTCTGATTCTACCTCCCGCACCTGCTC[G/T]AAAGTGACAACTTTTGTTGTGACGTGGACTAAATC K 2 1 2 1 101000 f 74 goat snp30469-scaffold336-584238 25 8351315 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419469 Affx-122945481 AX-123289817 25 8568443 ACTGGGCAGCTCTATCAAGTGTCAAACAGTATAGA[C/T]GGTCACAATTTTCCATTAGCCAGTGGAGTTGGTGA Y 2 1 2 1 101000 r 74 goat snp30470-scaffold336-625006 25 8392217 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436183 Affx-122932608 AX-123306522 25 8602527 TGCTAAGAACTAACCTGGCAGCTGGAAAACTCACA[C/T]GTCCTCCCACTCCTGCTAGAAAGAGCAAGAGGACA Y 2 1 2 1 101000 f 74 goat snp30471-scaffold336-659090 25 8426341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769534 Affx-122936244 AX-385256704 25 8634117 TAGTCAATATTTCACTCAAGAGAATGAAGCACAGA[C/T]GCTAACACCACATATCAATAAAGACAGTGGAAGGG Y 2 1 2 1 101000 r 74 goat snp30472-scaffold336-690680 25 8457947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384739 Affx-122972042 AX-123255097 25 8665710 CTGCCTGGACCACTCACTCCCTTACCTTTGGACAC[A/G]GATTCAGGATTTGGGCTCTGGATTAGACACATCTT R 2 1 2 1 101000 r 74 goat snp30473-scaffold336-722273 25 8489715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404996 Affx-122956391 AX-123275348 25 8744897 CTTCACTCTGGACTGGCCTTTTTCTTTACAGCTGA[C/T]GAGAAGAATCCACTGAAGGATTTTTAGCAGAGATA Y 2 1 2 1 101000 f 74 goat snp30475-scaffold336-801460 25 8568544 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275063 Affx-1111834573 AX-519548645 25 8781899 GTTCATTCAAACCAGC[A/G]GGAAGAGAAGATAAATGCTGAGCCTGCACACTTGG R 2 1 2 1 102000 r 74 goat GoatD01.041924 25 8781899 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38402173 Affx-122959188 AX-123272526 25 8800297 TATCACAGGGAAGGGCCATCCTGCTTCTGCCTAAA[C/T]GTGTCACATGATGGGAGCTGACTATTTTCACAAGC Y 2 1 2 1 201000 r 74 goat snp30476-scaffold336-856860 25 8624384 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421842 Affx-122944298 AX-123292189 25 8890456 GGGAGCCAGGAAGTAAAGGTTGTAGGCTCTGTCCT[A/G]CCACTCATCTGCTATGTGATTCTCTGTAAACGTGT R 2 1 2 1 201000 f 74 goat snp30478-scaffold336-947019 25 8715946 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381824 Affx-122974266 AX-123252182 25 8922171 GTTTCCAGGCCTCTCTGCCTGAGCTGAAATCATTA[C/T]GCTGTTTCTTTCACTGCACAGGAATATGGGGGTTT Y 2 1 2 1 101000 r 74 goat snp30479-scaffold336-978734 25 8748208 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433106 Affx-122935711 AX-123303447 25 8965754 GGGAATATAAAAGTGAGGTGCGGCTAAATTAAATA[C/T]ATTCCACAGCAGATGTCATAAAAGAGATGCAAACT Y 2 1 2 1 101000 f 74 goat snp30480-scaffold336-1022317 25 8791699 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425289 Affx-122940960 AX-123295635 25 9005979 ACAGTGGACGAATAAGCCACATGTCACACTTCCAG[C/T]AATAACTCTTCCTGGGATCGCTGGCAGCCAAACAG Y 2 1 2 1 101000 f 74 goat snp30481-scaffold336-1062542 25 8832163 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389834 Affx-122968172 AX-123260191 25 9035948 TGTGTTTTTTATTTGTGTATTTATAGTACCTCCAG[A/C]GGGAGAAAATTTGGATCCCAAGATGCCTACTGTGG M 2 1 2 1 101000 r 74 goat snp30482-scaffold336-1092511 25 8862601 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771250 Affx-122973092 AX-385258408 25 9092517 TAAAAATAAGTGAGATTTTGGCTTTGATTCAAAAG[C/T]ATACAATTTAAAGTTGGAAAGGAACTTAGAGGAAA Y 2 1 2 1 101000 r 74 goat snp30483-scaffold336-1149080 25 8919565 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407532 Affx-122954698 AX-123277883 25 9153581 AAGATACAACTGAATTCTTAAGAAAAAATATCAAA[C/T]GCCTTCAAGAAGTGGGCTTTGATTGGATTGATAGA Y 2 1 2 1 201000 f 74 goat snp30484-scaffold336-1210144 25 8981316 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410395 Affx-122952429 AX-123280745 25 9241789 AGTTACTGCTATCAGCTTTATTGTGGTGGGAATGT[A/G]TTCTGTGGTGCCTGGTACCTGGCGTATCTGAGTAG R 2 1 2 1 201000 f 74 goat snp30485-scaffold336-1298352 25 9071498 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439446 Affx-122930184 AX-123309783 25 9290669 TGTTAGTTATGGAAAGCTATTATCTGTTGGAATTT[G/T]TTTTTGTATGAAACTGTTCACTTAAAAATATAAAG K 2 1 2 1 202000 r 74 goat snp30486-scaffold336-1347232 25 9120663 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440450 Affx-122929399 AX-123310787 25 9330550 AAAATATGCAAACTACAGTTCCCTCAAAGGCAGTC[A/G]TCATCAGTAATACATTTGGTCCTAATATTTGCCTC R 2 1 2 1 101000 r 74 goat snp30487-scaffold336-1387113 25 9160822 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403082 Affx-122958508 AX-123273435 25 9369972 GCACCTCCTGTTCCCAGCACCCCCATCCCACCCCC[A/G]TTCTTCTCTGGATGAGATGACGCCAACATCCAAGG R 2 1 2 1 101000 r 74 goat snp30488-scaffold336-1426535 25 9200327 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421937 Affx-122943827 AX-123292284 25 9399905 TAGGTGGGAGGTGGGGCAGGTAGAGAGAGTGAAGA[C/T]GGGGAGGGGCTGAAGAGTTTCTTTAAAGCCCGAAA Y 2 1 2 1 303000 f 74 goat snp30489-scaffold336-1456468 25 9230275 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393745 Affx-122965221 AX-123264100 25 9455525 TGACTTAGTGGCTAAGCATAGCACTCCATACCCCA[C/T]GCCAAAGTGTGGCCTATGTGGGTGGGCTTAGAGTG Y 2 1 2 1 102000 f 74 goat snp30490-scaffold336-1512088 25 9286061 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437309 Affx-122931970 AX-123307647 25 9498690 AGGTGCTGTTTCACTCACGATCCTTTGAAATAGTC[A/G]AGGACTTACCTCCTTCCAGCCCATCGGAAGAGTGA R 2 1 2 1 101000 f 74 goat snp30491-scaffold336-1555253 25 9329639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443911 Affx-122927049 AX-123314248 25 9543693 GTAAGCCAGTAAGAGGAAGGCAGAGGGAGACTGAT[A/G]CAGAGGAAAAAGCGATGTGAAATAAAAGTGAGGCT R 2 1 2 1 201000 r 74 goat snp30492-scaffold336-1600256 25 9374861 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451186 Affx-122921335 AX-123321520 25 9572856 ATTAACACCCATTCCGAAGGTGGAAGCTTCAGATA[A/G]ACACTGAGTGCCCATGAATGCAGAATATTTTGGTG R 2 1 2 1 101000 f 74 goat snp30493-scaffold336-1629419 25 9403200 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399544 Affx-122961140 AX-123269899 25 9623745 AGGGAGCAGGAGGAAAAGAGGAACTTGTTTGATCC[A/G]CTGAGATGCTGACTGGGAGCTGCTTGTGGTAGATA R 2 1 2 1 201000 r 74 goat snp30494-scaffold336-1680308 25 9453614 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse405 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38411413 Affx-122951841 AX-123281763 25 9665920 GGGCTTGTGTCCCCATTTGAAACAAACTGCTAGCT[A/G]TTTGTTACAAGGATTACATGAAATTGTGTTGGTGG R 2 1 2 1 201000 r 74 goat snp30495-scaffold336-1722483 25 9495662 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384579 Affx-122972995 AX-123254937 25 9725385 TCCCTAGTTTCCCCAGGGGTGACGTCTTGCAAAAC[A/G]CTAGGACAGTGTCAGAAAGCAGGATATTCACATGG R 2 1 2 1 101000 r 74 goat snp2520-scaffold1074-21763 25 9555284 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse406 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38452275 Affx-122920756 AX-123322608 25 9775441 CAGGACAGCAGGCTGTGTTAGTCAAGACTCGGCTG[C/T]AGTTGACAGAAACCCAGCTCAGACTCACTGAGACA Y 2 1 2 1 201000 f 74 goat snp2521-scaffold1074-71819 25 9605253 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422822 Affx-122943191 AX-123293168 25 9831009 TGAGTGCTTAGCACAGAGCCTGGTGCTTATTGAAA[C/T]ACTCAATGGACTGTGTATGTTATGGCTCAAAATTA Y 2 1 2 1 201000 r 74 goat snp2522-scaffold1074-127387 25 9660942 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse407 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320798155 Affx-122968944 AX-385285090 25 9873527 GTTCTTTGTTATTATTGATATGGGGTCAGGGGCCT[A/G]CCAGAAGGCTCAGAATCCCATAAGTAAAAAGCCCA R 2 1 2 1 101000 f 74 goat snp2523-scaffold1074-169905 25 9703561 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428191 Affx-122939018 AX-123298534 25 9919128 AGAGCTCCGTGCCCTCTGGAGCAGACCACCCAGGA[A/G]GGGGAAGCAGGCAGTAAAGAAAATAAGTACAGAAA R 2 1 2 1 103000 r 74 goat snp2524-scaffold1074-215506 25 9749156 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse408 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38413397 Affx-122950719 AX-123283746 25 9958868 GTCCCTCAGTCAGACACGACTGAGCCACTGAACAA[C/T]GACACACAGATTATGGGAGATTACAGAGGCCGCTT Y 2 1 2 1 101000 r 74 goat snp2525-scaffold1074-255246 25 9788658 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445400 Affx-122925389 AX-123315737 25 10015090 GGGAATTTCTTGACCCTCTTCAGAAGAAATTGTGC[C/T]GTGATGTGATTGATGGTGGAGAACTATTGTAACTT Y 2 1 2 1 201000 r 74 goat snp2526-scaffold1074-311468 25 9843816 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse409 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38392407 Affx-122966209 AX-123262764 25 10046069 GTGTTTATCTAGACATGGTCTGCAAACCTCAGGGT[A/G]CCACCTCTTTTTGCTTGGCCTATGAGCTAAGAGTT R 2 1 2 1 101000 r 74 goat snp2527-scaffold1074-342447 25 9875260 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387346 Affx-122970487 AX-123257704 25 10156052 AAACATGCGCAATTGGAAACCACAGAAGAGGACAA[C/T]GAGAACTGGTCAGAAAGAAATCTTTGAAGAAGCAA Y 2 1 2 1 101000 f 74 goat snp2530-scaffold1074-452430 25 9985603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse410 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320803419 Affx-122976347 AX-385290250 25 10191722 CTCATACAAGTCTGTTTACACTATTTCTCTTCTAT[A/G]CAGTGAGAACTGATAATACTTGCCGCACAAGGGTT R 2 1 2 1 101000 r 74 goat snp2531-scaffold1074-488100 25 10021054 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437122 Affx-122932164 AX-123307460 25 10229561 ATGTGCCCAAGTCAAGTATCACTTTTATTTAAGAC[C/T]CTAAGAATTTGATGGATAAGCACAGACCACCTGGA Y 2 1 2 1 101000 r 74 goat snp2532-scaffold1074-525939 25 10058841 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse411 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38393835 Affx-122965161 AX-123264190 25 10291181 CTGGGGCATCTTTCAAAGTCTTAGGTTGCAATCGG[C/T]GAACTTCTCTTACAAAGGGCCAGGGAGTACGTGTT Y 2 1 2 1 101000 f 74 goat snp2534-scaffold1074-587559 25 10120560 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445753 Affx-122926080 AX-123316090 25 10344710 CACTGCCTTCCAGAGCAGGACTGAAGCCCAAACAC[A/G]TAATTCCCACTCCCAAGGCTGAATCTTTCATTACT R 2 1 2 1 201000 r 74 goat snp2535-scaffold1074-641088 25 10173913 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse412 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38421554 Affx-122943860 AX-123291901 25 10400223 GGCCCAAGTCACAGCGCGCCCAGCAGGGGCCAGGG[A/C]ACTGGGTTAGGAGATCCCAGCACTGATGGCCTTGA M 2 1 2 1 101000 r 74 goat snp2536-scaffold1074-696601 25 10229664 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398923 Affx-122961003 AX-123269278 25 10436214 AAGCCGCACCACTGTGCGTAGTAAAGTAGCAACAC[A/G]TCCTGTGGGAAGAAGAAGTTGGCTGTTACTGGGCT R 2 1 2 1 101000 f 74 goat snp2537-scaffold1074-732592 25 10265761 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse413 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38445148 Affx-122926163 AX-123315485 25 10469348 AAAACGCAGAAATAAAAGATTTCTGTCAGAGCTAG[A/C]TGTCAGGGCTAAAACCCAGCCCTGTAGAGTCCTAG M 2 1 2 1 101000 r 74 goat snp2538-scaffold1074-765726 25 10299008 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396624 Affx-122962877 AX-123266979 25 10527582 CCCCTGTCTTTCTTGGATGCGATCACCTCACACTC[C/T]CTGGGTCCAGGTCAATGAGAACCCAAGCGAAGAAT Y 2 1 2 1 201000 f 74 goat snp2539-scaffold1074-823960 25 10357393 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse414 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320801047 Affx-122950497 AX-385287961 25 10564697 ACAACATGAGATATACTCTCTTAAGTTTTTAAGTG[C/T]GCAAAACCATTTTTGAAAATGATTTTGATATCAGT Y 2 1 2 1 101000 r 74 goat snp2540-scaffold1074-861075 25 10391007 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789065 Affx-122950716 AX-385276078 25 10616398 AAAATGTATGGTGTTGGTTAATTTAACAATGAGGT[G/T]TCTTCTAAATAATCTTACTTGCATAAATGTGCAAG K 2 1 2 1 101000 f 74 goat snp2541-scaffold1074-912776 25 10442443 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse415 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320764991 Affx-122936047 AX-385252568 25 10652734 TCCTCAGTAAACCTCCAGGAGAGAAGGAAACATAC[A/G]TATCTCTCTGGATGCTATAAAGCTTTTTAAAGTTT R 2 1 2 1 101000 f 74 goat snp2542-scaffold1074-949112 25 10478916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379947 Affx-122975645 AX-123250305 25 10701108 TTGGATGTGGCTTCCTTGAAAAATACCCAGGTGGA[C/T]GGGCGCTTCTCCCATGCAGTCTTGACCTCATGGGC Y 2 1 2 1 101000 f 74 goat snp2543-scaffold1074-997486 25 10527654 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse416 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38396944 Affx-122963182 AX-123267299 25 10745562 TCCTTTTGCAGAGGTGGGGAGGGGTGTGGGAGAAG[C/T]AGCTGAGGCCCCAGGGGGAGGGAGGACCCTTCCTC Y 2 1 2 1 103000 f 74 goat snp2544-scaffold1074-1041940 25 10572119 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400040 Affx-122960779 AX-123270395 25 10826398 CAGCCACAATGGCCACAGAGCCTAAAGTGTTGACT[A/G]TCTGGTCCTTTTCAAAAAATTTTTGTTAATCCCTG R 2 1 2 1 10000 f 74 goat "snp2546-scaffold1074-1122776;SV_157" 25 10652032 A G SV_157 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406309 Affx-122955465 AX-123276661 25 10856957 GAGGATAATTATGCCAGTCCAGGCGAGATGGCAGA[C/T]GGGCCTGGCATCGGAGGAGAGGTTCTTCCTGGACG Y 2 1 2 1 10020 f 74 goat "snp2547-scaffold1074-1153335;SV_157_right" 25 10683092 C T SV_157_right 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382028 Affx-122974953 AX-123252386 25 10889973 TAAGTACTATTTTTACATAGGTATGCGACCGTTAG[C/T]GTGTACATGTAATTGTAAAAAGAAGTATGGTTGAT Y 2 1 2 1 101000 f 74 goat snp2548-scaffold1074-1186351 25 10716387 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse418 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38418616 Affx-122946347 AX-123288964 25 10929195 TCGCGTCTGCTCTCCTTGCCTATTCTTACCTCTTC[C/T]GGGGAGGGTGATTTATTGGAACACCCATTCTCACG Y 2 1 2 1 101000 f 74 goat snp2549-scaffold1074-1225573 25 10754913 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383236 Affx-122972757 AX-123253594 25 10971541 TCAGTAAGGACATCCTGAACTACACTTGCAACTTT[C/T]AAGTCTTTTTATTAATCTGAAATCAATATGGAAAT Y 2 1 2 1 101000 f 74 goat snp8811-scaffold1314-2739103 25 10796974 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse419 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468273052 Affx-1111833288 AX-519546723 25 10997729 TGATGGGCCCAAATGGATACAAACCCTGTCTTCTC[A/G]GAGGAAGGCTCTCACATCCCAGTGCAGAGGCTCCA R 2 1 2 1 201000 f 74 goat 25_10997729_AF-PAKI 25 10997729 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38412643 Affx-122950794 AX-123282992 25 11021683 GAGTCTTCATAACAACAGCATCCACCATTCTGAGC[A/G]CTTGCTGCTGCGGGAAGGGGAGGGTACGGTGAAGA R 2 1 2 1 101000 f 74 goat snp8810-scaffold1314-2688961 25 10847147 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415515 Affx-122948681 AX-123285864 25 11061602 GCGTGGTGACAGCTCCACATGACGTTGCTCCTCCC[A/G]TTCATGACATCACAGCATCCTCACTGCTGCAAGAA R 2 1 2 1 201000 r 74 goat snp8809-scaffold1314-2649042 25 10887023 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse420 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38416323 Affx-122947913 AX-123286672 25 11090608 GTTCCTTTCTGTAAACACAGCAGATAATGTTGTTT[A/G]CCTGGCATCATACAGTGGTCGTAATTATAACCCAT R 2 1 2 1 101000 r 74 goat snp8808-scaffold1314-2620036 25 10916063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376134 Affx-122978863 AX-123246493 25 11148271 GCCATGTCGTCTATCACTGTTTAGTCTAAAGTCCC[A/G]TAGGGACATTTCTTTCAGAGCTCTCTTTGAGGAAC R 2 1 2 1 101000 f 74 goat snp8807-scaffold1314-2562373 25 10973721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse421 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38440766 Affx-122929856 AX-123311103 25 11177621 GACATCTCAGTGCAGCAGAGACGGTCCCTGACTAA[C/T]GATGGTTGCACTCAGGACTGTAACTTTAGGATGGC Y 2 1 2 1 101000 r 74 goat snp8806-scaffold1314-2533023 25 11003361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398498 Affx-122961563 AX-123268853 25 11217637 GGAAGAGGGAAGACATGGAGGATGATAAACTGAGC[C/T]TCAAAGATGGAGGAGGTAGGGATCTCTGAAGACTG Y 2 1 2 1 101000 f 74 goat snp8805-scaffold1314-2493007 25 11043394 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse422 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38423747 Affx-122942854 AX-123294093 25 11276763 GGGTTATCTGAACGTAATAACACAGAGCATCTCCA[C/T]ACCTGCCTGGTCTGTTAGGACCTCAAAAGAGTGTC Y 2 1 2 1 101000 f 74 goat snp8804-scaffold1314-2433881 25 11103522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425495 Affx-122941481 AX-123295841 25 11305898 CAGCAGGGTCTGCTCTGGAATCTCAGGCCAGTCAT[G/T]TAACCTATGGAGCCTCAGCTGGCTCACCTGTAAAA K 2 1 2 1 201000 f 74 goat snp8803-scaffold1314-2404746 25 11132488 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse423 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38424525 Affx-122941727 AX-123294871 25 11339454 AACTGTAACAGAAGAGGGTAGTTAAGATAATACTA[C/T]GCGTTTCACAGCCCATCTGTGGACTTCTCAGCCTC Y 2 1 2 1 201000 f 74 goat snp8802-scaffold1314-2371190 25 11165871 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274949 Affx-1111834596 AX-519548531 25 11383421 TGACCTGCTCCTTGTCTGTCTCACCACCGTTCTGT[A/G]AGGTCTTTAGGAATGGGACCTGCAGCCTTGTCCAC R 2 1 2 1 202000 f 74 goat GoatD01.042587 25 11383421 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38378539 Affx-122976620 AX-123248898 25 11397147 TATACACAAATGATTTCTTAAGGTCTTTCTCAGCA[C/T]GAAGAATTCTTAAAAACCAAGATGGAGGATCAAAA Y 2 1 2 1 101000 f 74 goat snp8801-scaffold1314-2313497 25 11224027 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse424 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38420439 Affx-122944899 AX-123290786 25 11485442 AAAATTATTCACATTCCTGGAGAATGTTTTCATTC[A/G]TTCAGAAATGACTTTCTTTCCCCTTTTTGGCCACG R 2 1 2 1 101000 r 74 goat snp8799-scaffold1314-2225202 25 11311381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389066 Affx-122968601 AX-123259424 25 11514134 AGGTCGAAAGAGGGCTGACGCTGCCCACCTCCACC[A/G]TCTGGTCTTGTACTGCAGGGGTCCCCAACCTCTGG R 2 1 2 1 101000 f 74 goat snp8798-scaffold1314-2196510 25 11339974 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse425 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38402830 Affx-122958263 AX-123273183 25 11550583 AAACACAAGTCAGAATCTCAGTTTTTTTCACGACA[C/T]CAACCTTCAGCTTGTGAAGAAGTGTTGCTGACTCC Y 2 1 2 1 101000 r 74 goat snp8797-scaffold1314-2160061 25 11376491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277735 Affx-1111835996 AX-519551234 25 11558486 CAGGGAGAGGAAACAGCACATGCAGAGGCCTGGAG[A/G]TGGGAAGTGGTGGACCATGAGGGAGGAAATATGAG R 2 1 2 1 102000 r 74 goat Random2.2K-2134 25 11558486 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38429458 Affx-122938487 AX-123299800 25 11602031 TGTAACAACTTTGTTTTAAAACAAGGAAATACATC[A/G]ATACAGGGACTTCCTTGGTGGTCCGGTGGCTAAGA R 2 1 2 1 201000 f 74 goat snp8796-scaffold1314-2108613 25 11428236 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse426 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38453268 Affx-122920394 AX-123323601 25 11642130 GGATGAGGAACCTTTTCTTATTTATCTCTGTATTT[C/T]CAGCATTAAACATGATGCCAGATGCTTGTTGCAAT Y 2 1 2 1 101000 r 74 goat snp8795-scaffold1314-2068514 25 11468063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449662 Affx-122922574 AX-123319997 25 11700252 ATCTATAAAGAACAATAAACCAAAACTTAATAAAA[C/T]AAGACATGCCTGTAATTAATATCTCACTTTGTTCT Y 2 1 2 1 101000 r 74 goat snp8794-scaffold1314-2010392 25 11526429 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse427 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38412572 Affx-122951313 AX-123282921 25 11739617 CTGAGTGTTTCTCAAGTTCAACAGCTTGGTAAACA[C/T]ACCTGGAAGCCTCCTTTAAGACTTCTTCTTTTTAT Y 2 1 2 1 101000 f 74 goat snp8793-scaffold1314-1971027 25 11565838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415542 Affx-122948657 AX-123285891 25 11776425 AACCTACCTGAGGGTCAGCACAGTGGGCTCAGGGA[C/T]GGACTGAACTGTCCCATTCTCCTCTCCACCCAGGC Y 2 1 2 1 101000 f 74 goat snp8792-scaffold1314-1934219 25 11601406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse428 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38393903 Affx-122965108 AX-123264258 25 11811926 CACTGATTTCCTCTTTCTTCAGCCAAAGTCTTTGC[A/G]TTTCACATTCTACTCCTATATAAAATGAAAATGAT R 2 1 2 1 201000 r 74 goat snp8791-scaffold1314-1898718 25 11636858 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386314 Affx-122970892 AX-123256672 25 11844480 GGGATGCTGCCTTGTTTTTCAATGGGTCCCACAAA[A/G]TCACATTACAGTTCCCAGGTGACTGGGATTCAAGC R 2 1 2 1 101000 f 74 goat snp8790-scaffold1314-1866164 25 11669504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse429 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38377835 Affx-122977295 AX-123248194 25 11900373 GAGGGCATGGGGAGTTAGAATGTAATAGGTACAGA[A/G]TTTAAGTTTTGCTAGACGTAAAGAGTTCTGGAGGT R 2 1 2 1 101000 r 74 goat snp8789-scaffold1314-1810271 25 11725301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277607 Affx-1111835997 AX-519551106 25 11937789 TACCTCCGCCGTTCACTATGTGATCCAGATGAATC[A/C]GCTGTGTCTTACTCACCTTTGCAGCACAAGCGTGC M 2 1 2 1 101000 f 74 goat Random2.2K-2136 25 11937789 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392715 Affx-122966034 AX-123263072 25 11942612 ATGCGTGTGTGGTGGAAACTGGGCATTCTGTGTAG[C/T]GCTGGTGTGTCTGCAGGGATGTGTAAGATATGTGA Y 2 1 2 1 102000 f 74 goat snp8788-scaffold1314-1768032 25 11767998 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse430 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38453870 Affx-122919522 AX-123324203 25 11986585 GGAAGAATAGCACAGAAAGGAAAAAATGGCCAAAG[C/T]GTGTTGCTTTGTGGAGCAGGTATTACCCATCACTT Y 2 1 2 1 201000 r 74 goat snp8787-scaffold1314-1724059 25 11811861 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405876 Affx-122955606 AX-123276228 25 12032475 TGGCTCTGCCTCAGAGGACTGTTGAAAGGAGGGAA[C/T]AAGGCAATGTCTGCGCAGTGCCTAAACCAGAAGGA Y 2 1 2 1 201000 f 74 goat snp8786-scaffold1314-1678169 25 11854675 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse431 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38403752 Affx-122958007 AX-123274104 25 12077476 TCAAAGTGCTAAATGTCTCACTGATGGAAAGAAAC[A/G]CGAGCAAATATTCTCTTCATCTCTTTTATAGTTTC R 2 1 2 1 101000 f 74 goat snp8785-scaffold1314-1633168 25 11899694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387905 Affx-122970459 AX-123258263 25 12112063 CCTCAGTCAATCAGTTGGAGATCTGAATAGAAAAA[C/T]GGAGTCTTCCTTGGTGACTGAGATGGTAAAGAATC Y 2 1 2 1 101000 f 74 goat snp8784-scaffold1314-1598581 25 11935267 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse432 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38383854 Affx-122973147 AX-123254212 25 12158127 AGTGTGAGTTTGGTCTGTTGCAACTCCTTGGATAG[C/T]AGTTACAAGGAAGAGCCTACCTACGCTACCAAAAT Y 2 1 2 1 101000 f 74 goat snp8783-scaffold1314-1552517 25 11981503 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450331 Affx-122922127 AX-123320666 25 12194458 ATGAAAATTCCCTTTCCTCTTTGATTTTTCCATCT[C/T]CTCTGAGTTGGGCCCCACTTTTTGCTCAAATTGAT Y 2 1 2 1 101000 r 74 goat snp8782-scaffold1314-1516186 25 12018240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse433 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38444423 Affx-122926571 AX-123314760 25 12224992 GTGAAGCAGACATCTTCAACAGTCCAGCAGATGCC[A/G]CAAGGTAACGAACTGAAGACCCAGAAATACATCCC R 2 1 2 1 101000 r 74 goat snp8781-scaffold1314-1485652 25 12043028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409016 Affx-122953876 AX-123279367 25 12256963 TGCCCTTAAACAAGATTGATGTTCAGGTTATTCCA[C/T]AAGCGACAGAAAATAATGTCAAGAGGGAGAAAAAT Y 2 1 2 1 101000 f 74 goat snp8780-scaffold1314-1453681 25 12074122 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse434 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38420927 Affx-122945000 AX-123291274 25 12292381 ACCACTGACAAGAACAAAATTGACTACCAGGCTGG[C/T]ACCTAGCCCCATGAAGAAGGAGTCCTGTGGCAGGT Y 2 1 2 1 101000 f 74 goat snp8779-scaffold1314-1418263 25 12109478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447780 Affx-122923949 AX-123318116 25 12336060 CAGGAGTTTGACACTAAGAGTGCTATTTCTCAGAA[C/T]ACCTACCTGGTTCTGGTCCTTGAATGCCTGATCCA Y 2 1 2 1 101000 f 74 goat snp8778-scaffold1314-1374584 25 12153461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse435 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38387571 Affx-122970277 AX-123257929 25 12377031 GAAACTTACAGTTGATGGTCTCTTGGAGGCATTTG[C/T]GGTGAGAGCTTGGTGATGGAGTGTGAGCCCTGAGG Y 2 1 2 1 101000 f 74 goat snp8777-scaffold1314-1333613 25 12194393 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802800 Affx-122941113 AX-385289699 25 12405617 CAACCTTTCTAATGACTTTAGTCTGCTTAACTTAC[A/G]GTTGAACCACATGTCAGTCAGACCAGGGGATCACG R 2 1 2 1 202000 r 74 goat snp8776-scaffold1314-1305027 25 12222684 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse436 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468277609 Affx-1111835998 AX-519551108 25 12506990 GTAATTAACAGGTTGCTGTTCAATAGAGAGGAAAC[A/G]CACAGATGAGAAGCTGGGGGAACTTTGGCCAGAAA R 2 1 2 1 101000 f 74 goat Random2.2K-2138 25 12506990 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38409017 Affx-122953875 AX-123279368 25 12533318 TTAAACTCACAAATGGGTCATTTCAAATGATAGAT[A/G]TTCAGAGCCACTCACAAATTGTTAGAATCAGGAAA R 2 1 2 1 101000 r 74 goat snp8773-scaffold1314-1177326 25 12351751 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450859 Affx-122922230 AX-123321193 25 12573789 CATCTGCCTGGCTTTGTGGGACTAAGCGAGGGAAA[C/T]GGTCTTATGGATTCTCCTCTCTGTGGATTCTCTAA Y 2 1 2 1 201000 r 74 goat snp8772-scaffold1314-1136855 25 12392097 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse437 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38381306 Affx-122974449 AX-123251664 25 12617107 AGTAAAGATGGACATTCATCCAATAATGTCCTAGG[C/T]GTATAATTATAAACTGTGAGTAGTGTTCTGGAAAG Y 2 1 2 1 101000 r 74 goat snp8771-scaffold1314-1093537 25 12435980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440998 Affx-122928964 AX-123311335 25 12649341 ACAATTTAGTTGAAGTCAGGCTAAGTGAAGGTTCA[A/G]CAGTAACGGTGGTTAGGTAGCTGAGGGGTCAAGAC R 2 1 2 1 101000 f 74 goat snp8770-scaffold1314-1061303 25 12468151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse438 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468277741 Affx-1111835999 AX-519551240 25 12705630 TCGTGGGGAATTAGAGACGTGAACTGACACAGTGC[A/C]CAGATGTCAATCATTCTATGACAATTCTCGCCTTT M 2 1 2 1 101000 r 74 goat Random2.2K-2139 25 12705630 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38412603 Affx-122951287 AX-123282952 25 12707212 TTTCTCTGTCACGGTTGGGATATAGCAAAGGAATC[A/G]CTGTGGGCACCTGAGCAGTGAGGAGTTCATCACTG R 2 1 2 1 101000 f 74 goat snp8769-scaffold1314-1003432 25 12526222 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779225 Affx-122954167 AX-385266329 25 12777955 ACTCTAATAGAGATGAATAGTAATACTATTAACTT[C/T]GGTAGGCTTAGTAGGATTTGAAGTTGGATGTAAAC Y 2 1 2 1 101000 r 74 goat snp8768-scaffold1314-932689 25 12598246 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse439 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38415491 Affx-122948699 AX-123285840 25 12822517 AAACTTCACGATGGGTGGGTAGACAGCTCCGTGCA[C/T]AGGCACCGAGTCACTCCACAGTGGAATCATTGTTT Y 2 1 2 1 101000 r 74 goat snp8767-scaffold1314-888127 25 12642938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784766 Affx-122974451 AX-385271813 25 12863071 ATAAGTGATAGCCATTTGAAATATCCCATTTTGTC[A/G]TTTCTTCATGATCTGGTCCTTTCTTGACCTCTTAG R 2 1 2 1 101000 r 74 goat snp8766-scaffold1314-847573 25 12683852 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse440 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38398154 Affx-122961677 AX-123268509 25 12910363 CGGTCAGAACACCAACTGGCCTGTTCTAGAGGTGG[C/T]GGTCTTTCTTCGATTAGCAGTAGCAAGTCCCGTGA Y 2 1 2 1 101000 r 74 goat snp8765-scaffold1314-800281 25 12731435 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421008 Affx-122944555 AX-123291355 25 12939783 TACTGAGGCTTCCTCCTAGGTGTCCTTCACAATTA[A/C]CTACTGCCTCACTTGGTTGCCATGATACGGAGCTT M 2 1 2 1 101000 f 74 goat snp8764-scaffold1314-770861 25 12760909 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse441 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468277616 Affx-1111836001 AX-519551115 25 12993816 AGAAGAAACCTCTGTGTGTTTAGGTCTGAACGAGC[A/G]AGGATCGAAGACTCCGAGTGCCAGGCATCTCTCTT R 2 1 2 1 101000 f 74 goat Random2.2K-2140 25 12993816 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449101 Affx-122923589 AX-123319436 25 12997821 GCAATCTAAATGGCTGTTAATAGGGGATGGATAAA[C/T]GGAAACACACCTGAAAATATAAGGGAATGAACAAG Y 2 1 2 1 101000 f 74 goat snp8763-scaffold1314-712823 25 12819054 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392837 Affx-122965774 AX-123263194 25 13040838 TCATGTGAATATTCTACCACCACAAATCCTGTATA[C/T]GAAGACAGAACTTCTCTTCTTTCCAACTTTCCAAT Y 2 1 2 1 101000 f 74 goat snp8762-scaffold1314-669806 25 12862376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse442 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320789972 Affx-122926936 AX-385276978 25 13070993 AAACAGATCTTCATGTTTAGTAGAATAATTCCAAG[C/T]AAAGTCAGTCAGGAGTTGGAAGAGAATTGAGGTCA Y 2 1 2 1 101000 r 74 goat snp8761-scaffold1314-639651 25 12891723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433814 Affx-122935171 AX-123304155 25 13122411 GGTAAGCCGACATGGGAGGCAGTCTGGACAGACTC[A/G]AAGAGGTTGATGGTGACTATAGAATGTTTTAATCT R 2 1 2 1 201000 r 74 goat snp8760-scaffold1314-588233 25 12943345 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse443 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38390914 Affx-122967091 AX-123261271 25 13167505 TCCTGGCAACAGCTATTTATACTTCATTGTGTGTC[A/G]TCTGTTTCTATCTAGATGTTTTTTTTTCCTACCAG R 2 1 2 1 101000 f 74 goat snp8759-scaffold1314-543139 25 12988992 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425947 Affx-122941184 AX-123296293 25 13209263 AGATGGCAATATGCAAATAAGAGATTCAAGATGCA[A/G]TTATTCTTTAAATATTTCCATATTCCAAGCCTCAG R 2 1 2 1 101000 f 74 goat snp8758-scaffold1314-501381 25 13031089 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse444 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320765746 Affx-122945426 AX-385253202 25 13240357 AAGCGATTTGTGGAAGGAGGAATGAAGGAATGGTC[A/G]TTAGGTGACTTGGGATTATGTGACACAGAAAGTTG R 2 1 2 1 101000 f 74 goat snp8757-scaffold1314-470287 25 13062121 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397966 Affx-122961901 AX-123268321 25 13282233 GGGTCTGGATCTCTACCTGCTTCTTGGGGATACAG[C/T]AATCCTTGGGTGACACTGACCACAAGATGAGCAGA Y 2 1 2 1 101000 r 74 goat snp8756-scaffold1314-428411 25 13102768 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse445 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38424333 Affx-122941947 AX-123294679 25 13320139 CCACTCTGTGAACCGGGTCTGTTGGGGTCTATTTT[A/G]TAGACTTGTTTGTGAGAATTAAACATGACGTATGC R 2 1 2 1 201000 f 74 goat snp8755-scaffold1314-390505 25 13140708 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442600 Affx-122928482 AX-123312937 25 13349119 GTATTTTTTGTCTAGATGCTGTTATCGGGTCATTA[C/T]GGCTTAGAATGGAGCACACAGGCTTACTTCAGTTC Y 2 1 2 1 201000 f 74 goat snp8754-scaffold1314-361525 25 13169911 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse446 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38397280 Affx-122962338 AX-123267635 25 13389841 TATTTCAACCGAATTTTCTCTCCCCGAGAGGAGTC[A/G]AGGTCAGGCATATGAGGTAGTTTTGAGTAAATGAG R 2 1 2 1 201000 r 74 goat snp8753-scaffold1314-320803 25 13210615 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793616 Affx-122958543 AX-385280590 25 13423269 ACATCAACACTTTTACTAATTTGCTAAGCATTATC[A/G]TGTATCCAGACATTTTCAGAGTCGCTTCACTCATT R 2 1 2 1 101000 r 74 goat snp8752-scaffold1314-287375 25 13244222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse447 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38453855 Affx-122919534 AX-123324188 25 13471426 TGGGTGCGAGGGGGCTAGAAGGGAAGAAGGCAGGA[C/T]GAGGAAGAGGACTTGTTTATGGGTGGCATCACAAT Y 2 1 2 1 101000 r 74 goat snp8751-scaffold1314-239218 25 13292171 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412584 Affx-122951302 AX-123282933 25 13520291 AGGTGTTAAACTCTCGTATGATTGTGGAAGTGTCT[A/G]TTTGCCCCTTTCATTCTGTCATTTTTCATGTCATA R 2 1 2 1 101000 f 74 goat snp8750-scaffold1314-190353 25 13342035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse448 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 468273103 Affx-1111833289 AX-519546768 25 13571678 ATTGGCAGACACACTCTTCACCACAAGCGCCACCC[A/G]AAAAGCCCCAAATATCTACTATGTGTACGTATGCT R 2 1 2 1 102000 r 74 goat 25_13571678_AF-PAKI 25 13571678 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320774272 Affx-122962166 AX-385261409 25 13577212 CTTTTGAGTATGGTGGTTCTGTTGATTGACGACCT[C/T]ATTCCTTAATGATGCTGATGGTCATGTTTTTATTC Y 2 1 2 1 101000 f 74 goat snp8749-scaffold1314-133432 25 13399236 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392217 Affx-122966272 AX-123262574 25 13634501 ACACATACTGTGTGTGTAGATTCTGGGCAATGAAG[A/C]AGCCTGCCACACACTGCCCAAACTTGTGAAGTTCA M 2 1 2 1 101000 f 74 goat snp8748-scaffold1314-76143 25 13456599 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse449 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320798680 Affx-122970443 AX-385285612 25 13707740 TGTGTTTTCTTGAAACTCACTAAGTTTCCTTAAAA[C/T]AGCTACTTGAATTCTTTATTGGGTGAATTGAAGAT Y 2 1 2 1 102000 r 74 goat snp8747-scaffold1314-2904 25 13529689 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796866 Affx-122933433 AX-385283809 25 13712202 TATCCGCATAAAGGTGTTGGAAACGCTGCCTATGG[C/T]GAAAGTGAAGCGGTTGCTGATGGTCTGGCTCAGGA Y 2 1 2 1 101000 r 74 goat snp14025-scaffold1554-455329 25 13534960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse450 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38387468 Affx-122970359 AX-123257826 25 13751510 TCAACCAGAAACAGAAACGAGGATTAAAGTACAGT[C/T]GATATCTGACTGATTATGCTAACTGTAGGGAAAAA Y 2 1 2 1 101000 f 74 goat snp14024-scaffold1554-416021 25 13573914 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377391 Affx-122977627 AX-123247750 25 13802230 CCACACTTTATGTTGCTGTTGCAAATGCTACCAGC[A/G]CAGCTGAAAGACATGTAAACGTCAGCAGGGAACAG R 2 1 2 1 101000 f 74 goat snp14023-scaffold1554-365301 25 13624389 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse451 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38412971 Affx-122951037 AX-123283320 25 13838569 CTGAATGAACCAATTATTCCCATTTTTTCATGTTG[A/C]GTTTTAAAGTCTACTTTTAAAATAGATAATGTATC M 2 1 2 1 102000 f 74 goat snp14022-scaffold1554-328962 25 13660700 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431739 Affx-122936741 AX-123302080 25 13867636 AGGTGTAGGAAATGTGGTCAAAGTGGTGTAGGAAA[C/T]GGCAACCCACTCCAGTATTCTTGCCTGGAAACTTC Y 2 1 2 1 102000 f 74 goat snp14021-scaffold1554-299895 25 13690028 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse452 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38400978 Affx-122960101 AX-123271331 25 13924541 TGAGGAAATGAAGAGATGAAAGAAAAATATGTGAA[C/T]GGATGACTTACCTGTTTGGGAATTTAAACAATATG Y 2 1 2 1 201000 r 74 goat snp14020-scaffold1554-242990 25 13746974 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383409 Affx-122973490 AX-123253767 25 13955239 GCATCCCTGTTCTCTTCTACTAGATGCCAAACACA[C/T]CCCCACCACCCCAGTTATGACAGTGAAGAATGTCT Y 2 1 2 1 101000 f 74 goat snp14019-scaffold1554-212292 25 13777204 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse453 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38447676 Affx-122924635 AX-123318012 25 14020869 CCAGGGACCAGTCCTACCCACTTTTGTCTCCCCTG[C/T]GGTGCTCAGCACGGTTCCTGGCACATAGAATGTCC Y 2 1 2 1 201000 r 74 goat snp14017-scaffold1554-146662 25 13842602 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399601 Affx-122961097 AX-123269956 25 14112348 TTATTTCAGAGTATTTTAGTTCAGGGACAGTCTGC[A/G]CTGAGGGCTGGCAGCTTCAGACAGGGGTCCAGGGT R 2 1 2 1 101000 f 74 goat snp14015-scaffold1554-55183 25 13934224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse454 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38403721 Affx-122958028 AX-123274073 25 14141921 AAATAGAGAAAGCCTGTGCACAGTGAAGACCCAGC[A/G]CAACCAAAAATAAATACAAACAATCAAGGGGATCT R 2 1 2 1 103000 r 74 goat snp14014-scaffold1554-25610 25 13963825 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405475 Affx-122956024 AX-123275827 25 14181702 AATGGCTAGATCTAATCTTCCTCTGATGCTTGGCT[A/C]TTTGGGGGTGCACAGGGTCTGAGGCAGTTAACTAG M 2 1 2 1 101000 f 74 goat snp55832-scaffold866-1012370 25 14003576 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse455 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38421417 Affx-122943968 AX-123291764 25 14217827 TATTTAAGATGCATTCTGATTTCATAAGGAATTTT[A/G]TAGTGGCTCCAAGCACTTTTCGTTATACCTGTTTT R 2 1 2 1 101000 r 74 goat snp55831-scaffold866-976245 25 14039765 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791205 Affx-122921909 AX-385278199 25 14393720 TATCCAAAGACCACCAAGTTCAGAACCAATTACCT[A/G]TAACAGCGTCCTACAGCTGCTGACGCAAATTATTT R 2 1 2 1 201000 r 74 goat snp55827-scaffold866-800352 25 14216641 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse456 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38375572 Affx-122978745 AX-123245931 25 14463554 GGGCGATGGGCACGCGGCATTCTTACACTATTCTC[A/G]CCACTTCTGCATACACGTGAAATTGGTCATAATAA R 2 1 2 1 101000 r 74 goat snp55825-scaffold866-730518 25 14287336 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380214 Affx-122975485 AX-123250572 25 14571344 CCTGCCGTCGAGTGGTTGATGACCTGGGACAAGTG[A/G]CTTGACCTCACTGGAGCTTGATGTTTCAGGACACG R 2 1 2 1 101000 r 74 goat snp55823-scaffold866-622728 25 14394171 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse457 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38454155 Affx-122919327 AX-123324488 25 14602823 TAGCCGGCCACTATGAGGGGACCCGCGGCGTTGGC[A/G]TTGGAGCTGGTCACTCGCACAGTGGTGCTCGCCTA R 2 1 2 1 101000 r 74 goat snp55822-scaffold866-591249 25 14425614 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422535 Affx-122943274 AX-123292881 25 14631926 TCCACGGCAACACCCTGTTCTGGCTCTCCGTTTAA[A/G]GAAGAAACTGTACCATAGCAACTAGACAGACGAGA R 2 1 2 1 101000 r 74 goat snp55821-scaffold866-562146 25 14454665 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse458 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38391570 Affx-122966619 AX-123261927 25 14689077 TGGAACAAGGGCTAACACTGTCACATCAAGCCTCG[C/T]GGGAGGAAGACAACGCTTGCTTTCCTGAGTATTTT Y 2 1 2 1 101000 r 74 goat snp55820-scaffold866-504995 25 14511940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423004 Affx-122942981 AX-123293350 25 14719385 GAACAACTGAAAATTTAGAGACAGAAACAAGAAGT[C/T]ACATCTTATACTTTAAATCCCCAGCATGAGTCCTG Y 2 1 2 1 101000 r 74 goat snp55819-scaffold866-474687 25 14541160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse459 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38453810 Affx-122919565 AX-123324143 25 14760205 ACAGAAGTGACAAAGGACCACTTTTCAGCTTAGGC[A/G]TTAAAAAGCATCAATTATTTCTGCTCACCCCTTGG R 2 1 2 1 201000 f 74 goat snp55818-scaffold866-433867 25 14582315 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426674 Affx-122939918 AX-123297020 25 14889881 TGCAGATCTGTGCCTTCTTCCAAGACACTTTAGAG[C/T]CTGTGTCAGAGAGCAGGTCCAGTAAGGTTTGGGTA Y 2 1 2 1 101000 f 74 goat snp55815-scaffold866-304191 25 14712836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse460 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38404757 Affx-122957222 AX-123275109 25 15067973 CAAATAGGAAAGGGAGAACATTAGAATGCACTCTG[C/T]GGTGCTGGATGGAACTGAATGTACTAGCGCTGTTG Y 2 1 2 1 101000 f 74 goat snp55810-scaffold866-126099 25 14888919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442979 Affx-122928198 AX-123313316 25 15173701 ATCCAAGTGGAGATGTGCAGTAGCCATTGAACACA[C/T]GGAAATACTGAACCAGACATTCTCAAGAACTGGAA Y 2 1 2 1 101000 f 74 goat snp55807-scaffold866-20371 25 14994001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse461 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320780849 Affx-122976196 AX-385267937 25 15222795 ATCAGCAAAGCAGAATAGTGATGGAGCAAGAAGTG[A/C]TTTTTGCAGCCGTGGAGTGTAACAGAGAGAAGGCA M 2 1 2 1 101000 f 74 goat snp38374-scaffold485-2194757 25 15050462 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403932 Affx-122957466 AX-123274284 25 15255401 TCCTTGTCAATTTTTAATTTGGAAATAGTTATAGA[C/T]GCACATCAGATTTCATAGATCATACAAAGAGGTGT Y 2 1 2 1 101000 r 74 goat snp38373-scaffold485-2162151 25 15083445 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse462 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38440413 Affx-122929610 AX-123310750 25 15287821 GAAAGCAGTGACCAAAGTCCAGGACATGCAGATGA[C/T]AAGTGGAAGGAAGAGGGTCCTGGGCAGAAGAAATA Y 2 1 2 1 201000 f 74 goat snp38372-scaffold485-2129731 25 15115923 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406689 Affx-122955780 AX-123277041 25 15326442 ATGTCTCTTAGAGGACCCAGTCTGCTGAGCACCCC[A/G]TTTTCTCTTTCTGCAATGGCACTGATTTCTTGTCT R 2 1 2 1 101000 r 74 goat snp38371-scaffold485-2091110 25 15155258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse463 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38430963 Affx-122936820 AX-123301304 25 15392137 TGAGTCAGATCTATAACAAAAAGCAAAGAGGAAAC[G/T]ATTTATTTAGCTTAGTTCATGATACTGAAGGTGGA K 2 1 2 1 101000 r 74 goat snp38370-scaffold485-2025415 25 15221311 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782236 Affx-122978123 AX-385269314 25 15425296 ATCATAAGAATGGTCCATAAACTATTTCCTCCTGT[A/G]ATCCATGTATTGCAGTGTGAAACGTTACAAAAGAA R 2 1 2 1 101000 f 74 goat snp38369-scaffold485-1992256 25 15253450 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse464 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38377892 Affx-122977250 AX-123248251 25 15460884 ACTGCCAAAGAGTGTATTAGTACAGGATCCTTTCA[C/T]ATCAAGTTTCAACAATATATCAAAGATTACCATGT Y 2 1 2 1 101000 f 74 goat snp38368-scaffold485-1956668 25 15289140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791197 Affx-122951072 AX-385278192 25 15516168 TTTCTTTTCATTGTAGCATACTCTTGCGGTTGAGG[C/T]ATGAATGACAATCCACTTTATAGTTAGGCTTTCAA Y 2 1 2 1 101000 f 74 goat snp38367-scaffold485-1901384 25 15345093 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse465 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 320783759 Affx-122924121 AX-385270815 25 15545477 TGTGAATATGCCAAAACGGGTGAATTTTGCAGTAT[A/G]TAAATTAAGCCACAATAAAGCTCCTTTCCACGTTG R 2 1 2 1 101000 f 74 goat snp38366-scaffold485-1872075 25 15374711 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423403 Affx-122943117 AX-123293749 25 15596109 ACTTAGATCAGTGACAGAAAGCTCTTCAGACCCAC[C/T]ACTCACCTAAGGAGGCCGCCTCTCCTAGTTCAGAA Y 2 1 2 1 101000 f 74 goat snp38365-scaffold485-1821443 25 15425337 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse466 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38382741 Affx-122973604 AX-123253099 25 15632820 AGGTCGACATCCTCCTGCTCTATTCCAATAAAATA[C/T]ACACTGTCAGAGATAAAGCAAATATTTCTCTGAGA Y 2 1 2 1 101000 f 74 goat snp38364-scaffold485-1784732 25 15461788 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416332 Affx-122947904 AX-123286681 25 15688753 GGGCCTTGAAGGTATACATATTTATTTTCTTCATT[A/G]CTGTCACTAACTCTAACTGAATTTAGCATGCCCTT R 2 1 2 1 101000 r 74 goat snp38363-scaffold485-1728799 25 15518003 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse467 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38454316 Affx-122919246 AX-123324649 25 15771279 GACAAGTAAGACAAGAGTCCCTGACATGTGGAGGG[A/C]GGGTCTGAGGCAGAGACAGGTAGACAGTAGGGGGC M 2 1 2 1 101000 f 74 goat snp38361-scaffold485-1646273 25 15600791 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413693 Affx-122950092 AX-123284042 25 15821597 CTCCAGCACTCTACCTCAAGGCCACGTGGCCTCTC[A/G]GGGCTGTGTATACCTGGGAGCTCACCGCTGCAAAT R 2 1 2 1 201000 f 74 goat snp38360-scaffold485-1595955 25 15650601 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse468 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38432001 Affx-122935931 AX-123302342 25 15867667 AGAAAATTCAGGCACAGAGTAAGTGGACATGTAAG[C/T]GGATCTTTTCAGATGAGCTGGAAATATTGCTATTT Y 2 1 2 1 101000 f 74 goat snp38359-scaffold485-1549885 25 15696620 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447825 Affx-122923912 AX-123318161 25 15904945 AAAAAATCCTGAGAGGCAAGCACTGCTCTGAAAGG[C/T]GGCCCACATGCCCCACATCTGAGCAGGACTGCCTG Y 2 1 2 1 101000 f 74 goat snp38358-scaffold485-1512607 25 15733594 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 snp-genphyse469 SNP in QTL region (GenPhySE laboratory, INRAE) multi-breed 38399695 Affx-122960487 AX-123270050 25 15945666 CATAAAGAGTTGGACGCAACTCAGACTGAACAGCA[A/G]CAAGACCTCCTGAGACAGCTGTTGGGCATTAGGTT R 2 1 2 1 201000 r 74 goat snp38357-scaffold485-1471886 25 15774384 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782481 Affx-122970392 AX-385269557 25 15993426 TAGCTGATTTCTGCCCTAATACTTCTAGATACAGC[G/T]ATCTAGCCTATCAAAGTGCCAGGTGTAAATAATAG K 2 1 2 1 101000 f 74 goat snp38356-scaffold485-1424126 25 15822192 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382157 Affx-122974037 AX-123252515 25 16026638 AGGGGCTCTACACTGTGCGTGAGACCAGGCATCAG[G/T]ACAAAATCCAAAGTTCAGGTTCCAGCTCTGCCACC K 2 1 2 1 101000 r 74 goat snp38355-scaffold485-1390914 25 15855638 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421547 Affx-122943865 AX-123291894 25 16075785 ATTTGACTTACTTGGGGTGACTCCTTTAAAATCAA[A/G]CCATTTTAGGATGATTTGCATTTCTTTATCTTAAC R 2 1 2 1 101000 f 74 goat snp38354-scaffold485-1341767 25 15905043 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420879 Affx-122944625 AX-123291226 25 16109010 GACAGAGAATGCAGACTGCCTAGGTAGGAGGGGTT[A/G]CAGTGGATATCTGGGGATGCAGAGCAAAGGACTAC R 2 1 2 1 201000 f 74 goat snp38353-scaffold485-1308542 25 15938333 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439215 Affx-122931027 AX-123309552 25 16142879 CCCCTCAGCAGAGAATGATCCAGTCTCAAGCGTCA[A/G]GGGTGCTGATGATGAGAAACCCTCTTCTAAAACAG R 2 1 2 1 101000 r 74 goat snp38352-scaffold485-1274673 25 15972229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404802 Affx-122956661 AX-123275154 25 16174016 GTATCAGCCTTGAGTAAGAGGCTAAACTTCCTGCC[A/G]GTTGACAGGGATGGGGGTTCAGAGCCTAAGGGGCA R 2 1 2 1 101000 f 74 goat snp38351-scaffold485-1243536 25 16003432 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273105 Affx-1111833290 AX-519546770 25 16181098 AGTGTTCTTTACCACTAGCACCACCTGGAAAGCCA[A/G]GTGCAGGGTGTGTAAAACCATCTAATTGTGTGTGA R 2 1 2 1 101000 r 74 goat 25_16181098_AF-PAKI 25 16181098 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38430438 Affx-122937735 AX-123300779 25 16213850 TGAGTGGACACTCTTTTCTCCTTGCCTAGGTTCCC[A/G]CATCCAGGCCAGGCTGTTACTCCTGTGGACACTTC R 2 1 2 1 101000 f 74 goat snp38350-scaffold485-1203702 25 16043370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421465 Affx-122943930 AX-123291812 25 16266884 AGATTTAAAAAAATGTGTTATAAGAAACTATATCT[A/G]CTCATTGTAGACGAGTCCATTTGTCCTCCAAGGTT R 2 1 2 1 101000 r 74 goat snp38349-scaffold485-1150668 25 16096549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277618 Affx-1111836002 AX-519551117 25 16298614 CCCTGCAATTTAGAGATTAGGGCTATGATCACTTT[A/C]TAGTTGCCAGTCTTCACAGACAAACTTGAAAGGAA M 2 1 2 1 101000 f 74 goat Random2.2K-2143 25 16298614 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392946 Affx-122965696 AX-123263303 25 16315979 CAGTTTAGGTCTTGTGATACTAACTTAGAACGCTG[C/T]TGAGAGCACAACTCATCTCCTCCACCTGTAGGACT Y 2 1 2 1 101000 f 74 goat snp38348-scaffold485-1101573 25 16143109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384516 Affx-122973045 AX-123254874 25 16383842 ACAGTTTTTGGCTACCCTATTTGGTTTCATTACAG[C/T]AGCAGTTCTCAAAACTCACCTATTTAAGTTCTGAT Y 2 1 2 1 101000 f 74 goat snp38347-scaffold485-1033710 25 16212061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384781 Affx-122972010 AX-123255139 25 16451702 TCCACATGATTGAGGCAGAAAGGAAAGGATGTGTT[C/T]GCAGGGGAATGATAGGGTGCCTGGTAATGGAAGTG Y 2 1 2 1 101000 f 74 goat snp38346-scaffold485-965850 25 16280426 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771756 Affx-122947646 AX-385258913 25 16554591 AACTGTGGGCCAGCAAAAATAATCTAATCTTTGTG[A/G]CCACATTTACTGTAGAGAAGGTGCAATGGAATTAA R 2 1 2 1 101000 r 74 goat snp38343-scaffold485-862961 25 16400148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403351 Affx-122957806 AX-123273704 25 16610065 GAAGAGGAAAGAGAAAAGCCCTGGGAGGGCACCAT[A/C]GTTGAACAGCCTCACCAGCCATGGGCTGCCTGCTG M 2 1 2 1 201000 r 74 goat snp38342-scaffold485-807487 25 16455613 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376203 Affx-122978812 AX-123246562 25 16649484 GCCTCATCAGGCCACCTCACTTCAAACTCTCGTTC[G/T]GAGCATTTCTGGGAACAGCAGGGGCCTCCCACGAG K 2 1 2 1 101000 f 74 goat snp38341-scaffold485-768068 25 16495018 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418693 Affx-122946299 AX-123289041 25 16684131 GCAAAGAGTCAGGCAAAGGGGTTAAATGTCCACCC[G/T]CTTCAAAGGAGAGGGCCACAAGGAGTCATGTCAGG K 2 1 2 1 101000 f 74 goat snp38340-scaffold485-733421 25 16529261 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442702 Affx-122927872 AX-123313039 25 16719796 TTCCCACTAGGGTTTGAGCTTCTATAAGGATCTAA[C/T]GTTGCCGCTGATCTGACTGGAGGTGGAGCTCAAGT Y 2 1 2 1 101000 f 74 goat snp38339-scaffold485-697756 25 16564583 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438145 Affx-122931471 AX-123308483 25 16768563 AGGAAACCCTTAGCAAATGTGTAAAGGACTCTGAA[C/T]GTCTCTGATTACTCAAGACACTGAGTTGGCCGTTT Y 2 1 2 1 101000 f 74 goat snp38338-scaffold485-648989 25 16611642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379973 Affx-122975629 AX-123250331 25 16813191 AACTTTTTCTGTAAAGGCCTACATAGTAAGTGTTT[A/G]TTTTTCTTCGAGGGCTGAGTGATCTGTGTCACAAC R 2 1 2 1 101000 r 74 goat snp38337-scaffold485-604361 25 16656296 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277620 Affx-1111836003 AX-519551119 25 16854452 TGAGAAAAGCAGTCTAGGTTGGTTCCCTTTCCCCC[A/G]CAGCACCTTCTGGACACACTGCTGGGACTGCCCAC R 2 1 2 1 102000 f 74 goat Random2.2K-2144 25 16854452 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38395538 Affx-122963858 AX-123265893 25 16925581 GCAAATATTACAATACCTCACCCTCCACACATACC[G/T]CAAAAAAACATTTATTAGGTGCCTGAATCTGGAAA K 2 1 2 1 202000 r 74 goat snp38335-scaffold485-491971 25 16769301 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450959 Affx-122921751 AX-123321293 25 16974837 CTTGGAGGAAATGGAGCTGAACTCTGAGCGTGGAT[A/G]CCACGAGTCTCTGCTTTCTCATTATTTCCTTTGAC R 2 1 2 1 201000 f 74 goat snp38334-scaffold485-442715 25 16817708 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399805 Affx-122960280 AX-123270160 25 17005009 AGGTGGGGCTGGACAGGTCCTGCAAAGCCTGCTCC[A/G]CACATGGTAAGGAGAGTGCAGGTTCTAACAGGCGA R 2 1 2 1 101000 r 74 goat snp38333-scaffold485-412543 25 16848028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443541 Affx-122927766 AX-123313878 25 17035295 TCATCTTTAAGGAGCCAGCTTCAACTCTGCCTTCA[C/T]AGAGAGGCCTCCCTTATGCCTCCACATCCAGACAG Y 2 1 2 1 101000 f 74 goat snp38332-scaffold485-382257 25 16876987 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434296 Affx-122934763 AX-123304637 25 17076314 AATCCACATTCAAATCGAAAGGCAAAATAAAAAAT[A/G]TGTGGGAACCTGGAAGTACTTAAAAAGTTGACCAT R 2 1 2 1 101000 r 74 goat snp38331-scaffold485-341238 25 16918538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794035 Affx-122933903 AX-385281004 25 17119103 TTCCACTATATACAAGTTTCCCAAGTAACAAGCAC[A/G]TGCCAGGAGCAACAGAAATAAGATGTTTTTCATCT R 2 1 2 1 102000 r 74 goat snp38330-scaffold485-298449 25 16961247 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405376 Affx-122956307 AX-123275728 25 17159765 AGTATCTAATTTATCAAACAGTGTGCTAAGATGAA[C/T]GAACTTTATATTTCAGAACTTATTTATAATTAATC Y 2 1 2 1 201000 r 74 goat snp38329-scaffold485-257787 25 17001938 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445484 Affx-122925202 AX-123315821 25 17202671 ATCACAGACCCTACCTCATAGAGCTGTTACAAAGA[C/T]GGCGTGACTGAATATCACTAAAGAACCTAAAACAG Y 2 1 2 1 201000 r 74 goat snp38328-scaffold485-214881 25 17045246 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391726 Affx-122967497 AX-123262083 25 17231249 GAGCTGGCTCTGTGAACTGGTCCGGTCTGTGGGCC[A/G]TACTATTCTCCTGGACAAAGTTTTGCATAATTAAT R 2 1 2 1 201000 r 74 goat snp38327-scaffold485-186303 25 17073882 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391828 Affx-122967012 AX-123262185 25 17288764 GTAGGAGCTCTGACCATGGAAACTATCAACTCCAA[C/T]GTTCACCAGCCTCCCCAAGGTACGTCCCTACAAAA Y 2 1 2 1 101000 f 74 goat snp38326-scaffold485-128788 25 17131407 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376003 Affx-122978414 AX-123246362 25 17330990 GAGGTCACGTGGGCTTGAGCCTTAAAAGATAAAGA[C/T]AGAAGAAAGCAGAGATTGTCCAGTGAGAGGCAAAG Y 2 1 2 1 101000 f 74 goat snp38325-scaffold485-86562 25 17173720 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442141 Affx-122928327 AX-123312478 25 17367279 TTTATCCTGTCCAAAGGGATTCACTGACTCAGGAC[A/G]GGCAAGTAATCAATTCCACAGTGCTAAGAGGTGTG R 2 1 2 1 201000 r 74 goat snp38324-scaffold485-50273 25 17210597 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399204 Affx-122960612 AX-123269559 25 17402722 GACTCTAGACCAGCTGGAGTTGGAAAATTGATTAT[A/G]GAGCTTCCTGAAATACCATCCTCACTGTCTACCAA R 2 1 2 1 101000 f 74 goat snp38323-scaffold485-14830 25 17246423 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384806 Affx-122971993 AX-123255164 25 17464763 TGAACACTCCTGGTGCCCAGCCTCACGCTGGCCAA[G/T]CAAGTCAGATTCTCTGGAGGTAGGGACAGTCCATT K 2 1 2 1 101000 r 74 goat snp25505-scaffold2627-281951 25 17309905 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396832 Affx-122963270 AX-123267187 25 17535932 AGCACTAACCACACCTTGTTGCCATCATTTCCATG[C/T]TTTGCCCATATCTGCACCCTCAGGACCCAGATCAA Y 2 1 2 1 201000 r 74 goat snp25503-scaffold2627-210782 25 17381750 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777358 Affx-122923616 AX-385264480 25 17576661 CATCACACTCAGCCCAAATGGCAGAATACCGGCCA[A/C]AGCAGATGACTACGATTGCTTTAAACCACTAAGTT M 2 1 2 1 202000 f 74 goat snp25502-scaffold2627-170053 25 17422472 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376379 Affx-122978108 AX-123246738 25 17627934 TTTCAATGAAATGTGGTCTCTAGTTTTACCTTAAT[C/T]CCTTCTCTCAGACAGTTTGCATCCACTGCCAATCT Y 2 1 2 1 201000 f 74 goat snp25501-scaffold2627-118780 25 17474092 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413976 Affx-122950294 AX-123284325 25 17669862 ATTCTGGGAGTAAGGTGGCTGAGGCAAGGCGAGAG[A/C]ATAGTGTGAGGTGCAAGCAGAAGGGAACAGAAAGC M 2 1 2 1 101000 r 74 goat snp25500-scaffold2627-76852 25 17516265 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397509 Affx-122962059 AX-123267864 25 17703071 CTCTTTGAGCCTGTTTCCTCTTCCTTAAAATGGAC[A/G]TAATAATTGCATCCATCTGAAAGTGTTGTTGGATA R 2 1 2 1 201000 r 74 goat snp25499-scaffold2627-43643 25 17549558 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780007 Affx-122931419 AX-385267105 25 17734753 GATTTAGGGATTTGGAAAACTGCCATCATTGTCAG[C/T]GTTCCTCAGTGTTCATTCCAGATCAGATATTTGCT Y 2 1 2 1 201000 r 74 goat snp25498-scaffold2627-11961 25 17579958 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800674 Affx-122921056 AX-385287592 25 17746939 TTTCAACTCAGTTCTCTTTAGAGTTTTCAACCACA[A/G]CACTAAGCTTCCTCTTAGCCAGGAACTATGTCAGA R 2 1 2 1 101000 f 74 goat snp13484-scaffold1520-126 25 17595607 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423259 Affx-122942669 AX-123293605 25 17780174 CAGTGTTCAATTAAATGAATTTTGACAGTTATAAA[C/T]AACCGCCAAAAACAGGATATAATACCTTTCCTTCA Y 2 1 2 1 201000 f 74 goat snp13485-scaffold1520-33361 25 17628945 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421341 Affx-122944068 AX-123291688 25 17833853 CTCCTTTGGCGTGAAGCTGGGATAGTGATTTCATC[A/G]CAGCCCTATTGGATTCACCGTTTACTCCTGCTGGT R 2 1 2 1 101000 f 74 goat snp13486-scaffold1520-87040 25 17681472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796886 Affx-122966980 AX-385283828 25 17919336 AGTGGAGGACAAAGTCTGTCTCAGTCAATCACTGC[A/G]TTGAGTAATGCCGTAGCAGAACACAGCCTAATAGT R 2 1 2 1 101000 f 74 goat snp13488-scaffold1520-172523 25 17768157 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408122 Affx-122954248 AX-123278473 25 17978984 GAAGCCCCTCCAACTCCCACCCAGGGCTTAGGGCT[C/T]ATCTGTAGCCATGGGTCACCTGCCTGTGTTTGCTT Y 2 1 2 1 101000 r 74 goat snp13490-scaffold1520-232171 25 17827641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404622 Affx-122957328 AX-123274974 25 18018725 CAGACTGAAAGTAGGCATGAGGCTGAGGAGAAATA[G/T]AGTCCAAGATTAAGAGAATGAGCACATTAAGTGAA K 2 1 2 1 201000 f 74 goat snp13491-scaffold1520-271912 25 17867388 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382932 Affx-122973385 AX-123253290 25 18059682 TAACCTTGAGTCTAAATCACCATACCACACTGCCC[A/G]CATGGCCACACCTCAGATTTTGTACTTGGGAATTG R 2 1 2 1 101000 f 74 goat snp13492-scaffold1520-312869 25 17909039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423443 Affx-122942599 AX-123293789 25 18106962 TTGGATGTGAAAAATGTCATGAAGCAAAGAGTACT[A/G]TTAAAACACAGATTGGGAGACTGATCGAGAATAGA R 2 1 2 1 101000 r 74 goat snp13493-scaffold1520-360149 25 17956699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764055 Affx-986698582 AX-385251820 25 18188393 CCATTCACAGCCTCAGCTGCGGTGGAGGAGGGTTC[C/T]CTTGTGTCCACACCCTCTCCGCAACTCACTGTCTG Y 2 1 2 1 600010 f 74 goat 25_18188393 25 18188393 Ancestral_priority_1043 ancestry 0.446 neutral IMAGE 10K 10K ancestral 320767464 Affx-986698549 AX-385254731 25 18188409 CTGCGGTGGAGGAGGGTTCCCTTGTGTCCACACCC[C/T]CTCCGCAACTCACTGTCTGTGGAGGTTTTCACAGT Y 2 1 2 1 600010 r 74 goat 25_18188409 25 18188409 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 320767468 Affx-986698551 AX-385254735 25 18188476 CAGTGACCATTCTGACATGTGTGAGGTGATAACTG[A/G]TGGTAGTTCTAAAACTTAGTGGTGTTGACAACTTT R 2 1 2 1 600010 r 74 goat 25_18188476 25 18188476 Ancestral_priority_1043 ancestry 0.708 recommended IMAGE 10K 10K ancestral 320764026 Affx-986698553 AX-385251798 25 18190666 GACTGCTTGGATCACAAAATATCTAGGTAAAATTC[A/T]TAAAGATTTGGGCATACCTGGCCACATGACTGGCC W 4 1 2 1 600010 f 74 goat 25_18190666 25 18190666 Ancestral_priority_1043 ancestry 0.766 recommended IMAGE 10K 10K ancestral 320764034 Affx-986698561 AX-385251805 25 18191563 AGCAAAAGCAGAAGGAAAAGTGGATGAAAGGTGAT[A/G]AGATTGTTATATGGCATCACCAACTCGATGGATGT R 2 1 2 1 600010 f 74 goat 25_18191563 25 18191563 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 320804204 Affx-986696439 AX-385290845 25 18197194 GTTCACTTGGATTTCCTTGAGGAAGGCCAGCCAAT[A/C]TCCAGATTTTGGTGGGCTCAAGGAGATGGCATAAG M 2 1 2 1 600010 r 74 goat 25_18197194 25 18197194 Ancestral_priority_1043 ancestry 0.584 neutral IMAGE 10K 10K ancestral 38447560 Affx-122924035 AX-123317896 25 18212048 CAGTACTTTTAGATTGGCTCACTGTAACTACAACC[A/G]TATCTCATTTTATTGTTTCACTTCACTGTGCTTCA R 2 1 2 1 101000 f 74 goat snp13495-scaffold1520-465235 25 18065472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449993 Affx-122922868 AX-123320328 25 18260811 TGCTCTAGACCATACTTTGCATAACAGAGGCTAGC[A/G]GATTTCTATGCAGATAAACCAGGCCTGAAGTCCAT R 2 1 2 1 101000 r 74 goat snp13496-scaffold1520-513998 25 18115159 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277622 Affx-1111836004 AX-519551121 25 18288072 ACTCATCTGTATATGTGGGGGCACATTTCTATATG[A/G]AGATGTACATCTTTGTGGGCTTCTTTCCTGAAATG R 2 1 2 1 101000 f 74 goat Random2.2K-2146 25 18288072 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320782781 Affx-122927069 AX-385269853 25 18289418 ATTTTATTTTTACAAAACTGAAACTTGGTATGTAG[A/G]TTAGTATGAATCACATTGAGTTTATTTCCTCCTAA R 2 1 2 1 101000 f 74 goat snp13497-scaffold1520-542605 25 18143869 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411509 Affx-122951679 AX-123281859 25 18318696 TGTAAACTTACTCAGCTTGTTCTAGAGAGTTGCAG[C/T]ACCTGCATCCCTGCAAACATGACACAGCTGTTTTC Y 2 1 2 1 201000 f 74 goat snp36475-scaffold438-2726128 25 18172498 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380737 Affx-122975137 AX-123251095 25 18357800 CAGTATTGGATTATGCATTCAGGAGGCCATTCGTC[A/G]TCTTTCCAGTTTCCAATCTGTAGAGACCTGTACTT R 2 1 2 1 101000 r 74 goat snp36474-scaffold438-2687024 25 18207058 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432989 Affx-122935260 AX-123303330 25 18386870 TGCTGATAAGACTGGAATATGAAGGACTTTGCTAA[A/C]GTTTGGTGATATGATCAATTTAATAGGGTGAATAT M 2 1 2 1 101000 f 74 goat snp36473-scaffold438-2657954 25 18236573 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454285 Affx-122919272 AX-123324618 25 18438992 AGCTCACTGCAGGCTGAGCTGCCTGAACAGCTTCT[C/T]AGAAGAGGTGGGTCTTGAACTGGGCTTTGGAGGAT Y 2 1 2 1 102000 f 74 goat snp36472-scaffold438-2605832 25 18288877 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796984 Affx-122924828 AX-385283925 25 18471947 GCAACTCAGTTGTCCCCTGCTACTTTGTTGTAAAC[A/G]TTGGACAAACATGGGTTGTATAGGTTAGAAGTGAA R 2 1 2 1 102000 f 74 goat snp36471-scaffold438-2572877 25 18320809 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789667 Affx-122947444 AX-385276675 25 18502967 TTCTTCCTTTCAGATATAGGCATTTTACTTCCCTC[A/G]TCTTATTAGACTGCCTAGAATTTCCAGCACTATGT R 2 1 2 1 101000 f 74 goat snp36470-scaffold438-2541857 25 18351903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785569 Affx-122977604 AX-385272613 25 18562426 AATTCTGTTTCAGTGAACTACTGTTTAAAAGTATG[C/T]GTTAGACTGCCAACAAACTAAGGCAGAGACAAATC Y 2 1 2 1 101000 r 74 goat snp36469-scaffold438-2482398 25 18411314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406658 Affx-122955806 AX-123277010 25 18593939 CACAAGCCTGTTCTTTAAGAAGCAGCAGTTACTGG[C/T]TGGATTAAGAGTGGGGACCTGGCTAAAGAGGGAGC Y 2 1 2 1 101000 f 74 goat snp36468-scaffold438-2450885 25 18442860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784482 Affx-122972433 AX-385271531 25 18632569 TGGGAATCAGTTCTCTGCCTTCTACACCAATGAAA[C/T]TCTGGTTTAATTACATAAGAAACATCAGGATACCA Y 2 1 2 1 101000 f 74 goat snp36467-scaffold438-2412255 25 18482263 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391113 Affx-122966808 AX-123261470 25 18680923 AAGCTGACGTGGGTTCCACCATCATGTGTTGTACC[A/G]TCTGTATTGTCTTGTTTACCATGGCAAGGGAAAAG R 2 1 2 1 101000 r 74 goat snp36466-scaffold438-2363901 25 18531400 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273060 Affx-1111833291 AX-519546731 25 18721036 CCATCTGGGAGACCACAATGACTAAGGTAAAAATT[A/C]TAAAATCAGAGGATCTAGAATACAGAAGGTAAAGG M 2 1 2 1 101000 f 74 goat 25_18721036_AF-PAKI 25 18721036 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38447876 Affx-122923829 AX-123318212 25 18730815 TGGATTAGAGTTCTCCAAATTCAGTCATTCAGAGG[C/T]GCCTGTGTGATTTTGTCATCTCCACAACTACCTAT Y 2 1 2 1 101000 f 74 goat snp36465-scaffold438-2314009 25 18581870 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785676 Affx-122975433 AX-385272717 25 18759670 TGAGTAAGAAAAGCAAATGAAAGACAATATGCCAA[C/T]ATGTTAACCTGTAGATGGTAAAATTATATATATAT Y 2 1 2 1 101000 f 74 goat snp36464-scaffold438-2285154 25 18610764 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429023 Affx-122938325 AX-123299365 25 18823620 GAGAAAAAGAAGAATTGAAAAACCAAAGAAACAAA[C/T]AGAGAACTAAACAGTATTAGTAATGATCTGATAAA Y 2 1 2 1 103000 r 74 goat snp36463-scaffold438-2221204 25 18675105 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401923 Affx-122958822 AX-123272276 25 18861722 CAGCCCTTAGAGTGGCATACTTCTACTTCATTCAT[A/C]TGCCACTGGCTAGGAGTCAGCAATGTGGCCACCCC M 2 1 2 1 101000 f 74 goat snp36462-scaffold438-2183102 25 18714526 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445922 Affx-122925928 AX-123316259 25 19042730 CCCTGAACCGCAAGGGATCTGGCTTTCAAAAGCAC[G/T]CATTGTTTGCTCTTCAAAGCTATTCACATCTAATT K 2 1 2 1 201000 r 74 goat snp36459-scaffold438-2002094 25 18898423 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453393 Affx-122919919 AX-123323726 25 19184163 ACATCAACTAATAGTGATGACTTCCATTGCTATTA[C/T]GAAGACACATCAGGATCTTAACAAACTGCTAGCTT Y 2 1 2 1 101000 r 74 goat snp36457-scaffold438-1860661 25 19057454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416594 Affx-122947645 AX-123286942 25 19241827 AGAAGTTTCCTGGCATGTTTCTCTGTCACCAAGTA[C/T]GAAGTTTTTCCAGTTGTCAGACATAGCCTATGGTA Y 2 1 2 1 101000 f 74 goat snp36456-scaffold438-1802997 25 19115453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784494 Affx-122950642 AX-385271543 25 19286059 CACGTATACTCCCATATAAGAACAACCCTTGAAGT[A/C]GAAAGTGTGCTGTATGTGCTATTCTCAGTTGTTTC M 2 1 2 1 101000 f 74 goat snp36455-scaffold438-1758765 25 19159852 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792483 Affx-122936419 AX-385279464 25 19391209 TATAGAAAAAACTGGGACTTAAAGGTGGAAATCTG[A/C]CTTAATTAAAATTAATTCCTTGGACCATTGAAAGT M 2 1 2 1 201000 r 74 goat snp36452-scaffold438-1653615 25 19270809 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405830 Affx-122955878 AX-123276182 25 19428471 CGGTAGAAGGGTCAACACAGAACGAGGAGGCAATA[C/T]GACACTGGACCACCATATAATATATATATGTATAA Y 2 1 2 1 101000 f 74 goat snp36451-scaffold438-1616353 25 19308468 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437519 Affx-122931921 AX-123307857 25 19487186 ATTATTTTCTGTTTTAGCTCAACATATTATTTTTC[A/G]TTATCCACAATTTTGTTAATTGTTTTGTTGAGGTC R 2 1 2 1 303000 f 74 goat snp36450-scaffold438-1557638 25 19371518 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443607 Affx-122927309 AX-123313944 25 19517583 GAAACTGTCACCAATGATTGGAAAAGTTGATGCCA[C/T]GATTTCAGCCAGAAGTTTAGTTATTGATAAAAGCC Y 2 1 2 1 101000 f 74 goat snp36449-scaffold438-1527241 25 19402125 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422906 Affx-122943053 AX-123293252 25 19602364 TCTGGCATAATAAGCCAAAGTAGTTTCAAATTTCT[C/T]TAAGTTTTATTTCAGGATACAATTAATTGAATAGA Y 2 1 2 1 101000 f 74 goat snp36448-scaffold438-1442460 25 19488277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406256 Affx-122956101 AX-123276608 25 19657894 CTCTATATTTTTATATATTAATTTATGTACTTGTC[A/G]GCATTTATACTTTTATATGCTTTCCTTCCATTAAT R 2 1 2 1 303000 f 74 goat snp36447-scaffold438-1386930 25 19545103 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277624 Affx-1111836005 AX-519551123 25 19738999 TTTGCCTTGACTCTGGCTTCTGTTTCACAGAGGCT[A/G]CAGGGGGATGAGACCCAGCCTTCAGTCTGGGAGAA R 2 1 2 1 102000 f 74 goat Random2.2K-2147 25 19738999 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320797597 Affx-122963066 AX-385284536 25 19739204 GGATTAAAGAAAATCATACAATTTAAGACTAGTGG[A/C]TTTCAGAAAAAAATGACTCAGTATCAAATGCTATT M 2 1 2 1 101000 r 74 goat snp36446-scaffold438-1305620 25 19627244 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779365 Affx-122962576 AX-385266469 25 19779894 CACACCGCACTGATTGCTTGGTCTCTTGGGAAATA[C/T]GGAATCATCTGCAAGCAGGATCTGATTCATGAGAT Y 2 1 2 1 201000 f 74 goat snp36445-scaffold438-1264930 25 19667367 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786414 Affx-122943051 AX-385273448 25 19830353 GTGGACTGATGACAACATGGTCAAATCTGTTACAA[C/T]ATGGACCACTTGTAAAAAGGTTTGCATATACTACA Y 2 1 2 1 101000 f 74 goat snp36444-scaffold438-1214471 25 19717520 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772943 Affx-122967751 AX-385260087 25 19866728 GCATATCACCTTATCATTATTTTGCAAACTACAAG[C/T]AGTATTTTGCAAACTACAAGAGCATTTCATTTTGG Y 2 1 2 1 101000 r 74 goat snp36443-scaffold438-1178096 25 19754482 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777517 Affx-122945473 AX-385264636 25 19895269 TGCAGGAAATCTTGTGGGCCTCAGATTGCATGTTT[C/T]CAGGGACAGAGAGCTTACTATTTGCCATGGCAGTC Y 2 1 2 1 101000 r 74 goat snp36442-scaffold438-1149555 25 19783038 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401232 Affx-122959312 AX-123271585 25 19948542 TCATGGGGAGGCCCTCAAAAAGCAGCCAAGACCAG[A/G]ATTGGGCCCAACAAGCTTTGGAGATGAACAGATCT R 2 1 2 1 101000 r 74 goat snp36441-scaffold438-1096282 25 19832158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431241 Affx-122937135 AX-123301582 25 19979853 CGCTCTAAGTTCACTGAGCGTTCACCGTATGCTGA[A/G]TGCTTACACGGAACTCCTCAAGAACCACCACTCAG R 2 1 2 1 101000 f 74 goat snp36440-scaffold438-1064971 25 19863428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430499 Affx-122937229 AX-123300840 25 20010366 TGCTACACATATTCTTCCAAATGCTCTCAGAAAGA[C/T]GGCTTTGCTCTAAGACATGACAATACACACCTCAT Y 2 1 2 1 101000 r 74 goat snp36439-scaffold438-1034458 25 19894023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773078 Affx-122936869 AX-385260221 25 20120780 GCTCAAAACTCTTCAAGCAAGATGCTTTTATTTTT[A/C]GGACATGTAAGCTAAACTGTAAGATGTACATAAGC M 2 1 2 1 101000 f 74 goat snp36437-scaffold438-924044 25 20005504 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440889 Affx-122929229 AX-123311226 25 20159645 CCCTACTTCCATGCAACTGCAAAAGAACCAGATGG[A/C]GGGCTATGGAAGCCACATACCCAAATGAACACCAG M 2 1 2 1 101000 f 74 goat snp36436-scaffold438-885179 25 20044228 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428145 Affx-122939053 AX-123298488 25 20232458 GTTTTTCTTATGGTCGAATTTAAAGGGGAGAAAAA[C/T]ATTTCCTGGACCTGCGATTGAGAGACTGATAATTA Y 2 1 2 1 101000 r 74 goat snp36434-scaffold438-812366 25 20116852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430622 Affx-122936967 AX-123300963 25 20263495 GTACTCAACAAATATTTTTAATTCAGTGAAGACAA[C/T]GGCAGCAAAAGAAGGAAGAGGGAAATAAAGAGAAA Y 2 1 2 1 201000 f 74 goat snp36433-scaffold438-781329 25 20147643 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445938 Affx-122925915 AX-123316275 25 20295573 GAACACCAGAGTCACTCTTCATCAGAGCAGACTCC[C/T]CCACCAAACTCTCTCCTAATCTTATCCATCTGCTT Y 2 1 2 1 201000 r 74 goat snp36432-scaffold438-749251 25 20180199 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396400 Affx-122963015 AX-123266755 25 20325709 TTAAAAGAAAATTACTGGTCCTCAATTTCCTCTCA[C/T]GCTCCCTATGGGCTGGACCAACGATGTAGGGCTGC Y 2 1 2 1 201000 f 74 goat snp36431-scaffold438-719115 25 20210239 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766529 Affx-122958138 AX-385253889 25 20354401 AAATCCTCTAATGAGGCTTATAGCATCGTCTGGCT[A/G]CTTCCATAAAGCTTGCGGGCAATGGGAACTCAATA R 2 1 2 1 101000 f 74 goat snp36430-scaffold438-690423 25 20239001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773774 Affx-122945380 AX-385260914 25 20390802 CTTATACATCCTCCTGAATCATAACCATCAGTCAG[A/G]GTTCCCTGGAAAAATCTGGATGCCTAAGAGGAACA R 2 1 2 1 101000 f 74 goat snp36429-scaffold438-654022 25 20276053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404260 Affx-122957056 AX-123274612 25 20428262 AGAATTGGTTGTGTGGCCAATCATGTCCTATTTGC[C/T]CACAGATCCATTCTTGCCCTTCTGCAAGCTGTGTT Y 2 1 2 1 101000 f 74 goat snp36428-scaffold438-616562 25 20313532 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377485 Affx-122977500 AX-123247844 25 20457028 TTGTTGGTTTGTTAGAGCTATAAGGGGCTTCCTTC[A/G]TGGCTCAGATAAAAGATCTGCCTGCAATGCAGGAG R 2 1 2 1 101000 f 74 goat snp36427-scaffold438-587796 25 20342246 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453945 Affx-122919479 AX-123324278 25 20520893 AAGCACACTTACTGGCAAGGGCTTCTTGACTGTTC[A/G]TGACAAACTGCACAACAAAGCTACACACCAGTTCA R 2 1 2 1 101000 r 74 goat snp36426-scaffold438-523931 25 20407768 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434195 Affx-122934866 AX-123304536 25 20550418 GATACAGATCCCGATTATCTTGTGGGAAGGCATTA[C/T]GGTGTTCAGTTCTGTTTGAAAGAAACCACACAGAA Y 2 1 2 1 101000 f 74 goat snp36425-scaffold438-494406 25 20437234 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439978 Affx-122929806 AX-123310315 25 20608842 TCAAAAGTGGCAGAGGTTTGACCTCAGCTCTGTCC[A/G]ACCCAGGGCCTGCCTTGGAGGGTAAAGCTGCAGGA R 2 1 2 1 103000 f 74 goat snp36424-scaffold438-435982 25 20494327 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403265 Affx-122957870 AX-123273618 25 20654011 CTCTTCACATAGTTGCAGCTTATGTTATAGAGCAA[C/T]TGTTTATGTGACTCTCATCCTCATTAGTCTGGGAG Y 2 1 2 1 101000 f 74 goat snp36423-scaffold438-390813 25 20539010 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389484 Affx-122968320 AX-123259842 25 20690947 GAAGCTCACAGGTGAGAAAAAAGCAGCCAAGACCC[C/T]GAAGATCTCAGTGTCATTGGAGCAGTGGAGAAAAT Y 2 1 2 1 102000 r 74 goat snp36422-scaffold438-353877 25 20575996 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401002 Affx-122959692 AX-123271355 25 20739903 GTTAGTTTCAGAACCACAGATTTCAAGTGGTCATA[C/T]AACCTTCCCCAGAAACCTCATCACGTGTTCTTTGT Y 2 1 2 1 201000 f 74 goat snp36421-scaffold438-304921 25 20626470 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413009 Affx-122951009 AX-123283358 25 20812138 CATTTAAGGGCCTTCCTGGAACAGACAAGACAGAA[C/T]GGCACGTGGCCCTGTGTGTGTGTGTGTGCTTGCTT Y 2 1 2 1 101000 f 74 goat snp36419-scaffold438-232686 25 20699041 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779211 Affx-122961515 AX-385266315 25 20877778 CCAGTCATTGGGTATATAGGGGTAAACCAAGCAGC[A/G]TGGTACTGTGAAAAAATAGTGCCAGATCCCGTGGT R 2 1 2 1 101000 r 74 goat snp36418-scaffold438-167046 25 20764543 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768523 Affx-122956191 AX-385255703 25 20917922 TGCAAGAGTTTGTTTTAGAAACCTAGGTCCAGGTA[C/T]AATTTGGTATCAAATAAAACTGCAACCCAGGGAAG Y 2 1 2 1 101000 r 74 goat snp36417-scaffold438-126902 25 20804595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389430 Affx-122968360 AX-123259788 25 20950788 CCTCCAGAACTGTCAGGGAATACATTTCTGTGGTC[A/G]TAAGCCCCACCGTTTGTGGCGATTTGGTACAGCAT R 2 1 2 1 201000 r 74 goat snp36416-scaffold438-94036 25 20837325 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450701 Affx-122921891 AX-123321035 25 21083317 TTCTAAGTGCTGACATGAGCTGATTCATTTACTCT[A/G]CATGAGACACAGATATGGTTATTGTCCCATCTTAG R 2 1 2 1 101000 f 74 goat snp23709-scaffold239-2568142 25 20971180 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435984 Affx-122933508 AX-123306323 25 21133143 TTACCCCTTTTCTTAGCCTGGTGTTCACACTGTGC[A/G]TTCTCTTTCCAGCCTTTCCTCTCTGTACCTCATGC R 2 1 2 1 101000 f 74 goat snp23708-scaffold239-2518316 25 21021136 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384524 Affx-122973039 AX-123254882 25 21185565 TTGGTAGTGATGTCCTCCCTTTCATTTCTGATTTT[A/C]TTTATTTGAGTCCTCTTCCTTTTCCTTGGTGAACC M 2 1 2 1 103000 r 74 goat snp23707-scaffold239-2465894 25 21073811 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422415 Affx-122943371 AX-123292761 25 21216398 GGATCTTCATTAAATTTTTTAAAAGATGGTTAGCC[A/G]TTTGTCTACCACTTACTGAATTAGCCAATGATTTT R 2 1 2 1 201000 r 74 goat snp23706-scaffold239-2435061 25 21104585 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431006 Affx-122936679 AX-123301347 25 21250719 GGGGTATGGCATGCTCTGGGGTTGGTTAATCAAGC[A/G]TTCAGTGACCTTGTGGAGGTCTGAGGGACTTCCGA R 2 1 2 1 101000 r 74 goat snp23705-scaffold239-2400740 25 21138712 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432804 Affx-122935405 AX-123303145 25 21294811 TCAGAAATGATAAAAACCTGGAAACCACCTACATA[C/T]CCATCGTAAGGGAACGCAAAATTAAAAGTGACCTA Y 2 1 2 1 101000 r 74 goat snp23704-scaffold239-2356648 25 21181175 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273063 Affx-1111833292 AX-519546734 25 21334122 ATGCAAATGAACTCTCACGACACGTGGTCTCATGT[A/G]CTTGCTGCTTTTCACTTAGCATGATGTAGGTGCAT R 2 1 2 1 101000 f 74 goat 25_21334122_AF-PAKI 25 21334122 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38398290 Affx-122962160 AX-123268645 25 21339065 GAAAGTGATATAGGGAGCACCCATGTGCCCAGCAC[A/G]TAGATTGTAAAGTCAATTCCATACTTTATCATGTG R 2 1 2 1 201000 r 74 goat snp23703-scaffold239-2312394 25 21225575 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405467 Affx-122956032 AX-123275819 25 21380238 TTTTTTGCAGATGACAAGCAGCTGTGGCAACTGGC[C/T]AACCGTATGAGCAGCAGGGATGCCAACAGTGACCC Y 2 1 2 1 201000 r 74 goat snp23702-scaffold239-2271221 25 21266675 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440407 Affx-122929613 AX-123310744 25 21423263 GAAACTGAATTGATAAGAAATGTTGGTGTGTCCAA[C/T]GGGCAGGCCCCAGCAAACAGACAGCACACTCCTAC Y 2 1 2 1 101000 f 74 goat snp23701-scaffold239-2228196 25 21309667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386611 Affx-122970239 AX-123256969 25 21466624 GGCCCATTCACAGATCTGAGATCAGGTGAATTATA[C/T]GCATCCTTCCGGTTTTCTCTCCTTGGCCCTAAATA Y 2 1 2 1 101000 f 74 goat snp23700-scaffold239-2184835 25 21351400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386133 Affx-122971410 AX-123256491 25 21511712 GGTAGAAAGTGGATCAAGGTTATTATCCTCAGAGC[A/G]GATGTCAGGGGTCTGCAGGGCCACCTAATTAATGC R 2 1 2 1 101000 f 74 goat snp23699-scaffold239-2139747 25 21396475 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429623 Affx-122937694 AX-123299964 25 21547534 GTGGGATCTGGTGTCATGTGAAAGCAACATGAAAC[A/G]TCATGGCAGGGTCCCCATTTGGGGAGTCAAGATGC R 2 1 2 1 101000 f 74 goat snp23698-scaffold239-2103925 25 21434509 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383118 Affx-122973264 AX-123253476 25 21577904 GAGCTCATCTCTGACTCAAACCACAGTGCCTGCAA[C/T]GTCCACTGGCAACCAGAAGTGGCAAGAATTCTGAC Y 2 1 2 1 101000 f 74 goat snp23697-scaffold239-2073555 25 21464770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794091 Affx-122942948 AX-385281058 25 21619659 CCATCAGACTATTCCTGGAATTCAAGAATAAGCAC[A/G]TCATTCCAAGTTCACCCTATTGACTAAATGACCAA R 2 1 2 1 101000 f 74 goat snp23696-scaffold239-2031800 25 21506343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277626 Affx-1111836006 AX-519551125 25 21686399 AGCAGGTATGCATAAGTTTGTGTATATGTACGTAG[A/G]TATGTGCGTACAAACAGTGATGAAGAGTGGGGGAA R 2 1 2 1 101000 f 74 goat Random2.2K-2148 25 21686399 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431359 Affx-122937043 AX-123301700 25 21697597 AACCACACTCCTAGCTGCCTGTGGGGTTCAAGCTC[A/G]TTGCTCTTTCATGCAAGAGTTGTGTGGCAGGGTGG R 2 1 2 1 101000 r 74 goat snp23695-scaffold239-1953862 25 21561778 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784688 Affx-122959219 AX-385271736 25 21739553 TAAAAACTTTCAAGCACAGCTTTGACCACATCCTA[C/T]GCTTTACTCTGCCATCATTGTTCTAAATTTCTAAT Y 2 1 2 1 101000 f 74 goat snp23694-scaffold239-1911906 25 21603543 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439296 Affx-122930968 AX-123309633 25 21786868 TGGTTTAGTCTAATGAGGTTTTGTACAGCACAGCA[C/T]AGCACAGTGGTAAGAACACTGAATGGGTGTTCCAA Y 2 1 2 1 101000 f 74 goat snp23693-scaffold239-1864591 25 21650765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431810 Affx-122936111 AX-123302151 25 21822590 AGAGGGCTCACAGCTGGCGTGGGGCAAGTTTTCCT[A/G]CTTCCGGTCTATCACAGCCCCACCCTAGGTCTCTG R 2 1 2 1 101000 f 74 goat snp23692-scaffold239-1828869 25 21685882 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384001 Affx-122972916 AX-123254359 25 21873602 CTCAGAAGCCCTCCTAGGAATCCCTGCCGACGAGC[G/T]ATGGCACACAGACAGGTGATGGACAAACACGGAGC K 2 1 2 1 101000 r 74 goat snp23691-scaffold239-1777857 25 21737647 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382055 Affx-122974931 AX-123252413 25 21966740 AAGCCCAGCAAGCTCTGGCACTTGCTGTCCCTTCT[A/G]TCTGGAATGCTTTGCTCTGGTCCTTATCACTGACC R 2 1 2 1 101000 r 74 goat snp23689-scaffold239-1684719 25 21831044 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422992 Affx-122942989 AX-123293338 25 22007420 GAAAATGGCAGGATTCAGATAAGAAACCAGGTCTA[C/T]CTGACCCCAAAGCCCCTGCTATTATCTAATATTCT Y 2 1 2 1 201000 f 74 goat snp23688-scaffold239-1644039 25 21871644 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789687 Affx-122953160 AX-385276695 25 22116834 TTGTATATCTGGATTCTGTAAACTGTCAAAAACAC[A/G]TCATTTAATGCACAGCCCTCCCTGTGTCTCAAAAG R 2 1 2 1 101000 r 74 goat snp23686-scaffold239-1534625 25 -1 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408106 Affx-122954260 AX-123278457 25 22154263 CCACCATTCCTGTCTTGACTGCAAGATGAAAACCT[A/G]TTTTTCAAAGTCATTCCATTCATCCTTGAATTTCT R 2 1 2 1 101000 f 74 goat snp23685-scaffold239-1497196 25 22016549 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277759 Affx-1111836008 AX-519551259 25 22227293 CTCTCTAAAAGATGCCATCGGATGCCAGTTGCACT[A/G]TTTTATTTTCTCGGCTCGGATATCTACTTCCCGTG R 2 1 2 1 101000 r 74 goat Random2.2K-2151 25 22227293 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443901 Affx-122927056 AX-123314238 25 22233785 GTCAGTATAGGCTCAGGGTACAGAGAAGTTCCGGA[A/G]GTTACCTCCATTCAGGCTCATTCAGGGCTCCCATC R 2 1 2 1 101000 r 74 goat snp23683-scaffold239-1417674 25 22097936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394771 Affx-122964836 AX-123265126 25 22274010 TCAAGCCCACTGTACCTCCTCCCTCCACCAAGCAC[A/G]TGCATTTAGTAGATTCCTTACCTTAGTTCCTTTGG R 2 1 2 1 201000 r 74 goat snp23682-scaffold239-1377449 25 22138261 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777646 Affx-122974016 AX-385264765 25 22308024 GCCTTCTAAGATCAAGTTTAAATGAAGAAAACCCA[C/T]TTCCTATAATCTTTTTGAGTAAATATGTAAAGACC Y 2 1 2 1 101000 f 74 goat snp23681-scaffold239-1343435 25 22172049 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277762 Affx-1111836009 AX-519551261 25 22312116 TAGTTTACATCTTGGTAAACAGATATTACAACAGT[A/T]CGTCTATTTCTCCTCTTCCAGATTTTGAGTTATTG W 4 1 2 1 101000 r 74 goat Random2.2K-2152 25 22312116 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38391543 Affx-122966641 AX-123261900 25 22338691 GTCACACAAACAAATTATCACAAACATGAGAACTG[C/T]AGATATGTGAACACTAACTGGATATCTGAAAAGAA Y 2 1 2 1 201000 r 74 goat snp23680-scaffold239-1312768 25 22202732 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453921 Affx-122919902 AX-123324254 25 22369075 CAATGTAGTAGCAGCACTACTTATAATAGCCAAGA[C/T]GGGGAAGCAATTCAAGTGCCCACAGCAGATGAATA Y 2 1 2 1 103000 r 74 goat snp23679-scaffold239-1282384 25 22233061 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438375 Affx-122931313 AX-123308713 25 22425701 AACAAATAATATTTGAAAGAATAGAGTCAAAGATG[C/T]GGGCTGTTTTGAGGTTCCTTCTGCTTTCCTCCATA Y 2 1 2 1 101000 r 74 goat snp23678-scaffold239-1225758 25 22289506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433066 Affx-122935745 AX-123303407 25 22487895 AGAAACCATCCCAAACCTTACCTAGCAACTACCAA[C/T]GCATCTTTATCCCTCAATCCTGGGTAACCAAAGGC Y 2 1 2 1 201000 r 74 goat snp23677-scaffold239-1163564 25 22352536 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400440 Affx-122959963 AX-123270795 25 22518599 GAACAGGGAGACTGTAAACCCCTGCGCTGGTGGGA[A/G]GAAAGTGGACAGTTCAGTTTCACAGTGTAACGCAA R 2 1 2 1 101000 r 74 goat snp23676-scaffold239-1132860 25 22383234 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444070 Affx-122926849 AX-123314407 25 22558022 CTTTTCTGTTGCACCCAAAATAAATACAGTTTGGT[A/G]CAGGACAGAGTCTGGATTTTGGCTGCCAGTCCAGG R 2 1 2 1 202000 r 74 goat snp23675-scaffold239-1093437 25 22422591 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797451 Affx-122956372 AX-385284390 25 22596743 TAAGATGTGAATAAGCATGTCATGCTTAAGGAACC[A/G]TCAGATTCTTTCCTGAGGATTAAGATTGGGAGCAG R 2 1 2 1 101000 r 74 goat snp23674-scaffold239-1054716 25 22460983 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430596 Affx-122936987 AX-123300937 25 22646233 CTGTTTCCCAGAGATCATAGAGAGGTGCAAACTTC[A/G]CAGTGAGAAAACCTTTGGGACCAGCTATTTCTTCA R 2 1 2 1 101000 r 74 goat snp23673-scaffold239-1005226 25 22510501 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277635 Affx-1111836010 AX-519551134 25 22679330 TTTAAAAACACTTCCTTGATGTATACACGTAATCA[A/C]AAAAATACAGTATTTGGGGGGAGGAGTTGATTTTA M 2 1 2 1 201000 f 74 goat Random2.2K-2153 25 22679330 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38432851 Affx-122935366 AX-123303192 25 22710634 CCCTCCTTCCAATACAGTTACATTACAACTTTGGC[A/G]TATATTGCTATTTGATATATATATTACTATGTTCA R 2 1 2 1 101000 f 74 goat snp23672-scaffold239-940825 25 22574140 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447337 Affx-122924888 AX-123317673 25 22764516 AGTCGTGGTGGTGACCAGGTTGGTACAGTCGGAAT[A/G]AATCCCAGGAGTTGGATGGGAGTCGCAAAACCTAG R 2 1 2 1 201000 f 74 goat snp23671-scaffold239-886943 25 22627796 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454054 Affx-122919396 AX-123324387 25 22803513 CGTACTAGTTATCTGACATTTGTTGTGTTATCTAC[A/G]TCACCCATCCGAGAAGGCCATCCTCTCTAAGCACA R 2 1 2 1 101000 f 74 goat snp23670-scaffold239-847946 25 22666818 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404581 Affx-122957362 AX-123274933 25 22851117 AGCAGCAGAATAAGTAAAATAGTGAAACTTCTTTG[A/C]TTTTGCTTTTATTTTTATGACTTTGTTGTAAAAGT M 2 1 2 1 303000 f 74 goat snp23669-scaffold239-800342 25 22714278 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419904 Affx-122945339 AX-123290252 25 22884227 TGGCCATGACCTTTTTGGAGGAAACAAAGATAAAG[G/T]CTCAGAATATTCATCTTTGAGTTCTTCCACAAGAT K 2 1 2 1 101000 f 74 goat snp23668-scaffold239-767232 25 22747452 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390654 Affx-122967137 AX-123261011 25 22942271 TCATCTACATATCACAGCTGAAGCTCTGAGATGGG[C/T]GGGATCCTTGAGCAGTAGAGCACAGAGGAAACAGA Y 2 1 2 1 101000 f 74 goat snp23667-scaffold239-709188 25 22805185 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384873 Affx-122971938 AX-123255231 25 22985571 TCTGACAAGACAGCTCCTGCAACTTCTCAAGGGCA[C/T]TGCAAACATGTCTGTTTCCTCCTGGCCTGGAAGCT Y 2 1 2 1 101000 f 74 goat snp23666-scaffold239-665888 25 22849240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774969 Affx-122942303 AX-385262101 25 23018509 AAACAGAGGCTAATAACTCAATTTATTGCAGCCTT[A/G]TGAAGATCAAAGGAAATGAGCTCTGTCTAGAATCA R 2 1 2 1 101000 r 74 goat snp23665-scaffold239-632950 25 22882366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388880 Affx-122968866 AX-123259238 25 23055394 GGCAGGTCTGCAAAGTCTTTCTTCCTGAGGAATAA[C/T]GACCTCAGATGTGTCCCTTACTACCTGTGAAGGCA Y 2 1 2 1 201000 r 74 goat snp23664-scaffold239-596065 25 22919248 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375468 Affx-122979154 AX-123245827 25 23089680 ACTGAAAATGTACATAACATATAAAACAACAGTTT[A/G]TAAGACACTGACCACCTAGCAGTGAAGAATGGTGA R 2 1 2 1 101000 r 74 goat snp23663-scaffold239-561779 25 22951060 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376153 Affx-122978850 AX-123246512 25 23134713 TTCCTTCTTACCTTTGACTGGGTAATATTTCACTG[C/T]GTACATGTATCACCTCTTCTTCACCCATTCCATCC Y 2 1 2 1 101000 f 74 goat snp23662-scaffold239-516746 25 22996833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384474 Affx-122973077 AX-123254832 25 23169933 GAAGTCTTTTTGTTTAGTTGAGAGACTGCAAGACA[C/T]GCCTGTACATGTTTCCTTAGTATTAGCAAAGGATC Y 2 1 2 1 101000 r 74 goat snp23661-scaffold239-481526 25 23032793 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389100 Affx-122968574 AX-123259458 25 23203159 TTAAGAGACACAAGTAGAGAAGTGACAACGTGTAA[C/T]AGGGAAGAACAAATCTAACGCCACATTAGATCTTT Y 2 1 2 1 101000 f 74 goat snp23660-scaffold239-448300 25 23066806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446786 Affx-122925307 AX-123317122 25 23260506 CACAGATTTAGCTTTCTAATGTCATTTAAAAGTCT[A/G]CACTGTCATTATTGGTTTTCTTGTATTTTCTCTTT R 2 1 2 1 101000 f 74 goat snp23659-scaffold239-390953 25 23124309 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437137 Affx-122932153 AX-123307475 25 23293547 TATTTCAATGGAAATAATTCATGTTATTATGTCCA[G/T]ATCATTCTGAACATTTTCAAAAGCAGCTTTTATCT K 2 1 2 1 201000 f 74 goat snp23658-scaffold239-357912 25 23157474 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792082 Affx-122948379 AX-385279069 25 23359992 TTGTCTTTGAAGTACAACATTTTGGCCATGTTCAT[A/G]GAAACAATATCTTCAGACCACTCTCAAACACACCT R 2 1 2 1 101000 r 74 goat snp23657-scaffold239-291467 25 23223811 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445022 Affx-122926629 AX-123315359 25 23389712 AGTTTCCAAGATCAGACAAGATCAGGCATGTTCAG[C/T]ATAGTATGGCTGGAGACAGCAATGATTTGCTTTTA Y 2 1 2 1 101000 r 74 goat snp23656-scaffold239-261747 25 23253452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395944 Affx-122963577 AX-123266299 25 23421959 AGCATACAAATTAAACTTTTATTCTGAAATTTCAG[C/T]GTTCTCAACAGCATAACAGGGGCTGGAAACTCAAC Y 2 1 2 1 101000 r 74 goat snp23655-scaffold239-229500 25 23285656 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409796 Affx-122952969 AX-123280147 25 23458977 TAGAAATATGGGCAATCCACAGCAGCTTTAAAAAA[C/T]GGAACCATTCTGGAAAGTCTTAGAAGATTTGGAAG Y 2 1 2 1 201000 f 74 goat snp23654-scaffold239-192482 25 23323578 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388890 Affx-122968859 AX-123259248 25 23491588 TGAATAATCCCAGGCACTACAAAGGGTACCCTCTG[C/T]ATGTTACTTCCAATCCTCACAGCAACCTTGAAACG Y 2 1 2 1 202000 r 74 goat snp23653-scaffold239-159871 25 23356200 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794218 Affx-122965876 AX-385281184 25 23556915 ATGAGCATTAAGAAAGGGACACTGTGGGGTGCTAG[C/T]GGATTGTTCAGTCAGGGTAGAATTAGTCTCTCCTT Y 2 1 2 1 101000 f 74 goat snp23651-scaffold239-94544 25 23421968 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403362 Affx-122957796 AX-123273715 25 23592774 TTTTCATCCTTCTCTAGTCCACTGCTTGCTCATCC[A/G]TCTCCTGTCACTGGTCCCTTGACCACCCTAGTCTC R 2 1 2 1 101000 f 74 goat snp23650-scaffold239-58685 25 23457739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446131 Affx-122925774 AX-123316467 25 23628275 CTCAAGATCATCAAGCATTAGATCCCGGAGGCTGG[A/G]GAGCCCCACTCTACCCCATTCATAGCAAGCATTAA R 2 1 2 1 201000 r 74 goat snp23649-scaffold239-23184 25 23493100 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799109 Affx-122950368 AX-385286039 25 23718299 GACAAGGTCAGGAAAGGACACAATTTCCTGACCCT[A/G]CCCTCTATGTTTAAGCACCTGAGACTACACTGAGG R 2 1 2 1 101000 f 74 goat snp50734-scaffold734-66741 25 23583277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277637 Affx-1111836011 AX-519551136 25 23740953 ATGCTACTCATCTCAACATCACATGAAAACTCCAA[C/G]TGCTGAAATGCAATGAAATGCGACTATGCGACTGA S 4 1 2 1 101000 f 74 goat Random2.2K-2154 25 23740953 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38440477 Affx-122929378 AX-123310814 25 23787777 GGCGCCACAGGGGGCTTTGGGCAGCATGCAAATTC[A/G]CAACATAACAGACCTATCCTTTGAAAAATAAAGCG R 2 1 2 1 101000 r 74 goat snp50736-scaffold734-136219 25 23646916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781936 Affx-122928514 AX-385269017 25 23820857 TAAATATTTCCATGTGACTCATGGCTTTCACAACA[G/T]CCCAAAGTCATGCATTTAATATAAGATCTGAATGA K 2 1 2 1 101000 r 74 goat snp50737-scaffold734-169299 25 23679449 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406613 Affx-122955839 AX-123276965 25 23859136 GGGGGTCAAGGAGGGGCTTGGCTTTTCATAAAGCC[A/G]TTGGCTGAGTTCTCACCTGACTACTAGTTTCTTTA R 2 1 2 1 101000 r 74 goat snp50738-scaffold734-207578 25 23717724 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795043 Affx-122976704 AX-385282002 25 23893490 TCCTTACAGAAAAGTACAGATAATAAATATAGAAG[A/G]GATGATGGATTTGGAAGATTATCAATGAATTATAA R 2 1 2 1 101000 f 74 goat snp50739-scaffold734-241932 25 23752261 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792658 Affx-122933225 AX-385279638 25 23922155 AAGCAAAGTGATTGGTACATGGAGTTTCACTATAT[C/T]ATCTTCTCTGCTTTTGCATGTATTTGGCTTTCTTC Y 2 1 2 1 101000 r 74 goat snp50740-scaffold734-270597 25 23781038 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273065 Affx-1111833293 AX-519546736 25 23938036 TAAGAGACAAAGAAGATGACCTGTGTTTTCAGAGC[A/G]AGAATGCCATGGAAGTCTCAGTTCAGTTCAGTTCA R 2 1 2 1 101000 f 74 goat 25_23938036_AF-PAKI 25 23938036 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387654 Affx-122969845 AX-123258012 25 23956366 GGGACTGTGCACCACCATATGCACATATTTTGAGA[C/T]GACACACCTCTTCCTACTGTTGCCTGTCTCCTTGC Y 2 1 2 1 202000 r 74 goat snp50741-scaffold734-304808 25 23815488 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409527 Affx-122953618 AX-123279878 25 24003366 ATCTCAAGCAAATGATTAAACCTACAGGGCTGTAA[C/T]GGACTATTTTGGATGTCTGACCAAGTGATAAAACT Y 2 1 2 1 101000 f 74 goat snp50742-scaffold734-351808 25 23863924 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770448 Affx-122946266 AX-385257614 25 24052693 AAAAATTGGGGGAGATGAATGTTGGTAATGGTTTC[A/G]TAACATTGTGAGTGTACCTAATACATTGAACTGTA R 2 1 2 1 101000 f 74 goat snp50743-scaffold734-401135 25 23913158 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412043 Affx-122951722 AX-123282393 25 24094300 CCCACTGCTGTTGCAGTCCCTAGTTCTCTCCTCTC[A/G]CCTTACACCCCAGCTCTGCTACTAAATTGTGTGAC R 2 1 2 1 201000 f 74 goat snp50744-scaffold734-442742 25 23955338 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416565 Affx-122947668 AX-123286913 25 24143009 GGGCCACTATTTATGCTCGTTTGAAAACAACAAGC[A/G]CCAAGATACGTGACCTTGATCACAGGGCATAGAAA R 2 1 2 1 101000 f 74 goat snp50745-scaffold734-491451 25 24003813 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795854 Affx-122971865 AX-385282807 25 24190262 CGGCCTTAGCTCTCCATCAGGGGGTAATTTCCCAA[C/T]TGAAGAAGCAACTATGGTCCAAGCAGAGAACATCA Y 2 1 2 1 101000 r 74 goat snp50746-scaffold734-538704 25 24051433 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404921 Affx-122956443 AX-123275273 25 24240946 CCACAAGCACATTTCAGTGTCTACCCAGGTGGTAC[A/G]TGCCTTGAAGCAACTCAGGAAGATTGGGTAATGGT R 2 1 2 1 101000 f 74 goat snp50747-scaffold734-589388 25 24102153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769565 Affx-122947478 AX-385256735 25 24282754 CTATTTTTTTGAAGTGTCCCAGTGACAATATTAGC[A/G]TTTTAAGGTTCTCTTTGCAGCTTGGCTTGGCCAAT R 2 1 2 1 201000 f 74 goat snp50748-scaffold734-631196 25 24143856 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377347 Affx-122977661 AX-123247706 25 24311771 CATGCAGGACAGAATGCGTGAATAAGTAGAATAAT[C/T]ACAGAAAGAACAGGAAAGAGGCAACCTTGCAAGGA Y 2 1 2 1 201000 f 74 goat snp50749-scaffold734-660213 25 24172520 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792311 Affx-122963349 AX-385279293 25 24347967 TCTGTGTTCACAGCCTAAGGTCCTGAGACTTTATT[A/G]CCCTCTCACCCATCTACTGAACAACTTTTCTTACA R 2 1 2 1 101000 f 74 goat snp50750-scaffold734-696409 25 24208704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794998 Affx-122941847 AX-385281957 25 24409026 GCATGGGGTGAACACACAGACTAATTTATGTGAAA[G/T]AAAAACACGCTTTTACATGGTGTCCTGACACCAAG K 2 1 2 1 101000 f 74 goat snp50752-scaffold734-757468 25 24269382 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408239 Affx-122953827 AX-123278590 25 24457870 GTTGAATTTATTAAAAACTTAAAGTAATGACGTTT[A/G]CTCCGAGATGATGCCCTTCTTCCATGTTTTCAATG R 2 1 2 1 101000 r 74 goat snp50753-scaffold734-806312 25 24318439 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422983 Affx-122942997 AX-123293329 25 24491319 CCTGCTGTATCACACTCCAGGCCACTTCACTCACT[C/T]TGCTCACCTTCTGGCGCCTGTGTGAACTTGAGGCC Y 2 1 2 1 201000 f 74 goat snp50754-scaffold734-839761 25 24351585 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447110 Affx-122924475 AX-123317446 25 24536987 AACCTCAAAACCTAGCCTAGTGTCTGACACAGAAC[A/G]TGCTCATAATGGGTTAAATATTTTCTATATGTTAA R 2 1 2 1 101000 f 74 goat snp50755-scaffold734-885429 25 24397156 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391717 Affx-122967504 AX-123262074 25 24594211 TTTTTTTTTTTTTCAAGAAATACAGTGTTTATCCT[A/G]TGAAGTTTATAAACCACTGAGAGAGACACTAAGTA R 2 1 2 1 101000 r 74 goat snp50756-scaffold734-942653 25 24453950 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795797 Affx-122924762 AX-385282750 25 24622878 TGCCTTTATGCTATGCTAGTCATCAGTTTCAGGAG[C/T]GAGAGCGTGATAAGATCAGGTCCATTCACATTTCA Y 2 1 2 1 101000 r 74 goat snp50757-scaffold734-971320 25 24482771 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417028 Affx-122947538 AX-123287376 25 24667894 GTTGATAGATTTCAGCCCTTGGGATGAAGCCTCTG[C/T]GGCTCTGGATCTGGGGATCCTTGCAGAGTTAGGAT Y 2 1 2 1 101000 f 74 goat snp50758-scaffold734-1016336 25 24527859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378649 Affx-122977098 AX-123249008 25 24703981 GTGCTGCAGCCCATGGGACCACAAAGTGTTGGACA[C/T]GACTTAGGGACTGAACAATACAAGTGTTTAATCAA Y 2 1 2 1 103000 r 74 goat snp50759-scaffold734-1052423 25 24562599 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800618 Affx-122965824 AX-385287537 25 24736413 TGGGAGAGAGTACAAGGGAACCTCCTGGGGAATTA[C/T]AAAGGTTCTCTGTCTCTTTCTTGACAGTGATTATA Y 2 1 2 1 202000 r 74 goat snp50760-scaffold734-1084855 25 24595028 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429327 Affx-122938588 AX-123299669 25 24779507 AAGCAATTTATATAGTTTTTATATAAATCAGTAGT[C/T]GATTTGGAATATCACTGATGACCATGAGGCAATAA Y 2 1 2 1 101000 r 74 goat snp50761-scaffold734-1127949 25 24639382 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403975 Affx-122957433 AX-123274327 25 24813881 ATTCAAACAGCTGGTTACCGCTCACCGATTCCCCC[A/G]TTCTAATTGCCAAGGGAAGAATTATAAATAAATGT R 2 1 2 1 101000 r 74 goat snp50762-scaffold734-1162323 25 24673768 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376078 Affx-122978911 AX-123246437 25 24848568 GGGTGTGGGGTATAGGAAGACATGAGGGGGCTGCA[C/T]GAGGGTACTTGCTGTTTTAAAGTACAGACGGTCCC Y 2 1 2 1 101000 r 74 goat snp50763-scaffold734-1197010 25 24707131 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413324 Affx-122950178 AX-123283673 25 24884668 GGTGGACATCGGTCATGATGCCCGTTCTCCTCGTG[C/T]TGCCCTGCATGGATGGAGAAACTAAAAAAGGAAGC Y 2 1 2 1 101000 r 74 goat snp50764-scaffold734-1233110 25 24742439 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413933 Affx-122949808 AX-123284282 25 24937273 CTCCTTTTGGACTTTTTCTGAATGGAGCACGTATC[A/G]CCCTTCCAAGCCCAGCCTCCTTCGCTCAGCTTGTG R 2 1 2 1 101000 f 74 goat snp50765-scaffold734-1285715 25 24794806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437478 Affx-122932371 AX-123307816 25 25006332 TGCAGAGAGATCCCCACTGTGGAGGGAGGGAATTC[A/G]TTTCCGAGCTTTGACCTGCTACAATGCATTCCCAG R 2 1 2 1 101000 r 74 goat snp50766-scaffold734-1354774 25 24863747 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403652 Affx-122957521 AX-123274004 25 25041678 GGATTCTTGTAGGCATCCTGGAAGCAGGGTTTACC[A/G]TCTTTACTTATAAGGCTCAGAGAGGGGAAGTGTCC R 2 1 2 1 101000 f 74 goat snp50767-scaffold734-1390120 25 24899045 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437815 Affx-122932115 AX-123308153 25 25073034 AAGGCAGAGAAATGTGTTTGTTGAGTGAATAAAAA[C/T]GAGAATGAGTGAGCAAAGAAAACGGCAGACACCCA Y 2 1 2 1 303000 r 74 goat snp50768-scaffold734-1421476 25 24929837 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790052 Affx-122929989 AX-385277058 25 25102261 TTGAATATGTGCAAAGCCGCTGAGCTACAGCTGCT[A/G]TGGGCAGGGCTCCAAACGTTAAATCTTACAGAAAT R 2 1 2 1 101000 f 74 goat snp50769-scaffold734-1450703 25 24958662 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418723 Affx-122946278 AX-123289071 25 25156058 TAACCATTTCTAGCTGCCAGCTGCTGTTTAGGTTT[A/G]GAAAGGAAAAGAGGATCTTAGCAGGACTTGTTTAT R 2 1 2 1 201000 r 74 goat snp50770-scaffold734-1504500 25 25012417 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438413 Affx-122931281 AX-123308751 25 25199195 CGCAAAGAGTTGGACAGGACTGCTTATGCACAGCA[C/T]AGCATAGTCGATCGTCTCCTTTCTTTGGCCTCAGA Y 2 1 2 1 101000 r 74 goat snp50771-scaffold734-1547637 25 25055896 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441961 Affx-122928566 AX-123312298 25 25246736 TCCACTGACCATCAACCCTCAGCTGCATTTTAGCT[A/G]CTGGTCCAGCATCCTTCCTTCCCTCCGTCTCCTCC R 2 1 2 1 101000 f 74 goat snp50772-scaffold734-1595178 25 25103103 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445924 Affx-122925926 AX-123316261 25 25285310 AAATTGTTACTTCTCTCTGAAATGGAAAAGTAAGC[A/G]TGGTACCCTTAATGGGAATGCTGTCTAATGCTGTC R 2 1 2 1 101000 r 74 goat snp50773-scaffold734-1633752 25 25141825 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423760 Affx-122942846 AX-123294106 25 25343542 AATAGAATTTTGTCCTTGATTATAAAAATAATACA[C/T]GTAGGGAACTTAGAAGAGAAGGTGTCAAAGAAGAA Y 2 1 2 1 101000 r 74 goat snp50774-scaffold734-1691984 25 25200205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453448 Affx-122919862 AX-123323781 25 25427238 GCTGGATTACCTTGGACAGGCTATTTAAGTTCCCC[A/G]TGCCTCAGTTTCCCCTCCATGAACCACCCGCCTCA R 2 1 2 1 101000 f 74 goat snp50775-scaffold734-1775680 25 25283436 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391812 Affx-122967025 AX-123262169 25 25467269 TGGAGCCCCTTGTGACCATCCTATCTCCATAAGGA[C/T]GGGCTTGACTGAGACCGAAGCTAAAAGAAATCAGA Y 2 1 2 1 201000 r 74 goat snp50776-scaffold734-1815711 25 25323394 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391041 Affx-122966863 AX-123261398 25 25518765 ATGACTGCAGTGATCCAGGCTGAAATGGAAGAAGG[C/T]GCTGACTTTTTTTCCTTCTTAAGAGTAAGAAAAGC Y 2 1 2 1 201000 f 74 goat snp50777-scaffold734-1867207 25 25373752 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387159 Affx-122970633 AX-123257517 25 25567126 GGTCATGTGACTGGTTCTTGCCTATAAAATGTGAG[C/T]GTAAGTGATGCATGGCACTTCCTGAGGGGGTGCGT Y 2 1 2 1 101000 f 74 goat snp50778-scaffold734-1915568 25 25421979 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377902 Affx-122977241 AX-123248261 25 25606166 CCTGTGACCAAACAAGTTGCCTTATTCATCTGTGT[A/G]TCCCAACATCCACACCAGGAACTCAGGACATGGGG R 2 1 2 1 101000 f 74 goat snp50779-scaffold734-1954608 25 25461086 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778029 Affx-122967299 AX-385265145 25 25661146 TTTTCATGACAATGGCAGAGGTACAAGGCAGTGAG[C/T]ATGAGGCCTCTGAAGGCTTAGGTCAAACTGACATG Y 2 1 2 1 101000 r 74 goat snp50780-scaffold734-2009588 25 25516184 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408661 Affx-122953465 AX-123279012 25 25692329 AAATAGTTCACACAAAAAACGTGTGTGTGTGTGCA[C/T]GTGTGCAGGGCTTCCCTGATGGCTCAGCAGTAAAG Y 2 1 2 1 103000 f 74 goat snp50781-scaffold734-2040771 25 25547412 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446249 Affx-122925686 AX-123316585 25 25771390 TGCATTTAACTCATAGAATACCTTTAGCTTTCCAG[A/G]GAGTCTGAGACCAAAGACCTTTTTCATTATAACCT R 2 1 2 1 101000 f 74 goat snp50783-scaffold734-2119832 25 25627033 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443101 Affx-122928104 AX-123313438 25 25803210 CGCTGTAAATTTAGCCCCTGGCCCCATGCCTGATA[C/T]GGAGTGTGCACTCAAATAAGTATTTATTGAATGGG Y 2 1 2 1 202000 r 74 goat snp50784-scaffold734-2151652 25 25659066 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273867 Affx-1111833894 AX-125817087 25 25847578 TGCTCTGTGGCGGCCATTTGGTCACGGATCTTCCC[A/G]ATCTCGGTGCTGACACCTGTGGTGGCCACAATGCC R 2 1 2 1 202000 f 74 goat GoatD01.009730 25 25847578 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38394897 Affx-122964738 AX-123265252 25 25862523 GGGATCTTCACCCAGGCCATACTTTGTGCTCCCTG[C/T]AGGACAAGGAGGAGGGGACAAGCCCTTTCTAAAGT Y 2 1 2 1 201000 f 74 goat snp50785-scaffold734-2210965 25 25708527 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450695 Affx-122921895 AX-123321029 25 25914911 GATTTAAGGTGAGTTAATGACGCTACTGAAGGAGG[A/G]CATGGCAGCCCACTCCAGTCTTCTTGCCTGGGAAA R 2 1 2 1 101000 f 74 goat snp50786-scaffold734-2263353 25 25760491 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435162 Affx-122933662 AX-123305502 25 25977843 ATTAACTAAGGGGCCCAAACGGTGACACAGGCGGA[A/G]CAGGAGGCAGTGTGGAAGTTCAGGAGACAGATGAT R 2 1 2 1 101000 f 74 goat snp50788-scaffold734-2326285 25 25824235 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417153 Affx-122947347 AX-123287501 25 26010609 GAAAGCCACCAGCCAAGAGCTGCAAAAGGATCACC[A/G]TCAGGGAGGCTGGGTGTGAACTGGGATGGAGGCAC R 2 1 2 1 101000 f 74 goat snp50789-scaffold734-2359051 25 25857005 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452259 Affx-122920769 AX-123322592 25 26041772 TTTTCTTGAAGATGGCTACACAGCAACCCAAAGAA[C/T]AAAGAAACCAAGGGAAAAAAGCTGAGCTTATTAGA Y 2 1 2 1 103000 r 74 goat snp50790-scaffold734-2390214 25 25886629 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427138 Affx-122939646 AX-123297481 25 26085318 ATAATCCATTAAGAACTAAAATCAACCCTGGCTGG[C/T]GTAGATAGCTAATGAGTTTACACACACACAAATGT Y 2 1 2 1 101000 f 74 goat snp50791-scaffold734-2433760 25 25930078 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441251 Affx-122929494 AX-123311588 25 26120865 ACCCAGATTCCTTCCCCAGGATCACGCAGCCTGTT[A/C]GCCCAATCTTCTCTGGATTTCAATCCCCCAACCCC M 2 1 2 1 101000 r 74 goat snp50792-scaffold734-2469307 25 25965843 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428168 Affx-122939036 AX-123298511 25 26152676 CTAGCTACTGTTACCAGACAGCGGGATAAGTAATG[C/T]GAGAAAAACAAATTCAAACTGCAAGGTGGACCTCA Y 2 1 2 1 201000 f 74 goat snp50793-scaffold734-2501118 25 25997640 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403614 Affx-122957552 AX-112062878 25 26188006 GGACGATGCGATCCACAGTCTCCTCCGGCAGGGAG[C/T]GCCCCACAAACTCCAGGATCTTCTGAATCTCCCTT Y 2 1 2 1 101000 r 74 goat snp50794-scaffold734-2536448 25 26033086 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391834 Affx-122967007 AX-123262191 25 26215349 GAACTGAACTGAACTGAACTGATGAGCCAGAAGAG[C/T]GGATGGGGGAAGATGATGAAGGGCTTTGGATGCCA Y 2 1 2 1 201000 f 74 goat snp44163-scaffold6-1767044 25 26057185 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407888 Affx-122954493 AX-123278239 25 26288573 GGGGTGGGGTTGAGCGGCTGACCCCTTTAATTCCC[A/G]TGTGATGCTTTCCTCCAGGGAGCATTGCCAAGCGA R 2 1 2 1 201000 f 74 goat snp44162-scaffold6-1693820 25 26125933 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384658 Affx-122972143 AX-123255016 25 26353110 TAAGAGATGACACAGTTGTGACTCAGAAGGGCTCC[A/G]TTTAGTAGTTCTCAAATTCTGTAACCAGTACCTTG R 2 1 2 1 201000 r 74 goat snp44161-scaffold6-1629283 25 26189726 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440582 Affx-122929295 AX-123310919 25 26394943 CTGGAGCCAGTAGAGGTCATTTTTATTTTTATTTC[A/G]TTTTCTTAAATGTTATTTATTTTTTGGCCAAGCTG R 2 1 2 1 303000 r 74 goat snp44160-scaffold6-1587450 25 26232177 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463948418 Affx-1110238743 AX-515425769 25 26446812 AACTACCAAAGCTTGAGCGCCCTAGAGTTCATGCT[C/T]CGAGACAAGAGAAGCCACCACAATGAGAAGTTCGA Y 2 1 2 1 202000 f 74 goat 25_26446812_AF-PAKI 25 26446812 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413529 Affx-122950619 AX-123283878 25 26498301 GTGGGATCTCCCGTGGTGGCTCCCAGCACTTGGCC[G/T]CGTCTTTCCTGTTTCTGCTAGCTCTACATTTCTCA K 2 1 2 1 103000 r 74 goat snp44158-scaffold6-1484092 25 26334476 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427587 Affx-122939467 AX-123297930 25 26547858 TTTGTCCTATTGGAGAAAATCACACAACCCATCAC[A/G]GTCAGTGCGTCTAGTCACCCTTTAACACGGATCTG R 2 1 2 1 201000 r 74 goat snp44157-scaffold6-1434535 25 26384017 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431317 Affx-122937075 AX-123301658 25 26584492 CTGAGTTTGCATAGCAATTTAAATAGTGGCACTGA[C/T]GGATAAATGCATAAACTGTATCATTCATTGTGTAG Y 2 1 2 1 101000 f 74 goat snp44156-scaffold6-1397901 25 26420806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436390 Affx-122933038 AX-123306729 25 26616447 TCCACCTGGCTCTCTGTTGGAGTCTATGGGGAACT[A/G]TAACCTCACTTCTCAGACATTATGAATGATTTGGT R 2 1 2 1 101000 r 74 goat snp44155-scaffold6-1365946 25 26452516 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380326 Affx-122975379 AX-123250684 25 26670040 AACCAAGGAGCAAGTGTAGAATGACTCCACACCCA[C/T]AAACCCAGTTCCTGGAACCCTTTGGGGCTTATAGC Y 2 1 2 1 101000 f 74 goat snp44154-scaffold6-1312353 25 26506430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439770 Affx-122930513 AX-123310107 25 26701746 GGCTGCTCTGAGGATGAAATGAGGAGATAAATAAA[C/T]GCAAAATGCTTAGCACTATCATGAGACTCAGGGGA Y 2 1 2 1 102000 f 74 goat snp44153-scaffold6-1280647 25 26538069 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431926 Affx-122935989 AX-123302267 25 26754094 TAGAAGAAGAAACCTTGCAGAGGAGGGGCTGGTCC[A/G]CCTATTAATGAGTTAGATTGTTTTAAACTGTACTT R 2 1 2 1 101000 r 74 goat snp44152-scaffold6-1228299 25 26590525 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402971 Affx-122958157 AX-123273324 25 26853182 AGTGAGGAGGAGGCTGGGGCGTTCACTTCACCCGA[A/C]TGTTGTGTACCTCTTCCTGCAGGAGAGGAGGTTTC M 2 1 2 1 101000 r 74 goat snp44151-scaffold6-1129211 25 26687479 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426299 Affx-122940297 AX-123296645 25 26883209 TTGTCCTTTCTATCCACTGCCGTTTTGCTGTAACA[A/C]GGTAGGTAATCAATAAATATTTACTGATGGATTAA M 2 1 2 1 101000 f 74 goat snp44150-scaffold6-1099184 25 26717683 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408287 Affx-122953790 AX-123278638 25 26911775 CTCATTATTTTTGTCCTCTCCTGACAAAGTTAAAG[C/T]AAAGGAACTAACAGCAATGTATGAGACAGGGAATT Y 2 1 2 1 101000 f 74 goat snp44149-scaffold6-1070618 25 26746456 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413804 Affx-122949902 AX-123284153 25 26943426 ACAGATCACAAGGTATTTCCCTCAGTAGTTCAGCG[A/G]TAACGAGTATTTAGAAAGAGGCTTCCCAGGTGGCA R 2 1 2 1 101000 f 74 goat snp44148-scaffold6-1038967 25 26778271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379129 Affx-122976741 AX-123249488 25 26982660 CGAGGGGTGGGGTGAGCGCCTCCTTTTCCGTGGGC[A/G]TCAGATGCTTCTCCAGCCCCCAGTCTGGGTTCAAA R 2 1 2 1 101000 r 74 goat snp44147-scaffold6-999733 25 26817405 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431094 Affx-122936615 AX-123301435 25 27011752 TTGAGAATCAGTTGCACACATCTTGTTCCTTTACC[A/G]TGGTGGTTGTTATTGTTCAGTCACTAAGTCTCCTC R 2 1 2 1 201000 f 74 goat snp44146-scaffold6-970641 25 26846271 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439222 Affx-122931023 AX-123309559 25 27044971 CCATGTTTTATCTCATTTAATCTTCACTACACCCT[A/G]TGAGGGTTATGATCTCTATTTATAGATGAGAAACC R 2 1 2 1 201000 r 74 goat snp44145-scaffold6-937422 25 26879581 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439754 Affx-122930526 AX-123310091 25 27095209 AGAAGTTGCCAGGGTCTGGTTAATAAAAGTTCCAA[C/T]GTGGGTGTGGCTTCAAATGGTCACAGAACACTTCA Y 2 1 2 1 101000 f 74 goat snp44144-scaffold6-887184 25 26929760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453217 Affx-122920435 AX-123323550 25 27133826 CGGATAAACAGGAGTTCACCATAATGACAGGACCT[A/G]TAGGGCACACGACTATAAAATGACTTGGCGTTGCC R 2 1 2 1 101000 f 74 goat snp44143-scaffold6-848567 25 26968132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435624 Affx-122933777 AX-123305964 25 27185032 GAAGGACAGGTGCTCTGGGAAGTAACTCAGGTCCA[C/T]GGCAAAAATAAACCTTTGTTGTATTATATCATTCA Y 2 1 2 1 101000 f 74 goat snp44142-scaffold6-797361 25 27019168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433327 Affx-122935159 AX-123303668 25 27224331 TGGCGCTGACAGTCAGAGCAGCTGAGTGAAGTGGG[C/T]GTGTCCTCCATGGGGCAGTGTGGCAGAAACCTGGA Y 2 1 2 1 201000 f 74 goat snp44141-scaffold6-758062 25 27058487 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786336 Affx-122924088 AX-385273370 25 27289772 ATCAAAAGATAAATACAGTTTCCCACATGTGTGCA[C/T]TAGCTGTTTCATAAGCCATCCTCCCAACCTCTGAA Y 2 1 2 1 101000 f 74 goat snp44140-scaffold6-692621 25 27123253 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379409 Affx-122976121 AX-123249767 25 27338354 CCTGGTTGAGGAACTAAGATCCCACAGGCAGTGCA[G/T]CATGGCCAAAAGCTTAAAAACAATGTCTTCTGCAT K 2 1 2 1 101000 r 74 goat snp44139-scaffold6-644039 25 27171997 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442601 Affx-122928481 AX-123312938 25 27390491 GCTGCCATAAATAATAAATGAATAGAGATTGTCTT[A/G]CTAAGTGAAGTAAGTCAGGAAAAAAAAAATACAAT R 2 1 2 1 103000 f 74 goat snp44138-scaffold6-591902 25 27224939 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406242 Affx-122956109 AX-123276594 25 27423327 AGGGAGGCAGAGCTGGTGAAGTCAACTGGCAGCCA[C/T]GGGGCAGGGCAAGCAAAGTCAGATAGAGCCTGAGA Y 2 1 2 1 101000 r 74 goat snp44137-scaffold6-559066 25 27258200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398620 Affx-122961474 AX-123268975 25 27475480 GCATTTCAGTGCACCTTCCCACATTCTCAGGAAGA[C/T]GATGTCTTCTCTCTCTAAGAGCTGAGACAGAAGCA Y 2 1 2 1 102000 f 74 goat snp44136-scaffold6-506913 25 27309720 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435049 Affx-122933747 AX-123305389 25 27505380 TTCCAGGCCTCACCCTTGCTCATCATTCAGCCTCC[A/G]TGGTTATTCCTTAGCCCTCCTCTGATCACCTCTCT R 2 1 2 1 101000 r 74 goat snp44135-scaffold6-477013 25 27339194 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407131 Affx-122954865 AX-123277482 25 27534334 GTCCTTCAGGAGACTGAGGGGACCAGAATTTCTCA[G/T]CAGGCCTCTTCTGCTCCTCTGGGGCTGCTGATGTG K 2 1 2 1 101000 f 74 goat snp44134-scaffold6-448059 25 27368754 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378190 Affx-122976945 AX-123248549 25 27574081 TACCCTCTAAAGCAGGAGGAAGAGAGGAGGGCAGA[G/T]AGCAGAGGAACCCAAGGATGGCCTCTCTCCCAGGA K 2 1 2 1 201000 r 74 goat snp44133-scaffold6-408312 25 27408042 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799723 Affx-122977165 AX-385286651 25 27618051 GGCACTATGAACGTTACAGGCGCAACAGACTTCAC[A/G]TAATGGGATTTACTGATATGGGTCCAAATAACCAG R 2 1 2 1 101000 r 74 goat snp44132-scaffold6-364342 25 27450158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382765 Affx-122973978 AX-123253123 25 27717316 TTACAAAATAAAACCTCTTTTCCTAGTGCTACTCG[C/T]TTTGTTGTAGAAAAATATTACAAATAAAAATTAGT Y 2 1 2 1 103000 f 74 goat snp44130-scaffold6-265077 25 27548667 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451735 Affx-122921537 AX-123322068 25 27763743 GTATTTTAAAAAACAGGATACGGTTGTGCAAGGGA[C/T]GACCAGAGGAGAGGGGCTTATGGAGGAATAAATGG Y 2 1 2 1 101000 f 74 goat snp44129-scaffold6-218650 25 27595116 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403535 Affx-122957610 AX-123273888 25 27819275 GGGAAGACAGATCGCAGAATTGAAAGAAGCTCTCC[A/G]CTATTTGACAAGGATGGTGATGAACAACCAAAAAT R 2 1 2 1 101000 f 74 goat snp44128-scaffold6-163118 25 27650880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432584 Affx-122935517 AX-123302925 25 27849267 ATTAGAAAACCAATCTCACTAATTATCTCATAGAA[C/T]GGCCAAGATGGAAAGGATCTTGGAGAATTCCCTGG Y 2 1 2 1 201000 f 74 goat snp44127-scaffold6-133126 25 27680717 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780300 Affx-122929543 AX-385267395 25 27892189 ATGTTTAACTACTATTACAGGTGGACAAGGATGAC[A/G]TTAATTCAGCATTCCTATATGCTATATAGAGGGAA R 2 1 2 1 101000 f 74 goat snp44126-scaffold6-90204 25 27723435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432636 Affx-122935477 AX-123302977 25 27920890 ACACTGCCAGTACAATGAGAAATTGCATCTGGGCT[A/G]TAGCCTAGCCATGGGGACCGACTTGCCTAGAGACC R 2 1 2 1 101000 f 74 goat snp44125-scaffold6-61503 25 27752138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444642 Affx-122926923 AX-123314979 25 27960582 AGGCAGAGAAACGGCCAGTGAGGTTGAAGGAAAAT[G/T]AAGAGGATGTAGCTTCATGGAAGCATAGGCGCTTT K 2 1 2 1 201000 f 74 goat snp44124-scaffold6-21811 25 27792025 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453764 Affx-122919599 AX-123324097 25 27985726 TTTCTTCCCATCCTGAAGTTGTAGCGTAGCCGGGC[A/G]TGGAGAATTATTTCACTTACTGCGGAGGCAGCAGA R 2 1 2 1 101000 r 74 goat snp12260-scaffold146-3234 25 27820224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397486 Affx-122962077 AX-123267841 25 28021713 TGTTTAACCTCATGTATTCACCAGCGTGAGTCATA[C/T]ACCCTCCCCTGAACACACACACTTACCACTGGTAG Y 2 1 2 1 101000 f 74 goat snp12261-scaffold146-39221 25 27852622 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442299 Affx-122928251 AX-123312636 25 28082007 GACTTTCCTGGTGGTCTAGTGGCTAAGATGTTGCA[C/T]GGATACCACTTGCTGTGACTGAGAGTTCGCACCCC Y 2 1 2 1 201000 r 74 goat snp12263-scaffold146-99515 25 27913341 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432733 Affx-122935460 AX-123303074 25 28121785 CAGTCTGGTGCTAATGAAGAAGTACATAGGGTGAA[A/G]TCTGGAAGGGTCCCAAAACAAGCTTCTGGCCCCAT R 2 1 2 1 201000 f 74 goat snp12264-scaffold146-139293 25 27953203 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451919 Affx-122921023 AX-123322252 25 28232695 TAAGTGCCTGTCACATAGTATAAATCAGTATGTAA[A/G]TATTTGTTGAATAAATAAATGAGGTCATGATGAGT R 2 1 2 1 103000 f 74 goat snp12266-scaffold146-250203 25 28064512 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447564 Affx-122924033 AX-123317900 25 28266507 CCCGAGCTCTTGGTCAGGGCGGTTGCCCTGGGGCC[A/G]AGTCAGAAGCCAGGAAAGAACAGGTCTCTGCAGGC R 2 1 2 1 101000 r 74 goat snp12267-scaffold146-284015 25 28098240 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387473 Affx-122970356 AX-123257831 25 28364139 TGATACAGTTACCCCCATACACACATTTTGTTAAG[C/T]AGAAATAAGACATTCTATGTTTTCTTTTTTGGCAA Y 2 1 2 1 202000 r 74 goat snp12269-scaffold146-381647 25 28195993 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416416 Affx-122947844 AX-123286765 25 28438447 ACAATTAACATTTAACTTCCCACACCTCCTCCACC[A/G]CCGCAGAGTTTGTCCCTGTGTGTATTTACTTTTGA R 2 1 2 1 102000 r 74 goat snp9497-scaffold1343-18818 25 28265627 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453403 Affx-122919897 AX-123323736 25 28478181 CAATAGCTTCATTGCTACTGTGTACTCTTTTCCTC[A/G]TTTTATACTTTTTTCCTCTTTTCTTCACTCAGGCC R 2 1 2 1 103000 f 74 goat snp9498-scaffold1343-58552 25 28304384 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452471 Affx-122921002 AX-123322804 25 28528868 GTCCCCCAAGGACATTAGCCACACTGAGCAGGTTC[A/G]CTTAGATGCACATGCTCAAGAGTTCTGACCTCTGG R 2 1 2 1 101000 r 74 goat snp9499-scaffold1343-109239 25 28355519 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800125 Affx-122957828 AX-385287048 25 28564756 AACTCTGGAGGGCAGGCTTTATTATATGAAACTGT[A/G]TCTTCTTGGATGATCTGTTCATTGCTTGATTAAAG R 2 1 2 1 101000 r 74 goat snp9500-scaffold1343-145127 25 28391551 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453090 Affx-122920040 AX-123323423 25 28597312 CTGGAAAGCTGAAACAGTCCAAGAATTAATCACTG[C/T]GAGAACAGCTACCATCTCTAGGGCTGGGGAACACA Y 2 1 2 1 101000 f 74 goat snp9501-scaffold1343-177683 25 28424397 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386323 Affx-122970885 AX-123256681 25 28641340 TGGGAAACCCTCATAGCTGCCCTCTCCTGATGAAG[C/T]CGACTCTATCTAGGGGAGGAGGGTCAGTGGGTATG Y 2 1 2 1 303000 f 74 goat snp9502-scaffold1343-221711 25 28468460 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434431 Affx-122934664 AX-123304772 25 28680313 CAGGCAGGAGAGATATAGATCAACTTTTACTAATC[A/G]ATAATTGAGATAATTTGAAGATGAATTTGATTCTC R 2 1 2 1 101000 f 74 goat snp9503-scaffold1343-260684 25 28507288 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788163 Affx-122922561 AX-385275182 25 28713305 ATCTTTATTGCTTTGTTCACTTTAAACAGTACCGT[C/T]TGACCTCCCATCATGAAAGACGAGGTACTTCACAC Y 2 1 2 1 101000 r 74 goat snp9504-scaffold1343-293676 25 28540404 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442000 Affx-122928426 AX-123312337 25 28781758 GGAAGAGTGTATGGATTTGGGGAACCCTCCAAGGC[G/T]CCCCTTGTCAGAAGCTTCGATTTGGGAAACAAGGG K 2 1 2 1 201000 r 74 goat snp9506-scaffold1343-362129 25 28608952 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452127 Affx-122921682 AX-123322460 25 28831101 GGAACATAACTATGGATTTCTCTGAGTTATTCCTA[C/T]GACTGGGCTCCTGGACTCTTGCAACAGTGGTTCCT Y 2 1 2 1 101000 f 74 goat snp9507-scaffold1343-411472 25 28655599 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387799 Affx-122969693 AX-123258157 25 28870331 GAGCTGAGGGAGAAGTACCCAGGCTGAGGTGGAAA[C/T]GTCTTTCTGTGATTTGTCAGTGACACTGGTAAGTG Y 2 1 2 1 101000 r 74 goat snp9508-scaffold1343-450702 25 28695185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433024 Affx-122935776 AX-123303365 25 28921861 TGGGGTCAGATGAATGAGCGTTCCTGACAGTGATA[C/T]GTCACCCGGCCTCCTGAGAGGGAGCAAAAGCATAG Y 2 1 2 1 101000 f 74 goat snp9509-scaffold1343-502232 25 28747089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449470 Affx-122922647 AX-123319805 25 28968750 ACAAAACACAGCGGGGTTCGCAGCATGATACATTC[A/G]TGTAGTGTCAAGCCTGTGGGCACTTCACACACATT R 2 1 2 1 101000 f 74 goat snp9510-scaffold1343-549121 25 28794122 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273067 Affx-1111833294 AX-519546738 25 29010780 ACCCGATACACAGTATATACTCGATGGAATGAATG[A/C]GATGGGTCAGCAAGACCGAGAACTACGTATGATAA M 2 1 2 1 101000 f 74 goat 25_29010780_AF-PAKI 25 29010780 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38377612 Affx-122977891 AX-123247971 25 29020922 GAGTTGCAAAGTCCTGCCTGATAAGAACCTAACCT[A/G]CCTTGGCAGCTTCACCCAGCTCTCCTTCAGCACCC R 2 1 2 1 101000 f 74 goat snp9511-scaffold1343-601293 25 28846290 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421324 Affx-122944081 AX-123291671 25 29068132 AGTGCAACTGAGCATTGAAGTCAATTAAAATACAA[C/T]GAAGCAGCAGTGGCTGTTAGAAATGTTGTTATAAA Y 2 1 2 1 201000 f 74 goat snp9512-scaffold1343-648503 25 28893524 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396474 Affx-122962961 AX-123266829 25 29102396 CTCTCAGCTCCTGGGGGAAATTGACACAAGTCCCC[A/G]TCAGCTCTCTTCAAGGAAGATCAAAGAATGCTCTT R 2 1 2 1 201000 f 74 goat snp9513-scaffold1343-682767 25 28927673 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451655 Affx-122921597 AX-123321988 25 29157216 AAGCAGGCTTGCTTTGTTATCAGTAAACATACGTA[C/T]ATGTGACATCTATTTGCCTATTAGCAAATGATACC Y 2 1 2 1 101000 r 74 goat snp9514-scaffold1343-737587 25 28982418 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779536 Affx-122930944 AX-385266639 25 29189441 TAATCCGATGGCCCATGAAATGTAAAGTAAGGAGG[C/T]ATCAATGCTGAAAGAGTAGCCTAGGGCTGAGGTCT Y 2 1 2 1 101000 f 74 goat snp9515-scaffold1343-769812 25 29014588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788141 Affx-122962073 AX-385275161 25 29218577 AAAATCCAGACAATCAGATTGTATGTATCTCCTGA[C/T]GTGATGTGATAGGAAGTTTACAGCATCACCTGAAG Y 2 1 2 1 202000 r 74 goat snp9516-scaffold1343-798948 25 29043357 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406140 Affx-122956187 AX-123276492 25 29252846 CCCTGTTGAGAATCGCAGCCTGTGCTCTGAGTCCT[A/G]TGTAGTCGAGGGTACGATGGACATGATTAGGGGGG R 2 1 2 1 201000 r 74 goat snp9517-scaffold1343-833217 25 29077480 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38405386 Affx-122956299 AX-123275738 25 29284397 TTCTCACGAGGTAGCTCCCTGAAAGGTGGAGCCTG[A/C]GGGTCTTTCGTGAGGTCCAGGCAGCCAGGCTGACC M 2 1 2 1 101000 f 74 goat snp9518-scaffold1343-864768 25 29109056 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394895 Affx-122964739 AX-123265250 25 29341343 GCTGCCTGTTAGCTTTTTTGATCCCCATTTTGGCT[A/G]TTTGGTTGACTGGAAGCTTATTTACAAAACCCCTC R 2 1 2 1 101000 f 74 goat snp9519-scaffold1343-921714 25 29166023 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432080 Affx-122935877 AX-123302421 25 29391928 AAATACCCACTGGACTTGGATGATTCAAAATCTCC[A/G]TCGTTGGGCCAGAGCATCCTTCCTGACCCTCAGAC R 2 1 2 1 202000 r 74 goat snp9520-scaffold1343-972299 25 29216963 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425579 Affx-122941422 AX-123295925 25 29420975 CACAGGTGATGATGAAAGGATCTGGTGGAAGCAGA[C/T]AGAGGGACAGGGCAGGTGATGTGGGAAGGAGCGTG Y 2 1 2 1 101000 f 74 goat snp9521-scaffold1343-1001346 25 29246420 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386851 Affx-122970076 AX-123257209 25 29458289 AACAGCAGATCTCCTGGTTCTCAGCTTCAGGGCTG[C/T]GTAAGTGAGTCCAAACCTCTACATACAAATGGAGG Y 2 1 2 1 101000 r 74 goat snp9522-scaffold1343-1038660 25 29283761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449779 Affx-122922433 AX-123320114 25 29508529 AATTCGACTGGTGGATTCCAGAGAGACTGAACTTC[A/G]CTGAGCAGTCTTCAGGAGAAGAGGGGGATCTTGAA R 2 1 2 1 101000 f 74 goat snp9523-scaffold1343-1088900 25 29333786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785175 Affx-122919315 AX-385272221 25 29571771 AGTGCTGCGCTTATGCAATCCTGCCCTGAAATTCC[A/G]CCCTGTGTCCACTGCTTTTTTATTCTCAATTCCAA R 2 1 2 1 101000 r 74 goat snp9525-scaffold1343-1152142 25 29396873 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790283 Affx-122950706 AX-385277287 25 29616740 TTCCTTTTCATCTCTAAGTCTTCAAAATTCAGTTT[G/T]TATTTTATACCTGAATCAGATAGCCAAATCAGTGT K 2 1 2 1 101000 f 74 goat snp9526-scaffold1343-1197111 25 29442017 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411771 Affx-122951488 AX-123282121 25 29652569 GATCCAGCTGCCCCTCCTTTTCCAGCTCTCCCCTC[A/G]TCTCCTCTTACTTGGAACAAGGCTCACCATCAGCC R 2 1 2 1 101000 r 74 goat snp9527-scaffold1343-1232940 25 29478916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277639 Affx-1111836012 AX-519551138 25 29677122 GTGCCAAGACATTTCACATTCTTAACTGATTTATT[A/G]CCTTGGCTCCTCCACAGACTGTTTGCTCTACAGTG R 2 1 2 1 101000 f 74 goat Random2.2K-2157 25 29677122 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448320 Affx-122924148 AX-123318656 25 29695850 AGTCAGTCTTGATGCTTCTCCTCCCATCATCACCC[A/G]TCTGTCACCCCCGTTTCCAACCCAATCCTGTCAGC R 2 1 2 1 101000 r 74 goat snp9528-scaffold1343-1276221 25 29522134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398723 Affx-122961837 AX-123269078 25 29736183 ATCTTGGGGCGTTGAAAGGTGAAAACTGTGATTAA[C/T]GCAGAGCAAATGCGGTTGTGTGATGTGAATAATGA Y 2 1 2 1 101000 f 74 goat snp9529-scaffold1343-1316554 25 29562736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399103 Affx-122960867 AX-123269458 25 29776021 ATTTTACCAATTATTTTAAAAATATGACTTAGATG[C/T]ATTGCTGTCATAGAATATACTCTAAGTTGTCAGTC Y 2 1 2 1 101000 r 74 goat snp9530-scaffold1343-1356392 25 29602799 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423563 Affx-122942416 AX-123293909 25 29889853 GCCCTGCTGTAGCCCCTACCCTGCCACCTTGTCTC[A/G]TTCTCAGCCTCTCAAACTAGACCCAGGCATGGGCC R 2 1 2 1 101000 r 74 goat snp9532-scaffold1343-1470224 25 29715377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768602 Affx-122943882 AX-385255782 25 29926299 TTAAAGGTTTACTTCACACGGCTGGCCTGTTGATC[A/G]TCAAGAAAGGCTATGGATTCATGCAGTAATTTAAA R 2 1 2 1 101000 f 74 goat snp9533-scaffold1343-1506670 25 29751569 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383220 Affx-122972770 AX-123253578 25 29970816 ATGAGGGCTGAGGCACTATCTGTTTCCTTCACCAG[C/T]TCCTGACATTTGGCCTGCAGGTAGAAAGTGCTCAG Y 2 1 2 1 101000 r 74 goat snp9534-scaffold1343-1551187 25 29795749 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800032 Affx-122959974 AX-385286955 25 30020832 TTCCTATAAGATTTTTAAGAAGCCATAGCATATGA[C/T]AAACAATGACATGAGAACTAAGTTTGCAGGGTTCT Y 2 1 2 1 101000 r 74 goat snp9535-scaffold1343-1601203 25 29845418 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421290 Affx-122944731 AX-123291637 25 30063159 TCCTGTGCACCGAGGTTGTCCTTCTCATGACTCTG[C/T]AGGAGTCCTGAATAAAGCCCTTCTATCCGGTTTCC Y 2 1 2 1 101000 r 74 goat snp9536-scaffold1343-1643530 25 29887441 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415220 Affx-122948971 AX-123285569 25 30092867 AGATGACCTGCCATCTGTCCCGAGTCCCTCTGGAC[C/T]GGTCCCCAACCCCTCTGTCAATGTCTCCCAACATG Y 2 1 2 1 102000 r 74 goat snp9537-scaffold1343-1673238 25 29917235 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783353 Affx-122921619 AX-385270417 25 30127204 GGGATGACCAAAATTCCTTTGGACAAGTAAGTTAC[A/G]TTTTGTACCCTGGATAAATAATTTGCTAACCAGCA R 2 1 2 1 101000 f 74 goat snp9538-scaffold1343-1707575 25 29951587 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379927 Affx-122975662 AX-123250285 25 30178230 AAACTCCTCATGTATTTTATGCATCCCCACAAGGG[C/T]ACTGGGACCCCTAAATGGGGCCAAAAAAGTCTTTA Y 2 1 2 1 101000 r 74 goat snp9539-scaffold1343-1758601 25 30001969 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448839 Affx-122923297 AX-123319175 25 30210005 AGATAAAGCATTGTAATTCACAGAGAATACATACA[C/T]GTGTTATGCACTTATCAAAAATGGAACTGTAGATG Y 2 1 2 1 101000 r 74 goat snp9540-scaffold1343-1790376 25 30033526 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375385 Affx-122979218 AX-123245744 25 30265102 AAATGTACTGAGAAACATTACTCAGGCTTCCACAG[C/T]GCAATAAGAGGTGGAGGCACGGTCTGATTCAGATC Y 2 1 2 1 101000 f 74 goat snp9541-scaffold1343-1845473 25 30089040 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395001 Affx-122964236 AX-123265356 25 30324737 TTCTTAAGGAGCTTACAAACTAGTAAAGTGGTACA[C/T]AAAGTCAGAAGAGAAGACTAAAGGAAAGCTTTACA Y 2 1 2 1 101000 f 74 goat snp9542-scaffold1343-1905108 25 30148488 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775595 Affx-122966268 AX-385262726 25 30368383 CTGGTGACTACCTTCTTTCAAACTTGTAAAGCAAA[G/T]CACAAAGTGACATTTATGACATAACATGTAATACT K 2 1 2 1 101000 f 74 goat snp9543-scaffold1343-1948754 25 30192209 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420585 Affx-122945263 AX-123290932 25 30402813 AAATGGAAGTATAGCAGATTTGAAAGAACTCAGTG[C/T]ATGGTTTGAGACTAAAAACAGGCTCTGGGTAGATG Y 2 1 2 1 101000 r 74 goat snp9544-scaffold1343-1983184 25 30226704 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779621 Affx-122975774 AX-385266723 25 30436806 GTATCAAGAGGGCAGAGCCTTTGGTTTACTTACTG[A/C]TACTATATCCACAGAAACTAAAAGAGAAGCAGGCA M 2 1 2 1 101000 f 74 goat snp9545-scaffold1343-2017177 25 30260590 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277769 Affx-1111836013 AX-519551268 25 30471677 TCTGATGAATATTTAGATCTGCACCCTTTCTTAGC[A/G]TCCTGAATAGTCTGAGAAGCAATTTAGAAACTTGG R 2 1 2 1 101000 r 74 goat Random2.2K-2158 25 30471677 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38407784 Affx-122954957 AX-123278135 25 30477933 TGAAAGTGCCAATAAGCACCAAATCTCCTGTTCAA[C/T]GATATTTTAAAATATACCTCCACTAACATCAAAAC Y 2 1 2 1 101000 f 74 goat snp9546-scaffold1343-2058304 25 30302371 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421850 Affx-122944291 AX-123292197 25 30516777 TTTCCTTCTATGAGTAGCTGGGATAAACTGATTAG[C/T]AGAAAAGATTCAACCACTGCATCTTGCCCATCTTT Y 2 1 2 1 101000 f 74 goat snp9547-scaffold1343-2097148 25 30341242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423504 Affx-122942558 AX-123293850 25 30605766 AACTAACAATTCCAGGTTATGGAAAACATTATTTG[C/T]AGGAAGCAAATCTAATTTAATTTTTTCATTGCTAA Y 2 1 2 1 101000 f 74 goat snp9549-scaffold1343-2186137 25 30430590 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436504 Affx-122932954 AX-123306842 25 30657010 GGCAAAGTAGTTTAACTAAGTTGCTTCAATTTCCA[A/G]CTTCCAGACTTCTCCCCAGTTTTGTAGCAAAGCAA R 2 1 2 1 101000 r 74 goat snp9550-scaffold1343-2237381 25 30481879 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392693 Affx-122966412 AX-123263050 25 30689981 GATCACAAAAGCAGTTCTGAATTATGGGCTGTGGA[A/G]AACACCTTAAAAAACCTCATTTCTTCACCACTGCT R 2 1 2 1 101000 f 74 goat snp9551-scaffold1343-2270352 25 30515001 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447901 Affx-122923811 AX-123318237 25 30721231 AAGACGAGAAATTGTTCAGGGCAGATTACAGTCAA[C/T]ATAGAGCCACTGAAGGTTTCTAAAGGGAAGCATCT Y 2 1 2 1 201000 f 74 goat snp9552-scaffold1343-2301602 25 30547191 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429858 Affx-122938150 AX-123300199 25 30750199 GTTGCTAGTATTTTGTCAAATTTTCTTAATCTACA[C/T]ACTCACTTTAATTTCTCATGGAACCATATGAAAGC Y 2 1 2 1 101000 r 74 goat snp9553-scaffold1343-2330570 25 30576173 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277771 Affx-1111836014 AX-519551270 25 30779068 TGTTCAAAGTCCAGGTCTGCTCCCCAAAGGTTCTT[A/C]TTAAAGAGCTTGATCTTGGATGCTGTTTACTTAGT M 2 1 2 1 201000 r 74 goat Random2.2K-2159 25 30779068 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431961 Affx-122935962 AX-123302302 25 30800881 ATAATTATTTCTCTGAGGTTTCAACCCCTTGAGAT[A/G]GGTTCAGTTCCTCCAGGTTCAGTTCCTCCAAGTTC R 2 1 2 1 101000 r 74 goat snp9554-scaffold1343-2381252 25 30626591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802275 Affx-122974830 AX-385289179 25 30834287 CCCCTTCCGGGGCACAAAAACCAGGTCAACAGGAA[C/T]AATTTCCAACTCACTGACACAAGGTAGGAAAATTC Y 2 1 2 1 101000 f 74 goat snp9555-scaffold1343-2414658 25 30659928 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786066 Affx-122972494 AX-385273102 25 30878745 TAGGATCAATCCTTCCACTATTCCTCAAAACCAAA[A/C]AGTAATTACAGAACACTTGCCCTTTTCTTTTTCTC M 2 1 2 1 202000 r 74 goat snp9556-scaffold1343-2459116 25 30704294 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435871 Affx-122932795 AX-123306210 25 30918784 ATGTACTGTCTTAAGAGCAAGAAGTTCATATCTTA[G/T]AGGTCAGGAAAACCATATACTTGACTCCTATTACT K 2 1 2 1 101000 r 74 goat snp9557-scaffold1343-2499155 25 30744322 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429545 Affx-122937828 AX-123299887 25 30973348 ACATGACAAACAGTTGTTATAAATTTTCTGGTTCA[G/T]CAATAAACAGGCAAGATGCCTTACCCAACACGTCA K 2 1 2 1 201000 f 74 goat snp9558-scaffold1343-2553719 25 30798864 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447348 Affx-122924879 AX-123317684 25 31022266 TATGTGCAAACATCAAAATTACTCTAAACAATTAC[A/G]TTCCTACCTTCCCTGTACTCCCCCAATAATAACAT R 2 1 2 1 101000 r 74 goat snp9559-scaffold1343-2602637 25 30847828 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769712 Affx-122927108 AX-385256882 25 31081956 TCATTACGCTGTCTGCTACAGGGACGTGCCTCAAT[A/G]TAGTTAAAGCAATAAACTACCTGGGAGTAATCTTT R 2 1 2 1 101000 f 74 goat snp9560-scaffold1343-2662327 25 30907641 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394269 Affx-122964719 AX-123264624 25 31110683 GGTGAGATTTTTCTGAGTGGTATTTTAAGACATTC[A/G]TCCTAAAGAGCATCCTGGAGATATGGGACAGGAGC R 2 1 2 1 101000 f 74 goat snp9561-scaffold1343-2691054 25 30936278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420865 Affx-122944637 AX-123291212 25 31164843 AGCCAACACTGCCGACAAGAGCAAATCAGGCAGGA[C/T]TGATGTCTCAGAAGGACAGCTGGCAGGGAGGATAG Y 2 1 2 1 201000 f 74 goat snp9562-scaffold1343-2745214 25 30990548 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382043 Affx-122974942 AX-123252401 25 31200199 GTCATGTAAGGTGGCACTTTCTGAAATTTATCCCC[A/G]CTGGACTTTCCTGCCTCCTTTATTGCTTCTACTCT R 2 1 2 1 201000 r 74 goat snp9563-scaffold1343-2780570 25 31025967 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407668 Affx-122954598 AX-123278019 25 31231390 CAACTTGTGGCCAGGGAACTGCATTCCACATACCA[C/T]GGGGCAACTGAACCCTCACAGCACAACTACTGGGC Y 2 1 2 1 101000 f 74 goat snp9564-scaffold1343-2811761 25 31057461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421539 Affx-122943872 AX-123291886 25 31281596 TTGTGCAGGAGGTTTGGGTTGTAATTTTGACAAAC[A/G]GAGGGAAAAACTGTAATTTTCTCCTCTGGAGAAAT R 2 1 2 1 201000 f 74 goat snp9565-scaffold1343-2861967 25 31107645 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377405 Affx-122977563 AX-123247764 25 31314760 TATTAGAGAGATTTATTTTCTTCATTTCGAATTCT[A/G]TAGCCTCAAATTCCTAGAATAATGTTTTGCAAATA R 2 1 2 1 101000 r 74 goat snp9566-scaffold1343-2895131 25 31138574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399518 Affx-122961157 AX-123269873 25 31357576 AGAGAGAAAAAAGGACGATAGGTAAAGCCTGTTGC[A/G]TGAAGTGCTGTGCCTCACTCCCAAATACACTGGAC R 2 1 2 1 101000 f 74 goat snp9567-scaffold1343-2937947 25 31181622 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399868 Affx-122960231 AX-123270223 25 31448308 GAGTAGGGGCCCCAGCACAGTGCCTGTCCTGAAAT[A/G]TTGTTGTTGTTGTTTAGTTGTTAAGTCCCGTCTGA R 2 1 2 1 303000 f 74 goat snp9568-scaffold1343-3028679 25 31272467 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426229 Affx-122940350 AX-123296575 25 31501763 TCCTACCAGCCCTGCTGCCCCCACCAGGAAATACC[A/G]TGGGGGCAATATGCATTTCATCTGAGGACCGACTG R 2 1 2 1 103000 r 74 goat snp9569-scaffold1343-3082134 25 31328581 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273070 Affx-1111833296 AX-519546741 25 31521050 CTGTCAGGACTGTAAAATGTCTCCCCCCAATCACC[A/G]CACACACACTTTTTTTTTTTTAATCACCTTCGGGG R 2 1 2 1 102000 f 74 goat 25_31521050_AF-PAKI 25 31521050 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449853 Affx-122922376 AX-123320188 25 31542465 AGGAGCATGGATCCAGTCAGAGAAAGATCCAGAAA[C/T]TCAGCTCTGATGGATTGGTCACAGGGATGGTGCCT Y 2 1 2 1 101000 f 74 goat snp9570-scaffold1343-3122836 25 31369476 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782909 Affx-122936591 AX-385269979 25 31582589 TGCAAATATGTGAGTAGGACCTAATGGTTTGTGGT[A/G]TTGTCTTTCTTAGATCCTTAGTAATAGCAGTCCTC R 2 1 2 1 101000 f 74 goat snp9571-scaffold1343-3162960 25 31410566 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418206 Affx-122947059 AX-123288554 25 31674436 TACAAGTATGACCTTTGGAGTTGTTGGTATATAAA[C/T]GGTGTTTGAAGCTCCAAGGTAGGGAAAAAGTGTGG Y 2 1 2 1 101000 f 74 goat snp9573-scaffold1343-3254807 25 31498730 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385360 Affx-122971641 AX-123255718 25 31718386 AGGTAGGCAGTGGGAACTTGGTCTTTACTTGTGGA[C/T]GAGGGCAAGGCAAACCTTTTAGCAAGTTGCACTTG Y 2 1 2 1 201000 f 74 goat snp9574-scaffold1343-3298757 25 31542437 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429761 Affx-122938256 AX-123300102 25 31769739 ATCTAGTTTAAAATGTTAATGAATAGCTCCCCTTC[C/T]AATTGCCAAGCTGAGTATTTAAGGGAACCTGACAC Y 2 1 2 1 101000 r 74 goat snp9575-scaffold1343-3350110 25 31593841 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438302 Affx-122931385 AX-123308640 25 31808266 GTGTCATCCCTAAGATGCAAGAAGATGTCCACCTG[C/T]AGAGGGCAACCGTCACCAAGGCGACCGTCACCATG Y 2 1 2 1 101000 f 74 goat snp9576-scaffold1343-3388637 25 31632295 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409292 Affx-122953108 AX-123279643 25 31867951 GCAGGGTTGAAGACAAAGCACAATTCTAGGAGCTC[A/G]TACAAGAGCTGAGAGGCAATAGCGTTTGGGGTGGA R 2 1 2 1 101000 r 74 goat snp9577-scaffold1343-3448322 25 31692313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799967 Affx-122940836 AX-385286893 25 31924694 CAAAGCAGAAATATAAGCACATGGAATATATGCCA[C/T]GAAAACAGAACGAGATCAAACAGAAGCTCTCAGAA Y 2 1 2 1 101000 r 74 goat snp9578-scaffold1343-3505065 25 31749101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431720 Affx-122936756 AX-123302061 25 31976192 AAGGCTTGCATCTCTTCTCCCTCTTCCCTATAAGA[C/T]GATTCAGTTGAGAGCAAGGTGATCTCCTGCACCCT Y 2 1 2 1 201000 r 74 goat snp9579-scaffold1343-3556563 25 31800403 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446711 Affx-122924728 AX-123317047 25 32015760 ACTATGACGATTTACAACCCTATGTTCTGTAGCCC[A/G]CCAAGCTCTCCTGTCCATGGGATCTTCCAGGCAAG R 2 1 2 1 101000 f 74 goat snp9580-scaffold1343-3596131 25 31839218 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398334 Affx-122962126 AX-123268689 25 32061170 ACTAAATATGCAGTTGCCATTGCTGGGATAGATGG[C/T]ACCCTAATTCTGTGCTGTGCTTGGTCGTGTCCAAC Y 2 1 2 1 201000 f 74 goat snp11626-scaffold143-15810 25 31883472 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320799538 Affx-122964712 AX-385286468 25 32103013 TTTCCATTAAAGAAGAAACTATTGTTTGAGTCACT[A/G]CTGGGAAGACCAGTGATAATTCTCATGCTGTTTAC R 2 1 2 1 101000 r 74 goat snp11627-scaffold143-57653 25 31925241 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406849 Affx-122955662 AX-123277200 25 32133631 AAGATACAGATATTAATTTCCTGAAACACTGTATG[A/G]CTCTAGCTGCACAAAATTTGAAGCTAAGTAACAGA R 2 1 2 1 101000 r 74 goat snp11628-scaffold143-88271 25 31955812 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420975 Affx-122944576 AX-123291322 25 32167595 GCCATCACAGAGGGACATTATAATTATTATACAAA[C/T]GCTAAAATAATCCTGAGCTCTCAGCCCAGACTAAG Y 2 1 2 1 201000 f 74 goat snp11629-scaffold143-122235 25 31990109 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418623 Affx-122947150 AX-123288971 25 32198545 AAAAGAGATGAAAAGGAAGAAATGTGTTCACCAGC[A/G]TGGTTAACGGTTAACGGGCAATTGCCTGCATTCAC R 2 1 2 1 201000 r 74 goat snp11630-scaffold143-153185 25 32021674 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406554 Affx-122955108 AX-123276906 25 32247127 TTTGGTGATACTCACACAAGAAGAACAAAGATTTG[A/G]AACAGAGTAGAGATTCTCTGGGGTCCAGGTTCTCC R 2 1 2 1 101000 f 74 goat snp11631-scaffold143-201767 25 32070635 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393095 Affx-122965590 AX-123263452 25 32287859 GCCAGGAAATAAAAAAAATCAGAAGCTGGCTTTCT[A/G]CTGGAGAAATATCATTCAGATGTCCCATTTCTGAT R 2 1 2 1 201000 r 74 goat snp11632-scaffold143-242499 25 32111412 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448435 Affx-122923655 AX-123318771 25 32331661 TGTAATCTCATGGGACCGCTCAGTTTAGGGCCCCA[C/T]GCAAGGGAATCACAGCAACAGAAGCTCTGGAGACA Y 2 1 2 1 201000 r 74 goat snp11633-scaffold143-286301 25 32151304 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795696 Affx-122950205 AX-385282649 25 32361572 CCTCTTTAATTTTTCCAGCTAATTTAGAAGGTAGG[A/C]AGTGATGCTGCATTGTATATGGCCTCGCACTTGGA M 2 1 2 1 101000 r 74 goat snp11634-scaffold143-316212 25 32181036 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786450 Affx-122940464 AX-385273484 25 32393410 ACAGCTTCTTCAACGCAAACGTTTTCCTGTGAAAT[A/G]CCTCCCCAGTTGATGCTTCAGAGTTGACTAATTGC R 2 1 2 1 202000 r 74 goat snp11635-scaffold143-348050 25 32213492 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400474 Affx-122961300 AX-123270829 25 32431861 CTGGATGGGCTCTATTCCTGGGCCTCCAGTGATTG[C/T]TAACACTGTCAGAATTTGACAAAGTCCTAATGAAA Y 2 1 2 1 101000 r 74 goat snp11636-scaffold143-386501 25 32251766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422774 Affx-122943225 AX-123293120 25 32500071 CTGGAAATCAAAGTCTGAATGAAGTCAGTGAGCTC[A/G]TCCACCTGGTTCAGACAGAAGGCACAACTACTGAT R 2 1 2 1 101000 r 74 goat snp11637-scaffold143-454711 25 32317792 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443594 Affx-122927320 AX-123313931 25 32538122 CTCAGTGGCTTACAATTGCAAAGGTCAGCTGTGAC[A/G]GTTCCTGTGGTATTGCTCCATGAATCTTCTCAGTC R 2 1 2 1 101000 r 74 goat snp11638-scaffold143-492762 25 32356031 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801247 Affx-122931242 AX-385288160 25 32595382 AGGAGCATATCATTTGCTTGTCTTACTCTCCCACC[A/G]CCTAGTTTATAAACCTTACTTTCAGGAAGCTTTTT R 2 1 2 1 101000 f 74 goat snp11639-scaffold143-550022 25 32413233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403924 Affx-122957473 AX-123274276 25 32631715 CCAATTGTAGGCTCCAACCAGCTGCTCACCCCATA[C/T]GACTGTGGGGACTTAAATGAACCAAAATTAAAGCG Y 2 1 2 1 101000 r 74 goat snp11640-scaffold143-586355 25 32448929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767555 Affx-986698600 AX-385254808 25 32652754 CGGTGACCACACACCAGGCCGGGTGGTGACATGAG[A/C]TTCCAGAGCACGAGGCCTGACGGGCGGGCCCTCCC M 2 1 2 1 600010 r 74 goat 25_32652754 25 32652754 Ancestral_priority_1043 ancestry 0.414 neutral IMAGE 10K 10K ancestral 38412278 Affx-122950883 AX-123282627 25 32673974 TTGATGACCTGTTTAATCGAGTCATCCAAAAGTTA[C/T]AGATCCCTCCTTCTGCCCTGTGACATTTTCTCTCA Y 2 1 2 1 201000 f 74 goat snp11641-scaffold143-628614 25 32491415 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393673 Affx-122965271 AX-123264028 25 32782795 TTTGATTCAAACACCGGGTATGGTACTTTTACCGC[C/T]TCTGTGAGTCCAAGAGCTTGAGCTGAAAGTGCAAG Y 2 1 2 1 101000 f 74 goat snp11643-scaffold143-737435 25 32600135 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443363 Affx-122927416 AX-123313700 25 32839228 CTTAGATCAAGAAGAAAATTCAAGATATTTTAGTG[C/T]AACCTCTTTGTTCCATTATATTAGAAATGAGAAAT Y 2 1 2 1 101000 r 74 goat snp11644-scaffold143-793868 25 32656365 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383603 Affx-122972562 AX-123253961 25 32877016 TAGTCTTACCTCAAAGGGTTATTATAAGCTTTCAA[C/T]GAGCTAGTATCTATTGGGTGCTTAGAGCAGGGCCT Y 2 1 2 1 101000 f 74 goat snp11645-scaffold143-831656 25 32694279 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441826 Affx-122929061 AX-123312163 25 32920005 TCGATGACAGAGCATTATAAAGTGATTTAAAGAGA[C/T]AGGAAAATGCTTATGTTTTAAGCATATGTGTTTGT Y 2 1 2 1 101000 f 74 goat snp11646-scaffold143-874645 25 32736620 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404845 Affx-122956627 AX-123275197 25 32969300 AGGTCAGCAGTTGCCCTAAGTGAGTATGGGTTCAC[A/G]TCTAAATGTTTATGAAATGTATTTATTCTCCTAGG R 2 1 2 1 101000 f 74 goat snp11647-scaffold143-923940 25 32786258 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450318 Affx-122922137 AX-123320653 25 33029543 ATGGATTGGATGGTAATTCTCCCCTCAACTAATTT[A/G]TAAATTCAACGCCACCCCTAATCAAATCCTAATGT R 2 1 2 1 202000 r 74 goat snp11648-scaffold143-984183 25 32846506 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448263 Affx-122924191 AX-123318599 25 33061110 CTCAGCCTCCTGTTCCCTGGGTTGGGGTCTACCTG[C/T]GGGCACAGGGGAACTCATGGGAGGTGCTTGGTTAA Y 2 1 2 1 201000 f 74 goat snp11649-scaffold143-1015750 25 32877961 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386579 Affx-122970699 AX-123256937 25 33152549 CGTCACCTTGATCCCCAGGTCTCCTGCCTGGATTT[A/G]CTAACTTAGGAGGGAAAAGCCTTTGTGCTTCTGTG R 2 1 2 1 101000 r 74 goat snp11651-scaffold143-1107189 25 32967028 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442516 Affx-122928550 AX-123312853 25 33235235 ACTTATTATTTCAGCAATTTTTCTGTAAATTTGGT[A/G]TTCTTCAAGATAAAAAATTTTAAAATAGTGACTAC R 2 1 2 1 202000 r 74 goat snp11652-scaffold143-1189875 25 33050821 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776887 Affx-122940790 AX-385264011 25 33302713 AATGGATACAAAAAATTATTCGGGAGATATTTTGC[A/C]TTCTTTTTTGTATAAAGTCTTCAAACTGGAGTGTG M 2 1 2 1 101000 r 74 goat snp11654-scaffold143-1257353 25 33115894 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383605 Affx-122972560 AX-123253963 25 33344641 ACCACCCTCTCTGTCTGAGCAAGAGTCATGGCTCT[A/G]CCCGTGAAGCTGGTGCAAGAGAGGAGACACGGACT R 2 1 2 1 101000 f 74 goat snp11655-scaffold143-1299281 25 33157943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392065 Affx-122966386 AX-123262422 25 33474541 AGAGAGAGAGAAAGAGAGAGTGCATGCAAGCCAGG[C/T]GGGGCTGAGTGGGGGTTTCAAATGCTCTGAATGGG Y 2 1 2 1 101000 f 74 goat snp11657-scaffold143-1429181 25 33287997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407030 Affx-122954945 AX-123277381 25 33516048 GAGCACTGAACACAGAACCCAGAGCACAAAAAAAT[A/C]GGGAGGGAAAAAACTGGATTAACATAGAAATAAGT M 2 1 2 1 101000 f 74 goat snp11658-scaffold143-1470688 25 33329282 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379504 Affx-122976461 AX-123249862 25 33556248 ACTTACCTAAGTTTACAGCTAGGACATGTCGTCTG[C/T]AGACACCGCTGTGAGGACAAGAGGGAGCCTAAGGT Y 2 1 2 1 101000 f 74 goat snp11659-scaffold143-1510888 25 33369328 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425492 Affx-122941484 AX-123295838 25 33604021 CCATCTACTGGGGAAGAGAGGTGTGTGCATGTGAA[C/T]CCAGGGCCGAATGAAATTGCAGTTGCAGCTGAACA Y 2 1 2 1 101000 r 74 goat snp11660-scaffold143-1558661 25 33412939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803488 Affx-122978273 AX-385290310 25 33656253 TTTTCCATATCAATGTATAAAGCTTATCAAATTCT[A/G]TATTTTTCCTCTGAGCCTCTGGTCTCCATCGCCTC R 2 1 2 1 101000 r 74 goat snp11661-scaffold143-1610893 25 33465404 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774806 Affx-122934421 AX-385261940 25 33685668 TCATTCAAGCCAAATTTCTTGAGAATGTTGTCTCT[A/G]CTTTTTGACCATCAGTTTATTCCTTATGCTGTTAA R 2 1 2 1 101000 f 74 goat snp11662-scaffold143-1640308 25 33495045 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444905 Affx-122926253 AX-123315242 25 33720136 AATCCCTCTTCATGAGGGTTTCCAGGAGGAGTCCA[A/G]GGCTTTTCTCGTGAACCCAATTCCTTTTCTTTCTT R 2 1 2 1 101000 r 74 goat snp11663-scaffold143-1674776 25 33529430 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387218 Affx-122970588 AX-123257576 25 33782540 AACTGCAGGGAGAAATACCCAGTAGTTAAGAGACG[C/T]GCAGCAGCTATGGCAAGTGACACCTGGCGGCTAGA Y 2 1 2 1 101000 f 74 goat snp11665-scaffold143-1737180 25 33591584 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277773 Affx-1111836015 AX-519551272 25 33810563 GACCTCACCGAAGGAGAGGGCTGGCTTTGCCTGCA[A/G]CTCCTGGATGATGATCTCAAAGCCCTTCAAGTATC R 2 1 2 1 101000 r 74 goat Random2.2K-2162 25 33810563 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436981 Affx-122933152 AX-123307319 25 33874843 CTTAGCATGCACGCACATGGGGGCTCTGCAGAGAA[C/T]GACTGAGATATACCCAATGGGCAATGCTGCAGACG Y 2 1 2 1 101000 r 74 goat snp11667-scaffold143-1829483 25 33684108 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431185 Affx-122937178 AX-123301526 25 33911693 TTTATTTATAAGGCATGACAAATAGTCACTCCTTC[C/T]GGTTGTTTTCAGAATCATAATTCTCTCTTGAAGAT Y 2 1 2 1 101000 f 74 goat snp11668-scaffold143-1866333 25 33720805 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804206 Affx-986696440 AX-385290847 25 34008913 GGTGTTCCCAGCCCTCTGCCACGCTGGACTGGGAC[A/G]CGACTCAGGACTTAGGTTGAGATGTCAAGGAGACC R 2 1 2 1 600010 r 74 goat 25_34008913 25 34008913 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 320764081 Affx-986698608 AX-385251841 25 34009435 GGAGGTGTCTGACGCTGGAGGAGGGCCTGATGATT[G/T]GGAAAGGCCTGATGCTGTGGGAAGGTCTGATTCTG K 2 1 2 1 600010 f 74 goat 25_34009435 25 34009435 Ancestral_priority_1043 ancestry 0.49 neutral IMAGE 10K 10K ancestral 320767581 Affx-986698614 AX-385254833 25 34010026 GCGCCTCAGCAGCAGAGGGGCCCTGTCCCTGCAGA[C/T]GCTGAAGTGATGGAGCCTCTTGTCTCCGGAGCCAA Y 2 1 2 1 600010 r 74 goat 25_34010026 25 34010026 Ancestral_priority_1043 ancestry 0.506 neutral IMAGE 10K 10K ancestral 38399432 Affx-122961224 AX-123269787 25 34010094 CAGTGGTTGTGCAAAGAATGGGAAGAACCAAGGGC[A/G]TCATGGACAAAGATGTTTTTTCTTGCAACTGTGTC R 2 1 2 1 101000 r 74 goat snp11670-scaffold143-1964734 25 33819072 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764089 Affx-986698616 AX-385251848 25 34010559 GTAAAAGTTACATTTGATACTTACACAATCCAGAA[C/T]GGCTGTGTCATCACAATCTAAAAATGTACGCCTGG Y 2 1 2 1 600010 f 74 goat 25_34010559 25 34010559 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320767527 Affx-986698584 AX-385254784 25 34010795 CGTCTCACCGGAGAGGAGGGATCCGGGTCCATAGA[C/G]ACTAGGTTACGGCAGAGAGTTTCATAGTCTTCTAG S 4 1 2 1 600010 r 74 goat 25_34010795 25 34010795 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 320764060 Affx-986698587 AX-385251823 25 34012653 TGTGAGATGGGACATGGGGAAGGACTGGCTACTTG[C/T]GGGTCAGAGGCTGGGCACCTGTGGCCTAGAGCCCC Y 2 1 2 1 600010 f 74 goat 25_34012653 25 34012653 Ancestral_priority_1043 ancestry 0.506 neutral IMAGE 10K 10K ancestral 320767536 Affx-986698589 AX-385254792 25 34012669 GGGAAGGACTGGCTACTTGTGGGTCAGAGGCTGGG[A/C]ACCTGTGGCCTAGAGCCCCACGATCTGCTGTCCTG M 2 1 2 1 600010 r 74 goat 25_34012669 25 34012669 Ancestral_priority_1043 ancestry 0.414 neutral IMAGE 10K 10K ancestral 320767540 Affx-986698591 AX-385254795 25 34013153 TACACGGTTTATGCCCTGCCTATCTCACGCGGTTC[A/G]TAAAAGGTCACCTCCAATATATTCCCAACACCTCG R 2 1 2 1 600010 r 74 goat 25_34013153 25 34013153 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 320767543 Affx-986698593 AX-385254797 25 34013197 CACCTCCAATATATTCCCAACACCTCGCTCTAGGA[C/T]TGTTTCTAATTTATCTAAACTCTAATGTCTATGTC Y 2 1 2 1 600010 r 74 goat 25_34013197 25 34013197 Ancestral_priority_1043 ancestry 0.684 recommended IMAGE 10K 10K ancestral 468273118 Affx-1111833297 AX-519546783 25 34037453 TAAAGAGTCCTTTTGGTTTAACATGAATGAACACC[A/G]TGTGGTTATGTCCTGGTGAATAACTGACATTTTAA R 2 1 2 1 101000 r 74 goat 25_34037453_AF-PAKI 25 34037453 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38387404 Affx-122970413 AX-123257762 25 34043447 GTTACATCCTCATCCTCCTGGTGGTGGTTCCTGTG[C/T]GTGCGACCAGTACCTCCCAAATGCAGTATTTTAAC Y 2 1 2 1 101000 r 74 goat snp11671-scaffold143-1998087 25 33852777 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398976 Affx-122960963 AX-123269331 25 34072957 AAAGATGACTGCAATTGTGCTAAAGGGGAGAAGGC[A/G]TCAAGGTGAAGAGGGCCTCAGTAACTAAAGACTGG R 2 1 2 1 101000 f 74 goat snp11672-scaffold143-2027597 25 33882230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771569 Affx-122935168 AX-385258727 25 34102275 AGAAGAAGAAAAAATTTTTAAGGTAGGCTTTGACA[A/G]TATGAGTGGTTAAAAACTTAGAATAAGCCTTCTAT R 2 1 2 1 101000 f 74 goat snp11673-scaffold143-2056915 25 33911352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436039 Affx-122932725 AX-123306378 25 34148259 GAGTCCGAAGTACTGAACCACCAGGGAGTTCCCGA[C/T]GTGGTTTATTTTTAATCCGCTTCTGTCCTGAAGAA Y 2 1 2 1 101000 r 74 goat snp11674-scaffold143-2102899 25 33957532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416135 Affx-122948291 AX-123286484 25 34186599 GATGTGGGCGCTGGGTACACAATGGCGTTCAGTTC[A/G]CGAAAATCCATCAAGCTCTGCTTGTGTGACTTGTA R 2 1 2 1 101000 r 74 goat snp11675-scaffold143-2141239 25 33996045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402629 Affx-122958398 AX-123272982 25 34230936 CACTGTGTGTGAGGTGGGTTTTTTTGAGGTTTTTT[G/T]GTTTGGTTGGTTTGGTTTTGTTGACAGAAGCCCAA K 2 1 2 1 103000 f 74 goat snp11676-scaffold143-2185576 25 35177209 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433757 Affx-122934496 AX-123304098 25 34294534 TTAGCATCACCTTGTTTCTGGTCAGAAGGAGGCAT[A/G]TGTTCAGGGCTAGAGGGATTGAGCAGGAGTCTGGC R 2 1 2 1 101000 f 74 goat snp11677-scaffold143-2249174 25 35240786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438331 Affx-122931344 AX-123308669 25 34346905 GGTTTCCCAAATGTACTGTCATGGCTACTGGAAAA[C/T]GTGGGCAGTTTGCAAATTCTCCAGTTTTACATTCT Y 2 1 2 1 201000 r 74 goat snp11678-scaffold143-2301545 25 35293658 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786556 Affx-122970208 AX-385273589 25 34409970 GGGAGACAGGCACATATCCATAAATCCCAACCCTT[A/G]TTTGTATTGGAGTTATTTATCTGGGCATGTCTACC R 2 1 2 1 101000 f 74 goat snp11679-scaffold143-2364610 25 35355142 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406438 Affx-122955196 AX-123276790 25 34453640 CAGGGAGGGCTTAATAGGTAGACCCAGGAACCCAA[C/T]AGGCAGGCAGGAGGCTGACAGGAAGGAATTCTCAG Y 2 1 2 1 101000 f 74 goat snp11680-scaffold143-2408280 25 35398643 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432476 Affx-122935599 AX-123302817 25 34485404 AGAGCAAGACCTTGTGCAGAGCAGTAATGAGGGGG[C/T]CACGGACCCAGAGAGATGCATGGTCCTTTGCTCCT Y 2 1 2 1 101000 f 74 goat snp11681-scaffold143-2440044 25 35429303 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414078 Affx-122949756 AX-123284427 25 34520653 GTCAGATCCACTCTTCTGCTGATAGACCAAGCATC[A/C]TGTCTGGACCCAGGCTGCAAGCTTGCTGTGGGGCT M 2 1 2 1 101000 f 74 goat snp11682-scaffold143-2475293 25 35464496 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391951 Affx-122966537 AX-123262308 25 34555924 CCGTGGGAAGACGACAGGACGAGAGCAGAGGGTGC[C/T]GAAACTCGGGGCAAAGGGTCCCAGGAGGCACTGGA Y 2 1 2 1 201000 f 74 goat snp11683-scaffold143-2510564 25 35499789 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438061 Affx-122931536 AX-123308399 25 34584777 TTGAGTGAGGAGGCCAGTTCACAAAAGCAGAAGGC[A/G]TGGACCACGAGGAGCGACTATATTTAAGACTATTA R 2 1 2 1 201000 r 74 goat snp11684-scaffold143-2539417 25 35528738 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384173 Affx-122972419 AX-123254531 25 34620498 TGTGCTGGGTGGACTCTACTTGACATCTGTTTCTC[A/G]TGCTAACTTCAGAAGGCAGCCCTCACTCAAGCCAC R 2 1 2 1 101000 f 74 goat snp11685-scaffold143-2575138 25 35563807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393872 Affx-122965134 AX-123264227 25 34660502 AGTGCAAGGGGCAGGAACCGGATTCTTATCAGAGA[A/G]ATGGTTTGGAAGCTTTGCTCATTGGTTGAGTGACT R 2 1 2 1 101000 r 74 goat snp11686-scaffold143-2615142 25 35603812 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422691 Affx-122943661 AX-123293037 25 34722001 TCCGTGGGATCACAAAGAGTCAGACACAACTGGAA[C/T]GACTGAACAACAGCAGAATCTCTCTGATTCTATCC Y 2 1 2 1 101000 r 74 goat snp11687-scaffold143-2676641 25 35666094 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401035 Affx-122959667 AX-123271388 25 34779999 AGGTGGGCCAGGAAAGCAAGGCTGGAATTGTCCAG[C/T]AGGCACCTAGGGGTTCTGTCCTCTACTGTATGCCA Y 2 1 2 1 102000 r 74 goat snp11688-scaffold143-2734639 25 35724095 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395883 Affx-122963624 AX-123266238 25 34892508 GACTTTCATCTCTGAGCGTGTGATGTTTCCCAGGA[C/T]GGCCTGAATTAGATTTCCTACTAGTTAGAATTTCC Y 2 1 2 1 201000 r 74 goat snp11690-scaffold143-2847148 25 35835799 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771353 Affx-122979201 AX-385258511 25 34932563 GTGTTAAATGAAAGTTTATCTGCCTGTTTGAGAAA[C/T]GAATCTTATAGCACCCTGTAGCTGATGTTTTTTAA Y 2 1 2 1 101000 f 74 goat snp11691-scaffold143-2887203 25 35875839 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382440 Affx-122974231 AX-123252798 25 34963405 TCCTTGATACTAACACCAGTCCATCTGGAACCCCA[C/T]ATTTTTCCTAGCGCTTTCCTTCTTCTAGTGCATTC Y 2 1 2 1 101000 r 74 goat snp11692-scaffold143-2918045 25 35906818 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394563 Affx-122964453 AX-123264918 25 35027016 GCAGGAAAATGGCCTCCGATGGAGGTAAAGTCCCC[A/G]AAAACCCCAACCGCATGAAGGTGTATTGCTGCTCA R 2 1 2 1 101000 r 74 goat snp11693-scaffold143-2981656 25 35968871 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433405 Affx-122935100 AX-123303746 25 35073965 CTTTACCATCTGAGCTATCAGGGAAGCTCAGGGGT[C/T]GGGGCCCAATTCCCCGTGTCGTGAACTCACTTGTT Y 2 1 2 1 202000 r 74 goat snp11694-scaffold143-3028605 25 36015781 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422381 Affx-122943400 AX-123292727 25 35124678 TGACCACCATCTCTTCTGCAGGCATATCTGACTTC[C/T]CTCATCTTGCTCTTCTTTTCTTTTTGATGTGGGTT Y 2 1 2 1 101000 f 74 goat snp11695-scaffold143-3079318 25 36066514 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418092 Affx-122947143 AX-123288440 25 35160300 GACCTCCAACTGAAAACTTCCGTTCAGCAAAGGAC[A/G]CCATGAAGAGCCTGTAAAGGCAAGGCCCAGGCTGG R 2 1 2 1 101000 f 74 goat snp11696-scaffold143-3114940 25 36102289 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426191 Affx-122940575 AX-123296537 25 35195028 TCTCCCCCCGGCCCAGCCGTGCGGCCCCCACCCTG[C/T]GGTCTCTCTTTTCCATGAAATGGCTCTGCGGTCCA Y 2 1 2 1 101000 r 74 goat snp11697-scaffold143-3149668 25 36136578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449955 Affx-122922895 AX-123320290 25 35248662 AGGAATTTGTGAACTATGATGGGAAATAGAATTAC[A/G]TCTTAAAAAAAAATTTTTTTTTAATTTATTTTTGG R 2 1 2 1 103000 f 74 goat snp11698-scaffold143-3203302 25 36189332 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430342 Affx-122938211 AX-123300683 25 35310887 GAGCCACAGTACCTAGCTCTATGGTCAAATATGAA[C/T]GGATGTTGCCATGAAAGCATTTCTTTAGGTGAGAT Y 2 1 2 1 101000 f 74 goat snp11699-scaffold143-3265527 25 36251456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409328 Affx-122953081 AX-123279679 25 35346188 GGTCAGTGGGCAGCCTGCAGCCTGCAGCAGGGCCT[A/G]ATTCCAGAAGCTACCTTCTGGGGAAGAGGAAAGCC R 2 1 2 1 303000 f 74 goat snp11700-scaffold143-3300828 25 36282370 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409413 Affx-122954131 AX-123279764 25 35419384 CTAGGAGAAGGTGCTTGAGCTGAATCTAGGAAGAC[A/G]TCTATGAGTTAACAGGCTGAAGAGGGAAGCGAGCA R 2 1 2 1 101000 f 74 goat snp11701-scaffold143-3374024 25 36354447 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440435 Affx-122929412 AX-123310772 25 35460221 GGTCGGAATCGAGTGCGTATCCGGAATGTGGCCTA[C/T]GACACGCTTCCTGTTGTAGTCCATGGGAACGGTCC Y 2 1 2 1 101000 f 74 goat snp11702-scaffold143-3414861 25 36394999 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409419 Affx-122954126 AX-123279770 25 35499336 ACAGGAAATTTCATTTAATGGGTTTAAAATAAAAC[A/G]TCGTTGATTGGACTGTTAAAAGAAAACTACTATTC R 2 1 2 1 101000 r 74 goat snp56885-scaffold9004-12102 25 36624328 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376084 Affx-122978906 AX-123246443 25 35563119 CAATGAGTTGCCTCCTTCCCCTCCTTCACTGCCTG[C/T]AATCAAAGGGGTCTCTGGGGAGTGGGCCATGGGGG Y 2 1 2 1 103000 f 74 goat snp56886-scaffold9004-75885 25 36687078 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422034 Affx-122943620 AX-123292381 25 35614660 AGAAAACAACAAACCAACAAAAACGCCCACTGCGA[C/T]GTGGGGAGTGTGGGTGTTTGCGTCTCACCCCTATT Y 2 1 2 1 101000 f 74 goat snp27370-scaffold2909-803753 25 36732757 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406458 Affx-122955183 AX-123276810 25 35650693 AGCAGGTATGTTAACCCAGCTCTGCCCTCTGAGCC[A/G]TCAGGACAATGCCCTGAGGAGTCTAGTAGTTAACA R 2 1 2 1 101000 r 74 goat snp27369-scaffold2909-767720 25 36768658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412632 Affx-122950801 AX-123282981 25 35694750 CCCCTTGGCCCTTCCCGGATGGTCTGCTCCTTCAT[C/T]GAGGTGCCTGGGGTCATTCTGGACTCCATTATCTC Y 2 1 2 1 201000 f 74 goat snp27368-scaffold2909-723663 25 36812892 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391492 Affx-122966706 AX-123261849 25 35732045 ACTTCTCAGAGAGGGCCCCTGGATTAGTGATGAGC[C/T]GAGGCACGGATGAAAATCGCTGTTCTCTGGTTGAG Y 2 1 2 1 101000 r 74 goat snp27367-scaffold2909-686368 25 36850042 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396918 Affx-122963205 AX-123267273 25 35798441 TCTTAAGAAAACAGCAAGTCAGTGACAAGGTATCC[A/G]TTAGCATTACATCAGCGCCTCCTCAGTGAGTTCTC R 2 1 2 1 101000 f 74 goat snp27365-scaffold2909-619972 25 36916569 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424098 Affx-122942033 AX-123294444 25 35837556 TAGGAAGGTTCTTGCAACCCAGGAGCACGTGAACA[A/G]TTTGATTTCACCATGCACCCTCATTTCTCCCATCC R 2 1 2 1 101000 r 74 goat snp27364-scaffold2909-580857 25 36955706 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426150 Affx-122940606 AX-123296496 25 35883611 CTCTCCCACTGACAGTTTACCTTAAATGCTGAAAC[A/G]TAAGGGATGCCCTCCATCCCACCAAAATCATCCCT R 2 1 2 1 101000 f 74 goat snp27363-scaffold2909-534802 25 37001637 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410367 Affx-122952448 AX-123280717 25 35919911 ACCAGGGATCACACTTGATGCCGCTGCAGTGCAAG[C/T]GGGGAGTCTTAACCACAGAGCAGGCAGGGAAATCC Y 2 1 2 1 303000 f 74 goat snp27362-scaffold2909-498502 25 37037529 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409146 Affx-122953290 AX-123279497 25 35966369 CCCACATTTCTGGATCAGATGCTTCCCAGGTGAAT[A/G]TGGGTCTGAGGAGGGGGAACAGGAATGGAGTACCA R 2 1 2 1 101000 f 74 goat snp27361-scaffold2909-452044 25 37083751 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437681 Affx-122931771 AX-123308019 25 36003879 TTACCCTGACCTGGAAGGGCAGAGGCTCAGGGACT[C/T]TGTACTCTGTTAAGGACAGTGAAGGTGAGGGGACC Y 2 1 2 1 101000 r 74 goat snp27360-scaffold2909-414534 25 37121472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450367 Affx-122922096 AX-123320702 25 36090188 TAGGACTGGATACTGCATTGCCCAGGGAGGTGAGA[A/C]GGGAACCTGAGAGGGGAGCTCAATCCTAGGGAGGT M 2 1 2 1 101000 f 74 goat snp27358-scaffold2909-328225 25 37208897 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786639 Affx-122957312 AX-385273671 25 36190561 TCCTCCGTTTCTCAGAAACTACCTTAAATTGTCTT[A/G]CTCATAATTTCCCCCCCTTCATTTTCTCTGTTCTT R 2 1 2 1 201000 r 74 goat snp27357-scaffold2909-227852 25 37309143 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277648 Affx-1111836016 AX-519551147 25 36200455 GGGGTTTCGGGAGAGTGTTTAGTTGTTTGTTTTTC[A/G]GCTGGGCCAGGTCTTAGTTGTGGCACAGGGCATCT R 2 1 2 1 103000 f 74 goat Random2.2K-2164 25 36200455 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38417257 Affx-122947267 AX-123287605 25 36223332 TGCTCCTCGTCCTCTCAGCAGCTCAGGGAGCCCAA[A/C]CCCTGGGAGAATTCCAACACCCGAGTTCCAGATAC M 2 1 2 1 101000 r 74 goat snp27356-scaffold2909-195081 25 37341857 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395671 Affx-122963753 AX-123266026 25 36252057 TAAAAGTAAGAAGCTTTGGGGGAGCTGCAGTATTG[A/G]GAGAGCTGCCTATTTTCCTGGATTTTGCCTCCAGG R 2 1 2 1 101000 f 74 goat snp27355-scaffold2909-166356 25 37370518 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787542 Affx-122958550 AX-385274566 25 36286877 ATGCACTCCTTTAGGAGGAAAGCTGTTAACTCTCA[C/T]TATATAGTTTAGGCAACTGAGGTTGAGAAGGTTTA Y 2 1 2 1 101000 f 74 goat snp27354-scaffold2909-131536 25 37405278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384613 Affx-122972174 AX-123254971 25 36344124 CAGGGTGGAAATCACTCTCAGTTTGATTCTGAATT[A/G]CTTTTACATGATTTCCCCTGGGGGTTTGGGAGTTT R 2 1 2 1 103000 f 74 goat snp27353-scaffold2909-74289 25 37462519 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786849 Affx-122973301 AX-385273878 25 36375920 CTGAAAATTTATTTCATGGATATACTTGCACACAT[A/G]CATAAGTAAATCTGTATAATGACATTTATTCCTGC R 2 1 2 1 101000 r 74 goat snp27352-scaffold2909-42493 25 37495216 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407492 Affx-122954755 AX-123277843 25 36413499 TTTCATGAGAGAGAAAATACACTCCTTGATAACCT[A/G]TGGTGTTTCATCTCAATGGGCATTGAGAGGTCAAA R 2 1 2 1 202000 f 74 goat snp27351-scaffold2909-4914 25 37531956 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803649 Affx-986696445 AX-385290427 25 36420215 GTCACCATCAAGAAGCTCCTGAGCTGCTGTCCTTG[C/T]ATCTTCTGGGGCCGTGGTCTCTTCTCAGCCAAGTC Y 2 1 2 1 600010 f 74 goat 25_36420215 25 36420215 Ancestral_priority_1043 ancestry 0.552 neutral IMAGE 10K 10K ancestral 38423344 Affx-122943161 AX-123293690 25 36433188 TCTCCATGGTCCTGCTGGGAGATCCAGACCAGGCA[C/T]GGGCTTTAGAGGATGGTGGTGTCTCCCTCCGTCCC Y 2 1 2 1 101000 f 74 goat snp29753-scaffold3220-384471 25 37680078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383421 Affx-122973481 AX-123253779 25 36468735 ATCTATTCCTCCACAGCCTAATGTTTTTAGTAATC[A/G]CCCATGATTTTTTAGCAACCATTCATGTGATAGTT R 2 1 2 1 101000 f 74 goat snp29752-scaffold3220-348924 25 37715697 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764074 Affx-986698601 AX-385251835 25 36570220 CCCATCTCTCCAAAAGCAGTGCAGATGGTTCTCTC[C/T]GCTGTCCGGGCAGGTGGAGAGGGCAGTGGGGCTCA Y 2 1 2 1 600010 f 74 goat 25_36570220 25 36570220 Ancestral_priority_1043 ancestry 0.53 neutral IMAGE 10K 10K ancestral 38387541 Affx-122970300 AX-123257899 25 36593900 GAACAAAAGACCTGAAGACCCAGAGGCTTGCTCTT[A/G]TTTACACATGCCCATAAGGCTCTGACCTCTTTGAA R 2 1 2 1 201000 r 74 goat snp29750-scaffold3220-223759 25 37841461 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273075 Affx-1111833298 AX-519546745 25 36616701 AGGGGATCTTCCCAATGCAGGGATCGAACCCACGC[A/C]TCCTGCATCTCCTGCATTGCAGGCAGATTCTTTAC M 2 1 2 1 303000 f 74 goat 25_36616701_AF-PAKI 25 36616701 G T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320782046 Affx-122941509 AX-385269124 25 36631851 AGACTCAGTACCTGGTAATCGTCTTCTTCATCCTC[A/G]CTCTCATCAGAATCTAGGGATTTCTTCTCTTTCTT R 2 1 2 1 101000 r 74 goat snp29749-scaffold3220-185808 25 37879393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439855 Affx-122930450 AX-123310192 25 36668600 CCTCTTTTCTTTCAACAGTTTGGCTAAGCACATCA[A/G]AACTTGCTCTCCATAACATTTCACTTACAAATTTC R 2 1 2 1 101000 f 74 goat snp29748-scaffold3220-149059 25 37916164 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407234 Affx-122955371 AX-123277585 25 36749469 CTGTAAATATTCAGAATGAATCTCTGAATCTCTGA[C/T]AGACAGACTTAAAAGCTAACACCAAAATATCACAA Y 2 1 2 1 101000 r 74 goat snp29746-scaffold3220-68190 25 37996810 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388050 Affx-122969540 AX-123258408 25 36782346 AATAAAAGTTCCCCTAATTTTGATTTTTTGTTAAA[C/T]GTCATACCTCTCTGCCCTCCCCCTGAAAAAGGAAA Y 2 1 2 1 103000 r 74 goat snp29745-scaffold3220-35313 25 38029795 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421477 Affx-122943922 AX-123291824 25 36851957 TAAACTCCTTTCATCTTGTACTTTTTCATTTATCT[A/G]CGCAATGGGGTTCTCTCTTTCTTTCTGTTTAGTAA R 2 1 2 1 101000 r 74 goat snp30884-scaffold3408-34199 25 38099265 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411414 Affx-122951840 AX-123281764 25 36892158 AGCTCCTGGGAGGTGTAACCTCTGAAAGTTAAAAA[C/T]GACAAGGAAGCGTTTCCTACAGTTCAATCTGTACA Y 2 1 2 1 101000 f 74 goat snp30885-scaffold3408-74400 25 38139456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404744 Affx-122957234 AX-123275096 25 36928267 GAAAGCTTTCGGGTTTCACCAGAGACCTAGACAAA[C/T]AACTGTGTCCTGGTAATGAGACGGATAAGGAAAGA Y 2 1 2 1 101000 r 74 goat snp30886-scaffold3408-110509 25 38175483 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437234 Affx-122932026 AX-123307572 25 36998142 GATAAGTGGGCTTTCTATAGATTTGAAGGGGTGAG[A/G]GCATTCCCACGTTGCAGACAGCCCCACAAGGCCAG R 2 1 2 1 101000 f 74 goat snp12435-scaffold1473-242296 25 38245913 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767561 Affx-986698603 AX-385254814 25 37026267 GCGTAGCCCCATGGCCTTGCCCTCCTCCCGGGTGA[A/G]AAGACAGGCAGAGCCCTCAAGGCCAGACGGGAGGC R 2 1 2 1 600010 r 74 goat 25_37026267 25 37026267 Ancestral_priority_1043 ancestry 0.486 neutral IMAGE 10K 10K ancestral 38379645 Affx-122975947 AX-123250003 25 37029893 CCCCTGCCCTCAGTCCCTGCTGTTCTAAACATGGG[C/T]GGAGGACAGAGGAGGGGTCCTGCCAGTTACAGGCA Y 2 1 2 1 103000 f 74 goat snp12434-scaffold1473-210545 25 38277619 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383203 Affx-122972783 AX-123253561 25 37097586 GCATATGTAGGGTCTCTTCAGAACATTCTTCTTTC[A/G]TGCTATTTTCATGCTTGCTTATTTTTCTCTCTCCC R 2 1 2 1 101000 f 74 goat snp12432-scaffold1473-142852 25 38345701 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429250 Affx-122937904 AX-123299592 25 37142404 TCCCAACTGGGATTAATTTGAGTTGGGGAGTAAAA[C/T]AGAGATGGTCTAACTGGTTCTTATTGAAGAGGGGG Y 2 1 2 1 201000 f 74 goat snp12431-scaffold1473-98034 25 38390415 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427502 Affx-122939998 AX-123297845 25 37172678 TGGTCCCAGCATCACCCGTCCTCCTGCATCGAGGA[C/T]GATGGAAATGACCTGCACATGACAGGCTGACCCAA Y 2 1 2 1 101000 r 74 goat snp12430-scaffold1473-67760 25 38421122 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804217 Affx-986696446 AX-385290855 25 37179697 TTACCTCCTTCCCTCTCTCCCCACCAGCATCCCCC[A/C]ATGTGGTTCCAGTCACCCTGTCCCTGTGTCCACCC M 2 1 2 1 600010 r 74 goat 25_37179697 25 37179697 Ancestral_priority_1043 ancestry 0.544 neutral IMAGE 10K 10K ancestral 38404600 Affx-122957348 AX-123274952 25 37221413 GGTGACTGTGGAGGCAGCGCCTTGAATTTCCTCAG[C/T]GGTATGGCAAGAACAGGCAGTTACACCGAGTCCTC Y 2 1 2 1 101000 r 74 goat snp12429-scaffold1473-19025 25 38470692 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421331 Affx-122944076 AX-123291678 25 37279938 TTCCAGTCTCAACAAACAAACTGGGCCATCTGAGA[C/T]GTGCTGGTTTTAAAGCAGTTGGTTAATTGCTATCT Y 2 1 2 1 101000 r 74 goat snp11277-scaffold1406-39401 25 38528895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388918 Affx-122968839 AX-123259276 25 37391623 GCCTGTCCTGGGTGTTTTCCAAAGTTTGGCGTCTG[C/T]TCCACTTCCTGACTTCCTATTCTTTACCCTTTAGT Y 2 1 2 1 101000 r 74 goat snp11279-scaffold1406-151086 25 38639006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392475 Affx-122966149 AX-123262832 25 37440821 GAGACGTATCCCCCTCTTCAAGGCCCATCCTGCGG[C/T]TCCCTATTCCCTCATCTTTCTGCCCAGTCTCCTCA Y 2 1 2 1 101000 r 74 goat snp11280-scaffold1406-200284 25 38688987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410152 Affx-122952795 AX-123280502 25 37483915 GCCTGTTCTTCAGCAAGATGAGGGGGAGCAGTGGG[A/C]TGAGGAAGGCCAGGACAGGGGCTCCCTGGGCTATT M 2 1 2 1 102000 f 74 goat snp11281-scaffold1406-243378 25 38732005 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780202 Affx-122944906 AX-385267298 25 37524422 AAAGATAAGTTATTGGATATATCTATTGGAGATAA[C/T]AGAAAATATATATTGGCCTACATGGAAAGAGAAAA Y 2 1 2 1 101000 r 74 goat snp11282-scaffold1406-283885 25 38772268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476375 Affx-1251763886 AX-586011786 25 37537171 GCTGTCTAACATATGAGTCTTCAAGTTTTAATTGA[-/TTAAAATTAAATACAGAGGACTAGAAAAAAAGATGGCGGAGTAAGAATTAAGGATTTAAAATTTTTTAAAAAAGTACAAA]AAAAATTAAATACAACTTATCATTTAGGTTACAGT - 8 1 4 1 20000 f 74 goat SV_231 25 37537171 - deletion junction SV-TF-chip 539476631 Affx-1251763886 AX-586012014 25 37537171 GCTGTCTAACATATGAGTCTTCAAGTTTTAATTGA[-/TTAAAATTAAATACAGAGGACTAGAAAAAAAGATGGCGGAGTAAGAATTAAGGATTTAAAATTTTTTAAAAAAGTACAAA]AAAAATTAAATACAACTTATCATTTAGGTTACAGT - 4 1 4 1 20000 r 74 goat SV_231 25 37537171 - deletion junction SV-TF-chip 562165151 Affx-1251763886 AX-606940563 25 37537171 GCTGTCTAACATATGAGTCTTCAAGTTTTAATTGA[-/TTAAAATTAAATACAGAGGACTAGAAAAAAAGATGGCGGAGTAAGAATTAAGGATTTAAAATTTTTTAAAAAAGTACAAA]AAAAATTAAATACAACTTATCATTTAGGTTACAGT - 8 1 4 1 20100 f 74 goat SV_231 25 37537171 - deletion junction SV-TF-chip 562165438 Affx-1251763886 AX-606940849 25 37537171 GCTGTCTAACATATGAGTCTTCAAGTTTTAATTGA[-/TTAAAATTAAATACAGAGGACTAGAAAAAAAGATGGCGGAGTAAGAATTAAGGATTTAAAATTTTTTAAAAAAGTACAAA]AAAAATTAAATACAACTTATCATTTAGGTTACAGT - 8 1 4 1 20100 f 74 goat SV_231 25 37537171 - deletion junction SV-TF-chip 562165807 Affx-1251763886 AX-606941216 25 37537171 GCTGTCTAACATATGAGTCTTCAAGTTTTAATTGA[-/TTAAAATTAAATACAGAGGACTAGAAAAAAAGATGGCGGAGTAAGAATTAAGGATTTAAAATTTTTTAAAAAAGTACAAA]AAAAATTAAATACAACTTATCATTTAGGTTACAGT - 8 1 4 1 20100 r 74 goat SV_231 25 37537171 - deletion junction SV-TF-chip 38429341 Affx-122938578 AX-123299683 25 37553899 TACAATATAGGTTATTGAAATATTGGTACAGTCTG[C/T]CCTATATAGTATAAATTTTTATGATGTAAAATTTA Y 2 1 2 1 101000 f 74 goat snp11283-scaffold1406-313362 25 38801478 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429585 Affx-122937724 AX-123299926 25 37589081 TAAACTTCTAAGAGCCAGATTTCTACAACAGAAGC[A/G]TAAACGGGGCAGCGGGTGCACGGACACGGGAGGAC R 2 1 2 1 101000 f 74 goat snp11284-scaffold1406-348544 25 38836387 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387877 Affx-122969630 AX-123258235 25 37630173 AGGAACTGTCTGAGTCAGCTCTGGTTCCCCAGGCA[G/T]ATTCCCCACAGGAAAAACCTGTGCCAGCCTGAAGA K 2 1 2 1 101000 r 74 goat snp11285-scaffold1406-389636 25 38877168 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771018 Affx-122968651 AX-385258180 25 37677482 CAAGAAAATGCTAATGTAAGTTCACACTTAAAAAG[C/T]AACCTGCTTATCAAACTATTATGATCACGATTTTA Y 2 1 2 1 101000 f 74 goat snp11286-scaffold1406-436945 25 38924160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406027 Affx-122955490 AX-123276379 25 37710820 GAAATCCCGCTTCCTTACTGGTAAAGCTGGGATGA[C/T]GTCACTGCCAGCCTCTAGACTCGAGACTGACCCAC Y 2 1 2 1 101000 f 74 goat snp11287-scaffold1406-470283 25 38956960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408496 Affx-122954409 AX-123278847 25 37748215 GGAGAGTCCTGGGCATGGCCCCCATGCAGTTTAGC[A/G]TGACTGTAAGCTGCACGAGGCTGAGAGCCCACAGC R 2 1 2 1 201000 r 74 goat snp11288-scaffold1406-507678 25 38993941 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442964 Affx-122928211 AX-123313301 25 37778476 CTCTGAATGGGGTGGGATCGGAGTGCTAAGGAAAC[A/G]GCAGGCTGACTTTCAAGAGCAGAACTGTCAAGGTC R 2 1 2 1 101000 r 74 goat snp11289-scaffold1406-537939 25 39022585 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413707 Affx-122950082 AX-123284056 25 37808930 CTGTTTCCAGTAAAACCTGACCAGCTTGTTGCAGA[C/T]AACCCTTCTGCCAAAAAAACAACTAAAAAAGCTGA Y 2 1 2 1 101000 f 74 goat snp11290-scaffold1406-568393 25 39052903 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383862 Affx-122973142 AX-123254220 25 37861798 AGCCCTCAACCAGATGACTTTTGATATTACTTATA[C/T]ACTGAGAGCCAGAAATAACTTTCAAGTAATTTCTA Y 2 1 2 1 101000 f 74 goat snp11291-scaffold1406-621261 25 39106142 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801945 Affx-122948747 AX-385288850 25 37894583 TTGGAGAAGTTTTAAACTGGTTTAAACTAACTCAG[C/T]TTTCATTTAAAGCTGATTTTCATGTGTGGCTTGTA Y 2 1 2 1 201000 r 74 goat snp26898-scaffold2848-18793 25 39139431 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393917 Affx-122965097 AX-123264272 25 37951918 ACATTCCATTGGGTGCCACACCATACCTTCATAGA[C/T]GTATTATATAATGAAATAAATGAAGTAAAAAGATC Y 2 1 2 1 101000 f 74 goat snp26899-scaffold2848-76128 25 39196903 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377279 Affx-122978126 AX-123247638 25 38000621 CTTTCCAGGGTCAGCCTTTGGGGTCACTGACACAA[A/G]ACCCTAGTTTTGGGGCAATGGGGTGTTTGGGGTCC R 2 1 2 1 202000 r 74 goat snp26900-scaffold2848-124831 25 39245747 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410353 Affx-122952455 AX-123280703 25 38029781 ATGCTACAAGTTTTTCACAGAGAAGCCCCTGTGAA[C/T]AAGTCGTCTACCTATTTCTTCCAGAAACTACACCT Y 2 1 2 1 101000 r 74 goat snp26901-scaffold2848-153991 25 39274954 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420961 Affx-122944586 AX-123291308 25 38068816 GGATCTCCAGAGAGATCACTCACCCTTCTCCCAAC[A/G]TGAGGACTCAGCGATGGAGCCCTGGCTCTGAACCA R 2 1 2 1 101000 f 74 goat snp26902-scaffold2848-193026 25 39314067 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400566 Affx-122960418 AX-123270921 25 38132763 TCACTAACATGACTCCAACTGGAAACATTTATAAA[C/T]ACTTAAGGCTACTCTGTTAGTCAATAAGACAAGCA Y 2 1 2 1 101000 r 74 goat snp26903-scaffold2848-256973 25 39378524 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449441 Affx-122922673 AX-123319776 25 38202574 AGACCTGTCCTGGCTCAACTGTGCTGACTCCTGCA[C/T]AGGAAATGGTCCTGGTCAGGCTCTGCCACTTACCA Y 2 1 2 1 101000 f 74 goat snp26904-scaffold2848-326784 25 39449029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784522 Affx-122931375 AX-385271571 25 38294493 AATTGATAACTCCACTACTAACAGAACCAAGCAGT[A/G]TAGACAAATCACGGGAGCAGAGTTTTTTGTGGGTG R 2 1 2 1 101000 r 74 goat snp26906-scaffold2848-418703 25 39541343 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385609 Affx-122971195 AX-123255967 25 38367508 TCCCACTCCATCCTTACACGAGCTGTTCCCTGGGG[A/C]CAATGTGACCTGCCTTATCAAGAGAACTCTTACAC M 2 1 2 1 101000 r 74 goat snp26907-scaffold2848-491718 25 39613710 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433729 Affx-122934517 AX-123304070 25 38478038 AATGGGAAGGAGTGTAAGTGAGCAGGTGACCACCA[C/T]GGGCAACCAGCATTCAAGCCCCCTGGGAGATAGCA Y 2 1 2 1 101000 f 74 goat snp26909-scaffold2848-602248 25 39721638 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770214 Affx-122933284 AX-385257381 25 38523865 AGGACACTGACGACCATCACAAAACAATGAGGAAC[A/G]TGCTATGGGTCATTTCATCACTGAAACAGCGCTTG R 2 1 2 1 101000 r 74 goat snp21783-scaffold2133-227398 25 39765667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416102 Affx-122948315 AX-123286451 25 38587750 CGTTCTGGGGTCAGGCCTCGGCTCTGTCGCTGACA[A/G]ACTGTGCCTGGAGCAGATTCCTCCGCTGTTCTGTG R 2 1 2 1 101000 r 74 goat snp21782-scaffold2133-163513 25 39826196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428039 Affx-122939134 AX-123298382 25 38647259 GGCTTTTCGGATGACTGAAGCATTTAGTAAATCTG[C/T]GTCCCCACCAGTGCCCGAGTTGAGCTGTTAAATCG Y 2 1 2 1 101000 f 74 goat snp21781-scaffold2133-104004 25 39886724 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421439 Affx-122943951 AX-123291786 25 38677673 GAGTGAAAATCAAATAAAATTGAAAATGCAGGTTA[C/T]GCTACTCGTATTTCAAGGGGCTACCATATCAGACC Y 2 1 2 1 101000 r 74 goat snp21780-scaffold2133-73590 25 39915719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378877 Affx-122976506 AX-123249236 25 38762240 GCAGATATCGATGCGTTGTGCGTGGCACCGAGACA[C/T]GTTGATCGAAGCGACTTTTTCACCTCCTTCTATGA Y 2 1 2 1 101000 r 74 goat snp15386-scaffold1632-10878 25 39998747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769414 Affx-122975490 AX-385256585 25 38830400 AGCGAAAGCTGACACTTTTGGTGTCACTTCAGAAG[A/C]AGCAGCGATGGGGACGGACTGACAGCTGGCGGCTC M 2 1 2 1 303000 r 74 goat snp15387-scaffold1632-79038 25 40066214 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400944 Affx-122959707 AX-123271297 25 38864487 ACCAATGCTGGGCTCAGGGCCCTAACCTACTCAGC[C/T]ACACAGATATTAACATAAAAAAGGTGCTTTAGAGC Y 2 1 2 1 101000 r 74 goat snp15388-scaffold1632-113125 25 40099984 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448291 Affx-122924170 AX-123318627 25 38909133 AGTAATAAACAGAGTTCGGTAACAATGCCTGAGAA[C/T]GTATTACAGAGTGTAGGGTTGGAATCCCAACATTT Y 2 1 2 1 101000 f 74 goat snp15389-scaffold1632-157771 25 40144204 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407667 Affx-122954599 AX-123278018 25 38958268 GGTCTTCCTTTTTAATTTTGGACTAATGAGCAGAT[G/T]TTAAAGTTATGTTATGAATTAGCTTATTGTTAAAA K 2 1 2 1 101000 f 74 goat snp15390-scaffold1632-206906 25 40202212 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802205 Affx-122965775 AX-385289109 25 39016424 CTTGGCAGCTCTTTATGACAGTCATAAATTACCCA[C/T]GCTGTGTCAAAAATGACACACTGAGGTTCCTTTCT Y 2 1 2 1 201000 r 74 goat snp15391-scaffold1632-265062 25 40260315 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389899 Affx-122968122 AX-123260256 25 39045387 ATGGAGATGGTAAAACCCCTTGGCTGAGAGAGTGG[A/G]GTGGACGCATCCGGGCGAACATTCGAATTATCTTT R 2 1 2 1 101000 r 74 goat snp15392-scaffold1632-294025 25 40288614 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384394 Affx-122972211 AX-123254752 25 39094764 CTGCAGGTCCCAGGGCCCCTTCCTGTGGCTTTCTG[C/T]GTTCACATCGCGCCCTTTATCAAGCACTTGCTCAG Y 2 1 2 1 101000 r 74 goat snp15393-scaffold1632-343402 25 40337682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422281 Affx-122943491 AX-123292627 25 39128390 CAAGTGCAAAGACTACAGAGGCAGACAGAGACCAA[C/T]AAGAACGTGATCAAACGATGTTTTAAGGACCTCGA Y 2 1 2 1 201000 r 74 goat snp32743-scaffold3789-1474 25 40370061 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377507 Affx-122977485 AX-123247866 25 39189120 TGTCAAAGCTCACTATGCTCCTCAGGTCTCTTCTG[C/T]GCTCAGATCCTTGAGCATCTCTTTCTCCTAATTAC Y 2 1 2 1 201000 r 74 goat snp32744-scaffold3789-62204 25 40430072 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429597 Affx-122937715 AX-123299938 25 39227645 TCCTGCTGCCTCGGGGCCGCGTCTCCAGTCGCTCC[A/G]TAAATGAGGCTTTCCTCTGTACTCTGGCTCAGAGG R 2 1 2 1 101000 r 74 goat snp14102-scaffold1562-10041 25 40466797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775080 Affx-122955799 AX-385262212 25 39259727 TGTGGATTTAGCATCCGCGTGGTTGGACACCAGAG[C/T]GACCCACATTTCCAGGGACAACAGCTGATAACCTG Y 2 1 2 1 101000 r 74 goat snp14103-scaffold1562-42123 25 40499453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450302 Affx-122922150 AX-123320637 25 39295184 GACAGGGATTTCTTAAAAAGTCGAAGCTGACTTGA[C/T]GTATCAGTATAGATGCTAAAGGATCAAACCTGACT Y 2 1 2 1 101000 f 74 goat snp14104-scaffold1562-77580 25 40534561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391127 Affx-122966798 AX-123261484 25 39330442 GGAGTGAGGAGCGAGGGCGGCTGCGGGAGGGAGAG[C/T]GGTTTGTGTGGAAACACTGACTGTGGTCCGAGATG Y 2 1 2 1 101000 r 74 goat snp14105-scaffold1562-112838 25 40569535 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411060 Affx-122951948 AX-123281410 25 39362485 ACGATGCGACGCGGAGGGATTCATTTCATCGGGGA[C/T]GCTGCCCAGCAGAGATATATTTACTGATAACAGGG Y 2 1 2 1 101000 r 74 goat snp14106-scaffold1562-144881 25 40601769 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463956863 Affx-1110243050 AX-515434151 25 39385685 GTCAACAAGAAAGTTCAAATTAGGCTCTAGCTCAG[C/T]GCTGTGGAATTAGAATCGGTGAGCCTGGGTCCTGG Y 2 1 2 1 101000 f 74 goat 25_39385685_AF-PAKI 25 39385685 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38444820 Affx-122926322 AX-123315157 25 39394786 TCAGAAGCTTCAAAGCTCCTGCTTTTCCGCTGATA[C/T]GTTGCTGACATAGGAGAGGGGTGCTGCTACCTGCT Y 2 1 2 1 103000 f 74 goat snp14107-scaffold1562-177182 25 40633240 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429169 Affx-122937971 AX-123299511 25 39434199 CACTTTCTGTAGCTTAACATCTCTGATTAATTATA[C/T]GTACAATTATTTTGATATACAGTGAACAATAAGGA Y 2 1 2 1 101000 f 74 goat snp14108-scaffold1562-216595 25 40672746 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415936 Affx-122948442 AX-123286285 25 39476338 TGTCTCTGGATGTGGGTGTGTGAGCATGCACACGC[A/G]TGTGAGCAGGAGACACACCTGGAGGAAAGAGGATC R 2 1 2 1 303000 f 74 goat snp14109-scaffold1562-258734 25 40714551 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452783 Affx-122920243 AX-123323116 25 39517585 CGCTGGTGTAGGTGGTGAGCTCACTGTCGTTGTGC[A/G]TCCACTTGAACTCCAAAGGCCAGCTCCCTTCCGCA R 2 1 2 1 201000 r 74 goat snp14110-scaffold1562-299981 25 40770571 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400539 Affx-122960439 AX-123270894 25 39570913 CCAGGATGCTCAGAAACGCCATCCTGCTCTCGCTG[A/C]TTCCACCACCACCAACCCCCGGGATAAGTGTGTGA M 2 1 2 1 201000 f 74 goat snp14111-scaffold1562-353309 25 40823918 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769690 Affx-122947940 AX-385256860 25 39615885 CAAAAAGTCCTTTCATTTGTCAAAAGATATAGGTA[C/T]ATATAAGCTCATGCAAAATATACAGTCCTGAAAAT Y 2 1 2 1 201000 r 74 goat snp14112-scaffold1562-398281 25 40868934 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771456 Affx-122953554 AX-385258614 25 39661644 AAAAATAGATTTACTATCTTCAAGGTCACTTAAAG[A/C]TGAAGTTAGCAAATTCAGTTTCCCGTTGGCAATCA M 2 1 2 1 101000 r 74 goat snp14113-scaffold1562-444040 25 40914906 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416088 Affx-122948324 AX-123286437 25 39700669 AAGATTTTCAGTGATATAAATTACCCAGTGGCAGT[A/G]CCCCCATTATCAACGCTCTGTGCTGACACTTCTAT R 2 1 2 1 201000 f 74 goat snp14114-scaffold1562-483065 25 40954245 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443731 Affx-122927139 AX-123314068 25 39737763 CTTGAACATGGTCTAGAAAACACAAAACTAAGTTG[C/T]AAAACATAATGGCACAGGTATCAGACAGCCCAGGC Y 2 1 2 1 101000 r 74 goat snp26139-scaffold2728-393791 25 40991349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393875 Affx-122965131 AX-123264230 25 39794031 AGAGAGCTGGGCTCCTGCTCTGGCTTTATCACGGC[G/T]ACTTTGCGTCTATTAAACTTCCCTGGCTTGGTTCC K 2 1 2 1 101000 r 74 goat snp26138-scaffold2728-337523 25 41047465 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447544 Affx-122924045 AX-123317880 25 39824705 CAGAGTGCGTAAATATCTGGGAAAAAAGAAGGTCC[A/G]TCTCACTAGGAATCCGCCAAGTGCAAACCAGAGCA R 2 1 2 1 201000 r 74 goat snp26137-scaffold2728-306849 25 41078220 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400254 Affx-122960139 AX-123270609 25 39882919 TTCTTTCTCCTTACTTCTCTGTGTGTCTGTACTGG[C/T]GTTCCTACAATACAGCTTGACTTGGCACTGTGAGA Y 2 1 2 1 201000 r 74 goat snp26136-scaffold2728-248635 25 41137278 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463963930 Affx-1110243234 AX-515441175 25 39925953 TCCTGCCTGCTTTGCCCAGGGGTCGTAGCGCAGTC[A/G]GTAGGATTCACACCTGGGTTCGCCTGGCCTCTGCT R 2 1 2 1 202000 r 74 goat GoatD01.060070 25 39925953 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38419809 Affx-122945838 AX-123290157 25 39954241 TATATCCATTCAGCAGCGGGGCATGGGAGGAACTT[C/T]GGAAAACTCATGGATGGTTTAAACCCAGGATTCTC Y 2 1 2 1 101000 r 74 goat snp26134-scaffold2728-177313 25 41207662 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785300 Affx-122934013 AX-385272345 25 39984148 CCTTCAAATTGTTTACATTCTGTAAAATTAAGTGC[G/T]CTGTTATCTGCTTGGAACTTAACTGTGCGTGAAGT K 2 1 2 1 101000 r 74 goat snp26133-scaffold2728-147406 25 41237294 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406411 Affx-122955216 AX-123276763 25 40025081 GGCTCAGCCAATGGAGATCCAAAAGATCACTGGAG[C/T]GGGAGTCAGCAGGGGCACTGTATTTGCAGACAGAA Y 2 1 2 1 101000 f 74 goat snp26132-scaffold2728-106473 25 41278127 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386482 Affx-122970763 AX-123256840 25 40071160 GCCTCATGTTTCAGGGAGGCTGGGCAACTTCTGAG[A/C]GGCAAGAGGCGGATCTTTTTTTGGTCTCTACCTAA M 2 1 2 1 101000 r 74 goat snp26131-scaffold2728-60394 25 41318469 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437939 Affx-122931630 AX-123308277 25 40101041 ATTTTATGAATGCTTTGGAAGGAAGCAGGGCATGA[C/T]GCCATGAATACAATAAATGCAGCAAGCCTCCAGCG Y 2 1 2 1 201000 r 74 goat snp26130-scaffold2728-30513 25 41347872 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277777 Affx-1111836017 AX-519551276 25 40125012 GCAAATGACCCAGATTTTAAAAATAAGTTGCAAGC[A/G]GGAGGAAAGGAGGCGGAGGGGCAACGTGGACTAAA R 2 1 2 1 103000 r 74 goat Random2.2K-2165 25 40125012 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439724 Affx-122930549 AX-123310061 25 40142955 TGACAAGGAAAACAGGATACTGCTTAACAAATTTT[A/G]TTTCTTGTTGATAGGGAAGTTTGTAAAAGTTAGTG R 2 1 2 1 101000 r 74 goat snp41711-scaffold542-3112485 25 41389500 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476376 Affx-1251763887 AX-586011787 25 40171494 TGGCTTTATGCTTTCTGCTACCCAGAGACAACCAC[-/TACTATTTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTATTAATAATATGTTGATATTGACATTGTGGTT - 8 1 4 1 20000 f 74 goat SV_243 25 40171494 - deletion junction SV-TF-chip 539476632 Affx-1251763887 AX-586012015 25 40171494 TGGCTTTATGCTTTCTGCTACCCAGAGACAACCAC[-/TACTATTTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTATTAATAATATGTTGATATTGACATTGTGGTT - 4 1 4 1 20000 r 74 goat SV_243 25 40171494 - deletion junction SV-TF-chip 562165372 Affx-1251763887 AX-606940783 25 40171494 TGGCTTTATGCTTTCTGCTACCCAGAGACAACCAC[-/TACTATTTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTATTAATAATATGTTGATATTGACATTGTGGTT - 8 1 4 1 20100 f 74 goat SV_243 25 40171494 - deletion junction SV-TF-chip 562165797 Affx-1251763887 AX-606941206 25 40171494 TGGCTTTATGCTTTCTGCTACCCAGAGACAACCAC[-/TACTATTTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTATTAATAATATGTTGATATTGACATTGTGGTT - 8 1 4 1 20100 f 74 goat SV_243 25 40171494 - deletion junction SV-TF-chip 562166367 Affx-1251763887 AX-606941775 25 40171494 TGGCTTTATGCTTTCTGCTACCCAGAGACAACCAC[-/TACTATTTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTATTAATAATATGTTGATATTGACATTGTGGTT - 8 1 4 1 20100 f 74 goat SV_243 25 40171494 - deletion junction SV-TF-chip 562166379 Affx-1251763887 AX-606941788 25 40171494 TGGCTTTATGCTTTCTGCTACCCAGAGACAACCAC[-/TACTATTTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTATTAATAATATGTTGATATTGACATTGTGGTT - 8 1 4 1 20100 r 74 goat SV_243 25 40171494 - deletion junction SV-TF-chip 562166547 Affx-1251763887 AX-606941955 25 40171494 TGGCTTTATGCTTTCTGCTACCCAGAGACAACCAC[-/TACTATTTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTATTAATAATATGTTGATATTGACATTGTGGTT - 8 1 4 1 20100 r 74 goat SV_243 25 40171494 - deletion junction SV-TF-chip 562166581 Affx-1251763887 AX-606941989 25 40171494 TGGCTTTATGCTTTCTGCTACCCAGAGACAACCAC[-/TACTATTTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]ACTATTAATAATATGTTGATATTGACATTGTGGTT - 8 1 4 1 20100 f 74 goat SV_243 25 40171494 - deletion junction SV-TF-chip 38441750 Affx-122929124 AX-123312087 25 40200987 GTGCCGACCAGCTCTGCAGGTGCTCAGTGGTGTCC[A/G]GGCGACCGCTTAAAATTCAGCTCCAACTCAGTCCA R 2 1 2 1 101000 r 74 goat snp41710-scaffold542-3054453 25 41447447 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384083 Affx-122972854 AX-123254441 25 40205550 AATACCCCTCTGAGCACTGCTTCGCTGCAGTCCAT[A/G]AATTTTGATAAGCTATAATTCCATTTTCATTCAGT R 2 1 2 1 201000 r 74 goat snp52854-scaffold7929-3218 25 41494512 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401746 Affx-122959511 AX-123272099 25 40309585 ATCCCGCACAAGAGGCCCCAGTCCCTGCTCGTCTT[C/T]GGGACCACCACCCACGCACCCGCACCCCGCTGGGC Y 2 1 2 1 103000 f 74 goat snp28892-scaffold3102-295738 25 41586418 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427670 Affx-122939313 AX-123298013 25 40364099 AGGAGGACAGGAGGTGGAGGGAGCAGAAGTCAGGG[A/G]GGGCTTCTGGGGGGAGGTGTCACTGAGCCGAGGGG R 2 1 2 1 103000 f 74 goat snp28891-scaffold3102-241224 25 41639352 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418549 Affx-122946399 AX-123288897 25 40392889 TAGGGCTTGTCGTGGGCCATCGTAAGGACTGGAAA[C/T]GGGAAGACATTGGGCCCCAGTGATTGAGAGTTTGA Y 2 1 2 1 201000 f 74 goat snp28890-scaffold3102-212434 25 41668776 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433272 Affx-122935223 AX-123303613 25 40428388 ATCAATAAAAATAATTATTATTCTTAATGCCGTGC[A/G]TGCATAGAACGTTCTAGAATGCCCCGTGCATTAAT R 2 1 2 1 101000 r 74 goat snp28889-scaffold3102-176935 25 41701060 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407802 Affx-122954559 AX-123278153 25 40490390 ACACAGCTGGATTCAAAAGCAAGAGAGAGTGCCCC[A/G]TAGGGGGAACTTTAAGTTACAGGGATGAACAAAAA R 2 1 2 1 202000 f 74 goat snp28888-scaffold3102-114933 25 41764880 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771114 Affx-122965632 AX-385258274 25 40558844 CCCCGGTCAAGTGCTGTTATCAAAGCAAAGAAAGC[A/G]TGGAATTTATGCACTGAGTAAAAAACCTGGCATCT R 2 1 2 1 101000 f 74 goat snp28887-scaffold3102-46479 25 41831335 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441734 Affx-122929135 AX-123312071 25 40595177 TCAGTTATTGTAGCACAGACCGATGCAGAAACACG[C/T]GACATGTCGCGAGAACATCTAGCTATTCCCGGCCT Y 2 1 2 1 101000 f 74 goat snp28886-scaffold3102-10146 25 41866827 G A 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448084 Affx-122924329 AX-123318420 25 40669686 TGATGTAAGACGGGAAACCAGTCACAAGAAGAAAG[C/T]GGGAAAAGTCCCAAATATGTGGATCTTAAGTTACC Y 2 1 2 1 101000 r 74 goat snp14801-scaffold1597-131474 25 42149325 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786036 Affx-122933009 AX-385273072 25 40734809 GTCGTGCTAAGTCCTCTAAGTTTTCTTTTCAGAAT[A/G]TTTTCTGCTATTCCTAGTCCTTCACATTTCCGTGC R 2 1 2 1 101000 f 74 goat snp14800-scaffold1597-66351 25 42072592 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772052 Affx-122950443 AX-385259207 25 40884433 ATGTTCTCGTCAATATGAATCAAAGTATGGATTAA[C/T]GAAAACCTAAATTCGGGTTGAGCTTCATAAACTAG Y 2 1 2 1 201000 f 74 goat snp17477-scaffold1808-83174 25 42367533 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444655 Affx-122926464 AX-123314992 25 40955618 GTGTATGAGCCTCGTTTCATCAAGTCTGCAACTCC[A/G]TCAGTGCTGCGAATACCAGAACTTTATGGACCGTT R 2 1 2 1 101000 r 74 goat snp17478-scaffold1808-154359 25 42561830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425800 Affx-122940699 AX-123296146 25 41064031 CTGGCCTGCTCTAGCTCCTTCTGGATGGCCTAAAA[C/T]GATTAAGAAACTGTTTAAATACACAAGTTATGCAC Y 2 1 2 1 201000 f 74 goat snp17480-scaffold1808-262772 25 42481072 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376904 Affx-122977804 AX-123247263 25 41114007 GGTCCTCCGCTGCTGGCAGACAGGTGCCCTGTGAC[A/G]AGGCTCAGAGGCCACGAGTCCCAGCCCAGGGGAGG R 2 1 2 1 103000 f 74 goat snp17481-scaffold1808-312748 25 42429710 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439148 Affx-122931076 AX-123309485 25 41140116 AGTGGACATTCATGGAACCCTCCACTCAACAGGCG[A/C]GGAGTGCATGCTGTTCACAGCTGCCCGGGGACGTG M 2 1 2 1 101000 f 74 goat snp27438-scaffold2922-8403 25 42403449 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375716 Affx-122978637 AX-123246075 25 41276383 GGGACCCCAAGTCCTGTGATGTCACACAACCTCTG[C/T]GCACTAACTTGAACTTCCTGTCATATGACATGACA Y 2 1 2 1 101000 r 74 goat snp52310-scaffold7764-82924 25 42671997 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796846 Affx-122919949 AX-385283789 25 41346259 ATCTATTGAGACGGAAGAGTATATTGATTGGTTTT[A/C]TAGTATTAAACCACTATTTTATTTCTGGGATAAAC M 2 1 2 1 101000 f 74 goat snp37498-scaffold4593-150426 25 42707447 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395270 Affx-122964086 AX-123265625 25 41394914 CTCCCCGTCTGTGCCTTCTCATCCCAGTCACCATC[A/G]CCAAGGCCCTCTTTCACTCCAGCGGCCACCTAACC R 2 1 2 1 201000 f 74 goat snp37497-scaffold4593-101771 25 42755241 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793232 Affx-122947805 AX-385280210 25 41437793 TAATGGTTCACAGAACAACAGCTCGATTGCTGACA[G/T]GAAGGGTCTAGAAGGAGGGCCTGGCCTTTCCCAGC K 2 1 2 1 202000 r 74 goat snp37496-scaffold4593-58892 25 42798378 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430087 Affx-122937536 AX-123300428 25 41478468 CTGTAAAGGTCTTTTTTGAATCAAAACAGAAAAGG[C/T]GCACTCCCACCACTCTCCTCGCCAGGATTTTGGGC Y 2 1 2 1 101000 f 74 goat snp37495-scaffold4593-18217 25 42840364 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273124 Affx-1111833300 AX-519546788 25 42008731 GCATGCAGACTGTGTGTCTCTTCTGTCTTTTCATC[A/G]AGTTTGGTCCTTTTCTTGAGTCTTGAGTCCTCCCC R 2 1 2 1 101000 r 74 goat 25_42008731_AF-PAKI 25 42008731 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468272403 Affx-1111834139 AX-519546129 25 42562661 GCCACACTGTGGACGAAGGGAGACTGCAGCCCGGC[A/G]CTCTGCTGTGGGACATGAGGCTGCTCGCCAGGCTG R 2 1 2 1 202000 r 74 goat GoatD01.020884 25 42562661 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320804221 Affx-986696448 AX-385290858 25 42850780 CCCAAAGTGACTGAACAACAAATATTTGGCAATTA[A/G]GTTGAGACTGAATTAAAAATATTCAGGCATGATAG R 2 1 2 1 600010 r 74 goat 25_42850780 25 42850780 Ancestral_priority_1043 ancestry 0.634 recommended IMAGE 10K 10K ancestral 468273141 Affx-1111833308 AX-519546804 26 25745 TCCACCACACATTCTGTACCCCTTGGCCTTCATTA[A/G]GCAACTCAGTTGTTTGTGCACTTTTACCTGGTGGA R 2 1 2 1 101000 r 74 goat 26_25745_AF-PAKI 26 25745 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38428843 Affx-122938364 AX-123299185 26 59735 TCTTTGGTGCCTCTGGTGGCCTGGGTGTCTCTGGC[A/G]TCACAGATGCTGTTCATGCCTTGGTTGCCATTCTT R 2 1 2 1 101000 r 74 goat snp10485-scaffold1374-59735 26 51356166 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787688 Affx-122968538 AX-385274711 26 131169 TTATGCACCATATCAATATCAAAAATATATAATGC[A/G]CACTTCTTTTGCACAAGAGACTGTTAGATTTTAAA R 2 1 2 1 101000 f 74 goat snp10486-scaffold1374-131169 26 51283153 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774632 Affx-122959404 AX-385261766 26 162907 GCTTTTTATCCACCATGACATCTTTTCCTAACTAT[C/T]ATCTTTTCCTACTACAACACTACCTACAACACTGC Y 2 1 2 1 101000 r 74 goat snp10487-scaffold1374-162907 26 51249641 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432535 Affx-122935553 AX-123302876 26 205628 GAGGTGCTTGCACACCACCACTAGAGAAATTTGAA[C/T]GCACCACAACTACAGAGTTGATCCTGACAATGATA Y 2 1 2 1 101000 f 74 goat snp10488-scaffold1374-205628 26 51206587 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441287 Affx-122929466 AX-123311624 26 236378 TATATCCCACCCAGAGACATCTTGTCCAGAGACTG[G/T]TCCCCTTGTTTAATCTTGTTTCAATATTATCTCAA K 2 1 2 1 201000 r 74 goat snp10489-scaffold1374-236378 26 51175776 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398071 Affx-122961737 AX-123268426 26 278178 AAATACAGGGAAAAGGTTAGGAAACAGATCTAGTA[C/T]ATTTTATACTGGAGTCCTAAAGGGGAAAAATAGAA Y 2 1 2 1 101000 f 74 goat snp10490-scaffold1374-278178 26 51133143 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443494 Affx-122927804 AX-123313831 26 333237 CCCCCAAAACAGAAAATGTAATGTTAATTATTTCC[A/G]TCACAGACAAATATGTACATATTTTTCTTTCCTTT R 2 1 2 1 103000 f 74 goat snp10491-scaffold1374-333237 26 51077639 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411342 Affx-122952264 AX-123281692 26 374353 CTTCTTTCTTATCTGTAACATGTAATTTGTGATAA[C/T]GGATTTCCACTGTGGGATGAGGTCCCTAATACAAC Y 2 1 2 1 201000 f 74 goat snp10492-scaffold1374-374353 26 51036336 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423432 Affx-122942607 AX-123293778 26 422289 ATTTTTCATTATTCATCTTACTTCACTTTTAAAAG[C/T]AGTCTTCAATATGACCATGTCCTCCTTGAAACATT Y 2 1 2 1 101000 r 74 goat snp10493-scaffold1374-422289 26 50989640 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388537 Affx-122969195 AX-123258895 26 473023 CCTGGTGATCCATCCCCACTTACATTAGCTGTAGG[A/G]CAGCTCTTACTCTGTCTGGGTAAAGGGCACTAAAC R 2 1 2 1 201000 r 74 goat snp10494-scaffold1374-473023 26 50939906 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387560 Affx-122970285 AX-123257918 26 516609 TGCAGCTTTAGATCCTTGCTGGCCACTGCCCCTCT[A/G]CTTTGATGACCGCACCCCTGCTGTCCTCCTGATTT R 2 1 2 1 201000 r 74 goat snp10495-scaffold1374-516609 26 50899546 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380441 Affx-122975294 AX-123250799 26 557443 TCATTGGTGGGGAGTTAATGCCTATCAAGATACAA[C/T]ACATAAGTCAAAGTGGTGGATGGGTGCTCTAGAAC Y 2 1 2 1 101000 f 74 goat snp10496-scaffold1374-557443 26 50857626 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399108 Affx-122960864 AX-123269463 26 589539 GCAGCCTGACCCATGCAAAGGCACAGAATTAGCTC[A/G]TTGATTTGAATCCATGGTTCTTGTTATTAGACCTG R 2 1 2 1 101000 r 74 goat snp10497-scaffold1374-589539 26 50825541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449223 Affx-122923494 AX-123319558 26 641894 AGAAGAAAATACTCTTTGTTTCCCTTTTTCTGTTG[C/T]AAAACATAACAAAACAGACAATGTCTGCTTTCCAA Y 2 1 2 1 303000 f 74 goat snp10498-scaffold1374-641894 26 50774246 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428341 Affx-122938993 AX-123298684 26 656309 GATGCTGAGTCATCAAGGTAAGTGCATGCGCATTT[C/T]GCTCCTGTGTACCTGCTCCGGTCCTCAGGCTCTCT Y 2 1 2 1 101000 f 74 goat snp59203-scaffold973-5146 26 50759841 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452500 Affx-122920979 AX-123322833 26 695968 GTTAGTTTAGTGTTGATGTCTGATTTTTAGCAATA[C/T]ATGAGAGATAATTTGTAACCTTAACATAAAAAAAA Y 2 1 2 1 101000 f 74 goat snp59204-scaffold973-44805 26 50720006 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438055 Affx-122931541 AX-123308393 26 729021 AACCATAATTCAGAATCCAAGTACAGCCAGTGCCA[C/T]ATGACAACACATGCACATATAAGCCATATTTAATT Y 2 1 2 1 101000 f 74 goat snp59205-scaffold973-77858 26 50693978 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768013 Affx-122942990 AX-385255227 26 765817 AAAAGGAGTTTTGGTTAGGAGAGGATATCTTCAAA[C/T]GGTGTAACTTCTTTTGAAGAGGCTATGTAGATTCA Y 2 1 2 1 101000 f 74 goat snp59206-scaffold973-114654 26 50661395 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381269 Affx-122974479 AX-123251627 26 808017 ATACATGTTTTTATGACTTGAAGTCTCCCTTCTCC[G/T]CAGAAAATGATGGGACATGCTAGATTGAAAAATAA K 2 1 2 1 101000 f 74 goat snp59207-scaffold973-156854 26 50619164 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789085 Affx-122929793 AX-385276098 26 836954 CAATTTAAAGGAGTCTGGAGAATAGTACCACTGAT[A/G]TCTGCACATCTTTGTCTCCTAGAATTGTGTATAAG R 2 1 2 1 101000 r 74 goat snp59208-scaffold973-185791 26 50590101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438793 Affx-122931368 AX-123309130 26 870478 ATCTGGCATGCATTTTGTTGTTCTCAATATATACT[C/T]ATTGAATGATATATACCCACAAACTTCCACACAAA Y 2 1 2 1 101000 r 74 goat snp59209-scaffold973-219315 26 50556344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397539 Affx-122962035 AX-123267894 26 907504 TAGTCATGAAACCTGTGTGGTACCAGTCCTCCACC[C/T]AACCATCTTCCCTTTTTCAAACCCCAGGACTGTAG Y 2 1 2 1 101000 r 74 goat snp59210-scaffold973-256341 26 50518937 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453315 Affx-122919979 AX-123323648 26 981839 GTCCAAACTAACCATTCTTTGGGCTAAATGATAAA[C/T]AGTTAGAAATCAGTCAAAATGTCAATGGGAATATA Y 2 1 2 1 101000 f 74 goat snp59212-scaffold973-330676 26 50443099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779206 Affx-122921808 AX-385266310 26 1019664 TTGTATCATTCAGAATTATATGATTATATGCAATT[A/C]TGTAAACAAAATTGTACAGAATTGTATAACTGGCC M 2 1 2 1 201000 f 74 goat snp59213-scaffold973-368501 26 50405303 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423449 Affx-122942594 AX-123293795 26 1049608 CAATGTAAGTCTATTTGAGATCCTTTTCTGCATCT[A/G]CTCTTAGCAAGCTAATGTGGGCTGATACATCTGTT R 2 1 2 1 101000 r 74 goat snp59214-scaffold973-398445 26 50375042 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451559 Affx-122921701 AX-123321892 26 1090464 TACTGATAGCAGAGCCATGAATATAACTAAGAACT[A/G]TTTGATTTCAAACTTAGGATATTCCCCAAAGGGGA R 2 1 2 1 101000 f 74 goat snp59215-scaffold973-439301 26 50301886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790040 Affx-122923670 AX-385277046 26 1123620 TGTCAGTGTACTAAGATGCTACAAAAATATCAGAT[A/G]TTACATACCTAGAGAGTCTTATGCTGAGTGGAGTA R 2 1 2 1 101000 r 74 goat snp59216-scaffold973-472457 26 50267385 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784509 Affx-122959886 AX-385271558 26 1176158 GAGAAGCAAGAGAGATTTATTATGATAAGGAAGGA[C/T]ATTCAGATTTAATCAGATGGGTCCAGGGCAACTTC Y 2 1 2 1 201000 f 74 goat snp59217-scaffold973-524995 26 50211981 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772190 Affx-122919353 AX-385259345 26 1271422 ACCTTGACCTAATAAATGCTTTCAGTAAGCAGAGT[A/G]CAAGGTGAATTTTCAGCATTCATAGGCTTATTCAG R 2 1 2 1 101000 f 74 goat snp59219-scaffold973-620259 26 50120743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778574 Affx-122921806 AX-385265686 26 1314329 TAATTAAAAGGGTAAACTTACTTTCAGATTGGAAT[A/G]CATTGAAATATCAAAGAGGAAACTGGCACTAGGTC R 2 1 2 1 101000 r 74 goat snp59220-scaffold973-663166 26 50076869 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779402 Affx-122974360 AX-385266505 26 1360056 CATAATAAGGTAGAGGACAGTGAAGTGAATAGTAG[C/T]TCTAGGTGAAAATAGTAAATACTATACTTAATATA Y 2 1 2 1 101000 f 74 goat snp59221-scaffold973-708893 26 50030869 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768494 Affx-122935605 AX-385255674 26 1423199 AAATTTAGGTTATTGTCTTCTCTATTGTTAAGTTT[C/T]CAAAGATTCAGTCATCTTCCTCTTGGTTCCATAGT Y 2 1 2 1 101000 r 74 goat snp59222-scaffold973-772036 26 49968015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387462 Affx-122970363 AX-123257820 26 1467789 ATCTATTATGACCTGGTACAACTTAGAGAGTCCAT[A/G]CTAGGCAGGTTTGTCTATAAATATTTACCTGAAAA R 2 1 2 1 201000 r 74 goat snp59223-scaffold973-816626 26 49922299 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379603 Affx-122976019 AX-123249961 26 1538540 CATTAGGCCCTGCAAATCCTCTTGCAACCCCTAAT[C/T]GTCCCTATTCAGAAGACTATTGGGGAGTATTGGTT Y 2 1 2 1 303000 f 74 goat snp59224-scaffold973-887377 26 49851382 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450767 Affx-122921839 AX-123321101 26 1573308 ATTCAAACGATTTAACTTCTAACTGCACATTTCCT[A/C]GGCAACATAGTTAATGGCCTTGATCTAGAGTACAT M 2 1 2 1 101000 r 74 goat snp59225-scaffold973-922145 26 49816188 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446442 Affx-122925969 AX-123316778 26 1634423 TAGAGGAGACAACTCAGAAAGCTTCATACTTACTG[A/G]GAAAAGTCAAATTATTTATTTGCTAATGACCCTCA R 2 1 2 1 101000 r 74 goat snp59226-scaffold973-983260 26 49754814 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415062 Affx-122949477 AX-123285411 26 1666876 TAATTGGTGGACTTCTCAGTTTGCTTTGCTCATTT[A/G]CATTGCCTTCCTGACCACAAGAGCCACTGAAAAGG R 2 1 2 1 101000 r 74 goat snp59227-scaffold973-1015713 26 49722437 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787872 Affx-122959180 AX-385274894 26 1730452 ATGCAGAAAAATCACTCACTTTAATAATGCTTGAA[G/T]AATTCTTGATAAATTTACCACTGGTCTTTCCATCC K 2 1 2 1 101000 r 74 goat snp59229-scaffold973-1079289 26 49658997 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379422 Affx-122976111 AX-123249780 26 1769366 ATTGAGAACTTCTCAAAGAAAAGAAAGGGTTTTAC[A/G]GGGACAGATAAACAATGGATTTATCTCTGAGTCTT R 2 1 2 1 101000 r 74 goat snp59230-scaffold973-1118203 26 49620110 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777229 Affx-122957184 AX-385264352 26 1800419 AAAGAGACTATGGAGACCAAAAAATGTTTTCCGAA[A/G]TAATTTAAACACAACAGATTAAGATCCACATCATA R 2 1 2 1 101000 f 74 goat snp59231-scaffold973-1149256 26 49587744 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274316 Affx-1111834129 AX-519547913 26 1872686 CGCCTGCAGCCCCCGCCCTCGCACTGGCCAGCCCA[A/G]CACCCTGCCCGCCCCCCACGGCGCTCCTGTGGGCC R 2 1 2 1 303000 r 74 goat GoatD01.020381 26 1872686 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320777932 Affx-122947978 AX-385265048 26 1880045 ATCTCTAGCCTTTTGGAACTCTGTAAGTCTATTCA[C/T]TCAGACACAGCAGTTTGAATCTTGGTTGGATGCCT Y 2 1 2 1 101000 r 74 goat snp59233-scaffold973-1228882 26 49506278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397345 Affx-122962299 AX-123267700 26 1945697 ATTGTATTATTCTTACTGATACTGCCAGGCATTAG[A/C]ATATGGTGCTTTTGCAAAGTGGTAGATCAAAGACT M 2 1 2 1 101000 r 74 goat snp59234-scaffold973-1294534 26 49439721 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769547 Affx-122938538 AX-385256717 26 1990855 TTGGAAAATAGATGAATAGCAAAATGTTGTTTAAA[C/T]GTATAAGTGACAGGAAAAAACATGCTGTTCTTTAT Y 2 1 2 1 101000 r 74 goat snp59235-scaffold973-1339692 26 49393759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430761 Affx-122937492 AX-123301102 26 2036471 ACTATAATTAGGGATCCAAGGTTCCAGGGAGTCAG[C/T]GATTCTATAAAAATATCAAGTAAATAAATTTCAAT Y 2 1 2 1 101000 f 74 goat snp59236-scaffold973-1385308 26 49348110 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404470 Affx-122956732 AX-123274822 26 2118498 TTGGATACAATTTTAAATTAATATTATAATTGGTA[C/T]GTATTCCAGAATATATTTTTCAACACTGATTATGA Y 2 1 2 1 101000 r 74 goat snp59238-scaffold973-1467335 26 49264772 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395932 Affx-122963587 AX-123266287 26 2207124 ACACACCCCCTCTCTCCTTCTACATAAGACAAAAG[C/T]AGAATACAGGAAGTCAAAGAACTACTAAGCTACAT Y 2 1 2 1 201000 r 74 goat snp59240-scaffold973-1555961 26 49175021 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392005 Affx-122966493 AX-123262362 26 2236338 TATGCCCACAAGATGAGCAGGAAGCCACAATGTCA[C/T]GGTAATGGATGACAGGGAGGTTACTTAGTCATGCA Y 2 1 2 1 201000 r 74 goat snp59241-scaffold973-1585175 26 49145038 A G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781143 Affx-122962063 AX-385268228 26 2271556 ACCTTAGGGCTGAGACTCTCCTTACCCAGATTGCT[A/G]GAATTTTGGATTCTGATAGCTCAAAGCTGAGTCTC R 2 1 2 1 101000 f 74 goat snp59242-scaffold973-1620393 26 49119731 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800422 Affx-122966970 AX-385287343 26 2302738 GGAAACAACAACCAAGTAGACTGTTGTGACTGATC[A/G]TTATTATGAAAAGGTTGACTGCAAAGGTTGGCTAT R 2 1 2 1 101000 f 74 goat snp59243-scaffold973-1651575 26 49087980 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410400 Affx-122952426 AX-123280750 26 2361527 TGCATTGCCACTCTCGCCACATTTTATTGGTTGCA[A/G]GCAAATCACAGCCCACCTAGAATTAAGGAAAAGGG R 2 1 2 1 101000 f 74 goat snp59244-scaffold973-1710364 26 49032698 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797208 Affx-122964560 AX-385284147 26 2421276 AGTTGACACTTCAAAAGCACTAAGCAAAAAAGACA[C/T]TGAGAAATTCTCTACAATCCTAATGTACATCTTAT Y 2 1 2 1 101000 f 74 goat snp59245-scaffold973-1770113 26 48971441 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799446 Affx-122962406 AX-385286375 26 2450690 AGCTCTTCAGTCCTCCAGAGTTCCACTGTCTAATA[C/T]GGTAACCATTAGCTACCCGTGGTTATTTAAAATTA Y 2 1 2 1 101000 f 74 goat snp59246-scaffold973-1799527 26 48941118 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790973 Affx-122965560 AX-385277970 26 2492830 CCTGAAAGGAGAAAGTAATAAAGCAAAGATATTTC[A/G]TGTCTTTGTGGAATAGTTTAAAGACTCTGATGATT R 2 1 2 1 201000 f 74 goat snp59247-scaffold973-1841667 26 48897970 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785159 Affx-122964678 AX-385272205 26 2550183 ACATGAGGGACCAAAACATGGGATTAATTAAGGGC[A/G]TAGTATGGAGAGATACTCCTGCTAAAGTTGATAAA R 2 1 2 1 101000 f 74 goat snp59248-scaffold973-1899020 26 48840301 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273096 Affx-1111833309 AX-519546762 26 2586142 AAGAAATGAGATATCTGGGCCCTAGAAAGAAAGAA[A/G]GAAACTGAAGTCGCTCAGTCATGTCCAACTCTTTG R 2 1 2 1 201000 f 74 goat 26_2586142_AF-PAKI 26 2586142 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392446 Affx-122966172 AX-123262803 26 2630914 CCTAAAAGTTGAGAGTTGTGTTTTATTTTCATGTT[A/G]TAATGCAGGAAAAATGAGGAACATGGATGCTAAAT R 2 1 2 1 101000 r 74 goat snp59250-scaffold973-1979751 26 48742036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393914 Affx-122965100 AX-123264269 26 2662682 CCTGAAAAATAATTTTTAAATGTATGTCATAGAAG[C/T]AGATGATCTTTGATAGAGACCTGTCACCTCAGGGA Y 2 1 2 1 101000 r 74 goat snp59251-scaffold973-2011519 26 48710117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401804 Affx-122959467 AX-123272157 26 2711007 TGTCAAGTAATGGGAATACAGTATAATTTAAGAGA[C/T]GATATCATGATCTTCTTGAATCTTTTCTATGATGA Y 2 1 2 1 101000 f 74 goat snp59252-scaffold973-2059844 26 48355055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784454 Affx-122968357 AX-385271503 26 2773776 CAGAAGATCATATAGTAAGACCAGTGTGAATCCTG[C/T]AGTGAATAGCATAATGGTGTTTAGGTCTTTGTGTG Y 2 1 2 1 101000 f 74 goat snp59253-scaffold973-2122613 26 48289860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772268 Affx-122946911 AX-385259423 26 2812796 GAGCAAATACTCAGGCAATTAACAGGCTACAGTGG[A/G]CTTGTTCTGGAATATACCTGAGCTAGTAAACTGGA R 2 1 2 1 101000 f 74 goat snp59254-scaffold973-2161633 26 48249847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780351 Affx-122977849 AX-385267446 26 2858990 AATTTTTCATTCCTTTCTGAAGTGATTTGTATGTT[G/T]GAGGCATCATTTATTCCTAAGAAAGTAAAGTTTTC K 2 1 2 1 201000 f 74 goat snp59255-scaffold973-2207827 26 48202832 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799241 Affx-122970863 AX-385286171 26 2961787 AATTCACATTTTACTATTGTTGGAGTCATATATGT[A/G]CTTGTATGGTATTAAAGACACACTGGAGGGTTCAT R 2 1 2 1 101000 r 74 goat snp59257-scaffold973-2310624 26 48097789 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422361 Affx-122943433 AX-123292707 26 3005310 CACAAGACTGTGACTGATGAGATCACTGTAGGCCT[A/G]TCAAGTTCAACACTTGCTGTTTGGAGCATGGTAAT R 2 1 2 1 101000 r 74 goat snp11253-scaffold1403-435530 26 48055001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394363 Affx-122964645 AX-123264718 26 3039056 CTGAATAGTATCTTTAATACCCACCTCTTTTAACC[A/G]CCAAAAGAAAGAAACTAGGGTTTTACTAAAATTCT R 2 1 2 1 101000 f 74 goat snp11252-scaffold1403-401784 26 48020631 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408926 Affx-122953949 AX-123279277 26 3077910 CATAATACAGATGCAGTCATTTAAAAGTGTCTATC[A/G]TGTTATCATATTTCCACTAGTACGAGTGTCAGCTC R 2 1 2 1 101000 r 74 goat snp11251-scaffold1403-362930 26 47984340 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450942 Affx-122921764 AX-123321276 26 3124210 ATTTCTCAGGTCACGAATTTAACACTGTGAGAGTT[A/G]CATTTGCAGACAAGAAAACATGGAACTCAGGGTTG R 2 1 2 1 101000 f 74 goat snp11250-scaffold1403-316630 26 47936716 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444654 Affx-122926465 AX-123314991 26 3155166 GTAAAATTTGCTACTAGCTACAGTGAGTTTGCACA[C/T]AATTCTACAAAGGCACATTGAAATCTTGGCCATTT Y 2 1 2 1 101000 r 74 goat snp11249-scaffold1403-285674 26 47905480 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782119 Affx-122922668 AX-385269197 26 3220458 AGAATATCTGGACTGTGTGAACACTTAAAATTACT[A/G]TTGCAGATTTGCTTCTGCTGTTTATGACTGATAAA R 2 1 2 1 101000 r 74 goat snp11248-scaffold1403-220382 26 47839643 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419688 Affx-122945929 AX-123290036 26 3287196 ATGTATGGTTTGTTGGTCTTAAACACAGTAAAATC[A/G]CCTATGCAATAAAATGGTTAAATGTCTTCAAAATT R 2 1 2 1 101000 f 74 goat snp11247-scaffold1403-153644 26 47772753 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783102 Affx-122968976 AX-385270169 26 3342966 ATTTCCCTCTTCATACCGACCAGATGGATTAGGAG[C/T]CCACCTTACTCCAGCATCACTTGCTCTTAACTCAG Y 2 1 2 1 101000 r 74 goat snp11246-scaffold1403-97874 26 47716385 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449802 Affx-122922416 AX-123320137 26 3391795 TCATGTGAATTGAAGTTTTGGTATGTTCTAACTGG[C/T]AAGAATATTTTGTATATACCAGGCCTTGAATCATA Y 2 1 2 1 101000 f 74 goat snp11245-scaffold1403-49045 26 47667445 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277779 Affx-1111836018 AX-519551278 26 3411000 GTGGCTGGCCCCGGGGGCGGGTTGTGGACATTGCC[A/C]GGCAGTTTTTCTGGGCAGGTGGCATCAGTGGTTAA M 2 1 2 1 102000 r 74 goat Random2.2K-2169 26 3411000 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320788410 Affx-122938145 AX-385275428 26 3472049 GATTAAAATTTCTGTCAATTTCTGCTACATAATTC[A/G]CAGTCATGTGGGAAGAATTTAGCTCAAGAAGTGAA R 2 1 2 1 101000 r 74 goat snp11778-scaffold1434-996755 26 47565434 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415789 Affx-122948908 AX-123286138 26 3511991 TCATGTATTAATTCACTGAAGAAATATTTATCAAC[A/C]ACCTAAAATGTACCAGGTACAATACTAGGTTCTGT M 2 1 2 1 201000 f 74 goat snp11777-scaffold1434-956813 26 47525228 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795755 Affx-122931746 AX-385282708 26 3551713 CTAATGAATTGTTAGTTTTCACTCCAGTGATAATT[A/G]TTAATCTTAGCCAGTTCAGTTATTGCCATTAGTCT R 2 1 2 1 201000 r 74 goat snp11776-scaffold1434-917091 26 47484633 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439097 Affx-122931117 AX-123309434 26 3599541 AAAGAGACTCCAGGAAGAGTCACTGAACTTTCTTG[C/T]GAATTCCATTATTATAAGTGGGAGAGTGCCTTACT Y 2 1 2 1 102000 f 74 goat snp11775-scaffold1434-869263 26 47435843 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436478 Affx-122932972 AX-123306816 26 3632696 GGCAGGTGGGCAATTAAAGAAAGAAAAAAAGCAGA[C/T]GGATGGACAAAAAATTTAAAGGATATGTACTACTA Y 2 1 2 1 101000 f 74 goat snp11774-scaffold1434-836108 26 47402937 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274202 Affx-1111834105 AX-519547803 26 3638244 CAGAGGCCACATTCAGTGCCCTCCTGGCCACCAGA[A/C]CCCGGGATGGCTGCAGGGGCACCACAATTAGATTG M 2 1 2 1 202000 f 74 goat GoatD01.018577 26 3638244 G T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38431249 Affx-122937128 AX-123301590 26 3672942 TGTTGGACAATTCACCAAGTATAAGGAAAATACAA[C/T]GATAGATTATCTGTCATGGGAAGCAGGGTATAGAA Y 2 1 2 1 101000 f 74 goat snp11773-scaffold1434-795862 26 47362653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407199 Affx-122954812 AX-123277550 26 3703755 CCACACACAACTGATGCTCATTGATGAAATTCCAA[C/T]GATAGGTGGAAGTGTGAGGAAAATAAAGATTAGCA Y 2 1 2 1 101000 f 74 goat snp11772-scaffold1434-765049 26 47331618 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383296 Affx-122972712 AX-123253654 26 3744229 CAACGTAAGTAAACATGTTGATCATGTAAAAAGGT[A/G]CTAACTCAAAATATATTATTTTCCCAAAGGCTTAA R 2 1 2 1 101000 f 74 goat snp11771-scaffold1434-724575 26 47291338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428008 Affx-122939158 AX-123298351 26 3799746 AGAGAATTCTTAAAAAATATAATTGTGCCAGTCAT[A/G]CTCAAATCTGTAAAGGAGTGGTCAAGGCCTAAGGC R 2 1 2 1 101000 r 74 goat snp11770-scaffold1434-669058 26 47236194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788154 Affx-122952868 AX-385275173 26 3859473 TAAAATAGAACCTTTCCCACTGAATAAATACCTAG[C/T]AATATTAAAATACAACTTAAAGCTGTTAAGAGCAT Y 2 1 2 1 101000 f 74 goat snp11769-scaffold1434-609331 26 47174691 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384046 Affx-122972882 AX-123254404 26 3904211 TAGGAACGGATGAGAATTAACAGGACTATTGATAG[A/C]TTTATTTATTTTTTGCATCCAAAATGCAGAATTAT M 2 1 2 1 102000 f 74 goat snp11768-scaffold1434-564593 26 47129944 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411261 Affx-122952321 AX-123281611 26 3935425 CAGGATGGACATGACACATAATTCATATTTTACTC[A/G]TCCTTCTTCAGAAGGAAGTTGAAAAATCCTACAAG R 2 1 2 1 101000 f 74 goat snp11767-scaffold1434-533379 26 47098140 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376403 Affx-122978091 AX-123246762 26 3974306 GTTTTTCACTTTTTTTTTTACACAAATTTCACAGT[A/G]CATTGTCCCATGATCTTTGCTGTTCTTTTATTCCA R 2 1 2 1 101000 r 74 goat snp11766-scaffold1434-494498 26 47060386 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435320 Affx-122934014 AX-123305660 26 4005837 GTGTGCTCCATGGGGTCACAAAGAGTCAGACACGA[C/T]GAACAACTAAGCACAGCACACCATTTCTGTGCTGT Y 2 1 2 1 103000 r 74 goat snp11765-scaffold1434-462967 26 47028931 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776670 Affx-122972533 AX-385263797 26 4061607 TTCCTCACTAGTTTTGAACAATATACATTTACTTA[C/T]GTATTTGCCATTATTTTTCCCACCTTGCTCCACTG Y 2 1 2 1 101000 r 74 goat snp11764-scaffold1434-407197 26 46972700 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796732 Affx-122927848 AX-385283677 26 4107161 TACTCAATGGATCCATTTGATACAATGAAAGGGAC[G/T]ACAGTTACAAAGTAAAAATGTTCCTAAGTATGCAT K 2 1 2 1 101000 f 74 goat snp11763-scaffold1434-361643 26 46926874 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798093 Affx-122939612 AX-385285029 26 4162092 CACTTCCCCATAAGAAGAATCCTAACTACACAGGA[C/T]AGAAGGCAATATTGACCGTTTCAGAAATTGTGGCT Y 2 1 2 1 101000 f 74 goat snp11762-scaffold1434-306712 26 46872944 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419427 Affx-122945513 AX-123289775 26 4192798 ACAGTTAGATACCCCTGTCTTTTGGAAAATTCCTT[C/T]CTTTTAGAATGTCCTTCCATCAAGAGCACAGAATA Y 2 1 2 1 101000 r 74 goat snp11761-scaffold1434-276006 26 46843072 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432197 Affx-122936389 AX-123302538 26 4238284 GGTTTTCCTCCTGAAGAGTTTATAAATGTCTGTTG[C/T]ATATTTCTCTATTAGGCTATGGAGGCTGGCCTTAT Y 2 1 2 1 101000 r 74 goat snp11760-scaffold1434-230520 26 46795088 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796978 Affx-122952395 AX-385283919 26 4269676 GAGCAGTCATTTCTTAGCTGTTGCTACTGTCATTT[A/C]TGTACAGGTTTTTTATTGAAGCCACCTTTGGTAAT M 2 1 2 1 101000 f 74 goat snp11759-scaffold1434-199128 26 46764213 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417795 Affx-122947379 AX-123288143 26 4323175 ACTCCAGGGAACGAAACTATCACTAGAGTGGACAT[A/G]TACTGCCAAATTACCAGTTCTAAGAAAACAACTAA R 2 1 2 1 101000 f 74 goat snp11758-scaffold1434-145629 26 46709311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377384 Affx-122977632 AX-123247743 26 4359713 TTCTAGGACCAGGTATCCTACTGATAATAATACAT[A/G]CAAAATACATAATATTATTTGATTTTTGTTTTGTT R 2 1 2 1 101000 f 74 goat snp11757-scaffold1434-109091 26 46670073 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405358 Affx-122956319 AX-123275710 26 4403570 AGATGTCATCATTTGATTTTATTAATGCAATAGAC[A/G]TATGACCACTTCAAAATGATTTGGAAGAATTAAAA R 2 1 2 1 101000 f 74 goat snp11756-scaffold1434-65234 26 46625519 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440489 Affx-122929367 AX-123310826 26 4432333 AAAGAAATATTATTTTTCATTTAATGAACATTAGC[A/G]CATGAACAATTAAGACATAATTGAATGAAGCTAGT R 2 1 2 1 103000 r 74 goat snp11755-scaffold1434-36471 26 46596389 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799782 Affx-122952084 AX-385286709 26 4500588 TGGCTTTCCTGTCATAGTGTCCTCTTGAAACCGCT[G/T]CATATTCAATGTTTTATGAGAGACTAGAATTTAAC K 2 1 2 1 101000 f 74 goat snp26609-scaffold278-31685 26 46525940 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443954 Affx-122927012 AX-123314291 26 4539301 TGGAAGTGGATTGAAAGAGTGGCATGACTGGACAG[A/C]GGATTAGAGGAAGTTTTGCCCTGAGTCCTGACTCT M 2 1 2 1 101000 f 74 goat snp26610-scaffold278-70398 26 46486417 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387859 Affx-122969642 AX-123258217 26 4570469 ATTGGCATCCGAGAGGTCAGAGCAAGAAAGCAAAA[C/T]AAAACATAAGACTAGAACTCATGGTAGAAGTCAGG Y 2 1 2 1 101000 f 74 goat snp26611-scaffold278-101566 26 46455368 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800754 Affx-122927191 AX-385287670 26 4604922 TATTGAGTTTACTCCTCCTGGTCAGATTCTGTTCA[C/T]ACCTTTAATTTTATATCTCACAGTGGTTGATTTAC Y 2 1 2 1 201000 r 74 goat snp26612-scaffold278-136019 26 46420856 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767114 Affx-122947142 AX-385254401 26 4693416 CTTTATATGTGGGCAGCAATAACAAAACCAGAAGA[A/G]CGGTTGCTTGTATAATGTTATTATCATTATTATCA R 2 1 2 1 101000 f 74 goat snp26614-scaffold278-224513 26 46331538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771536 Affx-122922820 AX-385258694 26 4740568 AGGAAAAGTGATCAATACAGCTTGTAAGATTATTC[A/G]CATCAGCTTTATTCTTTAGAAACTATAAGTATGTG R 2 1 2 1 101000 r 74 goat snp26615-scaffold278-271665 26 46285296 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778817 Affx-122926367 AX-385265926 26 4777932 GAAGAATAAAGTCAGATGTTCTAGAGTTCAGGGAA[C/T]GAGAAAAATAGTGGTGGAAGGAACAGTCAGACAAG Y 2 1 2 1 101000 r 74 goat snp26616-scaffold278-309029 26 46247409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782504 Affx-122935685 AX-385269580 26 4851116 CTAGGGTGACACCATCAAGGCATTTTTTATAAGCC[A/G]CCAACCATATACTTTTGCTCATGATCAACTGAGAT R 2 1 2 1 101000 f 74 goat snp26618-scaffold278-382213 26 46172797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437550 Affx-122931899 AX-123307888 26 4883850 AAGAGAACAATCATCCATTATGCAGATCATTTAGC[A/G]CCATGTATTAAATGATTAGATCTTTATGGTTCTGT R 2 1 2 1 101000 f 74 goat snp26619-scaffold278-414947 26 46140116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779738 Affx-122946948 AX-385266838 26 4925606 CTGTTACTTCAGTGCATTGTTGACACAGGAATGAA[C/T]ATAAAACATGTATTGCCAGGTCAACCAATTTGATG Y 2 1 2 1 101000 r 74 goat snp26620-scaffold278-456703 26 46096194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430724 Affx-122936894 AX-123301065 26 4969939 TACTGAGCATGTGTCTTTCAGTTAGCAAATATATT[A/G]TGAGATTGAGTTTTGATCCTTGAAACACTTTCAGC R 2 1 2 1 101000 r 74 goat snp26621-scaffold278-501036 26 46053499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432222 Affx-122936369 AX-123302563 26 5017234 TTTTGATGTTATGTGCATGACTACACTAATATATT[G/T]CAAGATTCTATGGTGATTTCTCATCTTTATATGAC K 2 1 2 1 102000 r 74 goat snp26622-scaffold278-548331 26 46005656 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766447 Affx-122951789 AX-385253818 26 5050186 AATACTTCAGATTTTTCATCCAGGGCTTCTAGATA[C/T]ATTTTCCCCTATCTCTTACATACCAAATTTTATCT Y 2 1 2 1 101000 f 74 goat snp26623-scaffold278-581283 26 45972051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439759 Affx-122930522 AX-123310096 26 5154071 TCTTGATGATGAGAGAAAAGGAAAAGAATGAGGAG[C/T]ACTTCAATAAGAGAAACGTCAATTATGCTCTTCTA Y 2 1 2 1 303000 r 74 goat snp26625-scaffold278-685168 26 45870677 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273115 Affx-1111833318 AX-519546780 26 5168153 ACCTTGCTCCTCCACGCAAAGCTTCTGAAGGTAGT[A/G]AAATTTACATAGACGTTTATGATCCTGTTCTTATA R 2 1 2 1 101000 f 74 goat 26_5168153_AF-PAKI 26 5168153 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320799948 Affx-122937069 AX-385286874 26 5199157 CATTTCAAAAGTCATTTCTACAGACATAAGTTAGC[C/T]GTTTTCTACAGTAGAGCAAAATAAATATGATCCAA Y 2 1 2 1 101000 f 74 goat snp26626-scaffold278-730254 26 45827170 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440662 Affx-122929934 AX-123310999 26 5254291 GTTTTGACAAATGCATAACAAAAAACAGAATGGTT[A/G]CAGCACCCTTCAAAACTCCTTCATGGACTATAATC R 2 1 2 1 101000 r 74 goat snp26627-scaffold278-785388 26 45772230 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779351 Affx-122923687 AX-385266455 26 5311429 AGTTAGAAAGCATGATGTAGACAGCTATGAACTTA[C/T]GTGAAATAATTTCCATGCTATCCTGTTAAATGAAG Y 2 1 2 1 101000 f 74 goat snp26628-scaffold278-842526 26 45715365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440508 Affx-122929353 AX-123310845 26 5344552 AATTAAAGATTTCAGGGTAGTTTCCTCAAATGACT[A/G]TGTTATGCAGCCTAAATGCATTGTAAAATGTCAGA R 2 1 2 1 101000 r 74 goat snp16241-scaffold1708-198569 26 45172071 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407713 Affx-122955012 AX-123278064 26 5427435 TTTCTTTTCCTTGATATCTCTATTTGTCCCATTTC[A/G]TGGATCTTTACTGGCTCTCCCTCCTTTCCTACTTG R 2 1 2 1 101000 r 74 goat snp16239-scaffold1708-115686 26 45089276 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424648 Affx-122942164 AX-123294994 26 5473530 AAACAAATAGCTCTATCATGGACAAAATTGTGGAA[G/T]AAACTAATTGAAGAATTATTATGAGCTGGTGAATA K 2 1 2 1 101000 f 74 goat snp16238-scaffold1708-69591 26 45042425 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411026 Affx-122951973 AX-123281376 26 5507437 AGTGGCCGCTAACACAAAAAATGACAAAATTGAAC[A/G]TCATGATCCTCTCAGTAAAATACACAAAACACTTG R 2 1 2 1 201000 r 74 goat snp16237-scaffold1708-35684 26 45008492 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791491 Affx-122950143 AX-385278482 26 5540493 TCTCCATGTATAACAAAAATGGCTGGCATAAACAC[A/G]TTGACCTTGGCATGACACTCCATGTAGGCGGTTTG R 2 1 2 1 201000 r 74 goat snp16236-scaffold1708-2628 26 44975666 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411106 Affx-122951914 AX-123281456 26 5546600 TCTAGGGGTGCAAAAAAAATACCACAGACTGGATA[A/G]TTTAATCAAGAAAAAATTTTCACATCTAGAGGCTC R 2 1 2 1 201000 r 74 goat snp55172-scaffold847-2536546 26 44967715 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782908 Affx-122961868 AX-385269978 26 5576704 ACCACACCCAGAACATTAGCAAGCCTTTGTTATAA[G/T]AAATGCTCCTACTTGACTTTAGAAACTGTGTAATC K 2 1 2 1 101000 r 74 goat snp55171-scaffold847-2506442 26 44937573 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792384 Affx-122952861 AX-385279365 26 5611227 CTTTAGCTTATATCGCAGATACAACTTTTACATTT[A/G]TTTGTAACTCTTCCTTCCACCTTTCCAAAAGGACG R 2 1 2 1 101000 r 74 goat snp55170-scaffold847-2471919 26 44903061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422683 Affx-122943666 AX-123293029 26 5655406 ATTTTAAAAGATAAGAAATTTAAATAATCCTATTT[A/G]CCATACATGTTACATACAGAGGGCTAATTTCTATA R 2 1 2 1 202000 f 74 goat snp55169-scaffold847-2427740 26 44858581 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800124 Affx-122960641 AX-385287047 26 5687339 GTAGATAGCAGATAAGTGACTTTAAATAGAAGGCT[C/T]AGAACTCTAGATTCATATTTTTTTGACTTTCTAGA Y 2 1 2 1 101000 f 74 goat snp55168-scaffold847-2395807 26 44826267 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435475 Affx-122933448 AX-123305815 26 5750592 CTGCTAAAAATCCCAATATTTTACTTTTGAAACAT[A/G]TCTGACACCTTAGTAGGGATTGTGAGCTCTTTATT R 2 1 2 1 101000 r 74 goat snp55167-scaffold847-2332554 26 44764132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440002 Affx-122929788 AX-123310339 26 5792342 AATTTTTAGTTCTGGAAATCTAATCAGTTTGTATT[A/G]GGAATGTTTTGACACAATGAGATAGTGGAAGTGGA R 2 1 2 1 101000 r 74 goat snp55166-scaffold847-2290804 26 44721086 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392682 Affx-122966420 AX-123263039 26 5831117 TGAAAGCAGTCTCCCACACCCTTCTTGCTCTCCTT[C/T]TCCCTTCCTCTCCACATTGCTTCCAGAGCATGTAG Y 2 1 2 1 101000 r 74 goat snp55165-scaffold847-2252029 26 44681671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785700 Affx-122950322 AX-385272741 26 5872339 TATCTGCATGTAATAGAGATATTCATTTGACACTT[A/G]TCTGGGCCATTACTATTGAAATCATCAAGTTCATA R 2 1 2 1 101000 f 74 goat snp55164-scaffold847-2210807 26 44641785 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441765 Affx-122929110 AX-123312102 26 5905044 TTCCAATTCTGTTATTAATTTATCATTTCCCCATA[C/T]TGAAATCTATGTATTGTCAAATGCCAAATACATTT Y 2 1 2 1 101000 r 74 goat snp55163-scaffold847-2178102 26 44609097 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785601 Affx-122971739 AX-385272645 26 5943556 GCCATTTAGTGATAGAGCCAACCACTCTCAGCCTG[C/T]GATTCTAAATAGCAGCAGAAAGAGATTCTCCTGTC Y 2 1 2 1 101000 r 74 goat snp55162-scaffold847-2139590 26 44569839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411353 Affx-122952256 AX-123281703 26 6012803 TTGGATGCTATGACGGTGGGAAAAAAAGTACAGAG[C/T]ACAGTCATTTTTTAAAACAACACAGCATCTTAAAC Y 2 1 2 1 101000 f 74 goat snp55161-scaffold847-2070343 26 44499732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771422 Affx-122933231 AX-385258580 26 6048524 GGTCAGTTTGAGGTCAGTATCTCAAGCTGTGAAGC[A/G]ATGTCTGGCAATAAGGGAATACTGGAAAATGATGG R 2 1 2 1 101000 f 74 goat snp55160-scaffold847-2034622 26 44463526 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277656 Affx-1111836020 AX-519551155 26 6053017 AGTTTCCTAATTTTCACCATGATACTTAATGTACG[A/G]TACTTAATGATACTTATGTACAAATAATACTTAAT R 2 1 2 1 101000 f 74 goat Random2.2K-2171 26 6053017 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320764660 Affx-122977131 AX-385252296 26 6080084 TCAGGGACTCCAGAGCGGGAAGAAAAAAATAAGCT[A/G]TTTGCCTTCTTTCAGGACTATTAGATGTCTTGTAA R 2 1 2 1 101000 f 74 goat snp55159-scaffold847-2003062 26 44433255 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769164 Affx-122953311 AX-385256339 26 6112066 AGAAAGGGTTAAGCTCCTTTAGGTAGAAGCATGGT[A/G]TCTAATTTATAAAAGATCAACTGTTATTCTATATA R 2 1 2 1 101000 f 74 goat snp55158-scaffold847-1971080 26 44402098 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451640 Affx-122921609 AX-123321973 26 6169122 AGTCAAGCAGGAGTCAAGGAAGGCGCCCATATCAG[A/G]ACTTAGGATGTCAGAAGAGATGCAAAAAGATGACA R 2 1 2 1 201000 r 74 goat snp55157-scaffold847-1914024 26 44343939 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384748 Affx-122972036 AX-123255106 26 6268028 TTTTGTAAATTATGTTTTTCTTTACTATGTGTGAT[A/G]CATTTGATATTGTCTATTCCATTAAAACAAAGCTG R 2 1 2 1 101000 r 74 goat snp55154-scaffold847-1815118 26 44236854 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432151 Affx-122936423 AX-123302492 26 6358577 AGTTTGCAGAATCACAGTTACAAAACAGGGGTTTC[A/G]GCCATGAAGTGACAGAGACACAGGTAATGTCTAGT R 2 1 2 1 101000 f 74 goat snp55153-scaffold847-1724569 26 44146394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422367 Affx-122943428 AX-123292713 26 6387411 ATCTGATCCCTATAACTGTCCTAGGAAGCATTTGT[A/G]CATCCATATTTTCATAACTTTATTCAACACATGTT R 2 1 2 1 101000 f 74 goat snp55152-scaffold847-1695735 26 44117746 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399027 Affx-122960924 AX-123269382 26 6444839 TCACTTTATCTTTGGAGATAAGGATTTCCCTTTAC[G/T]CCAGATACAAGGAGGCACCTTCACATGAGAGTTTT K 2 1 2 1 101000 r 74 goat snp55151-scaffold847-1638307 26 44060546 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425002 Affx-122941895 AX-123295348 26 6477490 CTTTTGAATATGGTAGTTAAAGCGATTAAATAGCA[C/T]GCTTTATGGGGCATTGAGGAATACGAGTGGAAATA Y 2 1 2 1 201000 f 74 goat snp55150-scaffold847-1605656 26 44027816 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787016 Affx-122936392 AX-385274044 26 6511732 AAGTTTTATTCTATTTAGTCAATAATCCTTTTATC[A/G]TCTTTTCCCTCTGTGTGTTACTTCTAGCATCTTCC R 2 1 2 1 101000 r 74 goat snp55149-scaffold847-1571414 26 43993958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437549 Affx-122931900 AX-123307887 26 6555090 TTTCTTTCTTTCACATTAGTTTTCTTATGTACAGA[A/G]TCTTAAAATCAGAATGGTATTTAGGCATCATCAAA R 2 1 2 1 101000 r 74 goat snp55148-scaffold847-1528056 26 43950523 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436864 Affx-122932197 AX-123307202 26 6621953 ATGGCAGGTAAGAGGACTCACAGAGTAACTGAAGA[C/T]GAGCTGGAAAGGGCACTGCTTGCTTGGGGTAGCAG Y 2 1 2 1 101000 f 74 goat snp55146-scaffold847-1461193 26 43885157 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799415 Affx-122940051 AX-385286345 26 6657044 ATGGATGCTTTAAAACCAATTAAGCATTCATCCTA[C/T]GTCAAATAGTTTGCAGCTAGCAGTCAGGATTTGAA Y 2 1 2 1 101000 r 74 goat snp55145-scaffold847-1426102 26 43849934 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801094 Affx-122941165 AX-385288008 26 6715060 CGCTGTTCTAAGCATTGTACATGTATTAGTTCACC[A/G]TTAATGCTAACAGCAACCCTGTGACTAAGCACGGC R 2 1 2 1 101000 f 74 goat snp55144-scaffold847-1368086 26 43792712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444083 Affx-122926841 AX-123314420 26 6802129 AGAAGCCCATGTGATTTATGGGAACCTGGGTGGAG[C/T]GTATACAGGGAATCTTTGTGCTAACTTTGCAACTT Y 2 1 2 1 101000 f 74 goat snp55142-scaffold847-1281017 26 43705785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431488 Affx-122936250 AX-123301829 26 6874108 GCGGTCACACATCTGGATTGCTAAACTATACCTCT[A/G]TCTTGGCAGTCCCCACTAAGACACTGAATGAACTA R 2 1 2 1 101000 f 74 goat snp55140-scaffold847-1209038 26 43632513 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451894 Affx-122921042 AX-123322227 26 6928672 TTAAAATCCCATAGAATATATGCTTCCATGTTCCC[A/G]TTTCCCTGCTCTGTCATGTCCTCTGGATTCCAGAA R 2 1 2 1 101000 r 74 goat snp55139-scaffold847-1154474 26 22324546 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447665 Affx-122923958 AX-123318001 26 6959559 CTTAGCAATACCCAGCACAGGGGAGGGAGGTCGGA[A/G]GGGGTTTCAGGATGGGGAACACATGTACACCTGTG R 2 1 2 1 103000 f 74 goat snp55138-scaffold847-1123587 26 43558360 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375873 Affx-122978507 AX-123246232 26 7005877 GAAAAATAATTCAGGTCTTTTCAACTCTGTATAAA[C/T]AGCCCAGAAAAGACAAGATGTGACTAAACCTTCCA Y 2 1 2 1 102000 r 74 goat snp55137-scaffold847-1077269 26 43512353 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410227 Affx-122952554 AX-123280577 26 7043966 TGTCTTCACAGAGAAGATGAGGCTGATATCTCTTC[A/G]TCAAACATCATGTGCAGAAAGAGGATAAAGCACAA R 2 1 2 1 101000 r 74 goat snp55136-scaffold847-1039180 26 43473083 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799423 Affx-122938804 AX-385286353 26 7096817 CATAAATTGCTACCTTTAACAAAGAGTGATATTAA[C/T]GTATTTATTAACAGTGACAGTTGAGCATCTACTAT Y 2 1 2 1 101000 r 74 goat snp55135-scaffold847-986329 26 43419379 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796854 Affx-122970984 AX-385283797 26 7158361 GATATGGCTATGGCAGGAGTTGTGAGTCTTCTGTA[C/T]GAAATGTTGGATTGCAAATTAGATATTTAAAAGTT Y 2 1 2 1 101000 f 74 goat snp55134-scaffold847-924785 26 43357858 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406162 Affx-122956168 AX-123276514 26 7204509 TTTTTAAGTGTGAATATTGAAATATATTTCAGTTA[C/T]GGAGTTAGTGGCAAAAACAGGGATCTAAGATAGTT Y 2 1 2 1 101000 r 74 goat snp55133-scaffold847-878637 26 43313101 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274494 Affx-1111834325 AX-519548085 26 7245440 GGAAGGGAAATAGTCCACTCCAGTCCACTTGAGCC[A/G]TCCTGTCCCACCTGAAGGAGGAGGAACAGATAAAC R 2 1 2 1 202000 f 74 goat GoatD01.030086 26 7245440 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443863 Affx-122927515 AX-123314200 26 7291112 GCCTGAGAATATAAATGACCAACTTCCTTGCTCTC[C/T]TGGGCCACATTTCCAAGCTTCCACTACTTTTATTT Y 2 1 2 1 101000 f 74 goat snp55131-scaffold847-792034 26 43226281 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446719 Affx-122924723 AX-123317055 26 7324080 TTATTTCTTTTATGTACCGAGGGGAGTAAATCAAA[C/T]GTAAAATAGAGCCACAGATAATTTTTGGAAAAGAA Y 2 1 2 1 101000 f 74 goat snp55130-scaffold847-759066 26 43193337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451599 Affx-122921640 AX-123321932 26 7408431 GACGATAACCATTGCTTTCAGTGGTGCCCTGACTC[A/G]CTGTTCTAGTAGGATTAGATTGCTGGGAGCAGGGA R 2 1 2 1 101000 f 74 goat snp55128-scaffold847-674715 26 43109223 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769974 Affx-122923897 AX-385257141 26 7441904 CAATTTTTCATGTAACAATTTTACTTTTGACTCAA[C/T]AGGATTATGTTCAGAGAAAAATGAAGCTGTCCTTG Y 2 1 2 1 101000 r 74 goat snp55127-scaffold847-641242 26 43075262 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453795 Affx-122919577 AX-123324128 26 7470934 ATGTGCTCATTAACAAAGAAAATTGGAAACTGGGC[A/G]CCACTTTTCCATCAGAGCTTTGCTTTCTGAAGCAT R 2 1 2 1 101000 f 74 goat snp55126-scaffold847-612212 26 43046086 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425609 Affx-122940915 AX-123295955 26 7531020 GCATCCATTTAACTACTGTTTTCCTCTCCTTTCTC[G/T]TACTGCCTTCCACTCTTTAATCCTGTACTTTAATC K 2 1 2 1 201000 r 74 goat snp55124-scaffold847-552126 26 42987767 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774501 Affx-122925623 AX-385261636 26 7563023 TTTTAAGCCCTTTCATGAAGGAACCGCAGAGTCTT[G/T]AAGAAATTTTATATACCGTCTTCTTCACCTTGGTT K 2 1 2 1 202000 r 74 goat snp55123-scaffold847-520123 26 42955867 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393569 Affx-122965397 AX-123263925 26 7602557 CAGGTGGGTTAGAGAGTCCATGGCTGAACGTAAGA[G/T]GATATAACTGTCTCTGAATGCTGGATGGTGGGCTA K 2 1 2 1 101000 f 74 goat snp55122-scaffold847-480589 26 42916653 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386232 Affx-122970975 AX-123256590 26 7635831 TTCACAACATTCAGCTAACGCCAAAGAAATACATC[A/G]TCAGTAGAACCTGGAAGGACTTAGCTTTGGGGTTG R 2 1 2 1 101000 f 74 goat snp55121-scaffold847-447315 26 42883498 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382025 Affx-122974956 AX-123252383 26 7691719 CTGAATTAGGCGTAGCATCCTCTTTCATACCCCTG[C/T]GCACTTGTTCTGCTGTTCTTTCTCCCTGGAGTGCC Y 2 1 2 1 201000 r 74 goat snp55120-scaffold847-391427 26 42826442 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273117 Affx-1111833319 AX-519546782 26 7719611 TCTCCTTCCTCTTGAAATGCTATTTGCTTAAAAAA[A/C]AAAACAAAACAAAAAAAACAGCAGATCCCTTTAGC M 2 1 2 1 303000 f 74 goat 26_7719611_AF-PAKI 26 7719611 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38447545 Affx-122924044 AX-123317881 26 7757890 TTTTCACCACTTAGTACCTGCAAGATTTAAAATGG[C/T]GGCAGGGGCTGGGGGGTTGCTACTTGTCGAGTTTA Y 2 1 2 1 101000 f 74 goat snp55118-scaffold847-325256 26 42761017 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394541 Affx-122964469 AX-123264896 26 7803483 CAGTTGGTTATTTCAAGTATTTTGGTAAGGCACTT[A/G]TAATCTAGTAATGTGGTCTAGTATTGTCCCTCTCT R 2 1 2 1 101000 r 74 goat snp55117-scaffold847-279663 26 42715554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407060 Affx-122954922 AX-123277411 26 7839940 GTTATTTTATGGTAAGAATGTAGTTTTCAGAAATA[C/T]TTTGAAGTGCCATTTTGGGCATTTTAGGGGAAAAT Y 2 1 2 1 201000 f 74 goat snp55116-scaffold847-243206 26 42679009 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453722 Affx-122919629 AX-123324055 26 7880384 AAGCATACTTCTATTTGTTTCTCAGGATAACATGG[C/T]CAGTTCTTTGGGGGCATTTGGGTTCCAAAAGCTGT Y 2 1 2 1 201000 f 74 goat snp55115-scaffold847-202762 26 42638095 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428833 Affx-122938370 AX-123299175 26 7918583 GAGACATAAGCTAGGATTCATTCAGTTGCTTCTGT[G/T]GCCTCTCAGTTTTCTTTTGTATTTATTTTTGAAAC K 2 1 2 1 101000 f 74 goat snp55114-scaffold847-164563 26 42599459 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437804 Affx-122931680 AX-123308142 26 7948929 CCTTCCAATTCTTTGCATACCATATTTGATGACAA[C/T]GCCTTTATTATTAGAGTCATCTTTGAAGCATCCAG Y 2 1 2 1 101000 f 74 goat snp55113-scaffold847-134217 26 42568897 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453545 Affx-122919786 AX-123323878 26 7996512 TAACGGGAGTTCTCTGAAAGCACTGAGGAAGGAAA[C/T]GAGCATTAATTTATGGTTCATTCTGTGCCATTCAC Y 2 1 2 1 101000 f 74 goat snp55112-scaffold847-86634 26 42521322 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786110 Affx-122951339 AX-385273146 26 8029657 AGAAAAAAGTTTATTCTCTTTCACAGTTGGCATTA[C/T]ATTGCAATAACTAACCCCCCTTCCAAAAATATGCA Y 2 1 2 1 101000 f 74 goat snp55111-scaffold847-53489 26 42488237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782261 Affx-122956365 AX-385269339 26 8063219 AAAATAATGTTATTGTTCACTGTATGATGGGTACT[G/T]CCCTGAGTTCTTTTGTTGATTACTCTGTTTAATAG K 2 1 2 1 101000 r 74 goat snp55110-scaffold847-19927 26 42454555 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277785 Affx-1111836021 AX-519551284 26 8095979 TATATAATGTTTGATACTTTGGTGATATTGAGATG[A/G]GGTAAACATGTTTTGCATGCGAGATTAACGTGAAT R 2 1 2 1 101000 r 74 goat Random2.2K-2172 26 8095979 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418406 Affx-122946546 AX-123288754 26 8104294 CATATCCTGCAGGTCAGCTGAAAAAACAGGCAGGC[A/G]TGTTTTGCTAACTTATCTCATGAAAATCTTGAAGA R 2 1 2 1 201000 r 74 goat snp42284-scaffold556-1104447 26 42413773 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375577 Affx-122978742 AX-123245936 26 8138786 AAAAGAGCAGCTAGACAAGTCTGATGACTTTGTTT[A/C]GTTTCTTCAGGATTGGAGAATTTGCATTTTGAGCA M 2 1 2 1 202000 r 74 goat snp42283-scaffold556-1069955 26 42378812 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766651 Affx-122944029 AX-385253999 26 8193989 ATGTATGATGACTATCACTCTCCTGGGCTTAGTTC[A/G]CTGTGATAAGAAATTGATATCTATCTAGTATTGCC R 2 1 2 1 101000 f 74 goat snp42282-scaffold556-1014752 26 42324327 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452627 Affx-122920357 AX-123322960 26 8224135 TTGGCACACAGATACGTATAGAAGATGGTCATATG[C/T]GAGCCAGTGAGAAAGGCCTGGAACAGATCCTTCTC Y 2 1 2 1 201000 f 74 goat snp42281-scaffold556-984606 26 42293902 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770545 Affx-122921538 AX-385257709 26 8253991 TGAGCCTGGAGATATAAACTGATTTGTCCTGGAAA[C/T]GGTCACGTACAAAGCTCTGCTTAGACTTTTGTCTT Y 2 1 2 1 101000 f 74 goat snp42280-scaffold556-954750 26 42263563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786666 Affx-122955673 AX-385273698 26 8298145 ATATTTTGATTCAATAGGTCTAAGCGTTTTCCAAC[C/T]AGCTTCTAGGTACTGCTGCTGATCTGCAAGCCACA Y 2 1 2 1 101000 r 74 goat snp42279-scaffold556-910596 26 42218759 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378533 Affx-122976624 AX-123248892 26 8347596 TGGAGATTTGAGTGAAAATAAAATAAAAGGAATAC[A/G]TATCATAGCGTGAAGTGTAAAGGACTTATTAAACC R 2 1 2 1 101000 r 74 goat snp42278-scaffold556-861145 26 42168019 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393141 Affx-122965550 AX-123263498 26 8410125 TATGGTTTGGCTACATTGTTTTCACCAATATGCTC[A/G]CTATTTGATTGAACTAAGATAAATGTCCAAACTTC R 2 1 2 1 101000 r 74 goat snp42277-scaffold556-798616 26 42105031 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274113 Affx-1111834014 AX-519547716 26 8412278 A[A/G]CAAAGCCTTGTCCCAGGCTGATTCCAGGCAGAACC R 2 1 2 1 102000 r 74 goat GoatD01.013788 26 8412278 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320787891 Affx-122939263 AX-385274913 26 8451290 AAATAGTACAGTCACGTCTCAAAAGTCAAAATACG[C/T]ATATTAAATGATAAACAGGGAAAAGTCTCATTTCT Y 2 1 2 1 101000 f 74 goat snp42276-scaffold556-757451 26 42063807 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424049 Affx-122942070 AX-123294395 26 8481323 TCCCCACCCCCCCAAATCACATAGTACTCAGCACA[C/T]GCCTTGTGGAGAGAGTATAATAGCGTTATTTGAAA Y 2 1 2 1 201000 r 74 goat snp42275-scaffold556-727418 26 42033747 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787212 Affx-122957944 AX-385274238 26 8514718 ATGATGCTGGACATGGTTAGAGGCCACATCTCCTA[C/T]AGAGGTCAAAATTTTATTAACGAATCTATTTGTGG Y 2 1 2 1 101000 f 74 goat snp42274-scaffold556-694023 26 42000001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386605 Affx-122970244 AX-123256963 26 8608587 AATCTAATAGCTGCTAGCAATGAATGAGTAGTTAA[C/T]GTGTAATTACAAGAATCAAAATTACTGACACATTT Y 2 1 2 1 101000 f 74 goat snp42272-scaffold556-600154 26 41905654 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453215 Affx-122920437 AX-123323548 26 8685509 GCTTTCTCATCACTTAGAATTTTTATTTTATACTT[A/G]CTGAAAAAGGTCCTCTAGATTTGTTGGGACATATA R 2 1 2 1 101000 r 74 goat snp42270-scaffold556-523232 26 41827376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438851 Affx-122930765 AX-123309188 26 8731775 GGACTGTTCTCAGGCAGAAAAGCAAAATCCAAAGT[A/G]TGAGTGTTGATCCTCATTCATCCAACACAAACTTA R 2 1 2 1 101000 r 74 goat snp42269-scaffold556-476966 26 41780999 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411988 Affx-122951768 AX-123282338 26 8764473 TGCTAGATTGTGTCATTAACCCCAATTCCTCACCC[A/G]TCACTGTATCCATATGCCTTTTGTCACGTCTTCCC R 2 1 2 1 101000 r 74 goat snp42268-scaffold556-444268 26 41750380 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448273 Affx-122924184 AX-123318609 26 8816020 CTCTTGCTGCCCTTGAAGCTGGTTTCCTGGAGCAG[C/T]GAAGATTCCTGGGATTCTGCAAGCAAGCTCGAGTT Y 2 1 2 1 201000 f 74 goat snp42267-scaffold556-392721 26 41698785 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418786 Affx-122946183 AX-123289134 26 8879679 ATCTACCAAAGACTTTCTGATGGAGAGCAGCTAAC[A/G]TAGAGGGGGGTGGTGTGGGCAGAGAGGATCTATAA R 2 1 2 1 101000 f 74 goat snp42266-scaffold556-329062 26 41634968 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796924 Affx-122949526 AX-385283866 26 8950986 AAGAGTAAAAGGCAGAGCTGTCTACTAGGTAGTTA[C/T]AGAACTTTCCAATCCATTCCTTGGGACTCCTTGGA Y 2 1 2 1 101000 r 74 goat snp42265-scaffold556-257755 26 41562450 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379856 Affx-122975800 AX-123250214 26 8980306 TAAGTATGCAGATTCATTTCCTGTCTCTGGCCTTC[A/G]TTTTAAAAAGCTCAACTCCTGGTAAATTCTGTGAC R 2 1 2 1 202000 r 74 goat snp42264-scaffold556-228435 26 41532986 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440879 Affx-122929237 AX-123311216 26 9016950 GCTGCTGTTCTTAATATTATCAGCTTTCAGCGTCA[G/T]CCCTGGGATTTCTTTGGAAGGAATGATGCTAAAGC K 2 1 2 1 201000 f 74 goat snp42263-scaffold556-191791 26 41495936 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800487 Affx-122936736 AX-385287407 26 9074499 TGAACCACTATAATCTTCTCTTCCAATTACCTAAG[A/C]GATGATCCCCTTCAAGGTCTAAGGTCTTGAAGGGC M 2 1 2 1 201000 r 74 goat snp42262-scaffold556-134242 26 41438021 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786192 Affx-122936743 AX-385273227 26 9106530 AATTATTTAAATATAAGCATAATCCATAAAAAGAA[C/T]GAATTAGTGAATAGGACTTGAGCTCAGCAAATGAC Y 2 1 2 1 303000 f 74 goat snp42261-scaffold556-102211 26 41406417 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397632 Affx-122962623 AX-123267987 26 9152988 AAAAACAATATGGCCAGTTGGTCAAGACAAACCCT[A/G]CCTCCTAGAAGTCAGAGACTCCATTTTGCTTTTGA R 2 1 2 1 201000 f 74 goat snp42260-scaffold556-55753 26 41359508 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794106 Affx-122960354 AX-385281073 26 9197779 TTTTCAGCTGTTTAATGGAGACTCTGATACTTTCT[A/G]TCCAAAGCTGTTGTTAGTATTAAAAGAAATAAAGC R 2 1 2 1 101000 f 74 goat snp42259-scaffold556-10962 26 41314207 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412117 Affx-122951106 AX-123282467 26 9225892 TCCCAATTAATTATCATACACATATATCTAATGAG[C/T]GCTCTCTGTATTCCAGGAATTGCCCCAGATTCTGA Y 2 1 2 1 201000 f 74 goat snp13746-scaffold1532-175960 26 41286410 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801058 Affx-122948269 AX-385287972 26 9258763 ACATTGCTTATAATGGCTTAACTGGTAAGTAAGAC[A/G]CGAGCACTCTCTTTAAGGTGACCCTGTTGTCATTT R 2 1 2 1 101000 r 74 goat snp13745-scaffold1532-143089 26 41254418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437375 Affx-122932447 AX-123307713 26 9292520 TCTAATTGCAAAGACTAATAAAGATAACTATAGCT[A/G]TAGCTAGTCTCTATTCTTTACAGAGATTAAGAAAA R 2 1 2 1 101000 f 74 goat snp13744-scaffold1532-109332 26 41220609 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386399 Affx-122970828 AX-123256757 26 9341053 GATTGAGAACCATAATCATTGACTGGCTTGATATC[A/G]TAAGGCCAAATGAGTCTTCCCCTTCAACTGAAAAT R 2 1 2 1 101000 r 74 goat snp13743-scaffold1532-60799 26 41173886 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382177 Affx-122974021 AX-123252535 26 9391569 AAGGTGGATCAAGGATTTTTTTCCCTGTGAGTAAC[C/T]TAATCTCATGTTCTAGAATTAGAATATATTTGAAT Y 2 1 2 1 103000 f 74 goat snp13742-scaffold1532-10283 NW_017190560.1 9952 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409465 Affx-122954071 AX-123279816 26 9418098 CCAAGTTTGTTTAATATTCCACAGCACCAATTCCA[C/T]GCTTCAGATCAAGTCCTAACACAAAAAAGTCTTTC Y 2 1 2 1 101000 f 74 goat snp18935-scaffold1908-15787 26 40987899 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408197 Affx-122954189 AX-123278548 26 9454847 CTGTTGGTGGTGGCATTATTATCTCTACCATATTA[C/T]AGTGTTTCACCAGAATTTGGCTATATTAATCAATA Y 2 1 2 1 101000 f 74 goat snp18936-scaffold1908-52536 26 40951172 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803657 Affx-986696449 AX-385290434 26 9498121 CGGAGGCCTGGGGCTATATACACACAGCAGCTGAC[A/G]CCTGACCTCCTCCTCCCCTGGAGCCCAGCCCCGCA R 2 1 2 1 600010 f 74 goat 26_9498121 26 9498121 Ancestral_priority_1043 ancestry 0.506 neutral IMAGE 10K 10K ancestral 320801692 Affx-122965486 AX-385288600 26 9505561 TAAACTGATCAACCATTATGCCTTCATTATCAAAG[C/T]AGAATTTATACTATTGCATTAATACCGTTAACATT Y 2 1 2 1 101000 f 74 goat snp18937-scaffold1908-103250 26 40900721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389423 Affx-122968365 AX-123259781 26 9544999 TTTTTGCTGCTGCCAGATATGATGATCAAGGTATG[C/T]GACTCCTCAGAAAATTCCTTGCCTAGGCACAAGAG Y 2 1 2 1 101000 f 74 goat snp18938-scaffold1908-142688 26 40860700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768036 Affx-122954760 AX-385255249 26 9594054 AAAGAGACTCCCTCATTCCTCCATGTTTGCTGATC[A/G]TATCAGCGTAAGCCCAGGACGGCCTTTCATTCTAG R 2 1 2 1 102000 f 74 goat snp18939-scaffold1908-191743 26 40811982 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420381 Affx-122944940 AX-123290728 26 9637959 GGTCCCAGGATTGATCTGGATTTTAAAACTGTACC[A/G]TGACTGGTGCTTCCTGCAGGTCATTTCTTTCTTGG R 2 1 2 1 101000 f 74 goat snp18940-scaffold1908-235648 26 40767972 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401155 Affx-122959369 AX-123271508 26 9671827 TTTTTTGTAGCAGATGCAAAGTTGAAAGCAGTGGT[A/C]GAGGGGAGCAGAGAGAAGTGATTCAATGACAGGAC M 2 1 2 1 201000 f 74 goat snp18941-scaffold1908-269516 26 40733750 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395969 Affx-122963558 AX-123266324 26 9700713 GCATCAACAGCAACAAACATTCATTAAGCTATTTG[C/T]ATATATCAAGCATCAATTGTACTATTAATATATCC Y 2 1 2 1 101000 f 74 goat snp18942-scaffold1908-298402 26 40704992 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781275 Affx-122951604 AX-385268360 26 9739180 TCAGAAAGTTCCTGCTAACTTCCTCTACCCTCAAC[A/G]CACATTTGCTTTGAAGGTTCATCGTAAAATTAACA R 2 1 2 1 101000 f 74 goat snp18943-scaffold1908-336869 26 40666645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794014 Affx-122952618 AX-385280983 26 9779117 ATTGGAGTAGTAGGTCAAGGACTCAATCTGAAATC[A/C]GATAAATCCAAGTTCAGATTCTAGTTCTGCCGCTA M 2 1 2 1 201000 r 74 goat snp18944-scaffold1908-376806 26 40626640 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397544 Affx-122962031 AX-123267899 26 9820765 GGCACATAAACTTGCACAAGTCATCTGTAAAAGGC[A/G]TGAATGAAATTTGTCCCACATTACTATAGTCCCAG R 2 1 2 1 101000 r 74 goat snp18945-scaffold1908-418454 26 40585312 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428975 Affx-122938867 AX-123299317 26 9960861 CTTTATTTCCCACAAAGAAATTCTAGAAATTCCCT[A/C]GTCCACTGGTTTTTCACTGTGTTCCTTAGAGACCT M 2 1 2 1 101000 r 74 goat snp39724-scaffold508-69830 26 40439909 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398744 Affx-122961820 AX-123269099 26 9997053 GTTCATATTCACATTTCTTTTGTGTGAAAATGAAG[C/T]AGGGCGCTCCACCTGAGTGGCGTCAGGGCTACTGC Y 2 1 2 1 101000 f 74 goat snp39725-scaffold508-106022 26 40403278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274270 Affx-1111834103 AX-519547866 26 10017187 GAGTAGCTCTTTTTATCTTCCTCTACCTGAATTCA[A/G]TGTGTTGGTTAATGTCCTTTCATTGTTTCTGACTG R 2 1 2 1 101000 r 74 goat GoatD01.018440 26 10017187 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38400816 Affx-122959806 AX-123271171 26 10036024 AGCAAAGGCTTTGCGGATGGATATTAAAGGGAAAA[G/T]GAAGTGACTCTTCCAAGGACACGCCGATGATTAGA K 2 1 2 1 101000 f 74 goat snp39726-scaffold508-144993 26 40364644 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764109 Affx-986698636 AX-385251863 26 10079961 TACACTGATGGGACTGTCATTGCCCTGGAGCCACC[C/T]TTCCCCATCAGGCATGGGGACATGACTCAGGCTGT Y 2 1 2 1 600010 f 74 goat 26_10079961 26 10079961 Ancestral_priority_1043 ancestry 0.504 neutral IMAGE 10K 10K ancestral 320800251 Affx-122919813 AX-385287174 26 10092158 ATCTCAGGACTCCCAACCCAGTATACTCTGCTCTA[A/C]ATCATACTTCCCAGGGAGATCAGGTATCAAATATC M 2 1 2 1 101000 f 74 goat snp39727-scaffold508-201127 26 40309247 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392404 Affx-122966212 AX-123262761 26 10137643 CATTTCTGGCCTTTGGTTAGCTGTTTTAGTATTCT[A/C]GAGTTACTTCTGTGAAGCTTTTCCTTTTGTCTGAA M 2 1 2 1 101000 f 74 goat snp39728-scaffold508-246612 26 40262460 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386706 Affx-122970165 AX-123257064 26 10170845 TTCAGAACTTTCCTCTCATCAAATTATATATAAAA[C/T]AAATAAACTATTGATGAAATGCTTAAAGGAATGAT Y 2 1 2 1 101000 f 74 goat snp39729-scaffold508-279814 26 40229149 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404653 Affx-122957303 AX-123275005 26 10205010 GGTGTAGCAAAAAAAGACAAATCAACATTTTAATT[C/T]CATAGGTGAACATCATCATCACAACAGCAGACACT Y 2 1 2 1 101000 r 74 goat snp39730-scaffold508-313979 26 40194791 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406595 Affx-122956257 AX-123276947 26 10235364 GGCAAGGGAGAAGCAGAGGTGGGGTGGGGAAGTAG[C/T]AGGCCCTTTATGCCCTTCTGCAAAGTCTGAATGAT Y 2 1 2 1 101000 r 74 goat snp39731-scaffold508-344333 26 40167333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273131 Affx-1111833303 AX-519546795 26 10241791 TTCTTTTACTGCAATTTTGTAACCCAGGCCAATGT[A/G]TTTGAGTGGTTGTGGTAGTGACTTTGCTACTGCAG R 2 1 2 1 101000 r 74 goat 26_10241791_AF-PAKI 26 10241791 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446408 Affx-122925569 AX-123316744 26 10263916 ATTTTAATCCCCAGTTCCATGAAATGACCACTGGA[C/T]GCATTTGAAATGGCCCCGGAATTTGAAATCTCAGC Y 2 1 2 1 201000 r 74 goat snp39732-scaffold508-372885 26 40139123 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439091 Affx-122931122 AX-123309428 26 10341919 GGGTAGTGTTCTAGAGTGGAAGGAGCTTTGGAGTC[A/G]CCAGACCTGGATTCAGAGCCTCATTCTACTACTTG R 2 1 2 1 101000 f 74 goat snp20940-scaffold2052-291918 26 40060594 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429180 Affx-122937963 AX-123299522 26 10434125 TAAGTTTAGAGTTTTAAATTCACTTCACTTCTATG[C/T]ATATCTGCAATTTCATACTTAGATCGAACAATGTC Y 2 1 2 1 101000 r 74 goat snp20938-scaffold2052-199712 26 39967461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450967 Affx-122921745 AX-123321301 26 10496541 CCAATGTGCCTAATACATTGCCTTGCCTGTAGTAA[A/G]TGTTCAACAAACATCTGTGGAAAGGATAAATGAAG R 2 1 2 1 101000 f 74 goat snp20936-scaffold2052-137296 26 39906069 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406841 Affx-122955669 AX-123277192 26 10546219 GTATACACGCTGGCACAAACACAGCTGTATGGTCA[C/T]AGAGCACATCACAACAGCAACAGCAAACTGATAAA Y 2 1 2 1 101000 f 74 goat snp20935-scaffold2052-87618 26 39877859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379182 Affx-122976311 AX-123249541 26 10598387 TTCCCTCTCATGAATCCCTCCAGGAATTGCTTCCA[C/T]CCTCAGGAGTCTGGCAATTCTCGCTGTTGAAACAA Y 2 1 2 1 101000 f 74 goat snp20934-scaffold2052-35450 26 39826746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777128 Affx-122947092 AX-385264251 26 10628687 CAGGTATGGGAAAACAGGCAGGAAAATGACTTCCA[C/T]GAAGAAAGAAGTTGATACAGATCCTTAGAAACAGG Y 2 1 2 1 101000 f 74 goat snp20933-scaffold2052-5150 26 39796140 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379037 Affx-122976354 AX-123249396 26 10672892 TTTCTAGGTGATCTCATCAGCACTCATGCCTTTGG[C/T]GTCTTTCATGTAGGACAACCCACAATGGTTTGTTT Y 2 1 2 1 201000 r 74 goat snp34801-scaffold414-38956 26 39747185 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437036 Affx-122933111 AX-123307374 26 10715199 GATAATTTGGCTATATGCACTTTTTACCTTGTGCA[C/T]GGGCTTTGGAGCTAACCTCCATGGGAGAGGGGACC Y 2 1 2 1 201000 f 74 goat snp34802-scaffold414-81263 26 39702829 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446646 Affx-122924779 AX-123316982 26 10744031 TTAGTTTGAAATTGGGATAAGGACTGGCAGAGAGC[A/G]GGAGTATATTAAGGAGACCATTGGGGGAGATTATG R 2 1 2 1 101000 f 74 goat snp34803-scaffold414-110095 26 39673656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434955 Affx-122933851 AX-123305295 26 10780001 GGATCATGTACTGGTAAAAACTGCATCAAATTTTT[A/G]TAAAGCATCTACTGTGTACCAGGCACTGTGCTAGA R 2 1 2 1 303000 f 74 goat snp34804-scaffold414-146065 26 39642141 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376140 Affx-122978859 AX-123246499 26 10838487 ATGTTTCATCTGGCTAGACAGAGTAGGTTTACTGC[A/G]TCCTTCCCTCTACTTGCCCTGTGACTGCCAGAGAG R 2 1 2 1 101000 f 74 goat snp34805-scaffold414-204551 26 39585094 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794072 Affx-122928512 AX-385281040 26 10936452 ACGAAAAATGACTTTCAGCCTATTTCACCTTGCCT[C/T]AGTTCCCAGGCCCTAAAGGTTCAACCTTTTCCCTG Y 2 1 2 1 101000 f 74 goat snp34807-scaffold414-302516 26 39488847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444395 Affx-122926592 AX-123314732 26 10991493 CTAAATAGCCTGGGACCCCCATTTCTTCATTTCAA[G/T]AGCTGATCTCTAACATCTCAATTTGAAGAATCCGG K 2 1 2 1 201000 r 74 goat snp29891-scaffold3244-41688 26 39433076 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445921 Affx-122925929 AX-123316258 26 11037386 TGAATTGTAAGGAGACACAAACATTCAGGCTATGG[C/T]AATGATAGAAAATGTAGATAGGTATTATACCCATT Y 2 1 2 1 201000 r 74 goat snp6220-scaffold122-43889 NW_017214403.1 2314 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785984 Affx-122935084 AX-385273021 26 11071004 ATGCCTGAGTTTACTCAAGATTTATCAATATCAAT[A/G]TAAAAGTCCCCTCCACCTAATACTTGATACATTCA R 2 1 2 1 101000 r 74 goat snp6221-scaffold122-77507 26 39354384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443917 Affx-122927044 AX-123314254 26 11110755 TGGTTGCCCGGCAACTGCTTCATACGGGAGCTGCA[A/G]AGATTGATGACATATTAGATCCCAGCCTCGATAGT R 2 1 2 1 102000 r 74 goat snp6222-scaffold122-117258 26 39314173 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780536 Affx-122971013 AX-385267627 26 11142275 GGGGGCCATTATTCTGTCTAGAACAGACAGATTTG[C/T]CAATAAAGGCTTTATTCCAGAAACTATAAACCCCA Y 2 1 2 1 101000 f 74 goat snp6223-scaffold122-148778 26 39283383 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796950 Affx-122938379 AX-385283892 26 11188588 TACTTCATAATAGAGAGTTGCCTGGTATCTAATAG[C/T]AATTTGAAAGGGCCTTGAGACTTTCGCCAGCAAGG Y 2 1 2 1 101000 r 74 goat snp6224-scaffold122-195091 26 39238006 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800640 Affx-122931143 AX-385287559 26 11218053 TGTCTCTTTGCTCACAATTGCAAGAGACTTGTGTT[A/G]TTGTATGAAGTCACTAACAAACCTGAGCCAAAGAA R 2 1 2 1 101000 f 74 goat snp6225-scaffold122-224556 26 39214931 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418720 Affx-122946280 AX-123289068 26 11276729 CACAGTGAAAGATTAAAGAGGAGAAAGAACTGATA[G/T]CCTATGGGAAACACATTTTATGAAACATGTCTCAA K 2 1 2 1 201000 r 74 goat snp6226-scaffold122-283232 26 39150643 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765524 Affx-122959751 AX-385253008 26 11323579 TTGCATTGTCTTCCTTATAAGGAGTACATATGAGG[A/G]AGAAACGCTTCTTGTAGACTAGCCTTGCTCCAGCT R 2 1 2 1 201000 f 74 goat snp6227-scaffold122-330082 26 39103213 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440587 Affx-122929291 AX-123310924 26 11369090 TAGATTATTCTTTTATTTATTTGCACTGTGGCATT[A/G]CTTAAAAATCTCAGTTTACAAAAGTCCAGGGAATA R 2 1 2 1 101000 r 74 goat snp6228-scaffold122-375593 26 39057561 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781102 Affx-122947540 AX-385268187 26 11400192 AACAAATTAAAATGCTGAGAAAGCCATAAAGAGAT[A/C]TCCTGGATTTAAAAACCCTGGAGAATCTCAGAACC M 2 1 2 1 101000 r 74 goat snp6229-scaffold122-406695 26 39026577 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765325 Affx-122948965 AX-385252845 26 11441251 TTAGAATAAATACAACTCCAGGACTGCCTTCACTT[C/T]ACTTTACATGTTAACGGAATGAACAGAGACTGGCC Y 2 1 2 1 101000 f 74 goat snp6230-scaffold122-447754 26 38986108 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789224 Affx-122977693 AX-385276235 26 11487848 CTATCTTGTGATTCACTATGACAATTACATGAGAA[C/T]AGGCATGTAATTAAAGCTTTCACCCCACCTTCTAC Y 2 1 2 1 101000 r 74 goat snp6231-scaffold122-494351 26 38939639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419536 Affx-122945429 AX-123289884 26 11531263 TGAATATTCATTAATTTAATAATTAAACAAATACT[C/T]ACTGACTTTTTATCTTATGCCAGTGCACTGACAAA Y 2 1 2 1 101000 r 74 goat snp6232-scaffold122-537766 26 38895897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440883 Affx-122929234 AX-123311220 26 11562943 TTTCCAACATACTGAAAATAGACTTTTAGTTGTAT[C/T]GTTTGTGAATACTAGTTTCTGTTTAGGACCTGCTC Y 2 1 2 1 101000 r 74 goat snp6233-scaffold122-569446 26 38864008 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438239 Affx-122931432 AX-123308577 26 11651399 TTAGACATCATAATATTTAGAAAATTATTCTTTAG[A/C]TTCTTTCATTAAGGTCATTTACTTGCTCAAAGCTA M 2 1 2 1 101000 r 74 goat snp6235-scaffold122-657902 26 38775981 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782743 Affx-122961744 AX-385269815 26 11688633 TTCATTAAGGCTGAGCAGCTACTCTAACAGCTCTG[C/T]CTACTTCTAGCCTTTCTCTTAGAAAGATTAAACAA Y 2 1 2 1 101000 f 74 goat snp6236-scaffold122-695136 26 38738291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775819 Affx-122967469 AX-385262950 26 11732623 GAAGGAAAAGTAAAGTGTAATCATGAGTAACTGTT[C/T]CTCATCCTTTGTGAGAGGTAACAGAGAAGAGTCAA Y 2 1 2 1 101000 r 74 goat snp6237-scaffold122-739126 26 38693378 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397802 Affx-122962495 AX-123268157 26 11775864 AAGAGTTGAGCAGCTGGCATGGTTCAAGTCCTGTG[C/T]TGGGCACTCTGCGTGCGTGTGTGCTGAGTTGCTTC Y 2 1 2 1 101000 f 74 goat snp6238-scaffold122-782367 26 38650417 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411330 Affx-122952271 AX-123281680 26 11805464 AATGCACATCAACGCTATGAACTTAAGTTAACTTT[A/G]TTTTATTTTTTTAAATGTTTATTTTATTTATTGAT R 2 1 2 1 103000 f 74 goat snp6239-scaffold122-811967 26 38620490 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411546 Affx-122951650 AX-123281896 26 11854666 TCCTTCTGACCCTGAACTGACTGACTGGCAGTCGG[C/T]AGTCTAAACATCAGTAGGTGTCAGTGCTTTCTCAT Y 2 1 2 1 101000 r 74 goat snp6240-scaffold122-861169 26 38572217 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792902 Affx-122976226 AX-385279880 26 11898986 GCTTAAAAAAAAATCTTACTAAGTTAACTTTATAC[A/G]TAGTCTACAGTTTTATGATACTGTAAGTTAAGAAT R 2 1 2 1 101000 f 74 goat snp6241-scaffold122-905489 26 38527373 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404176 Affx-122957689 AX-123274528 26 11927614 TGGTAAAAATCACAGCCCATTATCGTACTGCAGCT[C/T]GTCAAGCACCAAAGGACAGAAGGGAGGTGGATCTC Y 2 1 2 1 101000 f 74 goat snp6242-scaffold122-934117 26 38498689 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401430 Affx-122958995 AX-123271783 26 11959063 CTTCCGCTCCCAGCTGATGTTCCTCCTGCAGATCC[A/G]TCACAGGGTCCCTGCAGGCCATGCAACAGTGACCC R 2 1 2 1 201000 r 74 goat snp6243-scaffold122-965566 26 38466767 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430863 Affx-122937419 AX-123301204 26 11989022 GATGATCAGTCGGCACATTTAACTTCTATGGCCAT[A/G]CAAAGACTTGCTCTCTGCTCCCTGACTCAGAACAC R 2 1 2 1 102000 r 74 goat snp6244-scaffold122-995525 26 38437284 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277787 Affx-1111836022 AX-519551286 26 12015331 CCCCTGTCTGTATTACTCTTCCCCTGTCAGTATTA[C/G]TCTTCCCTGTCTGTATCACTCTTCCCTGTCTGTAT S 4 1 2 1 202000 r 74 goat Random2.2K-2175 26 12015331 C G 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320780031 Affx-122936143 AX-385267130 26 12024997 GACTGAGCAGCTAAGCGTACACGCCTGCATTCTGC[A/G]TTTTGTCTCTGTTGCTGTTTCCCGCCTTCTTTGGG R 2 1 2 1 202000 f 74 goat snp6245-scaffold122-1031500 26 38401627 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764993 Affx-122930346 AX-385252570 26 12128786 ATTGCTTGCTATCACAGAGCAGGACAAAAGATTTG[A/C]GTGACTAGTGACATCCCAGAGTCAGTTTACACTGA M 2 1 2 1 101000 f 74 goat snp6247-scaffold122-1135289 26 38296616 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441137 Affx-122929579 AX-123311474 26 12158948 TGAGCAGTGGTGCCTTCGCCGGTTAACTATGAAAG[A/G]GGGGAAAAGATGGTTGTAGAGCAGCTCTGTGATAT R 2 1 2 1 201000 f 74 goat snp6248-scaffold122-1165451 26 38270677 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391751 Affx-122967478 AX-123262108 26 12194028 CAGCAATATAATGGAACAATTTCTCTGATGTTGGG[C/T]GCTTCTATTTTGCCCGGTCTTCCGCAACCAGCCCA Y 2 1 2 1 101000 f 74 goat snp6249-scaffold122-1200531 26 38234932 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436973 Affx-122933158 AX-123307311 26 12229665 CCTAATGACGTGTGTCCCACTCACCTCATGTAGTT[A/G]CTGGGAGACTCAGGCGAGTTGAGACGGTGCTTTGT R 2 1 2 1 101000 f 74 goat snp6250-scaffold122-1236168 26 38198956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397124 Affx-122962681 AX-123267479 26 12335687 TTAATAGAAATGTTGTATTTGTTCTTTGTCTATTC[A/G]TCGTTTGTATTTCTTAAAGATGCAGTGTTTGAAAT R 2 1 2 1 101000 r 74 goat snp30017-scaffold3275-17307 26 38091493 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780980 Affx-122924588 AX-385268068 26 12358868 AATCTTTTCTCCCAAATACCAAACACTTAATTTCT[A/G]TAATCAACAAGTATTTTTTGATCAGAGAATATGAA R 2 1 2 1 201000 r 74 goat snp1135-scaffold1029-2131350 26 38068259 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409263 Affx-122953128 AX-123279614 26 12395011 TATATAAAAATATGTGTGTATGTGTGTAATTCAAA[C/T]GATCTAAATCTCAGGATGAGGCGATTACTTCCGAT Y 2 1 2 1 101000 r 74 goat snp1134-scaffold1029-2095207 26 38031654 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445538 Affx-122925163 AX-123315875 26 12425167 AGGAGACTGCCTTGGATGGGACACTGTCTCTGCCA[C/T]GTGGTTATGCTCTCTATCTTCAAGAGGTTTGGTTA Y 2 1 2 1 101000 r 74 goat snp1133-scaffold1029-2065051 26 38001794 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784411 Affx-122940591 AX-385271460 26 12456222 CACAATTTACATCAATAGAAACAACTCCAGATATG[C/T]ATTTACTGTGAATAACTCTTACTCAAGATAAGAAA Y 2 1 2 1 101000 f 74 goat snp1132-scaffold1029-2033996 26 37970238 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446931 Affx-122924684 AX-123317267 26 12506548 GTTTCTCCTGTAGGAAACTGTAATTTGTTTAAACT[A/C]TAACACATACCAAATAATCAAGTCTAGCCCATCTG M 2 1 2 1 101000 r 74 goat snp1131-scaffold1029-1983670 26 37920042 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773442 Affx-122968197 AX-385260584 26 12555932 AACTAATCTATAGTCTTTTATGACCAGATTCTTTC[A/G]TTTAGCATCTTTAAAGGTTCACTGATGTTTTAGCA R 2 1 2 1 102000 f 74 goat snp1130-scaffold1029-1934286 26 37870606 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400370 Affx-122960022 AX-123270725 26 12585474 ATCCTTTCCTGTTTACAGACGTTCAGGTTGCTACC[A/G]TGTCCTGCCTACTGTAAATACTGTTGCCGTGAACG R 2 1 2 1 101000 f 74 goat snp1129-scaffold1029-1904744 26 37841168 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423094 Affx-122942925 AX-123293440 26 12633860 ATTTTGAAGGAGGTGACGGAAAAACTGACCACTGC[A/G]TCGTCTTACCTGCAAGACATCCTTTACCTTACTGT R 2 1 2 1 101000 r 74 goat snp1128-scaffold1029-1856358 26 37792306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784846 Affx-122927494 AX-385271893 26 12667008 AGGGAGACTTGGTCATATTCAGAAACTTGAAGCCC[G/T]AAGACTTGTGTTTAAAACTGTTCTTGCTAAAACTG K 2 1 2 1 101000 f 74 goat snp1127-scaffold1029-1823210 26 37759020 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396253 Affx-122963324 AX-123266608 26 12698463 GAATTGAGGCTAATTAGAATATTTCTTAATAATAC[A/G]TTTGAGATACTAGCAATCCAAAAGTGAGTTTCACT R 2 1 2 1 101000 r 74 goat snp1126-scaffold1029-1791755 26 37727857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273506 Affx-1111833640 AX-519547121 26 12723942 TTTCAATAAGATTTGGTGGGGGAGTCAAATATATA[A/C]AAATAACTCATGAGAAAATGTCTGCAGAATCCTTA M 2 1 2 1 201000 r 74 goat GoatD01.000179 26 12723942 T G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320776136 Affx-122936859 AX-385263266 26 12739793 ACTGGTTATGTCTCCCTGTACTAGTTACTTGCAAA[C/T]GGACTAGATTCTAACATTCATCTCTGAATCACCAG Y 2 1 2 1 101000 r 74 goat snp1125-scaffold1029-1750425 26 37686574 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401707 Affx-122959540 AX-123272060 26 12793486 CCTATGGACTATAGCTGGCCAGGCTCCTCTGTCCA[C/T]GGGATGAAGGAAGGTATGCTGTATCAGAAACAGTT Y 2 1 2 1 103000 r 74 goat snp1124-scaffold1029-1696732 26 37632534 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273133 Affx-1111833304 AX-519546797 26 12809717 TCCACCATGCTGTGTGGCCCGAGGGATCTTAGTTC[A/C]CCTACCAGGTATCGAACCAGAGTCCTTGGCAGCAA M 2 1 2 1 102000 r 74 goat 26_12809717_AF-PAKI 26 12809717 C A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394106 Affx-122965349 AX-123264461 26 12843111 ACCCAGGAACATTATGGCACCTAAAAGTCAATTCA[C/T]ACAAGGCTCCATTCACAGGCAACAGCTGGAGTTTG Y 2 1 2 1 101000 f 74 goat snp1123-scaffold1029-1647107 26 37582882 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402214 Affx-122959159 AX-123272567 26 12875996 ATTCCTTTAATCTGTCCCCTGGTGTTTCTCTTACT[A/G]CCTCATTCCCTCTTCCTAGAGTTCAGCAATTGAGA R 2 1 2 1 201000 r 74 goat snp1122-scaffold1029-1614222 26 37549976 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433011 Affx-122935788 AX-123303352 26 12934339 ACAGTAAGTGGTCCTGTTGTTGACTAACTCAGGCG[A/C]AGTAAAGAATAGTATTTTCCAGGGACATTTTACCT M 2 1 2 1 101000 f 74 goat snp1121-scaffold1029-1555879 26 37490858 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441991 Affx-122928433 AX-123312328 26 12989997 GTTATTCTTGCAGAACAAACCTTGTCAGAAATCAT[A/G]CTTAATTTACTTTTATTATTTTTTAGTAACTTCAG R 2 1 2 1 101000 f 74 goat snp1120-scaffold1029-1500221 26 37435155 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411759 Affx-122951498 AX-123282109 26 13065254 TTAAAATAATGACTAATACATAGAGCACTTACTAC[A/G]TGCCAGGCACTCACTGTTCCAAGTGCTTCACACAT R 2 1 2 1 201000 f 74 goat snp1119-scaffold1029-1424964 26 37361950 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402165 Affx-122959194 AX-123272518 26 13101625 TCCAACTGCATTTACAGCACTGCCTTGATATTCTC[C/T]ACTCATTTTTAATCTGCACACAAGGCTCAAATTCT Y 2 1 2 1 101000 f 74 goat snp1118-scaffold1029-1388593 26 37325580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799759 Affx-122934124 AX-385286686 26 13155572 AGCACAAGAAATTTAAGGAATACTCTAATAACCAT[A/G]TATGCAACTGAACAAATATTGATGTTTTTTAGCCT R 2 1 2 1 101000 r 74 goat snp1117-scaffold1029-1334646 26 37271740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444179 Affx-122927272 AX-123314516 26 13186537 GAATCACCTTTTGCTTTTTTTTAATGACTTTAATA[C/T]GCCTGTGTGGTCACAGAGTTCTTACATATAGATAG Y 2 1 2 1 101000 r 74 goat snp1116-scaffold1029-1303681 26 37240880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406348 Affx-122955436 AX-123276700 26 13229295 GTCATTTCAAAAGTTATGAATAGGAAACAAAAAGC[A/G]AGCATAATAAAAACAGAAATACTCAACTTAAGAAA R 2 1 2 1 101000 f 74 goat snp1115-scaffold1029-1260923 26 37198198 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392812 Affx-122965792 AX-123263169 26 13285117 TAATGTCCAGGTGCTTCCTTTAATTCAGTTGAAAG[C/T]ATTCTGTCAAACAATATTTTAAATGACAGAGCTGA Y 2 1 2 1 101000 f 74 goat snp1114-scaffold1029-1205101 26 37142289 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385929 Affx-122971563 AX-123256287 26 13352768 AAATGAAAGAATGTGGCACAGTCGCACAGTAGCCT[A/G]ACTCCAGAGTATATGCTTGCCATTACTGTACTGTT R 2 1 2 1 201000 r 74 goat snp1113-scaffold1029-1137450 26 37074265 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764117 Affx-986698644 AX-385251868 26 13383595 CTACAGATGGACCAAACACTGAAGCAGAGGCAAAT[A/G]TAAATGCATATGAAGAGTGTCCCTCTGGAATCCCC R 2 1 2 1 600010 f 74 goat 26_13383595 26 13383595 Ancestral_priority_1043 ancestry 0.668 recommended IMAGE 10K 10K ancestral 320767642 Affx-986698648 AX-385254885 26 13383614 TGAAGCAGAGGCAAATATAAATGCATATGAAGAGT[A/G]TCCCTCTGGAATCCCCTTGAATATGTGGAATGTAG R 2 1 2 1 600010 r 74 goat 26_13383614 26 13383614 Ancestral_priority_1043 ancestry 0.622 recommended IMAGE 10K 10K ancestral 320770364 Affx-122959849 AX-385257531 26 13403446 TTAAATCTAAAAAGTTCTTTTCTTAAGACCATCCA[G/T]CATATTGTTGGCTTTTTTGGCAAGTCTCAGGCTAC K 2 1 2 1 101000 r 74 goat snp1112-scaffold1029-1086772 26 37024298 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404853 Affx-122956622 AX-123275205 26 13441901 CCTCTGTTCATCCCTGCGTGGCGTCGGGTCTTAGG[G/T]TGTGCTGGAGAGAACGCCAGTGACACACGGTCCCT K 2 1 2 1 201000 r 74 goat snp1111-scaffold1029-1048317 26 36985865 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438713 Affx-122930852 AX-123309050 26 13472057 ATGCTCACTCCCCCAAGAGACCCCAGGAAAAAGCC[A/G]TCAGCACCAGCAGTTCCAGGACTCACTCAGAACTT R 2 1 2 1 101000 r 74 goat snp1110-scaffold1029-1018161 26 36956785 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394059 Affx-122964979 AX-123264414 26 13503427 TTCCATCACTGCACTTGATAACAATGTTTTGCTTT[A/G]TCCTCACAATAAATTTCTGTGGTAAGTGCTATTGT R 2 1 2 1 101000 f 74 goat snp1109-scaffold1029-986791 26 36925298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792020 Affx-122925114 AX-385279008 26 13539938 TCAGGAACTTCTGACTTCTAGCAAAATGTAGCTTA[C/T]ATTGGACTAACTTCTCCTATCGATAATTAGAAATT Y 2 1 2 1 101000 f 74 goat snp1108-scaffold1029-950280 26 36889045 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405823 Affx-122955884 AX-123276175 26 13582780 CAACAAAACAGCCCACATGCTGCACTAAGACCCAA[C/T]GCCACCAAATAGATTTAAAAGAGAAAAAAGATCTA Y 2 1 2 1 103000 f 74 goat snp1107-scaffold1029-907438 26 36846755 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450497 Affx-122922515 AX-123320831 26 13621500 TGGTTGACCTGTTAACCTTTCTGCTACATAGTTAA[C/T]GGGAGAGCAATATGTTAACCACCACAGCATTACTA Y 2 1 2 1 101000 r 74 goat snp1106-scaffold1029-868718 26 36807397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415844 Affx-122948869 AX-123286193 26 13668687 ATCACTTCCTCTATCCCTGGCGAAGCTAGCTTCCT[A/G]CCACTCTAGAGCAGTTTGTACATAATCTCATTTAG R 2 1 2 1 101000 r 74 goat snp1105-scaffold1029-821531 26 36759878 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433417 Affx-122935091 AX-123303758 26 13711230 TATCCTTTATGCTTTCCTGCCCTCACCTCCCAGAG[A/C]TTCCCTGGTGGCTCAGATGATAAGGAATCCACCTG M 2 1 2 1 303000 r 74 goat snp1104-scaffold1029-778988 26 36717275 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453992 Affx-122919443 AX-123324325 26 13754881 TGCAGTCCATGGGGTCACAAAGAGTCGGACACGAA[C/T]GAGTGACCAAGACAAGACATCAGTTATTTGAGTTT Y 2 1 2 1 101000 r 74 goat snp1103-scaffold1029-735337 26 36674101 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463977473 Affx-1110250032 AX-515454626 26 13780756 GACCCCACCTCCATCTTTGGGCACCAGTGACCCCA[A/C]AGTTCCGGGACTGGCTCCGATCCACAGCCTAAGAG M 2 1 2 1 202000 r 74 goat GoatD01.009467 26 13780756 C A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38406394 Affx-122955395 AX-123276746 26 13797863 ACAAAGTTTCCTTATTACTGTCACACCATAACATT[C/T]TAGCATATTTATAGCATTAGTAATATGAAGGAAAA Y 2 1 2 1 101000 f 74 goat snp1102-scaffold1029-692355 26 36630543 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408966 Affx-122953916 AX-123279317 26 13830031 GTGGTCAGTGTGACTTCATGAACTGAACTGCTAAC[A/G]TTATTTCATTCAAATATTCATGGATACATGAGGTT R 2 1 2 1 101000 f 74 goat snp1101-scaffold1029-660187 26 36598677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451969 Affx-122920946 AX-123322302 26 13868145 AGACCACCAACAGTAGCAGCAGCACCTGAAGCTTA[C/T]TGGAAATGGAGACTCTCAGGTTCTACCCCAGACTA Y 2 1 2 1 101000 r 74 goat snp1100-scaffold1029-622073 26 36560397 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406859 Affx-122955654 AX-123277210 26 13967680 TTTTTTTCTTTTCTGATGTGGGATCCAGGTTGGGA[G/T]AAGGTGGTTAAGGGCTGGAGGGAAAAACCAGACAG K 2 1 2 1 201000 f 74 goat snp1098-scaffold1029-522538 26 36460082 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784236 Affx-122971729 AX-385271286 26 13998691 TTAGACCCTGTAACTAGTTCACTTTGTCCTAATGC[A/G]TTTTACTTTATAGTTCACCGACAAGAAAATGTACA R 2 1 2 1 101000 f 74 goat snp1097-scaffold1029-491527 26 36429628 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38402888 Affx-122958218 AX-123273241 26 14028239 TGCCAGACTCCTCTCTCCATGTTTACGTAAATCCC[A/G]TCAGTTTTACCCCAGGTTATGTATTTCTCAAGTTT R 2 1 2 1 101000 r 74 goat snp1096-scaffold1029-461979 26 36399837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416295 Affx-122947935 AX-123286644 26 14076517 TTATTCACACCATTGCAGGCAAGAGCTGCATAAGT[A/G]CAGAATCCCAGTGGGATGATGTGTATTGAGCCTTT R 2 1 2 1 101000 f 74 goat snp1095-scaffold1029-413701 26 36351768 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393500 Affx-122965814 AX-123263856 26 14106442 ATAATGACACAACATTCACATTATGACAGACAACT[A/G]TAATAACACTACTCAGCTTATGTGGATTTAAGAAA R 2 1 2 1 101000 f 74 goat snp1094-scaffold1029-383776 26 36321777 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386258 Affx-122970955 AX-123256616 26 14150655 CCAGCAGCCAGGCAAATCCTTCCCTGAATGGGGAC[A/G]TGTGACTTCACCAATCCCTGTGTCCACTACAGGAG R 2 1 2 1 101000 r 74 goat snp1093-scaffold1029-339563 26 36278110 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450872 Affx-122922220 AX-123321206 26 14241766 TGTAGCCAGAGGTGAACCTTTTATTTTGGAAAATC[C/T]GAGAAAATAGGCTGTTAATTCTGTTGAGCAGAAGA Y 2 1 2 1 201000 r 74 goat snp1091-scaffold1029-248452 26 36185808 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277663 Affx-1111836023 AX-519551162 26 14253531 TTATCCCCTGCTTCCTTGAGGTATCAGAGGGTGTC[A/G]AAGCCAAAGAAATAATTATGTTGCTGTGCAAGTCT R 2 1 2 1 102000 f 74 goat Random2.2K-2177 26 14253531 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451257 Affx-122921933 AX-123321590 26 14287141 AGGGACTTGAAGGTCATCAGCAGTCATGGGGCAGT[A/G]CCTCTTGTGGGCCTCGCTGGGATAGCACTAGATGC R 2 1 2 1 101000 f 74 goat snp1090-scaffold1029-203077 26 36140000 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449772 Affx-122922440 AX-123320107 26 14320016 GATTGGGGTGGAACAAAGCAAGTACAGAAAAAGCT[A/G]TCCTTCCTTTCCCTTCTCAGCTGTCCTTACACTCA R 2 1 2 1 101000 f 74 goat snp1089-scaffold1029-170202 26 36107124 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405332 Affx-122956339 AX-123275684 26 14392307 TGGAGACAGGAGACACAGGAAGCAGCCCTGCTATA[A/G]CGTACTCATTCCTTAGCCAAGGAAAACATGATCTA R 2 1 2 1 201000 r 74 goat snp1087-scaffold1029-97911 26 36034363 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444234 Affx-122927230 AX-123314571 26 14422960 TCTGAGCCCCAAACTTGGCAAATGTCATATAAACT[A/G]TAGTTGGTATCCTAAAATTCCAAGAGACTCTCCGG R 2 1 2 1 101000 r 74 goat snp1086-scaffold1029-67258 26 36003645 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416113 Affx-122948307 AX-123286462 26 14467544 TGTAATCACCACAACATCTAATGAATGTTTAAAAT[A/G]TCTCACTGAGCACTGAGACACGATTTCATCGAAAC R 2 1 2 1 201000 f 74 goat snp1085-scaffold1029-22674 26 35959488 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799494 Affx-122941602 AX-385286424 26 14520936 AATCATATTTGTCTGTTTGCTAATTTCCACGGGAC[A/G]CATTCTTGTTTTTATCAGTCCAGGGACTGAAGTAG R 2 1 2 1 101000 f 74 goat snp15063-scaffold161-373737 26 35905994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376179 Affx-122978831 AX-123246538 26 14571491 CAGGAAGGGGAAAGGGGGGTCAGTGATGGTGTTGA[C/T]GGAGTTAAGCAATCAGACACTCAGCCTGCCCAAGA Y 2 1 2 1 101000 r 74 goat snp15062-scaffold161-323182 26 35849892 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433808 Affx-122935176 AX-123304149 26 14617559 TCCAGGTGAGAACAGGGCTTTCTCTCACTTCTCAA[C/T]GACCCCATAAGTAACGAATGTTAGGAGGTAATTGT Y 2 1 2 1 101000 r 74 goat snp15061-scaffold161-277114 26 35803436 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408385 Affx-122953719 AX-123278736 26 14646270 CAGCTTTGAAAATATTTCACTATTATTTCCACTTG[C/T]GAGTCCAAATCATACTGTTTTCATAACTTATCAAA Y 2 1 2 1 101000 r 74 goat snp15060-scaffold161-248403 26 35774540 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767589 Affx-122959965 AX-385254840 26 14680089 AATGAAGGTGTTGAGACCGTCCTCCAGTGTCTTGA[C/T]GTCATGCTGACTAAACGCAGAAAGCAAGTTTCTCA Y 2 1 2 1 101000 f 74 goat snp15059-scaffold161-214584 26 35740428 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431848 Affx-122936082 AX-123302189 26 14709290 ATCTGCTTCCAATCAGTAGACCAAAGCCCTACAAG[C/T]GCAGGGATGGTATCATTCTCGTTCTCATGCCCGGA Y 2 1 2 1 101000 f 74 goat snp15058-scaffold161-185383 26 35710998 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391867 Affx-122966983 AX-123262224 26 14744878 AGAAGGCACACATTCAGTCTATAACACTAGTCTAA[C/T]GGAGGAGTCCAGTCTGGGAGCTATTACTTCTATGA Y 2 1 2 1 101000 r 74 goat snp15057-scaffold161-149795 26 35674985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436224 Affx-122932576 AX-123306563 26 14790191 GCATTAATAAAATAGAAAGACTTGGAAAGAACAGG[C/T]GAGGGGGAATAAGCAAAAGTGTGGATTAGGGAAAT Y 2 1 2 1 201000 f 74 goat snp15056-scaffold161-104482 26 35629876 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400642 Affx-122960365 AX-123270997 26 14819714 ACAATGAGTGAGAAATATTGATTAGACAGACAAAA[C/T]ATCATATTCAATTTCACATTATCTTGAGGTTTTTA Y 2 1 2 1 101000 f 74 goat snp15055-scaffold161-74959 26 35599947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442742 Affx-122927844 AX-123313079 26 14862317 AGAGTAACAACCTACACAGGAATGTGTGCTTCAGG[C/T]AGCATTCTGCATTTCTCTTCATCAGTTTCTTCGTA Y 2 1 2 1 201000 f 74 goat snp15054-scaffold161-32356 26 35557423 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780021 Affx-122936841 AX-385267120 26 14928871 ACCAAGTGGGATTTACTTTATGTATGTAAGATTGA[G/T]CCATCATTTGGATCAATTAAGGTTCAATAGCAACA K 2 1 2 1 201000 f 74 goat snp12641-scaffold1481-200262 26 35307301 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775288 Affx-122954519 AX-385262419 26 15018694 TGAAATAGCCAGTGATGCAGGAACATGTCTGAAAT[C/T]ACATCCACAATGACTTCCCACAGTTACTCCATTTT Y 2 1 2 1 101000 f 74 goat snp12639-scaffold1481-110439 26 35400772 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803324 Affx-122928324 AX-385290162 26 15128227 AATTTGTGAGAGCTTTATTCAGTCAATTCCTTATT[C/T]TGAGCATCTGCACTCATTTCCTCCACCAAGCTGCC Y 2 1 2 1 201000 r 74 goat snp12637-scaffold1481-906 26 35507446 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439022 Affx-122930349 AX-123309359 26 15146675 AATCCAGCCCCCACTTAAGTCATTCAGACCTTGCC[C/T]ACCTCCATTTAAGTACTCAAATAGAGCATCTCTTT Y 2 1 2 1 201000 r 74 goat snp17598-scaffold1829-17443 26 34873240 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410301 Affx-122952494 AX-123280651 26 15196034 TTTTACTGCACGAGGAATAACAATGAAATAAGAAG[C/T]GGTCTTTAACGGCAGCAGACTTCCCAAGGGGTGAC Y 2 1 2 1 101000 f 74 goat snp17599-scaffold1829-66802 26 34823875 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428234 Affx-122939430 AX-123298577 26 15290557 CTAAGTAATCCCAAGCCCTGCTTATTCCCTGTCCT[A/G]GACACAGTCACATGAATCCTGCTCTCTTTCCCCCT R 2 1 2 1 201000 r 74 goat snp17601-scaffold1829-161325 26 34728872 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273089 Affx-1111833305 AX-519546756 26 15324985 TGCTTGGGTCAGGAAGGACCCCTGGGAAGGAAATG[A/G]CAACCCATTTTGGTATTCTTGCCTGGAAAATACCA R 2 1 2 1 303000 f 74 goat 26_15324985_AF-PAKI 26 15324985 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38416969 Affx-122948010 AX-123287317 26 15347997 TCACTGATAGTGGAAGAGGCTGTGCTTCCACATGC[A/G]CCCGGGGTTAATCAGCACTATCTCCTACCCCAGGT R 2 1 2 1 101000 f 74 goat snp17602-scaffold1829-218765 26 34671404 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776748 Affx-122976365 AX-385263872 26 15393160 TACTGGTTTTAGCTTTTGATTGATATGAGGTAGCA[A/C]TTTCCTCCAAATTCAGTAATTTCCTCCAAAGATAC M 2 1 2 1 101000 r 74 goat snp17603-scaffold1829-263928 26 34626173 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793615 Affx-122919313 AX-385280589 26 15439523 CATATTCTTCTTACTTTTTGCATTTGCAGAATTGT[A/C]TTTAAGTTTAAAACAGGAACATAAAACATTCCATT M 2 1 2 1 102000 f 74 goat snp17604-scaffold1829-310291 26 34579907 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429065 Affx-122938293 AX-123299407 26 15476308 CCTGGCAGAGCAACTCACATTTTCATATCTCCTTG[A/C]TGTACTCTTTCTAAGTGGAAAAATCTAAGTCTGCA M 2 1 2 1 101000 r 74 goat snp17605-scaffold1829-347076 26 34543322 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274246 Affx-1111834136 AX-519547844 26 15486571 ACTTCACCACCACCCAGGGCTTCTGGGTGGACTGC[A/G]CTGGCCCGTGGAGGCTTCCC R 2 1 2 1 103000 f 74 goat GoatD01.020635 26 15486571 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38431992 Affx-122935938 AX-123302333 26 15509573 ACTTGCCCAAGGTGAAACAACCAGCCGATGGCAGG[C/T]GTGGGTTCTGAACCCAGAATTATCTGTTTCTGAAA Y 2 1 2 1 101000 r 74 goat snp17606-scaffold1829-380341 26 34510076 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394645 Affx-122964388 AX-123265000 26 15552288 CCTTGATTAGTTAGCAAAAATCCACAGCTTCTGAA[C/T]AGGTAATCTCTTCCCATCTTCTAAGGACCTTTAGG Y 2 1 2 1 101000 f 74 goat snp17607-scaffold1829-423056 26 34468298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389242 Affx-122969039 AX-123259600 26 15609430 TGCACAATAGTTACCCTGGCCATTTCTTTTAAGAT[A/G]CATAAAAGCAGAGTACCTCTTTTCATGAGTTTTAT R 2 1 2 1 101000 f 74 goat snp17608-scaffold1829-480198 26 34410745 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443774 Affx-122927104 AX-123314111 26 15643490 TTAAGAGCGTAGACTTGCCAGACTCAGACAAGCTT[A/G]TGTTCAGATTCCAGCTCTGCACTCAGTGTCTGTGT R 2 1 2 1 201000 f 74 goat snp17609-scaffold1829-514258 26 34376727 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435692 Affx-122933321 AX-123306031 26 15692814 GGTAAGGATTTTCCTCTATAAAGACACTTAGGAAG[C/T]AGAAACTAAGTAAGTCCCAAGGAAACAAGAAGATA Y 2 1 2 1 101000 f 74 goat snp17610-scaffold1829-563582 26 34327100 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442868 Affx-122927669 AX-123313205 26 15738410 ACCATTAGGAACAAAATGGAAGGTCAAAGGGAAAT[A/G]TACCAATTAGATCTCAATATAGTGGGTTTGCAATT R 2 1 2 1 101000 f 74 goat snp17611-scaffold1829-609178 26 34280427 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795789 Affx-122974431 AX-385282742 26 15792685 TAATGATTATTATACATGGTCTGGAGTCATGCTAA[C/T]GGGCTTATTCCCAGAGACCCATATGTTGTGTTAGT Y 2 1 2 1 101000 r 74 goat snp17612-scaffold1829-663453 26 34226035 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780105 Affx-122936998 AX-385267202 26 15828405 AACTTGAACCTGTGAAACTGGGGAGACCACTCTTT[A/G]TAGTACACTAAAGTCAAGGAAAGTTAACATGAACT R 2 1 2 1 101000 f 74 goat snp17613-scaffold1829-699173 26 34189760 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393485 Affx-122965826 AX-123263841 26 15896413 GAAGAAGAAAATATGGAAGAAACAAGTTTGGGATC[A/G]TATAAATACACAATCTAATTCTTTCAAAACATGTA R 2 1 2 1 201000 r 74 goat snp17614-scaffold1829-767181 26 34120394 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400919 Affx-122959729 AX-123271272 26 15936296 CCGTGGGGTTGCAGAGAGTCGGACAAGCACACATT[A/C]TCAGGGTGACAACTGTGCCAGTACAGGCTGAAGAC M 2 1 2 1 101000 r 74 goat snp17615-scaffold1829-807064 26 34080607 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787916 Affx-122955385 AX-385274938 26 15973659 CTCTCCAGTCCCTCTGGGTTATGGGTTATGACCTC[A/G]TAGATGCTGCTGGCACCTTGTGACATGTACTTCAT R 2 1 2 1 101000 r 74 goat snp17616-scaffold1829-844427 26 34042336 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435498 Affx-122933428 AX-123305838 26 16006078 CCTTGCAGCAGCCCTATGAGATTGGTGCTATTATT[A/G]TCTCTATCTTTTTAGCTGAAGAAACTGGGACCGGG R 2 1 2 1 101000 r 74 goat snp17617-scaffold1829-876846 26 34010601 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414832 Affx-122949195 AX-123285181 26 16055180 TGCTTTATTGTGGTGGTCTGCAACGGAACCCACAA[C/T]ATCTCTGAGATGCGCCTGTGCTATGATGTCAAAGT Y 2 1 2 1 202000 f 74 goat snp17618-scaffold1829-925948 26 33961716 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277791 Affx-1111836024 AX-519551290 26 16055195 TTGATTCTTTATTCCCTAGCACATACAAACTCAAA[C/G]TCATTTGATTAGCTAAGGGCAAGCATGAATTTTTC S 4 1 2 1 101000 r 74 goat Random2.2K-2178 26 16055195 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380775 Affx-122975110 AX-123251133 26 16097318 GTGACAGTTTCTGCCCCTGGCTCAAGAGGCTGGAG[C/T]GGTCCTCTTTCTACCTGATTGGCCCCCTGCCTTGT Y 2 1 2 1 101000 r 74 goat snp17619-scaffold1829-968086 26 33919460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435666 Affx-122933338 AX-123306005 26 16138068 GCCCTCTGGACTGAGAGGACTTGTGTGCCCTTCCC[A/G]GGAGTAGCTGACCTGGCTGAGACCCTTTGGCCATA R 2 1 2 1 201000 f 74 goat snp17620-scaffold1829-1008836 26 33878785 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383094 Affx-122973282 AX-123253452 26 16200498 TCATTACAAAGAGCAAGAAATCAGATCCATTACCC[A/G]GATGGAGAGAACTGCAAGATGAGATTGCCTCTCCA R 2 1 2 1 101000 f 74 goat snp17622-scaffold1829-1071266 26 33814892 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277666 Affx-1111836025 AX-519551166 26 16246774 ACATCACCAGCTCAAATGAGCTATATACAGCCACA[A/G]GGAAGGCAAATGTGACAACAAATGTAACAGTGAAG R 2 1 2 1 101000 f 74 goat Random2.2K-2179 26 16246774 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777464 Affx-122946909 AX-385264584 26 16276252 GGCAATCCAAAGCATTATCTCTGTTTACAGTTAGA[C/T]CACATTAAGTTTGACAGGACCAATTTTTTTTAAAA Y 2 1 2 1 101000 f 74 goat snp17623-scaffold1829-1147020 26 33739710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419082 Affx-122945794 AX-123289430 26 16339999 CTGTGTTCTCGCACATTCCCCTGACCTCGAGGGAC[A/G]CTGATTCCATGACTCTGTTCCAAGGCGGGGTCAAG R 2 1 2 1 101000 r 74 goat snp17624-scaffold1829-1210767 26 33676128 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771663 Affx-122965331 AX-385258821 26 16372075 GTTGAGGACAGGCTTTGAGTGATGTTATTAACATA[C/T]ACGAACCCCAGGATGTCCATTAACCTTCTGATTTT Y 2 1 2 1 101000 r 74 goat snp17625-scaffold1829-1242843 26 33644114 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437487 Affx-122932363 AX-123307825 26 16408105 TCTCCCCCAACATAGCCTCCTAGTAATAAAACAGA[C/T]GTGTGGCTTTTGAGGTCAAAAGAAGCAAAGAATGT Y 2 1 2 1 101000 f 74 goat snp17626-scaffold1829-1278873 26 33607910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775702 Affx-122966732 AX-385262833 26 16438667 AGCTACCTTCCCAATTCCCTTAAATACAAAGTCTG[C/T]ATTACCAAATCTAAGGGAACTGTCACCGTTGATTG Y 2 1 2 1 101000 f 74 goat snp17627-scaffold1829-1309435 26 33577308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799685 Affx-122939041 AX-385286613 26 16470791 TACAAGTATGATGGAATAGAGAACCATCGTTCTGG[C/T]GTAACAGCAAAGTGAGGGAAAATGTAGGAAAAGAA Y 2 1 2 1 101000 r 74 goat snp17628-scaffold1829-1341559 26 33544161 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792245 Affx-122923071 AX-385279229 26 16510785 CAATTAACCCAAAGGAAATACAATTAAAAGAGTAA[C/T]ATGAGAGGCTCTCTTTCCAAAACAATGATACCTAA Y 2 1 2 1 101000 f 74 goat snp17629-scaffold1829-1381553 26 33503059 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446056 Affx-122925832 AX-123316393 26 16555950 CTTGTTTTGAGCTTTGTTTGTTCTTTTTCTAGTTC[C/T]TTGCGTGTCAAGTTGGATGTTGTGAGAGTTTTGTT Y 2 1 2 1 101000 r 74 goat snp17630-scaffold1829-1426718 26 33457253 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770482 Affx-122971921 AX-385257648 26 16604260 TTCAGCACTGCTGATAATGACTTCTCTGTCATCTT[A/G]TCCTAGAGAACCACAACTCAATAAGTATTCACAGT R 2 1 2 1 101000 f 74 goat snp17631-scaffold1829-1475028 26 33408874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425371 Affx-122941571 AX-123295717 26 16638590 CTACAACTAACGAAAGCTGAGTTGCGGGATAGAGC[A/G]CATGGTACAGTTGGGCCGCCTTCATTTTAGATTAT R 2 1 2 1 101000 r 74 goat snp17632-scaffold1829-1509358 26 33374587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414245 Affx-122949628 AX-123284594 26 16694308 CACATTCCTATGTTACTGATGGGAATGCAAGATGG[C/T]AGAACTCCAACAGAGGGGTATTGCCTGTTATCTAT Y 2 1 2 1 201000 f 74 goat snp17633-scaffold1829-1565076 26 33318945 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434796 Affx-122933874 AX-123305137 26 16752309 GTAGCAAATTACTGCTGTCTGGTAGAAAAGATAAC[A/G]TCAAGGGTTAGTTACTGCCTGTAAGATGTTAATCA R 2 1 2 1 101000 f 74 goat snp17634-scaffold1829-1623077 26 33260807 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385407 Affx-122971339 AX-123255765 26 16811062 TAAAAAGTCTTGTTTAATCATTTCCTCTCAGCATG[C/T]ACCCTTTTTGAGATGACCTGAGCTGGAGGGGCATC Y 2 1 2 1 201000 f 74 goat snp17635-scaffold1829-1681830 26 33202120 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786124 Affx-122919238 AX-385273160 26 16842963 AGGTGCTCATTTAGCAGGCCTCACAATGTACTAAG[C/T]ACTTTCCATACATTATCTTCAGTCCTCACAAGAAC Y 2 1 2 1 201000 r 74 goat snp17636-scaffold1829-1713731 26 33170119 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405174 Affx-122956933 AX-123275526 26 16850567 AGGGGAAGAGAGATGGATAAACAAGTAATTACAAA[C/T]GACGATTTCATGCTCTGGGGGAGGCATGGTGAGCC Y 2 1 2 1 101000 f 74 goat snp41203-scaffold532-4879953 26 33161888 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801515 Affx-122938966 AX-385288424 26 16896236 CATTTTGAGGATCTTTCGTTTTTCTAGAGTAATCT[A/G]TCAGTCAGATCATTTTAAGAACCACTGTCCTCATG R 2 1 2 1 101000 r 74 goat snp41202-scaffold532-4834284 26 33116864 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410985 Affx-122952010 AX-123281335 26 17026014 AACCTGAGTCACAGAAAAGTTAAGTTGCTAGTCCA[G/T]AGTCGCAGTGACAGGCTGGGATTTCAGCTTCTGAC K 2 1 2 1 101000 f 74 goat snp41200-scaffold532-4704506 26 32985894 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376729 Affx-122978959 AX-123247088 26 17064507 GCAGCATAAGCCTCCCGGAAAAGGTCCCAGCTTCC[A/G]TAGCTGCAGTAGACACAGCCCAGAGTCATGAAAAA R 2 1 2 1 101000 r 74 goat snp41199-scaffold532-4666013 26 32947639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797054 Affx-122946526 AX-385283994 26 17095603 TTAATCAAACACGTAGAAGATTGCTAACCTTTCAC[G/T]CTTAGTTGCTCCTTTGAAAATTTCTCTTATAATAA K 2 1 2 1 101000 f 74 goat snp41198-scaffold532-4634917 26 32916808 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436460 Affx-122932985 AX-123306798 26 17152355 TACGTGCCGGCATTATAAGGCTGACTGAAATAGCA[C/T]AGGCCCTGCTCTTCATGACTCATACCTAGCGGGCT Y 2 1 2 1 201000 f 74 goat snp41197-scaffold532-4578165 26 32860907 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778920 Affx-122925681 AX-385266027 26 17181420 TGTTACCATTGGGGTAAACAGGGTAATGGGTAGAT[A/G]GAATCTCCATGTATTGTTTCTTATCATGTGAATCC R 2 1 2 1 101000 f 74 goat snp41196-scaffold532-4549100 26 32831943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375985 Affx-122978426 AX-123246344 26 17222295 ACTTCTAAGGTGCATTAATACTCACTGTTGCTCCG[C/T]ATCAGTTAAGGAAAGTATCAACTGAAAGGAAATCA Y 2 1 2 1 101000 f 74 goat snp41195-scaffold532-4508225 26 32791244 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423815 Affx-122942803 AX-123294161 26 17270061 TTCTGGAATTCCCTCCAGCCCCAATTAGGGACAGA[C/T]ATAGTTCTATCCCTCTGATTTCTGTGTCCTGCCTT Y 2 1 2 1 101000 r 74 goat snp41194-scaffold532-4460459 26 32742694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384586 Affx-122972990 AX-123254944 26 17367627 AGAGCTGCCCAGCACCAGCAGAGAACCGCTCCCCC[A/G]GAAATGCCATGAACGCCCTGGGCTCTGGAATCCCA R 2 1 2 1 101000 r 74 goat snp41192-scaffold532-4362893 26 32644977 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277795 Affx-1111836026 AX-519551293 26 17377250 ATAGAAATAATCTAAAATCAAAAAGTAGCATGTCA[A/G]TTCCCTAGCAACAAAACTGACTCTTAGAGAAATAA R 2 1 2 1 101000 r 74 goat Random2.2K-2180 26 17377250 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38379394 Affx-122976134 AX-123249752 26 17398032 ATAAGGAAACAAAAGTCCTGTGAAAAAGCAGAGTC[A/G]GACGTCAAGGCTCTTCTGCCACTCAGTTTGGTACA R 2 1 2 1 101000 f 74 goat snp41191-scaffold532-4332488 26 32614783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449834 Affx-122922390 AX-123320169 26 17429197 GGCAACACATAATATTTATGTCATCTGAAAAAGAG[A/G]CATAAATATTTAGGGGACCCAGGGCCTGGTTATAT R 2 1 2 1 201000 f 74 goat snp41190-scaffold532-4301323 26 32583714 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795792 Affx-122958697 AX-385282745 26 17462266 GGCAAGTGCTAGTGAGTGAATGTATGTGAAGCTCA[C/T]GGCATATAGAAATCACCATAGGAACGTTAAGTAGT Y 2 1 2 1 101000 f 74 goat snp41189-scaffold532-4268254 26 32550668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452963 Affx-122920163 AX-123323296 26 17501411 AAGGCAGCTCTGGTGGCCAGACTGAAGGATTGCCT[A/G]GAGGCAGGCGATCATTATAGACCATTGTGACAGTC R 2 1 2 1 101000 r 74 goat snp41188-scaffold532-4229109 26 32512153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432863 Affx-122935357 AX-123303204 26 17540273 TGAATATTGTTTCCAATCTCAATCTTTTCCTGTGT[A/G]TTCATAGCCTAGAAATAAAAGGTGATTTGGGGGGG R 2 1 2 1 101000 r 74 goat snp41187-scaffold532-4190247 26 32473343 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444129 Affx-122926807 AX-123314466 26 17674177 GCTCTGTAACAGTGTTCCCCAAGTCTAACCCCACA[C/T]GCATAAACAGACGTTACATCTAGGGGAGCAATCAA Y 2 1 2 1 101000 r 74 goat snp41184-scaffold532-4056343 26 32339668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454067 Affx-122919386 AX-123324400 26 17728734 CTTTCACCAAGACCCGAGACAGTACATCCCATACA[C/T]GGTTTGGTGACCCAAGCGCTTCACTAGGCGCCACA Y 2 1 2 1 101000 f 74 goat snp41183-scaffold532-4001786 26 32284579 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767650 Affx-986698652 AX-385254891 26 17735627 TACGTATGGCTGAGTCCCTTCGCTGTTCACCTGAA[A/C]TATCACAACAGTGTTTTTCAGTTGGCTGTATCCCT M 2 1 2 1 600010 r 74 goat 26_17735627 26 17735627 Ancestral_priority_1043 ancestry 0.632 recommended IMAGE 10K 10K ancestral 38439218 Affx-122931025 AX-123309555 26 17770633 CTGTGCAGACCTTTGGGATCACTCACAGCCTGTCA[C/T]TTCCCAGGCCTGAGCCCTGGGCTGGGAACAGGAGG Y 2 1 2 1 101000 f 74 goat snp41182-scaffold532-3959887 26 32242601 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377683 Affx-122977423 AX-123248042 26 17801870 ATATTTATAACAGAGTAGACTCCATTGTGCTACCC[A/G]TTGTCTCAGCTTCTGGGGCTGCGGCAGCTACAGCA R 2 1 2 1 101000 f 74 goat snp41181-scaffold532-3928650 26 32211684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764127 Affx-986698654 AX-385251874 26 17810044 GAAGTAGAGTTCCTTGGTGAGCATGGAGACCACAC[A/T]TGGAATCTGCTTCTTCTCGTGGAAGCGTGGGTCAT W 4 1 2 1 600010 f 74 goat 26_17810044 26 17810044 Ancestral_priority_1043 ancestry 0.466 neutral IMAGE 10K 10K ancestral 320767598 Affx-986698623 AX-385254848 26 17810059 GGTGAGCATGGAGACCACACATGGAATCTGCTTCT[G/T]CTCGTGGAAGCGTGGGTCATCAGACTGGGATTCAA K 2 1 2 1 600010 r 74 goat 26_17810059 26 17810059 Ancestral_priority_1043 ancestry 0.48 neutral IMAGE 10K 10K ancestral 320764098 Affx-986698625 AX-385251855 26 17810087 TGCTTCTTCTCGTGGAAGCGTGGGTCATCAGACTG[A/G]GATTCAAAGTGCCTGGCCACCCTGTCATTCACCCG R 2 1 2 1 600010 f 74 goat 26_17810087 26 17810087 Ancestral_priority_1043 ancestry 0.554 neutral IMAGE 10K 10K ancestral 320803661 Affx-986696451 AX-385290438 26 17810137 GGCCACCCTGTCATTCACCCGGGTGAGGATCTGCA[A/G]GATCTCCAGGCTCTTCCCATGCTCATTCAGGATGG R 2 1 2 1 600010 f 74 goat 26_17810137 26 17810137 Ancestral_priority_1043 ancestry 0.56 neutral IMAGE 10K 10K ancestral 468277797 Affx-1111836027 AX-519551295 26 17835473 TACTGTAGTGGGTTGCCATTGCCTTCTCCAATATG[A/C]AAATACTACCCTGTTTTAAACACCGTACTTGAGCA M 2 1 2 1 201000 r 74 goat Random2.2K-2181 26 17835473 G T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378548 Affx-122976613 AX-123248907 26 17868689 ATATTTCACACAGGATTCATTTAACCCTCAAGGCA[A/G]CATTGGGGAGCTGTGGTTCAGAGAAGGGAGATAAC R 2 1 2 1 101000 f 74 goat snp41179-scaffold532-3861831 26 32145424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441764 Affx-122929111 AX-123312101 26 17913838 AACTAGAACCAGGTCTCCTGTGCCTGTTGTGTTGG[C/T]TTACTGCCATTCATTGCATATCCTTGGATATCTCC Y 2 1 2 1 101000 r 74 goat snp41178-scaffold532-3816682 26 32099022 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277799 Affx-1111836028 AX-519551297 26 17925934 TTATGGATGCCCCAATGGTTTGCAACCCTTTCCTG[A/G]TAAAAGCCAGTGTTTTTTTCTTCCCACAGTTGCGC R 2 1 2 1 202000 r 74 goat Random2.2K-2182 26 17925934 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 463980447 Affx-1110251573 AX-515457585 26 17944317 CCTCTGCTTAATGGAACCAGTTGAAAGCCATACAC[A/G]AAATCCCTGTTTCTATATGGAGACCATATAGAATG R 2 1 2 1 101000 r 74 goat 26_17944317_AF-PAKI 26 17944317 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320782851 Affx-122953163 AX-385269922 26 17951210 AAAGTGGCCTCTTCTTAGACTTTTAAGATAATATG[C/T]GGATAAGACATTTGTTAAGATTATGATAAAAAGAA Y 2 1 2 1 101000 f 74 goat snp41177-scaffold532-3779310 26 32061651 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787935 Affx-122945022 AX-385274957 26 17985317 ATATGAAGGTGTGGGATCATATGACCATATTTAAG[A/G]TGAAACCTGTCTGCCTGATTATATGTGCTTCCAGT R 2 1 2 1 101000 r 74 goat snp41176-scaffold532-3745203 26 32027027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377775 Affx-122977352 AX-123248134 26 18015617 GAGTGAAAAGGGGGTTGGGGACTGGGAGGTTGAAC[A/G]CGAGCAGATAAATCCCAGTGCAGGCCATGAGAGGA R 2 1 2 1 201000 r 74 goat snp41175-scaffold532-3714903 26 31996721 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779323 Affx-122936734 AX-385266427 26 18099792 CCCCCTGATTTTTATTCACAGGGTACAGTAACCCT[A/G]TGAAAATATATGTTTGGGTTCTTTTTAAACCAATT R 2 1 2 1 101000 f 74 goat snp41174-scaffold532-3630728 26 31911654 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793358 Affx-122925953 AX-385280336 26 18145124 TTGGTCTGCACTTATATACCTCAGTCCTCACTTCT[A/G]CTGTTGTAAGAAAATGAAGTATGGTGCATATAATA R 2 1 2 1 101000 f 74 goat snp41173-scaffold532-3585396 26 31865801 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379053 Affx-122976342 AX-123249412 26 18175684 TGAGAGACTAGTGTTCCACTAATGTGTTTGGACAA[C/T]GCTGACTTGGAATGTGAGCCCTGCTTTAGGTGAGA Y 2 1 2 1 201000 f 74 goat snp41172-scaffold532-3554836 26 31834794 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435153 Affx-122933668 AX-123305493 26 18208823 GAAGCTTAGAATAGTGAGAGCCAAGGAATAATGTC[A/G]TTTGTCAAGAAATGATGAGGAGTTCTAACATGGCA R 2 1 2 1 201000 r 74 goat snp41171-scaffold532-3521697 26 31801742 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782231 Affx-122943574 AX-385269309 26 18274311 CTAGTCCCAAAGCCTTTTGTTAAGACTTTGGTACT[A/G]TCTGCTATAGCATTACGTTTGTTCCCTCCTCCAGA R 2 1 2 1 101000 f 74 goat snp41170-scaffold532-3456209 26 31736102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437112 Affx-122932172 AX-123307450 26 18320457 CAGCCATAAAAATACATGAACACATGAGTGTTGCT[A/G]TATTCCAATAAAACTTCAGGGACACTCAAATTTTA R 2 1 2 1 103000 f 74 goat snp41169-scaffold532-3410063 26 31689831 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445397 Affx-122925391 AX-123315734 26 18356100 TGTCCACCCACACTATGAAACTTATAAAACATTAA[C/T]GGCACCCCCCCTCCCCTCTGTCACACTCTACTCAG Y 2 1 2 1 101000 f 74 goat snp41168-scaffold532-3374420 26 31653750 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794733 Affx-122938937 AX-385281693 26 18388696 AATTATAGTTTGCCCAAGACAGTGCTACTGCCTCT[A/C]GCATTGTGCAAAGAGAATACTGCAATGGTAGAGTT M 2 1 2 1 101000 f 74 goat snp41167-scaffold532-3341824 26 31621017 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442985 Affx-122928192 AX-123313322 26 18418438 TTATCTTTAAGCAGCTTTCCTTACCTTTGAGATTC[A/G]TAGAGGTTAATTGACTTGCCCATACAGCTAGTAAA R 2 1 2 1 201000 f 74 goat snp41166-scaffold532-3312082 26 31592301 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782998 Affx-122919849 AX-385270066 26 18447243 GAGAAAGATTGAAAGTTTCGATGAATGGCAGTTCC[A/G]TGGATTATTTAGGAGAACCTTGGACTTCCCCGTAG R 2 1 2 1 101000 r 74 goat snp41165-scaffold532-3283277 26 31563441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444704 Affx-122926427 AX-123315041 26 18506891 TAAATTTGCAACATTTTATATTACCTTTAGTGATG[A/G]AATGTAAGGTGTGTGTGTTTAGTTTGCTTATCTAA R 2 1 2 1 201000 f 74 goat snp41164-scaffold532-3223629 26 31503083 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777210 Affx-122935641 AX-385264333 26 18550897 TTCAGGAGTCTTTGTGTTAGGAGACTTGAGGAGAT[A/G]ATCATTACTTCCTGCTTTTCACCCATATTCTATAA R 2 1 2 1 101000 f 74 goat snp41163-scaffold532-3179623 26 31458164 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440790 Affx-122929839 AX-123311127 26 18594337 TTAAGGTCTGAAGGAGTAAGATAAGGCTTTGTGGC[A/G]AGGCAAAGGTGAAACTCCACTTGTTCCTTGAATGA R 2 1 2 1 101000 f 74 goat snp41162-scaffold532-3136183 26 31414202 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443739 Affx-122927132 AX-123314076 26 18653473 GTTAAAGGGAATTTAAATCTGTCTTTTAAAATTAG[A/G]TACAAGTGACCAGATGATTCAAAACATAACTGGTT R 2 1 2 1 101000 r 74 goat snp41161-scaffold532-3077047 26 31354845 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438177 Affx-122931835 AX-123308515 26 18697361 CAAGACCTTTGCATTTCTTGTTTATTTCTCCAGTT[C/T]CTTGCATTATTGATTCCTTCTCATCTTTCTTCCTT Y 2 1 2 1 201000 r 74 goat snp41160-scaffold532-3033159 26 31310843 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388727 Affx-122968969 AX-123259085 26 18757772 TGGCCCAGAGCAGGCGCTCATTAAAGCAGGATGGA[A/G]TGAACAAGTCAGCACCTAACAGTCCCTGAAGGTGT R 2 1 2 1 101000 r 74 goat snp41159-scaffold532-2972748 26 31250960 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382783 Affx-122973583 AX-123253141 26 18789791 GCCAGGGGAATTATCCTCATGAGTCTCACTGCTTA[C/T]GCTGAAAATGTATCCCAGCCCTGGATCAACTAACA Y 2 1 2 1 101000 f 74 goat snp41158-scaffold532-2940729 26 31218865 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410451 Affx-122952384 AX-123280801 26 18822530 ATAATGGGTAAGAATTGTGAACAAGGTGATATACT[A/C]GGTAAGAATCGGGGTCTTGGTTCAAATTTTAATTC M 2 1 2 1 201000 f 74 goat snp41157-scaffold532-2907990 26 31186249 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423453 Affx-122942591 AX-123293799 26 18918508 TTGGGTTATTGCAATAGTCTTCCCACTAGTTTCCC[C/T]GATTCCAGGATCAGACCGTTAACTCACCCCCTCCC Y 2 1 2 1 101000 f 74 goat snp41155-scaffold532-2812012 26 31089072 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787525 Affx-122954430 AX-385274549 26 18955900 GCATGACCAGTGTGAATGAAACAATCTTATATTAA[C/T]ACAAAGCAGTGTATAGTCATGTACTAGGCTACATG Y 2 1 2 1 101000 r 74 goat snp41154-scaffold532-2774620 26 31051973 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418122 Affx-122947123 AX-123288470 26 19027643 GTGCCCCCGTACAGCTGCTGGACTAATGATCACAG[C/T]TCCCTTTCAACTCCAGTATCCTCTGGGTTTCAGTG Y 2 1 2 1 101000 r 74 goat snp41153-scaffold532-2702877 26 30979884 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389871 Affx-122968145 AX-123260228 26 19067805 AAAAAGCAAGGTTAGTATGCTCTTACTTCTATGTG[C/T]AATCTAGAAAAGTAAAATATATGAAGCAGAGAACA Y 2 1 2 1 201000 f 74 goat snp41152-scaffold532-2662715 26 30938925 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438894 Affx-122930446 AX-123309231 26 19101671 TCGTGGGGCTGACAGAAAGAGGAGCCCAAAAAGAG[C/T]GAAACAGGAGAAAGGGGGGCAGGGCACAACCCTTC Y 2 1 2 1 103000 f 74 goat snp41151-scaffold532-2628849 26 30904895 T C 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38417605 Affx-122946875 AX-123287953 26 19155436 TGAGTTAATATTACACTGGAAGATAAAAGGCAAAA[C/T]GGAGAATATTTCCAGAAACTTCTAAGTTCCTTTGG Y 2 1 2 1 201000 f 74 goat snp41150-scaffold532-2575084 26 30850748 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418991 Affx-122946061 AX-123289339 26 19186244 TAAACCTACATATTTTAAAGCCACTTTCACATCCA[C/T]AGCTGAGGAATCCCTGGCCACCTGCCCTTGCTCAC Y 2 1 2 1 101000 f 74 goat snp41149-scaffold532-2544276 26 30819835 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402731 Affx-122958340 AX-123273084 26 19232394 GAGAATAGAGGCTCTGATTCTCCATTTGCAAACTG[C/T]GAATATAAATTTCAGAATTACAGAGGAGCAGATTC Y 2 1 2 1 101000 f 74 goat snp41148-scaffold532-2498126 26 30773980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425652 Affx-122940883 AX-123295998 26 19263257 GAGCTGACAATAATAAATCCTTATCTTTGAGTAGC[A/G]TTTTATAATTTCTACAGTATTTTTTTCTCACAAAT R 2 1 2 1 201000 r 74 goat snp41147-scaffold532-2467263 26 30743112 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428508 Affx-122938765 AX-123298850 26 19309923 AAAAGAGCATTATAATTTTATTAAACTCAAGCATC[A/G]TTTTAATTTTACTGTGTCTCTTAAGTCCAGTGAAC R 2 1 2 1 101000 r 74 goat snp41146-scaffold532-2420597 26 30700463 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773215 Affx-122952615 AX-385260358 26 19368482 AAATCAAGGCAAATCGATTCGATTCAGATGTCATA[C/T]ATTATCAGATAACAAAGGGACCTCCTTTTGTAGAC Y 2 1 2 1 101000 r 74 goat snp41145-scaffold532-2362038 26 30641851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446136 Affx-122925770 AX-123316472 26 19402517 TTCCATCCACCTGGTCTACTTTTTCTCCCTATAGC[G/T]CTAACCTTGTTAACTCCTATAGCGTCTTCACTTCT K 2 1 2 1 201000 r 74 goat snp41144-scaffold532-2328003 26 30607300 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389439 Affx-122968354 AX-123259797 26 19432307 GGACAGAGTTGACTTTCTGCAACTGTATAGGATAC[G/T]CTGAATTGAGTGTATTTAGCAAGATAGTCATTGAT K 2 1 2 1 101000 f 74 goat snp41143-scaffold532-2298213 26 30577486 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394786 Affx-122964824 AX-123265141 26 19470294 TGAGCTTTAAACCTGAAGTAATATAATTTTGACAC[A/G]ACATGATTAGTAGAAATGGTTCTTTGGTGTTTCTG R 2 1 2 1 101000 r 74 goat snp41142-scaffold532-2260226 26 30541694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437740 Affx-122931727 AX-123308078 26 19512878 TCAAGATGGGTAGAGTGGGACTGTTAGGAGATGTC[A/G]CCACCCCAAGGGAATGGCAGAGACAGAGAGTGATC R 2 1 2 1 101000 f 74 goat snp41141-scaffold532-2217642 26 30499144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792733 Affx-122958085 AX-385279713 26 19563102 TCAAGGAGGAAAGATGGTAGAAATGTAAAGCAACA[A/G]TGTCATGGTGTGATGAATACAATGGTGAAGGGGTG R 2 1 2 1 101000 f 74 goat snp41140-scaffold532-2167418 26 30448575 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389692 Affx-122968696 AX-123260050 26 19604959 GTAATAAAAACGGAAAAGATGGGCAGGGTTGAGAG[C/T]ATAAAGGAAGGTTTTAAAGAGAACCGAGCGACAGC Y 2 1 2 1 101000 f 74 goat snp41139-scaffold532-2125561 26 30406703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375714 Affx-122978638 AX-123246073 26 19683018 AATGCCAGACAGGATAAAACAGTTCAACTATCACT[A/G]TTTATTAGCCTGGATATTAGTATGAAGTGAAATCT R 2 1 2 1 201000 r 74 goat snp41137-scaffold532-2047502 26 30329111 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784431 Affx-122923442 AX-385271480 26 19736750 GGTCTTAGTGCCTGAAGAGCTTTTCAAGGGTAACA[A/G]CCTGTTTTGCAGTCAACTAGGTTGAAGCAGCTTCC R 2 1 2 1 101000 f 74 goat snp41136-scaffold532-1993770 26 30274666 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387002 Affx-122969943 AX-123257360 26 19779857 TAGCTCAGGCCAGAATGCTCAGCTGTAACAGGAGC[C/T]ACACCTGAATTCCACGTCTGTTTGTCTTCTTGCCA Y 2 1 2 1 101000 r 74 goat snp41135-scaffold532-1950663 26 30230958 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783655 Affx-122963726 AX-385270714 26 19812897 CTCTATTGGAATTCTATGGGTTTTATCATTTATGG[A/G]CCAGTTTGTTATTGTTTTGAATTGAGTTTCCCACA R 2 1 2 1 101000 r 74 goat snp41134-scaffold532-1917623 26 30197916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416915 Affx-122948053 AX-123287263 26 19851535 AGCATAGGGACACAGAGCATGTCATACAGAATGTC[A/G]CATTTCCAGAATACCACTCACATGAAGGCAACCTT R 2 1 2 1 201000 r 74 goat snp41133-scaffold532-1878985 26 30159545 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390191 Affx-122967801 AX-123260548 26 19888631 AGCATCTGGGTTCTAGCAACAGGGGTCTCAAGAAC[A/C]TGACAAAGGAGCTTCGAGTCATTTTGTAAGCAGTA M 2 1 2 1 101000 r 74 goat snp41132-scaffold532-1841889 26 30122588 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378810 Affx-122976557 AX-123249169 26 19950658 TCCTGGGCTCTCTTAGACTTTCCTCCCCAGGCTCG[C/T]GGTGAGCAGGAAAGGCAGCCCCAGTCTCAAGCCCA Y 2 1 2 1 201000 r 74 goat snp41131-scaffold532-1779862 26 30061008 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431154 Affx-122936569 AX-123301495 26 20002650 TCAAATTTGACCTGACTCTCTCAGTCCTAGAGTAA[A/G]TTAATGACTTTTATTTAAAATATCTTTTCCCTCTA R 2 1 2 1 101000 f 74 goat snp41130-scaffold532-1727870 26 30009081 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440661 Affx-122929935 AX-123310998 26 20051126 TACGGCCAGTGGGGGCAAGCTTACTGTTCTTCCTG[C/T]CTCTGAGATTAAGTGCCTCCAACACCCTTACTTCC Y 2 1 2 1 101000 r 74 goat snp41129-scaffold532-1679394 26 29960521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394184 Affx-122964920 AX-123264539 26 20098607 CAATAAGCATCAAGGCTCTTCTTTGTTTAAACTGT[A/G]TTTGAGAATGATGCAGATTTAGGTTGCAGGATGAA R 2 1 2 1 101000 r 74 goat snp41128-scaffold532-1631913 26 29916339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412380 Affx-122950808 AX-123282729 26 20131539 GTGATATTCATTTATTCTTTACTTGAAAGTCCCCA[A/G]CCGAGGGACTTCCCTGGCAGTCAGTGGTTAAAAAC R 2 1 2 1 303000 f 74 goat snp41127-scaffold532-1598981 26 29883400 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430182 Affx-122937358 AX-123300523 26 20161120 ACACAGGTTCGATGCAGCAAGGGGAGGCTCAGAAG[G/T]TGCGTGTGAATGGAAATGTAAGCACATGTGCGTGA K 2 1 2 1 101000 r 74 goat snp41126-scaffold532-1569400 26 29854352 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437525 Affx-122931917 AX-123307863 26 20191480 GTCTAACCCCCTCCCTAAACTCATCTCTCTTTTCA[C/T]AGCCCCCAAGGCCTTTCTCTCTCCTGGTTCTCTTC Y 2 1 2 1 201000 r 74 goat snp41125-scaffold532-1539040 26 29825821 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404864 Affx-122956486 AX-123275216 26 20234032 GGGGCTCTTAAAAAGGAATGCTTGCTATGCCTTCA[C/T]GGCTTTTTGGTTGTGGGAGGGTGCTGGGATTGCGA Y 2 1 2 1 101000 f 74 goat snp41124-scaffold532-1496488 26 29805583 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431664 Affx-122936802 AX-123302005 26 20271920 CCTAGAAATCCCTCAAGAAGAGTTATTTAAGTACC[G/T]CAAAGAAGACCACCCTACCTAACCTCTATTAAAGA K 2 1 2 1 101000 f 74 goat snp41123-scaffold532-1458600 26 29767809 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381031 Affx-122974646 AX-123251389 26 20304028 CCTAAGAAATGAATATAGATGTTTGAACGCAAGGG[A/G]GAAGGGAGCGTAACTCAATAAACAGGGTTGGGAAA R 2 1 2 1 101000 f 74 goat snp41122-scaffold532-1426492 26 29735679 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384633 Affx-122972160 AX-123254991 26 20357014 CCAGGGATGAAACTTGTGTCCCTTGCATTGCAAGG[C/T]GGATTCTTAACACCAGACTGACAGGTAAGTCCCTG Y 2 1 2 1 103000 r 74 goat snp41121-scaffold532-1373506 26 29682755 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399184 Affx-122960626 AX-123269539 26 20426403 TCTCATCTTCCTCTTCACCATGTTCTCCTCACCCT[A/G]AGACCCGGCCACAATGACCTTCCTCATGAGCTTTC R 2 1 2 1 201000 r 74 goat snp41120-scaffold532-1304117 26 29614784 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439573 Affx-122930081 AX-123309910 26 20460251 TTCCAGGCCCCAGAACTGGCAGCTCTGATTGTCTC[A/G]CCTTCAGGGCCCAACTGAGGTGAGCAGAGTCTTCG R 2 1 2 1 202000 f 74 goat snp41119-scaffold532-1270269 26 29580929 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765834 Affx-122954059 AX-385253281 26 20492338 AAGAACCGCAGGTCTAGGATGAAATTCTGAAGAAC[A/G]TTAAGATTTACAGGATGAGCAGAAGAGCCAGCAAA R 2 1 2 1 102000 f 74 goat snp41118-scaffold532-1238182 26 29548752 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780117 Affx-122928201 AX-385267214 26 20542517 AGGCCTGGGAATCACACACAACAATTTTTGATGAT[A/G]TGGGTTTGGCCTATACAACGACTTCAAATGAGCAA R 2 1 2 1 101000 f 74 goat snp41117-scaffold532-1188003 26 29498317 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387601 Affx-122970251 AX-123257959 26 20585083 AATGATCTGTTTAAAGATACACAAATTTATAAAAG[C/T]AAAGTCATGCCGCGCTATCAGGGATCAGACAAAAA Y 2 1 2 1 201000 f 74 goat snp41116-scaffold532-1145437 26 29455432 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273091 Affx-1111833306 AX-519546758 26 20614666 AAGAGGCCAAGAAACTGTATCCCTACAGAGTACAC[A/G]CAGAGTGTGACATGCACTTAATAATCTGTAGGGCT R 2 1 2 1 101000 f 74 goat 26_20614666_AF-PAKI 26 20614666 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320789242 Affx-122959571 AX-385276253 26 20617102 ACTGAGTAAAGATATCTATAGATAAACCATTGTTA[C/T]GACGTGACATAACATATATTAATGTGTAATATTAC Y 2 1 2 1 101000 r 74 goat snp41115-scaffold532-1113418 26 29423011 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380862 Affx-122975435 AX-123251220 26 20648218 TTGCAAACTGTCCACTGGTAATACACTCTAGTCAC[C/T]GCCCCTTAAAACAGAGTATTTCACTGCAGGCAGAA Y 2 1 2 1 101000 f 74 goat snp41114-scaffold532-1082302 26 29391796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421925 Affx-122943836 AX-123292272 26 20679063 GTGATGCTTTATAACGCTGTTTACTGCACTGACCT[C/T]TGAACACCCACACAACCACAGAACCAATCGGAAGC Y 2 1 2 1 101000 f 74 goat snp41113-scaffold532-1051457 26 29360632 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426980 Affx-122940391 AX-123297325 26 20729481 ATCCCAGAGGCAAGTGGAAGAAGCCTCTTGGGAAA[C/T]ACAACTGGGTCAGGCAAGCCCTACCTCCTCAGCAC Y 2 1 2 1 101000 f 74 goat snp41112-scaffold532-1001039 26 29310017 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463982451 Affx-1110252574 AX-515459568 26 20743605 ATGGCAGATACATCCACCCTGCAGAGCAGCCTAGC[A/G]CAAAAGGCACTGTTTCTCTCCACTGATTAGTCCCA R 2 1 2 1 101000 r 74 goat GoatD01.007646 26 20743605 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38436888 Affx-122933226 AX-123307226 26 20764646 TCATGGCCTTTAACTACTCTGCTACCCTGTCTGCT[G/T]CTTGGCCCATAAGGATCTTGCTGTCATTTGGGATT K 2 1 2 1 201000 f 74 goat snp41111-scaffold532-965874 26 29274659 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425318 Affx-122940940 AX-123295664 26 20797466 CAAACTTGTGCAAGGGCATGTTGAAGAGGAATGTG[C/T]GTAATGAATGAGAGTGCAGGCATCTGTACACTATA Y 2 1 2 1 101000 f 74 goat snp41110-scaffold532-933054 26 29241475 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426144 Affx-122940610 AX-123296490 26 20833328 TGAATGCTCATCTTCAAGGCTTCAACAAATGTATA[C/T]GCCCTAAGGCCACATTTTCACTGTTAGGAATTTAT Y 2 1 2 1 201000 f 74 goat snp41109-scaffold532-897192 26 29205485 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436205 Affx-122932590 AX-123306544 26 20893441 ATTTTCAAAGGCTGAGATGAAGGAAGGGTCTCTAC[C/T]GGCTTAATGTCACTCGGTTTTTTTTCTCTTTTAAG Y 2 1 2 1 201000 r 74 goat snp41108-scaffold532-837079 26 29145513 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416597 Affx-122947643 AX-123286945 26 20954148 AGAATTGAAACATGAGAGCTCTTGGATGGCTGATA[G/T]TTCATCTGATAGTTAACTACCATGAATCTTTTAGG K 2 1 2 1 101000 f 74 goat snp41107-scaffold532-776372 26 29084682 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450448 Affx-122922958 AX-123320782 26 20990570 GTGCCTTTCCTAAGTCGCCAGCTTGGTCTAATATC[C/T]CTCCTCTGTGTGCTCATGATACCCCTTGTTGACTC Y 2 1 2 1 201000 f 74 goat snp41106-scaffold532-739950 26 29048325 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787818 Affx-122928156 AX-385274841 26 21037799 TGGTGACTGGCTCACCTAAAATTTACTCTGCAGCC[A/G]CATGAGTATTCCTTATTTCTGTAAGAGGTCATGTA R 2 1 2 1 101000 f 74 goat snp41105-scaffold532-692721 26 29001146 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277801 Affx-1111836029 AX-519551299 26 21053597 GCTGGTGTCTGACTGGGATCCCCAACCTCAGCAGT[A/G]CTGACATTTCAGCCCGCCTCACTGGGTCCTGTACT R 2 1 2 1 202000 r 74 goat Random2.2K-2183 26 21053597 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38424047 Affx-122942072 AX-123294393 26 21081196 ACTTTTCCCCTCTGCCTTTTTCATTCTCAGAACCT[A/G]CTTTCAAGGAAAGGACCGATAAGCTCTTTAATTTT R 2 1 2 1 201000 r 74 goat snp41104-scaffold532-649324 26 28957065 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445647 Affx-122926159 AX-123315984 26 21149891 GGGAGCAGGGAACCTGGAGTGTCCCCCTTTCTCCA[A/G]TCAGTGTTTACAGGCTGAAGTCTGAGTCTGTGTCT R 2 1 2 1 101000 r 74 goat snp41103-scaffold532-580629 26 28888660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409339 Affx-122954184 AX-123279690 26 21185062 AAGCAGGGTAAGAAAGTTTTATCCTGGTTATTCTA[C/T]GGGAGTTCAAATTTTGTGTTACTCTCTCATTAAAA Y 2 1 2 1 101000 f 74 goat snp41102-scaffold532-545458 26 28853014 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274465 Affx-1111834213 AX-519548056 26 21208058 GTCGGGTGCAGAAACACAGCAGCGGGAGCAGCAAC[A/G]CCAGCACTGCCAACAGGTATTGAGCTGCAGAGGTT R 2 1 2 1 102000 r 74 goat GoatD01.025782 26 21208058 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38439662 Affx-122930597 AX-123309999 26 21249317 ATTACACTTAAACAGCTCTTCTAGCCAGAGGTAAA[A/C]TTGACCTCCCTGACTCCCTTCAACTCAATTCCACA M 2 1 2 1 201000 f 74 goat snp41101-scaffold532-481203 26 28788796 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788810 Affx-122952450 AX-385275825 26 21282360 TGGTAGTTTATAACGTCTACATCATTCCCACCCTA[A/C]TTCATGATGCCATGAAGACAGACAATATACACAAA M 2 1 2 1 202000 r 74 goat snp41100-scaffold532-448160 26 28756455 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 coat-colour SNP associated with coat colour multi-breed 38397326 Affx-122962304 AX-123267681 26 21320528 CCTTGAAGAAATGTTTCTTTCAAACACATATCTCC[C/T]CTATGATCCAGCAATTTCATCCTTAAGTATTTGTC Y 2 1 2 1 101000 f 74 goat snp41099-scaffold532-409992 26 28718026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776190 Affx-122934432 AX-385263318 26 21361551 GATCTTGCAGAATTCACTTATTATTTCTATGCTGG[C/T]TGTCTTTTTATAAATTGGGCAAAGGTCCTAAGCGT Y 2 1 2 1 101000 f 74 goat snp41098-scaffold532-368969 26 28677164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392279 Affx-122967541 AX-123262636 26 21398426 AGGCTTGTCTTGTCTCCTTGGTGGTCTTGGGCCTA[C/T]CACTCTGAATTCTTCAATCTGTGCTAAATCTGCCT Y 2 1 2 1 101000 r 74 goat snp41097-scaffold532-332094 26 28640142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405073 Affx-122957412 AX-123275425 26 21442217 AAAAAAAAGTCCCCAAGGGAGCACCTCTCTCTCCT[A/G]TCCTCACGTTGCAGGTGAGAACATGGCTGCTCCAA R 2 1 2 1 303000 r 74 goat snp41096-scaffold532-288303 26 28596788 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393155 Affx-122965540 AX-123263512 26 21480757 ATGGGAGTCGAAAAGCATGTGCTAGCAGAGAAGAA[C/T]GCTGGGACTTCGAGATCTGATCATGTCAAACCCAT Y 2 1 2 1 201000 f 74 goat "GoatD01.017079;snp41095-scaffold532-249763" 26 28558156 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320773670 Affx-122944294 AX-385260810 26 21556597 AAACTGTCATCAAATTGTCCATTCTTTGTAACCTC[A/G]TCATACTACCAACTTACACCGCACTCCCTCTGTCA R 2 1 2 1 101000 r 74 goat snp41093-scaffold532-173923 26 28481625 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277675 Affx-1111836030 AX-519551174 26 21583607 AGAACTGTTGCCAGGTCTTCCATCTCCTGTCTCCT[A/G]GGGTCCTGGGGAAGACCCCTCATCATCACCACAAG R 2 1 2 1 102000 f 74 goat Random2.2K-2184 26 21583607 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38405688 Affx-122956550 AX-123276040 26 21592562 GTACCTTTAAGGGCAAAGCAGACAGTCTCAAAGAC[A/G]CTCAAGAACACGGACCCACATCTATAGACACTCTC R 2 1 2 1 101000 r 74 goat snp41092-scaffold532-137958 26 28446812 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433844 Affx-122934443 AX-123304185 26 21623863 AAAATGAAAGACTTTACTTTCAGACAGAGATTCTG[C/T]GAAAAAGTTACTTAAAATTCCTTAACTTCCTATCT Y 2 1 2 1 102000 f 74 goat snp41091-scaffold532-106657 26 28416179 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446695 Affx-122924741 AX-123317031 26 21663430 ACACATGGGACACATTCAGCCCATGGTATGTAACC[A/G]CTCCCTCAGTGGCAAATCAATTCGCAGAAGACACT R 2 1 2 1 201000 f 74 goat snp41090-scaffold532-67090 26 28376492 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438189 Affx-122931827 AX-123308527 26 21708112 GCTGTCTGGCTTAGGAGCACCCAGTCTCCCATACG[C/T]TGGTTGTAAAGTACTTTAAAGGGGAAAGCTAAACC Y 2 1 2 1 202000 f 74 goat snp41089-scaffold532-22408 26 28331838 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403956 Affx-122957445 AX-123274308 26 21752519 TGCAAATTTGACCTGGTTTAGCCATTTCTGTGCTT[A/G]CTCTGTAGCCATTGCTCCTCTGGAAAGGGCTCAAC R 2 1 2 1 102000 f 74 goat snp11466-scaffold142-168434 26 28287078 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453416 Affx-122919888 AX-123323749 26 21838789 TGGGATAAGCCAGGTATCACTAAAGAAAATCACTC[A/G]TTTAGTTGACTTGCCTTCGCTGGAAAAGAGATGTT R 2 1 2 1 201000 r 74 goat snp11468-scaffold142-254704 26 28200537 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385191 Affx-122971725 AX-123255549 26 21871990 ATTTTGAGTTTTCTTTTAGAAATTAAGCAAAGAGA[C/T]CATTGTTTATTGCTTTTCTTTACTTTAGGATAAAT Y 2 1 2 1 201000 f 74 goat snp11469-scaffold142-287905 26 28167409 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771660 Affx-122960580 AX-385258818 26 21900839 CCTTCTTTCCCTCATTCTTTTCGGAGTGGTGTAAG[A/G]TTCTCTCTTAGCACCACCGTGAAGTCTCCACACAA R 2 1 2 1 101000 f 74 goat snp11470-scaffold142-316754 26 28138676 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783245 Affx-122936411 AX-385270310 26 21935026 TGTGATGACCTTCGTGTTGTCTAAGCCTTCTGTGA[C/T]ATGTGCCTCCTTAGATCCTGGTGCTTAGCTGGGCT Y 2 1 2 1 101000 r 74 goat snp11471-scaffold142-350941 26 28104044 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389761 Affx-122968241 AX-123260118 26 22002936 TCTGTCTGAACTCTGCTGTGGCCCCATGATGTGAC[C/T]GTAAGAGGATGGACTTGTCCCTCCAGTGGCCTCCC Y 2 1 2 1 201000 r 74 goat snp11472-scaffold142-418851 26 28035084 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787064 Affx-122920245 AX-385274091 26 22041442 AACCTCATCCTTCTTTAACAAGAGGTGCTGAAGCA[C/T]AGGCAAGTTTACATTGTCATATGTTTCACTTTTTA Y 2 1 2 1 102000 f 74 goat snp11473-scaffold142-457357 26 27996609 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419784 Affx-122945856 AX-123290132 26 22077244 GGGTGTGCCATGTCTATGAATTTTTAATACATTTA[C/T]AGACTGGTATAATAACCATCACAATCTGGAATCAA Y 2 1 2 1 101000 r 74 goat snp11474-scaffold142-493159 26 27960971 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395843 Affx-122964020 AX-123266198 26 22137817 CTTCCTGGTCAACTGACACAAGGGTGACCTCGCAC[A/G]AAACTACTCCCTTTCCTGGGCGTTGGCTTCCTCTG R 2 1 2 1 101000 r 74 goat snp11475-scaffold142-553732 26 27900413 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387688 Affx-122969818 AX-123258046 26 22170816 TTGAGATAGCAGCTTACAGGTACGTCACAGGGCAT[A/G]TTCACCTAGGCAGGTCCCGTCACCTAGGGCATCGC R 2 1 2 1 101000 f 74 goat snp11476-scaffold142-586731 26 27867328 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441916 Affx-122928600 AX-123312253 26 22224408 CTGGGACCCAGTGCAGTTTCAGTTGCAAGGAGAGC[A/G]CAGAAGAGCAAGGAAGATAAAGGACCAGAGAGATT R 2 1 2 1 101000 r 74 goat snp11477-scaffold142-640323 26 27813721 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397051 Affx-122962739 AX-123267406 26 22314750 TCTTCAGTACTTTAGAACCCCCTCCCCAAGAGATA[C/T]GGTCTCTGAGAACACAGGAAGACATCAGCTTCCCT Y 2 1 2 1 201000 r 74 goat snp11479-scaffold142-730665 26 27723121 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440431 Affx-122929416 AX-123310768 26 22351251 ATGAAGCAGTTTTAAATTTATATAGAGTCTTACTT[A/G]TCAGACTTTTCTTTTAGGATGCGCTGATCATCGTA R 2 1 2 1 101000 r 74 goat snp11480-scaffold142-767166 26 27686361 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429970 Affx-122938061 AX-123300311 26 22394387 TGAACATTTTCTCTGGCTTTTATGAGCTGGGTTTT[C/T]CCAAGAGGCCACATGGCAGAGGCCAGCACTGGTAC Y 2 1 2 1 101000 f 74 goat snp11481-scaffold142-810302 26 27643092 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450346 Affx-122922114 AX-123320681 26 22437349 GACCCAGCTTGTGGTCCAGCAACTAGCAGTTTTTC[C/T]GGTCAGCTTCTTATACAGCCAAATCTTGAGACTTT Y 2 1 2 1 101000 r 74 goat snp11482-scaffold142-853264 26 27600132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420126 Affx-122946011 AX-123290474 26 22495022 ACAAACCATCAGGGCTGAGAGAATCCTCAGACACT[A/G]TGAAGTGCAACCTGTTTTCTAGCCAGGTGAGAAAG R 2 1 2 1 201000 r 74 goat snp11483-scaffold142-910937 26 27545518 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414519 Affx-122949524 AX-123284868 26 22559566 CAGGGGCATCACCCCTGGCTCAGACCTAAAATGCT[A/G]TCATTGGGCTTTCAGCATGCACACCATGAGGTGGT R 2 1 2 1 101000 r 74 goat snp11484-scaffold142-975481 26 27481778 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775639 Affx-122920523 AX-385262770 26 22616129 TCTTGCTTTCCAGATGCACCTTGTTCTCGAACTTG[C/T]CACTGTTGTTTTCTAGTAGTTTTAAAGTTGAAAGT Y 2 1 2 1 101000 f 74 goat snp11485-scaffold142-1032044 26 27425543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424115 Affx-122942020 AX-123294461 26 22664499 TCAGTAATAGTCTGTCCCAGCAACATAAGATGTCA[C/T]AGAACAGGGAATTCCCTGAAGAAGCAGTGGTTAAG Y 2 1 2 1 101000 f 74 goat snp11486-scaffold142-1080414 26 27378811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799975 Affx-122935036 AX-385286901 26 22751509 GAATAAGCTAGAGATTTCAGAAAATCCAGATCATG[C/T]GAACATAGAAGCCAGTGGCAACCATATCAGGGCCA Y 2 1 2 1 101000 r 74 goat snp11488-scaffold142-1167424 26 27291739 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381046 Affx-122974632 AX-123251404 26 22787120 TCTGGGACTCAAAACCATCATGAAGAACTTTCCAG[C/T]GATTATGTTACCAGGTTTTAATGACCAAGAGAGCT Y 2 1 2 1 600000 r 74 goat snp11489-scaffold142-1203035 26 22787120 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769464 Affx-122974632 AX-385256634 26 22787120 TCTGGGACTCAAAACCATCATGAAGAACTTTCCAG[C/T]GATTATGTTACCAGGTTTTAATGACCAAGAGAGCT Y 2 1 2 1 101000 f 74 goat snp11489-scaffold142-1203035 26 27256215 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431861 Affx-122936071 AX-123302202 26 22821732 GTACTTTTTATGACTGTGAAAATGAGCCCTTTATC[A/G]TAATGGTGCATTTATTTTAGTTAAATTAGTTTATG R 2 1 2 1 101000 f 74 goat snp11490-scaffold142-1237647 26 27221682 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409308 Affx-122953095 AX-123279659 26 22860710 CTTTAATATAAAAAATCAGTTGCAAATATTTTGGC[C/T]GTGTAATCATCCACACTCTGCTTAATTATTCAAGC Y 2 1 2 1 101000 r 74 goat snp11491-scaffold142-1276625 26 27182765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405973 Affx-122955532 AX-123276325 26 22897750 CAACCCTCACTAATATTTAAAGTAAAAATGTACGT[A/G]TTCTATTTACCTTTAGGGCCTTGAACTCCCATGTC R 2 1 2 1 101000 r 74 goat snp11492-scaffold142-1313665 26 27146090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449394 Affx-122922708 AX-123319729 26 22939128 TCTTGTGTACTGTATCTTAAAATATAAGTATGCCC[A/G]TAGCTTTGAATTGAAATAGGCAGTATCGGAACAGG R 2 1 2 1 101000 r 74 goat snp11493-scaffold142-1355043 26 27104501 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778613 Affx-122946765 AX-385265724 26 23015429 AAGTAGTCCAACTCTATACTAATTAGGGGACATAA[C/T]AAAGTTGGAAATAAAGCAGTTGAAAAAGATATGTA Y 2 1 2 1 202000 r 74 goat snp11494-scaffold142-1431344 26 27028067 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421725 Affx-122944386 AX-123292072 26 23056613 AGAGAACCTACAAGAAAGCGATTTGTTCTTCCTGA[C/T]GGAGTGAAGGAAATGGACAGAGAGAGAACTGTCAT Y 2 1 2 1 201000 f 74 goat snp11495-scaffold142-1472528 26 26986492 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772257 Affx-122929480 AX-385259412 26 23096746 TCTTGTTCACATCATTATGATTGCTTAATTAGATC[G/T]TCAAAGTTTTCTGACCTTACGGCTTCTGCATATGC K 2 1 2 1 201000 f 74 goat snp11496-scaffold142-1512661 26 26946599 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792148 Affx-122921028 AX-385279133 26 23126525 TAATCATTAATTTTGAAGTAGACTAAACTCTTACT[A/G]TACTGAGGATAGCCACCTGAACAGTTGCATTTAAT R 2 1 2 1 101000 r 74 goat snp11497-scaffold142-1542440 26 26916684 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446623 Affx-122924794 AX-123316959 26 23159349 TCTCTGTATAAACAAGAGGCCAGAAGGTAATTTTT[C/T]GGTGAATTTTCTTCTGGAAGCAAAGGGGAAGCTGG Y 2 1 2 1 101000 f 74 goat snp11498-scaffold142-1575264 26 26883778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442880 Affx-122927660 AX-123313217 26 23195105 GCCTGGTAGAAAAGATGAAACTGAGCAGGACCCTC[C/T]TGGGTACAAAAGTCTATCACTCCTTTCTTAATTGT Y 2 1 2 1 201000 r 74 goat snp11499-scaffold142-1611020 26 26848039 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772394 Affx-122956338 AX-385259547 26 23223795 ATGTCATCTATTATTATCCAGATATATTACTGCTT[A/G]TAAAAGTAATAAGACAATGCTATCCCCTCCTGAAA R 2 1 2 1 101000 f 74 goat snp11500-scaffold142-1639710 26 26819340 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386415 Affx-122970816 AX-123256773 26 23269173 TGCCACCAGCTCAGAGACACTGATTCAGTTTCTGC[A/G]TTTGTTAAGTGAGGATAGTCATGCCTAGCTCACAG R 2 1 2 1 101000 r 74 goat snp11501-scaffold142-1685088 26 26774033 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772344 Affx-122976000 AX-385259497 26 23323804 TATCCCATAATTTAGGTATACAATTTTGGCAGAAT[A/G]TCACAGAAGTTATGCTGAGTTCTTCTCATTGCACC R 2 1 2 1 101000 r 74 goat snp11502-scaffold142-1739719 26 26718920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443039 Affx-122928152 AX-123313376 26 23353850 TCCCCACACCTCATCAACTCGCTCTCTTGTGTTGG[A/G]TCTTTGTAAGGATGAGCCCCCTCCTCCCAGCTGAA R 2 1 2 1 101000 f 74 goat snp11503-scaffold142-1769765 26 26688846 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401709 Affx-122959538 AX-123272062 26 23413600 GGGTGGGGTGGGAATGGCATTCCTATACTCTTCTG[C/T]GTAGATGTTTCCTTCAAAGGTGAGAACGAGGTATT Y 2 1 2 1 101000 r 74 goat snp11504-scaffold142-1829515 26 26628539 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383870 Affx-122973136 AX-123254228 26 23465216 TGCCTGTCTTTCTCTTCAGGCTGACTTATTGTACA[C/T]GCCTTTCATCTGCTCAGAATCTGATTTAAATATGA Y 2 1 2 1 101000 r 74 goat snp11505-scaffold142-1881131 26 26576786 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423059 Affx-122942954 AX-123293405 26 23508864 TCGCTAAGCAGGGGCCTGGTACTTGACCTGTGCTG[A/G]AAGAAACCTACCTTAGGGGAAAAGCTGACCATCGT R 2 1 2 1 101000 r 74 goat snp11506-scaffold142-1924779 26 26532923 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423370 Affx-122943141 AX-123293716 26 23544915 GCCCCATTCTGAGTGTGGCTGGGAGTGACCTGTTA[C/T]CCAGTGTACATTTCGTTGCTCCATCTATTGAGGAG Y 2 1 2 1 101000 r 74 goat snp11507-scaffold142-1960830 26 26496797 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415232 Affx-122948960 AX-123285581 26 23574535 GTAACAAGTCTATTTGGGGAGTGTTTCCCATGCCA[C/T]GAAACACTTTTCATATGCATCATTTCCTTAAAACC Y 2 1 2 1 101000 f 74 goat snp11508-scaffold142-1990450 26 26467498 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422097 Affx-122943577 AX-123292444 26 23638909 TTAAGGATTAGGAAATTGAGGTCCGTGACTACTTG[A/G]CCTCCATAAGATGACATTCCTAGTTTGCATAAAGA R 2 1 2 1 101000 f 74 goat snp11510-scaffold142-2054824 26 26402742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786898 Affx-122930477 AX-385273927 26 23788125 ACTGAAGAATCTGCTAGAGACTACTGCCATTAGCC[A/G]CTTGATGAACATCGGGAGCTACAGATAATTTGAAT R 2 1 2 1 101000 f 74 goat snp55582-scaffold861-1598308 26 26253087 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397587 Affx-122961998 AX-123267942 26 23826040 AAAGAAAAAATGCTCACCAGCCTGCATATTATCTA[C/T]CATCTACCATAAAACAAACCTAATGTATAAGCCAT Y 2 1 2 1 101000 f 74 goat snp55581-scaffold861-1560393 26 26214945 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273092 Affx-1111833307 AX-519546759 26 23847874 TGAATGCTGAGTTTTAAGCTAGCTTTTTCACTGTT[A/C]TTTTTCACCTTCAATAAGAGGCTCTTTAGTTCTTC M 2 1 2 1 303000 f 74 goat 26_23847874_AF-PAKI 26 23847874 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38397531 Affx-122962041 AX-123267886 26 23931881 CTTTGAGGTCTATGAGGAATATCTCACTAGGGCTA[G/T]CCCTCAGTGTCTGAACTGAGTAGACAGGGTAGAGA K 2 1 2 1 101000 f 74 goat snp55579-scaffold861-1454552 26 26109290 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399429 Affx-122961227 AX-123269784 26 23979272 AAGTATCTACAGACACCCAAAATTCATGGCCCCTC[A/G]TTTATTTTGATCCATAGCACTGCCATTCTCTGATA R 2 1 2 1 201000 r 74 goat snp55578-scaffold861-1407161 26 26061156 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377817 Affx-122977307 AX-123248176 26 24019042 GCAAGGAGAACTTAAGAACATCAACATTTTAAGGA[C/T]AGCAAGGGAAGGGGATCCAGGAAAGGAAATCAGGA Y 2 1 2 1 201000 f 74 goat snp55577-scaffold861-1367391 26 26021230 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777909 Affx-122976542 AX-385265024 26 24051630 TGGGCAAGACAAAGGAACTGGGAATTCTTTTAGGC[A/G]TACAGGTAAAGCTGAAATGATAAGATAACCAGTAC R 2 1 2 1 101000 f 74 goat snp55576-scaffold861-1334803 26 25988517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798599 Affx-122961778 AX-385285532 26 24111036 ATTGTGAATCTCATTCATACCTCCCGTGTCAGAGG[C/T]AAATTTATATTGGGAGAAAAGGTGTTTGGATAGGA Y 2 1 2 1 101000 f 74 goat snp55575-scaffold861-1275397 26 25928634 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401378 Affx-122959232 AX-123271731 26 24146174 AGGGAGGAGCCGGGTACTGGTGGTTTGGTGCTGTA[C/T]GGGCAGGGAGAGGATGGGAGGTTAGTGGAAAACCA Y 2 1 2 1 202000 f 74 goat snp55574-scaffold861-1240259 26 25893171 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782351 Affx-122969697 AX-385269427 26 24208112 AAATCACATTATATTAGGTAGCCTGATTATGAGCT[A/C]GTACCATATCCAAGAGGTCCTTTGGCTGTGGCAAT M 2 1 2 1 101000 r 74 goat snp55573-scaffold861-1178321 26 25830899 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426330 Affx-122940275 AX-123296676 26 24333261 TTCTTTTTTTTTAATGACTTTTCTGCCATAGGGTG[C/T]ATGTCTATTTTCTATGCTTAAAGTGTATAGGACAC Y 2 1 2 1 101000 r 74 goat snp55570-scaffold861-1053172 26 25703901 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438255 Affx-122931420 AX-123308593 26 24371796 CTGGTGTTTCTATAAAGATATGTTACAGTTTCTAT[A/G]TTGGACCAGACACACCTGAGAGGTCCCATCAAATA R 2 1 2 1 201000 f 74 goat snp55569-scaffold861-1014637 26 25665546 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450571 Affx-122922039 AX-123320905 26 24416383 ACATAAGCATATAGATATAATTATTAATTCCTGTC[A/G]TGTCCCCACATTCTAATTTTGTCTAGCTGCTCTGA R 2 1 2 1 101000 r 74 goat snp55568-scaffold861-970050 26 25620696 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398027 Affx-122961773 AX-123268382 26 24530146 AGGCAGAGGTTCTCAAAGTGAGACCACAGGGTCAG[C/T]ATTTGCAGCTTCACCAGGGAACTTATTAGAAATGT Y 2 1 2 1 101000 r 74 goat snp55565-scaffold861-856287 26 25507248 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435814 Affx-122932840 AX-123306153 26 24618347 CGGTAACAGCACTGCATATGCTAAGAAACAGCATC[A/G]CAAGAATTTTCAAGAATTTATCAGCAGCATGGTTG R 2 1 2 1 101000 f 74 goat snp55563-scaffold861-768086 26 25418129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777770 Affx-122974033 AX-385264888 26 24657995 AATTTGCAACTAACACATTGTCTTCCAATGGGACT[A/G]CTTGTTTTCAAATGGAACTACTTTCTATTTAGTTA R 2 1 2 1 101000 f 74 goat snp55562-scaffold861-728438 26 25378224 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435127 Affx-122933687 AX-123305467 26 24741373 CTCACTTGACCCCCAGCTTCCACTGTGAGCCCACT[A/G]TCCAGTTTAATTGTCAGCTGGGATTGTTCTACAGC R 2 1 2 1 201000 r 74 goat snp55560-scaffold861-645060 26 25294666 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768749 Affx-122924514 AX-385255926 26 24800239 AATAGGAACATACTCTCCAGGAAGAGTATATCACA[C/T]GGGAAATAGGAATGGTCAAGAAAACTGAGAGGGGG Y 2 1 2 1 101000 f 74 goat snp55559-scaffold861-586194 26 25236418 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277805 Affx-1111836031 AX-519551303 26 24873001 AAGAGGAAGGTAGATGAGGAGGTCAGGGTGATGAA[A/G]TGTGAGATGAAATCCAACTGCTATTGCTGGCATTG R 2 1 2 1 101000 r 74 goat Random2.2K-2186 26 24873001 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394383 Affx-122964631 AX-123264738 26 24911337 GGGAAAACACTCTTGCTTTTTTGGACCCAACAGTG[A/C]TGTGGCAGGGGAGAAAAAATCAGTCAGAAACTTAA M 2 1 2 1 303000 r 74 goat snp55556-scaffold861-475096 26 25124254 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277807 Affx-1111836032 AX-519551305 26 24917896 ACCTTCTACCTACACTTCATTCTGATTATTCACAA[A/G]TGAAAGCTCTCATGGTAATGAGCATCCCCCTTATC R 2 1 2 1 101000 r 74 goat Random2.2K-2187 26 24917896 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386597 Affx-122970686 AX-123256955 26 25084905 TTACTTTGATCTTTATACTTGCTGAGCATTAAATT[A/G]TCAATATATGTTCAACAATTTAACTTTACAGACCT R 2 1 2 1 101000 r 74 goat snp55552-scaffold861-301528 26 24950230 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396820 Affx-122963278 AX-123267175 26 25306306 CTCAGTTTCTACACAGTTTATACAGTTTATTTCTT[A/G]CTGCTAATCCTATTAGGTGTGTACTGTTATTATCT R 2 1 2 1 101000 r 74 goat snp55547-scaffold861-80127 26 24729767 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421193 Affx-122944152 AX-123291540 26 25427707 CTGTTTGCCAAGAGCAGTGTGTCACCTTTGGAACT[G/T]GATTTGGACAAACTATAAAAAGACATTTTTAGAGA K 2 1 2 1 101000 f 74 goat snp23636-scaffold2388-310522 6 113552425 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445486 Affx-122925200 AX-123315823 26 25460260 AAATTTTTCATGTTGGTTTGATACTGGGAGGTAAA[C/T]GGGTATTATCCATCTTGCAGCCGGAAAAGTGGTTC Y 2 1 2 1 201000 f 74 goat snp23635-scaffold2388-277969 6 113519909 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414277 Affx-122949603 AX-123284626 26 25498204 ACAGTCTTTGAAAAAGCAGTTCAGCTTTTCAGACC[A/G]GAAGTATTGAGTGGTGAGTAGTGAATCAGCAAGGA R 2 1 2 1 101000 r 74 goat snp23634-scaffold2388-240025 6 113481759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454283 Affx-122919273 AX-123324616 26 25734041 GAGGGCTGAGTCCCTCTGGGCAGAGGCAGCCGTAG[A/C]TGACAGCACGGGAGCTGGGGTCTGAGACCTTCTTC M 2 1 2 1 103000 f 74 goat snp23629-scaffold2388-4188 NW_017214680.1 11055 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406178 Affx-122956155 AX-123276530 26 25797985 GAATGCAAGCAGCAATGAAAATCAGATCAGTCTCC[A/G]TCTGACAGCCAGCAAGGAGATGAGGACCTCAGTTC R 2 1 2 1 101000 f 74 goat snp55587-scaffold862-59657 26 24590380 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788449 Affx-122978090 AX-385275466 26 25841396 AAAAAAATAGAAAGCTTGGTTAACACTGAAACTTC[C/T]GTTTGCTGAAGGAGAAAAATCAGCTGGAAACAAGC Y 2 1 2 1 101000 r 74 goat snp55588-scaffold862-103068 26 24546338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376720 Affx-122978965 AX-123247079 26 25869974 CCACACATTATACCAAAAGGAGTGCATCTGCCTAC[A/G]CACAGAGCACACAGACCTGCGTGCTCACTGAAAAG R 2 1 2 1 101000 f 74 goat snp55589-scaffold862-131646 26 24517786 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427492 Affx-122940004 AX-123297835 26 25937818 CCAAGTATTCCAGGAAGCCAATTAGGGGATAGTTC[A/G]AGGTAGATGACAGGCAGATTGATATATGAGTTGCA R 2 1 2 1 101000 f 74 goat snp55591-scaffold862-199490 26 24449877 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389272 Affx-122969015 AX-123259630 26 25975447 TATAAAATGAAAATACATATACATTCTTAATAAAG[C/T]GAAAAGTAAGGGTTCATAGACCTTCTTTTTCTGCC Y 2 1 2 1 103000 r 74 goat snp55592-scaffold862-237119 26 24412398 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424354 Affx-122941855 AX-123294700 26 26016043 GGGAAGGGAAATGTCTGTGAGACAATCAGCGGAAG[C/T]GGATCTTTCATACCTGAACAAACACATAATCATCC Y 2 1 2 1 101000 r 74 goat snp55593-scaffold862-277715 26 24371801 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275190 Affx-1111834756 AX-519548769 26 26044131 CCTGGGATGATTTCTCCACACTGCAGTCTGGAAGC[A/G]GTTG R 2 1 2 1 101000 f 74 goat GoatD01.051627 26 26044131 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320778433 Affx-122960759 AX-385265547 26 26095619 CTTGGAGGGCACACTGCATGCTTTACGACTATAGA[C/T]GAGCTACTTTCTACAGCAAGTCAATAATGGCGACA Y 2 1 2 1 101000 r 74 goat snp55595-scaffold862-357291 26 24290858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436020 Affx-122932740 AX-123306359 26 26137312 ATGGACACAATCATTTTGTTTTAGAGATAAGGAAA[C/T]AGTATTGTGGTGAGGTTAATAAGAAACAAACCAAC Y 2 1 2 1 101000 r 74 goat snp55596-scaffold862-398984 26 24248745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451059 Affx-122921430 AX-123321393 26 26166051 TTAACTGGGAGCTAAACTTCCCTCCCATATTACCA[C/T]GCAACGTCTTGTGTCTCTTGCAAATACCACCACCG Y 2 1 2 1 101000 f 74 goat snp55597-scaffold862-427723 26 24219710 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396987 Affx-122963152 AX-123267342 26 26245509 ATGAGTTCCAATCTGCACATCCTGGGAAAGGGCCT[A/G]TGCAATTAATTAACACTGAAACTTGCTTCATTTGC R 2 1 2 1 201000 r 74 goat snp55599-scaffold862-507181 26 24139888 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422129 Affx-122943551 AX-123292476 26 26315864 TTTTGCTGGTCAAGTGCCAGTACCCACATTTAGTA[C/T]TTGGTACCAGGTGATTTCAGACAAGTCTAATAATA Y 2 1 2 1 101000 f 74 goat snp55601-scaffold862-577536 26 24069988 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273145 Affx-1111833310 AX-519546808 26 26354395 CCTTCACCAGTCCCAGCAAGATCTAAGCCGCCCCA[A/G]ATCTCCGGGACTTCATCTCCTTCTGCTCTCTCTTG R 2 1 2 1 102000 r 74 goat 26_26354395_AF-PAKI 26 26354395 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38434070 Affx-122934183 AX-123304411 26 26389324 GAGCTATTCTGCAAGGAAAAACCAAGATGTGAAAT[A/C]AGAATTCTTCTAGAGATGGCTATTTACATCTCTGG M 2 1 2 1 101000 f 74 goat snp55603-scaffold862-650996 26 23996545 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443859 Affx-122927518 AX-123314196 26 26426028 ACCCACAATACTTGAGGGCCATTGTTGCATTTGTG[A/C]TTCTTTTCAAGCATTGTTAAAGAAAAAAATCTCAT M 2 1 2 1 101000 f 74 goat snp55604-scaffold862-687700 26 23959845 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398946 Affx-122960986 AX-123269301 26 26483747 ACAAAGGATAATGGATAGCATATCACCATGGACAA[C/T]GTCAGGATATTTACCATAACAAACAGCAGGAGGCA Y 2 1 2 1 101000 f 74 goat snp55605-scaffold862-745419 26 23902198 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453819 Affx-122919558 AX-123324152 26 26515591 CTTTCTAGAGAACCCAAACAGTGTCAGCAGTCATT[C/T]AACTTAAGAATTTTTGTTCATTGAAAGATGCTATT Y 2 1 2 1 101000 f 74 goat snp55606-scaffold862-777263 26 23870391 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402714 Affx-122959196 AX-123273067 26 26544113 GGATCTTTTCCCTCCTCTGAAGGACTCAGTAGAAG[C/T]GAGAATGATGACAAGGACTTGCTCCTCCACCGTGA Y 2 1 2 1 201000 r 74 goat snp55607-scaffold862-805785 26 23842041 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381239 Affx-122974502 AX-123251597 26 26585763 ATTAAGAAAGAGACATGTCAGAAATGAATTGTGAA[C/T]AGTTGGCATTTCATGTACTATGGAACTCAACAGAA Y 2 1 2 1 101000 r 74 goat snp55608-scaffold862-847435 26 23800178 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445896 Affx-122925949 AX-123316233 26 26630601 CAGAGCATCCTTCCTTGTTCTTCCCTGGCTTCTAG[C/T]GGAGGACACCAGTCTTGCTGGATGAAGTCCCACCC Y 2 1 2 1 101000 f 74 goat snp55609-scaffold862-892273 26 23753996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410622 Affx-122952095 AX-123280972 26 26659724 AGAAAATGCTTGCCATGGTCCAGAGAAAAACTCGA[C/T]AATTGTTAGCTATTATTGGGGAGCAGTTTATGATA Y 2 1 2 1 101000 f 74 goat snp55610-scaffold862-921396 26 23721419 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796545 Affx-122978703 AX-385283491 26 26693000 CGCCTGCCCCATCCCTATAACCAAAAGTAATTATT[A/G]CATTAATTTCTAGTATTATAGGTTACCATTGTCTG R 2 1 2 1 102000 f 74 goat snp55611-scaffold862-954672 26 23688041 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437530 Affx-122931912 AX-123307868 26 26738730 ACAAAGCTACCACAGGTGTTACTATCTTCCTGGAG[C/T]CACCTCCTTTCTGCTATTCCAGAATCCCTAATTCC Y 2 1 2 1 101000 r 74 goat snp55612-scaffold862-1000402 26 23641574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429116 Affx-122938014 AX-123299458 26 26792757 AGGTAATACCTGGCTTTGTTAAAATTATGGAACAC[A/G]TTCCACATAATCATGGCCTGCACTGTACTTATATG R 2 1 2 1 101000 r 74 goat snp55613-scaffold862-1054429 26 23588454 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783073 Affx-122941318 AX-385270140 26 26850613 CAAGATAAAGAGGCTTTTAAGAATCTTAAAGAGTA[G/T]TGTCTTCTGCATTCTGGTTCTCAGCCCAAGCAGAG K 2 1 2 1 101000 r 74 goat snp55614-scaffold862-1112285 26 23529735 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379448 Affx-122976094 AX-123249806 26 26887710 ATATGTATGCTTCTGTGCCAATCAAATCCTGGCAC[C/T]AGAGAAGCCAAATAGATAAGGGCATAGAGCCAAAG Y 2 1 2 1 201000 f 74 goat snp55615-scaffold862-1149382 26 23492263 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414444 Affx-122949951 AX-123284793 26 26998936 AGTAGCTTTAAATGGGAAAAAGAACAGTTCCCAAG[C/T]AAATGATGGGAAAACTACCTGCCATTTAGAAGCCA Y 2 1 2 1 101000 r 74 goat snp55618-scaffold862-1260608 26 23379762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424586 Affx-122942212 AX-123294932 26 27105945 CTTCAAAATGAGAACCAAGAAAGACTCTCCTCTTC[G/T]CCAGACCCTGGTATTTATAATGCAGGAGGAAATAG K 2 1 2 1 101000 r 74 goat snp55620-scaffold862-1367617 26 23272759 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450501 Affx-122922512 AX-123320835 26 27168566 TTCCTTAATCCCTCATGGATGCTTTTATTTAATAC[C/T]ACAAATAAGGCCCAAAAGTGCCCTAAACTCCAAAC Y 2 1 2 1 201000 f 74 goat snp55621-scaffold862-1430238 26 23211503 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765057 Affx-122969695 AX-385252625 26 27211332 TGTGAATAATCTTTGGTCCATTTCAATTAGGTCAG[A/C]TCTCTTGCACTCTGTTTGATAAATTAAACTGAGGT M 2 1 2 1 101000 f 74 goat snp55622-scaffold862-1473004 26 23168039 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785483 Affx-122942331 AX-385272528 26 27267605 ACATAAATAAATGACACCTATTCACAAAAGTCTGG[C/T]AAATAGCAATTCATCTTCCTTCCACAAAAGTGAGT Y 2 1 2 1 101000 r 74 goat snp55623-scaffold862-1529277 26 23110814 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408861 Affx-122954000 AX-123279212 26 27318648 TGCCAAGATTAGAGGTGTCTCAAAACCTCAGATAT[A/C]GTATAGAATATCTCAAGAGAATACACTCTGTGGTG M 2 1 2 1 101000 r 74 goat snp55624-scaffold862-1580320 26 23059233 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436883 Affx-122933230 AX-123307221 26 27355667 CCAGTCCTTATAGACTGCTCTCTACATTCATGTCA[C/T]AGACAACAAGCATGTTTTTAGAGAGTGGGAGAAAT Y 2 1 2 1 101000 f 74 goat snp55625-scaffold862-1617339 26 23024489 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452964 Affx-122920162 AX-123323297 26 27406919 AAAATGAAAAATGTGCCACTTAAATCTAATTATTC[G/T]ATGGTGTATCTCTACTCATCCTAGCCTCCTATTTA K 2 1 2 1 101000 r 74 goat snp55626-scaffold862-1668591 26 22973300 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450666 Affx-122921917 AX-123321000 26 27436061 AAGTATAAAGAAGACAATTTTACCAGGAAGACATC[A/G]TCAAGAGGGAGAAAAGCATTCTCTAAAAAGTGATA R 2 1 2 1 101000 f 74 goat snp55627-scaffold862-1697733 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451543 Affx-122921087 AX-123321876 26 27471297 GAAGAAATGTATTTTGAAAAATAATGTGTTTTAGG[C/T]AATTCAATTTGGGTATATTTCATTGAACAGTGGGA Y 2 1 2 1 103000 r 74 goat snp55628-scaffold862-1732969 26 22907643 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410432 Affx-122952401 AX-123280782 26 27582086 AGTCATTACCCTTTCAGATGGGAACTCCTTAAAGG[C/T]GATGTTTGAGAAAGAGTTTAAATAAGTAAATAAGT Y 2 1 2 1 201000 r 74 goat snp55631-scaffold862-1843758 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277683 Affx-1111836034 AX-519551182 26 27656916 GCTCCTTTTACAAAGTGCTTTGCCATTGCAATCTG[A/G]CGACCCCAGGGGGCTGGCAGGCATCACAGTTTCCA R 2 1 2 1 101000 f 74 goat Random2.2K-2190 26 27656916 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382858 Affx-122973528 AX-123253216 26 27697200 AGGCAGCTTGCTTGCCACAGTAATAATATTGATGG[C/T]AATAAATGGAAACAGTTTATTTGAACAAGAATAAG Y 2 1 2 1 101000 f 74 goat snp55633-scaffold862-1958872 26 22800771 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408475 Affx-122954424 AX-123278826 26 27757765 GGCTCACACTTCAAGGTAAAGCCACCAGTAGCATT[A/G]CAAGTGCTATCTGAATATGGGGAGAATAGAGAATT R 2 1 2 1 101000 f 74 goat snp55635-scaffold862-2019437 26 22739450 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277813 Affx-1111836035 AX-519551311 26 27785852 GAAATCTCAAATGATCCATTATGTGAAGAAAAATA[A/G]CTGTCATTATGTGTTCTCTCATATGTGATTATAAT R 2 1 2 1 101000 r 74 goat Random2.2K-2191 26 27785852 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320788364 Affx-122940456 AX-385275382 26 27787938 GGAGAGATATATTCAGACATTTCTGGAAGTCACTA[A/G]CTTGGTAACACTATTCAAAATTGCCTAAGCCCATT R 2 1 2 1 101000 f 74 goat snp55636-scaffold862-2049610 NW_017200173.1 6616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784012 Affx-122931369 AX-385271066 26 27826046 AATGGAAACTTGTGTTCTTTGACAGTGTAATTATT[A/G]CGCTCTGTCAAATTACTTGGCTTTTTTTAATAAAA R 2 1 2 1 201000 r 74 goat snp55637-scaffold862-2087718 26 22672614 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783688 Affx-122937147 AX-385270746 26 27867238 TGTCAAATGGACCAATTGCAATGCCATTGGGATGC[A/G]CCTAGTGCATTGCCCATCACATGGTAGGTATTCAT R 2 1 2 1 101000 r 74 goat snp31724-scaffold353-1134256 26 22631855 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415571 Affx-122948636 AX-123285920 26 27908373 CTGCATATATTACACATTATGAGTGACTCAAGAGA[C/T]ATTCCAGAATAATTTTGACAACATGTATTTTCCAT Y 2 1 2 1 101000 f 74 goat snp31723-scaffold353-1093121 26 22589870 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402881 Affx-122958223 AX-123273234 26 27965305 CAATTTGAATTACTGAAAAATAGGCTTATATAAAA[C/T]AAAAATCCATTTTCCTATGACTCTGGATTACTGGT Y 2 1 2 1 201000 f 74 goat snp31722-scaffold353-1036189 26 22532574 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781637 Affx-122928134 AX-385268721 26 28011282 AAAGTGTTTGACTATCATACTGGGAAGACAGCCAG[A/C]CACAAACTATTATTCTGAGAACCATGTTGAGGAAA M 2 1 2 1 101000 f 74 goat snp31721-scaffold353-990212 26 22486468 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783636 Affx-122945449 AX-385270695 26 28066121 ACATACTAAATGTGTTGAGATTTAATTTCAAAGCC[A/G]CAAAGCATGGGCATGATTACCATTTCAACTTTTCA R 2 1 2 1 101000 r 74 goat snp31720-scaffold353-935373 26 22438382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783749 Affx-122927572 AX-385270805 26 28096080 ATCCAAGTCCAGCTTTCTATCTAAGGCATCATCCT[A/G]TTTGAGTTCTAAAGAGTTAATTGCAGCCTTAATTT R 2 1 2 1 101000 f 74 goat snp31719-scaffold353-905414 26 22407910 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770717 Affx-122942481 AX-385257881 26 28129139 CCTATTCTGATTTTAATCTCAAGAAGTCAGGAATG[C/T]AACAGCAAAAGACTTAATAAGAATTATTACTTATT Y 2 1 2 1 101000 f 74 goat snp31718-scaffold353-872355 26 22378865 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421057 Affx-122944516 AX-123291404 26 28171400 GGACACACAATCTGCCTCATTGTACTTTTCTGAGC[A/G]TCTCTTCTCACTTTAAAAATCTCCCTGAGCAAATG R 2 1 2 1 101000 f 74 goat snp31717-scaffold353-830094 26 22256612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774317 Affx-122949515 AX-385261453 26 28256995 GATTAAAGAAGATCATAACCAGTATTAAGATATTC[A/C]TCATCCTTCTGGACATATTGGAGGTAGATTAAACA M 2 1 2 1 101000 r 74 goat snp31715-scaffold353-744499 26 22170314 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435288 Affx-122934039 AX-123305628 26 28292903 GGGAGCAGTTGCTGAGAGTGATCACAGATATTTAT[C/T]AAGTACTTTCTCTGTGCACAGCTTCTGCTGACTCT Y 2 1 2 1 101000 f 74 goat snp31714-scaffold353-708591 26 22133827 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393264 Affx-122965456 AX-123263621 26 28332849 TAATACTGTCCTCCTTCATCATTCTATCTCCATCT[A/G]TACTGCAGTTTTCTAACATTTATTTTCTAAACATT R 2 1 2 1 101000 f 74 goat snp31713-scaffold353-668645 26 22094411 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375848 Affx-122978525 AX-123246207 26 28373338 TTATGCATATGTGTGTGACACACACATAAGCAACC[A/G]TATACACACATATCCACATATTTATAGCATGTATA R 2 1 2 1 103000 f 74 goat snp31712-scaffold353-628156 26 22052275 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399470 Affx-122961195 AX-123269825 26 28430295 CAAGCAACTTGAGTAAGGTCACACAGCTATAAGAC[A/G]TATAACCCCTGTGACCACTGCATTTTACCACTTCC R 2 1 2 1 201000 r 74 goat snp31711-scaffold353-571199 26 21994882 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779566 Affx-122930156 AX-385266669 26 28472714 CAGAAAATCTTAAGTGCAAAATACTAAAATGTCTA[C/T]AGAGATGGGTGTATGGAATATATTAAAATAGGACT Y 2 1 2 1 101000 r 74 goat snp31710-scaffold353-528780 26 21951685 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432262 Affx-122936342 AX-123302603 26 28527838 GAATAAGTGATGTGGGACACATTTTTCTGTACAAG[C/T]AGATGACTTTTTCTGGGTAATGTTGATTAGTAGAT Y 2 1 2 1 101000 r 74 goat snp31709-scaffold353-473656 26 21895780 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425174 Affx-122941053 AX-123295520 26 28589115 GAAATTGTTCACTTTGGTCTTCTGTCATAGAAACA[C/T]ACAACACAATCCATTTGGTAAGGGATGTAAACTAG Y 2 1 2 1 101000 f 74 goat snp31708-scaffold353-412379 26 21834207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790979 Affx-122974778 AX-385277976 26 28641201 TGTAGGAGATGGTGTGTGTTATTTGAAGTCCTGAG[C/T]GCAATGCTTGGTGTGTATAAAATTCTCAGTAACTT Y 2 1 2 1 101000 f 74 goat snp31707-scaffold353-360293 26 21781180 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396431 Affx-122962991 AX-123266786 26 28693283 TACAGTTCATTTTCATGGCAATAATCTTATAATGT[A/G]CTCATTGTTCAAACACCTATCTTCCAAGATCACAT R 2 1 2 1 101000 r 74 goat snp31706-scaffold353-308211 26 21729040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411190 Affx-122952375 AX-123281540 26 28739781 GATGGGCTGAGATGTGTCAAAGTGCACTCAGAAGA[C/T]AGGACAAGAGTATCCAGGAAAGGAAACATTGGAGG Y 2 1 2 1 101000 f 74 goat snp31705-scaffold353-261713 26 21683492 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394394 Affx-122964622 AX-123264749 26 28776710 TGGTATCCCCTTATAGCCTCAGGAATTTCACACAT[A/G]ATTCATCAGAGACGGATAATGATGTAGTGCTTAAG R 2 1 2 1 201000 r 74 goat snp31704-scaffold353-224784 26 21646900 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375668 Affx-122978674 AX-123246027 26 28824450 ATGAAGTGGGGTGTAGGAGAGCAGTCCCCCTCCTC[C/T]ACCCCCACAATCATGCTTAGCACCAAGACCAAAGC Y 2 1 2 1 201000 r 74 goat snp31703-scaffold353-177044 26 21598241 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380807 Affx-122975087 AX-123251165 26 28863115 GGTGGGGGGTGCTTGTTTAAAATCTCCCTCCAGAT[A/G]TTGAAACCGAATCTCCAGGGCTGGGACCTGGGAAC R 2 1 2 1 101000 f 74 goat snp31702-scaffold353-138379 26 21559581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383392 Affx-122973503 AX-123253750 26 28893340 CACTTTCCATCCTATGATGCCACCATTCCAGCTGG[C/T]GGAAGGGGAGTAGTATGGAGAGGGCACATCTGACT Y 2 1 2 1 103000 r 74 goat snp31701-scaffold353-108154 26 21529500 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435461 Affx-122933459 AX-123305801 26 28928002 TGGAACACAGCACCTGACAAACACTCTTTAACAGA[C/T]GTTAGCCCCTGTGTGTCTTCCATCCTCCAGTCGCA Y 2 1 2 1 101000 f 74 goat snp31700-scaffold353-73492 26 21494899 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463980729 Affx-1110255141 AX-515457866 26 28944274 CTCATTCGAGGAGTCCATCAAAAGAATAAGTCTAC[A/C]TCTGGGTTTGACATTATCAACATGCTGATGGGCTT M 2 1 2 1 101000 f 74 goat GoatD01.005086 26 28944274 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38379464 Affx-122976084 AX-123249822 26 28962465 ACATTAAACATGGTGTGTTTCTTGGCCCCACCAGA[C/T]ACTTTCTACCTTTTCCTCCTGTGTTCTCTGCCCAG Y 2 1 2 1 201000 r 74 goat snp31699-scaffold353-39029 26 21460300 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791631 Affx-122946175 AX-385278622 26 28992004 GCCTTCAAACCAAATCCTTCCTGAAAACAGTAACA[C/T]ATTGACCCAAGTTTTCACCAAAATCTAAATGTCTG Y 2 1 2 1 101000 f 74 goat snp31698-scaffold353-9490 26 21430754 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375931 Affx-122978463 AX-123246290 26 29023488 GATTAGGAATAGGAATAATAGATCTTTGTATCACC[C/T]GAAATTTTGATCTTAATTTTTTTGATCGAGGAAGA Y 2 1 2 1 201000 f 74 goat snp13435-scaffold1519-389838 26 21399510 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380838 Affx-122975063 AX-123251196 26 29053967 GAGAATTCTGTTCCCTAAGGCTGCTACCTAAGGTC[G/T]CACAGAGTACTTATCTCTTGACTTCAGGCCAGTAC K 2 1 2 1 101000 f 74 goat snp13434-scaffold1519-359359 26 21369025 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412826 Affx-122950467 AX-123283175 26 29113307 GCTGAATACATCTCAGAGGTTTTCAGAAGGAAGAA[C/T]GTTTTTTAAAAATTTAGATAACAGCACAGAAGCTC Y 2 1 2 1 101000 f 74 goat snp13432-scaffold1519-300019 26 21309779 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375570 Affx-122978746 AX-123245929 26 29165846 AACCTACCACAGGAAGAGGTAGGAAGTTGGACTAC[A/G]GAGGGCAGAAAGAGTGCGGTGGGTGTGCCTCTTAA R 2 1 2 1 101000 f 74 goat snp13431-scaffold1519-247480 26 21257346 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780724 Affx-122937283 AX-385267814 26 29202064 ACTGTTGAGTGATCTTTTCCCTTAAGATGCTAATC[A/G]TCTCCCTGTGAGGATAAAGCTAATGTACAGCAAGC R 2 1 2 1 101000 r 74 goat snp13430-scaffold1519-211262 26 21221142 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785980 Affx-122973440 AX-385273016 26 29239884 TAAGAGTGCAGCCAAATTAATGGCAAGGATATGTA[C/T]GATTTAGAAGAAGCTATAAAAACACAGGCTTCTTA Y 2 1 2 1 102000 f 74 goat snp13429-scaffold1519-173442 26 21183085 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404734 Affx-122957240 AX-123275086 26 29289813 AAATATTGACAAGAGCAACAATAGCACCTGCACAA[C/T]GGGGCTGTGAGGAAGGAGAGAGACTGCTTGTAGGA Y 2 1 2 1 201000 f 74 goat snp13428-scaffold1519-123513 26 21133201 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766851 Affx-122950338 AX-385254172 26 29342522 GTTTTGTGTTGTTTTCCATCAGTGGCAGATAGATG[C/T]GATAAGCTCTAAAGTAAAATACGATGAATATAATT Y 2 1 2 1 101000 f 74 goat snp13427-scaffold1519-70804 26 21080024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416204 Affx-122948240 AX-123286553 26 29412072 CAACATAAGACCTTCTGGCCCCAGGTCCTTAATAG[C/T]GGAGGGAAATCTGCCCTTCAATTCACTCAACCCAG Y 2 1 2 1 101000 r 74 goat snp13426-scaffold1519-1254 26 21010188 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377646 Affx-122977864 AX-123248005 26 29439124 GAACCAAGCTCCGTCTCACTTTGAGGCTTTGCACA[C/T]GTCTGACTTGGAGCTGCCCTGGTGGCTCTAGTGGT Y 2 1 2 1 101000 f 74 goat snp47651-scaffold67-6530294 26 20983114 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382622 Affx-122973698 AX-123252980 26 29504244 GCCCAATAGGATAGCAGTAATTAAATCCAGGAACC[A/G]TGTTTCCTTCAGCAGTGGTAAGGGATTCAAAAGTG R 2 1 2 1 101000 f 74 goat snp47650-scaffold67-6465174 26 20919199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435833 Affx-122932824 AX-123306172 26 29553607 CTTGAGCAGAAACTGAAACAATACAAAGGGACCTA[C/T]GCTGCATGCATGCAGAAGTCTCAGGTAATTGCTTT Y 2 1 2 1 201000 f 74 goat snp47649-scaffold67-6415811 26 20869840 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436034 Affx-122932728 AX-123306373 26 29583997 CAGATGCTGGTGGTGCTTCAGATGCTGGTGGTGAC[A/G]TTGCGGGTGGGAGACAGGGTAGATGGAGCTACAGA R 2 1 2 1 201000 f 74 goat snp47648-scaffold67-6385421 26 20840000 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793179 Affx-122963994 AX-385280157 26 29635859 CCACATTCCAATTTGTGGATTTTTACCTCCATGGT[A/G]TTGTTTTGACATGTTCCTCTGTTCCCTGTGTTTTC R 2 1 2 1 101000 f 74 goat snp47647-scaffold67-6333559 26 20788538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429467 Affx-122938482 AX-123299809 26 29672014 AACCAGCAAATTCCCAATTTCAAGCAATGGTGGCA[C/T]GAACATTGAAAACCCTTCCCCAGATCTCCACTCTC Y 2 1 2 1 101000 f 74 goat snp47646-scaffold67-6297404 26 20752334 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380266 Affx-122975427 AX-123250624 26 29710973 TGCCATGAGAACTCCTCTGTTACTTAGCAACCAGG[C/T]TCAGCACACAGCCAGCTCAATGTGGAACAAAGCAG Y 2 1 2 1 201000 f 74 goat snp47645-scaffold67-6258445 26 20713614 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401773 Affx-122959491 AX-123272126 26 29768782 ACTTTTATTACAGTTAGCTTATTATAATAAATTTA[C/T]AACTTATTGCCAAAACTTTTGGAAATAGCCTGAAT Y 2 1 2 1 202000 f 74 goat snp47644-scaffold67-6200636 26 20655833 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433140 Affx-122935683 AX-123303481 26 29801265 TGGTTACCCAACTTCTCCAAGCCTCATTTTCCTCA[G/T]TTACAAAACTGGCACGAAGGAAACAGCATCAGCTT K 2 1 2 1 201000 r 74 goat snp47643-scaffold67-6168153 26 20623401 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273100 Affx-1111833311 AX-519546765 26 29820465 ACTTCAGTGGTGTCTGACTTTTTGCCACCCCATGG[A/G]CCACAGCTTGCCAGGCTTCTCTGTCCATGGGATTA R 2 1 2 1 303000 f 74 goat 26_29820465_AF-PAKI 26 29820465 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38432877 Affx-122935347 AX-123303218 26 29831741 TTCATAAACCTGGGAACTGAGGGAATGCTTACAAA[A/G]CTTCATAGCCTTTACCACGGGTGCCTGAGCATACT R 2 1 2 1 101000 f 74 goat snp47642-scaffold67-6137677 26 20592909 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421521 Affx-122943885 AX-123291868 26 29918628 TAACATGCACAAACCAACACTAAGTACAAAGACAG[C/T]AAATAACATTTTATATTTCTACCTAAAAATTCAGC Y 2 1 2 1 101000 f 74 goat snp47640-scaffold67-6050790 26 20506203 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396732 Affx-122962799 AX-123267087 26 29959100 GTTTAAATATACACACACACCCCTTCTTCCATAGA[C/T]AGACTGAAGAGAGCTGTCTTCTTTACAATTCTCCT Y 2 1 2 1 201000 r 74 goat snp47639-scaffold67-6010318 26 20465367 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382299 Affx-122973914 AX-123252657 26 30059851 AATGCCCAGATGGCTAAGATACCCATCACCAAGCA[C/T]GGAAAGCCTCAATTCCAGCTGGAACTCCCACCTCC Y 2 1 2 1 101000 r 74 goat snp47637-scaffold67-5909567 26 20364287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433542 Affx-122934996 AX-123303883 26 30089805 ATTAAAAAGCCCTGATACAAGAGCTCTTTGTCAGA[A/G]TTCAAAATGTGAGGGCGCTCTCTGCAAAACCATCC R 2 1 2 1 101000 r 74 goat snp47636-scaffold67-5879613 26 20334315 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453391 Affx-122919921 AX-123323724 26 30133588 ACCCAAAAATGAAGGAGAATAAGAGTGAAGGAACT[A/G]TCTGGGGATGGATAAGTATCTTACTGCTGAGCATC R 2 1 2 1 201000 f 74 goat snp47635-scaffold67-5835830 26 20290526 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432250 Affx-122936350 AX-123302591 26 30170821 TCCACATCCAATCAGCACCCAGGGTGTTTGAGCAC[A/G]TGCGTGATGCTCCTGGAAGATTGGGGGCAGGAGGA R 2 1 2 1 101000 f 74 goat snp47634-scaffold67-5798597 26 20253199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378982 Affx-122976397 AX-123249341 26 30200558 CCGGGTGGAGTCCACGTCCCGAGGCATAGACACTC[C/T]ATCGCAGAGAAAAGCCTGCAACGCAGGGTGTGGGG Y 2 1 2 1 101000 f 74 goat snp47633-scaffold67-5768860 26 20223006 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767893 Affx-122972334 AX-385255113 26 30239818 TCCTAGGGCAAATACAAGAGAGGTATATGGAAAGA[C/T]GTTACGCCCTGATTTTTTCTAGAGTATTTCTGAGT Y 2 1 2 1 101000 f 74 goat snp47632-scaffold67-5729600 26 20172668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384032 Affx-122972891 AX-123254390 26 30286616 CACAATACTTTGGAGCACTTGATTCTTTTCTTCTA[C/T]GAAGCTCTTTCCTTCCCTGTATGGTAATAATGAAT Y 2 1 2 1 101000 f 74 goat snp47631-scaffold67-5682802 26 20125468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787122 Affx-122950650 AX-385274148 26 30321537 CAGGGAGAAGGGTGCTGTTGAGAGATCCAGAAGCA[C/T]GGTCCATACAGTTGCTCACAATTCATAAGGTCCAG Y 2 1 2 1 101000 r 74 goat snp47630-scaffold67-5647881 26 20090537 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450952 Affx-122921756 AX-123321286 26 30372459 AGAAACGTCTAGTATAGTGGTTCTCTACTCTGGCC[A/G]TCCATTAAAATCATCTGTAGACTTTTTAAGGTGCC R 2 1 2 1 101000 f 74 goat snp47629-scaffold67-5596959 26 20039206 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768980 Affx-122961716 AX-385256156 26 30418074 CAATTTCTCAGATTCACAGAAGCACTTTGTGAAAT[A/C]GGGTCATGGAAGGCCTCTGTTGATAAGCTGCTCAC M 2 1 2 1 202000 r 74 goat snp47628-scaffold67-5551344 26 19993424 T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392979 Affx-122965669 AX-123263336 26 30456749 AGTCCTAATAATATCTCAAGGTCACTATGTAATTT[C/T]CTCTCTAAAATAAGGCTATCCACAAATGTGCTTCT Y 2 1 2 1 101000 r 74 goat snp47627-scaffold67-5512669 26 19954751 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409313 Affx-122953091 AX-123279664 26 30485685 TGTGTATGACTAGCCTCTGCACAAAATGAAAAAGT[A/G]TAATGTTACTCTTTTCTTCCCATTACAACTGGGTC R 2 1 2 1 101000 f 74 goat snp47626-scaffold67-5483733 26 19926529 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446847 Affx-122925262 AX-123317183 26 30542409 TTCTTCCTTCTTCTGGCATCCTTTCTCCATTAAGT[A/G]CTTAAAATTGTACTTTTGTGCCACTTTTAGTAAAA R 2 1 2 1 201000 r 74 goat snp47625-scaffold67-5427009 26 19869202 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402603 Affx-122958419 AX-123272956 26 30597044 GGGACAATATCAGTAACTTCAGTGAGCCCAGGGAA[C/T]GAGGTTTTGCTCATTATGGAATCTGCAGTGCCTGG Y 2 1 2 1 201000 r 74 goat snp47624-scaffold67-5372374 26 19813747 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408842 Affx-122954015 AX-123279193 26 30652745 ACTAAATTTCCTTAGTTTTTAAAAAAGAAGCTCTG[C/T]ACTGTTCTGCATAGTGGTTGTAGCAGTATATATTC Y 2 1 2 1 101000 r 74 goat snp47623-scaffold67-5316673 26 19756564 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382983 Affx-122973346 AX-123253341 26 30693036 TCTCATGAGTCCCATTAATATAATTTTTTACTCCC[A/G]TCCCTAGTGCTGCCTCCTGATTTCTATACTGTTCA R 2 1 2 1 101000 r 74 goat snp47622-scaffold67-5276382 26 19715782 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769491 Affx-122957642 AX-385256661 26 30734230 GAGCCCAGATCCCAGGTTGTAGAGGTATTGGCCCA[C/T]GATGGTTCATTGAAATCCAGAGAAGCCAAGAAGCA Y 2 1 2 1 101000 r 74 goat snp47621-scaffold67-5235188 26 19673721 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413903 Affx-122949832 AX-123284252 26 30785420 TTAATGGGTTTAAACTCACCTGAGCTACTTGTTTC[A/G]CTGCACTTGTTGAGCCAAGGCATTCAGCAAGTCCA R 2 1 2 1 101000 f 74 goat snp47620-scaffold67-5183998 26 19622319 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277815 Affx-1111836036 AX-519551312 26 30792729 AAGCTATTATCTCCCAGGAATCAAAAGTGAAAGTG[A/C]AGTCGCTCAAAGTTCTATTAATTATACTACAGGAA M 2 1 2 1 101000 r 74 goat Random2.2K-2194 26 30792729 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437293 Affx-122931983 AX-123307631 26 30841443 ATTGGAGTTAATGTTATGAGCCTAGAACATGGCAC[A/G]TGTTTTGGTGAGAGGGAAACAAGTTAAAGGTCATA R 2 1 2 1 101000 f 74 goat snp47619-scaffold67-5127975 26 19564435 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431563 Affx-122936194 AX-123301904 26 30898471 CTCATGTCCATTGGTACCATGTCTGGCATATGTGG[A/G]TGCTTGAACATTTTGGCATGGGGACTGTGAGACTC R 2 1 2 1 101000 f 74 goat snp47618-scaffold67-5070947 26 19506872 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38393512 Affx-122965806 AX-123263868 26 30941693 GGAGTGATGGGAAGAAGGCTGGTACCAATGGGCTT[A/G]GAATGAACAAGGTTTGGAGGTAGTTGTGGAGCGCA R 2 1 2 1 101000 r 74 goat snp47617-scaffold67-5027725 26 19463378 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426806 Affx-122940530 AX-123297152 26 30992240 CTTGTTTGACTGGTTAATTTTTCATTGACATATAG[C/T]AGTCACTAAAGGGTCTTTTTCGCAAAGTATAAAAC Y 2 1 2 1 101000 r 74 goat snp47616-scaffold67-4977178 26 19412494 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387574 Affx-122970275 AX-123257932 26 31021861 TGAAGCTGCTCCCCTCTTATGTAACATGCTTTAAG[C/T]GCCTGCTCTGTAGCTTGAATTTTCTCACTTAGTCC Y 2 1 2 1 101000 r 74 goat snp47615-scaffold67-4947557 26 19382673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422652 Affx-122943691 AX-123292998 26 31051595 AAAAAAAGATGGGTTGTGATGGGTAGTGAAATTTA[C/T]ATCATGAGAGGAATCTGGCTTGTAAGGGTATAGAT Y 2 1 2 1 201000 f 74 goat snp47614-scaffold67-4917823 26 19355580 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414009 Affx-122950270 AX-123284358 26 31083403 CCGGTGTACATGGGTGTAATTCAGCCTGCAGGCTT[A/G]CCTCATTTGGTAATTCAGAAATAAATGAATGGAGT R 2 1 2 1 101000 r 74 goat snp47613-scaffold67-4886015 26 19323750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420138 Affx-122946003 AX-123290486 26 31154200 GTTTGTGTTAAAACGTGTTTAAAATGAGTGACTCA[C/T]ACAAGGTTTAGCTAGTTAGCTGTAAGGAGTGCTTT Y 2 1 2 1 101000 r 74 goat snp47612-scaffold67-4815218 26 19252864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425276 Affx-122940971 AX-123295622 26 31183368 CACCTGGGAAGCCCATTAATCCAGGTAGCAAAACG[G/T]TATTAAGGAAGCGTTCATTCAGCATCGGTTAGGAG K 2 1 2 1 101000 r 74 goat snp47611-scaffold67-4786050 26 19224689 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406320 Affx-122955457 AX-123276672 26 31265313 CCATTTTAGGGCCCCTGAGTCTGTCCTGCATTCCA[C/T]GCCAGAAGAACAGAGGACAGCTTGACTCTGCTTTG Y 2 1 2 1 101000 r 74 goat snp47609-scaffold67-4704105 26 19141969 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401875 Affx-122958857 AX-123272228 26 31317676 AATGTCCAGAAAGTTCAAAGCAAAACAAACAGGCT[A/G]CTTAAAATAGGGAAAGACATTCAACTGCACTTACA R 2 1 2 1 201000 r 74 goat snp47608-scaffold67-4651742 26 19088847 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796412 Affx-122932937 AX-385283362 26 31376486 ATTAACTAGCCTTAGAATTGTTCTGAGTTTAAATT[A/G]TAAAGGAGACCTGCTTTTTCCATTATTTAGTTGAA R 2 1 2 1 101000 r 74 goat snp47607-scaffold67-4592932 26 19029860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771581 Affx-122920889 AX-385258739 26 31412040 CTGTTGAAAACCATAGTTTTCAACATTAGAACTAA[C/T]GAAGTGAACAGAAAGAAGTTTGAAAGTTCTCTTCC Y 2 1 2 1 101000 r 74 goat snp47606-scaffold67-4557378 26 18994423 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445760 Affx-122926075 AX-123316097 26 31466962 TCTTGTAAACCAGGTCATTTCAAAGCAATGAACTC[G/T]CTAACTTCATTTGTACTGCAATTTGTTTTCACCAA K 2 1 2 1 101000 r 74 goat snp47605-scaffold67-4502456 26 18939516 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414494 Affx-122949542 AX-123284843 26 31502588 AAATGCTAACCTCTGCCTTCAAATCATGAACCCAA[A/G]AGATGTTCCAGCCTACCTTTCAATTCTGTTTTCTA R 2 1 2 1 201000 r 74 goat snp47604-scaffold67-4466830 26 18903917 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796366 Affx-122949653 AX-385283316 26 31536591 ACTGAAATTGGGTTAGGTGTTGTACTCTTTACCAG[C/T]ATTAGTTTTAACCCTTTACATGTACAACTCTTTAG Y 2 1 2 1 101000 f 74 goat snp47603-scaffold67-4432827 26 18869917 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442740 Affx-122927846 AX-123313077 26 31593316 GGGGACAGCTAAAATCATAAAAATGCAACTGTCAT[A/G]AATACAAGCTAATACTAGAATAGTAGGATTATTTT R 2 1 2 1 201000 r 74 goat snp47602-scaffold67-4376102 26 18813028 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451597 Affx-122921642 AX-123321930 26 31626912 TCAACATTTTATTTAAAATATTTAATTATGCATTT[A/C]CTTTAACATGTGAAAAAATGCATAACTAACACACT M 2 1 2 1 103000 r 74 goat snp47601-scaffold67-4342506 26 18779393 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445819 Affx-122926028 AX-123316156 26 31665388 TCAACCAAGTTGGGTTAACATTCAAATGTTTGCTC[A/G]CATGGGTTCTAAACAAGTCCTACACTTGATGCAAA R 2 1 2 1 101000 r 74 goat snp47600-scaffold67-4304030 26 18740895 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442965 Affx-122928210 AX-123313302 26 31699595 GTTTTATAAAAACAAAACCAACAAAAGATAATTCT[C/T]GAAATAGGATTCTTTTGCATTATTCACCGTTTTGG Y 2 1 2 1 103000 r 74 goat snp47599-scaffold67-4269823 26 18706693 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430008 Affx-122938030 AX-123300349 26 31738976 GTCGCCTTCGTTTCTGGAGCCAACTTCTGGGACTC[A/G]AATCTGCCACAAACCAGTAGGGCAAATTACTTCAT R 2 1 2 1 101000 f 74 goat snp47598-scaffold67-4230442 26 18667341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435236 Affx-122934081 AX-123305576 26 31793173 GCAGTGTGTTGTCCCAGGAGAAGCTCAGGCTGGAA[C/T]GTCAGCACAGGAGGGAGGGTTTATTTCGCATCTAT Y 2 1 2 1 202000 f 74 goat snp47597-scaffold67-4176245 26 18613044 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412950 Affx-122951459 AX-123283299 26 31834694 AAGAATACAGGCCTTCCCGGGGCCACCCAAGTCTC[C/T]TTTGTAGCATGCAAAATATCCAAATCCAAAGCACA Y 2 1 2 1 101000 r 74 goat snp47596-scaffold67-4134724 26 18572258 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380041 Affx-122975579 AX-123250399 26 31865107 GGGCCCTCCTAGCTCTTTCACTTCTTAAGGGAGGA[C/T]GTCAGAGACCACTTTGCCCATCCGAAGCTAGGTTT Y 2 1 2 1 101000 r 74 goat snp47595-scaffold67-4104311 26 18541780 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798893 Affx-122960194 AX-385285823 26 31896390 TGTAAACAGCAACCAACAGGAGTCATAAATCTTTG[C/T]TACCCAGCAAAGATAGTCCACGTTATCAAATTTAT Y 2 1 2 1 101000 f 74 goat snp47594-scaffold67-4073028 26 18510383 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437180 Affx-122932123 AX-123307518 26 31940754 TTTCAGACACCGGCTGAATGTCTCAATTGTCCATT[A/C]GGCGCGGCGAAAGATGAAGGCAGGCTTTCTGTCCG M 2 1 2 1 101000 f 74 goat snp47593-scaffold67-4028664 26 18466209 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382337 Affx-122973886 AX-123252695 26 31982261 GACCCAATTAATCTGACATCAGTCAATTCTCTGCT[A/G]CAGTACAAGCATTTGAAAATTTACTTTGGGCTGAG R 2 1 2 1 101000 f 74 goat snp47592-scaffold67-3987157 26 18424664 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398574 Affx-122961504 AX-123268929 26 32014916 GGTGTTTCCAGGTTCAGTGAACACTTTACTATCGT[C/T]CATCAGAGAAGAAACAAAAGCAAGCCCCACCCCCA Y 2 1 2 1 101000 f 74 goat snp47591-scaffold67-3954502 26 18392250 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796052 Affx-122931922 AX-385283004 26 32048761 CATCCAACAATTCCTTCCGACCAAGTGACATGGAA[G/T]AGCCATTCTGAATTCATCCTGCTAATTAACCAGCT K 2 1 2 1 101000 r 74 goat snp47590-scaffold67-3920657 26 18358440 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383285 Affx-122972720 AX-123253643 26 32079634 ACCAAAGTTGCCCGTCAGACCCACACCAGGGTTCA[C/T]GCCAGCCTCTGCCATCACAACAAGCCTGGGAATGC Y 2 1 2 1 201000 r 74 goat snp47589-scaffold67-3889784 26 18327645 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415419 Affx-122948728 AX-123285768 26 32109081 AGCTAAGGAGCAGACCGATTCCTGCCTCCCGCTCC[A/G]TCTACATGGCTCTTGCTGAGGTCTGGGACAGAGGG R 2 1 2 1 101000 r 74 goat snp47588-scaffold67-3860337 26 18298059 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770497 Affx-122951383 AX-385257662 26 32151597 TCTGTCTGAGTAAGACTTAATCAAAGCACTTTCCT[A/G]TCTACCAAGTCATTTCACTTTCTACAGCCATAGCT R 2 1 2 1 101000 r 74 goat snp47587-scaffold67-3817821 26 18255467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769842 Affx-122943825 AX-385257012 26 32200323 ACCTCCCTATGAAGGGAATAAAGAGGGTGTTTTCA[C/T]CTCCATTTGCCTATTCTTGTATCTATTTCTCAATT Y 2 1 2 1 101000 f 74 goat snp47586-scaffold67-3769095 26 18206337 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404918 Affx-122956446 AX-123275270 26 32257713 GGCAGTGGTCAGTCCTAAAGGATATCTAGTGTGTC[A/G]TGGGGCTGAGCTCTAGACAGACCATTCTGGTGGAT R 2 1 2 1 201000 r 74 goat snp47585-scaffold67-3711705 26 18149468 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429314 Affx-122938598 AX-123299656 26 32294101 CCATGCTGGGCATGCAGAAGGTACTTAAAAAGAAA[C/T]GGCGGTTTAAAAGACCTGTCCCTCCTGATATCTGC Y 2 1 2 1 101000 f 74 goat snp47584-scaffold67-3675317 26 18112822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443200 Affx-122927590 AX-123313537 26 32352494 ACGGGCCATCCGTCTGCTCCCATGTGGATAAACAC[A/G]GCCTGCTAGAAAATGATTAAATGGTGACTCCACCA R 2 1 2 1 101000 r 74 goat snp47583-scaffold67-3616924 26 18054821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796695 Affx-122951284 AX-385283640 26 32388979 GCAGCAAAGCTTGTTTGGGGAATTTTGAAAATGGA[C/T]GAGGACAATCAGAAGGCATCTGATATTTTCTGGTT Y 2 1 2 1 101000 f 74 goat snp47582-scaffold67-3580439 26 18018306 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463989802 Affx-1110256249 AX-515466862 26 32396416 TTCAATTCCCATCTGTCGCTGAGCCACCTTATTGC[A/G]ATTGCTTCCTTCAGCAGCACTGATTTCGGGTTTGG R 2 1 2 1 101000 r 74 goat 26_32396416_AF-PAKI 26 32396416 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426688 Affx-122939907 AX-123297034 26 32433926 TTTTCTGTTAACCTCCACGGCCTCATGTGAACTAG[C/T]GACCTTCTGACTTTGTGGAGAGATTCCCAGAAAAC Y 2 1 2 1 201000 f 74 goat snp47581-scaffold67-3535492 26 17973373 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439345 Affx-122930290 AX-123309682 26 32480734 GGTCTGGGCAGGGCCGGCTTAAGGCTGAATCCTTC[C/T]GTCTCCTGAACTCCTTTTCTTGTGATGAGCTTTGG Y 2 1 2 1 101000 r 74 goat snp47580-scaffold67-3488684 26 17926618 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414562 Affx-122949386 AX-123284911 26 32526542 AAAAAAAAAAAAAATCAGGTCATTTTGTGCTGTCT[A/G]TGCATCAGATCCTATGTTTGCTTGTAAGCTTGTTT R 2 1 2 1 101000 r 74 goat snp47579-scaffold67-3442876 26 17880853 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433848 Affx-122934440 AX-123304189 26 32577604 AAGTTACTGTCTGGAGATCAACGGCCAGACCCAAG[C/T]AGATTGTTAGATAAACAACTGCTGTGTCACAGAAT Y 2 1 2 1 101000 r 74 goat snp47578-scaffold67-3391814 26 17829698 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428901 Affx-122938924 AX-123299243 26 32617864 AAATCCTCCAACTGCCCTCTTCAGTCACAAATGGA[C/T]CGTCTTGCCCTCTCAACTGAGAGGGACCGCTGTTC Y 2 1 2 1 101000 f 74 goat snp47577-scaffold67-3351554 26 17789628 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439240 Affx-122931010 AX-123309577 26 32685095 AGATTAGACCTCACACTTGGAAAACCCTGTAGATA[A/C]AGCCTTGGCAGCTATGGTTGTCCTTGCTCTAGCAG M 2 1 2 1 101000 f 74 goat snp47576-scaffold67-3284323 26 17722246 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382686 Affx-122973646 AX-123253044 26 32714090 CAGAGATAGTGTTTAAGCAAAGCTGTGATGCAGTC[A/G]TTTTAGAAAGTTCTTCCTGGCATTCTGGTAGGTTT R 2 1 2 1 101000 f 74 goat snp47575-scaffold67-3255328 26 17693213 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795491 Affx-122955524 AX-385282446 26 32747138 CAAAATACTCATCAGTAAGAAATGCTTAAAATAAC[C/T]AGGTAATACTATGCAGTCATATTCATATGACTAAT Y 2 1 2 1 101000 f 74 goat snp47574-scaffold67-3222280 26 17660160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426070 Affx-122941088 AX-123296416 26 32786602 CTCCTGAATCACTTAACACAAAAGCTAGGATCATA[G/T]GACTCACATCTGTTGGTCACCCTCATCTTGCCTCC K 2 1 2 1 101000 f 74 goat snp47573-scaffold67-3182816 26 17620432 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390905 Affx-122967097 AX-123261262 26 32817198 TTTAGACCTCAAACTGCTCTATAAGACGCCATCAA[C/T]GCAAGCCGCCCGAGAGACTCCCTTAAATCCATGAC Y 2 1 2 1 101000 f 74 goat snp47572-scaffold67-3152220 26 17589440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451293 Affx-122921297 AX-123321626 26 32853661 AGCTGCCTGAAGTGGGATAGCTCTAGTTCTAAGAA[C/T]GCAGGAACACAGAGAGAGGTAACTTAGGTGGCAAA Y 2 1 2 1 101000 f 74 goat snp47571-scaffold67-3115757 26 17552953 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402649 Affx-122958382 AX-123273002 26 32889818 AGTCAAAGTCTCTGGAATTTTCTCAGTCAGTGGTG[A/C]CTTAAAGGAAAACATCTTTTCCTCAATTGAGAGTA M 2 1 2 1 101000 f 74 goat snp47570-scaffold67-3079600 26 17516796 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433503 Affx-122935023 AX-123303844 26 32922694 AAAAACTCAATCTGATAACTTGCTTGCCATTTGGT[A/G]TTAAGAATGACTCACAGCTGTCCTAAATACCTCTG R 2 1 2 1 101000 r 74 goat snp47569-scaffold67-3046724 26 17484219 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447201 Affx-122924991 AX-123317537 26 32952326 TTATTTCTGATCTTTGAGGAAGAACTTTAAAAAGC[A/G]CTTGTTCACCCTGTCTCTACTAATGCTTTGAAGGT R 2 1 2 1 101000 r 74 goat snp47568-scaffold67-3017092 26 17454919 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776595 Affx-122922109 AX-385263722 26 32990650 TACTGTTTCCAGGCTCCGGGGAATCTTCTCTGTAG[A/G]ATATTTATCTGTCAATTTGGAATAAGAGCAGTTAA R 2 1 2 1 101000 f 74 goat snp47567-scaffold67-2978768 26 17416635 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802209 Affx-122935515 AX-385289113 26 33029619 TGTTTCACAGTACATTTGCTCTATCTGTAACTTAT[C/T]CTTGGACCTCTGATCTAAAGGCAGTCTTACTAGCA Y 2 1 2 1 101000 r 74 goat snp47566-scaffold67-2939799 26 17377367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764094 Affx-986698621 AX-385251852 26 33038144 TTTGTGAGTGACAGAAACCGTGTTTTAAATGTGAC[C/T]CTCCGAGAGGAGAAACTGCTGGTTTTACCCATGTG Y 2 1 2 1 600010 f 74 goat 26_33038144 26 33038144 Ancestral_priority_1043 ancestry 0.732 recommended IMAGE 10K 10K ancestral 320764129 Affx-986698656 AX-385251875 26 33038249 TGCCACCTCCAAACTTTAAGGGAGCTAAACTAACT[A/T]TTTTAAAAAAGATTCAATGGCTTGCTCATCCTTCA W 4 1 2 1 600010 f 74 goat 26_33038249 26 33038249 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 38422027 Affx-122943626 AX-123292374 26 33087162 TGAGAAACATCAACAGTATCCAAAAGCTCAGGTCA[G/T]AACATGAAACATACACAGCAAAGAAACAAAACATA K 2 1 2 1 101000 f 74 goat snp47565-scaffold67-2882256 26 17319432 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410267 Affx-122952523 AX-123280617 26 33134382 TGTAAAGTCCATGTCCTGTAGATAAGCACAGAAAG[C/T]ACCAGGTGAGGGTGTGCAGAAGGAACAGGCCAGGC Y 2 1 2 1 101000 f 74 goat snp47564-scaffold67-2835036 26 17271591 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405361 Affx-122956317 AX-123275713 26 33194985 CTCAGCCAAAGAGTCCTGCTGCTCATTTGCAAGGA[G/T]CTGTGGGGCCCCCGCTTTAGTCAAAGTCAGGAAAG K 2 1 2 1 102000 f 74 goat snp47563-scaffold67-2774433 26 17212918 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397929 Affx-122961929 AX-123268284 26 33223952 CCTCCAGCTCTCTCCCAGTCAACGGCAATACTCAC[C/T]CCAGGGAGTTTGGTTTTCCAGGAATGAAGTCGGAG Y 2 1 2 1 101000 f 74 goat snp47562-scaffold67-2745466 26 17184070 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447380 Affx-122924855 AX-123317716 26 33255693 AAGTAAAGCCTTGTCTAGCTGCCTCTGGGGTACGG[A/C]TTTGTGATTAGGGTCTTTCAGCTAACCAAAACCTC M 2 1 2 1 101000 r 74 goat snp47561-scaffold67-2713725 26 17152279 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403404 Affx-122957765 AX-123273757 26 33288485 CTGTGAAGAGTCAAGCCAGTAAAAATACTTGAAAG[C/T]GTATGTGGGAATCATGTGATCTGTGGCCAGGGAAG Y 2 1 2 1 101000 r 74 goat snp47560-scaffold67-2680933 26 17119351 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272391 Affx-1111834258 AX-515467746 26 33334393 GCCCCACCTGGAATAACCACCACACAATGGAGAGG[A/C]A M 2 1 2 1 102000 f 74 goat GoatD01.027983 26 33334393 G T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38435463 Affx-122933458 AX-123305803 26 33374958 GCCTGTGCCTATTCTCTGTGTCTGCCAGAACTGCA[C/T]GATGGCCCAGGAGAGTGTGGGCTTGGCTCCTTTAA Y 2 1 2 1 201000 f 74 goat snp47558-scaffold67-2594460 26 17032439 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421166 Affx-122944173 AX-123291513 26 33431180 GTGGGTGTAGTCTTCCTAATCCCACAGCAAGCCCC[A/G]TGATGCCTTCCTGCCCATGAAATGCAGGACAGGGG R 2 1 2 1 201000 r 74 goat snp47557-scaffold67-2538238 26 16976620 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793402 Affx-122968464 AX-385280379 26 33460261 TTTAAGTAGTTGACCCATACTGATCGAGTAATTCC[A/G]TGCCTTTTGGTATGATGTTGATCATATGTGTTCAA R 2 1 2 1 101000 r 74 goat snp47556-scaffold67-2509157 26 16947347 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416816 Affx-122948128 AX-123287164 26 33506722 AGGTGTGCCTAGGCTTCTTGCCAAGGAAGCTGTCC[A/G]CCCACTCTGCAGCAGCTCCTGCTGGCTCCTCCCAT R 2 1 2 1 103000 f 74 goat snp47555-scaffold67-2462696 26 16900409 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407201 Affx-122954810 AX-123277552 26 33552800 GTTTTCTTCATCCAGAGCCCATGCATTTACCCATC[A/G]CGTTGTTCTCCTTTGTTTATTTTTAGCTTTGGTTT R 2 1 2 1 101000 f 74 goat snp47554-scaffold67-2416618 26 16854329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427578 Affx-122939475 AX-123297921 26 33583166 TTGGAGGGTTCGCACACGCCCTGTGTGAAGCCTGC[A/G]CCTCCTGATGTGTTCGCTCTGTGCTTCCCTCCCTC R 2 1 2 1 201000 r 74 goat snp47553-scaffold67-2386252 26 16824075 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408913 Affx-122953959 AX-123279264 26 33611697 GCAGAGTCCTTATTAATGGCAGTATCCCATTTATC[A/G]TATGGGTGGTCTGCATTTTAGAAAGCACTTTATTT R 2 1 2 1 101000 f 74 goat snp47552-scaffold67-2357721 26 16795312 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434592 Affx-122934107 AX-123304933 26 33683134 TGAACAAGAAGTTCCACATTTTCATATTGCATGCT[A/G]CCTTGCAAATTGTATAGTCATACGCACATACACAT R 2 1 2 1 101000 r 74 goat snp47550-scaffold67-2286284 26 16723382 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798103 Affx-122923699 AX-385285038 26 33746970 AAATACAACAAAATTAGCAGTAGGTGTAAAATATG[A/C]TTCTACACACATGCTGTAGGATGTAGAGATGCAAA M 2 1 2 1 101000 r 74 goat snp47549-scaffold67-2222448 26 16659422 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441402 Affx-122928840 AX-123311739 26 33806900 GAGTTTAGAACAAGCCAGCCTGTTTTATTAAACAT[A/G]TGTGTCTAATATTTAAGTATTTCACATGCATAAAT R 2 1 2 1 101000 f 74 goat snp47548-scaffold67-2162518 26 16599522 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798751 Affx-122962211 AX-385285682 26 33843792 AGTTATGCAAGACTTCCAAATCTAGAGAGCCAATG[A/C]TTCCACCATGTTGGTAATTGCTGAAAGAAATGCCA M 2 1 2 1 101000 r 74 goat snp47547-scaffold67-2125626 26 16562987 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451959 Affx-122920953 AX-123322292 26 33888624 GAGAGAACTAGAAACAGCAGGTGAGGTCAAAGACT[A/G]GACAGTCTAGGGTCTTGCTGGCCATGGTAAAGATC R 2 1 2 1 101000 f 74 goat snp47546-scaffold67-2080794 26 16518472 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792737 Affx-122962090 AX-385279717 26 33927460 GTGAGCATAGAAATGGATAAATCAGTCTATCTCAG[C/T]AATCCCATGAATTCTTGACATGTGTAGAGAAAAGA Y 2 1 2 1 101000 r 74 goat snp47545-scaffold67-2041958 26 16479468 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787065 Affx-122955430 AX-385274092 26 33960670 ATCCTATTTGGACTTGTTACCCAAAAAAGTTGATT[A/G]CCAGCACTCAATTGCAAAAATGTGTCTTTTGTGAA R 2 1 2 1 101000 r 74 goat snp47544-scaffold67-2008748 26 16445581 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390250 Affx-122967759 AX-123260607 26 34014278 ACTACTGCTACACATGGTCATGTAACTTTAGATTA[C/T]GTATTTCTTGAGTCAAAGTTCCCCCATCAACAGGA Y 2 1 2 1 101000 f 74 goat snp47543-scaffold67-1955140 26 16386112 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431309 Affx-122937083 AX-123301650 26 34069684 TAGATACCTATAAATATTTATACCAAAAAATCATG[C/T]GATTTTACAACTATATTTTCACTTAACAAAACATC Y 2 1 2 1 101000 r 74 goat snp47542-scaffold67-1899734 26 16330568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406346 Affx-122955438 AX-123276698 26 34119997 AATTCAGCAGGAGGGAGAAAAGCACATTTCAGAGA[C/T]GAGAACCAGGAAAAATGCCCAGAAAAACCGTTTAA Y 2 1 2 1 201000 r 74 goat snp47541-scaffold67-1849421 26 16279850 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794070 Affx-122971015 AX-385281038 26 34161953 AACGTCCCAGTGGGTCTGAGTTCGTATTTCCCAGT[A/G]CAGTATCCAGCTTCATAATGCACATATTATTGGTT R 2 1 2 1 101000 f 74 goat snp47540-scaffold67-1807465 26 16238616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453100 Affx-122920032 AX-123323433 26 34215922 AAAAAGAGTCAATCCAAATTTTACTCCTTGGAAAA[C/T]AGAAAATAAAGAGATTTGTCCATAATTACTTGACA Y 2 1 2 1 101000 f 74 goat snp47539-scaffold67-1753496 26 16188912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787994 Affx-122976756 AX-385275015 26 34259865 GTAATTGTGTGTGCCTTATTTTGTGTCAGGGAAAT[C/T]TGAGAATAGCTGCTATTGTTACTAAAAAAGGTTAC Y 2 1 2 1 101000 f 74 goat snp47538-scaffold67-1709553 26 16144280 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786670 Affx-122943381 AX-385273702 26 34298370 ATTATAAATCATATGTGCTAGAACCAAAATTTCAT[C/T]GACAACACTTCATATATCCAAAAACTGAAGACAAC Y 2 1 2 1 101000 r 74 goat snp47537-scaffold67-1671048 26 16104354 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418368 Affx-122946576 AX-123288716 26 34337122 AAGGATACATAAATATATTTTTAAGATCTACAGGT[A/G]ATTCCAAAGTACCTGCTAGACTGAGAACCCCTGTG R 2 1 2 1 101000 r 74 goat snp47536-scaffold67-1632296 26 16064836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772165 Affx-122967739 AX-385259320 26 34414965 AGTGTATTTATGGATAACACATTTTTTCTCATGAG[C/T]AAGTTAGAGGTTTAAATAGAGAAGCTATATAGTTT Y 2 1 2 1 101000 r 74 goat snp47534-scaffold67-1554453 26 15986689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769998 Affx-122930642 AX-385257165 26 34443948 CAAACCCATCATCCTAGGCAGAGGTAAACCAAACG[C/T]AGTCTTTCCATATCATGGAATACCATACCACCATA Y 2 1 2 1 101000 r 74 goat snp47533-scaffold67-1525470 26 15957679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391734 Affx-122967490 AX-123262091 26 34516962 GCCTTGGTTAAAATCAGTATCCCCTTAATACGTAC[A/G]TGGTGATCATCATCTTAGGGCCAGTCTGCAAGAAT R 2 1 2 1 101000 r 74 goat snp47531-scaffold67-1452456 26 15888709 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395540 Affx-122963856 AX-123265895 26 34557139 ATTGCTTCTACTCCCATGCATACAAAGGTGGGAGG[C/T]AGTGGCGACAGTCTTCCCTGGGTGCAGGCAATAAA Y 2 1 2 1 101000 f 74 goat snp47530-scaffold67-1412279 26 15848289 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445462 Affx-122925218 AX-123315799 26 34596127 TGTAACATCCCCAAACTGGAGGTATCCCAAGTAAA[C/T]AGATAAACAAATCTGTAGTATATTCATACAGGTGA Y 2 1 2 1 102000 f 74 goat snp47529-scaffold67-1373291 26 15809261 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422470 Affx-122943329 AX-123292816 26 34630459 ATATTTGAATTGCTCAGAAGAAACACAGACATATG[C/T]ATTCATCCACCTAGAATATTTTAGAATACTGCCAG Y 2 1 2 1 101000 r 74 goat snp47528-scaffold67-1338959 26 15775045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397480 Affx-122962082 AX-123267835 26 34686031 TTGGGGTCAAAATACTTAAATTGTCCAATCAGAAG[C/T]TTCTGCATTTATAAAATGGACATAATGGCTGAGAA Y 2 1 2 1 101000 f 74 goat snp47527-scaffold67-1283387 26 15718663 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391773 Affx-122967462 AX-123262130 26 34818542 AAGTCAAACTCATTAAACAATGTGCAAGTTTGCCA[C/T]GCGGTATCAAAGGGCCACCTGCCCAGCTAGCAGCC Y 2 1 2 1 101000 f 74 goat snp47524-scaffold67-1150876 26 15585618 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446799 Affx-122925298 AX-123317135 26 34859204 GAAAGAGTCGGACATGACCGAAACGACTGAACACT[A/G]TAAGAAATGACAATATAGCTTAAGAAAGTGGTAGT R 2 1 2 1 201000 r 74 goat snp47523-scaffold67-1110214 26 15544992 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764131 Affx-986698658 AX-385251877 26 34878808 GTTGTGGGCTTACTTATTTTGGGGATATCAGCTTT[A/G]ATAGCTGCGATCACTTCTGTTACTGTAGCAGCAGT R 2 1 2 1 600010 f 74 goat 26_34878808 26 34878808 Ancestral_priority_1043 ancestry 0.634 recommended IMAGE 10K 10K ancestral 320767672 Affx-986698664 AX-385254911 26 34878913 GTTGATACTATGTCAAAAAATGTCTCTTTAACGCT[A/G]GCAAATCAGGAAATTATAGACAGAAAACTAGAGAT R 2 1 2 1 600010 r 74 goat 26_34878913 26 34878913 Ancestral_priority_1043 ancestry 0.622 recommended IMAGE 10K 10K ancestral 320764139 Affx-986698666 AX-385251885 26 34878958 GAAATTATAGACAGAAAACTAGAGATGAGGGTAGA[C/T]GCCTTAGAGGAGGCAACAATGCATATTGGGACTGA Y 2 1 2 1 600010 f 74 goat 26_34878958 26 34878958 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320764141 Affx-986698668 AX-385251887 26 34888333 CAATGACCAGAACCTTCTTGATATAACATCTATAT[G/T]TATGTCTGTATTTTCCTTCCTCTGTCTGGCTCATC K 2 1 2 1 600010 f 74 goat 26_34888333 26 34888333 Ancestral_priority_1043 ancestry 0.582 neutral IMAGE 10K 10K ancestral 320767682 Affx-986698670 AX-385254922 26 34888348 TCTTGATATAACATCTATATGTATGTCTGTATTTT[C/T]CTTCCTCTGTCTGGCTCATCACAGACACACACACA Y 2 1 2 1 600010 r 74 goat 26_34888348 26 34888348 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 320764145 Affx-986698672 AX-385251890 26 34888491 GACAAGAAAGCAGAGGGTTTGGGAAATCCATATTA[A/G]GAAGCCTGTTATTTGATGTGATTTTACCTTTGAAG R 2 1 2 1 600010 f 74 goat 26_34888491 26 34888491 Ancestral_priority_1043 ancestry 0.672 recommended IMAGE 10K 10K ancestral 38408127 Affx-122954243 AX-123278478 26 34892249 CGATGAATCTTTTCTGCTGCTCTCTGCACACTTGC[A/G]TTTCTGAATGCACATTTGAGAAAACAAATTCTTCC R 2 1 2 1 201000 r 74 goat snp47522-scaffold67-1077169 26 15511957 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273102 Affx-1111833312 AX-519546767 26 34900670 AGGGCAGGGAAGCGCGGGAGGTGCTGGCTGCAGAG[A/C]TTTGTAAGAATCGGGCAGGAATGCCCCACACGTAA M 2 1 2 1 303000 f 74 goat 26_34900670_AF-PAKI 26 34900670 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38394290 Affx-122964703 AX-123264645 26 34924267 TGAATGGATTCTATTCCAAGCTTCTGAGTTGCTAG[G/T]GGGTCAGCAAGTCTTGCAGTCCTGTATGGGCAGTG K 2 1 2 1 101000 f 74 goat snp47521-scaffold67-1045151 26 15480000 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764149 Affx-986698676 AX-385251892 26 34935350 TATTTCCCACCTTATCTACATTTTCCTACATTATC[C/T]ACATTTTCAGTTTTGAAATGCTCACTGTTCTTGCA Y 2 1 2 1 600010 f 74 goat 26_34935350 26 34935350 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320764151 Affx-986698678 AX-385251893 26 34936152 AATAAAATCTTTTGAAATCAAATACTTGCTCTATT[G/T]GTCATCTGTGTTTTAATAGCTAGACCTTAAACTGT K 2 1 2 1 600010 f 74 goat 26_34936152 26 34936152 Ancestral_priority_1043 ancestry 0.724 recommended IMAGE 10K 10K ancestral 320767702 Affx-986698680 AX-385254937 26 34956112 AGGTAGTATCACAGATGATGGACAGGATGAAATTT[C/T]TGGTTAGAAATTGGCAGGCAACATTGATGACTTTT Y 2 1 2 1 600010 r 74 goat 26_34956112 26 34956112 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 320764155 Affx-986698682 AX-385251895 26 34956172 TGATGACTTTTCTACTCTTCATCTGCCTAGAAGAT[A/G]TACAAGAAAAACTTCCTTAGTACATTTTCCTATCA R 2 1 2 1 600010 f 74 goat 26_34956172 26 34956172 Ancestral_priority_1043 ancestry 0.688 recommended IMAGE 10K 10K ancestral 320764157 Affx-986698684 AX-385251897 26 34956224 TTAGTACATTTTCCTATCATTGTATGAATTGCATT[C/T]AAATTGGAGTATAGTAAAACAGGAGAATGAAATAT Y 2 1 2 1 600010 f 74 goat 26_34956224 26 34956224 Ancestral_priority_1043 ancestry 0.624 recommended IMAGE 10K 10K ancestral 320767713 Affx-986698686 AX-385254947 26 34956230 CATTTTCCTATCATTGTATGAATTGCATTCAAATT[A/G]GAGTATAGTAAAACAGGAGAATGAAATATTTAACC R 2 1 2 1 600010 r 74 goat 26_34956230 26 34956230 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320767717 Affx-986698688 AX-385254951 26 34956326 ATCACTGTCCTCCCTACTGTGATGGAGTATCCTTG[A/G]TTTGCATCAGGTCAGGTGCAGTAGGGCTTCCATGG R 2 1 2 1 600010 r 74 goat 26_34956326 26 34956326 Ancestral_priority_1043 ancestry 0.612 recommended IMAGE 10K 10K ancestral 320767721 Affx-986698690 AX-385254955 26 34956460 TAAATGTACTTTTGTCAAAAGTTAATTCTACTCAG[A/G]TGCATTTGCAGTGGAAGGATTGACTCAACAAAATC R 2 1 2 1 600010 r 74 goat 26_34956460 26 34956460 Ancestral_priority_1043 ancestry 0.728 recommended IMAGE 10K 10K ancestral 320764132 Affx-986698659 AX-385251878 26 34956592 GTTCAAATACACCCTTTTGACCAAAAAAAATTTCC[C/T]CAAAATGTATTTTTTCATCCTCCCTTTTTTCTTTA Y 2 1 2 1 600010 f 74 goat 26_34956592 26 34956592 Ancestral_priority_1043 ancestry 0.638 recommended IMAGE 10K 10K ancestral 38428302 Affx-122939379 AX-123298645 26 34982805 CTTTGGGCCTGCAGACTTTCCTCATGAATAAAATG[C/T]ACAGCAAACCACCTGTTTTGCCCACTATCCAAGTG Y 2 1 2 1 101000 f 74 goat snp47520-scaffold67-986613 26 15421724 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795731 Affx-122973224 AX-385282684 26 35019208 ATGCCTTTAATGCATTCAATTAACATTCAGGGCTT[C/T]GTCACCAAATAAATGACACACATCGGTGGCACAAA Y 2 1 2 1 101000 r 74 goat snp47519-scaffold67-950210 26 15385208 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392108 Affx-122966355 AX-123262465 26 35048290 AGAAGGTGTTAACCCTGCTCTCCCTGAGAAGGTCA[C/T]CTGCCACTTTTGGACCTAGACTTCTTCAGTTTGAA Y 2 1 2 1 101000 r 74 goat snp47518-scaffold67-921128 26 15356586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401401 Affx-122959213 AX-123271754 26 35086553 GTGCACCTTGGAGACTGGGGGAAGGAGAGTGCTTC[A/G]TGGGTTCACATGCCGGGTGAGGATGCTGAGTTGAA R 2 1 2 1 101000 r 74 goat snp47517-scaffold67-882865 26 15318309 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448029 Affx-122923715 AX-123318365 26 35116038 CAGGCCGCAGGGCCACAACTGGCTGTAATGAAGGC[G/T]CAGAAGTATAATCTTTATTCTGTGGGGGCCAGATG K 2 1 2 1 103000 f 74 goat snp47516-scaffold67-853380 26 15288911 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764134 Affx-986698661 AX-385251880 26 35122063 AAATTATGAAGATGACACAGTCTGAATGAAACATT[A/C]AGTGCAGTGAAAACAAATCTTCTAATATTCTATTA M 2 1 2 1 600010 f 74 goat 26_35122063 26 35122063 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 320792978 Affx-122924392 AX-385279956 26 35163124 TTTTAAATTAATCACTGCCTTTTGTAATCAAGCTG[C/T]GGTAATATTAACACTTCAATATCTGCGTAATATGT Y 2 1 2 1 101000 r 74 goat snp47515-scaffold67-806294 26 15241228 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408413 Affx-122954472 AX-123278764 26 35213146 ATAGCTTTGACTAGATGGACCTCTGTTGGTAACCA[C/T]AGTTGGGAAAAACATCTGGGAGGTGGTCATATACC Y 2 1 2 1 201000 r 74 goat snp47514-scaffold67-756272 26 15191923 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789187 Affx-122937620 AX-385276199 26 35248264 CATGTTAACCCTTCACTTATCACTTGTTGCAAATA[C/T]GTTTTCCAAGTTTTGGGTGTGCATATGTGTTTGTG Y 2 1 2 1 101000 r 74 goat snp47513-scaffold67-721154 26 15156802 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767044 Affx-122960318 AX-385254335 26 35283546 TTGGGCTAGTGAGCTCACTGTGCTTTCCTCTGCCT[A/G]TAAAAAACCAGAGATAATCCTGGTTCCTAATATAG R 2 1 2 1 102000 f 74 goat snp47512-scaffold67-685872 26 15120388 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426409 Affx-122940838 AX-123296755 26 35331375 AGATGGTGATGTTATATCCTGTGAAAATAACCCTC[A/G]CCCTGAAAAAGGTCTAAATCTGACTGGTTGACTTA R 2 1 2 1 101000 r 74 goat snp47511-scaffold67-638043 26 15072552 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437484 Affx-122932365 AX-123307822 26 35369851 TTATAAAAATTAATTACTCTTCACTCCTTTTTTTC[A/G]TAGAATTTTAATTTTAATGGACATTTTTCAGTTCA R 2 1 2 1 303000 f 74 goat snp47510-scaffold67-599567 26 15033648 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395980 Affx-122963512 AX-123266335 26 35447073 CCAGCCTATTTAGTCACGGGGGCCCCAGGATTGAC[G/T]GGGCAGTTCAGCTGGGGGCCGTTGGGAGGCCGAGC K 2 1 2 1 101000 f 74 goat snp47508-scaffold67-522345 26 14956551 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764136 Affx-986698663 AX-385251882 26 35508100 ACAGATGCAACATGATCCATGTGAAAATGGATCAG[A/G]TTCTACTAGGATGGCTAGAATCAAAAAGACAGATA R 2 1 2 1 600010 f 74 goat 26_35508100 26 35508100 Ancestral_priority_1043 ancestry 0.734 recommended IMAGE 10K 10K ancestral 320767677 Affx-986698667 AX-385254917 26 35508260 GCTTTCTTCTAAGAGTTTTATAGCTTCAGTTCTTG[C/T]ATTAAGACTTTGATCTGCCACACCTCCTTCGAAGG Y 2 1 2 1 600010 r 74 goat 26_35508260 26 35508260 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 320767681 Affx-986698669 AX-385254921 26 35521958 GGTGTTTTACTACCTGGGAATTACTTGGAACAAGT[C/T]ACTATCTTTATATGCAGAAATGGAGATATAATAGT Y 2 1 2 1 600010 r 74 goat 26_35521958 26 35521958 Ancestral_priority_1043 ancestry 0.716 recommended IMAGE 10K 10K ancestral 38402953 Affx-122958169 AX-123273306 26 35550593 TCTGGAGCCTGACCGCCTGGTTTCATCTCTGGGCT[A/G]TGTCCTTTAACTCTCATGTGGCCCTAGCAAGTGGG R 2 1 2 1 101000 r 74 goat snp47506-scaffold67-418825 26 14853487 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786735 Affx-122930894 AX-385273766 26 35607580 TCAGGTCTAACTAAAGATTCTTTTATCCAAGAGGT[C/T]CTAACTAACATCTTTCAATTCTAGAAATTCTGTTT Y 2 1 2 1 101000 f 74 goat snp47505-scaffold67-361838 26 14796751 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406313 Affx-122955462 AX-123276665 26 35638115 TTTCTTCCTGGGATGTGATTTGACAGCCTTTTGTC[A/G]TTCTGAGATCCAGTTTGTTGATATGCCTCCTGCTT R 2 1 2 1 101000 f 74 goat snp47504-scaffold67-331303 26 14766109 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411222 Affx-122952351 AX-123281572 26 35693567 TCCTTTTGTAATGAGCACATGATTCGTTTTGGTGT[A/G]TTGGCAAGAGCTATAGACATTCTGTTCTTGTCACT R 2 1 2 1 101000 f 74 goat snp47503-scaffold67-275851 26 14711280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779310 Affx-122928298 AX-385266414 26 35723235 AAGTAGTTGTTTTCTTGTAACATAAGATGATTTAC[A/G]TGTATGTTTTTTGAATAGCTGAAGAAGTCACAGAC R 2 1 2 1 101000 r 74 goat snp47502-scaffold67-246183 26 14681616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423266 Affx-122942665 AX-123293612 26 35765520 TATTGTTGTATTCATTCAGTGTTTACCTTTACTGC[A/G]TCAGCCTAGTTTAAGTTTGGATGGCAGGGAGACAG R 2 1 2 1 101000 r 74 goat snp47501-scaffold67-203898 26 14639301 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425120 Affx-122941220 AX-123295466 26 35800984 AATTCCACTACCTCTCGTTAATGTGAACAAGAACC[A/G]TTATTGATTAAAAGCTTTTTTTTCTAATGCTGAGT R 2 1 2 1 101000 f 74 goat snp47500-scaffold67-168434 26 14602818 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399344 Affx-122961359 AX-123269699 26 35836843 ACCCAGTGCTTGCCAATGTCTCCAGCTCCATTTCC[A/G]CTTTCTCTCCTGATCCTGTCATTCTCTGCCCTTTT R 2 1 2 1 201000 r 74 goat snp47499-scaffold67-132575 26 14566933 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388985 Affx-122968660 AX-123259343 26 35877445 TGGCATACAGTAAGAGCTCAATAAAGTGAGTCACC[A/G]TTATTATTTCACTGGAGGAAATTAGTGAAATGTTG R 2 1 2 1 303000 r 74 goat snp47498-scaffold67-91973 26 14526178 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396899 Affx-122963219 AX-123267254 26 35913736 TCCTCCCACTTGTCCCTGTGGCCATTGCCCACGCA[C/T]GTGCTCGTGCATTTCCCCAGCAGCTCTGAACTGAT Y 2 1 2 1 101000 f 74 goat snp47497-scaffold67-55682 26 14488905 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403272 Affx-122957864 AX-123273625 26 35960932 TGAGGCTCAGAGAAGTGAAGCGACTTAGCCAAGAG[C/T]ATACGTGTGATAAACTGTGAAGCTGGAGGTCAAAG Y 2 1 2 1 101000 r 74 goat snp47496-scaffold67-8486 26 14442010 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432442 Affx-122935813 AX-123302783 26 35994242 TTCTCTGTCCCCTATTCTGCATCCTTGCTTTTGTC[A/G]CTTACCCAGAAGAGGGAACCGAGGCAGATCTTAGC R 2 1 2 1 201000 r 74 goat snp18565-scaffold1878-24725 26 14407310 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443426 Affx-122927369 AX-123313763 26 36042871 AAGTACTGTTTCTGTAATTAGCTCTTAAATGCACC[C/T]ATCCATTTGTTTACATATTAAATTATTTAGCATTT Y 2 1 2 1 101000 f 74 goat snp18566-scaffold1878-73354 26 14358378 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402193 Affx-122959173 AX-123272546 26 36095681 TAAACATCATCACAAACCTCTACTAGTCATAACTC[A/G]TATGGTGCCCATTATTACGCAAAGTATGGTACACA R 2 1 2 1 101000 r 74 goat snp18567-scaffold1878-126164 26 14305272 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399858 Affx-122960239 AX-123270213 26 36126446 AAAGATCAGATCTCTCCCTATATTTCTTCACCTTT[A/G]TCGTACATCCCTGTTTCAATACTCAGCATACCTAA R 2 1 2 1 101000 r 74 goat snp18568-scaffold1878-156929 26 14274647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407336 Affx-122955294 AX-123277687 26 36156488 TAGATCTCAAAAGTCTTTTCCAGCAGGAACATTCC[A/G]TAGTAATTATCTATCCATTTATTTCGATCTATGTT R 2 1 2 1 201000 r 74 goat snp18569-scaffold1878-186971 26 14244775 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406887 Affx-122955636 AX-123277238 26 36188743 TCCTGCATTTTGGCAGGTGGATTCTTTACCACTGT[G/T]CCACCTGGAAAACCCTGAGCTCTATCTATCTCTGC K 2 1 2 1 303000 r 74 goat snp18570-scaffold1878-219226 26 14212215 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428983 Affx-122938860 AX-123299325 26 36218778 CTTTGCTATAGCAGCCCTTGGAAACCCATATGGGG[A/C]TGGGGATTCCTATTCTCCCAAGTGTCAGGATCATC M 2 1 2 1 202000 r 74 goat snp18571-scaffold1878-249261 26 14182231 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386089 Affx-122971444 AX-123256447 26 36307398 TTCTGAGCATGCACAGATTCATGACAACCTGGCTG[A/G]GGCTTTTCTCAAAGCTTCTTCCTTTTCTCAGCACT R 2 1 2 1 101000 r 74 goat snp18573-scaffold1878-337881 26 14093322 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783751 Affx-122920565 AX-385270807 26 36374259 CTGGCACGTTTTCTTGGCACAACTGCCTCAGTTTG[A/C]AAACTCCTTGGCAAGCTTCTCCTCTAGAAGAGTTG M 2 1 2 1 101000 f 74 goat snp18574-scaffold1878-404742 26 14026532 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764918 Affx-122935398 AX-385252506 26 36407571 GGAGCCTCAGTGTTTAAACTAGGGAAACTTCTTGA[C/T]GGTCTGCTCTTATTTGCACTTTCTCAGTCTGTTCA Y 2 1 2 1 101000 f 74 goat snp18575-scaffold1878-438054 26 13993059 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380124 Affx-122975997 AX-123250482 26 36456985 TCAAAACCCACCATTTCACTTATTACGGCAGTGGA[A/C]GGGGACACTCATTAACACCTCAGCTGTCTGAAGGA M 2 1 2 1 101000 f 74 goat snp18576-scaffold1878-487468 26 13947714 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427798 Affx-122939762 AX-123298141 26 36500944 TACTACACAGGGATGTTATATTTTATAGAAATAAA[G/T]CTATCGACTTTCTATTTCCCGATAATGCAGACTGT K 2 1 2 1 101000 r 74 goat snp18577-scaffold1878-531427 26 13903549 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452438 Affx-122920574 AX-123322771 26 36541802 AAAACAAAGAAAGAACCAGGGAAGGAGAGGGTGAG[C/T]GAGCTATTTGTACCCCTTTCACTTCCAAACGAAAA Y 2 1 2 1 201000 r 74 goat snp18578-scaffold1878-572285 26 13862530 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402749 Affx-122958328 AX-123273102 26 36570519 TGAGGAGCCAGCACTGACTTGTCACAGAGCCTCCA[C/T]GAGCTGCTGTCAGTTGATGGGCAGCTGTCTTATTC Y 2 1 2 1 101000 r 74 goat snp18579-scaffold1878-601002 26 13833860 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442958 Affx-122928216 AX-123313295 26 36610670 AATGTTACCACATCAGAGAAGCCTGAGGTTCCTCC[A/G]CTCTTCACTCTCCATCTGTTAGCCTATTTCTCTCT R 2 1 2 1 101000 r 74 goat snp18580-scaffold1878-641153 26 13793940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775911 Affx-122958723 AX-385263042 26 36640067 AAGTACGCTTGTTTTCAGATTAATGTATCCTGAAT[A/G]TAAGCTTTTCAGTACCCTCTCTGAAGGAGTTAACG R 2 1 2 1 101000 r 74 goat snp18581-scaffold1878-670550 26 13764284 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386262 Affx-122970951 AX-123256620 26 36674434 CAGGAGAAAACTAATAGAAAAATGCCTAGAAATCA[G/T]GATCCAATGGAATGCACTATACATTTAATGGAGAG K 2 1 2 1 101000 r 74 goat snp18582-scaffold1878-704917 26 13729731 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428207 Affx-122939450 AX-123298550 26 36722916 GGGATCGCAAAAAGCCGGACACGTATAAGCGACTA[C/T]ACACAGCGCAAAGTACGAATCATAGAAGTTATGTC Y 2 1 2 1 101000 r 74 goat snp18583-scaffold1878-753399 26 13682234 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782489 Affx-122959146 AX-385269565 26 36758114 GCTGAAGTTATTCTGAAGGGATGTGCTGGCCATTA[A/C]TTTCTTTAAAAGCCACCAGAAAACCTATTGATCAA M 2 1 2 1 101000 f 74 goat snp18584-scaffold1878-788597 26 13647070 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388875 Affx-122969311 AX-123259233 26 36795156 CTTGGCAGAGGGTGGGGGGATGGAACAGGATGCCA[A/C]TGGTATCTAGTGGGTATAGGCGAGGTAAACCGCTA M 2 1 2 1 101000 r 74 goat snp18585-scaffold1878-825639 26 13610061 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427297 Affx-122940153 AX-123297640 26 36855468 TTATAGATGAGGAAACCAGCATGGAAAAGTGAAGT[A/G]ATTTGCCCAAAGTTACACACTCACTAAGCAACAGA R 2 1 2 1 201000 f 74 goat snp18587-scaffold1878-885951 26 13549612 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386771 Affx-122970116 AX-123257129 26 36912071 AAATAAAGATAACAGAAATTCACCTTCTGGGAAGA[C/T]AATGTCAATGTACTTTTCTCTACCCTTCCCTCAAA Y 2 1 2 1 101000 r 74 goat snp18588-scaffold1878-942554 26 13493002 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277688 Affx-1111836037 AX-519551187 26 36956388 CTAAACAAGACAATCAAGAACCTGCTGATTTCATG[A/G]GGAAGAGGGCTAAGCAATCATATAAATAAGAAATA R 2 1 2 1 101000 f 74 goat Random2.2K-2195 26 36956388 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38396428 Affx-122962994 AX-123266783 26 36972862 CCTCCAGCAAAGATGTAAATGGTCAGAATTCATCA[A/G]GAATGAACCAGGTAGGTGCAGCCTGTGTGAAAATG R 2 1 2 1 101000 f 74 goat snp18589-scaffold1878-1003345 26 13432176 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776963 Affx-122967284 AX-385264087 26 37010834 AGGCCCATTCTCAGACATGGGTTCTACTTCTGGCT[G/T]CACTCTTCTCAATATTGATACTGCCCTGTTGGTTT K 2 1 2 1 101000 f 74 goat snp18590-scaffold1878-1041317 26 13394419 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779497 Affx-122935583 AX-385266600 26 37025781 CATGATATTGTTTGAGGGAAAATGAAATATGTTGG[G/T]CTATTTGAGTATTGAAATTAGCTTAAAAATCTCCA K 2 1 2 1 101000 f 74 goat snp19930-scaffold1992-2732449 26 13379600 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420054 Affx-122945132 AX-123290402 26 37055900 CCAGCCATTCATTCAACTCAGAAAATATTTACTGA[A/G]TGTCTACAAGGTGTGAGGCTCTGTCAAAGGCCTTT R 2 1 2 1 201000 r 74 goat snp19929-scaffold1992-2702330 26 13349527 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406335 Affx-122955445 AX-123276687 26 37099536 ATTCTAGTAGCAGGAGACAGAGAAAAAAATGAAAA[C/T]GGAATAAATGAGATTATTTTAGATAGTGATGAGTG Y 2 1 2 1 102000 f 74 goat snp19928-scaffold1992-2658694 26 13305732 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418455 Affx-122946471 AX-123288803 26 37153527 TCTGGGAACAGGTGTCCACTGTGTAGGGGATAAAC[A/G]CACTCCTCTCTCAGTAGGGGAGAGAGGCAGGGATC R 2 1 2 1 101000 f 74 goat snp19927-scaffold1992-2604703 26 13251745 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772669 Affx-122958271 AX-385259816 26 37192078 CCTGCCATGCTCCTGAGTGAGTGCTTAGTAAACTA[C/T]GAGAACTAGCTTTAAGCTTTACAGTTTATCATATC Y 2 1 2 1 101000 f 74 goat snp19926-scaffold1992-2566152 26 13213348 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419545 Affx-122945421 AX-123289893 26 37248741 GCTGGGAACTTAGATTGCTTGGTAAAACTCACAAC[A/G]TAGAAGAAAAATCATGCTTCCTATGCAGGGGCTCT R 2 1 2 1 201000 f 74 goat snp19925-scaffold1992-2509489 26 13156527 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431011 Affx-122936676 AX-123301352 26 37306649 GGAAGAGGTCAGTATGGGCTCCAGGTGGGGAGAAG[C/T]GGCCCATTTTTTTTCTTGGTTTTATTAACTAAACA Y 2 1 2 1 101000 r 74 goat snp19924-scaffold1992-2451581 26 13098759 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413568 Affx-122950590 AX-123283917 26 37360443 TCTAGTTGGATTGCATTGTTTAGAAATGCAGTGTG[G/T]TATTGGCTTATAATTCTGGGAAATTGATAGTGTGG K 2 1 2 1 101000 r 74 goat snp19923-scaffold1992-2397787 26 13044870 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796660 Affx-122953958 AX-385283606 26 37394217 AGAAAAAAATTTCCATATAATGGTAACAGTAGTAA[C/T]AGCAGCAGTTGACTTTGAAAGTTAAGCGGCCTAAA Y 2 1 2 1 101000 r 74 goat snp19922-scaffold1992-2364013 26 13010761 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799021 Affx-122952811 AX-385285952 26 37423516 CTGTGTCCTGTAACAACTCTGGTACCAGATACTTC[A/G]TCAATCACAGTTCAGTCCAAGAAAACACTAGGTAT R 2 1 2 1 101000 f 74 goat snp19921-scaffold1992-2334714 26 12981461 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422979 Affx-122943000 AX-123293325 26 37474940 TCCTTGTCACTGGACCCAGGGACCTACCAGTTGGG[C/T]ATTTATTCCTTACAAAAGGACAAGCAAGGCAAGGT Y 2 1 2 1 101000 r 74 goat snp19920-scaffold1992-2283290 26 12929209 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386236 Affx-122970972 AX-123256594 26 37506837 ATGGGTAATTTCTTTGCAGATGGTTGGGAAGGGAA[C/T]GCTTTTCTTCAGCATCTCCACAGAAGGCCTCCTTG Y 2 1 2 1 101000 f 74 goat snp19919-scaffold1992-2251393 26 12898771 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376103 Affx-122978891 AX-123246462 26 37561530 CTCTTGCTGATGGCATCTATTGATTGTCTTTGCTC[A/G]TTTAGTTTGAGCTTGTCATGGGTCTTTATAGGATG R 2 1 2 1 201000 r 74 goat snp19918-scaffold1992-2196700 26 12845855 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429038 Affx-122938312 AX-123299380 26 37605523 CACTGTTGCAAGTGGGCATTTTTGTGAGGCTCTTA[C/T]ACAGTGAATAAATTGGGCAGCTGGGTCTTTAAGAA Y 2 1 2 1 101000 r 74 goat snp19917-scaffold1992-2152707 26 12802384 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387046 Affx-122969910 AX-123257404 26 37634971 GGATTCTTTTAAATAATTCCTCCCCAAAACACAAC[A/G]TCTCAGATTGCCAGAGAGGACCCTTGATATGATGA R 2 1 2 1 201000 r 74 goat snp19916-scaffold1992-2123259 26 12772581 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798684 Affx-122931175 AX-385285616 26 37683641 TATTGAAATTGCAGAGGCAGAAACTAAAAATTGGT[A/C]GTTTTCAGCCAATGAAAATGTGATCTCCTGCTCTC M 2 1 2 1 102000 r 74 goat snp19915-scaffold1992-2074589 26 12724005 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403587 Affx-122957570 AX-123273940 26 37722893 TGTAGGGCTTCCAGTTCATCGGCATCCAGGTGCAC[A/G]TAGGAGTGAAGTATGGTCCAGTCCTGTCGATGCCA R 2 1 2 1 101000 r 74 goat snp19914-scaffold1992-2035337 26 12684976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778154 Affx-122930861 AX-385265269 26 37755634 ATTATTGCTTTCAGTGACAAAGCCAGTGAATTTCA[C/T]GATGTGAACTGTGAAGTTGTTGCAGTGTCGGTGGA Y 2 1 2 1 101000 f 74 goat snp19913-scaffold1992-2002596 26 12652249 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446756 Affx-122925328 AX-123317092 26 37790578 TAGGCCTGATGCATTCCACCCCAAGCAATGGTTAG[C/T]GGTTTGGGGAACGAGTGTGTGGCAGAATAAGCAAT Y 2 1 2 1 201000 f 74 goat snp19912-scaffold1992-1967652 26 12617438 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444750 Affx-122926373 AX-123315087 26 37836548 CAGAGTTCACTCCTTGGAGAAATTTTTGTATCATA[C/T]GATTATATCACTGTTTTAAAAAAGAAAACATTGTA Y 2 1 2 1 103000 f 74 goat snp19911-scaffold1992-1921682 26 12571395 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397165 Affx-122962426 AX-123267520 26 37895604 CTTGGAACAAGGGGTGTTTAACGCGCTGAGGCAGA[C/T]GCTGGGGTTGACGCTGCCAAGGGGCTGCTGAAGAC Y 2 1 2 1 101000 f 74 goat snp19910-scaffold1992-1862626 26 12512390 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768567 Affx-122943088 AX-385255747 26 37988667 ACAAGGTTGGGGAAGATCAGGTTAAGCATAACAGC[A/G]CATATTAACAGCATGGCTTGGCCATACTTAGGCCC R 2 1 2 1 101000 f 74 goat snp19909-scaffold1992-1769563 26 12420230 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273104 Affx-1111833313 AX-519546769 26 38091909 AAGAAAAGACAAAGTGTGAGGAGAAAAATTTAATA[A/C]GACAGAAACAAGTGTTACTCAAATATAAAAGAATC M 2 1 2 1 101000 f 74 goat 26_38091909_AF-PAKI 26 38091909 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320786637 Affx-122935060 AX-385273669 26 38096486 AAAGCATATTCACCGTAGAAATTTTATAAAACATG[A/G]AAATATAATAATGAACATTAAGATCACCCATTATC R 2 1 2 1 303000 r 74 goat snp19907-scaffold1992-1661744 26 12313349 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379189 Affx-122976305 AX-123249548 26 38129948 AAATGGTAATGGTGCTCTACTGTAGGTTCATTTTC[A/G]TCATCTATTTGATGTACCGCAATGAAGAGGAATTG R 2 1 2 1 101000 r 74 goat snp19906-scaffold1992-1628282 26 12279892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410847 Affx-122952616 AX-123281197 26 38176890 TGGGCCATGTCCTTTCTCTGGTTAGAATGCTTGAA[C/T]GGCTCCCCATCGCCCTTTTTATCTCCAAATCCAAC Y 2 1 2 1 201000 f 74 goat snp19905-scaffold1992-1581340 26 12232817 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416378 Affx-122947870 AX-123286727 26 38205409 AGAGTGCACCTTTCACGCCTCCTGGGGTCTGGTTC[A/G]ACCCTTCTCCTGCTCCTAGGTCTGCGGGCACCTGT R 2 1 2 1 101000 f 74 goat snp19904-scaffold1992-1552821 26 12204271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379014 Affx-122976371 AX-123249373 26 38238078 AAGTCCAAAAAATACCCCATAGTTCATTTTGTTTA[C/T]AGCCTGGTGAGTGGGCAGAGGAAACCTTGGAAGTG Y 2 1 2 1 101000 f 74 goat snp19903-scaffold1992-1520152 26 12159233 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388835 Affx-122968888 AX-123259193 26 38278951 AAATGAAAGAATTGTGTGAAAGTACCCAGCACAAT[A/G]TCTGGCACATAAATGTTCAATAACTTTTACTTCAA R 2 1 2 1 101000 r 74 goat snp19902-scaffold1992-1479279 26 12118337 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452703 Affx-122920302 AX-123323036 26 38312396 TAAAAACCAGAATATTGACATTGATCATTTCTATG[C/T]GGGAGAATATTTTTTCCTCCTCCTCAGTTACAATT Y 2 1 2 1 101000 r 74 goat snp19901-scaffold1992-1445834 26 12084949 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444047 Affx-122926867 AX-123314384 26 38354121 TGAGAGCCTATACAAGATACTATGGACTGCACCTT[A/G]GAAAGTTACAACTGGAAAACTTCTTTCAAGCTTTA R 2 1 2 1 101000 f 74 goat snp19900-scaffold1992-1404109 26 12043228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450337 Affx-122922121 AX-123320672 26 38405574 CATTCAGCAAATTCTATTATGTGAACTTGCCCTTG[C/T]GCCAGACATGGGAGATACAAGAATGGCCAGACCAG Y 2 1 2 1 101000 f 74 goat snp19899-scaffold1992-1352656 26 11993899 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386422 Affx-122970810 AX-123256780 26 38442016 TTAAATAAGACCTTAGTGTTAAAATGCTCATAACT[C/T]ATTACAAATGACAGGAAGAACCCAAATCATTAAAT Y 2 1 2 1 101000 f 74 goat snp19898-scaffold1992-1316214 26 11957536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426811 Affx-122940525 AX-123201522 26 38539231 TCTGAGGTTCATGTTAAGAATGCCCCAAATTTCCC[A/G]TGAGGAACTGTACCTCTTCAATTCTGAGCTGTGTG R 2 1 2 1 101000 r 74 goat snp19896-scaffold1992-1218999 26 11859499 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385724 Affx-122971100 AX-123256082 26 38570627 GCAGTCACAACGAGTCAGACATGACTTAGCAACCA[A/G]ACAACAATCTATGAGAAGGACCAGGGACCAGGGGA R 2 1 2 1 201000 r 74 goat snp19895-scaffold1992-1187603 26 11827806 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401587 Affx-122958876 AX-123271940 26 38657569 ACCTTTTAGGGAAAAAATGAGCAAAGAACAGGAAA[G/T]GTAATTCACTCAACATCCAACAAATATTTGAGCTC K 2 1 2 1 101000 r 74 goat snp19893-scaffold1992-1100661 26 11741014 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389624 Affx-122968750 AX-123259982 26 38695155 GACATAGTTGGCTCTTCATATCAATGGGGATGAAA[C/T]AGACAATTCAGTAACTGTCACTGGAGAAATCTAAT Y 2 1 2 1 101000 r 74 goat snp19892-scaffold1992-1063075 26 11701921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770599 Affx-122955101 AX-385257763 26 38726317 GAAGAGTTTATGAGCCGCAAACTCTCTCAGTCTTT[A/G]TACGCCTATGGGTATCTTTATTTCATCATCTCTCT R 2 1 2 1 101000 f 74 goat snp19891-scaffold1992-1031913 26 11670645 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419200 Affx-122945705 AX-123289548 26 38777590 TGTGTGTGTACACATACATGAGAGACCTATCTCAC[G/T]CGTGACAATTATAGATAATAGGCTGGGGTACAGTC K 2 1 2 1 101000 f 74 goat snp19890-scaffold1992-980640 26 11621418 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441030 Affx-122928941 AX-123311367 26 38808383 TTTACTTGGCAACTTTTTCTTCTCCCCAGGATGAA[C/T]GTGAGTCCCCAGCAGGGGTGGATTGGGAGCAACCT Y 2 1 2 1 101000 f 74 goat snp19889-scaffold1992-949847 26 11590287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401828 Affx-122959447 AX-123272181 26 38863629 CTGCTCTTCCACGTCATCTCCACGCCTACAGCCAA[C/T]GAACAAACAGCCTTGGACAGACAATCAGGAGGCTA Y 2 1 2 1 101000 r 74 goat snp19888-scaffold1992-894601 26 11535066 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388176 Affx-122969440 AX-123258534 26 38897732 AGAGAACTGAGTTGTTTCCATTTTCAGTGCTATGG[C/T]CCTTAGAAAATTACCTGGCACAGAGTACAATAGGT Y 2 1 2 1 201000 r 74 goat snp19887-scaffold1992-860498 26 11501739 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445809 Affx-122926035 AX-123316146 26 38928311 TAAACCTTTTAAGCTTTGGATTTCTCATCCAAAAA[C/T]ATGAAGAATTATAAAACTCCTACCTCATAGGATTG Y 2 1 2 1 202000 r 74 goat snp19886-scaffold1992-829919 26 11470967 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399446 Affx-122961213 AX-123269801 26 38958359 TGGCCAGGGCAGGGCAGTGATAATACTACTGTCAT[C/T]AGCAAGAAGAAATATTAGAATATGGCACAGGGCCT Y 2 1 2 1 201000 f 74 goat snp19885-scaffold1992-799871 26 11440844 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770749 Affx-122935264 AX-385257913 26 38990992 GATAATTTTTCAATCCATATTTACAAACCCTTTAG[A/G]TTTGTTCCACAAAAGCAAACTCCCAGACACTCAGC R 2 1 2 1 101000 r 74 goat snp19884-scaffold1992-767238 26 11408365 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432011 Affx-122935925 AX-123302352 26 39080005 CACACATTCACATGGCCTGCCCAGGACCTGGTGGC[C/T]AGAGGCAGCAAATGTAGATGACTCCAAGGGACAAA Y 2 1 2 1 102000 r 74 goat snp19882-scaffold1992-678225 26 11320950 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444921 Affx-122926240 AX-123315258 26 39151095 CATGAGGATATTTTAAAATTCAGCATTAATTACAG[C/T]AATTCCTTCTTCCCATCCATTCAGGCACTTGCAGA Y 2 1 2 1 101000 r 74 goat snp19880-scaffold1992-607135 26 11249181 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401230 Affx-122959314 AX-123271583 26 39191581 TGGTGATCTCAAACCCAAGCCTCTGGACTAGGACC[A/G]CTTTGGAGGGATTAAGAAACTCATCCAAAGCCACA R 2 1 2 1 201000 r 74 goat snp19879-scaffold1992-566649 26 11211554 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769830 Affx-122947019 AX-385257000 26 39233458 ATTTCATTGATTTTTCAGAGATTTGAATTTCAACC[A/G]TAAGCACATCATAATGAAAGGAGCGGATTATCTAG R 2 1 2 1 101000 r 74 goat snp19878-scaffold1992-524772 26 11169673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788344 Affx-122930196 AX-385275362 26 39300590 AGAGCTGGAAGAAAAACCCCTATGTGTAATTCAGT[A/G]CTCTACTGGAGGTTAAACAAATTATGAAACTACCT R 2 1 2 1 101000 f 74 goat snp19877-scaffold1992-457640 26 11096856 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403069 Affx-122958519 AX-123273422 26 39349219 TGTCCTGAGAGGGAACAACCATACTTGGGATATTG[C/T]GTCCTTTTGGCAAAGGGGAAAGAACAAGAGACCAG Y 2 1 2 1 101000 f 74 goat snp19876-scaffold1992-409011 26 11049648 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448740 Affx-122923328 AX-123319076 26 39383674 TGGCTCAGGTACCACAGTACTTTACGTGGAGTAAT[A/C]GCTTTTGCTTTTGTTCAGTGGCCAAGTCATGTCTG M 2 1 2 1 201000 f 74 goat snp19875-scaffold1992-374556 26 11015234 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444502 Affx-122926511 AX-123314839 26 39443684 ATCAGAAAGAGGAAGACAGTCTGAGATTCTGAAAA[C/T]AGAACCTGACTTAACAGCCCTGGACAACTGAGAAT Y 2 1 2 1 101000 f 74 goat snp19874-scaffold1992-314546 26 10955534 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409783 Affx-122952979 AX-123280134 26 39480364 CCAATTCTATCATCCAAAAAATGGCATGGTTGATA[C/T]AGTATCAGTTTACTTCAAAGGGCAATTTTGAAAAT Y 2 1 2 1 101000 r 74 goat snp19873-scaffold1992-277866 26 10918716 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376004 Affx-122978413 AX-123246363 26 39518075 CGTTCTTTCAATTTTCAGGAATTTTGAATCCCCTC[A/G]GAAGAATGTAATAATTGTTCTTTCGCTACTGAAAA R 2 1 2 1 201000 r 74 goat snp19872-scaffold1992-240155 26 10881034 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433246 Affx-122935243 AX-123303587 26 39553511 TACATTGTGCATTCACAAGGGATGGTCTTGGTGCA[C/T]AGCCTGAATCAGTGGTTTCCCCGTTTGGTGTCCAG Y 2 1 2 1 101000 f 74 goat snp19871-scaffold1992-204719 26 10845474 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401243 Affx-122959304 AX-123271596 26 39606093 TCTAAAAATCACATCATCCAAGGCTACACTGTCTA[C/T]AGTATCTGAGGCCCCCAGAATGCACCCGGCACAAG Y 2 1 2 1 101000 f 74 goat snp19870-scaffold1992-152137 26 10793461 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389256 Affx-122969029 AX-123259614 26 39661054 GGGGTTTGGACCCTTCATGGCCCATCTTGCTGTAG[A/C]CACTCTTTGTGGATCCATTTTCCAGAAGAGCATCC M 2 1 2 1 202000 f 74 goat snp19869-scaffold1992-97176 26 10737598 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399557 Affx-122961130 AX-123269912 26 39710198 ACTGCGAGCCCCTCATCTTGTTTTCATTTCCCCAG[A/G]TGATGGGCGCATCAGCTTGGGATGATAACAGCTCT R 2 1 2 1 303000 r 74 goat snp19868-scaffold1992-48032 26 10688403 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423711 Affx-122942883 AX-123294057 26 39740800 CATCCTCTAGTGGTGTCTGTGGGAGCTCCAGAGGC[A/G]ATCAAGGGCATCCGGCAAAGTGATCAAGTCCCTCG R 2 1 2 1 101000 r 74 goat snp19867-scaffold1992-17430 26 10658243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440887 Affx-122929231 AX-123311224 26 39786432 CTAGTAATATGCCCCCTCTCAGGGCTGTTGCAAGC[A/G]CTGAACTCCACCTGCACGTACAGCTTGCATGGATT R 2 1 2 1 201000 r 74 goat snp1033-scaffold1027-1049823 26 10613436 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433155 Affx-122935672 AX-123303496 26 39840360 AGCTGGTAAGGGCTCTGCTGTTGCTATGTGGCAGC[A/G]CTGTCTCTGGGGGTCTCCTCACTCCACCCACGACC R 2 1 2 1 101000 f 74 goat snp1032-scaffold1027-995895 26 10558911 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399310 Affx-122960527 AX-123269665 26 39893186 GGCTGCCTGTGGTCCATGTTTGAGTCCTCCTTCTC[A/G]TGGCATCTATACCTTTGCCTGCCCTGTTCTCTGCA R 2 1 2 1 101000 f 74 goat snp1031-scaffold1027-943069 26 10505892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794946 Affx-122959951 AX-385281906 26 39935577 GGTTTGTACCACAATTCCTTATCTATTAAATAGAT[C/T]GCTAAGATTATACCAGGGAAGGTTTGCAAAGTGGA Y 2 1 2 1 101000 r 74 goat snp1030-scaffold1027-900678 26 10463408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434200 Affx-122934861 AX-123304541 26 39980692 TAATGAATCACTGGAAATTCAGCAGGCTTGAGCAG[G/T]AAAATCAGCTCTGAGAAACAGAGCCAGGTAAAGTA K 2 1 2 1 101000 f 74 goat snp1029-scaffold1027-855563 26 10418221 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405920 Affx-122955573 AX-123276272 26 40054531 AATCTGATTCCTATGGAATTTCTTTCAGAATGTTT[A/G]CTTAGTAAGAGAAGACACTGATGAGTACAAAGATT R 2 1 2 1 202000 f 74 goat snp1028-scaffold1027-781724 26 10345356 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801081 Affx-122960531 AX-385287995 26 40087583 AGAAGATTCTGTGCAGTTTTGTCGGTGTTCTTCTC[A/G]CCTTTGTTGTTCTTGCTTACCTCTGCTAGTCTTCC R 2 1 2 1 202000 f 74 goat snp1027-scaffold1027-748672 26 10312512 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419730 Affx-122945897 AX-123290078 26 40126731 GATTTGCTGTGTCCTGAGACGTATGTTTGGGTTCC[C/T]ATTGAGCAATGCCTGCCTTCACTTGAGAAATCCAA Y 2 1 2 1 101000 r 74 goat snp1026-scaffold1027-709524 26 10272621 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782679 Affx-122965649 AX-385269751 26 40185937 TAAGGCCTTTAGATGCTCACCTATCATAAAGTAAT[A/G]TAGTATATCCTAAGAGAGTTGTGTGAATAGGAAGA R 2 1 2 1 101000 f 74 goat snp1025-scaffold1027-650318 26 10212943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445318 Affx-122925431 AX-123315655 26 40231957 AGAAATCCCAGTCATGAGCTTTTCTTCATTGTACT[A/G]TTATCTAAGACTGATTTTATTTCTTCACAGTTTTA R 2 1 2 1 201000 r 74 goat snp1024-scaffold1027-604298 26 10166965 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439333 Affx-122930299 AX-123309670 26 40278388 CAGGGCAATAGACTAAAAAGCAGTAGACATATACC[A/G]TGTTTCTGATGTGAGATAAATACAATGAGAATTTC R 2 1 2 1 101000 f 74 goat snp1023-scaffold1027-557867 26 10120619 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387880 Affx-122969628 AX-123258238 26 40309161 TGCCATGACCCCTTTTCCTCAAGGCAATACTCTGA[C/T]GGGATCCCAACAGCAGTCTTATCACAATCTATACA Y 2 1 2 1 202000 r 74 goat snp1022-scaffold1027-527094 26 10089829 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407160 Affx-122954842 AX-123277511 26 40350578 CCATCCTAGGCTCCTTCCCGGCTCTAACACAGCAG[C/T]AGTGATACATTTTGGAAGATTAATTGCTGTCAAAG Y 2 1 2 1 101000 r 74 goat snp1021-scaffold1027-485677 26 10051515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447526 Affx-122924060 AX-123317862 26 40398379 TTGTTACCCACATGGAGATTAGCAGAAAAATAACC[A/G]TATCGAGAATAAAGGGAGCAGGTTCTCACAGTCAG R 2 1 2 1 101000 r 74 goat snp1020-scaffold1027-437876 26 10003122 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449438 Affx-122922675 AX-123319773 26 40459587 TGTCACAAATACCTTAACTTTGAGACAGTGTGCCT[A/G]TTTGATGAGGGAGATTGTGTTGTTTGTTGGAGCTT R 2 1 2 1 101000 f 74 goat snp1018-scaffold1027-376668 26 9942156 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415254 Affx-122948941 AX-123285603 26 40510797 AGGGGCAGGCAGCTGGGCTGTCGCATGTTCTAATA[G/T]TCCTTGTCCTGGACCCTATGTAACGGCCAGTGGGT K 2 1 2 1 201000 f 74 goat snp1017-scaffold1027-325458 26 9890925 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421885 Affx-122944267 AX-123292232 26 40565358 TTTTCCTAAATCCTCGTGGGGTTCTGTCTGTTGTT[A/G]CCATGCTTATTTGTCAGGCCAAGTCCTATTGGTCA R 2 1 2 1 201000 r 74 goat snp1016-scaffold1027-270897 26 9836404 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273152 Affx-1111833314 AX-519546814 26 40598859 GCTCATGACTTGCTGAAACAGGTAGCTGATATTCT[A/G]ATGCACCATATGATGCTGTGGGAAAAATACAGATC R 2 1 2 1 101000 r 74 goat 26_40598859_AF-PAKI 26 40598859 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38439696 Affx-122930571 AX-123310033 26 40650293 TCAGTAGGTATACTGTAAAATCTGTTAAGATCACG[C/T]AAAGATAATAAATTTTTTTCACACAAAAAAATACA Y 2 1 2 1 101000 f 74 goat snp1014-scaffold1027-185962 26 9751092 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447996 Affx-122923740 AX-123318332 26 40687586 AGCACATGGCACATGACCAATTTTTTCCACTCTTC[A/G]TTTCACCTATTGGACAGACACAAGTTCAAGTAGAT R 2 1 2 1 101000 r 74 goat snp1013-scaffold1027-148669 26 9714012 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430839 Affx-122937434 AX-123301180 26 40762461 CACGTAGGCTCTGCAGTGTATGAGAAAGGTTTGAG[G/T]ACTCCCACGTCACAGATCAAGACCCTGGACCTCAT K 2 1 2 1 201000 f 74 goat snp1011-scaffold1027-73794 26 9638875 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780708 Affx-122933969 AX-385267798 26 40811316 CAACTGACCAGTAAGTGACAGCCGGACCTATACTC[A/G]GATGGTTGCTCTTAACTATTTCACTGTTCTACCTT R 2 1 2 1 101000 r 74 goat snp1010-scaffold1027-24939 26 9589617 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388092 Affx-122969504 AX-123258450 26 40850447 TCTCATACCAGCATGTTCCTTCGCACATGCTGTTC[A/G]CTCTGCCTGGAACACACTTCTGACCTTTTGGCCTC R 2 1 2 1 201000 r 74 goat snp29705-scaffold322-14093 26 9537682 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396264 Affx-122963315 AX-123266619 26 40892158 TGGAAAATCGACTTCATTTTGTTCAACCTCAGATT[A/G]GTCACTGACCTCAGTGAAGAATTTTTCAAACAGTT R 2 1 2 1 101000 f 74 goat snp29706-scaffold322-55804 26 9496109 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392013 Affx-122966486 AX-123262370 26 40931928 TCTGAAGACAACGTCTGTAGTTCCTTGAGCATTTC[C/T]CGTTCTTCCTCTTGCTTGTAAGTCAGAAACCTCCG Y 2 1 2 1 101000 f 74 goat snp29707-scaffold322-95574 26 9455513 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277819 Affx-1111836038 AX-519551316 26 40978908 GCTTCTCTGGAAAGATTTGTCTTTCTTATTCCACC[A/G]TGCTGTTTATTCAGTGGATACAAAAAGGACTCCAG R 2 1 2 1 201000 r 74 goat Random2.2K-2199 26 40978908 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320790115 Affx-122938037 AX-385277121 26 41030259 CTATGGAATGATCTGTAAGATCATGGCCAGTAGCA[C/T]AGGGACTGACATTATGCATAGACCGTCTCTGGAAG Y 2 1 2 1 101000 r 74 goat snp29709-scaffold322-193905 26 9356539 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386152 Affx-122971396 AX-123256510 26 41101341 TTGATGTCACACAGGCTGTGGCCCAGTAGGGGTCA[C/T]AGCACCGGAGCTGGGGAGAGGCTGGGCTTCTTAAG Y 2 1 2 1 103000 f 74 goat snp29711-scaffold322-264987 26 9286556 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441360 Affx-122928871 AX-123311697 26 41133832 TTCATCAACAGTTCCCCGACCAGGGATTTAATCTT[A/G]CCCTCTTCAGTGACAGCGTTGACTGGATCCCAGGG R 2 1 2 1 201000 r 74 goat snp29712-scaffold322-297478 26 9254067 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389509 Affx-122968299 AX-123259867 26 41177223 CTTGGTTCATTGAACCATGAAGAACTGCCCGAGGC[A/G]CTAGATCTATCGTCATCCGGTTTGGCAGCCACCTG R 2 1 2 1 101000 f 74 goat snp29713-scaffold322-340869 26 9210418 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452838 Affx-122920731 AX-123323171 26 41279547 GACCTCCTATTTAAGAGAAAATTGGGGCAAACTCG[C/T]GTCCTGGGATGACTTCCTTCAGGTTGGCGTTCCAG Y 2 1 2 1 101000 f 74 goat snp29715-scaffold322-443193 26 9108110 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785103 Affx-122926292 AX-385272149 26 41321586 TTTATTTGTAAGTATTTTAGTGAAAACTTAGTGTA[C/T]ATCTGAACCCATCTTTTGAAATGTATTTTCTTCAT Y 2 1 2 1 101000 r 74 goat snp29716-scaffold322-485232 26 9070945 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442012 Affx-122928417 AX-123312349 26 41355323 CAAACCTGGATTTAAATCCTGGCTCCATCTCCAAG[C/T]TCCTAACCTCTGTGATCAGAAACTCCACATCTGTA Y 2 1 2 1 201000 r 74 goat snp29717-scaffold322-518969 26 9037746 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383769 Affx-122972429 AX-123254127 26 41412626 ACCCTCTGCACTCAGTGCTCTGCCTCCCAGAGCAC[A/G]TCATCCATATTTCTCTTCCTGAGCATTTGCAATGT R 2 1 2 1 101000 r 74 goat snp29718-scaffold322-576272 26 8980852 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449304 Affx-122923006 AX-123319639 26 41502222 GTATCTTTCATTTCAGTGATTGTATTCTTCAGTTA[C/T]GATTACTTTCTCTTAATATTTCCTGTCTCTTTTAT Y 2 1 2 1 101000 f 74 goat snp29720-scaffold322-665868 26 8891162 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383412 Affx-122973488 AX-123253770 26 41538683 TATAAAGTTTCTCTCCCCCTCTCCTGCAGAGGAAC[A/G]CTTACTGTGCCCCCTCTATTGTTTTTGAAAGTTTG R 2 1 2 1 201000 r 74 goat snp29721-scaffold322-702329 26 8854657 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434251 Affx-122934822 AX-123304592 26 41568553 CTCCTTCAGACTTTGAAGCGGTTCTATCACGAGTC[A/G]TGATGCTGATCAGAGCAGCTCTTAGCTGCCTGGGG R 2 1 2 1 101000 f 74 goat snp29722-scaffold322-732199 26 8824717 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447250 Affx-122924954 AX-123317586 26 41680287 AATCGTAACCACTGGATCACCAAGGAAGTCCCAAG[A/G]AGCAGGGCTTCTTACTGAGAGTGATGGAAGCAGGG R 2 1 2 1 201000 r 74 goat snp29724-scaffold322-843933 26 8713277 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379093 Affx-122976766 AX-123249452 26 41732314 AAGCTGGAAGTCCTGCTGATGAACATCTAATCATG[C/T]GAACTTGAACCCTGGTGTACCTTTCTCCTCTGACT Y 2 1 2 1 201000 r 74 goat snp29725-scaffold322-895960 26 8664420 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391631 Affx-122966575 AX-123261988 26 41779832 GTGGGAACAAAGTCTTTGGGAGCAGGGGAGATATG[C/T]AAGTGAATATCTCACTCTGATGCCAAGTATCTAAC Y 2 1 2 1 101000 r 74 goat snp29726-scaffold322-943478 26 8617316 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379819 Affx-122976224 AX-123250177 26 41840918 AAAATGTCTTTGCAGAGTACAGATACTTCCTTCCC[A/G]CAGAAGGTACATTTTTTTTTCATAAGGGTGTGATG R 2 1 2 1 101000 f 74 goat snp29728-scaffold322-1004564 26 8555843 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380849 Affx-122975445 AX-123251207 26 41874598 TGACCATATGTTTCCTCCTCCATGAATTGCCTCTG[C/T]GTATCTTTTACCCATTTTTCTCTTGGTTCTATTTT Y 2 1 2 1 101000 f 74 goat snp29729-scaffold322-1038244 26 8522608 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411359 Affx-122952251 AX-123281709 26 42073939 ATTACGCTGCATGTTGTTCACATGCGTAGGGGTGC[A/G]TGAGCAAAGTCCTTGTGACCACGGTTGGGGCCGAA R 2 1 2 1 101000 f 74 goat snp29734-scaffold322-1237585 26 8323453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413766 Affx-122949933 AX-123284115 26 42107393 TCCATGGAAGCCATACCGATAATGATTCTATTCAT[C/T]TTGCTCGGCTCCTTCGCAGCGCTGGCCTGCAGTCC Y 2 1 2 1 101000 f 74 goat snp29735-scaffold322-1271039 26 8289967 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415174 Affx-122949008 AX-123285523 26 42147148 AAATGCACATCCGCGTGGTGGGCACCAAACCTTTG[A/G]TGGATTGGAAAATGAAGGTTCTGGTCAAACTTGCC R 2 1 2 1 101000 r 74 goat snp29736-scaffold322-1310794 26 8250330 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419208 Affx-122945699 AX-123289556 26 42186632 TCTCTTTCATAATTTTTCAGGAAAACTGCGTCTTA[C/T]TATGAATTTGTTGTTTACCTGCTGCCTCACCAGCC Y 2 1 2 1 101000 f 74 goat snp29737-scaffold322-1350278 26 8210910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429702 Affx-122937627 AX-123300043 26 42310915 GTCCATGCTGCAGGAAGTCAGCCCTGAAATATTCA[C/T]GTTGTGGGTGTCACAGTAGCTTAAAGAGTGGACCC Y 2 1 2 1 101000 r 74 goat snp29740-scaffold322-1474561 26 8087282 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384542 Affx-122973022 AX-123254900 26 42413095 ATGATGCTATCATTAATCATTAGTGAAGTGAAGTC[A/G]CTCAGTCGTGTCCGACTCTTTGTGACCCAATGGTC R 2 1 2 1 103000 f 74 goat snp29743-scaffold322-1576741 26 7985263 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416320 Affx-122947916 AX-123286669 26 42456446 GCCCATCCTCTTGGCTGTGTCTGTCACTCACTGGT[A/G]CTGGGCACATGTTTGATCAGTAGCCTTAAAAGCGT R 2 1 2 1 101000 r 74 goat snp29744-scaffold322-1620092 26 7941784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391247 Affx-122967380 AX-123261604 26 42508602 GAGTCTCTTCCTTTCTTTCTCTCTGTCTGCAGGCT[A/G]TCCTTTCCTGCTTGTGTGGTGTGCAAGCCCTGGTC R 2 1 2 1 201000 r 74 goat snp52204-scaffold774-34130 26 7888996 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399757 Affx-122960317 AX-123270112 26 42546416 ATCCTTTACTGAAGTTGGTGAAGAACACAGATGCC[A/G]CTGGCTCACAGTGCAGGTCACCGTCCCCAAGAAGT R 2 1 2 1 202000 r 74 goat snp52205-scaffold774-71944 26 7853379 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407239 Affx-122955366 AX-123277590 26 42603806 CTGGACTGTCACTTACAGGAAGCCCGGGAGCTCAA[C/T]GACGGGTCAGGTGGTAGGTCTGGCTGGAGGTGGCC Y 2 1 2 1 101000 f 74 goat snp52206-scaffold774-129334 26 7797639 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414363 Affx-122950011 AX-123284712 26 42635096 GTCACCCTCCTTTTTCCCTAATGAAGAGGAGGAAG[C/T]GCTCATAGGGTGGCCTTGCAGAGGTCAACTCAGCC Y 2 1 2 1 101000 f 74 goat snp52207-scaffold774-160624 26 7766809 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393988 Affx-122965034 AX-123264343 26 42663961 TCTTCTCCACCTGTCAAGTACGGCGCTCACGCTGC[A/G]CCAAGCTCCTTCCGAGAGTCTCGGAGACCTCATAG R 2 1 2 1 201000 f 74 goat snp52208-scaffold774-189489 26 7739355 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413394 Affx-122950721 AX-123283743 26 42693962 AGGGAATGACTGTGCACTTGGGCATTTCCACCACC[A/G]TGCACCCTGAACCATACAATCGGGGGGACCAGAAA R 2 1 2 1 201000 f 74 goat snp52209-scaffold774-219490 26 7709822 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393049 Affx-122965623 AX-123263406 26 42724502 TTTTAACACGACTGAGTGGCTAAGCACACATGCGC[C/T]ATTATCATGAAGCACGCAAACCCTGCAGCTCCATC Y 2 1 2 1 201000 r 74 goat snp52210-scaffold774-250030 26 7679739 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386446 Affx-122970789 AX-123256804 26 42754347 CTCTTGGGTTAAATCAGTAATGACACCGTGAGGGA[A/G]GTGAACTTAGGGCCAGTAAGTGGTTTGTTCAGGGC R 2 1 2 1 101000 f 74 goat snp52211-scaffold774-279875 26 7649848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425225 Affx-122941012 AX-123295571 26 42797549 TTCTGCTGTGGGCTTTCACAGAGAGTGGTAAAACT[A/G]TTTCAGCAAAATGACCTTCAGGCAGGATGCATTAA R 2 1 2 1 101000 f 74 goat snp52212-scaffold774-323077 26 7606778 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427441 Affx-122940043 AX-123297784 26 42846229 CCAAACCAAACCCAGGTGGTGATAAGCGCTCTGCC[A/C]GTAATGTAATGAAAGTAGGGTGATGTGCTGGAGAA M 2 1 2 1 101000 r 74 goat snp52213-scaffold774-371757 26 7558349 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277693 Affx-1111836040 AX-519551192 26 42877666 TTTATATAATGCTCTTGTGGAAAGATCTAGGCCTG[A/G]TGGCTTTATTTTTATTTTATTTTTTAAAATTTATG R 2 1 2 1 101000 f 74 goat Random2.2K-2202 26 42877666 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38387989 Affx-122969585 AX-123258347 26 42963981 CTGACTTGGCAAGTGATACCTTTGGAAGGACTACA[C/T]GCACACAGGTCCTGGGGGGATTCTGTCTGCTCCAG Y 2 1 2 1 101000 f 74 goat snp52215-scaffold774-489509 26 7438580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394806 Affx-122964807 AX-123265161 26 43017673 GACGGACAGACTCCAGCATGGGCTCAGCCACCCTG[C/T]ACCTCCCTGGTCTCTCCACAGCCTGGGATTCATTT Y 2 1 2 1 202000 f 74 goat snp52216-scaffold774-543201 26 7388149 G A 2 parentage parentage neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412124 Affx-122951103 AX-123282474 26 43072065 CTCAGCTCCCATGTGCAAGCAGGAAGCTTGGTGAA[C/T]GGAGGAAGAAGATGCAACTCAGAGGAACGTTTCCA Y 2 1 2 1 101000 r 74 goat snp52217-scaffold774-597593 26 7333878 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410698 Affx-122952735 AX-123281048 26 43133954 AGTGAGATAGAACTTCACTTCTCCTTTATGTCAAG[C/T]GCAGTGTGGTGGTCCCAGGTTCCTCCCAGGTCCCT Y 2 1 2 1 101000 f 74 goat snp52218-scaffold774-659482 26 7271523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277825 Affx-1111836041 AX-519551322 26 43149250 TTATAAAATAAAGTTTCTTATAAAATAAACTATCT[A/G]TTCCTCTTAATTTCCATGGTAATAAGTAATTAGTA R 2 1 2 1 101000 r 74 goat Random2.2K-2203 26 43149250 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38438997 Affx-122930370 AX-123309334 26 43179289 TATGGCCAATGTTGACACCAAAAAATAAAGACCCC[A/G]TCCTCAACCTTGACACCTCACAACTCAGTAGACGG R 2 1 2 1 201000 r 74 goat snp52219-scaffold774-704817 26 7225642 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770834 Affx-122970524 AX-385257998 26 43219044 TTTGTCTTATCAGGTACCATACAATAAAGGCACTG[C/T]GGTAAAATCAATATGGTATTTATATCAGAACAGAC Y 2 1 2 1 101000 f 74 goat snp52220-scaffold774-744572 26 7185824 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428035 Affx-122939138 AX-123298378 26 43256173 GTGCTCCTCAGTTTCCTCAGCTGCAAAATGGGGCA[A/G]TAATAGAACTGGCATCTGAGGGTCTCGGGAAGTTT R 2 1 2 1 103000 r 74 goat snp52221-scaffold774-781701 26 7148138 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442723 Affx-122927857 AX-123313060 26 43300070 TGCTCTTCACTTCCTTTTCTGACCTTGAAAATGCA[C/T]GGACATATTTTTCTCTGAACCACTGTTCTGAGCTT Y 2 1 2 1 101000 f 74 goat snp52222-scaffold774-825598 26 7104328 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378579 Affx-122976592 AX-123248938 26 43354688 TCACAAGTGCTTGGGTAAAGTCAGGCAGCAGACGA[C/T]AGATTAAGGGAGAAAGCATTCTTTCTGGTAAGAAT Y 2 1 2 1 101000 f 74 goat snp52223-scaffold774-880216 26 7049635 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275083 Affx-1111834676 AX-519548663 26 43362741 GTAGAAGGAGGCCTCTCCCGTGTATAACTTGGAGG[A/G]A R 2 1 2 1 102000 f 74 goat GoatD01.045443 26 43362741 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38377357 Affx-122977653 AX-123247716 26 43410968 AGAGCAGGGCTCCAGAGCAGCAGGAGACCTTATTC[A/G]CAGCAGCTGGAAGAGAAGGGAGGAATATGGTGAAT R 2 1 2 1 201000 f 74 goat snp52224-scaffold774-936496 26 6993164 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377526 Affx-122977473 AX-123247885 26 43444943 CCATGAAGGTTTACATAATTCTTGACCTCTTCTAA[C/T]ACAGAACGTTTCACTATGTGATTTTTGAAGGCTAA Y 2 1 2 1 101000 r 74 goat snp52225-scaffold774-970471 26 6959022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780330 Affx-122959193 AX-385267425 26 43500435 CAAACAGAATCTTGAGTCTGGTACAGAATGGTCAA[G/T]ACAAAAGTGTTAGCCATTGTTATGGTCTTCATATG K 2 1 2 1 101000 r 74 goat snp52226-scaffold774-1025963 26 6903525 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426083 Affx-122941079 AX-123296429 26 43544416 AGTTGTTCGTCTTAACCAGAGTCCTAGGGGGAAAG[C/T]GGTTTTTGCCTTGGGCACTTTTCCTCGTGAAATGT Y 2 1 2 1 101000 r 74 goat snp52227-scaffold774-1069944 26 6859834 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404990 Affx-122956395 AX-123275342 26 43585263 CCTATACCTTTCAAATATCCAACAAAGAAATTAAA[C/T]TCATACAGCTATATATGTGAATATACACACAGAAA Y 2 1 2 1 101000 f 74 goat snp52228-scaffold774-1110791 26 6819019 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406742 Affx-122955740 AX-123277093 26 43623904 GCTGCCATGAGTCTTCAGAAGTACGGAAGAGCATT[A/G]CGATACATTAAATTAGCTTTGCAGAGCCATGGTAA R 2 1 2 1 101000 f 74 goat snp52229-scaffold774-1149432 26 6780203 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320793623 Affx-122948416 AX-385280597 26 43712773 TGAAGCAGGCAGGAAATAATCACTGTTATTTATAC[A/G]TTTGCAAGATTCAGGAATTTAGAAATACTCTTTAA R 2 1 2 1 101000 f 74 goat snp52231-scaffold774-1238301 26 6691231 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422056 Affx-122943608 AX-123292403 26 43768039 GAGGACCTGGGGGAAGGGCCATAGGGTCCTGCTTC[A/G]TTTCCCCAGAACGACCTGATTATTAACTTGTCCTC R 2 1 2 1 101000 r 74 goat snp52232-scaffold774-1293567 26 6636059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447623 Affx-122923989 AX-123317959 26 43802052 CTGGAATTTTTTTTTTTTTGTCAGTTGCTTTGCTT[A/G]TTGAAGAATTTCTGTGAAACACTTGTAATACTTGT R 2 1 2 1 201000 r 74 goat snp52233-scaffold774-1327580 26 6600915 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376007 Affx-122978411 AX-123246366 26 43834359 TTGACGTAGATGTACTTACTTCCCCTTGCAATTCC[A/G]GCTTCACTGTCAATCCTGAGGATGAAGAATAAATG R 2 1 2 1 201000 r 74 goat snp52234-scaffold774-1359887 26 6568273 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425892 Affx-122941629 AX-123296238 26 43877245 CACGCCTGGAAAATGACACCCAGGAGGAAAATCCA[C/T]GTCCACCAGAGGCCAGTGAGGGAGCCGGCAGTAGA Y 2 1 2 1 101000 f 74 goat snp52235-scaffold774-1402773 26 6525149 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274627 Affx-1111834331 AX-519548214 26 43905393 AAACACACAATTCCATTTTCA[A/G]AGCTGACAAAAGACTGAGCTCCAGAGGAATAGGTC R 2 1 2 1 101000 r 74 goat GoatD01.030216 26 43905393 C T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38410930 Affx-122952050 AX-123281280 26 43950058 GTGGCATACTTAGCCCTCAACCCCTTAAGGCCAAA[C/T]GCTCCAAGAAGCTCATTAATGGATGGACTCAACTG Y 2 1 2 1 201000 r 74 goat snp52237-scaffold774-1475586 26 6452034 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778947 Affx-122947796 AX-385266054 26 44002467 TCAGCCTGGAAACAGTGAGTCTGCAATAGTGAGAA[C/T]GCTGAATCGACCCAGAGTCAGAAGTCTTATGGTTT Y 2 1 2 1 101000 r 74 goat snp52238-scaffold774-1527995 26 6399739 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768317 Affx-122945859 AX-385255497 26 44036044 AATTGTTTCTATTCTGGCTTCTTTTCTGTAATCAA[C/T]TCATTCCACAAGATACAATCAATCAGCACGGCTTT Y 2 1 2 1 101000 r 74 goat snp52239-scaffold774-1561572 26 6366252 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773687 Affx-122927633 AX-385260827 26 44073404 TCAACTTCACTGAGGGATATTCTACTAAAAATAGC[A/G]TATGTATAACTTATTTTCCTTAATGCTTTTATTAA R 2 1 2 1 201000 r 74 goat snp52240-scaffold774-1598932 26 6328830 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426724 Affx-122939881 AX-123297070 26 44111205 CAGATCTATTAATAGTTTAATAAAATCCACATGCT[A/C]TGATGAAGATGTGTGGATAAAAAGAAGAGGAAAAG M 2 1 2 1 101000 r 74 goat snp52241-scaffold774-1636733 26 6290522 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434929 Affx-122934306 AX-123305269 26 44142209 TAGAACACCAGGCAAATTAAGCCTAAAGCTTCTGA[C/T]AGGCAGGTGAGGCTTCTTCTGCCAGAGTAGAAATG Y 2 1 2 1 201000 f 74 goat snp52242-scaffold774-1667737 26 6259845 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409454 Affx-122954080 AX-123279805 26 44171228 ATATATTGCTATGAGATTCCATGACTACGCTATGA[C/T]GAAAAAGACCAACTGCTGAGGGGGTCCAAAGGTTT Y 2 1 2 1 101000 f 74 goat snp52243-scaffold774-1696756 26 6231770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388803 Affx-122968913 AX-123259161 26 44227618 GGCCCTGGAAGGGTCAGACCCACCAGCGGGCTGTG[A/C]GCCAGAAGCAGGCATAGCGTCAGGTCAACGGGGAG M 2 1 2 1 101000 r 74 goat snp52244-scaffold774-1753146 26 6175463 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320793050 Affx-122942052 AX-385280028 26 44256242 GTCTCATTGTTAAATATAAACAGACTGCCAAAATA[C/T]AGACATTTGAAGCAACTCAAAGACTATACCATATA Y 2 1 2 1 101000 r 74 goat snp52245-scaffold774-1781770 26 6146702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419710 Affx-122945913 AX-123290058 26 44286607 ACTAGTGGCACTCATGCTCACTCACTCACTCAGTC[A/G]TGTCTGACTCTTTGCGACCCCATGGACTGTAGCCC R 2 1 2 1 103000 f 74 goat snp52246-scaffold774-1812135 26 6116324 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403521 Affx-122957622 AX-123273874 26 44318093 CATCCATCTGATTTGGTCAAGAGGCTGATCAAAAG[C/T]ACAGTGCAAGAGCACGCCCTAATTTTCTTCCAACC Y 2 1 2 1 101000 f 74 goat snp52247-scaffold774-1843621 26 6084895 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476378 Affx-1251763889 AX-586011789 26 44330056 TTTTATTGAAAATGAGTTTTATATTTGATTCTCAT[-/TCCCCGTTATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]CCCCGTTATTCTTGGAAGTGGTTCACTCGGCCATT - 4 1 4 1 20000 f 74 goat SV_252 26 44330056 - deletion junction SV-TF-chip 539476634 Affx-1251763889 AX-586012017 26 44330056 TTTTATTGAAAATGAGTTTTATATTTGATTCTCAT[-/TCCCCGTTATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]CCCCGTTATTCTTGGAAGTGGTTCACTCGGCCATT - 4 1 4 1 20000 r 74 goat SV_252 26 44330056 - deletion junction SV-TF-chip 562165658 Affx-1251763889 AX-606941067 26 44330056 TTTTATTGAAAATGAGTTTTATATTTGATTCTCAT[-/TCCCCGTTATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]CCCCGTTATTCTTGGAAGTGGTTCACTCGGCCATT - 8 1 4 1 20100 r 74 goat SV_252 26 44330056 - deletion junction SV-TF-chip 562166247 Affx-1251763889 AX-606941655 26 44330056 TTTTATTGAAAATGAGTTTTATATTTGATTCTCAT[-/TCCCCGTTATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]CCCCGTTATTCTTGGAAGTGGTTCACTCGGCCATT - 8 1 4 1 20100 r 74 goat SV_252 26 44330056 - deletion junction SV-TF-chip 562166463 Affx-1251763889 AX-606941871 26 44330056 TTTTATTGAAAATGAGTTTTATATTTGATTCTCAT[-/TCCCCGTTATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]CCCCGTTATTCTTGGAAGTGGTTCACTCGGCCATT - 8 1 4 1 20100 f 74 goat SV_252 26 44330056 - deletion junction SV-TF-chip 562166573 Affx-1251763889 AX-606941981 26 44330056 TTTTATTGAAAATGAGTTTTATATTTGATTCTCAT[-/TCCCCGTTATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCTCCCCCC]CCCCGTTATTCTTGGAAGTGGTTCACTCGGCCATT - 8 1 4 1 20100 f 74 goat SV_252 26 44330056 - deletion junction SV-TF-chip 38421455 Affx-122943937 AX-123291802 26 44352275 TTTTGCAAAAAAGAAAAACAAAACAGTAATGGTCA[C/T]AATCTAATCTTTCTCTGTCAGATATTAAGCTTATC Y 2 1 2 1 101000 r 74 goat snp52248-scaffold774-1877803 26 6050687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418552 Affx-122946397 AX-123288900 26 44385452 TTAATTGAGCCTGATCAATTAATGACCCAAAAGCC[A/G]TAAGAGAGCTGCCTAGGCTGGGCTTCTCTCATAGC R 2 1 2 1 101000 f 74 goat snp52249-scaffold774-1910980 26 6017828 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381716 Affx-122974702 AX-123252074 26 44414475 AGAGAGTAAGACATCCACATACATTTGGGAATTTG[C/T]GAAGAAGACATTTTGGGTCAAAGAGACTGGGGTAG Y 2 1 2 1 101000 f 74 goat snp52250-scaffold774-1940003 26 5988809 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384254 Affx-122972355 AX-123254612 26 44461304 CTGGAATTCAGAGACTGGATAAAGTTCTATGATTT[A/C]ATGTTCTTACCACACAGACCCATGAGGACATCTCA M 2 1 2 1 101000 f 74 goat snp52251-scaffold774-1986832 26 5944615 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782430 Affx-122963588 AX-385269506 26 44528617 TCTATAGCATCCAATTTCCTGTTACTACCACCTAG[C/T]AAAACTTCCATTTCAGATAGTATTAAAGAATCACT Y 2 1 2 1 102000 f 74 goat snp52252-scaffold774-2054145 26 5877258 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384883 Affx-122971931 AX-123255241 26 44559521 TCCTAGCCTTTCTAAGAAGAGATAATGTAGACAGA[C/T]CTTAAGGGGCCCCTACACCCCTCACTTTTCCCCTC Y 2 1 2 1 101000 f 74 goat snp52253-scaffold774-2085049 26 5846039 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426122 Affx-122940626 AX-123296468 26 44599087 TTCTTCTCCAGAGAAACTGATTTAACAACAGTAGC[A/G]TGAACAAGCCTCCCCACACCGCTGTCACTCTCTTG R 2 1 2 1 201000 f 74 goat snp52254-scaffold774-2124615 26 5806582 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775105 Affx-122946796 AX-385262237 26 44657352 ATATGAAAGAAAAACATGACATACAAGACCATTTC[A/G]TTTTTTAAAACTTCCTAGAAGAGTATGAATGTGGC R 2 1 2 1 101000 r 74 goat snp52255-scaffold774-2182880 26 5749588 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423882 Affx-122942300 AX-123294228 26 44726817 GAGCATTTCACGTATGGCCTGGAGGAAGGTGAGGT[A/G]TAGTAACTGTCAGCTGCTGTTATCAGTAGTGTCAG R 2 1 2 1 101000 r 74 goat snp30499-scaffold3363-149216 26 5680548 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383202 Affx-122972784 AX-123253560 26 44763296 CAGTCATAATTAGTAGCAGTGCTGGGTTAGATTTT[A/G]TCCCTCCCTCCTAAAAGTTATATTCAAATATTTAA R 2 1 2 1 101000 r 74 goat snp30498-scaffold3363-112737 26 5644028 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394440 Affx-122965088 AX-123264795 26 44804948 ACTGACTGTCAATCAAACAGCTGTCCCCCAAAAAA[C/T]GGTGGAGGTGGGGATGACTGGATCACTATTAAATC Y 2 1 2 1 202000 f 74 goat snp30497-scaffold3363-71085 26 5602695 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444635 Affx-122926929 AX-123314972 26 44843446 TGGGGGCCGCTGTCTAGGAGTAGCTGGTCGTCGGG[C/T]AAGTGGACTGTGAAGGCCGTATCCAGGGTGACATC Y 2 1 2 1 101000 r 74 goat snp30496-scaffold3363-32587 26 5564255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433497 Affx-122935028 AX-123303838 26 44899621 GGTTTTGGATCACAGGCAAGCTGTTGAGAGGTTCA[G/T]CTGATGAAATCAAGTGGCACTAGAGAGCTAAAAAT K 2 1 2 1 101000 r 74 goat snp11039-scaffold1397-23489 26 5510221 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393674 Affx-122965270 AX-123264029 26 44978946 TTAAGGACTGGATGCTGTATCTACCCCAAAGGAAA[A/G]TTTCCACGGTCATCTAAAAAATGAATTACACTGAT R 2 1 2 1 201000 r 74 goat snp11041-scaffold1397-102814 26 5431535 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778666 Affx-122953991 AX-385265777 26 45009817 CATCTCCACTTCACAGGCAGATGGTTTTTCAAAAT[A/G]CAACTTACTTGGTGTAGGCTTTTACTACTTTTTTG R 2 1 2 1 101000 f 74 goat snp11042-scaffold1397-133685 26 5400666 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386240 Affx-122970969 AX-123256598 26 45044886 ATTTACTGAAAGAACTTCAGAGAGCCCTAGGGACC[A/G]TGGCTGCAGGTAAACATGGATGTGCCCCCTTCCAC R 2 1 2 1 101000 f 74 goat snp11043-scaffold1397-168754 26 5365671 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377223 Affx-122978168 AX-123247582 26 45080393 CAAATCTAAAGAGAAAGAATAATTTCACAAGGATC[A/G]TAGAATTTGGAAGGAGTTTTCCAAATGGGTTATTA R 2 1 2 1 101000 f 74 goat snp11044-scaffold1397-204261 26 5330106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427804 Affx-122939758 AX-123298147 26 45126528 GAGCAGATTCATAGAGCTGCAGCTTTCCTGAGAGG[C/T]GTTGCCAAAGTCATAATTAGTAGAAAGTTACCAAG Y 2 1 2 1 201000 r 74 goat snp11045-scaffold1397-250396 26 5283994 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277697 Affx-1111836042 AX-519551196 26 45162388 ACAAATTAAAATTATCTTCACCATTTTAAATCTAT[A/G]AAGATCTTGCTTCCTGGAATCTCTTCCATATTTTA R 2 1 2 1 101000 f 74 goat Random2.2K-2204 26 45162388 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777325 Affx-122975770 AX-385264447 26 45203276 CAGCCTGGCTTTCACCACTCGTACTGTTCAAGAGA[C/T]ACCATTCCAGACTGGGAAGCAATTGCTTGGCAGTT Y 2 1 2 1 101000 r 74 goat snp11047-scaffold1397-327144 26 5207090 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396249 Affx-122963327 AX-123266604 26 45285103 GTCGACGGGTATGTTTTTCAGATTCCATTTTTGGC[C/T]GAAGGGATCAGGATCCATGGAGACAAAGTCACAGA Y 2 1 2 1 201000 r 74 goat snp11049-scaffold1397-408971 26 5124618 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783541 Affx-122959100 AX-385270603 26 45351328 GCATTTCTCTGTGTTAGCAAACAAAAGACGGTATG[A/G]TTACCCTGAAATAAGCACACATTAATGAGCTATAG R 2 1 2 1 101000 f 74 goat snp11051-scaffold1397-475196 26 5058578 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421744 Affx-122944373 AX-123292091 26 45366323 AGTTTGGTTTCTTGGAATGATCAGTGCTAACGGAT[A/G]TACACAGGTATAGCATACAGAATTACAAGACATAT R 2 1 2 1 101000 f 74 goat snp56382-scaffold885-9392 26 5047298 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414546 Affx-122949501 AX-123284895 26 45414614 ACACAGTGTTCCATCTCTGCCTGCTCCATAAACGG[C/T]GGCCAGCTGCTGCAGAACGCACCAAGCATCTCAGT Y 2 1 2 1 101000 f 74 goat snp56383-scaffold885-57683 26 4998899 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450298 Affx-122922154 AX-123320633 26 45464205 CCTTTGGACTGGTTAGTTCTCTCCAGCCCCTCTGC[A/G]CAGTATGGAGCCTGAATCCCAGGGAAGATCCAGGT R 2 1 2 1 101000 r 74 goat snp56384-scaffold885-107274 26 4949266 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399239 Affx-122960581 AX-123269594 26 45492835 GTATCTGAGACCTTGCATGGTTGGAGATATCATTG[C/T]GTTACTTTTGCACATGATCTAAATTTGGCTGGGTA Y 2 1 2 1 101000 f 74 goat snp56385-scaffold885-135904 26 4920172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391390 Affx-122967266 AX-123261747 26 45544761 CAGAGAGTCAGACACAATTGAGTGAATGAGCATGC[A/G]CGTGCACACACACACTGATTCAGAATCATACCATT R 2 1 2 1 303000 f 74 goat snp56386-scaffold885-187830 26 4868058 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798253 Affx-122966102 AX-385285188 26 45575997 GGTCTGCCTTCGCCCACGGGATGCTTACTATCATG[G/T]TCTCAGAGAAAGACACCGAGAAAACAGCCAAACTT K 2 1 2 1 202000 f 74 goat snp56387-scaffold885-219066 26 4837715 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405341 Affx-122956331 AX-123275693 26 45605084 AATGCTGAGTGATCATGTTGTGAGCTGAGCTGTGA[C/T]AAGAGGACAGGTTAGAATAAAGGTTAAAAGCTCAG Y 2 1 2 1 101000 f 74 goat snp56388-scaffold885-248153 26 4808511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797626 Affx-122949047 AX-385284565 26 45653010 CCGCAAATCCATGTATGATCTGAGGAGTGAGATAG[C/T]TTGTCCTCTAAAGACACCAAACTCTGTTCAAACGC Y 2 1 2 1 201000 f 74 goat snp56389-scaffold885-296079 26 4759960 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423538 Affx-122942437 AX-123293884 26 45690423 TTTTTTTTTTTAACATAGATGGAGAGAGAAGAGAC[A/G]CCTGCCTAGGGACCAAACAGCCAGTGCTTCTAGAG R 2 1 2 1 201000 r 74 goat snp56390-scaffold885-333492 26 4722242 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273108 Affx-1111833315 AX-519546773 26 45701546 GTTGACTGAAAAGGAATATTAAGGTGCTTATTGTT[A/C]TTGAGAGGAGCATGAGAAGGCATGAAGCCTTCTGC M 2 1 2 1 103000 f 74 goat 26_45701546_AF-PAKI 26 45701546 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38431652 Affx-122936811 AX-123301993 26 45760386 TGTTGGGAGCACAGGGTACATAATTGCTTTGATGG[C/T]AATTGCTTCTTAAATTGATCTGCTGTGGGGAAAAC Y 2 1 2 1 201000 f 74 goat snp56391-scaffold885-403455 26 4652135 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382109 Affx-122974887 AX-123252467 26 45798422 GCACTTCTTTGAAGTCTTTCCCTCTTAAGGGACAG[C/T]GACCCACCCTGTTGGGCTGGGCCAGCCTTCTGCCC Y 2 1 2 1 102000 f 74 goat snp56392-scaffold885-441491 26 4614406 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441427 Affx-122928820 AX-123311764 26 45858738 TTGGTTTGTCTTTATTAAACTTCAAGTCTGCCATA[C/T]ACAGTCGTGTAGGTTGCACACTGCCCAACTCCAGG Y 2 1 2 1 101000 f 74 goat snp56393-scaffold885-501807 26 4554412 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416405 Affx-122947852 AX-123286754 26 45898226 ATGGCTTGGGTGGTATATTAGTTCTCTAACCAAAC[A/G]TCACACCCTTAAACAAGAGAAATGTCTTTCCTCAC R 2 1 2 1 101000 f 74 goat snp56394-scaffold885-541295 26 4514998 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385140 Affx-122971764 AX-123255498 26 45930550 TGCTAAACCTCTCTGAACCTCAATTTTCTCACTTG[C/T]GAAAGGGGAAAGCCTTAAACTGGTTGACCCAAGTG Y 2 1 2 1 201000 r 74 goat snp56395-scaffold885-573619 26 4481400 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449648 Affx-122922584 AX-123319983 26 45965472 GAGGAGAATGGTGTCTCTGTGCCCGTTTCTGGCCA[C/T]GTGAACTCTCCCAGGTTGGGTTCTCTCTTGTATTG Y 2 1 2 1 101000 r 74 goat snp56396-scaffold885-608541 26 4446235 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415022 Affx-122949024 AX-123285371 26 45993267 TAGAATGGGGAAGTTAAGACAAAGAGACCCTACTT[A/G]TGTGTCTCAGTGGCCATAGCTTATCCTATGGTTGT R 2 1 2 1 101000 f 74 goat snp43588-scaffold5814-6429 26 4418733 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395282 Affx-122964078 AX-123265637 26 46022430 ACTGATGACAAACGCAGCATTAGAAAGAATGCCTA[C/T]GAGACGGGCTCGTTCCCAACTGCAAGTGCCTCTCC Y 2 1 2 1 101000 f 74 goat snp43589-scaffold5814-35592 26 4389536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452967 Affx-122920160 AX-123323300 26 46041610 GACAGCTGCTTACAGAGCCTGGGCAAGTCCTCTAG[C/T]GCTTTATGCCAGCATTGTGGTCCCACGGAGGAGTA Y 2 1 2 1 201000 r 74 goat snp26120-scaffold2722-8647 26 4371216 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427109 Affx-122939668 AX-123297452 26 46093927 GTATTCTATACTTCGATGCTCACTCGTGTAAGACT[A/G]CAGCCCCATGGACTGTACCCCTCCAGACTCCTCTG R 2 1 2 1 101000 f 74 goat snp26121-scaffold2722-60964 26 4319932 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277828 Affx-1111836043 AX-519551325 26 46108867 TATTAAATAATTTAGATAGGTATATATTTTAAATG[C/G]GTGAGTGAAAAACACAACTCCAAATATATGACCCA S 4 1 2 1 101000 r 74 goat Random2.2K-2205 26 46108867 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38397731 Affx-122962545 AX-123268086 26 46139597 CCCAGGCCTGTGAGTTTCACAGACCTCATTTACTT[C/T]TTTTACCAAAACATGAAGGCTTGAGAATAATGAGA Y 2 1 2 1 201000 r 74 goat snp26122-scaffold2722-106634 26 4274289 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414534 Affx-122949510 AX-123284883 26 46193763 CCAGTTTCCTTTCTGACTGTTCATTAAATGTGTAT[A/G]TGATAAAATACGGATTATTTGTGAATATGGGTGGG R 2 1 2 1 101000 r 74 goat snp26123-scaffold2722-160800 26 4220018 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391718 Affx-122967503 AX-123262075 26 46213986 TAAAGATGGCAGTGTTTAAACCACAAAACTCCAAA[C/T]AGAAAAATACAGCTGTCCTCCTCTTTTTGTCAAAC Y 2 1 2 1 101000 f 74 goat snp58601-scaffold954-1353631 26 4201021 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429017 Affx-122938329 AX-123299359 26 46251176 CTCACGTCTTTGAATATGTGCCCCTTGAAGGTTCA[C/T]ATGTGCTTTAGAGCCAGAGGCCGCCTGCACGGTCA Y 2 1 2 1 101000 f 74 goat snp58600-scaffold954-1316441 26 4164233 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410925 Affx-122952053 AX-123281275 26 46302639 GAAACACCGTAGCAGTAATTCACACAGGCAAGAAG[C/T]ATGCATGGAGACAACGCAAGTAAAAATTGGATAAG Y 2 1 2 1 101000 f 74 goat snp58599-scaffold954-1264978 26 4112939 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419175 Affx-122945725 AX-123289523 26 46347252 AATTCAGATCTTTCAAACACTTCTAAATGGAATCT[C/T]TGAGCAGGGTGGGCTTCCCCACAACCAAGGCCAAA Y 2 1 2 1 101000 f 74 goat snp58598-scaffold954-1220365 26 4068706 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780569 Affx-122957330 AX-385267660 26 46376585 TAAAATAAACTTGAGTGTTTGGGGAAAAGAGCATA[C/T]GGACGTTTTGTGAAATTCACGTCTTAGGGAGAACC Y 2 1 2 1 101000 r 74 goat snp58597-scaffold954-1191032 26 4039397 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453054 Affx-122920069 AX-123323387 26 46409382 TTAGTTTTTAATTTTTATGCAGTTATACTTTTTAC[A/G]TTATCATATGAGTTCTGCAAGCAGCTAAATATTCA R 2 1 2 1 101000 r 74 goat snp58596-scaffold954-1158235 26 4006356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277830 Affx-1111836044 AX-519551327 26 46409709 AGAAGAAAGATATGGATTTAAAAGCACAGACTTTC[A/G]GTTGCAAAAGGAATGAGTCACAGGTTTGAAATATA R 2 1 2 1 101000 r 74 goat Random2.2K-2206 26 46409709 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450287 Affx-122922163 AX-123320622 26 46442049 ACGTGGACATTTACTCAGCAGTGGGGATTTGAGAG[C/T]GCATCACTTAAAACATGCCCTGCCTGCAAGGAATT Y 2 1 2 1 101000 f 74 goat snp58595-scaffold954-1125568 26 3973839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451825 Affx-122921472 AX-123322158 26 46498948 GGAAGATGTCTGTGTGAATTTGCTAAGGCTACTGA[C/T]GCAAAATACCACAGGCTGGCAGCTGATAGAACAGA Y 2 1 2 1 201000 f 74 goat snp58594-scaffold954-1068669 26 3917186 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411128 Affx-122951898 AX-123281478 26 46528209 AAGTGTTAGAGCAAATAAGTAGAAAAAAAGAAACC[A/G]TAATTCATCCAACTAAAGCGTGGAAGACAACAAAC R 2 1 2 1 101000 r 74 goat snp58593-scaffold954-1039408 26 3888154 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389511 Affx-122968298 AX-123259869 26 46571726 CAACTGCATACAATGACATTTAACTTGTATTTTCT[A/G]GCACTATTTCTAACATGTCTCTTTGACCCAATTTA R 2 1 2 1 101000 r 74 goat snp58592-scaffold954-995891 26 3847630 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433750 Affx-122934502 AX-123304091 26 46627109 CTTGCTGCCTCACCTGGCTTCTTCCTCCTTCTTGG[A/C]TAAGGCAAGCCCATTTCAGAAACAGTAGACACTGT M 2 1 2 1 101000 r 74 goat snp58591-scaffold954-940508 26 3792132 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800257 Affx-122962918 AX-385287180 26 46674186 ATGATTGAGTGACTCAAACTGTCACAGCTCAGATG[C/T]GCTGTTTTTAGCAATGTTGCAGCTTTGTTCAACAT Y 2 1 2 1 101000 f 74 goat snp58590-scaffold954-893431 26 3744789 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392288 Affx-122967532 AX-123262645 26 46734647 CAAAGTGCAAAGCAGCCTGAAGATGCAGAGATTCC[A/G]TTTCCTTCGCAGTTTCTCAGGTGGGAAAACCTTCA R 2 1 2 1 101000 f 74 goat snp58588-scaffold954-832970 26 3684606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444231 Affx-122927233 AX-123314568 26 46919320 ACGAAAGGTTCTCCCATTTTGGTTTCTTGTAAATG[C/T]GTCACATGTAAGTTGTCCTTGTCATGTCATCTGAA Y 2 1 2 1 101000 r 74 goat snp58584-scaffold954-648297 26 3499977 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803308 Affx-122924396 AX-385290148 26 46961771 TTGCAAAATCGTGCCACATGAATTTAAACTTCTAG[A/C]GATGGAGTGTGCCTCGTCTTTCGTGCTAGAAATCC M 2 1 2 1 101000 r 74 goat snp58583-scaffold954-605846 26 3458181 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390263 Affx-122967750 AX-123260620 26 47002411 CATATGGAAAATGATCTGATTTTCTCCCTTCTCCC[A/G]TGGATGGAGGGCTTTCCAGGTGGCGCAGAAGATGT R 2 1 2 1 201000 f 74 goat snp58582-scaffold954-565206 26 3417990 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797012 Affx-122933340 AX-385283953 26 47061148 AGACATCTTGAAACTACAGTGGATTCATTTTCTCC[A/G]TTTTCAAAGTACTCTTTAGAAAAGTCAAATCAATA R 2 1 2 1 101000 f 74 goat snp58581-scaffold954-506469 26 3359682 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383664 Affx-122972513 AX-123254022 26 47112821 TTTATCGTTCATAAAAACCTCAAGGGGAGTTATTT[C/T]TGTCCCCATCCAGTAGCCCAGGAGCCTGAAGCTCA Y 2 1 2 1 101000 f 74 goat snp58580-scaffold954-454796 26 3308737 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379213 Affx-122976286 AX-123249572 26 47164898 CCTGAGCTGAGGAATTAGGGAGAGCTTTCACATCA[G/T]ATCTCAGCCTCCTCCAGAGTGGGAAGCAGAGCTCA K 2 1 2 1 101000 f 74 goat snp58579-scaffold954-402719 26 3256627 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413176 Affx-122950337 AX-123283525 26 47195344 CTTAATCATTCTCACCTTCCCAGGAGTCTGTAAGA[C/T]AGACAATTGTTAAGGGGAGCAACTCATAATATTAC Y 2 1 2 1 202000 f 74 goat snp58578-scaffold954-372273 26 3226094 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783976 Affx-122958192 AX-385271030 26 47248714 ACAGCATCACCCACAGGTGCTTCTTGTTGAATAAG[C/T]GTCACCAGTCATCTCAACAACCCACTACAAGCTGC Y 2 1 2 1 101000 r 74 goat snp58577-scaffold954-318903 26 3172914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444106 Affx-122926825 AX-123314443 26 47280864 CTCATTAACAAGTAAAATGTTTTTACTGCTTGAAA[C/T]GTTTTAATAAATAGAAAAAAGCAGAGCAGCTGACA Y 2 1 2 1 201000 r 74 goat snp58576-scaffold954-286753 26 3140122 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792786 Affx-122967042 AX-385279765 26 47311002 CCTGCCCTACAAACACATCCGACTGGTGAGTAATT[C/T]GCTTCATTATAAGTTTCCTTTATAAATTTTCAAGG Y 2 1 2 1 101000 f 74 goat snp58575-scaffold954-256615 26 3110199 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780652 Affx-122969010 AX-385267742 26 47344403 GTACACAAATATTGAAGTCTAGTTAAGTTTTCAAA[C/T]AGTGGTATGGTCATAAATTCTGTGACTACTTTCTT Y 2 1 2 1 101000 r 74 goat snp58574-scaffold954-223214 26 3077368 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434524 Affx-122934159 AX-123304865 26 47386822 GAGCTCTGCCCACCCAGCTCAGTGGGAGAGTTCTG[A/G]TGTTTCATGAGTCCAATACTAATGCTCAGAGATCC R 2 1 2 1 101000 r 74 goat snp58573-scaffold954-180795 26 3035615 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389051 Affx-122968613 AX-123259409 26 47426839 AGCTTCACAGCTGCTATTTACTGAGTGCCTAACAC[A/G]TGCCATGCACAGAATTAGGAACAGTCCTGTGGTTT R 2 1 2 1 201000 r 74 goat snp58572-scaffold954-140778 26 2995923 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429731 Affx-122937605 AX-123300072 26 47469324 GCGTGAATGGAGTGCAGACAGACGGGAGAATTTCT[A/G]CACAGCTCGGGGACCCTGGGATGCAGGGAGCAGGC R 2 1 2 1 103000 f 74 goat snp58571-scaffold954-98293 26 2953310 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797447 Affx-122956644 AX-385284386 26 47525772 CCAGAAGGCTCAGTCCTACTTTTTAAACCTCACAG[C/T]CCTGTTTCTTAAATCTGCTTAAAACTTGTCTCCTT Y 2 1 2 1 101000 r 74 goat snp58570-scaffold954-41845 26 2897711 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404292 Affx-122957033 AX-123274644 26 47586474 AGTGCCTGCATGACGTCATCACGGAGGGCCCGGAG[A/G]GGGGACGGGATTGAATTTTACAGCTGGGCCCAGAT R 2 1 2 1 101000 f 74 goat snp21476-scaffold2095-18758 26 2838139 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400607 Affx-122960387 AX-123270962 26 47644671 TGTACTGCCATAGGCTCAGGAGTTCATCCCCAAAA[C/T]ACCCAGACAGCAAGTGAAAGGAAAAACATTGTCCA Y 2 1 2 1 201000 r 74 goat snp21477-scaffold2095-76955 26 2780160 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432177 Affx-122936405 AX-123302518 26 47723222 TGGATTCCTCGGTGATTCTCCCTTGGCCTGGCCCA[C/T]GCCGCCTGCATCCCATGGTAATGGGCCTTCTTCAA Y 2 1 2 1 101000 f 74 goat snp21479-scaffold2095-155506 26 2704133 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399118 Affx-122960856 AX-123269473 26 47787734 TCCTGAGTTTTCAGATTTTTTTGTAGTTGAAAGTG[A/G]AAGTTGCTCAGTCGTGTCCTAAGTCGTGTCCTACT R 2 1 2 1 201000 f 74 goat snp21480-scaffold2095-220018 26 2639500 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273776 Affx-1111833835 AX-519547387 26 47799418 GTCCATGGCTGTCATAGGAGTGAGTGAAGTCCTCA[A/G]GAGGAAAGCCTTCAGGATTCTCTGCAGACAGAGAA R 2 1 2 1 201000 f 74 goat GoatD01.006398 26 47799418 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38404164 Affx-122957073 AX-123274516 26 47845376 ACACACAGTGTGCCCCCTGCCCCTCCTCCCCTTGC[C/T]GGTTCCAAATTCCAGAGAACCAGGCTCCGTGCACG Y 2 1 2 1 101000 r 74 goat snp21481-scaffold2095-277660 26 2585675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435615 Affx-122933784 AX-123305955 26 47885754 TGGTGGGGTGGATGGAGAGATGCACATAGATTGCA[G/T]TTAAGCCTCTATTTACCTTTCTCTCTGTTGGTCCA K 2 1 2 1 101000 r 74 goat snp21482-scaffold2095-318038 26 2547130 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400344 Affx-122960041 AX-123270699 26 47908579 CCTCTCCAGGATTTCCCACATATTCTCCAGTGGGC[A/G]TGCTTGCCCCAAACTCATTATGCTGGTTCTTCATG R 2 1 2 1 101000 r 74 goat snp35030-scaffold4187-10242 26 2525495 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771396 Affx-122940716 AX-385258554 26 47932586 AAAGACTGTTAACAGGATAAAAAAAAGTCAAGCTA[C/T]GGGCAGGATAAAATGGTTGTAAACCATATATTTGA Y 2 1 2 1 101000 f 74 goat snp34795-scaffold413-993146 26 2502077 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391771 Affx-122967464 AX-123262128 26 47961102 TTAAGAAGCCACTTCAAAGTCGCAGAGCCAGAAAT[A/G]AGAAGTCCTCTCCTTACTAAGGTTCAGCAAAGGAC R 2 1 2 1 101000 f 74 goat snp34794-scaffold413-964630 26 2473026 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277833 Affx-1111836045 AX-519551329 26 48003543 ATCTTTAACAGTGTGTTTCCTTAAATAATTGTCCA[A/G]TGAATTTAGTTTGTCCACTTTAAGGGCATATCGGG R 2 1 2 1 101000 r 74 goat Random2.2K-2211 26 48003543 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38387509 Affx-122970326 AX-123257867 26 48004514 TAATATTCCAACCAGCTTGGATCTCTGGATGCCTC[A/G]CTGCCCTGTGCGTGTCTCTGCAGGGGCTGCAAGTG R 2 1 2 1 101000 f 74 goat snp34793-scaffold413-921218 26 2431241 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416307 Affx-122947926 AX-123286656 26 48046536 TGATTACAGAAGAGGGGGGAGCGTCAAGCACCCCC[A/G]AATGTAACTCTGGCGGTCTCCCAGTACGACGACCC R 2 1 2 1 101000 r 74 goat snp34792-scaffold413-879196 26 2389305 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428056 Affx-122939123 AX-123298399 26 48115860 AGCAGGTTTGGATCCCACAGCCAACTCACCCCCTC[A/G]AGGCCCCATGACAGTGGGTCCCAGACTCATCTCAC R 2 1 2 1 201000 r 74 goat snp34790-scaffold413-809872 26 2318969 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415808 Affx-122948897 AX-123286157 26 48175375 CCAGCTGAGCCACGAGGGAAGCTCCAGCGTATATG[C/T]GCATGTAATACACATACACAAATGCTTATGATACA Y 2 1 2 1 102000 r 74 goat snp34789-scaffold413-750357 26 2262289 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389635 Affx-122968741 AX-123259993 26 48213861 GGAAACCTGTCCAACAGCATCTCTTATCTGTCAAG[C/T]AGACGAGGCCAGGGCTGGTCCTGGCCGTTCTGATA Y 2 1 2 1 101000 f 74 goat snp34788-scaffold413-711871 26 2223486 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400457 Affx-122959950 AX-123270812 26 48307328 CCTGCAGCCTGCAGCCAAAAGTGAGCACTCTCTGG[A/C]GGCTCACAGGAAGTGCTTCCCAGGCTCCAACCTCT M 2 1 2 1 102000 r 74 goat snp34786-scaffold413-618404 26 2132034 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273156 Affx-1111833316 AX-519546817 26 48323463 TCTAAGAAGTCGTTTGAAATTCTTTTGTGCCACTG[A/C]GTGACCACAGTATCCACTGGCGGATGAGGAACACT M 2 1 2 1 202000 r 74 goat 26_48323463_AF-PAKI 26 48323463 T G 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38413487 Affx-122950652 AX-123283836 26 48336605 CTCCGAGGTTATCACCTCGTGTGCTCTGCACCCTG[G/T]TGACCATCTCTGCCCTTCCATTTAAGGCTTTGCTT K 2 1 2 1 201000 r 74 goat snp34785-scaffold413-589127 26 2102030 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403823 Affx-122957955 AX-123274175 26 48376431 CGTTTCTCATCCACTTTGTTTGACTTCTCCAGGCC[C/T]GGGCTCTGAGCCTGCAGACCCTCTGTTCTCAGGAC Y 2 1 2 1 101000 f 74 goat snp34784-scaffold413-549301 26 2065748 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383829 Affx-122973166 AX-123254187 26 48415643 CTGATTAACTTACATTCTAGTCAGGAAGATAGATA[A/G]CAATCAAACAAATAGATAAAGCTTTAGGAGAGTGA R 2 1 2 1 101000 f 74 goat snp34783-scaffold413-510089 26 2028506 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803682 Affx-986696461 AX-385290455 26 48448028 CTGGTAACAGATAAGTAAGAATGATAGAGAAAAGT[A/G]CACACCACATTTGTATACAAATTGAAGGACACACG R 2 1 2 1 600010 f 74 goat 26_48448028 26 48448028 Ancestral_priority_1043 ancestry 0.754 recommended IMAGE 10K 10K ancestral 320767719 Affx-986698689 AX-385254953 26 48448042 GTAAGAATGATAGAGAAAAGTACACACCACATTTG[C/T]ATACAAATTGAAGGACACACGAGGCATTATGAAGG Y 2 1 2 1 600010 r 74 goat 26_48448042 26 48448042 Ancestral_priority_1043 ancestry 0.7 recommended IMAGE 10K 10K ancestral 38441663 Affx-122929189 AX-123312000 26 48464636 GGCTGTTTCATTGCTGAGCTGCCGTCCTTACTGTT[C/T]CGGCTTAACTGCTTTTCCTCTGCACCTGCACCCTC Y 2 1 2 1 201000 f 74 goat snp34782-scaffold413-461096 26 1979210 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403207 Affx-122957911 AX-123273560 26 48502025 AATAAAAGAATGCATAAACTTAACTCTCCTCAAAA[G/T]TAACTTTAATTGACTGACATTTAAAAATTAATGTG K 2 1 2 1 101000 f 74 goat snp34781-scaffold413-423707 26 1941676 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765477 Affx-122936145 AX-385252972 26 48592689 TCCTCTTTTCCTAAAGGAGACTTCTGTTAGCATTT[A/C]GGTGTGATAGTCAAACGCTTCCGACTCCTTTTGGC M 2 1 2 1 101000 f 74 goat snp34779-scaffold413-333043 26 1852044 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764169 Affx-986698696 AX-385251907 26 48593695 TAGCAGAAATTGGATGAAAGATTTACTCAGCATGA[C/T]CCTGCCCATGAGAGCAGACCTAGTTTTCCCCACAG Y 2 1 2 1 600010 f 74 goat 26_48593695 26 48593695 Ancestral_priority_1043 ancestry 0.578 neutral IMAGE 10K 10K ancestral 320767736 Affx-986698698 AX-385254967 26 48613558 TTAGCTGTGTACTCATCTATGGTACTGCAGCACTT[A/T]ACTGGATTCTGAAAACCTCATTAAAATTTTTACCT W 4 1 2 1 600010 r 74 goat 26_48613558 26 48613558 Ancestral_priority_1043 ancestry 0.822 recommended IMAGE 10K 10K ancestral 320767740 Affx-986698700 AX-385254970 26 48613647 CAGTGTTTCTATGGGAGAACAAGGGCTAGGTCACC[A/G]TCTTCCTGATGTCACTCTGTCAGTATATTTTTTTA R 2 1 2 1 600010 r 74 goat 26_48613647 26 48613647 Ancestral_priority_1043 ancestry 0.666 recommended IMAGE 10K 10K ancestral 539476379 Affx-1251763890 AX-586011790 26 48631890 AAAGGATCAGAGTTCACAACAGCATCAGAATTTAA[-/GACCAACTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGC]ACCAACTATCAAACTGGGTATTGATTTTATAAAGG - 4 1 4 1 20000 f 74 goat SV_264 26 48631890 - deletion junction SV-TF-chip 539476635 Affx-1251763890 AX-586012018 26 48631890 AAAGGATCAGAGTTCACAACAGCATCAGAATTTAA[-/GACCAACTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGC]ACCAACTATCAAACTGGGTATTGATTTTATAAAGG - 4 1 4 1 20000 r 74 goat SV_264 26 48631890 - deletion junction SV-TF-chip 562165136 Affx-1251763890 AX-606940548 26 48631890 AAAGGATCAGAGTTCACAACAGCATCAGAATTTAA[-/GACCAACTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGC]ACCAACTATCAAACTGGGTATTGATTTTATAAAGG - 8 1 4 1 20100 f 74 goat SV_264 26 48631890 - deletion junction SV-TF-chip 562165320 Affx-1251763890 AX-606940731 26 48631890 AAAGGATCAGAGTTCACAACAGCATCAGAATTTAA[-/GACCAACTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGC]ACCAACTATCAAACTGGGTATTGATTTTATAAAGG - 8 1 4 1 20100 r 74 goat SV_264 26 48631890 - deletion junction SV-TF-chip 562165445 Affx-1251763890 AX-606940856 26 48631890 AAAGGATCAGAGTTCACAACAGCATCAGAATTTAA[-/GACCAACTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGC]ACCAACTATCAAACTGGGTATTGATTTTATAAAGG - 8 1 4 1 20100 r 74 goat SV_264 26 48631890 - deletion junction SV-TF-chip 562165520 Affx-1251763890 AX-606940931 26 48631890 AAAGGATCAGAGTTCACAACAGCATCAGAATTTAA[-/GACCAACTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGC]ACCAACTATCAAACTGGGTATTGATTTTATAAAGG - 8 1 4 1 20100 f 74 goat SV_264 26 48631890 - deletion junction SV-TF-chip 562165584 Affx-1251763890 AX-606940995 26 48631890 AAAGGATCAGAGTTCACAACAGCATCAGAATTTAA[-/GACCAACTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGC]ACCAACTATCAAACTGGGTATTGATTTTATAAAGG - 8 1 4 1 20100 r 74 goat SV_264 26 48631890 - deletion junction SV-TF-chip 562165976 Affx-1251763890 AX-606941385 26 48631890 AAAGGATCAGAGTTCACAACAGCATCAGAATTTAA[-/GACCAACTGCCGCGGCCAGCACAAGCAAGAGTCGCACCTGGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGC]ACCAACTATCAAACTGGGTATTGATTTTATAAAGG - 8 1 4 1 20100 f 74 goat SV_264 26 48631890 - deletion junction SV-TF-chip 38396862 Affx-122963247 AX-123267217 26 48679972 GTTAAGTCAGTTACCATGTATCAATAAAAGTGAGC[A/G]CTCTTCAACCATTAGTAGAAGTGATTTGGAAGATT R 2 1 2 1 101000 f 74 goat snp34778-scaffold413-245760 26 1763523 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411915 Affx-122951171 AX-123282265 26 48730293 ACAGCGAAGGCAGAGCCTGGTTTTTCTTTCTGAAG[C/T]GGAGTGTCTAATCTCACCATAAATGCAGCTGTATG Y 2 1 2 1 101000 r 74 goat snp34777-scaffold413-195439 26 1713244 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436499 Affx-122932957 AX-123306837 26 48779294 AGAAAAATCAATGTAAATAAATAATCAAGAGATGG[C/T]GGGCAGTGAGGAGAACAGGTGTTAAAAAGGTGAGC Y 2 1 2 1 101000 r 74 goat snp34776-scaffold413-146438 26 1666996 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794396 Affx-122923556 AX-385281359 26 48821860 TGTGTAAGAGGTGGACTTAAAATAGATACATCAAT[A/G]TATTAAAAGAGGAACCTTGGACCTTAGAAACACAC R 2 1 2 1 101000 r 74 goat snp34775-scaffold413-103872 26 1624874 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399849 Affx-122960247 AX-123270204 26 48874956 TGCCGCACCATTCCTCCTGGAATTCCTTTTAAGAG[C/T]TGAAGCTTGATTATGTATCTTTCTTGAATTTCATT Y 2 1 2 1 201000 r 74 goat snp34774-scaffold413-50776 26 1572502 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451578 Affx-122921687 AX-123321911 26 48923088 GTGGACTATATCTTAGACCAAATGGACTAATGGAC[A/G]TATACAGAACACTCCACTCAACAAGGGCAGAACAC R 2 1 2 1 201000 f 74 goat snp34773-scaffold413-2644 26 1524652 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417320 Affx-122947747 AX-123287668 26 48932632 TCTAAGATGAGGTCATCCTGGCTTCTGAGTGGCCC[G/T]AAATCCAGTGACAGGTGTCCTTACCAAAGAGAGAC K 2 1 2 1 202000 f 74 goat snp31448-scaffold3488-6801 26 1314914 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382335 Affx-122973887 AX-123252693 26 48980676 CAAGAAGATCTGTAACCACAACGCTGTCCCGTCTT[A/C]AAGCTCTGGAGAGGCCACAGAACGACCCAGACAGA M 2 1 2 1 101000 f 74 goat snp31449-scaffold3488-54845 26 1267871 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414934 Affx-122949095 AX-123285283 26 49014663 GGTCAAAACCAGCTGACTCCAGGGGTTCTGCTGCA[C/T]GGCAGTTCCTGTAGGTGAAAATGCTCCGAATTGGG Y 2 1 2 1 201000 r 74 goat snp31450-scaffold3488-88832 26 1233702 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401307 Affx-122959852 AX-123271660 26 49044433 CAGGGAGAAGGCTGTCGGGACAGGCTTGATGCTCC[A/G]TCTGGGCTGAAATGAGTGTTTACTATTCGTGTTAC R 2 1 2 1 101000 r 74 goat snp31451-scaffold3488-118602 26 1203919 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378513 Affx-122976642 AX-123248872 26 49099589 CCCGCACCCGAGTTGAACGTTTCTTCTGACACAAA[C/T]ATGAAGTGAACCTAACACTTGCAGACAGCGCAAGC Y 2 1 2 1 101000 f 74 goat snp34225-scaffold4018-20189 26 1153201 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453941 Affx-122919483 AX-123324274 26 49129233 CCGACACCCAGCCTGGACCCGGACGCGCCCTTTTC[C/T]ACTTTCAGTATTTGATAAAGTCAACAATGAGTTAT Y 2 1 2 1 101000 r 74 goat snp29946-scaffold3266-9071 26 1127688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397344 Affx-122962300 AX-123267699 26 49178363 ACCTCACAGGGCAGCTGGCGTCTCAATCAAGCGCC[A/G]GTCCCATGCTGCATTTGGATAAATGGAAGCCACGC R 2 1 2 1 101000 r 74 goat snp29947-scaffold3266-58201 26 1082363 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422732 Affx-122943255 AX-123293078 26 49209498 TGTTAAAGCCCATGTGAGACTCTTCACAGCTCTAG[C/T]ACTGATGCTTTCCGTAGCCTGCTCAGCGTCCGGTC Y 2 1 2 1 101000 f 74 goat snp29948-scaffold3266-89336 26 1053441 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421749 Affx-122944368 AX-123292096 26 49253178 GTCTGCGTGGTGATGGCCTGGGGGATTCACACTGG[A/G]AAGTTGAAGAAACCCCGGCTCAGAGGTCAAGGCCA R 2 1 2 1 101000 r 74 goat snp26605-scaffold2776-131625 26 1000784 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395636 Affx-122963792 AX-123265991 26 49310247 CTTAGTGAATGCTCAACAAACGTTGTCAGGTCCTT[A/G]GTTAAATCTCCAGAGACAAAAGTCAGGCTGTATCT R 2 1 2 1 101000 r 74 goat snp26604-scaffold2776-74556 26 944283 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431277 Affx-122937104 AX-123301618 26 49349528 AATTTACTGGGTTTTGGCCTCCCTGAGTCTTTGCC[A/G]CCGCAGGCAGTCTTCGTCTAGCTGTGGCGAGCAGG R 2 1 2 1 201000 r 74 goat snp26603-scaffold2776-35275 26 908695 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387919 Affx-122970446 AX-123258277 26 49381843 GGGAGTATAATTCACATCACAATAAGCTTTGCATT[C/T]AGACAAAATTAACAACGTGTCATCAATAATCAGGC Y 2 1 2 1 101000 f 74 goat snp26602-scaffold2776-2960 26 880408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448089 Affx-122924326 AX-123318425 26 49404000 TGTTTGTGGTGTGGCGTGTGTGTATGGTGTGGGGT[A/G]TGTGTTTGTGGTGGGGTATCCGTGTAGTGCGTGTG R 2 1 2 1 103000 r 74 goat snp28929-scaffold3113-19098 26 857923 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405411 Affx-122956283 AX-123275763 26 49487391 AAGGGACATCCCTGAACTGGCCAAGTAGGAGACTC[C/T]GGTATTTCATCAGCTTTTCTGCAGGGGGGACCCTG Y 2 1 2 1 201000 f 74 goat snp28930-scaffold3113-102489 26 793069 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413347 Affx-122950158 AX-123283696 26 49570050 TTCTAGGTCTTCGTGCACAGCGTCTGACCCTCCTG[C/T]GTTATCCCTGTTACAGTCGCTGGATCTTCCTGCAC Y 2 1 2 1 201000 r 74 goat snp28931-scaffold3113-185148 26 716097 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382506 Affx-122973812 AX-123252864 26 49583839 GCTGGACAGAGACCCCCTGCAGAACTTGTTTCTGA[C/T]GCTGGAAATAGACAGCCGCTTGCTGGAGGTCGAGG Y 2 1 2 1 101000 r 74 goat snp23428-scaffold2352-346197 26 702626 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426670 Affx-122939922 AX-123297016 26 49613577 AGGAAAACGTCCCCCATCCCCAACCTGGCTCCTCG[C/T]TACCTGAGTGCTGCCGGCAGCCGGCTCTCCAGGCC Y 2 1 2 1 201000 r 74 goat snp23427-scaffold2352-316459 26 674556 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404498 Affx-122956711 AX-123274850 26 49657568 GAGGGAGCGTTTGCCCCCATGGACCTGAGCATCCA[C/T]ATTTTATCAAGCACTGGGCTCTACACTCTACCTAA Y 2 1 2 1 101000 r 74 goat snp23426-scaffold2352-272468 26 632993 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381860 Affx-122974184 AX-123252218 26 49711668 AAGCAGAAACAAAGGCGAGGCGGAGCCCACCCAGC[A/G]CCCTGCTCCCCTCCAGGGGAGCCCGTGCTGCTCCT R 2 1 2 1 103000 f 74 goat snp23425-scaffold2352-218368 26 582525 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787132 Affx-122973444 AX-385274158 26 49814744 GATTTGCCAGGGCAGTGCTGATCACACTAAGTTTA[C/T]TAAAGAATGTATATTTGATCAACATTTTACTTTCA Y 2 1 2 1 101000 f 74 goat snp23423-scaffold2352-115292 26 502215 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438763 Affx-122930812 AX-123309100 26 49856738 GAGGCAGGGTGGCTGGAGGCCAGCTCTGGACACGC[C/T]GTCTGGGGTCCTTGGCCACATCCAGCATCCACGCG Y 2 1 2 1 201000 f 74 goat snp23422-scaffold2352-73298 26 460123 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767759 Affx-986698710 AX-385254986 26 49868054 TGGTGATGCTTGCACATCTTTATAAACATACTGCA[C/T]ACCCCTGAAATGTACTTTAAAAGGTTAAATGTGAT Y 2 1 2 1 600010 r 74 goat 26_49868054 26 49868054 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 320764185 Affx-986698712 AX-385251918 26 49868472 CTAAGCTTTTGCAGAAATATAATCCTTGTGGAAAA[G/T]ATATAGATTTTTTTTCATACAGCTATTTACTTTTG K 2 1 2 1 600010 f 74 goat 26_49868472 26 49868472 Ancestral_priority_1043 ancestry 0.602 recommended IMAGE 10K 10K ancestral 38422290 Affx-122943484 AX-123292636 26 49922885 TGGGCGTCCAGGCTGCATGTTTGGACCCGAGTCAG[C/T]GGGGGTGGGGCGTGCAGGCCGCACAGCCTCGGGTT Y 2 1 2 1 101000 f 74 goat snp23421-scaffold2352-7151 26 402497 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391614 Affx-122966589 AX-123261971 26 49960966 CAGTTAGCCATTATTATTAACACTAAGACAACGGC[A/G]GACAACTAGATTCAAAAAACAAACATGAGCAGGCT R 2 1 2 1 101000 f 74 goat snp25266-scaffold2596-30831 NW_017206628.1 1775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392146 Affx-122966323 AX-123262503 26 50084076 AGGGAGTTTGCTCAGGGATGAGTCATCAACAGAAA[C/T]GACTGGTGAAGTGATGACAGCATCTGCTAGGACTG Y 2 1 2 1 101000 f 74 goat snp23483-scaffold2369-35756 26 253871 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407231 Affx-122955374 AX-123277582 26 50152710 ACACAGGGCAGGAGTATTTCCAGAATGTGTGAGGA[A/G]CAGCAGTAGCTGTGAAGTCTCTGGAATGAGGTGAC R 2 1 2 1 202000 r 74 goat snp23484-scaffold2369-104390 26 192337 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767770 Affx-986698716 AX-385254997 26 50637681 TATAGATAAATTAATCAATGTGATAGACTACATTA[A/G]CAAATTAAAGAACACAAATCATGTTGATGTATGGC R 2 1 2 1 600010 r 74 goat 26_50637681 26 50637681 Ancestral_priority_1043 ancestry 0.624 recommended IMAGE 10K 10K ancestral 468273158 Affx-1111833317 AX-519546819 26 51090891 GAACATTGAGAATTTGTTTTTTTAATGAGAAATGC[A/G]TTTCAGCAAGTTAAGCCAGAGATGGACAGCATGTT R 2 1 2 1 101000 r 74 goat 26_51090891_AF-PAKI 26 51090891 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320764191 Affx-986698718 AX-385251924 26 51411711 TTTCTCGAGTTGCGACTGGTGATCTTGACTTATGA[C/T]GGGGACCTCAGGAATCTGCTCTGGTGGCCTCAGGA Y 2 1 2 1 600010 f 74 goat 26_51411711 26 51411711 Ancestral_priority_1043 ancestry 0.596 neutral IMAGE 10K 10K ancestral 38386602 Affx-122970683 AX-123256960 27 14309 TAATATGGAAAGTAGAGCGGAAAGCACAGGGGAGC[G/T]TCCAGAAAAGGAAAGCTCTGTGCTGCTCAGTTCAC K 2 1 2 1 102000 r 74 goat snp59631-scaffold984-1634297 27 44514473 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380422 Affx-122975306 AX-123250780 27 64182 TGTCTGTCTGTATCTCCCTCTCGCCCTCTTGGAGT[C/T]TGTCTCGGAAGCTTCATCTCTTTCTGCCTCTGACT Y 2 1 2 1 201000 r 74 goat snp59630-scaffold984-1584424 27 44465432 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381302 Affx-122974453 AX-123251660 27 110146 TGAGGTTTTCGACGGTACGTGTTTACACTTGTAAG[C/T]AGTATAGTAAAGTAAAGGAATAAAACAAACCAGCT Y 2 1 2 1 101000 f 74 goat snp59629-scaffold984-1538460 27 44418790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383264 Affx-122972735 AX-123253622 27 164859 GTAAAACTTAGGGTATATAAGCACCTTTTGAAAAT[A/G]AAGTTATGGGGTTTTTGCACAAGCTTGGCCTCCCT R 2 1 2 1 303000 f 74 goat snp59628-scaffold984-1483747 27 44362689 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408440 Affx-122954451 AX-123278791 27 196269 TCTGTGTCCTCTCTAGTTGGGGTGTGCATGTCTCC[A/G]TGGGGGAGGTCCTTTGTGTTTTTGGCACTATGGGT R 2 1 2 1 101000 r 74 goat snp59627-scaffold984-1452337 27 44331284 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274514 Affx-1111834339 AX-519548105 27 216505 TCAGTCTTGATGCCTCATTCTGTATATGGAAAAAT[A/G]GCACAAAAGTGAAAGATTTTCCAAATTTTCTAATA R 2 1 2 1 201000 f 74 goat GoatD01.030465 27 216505 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38441120 Affx-122929593 AX-123311457 27 253396 TAATTCCTTTTCTTTTTTTCAGAACTTGTTGCAGA[C/T]ACTTTCTCCTCCCTGAAAAATTATTTGCAATAATT Y 2 1 2 1 201000 r 74 goat snp59626-scaffold984-1395210 27 44271909 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392880 Affx-122965743 AX-123263237 27 296061 TGCTGTGCCTGGGGAAGTCCTCTTTAGTTGTGGAG[C/T]GGGAACTCCTGTCCTATTGCATTGTGCTGCGCAGC Y 2 1 2 1 101000 r 74 goat snp59625-scaffold984-1352545 27 44228315 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804256 Affx-986696466 AX-385290886 27 298898 GAACCACTGAGATACTGGGCAAGGTTTGAAGTAGC[C/T]TGGATTCTCTGCTGTACCTGTATTCCATGTTAGGA Y 2 1 2 1 600010 r 74 goat 27_298898 27 298898 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 320767781 Affx-986698722 AX-385255007 27 299098 CTCACCTAGGATGCATTTATTTATTTATTTTCTTA[A/C]ATATAAATGTTTCAAGGGGTCAGTTTAAGTCTAGC M 2 1 2 1 600010 r 74 goat 27_299098 27 299098 Ancestral_priority_1043 ancestry 0.59 neutral IMAGE 10K 10K ancestral 320767784 Affx-986698724 AX-385255009 27 299186 CATATTTATGCAACCTATACTTACGTGCTGGTCCT[C/T]GTCCTCTTTGAAATCAAAGCTTTGTAGACACACAC Y 2 1 2 1 600010 r 74 goat 27_299186 27 299186 Ancestral_priority_1043 ancestry 0.722 recommended IMAGE 10K 10K ancestral 320764199 Affx-986698726 AX-385251931 27 299304 ACATTGTTACAAATGGCATTCTAGATACTGTCTTG[A/G]GCAGGAGCTGGAATCAAGATTGCCGGGAGAAATAT R 2 1 2 1 600010 f 74 goat 27_299304 27 299304 Ancestral_priority_1043 ancestry 0.66 recommended IMAGE 10K 10K ancestral 38405766 Affx-122956495 AX-123276118 27 346473 ATGTTCACAGGCCCTCACATGCTCTCACATGGCCT[C/T]ACACTCCCTTGAACATTTCTTTGCATGCGCTCACA Y 2 1 2 1 101000 r 74 goat snp59624-scaffold984-1302133 27 44177753 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794701 Affx-122921125 AX-385281661 27 385442 CTTCCTGCTGCTTTGTCCACCTTTGGTGTAAACTT[A/C]TGTTTCTCTTTCACTTCGTATGCAGTTTTTTCAAG M 2 1 2 1 101000 f 74 goat snp59623-scaffold984-1263164 27 44137412 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272157 Affx-1111833332 AX-519545913 27 419198 AGGAGGGGTGGGCCAGAAAAGAGCAATGAAGAGCA[A/G]GGGATGACGTACAGCCCAAAGACACGCTGTTCAAG R 2 1 2 1 201000 f 74 goat 27_419198_AF-PAKI 27 419198 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320794181 Affx-122953822 AX-385281147 27 435356 TGACTGATCAAAGGCGCACTAGGTCCAGAGTCCAA[C/T]GGGTCCCATTCACTTTATAACAGTTCTGCAACCTT Y 2 1 2 1 101000 r 74 goat snp59622-scaffold984-1213250 27 44087230 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787651 Affx-122932395 AX-385274674 27 464841 AAGTACAAGCCCTCTAACAAAACACATTTAATGTA[C/T]GTGATGGATGGACAAAATTCGGGATGACTACAAAC Y 2 1 2 1 201000 r 74 goat snp59621-scaffold984-1183765 27 44057369 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425702 Affx-122940776 AX-123296048 27 505577 TGGGCATCACCTGAAGCCCACAGGCATCCCACAGG[A/G]AACAACGAAAACATAATAAAAACCCAGGGAAAAAA R 2 1 2 1 202000 f 74 goat snp59620-scaffold984-1143029 27 44016272 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403401 Affx-122957768 AX-123273754 27 555040 CTCTAAGTCTGCGTCTCAATGCTGCCCAGAAAATA[C/T]GTTCATCAGCATTATTTTTCAGATTCCATATATAT Y 2 1 2 1 101000 f 74 goat snp59619-scaffold984-1093566 27 43965854 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404425 Affx-122956766 AX-123274777 27 599040 TACAAATATAAATGGAATTCTGCTGCAAAAGACAA[C/T]TGTGTGGCATTGGCTGAGCTGGAGAAAGAAATGCT Y 2 1 2 1 101000 f 74 goat snp59618-scaffold984-1049566 27 43921271 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432661 Affx-122936463 AX-123303002 27 700972 GCTAATTGGAGACTGATTCTGTCTTCTTAGAATGA[C/T]AGCGGTATTGTCCTGGGCTGCCGGGCCAGCCCTCT Y 2 1 2 1 101000 f 74 goat snp59616-scaffold984-947634 27 43820116 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379193 Affx-122976302 AX-123249552 27 757321 GGACGGGTAACAATCTGATTTTATGTGTCACCAAA[C/T]GATTTCAAAATATTAAAAAACAGAAGCTGACAAAT Y 2 1 2 1 101000 f 74 goat snp59615-scaffold984-891285 27 43766217 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428733 Affx-122938447 AX-123299075 27 800360 ACACCTAAGGATTCTGGACATGGGAGGCTCCTGCC[A/G]TTTCTTTTCTCAGCATTGACCGAATACTCAAGGGC R 2 1 2 1 101000 r 74 goat snp59614-scaffold984-848246 27 43722036 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394637 Affx-122964396 AX-123264992 27 835222 TAGAGGCAGAAGTGTGTATCTGACAAACTCCAAAT[A/C]ATTCACTCCTTTGGACCAAAACCTGGGCTCATATT M 2 1 2 1 101000 f 74 goat snp59613-scaffold984-813384 27 43687135 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378344 Affx-122976837 AX-123248703 27 888890 TGATCACACGCATCCCTCTTTCAGGCACAGCATAC[A/G]TGTGGAGCACACGTGACCAAGACAGAGTGTGAGAC R 2 1 2 1 201000 r 74 goat snp59612-scaffold984-759716 27 43633051 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449072 Affx-122923613 AX-123319407 27 941644 GCATCCTCGCGCATCCATTCTGTAGCATTTTTCTC[A/G]TCCCAGAATACTTGCACATCCATTATTGAGAACTG R 2 1 2 1 101000 r 74 goat snp59611-scaffold984-706962 27 43582416 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419539 Affx-122945427 AX-123289887 27 989072 ACTGTGTCAGTGGAAGGGGCTGTCACAAAGGACCA[C/T]GCATTACATGATTCTACCATATAAAGTGTGCAGAA Y 2 1 2 1 101000 r 74 goat snp59610-scaffold984-659534 27 43534918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411240 Affx-122952339 AX-123281590 27 1026508 TAAGCCTTCAGAGATTAAAGCAATAGCTGTAAACA[C/T]GAACATGAAAGATTTAAAATGAGGGACACATTTCA Y 2 1 2 1 101000 f 74 goat snp59609-scaffold984-622098 27 43498741 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405566 Affx-122955951 AX-123275918 27 1117615 GCACATTGGTGTGGGTTGCTGCGAGCACCAGGGCC[C/T]GGCACACCCAGCTGGGCCGCCAGGCAGGCCTGCAG Y 2 1 2 1 103000 f 74 goat snp59607-scaffold984-530991 27 43407654 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416810 Affx-122948134 AX-123287158 27 1226446 TGGGTTTTTATATCCACTTATTTGCCTGATTTAAG[C/T]GTTTCACCACATATAGTTATGGAAAGGAAATTTAC Y 2 1 2 1 101000 f 74 goat snp59605-scaffold984-422160 27 43298744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433536 Affx-122935001 AX-123303877 27 1263196 CTGTCGAGAGCCTCCACGTTGCCCGGCATGATCCA[C/T]GACATTGCTAAGTCGAAACGTCACTTTTGTCAGGG Y 2 1 2 1 101000 r 74 goat snp59604-scaffold984-385410 27 43261858 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420791 Affx-122944693 AX-123291138 27 1338482 ACTCCCCGGGGCTCGGGGCCAGCTCCCACAGGAAG[C/T]GGTGCTTCGTCTCAGCCAGGCGTCCCTTCATTCAA Y 2 1 2 1 101000 r 74 goat snp59602-scaffold984-310124 27 43185921 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802718 Affx-122957069 AX-385289617 27 1369287 ACAGGACGTAAGGAATAAATATGTGCTTTCAGAAA[C/T]GCTTGAGGCCAGCAAGAGTAGTAAACCATCACCAG Y 2 1 2 1 101000 f 74 goat snp59601-scaffold984-279319 27 43157191 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389975 Affx-122968066 AX-123260332 27 1406505 CACACACTCACCTCGCTGTCGGCAACTTCTCTGTC[A/G]TTGATGATAAAGCGGTAGCTGGAGTCTGGGGATAA R 2 1 2 1 201000 r 74 goat snp59600-scaffold984-242101 27 43119141 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448852 Affx-122923288 AX-123319188 27 1442224 AGTTGTGTTTACACTGCTGCTTTACTGGTTTACGA[C/T]GTCTGTGCTAAGCCATTCCCAGCCATGTGGAACAA Y 2 1 2 1 101000 f 74 goat snp59599-scaffold984-206382 27 43083484 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444683 Affx-122926444 AX-123315020 27 1474207 CCAGAGGTCAAGAAAGGCAAATCCTATTTGAAACA[G/T]GGACTGTTTCAAGCTCTTGCCATCAAGGAGAGCAA K 2 1 2 1 101000 f 74 goat snp59598-scaffold984-174399 27 43051376 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385435 Affx-122971320 AX-123255793 27 1503838 TTGGTCGCATACTCTCTGCTTTTGTTCTAGTTGCT[A/G]CTTGATGGAAGTTGTCTGCATAAAAACGTATTTTG R 2 1 2 1 201000 r 74 goat snp59597-scaffold984-144768 27 43021487 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788725 Affx-122943306 AX-385275741 27 1539077 GTCGCAAAATGTGTGAGGTTTAGATATAGAAAACA[C/T]GTCACTTTATCTTTCATCCTTTTTCTCTTTTGCAT Y 2 1 2 1 101000 r 74 goat snp59596-scaffold984-109529 27 42985313 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277835 Affx-1111836046 AX-519551332 27 1567458 CTGCTGCCTGCTGCTTTCTGCTCATTTCCTTTCTT[A/G]TAACCTTGTGGCTTAACTGTTTTTCTAACATACTG R 2 1 2 1 101000 r 74 goat Random2.2K-2215 27 1567458 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38426408 Affx-122940839 AX-123296754 27 1575417 AGAGTGGGTGCCCAGCAGTAGTGTGGAAGCTTCAC[A/G]CCAACTCCAAGAGCAGAGCCCTTGTCCCTCCTGTG R 2 1 2 1 201000 r 74 goat snp59595-scaffold984-73189 27 42949088 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793952 Affx-122929862 AX-385280921 27 1628139 GGGCAGGATGAGACCTCTGGCCACATAATACCTCA[C/T]GGAAGTGGGTGTCCTTCTTGACTGTTTACATGGCA Y 2 1 2 1 101000 r 74 goat snp59594-scaffold984-20467 27 42898455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409614 Affx-122953546 AX-123279965 27 1660576 ACTGTGCTTCTCTGTGGCCACTGCAAACCCAGACT[A/C]CCCCAGACCCTTCTTCCTTGGTTTTAGCTGAAGAA M 2 1 2 1 202000 f 74 goat snp30693-scaffold34-11871 27 42855614 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389648 Affx-122968732 AX-123260006 27 1695248 ATGTTTCACTCTATTTTCTTCATCCCACATTAATA[C/T]AGCCATCCATTTTCCCCTTTATTGTTGAGAAGTTA Y 2 1 2 1 201000 f 74 goat snp30694-scaffold34-46543 27 42820257 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407139 Affx-122954860 AX-123277490 27 1725078 AAAGATGAACACGCAGATTCAGGGACAGGAGGGCC[A/G]TGCCTCCATGAACCCTTGGTCTCTGTGGTCCAGAG R 2 1 2 1 101000 f 74 goat snp30695-scaffold34-76373 27 42789911 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438808 Affx-122930796 AX-123309145 27 1776299 CAGAAAAAGATGGAAGGAACTGCTTGTCTCTCTGG[C/T]GGGGAAACACTGAGCCCTGGAGACAAGAAACAGGC Y 2 1 2 1 101000 f 74 goat snp30696-scaffold34-127594 27 42738405 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400491 Affx-122961288 AX-123270846 27 1830380 ACACTCTTTAGGACTTGAATTAAAGTGGGATCTTT[A/G]CTCTTAGAAATAGCACCATTCTTCTCCGTGTGGAC R 2 1 2 1 101000 r 74 goat snp30697-scaffold34-181675 27 42683867 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386036 Affx-122971481 AX-123256394 27 1864065 AGAAGTGGGAGTAAGACTTTGGATCATTCTTTTGG[A/C]TCATTCGGACAAATGACTGTTGGCAAATTCCTGTA M 2 1 2 1 101000 f 74 goat snp30698-scaffold34-215360 27 42650127 T G 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404435 Affx-122956759 AX-123274787 27 1904913 ATACTCAAGCCAGTTTCCTTCCCAAGGTGATTGCC[A/G]CCCAGGGATCTTTGCTAATGCTTTCTTCCAGCTCT R 2 1 2 1 201000 r 74 goat snp30699-scaffold34-256208 27 42608260 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778135 Affx-122946760 AX-385265250 27 1999085 TTTGTTAAATATGTGAATTTCTTGGAGAGAATCTT[A/G]CAGAATGGAATCTGGGTAGAAAACAGATTTCCAAT R 2 1 2 1 201000 f 74 goat snp30701-scaffold34-350380 27 42512889 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403623 Affx-122957546 AX-123273975 27 2035072 GAGTGCTTACACAGGAGAGGTATGCCTGAAGCCAC[C/T]CCCTCTTCTCATGAAGGGAGAAAACTCTCTGTTCT Y 2 1 2 1 101000 r 74 goat snp30702-scaffold34-386367 27 42476593 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402032 Affx-122958738 AX-123272385 27 2071264 ACAAGAGTACAGAGATGGCCCTGAGTAACACGGAC[A/G]TGTGTATATATGTTTGTGTGTACATGAGTGTGCAC R 2 1 2 1 101000 f 74 goat snp30703-scaffold34-422559 27 42440629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446977 Affx-122924651 AX-123317313 27 2102114 CTGCTGAGCCCCCAGGGGAGCCCCAAGGTTGTAAC[A/G]TGCTGTGCTGTGTGCGTGCTGTGCTAAACTGTTTG R 2 1 2 1 303000 f 74 goat snp30704-scaffold34-453409 27 42409903 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768488 Affx-122960316 AX-385255668 27 2143698 TTTGTATCAAGTCTCTATTTGGCACACTCTGAAAG[C/T]GAAAGCGTTGGTCACTTAGTTTCGTGTCCGACTCT Y 2 1 2 1 101000 f 74 goat snp30705-scaffold34-494993 27 42367823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407665 Affx-122954600 AX-123278016 27 2175819 TGATTCCCAAGTGAGATCTCCTTCTGCTCTATAGG[C/T]ACCCAGGTCACCTGCGGCTAAGTCTGAGTTTTTTG Y 2 1 2 1 201000 f 74 goat snp30706-scaffold34-527114 27 42335504 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272466 Affx-1111834910 AX-519546190 27 2212702 AAAAAAGGCTGACAGAGATAACTGCACACAGCCTC[A/G]CACAGTGCAGGTGGAACTGCAGCAAACGAAACCCA R 2 1 2 1 201000 r 74 goat GoatD01.058457 27 2212702 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38441404 Affx-122928838 AX-123311741 27 2244633 TTTCCATGGTCTCCATATCAGAGTTTCACATACAA[C/T]ACGCTTATCCTGGGGGCAAATCCAAGATAAACTAT Y 2 1 2 1 201000 f 74 goat snp30708-scaffold34-595928 27 42266086 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423942 Affx-122942250 AX-123294288 27 2273540 GACATCTAACAGGCAGTCCCATGTATATTTGGTTG[C/T]GTGAAAAGATCAAAAACACTGCAACAAACCTTCCA Y 2 1 2 1 101000 f 74 goat snp30709-scaffold34-624835 27 42236908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400829 Affx-122959796 AX-123271184 27 2316383 TCTGTATTCTGCGCTCCTTCGCTGTGTGATCAGCT[A/G]TTAAGGGATGTTTTACATGGACTATGACACTTGAA R 2 1 2 1 201000 r 74 goat snp30710-scaffold34-667678 27 42194095 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441816 Affx-122929070 AX-123312153 27 2347676 CTCATATTATGAGATTAACAAATACCACATATAGC[A/G]TTATTTTTCTGAGTTGGGGAAAATAAACAATAATA R 2 1 2 1 202000 r 74 goat snp30711-scaffold34-698971 27 42162773 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802166 Affx-122932977 AX-385289070 27 2378702 GAAAGAGAAATGGCAAAGTTGTGCTCCCTGTGACT[A/G]TAGCTACATACAGTCTCACAATAAATTACAAAGGG R 2 1 2 1 101000 f 74 goat snp30712-scaffold34-729997 27 42131846 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390023 Affx-122968445 AX-123260380 27 2417870 TCAGCACTCTAGTATCTCGTGCTACTGCTGTTGCT[A/G]CTGCTAAGTCACTCAGTCCTGTCCGACTCTGTGTG R 2 1 2 1 103000 f 74 goat snp30713-scaffold34-769165 27 42092481 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409576 Affx-122953580 AX-123279927 27 2542229 GGGCCCTAAACCCAGACCTTAAACGTCAAATTTCC[A/G]CAAGAACCTTTCATGTGCTGTACCCCCTGCTCTTC R 2 1 2 1 101000 f 74 goat snp30716-scaffold34-893524 27 41968329 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405601 Affx-122955925 AX-123275953 27 2578827 CTCATATTTACATATGAAAAAGACCTTCTGAGGCT[A/G]GAAAGTTGTCCTCTACATTTACCTTGCAAAGCCTT R 2 1 2 1 101000 r 74 goat snp30717-scaffold34-930122 27 41924287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777713 Affx-122962116 AX-385264832 27 2608975 TGAACTATATTGTGAAAAGGGGTACATACAGATGC[A/G]TTTTAAATAACTAGGTTTCCCTGTACTGTGGAGGT R 2 1 2 1 101000 f 74 goat snp30718-scaffold34-960270 27 41893202 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421489 Affx-122943914 AX-123291836 27 2649318 TCAGATGTACAGAGGGGAGCTGGGAGTCTTACCTT[A/G]TCAGGATCCGTCGTAGTGATGACCCATACACAGTG R 2 1 2 1 101000 r 74 goat snp30719-scaffold34-1000613 27 41852653 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407419 Affx-122955234 AX-123277770 27 2677944 GAACCTAAATGTACATAAAGAACTTACAACATGAT[A/G]CACATAATATTTATATAAATGGATGATGTTTATGT R 2 1 2 1 101000 f 74 goat snp30720-scaffold34-1029239 27 41823387 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769970 Affx-122972221 AX-385257138 27 2732108 GATACCATCAAAATGCAAAGCTTTGTGAAATAATG[C/T]AAGAATTTATGGTAGAATATGGAAAGTACATATTT Y 2 1 2 1 101000 r 74 goat snp30721-scaffold34-1083403 27 41769030 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771589 Affx-122923361 AX-385258747 27 2766505 GAGTCTCAGTTCCATAATGTAAAATAGACATAGTA[A/G]TTTCTTAGATGGATTGTAAAAATTACTCTTTCTTA R 2 1 2 1 101000 f 74 goat snp30722-scaffold34-1117800 27 41734676 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782397 Affx-122964091 AX-385269473 27 2795599 AATTATTATAAATGCAAAGTTCATGTTGATGCTGG[C/T]AAAAGTCTGTGTAATCCCAGGATCTTACGGCTGTT Y 2 1 2 1 101000 r 74 goat snp30723-scaffold34-1146894 27 41705911 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450108 Affx-122922776 AX-123320443 27 2839285 ACTTGCTAGTTAATCACCATACTATGCACATCTCA[C/T]GACAGACATGATGCTCTTTTTACCCAGGATCTCAG Y 2 1 2 1 101000 f 74 goat snp30724-scaffold34-1190580 27 41662357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442007 Affx-122928421 AX-123312344 27 2894982 TTCCTTTCAGGCCCCAGGAAATCACTGTGCTTTCT[G/T]CACACACAGAAACCCATAATAAAAATTCACAATAA K 2 1 2 1 202000 r 74 goat snp30725-scaffold34-1246277 27 41606564 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419753 Affx-122945880 AX-123290101 27 2923692 AAAAATTCAGATGTCTTTATTTTTGTACCATTTTC[A/G]CTGCGCTGCTTATGGGTTTCCTTCAAATTGAGTCT R 2 1 2 1 101000 r 74 goat snp30726-scaffold34-1274987 27 41577759 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417509 Affx-122946951 AX-123287857 27 2961727 CCACCTAATATCACTTAAGAAACTGTGATGACTTA[C/T]ATTCGCGTTTCAGGCTATGCCCACACTTGTAGGGC Y 2 1 2 1 101000 f 74 goat snp30727-scaffold34-1313022 27 41539833 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775438 Affx-122937204 AX-385262569 27 2995650 ATTCATGCAATGGAAAGTCCGTAAAGGGACTGGAT[A/G]CTGCTTATAGTGTGGAACCACCACATCAGAACAAG R 2 1 2 1 101000 f 74 goat snp30728-scaffold34-1346945 27 41505414 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800800 Affx-122973535 AX-385287716 27 3025512 ATCGTCTTTGATTATCTATGCCACTCTTCCATAAT[A/G]TTATGTGAGGAAAATAAATCCACCCTTTCTTTATA R 2 1 2 1 101000 r 74 goat snp30729-scaffold34-1376807 27 41475406 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 463997139 Affx-1110263473 AX-515474144 27 3042986 CCACACCGCTGCCTCCTCACTTCGGGCTTCTCTTC[C/T]ATTCACCCTCTGCTGCCTCCTTTTGACTGGGGTGT Y 2 1 2 1 202000 f 74 goat 27_3042986_AF-PAKI 27 3042986 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38447297 Affx-122924920 AX-123317633 27 3054725 GAAGTTCAAGTTAAAAAGCCATGCCATGAATTGGC[C/T]TAATCCACTGTCCCACATGTAAGACACACCTCCTG Y 2 1 2 1 101000 f 74 goat snp30730-scaffold34-1406020 27 41446333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382757 Affx-122973591 AX-123253115 27 3089014 CAACCGTGGTTTGTGCTTATACAGTCTGCTCATAG[C/T]ATCTGAGTCCTTAGTTACCAGGGAAAAGGCAACAT Y 2 1 2 1 101000 f 74 goat snp30731-scaffold34-1440309 27 41411414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383675 Affx-122972504 AX-123254033 27 3123679 CTCATTTGCTCCATTTCACAAGCCTCCGCTGTCTT[A/G]TCAGGGCCATTTCCATCTCACAGACACCAGCCTGG R 2 1 2 1 201000 r 74 goat snp30732-scaffold34-1474974 27 41378401 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442905 Affx-122927640 AX-123313242 27 3152257 TTTGTAACAGGAAAAGTGAATGTTTGGATTTCCAG[C/T]GGTGAGCTGGTAAGGGACTCTTCGGGAAGAAACCT Y 2 1 2 1 201000 f 74 goat snp30733-scaffold34-1503552 27 41349527 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412247 Affx-122950903 AX-123282596 27 3219984 TTTCTCAGAGTATAAGAGAACAAAATGAAAGTGAA[C/T]GTTGGCAGCAATTAAACTTGGGATTGAGGCTTTTT Y 2 1 2 1 201000 f 74 goat snp30734-scaffold34-1571279 27 41281571 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391389 Affx-122967267 AX-123261746 27 3260342 CAGTGCGTCTCCAGCTCAGCACCTGTGGGCACAGC[C/T]CTGCCTTTCCTCAGATGGAGGCCACTCTTAGAGCA Y 2 1 2 1 101000 r 74 goat snp30735-scaffold34-1611637 27 41240695 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422848 Affx-122943099 AX-123293194 27 3292767 CCCCAGGCTCAGGTGTCCCTTTGTAAAAGGGAGAT[A/G]CTACAAAGTGAAAATCAGAGGACGAAATGCAACTA R 2 1 2 1 201000 f 74 goat snp30736-scaffold34-1644062 27 41208628 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794268 Affx-122938760 AX-385281233 27 3330663 AAAGGTGAAATAACTCACAACAGGAACCTGAGGAC[G/T]CTTCTGGGAAGGGAACTGTCTCACAAAGAGTGTTC K 2 1 2 1 201000 r 74 goat snp30737-scaffold34-1681958 27 41170706 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401193 Affx-122959342 AX-123271546 27 3367421 AGAACCAGTTTTAGGTAACATGCAAAAATAGCAAA[A/G]ATAATCCAACATAAAGATTTGGTTTTTACATGCAA R 2 1 2 1 101000 f 74 goat snp30738-scaffold34-1718716 27 41134009 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444377 Affx-122926605 AX-123314714 27 3400955 GTGTGTGTGTGCATGTGTGAGCACACTTGCAAAAA[C/T]GCATGTGTGTTTATGCCTGTGAGTGATACTTGTAA Y 2 1 2 1 202000 r 74 goat snp30739-scaffold34-1752250 27 41100818 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432901 Affx-122935325 AX-123303242 27 3450568 GAAAAGGCTGCTCTGAAACAGAACAAAGAGCCACC[A/G]TTTCCACTGCCTATTGTGGAAGTCAACCCAAGAGA R 2 1 2 1 201000 r 74 goat snp30740-scaffold34-1801863 27 41050386 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401075 Affx-122959637 AX-123271428 27 3494718 TAACTTGGAGTGTCAGAGTTCAGTTACAGAAGGGC[A/G]TGGGAGAGTAAGCCAGACCCTCTCCTCTCTGGGGC R 2 1 2 1 101000 f 74 goat snp30741-scaffold34-1846013 27 41005705 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770107 Affx-122947175 AX-385257274 27 3588827 TCAACATTAAATATTTCAGTTCTGAGGTTAGTACA[C/T]GTGCTTAGAGAAACGCACTGAGCCACCTGTATTAA Y 2 1 2 1 101000 r 74 goat snp30743-scaffold34-1940122 27 40910151 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801618 Affx-122968210 AX-385288526 27 3627510 GACTTACTTGAAACAATCATATCTTTACTGTGAAC[A/G]TCTACCTTTGTATGCACAGTATCAGTATCCGTTTA R 2 1 2 1 101000 f 74 goat snp30744-scaffold34-1978805 27 40871456 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378212 Affx-122976926 AX-123248571 27 3713305 ACCCGTGGCCCACTTTGCTGCCTTCTCCAACAGCA[C/T]GTTGGGTTTGTTAGTTCCCTCCTACAGCCACCTAG Y 2 1 2 1 101000 r 74 goat snp30746-scaffold34-2064600 27 40784030 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770159 Affx-122926043 AX-385257326 27 3747704 CTTTGCAGATTCACTATCATGTACAATAATAAAAG[C/T]CAATTAATATCTTACTGACTTTTGGACACCTTTAT Y 2 1 2 1 101000 r 74 goat snp30747-scaffold34-2098999 27 40749517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402053 Affx-122958725 AX-123272406 27 3779159 CTACAAACAAGGAAACCAGCCAAGTGACAAGTGAT[A/G]CCAGGGCTATAGAAGAACAGGTGAGAACGTTTCAG R 2 1 2 1 101000 f 74 goat snp30748-scaffold34-2130454 27 40717286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273503 Affx-1111833656 AX-519547118 27 3813865 ACCAAGTGCTGCAGGCATCATGTCTTTACAGTGGA[A/C]TCCTTAAGAGGTCAGTGCAACCGCAGA M 2 1 2 1 101000 f 74 goat GoatD01.000738 27 3813865 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38442278 Affx-122928265 AX-123312615 27 3816616 AGACCAGCCACCTTCCCCTCCCATGCATACACATC[A/G]CTATTCTAGAATTTGACGAGCTTAGCTTTCACTTC R 2 1 2 1 101000 r 74 goat snp30749-scaffold34-2167911 27 40679349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383871 Affx-122973135 AX-123254229 27 3900073 ACAGTGTCTCAGAGCAAGAAACAGAACAATTACAT[A/G]CTTCACTATTTTTAAAAAATTTAAAAAAAAAGAAT R 2 1 2 1 103000 f 74 goat snp30751-scaffold34-2251368 27 40596623 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443666 Affx-122927188 AX-123314003 27 3938777 CAAACCACCCGGCCATACCCTTCAGAAAGAAAACA[G/T]AGCTTCATTTTCATTGCGTATAAAACTCTGAACAT K 2 1 2 1 201000 r 74 goat snp30752-scaffold34-2290072 27 40557919 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408154 Affx-122954221 AX-123278505 27 4017760 TGCAGTTCCACAAAATCTCTGGCATAGTGTTCTTA[C/T]GGAAATAACATGCATTGCCTCTGCTTTGAATAAAG Y 2 1 2 1 101000 f 74 goat snp30754-scaffold34-2369055 27 40479333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403187 Affx-122958072 AX-123273540 27 4053757 ACATAGATGTGTGGGTGAATGGATAAATCAATGGG[C/T]GGAAAGATGGATGAATGGATAGATAAATGGATGAA Y 2 1 2 1 101000 f 74 goat snp30755-scaffold34-2405052 27 40443078 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422805 Affx-122943202 AX-123293151 27 4083168 TACGATCGTGTACTAATATGCTGTTTAAATATAGT[A/G]TCCCCCTTTTGGTAAATTGCAAGTTCTGCTGCCTC R 2 1 2 1 101000 f 74 goat snp30756-scaffold34-2434463 27 40413371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386214 Affx-122970987 AX-123256572 27 4153560 AATGTGTCTCGAGCTTTTTGCTCTTGGAAAAGCCA[C/T]GTCACTTCTGAGACCACTTTCTTATCTGTGAAACA Y 2 1 2 1 101000 f 74 goat snp30757-scaffold34-2504855 27 40344157 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376341 Affx-122978338 AX-123246700 27 4214227 AATAAGCAACAATGCAAATAATTTTGAAACAATCA[C/T]GTTGTAACGAATAGAGGAAAGAGTATTATAACAAG Y 2 1 2 1 101000 r 74 goat snp30758-scaffold34-2565522 27 40282386 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377228 Affx-122978164 AX-123247587 27 4267474 TCAAACAGGAAAGTATTATTCTCAGAATGAAAAAG[C/T]AAAAATCAAATGCAGAATCCAGAATGTTTCTGATA Y 2 1 2 1 101000 f 74 goat snp30759-scaffold34-2618769 27 40228271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766246 Affx-122949002 AX-385253642 27 4304595 CAGAATCCATCGCAATAGTGTTGGCCACTCCACTG[C/T]ATTTTTGAATGTAAAAGAAGTCTTTAAGCCAAAAG Y 2 1 2 1 101000 f 74 goat snp30760-scaffold34-2655890 27 40191156 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390515 Affx-122967244 AX-123260872 27 4339345 GTGAATTAAACAAAATCATATGTTGTTTACATGTT[A/G]CAAAAATGAGAAACCCCAAGTCCTGCTCTAAGTTG R 2 1 2 1 101000 r 74 goat snp30761-scaffold34-2690640 27 40156174 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770297 Affx-122938304 AX-385257463 27 4367885 TCGCATGTAAGTTGCCATGACCTTTTAGAGTTGTT[A/G]TAATCTTCTAAAAATGGACCAGTGTTTCAATGTTC R 2 1 2 1 101000 f 74 goat snp30762-scaffold34-2719180 27 40127089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782169 Affx-122956235 AX-385269247 27 4400481 ATGAACAGAGTCCACCTGCTTTGTATTAGAATTCA[A/G]CAGCAGAGGGCAGATTACACTTCAGGTTTAAACAG R 2 1 2 1 101000 r 74 goat snp30763-scaffold34-2751776 27 40094623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396395 Affx-122963018 AX-123266750 27 4432341 TTTGTTGTTATTTTTTTTTTTTCTGGTTGTTACAC[A/G]TGATGCACTTTCCTCTTTCTCCATCAGCAGTTCAG R 2 1 2 1 101000 r 74 goat snp30764-scaffold34-2783636 27 40062747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390886 Affx-122967114 AX-123261243 27 4490719 AAACTTATTTTAGTCACCCCCAAATTATTCTTATG[C/T]AACTGTGAATAACATACTTCATTAAAAATTGAAAA Y 2 1 2 1 201000 r 74 goat snp30765-scaffold34-2842014 27 40003933 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406134 Affx-122956193 AX-123276486 27 4544152 GGCATAAGCATTAAGACAAACTAGACAACCCTAGA[C/T]AGCATATTAAAAAGCAGAGCCATCACTTTGCCAAC Y 2 1 2 1 303000 f 74 goat snp30766-scaffold34-2895447 27 39948937 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785908 Affx-122972785 AX-385272945 27 4592731 TTCCATTCACAGGAAATAGCCTGTGAAAATGAAGG[C/T]GCAATGAAGACGGTTTCAGAAACAAAAACAGAATT Y 2 1 2 1 101000 f 74 goat snp30767-scaffold34-2944026 27 39900149 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433999 Affx-122934242 AX-123304340 27 4634988 CTCTGTGTTTCTAGACCCTCTTTTTTGAAGCTAAA[C/T]ATTATCAACTATGTCTTTAAGTACGTCTCCTTGAA Y 2 1 2 1 101000 f 74 goat snp30768-scaffold34-2986283 27 39858182 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386607 Affx-122970243 AX-123256965 27 4664775 TAAGGACACATACTATATAAATTCAATTATATGAC[A/G]TTCTGGACTCTGCCAACTCACAGGAACAGAACTCA R 2 1 2 1 101000 r 74 goat snp30769-scaffold34-3016070 27 39828583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774185 Affx-122941447 AX-385261322 27 4723859 TTTTAAATTTTTGTACTATTCTTAAATCTAATTGT[A/G]TCTCAGGACTCAGCAGCACTCAGAACTAGTGGCCA R 2 1 2 1 102000 r 74 goat snp30771-scaffold34-3075154 27 39769365 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448426 Affx-122923661 AX-123318762 27 4781125 CTCTGTTTGTCTCTTAAAAATGCAAACATTACTGG[C/T]AAGAGATGCAAACAACATGGATTCTAATAACTTTA Y 2 1 2 1 101000 f 74 goat snp30772-scaffold34-3132420 27 39711129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452646 Affx-122920342 AX-123322979 27 4827698 GAAATCTTTAAACGGATGCTCTGCTCACCAGTCTC[A/G]CACATCACAGCCCACGTAACCGGCAAGCGCTGTCA R 2 1 2 1 201000 r 74 goat snp30773-scaffold34-3178993 27 39664068 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415231 Affx-122948961 AX-123285580 27 4859909 CAGAAAGAATGCCCGTACCAGAGTCCCAAGAGCTG[C/T]GAGGCTTTTCCCAGAAAGTACCTACGTCTTTGCTG Y 2 1 2 1 201000 r 74 goat snp30774-scaffold34-3211204 27 39631712 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802309 Affx-122946972 AX-385289213 27 4908004 AATCTAGGAGACGAACCATGAAGAAGAGATACAGA[C/T]GGAAAATACAGCTGCAAAGACACGGCTTGATCCCC Y 2 1 2 1 101000 r 74 goat snp30775-scaffold34-3259299 27 39583442 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277837 Affx-1111836047 AX-519551334 27 4921690 CCATGCAACGGGAAATAGCAACCATGTCCACACGC[A/G]CAAAGAGTGACAATTTATGCCATTGCTGTTGTGCA R 2 1 2 1 101000 r 74 goat Random2.2K-2217 27 4921690 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38434384 Affx-122934697 AX-123304725 27 4967703 GTGTCTCCTGCTTTGGCAAATGGGTTCTTTACCAC[C/T]AGCACTACTTGGGAAGCCCTAAAGATGCAGCTACC Y 2 1 2 1 303000 r 74 goat snp30776-scaffold34-3318998 27 39523775 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768727 Affx-122950997 AX-385255905 27 4997438 TCTTAGCTCCTAGTCTCTAATTTATTCTCTGACAT[A/G]AAACGACTGGCTCTTTGCAATTGATAAAATTTACC R 2 1 2 1 201000 r 74 goat snp30777-scaffold34-3348733 27 39494053 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421636 Affx-122944461 AX-123291983 27 5093234 CTTTTATTCCCTATGAAATGTTACACTCAAACAAT[A/G]CTTAGCTATATAACCAGAAATACTTTCATCTCTGT R 2 1 2 1 101000 r 74 goat snp30779-scaffold34-3444529 27 39402057 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394962 Affx-122964277 AX-123265317 27 5125675 ATCCTTGGAACGCACATCTCATGAAGACGAAAAGT[A/G]TAAATGGACAATGCCAGCACCCAACTCTAGTCTTG R 2 1 2 1 101000 f 74 goat snp30780-scaffold34-3476970 27 39369345 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277707 Affx-1111836048 AX-519551206 27 5144994 ATGTGTCTGTGTTAATTGTCTGCCTGGCTTGGCCT[A/C]ATCCTGAGTGAGGGCCGTGGATGGATCACTCAATG M 2 1 2 1 102000 f 74 goat Random2.2K-2218 27 5144994 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468274176 Affx-1111834049 AX-519547777 27 5180733 ATGGGAGAGTCTGTCC[A/G]GTGGGCACGTGTGTGATGCAGACTTCCTGCAGGAC R 2 1 2 1 102000 r 74 goat GoatD01.015874 27 5180733 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38443244 Affx-122927554 AX-123313581 27 5218625 ATATTCATATGCTTCATAAGGAAATGTTCCACTGG[C/T]GAAGATTCACAAGGAGAGTTCTAAGAAAGAAATTT Y 2 1 2 1 101000 r 74 goat snp30782-scaffold34-3569920 27 39279491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440324 Affx-122930201 AX-123310661 27 5264175 AACAGCCGGATGGATCACTGTTCCTATAAAGGTAC[A/G]TCTTTCTACTAAATCATAGAGAGAACCATCCTCCT R 2 1 2 1 101000 f 74 goat snp30783-scaffold34-3615470 27 39234207 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411143 Affx-122951887 AX-123281493 27 5314360 TTACCAAAATGTCGAAGCCCCAAACTCTTCTCAAG[C/T]AGTGGCTGCACATGTCTGATACTTTCTGTAAACAT Y 2 1 2 1 201000 r 74 goat snp30784-scaffold34-3665655 27 39183806 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410317 Affx-122952483 AX-123280667 27 5396276 TTGTTTTGGAGAATCAACTTTTCATAGAATGGGAA[C/T]GCCTCTTACAGGACAGGGAGATCCAGGTCTCAGTC Y 2 1 2 1 201000 f 74 goat snp30786-scaffold34-3747571 27 39099792 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766720 Affx-122965440 AX-385254061 27 5427511 GATGATGACGATGAAGCTTGTTTATGGTATGAGAC[A/G]TTTTACTCTTCTGAAGGGTGAGAAGGGTTTCCCAG R 2 1 2 1 201000 f 74 goat snp30787-scaffold34-3778806 27 39068660 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432317 Affx-122936302 AX-123302658 27 5481892 GTTAATCCAGGATGTCAGACAGCCCCCCTCAATAC[G/T]TGGAGGCCACCTGCCCATGGAAAGTGGATGTTATG K 2 1 2 1 101000 r 74 goat snp30788-scaffold34-3833187 27 39014421 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432781 Affx-122935424 AX-123303122 27 5526170 CCTGGCGCTGGTATTTTTAATACTGTAAAACTCGC[C/T]CAGGTGGCCTCAGGATGCTGGCCAGTTCAAGAACC Y 2 1 2 1 10000 f 74 goat "snp30789-scaffold34-3877465;SV_234" 27 38969867 A G SV_234 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403046 Affx-122958537 AX-123273399 27 5559626 AGCATTTTGTATGTGGTATCTTGTTTAATCCTCCC[A/G]GCAATCCTAAAAGTTAGTTACTACAAGTTTGCACC R 2 1 2 1 101000 r 74 goat snp30790-scaffold34-3910921 27 38936230 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782059 Affx-122952703 AX-385269137 27 5611478 CCCAAAAAATATCATAGACAAGAAAAGTTAAAATC[A/G]TGTAAGGAACTGATGATCCCGTCTACGCTGAATTA R 2 1 2 1 101000 r 74 goat snp30791-scaffold34-3962773 27 38883511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775601 Affx-122955278 AX-385262732 27 5663663 TAACATTTAGCAGGCTATCTTTAAATAGATAAGAC[A/G]CAATATACTAGCAAGGATGTGTAGAAAAAGGAAGG R 2 1 2 1 101000 f 74 goat snp30792-scaffold34-4014958 27 38830329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272162 Affx-1111833334 AX-519545918 27 5691457 AACATGGATGGACCTAGAGGTTATCACACTCGGGG[A/G]AGTGAGTCAGACAGAGAAACAAATGCCGCCGGGTA R 2 1 2 1 303000 f 74 goat 27_5691457_AF-PAKI 27 5691457 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320798687 Affx-122921634 AX-385285619 27 5732679 ATATTATTCTTGGCATTTCCTGTGAACTAATGTCA[A/G]CTGCAGAAGATTATTAGGATTGTATAATTTGTGTT R 2 1 2 1 101000 f 74 goat snp30793-scaffold34-4083974 27 38760468 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398979 Affx-122960961 AX-123269334 27 5786050 ATGCTGGTTTCAGGATGAGAAATAGATTTGTTTTC[G/T]ACTTTAACTTTCAAAGCTTTCTTCTAAGGAAGTAG K 2 1 2 1 201000 r 74 goat snp30794-scaffold34-4137345 27 38707440 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798006 Affx-122951883 AX-385284942 27 5826016 CTCCAATATTAATTAGTGAGGAAATGAACACAAAC[A/G]TTCCTACATAGTGAACTATTGTCAATGACTTCACC R 2 1 2 1 101000 r 74 goat snp30795-scaffold34-4177311 27 38667160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785142 Affx-122932056 AX-385272188 27 5861257 TCCCATAAATACTGCTATGAGGAATACATTTGGGA[C/T]AAGACATTAAAAGTTTCAGTGTCTCAGTAAAGAGG Y 2 1 2 1 101000 r 74 goat snp30214-scaffold333-13000 27 38540447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424412 Affx-122941811 AX-123294758 27 5890925 AAGTTAACCATGGGAAGCTGTCCCAACATGTCCAG[C/T]GGCTCAGCACACCACATTACAGAGTCCCAATTTTC Y 2 1 2 1 101000 f 74 goat snp30215-scaffold333-42668 27 38511744 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392574 Affx-122966073 AX-123262931 27 5935883 CGCTGGACACCCTCCACTGGAGGAGATGCAGCCTC[A/G]GAGGTGGCTGAGGGTCAGTGGGGAGAATTCCCTTT R 2 1 2 1 202000 f 74 goat snp30216-scaffold333-87626 27 38467333 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420361 Affx-122944955 AX-123290708 27 5966878 TCTGTTTATTCACCAAGGGTGTCTGATTTTCTGAA[A/G]ATGTCTGTGAGGGGTCCCCAACACAAATACTCATA R 2 1 2 1 201000 f 74 goat snp30217-scaffold333-118621 27 38434445 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794043 Affx-122940411 AX-385281011 27 6005817 TTTATTGACAATAGAATGGAAGTTTACCAACAGCT[A/G]TCCTTCTGTTTCAGTTAAAGTGACTTAGGCTAGTT R 2 1 2 1 101000 r 74 goat snp30218-scaffold333-157560 27 38395320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409312 Affx-122953092 AX-123279663 27 6046164 GGACTCCTGATTTTTGTAGGCTTTCATTTCTTTTT[A/G]TTTATGCTTTCAACATTTCATTAAGATATATGTAA R 2 1 2 1 201000 r 74 goat snp30219-scaffold333-197907 27 38355765 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409480 Affx-122954057 AX-123279831 27 6078595 GTGTCCATGAATAGACAAAGGAGACATGGCATTTG[C/T]ATGTAAGGGAATACTGCTCAGTCATACAGAATAAT Y 2 1 2 1 101000 f 74 goat snp30220-scaffold333-230338 27 38323270 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438518 Affx-122931202 AX-123308856 27 6141059 GCAGTTATGCTGGAAGAGAAAGGGCCTCCTCAGCT[A/G]AAGAAGCTCACTGAAGGGCTGAGCAGTGAAATGAC R 2 1 2 1 202000 f 74 goat snp30221-scaffold333-292802 27 38595142 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415222 Affx-122948969 AX-123285571 27 6181728 GGATAACAGAGTTTGGAATACTAATGCATGTGCGA[A/C]GTGGGAAGAAAATGATTGGGCTGGGAAATGCAGAC M 2 1 2 1 101000 f 74 goat snp30222-scaffold333-333471 27 38234007 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768220 Affx-122922307 AX-385255405 27 6239285 CACATGGAGGTGGTTAAAAATCAAATCTCTGCATT[C/T]GACAATGTTAGTCTCTTTGATCTTACAGAATTAAG Y 2 1 2 1 101000 f 74 goat snp30223-scaffold333-391028 27 38175908 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396235 Affx-122963337 AX-123266590 27 6272573 GTGACTGAACTGAACTGAACTGAGTCTAATGTGGA[C/T]GGCACTTTGCTAACATATGTTTCCTATGTCAGTAC Y 2 1 2 1 201000 r 74 goat snp30224-scaffold333-424316 27 38142505 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403078 Affx-122958511 AX-123273431 27 6330611 AAATCTATCAGAACTGTTTAAATATTCTGCAGGCA[C/T]ATCAGTTCTCCTGAAGACATATATCATTCTTCTGA Y 2 1 2 1 101000 r 74 goat snp30225-scaffold333-482354 27 38084358 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442983 Affx-122928194 AX-123313320 27 6364544 TTAATTTCTGAAAGTGCAGCAAACACTAGTAAAGC[A/G]CAGCTGTCAAATCACAGGACACAGTTTTCTTAGGT R 2 1 2 1 101000 f 74 goat snp30226-scaffold333-516287 27 38050288 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443843 Affx-122927530 AX-123314180 27 6402551 AATATTCCTAAAAAGTAGATATGCTGAATTGCCAT[A/G]CAAATTAAAGTATATAAAACTGAGGCAAAGAGAGA R 2 1 2 1 101000 f 74 goat snp30227-scaffold333-554294 27 38013335 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784820 Affx-122944455 AX-385271867 27 6436487 TATCATACCAGTAATATTTATATGATAAAATTTTT[A/G]TAAACCCTTGAGCAAAATCCCTAATTACTAGTAAT R 2 1 2 1 303000 f 74 goat snp30228-scaffold333-588230 27 37978338 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375626 Affx-122978706 AX-123245985 27 6469225 GCTAAGATCTTGTTCTCCAAGATCGCTATCAGTAG[C/T]GAAAGAACTAACATTTTCAGCTCCATCTCCCAGAG Y 2 1 2 1 201000 f 74 goat snp30229-scaffold333-620968 27 37945607 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802352 Affx-122922886 AX-385289256 27 6527330 CTTAGAAAATCAAGTAACAGTTAACTTGGAACTGC[A/G]TTACACAGTTTAAAGCTAAACATGTGCTGGATATT R 2 1 2 1 201000 r 74 goat snp30230-scaffold333-679073 27 37880006 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781183 Affx-122958071 AX-385268268 27 6579403 AAACCTGAGGTCTAGTGAGAAAATATTGCCCTTAA[C/T]AAGCTTTTGTATTTGATATAAGTGGTTTCTCTCTC Y 2 1 2 1 101000 f 74 goat snp30231-scaffold333-731146 27 37827873 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277709 Affx-1111836049 AX-519551208 27 6607385 CAGTCCAGACCTTCTCCAAATCCTGAGGAAATATC[A/G]GCATCTTGGGATTATCCCAGAGCCAGGCCCCTTCC R 2 1 2 1 101000 f 74 goat Random2.2K-2219 27 6607385 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320764597 Affx-122947193 AX-385252244 27 6633429 ATTTAAAGCAAGCTGCACACTTGATGACAGAGATG[C/T]GCTGATGTTGCTATTTAAGAGCATCGATGGCATTT Y 2 1 2 1 101000 f 74 goat snp30232-scaffold333-785172 27 37774214 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445881 Affx-122925963 AX-123316218 27 6663202 GTGTTCTGTGGAGGCCAGAGGTACAGTGTCATGAA[C/T]ACTAGACTGGGTTTGGCTCGCAGCTTTTTCGTTAA Y 2 1 2 1 101000 r 74 goat snp30233-scaffold333-814945 27 37744648 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793386 Affx-122935835 AX-385280364 27 6702378 TCTTTTAAAAAGTATGAAGTCTGTGCAACTTTCAA[G/T]TTTAAAATTATATGCATTGTAAACTGACTTTTTTT K 2 1 2 1 202000 r 74 goat snp30234-scaffold333-854121 27 37705367 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446448 Affx-122925079 AX-123316784 27 6735050 GATATTATTCATTCTCCTTGGCTTGTGAATCTATG[C/T]GCTCCGCCTGCTCTGGTCAGTGGACACCTACACAC Y 2 1 2 1 101000 f 74 goat snp30235-scaffold333-886793 27 37674424 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776775 Affx-122956174 AX-385263899 27 6769175 CACCTTCCACTTCCATACGATTTAGGAGCGTCCTA[C/T]GATCTAAAGCATTTGCTCTTCCAAAATGAAAAAAA Y 2 1 2 1 101000 f 74 goat snp30236-scaffold333-920918 27 37640358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433885 Affx-122934411 AX-123304226 27 6822095 AGTGAACAGCACCAGGGCCCAACAGAGTCAGTGAT[A/G]TTCTGCTTGGTTAATGTTTTATACTCATAAAATCA R 2 1 2 1 201000 r 74 goat snp30237-scaffold333-973838 27 37589527 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418551 Affx-122946398 AX-123288899 27 6858910 CTCAGGTAGTGCCTTCTCCATCTGGGGAAGGATGT[A/G]TGTCCTGTCATCCCCCACTACTGCTTGCTTGGCCT R 2 1 2 1 201000 r 74 goat snp30238-scaffold333-1010653 27 37552695 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429510 Affx-122937855 AX-123299852 27 6892719 TCAAAGAATAATGCCTCACGGTTGAAGGTGTGTGC[A/G]TGGAGGGGGCCATTGATTATAAATCCAACACAGGG R 2 1 2 1 101000 f 74 goat snp30239-scaffold333-1044462 27 37519208 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445588 Affx-122925127 AX-123315925 27 6921933 GAGAGGAGACTAGAAGGCCAGGACGCCTCAGAGGT[A/G]TGTGCAAAGGTCTGGGCCGGAGGAGGAACTGAAGG R 2 1 2 1 101000 r 74 goat snp30240-scaffold333-1073676 27 37490163 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447263 Affx-122924945 AX-123317599 27 6978266 TTTCCTCTTTCCCTCTGCTTACCACTTCCAGTGGC[A/G]CTCCCATCACCATCAAGTGTTCAGTGCCAAGAAAT R 2 1 2 1 101000 r 74 goat snp30241-scaffold333-1130009 27 37434716 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779325 Affx-122976423 AX-385266429 27 7011194 ATTGACCCAGCTTTTCCTTAACTGCATATTATTTC[A/C]TTATTATTGTTTTCTCTGTGGCCACTGGTCCTTCT M 2 1 2 1 101000 r 74 goat snp30242-scaffold333-1162937 27 37401443 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434917 Affx-122934317 AX-123305257 27 7051515 TTTTCAGTACACTGCCAGCTTTTCTTGCCCAGGCA[A/G]ATCTGCACTGTCAACACACCAGTGATACCCAGTTA R 2 1 2 1 201000 r 74 goat snp30243-scaffold333-1203258 27 37360409 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774817 Affx-122965742 AX-385261951 27 7099595 TTTGTGATAAGCAAGTTATTTTCAGTTCTCTCACA[C/T]GTAATGTGCTTTAACTATTGAATGGTAGAAATTTT Y 2 1 2 1 101000 f 74 goat snp30244-scaffold333-1251338 27 37311970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435533 Affx-122933401 AX-123305873 27 7136005 TATTTCATTTCTACATTTTCAAAGCAAAGTGCTGT[G/T]TGCCTTTCTTTCCTTTGATTATTGAATTGTGATCC K 2 1 2 1 101000 f 74 goat snp30245-scaffold333-1287748 27 37277428 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796426 Affx-122929731 AX-385283376 27 7181367 TAGTTGATTTATGAACAAGATTATTTTAACTGACT[A/G]ACTAGAATATTTGACGTATACTACACTCCTGGAGA R 2 1 2 1 101000 r 74 goat snp30246-scaffold333-1333110 27 37231846 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400279 Affx-122960120 AX-123270634 27 7231002 GGAGGAGAGCTGGGAATGAGGAGCCAGTTCTCTAA[C/T]GAGCTGAGCTTTATAAGAGAGATTCACATAGTGAC Y 2 1 2 1 101000 r 74 goat snp30247-scaffold333-1382745 27 37182181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778675 Affx-122967326 AX-385265786 27 7270876 ACCACTTTCTATTAGACTACAAAATTGTCAGGGTT[A/G]TAAGAGAGATGAAATAGTATGAAGGACTATAAAGG R 2 1 2 1 101000 f 74 goat snp30248-scaffold333-1422619 27 37141908 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413582 Affx-122950580 AX-123283931 27 7301115 GACCATGAACATTTTCTTCATGCATATCACCAGAA[A/G]CAAGATGATGAAAAGCTGATTCAGCTCAGCTTCCA R 2 1 2 1 101000 f 74 goat snp30249-scaffold333-1452858 27 37111249 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441061 Affx-122928917 AX-123311398 27 7334219 AGTATTTATTTCTAATCCTTTAATACTCACTAACT[A/G]CGCAAAAATAAAAATACAAATGAATGGTTATCTGA R 2 1 2 1 101000 f 74 goat snp30250-scaffold333-1485962 27 37077821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794514 Affx-122948841 AX-385281477 27 7367768 ATATCTAGACACTCAAAGTAACAGTCAGTGGCAAT[A/G]CCCTTACATATTAAAGGTGCAAAATACCAAATCAC R 2 1 2 1 101000 f 74 goat snp30251-scaffold333-1519511 27 37044000 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425518 Affx-122941465 AX-123295864 27 7417540 TTAAGTGTAACACAAAATCAAAATCCCTCTATCCA[C/T]GAGCTGGGTGCCATTTATTTTCATAATTTAAGAAT Y 2 1 2 1 101000 f 74 goat snp30252-scaffold333-1569283 27 36998117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427290 Affx-122940158 AX-123297633 27 7449679 TTTTTGACCCTCATGCCTCTTCTTATCAGACCCTC[A/G]TGATTACGTTGAGCACACTCAGATAATTCAGGATC R 2 1 2 1 201000 r 74 goat snp30253-scaffold333-1601422 27 36966036 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417630 Affx-122946857 AX-123287978 27 7500353 GCTGATGGAAAGATTATTCTTCTGGGTAGTGAGGC[G/T]AAGGACCACTTGTGCACACACCTAGAGTAACCTCT K 2 1 2 1 101000 f 74 goat snp30254-scaffold333-1652096 27 36918250 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426566 Affx-122940167 AX-123296912 27 7534366 GTTAGTAGCTTTTTGGGTCCACGTATTGCCTTCAG[C/T]GTTGCCTTCCTCAGAAAAATATTTGAGGGACAATA Y 2 1 2 1 101000 f 74 goat snp30255-scaffold333-1686109 27 36884287 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790030 Affx-122960412 AX-385277036 27 7587036 CATGGCAGAGCAAACTTCGTGGTATCTTCCTGTCA[A/G]TTCAAACATCACCTGGCACCACTAACTGGTGTCAC R 2 1 2 1 101000 f 74 goat snp30256-scaffold333-1738779 27 36831840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787039 Affx-122953093 AX-385274067 27 7630506 CTGAAATCTTTTGACTTCTATAATCTGATGGGGCT[C/T]GTGACATAATTCATTGTGGCTCAGAAATATTTGAT Y 2 1 2 1 101000 f 74 goat snp30257-scaffold333-1782249 27 36787822 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775790 Affx-122924355 AX-385262921 27 7667786 AGTTTTAATATGGTGCAGTCTTGTGTTTATAACCA[C/T]AAACCTTATTGTAAATGTCAAAAGAATTCAGATCT Y 2 1 2 1 101000 r 74 goat snp30258-scaffold333-1819529 27 36749828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770398 Affx-122974466 AX-385257564 27 7696693 ATGTTTGTTGTGAGCATAAATCCATAGGCACTTTC[A/G]TACAGCTTGTAGAGTAAATATGCAAATAAAATCTT R 2 1 2 1 101000 f 74 goat snp30259-scaffold333-1848436 27 36720912 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777889 Affx-122960992 AX-385265005 27 7737646 GTGTACCCTTTTTTTGTTGACATAGATTACATGTA[C/T]GTTCTTATGATTTGTGCTTTCTTTCATTGAATTTT Y 2 1 2 1 101000 r 74 goat snp30260-scaffold333-1889389 27 36679922 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783911 Affx-122949689 AX-385270966 27 7783049 GTCTTCAAATAACTAGAAAGATGAAAGTAATTTGA[C/T]GTTCCTGTTGAATCAGGTTGGCTTCTGAGAAACGT Y 2 1 2 1 101000 r 74 goat snp30261-scaffold333-1934792 27 36633719 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789865 Affx-122936149 AX-385276872 27 7836682 TTAGAATATTTGGTAACTTGGTTATAACATCTATA[C/T]GCCTATTAAGTTTTAATATCTACAGGCCTATCAAG Y 2 1 2 1 101000 r 74 goat snp30262-scaffold333-1988425 27 36579494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380651 Affx-122975220 AX-123251009 27 7869128 TACTAGAGTTTGACCCTGGAGACTGATAGGGGGAC[G/T]GGCTACTTTTGGAGGAGAGAAATAAGCAATCCACC K 2 1 2 1 201000 r 74 goat snp30263-scaffold333-2020871 27 36546953 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437821 Affx-122932110 AX-123308159 27 7925907 TTCTACCATAGTAATTTCTTCTACCCAACTAATTA[C/T]TGTTTCATTCTTTCAATTAGTATCAGATGTCTCAT Y 2 1 2 1 101000 r 74 goat snp30264-scaffold333-2077650 27 36489891 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387418 Affx-122970402 AX-123257776 27 7961360 CTTTTGGGGAAAGGAAATAGGAGATAAACAACCAT[C/T]CTGAAGGGAGTTGATTTGAAAATAAATTAAACATT Y 2 1 2 1 101000 f 74 goat snp30265-scaffold333-2113103 27 36454434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389474 Affx-122968329 AX-123259832 27 7990614 TGAAAAGAAAGTGGTGCGTCCTATATATTCATGTA[C/T]AGATGCATAAATGCTTTTTCCTTTTTTGTTTTATT Y 2 1 2 1 101000 f 74 goat snp30266-scaffold333-2142357 27 36425082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441655 Affx-122929195 AX-123311992 27 8090457 TATACAAACACTTATTCTGGCTACAAGTTCTAGGA[C/T]AAAAGGTACTTTTAACAACTCTGCACAGTAAAACT Y 2 1 2 1 101000 f 74 goat snp30268-scaffold333-2242200 27 36325393 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452166 Affx-122921243 AX-123322499 27 8127672 TTCTCAGAATATTTCAGGTGATAAACCCATCCTCC[A/G]AGTGAAAGTGGAATTCCCTCAGTTGTGTCTGACAT R 2 1 2 1 101000 f 74 goat snp30269-scaffold333-2279415 27 36289420 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277711 Affx-1111836050 AX-519551210 27 8151542 TTTTTGGATCTAAACTCCTTCCTCTTGGACTCTGG[A/G]TCTCCTGACTCTCCCCGCATCCCCCCCCGCCCCGC R 2 1 2 1 102000 f 74 goat Random2.2K-2221 27 8151542 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38443053 Affx-122928140 AX-123313390 27 8177593 GCCCCTCTCCCATATTTATTAGACGGAAGCCTGAA[C/T]CCACAGATGGGCCTTAACTGGGAAGGAAAGCAAAA Y 2 1 2 1 201000 f 74 goat snp30270-scaffold333-2329336 27 36242254 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435031 Affx-122933759 AX-123305371 27 8208415 AGACAAATATGTGGATGTTTACCTACATGGGTCAA[C/T]GCTCCACAGCAGGTGTTTTCAAATGAGTGTTATTT Y 2 1 2 1 101000 f 74 goat snp30271-scaffold333-2360158 27 36211460 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273188 Affx-1111833335 AX-519546847 27 8276657 TGCCAAGTACTGTTCTGAGCGTTGTATGTGCATTA[A/G]CTCATTTTTACAACAGTCTGTTAACTTGCCTGTGG R 2 1 2 1 101000 r 74 goat 27_8276657_AF-PAKI 27 8276657 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320779037 Affx-122949948 AX-385266144 27 8290398 CTATTATGATTTAAATTATCTGCATGTTGTTTAAA[A/C]AGTATTTCCTACTTCACGCTCACAATGGCATTCTG M 2 1 2 1 101000 r 74 goat snp30273-scaffold333-2442141 27 36129096 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409436 Affx-122954096 AX-123279787 27 8330396 TTACCTTCTCCTCCTGAAGTCCGAAGTGACCAATA[C/T]GTGCTTATGGGTTTGGAGAAAAGAGATACAAACCC Y 2 1 2 1 101000 f 74 goat snp30274-scaffold333-2482139 27 36088057 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777741 Affx-122976860 AX-385264859 27 8363328 TGTGAAGAAGAGAACTTCAAAGACGTTAATTGGGG[C/T]GGAAACAGAGAAGTGTTACAAGGTTAGTGGCTGGA Y 2 1 2 1 101000 r 74 goat snp30275-scaffold333-2515071 27 36055101 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781552 Affx-122931389 AX-385268637 27 8397041 TTTAATTTGAGTTGATTCTGTCACAGACTCATATT[A/G]TTTGCATCTTATGGCAGCTGGCACCCGGGTTCTCC R 2 1 2 1 101000 r 74 goat snp30276-scaffold333-2548784 27 36020914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424259 Affx-122942002 AX-123294605 27 8465174 ATGAACTGCCTTTCAATAATCAAAACAGTTTTACT[A/G]CTCATGTTTTTCTCTGTTAGAAACGCTTGATATAA R 2 1 2 1 202000 f 74 goat snp30277-scaffold333-2616917 27 35956622 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787715 Affx-122930731 AX-385274738 27 8503991 CATACTCTATGAAGTATTAAAATCATCAAACTAAA[G/T]CAGCATGTAATGTAACCTCCCTCAGATCTTCCTTG K 2 1 2 1 101000 r 74 goat snp30278-scaffold333-2655734 27 35917947 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769995 Affx-122940921 AX-385257162 27 8561900 CCTGAAGGTCATACGTGGCTACACTCCTTTAAACA[C/T]GGCTGCATTTCCTGCTATGTCTTTGAGTGTTCATG Y 2 1 2 1 101000 r 74 goat snp30279-scaffold333-2713643 27 35859560 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277712 Affx-1111836051 AX-519551212 27 8570678 GGTCCTGGTTATCCTAATCGCAGTGAAGACTTCCC[A/G]GAGTCTCCTGGGATGTGGAGACGAGGGTCCTGCTC R 2 1 2 1 101000 f 74 goat Random2.2K-2222 27 8570678 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38442458 Affx-122927949 AX-123312795 27 8627890 ATGTGGTGTCTGTGAGGAGTCTTTGATTATATTTA[C/T]GCATTTTTTAAATTCTGTAAAATCAATGCATAGGT Y 2 1 2 1 101000 f 74 goat snp30280-scaffold333-2779633 27 35793099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397882 Affx-122961964 AX-123268237 27 8668471 AAACTAAAATATCAACTTTCTGCAAATACAAAATT[A/C]AAGCTTTTCCTAGTTGGGATTGTGCCTGTGTTGTT M 2 1 2 1 101000 r 74 goat snp30281-scaffold333-2820214 27 35752970 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779690 Affx-122954552 AX-385266789 27 8792800 TTCTTCCAACAAGAAAGAGGCTTTAAGTGACCTGG[C/T]TGCATAGTTAACTCTACTTTACAAAGGAGACAATA Y 2 1 2 1 101000 f 74 goat snp30283-scaffold333-2944543 27 35625004 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449026 Affx-122923082 AX-123319361 27 8832859 AAGCTTCCCCTTGAGTCTATTTAGCAGTGAGAAAA[G/T]CCTTCTATGGCCACTTCCCTGAAAAGAGAGATCTT K 2 1 2 1 101000 f 74 goat snp30284-scaffold333-2984602 27 35584570 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413159 Affx-122950350 AX-123283508 27 8887619 ACATCTCCTTCATGTGCTGTGCTAGTATCTTGGAT[A/G]CTGACACAGTCAGTGCAAAGCCAGGCTGATGTATT R 2 1 2 1 202000 r 74 goat snp30285-scaffold333-3039362 27 35529528 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407121 Affx-122954871 AX-123277472 27 8918546 TGTCAATGGAGACAAAATTCAGAAGCATGCTTTCC[C/T]GGAGCCCTAGCAGCACTGAACACAAACCTCCTTGG Y 2 1 2 1 101000 f 74 goat snp30286-scaffold333-3070289 27 35498585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417244 Affx-122947277 AX-123287592 27 8955261 GAGACCCTGCTCCACAACAAAGGAAGGCACCACAA[C/T]GAGAAGCCCAAACTAGAGAGTAGCATCTCCTCACA Y 2 1 2 1 103000 r 74 goat snp30287-scaffold333-3107004 27 35461787 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396231 Affx-122963341 AX-123266586 27 8992669 GACTACTGAATTACATGTTTTGCTGATCTGAAGAA[C/T]AGTGAATTTTGATTTTTAAATACTAATCACACTAA Y 2 1 2 1 101000 f 74 goat snp30288-scaffold333-3144412 27 35424370 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397357 Affx-122962291 AX-123267712 27 9032220 TTATAGCACATACTAAAAGGGAGAGGAGGGAGGGA[C/T]GAAAGGAGGGAATAGATAAAAGGAAAGGAACAAGA Y 2 1 2 1 201000 r 74 goat snp30289-scaffold333-3183963 27 35384841 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376715 Affx-122978968 AX-123247074 27 9068076 GGAACCCATGACTCCTACAGTGGTAGCATGGAGTC[A/G]TAACCACTGGACAACAGCAAACTTAACTTGCGTAT R 2 1 2 1 303000 f 74 goat snp30290-scaffold333-3219819 27 35349323 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428299 Affx-122939381 AX-123298642 27 9122179 CACCAACCTGGCACCTTCAGAAGATACAATTTTCA[C/T]GTTCACAGGGTACTGTTTAGTACACTTAAGAGTCA Y 2 1 2 1 101000 f 74 goat snp30291-scaffold333-3273922 27 35294766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429689 Affx-122937638 AX-123300030 27 9168247 TCATAGAGCACATGCTGTCCAGAAATAAATGGTCA[C/T]ACAGGACAAGGAACTGAGAGTACCGCTTTCCACAG Y 2 1 2 1 101000 f 74 goat snp30292-scaffold333-3319990 27 35247816 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445467 Affx-122925215 AX-123315804 27 9201175 TTGGAATAGCCATAATGGATATTTGGTTCAACCCC[C/T]AAATGGGATTGTCAGCCTTCAGAGTGAGGTGTAGC Y 2 1 2 1 201000 r 74 goat snp30293-scaffold333-3352918 27 35214390 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381751 Affx-122974318 AX-123252109 27 9237026 TTCATTATTCAAGAATTCTATGAAAGAAGATATAG[C/T]GTCTATTTATATTTCTGAAATATTAAAAAAAATGA Y 2 1 2 1 103000 f 74 goat snp30294-scaffold333-3388769 27 35178530 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778373 Affx-122974534 AX-385265488 27 9266022 CCATTAAAAATCTGTACATTAATGCTCTGTGCCAA[C/T]AATACTATGCATTTTTATTGGAGCTGGATGCTTGT Y 2 1 2 1 101000 r 74 goat snp30295-scaffold333-3417765 27 35149846 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277848 Affx-1111836052 AX-519551345 27 9309827 TCTAAGAATGCTAAATACTACATCTCCACAATTTG[A/G]CAAATTTTCCTAAGGGAAAATTTTTCCTTCCTGAA R 2 1 2 1 101000 r 74 goat Random2.2K-2223 27 9309827 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38383963 Affx-122972944 AX-123254321 27 9311487 TGTCTCTGCTCCAGTGTTTGCCCCAATTCTGTTTG[C/T]ATTGTGTTTGAAAAATTACCAGAGATAATACTATT Y 2 1 2 1 201000 r 74 goat snp30296-scaffold333-3463230 27 35104335 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789777 Affx-122947599 AX-385276785 27 9365892 ATATGTATGAAAGAATGTATGTAGAAAATACAGAC[A/G]TCATTACACTCAGCTCCTGACAGCATAGACTCCAT R 2 1 2 1 101000 r 74 goat snp30297-scaffold333-3517635 27 35050958 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453914 Affx-122919907 AX-123324247 27 9400776 TAAAGCTTGTTTATTCTTAAATTATGTCTGAATGG[C/T]GTAATTAGGCTTTATGAGACCTTGACCCCTTCTAA Y 2 1 2 1 101000 r 74 goat snp30298-scaffold333-3552519 27 35016281 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396007 Affx-122963489 AX-123266362 27 9466438 CTGAGATGCCTGGTATTTATTGGTCTTTTAGGGCA[C/T]AGAATCTATTTGGCTAATTCAGTTGGCAATAGTTT Y 2 1 2 1 101000 f 74 goat snp30300-scaffold333-3618181 27 34949742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784588 Affx-122972428 AX-385271636 27 9500650 TGAATATGTGTTCTCTTAATACAGAAAATCCAGGA[A/G]AGTGCAGTGACGCAAGAAGCTTGTGTCCATAGTTC R 2 1 2 1 101000 r 74 goat snp30301-scaffold333-3652393 27 34915535 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402020 Affx-122958749 AX-123272373 27 9558248 ACCATCTGAAATGTTCCATCCATTGAACTTAATTC[A/G]TTATTTTTCATATCTACTTTTTCTTCTCTTCTGTT R 2 1 2 1 303000 r 74 goat snp30302-scaffold333-3709991 27 34858207 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436857 Affx-122932202 AX-123307195 27 9610730 ACTTACAATTAGAATGAAACAAATACTAAACAGGA[C/T]GTGCAAGCTGGGGTTGTTATGATTGACTATTTTAG Y 2 1 2 1 201000 f 74 goat snp30303-scaffold333-3762473 27 34812829 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453711 Affx-122919683 AX-123324044 27 9659071 TATTCTGCAACGTTGGCAAGTGATTGAAAATTTTC[A/G]ATTTAGTGTCCTGTAAAAGAAATGGTGAGGGGCGT R 2 1 2 1 101000 r 74 goat snp30304-scaffold333-3810814 27 34763637 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446009 Affx-122925866 AX-123316346 27 9717485 GTATTTGAAATTCTCCCCTAAAATATGGTAATGCT[A/G]TATAATATGCATGTGTGCTAAGTCTCTTCTGTTGT R 2 1 2 1 303000 f 74 goat snp30305-scaffold333-3869228 27 34704413 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779965 Affx-122975872 AX-385267064 27 9761058 ACTGGCTTTAAAATGACAAATTAAATTACTAATTC[C/T]ATACTAGTAATAGGCAAACTTAGTAATTCAGTCAT Y 2 1 2 1 102000 f 74 goat snp30306-scaffold333-3912801 27 34660597 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794296 Affx-122978505 AX-385281260 27 9825000 GCATTGTAAGGAAAATTTGATAAATACATAATATC[A/G]TATCTGTCTCATGTATCTTTTCATCCCCTAAGGGT R 2 1 2 1 202000 f 74 goat snp30307-scaffold333-3976743 27 34596553 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779914 Affx-122929919 AX-385267013 27 9891307 CCCAAGGATATAAAAATCTGCAGAAGTTCAAGTCT[A/G]TTATATAAAATGGCCCAGTACTGTTGACGCTCTGG R 2 1 2 1 101000 f 74 goat snp30308-scaffold333-4043050 27 34528987 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320794481 Affx-122944172 AX-385281444 27 9939593 GCACCTAGATGAAAATGTTAACGACACTATAAAAA[C/T]ATGAAATGAGCTATTCTAAGACTCTCAAGACCTTG Y 2 1 2 1 201000 f 74 goat snp30309-scaffold333-4091336 27 34480890 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780706 Affx-122938018 AX-385267796 27 9975347 TAACACTTTGCTTGAAAGGTAATTAGATAACCTTC[A/G]TTAGTTAGAGTTCACAAAAGAGGCAGGGCTTTAAA R 2 1 2 1 201000 r 74 goat snp30310-scaffold333-4127090 27 34445495 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389661 Affx-122968721 AX-123260019 27 10008309 TAACTTGATTACAAAGACAAGAAGTTTTATGAGCT[A/C]TTCTGAATGGAAAATTTCTTTCTGTCTAGAGAAAA M 2 1 2 1 101000 r 74 goat snp30311-scaffold333-4160052 27 34412658 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452028 Affx-122920902 AX-123322361 27 10044623 TTAAAATGTATATGGAATGAACATTGATTACCAGT[C/T]GTGGAGGTGGGCATACTTGAATGACCAGAGATGGT Y 2 1 2 1 201000 f 74 goat snp30312-scaffold333-4196366 27 34377528 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437985 Affx-122931591 AX-123308323 27 10144495 ATGTTTTATCATTATCAGGAATCACTTCAATTGGA[C/T]AGTAAATGCTTACAATTGCATACTCTGCTTCATGA Y 2 1 2 1 101000 r 74 goat snp30314-scaffold333-4296238 27 34277431 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428002 Affx-122939164 AX-123298345 27 10203653 TGGACCCTAGCATGCCAGGCTCCTCTGTCCATGGG[A/C]GGACTCTAAATTTACTGCATGATAAGGTGACTATG M 2 1 2 1 101000 r 74 goat snp30316-scaffold333-4355396 27 34218361 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410572 Affx-122952132 AX-123280922 27 10232988 AGCAGTTTCAAAGCCTCTGGACTAGATACTGTCCC[A/G]TTGTATGAGTCTTTACACCCAGCACATCGTGTTCC R 2 1 2 1 101000 r 74 goat snp30317-scaffold333-4384731 27 34189354 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382992 Affx-122973338 AX-123253350 27 10270427 CCTAAGTTTGCATATCTGCTTTATATACTGTGCAG[C/T]GCACATAGATCAGGCCACTTCATTTCCTGCCTCCC Y 2 1 2 1 101000 f 74 goat snp30318-scaffold333-4422170 27 34151974 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788558 Affx-122974391 AX-385275575 27 10304672 AAAAAAATAGTTTAACAAGGATGAACTATGACTAG[A/C]GTTGTGGTTTAGGGAATAATACATTAGGTTTGTAA M 2 1 2 1 101000 f 74 goat snp30319-scaffold333-4456415 27 34116559 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464003621 Affx-1110266751 AX-515480576 27 10337952 CTTGGGCTTGAATCATTTCCTGTCAGCTTTGGAGA[C/T]GCCTTGAGTGCAGAACCAGACCGGCTTGGGCAGGG Y 2 1 2 1 101000 f 74 goat Random2.2K-2224 27 10337952 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38414814 Affx-122949209 AX-123285163 27 10385168 AGGGGAGAGAGTGCCAACTAGTTGCCGAGATTTTG[A/C]GTAGGTGGTTTTTAAAGGTGAGGGAAGTAGTTAAA M 2 1 2 1 201000 r 74 goat snp30321-scaffold333-4536911 27 34036081 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436751 Affx-122932288 AX-123307089 27 10440452 GTGCACCAAAATAAGTTTTAAAGATTTTTAATTGC[A/G]TTAGCCTTTATATAAGAAATAGTGCATAGCATTTA R 2 1 2 1 201000 r 74 goat snp30322-scaffold333-4592195 27 33982205 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401983 Affx-122958774 AX-123272336 27 10499609 TTATGAAGTTTACCTTCTAGTGGAGTCACATTACC[A/G]CACGTGACAAACAGAGCACCGTCTAGGAGGCGACA R 2 1 2 1 101000 f 74 goat snp44426-scaffold604-28010 27 33925840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785546 Affx-122961255 AX-385272590 27 10546791 TGAGCGTAACAGAATGTATAATATAATCCTAGATA[C/T]TAAAATCAATTTTCACATGCACAACTTCAAAGGCT Y 2 1 2 1 101000 r 74 goat snp44427-scaffold604-75192 27 33878579 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771801 Affx-122965380 AX-385258958 27 10620457 GTGTCATGTTCCAAATAGAGAAATGGCCACTTTCA[C/T]CCTTACTATCTCTGAATCTTGTCTCATCCATCTGC Y 2 1 2 1 101000 f 74 goat snp44428-scaffold604-148858 27 33804797 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782797 Affx-122944857 AX-385269869 27 10670394 ATCCAATAGTGAAAAACCAAACACGTGGTCAAAAC[A/G]TAATTATGTGATATTAAAAACATAGCTGAAAATAA R 2 1 2 1 201000 r 74 goat snp44429-scaffold604-198795 27 33755449 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782760 Affx-122978268 AX-385269832 27 10705193 TAAATCATGAAAACTTTGAGAATAAAAGCCCTGGC[A/G]TTCAAATCAGACATTTGCAAAGAAGACACTTTGCA R 2 1 2 1 201000 f 74 goat snp44430-scaffold604-233594 27 33720144 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430568 Affx-122937009 AX-123300909 27 10742104 ATGGCAAGTTCTTCCAGAAAATGAAGATTAGAAGA[G/T]ATACTATTTTTAAATATTTACAAGAGAAAATAATA K 2 1 2 1 103000 f 74 goat snp44431-scaffold604-270505 27 33682899 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448651 Affx-122923350 AX-123318987 27 10802878 TCTGACTTTATTTTGGACCACTTTCTTTGCTATTA[C/T]AGAGACACTGACTTTCTGTTTCAGGAACACAGTTG Y 2 1 2 1 101000 f 74 goat snp44433-scaffold604-331279 27 33621765 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387303 Affx-122970520 AX-123257661 27 10842640 CAATCTCTAATTTTTGTTTTTGCTTTTTTCTTAAA[C/T]GAGGTATAATGCTTATCTTACAAGATTTCACTTTC Y 2 1 2 1 103000 r 74 goat snp44434-scaffold604-371041 27 33581529 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764180 Affx-986698707 AX-385251913 27 10869486 AATTTGTAGATTGCTTTAGGTGGTATGGGAATTAT[A/G]ACCATAAGAATTCCCCCAATCCATGATCATTGGAT R 2 1 2 1 600010 f 74 goat 27_10869486 27 10869486 Ancestral_priority_1043 ancestry 0.766 recommended IMAGE 10K 10K ancestral 320764182 Affx-986698709 AX-385251915 27 10870070 TTGAAGGAATGTATAGAGATTTGATATGGTTTTAC[A/G]CAAATGTTTGGCAGAATTCAACAGTGACAACATCT R 2 1 2 1 600010 f 74 goat 27_10870070 27 10870070 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 38449946 Affx-122922902 AX-123320281 27 10876282 GTGCTTTCAGAAACTGCCTGGCACTTCCCAGAGCC[A/G]TGATTCAAACACAGGCTTGTTCTGATACCACCGTG R 2 1 2 1 102000 r 74 goat snp44435-scaffold604-404683 27 33547955 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768485 Affx-122942092 AX-385255665 27 10905332 CCTTACTGCAACATCCAATATCTTTAGACCAATGT[C/T]AAACAAAGAGGCAATCCCAGACATTTTAGACTGCT Y 2 1 2 1 102000 r 74 goat snp44436-scaffold604-433733 NW_017211829.1 10629 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449146 Affx-122923554 AX-123319481 27 10940612 GAAGAGAGATAACTTGGCAGACAGAATGGGAGGGC[A/G]TTCCAAGAATATGGCGCAGCTTGGAAACGGCTTGT R 2 1 2 1 201000 r 74 goat snp44437-scaffold604-469013 27 33483269 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767760 Affx-986698711 AX-385254987 27 10941863 CCACCCCTGGTAGTGGCAGAAGCTCTGACCCAGCA[C/T]TACATTCTAAGTTAAATTTCCCACCACTGTGTCTA Y 2 1 2 1 600010 r 74 goat 27_10941863 27 10941863 Ancestral_priority_1043 ancestry 0.684 recommended IMAGE 10K 10K ancestral 320764186 Affx-986698713 AX-385251919 27 10944619 TTCAAAAACATAACATGCTTGTTTAAAATTGGACC[C/T]TTCTACAAGATACAATAATAAAACAGAGTTTAAAT Y 2 1 2 1 600010 f 74 goat 27_10944619 27 10944619 Ancestral_priority_1043 ancestry 0.762 recommended IMAGE 10K 10K ancestral 320804262 Affx-986696469 AX-385290890 27 10944707 AATACTTTGATAAACATAAAGAATTTTTAAAAACA[A/G]TGCCATTAAAGCTAGTACATGAAAGTAAAAAGGGA R 2 1 2 1 600010 r 74 goat 27_10944707 27 10944707 Ancestral_priority_1043 ancestry 0.662 recommended IMAGE 10K 10K ancestral 320764166 Affx-986698693 AX-385251904 27 10945233 CATACTGATGCTGACTGCATTACGAAGTAATATGT[C/T]ATCCCTCTAAGCATCATTTAAAACAAAATGCAATC Y 2 1 2 1 600010 f 74 goat 27_10945233 27 10945233 Ancestral_priority_1043 ancestry 0.718 recommended IMAGE 10K 10K ancestral 468273119 Affx-1111833320 AX-519546784 27 10957513 GGGAAAGGAGTATGTCAATGCTGTATATTGTCACC[A/G]TGCTTATTTAACTTATACGCAGTATACCTCATGAG R 2 1 2 1 103000 f 74 goat 27_10957513_AF-PAKI 27 10957513 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320767798 Affx-986698732 AX-385255022 27 10963864 ACAGTCCATGGGTTCACAAAGATTTAGACAATTGA[A/G]TATGTCCATGAAAATACACAATATCATCATAATTG R 2 1 2 1 600010 r 74 goat 27_10963864 27 10963864 Ancestral_priority_1043 ancestry 0.746 recommended IMAGE 10K 10K ancestral 320777110 Affx-122946508 AX-385264233 27 11015199 TCATTTCGTAAGCATTCTTATCAGTACCTGCTAGA[A/G]TGAATTTTTAATTTGTGTTGATCTCCTGATTATCT R 2 1 2 1 201000 r 74 goat snp44439-scaffold604-543600 27 33408789 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786208 Affx-122946800 AX-385273243 27 11069196 ACTTTCTCAGTGAAGCCTTGCAACATTCACAGACC[A/G]CCATGCTTCTTTCATTGTTTGGCATGATTCATGAT R 2 1 2 1 101000 f 74 goat snp44440-scaffold604-597597 27 33356026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799886 Affx-122942703 AX-385286812 27 11106959 TTGGAAACTTTTAAAACTATTAGATAGATACCATT[A/G]CCCCTAATGGAAAGGAGTGAAAAAATATACATCTT R 2 1 2 1 101000 r 74 goat snp44441-scaffold604-635360 27 33318122 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448755 Affx-122923316 AX-123319091 27 11137395 GCCAGAAGTGGTTACTAGGCTGCCTTAACATAACA[G/T]AAAGCCTTCCCTGCATTTGTCAAAATGATGATGGT K 2 1 2 1 101000 f 74 goat snp44442-scaffold604-665796 27 33287365 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395091 Affx-122964170 AX-123265446 27 11169777 GAGGCATTTAAGTTATAGAACTTGATTTTTATGTT[A/G]CTATCATGAGAAATGGTTTCAACTCGGGGAAGCCC R 2 1 2 1 201000 f 74 goat snp44443-scaffold604-698178 27 33255232 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770151 Affx-122974361 AX-385257318 27 11210688 ACTTAAAATTGTATCAAATCCAAAGGAGAGTTTCT[A/G]CCTTGACTTTTGGAGAATTTTGGAGTAGGTTATAT R 2 1 2 1 102000 r 74 goat snp44444-scaffold604-739089 27 33214235 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383634 Affx-122972539 AX-123253992 27 11256185 CTTTGAAAAATGTCTCTAGTGCTGAGATTTAATGG[C/T]AATACTCAATGAATATTATATTTTCTATGAAAACA Y 2 1 2 1 101000 f 74 goat snp44445-scaffold604-784586 27 33168279 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38393780 Affx-122965194 AX-123264135 27 11291451 GGGTTTGGAGTTACTCTATGTGGATCAGAAACAGC[A/G]TGTCCTGTGGCCCCTGCCTTACTGTGAAATCTTCC R 2 1 2 1 101000 f 74 goat snp44446-scaffold604-819852 27 33134031 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382847 Affx-122973536 AX-123253205 27 11337427 CTGAAAGTAGATCAATTCTACAGTATTCTGAGGAC[A/G]ATTTATCAGGTCCTAGGGCAAACAAGGCAGGCTGG R 2 1 2 1 101000 f 74 goat snp44447-scaffold604-865828 27 33087836 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784222 Affx-122978083 AX-385271273 27 11384630 ACATGCCACAGATTTATTTAAAAGGGTTGTGTTCA[G/T]AGTGTTTGGAGTCATAAGGAAGATACTCTCTGAAC K 2 1 2 1 201000 f 74 goat snp44448-scaffold604-913031 27 33040949 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386493 Affx-122971546 AX-123256851 27 11414859 AGTCCCCACAAGAGAGAGAGCTGCCCTAAGCCCTC[A/G]TTCTCTGGCATAAAAATTCCACTAGGGTCTCCCTC R 2 1 2 1 101000 r 74 goat snp44449-scaffold604-943260 27 33010773 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416077 Affx-122948331 AX-123286426 27 11448725 AAAGCCTCTTTGAGTTATTATTTTGAGAATGTTCC[A/G]TATCACAGGCTGTAGCTCTTGCGTTGTATGTTTTC R 2 1 2 1 101000 r 74 goat snp44450-scaffold604-977126 27 32977955 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781053 Affx-122949648 AX-385268140 27 11481991 AGTCCACATCAATTCAGAATTTCTAAGTCAAGAAA[C/T]GAAGAGGCTGTACTATATTGTCCATTGAGAGTCAG Y 2 1 2 1 101000 r 74 goat snp44451-scaffold604-1010392 27 32944534 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412608 Affx-122951283 AX-123282957 27 11511711 AACTGCTGACCCTAATCAGCTGAGCGAGGAGAGGT[A/C]GTGGTTTGGGATGGAGCCCGACCCTGCAAAGGCTG M 2 1 2 1 201000 r 74 goat snp44452-scaffold604-1040112 27 32916253 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420670 Affx-122944814 AX-123291017 27 11562227 CTGCAGCTCAGAACCCAACACCGGAGATAACTAAA[C/T]AGATGATTGACGTCATGGGGGTCCTTGCTATGCCT Y 2 1 2 1 201000 f 74 goat snp44453-scaffold604-1090628 27 32865039 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453634 Affx-122919743 AX-123323967 27 11615679 TTGCTGTAGAATGTTCAGCATCTAATGAAGCTAAC[A/G]CTTTGCATGATTGTAAATGTGAACCATCCCATCTA R 2 1 2 1 101000 f 74 goat snp44454-scaffold604-1144080 27 32811529 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388371 Affx-122969330 AX-123258729 27 11710408 ACATCCTTAGGAACAATAATTCCTCAAGGGAGACT[A/G]TATAACTGCATTACTTATTTCTCAGTTTTAGAGCA R 2 1 2 1 101000 f 74 goat snp44456-scaffold604-1238809 27 32716974 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450127 Affx-122922762 AX-123320462 27 11739726 TACGCTCGGTGCCCTAAACATGCTCTGACAGGAAG[C/T]AGATGGATAAGAGAGGTAAATTAGTTATTTCAGGC Y 2 1 2 1 201000 r 74 goat snp44457-scaffold604-1268127 27 32686613 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393832 Affx-122965163 AX-123264187 27 11799153 AAGACTTAGAGATAATTTAGAAATTCACTCGCCTC[A/G]TCCAACACTTTCTTCCAAATTGGTCTGATAGGCAG R 2 1 2 1 101000 f 74 goat snp44458-scaffold604-1327554 27 32627052 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392150 Affx-122966320 AX-123262507 27 11885830 TAACATTTTTATGGACCAAACTGTAATCAAAAGCT[A/G]TAAATGGACTATAAGAAAGACAGTCTAGGCTGTTG R 2 1 2 1 101000 f 74 goat snp44460-scaffold604-1414231 27 32539798 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802706 Affx-122962923 AX-385289605 27 11926182 GAGCAGACCTGGGGGACATAGACCCATCTTGAAGG[A/G]TCAACCTTTTCAACCGATGCATACAGAGATGAACA R 2 1 2 1 202000 f 74 goat snp44461-scaffold604-1454583 27 32499525 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421679 Affx-122944420 AX-123292026 27 11956874 AAGGGTTATAAACCCATATGATCTAAGTTGGAATA[C/T]GGAAATGTATGTATATAATATATGTGATTAATGAA Y 2 1 2 1 101000 f 74 goat snp44462-scaffold604-1485275 27 32468851 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779245 Affx-122964025 AX-385266349 27 12003948 TGCATTTCAGCATAAAGACAAGGTGAGCAAGACAC[A/G]CCATTGCTTCCCAGGTATGTCTACAGCAGTGCCAT R 2 1 2 1 101000 r 74 goat snp44463-scaffold604-1532349 27 32421867 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379842 Affx-122975810 AX-123250200 27 12060375 GCTATTATATAGTTTTAAATGAATTTTTATAGCTT[A/G]CTAACTGATGTTTATAGACAGATCTAAGGTTTACT R 2 1 2 1 101000 r 74 goat snp44464-scaffold604-1588776 27 32365279 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377839 Affx-122977292 AX-123248198 27 12113573 ATGATCACATTATGTGATATTTTTTGTAATAACCT[A/G]ATAGCTAGCAGATGGTGCACTGCACATTCTATGAG R 2 1 2 1 101000 r 74 goat snp44465-scaffold604-1641974 27 32311470 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379522 Affx-122976073 AX-123249880 27 12175598 ATAACTTGGAAGCATCAATTAACCTAGGTTAACAC[A/G]TGTTTGTAAATATTTGCAAAGTTTGGTGAGCTTGT R 2 1 2 1 101000 f 74 goat snp44466-scaffold604-1703999 27 32249220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790858 Affx-122962944 AX-385277856 27 12219313 TTCTCAATATGTACCTAAAAATTCTAAATATTTGT[A/C]TGTAAGAATCTAGAGATGAATAAAAGGATAATAGT M 2 1 2 1 303000 f 74 goat snp44467-scaffold604-1747714 27 32205582 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387606 Affx-122970249 AX-123257964 27 12297957 ACTTAGCCACCAGGGAAGCCCTTCTTTGGACTAAA[A/G]GGTGCCCAATCGTGAAAAGGAGAAAACAAAAAGAA R 2 1 2 1 201000 r 74 goat snp44469-scaffold604-1826358 27 32126661 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788679 Affx-122948355 AX-385275695 27 12337573 TAAAATGGAAATCTAGCATCAATATTTGAACAAGT[A/G]TTGTTCACTAATAGGACGAGTTTTATGAAATGCAG R 2 1 2 1 101000 r 74 goat snp44470-scaffold604-1865974 27 32086665 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405896 Affx-122955591 AX-123276248 27 12369048 TTGTACGGATGCTGAGGAGGTGAGAGTTTTGGGGA[G/T]AAAATGCAAAAGAAAGGGCATAAAAATAATAATGG K 2 1 2 1 102000 f 74 goat snp44471-scaffold604-1897449 27 32054310 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387137 Affx-122970648 AX-123257495 27 12429925 ACCATATAGGCCCTGAAGTCTAGTATTCAGTAATA[C/T]GATTAGGAAGGTATTTCAGTTTTGTCCTGGTGAAA Y 2 1 2 1 101000 f 74 goat snp44472-scaffold604-1958326 27 31993550 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784203 Affx-122934504 AX-385271254 27 12473205 TGGTATAGATAAATACGTGCTCCAGCTACTTCTCA[C/T]GTCCTGTGAGCTGGAATCTTTAGAACTAGCATTGA Y 2 1 2 1 101000 r 74 goat snp44473-scaffold604-2001606 27 31950488 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428594 Affx-122938699 AX-123298936 27 12503140 AACTTTCTGGTGTCTACCGTTTCAGATATTTGTCC[A/G]TGCACATATACACCTAGGCTTCCCTGGTAGTTCAG R 2 1 2 1 201000 f 74 goat snp44474-scaffold604-2031541 27 31920568 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786532 Affx-122923827 AX-385273565 27 12540042 TTTGAAAGTCTCTGTGACCCGTTATAAAACTGTCC[A/G]TGTGACTGTTGCCAAGGAATCAATTGACTTCCTTC R 2 1 2 1 101000 r 74 goat snp44475-scaffold604-2068443 27 31884799 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798434 Affx-122949062 AX-385285368 27 12572217 GTCCAATAACAAACCTTCCTTTACCTGTAATTCCT[C/T]GTTTTGCATAATCGATTGTTTGCGAAAGTAATAGG Y 2 1 2 1 101000 f 74 goat snp44476-scaffold604-2100618 27 31852871 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389799 Affx-122968207 AX-123260156 27 12633497 CTGCTAGGGATGTTTGAGCAGAGAAGTGTTACCCT[C/T]GGGAGCAGGGGCATGGCATGGCTTAGAAGATGGAT Y 2 1 2 1 101000 f 74 goat snp44478-scaffold604-2161898 27 31790958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441204 Affx-122929529 AX-123311541 27 12673124 TCACTGAGGCCCGGTCCTCGCAAAAAATCGCTCCC[A/G]TAAGATTTCCCTTCCCGTCAAGCAGAAACTTTGTC R 2 1 2 1 101000 r 74 goat snp44479-scaffold604-2201525 27 31751892 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441190 Affx-122929539 AX-123311527 27 12724358 TGTAAGTAGCTGAAAAACAAGGGACAGCTCTGGGG[A/G]TTAGGACAAAAGCTAGCGGAATTTCCCCAGCCCAT R 2 1 2 1 201000 r 74 goat snp44480-scaffold604-2252759 27 31700477 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430322 Affx-122938227 AX-123300663 27 12769292 AAGGTGAGATTCATGTCGATGATGAAGGCAGGGCG[C/T]CAGGCATACATGGGAGCTCGCGTCACCAACAGACC Y 2 1 2 1 101000 f 74 goat snp44481-scaffold604-2297693 27 31655437 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767560 Affx-122932942 AX-385254813 27 12802027 CAACTCAGCACCTGAGAGAAGGTAAAACCACATGA[C/T]GGGTAACCAACTTTCAATGGTTAGGTTGCAATGTA Y 2 1 2 1 101000 f 74 goat snp44482-scaffold604-2330428 27 31622941 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437136 Affx-122932154 AX-123307474 27 12843500 CCACCCACACGGCCACATTCCCCGGTCCTTATTCT[A/G]CGGCTCTTCACTACCATTCTTCCACCAGAGGCCAC R 2 1 2 1 101000 r 74 goat snp44483-scaffold604-2371901 27 31581547 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452492 Affx-122920984 AX-123322825 27 12885355 AAATGTGTCTGTAGCAATCTGCATTCCCAGCCGTC[A/G]CTGATGACAATTCCTGTTGCTCCACATACTTACCA R 2 1 2 1 101000 f 74 goat snp44484-scaffold604-2413756 27 31539344 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773213 Affx-122949226 AX-385260356 27 12930363 AAATTTTACAAAGTTTAGGATCAAGCTGAAAATGA[C/T]ACAGAGATTTATGGCACATTTTTCTTTAGGATTTC Y 2 1 2 1 102000 r 74 goat snp44485-scaffold604-2458764 27 31494214 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779078 Affx-122921413 AX-385266183 27 12970854 TCACTTTTTGATAGAGTCAGAGTTGTACCTTAACT[C/T]TTTTGTCTTTTAGTAATTAAGGTCCATTTACATAT Y 2 1 2 1 201000 r 74 goat snp44486-scaffold604-2499255 27 31453688 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434632 Affx-122933999 AX-123304973 27 13014664 GAGCCCAGTGCTGGGCACTTTACATACATTATCTC[A/G]CTCATCCCCTTGACAGTCTTAGGAAAAGGGTGTGA R 2 1 2 1 201000 r 74 goat snp44487-scaffold604-2543065 27 31410017 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402187 Affx-122959178 AX-123272540 27 13043665 TAAAACCCATCCCAGCAATGAGAGCAAAATCCCCA[C/T]GAATTGCATTGCTACTCTCAAAACTAAAGCCATTG Y 2 1 2 1 201000 r 74 goat snp44488-scaffold604-2572066 27 31380991 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275087 Affx-1111834679 AX-519548666 27 13123887 CAGACGTCTGAGGCAGGGTAATCAATCACTTCATC[A/G]CTGCTACTGCAGATAAAGAGAGCGGTGAGACAGGA R 2 1 2 1 201000 f 74 goat GoatD01.045554 27 13123887 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320801002 Affx-122968597 AX-385287916 27 13150593 TGTATCTGAAATAACTGTTGGGAAATGGTTTCTAG[A/G]CATTCTATTTGTAGAATTTTAAAGGGACAGTCTAC R 2 1 2 1 101000 r 74 goat snp44490-scaffold604-2678994 27 31274319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790062 Affx-122977345 AX-385277068 27 13197312 GTGAATGGAACTTGAGTGCAATGTCCTATTTTACA[C/T]ATTCTCAATTTAACACTAAGAGAAACGTAAATACT Y 2 1 2 1 101000 f 74 goat snp44491-scaffold604-2725713 27 31227291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420977 Affx-122944575 AX-123291324 27 13228370 CAAAGAGGAACCTTAATGTTTTGCCAAAGGTGAGA[A/C]TCAGAGAGCAGGAGGTCATTTCACTTGCGCACAGA M 2 1 2 1 101000 f 74 goat snp44492-scaffold604-2756771 27 31196262 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432850 Affx-122935367 AX-123303191 27 13281748 GGGCTCCTCTGGGGACGGTCCTCAGTGGGAGGAGG[C/T]GTCGTGTTGTAATGTTACACCACTCTGCTACCGAT Y 2 1 2 1 101000 r 74 goat snp44493-scaffold604-2810149 27 31142823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794723 Affx-122977157 AX-385281683 27 13311672 AGTTTACAGAAGTAAGAAGAAATAGTTCATGAGAT[A/G]TCATTTAAATGAGATTTAAGGAGACCCCTATGTAC R 2 1 2 1 101000 f 74 goat snp44494-scaffold604-2840073 27 31112914 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448644 Affx-122923357 AX-123318980 27 13370485 AGGGGGTGTTTTATCAGGATTGCCTACCTGAAAAT[C/T]GAACAAAGTAAACATGTTAAAATAACCAGCGCATG Y 2 1 2 1 101000 f 74 goat snp44495-scaffold604-2898886 27 31053667 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774524 Affx-122919698 AX-385261658 27 13424671 GAAATACAGCTAAATCCAAATGTAACCTCAAAACA[C/T]GTCTGTCCATAAACCCATGTCTGCTCTGGGTGTTC Y 2 1 2 1 101000 r 74 goat snp44496-scaffold604-2953072 27 31001023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795152 Affx-122933863 AX-385282110 27 13456836 GCGTGGTCCTCAGGGGTATGTAGTACATCAAAAGT[A/G]TCTAAAACCCTCAAGGATTAGTAAGTAGTTAGCCT R 2 1 2 1 101000 f 74 goat snp44497-scaffold604-2985237 27 30968969 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434363 Affx-122934713 AX-123304704 27 13487520 CCCGTCTCCTCCATGAATCCTCCTGTGCCAGCCAT[A/G]CTAGACAGACCATTGGCTGTGCTCCAGAACCTCCT R 2 1 2 1 201000 r 74 goat snp44498-scaffold604-3015921 27 30938380 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273121 Affx-1111833321 AX-189922780 27 13498276 AGCACGCCAGGCCTCCCTGTCCATCGCCATCTCCC[A/G]GAGTTCACTCAAACTCACATCCATCGAGTCGGTGA R 2 1 2 1 303000 f 74 goat 27_13498276_AF-PAKI 27 13498276 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435040 Affx-122933753 AX-123305380 27 13526889 TGAAGCACTTTGGGCCTCTCTGCCTTCACTTGCAT[A/G]TTACCGTATTGAGCCCAGATTTCATTGGAATTAAA R 2 1 2 1 101000 r 74 goat snp44499-scaffold604-3055290 27 30898708 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381227 Affx-122974509 AX-123251585 27 13556632 ACCCTTTTCTAGTGCCTGCAGACAGCAGCCTGGCC[A/G]CCTCTTCCGACTCCATCTGTGTCCATCCGTTCCCT R 2 1 2 1 101000 r 74 goat snp44500-scaffold604-3085033 27 30869100 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410732 Affx-122952708 AX-123281082 27 13600627 GTGATGACGAGTGTAGCAGTACGAGCAACTGACAA[A/G]AGAGGAAGCAATGGAAAAGGAATGAAGGCTAACTC R 2 1 2 1 201000 f 74 goat snp44501-scaffold604-3129028 27 30825350 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800060 Affx-122922695 AX-385286983 27 13666220 ATGGGGCGTATGTAAATAACCCTTGAATTTGGAAA[C/T]ATCACTATGGTATATAATAAGTTCTATCACTATAA Y 2 1 2 1 101000 f 74 goat snp44503-scaffold604-3194621 27 30759745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773466 Affx-122926823 AX-385260608 27 13721478 AGTGTGCTTGTCTGATTTATAAGTTCGCTGAAATG[C/T]ACCTGATTTCAAACTTGCTGAGTCAATATGTCCTG Y 2 1 2 1 101000 r 74 goat snp44504-scaffold604-3249879 27 30703949 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776208 Affx-122962198 AX-385263336 27 13753897 AAGGTCAGGTTAGTCTCCCAAGTGCGTGTTTCAAG[C/T]GCATGTTTTCAATCAGCTAGAGCTCAAAAAGCACT Y 2 1 2 1 101000 f 74 goat snp44505-scaffold604-3282298 27 30671557 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432942 Affx-122935296 AX-123303283 27 13797511 GAGGAGGGAGGAAGATTGCTAAAGCATGCAACCCC[G/T]AAAAAGAAAAATTGTACCATTTTCACGACATTTTT K 2 1 2 1 201000 r 74 goat snp44506-scaffold604-3325912 27 30628010 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277716 Affx-1111836053 AX-519551215 27 13812292 TCCCAGCAAAATGGAGTATGAAGTACAACAAAGCA[A/G]TTTATTCCAGATCCAGGATAAAAAAAAAAAAAAAC R 2 1 2 1 101000 f 74 goat Random2.2K-2225 27 13812292 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38403759 Affx-122958002 AX-123274111 27 13842904 AGATTGTTCAGGATTGACCATACTAGACTTGGTCA[C/T]ATTCCAAATACTTATGTGAAGTATGTATATAACAC Y 2 1 2 1 101000 r 74 goat snp44507-scaffold604-3371305 27 30582402 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427818 Affx-122939748 AX-123298161 27 13887504 CAAAGTGAAAAATGAAAACAAAAATTTCATTGCTG[C/T]ATTATTAAAATTCCTTCAAATATTTTATAGGAAAA Y 2 1 2 1 303000 r 74 goat snp44508-scaffold604-3415905 27 30537492 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436121 Affx-122932653 AX-123306460 27 13921296 ATTTTGATCATACAAAGAAGGTTTAAGAGTTCCTG[C/T]TGAAGGATTCGTAGGATCCTGGCTCTGTTTTTACT Y 2 1 2 1 101000 f 74 goat snp44509-scaffold604-3449697 27 30504210 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417850 Affx-122946780 AX-123288198 27 13954273 TAATCTGGAGAGCCTATGAATTTTTGAACATAAAT[A/G]TGTAGTAATAATTTGGGAGAATGGCATTGAAACAT R 2 1 2 1 101000 f 74 goat snp44510-scaffold604-3482674 27 30471536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408668 Affx-122953460 AX-123279019 27 13990250 GCCTTTCCTCTGCCCCTCTGTCTTACTGAAATTTT[A/G]CCCAAGTCTAATAAAGGCAGTAGAGAAACTATCTC R 2 1 2 1 201000 r 74 goat snp44511-scaffold604-3518651 27 30436383 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416515 Affx-122947774 AX-123286863 27 14050435 GAAAGAGCAAAGTCCTAACCCTTTGGTTAGCAGAT[C/T]GGGGAGACAAAGTGTTCACCCGCCTTTGTAACTGA Y 2 1 2 1 101000 f 74 goat snp44512-scaffold604-3578836 27 30376742 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397113 Affx-122962691 AX-123267468 27 14078951 CTACCCTATAATCTGTTAGGAATGTCAGTTTCCCA[C/T]GTAGCATCTACTAGTTACCATCATCAGCTATAACA Y 2 1 2 1 101000 f 74 goat snp44513-scaffold604-3607352 27 30348253 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801149 Affx-122922893 AX-385288063 27 14136114 TCAAATGGGTACTGTTAACCACCAGTCATCCAAGC[A/G]ACGTTTGGTGACATTTCAATCTTCCTCTAACCTTC R 2 1 2 1 101000 f 74 goat snp44514-scaffold604-3664515 27 30290784 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379338 Affx-122976172 AX-123249697 27 14168577 TTCACCTTTCAGAGTGTTTGTATCTGGAAGATCAA[C/T]GACATGGTCACCACCTATACCCCGCCTCCTTTACC Y 2 1 2 1 101000 f 74 goat snp44515-scaffold604-3696978 27 30258112 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277718 Affx-1111836054 AX-519551217 27 14169644 AACCAGGTAACCTACATCTTCAAAGGAATTCACAG[A/G]GCACTCCTTCCTGTTTCTTCCCTCACTGCTGAGAA R 2 1 2 1 101000 f 74 goat Random2.2K-2226 27 14169644 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38437876 Affx-122931677 AX-123308214 27 14204367 AGGGGGAAAGTCCTTCCAGGTCACTGAGAAGAAAG[C/T]GCCAAACTAAGCCCTGGCACTGGCTTGGTCCTGGC Y 2 1 2 1 201000 f 74 goat snp44516-scaffold604-3732768 27 30222301 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448295 Affx-122924167 AX-123318631 27 14242105 CACCCTACTGGCCCTTCTCTTCTAAGCCCTTTTTG[C/T]AAAATAAATTATTTATTTTGGCTGCGCTGGGTCTT Y 2 1 2 1 103000 f 74 goat snp44517-scaffold604-3770506 27 30184594 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783498 Affx-122972001 AX-385270561 27 14334181 ATTTTAAGTGGCAACATTCAAGCAAGCATAAAATA[C/T]AGGGAGACTAAACTCCTGTCTGATAGTAAGCTAAG Y 2 1 2 1 101000 r 74 goat snp44519-scaffold604-3862582 27 30090972 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432823 Affx-122935389 AX-123303164 27 14369655 TCTAAATTGAGCTTTCTAAGACTCACAGTTTGAAA[C/T]GGTCTGGAATGGTTGATAAAATTTTTAAGATCTAA Y 2 1 2 1 101000 f 74 goat snp44520-scaffold604-3898056 27 30055737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439542 Affx-122930107 AX-123309879 27 14407622 ACAGAGTTTGCTCCTGTCTGCTCACGCCGAGCTTC[A/G]TCCTGCAGTCCTCTTATTTCTGCCAGCCCACAGGC R 2 1 2 1 201000 r 74 goat snp44521-scaffold604-3936023 27 30017696 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401558 Affx-122958898 AX-123271911 27 14454231 CTGCTCTATATAGATGCTGCACACGTGGGGGTGCC[A/G]TGCCCATCGTGCACCTTGTATAGAGTGTAAGTAGA R 2 1 2 1 101000 r 74 goat snp44522-scaffold604-3982632 27 29970967 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388443 Affx-122969261 AX-123258801 27 14493672 GTTAGAGCATACCTGCCAAGTTCTTGATATAAAAC[A/G]TAAGTTCTGAAAGAGAAATGATTAAAAATTAGTAA R 2 1 2 1 101000 f 74 goat snp44523-scaffold604-4022073 27 29932058 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394946 Affx-122964291 AX-123265301 27 14506974 GGGGTCTAGAATAGATTGCAGCTCTATTTTATCAC[A/G]TTTAGTTTCAAGTAATCAAGTGGTTAGGGGTCGTC R 2 1 2 1 101000 f 74 goat snp22220-scaffold2192-12249 27 29855610 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411766 Affx-122951492 AX-123282116 27 14537652 TCATTTAGAAAACAGCATTTTTATTTCTGAAAAGC[A/G]TCTTTCCTGTCTTGTGATAACTACATTATAATTTT R 2 1 2 1 201000 r 74 goat snp22221-scaffold2192-42927 27 29824534 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764207 Affx-986698734 AX-385251939 27 14565209 AACTGTGTGGCTACTGGTTATAGTTTAGATGATCA[C/T]TAGATACTTTTGAAATATTAGAAATAAAAAATAGA Y 2 1 2 1 600010 f 74 goat 27_14565209 27 14565209 Ancestral_priority_1043 ancestry 0.554 neutral IMAGE 10K 10K ancestral 320764209 Affx-986698736 AX-385251941 27 14565233 TTAGATGATCATTAGATACTTTTGAAATATTAGAA[A/G]TAAAAAATAGAAATAAGAGAATACTGAAGTATTAT R 2 1 2 1 600010 f 74 goat 27_14565233 27 14565233 Ancestral_priority_1043 ancestry 0.71 neutral IMAGE 10K 10K ancestral 320768568 Affx-122939581 AX-385255748 27 14600504 TTTAACATTGTCTCTAAAAAGTGCCTAATGTATTC[C/T]GAGGAAATAGTTTACACACACCAGGAAAATCAGGC Y 2 1 2 1 101000 r 74 goat snp24077-scaffold2457-11263 27 29761522 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387904 Affx-122970460 AX-123258262 27 14649213 CTAGTGGGTCTTTCCAGGCTTCTGTCTATAGAGGA[C/T]TGATACAATGAGGCCTGTTAAGACAGAAGGATAGT Y 2 1 2 1 201000 r 74 goat snp24078-scaffold2457-59972 27 29712851 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398678 Affx-122961873 AX-123269033 27 14688357 AGTTCTTCCCCCTTCAAAGCCGCTCTGTCTGCTGC[A/G]TGAGGGCTCTTTGACTACCCTATTTAACATGGACT R 2 1 2 1 101000 r 74 goat snp24079-scaffold2457-99116 27 29673801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445686 Affx-122926128 AX-123316023 27 14720290 ATGTTTGTTTATTATCTCTTTCCCACCCCAAGAAC[A/G]TAAGCTCAGAAGACCAGGGACTTTTCTCAGGAGAA R 2 1 2 1 201000 r 74 goat snp24080-scaffold2457-131049 27 29642119 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394205 Affx-122964906 AX-123264560 27 14758273 ATCTTAAATTCCCTTTGTTTAACTTATTTTAATAC[A/G]TGGAGGAGTTCAAGGTAAAAGATGCCTCCTAAAAA R 2 1 2 1 101000 r 74 goat snp24081-scaffold2457-169032 27 29604197 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389491 Affx-122968315 AX-123259849 27 14788315 TAGAAGAACATTAGAGCACCGGTTTGGAATCTGGC[C/T]GGCCCAAGTTTGATTCCTCCCTTCCCCTCAAGTGT Y 2 1 2 1 101000 f 74 goat snp24082-scaffold2457-199074 27 29574097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410991 Affx-122952005 AX-123281341 27 14818594 TGGTTTCCCTTCTCCACTGCTACCACTACCTGCCC[A/G]TCCCCCACCAGCACCATCTTTGTCGCCATCGTCAT R 2 1 2 1 101000 f 74 goat snp24083-scaffold2457-229353 27 29543781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786085 Affx-122927170 AX-385273121 27 14865153 GCTAGAAACGATGGTACCAGTTAGTAAAGCTGAAC[A/G]TCACAATCATTGGAACCAGTTCACAGGTTTCTCCT R 2 1 2 1 101000 r 74 goat snp24084-scaffold2457-275912 27 29497174 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277720 Affx-1111836055 AX-519551219 27 14869067 CCATTTCAACTCTACTAAGGCTGAATCTTTAAAAG[A/G]AACAAACATTAAAATGATTTCCGGGAGCTGAAGAC R 2 1 2 1 101000 f 74 goat Random2.2K-2228 27 14869067 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320776884 Affx-122975139 AX-385264008 27 14905908 TTAACCAAGAGATCAAATGCAGCATGGCTGAAGTT[C/T]GACATCATTAGAGTGTGACGCCATATAAAGCGTCA Y 2 1 2 1 101000 f 74 goat snp24085-scaffold2457-316667 27 29456865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382364 Affx-122973866 AX-123252722 27 14988589 GAAAGCATCGCCTGGTTTGTTAATTGGATTAATAG[C/T]ACCCACACCAACATCTCTGAGCTGTCAAACCATTA Y 2 1 2 1 101000 f 74 goat snp24086-scaffold2457-399348 27 29376038 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787988 Affx-122932548 AX-385275009 27 15035453 TTAGGTGTTTTAAGGACATACAGAGATGATCACAG[C/T]GTATTCTCTGAAATAGTCGCGTGAAAAGTATTATA Y 2 1 2 1 101000 f 74 goat snp24087-scaffold2457-446212 27 29329835 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454204 Affx-122919289 AX-123324537 27 15083388 GCATTTTTGTTAGAAATTCAGGTTTTTGTTGATGT[A/C]TTTATTAAAATATGATGTTTTTATTAAAATATTCA M 2 1 2 1 303000 r 74 goat snp24088-scaffold2457-494147 27 29281865 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403865 Affx-122957925 AX-123274217 27 15127256 CAAGTCAGCTTCACGTAGTGTTTCTAGTTTGCTTA[C/T]GCACTCGCTTTGCTGAAAGAATAACCTGGTAAATG Y 2 1 2 1 202000 r 74 goat snp24089-scaffold2457-538015 27 29237921 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399353 Affx-122961352 AX-123269708 27 15161685 CCCCTGCTCTGCGTAGGGGTTTGATCTAGGGCATT[A/G]CACAGAGAAGCTGTGGACAAGAAGCTGTACCTTAA R 2 1 2 1 102000 r 74 goat snp24090-scaffold2457-572444 27 29202782 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397617 Affx-122962633 AX-123267972 27 15209366 TGCCATGCATAGCCTCCAATTTCTTTTAAAAAATA[C/T]GTTAAAAAAAACCCTGAGCAATAATAAATAAAAAC Y 2 1 2 1 303000 r 74 goat snp24091-scaffold2457-620125 27 29154812 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442814 Affx-122927711 AX-123313151 27 15238623 TCGCAAGGGTTCTTAAGGGGAGCAACTTTCCCAGC[C/T]GTGGCTGGAGAGCTAGGACTACAACAGACAGACCG Y 2 1 2 1 101000 f 74 goat snp24092-scaffold2457-649382 27 29124912 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38385281 Affx-122972066 AX-123255639 27 15268030 TGGACTGATGGTAGCCCCTACCTGCCAAGCACAAG[C/T]GTGAATGCTCCTAGCAAGGCACCTGGCACATAAAA Y 2 1 2 1 101000 r 74 goat snp24093-scaffold2457-678789 27 29097265 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416685 Affx-122947577 AX-123287033 27 15314084 CCTTTTGGATAGGGTACAGTATTAAATAAAAGAGG[C/T]GTGGTTTCCATTTACTATTCTGAGTTTTGACTAAC Y 2 1 2 1 101000 r 74 goat snp24094-scaffold2457-724843 27 29050414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404576 Affx-122957366 AX-123274928 27 15350366 GGACAGATGGACGAGGATCGGGCATGGAAAACAGA[A/C]GGCAGGACCGAAGGGAGGCTGCTGGCAGGGGGATA M 2 1 2 1 101000 f 74 goat snp24095-scaffold2457-761125 27 29014369 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385934 Affx-122971559 AX-123256292 27 15380697 GTTGAGGGCTTGCATTACAAACCAAAATAAGATAC[A/G]TTTTTTTGATGAGTGGCTAGCTCGAGGGTAGAACT R 2 1 2 1 201000 f 74 goat snp24096-scaffold2457-791456 27 28984090 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791295 Affx-122922667 AX-385278289 27 15427782 AAAAGGTCTTTCCTAGGAGCCTTTCAAAGAAAGCT[A/G]CAACATTATTAAGTCCCAAATATTATCTTAGGTCC R 2 1 2 1 101000 f 74 goat snp24097-scaffold2457-838541 27 28937050 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425435 Affx-122941525 AX-123295781 27 15471426 CTGACGGGGAGGCATTAATGCTGTTTGATTCCATG[C/T]AGGCAGAATATATCCAGCTGTGGAGGCCTGGAAGG Y 2 1 2 1 101000 f 74 goat snp24098-scaffold2457-882185 27 28893409 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787673 Affx-122973731 AX-385274696 27 15525365 TGGATGCTTAATGGAAAATTGTTCTATAGTTGATC[A/G]TGCTATTGATTATGATTTATGATCAGAATTGGAGG R 2 1 2 1 101000 f 74 goat snp24099-scaffold2457-936124 27 28839439 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416935 Affx-122948038 AX-123287283 27 15531149 CTATCTCAAAGGCCCCAAACCACTTCCATTTACTG[C/T]ACAAAGAAATTCAAAGCCTTCTAGCCAAAGTCAAC Y 2 1 2 1 101000 r 74 goat snp47495-scaffold669-1264418 27 28833564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448182 Affx-122924251 AX-123318518 27 15585945 ATACTTCAAAGTATTAATTTTTATTTAAACCAGAA[G/T]AGAAAGATCGCTAATGCAGTTATTTCCTAAACTAC K 2 1 2 1 101000 r 74 goat snp47494-scaffold669-1209622 27 28778015 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435599 Affx-122933795 AX-123305939 27 15665234 TACTAGGATCCTACTTGCTCTAATGTCCATTCTTA[C/T]GCTTCACTTCCTTCTCTGTGTTCCTCATGCCAAGC Y 2 1 2 1 201000 f 74 goat snp47492-scaffold669-1130333 27 28698763 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411535 Affx-122951659 AX-123281885 27 15698128 AGCAAAGCAGAGTATAACACCCCCATCCAGGGCAC[A/G]CGGTTCTTTCAGGGGTTCTAAACGCTATATGCATC R 2 1 2 1 101000 r 74 goat snp47491-scaffold669-1097439 27 28666118 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438589 Affx-122931151 AX-123308926 27 15733537 TTGACTCTAGGCTCCTTGAAAATGTCCTAAGTCAA[C/T]AGCCTCACAAAAAATATTTTGGGGCTCTTATTATT Y 2 1 2 1 201000 f 74 goat snp47490-scaffold669-1062030 27 28630623 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776532 Affx-122926981 AX-385263659 27 15768914 ACTTCGTATCTATGGGGTTTCATTAGATTCTGTTC[A/G]TATGTTAGGGTCTTTGATTCTCATAACTTTATGAT R 2 1 2 1 101000 f 74 goat snp47489-scaffold669-1026653 27 28595004 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400521 Affx-122961265 AX-123270876 27 15831334 TTTAACCTCAGGGCTGCATGGGGACAACCATAGTT[A/G]TGCATGTTTGGAAGTAAAGATAAATTTCTTCTATA R 2 1 2 1 201000 r 74 goat snp47488-scaffold669-964233 27 28532609 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769497 Affx-122965530 AX-385256667 27 15860310 TGGTGTTTATTTAAAGTTCAAGGCATTTCTTAAAC[A/G]TAAGTATTTGGTCCAATGGGTCACTGATTTCATTT R 2 1 2 1 101000 r 74 goat snp47487-scaffold669-935257 27 28503673 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428113 Affx-122939077 AX-123298456 27 15890537 GGGCTGCTCCCTGTGGTCTGTGGTTACCCTCTGGA[C/T]GAGCATATTAAATGGAGAAGGATCCTTTAGATCTT Y 2 1 2 1 101000 r 74 goat snp47486-scaffold669-905030 27 28473625 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771295 Affx-122965588 AX-385258453 27 15923817 TTTACTTTCCACTAAATTTCTCATTCAACCTGATC[A/G]TTAAAAAATGTGCATTTATGAGAATGCCAAGACAA R 2 1 2 1 101000 r 74 goat snp47485-scaffold669-871750 27 28440558 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389787 Affx-122968219 AX-123260144 27 15967039 TTTGTCTTGTCTCTTACTAGGATTATAGCTAAGTA[C/T]GTCACGCAAACTATGTCTATTTAATTTGACCATTT Y 2 1 2 1 101000 f 74 goat snp47484-scaffold669-828528 27 28397268 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380405 Affx-122975318 AX-123250763 27 15995807 AAAGTTTTGAAGAGTTAGACTATAAATATGTAGTC[A/G]ACAGTGTCATTACTGATACCTGTAGGAATATTGAG R 2 1 2 1 101000 r 74 goat snp47483-scaffold669-799760 27 28367244 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416177 Affx-122948260 AX-123286526 27 16031404 CAACTCATCTTTCATGCTTCCCCTGGTCAGCCAGG[C/T]ACATCACAACACAGTTTTTGCCCTCCATCCTGCTT Y 2 1 2 1 101000 r 74 goat snp47482-scaffold669-764163 27 28331650 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273168 Affx-1111833322 AX-519546828 27 16050550 AGATGCTCATCTTGCTTGATTTGCCTTGGTTGATG[A/G]AATCATTTATCTCTGATGTCTCATGTCTTCTGCCG R 2 1 2 1 101000 r 74 goat 27_16050550_AF-PAKI 27 16050550 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38435351 Affx-122933595 AX-123305691 27 16061358 TTTTAAAACTGTTTATTTGCTGAGAGTATCTTCAC[A/G]TAGTGGCAAACAGTATTTGGGGGCTTTTGGTTTGT R 2 1 2 1 201000 f 74 goat snp47481-scaffold669-734209 27 28301863 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383117 Affx-122973265 AX-123253475 27 16099138 TTTGATTCTGCAGCTTATATTCTATCAGTACTGAT[A/G]TTGAATTACTGCATGTCAAACTTCCGAAATGGCGT R 2 1 2 1 101000 r 74 goat snp47480-scaffold669-696429 27 28263049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411243 Affx-122952337 AX-123281593 27 16139408 GTGCTGAGTTTAGTGGCAAGAGATCCAAAGTCTCC[A/G]TTTTCATGCGTGAGTATTTTCTAAGGTTTAGCTAC R 2 1 2 1 201000 r 74 goat snp47479-scaffold669-656159 27 28222528 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427942 Affx-122939210 AX-123298285 27 16189448 GCACAAGCTGCCTTAAAGAAATGTTATTGTTCTTA[G/T]AATGCTGTGGTTTTAAATTATAGTTCTTATTTTCA K 2 1 2 1 201000 r 74 goat snp47478-scaffold669-606119 27 28172453 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780621 Affx-122946285 AX-385267711 27 16227302 TTCATAGCATAGAGGCAAAACACTAAACCAGGTAT[A/G]TTTCTTGAGAAAAAGGAATGTGTTTATTATTTTTC R 2 1 2 1 201000 r 74 goat snp47477-scaffold669-568265 27 28134560 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797768 Affx-122934459 AX-385284707 27 16268211 ATTCTCAGAAATACATTATATAAATGTGTCTTCAA[C/T]GGAGATAGTGTGTCCTCAATGAAGGTAGGTGTGCA Y 2 1 2 1 201000 f 74 goat snp47476-scaffold669-527356 27 28093653 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389728 Affx-122968670 AX-123260086 27 16337228 CTCACATCACCCATATGCCTCTGGCTTTCAAACCC[A/G]TATCCCCCAGTGTCCTTTGCTCTCACCTCAGAACG R 2 1 2 1 202000 r 74 goat snp47474-scaffold669-458339 27 28024150 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416439 Affx-122947828 AX-123286788 27 16379748 ACCAGAGAAGTGCCCAGAATATTTTAAATAGAAGT[A/G]CGAACTCTGAAATTGAGAGAGACTATCTGAGTGCT R 2 1 2 1 201000 r 74 goat snp47473-scaffold669-415819 27 27981640 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400770 Affx-122959877 AX-123271125 27 16422954 CCGTGTCTCAGATAAGGACACTTGCCATTGGATCT[A/G]TTACCCAGGGAGTTGCCTAGATCTGCAAGGACCAA R 2 1 2 1 101000 r 74 goat snp47472-scaffold669-372613 27 27938352 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435167 Affx-122933659 AX-123305507 27 16456825 CTAGGGCATGAATTATAGTTGGGTGAATCCTAGAG[C/T]TGGAGGTCTTAGGCATAGCTGGGAATTCATGAATT Y 2 1 2 1 101000 f 74 goat snp47471-scaffold669-338742 27 27904416 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771061 Affx-122933116 AX-385258221 27 16506537 TTCCTTCCATTTCTAGACAAATGCTTGCATACCAC[A/G]TATGTTGTTCTGCACGTTGCTTTTTCTAAGTAAGC R 2 1 2 1 101000 f 74 goat snp47470-scaffold669-289030 27 27851239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410104 Affx-122952831 AX-123280454 27 16550861 CTGTTAAACAGTTAGACTCCAATAAAGAATAAAAA[C/T]GCTCAAAAAAGACTCTAATGTTTAATAATAATCAC Y 2 1 2 1 102000 r 74 goat snp47469-scaffold669-244706 27 27807144 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422871 Affx-122943080 AX-123293217 27 16588548 TCTACATCCTGACTATTCCTTCAATTCAACAAGCA[G/T]CACACAAAGATACACTTTTCTTACATTCTTTACTT K 2 1 2 1 101000 f 74 goat snp47468-scaffold669-207019 27 27769634 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277857 Affx-1111836056 AX-519551353 27 16611473 TCTAGTACAGTAAGCCCCAGACATGCGAACCATCA[A/C]GGTGCACACTTTCACAGATGCGAACATGTGTTCCC M 2 1 2 1 201000 r 74 goat Random2.2K-2229 27 16611473 T G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320785943 Affx-122952614 AX-385272980 27 16691300 GAACTCTGTTCTACATTATTGAATAATTAGTAGCT[A/C]AAGATGGAAGATAATCCATGAGAGTTTAACTAACA M 2 1 2 1 101000 r 74 goat snp47466-scaffold669-104267 27 27667708 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420207 Affx-122945545 AX-123290555 27 16726515 GGTCCTGAGCTCATAGTGAGCATGAGCTCTGAAAC[A/G]CTGATAAACAAAGTGCAAGGCCAACAGGATATTCT R 2 1 2 1 101000 f 74 goat snp47465-scaffold669-69052 27 27632488 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775451 Affx-122967689 AX-385262582 27 16757571 ACAAAGATAGAATTGCCTTAAGGGGAATATAAGTA[C/T]AGCTTTTCTTTTAAGGGAAAATCTATTGTCACAAA Y 2 1 2 1 101000 r 74 goat snp47464-scaffold669-37996 27 27601146 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799531 Affx-122951346 AX-385286461 27 16794138 ACAATCACATTCCCATAGCATGGTAATCTATTGCT[A/G]TAGAGCTAAGCAATAATTAACAGGAGTAGGATTTT R 2 1 2 1 201000 r 74 goat snp47463-scaffold669-1429 27 27563437 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378050 Affx-122977191 AX-123248409 27 16810530 AATACACATCCAATTTGTGATCATTATAAAATAAT[A/G]TCAGAGGAACCTACACAGATATATTTTACAAACTC R 2 1 2 1 101000 r 74 goat snp26284-scaffold275-2717923 27 27547125 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419215 Affx-122945693 AX-123289563 27 16844928 TACTTTAATCTGAAAAGATTCCAGATGCTACCTCA[C/T]GCTAACATCATTATCTACCTTCCCAGGAGATTCAG Y 2 1 2 1 101000 r 74 goat snp26283-scaffold275-2683525 27 27512107 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401885 Affx-122958850 AX-123272238 27 16940232 TGTTCCAAGTTGTTGTAAGCTGCTGGCATCTTTGA[C/T]GTATTTGCTAAGGAGGGTAGATCTGGCTCATAGGA Y 2 1 2 1 101000 f 74 goat snp26282-scaffold275-2588221 27 27416916 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388110 Affx-122969490 AX-123258468 27 16969240 ACATGAGCTTTTCTTATTTTATGAATATAAATTTA[C/T]GTATCATTATTAAGTGATTTTGATATCCTTTGAAG Y 2 1 2 1 103000 r 74 goat snp26281-scaffold275-2559213 27 27386720 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802661 Affx-122939414 AX-385289560 27 16999410 ATGGTTGGGCTAACATATCTGTTTTGGTTTTCCAA[A/G]ATGTGTGTATTTTTAGTCCACTCTCAAAAGATGGA R 2 1 2 1 201000 f 74 goat snp26280-scaffold275-2529043 27 27358358 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438880 Affx-122930741 AX-123309217 27 17040715 CCCTTTCTTGGTGGAAGGAACCCCTTGAGTGCTCT[A/G]TTTTAGGTGGGAGATTATCTTATAAGTCCCTGCTT R 2 1 2 1 201000 r 74 goat snp26279-scaffold275-2487738 27 27317107 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775278 Affx-122944204 AX-385262409 27 17070292 TTAGAAATCAGATTGTATCCTATAGAAAAGAAAAT[A/G]GTGTTTCCTGTAAATGAGAAATATTAGGGAAGCTG R 2 1 2 1 101000 r 74 goat snp26278-scaffold275-2458161 27 27287117 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397467 Affx-122962093 AX-123267822 27 17099845 TGCAACTAAGGAACTGAGGCTCAGAGATAATGGCC[A/G]TAAAGAAAAAGTGACAACAGGGTGATATAAACTAA R 2 1 2 1 303000 r 74 goat snp26277-scaffold275-2428608 27 27256587 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786908 Affx-122924213 AX-385273937 27 17148956 TGTTTTTTTTAGTTTATTTGAACAAGATATAAATA[G/T]TATGTTTATAGACCAGGCATTGAGTCAAGGAAATA K 2 1 2 1 202000 f 74 goat snp26276-scaffold275-2379497 27 27206852 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395971 Affx-122963556 AX-123266326 27 17181427 GTTTATTTATTTATATATTTTAGGACCCATATCTT[A/C]TTATCAGTTCTCCATTGACTACTTTTATTTTACTA M 2 1 2 1 103000 r 74 goat snp26275-scaffold275-2347026 27 27174821 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802255 Affx-122977929 AX-385289159 27 17299777 GCTATAACCTAAAGCACAAGGCCACATCGAAAATC[A/G]GTGTTTTTGTTCATTGTATCTTTGACATTTTTGCA R 2 1 2 1 101000 f 74 goat snp26273-scaffold275-2228676 27 27053938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383252 Affx-122972744 AX-123253610 27 17353583 ATCTTCTCTCTTACCAATAAATATCACTTTGATAT[A/G]TTTTATAAATGACCAATATTGCTATCTATAGCAAG R 2 1 2 1 101000 r 74 goat snp26272-scaffold275-2174870 27 26991715 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420814 Affx-122944677 AX-123291161 27 17421808 TTTTAGGACTAGTAAGAGGCTAAGTGTGGCTTTTA[G/T]AGGTGCTGCCCTGTGGAAGTGGTTTAACTTGTCCA K 2 1 2 1 101000 f 74 goat snp26270-scaffold275-2106645 27 26924344 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778729 Affx-122967308 AX-385265840 27 17478024 GGGGTGATTTCATTAAATCTCCAGATAATTTAAAC[G/T]AAAAACTATTGTGAAAAAAATGACCATTTGGAAGA K 2 1 2 1 103000 r 74 goat snp26269-scaffold275-2050429 27 26867547 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430628 Affx-122936963 AX-123300969 27 17522035 ACTGAAAACAAGTGGGGAGAAATGAAAGGAACTGT[A/G]TGGATGGTGTTACTGCACAAATATATCCTGGGTTG R 2 1 2 1 101000 r 74 goat snp26268-scaffold275-2006418 27 26823514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392584 Affx-122966065 AX-123262941 27 17576424 GAGGGGCTCTGGCTGCCTCATTCAGCCACAGATTG[C/T]GTTTCAGGCCCAGCGAGGAGGCAGGAGATACCTGT Y 2 1 2 1 201000 r 74 goat snp26267-scaffold275-1952029 27 26767756 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273646 Affx-1111833747 AX-519547259 27 17607218 AAGTCATAGCAACTTAGCCTGCAGACACAGACCAC[A/G]TG R 2 1 2 1 103000 f 74 goat GoatD01.003499 27 17607218 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38393256 Affx-122965463 AX-123263613 27 17607305 TACTGAGCCACCTGGGAAACCATTATAAAGAGACG[C/T]AGGGCTATTGGAATGTTAAGATCATGTTTATGAAG Y 2 1 2 1 201000 r 74 goat snp26266-scaffold275-1921148 27 26736858 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447540 Affx-122924049 AX-123317876 27 17637618 TTCTTGGCAGACTTTGGGTTCCCTTAAGGAAACTA[C/T]AGCACTTGCTATTCTTGGGAGATTATTAGAGGTAG Y 2 1 2 1 101000 f 74 goat snp26265-scaffold275-1890835 27 26706657 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784763 Affx-122963253 AX-385271810 27 17699515 AGCAAGATACACTGCTATCAGAGAATGACTGCTAC[A/G]CCATGGTCGATATTGTCCACTATCATTAAAAAATA R 2 1 2 1 101000 f 74 goat snp26264-scaffold275-1828938 27 26644690 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448553 Affx-122923426 AX-123318889 27 17735755 GCTATGCAATGTGTTTTAATTTATGTGATGATTTG[G/T]GTGATGTTTTCTGCTCACTGATTGAGAGCAGGGTC K 2 1 2 1 101000 r 74 goat snp26263-scaffold275-1792698 27 26608983 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770856 Affx-122927361 AX-385258020 27 17765013 TGTTTGAACTCAGAATTTGGAGAATAAAGGATATA[C/T]ATTGGTAAATAAGAAATATCCTCACTTTCATCCCT Y 2 1 2 1 201000 f 74 goat snp26262-scaffold275-1763440 27 26579718 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415441 Affx-122948712 AX-123285790 27 17794697 TAGGGCCTATAGTGATGAAGTAGTAAGTGCTAGAA[C/T]AGAATAAAGGGTGAAATATTATTGCTGGATACAGT Y 2 1 2 1 101000 f 74 goat snp26261-scaffold275-1733756 27 26549904 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794553 Affx-122944407 AX-140726646 27 17828899 GATGTAAATTAGTCAGGGTGTGACTGGACCATGAA[G/T]ATTCAAGACAGGTTATTGGAATGGCCATGAGTCAT K 2 1 2 1 201000 f 74 goat snp26260-scaffold275-1699554 27 26515754 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431255 Affx-122937123 AX-123301596 27 17906414 GCCTCTTTCCAATCCATTTTCTACATTATAGGCAA[C/T]GTGATATTAAAATACAAATATGATCATGTCACTTC Y 2 1 2 1 101000 f 74 goat snp26258-scaffold275-1622039 27 26438055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411386 Affx-122952229 AX-123281736 27 17944137 TGTTGGCCTGTGCAGGACAGAAGGCCCACAGCTTG[C/T]ACCTTCCCTTCCCTTTTACTTCGTCTCCAAAGGAC Y 2 1 2 1 101000 r 74 goat snp26257-scaffold275-1584316 27 26400243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784096 Affx-122926801 AX-385271148 27 18002588 GTTCATGGTTGAATAACAGCAACATGATAGATTTA[A/C]GTATGTTCCACAAAGTACCTGCCAATCAACAATAA M 2 1 2 1 101000 f 74 goat snp26256-scaffold275-1525865 27 26340434 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406165 Affx-122956166 AX-123276517 27 18038383 TACAGCTCTAATGCATTCTGTTAACATATCAAGAG[A/C]TGAGGGTTGTTGTAATTATTTTAGCCCTCAATGTA M 2 1 2 1 101000 f 74 goat snp26255-scaffold275-1490070 27 26303939 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797396 Affx-122949609 AX-385284335 27 18082363 AGAATGTATAGTCAATGCTAAAACTCAGTTTTAGC[A/G]TTGGTTTGCAGTGTAAAAGCAAGGGTTTTACAGTT R 2 1 2 1 201000 f 74 goat snp26254-scaffold275-1446090 27 26259938 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792378 Affx-122935371 AX-385279359 27 18150264 AGGCAGGAGCTACAAACAGAAGTTAAAGTATGTAT[A/C]GAAAAAATACAACCAGGCACCTCTTTCTATTAGCA M 2 1 2 1 101000 r 74 goat snp26253-scaffold275-1378189 27 26192111 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398196 Affx-122962638 AX-123268551 27 18189089 CACGATACTTGTTTAGCTCCCCTCCCACTTGTCTG[C/T]AAAATCATTTTTCTCTCCTTTAAAAGCTTTTCTTC Y 2 1 2 1 103000 f 74 goat snp26252-scaffold275-1339364 27 26153266 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787456 Affx-122963826 AX-385274481 27 18230525 ATGAGGACACAAAATGCCCCAAAACATGTTGATTC[A/G]TTGCAGAAGATTCAGGTAATTATGAATGATTGGCC R 2 1 2 1 102000 f 74 goat snp26251-scaffold275-1297928 27 26112006 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454278 Affx-122919277 AX-123324611 27 18259832 ATTTATTTAACCACCTTAGGTGAAATGGCACAAGT[A/G]CCACAAACTAACCCTGCATTAAGAAGATCAAACAT R 2 1 2 1 101000 f 74 goat snp26250-scaffold275-1268621 27 26083156 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380281 Affx-122975415 AX-123250639 27 18291029 GGCTCGTAATGAGTTTATTAAACTGCTGCTTATGC[A/G]TCTTGTTTATTGGAATTTCTGCTTTGGGGTCTGCA R 2 1 2 1 101000 f 74 goat snp26249-scaffold275-1237424 27 26052486 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801726 Affx-122959363 AX-385288634 27 18337373 AAAATTTATTGCAATTGTGATTGTATATTTATTTG[C/T]GCAATCCTTCAACTTTCCTGGAACCTTCCTGAAGA Y 2 1 2 1 101000 r 74 goat snp26248-scaffold275-1191080 27 26006552 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445814 Affx-122926031 AX-123316151 27 18371055 CTGGATTGTGTAAACTGTCTCAAAAAACATGCACC[C/T]GACTTCCAAGGTGTGGAACAGTTCTCCGACCTTTC Y 2 1 2 1 101000 f 74 goat snp26247-scaffold275-1157398 27 25972887 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454037 Affx-122919410 AX-123324370 27 18415864 GACAGGAGATTCCTCAAAGGTAAGTGAAAATTTAG[C/T]ATTATCTCCCCAGCCTGCTCTATTAGCAAGGTGCT Y 2 1 2 1 101000 f 74 goat snp26246-scaffold275-1112589 27 25927511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398597 Affx-122961491 AX-123268952 27 18450580 CTCATCATAGTAACAGTGTCCAAGGTGTGCTGAGC[A/G]CTGACTCTGTGCCAGGTTCTGTTCTAAGTCTTTTT R 2 1 2 1 202000 r 74 goat snp26245-scaffold275-1077873 27 25892653 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273125 Affx-1111833323 AX-519546789 27 18551024 CCATTTGATATTGTAATGCATTCTTAAATAAATGT[A/G]GTTTGTTATACATCATTTTAATGAGCATTTCTACC R 2 1 2 1 303000 f 74 goat 27_18551024_AF-PAKI 27 18551024 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38426377 Affx-122940242 AX-123296723 27 18558842 AAGGTCTCTGATATAAGAAGCCATTTGAAATAAAA[C/T]CCAAGCAAAATGAAAACATGAAAGATATGATTTGC Y 2 1 2 1 201000 f 74 goat snp26243-scaffold275-969611 27 25785014 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411151 Affx-122951881 AX-123281501 27 18601693 TCTTTTCTTCCAAAAGATGAAAAGAGAACTACCCC[A/G]TGATCCAGCAATCCCACTTCTGATTCACTGTCTCA R 2 1 2 1 103000 r 74 goat snp26242-scaffold275-926760 27 25741831 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412693 Affx-122950758 AX-123283042 27 18633316 GCTGAGCAGCACCCATGTTTGCTTTCAGATTTGGC[A/G]TATATGATTGGCTGTCTTGCCATTGTAAAGACTTG R 2 1 2 1 101000 r 74 goat snp26241-scaffold275-895137 27 25710213 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428124 Affx-122939068 AX-123298467 27 18662361 AATAAGGACAAATGAAAAAATTAAAAAAGAGCTCT[A/C]TCTGCAAAAGTGAAGACTAAAACTAAATGCCATGG M 2 1 2 1 101000 r 74 goat snp26240-scaffold275-866092 27 25680870 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390016 Affx-122968035 AX-123260373 27 18723782 GGGCTTAAGGAATGACAAAGACTAAAATAGGAAAT[A/G]TAAGGCAGATGGAAATAGAGAAGTCTAGTTTGGAA R 2 1 2 1 101000 f 74 goat snp26239-scaffold275-804671 27 25619444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785672 Affx-122962317 AX-385272713 27 18762329 AAAGCAATTAATTGGCCCAATTTGAAGAACAGTCT[A/G]TAATTCATATTATCCTTACTCCACATTAAAAAGGT R 2 1 2 1 101000 f 74 goat snp26238-scaffold275-766124 27 25580723 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273841 Affx-1111833877 AX-519547451 27 18778868 CCTTTTTCTGGGCTGAATATGCCACTCACTTGCCC[A/G]GTCTCCTCTGCAGGGGTAGCTTGCCCTGGCCAGGA R 2 1 2 1 201000 f 74 goat GoatD01.008872 27 18778868 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38377888 Affx-122977253 AX-123248247 27 18793963 CTCACACACTCCTACTAACAAGTGTATTTAAGGCC[A/G]GATTGAACCTGAATACTTTTCTATTTATTAAGATC R 2 1 2 1 101000 f 74 goat snp26237-scaffold275-734490 27 25549003 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433932 Affx-122934294 AX-123304273 27 18831495 CCACTCTGGTGGTTTGCTTATAACCTCTGTGTTGA[C/T]ACAATTTCCACATCTGTTTCCAGCCTGACCTCTCC Y 2 1 2 1 101000 f 74 goat snp26236-scaffold275-696958 27 25511467 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422053 Affx-122943609 AX-123292400 27 18870995 TGCACGCTGGTGCCTGTCTAATTAGTGCCTGGTTG[C/T]TGTTTAGTTGCTCAATCATGTCCCACTTTTTGTGA Y 2 1 2 1 201000 f 74 goat snp26235-scaffold275-657458 27 25473736 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449903 Affx-122922333 AX-123320238 27 18900558 TACAACAAACAAGTAAAGGAAAAATAGTAAATGAT[A/G]TCTTTTCAGATAATGGTAAATATTATGAAGAGGAC R 2 1 2 1 101000 r 74 goat snp26234-scaffold275-627895 27 25444314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380946 Affx-122975003 AX-123251304 27 18940906 ATTAATTAATTTTTTATTTTGTATTGGGTATAACC[A/G]TTTCACAATGTTGTGATGGGGTGGATAGTAAAGGG R 2 1 2 1 103000 r 74 goat snp26233-scaffold275-587547 27 25403965 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442573 Affx-122928504 AX-123312910 27 18979218 CTTTGTCCATGGAGCAGCCTGGAATTTCTCAGAGC[A/G]CAGAAAGAACCAGGCAGAAGCTTACTGCTTTAAGG R 2 1 2 1 202000 f 74 goat snp26232-scaffold275-549235 27 25365099 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799829 Affx-122926680 AX-385286755 27 19010588 AGGATAATGGGCAGAAAGAACTAGTGAACTAAAAG[C/T]AATAAAGGTTTAGGGTTTAAGAAGTAGAAGAGAGT Y 2 1 2 1 101000 f 74 goat snp26231-scaffold275-517865 27 25332631 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765251 Affx-122926350 AX-385252788 27 19041132 TCCTAGTTGACCAGGCAATAATTCAAACTGTAATC[A/G]CCTGATTTCATCGCTACTCAACATGCCTTGAAAGC R 2 1 2 1 101000 f 74 goat snp26230-scaffold275-487321 27 25301577 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442389 Affx-122928005 AX-123312726 27 19105061 CATACCCACAGAAATGACATTATCCCCAGGGTGAA[A/C]TTATACACAACATTATCATCCTGGCTGCTTTCAGT M 2 1 2 1 201000 r 74 goat snp26229-scaffold275-423392 27 25236847 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408571 Affx-122953668 AX-123278922 27 19196966 AATCCCCACGATACCACATCTTTTACCTTGTAGGT[A/G]CACTGTCTCCCCCTCTTTCTTGGAACCTTTAAACC R 2 1 2 1 101000 f 74 goat snp26227-scaffold275-331487 27 25143361 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387197 Affx-122970602 AX-123257555 27 19327674 TTATGTTCTTTGTTTCTTCATTCAAAGACTTTAAA[C/T]GCATTTGCAGCCTCCAGTTATATCATAAACGTTCC Y 2 1 2 1 201000 f 74 goat snp26224-scaffold275-200779 27 25011036 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404076 Affx-122957142 AX-123274428 27 19364202 AACCACCTCAGCAGCCGCAGGAAGAAAGTAAAAAT[C/T]AGTAAGTTTCTCTGCAAAGAAATATCACACACTAC Y 2 1 2 1 201000 r 74 goat snp26223-scaffold275-164251 27 24973860 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451034 Affx-122921448 AX-123321368 27 19393495 CTGAGTTACTGAAGTAGTGTTTACCCCCTTCTTCC[A/G]TATGGGTTCCTGTCTAATAGGAATGATAACTGAAG R 2 1 2 1 201000 r 74 goat snp26222-scaffold275-134958 27 24944646 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440124 Affx-122929697 AX-123310461 27 19425393 AAAGTGAACACAGATGATCAAATAAAGATAGGTTG[C/T]AAGTCTCAGCAGTCTTAAATTTATAGGTGCATATG Y 2 1 2 1 101000 f 74 goat snp26221-scaffold275-103060 27 24910975 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394921 Affx-122964312 AX-123265276 27 19476393 CAAAGTGATGGGGCTCGGATGGTACACTCTAGTAA[C/T]AACTCATCAAAAATACAGTACTTTCATTATGCCAA Y 2 1 2 1 101000 f 74 goat snp26220-scaffold275-52060 27 24859916 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409009 Affx-122953882 AX-123279360 27 19522974 GGACTGTGCTGGAAAGTCAAACTGATGGCCCCTAG[C/T]AATGCTCTACATGTCCTACAACTTATCCTCTCTGT Y 2 1 2 1 101000 r 74 goat snp26219-scaffold275-5479 27 24813002 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770415 Affx-122947502 AX-385257581 27 19543149 TTCAACCTAGGCTTGTGTACTGATTGTGTTTGAAG[C/T]ATCACAACTAAAATCTACATCTCCAAGTCAAAGCT Y 2 1 2 1 101000 f 74 goat snp37869-scaffold466-3731815 27 24792974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430043 Affx-122937567 AX-123300384 27 19572244 GCTGTTCTTGTGGTAGAATGAGAAGATCAAGAGAG[C/T]GAGTAAAGGATGCAATGGCTAGTACAGAGGTGGAG Y 2 1 2 1 101000 f 74 goat snp37868-scaffold466-3702720 27 24763930 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793896 Affx-122937836 AX-385280865 27 19625176 AAACACTTGTGCTTGGAAAGAGATTTCCAGTTACA[C/T]AGAATGATTGCATTGGTCAGTTTAACCAAAACTAT Y 2 1 2 1 101000 f 74 goat snp37867-scaffold466-3649788 27 24711376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802162 Affx-122924692 AX-385289066 27 19663024 CTTGGAAAGATTCCAAGAATTATGGAAAGATTCCC[A/G]TGGCTATTTGAACACCAAATTCAATAAAATCAAGA R 2 1 2 1 101000 f 74 goat snp37866-scaffold466-3611940 27 24673848 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452749 Affx-122920270 AX-123323082 27 19706617 GATTCTCCCCAACAATAAATGTAACAATCTGACAC[A/G]TGTCTGAGTTGATCTGCAGACACCAAGCTGCTCAT R 2 1 2 1 102000 f 74 goat snp37865-scaffold466-3568347 27 24630235 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388169 Affx-122969444 AX-123258527 27 19789422 GAGCCCATTTAATGTGCAGGCTTTAAAGAGCAGAG[C/T]GGCAGGAGATGAGACAGGTATATCAACATTCTGAG Y 2 1 2 1 101000 f 74 goat snp37863-scaffold466-3485542 27 24548610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429694 Affx-122937635 AX-123300035 27 19826271 CCCTTTCCTAGGACACTTTGTCCTCAAAGTCTCTA[C/T]GTTCCAGGGGCAGAGAGAAATTTTGAGGTATATAT Y 2 1 2 1 202000 r 74 goat snp37862-scaffold466-3448693 27 24512499 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774617 Affx-122973830 AX-385261751 27 19874147 GAAAACAAAGTGACATGTGATGCACAGTTAAGTTA[C/T]GAAACATTTTATTCATATTCCTCAATGAATTCTTC Y 2 1 2 1 101000 r 74 goat snp37861-scaffold466-3400817 27 24470442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447311 Affx-122924909 AX-123317647 27 19930249 TAAATTCAGAGCAATTCTGTTGCCTAGGAAAGAAA[C/T]GCACCTTGAAATAGCTAAGCAAAATGGGGAAATTG Y 2 1 2 1 202000 f 74 goat snp37860-scaffold466-3344715 27 24413877 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412961 Affx-122951044 AX-123283310 27 19966179 CACTCACAAAAATTACCCCATCTTATAGAGATAAA[C/T]ACCAATATGTTTTACATTTTCTGGTCATTTGTTAT Y 2 1 2 1 201000 r 74 goat snp37859-scaffold466-3308785 27 24376527 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430422 Affx-122937748 AX-123300763 27 19997224 TCCAAGCAGGCTCAACTCCAGGGAACAGCCAGGTG[C/T]GAGAGAAGCTCACATTCTTTTGCTTGACAGACTGC Y 2 1 2 1 101000 r 74 goat snp37858-scaffold466-3277740 27 24345459 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422011 Affx-122943773 AX-123292358 27 20063736 TATGATAGCTTTAACTTCTCTGTGAGTGCAAAATA[G/T]ATCACCTGTTTCTTTTCATGGAAAAAATTACTCAA K 2 1 2 1 101000 f 74 goat snp37857-scaffold466-3211228 27 24279094 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794570 Affx-122972422 AX-385281532 27 20100317 GCACTTTACCACGTTAGCTTTTTCATTAAATATCC[A/G]TATGTAACTTTTGTGTGTTGGCGTTCTTTTCTTTC R 2 1 2 1 101000 r 74 goat snp37856-scaffold466-3174647 27 24241930 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408653 Affx-122953470 AX-123279004 27 20157359 TTGGAGATTTTTTCTGTCTGTGCTATTGTTTCTGG[C/T]CTTCCTACTTACCTAGTATCATCCAGTCCAGGACA Y 2 1 2 1 101000 r 74 goat snp37855-scaffold466-3117605 27 24183966 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406498 Affx-122955153 AX-123276850 27 20202857 AATAACAATAGGATAATACCCACTTTTCATGAGCC[A/G]TATGAGACAATGTCACTGGCATACGCTGTTCTCAG R 2 1 2 1 101000 r 74 goat snp37854-scaffold466-3072107 27 24138612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453652 Affx-122919726 AX-123323985 27 20233736 TTCTAAAAAAAGAAAAAACACAGAAGGACAGAGAG[A/C]TGATGAAGTTTCTTTGTGTCACCGAGAGATGTACT M 2 1 2 1 101000 r 74 goat snp37853-scaffold466-3041228 27 24107672 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407662 Affx-122954602 AX-123278013 27 20322647 ATCCTTTTTAGATGGTAAAATTATATGAAATATGA[C/T]ATCTGAATGATTTATGGTAGTTTTGCTAAATAGCA Y 2 1 2 1 101000 r 74 goat snp37851-scaffold466-2952317 27 24018858 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779483 Affx-122966998 AX-385266586 27 20361861 CTTGATTATTGTGTCTTTGTAGAAAGTTTTGGAGT[C/T]AGGAAGTATGAGTCTGCTGACTTTGTTCTTTTCCA Y 2 1 2 1 101000 r 74 goat snp37850-scaffold466-2913103 27 23979314 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382165 Affx-122974031 AX-123252523 27 20390865 CACTTCCTGAAATGCCTTTACCCCTAAACTACCAT[A/G]TTCATTAATTTATTTGTGAAAGGTATATTGCATAC R 2 1 2 1 201000 r 74 goat snp37849-scaffold466-2884099 27 23949497 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782065 Affx-122955530 AX-385269143 27 20421027 AACCTAAATAATATGTCTGCTCTTAACGGGAATCC[A/G]CAGTCCAATCTGCCTTTTCCCCTCTTTTAAGTAGT R 2 1 2 1 101000 r 74 goat snp37848-scaffold466-2853937 27 23919392 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439893 Affx-122930032 AX-123310230 27 20452598 ACTCATCTATTCATTTATTCCACACTTTTTTTCAT[A/G]TGCTTCTCTATGCCAGGCCCTCTGAGATCGATGGG R 2 1 2 1 101000 f 74 goat snp37847-scaffold466-2822366 27 23886624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434159 Affx-122934897 AX-123304500 27 20485101 TCTAGGTGAAACATTCCCCCTCTCAGAAGGAGTGC[A/G]TTTTGACCATGCCTTGACTGAATGAATTGTTTAAT R 2 1 2 1 101000 r 74 goat snp37846-scaffold466-2789863 27 23854049 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442118 Affx-122928344 AX-123312455 27 20522067 TAGAGCAAAAACATTATTACCTACGAGAAAGGCTT[A/G]CAAATGAGTGGAAATTTACTATGTGTTATTAATGT R 2 1 2 1 101000 f 74 goat snp37845-scaffold466-2752897 27 23816558 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427721 Affx-122939275 AX-123298064 27 20551372 ATTGGTATGGGCGTTCCAGGATGCTTTTATGAATT[A/G]CTGCAGGAATGCTCATCAGTTTAGGAACAGTGAAA R 2 1 2 1 102000 f 74 goat snp37844-scaffold466-2723592 27 23787196 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415684 Affx-122948542 AX-123286033 27 20605902 GACACAGGGACAGCTGACTTGGGTGGAAGACCACC[A/G]TTAATCAGAAGTTTGCCACATGTCTGCTGGACTTT R 2 1 2 1 101000 r 74 goat snp37843-scaffold466-2669062 27 23732981 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393662 Affx-122965280 AX-123264017 27 20673233 CTCTTGGATTGCATTACTTGAGATATTCCAATGAG[C/T]GAACATCTCATATAAGCCAGAACTGCATGTCCATA Y 2 1 2 1 101000 f 74 goat snp37842-scaffold466-2601731 27 23666794 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398333 Affx-122962127 AX-123268688 27 20704986 AGTGAATTTTTAATATTCTAGATTTTAGACATGTT[C/T]GTTAGATATTCTCTTTTCTGCCTATGCCTGATCAA Y 2 1 2 1 101000 r 74 goat snp37841-scaffold466-2569978 27 23635099 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796321 Affx-122922389 AX-385283271 27 20734734 TTTCAGACTTTTTTTCTCAGTCTGAAATCAGTAAT[A/C]TAAAAATTCAAGCTTATTTTCAAATTAAAATTTAG M 2 1 2 1 202000 r 74 goat snp37840-scaffold466-2540230 27 23605441 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375478 Affx-122979147 AX-123245837 27 20793837 GGCTGTGGCAGATTTTGCAAAACTCAGTGTATATG[C/T]AGGTTTCATGGGGAGCTAAGTTGTCAATATCCATA Y 2 1 2 1 201000 f 74 goat snp37839-scaffold466-2481127 27 23546350 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397096 Affx-122962705 AX-123267451 27 20843331 AGTACCCTTGAAAATGATCTCGAGAAATAATATTT[C/T]AAAAATCAATTTCTAAATGCAAGCCTAGATTTGCA Y 2 1 2 1 201000 f 74 goat snp37838-scaffold466-2431633 27 23496785 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406201 Affx-122956135 AX-123276553 27 20876483 CAAAACCTTGAAAGTTCCAATTTACTATAGGCAAT[A/G]CACATGATTCTATGAACAGCATATGCATAAGTATA R 2 1 2 1 101000 f 74 goat snp37837-scaffold466-2398481 27 23463597 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376164 Affx-122978842 AX-123246523 27 20905893 AGTTACTGTCTAGATTCTACTGGGAAAAGTAACAG[C/T]GAGAAATACTGCTTTACTTTGAACCTTAGACTATA Y 2 1 2 1 101000 f 74 goat snp37836-scaffold466-2369071 27 23434410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440473 Affx-122929381 AX-123310810 27 20937025 TCCTTACTCTCCCAAAGACCTTAGATGGGGTTCCT[A/G]CTTCTCCCACTGCTTTGCATGGAGGCATAAGACTG R 2 1 2 1 101000 r 74 goat snp37835-scaffold466-2337939 27 23402857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450139 Affx-122922752 AX-123320474 27 20967950 TAAATACTGATTCTACATTTCATGTTGACTAATCA[C/T]GGGAAACCTTCTTAGCTTCTCTAGACCTTTCTTTA Y 2 1 2 1 101000 r 74 goat snp37834-scaffold466-2307014 27 23371969 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407522 Affx-122954705 AX-123277873 27 21013277 TGGAATTAGAATCAAATATATTGAGTTTTGAAGGG[C/T]GAGAATTGGTGGAGTATACAAATATAAGGAAAAGG Y 2 1 2 1 101000 r 74 goat snp37833-scaffold466-2261687 27 23326806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421561 Affx-122943856 AX-123291908 27 21052630 TTCCAATTATTTTTCCACAGAAAAAGAGCTTTCTT[C/T]TTAAATAAAAGAGAAGACTGCATTAAGTCTCATAA Y 2 1 2 1 303000 r 74 goat snp37832-scaffold466-2222334 27 23287431 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790118 Affx-122978652 AX-385277124 27 21083990 GTCAGACAGACAGATGAAATTCCCAAGAACAGGAA[C/T]AGTTTTTACAGGAACACTAGAGTATTTTGCAGTTT Y 2 1 2 1 101000 f 74 goat snp37831-scaffold466-2190974 27 23255923 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273127 Affx-1111833324 AX-519546791 27 21089780 TATAGAAAAGGGAAAGGAGGGGAGACTGACTTCAC[A/G]TTCTTAGGGGAAAAATGGGACTTGAAATAGAAATT R 2 1 2 1 102000 f 74 goat 27_21089780_AF-PAKI 27 21089780 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38425599 Affx-122940924 AX-123295945 27 21113537 TAACATAGGGAGAAAGTTTATCTGAGATCAGCTCA[C/T]GCCAGTGGAGTTCTGTACTGAATTCTGGAGCCAAA Y 2 1 2 1 101000 f 74 goat snp37830-scaffold466-2161427 27 23226133 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770514 Affx-122968042 AX-385257679 27 21173408 AGTGCATGAGAAAAAGCTAATTCTTAAACAACTAG[C/T]ACTTCTTTTTAATAAAAGGCTAATTCCCACCACAA Y 2 1 2 1 101000 r 74 goat snp37829-scaffold466-2101556 27 23165493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390772 Affx-122967888 AX-123261129 27 21217386 CAGTCACCTCTTCCCCTGCTGATTTAGATGCCAAC[A/G]TCATGACATATATGTAAAGTCACTGCATGGTTACA R 2 1 2 1 201000 r 74 goat snp37828-scaffold466-2057578 27 23121553 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405455 Affx-122956041 AX-123275807 27 21255345 AGAGACAAAGCTTTCTGAAAGTTTCCAACAGATGA[C/T]AGGACAGGATATGATCCGACGAATGAGGACTAAGA Y 2 1 2 1 201000 f 74 goat snp37827-scaffold466-2019619 27 23083526 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411011 Affx-122951982 AX-123281361 27 21290103 TTCCACTGACACAGTGGCTGTCTACTGCAGTGATT[C/T]AAGGTGCAGTTAAACATGAGTGGTTCTAAAGCACA Y 2 1 2 1 101000 r 74 goat snp37826-scaffold466-1984861 27 23048138 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412575 Affx-122951310 AX-123282924 27 21327525 ACCCACTATGTGCCTGGAAAAGATAACAGGATAAA[C/T]GAGATAATAAGACCTGATTCTGCTCCTTGAGGGAT Y 2 1 2 1 201000 f 74 goat snp37825-scaffold466-1947439 27 23008895 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383112 Affx-122973269 AX-123253470 27 21360407 AAGACCATCTAATGAAGAGGAAGACCTTAAAAGAA[C/T]ATGGACTTGTGGGGGTTTAAAACTTTAAGCCACAT Y 2 1 2 1 101000 f 74 goat snp37824-scaffold466-1914557 27 22976004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429530 Affx-122937840 AX-123299872 27 21403101 TACATTAGGACCCCAAAAGATATCTGTTAAGTGAG[C/T]GAATGAATGAAATAGAAAGCTAACCAGAAATTTAA Y 2 1 2 1 201000 r 74 goat snp37823-scaffold466-1871863 27 22935214 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796834 Affx-122949521 AX-385283777 27 21451160 TAAGGATAGAGATTATTGTCTATCTTTTGCCATCA[C/T]GTATCCAAGAGCACAGAGTAAAGCTTGATACATAA Y 2 1 2 1 201000 r 74 goat snp37822-scaffold466-1823804 27 22886297 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426209 Affx-122940366 AX-123296555 27 21482725 ATCAGATCTACCACCGTAACCTCAGCTAGTCCTAC[A/C]GGTACCTTGCTTGCCAGGCCCCAAAGGCTTTCATT M 2 1 2 1 101000 f 74 goat snp37821-scaffold466-1792239 27 22854403 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376678 Affx-122978997 AX-123247037 27 21513892 GAAAATGCTCAAATGTTCAAAGGAAAAATAAGATT[C/T]CTCCCAGATGGTAGGCACCTTTAGGAAATCTCTGG Y 2 1 2 1 201000 f 74 goat snp37820-scaffold466-1761072 27 22823772 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439710 Affx-122930559 AX-123310047 27 21607004 GTGCTGTGCCACTCACTCAGTTGTGTGAAGAATAA[C/T]TTCAGTGAACCCAGACTCTTGAATCTTCTCAAACA Y 2 1 2 1 101000 f 74 goat snp37818-scaffold466-1667960 27 22727821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389788 Affx-122968218 AX-123260145 27 21669194 TACCATGATATTATGTGAGACTCAATTTCTGGCAC[A/G]TGAACCACAGATATTAAAAAGTCATTTCTTGTTCA R 2 1 2 1 101000 f 74 goat snp37816-scaffold466-1605770 27 22665403 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786128 Affx-122976898 AX-385273164 27 21718531 TAATTGACAAGGTTTAGTTTACAAGGATAAGGGAG[C/T]GGGATACTTATATTTGACAGTAAAGTATCTCTATT Y 2 1 2 1 101000 f 74 goat snp37815-scaffold466-1556433 27 22615480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440991 Affx-122928971 AX-123311328 27 21764272 CCTGAGAAGGGGGTAACACCATGTGAATATAAAAG[C/T]AATTATTTCATAAGTGGCTGCTCTGTACCAGCCTC Y 2 1 2 1 101000 f 74 goat snp37814-scaffold466-1510692 27 22569718 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789370 Affx-122957827 AX-385276380 27 21796922 AGCAATTAAGTGTGGAACAGGTAGGACATGTCCAG[C/T]ATACTATATGTCATATCAGACAAATTAAGAATCAC Y 2 1 2 1 101000 f 74 goat snp37813-scaffold466-1478042 27 22536897 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431280 Affx-122937101 AX-123301621 27 21834608 CAATCTGCCACAGGGAATCATAAAATGGGTATTAG[C/T]GTCAGGCAAAAAAGCAACACAGGACTTAATTTCCA Y 2 1 2 1 101000 f 74 goat snp37812-scaffold466-1440356 27 22498169 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428295 Affx-122939384 AX-123298638 27 21880489 AAATTTTTGTGTTGCCCAGCCAAGTTTAAGAACCC[C/T]CAAAGGCCCTGGGTAAGGCCAAGGGAGTAAGAAAT Y 2 1 2 1 101000 f 74 goat snp37811-scaffold466-1394475 27 22452326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783612 Affx-122974224 AX-385270671 27 21925469 GTAGGTACAGAAAGAGTTACAGTGATCCATGCTCC[A/G]TAAGAGTCCTTGCTGGTCACCAGACGTTGCTAACA R 2 1 2 1 101000 f 74 goat snp37810-scaffold466-1349495 27 22407245 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447273 Affx-122924938 AX-123317609 27 21964324 TAGTCTCCCATAAGTCAGTCAGTCACCACCATCCT[A/C]CATTTGGTTTTACAACAAAAAATTGGTGTTTACCC M 2 1 2 1 201000 r 74 goat snp37809-scaffold466-1310640 27 22368005 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274624 Affx-1111834403 AX-519548211 27 22000570 TATGTTTATTGAGCGTCTACTGCAGGCACTGCATC[A/G]TCTCCTAGGAAGCTACTGCTTTCGTATTTTTACAG R 2 1 2 1 101000 f 74 goat GoatD01.033681 27 22000570 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38416900 Affx-122948066 AX-123287248 27 22029763 TATAGCAAATGTTGCATTTGTTAAGGTATTCAGGT[A/G]CTGTAACACAGACCTAAATTTACCGTGGCTGCTTT R 2 1 2 1 101000 r 74 goat snp37808-scaffold466-1245201 27 22303144 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386125 Affx-122971417 AX-123256483 27 22090032 GTTTTTTAATTATAAAAGTTTTTATACCATAAAAA[G/T]CTCAATTTTCCATAATGCCAGATATCGAACAAGAC K 2 1 2 1 101000 r 74 goat snp37807-scaffold466-1184932 27 22242923 G T 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781209 Affx-122942121 AX-385268294 27 22137966 AAAATTGTGAATTAGAAGGAAAACAAGTATACTGA[G/T]TGAAAAAGTCTGCTTCTATGGCAAAGGCAATAATG K 2 1 2 1 201000 f 74 goat snp37806-scaffold466-1136998 27 22195905 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446566 Affx-122924837 AX-123316902 27 22185022 CATGGCAGTGTATAATCCATTTTAAAAAGCTGTCC[A/G]TTAAAATAGTTAAAAATATTTTGGCACTTTTTGGA R 2 1 2 1 303000 r 74 goat snp37805-scaffold466-1089942 27 22148860 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802903 Affx-122960255 AX-385289800 27 22218083 GCAAAGCACGGACTATCAGAAATATCAAACCCAAT[A/G]CTTACCATTTGGTATGTATGTTAAATTTGGTTAGA R 2 1 2 1 101000 f 74 goat snp37804-scaffold466-1056881 27 22115017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408140 Affx-122954233 AX-123278491 27 22249373 TAAATTTCTTAATCATCTGGCTTCATGCAAGCAAT[A/G]CAACTATTGCCCATTCATTCTCTATCAAAAACATA R 2 1 2 1 101000 r 74 goat snp37803-scaffold466-1025591 27 22083798 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784993 Affx-122969196 AX-385272040 27 22307531 AAAAATCAAACAAATTCTAAAAGGAAATCTAAAAG[C/T]AAATGCTAGCATTAGATGTAAAAATGTGATGTATT Y 2 1 2 1 101000 f 74 goat snp37802-scaffold466-967433 27 22025474 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445090 Affx-122926205 AX-123315427 27 22337637 ATAGGTGCAGGGACACATTCACATGTGGGAAGCGG[A/G]AGGTGGGAAGCTCACAGGGACTTGCCGCCGCAGGC R 2 1 2 1 101000 f 74 goat snp37801-scaffold466-937327 27 21995292 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795950 Affx-122973303 AX-385282902 27 22389172 CCAAATGCTTTTAAACAATGAGGTTATTTACTTAG[C/T]AAATACGATGATAGTATTTATTATATGCCAAAGAT Y 2 1 2 1 201000 r 74 goat snp37800-scaffold466-885792 27 21943512 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379148 Affx-122976724 AX-123249507 27 22419808 GAGTGAACAATTCTTAGTACATAATTGGCCTTTCA[C/T]GTGAAGACAAACAGCTGCTAGAAATTTCTGGAAAA Y 2 1 2 1 101000 f 74 goat snp37799-scaffold466-855156 27 21912525 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795546 Affx-122934181 AX-385282501 27 22455483 TAAAAAAAAAAGTTTCTGCCTCCTTTTTCCAAACT[A/G]CTTAATAAAGAGTTAAGAATAAGGATGTCTAGATT R 2 1 2 1 202000 f 74 goat snp37798-scaffold466-819481 27 21876946 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441919 Affx-122928597 AX-123312256 27 22491531 GACTTGGAATAAATACCAGTAACATACTGATTAAT[A/G]TGTAGAATGAAGGATACTTTTAAAACACATTTCGC R 2 1 2 1 101000 r 74 goat snp37797-scaffold466-783433 27 21840735 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417081 Affx-122947499 AX-123287429 27 22543477 CGTTTCTATGGCTTTATGAATGATGACATAGAGAT[A/G]AGCGAAATGGGTAAAAGCACAGACCAGGTGAGTTT R 2 1 2 1 101000 f 74 goat snp37796-scaffold466-731487 27 21788845 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774000 Affx-122928521 AX-385261139 27 22586162 TAAATCTCAGGGGCAGAACTGAAGAATGGCAAGTT[C/T]AGGGAAGCTAAATTAGTATGCATGGATTTACTTCC Y 2 1 2 1 101000 f 74 goat snp37795-scaffold466-688802 27 21746840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402363 Affx-122959044 AX-123272716 27 22619603 TCCTAACAGGTGAGTTGGGAATATCCCTAAGATAT[A/G]AAGATGAGGGAACAAGTGGAGAAACAACCACTTCT R 2 1 2 1 101000 r 74 goat snp37794-scaffold466-655361 27 21713223 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384428 Affx-122972183 AX-123254786 27 22649177 CTCACTCTGTACAGAGCCCCTTCTGCAGTGGGTAT[A/G]CAAGCTCACACAGTCAGTTCTTTGAAAGAGAACCA R 2 1 2 1 101000 r 74 goat snp37793-scaffold466-625787 27 21683629 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792777 Affx-122938492 AX-385279756 27 22701443 AACACCCAAGCACTGAAGCCAACATACTTCCCTGT[A/G]CCTTTGTTAAATGATGCTAGGACCAAACAAAATAA R 2 1 2 1 101000 f 74 goat snp37792-scaffold466-573521 27 21631038 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439796 Affx-122930496 AX-123310133 27 22782338 CATTGAAGAGAATGAAAGCGACTCCCTGGTGGCCC[C/T]GATTGCCCATAACTTCTTTTAAAGTGGACCTTGAC Y 2 1 2 1 101000 r 74 goat snp37790-scaffold466-492626 27 21550117 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779774 Affx-122929102 AX-385266874 27 22813805 AAAGGAAGGAAAGACTCTTCTAAATGTCCTCCACC[A/G]TCTCTTTAACTCTCACTGCTTATGCGCTCTGTGGA R 2 1 2 1 101000 f 74 goat snp37789-scaffold466-461159 27 21518504 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425017 Affx-122941883 AX-123295363 27 22903569 CAGACTTCCCCCTCTTGCCTCATTAGCCAGAATTA[C/T]ATCCAATGTCTTTGCCTAAATCAAGTACCAGTTAA Y 2 1 2 1 201000 r 74 goat snp37787-scaffold466-371395 27 21427644 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400626 Affx-122960373 AX-123270981 27 22940880 ACTCAAAACCCTCACGGGCTGTTCAAACCACAGAA[C/T]GGGACTCTGTGTCCCTACCCTCGGGGTGGTGATCT Y 2 1 2 1 101000 f 74 goat snp37786-scaffold466-334084 27 21390326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802181 Affx-122920696 AX-385289085 27 23008776 CTCGAAGTCAAGTTGTTCTCTAGTTAGGAAACAAA[C/T]GTTTCTTATAGTCTAAAAAACTGTCAGATGATATT Y 2 1 2 1 101000 f 74 goat snp37785-scaffold466-266188 27 21343870 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416724 Affx-122947548 AX-123287072 27 23058201 TTCCTTTCTTCATACCTTCTTCTCCGAAAACACAC[A/G]TCCTACTTTCCTTAAACAACCATGAACTGTCTGCT R 2 1 2 1 101000 f 74 goat snp37784-scaffold466-216763 27 21294366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794743 Affx-122959962 AX-385281703 27 23113743 CTCAGATAGGTTTCCTTCCTTAGTTTATAAACAAA[C/T]AGTAGTGAACTTTGTAAGAAACTATATACTGAGCA Y 2 1 2 1 101000 f 74 goat snp37783-scaffold466-161221 27 21238755 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408553 Affx-122953680 AX-123278904 27 23193361 TGCTCTCACTGCGGCTGATAAGAGTGTTAGTCGCC[A/G]CCCAGAGAGGAAGGACTAGAGCATGTGGCTTTGGC R 2 1 2 1 201000 f 74 goat snp37782-scaffold466-81603 27 21159848 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780941 Affx-122960521 AX-385268028 27 23226663 TGGTACTTTGTGATAGCAACCTGAATGGACTGAGG[C/T]ACCAGGTTCTCAACTAGGCATTTCACATAACTTAG Y 2 1 2 1 101000 f 74 goat snp37781-scaffold466-48301 27 21126657 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378928 Affx-122976440 AX-123249287 27 23257560 AACTGTACAAAATGTGAGCCATACGACAAATCCTC[A/G]CTCTCAACCAAAGCAGGAGTCTGAAAGGAAAACCC R 2 1 2 1 101000 f 74 goat snp37780-scaffold466-17404 27 21095716 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780985 Affx-122933280 AX-385268072 27 23287665 GCTCTGCTTTGGAACACTCCCAGTTTTTGTCATGC[A/G]TGTTTTTGCTGGATCTTGGTTAAGGGTTCAGCAAG R 2 1 2 1 101000 f 74 goat snp55779-scaffold864-4284424 27 21066142 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449096 Affx-122923593 AX-123319431 27 23335067 ACGTTTAAAGGGGGAAAAAAAAGAAACTTAGGCCT[A/G]CAATCCAAAGACAGGGACTTAAAAAATGCTTAAAG R 2 1 2 1 101000 r 74 goat snp55778-scaffold864-4237022 27 21018572 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416782 Affx-122948165 AX-123287130 27 23383957 GTTCACAACTACCAGGAATAATAAAAGTCAAATAC[A/G]TATTTGGGAAAATGTCTGAATAATGGCTGAAGTTA R 2 1 2 1 101000 f 74 goat snp55777-scaffold864-4188132 27 20969806 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437988 Affx-122931588 AX-123308326 27 23422186 ATGCGGATCCACTGCACCCTCACTGGTCTCTGATA[C/T]GGGGAGGCTAGACTGGTCCTCATCCAAACTCATGG Y 2 1 2 1 201000 f 74 goat snp55776-scaffold864-4149903 27 20931753 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452884 Affx-122920224 AX-123323217 27 23463971 ACTGTAGTGCCCTTTAGAATAAGCAGATTACAAAA[C/T]AGTACTATAGCATGAAACCAATTAGGTTAAAAAGA Y 2 1 2 1 101000 f 74 goat snp55775-scaffold864-4108118 27 20889946 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771110 Affx-122931259 AX-385258270 27 23494071 GAAATAATTGGGCTGTAAATCAGAGTTTTGAGGAA[C/T]GAACTGGTGTTATTTTCTGTGAGGTAATACTTTGT Y 2 1 2 1 101000 f 74 goat snp55774-scaffold864-4078018 27 20859774 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397406 Affx-122962254 AX-123267761 27 23525979 ACTTGTTCACAGTCTTGCTCATCTATCAGTGTGTA[C/T]CTGCCAAGACCCTCTTGTTCCTACTCCCACCAGCA Y 2 1 2 1 101000 f 74 goat snp55773-scaffold864-4046110 27 20827886 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449926 Affx-122922917 AX-123320261 27 23559101 GCCAGATGACAAATGATTGGAAATGACTTTTATGA[C/T]AGATCACGCTGTGTATGTGTGCTAAGTCGCTTGTT Y 2 1 2 1 201000 f 74 goat snp55772-scaffold864-4012988 27 20794598 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801586 Affx-122939208 AX-385288495 27 23596871 ACAATCATAAAATCAAATGGGATCAGACTAGTTCT[A/G]CATTTAATCCTTGAATATGACACCTCCAATTTGCA R 2 1 2 1 101000 f 74 goat snp55771-scaffold864-3975218 27 20756929 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273129 Affx-1111833325 AX-519546793 27 23619664 TTTCTCTTCTGAATGCATGTAGTTGTAACTTTGCT[A/G]GAACACCTATCCTGATAAGACTTATATTTTGGTTA R 2 1 2 1 101000 f 74 goat 27_23619664_AF-PAKI 27 23619664 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38400900 Affx-122959741 AX-123271253 27 23644106 AAGCTAGATACTTTTTTTCTAAGACGTCTGAAGCC[A/G]TTGATGATTACAGCTTGAAACAGCCTGCAGAAGTA R 2 1 2 1 101000 r 74 goat snp55770-scaffold864-3927983 27 20709837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437103 Affx-122932178 AX-123307441 27 23686673 ACCATATTCTTTGTTTAATTAGCCTTTGTTTAATT[A/G]CATTCTACGCTAGTGTGGACTTGAGCTCAATCCAT R 2 1 2 1 101000 r 74 goat snp55769-scaffold864-3885416 27 20672514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797246 Affx-122939647 AX-385284185 27 23758687 TGTGGATATGACATAGGTGTGGCCTTTGCTGTTAA[C/T]GCAGGAGGCTGCTTGTTCTAAATAGTTCTCTGTGA Y 2 1 2 1 101000 f 74 goat snp55767-scaffold864-3813402 27 20600587 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776493 Affx-122943165 AX-385263620 27 23906077 AAAAAAAGAAGTTTAGGTTTGAGCATCGGAGAATG[A/G]TCTTAGTGTTATCATAAACTACACTTTCACTCTCA R 2 1 2 1 101000 f 74 goat snp55764-scaffold864-3666012 27 20451239 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403949 Affx-122957451 AX-123274301 27 24236856 ATGAGTAGAAGCTGTTTGAGCTAAATGGTGTTGTG[C/T]GTGCAGTTTCTCTGGCTGTTGCCCATTCCTTCATA Y 2 1 2 1 201000 f 74 goat snp55756-scaffold864-3335233 27 20121436 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799450 Affx-122978544 AX-385286380 27 24288789 GAACCTAGATGTACTTGTTTATTCAATAGTTTCAC[A/G]TACTCATCTAAGTCCTGGGCACAATGGAGTGAGCA R 2 1 2 1 101000 r 74 goat snp55755-scaffold864-3283300 27 20068826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776446 Affx-122935101 AX-385263573 27 24320790 TGAAAGTGAGTCAATTTAAGATCCTTTTGAGAAAA[C/T]GGTTCGACCCATACCCTCAAAATGCCTTAAGAATC Y 2 1 2 1 101000 r 74 goat snp55754-scaffold864-3251299 27 20037162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780566 Affx-122978319 AX-385267657 27 24361719 GTTTCAAAGAGCTACCCAAGACATTAAAGCATTGA[C/T]ATACCTTCACAGTTTCCAAGTCTCCGGCTTTAGAT Y 2 1 2 1 101000 r 74 goat snp55753-scaffold864-3210370 27 19996437 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391317 Affx-122967323 AX-123261674 27 24394567 GCGTTTTTCCTTTCCATCTCCGTTTATGCTGATAA[G/T]AGGTACAGATAAAAAATAAATCAGTGGGGGAAAAA K 2 1 2 1 101000 f 74 goat snp55752-scaffold864-3177522 27 19963842 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380734 Affx-122975138 AX-123251092 27 24449465 TCCCCTTGGCAATCAACTGTCCAGAGCCAGGAGAG[C/T]GGCCATCAAGACTATCCTCAACAGCCTGGAAAACT Y 2 1 2 1 201000 f 74 goat snp55751-scaffold864-3122624 27 19909422 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414693 Affx-122949285 AX-123285042 27 24507577 GTTTCAAACTTAAAGAAAAATTGAGCAGAAAGTAC[A/G]GAGTTCCCCCAGATGCCCCTTCTGCCCCACCACAT R 2 1 2 1 101000 r 74 goat snp55750-scaffold864-3064512 27 19851374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416004 Affx-122948389 AX-123286353 27 24537170 CTGGATTTGGCAATGAACACTCACGAATGACCTTC[A/G]TTGCCTGGTTTCAGTGAAGCAATGGGAGCGGAGGC R 2 1 2 1 101000 f 74 goat snp55749-scaffold864-3034919 27 19821984 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277862 Affx-1111836058 AX-519551358 27 24611254 CAGCAGAGATAATGTGAAGGAAAAAAAAAAAATCA[A/G]CACAGTTCTAGCCAGGTCTTTTGCATCAGCAAAGT R 2 1 2 1 101000 r 74 goat Random2.2K-2233 27 24611254 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376941 Affx-122977775 AX-123247300 27 24690964 GGTGGGGCTGGCACAGCAGGATTTCTAGAATATCT[A/G]TCTAAGAGCTTCATCCTCAGCGTGAGCTATTCAAC R 2 1 2 1 101000 f 74 goat snp55746-scaffold864-2881125 27 19666912 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387939 Affx-122970023 AX-123258297 27 24786359 GTGGTTTGACAGTTTCATCTTCCAATCTCCCCCAG[C/T]AATGCTTTCCAGGAATAGGGCCTCACCTATGCCTT Y 2 1 2 1 101000 r 74 goat snp55744-scaffold864-2785730 27 19571237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447288 Affx-122924926 AX-123317624 27 24861066 TATATTGACTAAGTTCAGCTGACGCAAAGCAAGAA[C/T]GGAAGAAAGCAGTGGTAGTGACTCATCGGCTGTCA Y 2 1 2 1 101000 f 74 goat snp55742-scaffold864-2711023 27 19497131 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424605 Affx-122942199 AX-123294951 27 25034598 CCGCCTTCGGCTGTGTGCAGATGCGACAGCCACAC[A/G]CGGGCATCTCGTCCTGCTGCCCATCTCACGGCTCA R 2 1 2 1 201000 f 74 goat snp55738-scaffold864-2537491 27 19328354 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447351 Affx-122924876 AX-123317687 27 25098178 TTCTGGAAAAAGGCAACATCCTGATGAATGAAATA[C/T]ATTTTTGGAATGACTTTTTTTAGGGTGATCAATTG Y 2 1 2 1 101000 f 74 goat snp55736-scaffold864-2473911 27 19264553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415140 Affx-122949418 AX-123285489 27 25136536 GAAAACACACACAACGGAGGGAAGACAAAGGAAAT[A/G]CCGTCAGACAACAGGCTTCCAAATGAACAGCTGAA R 2 1 2 1 101000 f 74 goat snp55735-scaffold864-2435553 27 19226144 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379291 Affx-122976211 AX-123249650 27 25280618 AGGATTGTGTATGCAAATGCACTGAGCAGCGAAAC[A/G]TGACCTGAAATGACAAGTTTTCATTTCTCCCCCTC R 2 1 2 1 201000 f 74 goat snp55732-scaffold864-2291471 27 19079852 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382411 Affx-122974254 AX-123252769 27 25310875 ACCCTCTTCAATTCCTTGTTTTGTGGCCTAGAGCA[C/T]GATAAATATTGAATGTAAAACAGATGTATATTCTG Y 2 1 2 1 201000 r 74 goat snp55731-scaffold864-2261214 27 19049768 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406933 Affx-122955079 AX-123277284 27 25403946 AAATTGTAATAGGTAAAGAGATGCGTTTCCCATAG[A/C]ACAAGCCCTTCACCTGACCACCCCCTGTAAGGAGC M 2 1 2 1 101000 f 74 goat snp55729-scaffold864-2168143 27 18956046 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408333 Affx-122953755 AX-123278684 27 25519965 TGTTTAGCCTTTGAATTCCCACAGCACTCCCTGTT[A/C]TGACAAAGCTGTTTGTGCTACTGTAATTGCATGAT M 2 1 2 1 201000 r 74 goat snp55727-scaffold864-2052124 27 18840355 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433052 Affx-122935756 AX-123303393 27 25621010 TAATGAACCTCCTTCTTCATGGGCTGCTCCGTGGG[C/T]GGTAAAACTTTGGTTACAGGCTTAGGCAAGTTCCG Y 2 1 2 1 102000 r 74 goat snp55725-scaffold864-1951079 27 18738981 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447117 Affx-122924470 AX-123317453 27 25665774 CCAGAAAATAAACCTTGTGCTCAATAGCAGTCACT[C/T]CTCATTCTTCCTTCTCCATCCCCTGGCGGCCACTG Y 2 1 2 1 101000 f 74 goat snp55724-scaffold864-1906315 27 18694008 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435792 Affx-122932857 AX-123306131 27 25697142 GTAGACAAATGTGGAGACTCTCAGGAACAAGAGAA[A/G]GATACTGCTGTTCCCAGTTGTAAAAAACAAAAGGT R 2 1 2 1 101000 f 74 goat snp55723-scaffold864-1874947 27 18661821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768181 Affx-122943560 AX-385255373 27 25755862 ATGATAAAATTGCTTAAAAGGTAATCTCTTTCTTG[C/T]CTATTATCTTTGCCCTGAGGGCAACAGACTGAATC Y 2 1 2 1 201000 f 74 goat snp55722-scaffold864-1816227 27 18603239 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378592 Affx-122976582 AX-123248951 27 25802892 AGGGCTTTATGCCTCTTGACTTGCCTGAATCCTCA[A/G]CATTGAGGACAGAGCAAATTAAGGGGTAGCGTAAT R 2 1 2 1 101000 f 74 goat snp55721-scaffold864-1769197 27 18555737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766478 Affx-122933554 AX-385253845 27 25853234 TTCTTACCATTTGCTAATTTACTTCAGAAACAGCT[A/G]TATTTTACATCTAGGTCCTTTAGCAATATGATTTA R 2 1 2 1 101000 f 74 goat snp55720-scaffold864-1718855 27 18505511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777918 Affx-122930567 AX-385265034 27 25883469 CCAAAGAGCATCTATCTAGAAAATGTTGTTAGCCA[G/T]CTATAACTAACCTATCTAGATTGCTTCTCACAAAT K 2 1 2 1 101000 r 74 goat snp55719-scaffold864-1688620 27 18475528 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428229 Affx-122939433 AX-123298572 27 25934999 CTCTGCTTTACCTGTTAGATGGAATGTCATTTAAA[C/T]AAAAAGTCCTACAGCTTGTCTGGAAAAAATAAGGG Y 2 1 2 1 201000 f 74 goat snp55718-scaffold864-1637090 27 18424070 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788712 Affx-122928897 AX-385275728 27 25983680 TGCAAATGTTTATTGAATGAAGACATAATAAGTAC[A/G]TACTTCTCAGTAATCCTTTTAAGTTGAGTTAGAAA R 2 1 2 1 201000 f 74 goat snp55717-scaffold864-1588409 27 18375318 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430574 Affx-122937005 AX-123300915 27 26092195 CTGCCACTCTTCTCAGTTGAAGGGAGAGGAAAGGA[C/T]GTGGGCAGTTACAGGGCACCCAAAGCTCCGGGTAG Y 2 1 2 1 101000 f 74 goat snp55714-scaffold864-1479894 27 18266867 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429539 Affx-122937833 AX-123299881 27 26121707 ATATAACTTTAAAGAGCAATAGGACAATTTGGCTC[A/G]ATCTATTTATTTCGATTTTCCCAGTATGATCTACC R 2 1 2 1 101000 r 74 goat snp55713-scaffold864-1450382 27 18236995 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273130 Affx-1111833326 AX-519546794 27 26207437 CTAGAAGAAAAGTCTTGCCTTTGCGAGAACACAGC[A/G]AGTTGGTAAAACTCCTACTTATTTACTTATTTAGT R 2 1 2 1 101000 f 74 goat 27_26207437_AF-PAKI 27 26207437 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38428839 Affx-122938366 AX-123299181 27 26474918 ACATAATGCCTGGAGCTGGCTGCACATGGCTGGAT[A/G]CATAGTCACATGGTCCATCCCATATGATAACCCAC R 2 1 2 1 201000 r 74 goat snp55705-scaffold864-1097171 27 17889271 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448100 Affx-122924318 AX-123318436 27 26520571 AACCTGAGATTTAATTTTTCACATCCTTCTTTCCT[A/G]TTCACCATGGGGAGTGGTTGATGGCTGCCAGATAG R 2 1 2 1 101000 f 74 goat snp55704-scaffold864-1051518 27 17843165 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796174 Affx-122954787 AX-385283125 27 26560113 ACTCATTGAGGTTAAGGAGCGAAAAGATTCAAAAC[A/G]TTACTTCTTAAGGCGAATTTCTATGCTCGAGTGGC R 2 1 2 1 101000 r 74 goat snp55703-scaffold864-1011976 27 17804256 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405052 Affx-122956349 AX-123275404 27 26680914 AATATAGGGGAAAAGAAAAGGCACTTCTTTCTCAG[C/T]GATGGACTCTTGAGCTCAACAGAAAGAGTCCTCAC Y 2 1 2 1 101000 r 74 goat snp55701-scaffold864-891175 27 17683530 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399721 Affx-122960464 AX-123270076 27 26795590 CTGAAGGCCAAGTTTAAGAGGCTTATGGAGTCTCC[C/T]TCCTCTGACTCCAGCTCCCTGTGTCTTTCTGTGTA Y 2 1 2 1 202000 r 74 goat snp55698-scaffold864-776499 27 17568202 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416432 Affx-122947832 AX-123286781 27 26829682 AAATGTCTTATCTCCAAGCAGTTTTTAGGATAAAA[C/T]AGATGGCCTAACCTCTTCTGGTTCACTGCTCCTCA Y 2 1 2 1 201000 f 74 goat snp55697-scaffold864-742407 27 17534185 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430167 Affx-122937370 AX-123300508 27 26912448 CTTTTCTTCCCTCCTCCTCTTCTCATTCATGAAAA[C/T]GATGATTCACTCCGGCGCCCTGCAGAGAGTGGGGC Y 2 1 2 1 201000 r 74 goat snp55695-scaffold864-659641 27 17451106 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428558 Affx-122938725 AX-123298900 27 26964155 AGGTAAGGAAAGCGAGAAGAAACAAATTACGTGTA[C/T]GTGTGAATGGAGGAAGGGGAGTCTAACCTGGGATG Y 2 1 2 1 201000 f 74 goat snp55694-scaffold864-607934 27 17400073 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384499 Affx-122973057 AX-123254857 27 27007471 CAGTGTTCTTTGCAGAACAATACGAAAGCAAAGTA[C/T]GACAAATATTACAAAAGAATCCTGTCTCCTAGAGG Y 2 1 2 1 101000 f 74 goat snp55693-scaffold864-564618 27 17357118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476382 Affx-1251763893 AX-586011793 27 27029693 TCCCAACCCAGGGATTGAACCCTAGGTCTCCTGCA[-/TTGCAGGCTGATCTTTTTTTTTTTTAATTTATTTATTTATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTC]TGCAGGCTGATCTTTATCATCTGAGCCACTAGGGA - 4 1 4 1 20000 f 74 goat SV_200 27 27029693 - deletion junction SV-TF-chip 539476638 Affx-1251763893 AX-586012020 27 27029693 TCCCAACCCAGGGATTGAACCCTAGGTCTCCTGCA[-/TTGCAGGCTGATCTTTTTTTTTTTTAATTTATTTATTTATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTC]TGCAGGCTGATCTTTATCATCTGAGCCACTAGGGA - 4 1 4 1 20000 r 74 goat SV_200 27 27029693 - deletion junction SV-TF-chip 562165485 Affx-1251763893 AX-606940896 27 27029693 TCCCAACCCAGGGATTGAACCCTAGGTCTCCTGCA[-/TTGCAGGCTGATCTTTTTTTTTTTTAATTTATTTATTTATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTC]TGCAGGCTGATCTTTATCATCTGAGCCACTAGGGA - 8 1 4 1 20100 r 74 goat SV_200 27 27029693 - deletion junction SV-TF-chip 562165794 Affx-1251763893 AX-606941203 27 27029693 TCCCAACCCAGGGATTGAACCCTAGGTCTCCTGCA[-/TTGCAGGCTGATCTTTTTTTTTTTTAATTTATTTATTTATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTC]TGCAGGCTGATCTTTATCATCTGAGCCACTAGGGA - 8 1 4 1 20100 r 74 goat SV_200 27 27029693 - deletion junction SV-TF-chip 562166078 Affx-1251763893 AX-606941487 27 27029693 TCCCAACCCAGGGATTGAACCCTAGGTCTCCTGCA[-/TTGCAGGCTGATCTTTTTTTTTTTTAATTTATTTATTTATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTC]TGCAGGCTGATCTTTATCATCTGAGCCACTAGGGA - 8 1 4 1 20100 r 74 goat SV_200 27 27029693 - deletion junction SV-TF-chip 562166145 Affx-1251763893 AX-606941553 27 27029693 TCCCAACCCAGGGATTGAACCCTAGGTCTCCTGCA[-/TTGCAGGCTGATCTTTTTTTTTTTTAATTTATTTATTTATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTC]TGCAGGCTGATCTTTATCATCTGAGCCACTAGGGA - 8 1 4 1 20100 r 74 goat SV_200 27 27029693 - deletion junction SV-TF-chip 562166443 Affx-1251763893 AX-606941851 27 27029693 TCCCAACCCAGGGATTGAACCCTAGGTCTCCTGCA[-/TTGCAGGCTGATCTTTTTTTTTTTTAATTTATTTATTTATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTC]TGCAGGCTGATCTTTATCATCTGAGCCACTAGGGA - 8 1 4 1 20100 f 74 goat SV_200 27 27029693 - deletion junction SV-TF-chip 562166482 Affx-1251763893 AX-606941890 27 27029693 TCCCAACCCAGGGATTGAACCCTAGGTCTCCTGCA[-/TTGCAGGCTGATCTTTTTTTTTTTTAATTTATTTATTTATTCTTGCCGTCCTATTCCTCCGCCATCTTTCCCTCCTCCTC]TGCAGGCTGATCTTTATCATCTGAGCCACTAGGGA - 8 1 4 1 20100 r 74 goat SV_200 27 27029693 - deletion junction SV-TF-chip 38377398 Affx-122977566 AX-123247757 27 27071744 GAGGGTAAGTAATCGGCCCAATGTCACACAGTTCA[C/T]GTGTGTGGTAAGGATGGATGGGAAGAGTATGCAGG Y 2 1 2 1 101000 f 74 goat snp55691-scaffold864-500345 27 17292975 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394743 Affx-122964859 AX-123265098 27 27104955 CACAGCAAACTGGACTGAGACAAGCAGATGTTAAG[A/C]AACTAGAACTGTGAGAGTGCAAGCCATCTAAAGAG M 2 1 2 1 101000 f 74 goat snp55690-scaffold864-467134 27 17259928 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772024 Affx-122972475 AX-385259180 27 27135889 GGCTCCATTTCCTCCCTTGCATTTGTATGATGTGA[C/T]AGAGAGACCAGGTTTTAGCAAGGCGGTTCTAACAA Y 2 1 2 1 101000 r 74 goat snp55689-scaffold864-436200 27 17228963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436438 Affx-122933001 AX-123306776 27 27189854 AATCCATTTCCTTCCATTAGATTATAAAATAATAC[A/G]TATATATTACTAGAATACATTTGAAAACTATGTAT R 2 1 2 1 101000 f 74 goat snp55688-scaffold864-382235 27 17175277 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385463 Affx-122971300 AX-123255821 27 27223634 GAAAACCCACTAAGAACAAAGTCAACATTTGCAGA[G/T]AAGTGAAGCATAAAGACAGAGAACCGATCATATCA K 2 1 2 1 101000 f 74 goat snp55687-scaffold864-348455 27 17141485 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378853 Affx-122976525 AX-123249212 27 27253086 CAAGTTTTTCTGCATTTCTAGAACATATGGCTCTC[C/T]CGCATACTGAACGACATGTCTGCAAAAGATATTTT Y 2 1 2 1 101000 f 74 goat snp55686-scaffold864-319003 27 17111775 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445902 Affx-122925944 AX-123316239 27 27296455 GCACTCATTCAGGATTGAGAATGTGAAGGATTTTG[C/T]AGCTGGCACCACCCAGGTTCTTGCATCCAGACACA Y 2 1 2 1 101000 f 74 goat snp55685-scaffold864-275634 27 17068366 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788467 Affx-122953879 AX-385275484 27 27325259 TGTGAAAGAAGTCATGAATGACCCAACTCTAGAGA[C/T]ATGAAACACATCTGATTTATTGAAATGTCTCCTCT Y 2 1 2 1 101000 f 74 goat snp55684-scaffold864-246830 27 17039767 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447076 Affx-122924500 AX-123317412 27 27381491 GACTTGGTTTTGCATGGAACTTGTACTGTCCACGT[G/T]ATGAAGGGCTGAGAATGAAAGAGTTGTTTGTGCTC K 2 1 2 1 101000 f 74 goat snp55683-scaffold864-190598 27 16983709 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405178 Affx-122956930 AX-123275530 27 27419146 AGTTTTCAACTCATCACTATGAACTAAAGGAAATC[A/G]TTTAAAAAAGAAGACACTGAGATACTGTCAATTAA R 2 1 2 1 303000 r 74 goat snp55682-scaffold864-152943 27 16945841 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378398 Affx-122976795 AX-123248757 27 27463592 TACAACACCAACATCTCAGAGCTCATAGACAACAA[C/T]GGTTTATTTCTAGCTCATATAACATGTCACTGAGG Y 2 1 2 1 101000 r 74 goat snp55681-scaffold864-108497 27 16901287 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400364 Affx-122960027 AX-123270719 27 27539989 ACCTGATGTTTTCGATGTTATTTTAACATGTTTGT[A/G]CTTCATTTTTTCTTCCATAAAATGGGGATAAACTA R 2 1 2 1 103000 f 74 goat snp55679-scaffold864-32100 27 16823859 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376445 Affx-122978061 AX-123246804 27 27587515 CCGGGCCAAGTCCCTTTCCCAGTTGCTCACAGGAA[A/G]TTTCAACTGATGTCATTGGAAATGGTATGTGTGTA R 2 1 2 1 101000 r 74 goat snp11990-scaffold1441-15327 27 16776289 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783985 Affx-122951633 AX-385271039 27 27636884 ATATTGTGGGAACAAGGAGTATGAGCCTTACACCC[A/G]TAGAAGAAATCAGTGATAAGAAGTTAGACTAGCAG R 2 1 2 1 101000 f 74 goat snp11991-scaffold1441-64696 27 16726994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436886 Affx-122933228 AX-123307224 27 27671038 GTAACTTGGAACTAGAAGAAAAGTTTGGCATTTGC[A/G]CTGATTTTCTGATGGTAGCATACTCAGTATCTGGG R 2 1 2 1 201000 r 74 goat snp11992-scaffold1441-98850 27 16693312 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801624 Affx-122971095 AX-385288532 27 27729165 GTTCTACCTTGCAGTGTTCAAGAAGTTTTACCGAA[C/T]GCCTTGCCACCGCATAACAAGATTACCGTTTTTCC Y 2 1 2 1 101000 f 74 goat snp11993-scaffold1441-156977 27 16635035 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441718 Affx-122929147 AX-123312055 27 27775703 ACTCTTCCGAACCACGTCTTGTACTAGTTCGTCTC[A/G]TCCAGTAATCCCCCAGAGGCTTATTCTTAGACTCC R 2 1 2 1 101000 f 74 goat snp11994-scaffold1441-203515 27 16588785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406058 Affx-122956251 AX-123276410 27 27807652 GGCCCCTAAGAGATCCCTGATGTATTGCTCACATG[C/T]AGAGAAAAAAGTTGGGCACTGTTTGGGTCCCCATA Y 2 1 2 1 101000 f 74 goat snp11995-scaffold1441-235464 27 16558326 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411203 Affx-122952365 AX-123281553 27 27865259 ATCACTTCCTTTTAGCACTTTTCCTTAAAAATGAC[G/T]CCTTTTTCAATGATTTATTCTAAAACAGGTCTACA K 2 1 2 1 101000 f 74 goat snp11996-scaffold1441-293071 27 16500546 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384947 Affx-122972318 AX-123255305 27 27917782 CAGCGGTCCCCCAACTGGGGGCGACAGATGGACCT[G/T]CAGAGAGCACCCTGAAGGCCGACAAGCTCCAAGAC K 2 1 2 1 102000 r 74 goat snp11997-scaffold1441-345594 27 16446940 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429125 Affx-122938007 AX-123299467 27 27957599 TGATGACTTAAAGTGAAAATGAAGTTTTTGCTGCC[A/G]TTTATTAAACTAAGTGTAAAAGCTGATGTCAGAAA R 2 1 2 1 201000 r 74 goat snp11998-scaffold1441-385411 27 16407120 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277864 Affx-1111836059 AX-519551360 27 27961648 AGAGTGTGAAAGTACTCCCTACCCATATCATGCAC[A/G]TATACAATTGTTCAGTGATGGAAAAATAGGTAACA R 2 1 2 1 201000 r 74 goat Random2.2K-2234 27 27961648 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388122 Affx-122969483 AX-123258480 27 27994843 GCAGGGAACGGAGGTCTCTCTAGCAGCTGTGTGAA[C/T]GGATATTGTGCCTTTGCCCATGTCCTGGCTGCAGA Y 2 1 2 1 101000 r 74 goat snp11999-scaffold1441-422655 27 16369744 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438870 Affx-122930749 AX-123309207 27 28049721 CCCACCTTGGAGTTTATGCTTTTGGGGTTCATGCT[A/G]TTGTTATCTGAAATATTTCTGTGTGCAGAGTGATA R 2 1 2 1 201000 f 74 goat snp12000-scaffold1441-477533 27 16314685 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777292 Affx-122974989 AX-385264414 27 28104294 TTTTTCATTCAACAATGCATTTTGGAAGTCTTTCC[A/G]TAACAGCTGTATATAGATAGCATCTTCATTCTATG R 2 1 2 1 201000 f 74 goat snp12001-scaffold1441-532106 27 16260026 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781036 Affx-122929297 AX-385268123 27 28138179 TTTGGGTGAACAACTTCCTCTGTAAAGTTTCAAAA[G/T]ATGTCCCCTTATACTAGTATTTGGAGACTTGGCAA K 2 1 2 1 101000 f 74 goat snp12002-scaffold1441-565991 27 16226123 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428364 Affx-122938973 AX-123298707 27 28189462 GAATAAGACACAGCTCTGCTTTTAGGAGCTTGTTC[A/G]CAACCTAGCAGAGGAGGCTAATTCCTTTATAATTA R 2 1 2 1 101000 r 74 goat snp12003-scaffold1441-617274 27 16172864 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451179 Affx-122921340 AX-123321513 27 28218993 GATGTAAACCAGATGCTTGGGGACACAGAGTTGGC[A/G]CATGTGGTCTCTCAGATGATCATGATGCTATAAAG R 2 1 2 1 101000 r 74 goat snp12004-scaffold1441-646805 27 16142910 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765792 Affx-122936281 AX-385253247 27 28275197 CTTGTAATAGTGAGCAGGAAAAAATTGATTAAATA[C/T]GATCATATAAAACCAGAATTGCTCCAAATTGATTC Y 2 1 2 1 201000 f 74 goat snp12005-scaffold1441-703009 27 16086034 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424862 Affx-122941338 AX-123295208 27 28298092 TCATAAGCTGGGTCTCTGACCTCCTAAGCAATAAC[A/G]TCAAGCTAATCGAAAGGCCATGCAAAGGGATTGAG R 2 1 2 1 101000 f 74 goat snp22394-scaffold221-2322089 27 16037689 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414993 Affx-122949046 AX-123285342 27 28386522 AAAACTGAAGTCTCCATGAGGAAACCCCACTTGCC[A/G]CATGGTATTCTCGGACCATTCTTATCTCAATGGGC R 2 1 2 1 201000 r 74 goat snp22392-scaffold221-2233659 27 15951675 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412445 Affx-122951412 AX-123282794 27 28433129 CTTTGTTGTGGCATGAGTGGAACATGGTGACATAA[G/T]GAGAGTCTAGAATCAACCCAGCAGGATGATTCTCT K 2 1 2 1 101000 f 74 goat snp22391-scaffold221-2187052 27 15904632 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400532 Affx-122960445 AX-123270887 27 28465168 GGTGCTATTGCCTATGGCTATACCTCCTTGAACAT[A/G]CCCCAATCTTGTCTGAACTCAGGGTGCTATCACTT R 2 1 2 1 101000 f 74 goat snp22390-scaffold221-2155013 27 15872079 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790442 Affx-122948570 AX-385277445 27 28630707 CCAGATGCCGATGTCTCACAGCAAGAGATTGGAGA[C/T]ATTCAGGTTTTCTCATTTGGATGAGTCTTATTGCC Y 2 1 2 1 101000 f 74 goat snp22386-scaffold221-1989474 27 15705687 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413629 Affx-122950549 AX-123283978 27 28660586 GACATGGTAATTAAAAGCAAAATTAGATAATACTA[C/T]ACAAACAATACCAGGTATGACAGGAGCAGGAGCCC Y 2 1 2 1 201000 f 74 goat snp22385-scaffold221-1959595 27 15675911 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414036 Affx-122949789 AX-123284385 27 28716141 GATTCCAATTTGTTTTAGTAGTTTATGGGTTGCAT[A/G]TCAATCTGGGGAGGATTTGGGTTCTGGAGTTGGAT R 2 1 2 1 201000 f 74 goat snp22384-scaffold221-1904040 27 15620214 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790495 Affx-122971084 AX-385277498 27 28748691 TAATCACACACAACATTTACAAAGTCAAAATGCAG[A/C]TAATAATAAAACTCAGAATAGAATTCTGAGGATGC M 2 1 2 1 102000 f 74 goat snp22383-scaffold221-1871490 27 15587727 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273132 Affx-1111833327 AX-519546796 27 28816085 ACTTGACTTTACCGTTGAGAAGGTCATTCTCTGTT[A/C]AGAAGAGAGATAGGAAGCAAAGATGACAATTATTG M 2 1 2 1 201000 f 74 goat 27_28816085_AF-PAKI 27 28816085 T G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468277729 Affx-1111836060 AX-519551228 27 28828736 TTATTTCCCAAGGGTTAGGGTCTTTGGATAAGAAC[A/G]TAACTGCAGAATATAGAAAGAAAGAAACATCATTT R 2 1 2 1 101000 f 74 goat Random2.2K-2235 27 28828736 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38445877 Affx-122925966 AX-123316214 27 28830142 CCCTTGCTATGAACCCTTCAGACTGAATTTCCATC[A/G]TGCCAAAGTGCTGTCTTTCTTTTATTTATGCAGAC R 2 1 2 1 101000 f 74 goat snp22381-scaffold221-1790039 27 15506120 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394111 Affx-122965345 AX-123264466 27 28951438 CAACCCTTTCATAGCACCACTATCCCTACACACAA[C/T]ACAGGGCACTTTACATGTTCTGTTTCTGCAGATTA Y 2 1 2 1 101000 r 74 goat snp22379-scaffold221-1668743 27 15384320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796656 Affx-122945056 AX-385283602 27 29019812 GTAGAAATACACAGCAGTCTTTATCAATTATAAAA[A/G]CATCACATGTTTTTGAAATTGTACAAACACATATG R 2 1 2 1 201000 r 74 goat snp22377-scaffold221-1600369 27 15315854 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386523 Affx-122970738 AX-123256881 27 29132759 CAGAATCAAATACAAATTTCTGAATTTTGGAATTT[A/G]TATCCTTTTACCCTTCCATACTCTGTCATTCATTC R 2 1 2 1 101000 r 74 goat snp22375-scaffold221-1487422 27 15201783 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464016535 Affx-1110273281 AX-515493385 27 29169198 AGTGGCTTCCTGATGGGCTTGAGCGTCATCGGGTC[C/T]GTTTTCAATATCACGGGAATTGCCATCAACCGCTA Y 2 1 2 1 202000 f 74 goat ilmnseq_rs664494080 27 29169198 T C 2 neutral Goat_IGGC_65K_v2 Illumina 468275868 Affx-1111835124 AX-519549429 27 29169203 AGCAATAGCGGTTGATGGCAATTCCCGTGATATTG[A/G]AAACAGACCCGATGACGCTCAAGCCCATCAGGAAG R 2 1 2 1 201000 f 74 goat ilmnseq_rs654837737 27 29169203 T C 2 recommended Goat_IGGC_65K_v2 Illumina 468275772 Affx-1111835001 AX-519549337 27 29169234 AGCTTGTCGTATCTGAGGCTGTGGCAGATGCAGCA[A/G]TAGCGGTTGATGGCAATTCCCGTGATATTGAAAAC R 2 1 2 1 101000 r 74 goat ilmnseq_rs639028962 27 29169234 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275976 Affx-1111835101 AX-519549534 27 29169276 CAGATCAGGAACACGTAGCAGAGGGAATTCGTGCC[A/G]CTATACAGCTTGTCGTATCTGAGGCTGTGGCAGAT R 2 1 2 1 101000 r 74 goat ilmnseq_rs651759989 27 29169276 C T 1 recommended Goat_IGGC_65K_v2 Illumina 468276178 Affx-1111835206 AX-519549728 27 29169282 CACAGCCTCAGATACGACAAGCTGTATAGCGGCAC[A/G]AATTCCCTCTGCTACGTGTTCCTGATCTGGATGCT R 2 1 2 1 201000 r 74 goat ilmnseq_rs663472455 27 29169282 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275781 Affx-1111835081 AX-519549346 27 29169321 TCCCTCTGCTACGTGTTCCTGATCTGGATGCTGAC[A/G]CTCGTGGCGATCGTGCCCAACCTGTGTGTGGGGAC R 2 1 2 1 101000 f 74 goat ilmnseq_rs648949715 27 29169321 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275863 Affx-1111835121 AX-174356637 27 29169396 CAGTACGACCCGAGGATCTATTCCTGTACCTTCAC[A/G]CAGTCGGTCAGCTCAGCCTACACGATCGCCGTGGT R 2 1 2 1 102000 f 74 goat ilmnseq_rs654513717 27 29169396 G A 1 neutral Goat_IGGC_65K_v2 Illumina 468275755 Affx-1111834992 AX-519549321 27 29169402 AACACCACCACGGCGATCGTGTAGGCTGAGCTGAC[A/C]GACTGCGTGAAGGTACAGGAATAGATCCTCGGGTC M 2 1 2 1 303000 r 74 goat ilmnseq_rs637617337 27 29169402 G T 3 not_recommended Goat_IGGC_65K_v2 Illumina 468276110 Affx-1111835172 AX-519549661 27 29169465 AGAACCAGGGCCCAGATTCTCAGATAACAGAAAAC[A/G]ACTACGAGCATCGGAACTATGAAATGGAACACCAC R 2 1 2 1 201000 r 74 goat ilmnseq_rs659448268 27 29169465 C T 2 recommended Goat_IGGC_65K_v2 Illumina 468276170 Affx-1111835275 AX-519549720 27 29169468 TGAAGAACCAGGGCCCAGATTCTCAGATAACAGAA[A/G]ACGACTACGAGCATCGGAACTATGAAATGGAACAC R 2 1 2 1 101000 f 74 goat ilmnseq_rs670508951 27 29169468 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275610 Affx-1111834995 AX-519549180 27 29169525 GCCCTGGTTCTTCAGGTCAGATGGAAGGTGAAACC[A/G]GACAACAAACCGAAACTGAAGCCCCAGGACTTCAG R 2 1 2 1 101000 f 74 goat ilmnseq_rs638037744 27 29169525 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468276123 Affx-1111835179 AX-519549673 27 29169615 GGGTCCGAGGCCACAACTAGACCAATGAAGTTCAG[A/G]GGAGCCCAGCAAATGGCAAAGAGGACAAAAACCAC R 2 1 2 1 102000 r 74 goat ilmnseq_rs660347541 27 29169615 T C 1 neutral Goat_IGGC_65K_v2 Illumina 468276202 Affx-1111835218 AX-519549752 27 29169633 GCCATTTGCTGGGCTCCTCTGAACTTCATTGGTCT[A/C]GTTGTGGCCTCGGACCCCACCAGCATGGCACCCAG M 2 1 2 1 202000 r 74 goat ilmnseq_rs664622021 27 29169633 A C 2 neutral Goat_IGGC_65K_v2 Illumina 468275980 Affx-1111835184 AX-519549537 27 29169711 AGTCCATATATGATTGCATTGAGGCAGCTGTTGAA[A/G]TATGCCATATAGTAACTAGCCACAAACAGCCACTC R 2 1 2 1 101000 f 74 goat ilmnseq_rs661503102 27 29169711 T C 1 recommended Goat_IGGC_65K_v2 Illumina 468275700 Affx-1111835041 AX-519549269 27 29169816 TTAATTCTATCTGCTACATGATTGGAGCTATCCAC[A/G]AAGAACATCTTGGTGGTACACAATGAGACTATAAT R 2 1 2 1 101000 f 74 goat ilmnseq_rs643693494 27 29169816 T C 1 recommended Goat_IGGC_65K_v2 Illumina 38376526 Affx-122978004 AX-123246885 27 29251696 TGAGAGCTTGATGCAAATGAAGAAAATGTTTCCTT[A/G]CACATTGAATTTTGGCCACATTTCGTCTTCTTTTC R 2 1 2 1 201000 r 74 goat snp22373-scaffold221-1368485 27 15081276 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396860 Affx-122963248 AX-123267215 27 29298461 TTGCTCTGTTAGATGCTTGAGAAGGCATTCTGGCC[A/G]TGCAGATGGTGGAAGAAAGCCGCTTTGCAGAAAAT R 2 1 2 1 101000 f 74 goat snp22372-scaffold221-1321720 27 15034384 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781658 Affx-122961442 AX-385268742 27 29344004 TTTATAAGAACAGGCTGCAAAATTCCCATTTGCAC[A/G]CACGTCCTTTATTGCTTCATTCACACCCCATGAAA R 2 1 2 1 201000 r 74 goat snp22371-scaffold221-1276177 27 14988739 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429647 Affx-122937675 AX-123299988 27 29373373 ACCTGGTAGATGGCATTCTTTCTTCACACCCCAAA[G/T]AGAAGACAGCTGAACCCATGAAGAGATGACTGCCC K 2 1 2 1 201000 r 74 goat snp22370-scaffold221-1246808 27 14959204 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277868 Affx-1111836061 AX-519551364 27 29428111 CGTGGCACTGGCTGGCTCACTTGAAGAGTTCATTG[A/G]CTTCAAGGGTGGATAATGCACCCCAGAGAAGCTAA R 2 1 2 1 101000 r 74 goat Random2.2K-2236 27 29428111 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38448387 Affx-122924095 AX-123318723 27 29483727 GTATTTTTTTTAATTTAAGTATAGTTGGTTTACAA[C/T]GTGGATTCAACATATTTTGATTCAGAAGGCAATAC Y 2 1 2 1 101000 r 74 goat snp22367-scaffold221-1136454 27 14852801 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423930 Affx-122942262 AX-123294276 27 29531699 CGTATTCATCAGTGTTATTTTTTTTCCCCTATAGT[A/G]TCTATAATAAAAGTGAAGATGACTTTAGACTCATG R 2 1 2 1 201000 r 74 goat snp22366-scaffold221-1088482 27 14804972 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383604 Affx-122972561 AX-123253962 27 29620490 ACATTCCAGGTGTTGACTTCATGGCAACTATCAAA[C/T]CTCAAGGGAATAACATCAGAAAGCCCCAATTCATT Y 2 1 2 1 101000 r 74 goat snp22364-scaffold221-999691 27 14718445 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437539 Affx-122931906 AX-123307877 27 29651409 CTTTGAAATAGTGAATGAACTCTACCTCCTAACGA[C/T]GACTGCCCGTTAAGGTTTAGCTTTGCCCCAAAATG Y 2 1 2 1 101000 f 74 goat snp22363-scaffold221-968772 27 14687656 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791248 Affx-122965451 AX-385278242 27 29826880 GATGTCTGGGAGAAAACACAAGCAATTACACACTC[A/G]CAAGGCAGTTTCATAAATAGATTTGGTCCTTACAT R 2 1 2 1 101000 f 74 goat snp22360-scaffold221-793301 27 14511592 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447834 Affx-122923907 AX-123318170 27 29859607 TAGCATGTGGAGGGGGGAAAAGCTCTTTAAAAGCA[C/T]GTCTAGGCTGGTGATAAAGTAAGTAAAAATTAGAA Y 2 1 2 1 101000 r 74 goat snp22359-scaffold221-760574 27 14478852 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794418 Affx-122939526 AX-385281381 27 29904658 ACATCTCATTCACATCTATGATTTCACAGGCTTCA[A/C]TTTTTCCATCAAAAAGCTTAGTCATTGTAACCATC M 2 1 2 1 101000 f 74 goat snp22358-scaffold221-715523 27 14433568 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432839 Affx-122935375 AX-123303180 27 29937883 CCCCTTCTTTCCTCCAGGTCCTTGGGCGCTGCTCA[A/C]GGATGGCGCCATCATCTTAAAAGGTGTATCTGGGG M 2 1 2 1 202000 f 74 goat snp22357-scaffold221-682298 27 14400254 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775182 Affx-122977419 AX-385262313 27 29971956 GAACATTTTCCGGGTAATTGCTGCCTGCATCCTCA[C/T]AGACAGGGATAGCTAGCGTGCATATGAGTGACGGA Y 2 1 2 1 101000 f 74 goat snp22356-scaffold221-648225 27 14366333 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277870 Affx-1111836062 AX-519551366 27 29996236 AAAAAAAATCAAAGTTATCATAGGTAATGAGCATT[A/C]TTTGATGAAACTGGATCACAATATAAAAAGTATTC M 2 1 2 1 101000 r 74 goat Random2.2K-2237 27 29996236 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38393923 Affx-122965082 AX-123264278 27 30008627 TGGCAGTGAATGGCAGTGAAAACTGCAAAAGCAAA[G/T]CTCAGATTTCTTTGAATGGGGATATAGCATGGAAA K 2 1 2 1 101000 f 74 goat snp22355-scaffold221-611554 27 14330134 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780066 Affx-122929972 AX-385267164 27 30052897 ATATATTTGATATTTGTGTGCACATATTGATTACC[A/G]TTTCTCAAATTTCTATGGTTTTTCTTTTAGTTGTA R 2 1 2 1 101000 r 74 goat snp22354-scaffold221-567284 27 14285860 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402985 Affx-122958146 AX-123273338 27 30133309 CGCCATGAAGGTTTGGCGGTCTTTAGATCCCATAA[C/T]GAATGCTCTCTCAAGGTCCCCACAATGACCTTCCT Y 2 1 2 1 101000 f 74 goat snp22352-scaffold221-486872 27 14204823 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412913 Affx-122950403 AX-123283262 27 30210591 CCTCTCCTTCCCTCATTTCCTTCCTCCTCCTTCCT[A/G]CATTCTTAATCTGTTGGCAAGATGTGGGTGTGCTG R 2 1 2 1 201000 r 74 goat snp22351-scaffold221-409590 27 14128766 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442713 Affx-122927864 AX-123313050 27 30302582 TCTCTACGTAACAGTGATGAAGAAAAACACAATAT[A/G]CAGTTTTCTTGTGAAAGAGTGTATTTATCTGGGCA R 2 1 2 1 101000 r 74 goat snp22349-scaffold221-317599 27 14036307 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769387 Affx-122969075 AX-385256558 27 30391437 TTCATAGTCTATAAGCTTAAGATTCATACCAATGA[C/T]GGGTATATTTTGCTGCTTTATCTGGGAGTCATCCT Y 2 1 2 1 101000 r 74 goat snp22347-scaffold221-228744 27 13945895 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767758 Affx-122932488 AX-385254985 27 30443205 TGCTAACTAGGAGAAATGATCGTTGGTCTGAAAGC[A/G]TTTGGTTTACATTACTACATTACATAACTTGCCAT R 2 1 2 1 101000 f 74 goat snp22346-scaffold221-176976 27 13894171 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444062 Affx-122926854 AX-123314399 27 30471893 GAAGGAAAGAGGGAAAACCAGAGACTAAGGAACCA[G/T]CAGGAAAGATCGGACCAAGACCGTGTTTTGAAGTT K 2 1 2 1 101000 f 74 goat snp22345-scaffold221-148288 27 13866089 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430498 Affx-122937230 AX-123300839 27 30618602 CTCCTAGAAAGACATAAACAAAAATATGGCATCAT[C/T]GACCTAAAGAATCCTAAAACGTTTACCAGAGTTTG Y 2 1 2 1 101000 r 74 goat snp22341-scaffold221-1579 27 13719105 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788751 Affx-122972960 AX-385275767 27 30636942 TAGATGGAAAATATCCCTAAGTACATGTGGTAACA[G/T]AAGTAGAAGACTAGCTTCTACATATAAGTTGTTGA K 2 1 2 1 202000 r 74 goat snp56380-scaffold883-1092994 27 13701737 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405717 Affx-122956530 AX-123276069 27 30675433 CCACTGACTCCCTGGGAGGAGCAACCCAAAACACT[A/G]TGGTATGAGAGAAGAGAGAAGATTCTGGTGGGTGG R 2 1 2 1 101000 r 74 goat snp56379-scaffold883-1054503 27 13663367 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442780 Affx-122927733 AX-123313117 27 30722307 CTACCATATTGGATTACAACTCTCTTTGCTTGGCA[C/T]GACATAGTCCCCCCAGATTTCAAGGTGAGGGTGTA Y 2 1 2 1 101000 f 74 goat snp56378-scaffold883-1007629 27 13619240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409974 Affx-122953287 AX-123280324 27 30756686 TTCTGAAATAGTGTTTCAAATTTGAAAAAGGAATC[A/G]CGTTTGGATTATTCCAATGACTTCTATGATTCAAT R 2 1 2 1 101000 r 74 goat snp56377-scaffold883-973250 27 13584930 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445308 Affx-122925438 AX-123315645 27 30812790 GATCACAGAAATGAAGTTCCATATCGCTAAACTCA[C/T]GAGAGGATCCTTGGAGGAAGAAGATCAAACAAGCT Y 2 1 2 1 201000 f 74 goat snp56376-scaffold883-917146 27 13528931 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784437 Affx-122960481 AX-385271485 27 30849199 CAGGAAAGCTCATCCCAGCAAAGTCATTGGAGAGA[C/T]GTTGCGTCAGGATTTTGTTCTTCAGGCCGTTGCAG Y 2 1 2 1 101000 f 74 goat snp56375-scaffold883-880737 27 13495004 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415733 Affx-122948505 AX-123286082 27 30879452 AATCTACCTACTTTGTCCACTTTTCTATGTGTTCT[A/C]TTCCCTCCTCTTCCTTTCAACATTAGCACTCCCAT M 2 1 2 1 101000 f 74 goat snp56374-scaffold883-850484 27 13464669 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450884 Affx-122922211 AX-123321218 27 30916392 TACAAATTTTGTGTAAATCTGAGTACCCTAATTGC[G/T]AAGGACTGATGTACAGAACACAATGTCATTTTTAT K 2 1 2 1 101000 f 74 goat snp56373-scaffold883-813544 27 13427824 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788348 Affx-122919257 AX-385275366 27 30946191 ATTAGTCATGGTTGGGGTTCACAGAGACTTAAATA[C/T]ATGTGTTGATGTCTTCAGTTTAAGATAATTCTCAG Y 2 1 2 1 101000 f 74 goat snp56372-scaffold883-783745 27 13398162 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437296 Affx-122931981 AX-123307634 27 30976361 AAATATCCCAGCAGGTCATAGGTCAGCAAGTCCAA[C/T]GGGGCTATTGGTCATATGTTAGAAGTAAGGAAGAC Y 2 1 2 1 201000 f 74 goat snp56371-scaffold883-753575 27 13367543 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398300 Affx-122962152 AX-123268655 27 31005822 GAATGATCGCCACGCAGATAAATCAAACTAGGCGT[A/G]TTCGAAGGTCAAACCAGAGCACTTGCAGCTCATTT R 2 1 2 1 101000 f 74 goat snp56370-scaffold883-724114 27 13338225 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771292 Affx-122963900 AX-385258450 27 31078152 AAGGGTCAAGAACAACTGCTTCCCAGAGAACATTC[A/G]CCATGTGTGGTTGGTGCCTTTTAAACTGTAAAGTG R 2 1 2 1 101000 r 74 goat snp56368-scaffold883-651784 27 13265590 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277736 Affx-1111836063 AX-519551235 27 31083141 CATTTTATTAAATGCTTACTTCAGAGTTGGAGAAG[A/G]GGTGAGTAGAGTAGGGAGGAGGAAAAGTCTGTTAA R 2 1 2 1 201000 f 74 goat Random2.2K-2238 27 31083141 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320769312 Affx-122920325 AX-385256483 27 31117801 CTCTCTCTCATACACACTTTGTAGCTTTCTTGTAG[G/T]CGACCTCGTTGTTGATTTCATGATAACTGAAGCTT K 2 1 2 1 101000 f 74 goat snp56367-scaffold883-612135 27 13226864 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426287 Affx-122940308 AX-123296633 27 31146724 CCTCTCCCTCCCCCACTTCCCTTTTCCAGCACTCT[A/C]TCTGGCTGATCTCTCTCACGAGCATCTACCTCGAT M 2 1 2 1 101000 r 74 goat snp56366-scaffold883-583212 27 13198242 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793096 Affx-122957969 AX-385280074 27 31192235 TGAGTTATTCAATTTCTTGTTGCTCTAGAATCAAT[G/T]GTCTGGCTATTTGTATTTTCCCCCTCATGGATCCT K 2 1 2 1 101000 r 74 goat snp56365-scaffold883-537701 27 13152868 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448282 Affx-122924177 AX-123318618 27 31253999 CTTTTACAAAAGTGCTTTTGGCGGGGGTAGGGATG[C/T]AGGGGTGGGGAGGGGAGAGAATGAAGAACTGGAAG Y 2 1 2 1 103000 f 74 goat snp56363-scaffold883-475937 27 13091039 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384520 Affx-122973041 AX-123254878 27 31291393 TGCTTGGGTCCAGCCCGAGCAAACATAACTCAAGT[C/T]CTGCACCCAGCTACGAAGGTGACCTGCCAGAGGAG Y 2 1 2 1 101000 f 74 goat snp56362-scaffold883-438543 27 13053819 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436050 Affx-122932716 AX-123306389 27 31326954 CCGCCCCTTGGGGTGCTACTCAGTTCTTTGGTTTT[A/G]CTCCTTCTTAAATCTCTCTCCCTCTCTCTACACAT R 2 1 2 1 201000 f 74 goat snp56361-scaffold883-402982 27 13019344 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389118 Affx-122968561 AX-123259476 27 31377935 CTATCTCGTTGAGTTTGATTATAAAGGTTATGCTA[G/T]CTTCATAGGATGAGTTAAGAAGAAGTTGTGTAAAA K 2 1 2 1 101000 f 74 goat snp56360-scaffold883-352001 27 12968366 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413992 Affx-122950282 AX-123284341 27 31407216 AAATTAGGCAGTATCTGAAGGTGAGTTTTCAAGTT[G/T]TCATGATCTCCTACAGGCTTTTGTGTAAAAAACAA K 2 1 2 1 101000 f 74 goat snp56359-scaffold883-322720 27 12939998 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377276 Affx-122978128 AX-123247635 27 31442813 TCTCAAACTTTTTTTTTTAATACCCTAAAGCTATG[C/T]GCTTGAAGTTTTGGTCATAGGGAGTTGCTTGAGAT Y 2 1 2 1 101000 r 74 goat snp56358-scaffold883-287123 27 12904211 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768015 Affx-122939554 AX-385255229 27 31473893 GCAGCTCAATCTCCAGTCTTTTGACTTAAACCCAG[C/T]GTTTATTTTTACTACTGTAAGCTGAAAATATGAAT Y 2 1 2 1 101000 f 74 goat snp56357-scaffold883-256043 27 12872882 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273182 Affx-1111833328 AX-519546840 27 31492100 TAGCATTTCCCTTGTGCAACTTTGTGTTTCTTGTA[A/G]ATGAATAACAGAGCTATAAATCTGATCAAATTCAA R 2 1 2 1 201000 r 74 goat 27_31492100_AF-PAKI 27 31492100 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38375405 Affx-122979204 AX-123245764 27 31511012 GGGGAGGATAGTAAACTAGCACAAACTCAGTCAGG[C/T]GGGAACCCTCATGGCCATTGTTCTGTCAGATGTAT Y 2 1 2 1 101000 f 74 goat snp56356-scaffold883-218924 27 12835786 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379444 Affx-122976096 AX-123249802 27 31561966 AGGACTGCAGGACTTAATAGCTGTAGCGTGCGCCT[A/C]GTGCCAGGCTAGGGTGGTAAATCCTACCTGTTACT M 2 1 2 1 101000 f 74 goat snp56355-scaffold883-167970 27 12785089 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445367 Affx-122925413 AX-123315704 27 31604630 GACCCGGTAATGGGGTGAAGGATGAACGTATCGTG[C/T]GCATTTCCTGGAAAAGGCTGAAGCAACATCCCGGA Y 2 1 2 1 201000 f 74 goat snp56354-scaffold883-125306 27 12742614 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782928 Affx-122960585 AX-385269998 27 31661317 CCCTTTGAACTTAAAGGACATCCTGTTGATGGCAC[G/T]TGTTTGTTAGTGACCATCGATTCTTATCACTCTGA K 2 1 2 1 101000 f 74 goat snp56353-scaffold883-68619 27 12685511 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420353 Affx-122944962 AX-123290700 27 31701910 CAGACAGACTGGTTAGTTGTCCCAAGCCAAGGAAA[C/T]AGACCATTCCCATTATTTTCCTATTCAGGCAGGTA Y 2 1 2 1 101000 f 74 goat snp56352-scaffold883-28026 27 12644718 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273491 Affx-1111833650 AX-515495343 27 31750648 TAACTGGCGAGGCTGCAGAAAGAGCCTGGATTGCC[A/G]CGAGGCCTGC R 2 1 2 1 102000 f 74 goat GoatD01.000568 27 31750648 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38440245 Affx-122930665 AX-123310582 27 31772741 GCATTTCCTGCAAGCGTTCTGAGGTTGAAAAACAC[A/G]TCTGGGGCTTAAGGTGTCTGTCCCGTTTCACACAC R 2 1 2 1 101000 f 74 goat snp7024-scaffold126-42706 27 12572855 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439527 Affx-122930120 AX-123309864 27 31805712 AAGACAAACTGCAGAGGAAGGAAACCTCTCCTTGG[C/T]GTGTTCCATCGGGTGAATTGCAAAAATATGAGCCC Y 2 1 2 1 101000 r 74 goat snp7025-scaffold126-75677 27 12539580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441178 Affx-122929548 AX-123311515 27 31834731 TTTCATTGTTTTCCCTAATTCTGCATTTAGCTTTC[A/G]TCTCCTTCAGACACATTCATTCATTCCATCTACTA R 2 1 2 1 201000 f 74 goat snp7026-scaffold126-104696 27 12510488 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380392 Affx-122975328 AX-123250750 27 31892121 AAAAGGTTTTTGTTAATTCCAGCCCAGCAGCTTTA[C/T]GTGGGAATGGCTATGATGTCGGTGGTACAGGAGAG Y 2 1 2 1 101000 f 74 goat snp7027-scaffold126-162086 27 12453012 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429667 Affx-122937658 AX-123300008 27 31935112 TTCTCATATTTACTGATGGGGAGTGGTTAGAGGGG[C/T]GGTGGGGTGCAGAAATCACTTACTTTTCTCTTTGC Y 2 1 2 1 102000 r 74 goat snp7028-scaffold126-205077 27 12410280 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388696 Affx-122968992 AX-123259054 27 31965019 GAATTTTTCAAATATACAGAAAAATTCAGATACTA[C/T]AATAGATGCCTGTTTATTCCTTATCTAGATTTGCC Y 2 1 2 1 102000 r 74 goat snp7029-scaffold126-234984 27 12380350 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448574 Affx-122923410 AX-123318910 27 32024506 TCTTGTGCTTCAGCCGTAATAAATATCTTCTTACC[A/G]GGAAAAAAATCCTGCGCTGAACCTGCTGAGTTGCA R 2 1 2 1 101000 f 74 goat snp7030-scaffold126-294471 27 12320839 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772787 Affx-122948802 AX-385259932 27 32057093 CCTGCAAGGTATATTTGTTCATTGTCTCCCATTTA[C/T]GTATTTCTTTATATCTGAATGGACCCATATTTATT Y 2 1 2 1 101000 f 74 goat snp7031-scaffold126-327058 27 12288197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384284 Affx-122972299 AX-123254642 27 32091433 CAGGTGCGGGACAGTGCAATTACAGCTGCAAAGAG[C/T]AGGGGTGACAGAAAGGAACAGAATCTCCAAGATTT Y 2 1 2 1 101000 f 74 goat snp7032-scaffold126-361398 27 12253989 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794131 Affx-122919395 AX-385281097 27 32150289 GGATAAGTGTGCTACAAAGCAGAGACGCTAAGAGT[G/T]AACCTCTAGAAACTATGATAATTTGACACTGCATG K 2 1 2 1 101000 f 74 goat snp7033-scaffold126-420254 27 12194788 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785558 Affx-122950033 AX-385272602 27 32200092 ATGATCTTTTGCAGAAAAGTACATGTGCATGATAA[C/T]GCAGTGATTAATTTATGAAATTAATGTGAAAAGTA Y 2 1 2 1 101000 r 74 goat snp7034-scaffold126-470057 27 12144990 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390255 Affx-122967755 AX-123260612 27 32230308 GAGGACTGACCCATGGCCTCGGCTTTTCTAGCCCT[A/G]CCTAAGCTAAACCGTGCCTGGCATCAGCCCACGTG R 2 1 2 1 201000 f 74 goat snp7035-scaffold126-500273 27 12114700 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406448 Affx-122955189 AX-123276800 27 32285976 TCGGTTCTCAACATGTTCCCCATTCTGGGGCCTTT[A/G]TGTGACGGGGGCCTTAGAATGTTTGGCAAATACTG R 2 1 2 1 102000 r 74 goat snp7036-scaffold126-555941 27 12058932 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772417 Affx-122976888 AX-385259569 27 32375013 CATTCCAGGAGTCTTTCTTAGGGGAGCAAAGAGAT[A/G]CTTTCCAAACAGGAGAGCATTCTCAAAGACTGCCT R 2 1 2 1 101000 f 74 goat snp7038-scaffold126-644978 27 11970130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277878 Affx-1111836065 AX-519551373 27 32394450 TCTACATCGCTAGGACTAGACTTGCACGCAGTGTC[A/C]GGGAGTGCTAATGTTCTCATCAGGCGTTCTGTTTC M 2 1 2 1 201000 r 74 goat Random2.2K-2240 27 32394450 A C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416694 Affx-122947571 AX-123287042 27 32433094 CTCTACGAGGTGGTTCCTCACTGGGTGTTTATAAC[A/G]TCAGACAATGGAAACAAGCTAATTGTCTGACAATA R 2 1 2 1 202000 r 74 goat snp7039-scaffold126-703059 27 11911893 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404414 Affx-122956775 AX-123274766 27 32467250 TGGTCCCAAGGTTTCTGTGAGCCTTTTCCTACACG[C/T]GACAGAGAAGCTCGTGTCGGGGAGCAAAGTGACCA Y 2 1 2 1 101000 f 74 goat snp7040-scaffold126-737215 27 11877719 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441514 Affx-122928721 AX-123311851 27 32497823 TTTGGTAAATACTCCTCCAAAGTTCTTCAGCTTTA[C/T]TTAAATAATTCTAAGTTAAAATGGTCACACCTGCC Y 2 1 2 1 101000 r 74 goat snp7041-scaffold126-767788 27 11847395 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795128 Affx-122937912 AX-385282086 27 32536254 AGAGGATCTCTTTCTCCAAGGAGATTCTGCACATG[A/C]CTTATATATTTACCAAAGCTTGCCTAAAAATAATC M 2 1 2 1 101000 f 74 goat snp7042-scaffold126-806219 27 11808881 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394721 Affx-122964335 AX-123265076 27 32600096 AGACAGAACTCAGGGATCAGTGCCAGCCACCGTCT[A/G]CAGATTCTCTGGATGGAACAAAGCTCCCAGGGCTG R 2 1 2 1 201000 r 74 goat snp7043-scaffold126-870061 27 11744789 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384353 Affx-122972244 AX-123254711 27 32676747 TCTTGGTTTCTAGTCCACTGAGGACTGGGAAACCA[C/T]ATAACTGGACCTTTTGAAATTAGATCTTCAGCCAG Y 2 1 2 1 101000 r 74 goat snp7045-scaffold126-946712 27 11667994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435821 Affx-122932833 AX-123306160 27 32747731 TTCAACCTGAGTGGATCAGCCAGTTTTGAGAATTA[C/T]TCTGTTCTCTTTGAGATGTTCTTTGACCCCGAATA Y 2 1 2 1 101000 r 74 goat snp7046-scaffold126-1017696 27 11597183 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426429 Affx-122940822 AX-123296775 27 32783591 TGATTGGTTCAGTGCGTAATGTTGATCCATGCTTA[C/T]GGCACTCATATCCATTGGACATTATTCTAGTAAAA Y 2 1 2 1 101000 f 74 goat snp7047-scaffold126-1053556 27 11561117 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777721 Affx-122952290 AX-385264839 27 32828705 TATCAAAATTGGGTTTCTCTGATTTGTAAGAGAGC[A/G]CTATTTTTATTACATGAATAGATGGAAAATTTTAT R 2 1 2 1 101000 f 74 goat snp7048-scaffold126-1098670 27 11516006 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793676 Affx-122934022 AX-385280648 27 32905720 TTGTGCTTAGTGGAGTAAATTAAGCTTCACTGAAA[C/T]AGAGTACCTTAATATCCCAGTGATGCAATTGAATA Y 2 1 2 1 101000 r 74 goat snp7049-scaffold126-1175685 27 11435943 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381477 Affx-122974967 AX-123251835 27 32955643 TAGGTGTGATGTTACGTGCTGTGGGTTTGTCTTAT[A/G]CGACCTTTGTTATGTTCAGTATATTCTTTTATAGG R 2 1 2 1 201000 r 74 goat snp7050-scaffold126-1225608 27 11384613 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430466 Affx-122937256 AX-123300807 27 33015588 CAAGAGCAACCCCTGGCAGATAGTGACAAAATGAA[G/T]CAACGGCTACAAAAAAAATGAATTCTTCACAGCCA K 2 1 2 1 201000 f 74 goat snp7052-scaffold126-1285553 27 11321220 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447346 Affx-122924881 AX-123317682 27 33061858 TGCCTCAGTAATTGAGACAGGAAGAATGGAAATGC[A/G]TCCACATCTGTTGCTTTCACATGCCCAGTGATTCT R 2 1 2 1 101000 f 74 goat snp7053-scaffold126-1331823 27 11274136 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425122 Affx-122941219 AX-123295468 27 33096099 TTATTGGATATGTGTATACATTCGATACCTATTGT[A/G]TGTCAGTTTTTGGGTAAAGTCCTAAGCACACAAAA R 2 1 2 1 101000 r 74 goat snp7054-scaffold126-1366064 27 11238647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801923 Affx-122939093 AX-385288829 27 33130787 TGATGATTAAGCCCTATTTTATTTGCTAAGACAGG[C/T]GGTATTGTCAGTTAATAGTATCTTGAAATTAAAGT Y 2 1 2 1 101000 f 74 goat snp7055-scaffold126-1400752 27 11202412 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777258 Affx-122924730 AX-385264380 27 33189887 ACCTTTCAATCATTGTACAAGGAACACTTAAAATC[A/G]TTAATTTCAAACCAAGCGTTTGTTCACAATATTCT R 2 1 2 1 201000 r 74 goat snp7056-scaffold126-1459852 27 11141316 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409511 Affx-122953630 AX-123279862 27 33242892 GGAACCAGTCTGTTGTTCCATGTCCAGTTCTAACT[A/G]TTGCTTCCTGATCCTAAACCATTCCAAATAAACTG R 2 1 2 1 303000 r 74 goat snp7057-scaffold126-1512857 27 11087150 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414188 Affx-122949665 AX-123284537 27 33336332 CTTATGATAATGTCTTAATTATAATAATTATAAAT[A/G]TAACACATTGAATACTGTGTTTGTAGCATTTTTGA R 2 1 2 1 103000 r 74 goat snp7058-scaffold126-1606297 27 10992348 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375719 Affx-122978634 AX-123246078 27 33386332 AGGGTTATATTAAGAACTTGCCTCCAGAATTTGAC[A/G]CATTCATTCATAAACATATTTTATAAGTTGATTGT R 2 1 2 1 101000 f 74 goat snp18606-scaffold1881-25106 27 10742872 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389159 Affx-122968533 AX-123259517 27 33471754 TGTGCACCATACATACATATCTTGGTCTAAGATAC[A/G]GAAGAAGGAAAAGCAAAGGTGGAAGGAACTGTGAA R 2 1 2 1 101000 f 74 goat snp18608-scaffold1881-110528 27 10656690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378519 Affx-122976637 AX-123248878 27 33519714 AACACAGTTATTAAAACTTAGCTCCACCGTTGTTC[C/T]AGAATTCACGTTCTAGATGCTTGCAACTAAACCAG Y 2 1 2 1 101000 r 74 goat snp18609-scaffold1881-158488 27 10607819 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405545 Affx-122955970 AX-123275897 27 33575454 GTAGGAGGCATAAGAAACTGATCTTCAAAACTGGA[C/T]GGATATTGGTCTAAGAGGAAGTAGATAGTTTTAAA Y 2 1 2 1 101000 f 74 goat snp18610-scaffold1881-214228 27 10551308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775436 Affx-122968493 AX-385262567 27 33614189 ACACATGCATGCGAAATCTGAAAAAGATCTCTGGT[C/T]TCACCATAACTTCTATGAAAGGACAAAGGGCAGGT Y 2 1 2 1 101000 f 74 goat snp18611-scaffold1881-252963 27 10512553 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429746 Affx-122937593 AX-123300087 27 33695574 GATTGGTAAAAATTAAAAAGTCTCTGTCTTCATTG[C/T]GGAGCTTAAGCTCTGATGGGAGAAGGCAAGCTGTC Y 2 1 2 1 201000 f 74 goat snp18613-scaffold1881-334348 27 10430594 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801926 Affx-122955710 AX-385288831 27 33725625 ACTTTTAAAGTTAACTTAATATGTAGTATATTTTT[C/T]TGAGTTGAAACTTGAAGGTATAAATGAAACATTGC Y 2 1 2 1 303000 f 74 goat snp18614-scaffold1881-364399 27 10394189 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796482 Affx-122927653 AX-385283432 27 33814837 GTGTTTATGGCATAATGACCGTCATGCATTTATAC[C/T]CCAAACAGGAGCAATCAGAGCAGCTTTCTATAGTC Y 2 1 2 1 101000 r 74 goat snp18616-scaffold1881-453611 27 10304461 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389711 Affx-122968682 AX-123260069 27 33849160 AGGGTACGAAATTCAAAGGGAACAGAACAATACAC[A/G]CTGAAAAGTAAGCCTCTGCCCCAACCATGCGTCAC R 2 1 2 1 101000 f 74 goat snp18617-scaffold1881-487934 27 10270995 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452849 Affx-122920722 AX-123323182 27 33901146 ATGGTTGTTTGATTGTCTTTAGATGGTTTCTTCCC[A/G]TCTTTCGCTTTCCCTTCTGACATTTTGGCAGGAGT R 2 1 2 1 101000 r 74 goat snp18618-scaffold1881-539920 27 10218643 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273722 Affx-1111833801 AX-519547334 27 33916075 TTTGATGCCTAGCAAGACATTTTCTTCTTCCTCAG[A/G]CATTTAAAAATGACCTGAGTCTGCAGACACAATCT R 2 1 2 1 102000 f 74 goat GoatD01.005520 27 33916075 C T 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468277880 Affx-1111836066 AX-519551376 27 33926366 GCTGCTGCATGTGTGTGCAAACTCCCTGCTTCCCA[A/G]AAACATCTATGAAGGAAGTGGGAGCACCAGCCCCC R 2 1 2 1 102000 r 74 goat Random2.2K-2241 27 33926366 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38431328 Affx-122937067 AX-123301669 27 33940351 ATATAGAACTCCTAGTACTGCCTCTAAAGAGCGGA[A/G]CCAAGCAGAGTCAGGAGCAAGAGAAAGATGCTGGC R 2 1 2 1 102000 f 74 goat snp18619-scaffold1881-579125 27 10179676 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423810 Affx-122942805 AX-123294156 27 33970023 GAAGCTGGTGTGACTTCAGTCTTGGGTCTGGGCAA[C/T]GGGTGGGAATAGGGGAGCATGGTGATCACGTGGAT Y 2 1 2 1 101000 f 74 goat snp18620-scaffold1881-608797 27 10150059 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38417026 Affx-122947967 AX-123287374 27 34003235 AGAAAGTTCTTGACCCATGGGATTCAGCACATTCA[A/G]TTGCAGACCATTCTGTCAACAGTCACAGTTGGCAA R 2 1 2 1 101000 r 74 goat snp18621-scaffold1881-642009 27 10116371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273136 Affx-1111833329 AX-519546800 27 34035706 AATTGCACCGAGTCGTCTGCAGCATTCACGTCTCT[A/G]AATCATTTGTAAGGAGGGAACGGCTTGAGAAATAC R 2 1 2 1 101000 f 74 goat 27_34035706_AF-PAKI 27 34035706 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320792836 Affx-122941212 AX-385279814 27 34041516 TGCTAAATTATTGACCACCTGGCAGAAAAAGGACT[C/T]GCAGTTTTTTGATGAGGTTAGAAATATTTTTATAT Y 2 1 2 1 101000 f 74 goat snp18622-scaffold1881-680290 27 10078506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785954 Affx-122925463 AX-385272990 27 34074791 ACAGTAATGTATGAGCAGATGAATCTCACTTTCTG[C/T]AAAGACGGAAACTTCCCGTGTCTGCATTCAGAGGC Y 2 1 2 1 101000 f 74 goat snp18623-scaffold1881-713565 27 10045474 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430861 Affx-122937420 AX-123301202 27 34105034 TGGACCACATTTTTAATTTTGTTTAGTCTCAATGC[A/G]TGCATCTGCCAAAAAAATCACTAATAGATAAGAAA R 2 1 2 1 201000 r 74 goat snp18624-scaffold1881-743808 27 10015855 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378995 Affx-122976386 AX-123249354 27 34142076 GGAATTCCTTTATCTATAGGCTACTGTCTTCCATT[C/T]GAGAAATTGGACTCTGGGGCCTTCCACAAAGAAGG Y 2 1 2 1 201000 f 74 goat snp18625-scaffold1881-780850 27 9978914 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801590 Affx-122971939 AX-385288499 27 34175977 AATATTAGGCCTACAATCCACTGAGATGAAATCCC[A/G]TCAGCTATAAAATATTGCTTTGATAGTTCAACCAA R 2 1 2 1 101000 f 74 goat snp18626-scaffold1881-814751 27 9945002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388157 Affx-122969455 AX-123258515 27 34218991 GGACACAGCAGAGATCTTCAGGGTAAAAGCTTTTC[A/G]CAGTATTTCACTTGCCACCACCCTGCTGTGGACTT R 2 1 2 1 101000 f 74 goat snp18627-scaffold1881-857765 27 9902477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400097 Affx-122960737 AX-123270452 27 34254857 TTCAGTTGGCTGGGTTTTTAATGTTCTGTGTTTTC[A/G]TTCTGTTTTCACTGTAGAAGTGATGTCCAGCCACC R 2 1 2 1 101000 r 74 goat snp18628-scaffold1881-893631 27 9866587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403526 Affx-122957618 AX-123273879 27 34284005 TCTACAGAGAGCCTAATGAAACAAAAATGCAGAAA[C/T]GGCCAAAGAATAAATTCAAATTTGAAGGTAATAAG Y 2 1 2 1 101000 f 74 goat snp18629-scaffold1881-922779 27 9837502 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397620 Affx-122962631 AX-123267975 27 34321060 TCTTTCCCCAAATCCATTCTCTACATCTCACCACA[C/T]AGCTTCTACCTCTGAGCACCAGCCATGCTGATTTT Y 2 1 2 1 101000 r 74 goat snp18630-scaffold1881-959834 27 9800529 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410903 Affx-122952067 AX-123281253 27 34359106 GCTTAGAAGCCCAGACAAAGCCACCAGGAGTCCTC[C/T]GAGCTTCTTTTTCTGCATCTGCTCATTAAGGACTC Y 2 1 2 1 201000 f 74 goat snp18631-scaffold1881-997880 27 9762473 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453562 Affx-122919772 AX-123323895 27 34389556 AAAGAGAATCAACAGAAAAGAAAGATGAATCCACC[A/G]CCATGGTGTTGATGTAGGACATTAAGGGTGTGACG R 2 1 2 1 101000 f 74 goat snp18632-scaffold1881-1028330 27 9731584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391109 Affx-122966811 AX-123261466 27 34423823 AGGAGGCGGGGCATTTTTCCCAACAGAACTGACCC[A/G]TGTCTTTCAGGTCCACCCACCACTTACAGGGTCTA R 2 1 2 1 101000 r 74 goat snp18633-scaffold1881-1062597 27 9697309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436181 Affx-122932609 AX-123306520 27 34466678 AGGAAGTTTGAGACCAAGCACATCACCTTCTCCCA[C/T]GGGGACACTGCTTCCTAGCCGGCCCTCAGACCTAA Y 2 1 2 1 101000 f 74 goat snp18634-scaffold1881-1105452 27 9654677 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432874 Affx-122935349 AX-123303215 27 34514969 CCCTGCAAGGACCTTCGACCTCGTCTCTCTGACTC[C/T]CTCCTTGTTCCCTCCTGGTCATCCACCCACACTCT Y 2 1 2 1 101000 f 74 goat snp36502-scaffold439-1227085 27 9606206 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431623 Affx-122936150 AX-123301964 27 34565036 AGCATTTCCCCAAAGTGAGTGTGGCCATGCTCTCA[C/T]GACTCATTTAAAACTTTTAGGAAATGTTCTAAGCT Y 2 1 2 1 101000 r 74 goat snp36501-scaffold439-1177018 27 9556271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277882 Affx-1111836067 AX-519551377 27 34587898 ACACTAATTTTTAATAAAAAGAATATTGTATATAC[A/C]AATGGGTGCCAATATCTCATTTAAAAATGCTCATT M 2 1 2 1 101000 r 74 goat Random2.2K-2242 27 34587898 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38413248 Affx-122950233 AX-123283597 27 34604742 AATGCCATTTACCTATTTTAAATCAAGGTTTGAAA[C/T]GAGCCATTTCATGAAGCCAACAGGATGAGGATGCT Y 2 1 2 1 101000 r 74 goat snp36500-scaffold439-1137312 27 9516831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384878 Affx-122971935 AX-123255236 27 34633768 CATGAAAAGGTGTGAGTCTGTGTGCACGTGCCTCA[C/T]GCACATGTGTTCATGGGTGTAACAGATCACAGCCC Y 2 1 2 1 101000 r 74 goat snp36499-scaffold439-1108286 27 9491745 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404484 Affx-122956722 AX-123274836 27 34665042 CCGGTGACGCAGAATGCCTTCCTCTCCACTTCCGG[C/T]GCACCGGTGACTACCAACAGACCACTGCCCTCTAG Y 2 1 2 1 101000 r 74 goat snp36498-scaffold439-1077012 27 9460431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412835 Affx-122950461 AX-123283184 27 34699222 GCTCCTCCCAACCCACCTCCGTCCATTCTTTCCTC[A/G]CCTCCTTGCTGAGGACTGCTGTGACCGTATTGATG R 2 1 2 1 102000 r 74 goat snp36497-scaffold439-1042832 27 9426818 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378960 Affx-122976415 AX-123249319 27 34755158 CTCGGCCCCAGAGGCTGGAGGTTTTGGATCACCCT[A/G]GTCTTGGTCGGGGTCCTCGTGGCATGGCTGAGTTG R 2 1 2 1 101000 f 74 goat snp36496-scaffold439-986896 27 9370965 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375407 Affx-122979202 AX-123245766 27 34815475 GGTTGCAAGGTTTTTCCCAAACTCTTTTCAGGCCT[C/T]ATTTACTTTATAAAGCAAAACCTATGTTAGGGTTG Y 2 1 2 1 101000 r 74 goat snp36495-scaffold439-926579 27 9310541 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432848 Affx-122935368 AX-123303189 27 34857358 TTTCTTTGGTCTCTGCACCTGACCCTTGAAGATGC[C/T]AAATCCTACCCTGCAGAGGGGTCTGTCCCTTCGGA Y 2 1 2 1 101000 f 74 goat snp36494-scaffold439-884696 27 9268193 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782325 Affx-122928133 AX-385269402 27 34918310 TTCAAAATCAAAACCCGTCAGACTTTTATAGAGGC[A/G]ATATTGTTTGTGAATTTTAGCATTCCTTGATAATA R 2 1 2 1 201000 r 74 goat snp36493-scaffold439-823744 27 9209376 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438989 Affx-122930376 AX-123309326 27 34949365 GAAAGTGGATACGGATCCTCTGTGACTTCTGATGC[C/T]GAACATTAAGCAGGAAAGAAAGTGTGTGACGTGGA Y 2 1 2 1 101000 f 74 goat snp36492-scaffold439-792689 27 9179806 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434109 Affx-122934937 AX-123304450 27 34978748 GAGTTTTCACTAGATTCTTAAAAAGGTTTGTGATA[G/T]AATTTATTTTTTGAAGGATTTTTATTTGTTTACTA K 2 1 2 1 103000 f 74 goat snp36491-scaffold439-763306 27 9150669 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277884 Affx-1111836068 AX-519551379 27 35031026 TATTTCATTTCTTTTTCAATCAACAAAGTTTTCAT[C/G]AGTTTCTCTTAGGGCTTCAGCATGAACTAGGATAT S 4 1 2 1 101000 r 74 goat Random2.2K-2243 27 35031026 C G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451853 Affx-122921074 AX-123322186 27 35042657 AATTACCAAACCTCCGAAGAGATACTGAAAAGCTC[A/G]CGGCACAGATCAACTTCCAGGAAATACCACTTCTT R 2 1 2 1 101000 f 74 goat snp36490-scaffold439-699397 27 9086572 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768200 Affx-122972489 AX-385255389 27 35114134 AATGTTTATCCAACCATATCTGAGGAGCTGTCTGA[A/G]ATGCAGTCCACTTCTGGCTAAGATAAGGCAACAAG R 2 1 2 1 101000 f 74 goat snp36489-scaffold439-627920 27 9016036 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423009 Affx-122942977 AX-123293355 27 35162955 CTCCTTATGTAGCAGAGGGCCAGATGGGTGCAGCT[A/G]TGGTCCTTATTTGATGGACGTTGTCAAGTGCCTGC R 2 1 2 1 201000 r 74 goat snp36488-scaffold439-579099 27 8968159 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784039 Affx-122944096 AX-385271092 27 35201582 AGCAAGGATTCAGTTCTTTCTGAATAATGAATTCT[A/C]TTATGCCATATCCCTTAGCACTGGAGGAAAATTCT M 2 1 2 1 101000 f 74 goat snp36487-scaffold439-540472 27 8926483 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388269 Affx-122969770 AX-123258627 27 35247234 CAACCACTTCTCTCTCCCTAGATTGTGCCTTCCAG[C/T]GTTTCTAAGTAATTATATCTTCTACCACCGGCTAG Y 2 1 2 1 201000 r 74 goat snp36486-scaffold439-494820 27 8880484 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443405 Affx-122927385 AX-123313742 27 35278047 TTTTAAGATGCTCACAGGTGGTGCTGATGCTGCTG[A/G]CCTGGGAGCAAGTGACTCCGAGATCCTTAATGTGT R 2 1 2 1 201000 r 74 goat snp36485-scaffold439-464007 27 8849860 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437120 Affx-122932166 AX-123307458 27 35320377 AATAAATAAGATCCAGTATTTATGATGCTGACTTG[A/C]TAAGTCCCCTGCATCTGAAGATGGGGATGGAAGTA M 2 1 2 1 201000 f 74 goat snp36484-scaffold439-421677 27 8807341 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797653 Affx-122966854 AX-385284592 27 35376531 TTGGACATGACTGCACACACGTGCCTTCTGTTGAT[G/T]ATGAAATAGTGGTATTTGAGGGAATATTTTCCCTC K 2 1 2 1 101000 f 74 goat snp36483-scaffold439-365523 27 8754027 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419747 Affx-122945885 AX-123290095 27 35415944 GAGGAACTCATCTCCTGTGCAGACTGCGGCAACAG[C/T]GGTAGGTGACCCTCTGTGCACGCACTCTCATGGGG Y 2 1 2 1 201000 r 74 goat snp36482-scaffold439-326110 27 8715163 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433566 Affx-122934977 AX-123303907 27 35463519 TTTGTGAAGACGCTTAAGCTAAAGTGTGTTTTCAC[A/G]TTGATAAACAGGAGAATCTGGAGATACTGTGATTG R 2 1 2 1 101000 r 74 goat snp36481-scaffold439-278535 27 8668282 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432456 Affx-122935802 AX-123302797 27 35500031 CCTGGACTGTGAGGTTAGACTGCCCTGGGCTAGAG[A/C]GGTGGCTGTTGACTAAGGGGCCGTTCTGTACCCAG M 2 1 2 1 101000 f 74 goat snp36480-scaffold439-242023 27 8631636 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448251 Affx-122924200 AX-123318587 27 35549746 CAGGAAGAAACCTGACGATTATTAACGATTGGGTT[A/G]TTTTAGTTTTTGGCTGTGCTGGGTCTTCCTCGCAG R 2 1 2 1 101000 f 74 goat snp36479-scaffold439-192308 27 8582112 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416912 Affx-122948056 AX-123287260 27 35606386 CTGTTCACTAACCATGACTGAGCGACCGAACTGAA[C/T]GGAACAATCTCTCACCTAATGGTTTGAGCATCTGT Y 2 1 2 1 201000 r 74 goat snp36478-scaffold439-135668 27 8525492 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410704 Affx-122952729 AX-123281054 27 35642647 GTCCAGAAAGATGCTGGAGGCCCTTCATTAAAAAG[C/T]GGGTACCTTCCCTCAAGGGCTTCAGTGTGTCTGAA Y 2 1 2 1 101000 f 74 goat snp36477-scaffold439-99407 27 8489142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441358 Affx-122928872 AX-123311695 27 35727026 GTGGTTTGTCACCTTAGCCCTAAGATTTCTCCCTG[C/T]CTCCCGTTTCTACACAGGACCATTTTTTAATCTGG Y 2 1 2 1 101000 r 74 goat snp36476-scaffold439-15028 27 8402731 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406251 Affx-122956104 AX-123276603 27 35770012 CTAGATTTCAATATTCAACAAATCTTTGTACATAC[C/T]GATTTCAGTGGCAGATTTTAAGAACTTTTTAAAAG Y 2 1 2 1 101000 f 74 goat snp42684-scaffold5672-37506 27 8358553 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414354 Affx-122950018 AX-123284703 27 35799650 CGCTAATAAATGGAGTCACTAGTTTTGGTTCTGTT[A/G]TAGATCAACATGTTCAAAGCATCAGATTGTAACAG R 2 1 2 1 201000 r 74 goat snp42683-scaffold5672-7868 27 8328986 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421143 Affx-122944190 AX-123291490 27 35825334 TGGCAACGCGCACTGCATTGGGAGTTCTGACACTT[A/G]GGTCAAAACGGCGGGGGAGACAGGTATCCCTTCAG R 2 1 2 1 101000 f 74 goat snp7577-scaffold1270-17717 27 8303381 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419751 Affx-122945881 AX-123290099 27 35859391 GGCAAAGTGATGTCACTGTACAGTTTTTCAGTCAA[C/T]ATCAGATGATTCCAGGACCTCCAGGAAGCCCATCC Y 2 1 2 1 101000 f 74 goat snp7578-scaffold1270-51774 27 8269494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431033 Affx-122936659 AX-123301374 27 35920713 TAACAAAAAAGCACAGAACAGAAAACCATTTAAGA[C/T]GGGAAATTTGGGAGGAGGATTTGATTTGGGGCCTC Y 2 1 2 1 201000 f 74 goat snp7579-scaffold1270-113096 27 8208070 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778696 Affx-122954838 AX-385265807 27 35987765 AACAAACCAGAAACATTTCCAGGCCTGTCCTCTAC[A/G]TCTGCTTCAATAACATCGATGACTTCAGTTTCTAT R 2 1 2 1 101000 f 74 goat snp7580-scaffold1270-180148 27 8140785 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451214 Affx-122921968 AX-123321548 27 36023379 TGTTTTCAGTCTCAGCTACGCAGAGCAAGTGGAAA[C/T]GGCTAAGGAGGAGAGATACCGTTTGGACCCACAGC Y 2 1 2 1 101000 f 74 goat snp7581-scaffold1270-215762 27 8105031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440788 Affx-122929841 AX-123311125 27 36081606 CACTCACGAGCAGTGCCAGCCGAGGGACTTAAGAT[A/G]TCATAATACTTGCAGTTTTGATTCTTCGCAAACAG R 2 1 2 1 101000 r 74 goat snp7582-scaffold1270-273989 27 8046359 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451911 Affx-122921029 AX-123322244 27 36137785 ACATTTTTACACAGCAATTAAGTGATGATGCAAAA[C/T]GAATTTCAGTTGTGTTTGTGTGTGTGTTTTGTTTT Y 2 1 2 1 202000 f 74 goat snp7583-scaffold1270-330168 27 7990634 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781132 Affx-122955992 AX-385268217 27 36243954 AGCCGCGTTGTGAGGCAGCTGTACAGAAGCTGTTC[C/T]TCATTATTGTCATTGCTCTTATAAAGTGATACATG Y 2 1 2 1 101000 f 74 goat snp7585-scaffold1270-436337 27 7878429 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777257 Affx-122955572 AX-385264379 27 36273261 AGCATCTCATCCTTCTGTGAACATAGCACTCATCA[C/T]ACCATATTGTAGCTTTACAAAATTATCAAGTAATT Y 2 1 2 1 101000 f 74 goat snp7586-scaffold1270-465644 27 7849034 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416543 Affx-122947753 AX-123286891 27 36323205 CCACACTGTTGCAGCTTCCTGCCTTGGGGTAAGTC[A/G]TTCGTCAATTCCGGGTGCTGAGGCAGAGAGAGAAA R 2 1 2 1 101000 r 74 goat snp7587-scaffold1270-515588 27 7799549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443352 Affx-122927424 AX-123313689 27 36354657 CTTTTCATGTGTGATTTTGGGATGCAAATAATTTT[A/G]TTTTGGAAGTTGCTACATTAATAAGAGTTCTGATG R 2 1 2 1 201000 r 74 goat snp7588-scaffold1270-547040 27 7767934 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424151 Affx-122942543 AX-123294497 27 36386797 CGTTTCCTCTTTATACAAATTTATTTGGTATTCTG[C/T]ATCTGATAACTTCAGCACTCGGGTCCTTGGAGTTC Y 2 1 2 1 101000 r 74 goat snp7589-scaffold1270-579180 27 7735492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766502 Affx-122956355 AX-385253866 27 36427107 TTAAATTTAGTCCTGCTGCTGAGTCCAGGCTCATA[C/T]TGCCCCTCACATGACACACCAGTAAATCGACTGAC Y 2 1 2 1 101000 f 74 goat snp7590-scaffold1270-619490 27 7696057 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429228 Affx-122937923 AX-123299570 27 36460745 TGCGTGCTCGTCCTGCCTGCTCCATCACTGCCATC[C/T]GTCCTCTTCAGGAATTAATTTGCTGAGTCCTCAAA Y 2 1 2 1 101000 r 74 goat snp7591-scaffold1270-653128 27 7662125 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774603 Affx-122950700 AX-385261737 27 36514669 TTATTGTTTCAAGAACTATTCTTTTAAAAGTGAAC[A/G]TTCCAAAAAACACTTGTAGATAATACAAATGGATA R 2 1 2 1 101000 f 74 goat snp7592-scaffold1270-707052 27 7608886 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390223 Affx-122967779 AX-123260580 27 36562000 ATGTGGTAGCATGAGCTGACAGCCTATTTAGTTTC[A/C]TTGTTAAAACAAGTGTGGTTTTGAATGATGTGGAC M 2 1 2 1 102000 f 74 goat snp7593-scaffold1270-754383 27 7561915 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273186 Affx-1111833330 AX-519546845 27 36596719 TTTTCCAGGCAAGAGTGCTGGAGTGGGGTGCCATC[A/G]CCTTCTCCCGAATTGCAGTCCTAGGCAGCCTCTAA R 2 1 2 1 103000 r 74 goat 27_36596719_AF-PAKI 27 36596719 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38430969 Affx-122936816 AX-123301310 27 36648499 CATCCCTTTCTCTGTAAACTCATCACCCATCGCCC[A/G]GGAAGAACTGTCTGCTCTTTCTGCATGTGACCACC R 2 1 2 1 101000 r 74 goat snp7595-scaffold1270-840882 27 7474580 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429184 Affx-122937959 AX-123299526 27 36706790 TCAGTGTTCTCATCTGTGCAATGGGCTCTGTCTTC[C/T]GTCCTTCATAGACTTCTTGTGACAGAGAAAGGGAC Y 2 1 2 1 201000 r 74 goat snp7596-scaffold1270-899173 27 7415531 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427953 Affx-122939202 AX-123298296 27 36787773 GGAGGCTGGGTATGGAATTTAGACAGAGAACAGAG[C/T]GGGTTTGGTGCTGGACAGGAGGAACAGTGTGACCG Y 2 1 2 1 101000 f 74 goat snp7598-scaffold1270-980156 27 7336663 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801741 Affx-122975206 AX-385288649 27 36817696 TTATTTCAGTGGTTGTGAAACACGTTTTGAAAATT[A/G]TTCTTTGATTTAAATCCCTTAAGACGTCATGAATG R 2 1 2 1 101000 r 74 goat snp7599-scaffold1270-1010079 27 7306590 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378709 Affx-122977055 AX-123249068 27 36860194 TCTAACCCAGGCTCATGGCTTTAAATACCAGTCAC[A/G]TGGCAACAATTTCCCAATTTAACACCCATCTGGGA R 2 1 2 1 101000 r 74 goat snp7600-scaffold1270-1052577 27 7264022 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775493 Affx-122969245 AX-385262624 27 36889979 ACCAGCTGAGAGACTCCCTCCAACTGTGTTAGTCA[A/G]AATCTGCTGGATTGTGCTGCAGGAATAAGCCCCAA R 2 1 2 1 201000 r 74 goat snp7601-scaffold1270-1082362 27 7234719 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447008 Affx-122924552 AX-123317344 27 36899018 CCAGTTTGTCATCACTGCCCAGGGAAACTAGTCTC[A/G]TTGGGGAAATTTTGCCAGGGACTATGGAGATGGTG R 2 1 2 1 101000 f 74 goat snp23619-scaffold2383-404950 27 7225679 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415327 Affx-122948799 AX-123285676 27 36948939 GCTACATGTCTGCGATATTTGCACAGTGAGGCACC[A/G]TTTACTTAGAAGTGAAGGAGGTTTTCTCAGGTTTT R 2 1 2 1 201000 r 74 goat snp23618-scaffold2383-355029 27 7176614 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396744 Affx-122962789 AX-123267099 27 36991222 GATTGCACATGAATTAAAAGTAAATGTTACTGGGA[C/T]TGAGTCACAAGGATTTGGGGATTTATCTGGTAAAC Y 2 1 2 1 101000 r 74 goat snp23617-scaffold2383-312746 27 7134442 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431490 Affx-122936248 AX-123301831 27 37041832 TGGCTGCAACACTGCGTTATCTACAGGCAATCACA[C/T]ATAGGGAACAAGAAAGACCAGTTTTACCATTTAAC Y 2 1 2 1 101000 f 74 goat snp23616-scaffold2383-262136 27 7086435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425244 Affx-122940997 AX-123295590 27 37084933 TGAAGCACTTACTTTCTTACTTCAAGGGTTGGGTT[A/G]CCTCAGATCCAAGTCATAGCACAGGCTTCTCCTTA R 2 1 2 1 201000 r 74 goat snp23615-scaffold2383-219035 27 7050141 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376306 Affx-122978365 AX-123246665 27 37118899 AAGATAATGAAAACATAATGAGAAAAACATGCCAC[A/G]TACCCACAGCTAGAAGCAGGTCCCATACAGTCTAA R 2 1 2 1 101000 r 74 goat snp23614-scaffold2383-185069 27 7017558 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445770 Affx-122926067 AX-123316107 27 37164929 AAATGACAGAAAAAGGAAGAGAGTCATCATTTCCA[C/T]GTCAAGTACAAATGTCTGACAGACGAGGAAATGGA Y 2 1 2 1 201000 r 74 goat snp23613-scaffold2383-139039 27 6971975 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422364 Affx-122943431 AX-123292710 27 37195987 ATCAATTAATTAAAGATTCGCCGGAAACCTCCCTC[C/T]TCCAAGTAAGAAGGAAGAAAGGAGGTGCTACTTGA Y 2 1 2 1 101000 f 74 goat snp23612-scaffold2383-107981 27 6940833 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782376 Affx-122929802 AX-385269452 27 37242633 AATTAAAAGTTTGAAACAAGTCCCTCATGGTGCAT[A/G]CCTTTAAGTATGTTAAGGTCTATTTTTTATTATCA R 2 1 2 1 101000 f 74 goat snp23611-scaffold2383-61335 27 6894086 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791288 Affx-122977523 AX-385278282 27 37329074 GTAAAAAATTCCAAATTTTTTTCCGAAATCTAATA[G/T]ACATGATGTGGGTGCCATACACTTATTCTAATGAT K 2 1 2 1 101000 r 74 goat snp26888-scaffold2837-25007 27 6807675 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436698 Affx-122932328 AX-123307036 27 37401983 CTCTGTAATCTGGATGAAAGATTATGAAAAAAAGG[C/T]ATATTTTCCTCCAGCCCCAGACTGGTTTGGTTCAG Y 2 1 2 1 101000 f 74 goat snp26889-scaffold2837-97916 27 6734997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415732 Affx-122948506 AX-123286081 27 37456698 CTCAGCCTCGGCCCCTGACCGCAGTGGTGGTGGTT[G/T]CACTTGAGTCGTTTTCTTAATTAACTGTAGTCTCA K 2 1 2 1 101000 r 74 goat snp26890-scaffold2837-152631 27 6681357 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422694 Affx-122943658 AX-123293040 27 37488332 TCTTTCTTGAAGGGATCAATGCCATCTGTCTTGAC[A/G]TCGCCCTGTTTCTAAATGTCCCAAACTTCATCCAT R 2 1 2 1 101000 f 74 goat snp26891-scaffold2837-184265 27 6650729 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449375 Affx-122922720 AX-123319710 27 37528405 TATTTATCACGAACATCCAAAGTGAGCCTGGCTGA[C/T]GTCACCTGCACTGATCTAACCAGCTGTGTCCTCCC Y 2 1 2 1 101000 f 74 goat snp26892-scaffold2837-224338 27 6610493 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782256 Affx-122957335 AX-385269334 27 37558046 CATTCTATCCATTCCTGGTTAAAGCGCTTCACATC[A/G]TGATAGCTCCCCTTGATGTTTAAGAGACAGTTTAG R 2 1 2 1 101000 r 74 goat snp26893-scaffold2837-253979 27 6580859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383852 Affx-122973149 AX-123254210 27 37601312 TTTACAAACTCTGTCTTTGAAATGTCTGGAAATCC[A/G]CCTTCGCCTTTCAGTTCTCATTCTCACAGCTCATC R 2 1 2 1 101000 r 74 goat snp26894-scaffold2837-297245 27 6537426 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446229 Affx-122925700 AX-123316565 27 37633626 AATTTCTGATGAGCACACACATTATGCCTAATGAG[A/G]TCCCAAGGAGCAGCTGCAAATACAGCTCAGTTTAA R 2 1 2 1 201000 f 74 goat snp26895-scaffold2837-329559 27 6505104 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421111 Affx-122944212 AX-123291458 27 37667143 ACCAGCCTCACCTCACAGTCCAGTGGAAAGATAGG[C/T]GAACACAGAGGCAAGCACGGCTCAGTGTGATCAAT Y 2 1 2 1 201000 r 74 goat snp51827-scaffold762-22636 27 6471428 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428075 Affx-122939106 AX-123298418 27 37698386 ACTTCATCTTGGAAACAATCGCACTGACTCTCTAG[A/C]TCCCTTAAAATTTCTTAAAATCTTACCTCATCTTG M 2 1 2 1 101000 f 74 goat snp51828-scaffold762-53879 27 6436236 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784703 Affx-122960788 AX-385271751 27 37744951 ATTTAGAAGAAAAGTTTGGAAGTATTAAACAAAAA[C/T]GGACTTTATCAAAACCAACAACAGACTTTATGACT Y 2 1 2 1 201000 f 74 goat snp51829-scaffold762-100444 27 6389662 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375850 Affx-122978524 AX-123246209 27 37787018 TCACACAGGACTTTGAAGTGACAAAAGGCGCAGCA[C/T]GTAGAGGCGCCCAAAGACATCGCATCAAGGTTACC Y 2 1 2 1 101000 f 74 goat snp51830-scaffold762-142511 27 6347694 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435720 Affx-122933300 AX-123306059 27 37826046 ACTGGATGGTAGAAAGCTTCAGAGCACAGGCTGGA[C/T]GACCAGGGGGAAGTTAAAGGGCCAATGCGGGCCCT Y 2 1 2 1 101000 f 74 goat snp51831-scaffold762-181539 27 6308681 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419647 Affx-122945959 AX-123289995 27 37865379 AACCCAGATATGATCAAAGCCCTACTCATCCCACC[A/G]GCTCACGCTCAGCCACACAAAGCCTCACACACCGT R 2 1 2 1 101000 f 74 goat snp51832-scaffold762-220872 27 6269536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445800 Affx-122926041 AX-123316137 27 37922303 AATTTGACCACTTAGAAGCTGGGTGTCAATGGTAG[C/T]GAGTTTTGTTTCCAAGTCCGTGGTTCAAACCCCTT Y 2 1 2 1 101000 f 74 goat snp51833-scaffold762-277796 27 6216918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277886 Affx-1111836069 AX-519551381 27 37955420 TTTACTGTTCTACTTTGTAGGATTGGGTTTCAGGT[A/G]TAAGAACTGCAGTTGTGCTTGAAATGTATTTTCAA R 2 1 2 1 101000 r 74 goat Random2.2K-2244 27 37955420 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444188 Affx-122927265 AX-123314525 27 37974190 GCAGGGCAGGGTCTGTCTTTAGGATCCTTGTACTC[C/T]AAGTCAAGGTGAAGGGAATAGCTTTGCTACACGTG Y 2 1 2 1 201000 f 74 goat snp51834-scaffold762-329683 27 6165107 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385591 Affx-122971209 AX-123255949 27 38035080 TTAGGAGGAAAAAGAGAGAGAAGTGCTTTGTAATA[C/T]AGATCTGGTTTTACCTCTCAAAAACAATGACCAGT Y 2 1 2 1 201000 r 74 goat snp51836-scaffold762-390573 27 6103872 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449703 Affx-122922541 AX-123320038 27 38064146 GATTTTTAGTCTCTTATTGCATCCAATTTCCCATC[A/G]TAATTTGGCTTTCCTTTTTCTGGTAATAACATCTA R 2 1 2 1 101000 f 74 goat snp51837-scaffold762-419639 27 6074049 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793807 Affx-122970444 AX-385280778 27 38094645 ACAGAGCATAATAGCACATAATACAGAGTTTCAAA[C/T]ACTTGGCCTCCAAAAGTTCTCAAATAAAAGAATGA Y 2 1 2 1 101000 r 74 goat snp51838-scaffold762-450138 27 6043316 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412246 Affx-122950904 AX-123282595 27 38142815 AATGCCTTATATTTCAGATTCCCTCATCATCTCAA[C/T]GAATTCCAGCCCTCCAGAGTGGTTCCTCATTCCTT Y 2 1 2 1 101000 f 74 goat snp51839-scaffold762-498308 27 5994996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788101 Affx-122944078 AX-385275121 27 38181694 CATAAAATTGTGATGATATACAAAATATAGGCCAG[C/T]GCAACATGGGACAATCCCAGCTTAGCTGAATACAT Y 2 1 2 1 101000 r 74 goat snp51840-scaffold762-537187 27 5955535 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384379 Affx-122972223 AX-123254737 27 38214009 AAGAAAAAAAAAATCAGGAAAAAAACCCGGCAGAG[C/T]AGGGGGGAAAAAAAACCACAAAGAGGAAAATAAAG Y 2 1 2 1 201000 f 74 goat snp51841-scaffold762-569502 27 5923093 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767844 Affx-986698758 AX-385255063 27 38252476 TTTCCCAGCTGACCTGAGGCTGCTCCAAGGTCACA[C/T]GACCTTGTCCAGAGTTTCTTAGCAAGTGACATCAG Y 2 1 2 1 600010 r 74 goat 27_38252476 27 38252476 Ancestral_priority_1043 ancestry 0.574 neutral IMAGE 10K 10K ancestral 38411718 Affx-122951528 AX-123282068 27 38258024 TGGATGGAGAAGCAAGAAGAGAATTGAGATAGCAC[A/C]GTGCCGTAGAAATTATAGAAGTGTTCAGGAAAGAG M 2 1 2 1 101000 f 74 goat snp51842-scaffold762-613517 27 5878779 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764233 Affx-986698760 AX-385251962 27 38262374 CTGTGCGTTTACTCATGTTTGGCTTCTCTCCTGTG[C/T]GTTTTCTCATGTTTCAGGTAGGAACTTTGGAGAGT Y 2 1 2 1 600010 f 74 goat 27_38262374 27 38262374 Ancestral_priority_1043 ancestry 0.568 neutral IMAGE 10K 10K ancestral 320767791 Affx-986698728 AX-385255016 27 38262379 CGTTTACTCATGTTTGGCTTCTCTCCTGTGTGTTT[A/T]CTCATGTTTCAGGTAGGAACTTTGGAGAGTTTCCC W 4 1 2 1 600010 r 74 goat 27_38262379 27 38262379 Ancestral_priority_1043 ancestry 0.644 recommended IMAGE 10K 10K ancestral 38401961 Affx-122958795 AX-123272314 27 38288069 GTTCATGGACTACATCTCCAGTTGATGGATTCTGA[A/G]CCAGGGCTATAGTAGAGCAACCAGAAGGGACGCGA R 2 1 2 1 101000 f 74 goat snp51843-scaffold762-643562 27 5848746 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440039 Affx-122929758 AX-123310376 27 38319760 GGATGGAGAGGAACATGCCTCAGTCATAAACCGCG[C/T]GGACAATAAAATCGATCTTCCCTGAATGGCCCTGT Y 2 1 2 1 101000 r 74 goat snp51844-scaffold762-675253 27 5816972 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383090 Affx-122923011 AX-123253448 27 38348708 AAAAAGAGTTGGATTGTGGAGCCGGGGAAAGACGG[A/C]GAAGACTGGGGTGCGAGTATAAATGATCACTGGCC M 2 1 2 1 101000 r 74 goat snp51845-scaffold762-704201 27 5787833 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384204 Affx-122972394 AX-123254562 27 38404354 CTGTCCATGTTTACAAAGCGCACACCCATTTGGGT[A/C]GTCCGATGCTAACTTGTTCTTGCTTTGTCTATTTT M 2 1 2 1 101000 r 74 goat snp51846-scaffold762-759847 27 5732122 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786377 Affx-122927691 AX-385273411 27 38434215 AAGACAGGGGTTTATATATTGTGAATTTCAAATTA[C/T]TAACCTTTTAAATAATGCACACCTTGGCTACTTCT Y 2 1 2 1 101000 r 74 goat snp51847-scaffold762-789708 27 5702065 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375397 Affx-122979210 AX-123245756 27 38479358 GCACATCCTTGGGCGGCTGTCCTTCCCGAGACTTT[A/G]TCTTACTGTGACCCTGTCTTGCAGTTGCTCAGTTG R 2 1 2 1 101000 r 74 goat snp51848-scaffold762-834851 27 5656831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764204 Affx-986698731 AX-385251936 27 38523402 TTGAACTCCTTTGAGAACAGAAAACTTTGTAAGTT[A/G]TAAAATGGCACATACCCAGACTCACGGCAAGGTCC R 2 1 2 1 600010 f 74 goat 27_38523402 27 38523402 Ancestral_priority_1043 ancestry 0.59 neutral IMAGE 10K 10K ancestral 320767800 Affx-986698733 AX-385255024 27 38523415 AGAACAGAAAACTTTGTAAGTTGTAAAATGGCACA[C/T]ACCCAGACTCACGGCAAGGTCCCCCCCATGCATGG Y 2 1 2 1 600010 r 74 goat 27_38523415 27 38523415 Ancestral_priority_1043 ancestry 0.42 neutral IMAGE 10K 10K ancestral 38420542 Affx-122945297 AX-123290889 27 38524813 TCTCAACACCTTAAACCTCGATTGAATAAATTTTC[A/G]CTTTACTTTTTGTTTTTGTTTTGTAATTTGCCGAC R 2 1 2 1 103000 f 74 goat snp51849-scaffold762-880306 27 5611148 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794410 Affx-122930529 AX-385281373 27 38565750 ACCAAAAATAAGTGCAGAGCTACTCACATGCCCTC[A/G]CTAGGTCTGACCCTATACTGATAGATTTCATGGGA R 2 1 2 1 101000 f 74 goat snp51850-scaffold762-921243 27 5569842 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803710 Affx-986696475 AX-385290472 27 38577240 TCTTTGATAAGATCAAGCCCACAGCATACCAGTTT[C/G]TTCCACTGATTTCACGATAAATACTCATTCCTGGA S 4 1 2 1 600010 f 74 goat 27_38577240 27 38577240 Ancestral_priority_1043 ancestry 0.676 recommended IMAGE 10K 10K ancestral 320764208 Affx-986698735 AX-385251940 27 38577545 AAAAAAAACAGAAATTTCCCCAGAAATTTCCAAAC[A/G]TCCCCCTGGTCAGGAACGGGAGGGTGGCACGGGGA R 2 1 2 1 600010 f 74 goat 27_38577545 27 38577545 Ancestral_priority_1043 ancestry 0.616 recommended IMAGE 10K 10K ancestral 320764210 Affx-986698737 AX-385251942 27 38577602 GGGTGGCACGGGGATGCCAGGTCCAACCATCCCAT[C/T]GAGCGTTTCTGGAAACACAAGCTCTGAGGGAAGAG Y 2 1 2 1 600010 f 74 goat 27_38577602 27 38577602 Ancestral_priority_1043 ancestry 0.5 neutral IMAGE 10K 10K ancestral 320767810 Affx-986698739 AX-385255034 27 38577607 GCACGGGGATGCCAGGTCCAACCATCCCATCGAGC[G/T]TTTCTGGAAACACAAGCTCTGAGGGAAGAGGAAAC K 2 1 2 1 600010 r 74 goat 27_38577607 27 38577607 Ancestral_priority_1043 ancestry 0.462 neutral IMAGE 10K 10K ancestral 320764220 Affx-986698747 AX-385251950 27 38578017 GCAGCTCTGGCTTACCTTTAACCTTTACAAGCCTG[G/T]TTGTTTCATCTTGTGAGTTTTTTTCTGGACCCTGG K 2 1 2 1 600010 f 74 goat 27_38578017 27 38578017 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 320803713 Affx-986696477 AX-385290476 27 38578050 TGTTTGTTTCATCTTGTGAGTTTTTTTCTGGACCC[C/T]GGGGGCTGGACAGGTCTCCAAGGGCTTGAGAAAAT Y 2 1 2 1 600010 f 74 goat 27_38578050 27 38578050 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 320803716 Affx-986696478 AX-385290478 27 38578628 GAAGGGCCCTGTTTATCTATCTTATAAACTCATTC[C/T]TTTAAAAAATGTTTATTGGTACATAGTAGATTGAC Y 2 1 2 1 600010 f 74 goat 27_38578628 27 38578628 Ancestral_priority_1043 ancestry 0.626 recommended IMAGE 10K 10K ancestral 320764229 Affx-986698756 AX-385251958 27 38578936 TTGTTTTCTATTTTATAAACTCATTCTTAATAAGC[A/T]AGAAACCAAGGCCCAGGAAGGGACTTGGTGAGGAC W 4 1 2 1 600010 f 74 goat 27_38578936 27 38578936 Ancestral_priority_1043 ancestry 0.702 recommended IMAGE 10K 10K ancestral 320764230 Affx-986698757 AX-385251959 27 38579492 CCATTATCTTTCTGACACATTCACTGTCGATGCTG[C/T]TAAAAAACAAAACCTGCTTTAGTTCTGAGCACTTT Y 2 1 2 1 600010 f 74 goat 27_38579492 27 38579492 Ancestral_priority_1043 ancestry 0.674 recommended IMAGE 10K 10K ancestral 320764232 Affx-986698759 AX-385251961 27 38579572 TCAGATGGTGAAATCTGCAGGTGGATCTGGGTGGG[C/G]GTGGGGGGGCTGTGGGTGGGCCAGGACGACCCGCC S 4 1 2 1 600010 f 74 goat 27_38579572 27 38579572 Ancestral_priority_1043 ancestry 0.442 neutral IMAGE 10K 10K ancestral 320767793 Affx-986698729 AX-385255018 27 38579581 GAAATCTGCAGGTGGATCTGGGTGGGCGTGGGGGG[C/G]CTGTGGGTGGGCCAGGACGACCCGCCTCCCATCCT S 4 1 2 1 600010 r 74 goat 27_38579581 27 38579581 Ancestral_priority_1043 ancestry 0.414 neutral IMAGE 10K 10K ancestral 320767871 Affx-986698772 AX-385255091 27 38579638 CCGCCTCCCATCCTGATGCCCGCACAGGGCCCTCC[C/T]CTATCCAGTAGCCAAACCGGAGGCCCAGTGAGTCC Y 2 1 2 1 600010 r 74 goat 27_38579638 27 38579638 Ancestral_priority_1043 ancestry 0.464 neutral IMAGE 10K 10K ancestral 320767874 Affx-986698774 AX-385255094 27 38579778 AGGAAGCTCTTCCTTCTGTGCACAGAGCACACGGC[A/G]TTGCCTGAGTCTTTTTCGTGTTGAAAAGACAGATT R 2 1 2 1 600010 r 74 goat 27_38579778 27 38579778 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 320764253 Affx-986698780 AX-385251982 27 38579912 TGCCCCTGGTCAGGGAATTACAATCCTTCAAAGCT[A/G]TGCAGCACAGCCCAAAATAAAAGACAGATTCTAGA R 2 1 2 1 600010 f 74 goat 27_38579912 27 38579912 Ancestral_priority_1043 ancestry 0.622 recommended IMAGE 10K 10K ancestral 320804284 Affx-986696481 AX-385290906 27 38579939 TCAAAGCTATGCAGCACAGCCCAAAATAAAAGACA[G/T]ATTCTAGAGTTTCACTGCTGGCAATTTTCAAGCAG K 2 1 2 1 600010 r 74 goat 27_38579939 27 38579939 Ancestral_priority_1043 ancestry 0.696 recommended IMAGE 10K 10K ancestral 320764255 Affx-986698782 AX-385251984 27 38579978 CTAGAGTTTCACTGCTGGCAATTTTCAAGCAGGAG[C/T]TATTTCGTGACGGTGTCCCTGGTGATTCTGATGGG Y 2 1 2 1 600010 f 74 goat 27_38579978 27 38579978 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 320797087 Affx-122956665 AX-385284027 27 38618461 TTTTTTTTAATCACCCTATCCAAAAAGTCCATAGT[A/G]CTCCTGGTTGAGTGCCTGCTTAGTGTGAATGGTTA R 2 1 2 1 101000 r 74 goat snp51851-scaffold762-973954 27 5517372 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440146 Affx-122929682 AX-123310483 27 38682187 AAAGCATCTCCCATAACAAATGATGGAGAAGATGA[A/G]TTTGTCCCTTCAGATGGCCTAGATAAAGATGAATA R 2 1 2 1 101000 r 74 goat snp51852-scaffold762-1037680 27 5453825 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764257 Affx-986698784 AX-385251986 27 38709330 TACTTAAACACAGAATTACCGTATAATCCAGCAAG[C/T]CCACTTCTGGGTAAATATCCAAACAAGTTGAAAGC Y 2 1 2 1 600010 f 74 goat 27_38709330 27 38709330 Ancestral_priority_1043 ancestry 0.648 recommended IMAGE 10K 10K ancestral 38451016 Affx-122921710 AX-123321350 27 38718037 TCTTGGTGAGCCTTGCGGATCTTCTCGGTGAGGTC[A/G]TCCAGCTCTGCCGTCATCTCGTAGCTCTCCGTGCA R 2 1 2 1 101000 f 74 goat snp51853-scaffold762-1073530 27 5417603 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445668 Affx-122926142 AX-123316005 27 38784182 ATGCCTGCCCCTCAAAGGCATGGACTACATAAATA[C/T]AAACTCAAAGAAAATGTAAACAGGTTCCTTTGAAA Y 2 1 2 1 303000 r 74 goat snp51854-scaffold762-1139675 27 5351790 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417963 Affx-122946695 AX-123288311 27 38824926 GGAGAATTAAGTGAACAACTGTACAATGTATCCAC[A/G]CTGGTTTCCACAGTAACCATGTCAGGAGCAGCATC R 2 1 2 1 101000 f 74 goat snp51855-scaffold762-1180419 27 5311001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390894 Affx-122967107 AX-123261251 27 38869114 GCCTTTAAAAAACTTTTCATTTTATAAAGATTACA[A/G]ACTCCTTGAGTGCAGAATTTATAATCTTCATCTAC R 2 1 2 1 103000 r 74 goat snp51856-scaffold762-1224607 27 5267092 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436502 Affx-122932955 AX-123306840 27 38916563 CTCCTCTACCATATCAGGTAGTACAGACACAAGAC[A/G]TTTCCATCAGCTCAAGGTGGTTGGAGCCGTGGGAA R 2 1 2 1 101000 f 74 goat snp51857-scaffold762-1272056 27 5220351 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390535 Affx-122967228 AX-123260892 27 39035489 TTAAAAAAACAACAACCTTAGCAGACAGTGGTTTG[C/T]GACAATAAAGCACAGGGAATATTGATTTTAAAAAA Y 2 1 2 1 101000 f 74 goat snp51859-scaffold762-1390982 27 5100867 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448752 Affx-122923318 AX-123319088 27 39081420 CTGTCCTCTCAGCGCTAAGGGACAGGGACAAGTAG[A/G]AGAGTGGACAGGGAGCAGATTTCAGTGTGAGAAGG R 2 1 2 1 201000 f 74 goat snp51860-scaffold762-1436913 27 5056119 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382520 Affx-122973801 AX-123252878 27 39127947 TTTAATTTATTTGGTAAATCTAAAGGAATTCTAAT[A/G]TAAAGTCAAAAATATCCCTTTCTTTTTCTCCATTC R 2 1 2 1 201000 f 74 goat snp51861-scaffold762-1483440 27 5009453 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778248 Affx-122956863 AX-385265363 27 39162137 TATATATTATACACAGAGGTATAAAATGAAAAATG[C/T]ATATATAGTTTCAGGCAACAGTATATTTGTTTCCT Y 2 1 2 1 101000 f 74 goat snp51862-scaffold762-1517630 27 4975015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383843 Affx-122973156 AX-123254201 27 39206495 CGCTATTGTTGAGCTGACAAGTATGAGCGGGAGCG[C/T]GGAAGAACTGGATCAGTACTCTTGGGATATAACCC Y 2 1 2 1 101000 r 74 goat snp51863-scaffold762-1561988 27 4930875 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272156 Affx-1111833331 AX-185779578 27 39220039 AACCATAGCCTTGACTAGATGGACCTTTGTTGGCA[A/G]AGTAATGTCTCTGCTTTTGAATATGCTATCTAGGT R 2 1 2 1 103000 f 74 goat 27_39220039_AF-PAKI 27 39220039 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38380285 Affx-122975412 AX-123250643 27 39246845 TGGGAGACGGGTTGACACATGTACACACTACTGTA[C/T]GTAAAGCAGCTTATTAATAGGGACCTACTACACAG Y 2 1 2 1 101000 r 74 goat snp51864-scaffold762-1602338 27 4890446 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403194 Affx-122958066 AX-123273547 27 39295283 GACAAGATTCACATAAAATGAAGAGATGAAATGAA[C/T]AATAATACTGCTAATCTATGCAATCAGGACAACCT Y 2 1 2 1 101000 r 74 goat snp51865-scaffold762-1650776 27 4842061 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772126 Affx-122949734 AX-385259281 27 39338296 CATTAGGACCACTTGAGCTGTGGTGGGAGAGCAAA[C/T]ATGGGAAAGCGGGCTTTACTTACAAGGAGTCAGCC Y 2 1 2 1 101000 f 74 goat snp51866-scaffold762-1693789 27 4799122 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439421 Affx-122930235 AX-123309758 27 39392482 TCTGCTTCCTGAATTTGGTTCATTAAGCAAATAAT[A/C]GTCATAGTGTAATGGAAAATAATCTCATTGTCAGA M 2 1 2 1 201000 f 74 goat snp51867-scaffold762-1747975 27 4745051 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800269 Affx-122971480 AX-385287192 27 39431437 CTAGTTCTCTCATTTAAGGATATTTTAGTAGTAAA[C/T]GAATTATATAGGCTTCCCCTCTTCCATAATGGTTA Y 2 1 2 1 101000 r 74 goat snp51868-scaffold762-1786930 27 4707524 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412562 Affx-122951322 AX-123282911 27 39464008 CCCTTGCAAGTTCCCAAGTAGGACCCTGGACAAGG[C/T]ACGTAACCTTCTTGAATCTGAGGAACAGCATCAGT Y 2 1 2 1 101000 r 74 goat snp51869-scaffold762-1819501 27 4675018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380924 Affx-122975017 AX-123251282 27 39495838 GCTATGTGCTATTTATGAGGGACACACAGAAAGCA[C/T]GAAACATTTTTAAATGATGGGGAAGACATACCAGG Y 2 1 2 1 101000 f 74 goat snp51870-scaffold762-1851331 27 4643836 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416995 Affx-122947990 AX-123287343 27 39568650 CTGATACGCTGGAACATTAGCAGGGCAAGATGAAA[C/T]GGAAAAGCGACAATAGAAGTACACATGGCCCAACA Y 2 1 2 1 101000 f 74 goat snp51871-scaffold762-1924143 27 4570665 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403335 Affx-122957817 AX-123273688 27 39605138 ACCAAGAAAGGCTTGGGGACCTTCACTGCTTTCTC[A/G]TACCTCCAACCCGCTGCTTGTAATCATGGGAGTAA R 2 1 2 1 101000 r 74 goat snp51872-scaffold762-1960631 27 4534344 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406023 Affx-122955494 AX-123276375 27 39640168 TTACACTTGCTTCACGTCACGGCTTTTGTGCAAGG[C/T]ATCATGCTGAGCTGTCTACGTGTGTTGTCTCGGAA Y 2 1 2 1 201000 r 74 goat snp51873-scaffold762-1995661 27 4498760 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774212 Affx-122964626 AX-385261349 27 39687230 TTCTCGAGTATTACTTCCCATTTATTCCCAGTTAA[C/T]GAATATTTATTGTGGGATTACCATGTATTAGTCCA Y 2 1 2 1 101000 f 74 goat snp51874-scaffold762-2042723 27 4452450 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442017 Affx-122928412 AX-123312354 27 39736787 GGTCAGGCCTAAAGAAAATTATTTTTGCAACTGTT[C/T]TAACCGCAAGAAAGAATAGTAGGAAAATGTATCAG Y 2 1 2 1 101000 f 74 goat snp51875-scaffold762-2092280 27 4402453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795261 Affx-122967866 AX-385282219 27 39769632 CAGTGCACGGGCAATCAGTTTGGTAAATGTGATAG[A/C]TTTTAATGTTGTCTTCATAATGCAAATTTTCAAAA M 2 1 2 1 101000 f 74 goat snp51876-scaffold762-2125125 27 4368734 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427514 Affx-122939525 AX-123297857 27 39802711 GTCCTTGTCTCTCAAAGTACAGTTCATGAAACAGC[A/G]GCATTGATATCATCTGGACATTTGCTAGAATTACA R 2 1 2 1 101000 r 74 goat snp51877-scaffold762-2158204 27 4335205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378153 Affx-122976972 AX-123248512 27 39851348 ACAGACAGCTTATCATACGGTGATAAATATTACTG[A/G]GAGGGGTAAGGTAATATGGTATAGAGATGACCACT R 2 1 2 1 101000 f 74 goat snp51878-scaffold762-2206841 27 4286343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402897 Affx-122958210 AX-123273250 27 39885139 AAAGGGCTCAGAAGCCAACTAGAAAGTCAACAAAA[C/T]AATTCTTAGCGGCAAAATGAATCATGGCAAACAAT Y 2 1 2 1 101000 f 74 goat snp51879-scaffold762-2240632 27 4252595 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429045 Affx-122938307 AX-123299387 27 39917708 GCCTGACGGGTCTTTATTCCTAGTGACCTGTGGAG[C/T]AGCTGCCTGACTTGGCTTTTATTTCTGGGGTAAAC Y 2 1 2 1 201000 f 74 goat snp51880-scaffold762-2273201 27 4220089 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774426 Affx-122936380 AX-385261562 27 39993826 CTTTTGGAAAATACAGGAGTAATTAATACCCTAAC[A/G]ATATTATTACTTGATGTGGTGATGACCCCAAAGAC R 2 1 2 1 101000 r 74 goat snp51881-scaffold762-2349319 27 4143759 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376232 Affx-122978789 AX-123246591 27 40066286 AAGAAAAAAATCTTTTTTACTTTTCACTCTCTTCT[A/G]TTCCTTCAGCCTCAATCCGTAGACAATAATAGTGT R 2 1 2 1 101000 r 74 goat snp51883-scaffold762-2421779 27 4071091 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395915 Affx-122963601 AX-123266270 27 40100336 TTATAACCATCAGATTCTGAGGGGGTCATGGACCC[C/T]CCGGGGAATGACTTTAAACTTACTGACTTTCCTGT Y 2 1 2 1 101000 r 74 goat snp51884-scaffold762-2455829 27 4037323 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404289 Affx-122957035 AX-123274641 27 40130029 GTATTATAGCAAAATTTGGAAGCCACCTCAGTGAC[A/G]CTGTTTTCCAGTTTTCCTCTCTGCTGTTTTCGTCT R 2 1 2 1 101000 f 74 goat snp51885-scaffold762-2485522 27 4015235 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402033 Affx-122958737 AX-123272386 27 40161282 TCAGGATTTGGTTGGAGAGAAGGAAGGATTCTCAA[A/G]GTGTCTGGCAAGTCTTCCCATGGAGCTGGGTTTTT R 2 1 2 1 101000 f 74 goat snp51886-scaffold762-2516775 27 3984003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381236 Affx-122974504 AX-123251594 27 40222911 AGCAGTCCAGCAGGCAAGTCAGTATTGGCAGAATG[C/T]GAAAATGGCAAATATTTTTAATATTATACATAAAT Y 2 1 2 1 101000 f 74 goat snp51887-scaffold762-2578404 27 3923321 C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395555 Affx-122964246 AX-123265910 27 40290136 AAAACCTGGGGATACCACTGACTCACAAGGAGGCC[A/G]TGCTAAGTCCTTGCCTTACGGAAGAGACAGAGCAA R 2 1 2 1 101000 r 74 goat snp51888-scaffold762-2645629 27 3855715 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798129 Affx-122930103 AX-385285064 27 40346207 TTTAAACACTCTGAAAGTCAAACCATGCAGACTGC[G/T]AGTGTGTGTATCCTTTTGATTAACATTTTGACTGA K 2 1 2 1 101000 f 74 goat snp51889-scaffold762-2701700 27 3810325 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768961 Affx-122966496 AX-385256136 27 40423682 AGGATGGTATCATCTGGGACGGCATTACAATCTTC[A/G]TGAAGATGGATAATAAACAGAGATGAGATCTCAAT R 2 1 2 1 101000 r 74 goat snp51891-scaffold762-2779175 27 3733665 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766759 Affx-122930310 AX-385254094 27 40481789 CCTGCAGGTCACACACTAAATGATTTTTCAAATTA[C/T]AGGTTAAATCTAATTTGACAAAATCCCTGTAGTGT Y 2 1 2 1 101000 f 74 goat snp51892-scaffold762-2837282 27 3674006 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420293 Affx-122945034 AX-123290641 27 40519540 TTATCATAGGAGAGATAAGAGAAGACAGAGCACCC[A/G]TGAGCTGGATGCTACAAAAAAGAAACAGAAAAGGC R 2 1 2 1 102000 f 74 goat snp51893-scaffold762-2875033 27 3636916 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385084 Affx-122971805 AX-123255442 27 40557819 GTTTGCTTGAATCTGTTTCCTAAGGCAAAGGAAAC[G/T]AGCAAACACAAACAAATGGCACCTGTTTAAATCTG K 2 1 2 1 103000 r 74 goat snp51894-scaffold762-2913312 27 3600156 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436040 Affx-122932724 AX-123306379 27 40613054 CCACTCCGTCCTGCTTAAAGGGAACCCTTGAAAAG[C/T]GGAAGCTAGTCCCTCCGTCATGTCCAGCTCTTTGT Y 2 1 2 1 101000 f 74 goat snp51895-scaffold762-2968547 27 3544999 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400016 Affx-122960798 AX-123270371 27 40691918 CTCTGAGCTCCAAGCTGCCACACCGCTGAACCAGG[C/T]GCCTTTAGCTCCTCTTTAACAGCCCTGGCACCTGC Y 2 1 2 1 101000 r 74 goat snp51897-scaffold762-3047411 27 3466041 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426331 Affx-122940274 AX-123296677 27 40720979 ACACGTTCTGCCCGGCTCATTACTGCCTTTCAAAA[C/T]GTCATTTGTTGTTTTTGTTTGATCGCACTGGTACT Y 2 1 2 1 201000 f 74 goat snp51898-scaffold762-3076472 27 3436994 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390788 Affx-122967877 AX-123261145 27 40753931 AGGAAGTGGTGGGACCGGGGCGTGAACACAGCGCT[C/T]GACATTTGACTTGCTGCCTGTGTCTCCATCCCTGA Y 2 1 2 1 103000 r 74 goat snp51899-scaffold762-3109424 27 3404032 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407102 Affx-122954887 AX-123277453 27 40804493 TCCACCACCTCTCATGGAGGGTGCTGAAACGATGT[A/G]TGGCTTTGAGCTGGCTCTCAGCTTTGACTACATAA R 2 1 2 1 201000 f 74 goat snp51900-scaffold762-3159986 27 3353819 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411692 Affx-122951547 AX-123282042 27 40834717 TATTTTGAGATTTGCTGAACTTGTGGAGATCAAAG[A/C]TCAGGTTGCCATCACACTCAGTAAACAAAACCATC M 2 1 2 1 101000 r 74 goat snp51901-scaffold762-3190210 27 3323775 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389295 Affx-122968514 AX-123259653 27 40863322 CTGGTAGCAAGTGCTGTCCACATCTAGATTTATGT[C/T]AAGGGACAAGATAACAGGTGCAGGGAATGTTGAGA Y 2 1 2 1 101000 r 74 goat snp51902-scaffold762-3218815 27 3295055 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410447 Affx-122952388 AX-123280797 27 40904179 CACAGCACACCAGCCAGAAATCCCCTCACACCCTG[C/T]AGCAAAGCGGGCAGTCCTGTTACGGTGCTCGAGAA Y 2 1 2 1 101000 r 74 goat snp51903-scaffold762-3259672 27 3254370 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404196 Affx-122957676 AX-123274548 27 40939692 TAGGAAACTAGGTAACTCTGCATGTCACGGGCCAG[C/T]GCTCCGCACATATCATTTACGCGTGCACCTGTCTG Y 2 1 2 1 101000 r 74 goat snp51904-scaffold762-3295185 27 3219123 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391387 Affx-122967268 AX-123261744 27 40995072 ACTCCATGTAATTCTTGTGATAGTCTAAAGGTTCT[C/T]ATTATTATTTTGTGACAGTGATCTGTGGCAGAAGA Y 2 1 2 1 101000 f 74 goat snp51905-scaffold762-3350565 27 3163932 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406129 Affx-122956197 AX-123276481 27 41033303 AAAAAAAGACACATGGAAAATATTGTTTTCCTGAG[A/G]AATGATCCTAGGTGGCTGCATGGTGAGAATATTCA R 2 1 2 1 101000 r 74 goat snp51906-scaffold762-3388796 27 3125743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393724 Affx-122965233 AX-123264079 27 41063865 TCAGTGTCCTTCTATATCTTGGTTACTATAAATAG[C/T]GGGGCTATGAACACTAGGAATGCACGCATCTTTGT Y 2 1 2 1 303000 f 74 goat snp51907-scaffold762-3419358 27 3094923 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402811 Affx-122958277 AX-123273164 27 41108071 CCTCGCTATAGTTAAGCTATAACATACTTGAACAG[A/G]ATATCTTTAGAAGAAATAATGGTGAAATAAAAAGA R 2 1 2 1 101000 f 74 goat snp51908-scaffold762-3463564 27 3050504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406114 Affx-122956208 AX-123276466 27 41137861 CATACCAAGCCTGCAGAGTAGCAAGCTGGATGGCA[A/G]TGTGGGATTCATTGTCCTCAGGCTTCAATCCTGGA R 2 1 2 1 101000 r 74 goat snp51909-scaffold762-3493354 27 3021357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277750 Affx-1111836070 AX-519551249 27 41192078 TGTCCCTTGGAAATTTCTTTAAATTCTCATTGCCA[A/G]TTTCTTCCTCCATACAGTGGGATAAAAATGATTAG R 2 1 2 1 101000 f 74 goat Random2.2K-2249 27 41192078 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38453308 Affx-122919984 AX-123323641 27 41218004 AATTCATGTGAGGTGTGATCCATCTTTCGGCTCCA[C/T]GAGTGGACATGTGCAAGAACCAGGACTAGACGGAA Y 2 1 2 1 101000 f 74 goat snp51910-scaffold762-3573497 27 2941270 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435399 Affx-122933562 AX-123305739 27 41265283 CATAGTTCTTTGTGAAAAACATGCTTTTGTTCAGA[A/G]GTACAGGCAGTGAAAGATAGAAATGGTTCCAATAG R 2 1 2 1 101000 f 74 goat snp51911-scaffold762-3620776 27 2892939 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427491 Affx-122940005 AX-123297834 27 41300303 CGATGCTGAGCATGTCTCCTACCTGTGGGTCTCCT[A/G]AAGTAGCATTTAATTATTTAGGGAGCAAATATATA R 2 1 2 1 201000 r 74 goat snp51912-scaffold762-3655796 27 2857992 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375421 Affx-122979192 AX-123245780 27 41330824 CCTTATTTTGATATTAATGTAAAATTAGGACTGCC[A/G]TCTATAATAGGGTTCACGCTGTGAAGTTGACACTG R 2 1 2 1 101000 r 74 goat snp51913-scaffold762-3686317 27 2827497 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779641 Affx-122955706 AX-385266743 27 41378438 AGAGAGATGATGTAACATGGCTAAATTCTGACAGC[C/T]GAGCAGATAAGTGGTTTGAAGCTAGTGATTCTGGC Y 2 1 2 1 101000 r 74 goat snp51914-scaffold762-3733931 27 2779435 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394523 Affx-122964532 AX-123264878 27 41415152 GTCGTTGTTGACAACATATAATAGAGATCTCCGGC[A/G]TCCTCTCTCCTCCGTTTGTGCGGGTGAAGTCGTGC R 2 1 2 1 101000 f 74 goat snp51915-scaffold762-3770645 27 2742278 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408433 Affx-122954455 AX-123278784 27 41446346 CATCCAAAGTCTAACTCTGTACCACATACCTCTAA[A/G]GCCATACTCTCTTTATATTTTCAACAACTTTCATA R 2 1 2 1 101000 f 74 goat snp51916-scaffold762-3801839 27 2710349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389049 Affx-122968614 AX-123259407 27 41487671 GAAGAGTTCAGGGTCTGGGGCTGGGATGAAAGACA[A/G]TTCACAGGAAGATACGAGGAAAATGTTTGCCAGGC R 2 1 2 1 101000 r 74 goat snp51917-scaffold762-3843164 27 2669314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386220 Affx-122970983 AX-123256578 27 41517041 CTACAGACTGAAATTTTAGCCCAGTGAATGAATAG[C/T]CTGGTTCCCAGATCCCTTATACTAAGTGTCCCCAG Y 2 1 2 1 101000 r 74 goat snp51918-scaffold762-3872534 27 2640845 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388107 Affx-122969492 AX-123258465 27 41557321 CTTTGCTGCTTTTTGACTATGAGAAATATTTTTTA[C/T]AAGCAGACTCCTTTTCCCATATTCAAAAGAAAATA Y 2 1 2 1 303000 r 74 goat snp51919-scaffold762-3912814 NW_017212815.1 10447 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390957 Affx-122967055 AX-123261314 27 41598245 ACAAACACATTTTAGCTTTTCCATTATAGAGGAAA[G/T]ATGTTTCTTTCAGCATACAGTGGCAGTTGGCATAC K 2 1 2 1 101000 r 74 goat snp51920-scaffold762-3953738 27 2564731 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788434 Affx-122932810 AX-385275451 27 41656686 TGGACAGGCATACCTGACTGGTGAGTCCTTTATTC[A/G]CTGAACAGTATCGGGACTTTAGAAATTGTAAGTTT R 2 1 2 1 101000 f 74 goat snp51921-scaffold762-4012179 27 2506517 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446050 Affx-122925836 AX-123316387 27 41707428 CTATCATTTTAGAATCTGCATTAGTTCACGTGTGG[A/C]GAGGAAAACCGTACATGCTGGGGGAAGGTGGAGAC M 2 1 2 1 101000 f 74 goat snp51922-scaffold762-4062921 27 2456077 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388595 Affx-122969154 AX-123258953 27 41745278 ATACTCAGAGTGCTGCGGTCTCTCAGTGAGAAAGC[A/G]CTTGTATGAAACGTGGTGCACTCGCTGCTCCGGGT R 2 1 2 1 201000 r 74 goat snp51923-scaffold762-4100771 27 2417869 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454051 Affx-122919399 AX-123324384 27 41784707 CAGGACACAGTCCGCTGGCATGTCTGCGCACCACA[G/T]GGGCCAAGGTTATTATCCCGCTTTGGAGACAGAGT K 2 1 2 1 101000 r 74 goat snp51924-scaffold762-4140200 27 2378079 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441066 Affx-122928914 AX-123311403 27 41836787 CAACTCCCAGGCACCCACTCACGCACTGTGGGCAG[C/T]GCTATCAGCCTTAGCAAGAAGAGAGCAGCATTGAA Y 2 1 2 1 101000 r 74 goat snp51925-scaffold762-4192280 27 2327903 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387868 Affx-122969637 AX-123258226 27 41868790 GCTGACCCTAGAGTAACAGGTTTGAACTGCACACA[C/T]GGGTCCACTACACTCAGATATTCTTCCATAGTAAA Y 2 1 2 1 201000 r 74 goat snp51926-scaffold762-4224283 27 2295631 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407124 Affx-122954869 AX-123277475 27 41910452 TTCAAACACAACTGGAAAGCTGGGATGAACTCACA[C/T]GGCCAGAGAGCTTGAGTCTATAGTCTCTCCCATTC Y 2 1 2 1 101000 f 74 goat snp51927-scaffold762-4265945 27 2253470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404109 Affx-122957116 AX-123274461 27 41968198 GGAAGCGTGATCTTCAGGAGGCTGCCGTGCGCTGC[A/G]CAGTACTTCTTGTGTCTGAAACTAGACTTGTGGTT R 2 1 2 1 101000 r 74 goat snp51928-scaffold762-4323691 27 2195231 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272160 Affx-1111833333 AX-519545916 27 41998189 AGGAGACAAAATTCTGTCCATAGCATCTCTGAAGA[A/G]TAGTTGATTAGCAGTTAATTCAATATTGTATGCCC R 2 1 2 1 101000 f 74 goat 27_41998189_AF-PAKI 27 41998189 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38376696 Affx-122978982 AX-123247055 27 42022515 TTCCCTTTGCCCCAGTCCTTACCTTTCTCGTGATC[A/G]TAGCTTTGTGCATTTTCCTTTGTTACCCAGTCCTT R 2 1 2 1 201000 f 74 goat snp51929-scaffold762-4378008 27 2140414 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427266 Affx-122939545 AX-123297609 27 42064547 CAGAAAGACATTTTTGAATAAAAAGAAATGGCCAG[A/G]TAGAAGGATTGTGTGGAAAATGAGCCCAAATTAGT R 2 1 2 1 101000 r 74 goat snp51930-scaffold762-4420040 27 2098208 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426402 Affx-122940842 AX-123296748 27 42118210 GATGCTGAGAATAAGAAGGGGGAAAGGAAGAACCA[C/T]GGAGAATCAGAAAGCATCCAGTTGTTAAATGCCGA Y 2 1 2 1 101000 f 74 goat snp51931-scaffold762-4473703 27 2044996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779932 Affx-122933790 AX-385267031 27 42148677 TCTCATTCTAGTTAATGTAATTAATTTGGATGTGC[A/G]TCTTAGCCTAGAATCTCGCAATTAAGTATTTCTTA R 2 1 2 1 101000 r 74 goat snp51932-scaffold762-4504170 27 2014100 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375723 Affx-122978631 AX-123246082 27 42157363 CCAGGAATGTATCCATGAATTACTTACACACAAAG[C/T]GCAAAGAGAGTAAAATGTTTAAAAAATCCAAATTA Y 2 1 2 1 103000 f 74 goat snp24620-scaffold2506-202350 27 2005753 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406188 Affx-122956147 AX-123276540 27 42193509 TGTAATAATGTAAGTTAAATGCTTTAAAAATGACA[G/T]AAACTCAATCACATAAGAAAATACCAAATACATGG K 2 1 2 1 101000 r 74 goat snp24619-scaffold2506-166204 27 1969555 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797312 Affx-122936622 AX-385284251 27 42228771 CAGGATTAAAGTGCGTTTAAAGTCGAGTTCCACTC[A/G]ACTAATCTAGGTCAAAAGAATTAAATGGAAGTACT R 2 1 2 1 101000 f 74 goat snp24618-scaffold2506-130942 27 1935745 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277891 Affx-1111836071 AX-519551386 27 42268149 AAATAAGACTTCTTGCTGTTTCCCAACAGTTTGTA[A/C]GTAATATTTTCAAACACATGACAAAGTTGAAAAAC M 2 1 2 1 201000 r 74 goat Random2.2K-2251 27 42268149 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38446500 Affx-122925043 AX-123316836 27 42280108 CTGTTCTGGGACACAGCAAACCATTCAAAATGATA[C/T]GTTAGACCACATCATCATTAACTGCTTTGGAAAAG Y 2 1 2 1 201000 r 74 goat snp24617-scaffold2506-79605 27 1884306 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379018 Affx-122976368 AX-123249377 27 42313005 AATACAAAGTATGACAATCGCTATTTTAAAGCACC[A/G]GAAACACTGAAGAACAACAGTATACTTATTTTTAC R 2 1 2 1 101000 f 74 goat snp24616-scaffold2506-46708 27 1851284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783152 Affx-122922469 AX-385270219 27 42370524 TAGAAAGAAGGAAAGAAGGACACTACGCAAACAGT[A/G]ATTGAGCTCTGGCGGTTGAGTGCGATAGCCAAAGT R 2 1 2 1 101000 f 74 goat snp22938-scaffold229-645256 27 1790759 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767910 Affx-986698794 AX-385255128 27 42400343 GAACTATTAAAGGTCCTTGACTTAATGACTGAACT[A/G]TCTTTATTTTGTCTTGCTGGGCTGCTTTCTGTGGT R 2 1 2 1 600010 r 74 goat 27_42400343 27 42400343 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 38414633 Affx-122949334 AX-123284982 27 42400468 CCGAGAATCCTAGCAGGACACAGCAGTCCATGAAC[A/G]TGCCTGTCAGAACAACATGCCCAGAAAGACCTCTT R 2 1 2 1 101000 r 74 goat snp22937-scaffold229-615312 27 1761115 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381139 Affx-122974564 AX-123251497 27 42440215 TTACCCATGCAGAGCTGACCCTGCCGTTTGTAAGC[G/T]CGCAGGCAGTCTATAAGTGATGAACACAGTGTTCT K 2 1 2 1 101000 r 74 goat snp22936-scaffold229-575565 27 1731724 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428750 Affx-122938436 AX-123299092 27 42509525 ATAGTCAATCCATCACTTTTTGAATGCCAAAATGG[C/T]GCAGAAATGCAATACTTTTCAGCTTTGGTTACTTC Y 2 1 2 1 101000 f 74 goat snp22934-scaffold229-506255 27 1663223 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407998 Affx-122954318 AX-123278349 27 42560062 ATTGCTCCTGTTCTATGCTTGGTCTTTTGATCGTG[A/C]GGCACGTGGGATTCTAGCTCACAGTTCACAGATCA M 2 1 2 1 101000 f 74 goat snp22933-scaffold229-455718 27 1612513 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426612 Affx-122939967 AX-123296958 27 42608338 GAAAGTTGTTTCAGCCATCTGAGGCTCAGATTCCT[C/T]ATCTAAAAATAGGAATGATTGTATTCTGTCTACCT Y 2 1 2 1 201000 r 74 goat snp22932-scaffold229-407442 27 1564814 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379681 Affx-122975917 AX-123250039 27 42644188 CACACAGGGCTGGACAGAGTAGGTGCTTAATAAAC[A/G]CTCAGTTGAATGCAGGGTAGTGTGACTCCAGCACC R 2 1 2 1 201000 r 74 goat snp22931-scaffold229-371592 27 1529098 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797098 Affx-122934718 AX-385284038 27 42691658 CATACGCTGGTAACGTTCCAAAACATCAATTTGTC[A/G]TTAATTAAAGGCTGTTTGAATCCTAGGAAACTGTT R 2 1 2 1 102000 f 74 goat snp22930-scaffold229-324122 27 1482289 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796335 Affx-122948878 AX-385283285 27 42735243 TCTGCACATCATCTGCTTTAAAGAGCTTACTTTAC[A/G]TGTTGTTGTGTAGACAGCAAGCAGAGCGGACCTGA R 2 1 2 1 201000 r 74 goat snp22929-scaffold229-280537 27 1440110 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793641 Affx-122961117 AX-385280614 27 42783964 AACTTATTTTTGTATCTTGGTCCCGAGGAATATAT[C/T]ATAGGCTTTGTTTAAAATCACAGTGGAAAACAGGA Y 2 1 2 1 101000 r 74 goat snp22928-scaffold229-231816 27 1390986 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789677 Affx-122957733 AX-385276685 27 42823372 AAACACATTTCAACAATGGTTGTCAAATTCCTGAT[C/T]GAATATTTTTTCGACCAATTCACTCAGCTTCTCTG Y 2 1 2 1 201000 f 74 goat snp22927-scaffold229-192408 27 1338446 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413612 Affx-122950561 AX-123283961 27 42854836 TGTTATACATTTTCCTTTCTAATGTGAAGACATGT[A/G]CTTTTCAAATTCTCTTACTCAATGGGGAAAATGAT R 2 1 2 1 101000 r 74 goat snp22926-scaffold229-160944 27 1307081 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441550 Affx-122928698 AX-123311887 27 42907169 TCATTTCTCCCGAGAGGCCTTGGTCTTGGCCTTAG[C/T]GACATCTTTTGTGGGATCCATCGCCCCCTGGCTCT Y 2 1 2 1 201000 r 74 goat snp22925-scaffold229-108611 27 1253745 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387212 Affx-122970593 AX-123257570 27 42938851 AGAGAACCAGAGGTAAGTTATGGAAATTTCCTTCC[A/G]GGTAACAGAAATGAAAGCATGCATGCTCAGTTGCT R 2 1 2 1 101000 f 74 goat snp22924-scaffold229-76929 27 1221882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390835 Affx-122967837 AX-123261192 27 42969809 TGTGTTCTCCAACAGAAGGGGAGGCTCTAGAGGCG[C/T]GAATGCTGTTGGACAGGGATTCGGGTATGAACAGT Y 2 1 2 1 101000 r 74 goat snp22923-scaffold229-45971 27 1190697 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428450 Affx-122938809 AX-123298793 27 43008041 TTTTTAATGTAAATAAAATCATAATTAGTAAAATT[G/T]ATTATTTGCCAAAGAAAGCGTATTGTTGTTTTGGG K 2 1 2 1 101000 r 74 goat snp22922-scaffold229-7739 27 1152256 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433801 Affx-122934462 AX-123304142 27 43016149 AGAGGAAAAAAGGGAATAAGTCATGGATTGTTGTG[C/T]AGAGATACCAATGAATGCTGGCCAGACAGTGATAG Y 2 1 2 1 101000 f 74 goat snp2231-scaffold1068-927167 27 1133013 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791214 Affx-122934945 AX-385278208 27 43052731 CTGACCTATGAATAGCTTTACTCTACAGTTGCATC[A/G]TGTTTGATCTGTAAATAATCGACAGAGGTAGTCTT R 2 1 2 1 101000 f 74 goat snp2230-scaffold1068-890585 27 1097136 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779071 Affx-122976805 AX-385266176 27 43098751 TTGGACTTAGCGCATAGAAAGAATCATAAAAAATT[A/G]CCATCAAAAGATGGTCAACTATCAGCAATTCCCTA R 2 1 2 1 201000 f 74 goat snp2229-scaffold1068-844565 27 1051338 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450905 Affx-122922196 AX-123321239 27 43127454 GTAATAAGCATTTTACAACTGTTTAGATAAAAGCC[A/G]TTTATTCTACAAAATTTAAAAACTTCTACAGTATG R 2 1 2 1 103000 f 74 goat snp2228-scaffold1068-815862 27 1022628 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410158 Affx-122952792 AX-123280508 27 43167250 CCCTTAGGCAGAACAAGGAGCTGCCCCAAGGTTGC[A/G]CTAGTGTTCCTTGTCTGCTTCTCTCTCGTCTCTGC R 2 1 2 1 201000 r 74 goat snp2227-scaffold1068-776066 27 983784 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436257 Affx-122932549 AX-123306596 27 43201293 AAGGGAGACAAGAATCCTTCAGGAGTTTTCCAGTG[C/T]GTGGGAGATAGCAGCACTGGGGCAAAACTTCTTGG Y 2 1 2 1 101000 f 74 goat snp2226-scaffold1068-742023 27 950305 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398998 Affx-122960947 AX-123269353 27 43230855 TCATTGGAGCTTGTCACAAAGAAAATGTCATCACA[C/T]GAAAAAGAAATGTTTAAACTCTCACACATTCTAGA Y 2 1 2 1 101000 f 74 goat snp2225-scaffold1068-712461 27 920783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775856 Affx-122955019 AX-385262987 27 43263781 GATCTCGCAAGTAACTGTGACAAAGCCAATCAGCA[C/T]GATTGTGATGGTAAATCCTCCTTGAAGCGGCTCTT Y 2 1 2 1 101000 r 74 goat snp2224-scaffold1068-679535 27 887123 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782335 Affx-122939460 AX-385269412 27 43340558 GCTGGAGACACCGTGAGTCTATAAATAGGATCAGC[A/G]TTTAAGTTTTTACACTCCTTGGTTACAGAGCTATA R 2 1 2 1 101000 f 74 goat snp2222-scaffold1068-602758 27 808668 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436214 Affx-122932582 AX-123306553 27 43380743 GGAAGAATATCTGAAAAGAATCTATCTATCTATAT[C/T]TCAGCTCAAAAGCAATTATCCCAGGTTAAATCATG Y 2 1 2 1 101000 r 74 goat snp2221-scaffold1068-562573 27 768452 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780659 Affx-122936529 AX-385267749 27 43424439 TGGTACTCCTCAGCAATAAAAATTAACCACTGATA[C/T]GTGCAAATACACAGATGGGTTTAAAAATATATGTT Y 2 1 2 1 101000 f 74 goat snp2220-scaffold1068-518877 27 724511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453063 Affx-122920062 AX-123323396 27 43467062 TCTGATTGCCATGCTGCGGGTTTCTTTGGGTGCAG[C/T]GCTTTCTGTTGTATTTGAAAATTTTAAGCCAGCAC Y 2 1 2 1 101000 r 74 goat snp2219-scaffold1068-476254 27 681323 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406958 Affx-122955060 AX-123277309 27 43496434 ATCTTGGAGGATTTATATGAGAGACCTGATTTTCC[A/G]CTATCTACTGAGTTTGTAAATGTTTTATCTGACTC R 2 1 2 1 101000 r 74 goat snp2218-scaffold1068-446882 27 652034 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393944 Affx-122965067 AX-123264299 27 43548739 CCACGTCTAGTGCGTGTAGCAGTTGCTAGCTAGTT[G/T]ATTGATATGAACATCACATAGTTGCCCACTGCTTT K 2 1 2 1 101000 r 74 goat snp2217-scaffold1068-394577 27 600400 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382250 Affx-122973950 AX-123252608 27 43601464 GAGGGGCTTCAGAAGATCCTGAAGATCGTGCTCAC[A/G]CAGATTTAGTCACTTCAGAAAAGAAATTTTGGCCA R 2 1 2 1 101000 f 74 goat snp2216-scaffold1068-341852 27 549876 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411313 Affx-122952284 AX-123281663 27 43650777 TGTAGAGTTCACTACGTGACAGATGACATTAAACC[A/G]CAACCACTGCTGTTTGTTCTGCAGATGAGATGATG R 2 1 2 1 201000 f 74 goat snp2215-scaffold1068-292539 27 500446 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451846 Affx-122921080 AX-123322179 27 43725986 AAAAGAAGCACCTGAGTTCCCCTTGTTCTGGCATG[C/T]AGCTCTTGTGTTTTAACATTACCAAAGAGTCCTTT Y 2 1 2 1 201000 r 74 goat snp2214-scaffold1068-217330 27 425175 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766834 Affx-122952161 AX-385254157 27 43779019 TTTAGAATAGTCTTTGTTAAAGAAGCTTAATAAAG[C/T]AACTATTCTGCAGTTCTTACTTATTTGCTGGCATT Y 2 1 2 1 201000 f 74 goat snp2213-scaffold1068-164297 27 372417 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781211 Affx-122936069 AX-385268296 27 43819659 TTCTAATAATTCTTGCTGTGTTAAAAAGGATTTGG[C/T]AGTCAGGGTAGGGAGAATAAGATCTTGATTTTGTT Y 2 1 2 1 201000 f 74 goat snp2212-scaffold1068-123657 27 331269 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786871 Affx-122944214 AX-385273900 27 43853491 AGCTCTACAGCTAAATGCTGAACTTGCTTTTTCAA[C/T]AGATAAGATTTTCCTTTGGCAGTTACCTGTAACTT Y 2 1 2 1 101000 r 74 goat snp2211-scaffold1068-89825 27 297870 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790645 Affx-122944896 AX-385277647 27 43885624 TGCCTGAGTTACAACCCTAGGGTCTCCTCATGATA[C/T]GAATCATGAGGTGGGGCACCTGCATGGCCAGGCTA Y 2 1 2 1 303000 r 74 goat snp2210-scaffold1068-57692 27 265727 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431426 Affx-122936519 AX-123301767 27 43935666 CTCAGTTGATTTTGATGCCCAAAGCCCACTACTCA[C/T]GTGAAACAAACCACCGTTTTCTTGGGTAGGCAGTT Y 2 1 2 1 101000 r 74 goat snp2209-scaffold1068-7650 27 215345 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384721 Affx-122972056 AX-123255079 27 43982873 GTTAGTGGTCTTGTTTTGAAAGAAACTGGAGAAGG[C/T]GGAGAAAAGGGAAATTACAAAGCAAGAGGTATTTT Y 2 1 2 1 102000 f 74 goat snp19312-scaffold195-135977 27 167943 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801040 Affx-122921356 AX-385287954 27 44022913 ACTTTAAGCTTACACTTTCCTTCAGCAAGCTGACT[A/G]TGACCAAAGAATTTAGACTTTTCACCCTTCTTTTG R 2 1 2 1 101000 f 74 goat snp19311-scaffold195-95937 27 130172 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411665 Affx-122951559 AX-123282015 27 44068311 TCATCACCCCAGTCTCCCACTCCGTCCTTCCGCCT[C/T]CCATCCTGGCAGCCCAGGGTCCATTCTCCACGTCT Y 2 1 2 1 103000 r 74 goat snp19310-scaffold195-50539 27 84452 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782604 Affx-122931575 AX-385269677 27 44099106 ACCCACTAAAAGCAGACCTGAAGACTGAAAAGATG[A/C]TAAAAATCTGTTTGTTACATTTTTTACTGTAACTT M 2 1 2 1 201000 r 74 goat snp19309-scaffold195-19744 27 52985 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767861 Affx-986698767 AX-385255081 27 44472748 GAGGTCACTGAGCTCTTCTTCCCCAGCACCTGAAG[A/T]TCACCACTAAACACCTGCACTGAACCCAATGGTAT W 4 1 2 1 600010 r 74 goat 27_44472748 27 44472748 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 468277754 Affx-1111836072 AX-519551253 27 44553984 AGAATAGTATGAGGTAGGGAATTACTGGTTTGGGG[A/G]GAAGGATGTTGATCTACTTAGGGATGAAGTATAGT R 2 1 2 1 101000 f 74 goat Random2.2K-2254 27 44553984 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777353 Affx-122974519 AX-385264475 27 AAGGAGAATGGTTTGTCTTTGAGTCTCTCTCAAGA[C/T]AAAGCTTTATCTAATACCTGATAAGACCTCCAGCA Y 2 1 2 1 101000 f 74 goat snp35506-scaffold428-82037 NW_017189517.1 21553353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767872 Affx-986698773 AX-385255092 28 2158 TTTGGCTAAGTGAGTAACTATTGTTTCATAGTGAC[C/T]TATATGATCCAATCCGACTGAGTGTTATAAACCCG Y 2 1 2 1 600010 r 74 goat 28_2158 28 2158 Ancestral_priority_1043 ancestry 0.66 recommended IMAGE 10K 10K ancestral 38436304 Affx-122933268 AX-123306643 28 30214 ATGTGCCATAAAATGGAAAATAATAAATAATTACA[C/T]AAAGATTTCTCTTTACAGAAATTTCAGCCATATTT Y 2 1 2 1 103000 r 74 goat snp57608-scaffold922-669638 28 44302456 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464026910 Affx-1110278517 AX-515503668 28 47375 ACAAGGTCTTTTCCTATAATACTGTCCCTTAGTGA[C/T]ACTCCATCTTTAATGTAATAGATGCCATGCTGGTT Y 2 1 2 1 101000 f 74 goat 28_47375_AF-PAKI 28 47375 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450203 Affx-122922291 AX-123320538 28 61370 CATGACTTCATTCCCCTGGAGTTCTCACTCTCAGA[C/T]GTATCTATACTCAGGTGCTGGTAATTCACCAGTTA Y 2 1 2 1 201000 r 74 goat snp57607-scaffold922-638482 28 44270922 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390399 Affx-122967658 AX-123260756 28 145675 AGAAGCCAAACTTTGAACCCACAGTCATCTGATGG[C/T]AAAGCCCATGAGGCTCCATGGGGTCCCTCTGAGGG Y 2 1 2 1 101000 f 74 goat snp57605-scaffold922-554177 28 44185307 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413768 Affx-122949932 AX-123284117 28 188050 GGGATCATGAGGTTCCCCACTACTCCGTTAGACAG[C/T]GCAAATTTGGGGATACTGTTGGTGCAAGTTTGGGG Y 2 1 2 1 101000 r 74 goat snp57604-scaffold922-511802 28 44142986 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439258 Affx-122930996 AX-123309595 28 216676 ATTAATGCCATCTTTTCTTGAGAAGACCCTGATTC[G/T]CTGAGGGTTACACTGGACAGTCTAATTAGAGTTTG K 2 1 2 1 101000 r 74 goat snp57603-scaffold922-483176 28 44114043 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436300 Affx-122933270 AX-123306639 28 259793 GCACCGAGAACATTTGGTCTGTTCATGACCCCATC[A/G]ATTCCAAACAAGTCTAAACCACAGAAATAAGTGCA R 2 1 2 1 101000 r 74 goat snp57602-scaffold922-440059 28 44071960 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400249 Affx-122960143 AX-123270604 28 311648 CTCTGCAGCAGAGACTCATGTCTGTTTCAATAGCA[C/T]TCTCCACTCAGCCTGGAGGGAGGATCAGGGTCACA Y 2 1 2 1 101000 f 74 goat snp57601-scaffold922-388204 28 44019692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786393 Affx-122957338 AX-385273427 28 382405 TCTCTTTGCTTGAAGTTGGATGACATACACATTGC[A/G]TGTCACGTATGTTTTACATGTCAAGTGCACAGTGC R 2 1 2 1 101000 f 74 goat snp57600-scaffold922-317447 28 43946758 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433920 Affx-122934303 AX-123304261 28 546413 TTATGACTGAAACACAGTCTTTGGAATTTCCTTTC[A/G]TGATAAAGTGTTGGTTGCAAAATATTTCCGTTTTT R 2 1 2 1 101000 f 74 goat snp57597-scaffold922-153439 28 43780704 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379756 Affx-122975857 AX-123250114 28 656131 ACAATGTACTATTGTCTATATACTATGTTGCACCC[A/G]CTCTGAATGTTGACATTTGTAGGATTAAGAGAATG R 2 1 2 1 101000 f 74 goat snp57594-scaffold922-43721 28 43670999 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387065 Affx-122969895 AX-123257423 28 692250 ACCCTGAGTCCCAACTTTCTGAGTCAATCATCAGT[A/G]CCTAAGTTTGCCCCTCTTTGACCTCAAATACACCT R 2 1 2 1 101000 f 74 goat snp57593-scaffold922-7602 28 43639001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402715 Affx-122958789 AX-123273068 28 707545 AAGTAAACACAGATAAATTCAGAATTATCTGGGTG[A/G]TCTTTAGCAAGTACTGGCATACAGTCTCAGTGCTC R 2 1 2 1 101000 r 74 goat snp12234-scaffold1457-7594 28 43622627 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392876 Affx-122965746 AX-123263233 28 745613 GCCACTTTTTAAATAAAATGAGACTAGGAACAGAT[A/G]CTTCATAGAAAAGATTTCAGTTCAGCTAACATTTA R 2 1 2 1 101000 r 74 goat snp12235-scaffold1457-45662 28 43584683 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277896 Affx-1111836073 AX-519551391 28 775358 AACTCCGGCAGAGGGACAGCACTCTTCAAGGGAGC[A/G]CAGATGCTGGTCTATCCGGGGAACCTGCATCCTTG R 2 1 2 1 202000 r 74 goat Random2.2K-2256 28 775358 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38392510 Affx-122966122 AX-123262867 28 800147 TCACTAGAGTTAAGGTAAGTCTTTTTATGACAAAG[A/G]AATCCATGCCCTAAGAAGATATAATAGCTCTAAAT R 2 1 2 1 101000 f 74 goat snp12236-scaffold1457-100196 28 43528728 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780819 Affx-122959388 AX-385267908 28 828777 TAAAATAACCCATAAAGCTCCCTTTGCTCTGACTC[C/T]GCTTAATTTTCCAATTACTACTTCAGATAACTTCA Y 2 1 2 1 101000 f 74 goat snp12237-scaffold1457-128826 28 43499940 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275106 Affx-1111834601 AX-519548685 28 845789 AATGTTCCGTGTGTGAGCTCTCTCTGGACTCCTTA[A/G]AGACTTCCCTTCTCTTCCCAGTATCTCTGGGGTGA R 2 1 2 1 202000 r 74 goat GoatD01.042768 28 845789 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320783340 Affx-122928390 AX-385270404 28 892714 AGCCTAATGCACTCAGGGAAAACTATTTGGCTTGA[C/T]AGGATTTTTTAGATCCTTGTTTAACACTTTGTTGG Y 2 1 2 1 101000 f 74 goat snp12238-scaffold1457-192763 28 43432556 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770904 Affx-122952373 AX-385258068 28 937357 CAAATCAAAAACGTAAATCCACTTCTGGACTGTTC[A/G]TCCAGGAATGGGTGAGGGGATGAATACCAGTGCCA R 2 1 2 1 202000 r 74 goat snp12239-scaffold1457-237406 28 43388223 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413304 Affx-122950193 AX-123283653 28 984733 TTACCCTTTAGCTTTTCTTTTCCTTGCAGCTGAGC[C/T]TATCAGTACCTGAGACTTGGTGGGGGGGCTGTTGT Y 2 1 2 1 201000 f 74 goat snp12240-scaffold1457-284782 28 43341968 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417163 Affx-122947339 AX-123287511 28 1013356 GGGACTGGTGCCAAGTGATGCCTGGCACCTGCCTC[A/G]TACATTCTTCCCAGTGGTGTCCAGAGAGTGTCAGT R 2 1 2 1 101000 r 74 goat snp12241-scaffold1457-313405 28 43313206 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766704 Affx-122966158 AX-385254049 28 1045048 GAGTTTCCTAGCAGTTCACAGAACATGAACCTCCT[A/G]CTTTATATACTTCATGAATCTTATCTCTTGTAATC R 2 1 2 1 101000 f 74 goat snp12242-scaffold1457-345097 28 43280455 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277898 Affx-1111836074 AX-519551393 28 1053086 GGGACATAACTACCATATTTTGGGAAACTTTATAT[A/G]AAGATTTTTTACGCTTTTAGGAGGACAAAGTCAGC R 2 1 2 1 101000 r 74 goat Random2.2K-2257 28 1053086 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38419123 Affx-122945763 AX-123289471 28 1073340 CCAAAGGAAGTTATCATGCAAGGGTCAAATGAGGG[C/T]GTCTACAATGTTTTTCTAATACCTCCATCTAAGAC Y 2 1 2 1 201000 r 74 goat snp26087-scaffold2713-4612 28 43251891 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405256 Affx-122956873 AX-123275608 28 1112793 TCCAGAGAGACACCTGCCAGAAGGCTCCAAGCAAA[C/T]GGCACTCTCCCTTCAGGCTGTGGGCTACTGTGGTT Y 2 1 2 1 202000 f 74 goat snp26088-scaffold2713-44065 28 43212387 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406909 Affx-122955620 AX-123277260 28 1203228 CATCTAGGTTGTTTGAGGTGACCTGAGTTCCTGGG[A/G]CCCCTGACAGGAACTAGGCTTCTACTTCCCCACTC R 2 1 2 1 101000 f 74 goat snp13193-scaffold1506-61124 28 43116423 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383077 Affx-122973741 AX-123253435 28 1237818 CACCCAAGCGGTGCTTTGTGATCCCCTCTCCTTGC[A/G]ATTGGAAACAGGAACAGGGTTAGCATCTGGAGAGG R 2 1 2 1 201000 r 74 goat snp13194-scaffold1506-95714 28 43081875 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409007 Affx-122953884 AX-123279358 28 1309727 TGTCTAATTTTGTCTGAGGACACCTCTAAGCCTTC[G/T]AATTCACCAGTCATCAGCCCCTCTCGCACCCTCCC K 2 1 2 1 101000 f 74 goat snp13195-scaffold1506-167623 28 43007949 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436233 Affx-122932569 AX-123306572 28 1378155 CATCAACATCGTATTTTAACCAACAGAGATCTCCA[A/G]TCCAGATGTTCAAGATGCATAAACAATGGGGTCAG R 2 1 2 1 103000 f 74 goat snp13196-scaffold1506-236051 28 42938403 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438887 Affx-122930736 AX-123309224 28 1424589 TTGAGGCATCTTCCTGTTAGGAAAACACACGATTT[C/T]CATTGCACATGGGCTAAGCCAGACACCATGCTTGA Y 2 1 2 1 101000 r 74 goat snp13197-scaffold1506-282485 28 42892523 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277760 Affx-1111836075 AX-519551258 28 1446350 GGGTCCTGAGGGAGTACCAGTTTCCCTTCAGAGCA[C/G]GTCCTCTCCACACAGTCAAAACTTTCCAAGGCATC S 4 1 2 1 202000 f 74 goat Random2.2K-2258 28 1446350 G C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439540 Affx-122930108 AX-123309877 28 1492624 CGTCTCTGTGTCGGCAAAGGGAAGGTAACAGTAGT[A/G]TGAAATTCACATTGGGAGGGAAGATGAAGTGGGGC R 2 1 2 1 201000 f 74 goat snp13198-scaffold1506-350520 28 42823559 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792077 Affx-122945457 AX-385279064 28 1531694 TCCCTACAGGATCCAGCATCTATGCCTGAACTTAG[C/T]ATGCAGATTCTAGCTACAGCTAGTTGCAGTGGTAA Y 2 1 2 1 101000 f 74 goat snp13199-scaffold1506-389590 28 42785979 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439350 Affx-122930287 AX-123309687 28 1582173 GCTCAATCAACAAATATTTATCAAGGACTAATAAA[C/T]AGAACAAAAATCTCTGCTGTTAGGGACAACTAGTT Y 2 1 2 1 103000 r 74 goat snp13200-scaffold1506-440069 28 42733859 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426052 Affx-122941103 AX-123296398 28 1656545 TGAAATAAAATGGGTTTTGGAGGTGCTGTGGAGAA[C/T]AGAGCTACAGAACATCCAGAATCACCCCATCATTT Y 2 1 2 1 101000 f 74 goat snp13201-scaffold1506-514441 28 42654567 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381373 Affx-122974395 AX-123251731 28 1719633 CATGGGTTTAAAGACCACATTAGGGATAAGAGTCA[C/T]AGGGTACATGATCATGTCTAGTTATTCTTCTGGCT Y 2 1 2 1 101000 f 74 goat snp13203-scaffold1506-577529 28 42589166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801109 Affx-122932892 AX-385288023 28 1729134 AGCAATTTTAGTGATTGACTATGGGAAAGCAGGGT[A/G]TGTGAAAACAAGCAGGAGAAAATAAGGTTTTTGTT R 2 1 2 1 201000 r 74 goat snp404-scaffold101-5416 28 41846726 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447135 Affx-122924457 AX-123317471 28 1764761 CAAGAAAATAAAATCTGCCACTGTTTCCATTTTTC[A/G]TGATCCATTTGCCATGAAGTGTTAGAACGAGACAC R 2 1 2 1 101000 r 74 goat snp405-scaffold101-41043 28 41811406 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378428 Affx-122976775 AX-123248787 28 1817402 CAATAATCCCCAAATCTCCTCAGCTACCAGGAGAA[A/C]TGGATGGGAATACTGGGTTTTATGAGAAAGCGGAA M 2 1 2 1 201000 r 74 goat snp406-scaffold101-93684 28 41760440 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410366 Affx-122952449 AX-123280716 28 1895102 CAGTCAGTCCAGCCTGCAGACGGTTACCACGCTAG[C/T]GCTCACCATGGACTTCCCATCCTAGAAGATGGCGT Y 2 1 2 1 101000 r 74 goat snp408-scaffold101-171384 28 41681740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768636 Affx-122968534 AX-385255815 28 1928280 TTCTTTTTGAAATAACACAAAGGGCCCTTCCTGCC[G/T]ACATTCCTAAATGTGGCTTTAAAGTGAAATCAACA K 2 1 2 1 102000 f 74 goat snp409-scaffold101-204562 28 41648721 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797681 Affx-122968307 AX-385284620 28 1970684 GCTCGCTCTAAATCCTAAATTTGTTGCTACATCTG[C/T]TCTTCTTGGAACAGAGAGGGATCAAGGTAGGTTTC Y 2 1 2 1 202000 r 74 goat snp410-scaffold101-246966 28 41606121 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273676 Affx-1111833734 AX-519547289 28 1972836 GGACTGAGGAGTTGAAA[A/G]CTGGTGGCAGCCATCAGGGTTGGTGCCCCTGACTG R 2 1 2 1 102000 r 74 goat GoatD01.003007 28 1972836 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38390105 Affx-122968016 AX-123260462 28 2012397 TGGACAGGTTCAGAGAATGCAAGTCTCTTGACTGG[C/T]GTGGCCTGAAAGGTTTACTTTCTCAGTACAGTTTT Y 2 1 2 1 101000 f 74 goat snp411-scaffold101-288679 28 41564525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783532 Affx-122934229 AX-385270594 28 2040908 TCAGGGATTTTGCTCTTCAGCAGAGAGGGAGCACA[G/T]ATATTTTTAGTGCAGGAATGATGAAATCTGCATCT K 2 1 2 1 101000 f 74 goat snp412-scaffold101-317190 28 41535814 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397352 Affx-122962294 AX-123267707 28 2074321 TGGACTCCATGCACGGTAACTTATGTGCCTGGTGG[A/G]GAAGTCAGCCCTGAGGATGAAGGAAAAGGCATTCT R 2 1 2 1 201000 f 74 goat snp413-scaffold101-350603 28 41502111 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795596 Affx-122972685 AX-385282551 28 2077688 GTTTCACAGGGAAGCATTAAACACACGGCCCATAC[A/G]TAATAATGTCTGTCATTATTCAAGAAGCAGTTGTT R 2 1 2 1 201000 r 74 goat snp13679-scaffold1528-600135 28 41498552 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415310 Affx-122948812 AX-123285659 28 2121232 GTCCAGCTCTCACCTGCCTCCTTTCCTCTCCCTCT[G/T]GGGGTTGGACCCCATCTCTAGTCCTGTGACTGCTC K 2 1 2 1 101000 r 74 goat snp13678-scaffold1528-556591 28 41454411 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433073 Affx-122935740 AX-123303414 28 2151339 CTTCCCTTCTCTCATGGCATCCTTTGCAAGCAAAG[C/T]GTTTAGAATAAAATCTCAGATGAAGCAAATTCACT Y 2 1 2 1 101000 r 74 goat snp13677-scaffold1528-526484 28 41423582 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424095 Affx-122942035 AX-123294441 28 2203567 TCTGAAGTCACCTCTACCACCCACCACCTTCTCCA[C/T]GCTGCTGTCACCTCTGACCTCACTCTGCTTGGAAC Y 2 1 2 1 202000 f 74 goat snp13676-scaffold1528-474256 28 41371318 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387105 Affx-122970672 AX-123257463 28 2241408 GGACAGGGAGGCTTTATCAGTGAGCATAGGTGAGA[C/T]GGTGGTTCTGTAACAAGTAGTCCTTACACCTCAGT Y 2 1 2 1 101000 r 74 goat snp13675-scaffold1528-436415 28 41333489 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375958 Affx-122978444 AX-123246317 28 2299259 GGTCCTCCTTTTACTAACTTCAAAGCAAGGGCAGC[G/T]CCACAATTTATGGACGGGATGGGGGACAGGGGCAG K 2 1 2 1 101000 f 74 goat snp13674-scaffold1528-378564 28 41275429 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436328 Affx-122933251 AX-123306667 28 2339149 CTAAAGAGCTCTTTACAACATGAGGTCAATATACA[C/T]GTTCATTTACCTCTTATTTAAAATATTTTTTGGTG Y 2 1 2 1 101000 f 74 goat snp13673-scaffold1528-338674 28 41235610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406029 Affx-122955489 AX-123276381 28 2381182 CCTGGGTTCTAGGGAAACGTGGGAGAGCATTCCAA[A/G]TAAAAGTATTAAATCGCCAGAACTGTGACCCTGAC R 2 1 2 1 101000 r 74 goat snp13672-scaffold1528-296641 28 41193788 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446240 Affx-122925693 AX-123316576 28 2426812 AATCTATGCAACTTCCACCATAAAATCAACAAAAT[A/G]CAAATAAAACCATACATTACCAGCCTTCAGAATTA R 2 1 2 1 101000 r 74 goat snp13671-scaffold1528-251011 28 41147339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792153 Affx-122921901 AX-385279139 28 2478050 GTAACTTCAAGCAAGGATCCAAAGGAAGAATTAAC[A/G]TGTGTACTTGCCTGGCACCTCAGCTCCAATCTGTG R 2 1 2 1 101000 r 74 goat snp13670-scaffold1528-199773 28 41100321 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403707 Affx-122958038 AX-123274059 28 2509061 AGAAGACCACACACTCCCTACCCCCACCCCCATGC[G/T]ATTTTTCTTTCTCTTTCTTTTGATTTGCTTTGCTT K 2 1 2 1 102000 r 74 goat snp13669-scaffold1528-168762 28 41068787 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273203 Affx-1111833342 AX-519546862 28 2551712 TCTAAACCAGATGGTGTGCCTCCAAGGTAGGGCGT[A/G]AGAAGTATTTGGTTGTGACTCAGTGACAACAGAAC R 2 1 2 1 101000 r 74 goat 28_2551712_AF-PAKI 28 2551712 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38447137 Affx-122924455 AX-123317473 28 2585645 AACACATCTGTATGCAAATTTTCATGAGTAAGATA[C/T]AAGAAATGATTCATTTTGGTAATTTTATGTACAGC Y 2 1 2 1 101000 f 74 goat snp13668-scaffold1528-92178 28 40991645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788237 Affx-122932117 AX-385275256 28 2675908 AGCTCTGAGGGTTGCCTTAAATCACCTGGGAAGAA[C/T]ACCAGGCCTTGTTAGATCTTTGCTTTAGACCAGAT Y 2 1 2 1 101000 f 74 goat snp13666-scaffold1528-1915 28 40901446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787869 Affx-122974273 AX-385274891 28 2703413 TATAAGGGCCTATTAAATGGATATGGCATATGATC[A/G]TGCATTGCCAATAAAGTTTTCTCCCCAACTTCTTA R 2 1 2 1 101000 f 74 goat snp26835-scaffold2821-25491 28 40863572 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405672 Affx-122956563 AX-123276024 28 2735888 TGGGGAGGTTTCAGACCCTTGGTTGAGTAGCTTTA[C/T]GGAGGGCTACTCAGACCCAAGGTTCTACAGGCGTT Y 2 1 2 1 201000 f 74 goat snp26836-scaffold2821-57966 28 40830658 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802122 Affx-122936172 AX-385289026 28 2785950 CATTCTTCATGCAAATGTAGACACTCATTTATTTA[C/T]GAATGAATAAATACCTAGTACCTTTGTCTAGTACC Y 2 1 2 1 101000 r 74 goat snp26837-scaffold2821-108028 28 40779454 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444532 Affx-122926487 AX-123314869 28 2816574 CTCTTTATCATCAGAGCCGCCAGGGAAGCCTGGAG[A/G]CGAAGGAGGGAATGAGCTACTAAGAGGGGAGACTC R 2 1 2 1 103000 r 74 goat snp26838-scaffold2821-138652 28 40749285 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786118 Affx-122922492 AX-385273154 28 2820300 AACACAACATACACACGTTATTTTATCCAAGACAC[A/G]GACATCAGAAAATTCAAACTGCTGCTTTGATTCCT R 2 1 2 1 201000 r 74 goat snp1084-scaffold1028-1974492 28 40745655 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405734 Affx-122956517 AX-123276086 28 2854018 AGACAAGACCTCTCAAAGCAAACAGGAAGAGACTA[C/T]AGAGATGGAGTGAGTGCCAGTACGGAAGGGGCCCT Y 2 1 2 1 101000 f 74 goat snp1083-scaffold1028-1940774 28 40711911 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432242 Affx-122936356 AX-123302583 28 2902758 AGAACAGGGGTGACCAGAGGTCAGGGATGGGGCGA[C/T]GGAGCGTTACTGTTTTGTGGATCTGGCCAATATCA Y 2 1 2 1 101000 r 74 goat snp1082-scaffold1028-1892034 28 40664734 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792176 Affx-122949274 AX-385279161 28 2942069 ACTTTGGCACTTTGGAAGATTACATGTCAGTTACT[A/G]TATAGAATTTCCTCCCATTTGAGTTTGTTGGGTAT R 2 1 2 1 101000 f 74 goat snp1081-scaffold1028-1852723 28 40626193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428417 Affx-122938835 AX-123298760 28 3030823 ATCTATAGATTTAGCTACCAGTTTATGGGAAATAC[A/G]TGGGAAAAAAGAAACATGTTAATGACTACAAAGAT R 2 1 2 1 101000 f 74 goat snp1079-scaffold1028-1763969 28 40535439 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385026 Affx-122971860 AX-123255384 28 3063361 AGACTTAAAATACATGACAAAGAGGGAATGAAAGG[C/T]ATGAAAATAGTTTCAGGTCCTTGAGTTTCCAGAAA Y 2 1 2 1 101000 r 74 goat snp1078-scaffold1028-1731431 28 40503498 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435986 Affx-122933507 AX-123306325 28 3092311 ATCAAGCACCACCAAGACTAATGGATTGGGCACCA[C/T]GCATTCCAAGTAAAGAGAAAGAACAGAAATCCAGG Y 2 1 2 1 201000 f 74 goat snp1077-scaffold1028-1702481 28 40474983 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415039 Affx-122949495 AX-123285388 28 3159140 ATCCCCTCAGATGTCTAGACTTCAAGCTTCTTTTC[G/T]CCTGCTCTTTCTGTGGTTAAGATCACGGAGGGTTT K 2 1 2 1 101000 f 74 goat snp1075-scaffold1028-1635652 28 40411235 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771781 Affx-122956880 AX-385258938 28 3197760 GATGATATTAGGGGCTGGGTCCTCTAAAGGCTTGA[C/T]GTCTATCAAGATCACTGCATCTTCCTCTGTAACCT Y 2 1 2 1 201000 r 74 goat snp1074-scaffold1028-1597032 28 40372320 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394830 Affx-122964790 AX-123265185 28 3238600 ATAGCATAGACACCTATTAGGTGTTAGTTACCCTC[A/G]TAAGATCATGTTAGGGCTGAAAAGAGGCATAGCAG R 2 1 2 1 101000 f 74 goat snp1073-scaffold1028-1556192 28 40332535 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417755 Affx-122947411 AX-123288103 28 3278720 AGTGTCTTGCTCAGAGGCAGTGAACACAGAACAGC[A/G]CAGAGGTGGAGCTGATGGAAGCCCCACGATTCCAT R 2 1 2 1 103000 r 74 goat snp1072-scaffold1028-1516072 28 40292504 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391780 Affx-122967457 AX-123262137 28 3308440 ATGCTCATGCCACATGGAGGACAGGTAGGCGTTTG[C/T]GACTGCAGTGTCCTGTAGGTCCTCCTGGAACTGGA Y 2 1 2 1 201000 r 74 goat snp1071-scaffold1028-1486352 28 40262996 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391091 Affx-122966827 AX-123261448 28 3392173 ATCTAGAAAACAGTTTGAGAGCATCAGGAATTTTC[A/G]CAGGAATAAGCAGCTTGCTGATGGCAGTGGGCAGA R 2 1 2 1 101000 r 74 goat snp1069-scaffold1028-1402619 28 40179436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385807 Affx-122971033 AX-123256165 28 3437066 CTCTGTTGAAAAAAAGCGTCAATCTGCTTACTTAC[A/G]AGAGCCCTCCTGTGTGCCATGAGCCAGCAGAATCA R 2 1 2 1 201000 f 74 goat snp1068-scaffold1028-1357726 28 40133993 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444335 Affx-122926728 AX-123314672 28 3481118 CAAAATACAGAAGCAGAACCTGTGCGGCAGGGTGT[A/G]CGGTGGGTGATGCTGAGCCTGGTGCCGGCCGCTCA R 2 1 2 1 303000 r 74 goat snp1067-scaffold1028-1313674 28 40090271 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274668 Affx-1111834431 AX-519548254 28 3519517 CTTTTCCTCTGAAGACTGCCACTGGCACTGGCCAA[A/G]CTGTGTGAGGCCTGCAGCTGACCTCACAGTGGGCC R 2 1 2 1 202000 f 74 goat GoatD01.035484 28 3519517 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38376689 Affx-122978988 AX-123247048 28 3537561 TTATCTATATATATTTTGGAGTGGGGGGTTGGTGC[C/T]GAGGTTAAGATTGACCCAAGGTTATTAAGTAGGTA Y 2 1 2 1 101000 r 74 goat snp1066-scaffold1028-1257231 28 40033960 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428255 Affx-122939415 AX-123298598 28 3569925 GGGGGTGTCAGAATAGATTCTACGTCTCCCTTAAG[C/T]TCTAACGTTGTGACTGAGTGGGTGGTTGATATTGA Y 2 1 2 1 101000 r 74 goat snp1065-scaffold1028-1224867 28 40001532 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396422 Affx-122962999 AX-123266777 28 3628470 GGGTCTCAGGTATCAAGTTGCTGGCGCCTTTGGAG[C/T]AGAAAGACATTTTGGAGGTGAGAGGAATAGGAAGG Y 2 1 2 1 101000 r 74 goat snp1064-scaffold1028-1166322 28 39944234 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388942 Affx-122968818 AX-123259300 28 3659409 ACGTATGGCTTTTTTAAAAAACTCATTTTAGAAGT[A/G]TGAGTCAAAGTTGCTTTCTGGACAGAGGTGCCTCC R 2 1 2 1 101000 r 74 goat snp1063-scaffold1028-1135383 28 39913444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376727 Affx-122978960 AX-123247086 28 3698889 CTTTAATCAAGAAAAAGATCATTTTACTGACATTT[C/T]CCAAAAGCGTTCAGTCTTTTTTCATTTTCCTCTCT Y 2 1 2 1 101000 r 74 goat snp1062-scaffold1028-1095903 28 39874132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403380 Affx-122957782 AX-123273733 28 3742888 AGGAAGAGGTTAGTATTCTGTCCTAGGTCTAACAC[C/T]TAGAGAGTTAGTCAGTCACAGGTGGTAACGGGGTT Y 2 1 2 1 101000 f 74 goat snp1061-scaffold1028-1051904 28 39829470 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409933 Affx-122952872 AX-123280284 28 3778536 CTATGTTTTAACCAGCACCCTGACTTTTTTTGTAA[C/T]GATCACAATACATTTTATTTAACTGAGTATATCCA Y 2 1 2 1 101000 f 74 goat snp1060-scaffold1028-1016256 28 39793600 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395581 Affx-122963838 AX-123265936 28 3808727 TTCGGTTTTCAAATTCAAAAAGTTTATGCCTTCTC[A/G]TTACTCAGCATCTATCTTCTCCAACTGGTTTTATA R 2 1 2 1 201000 r 74 goat snp1059-scaffold1028-986065 28 39762710 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406914 Affx-122955616 AX-123277265 28 3888344 GCTCAGAATTAAGTTGCGATGGCTGTCCCAAGTAG[C/T]GCTTAGACTAAGGGGTATTTGTAAGTAGGTTATGT Y 2 1 2 1 101000 f 74 goat snp1057-scaffold1028-906448 28 39682486 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451725 Affx-122921546 AX-123322058 28 3937809 TAAATCAACTATACCTCAATTTTAAAACTGCACAT[A/G]TGATGATTTATCAACCTCACTTATAATACTAAAGT R 2 1 2 1 201000 r 74 goat snp1056-scaffold1028-856983 28 39632191 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420062 Affx-122945124 AX-123290410 28 3995445 GTGACTTGGTCCAACATAGGTGTCCTCTTGCTCTG[C/T]AGGAGAGAAGGGTCCCACACCCAGCAGGTTTGGAA Y 2 1 2 1 101000 f 74 goat snp1055-scaffold1028-799347 28 39573726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378327 Affx-122977341 AX-123248686 28 4034688 ACAGCACCCTCCATCAAGAAGGTAATATAGGCACA[G/T]AACAATTAGCTACAAAATTTCATCAGTTCATCATA K 2 1 2 1 101000 f 74 goat snp1054-scaffold1028-760104 28 39535087 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392496 Affx-122966133 AX-123262853 28 4064578 AAATCTATTTGTTTGGGCAGTTTACATGGATATCT[G/T]CACTAAACGGACATCAATTAATAATAATAATTAAT K 2 1 2 1 101000 f 74 goat snp1053-scaffold1028-730214 28 39505342 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413125 Affx-122950375 AX-123283474 28 4096016 TGAGTAACAAACATATTTCTATATCTTTGTATAAA[C/T]GATTATTTTGAAAATGGTATGTAAAGCTGATTTAC Y 2 1 2 1 101000 f 74 goat snp1052-scaffold1028-698776 28 39473641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416475 Affx-122947804 AX-123286823 28 4139283 GACAGCAGTGCCCTGCAGCAGAAGGCTCTCCATGA[C/T]GCCCATCTGTAAACATGCAGTATACGAGTCTGTTT Y 2 1 2 1 101000 r 74 goat snp1051-scaffold1028-655509 28 39430207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418259 Affx-122947021 AX-123288607 28 4171769 CTCCCAAGCAATTATTTTCCTTTTGTCTTAAGGAT[A/G]TGAGAAACTCCTCAGTATCTTTCTATACTACTGGT R 2 1 2 1 101000 r 74 goat snp1050-scaffold1028-623023 28 39397084 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445559 Affx-122925148 AX-123315896 28 4231554 TTCTACTCCCCATATCCCTACCTGTGGATCAACAT[A/G]TCTGATCGCTTTCCCCAATTCTTTTGTTCCTGGTT R 2 1 2 1 201000 r 74 goat snp1049-scaffold1028-563238 28 39338090 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382918 Affx-122973394 AX-123253276 28 4260623 TTCCCTCTTGGCAGATTTAGGCTTTGAGTCCTGAC[A/G]TGTCTGGCCCATTTGCCCAGCTTAAATGGTGGGCT R 2 1 2 1 101000 f 74 goat snp1048-scaffold1028-534169 28 39309364 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382033 Affx-122974949 AX-123252391 28 4292526 ATCTGTGAATTACAATGAAATCCGATGAGAAATTT[A/G]CCTAGCATACACAGATGGCATTTCATTAGTATGGT R 2 1 2 1 101000 r 74 goat snp1047-scaffold1028-502266 28 39277115 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418974 Affx-122946073 AX-123289322 28 4333502 GCAGGAAGTTTTACTCGAGGAGATTGTCAGAGCCA[G/T]AGGTCCTACATCATCATTCTGATCCTATGACAACT K 2 1 2 1 101000 f 74 goat snp1046-scaffold1028-461290 28 39236017 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431360 Affx-122937042 AX-123301701 28 4408220 GTTTGAGCATCCATGGGTCATAATATAATGGTGTG[C/T]GTTTAGAAGTAGGGTGTGTCCTATAGGAGGACAAG Y 2 1 2 1 101000 f 74 goat snp1044-scaffold1028-386572 28 39162602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790409 Affx-122934339 AX-385277412 28 4451009 AGTCAATTCTCGCTAGCAACCCAGCGACGAATGTT[C/T]GAGCCCCTTTTTGTGCGACTTCAGTAAAGATTTTT Y 2 1 2 1 101000 r 74 goat snp1043-scaffold1028-343783 28 39120158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448716 Affx-122923848 AX-123319052 28 4539632 AGGCTTCAGGAAGAGACAAGCAGCATCCTGGGAGC[A/G]CTAGCAGAGGATAAGTCTCTGAGTCACTGTCCCGC R 2 1 2 1 201000 r 74 goat snp1041-scaffold1028-255160 28 39031231 C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799949 Affx-122943301 AX-385286875 28 4570645 TTATCTTATAAATGTAGCCTGTGTTATTGGCATTG[A/C]TGTTCTTCGGTCACAAAGTTGGTTCTGACACTTTG M 2 1 2 1 101000 r 74 goat snp1040-scaffold1028-224147 28 39003640 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777978 Affx-122924582 AX-385265094 28 4641492 TCCTAGTAATGATAGCTTATGCCAATCAGACTCAA[C/T]AAAAATGTTATCAGTTCTACAGCACTTTGGTGTCT Y 2 1 2 1 101000 r 74 goat snp1038-scaffold1028-153300 28 38930731 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441152 Affx-122929566 AX-123311489 28 4670397 ATATTTTATAGAAGATTTTTTTACCGGATTAGTCT[A/G]TACAGTTGGCCCCTGAACAATATGAGGGTTAAGGA R 2 1 2 1 201000 f 74 goat snp1037-scaffold1028-124395 28 38901491 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395191 Affx-122964509 AX-123265546 28 4703395 CTTTTTGAAAAATACCAATGCTACCAACCTGGCTA[A/C]AACAAAGGCCACTGTAAAACAAGGTAAATTAAGTT M 2 1 2 1 101000 f 74 goat snp1036-scaffold1028-91397 28 38867959 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781045 Affx-122936647 AX-385268132 28 4752913 AGTTTGCAGCCAACAGTTCCTGAAATTTTTCTAAG[C/T]CTTTAGCTTCACAGATATAGACTTCCAGAAAAACA Y 2 1 2 1 201000 f 74 goat snp1035-scaffold1028-41879 28 38818688 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423243 Affx-122942683 AX-123293589 28 4790560 CAGACTCCTGGCAGGTGGAAAATCTAGAGCCCTGG[A/C]TCTATTAAACCAGAATTGCAAGGGAAACAGATTGA M 2 1 2 1 201000 r 74 goat snp1034-scaffold1028-4232 28 38779805 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387728 Affx-122969749 AX-123258086 28 4804378 GCCAGGGGGGAAAAGCAAACCTATGTACAGACATG[C/T]AGAGTTAGGAGCAGTTAAAGTGAAAAACAAAAAAC Y 2 1 2 1 201000 f 74 goat snp58688-scaffold957-8343 28 38764592 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407498 Affx-122954750 AX-123277849 28 4833320 AATGAGCACTGTTATTGCCTGTTTTCCACATGAGG[C/T]ATAGAGATTAAGGAACTTGCCCAAGGTCACCCTGA Y 2 1 2 1 201000 f 74 goat snp58689-scaffold957-37285 28 38734919 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786361 Affx-122945218 AX-385273395 28 4884219 TTTAGTAAGGCAAAGGCAAGAATCAGATGAGAAAT[A/G]ATTGCTTAATCAGAAACTCCGAGGTGTTATAATAG R 2 1 2 1 101000 f 74 goat snp58690-scaffold957-88184 28 38686636 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801309 Affx-122929771 AX-385288221 28 4923323 TTTTTGAGTCTGTAAAATGATTGAATGCCTTGCAA[C/T]GCCAGACTACGCTAGACTCATTCACTACCGAAATT Y 2 1 2 1 101000 r 74 goat snp58691-scaffold957-127288 28 38648318 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446479 Affx-122925058 AX-123316815 28 4963797 AACTCTGAGGATACCCTAGGAACACCAGTTCAAGA[C/T]AAGCTTAAGATGAGATAGTTCAGGTACAAGGGTAA Y 2 1 2 1 101000 f 74 goat snp58692-scaffold957-167762 28 38607889 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442900 Affx-122927645 AX-123313237 28 5007318 GCGTGGGTGGTTTTGAGACTGTCTCAGAGTGGTCC[A/G]AAGCATTGTGGGTAAAAGCTCTTAACCTTTAGTGT R 2 1 2 1 101000 r 74 goat snp58693-scaffold957-211283 28 38564501 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414250 Affx-122949624 AX-123284599 28 5038338 TGGAATTTGACTGCTGAGCCCATTTAGATAACACC[A/G]CTGTCTGTGGCACCTTCTCCAATCACAGACTTGTC R 2 1 2 1 101000 f 74 goat snp58694-scaffold957-242303 28 38533498 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446801 Affx-122925296 AX-123317137 28 5091475 TTACTCTACTTAATCTACCAAAACAGAACAAACAC[G/T]AGAACAAAGCCCTTGAAGACACCATTCACTCATTC K 2 1 2 1 101000 f 74 goat snp58695-scaffold957-295440 28 38479922 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770839 Affx-122976051 AX-385258003 28 5124128 ATTTTGTATAATGTCATGATTGGCATCCGTTTTAC[A/G]TTACTGCATGACCAGTCAGGTGCCTGTAGCAATTT R 2 1 2 1 101000 r 74 goat snp58696-scaffold957-328093 28 38447340 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273171 Affx-1111833350 AX-519546831 28 5143440 CTGCTCTGTTGTTCATTGCAAACTTTTCCCTAAAT[A/G]GATTTAGAACATCTTCTGAAAATATGTTTCAGGGA R 2 1 2 1 101000 f 74 goat 28_5143440_AF-PAKI 28 5143440 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38395331 Affx-122964043 AX-123265686 28 5157454 GGAGACAAAAGACAGAACGGGAGGAAAGAGTCTTC[A/G]CCTATGTGTTCTGTCTTCTCCCATGTGATCTGTGA R 2 1 2 1 101000 f 74 goat snp58697-scaffold957-361419 28 38413903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428867 Affx-122938345 AX-123299209 28 5211487 CTCCCTTCACATCTGCCAGGCTCCTCTCTCCCAAG[C/T]GCAGCCCTAAGCCCATCCTTACCCTTCAAAGGATT Y 2 1 2 1 103000 r 74 goat snp58698-scaffold957-415452 28 38360204 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382991 Affx-122973339 AX-123253349 28 5303714 TGTGCTCCCCTTGAAGGCTTTCCCACATTCTGCAC[A/G]TCCATGATCTCAGGGACTGTGAACCCAGAGATGCT R 2 1 2 1 201000 r 74 goat snp58699-scaffold957-507679 28 38268397 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464031782 Affx-1110280978 AX-515508510 28 5321914 CTTGAATAGTCCTGGAACGCTTCCCTGCAGATCCA[C/T]GGAAAAATTGACTTTCACGAAAACAGGCCCTGGTG Y 2 1 2 1 201000 f 74 goat GoatD01.011416 28 5321914 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320798767 Affx-122959720 AX-385285698 28 5332618 ACAGTTAATGTAAATCAATCCCATCCAAAATGGCA[C/T]GTTATGAAATTGACCTTGTCCAAAACCCTTCTGTC Y 2 1 2 1 101000 r 74 goat snp58700-scaffold957-536583 28 38239308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774926 Affx-122937984 AX-385262059 28 5367500 ACAGAAAGTCTAAAATCATCTTTATTTGAGCCAGC[A/G]TGGAGATCAGAGATGAATATCGTTAATATTATTAA R 2 1 2 1 101000 f 74 goat snp58701-scaffold957-571465 28 38203244 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414685 Affx-122949291 AX-123285034 28 5406056 GCCGTTTCCGGCAGGGCTCGCACATGAAATCTTCC[G/T]GCCGGCGCTTGGCGCAATGTGTATAAAAACTCAGA K 2 1 2 1 201000 r 74 goat snp58702-scaffold957-610021 28 38164405 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791685 Affx-122975219 AX-385278676 28 5437443 TTACGGCACTGCCAGTGCTTTAAGCAAGTTAAGAT[A/G]CTTTAAGCTGAAATAAAGCATATTTACTTTGTCCA R 2 1 2 1 201000 r 74 goat snp19148-scaffold1927-19166 28 38133060 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396201 Affx-122963363 AX-123266556 28 5499284 GCACTATGTAGAGGTCAGTGAGTAGTCCTGTCCTC[C/T]GGGAGCTTACAATCTAAAATTAAAAAAAATAATAA Y 2 1 2 1 101000 f 74 goat snp19149-scaffold1927-81007 28 38071441 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376293 Affx-122978375 AX-123246652 28 5531490 TATTATCAGTGACACTAAGATCAGGCGGTCCCCTC[A/G]TATGAGTTTCTGTGGCATGTCCATTAGTCAGGAAT R 2 1 2 1 101000 r 74 goat snp19150-scaffold1927-113213 28 38039515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401200 Affx-122959335 AX-123271553 28 5581174 ACATTGCTCTTTTTTAAATTGCTGGCTTGCCTTTA[A/G]AGATGGTCAAGAGAGGCTCTGACTCAGCCCCACAG R 2 1 2 1 101000 f 74 goat snp19151-scaffold1927-162897 28 37989997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377053 Affx-122978298 AX-123247412 28 5613248 GTTGTAGACCTCGAAGCCATGATTCAGCCTAATGA[C/T]AGGGCCAAGTTACAAACACCTGAACTTAAAAGGAT Y 2 1 2 1 101000 f 74 goat snp19152-scaffold1927-194971 28 37957991 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445604 Affx-122925113 AX-123315941 28 5645873 GTAAAAGTGCTTATATCTCTTGCACTAGTAATTCT[A/G]CTTCTAGGTATTTATCTCAATAATCGTAACTGTGT R 2 1 2 1 101000 f 74 goat snp19153-scaffold1927-227596 28 37925657 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444118 Affx-122926816 AX-123314455 28 5681517 TTAAGCTCTCAATAATTATGTGTTACTTGTACTAA[C/T]GAGTGAGTGAGTTAGAAAGAGTTCCCTGGTGGCTC Y 2 1 2 1 201000 f 74 goat snp19154-scaffold1927-263240 28 37890371 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424713 Affx-122941682 AX-123295059 28 5755776 AGGAGGTGGACCAGGTGAGGAATTTTCGGGTGCCA[G/T]CTGGAAAGGGTTCTGGCTGGAAGGTGATTTGAGTA K 2 1 2 1 101000 r 74 goat snp19156-scaffold1927-337499 28 37815774 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379920 Affx-122975751 AX-123250278 28 5794651 GAAGGTGAGTGTGGCTATTGGGGCGGGGGGTAAGC[A/G]GTCATATCTAATGAAGCAGGGAGGTGAGTAGCAAG R 2 1 2 1 101000 r 74 goat snp19157-scaffold1927-376374 28 37777208 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794431 Affx-122972880 AX-385281394 28 5836531 ACTTCACACAGGTTTGCATTTAAATTTACTCACCT[A/G]TACAGTCTAGGAATCCCAAACCAATTAAATAACAT R 2 1 2 1 101000 f 74 goat snp19158-scaffold1927-418254 28 37735428 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794042 Affx-122974695 AX-385281010 28 5866618 TCTGTACACTCATAAGAAAGCGAGAGTGAAAAAGG[C/T]GAATGAGGCCTTAGCAGTGTTTTGAAAATAGTCTT Y 2 1 2 1 101000 f 74 goat snp19159-scaffold1927-448341 28 37704991 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382667 Affx-122973661 AX-123253025 28 5908661 TTTCTATTGGACAGAGATGCTTTAGAAAAAGGTTC[A/G]TTTTAGTCCAGGAGAATCAGGCAATCATTCTTCAT R 2 1 2 1 101000 r 74 goat snp19160-scaffold1927-490384 28 37662486 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437618 Affx-122931847 AX-123307956 28 5966987 GCATGCAAGCGCGCTACATTGTTTTAGTTGTGTCC[A/G]ACTCTTAGTGATCCTATGCACCATAACCTGCCAGG R 2 1 2 1 201000 r 74 goat snp19161-scaffold1927-548710 28 37605097 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430682 Affx-122936924 AX-123301023 28 6010840 TGGAAATCCAGCTGCCCCTGGTTTATTCCTATTTA[C/T]GCCCACAGATTCACCCTTTGGCCTAAGCACACTTG Y 2 1 2 1 101000 r 74 goat snp19162-scaffold1927-592563 28 37561552 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416109 Affx-122948309 AX-123286458 28 6043337 TCACAAGCTCTGGAGAGCAGAACTGAGCCTGTCCT[A/G]TTTCTATACCTGGGCTGAGTGGGGCAGCTGGCTTA R 2 1 2 1 103000 f 74 goat snp19163-scaffold1927-625060 28 37529154 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789078 Affx-122920893 AX-385276091 28 6071937 AGAGCTCTATGAGCAAATTCACTAAATGGAATCAC[A/G]TTTACCTTCCTATTGTCAACTGGAAACATTTGCTT R 2 1 2 1 101000 f 74 goat snp19164-scaffold1927-653660 28 37500668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396340 Affx-122963062 AX-123266695 28 6125096 AGGCAGGGACGACAAGCAACAGGCTGGATGAGCCA[A/C]AGAAGAGGCCACGGCTGGCAGGGTGAGCGGTGCTA M 2 1 2 1 101000 r 74 goat snp19165-scaffold1927-706819 28 37447306 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787444 Affx-122965400 AX-385274469 28 6231913 TGTCTAGTGAGCAAAAGAAACTGAACCATATAATA[C/T]GTAATAAACAGAAATTCTAAGCCATAGAATGCACT Y 2 1 2 1 201000 f 74 goat snp19167-scaffold1927-813636 28 37340344 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402995 Affx-122958139 AX-123273348 28 6255839 AATGACCTGTTTTTCAAGTTGGCAGGATAAGCACA[C/T]AGGAACAATTATTTCAATCCAATTTAAAATAAGTA Y 2 1 2 1 101000 f 74 goat snp13204-scaffold1507-6116 28 37316557 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777551 Affx-122961759 AX-385264670 28 6289102 AGTCATTCTCTTCAGGGACCTTTTCAAGAGCTTTC[A/G]TCAATCACCTTCCTCCTTTCTTTAGGCCCTACTAT R 2 1 2 1 101000 r 74 goat snp13205-scaffold1507-39379 28 37283319 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774933 Affx-122922172 AX-385262066 28 6324449 AAGTAGCACAAAAATAAGATAGAGGTATGATGGAC[G/T]ATTTCAGTGATCTTAAATTCTGCCAGAGATCCTTT K 2 1 2 1 101000 r 74 goat snp13206-scaffold1507-74726 28 37252172 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420884 Affx-122944622 AX-123291231 28 6394035 TGTTCATCTAACTGGGGCCGTCCTTTCTCCTGGAA[C/T]ACTCACCGTGTTCATGGGCTGAGCTTTATTCACCT Y 2 1 2 1 101000 r 74 goat snp13208-scaffold1507-144312 28 37181896 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277761 Affx-1111836076 AX-519551260 28 6423441 GCATGTCAATTTGTAATAATTCTCAACTCCACCCC[A/G]TCTTCTCCAACACTACCTCCTTTCCTAATCTAGAA R 2 1 2 1 201000 f 74 goat Random2.2K-2260 28 6423441 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38436612 Affx-122932510 AX-123306950 28 6485530 CCATGGGCTTGTGTTTGAAGGCTAGCTCTCAGATC[A/G]TCAGTAGAGTGGTCCTGAGACAAGGTGGCACCTAA R 2 1 2 1 101000 f 74 goat snp13210-scaffold1507-235807 28 37090119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384726 Affx-122972053 AX-123255084 28 6518887 GAGATGGGACTTTTGGTAGATAATTAGGTCATGAC[A/G]GTTGGAACTTCATGAATGGAACTGAGATGGGCTGG R 2 1 2 1 101000 r 74 goat snp13211-scaffold1507-269164 28 37057710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403025 Affx-122958555 AX-123273378 28 6549777 TCCAAGCATCGGGTTGATGGATGTCTTCTTACACA[C/T]GGCAGCATGTGTTTCTAAGTGGATGTAGAACCAGA Y 2 1 2 1 101000 r 74 goat snp13212-scaffold1507-300054 28 37026759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398471 Affx-122961583 AX-123268826 28 6603992 TTTCAATATTTCAAAGAATACAGAAAAGTAGAAAG[C/T]ATAAATACAATGAAAATCTGTATACTGACCACTCA Y 2 1 2 1 303000 f 74 goat snp13213-scaffold1507-354269 28 36973241 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770075 Affx-122931894 AX-385257242 28 6655073 AAGATTTTAGCCCACTGCTGTTTGGAACTACTGGT[C/T]TTACCTGAAGCCTTAAATCAAAACAGGAATGAATT Y 2 1 2 1 101000 f 74 goat snp13214-scaffold1507-405350 28 36922188 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800544 Affx-122928397 AX-385287463 28 6703800 TTAGCTTTACCAGTAGAAAGCAAATTTAATTCCAA[C/T]GTACAAATCTCAGGATAAATTATTTCCCCTTGAGC Y 2 1 2 1 101000 r 74 goat snp13215-scaffold1507-454077 28 36873213 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389767 Affx-122968236 AX-123260124 28 6733162 GATACATGAGAACTCAGACAATACTACACAGCCAA[C/T]GAATGAATAAACCACCACCAAGTTTCCTACCCTTT Y 2 1 2 1 101000 f 74 goat snp13216-scaffold1507-483439 28 36843811 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409838 Affx-122952938 AX-123280189 28 6772317 CAGGAAATGTACTATAAAGCACAGTCCCAGGACCA[C/T]TCGCCCCTCAGGATAGCCTCTCCTGCCTTGCTTCC Y 2 1 2 1 101000 f 74 goat snp13217-scaffold1507-522594 28 36804628 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427044 Affx-122939822 AX-123297389 28 6816279 CCCTATATGTGATAAACATGACTTCCCTGGTGGCT[C/T]AGTGGTAAAGAATTCACCTGTCATTGCAGGAGATA Y 2 1 2 1 103000 f 74 goat snp13218-scaffold1507-566556 28 36760518 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437290 Affx-122931985 AX-123307628 28 6853925 CCCTACCTCCTCCTGGTCCTCTCTCTGCTCCTCTC[A/G]CCCCTGGTCTGCCTTCCCTACCCTTCTAAAGGGCA R 2 1 2 1 201000 r 74 goat snp13219-scaffold1507-604202 28 36722642 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428420 Affx-122938832 AX-123298763 28 6924121 CTGGTGGTCAGCATGTTGTTCAAGATAATTTGAAA[G/T]AAGATAACTCTGAACAAAGTTTCCTGGTCCTTTGG K 2 1 2 1 101000 f 74 goat snp59570-scaffold982-1453785 28 36655745 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437692 Affx-122931763 AX-123308030 28 6961791 GTTCCCAAAGTGTGTACCCCAGAATACTGGTCCTA[C/T]AGACAGTCCTTGAGGAAAAAGACTCCTTGGGCCAA Y 2 1 2 1 101000 r 74 goat snp59569-scaffold982-1416115 28 36620293 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795977 Affx-122970194 AX-385282929 28 7002672 GTATAATAAACAAGGGAGCAAATATATTTTGCAGA[C/T]GGAAATTGAGGATGAAAGCTCTCCATCTACAGATA Y 2 1 2 1 101000 r 74 goat snp59568-scaffold982-1375234 28 36579288 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427534 Affx-122939509 AX-123297877 28 7040698 TCTTAAACACAGGACCACCAGGAAAGGCCCACCTC[A/G]TTGATTTAAACACAGCCTTGCTGATAACCATGGTT R 2 1 2 1 101000 r 74 goat snp59567-scaffold982-1337208 28 36541227 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389805 Affx-122968202 AX-123260162 28 7098707 CAAATACTGTACGTAATAATGCTTTTAACCCTGGC[A/G]GTCTTGCCCAGGGGTATTTTATGAACACTGGTGCT R 2 1 2 1 201000 f 74 goat snp59566-scaffold982-1279199 28 36482963 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427724 Affx-122939273 AX-123298067 28 7147228 TTGTTTTGTTGTCCACATCTTTGACAAAAATTGAT[A/G]ATGTTTAACTGTGAAATAGTATCTCATTTTTGTTT R 2 1 2 1 101000 f 74 goat snp59565-scaffold982-1230678 28 36434142 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384767 Affx-122972021 AX-123255125 28 7193865 ATAATGATTCCTACTAATGTCAAATCCTCCTAGGT[A/G]TTGTCAGTTGCTACAAACACACGTGTTTCAGCTCT R 2 1 2 1 101000 r 74 goat snp59564-scaffold982-1184041 28 36387247 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426875 Affx-122940478 AX-123297220 28 7248594 ATTTTCTTTCTAGATTCCACATTCATATTATATGA[G/T]TTATGTAGTTTTACTTGTAGTTGAATTTGAGAACT K 2 1 2 1 101000 r 74 goat snp59563-scaffold982-1129312 28 36332656 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395591 Affx-122963829 AX-123265946 28 7297990 ATAACCTAAGAAGAACACTCCTGACATGTGCAAAA[C/T]AAGAACAGAGTCTAACAAAGGGGGGGGGGAAAAAC Y 2 1 2 1 201000 f 74 goat snp59562-scaffold982-1079916 28 36284099 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787843 Affx-122951902 AX-385274866 28 7328874 GCCAATAGATGAAAAGGTTACTGAACCAAAATACC[A/G]TCTAAATGCGTATATGATTTAACCCATCACTTTTC R 2 1 2 1 101000 f 74 goat snp59561-scaffold982-1049032 28 36257858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399462 Affx-122961201 AX-123269817 28 7375898 CTCACGAACAGCTCTAGTTAAAAAAGAAAATGAAA[A/G]CGTGTACAGAAAGAAATCCATTCCCTCTGAAAATT R 2 1 2 1 103000 r 74 goat snp59560-scaffold982-1002008 28 36211060 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437249 Affx-122932015 AX-123307587 28 7420042 GCCACCTACGTCGTTCAGGTAAACTCAGTGGCGGA[A/G]AAGATGGAGTGTGTGCAGACGTTGTGGACACGCGA R 2 1 2 1 101000 f 74 goat snp59559-scaffold982-957864 28 36167215 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412097 Affx-122951120 AX-123282447 28 7448944 ATATCCAAACAATTCTTTTAAAATGGAGAAAAATA[C/T]ACAATTCAAGGTCACAGCATGCTTTTTTAAAACAG Y 2 1 2 1 103000 r 74 goat snp59558-scaffold982-928962 28 36138020 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399029 Affx-122961600 AX-123269384 28 7504901 CTTTTACATGCTTTATAGTTTTGACAGAGCTTGGA[C/T]AGTGGCCGGAATCATTTCTTAAAAGCTCTCTAACG Y 2 1 2 1 201000 f 74 goat snp59557-scaffold982-873005 28 36081491 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431902 Affx-122936005 AX-123302243 28 7535532 AGCAGTAAAAGCAATGGTCACAGGAGTCAAACCAA[C/T]AAACCTGAAGGAGGCTATGGGATCAATGCATCTGA Y 2 1 2 1 201000 f 74 goat snp59556-scaffold982-842374 28 36051332 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391798 Affx-122967036 AX-123262155 28 7576148 GAAGCCAGATTCCTTACTGCACGTTGAAGAGTAAA[C/T]GAAGTAAAGGAACAGGAAGGAACCAAAAATAAGGA Y 2 1 2 1 101000 f 74 goat snp59555-scaffold982-801758 28 36010831 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442240 Affx-122928292 AX-123312577 28 7614369 TAACTGGCTTTGGGCAAGATCATCTCAGGCTACAC[A/G]CTACACTTTATAAAATAGGAAATGATAGGGTGGTG R 2 1 2 1 101000 f 74 goat snp59554-scaffold982-763537 28 35972478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377410 Affx-122977559 AX-123247769 28 7646392 AGGGAGAAAAAGGACATCTTTGTTACTGAGAGACT[A/G]TGTCAAAGGTCACAGTCTAACAGGCTGATCAGAAT R 2 1 2 1 101000 r 74 goat snp59553-scaffold982-731514 28 35940395 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409344 Affx-122954180 AX-123279695 28 7678341 TATGACTTAGCAGATCACAGGTTCTAGGGAAAGGA[C/T]CACAGGAGGGGGCTCTGTAGCCCCACTGGTCCAGG Y 2 1 2 1 101000 f 74 goat snp59552-scaffold982-699565 28 35908303 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447747 Affx-122924583 AX-123318083 28 7706882 TCATCTGGATCTGTAAGCCTGCAGCCCAGGTGAGC[A/G]ATCCAAGCTGGAGATAAAACCTGGGACTTGTTGGC R 2 1 2 1 101000 r 74 goat snp59551-scaffold982-671024 28 35879616 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447993 Affx-122923743 AX-123318329 28 7740358 ACTGGGCTTGAGGTGTCTCTTGTATATTGGATGCT[C/T]GCTATGCTATGTTCTTCAAGACAGAGGAGTCTGGA Y 2 1 2 1 101000 r 74 goat snp59550-scaffold982-637548 28 35848285 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415091 Affx-122949453 AX-123285440 28 7770844 ACATTAGAGTCTCAGGCAAGGGACTGGTTTGTCAG[C/T]GAGAAACTGTCAGGGCTGAAACTGAAGTGTGCAGA Y 2 1 2 1 101000 f 74 goat snp59549-scaffold982-607062 28 35817645 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395330 Affx-122964044 AX-123265685 28 7819607 GTAGGGCTCCATGTCCAACAGTCATTTATTGAAAT[A/G]TCTGGCATTTTCCCCTTGATCACTCCCTACGGGTT R 2 1 2 1 101000 f 74 goat snp59548-scaffold982-558299 28 35768414 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446357 Affx-122925603 AX-123316693 28 7867596 ATAATAGTCAAGGAAGGCATCTCTGATGAAGCTTC[A/G]CCTCATGGCAGTAGAGACTTCAATCAAGCGAGGGA R 2 1 2 1 101000 r 74 goat snp59547-scaffold982-510310 28 35720482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447302 Affx-122924916 AX-123317638 28 7928388 GCTCAGGGAAATGAGAATTAGAATTGAAAATAATG[C/T]AGTCTCAAATATTTGTTTCAGAGGGTGTAAAAAAT Y 2 1 2 1 101000 f 74 goat snp59546-scaffold982-449518 28 35659604 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450641 Affx-122921984 AX-123320975 28 7961898 AGATCCTCCAGTTCCAACCAGTCCTTCAAATGATT[A/G]CAGCCCCTTGCATGCACTGATACAAACCAAAAAAA R 2 1 2 1 201000 r 74 goat snp59545-scaffold982-416008 28 35626333 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453664 Affx-122919717 AX-123323997 28 8007605 GGAATAAGAGCTCCTTAAAGGGGAGAATGAAACAG[C/T]GGTTTAGCAGTAGTATAGTGTTAGTCGCTCAGTCA Y 2 1 2 1 101000 f 74 goat snp59544-scaffold982-370301 28 35581490 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405060 Affx-122957422 AX-123275412 28 8043496 ACATGGCAATGAATGAGACCTGCTCCCTCAGTAGC[A/G]TGTAGATTTCTCTGTGGGATGAAAACCGTCTCCAT R 2 1 2 1 101000 r 74 goat snp59543-scaffold982-334410 NW_017215053.1 8984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397877 Affx-122961969 AX-123268232 28 8072749 GTTTAAGAATCTATGAAGTGACAGAGATATCCTCA[A/G]TTAAACTTCATCTGCAGATTTTCTCTAATCAGCAC R 2 1 2 1 101000 r 74 goat snp59542-scaffold982-305157 28 35514927 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273222 Affx-1111833351 AX-519546879 28 8077932 ACACACACATTAACTGGAGGAGGTTGTTGTTGTTA[A/G]TTGAAAAACAGAAACAATTGAGAACTTTTTGAAAA R 2 1 2 1 201000 r 74 goat 28_8077932_AF-PAKI 28 8077932 C T 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320793798 Affx-122923200 AX-385280770 28 8170074 CATATCCACTTAAACTCTCAGAGTTTGGAAGTTAC[A/G]TTTTGACAAATAGCACTAATAGAGAACTATGTTAA R 2 1 2 1 102000 f 74 goat snp59540-scaffold982-207832 28 35416446 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390627 Affx-122967160 AX-123260984 28 8228485 CCTGGGATTCTCAGAATTCCCTATATAAGGTAATG[C/T]GTTTGTCTATTAAAAACTTAATTAGGTTGGTAACT Y 2 1 2 1 101000 f 74 goat snp59539-scaffold982-149421 28 35356497 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400921 Affx-122959727 AX-123271274 28 8278419 GGATGATCTGACCCATCACCATGTTAAGAACATGA[C/T]AGCTGGTAAAAGCATCTAATAGAAAACTAGTCTGT Y 2 1 2 1 101000 f 74 goat snp59538-scaffold982-99487 28 35305729 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394179 Affx-122964923 AX-123264534 28 8321712 AAAGGCATTCTGAAATAGGATAAAGATTGTGGATA[A/G]CCCAGCAACTTGAATCATGTTTGCATTCAGAAAAG R 2 1 2 1 101000 f 74 goat snp59537-scaffold982-56194 28 35263726 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768671 Affx-122950263 AX-385255849 28 8354643 AATCTTTACTACAGTTTCACGAAGTAGATATACTA[C/T]GATCCTCATTTTAAACTGATGCTATTAATAGAAAG Y 2 1 2 1 101000 r 74 goat snp59536-scaffold982-23263 28 35230433 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392702 Affx-122966406 AX-123263059 28 8395001 AATTACATCAGGTACACTTCCCCCTCCGGCAAGAA[C/T]GCTCTTTCTACCACCAATCCCTGCTTAGTATTTTG Y 2 1 2 1 201000 r 74 goat snp51665-scaffold759-1131156 28 35187571 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799321 Affx-122956896 AX-385286251 28 8437005 TGCCTATCTCCTAGGTTTTACAAGTTACAGAAACA[A/G]ACACTTAAATAAGCATGTGTAACTGTTTATTTAAA R 2 1 2 1 101000 f 74 goat snp51664-scaffold759-1089152 28 35145051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383523 Affx-122972632 AX-123253881 28 8519787 AGGAGAGTCTATGAAAAGTGAGTGACTGCCCTGCA[C/T]GGCTATTGGAAAGCAGTGTTTGGGAACATGAACTT Y 2 1 2 1 101000 r 74 goat snp51662-scaffold759-1006370 28 35062897 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797567 Affx-122978132 AX-385284506 28 8548586 GCAGTCAGACAACTAGGGATACAAAGCTTCAGCTA[A/G]CATTAGTTTCAAGTTCATGTCTAGTAGTGTCAAAT R 2 1 2 1 101000 f 74 goat snp51661-scaffold759-977571 28 35034333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797077 Affx-122952192 AX-385284017 28 8583500 AATTTAAAAATGTGGTCTGCTTTTGTTGTTCTAGG[C/T]GAGAAAAACCTGTCATGCTCAGAAAAGTTACTTGA Y 2 1 2 1 101000 r 74 goat snp51660-scaffold759-942657 28 34999649 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387031 Affx-122969922 AX-123257389 28 8641724 TGCAGACAAAGAAACTGTATCTTAGAGAATGTAAC[A/G]TGCCCAGGGTTGGTAGGCCTGGCAAAAGAGCAGAT R 2 1 2 1 101000 f 74 goat snp51659-scaffold759-884433 28 34942549 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773551 Affx-122933355 AX-385260692 28 8687751 CAGATTAAGACACAAAATGAGTCCCTGGTTACAAT[A/G]TGGAAACAAATTTGCCCTGAACAGGAAGAGCTTTC R 2 1 2 1 101000 f 74 goat snp51658-scaffold759-838406 28 34896592 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773218 Affx-122931648 AX-385260361 28 8736511 CCTCAAGTGGACTTTAAAACCATAGGTTACTTTTG[C/T]ATATTTGTTATCATGCCGTATTTTTTGCTTTTGGA Y 2 1 2 1 101000 f 74 goat snp51657-scaffold759-789646 28 34850123 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419806 Affx-122945840 AX-123290154 28 8771942 TATCTATGGGAACTTAATGTTTCTTAATGAAAATA[C/T]CTCTTAAAGACTAGACTTTGTTACCTAGTTCAAGT Y 2 1 2 1 101000 r 74 goat snp51656-scaffold759-754215 28 34814468 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778937 Affx-122955540 AX-385266044 28 8823628 TTAAAACTAACTCTGGCATTAAAGCCTGTGATTTT[A/G]TTACTATCCAAATAGTTCTTATTCTATATCCTATT R 2 1 2 1 101000 f 74 goat snp51655-scaffold759-702529 28 34763030 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791565 Affx-122970638 AX-385278556 28 8868229 GGAAAATATTAGAAAATGGGTCTTATGAGATAAGT[A/G]CATTTAAAAGTTAACATGATATGGTGGAAATAAAA R 2 1 2 1 101000 r 74 goat snp51654-scaffold759-657928 28 34717585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273469 Affx-1111833638 AX-519547087 28 8881417 ATGATGCCCCTGCTGATACACAAACTGGTCAGAGT[A/G]CAGCAAACCAGGGAAAG R 2 1 2 1 102000 f 74 goat GoatD01.000119 28 8881417 T C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320784876 Affx-122932487 AX-385271923 28 8921072 TTTGACACCAGACATCTAGAAAAATCAAGACTGTT[C/T]ACTCAAAGGAAACATTCATCTGTGTACTGGTATTT Y 2 1 2 1 202000 r 74 goat snp51653-scaffold759-605085 28 34664517 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781318 Affx-122929809 AX-385268403 28 8967202 GTGGGAAAATGCTGGACAAATTGAGACGTGTTTTC[G/T]CCCAGATGTCAGATTCTAGTTGCCTGATGATACTT K 2 1 2 1 101000 r 74 goat snp51652-scaffold759-558955 28 34617620 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410723 Affx-122952715 AX-123281073 28 9004739 CAGAAGTTATACCTAGGGATACATATGTCTTGGTA[G/T]CCCTCATAGACAGCAGATGGGGACAGTTACTAAAT K 2 1 2 1 202000 f 74 goat snp51651-scaffold759-521418 28 34579506 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398296 Affx-122962155 AX-123268651 28 9038665 GTACAGGGCTATGTGGTAGTAGAGTCCATGAACTG[A/C]GAAGATGGGGACCATTGCTCCAGAGGCAGGGGTGA M 2 1 2 1 101000 f 74 goat snp51650-scaffold759-487492 28 34545890 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388920 Affx-122968837 AX-123259278 28 9089919 CGACTTAAGTCTAGAACCACTTAAAGCAAGTTCAC[A/G]TGAAAAATTCCTTGGACCACAGAGAGATACAGTGT R 2 1 2 1 101000 f 74 goat snp51649-scaffold759-436238 28 34493153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401844 Affx-122959432 AX-123272197 28 9127891 TTTAAAATAGAATTTAATCATTGAATGTGCAAATG[A/C]GAATTTTTTATTTTTTTCACCAAGAAAAGGCAACA M 2 1 2 1 103000 f 74 goat snp51648-scaffold759-398266 28 34454959 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800615 Affx-122935783 AX-385287534 28 9162865 AATTTGCCTAATTTAACATTCTTCACCTTTATTTT[A/C]TAAAACCAAAGCTTATGTTTTGCTCAGGATACTCA M 2 1 2 1 201000 f 74 goat snp51647-scaffold759-363292 28 34419790 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798423 Affx-122956476 AX-385285357 28 9294610 AGTTCAATAGTTCATTAAGCAGCATAGAGAAAGTT[C/T]CAACAGGTTCCAGGATATAGAAAAGCTGAGGAAAA Y 2 1 2 1 101000 r 74 goat snp51645-scaffold759-231547 28 34285195 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769204 Affx-122934685 AX-385256379 28 9411040 AAACAGATGAATCAATAAACAATCTCAGTCAGTAC[A/G]TAACAGATGCATCAGGAGAATCATTCAATTTTTAT R 2 1 2 1 101000 f 74 goat snp51643-scaffold759-115117 28 34172353 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794892 Affx-122968417 AX-385281852 28 9454582 ATACTCTTCTTGGTGCTGCATTTCACCCAACATAT[A/G]TGCAGATAATTCTTTAGTAACAGATTCAAAGGGAC R 2 1 2 1 101000 f 74 goat snp51642-scaffold759-71575 28 34127994 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433888 Affx-122934408 AX-123304229 28 9485623 CAAAACCAATATTTCATATCTATTCTTACATTGTC[A/G]TAATGATATGCTTTTTTAAACCCACATTTGACTGG R 2 1 2 1 101000 r 74 goat snp51641-scaffold759-40534 28 34096939 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768976 Affx-122938382 AX-385256151 28 9515438 AGCTACTTTCAAAAACCGCCTTAAGAGGCATACAT[A/C]TGGCCGATATTGTTCTGAGCTTTCCTTTCTGAATT M 2 1 2 1 101000 r 74 goat snp51640-scaffold759-10719 28 34067042 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429168 Affx-122937972 AX-123299510 28 9526391 CTTGAACAGTTCATTATTTAACTCTTAACTATTCC[C/T]ACTCCAGGACTCTTGTCTGGAAAATCCAATGGACA Y 2 1 2 1 201000 f 74 goat snp42248-scaffold5547-135 28 34053840 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406593 Affx-122956258 AX-123276945 28 9548917 TCTTGAAAATATCTGTAATTCTCATAGGACCAAGT[A/G]TATTGACTTTCACATTAGAGACAAGCAATAAAGGG R 2 1 2 1 101000 f 74 goat snp23863-scaffold2404-12128 28 33922636 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426530 Affx-122940195 AX-123296876 28 9594857 GTTAAGTTAATGAGAATGGACAGCTTCCCTGTGTC[A/G]TTTTGCAGTGAGGCCACAGAAAGATGCTCCCCATG R 2 1 2 1 102000 f 74 goat snp23864-scaffold2404-58068 28 33876434 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451785 Affx-122921502 AX-123322118 28 9624205 GATTGCTTTTACAACAATTTACAGCTTTAAAAGAG[A/G]ATGAGACAAGATCTGGGGAGAAGGGAAGCACATAA R 2 1 2 1 201000 f 74 goat snp23865-scaffold2404-87416 28 33846277 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439002 Affx-122930365 AX-123309339 28 9719603 GAACCATTGTTTACTTTTAGATCCTGCACACAAAA[A/G]AGAAATGGGTGGAGTTTGCCCTTCTATCATTTGTA R 2 1 2 1 101000 f 74 goat snp23867-scaffold2404-182814 28 33750424 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397044 Affx-122963103 AX-123267399 28 9757172 TTTTAGGAATAGTAGGTCAAAATGATTTTTGGAAA[C/T]GGGAGGAATTATTCTTGTAGTTCAGTGATTTCTGG Y 2 1 2 1 101000 r 74 goat snp23868-scaffold2404-220383 28 33712251 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777042 Affx-122963048 AX-385264165 28 9798356 ACAAAGTAATTATACCTGAGTCTGTCAATAGGATG[C/T]AGCACTTAGGCAGCCTGTCTTTACTAGCATGGTAA Y 2 1 2 1 101000 r 74 goat snp7632-scaffold1274-240780 28 33663694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386658 Affx-122970201 AX-123257016 28 9864960 TTCAGAAAACTTTCTCCTTAAATGATTTCATCATT[C/T]GATTTCCTCCTTATATAAGGAAACACGTTTTACAT Y 2 1 2 1 202000 f 74 goat snp7630-scaffold1274-174176 28 33590138 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277764 Affx-1111836077 AX-519551263 28 9883071 GTCATAAAAAAGAATGAATGACCGACTCACACTAT[A/G]ACACGGATGGACCTTGAAGATACACTAAATGAAAG R 2 1 2 1 202000 f 74 goat Random2.2K-2261 28 9883071 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320777930 Affx-122971968 AX-385265046 28 9902138 TCTGTTTAGGTTATTTAGTAGATAAAAAAATGATA[C/T]GTCTTCAGCCCTAAAAATAAGTTTCAAGGATATTT Y 2 1 2 1 101000 r 74 goat snp7629-scaffold1274-136998 28 33552914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424831 Affx-122941362 AX-123295177 28 9948973 GACATATAAATGCACATCCCATTCTCTTGACAAAT[A/G]TTATTATTAGGCTTTCAAATATTAAAAATATCAAA R 2 1 2 1 101000 f 74 goat snp7628-scaffold1274-90163 28 33505490 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389581 Affx-122968784 AX-123259939 28 10000836 TTGTTTCAGGACAACAAAATTAACCACATCTAATA[C/T]TGACAAATATTTGGGTCAACCTGATTTCTCCTATG Y 2 1 2 1 101000 r 74 goat snp7627-scaffold1274-38300 28 33452028 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436194 Affx-122932599 AX-123306533 28 10038696 CTGTAATAATTTTAATGAGGAAATGGGAGCACAAA[C/T]AAAGAACACTTAAAACACTTAATACACTGAGACTC Y 2 1 2 1 201000 f 74 goat snp7626-scaffold1274-440 28 33413463 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396971 Affx-122963165 AX-123267326 28 10041930 AAATATCATCCTCAAGAGAAGCCTGTCTTGCCCAT[A/G]CAGTCAAAATTCACTCCCGTAACTCTGTATTTATT R 2 1 2 1 201000 r 74 goat snp48828-scaffold696-2695 28 33410398 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385302 Affx-122971682 AX-123255660 28 10104568 AAAGGAAAATGTTGGCAAATATGGTAGAATTTCAG[C/T]AGGTGTCTAGTTTAGATGTTAGTATTACCTTCATG Y 2 1 2 1 101000 r 74 goat snp48829-scaffold696-65333 28 33347711 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451301 Affx-122921291 AX-123321634 28 10163066 AATCCCTGTTTGGGCGACTAAGTTCCCACATGCTG[C/T]GGGGAAACCAAACCCATGAGCTGCGACTAGAGTAC Y 2 1 2 1 303000 r 74 goat snp48830-scaffold696-123831 28 33288407 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394193 Affx-122964914 AX-123264548 28 10194853 GGAGTTCATTTGTATGATTTAAAAAGGCTCAAAAA[C/T]GATAGAAACCCATGGTATTAGAGGCTACCTGCTAA Y 2 1 2 1 201000 f 74 goat snp48831-scaffold696-155618 28 33256402 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439670 Affx-122930590 AX-123310007 28 10243231 ACGATACACATTTTGTTGTTTTGTGAAAAATGCTT[A/G]CCATAAAATGATGAACTTCTCTAGAATGCACTTGA R 2 1 2 1 101000 r 74 goat snp48832-scaffold696-203996 28 33207629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411124 Affx-122951901 AX-123281474 28 10337131 TGGACCTGTTTCAGTGTAGTAGGCCCTGAGTTATG[C/T]ACAGTAAACAAAGTTCCTGTATTCGTGGAGTTTAT Y 2 1 2 1 101000 f 74 goat snp48834-scaffold696-297896 28 33113562 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776517 Affx-122943211 AX-385263644 28 10380260 CCCTACCTGTAATATAATAGATGCTGAAGGTGTTG[A/G]TGAGATGACTGAATCCTTTTTCCTAGTACTTCTAC R 2 1 2 1 101000 f 74 goat snp48835-scaffold696-341025 28 33070155 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421183 Affx-122944160 AX-123291530 28 10411972 GTCCTGAAGTGAAAAGTGAAAACTGGGAAAAAAAA[C/T]GAAAAGCATTGTTCTCTAAACAAGCAGGTTATAGA Y 2 1 2 1 303000 r 74 goat snp48836-scaffold696-372737 28 33038011 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797573 Affx-122965802 AX-385284512 28 10448498 CTGCCTCCTAACTCTCTACTTGAATCAAATTAATT[A/G]CTGTCCTCCAAATGTTCCTTTTACTTTTCTACTTC R 2 1 2 1 101000 r 74 goat snp48837-scaffold696-409263 28 33000981 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412974 Affx-122951036 AX-123283323 28 10477546 CTCTATTTGTTAATAATTTTTTAATGGAAGCTAAT[A/G]TTACCTGTGTACCCCTGATACTGCCTTCAGAGGTT R 2 1 2 1 101000 r 74 goat snp48838-scaffold696-438311 28 32971640 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452405 Affx-122920600 AX-123322738 28 10484876 ATTTCTTATTCCAGGAGAGCCTGTCTCTCAAAACT[A/G]CAACCACAAGCCTTCAATTATTTTTGACATACAAA R 2 1 2 1 101000 f 74 goat snp19558-scaffold1970-1269039 28 32964350 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797348 Affx-122962421 AX-385284287 28 10542016 TGGCATATACAAACTAACTGTGGCAGAGAATCAAT[A/G]GCTGAATTCCTCAATTACGAAAACATCACTAACTG R 2 1 2 1 101000 r 74 goat snp19557-scaffold1970-1211899 28 32907965 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788083 Affx-122943674 AX-385275103 28 10570834 TGTATCTTTTTCATACAATCCTTGGAAACATTATA[C/T]TAGGTCATTGCAAGTTCTTACCCCTTGTTTTGAAC Y 2 1 2 1 101000 r 74 goat snp19556-scaffold1970-1183081 28 32879264 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417034 Affx-122947533 AX-123287382 28 10607426 CCTTTTCCTGCCTAAATTCCTGAGCCTGTTATCAG[C/T]ACCAGCCACCCAGCTGTCCCATATGCTCACTTTGA Y 2 1 2 1 101000 f 74 goat snp19555-scaffold1970-1146489 28 32842838 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273142 Affx-1111833336 AX-519546805 28 10613482 GACTCTGATGTGGAGATGGCTGGCTATACTTGAAG[A/G]AGCAGGGACCTAAAGCGTGGCATGGCCATTCCTGA R 2 1 2 1 101000 f 74 goat 28_10613482_AF-PAKI 28 10613482 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468274366 Affx-1111834158 AX-519547961 28 10643553 GACATGTGAAATGATCTCTAATCGATGCAACAGCC[A/G]TATAAAACCAGCACTCTGAACCCTACCGACGGATG R 2 1 2 1 201000 r 74 goat GoatD01.022459 28 10643553 T C 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468277907 Affx-1111836078 AX-519551402 28 10647000 CGTTCACCAGCAAGAAGAGTTGGGAGGACTACAGA[A/G]TTGAAGTGTCCTCAGAGTGACCTGGTCCCACTGTC R 2 1 2 1 101000 r 74 goat Random2.2K-2262 28 10647000 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38384870 Affx-122971941 AX-123255228 28 10718340 TGGACTTTATTCAGTGAATCATTCCTCAATGAGTG[C/T]CATACCAAAAATTCAACATTTGAGAATCACAACAA Y 2 1 2 1 101000 f 74 goat snp19552-scaffold1970-1035575 28 32731923 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421265 Affx-122944750 AX-123291612 28 10757654 TCCTTTCTGCTAGGACAGCAGGCCCTTCATACCAC[A/G]TCTCCTCTCCTTTAAGAGCTCCTCCCAGACCAAGA R 2 1 2 1 101000 r 74 goat snp19551-scaffold1970-996261 28 32692498 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399547 Affx-122961137 AX-123269902 28 10788811 TTTTGGCTGTTCTTGGAAAAATGTAGACAACTCTG[A/C]AGATACACTGGGTTAGAAGAAGAGGACTGGAGTCA M 2 1 2 1 101000 r 74 goat snp19550-scaffold1970-965104 28 32661435 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418001 Affx-122946666 AX-123288349 28 10828682 AAACTGCGGATATAATTTATATAATATTGTACAGA[A/C]ACCACATCTCAATTTCAAAAACAAACTATGGACCT M 2 1 2 1 101000 r 74 goat snp19549-scaffold1970-925233 28 32620168 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788971 Affx-122928241 AX-385275984 28 10865266 AGGTATAGTTCCAAATAGATACAGTGATTTAATAA[G/T]AAGCTGTACATGGGAATTATGGAAATAGGTATCCA K 2 1 2 1 101000 r 74 goat snp19548-scaffold1970-888649 28 32583519 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793311 Affx-122976936 AX-385280289 28 10952329 CACTGACATTCACACATAAGTCCTACATACTAAAG[A/G]ACTTTTCACATGTGTTAATGATGTCACATTTTTCA R 2 1 2 1 201000 r 74 goat snp19547-scaffold1970-801586 28 32501851 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396046 Affx-122963458 AX-123266401 28 10987208 ACATACTTTCAACTAACTCTGATGACTGTACAGTT[C/T]GATATAAATCTGATTCAAATAGAGTGAGCTGTTGA Y 2 1 2 1 101000 f 74 goat snp19546-scaffold1970-766707 28 32466181 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444067 Affx-122926850 AX-123314404 28 11041801 TGGGCGCTCAAAACAGCCCAAAGCGGCAAGCACTA[C/T]AGAGGTCTGCATTTTACAGATAAGAAAACCAAGTC Y 2 1 2 1 201000 f 74 goat snp19545-scaffold1970-712114 28 32411103 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798005 Affx-122974548 AX-385284941 28 11110674 CATACAATGAGTTTGATTTATGAATTTGATTTTTA[C/T]TTATTTTTCTCCTAGGTGTGCTATCTGATGTACCA Y 2 1 2 1 303000 f 74 goat snp19544-scaffold1970-643241 28 32341157 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425340 Affx-122941594 AX-123295686 28 11153800 CCTACACGCAACACTTCAAAATAAAGATTAATAAT[A/G]CTATCCACACTAAGAGCTAACCATTCTCCTTTGTT R 2 1 2 1 101000 r 74 goat snp19543-scaffold1970-600115 28 32298146 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772578 Affx-122919409 AX-385259727 28 11204289 TAAATTTATATGCACCAAAAACAGGGCCTCAAAAT[A/G]CATAAAGCAAAAACTGACAGGACTGAAAGGAAAAA R 2 1 2 1 303000 r 74 goat snp19542-scaffold1970-549626 28 32248494 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378551 Affx-122976611 AX-123248910 28 11237186 GGTAGACACAGCTCAGGGAAAGAGCATCACCAGAG[C/T]GAAGAGGGCTGAGCAGAAAGCCCTGACCCTCCGAG Y 2 1 2 1 101000 f 74 goat snp19541-scaffold1970-516729 28 32215562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410512 Affx-122952180 AX-123280862 28 11267728 CAACTCTGTTTCTGTTTTCCCTTTTCTCTTTTCCT[A/G]TTTTCCTTTTGCATAAATCAGGTCTGTGTTATGAT R 2 1 2 1 201000 r 74 goat snp19540-scaffold1970-486187 28 32184942 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792833 Affx-122942482 AX-385279811 28 11327028 ACTCCTGAGTCGATATCCTGGACTCCAGAAAAAGG[A/G]AGGGTCAGCAAAACAGGGCAGCACAGCGCTCGCTG R 2 1 2 1 202000 r 74 goat snp19539-scaffold1970-426887 28 32127973 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790229 Affx-122951207 AX-385277233 28 11370027 CCAAAAAAACAGTAAGTTAGGTTCCAGACATGTTG[C/T]AGATTCTTTAGGCACAGTGGTGGGCTAGTGATAAC Y 2 1 2 1 101000 r 74 goat snp19538-scaffold1970-383888 28 32084572 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447086 Affx-122924494 AX-123317422 28 11412149 TGGAGCTCTCCTGTTTCACTCTGATAAGCCAGCCT[A/G]CTCACTCCCATGTGGGTTTCCTCCGTCTCAGCTTA R 2 1 2 1 201000 r 74 goat snp19537-scaffold1970-341766 28 32042821 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395343 Affx-122964034 AX-123265698 28 11452662 GATGTATAGGCCCACCCAGAAGGTAAGCACCATGT[A/G]CAAATTCACGCAGAAGGGAGGGTGTGCCCCCACTG R 2 1 2 1 202000 r 74 goat snp19536-scaffold1970-301253 28 32002792 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781320 Affx-122968687 AX-385268405 28 11481814 TGATACTACAGCTAGCTTTTAAAAGAATTGGTTTC[A/G]CCCACTGCAGCAGAACCTATGGAAGAAAGTCACTG R 2 1 2 1 101000 r 74 goat snp19535-scaffold1970-272101 28 31973818 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402285 Affx-122959107 AX-123272638 28 11532448 GAAATCCTAGGGTTCCCTCAGTTGAGTTCCTTCTT[A/G]TGGAGCCTCTGATTCATTATCTGAAAGATGAAGAG R 2 1 2 1 101000 r 74 goat snp19534-scaffold1970-221467 28 31923279 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277768 Affx-1111836079 AX-519551267 28 11584330 ACCCACAGTCTTGGTAGAGATGAAAACTCTCTGAA[A/G]TCATCATTTGGTTCAAGGGGAAAAAGAGAAAAACC R 2 1 2 1 201000 f 74 goat Random2.2K-2264 28 11584330 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399006 Affx-122960942 AX-123269361 28 11587299 TAGCTCATTTCACAGTCTGCTCAGGGTTCACATGA[C/T]GAACAGGACTGCGCTGTGTGTCCCTGGCCACGTCT Y 2 1 2 1 101000 f 74 goat snp19533-scaffold1970-166616 28 31868988 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383111 Affx-122973270 AX-123253469 28 11627319 GGGCCACGGAAGTCCTCTGTATCACTGACAGCTGT[G/T]CTGGTTACTACATGCAAATCACTAAAAGGAGTTAT K 2 1 2 1 101000 r 74 goat snp19532-scaffold1970-126596 28 31830236 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795522 Affx-122933136 AX-385282477 28 11668442 TGTATGTATGTGGACCTCATTTTTATTTTGATAAA[C/T]GTTTGGTTATACCATACCATTAGGTAATGTAGAAT Y 2 1 2 1 303000 f 74 goat snp19531-scaffold1970-85473 28 31789181 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404579 Affx-122957364 AX-123274931 28 11718250 ATCTAAGAGCCTTCCAGACTAGGGGATACTGAAAC[A/G]ATGTGGGGGAGTGTCTCAAGAATGGGGATATGAAG R 2 1 2 1 201000 f 74 goat snp19530-scaffold1970-35665 28 31738761 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388025 Affx-122969558 AX-123258383 28 11769501 CTGCTACTCTTCTCTCACAGATGAACTGTGCCCCT[C/T]ATGCACCGCCCCCCACACTGCCATGACTGCTTGTA Y 2 1 2 1 101000 f 74 goat snp54764-scaffold838-15487 28 31686897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439822 Affx-122930472 AX-123310159 28 11823657 ATGTCATTTGTACTTGTCTGGAAAGAACTATTTCA[A/G]AAGCATCTAGATGTCTTGAGATTAAACTTCTCAGC R 2 1 2 1 101000 r 74 goat snp54765-scaffold838-69643 28 31632511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800004 Affx-122962194 AX-385286927 28 11854434 TGGTAGATATTTAAACATCCATTTAATACCTAGTA[C/T]GTACTAGTATGTAGAGACTGAGCTAGGCATTGAAG Y 2 1 2 1 101000 r 74 goat snp54766-scaffold838-100420 28 31601824 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785234 Affx-122965436 AX-385272279 28 11906404 TTTTGTTTGAAAAGTGCCAATTAGGAAAAGTCTTT[A/C]TTTTCCTGGTTGGGTTTCTGATTATTGTGAATTTG M 2 1 2 1 102000 f 74 goat snp54767-scaffold838-152390 28 31549903 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405331 Affx-122956340 AX-123275683 28 11947577 CCAACCCGGGTCTCTTGCACTGCAGGCAGATTGTT[C/T]ACTGTCTAGTTTTCTTGTGAGGCAACCCTAAATAG Y 2 1 2 1 101000 r 74 goat snp54768-scaffold838-193563 28 31508562 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420847 Affx-122944649 AX-123291194 28 11985466 CTTGTGTGCATGTCGCTTCATACTGCAGGAGGGCA[C/T]GGAGGGTTTCAGTGATGTGGAGGTTGAGTAGGAGA Y 2 1 2 1 201000 f 74 goat snp54769-scaffold838-231452 28 31470783 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437199 Affx-122932052 AX-123307537 28 12015529 AACAACTTGAGAAGCAGATATAGCGGAAGTGATTC[A/G]TGCCTCTGGTGGGGAGCTGGCAATTTGTGACATTT R 2 1 2 1 103000 f 74 goat snp54770-scaffold838-261515 28 31440633 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448198 Affx-122924238 AX-123318534 28 12052428 TGCTGGTAGACTGTCGTTGCTTGTTACTTGGTGCA[A/G]GGTTCATGGTGGGGTGGAGGGTGAGTTGATAGTCT R 2 1 2 1 102000 f 74 goat snp54771-scaffold838-298414 28 31404149 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444158 Affx-122926786 AX-123314495 28 12132328 TAGAGTGGGCAGAGACTCAAAACAATGAAATAAAA[C/T]GGGTCAACATTTGTGAGGTGGCTCATAGTTTATAA Y 2 1 2 1 202000 f 74 goat snp54772-scaffold838-378314 28 31324055 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772905 Affx-122935715 AX-385260050 28 12173591 TTCTTGTGAAAATTAGGTCTTTGAATTTAAAACAC[A/G]TTTGGTTTTTCACATCTCAGTATCCAGCCCTCCTG R 2 1 2 1 101000 r 74 goat snp54773-scaffold838-419577 28 31282298 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445671 Affx-122926140 AX-123316008 28 12209843 TAGTTCTAGGGCAGGTTGCTGATAAGGATTAGGGC[A/G]TGTGCAGGCCTCCATTCCTCAGGCGGTCTCCTCAC R 2 1 2 1 201000 r 74 goat snp54774-scaffold838-455829 28 31245424 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447457 Affx-122924363 AX-123317793 28 12255982 AAGATAACAGAAAACCAAAATTTGGTCTTGGTCAC[C/T]TGCTCTGAGTTCCAGCATAGAGTCAGCAGATTAAA Y 2 1 2 1 101000 f 74 goat snp54775-scaffold838-501968 28 31199184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403048 Affx-122958535 AX-123273401 28 12286752 TGAAGGAGAAGAGGGGAGGAGCTTGTAATAATCAG[C/T]ACTCAAATCCTGGCAGACCAAGCTTCTTTCTATAA Y 2 1 2 1 101000 r 74 goat snp54776-scaffold838-532738 28 31168107 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413610 Affx-122950562 AX-123283959 28 12321962 TAAGAAAAAAACTATTACTTTTTCACAAACATATT[A/G]TCATTTTTGATGACCTTCATTCCTTTGCTCAGAGG R 2 1 2 1 101000 r 74 goat snp54777-scaffold838-567948 28 31132059 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424056 Affx-122942063 AX-123294402 28 12360320 TAAGTTCATTAACATGGGGTAGTGGTCTGGCTCTT[A/C]GGAGGGAAGAGTGTCTGACTTACACCAGCAATGTG M 2 1 2 1 101000 f 74 goat snp54778-scaffold838-606306 28 31093553 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770508 Affx-122924663 AX-385257673 28 12404368 TGGGGAATATCTTTATGTTATATTTGGTGTTAATT[A/G]TTTCCAGAGTTGCTTTCACATTTGAAGTAGGTGTA R 2 1 2 1 101000 r 74 goat snp54779-scaffold838-650354 28 31048651 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414978 Affx-122949059 AX-123285327 28 12450889 TCCAAGTAGCCTGCGATACCTCTCAGATGACAACA[C/T]GGAAGCAGTCTTCCTTCCTACCTACGTGTACAGCC Y 2 1 2 1 101000 f 74 goat snp54780-scaffold838-696875 28 31001983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424506 Affx-122941740 AX-123294852 28 12482783 ATGAAATAGCTCAAGTTAAAGTCACTGTCATTGAA[G/T]ATTAGCATGGATCAATATGGAGTTATCAAACTATA K 2 1 2 1 101000 r 74 goat snp54781-scaffold838-728769 28 30971277 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389018 Affx-122968637 AX-123259376 28 12532585 TCACAACAAATAAAAATATCAGAGTCCTAACTGAA[C/T]AAAGACTGTTTGAGAAAAACAGGCATCTTTATGTT Y 2 1 2 1 201000 f 74 goat snp54782-scaffold838-778571 28 30915533 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434079 Affx-122934176 AX-123304420 28 12569660 GTCAGAAAACAGCCAGGCCATCCTAGCTGGTAGTT[A/G]GAGAGTCAGTGATGGACATATACATAAAAGCTGAG R 2 1 2 1 101000 f 74 goat snp54783-scaffold838-815646 28 30884374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376990 Affx-122977740 AX-123247349 28 12608042 CCACCAGACCAATGTGATTCCTTCTTCTGTGCCAC[C/T]GTCTATGGGCATTAAATAGAAAGAGAGAATAGAGT Y 2 1 2 1 201000 r 74 goat snp54784-scaffold838-854028 28 30839354 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798793 Affx-122951204 AX-385285724 28 12700195 GTAACTCATCAAATTGTACTGAAGTATCTGCTCAA[C/T]GCACACATATAATATGTACTCAAAACTTACAACTT Y 2 1 2 1 101000 r 74 goat snp54786-scaffold838-946181 28 30746832 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449716 Affx-122922530 AX-123320051 28 12733325 TCCAAAAGCTATGTGATCTGGAGGTGTCTTCTCAA[C/T]GGCAGTCACAAAAATCATAGCTCCATGTGAGTGTA Y 2 1 2 1 101000 f 74 goat snp54787-scaffold838-979311 28 30713406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398853 Affx-122961057 AX-123269208 28 12775888 TATTTCAAAGTATAATTAATGTATTACACTTATTA[A/G]GATGAAACTGATCTTTTTTTAATAAAAGGTTGTTG R 2 1 2 1 303000 f 74 goat snp54788-scaffold838-1021874 28 30670534 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792277 Affx-122919730 AX-385279259 28 12894183 CCATAGAATAGCTATTTCCAGCTATGGTATATCCA[C/T]AGAATAGCTATCCATAGACTAGCTAATATTTTAGA Y 2 1 2 1 101000 f 74 goat snp54790-scaffold838-1140169 28 30556154 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394063 Affx-122964975 AX-123264418 28 12933066 ATACAGCCACTGCTGACTGGCTTTACAACCAGGTG[C/T]GTTAGAGGGGTGCGGGGACTGCTGTCACTGATCAG Y 2 1 2 1 101000 f 74 goat snp54791-scaffold838-1179052 28 30516064 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402524 Affx-122958481 AX-123272877 28 12965580 CCTGGGAAGCCCTATAGTCCTCCATTACCAAGTCA[C/T]TGATACAGTGACTTGAATCTCATATCATTTATTTG Y 2 1 2 1 101000 f 74 goat snp54792-scaffold838-1211566 28 30483489 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393249 Affx-122965469 AX-123263606 28 12996613 AAGTACTTGTTCCCATTCTTCTTAATCAATGTCAC[A/G]TTACTGTCACTTGAGGCAGGAGATGGGGTCAACTG R 2 1 2 1 201000 f 74 goat snp54793-scaffold838-1242599 28 30452695 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382240 Affx-122973960 AX-123252598 28 13030631 CTCCAGTGCTTAGAGAAGGGATTGGTGCTAGTGAT[C/T]AAACAACAAATATTTATTTAATAAAATGAAGTAAA Y 2 1 2 1 101000 f 74 goat snp54794-scaffold838-1276617 28 30418067 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775968 Affx-122922298 AX-385263099 28 13063689 GAAATAAAGCCCAGGCAAACATCAGAGAGTAACAA[G/T]TTTCAGACACAGATTATAGTGTCCTTTCTCAGCTT K 2 1 2 1 101000 f 74 goat snp54795-scaffold838-1309675 28 30385186 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403229 Affx-122957895 AX-123273582 28 13135887 AGTGGCCACTGGATGAAACGCGGTCTTCCCTACGC[A/G]CTGCATTCCCTGTGGCTCTGCTTTCTTGAGCAAGG R 2 1 2 1 101000 r 74 goat snp54796-scaffold838-1381873 28 30311907 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400112 Affx-122960725 AX-123270467 28 13192979 AAGGAGTTATCAATAATCACTTTCACTTCGTGAGC[A/G]CATTGCCAGATACAGGTTGCCTCCCACACTCGACA R 2 1 2 1 102000 f 74 goat snp54797-scaffold838-1438965 28 30256478 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793731 Affx-122967103 AX-385280703 28 13228844 TCTTAACCAGCCTTTTTTTCCATGTTCGCAGTACC[A/G]GGAGTAAATGCATAGATACACGTTACATGTATGTT R 2 1 2 1 101000 f 74 goat snp54798-scaffold838-1474830 28 30220315 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401791 Affx-122959476 AX-123272144 28 13259139 TCAAAGTGTGTGTTCCTAGATCCCTCTGATGTTAG[C/T]GGTGCAGCTCCAATGAACACATTTTGGCCAGCCTC Y 2 1 2 1 101000 f 74 goat snp54799-scaffold838-1505125 28 30190311 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778080 Affx-122974542 AX-385265196 28 13292041 TGTTTATCCTTCTAAATAAGTCAACAGCAATCATA[C/T]ATTTGAAAAATACCAAAAAGTGCCAGAATGAAATC Y 2 1 2 1 201000 r 74 goat snp54800-scaffold838-1538027 28 30156247 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396190 Affx-122963370 AX-123266545 28 13333575 ATAAACCTAAAAAGGAAGTGCTCTTATTATTACCC[A/G]CACAGTTTGTCAATGATAAAAATGAACTAGAGAGC R 2 1 2 1 101000 f 74 goat snp54801-scaffold838-1579561 28 30114774 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448174 Affx-122924257 AX-123318510 28 13373475 AAGTGCTTCCTATGTGCTAGGCACATCGCTAGATG[A/C]TTGATGCCAAGAGATGCTGAGGAACTGATCCAGGG M 2 1 2 1 101000 f 74 goat snp54802-scaffold838-1619461 28 30075226 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781434 Affx-122953119 AX-385268519 28 13426258 AGCAGCATCAGAATTGTTTGTGGACTGCTTGTGAC[A/G]TCAGTTGGCTTGTACTACCCGCTAGACAAGTAAGG R 2 1 2 1 101000 f 74 goat snp54803-scaffold838-1672244 28 30021776 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273192 Affx-1111833337 AX-519546851 28 13437742 AAGGAAGTGTGATACTGAAAACATCAGCAGCAGCT[A/G]ATCAGGGCATTACATATCCTCGTTTGTTTGTTTGA R 2 1 2 1 101000 r 74 goat 28_13437742_AF-PAKI 28 13437742 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320797383 Affx-122977690 AX-385284322 28 13456955 AATAAAAAGAATGCCATTTCGTCTTTCTAAGGCCA[C/T]AGGGAGCCATAGAACAGAGCACACCTCACACCTAC Y 2 1 2 1 102000 r 74 goat snp54804-scaffold838-1702941 28 29991283 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433030 Affx-122935772 AX-123303371 28 13486290 TGTAAGAAAAAATGGATCTTTTAGGAAACTTGATT[A/G]CCTCTCATTACTTATGCACGGCCACGCAGGTCAGT R 2 1 2 1 101000 f 74 goat snp54805-scaffold838-1732276 28 29961779 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389059 Affx-122968606 AX-123259417 28 13559190 ACAAGAGTCCTTATTGGAAGGATAGTATGTATGTG[C/T]AAAATTACCTTCTTCTTTATAAGTTATGATGTCTA Y 2 1 2 1 101000 f 74 goat snp54807-scaffold838-1805176 28 29888457 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451120 Affx-122921385 AX-123321454 28 13591638 TTGGCATCGGTTCTTTGCTATTGCTATGTTGATCT[A/G]TTGTAGGCCATCACCTCCCTCTCTGTCCTTGCTAA R 2 1 2 1 101000 f 74 goat snp54808-scaffold838-1837624 28 29855703 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453640 Affx-122919738 AX-123323973 28 13624816 TCAAGTCGCAATCTTTCCTCAGAGCTCCAGACTTA[C/T]GTACTGACAAATGGCCTGAGTTCTTGATAGTTTTA Y 2 1 2 1 201000 r 74 goat snp54809-scaffold838-1870802 28 29822511 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405080 Affx-122957406 AX-123275432 28 13714073 TGGAATTAGGTGACACATTTAATAAAAGGAATGGT[A/C]GGTGCTGCCCTGATTATTGTAATTATTGTGACCTG M 2 1 2 1 101000 r 74 goat snp54810-scaffold838-1960059 28 29733121 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427204 Affx-122939591 AX-123297547 28 13755825 TGAGCATTTCAGGGGCGTTGGCTTTACGAACTGCA[C/T]GATTTAAGTGAACAATGTAAGTGTGAAAAAATGCA Y 2 1 2 1 101000 f 74 goat snp54811-scaffold838-2001811 28 29691670 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785889 Affx-122950098 AX-385272926 28 13788395 TTTAATATGGCCAGAAAAGCTGAGAGAGAAGAAGA[C/T]AACTAATTTCAACTGAAATTTGAGTAATGTCGAAA Y 2 1 2 1 101000 f 74 goat snp54812-scaffold838-2034381 28 29659198 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435568 Affx-122933375 AX-123305908 28 13835667 TGGATCTCATATTTCTTTGATTATATCACTATTAG[C/T]GCTGATTCAAAAGGAGCCCGCTCTGTGTTGATAGT Y 2 1 2 1 101000 r 74 goat snp54813-scaffold838-2081653 28 29611580 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764258 Affx-986698785 AX-385251987 28 13844718 CAATGGTAAAGGAATTATTACATAAAACTCTCTCT[A/C]TATATATATATGATAAATAGCATACAGCAAATATC M 2 1 2 1 600010 f 74 goat 28_13844718 28 13844718 Ancestral_priority_1043 ancestry 0.658 recommended IMAGE 10K 10K ancestral 38410862 Affx-122952608 AX-123281212 28 13901118 TTCCCATCCAGAAATGAAGAAATTAAGATCCTTTC[G/T]CCAGACACTGCTTTTGCTATAAATACACACACACA K 2 1 2 1 101000 r 74 goat snp54814-scaffold838-2147104 28 29545883 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790312 Affx-122974153 AX-385277315 28 13943877 TAGCTTTGGCAGGCAATTCAAAACTGAAGGAAATG[C/T]CTTTCAGTTCTCATGAAAATAGTAAACAAAGATTA Y 2 1 2 1 101000 f 74 goat snp54815-scaffold838-2189863 28 29503266 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766639 Affx-122955110 AX-385253990 28 13998793 CTCCTTACCAGTATGTTTTCAAAAACTAATGTTTA[C/T]GAAACAACATGATTACCACAAAAGACAAAAACAGT Y 2 1 2 1 201000 f 74 goat snp54816-scaffold838-2244779 28 29448529 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421626 Affx-122944469 AX-123291973 28 14040537 GACAGTCCCTGGGGTGTGAGAATTGTAAGAATCAC[A/G]CCACAATAATAAACCATACGACACTTATTATAGGG R 2 1 2 1 101000 f 74 goat snp54817-scaffold838-2286523 28 29406357 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403691 Affx-122958049 AX-123274043 28 14073817 TTAAAATTCCCTCATCAACCAGGTTAGCAACTGTG[C/T]CAACGCTAAGGAAAGTCTGATATGACAGCACCGCT Y 2 1 2 1 101000 r 74 goat snp54818-scaffold838-2319803 28 29373123 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776937 Affx-122938855 AX-385264061 28 14103109 GACCAAGGTGATACCACCAAAGTTTAACATGGAAC[A/G]CTTCTTACTGTACTCTCTGCAGACTCCTTTTATAT R 2 1 2 1 101000 f 74 goat snp54819-scaffold838-2349095 28 29343870 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415587 Affx-122948624 AX-123285936 28 14143537 TGAGTGCTTCTCAGAAACAAAAGATAAAGCGAGGG[G/T]ATATTATGACCTAGTAGTGCCCTGGGAGGTGGGGT K 2 1 2 1 101000 f 74 goat snp54820-scaffold838-2389523 28 29303604 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418252 Affx-122947026 AX-123288600 28 14174433 CTACTTGAAAGGTGAAAGATGAGGAGATGCTCCTT[A/C]TTTTCTTGACACTTCAATTCTAAAAACACAAAAAC M 2 1 2 1 202000 r 74 goat snp54821-scaffold838-2420419 28 29272711 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434358 Affx-122934715 AX-123304699 28 14207381 CACCAGAAGCAGTCTGCCTTGCTTATTAAGGGTGC[A/G]GTAACACCTTCAGTGCCTTGCCTTAGAGTCACCTC R 2 1 2 1 101000 f 74 goat snp54822-scaffold838-2453367 28 29239471 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379566 Affx-122976046 AX-123249924 28 14256485 TTTTTCTAACTTTCAAATGTTCATTTTCTCTTCAG[C/T]TGAAATGTCTGTGCTTTCCACTGGATGGAAACTAT Y 2 1 2 1 103000 r 74 goat snp54823-scaffold838-2502471 28 29190367 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421337 Affx-122944071 AX-123291684 28 14298454 TGGGCTATAAGCTGTAAGCTCTGGAGTGTGTTTCT[A/G]TGTGCCTCTCACTCACCAATAGAACCCAGTAGCCA R 2 1 2 1 101000 r 74 goat snp54824-scaffold838-2544440 28 29147762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788211 Affx-122921475 AX-385275230 28 14365217 GTAATATTTAAGCTTTGTGAATTTCAAAAAGCAAG[G/T]CCCTATCGTGAAGAATAGGTCTACATTTTTTGCAG K 2 1 2 1 201000 f 74 goat snp54825-scaffold838-2611203 28 29079399 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405891 Affx-122955596 AX-123276243 28 14399647 GGCCCTCTACCCTCTGATCAAGGCACCCTAAATTA[C/T]ATGGGCAGACTTCAGGGCTTTACTCATACAACTTC Y 2 1 2 1 101000 f 74 goat snp54826-scaffold838-2645633 28 29045029 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442712 Affx-122927865 AX-123313049 28 14455575 CTAGTCTGAGCTTTCAAAAGCCCTCTGAGCTAAGA[C/T]GAGATAAAACCACCCTTTCTGGTTCCAATTCTGGA Y 2 1 2 1 101000 f 74 goat snp54827-scaffold838-2701561 28 28988786 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400176 Affx-122960675 AX-123270531 28 14505478 AAAGTAGGTGTTTAAAAAACAGTTGCTGAATTGAA[C/T]GGGGGCTGTTTGATACATTTGATCAGTTCATATCA Y 2 1 2 1 201000 f 74 goat snp54828-scaffold838-2751464 28 28938732 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787197 Affx-122941597 AX-385274223 28 14551406 TAACTTGGTCCATTAAGAATCCTAGTGGAACAAAT[C/T]TGAGCGTCTTTGGAGAGTTAGCTCTGAAAGAAAGA Y 2 1 2 1 101000 r 74 goat snp54829-scaffold838-2797392 28 28892818 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394028 Affx-122965003 AX-123264383 28 14614708 CAGATATGGGTGTGAATTTTTTGATCAGGTGGAAG[C/T]GATGAACATGCTCTGTGACTTGATTTATCCTAAAT Y 2 1 2 1 101000 f 74 goat snp54831-scaffold838-2860694 28 28829385 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780885 Affx-122937733 AX-385267972 28 14653106 TTTGGTTGTTTTCAAAGATAGTAGTAGCCAGGATT[A/G]ATTAGGTTGGTCTCTAGTAATGAACAACCCTAACT R 2 1 2 1 101000 r 74 goat snp54832-scaffold838-2899092 28 28791816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402480 Affx-122958593 AX-123272833 28 14687418 AAATTGTTAGAACCTGGCCCATAGTAAGCATTCTC[A/G]TTAGATAGCCTGTGCCCTTAATAGAAAACTGTGTA R 2 1 2 1 101000 r 74 goat snp54833-scaffold838-2933404 28 28756859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434210 Affx-122934854 AX-123304551 28 14724263 CAGCCACTTGGGAGGTGTAACAATTGCCACCATAA[C/T]TGCCACGTGTGGTGAAGGAGATTCTGAGCTTAGAA Y 2 1 2 1 201000 f 74 goat snp54834-scaffold838-2970249 28 28719690 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420650 Affx-122944829 AX-123290997 28 14759253 GAGATGTCTTTCCCTTGCATCTTAGCCAAGACCAT[A/G]TGACTGGTTCTGGCCAATAGAATATGAGTAGAATT R 2 1 2 1 101000 r 74 goat snp54835-scaffold838-3005239 28 28684737 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789688 Affx-122943750 AX-385276696 28 14789085 AATTTTATTCATGGCAAACCCTTTATAATGTGAAA[A/G]TAACTTGGGTGATGAGTGATTCTGATGCGTGAGGA R 2 1 2 1 101000 r 74 goat snp54836-scaffold838-3035071 28 28654726 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783107 Affx-122932039 AX-385270174 28 14821511 CCCTTGTTCAGTTCTTTTGGCTAGACTTTTTTGCA[C/T]GTGCCGTTTGTTTTTGCTGGGAATGATACAGGTAT Y 2 1 2 1 101000 r 74 goat snp54837-scaffold838-3067497 28 28627349 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792924 Affx-122934723 AX-385279902 28 14852331 AAGGCCAGACAGCAGGTCACATTACAGCCAGTGGA[C/T]CACAGGTTGTTGACTTCTGATATACACACCATGTG Y 2 1 2 1 101000 f 74 goat snp54838-scaffold838-3098317 28 28596397 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38431657 Affx-122936808 AX-123301998 28 14895606 TAATACAACAAAAATTTGTATAATGCAGTCCAGAG[C/T]ATATCACAGGATGGGGAAAGGAAAGGACTTTGCTC Y 2 1 2 1 201000 f 74 goat snp54839-scaffold838-3141592 28 28552310 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793088 Affx-122943330 AX-385280067 28 14948614 GAGCAGCAAATAACCCGGTACTCTTGGAGCCAAAT[A/G]CTGAAACTACTGTCAGTTCTAAGTGAGTCTCTGTT R 2 1 2 1 101000 r 74 goat snp54840-scaffold838-3194600 28 28498787 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382592 Affx-122973721 AX-123252950 28 15004682 CACCCTTGTTCATACATGTAATTTTATTCTTGTCT[A/G]CTATTCTGCATTCTGACATGTTGCTTCTAACTACA R 2 1 2 1 101000 r 74 goat snp54841-scaffold838-3250668 28 28442304 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391106 Affx-122966813 AX-123261463 28 15128167 CAAGCAAAGAGAGCTAAATTAAAAGAACACACAGT[A/G]TGAACATAGAAAAACTCTCCTTTGTTTGGTCAAAT R 2 1 2 1 101000 f 74 goat snp54843-scaffold838-3374153 28 28318774 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435190 Affx-122933644 AX-123305530 28 15156867 ACCAAAATTGTATACCCCCATGTAAACTGTAGCAT[A/G]TTGGAGGGGAAGTGTTAGGAACAAGATCTCTAACC R 2 1 2 1 202000 r 74 goat snp54844-scaffold838-3402853 28 28290005 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476385 Affx-1251763896 AX-185810449 28 15159108 CTCAACTGGAATTTCATCACCTCCACTAGCTTTGT[-/TTGTAGTGATGCTTTCTTTTTTCTTTTTTTTTTTTTAGTAGGAGCTTCCTCACTTTGGGTGGGGTTCTATCAGTGGCTTC]TGTAGTGATGCTTTCTAAGGCCCACTTGACTTCAC - 4 1 4 1 20000 f 74 goat SV_171 28 15159108 - deletion junction SV-TF-chip 539476641 Affx-1251763896 AX-385251424 28 15159108 CTCAACTGGAATTTCATCACCTCCACTAGCTTTGT[-/TTGTAGTGATGCTTTCTTTTTTCTTTTTTTTTTTTTAGTAGGAGCTTCCTCACTTTGGGTGGGGTTCTATCAGTGGCTTC]TGTAGTGATGCTTTCTAAGGCCCACTTGACTTCAC - 4 1 4 1 20000 r 74 goat SV_171 28 15159108 - deletion junction SV-TF-chip 562165279 Affx-1251763896 AX-606940690 28 15159108 CTCAACTGGAATTTCATCACCTCCACTAGCTTTGT[-/TTGTAGTGATGCTTTCTTTTTTCTTTTTTTTTTTTTAGTAGGAGCTTCCTCACTTTGGGTGGGGTTCTATCAGTGGCTTC]TGTAGTGATGCTTTCTAAGGCCCACTTGACTTCAC - 8 1 4 1 20100 f 74 goat SV_171 28 15159108 - deletion junction SV-TF-chip 562165621 Affx-1251763896 AX-606941031 28 15159108 CTCAACTGGAATTTCATCACCTCCACTAGCTTTGT[-/TTGTAGTGATGCTTTCTTTTTTCTTTTTTTTTTTTTAGTAGGAGCTTCCTCACTTTGGGTGGGGTTCTATCAGTGGCTTC]TGTAGTGATGCTTTCTAAGGCCCACTTGACTTCAC - 8 1 4 1 20100 r 74 goat SV_171 28 15159108 - deletion junction SV-TF-chip 562166394 Affx-1251763896 AX-606941802 28 15159108 CTCAACTGGAATTTCATCACCTCCACTAGCTTTGT[-/TTGTAGTGATGCTTTCTTTTTTCTTTTTTTTTTTTTAGTAGGAGCTTCCTCACTTTGGGTGGGGTTCTATCAGTGGCTTC]TGTAGTGATGCTTTCTAAGGCCCACTTGACTTCAC - 8 1 4 1 20100 r 74 goat SV_171 28 15159108 - deletion junction SV-TF-chip 38378430 Affx-122976773 AX-123248789 28 15187120 AGGAGAAGGGTCTGGAATGAGGCTGCCTTCAAGTC[A/G]CAGTCTTCAAGCCTTGGCACCATCTCTTAAGTGAT R 2 1 2 1 101000 r 74 goat snp54845-scaffold838-3433106 28 28259549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382198 Affx-122974005 AX-123252556 28 15233287 GTGTTTGGGAGAGGTTGTTTTATTTTTTGTCTGAA[C/T]GACTCTAGAAACAGATTCTATTCCAAACACCATAT Y 2 1 2 1 101000 r 74 goat snp54846-scaffold838-3479273 28 28210425 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377213 Affx-122978176 AX-123247572 28 15270287 TTTATGACACCTCTATAGCATCTACAGGAAAAGAC[A/G]ACAGGAAGACTGGCTATCAGATAACTAATCCCACT R 2 1 2 1 101000 f 74 goat snp54847-scaffold838-3516273 28 28173396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769937 Affx-122937060 AX-385257106 28 15314246 ACATGAAACACAGTTGTAAATATCCTCCATATAAT[A/G]TTAGCTATCTAAATCTCACATTGTATTAAAAGAAA R 2 1 2 1 101000 f 74 goat snp54848-scaffold838-3560232 NW_017209136.1 13165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449147 Affx-122923553 AX-123319482 28 15355485 ACATGGCTGGCTACCTCTGCTTCAAGAGAAATTGG[C/T]AAATGTAATTTTTAAAGCCGTATACATTGCCACAT Y 2 1 2 1 101000 f 74 goat snp54849-scaffold838-3601471 28 28087376 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783101 Affx-122965762 AX-385270168 28 15413669 TATGAGAACTTGATCCTCCAGCATTCATTCATTGA[C/T]GATAGATCCAGCTGTCATTACTTCTAAAGAACTAC Y 2 1 2 1 101000 f 74 goat snp54850-scaffold838-3659655 28 28028784 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411419 Affx-122951837 AX-123281769 28 15456474 TTTATCACCTTGGTGTTGCTGATTCATTCACCTGC[A/G]GCACTATCCACGTTCATTCTCCGAAAAGCTATTCC R 2 1 2 1 101000 r 74 goat snp54851-scaffold838-3702460 28 27985377 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801238 Affx-122947189 AX-385288151 28 15512808 GAGAAAGTAGACAAGGATTGATCCATTTATTTTCT[A/G]TTGTCTTTTGTATTTTCCCCAAGTTGACCAGAGCT R 2 1 2 1 102000 r 74 goat snp54852-scaffold838-3758794 28 27928046 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774286 Affx-122931176 AX-385261422 28 15546695 AACACTCTAAAAAGTCCTTAGCTAAGAAATGAAAT[A/C]AAAATAATGAATCCAAAAGAAGACAGAAAAAAATG M 2 1 2 1 201000 r 74 goat snp54853-scaffold838-3792681 28 27893879 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452637 Affx-122920349 AX-123322970 28 15639373 CTTATTTTGCAAATAAGTTAGTCTTGCTTTGGCCA[C/T]GTTTGATGGAGATGAGAATAATTTAGAGGGGAAAA Y 2 1 2 1 101000 r 74 goat snp54855-scaffold838-3885359 28 27800008 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428704 Affx-122938472 AX-123299046 28 15691971 CCATCTACTGAATTGCTATTGAACCTTCAAGACAC[A/G]TGAACGACTACTTCCTTCATGAGGATTTTCCAAAA R 2 1 2 1 101000 f 74 goat snp54856-scaffold838-3937957 28 27747963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399583 Affx-122961111 AX-123269938 28 15725194 GACAGGGAGGAAGGCAGAGCCGAAAGAGGGGAGAC[A/G]TGAGTCCTGATGATGTTGGAGAAACTACAGATTCA R 2 1 2 1 101000 r 74 goat snp54857-scaffold838-3971180 28 27714120 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442879 Affx-122927661 AX-123313216 28 15763726 TTAACATTAAGGGGTGTTTGGGTTTATGTGTGACT[A/G]GGGTGAGGGAATGGGACTTGGATTTAATTTATAAA R 2 1 2 1 101000 f 74 goat snp54858-scaffold838-4009712 28 27675704 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795639 Affx-122929460 AX-385282594 28 15818764 TACTTCTTCTATTTTCGAATTACTAATTTTGACAG[C/T]AGGAATGGGCACTGGGTAATTTGTATTTGTTCCTG Y 2 1 2 1 101000 r 74 goat snp54859-scaffold838-4064750 28 27620801 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415730 Affx-122948508 AX-123286079 28 15851034 TCAAAGGCTTACAAGGCAGCTACAGTAATGGTATT[A/G]TGGTTCTTGGAATGACAGCAGACATAAACTAAAAA R 2 1 2 1 101000 f 74 goat snp54860-scaffold838-4097020 28 27588531 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419035 Affx-122946030 AX-123289383 28 15881506 TATTTCAGCATTTTAAATCCTGAGTTGGAGCTGTG[C/T]AAACCCCATGGTGTAGGTATAACAGAGTACAACCA Y 2 1 2 1 101000 r 74 goat snp54861-scaffold838-4127492 28 27558007 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777309 Affx-122971918 AX-385264431 28 15916456 GGCTTGGAGGGTTGGTAAAGGACAGATGATTAAGC[A/G]CCCACGTCATTGAGGCTGAGATTTCATAGTAGGTG R 2 1 2 1 101000 r 74 goat snp54862-scaffold838-4162442 28 27523564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277770 Affx-1111836080 AX-519551269 28 15938102 CAAAGCAACTGGGTCTCCATGTGCTCGCTGATGCT[A/G]AAGGACAAGGAACAGGAAGGGAAGGAATAAGTGAC R 2 1 2 1 201000 f 74 goat Random2.2K-2265 28 15938102 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38420960 Affx-122944587 AX-123291307 28 15972434 TTATACAACTCTATATCATCAAAACAAGGATCCAA[C/T]AGAAAGACCTGTAATCACTTTTTAAAATCCAGATG Y 2 1 2 1 201000 f 74 goat snp54863-scaffold838-4218420 28 27467086 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273194 Affx-1111833338 AX-519546853 28 15976173 GGAGAGTGAGCGCCTAGATAATGGGATTTCGGGGC[A/G]TATGGTTAATTCTCTTCAGCCCTGCATCACGACCC R 2 1 2 1 101000 r 74 goat 28_15976173_AF-PAKI 28 15976173 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438385 Affx-122931304 AX-123308723 28 16006119 GTTATTTACAGGAGAGAGAAAAGGAGAATCAGAGG[C/T]CAGAGGACGAAACCCTTAACTGCCTGTAAAAAAAT Y 2 1 2 1 201000 r 74 goat snp54864-scaffold838-4252105 28 27433152 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38402140 Affx-122958663 AX-123272493 28 16059681 AAACCAGAGACACAGATCAGAAGGCTATGTGAAGA[C/T]AGGGGCAGAGGTCTGAGTGATGCCTTTGTGAGCCA Y 2 1 2 1 101000 f 74 goat snp54865-scaffold838-4305667 28 27378852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794686 Affx-122958727 AX-385281646 28 16109450 ACTTTATTCTGCCCTAGATATCTATCCTCTATTTC[A/G]TTGCATACATCACATTTCACTGAAGATTACAAGAG R 2 1 2 1 101000 r 74 goat snp54866-scaffold838-4355436 28 27329079 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793948 Affx-122955773 AX-385280917 28 16142336 TTATAATCTCCTTTTTATCAAACCCGTATATTTAC[A/G]TGTATGTGTATTCTTCTGGCAGAAGGCTGAACAAC R 2 1 2 1 101000 r 74 goat snp54867-scaffold838-4388322 28 27295042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773125 Affx-122930364 AX-385260268 28 16197511 TTCGTATCCAATCAAGCTGCACTTTAGGTACCAAC[A/G]CTAAAGAAAAGCACTTTAAAGATACAAGATTGCGA R 2 1 2 1 201000 r 74 goat snp54868-scaffold838-4443497 28 27238835 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419579 Affx-122945394 AX-123289927 28 16242903 AGAAAATATGACAGTTTTATTTTGTGATATCAAAG[C/T]GAGAATTGAGATGGCTTGTTTACCACAAATATCAG Y 2 1 2 1 101000 r 74 goat snp54869-scaffold838-4488889 28 27193495 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393560 Affx-122965404 AX-123263916 28 16281163 AGTGTTCTGATTTCACTCTGAAAATATTCCTACCC[A/G]CCCATGACTGCATTTCTATATTTTTTTCCAAAAAT R 2 1 2 1 101000 f 74 goat snp54870-scaffold838-4527149 28 27154791 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449504 Affx-122922622 AX-123319839 28 16326652 AGCTTTTAGCAGGATAAGCTATGGGTCATATCTGT[A/G]GTAACCTGTTTGGTCCAGCTTAGAGAAGGTGCAGG R 2 1 2 1 101000 f 74 goat snp54871-scaffold838-4572638 28 27108707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437390 Affx-122932435 AX-123307728 28 16369592 CAGATAGTAGACAGATGACTCACCAGCTTTGGCCA[C/T]GGAAGCAAGCTGAGTCATCTAAAGTCGGCTGAATC Y 2 1 2 1 101000 r 74 goat snp54872-scaffold838-4615578 28 27067056 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790491 Affx-122965788 AX-385277494 28 16398206 GTGAGGTGCAAGAGCATAAGACCAGCTATACAAGC[A/G]TATCCCATTAGTCAAAGAATATCACTTGACTGCAC R 2 1 2 1 101000 f 74 goat snp54873-scaffold838-4644192 28 27038790 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444355 Affx-122926712 AX-123314692 28 16428666 ATAAGATCGATGTTACAGACTTGTGCTAAGGACCA[C/T]AGCTTAATTAACTCCTTCATTCCTATTTTCATCAG Y 2 1 2 1 101000 f 74 goat snp54874-scaffold838-4674652 28 27007713 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442501 Affx-122927916 AX-123312838 28 16533529 GACAAAGCAGTTTGTGGTCCCACATGAGAAATTAT[A/G]TAAAGAGAGAAGCACCAGACCGTGCAGAAAAAAAA R 2 1 2 1 101000 f 74 goat snp5605-scaffold1197-572379 28 26901483 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420424 Affx-122944909 AX-123290771 28 16570950 TTAGAGAGTGAAACCATTCCTGGGTTATATAACAG[A/C]CCACCAGCCAGTGTCTTTCAGAATAGATTTGAAGA M 2 1 2 1 101000 f 74 goat snp5604-scaffold1197-534958 28 26864047 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453180 Affx-122920462 AX-123323513 28 16612125 ATTTCTAGGGAGCAGATCAGGAAATTTCCTTGAGC[A/G]TATGGAGAGAAGGAGGTGGAGAAGGGGGAGGTGTG R 2 1 2 1 101000 f 74 goat snp5603-scaffold1197-493783 28 26822296 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451991 Affx-122920929 AX-123322324 28 16694975 GATGAATGGATTTTTAAAAGTAAGGGATCGTCTTT[A/C]GGCTGTGGGATTGCATATCAAGTCATGTGGATGTT M 2 1 2 1 101000 r 74 goat snp5601-scaffold1197-410933 28 26739075 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453541 Affx-122919789 AX-123323874 28 16729226 TTATCTCTTTTCTAACTGGTGAAAGTGGGAGGCAT[A/C]ATGTGTCCCATTTCTCTCAGGTAATCTTGGTTTAA M 2 1 2 1 101000 f 74 goat snp5600-scaffold1197-376682 28 26704923 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776950 Affx-122926229 AX-385264074 28 16988220 TCCCTCTTCTCCATCTTTAAAGAGTAAACTTGAGT[A/G]TAACTTCCTCTGATGATGCCGCAACACAAGCAACT R 2 1 2 1 101000 f 74 goat snp5595-scaffold1197-117688 28 26444649 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800062 Affx-122938876 AX-385286985 28 17072116 GGTCAGAATACAAAGTCACCCTCACAGAGCTTAAC[A/G]CCTCACCCTTAAACAACCTCTCTTCAGCATTCAGC R 2 1 2 1 101000 f 74 goat snp5593-scaffold1197-33792 28 26359064 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420357 Affx-122944959 AX-123290704 28 17126331 ACACTGAGTGTCTTCTTAGAGATTATTAGGTATTG[C/T]AAAATGCTTGAGAGTTTGTTTGATGAAACAATATT Y 2 1 2 1 101000 f 74 goat snp56815-scaffold90-20324 28 24128943 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796180 Affx-122955789 AX-385283131 28 17181649 TGTGTAGCTATAGTTCCATTTTCTTGTGATTGTTG[C/T]GAAGTATTTCAGTATATGAGTATAGTGCAATTTAT Y 2 1 2 1 101000 f 74 goat snp56816-scaffold90-75642 28 24185042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409467 Affx-122954069 AX-123279818 28 17224090 AATGGCACATTGTCTAACCTGTATATACCCATTCT[A/G]TAATCCATTGTTGTTTCTAATGATTGATATGAGAA R 2 1 2 1 101000 f 74 goat snp56817-scaffold90-118083 28 24226962 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277914 Affx-1111836081 AX-519551408 28 17254782 GAGGAAAATTTGGGGAAAACGGTAATTCCAAAAGG[A/C]CCAGTATAAACTGTGGGAATAAATAAAACCTCCTT M 2 1 2 1 101000 r 74 goat Random2.2K-2266 28 17254782 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38378320 Affx-122977346 AX-123248679 28 17265561 CAAAAGAAGAATCCTGAGGTCTATTATGATGCACC[A/G]TTAATTCTTTATTAGTATAATAAGATGTTAAACAA R 2 1 2 1 101000 f 74 goat snp56818-scaffold90-159554 28 24268719 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782584 Affx-122953329 AX-385269658 28 17336021 CCTGCAATATGAATTAAATTAAGACAACACAAAAT[A/G]TCTTATAATTATCTAAATGAATTTTATTTGTTAAT R 2 1 2 1 202000 r 74 goat snp56819-scaffold90-230014 28 24340986 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392002 Affx-122966495 AX-123262359 28 17446540 AATATTTATGTATATATAAATAAAACAATTACTTT[A/G]CACATAATTAGTATGGAATTAGACTCAAATTTCTA R 2 1 2 1 103000 r 74 goat snp56821-scaffold90-340533 28 24454039 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779567 Affx-122955981 AX-385266670 28 17497858 AGATGATATTTACATTCCTATTTCTTATTCTCTTC[A/G]TTGTCTGAAGTAATTTTCAGGGAATAAGAACACTG R 2 1 2 1 202000 f 74 goat snp56822-scaffold90-391851 28 24498237 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464048705 Affx-1110285976 AX-515525318 28 17501676 GCAGTTTTCGCTCTGATCTGTCACCTTGGGCAAGT[A/G]GTTTAATCACTGTGACTCAGTTTTCCCACCTGTTT R 2 1 2 1 101000 r 74 goat GoatD01.040669 28 17501676 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38453773 Affx-122919592 AX-123324106 28 17670868 AGCCCTTATCCAGCAATTGGTCACTGTTGGGCAGT[A/G]CTAAAGCCCATACTCCTTGCCTCAATAAAAACACC R 2 1 2 1 101000 r 74 goat snp56825-scaffold90-564861 28 24675076 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387364 Affx-122970471 AX-123257722 28 17701771 TGACGGCACCACAGAGAAGTATCAAGTGCAAGACA[C/T]GCACAAATACAAAATACCAGGGATAGAGTAGGGAG Y 2 1 2 1 101000 f 74 goat snp56826-scaffold90-595764 28 24705930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440261 Affx-122930652 AX-123310598 28 17753011 CTTTTCTCATGGACAAAGTACAGTTTTCTTACCTC[A/G]TCATTTTCTATTGTTTACTTTTCATAAAAGATTTG R 2 1 2 1 101000 f 74 goat snp56827-scaffold90-647004 28 24757321 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382743 Affx-122973603 AX-123253101 28 17794344 CAGAAAAAGGCTAAGAAATATGAATAATTGCATAA[C/T]GCAGACACTTCTTAGAAATATTTACAAAATTGGCT Y 2 1 2 1 101000 f 74 goat snp56828-scaffold90-688337 28 24798968 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385500 Affx-122971268 AX-123255858 28 17826235 TTTATATCTTCATTGTCAGGCTAAGATCTGGAGCA[C/T]GTCACAGCAGAATCACACAGGTTGAACTATACAGT Y 2 1 2 1 201000 f 74 goat snp56829-scaffold90-720228 28 24830986 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774646 Affx-122920866 AX-385261780 28 17857507 CTGCCTCCTTCACAGAGATGTGTGTGATAATACAT[A/G]TAATATTCCTTTGAGAGCTATAAGACTGAATATAT R 2 1 2 1 101000 f 74 goat snp56830-scaffold90-751500 28 24862231 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779600 Affx-122922439 AX-385266703 28 17888478 AGGAAGAAATGATTACTTTTTATGTGGAACAATGG[A/C]ACCATAAAATTCTGATGTAAAGTTTAGAGTTTTCA M 2 1 2 1 101000 f 74 goat snp56831-scaffold90-782471 28 24893410 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395923 Affx-122963594 AX-123266278 28 17996307 GGTAATCTTTTATTTTCAAAATGATATTTCTGAAA[C/T]GGTCTCTAAGGGTGGGAGAACTATCTCTGAATTCA Y 2 1 2 1 103000 r 74 goat snp56834-scaffold90-890300 28 25000948 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417997 Affx-122946668 AX-123288345 28 18073619 AGACTTTTTGTGATATCCTCTAGGTCACTGATCAC[A/G]TGATTTAATTTATGCTTAAGTGGACAGTCCAGAGA R 2 1 2 1 101000 r 74 goat snp56836-scaffold90-967612 28 25077699 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421487 Affx-122943916 AX-123291834 28 18107391 CTCTGAAATTGTTGTAATAATAAAGTATTTTCTGA[C/T]GATTAAAAAATTCTAAAAATGTAAGCACTAGCCAC Y 2 1 2 1 101000 r 74 goat snp56837-scaffold90-1001384 28 25111205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769683 Affx-122928540 AX-385256853 28 18137825 TGCGAGGTGTGGATGTGACCAGCATTGATGTCAAC[A/G]TATTACTATAAATATTATGACAGATTTGGGCATGA R 2 1 2 1 101000 f 74 goat snp56838-scaffold90-1031818 28 25141719 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411992 Affx-122951764 AX-123282342 28 18188517 TTAGCCCATTTCCAGGAATTTGAAAAGATTCAGTA[C/T]TAGTATTATGCATCTATCCCATGTAGACTATAAAC Y 2 1 2 1 201000 r 74 goat snp56839-scaffold90-1082510 28 25192904 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390395 Affx-122967661 AX-123260752 28 18217219 TAGTGAGAGAGAAAATCAAAAAGATGCAAGCACTA[C/T]GCAAGGGCTTCTGTGAACTGGCCATTTGGGCTTCT Y 2 1 2 1 201000 f 74 goat snp56840-scaffold90-1111212 28 25221712 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414728 Affx-122949261 AX-123285077 28 18250299 TTGAAGAAAAGCTTATCATACATATATCACTAAAA[C/T]GTTGTCCAGACACTTTCATAGAGGTTTCTGTATTT Y 2 1 2 1 201000 f 74 goat snp56841-scaffold90-1144292 28 25251815 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428539 Affx-122938739 AX-123298881 28 18318475 CCTTTTTGTTCTGATGCACTTAGATTTAATATTTT[A/G]TCCAGTTTTTCTAGCTCAATGGTCTGAAAAATCTT R 2 1 2 1 101000 r 74 goat snp56842-scaffold90-1212468 28 25319090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411610 Affx-122951598 AX-123281960 28 18370273 TATTCCCATGAATAAAAGATGTTCCCTGACACTAA[C/T]TCACCCTGCTTCTCTGACTGCCCACTGTGCCCTCT Y 2 1 2 1 101000 f 74 goat snp56843-scaffold90-1264266 NW_017216664.1 9038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388285 Affx-122969756 AX-123258643 28 18430292 CTATAAATCCCCAAATCAGAAAGACCAAGAGAGAA[C/T]AAGATGGTCAAAAAAGAATTTACAGGGAAAAGCCT Y 2 1 2 1 102000 f 74 goat snp56844-scaffold90-1324285 28 25429471 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769455 Affx-122958155 AX-385256625 28 18467133 TATTATTACTTTTGCACACCCCTGGTGATCAAGAA[C/T]ATAGTACTACTGTTAAACCCAGATAGGAGGAAAAA Y 2 1 2 1 102000 f 74 goat snp56845-scaffold90-1361126 28 25466314 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273149 Affx-1111833339 AX-519546812 28 18476650 CTCACAATGGCGCTGGGTGGGACTAGCTGGAAATT[A/G]GATGTGAGGGGCAGGCAGAGCACCTAGGAGTGGGG R 2 1 2 1 101000 f 74 goat 28_18476650_AF-PAKI 28 18476650 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38388207 Affx-122969417 AX-123258565 28 18497974 TGTCCATTCTCCCTGCAACTTCCCTGCGCTCTTCC[A/G]GGGCCCTCAGCTCAGTATCCTTTGGGCAAGGATCT R 2 1 2 1 101000 f 74 goat snp56846-scaffold90-1391967 28 25498073 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419897 Affx-122945344 AX-123290245 28 18550575 GCCTTGCACTAACAGTTTCCAAGCAATGGCCTTAG[C/T]GCACGGTCTCTGGTGTTAGACACACTGAGATCAGT Y 2 1 2 1 101000 f 74 goat snp56847-scaffold90-1444568 28 25550862 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436789 Affx-122932257 AX-123307127 28 18595273 GCAATTATTGCCTTGTAAAATGATGAGTCTCAAAT[A/G]CTCCCCTCCTGGGACTTCTCTGGTGATCCTGTGGC R 2 1 2 1 101000 f 74 goat snp56848-scaffold90-1489266 28 25596074 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454052 Affx-122919398 AX-123324385 28 18656281 AGGCTTTTTTTCATTGAGAGAAATTGAATCTTGCT[A/G]CTTTTTCTTTTTAGCTGGAAACCTTAGGAAAGCTA R 2 1 2 1 101000 f 74 goat snp56850-scaffold90-1550274 28 25657785 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414179 Affx-122949672 AX-123284528 28 18712054 AAGAAATAAAAGCAACTGAAGAAATCATCATCGCA[C/T]GGATCCAAAGCTAAGATCAGCAGCTAAGAAACCTG Y 2 1 2 1 101000 f 74 goat snp56851-scaffold90-1606047 28 25710920 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404383 Affx-122956799 AX-123274735 28 18742648 AACTGGTCTCTGGTGCCCAAAAGGCTGGGGACTGG[C/T]GCACGAACCTGTCTATTCTGAACTTCCACAGGCTC Y 2 1 2 1 201000 r 74 goat snp56852-scaffold90-1636641 28 25741458 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405541 Affx-122955974 AX-123275893 28 18838175 GGTGGAGGAATTGGGGAAGTACCTTTTGAAAATGT[A/G]ATACCTGAACTGAAACCCAAGGGATGAACAGCAAC R 2 1 2 1 201000 f 74 goat snp56854-scaffold90-1732168 28 25836574 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397470 Affx-122962091 AX-123267825 28 18900061 CAGAATATTAGCTGAGGCTTTTGAGAAGTGAGTGC[A/G]TCTCCCCACAGGCTCTTCTCTCGCCCTGCGGCTGG R 2 1 2 1 101000 f 74 goat snp56856-scaffold90-1794054 28 25898227 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801029 Affx-122958678 AX-385287943 28 19026782 TGTTTTGATCATCTACATGTAATTCTTGGTGAAGA[C/T]ATCCTGTAGTTCAAATTGATTAAAATAAGTAAAAA Y 2 1 2 1 101000 f 74 goat snp56858-scaffold90-1920775 28 26022387 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785203 Affx-122931184 AX-385272249 28 19092745 ATATCAAGTCTGGGAACTCTTAGTTCTTACCTGAC[A/G]TTATGTAAATCCTCACCCTTCGTTTGGAGTAAATA R 2 1 2 1 101000 f 74 goat snp56859-scaffold90-1986738 28 26088467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785553 Affx-122958881 AX-385272597 28 19168769 TGAAAAGAGACAGCCTTATGCCCAAACTTCTGTTA[C/T]GAACTTCTTCTGATATCCAATATGAGTTATTTTGA Y 2 1 2 1 101000 f 74 goat snp56860-scaffold90-2062762 28 26165011 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785457 Affx-122950414 AX-385272502 28 19201884 TACCCAAAATACGAGTAAATTCATTTATGTAAAAG[C/T]TGTCTTCAAATGACTATGGATTTGCTCAGGTCATC Y 2 1 2 1 101000 r 74 goat snp56861-scaffold90-2095877 28 26198140 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799304 Affx-122952581 AX-385286234 28 19248672 AATAGCCTCTACATCTAATGATCTACAAAATAGTG[C/T]AGATAGTAAGATCATAGTTGATAAATATGTAAAAG Y 2 1 2 1 201000 r 74 goat snp56862-scaffold90-2142665 28 26244957 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793309 Affx-122947690 AX-385280287 28 19307728 TTCGTCAAAGACTAACCAAGAGTTAAAATCAGATT[A/G]TTACTCAAAACGTATACTTCCTTGTTTTTTAATTC R 2 1 2 1 201000 r 74 goat snp56863-scaffold90-2201721 28 26304223 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413972 Affx-122950296 AX-123284321 28 19378919 ATGGAATCTGGCATTTCACAGGTAAAAAATGCACT[A/G]CAGACTTGGAGTTATGCACTGTCAGAATTTGTTTA R 2 1 2 1 201000 r 74 goat snp50732-scaffold732-120107 28 24046831 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773075 Affx-122948439 AX-385260218 28 19450456 TTATTCTAAAAATAGCCAATAATCTGTGTATCATT[C/T]GTTATTTTTTCCCATTGGAGATGTAGCCCATTTTC Y 2 1 2 1 102000 r 74 goat snp50730-scaffold732-48570 28 23975600 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784045 Affx-122941638 AX-385271098 28 19484297 GTTTGCTGTGAATGTAAATGCATGTTCAAAAGTTT[A/G]CTAATTTAACATTTTAGCAAAGTGGTGGCAAAAAC R 2 1 2 1 101000 r 74 goat snp50729-scaffold732-14729 28 23942887 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429309 Affx-122938602 AX-123299651 28 19515983 TGAATTGTGAAAAAAACACAACCCTGAGTGCAGAA[C/T]GGGTAATTATGTTCTCAGGCAGCCTCCAGGACAGG Y 2 1 2 1 202000 r 74 goat snp45623-scaffold626-591714 28 23902197 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787759 Affx-122956795 AX-385274782 28 19567201 GACCTCCAATTTAGCTGTAATTTCTATGATATGGT[A/G]TTTCCTTTCAGTGTCTCTTCCTTATTATCCAAGTT R 2 1 2 1 101000 f 74 goat snp45622-scaffold626-540496 28 23850255 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415794 Affx-122948905 AX-123286143 28 19629591 ATGGCTGCACCAATTTACATTCTTACCAAGAGTAG[C/T]GCTGTACATAACGTAATCCTCATTACAACTTTATG Y 2 1 2 1 201000 r 74 goat snp45621-scaffold626-478106 28 23789339 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436409 Affx-122933022 AX-123306747 28 19707566 AGCCACCTTCAAATCCCTGCAAAGTAAAGGAAGGA[G/T]AACACTTTTTACAGAGAGGAAAAGGAATTTGGGAG K 2 1 2 1 202000 f 74 goat snp45620-scaffold626-400131 28 23709489 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437727 Affx-122931737 AX-123308065 28 19737552 CATTCAAGCATCTGGTTCATTTCTTAGAGTTTCTT[A/G]TAAGACTGCCATGATTTCTTCCAGTTCACCCAACA R 2 1 2 1 101000 r 74 goat snp45619-scaffold626-370145 28 23678691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439942 Affx-122929996 AX-123310279 28 19767247 TATTTATTGAGACTCATTCAATCTCATTCAATAAT[C/T]ATGAGTAGGTCTCTCCACTTACAACCACTGATATA Y 2 1 2 1 101000 r 74 goat snp45618-scaffold626-340450 28 23648847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419303 Affx-122946231 AX-123289651 28 19880682 AATAGGGTCAGTTTTGGATGTGGCACCTTCTTGTT[C/T]ACATCAGCAGTTTTCTCTGGTCCCATAATGGACCA Y 2 1 2 1 101000 r 74 goat snp45616-scaffold626-227015 28 23537385 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378332 Affx-122977338 AX-123248691 28 19931276 AATCTGAAAATATTAGTTCTGGAGTGTGATCACAT[A/G]TAAAAAACACTTAAGTGTGTAATCATCATGCTTAG R 2 1 2 1 101000 f 74 goat snp45615-scaffold626-176421 28 23483338 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406176 Affx-122956157 AX-123276528 28 20022256 CCCAACACTCCCCTTGCCCCTTGTGATCTTGCTGT[C/T]ATTTTTTAAACTTATCCATATGCTTAATACTTTTT Y 2 1 2 1 201000 r 74 goat snp45614-scaffold626-85441 28 23401517 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436330 Affx-122933249 AX-123306669 28 20081422 TCCTTGATGTTTAAATATCATGTTTTGTAGAAGCA[C/T]AGGATTTTCACAAAACTAGAAACAATAATAACGAT Y 2 1 2 1 101000 f 74 goat snp45613-scaffold626-26275 28 23342312 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409282 Affx-122953114 AX-123279633 28 20130067 CTGGGCTGTTTCTGTATTTCTCAAATCACAAACAG[A/C]TTTCCCAGTAGATCTCAAAGGAAGTCATAGGATAA M 2 1 2 1 101000 r 74 goat snp7896-scaffold1285-22271 28 23293563 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387530 Affx-122970308 AX-123257888 28 20158880 TCTAACATTATAGTCATTTTAAGGCAGTAAGCTCT[A/G]TGAAGAAGATATAATATTACCATTTTCACCCTGTT R 2 1 2 1 101000 r 74 goat snp7897-scaffold1285-51084 28 23264816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797553 Affx-122933556 AX-385284492 28 20205138 TGATAAAAATGAAAGCCAGAACCCAAGTATAATAA[C/T]GTAGAAAGACCTAAGTGCTCAATTCCCTGATGACT Y 2 1 2 1 101000 r 74 goat snp7898-scaffold1285-97342 28 23218495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426817 Affx-122940520 AX-123297162 28 20239186 ACACATAGATAACTGCAGATAAAGCTGGAAAAAGC[A/G]TTCTATTTGGACACAGGAAAAAAAGAAAACAGGGT R 2 1 2 1 303000 f 74 goat snp7899-scaffold1285-131390 28 23184312 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768264 Affx-122923075 AX-385255445 28 20321846 AATATTCACATAGCTATCTCATAGAGTTGAAGAAG[C/T]GATCAAGTAATATACTGAGTAAATATATTCCATAA Y 2 1 2 1 101000 f 74 goat snp7901-scaffold1285-214050 28 23101732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444289 Affx-122926761 AX-123314626 28 20353468 CCTTGACCCCCATCTCAATGATTAATTGAGATTAC[A/G]TCCCTTCTTTCCTTTAAATGTTTTTATAATCTAGC R 2 1 2 1 103000 f 74 goat snp7902-scaffold1285-245672 28 23070058 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406683 Affx-122955783 AX-123277035 28 20403462 GGTCTCATATGACAATAAGAGTTCCTTGGGATTTT[A/C]TTTTTGATGGAAAACATATAACTGCAAGCTTTCAG M 2 1 2 1 201000 r 74 goat snp7903-scaffold1285-295666 28 23019955 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426758 Affx-122939855 AX-123297104 28 20443032 GTCGTAAAGAGCCGGATATGACTAAATGACTGAGC[A/G]TGCACATGACCTGGCAGAGGCTTTTTAAAATAACA R 2 1 2 1 303000 r 74 goat snp7904-scaffold1285-335236 28 22979747 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404034 Affx-122957173 AX-123274386 28 20448372 CATTTCAGAAGCTGTTCACTTATTCTGTTCACCTT[A/G]TTTACAGATCCCTTTGCTTCTGATTATGTTCTTGT R 2 1 2 1 101000 r 74 goat snp42456-scaffold561-1350557 28 22974685 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427596 Affx-122939459 AX-123297939 28 20487839 TACAAAGACAGATCAGTAGAATGAAAGAAATGTCC[A/G]TGAAAGAGACCTAATTAAGTGAATGTATTGGGGCA R 2 1 2 1 101000 r 74 goat snp42455-scaffold561-1311090 28 22935185 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770372 Affx-122949240 AX-385257538 28 20525624 TTAGAGGCAGTGGAGCTATACTGGCAATAGCTTTA[C/T]AATATATTTATATGGTTAGAGGAGATTACACTTGG Y 2 1 2 1 201000 r 74 goat snp42454-scaffold561-1273305 28 22897721 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382656 Affx-122973672 AX-123253014 28 20558672 AAGGAAATATTCAATGATTCATTATTTTGCTGACC[A/G]TTATTTGCTTTCTTGTAGTAACTGGAGAATGGGGG R 2 1 2 1 101000 r 74 goat snp42453-scaffold561-1240257 28 22864574 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444721 Affx-122926414 AX-123315058 28 20594776 AATATTAAAACACACAAAAAGTTAACTTGATTCTG[C/T]AGCTAATCAAAACCAGATTTACTTTAAATATTAAG Y 2 1 2 1 101000 r 74 goat snp42452-scaffold561-1204153 28 22828630 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791323 Affx-122944220 AX-385278316 28 20628705 ATGATTAGTGTTGCTATTTTTCTAGCATGTTGATA[C/T]AGAAATCATTAATGAATCTGGATGGATAGTTTTCT Y 2 1 2 1 101000 f 74 goat snp42451-scaffold561-1170224 28 22793415 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402646 Affx-122958385 AX-123272999 28 20666030 TCTTGACTTGATACTCGGTTGCAAAATTAACCTTC[A/G]TTTTCCTAGAGTTAGACTTGAGTGAAAGTGCATGT R 2 1 2 1 101000 r 74 goat snp42450-scaffold561-1132899 28 22757799 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795834 Affx-122977245 AX-385282787 28 20702287 TAATTGTTCAATCTGGCTTAATAATCTTATTTTCA[G/T]AAGTTTAAGAGAAAGTTTTTGATTTTCCATCTTCT K 2 1 2 1 101000 r 74 goat snp42449-scaffold561-1096642 28 22721402 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448078 Affx-122924334 AX-123318414 28 20731028 AACAATAATGCTAGAGAACTGAAGAGGGGAAATTG[C/T]TCTTCCAGTTATAAAAAATGAGGAAAACATAGGCA Y 2 1 2 1 103000 f 74 goat snp42448-scaffold561-1067901 28 22693099 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769139 Affx-122928484 AX-385256314 28 20772623 TAAGCTAATGATCAGGTTCCACACAGGAGCTAATT[A/G]CTATTTATTCTCTTACAAGACAAATTTGTTTTTAA R 2 1 2 1 101000 f 74 goat snp42447-scaffold561-1026306 28 22651231 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436554 Affx-122932915 AX-123306892 28 20851427 TTTATTTGTTTGTTATGAGCAAAGTTTGTTATCTG[C/T]AATGGCAAAGCTAGAGCCAACCTAAATATCTGTTA Y 2 1 2 1 101000 r 74 goat snp42445-scaffold561-947502 28 22573258 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434480 Affx-122934629 AX-123304821 28 20880871 CAGTCCCATGAAGGAGGCACTTATTAAGGTGACCA[C/T]CTCTTAGGTGAGAAAGCCCACTCTCTGCCCTAAGA Y 2 1 2 1 101000 f 74 goat snp42444-scaffold561-918058 28 22543770 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395844 Affx-122964019 AX-123266199 28 20998649 ATATATTTTGACTTATAATCAGTGTTATTTACACT[A/G]TTTAGCATTCTTAGTCTACAAAAGCCTATTAAATT R 2 1 2 1 101000 r 74 goat snp42442-scaffold561-800280 28 22425654 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273151 Affx-1111833340 AX-186035335 28 21022885 CTTTTAATTTCATGGCTGCAGTCACCATCTGCAGT[A/G]ATTCTGGAGCCCAAAAAAATAAAGTCTGACACTGT R 2 1 2 1 103000 f 74 goat 28_21022885_AF-PAKI 28 21022885 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38406782 Affx-122955711 AX-123277133 28 21030703 ATAACCTCTGAGATCTTACTATGTGCAAGCGCTGT[A/G]CTAGGTAATATGAGGGACAATTACATGTACAGAGT R 2 1 2 1 101000 r 74 goat snp42441-scaffold561-768226 28 22393166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444636 Affx-122926928 AX-123314973 28 21102712 CTCTGAAGCACATAGAGCTTTTTTCCATATATCTC[A/G]TATGGCAATTCAATTATTGTATTTTATATTTGCTT R 2 1 2 1 101000 f 74 goat snp42439-scaffold561-696217 28 22321621 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795090 Affx-122919320 AX-385282049 28 21177740 ACAATACATATTTATTATAAAACATGAGGATCATG[A/G]TTTCACTGTCCAAAGTTTGGCAATTATGCAAATTT R 2 1 2 1 202000 f 74 goat snp42437-scaffold561-621189 28 22246343 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389892 Affx-122968127 AX-123260249 28 21230858 CGCCTGGGAAACATGCAAATTCTGAACCCAGCTGC[A/G]TATTTGTGACAAAGAGATAGCTAATGATCTGAGCT R 2 1 2 1 201000 r 74 goat snp42436-scaffold561-568071 28 22193422 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407966 Affx-122954343 AX-123278317 28 21287404 GATAATCCCTTTCAGCTCTGAATTCTCTGACCTTG[C/T]GATATTCTCCGTACTTTGTGACATAGAAAGTCTGC Y 2 1 2 1 201000 r 74 goat snp42435-scaffold561-511525 28 22137142 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774682 Affx-122939754 AX-385261816 28 21344195 ATAAATTTGCTTACAGAAAATGGCTTCATAATAAA[C/T]GTGTAGCCAAGGACAATCTTCTAACATTTTACTAT Y 2 1 2 1 101000 r 74 goat snp42434-scaffold561-454734 28 22080805 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381678 Affx-122974731 AX-123252036 28 21448446 CACATTAAGCATTTTTATTTTTTAATTTGATCACT[C/T]CAGTTTTCCTGATGGTAATTTTCTCTGAAGGAGCA Y 2 1 2 1 101000 r 74 goat snp42432-scaffold561-350483 28 21977060 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796223 Affx-122947985 AX-385283173 28 21532458 AAATCACTGTGCAACAAATCATGGAAAGTTAATGC[A/G]TAAGATCCTGGAGACATCACTCTTGCAGGAAGCCA R 2 1 2 1 101000 r 74 goat snp42430-scaffold561-266471 28 21892331 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385243 Affx-122972093 AX-123255601 28 21614277 AGCACAACCCCTCTGGAAGTGTTATATTTTCCACT[C/T]CTGTTGGTAAGGAAAAATTAGAAATCATTTGCATT Y 2 1 2 1 201000 r 74 goat snp42428-scaffold561-184652 28 21810367 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389174 Affx-122969090 AX-123259532 28 21652758 ACAGAGGCGCAAAGTGTTGGAGACAACTGAAGTGA[C/T]TTGGCGTGCCTGCACTCTCTATTAGGTCTTCCCAT Y 2 1 2 1 101000 r 74 goat snp42427-scaffold561-146171 28 21770972 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402075 Affx-122958708 AX-123272428 28 21681790 TAGACTTTACGTGGTCTTGCATAATCATTTGCACA[C/T]AGATATAAGAAGCATTCAATTCCTTTTCAGATAAG Y 2 1 2 1 101000 f 74 goat snp42426-scaffold561-117139 28 21741891 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441258 Affx-122929489 AX-123311595 28 21714310 GGTATGAAATATGATAAAAGAAATAGGTTGAGACG[A/C]ATGTAAGTAAGTTAAAAAGCCGTCATTTAGCCGTT M 2 1 2 1 303000 r 74 goat snp42425-scaffold561-84619 3 79343761 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429373 Affx-122938554 AX-123299715 28 21744339 TATAATATGAAGTGTAATCTGATTGTTCAAAGGAC[A/G]GTTTCACAATTTCTTCAGAAATACTTGTTACTAAC R 2 1 2 1 101000 f 74 goat snp42424-scaffold561-54590 28 21672073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784448 Affx-122943305 AX-385271497 28 21787971 GACCTGAGATCAGGGAACACAATCTAAGATCTTGG[A/C]GTACACTAAAAAAACTGTTGATACTAAAGAGCATG M 2 1 2 1 101000 f 74 goat snp42423-scaffold561-10958 28 21628471 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384660 Affx-122972141 AX-123255018 28 21802422 ACCACATACCTAGAATGCCTCACTTTATTATCCCT[C/T]CAGTTTGTCTCTCTGCAGGGATATTGGGGACAGCC Y 2 1 2 1 101000 f 74 goat snp16590-scaffold175-3394 28 21612191 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449985 Affx-122922874 AX-123320320 28 21850269 AGTTGGGTAGCTTCTCAAATGTCACTAAGTTCTCT[G/T]CCATAAAGACATCAAAATAGGAAGCCATAGTCAAT K 2 1 2 1 101000 f 74 goat snp16591-scaffold175-51241 28 21563752 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434215 Affx-122934851 AX-123304556 28 21935795 AAGTTTCCTTAGTCATCAACTATGACTTCCCCACC[A/G]ATAGAGAAAACTACATCCACAGAATTGCTCATGGT R 2 1 2 1 101000 r 74 goat snp16593-scaffold175-136767 28 21476372 T C 1 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427435 Affx-122940048 AX-123297778 28 21966193 CTTCATTGCAGGCAGATTCTTTACCATCTGAGCCA[C/T]GAGGGAAGCCCTGATGTATAAGTAGACTAAACATT Y 2 1 2 1 303000 r 74 goat snp16594-scaffold175-167165 28 21446018 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439006 Affx-122930362 AX-123309343 28 22015261 TTACCTGCTGGGAAAACTCATGTTCTTTCTTTAAG[C/T]GTCACCTTCTGGGTAAAGCATTCCTGCAACTTCCA Y 2 1 2 1 101000 f 74 goat snp16595-scaffold175-216233 28 21398052 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773123 Affx-122923650 AX-385260266 28 22060241 GATGTATTGCATTTCCTTTCACAAGATTTTGTAGA[C/T]ACTGCATTGTATCCAGATTCTACCAGCTTCTTGGT Y 2 1 2 1 101000 r 74 goat snp16596-scaffold175-261213 28 21353037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783681 Affx-122962741 AX-385270739 28 22091743 GGCTGCCTGATGTACTTCCATATCACTAGTATCTC[A/G]AACATAAATTAGGGACCTAAAAGTATTTGTTAATT R 2 1 2 1 101000 f 74 goat snp16597-scaffold175-292715 28 21321504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792903 Affx-122968483 AX-385279881 28 22155758 TATATATTTCTATATTTAGGAACTATATATTTCTC[A/G]CCCATGTTTATATCCCATTATGTATCACATTGCCC R 2 1 2 1 101000 r 74 goat snp16598-scaffold175-356730 28 21257203 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777211 Affx-122956614 AX-385264334 28 22185110 TTTTGGAAATACTTGACTGATAGAAACTCTTGCCC[A/G]CTTTCAAATAATTTGAAATGGTTTCCTTGTTTCCC R 2 1 2 1 201000 r 74 goat snp16599-scaffold175-386082 28 21227537 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796002 Affx-122933654 AX-385282954 28 22222427 AGGATAGAATTTCTGACTAAGGACAGGGATTGAAC[A/G]AAAGGACAGAACGACCACATATCAAAAAAATGCAT R 2 1 2 1 101000 f 74 goat snp16600-scaffold175-423399 28 21190396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438725 Affx-122930842 AX-123309062 28 22267417 TTCCTTGTTAAATTTATTCTTATTATGGACCCTCA[C/T]CGTATCCTTCCACTTGACAATTACCAGTAATAAAT Y 2 1 2 1 101000 r 74 goat snp16601-scaffold175-468389 28 21145261 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277918 Affx-1111836083 AX-519551413 28 22354089 ATATCAAAGCATCTGCAAACAATGGAAAAGAAATG[A/G]GAGCGCAGAAATAAACCCACTTATACACTGACAAT R 2 1 2 1 103000 r 74 goat Random2.2K-2270 28 22354089 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320786523 Affx-122969800 AX-385273556 28 22368240 ATGTCTAAGAGAACTTTAACATCTGTCAAATGAAA[C/T]GTCCAAGAGAACACTTCTTAAAACCTGCTTCTTCC Y 2 1 2 1 101000 r 74 goat snp16603-scaffold175-569212 28 21044340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440481 Affx-122929374 AX-123310818 28 22411312 GCTAATTCAATCCAGTTATCACGAAACACTGAGAT[A/G]CCAAGTTTCTAATACAACTTTGCTTTTGTTAATTT R 2 1 2 1 101000 f 74 goat snp16604-scaffold175-612284 28 21001293 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440312 Affx-122930211 AX-123310649 28 22448458 AAAGTGTTGGCATGAGGACAGAACGCACCCCTGCT[A/G]TGTACCTGCTAGACTGTATTCCTTTGATTGTAACA R 2 1 2 1 101000 r 74 goat snp16605-scaffold175-649430 28 20963990 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395389 Affx-122963967 AX-123265744 28 22580645 ACAAACACATAAAGCACTCACATAGCACAATCAAA[C/T]GTGACCGTATACAGAACAAAAAGGATATCAATTTT Y 2 1 2 1 101000 f 74 goat snp16608-scaffold175-781617 28 20832175 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800176 Affx-122968850 AX-385287099 28 22614741 GCTATGCTTGTGCCAGAAATCAGCATGTCGGGATA[C/T]AGAATCAAATATCCAAAATCTTCATCTATTATCCA Y 2 1 2 1 101000 f 74 goat snp16609-scaffold175-815713 28 20798319 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413714 Affx-122950076 AX-123284063 28 22675021 TATTGTTTAGTTTGTCACAATTTATTCAACCTTTT[A/C]GTTTCTGTTATAATTATCAGACCCCTTTTCTAACA M 2 1 2 1 101000 r 74 goat snp16610-scaffold175-875993 28 20738050 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448673 Affx-122923332 AX-123319009 28 22768730 CCTCTCAGAATGAAGAGCCTTTTAGAAGGGTTGGA[C/T]GGTCTGGAGGGGTGACAGCGCTGTCTGAGTGGGGT Y 2 1 2 1 101000 f 74 goat snp16612-scaffold175-969702 28 20644216 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790658 Affx-122967059 AX-385277660 28 22846309 AATGTAGATCTAGAGAGTCGCATACATAAATTCTA[C/T]GTAGAACAGAAACTTGGTTGCTTTGCAGCTTTCTG Y 2 1 2 1 201000 r 74 goat snp16614-scaffold175-1047281 28 20566805 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444818 Affx-122926324 AX-123315155 28 22879357 TCCTGAGTCATCACAGTTGCTTGGGAAAGCCTTAC[A/G]TTTTCCTTTGGGAAATGGAAACAAAAGTCTGTATG R 2 1 2 1 201000 r 74 goat snp16615-scaffold175-1080329 28 20533946 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775680 Affx-122940941 AX-385262811 28 22949228 TGAAGCCTATTATGAAACCAGTAAACCTGCCTTCT[A/G]TAAAACACAACATATGACCACAGATATTAAAATTG R 2 1 2 1 101000 f 74 goat snp16616-scaffold175-1150200 28 20464090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423306 Affx-122942634 AX-123293652 28 22982724 CCTTAGGCCAAACCATTTGCTATACTTGGATATTA[A/G]TTAACTTTCAGTGTACTAGCAGCCAAGATCAAAGA R 2 1 2 1 101000 r 74 goat snp16617-scaffold175-1183696 28 20430811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386175 Affx-122971377 AX-123256533 28 23018798 TGGATAGGAATGGGTTGGTTTATCAAGTAGGACAG[C/T]GTACTTGTCCTTTAGGAGGAAATACTCGGGAGTGT Y 2 1 2 1 202000 f 74 goat snp16618-scaffold175-1219770 28 20394724 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398275 Affx-122962173 AX-123268630 28 23079590 GTTCTGAGCAATGCAGATCTAGAGGGAAGACTTTT[C/T]AAATGAAGAGAAGAGCTGGCCTTGGGGCTGACCGC Y 2 1 2 1 101000 f 74 goat snp16619-scaffold175-1280562 28 20333606 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435838 Affx-122932820 AX-123306177 28 23134971 GGGTTTTCAGCATAGCCCCCACTTTTTTGAGAACG[C/T]ATTAGCAAGGGAATCGAGGAAACTGAGTCTTGAGA Y 2 1 2 1 101000 r 74 goat snp16620-scaffold175-1335943 28 20277358 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277778 Affx-1111836084 AX-519551277 28 23153946 AAGACCTTTAAAACTCAATGGAATCAAGTAAACTA[A/G]CTCCTTCTTATTTCTAGTTCTACTGCTAAATTTCT R 2 1 2 1 101000 f 74 goat Random2.2K-2271 28 23153946 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468277780 Affx-1111836085 AX-519551279 28 23155420 AGAAGTGGCACAAGTTAGGTGACTTAAGATCCAGC[A/G]TTCCAGAGAGCAGCCAACTATATTCTCTGTAGCAG R 2 1 2 1 201000 f 74 goat Random2.2K-2272 28 23155420 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38418180 Affx-122947077 AX-123288528 28 23227332 AAAAACGGTTTCTGACAAATTAAAAACCTGGCAAA[A/G]CTTCCTAGCCTTCAGGCTGCTGGGTCCAAAAATGC R 2 1 2 1 202000 f 74 goat snp16621-scaffold175-1428304 28 20189279 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799807 Affx-122967996 AX-385286733 28 23276997 GTTGTCCTTAATGATGGGGAAACCAGGAAAATGGC[A/G]GAAATGAAAACTGAAGATGGCAAAGTAGAAAAGCA R 2 1 2 1 202000 r 74 goat snp16622-scaffold175-1477969 28 20139708 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387874 Affx-122969632 AX-123258232 28 23315509 AAATGTTTTTCTGTATTTTCTCTTGAAAATGTTGG[A/C]ACTTGTCTAACTTTAGCAGTTTTTAGCTACTTGAC M 2 1 2 1 101000 r 74 goat snp16623-scaffold175-1516481 28 20100991 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789352 Affx-122929391 AX-385276361 28 23359826 TTAGGGTTTGAAGCATAAAAACCCTCTCATTTAGG[C/T]AATAATTAGTGATTTTAGTGAATTTATCGAGTTTT Y 2 1 2 1 201000 r 74 goat snp16624-scaffold175-1560798 28 20056412 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442633 Affx-122928458 AX-123312970 28 23396599 ATGCAGGTTCAAAAGCGAATTTAAGTTCCTCTTTC[A/G]CACACTGTCACGTTTCTGTTTCCCCAGCTCTTTTG R 2 1 2 1 101000 f 74 goat snp16625-scaffold175-1597571 28 20019218 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412888 Affx-122950423 AX-123283237 28 23427932 TCTGGATACACAAAGAGACATCAGGGGTCTGTGCA[C/T]GAGAGAGAAGACCATATCAGGAAGCAGCCATCTGC Y 2 1 2 1 101000 f 74 goat snp16626-scaffold175-1628904 28 19987469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429910 Affx-122938110 AX-123300251 28 23462305 TCACTTGGGAAATGTCCCCTTTTTTTCTCATCTTG[C/T]CATTTATCACTCAGGATATTGTAAATATCAATCAG Y 2 1 2 1 201000 r 74 goat snp16627-scaffold175-1663277 28 19953126 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406032 Affx-122955487 AX-123276384 28 23511074 TCTAATTTATGCATTCGTCCAACCGTTATTTATTG[A/G]CCCAAGATGAAAAGTCACACCATCTGACAGGCCTT R 2 1 2 1 101000 f 74 goat snp16628-scaffold175-1712046 28 19904145 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435042 Affx-122933752 AX-123305382 28 23550021 AGTGTTTTCTTCCTCTTTCTCTGACTTTAGGGGGC[A/G]CAGTCTGAAGCTGCCTTGCACTGGCTACACCCCTC R 2 1 2 1 201000 r 74 goat snp16629-scaffold175-1750993 28 19866549 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273153 Affx-1111833341 AX-311427132 28 23571541 AAATTAACACACAGAAATCCCTTGCATTCCTATAT[A/G]TTAACAATGAGAAAACAGAATGAGAAACTAAGGAA R 2 1 2 1 303000 f 74 goat 28_23571541_AF-PAKI 28 23571541 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38392101 Affx-122966361 AX-123262458 28 23588102 TTTTGCCTCATTTTTCCTGATGGGGAGTTACAGTG[A/G]TCACCTTTCCACTGTTAGGAAAATTGATGAGGAGG R 2 1 2 1 201000 r 74 goat snp16630-scaffold175-1789074 28 19828526 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389718 Affx-122968676 AX-123260076 28 23633323 GCAGAGCAGGGCAACATGCATGATTGGCAGCCCAA[G/T]CAGAACCACATGGAATTCTCCAAAGGAGGGTGGAT K 2 1 2 1 201000 f 74 goat snp16631-scaffold175-1834295 28 19783507 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448497 Affx-122923463 AX-123318833 28 23667839 GCAGTGGAAAAGAAAATGTGATTTGAGCCAGACAC[A/G]CTGTGTTCCATTCTGGATTTCTGCACCTAGTAGCT R 2 1 2 1 201000 r 74 goat snp16632-scaffold175-1868811 28 19749370 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436291 Affx-122932526 AX-123306630 28 23719146 GGGTACCTGTGAGCTGTCCGCCAGGAAGGCCAGGA[A/C]GAGCTGCTTCTGCAGGACTTGAGTGTCCCAGCGGG M 2 1 2 1 103000 r 74 goat snp16633-scaffold175-1920118 28 19698320 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415017 Affx-122949027 AX-123285366 28 23768975 TCCTGGCCTGGATTGCTCTGTGGTTTATGACACAC[A/G]GAGGTCAGTGTGGGGTCAGCATCAGCAGTGATGGG R 2 1 2 1 202000 f 74 goat snp16634-scaffold175-1969947 28 19648494 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277782 Affx-1111836086 AX-519551281 28 23785601 AAAAGAGTTAGCTGACTTAGAACACTGGGATGGGT[A/G]GACATTCCTTTTTCCAGGGGATCTTCCCAACCCAG R 2 1 2 1 101000 f 74 goat Random2.2K-2274 28 23785601 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38444445 Affx-122926553 AX-123314782 28 23801924 GTTCCTGTTCCTTCCTGTGGAATCTGGAAGCGATC[A/G]TCTCACAGTGGCTGGGTGTGGTCTGGGGTACTGGT R 2 1 2 1 101000 f 74 goat snp16635-scaffold175-2002896 28 19616087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445444 Affx-122925354 AX-123315781 28 23851572 CTGGAAGCTGAAAACCAGAGAGAGAGACAGGTAGC[C/T]GAGGTCAAGAGGGGCCTTAGAGACACTTTGATCTT Y 2 1 2 1 201000 r 74 goat snp16636-scaffold175-2052544 28 19566176 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803496 Affx-122919626 AX-385290317 28 23900674 GGTAAATTAGAGTGTGTGCAGATAGACTGTTGTTA[C/T]GGGGATTAGAGATAGTGAGTAGGAAGAGCCCAGTC Y 2 1 2 1 101000 r 74 goat snp16637-scaffold175-2101646 28 19517207 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424954 Affx-122941929 AX-123295300 28 23945329 AGCTCTGTTGTAAGAATTCTACACGGATTATCCCA[C/T]GTAATCCCACACGGGCCACCATGCAGTGGAACTGA Y 2 1 2 1 101000 f 74 goat snp16638-scaffold175-2146301 28 19472516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379867 Affx-122975791 AX-123250225 28 23975870 GTGAAGGGGAAAGGAGAGAACTGTGGAGTGAGAAG[C/T]AGTCAGGTTGGAAGCCACCTTCTCATAAGACAGGA Y 2 1 2 1 201000 r 74 goat snp16639-scaffold175-2176842 28 19442864 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444556 Affx-122926983 AX-123314893 28 24018434 GGGAGCTGATCTGCGTAACAAAATCTCAGAAAGAC[A/G]TGGAAGAGGAGAGGGGCTGAACTTTTTCACAAGCA R 2 1 2 1 101000 f 74 goat snp16640-scaffold175-2219406 28 19400521 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775843 Affx-122973759 AX-385262974 28 24072101 GGTTTATTTGGGGGCTGTATTGCATTTTAATGAGA[C/T]GAGGAGTTTAAGCCAAAAGAATGAATCATTGCTGC Y 2 1 2 1 101000 r 74 goat snp16641-scaffold175-2273073 28 19347033 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454258 Affx-122919648 AX-123324591 28 24137194 ATGCTTCATTGAGCCTCTGCATTTGGGACCTAGCC[A/G]TGAAAAGTATGCTTTCCCAACAGGTCAGTACTGAA R 2 1 2 1 101000 f 74 goat snp16642-scaffold175-2338166 28 19281673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405977 Affx-122955529 AX-123276329 28 24176698 ATTTGATGACTTTCTCCATCCTTGCTATGACCAAG[A/C]CATGTAAGTTCCCATTGGTACTCTTATGAAAAATG M 2 1 2 1 201000 r 74 goat snp16643-scaffold175-2377670 28 19242244 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803732 Affx-986696486 AX-385290492 28 24242426 GGCTGACAGCAGGGCCGTTTTAATAGTCTTGAAAG[C/T]GGTCTCCATCCGCTCCGTCCAACTGAAAGGGGTGG Y 2 1 2 1 600010 f 74 goat 28_24242426 28 24242426 Ancestral_priority_1043 ancestry 0.584 neutral IMAGE 10K 10K ancestral 320767912 Affx-986698795 AX-385255130 28 24242810 GAGGTCATCTACATATTGTAACAAGGTTAGTTGGG[A/G]GTGTTGTTGTCTGAACTCACCCAGATCCTCATGGA R 2 1 2 1 600010 r 74 goat 28_24242810 28 24242810 Ancestral_priority_1043 ancestry 0.52 neutral IMAGE 10K 10K ancestral 320764273 Affx-986698800 AX-385252000 28 24242970 GACCATTCAAAGGCATAAAGGTCCTGGCTCTTGGA[C/T]GCCAGGGGGAGGCTGAAGAAAGCATCCTTTAAATC Y 2 1 2 1 600010 f 74 goat 28_24242970 28 24242970 Ancestral_priority_1043 ancestry 0.622 recommended IMAGE 10K 10K ancestral 320767925 Affx-986698802 AX-385255142 28 24242994 TGGCTCTTGGACGCCAGGGGGAGGCTGAAGAAAGC[A/G]TCCTTTAAATCTAAGACCGTATACCAGTGATGGTC R 2 1 2 1 600010 r 74 goat 28_24242994 28 24242994 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 38413146 Affx-122950358 AX-123283495 28 24256604 GGGAGAAAGAACATGTGAGTGGAAAAAGCAATGGC[A/G]TCTCCCATCCCAGCCAGCCTCCAGCTCAAACCCCA R 2 1 2 1 101000 f 74 goat snp16645-scaffold175-2457576 28 19161811 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449577 Affx-122923227 AX-123319912 28 24351631 AGGCCTAGAAGGGAACAGATTGGGGGTGGGGGTGA[C/T]TAAGAGTTCAGCATGTCCAGTACTGTGTTTGAGAT Y 2 1 2 1 101000 r 74 goat snp16647-scaffold175-2552603 28 19067949 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451284 Affx-122921305 AX-123321617 28 24390972 GAGATATCTGTCTGTGCTTGATCTTTACATCCAGT[A/G]AAAGTTAACTGCACACCTGCCTCACCCTGGGCTTC R 2 1 2 1 101000 f 74 goat snp16648-scaffold175-2591944 28 19028490 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418987 Affx-122946064 AX-123289335 28 24427846 ACGGTTATCCATCTAATAATGATGAGCATAAAAGC[C/T]GCTCGGTGCCAGCACAGTGCCAAGTACTTTGAAGT Y 2 1 2 1 101000 f 74 goat snp16649-scaffold175-2628818 28 18991633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438501 Affx-122931217 AX-123308839 28 24459788 CCCTGCAGCAGTTTGGCTTGATTTTGAGGTTTAGA[C/T]AAATGGAATCATATAGTGTTTGCTTAGTCTGGCTT Y 2 1 2 1 101000 f 74 goat snp16650-scaffold175-2660760 28 18959607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395207 Affx-122964496 AX-123265562 28 24509887 AGACACTGAAGCCTAATGAAGTTTTGTGACCAGCT[A/G]AAGGCAGGATCAGAACCTGTCTCCCAACTCCTCGG R 2 1 2 1 101000 f 74 goat snp16651-scaffold175-2710859 28 18909256 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414806 Affx-122949215 AX-123285155 28 24540255 TGATCACTGTAGAGAGGATTCACAGCCTCTCAAAG[A/C]TGCAAGGGGCCCCTGTGCCTCCCCTCGGGCTCTCT M 2 1 2 1 101000 f 74 goat snp16652-scaffold175-2741227 28 18878965 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393105 Affx-122965583 AX-123263462 28 24570445 CCCTCCAGGAGCCAGAAAAAACTTTGTGCAAGAGG[C/T]ACTGGGTATGGATGAGCTCATAGCTTTGATTTTGT Y 2 1 2 1 101000 r 74 goat snp16653-scaffold175-2771417 28 18848798 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384249 Affx-122972358 AX-123254607 28 24600923 CGGGCAGCTCCAAGGAGCTCCCTATCAGCACAAAT[A/G]ACCCTCATGTTATGAACACCTCCAGCTCAGCTTCA R 2 1 2 1 101000 r 74 goat snp16654-scaffold175-2801895 28 18818653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391537 Affx-122966646 AX-123261894 28 24656382 GTTTTCTGGTCTGGTGCTAGAAGAGGGTCAGCCTG[C/T]ACCCAAAGGGCTGTTTATCTGAATCCCTGGAATCC Y 2 1 2 1 101000 r 74 goat snp16655-scaffold175-2857354 28 18763236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433401 Affx-122935103 AX-123303742 28 24708005 CAGATCGAAGCCTCAGAGTCAGTTTCTTGGACCCC[A/C]CATCCCTGAGCCCTGTGTGGTTGTACCCCAAGGTC M 2 1 2 1 201000 r 74 goat snp16656-scaffold175-2908977 28 18711940 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792219 Affx-122939895 AX-385279204 28 24743957 CACGTCCTCATTTGAAAATCTAGCTTTTTATAGGT[G/T]TTGCTTTGCTCATTGGTGTTAGGAATTAAATCATA K 2 1 2 1 101000 f 74 goat snp16657-scaffold175-2944929 28 18676211 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441927 Affx-122928591 AX-123312264 28 24775898 TCTAATCAGATTTATTTTTTAAATCTCACTTTGTC[A/G]TACAAAATTGGCATTGGACTGTTGCTTTCTAAGGA R 2 1 2 1 101000 r 74 goat snp16658-scaffold175-2976870 28 18643968 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418188 Affx-122947071 AX-123288536 28 24821809 TGAGAGATTTATATGCTTCCATCTGGTGGCTCAGA[C/T]GGCAAAGCGTCTGCCTGCCATGTGGGAGACCCGGG Y 2 1 2 1 103000 f 74 goat snp16659-scaffold175-3022781 28 18599273 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394741 Affx-122964861 AX-123265096 28 24874474 GAAAAATGCATAACTGTTAGTCAGATCCTCCTGAC[A/G]TTTCCTTTAGAGTTTCTGAGTTTCATGCCTTGCTT R 2 1 2 1 101000 r 74 goat snp16660-scaffold175-3075446 28 18545901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438837 Affx-122930776 AX-123309174 28 24938218 CCACCTGGTTCCACTCCCTCCCTGGGGGCAGGATC[C/T]CTGCTCACAGGTGTCAATCTCTTCTTACTTACTTC Y 2 1 2 1 101000 r 74 goat snp16661-scaffold175-3139190 28 18482410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441756 Affx-122929119 AX-123312093 28 24968130 AATGCTCTGTATGTAATGAAATGGAATAATCTACA[C/T]GGTATATTGTTGAGAAAAAAAATCAAGGCACACAA Y 2 1 2 1 101000 f 74 goat snp16662-scaffold175-3169102 28 18452915 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793794 Affx-122950916 AX-385280766 28 25060474 AAACAAGTGCAGTGAAATGTTAATAGTGTATCAAC[A/G]TTCCCTGTAAAATTCCATCAGCTAGGCTATGTTTG R 2 1 2 1 101000 r 74 goat snp16663-scaffold175-3261446 28 18359211 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432342 Affx-122936283 AX-123302683 28 25097288 TGGTAACAAGCAACGTGCCTGTGTCCAGCAGTCCT[A/G]TGGGTAGGGAGACCTTTCAGACCTCCAATGCGAGG R 2 1 2 1 201000 r 74 goat snp16664-scaffold175-3298260 28 18321523 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434596 Affx-122934103 AX-123304937 28 25126215 TGTTAGGAAACTGAGATTGAGACAAGTAAGGGGTC[A/G]TGTTCAAATGCACACAACTGTCAAGGACAGGAGCT R 2 1 2 1 101000 f 74 goat snp16665-scaffold175-3327187 28 18291758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420416 Affx-122944915 AX-123290763 28 25193454 AGTAGCTGTGGCTCTCTACACCTAGGAGCAGGAGT[A/G]GGGGGTGCACTTCCTAGGGGGTGATGGAGATCTTC R 2 1 2 1 101000 f 74 goat snp16667-scaffold175-3394426 28 18224081 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403397 Affx-122957770 AX-123273750 28 25266733 GATGGGGAGTTTCCTTGGAAGACCTCTTCCTCCTC[G/T]CCCTGGCCACATGGTCCGGCAGCAGACGAGGAAGG K 2 1 2 1 101000 f 74 goat snp16668-scaffold175-3467705 28 18150814 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38440708 Affx-122929901 AX-123311045 28 25295854 AAACTGAGCGAGTGAGGCCTAGAGCCCAGCTCGCC[A/G]TGCAGTGTCAGTACTGGCTTCCTTTGTCACTGCTC R 2 1 2 1 101000 r 74 goat snp16669-scaffold175-3496826 28 18121845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781657 Affx-122930984 AX-385268741 28 25339672 AGAACCTACGTAAAAGGGTTATTGGGAGAATTAAA[C/T]GAATTATTGCCTGTAAAATGCTTAGAAAATATGCC Y 2 1 2 1 202000 r 74 goat snp16670-scaffold175-3540644 28 18077990 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387166 Affx-122970628 AX-123257524 28 25425365 TGGAAAATTTTGAACACAGGAAGGGGCAACAGAGC[A/G]AATAAGTTTTTCTTTTTCTACCCCACCTGTGGAAT R 2 1 2 1 103000 f 74 goat snp16672-scaffold175-3626337 28 17992772 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409986 Affx-122953278 AX-123280336 28 25545896 AGGCAGAGCGCGTCATTCAACAAGGGGCTTCTGGT[G/T]TCTAAATAATTTATAGAAAAAATCTTGCAAAGATA K 2 1 2 1 101000 f 74 goat snp16675-scaffold175-3746868 28 17872212 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275130 Affx-1111834711 AX-519548709 28 25570944 TTTGAGTTGGTGGTCAAGCAGACTAGGACATATAC[A/C]CTTTTTAAGAAGAGGTTATAAAAGATGACTGCAGT M 2 1 2 1 101000 f 74 goat GoatD01.047229 28 25570944 G T 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38404777 Affx-122956681 AX-123275129 28 25575968 TGGGCCTCCCCTTTTCAAGGAGGATGAGGAAATGT[A/C]CAGGCATTGAGTGGAATTTTATTAGGTACCATCGC M 2 1 2 1 101000 r 74 goat snp16676-scaffold175-3776940 28 17842192 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446952 Affx-122924671 AX-123317288 28 25606073 TCTGCCTTGGAGGTTTGGGTGGCTGGAGGAGAGTC[A/G]CTGAAGGAAGCCACCAGATGGTTGAACCCACCATC R 2 1 2 1 101000 r 74 goat snp16677-scaffold175-3807045 28 17812055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449008 Affx-122923097 AX-123319343 28 25657457 CAGAATGCCCCTCCTCCTAGCAGGCACCCAGCATC[C/T]GATTTACTACCAGAGGTGCTGGCTGCTCCCACGGA Y 2 1 2 1 303000 f 74 goat snp16678-scaffold175-3858429 28 17760696 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381645 Affx-122974758 AX-123252003 28 25716244 GTGGCCACCCTGACCAGTGCCCACCAAGGCTCAAC[C/T]GTGAGTGTCACCAGGGTATAGGACAGTGGCTGTGA Y 2 1 2 1 101000 r 74 goat snp16679-scaffold175-3917216 28 17703917 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398525 Affx-122961539 AX-123268880 28 25782614 GACACTGCGTATCTAGGGATTAAACAAGAAGCCCT[A/G]CATGAACAAAAACGAGAGGTGCCCAGCGAGATACC R 2 1 2 1 101000 f 74 goat snp16680-scaffold175-3983586 28 17637490 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409703 Affx-122953047 AX-123280054 28 25822846 CCTGGGGTCCAGTCATCCTCATCAAGGGATTTCCA[A/G]TCAAGGAGAAAGCAAACCGGTGACCACTGAGTCCA R 2 1 2 1 101000 r 74 goat snp16681-scaffold175-4023818 28 17596882 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769220 Affx-122941299 AX-385256394 28 25855043 CTCAGTCTATGTTTCCACCTTTGTATCCACTGGGG[A/G]CATCACAAAGTTCTGGCAATAAAAGTCCAGACTCT R 2 1 2 1 101000 f 74 goat snp16682-scaffold175-4056015 28 17564677 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409193 Affx-122953181 AX-123279544 28 25896536 CCCCACTCTCACCCCAAACCAGGGAGCAGAACTCA[A/G]TACCCCCTGAAAACTTGCAGGAAGAATCAGAAGTT R 2 1 2 1 101000 r 74 goat snp16683-scaffold175-4097508 28 17523370 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389122 Affx-122968558 AX-123259480 28 25930179 CAAACAATGCAGAATTTTCCTTGTAAGAGAAGTGT[A/G]TTATATGTGTGCAATAACAACAAAAATAATCCCAG R 2 1 2 1 101000 f 74 goat snp16684-scaffold175-4131151 28 17489644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392204 Affx-122966282 AX-123262561 28 25988097 CACTCTTATCTGTAATCCAGTCCAGATGGCCTCCT[C/T]CCCTTCTGCAAAGGTGTGGGCTAAATGCCAAATAA Y 2 1 2 1 101000 f 74 goat snp16685-scaffold175-4189069 28 17432026 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446898 Affx-122924709 AX-123317234 28 26043205 CTGCTATGGCCAGAGAGAGAGATGTGACAACAGAC[A/G]GAGGGCCAAACAGATGCAACGTTGTTAGTGCTGAC R 2 1 2 1 201000 r 74 goat snp16686-scaffold175-4244177 28 17375455 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794815 Affx-122949786 AX-385281775 28 26077923 TTCAGTGGGAGAAGAGATGTGTATCTTTTTACTGT[A/C]TGAATTATGAGTCATTTTTGTACTCCTCCTTATAC M 2 1 2 1 101000 f 74 goat snp16687-scaffold175-4278895 28 17342365 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433299 Affx-122935198 AX-123303640 28 26125611 CTGGCCCTGGTGGGAGGGGGGAGGTCATCGAGGTG[A/G]TTAGTGTATCTCATGGTCTGAAGGGCCCAAATGTT R 2 1 2 1 101000 r 74 goat snp16688-scaffold175-4326583 28 17294641 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451404 Affx-122921194 AX-123321737 28 26143965 ACATCCCCCAGAGGTAACCACTATCCTGACTTCTC[C/T]GAACTTGATATAAGTGGGTCATATAGGATGATTCT Y 2 1 2 1 201000 r 74 goat snp39888-scaffold509-6629674 28 17276436 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404898 Affx-122956459 AX-123275250 28 26205439 CTCCAGGGGGATTTCATGCTCCATAGGGACATTTT[A/G]CAGATTAGAATCCCAACCATCCATCAGTTAGCATC R 2 1 2 1 101000 r 74 goat snp39887-scaffold509-6568200 28 17215480 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273206 Affx-1111833343 AX-519546865 28 26207858 CTCCCAGTTTCCTCGGCTGCCTAGTTTTCTCTGTT[A/G]TGCTCAAAGATTTGTTCAGAGTTAAAACTAAAAAG R 2 1 2 1 201000 r 74 goat 28_26207858_AF-PAKI 28 26207858 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320792497 Affx-122929159 AX-385279478 28 26249325 CAAGCTGAAATTCAGACCCAGGCAGCTGATTCTAA[A/C]ATCTATATTCCTAGTCATTTAAATATATTACTTTG M 2 1 2 1 101000 f 74 goat snp39886-scaffold509-6524314 28 17171372 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792546 Affx-122935123 AX-385279527 28 26296674 AGATCATGATAAACCTAAAAATTTAACAACTCTGC[A/G]TTGTCTCTGTAATCAGTGAAGACAGGAAATGAGAA R 2 1 2 1 101000 r 74 goat snp39885-scaffold509-6476965 28 17123716 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275441 Affx-1111834803 AX-519549013 28 26334529 TTATTTGCCATAAAATGATGGGATTGGATGGCAAG[A/C]TGGGAATGTAACTTGGTTGCAACCTTGAGATGAAA M 2 1 2 1 103000 r 74 goat GoatD01.054085 28 26334529 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38418697 Affx-122946296 AX-123289045 28 26348774 TCTTTCAAATATTGATTGGTTTTGTTTTAAATGTT[A/G]CATCATCTGATTCAAGCTACCCTATACCCTTAGAT R 2 1 2 1 101000 r 74 goat snp39884-scaffold509-6424865 28 17071199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389924 Affx-122968102 AX-123260281 28 26442238 CACCAGTAATACTATAGCTTTGGTGTGCTTTTTCA[C/T]AGTGCAAAGCAAACAAAACTGTAAACAGCAAATGC Y 2 1 2 1 201000 f 74 goat snp39883-scaffold509-6331401 28 16977384 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380189 Affx-122975504 AX-123250547 28 26474661 CTAAGGATAGGTTTTGGCCCACAATTTATATTTCC[A/G]TATGCTTGAACAGCCTACATACATACAATGTAGGT R 2 1 2 1 101000 f 74 goat snp39882-scaffold509-6298978 28 16945046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420392 Affx-122944932 AX-123290739 28 26524406 TCAACTAACCCTTGTCTGAGTGTTATCCATGTATG[C/T]AGCACTGCTCTGGAGTCCATGAGGGACAAAAAGGT Y 2 1 2 1 101000 f 74 goat snp39881-scaffold509-6249233 28 16895286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376724 Affx-122978962 AX-123247083 28 26553841 GGAAGAAAAGGGAAGTAAGATGAGCATCTTCAAAC[A/G]TCCATTAAAACAAAACCAAACAAGACCATCTTTTG R 2 1 2 1 101000 f 74 goat snp39880-scaffold509-6219798 28 16865780 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775391 Affx-122932473 AX-385262522 28 26605453 AGAAAACCTGAACAGAACCATATTTCCATTCTTTC[A/G]TTCTTAGACATATTATTGGAAAAAAGTATATCTTA R 2 1 2 1 102000 f 74 goat snp39879-scaffold509-6168186 28 16816125 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451797 Affx-122921493 AX-123322130 28 26643101 CAATTTCCTCAAAGCAGCTTTTCAGCTGAACTTTG[C/T]AAGTTTCAGGGCCTATCTTGACTCACTCCAATTTG Y 2 1 2 1 101000 r 74 goat snp39878-scaffold509-6130538 28 16778437 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452389 Affx-122920612 AX-123322722 28 26697703 GAAACAAAACACCTGTGTTCATTCAACAGAGGCCA[C/T]GTAAAAACATAAGAAGCAACTCTCAGAATTCTTTT Y 2 1 2 1 101000 f 74 goat snp39877-scaffold509-6075936 28 16723697 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395563 Affx-122963851 AX-123265918 28 26731186 TCTGCAGCATAGCCAGCACCTAAGTTATTTAAAAA[C/T]GCAGGATCTTCACCTGACCCCAGACCTACTGAATC Y 2 1 2 1 101000 f 74 goat snp39876-scaffold509-6042453 28 16689553 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414093 Affx-122949745 AX-123284442 28 26768534 GCTTTTAGCCTTGAGAGCCTGTTTGTCTTTGACTG[C/T]GTCATTTCTATCTCAGTTTTCTCACCTCTCAAATG Y 2 1 2 1 101000 f 74 goat snp39875-scaffold509-6005105 28 16652198 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406629 Affx-122955826 AX-123276981 28 26817504 GGCAAGGTATGGCACAGTCAGTCTGGATGAAGTCA[C/T]GGAAACCAAAGCCGTGCCACACCCCAGACATTAGC Y 2 1 2 1 101000 f 74 goat snp39874-scaffold509-5956135 28 16602979 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773124 Affx-122960388 AX-385260267 28 26873390 AGCTATATATTTGTTGTAGCATGAATCAGCACTTC[A/G]TGCTTTTTCTTGTCTGAATAATACTCTTTTGTTGG R 2 1 2 1 103000 f 74 goat snp39873-scaffold509-5900249 28 16546321 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386350 Affx-122970864 AX-123256708 28 26903273 ACCATATAATTGGGAGTTTGTACCTTTTGACCACC[A/G]TCACCATGTCTCTCGTATTAGTTTTAGTTATGCAG R 2 1 2 1 201000 r 74 goat snp39872-scaffold509-5870366 28 16516482 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788165 Affx-122939705 AX-385275184 28 26934450 AAATGATCTTATCTTCAGATTACTTCTGATAGGGA[C/T]GACTGAGCTTTGAAAGAACCTTTGAAAGACAGCCT Y 2 1 2 1 101000 r 74 goat snp39871-scaffold509-5839189 28 16485392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790653 Affx-122958009 AX-385277655 28 26987747 GGTATCGAACTGCCAGTTCTTGAACCTGCTATGTT[A/C]GTTACACAAAATAAGAGTTGGAAAGGCTACTGCTG M 2 1 2 1 101000 f 74 goat snp39870-scaffold509-5785892 28 16433623 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421327 Affx-122944079 AX-123291674 28 27020908 GAGAAGATAATGACCCAGTTTGCACCTATGCTGGT[C/T]CCCTATATCTGGCAGAATCAGCCTTTCAATCTCAG Y 2 1 2 1 101000 f 74 goat snp39869-scaffold509-5752731 28 16400866 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386864 Affx-122970065 AX-123257222 28 27088570 TCCCTTCTACCTCTTATGCAGTTAAAACTGAAAGA[C/T]GAGAATCTGCTTGCAGAGCTCCACATGGTTCAGGA Y 2 1 2 1 101000 f 74 goat snp39868-scaffold509-5685069 28 16332636 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415001 Affx-122949040 AX-123285350 28 27171543 TTTCTCTATGTACAATCAAGTAAAGCCATATCACA[A/G]TGATGAAGTAATAATGCAATGTTTGTAAAGCGTAA R 2 1 2 1 101000 r 74 goat snp39867-scaffold509-5602096 28 16249015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376692 Affx-122978985 AX-123247051 28 27211941 TTTGATGATGTTCACAGAAGCAGGTAAGTGACATA[A/G]CTGGGGCCAGATGTGAGCAAAGTCAGGTCTTAGAG R 2 1 2 1 101000 f 74 goat snp39866-scaffold509-5561698 28 16208074 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799885 Affx-122959266 AX-385286811 28 27245984 TATCCCTGTCATGACTCTTCATAGATTGCTTCTGT[A/C]GTAGACCTTTCTTGATAGAATTTTATGCTCTCTTA M 2 1 2 1 101000 f 74 goat snp39865-scaffold509-5527655 28 16173961 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789697 Affx-122945809 AX-385276705 28 27337906 TAGGAAAAAATGTCTGCAGTATCTCAAGCTAGATA[C/T]GGAGATTTGGGGAACTCATTTAAGGAGAGTCAGAG Y 2 1 2 1 102000 r 74 goat snp39863-scaffold509-5435733 28 16081886 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390935 Affx-122967073 AX-123261292 28 27401749 ATACACACAAATAGTTTTTTTATAAAGTATATCTC[A/G]CACAATATTTGGTATGTAACTTTCTTTTTTCTTAA R 2 1 2 1 101000 r 74 goat snp39862-scaffold509-5371890 28 16016869 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764283 Affx-986698810 AX-385252007 28 27439814 GGGGACTCTAGATACCATGGCAGAGAAGGCATCCC[A/T]TCCCAGATGTATAAATTCATGGTGGGCATTAATGA W 4 1 2 1 600010 f 74 goat 28_27439814 28 27439814 Ancestral_priority_1043 ancestry 0.462 neutral IMAGE 10K 10K ancestral 320767966 Affx-986698824 AX-385255181 28 27439842 GCATCCCTTCCCAGATGTATAAATTCATGGTGGGC[A/C]TTAATGAGTTTCCATTGGAGGCTCCTGGGGACAAG M 2 1 2 1 600010 r 74 goat 28_27439842 28 27439842 Ancestral_priority_1043 ancestry 0.486 neutral IMAGE 10K 10K ancestral 38412550 Affx-122951330 AX-123282899 28 27451691 AGCACCTGGCTTACCCTGCTCTTCTGTGAATACTT[C/T]TGTGGTAAGAGGAATAAAGAAGAAAGTCTCGGAAG Y 2 1 2 1 101000 f 74 goat snp39861-scaffold509-5321948 28 15968432 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419811 Affx-122945837 AX-123290159 28 27489739 AATAACCTTTAAACAGTCCATTGTGTTACTGCTGT[C/T]GGAGGCTTATGGCCAGAGGTTTAGATTCAACAGCC Y 2 1 2 1 101000 r 74 goat snp39860-scaffold509-5283900 28 15930519 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404505 Affx-122956706 AX-123274857 28 27617245 CCTAACCATTTATTTTTCTCCCCACCCCATAAGGG[A/G]CACTTACTATAATATGTGTAATGTATATCCACTGG R 2 1 2 1 201000 r 74 goat snp39857-scaffold509-5156394 28 15803470 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767899 Affx-122937757 AX-385255119 28 27712533 TTAAATCCCTGCCAACATGTTTAGAACTCTCCCAC[A/G]AGTTAATAAAATACTCAGAGTTCATTACTGAGAAA R 2 1 2 1 102000 f 74 goat snp39855-scaffold509-5061106 28 15707370 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375845 Affx-122978527 AX-123246204 28 27776703 CCTACATTCTTTGCTTTCAGGGGGACTCCCTTTAC[A/G]TAGTGTGTGCTACCCAAGGCTATAGTCAAAAGATT R 2 1 2 1 201000 r 74 goat snp39854-scaffold509-4996936 28 15642955 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382101 Affx-122974894 AX-123252459 28 27828064 CACTATGAAGTGTAACATATTACTATATTTACCAG[C/T]AATTATCTTAAGTGTGGTGTGAAAAACAGCACTGG Y 2 1 2 1 101000 r 74 goat snp39853-scaffold509-4945575 28 15590943 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439965 Affx-122929815 AX-123310302 28 27879744 TGAAAAGAAATGAATCCTAGCATGCAGAAATTTTC[A/G]TGCCCTTTCTGCAAGACCCCTCCCCCCAAAATTCC R 2 1 2 1 201000 f 74 goat snp39852-scaffold509-4893895 28 15539017 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774516 Affx-122920651 AX-385261650 28 27922241 ATGCAGACAGTAAGAATCAACCTGCTTCTACTAAT[G/T]CAGACATTTAAGAAATTAGCAAAAATGTAAAACAT K 2 1 2 1 201000 r 74 goat snp39851-scaffold509-4851398 28 15495987 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385145 Affx-122971761 AX-123255503 28 28000750 TAAAATGACAGTCAAATAAATAAATATATAAAACC[C/T]CAAGAATAGTTACTTGTATTATGTAAGGAGCTGCA Y 2 1 2 1 101000 r 74 goat snp39849-scaffold509-4772889 28 15417546 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777388 Affx-122974998 AX-385264510 28 28039566 GTCTTTAAAGGTAAAAATGTCTCTCAGATGTATTC[A/G]TGCAGAAATTCTACAAAATCTGAAGAGAAACAATC R 2 1 2 1 101000 f 74 goat snp39848-scaffold509-4734073 28 15378865 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433833 Affx-122934452 AX-123304174 28 28086038 AATATGATTCTTATTCACAGTTATGTTCTAAGTGC[C/T]GAAAACACCGTCCAGCACATGCTAAGCACGTGAAC Y 2 1 2 1 201000 f 74 goat snp39847-scaffold509-4687601 28 15331798 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784725 Affx-122924411 AX-385271773 28 28120011 AGGAAAAGGAAAACTACACTGAAAAACTGAAAATG[C/T]ACAAGACTAGGAAATCTGTAAATAGTATAGAGGTT Y 2 1 2 1 201000 f 74 goat snp39846-scaffold509-4653628 28 15297761 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427482 Affx-122940012 AX-123297825 28 28154025 ACAAGTGATCTGTAAGAACCTACGGTGAGACGATC[A/G]TTCCTTTTGGTTATATTTTGTCTTGAAGTGATCCT R 2 1 2 1 101000 f 74 goat snp39845-scaffold509-4619614 28 15264096 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441105 Affx-122928886 AX-123311442 28 28202216 TAGTGTTTTTTCTTATAAGAGTGTAGCAATAAATC[A/G]ATAAGTATTTATTAATTTGATAATTTGCAGAGTAG R 2 1 2 1 101000 f 74 goat snp39844-scaffold509-4571423 28 15215712 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416106 Affx-122948311 AX-123286455 28 28232113 TAAATTCTATAGTTCAGTTACTAACACTGTACTAA[C/T]GTTGACTTCCAGGTTTTGATCATTATACCTTGGTT Y 2 1 2 1 101000 r 74 goat snp39843-scaffold509-4541526 28 15185576 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798872 Affx-122946392 AX-385285802 28 28285906 GCTAGGAAAGCTTTGCAGAAATTGGTTGCTGATTG[C/T]ACTTTGATAATTAAATACACAAACCTATGATCCTT Y 2 1 2 1 101000 f 74 goat snp39842-scaffold509-4487733 28 15126033 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430114 Affx-122937514 AX-123300455 28 28322888 AGGGCCACTCCCACTTTTGGTCATGTCATGGACCT[G/T]AGGTCCATGCTCGGGCTGCTGAGGCACAGTGTACC K 2 1 2 1 202000 r 74 goat snp39841-scaffold509-4450751 28 15089255 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451011 Affx-122921714 AX-123321345 28 28385416 CTCGGTACAGGGCTGTCCTTTAGCTTAGTTTCCTC[A/G]TCTATATAACAGGAATAATAAAAGTATCTACCTCA R 2 1 2 1 201000 r 74 goat snp39840-scaffold509-4388223 28 15026809 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440170 Affx-122930722 AX-123310507 28 28414125 CGGGCAAGCCATAGATTACATAATTATCAAGTAAA[C/T]CTCAAAACCACCCTGTAAGGTAGCATTGTTGCCCA Y 2 1 2 1 101000 f 74 goat snp39839-scaffold509-4359514 28 14997859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432727 Affx-122935466 AX-123303068 28 28455684 TGACCACCCAGAGTACTTGCAGCGAGTGACGACCA[C/T]GTGACTCAGCTCAAGGCAATGAAATATAAGTACAG Y 2 1 2 1 201000 r 74 goat snp39838-scaffold509-4317955 28 14956522 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419521 Affx-122945440 AX-123289869 28 28489095 ATTTGAATTGATCTGCTAGCACTTGTAACCTTTAG[A/C]TTGTTTCATTTAAGACAAAGGTAACCAGTTAATTC M 2 1 2 1 101000 f 74 goat snp39837-scaffold509-4284544 28 14923246 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785941 Affx-122970761 AX-385272978 28 28544036 TGCTTGCTGTTCATCATGTTTAAATATGAATGCCA[G/T]ATACAATCTCCCAAAGTGGTAATATTTAAGGACTT K 2 1 2 1 101000 r 74 goat snp39836-scaffold509-4229603 28 14868625 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394409 Affx-122964611 AX-123264764 28 28576855 CCCCACTGAGCACGTGCATACCAAGCCCGCTGGAC[A/G]TTCACAGAGACCACCTCTGTGCTGTGCTAGCAAAG R 2 1 2 1 102000 r 74 goat snp39835-scaffold509-4196784 28 14835908 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427159 Affx-122939626 AX-123297502 28 28605741 TCTCTGTCCATGTTCCAAGGCCACCTACTTTAAGA[C/T]GACTTTACTCTTTGTTAATGAAAAATCTTGCCTAG Y 2 1 2 1 201000 r 74 goat snp39834-scaffold509-4167898 28 14807250 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447148 Affx-122924445 AX-123317484 28 28664499 CTTCCATACAGTAAAAGGCATCTGTGTACCCACCT[A/G]TCCCAGTTCTGTTAACTGCCAGCTACAAGCATCCT R 2 1 2 1 101000 f 74 goat snp39833-scaffold509-4109140 28 14748229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783761 Affx-122936192 AX-385270817 28 28708973 AAATCAACCAGACTCCCACTGTAATTAACTGCAGA[C/T]GCCAATAATGGGTGGTCAAAGCATGGCTATACTCA Y 2 1 2 1 101000 f 74 goat snp39832-scaffold509-4064666 28 14703744 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273159 Affx-1111833344 AX-519546820 28 28722765 TACTTTGACTAAATCTATCGATTGATCGATGAATC[A/G]ATCGGTGGATAAGGGCTTCCCAGGTAGCACTGGTG R 2 1 2 1 201000 f 74 goat 28_28722765_AF-PAKI 28 28722765 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38420883 Affx-122944623 AX-123291230 28 28745448 GCTCTGAAAGTCACCTCTGCTCAAATGCTGCCAAG[G/T]TTCCATATCCTCCTAAACCAGGAAAAAAGGATAAT K 2 1 2 1 101000 r 74 goat snp39831-scaffold509-4028191 28 14666901 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418529 Affx-122946415 AX-123288877 28 28796470 AAGCTTCTCTATGCTAACAAATGCAGAAGGAATAA[C/T]GACAGCTTTCGCAGCCCCTTACAAATGTATGAATA Y 2 1 2 1 101000 r 74 goat snp39830-scaffold509-3977169 28 14616067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394413 Affx-122964608 AX-123264768 28 28865844 CATCAACAATGTTTTTCTTTCTATCTCTCAGCTCT[A/G]CTTTCCTTGAAATTCTTCCTGGGCACAGTCTAGTT R 2 1 2 1 201000 r 74 goat snp39829-scaffold509-3907795 28 14547581 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800879 Affx-122974144 AX-385287794 28 28922723 GGCGAGGCTGTAGACATTCAGTCAGACTGCTTAGT[A/G]CTGAGGTCCTCACCAGTATCACCCGAGAAGCCCAT R 2 1 2 1 101000 f 74 goat snp39828-scaffold509-3850916 28 14492510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801268 Affx-122952632 AX-385288180 28 28969709 CCCATTTTTAGAAGGCAAACGGGGAGACATGTGCA[C/T]GGACACACAAATATACTCTCTGTGCTCAGGCAACT Y 2 1 2 1 101000 r 74 goat snp39827-scaffold509-3803930 28 14446286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408376 Affx-122953725 AX-123278727 28 29033202 GTTCCTGGGATGCCTTTGTGTCTTCTCACATTAAC[G/T]CGTACATCTCAAGTATTCAACAAATGTTGGATGAA K 2 1 2 1 101000 f 74 goat snp39826-scaffold509-3740437 28 14383243 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411741 Affx-122951512 AX-123282091 28 29081817 CTATAAGAATTCTCTCTCTTCAGGCGATACTGCCA[C/T]TTCCAGATTAGCAGAAATAATCAAATAAATGTGCT Y 2 1 2 1 101000 f 74 goat snp39825-scaffold509-3691822 28 14334635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800365 Affx-122934311 AX-385287287 28 29112880 TTCTCCCAAAGGCACTGTATGGGTTACCTGAATAA[C/T]GTCATGTTCAGAAAACCAAAGGGAGCCAAGCACCA Y 2 1 2 1 101000 f 74 goat snp39824-scaffold509-3660759 28 14303589 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419675 Affx-122945939 AX-123290023 28 29161710 GTAATTCTTAACATTTTCCAAAAGTGTTAGAAAAA[C/T]AACCAAAAATGCTTAGATTACTCTAGGTTACTCAA Y 2 1 2 1 202000 f 74 goat snp39823-scaffold509-3611929 28 14254767 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380025 Affx-122975590 AX-123250383 28 29194327 TTTCTTTCACTGGCTGGTAGTTTTGGGGAGGAGAG[C/T]AGACAAAGCACAAGCTGGAATCAAGACTGCCAGGA Y 2 1 2 1 101000 f 74 goat snp39822-scaffold509-3579312 28 14222073 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791766 Affx-122936533 AX-385278757 28 29224277 ACCAGGATTAATACGTGACATAATCTCCAAGCGGT[G/T]AGTCAGCTCTGAGCTCCTATTATTCCAAAACGATG K 2 1 2 1 101000 r 74 goat snp39821-scaffold509-3549362 28 14192179 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381112 Affx-122974582 AX-123251470 28 29324900 ATAATATCATTTGATCAAAATCAATCTTTCCCTGG[C/T]GGCTCAGTGGTAAAGAATTTGCTTGCTAATACAGC Y 2 1 2 1 201000 f 74 goat snp39819-scaffold509-3448739 28 14090604 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431313 Affx-122937079 AX-123301654 28 29390381 GCAAAGGTTTCTGAGCAGTGGGACAGCTTAAACTG[C/T]ATCATTTCATGTAGGCTGAGCATCTGATGCACTGG Y 2 1 2 1 201000 r 74 goat snp39817-scaffold509-3383258 28 14024873 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395142 Affx-122964127 AX-123265497 28 29419267 ATACTCTGATCAGCAGACAGAAAACAGCTTAATTA[A/G]CTCATTTGATTACAGGATAATATTGAGGCCAAAGG R 2 1 2 1 101000 r 74 goat snp39816-scaffold509-3354372 28 13994362 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272420 Affx-1111834682 AX-519546146 28 29432345 GCAAAGTAAAATTTGTGCTGCAAGTTGCCATCTGT[A/G]TTCAAATT R 2 1 2 1 101000 f 74 goat GoatD01.045783 28 29432345 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38401479 Affx-122958958 AX-123271832 28 29452340 GTGCTGCTTACATCCGGGCTGTCTGGTGCGCTGCT[A/G]TATGGGAGAACCCCCAGGATGGATTTCCAAAACAC R 2 1 2 1 101000 r 74 goat snp39815-scaffold509-3321299 28 13961482 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403630 Affx-122957540 AX-123273982 28 29485089 AAAGAAGAAGCTAGTACATTCCCATCAAGATACAC[A/G]CACATACATATTTTACAAAAAATAAAAACAAAAAC R 2 1 2 1 101000 f 74 goat snp39814-scaffold509-3288550 28 13928659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443017 Affx-122928170 AX-123313354 28 29532779 TTTTTTTTTAAATTTCCATGTTGGCTCATTATTCA[C/T]ACTTATACACATACATCCTATATTCTCTATCTCCT Y 2 1 2 1 101000 r 74 goat snp39813-scaffold509-3240860 28 13881037 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427553 Affx-122939493 AX-123297896 28 29588447 TTTGGGGGTAGTCCATCATTAAAACCTGGGAATAG[C/T]GTGGATGCAAACTGGGATTGGCCTCCTCTATGATC Y 2 1 2 1 101000 f 74 goat snp39812-scaffold509-3185192 28 13825501 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387294 Affx-122970527 AX-123257652 28 29617974 TATTGAGAACAATAACATATTTGTGCTTTTATAGG[C/T]AGAATGATTGGTATTATGCAAAGATTTGGCGAACA Y 2 1 2 1 101000 r 74 goat snp39811-scaffold509-3155665 28 13796014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425623 Affx-122940904 AX-123295969 28 29656969 TTGCAAGAACCAGAATTTAATAAAAGTGGCTCAAA[C/T]GAAGAAACATTAAAGAAAGGACGCTTGAAAGCACA Y 2 1 2 1 101000 f 74 goat snp39810-scaffold509-3116670 28 13756999 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413760 Affx-122949937 AX-123284109 28 29691718 ACAATTAGTATGTTAATTACAGATGATCTTTAGTC[A/G]TCAAAAGAGGTCCTCAACCTTGGGGCCACTCGCTG R 2 1 2 1 201000 f 74 goat snp39809-scaffold509-3081921 28 13722247 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390460 Affx-122967612 AX-123260817 28 29727174 TCAGCATTAATTCTTTCTTGTTTGGGTCATTAGTA[C/T]ACATACTGGAAAGCTGAAAAGGAGAAACCTCGTGG Y 2 1 2 1 201000 f 74 goat snp39808-scaffold509-3046465 28 13686142 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393210 Affx-122965498 AX-123263567 28 29769458 TGTGTTCTTGTCAATGGAGTCAACTGTTAGTCACA[C/T]TGATGAAGCAGGGGAAGCAGGGAGAAAACCAAGAA Y 2 1 2 1 201000 f 74 goat snp39807-scaffold509-3004181 28 13644092 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770157 Affx-122963564 AX-385257324 28 29800079 CAGCTTAGATCTTCTTTCAATATTTCGCCCTTCAA[C/T]AGATACATCTCACCCCATCTGAGCGATCCTTTCAT Y 2 1 2 1 101000 r 74 goat snp39806-scaffold509-2973560 28 13613760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789131 Affx-122960477 AX-385276144 28 29833998 TTTCTTAATGTTTCATCAAAATTACCTTTATGATC[A/G]TCTCAGCAATCCCATGAGGAACAAAAGGCAAGCAT R 2 1 2 1 101000 r 74 goat snp39805-scaffold509-2939641 28 13579633 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436653 Affx-122932480 AX-123306991 28 29889627 TATGGACATTCCCTAGGAGGTTCTTACATAGGCTT[A/G]AGAGGAACATATCTATAAGGAAGGCTTCCTGAAAA R 2 1 2 1 101000 f 74 goat snp39804-scaffold509-2884012 28 13523678 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418968 Affx-122946077 AX-123289316 28 29931763 ATGACCATTAAAGATTAGACTCTATGAAAGAGAGG[A/G]GAGTCATGAGACTCAGGAGCTAGGCTGATCCAAAG R 2 1 2 1 101000 f 74 goat snp39803-scaffold509-2841876 28 13481503 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778123 Affx-122949305 AX-385265238 28 29967012 CTGTCCTCACACTCATCCAGAAGGTGTGAGACCAA[C/T]AGTCTGGAGAAGTAAATAATCCTTCCTTCTCTGGA Y 2 1 2 1 101000 f 74 goat snp39802-scaffold509-2806627 28 13446388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277784 Affx-1111836087 AX-519551283 28 29982170 CTGGACGTAGGACTTCGCTTTGTTTGGTATCTCGT[A/G]TGAGCTGAATTTTTGGTGAATGTTTTGCATCTGTT R 2 1 2 1 101000 f 74 goat Random2.2K-2277 28 29982170 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38388652 Affx-122969110 AX-123259010 28 30013993 GCCCCCTTGCCTTTAAATATTTTCTTAAAGGAAAC[A/G]TTTCGTTTCACTTTGAAATAATTTCATCCCCATTC R 2 1 2 1 303000 f 74 goat snp39801-scaffold509-2759646 28 13400867 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401020 Affx-122959677 AX-123271373 28 30049421 TGAAATTAAAAATAATATATCAAAAGGATTGGTTA[C/T]GTTTGTAGTTTTCAACTTTAGGAAGTGACTTTCCA Y 2 1 2 1 101000 r 74 goat snp39800-scaffold509-2724218 28 13365603 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388036 Affx-122969549 AX-123258394 28 30079629 GAAAGGATCTCAGGATACTTCTGAACCGCAGAGTT[C/T]GATACACACTCCTAGACATTGGCAGGTGGAGGAAC Y 2 1 2 1 101000 f 74 goat snp39799-scaffold509-2694010 28 13335580 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422877 Affx-122943076 AX-123293223 28 30136407 TTATTCACTTATAGGGATGATGTAAATATGTTAAA[C/T]AGGAGGCAATAAAAATCCAGGATGTTTTCAGTCTG Y 2 1 2 1 201000 f 74 goat snp39798-scaffold509-2637232 28 13278848 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801112 Affx-122920002 AX-385288026 28 30182541 GATTTCTGTTCACTCGGGTTAATTTCAGGAGAGGA[C/T]ATTAGCAGAATGGAAGTGAGATGGTAATAGAACAT Y 2 1 2 1 101000 f 74 goat snp39797-scaffold509-2591098 28 13232559 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797452 Affx-122948100 AX-385284391 28 30217540 CAGTATGAAAAGGCATAGAGAATAAGTACTACAAA[C/T]GTTTTCTGTGAAGAGAATCTACTGGGCATTGGTGC Y 2 1 2 1 101000 r 74 goat snp39796-scaffold509-2556099 28 13197261 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788585 Affx-122977552 AX-385275602 28 30304760 CCAAAATATGATACAAGAGTTTAAGACTGGTGAGT[A/G]TTGCAAGATAAGGATCTTCAAGCAAGTGTTCTAAG R 2 1 2 1 201000 r 74 goat snp39795-scaffold509-2468879 28 13109386 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396928 Affx-122963196 AX-123267283 28 30334301 CAGAGATGAGACTAGAACAAAGAAACTAGAGGTCA[C/T]GCAAATCTAGGAACAAAGCAAGTTCAGCTGTAGTG Y 2 1 2 1 101000 f 74 goat snp39794-scaffold509-2439338 28 13079904 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378521 Affx-122976635 AX-123248880 28 30393706 TTCTTTGCTTTTCCTAAAAGCCACTAAAATGAGGC[A/G]TATGATTCTCAAGTTAGAATGCACTGTTTGCCCCA R 2 1 2 1 101000 r 74 goat snp39793-scaffold509-2379933 28 13020884 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793985 Affx-122957595 AX-385280954 28 30435173 TGCTATAATGAATTAAGAAGCTCTCTTTCGTGAGA[C/T]TGGACACCAGTCTTTCAACATACTAAAAAAATCTT Y 2 1 2 1 101000 f 74 goat snp39792-scaffold509-2338466 28 12979452 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443398 Affx-122927389 AX-123313735 28 30468974 TAGCCCTCTATGAGGACACAGAGCATGTGGGGGTC[A/G]TGCCCCATTCCTTCAATCCTAACCCTTATATTTTA R 2 1 2 1 201000 r 74 goat snp39791-scaffold509-2304665 28 12946193 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383151 Affx-122973239 AX-123253509 28 30530340 TTATCTGCAGAACATCTTGAAAAATGGCTTGAGGA[C/T]ATGGACAGCTTTCCTTCCTGCCAAGCTGCCTACTG Y 2 1 2 1 101000 f 74 goat snp39790-scaffold509-2243299 28 12884866 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427460 Affx-122940028 AX-123297803 28 30560192 CAGAAAATGCCTGGACTTGACTTGATGCTGGATGC[A/G]CATAAGAAACACACAGTTTATGTTTTATATTCCTG R 2 1 2 1 201000 r 74 goat snp39789-scaffold509-2213447 28 12854797 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443119 Affx-122928090 AX-123313456 28 30621837 GCTAAAATTAGTTTATCCCAAGAAAGAGTTGTTCA[C/T]AGGACTTGACAGAACTTTAAAAACCAAAGAAGTCA Y 2 1 2 1 201000 f 74 goat snp39788-scaffold509-2151802 28 12793053 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434715 Affx-122933935 AX-123305056 28 30650552 CCCACCCTCATCACTTTGATTTTTTAAATATTTTC[A/G]TTTATTTTAATGCTTACAATTTGAAGGATACGAAC R 2 1 2 1 202000 r 74 goat snp39787-scaffold509-2123087 28 12764308 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395963 Affx-122963562 AX-123266318 28 30681426 TTTTTCCCTTGTTCTGCCTGTTTGGTTTTCCTCTC[A/G]TTGCACACAGCCCTTTTACTTCAGTGAAGAGTCTC R 2 1 2 1 201000 r 74 goat snp39786-scaffold509-2092213 28 12733428 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436286 Affx-122932529 AX-123306625 28 30725240 CCAGATCCTTTCCCTGCACTGCCCATGCATGTCAC[A/G]TGCTTCCCCGCCAGGCCCGGACCTGAATGTAGTAA R 2 1 2 1 201000 r 74 goat snp39785-scaffold509-2048399 28 12689910 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444523 Affx-122926495 AX-123314860 28 30788229 CGTGACACAAGTTAGGAGTTTGTGGGAACTCATGC[A/G]TTTACATGACCTTCATTTTGCTGAGAAAGATGTGG R 2 1 2 1 201000 r 74 goat snp39784-scaffold509-1985410 28 12627196 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422154 Affx-122943535 AX-123292501 28 30825208 AAGGAGGAGGAGGCCTTGTCCAGACAGCCCTGGAT[A/G]CACCTGCTTTCTGATTGCCTGACCAACTCCTGGAC R 2 1 2 1 201000 r 74 goat snp39783-scaffold509-1948431 28 12590334 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424335 Affx-122941946 AX-123294681 28 30856107 CAATTTCTTATTATCCAGGCCAGCAGAGGGGAGCC[A/G]GTGATTCCCCAAGTAATTTATGTTAGCTCTGGTAT R 2 1 2 1 201000 r 74 goat snp39782-scaffold509-1917532 28 12559605 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407705 Affx-122954569 AX-123278056 28 30891769 GCTAAAAAGCAGCGAGAGAGAAGGGTAAGAGCACG[C/T]GGGCATGCTATCTTATCCTGGGAGCTGCAGCAAGA Y 2 1 2 1 201000 f 74 goat snp39781-scaffold509-1881870 28 12524291 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395194 Affx-122964507 AX-123265549 28 30927250 GTTGAGTGAAGTTCCTATTCAAATATTTTCCCCAT[C/T]TCTAATTGGTTTGTTATTATTGAGGGGTTTTCCCA Y 2 1 2 1 103000 f 74 goat snp39780-scaffold509-1846389 28 12489349 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476386 Affx-1251763897 AX-586011795 28 30936180 TCAGTTGTTACACAGAGTACAATTAAGAGCAAACA[-/CGCAGAGGGGAGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAAATAAAAAAATTAAAAAAAAAAAAAGAGCAAACACG]CATACTGAGATATAAGATGAGAAAGTGACTAACCA - 4 1 4 1 20000 f 74 goat SV_212 28 30936180 - deletion junction SV-TF-chip 539476642 Affx-1251763897 AX-586012023 28 30936180 TCAGTTGTTACACAGAGTACAATTAAGAGCAAACA[-/CGCAGAGGGGAGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAAATAAAAAAATTAAAAAAAAAAAAAGAGCAAACACG]CATACTGAGATATAAGATGAGAAAGTGACTAACCA - 4 1 4 1 20000 r 74 goat SV_212 28 30936180 - deletion junction SV-TF-chip 562165386 Affx-1251763897 AX-606940797 28 30936180 TCAGTTGTTACACAGAGTACAATTAAGAGCAAACA[-/CGCAGAGGGGAGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAAATAAAAAAATTAAAAAAAAAAAAAGAGCAAACACG]CATACTGAGATATAAGATGAGAAAGTGACTAACCA - 8 1 4 1 20100 r 74 goat SV_212 28 30936180 - deletion junction SV-TF-chip 562165440 Affx-1251763897 AX-606940851 28 30936180 TCAGTTGTTACACAGAGTACAATTAAGAGCAAACA[-/CGCAGAGGGGAGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAAATAAAAAAATTAAAAAAAAAAAAAGAGCAAACACG]CATACTGAGATATAAGATGAGAAAGTGACTAACCA - 8 1 4 1 20100 f 74 goat SV_212 28 30936180 - deletion junction SV-TF-chip 562165845 Affx-1251763897 AX-606941254 28 30936180 TCAGTTGTTACACAGAGTACAATTAAGAGCAAACA[-/CGCAGAGGGGAGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAAATAAAAAAATTAAAAAAAAAAAAAGAGCAAACACG]CATACTGAGATATAAGATGAGAAAGTGACTAACCA - 8 1 4 1 20100 r 74 goat SV_212 28 30936180 - deletion junction SV-TF-chip 562166431 Affx-1251763897 AX-606941839 28 30936180 TCAGTTGTTACACAGAGTACAATTAAGAGCAAACA[-/CGCAGAGGGGAGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAAATAAAAAAATTAAAAAAAAAAAAAGAGCAAACACG]CATACTGAGATATAAGATGAGAAAGTGACTAACCA - 8 1 4 1 20100 r 74 goat SV_212 28 30936180 - deletion junction SV-TF-chip 562166435 Affx-1251763897 AX-606941843 28 30936180 TCAGTTGTTACACAGAGTACAATTAAGAGCAAACA[-/CGCAGAGGGGAGGAGGGAAAGATGGCGGAGGAATAGGACGAAAAAATAAAAAAATTAAAAAAAAAAAAAGAGCAAACACG]CATACTGAGATATAAGATGAGAAAGTGACTAACCA - 8 1 4 1 20100 f 74 goat SV_212 28 30936180 - deletion junction SV-TF-chip 38437551 Affx-122931898 AX-123307889 28 30958811 GGGCTTTGTTGGTGTTTTGGGGGCTTCATGATGTT[A/G]GAGAGGAGGTCCCTGCTGACCTTGAGTTCTTCCTT R 2 1 2 1 101000 f 74 goat snp39779-scaffold509-1814828 28 12457794 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425937 Affx-122941193 AX-123296283 28 31014523 TGTCACACTTTGCACACTTGTGCCGTATCTCTTAA[C/T]AGGATGAATGTGTTAGCTGATGAGTGATGAGAGGC Y 2 1 2 1 101000 f 74 goat snp39778-scaffold509-1759116 28 12402097 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803736 Affx-986696488 AX-385290495 28 31014982 GTCTACTTACTTGCCCTTGCTTTTAAGACCAGCGC[A/G]AAAGGGAGCCTAAGGAGGGGCACCCTTAGATATTC R 2 1 2 1 600010 f 74 goat 28_31014982 28 31014982 Ancestral_priority_1043 ancestry 0.456 neutral IMAGE 10K 10K ancestral 38420659 Affx-122944822 AX-123291006 28 31060902 AAGGCAGTATTTATATTTTACTATTATAAATACAC[A/G]TAAACATAGTTAGGGGAAGGACCTTGTCTCTGGTT R 2 1 2 1 103000 r 74 goat snp39777-scaffold509-1712737 28 12355770 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767010 Affx-122961863 AX-385254304 28 31115844 CTGCCATAACAGAGAACTCTTGGACCCTGGTGTCC[A/G]TCAGTCTGAGAACATCATTTTTATGGTCTCATTTA R 2 1 2 1 101000 f 74 goat snp39776-scaffold509-1657795 28 12301051 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410838 Affx-122952624 AX-123281188 28 31145142 AGCAGAAGGGCGGACCCAGCAGCCCTCTTTCTGCC[A/G]CTGAGTCTCGTTCGATAGTGTGTGAAGTTAAAGGC R 2 1 2 1 101000 r 74 goat snp39775-scaffold509-1628497 28 12271729 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789771 Affx-122956031 AX-385276779 28 31185012 TGATGAAAGGACTAATTATAAAGAGCTCCCTCCTA[G/T]AAAGGCCAGTGGAACAATTTGGGAACAATTACACG K 2 1 2 1 101000 r 74 goat snp39774-scaffold509-1588627 28 12232586 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378659 Affx-122977091 AX-123249018 28 31257329 GGTGGTGAGAACTGCTTGGCAGGGGAGAGGGGTTC[C/T]TGTGAGTTGGGTGGATTTTGGTCAAAGACACTCCT Y 2 1 2 1 101000 r 74 goat snp39772-scaffold509-1516310 28 12159158 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775456 Affx-122936804 AX-385262587 28 31291813 TCCTTCCTACCTTTTGCTTATCGTTTTCATTTTAT[A/G]CATATTTTTAAAGCCAGCAGTGTTATTGATTTACG R 2 1 2 1 201000 r 74 goat snp39771-scaffold509-1481826 28 12124628 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796859 Affx-122929895 AX-385283802 28 31330498 GAAAGCAGTTTGAGATATGTGACAAAGTAGAGTTG[G/T]CCCTCTATATCCTTGAGTTTCACATCTGAAGATTC K 2 1 2 1 101000 r 74 goat snp39770-scaffold509-1443141 28 12086172 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415099 Affx-122949448 AX-123285448 28 31364377 GCGCTTCACATTGCCAGTGAGCCACTCTAGGCTTG[G/T]CACTCATATCCCCCACGCTCTACGGGGTGACTGTG K 2 1 2 1 101000 f 74 goat snp39769-scaffold509-1409262 28 12052722 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421533 Affx-122943876 AX-123291880 28 31408908 CAGAGAAAGGGCCCCTGTCCTCACCTGTCCTCTGA[A/C]TAGAAGTGAAATAGACGTCTTTCTGCTGGAGCCCA M 2 1 2 1 101000 r 74 goat snp39768-scaffold509-1364731 28 12008208 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447585 Affx-122924016 AX-123317921 28 31439187 AGCAGCCAACTCATGAGCTTTGTGCTCTCCAGGAC[C/T]GAGGCCCTGCTGCCCCCACCATGCTGGCTGTTGGA Y 2 1 2 1 101000 f 74 goat snp39767-scaffold509-1334452 28 11977898 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388394 Affx-122969300 AX-123258752 28 31530785 TCACTGTCTCTTTACTTCTGAGCTGAAAGCAGGGG[C/T]GAGTACCACTCCTTTGGAAGGTAGAAGGGGAGCAA Y 2 1 2 1 101000 f 74 goat snp39765-scaffold509-1242854 28 11887538 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388126 Affx-122969481 AX-123258484 28 31571867 ACGTGCCTCAGAGTTATCCCATTAGGAGTGAGGGA[A/G]CTGGGGTATTTATACCCCAACTGTGGCCAGTCACT R 2 1 2 1 202000 r 74 goat snp39764-scaffold509-1201772 28 11846717 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452298 Affx-122920683 AX-123322631 28 31611571 AGCCAGGTGCCACCCTCCCTGGGCATATCTGTATC[A/G]TGCTGTGTCATCACCAGCAACCTCAGTATCTCTCT R 2 1 2 1 101000 r 74 goat snp39763-scaffold509-1162068 28 11806742 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401853 Affx-122959426 AX-123272206 28 31642501 GGGAGGTGAAGGTAAGGCAATGAGGAGGTGAGACA[C/T]GGAGGAAGGCAGTAATGACAGGGGTGTTTTCAAAC Y 2 1 2 1 101000 f 74 goat snp39762-scaffold509-1131138 28 11775851 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447506 Affx-122924075 AX-123317842 28 31671985 TTGACGCTTGCCCTATAAGACATGGCCTCATGCCC[A/G]GGAGGCCTGTGGATCGAGCTGGTCTCAGCAGACCT R 2 1 2 1 101000 f 74 goat snp39761-scaffold509-1101654 28 11746431 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389063 Affx-122968603 AX-123259421 28 31715592 TCTCCGGGCCTCAAAGCACCTGCCTTGAAGTCAAG[A/G]GCTGTCTTTGGAATGAGCCAATCAGACTGTAAAAG R 2 1 2 1 101000 r 74 goat snp39760-scaffold509-1058047 28 11706455 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404229 Affx-122957650 AX-123274581 28 31773865 AAAAAACTCCCCTGATGGTGAGATGCTACCTGTTG[A/C]GTGATGGTGGACATACTGTGTGCTATTGAATTTTT M 2 1 2 1 201000 r 74 goat snp39759-scaffold509-999774 28 11647748 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379114 Affx-122976750 AX-123249473 28 31819174 AATTTCCTGAGGGGCTGGTGCCGAGAGAAGCAAAA[C/T]GGATGCTCAGGAGGGACAAGACGCACTTCATAAAT Y 2 1 2 1 101000 r 74 goat snp39758-scaffold509-954465 28 11602409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382931 Affx-122973386 AX-123253289 28 31848828 TGGAGCCAGTGAAGCAGAGAAGGAAGGGAGGAGAC[A/G]GTTGGGAGTGAGCACTGGGCCGTGTCCTAAAGTGC R 2 1 2 1 201000 r 74 goat snp39757-scaffold509-924811 28 11572881 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787852 Affx-122972911 AX-385274875 28 31891271 TGAAAAGATTATGTTTCTTCCATACATAATGTAAC[A/G]TGAAGTTAATTCTAGTCTGTGAAGTACATGCAAGG R 2 1 2 1 101000 r 74 goat snp39756-scaffold509-882368 28 11530558 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377575 Affx-122977437 AX-123247934 28 31935000 TGTAGGGGTGATGAGAACCTGCCCAAGACAATGGT[C/T]GCAAGCTCAGGGTCATTGCTGAAAGGTCTAGAGAG Y 2 1 2 1 201000 r 74 goat snp39755-scaffold509-838639 28 11486711 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786279 Affx-122971520 AX-385273314 28 31969906 ATCTGGAGAAAGTGATGCTGTAACCAGTTCTGGGC[A/G]TAGCCCTTAACTGGTCTTGCAGCTTCCTCTTCCTA R 2 1 2 1 101000 f 74 goat snp39754-scaffold509-803733 28 11451884 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453714 Affx-122919634 AX-123324047 28 32000970 ATGAGACAGTACAAGAAAACTGTTTTGGATCCTTC[A/G]TAGAACATTGGCTCCCGAAACAAAGTGCCCACATG R 2 1 2 1 201000 r 74 goat snp39753-scaffold509-772669 28 11420341 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391367 Affx-122967282 AX-123261724 28 32031051 TTTAAATCCAAACATGAGGAGTTCTCCAAGCTCTG[C/T]GGTCTTGTGCCTGCCACATTCAGATGGACTTGAGA Y 2 1 2 1 101000 f 74 goat snp39752-scaffold509-742588 28 11390312 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390041 Affx-122968430 AX-123260398 28 32060010 CTCATGAGAATTGTCAGGCCTCCAAGTCTCAGGAC[A/G]CTCATCTCTAGATTGCAATTGTGCAACAGAGGTAA R 2 1 2 1 101000 r 74 goat snp39751-scaffold509-713629 28 11361204 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378442 Affx-122976699 AX-123248801 28 32089785 ATGCTCAGTTTCTTTATCTGTAAAATGGGGGTAAG[C/T]ATTACTACACACTTGAAGTGTTATAACAGTCTCTA Y 2 1 2 1 201000 r 74 goat snp39750-scaffold509-683854 28 11330903 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396229 Affx-122963343 AX-123266584 28 32130504 GAGTTATTTTCCAGGCTATAGACCTCAGTTTTGTG[C/T]AAGTGAAGGTACTTTCTATTCTTAGTATGGACTGT Y 2 1 2 1 201000 r 74 goat snp39749-scaffold509-643135 28 11290431 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767390 Affx-122958835 AX-385254663 28 32193616 TTTTGACCTAATGTGATTCTGTGGGGAACGATGAC[C/T]TGCCTGTTGCATAGATACTGACGGAAAGCAGGTGG Y 2 1 2 1 101000 f 74 goat snp39748-scaffold509-580023 28 11227360 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426174 Affx-122940588 AX-123296520 28 32224181 GGCCATTTTATTAATGCCCCATTCAATTTACCTGA[C/T]GCAGGTAGGGTTGGGGGAAAGCTTGGCACTGGCTG Y 2 1 2 1 103000 f 74 goat snp39747-scaffold509-549458 28 11196442 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410557 Affx-122952144 AX-123280907 28 32271643 AACCAGTCCAGGTCCAGAACCTATGTTCTAAAACA[C/T]GACAGCCTCCTCGCGGCAGAGTGCCCTTGTTTGGT Y 2 1 2 1 101000 f 74 goat snp39746-scaffold509-501996 28 11149021 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401589 Affx-122958875 AX-123271942 28 32348304 CATGCGGGCTCCCCACCTCCCTCCCCTGCCCAGGT[A/G]TAGGGGCCATGAAACCCATCCATGCTGCGAGGACA R 2 1 2 1 101000 r 74 goat snp39745-scaffold509-425335 28 11072113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378281 Affx-122976871 AX-123248640 28 32378025 GTTGGCCTCAACTTGTAGGTAAGTTGTTTGGTCGA[C/T]GCGGGATTGAAAAAAACCACCAATACTCGGAATGA Y 2 1 2 1 201000 f 74 goat snp39744-scaffold509-395614 28 11042035 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423776 Affx-122942833 AX-123294122 28 32410272 CCCAGGAAAGAACCAGACTTGGCATTGAGGAAGAC[A/G]TCCCTGTCCCAGCTCTCCAGGTATCAGCACCTGCT R 2 1 2 1 101000 f 74 goat snp39743-scaffold509-363367 28 11009847 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408098 Affx-122954713 AX-123278449 28 32442654 CCAGTCGGGGTGTTGTAAGCATTCCTGGTAAGTGG[C/T]GGTGGTGACCTGCAAGGGTAATGGGAAGCAGAGAT Y 2 1 2 1 201000 f 74 goat snp39742-scaffold509-330985 28 10977587 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765358 Affx-122932308 AX-385252875 28 32544980 CTGGCCTTGTCCAAAGGGATCATATCTATGAAACC[A/G]TTGGTTTGCTAAGCTAGTTATACATTTCTATATAC R 2 1 2 1 101000 f 74 goat snp39740-scaffold509-228659 28 10878536 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804305 Affx-986696491 AX-385290921 28 32554042 GCCCCCTGGGGGGACTATGTGGGTGCATGCTGGAA[A/G]GTGGTTTCTGGGAACCTGGGCCCCTGGAATGGCTG R 2 1 2 1 600010 r 74 goat 28_32554042 28 32554042 Ancestral_priority_1043 ancestry 0.448 neutral IMAGE 10K 10K ancestral 320764278 Affx-986698805 AX-385252004 28 32556593 TTTTTTTAAAATTACATGTACAAACTTATTTTTTC[A/T]ATGAAATAAAGTAAACTTTGATAGAAATGGAATTC W 4 1 2 1 600010 f 74 goat 28_32556593 28 32556593 Ancestral_priority_1043 ancestry 0.63 recommended IMAGE 10K 10K ancestral 320767935 Affx-986698807 AX-385255151 28 32556603 ATTACATGTACAAACTTATTTTTTCTATGAAATAA[A/G]GTAAACTTTGATAGAAATGGAATTCTATGACTTTT R 2 1 2 1 600010 r 74 goat 28_32556603 28 32556603 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320803743 Affx-986696492 AX-385290501 28 32556658 GAATTCTATGACTTTTTCAATTGTACGTGTGAGCC[A/G]CACGGAAAACATTCACTGCGTTCCATGACCCCGTC R 2 1 2 1 600010 f 74 goat 28_32556658 28 32556658 Ancestral_priority_1043 ancestry 0.636 recommended IMAGE 10K 10K ancestral 320767939 Affx-986698809 AX-385255155 28 32556665 ATGACTTTTTCAATTGTACGTGTGAGCCGCACGGA[A/G]AACATTCACTGCGTTCCATGACCCCGTCGACTGTC R 2 1 2 1 600010 r 74 goat 28_32556665 28 32556665 Ancestral_priority_1043 ancestry 0.628 recommended IMAGE 10K 10K ancestral 320767943 Affx-986698811 AX-385255159 28 32556698 GAAAACATTCACTGCGTTCCATGACCCCGTCGACT[C/G]TCTGTTGCAGAGCATCTGCATCCTATTTGACGCCA S 4 1 2 1 600010 r 74 goat 28_32556698 28 32556698 Ancestral_priority_1043 ancestry 0.696 recommended IMAGE 10K 10K ancestral 38420336 Affx-122944975 AX-123290683 28 32601220 CAAGGAGTCGGTCCTAATCGGAGGATCTCATCAGG[A/G]AGACTCTGATGAGCCAGGCTGGGGCTCCCAGAGAG R 2 1 2 1 101000 f 74 goat snp39739-scaffold509-172419 28 10824393 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777896 Affx-122955400 AX-385265012 28 32630773 TAATTCCTGTCCGTCTGTCTAACTCAGAAAGTATT[C/T]ACAAGGCCATGGCTTCAATGCATGCCTTAAAAGTA Y 2 1 2 1 101000 f 74 goat snp39738-scaffold509-142866 28 10794766 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435271 Affx-122934052 AX-123305611 28 32678624 GGGGTTCCACAGACCCGGCTTGAACTGTGCCCTGA[C/T]GCTCTCTAGCTGGGAGATTTCACACTGGCTGCTTC Y 2 1 2 1 101000 r 74 goat snp39737-scaffold509-95015 28 10747592 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782120 Affx-122953577 AX-385269198 28 32727825 CATTCGTTTATTCATCAAGTAATTATTAGGCTCCC[A/G]CTGTATACCAGGCTGTAGTCTAGGCACTGTGGATA R 2 1 2 1 101000 r 74 goat snp39736-scaffold509-45814 28 10698379 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391411 Affx-122966771 AX-123261768 28 32764316 AAGGATTCTCATCTCTCCGTTTCTCCACTCATCCC[A/G]TGAGAGGATGACAGCAGAGAGGTGTTCTGAGGTCC R 2 1 2 1 101000 f 74 goat snp39735-scaffold509-9323 28 10662444 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410266 Affx-122952524 AX-123280616 28 32790685 ACTTAGTCTGCGTGCCTGCTGTCTCCTCCCCAGCC[C/T]TCTCCCCAGGGACAGAGACCATGTCGATTCCTCTC Y 2 1 2 1 102000 r 74 goat snp39048-scaffold4955-16947 28 10636223 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411249 Affx-122952332 AX-123281599 28 32822203 AGATTATACATCCCAGCCACCACCACCCACACACA[G/T]ACACACAAGGGACCAAGCACCCTGAGACACACCCT K 2 1 2 1 202000 r 74 goat snp39049-scaffold4955-48465 28 10604775 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399404 Affx-122961244 AX-123269759 28 32839553 GTGTCCTGGTGATATGTCATTGGCGACTGATGGGA[C/T]GTTCAGACAGATGAGGACAGAGTGGAGGCATGGTT Y 2 1 2 1 101000 f 74 goat snp10920-scaffold1390-648378 28 10586645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438815 Affx-122930791 AX-123309152 28 32895118 AAGCCCCCTTTGCAAACATCTTCTCACCAGATTCT[A/G]CAAACAACCATTTTACTACCCAGAACACTGGGAAG R 2 1 2 1 201000 r 74 goat snp10919-scaffold1390-592813 28 10530955 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446512 Affx-122925032 AX-123316848 28 32931304 TTACCTACCCTCATGGCCTTGTTGAGCCTTTCAGC[A/G]AAGAAGGCTGGGGTATTCTTAAGACATTTCACTGG R 2 1 2 1 201000 f 74 goat snp10918-scaffold1390-556627 28 10494787 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426739 Affx-122939870 AX-123297085 28 32960682 GGCCTGGGCTCTTGAGTACTAGGCGATGTGACTGC[C/T]GCCAGCTACATCTTCCTCCAAAGTGAACAAGTGAG Y 2 1 2 1 101000 r 74 goat snp10917-scaffold1390-527249 28 10465544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388786 Affx-122968925 AX-123259144 28 32996916 CCTATTATTTATTACTTTTCTCCAGACTCTGTAGA[C/T]GTGCCCCTCCTGTTCTGACTCACTCAGCCATTCCT Y 2 1 2 1 201000 f 74 goat snp10916-scaffold1390-491015 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776031 Affx-122963274 AX-385263161 28 33049733 AAAATAGCAGTAAATGTTATGATTAGGAATATTTG[C/T]AATATAATTAGCAAGGTAACTACTAGCTTTTTTCA Y 2 1 2 1 201000 f 74 goat snp10915-scaffold1390-438198 28 10387339 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789935 Affx-122927894 AX-385276941 28 33085492 TTGTCCTCCATTGGTAGAAGATACAGAAAAATTCA[C/T]ATGTAATCCTTCATATTCTATGATATAACATGCAA Y 2 1 2 1 101000 f 74 goat snp10914-scaffold1390-402439 28 10350399 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771873 Affx-122954861 AX-385259029 28 33157084 TTCATTGATAGATACCCTTTGTAATATACATATAC[A/G]CACCCTGTGTGCAATTCAGCATGACATTAGGGGTA R 2 1 2 1 101000 r 74 goat snp10912-scaffold1390-330847 28 10278379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378684 Affx-122977072 AX-123249043 28 33195984 TTCAGAATTCTCTGCAGCAAAAAATGCCCCCCTTG[A/G]GCTTAATTAGATCTAGTTGTTTTTCTTATTTGCAG R 2 1 2 1 201000 r 74 goat snp10911-scaffold1390-291947 28 10238966 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379528 Affx-122976070 AX-123249886 28 33234161 GGCTCAGGGGAGGACTGTGTGCTCCTCTTACCAGA[C/T]GGGCTCTGGAACGACATCTCCTGTTCTTCCTCCTT Y 2 1 2 1 201000 f 74 goat snp10910-scaffold1390-253770 28 10200378 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420494 Affx-122944858 AX-123290841 28 33289750 TGATCCCTGAATCCTCCCACCTTTTTGCTTCCTAC[A/G]TCCAATGAGGTATCAAATCCCACTTCTGCTTTCCA R 2 1 2 1 101000 r 74 goat snp10909-scaffold1390-198181 28 10144789 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779404 Affx-122952122 AX-385266507 28 33337252 CTGGTTGCTTAGACATGGCTTTCTTACATCTTCAG[C/T]GTTATGTCTGTTATGTGGTTTCTTTTGTTTAATGC Y 2 1 2 1 101000 f 74 goat snp10908-scaffold1390-150679 28 10097930 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416926 Affx-122948045 AX-123287274 28 33366617 GGTATTTTGAAGGACTCTAGTAACAAACACTAATG[C/T]GCCCCAAGGCATGTTCTCCAGGAATAGTACCCTGC Y 2 1 2 1 101000 f 74 goat snp10907-scaffold1390-121314 28 10068049 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385576 Affx-122971840 AX-123255934 28 33396231 CACCAAACACTGAACAGCTGCTCCCGCTGTATCAG[C/T]GCAGGCCTGCCTCCTGGGCCTACGCTCTGGGTCTG Y 2 1 2 1 103000 f 74 goat snp10906-scaffold1390-91700 28 10038021 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405586 Affx-122955938 AX-123275938 28 33428632 GGGAGGGAATGATTGAGCTGGAATGAAAGAATCAG[A/C]GACACTTGGAGTGAGGAAGTCAGGGTCAAGTATGG M 2 1 2 1 101000 f 74 goat snp10905-scaffold1390-59299 28 10005420 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798094 Affx-122946726 AX-385285028 28 33462845 TCCAAAAGTTATTATAACAGAATAAAGCATTCATG[C/T]GGCAAGTAGGAGGCATTGTGTTTGTCCAAACATCA Y 2 1 2 1 101000 r 74 goat snp10904-scaffold1390-25086 28 9970999 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436648 Affx-122932483 AX-123306986 28 33516465 GACGTGCTGAGAATCCAAACAGTGAGTGGTGTGCT[A/G]CTGGGTTGGCCAAATCATTTGCACAAGGGGTCAGA R 2 1 2 1 101000 f 74 goat snp37486-scaffold4588-112729 28 9915973 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378193 Affx-122976942 AX-123248552 28 33558841 GCTGTGATACACGTGCAGCCAGATCAGCTCAGAAA[C/T]GCCAGGCAGCAGTACAGAGGGTACTCAGAGGTGAC Y 2 1 2 1 101000 f 74 goat snp37485-scaffold4588-70353 28 9873126 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277786 Affx-1111836088 AX-519551285 28 33594089 CCAAAGACTAAGAGAAGTGGGGAGAGAAGCCTGGA[A/G]CAGATACTTTCCTAGAGCCTTCAGAGGGAGGATGG R 2 1 2 1 102000 f 74 goat Random2.2K-2282 28 33594089 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38399317 Affx-122961376 AX-123269672 28 33606311 CCTGACACAGCCTGCCAAGGTCGCTGTCCTGCCCA[C/T]GTGTTCCTCCTCCCACCTCTCCTACTCATGCCCTG Y 2 1 2 1 101000 f 74 goat snp37484-scaffold4588-22883 28 9825684 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769728 Affx-122927681 AX-385256898 28 33638092 AGGAAGCCTACACAGGAGCAATGAGCAAAATGGAT[A/G]CAAGGGTGATTAAAAAGGACTTTCTTTAAAGGAAA R 2 1 2 1 101000 f 74 goat snp15934-scaffold1674-240136 28 9618616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423073 Affx-122942942 AX-123293419 28 33676677 TGCTTGCTAAAATGTAAAATGTTTTCAGAGACAGC[A/G]TTTGTTGACAACATGAAAAGAGAAGTGAACATAGA R 2 1 2 1 103000 f 74 goat snp15933-scaffold1674-201551 28 9579785 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792367 Affx-122964028 AX-385279348 28 33705510 ACTTTTGCATAAATAGGAAGGTTGGCAGCATAAGC[A/G]TGGTGAGCCTGTTGATGTAAACTCTAGAGAAAGTG R 2 1 2 1 101000 r 74 goat snp15932-scaffold1674-172718 28 9549899 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787887 Affx-122975372 AX-385274909 28 33806159 AATCGTTGTATACCTAAGTTAAAACTTAGTTGGTA[A/G]AATACCTTTCAAAATCTTGTTTTCAACCATGAGAA R 2 1 2 1 201000 r 74 goat snp15930-scaffold1674-72069 28 9447595 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443683 Affx-122927175 AX-123314020 28 33863304 TTCATTAGCGGATTGCATTTCTTTTCCATGAAAGA[C/T]AGGAGCTGGAAATCTATTACTATGCTGTGTAAATA Y 2 1 2 1 101000 r 74 goat snp15929-scaffold1674-14924 28 9389973 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273161 Affx-1111833345 AX-519546822 28 33863552 AGAAAGTGAAACCGTGGATAAGGTAGGAGTACTGC[A/G]TACTCAAAGGAAATAAAAACAGAAACTTGAGACAT R 2 1 2 1 101000 f 74 goat 28_33863552_AF-PAKI 28 33863552 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38434579 Affx-122934114 AX-123304920 28 33878825 AGGAATGATGCACATATGTTGCAGAATCTGCTCAC[A/G]GGCCAGTCCCGGGAGCTTGCTGGCTCCTAAAGGAA R 2 1 2 1 201000 f 74 goat snp44849-scaffold610-164989 28 9801627 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377634 Affx-122977873 AX-123247993 28 33911561 TATATTATGTTTATCAGATTAGAAAACATTTTCTC[A/G]TATCAGCTCATTCAATCCCCATAATGTTCTTGAAA R 2 1 2 1 101000 r 74 goat snp44848-scaffold610-132253 28 9768800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401799 Affx-122959471 AX-123272152 28 33953945 CGAGTTCTCCAATTACGATTTTTCAGTAGTAAAAA[C/T]AATTATTTCAATTTTCCAAGTCCTTTCACATATAT Y 2 1 2 1 201000 r 74 goat snp44847-scaffold610-89869 28 9725808 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423020 Affx-122943417 AX-123293366 28 33997176 AGGGGTAGAGAGTATCAGAAAGTTGAGAAAATACT[A/G]TTTATATAGAATAGTCATGACAGTCCTCACTGTTT R 2 1 2 1 103000 r 74 goat snp44846-scaffold610-46638 28 9680507 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401752 Affx-122959507 AX-123272105 28 34031050 ATACCTGGAGTTTGGAAATAAGGTTTCATGATTTG[A/G]CTCAACTGAATTATCCAATCAAGTGAAGAGTAGTC R 2 1 2 1 101000 r 74 goat snp44845-scaffold610-12764 28 9646248 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395281 Affx-122964079 AX-123265636 28 34055276 ATCATAACTCAAATCCTAATCACGGTACTACAACA[C/T]AGTGCATGTAATACCATGGTTAAAACTCAAACACA Y 2 1 2 1 101000 f 74 goat snp22555-scaffold2234-11363 28 9343476 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436105 Affx-122932672 AX-123306444 28 34135143 TCAGAAGAGGGCTTGAGATACTGATATTAAATCCC[A/G]TCATTGGTTGCATAGTGCCTTGAGCATACTGAATT R 2 1 2 1 101000 f 74 goat snp22557-scaffold2234-91230 28 9262582 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376922 Affx-122977790 AX-123247281 28 34170174 ACCATGACTTCTGAACTCATGGTTGATGTCTGAAG[C/T]AAGGACAATCTATAAGGACTGTTTCCCCTTAATCT Y 2 1 2 1 201000 r 74 goat snp22558-scaffold2234-126261 28 9227865 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773007 Affx-122968820 AX-385260151 28 34245568 AAGTCAGGCTCACAACTGTAATTTTAACCCTAGAA[C/T]GCACACGTTTTCAGAACAATTTCAGTCAATTTCAA Y 2 1 2 1 201000 r 74 goat snp22560-scaffold2234-201655 28 9151634 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422042 Affx-122943615 AX-123292389 28 34319754 AGATCGTCCTCATCCTTTTTCTTTTTTCCTGGCTT[C/T]CCTATGATCAAAAGGAAAAGCAAAGAGAGAGAAAA Y 2 1 2 1 103000 f 74 goat snp22562-scaffold2234-275841 28 9079584 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380499 Affx-122975703 AX-123250857 28 34364581 CTGGATCCCCCAATATTTCAGGCACATCAGCGACA[A/G]CAGTAATAACACATGCACAGCGAGGGATGCCTAGA R 2 1 2 1 201000 r 74 goat snp22563-scaffold2234-320668 28 9034314 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396356 Affx-122963049 AX-123266711 28 34445345 GATGCCTCGGGAGCCCCGAGGAAGGATGGCTGTAA[C/T]GTGAGGCTCTTGCCCTACTGGCCTGCCAGGTAGCT Y 2 1 2 1 102000 r 74 goat snp31318-scaffold346-17970 28 8952931 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383693 Affx-122972490 AX-123254051 28 34501420 ATTTTTTGAATTAAATTGCTAATTTACTGAAATGG[C/T]AACATACTCAGCTATTGGGTCTTGTCTTTAGTAGC Y 2 1 2 1 101000 r 74 goat snp31319-scaffold346-74045 28 8897064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774076 Affx-122919297 AX-385261214 28 34545370 AGCATCTTTAAAGGAAGGAGTAAGTTTATTCTCCA[C/T]GCATCTTTCAGTGCTTGTGAATGTCGTTCTCTTTT Y 2 1 2 1 101000 f 74 goat snp31320-scaffold346-117995 28 8853134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768482 Affx-122972703 AX-385255662 28 34575629 AGCTCACATATCTTCTCCTCTAAGTATAGTTATTG[A/C]TGAGACACTAGAATACCCTCTTCCCCTGTCAGCTG M 2 1 2 1 101000 r 74 goat snp31321-scaffold346-148254 28 8822742 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769252 Affx-122946298 AX-385256425 28 34614629 TCTATACCAAAACCTTGCTCTAGAAAACGAGAAAG[A/C]TATTTTCTACTTTAATGGAGGATATTGTCAAGATT M 2 1 2 1 101000 f 74 goat snp31322-scaffold346-187254 28 8783925 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773921 Affx-122953695 AX-385261060 28 34639885 TGAGTGACTAACATACATCCATACGTACCGGTTGA[C/T]ACTATATTCTCTTACCATCTCAAGACTGTTATCCT Y 2 1 2 1 101000 f 74 goat snp23210-scaffold232-7584 28 8756613 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443177 Affx-122927606 AX-123313514 28 34722419 TAACTATCTCCACACCTCCCTTCACTCATTATTTT[A/G]TTGATTGGTTGCTCATTTTAGATCTATAGAAATCC R 2 1 2 1 201000 r 74 goat snp23212-scaffold232-90118 28 8675616 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277788 Affx-1111836089 AX-519551287 28 34737733 CTATTTCCAAGACACATTTGAAAAATGGATCATGG[A/G]TTATAAAACTGCTGCAGTACAAGATATCACAAATC R 2 1 2 1 101000 f 74 goat Random2.2K-2284 28 34737733 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320779040 Affx-122959904 AX-385266146 28 34819324 AAAATAGACAAAAAAGTAGCAAGTGAAAAAAATGG[C/T]GAGTTACAACTATAATATTAAAACCTAAAATCTGT Y 2 1 2 1 101000 f 74 goat snp23214-scaffold232-187023 28 8578901 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793694 Affx-122946672 AX-385280666 28 34869563 TGGGCCAAGGTCTGTTTTAGACACTAGAGCCATGA[C/T]GGTGTACACAAGAGATAAACCAACTGTTCTTATGG Y 2 1 2 1 202000 r 74 goat snp23215-scaffold232-237262 28 8529966 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382160 Affx-122974035 AX-123252518 28 34901222 TTCTGACTACAGTTACCCATGAAAAGGTCCCCAAA[C/T]ATTTCTGACCTTTCAGCTTGCTAAAATAATGCACA Y 2 1 2 1 201000 r 74 goat snp23216-scaffold232-268921 28 8497973 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764302 Affx-986698829 AX-385252025 28 34920598 ATAGAAAATCAAGGCCCACATAAATGCTGCTTACA[A/G]GAAGCCCACTTCAGACCTAAACACACATATAGACT R 2 1 2 1 600010 f 74 goat 28_34920598 28 34920598 Ancestral_priority_1043 ancestry 0.686 recommended IMAGE 10K 10K ancestral 38379313 Affx-122976195 AX-123249672 28 34952804 TCTGTCTTCCAGCCTTACATTTTCTTCCCATTTTG[A/C]GTTTAATGAATTAACCACCACCATTTCCCACTGTG M 2 1 2 1 201000 r 74 goat snp23217-scaffold232-320503 28 8445974 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442080 Affx-122928371 AX-123312417 28 34993166 ATAGAAATTCTGTAAGCCTACATTTGCAACACATA[C/T]GTTGAAAGAATGATATCAAATATTTATTAAACTAT Y 2 1 2 1 101000 f 74 goat snp23218-scaffold232-360865 28 8405870 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407627 Affx-122954628 AX-123277978 28 35046350 TAGATAATGTTAAAATAAATATCTTTGACTTTTGC[A/G]TATCTCCTTGGCATTTACATTTGGATATGATTCTT R 2 1 2 1 101000 r 74 goat snp23219-scaffold232-414049 28 8352407 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38379963 Affx-122975636 AX-123250321 28 35075614 CCTTTTCAGGATGTTGAAGCAGAAGTCCCTAGAGA[C/T]GTGTGTGCATTCTGCTCTGAGCCAGCCTCCCTCTG Y 2 1 2 1 102000 f 74 goat snp23220-scaffold232-443313 28 8323080 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385911 Affx-122971575 AX-123256269 28 35143876 AGATGAGGTGAGAGAGCTGCCCCCAGCAATGTAAG[C/T]GTGCCCCAAAGCAACTGAAACCAAGTCTCAGTTAT Y 2 1 2 1 201000 r 74 goat snp23222-scaffold232-511575 28 8255523 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277790 Affx-1111836090 AX-519551289 28 35173062 TGAGAAGAGACCAGGAAGAACTCACAGAAAACCTT[A/G]CCAGGGACAGCAATTGCACTTGCCAGCGCTGTTCC R 2 1 2 1 101000 f 74 goat Random2.2K-2285 28 35173062 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320798047 Affx-122942021 AX-385284983 28 35175242 TTCCTTCAGCAGTTGCTTTATGGGTTGACACCTTA[A/C]AAACTTCATGTGAGCATTCCCTAAGGTGCCAGACC M 2 1 2 1 101000 f 74 goat snp23223-scaffold232-542941 28 8224222 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379881 Affx-122975781 AX-123250239 28 35208079 AAGACTAAAGGGCCGCGTGCTTTGGGGGAGATTCA[C/T]GATTGGCAGTTGCATCATGGTAGGTATTCCTGAGC Y 2 1 2 1 101000 r 74 goat snp23224-scaffold232-575778 28 8190865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383914 Affx-122972981 AX-123254272 28 35249490 CCAAATTAAAATGAATATGTACATCTTTGAAATAT[A/G]TCAAGGTGATCATAAGATCAGGACTTCCATTTTAT R 2 1 2 1 101000 r 74 goat snp23225-scaffold232-617189 28 8149372 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435586 Affx-122933362 AX-123305926 28 35298555 CCATCTCTTAAATTCCTGTTATAATCGAGTATACC[A/G]CCATCTCCCTCAGAGTCTCTACCCATTCACCCATT R 2 1 2 1 101000 f 74 goat snp23226-scaffold232-666254 28 8100532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440084 Affx-122929725 AX-123310421 28 35382865 CTCAAATGGTTTGTCATACCCATGTTGAAATGAAG[C/T]AGTTTTGATTTATTGCAGTTGAGGTGGAAGGGAGA Y 2 1 2 1 101000 r 74 goat snp5064-scaffold1172-4787 28 8016589 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396023 Affx-122963479 AX-123266378 28 35415165 AAAGAGAATACAAGCAGAAGGCCTTAGGCAATGAC[A/G]TTATGCCAGAAAAATGTCCCCCAAATAATAATTTT R 2 1 2 1 101000 f 74 goat snp5065-scaffold1172-37087 28 7984595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423923 Affx-122942268 AX-123294269 28 35458517 TCCCCTCTAAGAAGTGCTGAATCTGTTTTGAGTAA[C/T]GATCCTGGAAAGTTGTGTTCTTAGTAAGCACAAGT Y 2 1 2 1 101000 f 74 goat snp5066-scaffold1172-80439 28 7940396 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415171 Affx-122949009 AX-123285520 28 35491803 AGTATGCATGCTTGTTTCTGAAGATCACTTCACCA[A/G]TTTTCTGGCTTTCATTCATTTCTTTCCTTCACCTA R 2 1 2 1 101000 f 74 goat snp5067-scaffold1172-113725 28 7906778 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428490 Affx-122938778 AX-123298833 28 35520377 CTTCCATGAGGAATGGCTATAATCATGAGATACAC[A/G]AGAAAAATATATAGGTATATTAGTATGGTTTCTAC R 2 1 2 1 101000 f 74 goat snp5068-scaffold1172-142299 28 7878083 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410476 Affx-122952206 AX-123280826 28 35561042 TAACAAACTCACTCGGGAGGAACGAGTTGCCAGAC[A/G]GTGCCGAACAATGTCTCAGAGAAGACCAGGACATC R 2 1 2 1 201000 r 74 goat snp5069-scaffold1172-182964 28 7836729 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403941 Affx-122957459 AX-123274293 28 35606620 ATTGCCCCTTTTCATTTATTCAAAAATGTGGATAA[C/T]GTGATATTCTCTTAGGTTTGCTTTCTGTATTTTTT Y 2 1 2 1 201000 r 74 goat snp5070-scaffold1172-228542 28 7789262 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449573 Affx-122923230 AX-123319908 28 35681879 ATTATAGTCATAGCATTTTAGATATAAAAGAAATT[G/T]AATACTACAAATGTGTCTACTCTTCAAACCACAGT K 2 1 2 1 101000 r 74 goat snp5072-scaffold1172-303801 28 7714121 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790316 Affx-122976825 AX-385277319 28 35742732 GCTGGATATCTTCCCTAGGCTCTATCAGAGTTACA[A/G]TTCATTCATCTCTACCATCCTTTCTGCCCCAGAAG R 2 1 2 1 101000 f 74 goat snp5073-scaffold1172-364654 28 7648356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428491 Affx-122938777 AX-123298834 28 35777126 CTGTATTCCTTAATGTTCCCCTTGAGAATTACATT[A/G]TCGTTAAAAACACAGACTGAACAATTTATTCTCCT R 2 1 2 1 101000 r 74 goat snp5074-scaffold1172-399048 28 7613871 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384373 Affx-122972229 AX-123254731 28 35805751 CTCTTCCCTGTGGGGCATTCCAGCTCTAAGCAAAA[G/T]CCCTATTAAACCTCTGCCATACAAATTGCTTTTCC K 2 1 2 1 101000 r 74 goat snp5075-scaffold1172-427673 28 7584553 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795299 Affx-122974371 AX-385282257 28 35861569 TATTTGCCTTATTCTTTTAATATAATGCTTGACAA[C/T]ATTTGATATTTTATTGGGACGTAAGGTCTTGACAT Y 2 1 2 1 201000 f 74 goat snp5076-scaffold1172-483491 28 7528711 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780027 Affx-122976299 AX-385267126 28 35899448 GTCTCTACTTTCTCATTTGTGAAAGAAAGATAACA[C/T]GTGGACAACTTCCTACCAAGGAAGTTGTAAGAAAT Y 2 1 2 1 201000 f 74 goat snp5077-scaffold1172-521370 28 7488059 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422192 Affx-122943507 AX-123292538 28 35936425 ATTCAAAATAACACCAACAGTGTATTAGAGTATGT[A/C]TGCTTATGCAAAGATCAGATATAGACATATACATC M 2 1 2 1 101000 r 74 goat snp5078-scaffold1172-558347 28 7450944 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440171 Affx-122930721 AX-123310508 28 36008996 AAATTCAGGTAATAATGGCCCAATCATTTAACCTC[A/G]CTAAATGTTGTCTACCAATATAACATCAGTATGAG R 2 1 2 1 101000 f 74 goat snp5079-scaffold1172-630918 28 7377613 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389565 Affx-122968260 AX-123259923 28 36088466 TAGGGAAGGTATTCCCCCCTTAGAAACAGACCATT[A/G]CACAGAAACAGATGAGAAAAACTAGTTTATATTAT R 2 1 2 1 202000 r 74 goat snp5081-scaffold1172-710388 28 7297968 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416200 Affx-122948242 AX-123286549 28 36119106 ATACAAAGACTCTGAGGATAGAGACTGCCTGCTAA[A/G]TAGCTTCAGTCATGTTCGTCTCTGCAACCCTATGG R 2 1 2 1 101000 f 74 goat snp5082-scaffold1172-741028 28 7267205 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794774 Affx-122974167 AX-385281734 28 36151021 AAAATACCTAAGCCTCTAAAATGGTAAGTTAATTT[G/T]CCCAGGATCACCCAACAAAGTAAGTAGTAATTATA K 2 1 2 1 101000 r 74 goat snp5083-scaffold1172-772943 28 7234951 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402929 Affx-122958186 AX-123273282 28 36189862 AGCTTGGCCATAGGGCAATCTCGGACCAGAGAAAA[C/T]GAGCAGAAGCGATGGCCACCACGTGGCCCCATGAA Y 2 1 2 1 101000 f 74 goat snp5084-scaffold1172-811784 28 7196243 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416904 Affx-122948063 AX-123287252 28 36256468 TTAGGATGGTGGGGCTTACCTTGAAAAGGCAATGA[C/T]ATGAGCCTGATATAAAAATTTATTAAAATTACATT Y 2 1 2 1 101000 f 74 goat snp5085-scaffold1172-878390 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791051 Affx-122940286 AX-385278046 28 36287551 CCTCCACTGTAGTTTACCATTAATTATATCTTTTC[A/G]TTTTCCAATAAAGAAAATGGGCAATAAATAATTTT R 2 1 2 1 201000 r 74 goat snp5086-scaffold1172-909473 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423864 Affx-122942315 AX-123294210 28 36318414 GGCTGTATCTAGCAAGATTACAGATAAAATTCACC[A/G]TTTGTCAATCCAACCCACTTTTAAGTATGTAGAAC R 2 1 2 1 101000 f 74 goat snp5087-scaffold1172-940336 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273163 Affx-1111833346 AX-519546824 28 36370459 ACTTCACTAATCCTATCTTCTGCCTCCATTATTCT[A/G]CTATTTGTTCCCTCCAGAGTGTTTTTGATATCATT R 2 1 2 1 103000 f 74 goat 28_36370459_AF-PAKI 28 36370459 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320765364 Affx-122943398 AX-385252879 28 36426352 GTTTTAGGTTACCATAACTTTTCATACGTTGAACA[C/T]GAAATATCAAGAATTATAAGCCTTTTGGTTTTGTT Y 2 1 2 1 101000 f 74 goat snp5089-scaffold1172-1048274 28 6804611 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410669 Affx-122952757 AX-123281019 28 36460295 CATGTTATAGTATGTTACTGCTACAGTGAGAGGCA[A/G]CTGAGAGTAGAAAGCAACCTTTCAATCATGTCCTG R 2 1 2 1 101000 f 74 goat snp4332-scaffold1134-1355307 28 6764055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376767 Affx-122977967 AX-123247126 28 36504622 TGGGTCTTTGTTTTCCTATGGAAAATTGGGAACTT[A/G]TTTCCTTTAGCAAAAATGTTCATTCCACTCTAGGC R 2 1 2 1 102000 r 74 goat snp4331-scaffold1134-1310980 28 6720023 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439592 Affx-122930066 AX-123309929 28 36541619 CCATGAAAAATGGGATTCTGTGGAAATGAACAACT[A/G]TGTCACCTTTCTAAGATTTATCTCACAGCTTGTCC R 2 1 2 1 101000 r 74 goat snp4330-scaffold1134-1273983 28 6682971 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442854 Affx-122927679 AX-123313191 28 36610820 GACAAGAGCATGAACTGAGGCAAATGCAATGCAAG[C/T]AGGTAATTAACATGAGACCTTTTCAGAGGCAGACT Y 2 1 2 1 101000 f 74 goat snp4328-scaffold1134-1204782 28 6614203 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393599 Affx-122965373 AX-123263955 28 36675262 CCAGCTGTCTGGGACGAGACCATCTAGACACAGAC[A/G]TCTGCCCTTGGTACTTGGCATCCTGAGCTCTTCTG R 2 1 2 1 201000 f 74 goat snp4327-scaffold1134-1140340 28 6549845 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397900 Affx-122961951 AX-123268255 28 36733617 GGGGCCCCAGGTATCGGTCTTGGTCACACCTCACT[G/T]GTGGAGGTCTGTCTAGGCCCATGGGCAGGGGGCTG K 2 1 2 1 202000 r 74 goat snp4326-scaffold1134-1081985 28 6493619 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797735 Affx-122942700 AX-385284674 28 36830546 TCTCAACAGCAGCACTACTGACGTCTTGGGCTGGA[C/T]AATTCCTTGTTGTGGGTGTTATCCTGTCAATTACA Y 2 1 2 1 202000 f 74 goat snp4324-scaffold1134-985056 28 6398677 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410762 Affx-122952686 AX-123281112 28 36894154 GCCACTGCAAAGTAGGAACCCCAAAGAATAGGAGA[C/T]AATACAAGCTCACACTGCTTTGCCTTGGACATGGA Y 2 1 2 1 101000 f 74 goat snp4322-scaffold1134-921448 28 6334530 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411333 Affx-122952270 AX-123281683 28 36988495 TCTGGAACGAGATTCCCCTGTCCATCCAGGCTCCA[C/T]GGACAGGTCCTCTTTCTCTCTCAGCCCTTCATCTC Y 2 1 2 1 202000 r 74 goat snp4320-scaffold1134-827107 28 6239082 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437650 Affx-122931797 AX-123307988 28 37025254 TACAAGGGAGTGTGTGGACTTGAATTTTTACAGGC[A/G]TGGCCAGGAACCCAGGCTCACTGTCCACTTGCTGA R 2 1 2 1 101000 f 74 goat snp4319-scaffold1134-790348 28 6201770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427179 Affx-122939611 AX-123297522 28 37073994 TTAGCCCTCATATTCATTTCCCCTATTTTCTAAAC[C/T]TTATCTTCCTAATTTTTCTCAAGTCCTTTTTCACA Y 2 1 2 1 201000 r 74 goat snp4318-scaffold1134-741608 28 6153425 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383406 Affx-122973493 AX-123253764 28 37112292 TAAATGCAATCTCCACAGACTGGTATTATGATAAA[C/T]AATTGTTCAATAACTTCTAAGGAGCCCTCAGTCTT Y 2 1 2 1 101000 f 74 goat snp4317-scaffold1134-703310 28 6115276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450023 Affx-122922843 AX-123320358 28 37149064 CCTCTGAGCCCCACAGCTATATTTTGCCCGCAGGT[A/G]TTGGGGTGGGACCACCCCACTGCAGTTCTCCCTTT R 2 1 2 1 103000 f 74 goat snp4316-scaffold1134-666538 28 6078087 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379702 Affx-122975900 AX-123250060 28 37216964 AGAATTGGATTTTGCATTGTCATTTGATTGCCTAA[C/T]GGGCTAGGAAAAGATAGGTTTGATTGAATATGTGC Y 2 1 2 1 101000 r 74 goat snp4314-scaffold1134-598638 28 6010087 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444371 Affx-122926609 AX-123314708 28 37268312 TTGCTATAAGGAGTAAAGATTATGTTAGACAGCTC[A/G]TGTGTCCGGTCCTACATCCTCTCAGATCACTTGTT R 2 1 2 1 101000 f 74 goat snp4313-scaffold1134-547290 28 5958145 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423531 Affx-122942442 AX-123293877 28 37318247 CACAGATCTAAGATGGGGGATTCAGGGTGCTCATC[A/G]TCCAAAGTTTGTTACCATTAAGTGTCACTTGAGAG R 2 1 2 1 101000 r 74 goat snp4312-scaffold1134-497355 28 5904268 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377986 Affx-122977610 AX-123248345 28 37366847 GAGATCATTAGCATAATCTAAAAGAGAAATGACAA[C/T]GGCTTTGGAGCTTAATATGGAGTATAGCACTTGGA Y 2 1 2 1 101000 r 74 goat snp4311-scaffold1134-448755 28 5855207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384320 Affx-122972270 AX-123254678 28 37396541 TATTACCAGTATGGAAAGCAAACAGCTAGTATATG[C/T]ATTATCCAAACATTTTGGGAATTTGGGGATCTTGT Y 2 1 2 1 201000 f 74 goat snp4310-scaffold1134-419061 28 5825606 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396657 Affx-122962854 AX-123267012 28 37461717 TATTAATACATAATTGCACTTCTGGTACATGAGTC[A/G]TTAAACATATTGCTACATAAAATAAAAAGCCTAGA R 2 1 2 1 101000 f 74 goat snp4309-scaffold1134-353885 28 5758953 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785136 Affx-122979076 AX-385272182 28 37496080 ATCCTCTGAAATACAGAGCAGGGAAATAAGAGGAA[C/T]GGATTTTTGGTAACAAATAGACGAACTGATACAAA Y 2 1 2 1 101000 f 74 goat snp4308-scaffold1134-319522 28 5724150 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405743 Affx-122956511 AX-123276095 28 37533628 CTCAGGCATCTCCTGGGACACCAGGTCAAGTGGCA[A/G]AAGTTCATCCTCCAGCATTCTTGGTCTCCTGGACC R 2 1 2 1 101000 r 74 goat snp4307-scaffold1134-281974 28 5686558 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398932 Affx-122960996 AX-123269287 28 37570090 GAGGCTTTTGGAGTAGGTGATCACACCCCACCATG[A/G]GCACTTTTCATCTCCTCTGGGGAAAGGTGGAGCCT R 2 1 2 1 201000 f 74 goat snp4306-scaffold1134-245512 28 5649340 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434127 Affx-122934923 AX-123304468 28 37607173 ATTTACACAAAAGCCATTTGGGGCGGGGTGCTAAA[C/T]GGCCAGTGAGTATATTTAACCAGGACTGAGTAAAC Y 2 1 2 1 101000 r 74 goat snp4305-scaffold1134-208429 28 5612069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450493 Affx-122922517 AX-123320827 28 37612640 GGAAACAGCGACTTAACTGTCAAGATACGGTTCAC[A/G]TCTTGGAGCCTTTGGGAAGACCATTCCATTCACGT R 2 1 2 1 101000 f 74 goat snp3343-scaffold1102-1149 28 5604425 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442472 Affx-122927937 AX-123312809 28 37654162 ATTTGAGAGCAGAGTGTAGATGAGAATCTGGTCCC[A/G]TACTTATTTCTCCTTATAAATCTCATTTTCTGGGA R 2 1 2 1 101000 f 74 goat snp3344-scaffold1102-42671 28 5562788 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788596 Affx-122962490 AX-385275613 28 37745485 AAAAACATCATTTGAAGATTTTCAGATAGCCCTGG[A/C]GTCCAGCATAGCAATAGCTATAACATGATTCATAT M 2 1 2 1 101000 f 74 goat snp3346-scaffold1102-133994 28 5471490 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450148 Affx-122922745 AX-123320483 28 37776533 TGTAAACATTGTCATTACAAAGTATCTTAGCACTT[A/C]TACGGTACTTTTTAATTTAAAAATGTCATGGTCAA M 2 1 2 1 201000 f 74 goat snp3347-scaffold1102-165042 28 5441542 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423626 Affx-122942369 AX-123293972 28 37809910 CAGGACACAGTTTCATTTTGCTCAGCGCTACACCC[A/G]AGGGATGTTACAAGTATGCATTTTCCCTGACCTTC R 2 1 2 1 101000 f 74 goat snp3348-scaffold1102-198419 28 5408149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434133 Affx-122934918 AX-123304474 28 37839853 CACTCAATTCACAAGTGAGAAAAACAAAAGTAAAA[C/T]GTTGTTTCCAGCTGTTGAAAACCCTTTAGGCAGCC Y 2 1 2 1 103000 r 74 goat snp3349-scaffold1102-228362 28 5378154 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396434 Affx-122962989 AX-123266789 28 37883945 TTGGTGAGAATGGGCAGTTCACTGGGCACGTTTGG[C/T]GCCTGGCCAGAGAGAGACCAGATAGAAGCAGGAAA Y 2 1 2 1 201000 r 74 goat snp3350-scaffold1102-272454 28 5333210 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445034 Affx-122926621 AX-123315371 28 37913454 CCTTTACAGAATCTTCAACTCCTTTTCATAGAAAG[C/T]GTTGCATGGTACGTGGGTGAGAGCAAGGGTCTGGA Y 2 1 2 1 101000 f 74 goat snp3351-scaffold1102-301963 28 5303807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394877 Affx-122964754 AX-123265232 28 37962571 TCCTGCAGACGATGGCTCAAGATCCTTAAGGGAGA[C/T]GTCTGAGCAAACAACAAAGCAAGCTAATTAAAACG Y 2 1 2 1 101000 r 74 goat snp3352-scaffold1102-351080 28 5256038 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792832 Affx-122950303 AX-385279810 28 37998621 ATTTGGAATTGTTCTTTATCGCTATGTAATCCCCT[A/G]TAATACTGTAAGGCAAAAAGTCTAATTTGTCTAAT R 2 1 2 1 101000 f 74 goat snp3353-scaffold1102-387130 28 5219727 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277792 Affx-1111836091 AX-519551291 28 38008590 CCTCTTCGCAGAGTTTTCATGAGAAATAGCCTTTC[A/G]GAAGGTAGTCCAGCTCAGTCACTCAGTCGTGTCCG R 2 1 2 1 101000 f 74 goat Random2.2K-2286 28 38008590 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38376195 Affx-122978818 AX-123246554 28 38036199 GACGTCTAGGGAAACTTAGGAGTGTAAGATATGAT[A/G]TTCAAGGGCAAACAGGATTCCTTATCAGAAAGGTC R 2 1 2 1 201000 f 74 goat snp3354-scaffold1102-424708 28 5182122 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421036 Affx-122944532 AX-123291383 28 38094943 TTTTTTTCCAACTTTCAAGAGCTCTGTCCATACAA[A/G]GGCAAAAGAATGAGCAATTTCTTATATATGTCATG R 2 1 2 1 101000 r 74 goat snp3355-scaffold1102-483452 28 5124343 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787752 Affx-122939321 AX-385274775 28 38131810 GTAGAGAAGAAAACAGGGATGAAGTTCCCAGTAAC[A/G]TTCCATCCTTCTTGCCAGTCATCAGAGGGAAAGAT R 2 1 2 1 101000 r 74 goat snp3356-scaffold1102-520319 28 5086945 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418354 Affx-122946588 AX-123288702 28 38170644 TTAATGCAAAATCAACAGTTGAGCTGGAAGGCGAT[A/G]CAGATAGTGGTGAGGCCTGGCATGTGGAGCTAAAC R 2 1 2 1 101000 f 74 goat snp3357-scaffold1102-559153 28 5047364 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411343 Affx-122952263 AX-123281693 28 38209602 ACTCTTTAAAATCTGGCTTCTGTTGCTCAGCATAA[C/T]GTTTTTGAGATTCATCCTTGCCTCTGCAGTTAACA Y 2 1 2 1 103000 f 74 goat snp3358-scaffold1102-598111 28 5008566 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407805 Affx-122954557 AX-123278156 28 38260805 GAAGATCATGTCTGAAGCATTCTGGACTGTGTCTA[G/T]CCCACAGAGGGGCAGGTGGAGACATGAAAAAGAGC K 2 1 2 1 101000 f 74 goat snp3359-scaffold1102-649314 28 4957399 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416322 Affx-122947914 AX-123286671 28 38292149 AATTATGAATGTCCAATAATTTATTTATCCAGGCC[A/G]CTATGGTGAGAAGTACCTTGCAGCTCTTAGACATG R 2 1 2 1 101000 r 74 goat snp3360-scaffold1102-680658 28 4926024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399850 Affx-122960246 AX-123270205 28 38324697 GGATCCTGGTTCACCACACGACTTTGGGCAAGTGA[C/T]AGCATCTCCCTGCCTCAACGCCTTATCTCTGAAGT Y 2 1 2 1 101000 r 74 goat snp3361-scaffold1102-713206 28 4893514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419115 Affx-122945769 AX-123289463 28 38377459 GTACGCCTAGGTGGCCTTTCCCACAAGAGAGAGAC[A/G]TGTACTCCAGGCCAAGAGAACAGCAGGACCAAGGA R 2 1 2 1 101000 r 74 goat snp3362-scaffold1102-765968 28 4843175 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447685 Affx-122924628 AX-123318021 28 38409484 TTCCCTCTCCTGTGCTAGACTGTAAGCTCCACAAG[C/T]GCAGGAACCTTGACTCCGCTTTTCTCCTGGAGCCC Y 2 1 2 1 201000 r 74 goat snp3363-scaffold1102-797993 28 4811352 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411683 Affx-122952000 AX-123282033 28 38513840 CTGGATGTCATGCAACACGAAGCAAACAGACCTGA[C/T]GATACATCTCTCCACAAAGGCCTCACGTGGGCCAC Y 2 1 2 1 101000 f 74 goat snp3365-scaffold1102-902349 28 4707024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397088 Affx-122962711 AX-123267443 28 38551878 GAATGGGCACATGACTCGGGCTGGGCCAATCAGGA[C/T]GCTTCCACCCCTAGAAGCACTGATTGGTTCTTGAA Y 2 1 2 1 102000 f 74 goat snp3366-scaffold1102-940387 28 4669180 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784116 Affx-122937378 AX-385271168 28 38588127 GACATTTTTTTAATACTACTGTAAAAAATACTGTT[A/G]CATGGATTCCAGGCTTTATGCAATTATTTTTTACG R 2 1 2 1 202000 f 74 goat snp3367-scaffold1102-976636 28 4633085 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451772 Affx-122921511 AX-123322105 28 38657984 CCTGTATTCAGGCCCAATCAGTAAAAAAGAAAAAA[C/T]GTATAACCAGTGGTCTGAACAATAATTAATACAAT Y 2 1 2 1 303000 r 74 goat snp3369-scaffold1102-1046493 28 4563898 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386398 Affx-122970829 AX-123256756 28 38697523 CTTCTAAATTCTTTAGATATTTTCATAAGGATACA[C/T]AATTTCCATGGGATCTAAAGCATTATTATTACTTT Y 2 1 2 1 101000 f 74 goat snp3370-scaffold1102-1086032 28 4524984 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433606 Affx-122934951 AX-123303947 28 38754053 TCAATGGCTACTTCATTACAGGCAACCCTAAGCAA[C/T]AGTTAAATAACTTATTTCATAACTGCATGACATAG Y 2 1 2 1 101000 f 74 goat snp3371-scaffold1102-1142562 28 4468323 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440808 Affx-122929826 AX-123311145 28 38797559 GGACTAACAAAGATACCAAGTTGTTTCACAAAATG[C/T]GTAATGGAAGAAAGAAACATTTATAGATTGAAACA Y 2 1 2 1 101000 f 74 goat snp3372-scaffold1102-1186068 28 4424534 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375867 Affx-122978511 AX-123246226 28 38829670 TCACCATGTCCGAGGGCTCTTGGGGACCCACTGCG[C/T]AACATTCTTGACATAGAACTGTGGGATAAGAGGAG Y 2 1 2 1 101000 r 74 goat snp3373-scaffold1102-1218179 28 4392540 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780595 Affx-122977176 AX-385267685 28 38923850 CTAGCATTAACTCTCACAGCAAAAAGGATAGCACA[A/G]GAAAAGAAAGCAATAGGCCCTTCTCATCACCTAAT R 2 1 2 1 101000 r 74 goat snp3376-scaffold1102-1312359 28 4297994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273548 Affx-1111833666 AX-519547163 28 38959242 CCTGAT[A/G]TTCATAAAGGGGAACAGATTAATGGAAGGAGCCTG R 2 1 2 1 102000 r 74 goat GoatD01.001038 28 38959242 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38381395 Affx-122974378 AX-123251753 28 38973589 TTGTGATAATTAGGTAGATAATTTCTGCTTGTTCT[A/C]GAAAATTAGTAAACCCAATTGCTTTCCAGTGGGTT M 2 1 2 1 101000 r 74 goat snp3377-scaffold1102-1362098 28 4247854 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273165 Affx-1111833347 AX-519546826 28 38983176 AAAGAGCCTCTTGATGAAAGTGAAAGAAGAGAGTA[A/G]AAAAGTTGGCTTAAAGCTCAACATTCAGAAAACTA R 2 1 2 1 303000 f 74 goat 28_38983176_AF-PAKI 28 38983176 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320778525 Affx-122941544 AX-385265637 28 39016377 GGAAAATTCCTTTGAATTTGAATCATGGAAGAGAT[A/G]TCCCTAGAATCACAATCCCATAATTTGAAGAAGTG R 2 1 2 1 101000 f 74 goat snp3378-scaffold1102-1404886 28 4204901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384842 Affx-122971964 AX-123255200 28 39051357 TGGTTGAGGAGAGCGTCTACCTCGCAAGACTGCTG[C/T]ATGGTCTCCAAGCGTCCCTGTGGCCAGTAAGAAGT Y 2 1 2 1 101000 r 74 goat snp3379-scaffold1102-1439866 28 4169980 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405028 Affx-122956368 AX-123275380 28 39084492 CTTTCCTCCTCAGACCTGAGGTCACACACCTTGGG[C/T]GTGAAGATGGGCTAGGGAGTAGGGGATGTGAGGAG Y 2 1 2 1 102000 f 74 goat snp3380-scaffold1102-1473001 28 4138688 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444712 Affx-122926421 AX-123315049 28 39132836 CAATGCCAGGACCTGGGGACACAGAGAAAGGGCAC[A/G]GCACCAATGTTTAAGACAAATGCATCTCAAACACA R 2 1 2 1 101000 r 74 goat snp3381-scaffold1102-1521345 28 4090381 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376795 Affx-122977946 AX-123247154 28 39185085 ACCGCCCGAGCGAAAAGAAGGTGGGTTTGGGTTGA[A/G]CTGTGTGTGTGTTCACTTGTGTTGGCTCTTTATGA R 2 1 2 1 201000 f 74 goat snp3382-scaffold1102-1573594 28 4037755 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793534 Affx-122949235 AX-385280510 28 39229707 GTAATTTCATGAAGATCTAAGGATCCAATTCTGGA[C/T]GGAGAATATGCCATGGAAACTCTGGGTAGCTTCAG Y 2 1 2 1 101000 r 74 goat snp3383-scaffold1102-1618216 28 3992920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439838 Affx-122930462 AX-123310175 28 39259341 TCTGCAGCCTGAGAGATGGCATTGCCTTCCCGATG[A/C]GCACGCCCCTCACTTCTAAGTGTGGGCAAGTTCCT M 2 1 2 1 201000 r 74 goat snp3384-scaffold1102-1647850 28 3963156 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375983 Affx-122978428 AX-123246342 28 39306567 CTTTCGTTGTCAAGCACTCATGGAGCTTCCCCTGT[A/G]TGCAAGGAAGTGGGCCCCAGAGATGCAGAGGTGAG R 2 1 2 1 201000 r 74 goat snp3385-scaffold1102-1695076 28 3916249 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393027 Affx-122965640 AX-123263384 28 39342587 CACACACAAATTATTTGGAAATCTTGTTACAATGT[A/G]ACTGCTGATTCAGATGCTCAAGTGGGGCTTGACAT R 2 1 2 1 201000 f 74 goat snp3386-scaffold1102-1731096 28 3879833 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395454 Affx-122963919 AX-123265809 28 39375396 ACTACAAGTGAGGATAAACAGTATTTTTTCTGAAC[C/T]ATTTGAGTAAGCTGCCAACAAGAAGCCCCTCTTTT Y 2 1 2 1 101000 f 74 goat snp3387-scaffold1102-1763905 28 3846708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383835 Affx-122973161 AX-123254193 28 39430227 GAGACACCTGCATTTGTCTCCAGTGGTGGCTGTTA[C/T]GGGCAAGTGATGTGATGGGAAAACTGTGTCTCAGC Y 2 1 2 1 101000 f 74 goat snp3388-scaffold1102-1818736 28 3793782 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796337 Affx-122930583 AX-385283287 28 39471427 GAGCCTTGTCAGCCTACGAGAAAAAAAGCGTTGAG[C/T]ATAATTCGTCAGACAACTGGAACCCACAGCTGGTG Y 2 1 2 1 101000 r 74 goat snp3389-scaffold1102-1859936 28 3751968 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395370 Affx-122963981 AX-123265725 28 39507832 AAGGTAAACGCATGGCACAGACTGTTTTTTGCTGA[C/T]GGGAGGGCTCCAGAGCTGATAGGAACCTGTCCACA Y 2 1 2 1 101000 f 74 goat snp3390-scaffold1102-1896341 28 3715023 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783519 Affx-122946754 AX-385270582 28 39555233 GCTTGTGTTGGTTCTTTTCCATATTTCACACCTCT[A/G]TGTTGAAGTTCTTACTGTATTCACATATTTTCTCT R 2 1 2 1 101000 f 74 goat snp3391-scaffold1102-1943742 28 3667968 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381885 Affx-122974168 AX-123252243 28 39590023 TTTGTATGTACAAAAGAGTGATATATCTCAAAATC[C/T]ATTCTTATTAAATCTAAAAAGGTTATGGAACACAA Y 2 1 2 1 101000 f 74 goat snp3392-scaffold1102-1978532 28 3633225 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415045 Affx-122949490 AX-123285394 28 39647825 ACAGAACCAGAGTGATGTGTGCTTTCTGCTTCAGA[A/G]CAGCCCTGCTCCAGACTCTGTGCTCCTGAACAAAG R 2 1 2 1 103000 f 74 goat snp3393-scaffold1102-2036334 28 3573300 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375865 Affx-122978512 AX-123246224 28 39683427 TCAAGTGCCATGCCTTGGAAGAGGCAGTTGTCCTC[C/T]TCTCCTCCATGGGCAGCTCTGCCCCCAGAGGTATG Y 2 1 2 1 101000 f 74 goat snp3394-scaffold1102-2071936 28 3538025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428208 Affx-122939449 AX-123298551 28 39712205 TAAATTCTCTTTATATAATTTAATCTGTTCTTCAC[A/G]CCAATCCTATTCTGGTAGGATGGGCTGTCTGTCTT R 2 1 2 1 201000 f 74 goat snp3395-scaffold1102-2100714 28 3509335 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439778 Affx-122930508 AX-123310115 28 39797083 CAGCCAAGAGAGAATTCCCAAAGAATGTATTCCAA[C/T]AGATCCAGATGGAAGCTGCAAGGATTCTCTTGGCC Y 2 1 2 1 101000 f 74 goat snp3397-scaffold1102-2185592 28 3424938 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768928 Affx-122956545 AX-385256103 28 39826830 TTAGAGGTTAGGCTGCTCTCCAATAAAATGAGTTT[G/T]CTCTTTCCATCGTTTCTGAAGAAAGCCTCCCTCTC K 2 1 2 1 101000 f 74 goat snp3398-scaffold1102-2215339 28 3395789 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446371 Affx-122925594 AX-123316707 28 39856757 GAAGACACACGTTCTCCCCTTGACCTGGGGGACAA[C/T]GTGCCAGCCCCTCCTGCTCTTGGATCACCTGCGTG Y 2 1 2 1 303000 r 74 goat snp3399-scaffold1102-2245266 28 3365812 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767787 Affx-122933462 AX-385255012 28 39887863 CCCTTTTCTTCCTTAGCAGTAACAGTCTTCTTCTC[A/G]TAGGCACAAGATATTGTTTCTATAACAGACTAAGG R 2 1 2 1 101000 f 74 goat snp3400-scaffold1102-2276372 28 3334318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403284 Affx-122957853 AX-123273637 28 39921483 AAAAAGGGAAGGATTGTTAACTTATCCTGTGAGAC[A/G]TCTCTGTGTTGACTATTGGGCTACATTAGGATGCA R 2 1 2 1 101000 f 74 goat snp3401-scaffold1102-2309992 28 3300810 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798488 Affx-122937508 AX-385285421 28 39962404 GCTCTGGGTTAAACAGTTACAGTTTTGCTGAACTA[C/T]GGCACTTCTCACAGCTTTAGATTCCAAGGAGACTT Y 2 1 2 1 101000 f 74 goat snp3402-scaffold1102-2350913 28 3259894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445213 Affx-122925512 AX-123315550 28 39991215 TTCATTGGATGAATCAAATTTAAACTTTTTTAAGA[C/T]GCAGCCTCAGATCTCTTAGGCAACCCTCGTTCAAA Y 2 1 2 1 201000 f 74 goat snp3403-scaffold1102-2379724 28 3232505 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412319 Affx-122950851 AX-123282668 28 40051649 AAGTCTAAATTTATCTGCTTATATGTTTACTGTGT[A/G]TCACAATCAATAGAAGGACCATGAGGCTGGTGACT R 2 1 2 1 201000 f 74 goat snp3404-scaffold1102-2440158 28 3172620 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451952 Affx-122920959 AX-123322285 28 40081480 GTTAAAAGATTTCACTTTGTTCACTTTTATACAGC[A/G]TCTGTTATACATTTTATAGGTCAATGCCATCCAAT R 2 1 2 1 101000 r 74 goat snp3405-scaffold1102-2469989 28 3143863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430365 Affx-122937788 AX-123300706 28 40130390 ACATCATAGTGAAAGGCACGGGCAGGAGCAAATAG[C/T]GCAGTTTTCTTGCATTAAGCAACTTAGGGTACGGA Y 2 1 2 1 101000 f 74 goat snp3406-scaffold1102-2518899 28 3095888 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446064 Affx-122925826 AX-123316401 28 40145780 ATTTCCCCAGTATTTGCCACATTCCCACGTTATCC[A/G]TCCTAGTGAGACAAGTGTTTTGTCTTTGTTTTTGT R 2 1 2 1 201000 r 74 goat snp11424-scaffold1416-3438 28 3080416 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388753 Affx-122968950 AX-123259111 28 40175324 GAGACTTGAAGGGCACAGGGTGTGGAGGGAAGGTG[A/C]GATTCCTGGCATTTTGCATGCGGCGGATTTGGAGA M 2 1 2 1 101000 r 74 goat snp11425-scaffold1416-32982 28 3051052 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409430 Affx-122954116 AX-123279781 28 40282646 ATAGAGCATCTCAGCGCTTTCGTACTGTTTGCTAC[A/G]GTTCTCATTTTGTTATACACCCTCAGCCGCTGATT R 2 1 2 1 101000 f 74 goat snp11428-scaffold1416-140304 28 2942877 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448547 Affx-122923430 AX-123318883 28 40330054 CATCCTTGTCAGATGAGTCTCAGCCTTGTCTTTCT[A/C]TGGCCCACCCCTCACAAGGCAGCCAGAGGGCTCTT M 2 1 2 1 101000 f 74 goat snp11429-scaffold1416-187712 28 2897583 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433940 Affx-122934288 AX-123304281 28 40360225 ATTTTTTAGAGTCTTACCCTAAGCCTTAAGACAAA[C/T]AATAATCATTTCCATGACTGAACATTTTTCTGTGT Y 2 1 2 1 101000 r 74 goat snp11430-scaffold1416-217883 28 2867766 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797375 Affx-122935155 AX-385284314 28 40391252 GTACTCCTATTGCTATCCCAGGAATATCCAGTTGC[G/T]CTTGAAGGAATTAACAAGTTTCCCCTGAGACTGGA K 2 1 2 1 101000 f 74 goat snp11431-scaffold1416-248910 28 2836719 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790368 Affx-122934141 AX-385277371 28 40421026 CTGGAACTCTGGGGTTCTAAAGTCTGTCTTCCTTG[A/G]TTAGAAGCTTGAACTCAGGCTTTGATTTTCTATTA R 2 1 2 1 101000 f 74 goat snp11432-scaffold1416-278684 28 2807388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410399 Affx-122952427 AX-123280749 28 40454614 CCATAGGTGTATGCTCTGCTTAACAAGTCTGATCT[C/T]GCAGCTGGCTCAGCCTGGAAGAAGGGCCACCTTTG Y 2 1 2 1 101000 f 74 goat snp11433-scaffold1416-312272 28 2773938 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405834 Affx-122955874 AX-123276186 28 40493089 TCTGTTCAGATTGTTTGCTCAAATATTTGTTCAGA[G/T]AGTCATGTTCAAATAATTTCTGTTCATCAGTCTTC K 2 1 2 1 101000 f 74 goat snp11434-scaffold1416-350747 28 2735752 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407142 Affx-122954858 AX-123277493 28 40521920 CAGGGGTGGGATGACATGGGGGAAAAGGCAACTCT[A/G]TGCATTTGGTAGATTAGGGATACTGATAATAGGTT R 2 1 2 1 101000 r 74 goat snp11435-scaffold1416-379578 28 2707491 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403583 Affx-122957572 AX-123273936 28 40539457 TGAAAGGGTCGGTTAGGAATGCAGGTGAGAATGCT[A/G]CCAGATTCACACTGTGACCGCTTGGGGAAACACTG R 2 1 2 1 201000 f 74 goat snp57680-scaffold9257-16591 28 2688293 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427621 Affx-122939352 AX-123297964 28 40570414 CTTGCATGGAGATGAAAAGCCTCAAAAGCAAGCTA[C/T]AGTGGACATAGAATGATGGAGTGCAAGTGAAGGTG Y 2 1 2 1 101000 f 74 goat snp57681-scaffold9257-47548 28 2657300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385161 Affx-122971748 AX-123255519 28 40571449 AATCATGTATGGAAATCTATTAACAACAGCAACAG[C/T]AAAAAATCTGTTTGAAAAGTGTATCTTGAAAGAGT Y 2 1 2 1 201000 r 74 goat snp523-scaffold1015-464 28 2656096 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792899 Affx-122955920 AX-385279877 28 40602823 ATTTAAAAAGGGAGTTAAGTAACCATGATGTGTTT[C/T]ATGTGACTGCGTTGATGTAATTAGCGAGTGGCCAG Y 2 1 2 1 101000 r 74 goat snp524-scaffold1015-31838 28 2624740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402756 Affx-122958323 AX-123273109 28 40655006 CAGAGGATTTTTCTCCTCCTTGAGCCTGAGTTAAA[C/T]GGTCTCAAAGCTGGACAAACTGATTTCTTCTCCTG Y 2 1 2 1 201000 r 74 goat snp525-scaffold1015-84021 28 2572908 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391808 Affx-122967028 AX-123262165 28 40711700 TCTCTACTGGCTGCTCATTAGCCAAGTGGCCTTGG[C/T]GAATTTTTCCCAAATATAGCCCCTGACTCCATTCA Y 2 1 2 1 101000 r 74 goat snp526-scaffold1015-140715 28 2516213 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439877 Affx-122930045 AX-123310214 28 40745282 GAGCGCAGACACAAGCCTCACTCCTGGGAGTCCTG[C/T]GTGGCCTCACTGTTGGAATCATGGGTTCTTCTGGT Y 2 1 2 1 101000 r 74 goat snp527-scaffold1015-174297 28 2482239 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404066 Affx-122957149 AX-123274418 28 40780921 TGAAAAAGTTAAAAAAAAATTTCCTGGCAGTGCAA[C/T]GATCCCAACAATGAAGTGCCCAATAAAGGCAGCAA Y 2 1 2 1 101000 r 74 goat snp528-scaffold1015-209936 28 2446345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405002 Affx-122956387 AX-123275354 28 40849011 GCCAGCGGGTGCCCAGCACTCGTGATGTCTCCAAA[C/T]GCCAGGTATTCCTGGAGTCCTAGGGCCAAGCGTCC Y 2 1 2 1 201000 f 74 goat snp530-scaffold1015-278026 28 2378759 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779659 Affx-122923421 AX-385266761 28 40880860 TTCCTGACGCTCTCAAATTTACTTTGGTTCTGCTG[C/T]ATATAGATGGCTTTGCCTATGTCTTACTACATCCT Y 2 1 2 1 101000 f 74 goat snp531-scaffold1015-309875 28 2347211 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767993 Affx-986698838 AX-385255207 28 40888485 CCTCCCTCCCCGCAGCACAACTGAACAAGTGAGCC[C/T]AAATAAACGACCACCTTCGCCCCCTGTGTCAGGGT Y 2 1 2 1 600010 r 74 goat 28_40888485 28 40888485 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 38380323 Affx-122975381 AX-123250681 28 40933771 AGGCTCCATCCCTGTGCTGGCAGGACAGACCACAC[A/G]CTGGACTCGGGTCACAGAGACCCTGAGGATGCTTT R 2 1 2 1 201000 f 74 goat snp532-scaffold1015-362786 28 2294723 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383809 Affx-122973182 AX-123254167 28 40968617 TGACCCACCTGTCGATGGCCATCTCAGCAAATTTC[A/G]TTCGTGACAATGAGCTGTAGTGGCTGAATGCTGGC R 2 1 2 1 101000 r 74 goat snp533-scaffold1015-397632 28 2259853 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412131 Affx-122951098 AX-123282481 28 41019676 GAGAAAACCAGGGGCAAGCAAGAATCCCTGAGCAA[C/T]GGCGGACTCCTTCCCAATGGGCTCGAGGAAAACCC Y 2 1 2 1 101000 f 74 goat snp534-scaffold1015-448691 28 2212194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446680 Affx-122924753 AX-123317016 28 41057855 ATACCATATCCATATAAGGTCACAGGTATGTAGAG[C/T]AAATAATACTATTTAGAAATAGAAAATATTTATAA Y 2 1 2 1 101000 f 74 goat snp535-scaffold1015-486870 28 2174611 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401820 Affx-122959452 AX-123272173 28 41097754 TGCCATTCTAGGAGTCTAAACGATGTTTTCATGTG[A/G]GAAAATTACTGTGAACTTTACAACACTGAGAGATT R 2 1 2 1 101000 f 74 goat snp536-scaffold1015-526769 28 2135001 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453303 Affx-122919987 AX-123323636 28 41143998 GATTCTCCTGGTATACAGAGCAGTAACTCCTCACG[C/T]GGCAAACCACCAGGAGGCCTGACCGCCTAACCAGC Y 2 1 2 1 101000 f 74 goat snp537-scaffold1015-573013 28 2088989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380544 Affx-122975667 AX-123250902 28 41231160 GGCCATCTAAGTAGAGACGTCAAGTTAGATCTATG[C/T]GTCTGGAGCTCAAGGGAGAGATCAGTACAGAGATA Y 2 1 2 1 201000 f 74 goat snp539-scaffold1015-660175 28 2002285 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418738 Affx-122946220 AX-123289086 28 41267628 CTAGTGATCTTGAATAGGCAACCTAAAAGATGAGA[C/T]GCAATTTTGAGTTTGCAGAGTTAGGCTTCCAAAAA Y 2 1 2 1 101000 f 74 goat snp540-scaffold1015-696643 28 1965953 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405604 Affx-122955922 AX-123275956 28 41297603 ACTTTGGTACATGGTAAATATGACCACATTTCACA[C/T]GGAAGCTGACACACCTCATTATGACGCGCCCACAG Y 2 1 2 1 201000 f 74 goat snp541-scaffold1015-726618 28 1936058 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451015 Affx-122921711 AX-123321349 28 41327683 TGAGCAGAAACCGCGATTAAAGCCGTATATAAGGG[A/C]CCTGCCCACCTCCCGCCTCCCCCAACGAGGTCCTG M 2 1 2 1 101000 f 74 goat snp542-scaffold1015-756698 28 1906063 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395769 Affx-122963674 AX-123266124 28 41383001 TCCACAGTGGCGATAATTTCTACTATTTCACTAAA[C/T]AAGCTCATTCCAACTTCTATGGCCAACTCAATAAC Y 2 1 2 1 101000 f 74 goat snp543-scaffold1015-812016 28 1850193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764313 Affx-986698840 AX-385252035 28 41388709 ACCAAAAAACAAAAAACCAACCTGAAAAAACAATA[G/T]GAATGTGAAAGACTACAGATCTCTTCAAGAAAATT K 2 1 2 1 600010 f 74 goat 28_41388709 28 41388709 Ancestral_priority_1043 ancestry 0.64 recommended IMAGE 10K 10K ancestral 38428442 Affx-122938816 AX-123298785 28 41425853 ACTTCTCTACGTTACCATGTTTGCGACTGATGAGG[A/G]TATAGACTCTTTAAAAATATCTAGATTCCCTTAGC R 2 1 2 1 201000 f 74 goat snp544-scaffold1015-854868 28 1807466 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413148 Affx-122950356 AX-123283497 28 41466162 GTACAAAATAATGTCCAAAGTCACATTCAGAGCTG[C/T]AATGCCAGAATTCAAATCTAGGAGGCTCCCAGTCA Y 2 1 2 1 101000 f 74 goat snp545-scaffold1015-895177 28 1766762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273167 Affx-1111833348 AX-519546827 28 41497418 TGACTTCACTCATACTTCACTCCATTCCGTTTTAA[A/G]TAAGATCCCTTCAAGATCCCAAATAGTCTGGGAAA R 2 1 2 1 201000 f 74 goat 28_41497418_AF-PAKI 28 41497418 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320794401 Affx-122930033 AX-385281364 28 41553201 ATTAGTTTGAATGTGTGGTTTTAGGGCATAAGAGA[C/T]ACCTGGCAAAGCCTTTCGATCTCGATTTTGTGCAG Y 2 1 2 1 101000 r 74 goat snp546-scaffold1015-982216 28 1681086 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439936 Affx-122930002 AX-123310273 28 41591292 TGTTTGGTTATGGTGCCTTGGCAGTCTCTATTTTA[C/T]GGACCAGTCTTTTCTTCTTTAGAAATTAATTACTA Y 2 1 2 1 101000 f 74 goat snp547-scaffold1015-1020307 28 1642946 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433768 Affx-122934486 AX-123304109 28 41627413 CTGAGTATAAACGCTGTGCGCTCGGGAAGCTGTGC[A/G]CTCGGAAGAGACGCGATTTAGTTCTCCTGAGTTTC R 2 1 2 1 101000 r 74 goat snp548-scaffold1015-1056428 28 1606440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780464 Affx-122934464 AX-385267555 28 41663319 ATCAGGTATTCCATTCTTTGTCATGCTCATATCAG[C/T]CCATATCCGAAAGATAAGTGCTAAGGCTTCATATT Y 2 1 2 1 101000 f 74 goat snp549-scaffold1015-1092334 28 1570277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436863 Affx-122932198 AX-123307201 28 41692647 GTACCAGTTAGGACCAAAACCTTACGTTACCTTCA[A/G]TATCCCTTGGTCTCCCCTTCACCCCATCCTCTTAC R 2 1 2 1 101000 f 74 goat snp550-scaffold1015-1121662 28 1541057 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419430 Affx-122945511 AX-123289778 28 41728460 AGCCAGGCGGGGAGGATGGCAAAGAGCCCAGGGAC[A/G]CTTCCAAAGCTGGGGCTGCTTCTTCCCTCAGCTGC R 2 1 2 1 101000 r 74 goat snp551-scaffold1015-1157475 28 1505296 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800351 Affx-122974164 AX-385287273 28 41763374 AGGAAGTGTCTGTAGATGGCAGAGACTTAGATGGC[C/T]CTGCTTACTCTGTTCGTGATCATTTTAGAAATGAA Y 2 1 2 1 101000 f 74 goat snp552-scaffold1015-1192389 28 1470298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410066 Affx-122953219 AX-123280416 28 41820792 CTTCCTGAAGACTCCTGTCCAGGTCTTGCTGCGGT[C/T]TAGCAAATGCTGCTCTTGTTGGTCCTGGACACCTG Y 2 1 2 1 201000 r 74 goat snp553-scaffold1015-1249807 28 1412120 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430080 Affx-122937541 AX-123300421 28 41863601 ATTTTTTAGGTACTCTGTGCTAAGAAATTTTACAT[A/G]CTCTAGCTCATGTATTCTTTTAACCCCCTAGTAAG R 2 1 2 1 101000 r 74 goat snp554-scaffold1015-1292616 28 1368692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417318 Affx-122947749 AX-123287666 28 41903969 TAGAGAAAAGGAGGAAACTGCGGGTGTTTTCTGTG[A/G]CATCTCTAACCTGGCCTGCTTCTCTCTATAAAAGA R 2 1 2 1 101000 f 74 goat snp555-scaffold1015-1332984 28 1327890 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446787 Affx-122925306 AX-123317123 28 41940927 GGGTTCTCTGGGAATTCCCATTCCTGAGTTTGCAG[A/G]AAACATCTCTGTTAAAAGGCCAGCCGGGAGGGAGC R 2 1 2 1 101000 f 74 goat snp556-scaffold1015-1369942 28 1291336 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764315 Affx-986698842 AX-385252037 28 41956679 TTTGATGTTTCTGGTCAGTTTATTGTTGGTTTATA[A/C]ATCCTGTGACTATGATGTTTGCTATATTTGTTGCA M 2 1 2 1 600010 f 74 goat 28_41956679 28 41956679 Ancestral_priority_1043 ancestry 0.728 recommended IMAGE 10K 10K ancestral 320768011 Affx-986698848 AX-385255225 28 41956689 CTGGTCAGTTTATTGTTGGTTTATAAATCCTGTGA[C/T]TATGATGTTTGCTATATTTGTTGCACTTCTAAATG Y 2 1 2 1 600010 r 74 goat 28_41956689 28 41956689 Ancestral_priority_1043 ancestry 0.668 recommended IMAGE 10K 10K ancestral 320803751 Affx-986696496 AX-385290508 28 41958756 TAGGCCTCCTATTGGTAAATAAATAGTTGAATTTA[C/G]CCTGGAAGACTACTAGCATTTTTGGGTGGTTGAAA S 4 1 2 1 600010 f 74 goat 28_41958756 28 41958756 Ancestral_priority_1043 ancestry 0.576 neutral IMAGE 10K 10K ancestral 320768016 Affx-986698850 AX-385255230 28 41958772 AAATAAATAGTTGAATTTACCCTGGAAGACTACTA[A/G]CATTTTTGGGTGGTTGAAATTAAGTCATTTTCAAT R 2 1 2 1 600010 r 74 goat 28_41958772 28 41958772 Ancestral_priority_1043 ancestry 0.764 neutral IMAGE 10K 10K ancestral 320764325 Affx-986698852 AX-385252047 28 41958794 TGGAAGACTACTAGCATTTTTGGGTGGTTGAAATT[A/G]AGTCATTTTCAATGAGGTATACGTAGGTTTCCTTG R 2 1 2 1 600010 f 74 goat 28_41958794 28 41958794 Ancestral_priority_1043 ancestry 0.638 neutral IMAGE 10K 10K ancestral 320767986 Affx-986698834 AX-385255200 28 41959036 GGCTTCCAAAGAGTTGCACATGACTGAGCACACAT[A/G]CATATGATTGAATCAGTAGTGAAGATAGAATGATA R 2 1 2 1 600010 r 74 goat 28_41959036 28 41959036 Ancestral_priority_1043 ancestry 0.534 neutral IMAGE 10K 10K ancestral 320764310 Affx-986698837 AX-385252032 28 41959062 AGCACACATGCATATGATTGAATCAGTAGTGAAGA[C/T]AGAATGATACTTCTATAGAATTTGTGTAGAGAGAA Y 2 1 2 1 600010 f 74 goat 28_41959062 28 41959062 Ancestral_priority_1043 ancestry 0.748 recommended IMAGE 10K 10K ancestral 320767995 Affx-986698839 AX-385255209 28 41959151 TGGGTTGATCCTGCAAGCAACTATTGTTGCTATCA[A/G]TGATAATGCAGTAACTCTAAGCTTCCAAACATAAA R 2 1 2 1 600010 r 74 goat 28_41959151 28 41959151 Ancestral_priority_1043 ancestry 0.746 recommended IMAGE 10K 10K ancestral 320764314 Affx-986698841 AX-385252036 28 41959181 TATCAGTGATAATGCAGTAACTCTAAGCTTCCAAA[C/T]ATAAATTTTATTGGTACTGAAAAAAGAGGAAAACT Y 2 1 2 1 600010 f 74 goat 28_41959181 28 41959181 Ancestral_priority_1043 ancestry 0.704 recommended IMAGE 10K 10K ancestral 320768014 Affx-986698849 AX-385255228 28 41959221 ATTTTATTGGTACTGAAAAAAGAGGAAAACTTTTA[A/T]TATTTTGTTCATTCTTGCTTTTTCATTTTAAGTAA W 4 1 2 1 600010 r 74 goat 28_41959221 28 41959221 Ancestral_priority_1043 ancestry 0.608 neutral IMAGE 10K 10K ancestral 320768025 Affx-986698855 AX-385255239 28 41959256 TTATTTTGTTCATTCTTGCTTTTTCATTTTAAGTA[A/T]TAATCTGATGTTAATGAAATTTAGCATTAAGGGAC W 4 1 2 1 600010 r 74 goat 28_41959256 28 41959256 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 38406039 Affx-122955481 AX-123276391 28 41986715 CTTCTATAACCTGGGGCAATTTTTGAGGAACTTTC[A/G]CCTCTCTGTTGGCCACTGAGTCTACCTGAGGAGTT R 2 1 2 1 201000 r 74 goat snp557-scaffold1015-1415730 28 1245187 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442248 Affx-122928287 AX-123312585 28 42022182 TGATTCAAGACAGGGACTGTGAGAAGTGACTGGGA[A/C]GTCACCCAGGATTCAAAGGGAGAGAGCTGGGGTTT M 2 1 2 1 102000 f 74 goat snp558-scaffold1015-1451197 28 1209889 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451025 Affx-122921454 AX-123321359 28 42061926 ACTCCGAGAAGTGAGTGCTGGCCCTGGGGTCATCC[A/G]TTCAGACCACCTCAGGGTACAACAGCTAGATCTGC R 2 1 2 1 201000 r 74 goat snp559-scaffold1015-1490941 28 1169838 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452432 Affx-122920579 AX-123322765 28 42105868 CAGATAGTCAGGGAAGTCCCTTTCAGGTTGTTAAA[G/T]CTAAGAACAACATGCATCCTTCGACCCAGTTTAAG K 2 1 2 1 201000 r 74 goat snp560-scaffold1015-1534883 28 1125489 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440400 Affx-122929617 AX-123310737 28 42142800 AAGAGCTGGACAAACAGGCCTAAGGTGAAATCTGC[A/G]CAACATGGAAGAAAGGCAATAGACAGAGAGCTCAG R 2 1 2 1 101000 f 74 goat snp561-scaffold1015-1571815 28 1087880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796452 Affx-122948252 AX-385283402 28 42177322 ATTATGCAGTTTTAAAAAGCTGGGCAAAATATATG[C/T]GACATCTGCTTTTAGACATTGGACAATAGGCAGCA Y 2 1 2 1 101000 r 74 goat snp562-scaffold1015-1606337 28 1052800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420521 Affx-122944837 AX-123290868 28 42217652 AAGGGGAGTCTTTCGTCTTCCCATTGGGCTCTGCT[A/C]TCCTGGTAGGGCATGAGAGCACTTCCTCCTGGTCT M 2 1 2 1 101000 f 74 goat snp563-scaffold1015-1646667 28 1011821 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450757 Affx-122921848 AX-123321091 28 42248714 CATTCATAAATCTGTACTGAAGATGCAATAAATAA[C/T]AGTCCTGGGAAGAAGTAACTCATTATTCTCAGAGT Y 2 1 2 1 201000 f 74 goat snp564-scaffold1015-1677729 28 980723 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426097 Affx-122940643 AX-123296443 28 42332079 GGCATCCACTCTAATTTTTCAGTTTTCCTTCTGCA[C/T]GCTGTAGGTACAACTTGCTCTTTTTATCTGGTGTC Y 2 1 2 1 201000 r 74 goat snp566-scaffold1015-1761094 28 898154 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780899 Affx-122978042 AX-385267986 28 42391908 TGGAGGGGCCTTTATTAGTTATAAGGGATACAGAA[C/T]TGGTTTCAAAACCCTCTTCTGAAATTAACCTGTCA Y 2 1 2 1 101000 r 74 goat snp567-scaffold1015-1820923 28 838500 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764330 Affx-986698857 AX-385252052 28 42401753 TTACAAACCTGGGGAAAACATAGACATGCAGCTCT[A/T]CAAAACTACTAAAACGTCTACCATTCCAGTGCAAA W 4 1 2 1 600010 f 74 goat 28_42401753 28 42401753 Ancestral_priority_1043 ancestry 0.682 recommended IMAGE 10K 10K ancestral 38397132 Affx-122962675 AX-123267487 28 42425859 GTATTCTTAGGTGTGAGATGTGTACAAAGTAGTGT[G/T]TGTCCATTGAATGGCTATCCTTAAATAAACCTGGA K 2 1 2 1 101000 r 74 goat snp568-scaffold1015-1854874 28 804762 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389347 Affx-122968473 AX-123259705 28 42517844 TCCTCTCACGTTCAGCATCGTGCCTGACACACAGG[C/T]GGGGCTGAGCACAGGTAAGCGCAGCCTGACCTCAG Y 2 1 2 1 101000 f 74 goat snp570-scaffold1015-1946859 28 716381 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399487 Affx-122961180 AX-123269842 28 42562608 TGTGGCTGGAGAGAAAACTACCTTTTAAAAAAATC[A/G]TAGTAAAATGCACAGTGTAACATTTGTCATCGTAA R 2 1 2 1 201000 r 74 goat snp571-scaffold1015-1991623 28 670617 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764332 Affx-986698859 AX-385252054 28 42619359 GGGGTGCTGCCCCTTATAATACTCGATGACTGAGA[A/C]GTGCAGCTGGAACCCCGGTGCCCTGGGGACTGGCA M 2 1 2 1 600010 f 74 goat 28_42619359 28 42619359 Ancestral_priority_1043 ancestry 0.498 neutral IMAGE 10K 10K ancestral 38383525 Affx-122972630 AX-123253883 28 42628930 TGCATGTGTGTCTCTGGGAGCTTCACCTGTGGCCT[C/T]GGTCCAGGTGGGCAGCATTTCTGGAGAAAACCTGG Y 2 1 2 1 101000 f 74 goat snp572-scaffold1015-2057945 28 611664 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433366 Affx-122935129 AX-123303707 28 42673999 TAAATAGTTAAAAAGAAGCTATATATCCCCCATAA[C/T]GAAATAACTGCCAGTTAAGAAGCTGTTTTTCCCAT Y 2 1 2 1 101000 r 74 goat snp573-scaffold1015-2103014 28 566464 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449813 Affx-122922407 AX-123320148 28 42688297 ATGAACGGGAAGCAAAATGCGGCTCAAACATACAG[C/T]GAGCTGTTATTCAGCCTTAAAGAGGAAGGAGCAAC Y 2 1 2 1 201000 f 74 goat snp20336-scaffold2015-6159 28 552277 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802054 Affx-122971363 AX-385288958 28 42719671 ACTGCCGTTCTGCCTACAACATACAGAAATGCAGC[A/G]CACTTGAAAAGATCAGAACAGACCCTGTGAGGCCA R 2 1 2 1 101000 f 74 goat snp20337-scaffold2015-37533 28 520992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380574 Affx-122975272 AX-123250932 28 42772952 GGGAATTTATCATCCTTAAAAAGAATACCCCTAAT[A/G]TAAAAATATTCACAATTTGCAATAGTACAATACAG R 2 1 2 1 201000 r 74 goat snp20338-scaffold2015-90814 28 466318 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448564 Affx-122923418 AX-123318900 28 42877664 GAAAGGGGAAAATAAAGGTGCCAGCTTTCCAGTGC[G/T]CCTGATGAAATGCAATAGGAAAGACACAAACTGGG K 2 1 2 1 201000 r 74 goat Random2.2K-2255 28 360610 A C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38401534 Affx-122958915 AX-123271887 28 42910561 GATTCAAGGAACCTGCAAAGGGAAAGGAGATGTTT[A/G]CTTTAATAAGCTTCAATTAAAAAACAAAATAAAAC R 2 1 2 1 103000 f 74 goat snp20341-scaffold2015-228423 28 331640 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432448 Affx-122935809 AX-123302789 28 42945930 AGAGCAATGAACCCCAGGATGGGGCTCAAGTTTCT[A/G]CTTTGGGGAGACTGCACCTGTGGAATTGCAGGTCT R 2 1 2 1 202000 r 74 goat snp20342-scaffold2015-263792 28 296414 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393869 Affx-122965136 AX-123264224 28 43012762 ATGAATATCACACCGCCCATCGAGCACTTGGAAGA[C/T]GGGCCACTCGCAGCGCAAGCTCCGAGGAAGCGTTG Y 2 1 2 1 202000 r 74 goat snp20343-scaffold2015-330624 28 230885 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407833 Affx-122954536 AX-123278184 28 43075406 GTTTCAGAGTTACCAGTTTTTAGAAATTTTTTACA[G/T]CACAAGCATTAACACCACCTCCTAAATGAATATTT K 2 1 2 1 101000 r 74 goat snp20344-scaffold2015-393268 28 167880 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409288 Affx-122953110 AX-123279639 28 43106235 GCTTTCTTTCTCAGGTGGAAATGACTTTTACATTA[C/T]GACTGTTGTCCCTTGGCGATTTGCTTTACTCTCCA Y 2 1 2 1 600000 r 74 goat snp20345-scaffold2015-424097 28 43106235 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799400 Affx-122953110 AX-385286330 28 43106235 GCTTTCTTTCTCAGGTGGAAATGACTTTTACATTA[C/T]GACTGTTGTCCCTTGGCGATTTGCTTTACTCTCCA Y 2 1 2 1 101000 f 74 goat snp20345-scaffold2015-424097 28 136702 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433457 Affx-122935058 AX-123303798 28 43150685 TGTTCTTTGGGGAAAATTTATAGCCTTGAACAGGT[A/G]GGCATATTGGTGTTATGGGCTGCCACTGCGGAGCC R 2 1 2 1 101000 f 74 goat snp20346-scaffold2015-468547 28 92496 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395137 Affx-122964131 AX-123265492 28 43203961 CCAGAAGAAAAGAATTATCGCAACAACATCACATC[C/T]TACGTATAAAAATAAAAGGAGGGAGAATAACAGAG Y 2 1 2 1 101000 f 74 goat snp20347-scaffold2015-521823 28 39181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277794 Affx-1111836092 AX-185180718 28 43224983 AGCATCTTTTAATTTCATGGCTGCAATCACCATCT[A/G]CAGTGATTTGGAGCCCAAAGAGTCCTGATCAAATA R 2 1 2 1 103000 f 74 goat Random2.2K-2291 28 43224983 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273697 Affx-1111833746 AX-519547309 28 43234830 TAAAAAAAAATGCACTGCAGACAATG[A/G]TAAAATTACATCCAGTCTTGGAAGAGGTTAGGGTA R 2 1 2 1 101000 r 74 goat GoatD01.003443 28 43234830 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468274599 Affx-1111834389 AX-519548188 28 43589570 TGTTTGACCAACTCTAGGAGTTGGTGCTGTCCCAC[A/C]CATTTCACAGATGAGAGAGTTGAGGCTCAGGGAGG M 2 1 2 1 303000 f 74 goat GoatD01.033106 28 43589570 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468273169 Affx-1111833349 AX-519546829 28 44147017 CTGCAATGATTTTGGAGCCCAGAAAAATAAAGTCA[A/G]CCACTGTTTCCACTGTTTTTCCTCCATCTATTTGA R 2 1 2 1 103000 f 74 goat 28_44147017_AF-PAKI 28 44147017 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320803761 Affx-986696501 AX-385290516 28 44563958 TCAAATATGGTTTGTGATGTTTTCTTCTCATTTAA[A/G]AAACCGTTTCTTAGGCCAAGGTCACCAGCATTCTC R 2 1 2 1 600010 f 74 goat 28_44563958 28 44563958 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 320768039 Affx-986698863 AX-385255252 28 44633038 AAAGGGGGAAGAAATGTGTTCGCCGTTGCTCTGGT[A/G]TAAAGCCCTATCTCTCACTTCTGTTTTGTTGGGCC R 2 1 2 1 600010 r 74 goat 28_44633038 28 44633038 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 38422355 Affx-122943437 AX-123292701 29 10503 AAAGGAACCCTCATCATTAGCTGAGGAGGGGACAA[C/T]GGGGCTCCTCTTGTGTTGTGGCGAGACCATCAGTG Y 2 1 2 1 103000 f 74 goat snp20637-scaffold2034-10503 29 12994 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423143 Affx-122942760 AX-123293489 29 48575 TGGGCATATGAGGGTGTGTGCAGTCATCCAAGGGT[A/G]TGCAAGGGCATGCAAATGTGTGTGAGTACGTGCAA R 2 1 2 1 201000 f 74 goat snp20638-scaffold2034-48575 29 51322 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420688 Affx-122944799 AX-123291035 29 80562 CACTGGGCCCTGACACTTGTCCTCACTACTCATTG[A/G]CCTTGATCCTCACTGGACCCTGAATGTGGCCCTCT R 2 1 2 1 101000 f 74 goat snp20639-scaffold2034-80562 29 82916 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320804326 Affx-986696502 AX-385290937 29 90052 CTGCCTCTGTCCTCACTAGGGCCTATCTCTCTCCT[C/T]ACTAGGGCCTGATTTTGTCCTTACTGGGCCTGACA Y 2 1 2 1 600010 r 74 goat 29_90052 29 90052 Ancestral_priority_1043 ancestry 0.6 recommended IMAGE 10K 10K ancestral 38387324 Affx-122970502 AX-123257682 29 126675 GAACCAACAGAAGGGCTACTAAGTGGCCACGTTAA[C/T]GTCAATCCTCACAATGACCTTGGCAAAGCCATTAC Y 2 1 2 1 101000 f 74 goat snp20640-scaffold2034-126675 29 126416 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443870 Affx-122927509 AX-123314207 29 182977 AATTATATAGCCTACACATGTCTGAAAACTGTAAG[C/T]ACATACTAAAAATCACATTATCAGTGGTTAGCAGT Y 2 1 2 1 101000 r 74 goat snp20641-scaffold2034-182977 29 180512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387048 Affx-122969908 AX-123257406 29 235482 CATATAGTAGCTATTTAAGTGACAAAAGTATGCAG[C/T]AAGAAAAAGAAATAATTAGAAGGGAGGAATGAGGC Y 2 1 2 1 101000 f 74 goat snp20642-scaffold2034-235482 29 233477 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415289 Affx-122948829 AX-123285638 29 285466 TGGGGCCTGCCTTAGCTGAGACCTTCTTGAGACAT[A/C]GACCCCCAGGAAAAATGCTTCTGACCATCAAAGCA M 2 1 2 1 101000 r 74 goat snp20643-scaffold2034-285466 29 283634 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408104 Affx-122954709 AX-123278455 29 404088 ATTATTATTAAAAAAGAAAGGAAGAAAGAAGTAAA[C/T]GGCTAAGAGGCTTTGAGCTTCCCAACCTATGCAAG Y 2 1 2 1 102000 r 74 goat snp20646-scaffold2034-404088 29 401646 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785085 Affx-122923177 AX-385272132 29 449642 TTATTTTCCTGAGCCTAGCCAAAATTTTGTCCTAA[C/T]ACAGCGTTTCTTGATTGCAACAGACACTCCCTGTA Y 2 1 2 1 101000 f 74 goat snp20647-scaffold2034-449642 29 447964 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410651 Affx-122952772 AX-123281001 29 479213 AATGAGGGGAGGCCATTGGACTTGATGGATGTATC[A/G]CTGTCTAGCTGTGTATGCTATTTTTCAGGATAAGA R 2 1 2 1 101000 f 74 goat snp20648-scaffold2034-479213 29 478135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275282 Affx-1111834699 AX-519548857 29 530643 CATAAACTCTTATACTGCAGTCACCTCCCTCTCCC[A/G]GGGAAAAAGATTAAAGTATGCCAAAAATAATGTAC R 2 1 2 1 201000 r 74 goat GoatD01.046787 29 530643 A G 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38386108 Affx-122971428 AX-123256466 29 533683 ACTACCCATGAATATGATAAACTACCATGTATTCA[A/G]TTTCTATTGACTTACAATGTGGCTGCTGACCTTCA R 2 1 2 1 102000 r 74 goat snp20649-scaffold2034-533683 29 532584 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793222 Affx-122942814 AX-385280200 29 593143 TTAATTTCTATTCAAGTAGGATTCAGAAGTTCTGA[C/T]GACAATGAAATTTTGAGTATGGCATTCCATTACTG Y 2 1 2 1 101000 r 74 goat snp20650-scaffold2034-593143 29 592031 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272171 Affx-1111833369 AX-519545924 29 641047 TCGAGACCCCTGCTCTGGACTACAAAATTTAGCAT[A/G]AGGCCGTAAGCCACTCACCCTGGTTTCCGCTACAC R 2 1 2 1 102000 f 74 goat 29_641047_AF-PAKI 29 641047 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403516 Affx-122957627 AX-123273869 29 656573 GCTACATACACAGTTCTGGAGACTCAGAAAGTGTT[A/G]CTTTGACAGGTTTCCTTGCTTGCAGGACCATTTAA R 2 1 2 1 201000 r 74 goat snp20652-scaffold2034-656573 29 652673 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424281 Affx-122941986 AX-123294627 29 689378 TTCCTTTTCTCCTGCTGTAGCCACCTTTGTGCTGC[A/G]GTGGACCCTGTTCTGCCCCTGCTGATTGGGCCAGG R 2 1 2 1 101000 f 74 goat snp20653-scaffold2034-689378 29 684380 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785232 Affx-122962529 AX-313131463 29 745989 AACTTCCAATGAAGGATTTTACAGAGAGCAGAACA[C/T]GGTCATTAATAACACAATGTCCTCACCAGTCACGC Y 2 1 2 1 101000 f 74 goat snp20654-scaffold2034-745989 29 742064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423063 Affx-122942951 AX-123293409 29 781338 TTATGCCTGTGAGGGTCACAGGATGCCAAGTCACA[C/T]GTGATTTCCATCATCTCATTATCAACCTTGTTTCT Y 2 1 2 1 101000 r 74 goat snp20655-scaffold2034-781338 29 777772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377605 Affx-122977896 AX-123247964 29 838739 AGTCTCCTCCAACACTACAGTTCAAAAGTGTCAAT[G/T]CTTCGGAGATCTCTAGTTTTAGAATATTCCGTGGA K 2 1 2 1 201000 r 74 goat snp20656-scaffold2034-838739 29 834875 T G 2 parentage parentage recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399053 Affx-122960906 AX-123269408 29 890367 ACATTACTGGTGCAATCTCCTGCCTCCTCCTGGAA[C/T]ACCCTGATCCATTCTGATGAAGTATCTACGATTAG Y 2 1 2 1 201000 r 74 goat snp20657-scaffold2034-890367 29 886784 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392518 Affx-122966116 AX-123262875 29 944020 TTGGAGTCTCCTGGAGAGGGGAAGGGCAACTAGGA[C/T]TCCCCTGGGGATGGAGGTACTGGTGGCAACCATTC Y 2 1 2 1 101000 f 74 goat snp20658-scaffold2034-944020 29 940094 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413999 Affx-122950275 AX-123284348 29 1012635 ATGTTTTGAATAAGAACTTCCTTGACAAATGTAGT[A/G]CCAATGAGCTCTGTTGTGATAAGGTTCGAAATAGG R 2 1 2 1 101000 r 74 goat snp20660-scaffold2034-1012635 29 1009271 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386322 Affx-122970886 AX-123256680 29 1067857 GGACTTCTCTTCTCACACAATCTTGCTAAAGTACT[A/G]CCCATGTGGGTTTGTGCTAAGTGGCTTCAGTTGAG R 2 1 2 1 202000 f 74 goat snp14774-scaffold1596-2078 29 1076938 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767322 Affx-122963035 AX-385254600 29 1123546 TGAGCCTAGTAGTAAGTAGTGGTCTACTATAATTA[C/T]GCTATTATACATTCTCAGGCCCTGACTGTCATTTT Y 2 1 2 1 202000 f 74 goat snp14775-scaffold1596-57767 29 1130343 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420310 Affx-122945023 AX-123290657 29 1164748 GGGAAGCAATTTTCCTTCAATTAAAAATAAATAAG[A/C]TTTGGGTGGGGGAGTGTTAAATCTAAGGCTATCTA M 2 1 2 1 103000 r 74 goat snp14776-scaffold1596-98969 29 1172404 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391174 Affx-122967435 AX-123261531 29 1228616 AATCCATTTTCCAGTGGATGCCAGGCAGCCTTGGC[A/G]TCACATACTATGGGGGCGTGCCCCCTCCTTTGACC R 2 1 2 1 103000 r 74 goat snp14777-scaffold1596-162837 29 1236923 A G 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38423401 Affx-122943118 AX-123293747 29 1269953 TATTAGGAAGCACAGTGCTTTGAGCATGGGGAGGA[C/T]GAAAGGGAGGGAAGAGCAAAGCAGAGTCACTGCAT Y 2 1 2 1 101000 f 74 goat snp14778-scaffold1596-204174 29 1278036 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277937 Affx-1111836093 AX-519551432 29 1329570 CAGTGCCATTCTTCAGCAGAGAAAGCAGGCCCACA[A/G]GGCAGCAGAGACCAGATTAAGGCAGGTCTGGAGCA R 2 1 2 1 202000 r 74 goat Random2.2K-2294 29 1329570 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320800199 Affx-122939426 AX-385287122 29 1362123 CATTCATTTTTTATGGCACCATACTATTGCACTGA[C/T]GTTTCTTTTCCCAGTGCCCTGTGACATGCATTTAA Y 2 1 2 1 101000 r 74 goat snp14780-scaffold1596-296344 29 1371610 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277939 Affx-1111836094 AX-519551434 29 1412375 TTACCACTGGACCACCAGAGAAGAACCAGAGGTTT[A/G]AACATTCCCTGACGCAAGAGCCAAACTGTCAGTTT R 2 1 2 1 101000 r 74 goat Random2.2K-2295 29 1412375 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320795416 Affx-122920123 AX-385282372 29 1444609 TGCAAGTATGTGTGTTATCCATAAATGCTAAATAA[C/T]GGTTAAATTATAAACACTGTGCAGTGGAATCTGAC Y 2 1 2 1 101000 r 74 goat snp14782-scaffold1596-378830 29 1444738 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421786 Affx-122944340 AX-123292133 29 1486829 TGAATGACAAATGTCGCTAGTTCAGCTACTCTCAA[C/T]CTAATCAGAATGTGTGCGATACAAGTAAAGTGCCT Y 2 1 2 1 101000 f 74 goat snp14783-scaffold1596-421050 29 1486816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783918 Affx-122946364 AX-385270974 29 1578128 ATCCATATGTTGAAGAGTTAACCCCCTATGTGACT[A/G]TATTTAGAGCTAGGGCTCTTCAGGCATTAAGGTTG R 2 1 2 1 101000 f 74 goat snp14785-scaffold1596-512349 29 1579413 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788046 Affx-122960755 AX-385275067 29 1612294 ATCTTACATTCTGGTTATGTGCTCTGACTGCTCAA[C/T]AGCGGACTCAACTTGGAGGCAATGACAAGACAAGC Y 2 1 2 1 101000 f 74 goat snp14786-scaffold1596-546515 29 1613457 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421220 Affx-122944132 AX-123291567 29 1648291 AAAGTGTGGCTTATGATCTTTTTCAAAATGAAAGA[C/T]CTTTTTTAAGGGGGAGAGAAGATACTGGTAGAAAT Y 2 1 2 1 201000 f 74 goat snp14787-scaffold1596-582512 29 1647783 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446194 Affx-122925727 AX-123316530 29 1705377 GGGCCCTCCCTTAGGGACAGTTGACAGTGAGATGA[C/T]GATGGGACTGTTTCAACAAGGCTGTGACATCTTCG Y 2 1 2 1 101000 r 74 goat snp14788-scaffold1596-639598 29 1705064 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429641 Affx-122937680 AX-123299982 29 1758995 GGAGCCATGTTTTGAAACCCAATTAAAAAAATCTG[A/G]GAGAAACATCACTCGTTATGGAGAGCTTTCAAAGT R 2 1 2 1 101000 r 74 goat snp14789-scaffold1596-693216 29 1758453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412356 Affx-122950826 AX-123282705 29 1790513 GAATCACAGGCGGATTCCTTACCCACTGAGCCATC[A/G]CGGAAGCCCATAACACATGGGTTGGAAGGCAGCTT R 2 1 2 1 101000 r 74 goat snp14790-scaffold1596-724734 29 1790196 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383815 Affx-122973178 AX-123254173 29 1868312 CACACGTTTTCAGAAGCACTACCAAAATAGAAAGC[A/G]TTCTGAAGCATGCTGTGGATTCTGGCAGCAAACAT R 2 1 2 1 101000 f 74 goat snp14792-scaffold1596-802533 29 1867338 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426941 Affx-122940422 AX-123297286 29 1920919 CACTAAGTGCCCCAAATCACAACATTCTCTTCTAT[A/C]TTCTTCTACTATCATTTGGGACCTACTACTTAATC M 2 1 2 1 201000 r 74 goat snp14793-scaffold1596-855140 29 1920084 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434083 Affx-122934174 AX-123304424 29 1957936 AGATTGTTCCCAGCCTCAGATCCTTTCTGTGGTCC[A/G]TGCTAATTTGCATACCACCCCTAAGCACAATGACT R 2 1 2 1 102000 r 74 goat snp14794-scaffold1596-892157 29 1958256 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800899 Affx-122943410 AX-385287814 29 2014516 GGTTTTAAAAAGGTCTCGTTTTTATAACAGTTATT[A/G]CTTTGAAGCAATCTTTCCCTAATTATCTTCATAAA R 2 1 2 1 101000 r 74 goat snp14795-scaffold1596-948737 29 2015339 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273894 Affx-1111833878 AX-519547502 29 2058214 ACGCTGCAGAGGAGCAGACGCACAGGAGGGCAGAC[A/G]GTCTGTGTCACATGGCCGATCAGCAGTGGAGACCG R 2 1 2 1 202000 r 74 goat GoatD01.008899 29 2058214 A G 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320798885 Affx-122972152 AX-385285815 29 2071400 AGTAACAAACTGAGAGGCTGATCAATCTTTGGAAC[A/G]CAGTCAGCACTCATTGCTGAATAAATTAGATCAGA R 2 1 2 1 101000 f 74 goat snp14796-scaffold1596-1005621 29 2072141 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430064 Affx-122937553 AX-123300405 29 2108379 CAGGCCCCGGGCATTGCTGACTTTCAGCATGTATC[A/G]CAGTACACTGTAATTCCCCTTTGAGTCACAGGTCT R 2 1 2 1 101000 r 74 goat snp14797-scaffold1596-1042600 29 2109292 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768031 Affx-122954240 AX-385255244 29 2156532 ATAGACAGGCTAGTCCATTCTCAGGTCTCTGCCCT[C/T]TAAAGGTATACCACTTTTCCACTTGTACAGAGATT Y 2 1 2 1 101000 f 74 goat snp14798-scaffold1596-1090753 29 2157579 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399042 Affx-122960916 AX-123269397 29 2203584 CCAGGTGAAGAATTATCTCATTCTGCCTTGTACCT[A/G]CTAGTTCCACCAAGAAGAGCTTATGACAAGCCGCA R 2 1 2 1 101000 r 74 goat snp14799-scaffold1596-1137805 29 2204388 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425187 Affx-122941043 AX-123295533 29 2233788 TTCCGTTTCCTCCGGTCATCTCTCTTCCGCTTTCT[A/G]TCGTTTATGTCTTGACTCCCTCCTTCTAGGCTCCC R 2 1 2 1 102000 r 74 goat snp15402-scaffold1633-408550 29 2234792 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765041 Affx-122947834 AX-385252610 29 2262536 GCCCAGGTACCTCCTGCTGTTTCTAAAATCATTGC[A/G]TATTTTCCTTACGCTGTTGCCTTATTGCAAGCAGA R 2 1 2 1 101000 f 74 goat snp15401-scaffold1633-379802 29 2263485 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441924 Affx-122928594 AX-123312261 29 2388700 CCTGATACGATTGTTTATTATGACAGCATTGATGC[A/G]CTCTGTTGGATAGACTCAAGGAAAGGGCTTCATGG R 2 1 2 1 101000 f 74 goat snp15398-scaffold1633-253638 29 2390515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379345 Affx-122976166 AX-123249704 29 2572241 AGGGTTTGCTGGGCCAGGCAGCGACAGGCACAGAG[C/T]GGAAATTCTGATCCTAAGCCCTGCCTAGAATCTCC Y 2 1 2 1 101000 r 74 goat snp15395-scaffold1633-70097 29 2574400 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419049 Affx-122946019 AX-123289397 29 2613407 ATTTTTCACAAACACCCTAGGGCATGTCGCAGACA[C/T]AGCAGCAATGCTGTCAGACAGCAGTGAAGCAGAAA Y 2 1 2 1 202000 f 74 goat snp15394-scaffold1633-28931 29 2615589 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410986 Affx-122952009 AX-123281336 29 2654017 AGGATGACCTGCATGTTCCTAAGAATGGCCGAGAT[A/G]TGTCCCATCTGATGGCTAGAACTGAAGGCTCATGC R 2 1 2 1 101000 r 74 goat snp50893-scaffold738-155049 29 2667078 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393326 Affx-122965948 AX-123263682 29 2684956 TAAAAATTCAGACTAGGTCAGACTTATTCCTTTCT[A/G]CAGCACCTCCTCCAAGTCCAAGATCCATGGAGGTG R 2 1 2 1 101000 f 74 goat snp50892-scaffold738-124110 29 2698221 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277941 Affx-1111836095 AX-519551436 29 2722421 TGAGAAGCATTTAGAAACATAAATAAATACAAATA[A/G]AAATAACACAAGCCATTTTTCATGGAATAAAATGT R 2 1 2 1 101000 r 74 goat Random2.2K-2298 29 2722421 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320799160 Affx-122935318 AX-385286090 29 2783596 GCAAAACTGATTTCTTAAAAGAGGTGAATGTCCAA[C/T]AGAGGCTAACTTAAATCATAATGATAAAAGCGGTA Y 2 1 2 1 101000 f 74 goat snp50890-scaffold738-25470 29 2799047 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441128 Affx-122929587 AX-123311465 29 2822986 AAATACTAAATGTGAGATTTCCCCATTAATATTGA[C/T]AGACCAAGTCCTGCAAAGAGACCAACAGAGTCAGA Y 2 1 2 1 101000 r 74 goat snp36252-scaffold4331-5058 29 2848608 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783811 Affx-122960673 AX-385270867 29 2853029 TAGTATAGAGATCTTTAAAGTAAACACCCACACTG[C/T]ATTGCTTGTGTGTCTTACAGTGACACTTCCTCATT Y 2 1 2 1 101000 r 74 goat snp40462-scaffold517-24886 29 2882825 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772906 Affx-122930934 AX-385260051 29 2888487 GACGTATCTTGTAACTGACTGTTTATTCTGCTAGT[A/G]CTTCTATACAATCTCATATTCTATCTTAACATCAT R 2 1 2 1 101000 f 74 goat snp40463-scaffold517-60344 29 2920687 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792327 Affx-122951597 AX-385279309 29 2917738 AGCCTTGAGACTTTTGAGAGTGTAAAATTATTTAC[A/G]AGTGTAAAATTATTATCTTGAAACCTGAAAATTGG R 2 1 2 1 201000 f 74 goat snp40464-scaffold517-89595 29 2949842 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788911 Affx-122942367 AX-320624285 29 3022015 CAGTATCACATAGTGATGGAAAGTCCTATGGCTGG[G/T]GGTGTCTAGTGTTGAAAATAAGAGTGAGTTTCTTT K 2 1 2 1 101000 f 74 goat snp40466-scaffold517-193872 29 3054987 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438058 Affx-122931539 AX-123308396 29 3078977 TTATTAGAAGAAAACTTGTATATACACTAAAGAGA[G/T]AGAGGCACCAGAAATATTAAGTGGGTAAACATAAA K 2 1 2 1 101000 f 74 goat snp40467-scaffold517-250834 29 3112876 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415630 Affx-122948586 AX-123285979 29 3108086 GAGGGCTTATTTCATGTACAATCTATAAATGTGTT[A/G]CCATCATTCTTATCTTTTAAATAGTATATTTTATT R 2 1 2 1 101000 f 74 goat snp40468-scaffold517-279943 29 3140959 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391210 Affx-122967410 AX-123261567 29 3149923 ATTAATCATAGGTTAATACCATTTTGTACTCCCAG[C/T]AACAATCAGGAGCACAGACTCACCAACAGAGATTT Y 2 1 2 1 201000 f 74 goat snp40469-scaffold517-321780 29 3184277 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800556 Affx-122977660 AX-385287475 29 3188731 TATGTGCCTATACAGAGAATGTAATAATGTTTTTA[C/T]GCTCAGTTTTTACATAGAAGGCAGTATTTTATTAA Y 2 1 2 1 101000 r 74 goat snp40470-scaffold517-360588 29 3222811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272164 Affx-1111833360 AX-185909873 29 3224401 TAGGGTCGCTTCAGTCATGTCCAACTCTTTGTGAC[A/C]CTGTAGATTGTGGCCTACCAGGCTTCTCTTTTGGG M 2 1 2 1 103000 f 74 goat 29_3224401_AF-PAKI 29 3224401 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38446503 Affx-122925040 AX-123316839 29 3235880 CATTTTATGCAATCCTATTCTCTAAAAATAAAGTC[A/G]TGTTCATAGAGAGATGCCAGAGAGCAAATTGATCA R 2 1 2 1 101000 r 74 goat snp40471-scaffold517-407737 29 3271989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442421 Affx-122927980 AX-123312758 29 3273240 TGAACAAAATAAGCTGTTCTTTAACTTTCTTACAT[A/G]TGGAATAAATGTTGAATCAGGAAGTGCATTTTGGT R 2 1 2 1 101000 r 74 goat snp40472-scaffold517-445097 29 3309521 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776886 Affx-122943632 AX-385264010 29 3321278 TAGCAAATTTAATCTGGTGATCTCCAGTTGGCTAG[A/G]TGCATTATGGTTTATGTTTTGTCTGCCCCTGAAAC R 2 1 2 1 101000 f 74 goat snp40473-scaffold517-493135 29 3358944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795606 Affx-122951863 AX-385282561 29 3361223 ATCAAACATAAGGACACCTGAGAAATGATCTTAAT[A/C]TAGAAGATGTGGGATGAGGCATGATTAAGTGTGGT M 2 1 2 1 101000 r 74 goat snp40474-scaffold517-533080 29 3399752 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768058 Affx-986698874 AX-385255265 29 3369589 CTCACTCTGACCATGCGGGCCCTCACCTGGACATA[A/C]CACCACTCCAGTATTAATTTGATGATTGGATTCAT M 2 1 2 1 600010 r 74 goat 29_3369589 29 3369589 Ancestral_priority_1043 ancestry 0.592 neutral IMAGE 10K 10K ancestral 320775159 Affx-122922986 AX-385262291 29 3389917 GTACTTGCTTTGCAGATGAAAGGTATTATGTACAT[A/G]CACATAACTTACAAAACAAAGGGATTTCTCTAGTG R 2 1 2 1 102000 r 74 goat snp40475-scaffold517-561774 29 3428530 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798478 Affx-122934599 AX-385285411 29 3426664 ACTGCTATGCCTCACCTGGATTTATGCTCTTTATA[A/G]TTAGCATGATTTATTGCCTGCATATAGAAAATAAC R 2 1 2 1 101000 f 74 goat snp40476-scaffold517-598521 29 3466089 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415249 Affx-122948946 AX-123285598 29 3457804 ATTTTTTCTCATTGGATTTTGATCTTGAGGCATGA[A/G]TTAAGGGGAATTTTTCTTTATCATTTAGTTTAGGG R 2 1 2 1 101000 f 74 goat snp40477-scaffold517-629661 29 3497718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409150 Affx-122953214 AX-123279501 29 3481768 AACAGTTTTGTGCTTCAAGAATATTCTATGCTTAC[A/G]TATCTGTTTAGAACAATTTCCTCAAGTCTGTTGGC R 2 1 2 1 101000 f 74 goat snp35404-scaffold426-19429 29 3538564 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777609 Affx-122926271 AX-385264728 29 3537744 ATTCGAAGGAACTTAATTTTATCTGTGAGTAATAT[A/G]CAATAATTCTTATACGAAGGAGGCCATCTCTTGCT R 2 1 2 1 101000 r 74 goat snp35405-scaffold426-75405 29 3594504 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432321 Affx-122936298 AX-123302662 29 3595226 TGCGTGATGTTTCATTATGGTTACCTCAAGAAATG[G/T]AGACTCTGTAAACCCTTCCAGTGCTTCCTTTACTG K 2 1 2 1 101000 f 74 goat snp35406-scaffold426-132887 29 3653316 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780786 Affx-122963241 AX-385267875 29 3629018 AAAATTTAGTTTAGAAACCTTGTTGAATTCAGATC[A/G]TTATAGATATATATGGAGCTAGAATGTGTGTATGA R 2 1 2 1 201000 f 74 goat snp35407-scaffold426-166679 29 3690130 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394887 Affx-122964746 AX-123265242 29 3660779 TGTTGGAGGGAAAGACTAAACCATCTCTCTCACTA[C/T]GCACGTTCCAACAAGAGATGCTGGCTTTAAGTAAA Y 2 1 2 1 202000 r 74 goat snp35408-scaffold426-198440 29 3722052 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774659 Affx-122939649 AX-385261793 29 3695242 AATTAGCATTGCAAATTAAGCATTAGAACTCAATT[A/G]GATCTCAAAAACTATGGTGGTCTGAGCAAATTAAT R 2 1 2 1 101000 r 74 goat snp35409-scaffold426-232903 29 3756275 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426125 Affx-122940624 AX-123296471 29 3737843 TTTTAACTCTAAGAGTATGCAGAGGATTTTAGAGG[C/T]GATCTAGAGGATCACTGACTTGTAGATCTTATATT Y 2 1 2 1 101000 f 74 goat snp35410-scaffold426-275504 29 3799850 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409023 Affx-122953871 AX-123279374 29 3774599 AAGTATTAAATAAATAAATGTTGAGTTAATGAATA[C/T]GTGAGTGAATATAAGAAAGAAACAACAGCACTTAT Y 2 1 2 1 103000 r 74 goat snp35411-scaffold426-312260 29 3836761 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795196 Affx-122929596 AX-385282154 29 3823130 AATGGATAAAGTATCTCAGTAGAGACCACTCAAAA[C/T]GAGTAACTCACAGAAATCAATTCCTAGTAGGGAAA Y 2 1 2 1 101000 r 74 goat snp35412-scaffold426-360791 29 3886675 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382867 Affx-122973520 AX-123253225 29 3865104 TTGTCTTCAAATTATCTTTGAAACACTATTTAATC[G/T]CTGATACTGATAAACTTGTCTCATACTCATTACAG K 2 1 2 1 101000 r 74 goat snp35413-scaffold426-402765 29 3929073 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432024 Affx-122935917 AX-123302365 29 3898424 GTGCTCAAGGCAAAAATTATCATGCACATTTTAAG[C/T]ACATTTTTCTCAACCCAAGAAATCTCAATGAATAG Y 2 1 2 1 101000 f 74 goat snp45156-scaffold615-24565 29 3986786 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781086 Affx-122933713 AX-385268172 29 3940229 AAACAATAGTGCTTACTCTTTTTGATTAAATGCTC[A/G]TTTAATCCTAAGCATAAGTGAATGGCAAAATAGAA R 2 1 2 1 102000 f 74 goat snp45157-scaffold615-66370 29 4029656 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383759 Affx-122972438 AX-123254117 29 3968976 CTAGCCATGTACAATTCTTCTGTTTCTTAGATTCT[A/G]TTTCAATTCTTCCGCTCCTTGGAGGGAAAGCTATG R 2 1 2 1 101000 r 74 goat snp45158-scaffold615-95117 29 4058821 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452239 Affx-122920787 AX-123322572 29 4000377 TAAGCTACTAAGTTGTTTTTTCTTTTTATTTTCTC[A/G]TTTCTTTCTTTCTTCCTAACAGCAGCTACTCTTGT R 2 1 2 1 103000 r 74 goat snp45159-scaffold615-126518 29 4090477 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378065 Affx-122977181 AX-123248424 29 4041530 TTCAAGTAATCTAATATTCCAATGTTACACTAAGT[C/T]GTGTCTGATTCTTTGCAACCCCATGGACTGTATAG Y 2 1 2 1 303000 f 74 goat snp45160-scaffold615-167671 29 4131499 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392614 Affx-122966044 AX-123262971 29 4081866 ACTGTTAACCACTAGACTAGAGCACATCTCAAATA[C/T]AGGAGTTAATTTTTGTGTGCCAGGCACTGATCTAA Y 2 1 2 1 101000 f 74 goat snp45161-scaffold615-208007 29 4170842 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777378 Affx-122944083 AX-385264500 29 4118641 CCATGAGACCTCATGGTTCACATCAGGTAATGGTC[A/C]ATTTTTTATGACTGACAAAGTAAATCTCTCGTCTC M 2 1 2 1 101000 f 74 goat snp45162-scaffold615-244782 29 4207630 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415614 Affx-122948600 AX-123285963 29 4162030 AATAACCCTGAGCATTTGACTCTGAGTCTTTTTCC[A/G]TCACAATTTGCCTAGTTCACAGAACCTTCACAGTC R 2 1 2 1 101000 r 74 goat snp45163-scaffold615-288171 29 4251471 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277946 Affx-1111836097 AX-519551441 29 4182655 TTAATCCTGTTCTTACCACTCTCTTCTAGTGCTTG[A/G]AATCTCTTAATTTACAGAATAGTATTTTTAGGGCT R 2 1 2 1 201000 r 74 goat Random2.2K-2301 29 4182655 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320770441 Affx-122921039 AX-385257607 29 4253877 AAGTTATGAAATAAAACCAGACAATCTTTTTTCTA[C/T]AAGACTTGAGTGAAGTTAGTATAGGCTAGAGTTGA Y 2 1 2 1 201000 f 74 goat snp45165-scaffold615-380018 29 4347707 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769990 Affx-122945057 AX-385257157 29 4348315 AAGACAGATATGCCTGTGAGAAGAACAGATTCCAC[A/G]TACTTTACAATTACCTAGAGACAGGATAGTACCAC R 2 1 2 1 101000 f 74 goat snp45167-scaffold615-474456 29 4441327 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767528 Affx-122953829 AX-385254785 29 4406626 ATGATCTCAGTTCAGTACCTGCACTAGCTAATGAC[A/G]TAATTGTTACCATGTGTAATATTTTACTCTCATAG R 2 1 2 1 101000 f 74 goat snp45168-scaffold615-532767 29 4499393 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444212 Affx-122927248 AX-123314549 29 4454247 AATCAGGCCAATTTTGTGGCTGAAACCATTAATGC[C/T]CTGAAGATTGAGAGTAAGAACCAAAAACAAACAAA Y 2 1 2 1 101000 f 74 goat snp45169-scaffold615-580388 29 4546903 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774819 Affx-122928130 AX-385261953 29 4489296 GTACATCACTTGGTATGATGACTGAGGGTGTCTAG[C/T]GATTCTAAAATAAACCATTGCTGCCATCTTCTGGA Y 2 1 2 1 101000 f 74 goat snp45170-scaffold615-615437 29 4582222 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379939 Affx-122975651 AX-123250297 29 4555947 GGATATCTTGTAACAAAGAAATACTGTATAAAATT[G/T]AAAATGGCAAAATTGGTTCTGAAGGAAATAACAAA K 2 1 2 1 201000 f 74 goat snp45172-scaffold615-682088 29 4649671 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397029 Affx-122963116 AX-123267384 29 4589925 CATGAAGGGAAAGTGAAGAAAAATAAAAAGAATCC[A/G]CTTTGCAATGCAATAATGCCAGTTTGATCCCTGGT R 2 1 2 1 101000 r 74 goat snp45173-scaffold615-716066 29 4683737 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416373 Affx-122947874 AX-123286722 29 4641213 GTCGCAAAGAGTCAGATACAGCTGAGCCACTAAGC[A/G]TGCCCACAATGTGGTAGATAAATACCTAGTTTCAG R 2 1 2 1 101000 r 74 goat snp45174-scaffold615-767354 29 4735984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440556 Affx-122929314 AX-123310893 29 4670151 TAACATTTAACATCTGTCTTGATATTAAAGTGCTT[A/G]TAGTGACCATTCTGTTATCTGTATACATGTAAATT R 2 1 2 1 101000 r 74 goat snp45175-scaffold615-796292 29 4765474 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377034 Affx-122977708 AX-123247393 29 4713057 GCGTAAACAATGGCAAGTGTGCTGTGGGAAAATAA[C/T]GTTTAGTTTGAGATGTGTTGATTTAGTTATCTCTC Y 2 1 2 1 101000 f 74 goat snp45176-scaffold615-839198 29 4810044 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786289 Affx-122931882 AX-385273324 29 4761678 ATAATCAGGAAACGATAGTCAGCATGAATATAATC[A/G]TTTGTAGACTGATAACATCAATGACCGTGATAATA R 2 1 2 1 101000 f 74 goat snp45177-scaffold615-887819 29 4859084 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786737 Affx-122960010 AX-385273768 29 4792959 ATCCAAAAATCTGAATTATATATATAGAGATGAAA[C/T]ATTTATTTTTAGCAAATCCCATCTATTAACTACCA Y 2 1 2 1 201000 f 74 goat snp45178-scaffold615-919100 29 4890908 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389963 Affx-122968075 AX-123260320 29 4827236 AGTTCCTGATTCTCCACATTCTCTCAGTATTTGGT[A/G]ATGTCCCTCTTTGGGATTTTGATGATTCTTATACA R 2 1 2 1 101000 r 74 goat snp45179-scaffold615-953377 29 4921977 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780715 Affx-122948468 AX-385267805 29 4880942 AAGTTATCTAGAGATGACAAAGTATACAGGAGCAC[A/G]TGTATTTGTTATCTGCAAATAACATGGGATTATGT R 2 1 2 1 101000 f 74 goat snp23957-scaffold242-54951 29 4965702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788676 Affx-122941923 AX-385275692 29 4927402 GTGAAGAAGAAGGAATATCAAAATCCCCTTACTTC[A/G]CTCAGTTTTGCTATAAAGTTAAACTGCTCTAAAAA R 2 1 2 1 102000 f 74 goat snp23956-scaffold242-8491 29 5011824 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401628 Affx-122959597 AX-123271981 29 4960868 TTCTTTATCTTGGCTCGGTTTGCATCCTCTTCCTG[C/T]TCCATAAGACATTTTCCTGTTCAGTCAATGATTGG Y 2 1 2 1 201000 r 74 goat snp26608-scaffold2777-112391 29 5290621 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399874 Affx-122960227 AX-123270229 29 5011872 ACAGCGACTTCTCTCTTTCTCTTACCCTCTAATGT[C/T]GTTCCAGAGCCTGCTGGAAACCAAGTTGTGTAAAA Y 2 1 2 1 201000 r 74 goat snp26607-scaffold2777-61387 29 5341303 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384868 Affx-122971943 AX-123255226 29 5060524 CTGTATCTGCAGTTCCTAGAATGATATGTCTTCAA[C/T]GTATTTGTGGAAGGAATCCGAGAGTCATCTTGGAA Y 2 1 2 1 101000 r 74 goat snp26606-scaffold2777-12735 29 5390917 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405199 Affx-122956914 AX-123275551 29 5093861 TCTTTCAGGCAAAATCTTGGTAATCAAATAAAATT[A/G]CCTTTCAAAGCATATAGTAAGCACTTACCATGTAG R 2 1 2 1 201000 f 74 goat snp59593-scaffold983-980092 29 5418622 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768065 Affx-986698878 AX-385255272 29 5108042 TGAATGCTTTTGAATGGATGTTCTGACAAACCATG[C/T]TCACATACCCCTTGCCTTTCTGTTGTTTTGATATT Y 2 1 2 1 600010 r 74 goat 29_5108042 29 5108042 Ancestral_priority_1043 ancestry 0.67 recommended IMAGE 10K 10K ancestral 320764353 Affx-986698880 AX-385252068 29 5127248 TGCAGGACTTCAGAAATAACTCACCTGCTGAATCT[G/T]GAGAGTGAAGAAACTGAAGATTCTGCTGAGGTGTC K 2 1 2 1 600010 f 74 goat 29_5127248 29 5127248 Ancestral_priority_1043 ancestry 0.692 recommended IMAGE 10K 10K ancestral 320791123 Affx-122966603 AX-385278118 29 5135850 AGGGATCAGTTCTGACATTTGGGAGTTGTGTGAAC[A/G]TAACTCATCTATGGTTCAATTTTTATTTGGGAATT R 2 1 2 1 101000 f 74 goat snp59592-scaffold983-938103 29 5461500 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394756 Affx-122964848 AX-123265111 29 5181795 ACCATAATGTAGTAATTCCCAGGTTTGCAAACTTT[A/C]GTTTATAAATTCACCTTCATGCAGTCCATAGACAT M 2 1 2 1 101000 r 74 goat snp59591-scaffold983-892158 29 5508297 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764355 Affx-986698882 AX-385252070 29 5195484 TTTTAAACTGGACACAGACTTTGAGGAATAAAACA[A/G]GGAACAATGCAATTAAAAGCCATGCTACTAAATAA R 2 1 2 1 600010 f 74 goat 29_5195484 29 5195484 Ancestral_priority_1043 ancestry 0.642 recommended IMAGE 10K 10K ancestral 38418311 Affx-122946977 AX-123288659 29 5218458 TAACTGAGGAGTGAGTCCACAGCAGAATTCACTGC[A/G]CTAAGAAACAAACATCTGAAATCCCTTCCCAGCAT R 2 1 2 1 101000 f 74 goat snp59590-scaffold983-855495 29 5545071 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445894 Affx-122925951 AX-123316231 29 5331557 TATTTGATGATACCATGATTCAGCTAGATTTTACC[A/G]CATTATTTGTTCTATTTTATTTTTCTGACTTTATT R 2 1 2 1 101000 f 74 goat snp59588-scaffold983-742396 29 5658516 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427094 Affx-122939787 AX-123297437 29 5371477 ATTAGATGAAGTGAATAATTTTGCTAGCATTTTTT[A/C]TGTCTTACATATAATCAGTTAAAGCATCCTTTATT M 2 1 2 1 101000 r 74 goat snp59587-scaffold983-702476 29 5698193 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444082 Affx-122926842 AX-123314419 29 5431760 TGCCAAGGGAAGGCAGATTTCCCTAGACAAAGGAA[C/T]GAAGATGAAAGAAAAATATAAAAAAAATCAATACA Y 2 1 2 1 101000 f 74 goat snp59585-scaffold983-642193 29 5759601 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377157 Affx-122978218 AX-123247516 29 5464673 AAAGAAATAGTATTTGAAAATTTTGAAAGCATTTG[A/G]GCTGAGCAGCAAGCAATAAAGAAAATCATAATTAT R 2 1 2 1 201000 f 74 goat snp59584-scaffold983-609280 29 5792204 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476388 Affx-1251763899 AX-586011797 29 5492355 CCCCATGGACTGCAGCACACCAGGCTCCTCTGTTT[-/CATTATCTCCCATAATTTGCTTATTTTTTTTTAATGTTTTTATCGTTTATTATAGCCGTATATTGTTATTTAGCCGTTTT]ATTATCTCCCATAATTTGCTTAAATTCATGTCCAT - 4 1 4 1 20000 f 74 goat SV_141 29 5492355 - deletion junction SV-TF-chip 539476644 Affx-1251763899 AX-586012025 29 5492355 CCCCATGGACTGCAGCACACCAGGCTCCTCTGTTT[-/CATTATCTCCCATAATTTGCTTATTTTTTTTTAATGTTTTTATCGTTTATTATAGCCGTATATTGTTATTTAGCCGTTTT]ATTATCTCCCATAATTTGCTTAAATTCATGTCCAT - 4 1 4 1 20000 r 74 goat SV_141 29 5492355 - deletion junction SV-TF-chip 562165241 Affx-1251763899 AX-606940653 29 5492355 CCCCATGGACTGCAGCACACCAGGCTCCTCTGTTT[-/CATTATCTCCCATAATTTGCTTATTTTTTTTTAATGTTTTTATCGTTTATTATAGCCGTATATTGTTATTTAGCCGTTTT]ATTATCTCCCATAATTTGCTTAAATTCATGTCCAT - 8 1 4 1 20100 f 74 goat SV_141 29 5492355 - deletion junction SV-TF-chip 562165362 Affx-1251763899 AX-606940773 29 5492355 CCCCATGGACTGCAGCACACCAGGCTCCTCTGTTT[-/CATTATCTCCCATAATTTGCTTATTTTTTTTTAATGTTTTTATCGTTTATTATAGCCGTATATTGTTATTTAGCCGTTTT]ATTATCTCCCATAATTTGCTTAAATTCATGTCCAT - 8 1 4 1 20100 r 74 goat SV_141 29 5492355 - deletion junction SV-TF-chip 562165441 Affx-1251763899 AX-606940852 29 5492355 CCCCATGGACTGCAGCACACCAGGCTCCTCTGTTT[-/CATTATCTCCCATAATTTGCTTATTTTTTTTTAATGTTTTTATCGTTTATTATAGCCGTATATTGTTATTTAGCCGTTTT]ATTATCTCCCATAATTTGCTTAAATTCATGTCCAT - 8 1 4 1 20100 f 74 goat SV_141 29 5492355 - deletion junction SV-TF-chip 562165509 Affx-1251763899 AX-606940920 29 5492355 CCCCATGGACTGCAGCACACCAGGCTCCTCTGTTT[-/CATTATCTCCCATAATTTGCTTATTTTTTTTTAATGTTTTTATCGTTTATTATAGCCGTATATTGTTATTTAGCCGTTTT]ATTATCTCCCATAATTTGCTTAAATTCATGTCCAT - 8 1 4 1 20100 r 74 goat SV_141 29 5492355 - deletion junction SV-TF-chip 562165759 Affx-1251763899 AX-606941168 29 5492355 CCCCATGGACTGCAGCACACCAGGCTCCTCTGTTT[-/CATTATCTCCCATAATTTGCTTATTTTTTTTTAATGTTTTTATCGTTTATTATAGCCGTATATTGTTATTTAGCCGTTTT]ATTATCTCCCATAATTTGCTTAAATTCATGTCCAT - 8 1 4 1 20100 f 74 goat SV_141 29 5492355 - deletion junction SV-TF-chip 38401533 Affx-122958916 AX-123271886 29 5562645 TTGGATCACAGAATTTGTAAACAAATAGAGATTCA[C/T]GATGTATTCTGGAGGTAGAATTGACAAGTTTGGCT Y 2 1 2 1 101000 f 74 goat snp59582-scaffold983-511308 29 5890990 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784480 Affx-122941308 AX-385271529 29 5637731 AGATTTCAAAGCATTCTTTCTTTCTCATATTCAGC[A/C]TTACAAACATCCTATGAACCAGTATAATCTAGCTT M 2 1 2 1 101000 f 74 goat snp59581-scaffold983-436222 29 5965741 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424168 Affx-122942530 AX-123294514 29 5675156 GGAGTATTAGGTAGTGTGTACTGACTCATTACTCT[A/G]CTAGATAAGCCGTACATGATTCGTCTAGGACCATT R 2 1 2 1 101000 f 74 goat snp59580-scaffold983-398797 29 6003970 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439441 Affx-122930187 AX-123309778 29 5705006 CATGGATACCTCGGATACATTTTCCTGAAAACAAG[C/T]GCATCCCATAGATAAGAGACACTCGGGTATAACGA Y 2 1 2 1 101000 r 74 goat snp59579-scaffold983-368947 29 6033344 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452418 Affx-122920590 AX-123322751 29 5753076 AATCGGCAAAAATGAAGTTTGTTTCAGTCATAATG[C/T]AACCTTATAAAATTATTTGTTTTCTTTATACTTCA Y 2 1 2 1 101000 f 74 goat snp59578-scaffold983-320877 29 6077333 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275742 Affx-1111834985 AX-519549308 29 5789865 ATCTGGCCGTGGCTCACTGGGGCAGCTGTGGTTGG[A/G]TCTGTCCTTACTGCTGTGCTGGGAGGACTTACTAG R 2 1 2 1 102000 r 74 goat ilmnseq_rs636877924 29 5789865 C T 1 neutral Goat_IGGC_65K_v2 Illumina 38427186 Affx-122939605 AX-123297529 29 5795893 TAAGGATATTATGTACCTATAATTTGCCAGACTAC[G/T]GAAATACAGAAATGAACAAAACTAATCCTGTCTAG K 2 1 2 1 201000 f 74 goat snp59577-scaffold983-278060 29 6120100 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449279 Affx-122923024 AX-123319614 29 5824843 AAGAGCCACCATTTACTAGTACATGCAAAGCACCA[C/T]GATGCTAGGTACAGATCCTTCATACAGGCATAGAT Y 2 1 2 1 101000 r 74 goat snp59576-scaffold983-249110 29 6148751 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275763 Affx-1111835072 AX-519549328 29 5853660 CAAGGCATTGTGCATACTGCTTTGAGAGGCATCTG[A/C]TATCCCAGTAAGCGGACTAGCAAATCCTGTTGGCA M 2 1 2 1 101000 f 74 goat ilmnseq_rs647471401 29 5853660 C A 1 recommended Goat_IGGC_65K_v2 Illumina 38426431 Affx-122940820 AX-123296777 29 5857212 CTGACTGAATTCCTATACGGATCAATGCATAAGCA[C/T]GCCAAGGAGCTTCAGCCACGTGCAATGTGTTACTT Y 2 1 2 1 101000 f 74 goat snp59575-scaffold983-216741 29 6180426 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272170 Affx-1111833368 AX-519545923 29 5879034 CACTTCAAACTCTCAGTGCAAATAGGATCCTTTCT[A/G]TTACATGTAAGAAATTTAAATAAGTATCCTGGATA R 2 1 2 1 101000 f 74 goat 29_5879034_AF-PAKI 29 5879034 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276188 Affx-1111835211 AX-519549738 29 5899437 AGGTTTGCACAGATGAGTACATGGGAGGTCGCAAT[A/C]CTGCAAACCCTAATCTGCTCAGCCCAGCATCCTTC M 2 1 2 1 201000 r 74 goat ilmnseq_rs663881503 29 5899437 G T 2 recommended Goat_IGGC_65K_v2 Illumina 468276065 Affx-1111835148 AX-519549617 29 5899438 AAGGATGCTGGGCTGAGCAGATTAGGGTTTGCAGG[A/G]TTGCGACCTCCCATGTACTCATCTGTGCAAACCTC R 2 1 2 1 102000 r 74 goat ilmnseq_rs656850833 29 5899438 A G 1 neutral Goat_IGGC_65K_v2 Illumina 468275806 Affx-1111835018 AX-519549370 29 5899504 CAGAAGCTGACCGGGGATGAGAACTTCACGATTCC[A/G]TACTGGGACTGGAGAGATGCAGAAAACTGTGAGGT R 2 1 2 1 102000 r 74 goat ilmnseq_rs641173186 29 5899504 T C 1 neutral Goat_IGGC_65K_v2 Illumina 468275737 Affx-1111835060 AX-519549304 29 5899520 GTGGGAACAGGAAATCCAGAAGCTGACCGGGGATG[A/G]GAACTTCACGATTCCATACTGGGACTGGAGAGATG R 2 1 2 1 202000 f 74 goat ilmnseq_rs646167085 29 5899520 T C 2 neutral Goat_IGGC_65K_v2 Illumina 468276141 Affx-1111835188 AX-519549691 29 5899557 ATCCCCGGTCAGCTTCTGGATTTCCTGTTCCCACA[A/G]CAGCAAGAAGAGTCTATGCCAAGGCAGGAAACCCG R 2 1 2 1 201000 r 74 goat ilmnseq_rs661675571 29 5899557 G A 2 recommended Goat_IGGC_65K_v2 Illumina 468275909 Affx-1111835145 AX-519549467 29 5899705 ATCCAGACAAAGAGGTCATAAACACTGACGTCATT[A/G]AACAGGGGCGTTGTTCCGTGATTCATTTGGCCATA R 2 1 2 1 101000 f 74 goat ilmnseq_rs656411059 29 5899705 G A 1 recommended Goat_IGGC_65K_v2 Illumina 468275869 Affx-1111835051 AX-519549430 29 5900083 CCCCTGCCCGAGAGCCGGCCGCAGGGGCTCCCGTC[C/G]CCCGCCCAGGGCGGGCAGCACTGCTTCTCCATCAG S 4 1 2 1 303000 r 74 goat ilmnseq_rs645133246 29 5900083 G C 3 not_recommended Goat_IGGC_65K_v2 Illumina 38452618 Affx-122920365 AX-123322951 29 5910732 GTTAGCACAGATGCCAAGAAAGCAAGTAAAAACCA[C/T]AGCCTTGTCTCTGTCTATTTTTGCCCTGGATAATA Y 2 1 2 1 101000 r 74 goat snp59574-scaffold983-163221 29 6235128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381280 Affx-122974469 AX-123251638 29 5955775 AAAAAGTGTAGATGGAAAATGGAAATATAGTACTT[A/G]CCAACCTATTTTTCTTGGGTACATGTGATCAAAAT R 2 1 2 1 101000 r 74 goat snp59573-scaffold983-118178 29 6275925 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437435 Affx-122932403 AX-123307773 29 6011796 ACCCAGATGTTTTTCATGACTGATTTCCATTGTGC[A/G]TAAGAGCTCACTAAAGAGAGATCAATTGTGTTGGC R 2 1 2 1 101000 r 74 goat snp59572-scaffold983-62157 NW_017189549.1 49026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424216 Affx-122942492 AX-123294562 29 6042795 AACCTAGCCATGGTGGCATTTGCTCTGAGGAAAAT[A/G]AGCGTACCGTGTTTTGTTCTCTGGTGTTTTAAATT R 2 1 2 1 101000 r 74 goat snp59571-scaffold983-31158 29 6327660 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386147 Affx-122971400 AX-123256505 29 6098370 CAAATCCAGTCTGATCACATCACTCCTCTGTATGC[C/T]ACTCCCTTCAATAACTGCTGCTTTCCTCAGGATCA Y 2 1 2 1 101000 r 74 goat snp58944-scaffold966-816272 29 6384741 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776636 Affx-122933546 AX-385263763 29 6129520 AGAACCTACTGTGAGCTAGGCAAAGCACTTAATGT[A/G]TGTGGTCAAATGGTGACCAAGACATGGTCATTTTT R 2 1 2 1 101000 r 74 goat snp58943-scaffold966-785122 29 6415442 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795931 Affx-122940620 AX-385282883 29 6164785 ACTTACAGATCAATATTGACCCTATCTGGTTATTA[C/T]GAGTCCAGATTCCCTTTGGATTTGCTACAAATAAA Y 2 1 2 1 101000 r 74 goat snp58942-scaffold966-749857 29 6450879 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798015 Affx-122972795 AX-385284951 29 6203019 GTTCATAAATGCACAAACCTCTTGTGTTTCTACTG[C/T]ACCCAGTAGAGATTTGTGACTTACACTTGTTTGAG Y 2 1 2 1 101000 f 74 goat snp58941-scaffold966-711623 29 6489847 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441244 Affx-122929499 AX-123311581 29 6234614 TGATAATAGTCTAGTTCTGTGAGACTTAAAAACAA[C/T]GATTGAATTTGAGTCTCTAACAATCTGTAGTTATG Y 2 1 2 1 201000 f 74 goat snp58940-scaffold966-680028 29 6521378 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795383 Affx-122946088 AX-385282339 29 6337849 TCCTTGGGTGATCACCTCTACTCCACTAGATTCTA[C/T]GTTATTCTACTTCTTCCTGCTCTTTCATTTGCACT Y 2 1 2 1 101000 r 74 goat snp58938-scaffold966-576793 29 6623601 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437943 Affx-122931627 AX-123308281 29 6377050 TTCATTGTTTGATCCTCTGACCATAACACTGTTTT[A/C]TTGTACTCAGATTCAGTGATTTAGAGTAGTAACAG M 2 1 2 1 101000 r 74 goat snp58937-scaffold966-537592 29 6663203 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411320 Affx-122952280 AX-123281670 29 6425020 TTGATCACAGGAGGCACGGAAAAGTTGGCATGGCT[A/G]TTGGTGACTTTCTACTGATTCATTTAGATGCAGGT R 2 1 2 1 201000 r 74 goat snp58936-scaffold966-489622 29 6712207 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408113 Affx-122954255 AX-123278464 29 6499575 CAGCTAACGAAAGTCTGTTTATGAAGAGTTTGTAA[C/T]AATATTAAACATTATATTATAAACTATTTTATATA Y 2 1 2 1 101000 f 74 goat snp58934-scaffold966-415067 29 6786310 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429637 Affx-122937684 AX-123299978 29 6528272 CAGTGATGGAGAGAGCTGGGGAACCGCACAGATGC[A/G]GCACCGAGAACCTGAGTGACACAGAATTAGCAGGA R 2 1 2 1 101000 r 74 goat snp58933-scaffold966-386370 29 6815348 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442380 Affx-122928012 AX-123312717 29 6559626 ACAGAGTACTGAGGAAAAAGCAGACTGCTTTTCAG[C/T]GGGAAAGCATATTAAAACTAAAATCAAGGGCACTT Y 2 1 2 1 102000 r 74 goat snp58932-scaffold966-355016 29 6846807 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441184 Affx-122929544 AX-123311521 29 6608904 TTTGTGCTCACATTTAATCTTCATAACAGTGCTAC[A/G]TAATGAGTATTATTATTTCTCACCTTTACAAAAGA R 2 1 2 1 201000 r 74 goat snp58931-scaffold966-305738 29 6894080 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780386 Affx-122968402 AX-385267480 29 6642471 AAGGTAGGGTGCCAAATATTCTGTTGTAGGACAGG[C/T]AAAGTGATTTTTCTTAGATTAACACAATCTTCAAA Y 2 1 2 1 101000 f 74 goat snp58930-scaffold966-272171 29 6928300 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427899 Affx-122939685 AX-123298242 29 6685143 TTCCTCCAAGTGCTCTCACAGCCCTGTAGAGTCCG[A/C]TAGTATTTATGGAACTTCCTACTATATTGTAATTA M 2 1 2 1 201000 r 74 goat snp58929-scaffold966-229499 29 6970812 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440572 Affx-122929302 AX-123310909 29 6718639 GGTATTAGAAGGAATAGCGACTCTTTGATATTTCA[C/T]GTTACAACAAAACTTTCGTCAGGTTTCTCTAAGCT Y 2 1 2 1 101000 r 74 goat snp58928-scaffold966-196003 29 7005191 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383344 Affx-122972677 AX-123253702 29 6759118 CTCTGTCCTACTTGACTCCCCAAATGGATGATAAG[C/T]GTTCGGTCCAGTGGTCTGTCCATCTGCCTGTGTTG Y 2 1 2 1 101000 f 74 goat snp58927-scaffold966-155524 29 7045770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773859 Affx-122974650 AX-385260999 29 6814232 AGCCAACAGAGCCAACATTAAGTTGTGTTACTTAA[C/T]GGAAACTCTAGAGGAGAATCTATTTTCAAACTCAT Y 2 1 2 1 101000 r 74 goat snp58926-scaffold966-100410 29 7101825 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453277 Affx-122920387 AX-123323610 29 6895181 ATGTAAAAATTGAACCAAACAACTTTGAGAAAATC[A/G]TTTTATGTTTAGTTGATTTCACCTGAGGGCCCAAA R 2 1 2 1 201000 f 74 goat snp58924-scaffold966-19461 29 7183234 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376725 Affx-122978961 AX-123247084 29 6924948 AAAATGTGTCCATTTCATGTAAACTGTCAAACTTC[G/T]TAGCCCAAACGTCTTCACAGTGTTTCCTTATTTTT K 2 1 2 1 101000 r 74 goat snp46746-scaffold652-10207 29 7219091 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397063 Affx-122962730 AX-123267418 29 6954203 ACTTATTATTGCTTCTTCTCAAACTCCCATGAACC[A/G]TTACTTCTCGACAGTAAATGCATCCAATAGTGGCT R 2 1 2 1 101000 f 74 goat snp46747-scaffold652-39462 29 7248914 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783166 Affx-122944521 AX-385270233 29 6999856 TACTTATCTTTGTCATCTTTGATCCTTTCTGCAAA[A/G]CTTTCAATAATTATGTCCTGACTGGATAAATAAAT R 2 1 2 1 201000 r 74 goat snp46748-scaffold652-85115 29 7294659 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383617 Affx-122972552 AX-123253975 29 7043176 AATCCTGGCTCCTCCACTTAATGGTTGGATGTGTT[A/C]TTTGATATCACTATGCAAAACAGAGATACTATAAT M 2 1 2 1 202000 r 74 goat snp46749-scaffold652-128435 29 7338321 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434320 Affx-122934746 AX-123304661 29 7074857 ACTGACTGTGAGGCCGAGGATGTGGACTCCTAAGC[A/G]TAAAACAGAAAGAAGCGGAAACCCCAGCAGAACTC R 2 1 2 1 101000 r 74 goat snp46750-scaffold652-160116 29 7378712 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391340 Affx-122967304 AX-123261697 29 7108650 GAGTACTTTCTTATCTACCTGCATCCCTTCAGAAT[A/G]CTTGGTCCACCCTTTAAAGAAGAACTTACCAGCAA R 2 1 2 1 101000 r 74 goat snp46751-scaffold652-193909 29 7412919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421783 Affx-122944343 AX-123292130 29 7147162 TAATGAACTAGAGGAGCAGAGAAGGAGACAAATTA[C/T]AATATCTTCTTGTGAAAAGAACTGTTTGCCTTGCT Y 2 1 2 1 101000 r 74 goat snp46752-scaffold652-232421 29 7451185 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786034 Affx-122921287 AX-385273070 29 7201567 TTATGGTGAGAGTGTGTCTACCTCTCTGAAATATC[A/G]ATGTGGGTATTTTCAGTCATCAAAGTATTGAAATC R 2 1 2 1 101000 f 74 goat snp46753-scaffold652-286826 29 7507983 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799536 Affx-122933847 AX-385286466 29 7232193 TCTGATTGTGGGACATAGTGATCTCTAAATTGAGC[A/G]CTACTTCAGACCTATCTAATAAAGCATAAAAGCAT R 2 1 2 1 101000 f 74 goat snp46754-scaffold652-317452 29 7538613 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410987 Affx-122952008 AX-123281337 29 7263094 GGAACCGGAAAATCAGTGAGCTGCTAGCCTCTTGA[G/T]CCATCCAAACTGCTGCTCCCTGGAGACACGTGGCC K 2 1 2 1 101000 f 74 goat snp46755-scaffold652-348353 29 7568286 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384130 Affx-122972817 AX-123254488 29 7299998 ACATATACCCATCATTATAGTTTCATACAGAATAG[C/T]GAAGCAATCCAGGCTTGGATTCAGTAACAATTTTA Y 2 1 2 1 201000 f 74 goat snp46756-scaffold652-385257 29 7606146 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779548 Affx-122929970 AX-385266651 29 7385916 CAAAAGGATCCTTTACCCATGCTGCCTACCAGACA[A/C]GTCATCCTAAAAAGTTAATCATAATAAAATTTTGG M 2 1 2 1 101000 f 74 goat snp46758-scaffold652-471175 29 7693838 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422611 Affx-122943723 AX-123292957 29 7424441 GGTTAATTCCTTTCCTTCTAGTGAGTATTCTCCCA[G/T]TTTAGACTCCATAATTGATTAGGCCAAAGACAGTC K 2 1 2 1 201000 r 74 goat snp46759-scaffold652-509700 29 7732312 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784259 Affx-122934534 AX-385271310 29 7461397 TAAACAAAAAAGGCACAATCGTTATGAATAACGCC[C/T]ACTGGAACTGTACAGAGAGGCTTTTTCTTTCAAAA Y 2 1 2 1 101000 r 74 goat snp46760-scaffold652-546656 29 7769822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774231 Affx-122927106 AX-385261368 29 7496846 GTATGATCCTGTGGCAATTAATTAATTTCAAGCCA[C/T]AGGTTACTATAAAGTGAAAATAACAATAGCATCTA Y 2 1 2 1 201000 r 74 goat snp46761-scaffold652-582105 29 7805173 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792484 Affx-122963776 AX-385279465 29 7570764 AAGAATGAATAAATTGACAAGGATGACTGCCTATG[C/T]GAGGGCTCAGGACTCCAATTTTTTTGCATGTATTG Y 2 1 2 1 101000 r 74 goat snp46763-scaffold652-656023 29 7879469 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782726 Affx-122924771 AX-385269798 29 7620312 TCGTAAAAGAGCCAGAGAAGGACACTGTAGAATAA[C/T]AAAGGTGTCACCTCATCAATAGGATATAAAAATTG Y 2 1 2 1 101000 f 74 goat snp46764-scaffold652-705571 29 7928974 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435273 Affx-122934050 AX-123305613 29 7652538 GCCATGACACACCTTCAGGAATATTAGGGTATAAA[C/T]CTAAATTATTACTCAATGAGAAGAACTGACCATCC Y 2 1 2 1 101000 f 74 goat snp46765-scaffold652-737797 29 7961853 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780550 Affx-122958035 AX-385267641 29 7694313 TAAACCACTCAGGTTAGATTTTCTGCATTTTTCAA[C/T]GAAATCTCTCCTTAAGTAATTTTAACATACCACAG Y 2 1 2 1 101000 f 74 goat snp46766-scaffold652-779572 29 8003847 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451392 Affx-122921203 AX-123321725 29 7728074 CATCAACAATAACCAAGTTATTTGGCCCTTACGAC[A/G]TGCCAGTCAGTGTGCGCAACAATTTACGCACTATC R 2 1 2 1 101000 f 74 goat snp46767-scaffold652-813333 29 8037618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391209 Affx-122967411 AX-123261566 29 7758761 GGGAGAGATGGCTGGGCCCAGGGTGGATTGGCCCA[A/C]GTGAGGTCCTTCAGAATCTCAAGAGTTTGGGCATA M 2 1 2 1 101000 r 74 goat snp46768-scaffold652-844020 29 8067349 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392831 Affx-122965779 AX-123263188 29 7771844 TATGTGGGTCCGCTCACATACTCACAAACCACCAC[A/G]CAGACTGATCTTAACATTTTCCCACATTTATTTTA R 2 1 2 1 202000 r 74 goat snp222-scaffold1006-12500 29 8080276 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771556 Affx-122967962 AX-385258714 29 7829457 GTGAGGCATCAGTCCAGGATTATGCGTGGCCCTTA[G/T]CTGTCACTTCTTTTGCTTTCTTTAACCTGGAGAGC K 2 1 2 1 101000 r 74 goat snp223-scaffold1006-70113 29 8137681 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444824 Affx-122926319 AX-123315161 29 7859925 TTTTCCTATTCTCAGGCTTCCTCTTTGAGAATATA[C/T]ACCTGCGAGCAAATTTTGGGTGACTTTTGCTTTCT Y 2 1 2 1 101000 f 74 goat snp224-scaffold1006-100581 29 8168294 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415521 Affx-122948676 AX-123285870 29 7896192 CACATATAAGAAATTCATTTTAAAATACTAGGTTC[C/T]TAAATAAAGGTATATATTATCATGCATTTCATTTT Y 2 1 2 1 303000 r 74 goat snp225-scaffold1006-136848 29 8204223 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419235 Affx-122945677 AX-123289583 29 7942213 GGACTTGATGGACAATCAAATGGTCACACAAATAC[A/G]TTCATAATTACAGTTGTGATCAGTGGTAGAAGGTG R 2 1 2 1 101000 r 74 goat snp226-scaffold1006-182869 29 8250368 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781405 Affx-122951903 AX-385268490 29 7986537 GCACCGGGAATTTTCATATGTCTGTGTGATGGCTC[A/G]CTACTGACAATAGTGAGTCAAGATCGTCCATGCCT R 2 1 2 1 202000 f 74 goat snp227-scaffold1006-227193 29 8294899 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432995 Affx-122935256 AX-123303336 29 8015859 CTGACTGCGCTGTCAGAACCGGCACTGTGCAGAGG[C/T]GGAGCTGGCAGATGAAGGTGGTGGAGGAGAAGCTG Y 2 1 2 1 103000 r 74 goat snp228-scaffold1006-256515 29 8324459 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452271 Affx-122920759 AX-123322604 29 8046909 CCAGGCTTGGATTTTCTTTCCCCAAAAGACAGATC[A/G]TCCGTCAGGCCCATTGAATTCTCTGAATCACCAGT R 2 1 2 1 101000 r 74 goat snp229-scaffold1006-287565 29 8355455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768285 Affx-122955734 AX-385255466 29 8088916 TTATGTGTACTCCTGAATTTGTGTGCTGTGGATTC[A/G]AATTTGTACAAAACTTTTGTCTCCCTTTCTGGTGC R 2 1 2 1 101000 f 74 goat snp230-scaffold1006-329572 29 8397990 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425688 Affx-122940856 AX-123296034 29 8149093 TAGTCATTCTGAGCTCTAAAAGGGGCCATGGCAAC[A/G]CTGAAGGCAGGACACCAAATCCATTCCCCCAGTCC R 2 1 2 1 101000 f 74 goat snp231-scaffold1006-389749 29 8458285 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413764 Affx-122949934 AX-123284113 29 8192723 AGTAGATTTGTTCAGAGCAGGGTGCAGGAGAGGCC[A/G]TCAGTTCCAGCTCCTTTTTTCAGCAGTCATGCACC R 2 1 2 1 201000 f 74 goat snp232-scaffold1006-433379 29 8502230 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277806 Affx-1111836098 AX-519551304 29 8240721 GGGTCATGCCATGGATGCTCTCAAGATCCCTTTTG[A/G]AGGCCTCCATCCTACAGTTTCCTTGACTTTGACAA R 2 1 2 1 101000 f 74 goat Random2.2K-2305 29 8240721 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38415841 Affx-122948871 AX-123286190 29 8249243 CTTCTCCTCCAAGTCTCGATGCTTCTTCATGACAG[C/T]ACTCCTTTCCCAATCATCCTGTAAGCTTTGGTTGA Y 2 1 2 1 101000 r 74 goat snp233-scaffold1006-489899 29 8558805 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445523 Affx-122925174 AX-123315860 29 8294253 AAGTGCAATGATTTTCACTCACATTTTACGTGACT[A/G]TAAAAACAAAATCTGAAAACATATCAACTATTAAA R 2 1 2 1 101000 f 74 goat snp234-scaffold1006-534909 29 8604025 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774464 Affx-122953187 AX-385261600 29 8327185 GGAGAGTTGAATTCTGTTAAATAGATACTTGCTAG[C/T]ATACCATTTTAACGTCTTTATCATAATTTTTATTA Y 2 1 2 1 101000 f 74 goat snp235-scaffold1006-567841 29 8636859 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272173 Affx-1111833370 AX-519545926 29 8387400 ATCTACAGTCCATGAGGTCACAAAGAGTTGAGCAC[A/G]ACTTAGGGACTAAATAACAACAAAATAAAGCATAA R 2 1 2 1 103000 f 74 goat 29_8387400_AF-PAKI 29 8387400 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38428199 Affx-122939455 AX-123298542 29 8405163 TATATAATAAGACTGGAAAGCACAAACAGGAAAAT[A/C]AAAAGATTAAAAGTAACACCACCTACTAAGCCTTT M 2 1 2 1 101000 r 74 goat snp237-scaffold1006-645819 29 8715001 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437919 Affx-122931645 AX-123308257 29 8445942 TTTTATCATGTTCAGTCTTTAAGTTCCCAAAGAAA[C/T]GCTGGTCTTTATCCAGAATTAGCTTTATTTAGGCA Y 2 1 2 1 101000 r 74 goat snp238-scaffold1006-686598 29 8756719 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417637 Affx-122946852 AX-123287985 29 8476442 TGAAATTAAAATTCCTTAGTTTAGCACACAAGCCC[A/G]TTTTAGAGCTGACACCTGCTCTTTGTCGCTTTGTC R 2 1 2 1 101000 f 74 goat snp239-scaffold1006-717098 29 8787727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438684 Affx-122930872 AX-123309021 29 8514255 CACTGAACCACCAGGGAAGTACCCCTCACTACTTT[A/G]TTTTGGCACATTCTAATACCCAGACTTAGCTTGAC R 2 1 2 1 201000 r 74 goat snp240-scaffold1006-754911 29 8825397 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401541 Affx-122958910 AX-123271894 29 8553682 GAAGGGCTGAGTTGCTGGGAAAGTTGAATTTGGCC[A/G]TAGGCTGGGATTTGGAGGCTTGTTCAAGCAGGAAG R 2 1 2 1 101000 r 74 goat snp241-scaffold1006-794338 29 8864264 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415276 Affx-122948838 AX-123285625 29 8609650 ATAATATAAGCATATTATTTAAGAAATTGCTACTG[C/T]ATTCATAAGCTAGGGTTAATTGACAAATTGTATCT Y 2 1 2 1 101000 r 74 goat snp242-scaffold1006-850306 29 8920000 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788863 Affx-122946261 AX-385275878 29 8663040 ACCATATTTTGTGACCTTTTACACAAAAAATTGAA[C/T]GATGTAAGATGGTTCATTCTGTTTCCCAGACATCT Y 2 1 2 1 101000 r 74 goat snp243-scaffold1006-903696 29 8973014 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800266 Affx-122934345 AX-385287189 29 8700380 TAGCCGAAGAGTATTTTAAGCCAAGAACTCTTAAT[A/G]CTTAATCATTGTATTGTTCATAACCATGACATTCA R 2 1 2 1 101000 f 74 goat snp244-scaffold1006-941036 29 9010342 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422268 Affx-122943993 AX-123292614 29 8736116 AGCAAGGAACGGCGGGCTCATTTGAAAGCGGTAAC[A/G]CAGATTAGTGTCATATTGACTTAAAAGCAAGCCAA R 2 1 2 1 201000 r 74 goat snp245-scaffold1006-976772 29 9046101 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431366 Affx-122937037 AX-123301707 29 8783714 AGAATATATTTGTAATTTCAATAAATTCAAAGACT[A/G]ATAAATTGGGCACTATAAAACTATAAATTTTCCTC R 2 1 2 1 101000 r 74 goat snp246-scaffold1006-1024370 29 9094278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425771 Affx-122940722 AX-123296117 29 8825784 TGTTAAAATGTATTTCAGTGAAATGGCCAATCTGT[A/G]CCCCTGATTATTAAGTTAATGATGCTGGAAACATG R 2 1 2 1 101000 r 74 goat snp247-scaffold1006-1066440 29 9136457 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430536 Affx-122937199 AX-123300877 29 8868347 TGCAGAGAGGCTATGTAACTTGCCCAAGGTCACAT[A/G]TAAGTGGTAATTCTGAAATGTAAATGTGGATACCA R 2 1 2 1 201000 r 74 goat snp248-scaffold1006-1109003 29 9179623 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800524 Affx-122942190 AX-385287444 29 8897664 TTGGTGTATACCTCCTGTATTACCGCTTAATGTAG[C/T]ACTTGTATGAGGGTAGCTTGTGAAAGTGTTAGTCA Y 2 1 2 1 101000 r 74 goat snp249-scaffold1006-1138320 29 9209014 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274480 Affx-1111834317 AX-519548071 29 8918609 GTCCTTCGTAAATTATAAAAGTTAAGCATTGTCTT[A/C]CTGCAGGCTTTTCTGCCTGTACCTCCAGATCTACT M 2 1 2 1 201000 f 74 goat GoatD01.029876 29 8918609 G T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320778724 Affx-122929209 AX-385265835 29 8932646 AGGCAAACAAAACATCGTTGTATTCCTTGAGGGAC[A/G]CAAAGCCGGAGCTTAATCGAGGAAGTAGCTGCATA R 2 1 2 1 201000 r 74 goat snp250-scaffold1006-1173302 29 9243998 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783046 Affx-122956098 AX-385270114 29 8964171 CCTTTCAGAAAAAGAGCTGCATTAAATTAATCCTC[A/C]GTTATCCATGGGTGAATGAATTGTCTATAGATTTT M 2 1 2 1 101000 f 74 goat snp251-scaffold1006-1204827 29 9275649 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403875 Affx-122957919 AX-123274227 29 9049342 CTTACGAATTGATCTGATTTCATGTTAGATTGATG[C/T]AAGAAATAAAAGTTAATGATAGCTGTGTTATCCCC Y 2 1 2 1 101000 r 74 goat snp253-scaffold1006-1289998 29 9359482 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428003 Affx-122939163 AX-123298346 29 9090535 TTCAAAAATTGAAGTTTTTAGAATCCTGGAGTCAG[C/T]GATAGGGAAAATGCTAAGCCATGAGAAGCTAGGTT Y 2 1 2 1 101000 r 74 goat snp254-scaffold1006-1331191 29 9401414 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796622 Affx-122940932 AX-385283568 29 9119807 AGAAATATGTTTCCATGTACTATCCCAGTACTTTC[A/G]TTTCAGATAAGTTGATTTGATAATCATGTTTATAT R 2 1 2 1 101000 f 74 goat snp255-scaffold1006-1360463 29 9430789 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447984 Affx-122923750 AX-123318320 29 9158042 GCGAGGGGCCCTGTGGCTGGAGAGGGAGTGAGTGA[C/T]GGACAGACAGAATGGCAAGAATGAAGTTAGAGAGG Y 2 1 2 1 101000 r 74 goat snp256-scaffold1006-1398698 29 9469407 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771214 Affx-122962689 AX-385258372 29 9186654 TGAAGAAACAGAGGTGTATTGACTGTGTATCATGT[A/G]CATCTGGAATGGCATTTTAATGGATTGCCTCTGAC R 2 1 2 1 101000 r 74 goat snp257-scaffold1006-1427310 29 9498629 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415424 Affx-122948723 AX-123285773 29 9225151 AAGCTACACTTCAGTTTCTTTCTTTTTACATGTCT[G/T]TTAGTGTCTATTACTGCCAAGCTGAAAATTAGCAA K 2 1 2 1 101000 r 74 goat snp258-scaffold1006-1465807 29 9537567 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393352 Affx-122965929 AX-123263708 29 9279362 CTTGAGTTTTTCCTCATCGTGTGACCCTAACTCTC[A/G]CTGATGTGTTTAACTTATTTATTTGTTTATTGTCT R 2 1 2 1 101000 f 74 goat snp259-scaffold1006-1520018 29 9593541 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408943 Affx-122953934 AX-123279294 29 9319979 AAATTTAAAATAAATAATATACGAAAAAAATATGT[A/G]CTACTTGACATCTAGCAGTACTTAAAAAACATGTG R 2 1 2 1 102000 r 74 goat snp260-scaffold1006-1560635 29 9634781 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774835 Affx-122958525 AX-385261969 29 9349164 ACATGCATGTGGCCAGATTTTCACTTACGGTTTCC[A/G]AATGATTGGAAGGTTTATTTGGGCCCACTGAACAG R 2 1 2 1 101000 f 74 goat snp261-scaffold1006-1589820 29 9664267 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447225 Affx-122924974 AX-123317561 29 9389425 GCATAGTGCCTGGCACAGATGAATATTAAAGAAAT[A/G]TGATAGGGCATAGAAATTTTAACTTTATTTTTCTG R 2 1 2 1 101000 f 74 goat snp262-scaffold1006-1630081 29 9704845 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396236 Affx-122963336 AX-123266591 29 9470717 CTTAATCACAAATCAATTTAATAAAAGAATGCTCT[A/G]TTAAAATAGTGAACAATTAATATTTACATTCTGAT R 2 1 2 1 201000 f 74 goat snp264-scaffold1006-1711373 29 9786401 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415284 Affx-122948833 AX-123285633 29 9514486 CCTCCAGGGAGGCGTGTGTTTTGTTTGTCAGTCTG[C/T]AGCATTCCAAGGGGAAGACCAAACGTTTAGGTCAT Y 2 1 2 1 101000 r 74 goat snp265-scaffold1006-1755142 29 9830725 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394350 Affx-122964657 AX-123264705 29 9543331 CTCAATTTCCTCATTTGTGAAAAAGATATGATATT[A/G]CCTATATGTAAGCAGTGTGGCAGGAAAGTATTGAA R 2 1 2 1 101000 r 74 goat snp266-scaffold1006-1783987 29 9860097 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426323 Affx-122940280 AX-123296669 29 9603811 CCAAATTCATATTGAACACATACTGTGTGCCAAGC[A/G]TATACTGAGTCTGGGGTAATAGTAGGAAACGGTCA R 2 1 2 1 303000 f 74 goat snp267-scaffold1006-1844467 29 9921255 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413792 Affx-122949912 AX-123284141 29 9631345 CTTTTTCTACTGTATCCTTAATATATGGAGAAAAT[A/G]CATGTGTAATTACCTACGTGTCCTCTTCTTCTCTT R 2 1 2 1 101000 r 74 goat snp2759-scaffold1079-2273547 29 9950359 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440304 Affx-122930216 AX-123310641 29 9663093 AAAATTTAGGTCTCCAGCTTCAATAAACTTTCCCA[A/G]GTAAGATTATGAAGCTCAAAATGCAGAGCTTGGCA R 2 1 2 1 101000 r 74 goat snp2758-scaffold1079-2241799 29 9982266 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415719 Affx-122948516 AX-123286068 29 9692831 GGAAAATAGCCAAGTTCTATACTCTAGTTTTGGGT[A/G]CTTTCCACTTGACTTGATACCAAGGGTGGCAATGG R 2 1 2 1 101000 f 74 goat snp2757-scaffold1079-2212061 29 10014462 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38431554 Affx-122936201 AX-123301895 29 9737550 TCCTTTGGAGTTTCTGCTAAATAAACCCAAATGAT[A/G]GTGACTTATTCTTTTACTATACAGAAAGCTCTAAA R 2 1 2 1 101000 r 74 goat snp2756-scaffold1079-2167342 29 10059788 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409678 Affx-122953069 AX-123280029 29 9771025 TTATCCGTCTATGTGCATAAGCTCAATAAGAAATA[C/T]ACATGGAAATAGGACCTCGGGCCTCCCCTCCACCC Y 2 1 2 1 101000 f 74 goat snp2755-scaffold1079-2133867 29 10093466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390692 Affx-122967948 AX-123261049 29 9812819 CAAAGAAGAACATCTAAGAAACTAAGTCATGGGTA[C/T]AGCTAAAATTTTAAATCTTAACCTTTTTCTCCCCC Y 2 1 2 1 101000 f 74 goat snp2754-scaffold1079-2092073 29 10135627 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791940 Affx-122925238 AX-385278930 29 9853338 AGATAATACTGATTTTACTTGTCATTAAAAATCTG[C/T]AATACTTTACTTGAAATCTGCCCTATACAAAGGTC Y 2 1 2 1 101000 r 74 goat snp2753-scaffold1079-2051554 29 10175853 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419282 Affx-122946246 AX-123289630 29 9898806 TATCTTGGTTCTATTCACTTGTTTTCTACCTTAGG[A/C]TCTATTTTCATTTTTCTTTCTATTTTAAATAAATA M 2 1 2 1 101000 f 74 goat snp2752-scaffold1079-2006086 29 10221441 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394614 Affx-122964415 AX-123264969 29 9987301 AATAATTGGTGGCTTTAATTTAATTGCTATTAATA[C/T]AAGGAAACCCCTTCCAATAATCAGACTTGGGCAAC Y 2 1 2 1 101000 r 74 goat snp2750-scaffold1079-1917591 29 10310732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401013 Affx-122959683 AX-123271366 29 10038578 AATTTAGTATATTTCTGTGTGTGTTGGGGGAGGGT[A/G]GGGCTCTATCTAAGATTCTAGAATCTAGAAAAACA R 2 1 2 1 201000 r 74 goat snp2749-scaffold1079-1866314 29 10361506 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800008 Affx-122956284 AX-385286931 29 10089305 GTAAAGAATGATATGGAAGCCTGATAGGAACACTC[A/G]CCAGGGTGAAAGGGAAATGGTTAAAACTAAGGTTG R 2 1 2 1 101000 r 74 goat snp2748-scaffold1079-1815587 29 10411921 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414835 Affx-122949193 AX-123285184 29 10097044 CCGTCTGCTAACAGTCCTGGAAAGGCACTCTTCAC[A/G]CACTTATCTGCCAAAGCATGACTCATGAAATTCAG R 2 1 2 1 101000 r 74 goat snp4262-scaffold1132-665647 29 10419906 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413810 Affx-122949898 AX-123284159 29 10139286 CCACTCTAACTAAGCTCCTGCTCCTTTGGTGTCCT[A/G]CCAACCAGAAGCAGTGCCCAATCCCGGCTAAACAT R 2 1 2 1 201000 r 74 goat snp4261-scaffold1132-623405 29 10463352 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780619 Affx-122956656 AX-385267709 29 10202071 AAGGTGAAGCTGCCATTCCGGAAGTCCAAAGAAGT[A/G]TTAGATGTTGATACTCCGGCAAAACTGGAAAGGAA R 2 1 2 1 101000 f 74 goat snp4260-scaffold1132-560620 29 10526202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402717 Affx-122958788 AX-123273070 29 10233602 TTTCACAGTACCACAGATCCACCCTCCACTGCTTC[A/G]TCTTTGACACTTAAAGGATAAAGACAGTTTAAAAT R 2 1 2 1 201000 r 74 goat snp4259-scaffold1132-529089 29 10555217 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423655 Affx-122942346 AX-123294001 29 10264332 TTTTAAGTGATTCATTTCCTTCTCAAAAATGTCTC[A/G]CTTGGACAATGAATTATATATGACTACACGTACTG R 2 1 2 1 101000 r 74 goat snp4258-scaffold1132-498359 29 10585706 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443910 Affx-122927050 AX-123314247 29 10298344 TATAAAGAGGGAGTCTTGTTAATACTGTTACTGCT[A/G]TGATTGCTATTACCATTATTACTACATTCCATGCT R 2 1 2 1 101000 f 74 goat snp4257-scaffold1132-464347 29 10619457 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419471 Affx-122945479 AX-123289819 29 10365903 AAACTTTTCCCTGATAAATTAAAAATCTAAAAGAA[A/G]TGAACAAATTTCTTAATGAACTTCACTCAAAGAGA R 2 1 2 1 103000 r 74 goat snp4255-scaffold1132-396788 29 10687034 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452959 Affx-122920167 AX-123323292 29 10397326 CATGGCTTGTCACCCACCCCTGCAACCCAGAATCA[G/T]CCCCAGGAATTAGCAGCGCCTTTCAGCAGTGCAGA K 2 1 2 1 201000 r 74 goat snp4254-scaffold1132-365365 29 10716706 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775110 Affx-122930177 AX-385262242 29 10493731 ATATATGTGAAGGACTTAGAACAGTACGTGACACA[C/T]GATAGGTGCTCAGCATTTACTACTGCTTTTATACT Y 2 1 2 1 101000 r 74 goat snp4252-scaffold1132-268960 29 10813315 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448630 Affx-122923369 AX-123318966 29 10527021 TCCATGTGAACATACCCCACAATTTCCTAGGAGAG[C/T]GATGATTATTTAGATGATTTAAAAATACTCAAGTC Y 2 1 2 1 201000 r 74 goat snp4251-scaffold1132-235670 29 10845667 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387495 Affx-122970337 AX-123257853 29 10575529 TATACTAACTCCCATTCTTCAGAAACTAAAGCCTG[C/T]GCTGTTCTATGATGTCATACTGCTTTCAATGCCAA Y 2 1 2 1 101000 r 74 goat snp4250-scaffold1132-187162 29 10894443 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790971 Affx-122945142 AX-385277968 29 10621779 AACTTCTTTGACCTACAGTTTTCTTCTTGGTAAGA[G/T]AGAGGCTCTAAAACGTATGTCATAGACTGTTAAAA K 2 1 2 1 101000 f 74 goat snp4249-scaffold1132-140912 29 10940608 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391515 Affx-122966664 AX-123261872 29 10661770 CAAGGTCAAATGACAGATTTATGGGGACCTGGGAA[C/T]AGAAGAAGGGGTAGCAGGCTGTGGACACAATGGGC Y 2 1 2 1 101000 f 74 goat snp4248-scaffold1132-100921 29 10980725 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387875 Affx-122969631 AX-123258233 29 10699117 CACTGAGTTACTTAACCTATATAAAATCAAAGCTG[C/T]GTTTAATTTATCTTTGCAATCCTGGTGTCTGCTAC Y 2 1 2 1 201000 f 74 goat snp4247-scaffold1132-63574 29 11017126 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776550 Affx-122936881 AX-385263677 29 10743191 AGTTAAGGACTTGATGAATTAACCAACACTTATTA[C/T]GCTATTGACTGGACCAGGGCATGTTGGTGTTCATG Y 2 1 2 1 101000 r 74 goat snp4246-scaffold1132-19500 29 11061194 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396393 Affx-122963019 AX-123266748 29 10764059 TATGAGGCAAAGAAATACATTTATAGAGCTATACA[A/G]TGTCAAAACATCAATAAAGAATAGTCACCTCTCTA R 2 1 2 1 101000 r 74 goat snp45589-scaffold6239-1269 29 11081674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390210 Affx-122967788 AX-123260567 29 10787748 ATAGCCTTTAAAAATGTGTTGGCCCTTGGCAGCAA[C/T]GGAGACACAGACATAGAGAACAGACTTATGGACAC Y 2 1 2 1 101000 f 74 goat snp48291-scaffold683-1989559 29 11103533 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453464 Affx-122919851 AX-123323797 29 10835947 TGAATCCCAGCCTGGCCACACAGTGGAGGGTGATC[A/G]CGGGCATGTCAGGTACCCTCTCAAGCCTTGATTTT R 2 1 2 1 101000 r 74 goat snp48290-scaffold683-1941360 29 11152069 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390187 Affx-122967803 AX-123260544 29 10870444 ATCAGCAGAGGGAAGAAAGTGACACCAGAGAAACG[C/T]ACCCGAACTGACGGTCAATTAATGATAATTCAAAA Y 2 1 2 1 101000 f 74 goat snp48289-scaffold683-1906863 29 11186951 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783645 Affx-122963926 AX-385270704 29 10902990 TGCCTTTCTAAATCATGCTGTCATTGAATAAAATC[A/G]AACCAGAGAACAGCACAGTCTCTTTTCCAAGAATG R 2 1 2 1 101000 r 74 goat snp48288-scaffold683-1874317 29 11218845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273224 Affx-1111833352 AX-519546881 29 10905832 GAACTTCTTTTAACATCTCTTGCAAAGCAGGTCTG[A/G]CAATATATTTCTCCAATTTTTCGTTTTTGTCTCAG R 2 1 2 1 201000 r 74 goat 29_10905832_AF-PAKI 29 10905832 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38433216 Affx-122935623 AX-123303557 29 10958996 GCTCCGTGTCTTATCTGTGCCCAGACTGTTCTCCA[A/G]TGCTGGGCTGTTCTCTTTGGCTAGAAAGACGCTTT R 2 1 2 1 201000 f 74 goat snp48287-scaffold683-1818311 29 11274431 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389248 Affx-122969035 AX-123259606 29 11006768 CCTCTCACCAGAGTGAATTCCTCAAATAAAAAAGG[C/T]AGAGCTCTTCCCACGTCCCAGAGGTCAGCCTGGCC Y 2 1 2 1 101000 f 74 goat snp48286-scaffold683-1770539 29 11321463 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396306 Affx-122963085 AX-123266661 29 11054635 GCCTGTTCATGGGATGCTCCACGAAGGTCAATGCC[A/G]TTCACCTGAAAGAGAGGAAGCCAGAGAATTTTGGT R 2 1 2 1 201000 f 74 goat snp48285-scaffold683-1722672 29 11369215 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393626 Affx-122965309 AX-123263981 29 11090154 CTGTCCCAGCTTTATGTCATCTTTGAGTTAAAGCA[C/T]GAAAACAACACAGAGAGATGAACACCTCTAAGATC Y 2 1 2 1 201000 f 74 goat snp48284-scaffold683-1687153 29 11404711 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800077 Affx-122976335 AX-385287000 29 11121826 GTGGGAATCTCGAGGTTTTAGGTTGGGTCATAAAA[C/T]GAAACAACACGGTCTGTTTAAAGCACACCTCTGGG Y 2 1 2 1 202000 f 74 goat snp48283-scaffold683-1655481 29 11436128 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410902 Affx-122952068 AX-123281252 29 11169586 CCTTGCTACAAATCATTGTCTACACAGCAAGTAGA[C/T]TCTCCTAAAACAAAATTCAGACTCCAGCACTCCCG Y 2 1 2 1 101000 r 74 goat snp48282-scaffold683-1607721 29 11483316 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387239 Affx-122970573 AX-123257597 29 11209883 CATTTTCTCTCATATTTGATTCCCACACTTCTCTT[A/G]CTCTGTTTTATATCAAAACAGCTGACCCCACGCAA R 2 1 2 1 201000 r 74 goat snp48281-scaffold683-1567424 29 11523224 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383740 Affx-122972451 AX-123254098 29 11240669 ATTGAGAAAATGGTATAAAAAGTGAAGAAAATACA[C/T]AAGGAGAAAGAAAATCTAAAAGATGGCTTTCTCTG Y 2 1 2 1 303000 f 74 goat snp48280-scaffold683-1536638 29 11553821 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790611 Affx-122925882 AX-385277613 29 11277851 CCATAAAAACTAGGCAGGAATCCAATACTAGCAAG[C/T]ATGAAGTTGAGATTTTTAAATGCATAAACTTGAAA Y 2 1 2 1 201000 r 74 goat snp48279-scaffold683-1499456 29 11591704 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452131 Affx-122921678 AX-123322464 29 11314773 AGGCCCTCCATATCAGTATACGCACATATATACAC[A/G]TATTTATCGCTATTGTGTTGTTATTTATCATGGGT R 2 1 2 1 101000 r 74 goat snp48278-scaffold683-1462534 29 11629242 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410907 Affx-122952064 AX-123281257 29 11350847 TTATTTTGCATAATTTGCCTGCACCCCTTTCTCTA[A/C]CAATCAGTAACTCATGTGGGATCCTCCACATGTTC M 2 1 2 1 101000 f 74 goat snp48277-scaffold683-1426460 29 11665313 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277950 Affx-1111836099 AX-519551445 29 11396549 ACTCAAGGAACGTGCTTACTTGTGAGCTCCTGAAG[A/G]TAGGAGCTTGTTGTGTTGGAACTTTAGTCTCTGCA R 2 1 2 1 101000 r 74 goat Random2.2K-2309 29 11396549 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468277812 Affx-1111836101 AX-519551310 29 11413388 ATGATGTGGTTTTATCCATCTCTGCTGATGGAACT[A/G]CTGTCCACAATCTTCTAAGCTAGAAGCTTCTAATA R 2 1 2 1 101000 f 74 goat Random2.2K-2310 29 11413388 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38386976 Affx-122969962 AX-123257334 29 11450331 TTCAGGTCTAAAACCACCTTCCTCTGTGGGAAGCC[A/G]TGTGACCTTCCCACACAGAAGCTCCCTCCCTTCTG R 2 1 2 1 101000 f 74 goat snp48275-scaffold683-1326976 29 11763237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798786 Affx-122938496 AX-385285717 29 11486857 GTGAATAGAAAAAGGACTCCCAGAAAGCTGAGGAA[C/T]TGAGAAATGACATCATGGTTCCTATAAAGTTGGCT Y 2 1 2 1 101000 f 74 goat snp48274-scaffold683-1290450 29 11798415 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432327 Affx-122936293 AX-123302668 29 11522251 TTAATCTTCCAAATAGTCATGGCCTTCCTGGAGCC[A/G]TTCGAGTAGATTGGATGCTTCTAGTAGGAAAAGTG R 2 1 2 1 201000 r 74 goat snp48273-scaffold683-1255056 29 11834027 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431620 Affx-122936152 AX-123301961 29 11588975 CTGCCCTTTCCTTTCATTGGATTCTCTCCCTCCTC[A/G]TTAGAACCTCCTATTTCCCTTTCATTCTTCCTCTT R 2 1 2 1 101000 r 74 goat snp48272-scaffold683-1188332 29 11893326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404062 Affx-122957151 AX-123274414 29 11630471 ACTGTTTCCTCCTCTTCCTCCTTTATTTTACCTGT[A/G]CTCTTACAATGTTACTGTCAGGTTTTTTGTTGTGT R 2 1 2 1 201000 r 74 goat snp48271-scaffold683-1146836 29 11934975 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277956 Affx-1111836102 AX-519551451 29 11653053 GGGCAATTATGAATAATGATGCTATCAACATTTGT[A/G]TATAGATTTTTGTATAGAAATATACTCTTACTTCC R 2 1 2 1 201000 r 74 goat Random2.2K-2311 29 11653053 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38393522 Affx-122965798 AX-123263878 29 11670326 GCACAGAACAGTCCTGAAATTAGATGAACTGGCTT[C/T]TCAGAGCAGAAATCACCACCAGAAAATGATTTAAG Y 2 1 2 1 101000 f 74 goat snp48270-scaffold683-1106981 29 11975021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418291 Affx-122946994 AX-123288639 29 11742652 ACACACACAAAATAAAGCCCCACAAAACTTAACCT[A/G]CTCAGAAGCACGCTCATCTTAAAAATGAATAGTGT R 2 1 2 1 201000 r 74 goat snp48269-scaffold683-1034655 29 12047547 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384544 Affx-122973021 AX-123254902 29 11777274 ACTACCAGGATTTGAACCCAAATCTATCTATTTCT[A/G]GAGCCACCTCGCTCTTCCACGTATTAATAAAACGC R 2 1 2 1 201000 r 74 goat snp48268-scaffold683-1000033 29 12081941 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396725 Affx-122962803 AX-123267080 29 11813229 GCCAGTCATCCAAGCACAGCTACACCCTCCGTGCG[C/T]AGGTCTCTTTTCAGAGCTGGGTCCAGACTTTCCCC Y 2 1 2 1 101000 r 74 goat snp48267-scaffold683-964078 29 12118351 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772691 Affx-122939510 AX-385259838 29 11872284 ATTAATGGTTTTTTCCCTAAAATCTAATTATTAAT[A/G]TACTACATTAGTTTTGTCTTTGTTCATATTTGTTT R 2 1 2 1 201000 f 74 goat snp48266-scaffold683-905023 29 12177541 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430508 Affx-122937222 AX-123300849 29 11914373 TCCCTTCTTCCCCAAAGAAACTCATCTTCCTACAG[C/T]AGGAAGCAGCTTTTACCCTGAAGTTCTCTCTCCTC Y 2 1 2 1 201000 r 74 goat snp48265-scaffold683-862934 29 12220350 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446177 Affx-122925739 AX-123316513 29 11962665 TCTGAAGCCTGCCATGCAGGCAGAAGCCCCAAACT[A/C]GCAAAGACGTCTCCTTCACAAAAATACTGGGCAAT M 2 1 2 1 201000 r 74 goat snp48264-scaffold683-814642 29 12268897 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394747 Affx-122964855 AX-123265102 29 11997710 ATGAGTAGAGCTTAATAGTTTTTAAAATAGTGCTT[C/T]TACTGCCTTTCTCACCAAGCTGTATCCACCCTGCA Y 2 1 2 1 101000 r 74 goat snp48263-scaffold683-779597 29 12303647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388277 Affx-122969763 AX-123258635 29 12054000 GTGGCCAAAAAAAAAAAAAAATTACCCTGCAAGCA[C/T]AAAGCAGGATGGTCCCAGCAAACTGTGTGTTGTGG Y 2 1 2 1 201000 r 74 goat snp48262-scaffold683-723307 29 12359350 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772635 Affx-122950010 AX-385259783 29 12097987 CTCCCAGGCCAGGCACTTTAGATTCTATTACAGCA[C/T]AGCCCCTCTAACTGTGAACCTTCTTCTAATAACTG Y 2 1 2 1 101000 f 74 goat snp48261-scaffold683-679320 29 12403987 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437076 Affx-122932669 AX-123307414 29 12128648 TATTGTTCATTTGTGTTACCCCAGTGATCTTCCAG[A/G]TCCTAGAACCCAGGAGCAGACCCTTAGGTGAGTAT R 2 1 2 1 101000 f 74 goat snp48260-scaffold683-648659 29 12432852 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449474 Affx-122922644 AX-123319809 29 12171245 TGGTTGAGTTTTATTTTCCAAAAGCATGTATTAAA[C/T]GATTACACAGGCCACACAGACACACAAGCACACAG Y 2 1 2 1 201000 f 74 goat snp48259-scaffold683-606062 29 12475473 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277816 Affx-1111836103 AX-519551313 29 12182879 ATCAGGGCAACAGTTTGACAATTTGCAGGAAACTC[A/G]CATATCCTTTAGAAGCTCTTCACAGTACTCCAGAC R 2 1 2 1 101000 f 74 goat Random2.2K-2312 29 12182879 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320798316 Affx-122974314 AX-385285251 29 12228634 GGCTTCCTTATTCTTGCAGATGCAGTTAATTTATT[A/C]TGATATTAGTGACATTCCAATATATTTAGATAAAA M 2 1 2 1 101000 f 74 goat snp48258-scaffold683-548673 29 12532864 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375629 Affx-122978704 AX-123245988 29 12292364 CATATATGTACATATATATATATGATATCTATACT[A/G]TATCTTAGGGCTCCTTTCATAGAGTAATATCCAGG R 2 1 2 1 101000 r 74 goat snp48257-scaffold683-484943 29 12597822 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403578 Affx-122957576 AX-123273931 29 12328849 TTTTGTATTTGTTTGCAAATGCAACCAAGTTAATA[C/T]AAAATCCATTTTCAGAGGTGGGATAGAAGGCTGCT Y 2 1 2 1 201000 f 74 goat snp48256-scaffold683-448458 29 12634500 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443600 Affx-122927314 AX-123313937 29 12359925 CATGTGTGTGAAACTTTTGAAAACTGTAAAGTACT[A/G]TAGAGTTTTAAGAGCCTTTTTATCAATCCTCCCGC R 2 1 2 1 101000 r 74 goat snp48255-scaffold683-417382 29 12664430 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790070 Affx-122964933 AX-385277076 29 12388813 AGCAATAGATTAAGGATATGTGCAACAATCTGGAT[A/C]GATATTAAAGTCTAAACATACAATGATAACGTAGG M 2 1 2 1 101000 f 74 goat snp48254-scaffold683-388494 29 12692984 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383141 Affx-122973247 AX-123253499 29 12422356 TTTAACTGAACTTTGTTTATAAAAGGTGTATGGTT[A/G]CTGTGGTCTAGCTAGTGGTTGTACATGTGAACATT R 2 1 2 1 101000 r 74 goat snp48253-scaffold683-354951 29 12727035 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417588 Affx-122946890 AX-123287936 29 12481777 AAAGAATGAGAAGCAAAATAAGTTGTAAATATAGA[C/T]AAGTCTAAAAGAAAACTGACTATATAACATAATTT Y 2 1 2 1 101000 f 74 goat snp48252-scaffold683-295530 29 12786970 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383081 Affx-122973738 AX-123253439 29 12515160 GGAAGAAAATACCAGTTGTATTTTCTGTATTTCTT[A/G]TCTTCCATGCAGTCAGCACAAATGGGCAGTAAGCC R 2 1 2 1 101000 r 74 goat snp48251-scaffold683-262147 29 12820438 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444822 Affx-122926321 AX-123315159 29 12574128 GCTTAATTGGAGGTGTCTAAGGTATTCATGTAAGC[A/G]TAATTGGAAATACGAAATTTTATCTGTGGTATTCT R 2 1 2 1 101000 f 74 goat snp48250-scaffold683-203179 29 12880190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385316 Affx-122971672 AX-123255674 29 12619674 GAGGTTACGGAGACAGATAGTTAACCGAGTAGCCT[A/G]CTTAACTGGAGGTCTGTTAATAAGATATCCACTTT R 2 1 2 1 101000 f 74 goat snp48249-scaffold683-157633 29 12925462 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388201 Affx-122969422 AX-123258559 29 12676849 ACAGATTTGAGGTGGACTAAGACAAAGGCTATTTC[A/G]TGTTCACACCAAGAATGTTTTTCTTGGAGCTTTTA R 2 1 2 1 101000 f 74 goat snp48248-scaffold683-100458 29 12983250 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421059 Affx-122944515 AX-123291406 29 12716313 CAGAGGCTGGCAAACTTTTTCTGTAAAATGCCAGG[C/T]AGTAAGTATTTTCAGTTTCATAAGCCAAATTCCAG Y 2 1 2 1 201000 r 74 goat snp48247-scaffold683-60994 29 13022608 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773596 Affx-122945381 AX-385260736 29 12750114 CAAACTGTGTTTAATATCACAGAAGATAAATCTTC[A/G]GCTTAAAAATAAGAGACAGGCTATCAAGAGGCACC R 2 1 2 1 201000 f 74 goat snp48246-scaffold683-27193 29 13056674 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764367 Affx-986698894 AX-385252080 29 12762415 GGTTTCTATTTCCTCCAATAGGCATTTTTCCATGT[A/G]TCGAATGTTGGCTCCGCTTCTCTGTCCCTCCTGAT R 2 1 2 1 600010 f 74 goat 29_12762415 29 12762415 Ancestral_priority_1043 ancestry 0.678 recommended IMAGE 10K 10K ancestral 320804342 Affx-986696510 AX-385290950 29 12762490 TCAGTCTGGGTCTTCGTCTGGAATAGCAGCCGCTC[C/T]GGGTGGCCGGGCTGGGTCTGCTGGGTTGGCTAGGT Y 2 1 2 1 600010 r 74 goat 29_12762490 29 12762490 Ancestral_priority_1043 ancestry 0.406 neutral IMAGE 10K 10K ancestral 320764343 Affx-986698870 AX-385252060 29 12762715 CGAGTAGGAGCCTAGCCGCTGTTCGATATGGGCAA[G/T]GTCTTGGAGTGAAAAGGGTATGTGGACATGGGTGA K 2 1 2 1 600010 f 74 goat 29_12762715 29 12762715 Ancestral_priority_1043 ancestry 0.454 neutral IMAGE 10K 10K ancestral 320764348 Affx-986698875 AX-385252063 29 12762763 AAAGGGTATGTGGACATGGGTGAGACCCTCCGGGC[C/T]GGCCACCTGGCAGAGAGGAAGCAGGGGAGCTGGCG Y 2 1 2 1 600010 f 74 goat 29_12762763 29 12762763 Ancestral_priority_1043 ancestry 0.402 neutral IMAGE 10K 10K ancestral 320768064 Affx-986698877 AX-385255271 29 12762801 CCACCTGGCAGAGAGGAAGCAGGGGAGCTGGCGGC[A/G]GATTGGGAGCGGTCTGCGACCTTGTGTGTGAGCTG R 2 1 2 1 600010 r 74 goat 29_12762801 29 12762801 Ancestral_priority_1043 ancestry 0.45 neutral IMAGE 10K 10K ancestral 320764352 Affx-986698879 AX-385252067 29 12762836 GGATTGGGAGCGGTCTGCGACCTTGTGTGTGAGCT[A/G]ACTGGTGAGCCAGAAAGGGGTGGGCATGGAGGAAG R 2 1 2 1 600010 f 74 goat 29_12762836 29 12762836 Ancestral_priority_1043 ancestry 0.444 neutral IMAGE 10K 10K ancestral 38383027 Affx-122973309 AX-123253385 29 12806444 AATGTCCTTTCTTTCCTTCCCTGTTGAACTATGCT[A/G]CGGACCCTACTCTTTGGTGAAGTTTTTGTCAACTC R 2 1 2 1 201000 r 74 goat snp18549-scaffold1877-29038 29 13773631 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449022 Affx-122923085 AX-123319357 29 12836430 ATTTGGTGAGGAGGGGATTAAAGTTTATACTAACA[C/T]ATTTATTGATTTGTGAATTAACTCCTTTTTTCACT Y 2 1 2 1 101000 f 74 goat snp18550-scaffold1877-59024 29 13742881 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391321 Affx-122967320 AX-123261678 29 12865000 TGGATTTCTCACGGTCTGCAAACCATCTTCTTCCA[C/T]ATTTCAGCTAAAACCATCTTTCTAAAATCCAGTCA Y 2 1 2 1 101000 f 74 goat snp18551-scaffold1877-87594 29 13714236 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789879 Affx-122968786 AX-385276886 29 12912087 GTTTAAAGTCAAGGGAAACAGTTCTAGGCACAGAA[G/T]AGTAGTACATCAGAAAGAACCCATTAATGTGTTAT K 2 1 2 1 101000 f 74 goat snp18552-scaffold1877-134681 29 13666830 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421933 Affx-122943831 AX-123292280 29 12941232 CATATGCCCTTGGTCAATCAAGGCAGAGTGTTGTA[C/T]GTGCCCAGTGAGACAACACATGAAGGAACTACTTG Y 2 1 2 1 101000 f 74 goat snp18553-scaffold1877-163826 29 13637401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405926 Affx-122955569 AX-123276278 29 12989293 AAGGAAACAGCAATGAATGTAGGTTTAATGTAGTT[A/G]TGGTTCAAATTTGATGAGAATAAGCAAGGAAATTG R 2 1 2 1 101000 r 74 goat snp18554-scaffold1877-211887 29 13589618 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794513 Affx-122932812 AX-385281476 29 13034424 TCCAATGGTACAATTATGTTTCCAAACTAGATATT[A/G]GATCATCAGATTCACCTCACTCCTTTATGTAGCAG R 2 1 2 1 101000 r 74 goat snp18555-scaffold1877-257018 29 13547354 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446582 Affx-122924824 AX-123316918 29 13076116 CAGCATCCAAAGCCTACTCTAACACCATATCAATG[C/T]GTCATGTTCTTAAAGAAAACGCACAGTGCACACAG Y 2 1 2 1 101000 f 74 goat snp18556-scaffold1877-298710 29 13505892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778595 Affx-122924914 AX-385265706 29 13107413 GTAGATTCTTTGTAGAAGTCACGTCTTTTATAAAG[A/G]ATATGTATTCTTTCCCTGATTCTAATATTTTTGCT R 2 1 2 1 101000 r 74 goat snp18557-scaffold1877-330007 29 13475339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432668 Affx-122936052 AX-123303009 29 13204035 AAGGCTGTGTTGCCACGGTAAGGGAAAAAGATGTT[A/G]ACAGGAAAAAATAGCATATTCATCACATTCTACCT R 2 1 2 1 101000 f 74 goat snp18559-scaffold1877-426629 29 13377694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433953 Affx-122934276 AX-123304294 29 13252654 TGTCTTAATTACACTCAAGGGAGTAACTGTGTAAC[A/G]GGAGATGATAAAATGTTTGCTTTAATTTTACTCAT R 2 1 2 1 101000 f 74 goat snp18560-scaffold1877-475248 29 13328789 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792700 Affx-122972362 AX-385279680 29 13299366 ATCATGAGGCTGCTACATTTACATTTTCACTCAGT[A/G]ATATTCCATTCACTCAGTAATATTCCAAGATTTCT R 2 1 2 1 102000 f 74 goat snp18561-scaffold1877-521960 29 13282357 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405454 Affx-122956042 AX-123275806 29 13356120 ATGATGAGGAAAATAAATGTCCTTCCCCAGGCCAG[C/T]GTAAGAGAATGCCACAGACTCCTACCCTAAATGAT Y 2 1 2 1 201000 r 74 goat snp18562-scaffold1877-578714 29 13224291 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402787 Affx-122958297 AX-123273140 29 13405131 CACTGGTTCTGAAAGTGTTCATAGGAATCCAAAAT[A/G]TGAGGCATGTTAGTGGACATTTTAAAATAATTTCT R 2 1 2 1 101000 f 74 goat snp18563-scaffold1877-627725 29 13175202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431705 Affx-122936768 AX-123302046 29 13441851 CTTTTTCCCTAAGTGCTAGGATAAACATGTTTCTT[A/G]TGTTGGGGCCAGGTTATGGAGAAATTGTTGAATCA R 2 1 2 1 201000 f 74 goat snp18564-scaffold1877-664445 29 13137412 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799507 Affx-122941499 AX-385286437 29 13456984 CATTTAGTTATGAAAATGGCTTACAAGTCAAATAC[A/G]AAATTGTATCACACTTCTTACAAAATGTTTTGCTT R 2 1 2 1 101000 r 74 goat snp54876-scaffold8383-35874 29 13120171 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388713 Affx-122968979 AX-123259071 29 13490363 TTTATCCTATGCACATTTATTGAATATCAGCTAAA[C/T]TCTAGGGCTACTAAAGTTTATGAAAAGCCCCTAAT Y 2 1 2 1 101000 r 74 goat snp54875-scaffold8383-2495 29 13087344 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273176 Affx-1111833353 AX-185215326 29 13532541 ATCTTGATTCCAGCTTGTGTTTCTTCCAGCCCAGC[A/G]TTTCTCATGATGTTCTCTGCATAGAAGTTAAATAA R 2 1 2 1 103000 f 74 goat 29_13532541_AF-PAKI 29 13532541 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38450259 Affx-122922186 AX-123320594 29 13532994 CCATTGAGGGATGAGTAATCCAAGACAAACCATTT[C/T]ACTTCTCACAGTACAAGTTTCTGTTTCCTCACTTC Y 2 1 2 1 201000 r 74 goat snp16742-scaffold1752-899392 29 13842834 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404225 Affx-122957652 AX-123274577 29 13569902 ACCATGCGAATAAGCAGGTGGCAGTCATCTGAGAA[C/T]TGTGGGTCAAAGCTTTATCTGGAACTTATCAAAGA Y 2 1 2 1 101000 f 74 goat snp16741-scaffold1752-862484 29 13879554 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766918 Affx-122947498 AX-385254232 29 13603951 CGAATTGTTAATGTGTGTGCTGCAAATAATGGCAT[A/G]AATAATGACCGTGCCAAAGAAACAATCAGCGATTA R 2 1 2 1 101000 f 74 goat snp16740-scaffold1752-828435 29 13912555 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399213 Affx-122960604 AX-123269568 29 13649832 TTGAAAGCCAAGTTAAAGAGTGAGGTATGCAGACA[C/T]GTAAGCAGGAAGTAAAATTAAACCCTGGTAAGCAC Y 2 1 2 1 101000 f 74 goat snp16739-scaffold1752-782554 NW_017203572.1 18021 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764584 Affx-122945576 AX-385252236 29 13764123 AGGGGTTTCTAAATATTTTGGAGGAATCAACATCC[A/G]TAAAAAAACCTACAGTACTAATTTAATACACTATG R 2 1 2 1 101000 f 74 goat snp16736-scaffold1752-668263 29 14063596 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432897 Affx-122935329 AX-123303238 29 13808877 TAAATGTAGATTCCTCACCACCTTTTTTTCTCCCC[A/G]TGCTTTGGGTAAAACTAAATACCTGAGGCTTTAAC R 2 1 2 1 201000 r 74 goat snp16735-scaffold1752-623509 29 14108382 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797710 Affx-122949081 AX-385284649 29 13837710 ATGAGAGTATGCAGAAGCTCATGGTATTTTCAATA[G/T]ATAACAAGGTTATTCAGATACTAAGTGAAAGAGAA K 2 1 2 1 102000 f 74 goat snp16734-scaffold1752-594676 29 14137143 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378082 Affx-122977168 AX-123248441 29 13878491 ATAGACCAGGGCCAAATCTATCCATATAATTTTAT[A/G]CCTGGGGGACATCCTATTCCATTCAGTTCAGTTTA R 2 1 2 1 201000 f 74 goat snp16733-scaffold1752-553895 29 14178158 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792489 Affx-122928834 AX-385279470 29 13916239 TAGCTTGACTGTGATATCTCTGAAGATGCCTGCAT[A/G]TTTGGCTTTGATTATTGCCTTAACAAAGGACACTG R 2 1 2 1 101000 f 74 goat snp16732-scaffold1752-516147 29 14216633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434831 Affx-122934793 AX-123305172 29 13954805 CAAGCAAATCAAACTCATGTTCTAATTTAAAAGAA[C/T]AACCAAAAAGAAAAAAAGGGGAGGGGGGAAGGAAA Y 2 1 2 1 303000 f 74 goat snp16731-scaffold1752-477581 29 14255297 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789337 Affx-122932629 AX-385276347 29 13984851 CCTACATTAGCAAAGGGCAAAAATGCAAATATCTC[C/T]ACTGACAATAGGAATCCTTGGAGTAGCTCAAGACT Y 2 1 2 1 101000 f 74 goat snp16730-scaffold1752-447535 29 14285521 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772442 Affx-122938253 AX-385259593 29 14020518 CTTAGTAGGATCCTGATGACCACTGGGCTATGAAT[A/C]GACACACAAGTTAGATATTTATTCGTAATAGCATT M 2 1 2 1 101000 f 74 goat snp16729-scaffold1752-411868 29 14322296 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395479 Affx-122963902 AX-123265834 29 14064989 TCCAACATTTTCAGAACAGGATGATCAAATATGCT[A/G]CAAATAGTCAACCTAGATTCACAATTTGTTTAGGC R 2 1 2 1 101000 f 74 goat snp16728-scaffold1752-367397 29 14367650 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411790 Affx-122951267 AX-123282140 29 14099687 GGGTGGGTTATGTGTGTGTTTAAACATGTTAATGG[C/T]GAGAGAGTATAAAGGCTCTTCAGCTCTACTCAGGA Y 2 1 2 1 101000 f 74 goat snp16727-scaffold1752-332699 29 14402168 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391003 Affx-122966896 AX-123261360 29 14135598 ATCAGTGTATCAGAAAATAGTACATATATCAACGT[A/G]TATGAGACCATACCAATTTTTATTTATTCACAAAG R 2 1 2 1 101000 f 74 goat snp16726-scaffold1752-296788 29 14438493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443751 Affx-122927124 AX-123314088 29 14195881 AATAAGTTTTCCTCATTTGCTTTTTCTTGTTTATC[A/G]CTCCAGAGAAGGAACCATCATTAACCCCCTCTACA R 2 1 2 1 101000 r 74 goat snp16725-scaffold1752-236505 29 14496875 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778100 Affx-122947470 AX-385265215 29 14234484 ACTTCACATTGGGAGACTCAGTAGGGCACTTGGCA[A/C]GTTTTATTTCCTCCTCCCAATAAACTAGAGGGCAA M 2 1 2 1 101000 f 74 goat snp16724-scaffold1752-197902 29 14536231 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398263 Affx-122962181 AX-123268618 29 14291506 TCAGCCCTTTAGATAATTCCAGGCAAGTGGGTCTG[A/G]AGCAGTAGCAAAGATCAGAGGGGTAAAAGTTCAGA R 2 1 2 1 201000 f 74 goat snp16723-scaffold1752-140880 29 14592925 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409011 Affx-122953880 AX-123279362 29 14331407 AGGAGATGACACTAGAATGCCAGGCAGGGTCAGGT[C/T]ATGGATGAAACACTGAAGAGTCTAAAATTTTTCCT Y 2 1 2 1 201000 r 74 goat snp16722-scaffold1752-100979 29 14633703 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450043 Affx-122922828 AX-123320378 29 14361645 CTTCCAATCCCTGAAAATGTTTTAGCTTCTTAAAT[A/G]TGTAAGCCATTAGCCCCATCGATTGTTTCACTTCC R 2 1 2 1 101000 r 74 goat snp16721-scaffold1752-70741 29 14663796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403063 Affx-122958523 AX-123273416 29 14417203 TTGACAAGGGGTATAAATCAGCACAGGATGCGCCC[A/G]TCTTGCTCGGGGAAATTGCAGCTTTATAAATAAAA R 2 1 2 1 201000 f 74 goat snp16720-scaffold1752-15183 29 14720334 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376585 Affx-122979070 AX-123246944 29 14466979 AGTCTGAAGATGCAGACGAAGACCCCACCATGCAG[C/T]GCTACACTGCTGGCCACTAACAAAGAGCTGAGAAT Y 2 1 2 1 101000 r 74 goat snp19422-scaffold1961-34494 29 14770230 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381674 Affx-122974734 AX-123252032 29 14524463 CTATTGGTTTTCTATGACCTAGATTAATTAGCATC[A/G]TGATAGTTTAATTGAGACAAGGTAGCAAGCATAAT R 2 1 2 1 101000 r 74 goat snp19423-scaffold1961-91978 29 14827750 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784796 Affx-122940127 AX-385271843 29 14555460 CACTTGCCAGCTCCAGAGTGGTTTGCTTGGTGTGA[A/G]GGTAATTACTCTAGAGTTAATTACAGAGTCCTTCA R 2 1 2 1 202000 f 74 goat snp19424-scaffold1961-122975 29 14858759 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429081 Affx-122938279 AX-123299423 29 14604097 ATGTGAGGAGGTCAGAGTTACTCACATTGTGTGGG[C/T]AGCCTTTCTTTCTTAACTCATCTGGTTGGGTGATT Y 2 1 2 1 101000 r 74 goat snp19425-scaffold1961-171612 29 14907090 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791220 Affx-122929923 AX-385278214 29 14639990 TCTTGTAAAGTAAATGTCATGCAATCACAGTCACT[A/G]CGACAACTTTCTTCCGTACAATATGATGGTAAAAC R 2 1 2 1 101000 f 74 goat snp19426-scaffold1961-207505 29 14943419 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406734 Affx-122955746 AX-123277085 29 14715366 ACATGTATGTTTCTACTAGATTGTAGATTTCCTTC[A/G]CTGCCGTGTGCGATATAGTGTCTTGCACACAAATA R 2 1 2 1 201000 f 74 goat snp19427-scaffold1961-282881 29 15018770 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767582 Affx-122945125 AX-385254834 29 14787782 GCATGCATCAATTTCCTTTTTGTGCCAGGTCTTGA[A/G]ATACTGAAAAAAGCTATTGTAGTAAAAATCTCAAC R 2 1 2 1 101000 f 74 goat snp19429-scaffold1961-355297 29 15090525 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445150 Affx-122926161 AX-123315487 29 14817546 AAAAATGTCAACCAGTACAAGTATCATTTGGGCAA[C/T]GGTATTTGAGGTAAGCATAATTATATCAATCGCCA Y 2 1 2 1 101000 r 74 goat snp19430-scaffold1961-385061 29 15120330 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389908 Affx-122968114 AX-123260265 29 14857126 TATTCAGTGTAAAGTGCTGTGTAAATGCAAGATGG[C/T]GGCAGTGATGTAGTTGACAAGGAAGAAAACTTGAT Y 2 1 2 1 101000 f 74 goat snp19431-scaffold1961-424641 29 15160309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799686 Affx-122923648 AX-385286614 29 14887466 TGCAGTAAAGATGGTAGAGGAATCAGCAGCATTGC[A/G]TAGGACAGGAAGAGGGTTTACAATTTCAAAATCTT R 2 1 2 1 101000 f 74 goat snp19432-scaffold1961-454981 29 15191042 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797647 Affx-122957516 AX-385284586 29 14928709 AAGCAAATAATGGTCTGTGTTTCAAAATCCAATTA[C/T]GATTCACCAGAAAGAGTCTAGCAATACCTTGCACA Y 2 1 2 1 101000 r 74 goat snp19433-scaffold1961-496224 29 15232088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407489 Affx-122954757 AX-123277840 29 15033747 AAACACTCCATCATGAAGAGAACGGTGCCCCACAA[C/T]GAAGAATCATGTAGCCCCAATGAAAATAGTGTGAA Y 2 1 2 1 201000 r 74 goat snp19435-scaffold1961-601262 29 15338025 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430065 Affx-122937552 AX-123300406 29 15067150 AGCTGAGAATCCAATGATATTTGCTTGTGAGTATG[A/C]GTGCATGGTAGAAGGGTAGCACCAAATCAAAGAAG M 2 1 2 1 101000 r 74 goat snp19436-scaffold1961-634665 29 15372555 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450747 Affx-122921856 AX-123321081 29 15115873 CACTAGAAACTAGTTCAATATTACAGAAAGGAAGC[A/G]GGGGAGAATTCAAAAGACCTGGGACCTCATTCTGA R 2 1 2 1 101000 f 74 goat snp19437-scaffold1961-683388 29 15420916 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433977 Affx-122934258 AX-123304318 29 15246420 CATTAGTTATCATATCAATTCTATTATTTTCCAGC[A/G]ATCATTAGTAACTAGCTGGATGCAAGCAGTCTTGC R 2 1 2 1 101000 r 74 goat snp19440-scaffold1961-813935 29 15550340 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378531 Affx-122976626 AX-123248890 29 15293704 AATGGAAACGATCATAATTTATTTTAAAATACATC[A/G]TGGTATTTCTCACCCTCCATGATCTGAAATGATAT R 2 1 2 1 101000 r 74 goat snp19441-scaffold1961-861219 29 15596606 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765808 Affx-122964252 AX-385253259 29 15313909 AGAGGAAGAAGCAAGTAGTTTGACTCAGGCTATAC[A/C]CCTTTTAGCTGTGAAATTGATTAATACAAAATGTG M 2 1 2 1 101000 f 74 goat snp30344-scaffold3335-330766 29 15618156 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441591 Affx-122928667 AX-123311928 29 15351313 ACCTACCACCTACCGCTTAGACTGCTGCCCAGTCT[A/G]TGTCTTCCCTCTCCTCTTCCTAACTCTGTCCCTCT R 2 1 2 1 303000 f 74 goat snp30343-scaffold3335-293362 29 15656054 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394328 Affx-122964675 AX-123264683 29 15396808 GAGGTAAGGATGTTATGTCTGTCTTTGGTTTACAG[A/G]TGCTTCAGGTCATGTCTCCTCCGTGGCATGCATCC R 2 1 2 1 101000 f 74 goat snp30342-scaffold3335-247867 29 15701562 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400259 Affx-122960135 AX-123270614 29 15441034 TTCCAACTCCACCACATCGAAGTCATGCATCCTGG[C/T]GATCTACCTAAATGTGAGCTTCCATTTCCTCTTTG Y 2 1 2 1 101000 r 74 goat snp30341-scaffold3335-203641 29 15745717 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431767 Affx-122936718 AX-123302108 29 15494325 GGAGCAGGTGGACATGTTGAAATCATGCCATGGAC[A/G]CAAGGGATCACTTTGACTGAGCACTCAGGTCAGAC R 2 1 2 1 101000 r 74 goat snp30340-scaffold3335-150350 29 15798434 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277818 Affx-1111836104 AX-519551315 29 15520824 CCAGGAGTAGCTGCAGAGGCATCTGTTTTGCACAA[A/G]GTGATAGAACTACTTCTTCCACAGTTATCTGACCA R 2 1 2 1 101000 f 74 goat Random2.2K-2314 29 15520824 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38450153 Affx-122922740 AX-123320488 29 15537193 CCATGAAACATCTTTTCTGATCACATAACTCATGG[C/T]AGTTTCTGGCTAATTCATTTTTGATCAACTGGATT Y 2 1 2 1 101000 r 74 goat snp30339-scaffold3335-107482 29 15840803 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451315 Affx-122921281 AX-123321648 29 15578027 TGAGAGAGGTGCAGAAGAGCAGATGAGATGAAGAA[C/T]GCCAATTATTTTCATTTTCTTGAAGAGGGGGACTG Y 2 1 2 1 201000 f 74 goat snp30338-scaffold3335-66648 29 15882374 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427230 Affx-122939571 AX-123297573 29 15612678 GAACCCTCCAATGACTTCTTCCTTCAAAGAGTCAA[C/T]GTTTGCTAAAAAAATTAAAGTTCATTTTAAAATAG Y 2 1 2 1 102000 f 74 goat snp30337-scaffold3335-31997 29 15916886 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408464 Affx-122954432 AX-123278815 29 15642290 AACTGTTTTCTAGCTCAGAGAGAGCTAGTGGGTAG[A/C]GTATCTTTTCCTCTGATACCCTGGCTGCTAAAAAG M 2 1 2 1 101000 f 74 goat snp30336-scaffold3335-2385 29 15946835 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392840 Affx-122965771 AX-123263197 29 15647479 GTGGAGCACCTGTATGCGCCAGGCTTTTCACATGC[A/G]TTATTTCAAACAGCGGTTAAGACTAGAGACATTCA R 2 1 2 1 101000 r 74 goat snp32738-scaffold378-2705 29 15951787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394007 Affx-122965020 AX-123264362 29 15755328 TCACAGATGCAACAGTGGCAAGGTCAGCTGAGGTC[A/G]TGTCCCAGTGATCAGATTTAATGGATTTTAAATGA R 2 1 2 1 101000 r 74 goat snp32740-scaffold378-110554 29 16060025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786812 Affx-122929087 AX-385273841 29 15786020 ACATAATATACTGCGTTTGAGAGGAATTGTTCTGT[A/G]CTATCTAGCAGAGATGTGGCAACTACTCAAAGTCC R 2 1 2 1 101000 r 74 goat snp32741-scaffold378-141246 29 16090718 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385461 Affx-122971302 AX-123255819 29 15830427 CAGATTAGTTCCTTACCCAATACAGTAACTCTTCC[A/G]TCATTGAAGACTAACAATAGGGATGCTGGTAATGA R 2 1 2 1 101000 f 74 goat snp32742-scaffold378-185653 29 16134831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375457 Affx-122979163 AX-123245816 29 15833887 AGGGTAGAGTGCTTTTATGTAACTTTTTAAGAACT[C/T]TAATTTTCAGTCTGGGGGATGGTTATTATAAACCC Y 2 1 2 1 101000 f 74 goat snp19092-scaffold192-2366 29 16138152 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798248 Affx-122945129 AX-385285183 29 15862754 GTTTGATCCTCATGGTGGCCCTTAGGGAGTGTTAG[C/T]GTCATCGTTCCATTTTGCAGATTAGGAGGTCAAGG Y 2 1 2 1 101000 r 74 goat snp19093-scaffold192-31233 29 16167150 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378759 Affx-122977016 AX-123249118 29 15938576 AACGATTCTGAGAGACTTACCAGTCTTCTTGCTCA[C/T]GTCTTTGTGCTTGTAAGAAAAGGGAAAGCTGTGCT Y 2 1 2 1 101000 f 74 goat snp19094-scaffold192-107055 29 16244042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405225 Affx-122956894 AX-123275577 29 15981886 AAGCGTCCAACGGCAGAGCAGAGGAAACAAAGGGC[C/T]CTAAGTTTGTGCAGCCAAGAAAATAACATGAAACA Y 2 1 2 1 101000 r 74 goat snp19095-scaffold192-150365 29 16286826 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428405 Affx-122938943 AX-123298748 29 16018007 GCCATGGTTCCTTGACCTGCCTCTCCATGGATTTT[C/T]GTGTCATGAATGTCATCCTGCCTCCTTTTCTGCTC Y 2 1 2 1 201000 r 74 goat snp19096-scaffold192-186486 29 16322895 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273178 Affx-1111833354 AX-519546837 29 16040831 CAAGTTGGGGATAATGATGATTATTTGGTAGCATT[A/G]TTGAGAGGATTATCAGGAAAGAATGTGGCACTTTT R 2 1 2 1 201000 f 74 goat 29_16040831_AF-PAKI 29 16040831 G A 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468277962 Affx-1111836105 AX-519551457 29 16051936 CCGGACAGGGCCCCGTGGGCGTGGGCTGCACAGCA[A/G]CCTTGTTCCCAACTGCTCAGGTGGTTTATAACCAG R 2 1 2 1 101000 r 74 goat Random2.2K-2315 29 16051936 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38402351 Affx-122959055 AX-123272704 29 16064024 CTTGGATGGAGTCGTTGAACCTCCCTTGCCCTCCT[C/T]GGTAAAGCAGGTGACTGTCATGGTTGATACTGAAG Y 2 1 2 1 101000 r 74 goat snp19097-scaffold192-232503 29 16370024 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404565 Affx-122957375 AX-123274917 29 16092760 TTTTCCTTCCAGCTATTCAACAACAAGCTATCAAC[A/G]CTCTCCTTTATCTCCAGTCTACTTACATTGCAGTT R 2 1 2 1 101000 r 74 goat snp19098-scaffold192-261239 29 16398831 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377090 Affx-122978270 AX-123247449 29 16136908 CTGCATTCTCCCATACTTAGGGCTTTAACCCTTCA[C/T]ATGGTCTGGGTTGTATCTCCCCTACTGACTGTGAG Y 2 1 2 1 101000 f 74 goat snp19099-scaffold192-305387 29 16442833 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792521 Affx-122953607 AX-385279502 29 16199281 AAACTTCCCTGGGACAACATGAGTCAAAGGAAGAC[A/G]TCTCCTTTGATCACCCCAAGCTGCCTATGATCCCC R 2 1 2 1 101000 f 74 goat snp19101-scaffold192-367760 29 16504864 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793417 Affx-122934193 AX-385280394 29 16231099 TGGTTCACGTTCCCTCAACGAGGAACAGGACTATC[A/G]TGATTTACAACGTCAGGATCTATGACCTGACATGT R 2 1 2 1 101000 r 74 goat snp19102-scaffold192-399578 29 16536873 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438935 Affx-122930417 AX-123309272 29 16381346 ATGAGAAACATGCCCTGGTCTTCCTGGTCTGAGGA[C/T]GTTCACGCTCATTAAAGAGGAGAGTCCTTTTGTCC Y 2 1 2 1 201000 r 74 goat snp19105-scaffold192-549825 29 16684608 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389588 Affx-122968777 AX-123259946 29 16412452 GTAGGATTGAAAGCAGATCCTCCAGTTCAAATGCC[A/G]GTGCAGAACTGGCTTCAAGCCCAGGATTTCAGGAG R 2 1 2 1 101000 f 74 goat snp19106-scaffold192-580931 29 16715658 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452824 Affx-122920741 AX-123323157 29 16444330 GACTTATTACAGTCTTCCCGGGAGGTCACAGCTCT[A/G]CTTTCACATCCCTGGAGTTTTAAAGACAGCTTCAC R 2 1 2 1 101000 f 74 goat snp19107-scaffold192-612809 29 16747063 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398845 Affx-122961063 AX-123269200 29 16490370 ATGAGCACTCGTCCAATGCCTACTTGCTCTGACAC[A/G]TAAGTGTTTCATATCTCCTTTAATCCTCAGACATC R 2 1 2 1 101000 f 74 goat snp54972-scaffold840-1745867 29 16792670 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412224 Affx-122950921 AX-123282574 29 16534291 TCTATTTTCTCCTCCCACCTGGTCTTCAGTCTGAG[C/T]GAGCTCCTTGGTTCTCCCCTTTGCATTCTTACCTC Y 2 1 2 1 201000 r 74 goat snp54971-scaffold840-1701946 29 16836675 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418783 Affx-122946185 AX-123289131 29 16642349 GTACTTATCCCATCCCATAGCAAAGGGGTTCCTAA[C/T]GAGAGATACAAATGCCAGAGAAGGGGGTAAAAATA Y 2 1 2 1 201000 f 74 goat snp54969-scaffold840-1593888 29 16945767 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799372 Affx-122970694 AX-385286302 29 16703914 GTCATTCACATCAATAGTCTGTTAATTCTTATTTC[C/T]ATTACATAGGGATAATTTTTAACATAACTAATACA Y 2 1 2 1 101000 f 74 goat snp54968-scaffold840-1532323 29 17007422 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38432004 Affx-122935929 AX-123302345 29 16807483 ACCTCCTAGGTCACATCCCCAATTCAAAATAATCA[C/T]GGTGGCCGGGGGAATGGCACTTTCTGACTGGCCAA Y 2 1 2 1 101000 f 74 goat snp54966-scaffold840-1428754 29 17111489 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381411 Affx-122974366 AX-123251769 29 16851873 TTCTCCAGAGGATCTTCCAGACCTAGGGATCAAAC[C/T]CACATCTCCTGCATTGCATCTGATAGCTGAAAGGG Y 2 1 2 1 103000 f 74 goat snp54965-scaffold840-1384364 29 17154790 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781792 Affx-122924110 AX-385268874 29 16924077 GAAGATGAGTAAGGAAAGAATTTTGCAAACAATGG[C/T]GTAGGATTTTATAGGATGAGTGATCCCTGGAGAAA Y 2 1 2 1 101000 f 74 goat snp54963-scaffold840-1312160 29 17226980 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451474 Affx-122921139 AX-123321807 29 16983232 GAGAGGATTTCATTGATGGGCCACTCGGTGTGCTG[G/T]CACTGGACTAGGCCCCATGAATACCAAAAAGTCTT K 2 1 2 1 101000 r 74 goat snp54962-scaffold840-1253005 29 17283671 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375780 Affx-122978585 AX-123246139 29 17016633 CATCTGTAATAGCAGAGGTAGTATACAAAGTTGTT[A/C]GGCCCCCATGGGGTCAATGATAGGAGATGAAAGCA M 2 1 2 1 101000 f 74 goat snp54961-scaffold840-1219604 29 17317479 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390471 Affx-122967603 AX-123260828 29 17063114 AGATGATAGAGTCAATGAAAGGATTCACATAGGCT[A/G]TGACATGAACCTACTTGTGTTCTGTCAAGATCACT R 2 1 2 1 201000 f 74 goat snp54960-scaffold840-1173123 29 17362142 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375782 Affx-122978583 AX-123246141 29 17099799 GGTCTTGGAACTCTACTCGGGCCTACTTTTCACAA[C/T]ATTCACAATCTTGTACTATCTCTACCTTGTAACCC Y 2 1 2 1 101000 r 74 goat snp54959-scaffold840-1136438 29 17399310 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776706 Affx-122938392 AX-385263832 29 17183162 CCACACGCCTAGCAAACTGCAGGTACTTAATGTAT[A/G]TTTACTAAATGACTGATGTGGAATTAGGAGTTCTC R 2 1 2 1 101000 f 74 goat snp54957-scaffold840-1053075 29 17482801 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792915 Affx-122977883 AX-385279893 29 17260139 ATACTTAGAACTAACAATCCATCTCAAGAAAATTC[A/G]TAGAAAGCTGCCTGGTTTTTTAAGGTCCATATCAA R 2 1 2 1 101000 r 74 goat snp54955-scaffold840-976098 29 17557602 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379328 Affx-122976181 AX-123249687 29 17327038 ATGGAGAGTCAAGCAATCTTATATACCACCCAAAA[C/T]AGAGTGTCATGACATAAAGTTTATGCCTGCATTTC Y 2 1 2 1 101000 f 74 goat snp54954-scaffold840-909199 29 17624603 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786847 Affx-122939686 AX-385273876 29 17509382 GCTGGGCTGTTTCTGAAGAGGCTCCCTAGAGTTAA[A/C]TGACCTGGGTCCCCAGTTAGTAAAAAGATCTTTAT M 2 1 2 1 101000 r 74 goat snp54950-scaffold840-726855 29 17807833 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402701 Affx-122959610 AX-123273054 29 17573575 AGGGGATACTCATGCTTTCCCTGAAAGCTTGTTGT[A/G]TAGATTAGAGATAACACATGTAATTTTACTTGCTT R 2 1 2 1 201000 r 74 goat snp54949-scaffold840-662662 29 17873067 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786547 Affx-122941310 AX-385273580 29 17626443 GGAAGTTTATTGAGGCTTAGGAACAATTTCCACAC[A/G]CTATACCAGGAGGTAATATAATACAGTTGAAGACA R 2 1 2 1 101000 f 74 goat snp54948-scaffold840-609794 29 17927546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765866 Affx-122947836 AX-385253306 29 17802099 TTTCACTCAGGGACTGGATCACTCAGCTCTGTTAT[A/G]TGATAAGTAAAAAAATCACTTAGCCTGTCAGTTTT R 2 1 2 1 101000 f 74 goat snp54944-scaffold840-434138 29 18103838 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409095 Affx-122953325 AX-123279446 29 17833351 TTGTTTCTTCACAAAGAAAGAGATTTAAAAACCAC[A/G]GAGTGGCTGCCTGACAAGGCTGTGATTCAATAGAT R 2 1 2 1 101000 f 74 goat snp54943-scaffold840-402886 29 18135125 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403816 Affx-122957959 AX-123274168 29 17879099 GCATCCACTCTGTTTGTCCAATGGGCCACAGAGAC[C/T]ACCAACTGACACTAGCACTCTCAGGAGCTAGTGAT Y 2 1 2 1 101000 r 74 goat snp54942-scaffold840-357138 29 18181051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376118 Affx-122978876 AX-123246477 29 17913237 GATGAAAAATATCTGCTAGCCAGAACACTAATTAT[C/T]TCATTGAGAAAGAACACTGAGACCAAGAATATACA Y 2 1 2 1 101000 f 74 goat snp54941-scaffold840-323000 29 18211957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392386 Affx-122966226 AX-123262743 29 17964941 TAAACAAAAGCTGAGGAAGTTCACCTCCATTAAAC[A/C]TGCCCTACAAGAACTGTTGAAAGGAACTCTTCTAT M 2 1 2 1 101000 f 74 goat snp54940-scaffold840-271296 29 18264016 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787293 Affx-122961670 AX-385274318 29 18047751 ATATCAAAAACATTAAAGGAGGGGAGTGGGAGTAC[A/C]TACACAGGGTAATTGAAATGTGTTCAAACTTAAGG M 2 1 2 1 101000 f 74 goat snp54939-scaffold840-188486 29 18348288 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798086 Affx-122931722 AX-385285021 29 18105370 GAAAAAGCAAACCTAACTGAGTAATAGAAATTTAA[C/T]GGTATATTTTCTGACTGCAGTGCAGTCAAGTTAGA Y 2 1 2 1 102000 r 74 goat snp54938-scaffold840-130867 29 18407690 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399726 Affx-122960459 AX-123270081 29 18151197 ATAGACTGTAGCCATCAGTGTGAGTGGTGGAGATA[C/T]GCGGATGGTGGTCATGGGAAACGAAGATGCCAACA Y 2 1 2 1 101000 f 74 goat snp54937-scaffold840-85040 29 18453790 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441136 Affx-122929580 AX-123311473 29 18254507 ATGAACAGCCTTTCTCTAAAAGCAGTTACATTTTT[C/T]ACCCTGACTTCTCACAGTGCTCTCACCCAGCATGT Y 2 1 2 1 101000 f 74 goat snp19859-scaffold1990-274320 29 18560845 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391444 Affx-122966744 AX-123261801 29 18340993 AGGTAAATTGGAAGTGACATGTCCAGTCATTGAGC[C/T]CAACAGTGACTGAAAACTTTCGGTCATTATTGCTT Y 2 1 2 1 101000 f 74 goat snp19857-scaffold1990-187834 29 18646326 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449658 Affx-122922576 AX-123319993 29 18394000 TCTTAAAATTCCAGGACTGGCCCCACATACCTGAC[A/G]GCCTCCTGGGCTTGCTTGGCTGTCCCTCTAGCTGA R 2 1 2 1 101000 f 74 goat snp19856-scaffold1990-134827 29 18698866 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776416 Affx-122975631 AX-385263543 29 18434656 GTCAATCTGATTTGTGTGAATCTGATTTGATAATG[C/T]GATCTTGTGTTACCTCACCCATTTTTTCAACACCT Y 2 1 2 1 101000 r 74 goat snp19855-scaffold1990-94171 29 18740176 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387286 Affx-122970535 AX-123257644 29 18487757 TGTTCAGGTAACTGCTCCTCCTTTGTCCTCATTTG[C/T]AACCGAGTTCCTGCCTAGAAACCATATTTATGAAA Y 2 1 2 1 201000 r 74 goat snp19854-scaffold1990-41070 29 18794272 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390362 Affx-122967679 AX-123260719 29 18528403 GACGTGCATCTTGACCCGTATTTTCTGCCTAGCCT[G/T]CTGTTGTAGGTAAACATTTTGTGTTCCCAGAGCAG K 2 1 2 1 201000 f 74 goat snp19853-scaffold1990-424 29 18834768 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770684 Affx-122972387 AX-385257848 29 18549655 ATTGATGAGAACTGAATTTTCCACTTAAAATTTTA[C/T]GAGTCTGATGACCATAAGAACTTACGTAGGGTAGC Y 2 1 2 1 303000 f 74 goat snp19445-scaffold1963-20729 29 18856877 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273180 Affx-1111833355 AX-519546839 29 18557801 GATTATCCAGGACTGATTTCCTATAGGATTGACTG[A/G]TTTGATCTCCTTGCAGTCCAAGGGACTCTCTAGAG R 2 1 2 1 303000 f 74 goat 29_18557801_AF-PAKI 29 18557801 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320802449 Affx-122953706 AX-385289353 29 18578838 GCAGATGGAAAAAATAAGCTTAATTCATAAAGTAG[A/C]AAATGTTGCTTTATCACTCTAAACAGTGAAGCATT M 2 1 2 1 101000 f 74 goat snp19446-scaffold1963-49912 29 18886607 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783028 Affx-122973153 AX-385270096 29 18615804 ATGTATAAAATCAAACTATTCAGATGGTCTGAAGA[A/G]TTGTTGCCCAAAATAATGATAGTATGTGATCTCTG R 2 1 2 1 101000 r 74 goat snp19447-scaffold1963-86878 29 18923394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385627 Affx-122971181 AX-123255985 29 18657473 GAAGCCTCATCCAAGTTCATTTAAAAAATTATTGA[C/T]ATGTCACTACAGGTGTTAAGTTCGGGACCAGGCCT Y 2 1 2 1 102000 r 74 goat snp19448-scaffold1963-128547 29 18965219 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452999 Affx-122920112 AX-123323332 29 18692146 CAATTAGAGATGATGGCTAAGCATTAAAAATGGAC[A/G]TGACAGAGTGTGATACAGCCCATGCCTTTAGCGGT R 2 1 2 1 101000 r 74 goat snp19449-scaffold1963-163220 29 18999700 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403285 Affx-122957852 AX-123273638 29 18744970 CCTTTCCTGTTCCACAGTCCCATTCAGGACACATT[A/G]CATTTAGTCATCATGTCTCCCTGGGCTCCTCTTGA R 2 1 2 1 101000 f 74 goat snp19450-scaffold1963-216044 29 19052605 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436576 Affx-122932897 AX-123306914 29 18778518 ATGATTTGGAGCAGCTTACAACACAAACAGGGGCA[A/G]GCACTTAGAGATAAAAGGAGAACTGGAGAGTGAAA R 2 1 2 1 101000 f 74 goat snp19451-scaffold1963-249592 29 19086655 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387736 Affx-122969743 AX-123258094 29 18836539 CCTGCTATGAAATTCACTGTTTTATGTGTCTGTCA[C/T]GTTGAGAAAAATTAAATTTCACTTTAATCTTACCA Y 2 1 2 1 101000 f 74 goat snp19452-scaffold1963-307613 29 19144954 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792614 Affx-122921633 AX-385279595 29 18877255 CTTGGCTTGAGAAGTTACCCTAGGAACAGCATTTC[A/G]TCTATGGAAACAATTTTATCTGCAAATAGTGTCAA R 2 1 2 1 101000 f 74 goat snp19453-scaffold1963-348329 29 19186128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430412 Affx-122937754 AX-123300753 29 18938286 TTCTTTTATTCCTTCCTTTGGAATTCTCTCTTGTG[C/T]AATAAACATTTTCCTCCACTTAATCTCTGTGATAA Y 2 1 2 1 103000 f 74 goat snp38185-scaffold48-31385 29 19246538 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416485 Affx-122947798 AX-123286833 29 18985884 TTCAATCCTACACATTTTTATTATATAATTATGCC[A/G]TTGAGGAGGAGAAGTTTCCCCTCTACCTCTCTGAA R 2 1 2 1 101000 r 74 goat snp38186-scaffold48-78983 29 19296019 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448091 Affx-122924324 AX-123318427 29 19038547 CAATCTCATTGTTTCTTACTTGAATTATTATTTTT[A/G]TATTTCTGTTTCTACCTTCATTGATGCATTATCTA R 2 1 2 1 101000 r 74 goat snp38187-scaffold48-131646 29 19348242 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382550 Affx-122973778 AX-123252908 29 19077628 TATTGGATACAGTCCAAAAGAAGATCAGGAAATCT[A/G]TTATGTTGGCTAATTTTAGGTATAGGCATCCTTTA R 2 1 2 1 101000 r 74 goat snp38188-scaffold48-170727 29 19387436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777476 Affx-122949079 AX-385264596 29 19107869 TCATTTTAATAACTTTTTGGAAATACAGGTTTTCA[C/T]ATCTAAATTTTATTCCCTTCTCACCACTCATAATT Y 2 1 2 1 101000 r 74 goat snp38189-scaffold48-200968 29 19416350 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377257 Affx-122978142 AX-123247616 29 19143995 TTTAAACCTGTGAGAGAGAGACAAATAATTAAATT[A/G]CTAATGCAGACTTACAAGATTTAAAGACCTTAGAG R 2 1 2 1 101000 r 74 goat snp38190-scaffold48-237094 29 19452312 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426728 Affx-122939878 AX-123297074 29 19240694 TTCAGAATGTAAAACATACTGCAGAGATTTTGCCA[A/G]GGATACCAAAGAAAGGAAATATAAAAAGATGATCT R 2 1 2 1 101000 f 74 goat snp38192-scaffold48-333793 29 19549631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404529 Affx-122956688 AX-123274881 29 19282231 GTAAGAGCAAGGAGTCATAACATACCCCTAATCAA[C/T]AGAGTTGTATCTGGACTTCCCATGTAGAAACCCAT Y 2 1 2 1 101000 r 74 goat snp38193-scaffold48-375330 29 19590673 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774418 Affx-122979229 AX-385261554 29 19316825 CTCTGTTTTTCCTCTCATAAAACTAGATAACTGTT[A/G]TAACCAAAGGAGTGTTTGTATTAAGTGAGATGGCA R 2 1 2 1 101000 f 74 goat snp38194-scaffold48-409924 29 19625366 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394495 Affx-122964554 AX-123264850 29 19361280 GTACTCTGCTATATTGCACCCAATTCTATTAAAGC[A/G]GAGCTCTTAGGAGATGAACACATTCATATTTCACT R 2 1 2 1 101000 f 74 goat snp38195-scaffold48-454379 29 19670794 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778261 Affx-122957833 AX-385265376 29 19415025 GTTAAGATGCATATCTCAGGAATAATTACAATGAA[C/T]CTGATCCTCACATACTCCCATACACAGAAAAGTAC Y 2 1 2 1 101000 r 74 goat snp38196-scaffold48-508124 29 19725144 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451375 Affx-122921219 AX-123321708 29 19481314 GGCTTTAAGAATGGTGATCTTCCTGTGAGATGGAA[C/T]GGAGACTCAAAAAATTCAAAATACATATGAAAGAG Y 2 1 2 1 101000 f 74 goat snp38198-scaffold48-574413 29 19791722 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392846 Affx-122965766 AX-123263203 29 19510728 TACAACTGAAATGAGGAACAGAAACATACAAAAAA[C/T]GAATATTATTCTGAAGATCATCTGCAAGAAAGGAC Y 2 1 2 1 201000 f 74 goat snp44108-scaffold599-6146 29 19843157 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425008 Affx-122941891 AX-123295354 29 19607311 ATGAAGTTTCAAGTGAGGGTAGGAAAAAAACCAAC[A/G]TTTATTGAGCTCTTATTATGTTCAAGGACTTGAGC R 2 1 2 1 303000 r 74 goat snp44110-scaffold599-102729 29 19939251 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445825 Affx-122926023 AX-123316162 29 19660607 TACAGTCACACAACTATGAAACTTCTGAGATTAGA[C/T]AATAAACTAAGAAAACTAGTGAAACTAGAAAAAAA Y 2 1 2 1 101000 f 74 goat snp44111-scaffold599-156025 29 19992839 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792140 Affx-122952919 AX-385279125 29 19690150 TCTAATGGGATTGAAGTTAAAACAATCATATAGAA[C/T]AGATACTGCTTTAAAACCCCAGGCCAATAAAACAG Y 2 1 2 1 101000 r 74 goat snp44112-scaffold599-185568 29 20022180 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435750 Affx-122933277 AX-123306089 29 19728032 GGCTCTGATGTTTCCTGTCCACAACTTTGGATAAA[C/T]GGCTTAACCTCATTAAATGTGAAATGGCCAGCCCT Y 2 1 2 1 101000 f 74 goat snp44113-scaffold599-223450 29 20059772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781193 Affx-122960422 AX-385268278 29 19761014 TCAATGTCCAAACATCATTTGGCACACAAAATATG[C/T]GGACTATGGAGTCAAACCTGTTGCATCTCTCTAGT Y 2 1 2 1 101000 r 74 goat snp44114-scaffold599-256432 29 20091029 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442950 Affx-122928221 AX-123313287 29 19793626 TTGAGGTCAGGTTGCAAAATATTAAGGAGTTCAAG[C/T]AGTGTTCAGTAGGAAAATGTGAAAAAAAAGAAAAA Y 2 1 2 1 101000 f 74 goat snp44115-scaffold599-289044 29 20124306 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409038 Affx-122953860 AX-123279389 29 19857968 TAGAGCTTTATAGGTGAAGATATAAGTGGGATCAA[C/T]GAGAAAGAATTTCTCACGGATCAACTGGAATAGCA Y 2 1 2 1 101000 f 74 goat snp44116-scaffold599-353386 29 20186978 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434503 Affx-122934611 AX-123304844 29 19902863 TAAAATACATTTAAAATATAAATGAATATTTAACT[A/G]CCAATAAATGGTCCTTGGTTTAAATTTGATTGTAA R 2 1 2 1 103000 r 74 goat snp44117-scaffold599-398281 29 20229510 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768019 Affx-122945372 AX-385255233 29 19944700 CCCACCTGCTACTTAGCTGTCTAAAAGAAATTAAG[C/T]AAATGCTGTAATCTATGGAAACACAAATTTGACAG Y 2 1 2 1 101000 f 74 goat snp44118-scaffold599-440118 29 20271373 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792340 Affx-122945582 AX-385279322 29 20003501 TGATGGGTGGGATATTTCAGATAAAGGGACAGTGC[A/G]TGCAAAGCTCCATTATTTGAAAAGTTCTTTACACA R 2 1 2 1 101000 f 74 goat snp44119-scaffold599-498919 29 20329770 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772187 Affx-122965470 AX-385259342 29 20048071 ATGTCAGACTGTATATAAGATATTGATTTTCATCC[A/G]TGCCAGCAAATCGTGAGTGAAATACTGCCAGTCAG R 2 1 2 1 101000 r 74 goat snp44120-scaffold599-543489 29 20374879 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789353 Affx-122938903 AX-385276363 29 20123027 ATCTTCACTATAAATCTTACCTCTGAAGTCAAACA[G/T]AGATGAACCTAGATCTGAGCATTGCTGTCCAAAAA K 2 1 2 1 101000 r 74 goat snp44122-scaffold599-618445 29 20450341 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442527 Affx-122928541 AX-123312864 29 20153210 CTTTCACTTGCTCACACTCCCTCATTCTTTAACCC[A/G]TTTTAATCTGTTTCAGCTGCCCCTTGAGAAATAGC R 2 1 2 1 201000 r 74 goat snp44123-scaffold599-648628 NW_017204901.1 13036 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769235 Affx-122953576 AX-385256408 29 20166173 AAAAGTATCAGCATTAGGGGCATGAAAATTGAATT[A/G]CATTAGATATTTATCACCTCTAACTCTTCAGCAAA R 2 1 2 1 101000 f 74 goat snp38581-scaffold489-1177751 29 20607928 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379563 Affx-122976048 AX-123249921 29 20202707 TAGCCACAATAAAGGGAAGAAAAAGGAACTGTTAG[C/T]ACAAAAGTTTCAAAATGCAAGGTCTTTTGTTTGTG Y 2 1 2 1 303000 r 74 goat snp38580-scaffold489-1141217 29 20644474 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790241 Affx-122974437 AX-385277245 29 20236007 AGAATAATTTTCCTTAAAATATAGTGCTATATAAT[C/T]TAGGCTTTCATGTTTAAAATCTAGACTTGTTTTAA Y 2 1 2 1 202000 f 74 goat snp38579-scaffold489-1107917 29 20677790 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387215 Affx-122970591 AX-123257573 29 20271111 ATGTCCCTTGATGTTAGCCTCAAGAAAATTTGCAA[C/T]GTTTAATGTAAATCCAGGTAGCACAGTGGTAAAGA Y 2 1 2 1 201000 f 74 goat snp38578-scaffold489-1072813 29 20713461 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448891 Affx-122923258 AX-123319226 29 20307717 ATCAACAAGTCTTATTGATTTTACCTCCTAAATAT[G/T]CCTTCAATCCTCTGCAACTACATCCTGACTTTACA K 2 1 2 1 101000 r 74 goat snp38577-scaffold489-1036207 29 20750865 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402105 Affx-122958688 AX-123272458 29 20343943 TCAACTAGATTTAATATGACACATGCCAAATGCTT[A/G]CAAAATTGCTATAGACTTGGGATTGTTCATTTGCA R 2 1 2 1 101000 r 74 goat snp38576-scaffold489-999981 29 20787130 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433521 Affx-122935010 AX-123303862 29 20422832 CTAAGAGAAAAAGATTATTTTCCAGGTACTTTCCA[C/T]ATCTGACTTTTAAGAATTTATCTTATAATTAAAAA Y 2 1 2 1 103000 f 74 goat snp38574-scaffold489-921092 29 20866464 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426272 Affx-122940317 AX-123296618 29 20461276 GTAGAAGTAGCAGCCATAGGCACTAGCTATGATCA[G/T]AAGTATTCCCAGTCATTTTTATTCTTCAACAAAGA K 2 1 2 1 201000 f 74 goat snp38573-scaffold489-882648 29 20902183 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384729 Affx-122972050 AX-123255087 29 20521490 TCTAGGAAAGAAATATGGCCTATATATATGGAAGA[G/T]ATTTTGTTTCAAATTACTCAATAATTAAAGTCCAA K 2 1 2 1 101000 f 74 goat snp38572-scaffold489-822434 29 20962107 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800943 Affx-122951724 AX-385287858 29 20590550 TTAGAATACTACTCTATTTAATTAGCTAAGTCTAA[C/T]GGTCCTCCTATCAACTTGTGGGCTAATTGTTAAGG Y 2 1 2 1 101000 r 74 goat snp38571-scaffold489-753374 29 21031776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766761 Affx-122964241 AX-385254096 29 20621772 CATATGATAAATCCCTTCACTTTTGCCAGATAATG[C/T]AATATAATCATAGAACAGATATCTCTTCATATTCA Y 2 1 2 1 101000 f 74 goat snp38570-scaffold489-722152 29 21062945 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781257 Affx-122937039 AX-385268342 29 20660444 AGGATGATTTGCTTGTTATAAAGCTGTTCAGATAT[A/G]TGAAACCTTTGGCTTAGAATTTTAAAACTTTACTT R 2 1 2 1 101000 r 74 goat snp38569-scaffold489-683480 NW_017215923.1 2700 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450033 Affx-122922836 AX-123320368 29 20719734 ATCAATTTTTTAAAAATTTGTATGTAAACTTAAAC[G/T]TTCTCAAGTTCAGTGTGCTTTTCATGATTAAGATG K 2 1 2 1 103000 r 74 goat snp38568-scaffold489-624190 29 21159561 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377062 Affx-122978291 AX-123247421 29 20761194 CTAGTAGAAGTAGCAAATTAAGAAAGAAAAGGGGG[C/T]ATGGACTCTAAGATATTTTTAGCTATAAAGTTAGC Y 2 1 2 1 201000 r 74 goat snp38567-scaffold489-582730 29 21200557 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417162 Affx-122947340 AX-123287510 29 20796813 GGGGCAGGGAGTTGACCTTTTTTGATATAGTAATC[C/T]CATTACCTAGTGCTACAGATGAGTTATCTGACATT Y 2 1 2 1 101000 f 74 goat snp38566-scaffold489-547111 29 21238130 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771240 Affx-122974464 AX-385258398 29 20832423 CCAAGTAACTGTTTTAAGTAAATTAACCAATACAC[A/G]TTTATAGAATGTCAATATGTCAAAGAATAAGAAAG R 2 1 2 1 201000 f 74 goat snp38565-scaffold489-511501 29 21274401 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778796 Affx-122930719 AX-385265905 29 20887440 GGAATATTCTAAATAAAAATTGGCTAGTAGACACA[G/T]AGCTGCTTTGAACAAGAACCTCTGATAGAGTAGGA K 2 1 2 1 101000 r 74 goat snp38564-scaffold489-456484 29 21329542 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448114 Affx-122924307 AX-123318450 29 20937678 ATGAGTTATCTTATGTCAGAATGCTTATGAAGTCT[A/G]TTTCAGAGCTCCTTCTCACTGACTTTATTTTGAAA R 2 1 2 1 101000 f 74 goat snp38563-scaffold489-406246 29 21379861 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452227 Affx-122920796 AX-123322560 29 20995578 GTTGTGATGGAGAAGAAGTTAAATGAAGGTTTACA[G/T]AATTCTTTTGACTACTATTGTGATAGATGAAGAAG K 2 1 2 1 101000 r 74 goat snp38562-scaffold489-348346 29 21437953 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397012 Affx-122963132 AX-123267367 29 21026052 TATTTGGTGAGTGAACAAAGGGATATTCTCAGATT[A/G]CTACAGTTATATATTTCCATTTCCACTTTGCTTTT R 2 1 2 1 101000 f 74 goat snp38561-scaffold489-317872 29 21468237 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381014 Affx-122974659 AX-123251372 29 21073979 TTTCTAAACCTCCAAATAATGGCTTTATTTTTCCT[A/G]TTATGAATTCTCTAATATGATAGTCACAAGCCACA R 2 1 2 1 201000 r 74 goat snp38560-scaffold489-269945 29 21515965 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766251 Affx-122968044 AX-385253646 29 21106357 AAGTTCAAACCTGCCTCTGCCGTGATCTAACCATA[C/T]GATTTTGGTTGAGTCACCATTCCCCTTTGGGTTTT Y 2 1 2 1 101000 f 74 goat snp38559-scaffold489-237567 29 21548618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766838 Affx-122968910 AX-385254161 29 21134884 TGGATTAACGAATGGTGTTTTCTAGCAGTTTGCCT[A/C]TCCTTATTTAAACAGATCCATTGGGTAAAACTCCC M 2 1 2 1 101000 f 74 goat snp38558-scaffold489-209040 29 21577132 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448420 Affx-122923667 AX-123318756 29 21178743 AGATAGCTTATTCTGTTTCAGTTACTGCACTAGTC[A/G]TTTCTCATTTGATCCTGGAAGCACCTTTTGAAGTG R 2 1 2 1 201000 r 74 goat snp38557-scaffold489-165181 29 21621325 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779144 Affx-122934572 AX-385266248 29 21207584 TACTCACAGGCAATGACTCTAATAATGAAATTTAA[C/T]GTGAAGACATTAACAGGGAAGTAACTCCAGGAGAA Y 2 1 2 1 101000 r 74 goat snp3-scaffold489-136340 29 21649743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273231 Affx-1111833356 AX-519546886 29 21223802 GTTTCTGCCAAACCCATCATCTGTGATATTAAGGA[A/G]TGTTTCATTCCCCATCATGAAATTCAGTACAACAT R 2 1 2 1 101000 r 74 goat 29_21223802_AF-PAKI 29 21223802 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320790207 Affx-122971106 AX-385277211 29 21237184 TAGGGCTGATGTTTTAAAAGGCTGTCATTAAGAAA[C/T]ATGTTGTTTGTCTTGCTTTGTGTCTGTTGCTTCCA Y 2 1 2 1 101000 r 74 goat snp38556-scaffold489-106740 29 21679163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428788 Affx-122938408 AX-123299130 29 21273419 GTCTCCGTTCCACTGAGTTCCATGGGGGCAGAGCT[A/C]GGATCACATATTTCTCAGTTCTCTTTGTTTACCAT M 2 1 2 1 101000 f 74 goat snp38555-scaffold489-70505 29 21713917 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378871 Affx-122976512 AX-123249230 29 21310236 CTGGGCATCTGTTTCTCTCTAATTCTCCCTCTTCT[C/T]TTCTGACTTCCTCTCATTACATTTCCAATATGGTT Y 2 1 2 1 201000 r 74 goat snp38554-scaffold489-33688 29 21751349 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396559 Affx-122962931 AX-123266914 29 21340027 AGGAAATGCTGAGAACACAAATTTTCCCCATGAAA[C/T]GTTCACTGTTAATTACCTGTCATTTAATGTTGGCT Y 2 1 2 1 101000 r 74 goat snp38553-scaffold489-3897 29 21781031 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800688 Affx-122961706 AX-385287606 29 21348390 TTAAAATTGACCTGAACTATAAGACCTTTAGAAAG[A/C]GGGCATTTGAGTGGCCATAGTTGTACTACATGACT M 2 1 2 1 101000 r 74 goat snp22554-scaffold2231-222589 29 21793783 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378057 Affx-122977186 AX-123248416 29 21395845 AGCAGAGATTTACAGATTTCCATGTCAGAGAGTTT[A/G]GAATTCAGATGCCAGCTCTATCACTTGCTTTTTTC R 2 1 2 1 101000 f 74 goat snp22553-scaffold2231-175134 29 21841774 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393932 Affx-122965075 AX-123264287 29 21429045 ATGAAAGCAAAGTAGCCCTGTGGCTTGGCTGTGAG[C/T]GGGGTGAGGTGGAAGGCTTGAGTTGAAATTCTAAC Y 2 1 2 1 103000 f 74 goat snp22552-scaffold2231-141934 29 21874951 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428995 Affx-122938850 AX-123299337 29 21459025 GCTGAAATATTTTTAAAAACCGTTTTTCTTCCACA[A/G]TGCCTATTGTACATCATGAAGCAAATCTGAGCATT R 2 1 2 1 101000 r 74 goat snp22551-scaffold2231-111954 29 21905193 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394155 Affx-122964943 AX-123264510 29 21504788 ATGACAGAACCCCTGGTCATGGTATTTTTACTCAA[C/T]GATTTATGTTTTAACTGCTCTGCTTGCACAGCATC Y 2 1 2 1 101000 r 74 goat snp22550-scaffold2231-66191 29 21950861 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406469 Affx-122955176 AX-123276821 29 21562865 CATCCTACAGGTATGGACACTGATTTGAATAGAAT[A/G]CCTTTGGAAAGGATTTGGAGAAATGTGAGATACGG R 2 1 2 1 101000 f 74 goat snp22549-scaffold2231-8114 29 22009800 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388659 Affx-122969106 AX-123259017 29 21573055 CAAGACACCCAGTCTGTGGTGTTTGTAACAGCAGC[A/G]CAAGTTGACTAAAACAGTGCCTTTTCTCGCTTCTA R 2 1 2 1 201000 r 74 goat snp14510-scaffold1585-334522 29 22019844 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781100 Affx-122968137 AX-385268185 29 21632862 GATATTTCCATTTTTACTGCAACCACAGGATTAAA[C/T]GCCCTCGATTAGGTGCTTGGATAGACTGTGATAGG Y 2 1 2 1 102000 r 74 goat snp14509-scaffold1585-274715 29 22080804 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451439 Affx-122921165 AX-123321772 29 21675162 AACTGCTACAGCTTATAATAAAATAAGGAAGCTCA[C/T]AAGCAATACATATGAGTGCACTTGTCTGAGCTTCA Y 2 1 2 1 101000 f 74 goat snp14508-scaffold1585-232415 29 22123253 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277822 Affx-1111836106 AX-519551319 29 21680525 TTCTGATTGGAAGTGAAAAGGGAAGACATCAGAAG[A/T]GAAGCACCACAAATTAAAATTAAATTTGTGGTTCC W 4 1 2 1 202000 f 74 goat Random2.2K-2319 29 21680525 T A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38453847 Affx-122919539 AX-123324180 29 21727969 CACTGTGGTAGTGTCTACTTAACACTTGACGCCTG[C/T]TGACAAGCGCATTCAAAAACAATAAAGAAACCAAC Y 2 1 2 1 101000 f 74 goat snp14507-scaffold1585-179608 29 22176436 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799702 Affx-122972025 AX-385286630 29 21772158 TAGATGTCTAAGATATCAAACAATGAGGGAAATAT[A/G]TGAAGTTGAAATTTCCTATTCTGAGTTACACCAGG R 2 1 2 1 101000 r 74 goat snp14506-scaffold1585-135419 29 22221557 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796410 Affx-122954771 AX-385283360 29 21833043 TGCCATCTATGCAATATTTGTAGCAGAATGTTTGA[C/T]CTGATTCTAATGGAATGTCAGTCTCCAGAGGTTAC Y 2 1 2 1 101000 r 74 goat snp14505-scaffold1585-74534 29 22282469 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779595 Affx-122968451 AX-385266698 29 21910068 TCCCATTTTTTGATATGACTGATAACGTTGTCATG[C/T]TATTTAAAAATCAGGTTAGGAGAGACCTTAATGAT Y 2 1 2 1 201000 r 74 goat snp43838-scaffold592-2392 29 22370796 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774723 Affx-122967209 AX-385261857 29 21949661 TCATTTGCTGTTGACTGCATTCCAGATAATTAAAA[C/T]GTTCTACTTCCAAGCCCCTAATGTGAACTAAAGGA Y 2 1 2 1 101000 r 74 goat snp43839-scaffold592-41985 29 22411039 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380686 Affx-122975173 AX-123251044 29 22051863 GAAAGGATATGAACTCAAGTCTGTTCACAATGTGA[A/G]CACAATTCTTGGAGAAGAGCCTGAAAAACTCATTC R 2 1 2 1 102000 r 74 goat snp43841-scaffold592-144187 29 22514298 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417121 Affx-122947466 AX-123287469 29 22104461 GTAGTGGCTAAACCACCACCACATCACATCATGCC[G/T]ACATGATAAAGGAAGCCATCTTGCTAAGCTTAGTG K 2 1 2 1 101000 r 74 goat snp43842-scaffold592-196785 29 22567429 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376266 Affx-122978761 AX-123246625 29 22143898 TTAGGAATGTTTATAAGCACCTTCACTTTATAGAA[A/G]TATTACCTTGATTTTTAATTATATTTCATTAAGTA R 2 1 2 1 103000 f 74 goat snp43843-scaffold592-236222 29 22606956 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425533 Affx-122941456 AX-123295879 29 22176365 CATTTAATATTATATTGGCTGTGGGTTTGTCATAA[A/G]TAGCTTCTATTGTATTTAGATATCCCCCCTATAGC R 2 1 2 1 101000 r 74 goat snp43844-scaffold592-268689 29 22642043 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452595 Affx-122920497 AX-123322928 29 22206122 CTTAAGGTCTGCATATACTTTAGGATGACAATGCT[A/G]CATAAGACAGAGTTTGCTGAGATATGTTTATTACC R 2 1 2 1 101000 f 74 goat snp43845-scaffold592-298446 29 22672180 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422096 Affx-122943578 AX-123292443 29 22245655 GAGGGGAAAGGGTTTAAAGCCAAATAAATTCTGGA[C/T]ACTCTCAACATAAAGGCTCTGAAAAGTCCTGCAGT Y 2 1 2 1 101000 f 74 goat snp43846-scaffold592-337979 29 22712713 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800454 Affx-122929625 AX-385287375 29 22296905 ACAAAGCCCTTGACAAATACGAGGTATTATTATGA[C/T]GGTATTATCACAATAAAACTTAAATGCGCTTGGGA Y 2 1 2 1 101000 f 74 goat snp43847-scaffold592-389229 29 22765872 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443491 Affx-122927807 AX-123313828 29 22330014 TTGAGTCTGATCCTCTCTAAACATGATGATGAAGA[G/T]TGATGACAATTAACATTTTAAGTGACTATTACGTA K 2 1 2 1 101000 f 74 goat snp43848-scaffold592-422338 29 22799667 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439842 Affx-122930459 AX-123310179 29 22383244 TTTTCCCTCATTTTCTTTTGCAAATGACTAATTAA[C/T]GCAGGGAGTACAGGCATGGAGGCTGAATGACTTCT Y 2 1 2 1 202000 f 74 goat snp43849-scaffold592-475568 29 22853716 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399585 Affx-122961109 AX-123269940 29 22452097 ACATTGTGAATGATGGAACTGGTTTCTCGATGACA[C/T]GGGATGCCTCAGAAAAGACATTATAAAACCTCTGC Y 2 1 2 1 201000 f 74 goat snp43851-scaffold592-544421 29 22922205 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770319 Affx-122920862 AX-385257485 29 22519956 TCTCACACTGTTTTTATAGCTCATATTTACAAAAG[C/T]ATTTTACCTGCAAATGATTAGTAAAGTCATCGATT Y 2 1 2 1 201000 f 74 goat snp43852-scaffold592-612280 29 22989990 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429234 Affx-122937917 AX-123299576 29 22567310 TTTATCCTGAATGCAGACAAAAGCCTGAGCACTGG[C/T]CTCTGAATTGTTCCAAACACAGAGAGGGGCTGAAA Y 2 1 2 1 101000 f 74 goat snp43853-scaffold592-659634 29 23037664 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388329 Affx-122969362 AX-123258687 29 22596051 TTACCAGGTACTGATTTCTGATTCAAGGCTACTGT[G/T]GAGCATCCTAGATGTAGTAGTCAGAATAGTTAGGT K 2 1 2 1 101000 f 74 goat snp43854-scaffold592-688375 29 23065719 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445056 Affx-122926230 AX-123315393 29 22638037 AGCAACAACGAGAGAGCCCCAGATAGCACTCTAGA[C/T]GCCAACAAGGACAGGTGTTCCCCTTCCCCTATCCA Y 2 1 2 1 102000 r 74 goat snp43855-scaffold592-730361 29 23107529 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404578 Affx-122957365 AX-123274930 29 22711146 GTCAGGAGAGACGGCTAGGGTTTCAAAATAGAAAA[A/G]GTTTTGTTATGGAGAAGAAAGAAGTGACTCTAGAT R 2 1 2 1 201000 f 74 goat snp43857-scaffold592-803470 29 23180148 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779352 Affx-122959895 AX-385266456 29 22757764 AAAGAAATGTAGAAATTACATAACAAAAGTAAGGA[C/T]GCCATCTATACTTGAATTTCTCTAAAATCCTGACA Y 2 1 2 1 101000 r 74 goat snp43858-scaffold592-850088 29 23226781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791376 Affx-122936070 AX-385278368 29 22806138 AATCGTTTTTTCTGTGTTAGCATCTAATTCATATA[C/T]GCATTTCAAAATGGAGAGGGATGGAACATACATTG Y 2 1 2 1 101000 r 74 goat snp43859-scaffold592-898462 29 23275159 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428728 Affx-122938452 AX-123299070 29 22835055 ATTAACCCAAGGTATGAATCCACAATCAGAAATAA[C/T]AGCATCATCTGAGGGCCTGTTAGAAATGTAATTTC Y 2 1 2 1 101000 f 74 goat snp43860-scaffold592-927379 29 23304018 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445037 Affx-122926619 AX-123315374 29 22865838 AAATATATTCATGGAGATTGTGTTTGCTGGCCAAG[C/T]GAATGGATGCTAGCCAAAAGCAGTCCGCTGTTGCC Y 2 1 2 1 101000 r 74 goat snp43861-scaffold592-958162 29 23334824 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781079 Affx-122926619 AX-180660636 29 22865838 AAATATATTCATGGAGATTGTGTTTGCTGGCCAAG[C/T]GAATGGATGCTAGCCAAAAGCAGTCCGCTGTTGCC Y 2 1 2 1 600000 f 74 goat snp43861-scaffold592-958162 29 22865838 6 parentage parentage GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445387 Affx-122925399 AX-123315724 29 22900740 GATGAACTCAGCCTCTGAGCGTCTCTGGTACCCAG[C/T]TGGCTGTGTGGTGAGCATCCCAGAGGATAATTCTG Y 2 1 2 1 101000 r 74 goat snp43862-scaffold592-993064 29 23369270 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785426 Affx-122970430 AX-385272471 29 22949786 GCTGATCCCAGGTTTGCAGTCTAATTCTGAGTCAT[A/G]CCCATGATCTGAAAAACCTTAAAGAGATCATGCAA R 2 1 2 1 101000 f 74 goat snp43863-scaffold592-1042110 29 23417317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420488 Affx-122944864 AX-123290835 29 23000537 GGCAGGCTATAGTCCATGGCGTCACAACTACACAA[C/T]GACCACTGTCACTTAGCTTGCTTTACCCTTATCAA Y 2 1 2 1 101000 r 74 goat snp43864-scaffold592-1092861 29 23466832 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425261 Affx-122940983 AX-123295607 29 23034020 CTACTTAGAGAATAGTGGGAAAAGAAATCAAATGT[A/G]TGCCCCTCCCCTCAAAAAAGCTAGAAATTGGCGAA R 2 1 2 1 101000 r 74 goat snp43865-scaffold592-1126344 29 23499897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396640 Affx-122962868 AX-123266995 29 23064149 TAAAGCTGTCTCACTGGACTACATGTTCTATGAAC[A/G]CAGAGACCATGTGTGAATTTGCTCTTCACTGCATC R 2 1 2 1 101000 r 74 goat snp43866-scaffold592-1156473 29 23532989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421583 Affx-122944503 AX-123291930 29 23099746 ATTTTTGGCCTCAGTGGGCCTATCTAGGTTGACAT[A/G]CCAAAAAGTAGTACAAGGAAGGTTTACTGAACTCT R 2 1 2 1 101000 f 74 goat snp43867-scaffold592-1192070 29 23567558 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416617 Affx-122947626 AX-123286965 29 23180348 TCTTGAATTAAACTTGGTGCTTTCAATCTGGTCTG[G/T]CCAGGACACAGCAGAGCATCCCCTTCTGGTTCAAA K 2 1 2 1 201000 f 74 goat snp10133-scaffold136-839836 29 23647853 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429317 Affx-122938596 AX-123299659 29 23210565 CTTAGGCTACACACTCCAAATCCCCACTCCAGAAG[C/T]GCATTTATAGGAGGAGATTGAGGTACTCAGTTATC Y 2 1 2 1 201000 r 74 goat snp10132-scaffold136-809619 29 23677831 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396251 Affx-122963326 AX-123266606 29 23247643 GGTTTGGGGTCAGGCCTGCATTAGGTGCCAGCCCC[A/G]TGCCCTCCTTGCTAGGTGACACTGGCAGTGAACGT R 2 1 2 1 101000 r 74 goat snp10131-scaffold136-772541 29 23714945 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420117 Affx-122945083 AX-123290465 29 23278014 CCCTTTCCAGCCCTGGAAGAATTGAAGGGGGAGGG[C/T]GCTGGAGACGGTATGTGTGTGGGAGGTGTGTAGCG Y 2 1 2 1 101000 r 74 goat snp10130-scaffold136-742170 29 23745167 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413789 Affx-122949914 AX-123284138 29 23320786 CCTGTTGAGAAGCACAGGGTGATCTATGAGAGCCC[A/G]TCAGGGGCGTGTCCAGTGAGGACATGACAAAGAAG R 2 1 2 1 101000 f 74 goat snp10129-scaffold136-699398 29 23789018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438131 Affx-122931483 AX-123308469 29 23363975 CATTGAAATTAACATTTAAAACACCTAGAGATATC[A/G]TGTCAAAGTGATGGTAACAAGGAGGTTAAACTGTA R 2 1 2 1 101000 r 74 goat snp10128-scaffold136-656209 29 23832696 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430744 Affx-122937503 AX-123301085 29 23421452 TAATTCATCTGATATATAGCATTTCCTTGTTGCTT[A/G]TGTATCTGGTGGCTCATATGGTAGAGAATTTGCCT R 2 1 2 1 303000 f 74 goat snp10127-scaffold136-598732 29 23889661 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445269 Affx-122925469 AX-123315606 29 23454829 GAGTGTGTGTATCCTCTCCCCTTGCCCTAAGCTCT[A/G]CTCTGTGCTTGAGTTTTCTTTATCATACTACTATT R 2 1 2 1 201000 r 74 goat snp10126-scaffold136-565355 29 23923046 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422769 Affx-122943228 AX-123293115 29 23485532 ACTGCCTAGGAGTACCCCTTTAAGTTGGTTATTCT[A/G]TAGGAGCTGGTTTTTCATTTGAAGAGACTAACAAA R 2 1 2 1 201000 r 74 goat snp10125-scaffold136-534652 29 23953844 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398070 Affx-122961738 AX-123268425 29 23579843 AGAAACTCCCTATTTTACATACAGTACTTCTGAGA[C/T]GCTAAAGTAGGCTTTCTGAAGTTCAAAGTTTAGAG Y 2 1 2 1 201000 r 74 goat snp10123-scaffold136-440341 29 24046409 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449003 Affx-122923101 AX-123319338 29 23612223 CCCACGATGTCTACCCATCTCCGTTTGCAGCCCAC[A/G]CTGCTTCTGTGTCTGTTAGCTGCACTGCAGTCCAC R 2 1 2 1 201000 r 74 goat snp10122-scaffold136-407961 29 24078869 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399896 Affx-122960209 AX-123270251 29 23644361 TGAAAGGAGAAACTCTAAAAGACTGCAAGTAAAGT[A/C]AAGTCAAGTCACTCAGTCATGCCCGACTCTTAGCG M 2 1 2 1 101000 f 74 goat snp10121-scaffold136-375823 29 24111344 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445489 Affx-122925198 AX-123315826 29 23675364 CTTGCCTGAGGCTGAGGTGGGTTTCGAGGTTATTG[C/T]AGGAAAGGGAGAAGGAAAAGCCCCCCAAGACTTTT Y 2 1 2 1 201000 f 74 goat snp10120-scaffold136-344820 29 24142516 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778860 Affx-122955937 AX-385265968 29 23721387 TATCTGGTTCTGAAACCCATGCTTTTTCTGCCACA[C/T]GATGCTACAGTCACATTAGGTTGGACTTTGAGGGG Y 2 1 2 1 101000 f 74 goat snp10119-scaffold136-298797 29 24188128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397753 Affx-122962530 AX-123268108 29 23761668 AGGGACACCCCAGGTTGATCTGAACTTGGCCAGGA[C/T]GCACAGAGCCCTGTTTGTCAATGCTCACAGCATCA Y 2 1 2 1 101000 r 74 goat snp10118-scaffold136-258516 29 24228367 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440843 Affx-122929263 AX-123311180 29 23795850 TGCAGTAGCTCGAGAAGCGTGTGTTCACTGATTTC[A/G]CTCATTTAATCATCGAGCCTTGATTGCTCACTTGC R 2 1 2 1 101000 f 74 goat snp10117-scaffold136-224334 29 24262408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388312 Affx-122969376 AX-123258670 29 23840188 TGCTTCCCGTCCCTGCACCCCTGTTCCTTCATCCA[C/T]GTGGTCTGACCTACTGATGTTTAAAGTCCTTGAGC Y 2 1 2 1 101000 r 74 goat snp10116-scaffold136-179996 29 24306295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376540 Affx-122977993 AX-123246899 29 23869363 GTTATTATTTATTCTTTCATTTAGTTCATCACGAA[C/T]ATTTGTTAGGTACCTATCTCAAGAGTTCTAATCAC Y 2 1 2 1 101000 r 74 goat snp10115-scaffold136-150821 29 24335557 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437088 Affx-122932191 AX-123307426 29 23925257 CTCTATGGTTATCTTGTCCGTCCTTCATTTGCAGG[C/T]GGGGACTCAGCCGCATTCTCTTTTCTGTCCATTGC Y 2 1 2 1 101000 f 74 goat snp10114-scaffold136-94927 29 24391387 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393652 Affx-122965288 AX-123264007 29 23961485 ACTTGAAAATATCTCCACCCTTATTTGGGCTTCCC[C/T]GGTGGCTCAGCTGGTAAAGAATCTGCCTGCCAATG Y 2 1 2 1 103000 f 74 goat snp10113-scaffold136-58699 29 24427640 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385240 Affx-122972094 AX-123255598 29 23992145 CTTTGGTAAGGCATAGTTAGCCTGTGGTGGCTGCA[C/T]TGGGAACTGGTCAGTAGAGGACTACCAGTGTGCTC Y 2 1 2 1 101000 f 74 goat snp10112-scaffold136-28039 29 24458019 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430449 Affx-122937727 AX-123300790 29 24021382 ACCACACAGTTTTGGGAAAGAGTAAAACCATCATC[A/G]CCACACCCAACTCCAAAGTATCACATCATTCCAGA R 2 1 2 1 101000 f 74 goat snp54097-scaffold825-1099 29 24486481 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451893 Affx-122921043 AX-123322226 29 24064114 AAATAACATCAGTGTCTCAAGGCTGGAGTTGGGGG[C/T]GGGGGAATAATCAAACCATCCCTATTTGAGGAGAT Y 2 1 2 1 201000 r 74 goat snp54098-scaffold825-43831 29 24529281 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425166 Affx-122941060 AX-123295512 29 24119836 ACAATTAGTACAGTTTGCTTTAATGAATTTGTAAA[C/T]AAGTTTTATTGTTCCTCAGTGCTTGTGGGCAGTCA Y 2 1 2 1 201000 f 74 goat snp54099-scaffold825-99553 29 24584816 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376856 Affx-122977840 AX-123247215 29 24186949 AACAGGTGGCAGGCCAAATTTGGCCCAAGGGCTAC[A/G]CTTGACAGACCCTTGGGTAAACCAGTTACACCCTC R 2 1 2 1 201000 r 74 goat snp54101-scaffold825-166666 29 24651612 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444608 Affx-122926948 AX-123314945 29 24234961 GGTGCACATGGTTACGTGTGTGTGCATGTTTATAG[C/T]ATGCACAGTCACCTGTGTATTCATGGGTATCAACA Y 2 1 2 1 103000 r 74 goat snp54102-scaffold825-214678 29 24699716 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272393 Affx-1111834259 AX-519546121 29 24245663 TTTTAAGTCTTGTGTGCATTTTGTTGTCCAGAAGT[A/G]TCCCAGCCACATAACCCAGGCTCTGCCTTGGCTCA R 2 1 2 1 201000 f 74 goat GoatD01.027985 29 24245663 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 320792083 Affx-122936729 AX-385279070 29 24268150 ATCCAGAAATCAGCCTTTCCTCTAAGACTTTAATA[C/T]GGATTATGAGAGTTTTCTATGAGAAGAACTTTAAA Y 2 1 2 1 103000 f 74 goat snp54103-scaffold825-247867 29 24732701 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409371 Affx-122954161 AX-123279722 29 24297780 TTTTAGATTATTTCCTTAGGTGGGATTCCCAGCAG[C/T]GGCAGAGTGAACATTTTCAAAGCTCTAACACCGTC Y 2 1 2 1 101000 f 74 goat snp54104-scaffold825-277497 29 24762141 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396181 Affx-122963769 AX-123266536 29 24354504 CTAAATTTTGAGGTGATTTGTTATGCAATAAGATA[C/T]AACTGGAACAATCATCACCTCATCCAACAGATGAA Y 2 1 2 1 101000 r 74 goat snp54105-scaffold825-334221 29 24818341 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391822 Affx-122967017 AX-123262179 29 24386858 CAAACGCTTTGACATAATACAAAACATCCTCGGCA[A/G]CTACACACACAGCTGCTCATCTCCCAGAAACAGAG R 2 1 2 1 101000 f 74 goat snp54106-scaffold825-366575 29 24850418 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277827 Affx-1111836108 AX-519551324 29 24413888 CTCAGCATCAGCTCTGAAACGTCTGTCAAGGGGTG[A/G]CCGGGACTTAGGGTGGCCCTTCACTTTCTCATTTG R 2 1 2 1 202000 f 74 goat Random2.2K-2321 29 24413888 C T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 320790562 Affx-122977763 AX-385277565 29 24431947 AATGCAGATTTTATTTGTGCATGGGATAGCTTAAA[C/T]GATTCAATTGGATCTGAGATTTTTTGAAAAGCAAT Y 2 1 2 1 101000 r 74 goat snp54107-scaffold825-411664 29 24895343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397843 Affx-122962466 AX-123268198 29 24561910 CTTCCTGAGGCTGTGCTTTGCCATGATTCTGGCCT[A/G]CATTTAGCAGGTGCATGATTCAAGTCACTGAGCAT R 2 1 2 1 101000 r 74 goat snp54110-scaffold825-541627 29 25025234 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781837 Affx-122962283 AX-385268919 29 24604964 AGTTCTCGGATATCTTTCACTTATCCACAAAGCCC[C/T]GACACGGGCAGATTTAATTTGACTGTTTTAGAAGA Y 2 1 2 1 101000 f 74 goat snp54111-scaffold825-584681 29 25068161 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380385 Affx-122975332 AX-123250743 29 24645936 TTGTCATTACAGAACTTCTGGTGCTGATCAAGACA[G/T]AGCGAGCCCATGAGAGCCTCTCCCATTGATTATAA K 2 1 2 1 201000 f 74 goat snp54112-scaffold825-625653 29 25109151 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397466 Affx-122962094 AX-123267821 29 24675423 CTGGGGCTCTTCACCTGAAGTCCAGTTCTCTAGGC[A/G]TTTATTCTCCTTTCGTCAACCTGGATATCTGAGTG R 2 1 2 1 101000 r 74 goat snp54113-scaffold825-655140 29 25138769 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421997 Affx-122943784 AX-123292344 29 24712339 TAGGTCATGAAAGATTTAAGTGGCCTATGACTTAC[A/G]TTTTTTAAAAAGGAAATAGAATAAAAAACAAAAAT R 2 1 2 1 103000 f 74 goat snp54114-scaffold825-692056 29 25175690 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431795 Affx-122936123 AX-123302136 29 24743196 ATGGAGATATCTTGAATCCAATTACTTTTTCTAAA[G/T]AGTATATAAGTACCATTAAAGTTAATTAACTAAAG K 2 1 2 1 101000 f 74 goat snp54115-scaffold825-722913 29 25206548 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403177 Affx-122958078 AX-123273530 29 24788915 AATGGGAATAACGATGCCTGCTCCACAGAGGTGCT[A/G]AAAGGAGCCAGTGAGCAATGCACACAGAAGCGCCT R 2 1 2 1 101000 f 74 goat snp54116-scaffold825-768632 29 25252902 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785213 Affx-122954166 AX-385272259 29 24822624 AGTCTGTTACTTTCTTACAATCAGTTTTTATACAA[C/T]GAAAAGAATTCAATTTCCATCCAGCCCCAAAGAGT Y 2 1 2 1 101000 r 74 goat snp54117-scaffold825-802341 29 25286593 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449395 Affx-122922707 AX-123319730 29 24864180 AACCAATCAGAATCGACCAAAAGGAGAAAGAAGCA[C/T]GTAGCAAGACATTTGGGACAGTTTCAAACATGAAG Y 2 1 2 1 101000 r 74 goat snp54118-scaffold825-843897 29 25328810 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386614 Affx-122970236 AX-123256972 29 24901932 CTCCTTCCTGGCTGGACAATTTCAGTGAATGCTTA[G/T]AACCTGTCTGGGTCTCAATTTCTCCATCCAAAAAA K 2 1 2 1 101000 f 74 goat snp54119-scaffold825-881649 29 25366901 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403843 Affx-122957939 AX-123274195 29 24961607 CTCTCTCTGTGTTCACCTGTTCTGTCCCTTCCCCT[A/G]TCCCACTGTGCGTGCACACACATACATACACAAAC R 2 1 2 1 101000 f 74 goat snp54120-scaffold825-941324 29 25426077 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392839 Affx-122965772 AX-123263196 29 25006105 CATTCCACCCCAGGGGTTTTCAAGATGGTGGTTGC[A/G]GGTGATACGTGAATTACCGTGGCTCTGGATTTAGA R 2 1 2 1 201000 r 74 goat snp54121-scaffold825-985822 29 25470801 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417174 Affx-122947330 AX-123287522 29 25034758 TCTTATAGGTTAAGGTTTCTTTTTAAACCAGCACA[A/G]CAGCAAGGTTGAGTGGATAAGAATGTCATCTGCCT R 2 1 2 1 101000 r 74 goat snp54122-scaffold825-1014475 29 25497494 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380072 Affx-122975555 AX-123250430 29 25091100 AACCCACCATGGCACCCAGGGAGCTGTCTCCTGGC[A/G]TGTGGAGTATTTCCCATGAGATCTCTGGAAGAGAG R 2 1 2 1 101000 r 74 goat snp54123-scaffold825-1070817 29 25553934 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435978 Affx-122933512 AX-123306317 29 25186310 AAGATTTAAGAAAATGAAACATACTACTAACAACC[A/G]TCAAAGAAAATATATTTTTGGATTTAACCTGAAAT R 2 1 2 1 101000 f 74 goat snp54125-scaffold825-1166027 29 25649038 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388936 Affx-122968823 AX-123259294 29 25223979 GTAGACTTGTTTTATATCTTCGTTTACAAACACAG[A/G]AAGAGTTATCATACTATAAATTGAGAATTATGGCA R 2 1 2 1 101000 f 74 goat snp54126-scaffold825-1203696 29 25686314 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382122 Affx-122974880 AX-123252480 29 25252916 AATACTTTTGTAATCAAAAAATGGACATTAATGGT[C/T]AGTGATCTTGTCATTTCCTTTTCACTATTCAGTTC Y 2 1 2 1 101000 r 74 goat snp54127-scaffold825-1232633 29 25715042 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405301 Affx-122956844 AX-123275653 29 25299581 GAAGACATCTTGCCCAGTTTCTTCATTTCAGTTAT[A/G]CAAACATTAATAAGGAACCAGCTCTGTGCAAGTTG R 2 1 2 1 201000 r 74 goat snp54128-scaffold825-1279298 29 25762136 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396647 Affx-122962862 AX-123267002 29 25339925 GGGAAACCATGAAGATGGCGAGACTAGTCAGGCAG[C/T]GGCTGCAGGAACCCAGGTGAGAAATGGTGCTGGAG Y 2 1 2 1 101000 f 74 goat snp54129-scaffold825-1319642 29 25802314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388669 Affx-122969098 AX-123259027 29 25395051 GCCCTCCATGGTGCTAACTGACAAGTTCCTGTTTC[A/G]TACCAGGAAGGCTCTGAGACAGGCTCAGCACAGTT R 2 1 2 1 201000 f 74 goat snp54130-scaffold825-1374768 29 25858578 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444386 Affx-122926598 AX-123314723 29 25423633 GTGCTGGGTACATTCAGCTTAATCTCTGGACACTG[A/C]TCAAGTGTGCTGGATACATTCAGCTTAATCTCTGG M 2 1 2 1 201000 f 74 goat snp54131-scaffold825-1403350 29 25887195 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422322 Affx-122943463 AX-123292668 29 25463307 ATGAGTAATAAAAATTGGAAAATATTGATATGAAG[C/T]GGAGATGTGAAAACTCAGATTTGTACTGCATCTGC Y 2 1 2 1 101000 r 74 goat snp54132-scaffold825-1443024 29 25926997 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413326 Affx-122950176 AX-123283675 29 25508657 TTTTTGGGAATTTTTTTTGTCTTCTAGCATCTTTG[C/T]GAGAAGTCCTGATGCATCTTTCCTTGGAATATATC Y 2 1 2 1 201000 f 74 goat snp54133-scaffold825-1488374 29 25972909 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277970 Affx-1111836109 AX-519551464 29 25517178 TCCAACAAGTTTTGGATCTCTGCCCTGGAGGGGAA[A/G]GCACTCTTTCCAGTTTATTCCTACCTTGGATACTT R 2 1 2 1 101000 r 74 goat Random2.2K-2322 29 25517178 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320791886 Affx-122969411 AX-385278876 29 25553728 CTCTAACATACTTCCAATAAATGCATGTCTCCCAG[C/T]GAGTTCTGTTACTAGCCCTCATCTCCCTCCCCGAG Y 2 1 2 1 101000 f 74 goat snp54134-scaffold825-1533445 29 26019039 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779484 Affx-122963736 AX-385266587 29 25688861 TATCATCTCAAAAAGATATCTTATACCATTTAGCT[A/G]TCATTCTCTTATTACCTCTGTCAGCTTTGACTGTA R 2 1 2 1 101000 r 74 goat snp2822-scaffold1083-29437 29 26155981 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441913 Affx-122928602 AX-123312250 29 25726154 ATGGTCCATTTTTCTTCTATATCCTTACAATCAAT[A/G]CATCCTGTTATTTGGAGGACTGGTGTCCTTGTCTG R 2 1 2 1 101000 r 74 goat snp2823-scaffold1083-66730 29 26193377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795373 Affx-122921421 AX-385282329 29 25759521 GGAAAAGAGTATATAGACGACAGTCTTATTTAAAC[A/G]TTGTAATTCTCTGATGACACCTCCTACAGATGAGG R 2 1 2 1 101000 r 74 goat snp2824-scaffold1083-100097 29 26227086 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441605 Affx-122928656 AX-123311942 29 25799354 GACCAAACCTGAGAAACTGCAGGGCTCTCTGAAGG[C/T]GGTGATGGTCCCCAGTCTCTGAAAGGAGTCTCTCA Y 2 1 2 1 101000 r 74 goat snp2825-scaffold1083-139930 29 26266915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764360 Affx-986698887 AX-385252073 29 25838308 CTGCTGGCCTGCCTGACAAGTACTGAGCTGCCTCT[A/C]TCTCTGCTCAGGGGATGGCAAAGTGAGTCCCCAAG M 2 1 2 1 600010 f 74 goat 29_25838308 29 25838308 Ancestral_priority_1043 ancestry 0.47 neutral IMAGE 10K 10K ancestral 320768092 Affx-986698893 AX-385255294 29 25838330 CTGAGCTGCCTCTATCTCTGCTCAGGGGATGGCAA[A/T]GTGAGTCCCCAAGTGAGGGACAATGACCTAGAGAG W 4 1 2 1 600010 r 74 goat 29_25838330 29 25838330 Ancestral_priority_1043 ancestry 0.51 neutral IMAGE 10K 10K ancestral 320768794 Affx-122924877 AX-385255971 29 25839970 CCATGCTGTGGGATATTATAGCCACTAGTTATGTG[C/T]GGTCACTGAGCATTTGCAATGTAGTATGATTTTAG Y 2 1 2 1 101000 f 74 goat snp2826-scaffold1083-180546 29 26308027 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764368 Affx-986698895 AX-385252081 29 25864540 AGAGTTATGATTAAGCTAATCAGCATTTAAGAGAA[C/T]TGAATTAAAATATATCATACATTTATTTATGTGCC Y 2 1 2 1 600010 f 74 goat 29_25864540 29 25864540 Ancestral_priority_1043 ancestry 0.716 recommended IMAGE 10K 10K ancestral 320804345 Affx-986696512 AX-385290953 29 25870216 CCCTACGTGTTCATCTCATTACACCTACAGGAAAT[A/G]AATATGTCCCAAACCCAGAAAGAGGCATCATCCTA R 2 1 2 1 600010 r 74 goat 29_25870216 29 25870216 Ancestral_priority_1043 ancestry 0.648 recommended IMAGE 10K 10K ancestral 38445772 Affx-122926065 AX-123316109 29 25874599 GTCCCAGAATCTGTTCCCTTTCTTAGAGGAATTCA[A/G]AGCATTCCCAGGCTATAATGTTCCTCCTCAATTGT R 2 1 2 1 101000 r 74 goat snp2827-scaffold1083-215175 29 26340466 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421549 Affx-122943864 AX-123291896 29 25915639 ATGTGTTGGTGATACTCCTTATGTCTTCTTTTCCT[A/G]TATCAATAGACTGTCCCCTGGCCATTGGTACAAAT R 2 1 2 1 101000 r 74 goat snp2828-scaffold1083-256215 29 26381310 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773169 Affx-122921201 AX-385260312 29 25979751 GCCAGTGGTGACCACCTAGGAGTTTATGGATGTCA[C/T]AGACTCAACCTGACTCCCTCAATGATGAAGACCAA Y 2 1 2 1 101000 r 74 goat snp2829-scaffold1083-320327 29 26445566 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452469 Affx-122921004 AX-123322802 29 26036694 TGAAAAAAATACCAGTCTAGGTCAACTGTTTTATA[C/T]AAAAAGATCTTTTTAAATGAAAAACATACATATTG Y 2 1 2 1 103000 f 74 goat snp2830-scaffold1083-377270 29 26502551 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447310 Affx-122924910 AX-123317646 29 26065212 TAAAATACTGGTCGTAAGCCTCATGACCACTCTCC[A/G]CAGGGTCTTCTTATGTATTGGCCATGGGTCTGTTG R 2 1 2 1 201000 r 74 goat snp2831-scaffold1083-405788 29 26531269 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447395 Affx-122924412 AX-123317731 29 26095716 CATAGGAAGTCACAGAGGATTTAATGTGAGTGTAA[C/T]GATATAACGTACTCAGATACAGATATGGCAGCGGC Y 2 1 2 1 101000 f 74 goat snp2832-scaffold1083-436292 29 26561693 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273183 Affx-1111833357 AX-519546842 29 26097018 AGGGTGGCACACGTCCTCCCACTCATCATGCTGGC[A/G]TACCTGAGCGGGTAACTGATGGCCAGGAAGCGGTC R 2 1 2 1 202000 f 74 goat 29_26252389_AF-PAKI 29 26097018 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418023 Affx-122946648 AX-123288371 29 26129238 TTGATGGATAAGATAGGGATGTTTAGGGAGAGTGA[A/G]TTGGGCATAAGAGGCCCTGGCATAGAGTTTAGTGA R 2 1 2 1 101000 f 74 goat snp2833-scaffold1083-469814 29 26595181 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406615 Affx-122955837 AX-123276967 29 26178818 ATATTTTAAAAAGATTGGCATATCAAACACCTAGT[A/G]TTTGTGTTCAAAGGCATCTTATGATTTACAGAATA R 2 1 2 1 101000 r 74 goat snp2834-scaffold1083-519394 29 26645510 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424455 Affx-122941780 AX-123294801 29 26230813 AGGTGAAGGCAGTGTTGGTGTGAACCAAAATGATC[A/G]TCTTATTAGAAGACAAACCACAAGCTCATTGTTGC R 2 1 2 1 101000 r 74 goat snp2835-scaffold1083-571389 29 26697690 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378046 Affx-122977193 AX-123248405 29 26272894 TAAGGTGATCTGTGAGCACAGAAGAAAAAGGTTAC[A/G]TAGAGAACAATGACTCAATTTTCACACAATATCTC R 2 1 2 1 102000 f 74 goat snp2836-scaffold1083-613470 29 26740481 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405329 Affx-122956341 AX-123275681 29 26320670 CTTCCTCCATAGATCAACTGGCAAAGAATCTGACC[A/G]CAATGCAGGAGACCCTGGTTCAATTCCTGGGTTGG R 2 1 2 1 103000 f 74 goat snp2837-scaffold1083-661246 29 26787993 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416496 Affx-122947789 AX-123286844 29 26359510 CCACCAGCAACATCAGATATCCCCCCACCCCTCTT[C/T]GGAGAAATTGGGGAGAAACACATAACTCTGAAATT Y 2 1 2 1 101000 r 74 goat snp2838-scaffold1083-700086 29 26827360 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796970 Affx-122972470 AX-385283911 29 26412328 CATAAGAAACTATCATCACTTATGATGATTTAGCC[A/G]TATCAGCCTATCTTCTTTTTGCTTTTCAGGAATGC R 2 1 2 1 102000 r 74 goat snp2839-scaffold1083-752904 29 26880142 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798034 Affx-122966581 AX-385284970 29 26451118 TGAAATGTTCAATTTTTATTTTGAGGCTTCTCAAA[C/T]GAAAGATTTTTGACCAACTTTTAACACAATTTTGG Y 2 1 2 1 201000 f 74 goat snp2840-scaffold1083-791694 29 26919287 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779292 Affx-122939470 AX-385266396 29 26498662 ACAGTGACCCTTATCATGCTCATTCCAAACCTGAT[C/T]TTGAGTAATTAATAATATAAGCTCTCTCTTGAACA Y 2 1 2 1 101000 f 74 goat snp2841-scaffold1083-839238 29 26967921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389945 Affx-122968088 AX-123260302 29 26534611 GTACACAGAGGGATGTACACTCTGTTGATAACGTT[A/C]TCTTCTCTGGAGCTAACTTCACTCCTCCTGGAGTG M 2 1 2 1 101000 r 74 goat snp2842-scaffold1083-875187 29 27004688 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764370 Affx-986698897 AX-385252083 29 26575992 TTCTTGCTAAACACTCTTGGCTTCCTCTAGTGGCA[A/G]TGTAACGTGATTTCTTTGCTGCCGGTCACCTTTCT R 2 1 2 1 600010 f 74 goat 29_26575992 29 26575992 Ancestral_priority_1043 ancestry 0.604 recommended IMAGE 10K 10K ancestral 320768103 Affx-986698899 AX-385255305 29 26576013 TTCCTCTAGTGGCAGTGTAACGTGATTTCTTTGCT[A/G]CCGGTCACCTTTCTTTTATATCCTCACATTCTAGA R 2 1 2 1 600010 r 74 goat 29_26576013 29 26576013 Ancestral_priority_1043 ancestry 0.618 recommended IMAGE 10K 10K ancestral 320769199 Affx-122935244 AX-385256374 29 26581674 TCAATAGAAGGTTTCAAATGCCAAAATCAAGGTCA[A/G]CTCACTATCGGAAGCCATTAGGAACCATTCGAGAT R 2 1 2 1 101000 f 74 goat snp2843-scaffold1083-922250 29 27053016 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390477 Affx-122967599 AX-123260834 29 26619743 AGAGGGCCACGTGATGATAAATGCAAGCAGCCTAA[A/G]CAAACTGAGAGTGACCCGCAGCTGACAGTCAACGA R 2 1 2 1 101000 f 74 goat snp2844-scaffold1083-960319 29 27091483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399393 Affx-122961251 AX-123269748 29 26672718 GAGGAATTTGATTGTCAATTTCCCATTAGGGTAAA[C/T]AGCCCAATAACCCAACCTTGGATTAGTTTTCTATT Y 2 1 2 1 102000 f 74 goat snp2845-scaffold1083-1013294 29 27144973 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421040 Affx-122944529 AX-123291387 29 26717275 GATGAGAACTGGAAAGAGACCTAGAGATATCATGA[C/T]CTCTGACTCCATTGTTTCAGTCACCCCCTCACCCC Y 2 1 2 1 101000 r 74 goat snp2846-scaffold1083-1057851 29 27190122 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415267 Affx-122948843 AX-123285616 29 26746927 TGTTTCCTATGCTTTTATTCTCTCCAGCATCCTCC[A/G]TATCCACTCCACAGAGGGAAGGTCCAAAGCCTTCA R 2 1 2 1 101000 f 74 goat snp2847-scaffold1083-1087503 29 27221096 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447714 Affx-122924606 AX-123318050 29 26791899 TCATTATTTCTCAGGTTGAAAGTGGAATAGAAATA[C/T]AGGGGAGAAACCCTCTAAAATTCATGCACACACGA Y 2 1 2 1 201000 f 74 goat snp2848-scaffold1083-1132475 29 27266662 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388094 Affx-122969503 AX-123258452 29 26830357 TAAAAATTTAATAAATTAAGATTACTAAATAATAA[C/T]AAAGTGCTACACACAAGACCACCTACAGCAAAACA Y 2 1 2 1 102000 r 74 goat snp2849-scaffold1083-1170933 29 27305879 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378209 Affx-122976929 AX-123248568 29 26874782 TTCCCTTATGAAGGACAAAATGCTCATGCAGAGTT[A/C]TTAAAAGCCTACCTTCTTATGTCCCTCAACCTCCT M 2 1 2 1 101000 r 74 goat snp2850-scaffold1083-1215358 29 27350718 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388148 Affx-122969462 AX-123258506 29 26931285 AGGCTACAAACTAGAGCGTGCTTGCGTGCTAAGCC[A/G]CTTCAGTCATGTCCGACTCTTTGTGACCCTATGGA R 2 1 2 1 103000 f 74 goat snp2851-scaffold1083-1271861 29 27407592 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389360 Affx-122968463 AX-123259718 29 26968853 TGACAGTTCTGCTTATTTTCATCTTGTTGTCATCA[C/T]GATATAATCAGAATTTTACACCTTCTGACAACCCT Y 2 1 2 1 101000 r 74 goat snp2852-scaffold1083-1309429 29 27445104 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777212 Affx-122925375 AX-385264335 29 27018234 GTACACCAGAATCTGGATGTAGCCTGAGAAGCACT[A/G]CTTTAGACAACTACGATAATACTTTAGCCATGAAG R 2 1 2 1 101000 f 74 goat snp2853-scaffold1083-1358810 29 27494438 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768106 Affx-986698901 AX-385255308 29 27051171 TAGTACATGGGAGTGTGCAGGTGAGGGTTCAGACC[A/G]ATAAGAATAATCAAGCCAATGTTCCCTGCCACAGT R 2 1 2 1 600010 r 74 goat 29_27051171 29 27051171 Ancestral_priority_1043 ancestry 0.608 recommended IMAGE 10K 10K ancestral 320764378 Affx-986698903 AX-385252090 29 27051212 AATAATCAAGCCAATGTTCCCTGCCACAGTGACCA[C/T]ATAAATTGCTAAGAAAATGAAAAAGAGAGGCAGCT Y 2 1 2 1 600010 f 74 goat 29_27051212 29 27051212 Ancestral_priority_1043 ancestry 0.582 neutral IMAGE 10K 10K ancestral 320768113 Affx-986698905 AX-385255315 29 27051227 GTTCCCTGCCACAGTGACCACATAAATTGCTAAGA[A/T]AATGAAAAAGAGAGGCAGCTGGAGTTCTGGCTGCT W 4 1 2 1 600010 r 74 goat 29_27051227 29 27051227 Ancestral_priority_1043 ancestry 0.444 neutral IMAGE 10K 10K ancestral 38402251 Affx-122959132 AX-123272604 29 27054760 GATTTTTCTCATCGCCTTAGTTATCCTCAGGACCA[C/T]AGTCTCCTTACAGATCACATCCTCCGCCTCTACCA Y 2 1 2 1 101000 f 74 goat snp2854-scaffold1083-1395336 29 27531047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788241 Affx-122953483 AX-385275260 29 27065441 GAAATATCCAGAAGATAGCAACTCTTGAAGTCATA[C/T]AGAATGGGCATCTCTTGAAACGTATGTGTAGCCAG Y 2 1 2 1 101000 f 74 goat snp53027-scaffold796-2259243 29 27540806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430300 Affx-122937275 AX-123300641 29 27168532 TCCACGGTAAAGCCATGGAAAAGCCAGCGTCATTG[C/T]GGCCTCATTCCCCATTTACACATGCAGAGAAGTCA Y 2 1 2 1 201000 r 74 goat snp53025-scaffold796-2156152 29 27644547 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417291 Affx-122947240 AX-123287639 29 27202247 TGATGCATTTATCTGAGGTCACACAGCTACTATTC[A/G]GCCGAACCAGGCTATGAGTCAGGTGATTTAACTCC R 2 1 2 1 201000 r 74 goat snp53024-scaffold796-2122437 29 27678409 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401372 Affx-122959236 AX-123271725 29 27353663 AAACAAAGATCTTGCAGTGAACCACAAACACAATG[C/T]CTGGTACACAGTGGTAGGAAGAGCAAGTAGAATAA Y 2 1 2 1 101000 f 74 goat snp53021-scaffold796-1971021 29 27829603 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375919 Affx-122978471 AX-123246278 29 27387153 GTGTGATGCATGGTCCTTGTGGAAAAAATCCACTC[A/G]AGAACAAGGCTCTGAGGCTTCCTGGCTGCCTTCCT R 2 1 2 1 101000 f 74 goat snp53020-scaffold796-1937531 29 27863690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397530 Affx-122962042 AX-123267885 29 27433435 GCATGTGTCTGTGTGTAGTACGTATATGAAAATGC[G/T]CACGTATGCCAGTTGGTTTAAAGGAAAACCTAGAA K 2 1 2 1 101000 f 74 goat snp53019-scaffold796-1891249 29 27909951 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386778 Affx-122970110 AX-123257136 29 27462287 TCTGAACTTGTTGCAGCAAACTACTCAAGGGCAGC[A/G]ACCTGATGGTTACATGTGTTCATTCCATTTGTTTT R 2 1 2 1 101000 r 74 goat snp53018-scaffold796-1862397 29 27937357 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790435 Affx-122929977 AX-385277438 29 27492828 CTGTCTAAGGGGCAAGTCAGACCACACAAATAAAG[A/G]TTCAACTGCAAATGGCCTCAATGAAGAAGACGGCT R 2 1 2 1 101000 r 74 goat snp53017-scaffold796-1831856 29 27967983 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379998 Affx-122975610 AX-123250356 29 27522999 CATCAGAGATGCAACAATAAATAGAACAGAAAAGC[G/T]CCTGATTTCATGGAGCTCATATTCTAATAGTTCAC K 2 1 2 1 101000 f 74 goat snp53016-scaffold796-1801685 29 27998100 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443456 Affx-122927831 AX-123313793 29 27678648 CAAGAGAGAGGAGGTGTGGGTTAGTGGGCCAGGAC[C/T]GCTGGTTCCCCAGCTGGAACCGTGAGGTCCACCTT Y 2 1 2 1 101000 f 74 goat snp53013-scaffold796-1646036 29 28153060 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403701 Affx-122958042 AX-123274053 29 27719942 CCACTCAAGGAAGAAATTCCTGGAACAAACTGTGA[C/T]GGCAGGAAGAAATGAAGAGTGAAGGAAAGGACTGA Y 2 1 2 1 101000 f 74 goat snp53012-scaffold796-1604742 29 28194439 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396512 Affx-122963522 AX-123266867 29 27749974 CTGATTTCTGGGACCTTTCATACGAGGGATAGGGC[G/T]AGGGGGGCATGTGAGTTGGGAATGGGCAGTGGTGG K 2 1 2 1 101000 f 74 goat snp53011-scaffold796-1574710 29 28224599 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422410 Affx-122943376 AX-123292756 29 27844650 CTTCTCTTATCAAAGTGTTCATCCTGCTAAATTGT[A/C]ATCACTTATTTAATCTGTTTCCCCCATTTATATCC M 2 1 2 1 101000 f 74 goat snp53009-scaffold796-1480034 29 28315349 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390192 Affx-122967800 AX-123260549 29 27886352 CCACTCAGTCTAGGGCTCACCTGGAAACCCACAAA[A/G]GAGATCTGCATGGAAAGAATGGTGCCCAGGCAGTA R 2 1 2 1 101000 f 74 goat snp53008-scaffold796-1438332 29 28357594 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277831 Affx-1111836110 AX-519551328 29 27933548 ATTTGCAGTCAGACTCAGTGCAAGTCCAAAAGGCA[A/G]GACAGGAATGTACAGATGGCGCTGGACTGGAAAAG R 2 1 2 1 201000 f 74 goat Random2.2K-2324 29 27933548 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425897 Affx-122941626 AX-123296243 29 28025996 TCAAAAGCTACATTTTAAAACAATTAAATAGCTCA[C/T]GTGTGCTAATTTAGCCCTCACAATTCTTCTTGATA Y 2 1 2 1 201000 r 74 goat snp53006-scaffold796-1298688 29 28497863 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410122 Affx-122952817 AX-123280472 29 28076649 TAAAGCCAAGTCACCCGTGGCACTAGTCCTGTCGG[C/T]AAAGATTTAATAGGGCATCAGGGGTAGGTTTGGGG Y 2 1 2 1 202000 f 74 goat snp53005-scaffold796-1248035 29 28548526 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398850 Affx-122961060 AX-123269205 29 28148630 GTACATGCATGGGGGGGGACGTTGTTGGCTGGCAA[C/T]AGGGAGCATTGATCAGCACAGCAAAGGCAATCTTA Y 2 1 2 1 101000 r 74 goat snp53004-scaffold796-1176054 29 28620713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383458 Affx-122973454 AX-123253816 29 28177665 TTGACTGATGAACCAAAAAATTTTAGGACATTTCT[A/G]AGCCTCTCTGAGTGTTAGTTTCTTCGCAGATGAAC R 2 1 2 1 201000 f 74 goat snp53003-scaffold796-1147019 29 28650113 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277974 Affx-1111836111 AX-519551468 29 28241362 TTTTTTTAAAGAAATAAAATATTGGAATGTGGTAT[A/G]TCTATACGACAGAAGAGAGAGCCATAAAAAGAATG R 2 1 2 1 101000 r 74 goat Random2.2K-2325 29 28241362 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38390952 Affx-122967058 AX-123261309 29 28294665 GGGTGATAGCATGCTGAATTTTTATAAACATCTTC[C/T]GATTTTCTACCCTGGTGGTTGTACCATTTTTAATT Y 2 1 2 1 101000 f 74 goat snp53000-scaffold796-1030019 29 28766826 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415914 Affx-122948458 AX-123286263 29 28331434 CATACCGATTTTGCAGATTCAGGGAGGCCTGGCGT[A/G]CTGCCATCCATGGGGTCGCAAAAAGTTGGACACCA R 2 1 2 1 103000 f 74 goat snp52999-scaffold796-993250 29 28803764 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411215 Affx-122952356 AX-123281565 29 28396591 GTATATCTGAAAAATGCATAGGCATTCATTGTTTC[A/G]TTTATATATTCATTCAACATTTAATGATCACTTAG R 2 1 2 1 103000 f 74 goat snp52997-scaffold796-928093 29 28864590 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428683 Affx-122938636 AX-123299025 29 28434941 CACTGAACCAAGCACAGCCTTACTACTGCCCACCT[A/C]GTTTGCAGCATCCTAGCCGATTTCCCTGCTCTCAA M 2 1 2 1 201000 r 74 goat snp52996-scaffold796-889743 29 28903048 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390113 Affx-122968012 AX-123260470 29 28483313 AGTGTTGCATTGGGCTTCTCAGCCTCCAAGACCTC[C/T]TCCCACTTCCAGAATCCACATGTAACTTTGCATGT Y 2 1 2 1 101000 r 74 goat snp52995-scaffold796-841371 29 28950209 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407782 Affx-122954959 AX-123278133 29 28553314 ATTTCCCAGGGGAAGCATTTCCTCTCTAACTGGCC[A/G]TCTCTCTAGGAATGTGCCACTTGAGAAAAAAAGTC R 2 1 2 1 101000 r 74 goat snp52993-scaffold796-771370 29 29020408 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442074 Affx-122928376 AX-123312411 29 28657434 GGATGCTGGTTCCTAGTCTCATTTGACTGAGTGAC[A/G]TCCAAGGTCTCTTCTCACCCTGGGATTGACCATGA R 2 1 2 1 101000 f 74 goat snp52991-scaffold796-667250 29 29124089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409694 Affx-122953055 AX-123280045 29 28714505 GCCTTGCGGCTCCCGGTAGAAACAACGCTTCCTAC[A/G]TCAACATGAATTATTTAACGACGGAGAGTAAGTCA R 2 1 2 1 201000 r 74 goat snp52990-scaffold796-610179 29 29182191 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406267 Affx-122956093 AX-123276619 29 28760645 TACAGCCTCTTTCATTGCACAATACCCCTGGTGGC[A/G]TATTACGTGACATAGGACAGGGTGGGTTGGGGTGG R 2 1 2 1 303000 r 74 goat snp52989-scaffold796-564039 29 29228924 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273185 Affx-1111833358 AX-519546844 29 28800680 CCACCATCTTTCAGTGTAACTGGTGGTGGTGCCGG[A/G]TTTTCATTGCTGCCTGGGCTTTCTCTAGTCGTGGT R 2 1 2 1 102000 f 74 goat 29_28800680_AF-PAKI 29 28800680 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38449227 Affx-122923491 AX-123319562 29 28808847 GTGGACGGACCACTGTCAATTTAAGACAATTAAAC[A/G]TGGGATTGGAGTTCCAGTAACTTTAGTCTCATCTC R 2 1 2 1 101000 r 74 goat snp52988-scaffold796-515837 29 29276909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398879 Affx-122961036 AX-123269234 29 28847448 CTGGGCCCGGGGGGTAACAGCGAGGGATGAGAAAC[A/G]TCAGAGCCTGAACTCAAACACTGTGAAGGAAGAGC R 2 1 2 1 101000 r 74 goat snp52987-scaffold796-477236 29 29315438 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443866 Affx-122927512 AX-123314203 29 28897368 CCCTTAGGTAGACATCACTGTCTCCATTATACAGA[C/T]GAAGAAACTGAGGCTCTGGGAGGGTGAGTAACTGG Y 2 1 2 1 101000 f 74 goat snp52986-scaffold796-427316 29 29365811 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377377 Affx-122977637 AX-123247736 29 28960943 AAGGCTTTTCTGCTAAACAGAATTTAATATTATGA[C/T]GAGAGACTGTGGAGGAGCACAGAAAGCTAGATTTA Y 2 1 2 1 201000 f 74 goat snp52984-scaffold796-363741 29 29429357 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421406 Affx-122943977 AX-123291753 29 29039275 GAAGGGACCAACGGGTTTAGGCGCTTCCGTGTCCA[C/T]GACTAATCGTCTCAATTTAGGGTGCAGTTTCAGGA Y 2 1 2 1 101000 r 74 goat snp52982-scaffold796-285409 29 29506845 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386095 Affx-122971440 AX-123256453 29 29245423 GATAAAAAGAGTGCCTATTGGTTAGCCTTGAAAGA[A/C]AAGAAAAATCGCCATCATCTCCTCCACCAACGGAA M 2 1 2 1 101000 f 74 goat snp52977-scaffold796-79261 29 29711724 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412628 Affx-122951269 AX-123282977 29 29286434 GTGTCCATCTCTGCAAGGATGCTGCAGGCCTTATG[C/T]GGATGCTCATCTTTGCAAGGATGCCCTGTTTTCAC Y 2 1 2 1 201000 f 74 goat snp52976-scaffold796-38250 29 29752236 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447832 Affx-122923908 AX-123318168 29 29323765 CAGGTACTGAGCCTGGACTGGAGAAATAACAGTGG[A/G]TGATGAAGACCCGATTCCTCTCTGTCCTCCAGATG R 2 1 2 1 101000 f 74 goat snp52975-scaffold796-919 29 29788729 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416602 Affx-122947638 AX-123286950 29 29348127 TCTGCTCTGCAACTGTCTCCATCTCAAATGCAAAT[A/G]CAACTTAGGCAGATACCTCATCAGACAGCACATTA R 2 1 2 1 201000 r 74 goat snp26214-scaffold274-2165356 29 29813158 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768933 Affx-122926860 AX-385256108 29 29405554 TCCTTTCTCGTGAATGAACACCTGCAATTAGATAG[C/T]AAATGTTTTCCATAAGCTTGAAACTCAGCTGAGTT Y 2 1 2 1 101000 f 74 goat snp26213-scaffold274-2107929 29 29870615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433103 Affx-122935714 AX-123303444 29 29434259 TCCCCTTTTAAACAATTCCATTCAACTGAACAAAA[C/T]GGAGGCTATGATAGCCCCAGAGCTGCGCAAATCTT Y 2 1 2 1 101000 f 74 goat snp26212-scaffold274-2079224 29 29899207 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797062 Affx-122959544 AX-385284002 29 29491779 TTACCAGAGCACAGCACTTCTCCTTAGCACTAGAC[A/G]CTAAGTTCCTAAAGGGCAAGACACATCTTTATGGT R 2 1 2 1 101000 f 74 goat snp26211-scaffold274-2021704 29 29956709 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391311 Affx-122967328 AX-123261668 29 29536412 CTGCATCCCAGTAATTAATGCCAAGTTCTTAGAAG[A/C]AGTCTGTTCCCTTAAGGAGGCAGAATCTGTGTTTA M 2 1 2 1 101000 f 74 goat snp26210-scaffold274-1977071 29 30001618 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383619 Affx-122972551 AX-123253977 29 29594378 AAGAAAGAAAGAGGAAATTCTGAGCAGTATCCCTC[A/G]CTCAGTCCCCCAAACAGTGGCTTTCCAAATTGTAA R 2 1 2 1 201000 r 74 goat snp26209-scaffold274-1919105 29 30060317 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277976 Affx-1111836112 AX-519551470 29 29632354 CAAGATGTTAATCAAACAAAGAGGACAAAAGAGAC[A/G]ATGACGCCTTCCTTTCGCTTATGGAGATTGCTCTC R 2 1 2 1 101000 r 74 goat Random2.2K-2326 29 29632354 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38382401 Affx-122973836 AX-123252759 29 29638464 TCTGTCACCTGCAACAAAGAGTCCTGAAAATCTGC[A/G]TGTATATTCATGGGAAATAAAACCTGGGAGAGTAT R 2 1 2 1 201000 r 74 goat snp26208-scaffold274-1875019 29 30104358 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452693 Affx-122920308 AX-123323026 29 29704987 GTCAGGTTGAGACGTTTTGACACTGGAGCTATGAA[C/T]GCTGCGACAATCTATTACCACAGGAAGCATCCTGC Y 2 1 2 1 101000 f 74 goat snp26207-scaffold274-1808496 29 30171657 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439235 Affx-122931014 AX-123309572 29 29750127 GAATCACATGTTTGCATGCGTGGGGATGGGGGGAA[C/T]GGAGAATATGTAAGGGCAGCTATGAGTGGGCGATA Y 2 1 2 1 101000 r 74 goat snp26206-scaffold274-1763356 29 30216742 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430942 Affx-122936834 AX-123301283 29 29798547 TATGCAGTATGTTTTATTAAGATGTGTTCATTTTT[A/G]CATGTTATTTAAGAAATTCTCCTCTACTTCCAAGG R 2 1 2 1 101000 r 74 goat snp26205-scaffold274-1714936 29 30265378 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389530 Affx-122968284 AX-123259888 29 29846346 CAGTCACACGTTTCAGGTATTTCTAGAATCTTTAC[A/G]TTTTTTAGAGGGCAGAACTTCTCTTCTTCACCCAG R 2 1 2 1 101000 r 74 goat snp26204-scaffold274-1667137 29 30312736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447275 Affx-122924937 AX-123317611 29 29897083 GGTTGAATCTTGATTCAAAAGTTTTCCCCAAAGAT[A/G]CTCAGACCTCAAAATCTAGAGAGCCGACCCTCTCC R 2 1 2 1 101000 r 74 goat snp26203-scaffold274-1616400 29 30363747 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422996 Affx-122942987 AX-123293342 29 29955698 TTAAAACCGGTTTCACAAAATCAACATTTATTGTC[C/T]TACTTGATTGGAATATCTAAGGATTGTTCAAGCTT Y 2 1 2 1 101000 r 74 goat snp26201-scaffold274-1557785 29 30423291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382857 Affx-122973529 AX-123253215 29 29984516 GCAACAGATCAAAACCAAAGGACACAGCATGTACA[C/T]GGTCACTCCAGAATTTTAAACCAAGGTAATCTGAC Y 2 1 2 1 101000 r 74 goat snp26200-scaffold274-1528967 29 30452377 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778682 Affx-122949166 AX-385265793 29 30041334 ATTTAAGCAGATAAATCAGCTGTTGAGTCTAAAAA[C/T]AGTCCATAGAATCATGAGGAGGATGAACAGATTCT Y 2 1 2 1 101000 r 74 goat snp26199-scaffold274-1472149 29 30509113 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429408 Affx-122938525 AX-123299750 29 30095008 TCTCCTGAGACGCCAGGCAGCAGGGCTCATTTGAG[A/G]GCTGGAAGGATATTCTAGTGTACCCTAGAAAGTAT R 2 1 2 1 101000 r 74 goat snp26198-scaffold274-1418475 29 30563880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406398 Affx-122955228 AX-123276750 29 30141598 ATCATCTCAGATAAACTGGAAACAATTTAGCTTAG[C/T]GTGTTGAGCCACTGGATACTTTCCAGGCCCCATTT Y 2 1 2 1 101000 r 74 goat snp26197-scaffold274-1371885 29 30611582 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772463 Affx-122976155 AX-385259614 29 30184031 CAAGGTCTATGGGTGAAGGCAAATGCACATTGTTA[C/T]GCATCCCTCACTACAATATCATACAGCGTGGCTTC Y 2 1 2 1 101000 r 74 goat snp26196-scaffold274-1329452 29 30646769 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777522 Affx-122951772 AX-385264641 29 30220585 TAATGTTTTGTTTTTTGTTAAAACTGCTTGTCATA[C/T]TTACTTGATTCTTTCCTGTTGGTTACAAGTACCAG Y 2 1 2 1 101000 r 74 goat snp26195-scaffold274-1292898 29 30683237 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421924 Affx-122943837 AX-123292271 29 30258637 TGAAGAAATAATCGAAAGGAATCGCTAGAAATGAA[A/G]AACACCATAACAGAAAGAATAATGTCTTTTATGGA R 2 1 2 1 101000 f 74 goat snp26194-scaffold274-1254846 29 30721197 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397328 Affx-122963300 AX-123267683 29 30351551 TGTTTCCTGGAATAACACAAAGGGATTTTGATTAG[A/C]TGGGAAGGCAGTGCAAGTAGGGAGCATGTTCATTT M 2 1 2 1 201000 f 74 goat snp26192-scaffold274-1161932 29 30815176 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382418 Affx-122974248 AX-123252776 29 30403409 AAGTTTCAAAGACGTTTTCTTTTCATCCCCTCCTA[C/T]CATGCTAAGGGTCTACATTTTCTGCTCCAATTTGA Y 2 1 2 1 101000 r 74 goat snp26191-scaffold274-1110074 29 30867778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454279 Affx-122919276 AX-123324612 29 30432265 ATGGACTCCCTCCGACCCACACGTATTTGAGACAC[A/G]ACAACACACACATCAACATCCTGTCATCCCTCCCT R 2 1 2 1 201000 f 74 goat snp26190-scaffold274-1081218 29 30896627 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418476 Affx-122946454 AX-123288824 29 30501255 GAGACAGAGTAAGGCTGAATTTTCAGCCAGATCAA[C/T]GGCCAGAGTGACCAGGGAGATGATAGAATGCTTGT Y 2 1 2 1 101000 f 74 goat snp26189-scaffold274-1012228 29 30971703 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410312 Affx-122952486 AX-123280662 29 30560905 CAAGGAATCACCATGCCATGTGGTGGCCAAATGTC[A/G]TGAGACCTAAAGCTGCTTGTGGTAGTCTGCTGTTT R 2 1 2 1 101000 r 74 goat snp26188-scaffold274-952578 29 31030945 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396935 Affx-122963190 AX-123267290 29 30600715 ACAAAGCTTTGTACGTCGGGCAGGTTAATAGTACA[C/T]GGTGATGTGTGTACGTGCGTGTATTTAGGCACGCA Y 2 1 2 1 201000 f 74 goat snp26187-scaffold274-912768 29 31071079 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779457 Affx-122944783 AX-385266560 29 30630240 ATTCACAAACACGCACACTAATTTGAGCTACTGTC[A/G]TCTCTCACCTGGACAACAGGCAATAATAACTTTTT R 2 1 2 1 101000 f 74 goat snp26186-scaffold274-883243 29 31100849 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409427 Affx-122954119 AX-123279778 29 30663384 AGTGATGGGTGAGAGTAGAACCAAGGCCAGACTCC[A/G]GTCCTTGCTTCTTTGCCACCAGGCATATCACTTTC R 2 1 2 1 201000 r 74 goat snp26185-scaffold274-850099 29 31133298 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773785 Affx-122948924 AX-385260925 29 30730431 TAGGGTTTTAGGCCATCCAGAGTAAGTTAAAAGGA[C/T]AAGAGTCAGAGTTTGAAGAAATTCAAGTTCTGTGT Y 2 1 2 1 101000 r 74 goat snp26183-scaffold274-783052 29 31199781 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393060 Affx-122965617 AX-123263417 29 30770191 CTCAAAGCCTCAGGTGGTGCTACGGCTGTTACTGG[C/T]CTGAAGACTACACTTTGGGAACCACCAAGTTAATA Y 2 1 2 1 201000 r 74 goat snp26182-scaffold274-743292 29 31239001 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452566 Affx-122920518 AX-123322899 29 30818704 ATGTTGCTTTCCATAAATCTCTCAATGCCTTTATG[A/G]CTGTGGCTGACTGTGGTTATTGAACTTTTGGTCCT R 2 1 2 1 101000 r 74 goat snp26181-scaffold274-694779 29 31287681 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 464090713 Affx-1110307193 AX-515566863 29 30822129 AAGCCTGAACTCTCCAGGGAAATTATGTCAAGTCA[G/T]AGCCAAGGAAGTTGGATTATAAGAAAATCACTAGA K 2 1 2 1 101000 r 74 goat Random2.2K-2327 29 30822129 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380493 Affx-122975708 AX-123250851 29 30882159 AACTACCTGATATAATAGCCATAGCTATAATTCAC[A/G]GATTGTTTAGTGTAAGACAGGCACTGGACTAGTCC R 2 1 2 1 101000 r 74 goat snp26180-scaffold274-631324 29 31350789 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418658 Affx-122946324 AX-123289006 29 30915980 GCCTCAGACCATTAGAAATCCAGCCTGATGGTTCA[G/T]CATCATAAAAAATTTTCCAACCTTTTTCTTTTGCT K 2 1 2 1 101000 f 74 goat snp26179-scaffold274-597503 29 31383167 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476389 Affx-1251763900 AX-586011798 29 30944817 TCTAAAATCTGTGGAGCCAGAGCAGAGGTGTCTTA[-/TGCTCCTTCCAATTCTTTTTTTTTTTTTTTTATTTTTTTTTGCAATTCAACATGGCGGTGGCGGCGGCTGCGGGCAGAGA]GCTCCTTCCAATTCTATGTAAACTTGGTTCATGGA - 4 1 4 1 20000 f 74 goat SV_213 29 30944817 - deletion junction SV-TF-chip 539476645 Affx-1251763900 AX-586012026 29 30944817 TCTAAAATCTGTGGAGCCAGAGCAGAGGTGTCTTA[-/TGCTCCTTCCAATTCTTTTTTTTTTTTTTTTATTTTTTTTTGCAATTCAACATGGCGGTGGCGGCGGCTGCGGGCAGAGA]GCTCCTTCCAATTCTATGTAAACTTGGTTCATGGA - 4 1 4 1 20000 r 74 goat SV_213 29 30944817 - deletion junction SV-TF-chip 562165183 Affx-1251763900 AX-606940595 29 30944817 TCTAAAATCTGTGGAGCCAGAGCAGAGGTGTCTTA[-/TGCTCCTTCCAATTCTTTTTTTTTTTTTTTTATTTTTTTTTGCAATTCAACATGGCGGTGGCGGCGGCTGCGGGCAGAGA]GCTCCTTCCAATTCTATGTAAACTTGGTTCATGGA - 8 1 4 1 20100 f 74 goat SV_213 29 30944817 - deletion junction SV-TF-chip 562165588 Affx-1251763900 AX-606940999 29 30944817 TCTAAAATCTGTGGAGCCAGAGCAGAGGTGTCTTA[-/TGCTCCTTCCAATTCTTTTTTTTTTTTTTTTATTTTTTTTTGCAATTCAACATGGCGGTGGCGGCGGCTGCGGGCAGAGA]GCTCCTTCCAATTCTATGTAAACTTGGTTCATGGA - 8 1 4 1 20100 r 74 goat SV_213 29 30944817 - deletion junction SV-TF-chip 562165721 Affx-1251763900 AX-606941130 29 30944817 TCTAAAATCTGTGGAGCCAGAGCAGAGGTGTCTTA[-/TGCTCCTTCCAATTCTTTTTTTTTTTTTTTTATTTTTTTTTGCAATTCAACATGGCGGTGGCGGCGGCTGCGGGCAGAGA]GCTCCTTCCAATTCTATGTAAACTTGGTTCATGGA - 8 1 4 1 20100 f 74 goat SV_213 29 30944817 - deletion junction SV-TF-chip 562165993 Affx-1251763900 AX-606941402 29 30944817 TCTAAAATCTGTGGAGCCAGAGCAGAGGTGTCTTA[-/TGCTCCTTCCAATTCTTTTTTTTTTTTTTTTATTTTTTTTTGCAATTCAACATGGCGGTGGCGGCGGCTGCGGGCAGAGA]GCTCCTTCCAATTCTATGTAAACTTGGTTCATGGA - 8 1 4 1 20100 f 74 goat SV_213 29 30944817 - deletion junction SV-TF-chip 562166486 Affx-1251763900 AX-606941894 29 30944817 TCTAAAATCTGTGGAGCCAGAGCAGAGGTGTCTTA[-/TGCTCCTTCCAATTCTTTTTTTTTTTTTTTTATTTTTTTTTGCAATTCAACATGGCGGTGGCGGCGGCTGCGGGCAGAGA]GCTCCTTCCAATTCTATGTAAACTTGGTTCATGGA - 8 1 4 1 20100 r 74 goat SV_213 29 30944817 - deletion junction SV-TF-chip 38404839 Affx-122956632 AX-123275191 29 30948901 AGAGGAAATCCTGTTCCAAAACCCGGAGCCCCCAG[C/T]GAAAGGTTGCCAGCAGTTCCTCCCTCCCACCTGCG Y 2 1 2 1 201000 r 74 goat snp26178-scaffold274-564582 29 31416113 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405415 Affx-122956280 AX-123275767 29 30995114 TTAGTGGGTTTATCAAAATTCTGTTCATATCTCTG[G/T]GTATATTTCACATCAGATGAAATTCGTATCAAATT K 2 1 2 1 101000 r 74 goat snp26177-scaffold274-518369 29 31462125 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376401 Affx-122978092 AX-123246760 29 31075396 ACATGACCTTGTAATTGCTCATTTACTGAGCTTAC[C/T]TCCCCCTTCGATTGTGAGCTCCTTGAGAACAAGAA Y 2 1 2 1 201000 f 74 goat snp26175-scaffold274-438087 29 31542664 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439495 Affx-122930147 AX-123309832 29 31108817 TTGCCCTTCCCTAAAAGGGGCATGCTTGACAGTGC[A/G]CCTGGGGATGTTCTTTCATTCACATCCATCGGCTC R 2 1 2 1 101000 f 74 goat snp26174-scaffold274-404666 29 31576240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412609 Affx-122951282 AX-123282958 29 31141319 GTGTTCACAGAGCCCCTTCCACAGGGAAGCTGAGG[A/G]ACAGCCTGCCCCACAGGGGCCTAAGGGTGTGGGAC R 2 1 2 1 103000 f 74 goat snp26173-scaffold274-372164 29 31608715 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442539 Affx-122928533 AX-123312876 29 31172902 TGCCAGCAGTGCATCAGGTTTCTGATATGAGAGAA[A/G]TTTGCTTTTCTAAGATTTTTGTCTATCTTTCATAT R 2 1 2 1 101000 f 74 goat snp26172-scaffold274-340581 29 31640291 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419530 Affx-122945433 AX-123289878 29 31212736 GGAAAAAAGTCATAGTTTTGAGATCGTGTATTACC[A/G]AGACCAGCCTCCCAACTTTTATACCTAAAAATTTA R 2 1 2 1 101000 f 74 goat snp26171-scaffold274-300747 29 31680349 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418721 Affx-122946279 AX-123289069 29 31251389 TATTAATAGAAACTGCTGTTGTTCTAAATATGGTA[A/G]TTTAAAATTTCCTTTTATAAGTGAATCTGATCACC R 2 1 2 1 103000 f 74 goat snp26170-scaffold274-262094 29 31719033 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406665 Affx-122955795 AX-123277017 29 31301414 CCTTGTAGCTTCAGTTTCACAGCTTAGAACACCAA[G/T]CTGACTACTTCAGGTATGTCCCAGAGATGTTCTTC K 2 1 2 1 101000 f 74 goat snp26169-scaffold274-212069 29 31769093 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273187 Affx-1111833359 AX-519546846 29 31311004 GAGACAGACACACACTGAGACATACAGACACACAC[A/G]CACACAAACACACACACACACACAGAGACACAGAC R 2 1 2 1 103000 f 74 goat 29_31311004_AF-PAKI 29 31311004 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38432120 Affx-122936449 AX-123302461 29 31341186 CCAGTAGCCCTCTGTTTTCTGGAATTTCCACCTTC[A/G]TAGGTACTATCCCTTCGGTGACCCCCACGCTCTGT R 2 1 2 1 201000 r 74 goat snp26168-scaffold274-172297 29 31809586 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447785 Affx-122923945 AX-123318121 29 31373198 TTTATCATCACAGTTGCCTCATGAAGTTGTTACTC[A/G]TACTTTTTTTTAAATTATGATAAAATTTATGTAAC R 2 1 2 1 101000 f 74 goat snp26167-scaffold274-140285 29 31841655 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399691 Affx-122960490 AX-123270046 29 31404893 TGATTTTTATTCTGCTGGCAAGAACCCCAGGGAGG[C/T]GGTGGATGACAGGTGTCTCTAACCAAACCCCCAAC Y 2 1 2 1 201000 r 74 goat snp26166-scaffold274-108590 29 31873447 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442077 Affx-122928374 AX-123312414 29 31434392 TATCTGGCCAACAAGGAAAAGAGCCTTAACAATGG[A/C]AAACCATGGCAATCCTCGTAGAGCAAGCTCCAGAG M 2 1 2 1 101000 f 74 goat snp26165-scaffold274-79091 29 31903141 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430971 Affx-122936814 AX-123301312 29 31474993 TGTGTTTCTCGATAGTATTACTCCATTCAGAGCCT[C/T]AAGCCTGGTAAGTCCATCTTGAAGGAATAAGATTC Y 2 1 2 1 201000 f 74 goat snp26164-scaffold274-38490 29 31943691 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387052 Affx-122969906 AX-123257410 29 31516560 GATTGCAAACTTCTCCAGGACAGAATTAAAAAGTG[C/T]ATCGTTTTATGGACACAGGTTGGGGCGAGGGAAGG Y 2 1 2 1 201000 r 74 goat snp21645-scaffold2119-513161 29 31985352 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277836 Affx-1111836113 AX-519551333 29 31525525 ACGTCTCCAAAAACAGCCAATGCCAAACCTTCAGC[A/G]TTTGGGAGAATCTCAACTGCTTCTTTTGTTCTTTC R 2 1 2 1 101000 f 74 goat Random2.2K-2328 29 31525525 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320802338 Affx-122943675 AX-385289242 29 31550240 AAGTAACTAGATAGTATGAAAACCTCCAGGTTCCT[A/G]TCTACGTGCACAGTGGAGGGAACCTCCAGGTTCTA R 2 1 2 1 102000 r 74 goat snp21644-scaffold2119-479481 29 32019027 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437268 Affx-122932000 AX-123307606 29 31620669 GTGAAAGAAATTAGACAATTACTATTTTGGGCTGG[G/T]TGTCAGGATGCCTGGGGGTCACACCAGGCTCTGGA K 2 1 2 1 101000 f 74 goat snp21643-scaffold2119-409052 29 32086427 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277838 Affx-1111836114 AX-519551335 29 31632259 CTAATCTCAGAAGCCATTAGAAGGTGCAAAGAAGT[A/G]ACGAGGTGAGAACACCATGGAGTGGGCATGCCTGC R 2 1 2 1 101000 f 74 goat Random2.2K-2329 29 31632259 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38425452 Affx-122941514 AX-123295798 29 31660871 TGGTGGTTGAGGCTGGGGGAACAAGGCCATCCAAG[A/G]AGTCTTCCCTCCCTTCTGACTCTCCCCATCTTGCC R 2 1 2 1 101000 f 74 goat snp21642-scaffold2119-368850 29 32126504 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387107 Affx-122970670 AX-123257465 29 31697087 AGGGCCCTTCAAATCCTCACCCTGAATTCTACCAG[C/T]GAAGAACACATGTCGAAACCCTGGAACTGCTTTTC Y 2 1 2 1 101000 r 74 goat snp21641-scaffold2119-332634 29 32162704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391553 Affx-122966632 AX-123261910 29 31743731 TGAGGGACAGGGAGGCCTGCGGGCTGCAGTCCACA[C/T]GGTTGCAAAAAGCTGGACACTATGGACAACTGAGC Y 2 1 2 1 303000 f 74 goat snp21640-scaffold2119-285990 29 32210179 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388206 Affx-122969418 AX-123258564 29 31815497 AACTGACAGTGGGCAAAGCATGAGCCTGGATCCAA[A/G]ACAGTTTCCTGGTGGTGATGAAGTCTTTGTCCACC R 2 1 2 1 101000 r 74 goat snp21639-scaffold2119-214224 29 32282177 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431193 Affx-122937172 AX-123301534 29 31853805 TGGAAGAAGCCAATCCCATGTCAGGTTTCATGTGG[G/T]CATGTCACAGTTTGTCCTTGGTGGTGGTGGTGTCA K 2 1 2 1 101000 f 74 goat snp21638-scaffold2119-175916 29 32320556 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443850 Affx-122927525 AX-123314187 29 31893100 TTCTTCACCTGCTCACTGCCTCCCTCTGTGCTGAG[A/G]AGCCCATAGGGGATCTTGGGGATCTTGGCTCCAGG R 2 1 2 1 201000 f 74 goat snp21637-scaffold2119-136621 29 32358927 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411446 Affx-122951818 AX-123281796 29 31922214 TCCAAAGTACAGATTTTCCCAGGGAAGCCAAGGAA[A/G]GGGTGATAGGGAACCCGGGCATTCAGAGGGCACCA R 2 1 2 1 101000 f 74 goat snp21636-scaffold2119-107507 29 32387669 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406052 Affx-122955471 AX-123276404 29 31983391 CTGGGACTCAGCACACTTTCCCCCCACCCGGTGCC[A/G]CAAGCAGGGATGGATGTCTCAAAAGATTTTACTTG R 2 1 2 1 101000 r 74 goat snp21635-scaffold2119-46330 29 32448856 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794497 Affx-122922885 AX-385281460 29 32020634 TCCTGTCCCACGTCTCCAGAGCTTTAACCTACTTA[C/T]GCTATGCAGCCAAGGTCTAAAAAATACCAGAGGAG Y 2 1 2 1 101000 f 74 goat snp21634-scaffold2119-9087 29 32485176 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419561 Affx-122945408 AX-123289909 29 32053176 CAGAATCATTATTTGCATAAAATAACAATCTTTAT[C/T]ATTTCCTGGTAGATTGTTTTGTTGATCATTCTGCA Y 2 1 2 1 101000 r 74 goat snp53032-scaffold799-23356 29 32517753 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412010 Affx-122951749 AX-123282360 29 32104006 TTGCTTTATCATTTGTCTTTTTGAGTCCTATGACA[C/T]TGTCAGAGAATTCTTGAAAAGTGTTTCCCCTTTGG Y 2 1 2 1 101000 r 74 goat snp53033-scaffold799-74186 29 32568319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450651 Affx-122921976 AX-123320985 29 32140683 CCGGGCATTTCATGTGTGCGGCATCACACAGCATA[C/T]GGCTTTTGTGACTGACTTCCTCCACTCAGCATACT Y 2 1 2 1 201000 f 74 goat snp53034-scaffold799-110863 29 32604509 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400643 Affx-122960364 AX-123270998 29 32179674 CTTGCTTTTATAAACCCATATATTCTGTGCCCAAA[C/T]GTAAGCCTTCTTCCAAAAAACAAATCTGGACTTAG Y 2 1 2 1 101000 f 74 goat snp53035-scaffold799-149854 29 32643667 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272253 Affx-1111833414 AX-166900458 29 32194752 TAGGTTGGTCATAACTTTCCTTCCAAGGAGTAAGC[A/G]TCTTTTAATTTCATGGCTGCAACCACCATCTGCAG R 2 1 2 1 303000 f 74 goat 4_13373599_AF-PAKI 29 32194752 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38418703 Affx-122946292 AX-123289051 29 32316088 TGGGGCTCCCCATGTGCTACACATTCTCATCCATT[G/T]CTGGTGGCCCCTCCATCCCCTCCCCTTCCTAGCGC K 2 1 2 1 101000 f 74 goat snp53037-scaffold799-286268 29 32779368 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443764 Affx-122927112 AX-123314101 29 32344985 AGCTTACTAGTAGTATTTTTGCATGGTATCTGACA[A/G]ACATTGCTATTTCCGTCAAACATTTAAAACCCGGC R 2 1 2 1 101000 r 74 goat snp53038-scaffold799-315165 29 32808360 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381005 Affx-122974664 AX-123251363 29 32376803 CAAGGCCCTCCTGCCAGCCACAGACACACGTCAGA[G/T]CACAAACTCTCTTGCCTGAAAAATATCCTTCCCAG K 2 1 2 1 201000 f 74 goat snp53039-scaffold799-346983 29 32840649 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277983 Affx-1111836115 AX-192376098 29 32397350 TCCCACCCCCACTGCCTCCCAGTTTCTGTGCCACC[A/G]GAGGCCCTGGTCTGAGAACTCCGGGAGAGCAGATT R 2 1 2 1 103000 r 74 goat Random2.2K-2330 29 32397350 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275154 Affx-1111834625 AX-519548733 29 32445234 CAGTCAGTGCCCAATCGGGCAGTCTGGCAAAGCCC[A/G]GGACACCTGCAGTGAGTGTCTCCACAGTTTAAGAT R 2 1 2 1 202000 r 74 goat GoatD01.043841 29 32445234 C T 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38383109 Affx-122973272 AX-123253467 29 32472660 TAGTTCTTCTGATTTTCTTCTTACAATATTCTACT[A/G]CCTAAATTAAGGCTTCCTTATTTCTCTGGCTAGAC R 2 1 2 1 101000 r 74 goat snp53041-scaffold799-442840 29 32936725 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376571 Affx-122979080 AX-123246930 29 32563156 AGGGCCTGAAATTTTCTAGGCATCCCTGAACCTTA[A/G]GCTGATAGCTCAGCTAGCCTGTGTTGAGTACTATG R 2 1 2 1 102000 f 74 goat snp53043-scaffold799-533336 29 33027342 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277841 Affx-1111836116 AX-519551339 29 32629349 CAGGGCTTTCAATTCTGACCCAACATCAACCAATA[A/G]GGTAACTTTATATAGAAAAATTTTGCCCCATCTAA R 2 1 2 1 101000 f 74 goat Random2.2K-2331 29 32629349 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38439888 Affx-122930035 AX-123310225 29 32636891 CTGGGGCCTCTTTCATGCCCCGTGGAGTTCAGAGA[A/G]GGTTCACACAGCAGCAGGAAATGGGAACTGGAGAC R 2 1 2 1 201000 f 74 goat snp53045-scaffold799-607071 29 33100680 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392791 Affx-122965978 AX-123263148 29 32690620 ACAAGACAGGACAGGGGCAGTGGTGCACAGCACCC[A/G]TTGATTCTGGGGCCAGCCTTTTGTCTTTAAGCCCC R 2 1 2 1 101000 r 74 goat snp53046-scaffold799-660800 29 33154436 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775661 Affx-122967673 AX-385262792 29 32731389 ACTATGGAAGGAGTTGCTCCTTATTTGTATATTTA[C/T]GTTTACCACTGGGCTGAACACGGTAGTCTGATAAT Y 2 1 2 1 201000 f 74 goat snp53047-scaffold799-701569 29 33195108 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410710 Affx-122952724 AX-123281060 29 32805463 AAAAAGCCATGACGTAGGTGTTGGCTACAGACACC[A/G]TCATGGATACTGAGGGTCCAAAATGATACATCTGG R 2 1 2 1 101000 r 74 goat snp53048-scaffold799-775643 29 33267088 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439448 Affx-122930183 AX-123309785 29 32838800 GAACCTTGAAGTTGCTGGGCCTGCAGCTGTGGTTC[C/T]TCTGAGCTGGCATCCCAGTTGAAGCCTTTCCATCA Y 2 1 2 1 101000 r 74 goat snp53049-scaffold799-808980 29 33300410 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376001 Affx-122978416 AX-123246360 29 32887870 TCTTTGGAGAATAATTTCACTAAAAGGGAGGGTGG[C/T]GACCAGACAAATAGGATCAGAACTTCTTGGACTTT Y 2 1 2 1 201000 r 74 goat snp53050-scaffold799-858050 29 33349014 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434552 Affx-122934135 AX-123304893 29 32964574 AAGTGGTGTGCCTTTAAACTCCCATCCAAAACTGT[C/T]GAGTGTGAGACCATATTCAGATCAGGAACCTCTTC Y 2 1 2 1 101000 f 74 goat snp53051-scaffold799-934754 29 33425603 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385492 Affx-122971274 AX-123255850 29 33062055 GAGGCTCTGCCTGACTCCGGGATCCCATGATCCTT[C/T]GTATTATATGTGGGAAGGTGTGTGCAGGGAAATCC Y 2 1 2 1 201000 f 74 goat snp53053-scaffold799-1032235 29 33523072 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378378 Affx-122976811 AX-123248737 29 33136359 ACACTGGTATAACGTTTGCTGCATATATTAACCTA[C/T]GAGTCCAAGCTCTCTCTGGAATCCTAAAGGGGAAG Y 2 1 2 1 201000 f 74 goat snp53055-scaffold799-1106539 29 33597008 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387676 Affx-122969827 AX-123258034 29 33280752 ACAAAGAAGAGGTGCTGTGTCTGGAAGGTTGAAAA[C/T]GAAACATCTGGTGTTACAGGCTTCCCTAAAGTGGA Y 2 1 2 1 201000 f 74 goat snp53059-scaffold799-1250932 29 33739347 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399545 Affx-122961139 AX-123269900 29 33309731 GTCTCTGAAAAACATGCAAAAAGGACAATTTTCCA[C/T]GGAGAATAGGTGGAGTTGTGGTCATCAAGGGCACC Y 2 1 2 1 101000 f 74 goat snp53060-scaffold799-1279911 29 33768354 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421967 Affx-122943805 AX-123292314 29 33345323 CCAGCGCTGCCTTGTGTGTCTTTCCCCTTGCTGTT[A/G]CATGCTTCTCATCAGCACAGTAAATGCAGTTTCTC R 2 1 2 1 101000 r 74 goat snp53061-scaffold799-1315503 29 33803898 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277987 Affx-1111836117 AX-519551480 29 33361391 TCATGGCCCCGATCTCTGATCTCTGTCCACACTGC[A/G]TCTGGAGCTCACTTTTCATCCAGCTTTCTATGGAT R 2 1 2 1 101000 r 74 goat Random2.2K-2332 29 33361391 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38385779 Affx-122971054 AX-123256137 29 33383936 GAGCCACGCAGCAGCCTGGCCTGCACACAGATGCT[C/T]GTGGAGATGGAGCCAGATTCCGGAGGCAAGGTAAC Y 2 1 2 1 101000 r 74 goat snp53062-scaffold799-1354116 29 33842390 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434859 Affx-122934366 AX-123305200 29 33416307 AAGGAATAACTCTAGGAGTAAAGCGCAGCCTTGTG[C/T]ATACGTTAAATATTTTGTAGAGGACGGAAAGTGAA Y 2 1 2 1 101000 f 74 goat snp53063-scaffold799-1386487 29 33874555 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392725 Affx-122966028 AX-123263082 29 33477568 AGTTAGAAGTGCCCATATTATTCCCAATTAATAAA[C/T]GAAGAAACAGGCTGCAAAAGGTTAATCACACAAAC Y 2 1 2 1 201000 f 74 goat snp53064-scaffold799-1447748 29 33935069 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394932 Affx-122964303 AX-123265287 29 33555320 AACAAGGCTTATTTGGAGGCTGCAGGGCAACACAA[A/G]ATCTAGGAGGAATTGGAGCCACTTTATTCAGCCTC R 2 1 2 1 101000 r 74 goat snp53066-scaffold799-1525500 29 34011863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445617 Affx-122925103 AX-123315954 29 33587986 CGTTCCGCGGTGCATCCGTGACTCCACAGAAACTC[A/G]TTCTTCCCAGTTTCCTGTTAATTTCCCTGCTCCGT R 2 1 2 1 101000 r 74 goat snp53067-scaffold799-1558166 29 34043200 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392581 Affx-122966067 AX-123262938 29 33685263 GGCTTCTGAAGGAACTCGACCTTTGTACTGCATCC[A/G]CCTCCTGGCAACTTCAGAACTAGGTCCACAAGCAG R 2 1 2 1 101000 f 74 goat snp53069-scaffold799-1655443 29 34140540 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390462 Affx-122967610 AX-123260819 29 33732009 CGGATCCAGGAGAAAGAACGCAGAGGAAGAGGAAA[A/G]GCATCCTCTCGGGTGCTGAGGGCACAGTGCACCAC R 2 1 2 1 101000 f 74 goat snp53070-scaffold799-1702189 29 34187980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382382 Affx-122973850 AX-123252740 29 33793181 GCCATTTTCTCTCTGGCACACCACTCCTGCAGGAA[C/T]ACCAATTAGAAAGATCTTGTCTGGTGAAGGGCTTT Y 2 1 2 1 101000 r 74 goat snp53072-scaffold799-1763361 29 34249628 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416856 Affx-122948096 AX-123287204 29 33834618 CTCCTTCGAGCCCCTGGCACTTTATGAGGACTCCC[A/G]TATTCTCCTGTGCTAGACCCAGGGATCTCTTATCT R 2 1 2 1 101000 r 74 goat snp53073-scaffold799-1804798 29 34291090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468272166 Affx-1111833361 AX-185156931 29 33843394 ATGGACTGGTTGGATCTCCTTGCAGTCCAAGGGAC[A/G]CTCAAGAGTCTTCTTCAACATGACAATTTGAAAGT R 2 1 2 1 103000 f 74 goat 29_33843394_AF-PAKI 29 33843394 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320788591 Affx-122951280 AX-385275608 29 33886230 AATGTCTCTTTCTCAGATTCATTTATAACTCACTC[C/T]TCAGCGGATGTGCTCACAATGCCTTCTGAGGATTC Y 2 1 2 1 101000 r 74 goat snp53074-scaffold799-1856410 29 34342804 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784713 Affx-122952788 AX-385271761 29 33919730 GCCCAACTCTGTGAATTACATGGAACACTTGGAAG[C/T]ACCCTCTCCATCATGATATAGGATGCTACTCAGGA Y 2 1 2 1 101000 r 74 goat snp53075-scaffold799-1889910 29 34376297 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407948 Affx-122954357 AX-123278299 29 33948262 TTGAATGCATGCAACTTCTGCCTAGCAGGTTGTTC[A/G]CCTCAGCCCCAGGCATCTCAAACACAGTGTGTCCG R 2 1 2 1 101000 f 74 goat snp53076-scaffold799-1918442 29 34405394 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407296 Affx-122955323 AX-123277647 29 34018276 TAGTGACAAAAAAAAGGATGCCACCCCAGGCCTGC[G/T]GTCACCATTTGCCTTGTTCCCGTTAGTGAAACTGG K 2 1 2 1 101000 r 74 goat snp53078-scaffold799-1988456 29 34475294 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398637 Affx-122961460 AX-123268992 29 34075935 TATAAAGCCGGTTTACATTACAAATGGTGTGGCAG[C/T]GATTACCTCGATGCTGACAAGCACGGTAACATCCT Y 2 1 2 1 101000 r 74 goat snp53079-scaffold799-2046115 29 34532506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429107 Affx-122938258 AX-123299449 29 34117889 GGAACCAACTCTGAATTTTGCTGTGATGGAATCTT[C/T]AAGCTGGAGAGCTCCATCCTGCCCAAAAGCCTGTG Y 2 1 2 1 101000 r 74 goat snp53080-scaffold799-2088069 29 34574373 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395934 Affx-122963586 AX-123266289 29 34174211 AATCCTGGAGACCACGCAGACTCTGCTGGGACAGT[C/T]GTGTGAAGGCCTGTGCCTTTAAGCTTTGCTTACTA Y 2 1 2 1 201000 r 74 goat snp53081-scaffold799-2144391 29 34630565 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772999 Affx-122937753 AX-385260143 29 34202838 GTAGATGGTAGGCTGACAATGGGACCTGACGTCAC[A/G]AGGAACTCCTGCTCATGCGGTAATCAGTCTGAACG R 2 1 2 1 202000 f 74 goat snp53082-scaffold799-2173018 29 34659062 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386458 Affx-122970781 AX-123256816 29 34249099 GTGTAAGGAGCCCGTGGCCCTGATCTCAGAAGCAG[A/C]TATCTGGTCGTCTCGGATGGCCCACCCGATGTCTG M 2 1 2 1 101000 r 74 goat snp53083-scaffold799-2219279 29 34703974 A C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320790190 Affx-122923499 AX-385277194 29 34307733 ATTGTAAACTAGAGAAGCATGGGATTAAGAATTTA[C/T]GTGGATGGCTCTTCACAGCTCCATGCATATAAATA Y 2 1 2 1 101000 r 74 goat snp53084-scaffold799-2277913 29 34762659 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452781 Affx-122920244 AX-123323114 29 34377508 GTTGGTTCAAACAAAGTTGAACAGGTTTCTTTCCT[A/G]CTGAAGGGATTCTCAGAGCTTTCAATATGCTAACG R 2 1 2 1 101000 r 74 goat snp53086-scaffold799-2347688 29 34832728 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377111 Affx-122978253 AX-123247470 29 34455855 TAGCCACTTTGAATAGAAGGGGTTCCAAGCAATGA[G/T]CAATGTATGATGTACTTTGCAGTGGTAGCAGTAGT K 2 1 2 1 101000 f 74 goat snp53088-scaffold799-2426035 29 34911112 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387073 Affx-122969888 AX-123257431 29 34520664 GGCTGTGAACGTCATTCTTTTATATGAACGAGTAG[C/T]ATCCCACTGTGTGTGTGCCGTATTTTCTTTATCCA Y 2 1 2 1 101000 f 74 goat snp53090-scaffold799-2490844 29 34976628 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381379 Affx-122974390 AX-123251737 29 34566282 GTGTACCCGAAACCCAGTGAAGTTGGGAATTAGCC[A/G]CCTTCGCCAACCCAGAACCCAGCGCCCACCCAGCT R 2 1 2 1 101000 f 74 goat snp53091-scaffold799-2536462 29 35021001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782408 Affx-122927513 AX-385269484 29 34628183 AACAGGAGCCACACCCTAGAACTAAAGACAAAACT[A/G]AATTGGATCCACCCTAATAAAGAAAAGAAAAAATA R 2 1 2 1 101000 f 74 goat snp53092-scaffold799-2598363 29 35082775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410776 Affx-122952676 AX-123281126 29 34678577 CACTGAATCTTGGATGTAACCAAGAACTTTTGTTC[A/G]TCTCCATTCTGATTGTGTGAATTGCATTATTAACT R 2 1 2 1 101000 f 74 goat snp53093-scaffold799-2648757 29 35132985 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468275110 Affx-1111834603 AX-519548689 29 34753183 TGGTGCCTATGTGCTCACTGCAGGTCTGCCCCAGG[A/G]GATATGTGTTAAAGCCAATGAGCACAGCCCATGAC R 2 1 2 1 201000 r 74 goat GoatD01.042840 29 34753183 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38422299 Affx-122943479 AX-123292645 29 34765338 CTGATAAGGGTCCTTCTGTCCAGGTTAGTGATAGT[C/T]CTTTGAATTATGTCTTTTCCAGAATATGTAATCCT Y 2 1 2 1 101000 f 74 goat snp53095-scaffold799-2735518 29 35219551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393047 Affx-122965625 AX-123263404 29 34803282 TCTGCATTTATTCTCAGGAATGGACTGCCAGATCA[C/T]GTGGCAGCTCTATTTTTGACTTTAAAAGCCACTTC Y 2 1 2 1 101000 f 74 goat snp53096-scaffold799-2773462 29 35252448 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793281 Affx-122954667 AX-385280259 29 34841796 AATCTGTTAAGTTCTACAAGTTTTTTATGGAGTCA[A/G]CACTAAGCCACCTCTCCTGAAGCAACCACTTTCAA R 2 1 2 1 101000 r 74 goat snp53097-scaffold799-2811976 29 35291740 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425238 Affx-122941001 AX-123295584 29 34974117 CATATAAGCAGAGAAGTCTAAGGGTAAAGAAAGGA[C/T]GAAAAAGGCATCATAATGGGGTCCTCCGGGTATTT Y 2 1 2 1 201000 f 74 goat snp53100-scaffold799-2944297 29 35424459 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452215 Affx-122920806 AX-123322548 29 35042109 GACTTCAAGAATGGGGAGGGCAAGATGTGATATAA[C/T]AGTCATCTTCACATATATGATGAAAATGACCTCGA Y 2 1 2 1 101000 f 74 goat snp53101-scaffold799-3012289 29 35492071 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377421 Affx-122977550 AX-123247780 29 35073075 AGAAGTAAAGGAAGAGGTGGCCTTGCTGAGACTGA[G/T]GGGGGTAGATGCCTACAGAGGGAGCTGTAACCATA K 2 1 2 1 101000 f 74 goat snp53102-scaffold799-3043255 29 35523048 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400710 Affx-122959926 AX-123271065 29 35113216 TGATTCCTTTGCGTACCTTCACCTTTCTAGTGAGT[C/T]TTGTAATTATGTTTTTAAATTTGTAAGGACTTGCG Y 2 1 2 1 101000 f 74 goat snp53103-scaffold799-3083396 29 35562845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435325 Affx-122933617 AX-123305665 29 35154149 GGGTGTATGTCTGGGTTTGATATTAGATGAAGTCA[C/T]AAATATAACCCATTAGGAAACTGAAATTCGAGATA Y 2 1 2 1 101000 f 74 goat snp53104-scaffold799-3124329 29 35603775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776486 Affx-122929885 AX-385263613 29 35213818 CCTTGTCCCTCTAAGTGCCTCTTAAAATTTAATGA[A/C]TATCCTTGCTCTGCTCAACAATCTCCACTTCCCAT M 2 1 2 1 101000 r 74 goat snp53105-scaffold799-3183998 29 35663499 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768126 Affx-986698912 AX-385255326 29 35229362 GGCACCAGAGCCTCAGGGAAAGGCCTGTTCCTGGA[C/T]TGTTGGAGGGGAAAGTGCCAGCAGAAACACCCAAG Y 2 1 2 1 600010 r 74 goat 29_35229362 29 35229362 Ancestral_priority_1043 ancestry 0.474 neutral IMAGE 10K 10K ancestral 38377711 Affx-122977400 AX-123248070 29 35281698 CTGCAGGACACCTGCTGAGCAGAATTGTTCTAGAG[C/T]GGATAATGGCACTGCAGTTGCAGAGAGAGACAGAC Y 2 1 2 1 101000 r 74 goat snp53107-scaffold799-3251878 29 35731385 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437741 Affx-122931726 AX-123308079 29 35315323 TGGGGATGAGAAGTTCCTCTGAGGACTGGTGGCTC[A/G]GATGCCTGTGCATCTAACTGACCCTGGGGGTAGGG R 2 1 2 1 101000 f 74 goat snp53108-scaffold799-3285503 29 35758598 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426220 Affx-122940358 AX-123296566 29 35344601 CTCTACTTGCCCTCTTTCCTTCTCAGAAGAAAGAC[A/G]TAGATTTTACTGAGAGCCCTGAAACAGGGCTCCCA R 2 1 2 1 101000 r 74 goat snp53109-scaffold799-3314781 29 35787872 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409927 Affx-122952876 AX-123280278 29 35472840 TTGAGATCTGCCTGCACCATAAATTCTCCCTCAGA[C/T]AAGTGGACAAATTCCCCGTCCTGCCTCAGGTCACT Y 2 1 2 1 101000 f 74 goat snp53112-scaffold799-3443020 29 35915621 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437025 Affx-122933119 AX-123307363 29 35511444 TCTGTTTCTCTCTGTGTGTCTACGTCTGTATCTAC[A/G]TATCCTACTGGGTCTGTTTCTCTGGTGAATCCAGA R 2 1 2 1 201000 f 74 goat snp53113-scaffold799-3481624 29 35953950 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388223 Affx-122969404 AX-123258581 29 35558060 AAGACAGAGAGACTGACTACTCAGGAGATCAAGAC[G/T]AATGAGTTAAGATCTAAAAGAAGCTACAAGTTAAC K 2 1 2 1 101000 r 74 goat snp53114-scaffold799-3528240 29 36000968 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387696 Affx-122969814 AX-123258054 29 35602801 TCCTTCCCACCCCCCGTCCTGCCGGATCCCAACCA[C/T]GCTGCACTTGGCAACGTGTACATTTGGCTTTCAAC Y 2 1 2 1 101000 r 74 goat snp53115-scaffold799-3572981 29 36046085 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410839 Affx-122952623 AX-123281189 29 35643372 ATTTGACCTCCAACAGGACTTTTGAGTTCCTAATA[C/T]GATCAGTCTTTGAAGCACAATTCATTGAGAAAAAA Y 2 1 2 1 101000 f 74 goat snp53116-scaffold799-3613552 29 36087440 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425331 Affx-122940930 AX-123295677 29 35675023 TGGTTTCTGAGCTTGCAGTGAAGGTAAGACAGGGA[C/T]GGGGTGGAATGTGCATGAAGGCCAGCCTGTGACAC Y 2 1 2 1 101000 f 74 goat snp53117-scaffold799-3645203 29 36118367 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423951 Affx-122942244 AX-123294297 29 35715570 GGAAAGCAGAGAGCCAGAAACAGAAGGCAATCAGT[A/G]CCGCGTGCAAAGCGGCAGGTGCTCTGATGGGCGTG R 2 1 2 1 201000 r 74 goat snp53118-scaffold799-3685750 29 36158715 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426997 Affx-122940378 AX-123297342 29 35787391 CTCCAATTCACAAGGCCTGAAGTGTTGTTAATGAA[C/T]GCTGTCATCAGGAAAGGTCAAATGGCAGGATTTGT Y 2 1 2 1 101000 f 74 goat snp53120-scaffold799-3757571 29 36230705 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378039 Affx-122977570 AX-123248398 29 35818363 GGGAGATAGAGGCAGAAGTCACCAACAAATGCATG[A/C]TTATGTGTTACCTCAAGGTCAAGGTAACCTTTAAG M 2 1 2 1 101000 f 74 goat snp53121-scaffold799-3788543 29 36262526 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446160 Affx-122925752 AX-123316496 29 35852488 TCAAAGTGCCAGCAGGTTTGGTTTCTTCTGAGGCC[G/T]CTCACCTTGGCTAGTAAACAGCTATCTCTTCCCCT K 2 1 2 1 101000 r 74 goat snp53122-scaffold799-3822668 29 36296716 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415603 Affx-122948609 AX-123285952 29 35908420 CAAGAGCCTCTCTCCTCCAGCTGGCAACACCTCCC[C/T]TTCCCAACTGCTGTCACGGTGAAGGAACAAAACTG Y 2 1 2 1 101000 r 74 goat snp53123-scaffold799-3878600 29 36353229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769645 Affx-122923664 AX-385256815 29 35948243 CTCTTCTGACCTGCAGCTTTTGCAGGTTGCAGTTC[A/G]CTTTAGGACAGAAAGTGAAGTATTGATAAGTCACT R 2 1 2 1 101000 f 74 goat snp53124-scaffold799-3918423 29 36392776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396627 Affx-122962874 AX-123266982 29 35986830 GGGGATGGACATTTTATGAAAAGTTACTAAAACAA[A/C]CAAGACAGTGCTCCAGATGAGCAGGGCCCTGAGGC M 2 1 2 1 101000 f 74 goat snp53125-scaffold799-3957010 29 36431409 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421375 Affx-122944042 AX-123291722 29 36053843 GATTTGATGATTCTCGCACATACCCACATTCACCC[A/G]CTACTACCACCGAAGTATTTGAGCACATCAGTTGA R 2 1 2 1 101000 r 74 goat snp53127-scaffold799-4024023 29 36498886 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419052 Affx-122946017 AX-123289400 29 36107712 TGGAAATACAGCCTGACAATAGGGGCACTCGGGCA[A/G]AAGGGAACTTGAGAAAAGCAAAGAAAGAAAAGCAG R 2 1 2 1 201000 f 74 goat snp53128-scaffold799-4077892 29 36552789 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376458 Affx-122978052 AX-123246817 29 36137750 GGGAGGGGAGGAGGGATGGTGGTGTCTCTGAGCCC[A/G]CAACCTCCTTTCACACAAGGTGACTGGAGGCGGAG R 2 1 2 1 101000 r 74 goat snp53129-scaffold799-4107930 29 36582577 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423015 Affx-122943420 AX-123293361 29 36175047 ACGTGTTGCTGCCTCATACCCTTAGTGGAACAAGA[C/T]GAGGAATAAGCAAATGGTGGAAGTCAGAAACAGGA Y 2 1 2 1 101000 f 74 goat snp53130-scaffold799-4145227 29 36619963 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768129 Affx-986698914 AX-385255329 29 36212925 CTTTCAAAGGTCCTCGAAGGCAGAGGGTGTGCCCC[C/T]ATCCTTTGGGTGCACGAGGGAGTGTGGCCCCAGAC Y 2 1 2 1 600010 r 74 goat 29_36212925 29 36212925 Ancestral_priority_1043 ancestry 0.472 neutral IMAGE 10K 10K ancestral 320798976 Affx-122940919 AX-385285906 29 36349004 AATTTCCATTTTTTTCACCTAATTCTGCAACCCCA[C/T]GTTTCTCAGGTTTGGAACAGTCCTTAATATACCAT Y 2 1 2 1 102000 f 74 goat snp53134-scaffold799-4319184 29 36795042 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468271997 Affx-1111833362 AX-519545765 29 36350077 ATGGCCAGAGAAGGACCACAAGACAGTCAGCCATC[A/G]AACCTCCGTGGCATTCCTCCATAAGAGTTTACTTT R 2 1 2 1 101000 r 74 goat 29_36350077_AF-PAKI 29 36350077 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38402999 Affx-122958136 AX-123273352 29 36398278 TTACCTGCCACCTGGTAATGCTGGGCTCAGTCACC[A/G]CAGATTGAGAGTTGAGGAGAAGAGTGTCTTCTCCT R 2 1 2 1 202000 f 74 goat snp53135-scaffold799-4368458 29 36841752 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407607 Affx-122954646 AX-123277958 29 36471459 GAGCCAGGAGGAAGGAGCAGCAATGAGAAACAGCT[A/C]GATGGCTCTGAACTGTGCTCCAGAAAAAAGAGGCA M 2 1 2 1 103000 r 74 goat snp53137-scaffold799-4441639 29 36913578 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430584 Affx-122936996 AX-123300925 29 36585869 GTCATGGGAATTATGAGTAATTTCCACGCTGGTGG[G/T]TGGGGACACCACTAGACTTGGAGCAATTTGAGTCT K 2 1 2 1 103000 f 74 goat snp53139-scaffold799-4556049 29 37029122 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429318 Affx-122938595 AX-123299660 29 36640126 TCTGTGTACCCTGGGTCTCGTGATACACATGTTGC[A/G]TTCTCCCCAGCAGCATCAGAGGCCAAGGAAGGAGC R 2 1 2 1 101000 f 74 goat snp53140-scaffold799-4610306 29 37085071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421927 Affx-122943835 AX-123292274 29 36674089 ACTGTTCACCAGCATCCTGGGCAGCAGTGCCCAAA[C/T]TGTGAGTTAATGTGTGTTAGGAGAGTCCTTACTGA Y 2 1 2 1 101000 r 74 goat snp53141-scaffold799-4644269 29 37119468 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447479 Affx-122924346 AX-123317815 29 36706422 CTCCCTCATGACTCACCCCCTAGACCAAGTTACTG[A/G]TCTTGAGTCCAGGAGTAGGGTTGGGTTCCAATAAA R 2 1 2 1 103000 f 74 goat snp53142-scaffold799-4676602 29 37152694 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803789 Affx-986696515 AX-385290536 29 36707447 ACCATAACCCATAACTCTGACTGAGCCAGTGCTTC[C/T]GTTTTCCTGGCTCCACCAGGAGCTAAAGCACTGGC Y 2 1 2 1 600010 f 74 goat 29_36707447 29 36707447 Ancestral_priority_1043 ancestry 0.612 recommended IMAGE 10K 10K ancestral 320764415 Affx-986698918 AX-385252114 29 36710536 TGATGTTTGTAACTCAAGCCCTTCTCACATGGACA[C/T]TAAGGAGAGAAAACCTCAGATTCCTCCAGAGACCA Y 2 1 2 1 600010 f 74 goat 29_36710536 29 36710536 Ancestral_priority_1043 ancestry 0.654 recommended IMAGE 10K 10K ancestral 38432606 Affx-122935500 AX-123302947 29 36747811 CTTGATATTGCATAGTCTCTGGTCTATGACAACCC[A/G]TGGGACTAAGAGGTTAGTTTTGTAGTTATTGATGC R 2 1 2 1 101000 f 74 goat snp53143-scaffold799-4717991 29 37193934 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381403 Affx-122974373 AX-123251761 29 36809095 CACAGCAATGTGCTGGCATCAACCTTCAGTCTCTG[C/T]AGGTTTTTGTTTCTGGCCTAGAGTTGAGAGTGAAG Y 2 1 2 1 101000 r 74 goat snp53144-scaffold799-4779275 29 37255478 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422785 Affx-122943216 AX-123293131 29 36849343 TTTGAAGGTTTGCTGTAATGTTTTTCAAGCAGAGA[C/T]GAAACAAGTCTTTAGACCAGGTTTACTATTCCCCA Y 2 1 2 1 201000 f 74 goat snp53145-scaffold799-4819523 29 37297171 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429333 Affx-122938583 AX-123299675 29 36905908 GATGTCGGCTGGCCACAAGAAGGTACCTTCAGCCT[A/G]CCTACTATTCAAGCTGTCAGAGAGAAGGTGCTCAC R 2 1 2 1 303000 f 74 goat snp53146-scaffold799-4876088 29 37354422 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377674 Affx-122977843 AX-123248033 29 36952688 GAGAAGCAGAGGATAGATCATTTTGTAGGTAGACT[A/G]CAGCACCTGCCTTAAAGAACAACAACAACAAATAA R 2 1 2 1 201000 f 74 goat snp53147-scaffold799-4922868 29 37402566 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410392 Affx-122952431 AX-123280742 29 36982332 TGACAAGGTAGTGGGTACAATCCTCTCCCATCTGC[A/G]CAAACTTCTCCGGACCCTTTTAGTACCCTGGTCAG R 2 1 2 1 102000 f 74 goat snp53148-scaffold799-4952512 29 37432968 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430916 Affx-122936853 AX-123301257 29 37032312 ATCTTGGGAATTGTGAAGGACCAGAAAGCTAAGGT[A/G]CTTCAAAGAACAATGTGAACTGGACAGAAAGTTTA R 2 1 2 1 201000 r 74 goat snp50431-scaffold722-25740 29 39451497 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277989 Affx-1111836118 AX-519551482 29 37050885 GTACCCCTTCTAACTCTTTCCTGAGCTTCTGTGAG[A/G]AGGTTAGAGTGGGATGGCAACAGCAATGCTAATGG R 2 1 2 1 102000 r 74 goat Random2.2K-2334 29 37050885 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38416511 Affx-122947777 AX-123286859 29 37120852 TCCAAGGACTCAGTGAATTTCAGGTTCTTAGCATA[C/T]AGTGGTGACTGGGAGCCCCTAGTTATATATGCCCT Y 2 1 2 1 101000 f 74 goat snp50433-scaffold722-114280 29 37688482 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423191 Affx-122942722 AX-123293537 29 37199185 CTCACCTTAAAGGTATTCTTTCACCGAGCATTTGA[C/T]AAAGAAAACAAAGAAGATGCTACAACAAACTGTCA Y 2 1 2 1 103000 f 74 goat snp50434-scaffold722-192613 29 39479017 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402760 Affx-122958319 AX-123273113 29 37232046 GGGCAGGGAAATGTGATCCCACTTCAGAACATTCG[C/T]GACAAGTAGCAGGAGCCACCACCCTTCATTCACGT Y 2 1 2 1 201000 f 74 goat snp50435-scaffold722-225474 29 37637492 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454213 Affx-122919282 AX-123324546 29 37277953 AGGAAGTTGTCTCCCAGTACCCAGGTCTCTGTAGA[C/T]GAACTCATTCTGTGCTCTTGAAAGGTGGTATAGCA Y 2 1 2 1 101000 r 74 goat snp50436-scaffold722-271381 29 39716960 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405606 Affx-122956612 AX-123275958 29 37320779 CATTATGAGTGAAATCCTTTATTCTTTAATGAGAA[C/T]AGGGTGTTCAGAACAACAAATACAGTTCACAGGCA Y 2 1 2 1 303000 f 74 goat snp50437-scaffold722-314207 29 39761374 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438038 Affx-122931554 AX-123308376 29 37373278 GAAGGCCTGCCTGAGGAAGACACATTTGAGATGGT[A/G]CTGAATGTGGAGAAGGAACCAGCCATGCAAAAAGA R 2 1 2 1 101000 r 74 goat snp50438-scaffold722-366706 29 39814713 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391022 Affx-122966879 AX-123261379 29 37423728 CGGGGTCTCCTTTCTAGGGAGGACAGAGATGGCTC[A/G]TTGCTGGTATTTCACAAGTGAAGTATGTGATGAGT R 2 1 2 1 101000 r 74 goat snp50439-scaffold722-417156 29 39866212 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476646 Affx-1251763901 AX-586012027 29 37469389 TCAACTATACAATTATATAGATTAAAAGCTGATTT[-/TTTTTATTTTTATGATTATTTTTATTTTTTTTATTACTACTCCTCCGCCATCTTTCCCCGACCTCTCAAAAGCTGATTTT]TTTTTAATGCTTACATGTACAGACCCATGGATTTA - 8 1 4 1 20000 r 74 goat SV_230 29 37469389 - deletion junction SV-TF-chip 560378491 Affx-1251763901 AX-605230906 29 37469389 TCAACTATACAATTATATAGATTAAAAGCTGATTT[-/TTTTTATTTTTATGATTATTTTTATTTTTTTTATTACTACTCCTCCGCCATCTTTCCCCGACCTCTCAAAAGCTGATTTT]TTTTTAATGCTTACATGTACAGACCCATGGATTTA - 8 1 4 1 20000 f 74 goat SV_230 29 37469389 - deletion junction SV-TF-chip 562165843 Affx-1251763901 AX-606941252 29 37469389 TCAACTATACAATTATATAGATTAAAAGCTGATTT[-/TTTTTATTTTTATGATTATTTTTATTTTTTTTATTACTACTCCTCCGCCATCTTTCCCCGACCTCTCAAAAGCTGATTTT]TTTTTAATGCTTACATGTACAGACCCATGGATTTA - 8 1 4 1 20100 r 74 goat SV_230 29 37469389 - deletion junction SV-TF-chip 562166502 Affx-1251763901 AX-606941910 29 37469389 TCAACTATACAATTATATAGATTAAAAGCTGATTT[-/TTTTTATTTTTATGATTATTTTTATTTTTTTTATTACTACTCCTCCGCCATCTTTCCCCGACCTCTCAAAAGCTGATTTT]TTTTTAATGCTTACATGTACAGACCCATGGATTTA - 8 1 4 1 20100 f 74 goat SV_230 29 37469389 - deletion junction SV-TF-chip 38391371 Affx-122967280 AX-123261728 29 37533826 AGGGGAGGGCTTGGTACTTATTTTTTAAAATGTGC[A/G]TTAAGCTCCAGTGATTATTTGCTACTATTCTTTTC R 2 1 2 1 201000 r 74 goat snp50441-scaffold722-527254 29 39968111 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784087 Affx-122962971 AX-385271139 29 37604892 TTCATTGTACTGGTCAAGATTAGAGGAAACAATCC[C/T]TGAGCCTCAACTTGAGCCAAGGCTAATTTGTGTCA Y 2 1 2 1 10000 r 74 goat "snp50442-scaffold722-598320;SV_241_b" 29 40037566 T C SV_241_b 2 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375854 Affx-122978521 AX-123246213 29 37641280 GATGAGGACACTGAGCCTGAGTCTTCTCACTGAAG[C/T]GTCTCACTGAAGGACATAGGGCCTGTGAGTGGTAG Y 2 1 2 1 201000 r 74 goat snp50443-scaffold722-634708 29 40074043 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432997 Affx-122935254 AX-123303338 29 37670136 CAACCCAAAACAATATATGACCCTGGGTGAAATCC[C/T]GCAGAAGAAAAATCACTAAAAGGGACAGTTTTAGG Y 2 1 2 1 101000 f 74 goat snp50444-scaffold722-663564 29 40102623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444718 Affx-122926416 AX-123315055 29 37760047 TGCTCTTAACAGTGCGATTTTGGAATGTCCTCCCA[G/T]AAATGAGTATCAGCCCTAGATTAACCTTTAATTCT K 2 1 2 1 101000 f 74 goat snp50445-scaffold722-753475 29 40191346 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450630 Affx-122921993 AX-123320964 29 37815331 CTCTGCCCCAAAGCCAGCATATTTTAAAATTTTAT[G/T]TATTTTTGGTTGTGCTGGGTCTTCCTTTCTGCACT K 2 1 2 1 303000 f 74 goat snp50446-scaffold722-808759 29 40246745 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408416 Affx-122954469 AX-123278767 29 37845953 AAACTTTGAGGAGTTAGGGGCCTTGCCATCACTGT[A/G]TGCTCAGATTTTAACACAGGCAGGTGACTAGAATG R 2 1 2 1 101000 f 74 goat snp50447-scaffold722-839381 29 40277365 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453454 Affx-122919858 AX-123323787 29 37888254 CTATGAGTTTCCTGATGCAACCGTAGCCCCTTGGA[C/T]GTGGTTCCCACGTGTAGGTGCCATCCCCTCCGCAG Y 2 1 2 1 101000 f 74 goat snp50448-scaffold722-881682 29 40319597 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400649 Affx-122960360 AX-123271004 29 37924123 CCCGCGGGGAAGGCTAGGAGGAGTGGAGCCCGGGC[A/C]CGGGGACATGGTCCATATCCAAGGTTCATTCATCT M 2 1 2 1 101000 r 74 goat snp50449-scaffold722-917551 29 40355385 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797332 Affx-122971838 AX-385284271 29 37994710 TTTCTTGGTTATTGTTTTATGTCAGCTGAAAACTG[G/T]TTCCGCGTTCTTATTTTATGGCTGCAGATTACTTC K 2 1 2 1 101000 r 74 goat snp50450-scaffold722-988138 29 40422215 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789447 Affx-122962666 AX-385276457 29 38026624 GAAGGAATACTATACAGTTGTAAAAAGAATGAGGA[C/T]GCTTTCTCTTCTGCTAGGAAAAGACCACTAGGATA Y 2 1 2 1 101000 r 74 goat snp50451-scaffold722-1020052 29 40451974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437011 Affx-122933129 AX-123307349 29 38086474 CCTGCTCCTCTGAAGTGGCGGTTAAGACACGGCTG[C/T]GGAACTAGGCTAGGTGACCTGGGGCAAATCACTTC Y 2 1 2 1 201000 f 74 goat snp50452-scaffold722-1079902 29 40509555 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401607 Affx-122959620 AX-123271960 29 38167610 AAGTCCATGTGACTGGCGTCCTTGTCCTTTCTGCC[C/T]AGTTTGTCTCCATTAGCTAAGGGGTCACGCAGGCC Y 2 1 2 1 101000 r 74 goat snp16308-scaffold1719-56550 29 40587098 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453700 Affx-122919690 AX-123324033 29 38197276 TAGAAGTCACGTCAGCCTCTCTGGTTACAGGTTCC[A/G]TATCTAAATTAAAGAGGCCAGATTCCTTCCAGTGC R 2 1 2 1 201000 r 74 goat snp16309-scaffold1719-86216 29 40616872 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453071 Affx-122920056 AX-123323404 29 38227766 ACCAGCTGGGAAGCCCCAGTATGTACATAAGTTTT[A/G]CCTCAATAAAGCCTACCCAGAAAATTGGGCAAGGG R 2 1 2 1 201000 r 74 goat snp16310-scaffold1719-116706 29 40647357 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277991 Affx-1111836119 AX-519551484 29 38231388 ACTTGAATACACCAGGATATTTTGTACCTTGACCC[A/G]AGCTGATCTTTCTTCCTAGAAGACTCCACTCCACT R 2 1 2 1 101000 r 74 goat Random2.2K-2335 29 38231388 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 320789345 Affx-122967265 AX-385276355 29 38298668 GAGAGAACCAGCAGAGAAGAGCACCATCAAAAGCT[A/G]TTTCATCATTACACCCCATGCCAAGTTCGGGGGTG R 2 1 2 1 201000 f 74 goat snp16311-scaffold1719-187608 29 40719133 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439347 Affx-122930289 AX-123309684 29 38341143 GCTCCACCAACAGCTTTCATTTTTCTGAGGGCCTC[C/T]GGACCTTCCATGGCTTCTTTGGGCTTCAAACCAGG Y 2 1 2 1 101000 r 74 goat snp16312-scaffold1719-230083 29 40761394 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796459 Affx-122930464 AX-385283409 29 38377327 CCAAGGAATTCCTAAGGAGTTCAAGCTTTATACTT[C/T]AGGAAAAAAGGGAGTCATCAAAGGGTTTAAGCAAG Y 2 1 2 1 101000 r 74 goat snp16313-scaffold1719-266267 29 40797696 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403722 Affx-122958027 AX-123274074 29 38408047 TGGCTTAGAACTCTTGTTTTCTAATAAGCTGGGGT[A/G]GAATGAAGAGTGGGAGTGGGGTTCCCTGGGCAAGG R 2 1 2 1 101000 f 74 goat snp16314-scaffold1719-296987 29 40828432 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395789 Affx-122963660 AX-123266144 29 38465099 AAAAAGCAGAGGAATGCCAAGTGGGTTAGGATGTG[C/T]GGCTATAAGCTTCCTACATTACTGGAGGTCATGGG Y 2 1 2 1 201000 r 74 goat snp16315-scaffold1719-354039 29 40885721 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383048 Affx-122973291 AX-123253406 29 38497896 TCTGATGGTTGCTCCCGTTTCCTCCTTTCCAGTGG[A/G]CTCCTGGGCACAAGGCGTATGGTGTCATGCTTTAT R 2 1 2 1 201000 f 74 goat snp16316-scaffold1719-386836 29 40919254 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774912 Affx-122947097 AX-385262045 29 38570148 AAAAAAATGGGAAATTATTTAGCATGCACTATACA[C/T]GTTAGTCTAAAAGATTCTATCCATGCAAAGGAAAG Y 2 1 2 1 101000 f 74 goat snp16318-scaffold1719-459088 29 40988792 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453257 Affx-122920404 AX-123323590 29 38611327 TCAAAGCAAAATAAACCATGAGGCTGTCCGTGACC[A/G]CCCTGCTGGTTACTCTGGCCCTTTGCTACTACGAG R 2 1 2 1 101000 f 74 goat snp16319-scaffold1719-500267 29 41027753 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419840 Affx-122945811 AX-123290188 29 38657018 AGACAGAAGCCCAACAGACCCCAGCTGAATTCCAA[C/T]GAGGCACCAAAGCTTTTGGCTGCTTGCCGCCTATG Y 2 1 2 1 101000 f 74 goat snp16320-scaffold1719-545958 29 41073526 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403029 Affx-122958552 AX-123273382 29 38690609 CTCCCCTTCTAGAACAACATTCCCTTGTCCACGGG[C/T]GCCAGATCCCCGGGGCTTTGAACTCCTGAACTCTC Y 2 1 2 1 101000 f 74 goat snp16321-scaffold1719-579549 29 41107119 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409502 Affx-122953637 AX-123279853 29 38722707 ATATATTACTCCCACAACCTGCAACCAAAAGAACA[A/G]TGACTATTTATTTAATTTTTGGCCACCCCATGTGA R 2 1 2 1 201000 f 74 goat snp16322-scaffold1719-611647 29 41138747 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417726 Affx-122947437 AX-123288074 29 38752730 CTGAGATCAGAGCGCCAGCATGGCGGCGTTCTGGC[A/G]AGAACCCTCTTCTTGGTTTGCAGACGACCTCTTAC R 2 1 2 1 101000 r 74 goat snp16323-scaffold1719-641670 29 41168827 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452786 Affx-122920241 AX-123323119 29 38779483 GCAGAAAAGGCCCCTGGCATTATCCTCTCCTCCCT[A/G]CTCACATTCCAGCCCTCCCCACTGCCTGCCCACTA R 2 1 2 1 303000 r 74 goat snp42419-scaffold5602-14553 29 41198096 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400988 Affx-122960092 AX-123271341 29 38810658 GATGGCCCAGTGGTTAAGACTCCAAGTTCCCAATG[C/T]AAGGGGCCAAGTTCCAGCCCCAATCAAGGAACTAA Y 2 1 2 1 303000 r 74 goat snp42420-scaffold5602-45728 29 41229340 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273238 Affx-1111833363 AX-519546891 29 38887840 AAAGAACATTTGAACGCTGAGTAAATTCCACAAAA[A/C]AACTTCTGAATGCAGGCAGAGTACATCAGGCACTC M 2 1 2 1 103000 r 74 goat 29_38887840_AF-PAKI 29 38887840 A C 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38403382 Affx-122957780 AX-123273735 29 38916085 GGAGAAAACTTGTCTTTGCAAGATGACTGGAAAAT[C/T]TGGGTCCTGGTTTCCACATTTATTAGATGGGTGTA Y 2 1 2 1 101000 f 74 goat snp22977-scaffold2292-39826 29 41329816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775783 Affx-122926505 AX-385262914 29 38968588 ATCAAAGGGAAACCTGAGCCTCAGCAAGAGAAATT[A/C]ACCCCATACCTCTGACTGAGGTGAACTTCTGTTTT M 2 1 2 1 101000 f 74 goat snp22978-scaffold2292-92329 29 41382408 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420573 Affx-122945273 AX-123290920 29 39046322 TCACCGTATCCCCAGCGCCTATGACAGTGCCTGAC[A/G]TGGAACAGGTGCTCAATTAATACTTGTGGTGTGGA R 2 1 2 1 101000 r 74 goat snp22980-scaffold2292-170063 29 41460775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453156 Affx-122920481 AX-123323489 29 39094189 TCTGACAGTTCTCTTCACCAGCCAGTGTCCCTCCT[A/G]CAGGATTTGTAATAACAAATAATATGCCAACACTG R 2 1 2 1 201000 r 74 goat snp22981-scaffold2292-217930 29 41507839 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426769 Affx-122940558 AX-123297115 29 39135574 CCTTTGATCGTCTAGACTCAGTGTTGTTTCTGCCC[A/G]TTGTAGAAATGGAGCAACTGAGGCCCAGAGAAAAA R 2 1 2 1 101000 f 74 goat snp22982-scaffold2292-259315 29 41548685 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791358 Affx-122962017 AX-385278351 29 39183152 AGGTACCAAGTTAAACTGTGACTTGAAAGTAAGGC[A/G]ATGAATTATTAAGACTCACCGGGTCAATGAGTTGT R 2 1 2 1 101000 r 74 goat snp16191-scaffold1703-40971 29 41595597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277993 Affx-1111836120 AX-504620842 29 39214606 ATTCCTTTATGTTGACTAAAATGGAGGTCCCCCTG[A/C]AATCAGAACTCACTGAATGTCTTGTGAATGCTAGG M 2 1 2 1 103000 r 74 goat Random2.2K-2336 29 39214606 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38380742 Affx-122975134 AX-123251100 29 39229842 AGCCAGGCCCTCCTCCTTCCATGGCCTCCACACCC[C/T]ACTGCCTGCCTCTCCAGCCTTCTTTGTCTCTTGTG Y 2 1 2 1 103000 r 74 goat snp16192-scaffold1703-87661 29 41642591 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787013 Affx-122926278 AX-385274041 29 39281366 TAACTTGAGGGAACGTGTAATCCTTGCACAATCCA[A/G]TATTTTGAGGCAGTAGTTGGAAAAAGTTTTGAACT R 2 1 2 1 101000 f 74 goat snp16193-scaffold1703-139185 29 41693762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394891 Affx-122964742 AX-123265246 29 39313358 TTCCATGGTGTTTCTTTGTTTCTGAATCTGAATCA[C/T]CTTGTCTATTAATAATTTATTGATTAAATTCAAAA Y 2 1 2 1 101000 f 74 goat snp16194-scaffold1703-171177 29 41725797 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435734 Affx-122933291 AX-123306073 29 39376701 TGGGCAAGCAGCACCACCAACTCCTCTCCAGCCCC[C/T]GCCCCCCACAACAGGTTCAAACTCCTTAGAAAGGT Y 2 1 2 1 101000 r 74 goat snp16195-scaffold1703-234520 29 41786860 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790088 Affx-122947635 AX-385277094 29 39471263 CTTGATATGTGGGACAGCATATGGTGAACTGTCCA[C/T]AAATGTACAGAACAATATAAGATATGAAACCAAAA Y 2 1 2 1 201000 r 74 goat snp16196-scaffold1703-329082 29 41883704 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441247 Affx-122929497 AX-123311584 29 39523439 TTCCATCAGCCTAGAAAGACCTTTTGTGTTCATTC[A/G]TTAGTCAGAATTGTCCCCTAGACCTCATCTCTCCT R 2 1 2 1 101000 r 74 goat snp16197-scaffold1703-381258 29 41936810 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419484 Affx-122945469 AX-123289832 29 39563368 TCAGTGTGGTGAGTGCTATTTTATCAGCTGTGAGC[A/G]TTGTGTATGGGATACAGAAACAACATCTCCATCAG R 2 1 2 1 101000 f 74 goat snp16198-scaffold1703-421187 29 41976058 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436534 Affx-122932931 AX-123306872 29 39609664 TTTTTCAGGGCAACAAGACCAGAAGGAAGGTTCCA[C/T]GACTGTGCAAAATAGAGCATATGGAACTTCATATT Y 2 1 2 1 201000 r 74 goat snp25365-scaffold2619-14542 29 42035958 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442499 Affx-122927918 AX-123312836 29 39672163 CCAGCTCCCCCAGGTACCATCTCCTGAGGACACCA[C/T]GTGACCAATGGTTCTAGATGTCCAGTTTTAAGCCG Y 2 1 2 1 101000 r 74 goat snp25366-scaffold2619-77041 29 42098345 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384713 Affx-122972102 AX-123255071 29 39704025 TACCACTAGCGCCACCTGGGAAGCCCTTGACTTCT[A/G]TTGAGGACACTTCAAATCTGAGCAGCTTCACGGCA R 2 1 2 1 103000 r 74 goat snp25367-scaffold2619-108903 29 42131184 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383762 Affx-122972435 AX-123254120 29 39752772 CCTCTCTGTCCTTTTTGCTCATTTTTACTTATGGC[G/T]TACGGTTTTCTGTGCATGAAAAGATTCAGAGGTTC K 2 1 2 1 101000 r 74 goat snp12793-scaffold1490-44599 29 42386173 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409307 Affx-122953096 AX-123279658 29 39790088 TATAGGCCTGGCTAAAGAACTGATCAAAATTCATG[A/C]TAAAAGAAGCAACTTGCACAGGAAGGACTCCACAA M 2 1 2 1 101000 r 74 goat snp12794-scaffold1490-81915 29 42423917 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440454 Affx-122929395 AX-123310791 29 39828659 TAAATACCAAAGGAAAAGGAATAAACACTTCCCCA[G/T]ATTATCCAGTCTTTATTATAACCTTCTTCATGCTT K 2 1 2 1 201000 r 74 goat snp12795-scaffold1490-120486 29 42462627 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399882 Affx-122960220 AX-123270237 29 39866831 CAGCGTGCCTCGTGACCACTGGAGGGCTTAGCAAA[A/C]CAGATTCCTAGGCTCCACGCCAGTTTCTGATCCAT M 2 1 2 1 201000 f 74 goat snp12796-scaffold1490-158658 29 42500886 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 539476390 Affx-1251763902 AX-586011799 29 39874892 CCCCAAGAACTCTCAAGCTCATTTTGTGAAATCAT[-/GTAGGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]TAGGATATTGATGTTTTTCTTGAGGACTGTGAAAC - 4 1 4 1 20000 f 74 goat SV_239 29 39874892 - deletion junction SV-TF-chip 539476647 Affx-1251763902 AX-586012028 29 39874892 CCCCAAGAACTCTCAAGCTCATTTTGTGAAATCAT[-/GTAGGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]TAGGATATTGATGTTTTTCTTGAGGACTGTGAAAC - 8 1 4 1 20000 r 74 goat SV_239 29 39874892 - deletion junction SV-TF-chip 560378497 Affx-1251763902 AX-605230912 29 39874892 CCCCAAGAACTCTCAAGCTCATTTTGTGAAATCAT[-/GTAGGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]TAGGATATTGATGTTTTTCTTGAGGACTGTGAAAC - 8 1 4 1 20000 r 74 goat SV_239 29 39874892 - deletion junction SV-TF-chip 562165423 Affx-1251763902 AX-606940834 29 39874892 CCCCAAGAACTCTCAAGCTCATTTTGTGAAATCAT[-/GTAGGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]TAGGATATTGATGTTTTTCTTGAGGACTGTGAAAC - 8 1 4 1 20100 r 74 goat SV_239 29 39874892 - deletion junction SV-TF-chip 562165454 Affx-1251763902 AX-606940866 29 39874892 CCCCAAGAACTCTCAAGCTCATTTTGTGAAATCAT[-/GTAGGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]TAGGATATTGATGTTTTTCTTGAGGACTGTGAAAC - 8 1 4 1 20100 f 74 goat SV_239 29 39874892 - deletion junction SV-TF-chip 562165728 Affx-1251763902 AX-606941137 29 39874892 CCCCAAGAACTCTCAAGCTCATTTTGTGAAATCAT[-/GTAGGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]TAGGATATTGATGTTTTTCTTGAGGACTGTGAAAC - 8 1 4 1 20100 r 74 goat SV_239 29 39874892 - deletion junction SV-TF-chip 562166350 Affx-1251763902 AX-606941758 29 39874892 CCCCAAGAACTCTCAAGCTCATTTTGTGAAATCAT[-/GTAGGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]TAGGATATTGATGTTTTTCTTGAGGACTGTGAAAC - 8 1 4 1 20100 f 74 goat SV_239 29 39874892 - deletion junction SV-TF-chip 562166529 Affx-1251763902 AX-606941937 29 39874892 CCCCAAGAACTCTCAAGCTCATTTTGTGAAATCAT[-/GTAGGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]TAGGATATTGATGTTTTTCTTGAGGACTGTGAAAC - 8 1 4 1 20100 f 74 goat SV_239 29 39874892 - deletion junction SV-TF-chip 562166533 Affx-1251763902 AX-606941941 29 39874892 CCCCAAGAACTCTCAAGCTCATTTTGTGAAATCAT[-/GTAGGATTGCCGCGGCCAGCACAAGCAAGAGTCACACCTGCAGCTCCCAAGACTTAACCCTTCACGGGCAGTCCCCCGCA]TAGGATATTGATGTTTTTCTTGAGGACTGTGAAAC - 8 1 4 1 20100 r 74 goat SV_239 29 39874892 - deletion junction SV-TF-chip 38426019 Affx-122941127 AX-123296365 29 39900431 GACCAGATTGAATAACCTTCCCAGATGGGAGAGGT[C/T]TTAAAAATTGAAAATATCTATTTTTGGTTAGTAAA Y 2 1 2 1 103000 f 74 goat snp12797-scaffold1490-192258 29 42534695 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383822 Affx-122973172 AX-123254180 29 39932032 GTAAGTTCTCCCAATTGCCAACACCCAACAACACA[G/T]CCACGTTGTTTTAAAAGCACACTGGCATAAATGTA K 2 1 2 1 101000 f 74 goat snp12314-scaffold1463-684291 29 42567035 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440289 Affx-122930226 AX-123310626 29 39980878 CTCAAACTGCCTCCTGCTCCAGAAGAGCAGAGGAA[C/T]GGAAAACGGCAGCTGGGGAGCTCAGCTGACTCACC Y 2 1 2 1 303000 f 74 goat snp12313-scaffold1463-635445 29 42616997 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448700 Affx-122923861 AX-123319036 29 40046765 AATGTCACAACACTTGGCCTGGGACTCTCTCCAGC[A/G]TGCAGAGCAGGCACCCTTCAGAAGACCTTTGACCT R 2 1 2 1 201000 r 74 goat snp12312-scaffold1463-569558 29 42682769 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418392 Affx-122946556 AX-123288740 29 40079362 TGGGCAAGTCTCTCACCCTCTCTGCGCCTCTGTGT[A/C]TTCTTTGCTAAAGCAAGAAAAGCAATAGCACAGCC M 2 1 2 1 202000 f 74 goat snp12311-scaffold1463-536961 29 42715449 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453141 Affx-122919998 AX-123323474 29 40135633 CTCCACGATGCTTGGATGAGGAAACACGCACAGAG[C/T]GGTTCAGCCACCAGCCCGAGGGCACACAGAGCCTG Y 2 1 2 1 101000 f 74 goat snp12310-scaffold1463-480690 29 42810020 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431482 Affx-122936255 AX-123301823 29 40207897 CCTCGGTTTCCTCGTCTGTAAACCCGGGAGAGTGA[C/T]GCCTTCTCTGAAGGTGGTTTGGGGGATGGAGATGC Y 2 1 2 1 201000 f 74 goat snp12309-scaffold1463-408426 29 42881512 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277995 Affx-1111836121 AX-519551487 29 40249083 TCTGCAGGATGAAAATGATGGCTGTCCTGCCTTCC[A/G]CACTGGGATGTTTTAAGCATCAGCAAAGCAAATGG R 2 1 2 1 101000 r 74 goat Random2.2K-2337 29 40249083 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38422183 Affx-122943515 AX-123292529 29 40296388 TCCTGCGCTGAAGCCCAACTCCCACATTTTTGTAG[A/C]GGATCGGGGTCTTCTTAGTGAGGGGACAGAGGAGC M 2 1 2 1 101000 f 74 goat snp12307-scaffold1463-319935 29 42964376 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382812 Affx-122973562 AX-123253170 29 40366259 CAGCATGCATTTCCTGGACCTGTCCTCGCCTGGCT[G/T]CGTGACTTTCAGCAAGTCACTGTTCTTGCCTAAGC K 2 1 2 1 101000 r 74 goat snp12306-scaffold1463-250064 29 43033857 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393031 Affx-122965637 AX-123263388 29 40462348 AAGTTTAACCTGTCAAACTGAGCTCGCTTCCCACC[A/G]CCTTCACAGTCTCACTTATCGACAATTCCACACTC R 2 1 2 1 201000 r 74 goat snp12304-scaffold1463-153975 29 43115641 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797799 Affx-122969907 AX-385284738 29 40536517 AAAATGTGAAAAGAGATAGAATCTTTGGGAATGAC[C/T]ATCACCATGTCAGCAGTGTCTCTATGTGTCCAGGG Y 2 1 2 1 101000 r 74 goat snp12302-scaffold1463-79806 29 43189734 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420106 Affx-122945090 AX-123290454 29 40595207 AAACTTTTATATTGATATTTTTCCTGTCTTGCCTT[A/G]AGATGTCAATTTTTATTTTGTCGACTTCCATTAGA R 2 1 2 1 101000 f 74 goat snp12301-scaffold1463-21116 29 43249197 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442316 Affx-122928237 AX-123312653 29 40639985 ATGCCTACAGGAATCTGCTAGGCTGCTTACCTCTC[A/G]GCTTCGATTTTAACCTGGGAGGCCAAGACCTGTTC R 2 1 2 1 201000 f 74 goat snp15236-scaffold1624-23563 29 43283732 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413636 Affx-122950545 AX-123283985 29 40688329 GAAGATGACATGTCCCGATGGGTACCCTTGTCCAC[C/T]CACATGCACACACGCTTGCACACGCACACACACAG Y 2 1 2 1 201000 f 74 goat snp15237-scaffold1624-71907 29 43332349 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767378 Affx-122930324 AX-385254651 29 40819113 CCCCTCAACCAGCCTGAGAACCAAGATGTTACTTT[C/T]GTAAATTCCTGAGATCCTTCCTTACCCCAGCCCCA Y 2 1 2 1 101000 f 74 goat snp15239-scaffold1624-202691 29 43448321 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428771 Affx-122938420 AX-123299113 29 40878672 CTCAGCCCCCACTGAGCACAAGGAAAGGGGATTGT[C/T]GGCCCCATTTGCAGGCCTAACCCTGCTGGGCTTGC Y 2 1 2 1 101000 f 74 goat snp15240-scaffold1624-262250 29 43507559 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411592 Affx-122951613 AX-123281942 29 40936144 GAAGGTCTCACCTGCAATGCTTGAGAGGAGATTAA[C/T]GGATCTTCCCTTCTCTTTGTACTTGGTCAGGCCTC Y 2 1 2 1 101000 f 74 goat snp15241-scaffold1624-319722 29 43564402 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451577 Affx-122921688 AX-123321910 29 40974575 TAGATTTGATAGTGTTTTTGGTGCTAGATGACTTT[A/G]CCAAGTAGGCAGGGACCACCTGATGAGACTTAGGT R 2 1 2 1 101000 f 74 goat snp15242-scaffold1624-358153 29 43602944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418677 Affx-122946310 AX-123289025 29 41012300 TGGGGGTGGAGGTGGAGAGGGACTAAAGGGGACCC[A/G]CAGAGACTTCAGTGTGTCTGTGACATATCATTGCT R 2 1 2 1 202000 f 74 goat snp15243-scaffold1624-395878 29 43640788 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400292 Affx-122960079 AX-123270647 29 41084398 TGCGAGGAAGACTCAGTGCAGTGAAAAAAACCCAA[C/T]AACCTAGGAAGTCTTGAGCAAGGAGGGGGCATGTT Y 2 1 2 1 101000 f 74 goat snp15245-scaffold1624-467976 29 43716454 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436492 Affx-122932961 AX-123306830 29 41159971 GAGTATTTGCCGTCTGTATATTTTCTTTTGTGAAA[C/T]GTCTGTTAAAGGTTTGGCCTGTTTTAAAATCGGAT Y 2 1 2 1 101000 r 74 goat snp15247-scaffold1624-543549 29 43790139 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386700 Affx-122970171 AX-123257058 29 41234468 GCGTGCAGCGGGAGCTGCCCCCAAATCCAGAGGAC[A/G]TGTCATAATTTCTTTGACCATCACCCTGATGTTGG R 2 1 2 1 101000 r 74 goat snp15249-scaffold1624-618046 29 43864559 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277996 Affx-1111836122 AX-519551488 29 41247982 TTTTCCGGTGAGGAAGGTGCAGGGAAGGTGGGGCA[A/G]GGATTTGGGAAATGCACTCATATTCCTGAGTCAGA R 2 1 2 1 101000 r 74 goat Random2.2K-2338 29 41247982 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38449284 Affx-122923021 AX-123319619 29 41283330 CATTAGTGGAAAAACCAGTGACATTTATAAAGTCA[C/T]GAGCTAACAGTAACATACCAGTATTAATGCCTTCG Y 2 1 2 1 101000 f 74 goat snp15250-scaffold1624-666908 29 43914012 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408364 Affx-122953734 AX-123278715 29 41339498 CTGCCGCCTGCGTTGTGTATCCTGGCTCCTGGGTC[A/G]TGGGGAAGCCACCTAGACATCTCTTTCTTCCCTCG R 2 1 2 1 101000 r 74 goat snp15251-scaffold1624-723076 29 43970197 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416642 Affx-122947610 AX-123286990 29 41405610 TTACTGTCATTGGAATTTAAAGAGCATTAGTCATG[C/T]GTGTATGGGGAAATATGTTCCGGTAAGCTGTTGTG Y 2 1 2 1 201000 f 74 goat snp15252-scaffold1624-789188 29 44035425 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273240 Affx-1111833364 AX-519546893 29 41409661 GGATAGCTTCTTACTATGCTTACTATGTGAAAGCA[A/G]TCTTCAACTCTTTGCAGAATGAATAGACTCTGCTA R 2 1 2 1 101000 r 74 goat 29_41409661_AF-PAKI 29 41409661 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320777501 Affx-122941130 AX-385264620 29 41465270 ACAGGACACCATTCCTGTGGGCTTCGATGATGGGA[C/T]AGCACATTTCACTCAAGAGGCAAGTAATTCCTTGA Y 2 1 2 1 201000 r 74 goat snp15253-scaffold1624-848848 29 44095082 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415943 Affx-122948438 AX-123286292 29 41494544 TGTTTTGTGAGTGTGCCTGGCACTCTGTTAACTGC[A/G]CACATACATTCCAGCCCTGCCCCTGATGTTGGCTG R 2 1 2 1 201000 r 74 goat snp15254-scaffold1624-878122 29 44124275 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377558 Affx-122977449 AX-123247917 29 41565556 GGCTTCTGTCCATTCACAAGCCTAGCAGAGCGTTT[A/G]CACTGACAGAGGGAACAGGCCAGTGTGCTGCTCTA R 2 1 2 1 101000 f 74 goat snp15255-scaffold1624-949134 29 44173676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423808 Affx-122942807 AX-123294154 29 41656003 CCCAGGGCTTTCTTTTACCCTCTCCAAAGACATGA[C/T]ACTCATTCGTATTTCAAAGCCTTTTGCACCTGTTC Y 2 1 2 1 101000 r 74 goat snp15256-scaffold1624-1039581 29 44252966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395471 Affx-122963908 AX-123265826 29 41684777 ATTTCAGATGGAAAATTTTTTCTTTCCTTTTGCTT[C/T]GATCTTGGTCAAATTGTTGAATGGGCGTCCACAAG Y 2 1 2 1 101000 r 74 goat snp15257-scaffold1624-1068355 29 44282165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383060 Affx-122973752 AX-123253418 29 41736543 AAGGAAAACATTGATCTAACCTCCACAGCTCTTCC[A/G]TGTGAAGGCAGAGGGTGGAAGGGCCCCTAGCCCTC R 2 1 2 1 101000 f 74 goat snp15258-scaffold1624-1120121 29 44333236 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771924 Affx-122923153 AX-385259080 29 41787845 ATCCTGCAGGCTAGAGATCCAAGATCTGTGAGAAG[C/T]AGAGCCTCAGCCAAGATGTGAGTCCAAAATTAAAA Y 2 1 2 1 101000 r 74 goat snp15259-scaffold1624-1171423 29 44383597 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448022 Affx-122923721 AX-123318358 29 41802590 ATGGGCAGGGCTTTGTCCTATGTATCCCTGACTTG[A/G]GGTCTCCCAGCTTAGGGGTGCCTTTCTCTTTAGCT R 2 1 2 1 201000 f 74 goat snp53484-scaffold811-325023 29 44398903 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394894 Affx-122964740 AX-123265249 29 41847875 TCAACCACTGAACAGCTAGGGAAGTCCCTCTACAG[C/T]GATTTTGAAAGCCATGAACTAAGGATGGTGGGGCC Y 2 1 2 1 101000 r 74 goat snp53483-scaffold811-279738 29 44444233 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397890 Affx-122961959 AX-123268245 29 42000760 TCTGGGAAATTTCATTTCAGGATAGAAAAGGGGCC[A/G]TAAAATCTGAACTGTTGAGAACCAGTTACAAACCA R 2 1 2 1 201000 r 74 goat snp53479-scaffold811-126853 29 44576267 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413947 Affx-122950314 AX-123284296 29 42045334 ACATACAATGAAAAGAGTGGGGACAAAAAACAAGA[C/T]GCTTTTGGGGTAACAGATAAATCAATAAGAAGCCC Y 2 1 2 1 201000 f 74 goat snp53478-scaffold811-82279 29 44620546 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781507 Affx-122935025 AX-385268592 29 42078186 CCACTGTCACCAACATCAACCAAGTCTAAGACACC[A/G]TAACCTACCTCTGCAACAGGCTCCTAACCAACCTA R 2 1 2 1 101000 f 74 goat snp53477-scaffold811-49427 29 44653728 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389954 Affx-122968081 AX-123260311 29 42268493 AGTTTAAAAAATAACTCAGAAGGTTCAGATTCTGG[A/G]CACAAAAGGAATTCCTCTGAGTTGTGAACCATGTC R 2 1 2 1 201000 f 74 goat snp21575-scaffold2106-73453 29 44842702 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782697 Affx-122927672 AX-385269769 29 42317451 GCAGAAAATTAAATTTAATTGGGTGTTAAATTTAG[C/T]TAAATTGGGTATCCTACAATTTAACTCCATTTTAT Y 2 1 2 1 201000 r 74 goat snp21574-scaffold2106-24495 29 44891544 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768139 Affx-986698919 AX-385255338 29 42347707 AGTAACAAGGAACAAAGCCCGTCACGTGCTACAAC[A/G]TAAGTGAACATCAGACACATTCTCCTAAGTTAAAG R 2 1 2 1 600010 r 74 goat 29_42347707 29 42347707 Ancestral_priority_1043 ancestry 0.742 recommended IMAGE 10K 10K ancestral 320774786 Affx-122948427 AX-385261920 29 42350529 AATATACAATGTCAAGAGTGGTCCCTAATGTAAAC[G/T]ATGATCTTTGGGTGATGAGGTGCCAAGGTACATTC K 2 1 2 1 101000 r 74 goat snp23323-scaffold2330-8484 29 44924759 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764422 Affx-986698921 AX-385252120 29 42357272 TTCAGAACACTGAAGATAAGGAGAAGAGTCTATAA[A/G]CTTCCAGAAAGATAAAATTGGTCACATACAAAGGC R 2 1 2 1 600010 f 74 goat 29_42357272 29 42357272 Ancestral_priority_1043 ancestry 0.732 recommended IMAGE 10K 10K ancestral 320764427 Affx-986698923 AX-385252123 29 42357306 AGCTTCCAGAAAGATAAAATTGGTCACATACAAAG[C/G]CTCAAAAATCACAACGAATTCAGACTTCTCAACAA S 4 1 2 1 600010 f 74 goat 29_42357306 29 42357306 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320804357 Affx-986696524 AX-385290964 29 42357310 TCCAGAAAGATAAAATTGGTCACATACAAAGGCTC[A/G]AAAATCACAACGAATTCAGACTTCTCAACAAGAAT R 2 1 2 1 600010 r 74 goat 29_42357310 29 42357310 Ancestral_priority_1043 ancestry 0.664 recommended IMAGE 10K 10K ancestral 320764432 Affx-986698925 AX-385252128 29 42357948 GTGTACTTGATATTCCTCGATTTTTATATGAATCG[C/T]CTTTCACATTCACATATACATACTTATATATTTAT Y 2 1 2 1 600010 f 74 goat 29_42357948 29 42357948 Ancestral_priority_1043 ancestry 0.64 recommended IMAGE 10K 10K ancestral 38451360 Affx-122921249 AX-123321693 29 42380756 TGAGTTAAGTATTGCTTAAAAGGTGCAGTGTGGGG[G/T]AGGCCATCTTTCCAGGTATGCCTCGTGGCTGCGTG K 2 1 2 1 101000 f 74 goat snp23324-scaffold2330-38711 29 44954801 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446314 Affx-122925638 AX-123316650 29 42414125 GAGCCCCGCCCCTGCTCCCAAAGCCCTCCAGACCT[G/T]TCACTCTTTAATAACCTCACCTTGGTACCCCTGTC K 2 1 2 1 101000 r 74 goat snp23325-scaffold2330-72080 29 44988172 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419337 Affx-122945651 AX-123289685 29 42459140 TTTCTCTGAGGCAGGAATCTGGACACAGCTTAGTC[A/G]GAGCTTCTGGCTGAGTGTCTCTCAAGGCCTGATTT R 2 1 2 1 201000 r 74 goat snp23326-scaffold2330-117095 29 45031256 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443220 Affx-122927573 AX-123313557 29 42526423 TTGCCCTGAAACCCTCAGTGGCTGAGCCAGAGACA[A/G]CGGGGAAAGTCATCTACTTTAATACCTCACTGGAT R 2 1 2 1 101000 r 74 goat snp23327-scaffold2330-184378 29 45098688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429966 Affx-122938064 AX-123300307 29 42564023 GTCTTTGTACTCCACAGAAAGCAGAAATGTAAAGA[C/T]GCAGACTGTGACCCCTGTTTCCAAACTGTGTGTCC Y 2 1 2 1 101000 f 74 goat snp23328-scaffold2330-221978 29 45136160 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398797 Affx-122961416 AX-123269152 29 42597049 CTTTTATGGCTGTGTGGTTTGTAACTATTATCCAA[C/T]GGGCTTGTCTTTTCCTAATGAGTGCTAAATTTACA Y 2 1 2 1 101000 f 74 goat snp23329-scaffold2330-255004 29 45169117 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450083 Affx-122922795 AX-123320418 29 42645025 CCCTTTGCTCTGTTGTGACTTTCAGTAATGTCCCC[A/G]TGCCCCCTGGATTTTAATCTTCACACTTACTGCCT R 2 1 2 1 201000 r 74 goat snp23330-scaffold2330-302980 29 45217704 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277854 Affx-1111836123 AX-519551350 29 42682910 TCTTTGACTTAACTGGGGTACTCGGAATATTCTTC[A/G]TCTCTAGAAAAGATCCCGGTCCCCCCTTCACTCAG R 2 1 2 1 101000 f 74 goat Random2.2K-2340 29 42682910 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38435641 Affx-122933765 AX-123305981 29 42719631 ACAGTCCATGGGGTTGCAAGTTGGACACGACTGAG[C/T]GACATTTACTTTACTTTACTAGACTGATTTATGAG Y 2 1 2 1 103000 f 74 goat snp23331-scaffold2330-377586 29 45288600 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431198 Affx-122937168 AX-123301539 29 42752158 GTATTTTCATTCAAAAAACAACTGCTTCATCCTAC[A/G]ATTAAAACGTCCTCTTGCTCACCAGCTCAGGTAGG R 2 1 2 1 101000 r 74 goat snp23332-scaffold2330-410113 29 45321426 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382231 Affx-122973966 AX-123252589 29 42805005 TTCACTGCAGAGTGAGGACTCTTCTCTGCAGTACA[C/T]ATGCTCTCTACTTGCAGCACACACATTTACTTGAG Y 2 1 2 1 101000 r 74 goat snp23333-scaffold2330-462960 29 45374826 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401942 Affx-122958808 AX-123272295 29 42870474 ATAAGTCAGATTGTGGAAAGCCAGGGATTTCCCTG[A/G]TTTCCAATTCTGATTCTGCTATTTACCAGTTCTGT R 2 1 2 1 101000 r 74 goat snp23334-scaffold2330-528429 29 45440297 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412344 Affx-122950835 AX-123282693 29 42904474 ATAAAGTTCTGTATTTTGTATTTTGGGAGGGATGT[A/G]TGTGATCTCTTATGGAAATAAATTTCTACTTAGTA R 2 1 2 1 201000 r 74 goat snp23335-scaffold2330-562429 29 45474249 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796267 Affx-122978311 AX-385283217 29 42935227 TCCCACAGTATGGTACATACTCAGGATTCTTTTAA[A/G]TATAGGAATCTGTGAGGTCAAAACTGTCTTTGTAG R 2 1 2 1 201000 r 74 goat snp23336-scaffold2330-593182 29 45505077 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437905 Affx-122931656 AX-123308243 29 42988590 CACACATACTTGTTACTCTGCTGTAAACCGAGCAA[G/T]CCATTTTACCACCAGAGTTAGGTGTATAGGAGGGC K 2 1 2 1 101000 f 74 goat snp23337-scaffold2330-646545 29 45558515 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395484 Affx-122963899 AX-123265839 29 43020979 TTGCACATTCCCGTTCTCTGACCTTGGACTTTGGC[C/T]CTTCTTCCCCAGGCATAGCCCTTTCCGGCAGCACA Y 2 1 2 1 201000 r 74 goat snp23338-scaffold2330-678934 29 45588418 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787383 Affx-122944505 AX-385274408 29 43053661 CCCCACATTCTGGCCTAACTCAGGCCAGACATAAT[G/T]GTGGAGGTTGGGAAACAGTTTGGGTGAAGAAGGCT K 2 1 2 1 202000 r 74 goat snp23339-scaffold2330-711616 29 45620969 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404962 Affx-122956415 AX-123275314 29 43144521 GTCAGGTAGGAGATCAGAGGCAGAAGCCCTGTGGA[C/T]GCCTCCAGGGCCTGCCCTGCTTTGAGCCGGGTGCC Y 2 1 2 1 103000 f 74 goat snp1563-scaffold10434-6585 29 42758516 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398569 Affx-122961508 AX-123268924 29 43172630 CTTGCTCACCTGCCCCTACATTTAGGTTCTGAGTC[A/G]TGGCCCTACCTCTCACTTGCTGTGTGACCTCGGTA R 2 1 2 1 101000 f 74 goat snp24770-scaffold2531-21425 29 46405421 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399738 Affx-122960333 AX-123270093 29 43209038 AAATGAATATTCATAAAGTGTCTACTGTTTCATTT[C/T]CCTTTTTCCTATCCATATCTCCATTCAGATCCCTC Y 2 1 2 1 101000 r 74 goat snp24771-scaffold2531-57833 29 46441549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377585 Affx-122977429 AX-123247944 29 43271652 AGCCATAAATACTGGCCATGGCGTCATGACCGTTG[C/T]AGCAGTGGCGCCCCCGACCATGTGTCCTTCATGGC Y 2 1 2 1 101000 f 74 goat snp24772-scaffold2531-120447 29 46499162 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453729 Affx-122919623 AX-123324062 29 43352393 GGACCTCCCAATAGCTTGTGACAATCGTCATCCCC[A/G]TGGTTCTTAGTATTTTTTATGATTTCTTAAAATAG R 2 1 2 1 101000 f 74 goat snp32658-scaffold3751-12020 29 46580025 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439898 Affx-122930029 AX-123310235 29 43372720 GACAAGTGTTCAGCCCCATAGATACAGCGAGTGCT[A/G]TGTTGAGTCCACAATGTCTAGGTAGGGAGACAGTC R 2 1 2 1 101000 r 74 goat snp40848-scaffold5251-9667 29 46600056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442690 Affx-122927882 AX-123313027 29 43383668 CCTTGGGGCACTGCCTACACTTACTGATCCAAAGA[A/C]CACCCTGCCCCTTCTAAGAAGCATCTGGAGAGATT M 2 1 2 1 201000 f 74 goat snp17578-scaffold182-862350 29 46608534 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376056 Affx-122978928 AX-123246415 29 43419799 TATGTAAATGTATATTTCTGAAGCCAGCGTGAATC[A/G]TTTCCAGTGGAGGTATTGCCTTCTCTGCTGAGAAA R 2 1 2 1 101000 f 74 goat snp17577-scaffold182-826219 29 46642558 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384280 Affx-122972302 AX-123254638 29 43450597 AGACACGACTGAAGCGACTTAGCAGCAAAAGCTGT[A/G]TCACAGTAGTCCAGGGGCTGGTGATGAAACAATAA R 2 1 2 1 101000 r 74 goat snp17576-scaffold182-795421 29 46673437 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377182 Affx-122978201 AX-123247541 29 43503439 CCAGCAGTTTTTCCTTCCATCACCACCACAGCAGC[A/G]CCACCTCTCAAGTTGTACCCTTGCACGCTTTTTGT R 2 1 2 1 101000 r 74 goat snp17575-scaffold182-742579 29 46726258 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435639 Affx-122933767 AX-123305979 29 43567940 TATGACTAAAGAACTGTAAGCATCTCCTTCAGAGA[A/G]GCAGTATAGATTAATATTTGAGCTGACTCTAGAGT R 2 1 2 1 101000 r 74 goat snp17574-scaffold182-678078 29 46791144 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429004 Affx-122938845 AX-123299346 29 43632730 GGACTAAAGGCCCAGAGAGTCTGGAAAACTGCCCC[C/T]TCACAGGTCCAAAGTCCCTAACACAATCCTTCAGG Y 2 1 2 1 101000 r 74 goat snp17573-scaffold182-613288 29 46855996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392049 Affx-122966397 AX-123262406 29 43689683 CAGGTGGCCATCTCACCAACACCGGTAAGCGCCTT[A/C]CCCTTTGTCACCCTGGCCGTATTGTGCTTTGTTGT M 2 1 2 1 101000 r 74 goat snp17572-scaffold182-556335 29 46912378 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432117 Affx-122936451 AX-123302458 29 43817396 GGGAGGCAGGAAATCAAACACAGTTTGCTAAAGGC[C/T]GCAGAGAAATTCTTAGGTTGTCTTCAAGCTCCTCA Y 2 1 2 1 101000 r 74 goat snp17570-scaffold182-428622 29 47036049 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375508 Affx-122979125 AX-123245867 29 43850570 AAACCCAGCAAGCGGTACCCACCCGCTCTCCCTTT[A/C]GGCACCTCCCCAGCCCCATCCACTACAGCAACACG M 2 1 2 1 103000 f 74 goat snp17569-scaffold182-395448 29 47069283 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446362 Affx-122925599 AX-123316698 29 43900649 CAGGGGTGGGACCTCTGCCTTCAGCCCAGCACTGC[A/G]TTGTCAGGCTGACTGAATGTGCACGCCTGTGTCCT R 2 1 2 1 103000 r 74 goat snp17568-scaffold182-345369 29 47119551 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273242 Affx-1111833365 AX-519546895 29 43948563 CCCTCAGGCCTCTGACGCCAGAGAAGCTGTTGGTC[A/C]CTTGCACTAGGCCTGTGTTTAATCCTTGGCTCTTG M 2 1 2 1 101000 r 74 goat 29_43948563_AF-PAKI 29 43948563 G T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38438991 Affx-122930375 AX-123309328 29 43971595 CTTTCTCGGAACCTTTTTCAGACGGCTTGAAGTGT[C/T]GGACATTCCATCTTGCTACCAGGCCAGACTTGTGT Y 2 1 2 1 101000 f 74 goat snp17567-scaffold182-274423 29 47190465 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385394 Affx-122971348 AX-123255752 29 44007729 TAGGAATGCATTCGCTGTGTGTTGAAGCTCACTTG[C/T]CTTTCCGTGAACATTCCCCCTAACGCTGTGCGTTT Y 2 1 2 1 101000 f 74 goat snp17566-scaffold182-238289 29 47226986 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416865 Affx-122948091 AX-123287213 29 44041920 TTAGCATTAAGGTTTCAGTGCCAGGAGTCACGCGG[C/T]CCAAAGATCCTCTCAGCTCTCACTCCCGGTATAGG Y 2 1 2 1 101000 f 74 goat snp17565-scaffold182-204098 29 47261051 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798384 Affx-122935037 AX-385285318 29 44072360 TCTCTGTCATTGCCTAACATACATAGTCCATGGAT[A/G]TTGTTACAAAATAGGCTCTGTTTTTCGACGTTTAG R 2 1 2 1 202000 r 74 goat snp17564-scaffold182-173658 29 47291731 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391232 Affx-122967393 AX-123261589 29 44132271 ATGGATTCACCCTCTCTGGGCCCGATGAGGGTTTA[C/T]AGCTGACTCCTTCCCTGCAGAATGCTCATCTGTCT Y 2 1 2 1 101000 r 74 goat snp17563-scaffold182-113747 29 47356456 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791454 Affx-122937801 AX-385278445 29 44167621 TAAAACTCACGGAAACTCCGCTTCAGTGAGTCAGA[C/T]GCCGGCAGCGAGTTTCCTGGCAACTCAGGAGACGG Y 2 1 2 1 202000 r 74 goat snp17562-scaffold182-78397 29 47391643 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425998 Affx-122941143 AX-123296344 29 44242737 GGTGTTTCCGGATTTACTATCCTTTGAAAACCATC[A/G]TCATGGTTTCTATAAAACCTGCACGTACTTACTAT R 2 1 2 1 101000 r 74 goat snp17561-scaffold182-3281 29 47443099 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441447 Affx-122928770 AX-123311784 29 44275251 CAGACCACCTTACCTGCTTCCTGAGGAACCTGTAC[G/T]CAGGACAAGAAGCAACAGTTTCAGAGCGACAGGCT K 2 1 2 1 103000 f 74 goat snp14554-scaffold1587-844866 29 47476134 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442945 Affx-122928225 AX-123313282 29 44307300 AGAAAGAGCCCCACTGCCTCCAACGTGTGGCCTTG[A/G]GGAGAATCTCCTGTCCTCTCAGAAACACCACCCTC R 2 1 2 1 303000 r 74 goat snp14553-scaffold1587-812817 29 47507531 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422294 Affx-122943482 AX-123292640 29 44354352 GCGCGCTTCCCAGCCCTTCGCAGTCCTGTGGACCG[C/T]ATTCCCGCTTGGGAGCGGGCAAGGCTAACATACAT Y 2 1 2 1 202000 f 74 goat snp14552-scaffold1587-765765 29 47555203 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407561 Affx-122954678 AX-123277912 29 44428644 AACACCCCAGAGTGTGTGTGAGCATGTGTGTGTGG[C/T]GGGGCATAAGAGGGATATAAGAAAGTGGTGCTAAC Y 2 1 2 1 202000 r 74 goat snp14550-scaffold1587-691473 29 47630077 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392489 Affx-122966138 AX-123262846 29 44472168 CACTAAGCCATGTAACAGGAGCTAGCGTAGCTGTC[A/G]CTGTTGTTCAGTCACTAAGTCAGGTCCGACTGTCT R 2 1 2 1 103000 f 74 goat snp14549-scaffold1587-647949 29 47667204 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390275 Affx-122967741 AX-123260632 29 44516976 TGCAGGGGTCCCCGAACCATTGGTGGATGGGGTCG[C/T]CTGGGCCAGTGCTGCACTGAGATATTATTGCCCTG Y 2 1 2 1 101000 r 74 goat snp14548-scaffold1587-603141 29 47714224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385274 Affx-122972072 AX-123255632 29 44566361 TAGAGCCAGTTTCTGGCTCCTTGGGAAACAAGAGG[A/C]GCCTTCAGGACTTCCTCGATTCTGGAAAGGCTGAG M 2 1 2 1 201000 r 74 goat snp14547-scaffold1587-553756 29 47762830 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454075 Affx-122919381 AX-123324408 29 44651878 GGTCTGTAGGCCCCAGACTAGGTGAGGTCAGTGTT[A/G]TGGTCTACTACATAATTAATTTTTGTAAAAGTCCA R 2 1 2 1 201000 r 74 goat snp14546-scaffold1587-468239 29 47847605 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767337 Affx-122934425 AX-385254613 29 44682117 AATGGGCAAAAAAATAGAGCATATGATATAATTAC[A/G]TATAATGAAATTTTCTAGATACGTGTGTGTGATAG R 2 1 2 1 101000 f 74 goat snp14545-scaffold1587-438000 29 47877848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447472 Affx-122924351 AX-123317808 29 44727089 TGAACAGCATAAAGGAAACCCTGCAAGGAGAAATT[G/T]CAGGGTATGCACTTGGCTGAAAAGCAAAGGGTCTC K 2 1 2 1 102000 f 74 goat snp14544-scaffold1587-393028 29 47922546 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278001 Affx-1111836124 AX-519551493 29 44737101 CTGAGGACTGGAAGGAATTGAGAGTCACAGGCTGG[A/G]CACACAGAGCTAACCAGCTCCTGGAAGAAAGTCTC R 2 1 2 1 102000 r 74 goat Random2.2K-2341 29 44737101 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38447735 Affx-122924592 AX-123318071 29 44783798 TCTAGGATGATGAACAGTGTCCCCAGCCACTACCG[A/G]CAATGCACCAGTAACACCCCCCTGCCCCAGTCATG R 2 1 2 1 201000 f 74 goat snp14543-scaffold1587-336319 29 47979203 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391793 Affx-122967040 AX-123262150 29 44824736 GATAGAGGCCCAGAGACTTAAGCTGCCCATCTCTG[A/G]GTGGGGGAATCTTAAAAGCACTGCGTGGGCGTCTG R 2 1 2 1 201000 f 74 goat snp14542-scaffold1587-295381 29 48020353 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398435 Affx-122961616 AX-123268790 29 44862940 AGGGCCTCACCGCCAGAGAAAGGGGTAGAGTCAGA[C/T]GGCCCTTACAGCCGCCGAGAATGGAACACAGCCAC Y 2 1 2 1 201000 r 74 goat snp14541-scaffold1587-257177 29 48058445 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436548 Affx-122932920 AX-123306886 29 44896947 TGACTTTGCTGGAAGCAAACTTGGGGCCAGAGAAT[A/C]AAGACTCCTCTGCTCAGCCCTGGACCCTCAGCCTA M 2 1 2 1 101000 f 74 goat snp14540-scaffold1587-223170 29 48092656 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397956 Affx-122961909 AX-123268311 29 44945480 GTGGTAGGTGGATCCTCGTTTTCCTAAAATAAGTT[C/T]TTTCCGTTGCTTGGTGGCGACGCAGCCGGAGCCCT Y 2 1 2 1 101000 f 74 goat snp14539-scaffold1587-174637 29 48140601 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468277858 Affx-1111836125 AX-519551354 29 44950796 CAGACCTGGGTTTGTCAAATTCCCCATCACATGTT[C/G]CATTACAGCTCAGCCCTCACCAAGGGCAGTGAATC S 4 1 2 1 102000 f 74 goat Random2.2K-2343 29 44950796 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38377779 Affx-122977333 AX-123248138 29 44983365 AATACACATTCATCTACCAAGCATCCATCCATCCA[G/T]CCATCCATCCATCTATCCATCAAACACCCATCCAT K 2 1 2 1 103000 f 74 goat snp14538-scaffold1587-136752 29 48178825 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407740 Affx-122954991 AX-123278091 29 45032355 CACACCTGGTGCTTTCTCGCCCCAGGACTATCCAG[C/T]GAGTCCTCAGTAAAGTGAAGGAGCAGATGGCATTC Y 2 1 2 1 101000 r 74 goat snp14537-scaffold1587-87762 29 48226909 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445618 Affx-122925102 AX-123315955 29 45062225 CGGATATTTACAAAGTGATCTAAGAATACATCTCT[A/C]AGCATTTCATCGATGGGCAAATGGTGAACCTCTTT M 2 1 2 1 101000 f 74 goat snp14536-scaffold1587-57892 29 48257089 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405767 Affx-122956494 AX-123276119 29 45091254 AGTATGCATAACAGTGCCAGGAAAATAGCAAGTGA[C/T]CAAAGCACCACCTGCAGAATGCATGAACGAGCTAG Y 2 1 2 1 101000 f 74 goat snp14535-scaffold1587-28863 29 48286506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385954 Affx-122971542 AX-123256312 29 45145808 AAGGGACCCCCATGGGGAGAGGGTTCCCTCTGCAC[A/G]CTTTGGTCAGAAAGGTTTTGCACCTGTGGTTCAGA R 2 1 2 1 101000 r 74 goat snp19382-scaffold1959-388873 29 48341100 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449331 Affx-122922987 AX-123319666 29 45192949 TCCACCTCGTACCGCTGCTTCTTCTTCGCGTGCTC[A/G]TCGTGGTCCGAGGGGCTCTGGTGCTTCAGCCTCAG R 2 1 2 1 201000 f 74 goat snp19381-scaffold1959-341732 29 48388060 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394468 Affx-122964572 AX-123264823 29 45230973 GGGGGCCCTAGAAGGTACACACATGTCAAATCTCT[A/G]GAACTGTGAATGGGAACTTTCTTGGAAAAGGGTCT R 2 1 2 1 101000 r 74 goat snp19380-scaffold1959-303708 29 48425920 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453676 Affx-122919709 AX-123324009 29 45269268 GCTGCCCCAAAGCCGTTGGCATTATCCATCCTGGC[A/G]CCACCCCCTGCTATGTGGGAAACAATACCGACCTC R 2 1 2 1 201000 f 74 goat snp19379-scaffold1959-265413 29 48464532 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407260 Affx-122955351 AX-123277611 29 45300580 TCCCCCGACCCTCTCCAGGCAGGGGATTAGCTGGC[A/G]TGTCTCTTACAAAGAAGGCCCAGCTAGTTTGTGAG R 2 1 2 1 101000 r 74 goat snp19378-scaffold1959-234101 29 48495822 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402642 Affx-122958388 AX-123272995 29 45356213 AATCTAAAAATGCACGCCTAGGTCCACTCTTTAAA[C/T]GCGTCTACAAACAGGTGTAAAAAGGCGATTCACGT Y 2 1 2 1 201000 f 74 goat snp19377-scaffold1959-178468 29 48551052 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375818 Affx-122978556 AX-123246177 29 45396893 CTCCCCACAGCAGCCCAGGAGAGCTCACGCTTGCT[C/T]GCTTCACATTCTCAGGCAAGTCGATCCATTACATT Y 2 1 2 1 101000 r 74 goat snp19376-scaffold1959-137788 29 48589633 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278004 Affx-1111836126 AX-519551496 29 45431714 CTCCAGGCGTGTGTGAAGGGCGTGCTCCAGGGTCC[A/G]TCAGAGTGCAACCAGTGACAGCGGTAGTAGCAATA R 2 1 2 1 102000 r 74 goat Random2.2K-2344 29 45431714 A G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 38405237 Affx-122956886 AX-123275589 29 45453325 CCCTCCTCGCTGGGGAGAAACCCCATAAACTCCTG[A/G]CGGCTACTCAAAACCGTCCAGCTCAGCAAAAGCAA R 2 1 2 1 101000 r 74 goat snp19375-scaffold1959-81356 29 48643720 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438551 Affx-122931179 AX-123308889 29 45529998 GTCTGCTGTAAACAGACGAGACTAAACAGAACAGA[A/C]TTTTCGTGCTGAATGGGCTCTGTGCGTGGTGGAGG M 2 1 2 1 101000 f 74 goat snp19374-scaffold1959-4683 29 48720245 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380907 Affx-122975029 AX-123251265 29 45559379 CAGTAGCTTTGTCTATAACAGCCAAAACCTGGAAA[C/T]GACCCCAACATCCACTAATGGAAAGTGAAGTGGAG Y 2 1 2 1 202000 r 74 goat snp13753-scaffold1534-24599 29 48752040 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794174 Affx-122921174 AX-385281140 29 45612996 GGACCTGAATGTAACAGAGGGGTCAAGTGGTCCTG[C/T]CTAAAGTTCATTTAGCAAGAGAGGAGTTTGAGAGC Y 2 1 2 1 101000 f 74 goat snp13754-scaffold1534-78216 29 48803689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402376 Affx-122959033 AX-123272729 29 45668298 GTCCTTTATCTGTTCATCCAGTCACCTGTCTACCC[A/G]TCCTGTCCATTCAGCCACCCATCCGCCATCTATTC R 2 1 2 1 101000 f 74 goat snp13755-scaffold1534-133518 29 48859040 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450795 Affx-122921817 AX-123321129 29 45707882 AGACGGGCAAGCCCTCCGCCGGACCAGGATGATGG[C/T]AATCCCTCGGACCACTTTCTCCAAAAATTGGTGCT Y 2 1 2 1 101000 r 74 goat snp13756-scaffold1534-173102 29 48897748 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448121 Affx-122924303 AX-123318457 29 45742219 AGACCTAAAGGCGAAAAGACGGTGTGCATTTCCAG[C/T]TTGCCAGCAGCGAGGCTGACATCAGACGCCCTGCG Y 2 1 2 1 101000 f 74 goat snp11231-scaffold1402-16116 29 48929682 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434304 Affx-122934758 AX-123304645 29 45788982 TGACTGCCAGGGATGAAATGCAGGAGCAGAAACTG[C/T]GTCCTCTTACATTTACACAGGGCCATTGTCTCCCC Y 2 1 2 1 101000 r 74 goat snp11232-scaffold1402-62879 29 48972855 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402597 Affx-122958425 AX-123272950 29 45819135 CCAAAACCGTCCACGCTGATACAGTATGTGACAGG[C/T]GTGTATCAAGTAACACCGGAACCGAAAGGAAAGCA Y 2 1 2 1 201000 r 74 goat snp11233-scaffold1402-93032 29 49003096 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435151 Affx-122933670 AX-123305491 29 45852821 ATCACTCAGGTCACAGCAAGATGGCTGGCGCTGCA[C/T]GGGTGGACGTGAAAGTACTAATACTTAGCAACTAA Y 2 1 2 1 101000 r 74 goat snp11234-scaffold1402-126718 29 49035695 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468278006 Affx-1111836127 AX-519551498 29 45887042 AACATGCAAATAAACTCTGATATTACTTCAGCATC[A/G]TCCTTTCCAGCCCGACGAAGTGAGTAAAAATTTTA R 2 1 2 1 101000 r 74 goat Random2.2K-2345 29 45887042 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38394513 Affx-122964541 AX-123264868 29 45906134 CTTCCTAAATACTGGGCAGGACATGGGGTGCAAGG[C/T]GCTCAGTCGTGTCCGACTCTTTGTAAACCACTGGA Y 2 1 2 1 102000 f 74 goat snp11235-scaffold1402-180031 29 49086673 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427104 Affx-122939672 AX-123297447 29 45950072 TGCAAAAAAATACCCAATGGGCCTGAACTACATTC[C/T]AACGTCCTAGTCGCTGGATTAAATATTACTCTGAA Y 2 1 2 1 101000 r 74 goat snp11236-scaffold1402-223969 29 49129903 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427929 Affx-122939219 AX-123298272 29 46013910 CTTCTGGGTCGTAGAGGGCATTCCCAGTTCACATC[C/T]GCATTCTCTGAGCACAGATAAGTTTGACCGTCTCG Y 2 1 2 1 101000 r 74 goat snp11237-scaffold1402-287807 29 49193187 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397921 Affx-122961935 AX-123268276 29 46044539 TATGATAGCCACGCTTGAGAAAAGAAATCAGTAAA[C/T]GGGGTTAGCGGTAAACATATACTTGTTTCCATGAA Y 2 1 2 1 201000 f 74 goat snp11238-scaffold1402-318436 29 49223430 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391369 Affx-122967281 AX-123261726 29 46084801 CCACTTGGGAAAGAGTTTTAAAAATGATGGACCCC[A/G]TTGGAAGGACTGATGTTGAGGCTGAAACTCCAATA R 2 1 2 1 101000 f 74 goat snp11239-scaffold1402-358698 29 49263491 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792468 Affx-122950863 AX-385279449 29 46119011 GGAATTCCTGAGACTTTGAGAATTGAATTCCAGAC[C/T]GTTTCAGACGTAATTTGGTTAAGTCCCTACTTGGA Y 2 1 2 1 101000 f 74 goat snp11240-scaffold1402-392908 29 49298356 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782091 Affx-122954879 AX-385269169 29 46158519 AAGATGTCAAACACGCAAACCAGTTGAATAAATAG[C/T]AAAGTGAACACCCACACACCTAGATTCAGCAGCTG Y 2 1 2 1 101000 r 74 goat snp11241-scaffold1402-432416 29 49337020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413270 Affx-122950217 AX-123283619 29 46189740 CGGTTTTTCTCCAAGTATTCCATGAACAGACACAA[A/G]ATGACCACACTGACCCCCGCGTACCACGCCGAGAG R 2 1 2 1 101000 f 74 goat snp11242-scaffold1402-463637 29 49364498 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402383 Affx-122959029 AX-123272736 29 46221147 GCCCCTTCTCTGAAAAAAATTTACCATCAACTACA[C/T]GAAAAAATGCTTCCTCTTCCAAGTGATTCATGGAA Y 2 1 2 1 101000 r 74 goat snp11243-scaffold1402-495044 29 49395773 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444594 Affx-122926956 AX-123314931 29 46260177 GGCGGCCCCAAACCCTTGACCTAACAACCCAGATA[C/T]GCCAGACTTTCCTAGGAGGTTTTCAGATGGACAAT Y 2 1 2 1 101000 r 74 goat snp11244-scaffold1402-534074 29 49435407 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436292 Affx-122932525 AX-123306631 29 46315124 CACTCACTCAGGACATCAGGACAAAGGCCGCTTCT[A/G]TGGGTCAGCTTGCACTCAGGAGATGCTAAGAGCTA R 2 1 2 1 201000 f 74 goat snp42680-scaffold5667-24602 29 49491423 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409897 Affx-122952898 AX-123280248 29 46376410 AATACTCATGTAATTTAAAATTCAATGGCAAACAA[C/T]GTAAAGCAGCCCTGCTTTCTCTGAAGAGGACAAGG Y 2 1 2 1 101000 r 74 goat snp48827-scaffold695-225820 29 49654641 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382839 Affx-122973542 AX-123253197 29 46433584 TGATGAAATGATTTCAAAGTTCTGAGCACTGCTCT[C/T]GCACGACCCCACCCCAGGCCCACTCTTGATGTGGC Y 2 1 2 1 101000 f 74 goat snp48826-scaffold695-168646 29 49708185 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435811 Affx-122932843 AX-123306150 29 46487907 GGCACTTGCTGTGGGGCTGGGGAGAGGGCTTCCCC[A/G]CATGGCCTCCCTTAGACAGTAGCCCCCAGGCCCCA R 2 1 2 1 101000 r 74 goat snp48825-scaffold695-114323 29 49757396 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395594 Affx-122963827 AX-123265949 29 46525657 AGGGTGATTTATGGGCGTTATTCCCGCGCTCTTGC[C/T]ATGGGGGAGGGGTGTTCCCAAGTCCCGAGGAGTCA Y 2 1 2 1 101000 f 74 goat snp48824-scaffold695-76573 29 49792683 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785817 Affx-122932703 AX-385272855 29 46578150 CTCTTTCTCATTTATAAAAAATCACTTTGTTCTCT[A/G]TACTGTATTCTGGATACTGTCTTCTGATCCGTCTT R 2 1 2 1 201000 f 74 goat snp48823-scaffold695-24080 29 49845337 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394696 Affx-122964352 AX-123265051 29 46607074 CCCTGGAGCAGTCTTGTCTGTTCTTGAGGCTGCAT[A/G]GGATCAGATTTGCCTACAGCTTTGTCACTGGCGGG R 2 1 2 1 201000 r 74 goat snp29452-scaffold3187-246792 29 49874119 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422037 Affx-122943618 AX-123292384 29 46646767 TGCTTCAGGTTATCCGCTCTGAATGTCAAGGGGAC[A/G]AGCTGCCAGGGCCAGACCAACTCCAGGGAGACGAC R 2 1 2 1 201000 f 74 goat snp29451-scaffold3187-207099 29 49913522 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453727 Affx-122919625 AX-123324060 29 46679131 ACAGGGTGTATCAAGTGGATCGTAGCCTACGAACT[A/G]TAGTGGAGAGACTGTCCACCAAGTACAGTGACCAT R 2 1 2 1 101000 f 74 goat snp29450-scaffold3187-174735 29 49945660 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423555 Affx-122942423 AX-123293901 29 46720940 TTGGACTTTGGTTCGTTTCTCAATTCACAGGTAAC[A/G]TGAAGGCCACACTGTTCTGCTCCTTACTGTGGCTA R 2 1 2 1 101000 f 74 goat snp29449-scaffold3187-132926 29 49987423 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796016 Affx-122953965 AX-385282968 29 46773997 AATGAAAAACGCAAATACCCTTCAAAACCCTGACA[G/T]AATTTTATTCTACACTGATATTACACATTTACAAA K 2 1 2 1 101000 f 74 goat snp29448-scaffold3187-79869 29 50040131 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273243 Affx-1111833366 AX-519546896 29 46830837 ACCTAACCAGCCAGCCCTCAGTTTTCCCATCTATA[A/G]AATGAGCAGAATCCCTCTTCTGGTAGGAGGATTTC R 2 1 2 1 201000 r 74 goat 29_46830837_AF-PAKI 29 46830837 A G 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 38385592 Affx-122971208 AX-123255950 29 46833177 ACGTTCTGCTGTTGTTGGAAGGGCTGTCCTGTAAA[C/T]GTCAATTAGGTCCTTGTGATTGGCAGTGTTCTTGT Y 2 1 2 1 101000 f 74 goat snp29447-scaffold3187-20689 29 50092149 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427373 Affx-122940094 AX-123297716 29 46870731 TAGAATAGAGAGTCCAGAGATTAAACACACACATA[C/T]ACCGCATATACAGCCAATCAACTCACCACAAAGGG Y 2 1 2 1 101000 r 74 goat snp11292-scaffold1407-16766 29 50130491 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406042 Affx-122955479 AX-123276394 29 46911268 ACCACTCACCGTACCCATAGACCTTAGAGACCCCA[C/T]AGACCCACAAATCCCCGGGCTGGGTCACCTCAGGC Y 2 1 2 1 201000 r 74 goat snp11293-scaffold1407-57303 29 50170355 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408625 Affx-122953491 AX-123278976 29 46982452 AAGGGAAGGGCTCCAAACCCTGCCACGTCTCTCTC[C/T]CTCACTCTCTTTCTCTCCTTCTTTTTCCATATATA Y 2 1 2 1 101000 f 74 goat snp11294-scaffold1407-128487 29 50242034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376060 Affx-122978926 AX-123246419 29 47012421 CAGCATGTTAGCTGTCTGCGGCTGTGTGAGGCAGC[C/T]TGGCCCCAAATGTGGTACAGCAGGTCCCCTGCATG Y 2 1 2 1 202000 r 74 goat snp11295-scaffold1407-158456 29 50271854 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774808 Affx-122941651 AX-385261942 29 47055321 CTTCCCTAGTAAACAAGTTTTATAATGGGGATTGC[A/G]TTTTAAATGTTATGGAACATGTTTGGGCACTTATC R 2 1 2 1 102000 f 74 goat snp26537-scaffold2765-185379 29 50448685 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390734 Affx-122967916 AX-123261091 29 47129643 ACTTTAATGCCCCATTTGAGTCTTTTCTCCTGCAC[A/G]GACTGTGAGCTCCTTGAGGACAGACTCAGGGAAGG R 2 1 2 1 103000 f 74 goat snp26536-scaffold2765-111057 29 50514063 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417782 Affx-122947389 AX-123288130 29 47316632 TGAGGAGCTCCTACAAATAATAACTTAAAAAAAGA[A/G]CCTGACGTGTTACAGAGTTCAAGCTCATTCTACTC R 2 1 2 1 101000 r 74 goat snp27795-scaffold2976-18538 29 50693518 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445723 Affx-122926101 AX-123316060 29 47341229 ATTCTGCCAGTGCAGGGGTCCAGGTTCACCTCCTC[A/G]TCAGGGGGCTAGATCCCACAAGCCACAGCTAAAGA R 2 1 2 1 201000 f 74 goat snp15822-scaffold16584-5960 29 50718474 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381796 Affx-122974286 AX-123252154 29 47381929 AAATCAGAGAGGAGACTGCCAAGGAGCAATCTGTG[A/C]GGGGCTTCACAGGCACTTTTTAGCAGAAAAATGGC M 2 1 2 1 201000 f 74 goat snp22695-scaffold2252-58996 29 50745738 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443418 Affx-122927376 AX-123313755 29 47438716 GTGACACTCAGTGACATCAGCCAGGCTCAGAAGGA[C/T]GACTGCTGTCCGACTCCACTCTCAGGAGGTCCCTG Y 2 1 2 1 202000 r 74 goat snp22694-scaffold2252-2209 29 50789150 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447953 Affx-122923775 AX-123318289 29 47447525 GGAGTGAGGCTTTCGAGGGCAGAGAGCAGAGTCAA[C/T]GTGAGCTCTTCGAGTACAGCGGGCCGGCCTCCTGA Y 2 1 2 1 101000 f 74 goat snp22987-scaffold2294-293113 29 50812356 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416723 Affx-122947549 AX-123287071 29 47566408 CTCACAGTTCATCTGTGCTTAACCTGTGGGAATCG[C/T]CCAGTGAAGCCGGGGCTGGGTTCTCAGCTGCCTTG Y 2 1 2 1 101000 f 74 goat snp22985-scaffold2294-174230 29 50937674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453072 Affx-122920055 AX-123323405 29 47660243 ACATAAGCAGCAACTGGTTTCAGACGCTGGAGGAC[A/G]CGGGGGATGGTGCCCTGGACGGCAAAGAAGGCCTG R 2 1 2 1 101000 f 74 goat snp22984-scaffold2294-80395 29 51019102 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389497 Affx-122968311 AX-123259855 29 47801716 GCCACCTCAGCAAAGCCTTTACTCCTGGGGCCTGA[C/T]GCTCGCTCAGATCTTCGCGCTCACTCATCCTTCAG Y 2 1 2 1 201000 r 74 goat snp25314-scaffold2606-438718 29 45709872 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405764 Affx-122956496 AX-123276116 29 47922865 CCCCGAAGGTTAAGGACTCTGAGCACTTTCTCAGG[G/T]GCTTATTTGCCCACGGAACACGGTTAGGGTTAGGA K 2 1 2 1 201000 r 74 goat snp25311-scaffold2606-317569 29 45808908 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383100 Affx-122973278 AX-123253458 29 47971476 TCTCCAGGTTGCCAGAGCACTGGATCTGAGCTGCG[C/T]ATCACACAGCAAATACCCACAGGCTATCTGTTTTG Y 2 1 2 1 101000 r 74 goat snp25310-scaffold2606-268958 29 45857705 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386673 Affx-122970189 AX-123257031 29 48088034 TCTTTCATGTTCAGAACTTTGTTCTAACAGTTTTT[A/G]TTTTCAAAGAAGCTTGGGGGTCAGCTTATCAGCCA R 2 1 2 1 202000 f 74 goat snp25309-scaffold2606-152400 29 45960691 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400853 Affx-122959778 AX-123271208 29 48143582 CACAGGTCTCTCAGTGTACACACCTGCCTACACCT[A/G]CAACCTTTGCACACCTCTGCACACCCCTGCACACC R 2 1 2 1 102000 f 74 goat snp25308-scaffold2606-96852 29 46029585 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382295 Affx-122973916 AX-123252653 29 48173668 TGGAGCAGAGGAGAGCTGTCCTGAGGGGCCACATC[C/T]AAACTCTCAAACCACGAACTCCAGGAGCTTAAACA Y 2 1 2 1 102000 r 74 goat snp25307-scaffold2606-66766 29 46146541 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468274122 Affx-1111834052 AX-519547725 29 48188235 CTTGCTCCCAGACCACTGCAGCAGGCAGGCAGACC[A/G]GCTTTACCTCCCTTCCCATCCCTTCTAGGGCATTC R 2 1 2 1 303000 f 74 goat GoatD01.015971 29 48188235 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 38401275 Affx-122959280 AX-123271628 29 48208908 GACGCTGTGGTTTAAAAGCAAGAGAAAGACATGAA[C/T]GCATGTCTCTGCGCTGTTAGCTGAAGCACAGATTT Y 2 1 2 1 101000 r 74 goat snp25306-scaffold2606-31526 29 46111286 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453363 Affx-122919942 AX-123323696 29 48301204 CCTTGGAGTTGAGTCCTGGAGACAAGCCCTGAGCT[A/G]CCAGAGGGACCACTGTGAGCCCTGGGTGAGATCCC R 2 1 2 1 201000 f 74 goat snp27542-scaffold2947-60671 NW_017189536.1 4591 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451834 Affx-122921465 AX-123322167 29 48331944 AAGAGCATGGGGAGGAGTGGGAAAGCATTGTTTCC[C/T]TGCTGTGTTTCCTGTACTTTCTGCTGGGAGATTTA Y 2 1 2 1 101000 r 74 goat snp27543-scaffold2947-91411 NW_017189536.1 35710 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391008 Affx-122966891 AX-123261365 29 48364878 GGCAGTTTCCCAGCCGTGTGTCCAGGAGCAGAAGC[C/T]GATGTTCTCACGGGATTCAGGATCTGCCCAGCACC Y 2 1 2 1 101000 r 74 goat snp27544-scaffold2947-124345 NW_017189536.1 68690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 468273197 Affx-1111833367 AX-519546856 29 49331622 AAGGATGGTTTGGTTTGGTTTGGACTGCACTGCTC[A/G]TGGGATCTTAGTCCCCTAATCAGGGACTGAACCCA R 2 1 2 1 103000 f 74 goat 29_49331622_AF-PAKI 29 49331622 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 320804361 Affx-986696528 AX-385290965 29 50828942 TTGCTCGACTCAGTGACTCTAGAGGGAATCAAAAC[A/G]TCAAAGGGTTGAAGGCTCACTCTAAAGACCCCCAA R 2 1 2 1 600010 r 74 goat 29_50828942 29 50828942 Ancestral_priority_1043 ancestry 0.65 recommended IMAGE 10K 10K ancestral 350602325 Affx-1002478943 AX-413836695 MT 56 AAGCAAGGCACTGAAAATGCCTAGATGAGTGTACC[A/G]ACTCCATAAACACATAGGTTTGGTCCCAGCCTTCC R 2 1 2 1 202000 r 74 goat mtdna_00056 MT 56 A G 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602327 Affx-1002478944 AX-413836697 MT 100 AACACATAGGTTTGGTCCCAGCCTTCCTGTTAACT[C/T]TCAACAGACTTACACATGCAAGCATCCACGCCCCG Y 2 1 2 1 202000 r 74 goat mtdna_00100 MT 100 C T 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602329 Affx-1002478945 AX-413836699 MT 227 CTTGTAGCTTATAACGCCTCGCTTAACCACACCCC[C/T]ACGGGAGACAGCAGTGACAAAAATTAAGCCATAAA Y 2 1 2 1 201000 r 74 goat mtdna_00227 MT 227 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603689 Affx-1002479630 AX-413837823 MT 257 ACCCCTACGGGAGACAGCAGTGACAAAAATTAAGC[C/T]ATAAACGAAAGTTTGACTAAGCCATGTTGACCAGG Y 2 1 2 1 101000 r 74 goat mtdna_00257 MT 257 C T 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602282 Affx-1002478946 AX-413836653 MT 289 AGCCATAAACGAAAGTTTGACTAAGCCATGTTGAC[C/T]AGGGTTGGTAAATCTCGTGCCAGCCACCGCGGTCA Y 2 1 2 1 101000 f 74 goat mtdna_00289 MT 289 C T 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602285 Affx-1002478947 AX-413836656 MT 435 TTAAACTGTAAAAAGCCATAATTACAACAAAAATA[A/G]ATGACGAAAGTAACCCTACTGCAGCTGATACACTA R 2 1 2 1 201000 f 74 goat mtdna_00435 MT 435 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603690 Affx-1002479631 AX-413837824 MT 726 CAGCAAACCCTAAAAAGGAACAAAAGTAAGCTCAA[C/T]CACAACACATAAAGACGTTAGGTCAAGGTGTAACC Y 2 1 2 1 101000 r 74 goat mtdna_00726 MT 726 T C 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350603691 Affx-1002479632 AX-413837825 MT 797 CATGGAATGGGAAGAAATGGGCTACATTTTCTACC[C/T]TAAGAAAATTAATACGAAAGCCATTATGAAATTAA Y 2 1 2 1 201000 r 74 goat mtdna_00797 MT 797 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602336 Affx-1002478948 AX-413836704 MT 945 CCGTCACCCTCCTCAAGTAAATACAATGCACTCAA[A/G]CCTATTAACACGCATCAACTACATGAGAGGAGATA R 2 1 2 1 101000 r 74 goat mtdna_00945 MT 945 G A 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603659 Affx-1002479633 AX-413837797 MT 1024 CAAGGTAAGCATACTGGAAAGTGTGCTTGGATAAA[C/T]CAAGATATAGCTTAACCAAAGCACCTAGTTTACAC Y 2 1 2 1 201000 f 74 goat mtdna_01024 MT 1024 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602289 Affx-1002478949 AX-413836660 MT 1075 CCAAAGCACCTAGTTTACACCTAGAAGATTTCACA[C/T]ATTATGAATATCTTGAACTATATCTAGCCCAATCC Y 2 1 2 1 201000 f 74 goat mtdna_01075 MT 1075 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603661 Affx-1002479634 AX-413837799 MT 1112 TTATGAATATCTTGAACTATATCTAGCCCAATCCC[C/T]CCCCCCCATCTAAATTACCAAAACAGTCTAAAACA Y 2 1 2 1 201000 f 74 goat mtdna_01112 MT 1112 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350603694 Affx-1002479635 AX-413837828 MT 1368 CCCGAAACCAGACGAGCTACTCATGGGCAGTTTAT[C/T]AGAACCAACTCATCTATGTGGCAAAATAGTGAGAA Y 2 1 2 1 202000 r 74 goat mtdna_01368 MT 1368 C T 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602290 Affx-1002478950 AX-413836661 MT 1829 TTCTGACTGTTAACAGTAAATAAAAACAACCTAAC[A/G]ATAAATAATTTATTAATTACACTGTTAACCCAACA R 2 1 2 1 303000 f 74 goat mtdna_01829 MT 1829 G A 3 not_recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602293 Affx-1002478951 AX-191753799 MT 2268 CTAGCAGTTTTGGTTGGGGTGACCTCGGAGAACAA[A/G]AGATCCTCCGAGCGATTTTAAAGACTAGACTTACA R 2 1 2 1 201000 f 74 goat mtdna_02268 MT 2268 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602344 Affx-1002478952 AX-413836713 MT 2311 CCGAGCGATTTTAAAGACTAGACTTACAAGTCAAA[C/T]CAAATTATCGCTTATTGATCCAAAAAACTTGATCA Y 2 1 2 1 201000 r 74 goat mtdna_02311 MT 2311 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602297 Affx-1002478953 AX-413836667 MT 2663 AATTTTACAAACAAAACCTGCCCTAGAAAAGGGCC[C/T]AGTTAAGGTGGCAGAGCCCGGTAATTGCGTAAAAC Y 2 1 2 1 202000 f 74 goat mtdna_02663 MT 2663 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602299 Affx-1002478954 AX-413836669 MT 2922 TCGCTGATGCAATTAAACTTTTCATTAAAGAACCC[C/T]TACGACCTGCCACATCCTCAATCTCAATATTTATT Y 2 1 2 1 201000 f 74 goat mtdna_02922 MT 2922 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602351 Affx-1002478955 AX-413836720 MT 2978 ATCTCAATATTTATTCTAGCCCCCATTTTAGCTCT[A/G]ACCCTAGCCTTAACCATATGAATTCCCCTACCCAT R 2 1 2 1 201000 r 74 goat mtdna_02978 MT 2978 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603621 Affx-1002479636 AX-413837768 MT 3194 ATTTCATATGAAGTAACACTAGCAATTATCCTACT[A/G]TCAATCTTACTAATAAACGGATCCTTCGCCCTCTC R 2 1 2 1 201000 f 74 goat mtdna_03194 MT 3194 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_A SNP discriminating mitochondrial haplogroups multi-breed 350603674 Affx-1002479637 AX-413837809 MT 3197 TCATATGAAGTAACACTAGCAATTATCCTACTATC[A/G]ATCTTACTAATAAACGGATCCTTCGCCCTCTCTAC R 2 1 2 1 201000 r 74 goat mtdna_03197 MT 3197 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602303 Affx-1002478956 AX-413836673 MT 3248 GGATCCTTCGCCCTCTCTACACTAATTATTACACA[A/G]GAACAAGTATGACTAATCTTCCCAGCATGACCTCT R 2 1 2 1 202000 f 74 goat mtdna_03248 MT 3248 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602355 Affx-1002478957 AX-413836724 MT 3261 TCTCTACACTAATTATTACACAGGAACAAGTATGA[C/T]TAATCTTCCCAGCATGACCTCTAGCAATAATGTGA Y 2 1 2 1 201000 r 74 goat mtdna_03261 MT 3261 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602357 Affx-1002478958 AX-413836726 MT 3491 ACAACTCTCTTCTTAGGAGCATTTCACAGCCCCTA[C/T]ATACCAGAACTCTACACAATTAACTTTATTATCAA Y 2 1 2 1 201000 r 74 goat mtdna_03491 MT 3491 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602359 Affx-1002478959 AX-413836728 MT 3635 CACTTATTATGAAAAAATTTCCTACCCCTAACACT[A/G]GCCCTATGTATATGACACGTGTCACTACCCATTCT R 2 1 2 1 201000 r 74 goat mtdna_03635 MT 3635 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603676 Affx-1002479638 AX-413837811 MT 3949 CAATCATTTTTATTATTATTCTAATAACCGTTATA[C/T]TTGGAACCACAATCGTCATAATTAGCTCCCACTGA Y 2 1 2 1 303000 r 74 goat mtdna_03949 MT 3949 C T 3 not_recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602362 Affx-1002478960 AX-413836731 MT 3960 ATTATTATTCTAATAACCGTTATACTTGGAACCAC[A/T]ATCGTCATAATTAGCTCCCACTGACTACTCATCTG W 4 1 2 1 201000 r 74 goat mtdna_03960 MT 3960 A T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603629 Affx-1002479639 AX-413837775 MT 4119 TTCCTAACTCAATCAACAGCCTCAATATTACTAAT[A/G]ATAGCTATTATTATTAATTTAATATTCTCAGGCCA R 2 1 2 1 201000 f 74 goat mtdna_04119 MT 4119 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602364 Affx-1002478961 AX-413836733 MT 4131 TCAACAGCCTCAATATTACTAATAATAGCTATTAT[C/T]ATTAATTTAATATTCTCAGGCCAATGAACTGTGAC Y 2 1 2 1 201000 r 74 goat mtdna_04131 MT 4131 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602365 Affx-1002478962 AX-413836734 MT 4164 ATTATTAATTTAATATTCTCAGGCCAATGAACTGT[A/G]ACAAAACTATTTCACCCAACAGCCTCCATACTCAT R 2 1 2 1 201000 r 74 goat mtdna_04164 MT 4164 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603631 Affx-1002479640 AX-413837776 MT 4276 ACTTCTGAGTCCCAGAAGTGACACAAGGTATCCCC[C/T]TATCCTCGGGCCTAATCCTACTCACATGACAAAAA Y 2 1 2 1 202000 f 74 goat mtdna_04276 MT 4276 C T 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_D SNP discriminating mitochondrial haplogroups multi-breed 350602367 Affx-1002478963 AX-413836736 MT 4284 GTCCCAGAAGTAACACAAGGTATCCCCCTATCCTC[A/G]GGCCTAATCCTACTCACATGACAAAAACTAGCACC R 2 1 2 1 201000 r 74 goat mtdna_04284 MT 4284 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602369 Affx-1002478964 AX-413836738 MT 4363 TACTTTACCAAATCCTCCCATCCATCAACCTAGAC[C/T]TAATCTTAACCCTATCAATTTTATCCATTATAATT Y 2 1 2 1 201000 r 74 goat mtdna_04363 MT 4363 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602371 Affx-1002478965 AX-413836741 MT 4470 AAAATCATAGCCTACTCATCAATTGCCCACATAGG[C/T]TGAATAACAGCAATTTTACCATACAACCCCACCAT Y 2 1 2 1 201000 r 74 goat mtdna_04470 MT 4470 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602326 Affx-1002478966 AX-413836696 MT 4563 TATATTACCATGACCTCCACTATATTTTTACTATT[C/T]ATAGCTAACTCAACCACAACCACCCTATCACTATC Y 2 1 2 1 201000 f 74 goat mtdna_04563 MT 4563 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602376 Affx-1002478967 AX-413836745 MT 4601 AGCTAACTCAACCACAACCACCCTATCACTATCAC[A/T]CACATGAAATAAAATACCTATCATAACAACCCTAG W 4 1 2 1 202000 r 74 goat mtdna_04601 MT 4601 T A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601311 Affx-1002479641 AX-413835741 MT 4626 TCACTATCACTCACATGAAATAAAATACCTATCAT[A/G]ACAACCCTAGTCCTCATCACCCTCCTATCAATAGG R 2 1 2 1 202000 f 74 goat mtdna_04626 MT 4626 A G 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602330 Affx-1002478968 AX-413836700 MT 4749 ATAACAAAAAATAACAGCATTATCTTACCCACCCT[C/T]ATAGCAATCACAGCACTACTAAACCTATATTTCTA Y 2 1 2 1 201000 f 74 goat mtdna_04749 MT 4749 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602380 Affx-1002478969 AX-413836749 MT 5085 AATGCAAATCAACCACTTTAATTAAGCTAAATCCT[C/T]ACTAGACTGGTGGGCTCCACCCCCACGAAACTTTA Y 2 1 2 1 102000 r 74 goat mtdna_05085 MT 5085 T C 1 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602333 Affx-1002478970 AX-413836702 MT 5141 CCCCACGAAACTTTAGTTAACAGCTAAATACCCTA[A/G]ATAACTGGCTTCAATCTACTTCTCCCGCCGCGAAG R 2 1 2 1 202000 f 74 goat mtdna_05141 MT 5141 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602335 Affx-1002478971 AX-413836705 MT 5312 AAACCTCTGTTCTTAGATTTACAGTCTATTGCTTT[A/G]CTCAGCCATTTTACCCATGTTCATCAACCGCTGAC R 2 1 2 1 201000 f 74 goat mtdna_05312 MT 5312 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602386 Affx-1002478972 AX-413836755 MT 5658 AATATAAGCTTTTGACTCCTTCCCCCCTCTTTCCT[A/G]TTACTTCTAGCATCCTCTATAGTTGAAGCCGGAGC R 2 1 2 1 400000 r 74 goat mtdna_05658 MT 5658 A G Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602339 Affx-1002478973 AX-413836708 MT 5772 GCCCATGCAGGAGCCTCAGTAGACCTAACTATTTT[C/T]TCCCTACACCTAGCAGGCATCTCTTCAATTCTAGG Y 2 1 2 1 201000 f 74 goat mtdna_05772 MT 5772 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602390 Affx-1002478974 AX-413836760 MT 5791 TAGACCTAACTATTTTTTCCCTACACCTAGCAGGC[A/G]TCTCTTCAATTCTAGGAGCCATTAATTTTATCACA R 2 1 2 1 201000 r 74 goat mtdna_05791 MT 5791 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602343 Affx-1002478975 AX-413836712 MT 5850 AATTTTATCACAACTATCATTAACATGAAACCACC[C/T]GCAATATCACAATATCAAACTCCCCTGTTTGTGTG Y 2 1 2 1 201000 f 74 goat mtdna_05850 MT 5850 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601312 Affx-1002479642 AX-413835742 MT 6096 ATTCTTATTTTACCTGGATTTGGAATAATCTCTCA[C/T]ATCGTAACCTACTACTCAGGGAAAAAAGAACCATT Y 2 1 2 1 201000 f 74 goat mtdna_06096 MT 6096 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_B SNP discriminating mitochondrial haplogroups multi-breed 350602345 Affx-1002478976 AX-413836714 MT 6150 GGGAAAAAAGAACCATTCGGGTACATAGGAATAGT[A/G]TGAGCCATAATATCAATCGGGTTTCTAGGATTTAT R 2 1 2 1 201000 f 74 goat mtdna_06150 MT 6150 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602347 Affx-1002478977 AX-413836716 MT 6309 ACTGGAGTAAAAGTCTTCAGTTGATTAGCAACACT[C/T]CATCAATGATACTGAAGCTATGAGTATACAGACTA Y 2 1 2 1 201000 f 74 goat mtdna_06309 MT 6309 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602349 Affx-1002478978 AX-413836718 MT 6486 GCTCATTTCCACTACGTTCTATCAATAGGAGCTGT[A/G]TTCGCTATCATAGGGGGATTTGTACACTGATTTCC R 2 1 2 1 202000 f 74 goat mtdna_06486 MT 6486 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602400 Affx-1002478979 AX-413836769 MT 6528 ATCATAGGGGGATTTGTACACTGATTTCCCCTATT[C/T]TCAGGCTACACTCTTAATGATACATGAGCCAAAAT Y 2 1 2 1 202000 r 74 goat mtdna_06528 MT 6528 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602352 Affx-1002478980 AX-413836721 MT 6923 GAACCCCCTATTATTGGTTTCAAGCCAACACCATA[A/G]CCACTATGTCTCTCTCAATAAACGAGATGTTAGTA R 2 1 2 1 202000 f 74 goat mtdna_06923 MT 6923 A G 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602354 Affx-1002478981 AX-413836723 MT 7024 TACAGGTGAAAATCCCGTACATCTCATATGGCATA[C/T]CCCATACAACTAGGTTTTCAAGACGCAGCATCACC Y 2 1 2 1 201000 f 74 goat mtdna_07024 MT 7024 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601313 Affx-1002479643 AX-413835743 MT 7090 TCACCCATTATAGAAGAACTACTACATTTTCACGA[C/T]CACACACTAATAATTGTTTTCCTAATCAGCTCACT Y 2 1 2 1 201000 f 74 goat mtdna_07090 MT 7090 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_D SNP discriminating mitochondrial haplogroups multi-breed 350601434 Affx-1002479644 AX-413835852 MT 7108 CTACTACATTTTCACGATCACACACTAATAATTGT[C/T]TTCCTAATCAGCTCACTGGTACTTTATATTATTTC Y 2 1 2 1 201000 r 74 goat mtdna_07108 MT 7108 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_D SNP discriminating mitochondrial haplogroups multi-breed 350602405 Affx-1002478982 AX-413836774 MT 7151 TCAGCTCACTGGTACTTTATATTATTTCACTAATA[C/T]TAACAACAAAACTAACCCACACCAGCACCATAGAC Y 2 1 2 1 201000 r 74 goat mtdna_07151 MT 7151 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602407 Affx-1002478983 AX-413836776 MT 7318 ATCAACAACCCATCCCTCACAGTAAAAACTATGGG[A/G]CATCAATGATACTGAAGCTATGAATATACAGACTA R 2 1 2 1 202000 r 74 goat mtdna_07318 MT 7318 A G 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601315 Affx-1002479645 AX-413835745 MT 7342 AAAACTATGGGACATCAATGATACTGAAGCTATGA[A/G]TATACAGACTATGAAGACTTAAGCTTCGATTCCTA R 2 1 2 1 202000 f 74 goat mtdna_07342 MT 7342 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_B SNP discriminating mitochondrial haplogroups multi-breed 350602409 Affx-1002478984 AX-413836778 MT 7361 GATACTGAAGCTATGAGTATACAGACTATGAAGAC[C/T]TAAGCTTCGATTCCTATATAATTCCAACATCAGAA Y 2 1 2 1 201000 r 74 goat mtdna_07361 MT 7361 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602361 Affx-1002478985 AX-413836730 MT 7426 TCAGAATTAAAACCTGGAGAACTACGACTGCTAGA[A/G]GTAGATAACCGAGTTGTACTACCCATAGAAATGAC R 2 1 2 1 201000 f 74 goat mtdna_07426 MT 7426 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602413 Affx-1002478986 AX-413836782 MT 7642 GAAATCTGCGGATCAAACCATAGTTTCATACCAAT[C/T]GTTCTCGAGCTAGTTCCTCTAAAATATTTTGAAAA Y 2 1 2 1 101000 r 74 goat mtdna_07642 MT 7642 C T 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602366 Affx-1002478987 AX-413836735 MT 7669 ATACCAATCGTTCTCGAGCTAGTTCCTCTAAAATA[C/T]TTTGAAAAATGATCTGCATCAATACTATAAAGTCA Y 2 1 2 1 201000 f 74 goat mtdna_07669 MT 7669 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601316 Affx-1002479646 AX-413835746 MT 7839 ACAATTTTATCAATATTTCTAGCTCTCTTTATTAT[C/T]TTCCAACTAAAAATCTCAAAGTACGACTTCTACCA Y 2 1 2 1 201000 f 74 goat mtdna_07839 MT 7839 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_A SNP discriminating mitochondrial haplogroups multi-breed 350602418 Affx-1002478988 AX-413836787 MT 7842 ATTTTATCAATATTTCTAGCTCTCTTTATTATTTT[C/T]CAACTAAAAATCTCAAAGTACGACTTCTACCACAA Y 2 1 2 1 201000 r 74 goat mtdna_07842 MT 7842 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601440 Affx-1002479647 AX-413835858 MT 8055 TTCCCTCATCAAACCGACTAATTAACAACCGCCTC[A/G]TCTCTCTCCAACAATGGGCACTCCAACTCATATCA R 2 1 2 1 101000 r 74 goat mtdna_08055 MT 8055 A G 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_A SNP discriminating mitochondrial haplogroups multi-breed 350601318 Affx-1002479648 AX-413835748 MT 8102 CAATGGGCACTCCAACTCATATCAAAACAAATAAT[A/G]AGTATTCATAACACCAAAGGACAAACATGAACATT R 2 1 2 1 201000 f 74 goat mtdna_08102 MT 8102 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350601444 Affx-1002479649 AX-413835862 MT 8113 CCAACTCATATCAAAACAAATAATAAGTATTCATA[A/G]CACCAAAGGACAAACATGAACATTAATATTAATGT R 2 1 2 1 202000 r 74 goat mtdna_08113 MT 8113 A G 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602420 Affx-1002478989 AX-413836789 MT 8456 ACAGCAGGACACTTACTAATTCACTTAATCGGAGG[A/G]GCCACCCTTGCACTAACAAGCATTAGTCCTACAAC R 2 1 2 1 101000 r 74 goat mtdna_08456 MT 8456 G A 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601446 Affx-1002479650 AX-413835864 MT 8486 GGAGGGGCCACCCTTGCACTAACAAGCATTAGTCC[C/T]ACAACAGCACTCATTACATTCATTATTCTAATTCT Y 2 1 2 1 202000 r 74 goat mtdna_08486 MT 8486 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602372 Affx-1002478990 AX-413836740 MT 8597 TACGTATTTACTCTCCTAGTCAGCCTATACCTGCA[C/T]GACAACACATAATGACACACCAAACCCATGCTTAT Y 2 1 2 1 202000 f 74 goat mtdna_08597 MT 8597 C T 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601321 Affx-1002479651 AX-413835751 MT 8635 CAACACATAATGACACACCAAACCCATGCTTATCA[C/T]ATAGTAAATCCAAGCCCCTGACCCCTCACAGGGGC Y 2 1 2 1 202000 f 74 goat mtdna_08635 MT 8635 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_B SNP discriminating mitochondrial haplogroups multi-breed 350602424 Affx-1002478991 AX-413836793 MT 8668 CATATAGTAAATCCAAGCCCCTGACCCCTCACAGG[A/G]GCACTATCCGCTCTCCTACTAACATCCGGCCTCAC R 2 1 2 1 202000 r 74 goat mtdna_08668 MT 8668 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602375 Affx-1002478992 AX-413836744 MT 8758 TCAACCGTCCTACTAACCCTAGGTCTAACAACAAA[C/T]ATGCTTACAATATACCAATGATGACGAGATGTGAT Y 2 1 2 1 202000 f 74 goat mtdna_08758 MT 8758 C T 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601450 Affx-1002479652 AX-413835868 MT 8770 CTAACCCTAGGTCTAACAACAAACATGCTTACAAT[A/G]TACCAATGATGACGAGATGTGATTCGAGAAAGTAC R 2 1 2 1 201000 r 74 goat mtdna_08770 MT 8770 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602377 Affx-1002478993 AX-413836746 MT 8827 ATTCGAGAAAGTACCTTCCAAGGTCATCATACTCC[A/G]GCCGTTCAAAAAGGCCTTCGCTATGGAATAATCCT R 2 1 2 1 201000 f 74 goat mtdna_08827 MT 8827 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601452 Affx-1002479653 AX-413835870 MT 8968 ACACCCGAATTAGGCGGCTGCTGACCCCCAACAGG[C/T]ATTCACCCACTTAATCCCCTAGAAGTCCCATTACT Y 2 1 2 1 201000 r 74 goat mtdna_08968 MT 8968 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_D SNP discriminating mitochondrial haplogroups multi-breed 350602379 Affx-1002478994 AX-413836748 MT 9007 CACCCACTTAATCCCCTAGAAGTCCCATTACTTAA[C/T]ACCTCCGTCCTCCTAGCCTCAGGAGTTTCCATCAC Y 2 1 2 1 202000 f 74 goat mtdna_09007 MT 9007 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601454 Affx-1002479654 AX-413835872 MT 9010 CCACTTAATCCCCTAGAAGTCCCATTACTTAATAC[C/T]TCCGTCCTCCTAGCCTCAGGAGTTTCCATCACCTG Y 2 1 2 1 102000 r 74 goat mtdna_09010 MT 9010 C T 1 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_B SNP discriminating mitochondrial haplogroups multi-breed 350602381 Affx-1002478995 AX-413836750 MT 9085 CACCATAGCCTTATGGAAGGAGACCGTAACCACAT[A/G]CTACAAGCCTTATTCATTACCATTATACTAGGCTT R 2 1 2 1 202000 f 74 goat mtdna_09085 MT 9085 A G 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602435 Affx-1002478996 AX-413836804 MT 9086 ACCATAGCCTTATGGAAGGAGACCGTAACCACATA[C/T]TACAAGCCTTATTCATTACCATTATACTAGGCTTA Y 2 1 2 1 201000 r 74 goat mtdna_09086 MT 9086 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602385 Affx-1002478997 AX-413836754 MT 9139 ACCATTATACTAGGCTTATACTTCACATTATTACA[A/G]GCATCAGAATATTATGAAGCACCATTCACAATTTC R 2 1 2 1 201000 f 74 goat mtdna_09139 MT 9139 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602438 Affx-1002478998 AX-413836808 MT 9223 GGTTCAACTTTCTTCGTAGCCACAGGATTCCACGG[C/T]CTTCATGTTATCATCGGATCTACCTTTTTGATTGT Y 2 1 2 1 201000 r 74 goat mtdna_09223 MT 9223 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602440 Affx-1002478999 AX-413836809 MT 9297 CTTTTTCCGTCAACTAAAATTTCACTTCACCTCTA[A/G]TCATCACTTCGGTTTCGAAGCTGCTGCCTGATACT R 2 1 2 1 201000 r 74 goat mtdna_09297 MT 9297 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602442 Affx-1002479000 AX-413836812 MT 9346 TTCGAAGCTGCTGCCTGATACTGACACTTTGTAGA[C/T]GTAGTATGACTTTTCCTCTATGTATCCATCTATTG Y 2 1 2 1 201000 r 74 goat mtdna_09346 MT 9346 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602445 Affx-1002479001 AX-413836814 MT 9445 CAGTACAACTGACTTCCAATCAGTTAGTTTCGGTA[C/T]AATCCGAAAAAGAACAATAAACCTCATAATTACTC Y 2 1 2 1 202000 r 74 goat mtdna_09445 MT 9445 C T 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602447 Affx-1002479002 AX-413836816 MT 9470 AGTTTCGGTACAATCCGAAAAAGAACAATAAACCT[C/T]ATAATTACTCTCCTGACTAATTTTACACTAGCTAC Y 2 1 2 1 201000 r 74 goat mtdna_09470 MT 9470 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601325 Affx-1002479655 AX-413835755 MT 9546 TCGTAACTATCGCATTTTGACTCCCCCAACTAAAC[A/G]TTTACTCAGAAAAAACAAGCCCATATGAATGCGGA R 2 1 2 1 202000 f 74 goat mtdna_09546 MT 9546 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350601457 Affx-1002479656 AX-413835875 MT 9547 CGTAACTATCGCATTTTGACTCCCCCAACTAAACG[C/T]TTACTCAGAAAAAACAAGCCCATATGAATGCGGAT Y 2 1 2 1 202000 r 74 goat mtdna_09547 MT 9547 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602448 Affx-1002479003 AX-413836818 MT 9572 CAACTAAACGTTTACTCAGAAAAAACAAGCCCATA[C/T]GAATGCGGATTTGACCCCATAGGATCGGCTCGCCT Y 2 1 2 1 202000 r 74 goat mtdna_09572 MT 9572 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350601459 Affx-1002479657 AX-413835877 MT 9599 AGCCCATATGAATGCGGATTTGACCCCATAGGATC[A/G]GCTCGCCTTCCCTTCTCCATAAAATTTTTCCTAGT R 2 1 2 1 202000 r 74 goat mtdna_09599 MT 9599 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602399 Affx-1002479004 AX-413836768 MT 9677 ACATTTCTCCTTTTTGACCTAGAAATTGCACTACT[C/T]CTTCCACTACCATGAGCCTCACAAACAACTAATCT Y 2 1 2 1 201000 f 74 goat mtdna_09677 MT 9677 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602401 Affx-1002479005 AX-413836770 MT 9753 CAATGCTTACCATAGCCCTTCTCCTAATTTTTCTA[C/T]TAGCTGTAAGCCTAGCCTACGAATGAACTCAAAAA Y 2 1 2 1 201000 f 74 goat mtdna_09753 MT 9753 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602404 Affx-1002479006 AX-413836773 MT 9797 AGCCTAGCCTACGAATGAACTCAAAAAGGACTAGA[A/G]TGAACTGAATATGGTATTTAGTTTAAAACAAAATA R 2 1 2 1 201000 f 74 goat mtdna_09797 MT 9797 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602406 Affx-1002479007 AX-413836775 MT 9935 TTATAACAGCATTCGCAGTATCTCTCACAGGACTA[C/T]TGATATATCGATCTCACCTAATATCCTCCCTCCTA Y 2 1 2 1 202000 f 74 goat mtdna_09935 MT 9935 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602459 Affx-1002479008 AX-413836828 MT 9937 ATAACAGCATTCGCAGTATCTCTCACAGGACTATT[A/G]ATATATCGATCTCACCTAATATCCTCCCTCCTATG R 2 1 2 1 303000 r 74 goat mtdna_09937 MT 9937 G A 3 not_recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602462 Affx-1002479009 AX-413836831 MT 9943 GCATTCGCAGTATCTCTCACAGGACTATTGATATA[C/T]CGATCTCACCTAATATCCTCCCTCCTATGCCTAGA Y 2 1 2 1 202000 r 74 goat mtdna_09943 MT 9943 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602275 Affx-1002478913 AX-413836646 MT 10106 TTTTCGCAGCCTGCGAAGCAGCACTAGGCCTGTCC[C/T]TACTAGTAATGGTATCAAACACATATGGTACCGAT Y 2 1 2 1 202000 r 74 goat mtdna_10106 MT 10106 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350603605 Affx-1002479010 AX-413837755 MT 10229 AATACTTATACCCCTAACCTGACTATCAAAAAATA[A/G]CATAATCTGAATTAACTCCACACTTCATAGCCTAC R 2 1 2 1 201000 r 74 goat mtdna_10229 MT 10229 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602412 Affx-1002479011 AX-413836781 MT 10261 ATAACATAATCTGAATTAACTCCACACTTCATAGC[C/T]TACTAATTAGCTTCACAAGCCTACTCCTTATAAAC Y 2 1 2 1 101000 f 74 goat mtdna_10261 MT 10261 C T 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602226 Affx-1002478914 AX-413836598 MT 10302 ATTAGCTTCACAAGCCTACTCCTTATAAACCAATT[C/T]GGCGATAACAGCCTCAACTTCTCATTAACCTTCTT Y 2 1 2 1 101000 f 74 goat mtdna_10302 MT 10302 C T 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602466 Affx-1002479012 AX-413836835 MT 10374 TCCGACTCCCTATCTACTCCACTACTAATCCTAAC[C/T]ATATGACTCCTTCCCCTGATACTTATAGCTAGTCA Y 2 1 2 1 201000 r 74 goat mtdna_10374 MT 10374 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602416 Affx-1002479013 AX-413836785 MT 10416 CTCCTTCCCCTGATACTTATAGCTAGTCAACATCA[C/T]CTATTAAAAGAAAGTCCAACCCGGAAAAAACTCTT Y 2 1 2 1 202000 f 74 goat mtdna_10416 MT 10416 C T 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602417 Affx-1002479014 AX-413836786 MT 10430 ACTTATAGCTAGTCAACATCACCTATTAAAAGAAA[A/G]TCCAACCCGGAAAAAACTCTTCATCTCAATACTAG R 2 1 2 1 303000 f 74 goat mtdna_10430 MT 10430 G A 3 not_recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602473 Affx-1002479015 AX-413836842 MT 10440 AGTCAACATCACCTATTAAAAGAAAGTCCAACCCG[A/G]AAAAAACTCTTCATCTCAATACTAGTCCTATTGCA R 2 1 2 1 101000 r 74 goat mtdna_10440 MT 10440 G A 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602475 Affx-1002479016 AX-413836844 MT 10473 CGGAAAAAACTCTTCATCTCAATACTAGTCCTATT[A/G]CAACTATTCCTAATTATAACATTCACCGCTACAGA R 2 1 2 1 201000 r 74 goat mtdna_10473 MT 10473 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602228 Affx-1002478915 AX-413836600 MT 10545 CTAATTTTCTTTTACATTATATTTGAAGCAACACT[A/G]GTCCCTACACTCATCATCATCACTCGATGAGGAAA R 2 1 2 1 201000 f 74 goat mtdna_10545 MT 10545 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602423 Affx-1002479017 AX-413836792 MT 10557 TACATTATATTTGAAGCAACACTAGTCCCTACACT[C/T]ATCATCATCACTCGATGAGGAAACCAAACAGAGCG Y 2 1 2 1 303000 f 74 goat mtdna_10557 MT 10557 C T 3 not_recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602281 Affx-1002478916 AX-413836652 MT 10563 ATATTTGAAGCAACACTAGTCCCTACACTCATCAT[C/T]ATCACTCGATGAGGAAACCAAACAGAGCGTCTAAA Y 2 1 2 1 201000 r 74 goat mtdna_10563 MT 10563 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602425 Affx-1002479018 AX-413836794 MT 10776 AATGTTTTCTTATGATTAGCATGCATAATAGCCTT[C/T]ATAGTAAAAATACCATTATATGGACTCCACCTTTG Y 2 1 2 1 101000 f 74 goat mtdna_10776 MT 10776 C T 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603537 Affx-1002478917 AX-413837701 MT 10813 TAGTAAAAATACCATTATATGGACTCCACCTTTGA[C/T]TACCTAAAGCCCACGTAGAAGCCCCAATCGCAGGC Y 2 1 2 1 201000 f 74 goat mtdna_10813 MT 10813 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_B SNP discriminating mitochondrial haplogroups multi-breed 350602482 Affx-1002479019 AX-413836851 MT 10842 CTTTGATTACCTAAAGCCCACGTAGAAGCCCCAAT[C/T]GCAGGCTCTATAGTCCTTGCAGCAATCCTACTAAA Y 2 1 2 1 202000 r 74 goat mtdna_10842 MT 10842 C T 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602232 Affx-1002478918 AX-413836603 MT 10950 CTTAATCCAATCACCGACTATATAGCATATCCATT[C/T]ATTATACTATCATTATGAGGCATAATTATAACCAG Y 2 1 2 1 201000 f 74 goat mtdna_10950 MT 10950 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602429 Affx-1002479020 AX-413836798 MT 11001 TGAGGCATAATTATAACCAGCTCAATTTGTCTCCG[C/T]CAAACGGACCTGAAATCACTCATCGCATATTCTTC Y 2 1 2 1 201000 f 74 goat mtdna_11001 MT 11001 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602430 Affx-1002479021 AX-413836799 MT 11052 TCACTCATCGCATATTCTTCCGTCAGTCATATAGC[A/G]CTCGTTATCGTCGCCATCCTTATCCAGACACCCTG R 2 1 2 1 201000 f 74 goat mtdna_11052 MT 11052 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602233 Affx-1002478919 AX-413836604 MT 11073 GTCAGTCATATAGCGCTCGTTATCGTCGCCATCCT[C/T]ATCCAGACACCCTGAAGCTACATAGGAGCCACTGC Y 2 1 2 1 202000 f 74 goat mtdna_11073 MT 11073 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602432 Affx-1002479022 AX-413836801 MT 11163 CTTACATCATCTATACTTTTCTGCCTAGCAAATTC[C/T]AACTATGAGCGAATCCACAGCCGTACAATAATTTT Y 2 1 2 1 201000 f 74 goat mtdna_11163 MT 11163 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602287 Affx-1002478920 AX-413836658 MT 11256 CTTCCACTAATGGCTGCCTGATGACTCCTAGCAAG[C/T]CTAACTAATCTGGCCCTACCCCCAACAATCAACCT Y 2 1 2 1 201000 r 74 goat mtdna_11256 MT 11256 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602237 Affx-1002478921 AX-413836608 MT 11325 CTAATTGGAGAACTATTCGTAGTAATATCAACTTT[C/T]TCATGATCTAACATCACAATTATTCTAATAGGACT Y 2 1 2 1 201000 f 74 goat mtdna_11325 MT 11325 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_D SNP discriminating mitochondrial haplogroups multi-breed 350602291 Affx-1002478922 AX-413836662 MT 11569 GCCCCCTATACTGTAAATATAGTTTAAAAAAAAAC[A/G]TTAGATTGTGAATCTAACAATAGAAGCCTATCACC R 2 1 2 1 202000 r 74 goat mtdna_11569 MT 11569 A G 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602241 Affx-1002478923 AX-413836612 MT 11649 ACCGAAAAAGTATGCAAGAACTGCTAACTCTATGC[C/T]TCCATGTCTAACAACATGGCTTTTTCAAACTTTTA Y 2 1 2 1 201000 f 74 goat mtdna_11649 MT 11649 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602243 Affx-1002478924 AX-413836614 MT 11702 GGCTTTTTCAAACTTTTAAAGGATAGTAGTTATCC[A/G]TTGGTCTTAGGAGCCAAAAAATTGGTGCAACTCCA R 2 1 2 1 201000 f 74 goat mtdna_11702 MT 11702 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_B SNP discriminating mitochondrial haplogroups multi-breed 350602490 Affx-1002479023 AX-413836859 MT 11797 TTCTCTTGCACTAACCACCCTAACCCTATTAACCG[C/T]ACCCATCATAATAACCAACCTCAATATCTACAAAT Y 2 1 2 1 201000 r 74 goat mtdna_11797 MT 11797 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602437 Affx-1002479024 AX-413836806 MT 11849 AACCTCAATATCTACAAATCCACCAACTACCCACT[C/T]TATGTAAAAACGGTCGTTTCATATGCCTTTATCAC Y 2 1 2 1 201000 f 74 goat mtdna_11849 MT 11849 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602296 Affx-1002478925 AX-413836666 MT 11872 CAACTACCCACTTTATGTAAAAACGGTCGTTTCAT[A/G]TGCCTTTATCACTAGCATAGTCCCCACAATAATAT R 2 1 2 1 201000 r 74 goat mtdna_11872 MT 11872 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_B SNP discriminating mitochondrial haplogroups multi-breed 350602439 Affx-1002479025 AX-413836807 MT 11912 TTTATCACTAGCATAGTCCCCACAATAATATTCAT[C/T]TATACAGGACAAGAAATAGTCATTTCAAACTGACA Y 2 1 2 1 102000 f 74 goat mtdna_11912 MT 11912 T C 1 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602496 Affx-1002479026 AX-413836865 MT 11915 ATCACTAGCATAGTCCCCACAATAATATTCATTTA[C/T]ACAGGACAAGAAATAGTCATTTCAAACTGACACTG Y 2 1 2 1 102000 r 74 goat mtdna_11915 MT 11915 T C 1 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602247 Affx-1002478926 AX-413836618 MT 11957 CAAGAAATAGTCATTTCAAACTGACACTGACTATC[C/T]ATCCAAACCCTTAAATTATCGCTCAGCTTCAAGAT Y 2 1 2 1 201000 f 74 goat mtdna_11957 MT 11957 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602498 Affx-1002479027 AX-413836867 MT 11973 CAAACTGACACTGACTATCTATCCAAACCCTTAAA[C/T]TATCGCTCAGCTTCAAGATAGACTATTTTTCAGTA Y 2 1 2 1 101000 r 74 goat mtdna_11973 MT 11973 T C 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602249 Affx-1002478927 AX-413836620 MT 12014 CTCAGCTTCAAGATAGACTATTTTTCAGTAATATT[C/T]GTCCCAGTAGCACTATTCGTTACATGATCCATTAT Y 2 1 2 1 201000 f 74 goat mtdna_12014 MT 12014 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602500 Affx-1002479028 AX-413836869 MT 12044 ATATTTGTCCCAGTAGCACTATTCGTTACATGATC[C/T]ATTATAGAATTCTCAATGTGATACATACACTCAGA Y 2 1 2 1 201000 r 74 goat mtdna_12044 MT 12044 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602302 Affx-1002478928 AX-413836672 MT 12146 CTCCTATTTCTCATCACAATACTCATCCTCGTCAC[C/T]GCAAATAATCTCTTCCAACTATTTATCGGCTGAGA Y 2 1 2 1 201000 r 74 goat mtdna_12146 MT 12146 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602502 Affx-1002479029 AX-413836871 MT 12218 GGAGTCGGAATCATATCATTCTTACTGATCGGATG[A/G]TGATATGGACGAACAGACGCAAACACAGCAGCCTT R 2 1 2 1 201000 r 74 goat mtdna_12218 MT 12218 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602449 Affx-1002479030 AX-413836817 MT 12257 TATGGACGAACAGACGCAAACACAGCAGCCTTACA[A/G]GCGATTCTATATAACCGCATTGGAGACATTGGGTT R 2 1 2 1 202000 f 74 goat mtdna_12257 MT 12257 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603607 Affx-1002479031 AX-413837756 MT 12260 GGACGAACAGACGCAAACACAGCAGCCTTACAGGC[A/G]ATTCTATATAACCGCATTGGAGACATTGGGTTTAT R 2 1 2 1 201000 r 74 goat mtdna_12260 MT 12260 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602253 Affx-1002478929 AX-413836624 MT 12362 AACACTTGAGATCTCCAACAAATCTTTATACTAAA[A/G]CCAGAAAACTCAAACCTACCCCTGATAGGACTAAC R 2 1 2 1 201000 f 74 goat mtdna_12362 MT 12362 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602507 Affx-1002479032 AX-413836876 MT 12369 GAGATCTCCAACAAATCTTTATACTAAAGCCAGAA[A/G]ACTCAAACCTACCCCTGATAGGACTAACTCTAGCT R 2 1 2 1 201000 r 74 goat mtdna_12369 MT 12369 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603539 Affx-1002478930 AX-413837703 MT 12638 CTATTTACAGCAATATGTGCTCTTACCCAAAATGA[C/T]ATTAAAAAAATCGTCGCCTTCTCCACATCCAGTCA Y 2 1 2 1 201000 f 74 goat mtdna_12638 MT 12638 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602509 Affx-1002479033 AX-413836878 MT 12651 TATGTGCTCTTACCCAAAATGACATTAAAAAAATC[A/G]TCGCCTTCTCCACATCCAGTCAACTTGGCCTTATA R 2 1 2 1 202000 r 74 goat mtdna_12651 MT 12651 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602511 Affx-1002479034 AX-413836880 MT 12683 ATCGTCGCCTTCTCCACATCCAGTCAACTTGGCCT[C/T]ATAATAGTAACAATTGGAATTAACCAACCCTACCT Y 2 1 2 1 201000 r 74 goat mtdna_12683 MT 12683 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602254 Affx-1002478931 AX-413836625 MT 12743 CAACCCTACCTAGCATTCCTCCACATCTGCACCCA[C/T]GCCTTCTTCAAAGCCATGCTATTCATATGCTCCGG Y 2 1 2 1 202000 f 74 goat mtdna_12743 MT 12743 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602514 Affx-1002479035 AX-413836883 MT 12762 TCCACATCTGCACCCATGCCTTCTTCAAAGCCATG[C/T]TATTCATATGCTCCGGCTCTATTATCCACAACCTA Y 2 1 2 1 101000 r 74 goat mtdna_12762 MT 12762 C T 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603609 Affx-1002479036 AX-413837758 MT 12776 CATGCCTTCTTCAAAGCCATGCTATTCATATGCTC[C/T]GGCTCTATTATCCACAACCTAAACAACGAACAAGA Y 2 1 2 1 400000 r 74 goat mtdna_12776 MT 12776 C T Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602516 Affx-1002479037 AX-413836885 MT 12987 CGTATACCAACGCCTGAGCCCTCTTAATAACATTA[A/G]TCGCCACCTCCTTTACAGCTGTCTACAGTACTCGA R 2 1 2 1 201000 r 74 goat mtdna_12987 MT 12987 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602460 Affx-1002479038 AX-413836829 MT 13146 AACGCTTACTAATCGGAAGTCTCTTCGCAGGATTT[A/T]TCATCTCCAACAATATCCCCCCAATAACAATTCCC W 4 1 2 1 201000 f 74 goat mtdna_13146 MT 13146 T A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602307 Affx-1002478932 AX-413836677 MT 13157 ATCGGAAGTCTCTTCGCAGGATTTTTCATCTCCAA[C/T]AATATCCCCCCAATAACAATTCCCCAAATCACTAT Y 2 1 2 1 202000 r 74 goat mtdna_13157 MT 13157 C T 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602309 Affx-1002478933 AX-413836679 MT 13178 TTTTTCATCTCCAACAATATCCCCCCAATAACAAT[C/T]CCCCAAATCACTATACCCCACTATCTAAAAATAAC Y 2 1 2 1 201000 r 74 goat mtdna_13178 MT 13178 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_B SNP discriminating mitochondrial haplogroups multi-breed 350602461 Affx-1002479039 AX-413836830 MT 13271 GGCTTTATTTTAGCACTAGAAACCGCTAACATAAC[C/T]CACCACCTAAAATTTAACTACTCATCAAACATATT Y 2 1 2 1 201000 f 74 goat mtdna_13271 MT 13271 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602310 Affx-1002478934 AX-413836680 MT 13286 CTAGAAACCGCTAACATAACTCACCACCTAAAATT[C/T]AACTACTCATCAAACATATTCAAATTCTCCAACCT Y 2 1 2 1 201000 r 74 goat mtdna_13286 MT 13286 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_B SNP discriminating mitochondrial haplogroups multi-breed 350602523 Affx-1002479040 AX-413836892 MT 13382 CACCGCTTAACCCCCTACATAAACTTAACAATAAG[C/T]CAAAAATCAGCATCCTCTCTCCTAGATCTAATCTG Y 2 1 2 1 102000 r 74 goat mtdna_13382 MT 13382 T C 1 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602525 Affx-1002479041 AX-413836894 MT 13457 GAAACTATTCTACCAAAAACCATCTCACAAGCCCA[A/G]ATAAAAATAGCTACCACAACAACAAACCAAAAAGG R 2 1 2 1 201000 r 74 goat mtdna_13457 MT 13457 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602467 Affx-1002479042 AX-413836836 MT 13508 ACAACAACAAACCAAAAAGGCCTAATTAAGCTATA[C/T]TTCCTTTCCTTCCTGGTTACAATCCTTGTCAGCAC Y 2 1 2 1 201000 f 74 goat mtdna_13508 MT 13508 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602529 Affx-1002479043 AX-413836898 MT 13523 AAAGGCCTAATTAAGCTATACTTCCTTTCCTTCCT[A/G]GTTACAATCCTTGTCAGCACAATTCTATTTAATTT R 2 1 2 1 303000 r 74 goat mtdna_13523 MT 13523 G A 3 not_recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602531 Affx-1002479044 AX-413836900 MT 13526 GGCCTAATTAAGCTATACTTCCTTTCCTTCCTGGT[C/T]ACAATCCTTGTCAGCACAATTCTATTTAATTTCCA Y 2 1 2 1 202000 r 74 goat mtdna_13526 MT 13526 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602533 Affx-1002479045 AX-413836902 MT 13548 TTTCCTTCCTGGTTACAATCCTTGTCAGCACAATT[C/T]TATTTAATTTCCACGAGTAATCTCCATAATTACCA Y 2 1 2 1 201000 r 74 goat mtdna_13548 MT 13548 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602474 Affx-1002479046 AX-413836843 MT 13579 AATTCTATTTAATTTCCACGAGTAATCTCCATAAT[C/T]ACCACAACACCAATTAACAAAGATCAACCAGTAAC Y 2 1 2 1 201000 f 74 goat mtdna_13579 MT 13579 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602476 Affx-1002479047 AX-413836845 MT 13675 TATAAAGCAGCAATCCCTATGGCCTCCTCACTGAA[A/G]AACCCGGAATCCCCTGTATCATAAATAACCCAATC R 2 1 2 1 202000 f 74 goat mtdna_13675 MT 13675 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602312 Affx-1002478935 AX-413836682 MT 13681 GCAGCAATCCCTATGGCCTCCTCACTGAAGAACCC[A/G]GAATCCCCTGTATCATAAATAACCCAATCCCCCAT R 2 1 2 1 201000 r 74 goat mtdna_13681 MT 13681 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_B SNP discriminating mitochondrial haplogroups multi-breed 350602314 Affx-1002478936 AX-413836684 MT 13762 TCAAACACAATCTCTACTTCCTTATCTTTCAACAC[A/G]TAATAAACCATAAGAAACTCCATTAACAAACCAGT R 2 1 2 1 201000 r 74 goat mtdna_13762 MT 13762 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_B SNP discriminating mitochondrial haplogroups multi-breed 350602478 Affx-1002479048 AX-413836847 MT 13800 ATAAACCATAAGAAACTCCATTAACAAACCAGTAA[C/T]AAACGCCCCTAGAACAACTTTACTAGAAACTCAAA Y 2 1 2 1 201000 f 74 goat mtdna_13800 MT 13800 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602542 Affx-1002479049 AX-413836911 MT 14038 GGCGAAGGTTTTGAAGAAAACCCCACAAAACCTAT[C/T]ACAAAGATAACGCTTAAAATAAATACAATATATAT Y 2 1 2 1 303000 r 74 goat mtdna_14038 MT 14038 T C 3 not_recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602481 Affx-1002479050 AX-413836850 MT 14050 GAAGAAAACCCCACAAAACCTATTACAAAGATAAC[A/G]CTTAAAATAAATACAATATATATTATCATTATTCT R 2 1 2 1 303000 f 74 goat mtdna_14050 MT 14050 G A 3 not_recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602483 Affx-1002479051 AX-413836852 MT 14170 TCAACTACAAGAACACTAATGACCAACATCCGAAA[A/G]ACCCACCCATTAATAAAAATTGTAAACAACGCATT R 2 1 2 1 201000 f 74 goat mtdna_14170 MT 14170 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602485 Affx-1002479052 AX-413836854 MT 14266 ATCTCATCATGATGAAACTTTGGATCCCTCCTAGG[A/C]ATTTGCCTAATCTTACAAATCCTGACAGGCCTATT M 2 1 2 1 202000 f 74 goat mtdna_14266 MT 14266 A C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602487 Affx-1002479053 AX-413836856 MT 14284 TTTGGATCCCTCCTAGGAATTTGCCTAATCTTACA[A/G]ATCCTGACAGGCCTATTCCTAGCAATACACTATAC R 2 1 2 1 303000 f 74 goat mtdna_14284 MT 14284 A G 3 not_recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602316 Affx-1002478937 AX-413836686 MT 14288 GATCCCTCCTAGGAATTTGCCTAATCTTACAAATC[C/T]TGACAGGCCTATTCCTAGCAATACACTATACATCC Y 2 1 2 1 201000 r 74 goat mtdna_14288 MT 14288 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602489 Affx-1002479054 AX-413836858 MT 14341 GCAATACACTATACATCCGACACAATAACAGCATT[C/T]TCCTCTGTAACTCACATTTGTCGAGATGTAAATTA Y 2 1 2 1 201000 f 74 goat mtdna_14341 MT 14341 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602491 Affx-1002479055 AX-413836860 MT 14444 GAGCATCAATATTCTTTATCTGCCTATTCATACAT[A/G]TCGGACGAGGTCTATACTATGGATCATATACCTTT R 2 1 2 1 201000 f 74 goat mtdna_14444 MT 14444 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602493 Affx-1002479056 AX-413836862 MT 14524 TGAAACATTGGAGTAATCCTCCTGCTCGCGACAAT[A/G]GCCACAGCATTCATAGGCTATGTTTTACCATGAGG R 2 1 2 1 201000 f 74 goat mtdna_14524 MT 14524 G A 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602318 Affx-1002478938 AX-413836688 MT 14587 CCATGAGGACAAATATCATTTTGAGGGGCAACAGT[C/T]ATCACTAATCTTCTTTCAGCAATCCCATATATTGG Y 2 1 2 1 303000 r 74 goat mtdna_14587 MT 14587 C T 3 not_recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602559 Affx-1002479057 AX-413836927 MT 14593 GGACAAATATCATTTTGAGGGGCAACAGTCATCAC[C/T]AATCTTCTTTCAGCAATCCCATATATTGGCACAAA Y 2 1 2 1 201000 r 74 goat mtdna_14593 MT 14593 T C 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602562 Affx-1002479058 AX-413836930 MT 14650 TATATTGGCACAAACCTAGTCGAATGAATCTGAGG[A/G]GGATTCTCAGTAGACAAAGCCACTCTCACCCGATT R 2 1 2 1 202000 r 74 goat mtdna_14650 MT 14650 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602499 Affx-1002479059 AX-413836868 MT 14674 TGAATCTGAGGGGGATTCTCAGTAGACAAAGCCAC[C/T]CTCACCCGATTCTTCGCCTTCCACTTTATCCTCCC Y 2 1 2 1 202000 f 74 goat mtdna_14674 MT 14674 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602566 Affx-1002479060 AX-413836934 MT 14686 GGATTCTCAGTAGACAAAGCCACTCTCACCCGATT[C/T]TTCGCCTTCCACTTTATCCTCCCATTCATCATCAC Y 2 1 2 1 201000 r 74 goat mtdna_14686 MT 14686 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602503 Affx-1002479061 AX-413836872 MT 14720 TCTTCGCCTTCCACTTTATCCTCCCATTCATCATC[A/G]CAGCCCTCGCCATAGTCCACCTGCTTTTCCTCCAC R 2 1 2 1 201000 f 74 goat mtdna_14720 MT 14720 A G 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350603603 Affx-1002478939 AX-413837753 MT 14746 TTCATCATCACAGCCCTCGCCATAGTCCACCTGCT[C/T]TTCCTCCACGAAACAGGATCGAACAACCCCACAGG Y 2 1 2 1 202000 r 74 goat mtdna_14746 MT 14746 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_A SNP discriminating mitochondrial haplogroups multi-breed 350602570 Affx-1002479062 AX-413836937 MT 14767 ATAGTCCACCTGCTTTTCCTCCACGAAACAGGATC[C/G]AACAACCCCACAGGAATTCCATCAGACGCAGATAA S 4 1 2 1 202000 r 74 goat mtdna_14767 MT 14767 G C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602506 Affx-1002479063 AX-413836875 MT 14893 ATTCTTGTTCTAATATTACTAGTACTATTCACACC[C/T]GACCTACTCGGAGACCCAGACAACTATATCCCAGC Y 2 1 2 1 101000 f 74 goat mtdna_14893 MT 14893 C T 1 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602575 Affx-1002479064 AX-413836942 MT 14968 CCACTCAATACACCCCCTCACATTAAACCTGAGTG[A/G]TATTTCCTATTTGCATACGCAATCCTACGATCAAT R 2 1 2 1 202000 r 74 goat mtdna_14968 MT 14968 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602510 Affx-1002479065 AX-413836879 MT 14993 AACCTGAGTGGTATTTCCTATTTGCATACGCAATC[C/T]TACGATCAATTCCCAACAAACTAGGAGGAGTCCTA Y 2 1 2 1 202000 f 74 goat mtdna_14993 MT 14993 C T 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602320 Affx-1002478940 AX-413836690 MT 15007 TTCCTATTTGCATACGCAATCCTACGATCAATTCC[C/T]AACAAACTAGGAGGAGTCCTAGCCCTAGTCCTCTC Y 2 1 2 1 202000 r 74 goat mtdna_15007 MT 15007 C T 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602321 Affx-1002478941 AX-413836691 MT 15053 GAGGAGTCCTAGCCCTAGTCCTCTCAATCCTAATC[C/T]TAGTACTTGTACCCTTCCTCCACACATCTAAACAA Y 2 1 2 1 202000 r 74 goat mtdna_15053 MT 15053 T C 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_C SNP discriminating mitochondrial haplogroups multi-breed 350602579 Affx-1002479066 AX-413836946 MT 15076 TCAATCCTAATCTTAGTACTTGTACCCTTCCTCCA[C/T]ACATCTAAACAACGAAGCATAATATTCCGCCCAAT Y 2 1 2 1 201000 r 74 goat mtdna_15076 MT 15076 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 350602274 Affx-1002478942 AX-413836645 MT 15112 ACATCTAAACAACGAAGCATAATATTCCGCCCAAT[C/T]AGCCAATGCATATTCTGAATCCTGGTAGCAGATCT Y 2 1 2 1 201000 f 74 goat mtdna_15112 MT 15112 C T 2 recommended Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_G SNP discriminating mitochondrial haplogroups multi-breed 350602513 Affx-1002479067 AX-413836882 MT 15348 AATACACTGGTCTTGTAAACCAGAAAAGGAGAATA[A/G]CCAATCTCCCTAAGACTCAAGGAAGAAGCCATAGC R 2 1 2 1 202000 f 74 goat mtdna_15348 MT 15348 G A 2 neutral Goat_IGGC_65K_v2 mitochondrial markers Haplogroup_F SNP discriminating mitochondrial haplogroups multi-breed 468278715 Affx-1111836568 AX-519552193 NW_017189516.1 1436359 CTATTCTTTGGAACTCTGGTTTCAGATGCTTATAT[C/G]TTTCCTTTTATCCTTTTTTTTTCTTTGCTTCTCTT S 4 1 2 1 103000 f 74 goat Random2.2K_MT-1 NW_017189516.1 1436359 G C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276363 Affx-1111835299 AX-519549892 NW_017189516.1 3493160 TGGGGAGATCTGGGGACAGTTCTCTCATACTCTGT[A/C]TTTCGTTACTTGTGTCTCTGATGAAAGGAATGTTG M 2 1 2 1 101000 r 74 goat NW_017189516.1_3493160_AF-PAKI NW_017189516.1 3493160 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468279017 Affx-1111836635 AX-519552471 NW_017189516.1 4149435 CTCTCCAAGTTTTATAAAAATTGTGAAATCTGATG[A/G]GAGCAAAGGAATCTTCATCCCATAAAAAGACATGT R 2 1 2 1 101000 r 74 goat Random2.2K_MT-2 NW_017189516.1 4149435 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279027 Affx-1111836645 AX-519552480 NW_017189516.1 4617791 TTTTTTTTTTTTCCCAGAAGTTTCATTGTTTTGGG[A/C]TTTACATTTACATCTATGATCTATTTTGGGTTAGT M 2 1 2 1 103000 r 74 goat Random2.2K_MT-3 NW_017189516.1 4617791 G T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278889 Affx-1111836656 AX-519552357 NW_017189516.1 5816788 AGATTGCATCTGTGGATACAGTCAGGGAAGGAGCG[A/G]GTGAAATGAATGGAGAAAGTAGCATTGACATATAT R 2 1 2 1 102000 f 74 goat Random2.2K_MT-4 NW_017189516.1 5816788 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278911 Affx-1111836666 AX-519552378 NW_017189516.1 6411606 AAGCTGAAATCAAAATTGACGGGACAAATATCAAT[A/C]ACCTCAGATATGCAGATGACACCACCCTTATGGCA M 2 1 2 1 303000 f 74 goat Random2.2K_MT-5 NW_017189516.1 6411606 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276234 Affx-1111835309 AX-185439353 NW_017189516.1 7614997 TCTCAAGAGTCTTCTCCAACACCACAGTTCAAAAC[A/C]ATCAATTCTTTGGCACTCAGCTTTCTTCACAGTCC M 2 1 2 1 303000 f 74 goat NW_017189516.1_7614997_AF-PAKI NW_017189516.1 7614997 G T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278934 Affx-1111836676 AX-519552395 NW_017189516.1 8561943 AAGAAGGGAGAGGAGGATGTTGCAACATTGAACTT[A/C]AGGGGAATTTTATCACCAAGTTTGTATCCTAAGGC M 2 1 2 1 101000 f 74 goat Random2.2K_MT-6 NW_017189516.1 8561943 C A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275354 Affx-1111834746 AX-519548929 NW_017189516.1 9666401 ACGAGTCACCTAGTAAGTGTCCAGGAAACGTTATC[A/G]TTGATGTTTTTCATCAGAGCTAGGAGAGATAAAAC R 2 1 2 1 101000 r 74 goat GoatD01.051252 NW_017189516.1 9666401 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276348 Affx-1111835292 AX-519549880 NW_017189516.1 10199087 AAGGAAGTATGTTGCCATAAAAGATATACTGCACG[A/G]TTCTAAGCAAGAACTCAAGAAATCTGCAAGTGCCC R 2 1 2 1 101000 r 74 goat NW_017189516.1_10199087_AF-PAKI NW_017189516.1 10199087 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468274924 Affx-1111834495 AX-519548506 NW_017189516.1 12420183 AATCCTAGGGGCAGGCAGGCCAGCCCCCAGC[A/C]GCCTGTAGGGGTGGCCTGGGGCAGAGGAGAGTAAC M 2 1 2 1 103000 r 74 goat GoatD01.038273 NW_017189516.1 12420183 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276203 Affx-1111835293 AX-519549753 NW_017189516.1 14738173 TTAAGATTTACTTTAAAACTACAGTTATTAGAGGG[A/G]CTTACCAGGTGGCTCAGTGGTAAAGAATCTGCCCG R 2 1 2 1 201000 f 74 goat NW_017189516.1_14738173_AF-PAKI NW_017189516.1 14738173 T C 2 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468275404 Affx-1111834878 AX-519548977 NW_017189516.1 15554333 TTTCTGAGCTTCTTCTGCAGTGTTTCTAATATCCA[A/G]CTCATCTATCTCCTTTGCCTT R 2 1 2 1 101000 f 74 goat GoatD01.057329 NW_017189516.1 15554333 A G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278949 Affx-1111836683 AX-519552408 NW_017189516.1 16099092 GGGAAGGACTTTTGATTTGTTAGAGCTGATCCTGA[A/G]CCATTTGGATGCAGAGATAAGGTCTATTTCCTAAA R 2 1 2 1 101000 f 74 goat Random2.2K_MT-7 NW_017189516.1 16099092 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278970 Affx-1111836693 AX-519552428 NW_017189516.1 16697312 AGTGCCTTCTCTGGGCCTGAATATCTTCACTGACA[A/G]GGGAGACAGGGTTTTCTTCAAGGGTCCTAGTGAGG R 2 1 2 1 102000 f 74 goat Random2.2K_MT-8 NW_017189516.1 16697312 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279084 Affx-1111836702 AX-519552531 NW_017189516.1 16867904 TCTCAAACATGAACCCCCCTCCCACCTCCCTCCCC[A/G]TAACATTGGAGGCTAATTACTTTACAAGATTGTAT R 2 1 2 1 103000 r 74 goat Random2.2K_MT-9 NW_017189516.1 16867904 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275181 Affx-1111834641 AX-519548760 NW_017189516.1 18565813 GCAGAGTGGGAAGGATGTAAGCCAGCTTCAGTAGC[A/G]CCTCAACAATATCAACCTGCAGAGCTCAATGGCTG R 2 1 2 1 101000 r 74 goat GoatD01.044214 NW_017189516.1 18565813 T C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276353 Affx-1111835294 AX-519549884 NW_017189516.1 19353349 TTGAACTCTTAATGTGCCAAACACAATTTCAAGTT[A/C]TTAAATCTTTCTAAAGACTCTGTGAAGAAAGACTT M 2 1 2 1 101000 r 74 goat NW_017189516.1_19353349_AF-PAKI NW_017189516.1 19353349 T G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278717 Affx-1111836569 AX-317820332 NW_017189516.1 19768538 ACCCAAGTCCAAGAAACCCAGAGAGTCCCAAACAG[A/G]ATAAACCCAAGGCAAAACACCCCAAGACACATATT R 2 1 2 1 103000 f 74 goat Random2.2K_MT-10 NW_017189516.1 19768538 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278736 Affx-1111836578 AX-190483197 NW_017189516.1 19786093 AGTCCAAGGGACTCTCAAGAGTCTTCTCCAACACA[A/G]TAGTTCAAAAGCATCAATTTTTCAGCGCTCATCTT R 2 1 2 1 103000 f 74 goat Random2.2K_MT-11 NW_017189516.1 19786093 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278764 Affx-1111836592 AX-519552237 NW_017189516.1 22837858 TGCAATCAACATCTGCAGTGATATTGGAGCCCCCC[A/G]AAATAAAGTCTAACACTGTTTCCACTGTTTCCCCA R 2 1 2 1 103000 f 74 goat Random2.2K_MT-13 NW_017189516.1 22837858 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278780 Affx-1111836600 AX-519552253 NW_017189516.1 25406012 AAAGGAAATCATCAACAAAAAAGACAGCCTAGTGA[A/G]TGGGAGAAGATATCTGCAAATGATATGACTGATAA R 2 1 2 1 101000 f 74 goat Random2.2K_MT-14 NW_017189516.1 25406012 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276207 Affx-1111835295 AX-519549757 NW_017189516.1 26297200 CCCAGAAGAAAGTTACTGTGATTATTTTAAGCAAT[A/C]TATAAACCTATTTTAACAACCCAGCTTATGTAGTC M 2 1 2 1 101000 f 74 goat NW_017189516.1_26297200_AF-PAKI NW_017189516.1 26297200 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278813 Affx-1111836616 AX-192007750 NW_017189516.1 26738222 CATGGACTGTATAGTCCATGGGATCACAAAGAGTC[A/G]GACATGACTGAGAGACTTTCACTTCACTTATGTGA R 2 1 2 1 303000 f 74 goat Random2.2K_MT-16 NW_017189516.1 26738222 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273932 Affx-1111833937 AX-519547538 NW_017189516.1 26765724 AGATACAACAGCATCAAATACACCACCTGAGACCA[A/G]GGATAGTAATTTCTAATTGATGGAGTCAAAGAGAA R 2 1 2 1 101000 f 74 goat GoatD01.010986 NW_017189516.1 26765724 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468279006 Affx-1111836625 AX-519552460 NW_017189516.1 28705567 TATCCTTTCTGGCCTGGCAGAAAGAAATTTCTCTA[A/G]GATGTTTTGCTAAGCATTGAGCTGTGGTCATTTAT R 2 1 2 1 101000 r 74 goat Random2.2K_MT-17 NW_017189516.1 28705567 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276209 Affx-1111835296 AX-519549759 NW_017189516.1 28804601 ATTGTGAAATTATTTGTTCTAGCTCTGTGAAAACT[A/G]CCGTTGGTAGCTTGATAGGGATTGCATTGAATCTA R 2 1 2 1 303000 f 74 goat NW_017189516.1_28804601_AF-PAKI NW_017189516.1 28804601 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278847 Affx-1111836634 AX-519552318 NW_017189516.1 29666674 TGGAGTAGCCATCATGGTCAGCAAAAGAGTCTGAA[A/G]TGCAGTATTTGGATGCAATCTCAAAAACAACAGAA R 2 1 2 1 103000 f 74 goat Random2.2K_MT-19 NW_017189516.1 29666674 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278851 Affx-1111836636 AX-519552322 NW_017189516.1 30379754 ATGTTATCTATATAGTGTGATGAACTCTTGACCAA[A/C]GTTAAAGGATGTCTCAAAAGAAGGCAAAATCATGA M 2 1 2 1 101000 f 74 goat Random2.2K_MT-20 NW_017189516.1 30379754 G T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278852 Affx-1111836637 AX-185155164 NW_017189516.1 30980443 TCCATGGGATTTCCCAGGCAAGAATACTGGAGTGG[A/G]TAGCCATTCCCTTCTCCAGGGATCTTCCCAACCCA R 2 1 2 1 303000 f 74 goat Random2.2K_MT-21 NW_017189516.1 30980443 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275540 Affx-1111834866 AX-519549112 NW_017189516.1 31014688 GGTGAGGCAGTGAGGGCGAGCTTAAGGGGAGTTCT[A/G]TGAACAGAATCTAGAGGGGAGCAGAAAAGATGAAC R 2 1 2 1 102000 r 74 goat GoatD01.057063 NW_017189516.1 31014688 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276211 Affx-1111835297 AX-519549761 NW_017189516.1 31360179 ACCAAAGAAAGAAAGAAAAGAACCAAGCCTCAACT[A/G]AATGAGTTATTGAAAGCAAAATTAAACAGATGCAA R 2 1 2 1 103000 f 74 goat NW_017189516.1_31360179_AF-PAKI NW_017189516.1 31360179 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468274032 Affx-1111833997 AX-519547636 NW_017189516.1 32115421 AAAGAATATCACACTAAAATGAAGTCAGACAGAGA[A/G]AGACAAATACTATATGGGGGGCTCAGAGGTAAAGA R 2 1 2 1 303000 f 74 goat GoatD01.013302 NW_017189516.1 32115421 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468279020 Affx-1111836638 AX-519552474 NW_017189516.1 32946059 TTTCCGTTTTTCAGAAGGAGACTCACAGACTTAGA[A/G]AACGAACTTATGGTTGGGGGCAAGGAAAGGAGGGA R 2 1 2 1 102000 r 74 goat Random2.2K_MT-22 NW_017189516.1 32946059 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276360 Affx-1111835298 AX-519549891 NW_017189516.1 34201588 CTTCAATTTAAAAAAAGTCAAAGGGCACCAAATCA[A/G]TTTAGAGACTAGAACAGTTACATGAGGTTTAGGGG R 2 1 2 1 101000 r 74 goat NW_017189516.1_34201588_AF-PAKI NW_017189516.1 34201588 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468273967 Affx-1111833957 AX-519547572 NW_017189516.1 35430311 CGTACCTGTCCATGGCCTTCTACTTCGACGGGGAC[A/G]ACG R 2 1 2 1 102000 f 74 goat GoatD01.011556 NW_017189516.1 35430311 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276217 Affx-1111835300 AX-519549767 NW_017189516.1 37278599 TCTCCCAAATCATGCCACCCTCTCCCTCTCCCTCT[A/G]AGTCCAAAATACTGTTCTATATATCTGTGTCTCTT R 2 1 2 1 103000 f 74 goat NW_017189516.1_37278599_AF-PAKI NW_017189516.1 37278599 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278856 Affx-1111836639 AX-519552326 NW_017189516.1 37430997 ACAAGAGGAAGAGCTCTCCACCATTCAACACTATA[A/C]CACTATCCCCCATACTTATCTGATCACCTGATTTT M 2 1 2 1 101000 f 74 goat Random2.2K_MT-24 NW_017189516.1 37430997 T G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278858 Affx-1111836640 AX-519552328 NW_017189516.1 38304759 ATAAGTTTTAATAAACATGTGAACCCATTTTAAAA[A/C]TGAAAGAGACAAAATTAATCTTCTAGGATTACCTG M 2 1 2 1 201000 f 74 goat Random2.2K_MT-25 NW_017189516.1 38304759 A C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279023 Affx-1111836641 AX-519552477 NW_017189516.1 40704157 GAAGGACTAAACCCTGCAGGGCTGGAATGGTAACC[A/G]TGTTACCCTCCCAATGTTTTATTAGCTACACTCTG R 2 1 2 1 201000 r 74 goat Random2.2K_MT-26 NW_017189516.1 40704157 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278864 Affx-1111836643 AX-519552333 NW_017189516.1 41107455 TATGTCTATAAGTGGAAGTGGCCATTGAGTCAGCC[A/G]TGCTCCTTTCTCCTTTTCTTATGTTGTGCTTCTCT R 2 1 2 1 201000 f 74 goat Random2.2K_MT-28 NW_017189516.1 41107455 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276219 Affx-1111835301 AX-519549769 NW_017189516.1 43118405 ATCATCAGCTTCTATACGTCTTCTGCTGTTCACTC[A/G]CCCAGCCGTGTCCGACTCTGTGCGAACCCCCTGGA R 2 1 2 1 101000 f 74 goat NW_017189516.1_43118405_AF-PAKI NW_017189516.1 43118405 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468279026 Affx-1111836644 AX-519552479 NW_017189516.1 44780078 CAGGTTTGATGAGAGTACCTTCTGTAGGGCAAGAC[A/T]GCAGGTGGACAAAATGGAGAAAGAATATATAGACA W 4 1 2 1 202000 r 74 goat Random2.2K_MT-29 NW_017189516.1 44780078 A T 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278869 Affx-1111836646 AX-519552338 NW_017189516.1 44841855 CCTACCCAGTCCAGTCTATTCAGTCAACTTGTTAC[A/G]TAAGTGAGGGGATATATGATCAGATTGTGTTTTAG R 2 1 2 1 101000 f 74 goat Random2.2K_MT-30 NW_017189516.1 44841855 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276221 Affx-1111835302 AX-519549771 NW_017189516.1 45742049 GCCCAGGTGATCAGAGGCGGTGAGGATTCCTGAGA[A/G]CGCCGCACAGCACATGGGATCTGCGTCATCACTCC R 2 1 2 1 102000 f 74 goat NW_017189516.1_45742049_AF-PAKI NW_017189516.1 45742049 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468279029 Affx-1111836647 AX-519552482 NW_017189516.1 47342365 CTAAAATTAACACAGAAGAAAATCAAAAAAGCCAA[A/C]AAAACTTCACAATGTCAAATGCTGAAGGAAACGTG M 2 1 2 1 102000 r 74 goat Random2.2K_MT-31 NW_017189516.1 47342365 G T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276223 Affx-1111835303 AX-519549773 NW_017189516.1 48951902 TCTTGCTAAACCTAAAATGGGTGACAGCCTACTTA[A/G]AGAAAAGATTTAAGTAAGACTTTGAGTCTCCTAAC R 2 1 2 1 101000 f 74 goat NW_017189516.1_48951902_AF-PAKI NW_017189516.1 48951902 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468279030 Affx-1111836648 AX-519552483 NW_017189516.1 49109441 AATAATAAGAATAATAAAACTAAACATACATATAG[A/C]ATACAACCCAGCAATTGTATTTTGGGGCATCTATC M 2 1 2 1 102000 r 74 goat Random2.2K_MT-32 NW_017189516.1 49109441 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278874 Affx-1111836649 AX-519552343 NW_017189516.1 49698228 CAAGTGTCTATTTTCATGATATTCTTATATCTTTT[A/G]GAAAAAAGGCTACACCTTTTCACAGGTACCTGAAA R 2 1 2 1 201000 f 74 goat Random2.2K_MT-33 NW_017189516.1 49698228 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276277 Affx-1111835331 AX-185744231 NW_017189516.1 49840789 CACCAGGCTCCCCCGTCCCTGGGATTCTCCAGGCA[A/G]GAACACTGGAGTGGGTTGCCATTTCCTTCTCCAAT R 2 1 2 1 303000 f 74 goat NW_017189741.1_15937_AF-PAKI NW_017189516.1 49840789 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468275572 Affx-1111834884 AX-123273020 NW_017189516.1 51405953 TACAGTTCCAGAGAGAGAAATAAGACTG[A/C]TGCACAGGGGAAAATTGTATCCTACAGAACTGGGA M 2 1 2 1 102000 r 74 goat GoatD01.057468 NW_017189516.1 51405953 A C 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278877 Affx-1111836650 AX-312357516 NW_017189516.1 51532027 AAGTGAAAGTTGCTCAGTCCTGTCTGACTCTTTGC[A/G]ACCCCATGGACTATACAGTCCATGGAATTCTCCAG R 2 1 2 1 103000 f 74 goat Random2.2K_MT-34 NW_017189516.1 51532027 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279033 Affx-1111836651 AX-519552485 NW_017189516.1 52050928 ATAGTTGTACTCTCACATCCATACATGGCTACTGG[A/G]AAAACCAAAACTTTAACTAGACGGAACTTTGTTGG R 2 1 2 1 303000 r 74 goat Random2.2K_MT-35 NW_017189516.1 52050928 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278881 Affx-1111836652 AX-519552349 NW_017189516.1 52630220 TGAGCAGATGGTACAAAGGTTTCCCATACACCCAC[A/C]TCCTGCACGCAGTCTCCTCTGTTACCGACACTAGT M 2 1 2 1 101000 f 74 goat Random2.2K_MT-36 NW_017189516.1 52630220 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278883 Affx-1111836653 AX-519552351 NW_017189516.1 52670034 GCACTTTGAAAAGTCAAGAAACTCTATGCTTGATC[A/G]CTCAGTCATTTCTAACTCTTTCAACCCCATGGACC R 2 1 2 1 201000 f 74 goat Random2.2K_MT-37 NW_017189516.1 52670034 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273638 Affx-1111833714 AX-519547251 NW_017189516.1 52767204 GAAGCTCATCTCTTCCATGTGCTCCAGGCCTGCAG[A/G]AGGCAGGCAGATTAACGGCTCCCTAATACTTCTTT R 2 1 2 1 101000 r 74 goat GoatD01.002258 NW_017189516.1 52767204 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278885 Affx-1111836654 AX-519552353 NW_017189516.1 53731366 GAGTTCCCCTTGTCAATGGGATTGAATCAACCTGT[C/G]CCTTTAAGCTTTCATATAAGGGCTGGGAGATTAGA S 4 1 2 1 102000 f 74 goat Random2.2K_MT-38 NW_017189516.1 53731366 C G 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275213 Affx-1111834769 AX-519548792 NW_017189516.1 53755791 CTTTAGAGTCATAACCTGTTCAGGGTCCTGCAGTG[A/G]AGCTGGCTGGTTTGCAGTTTGATCAGCTTTGCTAT R 2 1 2 1 202000 f 74 goat GoatD01.052169 NW_017189516.1 53755791 G A 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276225 Affx-1111835304 AX-519549775 NW_017189516.1 54949003 TCCGACTCTAGCGACCCCATGGACTGCAGCCTCCA[A/G]GGCTCCTCCATCCATGGGATTTTCCAGGCAAAAAT R 2 1 2 1 303000 f 74 goat NW_017189516.1_54949003_AF-PAKI NW_017189516.1 54949003 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278887 Affx-1111836655 AX-519552355 NW_017189516.1 55671302 TGAGTTTGAGAGCATTAAGAGTTCTTAGAACAAGG[A/G]GGGGATCTTTGCAATCAGATTAATGAGGGGAAAGG R 2 1 2 1 201000 f 74 goat Random2.2K_MT-39 NW_017189516.1 55671302 C T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278892 Affx-1111836657 AX-519552360 NW_017189516.1 57155555 CTCCCTTGTAACTTGGCAGTGGACAGTTTGTATAA[C/G]TCTCTGAGAATTTTGGGAAAATTCTGGATTTTGGA S 4 1 2 1 101000 f 74 goat Random2.2K_MT-40 NW_017189516.1 57155555 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276375 Affx-1111835305 AX-519549904 NW_017189516.1 57467664 AGACTCAGAGGTGTGATGGATAAAGTGTCTCTTCA[A/G]TTTCCATTGATCCCAAATGCTCCTTTCTGGACAGT R 2 1 2 1 101000 r 74 goat NW_017189516.1_57467664_AF-PAKI NW_017189516.1 57467664 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276229 Affx-1111835306 AX-519549779 NW_017189516.1 59971908 CATCACTGCAAAGAGGTGAGAGAAAGCATAGCTCA[A/G]CGTAATCTAAACATTACCTCGGAACATATTTCAGC R 2 1 2 1 101000 f 74 goat NW_017189516.1_59971908_AF-PAKI NW_017189516.1 59971908 C T 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468279040 Affx-1111836658 AX-519552492 NW_017189516.1 61545364 CAACTTTAAGTTCCGCCCTGACGTCCCGGCCGGTT[A/G]CATCTGAGACTTACCACCCCCTGTTCAACGACAAA R 2 1 2 1 101000 r 74 goat Random2.2K_MT-41 NW_017189516.1 61545364 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276231 Affx-1111835307 AX-519549781 NW_017189516.1 62500127 GTTCAGGTTCAGAGGCTCAGGTTGCCATCCTCTGC[A/G]TTGTGATTTACCCAGCCCTCCCGAGGGAGCAGAGG R 2 1 2 1 102000 f 74 goat NW_017189516.1_62500127_AF-PAKI NW_017189516.1 62500127 G A 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468279041 Affx-1111836659 AX-519552493 NW_017189516.1 62936462 ATTTCCCTTCATCAATGACTATTTGCTTAAGATGC[A/G]CTTTTTCAGATGGAATTGCTAGCCCAAAGGACATT R 2 1 2 1 101000 r 74 goat Random2.2K_MT-42 NW_017189516.1 62936462 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279042 Affx-1111836660 AX-519552494 NW_017189516.1 64328770 TACAAAACATACATTCTTTATGATGTCTATATAGA[A/G]GTAAATGTTTACAGCACACTGTACTGAACTTATTT R 2 1 2 1 101000 r 74 goat Random2.2K_MT-43 NW_017189516.1 64328770 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278900 Affx-1111836661 AX-185910067 NW_017189516.1 64827710 TGTCCATGGGATTCTCCAGGCAAGAATATTGGAGT[A/G]GGTTGCCGTTTCCTTCACTTCATTTATTCTATTTG R 2 1 2 1 103000 f 74 goat Random2.2K_MT-44 NW_017189516.1 64827710 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276232 Affx-1111835308 AX-519549782 NW_017189516.1 65003790 AGATAGGTCCTGGTGATTCTTAGAAGAGAAGGTGG[A/G]TCTTCAGAGAGTGGCCACCATGAAGAGCTGGATGG R 2 1 2 1 102000 f 74 goat NW_017189516.1_65003790_AF-PAKI NW_017189516.1 65003790 T C 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278902 Affx-1111836662 AX-519552369 NW_017189516.1 65021182 TGGAAATAGAATCTAAAAACAGGCAGATACATAAT[A/T]TGTATCAGTTCTAATGAGACGGATGAAACTGGAGC W 4 1 2 1 201000 f 74 goat Random2.2K_MT-45 NW_017189516.1 65021182 A T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278904 Affx-1111836663 AX-519552371 NW_017189516.1 65449631 CCTGACACCCCAGAAAAAAAGAAAAGAAAATAGAG[A/C]TATTTCAGAATAAGGAGGAAAAATAAAAATAGAGC M 2 1 2 1 103000 f 74 goat Random2.2K_MT-46 NW_017189516.1 65449631 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273619 Affx-1111833729 AX-519547232 NW_017189516.1 65826995 GATTATCACTGGGCCTCTGTGTTCGCTCAGTGGCA[A/G]ATAATCCACCTGCAAATGCAGGAGACTTGGGCTC R 2 1 2 1 102000 f 74 goat GoatD01.002725 NW_017189516.1 65826995 G A 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276396 Affx-1111835315 AX-519549923 NW_017189517.1 26257 CAACTCTGGTCCAAAGGCTACCTGTAATAAACATC[A/C]AGTTGCACAGTACTTATCTCTCTAGGCGAGTCACA M 2 1 2 1 101000 r 74 goat NW_017189517.1_26257_AF-PAKI NW_017189517.1 26257 C A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468275105 Affx-1111834692 AX-519548684 NW_017189517.1 156344 GACCCAACCTGGAAAAGAAACCCTTCTGACAGGTA[A/G]ACAGCTGCATTACAGGCATACTGCAGATACCAAGA R 2 1 2 1 202000 f 74 goat GoatD01.046085 NW_017189517.1 156344 T C 2 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276399 Affx-1111835316 AX-519549926 NW_017189517.1 2671123 GCATACAATCCCCTCAAAAGCTCAATCCTGGAGGT[A/G]AGGATTGACAGGTGTGCTTTAGTTGTGTTCAATTT R 2 1 2 1 101000 r 74 goat NW_017189517.1_2671123_AF-PAKI NW_017189517.1 2671123 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468274318 Affx-1111834130 AX-519547914 NW_017189517.1 2767692 TAGTAGTAGGCCAGAGTTCTGGGATGGTTCTCAGC[A/C]GGGTGCTCTGGCTGGCAAGGACTAAAAACAGTTTC M 2 1 2 1 101000 r 74 goat GoatD01.020401 NW_017189517.1 2767692 C A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278906 Affx-1111836664 AX-519552373 NW_017189517.1 3016091 ACTCCACTCTTTAATAGCTCCTCTTATAAACTATT[C/G]CTACTTCATTTATCTAGGCCAGGGCTTCCCAGGTG S 4 1 2 1 101000 f 74 goat Random2.2K_MT-47 NW_017189517.1 3016091 G C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276417 Affx-1111835325 AX-519549944 NW_017189517.1 5527853 AGCTTCCCTAACCAGGAAAACTTGACAAGCCACCC[A/G]TACAACCCCACCCAGAGTGAGGAAACTCCACAATA R 2 1 2 1 103000 r 74 goat NW_017189517.1_5527853_AF-PAKI NW_017189517.1 5527853 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278909 Affx-1111836665 AX-519552376 NW_017189517.1 5963930 GACTTTTAGACTCTATGGGAGATGGAGAGGGTGCG[A/G]TGATTTGGGAGAATGGCAAACATGTATACTATCAG R 2 1 2 1 103000 f 74 goat Random2.2K_MT-49 NW_017189517.1 5963930 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279049 Affx-1111836667 AX-519552500 NW_017189517.1 7134258 TCCTATTCTCCCTGCTCCCAACATGGGTTTCAAAG[A/G]AAGTCCTACATACACCCTAAAGCTCCACTTAAATG R 2 1 2 1 101000 r 74 goat Random2.2K_MT-50 NW_017189517.1 7134258 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276267 Affx-1111835326 AX-185130607 NW_017189517.1 8122244 TCTCTTGTGTTGTTGGAAGAGGGTGTTTGCTATGA[A/C]CAGTGCATTCTCTTGGCAAAACTCTGTTAGCCTTT M 2 1 2 1 303000 f 74 goat NW_017189517.1_8122244_AF-PAKI NW_017189517.1 8122244 T G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278915 Affx-1111836668 AX-185185846 NW_017189517.1 9753016 GCAACCCACTCCAGTATTCTTGCCTGGAGAATTCC[A/G]TGGACAGAGGAGCCTGGTGGGCCACAGCCCATGGG R 2 1 2 1 103000 f 74 goat Random2.2K_MT-51 NW_017189517.1 9753016 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276236 Affx-1111835310 AX-519549786 NW_017189517.1 10688070 AAAAAATGAAGACCATAGCATCCAGTCTCATCACT[A/C]ACTTCATGGCAAATAGAAGGGAAAAAAATTGTAAC M 2 1 2 1 103000 f 74 goat NW_017189517.1_10688070_AF-PAKI NW_017189517.1 10688070 G T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468279051 Affx-1111836669 AX-519552502 NW_017189517.1 12585684 TCTAATGCAACTTCCAATGCAATGTGATAGAAACC[A/C]AGTGCAGAAGAGCAAGCGCATCACCTAGTGACGCA M 2 1 2 1 201000 r 74 goat Random2.2K_MT-52 NW_017189517.1 12585684 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279052 Affx-1111836670 AX-519552503 NW_017189517.1 12655559 GTATTCTATTATAGAAAGCATGGAGAATCAAATTA[A/G]AAAGCATAAGAAGCTGAAAAACTCAATGAATCTCT R 2 1 2 1 101000 r 74 goat Random2.2K_MT-53 NW_017189517.1 12655559 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468275030 Affx-1111834644 AX-519548612 NW_017189517.1 12783527 CATTTATTATTTCCTAGTTCTGCAGGTTTAGAAGT[A/G]TGGGTACGGGGTACGTTGGCTGGTTTCTATGCTTT R 2 1 2 1 201000 f 74 goat GoatD01.044331 NW_017189517.1 12783527 G A 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278922 Affx-1111836671 AX-186147319 NW_017189517.1 12803105 CTCCAGGGGATCTTCCCAACCCAGGGATTGAACCC[A/G]CGTCTCCTTTGCTTTCTGCATTGCAGGCAGATTCT R 2 1 2 1 303000 f 74 goat Random2.2K_MT-54 NW_017189517.1 12803105 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278925 Affx-1111836672 AX-187325786 NW_017189517.1 13173784 GTCATGTCCGACTCTTTGCGACCCCATGAATCGCA[A/G]CACGCCAGACCTCCCTGTCCATCAACTCCCGGAGT R 2 1 2 1 303000 f 74 goat Random2.2K_MT-55 NW_017189517.1 13173784 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276387 Affx-1111835311 AX-519549915 NW_017189517.1 13557939 GGAAATTTCTGAACACAATATTTTGATTAACCTAG[A/G]CTTAAACTAGCTGTAAACAAATTGTGTACTCTAGG R 2 1 2 1 101000 r 74 goat NW_017189517.1_13557939_AF-PAKI NW_017189517.1 13557939 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468274070 Affx-1111833989 AX-519547674 NW_017189517.1 14164522 TCTTGTTGGGGGT[A/G]GGGGAATGCAGCCCAGGGATATGCATTTTAGCCAC R 2 1 2 1 102000 r 74 goat GoatD01.012939 NW_017189517.1 14164522 A G 1 neutral Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278927 Affx-1111836673 AX-519552390 NW_017189517.1 14762409 TATACAGTCAGCAAAAATAAGACCGGGAGCTGACT[C/G]TGGCTCAGATCATGAACTCCTTATTGCCAAATTCA S 4 1 2 1 303000 f 74 goat Random2.2K_MT-56 NW_017189517.1 14762409 C G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273519 Affx-1111833667 AX-519547134 NW_017189517.1 14797611 GAGGGATTTGGCTATTTAAAGTCCCTCAAGGAAAC[A/C]AGGAGGTTTCCAGATTTGTTCTGCAGCCATGGTCA M 2 1 2 1 101000 f 74 goat GoatD01.001044 NW_017189517.1 14797611 T G 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468279056 Affx-1111836674 AX-519552506 NW_017189517.1 16001930 AAATGCATGGTATTGCTTCAGTACAACACTCTGCT[A/G]TTAGAAAACGTGGTAGCAAAGACCCTGCTCTGGGA R 2 1 2 1 101000 r 74 goat Random2.2K_MT-57 NW_017189517.1 16001930 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468274112 Affx-1111834045 AX-519547715 NW_017189517.1 17069969 CATGAGGAATTTTGTGGTATTGCCTGTAAATCAGT[A/G]TAGCAAAGGACAGCTGCTGCAGCCTTGTATTCTGT R 2 1 2 1 201000 f 74 goat GoatD01.015826 NW_017189517.1 17069969 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468278932 Affx-1111836675 AX-169387580 NW_017189517.1 18784078 GAAAAGCAGAGACATTACTTTGCCAACAAAGGTCC[A/G]TCTAGTCAAGGCTATGGTTTTTCCTGTGGTCATGT R 2 1 2 1 303000 f 74 goat Random2.2K_MT-58 NW_017189517.1 18784078 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276389 Affx-1111835312 AX-519549917 NW_017189517.1 19112187 AGTCAGAGAAGAAAAGAAAGAAGGAAGGAAGGAAG[A/G]GAGAAAGAACAAAGAAAGCCTGCATAGACTATGAG R 2 1 2 1 202000 r 74 goat NW_017189517.1_19112187_AF-PAKI NW_017189517.1 19112187 T C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276242 Affx-1111835313 AX-519549791 NW_017189517.1 21644504 CTCTGAAGACGTCTGGTCCTGGGCTTTTGTTTGCT[A/G]GAAGATTCCTGATTACAGTTTCAATTTCTGTGCTT R 2 1 2 1 103000 f 74 goat NW_017189517.1_21644504_AF-PAKI NW_017189517.1 21644504 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276244 Affx-1111835314 AX-187484744 NW_017189517.1 24683412 AGTCCCTTAAATCTATTTCTCACTTCCACTGTATA[A/G]TCATAAGGGATTTGATTTAGGTCATACCTGAATGG R 2 1 2 1 303000 f 74 goat NW_017189517.1_24683412_AF-PAKI NW_017189517.1 24683412 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276401 Affx-1111835317 AX-519549928 NW_017189517.1 27476520 TCCTAGGAGCACTGTGCACTGTGACCATGCAGTCC[A/C]GCTAAGGGACCCCGTGGCTATGTGGTCCACACACC M 2 1 2 1 202000 r 74 goat NW_017189517.1_27476520_AF-PAKI NW_017189517.1 27476520 A C 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276403 Affx-1111835318 AX-519549930 NW_017189517.1 30221152 ATAGATTATGTAATTCATCCAAGACTGAAAAATTG[A/G]TTCTGATAAAGGCTCAAACGCATTCTCCTAAAAGT R 2 1 2 1 101000 r 74 goat NW_017189517.1_30221152_AF-PAKI NW_017189517.1 30221152 G A 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276254 Affx-1111835319 AX-519549801 NW_017189517.1 32840546 ATTGTTTAGTCTAAAACAACCATCTTTAAAAAAAA[A/C]AAAAAAAAAACTCAGTACACTACCATTTAACTTGT M 2 1 2 1 103000 f 74 goat NW_017189517.1_32840546_AF-PAKI NW_017189517.1 32840546 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468274452 Affx-1111834296 AX-519548044 NW_017189517.1 35098242 AGACATTATCCATCAAATTGGCCAGGGACTGCAGG[A/C]AAAGGAATTTCTGTAGACATTTGATTAAGAAAAGT M 2 1 2 1 101000 f 74 goat GoatD01.029410 NW_017189517.1 35098242 A C 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276256 Affx-1111835320 AX-519549803 NW_017189517.1 35667371 GTGGGTTGCCATTTCTTTCTCCAAGGGAACTTCCC[A/G]ACCCAGGGATCGAACCCAGGTCTCCTGCATTGCAG R 2 1 2 1 103000 f 74 goat NW_017189517.1_35667371_AF-PAKI NW_017189517.1 35667371 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276410 Affx-1111835321 AX-519549936 NW_017189517.1 38413040 TTAATCTCCAATTAAATAAATTTATATTAAAAAAA[A/G]AAAAAAAGTGATGGGAGAGAGGGGCAACGACTCAG R 2 1 2 1 103000 r 74 goat NW_017189517.1_38413040_AF-PAKI NW_017189517.1 38413040 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278939 Affx-1111836678 AX-519552399 NW_017189517.1 38753958 TCTTGGATCGTGATTCCTCAAGTCCCTGTCATCTT[A/G]GCCTCCCTTGACTCCAGCTTCTGTCTCTGTAGTGA R 2 1 2 1 101000 f 74 goat Random2.2K_MT-64 NW_017189517.1 38753958 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278941 Affx-1111836679 AX-519552401 NW_017189517.1 39417067 TATAAGAAACAATAAAATTGTTTTTAAAAATAGTT[A/G]CGCCATTTTACAATCCCACCAGCAGTAGATGAGAT R 2 1 2 1 303000 f 74 goat Random2.2K_MT-65 NW_017189517.1 39417067 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279062 Affx-1111836680 AX-519552510 NW_017189517.1 40056374 TGCGCATGTAACAGGCCCCCAGGACAGGAGGCGGT[A/G]CAGTCTGGTTTCCAGCAGTTCCAGGTTCCCTGGTT R 2 1 2 1 102000 r 74 goat Random2.2K_MT-66 NW_017189517.1 40056374 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273500 Affx-1111833636 AX-519547116 NW_017189517.1 40384196 ATATCTGGGGCCAGGTCACCTGAAAGGTGAATGGA[A/G]AATGTAAGAATCTTTTTCTGCAGGTGAACATTTGC R 2 1 2 1 201000 r 74 goat GoatD01.000044 NW_017189517.1 40384196 C T 2 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468276260 Affx-1111835322 AX-519549807 NW_017189517.1 41262232 GTTGCCATTTTCTTTTACAAGGCATGAAAGTGAAA[A/G]TGGTGAAAGTGAAGTCGCTCAGTCCTGTCCGACTC R 2 1 2 1 103000 f 74 goat NW_017189517.1_41262232_AF-PAKI NW_017189517.1 41262232 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278945 Affx-1111836681 AX-519552404 NW_017189517.1 43404612 TCACCTAAAGTTACAAACATATCCGTGGATCAAAT[C/G]TCCACTCCACTTTTATGGAACATCTGGTCTATTGC S 4 1 2 1 201000 f 74 goat Random2.2K_MT-67 NW_017189517.1 43404612 G C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468273943 Affx-1111833942 AX-519547549 NW_017189517.1 43599037 AACTGCATAACATTAAACACATACTGCAGATATAC[A/G]TTCAAATTACAGATGTAACAAACTCTCCACTGAGA R 2 1 2 1 101000 f 74 goat GoatD01.011172 NW_017189517.1 43599037 G A 1 recommended Goat_IGGC_65K_v2 SNPs to be able to join with GBS data + fill remaining gaps (determined after mapping the SNPs on ARS1 assembly) 468279064 Affx-1111836682 AX-519552512 NW_017189517.1 43621115 ACCCAGCAGGACCCCATAGGAGATCCTAGGCATGG[A/G]TAATGTTTCTGTTCACCATCGGTGACCTTCCCTGA R 2 1 2 1 101000 r 74 goat Random2.2K_MT-68 NW_017189517.1 43621115 C T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276262 Affx-1111835323 AX-187714201 NW_017189517.1 44189636 TGTCCATCGAGTCAGTGATGCCATCCAACCATCTC[A/G]TCCCCTGTTGTCCCCTTCTCCTCCTCCCTTCAATC R 2 1 2 1 103000 f 74 goat NW_017189517.1_44189636_AF-PAKI NW_017189517.1 44189636 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276416 Affx-1111835324 AX-519549941 NW_017189517.1 46692184 GAAGCCAGTAGATATTGGTTCATGATGTTTAAGGA[A/G]AGAAGTTGGCTCCATAACATAAGAGTACAAGGAGA R 2 1 2 1 101000 r 74 goat NW_017189517.1_46692184_AF-PAKI NW_017189517.1 46692184 A G 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278952 Affx-1111836684 AX-519552410 NW_017189517.1 49445401 TGGCAAGGTGTGCAAATGATCTTTGGTTCTAAAAA[A/T]CAGTAGATAGTAGACACTGTATACAATAGGAACTG W 4 1 2 1 101000 f 74 goat Random2.2K_MT-70 NW_017189517.1 49445401 A T 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278954 Affx-1111836685 AX-426479540 NW_017189517.1 49507576 TTCAGTCATGCCCGACTCTGTGCGACCCCATAGAC[A/G]GAAGCCCACCAGGCTCCTCCGTTCACAGGATTCTC R 2 1 2 1 103000 f 74 goat Random2.2K_MT-71 NW_017189517.1 49507576 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278956 Affx-1111836686 AX-519552414 NW_017189517.1 49871858 GATCAAATTGCCAACATCAGTTGGATCATCAAAAA[A/T]GCAACAGAGTTCCAGAAAAACATCTACTTTGCTTT W 4 1 2 1 103000 f 74 goat Random2.2K_MT-72 NW_017189517.1 49871858 T A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278958 Affx-1111836687 AX-519552416 NW_017189542.1 20926 CATCCTACCTCTACTGAGTCAACATTATATGGCAT[A/T]CATGATCCAACTTCTGAGTTTGCACTATGGAATAC W 4 1 2 1 103000 f 74 goat Random2.2K_MT-74 NW_017189542.1 20926 A T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278960 Affx-1111836688 AX-519552418 NW_017189545.1 76460 CAGGTTAGCCACCATCTCATTCAGAGCTACCGGGG[A/G]CAAGGCCAGAGACTGGGGGTGGGGGGGCAATTGCA R 2 1 2 1 102000 f 74 goat Random2.2K_MT-75 NW_017189545.1 76460 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276269 Affx-1111835327 AX-519549813 NW_017189552.1 282898 TCTGATTCCCAAAGTAGCCCTCTTCCTAATAACCC[A/C]AGGTTTGTCCCTTCTGACTCCATGTTTGCATCACC M 2 1 2 1 101000 f 74 goat NW_017189552.1_282898_AF-PAKI NW_017189552.1 282898 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468279071 Affx-1111836689 AX-519552519 NW_017189554.1 18009 TTTTCCCCTTTTCTCTTCTCCTCCCCAGAAGTCCC[A/G]AGGTTGGAGACTTCTGGTCATAGAATCTGTATGTG R 2 1 2 1 201000 r 74 goat Random2.2K_MT-76 NW_017189554.1 18009 G A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278964 Affx-1111836690 AX-519552422 NW_017189563.1 302869 TAAGCAGAAGTGGCAATACTTATGTAAGAAAAATT[A/T]GATTTTGGAATAAAGACAATGATAAGAGACAAAGA W 4 1 2 1 201000 f 74 goat Random2.2K_MT-77 NW_017189563.1 302869 A T 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279073 Affx-1111836691 AX-519552521 NW_017189575.1 12303 ATGGACAAGGGCCCACCTCAACCCCAGAGCTTCTC[A/G]GGTGGCCCTCCTTCCAAATTTGGATTCTCTTCTGT R 2 1 2 1 202000 r 74 goat Random2.2K_MT-78 NW_017189575.1 12303 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276424 Affx-1111835328 AX-519549949 NW_017189596.1 459023 TTGCTGCTGTTATAATTATTATTTAACAGATATTA[A/G]TACTGTGCTAAGTGCCAAGCCCTATCCTAAGCACT R 2 1 2 1 101000 r 74 goat NW_017189596.1_459023_AF-PAKI NW_017189596.1 459023 T C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278968 Affx-1111836692 AX-519552426 NW_017189605.1 7854 GCATCAATGCATCCAGATGAACTGATTCCCAGATC[A/G]AGTAATAAATTTACCTTATAAAATGAAGTAATTCC R 2 1 2 1 101000 f 74 goat Random2.2K_MT-79 NW_017189605.1 7854 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272510 Affx-1111836718 AX-519546229 NW_017189618.1 399920 ACGGAGGCTGAAAATGCACTCTCCCCACTAGTTTC[A/C]GGAGGAGAGCTAGAGTTACAATTATCTATGTTGCC M 2 1 2 1 101000 r 74 goat Random2.2K_MT-80 NW_017189618.1 399920 A C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278972 Affx-1111836694 AX-185288592 NW_017189627.1 5832 CCAATTTGCCTTGATTCATGGACCTGACATTCCAG[A/G]TTCCTATGCAATATTGCTCTTTACAGCATCGGACC R 2 1 2 1 103000 f 74 goat Random2.2K_MT-81 NW_017189627.1 5832 A G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276426 Affx-1111835329 AX-519549951 NW_017189652.1 5481 CGTGAACGCGCAACCTCACGGGGCATGCACCTGCA[A/G]GCGCACGCAGGACGGCTTGACGTTTGAGAATATGT R 2 1 2 1 102000 r 74 goat NW_017189652.1_5481_AF-PAKI NW_017189652.1 5481 A G 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276427 Affx-1111835330 AX-519549952 NW_017189674.1 75060 AAACTTTTTGTCAAAGCAACCAAACAAAAAACCCC[A/C]TAAGTTTCTAACTTTGTCTCTTCATCTGAAGGAGG M 2 1 2 1 101000 r 74 goat NW_017189674.1_75060_AF-PAKI NW_017189674.1 75060 A C 1 recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468279077 Affx-1111836695 AX-519552524 NW_017189696.1 279577 TCCTCATAATGTTTGCTATGGGTGGAGTTCCTCAC[A/G]TTGGCCCCCAGCACAGGTGAAACCACCCTTTTGGC R 2 1 2 1 202000 r 74 goat Random2.2K_MT-82 NW_017189696.1 279577 G A 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278976 Affx-1111836696 AX-519552433 NW_017189707.1 148027 GGGATTTCTTTGGAAGCAATAATGCTAAAGCTGAA[A/G]CTCCAGTACTTTGGCCACCTCACGAGAAGAGTTGA R 2 1 2 1 103000 f 74 goat Random2.2K_MT-83 NW_017189707.1 148027 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278977 Affx-1111836697 AX-519552435 NW_017189740.1 378099 GACAAACCAGTATGTTTTACTCAGGCAAATGTTCT[A/C]TTCAGCTATGTTAATGAAACTGTATTTGCTTGGAA M 2 1 2 1 103000 f 74 goat Random2.2K_MT-85 NW_017189740.1 378099 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278979 Affx-1111836698 AX-519552436 NW_017189752.1 193276 AATGAATTGGGTCATGTGGGGCTTTATATGTAGGT[A/G]TGTATGTGTGTGTGTTTGTCTTTTTAACATTTTTT R 2 1 2 1 101000 f 74 goat Random2.2K_MT-86 NW_017189752.1 193276 A G 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278981 Affx-1111836699 AX-519552438 NW_017189754.1 24802 AGAATGTGGTCCACTGGAGAAGGGAATGGAAAACC[A/G]TTTCAGTATTCTTGCCTCAAGAACCCCATGAACAG R 2 1 2 1 303000 f 74 goat Random2.2K_MT-87 NW_017189754.1 24802 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276279 Affx-1111835332 AX-166846953 NW_017189774.1 174347 AAAAAAACATCTATTTCTGCTTTATTGACTATGCC[A/G]AAGCCTTTGACTGTGTGGATCACAATAAACTGGAA R 2 1 2 1 303000 f 74 goat NW_017189774.1_174347_AF-PAKI NW_017189774.1 174347 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468276281 Affx-1111835333 AX-519549823 NW_017189840.1 59814 AAGACCTGCCGTGGAAAGTGCACTCTTGCCTCGCA[A/G]CCTCTCTGTCCACATGGGGGCTTGGTTGGGGGAGA R 2 1 2 1 102000 f 74 goat NW_017189840.1_59814_AF-PAKI NW_017189840.1 59814 C T 1 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278985 Affx-1111836701 AX-519552442 NW_017189928.1 1135 AATGCGGAAAAGCCTTCAGTCAGTACTCAAATCTT[A/G]CTCAACACCAGAGAATTCATACTGGGGAGAGGCCT R 2 1 2 1 202000 f 74 goat Random2.2K_MT-89 NW_017189928.1 1135 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272440 Affx-1111836703 AX-519546166 NW_017189962.1 549181 TGCCCCTGCTGCTGCTGCTGCTGCTTCTCAGTCGC[A/G]TCAGTTGTGTCTGACTCTGTGCCACCCCATAGACT R 2 1 2 1 303000 f 74 goat Random2.2K_MT-90 NW_017189962.1 549181 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468272442 Affx-1111836704 AX-519546168 NW_017190018.1 3783 ACTGAAGATTGGGTTTTTAAAGGTAAAAAATTGAT[A/T]AGAAATACCAAAAAGCAAAGATTAAAAATCTGAAG W 4 1 2 1 303000 f 74 goat Random2.2K_MT-91 NW_017190018.1 3783 A T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468276284 Affx-1111835334 AX-519549826 NW_017190074.1 134189 GTGAATGGAAGGGGCAGAGGCTGACTTTGAGGAGT[A/G]CCCATCTGAGGACCCCAGATCGGGAATGAAACAAG R 2 1 2 1 202000 f 74 goat NW_017190074.1_134189_AF-PAKI NW_017190074.1 134189 C T 2 neutral Goat_IGGC_65K_v2 SNPs chosen in breeds not represented in the discovery dataset 468278989 Affx-1111836705 AX-519552444 NW_017190137.1 402752 ATGTCTTAAAGACTTTAACCACATAACACCATAAA[A/T]CTCTTGAAGAGAACACTGGAAAAAAAGTCTCTTAC W 4 1 2 1 101000 f 74 goat Random2.2K_MT-92 NW_017190137.1 402752 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278992 Affx-1111836706 AX-519552447 NW_017190138.1 98451 CAATGAAACCAAGCCATGCCTGTGGGGCAGCCCAA[C/G]ACCAGCGGGTCGTGGTGGAGAGGTCTGACAGAACG S 4 1 2 1 103000 f 74 goat Random2.2K_MT-93 NW_017190138.1 98451 G C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279087 Affx-1111836707 AX-519552534 NW_017190147.1 435614 ATCCCCAGGGCCGGGAGAACGCCTGCTGGCATTAG[A/G]GAAAGGACCCCTGAGGAGCTTGTGAACACCCGGAT R 2 1 2 1 102000 r 74 goat Random2.2K_MT-94 NW_017190147.1 435614 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279088 Affx-1111836708 AX-519552535 NW_017190152.1 24393 AAGTCCTTAACAAAATTCTAGCAAACAGAATCCAA[A/C]AACATATTAAAAACATGGCCAAGTGGGCTTTAACC M 2 1 2 1 102000 r 74 goat Random2.2K_MT-95 NW_017190152.1 24393 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278998 Affx-1111836709 AX-519552453 NW_017190155.1 50499 ATCCTGTCATCCCCTTCTCCCACCTTCAATCTTTC[C/G]CAGCATCAGGGTCTTTTCAAATGAGTCAGTTCTTC S 4 1 2 1 303000 f 74 goat Random2.2K_MT-96 NW_017190155.1 50499 G C 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279001 Affx-1111836710 AX-519552456 NW_017190155.1 81168 CTTCAGATTCTCCCTAAATAGGCCAGAAATAGGAG[A/G]CTCTGGGCCTCTCCTCCTGCTTCAGTGGAGCTGAG R 2 1 2 1 101000 f 74 goat Random2.2K_MT-97 NW_017190155.1 81168 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278798 Affx-1111836609 AX-519552271 NW_017190185.1 5184 CCGTCAATGCCGGGGTTAATATCTTGTGTGGAGTA[A/G]GTGCCGGAACCTGAGCATTCCTCTCCAGTGCTGAC R 2 1 2 1 103000 f 74 goat Random2.2K_MT-150 NW_017190185.1 5184 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278719 Affx-1111836570 AX-519552196 NW_017191871.1 9966 AGATGTCTCAGTCCATTCCAGGGAAACCTTGTTTC[A/C]CTGCACTGCCTCGACTTTCAAGCCGAGGATCGACT M 2 1 2 1 103000 f 74 goat Random2.2K_MT-100 NW_017191871.1 9966 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468277230 Affx-1111835745 AX-519550736 NW_017191943.1 1547 CTTAAATTTTTCTGGTTGGTTGACCACAACTAAGT[A/G]TGCATCTCTAGGAGATGTGTTCTGAAGTCTGAAAG R 2 1 2 1 101000 r 74 goat Random2.2K-1676 NW_017191943.1 1547 T C 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278721 Affx-1111836571 AX-519552198 NW_017192075.1 1949 AATGGACTGAGACATCTGGGGGACTCTGGGAATGG[A/T]GGCTCGACCCTGGAGTTCCTCTCGCCTTTCCTGTG W 4 1 2 1 103000 f 74 goat Random2.2K_MT-101 NW_017192075.1 1949 A T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278723 Affx-1111836572 AX-519552200 NW_017192111.1 5317 GAGTCCCCTGGCTGTCTCAGTCCATTCCAGGGAAA[A/T]CTGTTTTCATTGCACTGCCGCGACTTTCAAGGCCG W 4 1 2 1 303000 f 74 goat Random2.2K_MT-102 NW_017192111.1 5317 T A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278725 Affx-1111836573 AX-519552202 NW_017192135.1 5778 AAGCCTCATGGGAAAGCCTCGAGGGAAAGCCACAG[A/G]TCCCTTGATCCACGCGAAGGGAAGCTTGACACTGC R 2 1 2 1 103000 f 74 goat Random2.2K_MT-103 NW_017192135.1 5778 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278727 Affx-1111836574 AX-519552204 NW_017192274.1 11090 CGCCTCCTCTTGAAATGCTATGGGAACGCCAGGAA[A/T]TCTTTCCCAACCACGCAGGGAAAGGATCCATCGTC W 4 1 2 1 303000 f 74 goat Random2.2K_MT-105 NW_017192274.1 11090 T A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278732 Affx-1111836576 AX-519552209 NW_017192504.1 5115 GGTGTGATTAGCCTCGAGATGCCTCAGCGGAAATG[A/G]GCCTCATTTAGCCTGGAGGGGAGAACCTCCTGGAT R 2 1 2 1 103000 f 74 goat Random2.2K_MT-108 NW_017192504.1 5115 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278734 Affx-1111836577 AX-519552211 NW_017192597.1 13926 ATTGGAGGTGGCCCCTAGAAAGATGGGTCATGCAC[A/G]CCTTCTGTCCAGGCTCAGGCCTAACAGCTGTATGT R 2 1 2 1 102000 f 74 goat Random2.2K_MT-109 NW_017192597.1 13926 G A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278983 Affx-1111836700 AX-519552440 NW_017193322.1 3739 TCACGGAGTTCACAAGACTCATATCTATAGAGTCC[A/G]TGATGCCTTCCAGCCATCTAATCCTCTGTCGTCCC R 2 1 2 1 102000 f 74 goat Random2.2K_MT-88 NW_017193322.1 3739 T C 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278740 Affx-1111836580 AX-519552216 NW_017194271.1 17908 TTTTACTCTAAGTGTTTTATATTTTCTGGTCTTAC[A/C]CTTGCATCTGTAATCCATTTTGAGTTTATTTTTGA M 2 1 2 1 103000 f 74 goat Random2.2K_MT-113 NW_017194271.1 17908 T G 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278980 Affx-1111836611 AX-519552437 NW_017195230.1 4452 TCTTGGGGTACTTCTGGAGTCTCCCCAGGGGAGTC[A/G]GTACTCGTCTCCATGGGGGCATGCAGGTGCCATTT R 2 1 2 1 103000 r 74 goat Random2.2K_MT-152 NW_017195230.1 4452 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278742 Affx-1111836581 AX-519552218 NW_017195322.1 1560 GAAACCCTCTTGGGAAAGCCTCGTGTGAAAGCCTC[A/G]AGCGAAAGCCACAGATCCCTTGATCCACGCGAAGG R 2 1 2 1 303000 f 74 goat Random2.2K_MT-114 NW_017195322.1 1560 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278924 Affx-1111836582 AX-519552388 NW_017195346.1 7986 GGACATGACTGATTTACAGCAGGTCCAGAATAACA[A/G]AGTAGAAACTTCAGCAGAGTCAGCAGATGTGTGAG R 2 1 2 1 202000 r 74 goat Random2.2K_MT-115 NW_017195346.1 7986 T C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278746 Affx-1111836583 AX-519552221 NW_017195384.1 6477 TCCATGTCAGCACGGGCGGGGAATCCTAAGTTTCC[A/G]GCACAGACTCCACACAAGGTCTTAGGCCCCGGCAT R 2 1 2 1 102000 f 74 goat Random2.2K_MT-116 NW_017195384.1 6477 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278782 Affx-1111836601 AX-519552255 NW_017195965.1 11072 AGACATCTGGGGGACTCTGGGAATGGTGGCACGAC[A/C]CTGGAGTTCCTCTCGCCTTTCTTGTAGAGAGTGCC M 2 1 2 1 303000 f 74 goat Random2.2K_MT-140 NW_017195965.1 11072 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278750 Affx-1111836585 AX-519552225 NW_017196176.1 3464 AACGGGGCTCCTCTGGATGTGGGCGGGACTCTCGT[A/G]CTTCCTCTCGAGTGGAGACTGGTATGTCGGGGAAC R 2 1 2 1 303000 f 74 goat Random2.2K_MT-120 NW_017196176.1 3464 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278752 Affx-1111836586 AX-519552227 NW_017196749.1 2378 AAATAAGGGGACACAAAATCATCATTCTTTCCTTG[A/C]TTTCTTTCCTTTATTACTGCACATGCATGTCTTTG M 2 1 2 1 202000 f 74 goat Random2.2K_MT-121 NW_017196749.1 2378 A C 2 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278784 Affx-1111836602 AX-519552257 NW_017197521.1 6822 TCCCTCGAGGCTTTCCCATGAGGCTTTCCCACGAG[A/G]CTTTCCCACAGGGCTGTCCCACGTGCCACCGTGGT R 2 1 2 1 103000 f 74 goat Random2.2K_MT-141 NW_017197521.1 6822 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278836 Affx-1111836628 AX-519552307 NW_017197652.1 1834 CTGCCCTTTCCTGAGGCCACCACAGCGGGTCCCTG[A/T]GGTTTCCGTCGTAAGTCAAGAGCACCTGCCGCAAC W 4 1 2 1 303000 f 74 goat Random2.2K_MT-173 NW_017197652.1 1834 A T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278753 Affx-1111836587 AX-519552228 NW_017198179.1 1809 CAGGGTCGTGCCACCATTCCCAGAGTCCCCCAGAT[A/G]TCTCAGTCCATTGCAGGGAAACCTGTTTTCCCTGC R 2 1 2 1 303000 f 74 goat Random2.2K_MT-123 NW_017198179.1 1809 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278935 Affx-1111836588 AX-519552396 NW_017199166.1 4018 GACTCCAGTTTGTGCTTCATCCAGGCCAGCATTTC[A/G]CATGATGTACTCAGAATTTAAGTTAAATAAACAGA R 2 1 2 1 303000 r 74 goat Random2.2K_MT-125 NW_017199166.1 4018 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278757 Affx-1111836589 AX-186051754 NW_017199210.1 2329 AGGGTGGTGTCATCTGCATATCTGAGGTTACTGAT[A/G]CTTCTTCTGGCAGTCTTGATTCCAGCTTGTGCTTC R 2 1 2 1 103000 f 74 goat Random2.2K_MT-126 NW_017199210.1 2329 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278759 Affx-1111836590 AX-519552232 NW_017199275.1 4120 GGTCGGGAAAGAATTCCCGGTGTTCCCGTCGAATC[A/T]CAAGAGGAGGCGCTCTCCACAGGAAAGGCGAGAGG W 4 1 2 1 103000 f 74 goat Random2.2K_MT-127 NW_017199275.1 4120 T A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278770 Affx-1111836595 AX-519552243 NW_017199733.1 4393 CAGGGCTGTCCCACGTGCCACCGTGGTGTGAGTCG[A/G]TCCTCGGCTTGAAAGTCGAGGCAGTGCAGGGAAAA R 2 1 2 1 303000 f 74 goat Random2.2K_MT-132 NW_017199733.1 4393 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278766 Affx-1111836593 AX-519552239 NW_017200402.1 6038 AAAGGCGAGAGGAACTCCAGGGTCGTGCCACCATT[A/C]CCAGAGTTCCCCAGATGTCTCAGTCCATTCCAGGG M 2 1 2 1 303000 f 74 goat Random2.2K_MT-130 NW_017200402.1 6038 G T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278768 Affx-1111836594 AX-519552241 NW_017200603.1 14071 CGACCAAGCAGGGAAAGGATCCCTCCTCTCGAGCT[A/G]GGAGTCAGCACCGGGTCTCCTCTGGATGTGGGCGG R 2 1 2 1 103000 f 74 goat Random2.2K_MT-131 NW_017200603.1 14071 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278762 Affx-1111836591 AX-519552235 NW_017201843.1 5463 GGACAGCACTTTGGGAAAGCCTCGAAGGAAAGGCA[A/C]AGATCCCTTGACCCATGCGAAGAGAAGCGTGACAC M 2 1 2 1 303000 f 74 goat Random2.2K_MT-128 NW_017201843.1 5463 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278776 Affx-1111836598 AX-519552249 NW_017201989.1 4497 CCCCAAGATCCATATCAGCACTGGAGAGGAAACCT[C/G]AGGTTCCGGCACCGACTCCACACAAGGTCTTAGTC S 4 1 2 1 103000 f 74 goat Random2.2K_MT-137 NW_017201989.1 4497 G C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278788 Affx-1111836604 AX-519552261 NW_017202028.1 1763 GCAGAGAAAACAGGTTTCCCTGCAATGGACTGAGA[A/C]ATCTGGGGGACTCTGGGAATGGTGGAACGACCCTG M 2 1 2 1 103000 f 74 goat Random2.2K_MT-144 NW_017202028.1 1763 G T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278748 Affx-1111836584 AX-519552223 NW_017202432.1 17302 ATTTTCTCGAGTTGCAGCAGGTGCTCTCGACTTAC[A/G]ACGGGGACCTCAGGGACCCGCTCTGTTGGCCTCAG R 2 1 2 1 103000 f 74 goat Random2.2K_MT-118 NW_017202432.1 17302 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278738 Affx-1111836579 AX-519552214 NW_017203239.1 10557 AATTCCCTGTCACTGACTTTAGGATCAGTTCCCTC[A/G]AGCCCCCAGGGGATGCTAGTGGTAAGGAATCCACC R 2 1 2 1 102000 f 74 goat Random2.2K_MT-111 NW_017203239.1 10557 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278774 Affx-1111836597 AX-519552247 NW_017204228.1 3503 CCAGGCGAGATGAGGCCCATTTCCGCTGAGGCGTC[A/T]CGAGGCTAATCACACCTAACCTCTGGAACTTCCAA W 4 1 2 1 303000 f 74 goat Random2.2K_MT-134 NW_017204228.1 3503 A T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278729 Affx-1111836575 AX-519552206 NW_017205840.1 944 GAGATGAGGCCCATTTCCGCTGAGGCGTCTCGAGG[A/C]TAATCACACCTAACCTCTGGAACTTCCAAAGGGTA M 2 1 2 1 303000 f 74 goat Random2.2K_MT-107 NW_017205840.1 944 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278778 Affx-1111836599 AX-519552251 NW_017206180.1 1589 TCCACCGTGCCACCGTGGTGTGAGTTGATCCTCGG[A/C]TTGAAAGTCGAGGCAGTGCAGGGAAAACAGCTTTC M 2 1 2 1 303000 f 74 goat Random2.2K_MT-138 NW_017206180.1 1589 G T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278835 Affx-1111836627 AX-519552306 NW_017206393.1 2087 CGGGATTTCTCTCCCGTCGATGCCGGGGCATAAGA[C/G]CTTGTGTGGAGTCTGTGCCGGAACCTGAGGATTCC S 4 1 2 1 303000 f 74 goat Random2.2K_MT-171 NW_017206393.1 2087 G C 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278786 Affx-1111836603 AX-519552259 NW_017208803.1 9105 ACGTGCCACCATTTTGTGAGTCGATCCTCGGCTTG[A/G]AATTCGACGCAGTGCAGGGAAAACAGTTTTCCGTG R 2 1 2 1 303000 f 74 goat Random2.2K_MT-143 NW_017208803.1 9105 T C 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278790 Affx-1111836605 AX-519552263 NW_017211321.1 23915 AGACTTAAATAGGAGAAAGTAGGGAAGACCATTAT[A/G]CCATTCAAGTATGACCTAAATCAAATCTGTAAATA R 2 1 2 1 103000 f 74 goat Random2.2K_MT-145 NW_017211321.1 23915 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278792 Affx-1111836606 AX-519552265 NW_017211618.1 12538 CTGGCCTACATTGCCCTTGGCTATATACCTGGACA[A/C]AATCAAGGACAGAAATGGTGAAGGCCTAACTGAAG M 2 1 2 1 102000 f 74 goat Random2.2K_MT-146 NW_017211618.1 12538 C A 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278794 Affx-1111836607 AX-519552267 NW_017211877.1 8782 ACTGTAATAATGTTGGCCAGAATGTGCCAAATTGA[A/G]CAATTATTCACTGCTAATTAATGTAAACAGATACA R 2 1 2 1 101000 f 74 goat Random2.2K_MT-148 NW_017211877.1 8782 G A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278796 Affx-1111836608 AX-519552269 NW_017211974.1 6012 ATGGAGGAAGGAGCCTGGTAGGCTGCAAATCCATG[A/G]GGTCCCGAAGAGTTGGACAAGACTGAGCGACTTCA R 2 1 2 1 303000 f 74 goat Random2.2K_MT-149 NW_017211974.1 6012 G A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278800 Affx-1111836610 AX-519552273 NW_017212153.1 12634 CCCTTGGCGTTGCCGTTGCCCTTGCCTTGGTCTTG[A/G]GCTTGGCCTTGCCCTGCCCTTGAACTTGAACTTGA R 2 1 2 1 303000 f 74 goat Random2.2K_MT-151 NW_017212153.1 12634 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278804 Affx-1111836612 AX-519552277 NW_017212483.1 21148 GAAAAGTCTGTCTCGTCAAGCGTTTTACCTTTGGC[A/C]TGGGGGGTTTTCTTTTCAACCTGAAGAAAGCAGGT M 2 1 2 1 201000 f 74 goat Random2.2K_MT-153 NW_017212483.1 21148 C A 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278806 Affx-1111836613 AX-519552279 NW_017213222.1 10693 TTCCTGAGGCCACCAGAGCGGGTCCCTGACGTCCC[A/C]GTCGTAAGTCCGAGAGCTCCTGCCGCAACTCGAGA M 2 1 2 1 303000 f 74 goat Random2.2K_MT-155 NW_017213222.1 10693 C A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278808 Affx-1111836614 AX-185886261 NW_017213352.1 10510 ACAGTCCAACTCTCACATCCATACATGACCACTGG[A/G]AAAACCATAGCCTTGACTAGACGGACCTTAGTGGC R 2 1 2 1 303000 f 74 goat Random2.2K_MT-158 NW_017213352.1 10510 A G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278810 Affx-1111836615 AX-519552282 NW_017213486.1 10927 ATGGATCTTGGGGTATTTCTGGAGTCTCCCCAGGG[A/G]AGTCAGTCCTTGTCTCGAGAGAGGGCATGCACGTG R 2 1 2 1 303000 f 74 goat Random2.2K_MT-159 NW_017213486.1 10927 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278772 Affx-1111836596 AX-519552245 NW_017213741.1 7648 ACCTCTGGAACTTCCAAAGGGTACTTCACACCCTT[A/G]CTGCAACTCAAGAAGTTCCCCGACATACCCGTCTC R 2 1 2 1 303000 f 74 goat Random2.2K_MT-133 NW_017213741.1 7648 A 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278817 Affx-1111836618 AX-519552288 NW_017213763.1 11340 CCTGGCGATCCCGTCACATCTCAAGAGGAGGCGCT[A/C]TCCACAGGAAAGGCGAGAGGAACTCCAAGGTCGTG M 2 1 2 1 103000 f 74 goat Random2.2K_MT-161 NW_017213763.1 11340 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278821 Affx-1111836620 AX-519552292 NW_017213782.1 7760 TGGAAGATGCCCTACTGTTTGAGGGGCGTGTCCAT[A/T]AGGGTGCTGCCCACCACGCTCTGGGCCATTGGACT W 4 1 2 1 103000 f 74 goat Random2.2K_MT-163 NW_017213782.1 7760 A T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278999 Affx-1111836621 AX-519552454 NW_017213824.1 13330 AGACGAGTACTGACTCCCCTGGGGAGACTCCAGAA[A/G]TAACCCAAGATCCATGTCAGCACTGGAGAGGAATC R 2 1 2 1 103000 r 74 goat Random2.2K_MT-164 NW_017213824.1 13330 C T 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278825 Affx-1111836622 AX-519552296 NW_017214131.1 5778 GAGAGTGCATCCCTTGAGATGCGACAGGAATGCCT[A/G]GAAATCTTTCCCGACCATGCAGGGAAAAGATCCCT R 2 1 2 1 103000 f 74 goat Random2.2K_MT-165 NW_017214131.1 5778 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278827 Affx-1111836623 AX-519552298 NW_017214180.1 13219 TATTGCCAAATTCAGACTTAAATTGAAGACAGTGG[A/G]GAAAACCACTATACCATTCAGGTATGACCTAAATC R 2 1 2 1 103000 f 74 goat Random2.2K_MT-166 NW_017214180.1 13219 G A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278819 Affx-1111836619 AX-519552290 NW_017214328.1 9090 AGGCTTTCTAAAGAGGCTTTCCCATGAGGCTTTCC[A/C]ACAGGGCTATCCCACGTGCCACCGTGGTGTGAGTC M 2 1 2 1 103000 f 74 goat Random2.2K_MT-162 NW_017214328.1 9090 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278829 Affx-1111836624 AX-519552300 NW_017214858.1 18906 CTGGTAGGCTGCAGTCTGTGGGGTCACAAAGACTC[C/G]GACACGACTGAGTGACTTCACTTTCACTTTCTACT S 4 1 2 1 303000 f 74 goat Random2.2K_MT-168 NW_017214858.1 18906 C G 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278991 Affx-1111836617 AX-519552446 NW_017215003.1 21467 AAAACATTCCACAGCCAAGGTGCGAGGCTGTCTGC[A/G]CAGAAGTGACAAAAAAGAGTGACCAAAAAGTGATG R 2 1 2 1 102000 r 74 goat Random2.2K_MT-160 NW_017215003.1 21467 C T 1 neutral Goat_IGGC_65K_v2 SNPs with different MAF profiles 468277099 Affx-1111835680 AX-519550605 NW_017215097.1 2904 GTTTTGATAACCATAAACACTAAACAAATAAACTT[A/T]AAGTAAGAGTCTAAAGTGTCAGGGTGAATGAGCTT W 4 1 2 1 101000 r 74 goat Random2.2K-1571 NW_017215097.1 2904 T A 1 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278833 Affx-1111836626 AX-519552304 NW_017215575.1 5172 AATTCTAGACTTTACTATTTTCAAACCTACAGAGT[A/G]ATAAGCATAAACCAAGGGTCTTTCCAGTCAGTACT R 2 1 2 1 201000 f 74 goat Random2.2K_MT-170 NW_017215575.1 5172 A G 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278838 Affx-1111836629 AX-519552309 NW_017216187.1 8818 GAGCCACGTTTCCGCCTCCTACCTCGAGAGGTTTG[A/G]TCCCTTCCCTGCGTGGGGGGAAAGAATTCGCGGCG R 2 1 2 1 103000 f 74 goat Random2.2K_MT-175 NW_017216187.1 8818 T C 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279003 Affx-1111836711 AX-519552458 NW_017217089.1 2740 ACGGGGCTCCTCTGGATGTGGGCGGGACTCTCGTG[A/C]TTCCTCTCGAGTGGAGACGGGTATGTCGGGGAACT M 2 1 2 1 303000 f 74 goat Random2.2K_MT-98 NW_017217089.1 2740 A C 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278840 Affx-1111836630 AX-519552311 NW_017217366.1 7654 GGTTCTCCCCTCCAGGCGAGATGAGGCCCATTTCC[A/G]CTGAGGCAACAAATAGAAATTGACAATGTAATCTG R 2 1 2 1 303000 f 74 goat Random2.2K_MT-176 NW_017217366.1 7654 C T 3 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468279013 Affx-1111836631 AX-519552467 NW_017218062.1 18249 AACTTGCCAGGGCAAACGTGTGCAGAGGGAAAAGG[A/G]GAGGTTATGCAGGAAATTTTAGTTGACTAAATAGA R 2 1 2 1 201000 r 74 goat Random2.2K_MT-178 NW_017218062.1 18249 T C 2 recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 468278844 Affx-1111836632 AX-519552315 NW_017218079.1 7937 ACCCTTTGGAAGTTCCCGAGGTTAGGTGTGATTAG[A/C]CTCGAGACAGCTCAGCGGAAATGGGCCTCATCTCG M 2 1 2 1 103000 f 74 goat Random2.2K_MT-179 NW_017218079.1 7937 C A 1 not_recommended Goat_IGGC_65K_v2 SNPs with different MAF profiles 38451019 Affx-122921458 AX-123321353 X 94978 GTTTTCTCTAGTGAATTTTATAGGCCAGCACCAAA[C/T]AATCTGTCCATTCTCATTGATAAGACTGAATTTAC Y 2 1 2 1 201000 r 74 goat snp34315-scaffold403-94978 NW_017189517.1 48191827 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423766 Affx-122942842 AX-123294112 X 219114 TCTTCCTGTAATGATGCTCTATGATATGGCACTAA[C/T]AAGAGCAAGGACACTTGTGGCACCAGATATTCCCA Y 2 1 2 1 201000 f 74 goat snp34317-scaffold403-219114 NW_017189517.1 48998238 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377564 Affx-122977444 AX-123247923 X 302467 TGTTGTTTTGAATCATTGCTACAATGAGATAGGAG[C/T]GGAGAAATCCTGCCTGCTTGAGCATAATTAGTCTG Y 2 1 2 1 101000 f 74 goat snp34318-scaffold403-302467 NW_017189517.1 49081703 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448921 Affx-122923164 AX-123319256 X 416634 CCCAGTTCCCTAGCAAGATTTTTTTTTAAGTGAAG[C/T]AAAATGTTTATTAGGAGGAAAAAGAGGACGTGTGA Y 2 1 2 1 201000 f 74 goat snp34320-scaffold403-416634 NW_017189517.1 49195373 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801607 Affx-122947433 AX-385288516 X 510260 TACACTGAAATTAGAAAGAAGTCAATAAAGTAAAG[C/T]AAATTCTAAACTATATGGTTACTAATAATCCCCCT Y 2 1 2 1 101000 f 74 goat snp34322-scaffold403-510260 NW_017189517.1 49290290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773607 Affx-122946367 AX-385260747 X 572368 CAACCAGAATGCAATTTCCTTGAAAGCAGTGAGGG[A/G]AGGCATTTTATAGATATAGTTGTATTTATTACATA R 2 1 2 1 101000 f 74 goat snp34323-scaffold403-572368 NW_017189517.1 49352685 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401477 Affx-122958959 AX-123271830 X 609731 TGTTTGAGATTCAGTTAGAAGATCCTCATGAATTA[C/T]AATTTGGCATGATTATATTTAGTCTGTGTATTCCT Y 2 1 2 1 101000 r 74 goat snp34324-scaffold403-609731 NW_017189517.1 49390499 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451774 Affx-122921510 AX-123322107 X 646318 AGTAGCTTTTATTAAGTGGTTAGTGTCTACGTTTT[A/G]TGCATCTAGTTTATCTTTGCCTTATATTGTCAGCA R 2 1 2 1 101000 r 74 goat snp34325-scaffold403-646318 NW_017189517.1 49429680 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401870 Affx-122958861 AX-123272223 X 690869 AACATGGAAGGCCCAGATGTAATAATCAGCTGTTG[C/T]AATGTTACCAACATGAATTCATATTTTTGGTTTAT Y 2 1 2 1 101000 r 74 goat snp34326-scaffold403-690869 NW_017189517.1 49475583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447032 Affx-122924536 AX-123317368 X 831543 AATTTAAGGAACAAAAAATCCCATAAAGCCACTGG[C/T]GGTTTGTGATTCTGTCAACACCTTGATTTTGGACT Y 2 1 2 1 201000 f 74 goat snp34328-scaffold403-831543 NW_017189517.1 49619074 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387392 Affx-122970420 AX-123257750 X 907163 AGCTGTGCATAAATAAATGTGTTTTGAACTGTGTT[C/T]ACTGGTGAAATAATAGCTTCCCAGGTTTGCTTCCT Y 2 1 2 1 103000 r 74 goat snp34330-scaffold403-907163 NW_017189517.1 49695247 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422128 Affx-122943552 AX-123292475 X 937118 ATAGTGATGGAGAGCAGGGGAAAAGTTAAAAGGAA[C/T]GAAAAGCATAGTTGGTATCCACAGCTGCCTTTCCT Y 2 1 2 1 101000 r 74 goat snp34331-scaffold403-937118 NW_017189517.1 49725584 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772611 Affx-122938692 AX-385259759 X 1120552 AATTTGATGAATTTGGACATATTTATATACCCATG[C/T]AACCATCACTGTCAACAAGACTACAGAAAAATATA Y 2 1 2 1 101000 r 74 goat snp34334-scaffold403-1120552 NW_017189517.1 49912514 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797352 Affx-122924098 AX-385284291 X 1149549 AAATTTCCCACATAGTTTATCCCACATAAAGAAAA[C/T]GACTGCATTGAAAAGGTAGTTCAAAACATATTCTC Y 2 1 2 1 101000 r 74 goat snp34335-scaffold403-1149549 NW_017189517.1 48168543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412149 Affx-122951085 AX-123282499 X 1274121 TCCCTGTGTTTGTGCTGTGATTGTACTAAGAAAAT[A/G]TGATGACAAAATATTCACATGCAGGTAAACCAATT R 2 1 2 1 101000 r 74 goat snp34337-scaffold403-1274121 NW_017189517.1 48043215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797209 Affx-122972178 AX-385284148 X 1426016 GTAGGACATTTGGTCATATTCATATCCAAATGTAA[C/T]GATGTTTCAGTCAATTCAGTTTCTTTTCCATAATT Y 2 1 2 1 202000 r 74 goat snp34340-scaffold403-1426016 NW_017189517.1 47888679 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776699 Affx-122973310 AX-385263825 X 1524820 TCCTAACTTGCCATGCTTTAAATCATATCCCTTTT[A/G]TCAAAAATTTATAATCTACTCTGTGCATGATTGAG R 2 1 2 1 101000 f 74 goat snp34342-scaffold403-1524820 NW_017189517.1 47788565 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794529 Affx-122934368 AX-385281492 X 1615793 ACTAGATTGGTCTTTTAAAAATATGGTGTTTTGTC[A/G]CATGTATACTACATAGATTGTATACTACAATGTAT R 2 1 2 1 102000 f 74 goat snp34344-scaffold403-1615793 NW_017189517.1 47700064 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801102 Affx-122973930 AX-385288016 X 1694164 TCAGTGAGCTCAGGAATAAAATTAGTGAAGAAAAG[A/G]AATAGTTTACCAAAGAGATCAAAACTCCAAATAAA R 2 1 2 1 103000 f 74 goat snp34345-scaffold403-1694164 NW_017189517.1 47618787 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415503 Affx-122948690 AX-123285852 X 1802194 TGATCAGGAGTTCTCGGGTGGTTCAAAGTCCTGGA[C/T]TTGGGTCTCCCACCTCAGGGGTCCAGAATCAGCCC Y 2 1 2 1 202000 r 74 goat snp34347-scaffold403-1802194 NW_017189517.1 47537381 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386111 Affx-122971426 AX-123256469 X 1873642 GTCAGTCACCTGGATCCTTCTAGCTCCCTTCCTGC[A/G]TCATCCATCAGTTCCCTGAACCAAAACAGTAGCCA R 2 1 2 1 101000 r 74 goat snp34348-scaffold403-1873642 NW_017189517.1 47464321 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435944 Affx-122933539 AX-123306283 X 1928256 GTCCAGATAAGAAGAATAGACTAAAACTTGAATTA[C/T]ACACTTTGTCATCTGAAGTTGTATTTCCAATACTT Y 2 1 2 1 101000 f 74 goat snp34349-scaffold403-1928256 NW_017189517.1 47409994 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397906 Affx-122961946 AX-123268261 X 2114977 GCCCAAGGAGGGAAACTCTCCGCTATTCAAGTGGG[C/T]GCCAGTGGCCCACATAGGTGGTGCAAGCTTCTTGT Y 2 1 2 1 303000 f 74 goat snp34352-scaffold403-2114977 24 9817502 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784849 Affx-122930505 AX-385271896 X 2181436 TTGCATATAAACCCTCTATTGTCCTCACAAATACT[G/T]AGGTTCCGGAATCTTTTGTTTTCTTGTCTTATAAA K 2 1 2 1 201000 r 74 goat snp34353-scaffold403-2181436 NW_017189517.1 47180322 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430725 Affx-122936893 AX-123301066 X 2210152 ACGAACAACCAGGCACTCTCCTCAGAGCTCATTTC[A/G]AAGTTCAAACCACTCACTCCCAAGATCTCACGTCA R 2 1 2 1 101000 r 74 goat snp34354-scaffold403-2210152 NW_017189517.1 47153326 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403958 Affx-122957444 AX-123274310 X 2258447 AATGAGCCAAAGCATGTGAATTAGAAACTTTACAT[A/G]GGGATTTGACTTCAAATCACATCACATAAGCATCT R 2 1 2 1 101000 f 74 goat snp34355-scaffold403-2258447 NW_017189517.1 47105107 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790407 Affx-122972628 AX-385277411 X 2313358 TTATTGCTTATGTCCAGGATTGAGAATGCTTTTTT[A/G]CAGCTTTCTTCAAAGAACAACACTAATGAATATTG R 2 1 2 1 201000 r 74 goat snp34356-scaffold403-2313358 NW_017189517.1 47048325 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382923 Affx-122973390 AX-123253281 X 2393881 GTCTCTAACCAATTAATAAACTGAAATTTAGGGTT[A/G]AGAGACCAGATGGGGGAGCTCTCACACCTTGAAAT R 2 1 2 1 201000 f 74 goat snp34358-scaffold403-2393881 NW_017189517.1 45257404 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440596 Affx-122929286 AX-123310933 X 2446742 TCTATAGATGCAAAAAGCACAATGTACCAAGAGCA[C/T]AAATAAACACATGAAGAAAGCCACAACATGGCATG Y 2 1 2 1 101000 f 74 goat snp34359-scaffold403-2446742 NW_017189517.1 46965838 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424402 Affx-122941818 AX-123294748 X 2512381 AAGTCCTGTAATATTAACCAACTTGGGCCACCATT[A/G]CAAGACACCACAGAATAGGTGGCTTCAACAACAGA R 2 1 2 1 201000 f 74 goat snp34360-scaffold403-2512381 NW_017189517.1 46899441 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782013 Affx-122942246 AX-385269092 X 2555550 ATCCTCTAATAGTTCTCAAACTGTAGCTTGAAAAG[C/T]ATTGTTCTAAACCATAGTAATTGGTAAGTTTCTAA Y 2 1 2 1 201000 f 74 goat snp34361-scaffold403-2555550 NW_017189517.1 46855491 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432771 Affx-122935432 AX-123303112 X 2622492 CACACTGTTCTGTGGCTTGAATTTTCCAGGCCAAT[A/G]TGATATTTCCACTTAGAAGTGATATGATATCCTTG R 2 1 2 1 101000 f 74 goat snp34362-scaffold403-2622492 NW_017189517.1 46788038 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433203 Affx-122935633 AX-123303544 X 2714137 CAAATTTTGGAAATGGGTAAAAGAGATGGCTGGAT[A/G]CCTTTTCAATGGAGTTCTGTGTAATGTCTTGTGCA R 2 1 2 1 101000 r 74 goat snp34364-scaffold403-2714137 NW_017189517.1 46694057 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391085 Affx-122966831 AX-123261442 X 2784427 AAATCTTTACCCACGGTAAGATTTGCCATGTGTCC[A/G]TTTTATAAAACCAAAAATTCCTCTCTTGTTTATCT R 2 1 2 1 201000 r 74 goat snp34366-scaffold403-2784427 NW_017189517.1 46623292 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408153 Affx-122954222 AX-123278504 X 2834144 ATTTCATATGTCTCTTTTAAATTTATATATCCTTT[A/G]CTGTAAGCAGCCTGTTTCTATGATGTTGCCCATCA R 2 1 2 1 101000 r 74 goat snp34367-scaffold403-2834144 NW_017189517.1 46571727 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385008 Affx-122971876 AX-123255366 X 2867290 GTTATGGAAGCTATTCAAAAGCCACTACAATTACA[C/T]GGGATGCTGTAATACCTAGAACAGTCCCTCATACT Y 2 1 2 1 101000 r 74 goat snp34368-scaffold403-2867290 NW_017189517.1 46538256 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428288 Affx-122939388 AX-123298631 X 3042630 ATGGTTCCTATTAACAGGAGAGAAATTGCACTTAG[C/T]CTAAGAGTTCCAAAAATAGGGCACAATGAGGTGAT Y 2 1 2 1 101000 f 74 goat snp34371-scaffold403-3042630 NW_017189517.1 46360884 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425699 Affx-122940778 AX-123296045 X 3106695 ATCTCCTCTCTTTATCATTTTCAAGATATTTCTCA[C/T]AGGCTACACATATGCTTAAGAATTTTTCCTAAATA Y 2 1 2 1 101000 f 74 goat snp34372-scaffold403-3106695 NW_017189517.1 46296731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444341 Affx-122926724 AX-123314678 X 3153634 CTCATTCATCTTGATTCTTCCCACCATATAATTAT[C/T]TCCCAGAAGAATCATTAGAATTTAGCATGATATAA Y 2 1 2 1 102000 r 74 goat snp34373-scaffold403-3153634 NW_017189517.1 46249841 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785209 Affx-122941806 AX-385272255 X 3183655 TTTCACCTTTACTTTATGGCTGAAACTTTGAATGC[A/G]TGCCAATAAATCATGACTGAGATGAACAAGATCCT R 2 1 2 1 101000 r 74 goat snp34374-scaffold403-3183655 NW_017189517.1 46219690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419275 Affx-122946250 AX-123289623 X 3227842 TTCCCAGGGGCAGCTGGGAGCCTATCTCTCCAAAA[C/T]GCTCACCTTCAAGCACAACTAGAAGCATTTGGAGC Y 2 1 2 1 101000 r 74 goat snp34375-scaffold403-3227842 NW_017189517.1 46175245 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764813 Affx-122941954 AX-385252419 X 3323371 TATGTGTAAGACCCAAGTTATTGTTTTCTGAGAGA[A/G]GAGTGGCACTTTTGCTCTTTAATACTTGTTTTACT R 2 1 2 1 101000 f 74 goat snp9341-scaffold1340-772 NW_017189517.1 45794656 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378665 Affx-122977087 AX-123249024 X 3354649 AACAAAGAACAACACAGAGGGAAAAATCAACTTGA[A/G]TGCATCATGTCTTATTTCTTATATAACAGTAAAGG R 2 1 2 1 201000 r 74 goat snp9342-scaffold1340-32050 NW_017189517.1 45763386 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791856 Affx-122954753 AX-385278846 X 3386963 TGAAGACAGATTACAGATGCAAACATATACAAATC[A/G]CAATTTGAAATTTCCTGTTTTAGTGAGGTAAAAAA R 2 1 2 1 101000 f 74 goat snp9343-scaffold1340-64364 NW_017189517.1 45731078 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448653 Affx-122923348 AX-123318989 X 3421360 AATGCTATGATTATAGTTTTTTGGCTTTGTCTAGC[A/C]CTAATTGCTCTTTAATGTGTGAATGACGGTATTGC M 2 1 2 1 101000 r 74 goat snp9344-scaffold1340-98761 NW_017189517.1 45714618 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426689 Affx-122939906 AX-123297035 X 3453097 GTTGGAATTCATTAAAGTTTAGGACCATTGGAGGT[A/G]TCAGAGGTGCCAGTCATTGAGACAGTACAGAAAGA R 2 1 2 1 101000 f 74 goat snp9345-scaffold1340-130498 NW_017189517.1 45682844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384571 Affx-122973000 AX-123254929 X 3491378 TGAAAAGTCAATATTTTTTAGATGTGAAATCAGAA[G/T]AAAAACAGCTAAACTAATCTGTCCATTTATTTTAT K 2 1 2 1 101000 f 74 goat snp9346-scaffold1340-168779 NW_017189517.1 45644389 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766124 Affx-122924495 AX-385253533 X 3531987 GAGTGTATTGATGCCAACTTTAGAAATCAATCTTT[A/C]TCACAGGAATTTTGAGATAAATTAGTTATAAAACT M 2 1 2 1 101000 f 74 goat snp9347-scaffold1340-209388 NW_017189517.1 45603559 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429923 Affx-122938099 AX-123300264 X 3560533 TTTTGCTTTTTTTCCCACACATTTTCCTTCAAAAT[A/G]TTTAGTTGAATAGTCTGTTTTCTGTGTTAATAGAA R 2 1 2 1 101000 r 74 goat snp9348-scaffold1340-237934 NW_017189517.1 45574772 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385453 Affx-122971307 AX-123255811 X 3601208 TTATTTCAAAGAGGAAAAATGATAGATTATGCTTT[A/G]CTTTTGTATCAGAGCAGATAGGGTCTATTTGACAG R 2 1 2 1 101000 r 74 goat snp9349-scaffold1340-278609 NW_017189517.1 45533783 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38411776 Affx-122951484 AX-123282126 X 3634006 GAAAACATCACTGAGGAAGAAGAAAAATGTCTCCA[G/T]ACTTTAATTTGAACTGATTAGCCTTGTTGGTTAGT K 2 1 2 1 201000 r 74 goat snp9350-scaffold1340-311407 NW_017189517.1 45500958 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445697 Affx-122926120 AX-123316034 X 3678866 TCCATTTATTGAGTGAGGTCAGTATTTTGTTCTTT[A/G]TTGCCTATGAATTTTTTAAATAACATGTATTCAGT R 2 1 2 1 101000 f 74 goat snp9351-scaffold1340-356267 NW_017189517.1 45457985 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423848 Affx-122942776 AX-123294194 X 3727587 ATCTATATTCTTTTTTTAGTAAGTAATAAAAATGG[C/T]AATGTTCACTCATTAGCTGAATGTTTACCATGTAT Y 2 1 2 1 101000 r 74 goat snp57468-scaffold92-10338 NW_017189517.1 45406831 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389585 Affx-122968780 AX-123259943 X 3771083 GACACGGTGAGGGATTACAGTTTAGGTGACAAGCC[A/G]TGGGGCCATGCTGGGTGGTAAAGGAAGGGAGGCCA R 2 1 2 1 101000 f 74 goat snp57469-scaffold92-53834 NW_017189517.1 45362989 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419978 Affx-122945186 AX-123290326 X 3802093 CTACAGAAAGAGAGGCTTTTTCAAATAACTTATAC[A/G]TAATTCTAAAATTTGTCCCTCGGTTGTATATTCAA R 2 1 2 1 101000 f 74 goat snp57470-scaffold92-84844 NW_017189517.1 45331160 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432632 Affx-122935481 AX-123302973 X 3844147 TATCCTAGAATAGAAACTGAAGGTAGCACAAATGG[C/T]AAAGAATCTGCCTGCAATGCAGGAGACACAGATTC Y 2 1 2 1 303000 f 74 goat snp57471-scaffold92-126898 NW_017189517.1 45201555 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787849 Affx-122947866 AX-385274872 X 3882970 CTGATGAGCATTATAAAGTAATGAAGAGGTTAATC[A/G]TTGTTCCCTTGACTGAAACACTAAAAGGCAATACC R 2 1 2 1 101000 r 74 goat snp57472-scaffold92-165721 NW_017189517.1 45162774 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454041 Affx-122919407 AX-123324374 X 3914580 AATGATGTGAAGACCTCAGTCATCTTCTTAAAACA[C/T]ATTGTTTCTTTGTCAAATTTATTTCACATCAGTTG Y 2 1 2 1 101000 f 74 goat snp57473-scaffold92-197331 NW_017189517.1 45130740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410175 Affx-122952594 AX-123280525 X 3944788 ATGTATACACTTACAGCATTCTATTTGTAATGCTT[A/G]TTGCTTGTACAGTCAGAAATTCTATTCCACAGTTG R 2 1 2 1 101000 r 74 goat snp57474-scaffold92-227539 NW_017189517.1 45099597 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802711 Affx-122932610 AX-385289610 X 3986352 ATGAAGAATGTTTCTTTGTTCCTACTTCAGATACA[C/T]AAAACTGACCTTGATCAATGTCAGCAAACCAGGCC Y 2 1 2 1 101000 r 74 goat snp57475-scaffold92-269103 NW_017189517.1 45057893 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388910 Affx-122968844 AX-123259268 X 4073131 TCCAAAGCCACGTGTACATTTTTAAGGATTTGTTA[C/T]AGCAGCCCCTGACTTCCTGGTACCCAAATCCGTAT Y 2 1 2 1 201000 f 74 goat snp57477-scaffold92-355882 NW_017189517.1 44970941 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402132 Affx-122958669 AX-123272485 X 4137450 TAATGCATATCATATGTTTTTCTTTCTCTTTCATG[C/T]AGAAAGACAGAATTATTCACCCAAATCTGTCATCA Y 2 1 2 1 101000 r 74 goat snp57479-scaffold92-420201 NW_017189517.1 44906870 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433007 Affx-122935790 AX-123303348 X 4182208 TCCTGGGGCAGTTCATCTGCTGGTGCGGTATCTGG[C/T]GACCGCCTTGCTGGCCTCGGACACGGCGTACTTGC Y 2 1 2 1 103000 f 74 goat snp57480-scaffold92-464959 NW_017189517.1 45066163 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442726 Affx-122927855 AX-123313063 X 4246480 CATTCTCACTCAGTAGGTCTGTCTGTGGTGGGGCC[A/C]AAGATACTTTGCTTCCAATAATTCCCCAGATGATG M 2 1 2 1 201000 r 74 goat snp57481-scaffold92-529231 NW_017189517.1 44787804 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776393 Affx-122964714 AX-385263520 X 4279061 TATGCTGTTATAAATTAAGATAGTGGTTACTTTGG[C/T]GGTAGTGACTAGAAAGTGTTCCGAAATGGGCTTCT Y 2 1 2 1 202000 f 74 goat snp57482-scaffold92-561812 NW_017189517.1 44755118 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418690 Affx-122946301 AX-123289038 X 4321237 TCTTTAAAGACTCATCCCAGGTGGCACGTCCTCCC[G/T]AATTGAGTCTTAAAAGTGACACAGATTCAAAGACT K 2 1 2 1 201000 r 74 goat snp57483-scaffold92-603988 NW_017189517.1 44711576 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427593 Affx-122939462 AX-123297936 X 4378512 ATTGCAGAAACTTTGAGCTGGGGGCTACTAACACA[C/T]GCATTCTTTGTCTCTCTGGATAGGTACTCTCATCT Y 2 1 2 1 101000 f 74 goat snp57484-scaffold92-661263 NW_017189517.1 44653043 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432832 Affx-122935381 AX-123303173 X 4454144 TTTTAAAATGTTCTTTTTAAGCTTTTTTAGAGATA[C/T]ATTTGTTGATTGCAGACATCTTTATTTCTGAATAT Y 2 1 2 1 101000 r 74 goat snp57485-scaffold92-736895 NW_017189517.1 44577483 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422371 Affx-122943425 AX-123292717 X 4508124 CTGGGTTTTAATTTGCCTAAATGAGTGGACAGATG[A/C]TGATACTTTGAACTGAAATTGGTCCATGAAAAAAA M 2 1 2 1 101000 f 74 goat snp57486-scaffold92-790875 NW_017215857.1 7246 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453213 Affx-122920439 AX-123323546 X 4566416 CTTAAGCCCTTTCTCCCTCTCCTTCAGGAGATCAC[A/G]TTGTATATATACATTCGTAATTGGTGGACTCCACA R 2 1 2 1 201000 r 74 goat snp57487-scaffold92-849167 NW_017189517.1 44483983 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416114 Affx-122948306 AX-123286463 X 4603809 CCTAGATGTGCCCAGTGCTGGACTCTATTTTGTTT[A/G]CTTCTTTTTGTACAGTGCACAATATGAATTAATAA R 2 1 2 1 201000 r 74 goat snp57488-scaffold92-886560 NW_017189517.1 44446652 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378804 Affx-122976984 AX-123249163 X 4651716 AACAAGAGTACTTTTCTTTTTCCACCCCCTAAATT[A/G]TAGCATTCCATTTTTAACTGGTTGCTAAAGCAAAT R 2 1 2 1 201000 r 74 goat snp57489-scaffold92-934467 NW_017189517.1 44398332 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793101 Affx-122978519 AX-385280079 X 4727061 AACGCTTGCTTTCTGCGACTTTGAGAAAGTTGTTT[A/C]GTTGTGTGGTACCTCAGTTTCTATCTTTGTGACTT M 2 1 2 1 101000 f 74 goat snp57490-scaffold92-1009812 NW_017189517.1 44314335 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795181 Affx-122943402 AX-385282139 X 4785664 GCCAACGATATTCAGGAATATGAATGTAACTGCCT[A/G]CTACAGGATATTTTGCAAACTTCATGAATTCTCAG R 2 1 2 1 101000 f 74 goat snp57491-scaffold92-1068415 NW_017189517.1 44255408 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448494 Affx-122923466 AX-123318830 X 4816687 GGTTTGTATTAATTTTAGCTTATGACAGTGTGACT[A/G]CTACCTAAGAGTAATTTTCTATAGATCTGAGAAAT R 2 1 2 1 101000 f 74 goat snp57492-scaffold92-1099438 NW_017189517.1 44224352 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802123 Affx-122946342 AX-385289027 X 4860387 TTTATCAGAATAACCTAGGGTGCTTATTAAAAATG[C/T]AATGACAGTGTTCCTTATGCTCAAGGATATTCAGT Y 2 1 2 1 101000 r 74 goat snp57493-scaffold92-1143138 NW_017189517.1 44180288 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380446 Affx-122975746 AX-123250804 X 4922081 CAGATTCACAATCTTTTAACTAGTCATTTTCTTCA[C/T]CTCTTCTGGTGTTTCAGTCTTAGGAGATTATTTGT Y 2 1 2 1 201000 f 74 goat snp57494-scaffold92-1204832 NW_017189517.1 44118519 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800123 Affx-122928819 AX-385287046 X 4951248 GAAAGAAAATGAGTCTGAAATTGTGGAGATAAGAA[A/G]TACATATTGTCCAAATGGGTCACTGAGTAATGGTA R 2 1 2 1 101000 r 74 goat snp57495-scaffold92-1233999 NW_017189517.1 44089366 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417194 Affx-122947315 AX-123287542 X 4980891 ACAGTCTCTCCCCTGCAGGTGATGATCATCAATAA[A/G]GATTTTATTTTAAGTGTAGTGATAGTATCATATTT R 2 1 2 1 201000 r 74 goat snp57496-scaffold92-1263642 NW_017189517.1 44059204 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445356 Affx-122926380 AX-123315693 X 5015520 TTAGACTTTCCAGATATCTTATATTTTTTAAATAT[A/G]CATTTTTTTCTATTGTGTTTTCAAATTTGCATGGA R 2 1 2 1 103000 r 74 goat snp57497-scaffold92-1298271 NW_017189517.1 44024200 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406305 Affx-122956063 AX-123276657 X 5060906 ATCAAAAATTCACCCTGTAATGATGGGAAATATAT[A/G]GTCCAATTTTCAAAAAAACATTTTTCAACACAAAA R 2 1 2 1 201000 f 74 goat snp57498-scaffold92-1343657 NW_017189517.1 43978038 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442135 Affx-122928331 AX-123312472 X 5123392 GTTCATGCCTTGCACCTCAGTATCCCCAGTCACTA[G/T]ATTTACTACCTGGAATACAATTTCCCTAGTGCCCA K 2 1 2 1 201000 r 74 goat snp57499-scaffold92-1406143 NW_017189517.1 43917687 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391324 Affx-122967318 AX-123261681 X 5163437 ATTGGTTTAGTTAGTTCCCTATTCATGCTCACTGG[C/T]GTAGACTTTCATTCATTGCCAATACTAACAAATAC Y 2 1 2 1 101000 f 74 goat snp57500-scaffold92-1446188 NW_017189517.1 43877140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382680 Affx-122973651 AX-123253038 X 5206455 ACCAGACGTATCTCCAGTATCTCCAAACAATGATT[A/G]CAGTTTATATTTAATAAAAAATATTAACCACAAAA R 2 1 2 1 101000 f 74 goat snp57501-scaffold92-1489206 NW_017189517.1 43834106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768913 Affx-122932959 AX-385256090 X 5248256 CTGATATCCTTTCTGTATTGTTGAATAGGCAATAA[C/T]AACTTACTAGTGCTGTACATTTTCACATATAAAAA Y 2 1 2 1 101000 f 74 goat snp57502-scaffold92-1531007 NW_017189517.1 43792008 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403945 Affx-122957455 AX-123274297 X 5326079 ATTTTATCAATCCAAGGAGCCACCAGTCAGTATTT[C/T]AAGGCAAATCAAGTCTATGGACACTCTTTCCTCCT Y 2 1 2 1 101000 f 74 goat snp57504-scaffold92-1608830 NW_017189517.1 43710769 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765488 Affx-122973885 AX-385252979 X 5360778 TGAATCAGGCACTTTAACCTGTAAGAAACAGATTT[C/T]TCAGAAGATGATGATATTTTGGCCAGTAAGCATTT Y 2 1 2 1 101000 f 74 goat snp57505-scaffold92-1643529 NW_017189517.1 43676011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406206 Affx-122956132 AX-123276558 X 5392466 GGAGTCTTTCTTCTTCTTGGGTTCTGTTATCACTG[C/T]AAGACATGAGTGCTCCTCTTTCTTGTTTCTTGACC Y 2 1 2 1 201000 r 74 goat snp57506-scaffold92-1675217 NW_017189517.1 43643807 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395169 Affx-122964109 AX-123265524 X 5429939 AACAAACACCAACAGGTATCCCATAATCTCCAAAC[C/T]GGAATGTTAATTAAAAATGTAGCTCCATGTGATAA Y 2 1 2 1 101000 f 74 goat snp57507-scaffold92-1712690 NW_017189517.1 43606061 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778793 Affx-122927408 AX-385265902 X 5466128 GAGTAGTTTGTGAGAATTGGCTGGTTGTTTCCAGT[A/G]TACATTCTCCCCTTGTTTGTTTAATAATAAAGTGT R 2 1 2 1 101000 f 74 goat snp57508-scaffold92-1748879 NW_017189517.1 43568992 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383643 Affx-122972531 AX-123254001 X 5507239 GCAAACAGTGTGAACAGCAAGACACCAGGGATGAG[C/T]AGATGGCAGAAACTGGGAGATGTTGGTCAGAGTGT Y 2 1 2 1 103000 r 74 goat snp57509-scaffold92-1789990 NW_017189517.1 43528154 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442343 Affx-122928040 AX-123312680 X 5547561 GCCATGAAGTGATGGGACCAGATGGCATGATCTTA[C/T]GGGTATGGCTAAATTATAATATCTAGGATTAATAA Y 2 1 2 1 201000 r 74 goat snp57510-scaffold92-1830312 NW_017189517.1 43487218 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382142 Affx-122974048 AX-123252500 X 5643693 GGGAGACTCACAGGTGATTAGAATTCCAATATCTC[A/G]TTATTTGTTATCAAATGGTCTAAGACCATCCAGAG R 2 1 2 1 202000 r 74 goat snp57511-scaffold92-1926444 NW_017189517.1 43390332 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768701 Affx-122954970 AX-385255879 X 5694288 TCTAGAATGGAAATTGCATTCAAGGAAGTAAGTCA[C/T]ATTGAATATATAGCAGTGGTACATTTTTTAGTACA Y 2 1 2 1 201000 r 74 goat snp57512-scaffold92-1977039 NW_017189517.1 43338940 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796751 Affx-122978331 AX-385283695 X 5729487 ATGGCATGTAGTCTAGTTTAGTTATAGCATAGAGT[A/G]TGTGGAAGGGAAGTGGTTTGGAATAAAATTAGAAG R 2 1 2 1 101000 r 74 goat snp57513-scaffold92-2012238 NW_017189517.1 43303851 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418384 Affx-122946562 AX-123288732 X 5824168 ATACAATGACCATGAAAAAGAAGGGAATGCTACAA[C/T]ATGGATTAGCCTTGAGGAGATTATGCTAAATGAAA Y 2 1 2 1 101000 r 74 goat snp57515-scaffold92-2106919 NW_017189517.1 43208936 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445589 Affx-122925126 AX-123315926 X 5854113 CACATCTCCCACTTTCCTCTGTCTCTCATCCTATC[A/C]AACCAGTTCAATCACAAAGACCTTTAAGTGTACAT M 2 1 2 1 201000 r 74 goat snp57516-scaffold92-2136864 NW_017189517.1 43179643 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398838 Affx-122961385 AX-123269193 X 5903885 CTCTTCATTCTGGGGAGGGGCAGGGGATATAGACT[A/G]GACACCACCAAGGCAATTCTGGAAAGAGCTGAAAG R 2 1 2 1 101000 r 74 goat snp57517-scaffold92-2186636 NW_017189517.1 42720115 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377816 Affx-122977308 AX-123248175 X 5932578 GTGGATTTGATGTGCTACATTTCACTTAATCGTAA[C/T]GGTTAAAAATTCTCCAGACACATGAAAAGATGCTC Y 2 1 2 1 202000 f 74 goat snp57518-scaffold92-2215329 NW_017189517.1 42749294 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777884 Affx-122921928 AX-385265000 X 5978784 TATAGAAGAAATTATGCTGATATGGACAAAAATTG[A/C]TGTAATAGAGGCAATAATATTGGACAGATTTTTTA M 2 1 2 1 102000 r 74 goat snp57519-scaffold92-2261535 NW_017189517.1 42795571 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800137 Affx-122974816 AX-385287060 X 6062002 GCAGATCACTCACGTATTATCTGTTTTGTGATGCT[A/G]CATGGAAATCTAGTTGTACGGCTTTAACCTAATAC R 2 1 2 1 101000 f 74 goat snp57520-scaffold92-2344753 NW_017189517.1 42877102 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780776 Affx-122967227 AX-385267865 X 6156213 GGTCACCTGAATAAGAATGGTACATTCCCATCTCA[A/G]CACTTTTACTCATATTGCTCTTTCCTTTCCACTTT R 2 1 2 1 101000 f 74 goat snp57522-scaffold92-2438964 NW_017189517.1 42972855 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766218 Affx-122974543 AX-385253617 X 6250816 ATGAGTCTGCTCCTAGTTATCTCATCAGACAAGCT[A/G]TCTAAAGTCATTCTGTGTGCACAGCCATCTCTAAG R 2 1 2 1 101000 f 74 goat snp57524-scaffold92-2533567 NW_017189517.1 43068708 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435298 Affx-122934029 AX-123305638 X 6315376 TATTGCAGCTTCACCTCTAATTCACCCTAGGGGAA[G/T]CCAAAGTTACAAGTAATATCAACAGACCAAACCAG K 2 1 2 1 201000 r 74 goat snp57525-scaffold92-2598127 NW_017189517.1 43134324 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799096 Affx-122940231 AX-385286026 X 6398239 TACATTAATTATCACAAACACCTCATGAATTGATA[C/T]GGCAAGGATTACTCTTACCCATTTTTTAGATATAA Y 2 1 2 1 101000 r 74 goat snp57526-scaffold92-2680990 NW_017189517.1 42666882 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390994 Affx-122966903 AX-123261351 X 6428248 GATGGTAGAGTGGTTAGTAGTATGAGTTTTGAAAT[C/T]CAAGAGATCTAGATTCCAATTTTAGCTTCCTTATT Y 2 1 2 1 101000 f 74 goat snp57527-scaffold92-2710999 NW_017189517.1 19794591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393379 Affx-122965909 AX-123263735 X 6461837 CTTCCTAGACCGCAATTTCTGGAATGTATTGGACC[A/G]TATCCTCTTTGTACAGTTCAGTAATTTTCTAAAGT R 2 1 2 1 101000 f 74 goat snp57528-scaffold92-2744588 NW_017189517.1 42628466 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794157 Affx-122925828 AX-385281123 X 6515309 TTTACTTCAACCTGACATGACATATTCCCTTTATA[A/G]TCTGTTTATTGGTTTTCTAATAACCTCTAACACTA R 2 1 2 1 101000 f 74 goat snp57529-scaffold92-2798060 NW_017189517.1 42577254 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770338 Affx-122979171 AX-385257504 X 6556888 CTTTTAGATATTCTTGGTGTTTAAAACTCTAGTTT[C/T]ATCTCAAAGGAGTCTAACAAGTGTCATGACAGCTG Y 2 1 2 1 101000 r 74 goat snp57530-scaffold92-2839639 NW_017189517.1 42535400 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783928 Affx-122954848 AX-385270982 X 6607311 CAACAATGAAGAGTACATACTCAGTCCGGACTGAA[C/T]TTACACTACTTTATATAAATCAAAGAGCCATCAGA Y 2 1 2 1 201000 r 74 goat snp57531-scaffold92-2890062 NW_017189517.1 42484863 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438101 Affx-122931507 AX-123308439 X 6654648 CTGGAACTTTTCCATATGAAGTGTGGGAAGACACT[A/G]TAAATCCATAACAGGAACTAACTTGTTGGCAATAT R 2 1 2 1 101000 r 74 goat snp57532-scaffold92-2937399 NW_017189517.1 42437025 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442333 Affx-122928050 AX-123312670 X 6716685 ATCTACAGGAAAAACATACTTCTTTTCAAACCAAC[G/T]GTCCCTGAATGCCTGCTTCCTTTCTGGAGTTACTG K 2 1 2 1 101000 f 74 goat snp57533-scaffold92-2999436 NW_017189517.1 42374995 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387538 Affx-122970303 AX-123257896 X 6757483 CTCAGCAGTTTGGTGTTGGTCTAAGTGAAAAAAAC[A/G]TTTTGGGGAAGTGAAATTTTGAAGTGGGATTCATT R 2 1 2 1 101000 f 74 goat snp57534-scaffold92-3040234 NW_017189517.1 42333301 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420118 Affx-122945082 AX-123290466 X 6809044 AGGAGGTAGAAGGGATACTGTTGTGAGAGGGCAAC[A/G]CTGCAGCTATCCTGGTGCTCTAAGGCAGAAATCAA R 2 1 2 1 101000 f 74 goat snp57535-scaffold92-3091795 NW_017189517.1 42284652 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765127 Affx-122947612 AX-385252685 X 6839004 AAGAGAACAGGTGTTCCTGTTCTGGAATACATTCC[A/G]AATGAGAGGTCAGAGTATCATCTTAAGAATCTAGT R 2 1 2 1 101000 f 74 goat snp57536-scaffold92-3121755 NW_017189517.1 42254993 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770062 Affx-122919300 AX-385257229 X 6895169 TTCTATACCCACACTAGCAAAGCTGAAAATCAAGA[A/C]TAAATGATCTGATTTCACGTAACATAATTGTATGT M 2 1 2 1 101000 f 74 goat snp57537-scaffold92-3177920 NW_017189517.1 42003540 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426185 Affx-122940580 AX-123296531 X 7008536 GTTCTGCTTTCATGAATCTATGGATCAGGCCAATG[A/G]CAACCAGTAGTTACATAACCCCTGCACAAACGTCT R 2 1 2 1 101000 f 74 goat snp57539-scaffold92-3291287 NW_017189517.1 42121732 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423678 Affx-122942327 AX-123294024 X 7053661 ACACAGCAAATCAGTGACATGTTTGATGTAAGTCA[C/T]GAGCACTTTGTTAACCAAAATGCAGGGGATTATTT Y 2 1 2 1 101000 f 74 goat snp57540-scaffold92-3336412 NW_017212762.1 11470 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411066 Affx-122951944 AX-123281416 X 7154989 TTGGTATTCAACTGCTGACTCTAATAGGGACAATA[G/T]CTAGTCATTTCAAAAAGCAAACTAGTGTATCAGAG K 2 1 2 1 101000 f 74 goat snp57542-scaffold92-3437740 NW_017189517.1 41880605 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391962 Affx-122966529 AX-123262319 X 7210173 TGTTTTAAATTCATTTATTCATTCACTCACTTGAC[A/G]TTATTTGAATACCTGTGCACTCAGCACAATGCTAG R 2 1 2 1 101000 r 74 goat snp57543-scaffold92-3492924 NW_017189517.1 41854764 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417072 Affx-122947506 AX-123287420 X 7243854 GCCAGTAGGTGGGAGAAGTGATATATTTTTAGGAA[G/T]ACGACCCCTGAAATCCTACCCCTCGGGCTTCTACT K 2 1 2 1 101000 f 74 goat snp57544-scaffold92-3526605 NW_017189517.1 41821124 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375412 Affx-122979198 AX-123245771 X 7306458 CTTAATTTAAAAAAAAAATACATCTTTGGTCAGGC[A/G]CATGCTATTTTCCATCTATCCTCCTTGGCACCTAC R 2 1 2 1 101000 r 74 goat snp57545-scaffold92-3589209 NW_017189517.1 41756917 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384965 Affx-122971907 AX-123255323 X 7342405 CAATCTTGAAAACCAAAATATTAGGTCCTGGTACT[A/G]CTTAACTGATTTCACCAATTTGGATTCTAGGAGTG R 2 1 2 1 101000 r 74 goat snp57546-scaffold92-3625156 NW_017189517.1 41720311 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400102 Affx-122960733 AX-123270457 X 7374152 CTGACAATATTATAGCACAGTTTTGCAGAAATTGA[C/T]GAGAGCTCAAAGTTCATATGGAAATGTAAGGGATC Y 2 1 2 1 101000 f 74 goat snp57547-scaffold92-3656903 NW_017189517.1 41687848 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320799996 Affx-122972899 AX-385286919 X 7460814 TGTGGAAAGGTGTTTTTCATTGTTTCTCCTAATGA[A/G]AAGATAGCTATCTTTATGCAGGAAGCAACTATTTC R 2 1 2 1 101000 f 74 goat snp57548-scaffold92-3743565 NW_017189517.1 41638327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448681 Affx-122923874 AX-123319017 X 7568033 CTGCTAAACCTCTTCTTCCATGAGGAGGTCAAAGT[A/C]GCTTCTCTACTTTTAGGCTAATTTATGAACTTCAT M 2 1 2 1 202000 r 74 goat snp57550-scaffold92-3850784 NW_017189517.1 41528887 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803383 Affx-122956288 AX-385290215 X 7687192 TAGTGATCTGTGCATCCTGTGCCAACCCAAACATG[C/T]TCTTTCATTCTGCAGCATTCAAAACCAAAGACACA Y 2 1 2 1 201000 r 74 goat snp57552-scaffold92-3969943 NW_017189517.1 41409802 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788224 Affx-122972324 AX-385275243 X 7732953 AACACTTCTTTCTTCTTGATAGAAATAATGAAGGT[A/G]TTCAAGAGTGGGACAGCCACCGTGTTTCTTCCCAC R 2 1 2 1 101000 r 74 goat snp57553-scaffold92-4015704 NW_017189517.1 41364067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433507 Affx-122935395 AX-123303848 X 7799714 GGAATTCGAAGGGTGGACGGTGTTCGCGTGGAAAG[A/G]CTTGTTTATTGATTGATATAAGATTAGATTAAGAA R 2 1 2 1 103000 f 74 goat snp57554-scaffold92-4082465 NW_017189517.1 41297278 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426909 Affx-122940451 AX-123297254 X 7835477 TTGTCAACCTATATTCATATAAACTTGAAAATCCA[C/T]ATGAAATAGGTAACTTCCTAGATAAATACAGACTT Y 2 1 2 1 101000 r 74 goat snp57555-scaffold92-4118228 NW_017189517.1 41264434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404737 Affx-122957238 AX-123275089 X 7900274 AGCCCTATCCATTGGGAAGATCTTCCATCCCTGCT[A/C]CTTTTCAAGACCACCCTTAAATGTGGCTCAAATGC M 2 1 2 1 101000 r 74 goat snp57557-scaffold92-4183025 NW_017189566.1 49887 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780176 Affx-122973600 AX-385267273 X 7959698 TACTGAGTTGGTCATTGTTTCTTGTCCTTTTCAGC[A/G]CATGGAGTCAGTAAACATAGGTTTCATGTTTCAGA R 2 1 2 1 101000 f 74 goat snp57558-scaffold92-4242449 NW_017189517.1 41160929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417091 Affx-122947489 AX-123287439 X 7989217 GTGCAAGAATGATATCTGAGAATCTGCCTTATACT[A/G]TCAATATTGTCATTTTGGTGGATGGAATTGAATAG R 2 1 2 1 201000 r 74 goat snp57559-scaffold92-4271968 NW_017189806.1 13207 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389169 Affx-122969093 AX-123259527 X 8039711 ACTAACTTATCAGTTCCTTCAGGCAGTGACAATCT[A/G]TGGTGTCACTCATTGCCTTTCTTATTCTTATGATT R 2 1 2 1 101000 f 74 goat snp57560-scaffold92-4322462 NW_017189517.1 41109703 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395204 Affx-122964499 AX-123265559 X 8086537 ACATGTTCCTTGTTACAATTATTATTATCTTGAAC[A/C]TGTAATTTAAGTAAGCCTTTTTGGTCCATACAGTG M 2 1 2 1 101000 r 74 goat snp57561-scaffold92-4369288 NW_017189517.1 41062690 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424568 Affx-122942225 AX-123294914 X 8120860 ATGGGCTGAAGAGTGTCCTTTATGAGAATGCAAAT[A/G]CTCTTCAAAGAGTACCTTATCCAGCCATTACCAGC R 2 1 2 1 101000 f 74 goat snp57562-scaffold92-4403611 NW_017189517.1 41028356 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389482 Affx-122968322 AX-123259840 X 8159639 GACACAATTTAGTGACTAAACAACAATGATCCAAA[C/T]TGTAGTGCTGATGTCAAAAAGACGAGTGTGTACAG Y 2 1 2 1 101000 r 74 goat snp57563-scaffold92-4442390 NW_017189517.1 41211601 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451666 Affx-122921589 AX-123321999 X 8178962 TTTGTCTGAACTGATTCCTTACCCCTGGGATCTCC[G/T]CCTGTAGCCCCCATCCCCAGCCCTACTACTACTGT K 2 1 2 1 201000 f 74 goat snp25905-scaffold268-11384 NW_017189517.1 41227691 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768985 Affx-122964202 AX-385256160 X 8211277 TGCTAGTTGATGTCTAAACCACCATTGTGGATCTT[A/C]TCACTTGATGCTACTAAACTCCAATTTCTGATTTT M 2 1 2 1 101000 f 74 goat snp25906-scaffold268-43699 NW_017189517.1 40976200 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772314 Affx-122948811 AX-385259468 X 8260270 TTAGGTTAGATCATTAGGAAAGCATTCTCTGAGAA[A/G]GTGACATTTAAACTAAGCCCTGAATGACAAGGAAT R 2 1 2 1 201000 f 74 goat snp25907-scaffold268-92692 NW_017189517.1 40926679 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788251 Affx-122975785 AX-385275270 X 8339556 TTAGGCCTGCAGACCAACTCAGATAAATATCAGCA[C/T]TGATGATACAATATGATATTCATTACTCAAAACTG Y 2 1 2 1 101000 f 74 goat snp25908-scaffold268-171978 NW_017189517.1 40847108 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438637 Affx-122930909 AX-123308974 X 8427341 GAAGACGTGTCAGAAGAAGAGGCAGTCAAGTCCTT[A/G]CCGATTAACAATAAGGATGTGGAGTCTCTCAGAGG R 2 1 2 1 101000 r 74 goat snp25909-scaffold268-259763 NW_017189517.1 40758515 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435246 Affx-122934072 AX-123305586 X 8457781 ACCCTTGATGAAGGCAAGAACAAGATACAAAACGG[C/T]TCAATTAGACTGGGAAAAGAGGGTAGTAGGTCTGC Y 2 1 2 1 101000 f 74 goat snp25910-scaffold268-290203 NW_017190163.1 30858 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443190 Affx-122927597 AX-123313527 X 8488647 CCATAGACTGCTTTAAATTTTTCAGTAATAGAATC[A/G]TTTAAAAGTAATACAGCTGGGCTTCCCTGGTGGCT R 2 1 2 1 103000 f 74 goat snp25911-scaffold268-321069 NW_017190163.1 62549 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431559 Affx-122936197 AX-123301900 X 8540832 GTCAACTGAGTCCATGCAACTATACTTCAAACAGC[A/G]CCTGCAACCCATTAAACAAGGTTAATAAATATTAC R 2 1 2 1 201000 r 74 goat snp25912-scaffold268-373254 NW_017189517.1 40654857 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38439506 Affx-122930138 AX-123309843 X 8609862 ACTTCTGTGAATCTGTGCTTCTGCTCCCTATCATG[C/T]TTGTTGCTTTTATATTAGGCAGTGTACCCAGTTCC Y 2 1 2 1 201000 r 74 goat snp25913-scaffold268-442284 NW_017189517.1 40585436 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444999 Affx-122926647 AX-123315336 X 8648069 CCAGGGACTAGACAGGGAGATACAGACACCAGCAT[C/T]ACCAAATCTGACTCTATCTCCAGACTAGCCATTTG Y 2 1 2 1 101000 r 74 goat snp25914-scaffold268-480491 NW_017189517.1 40548127 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419965 Affx-122945198 AX-123290313 X 8761659 AACACCCATATCTCTCTTCCTATTGAAAAGAAATC[C/T]CTATAACTTTAACCCTGAAAGTGAAAGTGATAGTC Y 2 1 2 1 201000 f 74 goat snp25916-scaffold268-594081 NW_017189517.1 40433808 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415349 Affx-122948783 AX-123285698 X 8800642 ATTATATGGGCTGTTCTGGATGCAGCAAGTCCTTT[A/G]CATAGGAACCTTCACACTGAGAACTTTTAAAGATG R 2 1 2 1 101000 f 74 goat snp25917-scaffold268-633064 NW_017189517.1 40394815 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430458 Affx-122937263 AX-123300799 X 8830508 TGAACAAGGTCACGGTTAGGGGTGCCAACTGCAGT[A/G]CAGTTAAAAATCCACCTCTTATCTGCGATTTTTCA R 2 1 2 1 101000 r 74 goat snp25918-scaffold268-662930 NW_017189517.1 40365138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769590 Affx-122951677 AX-385256760 X 8889919 TGGTAACCACTGCTTGGTTTATAGCAATCAAACTC[A/G]TATCTCCCTACCTTGTCTGATTATATAGCTAATTT R 2 1 2 1 101000 f 74 goat snp25919-scaffold268-722341 NW_017189517.1 40305632 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794884 Affx-122946563 AX-385281844 X 8932593 AACATCATGGCTGTTACCATTACTACCATCATGCT[A/G]TTACCATTAGTGGGTTAGCTCAGGTCCTCTCAGAT R 2 1 2 1 101000 f 74 goat snp25920-scaffold268-765015 NW_017189517.1 40262376 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409672 Affx-122953505 AX-123280023 X 8966561 ACGAGTCTACATTGTCTGCTGTCTATACCAACCAT[A/G]TGATTTTGCCTGTGGCCCTGTGACTGAAGGGCATA R 2 1 2 1 101000 f 74 goat snp25921-scaffold268-798983 NW_017189517.1 40228493 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788642 Affx-122974720 AX-385275659 X 9033985 AAAGTTTCTAGAAGAACCTGTTCTAGGCAGACAAG[C/T]AATAATACAGGTAAGCATGAATCTAGGTTTACTAA Y 2 1 2 1 101000 f 74 goat snp25922-scaffold268-866407 NW_017189528.1 55271 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388161 Affx-122969452 AX-123258519 X 9113736 CTGGCAGAGGTCCCTGTGTGGTTTTCTCCACTACA[A/G]AGATCAGCTGTCTGATTATTTGGCTGAATAGATTT R 2 1 2 1 201000 r 74 goat snp25923-scaffold268-946158 NW_017189524.1 58694 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408220 Affx-122953842 AX-123278571 X 9209933 ATCCTGTCCATGCACCCTGCCTACTGGCCAGTGCC[C/T]AGAGAAATTGGAGATAGGGTTGGGGACATCAGGTT Y 2 1 2 1 202000 f 74 goat snp25925-scaffold268-1042355 NW_017189517.1 40704239 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774129 Affx-122971398 AX-385261267 X 9247846 ATGAATCACATAGTATTCTAGCATAGGTTTTGAGG[C/T]ATGAAATTTACATTTCTTAGAAGTCTAAGCAATGG Y 2 1 2 1 201000 r 74 goat snp7247-scaffold1267-1440349 NW_017189517.1 40127395 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442325 Affx-122928231 AX-123312662 X 9341143 TGTGAGGTGAACATAGTGGTAGAAACATATGGAAA[C/T]GGGAATGTTGATTCTATTTCAGGTAATACAAAAGG Y 2 1 2 1 101000 f 74 goat snp7245-scaffold1267-1347052 NW_017189517.1 40008946 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770594 Affx-122968362 AX-385257758 X 9373032 TGTATTTGAGTGAAGACACTTACACATATATATGC[A/G]TGTATATTCGCATGATTTAAAAAATCTGGGAGAAA R 2 1 2 1 201000 r 74 goat snp7244-scaffold1267-1315163 NW_017189517.1 39976041 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777380 Affx-122930238 AX-385264502 X 9402457 TTTTTGAAACTGTATCAGAGCACTTGAGAGAATGT[A/G]CTGGAGAGAATGTGCTGTTAGAAATCATATTTGAC R 2 1 2 1 202000 f 74 goat snp7243-scaffold1267-1285738 NW_017189517.1 39948200 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446850 Affx-122925259 AX-123317186 X 9442759 CTGTGTAGCATGACCCAGGGAAATGATGAACTTGC[A/G]CCAGAGCACCTGAAAGATGTAAAACTAAAATTCTC R 2 1 2 1 101000 f 74 goat snp7242-scaffold1267-1245436 NW_017189517.1 39892137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421728 Affx-122944384 AX-123292075 X 9488223 GTGTTCCATACATATTCCTTTTCAAGAAAGGACTT[A/C]TTTTTTCAGATTCTAGTTGTCCAGTTAGTAGAAAG M 2 1 2 1 201000 r 74 goat snp7241-scaffold1267-1199972 NW_017189517.1 39833303 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767486 Affx-122929408 AX-385254750 X 9542325 CCACATGAATTCAATGGGATCTTTTAAGTACTCTT[C/T]AGTTCTTTTCAAAACTGTGCCTATTAAAATCGATT Y 2 1 2 1 101000 f 74 goat snp7240-scaffold1267-1145870 NW_017189517.1 39778937 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453738 Affx-122919617 AX-123324071 X 9585760 TGCTAATGACTATTCCCAATGAGCCCTAGTAACAA[C/T]TGCATTTTTAAAAAAGACTCTTATGCATTCCTGCA Y 2 1 2 1 201000 f 74 goat snp7239-scaffold1267-1102435 NW_017189517.1 39735140 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773395 Affx-122954361 AX-385260537 X 9621784 GGTGTAAACAGCAGATCTTTAATGAAGAAACTTTG[A/G]AAGTAGTAGCCATGGGTTAAGGAAAGCAAGGCTAA R 2 1 2 1 101000 r 74 goat snp7238-scaffold1267-1066411 NW_017189517.1 39699045 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445838 Affx-122926015 AX-123316175 X 9684247 ATGAAGTAAAAAATGAAAAAGGAGAAGTTACTACA[G/T]ATACCACAGAAAAACCAAGTGTCATGAGATAACTA K 2 1 2 1 103000 r 74 goat snp7237-scaffold1267-1003948 NW_017189517.1 39638455 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798628 Affx-122961537 AX-385285560 X 9777873 AAGAAGAAAAATATTAATAGACTACCAGCAAAATA[C/T]GATTAAGAAAATTCTTATACTAAGGAGATTTATTC Y 2 1 2 1 101000 f 74 goat snp7235-scaffold1267-910322 NW_017189517.1 39545257 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428487 Affx-122938780 AX-123298830 X 9811116 ATTCTTTTGCAACTATATATACACTTGCATACACG[A/C]ACACAGAGTATTTGCTTACTTCAACTCTCTCAACA M 2 1 2 1 101000 r 74 goat snp7234-scaffold1267-877079 NW_017189517.1 39514016 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802192 Affx-122945078 AX-385289096 X 9846456 ATGGAAACATTATCCATTTGAGTTCTTGTTTATTT[A/G]CTTTATCTTGAGCCCAGTTTCCCTAGTATGGGTAA R 2 1 2 1 101000 r 74 goat snp7233-scaffold1267-841739 NW_017189517.1 39478657 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436432 Affx-122933006 AX-123306770 X 9893370 AGTAAATTCTGCTTGTGGACTGGCCACAATGATTT[A/G]CCCTCTTGTTATGTATATACGAGTCAAGTCCCATG R 2 1 2 1 101000 f 74 goat snp7232-scaffold1267-794825 NW_017189517.1 39431312 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796058 Affx-122938831 AX-385283010 X 9939383 AAAGTGTGATTATGGAACATGTTCCAGAAATTAAG[C/T]AATCTATGGAGAGTAATTTGGCTGGTGAAGATCTT Y 2 1 2 1 101000 r 74 goat snp7231-scaffold1267-748812 NW_017189517.1 39384635 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417063 Affx-122947512 AX-123287411 X 9990730 TGATTTTTTCAAGACCAAATTCACAGCATGCTGGC[A/G]TAACTGAAGTTAACATTCAGTCAGGCTGCTCAGCA R 2 1 2 1 101000 f 74 goat snp7230-scaffold1267-697465 NW_017189517.1 39332577 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793207 Affx-122939011 AX-385280185 X 10023453 AGTCCTTATATACCATTTATCCAGCTTCTTTTAAT[A/G]CAAACCCTAGTTAAAACTATGAAGTAGTGTTTTAG R 2 1 2 1 101000 r 74 goat snp7229-scaffold1267-664742 NW_017189517.1 39299646 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786198 Affx-122968013 AX-385273233 X 10092549 AGAAACATGTTTCCTTTTCCATTTATGTCATAGAT[A/G]TTAAAAGGGTCATTTACTGTCTTAAAGATGATCAA R 2 1 2 1 101000 f 74 goat snp7228-scaffold1267-595646 NW_017189517.1 39231138 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383491 Affx-122973430 AX-123253849 X 10140352 GCTTTAAATCCCACAGTAATTCTTCCTAATTTAAG[G/T]CATTTATGAACTCATAACAGAGGCTCAAGCTGTTC K 2 1 2 1 101000 r 74 goat snp7227-scaffold1267-547843 NW_017189517.1 39183127 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443007 Affx-122928177 AX-123313344 X 10182530 TGCCATCCTGGGCAAGGTGCTCACTTCTGTGTGTC[A/G]TTTTTCACATGTGGAAGGTTGGACTCATAATAACA R 2 1 2 1 101000 r 74 goat snp7226-scaffold1267-505665 NW_017189517.1 39134847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801956 Affx-122919737 AX-385288860 X 10212965 GAAGAACAATACAAAAAACATGCTGAGCCCTTCCA[C/T]GCTGCCAGAAGATGGTGATATTGTCTTTGCCCCTG Y 2 1 2 1 101000 r 74 goat snp7225-scaffold1267-475230 NW_017189517.1 39104415 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407401 Affx-122955248 AX-123277752 X 10250977 AGGATATTCATCTATGATCACACAGCTAGTAAGTG[G/T]TGGGGCTAGAACTTTAATCCACCTTTGTTCTAAAA K 2 1 2 1 101000 r 74 goat snp7224-scaffold1267-437218 NW_017189517.1 39066066 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426491 Affx-122940224 AX-123296837 X 10280425 TGGGCCCAGTGCAGGATTTGTGAATACTGGAAATA[C/T]GGGGATCTGTCAATAAACCACCATCAAAGACTGCA Y 2 1 2 1 201000 f 74 goat snp7223-scaffold1267-407770 NW_017189517.1 39036596 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773953 Affx-122962231 AX-385261092 X 10315593 TATAGTGAAAAAGGCTCTGCATTTGGCAATATCTA[C/T]ATCACCTAAAATCTCAAATTTGATACTACTTTAAA Y 2 1 2 1 101000 f 74 goat snp7222-scaffold1267-372602 NW_017189517.1 39001996 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439468 Affx-122930168 AX-123309805 X 10351549 CTGAACATTTCATATTGTTTCAGGCCTCCATGACT[C/T]ACATGTGTGGTTTCCTCTGCTTGGAATGTTCTCTC Y 2 1 2 1 101000 f 74 goat snp7221-scaffold1267-336646 NW_017189517.1 38965098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445033 Affx-122926622 AX-123315370 X 10380582 CTCCCAATACTCACATTGTCTCACCTAATCAGAAA[C/T]GATTTTATGGACGGCATAGAACAATTTGGGTATTG Y 2 1 2 1 101000 f 74 goat snp7220-scaffold1267-307613 NW_017189517.1 38841869 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394577 Affx-122964441 AX-123264932 X 10419742 CAGTGTAGTGCATATGTAAATGTATCTGTGGTTAT[C/T]GGACCATGACTGTATGTGATGATGGTTGTCTTTTC Y 2 1 2 1 201000 f 74 goat snp7219-scaffold1267-268453 NW_017189517.1 38880897 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411264 Affx-122952319 AX-123281614 X 10487738 CTACAATAAGATGCTAGTATCACAGAATCCACCAG[C/T]GCCAAAGGTGAAAGTGATTCATGCTAAGCACAGTG Y 2 1 2 1 101000 f 74 goat snp7218-scaffold1267-200457 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436398 Affx-122933032 AX-123306737 X 10522199 TTTAATGTTATTATTCTCTGGGACTCTGCATCACC[A/G]ACTTGAACAGAGAGGTCAATGCTACAAGCTCTATC R 2 1 2 1 201000 r 74 goat snp7217-scaffold1267-165996 NW_017189517.1 38815588 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794463 Affx-122929574 AX-385281426 X 10554092 AAAAATAATATACCTTGTCCCTATGCTGCCTTTGG[C/T]ATGATTCAGGTTTTCAGACTATTGCGAATGAATTT Y 2 1 2 1 101000 f 74 goat snp7216-scaffold1267-134103 NW_017189517.1 38783679 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403128 Affx-122958114 AX-123273481 X 10616916 GTAATTCTAGTACTTATTTTTTTTCTGAGCTTCTG[A/C]GGATTTTTATATCTTGAAAGATGCTACTGCCCTGC M 2 1 2 1 101000 r 74 goat snp7215-scaffold1267-71279 NW_017189517.1 38720720 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780156 Affx-122969424 AX-385267253 X 10664476 AACGAGCACTGAGTTCTGTGACTTAAGATGTAGTA[C/T]AAGATAAAGTCCATGTAAGCAGTTTTGTGTAAATA Y 2 1 2 1 101000 f 74 goat snp7214-scaffold1267-23719 NW_017189517.1 38672826 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779029 Affx-122945393 AX-385266136 X 10692892 GTTACCACTAATTAATAATGGGAGAATTAACCTAC[G/T]AGTTGGTAACCTGATTTCTGTGCTGGAAAATATCT K 2 1 2 1 101000 r 74 goat snp26157-scaffold273-836548 NW_017189517.1 38644748 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450875 Affx-122922218 AX-123321209 X 10721539 TGTATTCCTTTATTCATTCAGTGAATGTATGTTTG[C/T]TGAGCAATTATGATGCAGAAGCATACGATATTTAA Y 2 1 2 1 101000 r 74 goat snp26156-scaffold273-807901 NW_017189517.1 38615497 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417400 Affx-122947685 AX-123287748 X 10863794 CTTATCCATTGAGGCCTATCCCAGAATAGATTTGA[C/T]AAGCTCCATTCTAGTCCCGGGATTTGTACTGACCC Y 2 1 2 1 101000 f 74 goat snp26154-scaffold273-665646 NW_017189517.1 38471971 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443783 Affx-122927098 AX-123314120 X 10918575 GTCAAGACCAGACCTTCAGAGTAGAAGCGCTAGGG[A/C]CTGAAGCTGGTTTTACAGTATGGCCTCTTGGCCCT M 2 1 2 1 101000 r 74 goat snp26153-scaffold273-610865 NW_017189517.1 38416892 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380797 Affx-122975094 AX-123251155 X 10947718 ATTCATGGGGTCGCAAAGAGTTGGACACGACTGAG[C/T]GACTGAACTGATTGATAAATCCTATCAAAAAGTAT Y 2 1 2 1 103000 r 74 goat snp26152-scaffold273-581722 NW_017189517.1 38387497 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397969 Affx-122961816 AX-123268324 X 10977805 CAGTAAGCAGGCATTGGCCATTTGAAGACAGCCCC[G/T]CTGTGAAACTGAGAAGTATACATTTCTAGAGATTT K 2 1 2 1 201000 r 74 goat snp26151-scaffold273-551635 NW_017189517.1 38355934 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375573 Affx-122978744 AX-123245932 X 11015463 AAAGACAAGGTGTTTGCAAGAAGCTCCTTGCTTCT[A/C]AGAAGAGGCACTGGCACCAGCCTTGTTATTAGTTG M 2 1 2 1 202000 f 74 goat snp26150-scaffold273-513977 NW_017189517.1 38317236 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794413 Affx-122957329 AX-385281376 X 11048756 AGTTCTCTTGTCCATTACTCCATAAAATGTTTTCC[A/G]CACTAAGTGAGGCAAACAGGAAAATCCCAAAGCAA R 2 1 2 1 101000 r 74 goat snp26149-scaffold273-480684 NW_017189517.1 38283659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419546 Affx-122945420 AX-123289894 X 11098168 GCCAGATAGTATACTATACTATCATGACCTAGAGC[A/G]TAGGCTCTGACTCTGCATCACCTTGGGTCAAATCT R 2 1 2 1 101000 f 74 goat snp26148-scaffold273-431272 NW_017189517.1 38233494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405509 Affx-122955998 AX-123275861 X 11140005 TCTGGTGAGTACTTTCTGTGTGCCAGTCATGGTCT[C/T]GAGTTTCTATGTATTAACTCATTGAATTCTCAAAA Y 2 1 2 1 101000 f 74 goat snp26147-scaffold273-389435 NW_017189517.1 38191612 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773700 Affx-122974101 AX-385260840 X 11177459 TAAAAGTTATGCAGTGTACAATCTATGCTGCCCTT[C/T]TTCATCTTTGTTGGGATAAAATGAGTAAGGAATTT Y 2 1 2 1 101000 f 74 goat snp26146-scaffold273-351981 NW_017189517.1 38153349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781032 Affx-122948962 AX-385268119 X 11259733 ACACCAAGGACGAATGTTAAATTCTCTTATCTTCC[C/T]CCAAATGTGGATAGCTGTATGCAGAAATAAATATA Y 2 1 2 1 101000 f 74 goat snp26144-scaffold273-269707 NW_017189517.1 38074112 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417475 Affx-122947178 AX-123287823 X 11308901 TCTAGGGCCAGTGTCTAGAACACAGAATATTTCCT[A/G]TTTTTCTCCATCCTGACATCTTGAATCCTCCTCAT R 2 1 2 1 303000 r 74 goat snp26143-scaffold273-220539 NW_017189517.1 38025200 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403199 Affx-122958061 AX-123273552 X 11491290 GCTGGTGGCAGGGGTAGTGAACAGTGTCATGAAAA[C/T]GTAGCCATCTGAAAAGTCTCTGGAATCCCCATACC Y 2 1 2 1 201000 f 74 goat snp26140-scaffold273-38150 NW_017189517.1 37952118 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383966 Affx-122972941 AX-123254324 X 11564745 TAGGGGGTAGAGTCTACATTATGTGCATTTTGTTT[A/G]CCAGTGTTTTTATTGCTTTGCATCTTTCGTATGAT R 2 1 2 1 201000 r 74 goat snp21928-scaffold2153-96872 NW_017189517.1 37665401 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400369 Affx-122960023 AX-123270724 X 11611388 GATGGCAGAGAGAACAATGGCAACAAGGAAAAGTG[A/G]GAAAGTTGCAAAGGAGACCAAAGTGAGAGGCCTAG R 2 1 2 1 101000 f 74 goat snp21927-scaffold2153-50229 NW_017189517.1 37618114 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775049 Affx-122974485 AX-385262181 X 11647581 GACCATATTTAAATTGGAAATATTGAGTATGACTC[G/T]ATTAAAATATCATCTTCCACTTATCAATGTTGCCA K 2 1 2 1 101000 f 74 goat snp21926-scaffold2153-14036 NW_017189517.1 37581891 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416824 Affx-122948123 AX-123287172 X 11663165 TGCATATATGGGATAGATTCTTGAAGGTTGCTCAG[C/T]TCCCACCTATACCAAAGTAATAAAAGAATATATCC Y 2 1 2 1 101000 f 74 goat snp56619-scaffold894-3142986 NW_017189517.1 37565053 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376165 Affx-122978841 AX-123246524 X 11751164 GCAGTTAGCATCCAGGAAATGTTTAGATGTCTCTC[G/T]CATATCCAATTCTATATTCAGACTCTGGCCTATCC K 2 1 2 1 201000 r 74 goat snp56617-scaffold894-3054987 NW_017189517.1 37475451 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443052 Affx-122928141 AX-123313389 X 11780768 TAGCAAAGATGAGTGGACTAAAATTCAAGGGTGAG[A/G]GTCCTGAATTTGGGTATTGCTTATTTAGGCCAAAT R 2 1 2 1 101000 f 74 goat snp56616-scaffold894-3025383 NW_017189517.1 37446921 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788901 Affx-122947654 AX-385275916 X 11863081 TGTGCACACTGAGGAGCAACAAAAGACGCTTCACA[C/T]GTCTTATGTGTGTGGGCACAGGCATTACTTATTTA Y 2 1 2 1 101000 r 74 goat snp56614-scaffold894-2943070 NW_017211717.1 1300 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451396 Affx-122921200 AX-123321729 X 11964828 ACCTGATAATACTCACTGTCATCAGGTCACACAAC[A/G]CTTTGGAAAACCATACACAAAAACAAACTCAAAAT R 2 1 2 1 101000 f 74 goat snp56611-scaffold894-2841323 NW_017189517.1 37274272 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773206 Affx-122964229 AX-385260349 X 12216326 ACACTTTGATTCTGTATACTCCCTCCAAACATATT[A/G]TCACATGTTTTCATTCTCCCTATATTTAAATTCCC R 2 1 2 1 201000 r 74 goat snp56608-scaffold894-2589825 NW_017189517.1 37021013 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428576 Affx-122938713 AX-123298918 X 12286942 CTATAGAAAGTCACTTGGCCCTTGGCCCTAGTTTC[A/G]CAGTTGTTGTGCAAACCAGTGTTTCTAGCCACCAT R 2 1 2 1 101000 f 74 goat snp56606-scaffold894-2519209 NW_017189517.1 36950482 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444336 Affx-122926727 AX-123314673 X 12439208 TCAGCTCAAGTGGGTATCCAACCATTAGAAAACAA[C/T]GGATATTTTTTTAAACAAAGATTTCATGCACTCAA Y 2 1 2 1 101000 f 74 goat snp56604-scaffold894-2366943 NW_017189517.1 36787676 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790894 Affx-122969905 AX-385277891 X 12468088 GTAGTGAGCTCTGTGCTTCAGGATCTTTTCCTCAC[A/G]CACTTTAATATTAACGTGTCAAAATGTAAAATGAA R 2 1 2 1 102000 f 74 goat snp56603-scaffold894-2338063 NW_017189517.1 36759207 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394943 Affx-122964293 AX-123265298 X 12503598 CTCCCATCTCACACCACTTCCCCAGAGGGATGGTA[C/T]GGGGAGGGAGGTGGGAGGGGGGTTCAGGATCGGGA Y 2 1 2 1 103000 f 74 goat snp56602-scaffold894-2302553 NW_017189517.1 36723365 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409190 Affx-122953182 AX-123279541 X 12595713 AGGTTCTTCCCTGGGCGAGGAGGGTTCTTTTTCCA[A/G]GGGTTTCTCTGCCTGCCCCTCACTGGGTACTCCAG R 2 1 2 1 101000 f 74 goat snp56601-scaffold894-2210438 NW_017189517.1 36630053 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393090 Affx-122965594 AX-123263447 X 12635688 CCATACCCTACACGGATGGATGCTAAAGTCTCAGA[C/T]AGCACTGAAACAAAACAGACTTAAATCTCAATCTC Y 2 1 2 1 101000 f 74 goat snp56600-scaffold894-2170463 NW_017189517.1 36589810 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798160 Affx-122966479 AX-385285095 X 12687497 AGTCATATTGAAGGAGCTATTTCTAAGATAGAACC[A/G]TGCAGCAAAGGATTAAGGAACATATCCTTGTTGGT R 2 1 2 1 101000 r 74 goat snp56599-scaffold894-2118654 NW_017189517.1 36537687 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403328 Affx-122957821 AX-123273681 X 12789339 TCACAGTAATAAGGGAGGGACCATTCAGAAATCTG[C/T]TGCTGTACTAAAATAAATAATTCCTCTGTTGCTAT Y 2 1 2 1 101000 f 74 goat snp56597-scaffold894-2016812 NW_017189517.1 36433901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404335 Affx-122957001 AX-123274687 X 12828358 CAGGATGAAGATCAGAAAGAAAAAAGAATGAAAAC[A/G]TAACAGAGTATACAACCATTAAGCACTCTTATGTA R 2 1 2 1 201000 r 74 goat snp56596-scaffold894-1977793 NW_017189517.1 36394367 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380719 Affx-122975148 AX-123251077 X 12860610 GACTGACCAACTAAACAAAAACATAAATACACACA[C/T]GTGTGTGTGTGCATGTGTTATGTGTTTGTGCCTCT Y 2 1 2 1 303000 r 74 goat snp56595-scaffold894-1945541 NW_017189517.1 36363059 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772027 Affx-122972634 AX-385259183 X 12964002 CACCACCTCAAAGAACTCTGGAAAACACTTGACTT[A/G]CAATTTCTGGTTCAGAAATGCTGCAGTTTAGGAGC R 2 1 2 1 101000 f 74 goat snp56593-scaffold894-1842149 NW_017189517.1 36257985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445250 Affx-122925482 AX-123315587 X 13016470 TCCATTATAGTCTCAGAGATGACCATACTACTTGG[C/T]ACATAATAGGCTCTCAACAAATATTTATTTAATGA Y 2 1 2 1 101000 f 74 goat snp56592-scaffold894-1789681 NW_017189517.1 36203229 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426086 Affx-122941076 AX-123296432 X 13047858 GGAGAAAATATTTGATATGTATTCCTCTGTAGGTC[A/G]TTTGTGGTTAAATTCCTCTATTATAGAAATCAAGG R 2 1 2 1 101000 r 74 goat snp56591-scaffold894-1758293 NW_017189517.1 36171141 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425698 Affx-122940779 AX-123296044 X 13119859 TCTTCCCCAGCCCTCAGCCCAGTGCCAGGTAGGGA[G/T]TAGGTGCTTGTTAAATCAAAACTGTGGAGTGGAAC K 2 1 2 1 101000 r 74 goat snp56590-scaffold894-1686292 NW_017189517.1 36098528 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451914 Affx-122921027 AX-123322247 X 13220638 GAGAGATGCTCGAGGAAGACCTAGGGTTATCACTA[C/T]ATTAAGGAGATGCTAGAGAGTGTTAAGTACTTCAC Y 2 1 2 1 101000 f 74 goat snp56588-scaffold894-1585513 NW_017189517.1 35997191 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38451690 Affx-122921572 AX-123322023 X 13282435 TAAGCAGGTGAAGTAGTCCCAGCTAACAGGCAGAT[A/G]GGAAAGGACCAGGGAGGAGATGGAACCCAGACCAC R 2 1 2 1 101000 f 74 goat snp56587-scaffold894-1523716 NW_017189517.1 35833019 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419912 Affx-122945332 AX-123290260 X 13362512 CACGACTAAGTGCACACACACGTAATAGTGACCAC[A/G]GTAGTCTCACCCCAGAGGAATGATCTATAAGAATT R 2 1 2 1 101000 r 74 goat snp56585-scaffold894-1443639 NW_017189517.1 35752181 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418409 Affx-122946543 AX-123288757 X 13428714 CATTCAGCGCATGGTTGTGCTGCCTGTGACATCTG[C/T]GGCCACATTCCACCCTGCCATCTTGTTATGTGTGA Y 2 1 2 1 101000 f 74 goat snp56584-scaffold894-1377437 NW_017189547.1 26889 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443078 Affx-122928121 AX-123313415 X 13490477 GATCAAAATCAAAGTCTTGACTCCCACCTCCCCCA[A/G]CATATCTGACCTCAGTGTAAGGTAGCACCACCTAC R 2 1 2 1 201000 r 74 goat snp56583-scaffold894-1315674 NW_017190149.1 89189 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430391 Affx-122937768 AX-123300732 X 13591343 CCAGAAACATCCTGTGATAAAAACAAAATTTTAAT[A/C]CCATGACTTGAAAAGTCTCTTTTTCTATTTTAGGG M 2 1 2 1 103000 r 74 goat snp56581-scaffold894-1214808 NW_017189517.1 35664831 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445665 Affx-122926143 AX-123316002 X 13744142 TTATAAAACTACAGAAATTTAAACTGTGACATGAA[C/T]GCAACTATAAATAAATGGATCAGCAGAATCAAATA Y 2 1 2 1 101000 f 74 goat snp56577-scaffold894-1062009 NW_017189517.1 35611666 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787851 Affx-122959399 AX-385274874 X 13831240 GAGAAGCTATGTAATGACAAAAGCAGGAGAAAACA[G/T]AAAAAGTGTCAAATTCTGGTGGATTTGGTTTAAAG K 2 1 2 1 101000 f 74 goat snp56575-scaffold894-974911 NW_017189517.1 35523004 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765920 Affx-122962790 AX-385253349 X 13895653 ATACTGAGCAGTATGTTGCAGTGGTTAAGTGCTAG[A/G]GTTTTAGGGTAGAATAGCACTGGATTACCATTTTA R 2 1 2 1 101000 f 74 goat snp56573-scaffold894-910498 NW_017189517.1 35458536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427563 Affx-122939485 AX-123297906 X 13971383 TCAGTCAACCTGGTGCTACAATTCGGTTTGGATGT[G/T]TGCGTGATTCTTCATGGCTACCTCAGAAAGACCGC K 2 1 2 1 101000 f 74 goat snp56571-scaffold894-834768 NW_017189517.1 35382380 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451789 Affx-122921499 AX-123322122 X 14039117 TGCTGATGGTTTTTACAAACTAGCTACTCCAAAGA[G/T]CACTTGAAGGCAACCTCTTCCCTTCATGCTGAGGA K 2 1 2 1 201000 f 74 goat snp56569-scaffold894-767034 NW_017189587.1 46810 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798480 Affx-122958894 AX-385285413 X 14075227 ATCTTGAGTGGTCTGACCATATGGGTGTAAGGCTT[A/G]CTCACTAATACCATCTATATATTGAAATATGTAGC R 2 1 2 1 101000 f 74 goat snp56568-scaffold894-730924 NW_017189517.1 35337333 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391861 Affx-122966986 AX-123262218 X 14252570 AGATAATGAATGCCTTTCATATTACCAGGCAATGT[A/G]CTAGGTGCTAGGAATCCATAGCCCAGTTATATGTG R 2 1 2 1 101000 r 74 goat snp56564-scaffold894-553581 NW_017189517.1 35159186 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443462 Affx-122927828 AX-123313799 X 14357323 GCAGGGTAAGAACTATAGATACCAATTTATTTCAG[C/T]CACAGAACCAGTAATCAGGTTGATGTTTGTTTCAT Y 2 1 2 1 101000 f 74 goat snp56562-scaffold894-448828 NW_017189517.1 35053852 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428815 Affx-122938386 AX-123299157 X 14526995 ATGGCTCAAAGTTGCTTGAGCAGGCCAAAATATGG[C/T]ACATGGGATTCAAAGTACATGTTAAGGTGATGAAT Y 2 1 2 1 101000 f 74 goat snp56558-scaffold894-279156 NW_017189517.1 34882396 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443885 Affx-122927498 AX-123314222 X 14586189 GACCCCCTCTGCCACTCTGGGCCTCCCCCTTTCAT[C/T]CTCCATTCTCCCCCTCTTTCTGATTCTTTCCTTGA Y 2 1 2 1 103000 r 74 goat snp56557-scaffold894-219962 NW_017189517.1 34823458 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425477 Affx-122941494 AX-123295823 X 14686220 GAATTCCTCCTAATCTCACCACCACCAACACCAAC[A/G]CCATTAGCTTTTCAGTGTCTCATCCCTGAAACTGT R 2 1 2 1 201000 r 74 goat snp56554-scaffold894-119931 NW_017189517.1 34723160 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427268 Affx-122939543 AX-123297611 X 14777551 ATAGGAAGAGTAAATATTAAGATGCCAGTTGTCCA[C/T]AAACTGACCTAGACCTGCACTGTCCAATCTGGTAG Y 2 1 2 1 201000 f 74 goat snp56552-scaffold894-28600 NW_017189553.1 37428 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451778 Affx-122921507 AX-123322111 X 14822719 TCATGGAAAATGAGGAACTGGAGTGAGACTGTATA[C/T]GAGGAGGTGTCTTTATACTTTCCCAAATCATACCA Y 2 1 2 1 101000 f 74 goat snp25895-scaffold2678-15354 NW_017189517.1 34597975 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776003 Affx-122972257 AX-385263133 X 14859177 CATATGGTTCAGATATTGTAACTTTCTCTTACAGT[A/G]CTTTGACATGTATTTTCTCTTCTTCCATCCTCAGG R 2 1 2 1 101000 r 74 goat snp25896-scaffold2678-51812 NW_017189517.1 34635374 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768449 Affx-122964762 AX-385255629 X 14888953 TAAACAGGAGGCGAATAGAAGCTAGAAGATGAGAG[A/G]CCTGAGAAGATACCTGGGAATGTATAAAGACAGAT R 2 1 2 1 101000 f 74 goat snp25897-scaffold2678-81588 NW_017189517.1 34350240 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778618 Affx-122965815 AX-385265729 X 14938575 GCTTTTAAAAGCACCTATTACACTATCAGCACCAC[A/G]TCAGGTCCTATGGCTGACATTAAATACAAAAGATG R 2 1 2 1 101000 f 74 goat snp25898-scaffold2678-131210 NW_017189517.1 34300124 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398240 Affx-122962200 AX-123268595 X 14968533 ACCTCCATTCTGCCCCCATCTACTCTCTCACCCCC[A/G]TCTTAAAATTTTCATTCCCTTAGTGAGCTGATCCA R 2 1 2 1 101000 r 74 goat snp25899-scaffold2678-161168 NW_017189517.1 34270156 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449640 Affx-122922590 AX-123319975 X 15072235 TCCCAAGGTGGTTGTATTTTTTTACACTCCCACCA[A/G]TAATGTATGAGGATTCCAATTGTTTGTGGTTACTT R 2 1 2 1 201000 r 74 goat snp25901-scaffold2678-264870 NW_017189517.1 33900197 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442686 Affx-122927885 AX-123313023 X 15113633 TTTAACATATTTTTAATTAGATTCCAAGTAGCAAA[C/T]AAAATCCAAAGGACATCAAACCAAAATGATGTCTG Y 2 1 2 1 201000 f 74 goat snp25902-scaffold2678-306268 NW_017189517.1 33858706 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382485 Affx-122973827 AX-123252843 X 15209850 ATACTCAGTGGACCAGATCAACATTACTAAAAAAG[A/C]ATGGGCTGCAGGCTAGTGGTGGTTCATGGACTGCT M 2 1 2 1 101000 f 74 goat snp25904-scaffold2678-402485 NW_017189517.1 33761315 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445989 Affx-122925879 AX-123316326 X 15251137 AGGCAGTTTACAATCTAATATGCAACATGCAGTAA[C/T]ATTTTCCAGTCAAGAGTAGTGTTCTTAGGATACAA Y 2 1 2 1 101000 f 74 goat snp59535-scaffold981-935188 NW_017189517.1 33719068 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452047 Affx-122920887 AX-123322380 X 15350825 AACTTTGGCCTCAGTAGGATAGTTGCATCCAGGTC[A/C]TGTGCACCTATGTGTATCAACTCATTGGAGGGGAA M 2 1 2 1 101000 f 74 goat snp59534-scaffold981-835500 NW_017189519.1 519644 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396243 Affx-122963332 AX-123266598 X 15384318 CAGTGAGAATTGAGGCCCCGGATATAGGAACTTAG[C/T]CAAGCCATCCTGACCAGTTCCCAGCTGTTTTAGCC Y 2 1 2 1 202000 r 74 goat snp59533-scaffold981-802007 NW_017189519.1 485585 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419921 Affx-122945325 AX-123290269 X 15414729 CTATCCAGGCATGAAAGTGGAAGTTATGCTGGAGA[C/T]GGATGCTAGTGATTAAGCCTAGTGTGGCTTGACTT Y 2 1 2 1 201000 r 74 goat snp59532-scaffold981-771596 NW_017189519.1 455050 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427696 Affx-122939293 AX-123298039 X 15443923 CTAAAAACTAGAAATACAGCAGTGAACAAAAGATA[C/T]GAATTTTCTGCCCTTCATGGAGCTTAAAACTCCAG Y 2 1 2 1 103000 r 74 goat snp59531-scaffold981-742402 NW_017189519.1 425669 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799769 Affx-122959051 AX-385286696 X 15484374 CGTTGCACAGGGAAACAAAGCTCCTTGTCACTTCA[C/T]GTGACAATAATTGAATACCCAAGTGCCAGGCACCC Y 2 1 2 1 101000 f 74 goat snp59530-scaffold981-701951 NW_017189519.1 385220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419187 Affx-122945717 AX-123289535 X 15572195 CCTCTGGTATCACACCTAAGACATCATACTGGATA[C/T]GTGTGCAAAAGATCCCTGGAATTCCTCTGCAATAA Y 2 1 2 1 101000 r 74 goat snp59528-scaffold981-614130 NW_017189519.1 297288 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443442 Affx-122927357 AX-123313779 X 15604664 TTAGCTTGCCAGCTCAATCCATTTTTTGGCCCACC[A/G]TTAAGTGACTTTCTCCTGGAGACTTCTTTATTTCT R 2 1 2 1 101000 r 74 goat snp59527-scaffold981-581661 NW_017189519.1 264248 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386539 Affx-122970726 AX-123256897 X 15667368 TAAATTATAACTTTTTCTTTTTTTCCTATGAAGAA[G/T]ACTGTACTAATAAAACTGCCCATTTCTTTCAGGTG K 2 1 2 1 101000 r 74 goat snp59526-scaffold981-518957 NW_017189519.1 201480 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401883 Affx-122958851 AX-123272236 X 15706447 TACCCGCTGGTGTGACTAAACTCTCCTCATTTACT[A/G]TTAGTGGCTCAGATGGTAAAAAATCTGCCTGGAAT R 2 1 2 1 101000 f 74 goat snp59525-scaffold981-479878 NW_017189519.1 162397 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450602 Affx-122922016 AX-123320936 X 15771299 TGTATCTGCTGTTTCAACTGTATCAACACAGCACT[A/G]TTGCTACTGTTTCCTTGAGTACCTACCTCATTGCA R 2 1 2 1 101000 r 74 goat snp59524-scaffold981-415026 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449170 Affx-122923537 AX-123319505 X 15819633 TTATCAGAACAAACCAGTCAAGCCGAATGCATGGA[C/T]GGAAAATAACATTTCATATCATAACAGTAACAGTT Y 2 1 2 1 201000 r 74 goat snp59523-scaffold981-366692 NW_017189519.1 95035 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389539 Affx-122968277 AX-123259897 X 15877516 GATTTTTTCCAATGAATAACAAATAATATCCTTAA[C/T]GAAAATCAGATCCTATTATACTGATTTTCCTGCAA Y 2 1 2 1 101000 f 74 goat snp59522-scaffold981-308809 NW_017189519.1 37086 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404666 Affx-122957292 AX-123275018 X 15910923 AAGAGCTCCTGTTAGAAAACCACTCTGACTCTGGA[C/T]ACTCAAGGAGTTCAAGTTCTGGTTCATTGTGACCA Y 2 1 2 1 201000 f 74 goat snp59521-scaffold981-275402 NW_017189519.1 3723 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414154 Affx-122949690 AX-123284503 X 15955905 TTTCAATAGTGTCTCACTATTTTGAATTAATTCTG[C/T]AACTCTTCAGCTTAGTGTTTAAGACCATTCACAAC Y 2 1 2 1 101000 r 74 goat snp59520-scaffold981-230420 NW_017189517.1 33662881 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395641 Affx-122963788 AX-123265996 X 16008429 TGAAACCATTTAAAAGAAAAATAGGGTGGAAAAGA[C/T]AGAATGGGCAAAATGGAATTGAAGGTTGAAGGCAT Y 2 1 2 1 103000 r 74 goat snp59519-scaffold981-177896 NW_017189517.1 33587427 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381300 Affx-122974454 AX-123251658 X 16062135 GGAACCAAAACAATTTGTGTGCTCTGCTTTATTTG[C/T]ATATTTGCTTTATTGTGATAGTCTGGAACTGAACC Y 2 1 2 1 303000 f 74 goat snp59518-scaffold981-124190 NW_017189517.1 33533601 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401326 Affx-122959274 AX-123271679 X 16098349 GCTATACCCCAATACAAAATAAGTTTTTAAAAAAT[G/T]ACTGTCCACCTTATGAGATACTAGAGCACACTTGC K 2 1 2 1 101000 r 74 goat snp59517-scaffold981-87976 NW_017189517.1 32426732 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442561 Affx-122928515 AX-123312898 X 16141438 GGGGGCTTCTCTCTTTATCAACAGATAAGGTGAAC[A/G]CTTAACAACCAATGGCATTCTAGATGTCAGTGGAG R 2 1 2 1 101000 f 74 goat snp59516-scaffold981-44887 NW_017189517.1 32383637 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796855 Affx-122953691 AX-385283798 X 16181739 AAGAAGATACAGACAAGTCCACTATTTTAATTAGA[G/T]AGTTTAAAACCCCTCTATTAGTAATCAACAGATCC K 2 1 2 1 101000 r 74 goat snp59515-scaffold981-4586 NW_017189517.1 32342255 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452951 Affx-122920171 AX-123323284 X 16188662 TGCAAACTGTTAAAGAGCAGAGTCTCTGTTTTCTA[C/T]GGCCCTCAGTCTCTCCTGTATGCAAGCTCTGCTGA Y 2 1 2 1 102000 f 74 goat snp9159-scaffold1334-2238 NW_017189517.1 33052288 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418501 Affx-122946435 AX-123288849 X 16221371 AGTCTCACTGTCTTGTCTGTTTGATAAACAAGTCC[A/G]TTAGGGCTTCTGTGCCAATTCCTCTCTCTATTTGG R 2 1 2 1 101000 r 74 goat snp9160-scaffold1334-34947 NW_017189517.1 33019271 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450233 Affx-122922267 AX-123320568 X 16302373 CTGGGTTGGTATTTTTCCTCCCAGTTCTTCTCATC[A/G]TATGGAAATGGTCATCATTAATAAAAACTTGGAAA R 2 1 2 1 201000 r 74 goat snp9162-scaffold1334-115949 NW_017189517.1 32937713 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434931 Affx-122934304 AX-123305271 X 16366856 CAATACCTACTTAAAGATAATGGGCATGTGATAAA[C/T]GACTTCTATCAGAACTGAGACTTCAGTGCAGTAAA Y 2 1 2 1 102000 f 74 goat snp9163-scaffold1334-180432 NW_017189517.1 32872959 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396247 Affx-122963328 AX-123266602 X 16418107 AGACAAAATTCTGTAGAAGGACTGAAAAAATACAA[A/G]AGGACAAACAAACACCCCCGGGGAGTGATGCTTCC R 2 1 2 1 101000 f 74 goat snp9164-scaffold1334-231683 NW_017189517.1 32821284 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429019 Affx-122938328 AX-123299361 X 16479051 ACACATACACACACACACAACAAAGGCAACTGTAG[C/T]AAATGGATTCACTTCTCACCAACCTGCCATCCCTA Y 2 1 2 1 101000 r 74 goat snp9165-scaffold1334-292627 NW_017189517.1 32760332 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429237 Affx-122937916 AX-123299579 X 16538813 TTAAATCCAGTGAGTTGTCTCTATTCTGTTCTCAG[C/T]TCCCTGGCCTGTGGATTTCAACCCTGGCCTTTAGA Y 2 1 2 1 201000 r 74 goat snp9166-scaffold1334-352389 NW_017189517.1 32700150 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401615 Affx-122959606 AX-123271968 X 16593064 AAAAGGGACAAGACAAGGGAAAATCATTCCAGAAT[A/G]TCATGGAGGATGAAGTTGAAGATGGATCTCAAAGA R 2 1 2 1 201000 f 74 goat snp9167-scaffold1334-406640 NW_017213116.1 14144 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401873 Affx-122958858 AX-123272226 X 16652452 ACTCTGGGTTGATGGAGGAAGGAGCAACTGATTCC[A/G]CCTGGAGTTGGACTATGGTCTGGTCCATATGTTTC R 2 1 2 1 101000 f 74 goat snp9168-scaffold1334-466028 NW_017189517.1 31245467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394455 Affx-122964583 AX-123264810 X 16703506 CATGTTGGGAAAAACAAGCTGAATTATTTTGGAAG[A/C]CTTCAACAGCAGATAGTTGACCCTATTTACACACT M 2 1 2 1 201000 f 74 goat snp9169-scaffold1334-517082 NW_017189517.1 31296058 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411042 Affx-122951961 AX-123281392 X 16765218 TACAGTATTTCAATTAAACAAATAAACTAATTTTA[C/T]ATTACTATTTTGTTAGTGTGTTGGTGCACGTGGTC Y 2 1 2 1 103000 r 74 goat snp9170-scaffold1334-578794 NW_017189517.1 31359768 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446067 Affx-122925823 AX-123316404 X 16809842 TAATTTTTTCAGTGAAAGAAATAATCAGCTTACAA[C/T]AAAGACGGTGTGTTCATAGGTATACCAGGAGTCTA Y 2 1 2 1 101000 r 74 goat snp9171-scaffold1334-623418 NW_017189517.1 32652637 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320781089 Affx-122942955 AX-385268175 X 16839347 ATATTAAGTGTATCTTTACCTAACAGCCTTACTAT[A/G]AGGATTCAGAAGATACATGGCAGAACTATGAATGG R 2 1 2 1 101000 r 74 goat snp9172-scaffold1334-652923 NW_017189517.1 32622645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790239 Affx-122966285 AX-385277243 X 16889934 AACATGAGGTAACAAAGAGAATTCTCTGTGATCTA[G/T]AAGAGGATAGTGTCACCAAGTTTCCTTAGTAGAAA K 2 1 2 1 101000 f 74 goat snp9173-scaffold1334-703510 NW_017189517.1 32571810 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440995 Affx-122928967 AX-123311332 X 16919297 GGTGACAAAATGCTTAAAAATACAAAGTGATTACT[A/C]TGAAAGCCAGGATAATGATTGATTATGGTGGGGTA M 2 1 2 1 101000 r 74 goat snp9174-scaffold1334-732873 NW_017189517.1 32542648 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791124 Affx-122932913 AX-385278119 X 16960868 AGAATTTGGATCATGTTTGTAGTTCCATGAATTCA[C/T]TAGGGTTGTTATGTTATATATTTAACATCAGTTTA Y 2 1 2 1 101000 r 74 goat snp9175-scaffold1334-774444 NW_017189517.1 32499892 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397985 Affx-122961805 AX-123268340 X 17000024 CCTATCTCTGCATGGCTGTCTCCTTGTCATCACTG[C/T]GGTCTCAGCTCAATCGTCACTTCCTTAGACAGACT Y 2 1 2 1 101000 r 74 goat snp9176-scaffold1334-813600 NW_017189517.1 32460462 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450668 Affx-122921916 AX-123321002 X 17029842 TTCCTTAGTGTATGTAGGGGGTGAAATCTGGTAGG[C/T]AAGTCAAATCTCTTAGGAGTTGCAACTAGGAGCTA Y 2 1 2 1 101000 f 74 goat snp9177-scaffold1334-843418 NW_017189517.1 32257311 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789251 Affx-122956964 AX-385276262 X 17075967 AAATAGCAGGGCAGGACTATCAGCTAAAGGAAAAA[C/T]GGTGGCTTTTGATTAGTTATGCTGACAAAAATATC Y 2 1 2 1 101000 f 74 goat snp9178-scaffold1334-889543 NW_017189517.1 32211128 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448252 Affx-122924199 AX-123318588 X 17145756 CATATTTACTATGTGCTTGGTGTCATAGTACATGT[A/G]CTTGAAGTGAGGCTGACCATACATATGTACTATGT R 2 1 2 1 101000 r 74 goat snp9179-scaffold1334-959332 NW_017207893.1 25355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396606 Affx-122962894 AX-123266961 X 17196884 ACCAGTCAGAGTATCTATGCGTAGCATTTTGGAAG[C/T]AGAAAGAAATTGGAAACAGAACCATGGTGACTCCA Y 2 1 2 1 101000 f 74 goat snp9180-scaffold1334-1010460 NW_017189517.1 32111375 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800883 Affx-122973421 AX-385287798 X 17265324 TCTCATTGTGTACTATTATTTTAGTTGTTACAGTC[C/T]CTGACACATGATGCAATTCCGTTTCTATAACTATG Y 2 1 2 1 101000 f 74 goat snp9181-scaffold1334-1078900 NW_017189517.1 32042804 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406621 Affx-122955832 AX-123276973 X 17356520 ACAACTTCTCTCCTTGTACAATGTTGAGCAGAGCC[A/G]TTGGTTTTTAATCTCAACTTTGACCTGTTTTTAGG R 2 1 2 1 201000 r 74 goat snp9183-scaffold1334-1170096 NW_017189517.1 31950727 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436592 Affx-122932523 AX-123306930 X 17453175 AAAATGCTTTGGCATATTTCCTTCTCAAGAAAATC[G/T]TGGACCGGCTTATGTGAGCCACATCCCAGGTCAAC K 2 1 2 1 103000 f 74 goat snp9184-scaffold1334-1266751 NW_017189517.1 31853846 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779644 Affx-122979138 AX-385266746 X 17520156 GGTATTCTGATCCTGAATGAATGATGATGTCTACC[A/G]TTATTTTCTGTAGGGAAATTGACTGTGAGCTGTAA R 2 1 2 1 101000 f 74 goat snp9185-scaffold1334-1333732 NW_017189517.1 31785961 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769693 Affx-122941551 AX-385256863 X 17562111 AGACTCAGCCCAAACATGGGTTCCACTCTAGAATC[C/T]CTGGGTGCATCTTAGGAGCTATTGCAGAATTAAAT Y 2 1 2 1 101000 f 74 goat snp9186-scaffold1334-1375687 NW_017189517.1 31394584 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389991 Affx-122968053 AX-123260348 X 17632871 TGTCTAAGATAACAGTTTTCATACCCGGATGAATG[C/T]ACCCTTGGGGATACATGAAGACTTCCTAGGGGACA Y 2 1 2 1 101000 f 74 goat snp9187-scaffold1334-1446447 NW_017189517.1 31465627 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765507 Affx-122978981 AX-385252991 X 17678901 AAGTTCAGGGACTTGGTTTTCTACTTATGTGTCAT[C/T]GAAAACAGTACTTAGCATCGCTAGAAACATTGGGA Y 2 1 2 1 101000 f 74 goat snp9188-scaffold1334-1492477 NW_017189517.1 31512179 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778674 Affx-122925855 AX-385265785 X 17743166 AGACAATTTTCTGAACCATCTCATGTTTAAAATCA[C/T]AGGGTATATACATCAATACCATATGTACAGAAAAT Y 2 1 2 1 101000 r 74 goat snp9189-scaffold1334-1556742 NW_017189517.1 31577100 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432474 Affx-122935601 AX-123302815 X 17759331 CATTTTGTGCATTGGCCATCTACAACAGTTCAGTC[A/G]CTCAGTCATGCCCCACTCTTTGCAACCCCATGGAC R 2 1 2 1 101000 f 74 goat snp56700-scaffold897-2426 NW_017189517.1 31599533 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380717 Affx-122975149 AX-123251075 X 17854720 TGCTGACCAGCAGATGATTTCACAGGTCCATCTAC[A/G]TTGGGACACAGGCCCCAGGTCATCTCAATTTGTGC R 2 1 2 1 201000 f 74 goat snp56701-scaffold897-97815 NW_017189517.1 31192392 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382985 Affx-122973344 AX-123253343 X 17890824 AAAGGGAGAGTGATGAATAAAGCTAAGCAAGGATG[C/T]TACTTCACATGAAATCTACCATTACCTGATCACAC Y 2 1 2 1 101000 f 74 goat snp56702-scaffold897-133919 NW_017189517.1 31155163 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412722 Affx-122950735 AX-123283071 X 17935703 CATACCTCTCTTGCCAGAAGCACCCACAGTTCCCC[G/T]ATGTTACATGAAAATCTTCTCCCAAACTCCATGTC K 2 1 2 1 101000 r 74 goat snp56703-scaffold897-178798 NW_017189517.1 31109775 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423224 Affx-122942698 AX-123293570 X 17978531 CCTCAACCAGGTAGCCCTCCAGGAATTTATCTATA[C/T]ACCACTTACATAAGTATATCTGTTAGACAAAATGT Y 2 1 2 1 101000 f 74 goat snp56704-scaffold897-221626 NW_017189517.1 31066827 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405304 Affx-122956841 AX-123275656 X 18067360 GAATCCAGTATCACTTGGATTAATTCTGATGATGA[C/T]GGTTCCCCCCCTCCTCCTTCAAACAAGCATTTGCT Y 2 1 2 1 201000 f 74 goat snp56706-scaffold897-310455 NW_017189517.1 30977858 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431885 Affx-122936056 AX-123302226 X 18167644 ATGTTCCATGCCCTTCAGGCTATGCTGGCTGGGAG[A/G]TGGCCCTTGGGCCTTGTAGAAATCACTGGAACTTG R 2 1 2 1 101000 r 74 goat snp56708-scaffold897-410739 NW_017213182.1 4602 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429917 Affx-122938104 AX-123300258 X 18206997 TAGAAGTCCTGGCAGTAGTGAGTAGAACAGAATAA[A/G]CATTGGTTCACAGTGTTAGATGCCTCCATCCTAAC R 2 1 2 1 101000 f 74 goat snp56709-scaffold897-450092 NW_017189517.1 30868802 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376875 Affx-122977825 AX-123247234 X 18253819 ATTAAACTGAAGAGAAAGCATTTTAAAAAGCCTTG[A/C]ATTATATATCCTTTTGTAAATCGAAGGTATCAAGA M 2 1 2 1 201000 r 74 goat snp56710-scaffold897-496914 NW_017189517.1 30822144 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441161 Affx-122929560 AX-123311498 X 18343732 TTAAAAAAGTGAAAATATAGAGAAAGAAATCCATA[C/T]ATTTTACTTCCTTTTTCTTTACTTTCTCCTTGGTT Y 2 1 2 1 103000 r 74 goat snp56712-scaffold897-586827 NW_017189517.1 30731362 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407437 Affx-122954799 AX-123277788 X 18424079 GGCTTGGAATCAGATCTTGCCCTAGTTAAATCTCC[A/G]TGGAAATCATGAAATAATGAATTTGTCTTCTTTTA R 2 1 2 1 101000 f 74 goat snp1353-scaffold1037-658827 NW_017189517.1 30625590 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796878 Affx-122975197 AX-385283820 X 18483889 ATTACAAAATGATCACTGTGACAATACATTGAAAT[A/G]CCTTGGTATTTTGTCTTTGGAATGCATGCTGGAAA R 2 1 2 1 101000 r 74 goat snp1352-scaffold1037-599017 NW_017189517.1 30565307 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396839 Affx-122963266 AX-123267194 X 18522671 AACACTAATTGAATGTTCCTATGCCCCTGGTACTA[C/T]GATAGGTGCCAGAAACACAAAAAGGTGTACTATAT Y 2 1 2 1 101000 r 74 goat snp1351-scaffold1037-560235 NW_017189517.1 30525175 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774182 Affx-122953898 AX-385261319 X 18619621 TCAAAGGAAGTTTCCTGCATGATATGTGTTTAGAT[C/T]TCCTTCAGCAACTAGCACTCGTAAATTTTTAAAAA Y 2 1 2 1 101000 r 74 goat snp1350-scaffold1037-463285 NW_017189517.1 30426796 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771300 Affx-122951326 AX-385258458 X 18673080 TTACTGGCTCAAGGGAAGAAACTAGGAATTAGACT[A/G]CTTTCTCCCAACCATGTCACATTGTACAAAGAAGG R 2 1 2 1 101000 f 74 goat snp1349-scaffold1037-409826 NW_017189517.1 30372674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407611 Affx-122954642 AX-123277962 X 18715183 TATCAGACATTTGTGATTATCTCAGCTCTACAATA[C/T]ACTTTGAAATCAGCAAGTGTGAAGCTTCCAGCTTT Y 2 1 2 1 101000 f 74 goat snp1348-scaffold1037-367723 NW_017189517.1 30330111 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405969 Affx-122955535 AX-123276321 X 18798799 GCAGAAGGAGAAAGAGATTATGTAAAATTTTAACT[A/G]TTCAGTGATGGTACAAACAGCAGTAGCAGTTTCAA R 2 1 2 1 101000 r 74 goat snp1347-scaffold1037-284107 NW_017189517.1 30248169 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381602 Affx-122974789 AX-123251960 X 18844604 TGCTATGACAATGAATTTGGCTACAGACAGAGTAG[C/T]GGGCCTCATGGTCCACATAGCCTCTGGAGAATGAG Y 2 1 2 1 101000 f 74 goat snp1346-scaffold1037-238302 NW_017189517.1 30202109 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399498 Affx-122961173 AX-123269853 X 18951175 CTGATATAGTAATATTGACACCTGTCAGGCAAGGA[A/G]AGTGGCAAAATATCTACAATCTGGTTTTCACAAAA R 2 1 2 1 101000 f 74 goat snp1345-scaffold1037-131731 NW_017189517.1 30098378 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779414 Affx-122941593 AX-385266517 X 18982862 TGGCACATGCAAATCACAAAAACTCTATCACTTTC[C/T]ATAGGCGATACACTTGTATTGACAGGGCAGAATAT Y 2 1 2 1 101000 f 74 goat snp1344-scaffold1037-100044 NW_017189517.1 30066034 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392731 Affx-122966023 AX-123263088 X 19035986 GTAATCAACCTTTGTGCTTGACATAACTTTAGGCT[A/G]TTGTGACAAGTACATCTAGTCTCTAAACTTATGTG R 2 1 2 1 101000 f 74 goat snp1343-scaffold1037-46920 NW_017189517.1 30012812 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439102 Affx-122931113 AX-123309439 X 19072665 TTTTCCTTAGTGTGAGACTTTCATCTTTAATACCT[A/G]ATGGGATTTAGTATACTCCAGTAGCTCAGTGAATA R 2 1 2 1 101000 r 74 goat snp1342-scaffold1037-10241 NW_017189517.1 29975439 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800455 Affx-122967777 AX-385287376 X 19127228 TGCCAATCATCTCAACCCTCATTTCAGTGTGTTAT[C/T]ACACAGTCATGTAGTGTCCTCATGCCTCTTTTTCA Y 2 1 2 1 101000 r 74 goat snp43829-scaffold59-919093 NW_017189517.1 29905840 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391142 Affx-122966788 AX-123261499 X 19170825 TAGGGTATATCCATCACCTCAAAAATAGTGACATT[A/C]TTTACATAAGAAAGAAAACTGTAGGAAGTAGTTTG M 2 1 2 1 101000 r 74 goat snp43828-scaffold59-875496 NW_017189517.1 29862150 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452309 Affx-122920674 AX-123322642 X 19238494 GAAGAGGTGATAATGTTATTGCATTTCTCTCTCCC[A/C]ACATTTTCTAAGTACTTTATTATCTCTCAGTAGTA M 2 1 2 1 101000 f 74 goat snp43827-scaffold59-807827 NW_017189517.1 29795928 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391096 Affx-122966822 AX-123261453 X 19271469 TGAGTTAGCAAGTAAAGAGAAGAGTCCCTTCACTG[C/T]TCACCTAAAACTATCATAACATTGTTAATCATCTA Y 2 1 2 1 103000 f 74 goat snp43826-scaffold59-774852 NW_017189517.1 29762117 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397195 Affx-122962402 AX-123267550 X 19311156 TGTGGGTCTGGCACTGATGCTTGGCTCACCCATGT[C/T]GATCTTTTCTCCCTTTTCAGGCTGAATTCCCATCT Y 2 1 2 1 103000 f 74 goat snp43825-scaffold59-735165 NW_017189517.1 29722190 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379791 Affx-122975831 AX-123250149 X 19402428 TATCTCTCCTGATGATTTTATGATGGTTTCCTATT[A/G]TGCTGTAGGTTATTGAAATATTTACTTTCTACAGT R 2 1 2 1 101000 f 74 goat snp43824-scaffold59-643893 NW_017189517.1 29628881 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38382521 Affx-122973800 AX-123252879 X 19437714 TAATTAATTATAAATGCTGTCTCATTAATAAATGC[A/C]CCTCTTCATTTTGGTTTTGGAAAAAAAAAATAGAA M 2 1 2 1 201000 f 74 goat snp43823-scaffold59-608607 NW_017189517.1 29593211 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433275 Affx-122935220 AX-123303616 X 19479683 AAGGCTGACAGTATTAAATTATTTTGTTAAACCTC[A/G]CAACCCTACCTAATCATATGAATATGGAATTATGT R 2 1 2 1 101000 r 74 goat snp43822-scaffold59-566638 NW_017189517.1 29549852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423366 Affx-122943144 AX-123293712 X 19573595 TTATTTATAAGCTCCTCTGTTTTTATTTCTCTGCA[C/T]GTGATATTATTCCTTCTGGATGGGGCTGAGATTTC Y 2 1 2 1 103000 r 74 goat snp43821-scaffold59-472726 NW_017189517.1 29454015 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409089 Affx-122953330 AX-123279440 X 19607897 AATGGCTCATATTCCTACTCAACTTGCATGGCTTA[A/G]CATGGGATGGCAGCCAAGAGACAGAGGCTGCAACA R 2 1 2 1 101000 f 74 goat snp43820-scaffold59-438424 NW_017189517.1 29418237 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452557 Affx-122920525 AX-123322890 X 19637097 TGTTGTTCTTCATTGCTTTTTAAAGTGTTTATTTG[A/C]CTTTAGTTTTCAGTAAATTTACTCTGACGTGTTTT M 2 1 2 1 201000 r 74 goat snp43819-scaffold59-409224 NW_017189517.1 29390294 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800889 Affx-122946944 AX-385287803 X 19666496 TATGCATGGTTCTAAGGTATGGCAACCATAGTGTT[G/T]AAATTATTAATATGATTAAGTTAATTATTTAGCTA K 2 1 2 1 202000 r 74 goat snp43818-scaffold59-379825 NW_017189517.1 29360206 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453794 Affx-122919578 AX-123324127 X 19776641 CTCAGAGTCAGGACACAGTGAACTGCTAGATTTTA[C/T]ATCCTCTGTGAAGCCTGCTCTGAAAGTGCCAACCA Y 2 1 2 1 101000 f 74 goat snp43817-scaffold59-269680 NW_017189517.1 29249803 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784008 Affx-122923693 AX-385271062 X 19825712 AAAAAATGGTATTGAAGCACAGGAAAACAGTCAAG[C/T]AATCAAAATCATATAGTGCTGGTTTTCATTTCTGT Y 2 1 2 1 101000 f 74 goat snp43816-scaffold59-220609 NW_017189517.1 29199979 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452845 Affx-122920726 AX-123323178 X 19861121 CAGTCCTTGGAATCACAGAGTCGGACACGACTGAG[C/T]GACTAAGCACACAATATATCCCTGTATTTTGGTAT Y 2 1 2 1 103000 r 74 goat snp43815-scaffold59-185200 NW_017189517.1 29164604 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765544 Affx-122950667 AX-385253024 X 19896172 TTCTAGTCTAGATTCTATGTAAATTGCTTTTTCTT[A/G]GATGCAATGATGATGAACTTCAGGGAGAATATGTA R 2 1 2 1 101000 f 74 goat snp43814-scaffold59-150149 NW_017189517.1 29129501 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447909 Affx-122923806 AX-123318245 X 19961219 ATAGGTCCAGACACTTCAGAAAACCCCTCTTGATC[A/G]TTAGCTGACCATGAAACTAACTTAGCAAAAACTTT R 2 1 2 1 201000 r 74 goat snp43813-scaffold59-85102 NW_017189517.1 29063770 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781694 Affx-122961730 AX-385268776 X 20011941 CACTTCAGCCTTTATTCCTTGGCCCATTCCTAGGA[A/C]TCAACCTAGTCATGGTTGCAAAGGAATGAGGTACT M 2 1 2 1 202000 f 74 goat snp43812-scaffold59-34380 NW_017189517.1 29012282 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424876 Affx-122941329 AX-123295222 X 20106150 CTTAGTCTCCAGAGTTTCTTGGCCCATCTTGTGAT[A/G]TATTGGGTAGGATGTCTCTATGCTTTCATTATACA R 2 1 2 1 201000 r 74 goat snp40267-scaffold513-1541361 NW_017196818.1 25098 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376198 Affx-122978816 AX-123246557 X 20211787 CACCAGATTCAACCCAAAGCAAGCAGATGTCAAAG[C/T]GCAGAAATTGAAGAAGTTAACAAAGGAAAAATCAA Y 2 1 2 1 101000 f 74 goat snp40265-scaffold513-1435724 NW_017189517.1 28580004 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453694 Affx-122919695 AX-123324027 X 20279271 GCACACATTCATATAAATAGTCTGTTTTTTAGGAA[C/T]AGAAGGTATCTTCCTCACCATGATAAAATGCATAA Y 2 1 2 1 101000 f 74 goat snp40264-scaffold513-1368240 NW_017189517.1 28511174 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442204 Affx-122928790 AX-123312541 X 20326578 CTAGAACTATTTCCTTTCAATATTTGAAAATCACT[A/G]TGGTAAGCACTGGGGATAACCTCTCCCTCCATATA R 2 1 2 1 101000 r 74 goat snp40263-scaffold513-1320933 NW_017189517.1 28463676 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788003 Affx-122922856 AX-385275024 X 20438545 GGATACTTCCATTACTTTTGGTTTATATAGCTGAT[C/T]ACAGACTGCCCTTAAGTAATGGTGGCAATGCTTTT Y 2 1 2 1 101000 r 74 goat snp40261-scaffold513-1208966 NW_017189517.1 28336612 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416777 Affx-122948170 AX-123287125 X 20494463 AAAAGGTAACTCCTTTTATGTAAGCAACATAAAAA[G/T]GTTCTTGGAAAGTTGTTTAGGGGAATTCCTTGGGG K 2 1 2 1 102000 r 74 goat snp40260-scaffold513-1153048 NW_017189517.1 28280172 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406130 Affx-122956196 AX-123276482 X 20528878 GTAACAGTAACTGTGCTAGATATTGTACCAGGAAC[A/G]CAAAGATAGTATCCACAGTTATTCTTGTTCTCTGT R 2 1 2 1 101000 f 74 goat snp40259-scaffold513-1118633 NW_017189517.1 28244979 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431242 Affx-122937134 AX-123301583 X 20566964 AGAGCAAACTAGATGATATGTCTTCTCCAGAAGCA[A/G]TGCTGATGATGCCATGCTGTGAGTCACTGAGAAAA R 2 1 2 1 101000 f 74 goat snp40258-scaffold513-1080547 NW_017189517.1 28206541 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378348 Affx-122976834 AX-123248707 X 20611842 CTTCCATTTAATGTTCTGTCTTTGGTTAAATGAGG[C/T]AACAAGGAAGTAGTCTATATTGATTAGATCCCCGC Y 2 1 2 1 101000 r 74 goat snp40257-scaffold513-1035669 NW_017189517.1 28161148 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423412 Affx-122942623 AX-123293758 X 20680956 TTTGCCAGAAACTTATCATGAAGAATATTTGTGCC[A/G]TGAGCATAAGCTTGGAGGCCTTCAAGCCTTCAATA R 2 1 2 1 101000 r 74 goat snp40256-scaffold513-966555 NW_017189517.1 28091410 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785231 Affx-122978581 AX-385272277 X 20717592 TAACATCAGTAATTTTGTGTTATGGAATTGTTTTA[A/G]TGTAATGATCATTAGCGTAAATTACACTTTCCCTT R 2 1 2 1 101000 r 74 goat snp40255-scaffold513-929919 NW_017189517.1 28054161 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790804 Affx-122926123 AX-385277804 X 20857938 GCACCAAAAATATTAGTGTTTTAAACTTATGTTGC[A/G]TATTTTTAATGAAAAACTCAAAACATGTCTCTTCT R 2 1 2 1 303000 r 74 goat snp40253-scaffold513-789573 NW_017189517.1 27913610 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777312 Affx-122943889 AX-385264434 X 20887191 GATTCAGTGTCAATTCATTAATGTTGTGCAGCATA[A/G]TAATTACTGAATAGCATTTCAGATCTATGTCTAAG R 2 1 2 1 101000 f 74 goat snp40252-scaffold513-760320 NW_017189517.1 27885135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419241 Affx-122945672 AX-123289589 X 20955988 CTTTTGAAAAGTACTGACCAAGTGTTTCATAGGAC[A/G]TCTCTTAGTTGATGTTTATCTGATATTTTTCTCCT R 2 1 2 1 101000 f 74 goat snp40251-scaffold513-691523 NW_017189517.1 27815641 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776111 Affx-122927997 AX-385263241 X 21005214 ATAGATCAAATCCTATATCTGAGAATTGACCACTC[A/G]TTGCTATGCTTCACCCTGTATCCTTTAATCTATGC R 2 1 2 1 101000 r 74 goat snp40250-scaffold513-642297 NW_017189517.1 27767480 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417057 Affx-122947516 AX-123287405 X 21114483 TAGTCTCTTCAGCAAATGGTGATTGAAAAACTGAA[C/T]AAAAACCTGCAGAAAAAATGAAATTGAATCTGTCT Y 2 1 2 1 101000 f 74 goat snp40248-scaffold513-533028 NW_017189517.1 27656159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437671 Affx-122931780 AX-123308009 X 21253394 GTAAAACGTGTTTGCACTCCCTTAAACTAGGGTCC[C/T]CAAACACCAGGATCTAATGCATGATGATCTGAGGT Y 2 1 2 1 101000 f 74 goat snp40246-scaffold513-394117 NW_017189517.1 27515988 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787211 Affx-122964791 AX-385274237 X 21295038 CACATGCAGCCTCTATTAGGGAAGCTCTCACATTA[G/T]GACATCCTTCCAAGACTGCCATAGGTAACTGTTTC K 2 1 2 1 101000 r 74 goat snp40245-scaffold513-352473 NW_017189517.1 27421503 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425833 Affx-122940676 AX-123296179 X 21331808 GTTTGGCCAACTTCTGTAAAAGGAGATGAAAAGTA[G/T]CCCAATGGGATGGTGAAAACATTTGAAAGACTAGT K 2 1 2 1 201000 f 74 goat snp40244-scaffold513-315703 NW_017189517.1 27384331 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800903 Affx-122964865 AX-385287818 X 21371949 CTTTCTGTTAGTAAAATCTATGCTCATGCACATAT[A/G]TTCATGCATTTTTCTAGATAGCCAGTTATTAAACA R 2 1 2 1 201000 r 74 goat snp40243-scaffold513-275562 NW_017189517.1 27342205 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378783 Affx-122976998 AX-123249142 X 21409186 CTCCAGTGACCCAATTTTAAGATGTAAAATAGGGT[A/G]TTCCAAATTTATATGGAAATAATATAGCTAGCCTG R 2 1 2 1 103000 f 74 goat snp40242-scaffold513-238325 NW_017189517.1 27304567 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800834 Affx-122963201 AX-385287750 X 21439303 TGGTATTTAAAGTCTAGAGACAGACAGGCTTCACA[A/G]TGAAATAATATGAGTTCCTTGTATAATGAGTAAAT R 2 1 2 1 101000 f 74 goat snp40241-scaffold513-208208 NW_017189517.1 27279514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452375 Affx-122920624 AX-123322708 X 21477249 ACAGTTTGGGGGTTCCCCTTGAGTGCAATGGTTAC[A/G]TTACCCTGTCTGGCCATTAAAATGGGAGCTGTTAG R 2 1 2 1 101000 r 74 goat snp40240-scaffold513-170262 NW_017189517.1 27241314 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422711 Affx-122943644 AX-123293057 X 21522267 TCAGGGGGGTTGGGGGTTGGTGTAAAGAAAGTGAT[A/G]CAATCTGCCAGGGAGCATGTAGAGTTTGAAAAGGC R 2 1 2 1 101000 f 74 goat snp40239-scaffold513-125244 NW_017189517.1 27196414 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792421 Affx-122967929 AX-385279402 X 21555647 GTCCAAACTACTTCATGCTTTCATGTCATAAATAT[A/G]TAAACAAAGTCAGAGATGATGATTACAGATAGTTG R 2 1 2 1 101000 r 74 goat snp40238-scaffold513-91864 NW_017189517.1 27163134 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415175 Affx-122949007 AX-123285524 X 21615831 GTGCATTTCACTAAAATATGCAAAGGTCACTTCTC[A/G]AGTTCTCTTCAAGTGTTTCAAGTGGTGTGTTAATA R 2 1 2 1 101000 f 74 goat snp40237-scaffold513-31680 NW_017189517.1 27102474 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438322 Affx-122931349 AX-123308660 X 21670216 TCAAAGATTATTGATGCTATGTTATAAGCGTCCAT[A/G]TTTTGGGAAAGAAATATGTAAAGGGAGATAATATT R 2 1 2 1 202000 f 74 goat snp56043-scaffold873-1393966 NW_017189593.1 44583 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383781 Affx-122973202 AX-123254139 X 21731289 TGATACTGAGAAGCAAAAGCAGAGCTAATATAGAC[A/G]TGGAGTTCTGTTCAGTGCAAAGCTGACCAGGTCCT R 2 1 2 1 202000 f 74 goat snp56041-scaffold873-1332893 NW_017189517.1 26870627 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434378 Affx-122934701 AX-123304719 X 21761025 GGCAAGGGTCTGAATAGATTCTGAAGCATCCTGCA[C/T]GGGATGAAGTAATTCTTCAGTGTTCTTTATGGGAT Y 2 1 2 1 103000 f 74 goat snp56040-scaffold873-1303157 NW_017219117.1 3763 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431774 Affx-122936712 AX-123302115 X 21807490 CCCTCCCTTTGACAGCCTTGTTTCAGCACTTCTGA[G/T]GAGCGGCTTTTAACTCATCATGGTTGGTCTGTGTT K 2 1 2 1 101000 r 74 goat snp56039-scaffold873-1256692 NW_017189517.1 26793429 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785130 Affx-122943203 AX-385272176 X 21858785 CAATCAGGACCTTTGAAAACTGTATGAATGGAAAT[A/G]CTATCTCTTACTAGGGCCCTGGACATGATCCTATG R 2 1 2 1 101000 f 74 goat snp56038-scaffold873-1205397 NW_017189517.1 26741547 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421079 Affx-122944235 AX-123291426 X 21930719 CCTTTCTTGCATGTGACCTGTGTCTTAGGTTTGTC[A/G]ATACTATAGTTATCCTTTGCTGCCATTAATATAAT R 2 1 2 1 201000 r 74 goat snp56036-scaffold873-1133463 NW_017189517.1 26669474 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401286 Affx-122959867 AX-123271639 X 22008100 TGGGCAGTTTCCCTTGTGGTATTGTTTGCACTGTA[C/T]ACTGCACTAAATACACTATTTCTTCTGTCTGTGAA Y 2 1 2 1 101000 f 74 goat snp56034-scaffold873-1056082 NW_017189517.1 26591550 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797029 Affx-122932909 AX-385283970 X 22077774 ACTTAGATTAATATTTATACAAGGACATTGGCCAT[A/G]CAAATCCTCCTACTTTGTTCCTTTATCACACACGA R 2 1 2 1 101000 r 74 goat snp56032-scaffold873-986408 NW_017189517.1 26521616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380531 Affx-122975680 AX-123250889 X 22187553 ATCTTGAAATTGGCCATGGTGGAAGTATTTCCATC[A/G]TGAAAATCAGCACGTGCCACACATCAGCTCCCTCC R 2 1 2 1 201000 r 74 goat snp56030-scaffold873-876629 NW_017189517.1 25567714 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406902 Affx-122955626 AX-123277253 X 22234656 CATTCCAATTTTAGTATATGTGCTGCTGAAGCAAG[C/T]ACTTGCTGGGTTCTTTTATTCAAGCTTCATTTTCA Y 2 1 2 1 202000 r 74 goat snp56029-scaffold873-829526 NW_017189517.1 25519988 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440293 Affx-122930224 AX-123310630 X 22280405 GAATGAGTAGTCAGGGAGAAACCCATTAAACAAAT[A/G]GACCTTCCTCATCGGTCTTACTTTCAACAGACAGG R 2 1 2 1 101000 f 74 goat snp56028-scaffold873-783777 NW_017189517.1 25473241 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796388 Affx-122958426 AX-385283338 X 22323429 TTTGTAACACGGGGATCCTAATAATTCCTTATCTA[C/T]TGGATTCTCCTGAAGGTTAAATAAGTTACTATACA Y 2 1 2 1 201000 r 74 goat snp56027-scaffold873-740753 NW_017189517.1 25429845 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436772 Affx-122932271 AX-123307110 X 22482364 GCATGCTCCCCTAGAGAATCAGATGCAAACACAGC[A/G]CTGCCATCACCTTGATTTTAGCCCAGTGTGCAACA R 2 1 2 1 101000 f 74 goat snp56024-scaffold873-581818 NW_017189517.1 25269622 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790934 Affx-122924400 AX-385277931 X 22574598 AGAATTAAAAAGGACCATAGAGATCATCTAAGCAA[C/T]GTCTTTCCCAAAGCAATAATCCTTCCTGTACTTCA Y 2 1 2 1 101000 r 74 goat snp56022-scaffold873-489584 NW_017189517.1 26952717 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432655 Affx-122936468 AX-123302996 X 22632456 CACGCTAGTGGGAAGAGACTCCCTGGCACTTTGTA[C/T]GTGGGTGGAGATTTCAAAGAAGGGCCTACTGCCAA Y 2 1 2 1 201000 f 74 goat snp56021-scaffold873-431726 NW_017189517.1 27010720 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802840 Affx-122955231 AX-385289739 X 22666632 TTCCCTGAACACCTGCTCTTCTTCCTGTGTTTCCC[A/G]TCTCAGTGATGACAATATCTCCCATCCAGTTACCC R 2 1 2 1 202000 f 74 goat snp2761-scaffold108-1814 NW_017189517.1 25213594 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768915 Affx-122932811 AX-385256092 X 22700511 TTCATCAATCCAGGACCAGTTCCTTACTTCACCAT[G/T]AGAACAATAATGGTGAAACAGTCTCAAGAGGCTTC K 2 1 2 1 101000 f 74 goat snp2762-scaffold108-35693 NW_017189517.1 25178890 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444043 Affx-122926871 AX-123314380 X 22810516 ATTAGTGAGAAAACCTGTATCACAGTGGAATATCA[A/G]TTATTGGGGCAGGGGTAACAGACAGATATGAACAT R 2 1 2 1 201000 f 74 goat snp2763-scaffold108-145698 NW_017189940.1 38534 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383370 Affx-122972659 AX-123253728 X 22839260 CTCAAGTCTCAAATGAAAGGTACTTAAAGCCAGGT[A/G]CATCATAACTCTTCTTAAACGCTCCTGAGAGGACC R 2 1 2 1 101000 r 74 goat snp2764-scaffold108-174442 NW_017189940.1 67345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430068 Affx-122937549 AX-123300409 X 22895689 TACACTCCCTGATCAGTCCTGAGCTCTCCTTTACA[G/T]CCCGGCCCCAGGCCCACCCCTCCAGGAAGCCTTCT K 2 1 2 1 101000 f 74 goat snp2765-scaffold108-230871 NW_017189517.1 25085729 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403796 Affx-122957973 AX-123274148 X 22963434 GTACTCAGACTACAGGGGATATTTTCATTGACCAT[A/G]CTCCACAAGGCAGAATGTCAGATGTTATTTGTACA R 2 1 2 1 101000 f 74 goat snp2766-scaffold108-298616 NW_017189517.1 25102563 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769656 Affx-122971985 AX-385256826 X 22997994 TTCTCTAACTCCAAGGAAAATCTTATTGCATCTGT[C/T]ACTTCATAGTCTCTAATGAAAGTGTGTGGTTATGG Y 2 1 2 1 101000 f 74 goat snp2767-scaffold108-333176 NW_017189517.1 25068514 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435655 Affx-122933346 AX-123305995 X 23027290 GACAGAAAATGTAAAACAACAGGCAAATCAAAAGC[C/T]AAAAATGGCAGCTCCTTCCTCAAACATCCCCTTAG Y 2 1 2 1 201000 f 74 goat snp2768-scaffold108-362472 NW_017189517.1 25038798 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801650 Affx-122929581 AX-385288558 X 23103303 CACACAAACATGATCAACTGATTGTTGATAAAGAT[A/G]CAATGATGCTGGACCAAGCAGATATTCATAGTCCA R 2 1 2 1 101000 r 74 goat snp2769-scaffold108-438485 NW_017189517.1 24954320 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451718 Affx-122921552 AX-123322051 X 23155292 AAGTCAGAATTTAATAAACTCAGAGGCAGACTTCT[A/G]CCTTGAATTCTATAGCAAGTTTCCTAAGGAGTAAC R 2 1 2 1 101000 r 74 goat snp2770-scaffold108-490474 NW_017189517.1 24902048 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444997 Affx-122926649 AX-123315334 X 23196988 TATCCAGTCCTGAAACCAGCCATTGTTCTGAGATG[C/T]CTTGGTTCTCTTTTGTGGAAAATAGTATTTGGAAA Y 2 1 2 1 101000 f 74 goat snp2771-scaffold108-532170 NW_017189517.1 24860453 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416100 Affx-122948316 AX-123286449 X 23254458 CTCATCTCCAAGATGACCAAGGAAAGAAGGAACTG[C/T]GGTAGTGCCCAAAAGGGCCATGGCCACATACAACC Y 2 1 2 1 101000 f 74 goat snp2772-scaffold108-589640 NW_017189681.1 7740 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425747 Affx-122940744 AX-123296093 X 23308558 CAGGAATCATTTAAATCTATTTTTACATTTTGCAA[G/T]GGTTAAAATCAGATCATGTTATTCATGAATTCACT K 2 1 2 1 101000 r 74 goat snp2773-scaffold108-643740 NW_017189517.1 24785137 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402366 Affx-122959041 AX-123272719 X 23366250 GTTGATGTGTAGTGGTAATTTGGTTGTTTCTTATC[A/G]TTGAGTTTTAAGAGTTCTCTCTATGGTCCCTTATC R 2 1 2 1 201000 f 74 goat snp2774-scaffold108-701432 NW_017189785.1 29523 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380583 Affx-122975265 AX-123250941 X 23441336 ACAAAGGGTACTGAAAGGTGAAAGGAACGTCTTTT[A/C]AACAAATGGTGCTGGAATAAGTGGACATGTTTATG M 2 1 2 1 101000 f 74 goat snp21103-scaffold2068-74686 NW_017189785.1 105199 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799544 Affx-122933542 AX-385286474 X 23474643 TTGTGTTAGATTTAGAAATGAAGTTTGGGAATATC[A/G]CATGTAGAAAACGGAAACAAATCCTTGTAAACACC R 2 1 2 1 101000 f 74 goat snp21104-scaffold2068-107993 NW_017189785.1 138444 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789814 Affx-122965032 AX-385276821 X 23509270 TCAGATGGCAAAACTTAGTGCCTTCAAAGTTAAGA[C/T]ATTTTACTGTTGCATTTTATTCTTGGTGAAATGTG Y 2 1 2 1 101000 r 74 goat snp21105-scaffold2068-142620 NW_017189785.1 173182 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405794 Affx-122955908 AX-123276146 X 23558334 TCCCTTCAACTTCAGCGCAGGTCATCCGGAGCTCT[A/G]GGAGGAATGCCAAGGGACTCCATCATGTTTGTGCA R 2 1 2 1 101000 r 74 goat snp21106-scaffold2068-191684 NW_017189785.1 222301 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381326 Affx-122974432 AX-123251684 X 23634019 TCTCAGTCTTCTTCATTTCTGAAATGGGGACTACA[C/T]GCTTTCAATGGAGCACTCAGACCAAAAAACTTGGG Y 2 1 2 1 201000 r 74 goat snp11624-scaffold1429-260670 NW_017189517.1 24677567 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418109 Affx-122947131 AX-123288457 X 23703952 TGTCCTAAAGTTTTAGGATTAGTTTGGGAACAGCT[A/G]CCCACTCCAGTATTCTGGCCTGGAGAATTCCATGG R 2 1 2 1 303000 f 74 goat snp11623-scaffold1429-190737 NW_017189517.1 24609190 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389566 Affx-122968259 AX-123259924 X 23756136 GCAGAGAATAAGATGATCATTAAGTATGTAAAAGG[C/T]ACTGTACTACTTTAATTTGCATTTTCCCAGTCTGC Y 2 1 2 1 201000 f 74 goat snp11622-scaffold1429-138553 NW_017189517.1 24556648 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431510 Affx-122936236 AX-123301851 X 23816409 TCAGAAATTTAAAACAAAAAGATATCTTCATTTGA[C/T]AAATGAGACAAATATTCCCAGAGCCCTTCAGTAAT Y 2 1 2 1 101000 r 74 goat snp11621-scaffold1429-78280 NW_017189517.1 24495522 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444673 Affx-122926451 AX-123315010 X 23873654 TGCTTACTTTCAAATATCTGTCCCACAACTCTTCA[C/T]CCCCACTACATTGTTCTGTAATATCCAGATCGTGG Y 2 1 2 1 101000 f 74 goat snp11620-scaffold1429-21035 NW_017189517.1 24437416 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443140 Affx-122928073 AX-123313477 X 23914672 ATTTTGGCATTAAAAAAACTGGAAACATTCAGAAC[A/G]CCCATCAAGGGACTTGCTAAATGAATTATTGAACA R 2 1 2 1 101000 r 74 goat snp51592-scaffold757-2087300 NW_017190170.1 31881 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415766 Affx-122948926 AX-123286115 X 23950682 GTAAAAGCTGAACCCCTAAGAAATGTAGAGAGGGT[A/G]CCCTGACATCTTGACAAGGGAGGTCGTGGGCCAGA R 2 1 2 1 101000 f 74 goat snp51591-scaffold757-2051290 NW_017189517.1 19846325 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788480 Affx-122963185 AX-385275497 X 24002137 ATGATATGTATTGCTAGGCTATTACATATTTAAGA[C/T]GTAAAAGTTAAGTAGTGTACGTTTTAAGGTTTAAA Y 2 1 2 1 201000 f 74 goat snp51590-scaffold757-1999835 NW_017189517.1 10642774 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435696 Affx-122933319 AX-123306035 X 24032844 TGTGCCCTTGTGCCCAGTTCTGGGTCTCCATCAGT[A/G]GTATCACTGAGGCAGCCAGGAAGGCACCATTTTAC R 2 1 2 1 101000 r 74 goat snp51589-scaffold757-1969128 NW_017189517.1 10673493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393616 Affx-122965358 AX-123263971 X 24149569 AATAAAAACTTTATTAAAAGGGTTTGGGCTTTGGA[C/T]GCACATAGAACAGAGTCTAAATCCTGTGCTCTATT Y 2 1 2 1 201000 f 74 goat snp51587-scaffold757-1852403 NW_017189517.1 10789712 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444223 Affx-122927240 AX-123314560 X 24237224 TTAGGTCCAAATCCTTCTTTTACAGATGAGGAAAC[C/T]AAAAAAACTAATGATTTCTCCAAGGCTGTGAGCTA Y 2 1 2 1 303000 r 74 goat snp51586-scaffold757-1764748 NW_017189517.1 10877557 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453835 Affx-122919547 AX-123324168 X 24295043 ACTCCCTTCTCTCTGAGTCTTGGTTTCTATTGATA[C/T]ATCCATAATATAAAGGGGTTGAACTAGATGACCTT Y 2 1 2 1 102000 f 74 goat snp51585-scaffold757-1706929 NW_017189517.1 10914278 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417099 Affx-122947483 AX-123287447 X 24350418 AAAGAAATGGTGGGAGAGGGTTATTTGGACTTACA[G/T]ATCATAAAACATTTTCCAATAACATTTTTAAAGGA K 2 1 2 1 101000 f 74 goat snp51584-scaffold757-1651554 NW_017189517.1 11097748 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426609 Affx-122939969 AX-123296955 X 24388154 AATTACTACAAACTAAGCAGCTTAAAACAACGCAC[A/G]TTTATTATCTCAGGGTTCAGGGATCAGGGGCCTGA R 2 1 2 1 202000 f 74 goat snp51583-scaffold757-1613818 NW_017189517.1 11060060 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387900 Affx-122970463 AX-123258258 X 24423297 ACTTTTGGACTCAGAGGGAGAGGGAGAGGGTGGGA[C/T]GATTTGGGAGAATGGGAATTCTAACATGTATACTG Y 2 1 2 1 103000 f 74 goat snp51582-scaffold757-1578675 NW_017189517.1 11024343 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381094 Affx-122974594 AX-123251452 X 24490252 GATGGAAGAGCAATTTGAGGGAAATAACACAGTCT[A/G]CCAGTGAAGGTAGAGTCTGGCAGTGAAGGTAAATG R 2 1 2 1 101000 f 74 goat snp51581-scaffold757-1511720 NW_017195428.1 4091 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429861 Affx-122938147 AX-123300202 X 24629013 GCCCCGCATCACTTCCCACAACCTTTTACCTATTG[C/T]CACTACATGCTGTTCCTCTGTATTTCAGCTGTGCT Y 2 1 2 1 101000 r 74 goat snp51578-scaffold757-1372959 NW_017189951.1 68328 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768286 Affx-122957231 AX-385255467 X 24674354 GCACTCACACTTCTGGTACCAGATGTGTGGAGACT[G/T]TCCCCCACCAAGCAAATTCTCTGTGCCACCAGCTG K 2 1 2 1 303000 r 74 goat snp51577-scaffold757-1327618 NW_017189951.1 22404 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425434 Affx-122941526 AX-123295780 X 24703353 ATGTAAAGAGAATAAACTAACATTGTGTGGTATAG[C/T]AACATTGAGTGGTTGTGCTGGTGATTACAATTAAT Y 2 1 2 1 101000 f 74 goat snp51576-scaffold757-1298619 NW_017189517.1 11140940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448687 Affx-122923869 AX-123319023 X 24759736 TCCTTCCACCTCTGACAGTCTGTGTGTCTAAGATT[A/G]TGAACTCCTTGAAGGAAAAATTCTTGTACTTCTGT R 2 1 2 1 101000 f 74 goat snp51575-scaffold757-1242236 NW_017189517.1 11178348 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409222 Affx-122953159 AX-123279573 X 24854211 TCAAGAGACATAATTCAACTAATAGTGGTGTCTTG[G/T]GAAAAAAAGGTTCCTGGTGACCAAAGTTGTATGCA K 2 1 2 1 101000 r 74 goat snp51573-scaffold757-1147761 NW_017189517.1 11250666 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441484 Affx-122928743 AX-123311821 X 24904513 CAGGAGTGGAACATAAACACCCAGGACCTTCAAGG[C/T]GCCATCAGAAGTCTGTCTTTAGTTACCACACTCCC Y 2 1 2 1 101000 r 74 goat snp51572-scaffold757-1097459 NW_017189517.1 11301160 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390631 Affx-122967156 AX-123260988 X 25011988 AAGAAAGGAAACAAGAGCTTGGAGACGGAAAGAGA[C/T]AGCAATAGAGTAGTAAGTAGGTGGAGGCCCAAAGT Y 2 1 2 1 101000 f 74 goat snp51570-scaffold757-989984 NW_017206894.1 19202 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394003 Affx-122965023 AX-123264358 X 25052541 TGACCTCTTCCAATTCAGAGGAACCTGACATGCTA[C/T]AGTCCATGGGGTTGAAAAGCATCAGACACAACTGA Y 2 1 2 1 103000 f 74 goat snp51569-scaffold757-949431 NW_017189517.1 11431301 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428691 Affx-122938632 AX-123299033 X 25091937 GGTGAACTGAAGTGTAAACCACCCCTACTCCAACC[A/G]CCCCAGCAGTTGCAGGTGCCTCCAGGTCCTTGACT R 2 1 2 1 102000 f 74 goat snp51568-scaffold757-910035 NW_017189517.1 11470920 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795473 Affx-122978228 AX-139318716 X 25138609 CATCCGCACAAATCAAAGCCACCAAGTAATTCCAG[C/T]GGATATATTTGACCTAATTGCTATATGTTTACACA Y 2 1 2 1 101000 f 74 goat snp51567-scaffold757-863363 NW_017189517.1 11516358 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426814 Affx-122940522 AX-123297159 X 25222751 CCATGGGGTCACAAAGAGTCGGACATGACTGAGCA[C/T]ACACGTGCAATTACTAGTATAGATGAACGCTTTTT Y 2 1 2 1 102000 r 74 goat snp51566-scaffold757-779221 NW_017189517.1 11600965 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427483 Affx-122940011 AX-123297826 X 25281648 GCAAAGATACTGAGGCACGTGCGGGATCGATGAGG[A/C]TGAAGTGAGGGAGGGAAATGGTTGGAGACAAGTTG M 2 1 2 1 201000 f 74 goat snp51565-scaffold757-720324 NW_017189517.1 11660068 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429522 Affx-122937845 AX-123299864 X 25356730 ACTCCAAGCACCTGTGCATAATCAGAAGTAGCTGT[A/C]TCAATAATGGCGCCTGGTATGGTTCATATGGTTCT M 2 1 2 1 201000 r 74 goat snp51564-scaffold757-645242 NW_017189517.1 11734829 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424644 Affx-122942168 AX-123294990 X 25390084 GCCAGATATGCTGTGGCCATTTTTTGAGTCCTCAA[C/T]AGTAACAGAAGATATTAGTTTAAACTCAAAGCAAA Y 2 1 2 1 101000 r 74 goat snp51563-scaffold757-611888 NW_017189517.1 11768126 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436036 Affx-122932727 AX-123306375 X 25428785 GCTCCTTCCACAGGTCAGTGGTAGCTGTACTCCAG[C/T]GTTTACATGGATACAAGCCTACGATGTAGAACTAA Y 2 1 2 1 101000 r 74 goat snp51562-scaffold757-573187 NW_017189517.1 11806727 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393573 Affx-122965394 AX-123263929 X 25516604 ATCACTAATTGGGTTCAAAGATCTGAAGCTTCTAC[A/G]TAAGGAAGACTCATACATGCACACACACACACATG R 2 1 2 1 101000 f 74 goat snp51561-scaffold757-485368 NW_017189517.1 17436427 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398088 Affx-122961722 AX-123268443 X 25604406 ATTTCCTTCCCTGGTCTTAGCTTGACTCCCATGCA[C/T]GAATAATTTCCTTACCTGCTTGTGCTTCTGAATTG Y 2 1 2 1 101000 f 74 goat snp51560-scaffold757-397566 NW_017189517.1 11888009 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779280 Affx-122956469 AX-385266384 X 25633466 ATCCTTTTAGTGCTCTCATGATTTTCTGAGCAGTA[C/T]TCAGCACCAGTTACTTCTACAATTGCAAAATCACG Y 2 1 2 1 101000 r 74 goat snp51559-scaffold757-368506 NW_017189517.1 11919301 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396837 Affx-122963267 AX-123267192 X 25682449 TATTTCTAGAAGAAACAAAGTAAAAGCATCTGCCC[A/G]TTGCATGCTTTAACTTATCCTTTGTACTGACTCTG R 2 1 2 1 201000 r 74 goat snp51558-scaffold757-319523 NW_017189517.1 11967974 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438939 Affx-122930413 AX-123309276 X 25722346 GACACCGTCCTTCCTCCCTCCTTACATCCCCCACC[A/G]AATGGGTAGGATATGCACCTTGACCTTATCCCCTC R 2 1 2 1 103000 r 74 goat snp51557-scaffold757-279626 NW_017189517.1 12007834 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413643 Affx-122950540 AX-123283992 X 25811901 TCTTGTCAAATCCAAATGTTCATCTTTGCGCCCTT[C/T]CAGTTGGTGAACTTTGTCCCTTCCACTGACCCATT Y 2 1 2 1 201000 f 74 goat snp51556-scaffold757-190071 NW_017189517.1 12096578 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440794 Affx-122929836 AX-123311131 X 25866529 TTGTATAACCCATAGGCCTACGGTAATAGGTTCAA[C/T]ATTTTATCTACTGTTTTCAGAGAAACACGTTGGTG Y 2 1 2 1 101000 f 74 goat snp51555-scaffold757-135443 NW_017189517.1 12151904 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389987 Affx-122968057 AX-123260344 X 25905234 ACAAGAGATTAAGCCCTGAGCCTTTGGAGTGGAAG[C/T]ACTGATTCCAAGACCGTAGATGACCAGACAACTAA Y 2 1 2 1 201000 r 74 goat snp51554-scaffold757-96738 NW_017189517.1 12191422 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426476 Affx-122940787 AX-123296822 X 26029309 GCCTGGGTTCTGAAACAACTGAGGCTGAAAGAAAC[A/G]CTCTTGCATTGCTCTAAGAGACTGGGGGCCAAAGG R 2 1 2 1 102000 f 74 goat snp17153-scaffold179-1958504 NW_017189517.1 12309717 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406898 Affx-122955629 AX-123277249 X 26081357 TCCGCACATGATGTCTTCTCCACCTGGACCTCGGC[A/G]TTGGTTGGGGTAACTCTGTTGGGTCCACCAATGGA R 2 1 2 1 102000 f 74 goat snp17152-scaffold179-1906456 NW_017189517.1 12362217 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787524 Affx-122963656 AX-385274548 X 26121458 ATTCCAGAATTGTTGAAATTACAGTGCCCAGAAAT[C/T]GTCTGGAAATTAGATCTTTACATTGGTACTCCATT Y 2 1 2 1 101000 f 74 goat snp17151-scaffold179-1866355 NW_017189517.1 12386009 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433751 Affx-122934501 AX-123304092 X 26173014 ACCAAGAGAAATGGAATAGAGCATTCATCCTTAGA[C/T]GGTGAAAGTGTTAATCACTCAGTTGTGTCCAACTC Y 2 1 2 1 101000 f 74 goat snp17150-scaffold179-1814799 NW_017189517.1 12437673 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801577 Affx-122921577 AX-385288486 X 26224680 ATGTAGTGTCATGAAAATAGCACTGATAAAAATCA[G/T]ATGATAGCTTCTACTGGCTGATTTTATGACCTTAG K 2 1 2 1 101000 r 74 goat snp17149-scaffold179-1763133 NW_017189517.1 12489389 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785081 Affx-122930901 AX-385272128 X 26315520 AAAGCCTCCCTCAAATAAATTGAGTATATATATTC[A/G]CACCTAGAAAACTCTATGGTACATCTTGTAAGCTA R 2 1 2 1 201000 r 74 goat snp17147-scaffold179-1672293 NW_017189517.1 12580850 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442701 Affx-122927873 AX-123313038 X 26358889 CTAAGGGACAGAAATTCACAAAAATCAGCAATCGG[C/T]AGGCCATCAAATCTAGGTTAAAATTGGCTGAGTGA Y 2 1 2 1 101000 r 74 goat snp17146-scaffold179-1628924 NW_017189517.1 12630761 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427937 Affx-122939213 AX-123298280 X 26408459 TTTTGCATTCTGGAAGAATGATCAACATCTGTTAC[A/G]TGTTGCAATGATTATGGTGTGCCAAATCTAACTTT R 2 1 2 1 101000 r 74 goat snp17145-scaffold179-1579354 NW_017189517.1 12681105 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407092 Affx-122954896 AX-123277443 X 26478871 GAGATACCTTCTCCGGAGAATGTTCAAGATCTGGC[A/G]TCAGGGACAGAATCACCAATGTTCTCAAACAAAGA R 2 1 2 1 101000 f 74 goat snp17144-scaffold179-1508942 NW_017189517.1 12752668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437497 Affx-122932354 AX-123307835 X 26508124 GTGAGTATGCTACATTACATCGTAAAAGGAACTAT[A/G]CAGATGTAATTAAGGTTATGGACCCCAAGATAGGT R 2 1 2 1 102000 f 74 goat snp17143-scaffold179-1479689 NW_017189517.1 12783968 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399297 Affx-122960536 AX-123269652 X 26538050 ATCCTTGTCCTCACTCTCAACTTTCCAGCCAGACA[C/T]GCAACAAATCTGAACTCTGGAGGCTTCTGCTCAAA Y 2 1 2 1 101000 f 74 goat snp17142-scaffold179-1449763 NW_017189517.1 12814793 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443524 Affx-122927781 AX-123313861 X 26572663 ATAACTTGCAAATATTTTCTTCCATTCCATAGGTT[G/T]CCTTTTCGTTTTGTTAATTATATCTTTTGCTGTGC K 2 1 2 1 101000 r 74 goat snp17141-scaffold179-1415150 NW_017189517.1 12849261 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397137 Affx-122962672 AX-123267492 X 26604779 AAGCTGGGCTTCACTTGCCTCACTCCGTTTCCACC[A/G]TCCCTTGTTACTGCGTTCTTCCCTTACCCACCTCT R 2 1 2 1 201000 r 74 goat snp17140-scaffold179-1383034 NW_017189517.1 12881310 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798355 Affx-122963193 AX-385285290 X 26668386 GCAACAATGTACCTATAGCTGAAGAGTTCAAATCC[A/C]AGCAAAGGACAGGTGATAAAGGTTAGGAATAGCGA M 2 1 2 1 101000 r 74 goat snp17139-scaffold179-1319427 NW_017189517.1 12945059 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782990 Affx-122923084 AX-313231532 X 26707491 AAATATATTGTGTTCTGCTTGAATTCTTGTAGATC[A/G]TGAAGGCTAATTTATGTGTGCACACTGAAGACATT R 2 1 2 1 101000 r 74 goat snp17138-scaffold179-1280322 NW_017189517.1 12985548 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382249 Affx-122973951 AX-123252607 X 26747234 TGTCACGTGTTTTAATGGATTTCCTCTGTTAGACC[A/G]TCCCTTTGGCCCAGAGTAGCAAAGAAGATTGTCTT R 2 1 2 1 101000 f 74 goat snp17137-scaffold179-1240579 NW_017189517.1 13025318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433423 Affx-122935085 AX-123303764 X 26805091 CACATCTTGGAAGGCCTTAAGAAGACCTGAGGAAT[C/T]GGTTTCTCCTTCATTAGGGTCCCAATGCATGAATT Y 2 1 2 1 101000 r 74 goat snp17136-scaffold179-1182722 NW_017189517.1 16334839 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401964 Affx-122958793 AX-123272317 X 26839473 AGTTCAGGACAAGTCTCGGAATACCAGGGTTAAAT[G/T]GAAGAAAATGCTGGAAGTTCAAGCCTGGAGGAGAC K 2 1 2 1 101000 f 74 goat snp17135-scaffold179-1148340 NW_017189517.1 16369239 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441847 Affx-122929045 AX-123312184 X 26902017 TTTCAGGAATGGAAATTGGTCTGTTCATACTATCT[A/G]TTTCTTCCTGGTTCAGCTTGGCAGATTGGGCATTT R 2 1 2 1 103000 r 74 goat snp17134-scaffold179-1085796 NW_017189517.1 14649635 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801098 Affx-122968578 AX-385288012 X 26953473 CCCAACAATCTTATGATAGAGAACCAGAGTATGTC[A/G]TAGAGAAACTGCTAGACTTTGGCAGGAAAACTACC R 2 1 2 1 101000 f 74 goat snp17133-scaffold179-1034340 NW_017189517.1 14701796 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445352 Affx-122926383 AX-123315689 X 27001684 TGTCTCCCTGGGCCAGATCCACACAATGCCTGAGT[A/C]GCATTCAAAATCTTGTCCTTTTGTTGGTATATCTG M 2 1 2 1 201000 r 74 goat snp17132-scaffold179-986129 NW_017189517.1 2281173 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402433 Affx-122958626 AX-123272786 X 27073934 AGATACATGAGAGAGAAAACTCTCTCTCTCCAGCA[G/T]ATGACAATTCAACAAAAAGGTATCTCTATGCAAAT K 2 1 2 1 201000 r 74 goat snp17130-scaffold179-913879 NW_017189517.1 2354158 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402937 Affx-122958181 AX-123273290 X 27150966 TGCATCAAATCACAGGGTGGGGAAACAGGGCACCT[A/G]TGAGAGTCTTCGCTTGCCCCACAAGTATCCCAGTG R 2 1 2 1 101000 r 74 goat snp17129-scaffold179-836847 NW_017189517.1 2429844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435797 Affx-122932852 AX-123306136 X 27205929 GCACACACGCACGCATAAATGATAAACTACTAAGC[C/T]AATCCCCATCTGATGGACATTCTCCCTGGTATCAG Y 2 1 2 1 101000 f 74 goat snp17128-scaffold179-781884 NW_017189517.1 2485972 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800412 Affx-122956523 AX-385287333 X 27240824 GTTAGTAAAGAAGATGTCATGAATATTGGAGGGCT[A/G]TGACAAGAATGCTGACCATCCTGAGGTGGGGAGGT R 2 1 2 1 101000 r 74 goat snp17127-scaffold179-746989 NW_017189517.1 2520669 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378954 Affx-122976420 AX-123249313 X 27290402 ACTGACTTTTCTGCAAGCTGTGACAATTGCATTTG[C/T]GGATGTCAGTGGCTAGGGTTGGTTAGCAGGTGGAT Y 2 1 2 1 201000 f 74 goat snp17126-scaffold179-697411 NW_017189517.1 2570542 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770411 Affx-122946437 AX-385257577 X 27331943 AACTCTTTCTAATAGCAAACCAAACCAAACTAAGG[C/T]ACAGAACAGTATGATCCTGTTTGTGTGTAAATAGA Y 2 1 2 1 101000 f 74 goat snp17125-scaffold179-655870 NW_017189517.1 2611725 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431334 Affx-122937063 AX-123301675 X 27400628 AAATATATCAAACTTTCTTAGTTTTGTTGAGTCTC[A/G]ACTAATCATAATTTGACAAGAACCTTTTCCCTGTC R 2 1 2 1 201000 r 74 goat snp17124-scaffold179-587185 NW_017189517.1 2680620 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400662 Affx-122960349 AX-123271017 X 27452116 TGAGTAGAATCATCATTCATATGGTTGCAAAATCA[C/T]ACCTGTTATGGTCAGTTTTTCACTTACTCCTTTGT Y 2 1 2 1 101000 f 74 goat snp17123-scaffold179-535697 NW_017189517.1 2732553 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402859 Affx-122958243 AX-123273212 X 27503774 CTTGCAATGAGCAAGTGTCTTAACCTCTCTTAAAA[C/T]AATGTAATAATGCCTACATTTTCAAGTTATAAATA Y 2 1 2 1 303000 r 74 goat snp17122-scaffold179-484039 NW_017189517.1 2764687 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784382 Affx-122960953 AX-385271432 X 27535547 GTGGTGGCACAGTTCTTCATTGAGGGGGAATGAAA[C/T]GATGTGTGGGCATTTGTGGATTAGTTCCTGGGGAA Y 2 1 2 1 101000 r 74 goat snp17121-scaffold179-452266 NW_017189517.1 2796553 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384331 Affx-122972260 AX-123254689 X 27592595 GGAAAGAGTTCAAGTCCAGTCCCCAAGCAAAAACA[C/T]ACAGACATACATCTGCCCTACCTTATACCTGTACC Y 2 1 2 1 201000 r 74 goat snp17120-scaffold179-395218 NW_017189517.1 13144488 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395036 Affx-122964208 AX-123265391 X 27671078 TCATTTAATTCTCACAACTCTGTAGAGTGGTTCGC[A/G]TTATTATTATCCCTTTTAACAGTTGAGGACATGTG R 2 1 2 1 101000 r 74 goat snp17119-scaffold179-316735 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782333 Affx-122978041 AX-385269410 X 27751302 GGGAAGAACCATATGGCAGATTATTGCAAAAAATT[A/G]TTAAGATGAAAGAGCAGGAATTTGAAAATGGGTAC R 2 1 2 1 101000 f 74 goat snp17118-scaffold179-236511 NW_017189517.1 2120964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380328 Affx-122975377 AX-123250686 X 27784932 AACTTTTTGGCTGTTGATTAGCAATTTTCCATTTC[C/T]GCTGCCACTCAGCTATGGCAGCTACCATTATACTC Y 2 1 2 1 101000 f 74 goat snp17117-scaffold179-202881 NW_017189517.1 2154473 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432493 Affx-122935586 AX-123302834 X 27825679 GCCACTGAAGAAACCAATGACCAGCACAGCTGCCA[C/T]GGATTCCTGGAGATTATACCACTTTTTATCCCATG Y 2 1 2 1 101000 r 74 goat snp17116-scaffold179-162134 NW_017189517.1 2195326 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419447 Affx-122945497 AX-123289795 X 27855709 ACCACAGATTTAACAAAGGACAGGTATCCAGAGTA[C/T]ATTAAAAGCTGTTAAAACTCAATAGAAAAAGAAAA Y 2 1 2 1 101000 f 74 goat snp17115-scaffold179-132104 NW_017189517.1 2225736 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784716 Affx-122947408 AX-385271764 X 27890627 AAGATTACTTTGTGAGCACAGATTTATGTTTAGAT[A/G]CGGTAATTTACAAATAATCTGATATAAGCTAATGT R 2 1 2 1 101000 f 74 goat snp17114-scaffold179-97186 NW_017189517.1 2016243 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378523 Affx-122976633 AX-123248882 X 27933806 GCTCCCTGAAAGTGGGGACTTTTTCTTCTTACTCC[A/G]TACCTTCTCTCACCAGAGACAGTGTTGGCTGCTGT R 2 1 2 1 201000 f 74 goat snp17113-scaffold179-54007 NW_017189517.1 1971820 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786671 Affx-122931166 AX-385273703 X 27991192 GTCCAATAAAGTTCTGGAACAACTGGCTATCAATG[A/C]TGTAAAGTAAACCTAAACCTATACTTCATGCCATA M 2 1 2 1 101000 f 74 goat snp45823-scaffold63-3280 NW_017189517.1 1909505 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399286 Affx-122960544 AX-123269641 X 28041982 CTTGGCAACCACAAGTCTGTTCACTATACCTGATC[A/G]CTAACATTCTTTCTCACATGGAAATGAATCCCTAC R 2 1 2 1 101000 r 74 goat snp45824-scaffold63-54070 NW_017212738.1 8848 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423367 Affx-122943143 AX-123293713 X 28085711 ACAGAGACACAGAACAAAAGGGAGAGGAAAAAGTA[C/T]AGTACAATAAGGAAAGAGAAGGATTTCAAAAGTTA Y 2 1 2 1 101000 f 74 goat snp45825-scaffold63-97799 NW_017212738.1 52266 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420768 Affx-122944711 AX-123291115 X 28190702 AGCCTTCTGGCTTACAGCCCCGTGACCATAAGTTT[A/G]TGCTGCTGTAAGCCACTGTTCGTGGTATTCATGAC R 2 1 2 1 201000 r 74 goat snp45827-scaffold63-202790 NW_017189517.1 28991966 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779181 Affx-122967601 AX-385266285 X 28229063 GCACATATGTAATAACAAGGTGCTTTAATTTCAAA[A/C]ATTCCTTCCAGCTCTAACATTCTTTGACTTGGTCC M 2 1 2 1 102000 r 74 goat snp45828-scaffold63-241151 NW_017189517.1 13384231 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383791 Affx-122973195 AX-123254149 X 28282622 CATTAATGACATTAGAGGGATATTGTTGTTGTTTC[A/G]TTGCTAAGTCATGTCTGACTCTTTGCAACTTCATG R 2 1 2 1 303000 f 74 goat snp45829-scaffold63-294710 NW_017189517.1 13519914 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797672 Affx-122933415 AX-385284611 X 28317365 TTAGACAAATAAGGGTGACACTGTATAGGCTTTGG[C/T]AGTGACTAGTTTCCAAAGCTTCAAGTGGGAATATG Y 2 1 2 1 201000 f 74 goat snp45830-scaffold63-329453 NW_017189517.1 13484200 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433650 Affx-122934574 AX-123303991 X 28389040 GAAGCATCCCTGTTAAAATAAGAACATAAAAACTT[C/T]AGAGGTAATAGTTGCCAGTGCTTATGAATGCTGGT Y 2 1 2 1 101000 r 74 goat snp45831-scaffold63-401128 NW_017189517.1 13432816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441878 Affx-122928629 AX-123312215 X 28446631 GGGATGTACACTAGAGAGATCATGTCTACATGTGT[A/G]CATACACATATATGCATCCGTGCATATTTGGAATA R 2 1 2 1 201000 f 74 goat snp45832-scaffold63-458719 NW_017189517.1 13579546 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391410 Affx-122966772 AX-123261767 X 28486655 CATGTCCCCAGAGGAATGGTCTACCAGAAGACCCG[A/C]TGATTTGTCTAGCTTTTGCACCAGAATGATCATAT M 2 1 2 1 101000 r 74 goat snp45833-scaffold63-498743 NW_017189517.1 13539124 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398595 Affx-122961492 AX-123268950 X 28536047 CAAGCAACTAACTGTGAGGGGGCACAGCCCTATGC[A/G]CTAGCAGACAGGTTGCCTTAAGATCCTCTGAGCCC R 2 1 2 1 101000 r 74 goat snp45834-scaffold63-548135 NW_017189517.1 13652930 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440805 Affx-122929828 AX-123311142 X 28595410 CGTTCCAATCTCCTGACTCATCCCACCACCCACCC[C/T]TCCACAACTTCACTCTTCCAGATGTTATTTATTCC Y 2 1 2 1 101000 r 74 goat snp45835-scaffold63-607498 NW_017189517.1 13712107 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792234 Affx-122956081 AX-385279218 X 28659951 CATACTTCGCTAAAATGGGGGAAAAGTTTGTTGTT[C/T]AGTGATCATCAGTACCCATGAGGTACTGGTCACTA Y 2 1 2 1 101000 f 74 goat snp45837-scaffold63-672039 NW_017189517.1 13777950 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446492 Affx-122925048 AX-123316828 X 28697231 CCCCTTGTCTCTCAGAGTGAGCCACTATCATTGCC[G/T]CAGTCAAATTGACAGAAGAAAATGACTTTGTTCAA K 2 1 2 1 101000 f 74 goat snp45838-scaffold63-709319 NW_017189517.1 13815413 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450718 Affx-122921878 AX-123321052 X 28727346 TACTTCCCCCGGGTCTGAGGCCTCAGGTCATGGAG[G/T]TAATCGGGGGTGTGATTCCACAGGTGGGAGCCCAG K 2 1 2 1 202000 f 74 goat snp45839-scaffold63-739434 NW_017189517.1 13845795 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395807 Affx-122963646 AX-123266162 X 28789293 TAATCCTTTTGATTTCTAGTAAAGCATTGGACATA[C/T]AGTGGACATTCAGAGAATAATTCTTGAATGAATGA Y 2 1 2 1 101000 f 74 goat snp45840-scaffold63-801381 NW_017189517.1 13908539 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392176 Affx-122966302 AX-123262533 X 28841352 CCAACTTTAAATCCCTATTCTACAGCTTAGATCTG[C/T]ATGACCTTGAGCAAATAGTGTTATCTTCTGAACCT Y 2 1 2 1 101000 f 74 goat snp45841-scaffold63-853440 NW_017189517.1 13960714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428568 Affx-122938719 AX-123298910 X 28899240 GTCACTAGTCCTCCCAGATTTGTTTCCTCTGCCAA[C/T]TGGGTGAATATGCCCTCTGTATTGCCTTGTGACCT Y 2 1 2 1 201000 r 74 goat snp45842-scaffold63-911328 NW_017189517.1 14018774 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399131 Affx-122960665 AX-123269486 X 29002607 TCCCATTATGGATGTTTATAGCACTATCCCCATCT[A/C]AGTCATAGCATTTGTCATAAGTGCAGTCCTGTATT M 2 1 2 1 201000 r 74 goat snp45843-scaffold63-1014695 NW_017189517.1 16190898 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401235 Affx-122959309 AX-123271588 X 29040106 ATTTCTGAGCAATTCTGCATTCTTCAAAACTTTCA[C/T]GCCAAGATAAAGAATTCTTTCAGGGTGGCTTTTAC Y 2 1 2 1 201000 f 74 goat snp45844-scaffold63-1052194 NW_017189517.1 14108167 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425711 Affx-122940770 AX-123296057 X 29088777 TCTGGCTATACAACTGTAAATAAGATGAATAAGGC[A/G]TCTGAACTCATGGCACATCAATTTAGTGTGGAGAT R 2 1 2 1 101000 f 74 goat snp45845-scaffold63-1100865 NW_017189517.1 14157486 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408288 Affx-122953789 AX-123278639 X 29122051 GAACTTTTGGTTGAGGTCTTGGAACTAGTTTTTCA[C/T]GAATGTTTTGGATAAAAAATTAATTTTAAATGGAA Y 2 1 2 1 101000 f 74 goat snp45846-scaffold63-1134139 NW_017189517.1 14190950 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380857 Affx-122975440 AX-123251215 X 29188713 GCCCTTTTTGTCCTATACTTATTATCTTTCCAGGC[C/T]TATGTTCCAGGTGATTCCATCATCTTGTTCCTGTA Y 2 1 2 1 101000 f 74 goat snp45847-scaffold63-1200801 NW_017189517.1 14259012 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803391 Affx-122967959 AX-385290222 X 29259419 GAAGACTCTGTTCTTTAACTCCAAGAACTAAAATC[A/G]TTTAGTGTGGACTTCAAGTTTTGATGCTATGAACC R 2 1 2 1 101000 r 74 goat snp45848-scaffold63-1271507 NW_017189517.1 14329894 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437434 Affx-122932404 AX-123307772 X 29290547 CCAAGCAGAATAGACCTGAGGACCTGGTATTCTTG[A/C]TATGGATTTGTTCAGATTGTGATGAGGGTGGAATT M 2 1 2 1 101000 f 74 goat snp45849-scaffold63-1302635 NW_017189517.1 14361418 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803456 Affx-122970288 AX-385290283 X 29322384 GAGGAGAAACCATAAGGGAATAGTGGATGGAAACA[G/T]TTATTATTTGAAGAATAGGAGCAAAGATCTGGGCA K 2 1 2 1 201000 r 74 goat snp45850-scaffold63-1334472 NW_017189517.1 14393241 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418193 Affx-122947068 AX-123288541 X 29356393 CCTTAGGCCTAAAGGAAACTGTGTGGAAGGGAGTA[C/T]GGTCTTAGGGTTGCCAGATAAAACGTACAACACCC Y 2 1 2 1 201000 f 74 goat snp45851-scaffold63-1368481 NW_017189517.1 14427127 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787569 Affx-122926130 AX-385274593 X 29421286 AGCCAATTCTGTTATTTCAATTTGAAAGAGACCTT[A/G]TGTGGCTTTGATGAACAATTTCATTGGTGCTCTTA R 2 1 2 1 101000 r 74 goat snp45852-scaffold63-1433374 NW_017189517.1 14482104 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440438 Affx-122929409 AX-123310775 X 29473643 GATTATTCTTGATGAAAGAACCTCCCATGCTAAAA[C/T]GACTGTTCTAAAATAATATTCTTCCTCTTGATATA Y 2 1 2 1 101000 f 74 goat snp45853-scaffold63-1485731 NW_017189517.1 14535595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389516 Affx-122968293 AX-123259874 X 29530926 GTTCTCTGAGTGAGACAAAGGAGATGAGGTCTAAC[A/G]CCCTAACTGCCTGAGAAAAAGACATGTGTGGTATG R 2 1 2 1 101000 f 74 goat snp45854-scaffold63-1543014 NW_017189517.1 14593919 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433611 Affx-122934947 AX-123303952 X 29652036 TTCTTGCCTCATGTAAACTGCCTCATTGATGGAGC[A/G]TTTTGGATTGTCTTGTGTTTTCGCAAAGCATTGCT R 2 1 2 1 201000 r 74 goat snp45856-scaffold63-1664124 NW_017189517.1 14749061 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444780 Affx-122926349 AX-123315117 X 29711916 TATTCTCATTTTAAAGATGAGGAATATGGATTTTG[A/G]GAAATGTAAGTAACTTGCCCAAAATGTTACAGTTG R 2 1 2 1 303000 f 74 goat snp45857-scaffold63-1724004 NW_017189517.1 14780070 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445687 Affx-122926127 AX-123316024 X 29743604 TGAAATTGTGTTCCATCCTGTTCAAGGCACCCTTG[C/T]AACTATGGGATCTGATAGTAGATGCAGCTCTTGGG Y 2 1 2 1 101000 r 74 goat snp45858-scaffold63-1755692 NW_017189517.1 14812041 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449054 Affx-122923059 AX-123319389 X 29809609 ATTTTGCCACAAACTAATATATTGTCCCTTGATAT[A/G]TAATTCTTAATGTAAAGAGAGAGAGAGAGAGACAG R 2 1 2 1 101000 f 74 goat snp45859-scaffold63-1821697 NW_017189517.1 14873631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799840 Affx-122974823 AX-385286766 X 29877866 AGAGGCGCTGAATTTACAACGCCAGAGAACACTCT[C/T]CCTCTTAATAGCTAAAAGTGTAAGTTAAAAGCTTT Y 2 1 2 1 101000 f 74 goat snp45860-scaffold63-1889954 NW_017189517.1 14942976 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395356 Affx-122963991 AX-123265711 X 29916978 TGTCTACCCCTTCTTTGCTCCTAGTAGCCCCAGGG[A/G]TTCAGAATGTTTTATTGTTTGATATTTATCTGGCT R 2 1 2 1 101000 r 74 goat snp45861-scaffold63-1929066 NW_017189517.1 14982743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391069 Affx-122966843 AX-123261426 X 29958517 GGCTCAATATTCTGCTTCTTGTTTTTAAACTTAAC[A/G]TCTTATTCTGTTGAGTGTTATTGTAGGTGTTAAAT R 2 1 2 1 101000 r 74 goat snp45862-scaffold63-1970605 NW_017189517.1 15024479 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777230 Affx-122972753 AX-385264353 X 30070813 ATGAAATATAGTTGTGTCATTACTCCATCAAAAAT[C/T]GGTAGTTATTTGTGCCCAACTTAGACCCCAAATTA Y 2 1 2 1 101000 r 74 goat snp45865-scaffold63-2082901 NW_017189517.1 15137560 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436976 Affx-122933156 AX-123307314 X 30152572 ATAATCCAATGTGTTCTGTCTCTGCTATTCAGGAA[C/T]GGTCACAGACCTGTGAACAGTTTTCTGTTCATTAT Y 2 1 2 1 101000 r 74 goat snp45866-scaffold63-2164660 NW_017189517.1 15220816 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787309 Affx-122923685 AX-385274334 X 30183362 GAAAGGAAAAACAAAAATGAGCATTTTAAACCACA[A/G]CACACATCATCATTGTGCTGTGTCAAGTTTTATCA R 2 1 2 1 202000 f 74 goat snp45867-scaffold63-2195450 NW_017189517.1 15249397 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378879 Affx-122976504 AX-123249238 X 30229832 CTGGGAGGGAACTCAGAAAAAGGGAAAATATGTGG[A/G]TGGATACCTGTCCTGGGAAGTGAGTGGTTACAGCC R 2 1 2 1 101000 f 74 goat snp45868-scaffold63-2241920 NW_017189517.1 15296017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438996 Affx-122930371 AX-123309333 X 30261357 TCACTATCTCAGATGCCCAGTTCCAGTTAATTTCT[A/G]TGAAAGTATATAGAACTGTGAACTGAAACAGCAAC R 2 1 2 1 101000 f 74 goat snp45869-scaffold63-2273445 NW_017189517.1 15327524 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394344 Affx-122964661 AX-123264699 X 30316354 TGGCTTCTAGCACACTGCTTGCCACATAGTTGATT[A/C]TTATTAAATATCAAAAAGGCAGGCATAAAACCTAA M 2 1 2 1 201000 r 74 goat snp45870-scaffold63-2328442 NW_017189517.1 15382841 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410117 Affx-122952821 AX-123280467 X 30366020 TTCCTAAGGAAAAGATTTTCTCACCAAAGGGCAAT[A/G]TAGGAGAAAGCAATGTCACTGAAAAAATACTTGGT R 2 1 2 1 101000 f 74 goat snp45871-scaffold63-2378108 NW_017212851.1 2849 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778325 Affx-122966507 AX-385265440 X 30404373 CCAAACTTCAGAAGCTAGCACAGTAAAAGGAACTC[G/T]ATACCAATAGGATATTTTTCCTTCATAATAACAAA K 2 1 2 1 101000 f 74 goat snp45872-scaffold63-2416461 NW_017189517.1 15456561 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437321 Affx-122931962 AX-123307659 X 30465477 ATACAATGCAGATGAAGCATCTTGGTCATGCCCAG[A/G]AACTACTTCTCTCTGCTCAGGTTCCAAAACAATCT R 2 1 2 1 101000 r 74 goat snp45873-scaffold63-2477565 NW_017189517.1 15517837 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394009 Affx-122965019 AX-123264364 X 30508796 ACCTCCACTCCCTCCATGTCCTCTTCACCCACTCA[C/T]GTATCCTGTTTCTCCCTTTACCTTGATATTAATAG Y 2 1 2 1 201000 r 74 goat snp45874-scaffold63-2520884 NW_017189517.1 15561328 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390586 Affx-122967192 AX-123260943 X 30567267 CCCTAAGTCAACACTGGGATTCTTCTGAGCATAGA[A/G]CCTGGTTGACTGCACAGGATTCATGTCCATAAAGT R 2 1 2 1 101000 f 74 goat snp45875-scaffold63-2579355 NW_017189517.1 15620679 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401196 Affx-122959339 AX-123271549 X 30602101 TAGGTATGGATCTCTGAGTTTATTCTTCTGTAAGT[C/T]CATTGAGCTCCTTGGATGTATATATTAATGTTTTG Y 2 1 2 1 101000 r 74 goat snp45876-scaffold63-2614189 NW_017189517.1 15655646 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414512 Affx-122949528 AX-123284861 X 30788820 TTTATTGAAGTGGAACATATATGTCTCTGGTTTTT[A/G]CTAAACTGAACTGAATGGGATACATCTACAAATAT R 2 1 2 1 103000 f 74 goat snp45880-scaffold63-2800908 NW_017189517.1 15844460 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376764 Affx-122977968 AX-123247123 X 30996548 TGCTGAAGGCTATACCACTGGTAAGTGACAGCTGA[C/T]GATAGACACAGTCAGCCGGGTCCCAGAGCCTTTGC Y 2 1 2 1 101000 f 74 goat snp45884-scaffold63-3008636 NW_017189517.1 16009653 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385908 Affx-122971577 AX-123256266 X 31086851 TTTCCCTGAACTGAACATCTCTACCGCTTTCCCAT[A/G]TCTACATGGCCCATAAGAAACCACTTGAGACACCA R 2 1 2 1 201000 r 74 goat snp45886-scaffold63-3098939 NW_017189517.1 16100085 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773469 Affx-122940389 AX-385260611 X 31189362 CTTTTTAGTAGTCACTCACTCAATACAAAACACAG[C/T]ATTGAGAACAAGAGAGCGATTCCCTTGAGCCATTG Y 2 1 2 1 201000 r 74 goat snp45888-scaffold63-3201450 NW_017189517.1 16263036 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398159 Affx-122962665 AX-123268514 X 31224786 GACTTGGAAAACTGCACCAAAATGATCATTCTCCA[C/T]CAGGTTTTGAAAATTTAACCTGATACAGAGTCATG Y 2 1 2 1 101000 f 74 goat snp45889-scaffold63-3236874 NW_017189517.1 16298452 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426262 Affx-122940327 AX-123296608 X 31369261 TCTGTTGACATAGAAGAGAACAGGCTAAGCAACAG[A/C]TATTTAGGGACTTGGCTATGATTTCTTGTATATGA M 2 1 2 1 101000 r 74 goat snp45892-scaffold63-3381349 NW_017189517.1 16521195 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393338 Affx-122965939 AX-123263694 X 31414456 ACTTGCCTTGCTTCTCTAAACATAGTTTTGGAAAA[C/T]AAGAGGGCCTTCATGCAAATTAGTATGCAACAAGT Y 2 1 2 1 101000 f 74 goat snp45893-scaffold63-3426544 NW_017189517.1 16566595 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416315 Affx-122947920 AX-123286664 X 31581695 AATGGAGAAAAAAAATCCTGACCCCATTGCTTACA[G/T]AGGTTCATAAGTGCTTAGCATAAATCACTCATATG K 2 1 2 1 201000 r 74 goat snp45895-scaffold63-3593783 NW_017189517.1 16735066 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796284 Affx-122968147 AX-385283234 X 31636298 TTTGACCACCTCTACCAAAAGATGAGAATTCTCCA[A/G]GTACTAATGAACTTAAAAGTTCACTTATTTTGTTT R 2 1 2 1 101000 f 74 goat snp45896-scaffold63-3648386 NW_017189517.1 16787574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427234 Affx-122939568 AX-123297577 X 31666204 ATTAAGGTAAAACATGAAATGAAACCTACTATTAA[C/T]GTTAACTAGAGAGGGACACAAAGTCTGCCTAAAAT Y 2 1 2 1 101000 f 74 goat snp45897-scaffold63-3678292 NW_017189517.1 16817880 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788058 Affx-122962399 AX-385275078 X 31707968 TATGAGTATACAGTAGTTTCTGGTTAATTACTGGT[A/C]GTGATGGTTTTTAGTATTAAGTAGATCTATCTAAT M 2 1 2 1 101000 f 74 goat snp45898-scaffold63-3720056 NW_017189517.1 16859784 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433152 Affx-122935675 AX-123303493 X 31754778 AATGAGCCAATCAGAAAATGGAAGAAAACCTTTTT[A/G]TGGAGTATTGGGATCTTATTCTCAGATGAGACATA R 2 1 2 1 101000 r 74 goat snp45899-scaffold63-3766866 NW_017189517.1 16906694 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780901 Affx-122924834 AX-385267988 X 31830138 CATAAATCTTTCAACTTCTATGTTTGAAAATCTCC[A/G]TGGCAAAATGTTGAACAGGAAGGAATGAGAAGAGA R 2 1 2 1 101000 r 74 goat snp45900-scaffold63-3842226 NW_017189517.1 16982411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797088 Affx-122933465 AX-385284028 X 31914896 TGTTCTAGTAGTTTTGGCGCACCCTTTGGGATTCT[A/G]TACGTGCATGATCATGATGTCTGTAAATAAAAACT R 2 1 2 1 101000 f 74 goat snp45901-scaffold63-3926984 NW_017189517.1 17066906 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775030 Affx-122959278 AX-385262162 X 32001064 ATGCAATATTAAGTCATCGCCTTCTCCATTGATAC[A/G]TTTCTAGAGATTTAGTCAGTCTCCCCTCTTTTTCT R 2 1 2 1 202000 f 74 goat snp45903-scaffold63-4013152 NW_017189517.1 17153843 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423908 Affx-122942279 AX-123294254 X 32193464 CTCTATTAGTTTATCCAGGGGTGGGGAAACAAATC[C/T]GTTTCTCCCTCTTGGGATGGGAGAGGATGTCTTCC Y 2 1 2 1 101000 f 74 goat snp45907-scaffold63-4205552 NW_017189517.1 17346793 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426367 Affx-122940249 AX-123296713 X 32239197 GTATCCATGGGGGCACACAATGAACAAAGGATTTT[A/G]TATTTGGGGTTCCCTGAGAGCTCAGTTGGTAAAGA R 2 1 2 1 103000 f 74 goat snp45908-scaffold63-4251285 NW_017189517.1 17392615 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381805 Affx-122974280 AX-123252163 X 32303143 TCCTTTGACATTTGGATTGCTTAGGAAAATCTTCT[A/G]CTTAGACTCCTTCCATTCTCTTGGCATATTCTCTT R 2 1 2 1 101000 f 74 goat snp45909-scaffold63-4315231 NW_017189517.1 17547241 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392579 Affx-122966069 AX-123262936 X 32367818 AACTGCATGTGTACTGCTTTGAGGAGGAGGGACTG[C/T]CTGGAGAACCTAGAACTTTGGTGTGAAATAAAAGA Y 2 1 2 1 201000 r 74 goat snp45910-scaffold63-4379906 NW_017189517.1 17611843 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401364 Affx-122959241 AX-123271717 X 32401729 TCATTATATGAGTTCATTTTTAGAGGCCAGTTACT[A/G]TTGATAAATGAGGGCACCACAGGCTATTTTTGAAA R 2 1 2 1 101000 r 74 goat snp45911-scaffold63-4413817 NW_017189517.1 17646100 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407071 Affx-122954913 AX-123277422 X 32453189 TCTGCAGAAAGTGATCTATACTTTGATGTGCATCA[C/T]GAAAAACAGCAATGCAAATGCTATGTATTATCAAA Y 2 1 2 1 201000 f 74 goat snp45912-scaffold63-4465277 NW_017189517.1 17698184 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411929 Affx-122951158 AX-123282279 X 32745951 CAGACATCGCTCTGAATTTTAGCTTTTTCATCTGC[A/G]AAATGGGAATAATATCATTATAACCCTGTGTTGAA R 2 1 2 1 101000 f 74 goat snp45917-scaffold63-4758039 NW_017189517.1 17994690 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417567 Affx-122946906 AX-123287915 X 32796677 AGAGCCAGGCAGCCATGCCCACACCAAGCCTTATC[A/G]TCCCCTCCATCCAGACCTCACAGGCTCCACCATTC R 2 1 2 1 101000 f 74 goat snp45918-scaffold63-4808765 NW_017189517.1 18041636 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435066 Affx-122933734 AX-123305406 X 32937924 AAAGAGAATTAGATAAAATAGAGGACTATACAAAC[A/G]TGTAAAATTCTGCATGTTGACTATATAAACGTTGT R 2 1 2 1 101000 r 74 goat snp45921-scaffold63-4950012 NW_017189517.1 18183714 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791990 Affx-122970031 AX-385278978 X 33034273 ATTTAACATCATATAAGGAGCTTGTTAAAAATTCA[C/T]ATAACATGGTCCCCACTCCCAGATATTTTGATTCA Y 2 1 2 1 201000 f 74 goat snp45923-scaffold63-5046361 NW_017189517.1 18275959 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444870 Affx-122926282 AX-123315207 X 33083201 CTGCAGGGGAAGTGTAGAGTCTTAACCACCAGACC[A/G]CCTGGGAAGCCCAGAAAAGTGACATAGTCTCATTT R 2 1 2 1 103000 r 74 goat snp45924-scaffold63-5095289 NW_017189517.1 18325460 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420251 Affx-122945065 AX-123290599 X 33114865 AAAGGAATGGATTCTTCTCTAGAACCTCCAGAAGG[A/G]AATGCACCACTACTGATGCCTTGAGGTTAGCTCAG R 2 1 2 1 201000 r 74 goat snp45925-scaffold63-5126953 NW_017189517.1 18358096 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450091 Affx-122922789 AX-123320426 X 33171295 ACAATCAGAGGCGATCAATGCTTCTTACAATAAGG[C/T]GAAGAATTACAACTGTGTTTTATTTTATAGCTTTG Y 2 1 2 1 101000 f 74 goat snp45926-scaffold63-5183383 NW_017189517.1 18416051 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795107 Affx-122920398 AX-385282066 X 33200137 TTAAAAATGAACACAACCTTAATAGAAAAGTGGCC[A/G]TATTTCTTACCTTGCTGAAGAGTTAAAGAAAGAAA R 2 1 2 1 201000 r 74 goat snp45927-scaffold63-5212225 NW_017189517.1 18445374 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790588 Affx-122934579 AX-385277591 X 33237490 TTTGGCCTATTGGGGTGGGAATGTATTTACCAAAG[A/G]GTGAATGGCAAAATGTGCTATTCTCCAGGTAAATT R 2 1 2 1 101000 r 74 goat snp45928-scaffold63-5249578 NW_017189517.1 18484167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773533 Affx-122953948 AX-385260674 X 33281342 ATCTCAGTAATCCCAGCCACCTGAACACATGAGTC[A/G]CAATATTATGGTCACTGCTCAATACATCACTGATG R 2 1 2 1 101000 f 74 goat snp45929-scaffold63-5293430 NW_017189517.1 18528614 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437909 Affx-122931653 AX-123308247 X 33330833 AAGGAGCCACATTCAGACCGGGAGCTGACTGTTTA[C/T]CATCCTATGGAAAACCAGTTGTTCCAGCACAGTTT Y 2 1 2 1 103000 f 74 goat snp45930-scaffold63-5342921 NW_017189517.1 18579091 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798801 Affx-122978554 AX-385285732 X 33370029 CCCTCTATAAACTTCAAGGTGATACTATTATTAAC[A/G]TAGGAATCATAGTTTCTCTTCACCTTTATTATTTA R 2 1 2 1 101000 r 74 goat snp45931-scaffold63-5382117 NW_017189517.1 18618046 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764595 Affx-122947515 AX-385252242 X 33474468 ATGTAAAACGAAGAATGTGTCAAACCAATCCTAAT[A/G]TGGTAATGATTTTACCGTATATCAAATCATCATAC R 2 1 2 1 101000 f 74 goat snp45933-scaffold63-5486556 NW_017189517.1 18725022 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382558 Affx-122973772 AX-123252916 X 33556104 TTTATTCTTGTCTGACTCTTTGCGACCCTATGGAC[G/T]ATAGCCCCCCAGGTTCTTCTGATCATAGGAATCAT K 2 1 2 1 303000 r 74 goat snp45934-scaffold63-5568192 NW_017189517.1 18808960 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798369 Affx-122925950 AX-385285304 X 33595376 TAAAATGGGGACAGGTCCTGTTTTTTGGACTGCTA[C/T]GTGGATCAAGTGATATAACATGTAAAGTACCTTGC Y 2 1 2 1 101000 f 74 goat snp45935-scaffold63-5607464 NW_017189517.1 18848807 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392929 Affx-122965706 AX-123263286 X 33660419 TATAGGATTGAACCCTATATATAGCCTGCTTTTTC[A/G]TGTTAAAAGCAGCCCCCTTGCTTAGAGACAGCTAA R 2 1 2 1 201000 f 74 goat snp45936-scaffold63-5672507 NW_017189517.1 18914190 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774297 Affx-122932552 AX-385261433 X 33738317 CAGCTGCTCAGCACCTCAACTTTCTTTTCAACTTT[A/G]CATTGGGTGGTCTGTAGTTTTCACAAAGCACTGTC R 2 1 2 1 101000 f 74 goat snp45937-scaffold63-5750405 NW_017189517.1 18993605 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384710 Affx-122972105 AX-123255068 X 33933113 TTATATGTTTGATTTTCTTAGAGGAAAGGCAAGTA[C/T]GTAAATAAAGTAGCATTCAGAGTTTTCTAGAGCTA Y 2 1 2 1 101000 r 74 goat snp45940-scaffold63-5945201 NW_017189517.1 19190436 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386051 Affx-122971470 AX-123256409 X 34013386 TTGAGAGGTTTTTGTTGTTCCTGTTTGCTATTGTT[A/G]TTGCTGCTGTTTTCCTTTTTATAGTGGAAGAATTT R 2 1 2 1 103000 f 74 goat snp45941-scaffold63-6025474 NW_017189517.1 19271765 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422544 Affx-122943267 AX-123292890 X 34110280 CTCTTACTAAAGTTCCATTGGATTTGTTTTTGCTT[A/C]TACAGGTGCTCATAGTGTCACATGTTTCTTATGAA M 2 1 2 1 201000 r 74 goat snp45943-scaffold63-6122368 NW_017189517.1 19369617 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796431 Affx-122964779 AX-385283381 X 34267764 CAAAGCTGTATCTCAAAGCCTGAGTGATGTCACAA[C/T]GAGTAATGATAGAAATTTGAGAGATGAGATGATGC Y 2 1 2 1 102000 f 74 goat snp45946-scaffold63-6279852 NW_017189517.1 19529121 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433847 Affx-122934441 AX-123304188 X 34341143 TTCTCCCTGGTGCAGATTTACAAAGCCCATTCATA[C/T]AGAAAGTCTTTATAAGAAAGAAACACTTAAATATT Y 2 1 2 1 101000 f 74 goat snp45947-scaffold63-6353231 NW_017189517.1 19604316 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440269 Affx-122930646 AX-123310606 X 34386865 TAAAGTGGTATTTGTTGAATTTTGCTTAGGAAAAT[A/C]TAGGGTTATGTAGAGTGCCCTCAAGGAGGGAAATT M 2 1 2 1 101000 r 74 goat snp45948-scaffold63-6398953 NW_017189745.1 22451 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785832 Affx-122920615 AX-385272869 X 34453314 AGAATCTATCTCCCTATAGCCTAATTAACCTATGT[C/T]TCAGTAAAGTGCTCATTAAGCATTGAAGGTTGTCA Y 2 1 2 1 101000 r 74 goat snp45949-scaffold63-6465402 NW_017189517.1 19690927 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781231 Affx-122945747 AX-385268316 X 34624602 TGGGAGGCTCCAAATTTCCCAGAATAAGATTATTT[A/G]CTTTATTTCAAATCAATTTTCTTGCTGAGGTTCAC R 2 1 2 1 303000 r 74 goat snp45952-scaffold63-6636690 NW_017189517.1 21635295 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376021 Affx-122978401 AX-123246380 X 34657566 CTTTTTTCCCTAACTTTCTGCCAACTGCCAGCCTT[A/C]GGTAAGTAGATGCAACATGACACCCAGACAAGGAT M 2 1 2 1 201000 r 74 goat snp45953-scaffold63-6669654 NW_017189517.1 21665955 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794176 Affx-122920178 AX-385281142 X 34688840 TCATGCCACCTACCCTTATCTCCAAGCAAATGGTT[A/G]ATATCAGGATATAATGTAAGCAGCTCCTTGCAGGA R 2 1 2 1 101000 f 74 goat snp45954-scaffold63-6700928 NW_017189517.1 21698171 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775553 Affx-122959710 AX-385262684 X 34730783 ATTAATAGGAGAAAAATGAATTGTAAATCATGGGC[A/G]CAGAGGTCTCAAAGAGAAGTGCCCAAAGCAGGAAG R 2 1 2 1 101000 r 74 goat snp45955-scaffold63-6742871 NW_017189517.1 21740151 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430509 Affx-122937221 AX-123300850 X 34761023 CTTTCTGACATCCAAAGTCTGGTGAGAAATTGACT[A/G]TTAATCTTATTGGGGATCCCTTGTATTTGAAAAGT R 2 1 2 1 101000 f 74 goat snp45956-scaffold63-6773111 NW_017189517.1 21770505 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784751 Affx-122957160 AX-385271799 X 34818145 ATATAGATATATAGGTATAGTTTCTCTAGAGAACG[C/T]TAACTGATCCATGGGTTATGCTAACTTTGCTCTAG Y 2 1 2 1 101000 r 74 goat snp45957-scaffold63-6830233 NW_017189517.1 21828291 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426601 Affx-122939976 AX-123296947 X 34864296 TGAACCTCCAGTACTTTAGTTGAAAGATGTCTGAG[C/T]AAAAGTCACAGAGAAAGGACTGAAAGATAGGAAGG Y 2 1 2 1 101000 f 74 goat snp45958-scaffold63-6876384 NW_017189517.1 21875542 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403955 Affx-122957446 AX-123274307 X 34913472 AATCTCTGGTTCAGTACCTCTGTTTTAATAAGATG[A/C]TTCTGATGCATGCTGAAGTTGGAAAATCACTGGTG M 2 1 2 1 101000 f 74 goat snp45959-scaffold63-6925560 NW_017189517.1 21926068 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425162 Affx-122941063 AX-123295508 X 35010263 ATTTAATGCCTATGTACTTTTGTGATTTTTTAAAA[C/T]GAAGTGACTACTATTGTAATTCTGACTACAACCAT Y 2 1 2 1 103000 r 74 goat snp45960-scaffold63-7022351 NW_017189517.1 22024968 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402517 Affx-122958487 AX-123272870 X 35071313 AATCTTATAATTTCCTATAAAATTAAGTCTGAAAT[A/C]TCAGCCTGGCTGTCATAGTTGATTGTTGTCTTAGT M 2 1 2 1 101000 r 74 goat snp45961-scaffold63-7083401 NW_017189517.1 22087163 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794028 Affx-122926133 AX-385280997 X 35123039 TTGCATAATTGCTTCGTGCCAGGTATTATGCTACA[C/T]ACTTTTCAAAAGTTAAGACATTTATTTCCCATCAT Y 2 1 2 1 101000 f 74 goat snp45962-scaffold63-7135127 NW_017189517.1 22139299 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441146 Affx-122929571 AX-123311483 X 35164472 ACAAATTGCCAGAATACAGAAAGGTCACCTCAAAC[A/G]CAGCAACATAACCAAGATGAGGAGACAGAACCCAG R 2 1 2 1 103000 r 74 goat snp45963-scaffold63-7176560 NW_017190118.1 106985 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450946 Affx-122921761 AX-123321280 X 35201024 ACGACTGAGCGACTTTCACTCACTCAGGCACTCAT[A/G]CGTGCTAATAGAATCTAATTCAGAGCTGAGTCTAG R 2 1 2 1 201000 r 74 goat snp45964-scaffold63-7213112 NW_017190118.1 69447 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401264 Affx-122959288 AX-123271617 X 35238763 TAACTATCTTTTATTGACTGCTTACTATGTGCCTA[C/T]TTCTTTGAATCCAACACGTTTTTAAGTTCTCTCAT Y 2 1 2 1 101000 r 74 goat snp45965-scaffold63-7250851 NW_017190118.1 31468 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803149 Affx-122949908 AX-385290012 X 35372967 TCAGCACTGCAGTGTCTTTGCTTAGATAAGCATAA[C/T]GTTTATTTCCCTACATCCTATAGGTCTCTTCTCAA Y 2 1 2 1 201000 r 74 goat snp45967-scaffold63-7385055 NW_017189517.1 22217172 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792743 Affx-122961371 AX-385279723 X 35448773 TATTGTAGGTCCTGTACTACGGTATTTAGGGCACC[A/G]TTAAATCGGGCAAAAGATATAGAGCTGGCGATGCT R 2 1 2 1 101000 f 74 goat snp45968-scaffold63-7460861 NW_017189517.1 22292588 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422275 Affx-122943496 AX-123292621 X 35483560 ATCTCTGTCTCTCTCACACACACAAACCCTCCTAC[A/G]GTCTTCTCCTTCACTCTCCTCCACATTCCTGTTCT R 2 1 2 1 201000 r 74 goat snp45969-scaffold63-7495648 NW_017189517.1 22327488 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791590 Affx-122927965 AX-385278581 X 35520623 TATTGCCCTCAATCATTAGAATACTATGTCCAAGA[C/T]AATGGATACTTTAGTGCAGATTTCTGAATGGCAAG Y 2 1 2 1 101000 r 74 goat snp45970-scaffold63-7532711 NW_017189517.1 22365841 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770920 Affx-122919985 AX-385258083 X 35670165 CCCTTCTCCCCCCTCCTTTGGACAAAATTTTTCTA[G/T]AAAACCTTGCACTTCTATCACAGTATAATTTTTTG K 2 1 2 1 102000 f 74 goat snp45972-scaffold63-7682253 NW_017189517.1 22516290 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780387 Affx-122950324 AX-385267481 X 35722921 ATATACAACAAATTTATTGTCCTACTCCAAGACTT[G/T]GAGGAAATTTTTACTTTCTCCAATATATTTGGAGC K 2 1 2 1 201000 r 74 goat snp45973-scaffold63-7735009 NW_017189517.1 22570067 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782218 Affx-122964818 AX-385269296 X 35785967 GAACCAGAGAAGGAACTCTGTAAGAAGCCAGAGGA[A/G]ATCATGAAAGAATACAAGCTACCAGATGGGAATGT R 2 1 2 1 101000 r 74 goat snp57039-scaffold905-2143315 NW_017189517.1 22637214 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787055 Affx-122936239 AX-385274083 X 35870017 TTATAATGATATGGTTATACTGTTACAGTTATAAT[C/T]ATGTGTATGCAGTTATAGTGCTAGTCTTAACATTG Y 2 1 2 1 201000 f 74 goat snp57038-scaffold905-2059265 NW_017189517.1 22722343 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449913 Affx-122922327 AX-123320248 X 35927785 TTTTGTGCGAGTGTCGTTCAAAAACACTTGTGAGG[A/G]ATTTCACCCACATTTCTCAGGAATGAATAAAGTAT R 2 1 2 1 101000 f 74 goat snp57037-scaffold905-2001497 NW_017189517.1 22781026 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797000 Affx-122946320 AX-385283941 X 35971000 GAAGTTGGAGAGCTAGAGTAAACAGAGTCCATTGC[C/T]TTTCACTGAGTTGTTGCCATGCAAAAAAAGAAATC Y 2 1 2 1 101000 f 74 goat snp57036-scaffold905-1958282 NW_017189517.1 22825189 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779537 Affx-122959412 AX-385266640 X 36074384 ATGATTACTGAGCTCTTACAATGTGGTAAAAATTG[G/T]GCTGAGTTCTTTGTATTGTTCAATAATTATTTCAG K 2 1 2 1 101000 r 74 goat snp57034-scaffold905-1854898 NW_017189517.1 22923002 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776730 Affx-122957114 AX-385263855 X 36103204 GTACATAATATAGGACTATAATATAGTCCTAAAGA[C/T]TATTGATGTTAGAAATTAGGTATTTTGGTCTTTAC Y 2 1 2 1 101000 r 74 goat snp57033-scaffold905-1826078 NW_017189517.1 22952458 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391419 Affx-122966764 AX-123261776 X 36160892 ACTGTTTTATTGCCTTTGTTGAATTCTTGATGATT[A/G]TAAGTATGGACTCCTACTCTTAAAGATCTTACAGT R 2 1 2 1 101000 r 74 goat snp57032-scaffold905-1768390 NW_017189517.1 23008549 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396669 Affx-122962844 AX-123267024 X 36198275 CCTCTTCAGTATCTCTGAACTCTAAACTCCATCTC[A/G]TCAACTCAACAAGGCCACTGAGGATTGTTTGGATT R 2 1 2 1 101000 f 74 goat snp57031-scaffold905-1731007 NW_017189517.1 23046776 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415864 Affx-122948855 AX-123286213 X 36333721 TTGTAATTGTAAGCATAGCATGCCAGCTATCTCCA[C/T]GCACAGGGAAATGCACGTGGCAGCCATTCAATTGT Y 2 1 2 1 101000 f 74 goat snp57028-scaffold905-1595561 NW_017189517.1 23174823 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776149 Affx-122943393 AX-318997749 X 36411488 TTTCCTGATTTATAGTATCCTAGCAACCATCATGC[A/G]CATTAGTCCTAATGGATCTAAAAATGATGCACTGG R 2 1 2 1 101000 f 74 goat snp57027-scaffold905-1517794 NW_017189517.1 23259333 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451381 Affx-122921213 AX-123321714 X 36452999 GGTAGGATTCCATCTGTAGCCTGGATTATTGCTCT[C/T]GCTGTAGCTATTGGAACAGGTTTTTTCTGTATATG Y 2 1 2 1 101000 f 74 goat snp57026-scaffold905-1476283 NW_017189517.1 23300743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453411 Affx-122919892 AX-123323744 X 36503629 TCTCAGGAGCAAATTCTCTCCTTTTGAAAGACTCT[C/T]TTCCACATACCTCCTGAGCTGCTGATAATTATTAT Y 2 1 2 1 101000 r 74 goat snp57025-scaffold905-1425653 NW_017189517.1 23351767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769941 Affx-122961800 AX-385257110 X 36540431 GTGACCAGTTGGGTCATTTTCAAGGTTGACAGTCT[A/G]CAATTCTAGTACTTGGTTGATTTGTTGTAGTTTTA R 2 1 2 1 101000 f 74 goat snp57024-scaffold905-1388851 NW_017189517.1 23389003 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380884 Affx-122975046 AX-123251242 X 36576222 CTACCAGGTAGTTGTTATGACTCAGGCACTGTGGG[C/T]AGTCTACCCTGGGTGCTGTGAGAGGCCACAAGAAA Y 2 1 2 1 101000 f 74 goat snp57023-scaffold905-1353060 NW_017189517.1 23425329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785286 Affx-122960925 AX-385272331 X 36635709 ATTCACAAGCAGCCATTGATTTGACTTTTAATCAC[G/T]CTTCCTCTTTGTGTCCCTCACCTTTCATCTGATGG K 2 1 2 1 101000 f 74 goat snp57022-scaffold905-1293573 NW_017189517.1 23485415 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774706 Affx-122952880 AX-385261840 X 36669494 AAGCTACCCTTTAATTATCCTGCAGAAGCAGTGTG[C/T]ATCCTTCTCGGCTTGCTTGAGATTTCTAGTTGGAA Y 2 1 2 1 101000 f 74 goat snp57021-scaffold905-1259788 NW_017189517.1 23518511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452632 Affx-122920353 AX-123322965 X 36706249 ATGAGATAAGACACTGGAAAAGGTGGTATCAGAGA[C/T]AGGGGCAAAAATGGAAAGTTGTTAAGTCAGCAAAT Y 2 1 2 1 101000 f 74 goat snp57020-scaffold905-1223033 NW_017189517.1 23554895 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447754 Affx-122924578 AX-123318090 X 36751048 TTGGAAAGGGGAATGAAGGGTTGCAGAGAGGCCAT[A/G]TGGGTTTCCTTTGTGGAAACTTCCAAAACGAAACT R 2 1 2 1 101000 r 74 goat snp57019-scaffold905-1178234 NW_017189517.1 23599690 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444629 Affx-122926933 AX-123314966 X 36803831 ATCTACAGTGACCCATTGGAATTAATGATTTTGAA[A/G]TGACCCAGAACAGAACAGACTCAGAAACCTCAAAT R 2 1 2 1 201000 f 74 goat snp57018-scaffold905-1125451 NW_017189517.1 23653169 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416227 Affx-122948221 AX-123286576 X 36838745 CGAGTTCTTGCCATCTGCCCTTCTCTGCCTTGTGG[C/T]ATTTACATCTTCAGTTCCACCACCTGCCCTCTTGA Y 2 1 2 1 101000 r 74 goat snp57017-scaffold905-1090537 NW_017189517.1 23688272 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383578 Affx-122972590 AX-123253936 X 36942811 AGGTTCAGGTCTTGCATTTGCAATAGTTGCCCTAT[A/G]TGCTACCTTTATGCTTTTAAAAATTTCCCACTCTA R 2 1 2 1 101000 f 74 goat snp57015-scaffold905-986471 NW_017189517.1 23791086 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434643 Affx-122933991 AX-123304984 X 37013144 TACTTTTACAGAAGTAAGTTTCATATAAAAAGGAC[A/G]TTTTTTAAAAAATATCCTTGACAAACCCCTGAAAA R 2 1 2 1 103000 f 74 goat snp57014-scaffold905-916138 NW_017189517.1 23857459 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430110 Affx-122937517 AX-123300451 X 37061506 AATTCCTTCTGGCTCCCCAGTGTACACGTGCTTAT[A/G]CTGTCTGGAAAGCCCAGGTTCTTGTCAGATTACAC R 2 1 2 1 101000 r 74 goat snp57013-scaffold905-867776 NW_017189517.1 23904150 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778863 Affx-122953053 AX-385265971 X 37113277 TACTGTTTTTATCATTGACACAAGGTTATGCCAGT[A/G]CAGCCAACAGAATTGAATGATTTAAGGACTTTGGA R 2 1 2 1 101000 r 74 goat snp57012-scaffold905-816005 NW_017189517.1 23955782 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431790 Affx-122936127 AX-123302131 X 37237516 CTAGTGAGTCAGTTGGGCCAAGAGTTGAAGCCTGG[C/T]GGTCGGCCCCCAGAACCTGTGCTCTTAATCATTGT Y 2 1 2 1 101000 f 74 goat snp57010-scaffold905-691766 NW_017189517.1 24080130 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392400 Affx-122966215 AX-123262757 X 37267753 CCATCTTTGCTCTGTCTCAGCACACAAAGGTACCA[A/G]ATTTGAGGTGGTATAATACCCCACCTTATGTAAGT R 2 1 2 1 101000 r 74 goat snp57009-scaffold905-661529 NW_017189517.1 24109854 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400878 Affx-122959759 AX-123271231 X 37323411 GCCTGACATCCCGGTGAGGACCACCTAGCTAGTTA[G/T]CATCTTGTGTGGCAATGAAGTGCACAAGGGTTAGG K 2 1 2 1 101000 f 74 goat snp57008-scaffold905-605871 NW_017189517.1 24165624 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412502 Affx-122951369 AX-123282851 X 37358138 GAAAATGGACAGGCTACTTAAGCAATTCAATCCAG[A/G]CCTCTCCTTTCTCAGATGCAGGATCCACGCCCAGG R 2 1 2 1 101000 f 74 goat snp57007-scaffold905-571144 NW_017205676.1 34071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388341 Affx-122969353 AX-123258699 X 37403629 AGCCATGGCAACATTGTGAAAAACTGTTGTGAAGT[G/T]CTGTGTGGCCCCTTGCCCCCCAGGTACTCAAAGGA K 2 1 2 1 101000 f 74 goat snp57006-scaffold905-525653 NW_017189517.1 24203009 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385489 Affx-122971276 AX-123255847 X 37489429 CACCAGCATTTGGAAAAAGCAAGGTGCAGAACAGT[A/G]TGGAGTAGATTACTACTACTTTTTTGATTTTAAAA R 2 1 2 1 201000 r 74 goat snp57005-scaffold905-439853 NW_017189517.1 24288583 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779590 Affx-122934668 AX-385266693 X 37583444 ATCCCCATGTGTTGAAGTTTTTAACTAGTCACCTC[A/G]ATAAATAAGCAGAAGCAAATTCTCAGGGTGAAGAG R 2 1 2 1 201000 r 74 goat snp57004-scaffold905-345838 NW_017189517.1 24382034 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408618 Affx-122953495 AX-123278969 X 37639953 ACTGTGTGCCCAACCCTTGCTAGGCGCTGTGGGGG[A/C]GACAAGGGAAGGGGGTGGCGGGAGATGACTAAGAC M 2 1 2 1 303000 f 74 goat snp57003-scaffold905-289329 NW_017190167.1 60065 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387011 Affx-122969936 AX-123257369 X 37673481 ATCCGGGCTCGGGATCCTGGAGCCAGGGTAAGGCA[C/T]ACACTGTCTTGCTTGACACGTCTTGCTTGACTGTC Y 2 1 2 1 101000 r 74 goat snp57002-scaffold905-255801 NW_017190167.1 26482 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784789 Affx-122959657 AX-385271836 X 37702492 AGATTCAGGGGCAAAATGTTAGGTAGCAACAACTG[A/G]ACAGAAAACACAACATTAACCAAGGTTACTAGGGA R 2 1 2 1 101000 r 74 goat snp57001-scaffold905-226790 NW_017189517.1 24754329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418082 Affx-122946604 AX-123288430 X 37736450 ACGCCATTCCAGCTGCAGTGCCACATTGAGAGCAC[A/G]CACACTCCCCTTGAGTTTTCCAGTAAGTCACAGTC R 2 1 2 1 101000 r 74 goat snp57000-scaffold905-192832 NW_017189517.1 24720706 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428266 Affx-122939406 AX-123298609 X 37765940 CGTGAGAGGACATCGTGCGCATAGGCAGTGGTGCT[A/G]TTGCGAGAGGGGAGTACCGCGAGGCGGGAGGAGGG R 2 1 2 1 103000 f 74 goat snp56999-scaffold905-163342 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437800 Affx-122931683 AX-123308138 X 37812798 TGACTAGACAAAACAATTTTGGAAAAGAAGAATTA[C/T]GGTGAAGGATTCATACTACTCAATTAAAGCTGCAA Y 2 1 2 1 101000 r 74 goat snp56998-scaffold905-116484 NW_017189517.1 34181648 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445379 Affx-122925404 AX-123315716 X 37843334 AAATGGAGACACAAAGGAACTTGATGATGTAGGGA[A/G]TGAAGGTGAGGGAAGAGTTGATGATGACTGGAAGC R 2 1 2 1 201000 f 74 goat snp56997-scaffold905-85948 NW_017189517.1 34151212 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394386 Affx-122964629 AX-123264741 X 37912216 GGACTACTTTCTTTTCTCTTAAGCCCTCACTCCTT[A/G]CTCCACCCCGACCATACTGGAACCACTGCCTCATG R 2 1 2 1 102000 r 74 goat snp56996-scaffold905-17066 NW_017189517.1 34081933 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377826 Affx-122977302 AX-123248185 X 37954421 TAGTATGGATCACAAGTGGGAAAGGGTTGATGCCA[C/T]AGATGGAGTAGGGACTTTTGTGGAGGACTCCTACA Y 2 1 2 1 101000 f 74 goat snp14037-scaffold1556-157359 NW_017189517.1 20119221 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417296 Affx-122947237 AX-123287644 X 38010101 ACTCAGCTTTCTTCACCTCAGAGCCCCACTGCCTT[G/T]GGCATGGAGCCAGTGTGCCAAACAGAAATAAATGG K 2 1 2 1 101000 r 74 goat snp14036-scaffold1556-101679 NW_017189517.1 20059507 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797610 Affx-122978498 AX-385284549 X 38088154 TCCACCCACAGCCATGGTAGAATATAAAGAAGATA[C/T]TGAGTTTAAGATTCCGCCCATTTAAATGTTTGGAG Y 2 1 2 1 101000 f 74 goat snp14034-scaffold1556-23626 NW_017189517.1 20002065 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400974 Affx-122960104 AX-123271327 X 38122350 TCTTACAACTCAATAATAAATAAACAAGCTAATTT[A/G]TTAAAGGAGTAAAAGATTTGAGTGGATACCCTACA R 2 1 2 1 102000 r 74 goat snp13483-scaffold152-2543290 NW_017189517.1 19928068 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420562 Affx-122945280 AX-123290909 X 38290163 TGCATCATGCAAATATTCCCCCTCAGTGATGACAC[A/G]TTTTTTTCTTACACTATTTGCTTTGGTGGCTTCAA R 2 1 2 1 202000 r 74 goat snp13480-scaffold152-2375477 NW_017189517.1 20719859 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390533 Affx-122967230 AX-123260890 X 38338917 ATCAGGCTGTTACAATAAGCCCCAACACCAAACCC[A/G]GAAGTGCCTGAGAAACCTTCTCTGCCATCCACACA R 2 1 2 1 201000 r 74 goat snp13479-scaffold152-2326723 NW_017189517.1 20670262 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770652 Affx-122956898 AX-385257815 X 38380252 ATATTTTCTCAAGTAGTACAAGGTTCCAAAGATTC[A/C]CATGACATTTACTGCCTACATCCTTCTTGTGCCCT M 2 1 2 1 101000 r 74 goat snp13478-scaffold152-2285388 NW_017189517.1 20628671 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797446 Affx-122950411 AX-385284385 X 38416726 GGTTTTTAAAAGGTGTAAATAGATGAATTATAATA[A/G]TAGTGACAAGAAGTAACTACTCCTTTATTCCCAAA R 2 1 2 1 201000 f 74 goat snp13477-scaffold152-2248914 NW_017189517.1 20591564 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386580 Affx-122970698 AX-123256938 X 38459396 CCTCTCCCGCAGGTTGTGGATTAAAGGCAACTAAA[C/T]GGCTACTGTGTACTACATCGGCTGTCTTTTGTTCT Y 2 1 2 1 101000 r 74 goat snp13476-scaffold152-2206244 NW_017189517.1 20548843 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377560 Affx-122977447 AX-123247919 X 38529356 TATACTGACAGAGAACCATAAAATTGAAAGGCTCC[A/G]CTGCTTTTTCTCTTAGCCTCTAGAAGGGCAATTTT R 2 1 2 1 101000 f 74 goat snp13475-scaffold152-2136284 NW_017189517.1 20480018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449620 Affx-122923197 AX-123319955 X 38561096 AGAAGGGGTAAAAACAAAAGATATTTGGTCAATAC[A/G]TATGTAAACATATTTATATCAAAATAAGAAAGGAA R 2 1 2 1 101000 f 74 goat snp13474-scaffold152-2104544 NW_017189517.1 20451014 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406091 Affx-122956228 AX-123276443 X 38604549 TACAAGTAAAGAGAAGGGGACTAACTTTTACTGAG[G/T]GTACCCCGCTTGCCACGTGTTCAGGGCCTCCAAAT K 2 1 2 1 101000 f 74 goat snp13473-scaffold152-2061091 NW_017189517.1 20407395 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379530 Affx-122976069 AX-123249888 X 38664731 TTGATTAAGGCCACTACTACAGAACACAGGAAAAA[C/T]AGCAGTGTGAGAAGCTGCAGCAGGAGCAGCCTAGT Y 2 1 2 1 101000 f 74 goat snp13472-scaffold152-2000909 NW_017189517.1 20347064 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440618 Affx-122929968 AX-123310955 X 38694609 TGTGGTATGAAAAGTTCTCTGCGGGAGAGGAGCCT[A/G]AGGTGCTGCTGGGCCCCAGAGGTACAGGCACCAAA R 2 1 2 1 101000 f 74 goat snp13471-scaffold152-1971031 NW_017189517.1 20316989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433437 Affx-122935074 AX-123303778 X 38733124 GTTTTTTACAAGACATACAAAGCACTGACATAGAA[G/T]AAAAAATAAGGATAAATGAAACTTCCTCAACATAA K 2 1 2 1 101000 f 74 goat snp13470-scaffold152-1932516 NW_017189517.1 20278473 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399314 Affx-122961378 AX-123269669 X 38906584 TAAATGTCAGTTGAGAGTTTATGGAACAGGATAGA[C/T]ACTATTACACAAAATGGGAAAGGAATTTTTAAATC Y 2 1 2 1 101000 f 74 goat snp13467-scaffold152-1759056 NW_017203560.1 18455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428475 Affx-122938790 AX-123298818 X 38946168 CTGATAACCAGGTGGGTTAGCAGCAGCAGCAATTC[A/G]CTTCAAAGGAAGCTTCTAAGACAGTGTCTCAGAAC R 2 1 2 1 103000 r 74 goat snp13466-scaffold152-1719472 NW_017189517.1 10381881 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447309 Affx-122924911 AX-123317645 X 39002769 CTGCTGATGACAAAAATACAACATATCAAAATTTA[C/T]GGACTACAACTTAAAGCAGTACACAGAAAGATATT Y 2 1 2 1 102000 r 74 goat snp13465-scaffold152-1662871 NW_017189517.1 10439059 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398085 Affx-122961724 AX-123268440 X 39040886 ATAGAATGAAAACTACAATGGATGAGGCTGTCCCA[C/T]CACCAGCACTGAGATGGTGGGAGAATGACTACAGC Y 2 1 2 1 101000 f 74 goat snp13464-scaffold152-1624754 NW_017189517.1 10477511 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430874 Affx-122936887 AX-123301215 X 39096175 TGGGCGCTGTTGGGGGATAGAGATGAGTATGCCAC[C/T]TCCTGCCCGGGGGATGGTGATACAGAGGATTCAAG Y 2 1 2 1 201000 f 74 goat snp13463-scaffold152-1569465 NW_017189517.1 10533606 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438911 Affx-122930433 AX-123309248 X 39137047 TTCAGTAATGGAAACTGTGGACTTTGGGAAGTTCA[A/C]CTTTGCACATTTAAGAGTGAATTTTCATGGGAAGA M 2 1 2 1 201000 r 74 goat snp13462-scaffold152-1528593 NW_017189517.1 10575098 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442322 Affx-122928233 AX-123312659 X 39194318 TGTAAGACCAAGTTATCACATTGCTGATGTCCACT[A/G]CCCAGAACCAAGTCAAAGGGAGGGGATTCGTGGTC R 2 1 2 1 101000 f 74 goat snp13461-scaffold152-1471322 NW_017189517.1 10315172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427868 Affx-122939709 AX-123298211 X 39279834 GTTGTCTGCTATGAATATCATGAATGCATCCATGC[A/G]TAGTCACTCAGTCGTATTCAACCCTTTGTGATCCC R 2 1 2 1 201000 f 74 goat snp13459-scaffold152-1385806 NW_017189517.1 10228558 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396699 Affx-122962824 AX-123267054 X 39412604 TGCAAATGGTATTTCTTTATTGCTGTAATGTTAAT[G/T]TCATGATTCCATGTGCGTTTGGACATCTCTCATGC K 2 1 2 1 101000 f 74 goat snp13457-scaffold152-1253036 NW_017189517.1 10095445 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800703 Affx-122969866 AX-385287620 X 39451939 TTACAATAGTGTGAGTATTGATTTAGACCAACATG[A/C]AAACGGCCCATAAAATGGGTTTGCCCTCAAGACAT M 2 1 2 1 101000 r 74 goat snp13456-scaffold152-1213701 NW_017189517.1 10055408 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418620 Affx-122947152 AX-123288968 X 39522404 ATTTTTGCTAGGAAGTCTGCTGAAATAAAGAAGAA[C/T]GAGCCAGCACTAGGCATTACCAGGCAGAGAAAAAG Y 2 1 2 1 201000 f 74 goat snp13455-scaffold152-1143236 NW_017189539.1 37414 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784476 Affx-122937448 AX-385271525 X 39607377 TTTCAGTTTGGTGCTTCAAAGTTGAGTGGATTCCC[C/T]ACCCCTTCATCTGTGCTACAACTTTGATGTTAAAA Y 2 1 2 1 101000 f 74 goat snp13454-scaffold152-1058263 NW_017189517.1 9725994 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377684 Affx-122977422 AX-123248043 X 39694563 ACTAGAAGTAGCAGTAAGATATCAAGGTGAATTTC[A/G]CAAGTCAAGCTGACAACTTTAGGGTTTTAAGTGAG R 2 1 2 1 101000 f 74 goat snp13453-scaffold152-971077 NW_017189517.1 9908570 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401530 Affx-122958918 AX-123271883 X 39777622 CCCACACTGCCAAATTCCTGTTCTTACAGCCAAGC[A/G]TGCTTCCACTCAGGCTTTACTGCCTCTGCTACATG R 2 1 2 1 201000 f 74 goat snp13451-scaffold152-888018 NW_017189517.1 9850736 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790574 Affx-122971012 AX-385277577 X 39813764 GCCAGTGTTCAGCTAAGACCAAGGCTCAGCAAAAT[A/G]ATTGCAGAATATTACTGTGCAGAGTCAATTGAGAC R 2 1 2 1 101000 f 74 goat snp13450-scaffold152-851876 NW_017189517.1 9814387 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425159 Affx-122941065 AX-123295505 X 39852703 CCCATAGATTCTGTTGTATCCTTTCTCTATTTTTG[C/T]AAGGAAAAAATACACACATAATATATATATTCTCA Y 2 1 2 1 103000 f 74 goat snp13449-scaffold152-812937 NW_017189517.1 9775193 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399609 Affx-122961092 AX-123269964 X 39932717 CTGTGTGTGAAGGCACATACATATATATGAAAATA[A/G]ATATAAAATTATCTTAACATTCATAGTAAATTTAG R 2 1 2 1 303000 r 74 goat snp13448-scaffold152-732923 NW_017189517.1 9575701 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444099 Affx-122926829 AX-123314436 X 40004962 GGTGTACCTATTTCAGAGAGTTTGGAGGATCAAAC[A/G]TCTTAATTTAATATGAAGCTCACAGAACAATGCCT R 2 1 2 1 101000 r 74 goat snp13447-scaffold152-660678 NW_017189517.1 9503154 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793334 Affx-122954489 AX-385280312 X 40066251 TTCAAAGGTATTCTATTCACTAGAAACAAGTCACT[A/C]GGTCTAACCCATGGAAAAAGGGAACGGCTTACACA M 2 1 2 1 101000 r 74 goat snp13446-scaffold152-599389 NW_017189517.1 9442912 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785381 Affx-122974460 AX-385272426 X 40112898 GTGGAATAACTTCATTGTTATGTTTATTTCTAATC[A/G]TGTCCCTTATTCCCAGGCAGAATGACATCTGATTT R 2 1 2 1 101000 r 74 goat snp13445-scaffold152-552742 NW_017189517.1 9396550 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795747 Affx-122967969 AX-385282700 X 40156040 GTTGTATGTGGTCTGGTCTAAATATCCACATGTCT[A/G]TATGGATAGGAAATATAATGGGATCCTTTCCCTCA R 2 1 2 1 101000 f 74 goat snp13444-scaffold152-509600 NW_017189517.1 9353337 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787037 Affx-122926428 AX-385274065 X 40191470 TTGTATTTGAATATTGCTTTTATAATTTCCAAAGC[A/G]TTTTCACATAGCCCTTTTTGAAATTTAGTTTAACT R 2 1 2 1 202000 f 74 goat snp13443-scaffold152-474170 NW_017189881.1 13041 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431472 Affx-122936264 AX-123301813 X 40250639 CTTGCTCCACTCCTTAGTAGTTTTGTAATTTGAGG[C/T]AAGTCATTTAAACTCTTAGACTTGGTTTTCTCATT Y 2 1 2 1 101000 f 74 goat snp13442-scaffold152-415001 NW_017189517.1 9275393 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774024 Affx-122971795 AX-385261162 X 40288567 GAAGGGAAAGTGGATGTTTGCAAGCCTGCCTACCA[C/T]GCATTTAGGATGATTCATTGTTATCTTACTTGGGA Y 2 1 2 1 101000 f 74 goat snp13441-scaffold152-377073 NW_017189517.1 9236735 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799619 Affx-122939585 AX-385286549 X 40346262 TGAACTTTCTGTTGTTTTTAGCCACAAATTATGTG[A/G]TAATGATACAATAACCTCAGGAAATTAATATAACA R 2 1 2 1 101000 f 74 goat snp13440-scaffold152-319378 NW_017189517.1 9178381 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378091 Affx-122977160 AX-123248450 X 40397082 GTGGATAACTGGTTGTTTTCACCCTTGGCTATTAT[A/G]AATAATGCTGCTATGAGTGTAGGTATTCAATGGGT R 2 1 2 1 103000 f 74 goat snp13439-scaffold152-268558 NW_017189517.1 9127444 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444917 Affx-122926243 AX-123315254 X 40431344 TTTCCTTTCCCCATCGTGAAGATGCAGTCTCCCAC[A/G]GTGATCAATACTTGCATTTTCCACCAGCATGTCAG R 2 1 2 1 201000 r 74 goat snp13438-scaffold152-234296 NW_017189517.1 9093122 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393491 Affx-122965821 AX-123263847 X 40564625 ACACTGCTGCTTCTTTCTAGCATATGAATGCTATG[C/T]AGAGCCTAATTTGATTTATGTTTTATTGGTGATGC Y 2 1 2 1 101000 f 74 goat snp13437-scaffold152-101015 NW_017189517.1 8958353 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451976 Affx-122920941 AX-123322309 X 40617862 TACTTGTTCCATGCCTGTCTTCCTCCTTTAAACCA[C/T]AAATTTAATGAGAAGAAAGGTCTTGACCATCTGTT Y 2 1 2 1 201000 r 74 goat snp13436-scaffold152-47778 NW_017189517.1 8904453 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38403304 Affx-122957839 AX-123273657 X 40673852 AAGATACAACGTATGGGAGTCATTAGACAATATCA[A/C]AGCCATATCATTGATGAGCTCACCTAGGGAGAGTG M 2 1 2 1 101000 r 74 goat snp20199-scaffold200-8113 NW_017189517.1 8848828 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451927 Affx-122921016 AX-123322260 X 40703067 AAGAATAGGAAGCTTAGGGAGTTTGACTAACTTGT[A/G]TGATGGTTAATTTTATGTGTCAGCTTGATGGGGCC R 2 1 2 1 201000 f 74 goat snp20200-scaffold200-37328 NW_017189517.1 8819586 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424181 Affx-122942522 AX-123294527 X 40801013 GGTCTAAGAAGTTTATTTATTTATTTATTTTTGAT[A/G]TGCTATATTCCTTTTTTCTTGCCATTTACATAAGC R 2 1 2 1 101000 r 74 goat snp20202-scaffold200-135274 NW_017189517.1 8719824 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405512 Affx-122955996 AX-123275864 X 40836988 CTGGATCGTAGTAGCAAAAAAAGACCTGTGTATTG[C/T]AGGGAGGCATTTGGAGGAATAGTAAAGGATTCCAG Y 2 1 2 1 101000 f 74 goat snp20203-scaffold200-171249 NW_017189517.1 8683029 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391175 Affx-122967434 AX-123261532 X 40865598 TCCAGGGACATTCTAATTTTCACAGGAAAACAAGA[A/G]ATCATGAGCCAAAAGAGTGAATTTGGCCACCAATG R 2 1 2 1 101000 f 74 goat snp20204-scaffold200-199859 NW_017189517.1 8654334 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418340 Affx-122946597 AX-123288688 X 40936315 CTATAAATCTTGTCTAAAATTATAGACAAGATCAT[A/C]ATTTTGTTTATGATTTCAGAAGGTTGATAGATTCC M 2 1 2 1 303000 f 74 goat snp20205-scaffold200-270576 NW_017189517.1 8588500 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411585 Affx-122951619 AX-123281935 X 41005989 AGAACTAGACAGTCCAGACACAGATTTCCTCTTAG[C/T]TGCCCACTGCCTGGTGACCTACTTTCTCTCTGCTT Y 2 1 2 1 101000 f 74 goat snp20206-scaffold200-340250 NW_017189517.1 8518816 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779589 Affx-122935747 AX-385266692 X 41038478 AGTGTGCAGATCTAGATCTTTCCTTCTTCAGAAAT[A/G]TTTTCCTTCTTATATCTTGCTGATTTTGGTTTCTC R 2 1 2 1 202000 f 74 goat snp20207-scaffold200-372739 NW_017189517.1 8486255 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422882 Affx-122943072 AX-123293228 X 41103596 GGGGGTGATCAAAGATTACAGACAGCAGAAAAAAA[C/T]GTAAGAAAGAGAAAGCTGAAAAACTCATACTTCAG Y 2 1 2 1 102000 f 74 goat snp20208-scaffold200-437857 NW_017189517.1 8420554 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437366 Affx-122931928 AX-123307704 X 41134138 AGTTGTATCCTGCAGAACCCAAAGAGTAGAAGGAT[A/G]TAAGCTCCCTCACCTGTGTTTCAATTGTAACACTT R 2 1 2 1 101000 r 74 goat snp20209-scaffold200-468399 NW_017189517.1 8389939 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790866 Affx-122919766 AX-385277864 X 41221117 AGTGACCTCATTCAGTCCTATAGCTTTAAATACTG[C/T]CTATGTACTGATGACTCCCAAACTTACATTTCCAC Y 2 1 2 1 101000 r 74 goat snp20211-scaffold200-555378 NW_017189517.1 8302816 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417397 Affx-122947687 AX-123287745 X 41251852 AGCATGACATGATACTGTAAGAACTTGTATATGAG[C/T]TAGAAAATGGCATTGAATACCAACCACCTGGAAAC Y 2 1 2 1 101000 f 74 goat snp20212-scaffold200-586113 NW_017189520.1 67780 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380656 Affx-122975198 AX-123251014 X 41281973 TGGGTTTTGTCCCCACCACCATTTAAAGCATGTGA[A/G]AAAGAAATGCTTAGACATACACTGGACCTGAGAAC R 2 1 2 1 201000 r 74 goat snp20213-scaffold200-616234 NW_017189520.1 36857 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787991 Affx-122925589 AX-385275012 X 41342353 TTAATTACATATTTAGTGACTCTTGGCAAAGGACA[C/T]GTTGTTAGTCCCACCTTTTACATGTGGGACATAGG Y 2 1 2 1 101000 r 74 goat snp20214-scaffold200-676614 NW_017189517.1 8266264 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395650 Affx-122963768 AX-123266005 X 41399917 TGTTTTGCTTTGTTTCAGAATCAAGTTAAAAGTGT[C/T]ATGTCCTAAGCTTCTGTATCAGCTTGCGGTAGGTT Y 2 1 2 1 101000 f 74 goat snp20215-scaffold200-734178 NW_017189517.1 8208855 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443897 Affx-122927058 AX-123314234 X 41453023 ATAGGAAGGAAATAAACTATTCTGAGATTTATAAA[C/T]GAAAAAAAGAAGTTAACGTCATTGAACATACATGA Y 2 1 2 1 102000 r 74 goat snp20216-scaffold200-787284 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437469 Affx-122932378 AX-123307807 X 41508043 GTCTTCAGCAGGGCCAAGGACAATCAGGTCTTCTG[A/G]GGATGAGCACTGGAGTAGGCTACAAACACTGTGCA R 2 1 2 1 201000 r 74 goat snp20217-scaffold200-842304 NW_017189517.1 8101714 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446497 Affx-122925045 AX-123316833 X 41584867 AACACACTCCCTGGGCGTCCCCATAGGTACCAAGA[A/G]CAGCAACAACATCCCATCTGTCTCTGTTCTCTTGC R 2 1 2 1 101000 r 74 goat snp20219-scaffold200-919128 NW_017189517.1 8024679 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800750 Affx-122924892 AX-385287667 X 41620375 AAAGAGTTTCTCCTAATCCTATACATATATGCTAC[A/G]CCACCCTCTAGAGGTAATGTCCTGTTAAATCCAAG R 2 1 2 1 101000 r 74 goat snp20220-scaffold200-954636 NW_017209577.1 7781 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379303 Affx-122976202 AX-123249662 X 41657077 ATGACATGCGTATACATACGAAACTTCATTTCTCT[A/G]AAGCTTAACTGACCCCTTAGGCCCCCTATTTATGC R 2 1 2 1 101000 f 74 goat snp20221-scaffold200-991338 NW_017189517.1 7989345 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789124 Affx-122966712 AX-385276137 X 41701123 TTCTGAAGTGCAAATGGAATAATCTGGGAGGCAAT[A/G]TTTTTAGGAGAAGATGGATCAAAAGCTAAAGACAC R 2 1 2 1 101000 f 74 goat snp20222-scaffold200-1035384 NW_017189517.1 7915811 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435229 Affx-122934086 AX-123305569 X 41749329 CAGGCAGTGCAGTGGAGTTGACCAGGCACTGTATG[A/G]CACCCGTGCTAAGCAGAACAAAGGAATGCACGTGA R 2 1 2 1 101000 r 74 goat snp20223-scaffold200-1083590 NW_017189517.1 7867644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447132 Affx-122924459 AX-123317468 X 41786324 ATTACCCACAGAGTCATGTGAAGACTAGGACCAAA[C/T]ACTGACGCCAGGAATCAAATACAGCACCACCAATG Y 2 1 2 1 101000 f 74 goat snp20224-scaffold200-1120585 NW_017189517.1 7829037 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448778 Affx-122923304 AX-123319114 X 41829632 CATGGATTCATACTTGACTTTATATTGAACTTTTT[A/G]GAATTATACTCTATGATAGGCTTTTGTGCACAGCC R 2 1 2 1 101000 r 74 goat snp20225-scaffold200-1163893 NW_017189517.1 7785668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395477 Affx-122963903 AX-123265832 X 41899423 AAGATTTCATGATTATACACAGTTCAGTTGGAATG[C/T]GGAATGGAGCAGGTCACTTAGGAGTCAGAAGAGAG Y 2 1 2 1 101000 f 74 goat snp20226-scaffold200-1233684 NW_017189517.1 7735120 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379045 Affx-122976348 AX-123249404 X 41937194 AGAGGCTGACAATCAGAGCTGTCTTTGGGCAGAAA[A/G]AATGCTCAGCAGTCTATTGAACAGAAGAAATTAAT R 2 1 2 1 101000 f 74 goat snp20227-scaffold200-1271455 NW_017189517.1 7697214 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387181 Affx-122970618 AX-123257539 X 41986996 GTTCTTCATCCTGCCCATCAGGCGTTGTAGTTCTC[C/T]ACTGGAGCAACTCACTGCTTCTCTGTCCTTAGCAG Y 2 1 2 1 101000 f 74 goat snp20228-scaffold200-1321257 NW_017189517.1 7647180 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394623 Affx-122964407 AX-123264978 X 42020660 AAAAAGGAAAAAACTCTTTCCTCTTTGACTCTCCT[A/G]TATGATAAAAAGTCCTTGCTACCAAGACCGAGAAC R 2 1 2 1 101000 r 74 goat snp20229-scaffold200-1354921 NW_017189517.1 7613541 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444924 Affx-122926238 AX-123315261 X 42066147 TTATTTTTATTCTTTCATGGACTCTAGGTTGATAT[A/G]GTTTCATTGTCTTTTTCTGACTTTCCTTAATGTCA R 2 1 2 1 101000 f 74 goat snp20230-scaffold200-1400408 NW_017189517.1 7567531 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423873 Affx-122942308 AX-123294219 X 42103818 TAAGCTATCACATCCAGAAAAGTACAGATCGTTGG[A/G]TTATACCAACCCCTAGTAGCACGAAGTGGATTTCT R 2 1 2 1 201000 f 74 goat snp20231-scaffold200-1438079 NW_017189517.1 7529817 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797187 Affx-122963598 AX-385284126 X 42160276 AAACTAATATTGGAAAAATCTGTTATATCTTAACT[A/G]TTTTGAGGGTCACTGAAGTGATTGGAAATGATTTC R 2 1 2 1 101000 r 74 goat snp20232-scaffold200-1494537 NW_017189517.1 7473124 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403728 Affx-122958023 AX-123274080 X 42260260 GCAAAAGGACAGCTCTCCTTATCGGTGGGTTCCAC[A/G]TCTGTGGATTCCAGCAACTTCAGATTGAAAATATT R 2 1 2 1 101000 r 74 goat snp20234-scaffold200-1594521 NW_017189517.1 7372784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399562 Affx-122961126 AX-123269917 X 42337436 AATTGAGAGGTTAGGGAACATGCCCAAAGTCAGAG[C/T]TTGACAATTGCAGAGCAAAGAGTCAAACGGGTCTA Y 2 1 2 1 102000 f 74 goat snp20235-scaffold200-1671697 NW_017189517.1 7296854 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377230 Affx-122978162 AX-123247589 X 42393946 AAAGGGTCTAGTACAGGACATAAAAATACCCAGGA[C/T]GTAAAGGGACTAGTACAATGTCTGGCAAGTAGTAC Y 2 1 2 1 101000 f 74 goat snp20236-scaffold200-1728207 NW_017189583.1 12920 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423762 Affx-122942845 AX-123294108 X 42433700 ACCCTTTTCCCTATACCTCTCTCATTGTAAGGCCT[A/G]CTTTTTGTTCTCCCCATCGACATTGGGGAGGATTG R 2 1 2 1 102000 r 74 goat snp20237-scaffold200-1767961 NW_017213293.1 28537 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774811 Affx-122956613 AX-385261945 X 42467220 AAAAATCACACAACTAGTACCTGAAAGATTTCCTT[A/G]TAAGAAAGTCAAAAGTAAAAAGTTGCAGTGTAAAA R 2 1 2 1 101000 r 74 goat snp20238-scaffold200-1801481 NW_017189569.1 34507 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453577 Affx-122919762 AX-123323910 X 42566709 GGAAACACCAAAGGAATGGCAAGGAGAAATAAATT[G/T]ATGGTGGGAAATTTCAACACTTATCTCTTGGTTAT K 2 1 2 1 101000 f 74 goat snp20239-scaffold200-1900970 NW_017189517.1 6997347 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771875 Affx-122955027 AX-385259031 X 42605543 AAACCTTAGAAATCATTGATTCTAAATTTTTCTAG[C/T]GATGCAAGAATTCTTTCTGCCATCTATTACATAAG Y 2 1 2 1 101000 r 74 goat snp20240-scaffold200-1939804 NW_017189517.1 7036350 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401862 Affx-122959420 AX-123272215 X 42735366 CTAACACACTGAGCTCAGAGGTAAAGTAGAAAAGA[A/G]AGAAGAGATCCCTGCCCTCATCTTGGGAAAGAGAA R 2 1 2 1 101000 f 74 goat snp38760-scaffold491-5155073 NW_017189517.1 7168448 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395907 Affx-122963606 AX-123266262 X 42807773 TGTCTAGGCAGTTCCAAATATCTTTTGGAAGGAGA[C/T]GATATGCCTCCCTCCCCCCAAATATACCTTCCCAT Y 2 1 2 1 101000 f 74 goat snp38759-scaffold491-5082666 NW_017189517.1 7242006 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803306 Affx-122940556 AX-385290146 X 42850210 TCTATAGGGTTTAGGGCAGGTAAATAGTACTATAT[A/G]TGAGAGTAAGACTCTTCTGTGGATTCCTTGTTATA R 2 1 2 1 101000 r 74 goat snp38758-scaffold491-5040229 NW_017189517.1 7285426 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424628 Affx-122942180 AX-123294974 X 42887432 GTATCCCCCTAAGACCTTTATTGTGATTCCAAATA[A/G]GAGGAGGAAACAGTTTTTAAGCGCAGAAGGAAGGG R 2 1 2 1 102000 r 74 goat snp38757-scaffold491-5003007 NW_017189517.1 6945787 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391170 Affx-122967437 AX-123261527 X 43003299 CAAGCAACCGAAATTGTGTTCTGCTTGTCTTTGTC[A/G]CTTTAGAGGAGGAAAAGAAATGAAAGGCCAAGTTG R 2 1 2 1 101000 f 74 goat snp38755-scaffold491-4887140 NW_017189517.1 6829667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432749 Affx-122935448 AX-123303090 X 43044748 GCTCAGAAAGGTTAAGTAACATGCCAAATGTCCCA[C/T]AGCCAGTAAGTGAAACAACCAAGAATTAAATGGAC Y 2 1 2 1 201000 r 74 goat snp38754-scaffold491-4845691 NW_017189517.1 6787848 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451681 Affx-122921579 AX-123322014 X 43085930 TTTCAGCTGATACATACCAATGAGCATTCTTTTAT[A/G]CAAACAAGAAAAGGTCATAAGTTGACATAGAAATG R 2 1 2 1 101000 f 74 goat snp38753-scaffold491-4804509 NW_017189517.1 6745972 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401857 Affx-122959424 AX-123272210 X 43169589 AATGCCTCAGGCATCTCTAATGTTTGATCTTAGAA[A/C]TAGGTATCTCTATAGTTCCATCACCTGGCAGAATT M 2 1 2 1 101000 f 74 goat snp38752-scaffold491-4720850 NW_017189517.1 6661872 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442268 Affx-122928270 AX-123312605 X 43238960 GTCACACTGTTGCTTAAACTCCTCTCTGGTTCCCC[A/G]TTGCTTTTAATAAGGTGGGGTGGAGGGGGAAGCTA R 2 1 2 1 102000 f 74 goat snp38751-scaffold491-4651479 NW_017189517.1 6591926 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413725 Affx-122950067 AX-123284074 X 43283899 TCAGGCACTGTGACATCCCTTCGGTTCTGGAATAG[G/T]TGGGGTCCTTGGTAGACATTCAGAATATGCACCTC K 2 1 2 1 201000 f 74 goat snp38750-scaffold491-4606540 NW_017189517.1 6546906 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421791 Affx-122944336 AX-123292138 X 43366578 TTCATACATAGTATTCATTCATTTGCTCAAAAATA[C/T]GTACTGGTATCCTAGTATGCCAGGTACTGTTATTG Y 2 1 2 1 103000 r 74 goat snp38749-scaffold491-4523861 NW_017189517.1 6462098 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448746 Affx-122923324 AX-123319082 X 43420474 ACCAAAGAGCTCCTCTGGCTGTCCACTTAGTTTTC[A/G]CACTGCTTACTAACTGCTTTTATCTTGTCATTATC R 2 1 2 1 101000 r 74 goat snp38748-scaffold491-4469965 NW_017189517.1 6408328 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320782435 Affx-122919636 AX-385269511 X 43469209 TACTTTACATTTAATTTACCCACTCAAAATTTTGA[G/T]ACGGTTTCTGCCTCTTGACTGAGCATTGACTGACT K 2 1 2 1 101000 r 74 goat snp38747-scaffold491-4421230 NW_017189517.1 6358726 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377113 Affx-122978251 AX-123247472 X 43512198 TATCAGTTGACAATGGGTTCTCCAGTATGATAATG[C/T]AGTAATAAGTCAAATTTCTTAAAATTAGATTTATC Y 2 1 2 1 101000 f 74 goat snp38746-scaffold491-4378241 NW_017189517.1 6317345 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770397 Affx-122976803 AX-385257563 X 43587889 GAGTTGAAGAGTTAGAGCTAGATCTCCACAGAGAA[C/T]AGCTTCCACCAGAATGAATGAACTTGAGGTGTTTT Y 2 1 2 1 202000 r 74 goat snp38744-scaffold491-4302550 NW_017189517.1 6241505 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768466 Affx-122951824 AX-385255646 X 43654045 CAGAAATACAGGCCCTCAAGGAGTTTCCATTCAAG[C/T]GTGTGTAGTAAGGAGGTACAGTAAGTAAAGTGCAG Y 2 1 2 1 101000 f 74 goat snp38743-scaffold491-4236394 NW_017189517.1 6174844 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436118 Affx-122932655 AX-123306457 X 43717165 TCAAGTCTTTTTTTCAGTGTCCTTCTTTGCCTGTT[A/G]CCTTGTCATGCTCACAAAATATCTAATTCAGGTCT R 2 1 2 1 201000 r 74 goat snp38742-scaffold491-4173274 NW_017189517.1 6108530 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435975 Affx-122933514 AX-123306314 X 43779006 CTTTCCTCATTCTCTCTACTCCAATATCACTTGAC[A/G]TCACCTAAATTTCTTTGTATACTTTCAGCACATTC R 2 1 2 1 101000 f 74 goat snp38741-scaffold491-4111433 NW_017189517.1 6045659 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441906 Affx-122928609 AX-123312243 X 43840251 AAAGCTAGAGCAGGTAAGAAAATATATATTTCTAA[C/T]TATATAGTATTTATACTACCTTAAACTAAGTCAGT Y 2 1 2 1 303000 r 74 goat snp38740-scaffold491-4050188 NW_017189517.1 5984253 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402668 Affx-122958367 AX-123273021 X 43876682 CAATCTCTTTTCCCACAGAGCTTAAAATCTAAAGG[C/T]AAATAGAGAAACATATATGAACAATTAGATACAAC Y 2 1 2 1 101000 f 74 goat snp38739-scaffold491-4013757 NW_017189517.1 5947487 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393373 Affx-122965914 AX-123263729 X 43958974 ATAATTCTTGATTAATGGAATGAGCCAGAGAACTG[C/T]ATAAACTCCCTGCTGAATTCACCATCTGCCCATGT Y 2 1 2 1 101000 r 74 goat snp38738-scaffold491-3931465 NW_017189517.1 5865371 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437661 Affx-122931787 AX-123307999 X 44032510 TTCAAAATGAGGTTGCAAATACTTGTATGCTTTTT[A/C]TGCACTATTCATATAGGGATATTAAAACAGAGATA M 2 1 2 1 101000 r 74 goat snp38736-scaffold491-3857929 NW_017189517.1 5792753 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377753 Affx-122977370 AX-123248112 X 44065268 CTGTTGGTGGGCTATGTTGCTAAAGATAGAAAGTC[A/G]CAAGATTCAGATTTGGGAAAGAGGAGAAAAAAAAT R 2 1 2 1 101000 f 74 goat snp38735-scaffold491-3825171 NW_017189517.1 5759133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438434 Affx-122931264 AX-123308772 X 44098833 TGTGCAACAAAAATTTAATAAACTGCTCTCAGTTC[A/G]TTGGCCTCATATTACTCACATTACTTCAAATCTGG R 2 1 2 1 101000 r 74 goat snp38734-scaffold491-3791606 NW_017189517.1 5725517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435775 Affx-122932869 AX-123306114 X 44171619 GCTGGCAAGTATGTTACCAAACAATATGCTAACCT[A/G]TATTGAGCCATTTTGTAACATCATGAACACTGTGA R 2 1 2 1 101000 f 74 goat snp38733-scaffold491-3718820 NW_017189517.1 5656846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421871 Affx-122944277 AX-123292218 X 44224831 CATAAACACATGATCATGTCTTTGGTTGAAACTTT[A/G]TTACTTGCTCTCTGTTTAAACATTAACGACGAGAA R 2 1 2 1 101000 r 74 goat snp38732-scaffold491-3665608 NW_017189517.1 5602642 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783995 Affx-122954280 AX-385271049 X 44255766 TGGAACCCAAAGAGAAACATAATATTGATTAAGAA[C/T]ATGCCTCTTGCAAACTGCAAAACATACCAGTTTGG Y 2 1 2 1 101000 r 74 goat snp38731-scaffold491-3634673 NW_017189517.1 5570968 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436813 Affx-122932239 AX-123307151 X 44290881 AGTCACTAAATGACTTTGGTCACTTTTCTTCTGTC[C/T]TTGCCCATAAAATTATAGATCTCTCTTCTGAGAGA Y 2 1 2 1 101000 r 74 goat snp38730-scaffold491-3599558 NW_017189517.1 5535607 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425755 Affx-122940736 AX-123296101 X 44321198 TTTGTTTCCCAAACCAGTGTGGCCACAAGCATGCC[C/T]GTCATCTTATCTGTTAATTGTTGAGCTCAGTGTGG Y 2 1 2 1 201000 r 74 goat snp38729-scaffold491-3569241 NW_017189517.1 5506380 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802496 Affx-122966749 AX-385289400 X 44395566 GATATTGTTCTGTTGTACCACTTAAAGCAATAAAA[C/T]GATCAAGGAACAGGTGGAATTATATAAAAAAAAGA Y 2 1 2 1 101000 r 74 goat snp38728-scaffold491-3494873 NW_017189517.1 5431564 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779709 Affx-122926646 AX-385266809 X 44444859 TATATTGCATTATTTAGTTCCAGGGTGTCATCTCC[A/G]CCATATAATTTATCATAGCACAAAATGAAATGTGA R 2 1 2 1 101000 f 74 goat snp38727-scaffold491-3445580 NW_017189517.1 5381031 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444172 Affx-122927278 AX-123314509 X 44494192 TAATATTAGTAATGTGCTTCTCTGTAGTCATATCA[G/T]CATATCAATTACAAGAGCCTCAGACAACACACACC K 2 1 2 1 101000 r 74 goat snp38726-scaffold491-3396247 NW_017189517.1 5331381 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448458 Affx-122923638 AX-123318794 X 44550275 ATATTTAACATCTAAATATTTATAATTCAGATGTC[A/G]CTCCAAATCACTGTCCCAGCAGCTAGAAGGATCTT R 2 1 2 1 101000 r 74 goat snp38725-scaffold491-3340164 NW_017189517.1 5274590 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453585 Affx-122920150 AX-123323918 X 44630320 AATGCCATTAACGGCATTGATATCTGTCATTTTTG[G/T]GTTTGGGGAAAGTCCTTCTTGTCTCACATCTGGAA K 2 1 2 1 201000 f 74 goat snp38724-scaffold491-3260119 NW_017189517.1 4572422 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444406 Affx-122926583 AX-123314743 X 44659416 TTATGAAACAGAGTTTTTGTTTGTTTGTTTTAAAG[A/G]AGGGTTTGGGTCCTGTATTCTGTGAGTTCTTTCAA R 2 1 2 1 103000 r 74 goat snp38723-scaffold491-3231023 NW_017189517.1 4601467 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384659 Affx-122972142 AX-123255017 X 44692991 GCAAGTAGGTAGTGCTTGAGTGACACCAACTGCAG[C/T]GTAATAAGTTCATGGTGTCCTCAGGTTTTCCATAT Y 2 1 2 1 101000 r 74 goat snp38722-scaffold491-3197448 NW_017189517.1 4635040 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772863 Affx-122952552 AX-385260008 X 44783741 TATTGTCACCATGAGTAAGATTCCCATAAGGTTTC[A/G]TAAGTTATCTTCATTGTTATAGCCTTACTTCAAAG R 2 1 2 1 101000 f 74 goat snp38721-scaffold491-3106698 NW_017189517.1 4728546 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436175 Affx-122932613 AX-123306514 X 44871445 AAGAACCTAATTTTATTTATCTGAGGTGTGTGTAA[C/T]GGAGGCATCAGAATTTTGAAAATTTTCTAAAGTGA Y 2 1 2 1 201000 f 74 goat snp38720-scaffold491-3018994 NW_017189517.1 4814632 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376773 Affx-122977962 AX-123247132 X 44934157 AGAAACCAAAATCTATAAATATGAACTAGTTCTCA[C/T]GCAGCTGAGAAAATCTACAATGGAGACTGTGGTAC Y 2 1 2 1 101000 f 74 goat snp38719-scaffold491-2956282 NW_017189517.1 4877866 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784545 Affx-122937811 AX-385271594 X 44964518 TCTTCATTATGGTAGAGCAAGCTTTCCCAACTCAT[A/G]TATTTTCTTCACAATTATATCAGTCATTCTTACCA R 2 1 2 1 101000 f 74 goat snp38718-scaffold491-2925921 NW_017189517.1 4908901 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780886 Affx-122976130 AX-385267973 X 45049867 AACAGCTGCTAGGAGACAGCTAACTGTATACCATG[C/T]ACTTAATTACTGGTGATATTGTGGGTGTGAATGGA Y 2 1 2 1 101000 f 74 goat snp38717-scaffold491-2840572 NW_017189517.1 4994765 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401803 Affx-122959468 AX-123272156 X 45101658 TCTGATGAATATAAATGCTCAAACTTCACAGTCTA[C/T]GCTATATTGTTGGAGCCCTATCCTTGATAAAAACT Y 2 1 2 1 101000 r 74 goat snp38716-scaffold491-2788781 NW_017189517.1 5046857 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380612 Affx-122975245 AX-123250970 X 45227033 GCCTGAGAAGAACCATTGCTCAGTGAGTGCATAGT[G/T]TTTCCACTAAGGGAAGAATCTAGCTGTACAAGTCA K 2 1 2 1 101000 f 74 goat snp38715-scaffold491-2663406 NW_017189517.1 4422718 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406133 Affx-122956194 AX-123276485 X 45420340 TAAAAAAATAATCCTCACTATTGCAAAATATAAAA[G/T]CATTTGCATCGTGCAGAAGTTGTGCTACATACCTG K 2 1 2 1 202000 f 74 goat snp38714-scaffold491-2470099 NW_017189517.1 4226308 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774448 Affx-122921749 AX-385261584 X 45459060 GTTGAAACCTTGTGCATATTAGCTTCCAGGTTTAT[A/G]CTCTTTCATGTTTGTGGCAGAAATGAAACTGGGTA R 2 1 2 1 101000 f 74 goat snp38713-scaffold491-2431379 NW_017189517.1 4187111 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377082 Affx-122978276 AX-123247441 X 45508212 GAACTAGCATTTCACTGAACTTTATTTAACTGGTT[A/G]TTAGTACAGCAGTCAGTATGTTTAAAGGAAGAAGT R 2 1 2 1 101000 r 74 goat snp38712-scaffold491-2382227 NW_017189517.1 4137950 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386177 Affx-122971376 AX-123256535 X 45537507 TAGTGTCCTCACCTGTAAAGTGGAGGTAATGAGAG[C/T]ATGTAACTCAAAGGGTTATTGTATTGAATATTCTG Y 2 1 2 1 201000 r 74 goat snp38711-scaffold491-2352932 NW_017189517.1 4108730 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768440 Affx-122927375 AX-385255620 X 45590207 TTGTCTGCATCCTTTTCCCTTGCTGATATTCATGG[C/T]AGCTTTTGATTTATAGGTTCAGAAGGAAGGAGACA Y 2 1 2 1 101000 f 74 goat snp38710-scaffold491-2300232 NW_017189517.1 4056109 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788985 Affx-122965724 AX-385275998 X 45623873 AAATTATTTTGTTGACATGATAAACTCCTACATAG[C/T]AGCCCTCAAGAGGACTGCAAACTTTTTGGATCAGA Y 2 1 2 1 101000 r 74 goat snp38709-scaffold491-2266566 NW_017189517.1 4021848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420720 Affx-122944776 AX-123291067 X 45737867 GTTACTATTGTTAAATAATTTGCATCTTCTTTTGA[A/C]TATGTTAGCATAAAGGAAGGATTGAGTTATATGGG M 2 1 2 1 101000 r 74 goat snp38707-scaffold491-2152572 NW_017189517.1 3905847 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787557 Affx-122955680 AX-385274581 X 45816308 AAATTTTTAAGATTCAGCCATTTACCTGGCTATTC[G/T]GAATTAAATGGATATTACTCATAATAAGAAATAAG K 2 1 2 1 101000 f 74 goat snp38706-scaffold491-2074131 NW_017189517.1 3669175 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404821 Affx-122956645 AX-123275173 X 45861581 AACTTATTTCATTATAGACTGCAAATCTAGACAGA[C/T]GAAAGATCTAGGGGAAATCTAAATTTAGAATAATT Y 2 1 2 1 102000 f 74 goat snp38705-scaffold491-2028858 NW_017189517.1 3730588 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389364 Affx-122968459 AX-123259722 X 45921360 TCCAGCATCAGAGTCAAGAGTCTAAGAAACCATTC[A/G]CTACAGACTGGTCAAATATACTTTACCTTTCATGG R 2 1 2 1 101000 f 74 goat snp38704-scaffold491-1969079 NW_017189517.1 3791966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388711 Affx-122968981 AX-123259069 X 45952198 CCCAAGGTGTTCCGCCAAGACTCAGGTAAGTTGTG[A/G]TTTAGCCATTTGCCTATGTGGTCCATGTGGATACA R 2 1 2 1 101000 r 74 goat snp38703-scaffold491-1938241 NW_017189517.1 3823757 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791512 Affx-122954897 AX-385278503 X 45992896 GCACATATATCACATGGCAGCCGATTCTCTAGAAA[C/T]AGGGTAAATAACTCACTTACCAGTGCAGGAGACAT Y 2 1 2 1 101000 r 74 goat snp38702-scaffold491-1897543 NW_017189517.1 3865133 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387534 Affx-122970305 AX-123257892 X 46032378 ACAACCCTGTGTCCAAGGAGGGGTGGCTGCCAGGG[C/T]GCAGGAGGGCCTAGAGGAGCCATCCCACGCTGAAG Y 2 1 2 1 103000 f 74 goat snp38701-scaffold491-1858061 NW_017189517.1 3602757 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387482 Affx-122970348 AX-123257840 X 46121811 ATAGTGACAAATGACTGTAATTAAGACAGTGGTTG[C/T]AATTCCCAGTCCAATAGTCAAACAGATAGAAATCT Y 2 1 2 1 101000 f 74 goat snp38700-scaffold491-1768628 NW_017189517.1 3511672 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444081 Affx-122926843 AX-123314418 X 46168143 TTGAGGCCATGTTTTGATGGCCTATTTAAGATATC[C/T]GCATGGATGCGTCCAGAACTGCTTATGCTTACCAT Y 2 1 2 1 101000 r 74 goat snp38699-scaffold491-1722296 NW_017189517.1 3465674 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416615 Affx-122947627 AX-123286963 X 46199018 CTCTCATACACCAAACTAATAGTATTTGCCTTTCC[G/T]TAACTCATGTCAGAGCAAGTTATGAGGCAACCAGA K 2 1 2 1 101000 f 74 goat snp38698-scaffold491-1691421 NW_017189517.1 3433651 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422836 Affx-122943107 AX-123293182 X 46251026 ACTACTGTGACTATTCAAGTCCAAGTCTTTGTGTG[A/G]CTCTATCTCTGTGTGAATCATTTATCTTAAGTAAA R 2 1 2 1 201000 r 74 goat snp38697-scaffold491-1639413 NW_017189517.1 3382271 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780113 Affx-122945045 AX-385267210 X 46285453 TTGTGGGAACCCTGTCACCCAGCAAATGTTATTGG[C/T]ACCATCTTCCAATAGCACTAGTTTTCTTTTCTTTT Y 2 1 2 1 101000 f 74 goat snp38696-scaffold491-1604986 NW_017189517.1 3347699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387718 Affx-122969798 AX-123258076 X 46320931 GCCTTCCTCACATCTTTAAATTTCTTACACAACTT[A/G]TTGGAATTGTTCCCAGTAGTTCTGTTCAATGTTTA R 2 1 2 1 101000 r 74 goat snp38695-scaffold491-1569508 NW_017189517.1 3312277 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408051 Affx-122954278 AX-123278402 X 46384140 TTGTTGTTGTTGTTGTTGTTCCTAAAAGACCTTTC[A/G]TTGAAACATCTCTGTTTCTTTAGCTGAGGGACAAC R 2 1 2 1 303000 r 74 goat snp38694-scaffold491-1506299 NW_017189517.1 3249119 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769905 Affx-122951540 AX-385257074 X 46428222 CTTTGCTTTTATAGATGTAACTATAAACTCTCTAC[A/G]CACTACAACTAAAGCCAAGCACATTTCTGCTCCCT R 2 1 2 1 101000 r 74 goat snp38693-scaffold491-1462217 NW_017189517.1 3204169 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409298 Affx-122953103 AX-123279649 X 46463582 CATAGCCTTGAACAAAGGCCTGTTAGCACTAACCA[C/T]GTTGGAGCAGAGGTCAGAGCCTCTTCGTCATTTTT Y 2 1 2 1 201000 f 74 goat snp38692-scaffold491-1426857 NW_017214902.1 6027 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389969 Affx-122968070 AX-123260326 X 46510248 GTCTGTCTCCCATTTTTAGATCATTAGCTACTTCA[C/T]GATGATGCACTCTTCCTTAATGCTGTCTCTTTGGT Y 2 1 2 1 101000 f 74 goat snp38691-scaffold491-1380191 NW_017189517.1 3146332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411379 Affx-122952235 AX-123281729 X 46539002 TGTAGCCCTCCTGGCATCTTTCTCTTCTGTAAAAG[C/T]GTTCTTCCCTTGCCCTGCAGGGACTTCCATGTAAC Y 2 1 2 1 303000 r 74 goat snp38690-scaffold491-1351437 NW_017189517.1 3117178 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385675 Affx-122971142 AX-123256033 X 46599224 CAGGTCAAAGTGAGAAAGAGAGCAAATTTGGAAAG[C/T]GGAGAGAAGGCCCCCCACTCCATAAAATGAAGACT Y 2 1 2 1 101000 f 74 goat snp38688-scaffold491-1291215 NW_017189517.1 3056987 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428117 Affx-122939073 AX-123298460 X 46637164 AGCAGTGTTCTAGGTACTCGCAAAACAGAAGTGAA[G/T]AAGAGAGATACAGAGCCTTGCTCTCATGCAGCTCA K 2 1 2 1 201000 f 74 goat snp38687-scaffold491-1253275 NW_017189517.1 3018824 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436758 Affx-122932282 AX-123307096 X 46671041 AAGATAATTATCTACTTGTTATTCATTGTTCTATA[C/T]CACATAGATGGAAAGGGAGCTAAATACCTTACATG Y 2 1 2 1 202000 f 74 goat snp38686-scaffold491-1219398 NW_017189517.1 2984727 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441288 Affx-122929465 AX-123311625 X 46714395 ATGGTCACCATGAGCCAAAGAGGCCGAGATCTGCA[G/T]GGTATAGCAGCTGAGTTAGTCAGAACCCAGGGATG K 2 1 2 1 101000 r 74 goat snp38685-scaffold491-1176044 NW_017189517.1 2939865 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430583 Affx-122936997 AX-123300924 X 46766619 CAAGTGCTATTTATAAATAGTTTTCATCTCTTTGA[C/T]GGTTACATCAGATTTGAACTTGTGTTCTTGAACTA Y 2 1 2 1 101000 r 74 goat snp38684-scaffold491-1123820 NW_017189517.1 2886321 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430208 Affx-122937339 AX-123300549 X 46800510 ACATTTCCGTTTCATGGAAAAGCAGCCAGAGACTT[A/G]CAAAATGCCAGAAAAAGGATAAATGATAGCATAGG R 2 1 2 1 101000 f 74 goat snp38683-scaffold491-1089929 NW_017189517.1 2851071 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381591 Affx-122974799 AX-123251949 X 46849149 GTCTCAGTAGAAATCTATAGGACAGGAGAGTGGGA[C/T]GATATATGCAAAGTGCTAAAAGAAAAACTGCTAAC Y 2 1 2 1 103000 f 74 goat snp38682-scaffold491-1041290 NW_017189517.1 2801527 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772972 Affx-122956414 AX-385260116 X 46914930 CCTTTAGCCAATTTAGTGTATGATTAAGTATGAAT[A/C]TTTTATTTTCAATACAAGACAAACAAATTTCCTCA M 2 1 2 1 201000 f 74 goat snp38681-scaffold491-975509 NW_017189517.1 5136141 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799896 Affx-122971949 AX-385286822 X 46953147 TGCTCTAAAGGAACAATGCATTTTACTCCTGCTCA[C/T]AACAGTGGTTTACATAGAATTTTTGATACCTGAAT Y 2 1 2 1 101000 f 74 goat snp38680-scaffold491-937292 NW_017189517.1 5174243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397349 Affx-122962296 AX-123267704 X 47045983 TTCATAGGAATTGGGTGTTATAATTCAATTTGGCT[A/G]TAGATGATTCTCTGAAATTCACTGACAATCTTGGA R 2 1 2 1 201000 f 74 goat snp38679-scaffold491-844456 NW_017190018.1 8823 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788723 Affx-122943964 AX-385275739 X 47075788 TAAATTTATTATTAACCCTCATAACACCTAACATA[G/T]CAAGAATTCTAACCATTTAACAGCTAGAAAAAGTA K 2 1 2 1 101000 r 74 goat snp38678-scaffold491-814651 NW_017190018.1 39064 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790569 Affx-122967814 AX-385277572 X 47122070 AGATATGTCGGATTGGGTGTTGAAGGAACTGAGTT[A/C]GAATGAGCTCTAGACTTTAATTGAAGATGTTTGTT M 2 1 2 1 201000 r 74 goat snp38677-scaffold491-768369 NW_017190018.1 86778 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432008 Affx-122935926 AX-123302349 X 47178205 CAAAGTCAAGTTGTCTGTGTTGACATATGTCTATT[G/T]TCTGGGTTTTTATTTAGTTTCATTTATCTATGTGT K 2 1 2 1 101000 f 74 goat snp38676-scaffold491-712234 NW_017190018.1 152805 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434567 Affx-122934125 AX-123304908 X 47220344 GAAATCTTTAAACAAAGAGGGATTTGAAACGCCAG[A/G]TCCTCAAAGGTATTGTAACGCCACAGTAAATGAAA R 2 1 2 1 101000 r 74 goat snp38675-scaffold491-670095 NW_017189631.1 24192 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450486 Affx-122922929 AX-123320820 X 47296471 TCTTTGAGCAAGAGCAATTTAAATGAGTCTCACTA[G/T]CCATCATAGGCAATAAGTAAGTGATTTATCTAACA K 2 1 2 1 101000 f 74 goat snp38674-scaffold491-593968 NW_017189517.1 13257860 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783303 Affx-122967640 AX-385270368 X 47333250 CAAGTCAAAGCTCTAAAATGTAAAGAGTTGGAAGC[C/T]GGAATATGGAATAGTGATACTTGTGTAAATGAATT Y 2 1 2 1 101000 f 74 goat snp38673-scaffold491-557189 NW_017189517.1 5239570 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423828 Affx-122942793 AX-123294174 X 47369561 ACAATGATTCCCTTTACCCCTTGTCATGCCTTCCC[C/T]GCAGAATATATTCCTCTGCCCCACTGATTTTGTGC Y 2 1 2 1 201000 r 74 goat snp38672-scaffold491-520878 NW_017200558.1 757 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774873 Affx-122921744 AX-385262007 X 47408178 AAAATCTTTTCTGTAAGTTCATCTTTCATAAAAGA[C/T]GTTAGTTAGGACATGCTTGAGTACAGTTTAGAGCC Y 2 1 2 1 201000 f 74 goat snp38671-scaffold491-482261 NW_017189517.1 1797777 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789431 Affx-122951774 AX-385276441 X 47439946 GCCAACCTCATATTCTGGTCACAAGTGATGTATTA[A/C]TATAGTTCTGACATAAATGTTGGTTGATATCTTCA M 2 1 2 1 102000 f 74 goat snp38670-scaffold491-450493 NW_017189517.1 1765695 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774915 Affx-122958433 AX-385262048 X 47493741 TCTGTCCTTCAACACAATTGTTGTTACTGAAATCA[C/T]AGGACCATGTGCCTGACATAGAATGAGACCCATGA Y 2 1 2 1 101000 r 74 goat snp38669-scaffold491-396698 NW_017189517.1 1710993 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375939 Affx-122978458 AX-123246298 X 47566295 AAAGGCTATCTTCTAAGGACTGTGCTCATCCTGCT[C/T]TGTTCAACTGTGAATAGAATAAGAATCACTGTGAG Y 2 1 2 1 201000 r 74 goat snp38668-scaffold491-324144 NW_017189517.1 1636950 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381676 Affx-122974732 AX-123252034 X 47701819 CTAGAAGGACAAAAGAGAGAAAAGAGGGTAAAATG[C/T]GTTTGATGAATTTATGGCTGAAAACTTCCCAAACC Y 2 1 2 1 101000 f 74 goat snp38667-scaffold491-188620 NW_017189517.1 1465714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450401 Affx-122922071 AX-123320736 X 47737702 TAGAGATGTTGATGGACCCATTGTGCTTTTTAACT[A/G]ATAGGCTTATATTTACTTCAGCTTTCCAACATAGC R 2 1 2 1 101000 r 74 goat snp38666-scaffold491-152737 NW_017189517.1 1429663 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380028 Affx-122975588 AX-123250386 X 47766566 AATTATCCAGGAGATCGGCTTAGTGTGAAATCCCC[A/G]TATTATGCAAAATCTGATAAAGGATCAGAGAAAGT R 2 1 2 1 201000 r 74 goat snp38665-scaffold491-123873 NW_017189517.1 1400311 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380582 Affx-122975266 AX-123250940 X 47809741 ATAAATCATGTGAAAAATTCTGGAAAAAATAAATC[A/G]CAGAGGGAACGGCAGCTCTAAATGCCCTTCGTGGG R 2 1 2 1 101000 r 74 goat snp38664-scaffold491-80698 NW_017189517.1 1357111 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419694 Affx-122945924 AX-123290042 X 47859133 TCTGCAATATATGAATTGACATCTAGTTCCAGGAG[A/G]GACATGATTCATATTTCAAAATAAAATGGCCCTGT R 2 1 2 1 101000 f 74 goat snp38663-scaffold491-31306 NW_017189517.1 1307390 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405718 Affx-122956529 AX-123276070 X 47906870 TCTATTCAAAGTCGTATCTGAACTTTTTTCCCCTC[A/G]TGTTCACAAAACCTGCTGAGAAATTCACATGATAT R 2 1 2 1 201000 r 74 goat snp18521-scaffold187-2453204 NW_017189517.1 1260477 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771490 Affx-122960736 AX-385258648 X 47945213 ATCTAAATATTACCACTCTGGATTGTTTAACTAAT[A/G]TTAGTAACAAACAAAGCCTGTCTTTACAGTTTGGC R 2 1 2 1 201000 r 74 goat snp18520-scaffold187-2414861 NW_017189517.1 1221780 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401619 Affx-122959603 AX-123271972 X 47985255 AGCTGACTGTGGCCTACCTTCTCAGCCTCATCCTG[A/G]CCATTCTCACTGTATGCTCTAGCCTAGAGTTAGCT R 2 1 2 1 101000 r 74 goat snp18519-scaffold187-2374819 NW_017189517.1 1181016 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418288 Affx-122946996 AX-123288636 X 48015468 CATCTGTGGTAGTGTTTTCATGCACAGTTTGGAGA[G/T]CCTCTGCAATCATTTCTCTTTTAGACATTCTTATC K 2 1 2 1 101000 f 74 goat snp18518-scaffold187-2344606 NW_017189517.1 1151104 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778571 Affx-122965107 AX-385265683 X 48057361 TTGTGTCCCACATTATGCCTTTTGAAATATATATG[C/T]ATACTCCTTGGCCAATCTCCCTTATTTATTCTGGC Y 2 1 2 1 101000 f 74 goat snp18517-scaffold187-2302713 NW_017189517.1 1108974 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395877 Affx-122963997 AX-123266232 X 48115616 CCTCCACCTTGAGGCAATGCATTGTTCAGTGTCCC[A/G]CCATGAGAGATGCTATTAACTTAAGCCAGTAAACA R 2 1 2 1 101000 r 74 goat snp18516-scaffold187-2244458 NW_017189517.1 23320 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396154 Affx-122963384 AX-123266509 X 48160298 TGGTCTTTTGCTTTCAGTGTGAACACACAGAGTGT[A/G]CAGAAGGAAAGATGATTCCTAAGAGGAAAAAAGAG R 2 1 2 1 101000 f 74 goat snp18515-scaffold187-2199776 NW_017189517.1 1073317 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795809 Affx-122929141 AX-385282762 X 48215686 AAAAAATTAAAATTTCTGCATGACAAAATTTATCA[G/T]TATTTATCATAAGCAAAGTTAAAAGACAACTGACA K 2 1 2 1 101000 r 74 goat snp18514-scaffold187-2144388 NW_017190153.1 21704 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389478 Affx-122968325 AX-123259836 X 48271109 CAGAAGGAACTAGGAATCTGGGAACTCTATCCTAC[G/T]AACTGCTTGAATCTGCCCTTTGGAACTCAGAGAAG K 2 1 2 1 201000 f 74 goat snp18513-scaffold187-2088965 NW_017190153.1 77243 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412670 Affx-122950774 AX-123283019 X 48324122 TAGTTTAGCCCTTCTCCTATGTAACAACTCTGAAC[A/G]TAACTACCATATTCCCTTTGAATTTTTTTTTCTTT R 2 1 2 1 101000 f 74 goat snp18512-scaffold187-2035952 NW_017189517.1 1025486 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449809 Affx-122922411 AX-123320144 X 48358121 ATCGTTATCATCAAGAGTATTCAACTGGTAGGAAA[G/T]CACAGTTTTAGAGAGAAAATTCCATGATTTTGGCT K 2 1 2 1 101000 f 74 goat snp18511-scaffold187-2001953 NW_017189517.1 991433 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797586 Affx-122938363 AX-385284525 X 48403341 TACTTCTCTTTAGCCATCTGAACATCCACTACTTT[A/G]TGGTTATTACATATACTAGATCTCTGTTACTCTTG R 2 1 2 1 101000 f 74 goat snp18510-scaffold187-1956733 NW_017189517.1 944077 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376592 Affx-122979065 AX-123246951 X 48488540 GGATTTTCCAGGCAAGAGTACTGGAGTGGGATGCC[A/G]TTGCCTTCTCCAAAATACATGTTAATAACTTTAAA R 2 1 2 1 103000 r 74 goat snp18509-scaffold187-1871534 NW_017189517.1 857704 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388461 Affx-122969249 AX-123258819 X 48521541 TACTTTCAGTTTCTCCCAAGTACCCTGTTCTCCCA[C/T]GTCCTGGCCTGTAACATGCTTTTGCTTTGGGTACC Y 2 1 2 1 201000 r 74 goat snp18508-scaffold187-1838533 NW_017189517.1 823982 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403104 Affx-122958491 AX-123273457 X 48561863 AGTCTTTTTCATTTTAGCCATTTGGATGAGGGTTT[A/G]TTGTCATCGTGTGTCTTTACTTTGCAATTACATGA R 2 1 2 1 101000 r 74 goat snp18507-scaffold187-1798211 NW_017189517.1 784079 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786053 Affx-122947293 AX-385273089 X 48597232 GCTATGATTATGAAAAGGACGCTTAGCCTCATTTG[A/G]TAGTTAACAAAAGACCCCTGGTGCAGTGTAATGGG R 2 1 2 1 101000 r 74 goat snp18506-scaffold187-1762842 NW_017189517.1 748586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801724 Affx-122942260 AX-385288632 X 48769537 AGGATAAATAATTTATGTAGGATAGAGTTTAAGAG[C/T]AGAGATACTGAAGAGCTGCTAGATTCATTTTATGA Y 2 1 2 1 101000 r 74 goat snp18503-scaffold187-1590537 NW_017189517.1 582864 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772283 Affx-122921408 AX-385259438 X 48791597 GAGTTTCTGAACCAAAAAATGATAACTTACATCTT[A/G]TACTTATAAAAGTGGGACAGGATGATTTTTAAATA R 2 1 2 1 101000 f 74 goat snp1332-scaffold1035-1783460 NW_017189517.1 559398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437504 Affx-122932349 AX-123307842 X 48826771 TAAGTTAAGATAAGCCTGTTTTATTATCTCCAGGT[A/C]TAGATAAGGAACTTAGGTTCAGAGAGATGAAATGA M 2 1 2 1 101000 r 74 goat snp1331-scaffold1035-1748286 NW_017189517.1 522997 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774083 Affx-122952089 AX-385261221 X 48856970 AATATGATCAATACAGTCCTTCTTACCACAGAAGT[A/G]TTTAAGTAAAATATGAATTAATCATTGGAAACACA R 2 1 2 1 303000 r 74 goat snp1330-scaffold1035-1718087 NW_017189517.1 492280 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429989 Affx-122938046 AX-123300330 X 48927721 ATGAGGTTGAACATTTTTATGTTTATTGACAAGTT[A/G]CATCTACTTTTCTATTAATGAACTGTTCATACTTT R 2 1 2 1 101000 r 74 goat snp1328-scaffold1035-1647336 NW_017189517.1 -1 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424253 Affx-122942463 AX-123294599 X 48999471 AATCTAAAGGGTAAGTTCTTCTCTAGGTACTTTCT[A/G]CTTTGAGCTAAGGACAAAATGTTATCATGACCTCG R 2 1 2 1 101000 r 74 goat snp1327-scaffold1035-1575586 NW_017189517.1 386530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418388 Affx-122946559 AX-123288736 X 49044379 TGTTCATAGTGTTTAACATCTGATCAGTTTCTTAT[G/T]ATGCCTCTTATTTTAATAAAATCCGTGGGATGTTT K 2 1 2 1 101000 f 74 goat snp1326-scaffold1035-1530678 NW_017189674.1 359507 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431534 Affx-122936220 AX-123301875 X 49165021 GTGTCTTGATTATTAATTTTTTTCTCTATTTCAAT[A/G]CTTCTTTCCTGTCATATCATTTTGCAATTTTGTGC R 2 1 2 1 103000 r 74 goat snp1324-scaffold1035-1410036 NW_017189674.1 237560 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422846 Affx-122943101 AX-123293192 X 49226133 TCTCCAAAGCACAGAACTGTAAAAAAAATTAAATG[C/T]AAAACTCATAGAATCCAAAAAACAATTTAGGGAAT Y 2 1 2 1 303000 r 74 goat snp1323-scaffold1035-1348924 NW_017189674.1 176028 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380767 Affx-122975116 AX-123251125 X 49265598 TCATTTTTAGTGCATGTTTTGGGAGTTTTGTGCTT[G/T]TGTGTGTCAGGATATATGCTATGGTTGGGTTTTTT K 2 1 2 1 201000 r 74 goat snp1322-scaffold1035-1309459 NW_017189674.1 136382 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779094 Affx-122954149 AX-385266199 X 49316677 GCTCACTAGATGGCTGTTGAATGAAAGAATTAGAG[A/G]AAAAGGTATTTATTTGGCCCATGATAGAGTGAAAT R 2 1 2 1 101000 f 74 goat snp1321-scaffold1035-1258380 NW_017189674.1 89541 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779906 Affx-122951763 AX-385267005 X 49351623 TGGGTTGCATTTTGGTGTATGAATTTTCCTGCACC[A/G]TGATGACTAAAATTTCCAAACTGAATGATCAACAA R 2 1 2 1 101000 f 74 goat snp1320-scaffold1035-1223434 NW_017189674.1 54511 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451663 Affx-122921592 AX-123321996 X 49394581 TGTACTCTTAGAAAGGCAGGAAGTGGGGACAGGCT[A/G]TCAGCTACAGACCCGAAGTGGAAGAGGCATTTCAG R 2 1 2 1 201000 r 74 goat snp1319-scaffold1035-1180476 NW_017189674.1 10322 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394519 Affx-122964536 AX-123264874 X 49434182 CTGACATCCTCCACCAAGGAGGTATAACTCAGTTA[C/T]GAGTTCTTGTTAGCAAGTAAGATTGAGATTATCAA Y 2 1 2 1 201000 r 74 goat snp1318-scaffold1035-1140875 NW_017189517.1 251392 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419122 Affx-122945764 AX-123289470 X 49462761 GTTCAGCCTGTTAACTTCAATCTGGGCCATAGGCA[G/T]CCTACTTGTTAGATGATTGTCCTTTGTTATGTTTG K 2 1 2 1 101000 f 74 goat snp1317-scaffold1035-1112296 NW_017189517.1 280489 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418887 Affx-122946107 AX-123289235 X 49669578 GAAAATGTTTGTTGTTTAATCCACCCTGTCTGTTG[C/T]ACTTTATTATGATGGCCCTACCAAACTAAGACAAT Y 2 1 2 1 201000 r 74 goat snp1313-scaffold1035-905479 NW_017189741.1 121230 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399255 Affx-122960570 AX-123269610 X 49702248 TCCCCATCTATTTGCCATGAAGTGATGGGACTGGA[C/T]GCCGTGATCTAGAGGTATACTTATCCTTATTTTAC Y 2 1 2 1 201000 r 74 goat snp1312-scaffold1035-872809 NW_017189741.1 154052 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790975 Affx-122954447 AX-385277972 X 49732518 ATCTAACTTTAAAGATCAATTATGTTTCAGCAGAC[C/T]CTGGGCACATCTAAAAAGGTTGCTCACTTAAACTT Y 2 1 2 1 101000 f 74 goat snp1311-scaffold1035-842539 NW_017189741.1 184891 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772552 Affx-122971045 AX-385259702 X 49785560 TATCATGGTAACATAGTATAGTGGAAATAGCATCT[A/G]TATAGGAAATAGGAGATCTGACTTCTCCACCTATC R 2 1 2 1 101000 r 74 goat snp1310-scaffold1035-789497 NW_017189741.1 238323 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436833 Affx-122932222 AX-123307171 X 49874944 CTCATCCCTCTCCTCTCATCACTCTGGACAGCCCT[C/T]GCCTCTCTCTTCCCTGCTCTCTCTCCCTCCCTCCT Y 2 1 2 1 103000 f 74 goat snp1308-scaffold1035-700113 NW_017189596.1 460086 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395038 Affx-122964207 AX-123265393 X 50010154 GGACTGCATCTGGAATACCATGTGCAGTCCTGGAC[A/G]TCACACACTCAAGAAAGAGTGACAACTGTCAGGCT R 2 1 2 1 101000 r 74 goat snp1306-scaffold1035-564903 NW_017189596.1 324714 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402605 Affx-122958417 AX-123272958 X 50078052 CCACCACAGAACCACTGAGTCAAAAACTCTAGGAG[C/T]GGAGCCCAGAAAATTGGGTTTTAAGAAGTCTTTCA Y 2 1 2 1 201000 f 74 goat snp1305-scaffold1035-497005 NW_017189596.1 255913 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452262 Affx-122920766 AX-123322595 X 50144960 GTGTTTGATAATCACCGATTTAACTTGAAACAAAA[C/T]GTATCAAATGTTCCTTGACATGCCATTCAGATTAA Y 2 1 2 1 101000 f 74 goat snp1303-scaffold1035-430097 NW_017189596.1 188580 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786718 Affx-122934896 AX-385273749 X 50181298 AAATAATCTTTCAATAACAAAACAACAGATTATAC[A/G]TAAGACACATGCTTAACTGGAATCACAGTCTCTAG R 2 1 2 1 101000 r 74 goat snp1302-scaffold1035-393759 NW_017189596.1 151947 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386589 Affx-122970691 AX-123256947 X 50223390 CCACAAGGGGAGGCAAGGTGAAGGTGCTCTGGGGG[C/T]GGTTCTGATTTGAGCCATCCCTGTCCAGCAACTGG Y 2 1 2 1 101000 r 74 goat snp1301-scaffold1035-351667 NW_017189596.1 109552 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399009 Affx-122960939 AX-123269364 X 50254903 TTCAAACTGCACACTGTGATAACCAGATCCACCCA[C/T]AGCACCCGAGTCGGGGGTAATCCATGTGAAGTCTT Y 2 1 2 1 101000 f 74 goat snp1300-scaffold1035-320154 NW_017189596.1 78111 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775860 Affx-122935445 AX-385262991 X 50308685 ATCAGTGGTGAGATTCACAATATAGAAAGCCAGTG[C/T]ACTTTTCAAAACCTTGTCCTGCAATAGGAACCACA Y 2 1 2 1 101000 f 74 goat snp1299-scaffold1035-266372 NW_017189596.1 23290 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452524 Affx-122920548 AX-123322857 X 50347151 ATGAGCCCAATAAAGACAACTGAAATAAACCAAAA[C/T]TAAAGACTCTGGAGACATGTTTTTGTTCCCTCATT Y 2 1 2 1 201000 f 74 goat snp1298-scaffold1035-227906 NW_017189517.1 109512 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400014 Affx-122960799 AX-123270369 X 50461202 ATGGACCTGGGAGCAAGTGTTCCAGAGAAGCAGAC[A/G]TACCTCTGCTCTCCCTCCACCACATGATTCATGAA R 2 1 2 1 101000 r 74 goat snp1296-scaffold1035-113855 NW_017189552.1 437445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446322 Affx-122925631 AX-123316658 X 50512819 GGAGTAGTCCTCTTGAGCTCCACAGTGGCCAGGAA[C/T]TCATTTTACTGGTCACATATCACAAGTCTGTACTG Y 2 1 2 1 201000 r 74 goat snp1295-scaffold1035-62238 NW_017189552.1 385715 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378718 Affx-122977048 AX-123249077 X 50628257 CTATATACTCCCTGGCTTGTTCTTAAATATGCTCA[C/T]GGGGTGGGGGAGAGTTTTAAATTATGTTGCTTATG Y 2 1 2 1 101000 f 74 goat snp7616-scaffold1271-737138 NW_017189552.1 269509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389219 Affx-122969056 AX-123259577 X 50677081 AGGGGAGGAGGCCTGGGCTGAAGAACTAATGGAGG[C/T]GAGGGTGGCTGGGGGCGGAGCCATGGGGGTAAACT Y 2 1 2 1 101000 f 74 goat snp7615-scaffold1271-688314 NW_017189552.1 220317 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387146 Affx-122970642 AX-123257504 X 50714309 TTCTGAAGCAATCCGATGACATGGGATAACGTTCA[C/T]GATACTACTTTAAGAGAAGCTAAATGAGGTGCAAA Y 2 1 2 1 101000 f 74 goat snp7614-scaffold1271-651086 NW_017189552.1 182642 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405542 Affx-122955973 AX-123275894 X 50802902 GGTTTCTTCTCAATTCCAGTTCTCCCAAAGACAGG[C/T]GCTATGCAGTCTTTTACTCTGTAACCCAGACCAGA Y 2 1 2 1 201000 r 74 goat snp7613-scaffold1271-562493 NW_017189552.1 93835 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768776 Affx-122946302 AX-385255953 X 50840475 TTTCATCATACTTTTATTTACATGGAATTAAAAGA[C/T]AACAAATCTGACCTGAACCATGATTTTGATTTTAA Y 2 1 2 1 201000 f 74 goat snp7612-scaffold1271-524920 NW_017189552.1 56478 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432505 Affx-122935577 AX-123302846 X 50885329 AAGGCCAGTCTCTTTCAAACATATGTCTTTTTATA[C/T]AGCCATTATAGGAAAATAACTTCATTCAAATTATT Y 2 1 2 1 101000 f 74 goat snp7611-scaffold1271-480066 NW_017189774.1 14229 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376994 Affx-122977737 AX-123247353 X 50984417 CCTTTTGTGAACTTGCTTGCTCGGTGGAGCTGCCC[A/G]TTTCTTTGCCCATGACCCTAACTCCATGTGCTTTC R 2 1 2 1 101000 r 74 goat snp7609-scaffold1271-380978 NW_017189774.1 112704 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444935 Affx-122926698 AX-123315272 X 51017982 TGCACAGGCTCACAGAAGAGGCACTGTGGAGTTTC[A/G]CTGGTTAAAATAGTTGAAGCACTTTGAAGATCTAA R 2 1 2 1 201000 r 74 goat snp7608-scaffold1271-347413 NW_017189774.1 146208 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780736 Affx-122973977 AX-385267826 X 51085857 TAGTGTATCTTTGAGTAGATCCTAAGAGCCAATTA[A/G]CATGAATCTTTAAAGACAGATTCTTAGTTATCAAT R 2 1 2 1 101000 f 74 goat snp7607-scaffold1271-279538 NW_017189774.1 216073 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422985 Affx-122942996 AX-123293331 X 51123530 CCTTGGCTCTGTGTGGGGTAATAGCAAGCCCAAAC[A/G]TACTGATCTTGACCTTGCTTAACCCTTGGCTTCTT R 2 1 2 1 101000 r 74 goat snp7606-scaffold1271-241865 NW_017189774.1 253671 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423802 Affx-122942813 AX-123294148 X 51166348 GTTTCCTGTTTGTTCATTCTGCACTCATTCATTCA[C/T]AAATGTTTGTTGGACCCCTTTTATGTGTCAGGCAC Y 2 1 2 1 101000 r 74 goat snp7605-scaffold1271-199047 NW_017189517.1 218940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438848 Affx-122930767 AX-123309185 X 51247971 AGTTGCCACTCTGCAGTCCTCCATGTGAGGCTGGG[C/T]GAGGTAAGCCTGCAGGAAAGGGGCTTGTAAGTGAA Y 2 1 2 1 201000 f 74 goat snp7604-scaffold1271-117424 NW_017190074.1 36762 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782163 Affx-122932849 AX-385269241 X 51324682 TCAAAAAGGGCACTCAAAGTGATTGGAAATTGCCA[A/G]CTTGGGGTATTCAAGCTGTCTTTTACAAGAGGTAT R 2 1 2 1 102000 r 74 goat snp7602-scaffold1271-40713 NW_017190074.1 113865 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779516 Affx-122929025 AX-385266619 X 51382298 TAAATCCACATGGAAAGGATAAATCCACTTTTCAA[C/T]AAGTCGGGGATCCACCTGCAAAAAATGTGAGTTTG Y 2 1 2 1 102000 r 74 goat snp31444-scaffold3481-107314 NW_017189574.1 359427 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780457 Affx-122968940 AX-385267548 X 51422420 AGACCAGAAAGACAAAGTGCCATTCTTATCACATC[A/G]TATCAAGGGCACATTCTATCAACATGATTTATCAC R 2 1 2 1 103000 f 74 goat snp31443-scaffold3481-67192 NW_017214082.1 11065 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795895 Affx-122953606 AX-385282847 X 51468537 TGAGAGTCTGGGTGTGGGACTGGAGGAAATCCTAA[C/T]GAAAGTCACCTGTCTTCACTGTTAATGGACAGTTG Y 2 1 2 1 201000 r 74 goat snp31442-scaffold3481-21075 NW_017189574.1 314360 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770630 Affx-122919379 AX-385257794 X 51543910 AATAATAAGCCATATCTCAGTGTCTGGTGAGTATG[C/T]ATTTCTAGTTGAGGTTGTGCATACCTATACATATA Y 2 1 2 1 101000 f 74 goat snp6395-scaffold1228-54199 NW_017189574.1 231631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781188 Affx-122925562 AX-385268273 X 51603337 GCTGGGATTCACCATCAGGTTCCACACACCTGATC[A/G]TACTTTCTTAGATTTTGGTTCTGTAGATGTTCAGA R 2 1 2 1 101000 r 74 goat snp6396-scaffold1228-113626 NW_017189574.1 172534 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410017 Affx-122953258 AX-123280367 X 51666473 AAGACTTATTATAGAATTAGATGAAATCATATGCG[C/T]GAAATCTTTGAAACTGTAAAGCACAAAGGAGTTTA Y 2 1 2 1 101000 f 74 goat snp6397-scaffold1228-176762 NW_017189574.1 109228 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787480 Affx-122973184 AX-385274505 X 51808735 CTGGACAAGATAAGAGCACCTGCCAAGACCTAGAA[A/G]CTAGGTCTTGAATTTAGTCAAAAAGCTAAGACACC R 2 1 2 1 101000 f 74 goat snp13737-scaffold153-2561897 NW_017189517.1 35893260 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767283 Affx-122946315 AX-385254565 X 51864850 TGTCTTTCTTTTGGAATAGTTGCACTCCTCAGCAA[C/T]GATCAATGCTCAGCAACTCCTAAGATTACCACAGC Y 2 1 2 1 101000 f 74 goat snp13736-scaffold153-2505782 NW_017189517.1 82893 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797643 Affx-122969704 AX-385284582 X 51896654 AATATTCAAATATATAACAGATGCATAAACGAAAC[A/C]CTGATAAACAGGATTGCTCTAGAGAGAAGAAGGAT M 2 1 2 1 101000 r 74 goat snp13735-scaffold153-2473978 NW_017189517.1 50637 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397415 Affx-122962248 AX-123267770 X 51967822 GACTTTCTGATTCTATTAGGTCACCAGATAAATGA[C/T]CTTGGAATAACTAAAGTGTCTCTGCACTGTATACA Y 2 1 2 1 101000 f 74 goat snp13734-scaffold153-2402810 NW_017189874.1 51494 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425790 Affx-122940708 AX-123296136 X 52006662 TTTCAGTCTCCAACTCTCTCTCTCTTCCACTGACT[A/C]ATAACAAAGTGCCATCATTCCAACTTTCTCTTCTA M 2 1 2 1 201000 r 74 goat snp13733-scaffold153-2363970 NW_017189874.1 90515 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782475 Affx-122958702 AX-385269550 X 52122294 CCAGGGATAAATCTGTCACAAGAGGAATTTGAGGA[A/C]TTCTTTAGGCTCTCAGATTCCACCTTTTTTATTTT M 2 1 2 1 101000 f 74 goat snp13731-scaffold153-2248338 NW_017189630.1 6734 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406352 Affx-122955432 AX-123276704 X 52341365 GTTAGACGTTCAGAGTGGGCAGGGGAGGTACCCAG[C/T]AGTAAGTCTTAACGTGGGAACAGGCACACAGAGAG Y 2 1 2 1 101000 r 74 goat snp13727-scaffold153-2029267 NW_017189630.1 228196 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417887 Affx-122946753 AX-123288235 X 52379827 CTTGGCCTCCAAGAGAGAAAAGAAGTGAGATCACT[G/T]TTACGTATCTATATACTTTTTTTTCAGGTTTACTG K 2 1 2 1 201000 f 74 goat snp13726-scaffold153-1990805 NW_017189630.1 266867 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405579 Affx-122955943 AX-123275931 X 52414598 ATTCAGCCACAGCCACGCCTTCCTCTGGGAGGCAT[A/G]ATCGATAGTATCCGGTGGCTTGGATGAAGCAAGTC R 2 1 2 1 201000 r 74 goat snp13725-scaffold153-1956034 NW_017189630.1 301687 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450924 Affx-122921778 AX-123321258 X 52612447 TCAGTTATTTGTCTCTTGCATTGGGAAAATATGCA[A/G]GTAGAAGGTTTTGTCCTGCTTCACTTGGCACGCAG R 2 1 2 1 103000 r 74 goat snp13721-scaffold153-1758185 NW_017189518.1 54711 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772195 Affx-122924782 AX-385259350 X 52650939 ATACATTCTTACTGTCAGGTTGTTTTGGCAGCTCT[A/G]AATACAAAGTTGTACTGAATGTGCATGGAGAGCAC R 2 1 2 1 101000 f 74 goat snp13720-scaffold153-1719693 NW_017189518.1 93400 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439805 Affx-122930487 AX-123310142 X 52682991 TGCTCCTAAGAAGCACCAGGGCTGACCTGCTGAGA[A/G]ATCCTACCTTCCATGGATATGCAGGAGTATGCTGG R 2 1 2 1 101000 r 74 goat snp13719-scaffold153-1687641 NW_017189518.1 125509 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437352 Affx-122931939 AX-123307690 X 52744847 TGCAGCAGAGTGGTGGGGACTGGGGAGGGGGTTCA[A/G]TGGTCTAGGATGAAGCCCTGAGAGGCATAGTCCCT R 2 1 2 1 101000 r 74 goat snp13718-scaffold153-1625785 NW_017189518.1 187722 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377120 Affx-122978246 AX-123247479 X 52777340 TGCATTACATATGCTAAGCAAACTTAAAAGTGGAC[C/T]ATTGCTTGGCCACTCCAAGAGCATTTTTTACACAG Y 2 1 2 1 101000 r 74 goat snp13717-scaffold153-1593292 NW_017189518.1 220155 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434049 Affx-122934200 AX-123304390 X 52831040 GTGATGGACAGCCAGGGGCTAGTAGAACAGGGTCC[A/G]TTAAAGGGCCTTCCTGCACGACCTAGAGGAATTTG R 2 1 2 1 101000 r 74 goat snp13716-scaffold153-1539592 NW_017189518.1 274592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782488 Affx-122956334 AX-385269564 X 52879094 AAACTAGAAGAGTTTAGACAATTTTGTAGCACATG[A/G]GGAGTGATCGGAAGAGTGCTAGGATCAAAACTCTG R 2 1 2 1 101000 r 74 goat snp13715-scaffold153-1491538 NW_017189518.1 322692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427796 Affx-122939764 AX-123298139 X 52949477 GGTCCTAGATAAGAGTGTATCTAACGAAGAATTTT[A/G]AGGAGCCCAGACTTCCCATACATAGAAAAGTACTA R 2 1 2 1 202000 f 74 goat snp13714-scaffold153-1421155 NW_017189518.1 393173 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448168 Affx-122924263 AX-123318504 X 53001959 CACCAGGGAAGGCCTCATGTAAAGCGCTGCTAATA[A/G]TAGTACAGAGTACCTAATGTGTCCAGTGCCTCCTG R 2 1 2 1 101000 r 74 goat snp13713-scaffold153-1368673 NW_017189518.1 445990 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778824 Affx-122938017 AX-385265933 X 53043312 GCTTTTTATTCCTATCATATCAGTAGTGATGTTCC[A/G]TCTTTCATTCTTGATTATAGTAATATGAGTCTTCT R 2 1 2 1 201000 r 74 goat snp13712-scaffold153-1327320 NW_017189518.1 487652 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788753 Affx-122970820 AX-385275769 X 53083232 ATGGGACCTCATGGAGGACTCACGGAGGAGATATA[G/T]ATATATATCTCCATCTCTGCCTCATAGAGTTGGGA K 2 1 2 1 202000 r 74 goat snp13711-scaffold153-1287400 NW_017189518.1 528845 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394988 Affx-122964257 AX-123265343 X 53178239 AGATTATGGGTGTCATATGCTATCCAACATCAAAA[C/T]GAAGAAGAGAAATATGGTATAGATGTGGTAAAAGC Y 2 1 2 1 101000 f 74 goat snp13710-scaffold153-1192393 NW_017189518.1 624925 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446858 Affx-122925253 AX-123317194 X 53236699 TCGGGCTGGGGGTGGGCTGGGGGCAGGCACTGGGC[A/G]CCAGTCACATAGCTCAGGACAGTGGGACAACTGTT R 2 1 2 1 101000 r 74 goat snp13709-scaffold153-1133933 NW_017189518.1 683821 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393736 Affx-122965227 AX-123264091 X 53286941 CAACAGCTCAGAGTGCTGGAGCCCTGGCCCTCCAA[A/C]AGGAAGTACCTTGACAGAGCTGGCGAGGGGATGCA M 2 1 2 1 101000 r 74 goat snp13708-scaffold153-1083691 NW_017189518.1 734285 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420233 Affx-122945526 AX-123290581 X 53363224 AATATACTCCAAACAACATGGGCTGAGTGGGAACG[A/G]TGGAGTAAGCTGGAAGGTCACTTCCTTTCTAGATT R 2 1 2 1 201000 r 74 goat snp13707-scaffold153-1007408 NW_017189518.1 811491 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441970 Affx-122928560 AX-123312307 X 53410340 CTATTACTTTTGGGTGTAAGAAAATGAACAAAATT[A/G]TTGCTTTTACTCTGCGGACTATTTAACTGAAGTAA R 2 1 2 1 101000 r 74 goat snp13706-scaffold153-960292 NW_017189518.1 858874 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783831 Affx-122978587 AX-385270887 X 53450108 AGTAATGCCATGTTTTCTTATTCCAGATAGTAAAA[C/T]ATAATGAAAGGTTTCCCAATTTGTTTCACAAAATA Y 2 1 2 1 101000 f 74 goat snp13705-scaffold153-920524 NW_017189518.1 898591 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440797 Affx-122929833 AX-123311134 X 53511922 CCTACAAAAGGCATGGAAGTGTGCCTGCTGAGAGA[C/T]GGCAAAGGGAACACAGACTCCTCCATCTATGTGCG Y 2 1 2 1 101000 f 74 goat snp13704-scaffold153-858710 NW_017189518.1 961215 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404958 Affx-122956418 AX-123275310 X 53555033 TCCAAAGCCTAGAACCTCTCACCAACTATGCTCCT[A/G]TGAAAGGACATAGAAGGAAGGCCATGAAGATGACT R 2 1 2 1 201000 r 74 goat snp13703-scaffold153-815599 NW_017189518.1 1004291 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420064 Affx-122945122 AX-123290412 X 53618470 TGCTCCCTCCCAGGTTGCCCCCTGAAGCCATCTTT[C/T]AAGTGGACTTCATCTACTTGTCAGTCATCTGAGGG Y 2 1 2 1 101000 r 74 goat snp13702-scaffold153-752162 NW_017189518.1 1065710 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795598 Affx-122939837 AX-385282553 X 53652092 AATGGATTTCTAATATGAGGGTACTGTTTTGTACA[C/T]GCTGCTACAATATGAAGGAACTAACAGAACCACTG Y 2 1 2 1 101000 r 74 goat snp13701-scaffold153-718540 NW_017189518.1 1099957 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800724 Affx-122963632 AX-385287641 X 53695870 TTTAAGTATTTGAATTAGTTATAAAGCTATGGAGT[A/G]TTTATTTCCACTTGGTTTCATAGTATGCCAAACCT R 2 1 2 1 101000 r 74 goat snp13700-scaffold153-674762 NW_017189740.1 660447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450801 Affx-122921812 AX-123321135 X 53810596 CTGGATCAAGTAATTGATTTACATATTCTGGCTTC[G/T]TGATCATATATTCTGACTACCTATGCAATTTCCAC K 2 1 2 1 101000 f 74 goat snp13698-scaffold153-560036 NW_017189740.1 542733 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768282 Affx-122921532 AX-385255463 X 53839988 TTGCTTCTTGAATAAATAACTCTTATGCAAAGATC[A/G]TAATTGAAAGAGTAAAAAGTGGTATACAGTGAAAA R 2 1 2 1 101000 r 74 goat snp13697-scaffold153-530644 NW_017189740.1 513257 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402203 Affx-122959165 AX-123272556 X 53883811 AGATAACATGTCGTGTTGCACAGCTGAAACTCTCA[A/G]TGAGCCAGGACTCTTTCCAGACCTCCCAACTCTCC R 2 1 2 1 101000 f 74 goat snp13696-scaffold153-486821 NW_017189740.1 469244 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449090 Affx-122923599 AX-123319425 X 53937850 TTCTTTCAGGTTATCAGAGAGACTTAAAGTCCAAA[C/T]TCAAGTCTTCTAATCATTGCACTCATCTCACATGC Y 2 1 2 1 101000 f 74 goat snp13695-scaffold153-432782 NW_017189740.1 414586 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438433 Affx-122931265 AX-123308771 X 53967932 TGCTCTCAGAAATATTTTTGGTTTTCAGACTTGCA[C/T]ATCTTTTTCTAGGTTTATCGCTCATTTCTTTTGGC Y 2 1 2 1 201000 r 74 goat snp13694-scaffold153-402700 NW_017189740.1 384185 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786130 Affx-122944653 AX-385273166 X 54011784 AGTGTTGAGGAGAAGCGACAACTGGGGAAAAGCTG[A/C]TTTTACTTTCAAAGTGAACAAATGGTCATTTTTAG M 2 1 2 1 102000 f 74 goat snp13693-scaffold153-358848 NW_017189740.1 340276 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429750 Affx-122937591 AX-123300091 X 54043499 GGTTGAACAAAAAAATCATTTAGATATGGAAGGGT[G/T]AGAGAAGTAAAAAGAATAATGGATGACTCACAAAT K 2 1 2 1 101000 r 74 goat snp13692-scaffold153-327133 NW_017189740.1 307496 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429979 Affx-122938053 AX-123300320 X 54108845 AGGAAGGAGACCACATCCCCCTTCTCTTACCCCAT[A/G]TCCCTTAAAGTAGTGGTATAGTTAGTGGGCAGCAA R 2 1 2 1 101000 r 74 goat snp13691-scaffold153-261787 NW_017189740.1 242074 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385066 Affx-122971819 AX-123255424 X 54178358 TTAACTCTTGTCCTGCATTCCCACATTTATGCCAC[C/T]GCCAAACAACTTCTCAAGCACACATTGTACCCATG Y 2 1 2 1 101000 f 74 goat snp13690-scaffold153-192274 NW_017189740.1 171392 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381116 Affx-122974580 AX-123251474 X 54331962 AAGACCCTGGAGACGCGGTGGCGGCCCGTGCTACG[C/T]GGCCACCAGCACTGTACCTTGGCAGTCCACATCGC Y 2 1 2 1 202000 r 74 goat snp13687-scaffold153-38670 NW_017189608.1 44900 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420935 Affx-122944993 AX-123291282 X 54448315 AAGCAAATGGTGGACCCAAGGGGCTTCTCATGTTC[A/G]TTTTGAGAACAAGTCCTGGATCATGGGAACATGGG R 2 1 2 1 101000 r 74 goat snp16294-scaffold1715-412556 NW_017190133.1 18984 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790596 Affx-122964845 AX-385277598 X 54546567 TTCAGAAGTCCTCTGTTCACTGAAAAGAAACATGG[C/T]TTCGGCCTTCCTAGGCTGAGTAATGCTCATGAGGC Y 2 1 2 1 101000 f 74 goat snp16293-scaffold1715-314304 NW_017189840.1 77308 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454034 Affx-122919664 AX-123324367 X 54610794 TTTGGAGAGTGGGGACAGGAAGTCCTTGGCCTGCC[A/G]GGTGCTTGTGTGCAGAAGTTTGGGCGGTGATGGGC R 2 1 2 1 201000 r 74 goat snp16292-scaffold1715-250077 NW_017189840.1 140517 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429436 Affx-122938505 AX-123299778 X 54645779 TTCCATCCCTGGTTGAGGAACTAAGATCCCACATG[C/T]TGCAGCAACAGATAAAACAATATCCCCCTTTCATA Y 2 1 2 1 101000 r 74 goat snp16291-scaffold1715-215092 NW_017189840.1 173863 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383223 Affx-122972767 AX-123253581 X 54695430 CTGACCCTGGTCTTCTCACTCAAAGATAACTATGA[C/T]GCATGAGGGCATGGATTTGGGTCTGCAGCCACCTA Y 2 1 2 1 101000 f 74 goat snp16290-scaffold1715-165441 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385115 Affx-122971781 AX-123255473 X 54779117 AGGATGGGGGCAAGAATCTGGGTGGGCTGGCGCTC[A/G]GGCTGGGGCAGGCGCTCTCTGAGCCTCTGGGAGCC R 2 1 2 1 103000 f 74 goat snp16289-scaffold1715-81754 NW_017190169.1 73943 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394734 Affx-122964867 AX-123265089 X 54832778 GTCTGGGCTTGAAGGGAAGCCAGGACCCCTCTAAG[C/T]GGAGCTGCACAGAGACCAAGAGCAGCCGCCCAAGG Y 2 1 2 1 201000 r 74 goat snp16288-scaffold1715-28093 NW_017214957.1 61524 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390446 Affx-122967624 AX-123260803 X 54899958 ACCTCCCACATCCAGATTTCTCTTCTCTCATTCTC[C/T]GATTCAAGGCCTGTGGGTTTAAATACCTTGAAGGT Y 2 1 2 1 101000 r 74 goat snp31514-scaffold3494-38988 NW_017189670.1 3638 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442763 Affx-122927746 AX-123313100 X 54974903 GTGTGGCTTTCTTATCAGTGAAGCCGCTTGCAGTG[A/G]TGGATGCTGGGCTCAGCCGTCCTCAGTCTTTGGGC R 2 1 2 1 202000 r 74 goat snp37954-scaffold47-1466820 NW_017209003.1 16761 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377206 Affx-122978181 AX-123247565 X 55008662 TCTCTGTATGTGTGTGTCTCTCACTGTGTGTGTTT[C/T]TCCAGTGTGTGTGTCTCTCTCAGCCTGTTTGTGTC Y 2 1 2 1 103000 f 74 goat snp37953-scaffold47-1433061 NW_017189543.1 9076 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448834 Affx-122923301 AX-123319170 X 55059091 ATTTCAATATCAGCTCATCAGGGACTTCTCTGGTT[A/G]TCCAGTGGTTGACACTCTACCTGCCAATGCAGGGA R 2 1 2 1 201000 r 74 goat snp37952-scaffold47-1382632 NW_017189652.1 28880 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375909 Affx-122978479 AX-123246268 X 55104705 TGGTGAGAATTCTGGCCTGAAGTGCAACACGAAAA[A/G]AGACAGGGACCACTTGGAGGAGTGGTTTTCCGTTT R 2 1 2 1 101000 f 74 goat snp37951-scaffold47-1337018 NW_017189652.1 57698 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419563 Affx-122945406 AX-123289911 X 55150849 TGCTTCCACTGGAATCATAAATTATCCTAGGAGAC[A/G]CGCACCTGGACACCTTGCCCCACTGGAAAACACAG R 2 1 2 1 101000 f 74 goat snp37950-scaffold47-1290874 NW_017189652.1 105435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443142 Affx-122928071 AX-123313479 X 55199860 TGATGCACTATCTTTTATATTTCACACGAGGAACT[A/G]TGTTTATGGCTTTAAAGGTTATATTAGAAACCAAT R 2 1 2 1 101000 f 74 goat snp37949-scaffold47-1241863 NW_017189652.1 155845 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450126 Affx-122922763 AX-123320461 X 55231383 GGTCCAGTCTCTCCTAAATGTGGTCATGGTTTCAC[A/G]TAGAAGACCTGGTGGAATCACTAGACACCTTGCAG R 2 1 2 1 101000 r 74 goat snp37948-scaffold47-1210340 NW_017189652.1 187605 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385762 Affx-122971066 AX-123256120 X 55299298 AGGGGTGGCCTGACCCCAGAAACTGGCTGATTTCT[G/T]ATTTCCTGAGGTTCACCTTCCCTCCGAGGAAGCTG K 2 1 2 1 101000 r 74 goat snp37947-scaffold47-1142425 NW_017189652.1 256548 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448378 Affx-122924101 AX-123318714 X 55331237 AGGGAAAGCTCTGAACTGTTTCTTCAGCTACTTCC[A/G]TCACCTGGTTGTTCCCACCAAGAGTGTCAAGGAAA R 2 1 2 1 101000 f 74 goat snp37946-scaffold47-1110486 NW_017189652.1 289789 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798888 Affx-122920064 AX-385285818 X 55364716 TATCCTGTCCTACATGCTTCTTGTACAATGACCTT[A/G]CCATTCTCCCTTTCAAAAGGTAGTCTAATTCCCCT R 2 1 2 1 101000 r 74 goat snp37945-scaffold47-1077007 NW_017189652.1 323446 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783401 Affx-122957039 AX-385270464 X 55401524 ATATCCCTTAGGTCTTCCAGCTTCTTAATCATGCT[A/G]TTTATTAGTATCTGATCATTTTTTCTTCTAAAGAT R 2 1 2 1 101000 f 74 goat snp37944-scaffold47-1040199 NW_017189652.1 360816 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449628 Affx-122923191 AX-123319963 X 55444438 ATCTTGGACCTGGGTTCATTTTCTTTTTTCTCCCT[A/G]CTTTCAATTCCTAGTTGGTCTTATCCATGCTCATG R 2 1 2 1 201000 r 74 goat snp37943-scaffold47-997285 NW_017189652.1 404142 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414362 Affx-122950012 AX-123284711 X 55477897 CAAACGACACCACCTAGGAACAGAAGACAGCACAG[C/T]GGATTACTCAGCTGAGGACGCTGTTATTGGGGAGG Y 2 1 2 1 201000 r 74 goat snp37942-scaffold47-963826 NW_017190062.1 145704 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771460 Affx-122969238 AX-385258618 X 55512270 GTATGTCCAAGATGGAAGAAACAGACTGGAGAATC[A/G]TTAAGAAGAATCTGCAAGATTCTGGAGATTATGCA R 2 1 2 1 101000 f 74 goat snp37941-scaffold47-929453 NW_017190062.1 111355 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443810 Affx-122927076 AX-123314147 X 55567771 TTTCAGGTTTGTTGGTCATTTGTTTATCTTCTTTG[A/G]AGAAATGTCTACTTAAGCCCTTTGTCTATGTTTAA R 2 1 2 1 303000 r 74 goat snp37940-scaffold47-873952 NW_017190062.1 55299 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388558 Affx-122969179 AX-123258916 X 55621381 CATATCCCACTGCTCCAGTGAAAAGAGTCGGACAC[A/G]AGTCAGCATGTTCATGCACAGACACACCCATATAC R 2 1 2 1 103000 r 74 goat snp37939-scaffold47-820342 NW_017190062.1 1106 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774164 Affx-122944484 AX-385261301 X 55656427 ACAGTGATTTTTGTCTGTTCATTGATGAATCTTGG[C/T]GTTTAGCATATAATAACTGCTTAATTGGTATTTGC Y 2 1 2 1 101000 f 74 goat snp37938-scaffold47-785296 NW_017190073.1 33354 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404445 Affx-122956751 AX-123274797 X 55698657 ATCATGGGACTCAAGAGTAGTAACAGGAAAAATCA[C/T]AGACAAGGTCTCTGAAATCATCACAACTGAAATGT Y 2 1 2 1 101000 f 74 goat snp37937-scaffold47-743066 NW_017190073.1 75927 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410460 Affx-122952217 AX-123280810 X 55778315 TTCTGGATGAAATTGATCCAGACAGTGCTGAGGAA[C/T]GCACAGTCTCCAGAAGATTGTTCTTGGATGGCGAT Y 2 1 2 1 101000 f 74 goat snp37936-scaffold47-663408 NW_017190073.1 156995 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434053 Affx-122934197 AX-123304394 X 55833655 TGAGAAACATGGATATAAAAAAATTGGAAACTGAA[A/C]AGTGCTATACAGATTTTAGCTATTATTGTAATTGT M 2 1 2 1 101000 r 74 goat snp37935-scaffold47-608068 NW_017190073.1 212903 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408016 Affx-122954306 AX-123278367 X 55894368 AAATAACGTAATAAATGCTAATAAAAGAATGTGAT[A/C]TTTTCCCTAGAACTGCAATATGCTAACAATGTGAT M 2 1 2 1 101000 r 74 goat snp37933-scaffold47-547355 NW_017190073.1 274994 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405985 Affx-122955522 AX-123276337 X 56062684 GAGATCATATAACTTGAGTGACAAGAGAGGAGAGC[A/G]CAGCTGGGACACATAGGTCATCTACAAAAGGCAAC R 2 1 2 1 101000 f 74 goat snp37931-scaffold47-379039 NW_017190073.1 446249 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413517 Affx-122950628 AX-123283866 X 56120973 GATGCAGGTGATTCACAGGACCACATTTTGTGAAA[C/T]GCAGCAATTATATTGAGGTGAGGGATTCCCTCTTG Y 2 1 2 1 101000 r 74 goat snp37930-scaffold47-320750 NW_017190073.1 504570 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384403 Affx-122972204 AX-123254761 X 56175855 ATGTCTGGGGAACTGTGAGAAAAATAAAAATAGAG[C/T]AACTAGCCTGCAATTAGTGGAGGCTAACAGCTAGG Y 2 1 2 1 103000 r 74 goat snp37929-scaffold47-265868 NW_017190073.1 560906 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442090 Affx-122928364 AX-123312427 X 56230208 ACAGAGAGTGTGGGCAAAGCTTCAGTCAGAACTCC[C/T]ATCTCATCACACACCAGAGGACACACGCAGGAGAG Y 2 1 2 1 101000 f 74 goat snp37928-scaffold47-211515 NW_017190073.1 615408 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396137 Affx-122963396 AX-123266492 X 56295867 CTATCCAATCATCAATCGATCATTTCCCTTGGTGC[A/G]TTGTGGCAAATTATAGACATCAGTATGTGTCTCCT R 2 1 2 1 101000 f 74 goat snp37927-scaffold47-145856 NW_017189740.1 16917 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412103 Affx-122951116 AX-123282453 X 56335337 TGAGGCATAGTATGAATGACTTCAGGAGAAAGAGA[G/T]GAAGTTGACAGGAGGAGAGAAGACAATGATTATGG K 2 1 2 1 201000 f 74 goat snp37926-scaffold47-106386 NW_017189556.1 27296 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378492 Affx-122976660 AX-123248851 X 56364843 CAGCAGAGAGGTCTACAGATATAGCAGGCTCTAGA[C/T]GCAGAGCTCCAGTTTCACTTCTTTGTGATTCCCTT Y 2 1 2 1 101000 r 74 goat snp37925-scaffold47-76880 NW_017189556.1 56371 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801123 Affx-122953221 AX-385288037 X 56426542 TTTCTTGGCAGCAAATATTGGAGTTGCTTCTACAG[C/T]ATCAGTTTTACCCTTTCCAAATTGTATATCATGCA Y 2 1 2 1 102000 f 74 goat snp37924-scaffold47-15181 NW_017189627.1 10929 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422904 Affx-122943055 AX-123293250 X 56458172 CACTTTCTTCGGGCTGGACACTGTTCTAAGTTGTG[A/G]AGATACAGCTGCGAATGAGAGACAAAGTCTTCACC R 2 1 2 1 101000 r 74 goat snp3285-scaffold110-870159 NW_017207382.1 9787 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448620 Affx-122923377 AX-123318956 X 56495142 GGGAGCCAGCAGAAAGAGAGTAAAAGGAGGATGGG[A/G]GGAAGGAAGAAGGAGGGTGGGAAGGGTAAAGATAA R 2 1 2 1 303000 r 74 goat snp3284-scaffold110-833189 NW_017189517.1 25637768 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784977 Affx-122939656 AX-385272024 X 56530704 TATGCTACATAACAAATCACCTTAAAAGTTAGTGG[C/T]TTAAAACAGTAACTATCATGTACTTTTGCTTGTGA Y 2 1 2 1 101000 f 74 goat snp3283-scaffold110-797627 NW_017189517.1 25674339 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422897 Affx-122943060 AX-123293243 X 56637664 TTTCAATAATTTCCTTTCCATAGATATCACCAAGA[G/T]GTTACCACATTTAATATCTTTTGTCTATAAGTTCA K 2 1 2 1 101000 r 74 goat snp3282-scaffold110-690667 NW_017189517.1 25783401 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794577 Affx-122966322 AX-385281539 X 56693350 AAGGATCAAACAGACGAGCAGCAATGGCCAGAATC[C/T]CACCCGATAATCTGGCAGAGTGAAGAAAGGAGGCG Y 2 1 2 1 201000 r 74 goat snp3281-scaffold110-634981 NW_017189517.1 25839158 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389676 Affx-122968710 AX-123260034 X 56753292 AGAGAAGACTCATGTATCAGTTCATTTTAACAATT[C/T]GTGACAAAAGTCATACAGCCTTTTGTACAGTGAAT Y 2 1 2 1 201000 f 74 goat snp3280-scaffold110-575039 NW_017189517.1 25899407 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408371 Affx-122953728 AX-123278722 X 56802302 GCTTTACTTTCATGACTCATAATTCTGCAGTAGCA[C/T]GTGTAATGCTCTTTGTGCACATATTTTGGTGATAG Y 2 1 2 1 101000 f 74 goat snp3279-scaffold110-526029 NW_017189517.1 25948647 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795562 Affx-122961937 AX-385282517 X 56838063 TTTATAACAAATGATGTTGCAACAACTGGATATTC[A/G]CAGGCAAAAGAATCTAAGAGAAGTTAGATTCTACT R 2 1 2 1 101000 r 74 goat snp3278-scaffold110-490268 NW_017189517.1 25984817 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776184 Affx-122975847 AX-385263312 X 56984032 TTGAGGTTGAATTTAGGTACCATCTGATGTCTTTT[C/T]AGTAAATTTATAGAATTGCATAGCTATTATATTAT Y 2 1 2 1 101000 f 74 goat snp3277-scaffold110-344299 NW_017189517.1 26138970 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415516 Affx-122948680 AX-123285865 X 57037506 CTAATAGGTAGTCTGAGCACATGCTTATAAACCTG[A/G]GTCACAAATTGCAGGGTGGCAAAACTTGGTTTTAT R 2 1 2 1 101000 f 74 goat snp3276-scaffold110-290825 NW_017189517.1 26193582 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411482 Affx-122951792 AX-123281832 X 57084071 TATACAAGAAAGTTAAAAACCTTTTCTTTCATCTT[A/G]CCACTTTGTCAATTCTGCTTCACCTCACATATGTT R 2 1 2 1 101000 r 74 goat snp3275-scaffold110-244260 NW_017189517.1 26239824 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774020 Affx-122938480 AX-385261158 X 57155932 TTCCAATGAGTGAAGATGGTGTTTATAAATGCTGT[A/G]TTTTAATTTTCAAGATTACTATGTTTTTTCACATC R 2 1 2 1 102000 f 74 goat snp3274-scaffold110-172399 NW_017189517.1 26309773 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393084 Affx-122965600 AX-123263441 X 57193185 TTGAGCTTTCATTTGCCATTAAAACTTTAGAAAAG[A/G]GAGATGCTAAACATCTCCAGATGCTTAGATAAACA R 2 1 2 1 101000 f 74 goat snp3273-scaffold110-135146 NW_017189517.1 26348196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424290 Affx-122941979 AX-123294636 X 57239341 TATTGAATCTAAAAAATAGACTTTTTACAAATCCT[A/G]TGTAACTGAGTCAGTACCCCCAGTGCCTACCCACA R 2 1 2 1 201000 f 74 goat snp3272-scaffold110-88990 NW_017189517.1 26394448 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425853 Affx-122940660 AX-123296199 X 57395048 GTTACACACTCTGAATTGAGAACGCTGGAGAGATC[A/G]GCATGTGGCCACACTTAGCAGCAGCAAAATGTTAC R 2 1 2 1 101000 f 74 goat snp43894-scaffold594-59718 NW_017190085.1 81940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444101 Affx-122926828 AX-123314438 X 57440830 TCCACAGGGTCAGAAAGAGTCAAACACGACTTAGC[A/G]ACTGAAGAACAGCAACAAAAATAGACAGGCTAGAT R 2 1 2 1 103000 r 74 goat snp43895-scaffold594-105500 NW_017189543.1 67015 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440068 Affx-122929736 AX-123310405 X 57506223 TGTGAAATGCTGCTGCTTCAACTGAAAAGGGACCA[C/T]GGGGGCCAGACAGAAGCCTGCATGGGGTGTGGGCT Y 2 1 2 1 101000 f 74 goat snp43896-scaffold594-170893 NW_017189680.1 11380 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791908 Affx-122934551 AX-385278898 X 57574257 CTTAAAATTGTAGTCACTTGACAGCAACACTTCAT[A/G]CAATCTTTTATCAGATAAAATCATGAGATTTCTTC R 2 1 2 1 201000 r 74 goat snp43897-scaffold594-238927 NW_017189516.1 4509889 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453130 Affx-122920008 AX-123323463 X 57611491 AGGTGGGCTTGCAGTAGGACACCTGGATCTGGCCT[C/T]ATGGACAGGGTCAGTGTCCAGTCCTCAGCAACACA Y 2 1 2 1 101000 r 74 goat snp43898-scaffold594-276161 NW_017189863.1 201993 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782636 Affx-122955486 AX-385269709 X 57666492 GACTAAGGTGACTGGGAAGACACAAAGCTCTAGAG[A/C]TGTTTTGGAACAGCCTACTCCAGATACCCAGGAGG M 2 1 2 1 202000 f 74 goat snp43899-scaffold594-331162 NW_017189863.1 146593 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419824 Affx-122945825 AX-123290172 X 57721535 CAGTGGGCAGGAACCATACACACACACACACACAC[A/C]CACACACACATATGCAACACAAGCACACATGTGTA M 2 1 2 1 303000 f 74 goat snp43900-scaffold594-386205 NW_017189863.1 91103 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780299 Affx-122926011 AX-385267394 X 57778614 CATAAGTATGATAAAAAGAGATATTCTCCTCTATA[C/T]GTGTGATAAACAGAAAGGTTTACATGAGTTCATTT Y 2 1 2 1 101000 r 74 goat snp43901-scaffold594-443284 NW_017189863.1 33459 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419494 Affx-122945463 AX-123289842 X 57825254 TTTGAAGTGTTTAATAATTGAGACCAAGCTCAGGA[A/G]GAAGAGAGAATCCCAATGTGAGAAAGTATAGGCCA R 2 1 2 1 101000 f 74 goat snp18856-scaffold19-11278295 NW_017189718.1 286052 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775881 Affx-122946612 AX-385263012 X 57861145 AGTTGAAATCTGTTCCATTCAGAATCTTCTGCTGT[A/G]GGTCTCTAACTGTTCAATACGCCCATTTGCACAAA R 2 1 2 1 201000 f 74 goat snp18855-scaffold19-11242404 NW_017189718.1 249463 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390649 Affx-122967142 AX-123261006 X 57918190 TGGCAGCCAGATTATTCACTATCATATTGGCATAC[A/G]TATTGCATTGCACTTAAAATTTGTTTAAATTAATG R 2 1 2 1 101000 f 74 goat snp18854-scaffold19-11185359 NW_017189718.1 191022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430752 Affx-122937498 AX-123301093 X 58006090 GCATTCAGCCCCTGCTCTCTGCTGGTGGCCACAAG[C/T]ATCTGGGCTACTTCTCCACTGGGAGTTGTGATTAG Y 2 1 2 1 303000 f 74 goat snp18853-scaffold19-11097459 NW_017189718.1 88851 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782457 Affx-122965103 AX-385269533 X 58143443 ACTCCAAGTATGTGTGATGACTATTTCATAAACTT[A/G]GATAGTGCATACAGACAGTTCATCTGAATGAATTA R 2 1 2 1 101000 r 74 goat snp18852-scaffold19-10960106 NW_017189729.1 10127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377657 Affx-122977855 AX-123248016 X 58355844 CTTTCAGACAGTTATGTGCTAGTAAATGTTTAATA[A/G]CTGGCTAGGGTTTAGGGTGGGAATGGAGCCCTGAT R 2 1 2 1 201000 f 74 goat snp18849-scaffold19-10747705 NW_017189729.1 223837 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801567 Affx-122958637 AX-385288476 X 58557559 GTATAATTGATTAGATTTTCAAGTGATCTCTATGA[A/C]TATTTTAAGTCAAGGGATACTAAGTTGAAAAGAAT M 2 1 2 1 101000 r 74 goat snp18848-scaffold19-10545990 NW_017189516.1 5667632 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378397 Affx-122976796 AX-123248756 X 58604861 CTGCACCAGAGTCTTGGACATCACCAGATCGTCAA[C/T]ACCAAAATCAGATTGATTATATTCTTTGCAGCCAA Y 2 1 2 1 303000 r 74 goat snp18847-scaffold19-10498688 NW_017189516.1 5620604 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388932 Affx-122968827 AX-123259290 X 58663389 GCTAATTAAATTTCAGAAGATTACAGCATTTCAGT[A/G]TATGAGAAGCTACATTTAGGCCCAAATCATTCCAC R 2 1 2 1 101000 r 74 goat snp18846-scaffold19-10440160 NW_017189516.1 5564389 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449745 Affx-122922458 AX-123320080 X 58813107 CAGACTGTGCTGAATGGATACAAAAACAAGACCCA[C/T]GTATATGCTACCTAAAAGAAACACACTCAGACCCA Y 2 1 2 1 201000 r 74 goat snp18845-scaffold19-10290442 NW_017189516.1 5412609 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393252 Affx-122965466 AX-123263609 X 59012908 TCTAGAAGTTAATAGCTTATGCAATATTGATATAT[A/G]CCATCAGGGAACTCATAGGAACTCCTACTTAAAAG R 2 1 2 1 201000 f 74 goat snp18844-scaffold19-10090641 NW_017189516.1 5210896 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440096 Affx-122929716 AX-123310433 X 59130239 CATCCTTGCACATTCCCTTGGCCTCAGTATGGCTC[A/G]ACAGGACTCCCCATAAAAGGTCTGTCACACTCAGT R 2 1 2 1 101000 r 74 goat snp18843-scaffold19-9973310 NW_017189516.1 5101866 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779430 Affx-122955317 AX-385266533 X 59173703 TAAATCCTACTATGAGGGACTTGCTTTCTACTAAG[G/T]CAGTTCTTAAAGCAAATCCTAGCTAGGACATGGTT K 2 1 2 1 101000 f 74 goat snp18842-scaffold19-9929846 NW_017189516.1 5057655 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789500 Affx-122939738 AX-385276509 X 59261410 GCAATTTGGAATCAGAGTTTCCACTGATGCAAAAT[G/T]AGCAACTTGGGACTTAATTTTAGACATGCATCTTC K 2 1 2 1 201000 r 74 goat snp18841-scaffold19-9842139 NW_017189516.1 4967446 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786749 Affx-122959755 AX-385273780 X 59321971 AAGCAGTTTTACACTGAAGAAAACCTTGAAGGCAA[A/C]ATTAAGGATGGGAAATTATCTAATCAAACTGATGC M 2 1 2 1 101000 f 74 goat snp18840-scaffold19-9781578 NW_017189516.1 4905157 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445830 Affx-122926020 AX-123316167 X 59586185 ATTTGTAATTGTTCTGTTGGTTATGTGATAAAGCA[A/G]TTATTCTAATTAAATTTAAAATAGTACATTGTTTT R 2 1 2 1 103000 f 74 goat snp18837-scaffold19-9517364 NW_017189516.1 4626456 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780212 Affx-122934232 AX-385267308 X 59647324 TGAGACAATTTAGGATCAAATAGTTGATGATAGGA[A/G]TTGGGTTTCAGAAAGGACTATCTGCCATTGAAAGG R 2 1 2 1 101000 r 74 goat snp18836-scaffold19-9456225 29 39535796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434980 Affx-122933834 AX-123305320 X 59696845 ATCCTCCAAGACCAGCAGGTAGGTCAGACTCAGGC[C/T]CCTATGAACTTACTGCTTCTCTCTGCATCCCAGTG Y 2 1 2 1 101000 r 74 goat snp18835-scaffold19-9406704 29 39575688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414026 Affx-122949797 AX-123284375 X 59768645 GAAGTGACTAGTTTTCTTCCTCAACAGTTACATGA[C/T]TCCCAATCAGCTGGTCTGTAAGTATTATAACTTCG Y 2 1 2 1 101000 r 74 goat snp18834-scaffold19-9334904 29 39649335 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385633 Affx-122971176 AX-123255991 X 59933672 TAAAGGCTGCTTTAGCTAGATCCCATAACGGGTCC[A/G]ACGTTTCAAGGTTGGAGGTGGAGGACAAGGGGTTG R 2 1 2 1 102000 f 74 goat snp18833-scaffold19-9169877 15 36549390 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392339 Affx-122966684 AX-123262696 X 60130696 GATAGTGGTATTAGAACTATGTTACTCAGAGTCTA[C/T]ATTCGTTTAATAAGTTATCTAGTTGCAATTCTGCA Y 2 1 2 1 101000 f 74 goat snp18831-scaffold19-8972853 NW_017189663.1 35790 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454020 Affx-122919423 AX-123324353 X 60185800 TACCCCATGGCTTCTGCATCTGTGAAACACTTGCT[A/G]AAGGCAGAAAAATGCCAAATGGCCTCAGATTCTAT R 2 1 2 1 201000 r 74 goat snp18830-scaffold19-8917749 NW_017189663.1 91982 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408969 Affx-122953915 AX-123279320 X 60229034 CCTTTCATTAGAAATAAATCATGATATGGTAATTT[A/C]ACAAGGATATGAGAAGCAGAAGATGAGGACCATTG M 2 1 2 1 102000 r 74 goat snp18829-scaffold19-8874515 NW_017189663.1 135935 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795119 Affx-122933885 AX-385282077 X 60370313 TGCTTTCCATTTTATTATAGCTAACCTAGAATGTA[C/T]AAATTGGCAAGTCATGGTAGCTTTGATTTTCAGTT Y 2 1 2 1 101000 r 74 goat snp18828-scaffold19-8733236 NW_017189663.1 278957 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769569 Affx-122967170 AX-385256739 X 60509756 GACTTCATCCAAAATCCAGTGATCCAAAGATGCAG[G/T]CTATTGACTGGTAAAACTATAGAACTTGTTTGAAG K 2 1 2 1 101000 f 74 goat snp18827-scaffold19-8593793 NW_017190146.1 20043 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453789 Affx-122919581 AX-123324122 X 60596894 TAGTTAATTTCCTATCCTTGCCTTGTGCAGAGGCT[A/G]CTGGGTGTTGGTTGGCAGAGCCTCATCACATGGAG R 2 1 2 1 101000 f 74 goat snp18826-scaffold19-8506655 NW_017190146.1 107573 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414739 Affx-122949724 AX-123285088 X 60743589 TTTCTAGAAATAAGAACAATTTATCTGATGTAATA[A/G]TATGCTCATTATGTCTTGCCCACCCTATCATCCTA R 2 1 2 1 101000 r 74 goat snp18825-scaffold19-8359960 NW_017189974.1 55674 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798800 Affx-122954688 AX-385285731 X 60840287 AATAATGGAGAAACATTTCCAGATAAATATAAAAC[C/T]GAGTCAATTTATTACCACTAAATTTTTTCTGCAAG Y 2 1 2 1 201000 f 74 goat snp18824-scaffold19-8263262 NW_017189516.1 7264122 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405260 Affx-122956871 AX-123275612 X 61021142 TTCCCTTTTGTATAAACTGACTCATCTGAATGGAG[A/G]TCAAACATGTGACCTGTGTCTCAGAACTGTGAGCT R 2 1 2 1 303000 r 74 goat snp18823-scaffold19-8082407 NW_017189641.1 79247 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777554 Affx-122944647 AX-385264673 X 61212084 CCATAGACAGAAGACAGTATATTAGACTAGGCTAG[G/T]ATGCTCAGCTAAGCTACAAAAGAGAGCAAAGATTA K 2 1 2 1 101000 f 74 goat snp18821-scaffold19-7891465 NW_017189641.1 272960 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421960 Affx-122943810 AX-123292307 X 61244786 ATTAATTAAGCTCTGCATTCACAGCATATGGCTGG[G/T]GTTCAATAAACGTGCTGGATGGACAAACAACATTT K 2 1 2 1 101000 r 74 goat snp18820-scaffold19-7858763 NW_017189641.1 306093 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375569 Affx-122978747 AX-123245928 X 61394505 TTGTTTCTCTCTTAGTAAGTAAGGGCTTTTTATGC[A/G]CTGTGATGAAATAATGAATTTATATTCTCATAAAT R 2 1 2 1 101000 f 74 goat snp18818-scaffold19-7709044 NW_017189516.1 7139996 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768964 Affx-122958718 AX-385256139 X 61580594 TGAAAAAGAATGTTACCTCTCTATGTAGCGAGCTG[A/G]AAACATGTCCAGTATAAATATAAGTGAAAAAGTCA R 2 1 2 1 101000 f 74 goat snp18816-scaffold19-7522955 NW_017189516.1 5760287 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399388 Affx-122961324 AX-123269743 X 61813536 ATATATAAACAGCCACCTATAAGCCAAAGAGAGAG[G/T]CATGAAACAGAGCTTTCCCTCACTTTCCTCAGGAA K 2 1 2 1 201000 f 74 goat snp18814-scaffold19-7290013 NW_017189516.1 5995975 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782775 Affx-122932687 AX-385269847 X 61902148 TTTTCAAGTTTCCTATTCTCTATAAGAAATTTGAT[G/T]TAACCATCACTTCTAGAATTTGCAGACTGATTTTG K 2 1 2 1 101000 r 74 goat snp18813-scaffold19-7201401 NW_017189516.1 6085215 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380015 Affx-122975598 AX-123250373 X 61975978 ATTTCCCTTATTTCCAATCTAGATTATTTTTAATT[A/C]TTTTTCTTCTCTGATTGCTGTGACTTATACTCTCA M 2 1 2 1 303000 f 74 goat snp18812-scaffold19-7127571 NW_017189516.1 6162208 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797650 Affx-122971510 AX-385284588 X 62233031 ATTTCACAGCTAAATTGACTAGAACTTAACAGTGA[A/G]TCTACCTAATTCTCAACCAATAAGATGTCTTCCTT R 2 1 2 1 101000 r 74 goat snp18810-scaffold19-6870518 NW_017189516.1 6421079 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438575 Affx-122931160 AX-123308913 X 62326207 ACCCTCTTACACTTTTGGTGGAAATGCAAACTAGT[A/C]CAGCCACTATGGAGAACACCACCAGGGAAGCCCTT M 2 1 2 1 303000 f 74 goat snp18809-scaffold19-6777342 NW_017189516.1 6516704 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395790 Affx-122963659 AX-123266145 X 62380664 ATCCCATCAGCATAAAAGGGCTTTTTTTCTTTTTC[C/T]CAATCTTGGGGCCATTGTTGAGAAGAAATTACTGA Y 2 1 2 1 103000 f 74 goat snp18808-scaffold19-6722885 NW_017189516.1 6571145 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779530 Affx-122920994 AX-385266633 X 62447737 CTTTGCCTATGCTTTAGTTGCTAAAGCCTCATTTT[A/G]TGGCTAGCTAGTATCTGAGCAAAAGTTTTCTACAG R 2 1 2 1 101000 r 74 goat snp18807-scaffold19-6655812 NW_017189516.1 6638692 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431473 Affx-122936263 AX-123301814 X 62634486 ACGTCTCTTTTTGAAATAAACATGCTAAGACATGT[C/T]TGTTAAAGGTGCTTTACAAAACATATTTTTCCAAA Y 2 1 2 1 101000 r 74 goat snp18806-scaffold19-6469063 NW_017189516.1 6826644 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377010 Affx-122977724 AX-123247369 X 62769436 ATAAATGTATAACAAAAAAGGTCTTAGGGGTTTTA[A/C]ATCATCTTCTGGCCATAAGGCCTGCTGACATTTTA M 2 1 2 1 303000 f 74 goat snp18805-scaffold19-6334113 NW_017189516.1 6964586 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436635 Affx-122932493 AX-123306973 X 62863498 GAGGATGACCCAGAGAGATGTTATGAGGAGGGAGG[G/T]GGGAGGGAGGTTCATGTTTGGGAAGGCATGTAAGA K 2 1 2 1 303000 f 74 goat snp18804-scaffold19-6240051 NW_017189516.1 52406 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401904 Affx-122958834 AX-123272257 X 62917027 AAATCTTGAAATCAAAATGGAATCACAGATAAATA[A/G]CCTGGAGACAAGGATTGAGAAGAGTTTACATTATT R 2 1 2 1 303000 f 74 goat snp18803-scaffold19-6186522 6 92660895 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423954 Affx-122942144 AX-123294300 X 62994687 GTAAAGAAGACATGGGGGAAACCAGTCCAGTGACT[G/T]GCCCATCCTCTATTGTCCAGAAAGGCCTTATATAC K 2 1 2 1 103000 f 74 goat snp18802-scaffold19-6108862 NW_017189516.1 16953927 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446955 Affx-122924668 AX-123317291 X 63087066 TCCTATTAACATTGTTTCAGATTCTCAATATGCTG[C/T]TCCCTCCCCATGTCTCCCTTCCATTGACTCTTAAA Y 2 1 2 1 303000 f 74 goat snp18801-scaffold19-6016483 NW_017189516.1 17862226 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387400 Affx-122970415 AX-123257758 X 63185534 GAAGATATTCCATGCAAAAGGAAATCAAAAGAAGG[A/C]TGGAGTAGCCATATTCATATCAAACAAAATAGATT M 2 1 2 1 303000 r 74 goat snp18800-scaffold19-5918015 NW_017189516.1 17763152 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378688 Affx-122977070 AX-123249047 X 63292598 CTGGGCTGGATGAAGCACAAGCTGGAATCAAGATC[A/G]CCAGGAGAAATATCAATAACCTCAGATATGTAGAT R 2 1 2 1 303000 r 74 goat snp18799-scaffold19-5810951 NW_017189516.1 17655374 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427996 Affx-122939169 AX-123298339 X 63377365 ATCCTTTTCTGGGAAACCTATAATTGGAATATTAA[C/T]GCATTTGATATTGTCCCAGAGGTCTCTGAGACTGC Y 2 1 2 1 303000 f 74 goat snp18798-scaffold19-5726184 NW_017189516.1 17562691 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414054 Affx-122949773 AX-123284403 X 63481006 TGCTCTGATAGCTACTTCCTTAATCCAGTACAACA[C/T]GGGCGGCTGCACAAATTGTAATCGCACAGCAGTTT Y 2 1 2 1 101000 f 74 goat snp18797-scaffold19-5622543 NW_017189516.1 17456649 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452210 Affx-122920809 AX-123322543 X 63524760 TTCGTTCATTAGGAAGAGCCAAAAAGGGGTGATAA[G/T]GTAGGAGAAGTATTTGAGCAATATGTTCCCCAACT K 2 1 2 1 103000 f 74 goat snp18796-scaffold19-5578789 NW_017189516.1 17412065 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771332 Affx-122953601 AX-385258490 X 63581166 TCTCTGCTTTGAACCACTTCAGAGTGCATTGGCTG[G/T]TCCCTTATCAGGAGACTGGCTAAGAAAACAATAAA K 2 1 2 1 101000 f 74 goat snp18795-scaffold19-5522383 NW_017189516.1 17373108 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422339 Affx-122943451 AX-123292685 X 63741157 ATGGGTTTGCAGGAGAACCAGGTCCTATAGATATA[A/G]CTAGCTCTGGATTTTCCATAAGTATTACTTGATAT R 2 1 2 1 201000 r 74 goat snp18793-scaffold19-5362392 NW_017189516.1 17211244 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791030 Affx-122927141 AX-385278025 X 63823543 ACCAGTGGAAGTGGAAAGTCTAATTTACCCTTGTC[A/G]CAAATTGTTATTGATACAGTAGTGGAAGAACTCAG R 2 1 2 1 101000 f 74 goat snp18792-scaffold19-5280006 NW_017189516.1 17134967 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416569 Affx-122947664 AX-123286917 X 63977300 TTTTGTACTTCCTCAGCCAGCCCTCATCTGAAAGC[A/G]TCTTCCCACAGGCCTGGCAGGTGATCTGTTCCTGG R 2 1 2 1 101000 f 74 goat snp18791-scaffold19-5126249 NW_017189617.1 12095 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800649 Affx-122929461 AX-385287568 X 64058920 AGTAACCATGAACTATCCTTTAAATCAACAATATG[C/T]AGATTGGTGAACATAAATCCTAACAATAATTTCTT Y 2 1 2 1 303000 r 74 goat snp18790-scaffold19-5044629 NW_017190150.1 53700 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400203 Affx-122960180 AX-123270558 X 64155236 TTTGTCTGGTTTTGGGTGATGGTGGCCTCATAGAA[C/T]GAGTTTGGAAGTTTACCTTCCTCTGCCATTTTCTG Y 2 1 2 1 103000 f 74 goat snp18789-scaffold19-4948313 NW_017189516.1 554364 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387340 Affx-122970491 AX-123257698 X 64340842 TATTTTAATTGGAGGCTAATTACTTTACAATATTG[C/T]AGTGGTTTCTGGTGAAGGCATTTTTGGGTGAACCT Y 2 1 2 1 303000 f 74 goat snp18787-scaffold19-4762707 NW_017189516.1 366256 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406571 Affx-122955095 AX-123276923 X 64453594 GGAAGTGACCCCACACTGCCCACATCAGAGAAGGG[C/T]CAGATATATCTTTACTATTTTTGCAATCATTCCTT Y 2 1 2 1 303000 r 74 goat snp18786-scaffold19-4649955 NW_017189516.1 251385 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431927 Affx-122935988 AX-123302268 X 64513983 GTTTCCTAGTATTTACTAATTGGCTATTGGCTGCA[G/T]GGGGATGTCTTTTACATCCTGAAAAACTCAAACCA K 2 1 2 1 303000 f 74 goat snp18785-scaffold19-4589566 NW_017189516.1 184533 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439444 Affx-122930185 AX-123309781 X 64678140 ATTGTTTTCCATAAAATATTTTTGAATTGTCATTT[G/T]CCATTATTGTTTCAGCCTCTTAACCTGGTTTTTGC K 2 1 2 1 101000 r 74 goat snp18784-scaffold19-4425409 NW_017189516.1 750831 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381342 Affx-122974420 AX-123251700 X 64893172 ATACAAGCAGCTCAAAGTTACTCCAAAACCATTGA[C/T]GTCTCATAACACATTACTGGTCACTCCACTGCACT Y 2 1 2 1 103000 r 74 goat snp18782-scaffold19-4210377 NW_017212088.1 14466 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411135 Affx-122951893 AX-123281485 X 64964478 GATGTGTTACAATACAGAAAGTGAAAAGTGAAGCC[A/G]CTCAAGTTTTGTCTGACTCTTTGCAATCCCATGGA R 2 1 2 1 103000 r 74 goat snp18781-scaffold19-4139071 NW_017189516.1 1032717 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402919 Affx-122958194 AX-123273272 X 65191738 GCGTTCATGAGCTGGCATGCTTTGCAGTTTGATAC[A/G]ATGTCTCCTATTATCGTCCTGACATCTTTCATGGT R 2 1 2 1 102000 f 74 goat snp18779-scaffold19-3911811 NW_017189516.1 1263364 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773769 Affx-122934634 AX-385260909 X 65452803 AGTATAATTAACACCAGATTAAGTTTCCTGCCATT[A/G]TAGTTTACTGCTGAGACTGATGAGTTTTTGCTGTT R 2 1 2 1 101000 r 74 goat snp18777-scaffold19-3650746 NW_017189516.1 1527343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377836 Affx-122977294 AX-123248195 X 65544190 TTCTTTTGTATAAACCTGAATTATGCTATAAGGAC[C/T]TGATGATCTGGGCCACAGTCAGTCCAAGTCTTGTT Y 2 1 2 1 201000 f 74 goat snp18776-scaffold19-3559359 NW_017189516.1 1620822 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375974 Affx-122978433 AX-123246333 X 65611702 AGTAGTTTTGATGTTAGCAACACTAGACTTTTGAG[C/T]TAATTAATTTTCTCTTTGTTATAAATCACTGTACT Y 2 1 2 1 103000 f 74 goat snp18775-scaffold19-3491847 22 16348809 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450270 Affx-122922177 AX-123320605 X 65679244 GATTCAAGCATTAGAGAGAGCTAAAGGAAAAAGAA[C/T]AACTATTTTTACTGACAGTCGCTATGCTTTTGGCA Y 2 1 2 1 303000 f 74 goat snp18774-scaffold19-3424305 27 15133048 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767734 Affx-122923478 AX-385254966 X 65812658 ATCTACTCTTAACCTTTGTAGTCAGCAAGTGGAAA[G/T]AAATGTTCAGAATCCAGTAGGAAAAAGTGAGTGCT K 2 1 2 1 101000 f 74 goat snp18773-scaffold19-3290891 NW_017189516.1 2491604 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797855 Affx-122964932 AX-385284794 X 65945593 TTATTTCTTCCAAAGTACCTGGAAGATATATATCT[C/T]CCATATACTTTGTGCTTATATAGATTAGCACAGAA Y 2 1 2 1 201000 f 74 goat snp18772-scaffold19-3157956 NW_017189516.1 2350848 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379868 Affx-122975790 AX-123250226 X 66147987 GCCAGTCCCATTCCTGCTGTTTCAGCCCAGGCCTG[A/G]GGGTATCTCCAAACCCATGGCTGTACTTTAGGACT R 2 1 2 1 303000 f 74 goat snp18771-scaffold19-2955562 24 12946666 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391910 Affx-122966948 AX-123262267 X 66240028 CTATACAAAAAAGATTTTAATGACCCAGATGATCA[C/T]GATGGTGTGATCATTCACCTAGAGCCATACATCCA Y 2 1 2 1 303000 f 74 goat snp18770-scaffold19-2863521 1 66975297 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419198 Affx-122945707 AX-123289546 X 66328339 CATTCCCCTGGTTGATTTTCAGTTTATTTCTTTAC[G/T]GGAAACCACTGCCTAGCCATTAAGAGGGCATGTTT K 2 1 2 1 101000 r 74 goat snp18769-scaffold19-2775210 NW_017189516.1 2110966 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397169 Affx-122962423 AX-123267524 X 66489498 TAATTCCAAGAACAAAATAATGTTTTGATATTTAT[A/G]TATATTTTGAAATGAGCAGCACACTAAGTATAGCT R 2 1 2 1 103000 r 74 goat snp18767-scaffold19-2614051 NW_017189516.1 1946480 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393771 Affx-122965200 AX-123264126 X 66621241 GGATGACCTCACTGGGCAATGACTCAGCCTTTCCC[A/G]TGAGTCCTACCTTAGTCCCTGAAGCCTATCATGGC R 2 1 2 1 303000 f 74 goat snp18766-scaffold19-2482308 NW_017189516.1 2559070 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410414 Affx-122952417 AX-123280764 X 66740363 GCAGATTCTTAATCTCCTTTCCTCATCTCTCTATC[A/G]TTTCTTTTCCATCCTCTCTGTCTTCATTACATACT R 2 1 2 1 201000 r 74 goat snp18765-scaffold19-2363186 NW_017189516.1 2711063 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375602 Affx-122978721 AX-123245961 X 66854648 GAGTATTCCTCTTCCGATCTAAGTTGGATCCAAGA[A/G]AATACCAACTGTCCGGAGGGCAAAGACGGATGGTA R 2 1 2 1 202000 f 74 goat snp18764-scaffold19-2248901 NW_017189516.1 2816908 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418429 Affx-122946527 AX-123288777 X 66917390 GAAGAGTTACCCCATTTCAGTTTGAGGCTCTGGTG[C/T]CCATAGACCACACAGTCAAGTCGTGGAGGCTCAGG Y 2 1 2 1 101000 f 74 goat snp18763-scaffold19-2186159 NW_017189516.1 3477261 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385149 Affx-122971757 AX-123255507 X 67095078 GTCAAGTTTATTTTCATTTTCCTATTATTACCTTC[A/G]TTAGTAACCCCTACATCACTCTGAGATTTTCACAG R 2 1 2 1 101000 r 74 goat snp18762-scaffold19-2008471 NW_017189516.1 3298506 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777349 Affx-122951286 AX-385264471 X 67141258 GAAACCTGTTCATATAGACTTAGAGGGATCATTGC[A/G]TTTCGCCTTCATGTCATACCAGTCCTGGGTGGACA R 2 1 2 1 101000 f 74 goat snp18761-scaffold19-1962291 NW_017189516.1 3250817 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441017 Affx-122928949 AX-123311354 X 67363737 GTGTTTATCAAAATAGAATTAAACACCAATCAAAG[A/C]ATTTAGAAATACAAGAAAAAGATACATAACATGGA M 2 1 2 1 101000 f 74 goat snp18759-scaffold19-1739812 NW_017189516.1 3061904 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769380 Affx-122934921 AX-385256551 X 67474291 GTAAATAACATTTTTGGCTCTTATATTTCAATTTA[A/C]TGCATAAATTCTTCCAATCAAATGAAAACATACAA M 2 1 2 1 101000 f 74 goat snp18758-scaffold19-1629258 NW_017189516.1 2950531 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787681 Affx-122963570 AX-385274704 X 67629405 AAGTATACTTATTTCTGGAAGTTGTTTAAAATCAG[C/T]AAATGTGGTAAGAAAAGTCTGGCAAAAATTCCTTT Y 2 1 2 1 101000 r 74 goat snp18757-scaffold19-1474144 NW_017189516.1 10072437 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451213 Affx-122921969 AX-123321547 X 67756825 TTCATTTTTTTAAGAAGCAGTCCATGTAACTCTGA[C/T]GCAAATGGTTTGTGGATCACACTTGGAGAATTACA Y 2 1 2 1 101000 f 74 goat snp18755-scaffold19-1346724 NW_017189516.1 3537692 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436594 Affx-122932522 AX-123306932 X 68200673 TCACAGATTGAGAAACTGAAGTAAGTAAAATTAAA[C/T]AATACTCAAGGTCACTCATTTATTAAATAGCAGAA Y 2 1 2 1 201000 f 74 goat snp18752-scaffold19-902876 NW_017189516.1 3970936 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380067 Affx-122975559 AX-123250425 X 68259238 TTGGTTCATGAGGATGTGTGATACAGATTCTATTC[A/G]TTGGTGTGGTAGTTCAGAAAGATACCTTGGAAAGC R 2 1 2 1 201000 f 74 goat snp18751-scaffold19-844311 NW_017189516.1 4030283 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404135 Affx-122957095 AX-123274487 X 68362966 ATGTGCTGTAATTCAGGTATACTTAGGAAGAACTG[A/G]GTTTTTGTTAAGTCAAGAAGATGGAGAGAGCTCAC R 2 1 2 1 101000 f 74 goat snp18750-scaffold19-740583 NW_017189516.1 7329174 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801006 Affx-122978753 AX-385287920 X 68397728 ATTTTGAGGACAATTAGTACATTGATGATTTCTTG[C/T]CCTTGCACTGAGTACCCAGACAGAATAGTATTTAT Y 2 1 2 1 101000 r 74 goat snp18749-scaffold19-705821 NW_017189516.1 7363828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401151 Affx-122959371 AX-123271504 X 68490675 TGTATAAATATAGAGGGCTGGGGTGGGGTGGGAGA[C/T]GGGAAGGAGGTTCAAAAGAGAGGGGATATATGTAT Y 2 1 2 1 303000 f 74 goat snp18748-scaffold19-612874 NW_017189516.1 7458319 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436189 Affx-122932603 AX-123306528 X 68592025 ATACCAAAATTAAGGTTAAACGTAAATGGGATAAA[C/T]GCTCCAACCAAAAGATACAGATTGAATGAATGGAT Y 2 1 2 1 303000 f 74 goat snp18747-scaffold19-511524 NW_017189516.1 7561167 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771722 Affx-122956660 AX-385258879 X 68684225 CAATCTGCCATGGTGACTTATTTTGAAGATCAGAA[C/T]GGTTCCCAACACTGAACTCTGTAAACTTCATTGGA Y 2 1 2 1 101000 r 74 goat snp18746-scaffold19-419324 NW_017189516.1 7651630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784318 Affx-122977290 AX-385271369 X 68763153 ACATCATTTATAAAAAACGGGCATCTTCAAATGAA[A/G]CTTTATCTAGGAGTATCTTATGTTAGATTACTAAA R 2 1 2 1 101000 r 74 goat snp18745-scaffold19-340396 NW_017189516.1 4163803 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775909 Affx-122946953 AX-385263040 X 68801208 TTCCTGATGATGCTACTTCTCCACTGCAGGAAAAC[C/T]GCAACAACCAGGGCACTGTAAATTGGTCTGTTGAT Y 2 1 2 1 201000 r 74 goat snp18744-scaffold19-302341 NW_017189516.1 4125450 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400183 Affx-122960669 AX-123270538 X 68892664 TCCAGTTGAAGGGAATTCCATGTGAAGGAAATGGC[A/G]TGTTTAACAGCAAGAAGGCATGAGAAAACATCTCC R 2 1 2 1 101000 f 74 goat snp18743-scaffold19-210885 NW_017207722.1 3203 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775356 Affx-122927910 AX-385262487 X 68941243 TATACAACTGTAACAATTCAAAGCAGGGATTCAGG[C/T]ATTTGTACATCCATTTTTATAGCATTATTACTCAC Y 2 1 2 1 101000 f 74 goat snp18742-scaffold19-162306 NW_017189516.1 7714203 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423619 Affx-122942374 AX-123293965 X 68990086 ATTATACAGGGCAGTTTTTATATTATAGTTATTTT[A/G]TCCAAGGTTCAGTATACTATTTTTCTAGTCTCTTT R 2 1 2 1 101000 r 74 goat snp18741-scaffold19-113463 NW_017189516.1 7760186 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794812 Affx-122965418 AX-385281772 X 69039294 CTGGTCATTAAAAGTATGACAGCTTAATGTTAAGT[A/G]AAAGCACTGTAATTTGCTACCATTTTGCCCATATT R 2 1 2 1 101000 r 74 goat snp18740-scaffold19-64255 NW_017189516.1 7809738 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767320 Affx-122931168 AX-385254598 X 69129730 GAAACTGGGTGTTCACTATAAGGGGACTCTCTGCT[A/C]TCATCAAAATTATTCTGTAGCTCTAAAGCTGTTGT M 2 1 2 1 101000 f 74 goat snp7762-scaffold1279-990185 NW_017189516.1 7900996 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404375 Affx-122956804 AX-123274727 X 69166323 CAATGGCAGTTTTTTGAGAATAATGTTTCCTAAAG[A/C]AACCAATTTGAAAGGAGAAATAGTATTTACATATG M 2 1 2 1 102000 f 74 goat snp7761-scaffold1279-953592 NW_017189516.1 7936282 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776546 Affx-122969545 AX-385263673 X 69207062 CTGATTTTGTATTCTTGCTAGTTTAGTTTTTAGTA[C/T]TCATTTTCACTTTTGAGTTTGTTCGTTGGTTTGAT Y 2 1 2 1 103000 r 74 goat snp7760-scaffold1279-912853 NW_017189516.1 7977339 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446356 Affx-122925604 AX-123316692 X 69261365 AAGGAAAATGAAATCTAACTACATTTAAATGATGT[A/G]ATCGCAATTGGCCTTTGTATCAAACACAGATAAAG R 2 1 2 1 101000 r 74 goat snp7759-scaffold1279-858550 NW_017189516.1 8031474 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449124 Affx-122923572 AX-123319459 X 69315119 AGAAAAAAAGGTACTTTAAAATGGCAGTTCTTTTC[A/G]GAGAAAGGGATAAACCATGTCCTAGATTAGGCTCC R 2 1 2 1 101000 r 74 goat snp7758-scaffold1279-804796 NW_017189516.1 8085522 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409359 Affx-122954170 AX-123279710 X 69409627 AGCTACATTGTTAGGAAAACAAAGAAATCTAGAAA[G/T]ATAAATCAAAAGCTTAATATACCTCAGCAGGGTAG K 2 1 2 1 102000 r 74 goat snp7757-scaffold1279-710288 NW_017189516.1 8180324 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384696 Affx-122972115 AX-123255054 X 69487646 CTGCTCTGTCGCTACGCTGCTTCATGACCCTGGGC[A/G]GGCTCCTTCCTCCCTGGGGCTCTCAGCTTCCTCAT R 2 1 2 1 303000 f 74 goat snp7756-scaffold1279-632269 NW_017189516.1 8471645 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383444 Affx-122973465 AX-123253802 X 69555031 GGGCCTTGACTTCTCCCCTTAAGTGATAAGAAAGC[C/T]GGGCCTCCCAGAAACTTAGTGGTGCTTAGAACCAA Y 2 1 2 1 201000 r 74 goat snp7755-scaffold1279-564884 NW_017189516.1 8315997 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436473 Affx-122932976 AX-123306811 X 69639343 TTCATCTAGCAACCATTTCTTTGGGATTTTATATA[C/T]AGCATGAGATGAAACACCAGATTTTGCTCTAGCCT Y 2 1 2 1 201000 f 74 goat snp7754-scaffold1279-480572 NW_017189516.1 8403386 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409262 Affx-122953129 AX-123279613 X 69772581 TTATCCAAACACCAAAGAGAAAAACCAAGAACATT[A/G]TGTTATGAAGGCACCATCTCAAACCATCCCTATGA R 2 1 2 1 101000 r 74 goat snp7753-scaffold1279-347334 NW_017189516.1 8540416 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802295 Affx-122975664 AX-385289199 X 69817226 GTGTTCTTACTATAAAACATTTAATCTTGTTATTA[C/T]AAAACTGAAATGACCCTTATTAGCTATAAACCCAG Y 2 1 2 1 101000 r 74 goat snp7752-scaffold1279-302689 NW_017189516.1 8585979 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773021 Affx-122921257 AX-385260165 X 69898218 AATGTCCACTTTTGACATAATTGGAGTTTTTACTT[A/G]CCAGAACCAAAGTTGGCACAATAAGCTCAATTAAT R 2 1 2 1 101000 r 74 goat snp7751-scaffold1279-221697 NW_017189516.1 8667325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783033 Affx-122978302 AX-385270101 X 70080088 AAGGAGGGCATGGGAATCTCAACTAACAGAAGGGA[A/C]AGTAGCTCTAATTGAGGCCATTAACTATTCCAAAT M 2 1 2 1 101000 f 74 goat snp7750-scaffold1279-39827 NW_017189516.1 8846917 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424353 Affx-122941856 AX-123294699 X 70193223 CAAAACTCACTCTTAGTGTCATTCAGAGTGCCCAG[A/G]GGGGATCAGTCATGAGGTGAAGGGTGATGTGAGTG R 2 1 2 1 101000 f 74 goat snp57462-scaffold919-73209 NW_017189516.1 8961146 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381173 Affx-122975207 AX-123251531 X 70334316 CAGTTCAGACTCTGCATGCTCTTGTGGCACTTCTG[C/T]ATGTATTTGCTGACAATGGCCACTACAATGCCACC Y 2 1 2 1 201000 r 74 goat snp57464-scaffold919-214302 NW_017189516.1 9104298 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377071 Affx-122978283 AX-123247430 X 70384355 TGAACAAGTTGATGAAAGAAACATGATGTGTGGTC[C/T]TTTTAGAAGTCAAGGTGGCATTCTGTGAGGGATTG Y 2 1 2 1 101000 f 74 goat snp57465-scaffold919-264341 NW_017189516.1 12069626 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779900 Affx-122955223 AX-385266999 X 70413866 GCTCACATCTGTGCATATATGTACATGATTTAACG[C/T]AGAATATGCTAGTAACAATTGGAAATGATACATAG Y 2 1 2 1 101000 f 74 goat snp57466-scaffold919-293852 NW_017189516.1 9249069 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417895 Affx-122946747 AX-123288243 X 70463837 TGCCAGCAACAACAACAGTCAGAATTACCATGCCT[C/T]GTCGTGGAATTATCCCCAGCAACCCAAGGAAACAC Y 2 1 2 1 101000 f 74 goat snp57467-scaffold919-343823 NW_017202354.1 32568 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431820 Affx-122936103 AX-123302161 X 70491532 GCCAGCAAGTCCAAAATTTGTAGGGTAGGCTGGCA[C/T]GTTGGAGCCCTAGGGAAGAGTTGCAGTTTGAGTTC Y 2 1 2 1 101000 f 74 goat snp37104-scaffold450-1149334 NW_017189516.1 9156255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789675 Affx-122930416 AX-385276683 X 70541572 GGTGATTTCTGTCATTCTATCTTCCAGATTACTTA[C/T]GCATTTTTCTTATCACCTAGTCTGCTGTTCTTACT Y 2 1 2 1 303000 f 74 goat snp37103-scaffold450-1099294 NW_017189572.1 13918 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382539 Affx-122973787 AX-123252897 X 70588127 AGCTGAGAGAAGAAAGGGGATCAAGTACAAATTTA[C/T]TGAGATTATTATATTGACTTTTTTTCCCATTTTGC Y 2 1 2 1 101000 f 74 goat snp37102-scaffold450-1052739 NW_017189572.1 59630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398783 Affx-122961425 AX-123269138 X 70635100 GCGGGCTCCAAATCAACACAGACAGTGACTTCGGC[C/T]GTGAAATTAAAAGATGATTGCTCCTTGGAAGAATA Y 2 1 2 1 101000 f 74 goat snp37101-scaffold450-1005766 NW_017189516.1 9584932 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383067 Affx-122973747 AX-123253425 X 70695944 CCTCTCTCCCTGAATCAGCAAGTTTCAAGTTTCCA[A/C]TGCAAAAAAAAAAAAAAAATTCTGTACAATATAGG M 2 1 2 1 101000 f 74 goat snp37100-scaffold450-944922 NW_017189516.1 9525553 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427646 Affx-122939331 AX-123297989 X 70740095 GCCAGTGCAAGGTTGAGTCCAGATTTGAGTCCAAG[C/T]CAACCTGCCTCCATGGGTCTACTTTTATCCACTAT Y 2 1 2 1 201000 f 74 goat snp37099-scaffold450-900771 NW_017189516.1 9481178 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421281 Affx-122944738 AX-123291628 X 70795080 ACTTATTCCAAGAAGACATTCATTCCTTGCCTCAT[A/G]CAACCTTACCAAGCATGCTGTGTGAGATGGGGAAG R 2 1 2 1 201000 r 74 goat snp37098-scaffold450-845786 NW_017189516.1 9425551 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427678 Affx-122939309 AX-123298021 X 70842413 CAGACTGCCAGGCCTCACTCCAGCCTTTCTGATTT[A/C]GTAGGCCTAGGATAGGAACCAATATTTTACATCTC M 2 1 2 1 201000 r 74 goat snp37097-scaffold450-798453 NW_017189516.1 9377838 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400740 Affx-122959901 AX-123271095 X 70912772 AAGCCCAAACACTTCAGTACAGTACACAAGGTCCT[G/T]AAAGATCTGGCCTCATCTGAGTTCCCAGCCTTACC K 2 1 2 1 101000 f 74 goat snp37096-scaffold450-728094 NW_017189516.1 9306013 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409793 Affx-122952972 AX-123280144 X 70957634 GAATAAATTCTTGTGCTTTAAACAGTCCTGACTTA[C/T]ATTTCAGAGGCCATGTCAGGATCTAAGGAAAATTC Y 2 1 2 1 101000 f 74 goat snp37095-scaffold450-683232 NW_017189538.1 62714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431222 Affx-122937149 AX-123301563 X 70995177 AAAGCCAAGGCAATTAAAAATTGTGGGAACAGAAA[C/T]AAGCTACCCCCAAAAAAGAGTAATAGAAATATGCA Y 2 1 2 1 201000 f 74 goat snp37094-scaffold450-645689 NW_017189538.1 26078 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388153 Affx-122969459 AX-123258511 X 71033588 AAAGTACTTTTGCTTTGTGGGCATTCAGTTGGATT[A/C]TAATACCTAACTGATGAGAAAGTTCCCCTTTGGTG M 2 1 2 1 101000 r 74 goat snp37093-scaffold450-607278 NW_017189599.1 14269 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425953 Affx-122941178 AX-123296299 X 71132409 GGTAGGTTGCTCTCTCCTCAGTGTTCTCAGAGTTC[A/G]GGACTCCTGTTTGTTACAGAGCATGAAGCATGTTG R 2 1 2 1 101000 r 74 goat snp37092-scaffold450-508457 NW_017189516.1 9655315 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770054 Affx-122965183 AX-385257221 X 71227861 GGAAACTGAGGCACAAGGAAGATTTAATAAGTTAC[A/G]CAAGTTTGTATAGCTTGTGAGTGGTAAAGTTGAGT R 2 1 2 1 201000 f 74 goat snp37091-scaffold450-413005 NW_017189516.1 9752107 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791228 Affx-122939420 AX-385278222 X 71282448 GCTCTGGATGTGTTTCCCACAGTTGATCACTACCA[A/G]TCCAAACCAAGGAGTGCCTAAACTGTGCCTGTTCA R 2 1 2 1 101000 f 74 goat snp37090-scaffold450-358418 NW_017189516.1 9807568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396954 Affx-122963175 AX-123267309 X 71320262 AATGTGATTTGGACTTGTTCTAGACTCAGCCCCAG[C/T]AATGAAACCAATGAGGTATGGAAGGTGTTCTATGT Y 2 1 2 1 101000 r 74 goat snp37089-scaffold450-320604 NW_017189516.1 9846398 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377327 Affx-122977676 AX-123247686 X 71384324 TTCAGAATGCAAGCCTAGGCCTTGGGAAACACAGC[G/T]CACGTGCAGTCTGGGTTCCCAGACACTTGAGGTTA K 2 1 2 1 101000 f 74 goat snp37088-scaffold450-256542 NW_017189516.1 9910423 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395880 Affx-122963627 AX-123266235 X 71435824 AGTGAGCATTTCCTCTGTGCCAGGCACTTTTCTAG[A/G]CACTGGGGACAAATCAGCGAGCACATCTTGCTGGA R 2 1 2 1 201000 r 74 goat snp37087-scaffold450-205042 NW_017189516.1 3523762 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453627 Affx-122919748 AX-123323960 X 71467160 TCTTTACCAGTAGCAACACCTGGGTATAATTTCAT[G/T]ATCTTAGGCACCCCTTTCTCATCCCCTTGCTCTTT K 2 1 2 1 101000 f 74 goat snp37086-scaffold450-173706 NW_017189516.1 3492760 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415426 Affx-122948722 AX-123285775 X 71516550 CTATGAATGGGTGCTGGCAAGAAGATGGTAGCCTC[C/T]GGTCTTAGCTTGCCTCTCCTAGGTTTCTCCATCTT Y 2 1 2 1 101000 r 74 goat snp37085-scaffold450-124316 NW_017190142.1 128325 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391802 Affx-122967033 AX-123262159 X 71617305 ATCAGATCAGTGTATCTCCAAAGCCCACATTTGAC[C/T]GTCACCACTATGCTGTGCTGCATAACTTCCCAGGA Y 2 1 2 1 101000 f 74 goat snp37083-scaffold450-23561 NW_017190142.1 26614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446078 Affx-122925815 AX-123316415 X 71651715 CCAACCCTCGTGCTCTGTCCACCTGACCTCATGCC[A/G]TGAGCCGCGGAAGGAAGTCAACGTGAGAATATGGG R 2 1 2 1 102000 f 74 goat snp32938-scaffold3811-16069 NW_017189516.1 10189208 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424159 Affx-122942536 AX-123294505 X 71707560 AGCTTCTTCCCAACCTCCTGACTAATTTGAAACAA[C/T]GAAATCTGTCCCATTTACTGTCAGTTACAGCTAGA Y 2 1 2 1 201000 r 74 goat snp4574-scaffold1147-39315 NW_017189516.1 10241430 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378721 Affx-122977045 AX-123249080 X 71756010 CCCACAGATAGAAGGCCCCAGAACTGGATCAAGAT[A/C]TGTGGGCACTCCAGGAAGACACCTCGAAATGGATT M 2 1 2 1 201000 f 74 goat snp4575-scaffold1147-87765 NW_017189516.1 10289827 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781655 Affx-122963134 AX-385268739 X 71857229 CAATTTCAAAATCTCTTAATTATTGCTTTATAATA[C/T]ATTTTGATATATGAAAGTTCAGATTTCCTCACCTT Y 2 1 2 1 201000 f 74 goat snp4576-scaffold1147-188984 NW_017189516.1 10391706 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438579 Affx-122931158 AX-123308917 X 71933841 AAAACATGAGGAAAGAATAAACAAAACATTTCATG[A/C]TCCCTTCAATTCTAGCAAAGGGAAAAGGAGTCTCC M 2 1 2 1 303000 r 74 goat snp4577-scaffold1147-265596 NW_017189516.1 10468478 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450150 Affx-122922743 AX-123320485 X 71962939 TCCAGGAGAAGAGATAAGTGGCTCACGCTGGCAAT[A/C]TTAAATGCTATCAAGGGAATTTCCCCTTTTTTCTC M 2 1 2 1 101000 r 74 goat snp4578-scaffold1147-294694 NW_017189516.1 10497713 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403142 Affx-122958103 AX-123273495 X 72019893 GACATGAAGCTGAGAGAAAAGAATTACAGGGGTAG[A/G]AACAATCCCAGAAGGTCAGAACACATTATTATGAC R 2 1 2 1 101000 f 74 goat snp4579-scaffold1147-351648 NW_017189557.1 12470 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418483 Affx-122946449 AX-123288831 X 72052693 GGGGCTGGGGCAAATCCCTCTTCACCTGAGGGGCT[A/G]CTAGAGCCTTTGGCTCCAGATTCTCCAATAACTCT R 2 1 2 1 101000 r 74 goat snp4580-scaffold1147-384448 NW_017189557.1 45190 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444141 Affx-122926798 AX-123314478 X 72084627 CTGGGCCTCAGCCTTCAGCCTTCCCTCACCCACTG[A/G]CCATAGGTAGATCCGGTGTGTGGACGAGCTACAGA R 2 1 2 1 101000 r 74 goat snp4581-scaffold1147-416382 NW_017189516.1 10551453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398281 Affx-122962167 AX-123268636 X 72137542 GGTCAGGGTCAGCAGCCAGCACTTGGCTAGTTCTT[A/G]TGCTGTTCCAAGAGCTACTCACCCTCAGAATGATG R 2 1 2 1 101000 r 74 goat snp4582-scaffold1147-469297 NW_017189516.1 10604651 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386613 Affx-122970237 AX-123256971 X 72185101 TTCTCTCTGCCCAGCGTGGATGCACAGAAACTCTA[C/T]ACGTTCCGTGTTCGGAGCCGTTATAACCCACTTTG Y 2 1 2 1 201000 r 74 goat snp4583-scaffold1147-516856 NW_017189516.1 10650436 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392058 Affx-122966390 AX-123262415 X 72282639 AGGGGAAGGAAAACAGTTGGTACCAAAGTCCTCAG[C/T]GAATGTCAGGGGGAGATCTGAAAGTTGACATTTAA Y 2 1 2 1 101000 f 74 goat snp4584-scaffold1147-614394 NW_017189516.1 10749296 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406833 Affx-122955674 AX-123277184 X 72344108 ATTATTTGGAATCTGCAAGGCTCAAGAACTCCCCT[A/G]CCACTCCCAATGTTGGGGGAAGCCACAGTGCTGTG R 2 1 2 1 102000 f 74 goat snp4585-scaffold1147-675863 NW_017189516.1 10811385 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400123 Affx-122960718 AX-123270478 X 72398241 GTTACTGAGGAAAATTATAGAAGTTTTTGTGAGAG[C/T]AAACAAGAATAACAACAACTAAAAAAAACCCCAAA Y 2 1 2 1 101000 f 74 goat snp4586-scaffold1147-729996 NW_017189516.1 10866471 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380779 Affx-122975106 AX-123251137 X 72447935 TTTATTTCCCCTTAGTACTCTAGGAGTGGAATGGC[C/T]GAGTCATGTTAGATGTATGGTTAATATTTTTAAAA Y 2 1 2 1 201000 r 74 goat snp4587-scaffold1147-779690 NW_017189516.1 10916210 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428502 Affx-122938770 AX-123298844 X 72517342 AGTCCATGGGGTCACAAAGAGTCAGACACGACTGA[A/G]CAACTTCACTTTCACTTATGTTATGCCTTCTATTC R 2 1 2 1 303000 r 74 goat snp4588-scaffold1147-849097 NW_017189516.1 10986540 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449897 Affx-122922338 AX-123320232 X 72571997 TGCCTATAAAGAGTAAAATTTCTGAAATTTTTATA[G/T]TAATATTTTACCTACAAAAATTTAACATACAGAAG K 2 1 2 1 103000 r 74 goat snp4589-scaffold1147-903752 NW_017189516.1 11042078 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796157 Affx-122970021 AX-385283108 X 72683070 CACACAGGCAAAAGGATCTCCATGCAGCTCTTTTA[C/T]GCATCTGGTATACCATGTGTGCCCACATGTGAGAG Y 2 1 2 1 101000 f 74 goat snp4590-scaffold1147-1014825 NW_017189516.1 11153365 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450436 Affx-122922968 AX-123320770 X 72729098 CCACGTGGCACAGGTTTGTGCCATTGCTTTGATTC[A/G]AGCCAGGGTGCTAGCAGTTTTGTCCACTATTGCTT R 2 1 2 1 101000 r 74 goat snp4591-scaffold1147-1060853 NW_017189516.1 11199597 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432757 Affx-122935441 AX-123303098 X 72774617 CTCTCTCTTCTATATATGTGACTTCTCTCTTTTTA[C/T]GGTATCCTTCCTATTAAGATTAAACCATGTTCAAG Y 2 1 2 1 101000 r 74 goat snp4592-scaffold1147-1106372 NW_017189516.1 11245120 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428719 Affx-122938459 AX-123299061 X 72925288 GGAAGGGAAGAGTGGGTGAGGTCTTGCCAATCCCT[C/T]TACTTCTTCTGGAGGTGGAGGGATCTTCCTAATGT Y 2 1 2 1 202000 f 74 goat snp4593-scaffold1147-1257043 NW_017189516.1 11409114 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401802 Affx-122959469 AX-123272155 X 72988487 TTTTTTTTTTAAACAAACCCTTGTGTTGAGGGCTG[A/G]CTTTCAATAGATCACAGTGAGGCAGCTGCTCTGCT R 2 1 2 1 102000 r 74 goat snp4594-scaffold1147-1320242 NW_017189516.1 11470766 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397261 Affx-122962352 AX-123267616 X 73029483 TGGTGGCTTCACCCGAGCCGCCCTGGTCACTGCAG[C/T]CCCCCAGCCCCCAACTGAACAGATCTAAGAAGGCT Y 2 1 2 1 303000 f 74 goat snp4595-scaffold1147-1361238 NW_017189516.1 11511359 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387098 Affx-122970677 AX-123257456 X 73075128 CAACACCCCCCAAAGGCACCTAGCAGGTAGGAAGT[A/G]CTCAAGCTGATTTTAAGAACAAGGGGAAAAAGCTT R 2 1 2 1 101000 r 74 goat snp4596-scaffold1147-1406883 NW_017189516.1 11557005 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38435798 Affx-122932851 AX-123306137 X 73132918 TCTTTAGGAATGTATCCCTCTGTTGCTTCATTTAG[C/T]CTAGTTTGCTGTTTTTATTTCTATGTATTCAGTAT Y 2 1 2 1 101000 f 74 goat snp4597-scaffold1147-1464673 NW_017189516.1 11593760 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401979 Affx-122958777 AX-123272332 X 73170954 AGTAGATATAGGATGTCCCTAGGAGAGATGAGGTC[C/T]TTATGAGGGTGATCTTGAGAGGTCCAAATGCCATC Y 2 1 2 1 101000 f 74 goat snp4598-scaffold1147-1502709 NW_017189516.1 11632024 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797252 Affx-122956088 AX-385284191 X 73200269 CTTCCCATTGACAGAGAAACCTCAGTGAATAGTTC[C/T]GTCAGCTATCACTTTTCCTAGAATGCCAAGCAGGC Y 2 1 2 1 101000 f 74 goat snp4599-scaffold1147-1532024 NW_017189516.1 11661251 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387484 Affx-122970346 AX-123257842 X 73253591 CCAGATGGACTCAGAGGTTATCATTCTAAGTGAAG[C/T]AAATCAGGCAGAGAAAGACAAATAAATGGTATAAC Y 2 1 2 1 103000 f 74 goat snp4600-scaffold1147-1585346 NW_017189516.1 11714776 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435017 Affx-122933806 AX-123305357 X 73381994 CTTCATGGTCCTTTGTAACCACAAATTTACTTCTG[C/T]ACTGATTGTCTCTGCCATTAGGCTGTAAGTGAAAT Y 2 1 2 1 101000 f 74 goat snp4602-scaffold1147-1713749 NW_017189516.1 11843230 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419798 Affx-122945847 AX-123290146 X 73448517 TCTAAAGTCACAGCCATTTTCTTTTCTTAGCTTCT[A/G]CAGCTGACTCAAGACATCAGAGCTAGAACACCTTT R 2 1 2 1 201000 r 74 goat snp4603-scaffold1147-1780272 NW_017189516.1 11910282 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393899 Affx-122965111 AX-123264254 X 73511048 TTCTTAACTATTCGATCAATGAGTGAATAAATGAA[C/T]GCATGATGCTTAACCCTTTGGGGAGTCTCCACTCT Y 2 1 2 1 103000 r 74 goat snp4604-scaffold1147-1842803 NW_017189516.1 11973994 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384247 Affx-122972359 AX-123254605 X 73558118 GATAATCCCTGTTGCACAAGGTTATTGTGAGGAGC[A/G]CAAGACACTGTGTGTACATGTTCAGTGCAAATGGA R 2 1 2 1 201000 r 74 goat snp4605-scaffold1147-1889873 NW_017189516.1 12021327 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443838 Affx-122927534 AX-123314175 X 73600301 AAATGATAAAGAAAGAGAAATCCATGCTAAGTAGG[C/T]AACTGGAAGCATCTGCCATGAACCCCAACCACCAA Y 2 1 2 1 201000 r 74 goat snp4606-scaffold1147-1932056 NW_017216339.1 12021 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407308 Affx-122955314 AX-123277659 X 73697668 TACTTAATCTTGCTGCTAACCACCTCTCTGACTTT[A/C]TCTCCCACCACTTCCCTGTCTGTCTACTTTCCTTT M 2 1 2 1 101000 f 74 goat snp4607-scaffold1147-2029423 NW_017189516.1 18615400 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450442 Affx-122922964 AX-123320776 X 73781708 ACCCTTTGCCCCACCCCAGGGCCAGAGACTCAAGA[C/T]GAAGGGAGGCCCAGCTGTGAAAACTCCAGCTCCAC Y 2 1 2 1 101000 r 74 goat snp4608-scaffold1147-2113463 NW_017207892.1 22551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768751 Affx-122937569 AX-385255928 X 73840492 GAGTAGAAAGAGAAGTACTAGACTAAGAATCTTAG[A/G]AATCAGCTGACAGCTCTCAAATTTCTCCAGCCCAG R 2 1 2 1 101000 r 74 goat snp4609-scaffold1147-2172247 NW_017189521.1 10298 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800864 Affx-122923742 AX-385287779 X 73930672 AAAGCATAGTAAAAATAATGATGGTAGGAACACAT[C/T]CAAACAGACTGTAGAGGTGAAGGACTTAAAATTCT Y 2 1 2 1 101000 r 74 goat snp4611-scaffold1147-2262427 NW_017189516.1 12115321 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403565 Affx-122957585 AX-123273918 X 73992398 ATCCTCACACTCCACAGCCTCTCATTTGTGGAACT[A/G]CAGCAAGAGAAGAAGACTGGGCACTTACATGCCTA R 2 1 2 1 201000 f 74 goat snp4612-scaffold1147-2324153 NW_017189516.1 12176464 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380216 Affx-122975484 AX-123250574 X 74049033 TTTGCCTAAAGCCACACAGTCCATGGGGGCAGTCC[A/G]GAAAGGAATACAGGCAGGCTGACTCTTGAGCCCTG R 2 1 2 1 201000 r 74 goat snp4613-scaffold1147-2380788 NW_017191278.1 28611 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433834 Affx-122934451 AX-123304175 X 74097603 TCAGGCAGGATTACTGGCCTAATAATCAGACCTAG[C/T]GCAGGGAGAGAGATGTAGAACAAAGCAACTCAATA Y 2 1 2 1 101000 f 74 goat snp4614-scaffold1147-2429358 NW_017189516.1 12268739 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425218 Affx-122941018 AX-123295564 X 74167799 AAATAAAACCCATCCTCGGTCTCCAGGAATAATGT[C/T]AGCAGCCATCAGCCGTGCATCATTCTCAACATGCC Y 2 1 2 1 101000 f 74 goat snp4615-scaffold1147-2499554 NW_017216067.1 27225 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383037 Affx-122973300 AX-123253395 X 74221251 AGCATCTAGGAGCCCTAGCCACCTCCCTCCTCACC[A/G]CCACCAACTGGGCAGAGGGTCCTAATGAAGGGCCA R 2 1 2 1 303000 r 74 goat snp4616-scaffold1147-2553006 NW_017189516.1 12235251 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445823 Affx-122926025 AX-123316160 X 74275405 AGATAGGCCAGAGGGAATGAGAGGGCACCTCGATA[A/C]AGAATGACGCAAAGAGGAAAGGTTATGGGACAGAG M 2 1 2 1 101000 r 74 goat snp4617-scaffold1147-2607160 NW_017189655.1 40420 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397075 Affx-122962721 AX-123267430 X 74308823 CGCAAACTATGTCCCCAATCAACCATGACCCTGAG[C/T]GCTGTTACCAATTGATTGGGAAGTATCCTTTCCCT Y 2 1 2 1 101000 r 74 goat snp4618-scaffold1147-2640578 NW_017189516.1 12335990 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429754 Affx-122937589 AX-123300095 X 74331968 TGTTAAGTCATCCAATTTCTATAATAACAATTATC[C/T]GTCAACCACATATATGTATTACATTTAATGGTTTG Y 2 1 2 1 101000 r 74 goat snp59929-scaffold997-2516922 NW_017189516.1 12362965 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387792 Affx-122969700 AX-123258150 X 74366150 TCCAGCCTCAGTTCCTCCAGACTGCCCAGGATGCC[A/G]GTGTGCTGACAGTTGAGGAGGTTGGGTTTCTGGCT R 2 1 2 1 101000 r 74 goat snp59928-scaffold997-2482740 NW_017189516.1 12425311 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400782 Affx-122959833 AX-123271137 X 74435762 TGTTCCCAGTTATAAAGTGAAGTGCTTGGTCCAAA[C/T]GGCCTCTAAGGTATCTTACTGCTCTGAATGAAATT Y 2 1 2 1 101000 r 74 goat snp59926-scaffold997-2413128 NW_017189516.1 12459045 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448215 Affx-122924227 AX-123318551 X 74480463 ACCTTAGCAGAACCCGCCCCACCTCACCTTATGGG[A/G]AGTCCTGGAATGTTCTAGCACTGCAGCAAGTGGAT R 2 1 2 1 101000 r 74 goat snp59925-scaffold997-2368427 NW_017189516.1 12504297 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438822 Affx-122930785 AX-123309159 X 74562529 ATAACTTGTTCTTTTTTTTCTGAGTACTAGAGCAG[C/T]ACATTAGCAGCATCTGAGAAACACACAAGAGCAGT Y 2 1 2 1 101000 r 74 goat snp59924-scaffold997-2286361 NW_017189516.1 12585959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398049 Affx-122961755 AX-123268404 X 74592355 TGAGTAGGTCCAAGTTCTCATGGAGTATTTGTGAC[C/T]TTGAGGAAATCACTCTGAACCCCAGTTTTGCCTTT Y 2 1 2 1 101000 f 74 goat snp59923-scaffold997-2256535 NW_017189516.1 12616084 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379417 Affx-122976114 AX-123249775 X 74667639 CACAGAATGCAGGACCCGTTTAGGAAGCTGCAGCC[G/T]CCCTCCCTTTAGAGGACAGATACCTGTTCAGATGA K 2 1 2 1 201000 r 74 goat snp59922-scaffold997-2181251 NW_017189516.1 12693160 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387316 Affx-122970509 AX-123257674 X 74710831 TTGGCATAATAATACCCTGTCAATGCTCTCTACCT[A/G]TACATTAGGAATAAAAATAAAAAATTGTCCAACTG R 2 1 2 1 101000 f 74 goat snp59921-scaffold997-2138059 NW_017189516.1 12736204 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796164 Affx-122955785 AX-385283115 X 74742682 TCCCATGAGGTTTTCATAAAGATTAACTTGAAATA[A/G]AGTAATTATAGCACTTAAGAGCTTAGTGGTAGTAG R 2 1 2 1 101000 r 74 goat snp59920-scaffold997-2106208 NW_017189516.1 12768590 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445705 Affx-122926114 AX-123316042 X 74826604 GGGTAGGGGAGGAAACAGACACCAGAGGACAACAT[A/C]CAAAAAGAGACTATGCCAAAACCTAAGCTAACAAT M 2 1 2 1 201000 f 74 goat snp59919-scaffold997-2022286 NW_017189516.1 12853179 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392473 Affx-122966150 AX-123262830 X 74898198 GAAAGAGATGCAGTCAAGCAATAAATTCCTGGCAT[A/G]TTGTAAAAGGCCTTCATTTAGCCCTACCTTCACAG R 2 1 2 1 101000 f 74 goat snp59918-scaffold997-1950692 NW_017189516.1 12924797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385733 Affx-122971091 AX-123256091 X 74953920 ACTCAGCAGCCCAGAATACTCAGTGAAACCTACAC[C/T]GAAATCTTCTAATACTTCTAGGAAGGTCTCTGAAA Y 2 1 2 1 101000 r 74 goat snp59917-scaffold997-1894970 NW_017189516.1 12981677 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414857 Affx-122949152 AX-123285206 X 75043825 TCCCTCTGTGCACCCAGGAAACCGAGCGACTGGGA[C/T]GGTGATAAGATGCACCGTCCCACCTGCAGAGTGTG Y 2 1 2 1 103000 r 74 goat snp59915-scaffold997-1805065 NW_017189516.1 13071858 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440698 Affx-122929907 AX-123311035 X 75140193 AGCCTTTTGGCTCTGCCATTCAGTGACTCTATGAG[C/T]ATCCTCTCTGGAAAATAATTAGAAAAAAAGACAGT Y 2 1 2 1 103000 f 74 goat snp59914-scaffold997-1708697 NW_017189516.1 13140388 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396404 Affx-122963012 AX-123266759 X 75233659 GTTCTGACTGTTTTTTGTTTTTCTTTTTGGGTATG[A/G]GCCATGCTTTCTTGTTTTATTACATATCATATTTT R 2 1 2 1 201000 r 74 goat snp59913-scaffold997-1615231 NW_017189516.1 13235246 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427508 Affx-122939530 AX-123297851 X 75289274 CTTTCACTTTCTTTCAAAAGCCTTGGTTGGCTATG[C/T]ACAGAAGAACAATGGAGCAGGAACTAGAAGTGTGT Y 2 1 2 1 101000 f 74 goat snp59912-scaffold997-1559616 NW_017189516.1 13291194 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399011 Affx-122960938 AX-123269366 X 75368669 TCACACTTCAACTGACCTAAAGAGATGGGTGAGAT[A/C]AAATGTGGACAAAGTTTCCTAAGTTTAGCATCTTA M 2 1 2 1 101000 f 74 goat snp59911-scaffold997-1480221 NW_017189516.1 13371443 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452329 Affx-122920659 AX-123322662 X 75400944 TTTAAGCTCCCTCTTTCCAACAGAATCTTATTGAA[A/C]AAAGGAATTGTTAAATAATACAAATCTTGACTAAA M 2 1 2 1 101000 f 74 goat snp59910-scaffold997-1447946 NW_017189516.1 13403941 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767799 Affx-122923977 AX-385255023 X 75467030 GCTAAGAAAAAAGTTATCCACAGAGATAAAATATC[C/T]ATAAAATGCAAATTACAGGCCTTATTGAAAGCAAT Y 2 1 2 1 201000 f 74 goat snp59909-scaffold997-1381860 NW_017189516.1 13470768 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776520 Affx-122967229 AX-385263647 X 75529070 TTTAGTGTAGAATTAAGACAGCTTCCATATCAATA[C/T]GGAATGTATAGATTACTGAATAAATGATACTAAGA Y 2 1 2 1 201000 r 74 goat snp59908-scaffold997-1319820 NW_017189516.1 13533094 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797218 Affx-122954743 AX-385284157 X 75572216 AAAGACACTGACACATGGAGGCTAAAGAGTTTGTT[A/G]CAAAACAACCAATGGATTAACGAAGAAATCAAAGA R 2 1 2 1 102000 f 74 goat snp59907-scaffold997-1276674 NW_017189516.1 13577353 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790246 Affx-122951334 AX-385277250 X 75608015 GGAACCACATCACACTCTTCACTTGGATGCTATTA[A/G]ACTTGGTAGACTTCTAGATGCTCTGACCAGGCTTT R 2 1 2 1 101000 f 74 goat snp59906-scaffold997-1240875 NW_017189516.1 13613157 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778398 Affx-122973925 AX-385265513 X 75674085 ACTATGGAAATTCTTCAACAGCAACTTAAATATGC[C/T]CATATGGGGCCATTCCAAAGTTGATGAAACTTGGA Y 2 1 2 1 202000 r 74 goat snp59905-scaffold997-1174805 NW_017189516.1 13681178 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416516 Affx-122947773 AX-123286864 X 75708156 CTGGAATTCTTGCAACTAAGTCATGAAGAAATCAG[C/T]CTTAAATGAAGGTTTGAGCCTGATCTCCTCCCCCA Y 2 1 2 1 101000 f 74 goat snp59904-scaffold997-1140734 NW_017189516.1 13715728 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781016 Affx-122969828 AX-385268103 X 75743345 TATGCACAAAGATTGTTACCTTCCTCTTTTGTTAA[C/T]GCCCCTGTTATAACATTCACCAGTTTGACATTTTC Y 2 1 2 1 201000 r 74 goat snp59903-scaffold997-1105545 NW_017189516.1 13750942 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769617 Affx-122965527 AX-385256787 X 75876011 TTCCCTTCTTGCAAGTCCTCCTTGCACTCAGCTGA[C/T]TATCCACTATTCCTATTATGGCTCATAGTGGCTTC Y 2 1 2 1 202000 f 74 goat snp59902-scaffold997-972879 NW_017189516.1 13884231 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431281 Affx-122937100 AX-123301622 X 75909815 TTTTTATCACCTTTTGCCTTGACTAGTGCAGCAAC[C/T]TCATGCATGCTCTCCTTAGTCCTCTGTGCTGCTCT Y 2 1 2 1 101000 f 74 goat snp59901-scaffold997-939075 NW_017189516.1 13918193 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407487 Affx-122954759 AX-123277838 X 76016570 TTGAAGAGTGTGCTCCACACATACACAGATTATAC[C/T]TCCAATAAACCTACCACATTCTCAAAGTAAAGAAC Y 2 1 2 1 201000 r 74 goat snp59900-scaffold997-832320 NW_017189516.1 14025038 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802258 Affx-122978840 AX-385289162 X 76097018 TAAGGGTATTACTGTAACAATACGGTAGGAGTTTG[C/T]GGTAAATTTGCTGAGACAGTGCTATCTTCCCCATA Y 2 1 2 1 101000 r 74 goat snp59899-scaffold997-751872 NW_017189516.1 14107778 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404433 Affx-122956760 AX-123274785 X 76199389 AAATGATCTGATTAACTGTCTGAAATATTCTGAGT[C/T]GAACTCCACTATGACCCACATAAATCTTCCTCCAG Y 2 1 2 1 101000 f 74 goat snp59898-scaffold997-649501 NW_017189516.1 14210734 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398668 Affx-122961881 AX-123269023 X 76324741 CAGCCCCAGTGGATCCAGGGAATTCAAAGGGTGGA[C/T]GGAGTCGGCAAGGAAAAACATTTATTTATTAATAT Y 2 1 2 1 303000 r 74 goat snp59897-scaffold997-524149 NW_017189516.1 14336962 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377354 Affx-122977656 AX-123247713 X 76412307 GGTTCAAAATGTAAAACTTTCGTGCCCTAAGCAAT[A/G]CCACCAACAAAGTGAAAAGACAGCTTATCAAATGG R 2 1 2 1 201000 f 74 goat snp59896-scaffold997-436583 NW_017189516.1 14426943 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453552 Affx-122919780 AX-123323885 X 76531804 ATGCCTCCAGCTTCCCCCCCCCACTTAAGATTGCT[G/T]TGGCAATTTTGGTCTTTTTGTTTCATACAAATTTG K 2 1 2 1 201000 r 74 goat snp59895-scaffold997-317086 NW_017189516.1 14547945 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403662 Affx-122957513 AX-123274014 X 76642991 TCTTTGTCTCCACTTCAGTTCTAAATGACAATCTT[A/G]CTGTACAGTGTCCTAGGTAATATTTTTTTTTCTTT R 2 1 2 1 101000 f 74 goat snp59894-scaffold997-205899 NW_017189516.1 18234472 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416154 Affx-122948276 AX-123286503 X 76725151 GGAAGGGCCTGGCTTTCAGTTACATGGTGGATCTG[C/T]GTTAGAACCTTGTTTAATTTCCCCATCTTCCTACC Y 2 1 2 1 101000 f 74 goat snp59893-scaffold997-123739 NW_017189516.1 18150388 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801669 Affx-122957195 AX-385288577 X 76849785 GACAAATGCATTTAACATTTGGAACATTCAAACAT[C/T]GTTTCTGAGATTTTTATATAGTAAGTAGGCAGAAG Y 2 1 2 1 101000 r 74 goat snp22032-scaffold217-796 NW_017189516.1 20404723 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411764 Affx-122951494 AX-123282114 X 76930567 GACCGTTTTTTAATCCCTTACTAACTCCACTTTTG[C/T]GAAGCAACAAAATAAACTTCCTCTCGCCTATGCCC Y 2 1 2 1 101000 f 74 goat snp22034-scaffold217-81578 NW_017189918.1 97602 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789767 Affx-122961184 AX-385276775 X 76984432 AATTTTATCCAGTAATTGGGGTGATAATATAGGCT[A/C]GCTAATTGATTTTATATAGAGGTAAAACAAACTTC M 2 1 2 1 101000 f 74 goat snp22035-scaffold217-135443 NW_017189918.1 43233 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384768 Affx-122972020 AX-123255126 X 77039833 CTTTTCCCCCATCCCAACCATCCATCATCCTTCAT[C/T]CAGTTAACTCTGACACTGCCTTCAGATCTCGGCTC Y 2 1 2 1 201000 r 74 goat snp22036-scaffold217-190844 NW_017189516.1 14672458 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382180 Affx-122974019 AX-123252538 X 77079349 AAAGTTTGTGAAGCAAAGATAAAGTTGAAACAAGG[C/T]CAGGACCATCCAAGGGATCTGGTGCAAAGCTGCTT Y 2 1 2 1 201000 f 74 goat snp22037-scaffold217-230360 NW_017189516.1 14712350 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402809 Affx-122958279 AX-123273162 X 77160171 TTTGCTAACTGAAAAAGGAGTCACAACTTGACATT[A/G]TGTGCCTCTGTATGGAAATACTCAAAATTCCTCTT R 2 1 2 1 101000 f 74 goat snp22039-scaffold217-311182 NW_017189516.1 14793906 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445164 Affx-122925548 AX-123315501 X 77191355 GAATGTGATCTCCACATTTTATGCGTTCACCATCT[C/T]AAAGGTCTCTCCCATCATCCCTTTTTATACCTTCA Y 2 1 2 1 101000 f 74 goat snp22040-scaffold217-342366 NW_017189516.1 14825165 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381177 Affx-122975203 AX-123251535 X 77241366 TTGATTTGGGAAAGATTCTGAGTTGGGTAACTGAG[C/T]AATGCAAGAGCCCTTTAATGAAAAATTGAATAAGA Y 2 1 2 1 101000 r 74 goat snp22041-scaffold217-392377 NW_017189516.1 15028847 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451452 Affx-122921154 AX-123321785 X 77270847 ATGACAGATATCCCAGCATCTGCCAGATGATCTCA[C/T]TGTGGTTTGACTTAGTTGCATTTCCCTGAAGATGA Y 2 1 2 1 101000 f 74 goat snp22042-scaffold217-421858 NW_017189516.1 14999240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405113 Affx-122956976 AX-123275465 X 77324243 TGGAACTATCTCATAAAGATTTTAAAGTAGTCACT[A/G]TAAAACTGCTGCAAAAGTAATTACAGGTAACCTAC R 2 1 2 1 101000 r 74 goat snp22043-scaffold217-475254 NW_017189516.1 14945309 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802764 Affx-122948692 AX-385289663 X 77359149 TTTAATTCCTACTCTCCTAAGTTCACCCATAAGGA[A/G]TGAACATACAAAACCTTAGATGCCTCAACCTCAAC R 2 1 2 1 101000 f 74 goat snp22044-scaffold217-510160 NW_017189516.1 14909512 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415317 Affx-122948807 AX-123285666 X 77442399 GAAGGAAGAGCAGAATGGATGAAGCTCTGTGGAGA[A/G]TAAAAAAGAGAACTAAGAAAACAGTAAGATTTCCA R 2 1 2 1 101000 f 74 goat snp22045-scaffold217-593410 NW_017189751.1 12623 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445696 Affx-122926121 AX-123316033 X 77494817 ACGGATCAGACACCCTGACCAAGTTCCCTATATCA[C/T]AGTATGGGAAAATATCATATTGCGCCCCCCTCCTT Y 2 1 2 1 303000 r 74 goat snp22046-scaffold217-645828 NW_017189516.1 15112047 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390971 Affx-122967046 AX-123261328 X 77548168 TTCTGGGGATTGGACACTACTTGGATGCAGGGACA[C/T]AAAGGGAAGACTACATCTTTCCATTATACTAGAGG Y 2 1 2 1 101000 r 74 goat snp22047-scaffold217-699179 NW_017189516.1 15154268 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451389 Affx-122921205 AX-123321722 X 77593114 AATAACTTTCAGGAAAGGTATAAATGAAAAAGTTT[A/C]TGGAATTTTCTGTTGCTTCTAACAGGGGAATCTTG M 2 1 2 1 201000 f 74 goat snp22048-scaffold217-744125 NW_017189516.1 15199478 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415486 Affx-122948702 AX-123285835 X 77632184 GCTTTCTTATTGGAAAGCAGAAATAATTTTGACCT[A/G]GAAGACTGGATTCCCAGAAATGCTTACCTCTAACA R 2 1 2 1 101000 r 74 goat snp26056-scaffold270-1701610 NW_017189516.1 15240451 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781054 Affx-122937986 AX-385268141 X 77673572 CAATGTAGCCTCAAGGAATATGTGTGAAAGGGAGA[C/T]TTAGAACACATACACCTGTATATTATTTGCATTTT Y 2 1 2 1 101000 f 74 goat snp26055-scaffold270-1660222 NW_017189516.1 15282140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778560 Affx-122925008 AX-385265672 X 77743765 AAAGAAGATGAGGCCTTGGAGGAAAGAAAGAGAAC[G/T]CTTTAAATCAGTCAGCCAGGACCAGAAAGCTCTCT K 2 1 2 1 101000 f 74 goat snp26054-scaffold270-1590029 NW_017198834.1 17051 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429612 Affx-122937702 AX-123299953 X 77780904 ATCAAAAAAATTGCACTGCTTAGAACATATGCACT[A/G]CATTCAACATTCTTTTCTAAGATACTTATAACACT R 2 1 2 1 101000 f 74 goat snp26053-scaffold270-1552890 NW_017189516.1 15370298 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794252 Affx-122968550 AX-385281217 X 77815568 CATTCTGAACATCAGATGGACAGATAATCTTCTTT[A/G]CTAATAAAAATCACTGCTAGGACTTCCCTGGTGGT R 2 1 2 1 102000 r 74 goat snp26052-scaffold270-1518226 NW_017189516.1 15405295 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380598 Affx-122975256 AX-123250956 X 77892689 AAAGAGTCAGACACAACCAACTGAGAGACTGAACA[A/G]TGAACAACACTACATGCCAGGTATTATAGGCACTG R 2 1 2 1 102000 r 74 goat snp26051-scaffold270-1441105 NW_017189516.1 15483183 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384142 Affx-122972808 AX-123254500 X 77952086 CTTGTTTTCTTGATTAAATTTGCTAGAGGCTTATC[G/T]ACTTAATTCATCCCCCCATTAAAAAAGCTTACTCC K 2 1 2 1 101000 r 74 goat snp26050-scaffold270-1381708 NW_017189516.1 15543154 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413948 Affx-122950313 AX-123284297 X 78000325 TAAACAATAGTTCTCAAAGTTTGTCTCATATAGCA[G/T]CATCAGCATCACCTGGGAAATTGAAGGAAATAAAA K 2 1 2 1 201000 f 74 goat snp26049-scaffold270-1333469 NW_017189516.1 15593250 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449743 Affx-122922460 AX-123320078 X 78038023 TAGCCTTTTCCACCATAGAAAGCATTTTCTTGGAC[A/G]TTGCAGCCCTTGAGATGACTTTGAGAACTCCTGCT R 2 1 2 1 101000 f 74 goat snp26048-scaffold270-1295771 NW_017189516.1 15679134 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409753 Affx-122953007 AX-123280104 X 78080671 GGAAACAGTATTCAAAACCAGGTAGTGTGGGGTCC[A/C]ACGCCAAGGCTTTAAACTGCCTCCCTAGAGGAGAA M 2 1 2 1 101000 r 74 goat snp26047-scaffold270-1253123 NW_017189516.1 15636400 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768695 Affx-122962203 AX-385255873 X 78111452 TAGAAATTGTTTGTTGCTGCAACAAAAACTAATTA[A/C]TTCAAAGTTGAAGAATATATTGGCTACTTGATCTT M 2 1 2 1 101000 r 74 goat snp26046-scaffold270-1222342 NW_017189516.1 15709985 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799165 Affx-122978616 AX-385286095 X 78229216 TATTTCTAAGACTATAAGGTCTTCATAGTTGTAAT[C/T]GAAGGACCGACTTCTTGATCTTCTGTCATAACTTC Y 2 1 2 1 101000 r 74 goat snp26045-scaffold270-1104578 NW_017189516.1 15828199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377148 Affx-122978224 AX-123247507 X 78304524 TGTAATAAGTATTGAAGGTGTAAAGACACATGTGC[C/T]GTGTGTTGTCTTCAGTCACTCAGTTGTGTCCAGTC Y 2 1 2 1 201000 f 74 goat snp26044-scaffold270-1029270 NW_017189516.1 15904126 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443090 Affx-122928111 AX-123313427 X 78342081 CAAAGTTTGAATATAGATGCTGCTTAGTGTCAAAA[C/T]GGCCCTGTATAAGATGCGTGGGAGGGGGAATCAGT Y 2 1 2 1 101000 f 74 goat snp26043-scaffold270-991713 NW_017189516.1 15941927 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453287 Affx-122920379 AX-123323620 X 78391344 GAAGGCCAGATGGAATAACTGTACTACCCCCCGGA[A/G]GACACTAGATAACCCTAAGGAAGTTCTCCATCATC R 2 1 2 1 101000 r 74 goat snp26042-scaffold270-942450 NW_017189613.1 19626 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395289 Affx-122964075 AX-123265644 X 78436114 TCTTCTTTCTTTTCCTTTCTCTGCTCCCAGCTAAT[A/G]CTGGGTTTTACTTGGCAATGAAGTAGGCAGCAAGC R 2 1 2 1 101000 r 74 goat snp26041-scaffold270-897680 NW_017189516.1 15975511 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390305 Affx-122967719 AX-123260662 X 78489194 CTACAGAGTGGTTCTTCTTTCTGGTTATGTTCCCA[C/T]GGTCATCTAGTTTTTCAATGTGACTTCTGCCTTGT Y 2 1 2 1 201000 r 74 goat snp26040-scaffold270-844600 NW_017189516.1 16029278 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446744 Affx-122925337 AX-123317080 X 78549828 GAGTAGATCTTAAATAAATAAAATTGATCACAAAT[A/G]CTGCTGATTATTACCAAACAAGAAAGAGATTTCTA R 2 1 2 1 101000 r 74 goat snp26039-scaffold270-783966 NW_017189516.1 16088318 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452537 Affx-122920539 AX-123322870 X 78617281 GGCTGTGAAGAATTTATCATTCTATACCTTTGTTC[G/T]CTGCAAATTTTTTTCAAACTGCTGTAAAACAAGGA K 2 1 2 1 101000 f 74 goat snp26038-scaffold270-716513 NW_017189516.1 16157476 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412647 Affx-122950792 AX-123282996 X 78703458 TCTGCCATAATCCACCTCTTGACTTCCAATGATTT[A/G]CATCCCTCCTACACTCAAAAACATTCACTCCCTCC R 2 1 2 1 101000 f 74 goat snp26036-scaffold270-630336 NW_017189516.1 16243712 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386403 Affx-122970825 AX-123256761 X 78739239 TTTCTAAACAGATTTCCTAAAATTGTGGTGTGCCC[A/G]TTCCCCAAGTCATGAACTGAATTGAATGCTGTGCC R 2 1 2 1 201000 f 74 goat snp26035-scaffold270-594555 NW_017189516.1 16279308 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784891 Affx-122959730 AX-385271938 X 78768752 TCTAGAAACCTGGAATACCTACTGTTAAGATTGAG[C/T]GCTTTTATAGGTTTGTTGAACGTAGTAAATCCCAG Y 2 1 2 1 101000 f 74 goat snp26034-scaffold270-565042 NW_017189516.1 16308885 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404058 Affx-122957155 AX-123274410 X 78857773 AAATATGTGGTCTAAGCTTCCCCCAAAGAAGTTCT[A/G]TGGAGGAAGACTTTTAACAAAAGAACCACTTTCCC R 2 1 2 1 201000 r 74 goat snp26032-scaffold270-476021 NW_017189516.1 16387966 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429604 Affx-122937709 AX-123299945 X 78889832 TTCCCTGCAACATGGCCCTCTTCATAGGCACTTCA[C/T]AACATAGTAGTTCACTTCATCAAGGCCAGCAAAGG Y 2 1 2 1 101000 r 74 goat snp26031-scaffold270-443962 NW_017189516.1 16420008 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408297 Affx-122953781 AX-123278648 X 78927567 GTAGATGGCTGACATCAGGTGGAAGTTGCAGTGAC[A/G]CAGGGTGGTCATGGGCCCCTTCTGTTCCTCCTCAT R 2 1 2 1 101000 f 74 goat snp26030-scaffold270-406227 NW_017189516.1 16457732 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441077 Affx-122928907 AX-123311414 X 78967097 AACTTATAAAGCTCACTGGTCTACCAGCCCAGGGA[C/T]AGCAGGGGAGTGACATGTTGGCCCCCTCCCTGATT Y 2 1 2 1 101000 f 74 goat snp26029-scaffold270-366697 NW_017189516.1 16498090 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386799 Affx-122970911 AX-123257157 X 79037810 GTATTTCAGAACCTCTAACCTTGAACTCAAAGCCC[A/G]CCCCATAGAGCATGATCAAACTTTGGTACTAATGC R 2 1 2 1 101000 f 74 goat snp26028-scaffold270-295984 NW_017189516.1 16568909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437790 Affx-122931691 AX-123308128 X 79100202 GTTTCACTCATTTAACTGATTTGACAAAATGCAAA[C/T]GTGGAAAAATGCCTTTTATTTATTTTTCTTCTTTA Y 2 1 2 1 303000 f 74 goat snp26027-scaffold270-233592 NW_017189516.1 16607110 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432376 Affx-122935861 AX-123302717 X 79166745 ACAAGTGCCCTGGGGTTTCTCAGTTATTGTAGCCC[C/T]ATCCCCTGCCTATTGTTAGGATATGCTGTGGTAGA Y 2 1 2 1 101000 r 74 goat snp26026-scaffold270-167049 NW_017189516.1 16674271 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413849 Affx-122949870 AX-123284198 X 79249661 AGACAGGATGCACTGAGTTGCCACTGATAGTTGGG[C/T]ATGGTTGGAGAAGGGGGTGGGTGTGAGACAGAAAC Y 2 1 2 1 201000 f 74 goat snp26025-scaffold270-84133 NW_017190157.1 30468 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384282 Affx-122972301 AX-123254640 X 79313226 TTAGAACTCTGTCCTACTCTAACCCCTGCTCACTG[C/T]GGGCCCTACCACTGCCTCACTCAAAGCTCCACCCC Y 2 1 2 1 201000 r 74 goat snp26024-scaffold270-20568 NW_017190157.1 94099 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389584 Affx-122968781 AX-123259942 X 79374999 AGATGAATTCCTAAGTCTTTAATCCTTTTTAGTTT[A/G]CTTTTCAAACTAGCAGTCTGATATTTACTTACTTA R 2 1 2 1 102000 r 74 goat snp23648-scaffold2389-573974 NW_017190143.1 40792 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420167 Affx-122945577 AX-123290515 X 79406530 TGAGCCCAGAAGGACAGGGGTCCCATTATACCTTC[C/T]CCTTGAACTTGGAGGTTCCACTGTACCCATTATCT Y 2 1 2 1 101000 r 74 goat snp23647-scaffold2389-542443 NW_017190143.1 71076 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453891 Affx-122919506 AX-123324224 X 79450612 TCAGAATCTTCCTAACGCTTCTGCCTTCCCTTTCT[C/T]CATTTAGCAAACATCTTTCTGATGTTCAAGCTGCT Y 2 1 2 1 101000 f 74 goat snp23646-scaffold2389-498361 NW_017190143.1 115301 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397720 Affx-122962553 AX-123268075 X 79550009 TGATCACAGGCACCTTGCAGGATGTGTCTTTTTTT[C/T]CTGCATCTGAGTTGTGTGATCTTAGGCAAGTTGTC Y 2 1 2 1 303000 f 74 goat snp23645-scaffold2389-398964 NW_017190136.1 60577 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423164 Affx-122942744 AX-123293510 X 79597083 CCCCAACCTCAGATCTACTGCGGTCGTTACATCAA[C/T]GCTCATATGCTCCAACACCATGAAGGTTCGGGACA Y 2 1 2 1 101000 f 74 goat snp23644-scaffold2389-351890 NW_017190136.1 14940 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396664 Affx-122962848 AX-123267019 X 79629217 AAACCTGTCTCTGGACTGCCAAACCCTAGCTCCAC[A/G]CTCTTAACCCCATCGATGCCTCTCAAATCCCATAC R 2 1 2 1 101000 r 74 goat snp23643-scaffold2389-319756 NW_017189516.1 21027616 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790177 Affx-122946825 AX-385277181 X 79663766 TAGGACAAAATAAATACAGGACAGGCCCTGTATAT[A/G]TAGGATGCCTGATAAGCCTGCCCCATACCTTGGCA R 2 1 2 1 101000 f 74 goat snp23642-scaffold2389-285207 NW_017189516.1 20992660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796394 Affx-122929463 AX-385283344 X 79729616 CCCCGAACCTCAGAAATCTGACAACCTGGAACATG[C/T]ACACACCAATGGCACAGAGAACTCATATCCTTGGA Y 2 1 2 1 101000 r 74 goat snp23641-scaffold2389-219357 NW_017189516.1 20921171 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385756 Affx-122971071 AX-123256114 X 79768293 GTGAGTGCAAGTCATTGGGCTTATCATGCTTCTTG[A/G]GGGTTCCTGGGTATTCACTGGATTACTGAGAAGTA R 2 1 2 1 201000 f 74 goat snp23640-scaffold2389-180680 NW_017189852.1 185571 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410696 Affx-122952736 AX-123281046 X 79814586 GCTGCATGCCAGAAAGCTTTCCCTACCAAACTGCC[A/G]TGGAAATGCCCCAGACTCCCTGGAGTAGCTTGGGT R 2 1 2 1 201000 f 74 goat snp23639-scaffold2389-134387 NW_017189852.1 139186 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428181 Affx-122939025 AX-123298524 X 79869901 AATAAGCAGATATAAATTTTTTTTTAATTCCCTCC[A/G]CCTGGTTTCTACCCTAAAGGTAACATATGAATGAC R 2 1 2 1 101000 r 74 goat snp23638-scaffold2389-79072 NW_017189852.1 83843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413323 Affx-122950179 AX-123283672 X 79901440 AGCACTTTATTGACTGTTAGGACCTGAATTGTGTC[A/G]TCCCACAAATTCATAGGGCTTCCCTGGTGGCTCAG R 2 1 2 1 101000 f 74 goat snp23637-scaffold2389-47533 NW_017189852.1 52127 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412922 Affx-122950395 AX-123283271 X 79962748 GATGCTGGAGTGGATACAGAAAAAAACATGATTTT[A/G]CAAGAACAGTAAAAATGGTGAGATTAGGAAGTACA R 2 1 2 1 201000 r 74 goat snp46117-scaffold634-247386 NW_017189516.1 16799863 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391883 Affx-122966969 AX-123262240 X 80005954 AGGTGAAGGAGGTGCTGAGAATGAGTAAAGGGAGG[C/T]AATGTGGAGCAGAGGGTGAGGGCACAGTAGTCATA Y 2 1 2 1 101000 f 74 goat snp46116-scaffold634-204180 NW_017189516.1 16756626 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420998 Affx-122944560 AX-123291345 X 80090991 TTGCTTACCTTTCTTATAATTTCATATAATTGCCA[A/C]ACTGTCTTCCAAAATGGCTTTACATTCCCAACAGC M 2 1 2 1 201000 f 74 goat snp46114-scaffold634-119143 NW_017199031.1 34380 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801139 Affx-122978303 AX-385288053 X 80205807 CAGACGCTTTTTCTCTCCTTCTCTATATGTGCTGA[C/T]GACACCTAGCTCTACCATGAGCTAACCAATATGTT Y 2 1 2 1 101000 f 74 goat snp46112-scaffold634-4327 NW_017204212.1 3011 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375730 Affx-122978625 AX-123246089 X 80246351 ATCAAACCCACGTATCTTGTTCGTCTCCTACCCTG[G/T]CAGTCGGATTCTTTACCACTATTGCTCAGGTAACG K 2 1 2 1 202000 f 74 goat snp58829-scaffold961-36118 NW_017189516.1 30104953 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388469 Affx-122969242 AX-123258827 X 80286534 CTGGGGTCACATGGTTTGCAGCCACCACTCATCCC[G/T]CCTATTGCATTCATGAAGGATTCCTGCAGTCTGCA K 2 1 2 1 101000 r 74 goat snp36790-scaffold446-504273 NW_017189516.1 17987379 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428703 Affx-122938473 AX-123299045 X 80419455 GAGGAGACATATGGCACATCTTAGATGGCGTTCTC[A/G]CTGTGCCTCCAGGAAATTGAGCAGCTGAGACCGGG R 2 1 2 1 101000 f 74 goat snp36789-scaffold446-371352 NW_017189516.1 18283760 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796308 Affx-122928054 AX-385283258 X 80525831 ATGGAAAGACTGAAAGGTAGTTATGTGGTGGAAAG[G/T]TAGTTATGTGGTGGAAAGGTAGTTATGTGATGGAA K 2 1 2 1 201000 r 74 goat snp36788-scaffold446-264976 NW_017189516.1 18392322 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391796 Affx-122967038 AX-123262153 X 80701814 TGGTAGGGAAAGTACACTGCTACATCCACTAGAGA[A/G]TGGAGAACAGTGTGGAACTTCCTTAAAACTATAAA R 2 1 2 1 101000 f 74 goat snp36786-scaffold446-88993 NW_017213149.1 7707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434076 Affx-122934179 AX-123304417 X 80732981 CATCAATGGTAGAATGAGGAGGGCTGAAGGCACCC[A/G]CATCAGTAAGTGACAGAAAAGTCTGACCAATGAAA R 2 1 2 1 101000 r 74 goat snp36785-scaffold446-57826 NW_017189516.1 18736466 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391517 Affx-122966662 AX-123261874 X 80780647 CTGATTTTAAAATGATGATTGTATAGCTGATTCTT[C/T]TTGTTGTACAGCAGTAACTAACACAACATTGTAAA Y 2 1 2 1 202000 f 74 goat snp36784-scaffold446-10160 NW_017189516.1 18784554 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414763 Affx-122949247 AX-123285112 X 80860180 ATACTTTACCCCCCACGTGTTATAAGAATGATGAG[A/G]ATGTTCCTTGGTGGACAGACAAAAGGGGTGTCCCC R 2 1 2 1 303000 f 74 goat snp24699-scaffold2520-69274 NW_017189516.1 19307145 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419419 Affx-122945519 AX-123289767 X 80911078 CGCCTGGACGTTCTCAGGTTCATATCCTGCTGAAA[C/T]CTAGCTTGAAGGATTTTGAGGGTTACCTTGCCAGC Y 2 1 2 1 201000 f 74 goat snp24700-scaffold2520-120172 NW_017189516.1 18826539 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442918 Affx-122927629 AX-123313255 X 80950817 GTTACATACAGACATTTTCTGATGGAAATGCAAGT[A/G]TAAATGATAGGGATAGAGTAGGATATTTAGGGCTT R 2 1 2 1 101000 r 74 goat snp57844-scaffold934-38277 NW_017189516.1 19046025 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395945 Affx-122963576 AX-123266300 X 80981978 AGTCACCATAAACCGGGACACTCAGCATGTTGTCC[C/T]AGCGTTGGAAGAAGCCACACTGTGGGGGCAATCTA Y 2 1 2 1 202000 f 74 goat snp57845-scaffold934-69438 NW_017189516.1 19075711 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445794 Affx-122926045 AX-123316131 X 81011974 TCAGTGATAACACCTGAGATTCTTGCTGGGATCCT[A/G]CAGAGACACAACTCTGTAGTCCCACATATATTAAA R 2 1 2 1 102000 f 74 goat snp57846-scaffold934-99434 NW_017189516.1 19105573 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414706 Affx-122949275 AX-123285055 X 81049865 CTTTCTCCATAAATTCTTTCCCTACAGTGGTGTGC[C/T]CAGTAGTTAACATTAGAGGAAAGAATAGCTGTAAC Y 2 1 2 1 101000 f 74 goat snp57847-scaffold934-137325 NW_017189516.1 19144381 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798614 Affx-122976685 AX-385285547 X 81124214 TTCATGAGGACTCTGTTGGAGGGATGAATGTTCTA[C/T]ACCTTAATTTTGGTGGTGATCACACAAGGGTGTGT Y 2 1 2 1 101000 r 74 goat snp57848-scaffold934-211674 NW_017189516.1 19219664 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407392 Affx-122955256 AX-123277743 X 81159420 CATATTTTTTCCTCCCAGAGGAGTTTGCATTTTTA[C/T]GAGGATTCATTGAAGAAAGCAAAGTTTAACTAAAA Y 2 1 2 1 201000 r 74 goat snp57849-scaffold934-246880 NW_017189516.1 19255378 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443585 Affx-122927327 AX-123313922 X 81189273 ATCTGTTTGATGCACATCATAGAGTGCTGTCAACA[C/T]CATACCTGGAATGGAAGAATCGCCACAGTAAACCA Y 2 1 2 1 101000 f 74 goat snp57850-scaffold934-276733 NW_017189516.1 19285308 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796064 Affx-122951733 AX-385283016 X 81219153 CAAAATAAATAGGCAGATTTCAGTTTCAAACAGAA[C/T]GTTTGCAAAGGAATATTCCTTTACTCTGCATTATT Y 2 1 2 1 101000 r 74 goat snp57851-scaffold934-306613 NW_017189516.1 19315648 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375438 Affx-122979178 AX-123245797 X 81275689 AGAGGCCAATGAGGATAAGAGGTTAATAAAGAAAA[C/T]ACAGCTTTTGTTGCTCTGACTCACCCACCACCTTG Y 2 1 2 1 101000 f 74 goat snp57852-scaffold934-363149 NW_017189516.1 19371659 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379396 Affx-122976132 AX-123249754 X 81343721 CTCCTGGTCTCACCACATACTACACTGAACTCATC[A/G]CATTTCTCCTTCCTAGATGGTCTCCCTGTCCTGGC R 2 1 2 1 101000 r 74 goat snp57853-scaffold934-431181 NW_017189516.1 19443047 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397498 Affx-122962068 AX-123267853 X 81412041 TTTTGCTTTGTATCTCTTCACTGTAATAAATCATA[A/G]GGGATGAGTGGTTATATGCTGAGCTCTGTGAATCT R 2 1 2 1 101000 r 74 goat snp57854-scaffold934-499501 NW_017212961.1 9629 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411119 Affx-122951905 AX-123281469 X 81496973 AGCACCTCCTATGAACTAAGAGCTGAGCTAGAAGA[C/T]AGAGCAGCGAGCAAGACAGAATTCCTTCCTTCAGA Y 2 1 2 1 101000 f 74 goat snp57856-scaffold934-584433 NW_017189516.1 19567991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412244 Affx-122950906 AX-123282593 X 81728333 GATAATTATCAGAGTCTGAGGAGAAGGCACGAAGA[C/T]GCTTTTCAATCTGAGATAGATTGGTGCAGCAGAAT Y 2 1 2 1 101000 r 74 goat snp57859-scaffold934-815793 NW_017189516.1 19802912 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782654 Affx-122946905 AX-385269727 X 81797162 TTTGGAAGACACAATACAACCCATAATAGTTTCCC[A/G]TTATGCAGTCCTCACTATGGGCAAATCCCCATGTT R 2 1 2 1 101000 r 74 goat snp57860-scaffold934-884622 NW_017189516.1 19872073 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794184 Affx-122977539 AX-385281150 X 81848359 CCCATGGAAATAGAGAAATGTGCTATTTATTGTGA[C/T]GGTGAAATCAAGTGTAAAATATCTAAGAATGAACT Y 2 1 2 1 101000 f 74 goat snp57861-scaffold934-935819 NW_017189516.1 19923968 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418772 Affx-122946192 AX-123289120 X 81900453 CTGTTGAAGGCAGGGGTCGAATTGGTAAGAGGAAG[C/T]GTTAGTGCCAGAGACCTAGCCCCTCCCTTCCAGCT Y 2 1 2 1 101000 f 74 goat snp57862-scaffold934-987913 NW_017189516.1 19976702 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376029 Affx-122978394 AX-123246388 X 81944289 GAAGTGACTTAGCAGCAGCAGCAGGGACATTGTCA[A/G]TTAAAACCATAATACAATGCCACTACCCACTCAAG R 2 1 2 1 202000 r 74 goat snp57863-scaffold934-1031749 NW_017189516.1 20020522 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398714 Affx-122961845 AX-123269069 X 81982394 TGAGACTGCCTTATACCAGCGTTATGAGATCAAGA[C/T]GACTAAGGTAACCCTTCAGTTCTTGCCCCAGCAGT Y 2 1 2 1 101000 f 74 goat snp57864-scaffold934-1069854 NW_017189516.1 20058672 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450226 Affx-122922273 AX-123320561 X 82041917 TCCCTTTATGCCTCTCCTGTCCTTTTACATATACA[A/C]TGTCCTTGCTCAGTGTCTGTGTCCCCATAGGGTCC M 2 1 2 1 201000 f 74 goat snp57865-scaffold934-1129377 NW_017189516.1 20118738 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427961 Affx-122939196 AX-123298304 X 82088525 TACATAGTGGAAATACATGTTCCTGATCTTTTATT[A/G]TTATCTAGTCTGCTGAATTCCTGCTAATCAAAATT R 2 1 2 1 201000 r 74 goat snp57866-scaffold934-1175985 NW_017189516.1 20165641 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787228 Affx-122963657 AX-385274254 X 82117330 GTCCAGAGACCATTTAAGGAACAAGCTGGGGAGAC[A/G]TTTCAGCATTTTCCTGGCAATGAGTGACACTCAGG R 2 1 2 1 201000 f 74 goat snp57867-scaffold934-1204790 NW_017189516.1 20195054 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773247 Affx-122928296 AX-385260390 X 82166282 TCCTTCCATTTGCGTAACTCACTTCTAAGCAGTAA[C/T]GTACCTTTAACATTGAGGAGATGCCACCTTCGTGG Y 2 1 2 1 101000 r 74 goat snp57868-scaffold934-1253742 NW_017189516.1 20244302 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381165 Affx-122975214 AX-123251523 X 82217171 TTAGTATTTCTTAATTTGACCTACATTTCACATTG[A/G]CTGCCAAGCTGCCTTGTTGCTAAAGTGTCCTCTCT R 2 1 2 1 201000 f 74 goat snp56867-scaffold900-44077 NW_017189516.1 21112363 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442223 Affx-122928775 AX-123312560 X 82254787 ACATTTTCTTTTCTGGTTTTTCTTCCCTCACACCC[A/G]TGCTATCTTTACTTCATTTCAGCAGTGAGCTCACT R 2 1 2 1 201000 r 74 goat snp56868-scaffold900-81693 NW_017189516.1 21154310 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404277 Affx-122957044 AX-123274629 X 82283793 ATAAGATGATTGCAGGAAGTTTATAGATGGTGGTA[A/G]AAAGAAGAGCATCATAGGCATTCTAGAAAAGTATC R 2 1 2 1 101000 f 74 goat snp56869-scaffold900-110699 NW_017189516.1 21183328 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400080 Affx-122960750 AX-123270435 X 82329187 GTAGTTTTTAGAGTTAGAAAGCAGAGAAGGTAATG[A/G]CAACCCACTCTAGTACTCTTGCCTGGAAAATCCCG R 2 1 2 1 103000 f 74 goat snp56870-scaffold900-156093 NW_017189516.1 21228269 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424338 Affx-122941943 AX-123294684 X 82392168 TTGTGACTTCCTACTATGTTCACTTGTTCTATACA[C/T]AGACAAGTGGTTTTTTGCAGGAGACTGCCTATACA Y 2 1 2 1 201000 f 74 goat snp56871-scaffold900-219074 NW_017189516.1 21316561 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445065 Affx-122926223 AX-123315402 X 82436793 TTCAGTATTATCTCCATGTCAGGATTATAGGAGCT[A/G]AGGTATCCTCTTATTGCATTTCTCACCCACTGTGA R 2 1 2 1 101000 f 74 goat snp56872-scaffold900-263699 NW_017189516.1 21363178 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438096 Affx-122931512 AX-123308434 X 82470411 AAAAACTTTGATTAAAATATTCTCCCTTGGTGTGA[A/G]CACTACTGTATTGTGTGGAGACATGGCAAAAAGGA R 2 1 2 1 101000 f 74 goat snp56873-scaffold900-297317 NW_017189516.1 21397134 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394538 Affx-122964520 AX-123264893 X 82581130 TTGTGTTGCTGCATTGCCCATAGTCCAGCAAAGAC[A/G]GACTGACAAAGCCCAGGGCTCTGGAGTATCATTTC R 2 1 2 1 101000 f 74 goat snp56874-scaffold900-408036 NW_017189516.1 21513245 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443952 Affx-122927014 AX-123314289 X 82614138 AGACAGGTTTTGTCCAAAGGCCACAGCCTATTAAT[A/G]TGGGGTCTGAAGTAGAAACCCAGAGTTTAGGCTGA R 2 1 2 1 201000 f 74 goat snp56875-scaffold900-441044 NW_017189516.1 24168556 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377520 Affx-122977477 AX-123247879 X 82677509 AGGATAACAGCTGATCTTTCTATAGAAACTCTTCA[A/G]GCCAGAAGGGAATGGCAGAGTGTACTTAAAGTGAT R 2 1 2 1 103000 f 74 goat snp56876-scaffold900-504415 NW_017189529.1 33441 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447375 Affx-122924859 AX-123317711 X 82814877 AGGAAAGTGTTTTCATTTAAAAGAATAGTCACTGG[C/T]TGACAGGCACTGTGATAAGCCCCAGGTCTAGAAAG Y 2 1 2 1 101000 r 74 goat snp56877-scaffold900-641783 NW_017189516.1 21778935 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431759 Affx-122936725 AX-123302100 X 82908335 TCATCTGCTGAGTATTTGTCACATTCATCTAAGGA[A/G]GCCTCTTTTCTTCACTGCCTTGGGAAATGGAAAGA R 2 1 2 1 101000 f 74 goat snp56878-scaffold900-735241 NW_017189963.1 26199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422463 Affx-122943335 AX-123292809 X 83168858 GGGGAAAAAACTGTGGGCTGTGTCTAAGCAGAACT[A/G]CAGACACCTACACAGCCAGAGCATCAGACATCTGT R 2 1 2 1 101000 f 74 goat snp56880-scaffold900-995764 NW_017189516.1 32569875 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408811 Affx-122954038 AX-123279162 X 83283010 AGCCCCAATTAGCCGGAGAGTGTGGACTTTGGGGG[C/T]AACTGTGGATTTCAAAGCAAGTATAAGCTGAAGTA Y 2 1 2 1 201000 r 74 goat snp56882-scaffold900-1109916 NW_017189516.1 22209214 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441685 Affx-122929174 AX-123312022 X 83370238 CACAGCAGCCTGAGAATTGGCTCTAGAGAAGCCTG[C/T]GGTTAGACAGCCTCCTGAGAGCAAGAGTGAGGGAA Y 2 1 2 1 101000 f 74 goat snp56883-scaffold900-1197144 NW_017189516.1 22129250 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421634 Affx-122944463 AX-123291981 X 83608636 TTTCCCTTTCTTTCCTTTCAGCCTCTGAATATTAA[C/T]CTGCCTTCTTGCCTCTCTCCCTCTTAGCAAATTCT Y 2 1 2 1 102000 f 74 goat snp55285-scaffold852-149263 NW_017189516.1 22737972 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406616 Affx-122955836 AX-123276968 X 83664523 AGCAGGTATTGGTATTTATTGTACCTGTAAGCAGG[C/T]GAGGTCTAAACAGATCTACTTGCAAATGCTTTCCA Y 2 1 2 1 101000 f 74 goat snp55286-scaffold852-205150 NW_017189516.1 22795159 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387674 Affx-122969829 AX-123258032 X 83704840 GAGGCAGAGAAAAGCAGGCAAAAGATGAAGATGTT[C/T]ATTAGCAGTTCAAATAAATGAATGTGGCCTCCTTT Y 2 1 2 1 101000 f 74 goat snp55287-scaffold852-245467 NW_017189516.1 22835536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430722 Affx-122936896 AX-123301063 X 83774607 AGATCTCTTTTAGCAGGTTTGGGATGCACAGGGTT[A/G]TTTTGGAGGTAGTAGACTTGCCTTCCTAATTATAT R 2 1 2 1 201000 r 74 goat snp55288-scaffold852-315234 NW_017189516.1 22906078 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791605 Affx-122971420 AX-385278596 X 83811280 TAGTCTTGAGGTGCAATCCAAAGGAGTTATATAAC[A/G]TGAGGACAACTGACCAAACCATTCTCTTCCCTTCA R 2 1 2 1 101000 r 74 goat snp55289-scaffold852-351907 NW_017189516.1 56711248 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421793 Affx-122944334 AX-123292140 X 83943848 AAGAGGGACAGTTCAACAAAATCAGGGAAACATTG[C/T]GAACAAAATAAGAAATTTAACAGAGGAAATTATAA Y 2 1 2 1 101000 f 74 goat snp55291-scaffold852-484475 NW_017189516.1 56845034 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802015 Affx-122952531 AX-385288919 X 84045114 ACCTCCCTGCTCAACCTATCTAAATCATTATGACA[A/G]TGGAATTAGTATACTGCTCCCTGATTCTGCTACAT R 2 1 2 1 101000 r 74 goat snp55293-scaffold852-585741 NW_017189516.1 56947018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438511 Affx-122931209 AX-123308849 X 84172607 TCTAGTTTTTAACATTGAATTTTATGTCTGTTAGT[G/T]AGCTGCTAATCGGATAGGAGAAACATCTCATGGCT K 2 1 2 1 101000 r 74 goat snp55295-scaffold852-713234 NW_017189516.1 57077511 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799750 Affx-122946018 AX-385286677 X 84229376 TTGTCAGCACTCAACTTTTCTTCTCCTACTTTGAA[G/T]CACAAATCCACTCAAAGTTCTCATCACCCCATATC K 2 1 2 1 102000 r 74 goat snp55296-scaffold852-770003 NW_017189516.1 57019358 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800168 Affx-122965791 AX-385287091 X 84305957 AATCTGGATGTAACATTACCTCTCCAGATTACTCT[A/G]CATCAAAATGAGTTATTCAGTCTCTGCTGTACATT R 2 1 2 1 101000 f 74 goat snp55297-scaffold852-846584 NW_017189516.1 22610964 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385833 Affx-122971011 AX-123256191 X 84423101 TATGCAGGCTGTAGAGAGTGGTGGCAGGATATACT[C/T]AAAGTAATGAAAAGAAAAAACCTACAACCATGATC Y 2 1 2 1 101000 f 74 goat snp55299-scaffold852-963728 NW_017189516.1 22489733 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433597 Affx-122934957 AX-123303938 X 84448275 CCCATGACCTCAATAGAACAATCCTTTCTCCTGAG[A/C]GCCTTAGAAGGTATGACTTGGAGGTCAACGATGGC M 2 1 2 1 101000 f 74 goat snp35004-scaffold4173-18858 NW_017189516.1 20567937 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451053 Affx-122921435 AX-123321387 X 84495469 AAATCTAGCATTCTATTCATACTTAGTCAAACAAG[C/T]GGAATCAAAATGTCATGATTTCTTTGGCTATGCAA Y 2 1 2 1 103000 r 74 goat snp35005-scaffold4173-66052 NW_017189620.1 36471 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786807 Affx-122977022 AX-385273836 X 84524220 ATGTGCCTTCCTGCCTTAACCCGTGTGTCTACTAA[C/T]ATATCAACTAGAAATATTCCTTGCAGACTTCTTTA Y 2 1 2 1 101000 f 74 goat snp35006-scaffold4173-94803 NW_017189606.1 30551 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378203 Affx-122976934 AX-123248562 X 84554993 GACCTAGACTAACATGATGGCCCACCAGTCAGAGA[C/T]GTATAAGGTCATACATGAAGATTCAGCCTGAGTCC Y 2 1 2 1 101000 r 74 goat snp35007-scaffold4173-125576 NW_017189516.1 20556188 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419905 Affx-122945338 AX-123290253 X 84628767 TCAGCTCTGCTTCCTTTGCAGCCCTAAAAATAATA[A/G]CTGTCATTTACTGAGGACCTACTTTTAGCTAGGCC R 2 1 2 1 101000 f 74 goat snp35008-scaffold4173-199350 NW_017189561.1 43269 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380647 Affx-122975222 AX-123251005 X 84680954 AAAACTCAAGCTTTCTCTTCTATTCCAGCCTGCTC[A/G]CAAAGATGAATGAAGACATGTTTCTGGCTTTAAGG R 2 1 2 1 101000 f 74 goat snp42418-scaffold560-661326 NW_017189516.1 22944120 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386769 Affx-122970118 AX-123257127 X 84714107 AGTTGAGAATCAAAGTGGATCATAGCTTCAGCAAG[C/T]GGCAGTATAAGAGTGATTGGATTGAAAGGGGCCTG Y 2 1 2 1 101000 f 74 goat snp42417-scaffold560-628173 NW_017189516.1 22977240 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770067 Affx-122952704 AX-385257234 X 84781756 CAGAGTAATAGTAGCTACTGGTTATTGTAGCTACT[A/G]TCGTACTGATGCTTGTGCTTTATTACAGCATCTCA R 2 1 2 1 101000 r 74 goat snp42416-scaffold560-560524 NW_017189516.1 23045066 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410841 Affx-122952621 AX-123281191 X 84850632 TTCAACTTTTTAATTTTTCTTAGGATTTCATCTTC[A/G]ACCCATGGTGTGCTGGTTATCAACTTATTGCCACT R 2 1 2 1 101000 r 74 goat snp42415-scaffold560-491648 NW_017189516.1 23114136 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444351 Affx-122926715 AX-123314688 X 84896625 ACTACTTGTGTAGTTATCTCTTTCTCAAAAATGTC[A/G]CTGGAGCTGAGTTGATACGGGAGTCAGTTTGACTA R 2 1 2 1 101000 r 74 goat snp42414-scaffold560-445655 NW_017189516.1 23160733 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786209 Affx-122934964 AX-385273244 X 84967069 GGGCTATTTTTAATTTGCATATCTTGAATAAATGG[C/T]GATATGAAATACCTTTCTAGTCTTTGTGGAAAGGT Y 2 1 2 1 201000 f 74 goat snp42413-scaffold560-375211 NW_017189516.1 23231342 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431667 Affx-122936800 AX-123302008 X 85018789 AGTTCCTACATCATATTTGTTGAGTCAGATTATGT[A/G]TATGGGCAGACATTTTTAGTTTTACTAAATAAGTG R 2 1 2 1 101000 f 74 goat snp42412-scaffold560-323491 NW_017189516.1 23284227 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426918 Affx-122940442 AX-123297263 X 85095754 TCAAGGCATTCAGTCTCCACCAGAGTAAACCAAAA[C/T]ATGTTACTCAAAAAAAGATCAGTGCTTGAGGAAAG Y 2 1 2 1 101000 f 74 goat snp42411-scaffold560-246526 NW_017189516.1 23362022 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434957 Affx-122933850 AX-123305297 X 85133524 GTATAGCTACCCTATGCTCTCTTGATTACTTTTTG[C/T]ATGAAATATCTTTTTCCATTTCTTCACTTTAAGAC Y 2 1 2 1 103000 f 74 goat snp42410-scaffold560-208756 NW_017189516.1 23401634 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431616 Affx-122936155 AX-123301957 X 85193694 ACATGGACTATGTCTCCATTTATCATCTTTGATTT[A/C]TTTTATCAGAGTTTTACAAATTTCTTTATATAGAT M 2 1 2 1 303000 r 74 goat snp42409-scaffold560-148586 NW_017189516.1 23462977 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445531 Affx-122925168 AX-123315868 X 85270803 ATCTTCCCAGACCAGGGATCAAGCTCATGTCTCCT[A/G]CATTGGTAAACAGATTATTACTATTAAGCCTTCAG R 2 1 2 1 303000 r 74 goat snp42408-scaffold560-71477 NW_017189516.1 23541754 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439136 Affx-122931084 AX-123309473 X 85470869 TTTTCTTATGAGAGGAGGTGAACTCTGCGACTGTG[C/T]GCCGCAAACTTAATAGGTGGCAGCGTGGGGGAGAT Y 2 1 2 1 101000 f 74 goat snp12055-scaffold1445-128490 NW_017190160.1 35097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442610 Affx-122928475 AX-123312947 X 85504861 CTCTCTACTTGTCCTGAGCTCTGGGGCCTATAAGC[A/G]CAATGCAACTTCCACCTAGCCCCCAAAGCCTGGGC R 2 1 2 1 303000 r 74 goat snp12056-scaffold1445-162482 NW_017206140.1 2831 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781621 Affx-122946444 AX-385268705 X 85633111 AGTCATTTAACTTCTTCATCTATAAAGCAGAGATT[A/C]TGTTATATTCCTACTTAATTCTAAGACTTTGAAAT M 2 1 2 1 101000 f 74 goat snp12057-scaffold1445-290732 NW_017189516.1 23792584 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787409 Affx-122926986 AX-385274434 X 85715308 AAATGGAATTCTAGGACACCAGAAACAGTGGCAGG[G/T]AATAAGTTTGATCTAAATGTAGCACGTGGACATTT K 2 1 2 1 101000 f 74 goat snp12058-scaffold1445-372929 NW_017189516.1 23876217 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431000 Affx-122936682 AX-123301341 X 85817822 CCATACACAATATGTAAATGAATGGGTGTTGCTGT[A/G]TTCCAACAAAACATTTTTTACAAAAATAGGCAGGG R 2 1 2 1 103000 f 74 goat snp12059-scaffold1445-475443 NW_017189516.1 23981301 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375870 Affx-122978508 AX-123246229 X 85975672 TCTATCTGACATGCTATGGCCCTGGGGTGGCAGCT[C/T]TGGAGTCTCTCCACCCTCTGGAAGGGCCCAGTCTC Y 2 1 2 1 101000 f 74 goat snp12061-scaffold1445-633293 NW_017218564.1 6968 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387891 Affx-122969620 AX-123258249 X 86225880 GGATGGGGAGAGGGAGCTGCCATTTATGGCTTAGC[A/G]TTTAAGAGTGCAGGCTCCAAGGACTCAGTTGCTGC R 2 1 2 1 201000 r 74 goat snp13552-scaffold1524-69558 NW_017189516.1 25737677 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401297 Affx-122959859 AX-123271650 X 86278630 TGCATTAACTTTGAAAACAGTGCTTTGAATGTATG[C/T]ATGTATTCATACATCACCTCATCATGACTGGAATG Y 2 1 2 1 101000 f 74 goat snp22791-scaffold228-5909 21 37502153 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408631 Affx-122953487 AX-123278982 X 86309626 CTGACAAATTGCAAAAAAAAAAAAAAAAAAGCCAA[C/T]CAAACATAAAAAGTCCCACCAACTTCTTCAGGACT Y 2 1 2 1 101000 r 74 goat snp22792-scaffold228-36905 NW_017190162.1 91003 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399998 Affx-122960808 AX-123270353 X 86360164 AATTGTGGATGATGAACAGTATAACAACAATTACA[C/T]AGAGAAAGGCAATGCAGTGTCTAAAAGTGCATGTG Y 2 1 2 1 201000 f 74 goat snp22793-scaffold228-87443 NW_017189516.1 25806490 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391338 Affx-122967306 AX-123261695 X 86399249 CAGAGGACACTGCAGGTTCAGTTCTTCTAGAACCT[A/G]CTATATTCTGACCCACTTCCCTCTAACCAGAGCAT R 2 1 2 1 101000 r 74 goat snp22794-scaffold228-126528 NW_017189516.1 25844864 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803182 Affx-122941004 AX-385290044 X 86435379 TAGGTTGTTTTCTACTTTTGAATGAATTCTCACAT[A/G]CCTAGTTCTGGAGTCAAGAAACCTGGCATACATGA R 2 1 2 1 101000 r 74 goat snp22795-scaffold228-162658 NW_017189516.1 25881721 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443546 Affx-122927763 AX-123313883 X 86476269 CAAATTCCGTGCAGATGCTTTTACTTCATGTGTTC[A/G]TGCAGAGATTTAAATGAAGTAGGGAGGGGGCAAGG R 2 1 2 1 101000 f 74 goat snp22796-scaffold228-203548 NW_017189516.1 25922828 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393277 Affx-122965449 AX-123263633 X 86512053 GGATTTTCCAGGCAAGAGTACTGGAGTGGGGTGCC[A/G]TTGCCTTCTCCGTTACTGCCCCTAAGAGCCCAGAT R 2 1 2 1 103000 r 74 goat snp22797-scaffold228-239332 NW_017189516.1 25959104 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382031 Affx-122974951 AX-123252389 X 86557204 TTTTTTAAAAAACAGGTAGATGAAATCTGGGTTCA[C/T]ATATTGGAGAATCACTCTTCTGCCTGGGGTATAGT Y 2 1 2 1 201000 f 74 goat snp22798-scaffold228-284483 NW_017189516.1 26005183 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779941 Affx-122964724 AX-385267040 X 86600401 TTAACCTAATTTGAATCTTGGTTTTACAATTTGTA[G/T]CTTTGTGACCTTAGGAAAGACACAACCACTCTTGG K 2 1 2 1 101000 r 74 goat snp22799-scaffold228-327680 NW_017189516.1 26049137 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438652 Affx-122930896 AX-123308989 X 86649406 TTCTACTTCTGACCCAGATTTATTTTTCCTCAGAT[C/T]GACAACTGTCATATTACCTGTTTATTTTCCTTTGA Y 2 1 2 1 201000 r 74 goat snp22800-scaffold228-376685 NW_017189562.1 28288 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428310 Affx-122939373 AX-123298653 X 86748114 GCTAGTGAATGGCTTTGGTTTTACAGTTCTGAGTA[C/T]AGTAACTCAATTTGAAGTTGTTAAAGGCACTTTAT Y 2 1 2 1 101000 f 74 goat snp22801-scaffold228-475393 NW_017189516.1 26178572 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399746 Affx-122960325 AX-123270101 X 86799158 ACTTCATTGAATTCTTCTCTAAAGAAATTTTCCCT[A/G]TCAATGCAACCATTTATTAATCTTGTGTGTCCAAT R 2 1 2 1 101000 r 74 goat snp22802-scaffold228-526437 NW_017189516.1 26229801 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431566 Affx-122936193 AX-123301907 X 86845543 ATAAAATAAGGAAAAATAAACTCAGTGCCCCAGTT[A/C]TCCAAATTAGTACTGGACAGTTTGTGGGCCATGAA M 2 1 2 1 101000 r 74 goat snp22803-scaffold228-572822 NW_017189516.1 26276539 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451539 Affx-122921090 AX-123321872 X 86899270 ATAAAATTTCCAGACTAATGCTTTCATGCTCCTTC[A/G]TCTTCAGGGAGGAGGCAAGGGAAAAGATGTTTGAC R 2 1 2 1 201000 f 74 goat snp22804-scaffold228-626549 NW_017189516.1 26330540 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777015 Affx-122963717 AX-385264138 X 86939177 TCTTTAGGCTTATTTTGCCCTTAATGTCTTGAGAT[A/G]CATAATGGCTTTGTAATTTTCAGCTATTCTTATTT R 2 1 2 1 101000 f 74 goat snp22805-scaffold228-666456 NW_017189516.1 26370342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400904 Affx-122959738 AX-123271257 X 87008487 TTTTGTCCTCTTTGAGCCAGTCCTTTCAAGGCTAT[A/G]CTATCCTTCAGTGCTAAGTGCCTCTCCTGGTCTCT R 2 1 2 1 101000 f 74 goat snp22806-scaffold228-735766 NW_017189516.1 26440140 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398497 Affx-122961564 AX-123268852 X 87041013 GGTGACCCAAGCTTTATCTAGTCTGTAGCTCCATG[C/T]GACAGACTGGCTGAATTCTCAAGAATCCAGCCTGA Y 2 1 2 1 102000 r 74 goat snp22807-scaffold228-768292 NW_017189516.1 26490910 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796967 Affx-122929662 AX-385283908 X 87102483 TAGATCCCTAATCATATCTTGGAAATTTCTTGGAG[C/T]ATTTTTTGCCTGAAGATCTCAGATGCTGTTCCCAT Y 2 1 2 1 101000 f 74 goat snp22808-scaffold228-829762 NW_017189516.1 26552619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410272 Affx-122952519 AX-123280622 X 87143236 ATACTCATGCAAAAACCCGAGAGTATTTTAATAAG[C/T]ATCACTTAGAATTCTTTTTTCCTGGACGACAGTGA Y 2 1 2 1 201000 f 74 goat snp22809-scaffold228-870515 NW_017189516.1 26593609 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448265 Affx-122924190 AX-123318601 X 87207718 CAAGGGGGAAGTGCAGCCCTTCATTTCCTTATTTT[A/G]CTATTCATCATGTTATTTTTCTCTCACCTGAATAG R 2 1 2 1 102000 f 74 goat snp22810-scaffold228-934997 NW_017189516.1 26637615 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409555 Affx-122953596 AX-123279906 X 87269567 CATTACATGTGTGTATACACACTACATCCTTATCC[A/G]TTCATCTGTTGATGGATGGACATTTAGGTTGCTTC R 2 1 2 1 103000 f 74 goat snp22811-scaffold228-996846 NW_017189516.1 26700051 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417450 Affx-122947198 AX-123287798 X 87299049 CAGCCTTCAGAATGTAGAGGTGAGTATGGAAGAAA[C/T]ACAGATGGGGCACCAATGGTATTGCTACAATCACA Y 2 1 2 1 101000 f 74 goat snp22812-scaffold228-1026328 NW_017189516.1 26729714 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795841 Affx-122951690 AX-385282794 X 87343038 GTCCATGACATGTGCAGCTGCAGGAAGAGATTTTC[A/G]TTTCTCTTCCTTAATTGTACAGCCCCTGGGGTTCA R 2 1 2 1 101000 f 74 goat snp22813-scaffold228-1070317 NW_017189516.1 26773605 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799195 Affx-122970107 AX-385286125 X 87380520 ACTGAGAAGGAGCAAACATTAAAGTGAAGATTGAA[C/T]GATGTTTTGAAAACCAAGTGAAAAACATGTGATCA Y 2 1 2 1 201000 r 74 goat snp22814-scaffold228-1107799 NW_017189516.1 26810951 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398271 Affx-122962176 AX-123268626 X 87436480 TATTTCTGTATAATCAACCTCCCCAAACACGGTGA[C/T]GTGAACCAAAAAACATTTTGTTCTGCATGTGGAGT Y 2 1 2 1 101000 r 74 goat snp22815-scaffold228-1163759 NW_017189516.1 26867258 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377049 Affx-122978301 AX-123247408 X 87475539 CAGCCCAGCACATGTGAAAGGAATCAAGCCTGTCA[C/T]GGGAGCCAGTGGAGAATCTGACTTAATAACACAAT Y 2 1 2 1 201000 f 74 goat snp22816-scaffold228-1202818 NW_017189516.1 27277954 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772675 Affx-122966874 AX-385259822 X 87532908 TAGATTTTCAAGTTCAATATTTGCCAAATTATTAA[C/T]TAACTGGATAAAATGTCTCCATGCTTTCAAGCATT Y 2 1 2 1 101000 r 74 goat snp22817-scaffold228-1260187 NW_017189516.1 27223601 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387756 Affx-122969727 AX-123258114 X 87567602 CTTACTTCAAAAAAGTTACTTTTTAAGTGGTTTTT[A/G]CCTAAATCTGTTAAAAATTGGGGGTAGTAAAAAAG R 2 1 2 1 202000 f 74 goat snp22818-scaffold228-1294881 NW_017189516.1 27189137 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444299 Affx-122926755 AX-123314636 X 87651765 TGTTCTCTAAAAATAAACATTTAGCTGGAGCTGGG[A/G]AGGTTCTCATCTTGCAATGTTTTCAATGAAAAAAG R 2 1 2 1 101000 r 74 goat snp22819-scaffold228-1379044 NW_017189516.1 27104601 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391630 Affx-122966576 AX-123261987 X 87747487 AAGGTCTGACAAACTGGATGTTGGGTACGCAGGTA[C/T]TTATTATCATATCCAGCAGACTTTAGGATTGCTTG Y 2 1 2 1 201000 r 74 goat snp22820-scaffold228-1474766 NW_017189516.1 27011919 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423346 Affx-122943160 AX-123293692 X 87814188 ATTCACCATGCTCCTAAATGTATTTATCTTCAGTG[C/T]AATAGCTATTTTTCTTACCTTTGGCTGCCAAGAAT Y 2 1 2 1 101000 f 74 goat snp22821-scaffold228-1541467 NW_017189516.1 26945776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424349 Affx-122941933 AX-123294695 X 87847077 TACAGGGCTACAAATTGATCTTGCCTCTTCAAAGT[C/T]ATTGAAATGCAAATTTAAAAGACATGGAGACAGTT Y 2 1 2 1 101000 f 74 goat snp22822-scaffold228-1574356 NW_017189516.1 27322072 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442244 Affx-122928290 AX-123312581 X 87917668 ACATTCTTTTAAAGAACACTATAGAGGTGATGTTG[C/T]ATGCTTCATATATGTCACTTCAAAAAGCCTATTTT Y 2 1 2 1 101000 r 74 goat snp22824-scaffold228-1644947 NW_017189516.1 27391978 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388500 Affx-122969220 AX-123258858 X 87979120 AGATAGAAATAGAAAAGGGAGCCATGAGAAATGTC[A/G]GCCAAAGTATAGTCGTGAAGATGGACCTCTTACTG R 2 1 2 1 101000 r 74 goat snp22825-scaffold228-1706399 NW_017189516.1 27453951 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378100 Affx-122977153 AX-123248459 X 88008448 CAGCTGCAGTGCTTATAAGTTCTTTCTTAGGCCAT[A/G]TGCTTGTAGTTAACAGGGAATGTCAGGTCTGTTGC R 2 1 2 1 101000 r 74 goat snp22826-scaffold228-1735727 NW_017189516.1 27483306 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387088 Affx-122969876 AX-123257446 X 88146539 GACTATTCAAGTTAAAGGGACAGTTCCAGCCAGAG[A/C]TGAAAATCCCTTCTTCTGCATTTTAGACAGATGGT M 2 1 2 1 101000 r 74 goat snp22828-scaffold228-1873818 NW_017189516.1 27622860 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390126 Affx-122968002 AX-123260483 X 88189241 ACCTTCATATTAGTGGAATCTTACAGTGTGTCTTC[C/T]CTGGAGTCTGTTTGGGATTTAAGATTTGAGGCGCA Y 2 1 2 1 101000 r 74 goat snp22829-scaffold228-1916520 NW_017189516.1 27666929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427488 Affx-122940007 AX-123297831 X 88260201 TTTTTCCCAAGTGTATGTGGGGTTTGTAATATTGT[C/T]CTCATGACAAAACAGATGACACTTAATTTATCTGA Y 2 1 2 1 101000 r 74 goat snp22830-scaffold228-1987480 NW_017189516.1 27738714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401838 Affx-122959438 AX-123272191 X 88334655 TTGTATGGTATCAAAAAGGGCAAAAAGAAAATTGG[C/T]ATGTCTCCTCATACTCCACTAGGTAGCAAAGCCAC Y 2 1 2 1 101000 r 74 goat snp22832-scaffold228-2061934 NW_017189516.1 27813937 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378651 Affx-122977096 AX-123249010 X 88367393 TGCATTTTGGGGGTCTGCAGCCATGATAAGCCATG[C/T]GCAAGTTCCTTCATGGCAAGGGAAGGAGAACACTT Y 2 1 2 1 201000 f 74 goat snp22833-scaffold228-2094672 NW_017189516.1 27846714 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767801 Affx-122956105 AX-385255025 X 88433612 CATATATTATGTACTTCTTGATGGAAGAATGCACT[A/G]CCATTTATGAAGCAGTCTTCTTAAAAAAGAGAAAA R 2 1 2 1 201000 f 74 goat snp22834-scaffold228-2160891 NW_017189516.1 27913413 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793007 Affx-122973616 AX-385279985 X 88476661 TTTTAAATCTCTACTTCCTCTTGAAAGGGAAAATT[A/G]TCTTTTACTAATTTGATCTTAGCACCATTTTTTTT R 2 1 2 1 101000 f 74 goat snp22835-scaffold228-2203940 NW_017189516.1 27956913 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433486 Affx-122935038 AX-123303827 X 88523194 GAAAATGGTTGCGGACCCAGGAAACTGCCAGAGGA[C/T]ACTTCCACTGGATCCTGGGGCTCTGTACCCATAAC Y 2 1 2 1 101000 f 74 goat snp22836-scaffold228-2250473 NW_017189516.1 28003915 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379407 Affx-122976122 AX-123249765 X 88593989 CATATTTTCCAAATTCTCTGAAAGCCATAGAAAGT[A/G]TTTCCTTCCAATTCTATTACGTGGTCTATTGTCAA R 2 1 2 1 101000 r 74 goat snp22837-scaffold228-2321268 NW_017189516.1 28095132 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377880 Affx-122977259 AX-123248239 X 88640166 ATGCAAGCAACATGATTATGCTCCTGTGTCTCTCC[A/G]CCATACCTTCTATCATACCCTTCAGATTCTCTTCC R 2 1 2 1 201000 r 74 goat snp22838-scaffold228-2367445 NW_017189516.1 28141318 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452225 Affx-122920798 AX-123322558 X 88698833 ACAGCAGTAGCTATTGTTTTCCTGTACAGGTTGGC[A/G]CTAGTATTCATTTTTGTGTGGCAGGTCCTCTTTTG R 2 1 2 1 201000 r 74 goat snp22839-scaffold228-2426112 NW_017189516.1 28200354 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413268 Affx-122950219 AX-123283617 X 88835650 TCATTTCTTCGTGGCATCTTTATGGTCTAGGCATA[C/T]ATACTGTTCACTCATTGTTAAAACATGTCAATCTC Y 2 1 2 1 101000 r 74 goat snp22841-scaffold228-2562929 NW_017189516.1 28304583 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768947 Affx-122953555 AX-385256122 X 88885888 GCTTTTCTTAATCACTACAAAACCATACAGTATGT[A/G]CTGCCAAGTTCTGGGTTAAAATGCCTAAAACGCTG R 2 1 2 1 101000 r 74 goat snp22842-scaffold228-2613167 NW_017189516.1 28281279 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38451727 Affx-122921544 AX-123322060 X 88953489 AGGAGTTATCCATCAACGGGTGCCTTTCATTTTCT[A/G]CTGGACTGTTAGACCAAGGCTTGGTTCACAAATCT R 2 1 2 1 101000 r 74 goat snp22843-scaffold228-2680768 NW_017189516.1 28380201 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390365 Affx-122967676 AX-123260722 X 88994068 CCGCAGCTAACTTATGTGTGTAGGAAAATATGTCA[C/T]GCAAAAGAACAATTTTCCTTTGCCTTCTACTTCTC Y 2 1 2 1 101000 f 74 goat snp22844-scaffold228-2721347 NW_017189516.1 28420985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797885 Affx-122921383 AX-385284823 X 89042305 AAAAGTCACTCAAGTTAGAAATTTAAAAACAGTCA[C/T]TTGTAAGAAATTCTTCTTAATTGCTGTTTATCTGT Y 2 1 2 1 101000 f 74 goat snp22845-scaffold228-2769584 NW_017189516.1 28469191 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425291 Affx-122940959 AX-123295637 X 89092531 CTTTGAACAGGCCATGTGGTGAGCCATGTTTTAGA[C/T]TATGATTAGTTCTCTATGCTTCCACTTCAGGGAAT Y 2 1 2 1 101000 f 74 goat snp22846-scaffold228-2819810 NW_017189516.1 28520533 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782463 Affx-122938446 AX-385269539 X 89175617 GTTCTCCTTTGAAAAAGTTACATGCATTTGCAGAC[A/G]CTTGTGTGTGCATTCAAGTGTGCTATGTGTGCGTG R 2 1 2 1 101000 f 74 goat snp22847-scaffold228-2902896 NW_017189516.1 28605136 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381843 Affx-122974196 AX-123252201 X 89226119 GTTAGGAAAGCAAAAACCTTTTCAGATCTGATTAA[C/T]ATTTTCATATGTGTCTCTTACTAGAGTATTGAACA Y 2 1 2 1 101000 f 74 goat snp22848-scaffold228-2953398 NW_017189516.1 28655606 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773849 Affx-122968435 AX-385260989 X 89326888 ATTGGGTTTTTTCCTCTCATGGAATCCTGATTGAT[A/G]CAATTTATTAAGCCAATTTCTACTGTGGACAGCTG R 2 1 2 1 101000 r 74 goat snp22850-scaffold228-3054167 NW_017189516.1 28757795 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452361 Affx-122920634 AX-123322694 X 89399288 CACTGATTCTATCATCTCACTTTTTGTTCTCCTTG[G/T]TACAATCTATATGACTTAAAAATTTTTTTCTTTGA K 2 1 2 1 101000 f 74 goat snp22852-scaffold228-3126567 NW_017189516.1 28830854 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378567 Affx-122976601 AX-123248926 X 89431902 GCCTACAGTGTGGCAGGGCCTATGCTAAGAGCTTC[C/T]CATTCACTGTCTTATGTAATCCTCACAGGCTTCAT Y 2 1 2 1 101000 f 74 goat snp22853-scaffold228-3159181 NW_017189516.1 28864551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788612 Affx-122977001 AX-385275629 X 89487200 AGAGAACTGGGATATGACCTGGTATTAAATTTCCC[A/G]CTATTCATAGTGACTCCTTAATTAGGAGTTTCCAA R 2 1 2 1 101000 f 74 goat snp22854-scaffold228-3214479 NW_017189516.1 28920004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449997 Affx-122922864 AX-123320332 X 89519502 TATATTCAGTCACAAGAAAAATATCAGTAATTTCC[A/G]TTATGTAGAAGTATTGCAAATAGCATATCTGATCA R 2 1 2 1 101000 r 74 goat snp22855-scaffold228-3246781 NW_017189516.1 28952285 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442662 Affx-122927903 AX-123312999 X 89587015 GCTCAGGCGGTCTCACCTAGCAGATGGTACCTGAA[C/T]AGGGGAAATTTTCAGATAACTGAAAGTCAAAGACC Y 2 1 2 1 201000 f 74 goat snp22856-scaffold228-3314294 NW_017189516.1 29020548 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446770 Affx-122925317 AX-123317106 X 89631850 GGGACCAAAAGCCAGAAGGAAGCAGATGGAGAGAG[A/G]AGTGGGAGGACAGGAAAGTTCTATATTCTGGAATC R 2 1 2 1 202000 f 74 goat snp22857-scaffold228-3359129 NW_017189516.1 29065648 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766996 Affx-122929857 AX-385254291 X 89711798 GAAATTATAGAGTTCTTTCTGTATTTGAAAGCACT[A/G]TCTTGGGCCTTCTAGAATAATCAAAGAAATAGCTC R 2 1 2 1 101000 f 74 goat snp22859-scaffold228-3439077 NW_017189516.1 29146389 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432087 Affx-122936486 AX-123302428 X 89774412 CCAGCACTGATGTTCTGGGTTCCAGATTTGCCTCT[G/T]CCACTTTCTACCTTGTGTCACTTTGCATCTTAATT K 2 1 2 1 101000 r 74 goat snp22860-scaffold228-3501691 NW_017189516.1 29209515 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419244 Affx-122945670 AX-123289592 X 89845606 ATCCAGGGGGTTCTAAAGAGTCAGACACAACTTTG[C/T]GACTGAACAACAACACTTTGGCTATGGGGAAATGG Y 2 1 2 1 303000 f 74 goat snp22861-scaffold228-3572885 NW_017189516.1 29281573 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407162 Affx-122954840 AX-123277513 X 89883559 GCTGTATCCACAATAAACTCTCAAAAAATGGATAA[C/T]AGAACGAGGAGAGAAAAATTAGTGCTGGTTAAGTC Y 2 1 2 1 201000 f 74 goat snp22862-scaffold228-3610838 NW_017189516.1 29319848 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411798 Affx-122951262 AX-123282148 X 89951197 AAAATTTTGGAACTTATGGTTTACCCCATCACCCC[C/T]AACACACACGCACACTGTAATCCTAGAAGCAGACA Y 2 1 2 1 202000 r 74 goat snp22864-scaffold228-3678476 NW_017189516.1 29387782 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400543 Affx-122960436 AX-123270898 X 89993091 CACAGAATGTCAGGCATATAACATCTCTATTCCAC[A/G]TTGGTATTTTTTGATATATGTGAAAAACAGTTTAG R 2 1 2 1 101000 f 74 goat snp22865-scaffold228-3720370 NW_017189516.1 29429794 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392738 Affx-122966017 AX-123263095 X 90046417 TATATCTACTAAAGCTAAAAAAACAACAAAAATGC[A/G]TTCACATGGTCACCAACATACTAACTAAAAAGTTA R 2 1 2 1 101000 r 74 goat snp22866-scaffold228-3773696 NW_017189516.1 65926317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439482 Affx-122930159 AX-123309819 X 90097323 TTATGTCCCTAAGAGCAAGATTCAGAGTGCAGTTT[A/G]CCCCCAGTGTTATTAACACCTCCTTCCCTTGTTTG R 2 1 2 1 101000 f 74 goat snp22867-scaffold228-3824602 NW_017189516.1 65977751 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424146 Affx-122942547 AX-123294492 X 90139130 AACACAGAACAGGGCAGACAAGTTGGGAGAAAATG[G/T]ACCTAGACCCAGGGGAAAGGCATTAACAGAGAATA K 2 1 2 1 201000 f 74 goat snp22868-scaffold228-3866409 NW_017189516.1 29460020 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402863 Affx-122958239 AX-123273216 X 90188953 CACACAGAAATGGTTAAAATGGTAATTTTATGTTA[C/T]GCATATTTTGCCACGAAGAAAAGATGAACGTGAAT Y 2 1 2 1 103000 r 74 goat snp22869-scaffold228-3916232 NW_017189516.1 29509898 T C 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38407829 Affx-122954538 AX-123278180 X 90223060 GACAGGGCAGATCACGATCAACTCCACTGGGAGGG[C/T]GGCAGAGGAGGAGGAGCAGGCCACCAAGTTCTCTC Y 2 1 2 1 101000 f 74 goat snp22870-scaffold228-3950339 NW_017189516.1 29544157 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453126 Affx-122920011 AX-123323459 X 90251644 TTACTTGTGTCGAGCAAAAAGCATTTTAAGATACC[A/C]TGGTTCTCTACTCCATTCTATTGCAAACTTCTACC M 2 1 2 1 101000 r 74 goat snp22871-scaffold228-3978923 NW_017189516.1 29572895 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387658 Affx-122969843 AX-123258016 X 90308938 TATCACAACCTACAGCTGCCATTTTTAGAAACACT[A/G]CGCTGTGAGCACAAGATGATTGGGTTAAGTGGCCT R 2 1 2 1 201000 r 74 goat snp22872-scaffold228-4036217 NW_017189516.1 29629169 A G 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38418278 Affx-122947005 AX-123288626 X 90356931 AGGACTTTTTAGGTGGTGCTTCTATAAGTTACGGA[C/T]ATGTGTGGTGCTATAAATGATCTCAGCTGTTACAT Y 2 1 2 1 101000 f 74 goat snp22873-scaffold228-4084210 NW_017189516.1 29678226 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381506 Affx-122974866 AX-123251864 X 90409277 AAAAAAAAAGAAATACATTATTAGCTTTAAAACAA[C/T]ACTCTGTCACTCCTACTGAAAGTGAGATGAGGTGC Y 2 1 2 1 101000 r 74 goat snp22874-scaffold228-4136556 NW_017189629.1 885805 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778630 Affx-122928873 AX-385265742 X 90491062 TTTGGGGGGCTGCTTAAACTACTGTAATTATTTTC[G/T]AGTTTTATTGCATTGTGCCTAAGTGCACAGCCTGC K 2 1 2 1 101000 f 74 goat snp22876-scaffold228-4218341 NW_017189629.1 803244 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446019 Affx-122925859 AX-123316356 X 90524107 AAAGATGATAAAATAAGAGTTGAAGTAAGTAGAAC[A/G]TTGATTAATCAGAAATCAACACTGCCTGGCTCTAC R 2 1 2 1 101000 f 74 goat snp22877-scaffold228-4251386 NW_017189629.1 770958 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404819 Affx-122956647 AX-123275171 X 90555383 TGGAGATGGTGCTTGAATTATTGCATTTTGTAAAT[A/G]TTTTCACATTTTAAATCTGGCAGAAATGGTTTAAA R 2 1 2 1 101000 f 74 goat snp22878-scaffold228-4282662 NW_017189629.1 739275 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388549 Affx-122969186 AX-123258907 X 90627706 TCTTCATATGCTTATTTTTCAAGAGCCCTGTTCTT[A/G]TTTTCTGAAAGTTCCATTTTTGTTTCATAGTTATG R 2 1 2 1 101000 f 74 goat snp22880-scaffold228-4354985 NW_017189629.1 668164 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390327 Affx-122967702 AX-123260684 X 90693923 ATATATTGCCTGGATGAAATAAGGTGGCTCTCCCC[A/G]TCCTTTCCAAAGCAGTTTTGCTCTCACAGATCACA R 2 1 2 1 101000 r 74 goat snp22881-scaffold228-4421202 NW_017189629.1 601606 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451979 Affx-122920938 AX-123322312 X 90734360 TTCAGATCCCTCCAGAAAGCCTTCCTCTGGCTCTA[A/C]GGATTCTTATTGCTTTATGATGCAATCAGTTTAGC M 2 1 2 1 101000 r 74 goat snp22882-scaffold228-4461639 NW_017189629.1 560777 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792779 Affx-122920252 AX-385279758 X 90791738 GCTGTCTGGCCTACATGCCTTCATATAGCATTTCA[C/T]GCAGGGATTTGTAATTATATCAAAGACTGAGCTTT Y 2 1 2 1 101000 f 74 goat snp22883-scaffold228-4519017 NW_017189629.1 503517 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775473 Affx-122930745 AX-385262604 X 90820559 CGTTAACCCTGGACTTATGGAAATCTGAAAGTTGC[A/G]TGGAATCATCATCAAGATCACTTCTCTATTTTTTG R 2 1 2 1 101000 f 74 goat snp22884-scaffold228-4547838 NW_017189629.1 474189 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443875 Affx-122927505 AX-123314212 X 90876518 TGGGGATGGAAATGGGAAGTATTCTTGGGGATTCA[C/T]ATTCATTTTGTGAGACCAGTAACACTTCAAGGGGT Y 2 1 2 1 101000 r 74 goat snp22885-scaffold228-4603797 NW_017189629.1 418152 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408426 Affx-122954461 AX-123278777 X 90922239 TTGGCAATTTGCATTCAGAAGGCATCTTCTGAGCC[C/T]GTCCCGTTGGCAGTGAGGTATCCAAAGATGCTGCA Y 2 1 2 1 101000 f 74 goat snp22886-scaffold228-4649518 NW_017189629.1 372155 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388583 Affx-122969162 AX-123258941 X 90957608 CTTTCTCTCATGAGAGCTCATAATGGCCACAATTC[A/G]CTGGGAACTCGTTCCAGGCAGCTCTGGATCTGTTT R 2 1 2 1 101000 f 74 goat snp22887-scaffold228-4684887 NW_017189629.1 336559 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451710 Affx-122921559 AX-123322043 X 91024059 AATTGTTGAGCAGGCTGAGTTCCTCAAACAAGTAC[A/G]TGCAGATGCGCATGAAAATTACAGAAGACAATTAT R 2 1 2 1 101000 f 74 goat snp22888-scaffold228-4751338 NW_017189629.1 270379 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801033 Affx-122975091 AX-385287947 X 91078132 TAACACGGAACATGTCAGCATTTGGAAGGTTTATT[C/T]CGATTCATTAATGGAAAAAACGCTCTCCCCCTAAC Y 2 1 2 1 101000 f 74 goat snp22889-scaffold228-4805411 NW_017189629.1 216372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400283 Affx-122960087 AX-123270638 X 91166071 GGTGGTGAAGGGAAGGTGAGGCTGGGGCAGCTGGT[A/G]TTTGAACTGTCATTTACGTGAAAAAAGCCCACCAC R 2 1 2 1 101000 r 74 goat snp22891-scaffold228-4893350 NW_017189629.1 128243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376547 Affx-122977987 AX-123246906 X 91257824 TTTATATTCAAACTTAGCACCTTCCAAGATGGGAA[C/T]AGCATCACGTTTACCTGGATAAAGCTTGGTCACCC Y 2 1 2 1 101000 r 74 goat snp22892-scaffold228-4985103 NW_017189629.1 36370 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430275 Affx-122937294 AX-123300616 X 91328503 GGCTGAAATCAAATTGTTGGCCAGGTAGAGTTCTT[A/G]TCTGTCAGTTCTATGGGGAAAAATGCACTTCCAAG R 2 1 2 1 101000 f 74 goat snp22893-scaffold228-5055782 NW_017189516.1 4449517 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774333 Affx-122920665 AX-385261469 X 91415360 TCTCAAATACATCTCAGATGTTTTGAACTTGTCAG[G/T]AAAGATCTCAGCCAAGTTGAGGAAAGATTCAAGAA K 2 1 2 1 101000 r 74 goat snp22894-scaffold228-5142639 NW_017189516.1 4362039 T G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38437322 Affx-122931961 AX-123307660 X 91468442 AGGCTGGAAAAGAGGGGAAGTTCAACTAGACAGAA[A/G]AATAATGGTAAGCATCTGCAATGATCCAGACACTG R 2 1 2 1 101000 f 74 goat snp22895-scaffold228-5195721 NW_017189516.1 4309167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454147 Affx-122919331 AX-123324480 X 91519756 GTGCTGCTGAGTGAAATGGAGGACCAGGTTTGTGA[C/T]AGAGGAATGAGGGTTGAGTTTCAGGTGACTTTGTG Y 2 1 2 1 101000 r 74 goat snp22896-scaffold228-5247035 NW_017189516.1 4257802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387748 Affx-122969733 AX-123258106 X 91581690 TGATTCTCACAGTGGTCGGTGTGTGCACCTCAGGA[C/T]TGGGGTTGTTTCAGGAATTATATGGCCTAATACCA Y 2 1 2 1 201000 r 74 goat snp22897-scaffold228-5308969 NW_017189516.1 24200936 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451265 Affx-122921927 AX-123321598 X 91613104 AGGGTATTATTAGAAATAGAAGCAGAAAGGAACCC[A/G]TTTAGAATGCAATTATATTCTTCATGAAGAGAGGA R 2 1 2 1 101000 r 74 goat snp57461-scaffold918-741887 NW_017215380.1 18350 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424141 Affx-122942551 AX-123294487 X 91697412 TCTACACGGGGCTAGTGGAACAAAAAACGTTATCT[A/G]CCTGTTCCCCCAAGGACAACTGAAACTCTCTTGCT R 2 1 2 1 101000 f 74 goat snp57460-scaffold918-657579 NW_017189516.1 30188910 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415456 Affx-122949171 AX-123285805 X 91746499 CTACCATGAATTCCCTGTGTCACCACGGCACATAA[G/T]ACAATCTCTTAAACCTTCCTGTCCCATTTGTAAAC K 2 1 2 1 101000 f 74 goat snp57459-scaffold918-608492 NW_017189516.1 30238364 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420837 Affx-122944659 AX-123291184 X 91778909 AGGTAGGTCACAGGTATGTAGTGGGACGTCAGTGT[A/G]TCTTTCCTTCTTTGAGCTGTGCAGCACAGCTTGCA R 2 1 2 1 101000 r 74 goat snp57458-scaffold918-576082 NW_017189516.1 30270752 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377008 Affx-122977725 AX-123247367 X 91831740 ATTGGAAGCTCGGCACTAAATCCTGCACAGCAAGG[C/T]CCCTGTTTCTTGGGGCGAGTTCCTCCTGCAGTAGT Y 2 1 2 1 101000 f 74 goat snp57457-scaffold918-523251 NW_017189516.1 30330199 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418962 Affx-122946081 AX-123289310 X 91887517 ATGCTCCTTCAGCCTGAGACTCCTACAACTTCATC[C/T]ATTTGTCCTGCTTCCAGACTGCCTAGCTTACATCA Y 2 1 2 1 101000 r 74 goat snp57456-scaffold918-467474 NW_017211574.1 13027 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784666 Affx-122958679 AX-385271714 X 91928808 CACAATTCAACCCATAAGAGATGGTAACGACTGTG[A/G]TTAGAATAGCAAGAAATGACAGGGTAAGCACGATA R 2 1 2 1 101000 f 74 goat snp57455-scaffold918-426183 NW_017189516.1 30647718 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38436174 Affx-122932614 AX-123306513 X 91973214 ACCTTAGTATTTTTTGGGAACCTTTTCCTTCAACA[C/T]AGCCGTGTCGAAGGATGACTCAGCTCTGAGGTGTG Y 2 1 2 1 101000 f 74 goat snp57454-scaffold918-381777 NW_017189929.1 27453 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437407 Affx-122932422 AX-123307745 X 92005537 TTGGAGCAGCGCTCATCAAACTGAGCAGCTGGTCA[G/T]CCTCTCTGAGCCCTCCCTCTCCATCACTTGCCAGC K 2 1 2 1 101000 f 74 goat snp57453-scaffold918-349454 NW_017189929.1 59705 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450851 Affx-122922235 AX-123321185 X 92040000 CTGTGACTCATGCAGGTTGGCGTATTAGAACCTCT[C/T]AATAAACCTGAACTCTGGGCACACAGAGGGGCCCA Y 2 1 2 1 101000 f 74 goat snp57452-scaffold918-314991 NW_017189929.1 94641 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786018 Affx-122975418 AX-385273054 X 92106388 TGTGACTTGTACTTATGTGACTACATAATATTCTG[G/T]TCAGTGTGTTTTAGAGGTTCATCTATGTTGTGTGT K 2 1 2 1 101000 r 74 goat snp57451-scaffold918-248603 NW_017189929.1 140083 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393691 Affx-122965257 AX-123264046 X 92155599 TACTTTTAACTACGCTTTCTATCTCTACCAAAGGC[A/G]TTTTTAGTTTTTTATTAAAAATATAATTGATTTAC R 2 1 2 1 101000 f 74 goat snp57450-scaffold918-199392 NW_017189516.1 21590044 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38406004 Affx-122955507 AX-123276356 X 92201015 CAAACTGTCTCGACTAGACTTTCCCCTAAAGACCC[A/G]TGTGTGTGGTAAGGATGGAAGGGGAAACTGCTTTA R 2 1 2 1 201000 f 74 goat snp57449-scaffold918-153976 NW_017189516.1 21632495 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422917 Affx-122943045 AX-123293263 X 92236632 TATCACCTTCGAATGCGGAATGAAGGCAGAAGTCA[C/T]GAAGAGATTTACACGGAGAGTGACAAAGAAACAAA Y 2 1 2 1 201000 r 74 goat snp57448-scaffold918-118359 NW_017211629.1 16961 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454197 Affx-122919294 AX-123324530 X 92299074 CTCACAGACATGCGGCGGCTACACACCTCCACCAA[A/G]TATCACGTAAGGCATTCTAAGCAGTGCTGTTAGGT R 2 1 2 1 101000 r 74 goat snp57447-scaffold918-55917 NW_017211629.1 75417 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376005 Affx-122978412 AX-123246364 X 92350293 AGCCCTGAATAGACAAGCAGCCGAGCTGAAAAAGA[C/T]GCCTGCTAGCCCCTTCTCTCTCCAACCCCCCAACC Y 2 1 2 1 101000 f 74 goat snp57446-scaffold918-4698 NW_017189516.1 30374459 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792429 Affx-122962226 AX-385279410 X 92385220 TCTATTCATTCAACATCTTGCGTTCATCTTGCAGT[A/G]TCCATCAGATCATTCAGATTATTTTGGTTGTATCC R 2 1 2 1 101000 r 74 goat snp8120-scaffold1299-30130 NW_017190007.1 141032 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784986 Affx-122935131 AX-385272033 X 92429558 AAATTTTTTATTCTGGCCCAAACAGACTGTAATCC[A/G]TTTGCAGGGAAACCCACTCCCACCACAAAATAGAT R 2 1 2 1 101000 r 74 goat snp8121-scaffold1299-74468 NW_017190007.1 96879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379040 Affx-122976352 AX-123249399 X 92522494 CTAGACTCTCTGCCTGCTCCAAGAATGGCAGTCCG[C/T]AGCCCAAAGACAGATGAAGTGGAGGGCTGTTTTTT Y 2 1 2 1 202000 r 74 goat snp8122-scaffold1299-167404 NW_017190007.1 4600 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427377 Affx-122940091 AX-123297720 X 92578196 GTAGGGAGCTGAGCTGCCCTTGGTTCCTGGGGGCC[A/G]TCAGTGGTCCTCGCTGGTTCTTTCAGTGAAAGGTA R 2 1 2 1 101000 r 74 goat snp8123-scaffold1299-223106 NW_017189516.1 30682569 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395491 Affx-122963893 AX-123265846 X 92607102 TAATCATGGAATGAGCCCATTATGACTCAATTTTA[C/T]GTATACAATTCAACCAATGACAAATTCCTATTCAC Y 2 1 2 1 101000 f 74 goat snp8124-scaffold1299-252012 NW_017189516.1 30427929 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423253 Affx-122942674 AX-123293599 X 92669711 AGTGCCATGTGTTTCATCAGCTCCCGAGGCCATGC[A/G]GCTGGCTGATCCATCCTCCTCTCTTCCCGTGCCTT R 2 1 2 1 201000 f 74 goat snp8125-scaffold1299-314621 NW_017189516.1 30490431 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423693 Affx-122942896 AX-123294039 X 92710209 CTTCCCCTAGGAAACGGAGTGTGATTGTTCATGCA[C/T]GTGTGTTTGTTGGTGTGTATGTATGTGTGTGTGTG Y 2 1 2 1 201000 f 74 goat snp8126-scaffold1299-355119 NW_017190148.1 93814 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395181 Affx-122964516 AX-123265536 X 92767418 AACCACACAGATACACACGTGCGCACATGCACTCA[G/T]CACAAACAGCAGGGAGGCAGCGAGCTAGAGGGGTC K 2 1 2 1 101000 f 74 goat snp8127-scaffold1299-412328 NW_017190148.1 36532 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454082 Affx-122919375 AX-123324415 X 92834474 TAATGTTGTGAAAGGGTAATAATAATAGCACCTAC[A/G]TTATGGGATTGTTTGGAGGATTTGATGAGTTAGTA R 2 1 2 1 201000 r 74 goat snp8128-scaffold1299-479384 NW_017189516.1 30538635 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408275 Affx-122953801 AX-123278626 X 92881672 TCACAGTGGATGCTATCACTGCATTAAAATGTTTT[A/G]TTTTGTATTTCTTCTCAGATGTTTAAAAGTGTTTC R 2 1 2 1 101000 r 74 goat snp8129-scaffold1299-526582 NW_017189516.1 30774411 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410804 Affx-122952652 AX-123281154 X 92945096 TCCTCAAGGTGCCTAAGCTAAAGCTAGGGAGGTAA[C/T]GGAAGAATTTTATGCAGAGAAAAGACCTGATCAGA Y 2 1 2 1 101000 f 74 goat snp8130-scaffold1299-590006 NW_017189516.1 30844936 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440150 Affx-122931145 AX-123310487 X 92991723 CAATTTCTGCATCTGTTAAATGAGGGCAATAATCA[C/T]AACAACCTCATAAGGTTGATTTGAGGACCAAGTGA Y 2 1 2 1 101000 f 74 goat snp8131-scaffold1299-636633 NW_017189516.1 30887193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380690 Affx-122975170 AX-123251048 X 93086087 CCTGTAGTTTTGCCCATCTAGTGGCTAAGAAATGG[C/T]ACCCCATTACATGACTTTGACACCTTGACATATGC Y 2 1 2 1 101000 f 74 goat snp8132-scaffold1299-730997 NW_017189516.1 30978331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772424 Affx-122951344 AX-385259576 X 93125826 TTTGGTTTTGGTTTTGAACACTTGCAATCAAAACA[G/T]CCTAACTACTACAGAAATAAGATCAAATGATTACA K 2 1 2 1 201000 r 74 goat snp8133-scaffold1299-770736 NW_017214769.1 5893 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420588 Affx-122945261 AX-123290935 X 93155414 TCTTCTATACCCTCCCTCTCCCAGCTTCAGGAGTG[A/G]AGGAAGCAAAATGGCAACCAACAAATGGAACTAGT R 2 1 2 1 201000 r 74 goat snp8134-scaffold1299-800324 NW_017189516.1 31046654 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436486 Affx-122932965 AX-123306824 X 93247498 ATAGATACCACTACATGAAAGAGAAAGGAGATCTC[A/G]ATGAGGAGTAGGGCAAGCCAGGGCTTGAGAAGAAA R 2 1 2 1 201000 f 74 goat snp8136-scaffold1299-892408 NW_017189516.1 31075013 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453846 Affx-122919540 AX-123324179 X 93291660 GGGAGGGGTTTTTAATCATTAACTCCAGTTTGAGA[A/G]TAAATCACAAACCCAGCTTTGATTTTTCTGAGCTA R 2 1 2 1 101000 f 74 goat snp8137-scaffold1299-936570 NW_017189516.1 31119874 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397670 Affx-122962593 AX-123268025 X 93333537 GTCGAAACAAATATATTTCATGATATGTCTAGCAA[C/T]GTTTGGCATAAAAGTGGTGTGATAATATGTGTTGA Y 2 1 2 1 101000 r 74 goat snp8138-scaffold1299-978447 NW_017189516.1 31161956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452673 Affx-122920322 AX-123323006 X 93376165 ACTAAACTGAACTGAACAGTATATTGTATTAGTCT[A/G]TATCATGAGGCTGTATATGAGGACTGTGAATGACA R 2 1 2 1 201000 r 74 goat snp8139-scaffold1299-1021075 NW_017189516.1 31204440 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453249 Affx-122920410 AX-123323582 X 93463318 TGGACAGGACCCTGATTGTATGCTTGAGTCTGACC[A/G]TCTGCAGCTTCTCTTGGCCAGGTGAGGGTCACTTC R 2 1 2 1 101000 f 74 goat snp8140-scaffold1299-1108228 NW_017189516.1 31292166 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442933 Affx-122927619 AX-123313270 X 93509259 AGCGTGGAGCATTCCTGGGATGCTGTGAACTCTGG[C/T]GAGTTACCTCATTGGTCTTTTACAGCAAAGATACC Y 2 1 2 1 101000 r 74 goat snp8141-scaffold1299-1154169 NW_017189516.1 31337957 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415623 Affx-122948592 AX-123285972 X 93578754 CTATACTCCTGGGGGGAAGAAGATTGATTATTCAG[C/T]AGGCCTGGTAACTACCAACACCCACTCCTAAACCA Y 2 1 2 1 101000 f 74 goat snp8142-scaffold1299-1223664 NW_017189516.1 32356942 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382207 Affx-122973999 AX-123252565 X 93623050 GCAAACTATCTCCAGCAGGGATTGTTGGCCTGGAC[A/G]CTTACAGGTGGCCTCTCCATGTAGCAACCCACTGC R 2 1 2 1 101000 f 74 goat snp8143-scaffold1299-1267960 NW_017189516.1 32312777 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800382 Affx-122954523 AX-385287304 X 93656176 ATAAGCAACAAACGAGTGTTAAGTCACAAATGAAG[A/C]TTGGAAGAGGTTCACTATCAATTCTTTTGAGGTTG M 2 1 2 1 101000 r 74 goat snp8144-scaffold1299-1301086 NW_017189516.1 32279308 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386034 Affx-122971482 AX-123256392 X 93711035 CATGTATTTGCCACACAAAAATGGACAGATGCTAT[A/C]ATTTCCATTCTGGAATTTTGAAACTGTGACAGAAA M 2 1 2 1 101000 f 74 goat snp8145-scaffold1299-1355945 NW_017189516.1 32414340 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412583 Affx-122951303 AX-123282932 X 93787101 AAGTCATAGATCTGTAAATAAATAACCATAATTGA[C/T]GCCTATAGAGGACACCTTATTAGAGACGTCCAGGT Y 2 1 2 1 101000 r 74 goat snp8147-scaffold1299-1432011 NW_017189516.1 32214094 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769890 Affx-122923407 AX-385257059 X 93823806 TCCATAGAGCTTTTTGTGACTATTCAACTTTTTCC[G/T]TGTGTCATTCTCTAAAGTGCTTCAGCATTCCACCA K 2 1 2 1 101000 r 74 goat snp8148-scaffold1299-1468716 NW_017189516.1 32177494 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796919 Affx-122946534 AX-385283861 X 93915707 TGGGTTTCCTTGTACCAGATCATATACTCAAGAGA[C/T]ATGTCACTGTGTATCCTCCTTTTAAAGAGAAGTGA Y 2 1 2 1 101000 r 74 goat snp8150-scaffold1299-1560617 NW_017189516.1 32085289 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766060 Affx-122922346 AX-385253477 X 93949701 CACAATAGGATAACATATCTGTATCTGACACAGGT[A/C]TATAATTTTTGTCCCTTTAAGCAAACCCAGTTCCA M 2 1 2 1 101000 f 74 goat snp8151-scaffold1299-1594611 NW_017189516.1 32051291 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388012 Affx-122969567 AX-123258370 X 94032152 CACATGGGCTTAGTTGCTCAGCGGCATTCCATCTG[A/C]TTTTTGACCCACCACACATTTGATTTATACCTGTT M 2 1 2 1 101000 r 74 goat snp8152-scaffold1299-1677062 NW_017189516.1 31967107 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424387 Affx-122941829 AX-123294733 X 94075889 CTGTGTCCATCAAGGCACAAGGCCCACAGGAAGAA[C/T]GTGTGTGGTAGCAGCAGATGGTGGCACCATGGGGG Y 2 1 2 1 101000 f 74 goat snp8153-scaffold1299-1720799 NW_017189516.1 31923374 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393024 Affx-122965642 AX-123263381 X 94148880 GGGTCCATGTTTCAACAGTTCTTACAGAGTGGGCC[A/G]AATACCATGGGTCAAAGAGTGGATGATTATTTTCA R 2 1 2 1 201000 r 74 goat snp8154-scaffold1299-1793790 NW_017189516.1 31850067 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426583 Affx-122939990 AX-123296929 X 94182603 ATTTGCAAGGGACCATTAGTCTCAAGGCTGTGTCC[A/G]TCTCCTTGGCAGAGCATCTTGTTTGTAAGCAGCAC R 2 1 2 1 303000 r 74 goat snp8155-scaffold1299-1827513 NW_017189516.1 31816331 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779447 Affx-122968900 AX-385266550 X 94223608 TGAAGCTTTCATGTGCATTTACCTAGGGAAAAATA[C/T]GCACATTTCCCCAGGAATACAGTTAGTATTTGCTT Y 2 1 2 1 101000 r 74 goat snp8156-scaffold1299-1868518 NW_017189516.1 31774372 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415036 Affx-122949498 AX-123285385 X 94289740 CACTTCAGTCACTCAGCGAATATTAATTGAGCATC[G/T]ACTATGTAAGCTTTATCACAGAACTCAATCCACTG K 2 1 2 1 101000 r 74 goat snp8157-scaffold1299-1934650 NW_017189516.1 31707208 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776736 Affx-122946610 AX-385263861 X 94326047 AACAAATGATGGCAGAATATGAAAATCTCTCTGAA[C/T]GAACTCCACAGAAACTCACTGCATGCTTCACAATT Y 2 1 2 1 101000 r 74 goat snp8158-scaffold1299-1970957 NW_017189516.1 31670762 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445309 Affx-122925437 AX-123315646 X 94385565 ACAAAAATATAACAATGTATATATACATGCATGTG[C/T]CAGAATCTCACTTGTGACAATTTTTTATCTTCTAG Y 2 1 2 1 101000 r 74 goat snp8159-scaffold1299-2030475 NW_017189516.1 31613843 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408214 Affx-122953848 AX-123278565 X 94418926 TGGGAATCTGACAAATTAAGGTTTTGCACATTTGG[A/G]AAAATCAACTGCTTCCACACTCTTAACACCACAAA R 2 1 2 1 101000 r 74 goat snp8160-scaffold1299-2063836 NW_017189516.1 31580138 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441304 Affx-122929452 AX-123311641 X 94462831 CTTTTACATTTGCACCAGCTATTTTCACTGAAACC[A/G]TCTCAGCCCTACTGTCTTTTCAGTAGGACTGTGAG R 2 1 2 1 101000 f 74 goat snp8161-scaffold1299-2107741 NW_017189516.1 31536329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445153 Affx-122925558 AX-123315490 X 94492241 AAGAAACCGTGAAGCCACATTGCAGAGGACATGGA[C/T]ACAGAGAGTAGTGGAAACTCAGGGCCAGATGGCAA Y 2 1 2 1 101000 r 74 goat snp8162-scaffold1299-2137151 NW_017189516.1 31506806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772132 Affx-122970586 AX-385259287 X 94533978 TGTTCCTTGTAATGCCTAAAGAAATTGCATATATG[C/T]AATTAAATATGGGGGAAGGAAAATGCAAAAGGAAA Y 2 1 2 1 102000 r 74 goat snp8163-scaffold1299-2178888 NW_017189516.1 31465087 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772129 Affx-122949063 AX-385259284 X 94570660 TAAGAATTATAAAGTAAACATGACACAATATTAAT[A/G]CATGAAACTGAGTGAAGGATAAAGGAATTCCTTCC R 2 1 2 1 202000 f 74 goat snp8164-scaffold1299-2215570 NW_017189516.1 31428060 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426617 Affx-122939963 AX-123296963 X 94607960 AACTCTGATTATCCCCGTCTTACAGGTGAGGAAGC[C/T]GCTGCTCACAGGAGACAGACGGATGTTCAAGATAA Y 2 1 2 1 202000 r 74 goat snp8165-scaffold1299-2252870 NW_017189516.1 31390409 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435206 Affx-122933633 AX-123305546 X 94671321 GACTTAGGGACTACACCACCACATCCGTAACATAA[C/T]AGACCTGGTGACTCAGGCTAATTTCCTTTCAGCAA Y 2 1 2 1 101000 f 74 goat snp8166-scaffold1299-2316231 NW_017189576.1 40751 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413880 Affx-122949847 AX-123284229 X 94748400 TCTGTCCCTGTACCCCCCACTCGTCCCACCTCAGG[C/T]GTATTTGAAGAGGAAAAGTTAAAATTTTACATAAC Y 2 1 2 1 103000 f 74 goat snp8167-scaffold1299-2393310 NW_017189516.1 32653976 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779856 Affx-122950832 AX-385266955 X 94774890 AGTAGCATGAAAATCTAAGGGAGGCATTAAGAAGA[C/T]ACAGTCATTAAGTGTGCAAAACTAAGATACAATCT Y 2 1 2 1 101000 f 74 goat snp3553-scaffold111-2393012 NW_017189516.1 32681691 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795105 Affx-122924749 AX-385282064 X 94811208 GTAGCAGTTTACTGTCATGGATTCTTGAACACAGA[C/T]GCTCTGAGTTCAAATGCCAGTTAAAATACTTACAA Y 2 1 2 1 101000 r 74 goat snp3552-scaffold111-2356694 NW_017189537.1 64381 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787926 Affx-122938703 AX-385274948 X 94861810 AACCTGGAATGAATATGGGGACATCACTACTGATT[C/T]TACAAAAAATAAAGTATCTAACATAATGCAATGAA Y 2 1 2 1 201000 r 74 goat snp3551-scaffold111-2306092 NW_017189516.1 32799161 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418901 Affx-122946099 AX-123289249 X 94945477 GTGAACCATGAAGTGAACCCTCTTTGCTTCATGGC[C/T]TTCAGAGATAAATGATTCTAATTTTAAATATTCCT Y 2 1 2 1 201000 r 74 goat snp3550-scaffold111-2222425 NW_017189516.1 32873257 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768613 Affx-122938023 AX-385255793 X 94996305 AAAACCTACCCTTTGTTCCTTATCATCTTGGAATC[A/G]CCTCTCTGCTAGAATAAAAGGAGAGACATCATGTT R 2 1 2 1 101000 r 74 goat snp3549-scaffold111-2171597 NW_017189516.1 32924127 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433879 Affx-122934416 AX-123304220 X 95041216 TGGCTACTTTGATGATTCATAAATATTCTGAGGAT[A/G]TCATGAGATTTAAAATTTTGAGGGCTTCCCTGGTG R 2 1 2 1 101000 f 74 goat snp3548-scaffold111-2126686 NW_017189516.1 32969167 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428799 Affx-122938400 AX-123299141 X 95131808 TTTTAGGAGATGTGTGATTACTGACTCAGTCTCCT[A/G]ACTAGTAATTTGTCTTTTTCTTTTCTTCCTGGTTC R 2 1 2 1 101000 f 74 goat snp3547-scaffold111-2036094 NW_017189516.1 34965406 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387849 Affx-122969649 AX-123258207 X 95180836 ATTTTTAATTAGAAAATAAACTCAGGATACTAAGG[A/C]GTCACCCTGGGTATAGCCTCCATCTAGATTTCTTT M 2 1 2 1 101000 r 74 goat snp3546-scaffold111-1987066 NW_017189516.1 34915015 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381416 Affx-122974363 AX-123251774 X 95229399 CAAGAGTACTGGAGTGGGGTGCCATTGCCTTCTCT[A/G]TCCCTACCTCTCCTTTAACATGGCCCTGTTAATGA R 2 1 2 1 101000 r 74 goat snp3545-scaffold111-1938503 NW_017189516.1 35168149 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440817 Affx-122929820 AX-123311154 X 95386098 GGGTCACTGCAATTCACTGTCATCAACCAAGTTGA[C/T]GACCCACAGCCAGTCCAGCCATAGTGACAAGCAAG Y 2 1 2 1 102000 r 74 goat snp3543-scaffold111-1781804 NW_017189516.1 33309815 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387577 Affx-122970272 AX-123257935 X 95512653 ATTCTACCCTTCAAATTCTAGTGCCTCAATCTTTA[C/T]GAACATTGCTATCTGTCTTATCAACTTGGAGAGAT Y 2 1 2 1 101000 r 74 goat snp3540-scaffold111-1655249 NW_017189516.1 33438848 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389205 Affx-122969066 AX-123259563 X 95544929 TCTCATGGTTATATCATGGGCAATGCGGACATGAT[A/G]CTGGCAGGAAGATTAACATACCCAGTATACTTGAA R 2 1 2 1 101000 r 74 goat snp3539-scaffold111-1622973 NW_017189516.1 33469092 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785571 Affx-122955899 AX-385272615 X 95602532 ATGGCTAAGGCAATCTGTACCATAACAAAGTAGGT[A/G]TTTTTGTTTCTTAAGTAAGAGAAGTTGTAGATCAA R 2 1 2 1 201000 r 74 goat snp3538-scaffold111-1565370 NW_017189516.1 33526330 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390367 Affx-122967674 AX-123260724 X 95682608 TTAACAACAGCTTGATATTCTCTCTTTCCCCCTTT[A/C]TCTTCCTCTCTTTTGCATAAACACAATGATGTGAT M 2 1 2 1 201000 r 74 goat snp3536-scaffold111-1485294 NW_017189516.1 33607542 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385202 Affx-122971717 AX-123255560 X 95753637 TGAGTTCACAAATATTGCAGCATAGTTTGTACCCT[A/G]CATATTAGGGGCACTGTCTCACATTAGCCCTTCTA R 2 1 2 1 201000 f 74 goat snp3535-scaffold111-1414265 NW_017189516.1 33678900 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801621 Affx-122941710 AX-385288529 X 95820334 AATATATTATCATGCTCTTATTACAAAATCAGTTG[C/T]AACTTAATTAAAATGTACACAATTAGGGCTTTAAA Y 2 1 2 1 101000 r 74 goat snp3534-scaffold111-1347568 NW_017189516.1 33746341 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779461 Affx-122963473 AX-385266564 X 95875557 GTGCAAATTTTTGAAAAAATCAGAATAAATGATTA[C/T]AATAAAACCTGAGCATAAAGCATTAAATTCAACTT Y 2 1 2 1 202000 f 74 goat snp3533-scaffold111-1292345 NW_017189516.1 33801895 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432393 Affx-122935850 AX-123302734 X 95906606 CTTTTGCAACTGGATCATTTGTTGATATTTTACTC[G/T]TATTCAAAGATTTATTTCTCTGTATCTATCACCTA K 2 1 2 1 101000 f 74 goat snp3532-scaffold111-1261296 NW_017189516.1 33844562 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408397 Affx-122954483 AX-123278748 X 95948715 GTGGGAACAGTGGTTCTTAGAGAGTTTAGTACTAG[C/T]GTCCATAAAGTAAGCATAATTCCTTTCAATCATCT Y 2 1 2 1 101000 f 74 goat snp3531-scaffold111-1219187 NW_017189516.1 33886807 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794826 Affx-122933964 AX-385281786 X 95979452 GTGTAGTCAAGTCTGTGATTTAAGTAAGTGACTTG[C/T]GAGCAATGTAAATATACCATAGTAAATGTTGTAAA Y 2 1 2 1 101000 f 74 goat snp3530-scaffold111-1188450 NW_017189516.1 33914068 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412811 Affx-122950478 AX-123283160 X 96028650 TTCCATCAGATCAAGGCCAAAGAGCATCTTCATGC[A/G]TTCAGAGGCTCTCAGAAAGATCTCAGGGAAGTGGA R 2 1 2 1 101000 f 74 goat snp3529-scaffold111-1139252 NW_017189516.1 33958089 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782008 Affx-122924126 AX-385269087 X 96060173 TGGTAAATTTATGGTTCCCTATGCGAGGGAGAGCT[A/G]TAATTTTATTAAGGGTTACATTAGAGTGTAAGGAC R 2 1 2 1 201000 r 74 goat snp3528-scaffold111-1107729 NW_017189516.1 33989841 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779475 Affx-122952999 AX-385266578 X 96103472 TTAAGATAAATCTGCAAATTTTAGTACCAGAATTG[A/C]GCACTTAAATTCAGTCTATAATTTAGGTTAATGTG M 2 1 2 1 101000 r 74 goat snp3527-scaffold111-1064430 NW_017189516.1 34033150 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428478 Affx-122938788 AX-123298821 X 96151904 CTAAGCTACTCGATGGTATTATTGCTTCAGCATCC[A/G]TTTTGTTCAGCCAAGCAGCCTGCAGAGACCTTAAA R 2 1 2 1 101000 f 74 goat snp3526-scaffold111-1015998 NW_017189516.1 34081742 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445300 Affx-122925446 AX-123315637 X 96197197 AGATTTAAGTGGAACCCTCAGTTATTAATACATCA[C/T]AGTCTATGACATTTGGATGCCTCCTATTTTGGTCT Y 2 1 2 1 101000 r 74 goat snp3525-scaffold111-970705 NW_017189807.1 1539 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774412 Affx-122951716 AX-385261548 X 96233783 GGAAATAGAGAATAAAGTTACAAACAAGTTTAGCT[A/G]TAAAAAAAAGTTTATGGTTAAAATGTGGATTAATA R 2 1 2 1 201000 r 74 goat snp3524-scaffold111-934119 NW_017189807.1 39859 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397823 Affx-122962481 AX-123268178 X 96315205 AATTTCTAGAATAAAAAAGCATATGAGAAGAAGGG[C/T]ATAAATATTTTTTATTCTAAAAGCAGAAATGGTCC Y 2 1 2 1 101000 f 74 goat snp3523-scaffold111-852697 NW_017189807.1 119582 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798193 Affx-122931123 AX-385285128 X 96412625 AAACATACTGTTAAAATATTAATGACATAAGCTCA[C/T]AGATAATTCTTACTTTACCTTAAATTTTCTACCTA Y 2 1 2 1 101000 f 74 goat snp3522-scaffold111-755277 NW_017189807.1 218304 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438027 Affx-122931561 AX-123308365 X 96472547 GAGTTAATCCACTCACCTTCTTTCATAGAATCTGT[G/T]ACAAATGGTATCCAGCTTCAGAGGACCAGCATGGC K 2 1 2 1 101000 f 74 goat snp3521-scaffold111-695355 NW_017189516.1 34279967 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421354 Affx-122944058 AX-123291701 X 96504307 AAGAACAGGCCTCTGGATCTTGTGTTAACATCATG[C/T]GGTGACTATAGTAACAGTGTTACAACTAACAGAGA Y 2 1 2 1 101000 r 74 goat snp3520-scaffold111-663595 NW_017189516.1 34312107 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399194 Affx-122960619 AX-123269549 X 96533776 GAGTCACAGAATGGAAAACTCAGAGTTTGTTGTAA[C/T]GGTCCTTTTGTGTCCTTTTGTGGATGGTCACCAGG Y 2 1 2 1 101000 r 74 goat snp3519-scaffold111-634126 NW_017189516.1 34341710 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424920 Affx-122941295 AX-123295266 X 96565181 AAACTTTCAAAATTTGATAAAAATATTAATTTACA[C/T]ATCTAAGAAGTACAAAATATTCTGTGAAGGATAAA Y 2 1 2 1 101000 r 74 goat snp3518-scaffold111-602721 NW_017189516.1 34372976 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767447 Affx-122974587 AX-385254718 X 96595757 GGACTTGGGAGGTCTGAAATATAACACTGCAGTTG[C/T]GGCCTTTATTAACCAGAGTAAAAATAAACAGGTAA Y 2 1 2 1 101000 f 74 goat snp3517-scaffold111-572145 NW_017189516.1 34403776 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429079 Affx-122938280 AX-123299421 X 96637775 GTTTCACCTGGTCCGACATATAAAATAGGAGGTCC[A/G]TGAAACCATTCTCCTTCTATAGTAACTTGAAATTT R 2 1 2 1 101000 r 74 goat snp3516-scaffold111-530127 NW_017189516.1 34445902 A G 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38422591 Affx-122943741 AX-123292937 X 96671587 CAACTAGGCTGGACTATGGTGTCCAGTTGTTTGAT[C/T]ACACACCAGTCTAAATGTTGGTAGGAAGATACATG Y 2 1 2 1 101000 r 74 goat snp3515-scaffold111-496315 NW_017189516.1 34479782 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794424 Affx-122963005 AX-385281387 X 96728055 TTTACAGAAAGTTAAATAAGAATTTGGGTGAGAGT[A/G]TTCCAAGCAGAAGTGTAAGCAATGTAAAAGCTTAA R 2 1 2 1 101000 f 74 goat snp3514-scaffold111-439847 NW_017189516.1 34536610 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788218 Affx-122927028 AX-385275237 X 96764800 ATGACATTGAAAGAATCATGTTTCCATCTCAAACT[A/G]TCATTTGTCAGTGACCGAAGATGGGTCTTCTAGTA R 2 1 2 1 201000 f 74 goat snp3513-scaffold111-403102 NW_017189516.1 34150449 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384494 Affx-122973060 AX-123254852 X 96841578 ACAGATTAACTCACATGCAAAGATTCTGGGGTAAA[A/C]AATACAAGGAGAGCTGTGACTGTTATCCTCTGCTG M 2 1 2 1 101000 f 74 goat snp3512-scaffold111-326324 NW_017189516.1 34227781 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406561 Affx-122955103 AX-123276913 X 96905552 TGAGGCCAGTCAGGAACCCAGGGATTCTTCTTTAG[C/T]TTTAACAGGATTTGAGTTTGATAACTGCGTACCAA Y 2 1 2 1 201000 r 74 goat snp3511-scaffold111-262350 NW_017189516.1 34597724 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793638 Affx-122927751 AX-385280611 X 97019092 ATTAGCAATGATTTCAGCTAATCAAAGTAAACCAA[C/T]CTCTACTCTAGCTGAAATTCATTCAGCTATTAAAG Y 2 1 2 1 101000 f 74 goat snp3509-scaffold111-148810 NW_017189516.1 34710553 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400366 Affx-122960025 AX-123270721 X 97049539 TACGAGAAAGATGGGGAAAAAAACGACCCAAGTGA[C/T]GTGACTGGAGAAAAACATTGAGAAGAAAAAATTCT Y 2 1 2 1 101000 f 74 goat snp3508-scaffold111-118363 NW_017189516.1 34741158 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431081 Affx-122936625 AX-123301422 X 97093718 TCTCATTCAAAAATCCATTGGCTCTCTTTGATAAG[C/T]AGAATTGAAGACTCTTCAAGTTGTTTTTTCTTTCT Y 2 1 2 1 101000 f 74 goat snp3507-scaffold111-74184 NW_017189516.1 34785459 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787177 Affx-122919669 AX-385274203 X 97130642 CCAATGGGCAGCTCTTTGTATTAGTGACATCTGAC[A/G]TGACTATTACATACCTCAAGTGAAAAAACCAATTA R 2 1 2 1 101000 f 74 goat snp3506-scaffold111-37260 NW_017189516.1 34822307 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408587 Affx-122953656 AX-123278938 X 97169073 GGCCGAAGTGGGTTGACCTTTTGAAAAGAGTGACA[A/G]TGTCTGCTCAGGACAACCCTGAGGGTCTTGACTTC R 2 1 2 1 101000 f 74 goat snp49716-scaffold71-5001139 NW_017189516.1 33307138 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404308 Affx-122957023 AX-123274660 X 97210397 AATGAAGACGCATGTAGCCCTGCCACGCGGGTCTC[C/T]CTGTGCTGTGTTTCTGCTCCTCTCCAGGCAGCTGC Y 2 1 2 1 201000 f 74 goat snp49715-scaffold71-4959815 NW_017189516.1 33265739 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414372 Affx-122950004 AX-123284721 X 97267468 GCTGAATTAAATTGAATGATGAGAGGAAGAAACTC[A/G]TGGCAGACATTTATAATACATTTTCTTGCTAAAGT R 2 1 2 1 101000 f 74 goat snp49714-scaffold71-4902744 NW_017189516.1 33207933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438755 Affx-122930818 AX-123309092 X 97307297 TTTAATATTAAAGTCCTGTTGGCTTCATAAAATAC[A/G]TTAGAGAGACTTTCATCTTTTTTTCTGTTCACCTG R 2 1 2 1 201000 f 74 goat snp49713-scaffold71-4862915 NW_017189516.1 33168067 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434032 Affx-122934213 AX-123304373 X 97387639 TGGATCTCCCATTTCTTTGAGAAAACCAACCAACC[A/G]TATATGTGTGCTGCAGGCAGTTCCAAGGTGGTGAT R 2 1 2 1 102000 r 74 goat snp49712-scaffold71-4782573 NW_017189516.1 33086952 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379573 Affx-122976041 AX-123249931 X 97417635 ATTGTATATATTATTAATTGCATATATAATATAGA[C/T]AGGTAGGGGAAACCTTGATAAGTGGTACATTATGT Y 2 1 2 1 202000 f 74 goat snp49711-scaffold71-4752577 NW_017189516.1 33052274 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387209 Affx-122970595 AX-123257567 X 97452847 AATAGAGGGATTCAGACAATGTCAAGAGGCGAAAG[C/T]GCTATTTGAGGCAGTGGATTTGGGAAGAAAAATCC Y 2 1 2 1 101000 f 74 goat snp49710-scaffold71-4717365 NW_017189516.1 33017508 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398532 Affx-122961534 AX-123268887 X 97484125 AGTACTTTCTTCTGATTTAGGAGAGAAAAACACAG[C/T]GAAAGTTCAACTGTTGAGAGTGGGCAGGACTGTGC Y 2 1 2 1 201000 f 74 goat snp49709-scaffold71-4686087 NW_017189516.1 32985840 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775260 Affx-122954372 AX-385262391 X 97557553 TTGAAACCTTGGTTGATAGTGTTATGAGTGTGAGG[C/T]ATTACTCTGAAATCCTCAAAGGAATCAATTAAGTG Y 2 1 2 1 101000 f 74 goat snp49708-scaffold71-4612659 NW_017189516.1 35282428 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441704 Affx-122929158 AX-123312041 X 97617922 ACAATTGGGGCAGCCTCCATTTTGTGGGTCCTGAT[A/G]TACAGATTAACTTTATTAGTCCAGATATCTAAAAC R 2 1 2 1 101000 r 74 goat snp49707-scaffold71-4552290 NW_017189516.1 35344240 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429558 Affx-122937819 AX-123299900 X 97650130 AAGCTGAACAATAGTAAGAAGAAAAATAATAAGTT[A/C]TTTTGTTTTCCTAAAGAAAATTAAAATGATCATTT M 2 1 2 1 103000 r 74 goat snp49706-scaffold71-4520082 NW_017189516.1 35378254 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800263 Affx-122954540 AX-385287186 X 97716409 CTCCTTAGTATGAACTTATTCCAAAAATGAATGCT[A/G]CAATACTGACAACCAAAAGCAACACCACCAAGCTA R 2 1 2 1 101000 r 74 goat snp49705-scaffold71-4453803 NW_017189516.1 35435592 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442735 Affx-122927849 AX-123313072 X 97783472 TTTGACAATGTTAGATAGCTCATATAAGTGGAATG[C/T]AGTATTTGTGCCTCTGAGACTGCATTACTTCAGTT Y 2 1 2 1 101000 r 74 goat snp49704-scaffold71-4386740 NW_017189516.1 35503580 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802985 Affx-122934655 AX-385289869 X 97843483 GAGCTATTTACCTTTAAACATAACAATCTGAATCT[A/G]TATGGAACAATCTGAACTGAATTACTTGTTCCTAA R 2 1 2 1 101000 r 74 goat snp49703-scaffold71-4326729 NW_017189516.1 35564667 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775826 Affx-122960719 AX-385262957 X 97906369 TGTGGTTATGTACAGTGTCAGTGCCTGATGTTTGT[A/G]CATAGCTATTTGATGCTGAGGATTCTGAGCTTCCT R 2 1 2 1 101000 f 74 goat snp49702-scaffold71-4263843 NW_017189516.1 35628494 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427462 Affx-122940026 AX-123297805 X 97973575 CAGGAAATAACAAGCCATCACATCATATTTCTTCA[C/T]GGACCTATTAATGTGATAAATTATGTTCAGTGCTT Y 2 1 2 1 101000 f 74 goat snp49701-scaffold71-4196637 NW_017189516.1 35694607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786368 Affx-122942816 AX-385273402 X 98032278 ACATAAACAAGTCCGTTCAAAGAATAAACATTGGA[C/T]AGCATTTTGCAGACAGTCATAGTTCTCAAATTAAA Y 2 1 2 1 101000 r 74 goat snp49700-scaffold71-4137934 NW_017189516.1 35754749 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447579 Affx-122924021 AX-123317915 X 98067168 CATGACAACATCCAACACTTTGCCTAAGTGAGGCC[A/G]TGGAATCATTCTCTACACATCATTCCATGCATCTG R 2 1 2 1 102000 f 74 goat snp49699-scaffold71-4103044 NW_017189516.1 35789761 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450451 Affx-122922955 AX-123320785 X 98110262 AAATTGGAGGCTGAGAGGGTCTCTAATGAGATCCA[C/T]GGGGGAAGAGTGATGTGAGTAAAGTGAAACTATTC Y 2 1 2 1 201000 f 74 goat snp49698-scaffold71-4059950 NW_017189516.1 35833232 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779923 Affx-122932270 AX-385267022 X 98139111 ACTGAAGAAGAAAAACCATTTTCATTCAACTTAGT[A/G]CATTTATAGAATTATGCTATATTTTTGCTTTTCAA R 2 1 2 1 101000 f 74 goat snp49697-scaffold71-4031101 NW_017189516.1 35862373 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444308 Affx-122926747 AX-123314645 X 98185233 GTTAGTGTGTCACAATCAACCTAAAGATAAATGGG[C/T]AGAAACAGCAAGATAAAATATGAAAAAATCCAAGT Y 2 1 2 1 101000 f 74 goat snp49696-scaffold71-3984979 NW_017189516.1 35910209 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402457 Affx-122958610 AX-123272810 X 98273573 GTAATGGAAACTCCTTTTCCATTCTCATCATTCAT[A/G]CCATGACTAAAACGTCACTGTGTCAGAAAGTTCCT R 2 1 2 1 101000 r 74 goat snp49695-scaffold71-3896639 NW_017189516.1 35980029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438884 Affx-122930738 AX-123309221 X 98341342 GGGGTTTGGTCAGGATGTGGCAGAGAAACAGAGGT[A/G]TGTTAGATTTTCCATCATATATTGGGGGAGACATA R 2 1 2 1 202000 r 74 goat snp49694-scaffold71-3828870 NW_017189516.1 36046972 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443521 Affx-122927784 AX-123313858 X 98389823 GTGTATGTAAGTCCCAAAGACATGAGACTCAAAGG[A/C]GAATGACTGAGGCTTATATGCTGTCTTGAGCCAAA M 2 1 2 1 101000 r 74 goat snp49693-scaffold71-3780389 NW_017189516.1 36095289 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798235 Affx-122941609 AX-385285170 X 98435590 TTATTTTAAGCAATGCCACTTTCAAATGTGGCTAC[A/G]CTTTCAAATGTAGCCAATAGATTTAATCATTAATC R 2 1 2 1 201000 f 74 goat snp49692-scaffold71-3734622 NW_017189516.1 36141067 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426595 Affx-122939982 AX-123296941 X 98473353 TTAACTGAACCATGAGTGAGTCACTATTCTATGCA[A/G]TATTTTATCAGATCAGAACAGCTGTTTCTGGATGA R 2 1 2 1 101000 f 74 goat snp49691-scaffold71-3696859 NW_017189516.1 36180029 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419870 Affx-122945363 AX-123290218 X 98508745 ACAGATCTGAAGTAAATCCAGACCAGGTTTTAATC[A/G]TTAGAAAGTTAATCATTTTCATTTTCACCAACCAC R 2 1 2 1 101000 f 74 goat snp49690-scaffold71-3661467 NW_017189516.1 36215604 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802083 Affx-122930723 AX-385288987 X 98543965 TTGGGGGAAAAGAGGAAACAGCAGAGAGACATAGG[C/T]ATTGCCAGTGTAACAAGTTCTTTGGTTTGCTTTTT Y 2 1 2 1 101000 f 74 goat snp49689-scaffold71-3626247 NW_017189516.1 36250899 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381911 Affx-122974148 AX-123252269 X 98583851 CCAACATGGAGCAATATTTGCAATAAATACTTTGC[A/G]TGACTTTAGAGAAGGGAGCAATGGATTCTGTAAGA R 2 1 2 1 101000 r 74 goat snp49688-scaffold71-3586361 NW_017189516.1 36290758 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792053 Affx-122956065 AX-385279041 X 98618530 AAAACAGAAATGTTTAGAGCTGTGACAAACTTCCA[C/T]GTATCTTCCTTCTCTCAGTCCTCTACACAAAATGA Y 2 1 2 1 101000 r 74 goat snp49687-scaffold71-3551682 NW_017189516.1 36325421 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794311 Affx-122957544 AX-385281276 X 98716379 TAAACTATTAATATTTTCACCACACCTCAAATACC[A/G]TATCTATTACAACATAATATTTTCTGCTTTTATTG R 2 1 2 1 201000 r 74 goat snp49686-scaffold71-3453833 NW_017189516.1 36425280 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788993 Affx-122932624 AX-385276006 X 98768729 TTGCAAGCTGCCTCAGGCCCAATATTGACTGCACT[C/T]TACTTCAATAGCATTTTCCTAGGCACTCTGAGCGT Y 2 1 2 1 101000 f 74 goat snp49685-scaffold71-3401483 NW_017189516.1 36479619 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776702 Affx-122922450 AX-385263828 X 98798680 GCTCAACAGAGAATTGATGGAGGATTGGAAGAGGA[C/T]GAGATGATGAGCAAGACAACTTAAGAAGAATCATT Y 2 1 2 1 101000 r 74 goat snp49684-scaffold71-3371532 NW_017189516.1 36508962 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776245 Affx-122956650 AX-385263373 X 98849612 CTTGTGCACTTTAAACTATGTTTGTTACATTTCAA[G/T]AAAGAACTTTTGAAAACCAAGCCAGACAGAACTGC K 2 1 2 1 101000 r 74 goat snp49683-scaffold71-3320600 NW_017189516.1 36559078 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788916 Affx-122973524 AX-385275930 X 98881913 GGTGGCAGCTCACTTTCTAGCTAAGGCCTTATGGA[C/T]GGTACTCATTTACTGTTTCATCTCAGTTTGGGAGG Y 2 1 2 1 101000 r 74 goat snp49682-scaffold71-3288299 NW_017189516.1 36591214 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410185 Affx-122952586 AX-123280535 X 98910573 TCCTCACACAGCTCAGAGAGGGGACCCCTGTACAA[C/T]GTTGGTGGGAACATAAATTGGTATAGTCACTATGG Y 2 1 2 1 201000 f 74 goat snp49681-scaffold71-3259639 NW_017189516.1 36619903 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451273 Affx-122921315 AX-123321606 X 98957925 ATAACTACACTGGACAGCTTTTAGGAGCATCATTA[C/T]AAAAATGACTGCTCAAGGAATTTGCTCAAGTTCCC Y 2 1 2 1 101000 f 74 goat snp49680-scaffold71-3212287 NW_017189516.1 36667402 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434600 Affx-122934099 AX-123304941 X 99006846 ATACTAGAGGGAATTTTTCTGGAGTTTTCTAGTTA[C/T]AAATTCAGTTTGTTAATGGTTATACAGTTATTCAT Y 2 1 2 1 101000 f 74 goat snp49679-scaffold71-3163366 NW_017189516.1 36716802 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397221 Affx-122962383 AX-123267576 X 99039782 TCTGGACACATCTGATTTTATTATTTTATCTTCCC[A/G]TTCCTTAATCCAGTCTATCTTTTTCAAAATTAATT R 2 1 2 1 201000 r 74 goat snp49678-scaffold71-3130430 NW_017189516.1 36749706 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453897 Affx-122919502 AX-123324230 X 99093293 GAGTTCAAGAAGGACACCTCGTTGGTGGCAAGGCC[A/G]TGGTGTTGATGAACTGGTCAGAGATACAGTAACAT R 2 1 2 1 201000 r 74 goat snp49677-scaffold71-3076919 NW_017189516.1 36803234 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436985 Affx-122933148 AX-123307323 X 99160434 TTCAATTGTTCTTGCTCTCACAAGAGTATAAATGA[C/T]AATCACCACCAATAATTGAATATTTACTATATGCC Y 2 1 2 1 101000 f 74 goat snp49676-scaffold71-3009778 NW_017189516.1 36870286 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383902 Affx-122973112 AX-123254260 X 99219479 TCTTGTGTATCTCTCTCTGGGTTAGAAGTATACAG[C/T]AATTCATTTAGGAAACATCGTCATCATTTCCAAAC Y 2 1 2 1 101000 f 74 goat snp49675-scaffold71-2950733 NW_017189516.1 36929660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802862 Affx-122956823 AX-385289760 X 99262068 ATTTTTAAAAGAAAATCTATTAATTGATTAAATTT[A/G]CAACTTACTTTGGCATGTTAAGCATAGCTTATGCA R 2 1 2 1 202000 f 74 goat snp49674-scaffold71-2908144 NW_017189516.1 36972795 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765692 Affx-122929255 AX-385253155 X 99296417 GAAGGGGTTTAGGGACAGAGCTATTTTTAAAGCAG[C/T]GATAAGAAAACAATGGTGTCACATCACATAACACT Y 2 1 2 1 101000 f 74 goat snp49673-scaffold71-2873795 NW_017189516.1 37007084 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406557 Affx-122955106 AX-123276909 X 99345963 ATCAGCCCCCCAGGGAAGAAAAAGGCAGAGAGAGG[A/C]TCTAGAAGAATAAACCAAAGACACATTCAACATTC M 2 1 2 1 201000 r 74 goat snp49672-scaffold71-2824249 NW_017189516.1 37056861 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772439 Affx-122932607 AX-385259590 X 99405328 ACTCTCATATTAACACATTATTTGTACAGAAAGAG[C/T]AACTCTATTCTTGGCAAAGTTAGAATGTAACCTTG Y 2 1 2 1 201000 f 74 goat snp49671-scaffold71-2764884 NW_017189516.1 37117316 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450325 Affx-122922131 AX-123320660 X 99467779 TCGTGTGTACTGTTACTTTAAGTTACAGGAACTAC[A/G]CATTTGATTTAAAATACAAACAACCAATTTTAAGA R 2 1 2 1 101000 f 74 goat snp49670-scaffold71-2702433 NW_017189516.1 37180549 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446422 Affx-122925984 AX-123316758 X 99529189 TGTTTGGGGGAACTCAAAGTGTTTATTAAATCAAC[A/G]TGGGCATCTGAGCCCTAAGTTATGCAAGGAACACA R 2 1 2 1 101000 r 74 goat snp49669-scaffold71-2641023 NW_017189516.1 37241669 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381231 Affx-122974507 AX-123251589 X 99574602 CCCTGGGTATAGAGTTTTGTTTGTTTTGTTCACTG[C/T]AGTGTCTGACAAAGAGTAGAACATACTAAATCTTT Y 2 1 2 1 201000 r 74 goat snp49668-scaffold71-2595610 NW_017189516.1 37286528 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444685 Affx-122926442 AX-123315022 X 99638738 ATCCCCTGAGCTTTTAGGAATAATGCATATGTTTG[C/T]AAGCTAGGTAAACATTAGGCACATAAATGAGAAAT Y 2 1 2 1 101000 f 74 goat snp49667-scaffold71-2531474 NW_017189516.1 37350713 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382762 Affx-122973981 AX-123253120 X 99691998 ACATTTACATAAACTTTAATTCAGTCGCTTTCAGT[A/C]TACCACTTGGAACTCATCATTCCCAAATGTGTAAA M 2 1 2 1 101000 r 74 goat snp49666-scaffold71-2478214 NW_017189516.1 37404229 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786250 Affx-122962959 AX-385273285 X 99731742 CTATGAATGACCTTACATCTTTTTCATAAATCAAA[C/T]ACAGATGTTCCTTTACAACTCTCATCTCAAAATTG Y 2 1 2 1 201000 f 74 goat snp49665-scaffold71-2438470 NW_017189516.1 37444249 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428345 Affx-122938989 AX-123298688 X 99784832 TACCAGAATTAGAAGATTATTATCCAGAAATTGAG[A/G]TAAAGGAACCGTAAGCTCATTTTTTTTTCTTACTT R 2 1 2 1 101000 f 74 goat snp49664-scaffold71-2385380 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797875 Affx-122921254 AX-385284813 X 99835626 AAAAACTTCGTGCTCACTCTTGATATCCATGAGGC[A/G]TTCCTATGTCCTTATGACCATCTCCCCTCCCTCAT R 2 1 2 1 101000 f 74 goat snp49663-scaffold71-2334586 NW_017189516.1 51844362 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383558 Affx-122972606 AX-123253916 X 99884289 AGCCAACAGAATTTGAAGTGAATTCCATGGATAAT[A/C]TAAAAGTAGGAGGAATCAAAGATGATGTTTAGGTT M 2 1 2 1 101000 f 74 goat snp49662-scaffold71-2285923 NW_017189516.1 51793661 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387912 Affx-122970453 AX-123258270 X 99925736 ATCTTATTATTTTGATATAGAACAAAAAATCCAGT[A/G]TGTGTGATCAAGCAAGTTCATACAATTATTCAAGA R 2 1 2 1 101000 r 74 goat snp49661-scaffold71-2244476 NW_017189516.1 51751743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431747 Affx-122936735 AX-123302088 X 99960134 CCTCTGCCCTGTTTTAGTGCTTTTTAAAGCTCCCC[G/T]CAGGCCAAAGAAAACAACCAAGCAAAGCAAATCCT K 2 1 2 1 201000 r 74 goat snp49660-scaffold71-2210078 NW_017189516.1 37520662 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447880 Affx-122923826 AX-123318216 X 99990837 AAACTTTATAAAGTACTTGAAAATAAATAATTTAC[A/G]CCTTGTTGGTCACGCAACCTTTATTACAACTATTG R 2 1 2 1 101000 r 74 goat snp49659-scaffold71-2179375 NW_017189516.1 37551243 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798623 Affx-122932368 AX-385285555 X 100081227 CTAATATTCTTGCTGTATCAAGGACTCTCAGAGAC[A/G]TGGCTTTTCTACACTAATCAAAGAAGATGAAACAT R 2 1 2 1 101000 f 74 goat snp49658-scaffold71-2088985 NW_017189516.1 37642386 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787304 Affx-122953295 AX-385274329 X 100140980 TGGTACCAAGTTAACTGTTGTAATTACTTTTGAAC[A/G]TGGTACTTCCCTCTAGTGGTACTGTCATTCGGAGA R 2 1 2 1 101000 r 74 goat snp49657-scaffold71-2029232 NW_017189516.1 37702190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378458 Affx-122976686 AX-123248817 X 100218539 CTTCCAATAAAGTTAAGATAGACTGAGAGATTTTA[C/T]ACAACTGAAATGAAAATAAATTGATTTAGGATGTA Y 2 1 2 1 101000 f 74 goat snp49656-scaffold71-1951673 NW_017189516.1 37779835 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403563 Affx-122957586 AX-123273916 X 100276470 CAGTAGTAACTCTCATCTACTGCCTAAGTTCCAGC[A/G]TCTAAATAACTTTAAAAAGTCAGATATATACTGCC R 2 1 2 1 103000 f 74 goat snp49655-scaffold71-1893742 NW_017189516.1 37837927 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769680 Affx-122929962 AX-385256850 X 100329125 GCCAAATCTTAAGAGATTCTACCCAGGAAGGGGAT[A/C]TATGTATAATTATAGGCTATTTGTGTTATACAGCA M 2 1 2 1 201000 r 74 goat snp49654-scaffold71-1841087 NW_017189516.1 37890599 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403031 Affx-122958551 AX-123273384 X 100358885 GGTGATAAACTCTTGCCTGCAAACCTGGGGTTCCA[C/T]GGTTCACTGGCTCCAGGCCTAATCTATCAATCCAT Y 2 1 2 1 101000 f 74 goat snp49653-scaffold71-1811327 NW_017189516.1 37920172 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381857 Affx-122974186 AX-123252215 X 100388033 CACATGATGGCCACACCTGAATTTTGTTATTGTTG[C/T]TGAAGATCTGAAATGCATAATACATGATGAGGTAA Y 2 1 2 1 201000 r 74 goat snp49652-scaffold71-1782179 NW_017189516.1 37949496 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435122 Affx-122933692 AX-123305462 X 100419598 TTTCCTCCCCTTTTAAAATAAAATCACAAAGATTA[C/T]GGCTATAGCTTCTGTTGCTTTTGTTTTTCCCTGCA Y 2 1 2 1 103000 r 74 goat snp49651-scaffold71-1750614 NW_017189516.1 37981069 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777919 Affx-122920051 AX-385265035 X 100465573 GAAGTGGCATTATGGTAGGGCTTTTCTGCTCATCT[A/G]CTTCTTTGGAAGACCATTCTATCTTTGTAGAAGTG R 2 1 2 1 101000 f 74 goat snp49650-scaffold71-1704639 NW_017189516.1 38027166 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778028 Affx-122959079 AX-385265144 X 100519684 TTTTCTCTAAGATAGTGGCCAAAGCAGGTGTTAAT[A/G]AGGTCAGTACTTCAATTAAAACTTCACAAAGCTAG R 2 1 2 1 101000 f 74 goat snp49649-scaffold71-1650528 NW_017189516.1 38081480 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796204 Affx-122966853 AX-385283155 X 100550308 CTTAAATGGTGAGTGGGGGCAGGATTTAAACCACA[G/T]TTGCCCATCTTAGATCCACTGCTTTCAGCACCACA K 2 1 2 1 101000 f 74 goat snp49648-scaffold71-1619904 NW_017189516.1 38112865 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398446 Affx-122961608 AX-123268801 X 100595539 AAAAATTTTCTTAGAGCATAGCCCCATGGTTGGCA[C/T]ATGGTATACTTTTGATAACTGCCAAATGAATTGTC Y 2 1 2 1 201000 r 74 goat snp49647-scaffold71-1574673 NW_017189516.1 38158392 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435754 Affx-122932886 AX-123306093 X 100624592 GAAAGAGAAGCAGGTTGCATCTGGAAAAAGAGGTT[A/G]TAAGAGGAAAAAGATGAGTTCAGCTTTGGGGCTAT R 2 1 2 1 101000 f 74 goat snp49646-scaffold71-1545620 NW_017189516.1 38187789 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413770 Affx-122949930 AX-123284119 X 100660113 TCCTAAAACAATTTCTCCTCTTTAATTCTGCAACT[C/T]TGTGTAGGCATCTGGTCATATCAAATGGTAAGCAG Y 2 1 2 1 101000 r 74 goat snp49645-scaffold71-1510099 NW_017189516.1 38227897 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429695 Affx-122937634 AX-123300036 X 100701931 GAGACTAATAGCAATAAAACTGCTGACAACAAATC[A/G]TACTGACTAATCTTCACTGACTGCATTTTATGTCC R 2 1 2 1 101000 r 74 goat snp49644-scaffold71-1468281 NW_017189516.1 38270035 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789481 Affx-122961646 AX-385276491 X 100809743 ATCACAAGGTAGAGAGAGATACATTCTTTTTAGGA[C/T]AGTGGTGGTTTGAACACAGACGGAAAGTTGGATAA Y 2 1 2 1 101000 f 74 goat snp49642-scaffold71-1360469 NW_017189516.1 38378012 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439510 Affx-122930134 AX-123309847 X 100847947 AAAAACTGAACCATTTACTATGAGAAGGCTCTCTA[G/T]AAGGGTGTTTGGGGATGAGGGTTTTAAAAGCTAGA K 2 1 2 1 201000 f 74 goat snp49641-scaffold71-1322265 NW_017189516.1 38396951 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377812 Affx-122977311 AX-123248171 X 100904980 TGCAAAGAATTGGACGCAACTGAAGCAACTTAGCA[C/T]GAAAATACTACAACGAACTGTTCAAACAAAAGAAC Y 2 1 2 1 201000 r 74 goat snp49640-scaffold71-1265232 NW_017189516.1 38454040 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449055 Affx-122923058 AX-123319390 X 100960032 ACATAAGAAATCCCTTTCTGGACAAAAGGGGTATA[C/T]GGAGACTACGTGTGAAATTGGAAAGGGGGATATTC Y 2 1 2 1 201000 f 74 goat snp49639-scaffold71-1210180 NW_017189516.1 38508703 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405041 Affx-122956358 AX-123275393 X 101020047 TTAGAAAGTGAGGCTTTCTCACAGAACTCAGCTGA[G/T]AGCTGCTCAATTTATCCGTGGTACTTGTTGTATAG K 2 1 2 1 101000 r 74 goat snp49638-scaffold71-1150165 NW_017189516.1 38550182 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442627 Affx-122928463 AX-123312964 X 101049406 AAGTTTTGAAAGCTGAAAATCAAATTTCAACACTT[A/C]GTTCATTTCCAAGATGTTTGTTGTTAGGAGGGCAA M 2 1 2 1 101000 r 74 goat snp49637-scaffold71-1120806 NW_017189516.1 38579641 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771434 Affx-122953143 AX-385258592 X 101089348 TCGCTGATACATTTGCTTCATATCGAAGCTTCCAC[A/G]TAAATGTCTAGATTACACGGATAATCTGGATGGAA R 2 1 2 1 101000 f 74 goat snp49636-scaffold71-1080864 NW_017189581.1 47854 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434360 Affx-122934714 AX-123304701 X 101132537 AGTTTCGGTGTTTGAGCCCCTGCAATTTGTGATAG[C/T]ACAGCACTGAATGAGGGGAACGCAACATGTCTGAG Y 2 1 2 1 101000 f 74 goat snp49635-scaffold71-1037675 NW_017189581.1 4535 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416996 Affx-122947989 AX-123287344 X 101283600 GAATACATTAAATAAACCTGTAGTGATGAACAGGG[C/T]AGGATGGTGCTACCCAGCCTCACCCCGGGAGTCTT Y 2 1 2 1 101000 f 74 goat snp49633-scaffold71-886612 NW_017189516.1 38875090 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375966 Affx-122978438 AX-123246325 X 101334897 CCAGGAAGTTGGAAGTGTCAGCCTAAACTCTTCCT[A/G]TTCAACTTGAGTGGGTCCAGGTTTGCAGCAACACT R 2 1 2 1 101000 r 74 goat snp49632-scaffold71-835315 NW_017189516.1 38926173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447783 Affx-122923947 AX-123318119 X 101382490 TGGTCCTATGCTACCCACTTATTATTCTTTATTTT[A/G]CAGTGGTTAGTTAAGTGCATGGCCATTTTTTTTAA R 2 1 2 1 101000 r 74 goat snp49631-scaffold71-787722 NW_017189516.1 38974249 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440504 Affx-122929356 AX-123310841 X 101429006 GAAAATTAACCTCAGAAGGTCACAGTTCTTTTTCT[A/G]TTCCAATATATACCAGAATGCTCATCTTGAAAGAT R 2 1 2 1 101000 r 74 goat snp49630-scaffold71-741206 NW_017189516.1 39018146 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400470 Affx-122961303 AX-123270825 X 101464781 CCAGACGAAAGTTACTGCGCCTGCGCGCGGAACGA[C/T]GAGGACGCATGCCCAAAACAACTCCTGAACTAGTA Y 2 1 2 1 101000 r 74 goat snp49629-scaffold71-705431 NW_017189516.1 39054020 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442148 Affx-122928321 AX-123312485 X 101499342 GGGGCAAGTGGTTCTTTTCCAAGTATCATCACAAT[C/T]AGACTCTTCTTTTCCTTTAGGTCACAAATATTTTC Y 2 1 2 1 101000 f 74 goat snp49628-scaffold71-670870 NW_017189516.1 39088603 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388738 Affx-122968960 AX-123259096 X 101594124 GATCTCTCCTAGGAAATGAGCTTGCTTGTTAGTTA[C/T]GGAATATTACTTTTAGGGCATATTCTTACCCAATA Y 2 1 2 1 101000 r 74 goat snp49626-scaffold71-576088 NW_017189516.1 39184137 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444042 Affx-122926872 AX-123314379 X 101633821 AAATAAATTGACCCTCATTCTTACTTGCATTTCTC[A/G]TTTCCAGACTAGAACTTAGATCAAAGTTAATTGAG R 2 1 2 1 101000 r 74 goat snp49625-scaffold71-536391 NW_017189516.1 39223896 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782476 Affx-122951816 AX-385269552 X 101695263 CCTTAGAGTTTAAATGTTTCTAGCTCATCATTCAA[A/G]GGCTATTCTGTTTCTTCCTTGGCTAATTTGTCTCT R 2 1 2 1 101000 r 74 goat snp49624-scaffold71-474949 NW_017212184.1 1099 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406723 Affx-122955752 AX-123277074 X 101752145 AAGCTCTTGAAAATGGAGTAATCTCTCTTTACAAG[A/C]TGAAAAGTCTGTTCTTTTAACTGTTTCATAAGTTG M 2 1 2 1 101000 f 74 goat snp49623-scaffold71-418067 NW_017189516.1 39311764 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780639 Affx-122921000 AX-385267729 X 101784487 CATTTACTTTGCATATATCCTGCCACACAGAAAAA[C/T]GCTTATCACAGCTTCATCCAGCAAATAATTGAGAG Y 2 1 2 1 201000 r 74 goat snp49622-scaffold71-385725 NW_017189516.1 39344411 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380466 Affx-122975729 AX-123250824 X 101818413 ATAGCAGATTTTGTAATACCTAGGAAATATCCAAC[A/G]CAAATTGATTAAAAGAGTGAGTAAATGGGGTAATG R 2 1 2 1 101000 f 74 goat snp49621-scaffold71-351799 NW_017189516.1 39378873 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443344 Affx-122927431 AX-123313681 X 101864380 AACACTCTCTTGTGTACCAGCAGGGCCAATGTTAC[A/G]TACAGCCTGGATTATAGCACTTCAAGTTTTTGTGA R 2 1 2 1 101000 f 74 goat snp49620-scaffold71-305832 NW_017189623.1 11107 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781922 Affx-122923488 AX-385269003 X 101926247 AATCACCTTCTTAATGGAAAGTGACATAAAGCTAC[A/G]TTCTTCATGTTGCCAGATCTCTGCAAAAGTGTACT R 2 1 2 1 101000 r 74 goat snp49619-scaffold71-243965 NW_017189516.1 42126792 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790322 Affx-122941832 AX-385277325 X 102000890 TGAGTCAGCATCAAGCTAGTAGTTTGTCAAAGTAA[C/T]AGCTGTAAGCATTTCAACTTTCCCATCCCATGACA Y 2 1 2 1 201000 r 74 goat snp49617-scaffold71-169322 NW_017189516.1 42051838 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787968 Affx-122953320 AX-385274989 X 102045746 TTCATCACAGTCCCATGTGCTGTCCCAATCTCTAA[C/T]ATAGGTAAAATTCCTCCAAAGTTCACAGCTAAACT Y 2 1 2 1 101000 f 74 goat snp49616-scaffold71-124466 NW_017189516.1 42006829 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452620 Affx-122920363 AX-123322953 X 102142220 TGGTGGGCTGCATAGTTTAAAGACAAAACCTGGGA[C/T]GGGGAACTGCCCTTAACAGTTAGAGGCACACTTCA Y 2 1 2 1 102000 f 74 goat snp49615-scaffold71-27992 NW_017189516.1 41558158 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386982 Affx-122969957 AX-123257340 X 102254524 AAATGCCCAACTTAACAATCAAGTATAGGAAAGAC[A/G]TGCTGTGAGAAGCGTGGTCAGCAGGCAGCCTCCAG R 2 1 2 1 101000 f 74 goat snp2133-scaffold1064-1709444 NW_017189516.1 39452699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776511 Affx-122977033 AX-385263638 X 102293472 TAACATTCGGTTGCCCAATGAAACTAGAAAACATG[C/T]GATTGTAACTGAGCCTGAAAAGTCTGGTCTTTCAA Y 2 1 2 1 101000 f 74 goat snp2132-scaffold1064-1670496 NW_017189516.1 39491738 T C 1 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38418035 Affx-122946639 AX-123288383 X 102342472 AGCAACTGCTGTTATTTTAAACCCGTGGTATGCTA[C/T]GCTGGCTTCAAACCAGAATCAACAGGGGAGAATTT Y 2 1 2 1 201000 f 74 goat snp2131-scaffold1064-1621496 NW_017189516.1 39540724 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451175 Affx-122921343 AX-123321509 X 102371838 AAACATAGCAACTCAGCAGCTCATGCTCTTGGTTG[C/T]ATTCCAGTTAATGTCTTGTGGGGACTGATTCAGCA Y 2 1 2 1 201000 r 74 goat snp2130-scaffold1064-1592130 NW_017189516.1 39569907 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395580 Affx-122963839 AX-123265935 X 102407571 ACCTCATCTTGCCTAGGAGATAACTTTCCCCTGGC[A/G]CACACTCTTTATACCGCCCCGTCAATGACTTCCTG R 2 1 2 1 101000 r 74 goat snp2129-scaffold1064-1556397 NW_017189516.1 39606918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377070 Affx-122978284 AX-123247429 X 102444838 ATTTCTACTATAGTAATCCCTGTTCTAAGGAAAAG[C/T]ACTCATGTATGTATAGATCAGTGAAGGAGTTATTA Y 2 1 2 1 101000 f 74 goat snp2128-scaffold1064-1519130 NW_017189516.1 39644061 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390841 Affx-122967833 AX-123261198 X 102508903 ATTGTGATGCCCTGGAAGGCTTGTTAAAATACAAG[C/T]TGTTGGGCTCCATCCTTCAGAGTTTCAAACTCAGT Y 2 1 2 1 202000 f 74 goat snp2127-scaffold1064-1455065 NW_017189516.1 39708922 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401815 Affx-122959457 AX-123272168 X 102554300 ATTCTAACTCCCATGCATACTGTTTCCACAAAACC[A/G]TGTTGTTAGATCGCTGATGAAGGATGAGGAAACCC R 2 1 2 1 101000 r 74 goat snp2126-scaffold1064-1409668 NW_017189516.1 39754118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793339 Affx-122950648 AX-385280318 X 102587041 AAAAGAGAGTGCAAATGTACAAATTAAAAATGTAC[A/G]TTAAAATCTTCACCCCATAGTTTGTCCATGATCCC R 2 1 2 1 201000 f 74 goat snp2125-scaffold1064-1376927 NW_017189516.1 39787075 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395340 Affx-122964036 AX-123265695 X 102637199 AAGTTAAGAAAAGATGAGGAGCCTGAAAGAAAGCT[A/G]TGAGGAAAACCCATGGTATTTCATGCCATCACTAA R 2 1 2 1 101000 f 74 goat snp2124-scaffold1064-1326769 NW_017189516.1 39837368 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445306 Affx-122925440 AX-123315643 X 102667144 ATCCCATTGTTGATCAGGACTTAGTGAACTTGCCA[A/G]TAAACTGTGTCGGTCAGATTTCACTCAGCAAGGGA R 2 1 2 1 101000 r 74 goat snp2123-scaffold1064-1296824 NW_017189516.1 39867740 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452573 Affx-122920512 AX-123322906 X 102707153 AAAGTATAACAATGTGTTCAATTAAAATATATGAA[A/G]TTTCCATTTATGAGAGATTTAGTAGCAGCAAAAAG R 2 1 2 1 101000 r 74 goat snp2122-scaffold1064-1256815 NW_017189516.1 39907874 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395746 Affx-122963693 AX-123266101 X 102739752 ACAGGGTTACCTGCTTGTTCATACACCTTTTATTG[G/T]CTTTCTTCGTTCTCATTCTCATTTCTTATTCTGCT K 2 1 2 1 101000 f 74 goat snp2121-scaffold1064-1224216 NW_017189516.1 39940363 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778412 Affx-122920045 AX-385265527 X 102812223 TTCATTCATGGTGACACTTATTCTCAAGAAAGGTT[A/C]GAAAGTATGCAACAATGGATCTGTAAAGACTTAAT M 2 1 2 1 101000 f 74 goat snp2119-scaffold1064-1151745 NW_017189516.1 40013128 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764626 Affx-122976573 AX-385252268 X 102872946 GCAAGCTGGCCTGGTAGAAACTGCCAAAGAATAAT[A/G]AGGCCCACTTACCCTGACAAGTCATATCAGCTGCT R 2 1 2 1 101000 f 74 goat snp2118-scaffold1064-1091022 NW_017189516.1 40073700 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445702 Affx-122926117 AX-123316039 X 102917890 TATAAAGTAATCTCCACTTTACTTTCTCAGACGTA[C/T]ATGTATGTGTGCACGCACACGTGCCCATGCAAATA Y 2 1 2 1 201000 f 74 goat snp2117-scaffold1064-1046078 NW_017189516.1 40118726 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451437 Affx-122921166 AX-123321770 X 102966089 CCTCTTTCATAGTGTCTTTCTTCTGTTTGGTTACA[C/T]GAATCAAGCTGTTGAGTATTTTTTTTTTTTCAATC Y 2 1 2 1 102000 f 74 goat snp2116-scaffold1064-997879 NW_017189516.1 40168407 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774970 Affx-122968628 AX-385262102 X 103038844 AACAAGCCAACACATTTTTCCATATATTAATACAT[A/G]CAACTGTGATGCTTTCAGGTTTCTAGATAACATAT R 2 1 2 1 101000 f 74 goat snp2115-scaffold1064-925124 NW_017189516.1 40243158 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425611 Affx-122940913 AX-123295957 X 103111236 GTTGACAGAAATAATTTACATTGTCTTAACCAAGC[A/G]TCTTAATATAAATACACTACAAAAAAGGCACTCTT R 2 1 2 1 101000 r 74 goat snp2114-scaffold1064-852732 NW_017189516.1 40316343 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452415 Affx-122920592 AX-123322748 X 103168930 GAAATTCTCATCTGTCACCCTATCCCCTTCCCCCA[C/T]CCTCTATTCCTATTTCATTCTTTAAATACGTTTTT Y 2 1 2 1 303000 r 74 goat snp2113-scaffold1064-795038 NW_017189516.1 40374326 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792574 Affx-122922107 AX-385279555 X 103209705 AAACAGAACTTTGCATATACATCAAAGTACAAATA[C/T]ATTAAAAGAATGGGAATGGCTCTTCATTTGATAAA Y 2 1 2 1 201000 r 74 goat snp2112-scaffold1064-754263 NW_017189516.1 40415190 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798467 Affx-122935602 AX-385285400 X 103262008 CAAGTTAAGGAATAGAAAACTCCCATGTTAATCAT[C/T]GTCTAGGGACTAACCACTCTCATACCAAATTTTTA Y 2 1 2 1 101000 r 74 goat snp2111-scaffold1064-701960 NW_017189516.1 40467697 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782906 Affx-122977428 AX-385269976 X 103312185 TATGAAGGAGCTGTTAAACTACTGAGTAAATAACA[C/T]GGCTTTTGAAATCATAATCACACATATTTATGTAA Y 2 1 2 1 101000 r 74 goat snp2110-scaffold1064-651783 NW_017189516.1 40518477 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424014 Affx-122942095 AX-123294360 X 103342763 TACCGCAAAGATCATACTCTTGCATAAAGAAGCAA[G/T]GCCTCTGGGAAGCTGCTGTCCACCAGCAAACAATA K 2 1 2 1 101000 f 74 goat snp2109-scaffold1064-621205 NW_017189516.1 40549081 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453044 Affx-122920077 AX-123323377 X 103436625 TTTTCTAAATTGTGTTACTTTAATGGAGGTCTCTC[C/T]GGAAGGGATTATTTATGTTATGTTTTTTTAAACCT Y 2 1 2 1 101000 f 74 goat snp2107-scaffold1064-527343 NW_017189516.1 40645024 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769032 Affx-122934788 AX-385256207 X 103507619 AAACTCTACTACATCACTGTCCTCATAATGAGATC[A/G]TTCTGCCTGATAAACAAGCTCCCTACGGGCCCTAC R 2 1 2 1 101000 f 74 goat snp2105-scaffold1064-456349 NW_017189516.1 40715112 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410216 Affx-122952563 AX-123280566 X 103541186 TTGACTAGTTTGCCATTAGTGGATTGGTTTACAAT[A/G]TCAAGACAAGAAACACAGCCTAGCTCTCAATTCTA R 2 1 2 1 201000 f 74 goat snp2104-scaffold1064-422782 NW_017189516.1 41492682 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377119 Affx-122978247 AX-123247478 X 103584685 ACATACCTTTTTAAGTGAAAGTGCCCCACTGAGAG[C/T]ACAGACTCAAGCTCAGCTGAAGGCACCTTAAACAT Y 2 1 2 1 201000 r 74 goat snp2103-scaffold1064-379283 NW_017189516.1 41449250 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398486 Affx-122961574 AX-123268841 X 103670504 AATAAGAATTCTTTCCCCAGGGTTTTGTTGTTGTT[A/G]TATTTTTAATGACTATTGAGACTCTTCAAATAAAA R 2 1 2 1 201000 r 74 goat snp2101-scaffold1064-293464 NW_017189516.1 41363962 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421002 Affx-122944558 AX-123291349 X 103714055 CCACATTAACAGTGGTAAATAATGAATGGAAAACA[C/T]GGGCAGCAATTTAAAACTAATTTTCATTTCAGTTT Y 2 1 2 1 101000 f 74 goat snp2100-scaffold1064-249913 NW_017189516.1 41320457 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399125 Affx-122960852 AX-123269480 X 103755693 AGAGAACTGGCTTCAAAGTCCCAATAGTATAATAG[C/T]ATAAACATGGGAAGTGGTTGTTTTTAACAAGCTTT Y 2 1 2 1 101000 f 74 goat snp2099-scaffold1064-208275 NW_017189516.1 41278559 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776717 Affx-122949691 AX-385263843 X 103809383 CATCGTATATTCTTTATACTGAACTAAGGGTATAG[C/T]GATGGGACAATATGATAAAATGCGAGGATTAGGCT Y 2 1 2 1 101000 r 74 goat snp2098-scaffold1064-154585 NW_017189516.1 41224345 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417520 Affx-122946942 AX-123287868 X 103913683 AGTGTTTTCTAGTGAGTTTTTGCCTACATCATAAC[A/G]TCATTACTCTTCATAGATAAATTTACATTTATGGC R 2 1 2 1 101000 f 74 goat snp2096-scaffold1064-50285 NW_017189516.1 41120137 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452578 Affx-122920509 AX-123322911 X 103953559 AAATGTCTCTTTTTCTTTCTTCACACTATCTCCAT[C/T]AGCTCTCGCCATGTTGGGGAATGATGTAGATGTTG Y 2 1 2 1 102000 r 74 goat snp2095-scaffold1064-10409 NW_017189516.1 41080132 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395507 Affx-122963882 AX-123265862 X 103971258 AAATTAGTAGTTTTAAAAGTATAAGTAAAATGCTG[A/G]AAGACAGGCAGTTACATAGCTGGTAAGATTATAAT R 2 1 2 1 101000 r 74 goat snp19692-scaffold1989-7191 NW_017189516.1 41061668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432773 Affx-122935431 AX-123303114 X 104011775 ATATTTAAGAGCAAAATAATATTATGCAGAGTTTT[A/C]TGATTATAAAAAGACAGATAGTTAGTGACTTTGGG M 2 1 2 1 101000 r 74 goat snp19693-scaffold1989-47708 NW_017189516.1 41020875 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447372 Affx-122924861 AX-123317708 X 104074465 ATCAACGCGAAATGTTATTTTTATCACTAGTACTT[A/G]CTGCATTAACTATAAACTGTGGAATTGTGCTCTGT R 2 1 2 1 101000 r 74 goat snp19694-scaffold1989-110398 NW_017189516.1 40957273 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790757 Affx-122977062 AX-385277758 X 104125222 TCTCATTACTCATCTGCTCAAAAGCTCCCATTTCA[C/T]GTTGTGAGCAACAATCCTTACAATGGCTTACAACA Y 2 1 2 1 101000 f 74 goat snp19695-scaffold1989-161155 NW_017189516.1 40906306 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781939 Affx-122973971 AX-385269020 X 104158570 TAAAACACTTGATAGAAATGGTAATATAAAACATG[A/C]TTTTATTACCTTTTTTAGGCTAACTTTAAGGTCTA M 2 1 2 1 101000 f 74 goat snp19696-scaffold1989-194503 NW_017189516.1 40872453 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430196 Affx-122937349 AX-123300537 X 104214173 AAAGGTGGGTTTAAGGACACCTTAAGTATGTAAGA[C/T]TGATTAAAGGAAATAAGGAAGCACTTGAAATTCCA Y 2 1 2 1 101000 f 74 goat snp19697-scaffold1989-250106 NW_017189516.1 40817586 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402834 Affx-122958260 AX-123273187 X 104268726 TGAGATATTAGAAATGGTTAAAAGATATTGAGACT[A/G]CACCAGAATGCCTCTGGTAACACTTAAGATGAAAA R 2 1 2 1 101000 r 74 goat snp19698-scaffold1989-304659 NW_017189516.1 40761517 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419160 Affx-122945738 AX-123289508 X 104319837 GGGTCTTATTTTGTTGACTTTGCCAACAAGGGTCT[A/G]TCTAGTCAAAGTTATTTTTCTCCAGTAGTCATGTA R 2 1 2 1 202000 r 74 goat snp19699-scaffold1989-355770 NW_017189516.1 41611143 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379458 Affx-122976087 AX-123249816 X 104359531 AAACAAGGAATGCTCAGCTAAGAGCTAAAGGCCTC[A/G]AGAGGGCCATGTTCATGAGGGGACAAGACTGCTAC R 2 1 2 1 101000 f 74 goat snp19700-scaffold1989-395464 NW_017189516.1 41648738 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408030 Affx-122954294 AX-123278381 X 104427207 AAAGGGGACGCAACCACCCAATAAACAAAATACAG[A/G]GCCCAGCATTTGATGCCCAGGGTGAAAACTACCAA R 2 1 2 1 101000 f 74 goat snp19701-scaffold1989-463140 NW_017189516.1 41716671 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452744 Affx-122920274 AX-123323077 X 104492985 AAGTAATAATCCCAAGACATAATATACCAAGAATA[C/T]ATCAAGCATTTATTTAGAATATACCAAGAATATAT Y 2 1 2 1 101000 f 74 goat snp43811-scaffold589-1691694 NW_017189516.1 42240846 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422146 Affx-122943539 AX-123292493 X 104532233 TAAGCCATCACTCAAACCAAAAAGAACAGAAAAAA[C/T]ACTCCCATAAACTTCTATACATAATCAGACTAAAG Y 2 1 2 1 101000 r 74 goat snp43810-scaffold589-1652446 NW_017189516.1 42280908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398469 Affx-122961585 AX-123268824 X 104571885 TACTTCTAAGTCGAAAGTGTGCAGCTTAAAAAGAC[C/T]GAAATACTTTGCTGTTTATCTTTGCATACTGCTAT Y 2 1 2 1 101000 f 74 goat snp43809-scaffold589-1612794 NW_017189516.1 42321103 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416584 Affx-122947653 AX-123286932 X 104606312 TCCTAGAAATGCAACAGGACCACTAAATCCTCTGA[C/T]GGTCATATCTTGTGCTTTACAGTAAGAAAGAAATG Y 2 1 2 1 101000 f 74 goat snp43808-scaffold589-1578367 NW_017189516.1 42355410 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430005 Affx-122938033 AX-123300346 X 104683503 TAAAGTGTTGGAGCAGCTATGATGTAAGGAATATT[A/G]TAAGATATCCCCTACAACTAAAAGGACAAGTCAAA R 2 1 2 1 101000 r 74 goat snp43807-scaffold589-1501176 NW_017189516.1 42432521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415772 Affx-122948922 AX-123286121 X 104731550 ATTTCTAAGTATTTCACAGGATTGATGAGACATGC[A/G]TTTGTTAAAGCTCTTAAAAATTCATTTAAAATGGA R 2 1 2 1 103000 f 74 goat snp43806-scaffold589-1453129 NW_017189516.1 42480905 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788100 Affx-122976068 AX-385275120 X 104790043 CAAAGGTGTAGTATTCCACCTGCTACAATTCCCCT[A/G]TTCATATGAACAGAGACTTCATCACTCACAAAAAT R 2 1 2 1 102000 f 74 goat snp43805-scaffold589-1394636 NW_017189516.1 42540738 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452807 Affx-122920226 AX-123323140 X 104844154 GAAATATATAATCACTCAGTCATATTAATATATTT[A/C]GGGAACATCATTTTCAAAATAAGTCATTAAGTTCA M 2 1 2 1 303000 f 74 goat snp43804-scaffold589-1340525 NW_017189516.1 42619576 A C 3 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 320797530 Affx-122919653 AX-385284469 X 104927517 TTGGAATTAAGGTATTTACATGTACATAAAGAAAA[G/T]AAAAACTACTTAATTTTCTTCAAGATGTAAATATT K 2 1 2 1 303000 r 74 goat snp43803-scaffold589-1257162 NW_017189516.1 42703025 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787860 Affx-122954912 AX-385274883 X 104968280 CTTTTGAGAACCTAAAAAAATGGGCAATTTTCTTA[C/T]GGTTCACAATCTCAAATACATATAAAGCTCTTTGT Y 2 1 2 1 101000 r 74 goat snp43802-scaffold589-1216399 NW_017189516.1 42751294 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800377 Affx-122944758 AX-385287299 X 105000444 CAAATAATAACATATCTGTTAAGTAATAAAGAAAT[A/G]TTTTAGTACTTCTTATCTTGAAGTATTAAGATAAG R 2 1 2 1 201000 f 74 goat snp43801-scaffold589-1184235 NW_017189516.1 42783519 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416268 Affx-122947955 AX-123286617 X 105044977 GAGACATGAATAACATTTGAAAGAAAATTTCTCAT[G/T]AAATAGATCTTCATTGAGATGTCACTGCCTGTCAG K 2 1 2 1 101000 r 74 goat snp43800-scaffold589-1139702 NW_017189516.1 42829609 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399558 Affx-122961129 AX-123269913 X 105102111 CTAAGGGCCTCCACTTAGAATCTGCAGAAGCATGT[A/C]ACCCAGATGTACCTGCCCAGAAAACCAATTACCTC M 2 1 2 1 201000 r 74 goat snp43799-scaffold589-1082568 NW_017189516.1 42887151 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776305 Affx-122978332 AX-385263433 X 105174161 TGAGGGAGCTATGGAGAGGACTAGGGCAGAAGTCT[A/G]TGTGGGAATGCACAACAGGTCTTTGGTCAAGGGTT R 2 1 2 1 101000 f 74 goat snp43798-scaffold589-1010518 NW_017189516.1 42956073 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764902 Affx-122938928 AX-385252494 X 105202950 GACTACCCAGCAGGCAATAAAAATAACCATACATG[C/T]GGAAGTATAAATGGGAAGGATTAACAACAGGCCTT Y 2 1 2 1 101000 f 74 goat snp43797-scaffold589-981729 NW_017189516.1 42984837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443432 Affx-122927364 AX-123313769 X 105232779 GCACCAAGAAGTAACTAGGATAGAACATTTATACA[C/T]CTGAGGAACAAACCCTAAGGCTGTGAATCCTGTTA Y 2 1 2 1 201000 f 74 goat snp43796-scaffold589-951900 NW_017189516.1 43015276 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388137 Affx-122969472 AX-123258495 X 105270110 TTACTGTTCTTTTCAATAACCTTAAAAGAAGAACC[A/G]CAGTAAGTTCTAAGCAACAAATAAATGGATAATAA R 2 1 2 1 101000 f 74 goat snp43795-scaffold589-914569 NW_017189516.1 43050739 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785160 Affx-122974340 AX-385272206 X 105323043 GTAGAAAAGATTCAGTTCCCAGTAGGCATCTCTAC[A/C]AGGGAAATGAGCTGAATCAAATCAGAGGAACCATA M 2 1 2 1 101000 r 74 goat snp43794-scaffold589-861636 NW_017189516.1 43104117 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385905 Affx-122971579 AX-123256263 X 105383766 ATTTTATATTTTCTGGGCAAGAGTACTATTGATGC[A/G]CATAGAGCCTACTTGGAAGATAACCGTCAAACCCT R 2 1 2 1 101000 r 74 goat snp43793-scaffold589-800913 NW_017189516.1 43170354 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432078 Affx-122935878 AX-123302419 X 105423763 ATTGTGAATTGCAATTCTGGGTGGGAAAATATAGG[C/T]TGGTAAGGACCAATTTAAATTGGGTCATTTGAACA Y 2 1 2 1 101000 f 74 goat snp43792-scaffold589-760916 NW_017189516.1 43211280 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402560 Affx-122958453 AX-123272913 X 105455394 GAGTCACAAAGAGTCAGACATGACTGAGCAACTAA[C/T]ACTTTCACTGCTTTCATAAGTACAGTGTTGTTAAA Y 2 1 2 1 201000 r 74 goat snp43791-scaffold589-729285 NW_017189516.1 43243478 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395919 Affx-122963597 AX-123266274 X 105502276 TTACACCATTAGCTGGAAGTAATCTTTGAGCATCA[G/T]TAGTGGTGAGTTGGATGTCAGGCAAGTTCTTGATC K 2 1 2 1 101000 r 74 goat snp43790-scaffold589-682403 NW_017189516.1 43289547 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418817 Affx-122946160 AX-123289165 X 105541103 AGATGGGACTAGTTGTGACTTTGGGTAAGCTAAAA[C/T]AGTCAAACTGTCAGTTTCCTCATCTATATCACTGG Y 2 1 2 1 101000 f 74 goat snp43789-scaffold589-643576 NW_017189516.1 43328389 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418802 Affx-122946172 AX-123289150 X 105579970 GTCAGAAGTTAATTGTGTAAAAGACAAATACTCGA[C/T]GCAACTCTAGTGAGATTTAGCAAGGGGAAAAAAGC Y 2 1 2 1 201000 f 74 goat snp43788-scaffold589-604709 NW_017189516.1 43366981 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413645 Affx-122950539 AX-123283994 X 105667683 GTGGACAGAGTTATCACTAGTTAAAACTGTCAATG[C/T]AATGATGATCCAAAAGAGCCAGACACAACTGAGCA Y 2 1 2 1 201000 f 74 goat snp43786-scaffold589-516996 NW_017189516.1 43457133 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794854 Affx-122923367 AX-385281814 X 105725812 AAAATAAGATTCCTATAAAACTTTATTGGTAAAAT[A/G]ATTGGAAATTTATTTTGAAACTATCTTTGGTATGC R 2 1 2 1 103000 r 74 goat snp43785-scaffold589-458867 NW_017189516.1 43516413 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802461 Affx-122943505 AX-385289365 X 105754361 GGGAAAAAGTTGGGATCTTTAATAAAAGAGAATTT[A/G]TACATATTTAGAAAAATCTAGTCAGATTTTTGCCT R 2 1 2 1 101000 f 74 goat snp43784-scaffold589-430318 NW_017189516.1 43545034 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426737 Affx-122939871 AX-123297083 X 105792349 TTAGTTTTCATTATTTTGTGCTAAGGATCCTATTT[A/C]TGCACTCACTGCTACAGGGGACTGTTTATACAATA M 2 1 2 1 201000 f 74 goat snp43783-scaffold589-392330 NW_017189516.1 43582301 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410882 Affx-122952595 AX-123281232 X 105827734 TGTTGGCCATTTGTAGGTTTCTTCAGAAAATGTCT[A/G]TTCAGGTCTATTCCCCATTTTTAAAAGCAGTGTAT R 2 1 2 1 101000 f 74 goat snp43782-scaffold589-356945 NW_017189516.1 43618207 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799921 Affx-122932060 AX-385286847 X 105868715 CCTAGATTTATGAAAGGAGTTGCTGATCAGCAATG[G/T]CTGTGGTGAGCAGACTGTCTGCAACTGTAAGTTCC K 2 1 2 1 101000 r 74 goat snp43781-scaffold589-315964 NW_017189516.1 43659369 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792299 Affx-122939161 AX-385279281 X 105915854 GAAGTGTATCCAATGTGCTTAAAATTAACTACATC[A/G]TCCTTCATCTTATAAGAAAGATCACTGAACTAGCC R 2 1 2 1 101000 r 74 goat snp43780-scaffold589-268825 NW_017189516.1 43706836 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786574 Affx-122967925 AX-385273606 X 105947235 GCCTTTATGGTTCTTTTAAATGCAAATCTCGACAC[A/G]TCTCATGTTTTCTTCTCTACTGCCATTTAAGCTTT R 2 1 2 1 101000 r 74 goat snp43779-scaffold589-237444 NW_017189516.1 43738007 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791737 Affx-122933895 AX-385278728 X 105978899 GCAGATAGTGATATAACTAAAGATAATTATCAAGT[A/G]TTTATTTAAATAAGAAAGTGTGTTCTATTCAAAAG R 2 1 2 1 303000 r 74 goat snp43778-scaffold589-205780 NW_017189516.1 43770275 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444353 Affx-122926714 AX-123314690 X 106048209 ATGCTGATCTGGAGACTGCGCTTTGAGAATCATGA[C/T]AGAAAATAAACAGATGCAGGTTCTTATTACAAACT Y 2 1 2 1 101000 r 74 goat snp43777-scaffold589-136470 NW_017189516.1 43839992 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416294 Affx-122947936 AX-123286643 X 106091389 CCATTTTAACTGGATTCTGGTTTACATGTGCTAAC[A/G]AAACCAGCCAAATGCTATTTTCAGAAGAAATCCTG R 2 1 2 1 201000 f 74 goat snp43776-scaffold589-93290 NW_017189516.1 43883004 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780669 Affx-122950653 AX-385267759 X 106135566 ATCTCAAAGTCTGAGAGAATCTCACCTTCTACCAA[C/T]GTCTTCTTCCCAACACCTCTGGGAAGAGACCTTTT Y 2 1 2 1 101000 r 74 goat snp43775-scaffold589-49113 NW_017189516.1 43927317 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409294 Affx-122953106 AX-123279645 X 106164340 GGTATTCTTTCCAAAGTTTTTTTCCATATGTATGA[C/T]GGGTATACAAATGAAGCATATAAAGGAGACTTACC Y 2 1 2 1 101000 r 74 goat snp43774-scaffold589-20339 NW_017189516.1 43957037 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802219 Affx-122950670 AX-385289123 X 106214148 GTAATAGGAAAAAGCTTGAAGATGAAGGTTTAATT[A/G]CTAGTAAATAACCTAATCCTAAGGTGACACTGTGC R 2 1 2 1 101000 r 74 goat snp13110-scaffold1501-29370 NW_017189516.1 44007959 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439590 Affx-122930068 AX-123309927 X 106272215 CACTATTTGAGGCTTGTGAAAACTGTTCTGGGCTG[C/T]GCACAAGCATGGCCATTCTAGTGAACACATCTATT Y 2 1 2 1 201000 r 74 goat snp13111-scaffold1501-87437 NW_017189516.1 44066005 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453780 Affx-122919587 AX-123324113 X 106335323 GCTAAATGAACAAGTAAAGTAAGATGAGAGTTTAG[C/T]AACTGGAGTTTGGTCAGTGTGGTGTGGCTCAGAAC Y 2 1 2 1 201000 f 74 goat snp13112-scaffold1501-150545 NW_017189516.1 44129114 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454136 Affx-122919337 AX-123324469 X 106377986 CCCCGTGGGAAACATTGTTATCAACTAGAGTACTA[C/T]ACTATGTACAGTTTCTTTTGCCTCAGTCTTACATA Y 2 1 2 1 101000 f 74 goat snp13113-scaffold1501-193208 NW_017189516.1 44169996 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392182 Affx-122966297 AX-123262539 X 106407157 GCTTCCCAGGGGATCCTAAATTAAAAGATAAATAG[C/T]ATAAAAATGATGAAATCAGGATCTGTCATGAAGTG Y 2 1 2 1 102000 f 74 goat snp13114-scaffold1501-222379 NW_017189516.1 44199275 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390445 Affx-122967625 AX-123260802 X 106507044 AGAATGGAACTGGAGGCTTGTCTCCACATTTTGCC[A/G]CAAATAAGTGAGCCATGCATTGCCTGAAAGCCTCT R 2 1 2 1 101000 r 74 goat snp13115-scaffold1501-322266 NW_017189516.1 44300531 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434090 Affx-122934169 AX-123304431 X 106543428 AGTCCCACGTGGTTGTGGGAAGAGGAGATGAAGAA[C/T]GGAGTGAGTCTTCTCATGACAAGATGGAAGACAGG Y 2 1 2 1 101000 f 74 goat snp13116-scaffold1501-358650 NW_017189516.1 44336743 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769732 Affx-122943444 AX-385256902 X 106578467 GGAGTTTTATCAAAGTAAATAGGATGTGAATGCAC[C/T]GAATGATGATATATTAAATAAGACTCCAATCATAT Y 2 1 2 1 101000 f 74 goat snp13117-scaffold1501-393689 NW_017189516.1 44372045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419699 Affx-122945920 AX-123290047 X 106616569 AAACTTCACCCTTTTAAAGTATATAATTCAGTACC[A/G]TTTCCTATATTCACAGAGTTATGCAAATAAACCCA R 2 1 2 1 101000 r 74 goat snp13118-scaffold1501-431791 NW_017189516.1 44409996 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787504 Affx-122942933 AX-385274529 X 106656036 GATTGATACTGAAGCGGATACCCAGTCAATCTCTA[C/T]GCCACACAGCCTTTCAATTACAGATTGAAGGAATA Y 2 1 2 1 101000 r 74 goat snp13119-scaffold1501-471258 NW_017189516.1 44449673 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393793 Affx-122965186 AX-123264148 X 106686560 TTACTTGCAGATTTCTTTTCACTATTATTTTTAGT[A/G]TCTTCAGAAGAAGAATCCTTCAGAAGTCTAGACTG R 2 1 2 1 201000 f 74 goat snp13120-scaffold1501-501782 NW_017189516.1 44480244 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789362 Affx-122954539 AX-385276372 X 106738862 ATTGACAGCGTCCTCTTAAGAACAGCTGTTGCCTC[A/G]TAGACTACAGTGTGAACATACCCCTGAATTTAGAA R 2 1 2 1 101000 f 74 goat snp13121-scaffold1501-554084 NW_017189516.1 44532374 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378066 Affx-122977180 AX-123248425 X 106770493 AGTTTTCGGCCCCCATTTCCTTACAGCTTGTTTTG[C/T]ACTCTTTTTTACCTCTTATGGGTGCTTGCCATCAA Y 2 1 2 1 201000 r 74 goat snp13122-scaffold1501-585715 NW_017189516.1 44564058 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451290 Affx-122921300 AX-123321623 X 106813496 TTTGCGACCCCGTAGACTGTACAGTCCATGGAATT[C/T]TCCAGGCTTTATATATGGCTGATATATCTTGCTGC Y 2 1 2 1 201000 r 74 goat snp13123-scaffold1501-628718 NW_017189516.1 44607511 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772846 Affx-122926471 AX-385259991 X 106870748 TCTCATGAGCCCTTCAAAGTTCACGTGCTTGTCTT[C/T]GACGGATTTCCCAAGTGGTAGGAAAGAAAAAGAGA Y 2 1 2 1 101000 f 74 goat snp13124-scaffold1501-685970 NW_017189516.1 44664067 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403738 Affx-122958017 AX-123274090 X 106903214 TTGCCTGGACTCCATGCTTTTCAGGTTTACCTCAC[C/T]GAGTAGAACATGAGTCAACAACTGCTGTTCAGAGC Y 2 1 2 1 101000 r 74 goat snp13125-scaffold1501-718436 NW_017189516.1 44696969 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402997 Affx-122958137 AX-123273350 X 106995259 AGAAAGCACAAAGTCCCCAAGTTTAAAGCAGGTGA[C/T]ATTTTTTTGTGGAAAACATAGAAAGAAAGACAGGG Y 2 1 2 1 101000 f 74 goat snp13127-scaffold1501-810481 NW_017189516.1 44789744 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385032 Affx-122971855 AX-123255390 X 107028452 AAACTGGATGCTTACAATAAAAATAACTAACAATG[C/T]GAAGAGGTTTGTTCTGCACCAATGGGTCAGAGATG Y 2 1 2 1 101000 r 74 goat snp44728-scaffold608-1409658 NW_017189516.1 44990282 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774377 Affx-122962585 AX-385261513 X 107058066 AATTTAATACAGTCCTTCTTCTGAAGTCCCATCTT[C/T]GGGATTTTTTTGTGAGGAGTCTTTAAACTTATATA Y 2 1 2 1 101000 f 74 goat snp44727-scaffold608-1380044 NW_017189516.1 45020423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375549 Affx-122979094 AX-123245908 X 107089380 TGAAGAGGCAGAGCCTATGAGGGAACCCTGAACTT[C/T]GACCCCAGGGACCACTTAATCTGTCAGAAATCACC Y 2 1 2 1 101000 r 74 goat snp44726-scaffold608-1348730 NW_017189516.1 45073103 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412398 Affx-122951447 AX-123282747 X 107227113 AAAACTTGTTCTGAGATGTCACCTAAGCCAGAGTA[C/T]ACCTTAACAGCCAGGTCAAATTACACAGTTAAGTT Y 2 1 2 1 101000 f 74 goat snp44724-scaffold608-1210997 NW_017189516.1 45209264 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385672 Affx-122971144 AX-123256030 X 107266347 TAACCTATCATAACAGTTTGGGAGTGCTCCATTAT[G/T]CTTTGAGCAAACTGATGGCAGAGTATGGTCCTTGC K 2 1 2 1 101000 f 74 goat snp44723-scaffold608-1171763 NW_017189516.1 45248585 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376644 Affx-122979022 AX-123247003 X 107313096 TGACTATTTCTCCCTGTCAGAATACCTCCTGAAGT[C/T]TGTCTGGTGGCATGTTGCATGGCCAGGTGTTCCAT Y 2 1 2 1 202000 r 74 goat snp44722-scaffold608-1125014 NW_017189516.1 45295200 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800458 Affx-122937474 AX-385287379 X 107394696 GCATGTGTAAAAATTCATCCTTTTAAACGATGCCT[A/G]CATTTTGTCAAGAATTAGATCGGGAAGGTACTGGG R 2 1 2 1 101000 f 74 goat snp44721-scaffold608-1043414 NW_017189516.1 45367560 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413911 Affx-122949826 AX-123284260 X 107423376 GTGATCCTGGTTCTAGGGAAAATGTTTTTCCCCCT[A/G]CACTGATCTAGGATGTCTCCCTAGTTTTCGAGGTG R 2 1 2 1 201000 r 74 goat snp44720-scaffold608-1014734 NW_017189516.1 45396702 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439673 Affx-122930588 AX-123310010 X 107457657 CGAACTCAATAAAATAAGCTGGTGAAATTCATGAG[C/T]CAACATACAAATTTCTCCAAATCTGAGGTAATATG Y 2 1 2 1 101000 f 74 goat snp44719-scaffold608-980453 NW_017189516.1 45430937 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427002 Affx-122939852 AX-123297347 X 107488494 GGGGGTGGGTAGTGAAAGAATAAATTTAAAAGAAT[A/C]GGAGAAACGAATTCATTGACCCCATGTTCAATATG M 2 1 2 1 101000 r 74 goat snp44718-scaffold608-949616 NW_017189516.1 45461874 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384012 Affx-122972907 AX-123254370 X 107531666 GGGAGAAAGGTCAAGCGAGACAGAGACTCTCAGTG[G/T]GTAATATAGTGCTCTGGAAAGTGCCATGTCTTCAG K 2 1 2 1 101000 r 74 goat snp44717-scaffold608-906444 NW_017189516.1 45505167 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388078 Affx-122969514 AX-123258436 X 107600468 ACTGAGGAAATAACCCTTTTTTTCCCCAACCATAG[C/T]ATCTTGACCTCCCCCTCAGCACCCCCACAGAGGTG Y 2 1 2 1 102000 f 74 goat snp44716-scaffold608-837642 NW_017189516.1 45573765 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766091 Affx-122961717 AX-385253507 X 107652248 TGTCTTCATAGCCCAGTGAGAACATTGTTTTCTAC[A/G]TTTGAATTCATACCCACTTTTTAATGGCATGCAAC R 2 1 2 1 201000 f 74 goat snp44715-scaffold608-785862 NW_017189516.1 45625927 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403451 Affx-122957727 AX-123273804 X 107736235 TCTGACTCTCAGGCCATTACAAAGGGTGAGAGGGA[C/T]GGGTCTGCTCCAGTCCGTCAAGGGTGTTGAATTAG Y 2 1 2 1 101000 f 74 goat snp44714-scaffold608-701875 NW_017189516.1 45710266 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430423 Affx-122937747 AX-123300764 X 107768107 GGGTACCAATTCTGGAGATAAGGGAGGAGCCAATC[A/G]CCAGAGCACAAGGGTGGAATGGGAGTGATGACGCA R 2 1 2 1 101000 f 74 goat snp44713-scaffold608-670003 NW_017189516.1 45742106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380129 Affx-122975993 AX-123250487 X 107800040 CACATGGCTCAACTGAAACTTAAGGACTGAGCTTG[C/T]ACATTTGGCCTTTTGATGGAAAGAGGTGTAAAGCC Y 2 1 2 1 101000 r 74 goat snp44712-scaffold608-638070 NW_017189516.1 45774612 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453176 Affx-122920466 AX-123323509 X 107844870 GGCCTTTAAGGAAGACTTTTTCCTAAATATGTCTT[A/G]TCATTCTATCTTGCATGACATTGTTCCTATACACA R 2 1 2 1 101000 r 74 goat snp44711-scaffold608-593240 NW_017189516.1 45820184 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412101 Affx-122951117 AX-123282451 X 107874486 AAACTGACAAGAGCAAGGACTCTCTGGAATTCAAG[C/T]TTGGGATGCCTCACACCTGTCAAGGCAAGAGGAGT Y 2 1 2 1 101000 f 74 goat snp44710-scaffold608-563624 NW_017189516.1 45849704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780529 Affx-122939521 AX-385267620 X 107921032 AACAGGTATAACTATTTGGGTTGTTCCACTTCCCA[A/G]CTACCATATTTGGAGTTGGTTGTCAAATGGACAAA R 2 1 2 1 201000 f 74 goat snp44709-scaffold608-517078 NW_017189516.1 45896247 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792791 Affx-122951001 AX-385279770 X 107957179 ACCTTACCAAGAATGGTTTAATGTTTTAGAAAATC[A/G]CACCAATGACATCAATGCCATTTATGGGCTGTGCT R 2 1 2 1 101000 r 74 goat snp44708-scaffold608-480931 NW_017189516.1 45933226 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400027 Affx-122960789 AX-123270382 X 108113852 TAAATAAACCAGGGCTCCATAAGCAAAAGAGTTGC[A/G]GAATGGTTGATAGGCAGGCAATCAACAATGCGTCA R 2 1 2 1 101000 r 74 goat snp44706-scaffold608-324258 NW_017189516.1 46094197 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437879 Affx-122931675 AX-123308217 X 108161698 GTGACAGGTCTTAGTTAACAAAAGTTCACTTTCTG[C/T]ACTGAAGAGCAACAGGAATCTGACCAAGTAAATGA Y 2 1 2 1 101000 f 74 goat snp44705-scaffold608-276412 NW_017189516.1 46142401 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405737 Affx-122956515 AX-123276089 X 108193571 GAGAAATATAATCATATCTAGTGTCAAATCTCTGA[C/T]GAACATGTGTGACTTCCTGGCTGCTTACCCACTAG Y 2 1 2 1 101000 f 74 goat snp44704-scaffold608-244539 NW_017189516.1 46175015 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415598 Affx-122948614 AX-123285947 X 108247693 TTTCAACTGCGGCCTAAAGTCATATAATACTTTAT[G/T]TTTACAAAGAGAAGTCTTACACTTTTCATGGTTTA K 2 1 2 1 201000 r 74 goat snp44703-scaffold608-190417 NW_017189516.1 46229239 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417538 Affx-122946929 AX-123287886 X 108280537 TTAACAGGAACCTCCTCACCCAGGCCCGTGGACAC[A/G]TCACAATCTACTCATATGGCTATCTTCATAAGTAG R 2 1 2 1 101000 r 74 goat snp44702-scaffold608-157573 NW_017189516.1 46262405 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383143 Affx-122973245 AX-123253501 X 108316019 GAGCACACTAATGTGAAGTGAACTCTTAAGAAAAC[G/T]AAAAGACATCATCCTTGACGACTTCCCAGTGAAGA K 2 1 2 1 101000 f 74 goat snp44701-scaffold608-122091 NW_017189516.1 46297860 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411336 Affx-122952268 AX-123281686 X 108345793 CTCAGGCAAATGACAAAATGTTGCAGAAAAGTTGT[A/G]TCTCCTATAGGCTGAGGATCACAGGAACTAGTGTC R 2 1 2 1 101000 f 74 goat snp44700-scaffold608-92317 NW_017189516.1 46327651 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376121 Affx-122978873 AX-123246480 X 108592673 AGTTATCATACCTGAATAAGAAGATTTTTGGATGG[C/T]ACATCACATATTAATAACAGTTCAGCTTGACATAT Y 2 1 2 1 101000 f 74 goat snp34227-scaffold402-154464 NW_017189516.1 46573477 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452797 Affx-122920234 AX-123323130 X 108691861 ATCAGACTTTATCTGTCATCCCCGTTGAAAGGGAA[C/T]AGGTGCCTCAAAAAGATGTTCATTTCTGAACAGTC Y 2 1 2 1 201000 r 74 goat snp34229-scaffold402-253652 NW_017189516.1 46667973 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391640 Affx-122966568 AX-123261997 X 108731454 TCAAAGCACAGTCTGAGGGTCAGCTGTATTAGCAC[A/G]TTAGGGGAACTGGTTAGAAATGCGCCACCTCAGAC R 2 1 2 1 101000 f 74 goat snp34230-scaffold402-293245 NW_017189516.1 46708311 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453369 Affx-122919937 AX-123323702 X 108770787 AATAGTGTGCAGAGGGAAAGAGGTGAGGGACAGAT[A/G]CAAACTCAGTCGTTTAGATGCCCACACACAGGCAC R 2 1 2 1 201000 r 74 goat snp34231-scaffold402-332578 NW_017189516.1 46747658 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378975 Affx-122976403 AX-123249334 X 108838358 CTCAACAGATTAAAGCCTTTTCATAAAAGTACATT[A/G]CTATTAACATCAAACAGAATCACCACAACCTGGTC R 2 1 2 1 101000 r 74 goat snp34233-scaffold402-400149 NW_017189516.1 46814935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447962 Affx-122923768 AX-123318298 X 108920781 CTGAATTGGTTAGGATTAACCAAACAATGCTGTAG[C/T]AAGAATATTACAGTGTGACAGACATGGACATAGAT Y 2 1 2 1 101000 f 74 goat snp34235-scaffold402-482572 NW_017189516.1 46899034 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452933 Affx-122920187 AX-123323266 X 109056899 ATGGCAAACTTCAATGTAACCAAAGGCCAGATTTG[A/C]TTCTGTGACAAGAGCATCAGAGACAGTGATTTCTG M 2 1 2 1 101000 f 74 goat snp34237-scaffold402-618690 NW_017189516.1 47036667 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405230 Affx-122956890 AX-123275582 X 109215175 TTGTTATACTTGCGCAGTTGTCTGGGACTGTTTTG[C/T]GACCCCATGGACTATACATGGGGTTTCCCAGACAA Y 2 1 2 1 103000 f 74 goat snp34241-scaffold402-776966 NW_017189516.1 47195635 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794512 Affx-122976217 AX-385281475 X 109276464 TTTAATGACAGAAGCTGAGTAATTTGAAAGGAAAT[A/G]TAAGAAATATCCATGAATCTATAATCAGACAGTAT R 2 1 2 1 101000 f 74 goat snp34242-scaffold402-838255 NW_017189516.1 47257005 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395952 Affx-122963572 AX-123266307 X 109433393 TTAAGCTTAGTTACCAGAATGAACATATGTCATAG[C/T]ATGCCCAGTACCATCTAGATTTGCACCTGTTATGT Y 2 1 2 1 101000 f 74 goat snp34246-scaffold402-995184 NW_017189516.1 47417587 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434228 Affx-122934839 AX-123304569 X 109474735 TTCCACCTGATTTTAAGGCTTACCATATGTGTACA[A/G]TAGTAAGGAAAACAGTGTGGAAATAGCAGGGGAAT R 2 1 2 1 202000 f 74 goat snp34247-scaffold402-1036526 NW_017189516.1 47459249 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383325 Affx-122972690 AX-123253683 X 109506524 ATTACTGGTGTCAGAGTCATTCACTTACTCATTCA[G/T]CAACTATTAATTGAGCACCTTCCATTTACTATACA K 2 1 2 1 201000 r 74 goat snp34248-scaffold402-1068315 NW_017189516.1 47491213 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398929 Affx-122960999 AX-123269284 X 109615574 GGTAAGGCATGCTAAGGAGACTTACTTACCCTGAC[A/G]TATACACGGAGGATTCAGCTCTTACCATATCCTTC R 2 1 2 1 201000 r 74 goat snp34250-scaffold402-1177365 NW_017189516.1 47602055 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451434 Affx-122921169 AX-123321767 X 109716050 CATACATGTCTCTGAGTTGTAAATACTAGGAGAGT[A/G]CCATTCCTTAAATAATTTTGGCACATTTAGCATCA R 2 1 2 1 101000 f 74 goat snp34252-scaffold402-1277841 NW_017189516.1 47702935 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450446 Affx-122922960 AX-123320780 X 109754288 TTTTGGTAGATATTTAAGAAAATTCTGTAAGGCTA[C/T]ATTCTCACAGTTGGAAGCAACAACGGGATTATGAC Y 2 1 2 1 101000 r 74 goat snp34253-scaffold402-1316079 NW_017189516.1 47741477 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385810 Affx-122971031 AX-123256168 X 109788588 TTATTGGGTGCTATGGCCCTACCCCTACTAGAACC[A/G]TTATGTATTATACAGGCTACAAACCATACTACCTT R 2 1 2 1 201000 r 74 goat snp34254-scaffold402-1350379 NW_017189516.1 47775844 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454189 Affx-122919301 AX-123324522 X 109822783 CTGGAGTCTCCTTTCTACACATCCAGTCCTCTCTC[A/G]TCTGTGAAGTTTCCCATCCTTGATGAAATAAATCA R 2 1 2 1 201000 r 74 goat snp34255-scaffold402-1384574 NW_017189516.1 47810256 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379680 Affx-122975918 AX-123250038 X 109904539 TGCTATTCTAAAAGCAATTTTCTTCCCTTTTTTCA[C/T]GTCGTTTCTTCCATTTGGAATGGGTTTAAATCCAT Y 2 1 2 1 101000 r 74 goat snp34257-scaffold402-1466330 NW_017189516.1 47892644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435567 Affx-122933376 AX-123305907 X 109966518 AAAAGGCTCCTTTGGGTGCCTTTCCAGTTAATAAG[C/T]GATGCACCCTAAAGATAACCACTATTCTGACCTCT Y 2 1 2 1 101000 f 74 goat snp34259-scaffold402-1528309 NW_017189516.1 48003503 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441412 Affx-122928832 AX-123311749 X 110036806 AGCAAGGTCATCCCATTGAAATCTCATAACAACAG[C/T]GAAAAGCAAATTCAAATCAACCTTTCATTACACCT Y 2 1 2 1 101000 f 74 goat snp34261-scaffold402-1598597 NW_017189516.1 48028557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421813 Affx-122944319 AX-123292160 X 110083958 CTAACAATTTAAGTGATAAAAATCTGCTTTCTTCA[C/T]GGGGCAGGGCAACTGATATTTCAATGTTATTATTA Y 2 1 2 1 201000 f 74 goat snp34262-scaffold402-1645749 NW_017189516.1 48076184 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409784 Affx-122952978 AX-123280135 X 110113562 GCCAACCTGTTTAGTAACCCATCATCTAGGGTCCT[A/G]CAGTGGGAATTGGCCCAAGTGCCTCTGACCAGCAT R 2 1 2 1 101000 f 74 goat snp34263-scaffold402-1675353 NW_017189516.1 48105542 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437022 Affx-122933122 AX-123307360 X 110143975 ACTTGGTGCCCTGGCAAAAAGGCAGGGAAATATGC[C/T]CTGGTTAGATTTCCACTTCTTCAGCTTTAAGAGGC Y 2 1 2 1 201000 r 74 goat snp34264-scaffold402-1705766 NW_017189516.1 48135983 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383034 Affx-122973302 AX-123253392 X 110185493 CTTCCATTTGGAAAAGAGAAGAAAGGAAAGCACTT[A/C]GCAGTCATTGGTGCATAGGAAAAATGAACCATGTT M 2 1 2 1 101000 r 74 goat snp34265-scaffold402-1747284 NW_017189516.1 48177508 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802675 Affx-122926690 AX-385289574 X 110256599 CTTATGTGAAAAGGGGAGATGCTCAATCCGTTGTT[C/T]TCCAGCCAGTCTTCATAAGAATGCTTAAAATATAC Y 2 1 2 1 101000 f 74 goat snp34267-scaffold402-1818390 NW_017189516.1 48249236 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789291 Affx-122973244 AX-385276302 X 110311193 CACACACTGCAAACTGGTAACATACAGTTTGCAAA[C/T]GGGCACTGCTGCATGGACCACCATTTGAGGAGCAC Y 2 1 2 1 102000 r 74 goat snp34268-scaffold402-1872984 NW_017189516.1 48303872 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407913 Affx-122954384 AX-123278264 X 110340389 TGAACAGTAGTTGGAAGAAAAAAGGTGAGTGAAAA[A/G]CTATTTCCTTTATCTCAAAAAGACCACTATAAAAA R 2 1 2 1 101000 f 74 goat snp34269-scaffold402-1902180 NW_017189516.1 48333126 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802907 Affx-122929638 AX-385289804 X 110391705 CTTTCTTAGCCACCTGAAAATACAGCAAGACAACC[A/G]TCTATAAGCTAGGAAGAGAGTTCTCATCAGGAACC R 2 1 2 1 202000 r 74 goat snp34270-scaffold402-1953496 NW_017189516.1 48516775 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400715 Affx-122959922 AX-123271070 X 110459483 ATTTTACTAAGAAGCTCTACTTCAAGTCTTTAATG[C/T]GAACTATGTGGCAGAGGGGAAAACCTTAGGAAGAT Y 2 1 2 1 201000 f 74 goat snp34272-scaffold402-2021274 NW_017189516.1 48584540 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770176 Affx-122973266 AX-385257343 X 110765830 ATTTTGAGATTATAAAAATGTCAGTCCCTTCATAG[C/T]CCTTCAATGGCTTTCTACTCCACCAACAATAAAAT Y 2 1 2 1 101000 r 74 goat snp34277-scaffold402-2327621 NW_017189516.1 48891018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772302 Affx-122936170 AX-385259457 X 110805088 AATAAGACATGTATTCCATGTACGAGGTTACTTAA[C/T]GTAACATTCTTTTAGAAGTGCCAGAATACCTTAAA Y 2 1 2 1 101000 r 74 goat snp34278-scaffold402-2366879 NW_017189516.1 48930879 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417402 Affx-122947683 AX-123287750 X 110864484 GAGGTGTATAATGCAGCCTTGTGTTTTGTAGTGAT[A/G]CAGAATCCAGCACTGGATTTCCATGGGGGTTAGTC R 2 1 2 1 101000 f 74 goat snp34279-scaffold402-2426275 NW_017189516.1 48993929 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383681 Affx-122972499 AX-123254039 X 110895509 AGCACACGATAGGCCCGCAGGACGTGTGCTCTCCA[C/T]GGTTCTCTGCTTCCTCCTTCCCTTCTCTACATGTG Y 2 1 2 1 201000 f 74 goat snp34280-scaffold402-2457300 NW_017189516.1 49025418 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391465 Affx-122966727 AX-123261822 X 110927689 GGGTGAACTTGCCCAATTTTACATCGATTATTATT[A/G]CATTATGTTCATTTAGAAAAATGTTAAATGTTCCT R 2 1 2 1 101000 f 74 goat snp34281-scaffold402-2489480 NW_017189516.1 49057605 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399405 Affx-122961243 AX-123269760 X 110990139 GGCTGTAGATGCAATTGTGATCCAAAACCTGAGTT[C/T]ACCTCTTGGTGAGTGTCGAGACAAATGAAAGAACC Y 2 1 2 1 101000 f 74 goat snp34282-scaffold402-2551930 NW_017189516.1 49120843 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798910 Affx-122944105 AX-385285840 X 111070501 TATGCTGAATTTTGAACATACCAAAATAATACTCC[A/G]TATTGAAAGTCATTTATTTAATGATATTAACTACT R 2 1 2 1 202000 r 74 goat snp34283-scaffold402-2632292 NW_017189516.1 49201913 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770947 Affx-122926874 AX-385258110 X 111164199 AGGATGTGTTCAAGTTAAGGTTACCATTATTCAGC[G/T]ATTTCTTTTTAGACCCATATGTCTTCCTGTTTTGC K 2 1 2 1 101000 f 74 goat snp34285-scaffold402-2725990 NW_017189516.1 49297810 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386104 Affx-122971431 AX-123256462 X 111258024 CTAACCCTCTGAATACCTTCCAGATTGGCTTTGCC[A/G]CTGGGGACCAGACCAGGATTCCATGCAAATGACAC R 2 1 2 1 201000 f 74 goat snp34287-scaffold402-2819815 NW_017189516.1 49392266 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797572 Affx-122930593 AX-385284511 X 111287438 ATCTGTGAAGCTGTCAAATCAACAAAATCCACTGC[A/G]TTCCACAAAACTGCTATATGTAACACAACATCCCA R 2 1 2 1 101000 f 74 goat snp34288-scaffold402-2849229 NW_017189516.1 49421544 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792411 Affx-122964254 AX-385279392 X 111328638 GGACACACATTCTGATTAAACAATGAATATACTCT[A/G]TATTTTTGAACATCGTGAACCTACAAGTATCATTT R 2 1 2 1 101000 f 74 goat snp34289-scaffold402-2890429 NW_017189516.1 49463114 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435956 Affx-122933530 AX-123306295 X 111365215 AGGTCTCCAAGAGTAGCCGTGCACCCCTAGATCAG[A/G]ATCGCTGGGGGAGCTTGTGGACTGTGCGGATCCCT R 2 1 2 1 101000 f 74 goat snp34290-scaffold402-2927006 NW_017189516.1 49499591 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795296 Affx-122957553 AX-385282254 X 111401412 TTTTTTTAAGTTGAAAAACAGGCAAAGCAAATATA[C/T]GGTTTTAAAAGTTAGAATGTGAGCTACCTTGACTG Y 2 1 2 1 102000 r 74 goat snp34291-scaffold402-2963203 NW_017189516.1 49536084 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415652 Affx-122948568 AX-123286001 X 111489482 AGGTCAGTGTTTCTCAAGCTATTGTCACAGACCAA[G/T]AATTTTATAAATTACAATGAAAATAAATTATTAGG K 2 1 2 1 103000 f 74 goat snp34293-scaffold402-3051273 NW_017189516.1 49624356 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390795 Affx-122967871 AX-123261152 X 111546370 ATGGGAATGAAGATGAGGCTAACAGCCCACTCCCA[C/T]ATCTATCAGCCAAAAAGACTTGACAGAAGTTGATA Y 2 1 2 1 101000 r 74 goat snp34294-scaffold402-3108161 NW_017189516.1 49681647 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402267 Affx-122959119 AX-123272620 X 111594043 TTATTGAGTTAGGATTTGAAAACAATGGGAAATTC[C/T]AATGAGTGTTCTCTTCTGTATAAAATTGATACCTT Y 2 1 2 1 101000 f 74 goat snp34295-scaffold402-3155834 NW_017213196.1 9259 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416848 Affx-122948103 AX-123287196 X 111653222 ATTCTTCCAGTCCTCTTGCTCTGTTTTTACCATTA[C/T]GTCTGTTCTTAGTACAGAGACCTCTGTCCCCTTGA Y 2 1 2 1 101000 f 74 goat snp34296-scaffold402-3215013 NW_017189516.1 49785703 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415347 Affx-122948784 AX-123285696 X 111683237 ATAATTCTTCCCCTTCAAACAACCCTGAAACAAAA[C/T]GACACCTCTAAGGATTAAACATTTTGGAAACCAAT Y 2 1 2 1 102000 f 74 goat snp34297-scaffold402-3245028 NW_017189516.1 49815656 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415687 Affx-122948540 AX-123286036 X 111747455 GGACCAGGGCATTAAAATTATATCCTTAGTGTCCT[A/G]CTCTGTGTCACTATTTTTTATAACTTCATACTCAG R 2 1 2 1 101000 f 74 goat snp34299-scaffold402-3309246 NW_017189516.1 49880195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797687 Affx-122931652 AX-385284626 X 111854353 CCCTGTGGTAGGGAGTGATGGATCACTTCACTCTG[C/T]GGGTGAAGTGATGTTGATGCTGATGTGTGCGTGTG Y 2 1 2 1 102000 r 74 goat snp34301-scaffold402-3416144 NW_017189516.1 49979125 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432234 Affx-122936361 AX-123302575 X 111884442 AAAGTGTTCTCTTCAACAGCCAGAGTTTGCCTTTT[A/G]CCATGACAGCATCAGTTGAAAACTGGCCTGCATCT R 2 1 2 1 101000 r 74 goat snp34302-scaffold402-3446233 NW_017189516.1 50009559 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785958 Affx-122932103 AX-385272994 X 111948869 TATCAAGGTGTGAGGGTTCCATTTTCAACACATCC[G/T]CACCAACAGCTGTTATGGTTCATCTTTTAAATAAG K 2 1 2 1 102000 f 74 goat snp34303-scaffold402-3510660 NW_017189516.1 50075351 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439878 Affx-122930044 AX-123310215 X 111995412 ATCAGATCTAGGCAGGGTAGGGTTCAAGAAAATTC[A/G]CAGTAACTGAGTTTTAGCCAGGCTTTATGAGTTTC R 2 1 2 1 101000 f 74 goat snp34304-scaffold402-3557203 NW_017189516.1 50122423 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402341 Affx-122959062 AX-123272694 X 112048076 TGTATTGTCAGAAGTTTGGAGTGGGCAGCAGTTGG[C/T]ATAGGAGCCTTGGAATATTTTTTAAAGTTCAGGTG Y 2 1 2 1 201000 f 74 goat snp34305-scaffold402-3609867 NW_017189516.1 50174987 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798441 Affx-122971956 AX-385285374 X 112082105 ATTTAAGACAGGCAGACGTGGAGTACAACAAGAAA[C/T]GGATAGGCCCACAATTTGTTCTGAATTATGCACAT Y 2 1 2 1 101000 r 74 goat snp34306-scaffold402-3643896 NW_017190168.1 83215 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394935 Affx-122964300 AX-123265290 X 112138748 TTTATCTGTGCTGTCTTGCTTACCCCTTTTTCCTA[C/T]GTAGATTTTGGTTATTGTTGGCTTTTGTAAATAGG Y 2 1 2 1 201000 r 74 goat snp34307-scaffold402-3700539 NW_017190168.1 26604 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783393 Affx-122964056 AX-385270456 X 112205578 TTCTTACGGTGCTTACAGTAAAGTGTTATAGGATC[A/G]CTGACATTTTGGTGTAATTTTTGTATTCATTGCCC R 2 1 2 1 101000 f 74 goat snp34309-scaffold402-3767369 NW_017189516.1 50243127 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772267 Affx-122972739 AX-385259422 X 112358034 TTATTTTAAGAAAGTGCAGTAGGAGATTAAAGATG[C/T]GGTTGTAAGTCAGAAGCCTTTTTCCACTCTCCCTT Y 2 1 2 1 101000 r 74 goat snp34312-scaffold402-3919825 NW_017189516.1 50466422 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453967 Affx-122919460 AX-123324300 X 112475755 CCCACTCATGTAATGGGACAGCGTAGACCTCCCAG[C/T]ACCACTGTCTCCAAAAAAGTCACTTTCACCCCACC Y 2 1 2 1 101000 r 74 goat snp34314-scaffold402-4037546 NW_017189577.1 46123 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427848 Affx-122939726 AX-123298191 X 112591772 GCAACCAATCAGGGCCTTCTGTTACCTGGAAGAAT[A/G]CATTCTCTGTTCAAGAGAATGTTCAGACTGATAGC R 2 1 2 1 101000 f 74 goat snp30962-scaffold3419-47778 NW_017189516.1 53814720 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793867 Affx-122976521 AX-385280836 X 112622806 TGGAAATCTTAAAGTATGCATTCATTGAGTTTTGA[C/T]AGCTGCACACAACTGGTTAATCCAAAATGCTATCA Y 2 1 2 1 101000 r 74 goat snp30961-scaffold3419-16744 NW_017189516.1 50953944 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393081 Affx-122965602 AX-123263438 X 112656284 CCTCAGAACAGAGCTCCTTCTAGGCTGCTTCATAG[C/T]GGTGTCATGTAACAGTTCCACATGGAGAAGTAACT Y 2 1 2 1 102000 f 74 goat snp32857-scaffold380-16635 NW_017189516.1 50996592 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403161 Affx-122958090 AX-123273514 X 112702894 AGCCTTAGAATGGAATGTCATGAGAGTAGAGAATA[C/T]GTATATCTTGGCCCCTTCCTCAGTCCTAGCATCTC Y 2 1 2 1 201000 f 74 goat snp32858-scaffold380-63245 NW_017189516.1 51043525 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793627 Affx-122935706 AX-385280601 X 112735874 CCTCTTAAAAGTCTGCATATAGTTTATTGCCCCAC[A/G]TTCTTCCGTTGTCTAGTCTAATCAGGGTCCTGTCC R 2 1 2 1 101000 f 74 goat snp32859-scaffold380-96225 NW_017189516.1 51076928 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450241 Affx-122922260 AX-123320576 X 112797103 GCCATGTGGGATTGGATTTGAGGAAGTGGTGGCAA[C/T]AACTCTCGAAGAATGTGCCAGGGAGGTGATGTAGG Y 2 1 2 1 101000 f 74 goat snp32860-scaffold380-157454 NW_017189516.1 51137980 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796474 Affx-122942263 AX-385283424 X 112845205 GGCAGCAGGCATGCTGTGAACGTAAAGTCAGACCA[A/G]CGATTGTCCTGTCTCCTGAGATTGCTTTCTGAGGT R 2 1 2 1 101000 r 74 goat snp32861-scaffold380-205556 NW_017189516.1 51186138 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446147 Affx-122925761 AX-123316483 X 112904382 TGGTGCCTACCCGTTAGGAGGACTGTGCGACAGTG[C/T]GTGTACAGAGCTCAGCACTGTGCCTGGTGCGGGGT Y 2 1 2 1 202000 r 74 goat snp32862-scaffold380-264733 NW_017189516.1 53930057 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769777 Affx-122937502 AX-385256947 X 112957760 AGACCACAATCCTTGACCTTTCAAAATGTAAATAA[C/T]CCCAAGACATTTACAAGTCTTTTAAAATGGCTAAG Y 2 1 2 1 201000 f 74 goat snp32863-scaffold380-318111 NW_017209417.1 1077 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433298 Affx-122935199 AX-123303639 X 112991983 TCAAGTAAACAGACTAGCCTTTGCTTTCTACTGCT[A/C]CTGAACCAATCAAAGCAAATTTACCTGAGTGATCA M 2 1 2 1 101000 f 74 goat snp32864-scaffold380-352334 NW_017189516.1 51236240 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778686 Affx-122964798 AX-385265797 X 113057629 TACCCCAATATTTTGTGGGGGCAGTTGATGATGTT[G/T]TATAAGAAATTAAATTTAGGAGTAACAATGTCTGT K 2 1 2 1 201000 r 74 goat snp32866-scaffold380-417980 NW_017189516.1 51302546 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792973 Affx-122926434 AX-385279951 X 113100227 CACTTTAAAGGTCACAGAGGCTTTTAAAATTACTT[A/C]GAATTTACACACAGGGCAAGAAAACCAAGATACTT M 2 1 2 1 101000 f 74 goat snp32867-scaffold380-460578 NW_017189516.1 51345304 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411672 Affx-122951552 AX-123282022 X 113225430 AGGCTACAGAAGTAAAAATAATGAATTCAGACACA[C/T]GTTCTATTATTGCTTTTAATATACTCTTTGAATGA Y 2 1 2 1 101000 f 74 goat snp32870-scaffold380-585781 NW_017189516.1 51470623 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791858 Affx-122977827 AX-385278848 X 113294647 TGAGAGAAAATACTGTTGGAAGATGTGCTATTATG[C/T]ACCAGAAATCCCTGGGTTTTAAAATTCAAGGAGTA Y 2 1 2 1 202000 r 74 goat snp32871-scaffold380-654998 NW_017189516.1 51539929 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424776 Affx-122941403 AX-123295122 X 113338960 AAGTTGTCTTCAAGCCTTACTGAATGCATTCTAAG[C/T]AGAATAATGAAGTGAGAAAACCCAAAATGTGATGA Y 2 1 2 1 101000 f 74 goat snp32872-scaffold380-699311 NW_017189516.1 51584255 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448188 Affx-122924245 AX-123318524 X 113405785 CCTAGCCTGTCCCCAGAGTGCTTATCTGATCTTTC[A/G]GTCCCCTATCTCCCCTACTGGAAACTTTCCTGGTG R 2 1 2 1 201000 r 74 goat snp32873-scaffold380-766136 NW_017189516.1 51650695 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770595 Affx-122951544 AX-385257759 X 113440245 TAGTATATGTCCTATGTTTCTCTCCATGCTTAAAT[A/G]ACTTCAATCTGTTATTCATGTAATCCTGTAGAGAC R 2 1 2 1 101000 f 74 goat snp32874-scaffold380-800596 NW_017189516.1 51680737 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415423 Affx-122948724 AX-123285772 X 113580721 ACCTATATGAAAGGAAAGCACATACTTTACTGAGC[A/G]TCATGTAAAAAAGCTTGAGTAAGAGACACAAAGAG R 2 1 2 1 101000 r 74 goat snp32875-scaffold380-941072 NW_017189516.1 52214380 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403163 Affx-122958089 AX-123273516 X 113617794 GGTCCGTGGACCAGCAGCTGCAGCACTGGAAAGCT[C/T]GTGAGAAAGGCAGTCTTGAGTTTCATACCAGACTA Y 2 1 2 1 101000 r 74 goat snp32876-scaffold380-978145 NW_017189516.1 52251414 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801082 Affx-122951520 AX-385287996 X 113693240 AATAGGGAAGAAGCAGCACAAGTTCAATTTTGAAC[C/T]GAAGCCTTAAGAGAACTCACATGTTTCCTTCTCAT Y 2 1 2 1 101000 r 74 goat snp32877-scaffold380-1053591 NW_017189516.1 52328189 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800845 Affx-122974086 AX-385287760 X 113741877 CGGTCATTTGAATTAGGGACACTTTTCTGACAACA[C/T]ATGGGTTCTTTTTTCCACCTATTCTATCATCTATG Y 2 1 2 1 201000 r 74 goat snp32878-scaffold380-1102228 NW_017189516.1 52378155 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387725 Affx-122969752 AX-123258083 X 113775164 TAGATTCGAGTTTGATGCTGGTGCCAGCCTATGAT[C/T]ACTCCTGGCATAGTTCACCCTGTAGCTTAGTGGCT Y 2 1 2 1 101000 f 74 goat snp32879-scaffold380-1135515 NW_017189516.1 52411956 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400684 Affx-122959945 AX-123271039 X 113854304 TATTTATAATGGATGCTTTGTACCTATCCATGTGA[A/G]CCAGAATTTGGTTGCTTAATTGGGAAAAAAACAAT R 2 1 2 1 101000 f 74 goat snp32880-scaffold380-1214655 NW_017189516.1 52579199 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444116 Affx-122926817 AX-123314453 X 113941583 AGAGATGACCTGTGGGGCTTATATTTGAGAGGTGA[C/T]ACAGGTGTGATGAGCTGAACTGACTGCCTCAGCAG Y 2 1 2 1 101000 f 74 goat snp32881-scaffold380-1301934 NW_017189516.1 52666402 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421060 Affx-122944514 AX-123291407 X 114001990 TTGTCTTTGGGCAGAAACGGGCACAAAGGGCAGTC[A/G]TCTTAGAAGGTCTCTCCCTCCCTCCAGCTGACGGA R 2 1 2 1 103000 f 74 goat snp32882-scaffold380-1362341 NW_017189516.1 47976182 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407925 Affx-122954375 AX-123278276 X 114037327 GAAATTAAGCCATAATTGAATCCTCATCATAAAAA[C/T]GTCAGTCTGTACAGAAGCCCGTAAGGTAAGTTGAG Y 2 1 2 1 201000 f 74 goat snp32883-scaffold380-1397678 NW_017213847.1 39521 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448122 Affx-122924302 AX-123318458 X 114098138 GGTTGCTGAAGGGAAGATTTCCTTTCCGGGACTTT[C/T]GGCTTTCTTTTGCTGCCTCCAGGAGACAATGGGCC Y 2 1 2 1 101000 f 74 goat snp32884-scaffold380-1458489 NW_017189516.1 52715966 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387730 Affx-122969747 AX-123258088 X 114134715 CATTGATTCTCCACAATCTTCCTGGTACAGCATCA[C/T]ATCACCTGCAACTAGACCTAGGTTTACTTCTTCTT Y 2 1 2 1 101000 r 74 goat snp32885-scaffold380-1495066 NW_017189516.1 52752991 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783165 Affx-122968400 AX-385270232 X 114204568 TGGATGTGAATTAGGTTTATTTAGTTTGGCTACCT[C/T]AGATAAGGAAATTCCAGAAGCTTTCCAATTGCTAT Y 2 1 2 1 101000 f 74 goat snp32887-scaffold380-1564919 NW_017217174.1 21619 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447162 Affx-122924435 AX-123317498 X 114296339 GAGGGAGCAAGGGCGCAAACCCATGCTAGGTCCTC[A/G]TTCTCCCAGCAACATCTCGACGCAGCTCTCAAGAT R 2 1 2 1 201000 r 74 goat snp32889-scaffold380-1656690 NW_017189516.1 52859538 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768835 Affx-122923542 AX-385256012 X 114324928 TGTACATTTTGCATGTTCCCATCCACTTAGCGAGC[A/G]TTTCTTTTTTGAGATGCTATTGTGTGCCTGGCCCT R 2 1 2 1 101000 f 74 goat snp32890-scaffold380-1685279 NW_017189516.1 52888129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419974 Affx-122945190 AX-123290322 X 114399576 TTCGGGCTCAGTGTGCCTGTGTGCGTCTCTTTCTG[C/T]GTTGTGCATCTCAAAGTGGAATTCATCATCCTCAC Y 2 1 2 1 101000 r 74 goat snp32891-scaffold380-1759927 NW_017189516.1 52946106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422626 Affx-122943711 AX-123292972 X 114529123 GATGTCTGGGCCTTTGGAAGCTGGAAAGAGACTTT[A/G]CTGTGCTGTGAAGAAACAGTGAGGGGTGGTGAGGG R 2 1 2 1 101000 f 74 goat snp32893-scaffold380-1889474 NW_017189516.1 53075336 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419989 Affx-122945178 AX-123290337 X 114579638 ACTAGAGATGTAGAGCTGGGCTTCCACTGGGATTA[C/T]TCACAGAAAATGATGTTCTCATTTCATCCTCACAA Y 2 1 2 1 101000 r 74 goat snp32894-scaffold380-1939989 NW_017189516.1 53126243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796895 Affx-122964888 AX-385283837 X 114623631 CACTTCCCTATTGGTGTTTCCTTTACCTCTAAATA[A/C]ACTACTTGCACTTGAATCTTTGTCTCAGGGCTGGT M 2 1 2 1 102000 r 74 goat snp32895-scaffold380-1983982 NW_017189516.1 53169473 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441759 Affx-122929116 AX-123312096 X 114720945 TTGGTTGGGGAACTAAGATCCCACATCCCACGCAG[C/T]GTGGTCAATAAATAAGTAAGCAACCAAGCAAGCCG Y 2 1 2 1 101000 r 74 goat snp32896-scaffold380-2081296 NW_017189516.1 53269232 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450972 Affx-122921741 AX-123321306 X 114798850 CAGCTGACTGGCCCATGGCTCCAATCCCTTACCAA[C/T]AATGGCCTTCTTTCCCTTTAAAGAGACAGACGTAT Y 2 1 2 1 101000 r 74 goat snp32897-scaffold380-2159201 NW_017189516.1 53348469 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799328 Affx-122957644 AX-385286258 X 114829735 AAAATAAATTACATCACAATAAGCCATCTATCTGC[A/G]TGTGACTAACTCTCCACTAGGCTAAGCTCTATGAA R 2 1 2 1 101000 r 74 goat snp32898-scaffold380-2190086 NW_017189516.1 26880307 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387906 Affx-122970458 AX-123258264 X 114881046 TTAGATTATTAGGATAGTTGAGTTTCTCCAATCTG[C/T]AAAAATCACTTTTTCCTACAAGTCCATGTTCCAGC Y 2 1 2 1 101000 f 74 goat snp32899-scaffold380-2241397 NW_017189516.1 26933009 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447741 Affx-122924587 AX-123318077 X 114963060 ATGGCCTTCTTTGCTTTTCTTGCCATTGACAGTTG[C/T]GAAGAGTACCGGCCACTTGTATTATGGAAGGTCCC Y 2 1 2 1 201000 r 74 goat snp32900-scaffold380-2323411 NW_017190135.1 64797 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768426 Affx-122972868 AX-385255606 X 114991908 CAAGAATTAAATGAAGCAATCTTGCTGTAACTTCT[A/G]CACCTCATAAATATGTATTAGGAGACAAATTTTCC R 2 1 2 1 101000 f 74 goat snp32901-scaffold380-2352259 NW_017190135.1 36046 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405540 Affx-122955975 AX-123275892 X 115027876 TTAGAATGGTCTGTTTTTATCAAATATGGAACATG[C/T]GGGTGGACTGTCCCATCAGAGTTCAATGCTGCCCC Y 2 1 2 1 101000 f 74 goat snp32902-scaffold380-2388227 NW_017190135.1 405 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415436 Affx-122948716 AX-123285785 X 115076656 CCCGCATGCCATGAAGCAACTGAGCCCAAGAGCCA[C/T]CTCACAAAAGGATCCCATGTGCCAGATGCACAACT Y 2 1 2 1 101000 r 74 goat snp32903-scaffold380-2437007 NW_017189516.1 53726487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434759 Affx-122933901 AX-123305100 X 115111243 AACAGTTACCAACAGAAATGCAATTCCCTAGGCCT[A/G]TACCCTACTATTGCAAAAAATGAACAAATTCACTC R 2 1 2 1 101000 r 74 goat snp32904-scaffold380-2471594 NW_017189516.1 53659341 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794908 Affx-122931612 AX-385281868 X 115165531 ATCTAAGAGGCATCTCATACACATCAAATGAGAAA[C/T]GGTTTACTAAGAATGAAGGTAGACTCTGAGTCTGG Y 2 1 2 1 101000 r 74 goat snp32905-scaffold380-2525882 NW_017189516.1 53604884 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440217 Affx-122930688 AX-123310554 X 115231963 GATAGGATCTAGCCCTGCATCTCCCTCACCTGCCC[A/G]TCTCCGGCCGGCTGTACAACGTTCTTATCCAGTAT R 2 1 2 1 201000 r 74 goat snp32906-scaffold380-2592314 NW_017189516.1 53538423 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416107 Affx-122948310 AX-123286456 X 115269301 CTTATGCCACTGCCTCATTAGTAGTGGGACAAAGT[A/G]TCCTGAAGCATTCCTTTTCTTATTTTCCTTATCTG R 2 1 2 1 101000 f 74 goat snp32907-scaffold380-2629652 NW_017189516.1 53500889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393396 Affx-122965896 AX-123263752 X 115315380 TGTTATTTTTTTTAAAGGAAATAAATTCTTTTTCT[A/G]TTTAAATCAAGGGACTTTGGAGACAGACTCGGTAA R 2 1 2 1 102000 r 74 goat snp32908-scaffold380-2675731 NW_017189516.1 53454481 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430158 Affx-122937377 AX-123300499 X 115353573 GTCCATGGGGTCACAAAGAGTCGGACATGACTGAG[A/C]GACTAAACTGAACACCTATATAACTGCCATCACCT M 2 1 2 1 101000 r 74 goat snp32909-scaffold380-2713924 NW_017189516.1 53416100 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454109 Affx-122919357 AX-123324442 X 115392580 ACGCCAAATACAATAACACTCAAAGTTAAATCACA[C/T]GCATGATCTGAGGTCTCATCATTTATTTTGTTTGT Y 2 1 2 1 101000 f 74 goat snp32910-scaffold380-2752931 NW_017189516.1 53376997 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800949 Affx-122953145 AX-385287864 X 115433735 TATTTGTTTCTTGGGACATAATTCTCCATGGGTGT[C/T]TCGCGTTTCTGCACATCTTCTGAGCAAAGGCATCA Y 2 1 2 1 101000 r 74 goat snp32911-scaffold380-2794086 NW_017189584.1 22870 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393999 Affx-122922536 AX-123264354 X 115477119 GTATATCTGCCCACTTTCTGAACTATGGCTTCATC[A/C]TTTTCACAACCACCACTCCCTTCCGAGTGACAACC M 2 1 2 1 102000 f 74 goat snp32912-scaffold380-2837470 NW_017189516.1 53768972 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427733 Affx-122939265 AX-123298076 X 115531446 TGGGTCACAAATCAAACTTGATAAGTTTAAGAAAA[C/T]GAAAATCATATCAAGCATCTTTTCTAATCACAAAT Y 2 1 2 1 103000 f 74 goat snp32913-scaffold380-2891797 NW_017189516.1 53955775 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392391 Affx-122966222 AX-123262748 X 115579799 CAAGCAATTTGTGAATTCAATATTGGCCCCATTTC[A/G]TTTATCTTCAATGCTGTGATTCTTCTCTGGTCTTA R 2 1 2 1 101000 r 74 goat snp32914-scaffold380-2940150 NW_017189516.1 54004496 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788978 Affx-122968413 AX-385275991 X 115638610 TAACAGAACTAACAGACCATCTTGAAAAGATCCTA[C/T]GAACTGGATCTCTAAGCAATGGTTTTCAAACTAGA Y 2 1 2 1 101000 r 74 goat snp32915-scaffold380-2998961 NW_017189516.1 54086972 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772514 Affx-122954776 AX-385259665 X 115688695 AGTCTTTCTGTGTTTTCATCATAAATACCACTCGA[G/T]CTACATTTGGACTAGAAGGCCAAAATTGCCACAGA K 2 1 2 1 101000 r 74 goat snp32916-scaffold380-3049046 NW_017189516.1 54136787 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426570 Affx-122940163 AX-123296916 X 115730521 GTAAATAATTAAGAGGGTTGTCTGAGAACCAGGAT[A/G]TCGGATGACAACAGTTTAAACGCATAGAGAAATCG R 2 1 2 1 101000 f 74 goat snp32917-scaffold380-3090872 NW_017189516.1 54178872 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449453 Affx-122922663 AX-123319788 X 115764617 CCAGACTTCCAGCTTAATCTCTAGCAATCAATTTA[C/T]TCCAGATGGTGTCAGGTAAATGCACTCCCATCCTG Y 2 1 2 1 101000 f 74 goat snp32918-scaffold380-3124968 NW_017189516.1 54213020 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800221 Affx-122965336 AX-385287144 X 115806814 TCTAGAAGCACCTTATGGAATGCAAGCAGCTTCCT[A/G]GATATTTGTAAAATTTCAGATGGACACACAAATCT R 2 1 2 1 101000 f 74 goat snp32919-scaffold380-3167165 NW_017189516.1 54256287 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418881 Affx-122946112 AX-123289229 X 115882387 CAGAAGACTAAAAGGCTAACAATTTAACTTCCACT[A/G]TTAGAGTTCACCATATCACCAGGTTCTTGCCACAA R 2 1 2 1 101000 r 74 goat snp32921-scaffold380-3242738 NW_017189516.1 54333015 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799448 Affx-122945288 AX-385286378 X 115922231 TTGAAAATTTATGGCTCACACTCAACCTACCTAGC[A/G]ATCTTCCCCAATTCCCCAGAGATCACTGCTGATGG R 2 1 2 1 101000 r 74 goat snp32922-scaffold380-3282582 NW_017195920.1 12193 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441317 Affx-122929442 AX-123311654 X 115970234 CAACATTAAGCAATGTCAGGCAGAAATTTTCACTA[C/T]GTCTGCAGTTCTGCTGGTGTTTGTGGGAAGATAAT Y 2 1 2 1 101000 f 74 goat snp32923-scaffold380-3330585 NW_017189516.1 54399875 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432041 Affx-122935905 AX-123302382 X 116024568 AATATATATTTTTTAACCTTTTCTGTAACAAGTTT[A/G]TTATTTGTCTTGAGAATTCTATTTGACAGTAACCT R 2 1 2 1 101000 r 74 goat snp32924-scaffold380-3384919 NW_017189516.1 54454205 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437245 Affx-122932018 AX-123307583 X 116062129 CTAACACTAGAATCTAAGTTAGGACTGATGACAAA[C/T]GGAAAACATATATATCACACACATGACAGATATAG Y 2 1 2 1 201000 f 74 goat snp32925-scaffold380-3422480 NW_017189516.1 54491753 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424580 Affx-122942216 AX-123294926 X 116109671 GAGCCACCAGGGAAGCCAGATGACCTCAACATAAA[C/T]GACAAGGAGAGCAAGGAAGGTAGAACAGGACTCAT Y 2 1 2 1 101000 f 74 goat snp32926-scaffold380-3470022 NW_017189516.1 54539198 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377544 Affx-122977458 AX-123247903 X 116142998 TAGAAATGGATGGACAGACATGAGTGTCTGGCTGG[C/T]GAGAGAGACAGATAAATGGAAATATCAATAAGTGC Y 2 1 2 1 201000 f 74 goat snp46932-scaffold655-7890 NW_017189516.1 54665558 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415865 Affx-122948854 AX-123286214 X 116175879 CTGAGGGTGGAGGGTTCCCTGGGAACTTGTTGGAC[A/G]CCAAGTCACTGCCTATATGTTAAGGTTCCTTTCAG R 2 1 2 1 101000 r 74 goat snp46933-scaffold655-40771 NW_017189516.1 54698455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771742 Affx-122936559 AX-385258899 X 116229462 TTTCAGCAGTCAATCAGACACAATTAAAAAGAGTG[A/C]TAGTACCCAGGGTCAGTGAGAATGAAGTGTTGCTC M 2 1 2 1 101000 r 74 goat snp46934-scaffold655-94354 NW_017189516.1 54752225 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794699 Affx-122968166 AX-385281659 X 116315995 GAGACCTCATGTCCCTTGGGCCAAAAAACAGCCTG[C/T]TCACTAATTAGCCCATGTTATGGGCTGGCATGTGA Y 2 1 2 1 202000 f 74 goat snp46935-scaffold655-180887 NW_017189516.1 54839163 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798365 Affx-122926697 AX-385285300 X 116348910 GGCAAACAAAAATATTTGCAATTCAATTGTTTTCC[A/G]TTAAATTTTCCTTAACTGCACTATTAGATTTAACA R 2 1 2 1 101000 f 74 goat snp46936-scaffold655-213802 NW_017189516.1 54871992 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435287 Affx-122934040 AX-123305627 X 116407951 ACTTAAGGTGGTTCTAGTTAAGGTTTCCTTGGTAT[A/G]CAGCTCCTGGGAGAGAGATTGGTATTCAGGAGTTT R 2 1 2 1 201000 f 74 goat snp46937-scaffold655-272843 NW_017189516.1 54932145 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428681 Affx-122938637 AX-123299023 X 116478350 TCTGTTGCTTGATTAGCTTAGCTGGTAAAGAATCC[A/C]CCTGCCATGCAGGAGACCCCAGTTCGATTCCTGGG M 2 1 2 1 103000 f 74 goat snp46938-scaffold655-343242 NW_017189516.1 55002208 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425617 Affx-122940908 AX-123295963 X 116542022 CCAGACTGATGAAGCCTATACCTGAAGCTTCAGTG[A/G]TCACCACGGCAAGAGGAAAGGGAGACGGATGGTCT R 2 1 2 1 202000 r 74 goat snp46939-scaffold655-406914 NW_017189516.1 55066267 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789083 Affx-122965391 AX-385276097 X 116613286 TTTCTGCACATGTAAATTGAAGATAGATAATTTGA[A/G]GTCACCCCAAGTTAGGTTAGCATAGGATGTGGCTA R 2 1 2 1 101000 r 74 goat snp46941-scaffold655-478178 NW_017189516.1 55137704 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410579 Affx-122952127 AX-123280929 X 116677873 CTCAAACACATCAGCTCCACAGACATTCTCTGTGG[C/T]GAGGGAAGGCAGCTAGAAAGCCTTTGTTCATTTCT Y 2 1 2 1 202000 f 74 goat snp46942-scaffold655-542765 NW_017189516.1 55203380 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430804 Affx-122937461 AX-123301145 X 116713558 CCTTTCCTTCTCACTTGCCCCCTTCCTTACTGGTG[A/C]TTCCTGGGATTTCTCCCAAATAAAACACTTTAAGT M 2 1 2 1 101000 r 74 goat snp46943-scaffold655-578450 NW_017189516.1 55240101 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389038 Affx-122968623 AX-123259396 X 116768193 GATTCATCCCCAAGCATTCTCTGTTGCATTTACAG[C/T]ACTTCATTGCATTGTATAGGAGTTCTTAGTTTGAA Y 2 1 2 1 201000 r 74 goat snp46944-scaffold655-633085 NW_017189516.1 55294550 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798192 Affx-122933275 AX-385285127 X 116816186 CACCTTACTTGATTTAGGCTCCAATGACTTTGCTG[C/T]TCCTCACACAGGCCAGGAACACAGCTTTTTCATTT Y 2 1 2 1 101000 r 74 goat snp46945-scaffold655-681078 NW_017189516.1 55343014 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791625 Affx-122973109 AX-385278616 X 116875026 TGCAGTTCAGATGAAAATGCAATTTAAAGGATTGA[C/T]GGAATTTCTAAGTGTGACTAAAAGTTATCTAATAA Y 2 1 2 1 101000 f 74 goat snp46946-scaffold655-739918 NW_017189516.1 55402314 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395570 Affx-122963846 AX-123265925 X 116909343 GTTGGCTGTGGATTTCATCCATCCATCCTTTTACT[A/G]CTTTATTACAAACAGGAATTAAGGCAACTTACAAA R 2 1 2 1 201000 r 74 goat snp46947-scaffold655-774235 NW_017189516.1 55436580 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384593 Affx-122972985 AX-123254951 X 116937948 GTTCCTGAGAGCCTCATTTTGCCTTTGCAGACTGA[C/T]GCCAGCTGCCTGAGTCCCTTCCTGTTTTCCTCTGT Y 2 1 2 1 101000 f 74 goat snp46948-scaffold655-802840 NW_017214303.1 3867 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770783 Affx-122952569 AX-385257947 X 116992461 GCTGTACTTGCAAGTTCCCCATTACTTACTAATAC[A/G]CTTGGAAAATATCCAATTACTTGCTTTTAGTATCA R 2 1 2 1 101000 f 74 goat snp46949-scaffold655-857353 NW_017189516.1 55500615 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768236 Affx-122925401 AX-385255417 X 117078194 TTAAGAAACACTACTCTGTTCCTTACTCTGACTTT[A/G]CCAGGTTGTTCAACCTCTCTTTACCTCCCTTCCTC R 2 1 2 1 101000 r 74 goat snp46951-scaffold655-943086 NW_017189516.1 55585492 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799065 Affx-122919418 AX-385285995 X 117141690 AATGATAAGCACAGTGAATACACTTCCCAAGACAA[C/T]ACATTTAGAGCCATGATTCTCATCCCTGGCTACAC Y 2 1 2 1 101000 r 74 goat snp46952-scaffold655-1006582 NW_017189516.1 55649793 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428561 Affx-122938723 AX-123298903 X 117197338 ACATCTTATCCAGTTCTTTGGGAACATGATTTCAC[A/G]TTGCAGATAAAACAACTCTTCACCCTGCAGCAGTA R 2 1 2 1 101000 r 74 goat snp46953-scaffold655-1062230 NW_017189516.1 55705471 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406229 Affx-122956117 AX-123276581 X 117268680 CTGGAATAGAACAGAAAGAAAAATTAAGATGAAGA[C/T]GAGCAGAGTTAACAAAGGAAGTAGAAAGTCAGAGG Y 2 1 2 1 101000 r 74 goat snp46954-scaffold655-1133572 NW_017189516.1 55775332 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444970 Affx-122926670 AX-123315307 X 117300622 GACATCCCAGTTCGTTTAAGGTAGAGATACCCTCA[C/T]ACTTCAGTGGTAACCCTGGGTAATGCTTGCCTGAT Y 2 1 2 1 101000 f 74 goat snp46955-scaffold655-1165514 NW_017189516.1 55807416 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440710 Affx-122929899 AX-123311047 X 117398684 AAATGGCATTCCTCTGCCATTTGCTTTTTTAATTT[A/G]GTATTGTTTCTATGATTAATCCATGTTGATAAGTT R 2 1 2 1 201000 r 74 goat snp46957-scaffold655-1263576 NW_017189516.1 55906044 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391569 Affx-122966620 AX-123261926 X 117432580 ATGTGTTAAAATAGCAATAGTGAAAATCATGAGAG[C/T]GGATCCATGTGAGGAGCAGACAATATTAGCCTCCA Y 2 1 2 1 101000 f 74 goat snp46958-scaffold655-1297472 NW_017189516.1 55939941 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449604 Affx-122923208 AX-123319939 X 117492617 AGAGCACTCACTTTCTCGGTGGACATGCGTTTGAA[C/T]AAGCCCCAGAACAGCTGTTCGGAGAGGACTTAGAG Y 2 1 2 1 103000 f 74 goat snp53293-scaffold803-639196 NW_017189516.1 55997448 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774914 Affx-122922193 AX-385262047 X 117571808 GTGTTAGCTCACAGTTCTTGCTTGATAGTAAAGTG[C/T]GTTTGACAAATGGTGAGTCAATTGTAGTCTTGTAG Y 2 1 2 1 101000 f 74 goat snp53292-scaffold803-560005 NW_017189516.1 56074776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792359 Affx-122935118 AX-385279340 X 117634731 CAGGTTATTAATTCATTCAAGAGGATTATAATGAT[A/G]TTAACATTATCAAATGCCCATGTTCAAGGCATTCT R 2 1 2 1 201000 f 74 goat snp53291-scaffold803-497082 NW_017189516.1 56139296 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789119 Affx-122967190 AX-385276132 X 117675502 TTTCCCTTCATATGTAGTTAATACTCTTACAAACT[A/G]TAACTCTGTGTTGTGGCATATAAATTGCTGATATT R 2 1 2 1 101000 r 74 goat snp53290-scaffold803-456311 NW_017189516.1 56178962 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424234 Affx-122942477 AX-123294580 X 117728586 GTGGCAGGAGCGAGAAGCAGGGCAGAGTTGTCTTC[A/G]AAATGTATCTGTTTTGGATTCCAAATGGAAGACTG R 2 1 2 1 101000 r 74 goat snp53289-scaffold803-403227 NW_017189516.1 56236196 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403427 Affx-122957745 AX-123273780 X 117763518 CTCTTCTGACAGTTTTCATCTTTCTTTGCTTTTCA[C/T]GACCTTGAGGGTTTTGAAGAGGACTAGTTGGGTAT Y 2 1 2 1 101000 r 74 goat snp53288-scaffold803-368295 NW_017189516.1 56271271 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771339 Affx-122942148 AX-385258497 X 117849123 TATAAAAGTTTTACATCATACCAGCCTATTAAGTG[C/T]GCAATAATAGCATTATGCCCTCCCCCAAAAGTACA Y 2 1 2 1 101000 r 74 goat snp53287-scaffold803-282690 NW_017189516.1 56356939 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396705 Affx-122962820 AX-123267060 X 117893331 TGTATAGCATTTGTCCTTGTCCCTGGTGTAAATAC[A/G]TGGCCAGCTGTAAGCTACCCATGTGATGTTGCTGA R 2 1 2 1 101000 f 74 goat snp53286-scaffold803-238482 NW_017189516.1 56404453 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445541 Affx-122925161 AX-123315878 X 117928406 TTGAAAAGTAATTAATTTAAAAAGTGAAATGGCTC[A/C]GTTTAGGGGAGAGTCAAGGACTGTTCTACCCAAGC M 2 1 2 1 101000 r 74 goat snp53285-scaffold803-203407 NW_017189516.1 56439738 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384640 Affx-122972154 AX-123254998 X 117958789 GGGCTTTTGGCTACCATCTTGGACAGAAGAGATAC[C/T]GGAGATTCTCTCACTGGAGAACACTGCTGTTGTGC Y 2 1 2 1 201000 f 74 goat snp53284-scaffold803-173024 NW_017189516.1 56470470 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390157 Affx-122967980 AX-123260514 X 118018548 TTTGTCCAAGATGGCTGGAGGGAATGAACTACAAA[C/T]GGACTGGTCCATGCTGGGAGTGGGAGAAACTTGCA Y 2 1 2 1 101000 f 74 goat snp53283-scaffold803-113265 NW_017189516.1 56530651 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432819 Affx-122935393 AX-123303160 X 118072431 AAAGTGCAGCCTTAAAACTATCCCCACTCTTTTCT[A/G]TCAAGCATTTCAAGTGCCATTTTCAGGTGTCTTCA R 2 1 2 1 201000 r 74 goat snp53282-scaffold803-59382 NW_017189516.1 56584543 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770218 Affx-122954681 AX-385257383 X 118120040 ACTCTCATAGAATAGTCCACATCACAGGTAGATGC[A/G]TTCCTCATGGTAACAAGTCACTGACAGAGTGATGT R 2 1 2 1 101000 f 74 goat snp53281-scaffold803-11773 NW_017189516.1 56633438 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395265 Affx-122964090 AX-123265620 X 118192298 TGAACATGAGTGTGTCCAGGCATGCCTGCACATGC[A/G]TGTGTGGCATTGGGGAAAGGAGACTTGCTCTTTGT R 2 1 2 1 101000 r 74 goat snp15780-scaffold1655-60386 NW_017189516.1 57185918 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443172 Affx-122927610 AX-123313509 X 118221820 CTGGTGATAGAAAGATCTTCCATTTAAGGTTCTTG[C/T]GAAAATTAAATGAAAATTATTTTGAAAGTAAAGTG Y 2 1 2 1 101000 f 74 goat snp15781-scaffold1655-89908 NW_017189516.1 57215463 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376871 Affx-122977829 AX-123247230 X 118282009 CTGTATGTTAGTATGTTGGTAAATAACTGTATGAA[C/T]GTTAGTAACGGCTTTGAAGTGAAGTGAAGTCGCTC Y 2 1 2 1 201000 f 74 goat snp15782-scaffold1655-150097 NW_017189516.1 57275735 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775538 Affx-122967157 AX-385262669 X 118345346 ACTATCAGAAGTTGCCCAGTTTTGTGACTATCAAA[C/T]GACCTGATATAGGTTTAGGCCTATATCCTGACTTA Y 2 1 2 1 201000 f 74 goat snp15783-scaffold1655-213434 NW_017189516.1 50783949 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412420 Affx-122951429 AX-123282769 X 118373883 ACCTAAGGAATGGTGATGTTGACCTCTTCAGACCC[C/T]CATGACTTCAACAGACTAAAACTTGGACTCTGTCA Y 2 1 2 1 101000 r 74 goat snp15784-scaffold1655-241971 NW_017189516.1 50812974 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434938 Affx-122933864 AX-123305278 X 118420817 AACATAAAGGTGAGGGAAGATGTCAAAGGATAAAT[A/G]TCAATAGAAGGACAACTCATTTATTTAGTTACTAA R 2 1 2 1 101000 f 74 goat snp15785-scaffold1655-288905 NW_017189516.1 50929707 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776596 Affx-122953421 AX-385263723 X 118461369 AAAGTCACATGATGATTGCATCACTTCAAGATACC[G/T]AGCAAGTTAGGACCAAGTATGGACATAAATCTTCA K 2 1 2 1 101000 f 74 goat snp15786-scaffold1655-329457 NW_017189516.1 50888706 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437273 Affx-122931997 AX-123307611 X 118490250 ACCTGAGTAGATACTAATTTGGGGGTGGGTGAGTC[A/G]GGTGGAGGGAGATTCCAGGGCCTGATTTCCCCAAG R 2 1 2 1 303000 r 74 goat snp15787-scaffold1655-358338 NW_017189516.1 50859082 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437066 Affx-122933085 AX-123307404 X 118564042 TCTCTGAACTGGCCATTTCTGCCTCAGAAATGCAG[C/T]GTTCCCTATGTGGCTGTGGTCAGAATGCTTTGCAG Y 2 1 2 1 201000 r 74 goat snp15789-scaffold1655-432130 NW_017189516.1 50545866 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417006 Affx-122947981 AX-123287354 X 118594153 AGGGTTTTTTCCCCTTCTGATTTTTAGAAGAAAAT[A/G]AAGTAATTTGTGGGCCCTCAGCTCTGTGCCTAATG R 2 1 2 1 101000 r 74 goat snp15790-scaffold1655-462241 NW_017189516.1 50576072 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431550 Affx-122936204 AX-123301891 X 118653610 CCAACTTATGCAGCGCCCTCATCTCTTCTGCCAGG[C/T]GCCATCTTAGCTCTAAACCGCAAAGCTAGCCCTTC Y 2 1 2 1 103000 f 74 goat snp15791-scaffold1655-521698 NW_017189516.1 50629141 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391964 Affx-122966527 AX-123262321 X 118694124 GGTAGGTGACCCAGGCAATACTGTGTTTGCTTGCC[A/G]CCTAAGCAGATCTCAGCCTATGTGATTTTCAAGTG R 2 1 2 1 101000 r 74 goat snp15792-scaffold1655-562212 NW_017189516.1 50669150 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452739 Affx-122920277 AX-123323072 X 118728171 AGGTCCAAAGTTTCTAGATTCTTCAGACTCTGTAG[C/T]CCTTTCCAACTGAAAGACTTGAGCCCATTTTTGGC Y 2 1 2 1 101000 f 74 goat snp15793-scaffold1655-596259 NW_017189516.1 50703293 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433516 Affx-122935014 AX-123303857 X 118761758 CTGCTTTAAATCAACTGGTTTTAGTCACTGTTAAC[A/G]TGTCTATGATGGGATGCCAAGATGTCTCGTTGCGT R 2 1 2 1 101000 r 74 goat snp15794-scaffold1655-629846 NW_017189516.1 50736788 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387295 Affx-122970526 AX-123257653 X 118795737 CTTTCCATTTTAGATCAACGTGATGTACAAGAAAC[A/G]TACTTCTTCCTTATGATATTATTTCCTGCTTCTAA R 2 1 2 1 101000 f 74 goat snp15795-scaffold1655-663825 NW_017189516.1 57411206 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795079 Affx-122941215 AX-385282038 X 118850811 CAAATCAGAATTGACATTTAGAACATCTTGACCCA[C/T]GACATCCTACTATATTTCCATAGGCTGAATACTTA Y 2 1 2 1 101000 r 74 goat snp15796-scaffold1655-718899 NW_017189516.1 57466178 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378714 Affx-122977051 AX-123249073 X 118862598 CTCATTTCTGGAAGCCTTATTTTTTAAAAAATTAT[A/G]TCCCAGAATCAGACAGAGACTGCAAAACATACTAT R 2 1 2 1 101000 r 74 goat snp19230-scaffold194-5463 NW_017189516.1 57477891 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412311 Affx-122950857 AX-123282660 X 118925897 TCTTCGCACTTTTGGAAGCTTTCTCCAAACGTGGT[A/G]ATTTTTATTATAAATCTCAAAAGAGGTTTCTTTTG R 2 1 2 1 101000 f 74 goat snp19231-scaffold194-68762 NW_017189516.1 57540771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787846 Affx-122966539 AX-385274869 X 118963017 GCTGTTCAAAGGCAGGTGAAGAGCACAAATGGTCT[A/G]CTAAGATTAAACAATGGCAACTTAAAAAAAAACTG R 2 1 2 1 101000 f 74 goat snp19232-scaffold194-105882 NW_017189516.1 57577962 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400632 Affx-122960370 AX-123270987 X 119046248 GAATGTCCAGTTCTTAGCACAGTATTTGACATAGG[C/T]GAGTGCTCAACATACTTTAGTGGGGGGAAAAAAGC Y 2 1 2 1 201000 f 74 goat snp19233-scaffold194-189113 NW_017189516.1 57662518 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427740 Affx-122939258 AX-123298083 X 119084324 GTGAGCTCCAGATTGAAAGCTCGTTCCTAGACGGA[C/T]AGAAGGAAAGGTAGAAGGACCTGAGGGCGTCCTTT Y 2 1 2 1 101000 f 74 goat snp19234-scaffold194-227189 NW_017189516.1 57700863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377893 Affx-122977249 AX-123248252 X 119124040 CTGTTAAACTGCATGTTGTCACTTTCAAGCTATGG[C/T]AGTGTAAAAAAATTTATAGAAAGAAAACTCAAATA Y 2 1 2 1 101000 f 74 goat snp19235-scaffold194-266905 NW_017189516.1 57738532 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398781 Affx-122961427 AX-123269136 X 119162634 TCTACCCTCTTGTGCTTGGACTGTTCTCACACAAG[C/T]GGTTTACAAAGATACAAAATCACAGTAAGGCCCAC Y 2 1 2 1 101000 r 74 goat snp19236-scaffold194-305499 NW_017189516.1 57777694 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443429 Affx-122927367 AX-123313766 X 119256557 ACTGCCCTTTTACACTTACAGAAACAGGCTCAGCT[A/G]CAATAACTTACTTCTTCAAAACTTAAAGTGCCATA R 2 1 2 1 201000 r 74 goat snp19238-scaffold194-399422 NW_017189516.1 57870451 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447043 Affx-122924528 AX-123317379 X 119314876 ATGGTAATCTGTAGACTGGGGTTATGTGAGAAAGT[A/G]TCCAGGATTTCTCAGTGGAAAAAGAAAAATGAAAT R 2 1 2 1 101000 f 74 goat snp19239-scaffold194-457741 NW_017189516.1 57928424 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445690 Affx-122926125 AX-123316027 X 119430231 ATGTGGTTCCCTCCTCTGGAACTTTCCCCCTAGAC[A/C]TCCCAATGGCTTGCTCTCTCACCTCTTCCAAATTT M 2 1 2 1 101000 r 74 goat snp19240-scaffold194-573096 NW_017189516.1 58044326 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391792 Affx-122967041 AX-123262149 X 119459414 ACATATATATGTCCCTATCAATTGTTCAGAAAATA[C/T]TTGACCTGTCCATTTACCATTTTTAAAGCCAAGTT Y 2 1 2 1 201000 f 74 goat snp19241-scaffold194-602279 NW_017189516.1 58073718 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444736 Affx-122926403 AX-123315073 X 119508714 ATACAATTAACGTCAGCAAAGTGGTTATTTTTCTT[A/G]TGCTAAAGTCCCAAGCAGTATGGTGGCTGTGTGAT R 2 1 2 1 101000 r 74 goat snp19242-scaffold194-651579 NW_017189516.1 58123645 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396947 Affx-122963180 AX-123267302 X 119564559 TTGCTATGAATGCATTGTGCAAATAAAAGTCATTC[A/C]GGGACTCTTGGGAGGCACAGCTCTAATGAGACAGC M 2 1 2 1 201000 f 74 goat snp19243-scaffold194-707424 NW_017189516.1 58179759 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425578 Affx-122941423 AX-123295924 X 119597130 GCAGTCCAATTCTTACCTAGTTATTATTCAAATGA[C/T]ATCATAATTGAAGGACACCGTGTAATGTGCTGCTC Y 2 1 2 1 101000 f 74 goat snp19244-scaffold194-739995 NW_017189516.1 58213063 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425189 Affx-122941041 AX-123295535 X 119628471 CAGGACAGCTGGCTGTCCACTCCAGGGCCTAATTG[C/T]GGAAGTTAATATAGAGGGATCAGTCTCTGAAGGGT Y 2 1 2 1 101000 r 74 goat snp19245-scaffold194-771336 NW_017189516.1 58244462 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397227 Affx-122962378 AX-123267582 X 119686311 TAAGATCTCCATGTTGTAGAGGCTACTAGCTGTCT[A/G]TCAAACATTATTTTATCTTTTCTGAGTTACATGAA R 2 1 2 1 101000 f 74 goat snp19246-scaffold194-829176 NW_017189516.1 58303804 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778411 Affx-122962554 AX-385265526 X 119745425 ACTGTATTTGTTGGTGTGTAAGGACAGATGTAATA[C/T]GTATGCTTTTGATGCCAGAGGTACATTGGCAACAC Y 2 1 2 1 101000 r 74 goat snp19247-scaffold194-888290 NW_017189516.1 58363507 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771998 Affx-122929344 AX-385259154 X 119797168 AAGGGGTGAATTATGTTGACTAATGTCATGCCAGA[G/T]CTAAGGACCCTTGAAGCAACTTGAGAAGAACTCTA K 2 1 2 1 101000 r 74 goat snp19248-scaffold194-940033 NW_017189516.1 58415411 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403201 Affx-122958060 AX-123273554 X 119825923 CTTAGCACTCTCCATCCCTGCCTAAACCCTACCCA[A/G]TGGCTGCAGGCTTTTGACAGTAAGTGGCAGGCACC R 2 1 2 1 201000 r 74 goat snp19249-scaffold194-968788 NW_017189516.1 58444228 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435251 Affx-122934068 AX-123305591 X 119856774 AGAATCATTAGCAAATAAGGGACTCAGAGGGAGCT[A/G]CTGGTACCTTTAAAAATGTTTGCTGGTTAAAAAGA R 2 1 2 1 201000 r 74 goat snp19250-scaffold194-999639 NW_017189516.1 58475576 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425791 Affx-122940707 AX-123296137 X 119938627 GACTGTTATGTTTTAGCTGTGATTTTAAATAATCA[A/C]ATCAGAGTTGTTAATTTTGTTACAGATGTCAGTAT M 2 1 2 1 101000 r 74 goat snp19251-scaffold194-1081492 NW_017189516.1 58557018 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436533 Affx-122932932 AX-123306871 X 119971870 CTTCTGGGGAATGATCTGACAGGCATAGAATTTAA[C/T]AGTGATTTTCCCCACCATTATTTACAGCTCCACAA Y 2 1 2 1 101000 f 74 goat snp19252-scaffold194-1114735 NW_017189516.1 58590306 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444575 Affx-122926968 AX-123314912 X 120062012 GGGAACGAATGTTCTATTCAAATTGCCGCCTTGGG[C/T]AGACTCTGGAATTTGCATTTCATCTCCTGAATCCA Y 2 1 2 1 101000 f 74 goat snp19254-scaffold194-1204877 NW_017189516.1 58673989 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388323 Affx-122969367 AX-123258681 X 120094939 ATAGGACAGACTGCTTGTTAAAGCCTTGAGTGGAC[A/G]TTTGGATTATGTGGTTCCTGGCATGTACCTTTGCT R 2 1 2 1 101000 f 74 goat snp19255-scaffold194-1237804 NW_017189516.1 58706975 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439502 Affx-122930142 AX-123309839 X 120135552 ATTAATCATCGCATTCCTCCCACCCCCACACACTA[C/T]GTCACTTCAGTAGATTCTGCTTAACAGGTTACCAG Y 2 1 2 1 201000 r 74 goat snp19256-scaffold194-1278417 NW_017189516.1 58747950 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397832 Affx-122962475 AX-123268187 X 120212584 CTCAAAGCAAACCTAGATTATTTGCATTTTGCAGA[C/T]GAGGCAGCTGAGACACAACAAGTTTAAGTCACTTG Y 2 1 2 1 101000 f 74 goat snp19258-scaffold194-1355449 NW_017189516.1 58825176 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802483 Affx-122940322 AX-385289387 X 120258376 CGAGGGAGAGGAAGGAAAATGTAGATCATATTATA[C/T]GCTTTTGCAATCTTTCTCCTCATTTTATTTAACTA Y 2 1 2 1 201000 r 74 goat snp19259-scaffold194-1401241 NW_017189516.1 58871125 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767756 Affx-122941189 AX-385254983 X 120290208 CAGAGATGAAACTGGCCTTTTGTTCTGACGTTTTC[A/G]CCTTTGGGAACTTCGAATATGTGGTTGTGTCTCTT R 2 1 2 1 101000 f 74 goat snp19260-scaffold194-1433073 NW_017189516.1 58902963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391859 Affx-122966988 AX-123262216 X 120327025 GATCATGCTGAGTAAGTAAGCCAGATAGAAAAAGA[C/T]ATATGATATCACTTATATGTGCAGTCTTAAAAAAA Y 2 1 2 1 303000 r 74 goat snp19261-scaffold194-1469890 NW_017189516.1 58939646 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386407 Affx-122970822 AX-123256765 X 120363815 AAGGCTACCTTTCTCAGAGTCAGTTCACCATTCAC[A/G]TAAGCATTCTTGATCTCCTTAGACAACCTTTGAGA R 2 1 2 1 201000 r 74 goat snp19262-scaffold194-1506680 NW_017189516.1 58976418 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419871 Affx-122945362 AX-123290219 X 120424963 AATTCCCTTTGTCTCCCACAATTCTTCTACTCATC[C/T]AGAGTTTTCTGTTTTTTCTAATAATTTCTTGGTTT Y 2 1 2 1 101000 f 74 goat snp19263-scaffold194-1567828 NW_017189516.1 59037545 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404989 Affx-122956396 AX-123275341 X 120524665 ATGAGGACACAAGAAGGAAATGGTAAAAATGGGTA[G/T]AAAGTATCTGTCTTCTTTCATATGCTTTATAATAG K 2 1 2 1 303000 r 74 goat snp26023-scaffold27-789114 NW_017203792.1 9732 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435588 Affx-122933360 AX-123305928 X 120555436 TGGTGAAGAATTTAGTGGTTGCCAAAGGTTAGAGA[C/T]GGTAAGGAGGAGTGGGCGTGACTCTAAGGGGCAGT Y 2 1 2 1 101000 f 74 goat snp26022-scaffold27-758343 NW_017189649.1 10964 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407990 Affx-122954323 AX-123278341 X 120583955 CTGTATTAGTAGCTTATAACTGGGATGCCTGCCTT[C/T]CCTCATGATTCCCTATAATTTATTCTTCAGAGGAA Y 2 1 2 1 101000 f 74 goat snp26021-scaffold27-729824 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408011 Affx-122954310 AX-123278362 X 120628532 ACCATTTGGTTCAGATAACAAGGCTCAAGTAAATG[C/T]AGCCTGCACAATAAGAATATAATCGCTGCTTAAAA Y 2 1 2 1 201000 f 74 goat snp26020-scaffold27-685247 NW_017189516.1 59138695 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440754 Affx-122929866 AX-123311091 X 120686407 CCTTCCAAAGCTGAAGATCACTCTCTTCCAATAGA[G/T]TTAAGAGCCAACACCAGGAAGGCAAAGAACCACAG K 2 1 2 1 101000 f 74 goat snp26019-scaffold27-627372 NW_017189516.1 59237280 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431644 Affx-122936133 AX-123301985 X 120751457 GATTACGGGCACTGGCTGCGAGCTTGTCAGCCTTC[A/G]TTGATCCTTTCCACAGTTCTGCAGGATATGCCTCC R 2 1 2 1 101000 r 74 goat snp26018-scaffold27-562322 NW_017189516.1 59302355 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801129 Affx-122977231 AX-385288043 X 120782775 GCTATTTATATGGCTCTGGACACAAGTTTCATGTT[A/C]TGGACCAATTTTCAAACATTAAGTTCTTTTGAAAG M 2 1 2 1 101000 f 74 goat snp26017-scaffold27-531004 NW_017189516.1 59333491 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798052 Affx-122934076 AX-385284988 X 120820712 TAAAAAATTCCACTATATCTTTTTAAGCCACTGAT[A/C]GTGGATAAAGCTATGCAGGCAAGGGTACAATACAA M 2 1 2 1 101000 r 74 goat snp26016-scaffold27-493067 NW_017189516.1 59371570 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396373 Affx-122963034 AX-123266728 X 120853197 CCCCTCTGGGAAGATGTACCCCCTCCACTCTCTGG[C/T]ACCAAGAAGAGGAGATAATATATCACAGGTGATGG Y 2 1 2 1 101000 r 74 goat snp26015-scaffold27-460582 NW_017189516.1 59405019 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449910 Affx-122922329 AX-123320245 X 120888080 TATCCAGATGACAAATTGTAAACAGCAGAAGGAGA[C/T]GGTGATTTTTAAAAATAAGTCGTAAGGAAATGACC Y 2 1 2 1 101000 f 74 goat snp26014-scaffold27-425699 NW_017189516.1 59439813 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800684 Affx-122968214 AX-385287602 X 120919780 TATGGAATTTTAATAGGAGCAGCTGTGTAAGACAT[C/T]TGGGAAAATTCCTTAAAGGAAACACACACTGTATG Y 2 1 2 1 101000 r 74 goat snp26013-scaffold27-393999 NW_017189516.1 59471295 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441853 Affx-122929040 AX-123312190 X 120993965 TTTCCATGTTTCTGTTGAGTGTGTGTATGTCTGTG[C/T]GTGTGTGTGTCAGGGGGGTGCGGTTTGACCTATGA Y 2 1 2 1 303000 r 74 goat snp26012-scaffold27-319814 NW_017199957.1 3779 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398452 Affx-122961603 AX-123268807 X 121034127 GGAATTACTTTCTGTTCCTGTTCCTGGATGCAACC[A/G]TCTCCTCTACAACTTCCAGAGAAGTGAATATACTT R 2 1 2 1 101000 f 74 goat snp26011-scaffold27-279652 NW_017189516.1 59579841 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770566 Affx-122947996 AX-385257730 X 121108033 AGGATAACCCACTCATATTCCTAGACCTTTATCAA[C/T]AGCAGTCTGGCGTGGAAGCGAACAATAATAGCATT Y 2 1 2 1 201000 f 74 goat snp26010-scaffold27-205746 NW_017189516.1 59664839 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432521 Affx-122935563 AX-123302862 X 121193180 ATACATGCATACATATACCATCTAGTCCATATCCC[A/G]TATCCAGGTATATGGACATTGGGGTATCTTTTGGA R 2 1 2 1 201000 f 74 goat snp26009-scaffold27-120599 NW_017189516.1 59750573 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404358 Affx-122956818 AX-123274710 X 121309151 TCCTCTGGCACTCCCCATCCTAGACTGCAACCAGG[G/T]AATTATGTGTTTTTTCCCTTTAAAGAGTAGTGTGC K 2 1 2 1 101000 r 74 goat snp26007-scaffold27-4628 NW_017203041.1 4160 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399334 Affx-122961365 AX-123269689 X 121318783 GCCTAAAAGATAAAGAATATGGAGGCCTGGCAGCA[A/G]TCATTGAGTCAACAGTGAAATCCGTCACCAATATG R 2 1 2 1 103000 f 74 goat snp8119-scaffold1297-229804 NW_017189790.1 27958 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428906 Affx-122938920 AX-123299248 X 121407824 CATGAGGTAATCCACATATTGCAATAGGACAACGT[C/T]CAGGTGGCTAGTCCGGTACTCACAGAGGTCCTCGC Y 2 1 2 1 102000 f 74 goat snp8118-scaffold1297-140763 NW_017189516.1 52085445 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771004 Affx-122946789 AX-385258166 X 121462827 TGAATTTCCTGAGATGAATGTCAAAATGTGTCCTG[A/C]GTATATTTTCCTCAAGAATATCATAGTCTCCATCT M 2 1 2 1 101000 f 74 goat snp8117-scaffold1297-85760 NW_017189516.1 52030011 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384650 Affx-122972148 AX-123255008 X 121544573 CCCGTCTGCCTGCCCTCTGTGTGTCCTGCCCCACA[C/T]TTTCCAGGAGCACTGGGGTCTAGACTGTGGTACTT Y 2 1 2 1 103000 r 74 goat snp8116-scaffold1297-4014 NW_017189752.1 2083 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396667 Affx-122962846 AX-123267022 X 121562901 CCGTGGTGAGTGGATTACTGGGGTTCCATGAGCGG[C/T]GTCACCTGGTGCCTGAATCAGCCTCATGCAGTGAG Y 2 1 2 1 102000 r 74 goat snp8817-scaffold1316-255287 NW_017197339.1 10078 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380354 Affx-122975356 AX-123250712 X 121593048 AAGTGAAAAGGGCAGAGATTTTGAAAGCTCCAGGA[C/T]GGTTCCACTGTGCAACTAGGGTGTGAGAACTACTG Y 2 1 2 1 101000 f 74 goat snp8816-scaffold1316-225140 NW_017189685.1 14329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435584 Affx-122933363 AX-123305924 X 121640229 GTGCAGGCAGTAGGGCATCGTACTGTGGCTCCCTG[A/C]AGGCAAATCAGGTGGGGAACACGTCACCCCCTGAG M 2 1 2 1 102000 f 74 goat snp8815-scaffold1316-177959 NW_017189752.1 19215 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439835 Affx-122930463 AX-123310172 X 121695220 AAATGTCATGCATGCAAGTGGAGACACATTGAAGC[A/C]CCTACCTGAAAAAGCTTCATCCACAGGCCCCCACA M 2 1 2 1 101000 f 74 goat snp8814-scaffold1316-122968 NW_017189752.1 75704 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409448 Affx-122954086 AX-123279799 X 121748953 TGTCTCCTTAAACAAACAAACAAAAAATAGTTCTA[C/T]GGAATGTCTACTATTGAAGTCCCCATCAGTCAGAA Y 2 1 2 1 101000 r 74 goat snp8813-scaffold1316-69235 NW_017189752.1 129542 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435689 Affx-122933324 AX-123306028 X 121779929 GATATTTGTGCCTTAAAGAAATAAAAATGTATGTG[C/T]GCATATATGTACATGAAAATATATGGTTTCTGATG Y 2 1 2 1 101000 r 74 goat snp8812-scaffold1316-38259 NW_017189752.1 160485 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408125 Affx-122954245 AX-123278476 X 121824403 ACATTTTCAGAAACAATATATAAGAAAGTCATTAG[C/T]AGTTGCCTTTGGAAGGGGGATGAGGGACTGGGAAT Y 2 1 2 1 201000 f 74 goat snp32736-scaffold3775-128450 NW_017189752.1 204835 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436738 Affx-122932297 AX-123307076 X 121874958 CTAAGGTGAGAAGCAACAGTCAACACATACTTACT[A/G]CTCATTTTCATGAAAGTGAAAGCATTAGCTGCTCA R 2 1 2 1 101000 f 74 goat snp32735-scaffold3775-77895 NW_017189752.1 255617 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384808 Affx-122971991 AX-123255166 X 121916336 CAGTCCCCTCCATCCCTGCCCCACCAGAGACACTC[C/T]TCAACACTACTTTCACACCAACTCTGATCCATCTT Y 2 1 2 1 201000 r 74 goat snp32734-scaffold3775-36517 NW_017189752.1 296743 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792694 Affx-122968611 AX-385279674 X AGTTCTGAAAGCAGCATTATTACTTCATTTCACTA[C/T]AGGTGTGTCCTGGTTTCCCTTATGATTTCTCCCTC Y 2 1 2 1 101000 f 74 goat snp10417-scaffold1372-782844 13 53694960 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 350603560 Affx-1002479130 AX-413837722 Y-CHROMOSOME AGAACATAGGCAAAACACTCTTCGACATAAACCAC[A/T]GCAGGATCCTCTATGATCCACACCCCAGAATTCTG W 4 1 2 1 103000 f 74 goat NW_017189563.1_120312 Y-chromosome A T 1 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602617 Affx-1002479127 AX-413836984 Y-CHROMOSOME CTTTCTTTAATTAGCAGACTGTTAGTAGCTATATA[A/G]CATCCAGCTAAAGACTAACAGAGGAATACTCTTTT R 2 1 2 1 303000 f 74 goat NW_017189563.1_12235 Y-chromosome G A 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602708 Affx-1002479131 AX-413837069 Y-CHROMOSOME AGGCAAAAGTACCGGAGTGGGGTGCCATTGCCTTC[A/T]CCCAATGTTAAAAGGATAAGGTGAAATAAGGCAGT W 4 1 2 1 201000 r 74 goat NW_017189563.1_173388 Y-chromosome T A 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602625 Affx-1002479132 AX-413836991 Y-CHROMOSOME TGTCCAATTCTAACTGCTGCTTCCTGAACTACATA[C/G]AGGTTTCTCAAGAGGCTGCTCAGGTGGTCTGGTAT S 4 1 2 1 303000 f 74 goat NW_017189563.1_226106 Y-chromosome C G 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602627 Affx-1002479133 AX-413836993 Y-CHROMOSOME ACCTTCAACATGGGATAGTTTCTCTAGGCCCTTCT[C/G]TGCCCATACAGCCACTGCTCTTTGGACGTGGTGTG S 4 1 2 1 202000 f 74 goat NW_017189563.1_250584 Y-chromosome C G 2 neutral Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602714 Affx-1002479134 AX-413837075 Y-CHROMOSOME ATTATTTTTTAATCATTGTATTATCAATTTTTAGG[C/T]CTTCTATTCTCCAATGTATAACTCAGTGTGTAACC Y 2 1 2 1 201000 r 74 goat NW_017189563.1_289604 Y-chromosome T C 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602630 Affx-1002479135 AX-413836996 Y-CHROMOSOME AGAGAACGAAGATCATTGCATCTGGTCCCATGACT[C/T]CATGGGAAATAGGTGGGGAAACATTGGAAACAGTC Y 2 1 2 1 303000 f 74 goat NW_017189563.1_308690 Y-chromosome T C 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602718 Affx-1002479136 AX-413837079 Y-CHROMOSOME GCGAACAGGCTTCTTTGCTAAGACTTCTGGGGGTG[C/T]TGGACAGTCACCGTCAGTCTCACAAGGGGCGCCAG Y 2 1 2 1 202000 r 74 goat NW_017189563.1_364368 Y-chromosome T C 2 neutral Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602619 Affx-1002479128 AX-413836986 Y-CHROMOSOME TTGACTACATGGCTGTAGTCACCATCTGCATCACT[G/T]TTGGAGAACCCCAAAATAAAATCTGTCACTATTTC K 2 1 2 1 303000 f 74 goat NW_017189563.1_37843 Y-chromosome T G 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602634 Affx-1002479137 AX-413837000 Y-CHROMOSOME TGGCCATGTAGACTTTTATTATTCTACATGGATTA[A/G]TGTTTTTCAAGTCCTCACCCAGAAAATATGCTGTG R 2 1 2 1 201000 f 74 goat NW_017189563.1_409641 Y-chromosome G A 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602636 Affx-1002479138 AX-413837002 Y-CHROMOSOME AGGGATCAAGACCATTCCCATGGAAAAGAAATGCA[A/G]AAAAGCAAAATGACTGTCTGGGGAGGCCTTACAAA R 2 1 2 1 303000 f 74 goat NW_017189563.1_451126 Y-chromosome A G 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602637 Affx-1002479139 AX-413837003 Y-CHROMOSOME AAGTGAGCCTGGCCCATGCTGTGTAAAAGGGATCA[A/G]CGTTAAGACAGCTGCAGGTAAACTTTCCCCAAGAA R 2 1 2 1 201000 f 74 goat NW_017189563.1_483280 Y-chromosome A G 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602700 Affx-1002479126 AX-413837061 Y-CHROMOSOME ATGGAAAAGGAAATAGTCAATCAAATCAAACAGGC[A/G]CAAAGAGCCCCGTACAGGATACTCCAAAGCAGAAA R 2 1 2 1 202000 r 74 goat NW_017189563.1_4866 Y-chromosome A G 2 neutral Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602639 Affx-1002479140 AX-413837005 Y-CHROMOSOME CTGGCTCTAGGTGACTGATCACACCATCATGGTTA[A/C]CTGGGTCATGAAGATCTTTTGTGCATAGTTCATCT M 2 1 2 1 303000 f 74 goat NW_017189563.1_495691 Y-chromosome C A 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602728 Affx-1002479141 AX-413837089 Y-CHROMOSOME CCTGTCACTTGAACAACTGAGTCAATAATGACTTT[A/C]TTTCTTTACATGAAGCAAATGATTAAAATTGTGAA M 2 1 2 1 201000 r 74 goat NW_017189563.1_527775 Y-chromosome C A 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602706 Affx-1002479129 AX-413837067 Y-CHROMOSOME GCCAACATATCCACTATATCTGTGAATTCACTCCC[A/G]CTGTAAAGATGACATCACACCACTTTATATGGCAG R 2 1 2 1 101000 r 74 goat NW_017189563.1_65603 Y-chromosome G A 1 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602691 Affx-1002479122 AX-413837054 Y-CHROMOSOME AGGCCAGTGTTGTCAAAAGGAGAACATTAGTGGGG[A/G]AAATAGTGGAGCAGAAGGACATAGAATGGAAGAGA R 2 1 2 1 303000 r 74 goat NW_017189610.1_12002 Y-chromosome G A 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602610 Affx-1002479123 AX-413836977 Y-CHROMOSOME GGGAGAGCTGACTCATTAGAATATATCTTAATGCC[A/G]GAAAAGTTTGAAAGAAGGAGGAGGGGATGACAGAG R 2 1 2 1 103000 f 74 goat NW_017189610.1_42889 Y-chromosome A G 1 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602588 Affx-1002479071 AX-413836955 Y-CHROMOSOME TTTCATTCCAGTCTCCTATAGTGAAAGGTTCCATT[C/T]ACTTCACACCCTATCCAACATATATTGTTTGTAGA Y 2 1 2 1 201000 r 74 goat NW_017189618.1_130945 Y-chromosome C T 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602590 Affx-1002479072 AX-413836958 Y-CHROMOSOME TAAAGACATTCTGAATAAAACCTTACTTGCCCTAA[A/G]TTCTTTGAATGTTTGAAGCAAGAGAAATCTATCAG R 2 1 2 1 201000 r 74 goat NW_017189618.1_174211 Y-chromosome G A 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602517 Affx-1002479069 AX-413836886 Y-CHROMOSOME TTCAGAATATACTACAAAACTATAGTTCTCAAGAC[A/G]GTAGCACAAAGACAGAAATCTAGATCAATGGAACA R 2 1 2 1 201000 f 74 goat NW_017189618.1_19294 Y-chromosome A G 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602592 Affx-1002479073 AX-413836959 Y-CHROMOSOME TTTTGCAGTTTCCAGGTGATTCTGATGGGTTGGTG[C/T]GGGTTCACACTGGCAGCTTTGGAGCGGAGTAACAT Y 2 1 2 1 202000 r 74 goat NW_017189618.1_207020 Y-chromosome T C 2 neutral Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602594 Affx-1002479074 AX-413836962 Y-CHROMOSOME GCCTGGATAATTTGGGGATTGAAGGTTCAGCCTTG[C/T]GGCCATCCGAAGTCAAAGGTGGGCCACTTGGCAGA Y 2 1 2 1 303000 r 74 goat NW_017189618.1_212234 Y-chromosome T C 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602596 Affx-1002479075 AX-413836963 Y-CHROMOSOME GGGTTCCATTTTCTCTGCATCCTCTGCAGCATTTA[C/T]TGTTTATAGACTTTTCTGAAAGCAGACATTCTGAC Y 2 1 2 1 201000 r 74 goat NW_017189618.1_247972 Y-chromosome C T 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602598 Affx-1002479076 AX-413836965 Y-CHROMOSOME GGAGCAGCCATGAAGAGATATCCTACGTCCAAGGT[A/G]AGAGGACCCCAAGTGAAATGGTAGGTGTTGCAAGA R 2 1 2 1 202000 r 74 goat NW_017189618.1_298440 Y-chromosome A G 2 neutral Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602532 Affx-1002479077 AX-413836901 Y-CHROMOSOME TGTGGCTCAGTGTGTTTATCTCTCTCCCAGGGTTT[C/T]CATCCAATTCAGTGTCTGTGTGTGTGTGTCTCTAA Y 2 1 2 1 202000 f 74 goat NW_017189618.1_345937 Y-chromosome C T 2 neutral Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602534 Affx-1002479078 AX-413836903 Y-CHROMOSOME TAGTCTGCCCAGTTGTTCCTCTGGCCAGAGTGGTG[A/T]CCTGTCTGTCTTTTGTATGTCTTGTATGTTTTATG W 4 1 2 1 103000 f 74 goat NW_017189618.1_388898 Y-chromosome A T 1 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602535 Affx-1002479079 AX-413836904 Y-CHROMOSOME TGTATAATCAAGGGGAGAACAGGGTGAGAATCTCT[C/G]GTAAGCATTTCCCAAAATATATGTCACCCAGTACT S 4 1 2 1 303000 f 74 goat NW_017189618.1_421000 Y-chromosome G C 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602606 Affx-1002479080 AX-413836973 Y-CHROMOSOME ATTTCACAGTTAAATATGAGAATATCAATGTGAAT[A/G]AACGTACTGATAGATTGCCTCGAGGTGCACATTCA R 2 1 2 1 303000 r 74 goat NW_017189618.1_446461 Y-chromosome G A 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602583 Affx-1002479068 AX-413836950 Y-CHROMOSOME TGCAAGATAACCTGGCTCTGAAAGCGTGCTGTGGA[G/T]AAGGTGATCGAGAAGCTATGATGTGAGTTTGGCCC K 2 1 2 1 201000 r 74 goat NW_017189618.1_5539 Y-chromosome G T 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602586 Affx-1002479070 AX-413836954 Y-CHROMOSOME AAGTTTTGTTTAATTGTTTTTACTCTGATGGGCAA[A/G]ACTAATAAGGTGGCAATCCTCTCTGCTGATGACTG R 2 1 2 1 201000 r 74 goat NW_017189618.1_78416 Y-chromosome G A 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602685 Affx-1002479119 AX-413837049 Y-CHROMOSOME ATCATCCACCCTAGATCTAGACAGTCAGTCTTTCG[C/T]CTCCATACCAGCGTTTCAATGCTGTGACATGATTT Y 2 1 2 1 201000 r 74 goat NW_017189628.1_11428 Y-chromosome C T 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602687 Affx-1002479120 AX-413837051 Y-CHROMOSOME ATTCCTTGAATTCTCCTTTTTACAGTCCTGAGTTC[C/T]GCTTGTGTCATGTTTAATGTCCTTGTAATGCCTCC Y 2 1 2 1 201000 r 74 goat NW_017189628.1_20501 Y-chromosome C T 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350603618 Affx-1002479118 AX-413837765 Y-CHROMOSOME TTTGATCTCCTTTGCAGTTCAAGGACTCAAGAGTC[C/T]TCTCCATCACTACAGTTCTAAAACATCGATTATAT Y 2 1 2 1 303000 r 74 goat NW_017189628.1_2340 Y-chromosome T C 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602689 Affx-1002479121 AX-413837052 Y-CHROMOSOME AGAAAGAAACCTTTTTCATTTTTTTCCAATTATTT[C/T]AATGGGAAGACATTCAATTTACAATATTGGGTTGG Y 2 1 2 1 303000 r 74 goat NW_017189628.1_45168 Y-chromosome T C 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602543 Affx-1002479083 AX-413836912 Y-CHROMOSOME AGGGAGACAGTGACAGCCTTTATCTTTTGGACTCC[A/G]AAATCACTGTATGTGGTGACTGCAGCAATGAAATT R 2 1 2 1 303000 f 74 goat NW_017189685.1_107939 Y-chromosome G A 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602544 Affx-1002479084 AX-413836913 Y-CHROMOSOME GGTATTGGCCATCTGGTGATGTTGATGTGTAGAGT[C/T]GTCTCTTGTGTTGTTGAAAGAGGGTGTTTGCTGTG Y 2 1 2 1 303000 f 74 goat NW_017189685.1_155746 Y-chromosome T C 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602546 Affx-1002479085 AX-413836915 Y-CHROMOSOME TCTTGTGCAGATTTGTGTGGACTTAGTTTTTAACT[C/T]GTTCAGGTAAAGACTGAAGAGCATGATGAATGGAT Y 2 1 2 1 201000 f 74 goat NW_017189685.1_203656 Y-chromosome C T 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602620 Affx-1002479086 AX-413836987 Y-CHROMOSOME GCAGGCAAAACACTGTATGACATAAATTTAGCAAG[A/G]TCCTTTATGACCTAAACCCTAGAATAGTGGACATA R 2 1 2 1 201000 r 74 goat NW_017189685.1_251624 Y-chromosome A G 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602550 Affx-1002479087 AX-185655617 Y-CHROMOSOME CAGTACTTTGGCCACCTCATGTGAAGAGTTGACTC[A/C]TTGGAAAAGACTCTGATGCTGGGAGGGATTGGGGG M 2 1 2 1 103000 f 74 goat NW_017189685.1_294550 Y-chromosome C A 1 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602624 Affx-1002479088 AX-413836990 Y-CHROMOSOME ATTAAAAGAAATAAAATGTGTTTGAGAGGGAACCT[G/T]AGAGTTTGGCTGGCATTGATAAGAAGATTGGTGTG K 2 1 2 1 201000 r 74 goat NW_017189685.1_345716 Y-chromosome G T 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602554 Affx-1002479089 AX-413836922 Y-CHROMOSOME GGAGTGTGTTAAGGGTCCAGTCAGACTAATTTATG[G/T]ACACTTGAGACTAATTCATGAATACATGGACTTTA K 2 1 2 1 101000 f 74 goat NW_017189685.1_371859 Y-chromosome G T 1 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602541 Affx-1002479082 AX-413836910 Y-CHROMOSOME CCCATTCACCATTGGAAATGCTTTCAGTTTTTTAC[C/G]ATTGAGGATAATGCTTGCTGTGGGTTTGTCATAAA S 4 1 2 1 303000 f 74 goat NW_017189685.1_55458 Y-chromosome C G 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602539 Affx-1002479081 AX-413836908 Y-CHROMOSOME TTCTTTAATAATTAGTGGTGGTCAAGGTGAATTTC[A/T]TGATTCCCAGTGTCATGCTATGGTGACTGGTGTCA W 4 1 2 1 201000 f 74 goat NW_017189685.1_7331 Y-chromosome A T 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602633 Affx-1002479092 AX-413836999 Y-CHROMOSOME GCCCCTAGCAAAATGTACATCAGTCTCACTGAGAT[A/G]CTACTTCACACCGATTAGGTTGGCTATAATCAAAA R 2 1 2 1 201000 r 74 goat NW_017189696.1_100764 Y-chromosome A G 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602561 Affx-1002479093 AX-413836929 Y-CHROMOSOME AAAAAGAAAGAGGGAAATTCCCTGGAAAGCCAGTG[A/G]TTAGGGCTTAGAACTTTCACTGCCAAGGGCCCAAG R 2 1 2 1 303000 f 74 goat NW_017189696.1_128567 Y-chromosome G A 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602563 Affx-1002479094 AX-413836931 Y-CHROMOSOME AGGTAAATCTTCACGTATAAGCAAAACCACAGTGT[A/G]CAATTGACAAAGTGATTGAAAGGCAAAGAATATTC R 2 1 2 1 201000 f 74 goat NW_017189696.1_143795 Y-chromosome A G 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602640 Affx-1002479095 AX-413837006 Y-CHROMOSOME TGGTTCAAGTTCCAGGAATCCACTTAGCCTTCTCT[G/T]GTACTGCCACATTAGTGGGTGGGTGTACTGTTATT K 2 1 2 1 202000 r 74 goat NW_017189696.1_195210 Y-chromosome G T 2 neutral Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602642 Affx-1002479096 AX-413837008 Y-CHROMOSOME GATACTTCTTTATGAATTATGGACATCTCCCCATT[C/T]CATTTGAGAAAGTCTTGGTGGCTATTTTACTTCTT Y 2 1 2 1 201000 r 74 goat NW_017189696.1_241612 Y-chromosome T C 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602569 Affx-1002479097 AX-187368826 Y-CHROMOSOME ATAGGTTGCAATCACCATCTGCAGTGATTTTGGAG[C/G]CTCAAAAAGCATGGTCTGACACTATTTCCACTGTT S 4 1 2 1 303000 f 74 goat NW_017189696.1_290559 Y-chromosome C G 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602647 Affx-1002479098 AX-413837013 Y-CHROMOSOME CATTGCAGGCAGACGGTTTTTCACCTGAGCCACCA[A/G]GGAAGCCCTTTTACTGTGAGGGTATCAACAAATTG R 2 1 2 1 201000 r 74 goat NW_017189696.1_333356 Y-chromosome A G 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602572 Affx-1002479099 AX-413836939 Y-CHROMOSOME CAGTTCCAAAGAAAGGCAAGGCCAAAGAATGCTCA[A/G]TCTACCACACAATTGCACTCATCTCACATGCTAGT R 2 1 2 1 103000 f 74 goat NW_017189696.1_351673 Y-chromosome A G 1 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602574 Affx-1002479100 AX-413836941 Y-CHROMOSOME GCCTTTTGTAAAACCTGTTCAAACTAATGGAAGTT[C/T]ATGGTTCATGTATTACTGAAGCCTGGCTTTGAGAA Y 2 1 2 1 201000 f 74 goat NW_017189696.1_363587 Y-chromosome T C 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602576 Affx-1002479101 AX-413836943 Y-CHROMOSOME ATACTCAAGAACCCGGGTTCAGGAGTGATGGGATG[C/T]ATGCTCTACTGTGCAGTCTCAGTGACAGCAACGCA Y 2 1 2 1 202000 f 74 goat NW_017189696.1_368588 Y-chromosome C T 2 neutral Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602631 Affx-1002479091 AX-413836997 Y-CHROMOSOME CAAGGGCTTTCTCTAGCTGAGGCAAGTGGTATGGT[A/G]CACTTCAATATGGTGCATAGCCTTCCCATTGTGAT R 2 1 2 1 201000 r 74 goat NW_017189696.1_57126 Y-chromosome A G 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602629 Affx-1002479090 AX-413836994 Y-CHROMOSOME TGTGCATTTAAGATACATTTTCTTCCAATTTTACT[A/T]CAAAACAAGATGTCATTGAATAGCTGATGCCTTTT W 4 1 2 1 303000 r 74 goat NW_017189696.1_8239 Y-chromosome T A 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602582 Affx-1002479104 AX-413836949 Y-CHROMOSOME GAGAAAAACGTACAACCCAAATTACTATACCCAGC[A/G]AAGATCTCATTAAAATATGAAAGAGAAATCAAAAG R 2 1 2 1 303000 f 74 goat NW_017189885.1_111694 Y-chromosome A G 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602584 Affx-1002479105 AX-413836951 Y-CHROMOSOME ACCAGATTGCTACTCAATTAACTGTTCAAATATCT[C/T]GATGCTTACAATTTAATGAAAACTGGCAAATTTCT Y 2 1 2 1 201000 f 74 goat NW_017189885.1_160611 Y-chromosome T C 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602587 Affx-1002479106 AX-413836953 Y-CHROMOSOME CCTGGTGGGCTACAGTCAACGGGGTCGCTAAGAGG[C/G]GGACACGACTGAGCAACTTCACTTTCAATTTTCAC S 4 1 2 1 303000 f 74 goat NW_017189885.1_190101 Y-chromosome C G 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602657 Affx-1002479102 AX-413837023 Y-CHROMOSOME TGAACGGATAAGAAACCAGTGGTACATATACACAA[C/T]GGAAAATTACTCAAGTATTAAAAGAACACATCTGA Y 2 1 2 1 201000 r 74 goat NW_017189885.1_4277 Y-chromosome C T 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602659 Affx-1002479103 AX-413837025 Y-CHROMOSOME AATATCAAGGGCTGTTACGTGAAAATCCTAACCTC[C/T]GTACTGAGCACTTTACCAGACTTTAGACCAGCCAC Y 2 1 2 1 101000 r 74 goat NW_017189885.1_58695 Y-chromosome C T 1 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602591 Affx-1002479109 AX-413836957 Y-CHROMOSOME ATCCTGGAATGAGATGGGTCTTAGGAAGCATCACT[A/G]CAAACAAAGCTAGTGGAGGTGATGGAATTCCCATT R 2 1 2 1 303000 f 74 goat NW_017189985.1_105414 Y-chromosome A G 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602593 Affx-1002479110 AX-413836960 Y-CHROMOSOME CACAGCATCAATGAATGATGGTAATTTAATGGATG[A/G]AATGGAGGAGACTCAAAACCTGTCACAATACAGAA R 2 1 2 1 201000 f 74 goat NW_017189985.1_152991 Y-chromosome G A 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350603549 Affx-1002479107 AX-413837712 Y-CHROMOSOME TCACACTCCAGAGACTGCATGCCATGGTTAGAGTC[A/G]GCTTGTCTCAAGGACTATCTTACGTGACACAACTA R 2 1 2 1 303000 f 74 goat NW_017189985.1_341 Y-chromosome G A 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602669 Affx-1002479108 AX-413837035 Y-CHROMOSOME GAGAATCATGGTCACAGATCAGAGAGGACACCCAG[C/T]GATTGACACTGAAGTTCCCTTTATTTATTTGTAAC Y 2 1 2 1 201000 r 74 goat NW_017189985.1_54777 Y-chromosome T C 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350603614 Affx-1002479116 AX-413837763 Y-CHROMOSOME GGGATTTCCTCACTGTGGGTGGGGTTGTAGCAGTG[A/G]CTTTTCAAGGTTCCTTGGTTAGAGAGGCTTGTGTT R 2 1 2 1 201000 r 74 goat NW_017190040.1_111693 Y-chromosome A G 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350603616 Affx-1002479117 AX-413837764 Y-CHROMOSOME GAAATGGTACCTCATTGTAGTTTTGATTTGCATTT[A/C]TCTGATAATGAATCCTGTTGAGCATCTTTTCATGT M 2 1 2 1 201000 r 74 goat NW_017190040.1_155478 Y-chromosome C A 2 recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602601 Affx-1002479114 AX-413836968 Y-CHROMOSOME CAAGATATGTTCTGCATATAAGTCAAATAAACAGG[G/T]TGGCTTTTTTTTTTTTTTTTTTCCCCCAATTTCAA K 2 1 2 1 303000 f 74 goat NW_017190040.1_3830 Y-chromosome T G 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350603613 Affx-1002479115 AX-413837762 Y-CHROMOSOME ATTCTGGGAGTCTTGCTGGAGCAGAATCTCTGATT[A/G]TGTTGTAGGGAATCTGCACCCAGGTGACACTCAGA R 2 1 2 1 202000 r 74 goat NW_017190040.1_56105 Y-chromosome G A 2 neutral Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602681 Affx-1002479113 AX-413837045 Y-CHROMOSOME ATGTTTGTATCATAGAATAAGCAAGGAGATAGCAT[A/G]CAATCATCTATATCTATTAACTATCTCTGCTACTG R 2 1 2 1 202000 r 74 goat NW_017190154.1_102884 Y-chromosome A G 2 neutral Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602597 Affx-1002479112 AX-413836964 Y-CHROMOSOME GGCATCCAGAGGCCCAGCACCTTATCTCCAGTTTA[A/T]CTGCATCATTAGTTATTTGGGGTTCAATAGCTTAA W 4 1 2 1 303000 f 74 goat NW_017190154.1_55387 Y-chromosome T A 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602595 Affx-1002479111 AX-413836961 Y-CHROMOSOME CTGTAGTACTGGAGAAGACTCTTGAGTCCCTTGAA[A/C]TGCAAAGGGATCAAAGCAGTCAGTCCTAAAGGAAA M 2 1 2 1 303000 f 74 goat NW_017190154.1_6843 Y-chromosome A C 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602612 Affx-1002479124 AX-413836979 Y-CHROMOSOME GTAATCCACTCTAGCACTCTTGCCTGGAAAATCCC[A/G]TGGATGGAGGAGCCTGATAGGCTACAGTCCATGGT R 2 1 2 1 303000 f 74 goat NW_017195709.1_1423 Y-chromosome A G 3 not_recommended Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602614 Affx-1002479125 AX-413836981 Y-CHROMOSOME AATGTTATTAAGAAGAAATCAGACAAATGGAAAAA[C/T]GTTACAAGATTTGAGAGCTATAAACGCAACTATGG Y 2 1 2 1 202000 f 74 goat NW_017195709.1_41106 Y-chromosome T C 2 neutral Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602680 Affx-1002479164 AX-413837044 Y-CHROMOSOME CATAGTCTTGACTGCTGCTGCTGCTGCTGCTAAGT[C/T]GCTTCAGTCGTGTCCAACTCTGTGCGACCCCACAG Y 2 1 2 1 400000 f 74 goat Y-chrom_23 Y-chromosome C T Goat_IGGC_65K_v2 Y markers Y-chromosome SNP on Y chromosome scaffold multi-breed 350602730 Affx-1002479142 AX-413837091 Y-CHROMOSOME AGAATTTTTTATGGCTCTGATTGTAGCTTACTGTC[A/C]ATATAAATTTGACAGTTGACAAAACCAAAATGGTT M 2 1 2 1 201000 r 74 goat "chr-Y-toconfirm-1;Y-chrom_1" "NW_017189885.1;Y-chromosome" 11760 "A;T" "C;G" 2 recommended Goat_IGGC_65K_v2 Y markers 350602749 Affx-1002479151 AX-413837110 Y-CHROMOSOME GATGGAAAGCTCCCTACCTTCTAAAGCACTTTCTG[A/G]TACAAGCTCTGTTCTTTGGTCTTTCTAGCTACTTT R 2 1 2 1 201000 r 74 goat "chr-Y-toconfirm-10;Y-chrom_10" "NW_017189563.1;Y-chromosome" 280433 "A;G" "A;G" 2 recommended Goat_IGGC_65K_v2 Y markers 350602660 Affx-1002479152 AX-413837026 Y-CHROMOSOME AGGGAGGTCATCCTATAGATTAGATTTTAAGCAAA[A/C]TATTGGTTATTCATTTTTAACTCTAAAAGGTCTTT M 2 1 2 1 201000 f 74 goat "chr-Y-toconfirm-11;Y-chrom_11" "NW_017189685.1;Y-chromosome" 43279 A C 2 recommended Goat_IGGC_65K_v2 Y markers 350602661 Affx-1002479153 AX-413837027 Y-CHROMOSOME AATATGTATAAATTAGATAAGCACAGCTAAATTAG[C/T]TCTCATTTCACAAATGAGTCATCCAGTATTGAGTT Y 2 1 2 1 101000 f 74 goat "chr-Y-toconfirm-12;Y-chrom_12" "NW_017189685.1;Y-chromosome" 43464 C T 1 recommended Goat_IGGC_65K_v2 Y markers 350602663 Affx-1002479154 AX-413837029 Y-CHROMOSOME TGCTGGGGAACAAGGAAGGGAGGGCCCAGGTCTTT[A/G]GAAAGCGAGGGGCCCAAGGGGACTGCTCTGGGTTG R 2 1 2 1 202000 f 74 goat "chr-Y-toconfirm-13;Y-chrom_13" "NW_017189618.1;Y-chromosome" 315506 G A 2 neutral Goat_IGGC_65K_v2 Y markers 350602665 Affx-1002479155 AX-413837031 Y-CHROMOSOME TTATGTAGGGTCCTTCTTTGCGTCTTCACAGCCTT[C/T]ATTTTAAGTCTGTTTAATCTTATATAAGTATTGCA Y 2 1 2 1 101000 f 74 goat "chr-Y-toconfirm-14;Y-chrom_14" "NW_017189618.1;Y-chromosome" 319904 T C 1 recommended Goat_IGGC_65K_v2 Y markers 350602666 Affx-1002479156 AX-413837032 Y-CHROMOSOME GGAAAAAACTATAAAGGAAGAAAATGAGTATGTTA[A/C]AAAAGTGTCTATTAAATAATAACTTTACTATGTTT M 2 1 2 1 201000 f 74 goat "chr-Y-toconfirm-15;Y-chrom_15" "NW_017189685.1;Y-chromosome" 177262 A C 2 recommended Goat_IGGC_65K_v2 Y markers 350602668 Affx-1002479157 AX-413837034 Y-CHROMOSOME TAGGCACTGTGGTGCTTTTTGTTCTGCGAAGTTAC[G/T]AAATGATTGATTCAGTTTAAATAGTTATATGCTTA K 2 1 2 1 201000 f 74 goat "chr-Y-toconfirm-16;Y-chrom_16" "NW_017189685.1;Y-chromosome" 207149 T G 2 recommended Goat_IGGC_65K_v2 Y markers 350602670 Affx-1002479158 AX-413837036 Y-CHROMOSOME GCACTAATATTCAGACTTCACATAGGATGCTGCCT[A/T]CTAGTTCAGTAACACAGGGAATTGCTTTCAATCAC W 4 1 2 1 101000 f 74 goat "chr-Y-toconfirm-17;Y-chrom_17" "NW_017189685.1;Y-chromosome" 210907 A T 1 recommended Goat_IGGC_65K_v2 Y markers 350602671 Affx-1002479159 AX-413837037 Y-CHROMOSOME TTGAAGTTGGAACTATTTATCATAAGTACACAGTT[A/G]CCAACAATCTATTTCGGTATATATATATATGCCAT R 2 1 2 1 201000 f 74 goat "chr-Y-toconfirm-18;Y-chrom_18" "NW_017189685.1;Y-chromosome" 250581 G A 2 recommended Goat_IGGC_65K_v2 Y markers 350602673 Affx-1002479160 AX-413837038 Y-CHROMOSOME GCCTTGCTCATGTAACACTATATATAAAGTGTATA[A/G]TGGAAATCACACTCCAAGTCAGCTATTTGGGGGTT R 2 1 2 1 201000 f 74 goat "chr-Y-toconfirm-19;Y-chrom_19" "NW_017189685.1;Y-chromosome" 267240 A G 2 recommended Goat_IGGC_65K_v2 Y markers 350602732 Affx-1002479143 AX-413837093 Y-CHROMOSOME GTTTATGAATGTTTTCCCCAGATATCTAAGCAAGT[A/G]TGGCTTTCAATTTTTCCTGCTTCATGTATTTTAAT R 2 1 2 1 201000 r 74 goat "chr-Y-toconfirm-2;Y-chrom_2" "NW_017189885.1;Y-chromosome" 11686 "A;T" "C;G" 2 recommended Goat_IGGC_65K_v2 Y markers 350602675 Affx-1002479161 AX-413837040 Y-CHROMOSOME ACTATCTCATCCTCTGTCGTCCCCCTCTCCTCCTA[C/T]CCTTCAGTCTTTCCCAGAATCAGGGTCTCTTCCAA Y 2 1 2 1 303000 f 74 goat "chr-Y-toconfirm-20;Y-chrom_20" "NW_017189685.1;Y-chromosome" 315794 C T 3 not_recommended Goat_IGGC_65K_v2 Y markers 350602676 Affx-1002479162 AX-413837042 Y-CHROMOSOME ATATGATGGATTTGAAGCTGTAAGCCATGTGAGGG[A/C]TTGGAGGTTTTGTTATTTATTTATTTATTTATTTT M 2 1 2 1 201000 f 74 goat "chr-Y-toconfirm-21;Y-chrom_21" "NW_017189685.1;Y-chromosome" 356782 C A 2 recommended Goat_IGGC_65K_v2 Y markers 350602678 Affx-1002479163 AX-185186147 Y-CHROMOSOME CTGTGGGGTCGCACAGAGTTGGACACGACTGAAGC[A/G]ACTTAGCAGCAGCAGCAGCAGCAGTCAAGACTATG R 2 1 2 1 303000 f 74 goat "chr-Y-toconfirm-22;chr-Y-toconfirm-23;Y-chrom_22" "NW_017189563.1;Y-chromosome" 8317 G A 3 not_recommended Goat_IGGC_65K_v2 Y markers 350603563 Affx-1002479165 AX-413837725 Y-CHROMOSOME TGAGTATGCCATCCAAAGCAATCTATAAATTCAGT[A/G]CAATCCCTATCAAGCTACCAACGGTATTTTTCACA R 2 1 2 1 303000 f 74 goat "chr-Y-toconfirm-24;Y-chrom_24" "NW_017189563.1;Y-chromosome" 201736 G A 3 not_recommended Goat_IGGC_65K_v2 Y markers 350602682 Affx-1002479166 AX-413837046 Y-CHROMOSOME CCCCAACTCACCCAGCATCGGTCTTTTGCAATGAA[C/T]CATCTCTTCACATGAGGTGGCCAAAGTACTGGAGT Y 2 1 2 1 202000 f 74 goat "chr-Y-toconfirm-25;Y-chrom_25" "NW_017189563.1;Y-chromosome" 318724 T C 2 neutral Goat_IGGC_65K_v2 Y markers 350602684 Affx-1002479167 AX-413837048 Y-CHROMOSOME ATAGTCAATACAACAGAAATAGATGCTTTTCTGGA[C/G]CTTTCTTGCTTTTTTGATGATCCAGCAGATGTTGG S 4 1 2 1 303000 f 74 goat "chr-Y-toconfirm-26;Y-chrom_26" "NW_017189618.1;Y-chromosome" 142595 C G 3 not_recommended Goat_IGGC_65K_v2 Y markers 350602686 Affx-1002479168 AX-413837050 Y-CHROMOSOME TTCTCTGATTATGAGTGATGATTAGCATCTGCTCA[A/T]GTGTTTGTTAGACATTTGTGTGTCTTCTTTGGAGA W 4 1 2 1 201000 f 74 goat "chr-Y-toconfirm-27;Y-chrom_27" "NW_017189618.1;Y-chromosome" 166198 T A 2 recommended Goat_IGGC_65K_v2 Y markers 350602688 Affx-1002479169 AX-185274797 Y-CHROMOSOME GGGAAACAGTGGAAACAGTGTCAGACTTTATTTTT[G/T]GGGGGGCTCCAAAGTCACTGTAGATGATGACTGCA K 2 1 2 1 303000 f 74 goat "chr-Y-toconfirm-28;Y-chrom_28" "NW_017189618.1;Y-chromosome" 186490 T G 3 not_recommended Goat_IGGC_65K_v2 Y markers 350602788 Affx-1002479170 AX-413837143 Y-CHROMOSOME GCAAAGCAGCAGCAGCACTTCCTGAAGTAGCAGAC[C/T]GTTAGTCCGATATAATCATCTGTGGTCTTTTTAAC Y 2 1 2 1 201000 r 74 goat "chr-Y-toconfirm-29;Y-chrom_29" "NW_017189618.1;Y-chromosome" 421370 C T 2 recommended Goat_IGGC_65K_v2 Y markers 350602646 Affx-1002479144 AX-413837012 Y-CHROMOSOME GAATATTTCACTGATCTAGAAAGAAAACCTGAACA[G/T]CTTAGCAGTTATTTCCCATGCTCCCTCCCTTTTAT K 2 1 2 1 201000 f 74 goat "chr-Y-toconfirm-3;Y-chrom_3" "NW_017189563.1;Y-chromosome" 277537 G T 2 recommended Goat_IGGC_65K_v2 Y markers 350602790 Affx-1002479171 AX-413837144 Y-CHROMOSOME TCTTATGTTGGGTGCATATATATTTATAATTGTTA[C/T]ACCTTCTTGAATTGCTCCTTTGGTCATTATGTAGT Y 2 1 2 1 201000 r 74 goat "chr-Y-toconfirm-30;Y-chrom_30" "NW_017189685.1;Y-chromosome" 60244 T C 2 recommended Goat_IGGC_65K_v2 Y markers 350602694 Affx-1002479172 AX-413837055 Y-CHROMOSOME GGCTTTAGTTGCTCAGAGGTCTGTGGAATCATCCC[C/G]AGCCAAGGATGGAACCATTTCCCCAGCACTGGCAG S 4 1 2 1 202000 f 74 goat "chr-Y-toconfirm-31;Y-chrom_31" "NW_017189685.1;Y-chromosome" 76889 C G 2 neutral Goat_IGGC_65K_v2 Y markers 350602695 Affx-1002479173 AX-413837057 Y-CHROMOSOME ATGTCCATCGAGTCGGTGGTGCCATCCTGTCATCT[C/T]GTCCTCTGTCGTCCCTTTTTCCTCCTGCCCCGAAT Y 2 1 2 1 303000 f 74 goat "chr-Y-toconfirm-32;Y-chrom_32" "NW_017189685.1;Y-chromosome" 87708 C T 3 not_recommended Goat_IGGC_65K_v2 Y markers 350602697 Affx-1002479174 AX-413837058 Y-CHROMOSOME TACCAAGATTTCCATGAAACATTTCCATGACAAAG[A/G]ACTCCTTGGCTGGCTTGAAGGAGAAATGACACATT R 2 1 2 1 201000 f 74 goat "chr-Y-toconfirm-33;Y-chrom_33" "NW_017189563.1;Y-chromosome" 112824 G A 2 recommended Goat_IGGC_65K_v2 Y markers 350602799 Affx-1002479175 AX-413837148 Y-CHROMOSOME CACTCCACCACCTCTGTATCTCCCCTTCCCCTCCC[C/T]GCTATTTACTGGTAACCAGGCGATGTTCTATATAT Y 2 1 2 1 201000 r 74 goat "chr-Y-toconfirm-34;Y-chrom_34" "NW_017189563.1;Y-chromosome" 122612 C T 2 recommended Goat_IGGC_65K_v2 Y markers 350602701 Affx-1002479176 AX-413837062 Y-CHROMOSOME GGGAATATGGAGTTGTGTTTCTGTTTGTTTGTTTG[A/T]TTTATTTTGTTTTATTTTTAATTCAATTTTCTTCA W 4 1 2 1 103000 f 74 goat "chr-Y-toconfirm-35;Y-chrom_35" "NW_017189563.1;Y-chromosome" 144258 T A 1 not_recommended Goat_IGGC_65K_v2 Y markers 350602736 Affx-1002479145 AX-413837097 Y-CHROMOSOME TAAACATTTACTTCCACAGTAAGATGCATGTTTTT[A/G]ATTGCATCAAGTAATAATGTTTTCACATTTTGTTT R 2 1 2 1 201000 r 74 goat "chr-Y-toconfirm-4;Y-chrom_4" "NW_017189563.1;Y-chromosome" 277871 A G 2 recommended Goat_IGGC_65K_v2 Y markers 350602738 Affx-1002479146 AX-413837099 Y-CHROMOSOME CTAACATACCACACACCAACCCCCCTTTCACCTCC[A/G]CACCCAGTCCCCCGCCCAGCCTCACACTTTCCCTA R 2 1 2 1 303000 r 74 goat "chr-Y-toconfirm-5;Y-chrom_5" "NW_017189563.1;Y-chromosome" 278523 A G 3 not_recommended Goat_IGGC_65K_v2 Y markers 350602740 Affx-1002479147 AX-413837101 Y-CHROMOSOME AGGTATTGGGGGCGGAGAAATAAATATTTCACTGC[A/C]AATTTTGCACTAAGTCAGTCTCTGGTAAGAACAGC M 2 1 2 1 201000 r 74 goat "chr-Y-toconfirm-6;Y-chrom_6" "NW_017189563.1;Y-chromosome" 279212 A C 2 recommended Goat_IGGC_65K_v2 Y markers 350602653 Affx-1002479148 AX-413837019 Y-CHROMOSOME ATTTTACTACAATTTCACCTCCGACTTAATTTTAA[A/T]CTAAGGCAAATAAGTACATTTAACAAGTAAAGAAT W 4 1 2 1 201000 f 74 goat "chr-Y-toconfirm-7;Y-chrom_7" "NW_017189563.1;Y-chromosome" 280046 "A;T" "A;T" 2 recommended Goat_IGGC_65K_v2 Y markers 350602745 Affx-1002479149 AX-413837106 Y-CHROMOSOME GAATTTGGACTTTCCAAAATAATTGCTCCTCTGTT[A/G]ATCAGTTCTTTCTGTAAGAGTATTTTTTGTAAGAA R 2 1 2 1 201000 r 74 goat "chr-Y-toconfirm-8;Y-chrom_8" "NW_017189563.1;Y-chromosome" 280113 A G 2 recommended Goat_IGGC_65K_v2 Y markers 350602656 Affx-1002479150 AX-413837022 Y-CHROMOSOME TATTAATAATCTGGAAATAGCCACTATAGACAATA[A/T]AACTTTTTATTTTAAATGCTGTAACTCCAAACTAT W 4 1 2 1 201000 f 74 goat "chr-Y-toconfirm-9;Y-chrom_9" "NW_017189563.1;Y-chromosome" 280306 "A;T" "A;T" 2 recommended Goat_IGGC_65K_v2 Y markers 350601358 Affx-1002479806 AX-413835785 TGGTGCCCCAGGCCTATCGGCGGCTGCTCGGACTC[G/GAGTCCGAG]AGTCTGGCGCCGGGACTTTGCGTGCACAGCTGTGC - 2 1 2 1 400000 r 74 goat snp-genphyse638 G GAGTCCGAG INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601286 Affx-1002479827 AX-413835718 GCCCGGGGCCCCCGGCCCACTGCCGCTTCCCCCCC[-/C]AGACACTTCTACAAGCCCATGCTCCGGCGGGGCAG - 2 1 2 1 400000 f 74 goat snp-genphyse661 - C INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601360 Affx-1002479831 AX-413835787 CTCTTTCTTTTAGCAAATGAAAGCTGGAAGCAGTT[-/T]GTCAAGTGAGGTATACCATTTTTATGTTAATTAAG - 2 1 2 1 400000 r 74 goat snp-genphyse670 - T INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601362 Affx-1002479832 AX-123315939 CTCTTTCTTTTAGCAAATGAAAGCTGGAAGCAGTT[-/C]GTCAAGTGAGGTATACCATTTTTATGTTAATTAAG - 2 1 2 1 400000 r 74 goat snp-genphyse671 - C INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601365 Affx-1002479835 AX-148662459 CATCCTGCAATAAATCATCACAGAAAAGAATATGT[G/GTA]TATATATATGTATATATATATGTGTGTGTGTGTAT - 2 1 2 1 400000 r 74 goat snp-genphyse681 G GTA INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601373 Affx-1002479840 AX-413835794 TGATCACCTCCCAGGGCACCATGCACAAAGTTTCG[T/TG]GGGGCTTCTCATCTGGGGAATGAACAGGCACACAG - 2 1 2 1 400000 r 74 goat snp-genphyse687 T TG INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601375 Affx-1002479845 AX-413835796 GGCAGCTGGAGCTGGCAAGATTACCAAGTGTGCCC[A/AGAAAGTTCAGAATATTACCCCCAATACCTGCCACCCTCATCTGTTACCAAGTGTTCAGAAATTG]GAAAGTTCAGAATATTACCCCCAATACCTGCCACC - 2 1 2 1 400000 r 74 goat snp-genphyse705 AGAAAGTTCAGAATATTACCCCCAATACCTGCCACCCTCATCTGTTACCAAGTGTTCAGAAATTG A INDEL in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 38378727 Affx-122977041 AX-123249086 CTACAGATATCTCAGAGTCTATAACTGAAGATGAC[C/T]AGAAACCAGGAAAACAGAAGCAGTCTCTCTCTCCC Y 2 1 2 1 201000 f 74 goat snp18947-scaffold1909-11495 2 124129066 T C 2 recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 38438477 Affx-122931232 AX-123308815 TTAATATCTTCTATATTAGACCTGCCCTTTGCCTT[C/T]ATAAATAGTTCTTTTCAATTTTTCACTAACATTTC Y 2 1 2 1 103000 f 74 goat snp21252-scaffold2077-98445 23 20370768 T C 1 not_recommended GoatSNP50 chip anonymous SNP "10.1371/journal.pone.0086227; 10.1186/s12711-018-0423-9" 195-SNP-parentage SNP from the 195-SNP assignation panel multi-breed 350603039 Affx-1002479362 AX-413837258 CAATTGGCAAAATTATTAGTGTGAATTTCCAGATC[A/T]C W 4 1 2 1 400000 f 74 goat CSN1S1-Ab-allele-1-2 0 0 A T Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603139 Affx-1002479363 AX-413837332 A[A/C]ACATGCAAAGCATTTCAAAAAGTTTGCTTCTTACA M 2 1 2 1 103000 r 74 goat CSN1S1-Ab-allele-2 0 0 a c 1 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603041 Affx-1002479364 AX-413837259 TGGCAAAATTATTAGTGTGAATTTCCAGATCTCGA[A/G]CATGCAAAGCATTTCAAAAAGTTTGCTTCTTACAT R 2 1 2 1 201000 f 74 goat CSN1S1-Ab-allele-3 0 0 a G 2 recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603042 Affx-1002479365 AX-413837260 AATTGGCAAAATTATTAGTGTGAATTTCCAGATCA[C/T]ATGCAAAGCATTTCAAAAAGTTTGCTTCTTACATT Y 2 1 2 1 201000 f 74 goat CSN1S1-Ab-allele-4 0 0 c T 2 recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603026 Affx-1002479355 AX-413837251 TCTTTAGGTGGTATGTCGAAAAATGCTTTGTGCAG[A/T]G W 4 1 2 1 103000 f 74 goat CSN1S1-B1-allele-1-2 0 0 t a 1 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603128 Affx-1002479356 AX-413837322 A[A/C]GAAAAACATTTTAGAAAAAAAATTTCCTGTAACAT M 2 1 2 1 103000 r 74 goat CSN1S1-B1-allele-2 0 0 c a 1 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603029 Affx-1002479357 AX-413837252 TTAGGTGGTATGTCGAAAAATGCTTTGTGCAGTAC[A/G]AAAAACATTTTAGAAAAAAAATTTCCTGTAACATT R 2 1 2 1 201000 f 74 goat CSN1S1-B1-allele-3 0 0 g a 2 recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603132 Affx-1002479358 AX-413837326 TCTTTAGGTGGTATGTCGAAAAATGCTTTGTGCAG[A/C]AAAACATTTTAGAAAAAAAATTTCCTGTAACATTT M 2 1 2 1 303000 r 74 goat CSN1S1-B1-allele-4 0 0 a c 3 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603019 Affx-1002479350 AX-413837247 AGGACAACCTCAAATTGAAGGCACTCTTTCTTCTT[A/T]T W 4 1 2 1 101000 f 74 goat CSN1S1-E-allele-1-2 0 0 T A 1 recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350603021 Affx-1002479352 AX-413837248 TACGTCAGACATGGACTGGCGATTCAATTCTTACA[C/T]GACAGTATACATGTTATAATTCCCATTCTCCCAAA Y 2 1 2 1 303000 f 74 goat CSN1S1-E-allele-3 0 0 T C 3 not_recommended Goat_IGGC_65K_v2 candidate gene ou candidate region CSN1S1 CSN-variant SNP in casein gene multi-breed 350601635 Affx-1002479805 AX-413836034 CCTGATATGGGGCCACTGCGACCCAACCTGGTGCC[A/C]CAGGCCTATCGGCGGCTGCTCGGACTCGAGTCTGG M 2 1 2 1 400000 f 74 goat snp-genphyse637 C A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601734 Affx-1002479807 AX-413836125 GACTGATGGGAAGGAGTTGGGGGAGCAAGCTGTGG[C/T]TGAAAGGGAGGATCTGACCTACGTGGGCATCGGCT Y 2 1 2 1 400000 r 74 goat snp-genphyse639 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601639 Affx-1002479808 AX-413836038 TGGCTGAAAGGGAGGATCTGACCTACGTGGGCATC[A/G]GCTAAGTCCTGCTGGCTGCCTCCAGGCGCCCCCTT R 2 1 2 1 400000 f 74 goat snp-genphyse640 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601641 Affx-1002479809 AX-413836040 GGAGGAAATGGGCAACAGGTCAGTCAGCAAGGATT[C/T]GCTATCTTCTTCACTGGGTGCTGTGGGGAGTGGAG Y 2 1 2 1 400000 f 74 goat snp-genphyse641 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601739 Affx-1002479810 AX-413836130 TTGCCTGCTCTACACAGGCCAGATGGGCAGAAGCC[G/T]CTCCTGTCCTCTTGGTGGCCCACCTTCGAGGTCTG K 2 1 2 1 400000 r 74 goat snp-genphyse642 G T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601646 Affx-1002479811 AX-413836045 GGGCCCTCGGGAAGAGGAGCAGTTGGTGGCGAGGA[C/T]GGGCCACCGGAGCCCCTCCTGATTTCCAGAACACG Y 2 1 2 1 400000 f 74 goat snp-genphyse643 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601648 Affx-1002479812 AX-413836047 TCTGGGGGCAGGGCGCTGCCCAGGTGGGATGATCG[A/G]AAGGCTGGTAGAGGGACCTGAGGGGTCTGTGTGGT R 2 1 2 1 400000 f 74 goat snp-genphyse644 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601745 Affx-1002479813 AX-413836136 GGTAGAGGGACCTGAGGGGTCTGTGTGGTGGCTGG[A/G]GGCAGGCCTCAGGAATTTGACAGCAGGGATCTGGA R 2 1 2 1 400000 r 74 goat snp-genphyse645 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601747 Affx-1002479814 AX-413836138 TCCTCCCCAGCCGTCCGTCTCCTGGGTGCAGCCAT[C/T]TGAGTGCTGACCCCAGCCACCCCCGGAGGCTAGCT Y 2 1 2 1 400000 r 74 goat snp-genphyse646 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601305 Affx-1002479815 AX-413835735 CCCCAGCCGTCCGTCTCCTGGGTGCAGCCATCTGA[C/G]TGCTGACCCCAGCCACCCCCGGAGGCTAGCTGTTC S 4 1 2 1 400000 f 74 goat snp-genphyse647 G C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601748 Affx-1002479816 AX-413836139 CAGCCACCCCCGGAGGCTAGCTGTTCTCCGGTGCC[C/T]CACTCCTGGGGACATGTGTCCACAGGAGGGAAAAG Y 2 1 2 1 400000 r 74 goat snp-genphyse648 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601750 Affx-1002479817 AX-413836140 CCTCGGTGGCCCTGCCTGAGGAGGGGGATGTGTGG[G/T]CAGCGGGGCGGCCTTGCTGCCATATGCTCTGCTCC K 2 1 2 1 400000 r 74 goat snp-genphyse650 G T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601656 Affx-1002479818 AX-413836053 CCTTGCTGCCATATGCTCTGCTCCGAGTGTCCATC[A/T]CCGCTCTCCAGGTGTCACCGCCTGCAGGACTCCCT W 4 1 2 1 400000 f 74 goat snp-genphyse651 T A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601658 Affx-1002479819 AX-413836055 CTGCCATATGCTCTGCTCCGAGTGTCCATCTCCGC[C/T]CTCCAGGTGTCACCGCCTGCAGGACTCCCTGTTCA Y 2 1 2 1 400000 f 74 goat snp-genphyse652 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601660 Affx-1002479820 AX-413836057 CCCCAGGGGGCGAGAGAGAGTAGGCAGGGACGGTC[C/T]GGTGGCCTTGGGTGGGGGATGGCTACTCTGTGGGC Y 2 1 2 1 400000 f 74 goat snp-genphyse654 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601757 Affx-1002479821 AX-413836146 CCAGACCCAATAGTCCATGCGTCCTGGTTTCGAGG[C/T]CACGGCTGGTTCAGGACTGTGGCAAGGTGGTCGTG Y 2 1 2 1 400000 r 74 goat snp-genphyse655 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601759 Affx-1002479822 AX-413836148 TCGAGGCCACGGCTGGTTCAGGACTGTGGCAAGGT[A/G]GTCGTGCAGGGCAGGCCCTCAGCAGCCTGTCTGTT R 2 1 2 1 400000 r 74 goat snp-genphyse656 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601667 Affx-1002479823 AX-413836064 GGCAGCCTGGGCTTCCAGGTGGGTGGGCCTCTTGG[A/C]AGCTCCAACTCTTGCCTGCGGTGGGCTCTCAGGAC M 2 1 2 1 400000 f 74 goat snp-genphyse657 C A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601763 Affx-1002479824 AX-413836152 CCCAGGAGGCCTCAGGCCAGCGGTGGGCGGGACAG[A/G]GCTGACCTGGGCCTGAACCTGCCCTGGGTTGCTTC R 2 1 2 1 400000 r 74 goat snp-genphyse658 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601765 Affx-1002479825 AX-413836154 TGGCCTTCCTGGGAGGGGCTGCACTTCAGGCCTGG[C/T]GGCCCTTCCCCAGGGAGATCCTCTGAAGGGAGGGG Y 2 1 2 1 400000 r 74 goat snp-genphyse659 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601767 Affx-1002479826 AX-413836156 CTGCACTTCAGGCCTGGCGGCCCTTCCCCAGGGAG[A/G]TCCTCTGAAGGGAGGGGGTCCCTGGCTGAGTGCTC R 2 1 2 1 400000 r 74 goat snp-genphyse660 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601676 Affx-1002479828 AX-413836073 CTCACCCCAGGGAGCCCTGACGGAGCAGGCGGGCC[A/T]GCTGCTGCACGGGGTCAACCTGGCCACCATTCTCT W 4 1 2 1 400000 f 74 goat snp-genphyse664 T A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601771 Affx-1002479829 AX-413836160 CCCCGCCCCCCGCCCCGGCCCACGCTGTCTCGGCC[A/G]CGGGGGGCATGGCCTGAGCTTGCCTCTCCCACAGT R 2 1 2 1 400000 r 74 goat snp-genphyse665 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601680 Affx-1002479830 AX-413836077 CTGCTCCGGGCTGGGGCCACTGGGCTGTCACCTGC[C/T]GCGGGACCGGCAGGGGCTCGGCTCACCCCCGCCCC Y 2 1 2 1 400000 f 74 goat snp-genphyse666 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601685 Affx-1002479838 AX-413836081 TCTGTACTGCATTTCATACCAGTGGTTATGACACA[A/C]AAGCCATAGTACAAAACAATGACAGCACAGAATAT M 2 1 2 1 400000 f 74 goat snp-genphyse685 C A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601779 Affx-1002479839 AX-413836167 TGGGAGCGGAGGCTGCTGCGGGCTGGAGGCCCCCC[C/T]AGACCCAAAACCTTCTTCCTCCCATCTGGGTGCTA Y 2 1 2 1 400000 r 74 goat snp-genphyse686 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601689 Affx-1002479841 AX-413836084 TGTTGCCCCCGGCAACAAACAGCTCTCGACCCAGG[C/T]GGGAGCACTCAGCTGCAGTGAGAGAGGGGACTGTC Y 2 1 2 1 400000 f 74 goat snp-genphyse688 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601782 Affx-1002479842 AX-413836170 TCTTCAAATGGCCATCACGTGGCATCTGGGTCGCC[A/G]CCAGCCAGACATGGTAAGAGAGGACTCTGGGGAAA R 2 1 2 1 400000 r 74 goat snp-genphyse689 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601784 Affx-1002479843 AX-413836172 TGGCAGAGAGCAGGAAAATTGACGTAGCCCTGGGG[A/C]AAGACTGTGAAGTTATATTGTTGGCCTTGCCAAGT M 2 1 2 1 400000 r 74 goat snp-genphyse703 A C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601695 Affx-1002479844 AX-413836090 TCAACACTTATGTTAAGAAAGTTGAATCCAACCCT[A/G]ACATAGTAGCATTGGTGCCAATTTCTGGATGGAAT R 2 1 2 1 400000 f 74 goat snp-genphyse704 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601697 Affx-1002479846 AX-413836092 CGGGGCAGACTTTCCAGTGGAAGAGCTTGAGAGAG[A/G]GGGGGAGAGAGAGAGCTGGAGCCAGACCCCTCCCG R 2 1 2 1 400000 f 74 goat snp-genphyse706 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601790 Affx-1002479847 AX-413836178 GGGCAAACAATTCTGGGAATTCCCTGATGGTCTAG[C/T]GGTTAGGACTCGGCATTTTCACTGCCGTGGGCCCA Y 2 1 2 1 400000 r 74 goat snp-genphyse707 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601701 Affx-1002479848 AX-413836095 AAGAAAACAAATACACTGAAGCATAAACAAACAAA[A/C]AAAAAAATCAGAGCAACACATTCCCGAAGGAAAGA M 2 1 2 1 400000 f 74 goat snp-genphyse708 C A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601793 Affx-1002479849 AX-413836182 CAGAGGGTCAGCCTGGGGCTCTGAAAGCACCGTCC[C/T]GGAACAGCACTGAGTGTGCTGCTGCCTGTGACGCT Y 2 1 2 1 400000 r 74 goat snp-genphyse709 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601706 Affx-1002479850 AX-413836100 TGAATCCAAACTGATGGGGCAAGAACAGAATATAC[C/T]GCCACTTTTCTAGATCTTTGAGTTGCACAGCAAAT Y 2 1 2 1 400000 f 74 goat snp-genphyse710 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601709 Affx-1002479851 AX-413836102 GGCTGATCACATCACGACAGTTGTTTAATCTGCCC[A/G]TAAAGTTCACAGTTTTGCCTGCTTTGTGATCACTA R 2 1 2 1 400000 f 74 goat snp-genphyse711 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601711 Affx-1002479852 AX-413836105 TAGACTTCCCTTTCTTTTTGGTATAACTGAGGCTC[C/T]TGAGAGCAACAGCCAGGACATTCACATGCACCATT Y 2 1 2 1 400000 f 74 goat snp-genphyse712 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601713 Affx-1002479853 AX-413836107 CAGGAATTGGGGTCTCAACTGCTTTATCCGTTTTT[C/T]CCCCCTCTCCTCCCTGGCCATATTTGAGTATCTGT Y 2 1 2 1 400000 f 74 goat snp-genphyse713 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601802 Affx-1002479854 AX-413836189 AGGACGAGGCGCCGGGAATTTGTTCATTCTCTTCC[C/G]TTAGGTCCACACCCTCAAAGGTTTTGGTTAGAGCC S 4 1 2 1 400000 r 74 goat snp-genphyse714 G C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601718 Affx-1002479855 AX-413836111 GTAGAAAAGGGAAGCGTCGGGGTCCTTTCCAACAA[A/C]GTAGCCTCCAGAAAGCCTTTTTAAAAACATCTCAT M 2 1 2 1 400000 f 74 goat snp-genphyse715 C A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601806 Affx-1002479856 AX-413836193 TGTGTGTGACATGATTCCCCCCACCCCTCTGCCCC[A/G]CAGGCAAGTACCTTCATAGGCCTCCTCCGTGTACT R 2 1 2 1 400000 r 74 goat snp-genphyse716 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601722 Affx-1002479857 AX-413836114 CCTCACCTAGATCTGCCATCCACTGGACCAGCATA[C/T]GGACAAACGTGGCCAGCACGTTCCCCCCGTTGAGT Y 2 1 2 1 400000 f 74 goat snp-genphyse717 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601810 Affx-1002479858 AX-413836197 ACACCTGCAGGTGAAAAGAGAAGGTGCTCACCTCT[C/T]GTGGGAGAGTGACTGATCTTTAATGAAGTCCATGA Y 2 1 2 1 400000 r 74 goat snp-genphyse718 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601812 Affx-1002479859 AX-413836199 TCTCAGACATCACAGCTGCCGAGTGTTTCTTTGAA[C/T]TGTACGATGCGACAAGATGCAACGGTGTCTCCTGG Y 2 1 2 1 400000 r 74 goat snp-genphyse719 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601814 Affx-1002479860 AX-413836200 CCCCGGGCCAGGTCTGCTCACCTCCGGGCCCTGGG[A/G]CTGGGAGCTGGCATCTTTGCTGGCTTTCTCCTTCT R 2 1 2 1 400000 r 74 goat snp-genphyse720 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601816 Affx-1002479861 AX-318633499 TTTTTCAAGAACCACAATGTTTTTCTCCTGGGAGG[C/T]GATCTCTTCCATGACCTTACAAAAAGGGTTAGAGT Y 2 1 2 1 400000 r 74 goat snp-genphyse722 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601818 Affx-1002479862 AX-413836203 ACACCCACTTTACAGATGGGACCCAAGGGCTCAGA[A/T]AAAGGACATGCACTGTGCAAGGTTACCCAGTAAGA W 4 1 2 1 400000 r 74 goat snp-genphyse723 T A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601735 Affx-1002479863 AX-413836126 CACTTTACAGATGGGACCCAAGGGCTCAGATAAAG[A/G]ACATGCACTGTGCAAGGTTACCCAGTAAGAAACAA R 2 1 2 1 400000 f 74 goat snp-genphyse724 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601738 Affx-1002479864 AX-413836129 GTGGAAAAGACTTCAATCAGAGCTCCAACCTGGTT[C/T]GACATAAGAGAATTCATAATGGTGAGAATCCCTAT Y 2 1 2 1 400000 f 74 goat snp-genphyse725 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601740 Affx-1002479865 AX-413836131 AATGTGGGAAAGCCTTTGGCCAGAGGTCGCACCTT[A/C]TGACACATTAGAAAATTCACACTGGAGAGAAACCC M 2 1 2 1 400000 f 74 goat snp-genphyse726 A C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601742 Affx-1002479866 AX-413836133 CATCAGAGGATTCATTCAGGGGAGAAGCCCTACAA[A/G]TGTAATGAATGTGGGAAAGCCTTCAGCCAAAGCTC R 2 1 2 1 400000 f 74 goat snp-genphyse727 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601744 Affx-1002479867 AX-413836135 ACAAGAAATGTTATGAAATGGCTTCTCACCTGCGG[C/T]GTTCCCAGTACTGACCTCGTCTGGCCCTCCCCTCA Y 2 1 2 1 400000 f 74 goat snp-genphyse728 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601746 Affx-1002479868 AX-413836137 AATGGTGAATTTGGGAATCTGGTCTCCCAGAAGTA[C/T]CTGCCGCTCTACCCCTGGTTCTGCAATGGCTGCCA Y 2 1 2 1 400000 f 74 goat snp-genphyse729 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601749 Affx-1002479869 AX-122790867 GAGGAGGAGGAAGAGGAGGAGGAGGAGGAGGAAGA[C/T]GAAGAGGAGGACGAGGAGGAGGATTTTGAGGAGGA Y 2 1 2 1 400000 f 74 goat snp-genphyse730 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601751 Affx-1002479870 AX-413836141 TCCTGTGCTGCAGGAGGTGCAGCTCGAGGTCGAAG[C/T]CTCCCTATATCTGGGGCGCCTCCTGCTGGTGAAGC Y 2 1 2 1 400000 f 74 goat snp-genphyse731 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601753 Affx-1002479871 AX-173673717 TGATTCCACACTTTCGCTACACCATGGAGATCAAC[A/G]TGCTGGCCCGGAGTAATCTTGTCTCTGAATGGGGA R 2 1 2 1 400000 f 74 goat snp-genphyse732 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601837 Affx-1002479872 AX-413836221 GAATGGCGGCCACGTAGACATTCTCCAGAGAGCCA[C/T]AGCTGGTCTGACGTATCGCTCCTTCTGCCCTCCTG Y 2 1 2 1 400000 r 74 goat snp-genphyse733 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601758 Affx-1002479873 AX-413836147 AACAGAGGCACTGGATACCAAAGTCCCCCTGCCTG[A/G]GGAGGGGCTGGGAGAGGATTGAACTCCAAGAAGGG R 2 1 2 1 400000 f 74 goat snp-genphyse735 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601760 Affx-1002479874 AX-413836149 CGAAGAATAGTAGGCTCCCTCCCACAGGAGCCAAA[A/T]TCTGGAAGCTGGGGTCTCCACTCAGAGCCTGGTAG W 4 1 2 1 400000 f 74 goat snp-genphyse736 A T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601762 Affx-1002479875 AX-413836151 GGCCAGTGAGAGGATGAAAGTCCACTGTAGCCCTT[C/T]CAAGGAGAGGCCGAGGGCCCTGCCGTCCCCCTCTC Y 2 1 2 1 400000 f 74 goat snp-genphyse737 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601764 Affx-1002479876 AX-413836153 GAACTCCAGATCTGTTCCTGGTTCCTTGGGTGGAG[C/T]CCACGGAGGAGCCCGGTGGATAACTGAAAGGTTCT Y 2 1 2 1 400000 f 74 goat snp-genphyse738 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601847 Affx-1002479877 AX-413836231 GCTCATCCTGGTCCAGGCACACAGCAAACGGGCAG[C/G]TGTTAGAGCCGATGATCTGCACCTTGTCCACTTTG S 4 1 2 1 400000 r 74 goat snp-genphyse739 C G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601377 Affx-1002479878 AX-413835798 GAGTGCCTGTCGCTGTCCAAGTCCTCCTCCTCCTC[G/GTCCTCA]TCCTCATCCTCCTCCTCCCCGTCCTCATCCTCGTC - 2 1 2 1 400000 r 74 goat snp-genphyse740 GTCCTCA G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601849 Affx-1002479879 AX-413836233 AAGGACGAAGCATAACCACAGCCAGTGGAATTTCA[A/G]TGAAGCATTTTTGGACCGTGACACACAGTAAAAAT R 2 1 2 1 400000 r 74 goat snp-genphyse741 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601770 Affx-1002479880 AX-413836159 GTACGGGACAACCTGTGTGTGTGACTCACTCAGTC[A/G]TGTCTGACTCTTTGTGACTCCATGCACTGTAGGCC R 2 1 2 1 400000 f 74 goat snp-genphyse742 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601853 Affx-1002479881 AX-413836237 TCGAGATGACAGTTACCAGTTCAGCCTGGGATTAT[C/T]GCTTTTGTTTTGAGCTGACTAGTGTGTTAGCGCTT Y 2 1 2 1 400000 r 74 goat snp-genphyse743 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601855 Affx-1002479882 AX-413836239 TCTTGGCAGCCTGGGCTGCGGTGCTCGCGAGCGGA[A/G]CCAGCATGCGGTTTGGCTTGATGACCTGCGTGCTG R 2 1 2 1 400000 r 74 goat snp-genphyse744 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601776 Affx-1002479883 AX-413836165 CAGGAAGGCAGCCGTGGGACAAGGTCAGAAGTTCG[A/G]CGTGTGGGTGTGGTTCTCACCACAGCGAACAGTTA R 2 1 2 1 400000 f 74 goat snp-genphyse745 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601778 Affx-1002479884 AX-413836166 AAGGCCCCTCCCAGGGGGAGAAAGTAGGCACAGGG[C/G]CCTCCAGCTGGGCCAAGGTGAGGCCAAGTGTGGGG S 4 1 2 1 400000 f 74 goat snp-genphyse746 G C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601860 Affx-1002479885 AX-413836244 CGATGCTGTCCCCGCTGATGGTCCTGTGGCTGACC[A/G]CCTTGCTCCGGACCACCTGGGGGCTCAAGGGCACT R 2 1 2 1 400000 r 74 goat snp-genphyse747 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601862 Affx-1002479886 AX-413836246 CAGGAAGCGGTCCCAGGGGCTGCTCCCGCGGGGGC[A/G]GAACTCCAGCTGAGTCCTACGCACAGCCCAGCAGC R 2 1 2 1 400000 r 74 goat snp-genphyse748 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601864 Affx-1002479887 AX-413836248 CTTGCCCCTCACCCTGGAAGGGCAGGCCTGCGGTC[C/T]GGCTCACGTCATGGAGGAAGTGGGTGAGGTGCGGC Y 2 1 2 1 400000 r 74 goat snp-genphyse749 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601866 Affx-1002479888 AX-413836250 CCCTGGAAGGGCAGGCCTGCGGTCCGGCTCACGTC[A/T]TGGAGGAAGTGGGTGAGGTGCGGCTGGAGGACCTC W 4 1 2 1 400000 r 74 goat snp-genphyse750 A T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601789 Affx-1002479889 AX-413836177 GTGATCTGCTTCACGACCTGGCAGTAACACTCGTC[C/T]CGCATGACCTCATGGTCCCTGCACAGCTGTGGGAG Y 2 1 2 1 400000 f 74 goat snp-genphyse751 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601870 Affx-1002479890 AX-413836254 ACGGTGGAAGAGCCAGGCCGTCCTCCCCATGGTCC[A/T]TGGAGCCAGCTCTGACTGGGGGCCCCTGCAAGAGG W 4 1 2 1 400000 r 74 goat snp-genphyse752 T A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601794 Affx-1002479891 AX-413836181 TGTGCTGTACATCTGGACAGCAGGGCTGACGGACA[C/G]CCTGGTCCCTACATGGGAGGATGGGGCCGCCCTCC S 4 1 2 1 400000 f 74 goat snp-genphyse753 G C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601291 Affx-1002479894 AX-413835721 TGAGGGGCCTCCTGAGGCAGCGTTGTTCTGTGTCA[G/GC]ACCAAGTTCCTGCTGACCGGTCTGCAGTGGGCAGA - 2 1 2 1 400000 f 74 goat snp-genphyse756 GC G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601798 Affx-1002479895 AX-413836185 GGGGCCTCCTGAGGCAGCGTTGTTCTGTGTCAGCA[A/C]CAAGTTCCTGCTGACCGGTCTGCAGTGGGCAGAAC M 2 1 2 1 400000 f 74 goat snp-genphyse757 C A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601292 Affx-1002479896 AX-413835722 GTGAACACGAAGATTTGAACCTCTTGATTTGCATG[A/AT]TTTTGTGGGGTTTTCTGGGTCAAGTGAATAGCGCA - 2 1 2 1 400000 f 74 goat snp-genphyse758 A AT SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601800 Affx-1002479897 AX-413836187 CTGCTGGGAACGGACTTCTAAAACGACAAATATGT[C/T]TGGAAGGCTGTGGTCCAAGGCAAGTTTTGCTGGCT Y 2 1 2 1 400000 f 74 goat snp-genphyse759 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601803 Affx-1002479898 AX-413836190 AAGGCTGTGGTCCAAGGCAAGTTTTGCTGGCTATA[A/G]ACGGGGCCTACGGAACCAAAGGGAACACATTGCTC R 2 1 2 1 400000 f 74 goat snp-genphyse760 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601805 Affx-1002479899 AX-413836192 TGAAACTGAATTCTATTTAGGCAAGAGATGTGCTT[A/C]TGTGTACAAAGCAAAGAACAACACAGTAACTCCTG M 2 1 2 1 400000 f 74 goat snp-genphyse761 A C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601885 Affx-1002479900 AX-413836267 AGTAACTCCTGGTGGAAAACCTAACAAAACCAGAG[C/T]AATCTGGGGAAAGATCACTCAAGCTCATGGAAACA Y 2 1 2 1 400000 r 74 goat snp-genphyse762 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601809 Affx-1002479901 AX-413836196 TGGCCGGTCTGGTGAGACTGTTAAACATGAGACTA[A/G]TTACCGGTCTCGGCACTTGGAGCAGACTCCTGTAA R 2 1 2 1 400000 f 74 goat snp-genphyse763 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601811 Affx-1002479902 AX-413836198 AGGCACTTGCTACCAGCAAGCGAAACAGGTCCTGA[C/G]TACAGCTGTCCCGGATCAGCTGCCTGCCAGGGAAA S 4 1 2 1 400000 f 74 goat snp-genphyse764 C G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601891 Affx-1002479903 AX-413836274 TATCCAGGCCAGCTGGGAAGGACATGATGAGGAAA[A/C]TGGAAAACCATATGACTGCAGAGAAGGGCCCCATG M 2 1 2 1 400000 r 74 goat snp-genphyse765 C A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601893 Affx-1002479904 AX-413836276 GAGAGCTTGGAGGAGGTGGTACATTATCCTCAGCA[A/T]CATCAGCATCAAGCTCTGTTACTTCAAATGGAAAG W 4 1 2 1 400000 r 74 goat snp-genphyse766 T A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601817 Affx-1002479905 AX-413836202 CAACATTTATTCTTTTTTCTCGTCTTCTGGTACGG[C/G]ATCTGTCGGTGGCTCCTCCACGGCTGCGCTGTTGC S 4 1 2 1 400000 f 74 goat snp-genphyse767 C G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601898 Affx-1002479906 AX-413836281 TTCTGGTACGGCATCTGTCGGTGGCTCCTCCACGG[C/T]TGCGCTGTTGCTTTCGGAGCCAGTGTTGCTATCAC Y 2 1 2 1 400000 r 74 goat snp-genphyse768 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601821 Affx-1002479907 AX-413836206 CGCCATGGCTACAGCGGCTGGTGAGGAGGAGCTAC[G/T]AGACAGGAGCTGAGGCCAGGAGAGTGACAAGGAGG K 2 1 2 1 400000 f 74 goat snp-genphyse769 G T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601293 Affx-1002479908 AX-413835723 AGCACCTACTAGCAGAACAGGCAGCCCTGGGCCTG[A/AT]TTCACCATGACCTACCGGTGCCTCCTCCAGATGGT - 2 1 2 1 400000 f 74 goat snp-genphyse771 AT A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601902 Affx-1002479909 AX-413836285 GAGACATCCTCAGAGTGTTTCCCAATAAGAAGAAA[A/G]TGTGAAGCATAGCACTGGGATGTGACATGAGAAGG R 2 1 2 1 400000 r 74 goat snp-genphyse772 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601826 Affx-1002479910 AX-413836211 TATTTCGAATCATTTGGCACTTACTCCACAAAGAT[A/G]CCCTTTGACTTATTCATCTATTTCCCATATGTGCT R 2 1 2 1 400000 f 74 goat snp-genphyse773 G A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601906 Affx-1002479911 AX-413836289 TGGCACTTACTCCACAAAGATGCCCTTTGACTTAT[C/T]CATCTATTTCCCATATGTGCTGAAAATATATCTCA Y 2 1 2 1 400000 r 74 goat snp-genphyse774 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601830 Affx-1002479912 AX-413836215 CATTTTTGCAATTCTGGATCCAAATTGCATGGCCC[A/G]CTTTGGCAGAAGAGCAGAGGCTGTTAGACCAAGTT R 2 1 2 1 400000 f 74 goat snp-genphyse781 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601387 Affx-1002479913 AX-413835808 ATTGCATGGCCCGCTTTGGCAGAAGAGCAGAGGCT[G/GTT]AGACCAAGTTCCACTGCTGCAAGACGCAAAATTAG - 2 1 2 1 400000 r 74 goat snp-genphyse782 GTT G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601390 Affx-1002479914 AX-413835811 TTGCATGGCCCGCTTTGGCAGAAGAGCAGAGGCTG[T/TTG]GACCAAGTTCCACTGCTGCAAGACGCAAAATTAGT - 2 1 2 1 400000 r 74 goat snp-genphyse783 TTG T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601832 Affx-1002479915 AX-413836217 ACCAGAATTGTATTTCCAAGGATACAACTTTAAAA[C/T]GACAGACTGGGAAATGGAAACAGATTTGAGATCAA Y 2 1 2 1 400000 f 74 goat snp-genphyse784 T C SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601913 Affx-1002479916 AX-413836296 AAACCATAAAGAATGGCTAGATGCTTGATAATATA[A/T]AAAAGACCAAGGACCTTGGACTTTTGAGAAGAGCG W 4 1 2 1 400000 r 74 goat snp-genphyse785 A T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601836 Affx-1002479917 AX-413836220 TGAGTGTATCCTCAGTGTGAATTTGGAGTTTGTGT[G/T]AATTGCTACTAGATGAAAGGGGAAGACTTCCAATG K 2 1 2 1 400000 f 74 goat snp-genphyse786 T G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601917 Affx-1002479918 AX-413836300 ACTTCCAATGGGGAAGACTGCAAGACTTTTTCTTG[C/G]TTGAGATGCATGAAGAGTTAAATACATGAACCAGG S 4 1 2 1 400000 r 74 goat snp-genphyse787 C G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601920 Affx-1002479919 AX-413836302 GGAAAGAAGCAGATGGCAGGACATGGGCTGGAGTG[C/T]GAAGAAGCTAGAGTAAAACAGAAAAATAGGGTTCC Y 2 1 2 1 400000 r 74 goat snp-genphyse788 C T SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601922 Affx-1002479920 AX-413836305 CTGTGGATGTTGGCGGTACAGACCAAGAATTTGGC[A/G]TTGAAATTGGGCCAGTTTGTTTTGTGTAAAGCAAG R 2 1 2 1 400000 r 74 goat snp-genphyse789 A G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601924 Affx-1002479921 AX-413836307 ATCACCCTTTGGTCCAGAGATCCCAGGGCTGCCAG[G/T]AGCACCATTACTACCAGGTGGACCTGGGGGGCCAT K 2 1 2 1 400000 r 74 goat snp-genphyse790 T G SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 350601392 Affx-1002479922 AX-413835813 GCAATCTTCTGCTCAAGCCACTGGACATAGAATCT[A/ATG]TGATGCTGTACCCCTCAAGATTTTAAACTTATTGA - 2 1 2 1 400000 r 74 goat snp-genphyse791 ATG A SNP in QTL region (GenPhySE laboratory, INRAE) Alpine/Saanen 320780800 Affx-122976890 AX-385267889 AGCTTTCTAGACTAACCTGGAAACAATACACAAAC[C/T]ATTGAATTGCCTCACATATGATTTTAGTGCTTCTC Y 2 1 2 1 101000 f 74 goat snp10134-scaffold1361-15149 26 35254506 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414022 Affx-122949800 AX-123284371 TGAACTGAACTGAACTGATGATGGTAATTGTTACC[A/G]TTTCCATTTCCATCTGTTATGCTAGGCAATGGCCC R 2 1 2 1 103000 r 74 goat snp10135-scaffold1361-44576 26 35281662 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422579 Affx-122943749 AX-123292925 AGAGTATACTGCTTATGTTTTCTTCTAGAGTTTTA[C/T]GGCTTCTTGTCTTACATTTAAGTCCTCAACCCTTT Y 2 1 2 1 103000 r 74 goat snp10136-scaffold1361-91495 26 48555315 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785191 Affx-122976369 AX-385272237 TAACAGACTACTGAGATACTTTTCACTCAGTTTTT[A/G]TATGCCAGATACAGAGAATTTGTAGCAGTTATTTT R 2 1 2 1 202000 f 74 goat snp10412-scaffold1372-579082 3 20362549 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428532 Affx-122938745 AX-123298874 ACAGTATTACAAAAAAAAAAAAATAAAGAATTTAA[C/T]GTACCGTATCCCTTCCATACAAAGGTCTCGTCTGA Y 2 1 2 1 101000 r 74 goat snp10413-scaffold1372-610565 13 53868636 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418893 Affx-122946103 AX-123289241 CCCAGTGCAAGATACCGTCTCTTCTGGAAGGCCGG[C/T]GAGGACTGCCCCGTGGCCTGTGCTCAGCGTTCTGG Y 2 1 2 1 101000 f 74 goat snp10415-scaffold1372-688806 13 53790524 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424372 Affx-122941841 AX-123294718 AAACTAGGCGTCAGAGGGCCAGGAGAGTTGTTTGC[C/T]AGCTTGTCATCTTCCAACTAATTATTTAATTACCC Y 2 1 2 1 201000 r 74 goat snp10416-scaffold1372-741571 13 53737265 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784205 Affx-122945934 AX-385271256 AACGGCGATAAACACATCCGTGATAAAACGAGCCC[A/G]AGAGCCCAACACCTCTGCTTGGCTAAAAACAGAAC R 2 1 2 1 101000 r 74 goat snp10418-scaffold13729-10228 25 42014044 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427162 Affx-122939624 AX-123297505 TGAAAAAACAAACTTCAATCCACACCTCATGTTAA[C/T]AAAACCAATTCATTCTTGATGGATCACTTGCTTAA Y 2 1 2 1 101000 f 74 goat snp10742-scaffold1381-10460 19 23940928 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430837 Affx-122937436 AX-123301178 GCCTGCCGCTTCTGACAACTTGGGTGGACCTTCAG[A/G]GCATCGTATGAGCCGAGTGAAACAGGCCAGGGAAA R 2 1 2 1 201000 r 74 goat snp10743-scaffold13815-5509 22 48360548 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439763 Affx-122930519 AX-123310100 ACATAAATATGCCATCAAAATGGATTATGGGAAGA[C/T]CTTCGATAGAGTCATGTGATGAGCACCGGAGATGG Y 2 1 2 1 101000 r 74 goat snp10921-scaffold1391-147 15 12673599 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788037 Affx-122938528 AX-385275058 TCTATTATCATCACATGCTAATAATTGATAGCTGA[A/G]TTTTGCTGTAGTAAATTTAATTCTTAATTGTTGAA R 2 1 2 1 101000 f 74 goat snp10922-scaffold1391-50229 15 12623215 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437362 Affx-122931930 AX-123307700 TCGCTGAGCACAGCTATCCGCACTTTATATGCCCC[A/G]TGTGTCATGACTGTTCCGTTTGGAGTAATCCAAGA R 2 1 2 1 101000 r 74 goat snp10923-scaffold1391-79003 15 12594481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389632 Affx-122968744 AX-123259990 TCTAGTCCCAGAGAATGAGAAACTCTATGTCCCAT[C/T]CAGTTTTAATACAAACCATGATCTCAAATGCTGAC Y 2 1 2 1 101000 r 74 goat snp10978-scaffold13932-19256 18 64495025 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776640 Affx-122948058 AX-385263767 TTTCCATAATTCCAGATCTCCTGTGTTCAAGTCAC[C/T]TTAGTGTTTGCACTTTACCAACCGAGGCTCCCCAT Y 2 1 2 1 101000 f 74 goat snp11205-scaffold1400-547534 15 15028639 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427348 Affx-122940112 AX-123297691 CTGCACTGCAGACAGAGTCTTTATCAACTGAGCTA[C/T]GATTAGAACCCTATTATTTGTAGAGGACCATTATT Y 2 1 2 1 201000 r 74 goat snp11218-scaffold1401-11134 12 86559555 G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401591 Affx-122958874 AX-123271944 ATGCATATACACACAAAGTGCTCACACAGGATATG[C/T]ACGCCAGTGTCAGGTGAGCAGTTGGAATATCTGAC Y 2 1 2 1 101000 r 74 goat snp11219-scaffold1401-101725 12 86650320 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427652 Affx-122939327 AX-123297995 TTAGGCACAGCCTGATGCCCTGACTGATTGCAGAG[C/T]ACAACATAAGGACCTATCTTGACTATGAAGCACAG Y 2 1 2 1 101000 r 74 goat snp11220-scaffold1401-145822 12 86695551 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426529 Affx-122940196 AX-123296875 CCATTAAAAGACAAGCTTTTGGAGTTTTTCGAAAG[C/T]GAACACAAACAACAGATGTAATTGTTGAAAGCCAT Y 2 1 2 1 101000 f 74 goat snp11221-scaffold1401-191827 12 86741395 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447790 Affx-122923942 AX-123318126 TGGCAATGCTGCTGTTCATCCAACCAGGAAGATTT[A/G]TGGATAAGGCTGGTCCAGGCCCCCAAAATCATCCT R 2 1 2 1 101000 f 74 goat snp11222-scaffold1401-224602 12 86774738 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387234 Affx-122970576 AX-123257592 TGAATGTCAATGCATTATTTATTATTAACTTCAAT[A/G]TAGTCAATGTTTAACCATGCAGAAATCAGAAGAAA R 2 1 2 1 101000 r 74 goat snp11223-scaffold1401-259445 12 86809598 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408077 Affx-122954729 AX-123278428 ATTTTGTCACAATTCCAAGGAAAAGAAGGAAAACA[A/G]CATAAAAATAATCAAGATCACACTCTTCCTTTCTG R 2 1 2 1 201000 r 74 goat snp11224-scaffold1401-309305 12 86860815 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378801 Affx-122976986 AX-123249160 CCTTCTTCTGCCACATCCCTCTGACTAACACCAGA[C/T]GGAGAAATTTCTCTGCTTTAAGATTTCAAGTGTTT Y 2 1 2 1 201000 r 74 goat snp11225-scaffold1401-351474 12 86903859 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399535 Affx-122961146 AX-123269890 CATAACCATACTATCATGTGGAAAGAAAGCAATTG[C/T]ATGATAGGTTGAACAATCTTTGAAATCCCCCTTCT Y 2 1 2 1 101000 r 74 goat snp11226-scaffold1401-380878 12 86933380 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451169 Affx-122921348 AX-123321503 CACTCCCTGAAGTAGCAGACTGTAAGTCCGAAATC[A/G]TCATTTGAGATCCTTTTAATGAGGCATTGACTGGT R 2 1 2 1 202000 r 74 goat snp11227-scaffold1401-414877 12 86967655 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452214 Affx-122920807 AX-123322547 AACACATGGGATCCACACATTTTCCAACTTATTAT[A/C]GATTTTATCAGTGCTTTAGAAAACAAACAAACAAC M 2 1 2 1 101000 f 74 goat snp11228-scaffold1401-445100 12 86998246 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788675 Affx-122945494 AX-385275691 TCTCAATGAAATTTTCATTGAGTAGCAATTTTGAC[G/T]CATATGAAAAAGTCCGCATCTGACAGCACAAGGCA K 2 1 2 1 202000 r 74 goat snp11229-scaffold1401-477987 12 87030827 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796609 Affx-122940568 AX-385283555 TTAACCATGACTTTGGACAATACGATAGAGAAAAT[A/C]TAAAGTAGGTGGTCAGATTTCTTTGGTGTGTCATG M 2 1 2 1 101000 r 74 goat snp11230-scaffold1401-556817 12 87110004 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404343 Affx-122956828 AX-123274695 GGTCTTATTTTTATCATTTGTAAATAGAATTGGCT[A/G]TGTGAATAGAAGTTGCCCCATAGGTACTAGTTTCC R 2 1 2 1 101000 r 74 goat snp11276-scaffold1405-7092 3 51662417 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403783 Affx-122957983 AX-123274135 CAGGAGGCTCTTCAGCGCCCAGTGGGTGGGGAAAC[A/G]CCAGGTGATTCCCTGCTCCTTGAACCGTTTGTGTG R 2 1 2 1 101000 r 74 goat snp11422-scaffold1414-3694 23 46896908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794831 Affx-122931101 AX-385281791 TTCTATTCTCCTATTGAACCAAATACAATACTGTA[C/T]ATAGTTTGAGTGCTTGGATCTCAAAAAATAAATGT Y 2 1 2 1 101000 r 74 goat snp11423-scaffold1414-41853 23 46936276 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394590 Affx-122964432 AX-123264945 ATTTTCCTTTTAGAGTGCCGTTATTGGCCCTTATA[C/T]TATCTACCCCATCCTAGAAAGTGTACATCCTACTC Y 2 1 2 1 101000 f 74 goat snp11600-scaffold1424-45654 14 85005904 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391655 Affx-122966559 AX-123262012 CAACACCTTTCTCTGGGAAAATTTAACTTAGAACT[A/G]CAACTGGTCTCCTGCATATGAAAGGAGTGTCTTAG R 2 1 2 1 103000 f 74 goat snp11779-scaffold1436-30078 13 42000 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449860 Affx-122922370 AX-123320195 AGCTTTTTTTCCCTCTACCTTTTTTTCTGCTGTTT[C/T]TTAGCAACTTTATTACATTCCCATGTATTACAGAT Y 2 1 2 1 201000 r 74 goat snp12153-scaffold1450-10837 11 3884913 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786069 Affx-122922685 AX-385273105 AGAAAGTGGTTCGTTTTATAAAAGTTTGAAAATTT[A/G]CTTTATATAGAGTAGAGCAAAGTACTTGTTCTTTT R 2 1 2 1 303000 f 74 goat snp12154-scaffold1450-69534 11 3825082 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400365 Affx-122960026 AX-123270720 TTGGCACAAACAACAGAAGCTAAGACCTGCTAACT[A/C]GAGCTCGTGTAAAGAAAAGGGGGCACCCAGACACC M 2 1 2 1 101000 f 74 goat snp12171-scaffold1452-15834 19 14120984 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418765 Affx-122946197 AX-123289113 TCTTGGTGGACAGGTTGGTTCTGTAAGCCGTGGGG[C/T]TGCCCACTGGTGGGTGGAGCTGGATTCTGAGCCTT Y 2 1 2 1 101000 f 74 goat snp12172-scaffold1452-46218 19 14097941 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453471 Affx-122919845 AX-123323804 GCTTCACCACTCGCATAAATGCAGATGAGAGAAGA[C/T]CAAGGGAAATATTTGAAGAGATTGGAGGTGCCATG Y 2 1 2 1 101000 f 74 goat snp12173-scaffold1452-90511 19 14053215 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767676 Affx-122951485 AX-385254916 GGAACTCCTAGCTTCACTGCCTCTTATACGTGATG[C/T]GCTTCAGCTACTGTGTCGTAAACTTCAAGAGTACA Y 2 1 2 1 202000 f 74 goat snp12174-scaffold1453-41167 NW_017214591.1 20872 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434367 Affx-122934709 AX-123304708 TGAACCTTTAAATAACACTCTTAGGTGCCACTGGG[C/T]CTCTGCCCAGGTAAGGCCTGCAGGACAAGGGACCC Y 2 1 2 1 101000 f 74 goat snp12175-scaffold14538-2873 24 33406396 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439315 Affx-122930953 AX-123309652 AGGAGTGAAGTTGTAGTGTATGAGAACCTCTGTTC[C/T]GGGGTGACTGGACCCCCTCATCCTCATTCAGGAGG Y 2 1 2 1 101000 f 74 goat snp12243-scaffold14578-3315 NW_017203637.1 10459 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429233 Affx-122937918 AX-123299575 TACAGTTAATTCATTTTTGACAGAGGAACTAGGAA[C/T]ATGCAATGCGGAAAGGACAGTCTCTTCAATAAATG Y 2 1 2 1 303000 f 74 goat snp12299-scaffold1462-1469 NW_017214048.1 15041 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800751 Affx-122957930 AX-385287668 TGGTCAAGATGATGCTACCAAATGTATGAGATTAC[C/T]TATATTTTGAATCTCTAGGGAGGCTGGGCATTGAG Y 2 1 2 1 201000 f 74 goat snp12300-scaffold1462-102225 5 101107963 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402914 Affx-122958198 AX-123273267 TCATATGAGCCAGCCTCCAACCAAAATGTAATAAA[C/T]CGGGAAGAAAAGACCAGCTTCTAAAAATCCCCATA Y 2 1 2 1 201000 f 74 goat snp12370-scaffold1467-56316 22 48306691 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401043 Affx-122959661 AX-123271396 CTGGCGATGCTCTAAATTCCTTCCTTGCAAACAAC[A/G]GAGTCTCTCAAACTGGTTGGAGTCTTAAACACGGT R 2 1 2 1 101000 r 74 goat snp12371-scaffold1467-85946 22 48280134 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408590 Affx-122953653 AX-123278941 CAGAAGAGAATGAGAATGTAGGGAAAACCCTTCAG[G/T]GTCAAGGAGGAGAACATAGATTCTAACACTTCAGC K 2 1 2 1 201000 r 74 goat snp12373-scaffold1467-180788 NW_017189526.1 64139 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381996 Affx-122974081 AX-123252354 TTGCCAAGTGTTTTTGTCTTTCAGTTACTTTGCTT[A/C]GTGCTTTAAATGTGTGAATTCAATTTTCACAGCAC M 2 1 2 1 201000 r 74 goat snp12393-scaffold1471-8691 3 109237161 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390859 Affx-122967820 AX-123261216 AGTGGATTCTAACTGGAGCCATTCTCTACTCTCAG[C/T]GCTACTGATGCAGAAAGCTCAACTTCTCTGTACAC Y 2 1 2 1 101000 f 74 goat snp12394-scaffold1471-55356 3 109189735 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410745 Affx-122952699 AX-123281095 AATGAAACAGGGGGAGAGGATGGAGACTCTCACAC[A/G]CCCTTCTTCAGGAAACAAAACTGAGACACTGATTT R 2 1 2 1 101000 r 74 goat snp12472-scaffold1477-1470 28 44330028 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398917 Affx-122961007 AX-123269272 TGTGTCCAATGCACACCTGTCATCACATAGATAGG[C/T]GGGTTAAGAAGGTGGATCGCACCCAATGTGCAGTG Y 2 1 2 1 101000 f 74 goat snp12473-scaffold1477-35332 28 44365290 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378742 Affx-122977029 AX-123249101 GCATAGGTTAACAAAGGAGATAGAGTGGGGAGTGG[A/C]GAGGGATGTACCTAATTACCCCCTTGGACACATTT M 2 1 2 1 101000 r 74 goat snp12474-scaffold1477-112961 28 44443616 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412709 Affx-122950745 AX-123283058 ATAAAAGATCATAACCTAGAAAATATATGGCCACA[C/T]AAAAAACTGCAAATGGATTTTTTACAGCAGCTTCA Y 2 1 2 1 101000 f 74 goat snp12476-scaffold1477-205035 28 44536284 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450460 Affx-122922948 AX-123320794 TGGTGGGTGCCTGAGGCGTCTGCTGCTGTGTTTAC[A/G]GTCGTGGACCAGAGCCACCTGGTGGTTACCTTTGG R 2 1 2 1 101000 f 74 goat snp12712-scaffold14886-4018 NW_017189530.1 463767 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799416 Affx-122976591 AX-385286346 CGTCTGTATTTGGTGAAATGTAGGAGTCCAACTTC[A/G]TTCTATTGCACGTGGATATCCTGCTGTCCTCGTAC R 2 1 2 1 101000 f 74 goat snp12811-scaffold1494-34470 NW_017189517.1 40185992 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379786 Affx-122975836 AX-123250144 CTCCAGGAGAGCTTTGAGTTTCAGTGAGGGCTCAG[C/T]GTACCTCTGGAAGCTGCCTCTCCATGGGCCAATAC Y 2 1 2 1 102000 r 74 goat snp12812-scaffold1494-64052 NW_017189517.1 40155059 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433000 Affx-122935795 AX-123303341 TTCCTCCTTGCATCTCTCAGCGCGAATCATAAAAA[C/T]AGGGGAGATGGTGAGGGAAACCAGAAGGACCCAGC Y 2 1 2 1 101000 f 74 goat snp13107-scaffold1500-68077 29 51310028 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387764 Affx-122969723 AX-123258122 TGGGGTCGCACAGAGTCGGACAGGACTAAGGTGAC[A/G]TAGCAAGGAAGCTTTGCCCAGCCCCAGGTCAGGAA R 2 1 2 1 101000 r 74 goat snp13108-scaffold1500-139902 29 46300691 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446484 Affx-122925055 AX-123316820 AGGATATTGGCCTGGAGGTCGTCCGAACAGATAAG[C/T]GTCGGGGTAAAATTCAGGAACTGTGTGGAGGTCTT Y 2 1 2 1 201000 f 74 goat snp13109-scaffold1500-202355 29 46239691 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782513 Affx-122971906 AX-385269589 AGAAAACACAAAATAAAACTATATTAGAGAAGAAG[C/T]ACTTCAAAGCCCAAATTTGCCAATAACCATTACCT Y 2 1 2 1 201000 f 74 goat snp13188-scaffold1505-9168 26 45702920 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770010 Affx-122974203 AX-385257177 TAGGAGGCTGTAAATTTTATAGACTTCTTTATAAA[G/T]AAGAATATTTGACTGTAAAGATTCCTCATTAGAAG K 2 1 2 1 102000 r 74 goat snp13189-scaffold1505-57602 26 45653784 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789925 Affx-122923480 AX-385276931 TAGATAGCCATGTCTTCTTGATTATCACTCATTTT[A/G]CCAAAGGAAAATAATTTCTGGCATATATTTTATTG R 2 1 2 1 202000 r 74 goat snp13190-scaffold1505-86515 26 45625492 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451408 Affx-122921190 AX-123321741 TTAGGGCCCTTATAACCACATGAAAAGATAGAGTT[A/C]TCTCTCTCTTTCACTAAGTGACTGCATTAAGAAAT M 2 1 2 1 101000 r 74 goat snp13191-scaffold1505-153770 26 45556579 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406049 Affx-122955472 AX-123276401 TTTTAAACACTGAGCAAAAGTCAAAAGGCAGAAAA[C/T]AGGAAATTGGGTTTTTAGGTATTTTTTTTTAACAT Y 2 1 2 1 303000 f 74 goat snp13221-scaffold1508-12920 18 59539005 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789505 Affx-122935102 AX-385276514 ATGAAAAATATACAAATTCCAATCAACAGTGGGTC[A/G]TTGATGCAGAAGTGTTATGTTCTACACACTGAGTG R 2 1 2 1 101000 f 74 goat snp13222-scaffold1508-49074 18 60274060 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377712 Affx-122977399 AX-123248071 CAGAAAACACGGACTCTTAACTGCACTGTTGGTGG[C/T]AATGTTAATGGTTCTGCTGTGTTGGAAAATAAAAT Y 2 1 2 1 101000 r 74 goat snp13504-scaffold1522-6672 NW_017189516.1 64741532 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434821 Affx-122934802 AX-123305162 AAGAGGTGGCCAATGTATTCGAGTTTTAGTATTAG[A/G]CCTTCCAGTGATTATAGGTATATACCTATAGGTAT R 2 1 2 1 101000 f 74 goat snp13505-scaffold1522-38883 NW_017189516.1 64775865 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441491 Affx-122928738 AX-123311828 TAAAAGTTCCAGGCAGAGTTGAAGTCCTATTACAA[C/T]GCAGTGACAGGTTAAAAAATAAATGAACGGTATTG Y 2 1 2 1 103000 f 74 goat snp13506-scaffold1522-69943 NW_017189516.1 64805830 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435520 Affx-122933410 AX-123305860 TCTTCAGTCTTTGAGGAGAAAGTTAGATATGTCAC[A/G]TAGTTACATGTATTTTGTATGCATGTATTAAAATG R 2 1 2 1 101000 f 74 goat snp13507-scaffold1522-101835 NW_017189516.1 64837771 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768970 Affx-122964409 AX-385256145 CAATGTATTTCACACACAGATTAAGAATATTTCCA[C/T]AGTGTCCTAGCCTTCTCTCCCCTTGAATTTTGTGC Y 2 1 2 1 101000 r 74 goat snp13508-scaffold1522-143092 NW_017189516.1 64878888 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441532 Affx-122928710 AX-123311869 GGCCGGCTCATTTTGCCATACAGCAGAAACTAACA[C/T]GCCATTGTAAAGCAACTATATCGCAGCAAACATTA Y 2 1 2 1 303000 r 74 goat snp13509-scaffold1522-185181 NW_017189516.1 64921088 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395936 Affx-122963584 AX-123266291 CGCTGTTTGAGGACTGGACTGCTGCTCAGGGCAAA[C/T]GCTCCACGTCTGTAACTCATTGAAGATCTTCCTGC Y 2 1 2 1 101000 r 74 goat snp13510-scaffold1522-236179 NW_017189516.1 64970090 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427908 Affx-122939678 AX-123298251 ACGAAGCAGGTGTGTCGTCTTTATATAAAAATGCT[C/T]GTCAATGAGCAGACAAGCTCAGAGGCAGTTCAGCT Y 2 1 2 1 101000 f 74 goat snp13512-scaffold1522-317912 NW_017189516.1 65052142 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383475 Affx-122973442 AX-123253833 CACTTCCACCGAAGAGAAGCAGGTAGACTTGATGG[C/T]GGACAGGAAAAGTCCGAAATGTTGTTGTTGAGAAG Y 2 1 2 1 101000 r 74 goat snp13515-scaffold1522-466642 NW_017189516.1 65207338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409788 Affx-122952975 AX-123280139 GCACCTAGCTTTGCACAGTCATGTCTAGGCAGAGG[C/T]GGGGTTCAGGGGATGGTGTTGGGATCACAGCTCTC Y 2 1 2 1 103000 f 74 goat snp13740-scaffold1530-951 13 62113127 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418156 Affx-122947095 AX-123288504 GAGTGCATACTGAGGCTCAGGGTCTAGCAGAAGTG[A/G]ACTCATCTGCATCTTGGACCTATTTGGATAAATAA R 2 1 2 1 102000 f 74 goat snp13741-scaffold1531-2162 23 21921453 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796879 Affx-122978097 AX-385283821 CAAAGTCTAAGAATAACCACTAACGGCTATTGTGT[A/G]TGCTGTGTGTGCAGTTATAGACATAGAGAAAGCAA R 2 1 2 1 201000 r 74 goat snp13766-scaffold1537-17466 29 5243517 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447176 Affx-122924423 AX-123317512 ATAGTTTTAAAAGTTGCTCTCTTTTCCATCTAGGT[A/G]CTTCTATACTCCTCTCCTCTACTACAGAGTAACAG R 2 1 2 1 101000 r 74 goat snp13767-scaffold1537-52898 29 5207601 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795810 Affx-122921259 AX-385282763 GAACACGTCTCAGATCTTCAAACACAGGGACATGA[C/T]GAGTGACTCTTTTATTATCCAACACAATGTACGCA Y 2 1 2 1 101000 r 74 goat snp13768-scaffold1537-81943 29 5178078 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397225 Affx-122962380 AX-123267580 CAGAGACTGACAAATCAGTAAATGGTTATAAATGC[A/G]TGGTCCGTGGAAAACTTATCATCAGTCTTTGGTGA R 2 1 2 1 101000 f 74 goat snp13769-scaffold1537-123620 29 5136038 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420914 Affx-122944599 AX-123291261 GTTGCCATTCCCTTGCCCTGTCTTTCTGAAGGCCT[A/G]TACTGTTTTGAATTCCCATCATCAGTGAATCAACT R 2 1 2 1 101000 r 74 goat snp13770-scaffold1537-171977 29 5086848 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800981 Affx-122937998 AX-385287895 GAACTTGGGATACTATTTGGTTCTTAGACTACTTG[A/G]AACTGTGCTCCAATCTTGACTCCTCCTGCTTCTCC R 2 1 2 1 101000 r 74 goat snp13904-scaffold1542-5264 14 84708695 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770347 Affx-122972226 AX-385257513 GCTTTCCTTCTCTGATGCATAATATGATTTGAGTG[C/T]AGTTCTAAGATTGTCATGTAATTCTAGTTATGTGT Y 2 1 2 1 101000 f 74 goat snp13905-scaffold1542-37729 14 84674964 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420869 Affx-122944634 AX-123291216 GTCATACAGATCTAATTCTGCTTCAGTGCAAATGT[A/G]ATTTGCTGGTGACTGTGTTTGTTTAAACCCATTGA R 2 1 2 1 102000 f 74 goat snp13906-scaffold1542-68606 14 84643919 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425226 Affx-122941011 AX-123295572 TTAGTGATTTTCTTTCCTTTGTGCTTAGTGGAGAT[A/G]GTATTTAAGCCTCTGCATAGACCCTTCTGTTGCTT R 2 1 2 1 101000 r 74 goat snp13907-scaffold1542-129682 14 84582409 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443124 Affx-122928086 AX-123313461 GAAAACCCCATGTAGATGGCCTAACAGAATATGTT[A/C]TTCAATATTCAGGGGATATTTTGTAAGATTTCCAT M 2 1 2 1 102000 f 74 goat snp13908-scaffold1542-183098 14 84528698 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422916 Affx-122943046 AX-123293262 TGTCCTTCCTGGGGAAAAGACATGGACAGGCCTGC[A/G]CACGGAGCACATCGTGTGACATGGAGCAGAGCTGG R 2 1 2 1 201000 r 74 goat snp13935-scaffold15446-6258 NW_017189534.1 8381 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414088 Affx-122949749 AX-123284437 ATCTTTAATTAAGCAATTGATTCCTCAGACACCGA[C/T]GCCATCCCCGCTTCAAATTCCCTGGATCCACCAGG Y 2 1 2 1 101000 f 74 goat snp13939-scaffold1546-56443 18 59723768 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445313 Affx-122925435 AX-123315650 GTCATCAACAAAACAGCACGTTAGAGAAAGATCTC[A/G]TCCACCTTACTGGGGAGAAAAATCTTTCACTCTAA R 2 1 2 1 202000 r 74 goat snp13940-scaffold1546-88619 NW_017190029.1 68638 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399116 Affx-122960857 AX-123269471 CTCTTCTGTGCCAACGGTCTGGTATTCTGAGCACA[A/C]AATCCTTAGCAGAGAGTCACAGGGGACAGCATTCA M 2 1 2 1 202000 f 74 goat snp13946-scaffold1548-2349 23 20924117 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432652 Affx-122936470 AX-123302993 TTCCTCGTGGCCATCCATAATGTTCATTACCACTG[C/T]AATGTTCGTTGGGCTCCCAGAGCACCATAGGCAAC Y 2 1 2 1 202000 r 74 goat snp13966-scaffold155-2673 13 43075894 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376837 Affx-122977913 AX-123247196 ACAAACATATGGAGATTAAACAACACATCTCTAAA[C/T]AACCTACAGTTTAGTGAAGAAATCAGAAGAGAAAT Y 2 1 2 1 103000 r 74 goat snp13967-scaffold155-43026 13 43036953 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435989 Affx-122933506 AX-123306328 AGAATAGCTGCATTCAACTTACTGCTGAAATTTTT[A/G]TAAAAATGCAAAATCCTGGGCCCACATTGGGATTT R 2 1 2 1 102000 r 74 goat snp13968-scaffold155-79657 13 42987369 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429126 Affx-122938006 AX-123299468 TTTCTGATAGAGAAGGACAACCAAAGCTGGAGTTC[A/G]CTTGTGCTTTTTGGCAATGGCACGAAGAACCAGGT R 2 1 2 1 101000 f 74 goat snp13969-scaffold155-118624 13 42947329 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411116 Affx-122951907 AX-123281466 ACCTTTTCTCGAGTCATATCAGTCCTGGAGGCCGT[C/T]TCTGCTGGTGCCCTGGACGTCCTACCCCTTATGCA Y 2 1 2 1 101000 f 74 goat snp13970-scaffold155-173875 13 42889673 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409277 Affx-122953118 AX-123279628 ATGAAGAGTAGTTGGTGTCTCTGCCTAACAGATGT[A/G]CAGAAGTGGGAGAGATTGTGCAGAATTATCTCCAA R 2 1 2 1 202000 r 74 goat snp13971-scaffold155-241439 13 42824328 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412260 Affx-122950896 AX-123282609 AGATTCAACTTTTCTTTGGGTAGTTCTGTATGCGC[A/G]TGATGAACCCATGACAGTTTCCTGAATGTCCCTGG R 2 1 2 1 201000 r 74 goat snp13972-scaffold155-312654 13 42749791 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445107 Affx-122926193 AX-123315444 CAACCAACTTGAGGGCTGCCTGGGAACTGGTGCCT[A/G]TTCCACTTAACTCTAACCTTAAACTGAAGAGCAGC R 2 1 2 1 201000 r 74 goat snp13973-scaffold155-343292 13 42718937 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782084 Affx-122926276 AX-385269162 CTTTTCCATGTGATTCTCATGATATTTCTTTACTT[C/T]TAAATCTCAAATATCATGACATTTTAATCCAACTT Y 2 1 2 1 101000 f 74 goat snp13991-scaffold1552-18110 23 20167247 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405720 Affx-122956527 AX-123276072 TGCCATCTGGGCAAAGAGACTCAGAAGGGAAGCCT[A/C]GAAACACAGACGATGGAGGGGGAGGCCAGCCCAGG M 2 1 2 1 101000 f 74 goat snp14026-scaffold15549-6738 16 79214040 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394702 Affx-122964348 AX-123265057 CAATTTCAGTGCATAAGCAATAAATGAAAATATAG[C/T]GGCCTGATTTATTGCCTTAACTAAAGTTAGATTGA Y 2 1 2 1 101000 r 74 goat snp14027-scaffold1555-4213 6 8790711 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408021 Affx-122954302 AX-123278372 AATACCATTTTAAAAGTGGAAATTAGTATTAATTG[C/T]AGACTTTCTAGCATATATTCTGCCTCTTGAATAGA Y 2 1 2 1 101000 r 74 goat snp14028-scaffold1555-57576 6 8844631 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397453 Affx-122962106 AX-123267808 ATGGTTGGCCAAGACCTACCTGCTACAGTGCCATC[A/G]TCTTTGGAAGAAGTGACAGCAACTGATAAATCTAC R 2 1 2 1 101000 r 74 goat snp14029-scaffold1555-103006 6 8888342 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443042 Affx-122928149 AX-123313379 CTATTTTAAATGTGCTTAATTACACAGTCCCTCCT[C/T]TTAGGGATGGAAAACCTCGAGTCCATGAAAACCAT Y 2 1 2 1 101000 r 74 goat snp14030-scaffold1555-143825 6 8929920 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433076 Affx-122935738 AX-123303417 CAACAAATTTGTAATGTTCAAGGAGAGAAGGTGGA[A/C]AGGTTAGCGAGACAGGTTGTGTCTGACTTTTATAG M 2 1 2 1 101000 f 74 goat snp14031-scaffold1555-192327 6 8980534 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775510 Affx-122943322 AX-385262641 ACAACGAAATTTTCATTATCCGTAGTTGTGTCACC[A/G]TCTGCCTGACTTGCGGGTTTATCCTCTATACAGCG R 2 1 2 1 101000 f 74 goat snp14032-scaffold1555-223175 6 9011534 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399023 Affx-122960927 AX-123269378 ATCTACAGCCATAATAATTTGCCTGCCTTCACTAA[C/T]GGAGTTATTTCTCAGGATCCCTAGGTTTTTGTTTT Y 2 1 2 1 101000 r 74 goat snp14033-scaffold1555-252247 6 9041313 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442016 Affx-122928413 AX-123312353 ATACTTTTAGATAGTGACTCTTTGCTGACCACAGG[C/T]ACTAGATAGACCTCAAACTGGTTGGAACCAAAAGA Y 2 1 2 1 101000 r 74 goat snp14075-scaffold156-2909 21 52077478 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387099 Affx-122970676 AX-123257457 TTTGAAAGTTAATATATGCATAAAGCAAAAACAGA[G/T]TGTGATATAAGAGGAATTCTGAGAGCATAAGAGAA K 2 1 2 1 101000 r 74 goat snp14076-scaffold156-39128 21 52040333 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429786 Affx-122938208 AX-123300127 CCAGTTCTGAGAAATACACTTTCTTTCTGTTTGGC[A/G]TTACTGATTCGTTGAAGCAGTATTGCCGAGGCCCA R 2 1 2 1 101000 r 74 goat snp14077-scaffold156-77464 21 52000410 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453406 Affx-122919896 AX-123323739 TTATGGCCTAATATCAAGCCAAAAGTGCCTTTAGG[C/T]GGTGGTCTAAATATATTTGTTTTTAATTTATAAAT Y 2 1 2 1 303000 r 74 goat snp14139-scaffold1565-22105 5 58284870 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431132 Affx-122936584 AX-123301473 TGGATTCATCCATCTGATTATAAATGTAACAGGAG[A/G]GAAAAATCAGAAGCTTGTTATGATACGGGCACACT R 2 1 2 1 101000 r 74 goat snp14425-scaffold15749-19135 25 1273055 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420045 Affx-122945137 AX-123290393 GCAAACTGCAAGTGTCAGGTATTTCCCCCTTTTCT[A/G]TTCAAAATTTTAATTTTGTAAACGAGGTTTCTCTT R 2 1 2 1 303000 r 74 goat snp14427-scaffold1575-36187 18 60678638 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780189 Affx-122944652 AX-385267286 GAAATCTCCTTGTTATTTCAAACAAGCTTCTCTAC[A/G]TTCTCCTCTGGTCATAGTTTCCACTCTAGATTTCT R 2 1 2 1 103000 f 74 goat snp14802-scaffold1598-5149 NW_017212733.1 2064 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429063 Affx-122938294 AX-123299405 CACCACATAACCCTCCCTCTGGGCTCACAGGAGCT[A/G]TGAGTCTCAAAGACTTCCTCTATGCAGAGTGGAAG R 2 1 2 1 102000 f 74 goat snp14991-scaffold1601-994 NW_017210437.1 24193 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791337 Affx-122960753 AX-385278330 GTTAGGGTCATCCCTGGGAATGGCAGCTGAGCCTA[C/T]AGGATTAGTATCATCAGTTTGATGCACTTCATGGG Y 2 1 2 1 202000 f 74 goat snp14992-scaffold1601-30158 4 6603199 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426274 Affx-122940316 AX-123296620 GACAAAAATTCGAGCACAGGCCTGATGAGTCAGTC[C/T]GGATGTCAGAAAACTTACCCAACACTCTGTCCAAA Y 2 1 2 1 101000 r 74 goat snp15015-scaffold1605-27873 25 34166029 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432582 Affx-122935519 AX-123302923 CCATTCTTACAACACAGAGGTCAGGAGAGCTGCCA[A/G]TGTAGGGTATGGAAGGAAAATGAGAGCTTCCTAAA R 2 1 2 1 101000 r 74 goat snp15017-scaffold1605-136155 25 34276826 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770042 Affx-122924616 AX-385257209 GGTGTGCACCATCGAATTCCTTTCAAATAATCAAC[A/C]CAATGCATAAAAAATGTGTCTCTGAATAATCTGAA M 2 1 2 1 101000 f 74 goat snp15018-scaffold1605-204832 25 34348467 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424567 Affx-122942226 AX-123294913 TCATGATTTATTTATTTATTTATTTTTATTGGCTG[C/T]GCCACAGGGCACAGCCTTGTGAGGTGAGGTTAGTT Y 2 1 2 1 103000 r 74 goat snp15019-scaffold1605-234785 25 34378956 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443333 Affx-122927439 AX-123313670 ACTGAATCATACTGTGTGTAGACTTTCCCTCCTAG[A/C]TTTATTGGAATATAATTGACAAACTAAAGTATATA M 2 1 2 1 103000 f 74 goat snp15020-scaffold1605-274313 25 34418584 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793544 Affx-122951550 AX-385280520 TAAGTTTGTCTCAAGTATTACACCTTTGTAAGTTT[A/C]TAAATGGTTTACATATTCATGGAATTCCCTTCTCA M 2 1 2 1 101000 r 74 goat snp15021-scaffold1605-360097 25 34525983 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426333 Affx-122940273 AX-123296679 AAAGTATTCTCCATCCTTTACAAACTCAAAGTTCA[A/G]CAATGCTGTAAGAAGACAGGAAAGCAGAGCTGATT R 2 1 2 1 201000 f 74 goat snp15022-scaffold1605-419966 25 34586865 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424179 Affx-122942523 AX-123294525 TGTTTTTTTGGCTGTGTCGGGAAGGTTGTGTGGAA[A/G]TAAGCAATTTTTAAAAAGTACGGCATCATATATAA R 2 1 2 1 103000 f 74 goat snp15023-scaffold1605-478399 25 34646660 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388365 Affx-122969336 AX-123258723 CTGTCTTCAAATCGACCTCCTCTTGGACTAAGTAA[A/C]TTTCAACATAAAAAATATGATGCATTCAAAACAGA M 2 1 2 1 101000 f 74 goat snp15024-scaffold1605-522656 25 34691152 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426390 Affx-122940851 AX-123296736 AAAGCATGTCTTAAGAAGAAAATGCCTTCCTTAGA[C/T]ACAATTAAAAGAAAAACAATCTATGGGGTTTCCCT Y 2 1 2 1 303000 f 74 goat snp15025-scaffold1605-568618 25 34739091 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381339 Affx-122974422 AX-123251697 CTCCAATTAAAAAAAAATAAAAAAGCACCAAAATC[G/T]ACATTTCTGAGAAACATTTCCCGCACCAGATGAAC K 2 1 2 1 101000 r 74 goat snp15026-scaffold1605-614235 25 34786677 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389237 Affx-122969042 AX-123259595 AGGAATTGAAGTTACTTAAGAATATTTAAGGCATA[G/T]CTTATCCCTCCAATATGATAATCAGCTGTACATCA K 2 1 2 1 101000 r 74 goat snp15027-scaffold1605-670000 NW_017215104.1 8637 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390858 Affx-122967821 AX-123261215 GTAGAATAACAGAGTGAAATATCAATTGGGCAGGC[A/G]CTTGTCATGCTTCCTTTTTGCATGAAAGATGTTCT R 2 1 2 1 101000 f 74 goat snp15028-scaffold1605-715821 25 34900749 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428991 Affx-122938853 AX-123299333 ATATTTACCTCAGTTTTTCAGTAAACAGGCACAGG[A/G]ACTGTAAGGAAATAACCATTTGCTGATACTGCATT R 2 1 2 1 201000 r 74 goat snp15029-scaffold1605-750024 25 34939665 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384064 Affx-122972869 AX-123254422 CTGTTTCAACCACTTTCTGCTTTTGATTTTTAACC[A/G]TCATTAAAAGTCTGCCATGTTGTTTAGCACTAAAT R 2 1 2 1 101000 r 74 goat snp15030-scaffold1606-10170 6 11521338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381134 Affx-122974567 AX-123251492 AATCATGGCCAACGGCACTGTAACTCATACCTAAA[C/T]GAAGCTTAACTGACGCATGTATTTTGTCAATGAAA Y 2 1 2 1 101000 f 74 goat snp15031-scaffold1606-46207 6 11485760 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440091 Affx-122929719 AX-123310428 TATGGAACACAAAATGTCTCACCCCATCATTTGAA[C/T]AGAGTTATACCCACTTGCATAGTGCCTCAAAATAC Y 2 1 2 1 201000 r 74 goat snp15032-scaffold1606-76319 6 11455084 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414071 Affx-122949760 AX-123284420 TTTCACCCCAGACCTCTTGAATGAATCTGGGAAGG[C/T]GCAGTTCAAAAATCTATACACTGACAACTCAGAAA Y 2 1 2 1 201000 r 74 goat snp15033-scaffold1606-133838 6 11396672 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408783 Affx-122953374 AX-123279134 CAAAGGCCGGGAATTGGCATCAAATGGCGCTGGGC[A/G]AGGGGGCATGACTGCCAAGCTCAGGAACAGCAAGG R 2 1 2 1 201000 f 74 goat snp15072-scaffold16103-2665 25 42026121 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446881 Affx-122925233 AX-123317217 CAGTGAAATCAGCAGTTCTTGATGATTAAATGAAC[G/T]TGGGGCATGGGAAGTGAAAGAGGCAACAGACTTCA K 2 1 2 1 102000 f 74 goat snp1517-scaffold1040-25179 3 111459839 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434710 Affx-122933939 AX-123305051 GGAATTCAACAGTTGTTTGGAGAAATAAAATTCTG[C/T]AAGCTGCTGCTTTTTGTTGTTCAGTTGGTAAGTTG Y 2 1 2 1 303000 r 74 goat snp15260-scaffold1625-7565 18 61158064 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411349 Affx-122952259 AX-123281699 TGAGTACTACCTGTTTCAAGTCTCTGACAAACTCT[A/G]TGTCTCGCCCTGGTTTTTTCTTCCTGTTAGTTCTT R 2 1 2 1 201000 r 74 goat snp15261-scaffold1625-41393 18 61422308 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385214 Affx-122971708 AX-123255572 TTAACTATTTTCTTATAGCATGAGAAACTGGCAGG[C/T]GCATAGATCCTAGTGGAAACATATCCTCAAAGCCT Y 2 1 2 1 101000 r 74 goat snp15385-scaffold1631-4992 4 120659288 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768314 Affx-122932980 AX-385255494 GTAGTTGATAACAGTAGACCTCTGGCAGAAGATGG[C/T]ACAACCTATATTATCTTTCCCTAAAATACATGAGA Y 2 1 2 1 101000 f 74 goat snp15447-scaffold1639-16664 26 35544431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771528 Affx-122960590 AX-385258686 GTGTTTTCTTTTTCGTGCATTTTCATTCACAAACA[A/G]TGCATTTAAGACACTGAAGAAAATGCATTTTATTG R 2 1 2 1 202000 r 74 goat snp15521-scaffold1640-12870 12 13621251 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405131 Affx-122956965 AX-123275483 GAGGTCGTGTGTGTGATCTCTCCCTGGCTTAGAAC[G/T]AAATCATCCAAGAACTGTTTTACCAAGAGAAATGT K 2 1 2 1 201000 f 74 goat snp1561-scaffold1043-6362 18 64329796 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780161 Affx-122948176 AX-385267258 CCCCAAAATGCCGTGAGTGTTAACTGATCAATAAA[A/C]CCATAAGATATGCACAAAATGTCATCAATAAGTAG M 2 1 2 1 202000 r 74 goat snp1564-scaffold1044-47934 21 1134943 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402620 Affx-122958405 AX-123272973 AAGTAACTCATGACAAAAGTCTTTCAGGGTGAGAG[C/T]ATTAAGGTACTGCTTTTACTTTTTAAAATTTTCTG Y 2 1 2 1 101000 f 74 goat snp1565-scaffold1044-81187 21 1101653 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413785 Affx-122949918 AX-123284134 AGATCCCCTATATAAAAATAAATAGGGTATATTTT[A/C]ACACTTATGTGCTGTAATGAAGAGTAATATTGGTA M 2 1 2 1 102000 r 74 goat snp1566-scaffold1044-115638 21 1067001 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775001 Affx-122922794 AX-385262133 TTGAGGAAAGTTAATTATGCTGCTTCAGATACAGT[A/G]CCTTATAAACATCAATTAGACCCACCTTGTCTAAT R 2 1 2 1 101000 f 74 goat snp1567-scaffold1044-161951 21 1019173 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776529 Affx-122972150 AX-385263656 AGAACCATGGTTGTAAAATTGGTGACAATAAAATT[A/C]GGGTAAGAGGCTTGTGGATAGATTACTCTTAGCTG M 2 1 2 1 101000 r 74 goat snp1569-scaffold1044-289141 21 889206 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397887 Affx-122961961 AX-123268242 CTGAGTTATTTTCCTTGCCCACAAATTAGGTAACT[A/G]TCCAAAAAAATAAAAAAACTAAAAACACAAAAATG R 2 1 2 1 101000 f 74 goat snp1570-scaffold1044-372338 21 804288 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766277 Affx-122919292 AX-385253669 AATGTGGTTTCCTGGGAAAGATAAGACACATTAAG[C/T]AAACATTAAGGACTGAGTATACTATGACTTTTAAT Y 2 1 2 1 101000 f 74 goat snp1571-scaffold1044-436472 21 739620 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409644 Affx-122953526 AX-123279995 ACAACATCTTCCTCATGGTTCAGCCCCCTAGATGA[C/T]TGTTTTCAGTTCTGTCCCTAGAAAGAAAATCAGTA Y 2 1 2 1 201000 r 74 goat snp1572-scaffold1044-471264 21 704070 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375424 Affx-122979189 AX-123245783 AAATCCGTGAGAAATTTGAAAACTGAGCCATAGAC[A/G]CAGGACTGGAATCAGTCAGTTTTCATTTCAATCTC R 2 1 2 1 101000 f 74 goat snp1573-scaffold1044-506748 21 668364 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446274 Affx-122925669 AX-123316610 CATGCACCATGTTGGATTTTGTTTTTTGTTTTCTT[A/G]TTTTCTACCATTATGTGGTCGTTTAGGTTCACTCT R 2 1 2 1 201000 r 74 goat snp1574-scaffold1044-542638 21 631263 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417812 Affx-122946810 AX-123288160 CTTGCCTGGATAATTCCATGGACTTCCAAAGAGTC[A/G]GACATGACTGAGCTTTTCTTTTTTCCCCCTCTACC R 2 1 2 1 303000 r 74 goat snp1576-scaffold1044-621896 21 549881 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423327 Affx-122943175 AX-123293673 CTTTTTCTTCTCAAAGTATAGCATCATCAATGTAG[C/T]ATAGCTGAAGAAATCTACACACACGCACACACCCC Y 2 1 2 1 201000 f 74 goat snp1577-scaffold1044-661421 21 510343 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770334 Affx-122928630 AX-385257500 CTCGGATTGACAACATTCTGCATTTCTTGTTCATA[A/G]CTCTTCCATACGGTAGGAAATCAATGAATTTTTGT R 2 1 2 1 101000 f 74 goat snp1578-scaffold1044-704703 21 466055 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765446 Affx-122936858 AX-385252947 AACACATATAGAGGCAAAATAAATGGCAAGAAGAA[C/T]ATAGAACTATGAAGAGTCTAAACAGAATTTCACTG Y 2 1 2 1 103000 f 74 goat snp1579-scaffold1044-733537 21 437185 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788617 Affx-122966621 AX-385275634 TCAGTGTATACACTGTAGCTAAGAGTCAAATACCT[A/G]TGGTACATGTTTGAACTCTTAGTACCTTGTTGAAG R 2 1 2 1 101000 f 74 goat snp1580-scaffold1044-763510 21 407168 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391821 Affx-122967018 AX-123262178 CTGAAGTCGAGTTGCCAGCATAGTTGTGTTCTTAG[C/T]GAGGCCCTTTTCGTTTTTTGCAGATGGCCACCTTC Y 2 1 2 1 101000 r 74 goat snp1581-scaffold1044-793182 21 377235 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436140 Affx-122932638 AX-123306479 CGAGGCTCTTCGGGAGGCTCCAGGGTACTTCTCCA[C/T]GGAAGCAGGGCTCTCCCGGTGAGGCCAAGGCCAGC Y 2 1 2 1 202000 r 74 goat snp15828-scaffold16602-10999 NW_017189661.1 31577 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393765 Affx-122965205 AX-123264120 AAATGAAGCAGTGAGCTTTTCTGGCAGGTGTCATT[A/G]CAATACCCAGCTTTTACAGTGGGAAAATATTATTT R 2 1 2 1 101000 r 74 goat snp1582-scaffold1044-859138 21 310908 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400153 Affx-122960694 AX-123270508 GGTTCCAAAAGATTTGGCATCAACACTTGGCATGA[C/T]GAGAGTGGGATTTATGCCAATTCATATGTAAAACG Y 2 1 2 1 201000 r 74 goat snp15837-scaffold1662-22314 8 45859330 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790550 Affx-122922316 AX-385277553 GAATATCTCAGAAATGGTTCTGCCCTACGAAAGAT[A/G]CATGTGATTGTACTCTGTGAGTTAAATCTCAAGAA R 2 1 2 1 201000 f 74 goat snp15838-scaffold1663-7057 23 23459198 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432302 Affx-122936311 AX-123302643 AATTTACTCAACTGAATTTCTACAGGTAGAAAAGG[C/T]AAAGGTATTCCTTGACTAAAACCAGCAGAAATCCC Y 2 1 2 1 101000 r 74 goat snp15839-scaffold1663-43069 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401380 Affx-122959231 AX-123271733 AGATCCATCTTTGTGGTGGAGTCTGTCCTATGCCT[A/G]TAGGATGTCTAAAGCATCCCTGGCCTCCATGAATC R 2 1 2 1 201000 f 74 goat snp1583-scaffold1044-929641 21 243968 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450512 Affx-122922502 AX-123320846 AGGGTAACCAAAAAAAAAAAAAATGTGAAGATATG[A/C]TAGGATATATAAGTAAGAGAGGATGTGATCCCTGT M 2 1 2 1 103000 r 74 goat snp15840-scaffold1664-41345 NW_017189516.1 22434371 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449891 Affx-122922343 AX-123320226 GAAGCACTGCCCCAAAGTCTACTGTGGACTTGTAC[A/G]TAACCTTAGATTGGGATCTTGAGAGATGAAGTATT R 2 1 2 1 201000 r 74 goat snp15841-scaffold1664-69993 NW_017189516.1 22405749 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440283 Affx-122930230 AX-123310620 CTCCAGGGAGAACATCCCTGGGCAATAATGACATC[A/G]TCCACAAATGAAGGGTTGAGGTCTCTCTGCCAGGC R 2 1 2 1 101000 f 74 goat snp15843-scaffold1665-67356 21 58764110 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425302 Affx-122940951 AX-123295648 GCAACACAGAGAGAATTCCTTCCAGAAGAAAGGCC[A/G]CCAGGTGCTTTCAGCTTACTCAGATCGGCATGGAG R 2 1 2 1 101000 f 74 goat snp1584-scaffold1044-985422 21 187918 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430244 Affx-122937312 AX-123300585 AAGGCTGTCAAGGACCATTTTGGGGCTCAAGAGAG[A/C]AGATGGGCTTTCTCTCCAGACACCGCAGGGGAAAG M 2 1 2 1 101000 f 74 goat snp1585-scaffold1044-1026132 21 147565 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429335 Affx-122938582 AX-123299677 CTCAAGAAGAGCCCAGTTTTTCCCTCCTCACCTCG[A/C]GATGAGGGTCCTTTTCCCTACTTCTTATGGAAAGG M 2 1 2 1 303000 f 74 goat snp1586-scaffold1044-1073136 21 99614 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419614 Affx-122945986 AX-123289962 GGTTATGAGGAAGGAAGCCTGACATACGCAAAGGC[A/G]TATTCTGGCTTCAGGTGTTCCCTCTGGATTTTACT R 2 1 2 1 101000 r 74 goat snp1587-scaffold1044-1106115 21 66849 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409639 Affx-122953529 AX-123279990 CTGTGATGACCGGGGTCCAGATGTCTCCTTGCTGA[C/T]GGTCTGTCCTTTAGAGCCAGCTGTAGAGGTCACAA Y 2 1 2 1 202000 f 74 goat snp15883-scaffold1669-9047 NW_017190616.1 13609 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393183 Affx-122965517 AX-123263540 TTCACTCGAGAGGAACACTGTGGGTCCAGCCACAA[C/T]GAAAGAAGAGCCCCATTTTTCTCTCCTCGTGTCGA Y 2 1 2 1 202000 f 74 goat snp1588-scaffold1044-1157596 21 14692 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790767 Affx-122925635 AX-385277768 ACTATCATAATCTGCTTAACTTCTTAAAAATCTCC[A/G]TGTCCTTTGATCCTATAGTCTTAAAGAATGTATGT R 2 1 2 1 101000 f 74 goat snp15957-scaffold1678-31543 9 44603697 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389542 Affx-122968276 AX-123259900 TTCACAAAGTATGGTCATTAAAATAAAAACTGAGA[C/T]AATAACACAGGACCACATGCCTGAACCAGAAGAGT Y 2 1 2 1 101000 r 74 goat snp15958-scaffold1678-100122 9 44534595 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406357 Affx-122955427 AX-123276709 TGATGTTGATACTGCCCACCTGAGGACTGTCCTAT[A/G]TGAACCTCTGCTATACTGGAAAGCTTTACATTTAC R 2 1 2 1 101000 r 74 goat snp15959-scaffold1678-135347 9 44501689 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782048 Affx-122920782 AX-385269126 TTTACTCCAATGGTGTATCTTAGAGTTCAGAGTAA[C/T]GGGTTGTGATTCAAGTGAATGCCAGTCACTACCAT Y 2 1 2 1 101000 r 74 goat snp15990-scaffold1682-50633 NW_017189516.1 65711239 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436006 Affx-122933494 AX-123306345 AAGACTGAGTATTGGGCTCCCGTGTCCACCATGAA[G/T]CCAACCGGTTTCCCCTCTACATGTATAGTTACCCA K 2 1 2 1 303000 r 74 goat snp15992-scaffold1682-263920 NW_017189516.1 29971822 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782406 Affx-122974151 AX-385269482 CCAAATGTTCACATGATCTAATATTTAATAAATAA[A/C]AGCTAGTTTAAATTTGTTGGTTTAATGAAAACAAG M 2 1 2 1 303000 f 74 goat snp15994-scaffold1682-488077 NW_017189516.1 22318103 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389139 Affx-122968547 AX-123259497 TCTCGAGTTACAACGGGGACCACAGGGAACTGCTC[A/G]CAGGGCTACAGGAATGGCCAGTCTCCATGCGAGTT R 2 1 2 1 102000 f 74 goat snp15995-scaffold1683-88540 27 44641700 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405075 Affx-122957410 AX-123275427 GGTCCTCTTTTAAATAAAAGAAGGTGACCTTCAAG[C/T]CTTCCTTTCAGTCCTCCATTCCTGGGGTGGTGTCC Y 2 1 2 1 101000 f 74 goat snp15996-scaffold1683-141593 27 44588263 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403313 Affx-122957834 AX-123273666 AAAATGTTAGCAGGCCTCTTGGCCAGAAGATGATG[C/T]AAATCACCTGAGAACTGTGTATATCGGAAGGAATG Y 2 1 2 1 303000 r 74 goat snp15997-scaffold1683-189321 27 44539665 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779889 Affx-122966999 AX-385266988 CATATTTCACTGTGAACCTAAGTGTACTCTCATGT[A/G]TTTCTCATAACTTTGTCTTCCGCACTCAATTATCA R 2 1 2 1 101000 f 74 goat snp16107-scaffold1696-48457 23 23226747 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427374 Affx-122940093 AX-123297717 ACCCAGCAAATACTTAACCAAAACAAGACTGAACA[A/C]GCTCAATTCTGAAAGGATAAAGAAAACATAAAAGT M 2 1 2 1 101000 f 74 goat snp16108-scaffold1696-80264 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404192 Affx-122957678 AX-123274544 CAATCTTCCCCTAAAACTACTGGCTTCTTTTAACT[A/G]CTTTTCTCTTCTTTTTGTTTCTCAGATGAGATTGC R 2 1 2 1 103000 f 74 goat snp16109-scaffold1696-114951 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430751 Affx-122937499 AX-123301092 GTTAGAATTCTCAGCCATGACCCGTCTGCCTTGGG[C/T]GGCCCTGCAAAGCCTGGCCTGTAGCTTTTGAGTTA Y 2 1 2 1 202000 r 74 goat snp16181-scaffold1700-53962 NW_017189717.1 7866 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439286 Affx-122930974 AX-123309623 CCTGACGCAGTTCGAGCTGTGCCCGCGAGACACCT[A/C]CATGCTGCTGCTCTGGGTGCAGAACCTCTACCCCA M 2 1 2 1 303000 f 74 goat snp16272-scaffold17131-4297 21 67114024 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447295 Affx-122924921 AX-123317631 AGGCCTCATTACTTGACGCTAACTGCTCCTTGTCC[A/G]CCTGCCCCACATAATCATCTTAGGTTTAGTGTAGC R 2 1 2 1 101000 f 74 goat snp16301-scaffold1717-29128 18 61358258 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385877 Affx-122971600 AX-123256235 AACCTAAAGAGCTCTTTAACCAATTTCTCCCTAAG[C/T]AGTTATTTTTTCCCCTTTGATGGCATATCACACTG Y 2 1 2 1 101000 f 74 goat snp16353-scaffold17213-6456 1 26970434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776732 Affx-122940299 AX-385263857 TGGATTACTAGCACTTTGTTAATGAAATATCACTA[C/T]TTAAATACAGTAATTTCATTAAACAATTGTCATTA Y 2 1 2 1 201000 r 74 goat snp16354-scaffold1724-8013 5 4937988 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420111 Affx-122945087 AX-123290459 GGGGCGAGTCTCCGTCTGTGGGTTGAGGGTCAGCC[A/G]TCTGTCTGCGTGTGTTTCCTCTTCGCCGTCTCCCC R 2 1 2 1 101000 r 74 goat snp16370-scaffold17264-2630 16 78626749 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392793 Affx-122965976 AX-123263150 AACCAAAGGTGGGCTTAAAAAGTGTTGCCACCTTG[C/T]GGATATTTTCTGTAAATAAAATTTGATCACAGGTT Y 2 1 2 1 102000 f 74 goat snp16426-scaffold1731-3753 NW_017189605.1 48530 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774622 Affx-122965839 AX-385261756 CTCATGTCCTAAGGATATGTATGGTAGTTGGGACA[C/T]AGTCCTTGGTCTTTCTTCATTGACCCTTCTAGCAG Y 2 1 2 1 101000 r 74 goat snp16450-scaffold1733-13456 14 84255487 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795722 Affx-122972187 AX-385282675 TAAAGGAGGCAATGGAAGATGTCAGCTTCCAAAGA[C/T]GGTAGAGATACATTGCTCAAAGACATGCCTGTGGA Y 2 1 2 1 101000 f 74 goat snp16451-scaffold1733-48385 14 84289787 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431130 Affx-122936586 AX-123301471 CAATACAACTCGATCCATCATTAGTAATTACTATA[C/T]GGCTTTGTTATTGTTCAGTTGCTAAGACATGTCTG Y 2 1 2 1 202000 f 74 goat snp16452-scaffold1733-80786 14 84316572 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378224 Affx-122976917 AX-123248583 AATAAATCTGGTTGTTATTATTAATGAAAATTAAC[A/C]CAGTGAACCTAAGTCATTACACTCATAAATGTATA M 2 1 2 1 101000 r 74 goat snp16453-scaffold1733-110135 14 84346158 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778376 Affx-122960584 AX-385265491 TCTTCATCTCTGAATAGCTCTGAGCTTTCTATCAA[C/T]GAAGTCAAAATAGAAACCTGAGAATATAGTGTAGC Y 2 1 2 1 101000 f 74 goat snp16454-scaffold1733-169128 14 84404364 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399540 Affx-122961142 AX-123269895 TCCTGGCATCAGAGGGTCTGGATGCCTTTTCTCAG[C/T]CCCCTCCTTCTAGCTCCAGGCCCAAGGTTACTTGA Y 2 1 2 1 102000 f 74 goat snp16556-scaffold1740-19845 15 28006871 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438744 Affx-122930827 AX-123309081 ACATATGCATATTCCCACAGTGTGCCGAGTGTGAC[A/G]TAAAGGCCAGCAGTGAGACGTTAGGACACAGAGGA R 2 1 2 1 101000 f 74 goat snp16557-scaffold1746-7851 21 68977195 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450810 Affx-122921804 AX-123321144 GGCTATTGGGTCATAGGGTTAAAACAGGATTCTGT[A/G]TATAATGCCTTTGAGTCCTCCTTCTCAACTCCTGG R 2 1 2 1 101000 r 74 goat snp16754-scaffold1755-16483 15 34806445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448941 Affx-122923147 AX-123319276 TGCCACAGTTCCTTCATTTCTTTGTGATTTCATAC[A/G]CTCAAAAGACCCAATAGGAATTGTTGTCTAAAAAA R 2 1 2 1 201000 r 74 goat snp16755-scaffold1755-49861 15 34840513 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800892 Affx-122920465 AX-385287807 GACCCTTAACAGAGTTGGACATCAATGATATAATC[A/G]GTATTTATGACTTTTCTAACCCTTCAGTATACCAC R 2 1 2 1 101000 f 74 goat snp16756-scaffold1755-93078 15 34884429 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429151 Affx-122937988 AX-123299493 AGGCATATTTCAAAGCTTGAAATAATGGGTGCAAA[C/T]ACAAAAAACCTCGAATAGCCAAAGCAATCTTGAGA Y 2 1 2 1 101000 f 74 goat snp16757-scaffold1755-122518 15 34913909 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770346 Affx-122922640 AX-385257512 TCAATAAGCATTATTAAATGGGGAGATGAACTAAT[A/G]CATGAATAAAAGAAGAAATGTTAACAAATAAATCA R 2 1 2 1 201000 r 74 goat snp16758-scaffold1755-180781 15 34972358 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453370 Affx-122919936 AX-123323703 TCTCTTACTTTGAAATGGTACCCCTCTGTGCAAAC[A/G]CTTTACCCACAGTATTCTGTCTGAATTCTCTGCAC R 2 1 2 1 202000 f 74 goat snp16759-scaffold1756-421 10 78187308 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800909 Affx-122975370 AX-385287824 GTGCAATGTTCACTTTGTTTTAGACCATAAATAAG[C/T]ACATTAATATTAGGAAAACCAGAAAACAGCCACAA Y 2 1 2 1 101000 r 74 goat snp16927-scaffold1769-76854 7 99947301 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380961 Affx-122974992 AX-123251319 AGCCCCCAACATCTCTCCAGGTTTCTTATGCAACC[A/G]TCTTAGTTGTTTTTTAGGAGTCAAGTGCTTCTATT R 2 1 2 1 201000 r 74 goat snp16928-scaffold1769-117824 7 99996111 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406618 Affx-122955835 AX-123276970 CTTGGGTGAATAGCTGTCCCTCCCTGGGTCTCTTT[C/T]CTCCTCTGTAGGATGGAGAGGCCAGGCCTCTAAAT Y 2 1 2 1 102000 r 74 goat snp16929-scaffold17692-3426 1 40979443 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795849 Affx-122941385 AX-385282802 TGGGACTGAGACAGCCCTTGGGAACTACTGCTGGC[A/G]CTGATACTACCTTCCAGTTCAATCCTTTTCATACG R 2 1 2 1 202000 f 74 goat snp16997-scaffold1773-19440 NW_017212022.1 6253 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405699 Affx-122956542 AX-123276051 AAGGTCACTACCGTGAATCTGTGTGTGTGTTCAGA[C/T]GCTCAGTCAAGTCCCACTTTTTTGTGATCCAACAG Y 2 1 2 1 103000 f 74 goat snp17072-scaffold1780-10430 NW_017189517.1 33412913 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433270 Affx-122935225 AX-123303611 CATACATATAGGGAAGAAAATGTGGGGAGGTATAG[A/G]GAGATTTCAGCTATTTACAAGCCAAGGAAAGTGGC R 2 1 2 1 103000 r 74 goat snp17073-scaffold1781-5023 NW_017189517.1 37716736 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791143 Affx-122946766 AX-385278138 CACAACATTGACAGTGGTGATAAAGGAGTGAAAGA[C/T]GGTAGTAATATTGTTGAATTGGTGTAAGAGAAAGA Y 2 1 2 1 201000 r 74 goat snp17074-scaffold1781-47400 NW_017195224.1 4621 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430284 Affx-122937286 AX-123300625 TCCGATCAGCTCGCATTGTGGCAGTAACGGCACAC[G/T]CAATCGAAAGAGGTCATGTGTGTGAAGACCGTGTG K 2 1 2 1 201000 f 74 goat snp17093-scaffold17858-20719 16 78112479 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445105 Affx-122926194 AX-123315442 CAAAGAAGCAAAGCATTTATTTAACTTCACTGTAG[A/C]TTTTTCAGGGGAAAAACACACACAGATCACAATGC M 2 1 2 1 103000 f 74 goat snp17103-scaffold1788-26861 1 13663155 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797094 Affx-122966627 AX-385284034 GTCCTCTGGTACAGAAATTTCCTAAGCAAGTGCCT[A/G]TTAACTTATTAAGATACCTGTGTATATTCACAGAC R 2 1 2 1 101000 f 74 goat snp17104-scaffold1788-77512 1 13714329 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795279 Affx-122924664 AX-385282237 ACAGTAAACCTTCATTCTTGCAGACCCTAAATCAT[G/T]ATAAGTGCTCCATACAATTATTGCTCATTCCTTCC K 2 1 2 1 101000 r 74 goat snp17184-scaffold1793-10388 NW_017189516.1 64694187 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785312 Affx-122929259 AX-385272357 CATTGGTTGAATGAATAGATTATATTGATATTGAT[A/C]GATTTTCAAACACAGAAAGGCCTCATCATTCATCC M 2 1 2 1 101000 r 74 goat snp17185-scaffold1793-39344 NW_017189516.1 64722528 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798274 Affx-122946658 AX-385285209 AGATAGTAAAACGCTGGTTGGAGGTTGTACAAAAG[A/G]AAACGAATGAAACGAACACCAAGGGAAGAAAAGTC R 2 1 2 1 201000 r 74 goat snp17197-scaffold1795-4692 NW_017216965.1 2584 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410722 Affx-122952716 AX-123281072 GAAAATAGTTTTCACAGCATTGCAAATTGTGTGTC[C/T]GTGTGTGTATTAGCCAGTCAGTCCTGTCCAACTCT Y 2 1 2 1 303000 r 74 goat snp17198-scaffold1795-45173 9 74335093 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445298 Affx-122925447 AX-123315635 GTTCCCCCAAAGGGTATGAGGTCTGGGGCTCCAGG[C/T]ACCGGCCCACCAAGCCCTCTCTGGCCTGGACGCAG Y 2 1 2 1 303000 f 74 goat snp17222-scaffold17973-672 5 113877773 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424732 Affx-122941667 AX-123295078 ATGACTGTTGTTTTCCTTTTTCTCATTTTTTATAT[A/G]TGGTTTGATGAAAAGTTTATTTCAGACCTAAGGCA R 2 1 2 1 303000 r 74 goat snp17524-scaffold1812-13432 12 25646820 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447354 Affx-122924873 AX-123317690 TGACATGGCAAAGAGGAGTTTTAGAATTAATCCAG[C/T]GATGACTGAGAAAATAGATTCTATTGCTATTTACA Y 2 1 2 1 101000 f 74 goat snp17525-scaffold1812-77110 12 25710775 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802099 Affx-122974090 AX-385289003 CTTTATTTTCATTAATCACAGGGACCGATTTTGAC[A/G]TTTTTACAGACCAATTTCATACGGAATTCATCCAA R 2 1 2 1 101000 f 74 goat snp17526-scaffold1812-117243 12 25751800 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768910 Affx-122944545 AX-385256087 CATTTAAATTAGCTCAAGTGTGATATTTAGATTTA[C/T]GTGAGTTTATGCATTTTTGTTTGTGCATATACAAA Y 2 1 2 1 101000 r 74 goat snp17527-scaffold1812-153089 12 25787379 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447204 Affx-122924989 AX-123317540 TTCCGCCTGGAGCCTGAGGGACCAAGTCAGAGATC[C/T]GACTCATCAGCCAGCGACTGAGGAGGGAGTGCAGG Y 2 1 2 1 102000 f 74 goat snp17557-scaffold1816-12146 7 92698716 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385521 Affx-122971252 AX-123255879 ACCCTTTACCATTGAGCTACCAAGGAAGCTTCTAT[A/G]TTTTCTTAACGTTTCCTCAGCATCTGCAGTCTCTG R 2 1 2 1 101000 r 74 goat snp17558-scaffold1816-56836 7 93939742 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378965 Affx-122976411 AX-123249324 CATGAGCTGGATCTCCTCTGCTATAGGCTGGGTAC[C/T]GATGTCCTTGAGTGTACCAGCTGAAGACTGGGAGC Y 2 1 2 1 202000 f 74 goat snp17559-scaffold1817-8578 13 37145727 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441073 Affx-122928909 AX-123311410 GTGTCCTTGTGTTTCCCAACTTCCAGAGGCTGCCC[A/G]CTTGCCCTGGCTTGTGGCCCCTTCCTCCTCCTGCG R 2 1 2 1 303000 f 74 goat snp17560-scaffold1819-10957 19 18924313 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434760 Affx-122933900 AX-123305101 GTACTAATTGGTCTATGATTTCTAAATGATATTCT[A/G]TCTCATGAAACTTGAGCTAAGTATTTTGTTATTAA R 2 1 2 1 101000 r 74 goat snp17579-scaffold1821-419 15 9891152 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782545 Affx-122953457 AX-385269620 GCTGCTATGAACTGAGAGTGTTGATTAATATGTCT[A/G]TTTTCAATCAGTTCAGTAAATCAGTATCTTTTCCT R 2 1 2 1 201000 r 74 goat snp17580-scaffold1821-51648 15 9942075 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397140 Affx-122962670 AX-123267495 CGGTAAACCGTAGCTTTAATTCACATGTCCCTATT[C/T]ACTGTGGGATTTTGTGGTGTGTGTGTTTTCAATTA Y 2 1 2 1 101000 f 74 goat snp17581-scaffold1821-99181 15 9989369 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320765637 Affx-122949457 AX-385253107 GGAAGATGGAGATTTAGCTGTCTTTGCCCACTGCC[A/G]CCTCATATGTACACGCACACCTCATCTCTTCACCC R 2 1 2 1 101000 f 74 goat snp17582-scaffold1821-130444 15 10020650 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390964 Affx-122967051 AX-123261321 GAAACCACAAACCAGGTGAATTTAACCAAAATGGT[A/C]GTACCTCTAATCTGGTAAATCTCCTTGAACTGTGA M 2 1 2 1 101000 f 74 goat snp17591-scaffold1825-76237 3 17794330 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451535 Affx-122921092 AX-123321868 CTTTAGAAAAAGATTAAATAATTACAGATAAAATT[A/G]AAGTGCTCTTTGACTATTTCCACTTCTCTGAATCA R 2 1 2 1 303000 f 74 goat snp17592-scaffold1825-107891 3 17826441 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438465 Affx-122931239 AX-123308803 GACTGAAGAGGCCAATGGGTAGTTTCAGACCTCCA[C/T]GGGCACCATTGTTTACTAGACACGTATTAAAATGT Y 2 1 2 1 101000 r 74 goat snp17593-scaffold1825-142414 3 17861936 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777532 Affx-122936081 AX-385264651 GACTAAATGTACCTATTAATGCCCTGGTAACACCA[C/T]GCATCTCTCCAGTTTAGTACTTCTAACAATTGGGA Y 2 1 2 1 101000 f 74 goat snp17594-scaffold1825-174652 3 17895202 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393425 Affx-122965872 AX-123263781 CGTTTTAGAACTCCCGCTAGGAGATTAAAGACTGG[A/G]GGGAATTTCTGTAGTGGTGGCCTTCCTAGGCTGAA R 2 1 2 1 101000 f 74 goat snp17595-scaffold1826-12190 28 42514536 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448726 Affx-122923840 AX-123319062 GTTTAACATGGCACACACTTGACAGATTTTGTGAC[A/G]CAGAGGCAAGATATAAAATTGTTCATAGACAACAG R 2 1 2 1 201000 r 74 goat snp17596-scaffold1827-17666 NW_017196442.1 8463 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445088 Affx-122926206 AX-123315425 CCTGCCTCCTGAATTTACTGAGTGGGCGACAAGTC[A/G]CCCCCGGACCGGAAGAACACCTTTCCCAACCGAGT R 2 1 2 1 201000 f 74 goat snp17683-scaffold1832-5197 18 60063115 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387710 Affx-122969804 AX-123258068 AAGAGTTAGATATGGGGAAATAGTTGTGAAGATGA[C/T]CTGTAAAATCCAATTTTACCTGTTAGTGATTAAGC Y 2 1 2 1 101000 f 74 goat snp17706-scaffold1839-14749 NW_017189661.1 5520 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449618 Affx-122923198 AX-123319953 GAATAACTATAATGACTATCTTTGAGAGAATTGCA[C/T]TATCAAAGAACCACCAGCCCATGGTGGTGGTTTTC Y 2 1 2 1 201000 f 74 goat snp17746-scaffold1841-4055 21 51155995 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413563 Affx-122950594 AX-123283912 AGAAAGAAGCAACAGCAACCATCATAGAGAATTCT[A/G]TAAAATGGAGCCCCAATACACGTTTAAAAGAACTT R 2 1 2 1 101000 r 74 goat snp17747-scaffold1841-49169 21 51237332 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390432 Affx-122967635 AX-123260789 CTCATTTTCTGGATACGACCAAATGAGGGTTAGAA[C/T]GGAAGAGGAGGAAGAAAAGTTAATCTCTGGGGAAC Y 2 1 2 1 101000 f 74 goat snp17748-scaffold1841-112299 21 51297623 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436559 Affx-122932910 AX-123306897 AGAGGGCAAAATTTCAAACATGTAGCAAAGCCACA[C/T]GCATACACACATGTGTATAATCCTGTGAGTCTGGC Y 2 1 2 1 101000 f 74 goat snp17749-scaffold1841-147000 21 51332237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400936 Affx-122959713 AX-123271289 ATTCACAGAGAGGAAGTTTAATTTTTTGATAGGAG[A/G]TATAGTTAATATTTCCAAAACAATTCTTAAGTGAA R 2 1 2 1 101000 f 74 goat snp17750-scaffold1841-182130 21 51367413 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407535 Affx-122954696 AX-123277886 CTTTTTTAAAAGAGATGTTCAGTGTAATTGTGCCC[A/G]TTGACACAATTTGATGGGAAAATTTGATGGAAGAA R 2 1 2 1 101000 f 74 goat snp17751-scaffold1841-222829 21 51408216 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375501 Affx-122979130 AX-123245860 ATATGATAGTCCTTAAATAAGAGTATAACTAAAAA[C/T]GACAACAAAGCATTGAGTTTAGTGACAGAAGAAAA Y 2 1 2 1 201000 f 74 goat snp17752-scaffold1841-254607 21 51439292 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416019 Affx-122948377 AX-123286368 TCAGCCTGAGATAGAAGCTGAGTCTGCTGACACCA[C/T]GCAGAGACGCAGGAAGATGGAAAGTTTGTGTCGTC Y 2 1 2 1 102000 r 74 goat snp17779-scaffold1847-9682 21 68994713 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389369 Affx-122968454 AX-123259727 CCTGAATTAACTTTTTCCAGAGAGTGTCAGAAAAG[C/T]AGAAAAGTACAATAAGGCAGGCAGATTCTTATTTT Y 2 1 2 1 303000 f 74 goat snp17780-scaffold1847-60114 21 69045400 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407694 Affx-122954578 AX-123278045 TCTACTTACATTAAATCTGGTCTAAAGTGGTGTAA[G/T]ATTGCACAAAAAGATAAACCATTCCTCCATGATGT K 2 1 2 1 101000 r 74 goat snp18103-scaffold185-12751132 11 61118657 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397674 Affx-122962591 AX-123268029 TTTAGCAAAGCTGAAAACCAGAGATTTTCTGCTTC[A/G]ATTTGCAGTATTTTGCTGATTTTCTTGGATAGGAA R 2 1 2 1 101000 r 74 goat snp1823-scaffold1051-630 4 15028925 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419366 Affx-122945629 AX-123289714 ACAGATGGCCTGTAAAACAAAAGTCTCCACCCTCC[A/G]TCATCTCTACTCCAGGAACAGTTCTAGCTTCTCCT R 2 1 2 1 101000 r 74 goat snp1824-scaffold1051-31157 4 14997898 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421411 Affx-122943972 AX-123291758 CTCTGTACTGCTCTTTGAGACTGTGCCTGCTCAGC[A/G]CTGCTCTTCTATACTAAGCAATAAGTTCAGCTTTC R 2 1 2 1 201000 r 74 goat snp1825-scaffold1051-61141 4 14967544 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446151 Affx-122925758 AX-123316487 CAGAAATATTTTTTTATTTTGGTTTTAGAAACTAC[A/G]CTTTGGAGGATTAGGAAAAGGAAAGTAGTAGGCAC R 2 1 2 1 101000 r 74 goat snp1826-scaffold1051-111599 4 14916068 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440503 Affx-122929357 AX-123310840 GTGTGACTTCATGGGAATGTACAGGCTAGCTCAGG[A/C]TGGGCAGAGCAGAAGACAAGAAGTGAGCTAAGGGC M 2 1 2 1 202000 r 74 goat snp18272-scaffold1854-10423 NW_017189517.1 33231342 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451489 Affx-122921127 AX-123321822 ACTTTTGTTAGCAGACTAATGTCTCTGTCTTTTAA[C/T]ATGCTGTCTAGGTTTGTCTAGTACTGCCCCACTCC Y 2 1 2 1 303000 f 74 goat snp1827-scaffold1051-170702 4 14856834 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417136 Affx-122947360 AX-123287484 GGATGTGGGTTGCTGAGATCACAGTCTCAATGTAC[A/G]CTCCTCAGACTCCACGGACACTTTAGTGTATTTGT R 2 1 2 1 101000 r 74 goat snp18281-scaffold1856-25548 NW_017189516.1 20653088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772327 Affx-122967474 AX-385259481 AGAACCATGCAATTATCAGCAATTTGGAAAACACG[C/T]ATGTGAAAGATACTAAGTTGATTACATGGGAAGAA Y 2 1 2 1 101000 f 74 goat snp18282-scaffold1856-55069 NW_017189706.1 16212 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795480 Affx-122949720 AX-385282435 TTACTATAGAGGTGTAGCAATTATTCCCTTCTTAG[C/T]AGAAATGTCTGATCATACAGTCTTTTACCTCCACA Y 2 1 2 1 101000 r 74 goat snp1828-scaffold1051-213638 4 14776934 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771478 Affx-122932322 AX-385258636 CTTAACTGTTAGAGCAAGGAAGGCTACTCTAGTTT[A/G]TCCTTATCACTTGTGGTCCTCAACATGCCCCCCAA R 2 1 2 1 101000 f 74 goat snp1829-scaffold1051-257942 4 14770876 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436312 Affx-122933262 AX-123306651 TCACCACCACCGCCTGTGCTGCCACCACAACCATC[A/G]CAGGGGTTCAGTTCAGTTCAGTTGCTCAGTTGTGT R 2 1 2 1 201000 f 74 goat snp18376-scaffold1860-8053 1 136213555 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796077 Affx-122925513 AX-385283029 TGACTAAATTACCACCAGCCCAATTTTACAGTTGG[A/G]GAAACCTAGGTACAAAGATGTTAGATTAACTTGCT R 2 1 2 1 201000 r 74 goat snp18377-scaffold1860-39554 1 136181524 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427571 Affx-122939480 AX-123297914 TTTCTCAAGCTTTCCTTCCTTTCTCTTATCCCCTT[A/G]CTACTCTTTCTTTACTGTTTCCGTCTTTGTCTCAC R 2 1 2 1 103000 r 74 goat snp18404-scaffold1862-18803 23 23252192 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377336 Affx-122977669 AX-123247695 TTCCACATGCAGTTTCCTTACCCTGGTTGACAGAG[C/T]CTCCTCACAAGGGCCAGGTCACCAGGTCATGGGGA Y 2 1 2 1 103000 f 74 goat snp18427-scaffold1865-21743 18 60055879 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444205 Affx-122927254 AX-123314542 ATTAAGAAAATATTATATTATATTTAATATCCCAT[A/G]TTTTACAGTGAAACATTATCTCAAACTTGAGAATT R 2 1 2 1 103000 r 74 goat snp18428-scaffold1867-5965 1 11460928 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412145 Affx-122951088 AX-123282495 AGGACAAACGGATACTCATTGAGCTTGAAGCAGTG[A/C]ACCATATTCCTCCACAAGATAATAAGCTCCACACA M 2 1 2 1 101000 f 74 goat snp18429-scaffold1867-36157 1 11491325 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771400 Affx-122924896 AX-385258558 ATATTTTACTATTAAAAAACTAACTTCTTTACATT[A/C]TACTTTTCCTAAGGTAGCAATGTAATGAACATATA M 2 1 2 1 201000 f 74 goat snp18430-scaffold1867-78532 1 11534334 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790938 Affx-122976197 AX-385277935 ATGTCTGTCTTATTATATTACCCATTTTGCATGCT[A/G]TCTGCTTTATCCACTGGAGCTTTTAGTATTCTAAT R 2 1 2 1 101000 r 74 goat snp18431-scaffold1867-116290 1 11571985 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418390 Affx-122946557 AX-123288738 TTACCCGCCCCCGGGAGTTCTGCCTGAGAGCGACC[A/G]CCCAATAAAAGGCCCTGATCAACGGTCCATAGGGG R 2 1 2 1 303000 f 74 goat snp18658-scaffold1885-33806 3 21564616 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797685 Affx-122926660 AX-385284624 GGAGTTGTGTGTCCAATATATGGCTCAAACCACTC[A/G]CACCCAGGGCATATCTCCAACCGTGTAATCTCCCT R 2 1 2 1 102000 r 74 goat snp18681-scaffold1888-11742 NW_017216379.1 4833 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412953 Affx-122951050 AX-123283302 AACTGGAGTTGGTAACAGTGTCTATAATGTTGTAC[A/G]TGGGATAATGTAGGCATTGTCTCAAAGCAGAAATG R 2 1 2 1 101000 f 74 goat snp18715-scaffold1892-30385 4 6869291 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377884 Affx-122977257 AX-123248243 TTTCATAAAATTCCTTGGTCTGGAAAAAACCCTCC[A/G]TACAGCCATACTTGAAGTCCCGCTTTCTGCCACGT R 2 1 2 1 202000 r 74 goat snp18719-scaffold1894-33682 NW_017212532.1 5558 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402966 Affx-122958160 AX-123273319 GCAATTACACCAGATGGGGAATAAGGGGTATGAAA[C/T]ATGATAAGAGAAATAGGTTGAGATGCATGTAAGTA Y 2 1 2 1 303000 r 74 goat snp18734-scaffold1896-5798 6 79096133 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436581 Affx-122932894 AX-123306919 TAGCTGCAAGAGAGAGTCATGCTGGTACAAGCCAA[C/T]GTCTCTGCCCTTCGTGCTCCTTCCTGATGCCTTCC Y 2 1 2 1 101000 f 74 goat snp18735-scaffold1896-38667 14 84865104 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786815 Affx-122972116 AX-385273845 TTAAAAGCTAGTGCCTCCATGGGAAGAAGCCCACT[A/G]CATTTCCAGTCTGCCCAAACATGGGCAATCTACAA R 2 1 2 1 102000 f 74 goat snp18736-scaffold1896-86172 14 84817567 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417389 Affx-122947695 AX-123287737 GCAGGACTGACACATTCACTGGGCTGCAGGCAACC[G/T]CAGGTTACTGCTAGCTGCGGTAAAAGCCACTGGTG K 2 1 2 1 101000 r 74 goat snp18737-scaffold1896-119824 14 84784346 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453014 Affx-122920102 AX-123323347 AGCTTTATTGGGACTTTTGCTGCAGTAAGGAGAGA[C/T]AGAAAGAGAAGTGTGTGCCCTTGCTCCTCCCAAAA Y 2 1 2 1 101000 f 74 goat snp18739-scaffold1898-7035 NW_017190029.1 91044 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382380 Affx-122973852 AX-123252738 TGTCTATGTCTTAAAAAAATATTTTGATAGAAATT[A/G]CTATCAACCTATTGACCAATTCTACCCACTTTCAA R 2 1 2 1 103000 r 74 goat snp18948-scaffold1909-55356 2 124173297 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382272 Affx-122973933 AX-123252630 GAATATATAGGGCACTTTCTGGGAGAAAATATTTG[C/T]AAAATATATATCTAAGCAAATACAGGTATTAGTTC Y 2 1 2 1 303000 r 74 goat snp18949-scaffold1909-88165 2 124207094 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445555 Affx-122925151 AX-123315892 GAAATTTAGGAAAATAAATTATGTCCTTTCTAGAG[A/G]CAAATTAGTCAAATATCAAAAGTTTTATTTACTTC R 2 1 2 1 303000 r 74 goat snp18950-scaffold1909-122280 2 124241388 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381760 Affx-122974312 AX-123252118 CAGATTCAATGTGGTGTGCCTACTGCTCATTCTCA[C/T]GTCCAGTCTTTGCTCTTCAATGCTCCAGGATTCCA Y 2 1 2 1 101000 f 74 goat snp18951-scaffold1909-154539 2 124274340 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426671 Affx-122939921 AX-123297017 ACCAACACATTAAAGTTGAATCAATTATCTTCCAG[C/T]AAGAAAAAAATCTCAAAATAGAAAACAGATCATAT Y 2 1 2 1 103000 f 74 goat snp18952-scaffold1909-183749 2 124303823 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427715 Affx-122939279 AX-123298058 ATTGCTGTAAGGATTAAGAATGGTATTAATTCTTC[A/C]GACCAAACACACAAACAAGGTCTTTTATAAAATAT M 2 1 2 1 101000 f 74 goat snp18953-scaffold1909-244734 2 124366417 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797138 Affx-122974647 AX-385284078 GTTAGTGAACTTTAAGTCAAATTGGCTTGGGCTAA[C/T]CAAATACATTGTTCTTATAACTAAAAAGACACAAT Y 2 1 2 1 101000 f 74 goat snp18954-scaffold1909-280129 2 124402228 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773161 Affx-122920543 AX-385260304 GATGCTTTATATAAACTAATTAATTTTCTACTAAA[C/T]ACTGGCCTAATTTGTCAAAAGATTCTTCTAGTATC Y 2 1 2 1 202000 f 74 goat snp18955-scaffold1909-332100 2 124456523 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789914 Affx-122946862 AX-385276920 GTTAACATCCAGATCCTTGTCTAACTAGAAAAACT[A/C]TCCCATAGCTTCTGGGCCTTCTTTGTTGGACAGAG M 2 1 2 1 101000 r 74 goat snp19056-scaffold1913-6125 NW_017189517.1 31742954 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375689 Affx-122978657 AX-123246048 TTCCCTACGCATTGGCCCTGCTTCCCTCTTTCAAC[A/G]GTTGATATCTAGAGTATTCTGCAGGGGAGAGGCTC R 2 1 2 1 101000 r 74 goat snp19061-scaffold1917-56986 4 24479266 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428136 Affx-122939058 AX-123298479 AGGCAGCTCTCAGAAGAGGGAGTGAGCTGGGCAAA[C/T]GCAAGTGTGTTCATGACGAGCAGTGAGCTGAGTAC Y 2 1 2 1 101000 r 74 goat snp19064-scaffold1917-176452 5 9371147 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421047 Affx-122944523 AX-123291394 TCGATTGGGGGCATGCACGTGCGATTTCCTCCCGA[G/T]CTGTAGCAGCAGTGTCATGCTTCCTTTCGCGTGGA K 2 1 2 1 303000 f 74 goat snp19209-scaffold1932-14004 NW_017190571.1 15951 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785615 Affx-122937192 AX-385272658 ATTGCAAAGGTCAAATTTTCAATGCTAAACGGTTA[C/T]ATAAATTCTTGTCCCTGTTTGTACATTAAAACATA Y 2 1 2 1 101000 f 74 goat snp19268-scaffold1942-20778 14 86223277 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775422 Affx-122932872 AX-385262553 AGAAAGATAAATGGTGGAAAGGTAGATAAATAGAT[A/G]GATATGATAGGCAAGTAGGTAGGTGGGCAGATAGA R 2 1 2 1 101000 r 74 goat snp19269-scaffold1942-62249 14 86181986 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410006 Affx-122953265 AX-123280356 TGCATCAGGGGTGAGAGAGAATAAATAACTGTTTT[A/G]ATTGCCTGCTCCCTGAGGTAGGAAGGACAATCTGG R 2 1 2 1 201000 r 74 goat snp19270-scaffold1942-123213 14 86120714 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783177 Affx-122964026 AX-385270244 TTAAAAAGAGTTGATTCTGCAAATTTCTCTCCTCC[A/G]TATTCCCTTTCATGTTTCAGCCACTAGTTTATTTA R 2 1 2 1 101000 r 74 goat snp19271-scaffold1942-168876 14 86075331 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451760 Affx-122921519 AX-123322093 CTCAGTAGACCTAACCATTTTTTCTTTGCACCTGA[C/T]GGGTGTTTTCTCAATTTTAGGGGCTATTAACTTCA Y 2 1 2 1 101000 f 74 goat snp19272-scaffold1942-205646 14 86038139 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422605 Affx-122943729 AX-123292951 GGAAAAAATTCAACTGAAAGCCAGGGCCTTACGAT[C/T]GGAATCTACCTCGGTGTCCACGGGGCAGAGCGCGC Y 2 1 2 1 101000 f 74 goat snp19274-scaffold19420-140 20 71144009 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442682 Affx-122927888 AX-123313019 TCACACACACCCCCAGTGCACGCACATACACACAT[A/G]CATCCATGTGTGTACACACCCTCCCCAGTGCACGT R 2 1 2 1 303000 r 74 goat snp19296-scaffold1947-15674 NW_017189634.1 41356 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411563 Affx-122951636 AX-123281913 AGCTGGAACAGTGTCCTGATGGAAACCGCTCCCAA[C/T]GCCTCCACTGCTACTGGGGAGTAGATTTCAGCTCA Y 2 1 2 1 102000 r 74 goat snp19297-scaffold1947-67440 11 105917429 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394464 Affx-122964575 AX-123264819 ATGAATTCAGTTGATAGCTCCTGGTAAGACTGATC[C/T]GGAAAGTAAAAGTAGGGGGAGAGAGACGTGGGGGT Y 2 1 2 1 101000 f 74 goat snp19299-scaffold1947-133705 11 105863726 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416071 Affx-122948335 AX-123286420 GAGGCCCAGAACACTTGGTGAGGAAGCACTGGTGT[A/G]ATCATCACCTGTGCAGAAGCTTCTGAGCCAAGGTC R 2 1 2 1 101000 r 74 goat snp19364-scaffold1956-21098 7 108372469 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406445 Affx-122955191 AX-123276797 TGTCGAGGGGTGATGTGGTTAAGGTGTACTGACGA[C/T]GGTGGGATTTCTAAGCATCTTCGGGGCCTTACGTG Y 2 1 2 1 101000 f 74 goat snp19414-scaffold1960-10986 15 30972965 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381208 Affx-122974527 AX-123251566 TCTAGCTTACCTATAATTCCTAATGCAATGTAAAT[A/G]CCAAGTAAATAGTTACTGGCCCATGGTAAATTTAA R 2 1 2 1 101000 f 74 goat snp19415-scaffold1960-39536 15 31003291 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413311 Affx-122950188 AX-123283660 GAGTGACGGCAAATAGAAAGTGGTCATCCTCACCA[C/T]GCGCCGCGTGCTGACCCCATGAGGCCGCCTGCTCT Y 2 1 2 1 101000 f 74 goat snp19416-scaffold1960-88724 NW_017189667.1 36225 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380843 Affx-122975449 AX-123251201 CAGACAGATGACTTACTCCAAGTGATGACTCAGAG[C/T]GACGACAGTCACCGGGGGCTCTGAGACGTGGAAGG Y 2 1 2 1 101000 f 74 goat snp19417-scaffold1960-168938 15 31088118 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409199 Affx-122953176 AX-123279550 ATTCTGTGAATGGATTATCGTTTATCACTATGTCA[C/T]GATGTTTCCCCATAAATTCCGTTCCATTTCATTAT Y 2 1 2 1 101000 r 74 goat snp19418-scaffold1960-220701 15 31139614 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421633 Affx-122944464 AX-123291980 CTACTCCGTGTTCTGGGTCAGAGAGAGAAATGTCC[A/G]TCTGGAGTGGACAGCTGTCTGGCTCAGATTACGGG R 2 1 2 1 201000 r 74 goat snp19420-scaffold1960-340547 15 31254796 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764641 Affx-122937457 AX-385252281 ATTCTTTACCATCTTAGCCAACAGTGATGAGGAGA[C/T]GCTTTTAAACAATTGCTGTTTAGACTAAGACTACT Y 2 1 2 1 101000 f 74 goat snp19487-scaffold1968-19364 6 84931045 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419778 Affx-122945861 AX-123290126 TCCTTCTTTCGTTCCATCACTCCATCCATCTCCTC[A/G]CTCACTGGCAGACTCACGGCCTGTGGCAACCGCTG R 2 1 2 1 102000 f 74 goat snp19489-scaffold1969-21094 21 19005297 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427691 Affx-122939297 AX-123298034 GCTTGTCCACCGAGATGTGATGCTAAATAAATACT[C/T]GGTGTCTTAACTCGTTTAAGTACCCAGTGCCCAGT Y 2 1 2 1 101000 f 74 goat snp19559-scaffold1971-21103 24 2317534 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783815 Affx-122977664 AX-385270871 GGAAGACATGTCAGGTGAGAACTGAGGAGAAGAAT[C/T]AGCAAAGCCTGCTCCTGGGAGATTGAAGTACAGAA Y 2 1 2 1 102000 r 74 goat snp19597-scaffold1976-4282 6 25976206 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420240 Affx-122945072 AX-123290588 CAGGACTGGCTCTGGAGTTGGTTGATTTAGTGGTT[C/T]GGTGATGTCAGTAAGAACCCTGACTTTATTTTTTT Y 2 1 2 1 201000 r 74 goat snp19598-scaffold1976-57386 6 25702801 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386796 Affx-122970913 AX-123257154 TTACATATGGTCTTTATTTTTGGTGCTTTCTAATG[C/T]AGTCTTCATCACATTTATTGAGTTCTTTGGTTCCA Y 2 1 2 1 103000 f 74 goat snp19599-scaffold1976-86366 6 25893550 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423968 Affx-122942133 AX-123294314 CCTTCCCTGAGTCTCCAGCCTGCTTGCCAGCCCTG[C/T]ACCTCTGGACACACAAGACCCCTAGGCTCATGAGC Y 2 1 2 1 303000 f 74 goat snp19600-scaffold1979-4650 23 20922538 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431470 Affx-122936266 AX-123301811 ATATGTTCTTCTCAAATTGCTTATCTCAAGTAATA[C/T]AATGTCCAATTTGTTCAAAGCATTTCTTAGAATTA Y 2 1 2 1 101000 f 74 goat snp19690-scaffold1988-19825 23 46810458 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429005 Affx-122938844 AX-123299347 TGACCAAGTGCATAAGCACTGAGTACCCTCCTCCC[A/G]TTCTTTTAACTTTGGTAACCATTGGTTTGTTTTTG R 2 1 2 1 101000 r 74 goat snp19691-scaffold1988-50502 23 46841547 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419329 Affx-122945655 AX-123289677 TGTTGCTTTGATAAGCCAGTAGAGATTCTTACTGG[C/T]ACAGCAAGTCCAAGCAGGAAATTTGTAAAGTGTTT Y 2 1 2 1 101000 r 74 goat snp1977-scaffold1056-165859 2 125505296 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424109 Affx-122942025 AX-123294455 GAACAGAGGACCTGTAAGCATTTTTCCAAGGAAGA[C/T]ATACAGATGGCCAACAGACTCATGAAAAGATGTTC Y 2 1 2 1 201000 f 74 goat snp1979-scaffold1056-249174 2 125589983 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786295 Affx-122925191 AX-385273330 TCCAGGGCTCCTTTGCTGGTCTTCTGTTGAATAAC[G/T]ACTTAAACAAACATTAGGATTTGAACAATCAGAGA K 2 1 2 1 101000 f 74 goat snp1980-scaffold1057-5026 8 13295157 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391994 Affx-122966500 AX-123262351 TTGGGCAAGGAGCCATAGCAGCAGCTTCAATCTCC[A/G]TTTCTTTCTTTCATATTTCTCTATTTTGTGTTCCT R 2 1 2 1 103000 f 74 goat snp1981-scaffold1057-47854 8 13339604 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421707 Affx-122944400 AX-123292054 ACTGAGAAAATGAAGCTGTAAAGAATCAGCTTCTT[C/T]GGGGATTGTTGAGGAAGCATTTGCTGTGACTATGC Y 2 1 2 1 202000 f 74 goat snp1986-scaffold1057-289223 8 13582679 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378978 Affx-122976400 AX-123249337 TGAACAAACTCTCTAAAAAGATTTTTAATAATTTA[C/T]GGTGGCAGCAGGAATATATAAATATGCATTTGCTT Y 2 1 2 1 303000 f 74 goat snp1987-scaffold1058-18044 4 87744005 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403179 Affx-122958077 AX-123273532 GCTAATAAAACAAAATGAAGTGGAAAAATATAGTA[C/T]GACTAACAGCAAAACACAGGTCATAACAAAGAAAA Y 2 1 2 1 201000 f 74 goat snp1988-scaffold1058-50675 4 87711073 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390714 Affx-122967932 AX-123261071 ATAATATGTACCTTTTTCTATTCATTTTGCTCAGC[A/G]TTATGTTTGTGAGATTCATCCTTTTTGTTGCACAT R 2 1 2 1 303000 f 74 goat snp1989-scaffold1058-80706 4 87678439 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405769 Affx-122956492 AX-123276121 CCGCCGCTGCTAGTTTGATTAACAGAAGGGAATGA[C/T]AACCCACTCCAGTATTCTTGCCTGGAGAATCCCAT Y 2 1 2 1 303000 f 74 goat snp19938-scaffold1994-28037 9 74365807 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422819 Affx-122943194 AX-123293165 AAGTAAAATTTTAAGTGATTGACTAATTTTAGTAC[A/G]TAGGCCAGGCTCTGCAAAGCACTTTATTAACTAAT R 2 1 2 1 201000 f 74 goat snp20256-scaffold2002-32958 16 10343282 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782441 Affx-122936663 AX-385269517 TGATTACTGAGATTATACACTAATCAAAACTGACC[A/G]CTTTAAATCAGAAGCAATTCTAGTCCTTAGCAACC R 2 1 2 1 101000 r 74 goat snp20257-scaffold2002-73377 16 10302707 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398482 Affx-122961576 AX-123268837 AAGCTTGAATAAAAAGGGATGACTTCCTGTGCCTG[C/T]ATTTTTCCACCAAGAAGAAAGAGAAATTGGAAACT Y 2 1 2 1 101000 f 74 goat snp20258-scaffold2004-13701 NW_017189516.1 63518709 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446006 Affx-122925868 AX-123316343 TCCCTAATTTTTCCAAATTTGCAGAGTCTATCCCA[C/T]GAATAATTGGGCAAACCATGATGGTGTACGCCTAC Y 2 1 2 1 201000 r 74 goat snp20259-scaffold2004-67250 NW_017189516.1 63468443 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779837 Affx-122954232 AX-385266936 TGGTTCAATATTCTGAATCAGAACTTGGCAGCGTC[G/T]AAAATCTAACATTAGCACAACAGAAAGATGGTGGA K 2 1 2 1 101000 f 74 goat snp20260-scaffold2004-104020 NW_017189516.1 63431962 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768769 Affx-122947398 AX-385255946 TTTAGTTTGCATTTTGCTTAAAAATGGCCCAAGTC[A/G]TAACTAGTGCTACTTTTATGATATTCCATTGCCAT R 2 1 2 1 101000 f 74 goat snp20261-scaffold2004-162739 NW_017189516.1 63372798 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398455 Affx-122961595 AX-123268810 TGCTCGGTCTTCACAAAAGCCTTGAGGTTGTGTGC[A/G]CCGCCATCGGCAGTGATTGTCTTCAGCTGCAGGAA R 2 1 2 1 101000 f 74 goat snp20262-scaffold2004-224674 NW_017189516.1 63311506 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777589 Affx-122956932 AX-385264708 ATGGAAATTTGCTTGTGTGCACATGAAAAATAAGC[A/G]GGTGTTTCTGATGTTCTGGGAATCCTTGAAAAAAG R 2 1 2 1 101000 f 74 goat snp20263-scaffold2004-284892 NW_017189516.1 63251738 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389037 Affx-122968624 AX-123259395 AATTAGGCAGAGATGACTGGACGTGGCCCAACAAC[A/G]CATTAGCATCTTTTTAGCCAGATATTATGAGGTGA R 2 1 2 1 101000 r 74 goat snp20264-scaffold2004-331279 NW_017189516.1 63209875 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433356 Affx-122935136 AX-123303697 CTAAACCATATGCCAAGCACATTAACAGGGTTTAA[A/G]ATGATCAGTTACTGAAGAAAAGACCAACCTACTCA R 2 1 2 1 101000 f 74 goat snp20277-scaffold2007-90800 28 41951082 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771601 Affx-122947122 AX-385258759 TTTTCCATGCCGTTAAGTTTTTTTCTACCTCATCA[C/T]GTGAATGATGGAAACAGTAGTAAGAGTATTGACAT Y 2 1 2 1 101000 r 74 goat snp20327-scaffold2011-26424 18 60790415 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405216 Affx-122956901 AX-123275568 GGTGCCAGGCTCTAGAGCATAGGCTTAGCTACTCC[A/G]AGGCATGTGTGGTCTCCCCAGACCAGCACTTGAAC R 2 1 2 1 303000 r 74 goat snp20328-scaffold2011-89596 NW_017212294.1 4371 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427333 Affx-122940124 AX-123297676 GAATGTCCTAGATAAACTTATTTACAATAATTCCA[C/T]GGGGAATATACTGAAGAAAATGTTGACAATATTAT Y 2 1 2 1 103000 f 74 goat snp20353-scaffold2017-15604 6 9075933 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435511 Affx-122933416 AX-123305851 AAGGTTTGATCACAATCTTTTAATTTCCTTTGCTC[A/G]TAATATTCAAGCCTGGTCTTCTTCCACACAGTTCA R 2 1 2 1 101000 r 74 goat snp20354-scaffold2017-74032 6 9134065 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798056 Affx-122946878 AX-385284992 ATTTATAATAGAATTGCTAGTAAAAGCCATAGATA[C/T]AACTGAGGAACAGCTCAGTAAGATTGTAGAGAAGC Y 2 1 2 1 101000 r 74 goat snp20355-scaffold2017-123081 6 9183107 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413289 Affx-122950202 AX-123283638 TGTAAGCCATGCAAAACAGAGCAGACAGCTGCACT[A/G]TCCGCCCCCACCGGCCTAGGCCCTTTGGAAACAAA R 2 1 2 1 101000 f 74 goat snp20356-scaffold2017-182167 6 9242064 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446639 Affx-122924783 AX-123316975 TCACTTGTGTCTGCTTAGGAAATTTCTGGAATGAT[A/G]CAAAGTTGTTTTTTAATTTACTTATTTTAATAGGA R 2 1 2 1 102000 f 74 goat snp2042-scaffold1061-20259 NW_017189639.1 20642 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421086 Affx-122944231 AX-123291433 GAAAGGAACCCTCATTTCGAGGGGAGCAGGGGGAT[A/G]CATGCTCCTCTTGTGTTCTAGCTGGACTCTCGGTG R 2 1 2 1 101000 r 74 goat snp20553-scaffold2020-11113 17 68540743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395855 Affx-122964012 AX-123266210 CCATTTCCCTGCTTCGTTGGGAAAGGAATCCCAGC[G/T]ATCACATCACAACTCAAGAGGAGGTGGTCTGCACT K 2 1 2 1 102000 r 74 goat snp20554-scaffold2020-61829 17 68591741 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452277 Affx-122920755 AX-123322610 CTTTTACAGCTCAAGAGGAAAGCGGACTTGCATGT[A/C]TCCACACAAGACGAGGCCTGACTGCCCTGTGGAAA M 2 1 2 1 103000 f 74 goat snp20556-scaffold2020-149996 17 68458106 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773674 Affx-122920443 AX-385260814 TCTTCTAGAGTGGGCAGAGGGAAAACTGTGAAAGG[A/C]TAATGACAAAACCCAGGGCAGGACACCTCCATTTC M 2 1 2 1 102000 r 74 goat snp20674-scaffold2036-2372 25 34107941 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436796 Affx-122932251 AX-123307134 TGCCATTTCAACACTGTTATGTGACAGAGGATCCT[A/G]GTGGAGAATGGATTTGAAGACCCAAGTCTGCATGT R 2 1 2 1 202000 f 74 goat snp20675-scaffold2037-21188 7 99171802 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454182 Affx-122919306 AX-123324515 GCGACCCCATCAATGGCAGCCCACCAGGCTCCCCC[A/G]TCCCTGGGAATAATCATTACTGGTCTTTTAATCCC R 2 1 2 1 103000 r 74 goat snp20676-scaffold2037-57586 7 99209063 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399398 Affx-122961248 AX-123269753 TCTTTAGAAGGAAGTCACCATACACAGCCCACACT[C/T]AAGGGGTGCTCTTCTATCAGCAAGTTTTTCAGGGG Y 2 1 2 1 101000 f 74 goat snp20677-scaffold2038-4835 23 21322736 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392608 Affx-122966047 AX-123262965 TTCCGCACCTCTCTGGAGTTTCACTTTCTCTTCGC[G/T]CAAACTGTGTCGGGCCTTTCTGCCTGGATACTCAT K 2 1 2 1 202000 f 74 goat snp20678-scaffold2038-42681 23 21360156 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398473 Affx-122961582 AX-123268828 CATTTCCTCTTCCCCAGGCCATGTCACATGTTGGA[A/G]CAATACCAGGCAATCCGGGGAATGGTTTTAGCCCC R 2 1 2 1 202000 f 74 goat snp20679-scaffold2038-120627 23 21370791 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388820 Affx-122968899 AX-123259178 GCTGTCCCTCTACTTCTTCAATATATGGACCCAAA[G/T]GTTAAGAACAAAAGATCCTGGGACTTAGTTTCTTT K 2 1 2 1 201000 r 74 goat snp20848-scaffold2046-10960 6 85532905 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393719 Affx-122965237 AX-123264074 GCCCTAGTGTTCTCTGGTGGGTGGAGATGGGGAGA[C/T]AGATTCACTGGAAAATCTACAAAGCTCTTACGCTT Y 2 1 2 1 101000 r 74 goat snp20849-scaffold2046-56069 6 85575990 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413113 Affx-122950383 AX-123283462 TAAATTCATCCTGCTCTGCCCTGAATGACCGGCAG[G/T]TGGCGCACAAACCCTCATTTCTTCTGTGTGGGTAA K 2 1 2 1 101000 r 74 goat snp20850-scaffold2046-113028 6 85633298 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435459 Affx-122933460 AX-123305799 ATTCTTCGGGATCGATGGAGAAGAGTGTGCACAGC[A/G]TTCACAAGAGGAGCGACAGCAAAAGAGCCCGACCA R 2 1 2 1 303000 f 74 goat snp21051-scaffold2060-12570 NW_017189575.1 14567 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381878 Affx-122974174 AX-123252236 TTGTCAGGGTTGAACATGAAAATGTCTGCTGCACA[C/T]CTGGTAGCTGATTTTCCTGAATGCTCTGCAGGTGC Y 2 1 2 1 101000 r 74 goat snp21098-scaffold2065-55125 NW_017189558.1 13878 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417552 Affx-122946917 AX-123287900 CAATGGTTATTCCTATTTCATAGGAGAGGAAGTTC[A/C]CAGACACTGTGTCATCATCCTCACTAAGGTTCATT M 2 1 2 1 101000 f 74 goat snp21099-scaffold2065-114352 12 14269249 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799051 Affx-122952989 AX-385285981 GAACACCTACTATTCCAGGAACTAGGGATACATAA[G/T]TGAACAGGATGATTGGTATAAAGTAGAGTCTCAGT K 2 1 2 1 201000 f 74 goat snp21101-scaffold2065-220715 12 35285734 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401504 Affx-122958937 AX-123271857 TTAAATTGCTCTTTGGAAGTGGGGAAAGGCTTAGA[C/T]GACAAAAGTTTTTCTGCAAACAAGTGACAGGGAAC Y 2 1 2 1 101000 f 74 goat snp21227-scaffold2070-31093 NW_017189516.1 20732292 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421928 Affx-122943834 AX-123292275 GAGTGCTCATGACCACAGTTTACCAGGCTCGTCAT[A/G]TTCAAGACCTGTAGGCTTCTCCACATGCTGATTCC R 2 1 2 1 202000 f 74 goat snp21228-scaffold2072-18453 12 121458 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797509 Affx-122939978 AX-385284448 ATGTGCTCACCTAAGATTTGGTATGATGAAATTGA[A/G]CTGAGTGTCAGCATAGATATAATCTCAAAGAACAC R 2 1 2 1 101000 r 74 goat snp21251-scaffold2077-21932 23 20294614 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769865 Affx-122943147 AX-385257034 AACTTGTTCTGGCCAAATCAATCTCTCTGTTTCCA[C/T]AAAGTTATAATGTACTGAAACTGCTTGCTAACTCC Y 2 1 2 1 102000 f 74 goat snp21253-scaffold2077-147222 23 20419218 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802224 Affx-122971166 AX-385289128 AATTGTCTTGTATTCTGCATTGTCCTGTACATTGC[A/G]CTTCTTTTTCATTGTGCTGAAAACGCTGAGACCAA R 2 1 2 1 101000 r 74 goat snp21254-scaffold2077-185403 23 20509185 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393161 Affx-122965535 AX-123263518 GAGATAGATTTTACAGAGGTAAGGCCAGGCAAGTA[C/T]GGCTATCGTTACCTGTTAGTTTCGGTTGATACATT Y 2 1 2 1 103000 r 74 goat snp21322-scaffold2081-15188 NW_017189516.1 20775955 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391862 Affx-122966985 AX-123262219 TCATACATGTAAAATTGAGCCTCATAGAGGTGGAA[G/T]CCACTTGTTCAAGGCCCCTAGGTGGAAAGTGGCCA K 2 1 2 1 102000 f 74 goat snp21466-scaffold2091-1064 19 19078487 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400583 Affx-122960406 AX-123270938 CAGCCTGGGAACATAGAGGGCTTGTTTATCAAATA[C/T]GTACTTAACTCAAAGTTAAAAGAAATAGTAGTTGT Y 2 1 2 1 101000 f 74 goat snp21568-scaffold2101-43698 14 7935498 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776032 Affx-122958234 AX-385263162 CTTTTGATGGTGAATAACACTGTGTATGTAAAGCA[C/T]GTTCTCTTGATCTGATCATCCATTGATGGTTAGTT Y 2 1 2 1 201000 r 74 goat snp21573-scaffold2103-122544 6 113124964 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785722 Affx-122919322 AX-385272763 GTGTTCAGTGTTGACATCTCCTTACGAGAGGTACT[A/G]TAAGAAGAAAACTTTTATATTGATTCCTGGTGCCA R 2 1 2 1 201000 r 74 goat snp21588-scaffold2109-34147 13 37866236 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445964 Affx-122925896 AX-123316301 AAGAGGGGGATATATACATATATATCTATGTGTCG[C/T]TGTTGTTTGGTCGCTGAGTTGCGTCTGACTCTTTT Y 2 1 2 1 103000 r 74 goat snp21595-scaffold2111-652 5 102007244 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422752 Affx-122943242 AX-123293098 GAATGCTGAGAAAGAAATACTCACTTCCGTAGGGC[A/G]AATCTCCTCCCTCCCTACAACGTGTCTGCCTGGAC R 2 1 2 1 101000 f 74 goat snp21603-scaffold2114-36612 NW_017189516.1 62695463 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401295 Affx-122959860 AX-123271648 AGACACCAACCTGTAGCAACTGGAATTACAAGGGA[C/T]GGAGCCTTGACTATGTCTGAGGCTCATGTATTTAA Y 2 1 2 1 101000 f 74 goat snp21604-scaffold2117-19429 3 234850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432683 Affx-122936041 AX-123303024 GGTTTGTATGATAGGAGGATGAAAGACAGAAAAGA[A/G]TACAAGAATTAGACTATATATGAGCTGACACAAAT R 2 1 2 1 101000 f 74 goat snp21681-scaffold2120-42831 25 35056189 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393804 Affx-122965178 AX-123264159 GGAGTTCCTCTCGCCTTTCCTGTGGAGAGCACCTC[A/G]TCTTGAGTTGCTTCGGGAACGCCGGGTATTCTTTC R 2 1 2 1 303000 f 74 goat snp21682-scaffold2120-87062 NW_017216914.1 7687 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427412 Affx-122940066 AX-123297755 AACCTAGGAATACATGAAAGAGCTCACCTTGGAAA[C/T]GAACATTTAATGAAAGACCAGGAATATACGGGGGT Y 2 1 2 1 103000 r 74 goat snp21708-scaffold2123-20961 18 59803111 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407651 Affx-122954610 AX-123278002 TCACTAGTTACCCGATCACATAAAAGAGAGGAAAA[C/T]GGAGTATCAGATGAACTGCTTAAATTAGGTCGTGA Y 2 1 2 1 101000 f 74 goat snp21787-scaffold2138-22615 18 61667177 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400127 Affx-122960714 AX-123270482 TCAAGTTAGCTAGGTCCCTGCCCATGAGTGGATCA[C/T]GGCTGAGGCTTGTTTCTGGAGGACCTTCACTCCCA Y 2 1 2 1 201000 f 74 goat snp21788-scaffold2139-46203 4 14715830 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800009 Affx-122939221 AX-385286932 CTAGTAAATATACCATACTAATCTGTAGAGGAATC[A/G]TTTTATAAGCATAGATAGAGTGGAAATACACCATA R 2 1 2 1 201000 f 74 goat snp21789-scaffold2139-99782 4 14662814 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793236 Affx-122973401 AX-385280214 TTGTATGTTTCATTGCCTGAGAGGGAAGTGAGGAT[A/G]GGAGGAGGCAAACTGACAAATTTGAAAAGCAAATA R 2 1 2 1 101000 f 74 goat snp21790-scaffold2139-154627 4 14606364 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766825 Affx-122957162 AX-385254148 GAGATGGCTCACTTGTACAACGGAGAGGTAATGCT[A/G]TAGAATAAAGGACATAAGATTTGGAGTTGTAAAAA R 2 1 2 1 101000 f 74 goat snp21859-scaffold2144-14867 3 73588699 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394837 Affx-122964785 AX-123265192 TCCAGGAGTTTACAATCTCTTTAGGCAGATAGAAC[A/G]TGTATAAGTTACTGCTAACAGTACAGGTAACATGC R 2 1 2 1 101000 f 74 goat snp21860-scaffold2144-53078 3 73550114 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397287 Affx-122962332 AX-123267642 GGATTCAAGGGGCCTGTGCAGAAATGTAAGCCTAC[A/C]GAAGTAAGCAAAGTCATAGGGGTTTCATATGGGGA M 2 1 2 1 101000 f 74 goat snp21861-scaffold2144-109130 3 73494109 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444390 Affx-122926595 AX-123314727 ATCCAATGGGGCACAGAGCTGAGTCCAGAAGATGA[G/T]AGTGGATCTGGAGGCGAAAAACTAGCACACGGACT K 2 1 2 1 101000 r 74 goat snp21862-scaffold2144-140583 3 73462849 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801553 Affx-122952299 AX-385288462 ACCATTAATGTTACCTGACAAATAACTCCCATATG[C/T]GGTTGTGGAACCTGTTTACTTCCCCAATTCTCCCT Y 2 1 2 1 101000 r 74 goat snp21863-scaffold2144-192272 3 73411660 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787279 Affx-122961573 AX-385274304 GCCCAAGATCTCGAGTATAAGGTAGTATAAAATCT[A/G]TGATGCACACTAAGCCAGCACCTGGGAACAGCTTA R 2 1 2 1 101000 r 74 goat snp21864-scaffold2144-221443 3 73381947 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420994 Affx-122944563 AX-123291341 TCAGGTAGGAAAGGAAATCACATCTAAGCATGTAA[C/T]GGTCAAATTAATGAAAGTCAAAGAGAAAGAGAAGA Y 2 1 2 1 103000 f 74 goat snp21865-scaffold2145-8943 21 34319124 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380903 Affx-122975032 AX-123251261 CTCAGATTCCTGTCTCCAGAGCCTCTCTCTCTCCT[A/G]TGAGGGCAGGCTGCTCCCATACTGGAACTGTCTGG R 2 1 2 1 102000 f 74 goat snp21866-scaffold2145-46298 21 34247526 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779002 Affx-122973167 AX-385266109 AGAACTTACTTGGTTCTAAATAGACATGGAAAATA[A/C]ATGTGGAAAAACCCATGACCAAAAATAGCCAAGTC M 2 1 2 1 101000 r 74 goat snp21867-scaffold2145-89583 21 34205273 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779504 Affx-122945074 AX-385266607 AGTAAAAAAATATCAAGATGCCAGTGGATACTTAC[A/G]TAAAATATAGGACCAAACATTTCACAAAAAGAAGA R 2 1 2 1 201000 r 74 goat snp21868-scaffold2146-43557 6 25841382 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421952 Affx-122943818 AX-123292299 ACAGCCTTTAGGCTGCCCCACTGGGAATCTTCCCA[G/T]TCTCCTCAACCCTGGCACAGAGACTTACTTCATTG K 2 1 2 1 102000 r 74 goat snp21924-scaffold2152-10100 10 75971689 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450254 Affx-122922251 AX-123320589 ATATATTGCTAGGCATTTTAAAACTATTCTTTCTG[C/T]AATCTTCAAAATCCCCTCTGTAGTCGTATTCACTT Y 2 1 2 1 101000 r 74 goat snp21925-scaffold2152-60365 10 76023044 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778771 Affx-122920820 AX-385265881 AGTATAGTCTGATATGTACAAAATCAGGCAGACAG[A/G]ACATAGGAACCTCTGAAATCTTCCTCTTGTATGGC R 2 1 2 1 101000 r 74 goat snp21963-scaffold2159-525 NW_017212856.1 2757 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794801 Affx-122948584 AX-385281761 ATTAAGTAAATCAATATTGATGGGTTAATAAATAC[A/G]TAGCATTTAATAAGGTCAGCAACCAAGCTTAGGAC R 2 1 2 1 101000 r 74 goat snp21978-scaffold2162-24019 14 84211223 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376954 Affx-122977767 AX-123247313 ACTGTAAAGTGTCTACCTGCAACGTGGGAGAGGTG[C/T]GTTCATTTTTTTCCTTTCCTTGAATCTTCTCAACA Y 2 1 2 1 101000 r 74 goat snp21979-scaffold2162-53219 14 84180647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407589 Affx-122954658 AX-123277940 AGAGGGTGGAAAGAGGCAGACAGCAAGGCAGAGGG[G/T]CCTAAGGGACCATGTAATTAACTTGTGCTTGCCCA K 2 1 2 1 103000 f 74 goat snp22025-scaffold2167-37555 23 23513453 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781786 Affx-122946148 AX-385268868 CTTATAGGAATTTCATAAGCTGATAGTCATATCTG[C/T]ATTATGTATACATTTGGTGTAAATTTTATTTGATG Y 2 1 2 1 201000 r 74 goat snp22026-scaffold2167-91685 23 23454365 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418163 Affx-122947091 AX-123288511 CTTCTGAGGGGATTTGATTACAGAAGTGAGAGTTC[C/T]ATATCTGACCAAGGCTGGCAATTTGATATCTACTA Y 2 1 2 1 201000 r 74 goat snp22027-scaffold2167-127770 23 23416514 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399521 Affx-122961155 AX-123269876 TGGGGGTGGGGAAAGACAAAAACAAAATGTTTAAG[A/C]GTTTTAAAGTCCTTCTCCTAAGGCAACACATTTCT M 2 1 2 1 303000 r 74 goat snp22118-scaffold2183-28635 12 15670487 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801067 Affx-122965566 AX-385287981 TTTCCATGGATTAAAGTCCTGCATAGTACCTACTA[C/T]ACTTTCCTAATGATGGTAACTTCCAGGAATCATGA Y 2 1 2 1 201000 f 74 goat snp22119-scaffold2183-68107 NW_017189558.1 18240 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399536 Affx-122961145 AX-123269891 AAAGAGTGAAGCATCAAATGACCTCTAAGTCTGAA[C/T]ACTTCTCACTACTCTCCACCCCACCCCTCAACCAT Y 2 1 2 1 101000 f 74 goat snp22120-scaffold2183-110035 NW_017218329.1 11610 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449748 Affx-122922456 AX-123320083 TACTTCCAGCATTGGTTGGACTCTATCTGAACTGG[A/G]CATTTGATCATTCATTAAATTCATTAAATGTGAAT R 2 1 2 1 101000 f 74 goat snp22146-scaffold2186-4792 3 66494688 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431839 Affx-122936089 AX-123302180 ACTAATTTCCATAGATAAAATTAAATAGAAAAGTG[C/T]ACTTAGCGAATCAATATTTATATAGCTGTGAATGT Y 2 1 2 1 101000 r 74 goat snp22158-scaffold2189-658 14 83755725 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390526 Affx-122967235 AX-123260883 GAAATAGGGTTGAAATTTTAGTTGGTAGAACTCTC[A/G]TATCACTTCTTTGCTTAGGTATTAGAAGTGTAGAG R 2 1 2 1 101000 r 74 goat snp22159-scaffold2189-41433 14 83796607 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424090 Affx-122942038 AX-123294436 CCAAACAAATAAAAGAATGAGATGACAGTGTGACA[G/T]CACATAATTAGGGGTTGGAAAAAGGCCTTAGTAGG K 2 1 2 1 202000 f 74 goat snp22223-scaffold2195-17488 3 111576031 A C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768785 Affx-122948849 AX-385255962 TACTAATTTGGACAATACAGCCAACTCTTCCCAAC[C/T]GTGAAATGCCAGGTTTTTCAACTTCTATTTTCTTC Y 2 1 2 1 102000 f 74 goat snp22224-scaffold2196-12660 3 111059029 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794656 Affx-122923889 AX-385281617 ACTGGGTGCTGGCCACCTGAGCACTGGGGGTTCAA[C/T]AGCTTAATAAAGAGGCCTAGAAGTGGAGAGGGAGA Y 2 1 2 1 202000 f 74 goat snp22225-scaffold2199-13658 10 77631245 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788728 Affx-122947229 AX-385275744 CAAGTGATTCCTCATACCCAAATCTTCTCCAAGGA[G/T]CCCTCTAAATGGTACTCTCTAGATGACAATAAAAG K 2 1 2 1 102000 f 74 goat snp22337-scaffold2207-12992 10 78244389 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376081 Affx-122978908 AX-123246440 CAGCTTTGTTTCTTAAAAAATTAGACAATTTTAAG[C/T]AGTGATAAGCACTTTAAACAAAACTGTGTTAAGAT Y 2 1 2 1 103000 r 74 goat snp22338-scaffold2207-43343 10 78274885 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395028 Affx-122964214 AX-123265383 TTTTTGAAAGAAAATAAAAGTTTTCTTCTGATTTA[C/T]GATTAGCAGGATTAAGCAAGCTACTTACTCAAAAA Y 2 1 2 1 103000 r 74 goat snp22339-scaffold2208-13494 4 87519155 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419844 Affx-122945383 AX-123290192 TTGTGGTTAAATAACAAACAAAAACGGCAGTCAGT[A/G]TGGAGAACACAAGGTGAGTTCTAACACTTGGGCAA R 2 1 2 1 102000 f 74 goat snp22423-scaffold2217-16723 NW_017189517.1 28921256 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784124 Affx-122928442 AX-385271176 ATGTAGTGTACTATTCATCAGCTCTTGTACATAAG[C/T]GGGATCTCAATAAATTGTGCTATCAAAAAGTCTAC Y 2 1 2 1 101000 f 74 goat snp22424-scaffold2217-68369 NW_017189517.1 28867726 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782284 Affx-122977925 AX-385269362 TTTCTTGGACAAATTTGACTTACGAACGTGGCTCT[C/T]GGAAGGGAACTTGTTTTTACATAGGGAACTTACTG Y 2 1 2 1 101000 f 74 goat snp22466-scaffold2220-11612 3 107487287 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791833 Affx-122945969 AX-385278823 CAGGGTTTCACTTTTTCTAATTGATTGGTGAATAA[C/T]TTTGCTTTTGGTATTTATAGTGATGCGTTAATTTT Y 2 1 2 1 101000 r 74 goat snp22487-scaffold2225-22166 5 118689843 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420982 Affx-122944571 AX-123291329 CGACTCACGCTGCGGATTGAGCGCCTCTCTGTGCC[G/T]GGAAAGGTGCGGGGTCTGGGCTCACCGCTTGCTCT K 2 1 2 1 101000 f 74 goat snp22488-scaffold2225-59940 5 118652325 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393773 Affx-122965199 AX-123264128 GGGGGCTGTACTTCTTCCGCGTGACATACTGCCGC[C/T]CCATGGTCTTCTTGGCGTTCTTCACCAGGTTCCGG Y 2 1 2 1 101000 f 74 goat snp22489-scaffold2225-111916 NW_017191023.1 4731 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767147 Affx-122945180 AX-385254432 TGAGTAACTGATCAATATCCTCCCTAGTGATCCTT[A/C]AGAAATTCTGGCCTGTGTTTTCCATCAATAACCAA M 2 1 2 1 101000 f 74 goat snp22490-scaffold2225-174369 5 118772593 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408312 Affx-122953769 AX-123278663 CAGGAAGACGGTCTAGTGGGCCATGGCACTCCTTG[C/T]GCCACAGGGGGTCTGGAGGCTGGCCTGGAGGGCGT Y 2 1 2 1 101000 f 74 goat snp22492-scaffold2225-288080 5 118885607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383929 Affx-122972970 AX-123254287 CTTCAGTCCCTCGCTTGCAAAATAGTGAGGGTGTC[C/T]AGGTGCTCTGCCAGGGCAGCAGGGGGACTCAGCGT Y 2 1 2 1 103000 f 74 goat snp22493-scaffold2225-351744 5 118948638 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434863 Affx-122934364 AX-123305204 TTAAGAGTTCCCAGGCTGAGGTATTCAGGGTCTCT[A/G]AGGTTAAGGAAATTTGGTCTGTCTGCAGGTGCTAT R 2 1 2 1 102000 r 74 goat snp22494-scaffold2225-427254 NW_017213422.1 11834 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422702 Affx-122943652 AX-123293048 GAGGATGTAGGCTGCTGTGAGAAATCATAATGGGA[A/G]AGTAATAAAATTGGAGCAACTACTGTCAACTTAAG R 2 1 2 1 201000 r 74 goat snp22505-scaffold2228-5143 1 102502389 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767037 Affx-122921341 AX-385254329 TTATTTAATGCCACTTCCCAGTGAATTTATTTGCA[C/T]GCTTAATATGGAGAACTTCTCTTTAAAAATTTAAG Y 2 1 2 1 101000 f 74 goat snp22507-scaffold2228-69650 1 102438707 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438484 Affx-122931227 AX-123308822 TTCACCTGGTCATCATCTTTATAAAATGTATGTCT[A/G]TTTTTTATCATTTTTTCCAATGCAGTTATCAAGTG R 2 1 2 1 101000 r 74 goat snp22508-scaffold2228-101845 1 102406935 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799440 Affx-122968919 AX-385286370 TTTATCTACATTGAAAGCAGCCTATAGAAGTCAGA[A/G]CATTGAAAAAGTATCAAAAACTCTTTCATCAAACT R 2 1 2 1 101000 f 74 goat snp22689-scaffold2250-17042 15 70649888 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774004 Affx-122955065 AX-385261142 CAAATACCTTAAATTTCTGAGAGTGAAATCTCATA[C/T]GTCCAGCTTTGCAGTTTGAAGAATGCATTAGATTC Y 2 1 2 1 101000 r 74 goat snp22690-scaffold2250-69837 15 70702015 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415188 Affx-122948997 AX-123285537 ATATTTAGGTCTTCTTTAATTTCTTTTAGCAAAGT[A/G]CTGTATATGCATATGCCACATGGCAAGCTCTTTGA R 2 1 2 1 103000 r 74 goat snp22691-scaffold2250-99629 15 70731405 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376760 Affx-122977971 AX-123247119 CTTCCATTACGATAGTCTTTAATATTAGAATGCCT[A/G]CATTCACTGACAGTTGACTCTGTCCCTTCACACAA R 2 1 2 1 101000 r 74 goat snp22692-scaffold2251-22471 NW_017194272.1 4640 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390322 Affx-122967707 AX-123260679 ACAGTTTTTTTTAAGATCACAGTTATGTAACACTC[G/T]ATATGAAATCCAGTCTATGTAGCCATACAGACATC K 2 1 2 1 101000 f 74 goat snp22701-scaffold2257-34398 16 4532088 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800094 Affx-122947652 AX-385287017 TACCAGTCTCTTAAAACGGTTAATTTTGGCCTAAC[A/G]TATGTTCTCTCATAGAGAATGGTTTATGTGTCCTT R 2 1 2 1 201000 r 74 goat snp22702-scaffold2258-14547 18 60429865 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422372 Affx-122943424 AX-123292718 GAACAATCCATCTGAACAAACACCAGCTCATCAAA[C/T]AACACCCCTCCTGGGAGGAAAGCAGAGGTCACCGA Y 2 1 2 1 101000 f 74 goat snp22717-scaffold2261-23263 29 51166148 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398834 Affx-122961387 AX-123269189 AAAATAATAATTAAAAAAAACGCTCTGGCAAGGGG[C/T]GCAAGTCGGTGTGAAGAAGTGGAATGACATCCCAC Y 2 1 2 1 101000 r 74 goat snp22718-scaffold2261-56211 29 51132979 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771454 Affx-122962237 AX-385258612 TATGATTCCAAATTAAAGTCCAAGTGACTAATATA[C/T]TTGAAAACCAGTTTTGGTGGACTTAGTAGTTCAAA Y 2 1 2 1 101000 r 74 goat snp22719-scaffold2263-5928 NW_017189516.1 63694167 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778133 Affx-122975476 AX-385265248 AGAGTGAAAACTCAATCAACCCTGGAAAATATGTC[A/G]TGATTATCTAGGATTAGCAATGCCCACAGCCATCT R 2 1 2 1 101000 f 74 goat snp22720-scaffold2263-65552 NW_017189516.1 63631668 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431229 Affx-122937144 AX-123301570 TAGTCTTTTTCTCTAACGCCTCCACCAGAGAGAGA[C/T]GTCCATGAATGCGGTCTCAACATTTTAAATTCATC Y 2 1 2 1 101000 r 74 goat snp22721-scaffold2263-126741 NW_017189516.1 63569902 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411956 Affx-122951140 AX-123282306 TCAAACGTAGGTTCAGCTACTGAACAGAAGGGTGA[C/T]GTGACAAGGAGGTGTATTTTCCTCTCGTGGGAAAG Y 2 1 2 1 101000 f 74 goat snp22748-scaffold2268-9652 18 64848103 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430562 Affx-122937014 AX-123300903 AAACCCTGACTACCTCCCAGCCAGTGCTGACGATC[A/G]GATTAGTCAAAGGACTGGAAGCTAGCTGTAAACCA R 2 1 2 1 101000 r 74 goat snp22749-scaffold2268-39998 18 64817875 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411906 Affx-122951179 AX-123282256 AATACTTGCTACATCCCTGTGCGACCCGGTATATC[A/C]TTCCTGTTTCTCTCATATGTAGCAGTCTGTGTCTC M 2 1 2 1 101000 r 74 goat snp22750-scaffold2268-102722 18 64759022 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795164 Affx-122919298 AX-385282122 ATTAGGATTATGGTGTATTATTGCTTTAATTGCAT[A/G]CATAATATCTTTAAGCAAGTTCCATCTTTGCTTGC R 2 1 2 1 201000 f 74 goat snp22781-scaffold2274-3901 6 85370210 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433526 Affx-122935008 AX-123303867 TGTCTCACCATATTCTGTTTTCTTTTCTTTAGATA[C/T]GTAGCAGGAAGAGAGAACACTGAATAGTGGAGTGG Y 2 1 2 1 103000 r 74 goat snp22782-scaffold2274-61049 6 85428688 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408136 Affx-122954237 AX-123278487 ATGCACATAACAGGTGTAGGTTCTCAGAGTGTGAC[A/G]CCCCTCAGACCTCACACTCTCTCTCTGGTTCTCTT R 2 1 2 1 202000 r 74 goat snp22789-scaffold2277-25429 17 505543 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430827 Affx-122937444 AX-123301168 TGCTGGAAAAGAGACCCATGGTTCTCTTCTGCATG[C/T]GTGCTAAGCTGCCAAAATCGTGTCTGACTCTTTAG Y 2 1 2 1 103000 f 74 goat snp22900-scaffold2281-3802 NW_017189516.1 65252901 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783909 Affx-122928692 AX-385270964 CCTTCCATATATATTGTTCCATAATTCTGTGATTA[C/T]ATCTCCATCTATAAGAGGACTCTTTCCATGAAACA Y 2 1 2 1 101000 r 74 goat snp22919-scaffold2285-4762 NW_017189779.1 8758 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383455 Affx-122973457 AX-123253813 TACTCATTTTTCTGTTTCTCTTCTATGCAAGAGTT[A/G]CTGTCAATGAAAGAAAAAATCCCTATTATGGCCTC R 2 1 2 1 101000 r 74 goat snp22976-scaffold2291-52285 NW_017189517.1 34511426 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784262 Affx-122932738 AX-385271313 TTGTTTTTCACTCATGCTTTCAAGATGTATCTATA[G/T]TCTTATAGCTAACTGTAGATCATAGGCTGGAACAC K 2 1 2 1 101000 r 74 goat snp22988-scaffold2299-65451 7 99235373 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802737 Affx-122944366 AX-385289636 AAATTTTATTCATTGCAATATATTCTCTGTGACAA[C/T]ACCATCTCTGATCAATCAGTATATCACGGCCATCT Y 2 1 2 1 101000 r 74 goat snp23107-scaffold2302-11269 7 98681470 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449237 Affx-122923483 AX-123319572 CAAAATGGAGGAAACAATTTGAATATAAGAGAAAA[C/T]GATTCCAAAAAGAGGAACACCAGCAAATAAGCTAG Y 2 1 2 1 101000 r 74 goat snp23108-scaffold2302-86700 7 98756660 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452898 Affx-122920213 AX-123323231 CTGTGAACAAAACCTATGTGGATGAAAAACTACCA[C/T]CTGCCTCTGTAAGGATGAAGTCACTAGCCACTGCA Y 2 1 2 1 101000 f 74 goat snp23109-scaffold2302-128665 7 98798291 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397567 Affx-122962012 AX-123267922 GGAAGGGAAACAGCTTCTGTGTTATAAGCACTCAG[A/C]TTCTTCTGTGGATAAGATACTGCTGTAACAAAATA M 2 1 2 1 101000 f 74 goat snp23121-scaffold2306-24289 3 116409544 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387326 Affx-122970500 AX-123257684 ATCATCAGCAGTTTTTAGTACTACCAGAGAGAAAA[G/T]AAAATGATGGATCCAGTGGTTCCAAGAATTCTATT K 2 1 2 1 201000 f 74 goat snp23124-scaffold2306-165424 3 116267705 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375456 Affx-122979164 AX-123245815 ATAACATGTAGTGCTGCTGCTGGTGGTACTCATGA[C/T]ACCAACGTAGAACATACCCTCTACTGCCTGTACGA Y 2 1 2 1 101000 r 74 goat snp23125-scaffold2306-199323 3 116234624 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376380 Affx-122978107 AX-123246739 TGGATAGGAATGAGCAGTTTCATTAAAAGAAATGT[A/G]TGCTGATTTATAGACAAAATAATATCATTTTAATT R 2 1 2 1 101000 f 74 goat snp23126-scaffold2306-241882 3 116191095 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793962 Affx-122951482 AX-385280931 CTTCCAGTCATTCATCTGGCTAGCACTGGAATTTA[A/C]TTTTAGTGCTAAAATCAATTGGTATTTTCCTGAAA M 2 1 2 1 101000 f 74 goat snp23179-scaffold2313-75 28 34043604 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390430 Affx-122967636 AX-123260787 CATCTGTCTCTAGAATGTATTTACAGGGTGTTTTC[C/T]GCTTTATTAATAATTACATTTCCAGAAGTAGTTAT Y 2 1 2 1 101000 f 74 goat snp23180-scaffold2313-61740 28 33980095 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400541 Affx-122960438 AX-123270896 CTCGAAAATGTTTTCCAAAGAATAGAGTGAAAAAC[A/G]CCACTAGTACTATTGATACACAGCATAGCCTCGTT R 2 1 2 1 103000 r 74 goat snp23229-scaffold2320-5573 NW_017189516.1 62737613 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375924 Affx-122978468 AX-123246283 CTCACTCTCCTGAGTCACACCCTCAGGTCTTGTGC[A/G]CTAATGAAATAGGACTCTTTTCCACAGAGGAAGCA R 2 1 2 1 101000 r 74 goat snp23230-scaffold2320-34963 NW_017189516.1 62766369 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792371 Affx-122973366 AX-385279352 GTGTTTACTACAAGTATTTTTACTGAATCCCTGAT[A/G]TTGTCATGCTTTACCCTTTGGGATAAGGTCAGGAA R 2 1 2 1 101000 r 74 goat snp23231-scaffold2320-72026 NW_017189516.1 62803868 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453237 Affx-122920418 AX-123323570 CCTTGACCCCCTATTGCTTGTGGCTCTTGTAATGA[C/T]GACTTTCTAGGAGCTGCTCGGGGAGTGAGGAATTT Y 2 1 2 1 101000 f 74 goat snp23232-scaffold2320-117731 NW_017189516.1 62850862 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382306 Affx-122973909 AX-123252664 ACGTACAATTGCTGAAGACCAAAGCAGAAAATAGA[C/T]GTTACAGATATTTGCTTCTCTCATGGCTCAGACAG Y 2 1 2 1 201000 f 74 goat snp23233-scaffold2320-156462 NW_017189516.1 62888943 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390419 Affx-122967645 AX-123260776 TCTCTCTCCTTTCTGATCTGACCTACCCTGCTGGT[C/T]GACCTTCAAGCCCTACAGCCTCTGCACAGAGTCTA Y 2 1 2 1 101000 f 74 goat snp23234-scaffold2320-203109 NW_017189516.1 62933562 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396948 Affx-122963179 AX-123267303 TATGTAGGAGCTCTATCCATCTAGCTAAAGATTTG[C/T]ATGCCTGTCACTCACCAGACGAAGCAACTAACACT Y 2 1 2 1 101000 r 74 goat snp23235-scaffold2320-244639 NW_017189516.1 62975221 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433167 Affx-122935664 AX-123303508 TGCTGTTTTGATTTGTAAACTTGTTTATCTTTTGC[A/G]TGCGTGTTTTTTTAAACTTATGTGCTTGAAATCTT R 2 1 2 1 101000 r 74 goat snp23236-scaffold2320-303351 NW_017189516.1 63034379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406018 Affx-122955498 AX-123276370 GAGACGTGAGGTGTGGGGTGCTCTTCAGGCACACA[C/T]GTCTTCCTTCACAGTCTCCGTATGTGAGGTTTTTC Y 2 1 2 1 101000 r 74 goat snp23271-scaffold2327-16584 25 37640918 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782390 Affx-122926721 AX-385269466 GTTTCTCACACCAGGTTAATACTGATTCTGAAGAA[C/T]GACTTTCAGAGTATTCTCTCATACTCTATTTGTTT Y 2 1 2 1 101000 f 74 goat snp23272-scaffold2327-45140 25 37612108 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406132 Affx-122956195 AX-123276484 ACACACAGCTGAAAGGAAACTCAGAGGAGGGAATC[A/G]CCAAGAAAAGTGGCCATGGAGCTAATCCCAAGCTT R 2 1 2 1 102000 r 74 goat snp23273-scaffold2327-82964 25 37574017 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451658 Affx-122921595 AX-123321991 AACAGAGGCCAAACCACAAGGCTTCAAAGGTCCCA[A/G]TGAGGAGCTTGGACAATATCTGAAGGGCAATGGGC R 2 1 2 1 101000 r 74 goat snp23344-scaffold2334-3823 18 58437079 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450414 Affx-122922062 AX-21718316 GTCGTAGCTGCATGACCCTTTGAATAACCAGATCC[C/T]GGCAAATTTTTGTTGAATGAATGAAGCTACAAAGG Y 2 1 2 1 101000 f 74 goat snp23345-scaffold2334-35988 18 58469849 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395174 Affx-122964106 AX-123265529 AGGTCGGAGGGTCCTGACCAAGGGGAAGTGGAGGA[C/T]ACTCAGGACAGAGATTTGTGAGGGTCTTCAGTGTG Y 2 1 2 1 101000 r 74 goat snp23346-scaffold2334-80341 18 58512554 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441092 Affx-122928896 AX-123311429 GAATTGTAAGAGGAGGTTATGGGCTAGGACTACAG[A/C]GAATTCACCCTAGGGAAGACAGACAAGACCAGCCT M 2 1 2 1 101000 f 74 goat snp23347-scaffold2334-122086 18 58554898 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381851 Affx-122974190 AX-123252209 TTTTTGCTGCTATTGTTTTGAACAAACTATTATCT[A/G]CTATTTCATTTTAGAAAAAGTAAAATGAAAGATTT R 2 1 2 1 103000 f 74 goat snp23366-scaffold2339-5014 6 25819661 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397514 Affx-122962054 AX-123267869 GGGAATGGAAATTGAAGAAAGGGACCCCAGCAGGG[A/C]ACTTTTGTACCTTTCAGACAGACGGTGAATCTGTA M 2 1 2 1 101000 r 74 goat snp23403-scaffold2346-9759 NW_017189516.1 62663350 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376815 Affx-122977930 AX-123247174 TGTGATTTTGAATGATTTTGGGAGATGTATCATAT[A/G]TAAAGATGATTTGTCATTTATTTACCTTTTGATAA R 2 1 2 1 101000 f 74 goat snp23406-scaffold2348-39685 12 15760721 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774363 Affx-122953285 AX-385261499 TACTGATCACCTTTTCTGGGGCCTCACTGAAGTGA[C/T]TCTTTCAAACTACAGTGGGAACAACAAAAATGCAA Y 2 1 2 1 202000 f 74 goat snp23429-scaffold2354-4662 3 66382535 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772002 Affx-122978879 AX-385259158 ATCCAAGTTATAATCATGCTAATGGTTTCTTCCAT[C/T]TTCCTGTGGAAATTCTGTAGACCTTCTAGATCACT Y 2 1 2 1 102000 r 74 goat snp23430-scaffold2355-9230 3 66536435 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417444 Affx-122947203 AX-123287792 TCATGTAGGGAAGGTGTTGGAGAGCCTGGGGACTG[A/C]TTTAGTTTCAATATATGAAATTTGAAGGAACACAA M 2 1 2 1 103000 f 74 goat snp23431-scaffold2357-10804 2 67698125 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423834 Affx-122942788 AX-123294180 TTAAAAGAAACTCATTTTAAATGTGAGGGGGGATC[A/G]CAAAGGACAATGCAACAGAACTAGAGGAACATAGG R 2 1 2 1 201000 r 74 goat snp23432-scaffold2357-52900 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444963 Affx-122926675 AX-123315300 TAAACTATCCTGCTTCTAAAGTCAATATTCAAACA[C/T]AGCTTTTGACCAATGTGCTAAATGGCAGATAAGCA Y 2 1 2 1 101000 r 74 goat snp23433-scaffold2357-90814 2 67778642 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802328 Affx-122945234 AX-385289232 ATCTTTCAGAATATGCTTTAACTTTTTCATAGCAA[A/G]ATATGGGAACCTGTGCTAGGAAGCAGGAAATATAT R 2 1 2 1 101000 r 74 goat snp23436-scaffold2359-44372 NW_017189516.1 62568339 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384923 Affx-122972336 AX-123255281 CTCTCCCTCTCCAAGCTTCTTGCAGCCATGCCTTC[A/G]CCCCCAAACCAGGGGCATCTAGAGAGTCAGCCAGG R 2 1 2 1 201000 r 74 goat snp23437-scaffold2359-81692 NW_017189516.1 62532564 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430417 Affx-122937751 AX-123300758 AAAAAAAAAACACCCGAGAGTGTCTTGGCCTTCCC[A/G]TAAAGCAGAGAAACAAACAGGTATATGGTCCCTGT R 2 1 2 1 102000 r 74 goat snp23438-scaffold2359-139324 NW_017189516.1 62477198 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787257 Affx-122959362 AX-385274283 TGCATTCTCAACTTCTAACCATTCCTAGAAAAGCG[C/T]GGATTGTAAAAAATCTTGTCTCTTTAAATCAGAGA Y 2 1 2 1 101000 f 74 goat snp23452-scaffold2364-12194 5 4964269 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392383 Affx-122966229 AX-123262740 GTGGTGAGAACCTAGTATGCCTAGGCTATCTCTAA[C/T]GCCTACTGGGGAGGTCAGCAAAAAACTCCTGGAGA Y 2 1 2 1 101000 f 74 goat snp23453-scaffold2364-43431 5 4995403 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443821 Affx-122927068 AX-123314158 ACCGCTACACTCTGTGCCTAACCAAGCTCCCCCTA[C/T]GTTACTTTCCAGGCCATTTTTCCCTATGAGTTCCC Y 2 1 2 1 101000 r 74 goat snp23454-scaffold2364-91790 5 5042607 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402542 Affx-122958469 AX-123272895 ATGGCACTTCAGTTAACATTCCTTTGGTCAGTCAC[A/G]TGGTCACAGTAGGCCAAAAAGGAAACCAGGAAATG R 2 1 2 1 101000 f 74 goat snp23455-scaffold2364-125603 5 5076544 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376611 Affx-122979049 AX-123246970 CCTCAAGCCTCCCTACTTCAAATATCTCAAGCATG[A/G]CTGGGGAATCTCTGTAGAAAAATCCATCCAAATGT R 2 1 2 1 202000 r 74 goat snp23481-scaffold2368-2834 4 120675363 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432023 Affx-122935918 AX-123302364 TGTAGCCTTACATTTAGAGAAATCTGGAAGTAGAG[A/C]TTTGGAGAGTTCAGGACAAGGAAAGGCATTATTTT M 2 1 2 1 201000 r 74 goat snp23482-scaffold2368-42352 4 120714410 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450601 Affx-122922017 AX-123320935 ATCCTGGCACTTGAAACTGTCCACTGGGCAAGAAC[G/T]CCTTACTCTTGGGCTGAACATCTACCAACTGTAAA K 2 1 2 1 101000 r 74 goat snp23548-scaffold2370-15554 22 9249594 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398411 Affx-122961631 AX-123268766 GGAAATTATGTGCATGCCCCCAAAGGAATGAACCA[C/T]TACTCTCTTGGCTTGTCACTCTGCTCCATTGGACA Y 2 1 2 1 201000 r 74 goat snp23549-scaffold2370-51437 22 9285679 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414529 Affx-122949514 AX-123284878 AGAATGTAACAAAAGTGAATAAGTATAGATCAAAA[C/T]AGGAAGATATTTCTCCCAGTGCTATGTCCTTCACT Y 2 1 2 1 201000 f 74 goat snp23550-scaffold2373-48312 12 16004586 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451534 Affx-122921093 AX-123321867 GTATCCATCCTAAGTACTTCTGATATTTCCACTCA[A/G]TGAAACACTTGAACTGCCATTCAACCTCTTTCCAA R 2 1 2 1 201000 r 74 goat snp23609-scaffold2381-38250 1 146671574 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784217 Affx-122971666 AX-385271268 TCCATTATAATCTATTATTTCATGTAGTACATGCT[A/G]TATCTGATTCATTAGGGCAGCTCTGTTAATGGCCT R 2 1 2 1 101000 r 74 goat snp23711-scaffold2391-21947 23 47012286 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437677 Affx-122931774 AX-123308015 CCAGGCACAGAGCATTTCAGAAGGAAGTGAATTTA[C/T]TAGGAACAAAGAACAGAGATAATGGGGATACTGGG Y 2 1 2 1 303000 f 74 goat snp23712-scaffold2391-62540 23 47051768 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419566 Affx-122945404 AX-123289914 GGATGGACCTTAAAGTTTCTCAACACAAAATAAAA[C/T]GGTAAATATATGAAGTGTTTGATGTGTTAACTAAC Y 2 1 2 1 101000 f 74 goat snp23713-scaffold2391-101901 23 47091505 A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395367 Affx-122963983 AX-123265722 AAAGCCGTGTTCGAGTCCAGGTTCAGTGAGCAGCC[A/G]GTGACTAGAAGCTGCCAGAGAGGGAGTGGGGTCAC R 2 1 2 1 303000 r 74 goat snp23714-scaffold2393-15566 4 7274204 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428743 Affx-122938441 AX-123299085 AGGTTAGATAGGTAAAAATGCCTCCTTGCTCTCCC[A/G]TGGTGGTTACCCTTGGAATTTGCCCACCATCTTGT R 2 1 2 1 202000 r 74 goat snp23715-scaffold2393-61676 NW_017189832.1 1643 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770708 Affx-122930353 AX-385257872 TGGAATGCAGAATCTAAGATTCAGTTCAACCCAGA[C/T]GATAATTAACTACTTTTCACTGAAGCAGTCCTTGA Y 2 1 2 1 101000 r 74 goat snp23719-scaffold2396-20585 23 20540970 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385467 Affx-122971298 AX-123255825 CCATTCTCTAATCCATGTTTTTGATCACTGCTTAT[A/C]TCTTCCTTCATCTTTTTCAATCTTTGCTTCCATTT M 2 1 2 1 101000 r 74 goat snp23720-scaffold2396-50737 23 20571167 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445084 Affx-122926209 AX-123315421 GAACCGATGGATACTCATAATGGAAAACACATGTC[G/T]CTATGTCCTGTTAACTTTTTCATTCCTTCTCTAGA K 2 1 2 1 303000 r 74 goat snp23721-scaffold2396-95206 23 20612381 G T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778278 Affx-122925078 AX-385265393 GCCAAAGATAAAGAACTGGGTCAAGCAACCAATCA[C/T]AGAGATGAATGCCTTCTGCAGGAAGTCCTCCAACA Y 2 1 2 1 201000 r 74 goat snp23722-scaffold2396-155269 23 20673081 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452864 Affx-122920711 AX-123323197 TTTTCAATAATCAATTTATTCATTTTCTGACAAAT[A/G]CCGTATTTAGCATTCCAAGTACTAGAGATACGTAA R 2 1 2 1 101000 r 74 goat snp23723-scaffold2396-199027 23 20716011 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389627 Affx-122968747 AX-123259985 TCTCTGGTCCATGGTTTTAAGCTAGTTTTGCTGCC[A/G]AGTCCGGGCTGCACACCTGCATCTGAGGAGAGGCA R 2 1 2 1 101000 f 74 goat snp23852-scaffold2400-17692 NW_017189851.1 54530 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420156 Affx-122945584 AX-123290504 AGTGATTTTTTTTCCTGTCCTTACTGTCGCTCCTC[A/G]TGACAAAGAGGCTCAGAACATTGTCAAGAATTTAT R 2 1 2 1 101000 f 74 goat snp23853-scaffold2400-78472 NW_017189851.1 110434 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416950 Affx-122948026 AX-123287298 TTTCAGAAGCCTGCATGTCAAGGACACTGGATCAA[C/T]GTTATCATTAATATTAGTTATTACCAATTCAAAAA Y 2 1 2 1 201000 r 74 goat snp23884-scaffold2406-7067 5 73151914 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385410 Affx-122971338 AX-123255768 GAAGTCCAGTGACCCCCATTCTCACCTCAGCTCCA[C/T]GCAAGTTCATCTCAGGATGACCTTGGCCCAGCCCC Y 2 1 2 1 303000 r 74 goat snp23885-scaffold2406-35937 5 73014663 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442054 Affx-122928391 AX-123312391 AGGAGAGGCTCTGACTCCTTGTCCTCCTCCACCCC[A/G]TCTGCTTCCTTTAATTTCCTAAATGGCTGAGTACC R 2 1 2 1 103000 r 74 goat snp23886-scaffold2406-87592 5 73049970 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430124 Affx-122937405 AX-123300465 GCGTCAGGATTTCCTGACTTGCCCCAAAGGAAATT[A/C]TGCTTGGTTCTCATCACCAGAGAGAAAATTCTTCC M 2 1 2 1 201000 r 74 goat snp23887-scaffold2406-121226 NW_017212970.1 8316 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451384 Affx-122921210 AX-123321717 CAGGGCCAAGGCAGTATAGTAGTTACACATGAACA[G/T]AATGTTAGGAACTTTGCTTCACTGCCACTCTCAGT K 2 1 2 1 101000 f 74 goat snp23888-scaffold2408-5847 6 85066602 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799734 Affx-122921527 AX-385286661 AGGGCATGCCAGAAATTATTCTCTTAAAGATATAG[C/T]GGAGTCATTTAGTCTGACAGGAATGGTATCAGGGG Y 2 1 2 1 101000 r 74 goat snp23889-scaffold2408-81370 6 85141783 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795382 Affx-122928106 AX-385282338 TTCCTCTGCATGTTAGCACTTATTTCTGGACTATG[C/T]TTGTCCCTTTGTAATTATTCTTTAATGAATAGTTT Y 2 1 2 1 101000 f 74 goat snp23890-scaffold2408-140740 6 85202493 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791481 Affx-122934105 AX-385278472 CCAGTCAGTCAGAATAATATGTTGATTAGGTCAAG[A/C]TGCTAATGGCCAGGACTAAGAGACCTTAAGACTTC M 2 1 2 1 101000 r 74 goat snp23891-scaffold2408-228816 6 85289854 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385844 Affx-122971002 AX-123256202 TTAATCAGGTCTGATGCCTCCAGGTAATAAACAAG[C/T]AAGCTGAGGCCCTAAGTGATTAGGTAATGAGTGTT Y 2 1 2 1 101000 f 74 goat snp23892-scaffold2408-266677 6 85328075 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432725 Affx-122935467 AX-123303066 AAAGGAACATTTCTCATAATGTGTTAAACTAGGTT[A/G]TTTTCATACACCCTCCATTAGACTATTCCTGTCCT R 2 1 2 1 101000 r 74 goat snp23943-scaffold2413-27513 3 51921664 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409849 Affx-122952930 AX-123280200 ATAAATCATTGGTGAGTCCACTGTCAAGAATCATT[G/T]TTTGTTCATTTACTTATAGGAGCTTTATACACTAG K 2 1 2 1 101000 r 74 goat snp23962-scaffold2422-16829 18 61290208 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442660 Affx-122927904 AX-123312997 TGATATTGTCTTCTTGCCTTGATGTCTGTATCACT[A/C]TATACTGCCTTTCTTTGTCTTTTGTTATACAATTT M 2 1 2 1 10000 f 74 goat "snp23963-scaffold2428-10889;SV_312" 7 68095028 C A SV_312 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415700 Affx-122948530 AX-123286049 GAAAACGATCCATGGATTGGGATATACAATGCCTC[A/G]GCAGTGGAACTCTGAGGGATTTTGGGCCAGAATGA R 2 1 2 1 102000 f 74 goat snp23964-scaffold2431-15287 6 1362639 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431782 Affx-122936706 AX-123302123 AAATGCCCTTAAAACATCCACTTTAGGATTGAGGA[C/T]ACTAAGGCATACAGAGATGAAGTTACTTGTCCAAG Y 2 1 2 1 201000 f 74 goat snp23965-scaffold2431-45016 6 1390060 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797786 Affx-122950827 AX-385284725 TAGTCAAGAGTATCCTGATAAATTTTATCATGAAA[C/T]GACAGCATATAATTGAGACAAAGAGAGTGAGAGTA Y 2 1 2 1 201000 r 74 goat snp23966-scaffold2431-95923 6 1441278 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376933 Affx-122977781 AX-123247292 CTAGGGGATGAAAAGCACCACAAAGCAAGGAGCCT[A/G]CACCCCTGAATCACTGCATGGAGCAGATTTGCTCT R 2 1 2 1 202000 r 74 goat snp24031-scaffold2444-8584 10 78073975 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783449 Affx-122977880 AX-385270512 CTAATACAAGAGAAGAAGGCTGTGACCCTGGACTG[C/T]ACATATGACACCAGAGATTCAAGTTATAGTCTATT Y 2 1 2 1 102000 f 74 goat snp24032-scaffold2444-38486 NW_017189654.1 17918 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420345 Affx-122944968 AX-123290692 CTGGCCCCAAGACTCTATATTCTTCAGAGCAGGGG[C/T]GAAGGCACCTCAGTAACTGGGCAAGGGATCATGAA Y 2 1 2 1 202000 r 74 goat snp24033-scaffold2444-69291 NW_017189814.1 8900 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447217 Affx-122924980 AX-123317553 TATATGTTGCATGAGAGATGCAAAGATAGAATTTG[A/C]GAGTTCAAGGGAAATAGATTGCATCGTCTGGTGGA M 2 1 2 1 201000 f 74 goat snp24066-scaffold2450-44253 23 23596546 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416999 Affx-122947986 AX-123287347 CGCCCAAGTTGTAGCAGTAGTGTCACCTTCCCGTC[A/G]CCTTGTTCAATATATCTGTGGCTTTCCCTTGAGGC R 2 1 2 1 201000 f 74 goat snp24070-scaffold2452-4802 6 22368 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435634 Affx-122933771 AX-123305974 GGATCTAGAATACCTTTGGTGTCTACACAATGAAG[C/T]CAGGCCTCGTCTCGAGTGGAGACATGCACGTCAGT Y 2 1 2 1 101000 f 74 goat snp24071-scaffold2452-43628 6 61207 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439290 Affx-122930971 AX-123309627 AGTTGAAACCGCCTCCTCCTGAGGTGTGATGAGAA[C/T]GCTGGGATTCCTTTCCCAATAAAGCAGGGAAATAG Y 2 1 2 1 303000 f 74 goat snp24072-scaffold2452-83615 6 101266 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385561 Affx-122971222 AX-123255919 GCGAAAAAATCTGCATGAAGCCATTCATCCGCCCA[G/T]CCCCTAAGAAATTCCATACAGTAGGGTGAGGTAGG K 2 1 2 1 101000 f 74 goat snp24073-scaffold2452-121315 6 139199 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418899 Affx-122946100 AX-123289247 TAATCTGTGTTCTAATCTCTCCTTTATATGAACCC[A/G]TATGTTTATATATACCTATATACACAATGATTGGG R 2 1 2 1 103000 f 74 goat snp24074-scaffold2454-34180 18 51199791 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434047 Affx-122934201 AX-123304388 CGTATATAGAATAGCATTCATTTTCTTGGAGTCAG[C/T]GCTTTTATCTGCTCACCAAAATACCAAATTAGCTA Y 2 1 2 1 101000 r 74 goat snp24100-scaffold2458-3202 23 18953175 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792002 Affx-122931243 AX-385278990 TAGCTAACATTCATTGAGCATTTAGTGCCAGGAAC[A/G]TCTTAGTATGGTCTACAAACTAATTCATTTGCCAC R 2 1 2 1 101000 f 74 goat snp24101-scaffold2458-32297 23 18982313 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451753 Affx-122921524 AX-123322086 TGGGGTAAATGACACTCCCCAGTTTACCCAGGACT[A/G]CTGAGTTGTCTCCTACTGCAGTTTGGTAATAGAGC R 2 1 2 1 202000 f 74 goat snp24102-scaffold2458-73071 23 19023323 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391522 Affx-122966658 AX-123261879 TTCACTCTTCCATCACTTCCCACTCCTGGGGTATT[A/G]TCTGGGCTAAATCTAGATGCTAACAGTTATTATAT R 2 1 2 1 201000 r 74 goat snp24103-scaffold2458-107389 23 19058641 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766539 Affx-122940653 AX-385253899 ATATTGCTTTGAACTTAGGTCTTGGCACAAATTAA[C/T]AATCCCTGACTTCCTCTTTAGTCAAACATCTATTA Y 2 1 2 1 102000 f 74 goat snp24412-scaffold2474-6861 9 74530140 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418334 Affx-122946959 AX-123288682 CTTCATGGGATTGCTGTGAGGACTAAATGAGATCA[C/T]GTATGCAAGGCCTTTACTCCTGGCACATAGTAAGA Y 2 1 2 1 303000 r 74 goat snp24424-scaffold2478-15073 NW_017211724.1 2151 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432361 Affx-122935871 AX-123302702 TGCCTCCTCCAAGACTTGGGCTGTTATCCCATCCC[G/T]GGACCCGGAGCGGGCTTGAGTCCTAGGGCTGGGCT K 2 1 2 1 303000 r 74 goat snp24519-scaffold2486-19173 NW_017189605.1 4080 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400857 Affx-122959776 AX-123271212 CAAAAGACCATGTAAAGCCAGTCATATGACCGCAC[A/G]TCCCTGCCAGGATGGCTGATCTAGGGCTGTACATG R 2 1 2 1 101000 f 74 goat snp24520-scaffold249-35236 29 38755189 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391820 Affx-122967019 AX-123262177 AGAGGCGTCACCTGGTAAGGAAAGAAGATTGCAGA[C/T]GTCAGAGTTAAAGGGTGTTCTCTGAATGACCCACC Y 2 1 2 1 101000 f 74 goat snp24521-scaffold249-93325 29 38814286 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377139 Affx-122978232 AX-123247498 GTTGTTACTGTCCTCCAAAGATCTCCCCCTCTTTT[A/C]TCTCTACAGATGCAGGGGAGGGGCAGTGTGGTGAT M 2 1 2 1 303000 r 74 goat snp24522-scaffold249-152282 29 38874365 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446671 Affx-122924760 AX-123317007 ACTCCATACAGTTCTGTACAGTAAAGTACACAAAT[G/T]CACACCAACTTGTCTTGGATGTGCCCACAACAATG K 2 1 2 1 103000 f 74 goat snp24523-scaffold249-210123 29 38932557 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770650 Affx-122927133 AX-385257814 TCATATAGTTTCTGTTATTGTGACAGAATAGTATG[C/T]ATGTTAACAGGTACAAGCAAGACAATAATTAAAAC Y 2 1 2 1 101000 f 74 goat snp24524-scaffold249-256270 29 38978824 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410239 Affx-122952546 AX-123280589 AATCTGCAAAAACCAGGTGACCAGCTGCTAGAGGG[C/T]GAGGCTTGAGGTAAACATTCTGCAGTAGGTGGAAA Y 2 1 2 1 101000 r 74 goat snp24525-scaffold249-291362 29 39014568 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430996 Affx-122936685 AX-123301337 AGACTTTTAATGTGTGAACCTAACTTGTGTAGCTG[C/T]AGACACAAGAGATGAGTGTCATCAGGTGCTAAGGG Y 2 1 2 1 102000 f 74 goat snp24526-scaffold249-328429 29 39052234 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446740 Affx-122925341 AX-123317076 ACAACAGGTCCCACACTTTTGTGTCCCACACTTTC[A/G]TTTTTCACTGGGTCCTACAAATCGGGTAGCTGGTC R 2 1 2 1 303000 r 74 goat snp24527-scaffold249-359610 29 39083418 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417175 Affx-122947329 AX-123287523 TTCATCAGCTTCATGACTATAAAGATTATTATTCT[A/C]GGAAGGATTTTAATGTCTTTCCCAGCTAATTATGT M 2 1 2 1 101000 r 74 goat snp24528-scaffold249-442500 29 39167571 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383916 Affx-122972980 AX-123254274 CTTGGGTATAGAATTCTGAGTCAATTATATTTATC[G/T]CAGCATTTAAGATGTGGCACCAGTGTCCTCTGGCT K 2 1 2 1 103000 r 74 goat snp24529-scaffold249-474481 29 39199553 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413870 Affx-122949855 AX-123284219 GTGTAGAGAGAAGAGAGGAGGGGATCCTTTGAAGA[C/T]AGTAACAACAGCACTGTCTGAGAGCTGTGCTGGTC Y 2 1 2 1 101000 f 74 goat snp24530-scaffold249-532532 29 39258119 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452050 Affx-122920885 AX-123322383 ATGTAGAAAAGTGCTATTCCACAGGACCATATTGA[C/T]ATCTGCATAGACTGTGCACTTAATAGTTTCAAGGA Y 2 1 2 1 101000 r 74 goat snp24531-scaffold249-578815 29 39305016 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439667 Affx-122930592 AX-123310004 AAATGTTTTTTCTGATAAAAAGATACCTTATAATT[A/C]TTGGCAATTTGCATCTTACAGAGCTCACTGACACA M 2 1 2 1 201000 f 74 goat snp24534-scaffold2491-10446 3 66351175 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453779 Affx-122919588 AX-123324112 AATTAACATAGAGCATATTGTAGCAGTCTTGAGCT[A/G]CCTTAACTGACTGGAAATATCTTTCCCAGAATGTG R 2 1 2 1 101000 r 74 goat snp24535-scaffold2494-2765 10 78363711 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390001 Affx-122968045 AX-123260358 CTTCCGGAACTTTCCTGGTGTTTTCTCCAGAAACA[C/T]GGTCAGCTGGACAGGAGAAAATGCTGGTGGGGTCA Y 2 1 2 1 102000 f 74 goat snp24548-scaffold2497-10312 16 78815205 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428014 Affx-122939152 AX-123298357 TGACCTGCTTATCATCAATATAGTGACAGGTGTCC[A/G]TCCTGAGGCATCACAGGGAACGCTTCAGCCCCCTT R 2 1 2 1 102000 f 74 goat snp24561-scaffold2499-14170 1 157396598 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429192 Affx-122937953 AX-123299534 CAACAGGGGAGTCAGGCCTCATCTCGTCTGGAGAC[A/G]TGCAAGTCCCCTTTCCTATTGAGCTGTGACAGTAG R 2 1 2 1 103000 r 74 goat snp24602-scaffold2501-9793 20 60433657 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380873 Affx-122975054 AX-123251231 ATCATCTTCTGGCCAGAGGGCCAATTAACATTTTA[C/T]GGCTGTTTTCTGATAAGGGTCTGTCAACCAGAAAA Y 2 1 2 1 303000 f 74 goat snp24603-scaffold2501-59149 NW_017189883.1 3207 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437030 Affx-122933115 AX-123307368 AGATTCAGTCACAGATTCAACCAAACAGCAGTGAA[C/T]AAAACAATCAGAAACCAAACAAAATACAGGACAGA Y 2 1 2 1 103000 f 74 goat snp24621-scaffold2507-389 NW_017212140.1 6528 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443255 Affx-122927545 AX-123313592 ACACAAGATGTGGTGGGGTTATTTTTGTTTGTTTA[C/T]GGGTTTAGTTTCAGTGAAGTATTCTAATCTAAACC Y 2 1 2 1 303000 r 74 goat snp24680-scaffold2515-33494 3 101531483 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782914 Affx-122971359 AX-385269984 TGTTAAGGTAGCCTGAAATAAGAGATCAGCCAGTT[A/G]TTAAATGTGCACATCCAGATGGCAAAAATATATTC R 2 1 2 1 101000 f 74 goat snp24681-scaffold2515-65177 3 101510082 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437799 Affx-122931684 AX-123308137 CTTTGCCTCCCAGCCCAGGCCAAAAGAAAAGAATA[A/C]GTATCACCATCACATTAGCCATAACCAAGTGGTTT M 2 1 2 1 201000 r 74 goat snp24682-scaffold2515-102467 3 101476283 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386555 Affx-122970714 AX-123256913 GTGGAAGATGTTCACTGCATGGTGCTCACACGGTC[A/G]TAGACCCCAGAAGCTTGATGATATTGGCTCCCGAT R 2 1 2 1 102000 r 74 goat snp24683-scaffold2517-2155 19 19035384 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408472 Affx-122954426 AX-123278823 TAAAACCCAGAAGCTTGATGATATGGCTCCCGATT[A/G]CGTCACCACCAACCAATCAGAAGACATCCTTGAGC R 2 1 2 1 103000 f 74 goat snp24684-scaffold2517-51236 19 19071935 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409083 Affx-122953335 AX-123279434 AGACCAGAATAATTTATATATTTTTCCCACTAGCC[A/G]CCTAAATTATAAATTACCAACAAATTAAAATAGAT R 2 1 2 1 201000 r 74 goat snp24721-scaffold2528-24438 14 83621959 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387806 Affx-122969687 AX-123258164 GGGGAGTAAATTGGGAGAAATGTAACAGATCAGGG[C/T]GATCTAGACAACTGAGTTAGTCTCCAATGTTCACT Y 2 1 2 1 101000 f 74 goat snp24722-scaffold2528-76686 14 83674859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390513 Affx-122967245 AX-123260870 TTGCTATGAGGACATTATTTAATTAAGGAATGGGA[C/T]GAATTTTCCTACTATAAGGCAGTAAGAGACAGAAA Y 2 1 2 1 101000 r 74 goat snp24723-scaffold2528-111259 14 83709030 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437144 Affx-122932147 AX-123307482 TTCACCCAGCAATATCCCAGTCCTGGTTAAGAGGA[A/G]TCAGATCTCAGTCGGCAGCTCCTTCAGGGCCACTT R 2 1 2 1 103000 f 74 goat snp24769-scaffold2530-14952 NW_017216379.1 9829 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790349 Affx-122962891 AX-385277352 ACAGGTTTGGGTACAGATAGTGGATGTCTGGGAAG[C/T]ACTGTGTACTTGCTGCACAGAAGTAGACAGCTGAG Y 2 1 2 1 102000 r 74 goat snp24775-scaffold2534-3371 NW_017189764.1 9341 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414549 Affx-122949397 AX-123284898 CTATGATGGATCTTCTGTGAGGGGAAGAGAGGGGA[A/G]AGAGAGACACCAGGCAGAGCAAGCTGAGTCTCCCA R 2 1 2 1 202000 r 74 goat snp24780-scaffold2536-12443 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380603 Affx-122975252 AX-123250961 ACTGAGCTATGAGGGAAGTTTATCACCTTAAGGTT[A/G]TAATTGTTCAAAACTGCCCATCGCTGGAGATAATC R 2 1 2 1 201000 r 74 goat snp24787-scaffold2538-62940 23 22024461 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395786 Affx-122963663 AX-123266141 AGATCATTGTCTTTGGTTGAAAATAATCAGCAGTT[A/C]GTTTGTCAACATGTGTAACATGCCAGAGTAACCCT M 2 1 2 1 103000 r 74 goat snp24933-scaffold2550-6951 NW_017189986.1 14609 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795284 Affx-122934665 AX-385282242 TAGAGGACATAAGTCCCTTGATCCCTCCACATTTC[A/G]CATTTAGTCTTCTGAGCAAACCAGTTTCTCCAGAG R 2 1 2 1 101000 f 74 goat snp24945-scaffold2554-7579 10 63321338 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400194 Affx-122960187 AX-123270549 GCAGATCCAGGGAGAAAGTGACTATCTGATAAGAT[A/C]ATCTCTGGTAAGAGATGAAAATGAGGTGGGAGCCT M 2 1 2 1 101000 f 74 goat snp25019-scaffold2577-422 5 97074769 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379502 Affx-122976463 AX-123249860 TCTTGTCACCAGATAGACACAGTTATAGTTGGGAC[A/G]TATCCCAGCAGGATGGAGTGGATACAATGTTATCA R 2 1 2 1 101000 f 74 goat snp25020-scaffold2577-29470 5 97092791 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377744 Affx-122977376 AX-123248103 GTTTGAAGCTTCACCCCCAGAGCTTGAGGGGTCAC[A/G]GCTCTAAGTCTGTCTCCTGAGAGGAAGCACCTCCC R 2 1 2 1 103000 f 74 goat snp25267-scaffold2597-13989 17 539575 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440770 Affx-122929854 AX-123311107 GACTAACGCACACACACACACAAACTGTGCTGAGG[G/T]TTAGTGAGATGATCCATGCACAGTGAGTGTTTGGA K 2 1 2 1 101000 r 74 goat snp25281-scaffold2599-31134 10 85433027 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784959 Affx-122971174 AX-385272006 CTAGTTCAGATGTTTTCCTAACTGCCAGAAACCCT[A/G]ATTCAAATGTTCGCCAAGATTCCTCTCAAACCATG R 2 1 2 1 101000 f 74 goat snp25282-scaffold260-8025 10 77573702 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442276 Affx-122928266 AX-123312613 GTTGTGTCCCCAACGACAGAACACTCTTGCCCACC[A/G]TCCTGGTCACTGGTTTCTGGTGTCCCAGCACCCAC R 2 1 2 1 103000 f 74 goat snp25296-scaffold2602-10498 13 37188239 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414865 Affx-122949148 AX-123285214 GCGAAGGGCTTCTGCCTCCTTTGGGTCTCAAGTTA[C/T]GGGGAGATGAGCTGGCTTTTCCCCCTTCCGTGGGA Y 2 1 2 1 303000 r 74 goat snp25297-scaffold2602-43445 13 37221614 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437996 Affx-122931583 AX-123308334 CCCAGATGCCAATGCCATACTAACTCTCTGTGTCC[A/G]TGCTGATCTTTTGTTGCTATTGTTTTAAACCTCAA R 2 1 2 1 101000 f 74 goat snp25298-scaffold2604-35013 26 35176627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793089 Affx-122948055 AX-385280066 AAAGAGGCAGGGATGTAAGGAGACATTTTAGAAGC[A/G]CCTTCTACAGTTTTGCACCTAATTTGTGCCTTAAA R 2 1 2 1 101000 f 74 goat snp25343-scaffold2610-53075 3 106754921 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786835 Affx-122947597 AX-385273864 TCTTTCAAGGCAACTCAGTAAAACACTTAACTCTC[A/G]TTAATTTCAAAACGGTTAATTATCCTGAAGGAAAC R 2 1 2 1 101000 f 74 goat snp25364-scaffold2614-5488 NW_017189779.1 5473 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444601 Affx-122926952 AX-123314938 CAAGTTAATAGGTGGGTTATAACATGTGTAGCTTC[A/G]CCTTGGGGAGGTGTGGCCCATATAAAAGAAGAATT R 2 1 2 1 303000 f 74 goat snp25481-scaffold2620-9186 NW_017190029.1 33335 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428758 Affx-122938431 AX-123299100 ACAGCAACACGGCCCAGGCTCAAAAGCCAAGGAGC[A/G]CGTAAAAAGCACTAGCTGCAGAATGTCACCTGCGG R 2 1 2 1 101000 r 74 goat snp25494-scaffold2626-148954 NW_017189516.1 10122878 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790259 Affx-122925361 AX-385277263 ATAGGTTAGTTTGTGTGTCTCTTCTTTCACTCGCC[A/G]TAATGTTTATGCAATTCACCCGTGTTATTCAACCC R 2 1 2 1 101000 f 74 goat snp25495-scaffold2626-181912 NW_017189516.1 10156055 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415683 Affx-122948543 AX-123286032 GCAATATTGCTACTACCAGGTGGACAGAAGGGAGA[A/G]GCAGGGAGATTTGCAGCCTAACAGGTTCATTCCTT R 2 1 2 1 101000 r 74 goat snp25496-scaffold2626-219888 NW_017190151.1 88247 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404593 Affx-122957352 AX-123274945 TGCCACCTTGTGATAGCCAGAAAGCTGGAGAGTTG[C/T]CAGCTGCAACTGGAGATGAACCCTAGAATCCCCAG Y 2 1 2 1 101000 f 74 goat snp25497-scaffold2626-250117 NW_017190151.1 57832 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450223 Affx-122922275 AX-123320558 ATGTTAGGGAAGTTTTCAGCTATTATGTCTTCAAA[C/T]ACTTTTTTTCAGGTCCCTTCTCAGGTTATTTGTTT Y 2 1 2 1 103000 r 74 goat snp25507-scaffold2628-9166 15 3983895 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404631 Affx-122957322 AX-123274983 GTAAATTCTCAAACATATTAGCTCTCTTTCCTATA[C/T]GTGTGCCTCTGGGCTTCCCTGGTGGCTCAGATGGT Y 2 1 2 1 103000 f 74 goat snp25595-scaffold2631-8933 NW_017198811.1 18143 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401390 Affx-122959221 AX-123271743 GCAACCAGTGAGCGTGGTGTAGGAAGCCTTCACAG[G/T]AGTGCTGGAAGTGCTGCTTAGTTACACTATTTCTT K 2 1 2 1 201000 r 74 goat snp25596-scaffold2632-618 16 33751776 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428400 Affx-122938947 AX-123298743 AACTTCATTCACTAAATAAATAGTTCTATTTAGTA[C/T]GTAGACACTGAGCTAGGCATGGTGATGAACATGAG Y 2 1 2 1 101000 r 74 goat snp25597-scaffold2632-35713 16 33717447 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791611 Affx-122945780 AX-385278602 CAATTGTGCTTAATCTTTATGCCCTCTGTGCCTAG[C/T]AGGTGCTCTGCACCAAGGATGCAGACGCTGAGAGA Y 2 1 2 1 202000 r 74 goat snp25598-scaffold2639-4534 10 78039665 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783153 Affx-122969926 AX-385270220 TTTTTTTCCTCATCCTTTTGGTGTGATACCCAGCT[A/C]GTTACACTGATACACTTAGGGTGCTGAAAGGACAC M 2 1 2 1 101000 f 74 goat snp25599-scaffold2639-56258 10 77987200 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783705 Affx-122951940 AX-385270762 TGAAAACCTCTTTTGTGATGGTTCCCTTGTGAATG[C/T]GCCCTTTGATTGGTTGATCAGTTTCAGCCTTATTC Y 2 1 2 1 101000 f 74 goat snp25774-scaffold2653-6202 7 68555846 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448770 Affx-122923312 AX-123319106 CTATGACCGCTATGTGGCCATTTGCCATCCTCTTC[A/G]TTACTCTGTCCTCATGAGCCACAGAGTGTGTCTCC R 2 1 2 1 101000 r 74 goat snp25775-scaffold2653-48385 7 68514419 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780970 Affx-122977436 AX-385268057 TCAACTTTAGTATTTATTAAACAGATGAAGGAACT[G/T]TTCTCCAGAGAAAACTTGTACTCTTAAAAGGTACT K 2 1 2 1 101000 f 74 goat snp25776-scaffold2653-84460 7 68478370 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430061 Affx-122937555 AX-123300402 GTTTTAAAGTCAAGGGTAAATCCTCCTTCTCTGCC[A/G]TCTCCCACCATGCCAAGTATAGGCTTGGGAACAAG R 2 1 2 1 201000 r 74 goat snp25777-scaffold2655-2173 21 58181424 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386065 Affx-122971461 AX-123256423 AAGCAGAGGGAGCCACACAGGGCTGCTGTCTCCTG[C/T]GATCCCAACTCCAGGGAACTCTTTTCACTGGGTCA Y 2 1 2 1 103000 r 74 goat snp25778-scaffold2655-35362 21 58157922 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412432 Affx-122951421 AX-123282781 GTCGGCACAGACTGATGTAAACGGAAGAGGAGCTG[C/T]GCCAGCTGCGGACACTCTAGAACAGAAGTTTAGAT Y 2 1 2 1 101000 f 74 goat snp25779-scaffold2657-13001 5 99175789 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432601 Affx-122935503 AX-123302942 GCAGCAAAGAGAATGTCCCAGCACCAGTCACTGTC[A/G]TCCCCAGTATCTGTGTCTTCCCTCCTCGACAGGGA R 2 1 2 1 303000 f 74 goat snp25780-scaffold2657-95926 5 99226053 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395453 Affx-122963920 AX-123265808 GTGACATCTAAGGTCAGATTAGAGGCATGTGAATT[A/G]GGGAGATTTCCTTGTACTGGGGTTTTATGTGGACA R 2 1 2 1 101000 f 74 goat snp25858-scaffold2668-9074 17 25212423 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786862 Affx-122953808 AX-385273891 CAAATGAAAGGAATTACAAGGCTGAAATGCATCTT[A/G]CATTGAGCATTAGCACTACCTGTGAAACATGTTAC R 2 1 2 1 201000 f 74 goat snp25859-scaffold2669-26283 4 6238621 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780312 Affx-122975405 AX-385267407 TACAATAATCAAGGCAGGAAAGATAGATGAACCTT[A/G]TATTTGTGGAGTAAAGTCTGAGATATTAGATAGAC R 2 1 2 1 101000 f 74 goat snp25883-scaffold2670-951 1 102383262 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793079 Affx-122951089 AX-385280057 CATTTTGCATGGAGGGCAGAAGTTTGGAGTTCTTA[C/T]GAAATCAAATCAATACTAATCCTCAGCAAATGAAA Y 2 1 2 1 101000 f 74 goat snp25884-scaffold2670-35572 1 102349009 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448958 Affx-122923134 AX-123319293 ACAGTGAGGAGGGCAATGGGACAGGCACAGCATGA[C/T]GGGGGGAGAGTGAGGGGATTGGGTGACAGAAGTGA Y 2 1 2 1 303000 r 74 goat snp25963-scaffold2689-4643 NW_017189516.1 20876277 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798027 Affx-122945094 AX-385284963 ATGAGTTAATTTATAGCTAAGATACCTCTTAAGAT[A/G]CTCGTAACACTGAAGTGGAATTACAATGCAATTTG R 2 1 2 1 102000 r 74 goat snp26057-scaffold2703-15117 NW_017189516.1 54654593 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774131 Affx-122977460 AX-385261269 TGTTGACATTTGTATAGAGTTAGCCCTTTCTAAAA[C/T]ATCCTTGTAGAGATGGAATTTAAGATAGCTATATG Y 2 1 2 1 201000 r 74 goat snp26085-scaffold2710-130224 5 98960892 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434188 Affx-122934873 AX-123304529 TCTGTCCACACCGAGGTGGGCAGGCCAGGGCCCAA[C/T]ATCCTCACTGAAGGACAAGAGTGGGCCTGAGGGAC Y 2 1 2 1 101000 r 74 goat snp26108-scaffold2719-11862 3 875660 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429743 Affx-122937595 AX-123300084 TATGATACACACACACCTTTCTAGTACCAGGTGGT[A/G]TAATACAGGATTTACTGGAGGGAAAACTTAGAAAG R 2 1 2 1 101000 r 74 goat snp26110-scaffold2719-108944 3 799244 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792575 Affx-122956077 AX-385279556 TGATATAGCTCATTTGGATTTTCTTCACCCCTTTC[A/G]TCTATGTAGGAGGTAGGGTTGTATATCTCCCTTAT R 2 1 2 1 202000 f 74 goat snp26111-scaffold272-35758 12 14994938 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777291 Affx-122967253 AX-385264413 GAGCACAGGTCACAGCCCAGTAGCGCATTTTCTAT[A/G]CTTGTTCAGTGTGTCCTCTACACGGTGCAGAGTAT R 2 1 2 1 201000 r 74 goat snp26112-scaffold272-93127 12 14252650 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417286 Affx-122947244 AX-123287634 GAAAGAGTTTATTTTAATTTGTTTTTTATACACTA[C/T]GATCTTGGGAAAGAAGTAATGAGAGTAAAGTAAGG Y 2 1 2 1 103000 r 74 goat snp26113-scaffold272-167190 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770495 Affx-122935422 AX-385257661 GGTCCTAAGGTTGAAGAAGGTCCCTGGAAGCAGAA[C/T]AGACCACTTTTAAACCTTCAGAGATTTTTAAAATA Y 2 1 2 1 101000 f 74 goat snp26114-scaffold272-244437 NW_017189517.1 34367959 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424118 Affx-122942018 AX-123294464 GAGTTGCTTCCAGGCTTTTCTTTATGGAGGAGACT[A/G]CCTGTCGTGGGTGTTAGTTTCTATACAGCCACCAC R 2 1 2 1 101000 f 74 goat snp26124-scaffold2724-27295 11 106002465 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381325 Affx-122974433 AX-123251683 AGAAGCGATCGCGCCGGGCCCACACAGCTCCCACG[G/T]AAGCCCAGAAAGTCTCACCATTAATTAACATAATT K 2 1 2 1 101000 r 74 goat snp26125-scaffold2724-87157 11 105952406 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383657 Affx-122972520 AX-123254015 ACAAATGACGAGTCGTTGGACCGCAGAGAACTTAT[A/C]GGGCAATCAAAGCATCCTGCATGATGCTGTGATGG M 2 1 2 1 303000 f 74 goat snp26163-scaffold2739-22429 1 144009876 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385977 Affx-122971527 AX-123256335 ACCGCCCCGGTTTCTAGTGGGTTTGGCCATGTGCC[A/G]CCCCCGTACCAGATCTGCTTCTCTCCTGTGTGATG R 2 1 2 1 102000 r 74 goat snp26215-scaffold2742-16724 26 48490650 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800289 Affx-122932906 AX-385287212 GTGGAAATTGAAGTGACAAAGCAGCTGTGACGGAT[A/G]GACACCAGTGTCCAAATGTGGTTATAAGCAGAATG R 2 1 2 1 202000 r 74 goat snp26216-scaffold2742-63731 26 48443072 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426379 Affx-122940240 AX-123296725 TAACAACCTTTGCATTTTGTGCCAAATGAACTCAA[C/T]GGAGTTAATCTGGTATATTTTCTTAACCTCTCAGA Y 2 1 2 1 101000 r 74 goat snp26217-scaffold2744-48151 5 100814305 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772437 Affx-122968742 AX-191755027 TGTACTTAGCACATGGGTTGTATCTTTTTAAGATC[A/G]TTTGGTATAATTTGAAACTGTTAAATTATCAACAT R 2 1 2 1 101000 f 74 goat snp26218-scaffold2744-90576 5 100771913 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422801 Affx-122943205 AX-123293147 GAAAAGAAAATAGAACACAAGCTGGATGATCAGGA[C/T]GCTGCAAACAACCATCACAACAGCTTGTCTGGATA Y 2 1 2 1 202000 f 74 goat snp26299-scaffold2754-17438 9 73938194 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440746 Affx-122929872 AX-123311083 ATTATGGAATCTCGGATGTCCACTGAAGCTCCTGC[A/C]AGAGTCCCCATTTCAACAAGAGGGGCACACCGCTC M 2 1 2 1 201000 r 74 goat snp26300-scaffold2756-4032 11 5822237 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418061 Affx-122946619 AX-123288409 ATAGGTATCAATACAGAACAGATAGATGATAGATA[A/G]CAGATATATGATAGATCAAGAGATACATATACATA R 2 1 2 1 303000 r 74 goat snp26301-scaffold2756-45596 11 5862112 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452184 Affx-122921228 AX-123322517 GATGATTTTTTTTTTCTCATTATTTTTAGATGATC[A/G]TTTCTGTCTTAATTTGCACAGCTGCACAAGGAGAT R 2 1 2 1 101000 r 74 goat snp26302-scaffold2756-82099 11 5899033 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422731 Affx-122943256 AX-123293077 GAACTGTGTGAAGAATCACCTGCGATCCCAAGCCC[A/G]TGGACAGACCAGAGCACTTCAGCTATGAGCTGGCC R 2 1 2 1 201000 r 74 goat snp26303-scaffold2756-135123 11 5952098 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449937 Affx-122922909 AX-123320272 AGAGGCCTGAGTACCTGAATCAATACCACAGGCCC[A/G]AGACAAATCTCCACCCCAGTGCCTCCTCCCTTACC R 2 1 2 1 201000 f 74 goat snp26304-scaffold2756-172330 11 5989109 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392159 Affx-122966314 AX-123262516 TCATGCTTCCTTCCCTTCTTCTGCCCATGGACCCC[C/T]AGAGGATAGCTTTCTTTCATTCTCTGGAACTTCTG Y 2 1 2 1 303000 f 74 goat snp26305-scaffold2759-2450 7 99097605 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452707 Affx-122920300 AX-123323040 ATTTTTTAGCTCAATTTCTTTTCTTTTCTTTCTTT[A/G]TCCATTCTCTCCCTATCCTGTAGACACACTCAGCT R 2 1 2 1 101000 r 74 goat snp26597-scaffold2770-45708 NW_017217042.1 1182 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407137 Affx-122954862 AX-123277488 ACTCATTCAATCTGCCCAACCCACAACAAGGAGGG[C/T]GCCATTTGCAGATGGGAGCCCAACCCAAAGCCCAG Y 2 1 2 1 202000 r 74 goat snp26629-scaffold2781-36998 NW_017189517.1 28718042 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447521 Affx-122924063 AX-123317857 CTTGAGTTGCAGATACAGATATAAAGAGGGAAAAA[G/T]ATCAGATTTGAGAAATACTCAACTGGTCAGCTGGA K 2 1 2 1 201000 r 74 goat snp26664-scaffold280-702 4 119371740 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768539 Affx-122942389 AX-385255719 GTGTGGAAAGAGATTGGAATCCTCTAGTGCTGCTG[A/G]TAGGAGTATAAAAGGTAGTAACCAAAGTGGAAATG R 2 1 2 1 101000 f 74 goat snp26665-scaffold280-36829 4 119407667 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782907 Affx-122952657 AX-385269977 CATCTTTTCCTCATTGATCTGTAATGATCCAAATA[C/T]AATATATATGGTAATCAACTATCTGTCATATATGT Y 2 1 2 1 101000 f 74 goat snp26666-scaffold280-82672 4 119453633 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386698 Affx-122970173 AX-123257056 ATGTGTGTTACTTTTAGAAAAAGCTAAGCATGTAC[A/G]TAAAAAGAACATCTTATAAATTTTTTGCATAAATA R 2 1 2 1 101000 f 74 goat snp26667-scaffold280-124236 4 119494463 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769117 Affx-122945312 AX-385256292 TTCACATAAGCCTGAAAATAAGAGCTATTCTCTGC[C/T]ATTTGTATTGCAATTTTGATACATACCTGGAAAAT Y 2 1 2 1 101000 f 74 goat snp26668-scaffold280-185182 4 119550640 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412593 Affx-122951295 AX-123282942 TCACCAACACATGAGTGTCTTGGGCCATAGGTTTG[A/C]TGGTATTTTGTGTCTAAACAACAATCTTACTGCTC M 2 1 2 1 201000 r 74 goat snp26669-scaffold280-226802 4 119594652 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385818 Affx-122971025 AX-123256176 ATTGCTTGTTTTGAATAGCTGTCAGATTTCCCATC[A/G]CTACTAGATTAAGGTCAAAGTTGACAACTGAACAG R 2 1 2 1 101000 f 74 goat snp26670-scaffold280-258292 4 119626816 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422686 Affx-122943664 AX-123293032 GGAAAATGTGGGAGTAGAAAGTACAATCTTAGATT[A/C]TATTTATAGCTCAGATCCAACTTTCTAAGCCACAA M 2 1 2 1 101000 r 74 goat snp26671-scaffold280-293792 4 119659370 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788699 Affx-122962683 AX-385275715 AAATCAGGCTGACCCTCCATATAATTAACTTTATA[G/T]AAATGCATTTTGATTTGTTGCTAGCAACTTATATT K 2 1 2 1 202000 r 74 goat snp26672-scaffold280-339395 4 119705001 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773298 Affx-122946975 AX-385260441 TGAGATGGAATTTTATTTGAATGACTCATTTATGA[G/T]GTATTATAGATACTTAAGGCAATAACTACATTACT K 2 1 2 1 201000 f 74 goat snp26673-scaffold280-399551 4 119765385 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395547 Affx-122964251 AX-123265902 CTTATTCTTAGCTTTAATTTTATCCATTTACTCTA[C/T]GAACTCCAACAACTTCTAGATCACAGATCTTTCAA Y 2 1 2 1 101000 r 74 goat snp26674-scaffold280-428066 4 119793918 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382244 Affx-122973956 AX-123252602 ATGGATGCAAAACGAAGAGGGTTCTGTGTATCTAA[C/T]TGAATGTGTCCAACTAACACAACCAGCCTTCTTAA Y 2 1 2 1 101000 f 74 goat snp26675-scaffold280-458935 4 119816467 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408596 Affx-122953649 AX-123278947 TTCTTGCTACAGGTCAGTATGTAGCCAGGCTTACA[C/T]GCTAAGAGAGGGAAAGAGAGCACCCTGAATTGAAA Y 2 1 2 1 102000 f 74 goat snp26676-scaffold280-499766 4 119857677 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419085 Affx-122945791 AX-123289433 GGTCAACTACATTTCTTCTTCTAGCACCACAAGGA[A/G]CATCCAAGCCCTGCTTGGAATGTGGTGATTCCCTA R 2 1 2 1 102000 f 74 goat snp26677-scaffold280-532752 4 119890764 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771258 Affx-122961355 AX-385258416 TATATTTTGTGCTCTAGAAATTTGAAGTAGCACAA[G/T]AATTATTGACTATCCTAGGATTTAGAAATATGAAA K 2 1 2 1 201000 f 74 goat snp26678-scaffold280-577892 4 119936541 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428904 Affx-122938922 AX-123299246 AGATCTCTGAACTGTTGTCTTGGCACCTCCTAATA[C/T]ACATCTCATGAATACAGTGTTTTATTTAGCTTTGA Y 2 1 2 1 101000 f 74 goat snp26679-scaffold280-623673 4 119984056 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782668 Affx-122958022 AX-385269741 ACAAACCAGAAGATCATCTCTATAGGACCAGCAGC[A/G]CCAAGTCTAAGGTCCTAGACTGGAGCCTGAAGCAA R 2 1 2 1 201000 r 74 goat snp26680-scaffold280-654889 4 120015103 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766698 Affx-122931169 AX-385254042 AATCTCGGTCTCTATGAGAGGGAAGCTAGGGTAGT[A/G]ATCTGGAAATAGTAATGAGAAACATTAAGAACTTC R 2 1 2 1 101000 f 74 goat snp26681-scaffold280-693731 4 120054852 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775998 Affx-122976043 AX-385263128 AGTACTGAGTTTGCATCTATATTCTTGCTTTCACA[G/T]ATATCTTAGTGGAATATTTGTAAAGGTTGTTTAAA K 2 1 2 1 101000 f 74 goat snp26682-scaffold280-774793 4 120137543 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450772 Affx-122921835 AX-123321106 TGGGAGGCTGCTGTGGGGGTGCAGCCTGTCAGCAG[C/T]TCTGGGGCTGCCATCTTGTTCTGTCACCTTAACCA Y 2 1 2 1 101000 r 74 goat snp26683-scaffold280-823527 4 120185234 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378547 Affx-122976614 AX-123248906 CATAGTTATAATACAATTAACAATATTGTATCACT[A/G]TCAAACTGGGAAGACACAATGATCAAACTGAAGAG R 2 1 2 1 101000 r 74 goat snp26684-scaffold280-856932 4 120218907 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400821 Affx-122959802 AX-123271176 GCCTCATTTTGAGTTGAGAGAGGGAAATCAGTATT[A/G]CTTTCAAGATGCTGCAGGGAATCAGGCCTCATATT R 2 1 2 1 201000 f 74 goat snp26685-scaffold280-895438 NW_017212635.1 10117 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796353 Affx-122962958 AX-385283303 AATAAGTGTGGGTATGATACTCTGATTTCCTTCTG[A/C]TAGCAGCATGATTCCTGTTGAACAAAGGGCCAAGC M 2 1 2 1 102000 f 74 goat snp26686-scaffold280-960388 4 120285508 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454168 Affx-122919316 AX-123324501 TGTACAATTTCATTAGAACACTTGGTTTAAGATGC[A/G]TGTTTCCTTATTTTCCTCTAGATTTTCTCACAACA R 2 1 2 1 101000 f 74 goat snp26687-scaffold280-996900 4 120316908 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392593 Affx-122966057 AX-123262950 GAGGGTGTAGAAGAGAACATCTTGTCTTCTGGAAA[C/T]ATCGTGGCCGGCCTAATGTAAATGAAGAGAATAGG Y 2 1 2 1 101000 f 74 goat snp26688-scaffold280-1028334 4 120348697 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421776 Affx-122944347 AX-123292123 TTTTTTGTTTCAGTTTTTCATATTTATGCTTTATA[C/T]AGAAGAGGACATTTAAATCTAAAAAGACCGTCCAG Y 2 1 2 1 303000 f 74 goat snp26689-scaffold280-1064502 4 120385781 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795620 Affx-122927354 AX-385282575 GGATGTAAAAGTTATGAATGGCTAATGGATTTTCT[C/T]GCTACTCTTAGGAAATGGGAAACCGTGTAAGGTAA Y 2 1 2 1 101000 r 74 goat snp26690-scaffold280-1131070 4 120453736 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781603 Affx-122941107 AX-385268687 TATCTGTGGTTCTGAAAACTGCAAAAGTCAAATGT[G/T]TATAGAATATACAACTACAATTAAATGCTTAAAAT K 2 1 2 1 101000 f 74 goat snp26691-scaffold280-1171906 4 120493013 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775635 Affx-122957182 AX-385262766 CTGTAAGAATGTGGAAGCTCTGGCTGAATCATTCC[A/G]TTGAAGTGAAAGTGCTTCGGTTCTCAGAATGCACT R 2 1 2 1 101000 f 74 goat snp26692-scaffold280-1209490 4 120531943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768619 Affx-122942451 AX-385255799 ATTCTGGATAATTTCCATATGTCCCTCTGAGGTTT[A/G]CCATTCTCTCATTCCATAAAGTAACCTCAAGTATA R 2 1 2 1 202000 f 74 goat snp26818-scaffold2814-21206 26 41035595 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429276 Affx-122937883 AX-123299618 GAGTTCATAGGGTCCCCACACCCATATACAATTAA[C/T]AGAAACCAAGTTTACTTAACTGCTGAAACAACAAA Y 2 1 2 1 201000 r 74 goat snp26819-scaffold2819-16070 NW_017190155.1 71433 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397621 Affx-122962630 AX-123267976 GGGGATAATAAATTATTTTTCTGCAAAATATGCTA[C/T]GACAAATGACTGTTCATTTATAAATAATTTAATAT Y 2 1 2 1 101000 f 74 goat snp26820-scaffold2819-64322 NW_017190155.1 22467 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446891 Affx-122925225 AX-123317227 TTCCCTATATACTAAGGACAGAGTGTTTACTAAAC[A/G]TCTATTCTGGGTGTACAATGGGGAAAGCATCTTGA R 2 1 2 1 102000 r 74 goat snp26834-scaffold2820-54714 NW_017189550.1 45947 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444073 Affx-122926847 AX-123314410 AACACATCCATCCTGCCTTGCCTTACAACTTCCCT[A/G]TTTCACATCACTCCTGGGACAGGAACCCAGTCTCT R 2 1 2 1 202000 r 74 goat snp26859-scaffold2828-36711 NW_017189516.1 41534103 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383377 Affx-122972653 AX-123253735 CTGCACCTTGGGCCAGCGCAACTTCTCCATCTCTG[C/T]GATGGAAGAGCAGCTTCTGAATGATCTCTTCCAAT Y 2 1 2 1 101000 r 74 goat snp27037-scaffold2873-24216 18 53825680 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387692 Affx-122969816 AX-123258050 AGAGCTAGCAGCTGGTGGAAGCAGGATTCGAACTC[A/G]AGCACTCTGATTCTTACCGTGAACCAAGAGGCTAC R 2 1 2 1 101000 r 74 goat snp27038-scaffold2873-88498 18 53760914 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440485 Affx-122929371 AX-123310822 AAGTAGATGATGGGGTAGTAGTCCCCACTCACGGC[A/G]TCGAACTTCACATCTGCAGACACACGGGGCAGGGC R 2 1 2 1 201000 r 74 goat snp27039-scaffold2873-128823 18 53742700 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404699 Affx-122957266 AX-123275051 CCCCTAAGGTGGTTCATGATGGTCACAAACTAATA[C/T]TGCAGATAAAACATTTAATTTTTGGTAAGTTTTTC Y 2 1 2 1 101000 f 74 goat snp27041-scaffold2873-219718 18 53650535 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401716 Affx-122959532 AX-123272069 CTTAAGGAATGATGCACAAATACACTTTACCTTCA[G/T]AGGCATCCTTCTCCTCCTCTTCATCACTATTCACT K 2 1 2 1 303000 f 74 goat snp27049-scaffold2883-58782 NW_017189516.1 20460116 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385459 Affx-122971304 AX-123255817 TGCTCCCCTCTCCTCCCTGTGACAGTGAGCTTTTA[A/C]GGGTAGGGTGTGTCTTGTGTGTCTGACTCCTGACA M 2 1 2 1 202000 r 74 goat snp27050-scaffold2884-64391 NW_017189662.1 31024 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442680 Affx-122927889 AX-123313017 AGCACAATGCTTAGATATATGCACGCGCTGTAAGA[C/T]AGTCCCCACGACAAATTCGGTTAGCACCCCCCGCT Y 2 1 2 1 101000 f 74 goat snp27051-scaffold2884-133127 NW_017189530.1 554963 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399421 Affx-122961232 AX-123269776 CCATTTCCCTGCTTCATCAGGAAAGGAATCCCGGC[A/G]TTCCTGTCACAACTCAAGAGAAGGCAGTCTCAACA R 2 1 2 1 303000 f 74 goat snp27052-scaffold2888-12234 10 77805163 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388740 Affx-122968958 AX-123259098 CCTCCTGGGACTATGCCTGTCTGAGCATTGCTTAA[C/T]GATCAACCACCCCTCTGGGGTGCTCATGTCGTGTG Y 2 1 2 1 101000 f 74 goat snp27053-scaffold2888-46290 10 77771293 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798361 Affx-122967778 AX-385285296 TGGAGGAGAAGAAAAGGGTAAATTCGTACATGGTT[A/G]CTGTTGCCACAGAGAAGCAGAATAATATAATGCTA R 2 1 2 1 201000 r 74 goat snp2706-scaffold1078-9894 NW_017189869.1 2313 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449567 Affx-122923236 AX-123319902 TGGACTTTATAAAATGATTTTTTATTTAAATAGTC[A/G]TTAGGTTTTCATTTTTAGTCTGTTCCTATGGTGGA R 2 1 2 1 101000 r 74 goat snp27130-scaffold2895-4311 6 117296452 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375794 Affx-122978573 AX-123246153 TTGGTTCTTTGTCTCATCACAACAAAGATTTGGAG[C/T]AACGGACATTAGAGCCCTCAGCTCGTCACAGGTCT Y 2 1 2 1 303000 r 74 goat snp27342-scaffold2901-665 NW_017214004.1 16235 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383448 Affx-122973462 AX-123253806 TGAGCGTGTTCACAGCACAAAACTTGGGCATCTGA[C/T]GGTTGGTTTATGGACTTTCTGTATCCAGTTGCTGA Y 2 1 2 1 101000 r 74 goat snp27345-scaffold2905-5863 16 79167099 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410255 Affx-122952532 AX-123280605 AGGAAGTCCCGGCTGAACAGGGCTAGTCGGGGTTC[G/T]CTATTGCAGGACTTCTCAGAGCCTGTGGAGTCACT K 2 1 2 1 201000 f 74 goat snp27346-scaffold2905-34820 NW_017189732.1 26863 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772284 Affx-122944060 AX-385259439 TTTAAAAAGTGTAAAGAACCGTTGGTTTGAAATAC[A/G]TGTATTCTAGTCCCAGCGTACTGTTCTGTCCGTCC R 2 1 2 1 101000 r 74 goat snp27347-scaffold2905-69098 16 78964801 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443966 Affx-122927003 AX-123314303 CCAACATGAGAGAGCCCCAGTACCAGGTGTGAAGC[A/G]TCCCCCAGACCCTAGTAACCGTGCAGCGCGTAGAG R 2 1 2 1 101000 f 74 goat snp27348-scaffold2906-25758 21 69131743 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448662 Affx-122923341 AX-123318998 ACTCTGGCTGTCTAGTTTTCTGCTCTGCCCGGCAC[A/G]TGCTGGGCACACAGCGGACACTCACAACTGCTTGC R 2 1 2 1 201000 f 74 goat snp27401-scaffold2911-31961 18 44771479 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801369 Affx-122952785 AX-385288280 TTGTAAAATAATAACATAACGATATCTACCACTTT[A/G]AAAGTTCATTTTATTCAATGCCCTCCCTAGCAGAA R 2 1 2 1 101000 r 74 goat snp27402-scaffold2911-65939 18 44801218 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408978 Affx-122953909 AX-123279329 ATATGAATACAAAAGTAAGTGCTAGAACACGCCAC[A/G]ACATGCCACCTGCCCCATCAGAAGCTCGTTTTGTT R 2 1 2 1 101000 f 74 goat snp27403-scaffold2911-98718 18 44833974 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407203 Affx-122954809 AX-123277554 TGTCATCAGCTGGTATGTTCCATTCCTTAACAATC[A/G]TCCAGCTCAAACTCAAATTTATATGAAGCTCAAAG R 2 1 2 1 101000 f 74 goat snp27440-scaffold2923-64506 11 89753585 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773958 Affx-122951744 AX-385261097 GAAAAACACTTTCATTTAGCCCTTATTTAAGCAAA[C/T]AGGATTTTCACAGCATTCAGTTTTGGGTCTTACTT Y 2 1 2 1 101000 r 74 goat snp27441-scaffold2923-103412 11 89793061 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775113 Affx-122958264 AX-385262245 ATTTAAAGATGAAGATGATGAAACCTTGAAAAGAG[C/T]AATAATTTTCCAAGGTCATCTAGCTTGTAAATCTG Y 2 1 2 1 201000 f 74 goat snp27442-scaffold2923-132084 11 89821728 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398805 Affx-122961409 AX-123269160 GCCCAGAGATCACAGTTACTTTCGTGAATGCCCCA[C/T]AGTGAGTGTGGAGATAGTTAACAGATCATGGTACC Y 2 1 2 1 101000 r 74 goat snp27521-scaffold2930-31428 28 44604810 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447871 Affx-122923880 AX-123318207 TTTTCTAAAACCAGCTTGAACATCTGGAAGTTCAC[A/G]TTTCACGTGTCCAGGGAGAGGGTAACTCTAAAAGA R 2 1 2 1 303000 r 74 goat snp27534-scaffold2932-48964 NW_017189793.1 16963 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777591 Affx-122978695 AX-385264710 TTATAGTTTAAATGTGAAAACATCTGCACAATTAG[C/T]ATTTTGGAGTTTTTTTGGATAACTAAAAGCAGAGA Y 2 1 2 1 101000 f 74 goat snp27535-scaffold2938-7756 1 138009225 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454315 Affx-122919247 AX-123324648 ATTAGCTGTTTCAGCTTGGTGTCAGAGGGTGCATC[A/G]TTCCTTAGTGATCATCTTTGTCCAGAGTCCGATGC R 2 1 2 1 101000 r 74 goat snp27541-scaffold2946-13615 3 51906208 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397756 Affx-122962527 AX-123268111 GCATGACTCAACTAAGTCAGTGCAGCCAAAATAAA[C/T]AAATATTTAAAGAAAGAAAAGAAAACGAGTGAAGT Y 2 1 2 1 103000 f 74 goat snp2760-scaffold10794-8610 2 554868 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436938 Affx-122933185 AX-123307276 CTTGATGAATATTTTCCACTTAGAAAGGGCGACTG[C/T]ACTGAACTGGCTAACAGAGAACACCGCTGACCTCA Y 2 1 2 1 10000 r 74 goat "snp27699-scaffold2950-529;SV_321" 9 74225430 G A SV_321 2 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446836 Affx-122925271 AX-123317172 CCCAAAATCTTTTAATTTCTTGTGTTATAGATATT[A/G]TATTTGTAAATTTGCTTTTAAGATTAAGTTAACCT R 2 1 2 1 103000 f 74 goat snp27711-scaffold2955-32274 3 51826062 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445023 Affx-122926628 AX-123315360 GAGTGGAAAGCGCATTTCCTTGTCTCCACACGAGA[C/T]GAGGCCTGACACCCCTGTTGAAACTCCATAGGAAC Y 2 1 2 1 103000 f 74 goat snp27724-scaffold2959-15765 17 68695194 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377658 Affx-122977854 AX-123248017 AGCGGCCGAGGAATTGCAATTCAGGACATTCAACC[G/T]GTGGCAAACCAGCGTCAAGTCCAGAGAGCAATGGA K 2 1 2 1 101000 f 74 goat snp27761-scaffold2961-13578 18 64663612 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779132 Affx-122931456 AX-385266237 TTTAGAGCAATTTTAGGCTTACAATAAATGTTGCA[A/C]AGATAATTCAGAGTCCTGCCTATCCTACACCTAGT M 2 1 2 1 101000 r 74 goat snp27762-scaffold2961-47017 18 64629491 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773593 Affx-122944163 AX-385260733 GAGAGAAAAAGGACAGATTATTTTCAAAGGAGCAA[C/T]GAGAAGATCTGCAGTTCATTTGCAACAGAAATGAT Y 2 1 2 1 101000 r 74 goat snp27763-scaffold2961-89433 18 64587854 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383576 Affx-122972591 AX-123253934 GTCAGAATGTGCTATGAAGAAAACAAATCCAGGTA[C/T]AAAGGAGAGAGTGGTAGGGGGTGTTATTTTGTCCT Y 2 1 2 1 303000 f 74 goat snp27764-scaffold2964-8032 7 99842640 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427895 Affx-122939689 AX-123298238 TAACCAGTGTAGACTGAAATAAACACAGGTCAAAT[A/C]GCGTCAGTCAGAAGAGAGGAGGCTGTGCTGTGGAG M 2 1 2 1 101000 f 74 goat snp27790-scaffold2974-41549 16 78770240 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390540 Affx-122967223 AX-123260897 GGCATAAAGGGAAGAGCGGCTTGTCCTGCGTCCGC[A/G]TGAAGCTCTGCTCGTGTCTGCCTTCTGCCTCCCGC R 2 1 2 1 202000 f 74 goat snp27791-scaffold2974-71822 16 78741009 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397363 Affx-122962286 AX-123267718 GGACTGCGATCCTGCCCACAGTCATAGAGCTGGTA[C/T]GTGGCAAAGCCAGGGCTCAGAGCCAGGCCTCTGGG Y 2 1 2 1 101000 f 74 goat snp27792-scaffold2974-108160 16 78704823 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407701 Affx-122954572 AX-123278052 CACGCTGGTCCAATGCTCCAGAAGGCGTAAGCGAT[C/T]AGGTGTGAGACTTTCAAACTGAACCAGAGAGACCC Y 2 1 2 1 101000 r 74 goat snp27793-scaffold2974-141129 16 78671829 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416036 Affx-122948363 AX-123286385 TGTAGTGTATGTTCTGTGGGTGTGTGGTGGATGAG[C/T]GTGTGTAGTGTGTGTGGGTTGTGTGTGGTGGTGTC Y 2 1 2 1 103000 f 74 goat snp27794-scaffold2974-186548 16 78632096 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421126 Affx-122944201 AX-123291473 CTGAGCCCTGTCTGCTCCTCTTCTTGTTTGTAAAG[A/G]AGAGCTGACCGGCAGGCACTGAGCTTACTGAGTTG R 2 1 2 1 202000 f 74 goat snp28226-scaffold3007-1472 16 5942852 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405937 Affx-122955561 AX-123276289 CTGTGCCTATTGTGTATATATAACCTAAAAGTACA[C/T]GCAAAATATTAATTGCAGAGGGGACACAGAGAGTC Y 2 1 2 1 303000 f 74 goat snp28322-scaffold3014-18412 28 42553776 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382301 Affx-122973913 AX-123252659 CCCCACAGAGTCAGACACAATGAAGGGACTGAGTA[C/T]GCATGCATGAGGCTGAGAGCAGATCCAACAGCTAA Y 2 1 2 1 202000 r 74 goat snp28323-scaffold3018-35184 18 64390773 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435762 Affx-122932880 AX-123306101 AACCATTCCGATGTAAAGAATGTGGCAAAGCCTTT[A/G]CCCAGAGCTCAAGTCTTTGTCAACATCAGAGAATT R 2 1 2 1 303000 r 74 goat snp28337-scaffold3020-12129 18 7865369 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422649 Affx-122943694 AX-123292995 CAGAGATATCCCACATGCAAGTCTCTGAATGATTG[A/G]TGGTAAGCTGTCATATCACCTTTTAGGATCTGAAA R 2 1 2 1 101000 f 74 goat snp28354-scaffold3023-13301 1 11416440 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451550 Affx-122921708 AX-123321883 TGGAGTTTTGGTCCACAGGGCTGTTGTTGTTCAGT[C/T]GCTCAGTCGTGTCTGACTCTTTGTGATGCTGTGGA Y 2 1 2 1 103000 f 74 goat snp28355-scaffold3023-44112 1 11386412 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779432 Affx-122973487 AX-385266535 GGGTGGAGGTTTCTTAAACAAGGGGAAAGAGAAAG[C/T]ATTTACATCTCTGACTAACCGCTTACAGACAAACT Y 2 1 2 1 103000 f 74 goat snp28356-scaffold3024-13902 18 59950680 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427250 Affx-122939557 AX-123297593 GGGGCATTTGCCATCTTCCCAAACAAGGCCTCAAA[C/T]GCATATCTTAAGCACTGGCTCAGAAGGGAAAACCC Y 2 1 2 1 102000 r 74 goat snp28484-scaffold304-77635 29 37575814 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421942 Affx-122943823 AX-123292289 TCTATCTTGTTTTTGATATGTGTTTTTATTGGGTA[C/T]AGAATTGTGAGTCAATTATATTTCTCTCAGCAATT Y 2 1 2 1 303000 f 74 goat snp28485-scaffold304-116554 29 37917766 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404665 Affx-122957293 AX-123275017 GAGGCCTGTTTTGTTGCTGAACATGTAATCACAAA[A/G]AGTCAGACATGGCTTAGCAACTGAATGATACCAAT R 2 1 2 1 303000 f 74 goat snp28486-scaffold304-162422 29 37964026 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377792 Affx-122977325 AX-123248151 CAAAACCAATAAAGTACTGTAAAGTAAAATAAAGT[A/G]TAAATAAATTTTAAAAAATGATGGTAAGTTCCACT R 2 1 2 1 303000 r 74 goat snp28487-scaffold304-253637 29 38059821 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439912 Affx-122930018 AX-123310249 TCCTCAGGGTGTGAATAATTATATTTGAGCCACGA[G/T]AAAAAATCTGGAACAGTCTGTAAGCATGTTCCTTG K 2 1 2 1 101000 f 74 goat snp28492-scaffold304-466848 29 38274792 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407359 Affx-122955275 AX-123277710 AAAATCAAACTGATCTGCATGGACATCTAAGAAGA[C/T]GGAGAATCTTGCCTACTTGCAGAAATAACTGCTAA Y 2 1 2 1 303000 r 74 goat snp28493-scaffold304-524661 29 38333048 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449975 Affx-122922881 AX-123320310 CAGGCACAGAAGTCAGTGCCTAGCATTCACAAGGC[A/G]TTCAGTGAGTTCTGATTGGAGGCGGGCCTCCATTT R 2 1 2 1 103000 r 74 goat snp28494-scaffold304-565978 29 38375691 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433484 Affx-122935039 AX-123303825 AAACGAATGAATTACAGAGACATGAATGAAGGGTG[A/G]TGGCCCTTGTTGCTCATCATGAATGTTCTTCAGTA R 2 1 2 1 103000 f 74 goat snp28495-scaffold304-604705 29 38399411 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786914 Affx-122922528 AX-385273943 CTGAACTAATAGTATAAGAAAGAGAATTAAAATTG[C/T]ATTGCATTTAAGACAATGCTATTTAAGGTTTGATT Y 2 1 2 1 101000 f 74 goat snp28496-scaffold304-641584 29 38436658 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417277 Affx-122947250 AX-123287625 GTGTATTTACTAATTAATTTTTTCCCTCATTTTGG[A/C]TAGTTTCTTGCTTCTTTACACATTGGGATTTTTTT M 2 1 2 1 103000 f 74 goat snp28497-scaffold304-717944 29 38514254 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413973 Affx-122950295 AX-123284322 CATGATGAGTAACAAGGGGCACCACCCTTCATTCA[C/T]GTCCCTGTAATTCATTCTTCTTTGGTTCTCCCCAC Y 2 1 2 1 103000 f 74 goat snp28499-scaffold304-832173 29 38629504 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407708 Affx-122954568 AX-123278059 CGGCATTTTCTCCTACAATTGTTTTCTCTTCCCTC[A/G]TTTTATCTTTCCTTCTCTTATAGATGAACTGGATA R 2 1 2 1 303000 r 74 goat snp28501-scaffold3043-40451 18 64541435 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377738 Affx-122977380 AX-123248097 CACTGATTCCTGTTTTTATGTTTTTCATGGTTCTC[A/G]GGAAAAGTATTTGGTATTTTCTCCTGGAAGAAGCC R 2 1 2 1 101000 r 74 goat snp28555-scaffold3050-12869 23 46519106 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401880 Affx-122958853 AX-123272233 CGTCCCCCCTGTGGATGAAAGCACCCTCCCCAGAG[C/T]GGTGTTGCAGGAACTGGGATTTGGCCAGGGAACAG Y 2 1 2 1 303000 f 74 goat snp2855-scaffold10839-12830 21 24529606 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423973 Affx-122942130 AX-123294319 CTTTCTAATTGACTAAGTGCCTAAAGGTATACATA[C/T]AGATTTCTCTTTCATTTTATGTTTCTTTTCTACTG Y 2 1 2 1 101000 f 74 goat snp28580-scaffold3060-19084 8 32147554 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380269 Affx-122975425 AX-123250627 AACAAATGTATGCTATAATAAGACTTCCCTTGTGG[A/C]TCAGCCAGTAAGGAGTCTGCTTGCAATGCAGGGGA M 2 1 2 1 102000 f 74 goat snp28581-scaffold3060-58858 8 32187785 A C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416800 Affx-122948142 AX-123287148 AATCCACATTGTGTTTGAATAGATGGTCTCAGCTA[C/T]GAAGGCAGAAAAGTATCATGTTTTGAGACGTGGGG Y 2 1 2 1 101000 f 74 goat snp28582-scaffold3060-91473 8 32220372 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385075 Affx-122971811 AX-123255433 CAGCGTTCATGCGTGTCTTAGCCTCCTAAAAGTAA[C/T]ACGCAAAAAGGCGAGTTGCTGAAATGAAGCCCTCC Y 2 1 2 1 101000 f 74 goat snp28686-scaffold3091-14925 27 10830184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390310 Affx-122967714 AX-123260667 AGACTCCTCGCATGCCTGGGGAGCACTTGAGGACT[A/G]CTTGGCACTTTCACCTGGGAAGCCAAGCTTCCAAG R 2 1 2 1 101000 f 74 goat snp2868-scaffold1085-30691 3 1556096 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376039 Affx-122978939 AX-123246398 ATGTCCTTTAAAGCAAGGACAAGGAGATGGAAGCC[A/G]TTCTTGCAGAGTAGACTCTCAGCTTGACATGAGCC R 2 1 2 1 101000 f 74 goat snp2869-scaffold1085-77367 3 1608297 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443499 Affx-122927800 AX-123313836 CTGCCTCCGTAACCCTTCAGTCCATCTTCCCCGCC[C/T]TCCAGGCTCCTCAGGCCTTGACGACCCCTTTTCCG Y 2 1 2 1 103000 f 74 goat snp2893-scaffold1087-42518 NW_017190139.1 36835 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385043 Affx-122971846 AX-123255401 TACAGCCTCACAGGCGCTTACAGATGACTAAATGA[A/G]CTCTCTATCCCAGGTTCCCCTGTGGGTGCTGCAAA R 2 1 2 1 101000 f 74 goat snp2894-scaffold1087-93561 NW_017190139.1 88617 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443214 Affx-122927577 AX-123313551 TTTGGGGCCCTGAGCCTGCCGCCGGCCGCAGGGCC[A/G]CTACCAAGGCCTGGGTTTGCTGGTTTAGGAGGCTT R 2 1 2 1 303000 f 74 goat snp2895-scaffold1087-194457 NW_017190141.1 70407 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446867 Affx-122925245 AX-123317203 AGAGGCATCTCTCTAAGTTTGTCTAATTAAAGGGG[C/T]GTCACAGGGCCCTGAAGCACAGGGCCTGAGTATGG Y 2 1 2 1 101000 f 74 goat snp2896-scaffold1087-236524 NW_017190141.1 27359 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424883 Affx-122941324 AX-123295229 CCAGCCACTCTCCCCAAAGCAGACCTTCCATTCAT[C/T]GCTGTCTGGTTCTTCTTTCCTCCTAGGGAAGCAGG Y 2 1 2 1 201000 r 74 goat snp2897-scaffold1087-335720 NW_017189818.1 167713 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432967 Affx-122935275 AX-123303308 TGAGCCAGCTTCCAACACCGTCTACACACAAGCTC[A/G]CCCGGCCCTCCTGGCTCTGTGCTGTCAGCTTCTCC R 2 1 2 1 101000 f 74 goat snp29137-scaffold3120-3777 NW_017189555.1 41335 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799290 Affx-122929808 AX-385286220 TTCCTAAACCACATTCTGATTCTCTCTTTCCCTTC[C/T]ATTGTGGCAGAGCAATACCTACCCACAAACTTCGC Y 2 1 2 1 102000 f 74 goat snp29139-scaffold3123-21247 NW_017189691.1 15980 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390470 Affx-122967604 AX-123260827 AGGGTGTCTGACACAGACAGGGCACAGGCAGAGTC[A/G]GTTGGAGCTGAGGCACAGTAGGAGGAAGGGGATGA R 2 1 2 1 103000 r 74 goat snp29179-scaffold3135-7671 NW_017218506.1 14695 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422222 Affx-122944026 AX-123292568 GTCATGGGTAAGATCCAATGGCTATGGCAAAATAC[A/G]TACAATAACAGCTACCACATAAATTGATCTTACAT R 2 1 2 1 101000 f 74 goat snp29230-scaffold3149-30675 NW_017189516.1 20326241 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788524 Affx-122925952 AX-385275541 TATCTTGAGAATATCGTGTTTTGAAGAATTCAACA[C/T]GGATGTTTGCATAAAGAGAGAAATGCTTCATCAGT Y 2 1 2 1 101000 r 74 goat snp29371-scaffold3177-25609 12 25821420 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779853 Affx-122969669 AX-385266952 TCCAGGTATATTAAGTATGTTCATTCTCAACAGTA[C/T]ATTAAAGTAAGCTAATAAAAATATAACCGGATTCC Y 2 1 2 1 101000 r 74 goat snp29373-scaffold3179-80962 NW_017189516.1 61734270 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383614 Affx-122972554 AX-123253972 ATGATATATGCTCTGGGACTTCTCTCATAGTTTCC[A/G]CAGCACCAAAGACAGTAACTTGCATCCCAAAAGGC R 2 1 2 1 101000 r 74 goat snp29374-scaffold3179-143327 NW_017189516.1 61794240 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379551 Affx-122976055 AX-123249909 TTACATGGGAGATGGAGTTCAGCCATGAGCGTTCC[A/G]CTCAGCCAGCTGGAGGTTTCGCTGAGACTCAAGAG R 2 1 2 1 101000 f 74 goat snp29375-scaffold3179-182301 NW_017189516.1 61832943 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418926 Affx-122946513 AX-123289274 AATGTAATGAACTACCTTAATGATTTTCTGATGGT[G/T]AACCAAATTGCATCTTGAGATAAGCTCAACCTTGT K 2 1 2 1 101000 r 74 goat snp29465-scaffold3192-12733 1 146613837 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798487 Affx-122941808 AX-385285420 GTCATTGAAATCTTAGGAGAAGTGATGTGTGGGAA[C/T]AAAGAGTTAGTGCATGATTTGTCCCATTCCCTTCC Y 2 1 2 1 101000 r 74 goat snp29568-scaffold3208-1390 NW_017189517.1 33105205 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381755 Affx-122974316 AX-123252113 AGGCACAGATCATTATAAATAGATTTTTTTCATCT[A/G]TGTGAATAACTGGGTAGGGGAGGTGGCATTCAAAA R 2 1 2 1 103000 r 74 goat snp29569-scaffold3208-51068 NW_017212306.1 23152 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447167 Affx-122924431 AX-123317503 GAGGAGGCAGAACCTGGGGGTATGGCGGGCTGACC[A/G]TGGTTCTTATTTCTCATATCTATTGTGTGAAGAAA R 2 1 2 1 101000 r 74 goat snp29842-scaffold3232-47453 NW_017219307.1 1839 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406412 Affx-122955215 AX-123276764 GCTTCTGGGACCTGATGACACTCTAACCCAGCCCC[A/G]TGTGACGCACACTCTCTCTCTGTCCTTTGGAACTT R 2 1 2 1 101000 f 74 goat snp29845-scaffold3232-161172 26 1482379 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404254 Affx-122957061 AX-123274606 CCTCTGAGGAGGCAGACACTGCACTTCTGGCGCTG[C/T]AGACGTTGCTCGGCCCGGACGCCCCGCCCCAGGCA Y 2 1 2 1 201000 r 74 goat snp29892-scaffold3246-24822 NW_017189621.1 13637 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320780096 Affx-122944047 AX-385267193 TTTTGAGAACAGCCAAGATGGAATTTTAGAAAGAC[A/G]CTAAGCTTTCTTCCACTTATGAGCACACCAAACCA R 2 1 2 1 201000 f 74 goat snp29928-scaffold3251-8725 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432790 Affx-122935418 AX-123303131 ACAACTATGATCTTTCAAATAAACAGTTGGAGGTT[A/G]CCACTACCCCCTCATACTGGTTATTTGTCATTTTG R 2 1 2 1 101000 f 74 goat snp29929-scaffold3258-20924 7 100059637 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406754 Affx-122955731 AX-123277105 TCACATGTTTAGTGCCATGTCATCCTGCCCAAATC[A/G]TCAGTTAAATGTAAATATTAATCCAAATTAATTTC R 2 1 2 1 101000 f 74 goat snp29944-scaffold3262-39542 8 65148631 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392542 Affx-122966097 AX-123262899 CCTCAGCATTTATGATATTATTAGTGGGCTCTTTG[A/C]TAATTGTTATTCTGACTGGCATGAGATGATGCATG M 2 1 2 1 103000 f 74 goat snp29949-scaffold3269-7401 18 59883935 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452593 Affx-122920498 AX-123322926 GGGTGACGTAGGAAGACCCGGTGACTTCAGTGTCC[A/G]TCCACAGCTGGTGGCACACCAAGTCTGGATAAGGT R 2 1 2 1 201000 f 74 goat snp30020-scaffold3278-4086 NW_017217295.1 3824 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766830 Affx-122951808 AX-385254153 ATGTCAGTCTTAAACTTCCAATCTATCTCTCCCCC[A/G]TCCTTTCCCTCTGTAACTCTAAGTTTTTTCCTAAG R 2 1 2 1 103000 f 74 goat snp30038-scaffold3288-45111 18 64400526 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419352 Affx-122945639 AX-123289700 TCTCATTCGATCTTTGACTGTCTCATCTTGAGGGC[A/G]TGTTCAGGACTGCCCTGCCCACCCCCAGGGCCTGG R 2 1 2 1 103000 f 74 goat snp30039-scaffold3288-77289 18 64433530 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397765 Affx-122962521 AX-123268120 CTTCTCAGTGTGGATGTCTCTCTGTCTCTCAGTGT[A/G]TGTGTCTCTCAGTGTGTGTGTGTCTCTGTATGTTG R 2 1 2 1 303000 r 74 goat snp30040-scaffold3289-6907 NW_017190085.1 5305 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452991 Affx-122920118 AX-123323324 CTGCATGGCAGGTGGATTCTTTACCAGCTGAGCCA[C/T]AAGGGAAGCCCAACTGCAGTATTAAACCAATGGCT Y 2 1 2 1 103000 r 74 goat snp30121-scaffold3305-540 12 35078425 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781963 Affx-122972860 AX-385269043 CAGAAAGTAAACTTTTTTAATAACTGAAAAAGGTT[G/T]TAGAAATCATCCATTCCAATTATAGTAATTAGTAC K 2 1 2 1 202000 f 74 goat snp30122-scaffold3309-11669 3 51889236 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425419 Affx-122941536 AX-123295765 ATGCTGTTAAATGATTTACTCTGGCAATAAGATAA[C/T]ATCTTTTGATGTAATAATTTTTACTATTCAGTTGG Y 2 1 2 1 101000 f 74 goat snp30158-scaffold3310-1954 6 85520188 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777424 Affx-122943692 AX-385264545 CAAGTGAAGATCTGCTTAATGCTTTGAAAGCAGTT[A/G]TTAACAACCCTTTGTGAGTAGAGAATATATACATT R 2 1 2 1 101000 f 74 goat snp30159-scaffold3310-35990 6 85485282 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790874 Affx-122946887 AX-385277872 CATTCTAAAAACCCTAATGAGGGAAATCTGCTGTA[C/T]GAGTTCCTTGAAAGCAAGAACCTATGTTTATTGCT Y 2 1 2 1 202000 r 74 goat snp30160-scaffold3311-17373 25 34027295 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768694 Affx-122927000 AX-385255872 ACAATGGTGGTTTCACTCTCTACCTTGCATCTACC[C/T]TCAAATGTCATACCTATCTCTTTTATTGCTCTCCT Y 2 1 2 1 101000 f 74 goat snp30323-scaffold333-4665714 15 37690004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443772 Affx-122927105 AX-123314109 ATTCAGGTGTGGCTTTCTGCAGTTCTTGTGATTTC[A/G]TGTATCCCGTAATTCAGGGGGAAGTTTTAAGGCTG R 2 1 2 1 101000 f 74 goat snp30324-scaffold333-4695771 15 37659220 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452037 Affx-122920896 AX-123322370 GCCAATGGAGCACTGCATGATCAATCCTTTCGGTG[G/T]ATCTCTCCTCCTGGTTTGCCACGGCTTCTTTATTT K 2 1 2 1 101000 f 74 goat snp30325-scaffold333-4751936 15 37603025 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773885 Affx-122967767 AX-385261024 TAAGATCTAGGCACAGAAATTCAGTCTGTATGACT[A/G]GATGACTGTCAATGATGTTGAAGGGTTATAACTAT R 2 1 2 1 101000 f 74 goat snp30327-scaffold333-4837379 15 37516467 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773701 Affx-122932245 AX-385260841 ACATCCTGAATCAGATGAGCCATCCATTATTAGAA[C/T]AGTCTCCATAACCATTTTGCTTCCATGATCTGCCT Y 2 1 2 1 101000 r 74 goat snp30328-scaffold333-4867029 15 37486518 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407109 Affx-122954882 AX-123277460 TACAATTGTCTGGAGACATTTTTCAATCTATAAAT[C/T]AATAACTCAAGGTAGCTTGAAGAAAATAAATAGAA Y 2 1 2 1 303000 r 74 goat snp30329-scaffold333-4906568 15 37446670 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442022 Affx-122928409 AX-123312359 AGCTAGCGCTTTCCCTTGACAACGTGTGTGCGTGC[A/C]CAGACGTGTGTGTGACCCCCTTTGACGCTCACTTC M 2 1 2 1 103000 f 74 goat snp30379-scaffold3340-7738 16 79017329 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426499 Affx-122940217 AX-123296845 GGGACCCGACGCCATGCTCTTGTTAGTTTTCTGAA[C/T]GTTGAGTTTTAAGCCAGCCTTTTCACTCTCTCACC Y 2 1 2 1 103000 f 74 goat snp30381-scaffold3340-121274 16 79118563 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426031 Affx-122941119 AX-123296377 CTTGGAGCTCTGAGGTGTGGAGCCTGCGTGCCCAC[C/T]CCACTCGGTTCTGTCCAGTGTGGACATATCCCGGA Y 2 1 2 1 102000 r 74 goat snp30382-scaffold3340-153835 16 79150419 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377760 Affx-122977363 AX-123248119 TGGGGCCGGAAGATGCACTGACCACATTCCATTCT[C/T]ACACGCTGGGCTGCTTCTGACTGCTCACTCTGCTG Y 2 1 2 1 101000 f 74 goat snp30383-scaffold3340-189219 NW_017189671.1 20135 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778267 Affx-122966651 AX-385265382 GAACAATGTGACATTAATTCTTGTCTTATGTTTAT[A/G]TTCTCTTTAAATATTGAATTTAAGCCCAACAAACT R 2 1 2 1 101000 r 74 goat snp30386-scaffold3342-5525 6 25688756 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410095 Affx-122952837 AX-123280445 TGGGCAAAATGCTATACTCAGAGGAATGCTAACCT[A/G]TTCTCCTGTCAAAAGTCAGTCATACAGCTTCATTT R 2 1 2 1 101000 f 74 goat snp30387-scaffold3348-11199 10 77870741 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392686 Affx-122966417 AX-123263043 TCAACCCCCAGTATAAATCCACCTCACCCTGCCTC[A/G]TCTTTGCTCTTTTGTTAAAATTTGAAAGAAGTAGA R 2 1 2 1 303000 r 74 goat snp3041-scaffold1092-9565 18 61489143 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433771 Affx-122934484 AX-123304112 GGGTCTTTTCCCTTGTGTCACAAGAATGTAGATAA[C/T]GTTCAGATCAGAAACAGAAATACCAACTCAGAAGT Y 2 1 2 1 101000 f 74 goat snp3042-scaffold1092-43151 18 61523029 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412282 Affx-122950880 AX-123282631 CACTTACCATAATATTCTCTACATTCATCCAAGTT[A/G]TCCCAAGTGAGGCAAAGCTCCATAATTGTTTATAA R 2 1 2 1 101000 r 74 goat snp3043-scaffold1092-127122 18 59749121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781568 Affx-122930766 AX-385268653 AAACTGGCATATTTCATAGCTACAAAGTCATCCTC[A/G]TGATAGCAGTGGTTTCTTAACAAAAAAAAAAATAA R 2 1 2 1 101000 f 74 goat snp30500-scaffold3364-56517 NW_017214180.1 23574 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440089 Affx-122929720 AX-123310426 TCTTACAGAGTTACTATGAGGACGGGAGGAGAAGG[C/T]GGTGACAGAAGATAAGACAGATGGATGGCACCACC Y 2 1 2 1 103000 f 74 goat snp30501-scaffold3367-5901 NW_017191234.1 8839 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413929 Affx-122949811 AX-123284278 ACCAGGCTTAGAATGCGTATAATCTGAAAAATGGT[G/T]CAGGGGAATGTGGAATAGATGCAAGCAGTGAGAAA K 2 1 2 1 201000 f 74 goat snp30541-scaffold3372-1628 6 9477810 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436579 Affx-122932896 AX-123306917 AGGGAAGGCTAGCTGTCTTCAGGAAAAATGTAGAA[C/T]TAGATGACTCCTGGGTTTCCTTTCCCAGTTATTCC Y 2 1 2 1 202000 r 74 goat snp30542-scaffold3379-6590 NW_017189516.1 20279589 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400788 Affx-122959828 AX-123271143 GGTGATGACACTGACATTTATCTCAACATTCAAAA[C/T]GATCCTTGGCTTTCTCTTCTCTCTCTCTCTGTAAC Y 2 1 2 1 303000 f 74 goat snp30554-scaffold3386-3408 NW_017189989.1 14642 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410855 Affx-122952611 AX-123281205 GTGGGAGAAACACACAGTCCTGAGAGCAAACAAAT[A/G]CAAACACTGAGAATCAGACACACTCACACTGAGAC R 2 1 2 1 101000 f 74 goat snp30555-scaffold3387-19586 NW_017191587.1 5391 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777558 Affx-122962558 AX-385264677 GAGGCCTCTTATCTACTAGGTGGTTCATGCGGGAA[A/C]TGTCCTTCTGGAGTAAAGCCTTCTACATATCTGCC M 2 1 2 1 201000 r 74 goat snp30556-scaffold3389-9134 23 46754673 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392085 Affx-122966372 AX-123262442 GGATGCCACAGCTGCATTGAGAGTCCTTTGGGCAG[C/T]AAGGAGATCAAACCAATCAATCCTAAGGGAAATCA Y 2 1 2 1 303000 f 74 goat snp30883-scaffold3407-14018 5 100897981 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407192 Affx-122954817 AX-123277543 TTTCCGTTTTTTATCCTGTGTTTATCTGCTTCTCA[A/G]TCTGGCCAGAAGACTGTTTGTTATGTTGATAAGGA R 2 1 2 1 101000 f 74 goat snp30958-scaffold3410-28140 NW_017189565.1 45047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381780 Affx-122974297 AX-123252138 CACACCTAGGAGAGGGAGACAGAGGGCGCAGGACC[C/T]GGTGGCCGAAGATCGACAGTAAGTGAAAAAGCAAA Y 2 1 2 1 101000 r 74 goat snp30959-scaffold3410-62272 NW_017189565.1 10858 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800222 Affx-122938573 AX-385287145 TGAACCAATATGGCAAGCACAAATAATAGAGTATT[A/C]TTCATCATTAAAAAGGAAGGGGATCCTAACACATA M 2 1 2 1 303000 r 74 goat snp30960-scaffold3415-10146 18 62916115 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384945 Affx-122972319 AX-123255303 CTGCAGTCCTAAATTCACTGCAGCATTTTCCTCAA[C/T]AGCCTAGATACATAACCAGCTTCACACAACAAATA Y 2 1 2 1 101000 r 74 goat snp31007-scaffold3424-53240 3 103188640 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423173 Affx-122942737 AX-123293519 TTCTGAGATAGGATGGAGGTGAGGAAGGTTATCAG[C/T]GATGGAGTTAAGATCTTGGGAATCTGAGATCCTGT Y 2 1 2 1 101000 f 74 goat snp31079-scaffold3431-25123 4 88019195 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791318 Affx-122958950 AX-385278311 TGTAGTTATGAGAGCAGTTTGTTTAACTACTTCCC[A/G]TGGTACCGACAATATCCTGGTAAAGCCCCTGCATT R 2 1 2 1 101000 r 74 goat snp31125-scaffold3442-18196 10 78303002 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452553 Affx-122920528 AX-123322886 CCCTGCCCCAAGTGCTCTTCTTCCTCCTCTTGAAA[C/T]GGACACAAAACCGAAAGTCCCCTCAATTCAAGAAC Y 2 1 2 1 103000 r 74 goat snp31126-scaffold3444-12443 18 60212102 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440767 Affx-122929855 AX-123311104 GACTTAGTCCGAAGAAAATCAATCAATTTAGATGA[C/T]GGATAGTGATTAGAAAACGAACCAGGAAATGAGGC Y 2 1 2 1 303000 f 74 goat snp31127-scaffold3444-44647 18 60178927 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381962 Affx-122974107 AX-123252320 AACGTGGCTTGAGACACCACCTAGAAGAGGTGGAT[A/G]CCACAGGTGGATGCCACGGCCGGCTGCTGGGCTTG R 2 1 2 1 101000 f 74 goat snp31128-scaffold3446-32156 5 27102207 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769614 Affx-122964715 AX-385256784 GCTTGTGCCCGTGACCGAGATGGAGTGTATCATCA[C/T]TGGAGATGGGCAGTTTGGAGAAATTGAAACGTTGA Y 2 1 2 1 102000 r 74 goat snp31129-scaffold3446-82168 5 27052679 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376595 Affx-122979063 AX-123246954 GTGTGTCATTCCTAGAGTGAGGCAGTCAGCAGCCC[A/G]CATACTTCTCGAATCTCTCTTTTCTCCTATCCTAG R 2 1 2 1 101000 r 74 goat snp31130-scaffold3446-120437 5 27014657 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453739 Affx-122919616 AX-123324072 GGAAATTGGTATGGATGCTAGCCTCAGATTCTCCC[A/G]CTGGAACTTAATTTCCCCCTCCCTAAACTCCATAC R 2 1 2 1 101000 r 74 goat snp31131-scaffold3446-150055 5 26985089 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424756 Affx-122941646 AX-123295102 ACCAGTGTCTTTAATATTTATTACTTAATACAAGT[A/G]CCAGTAGAACAAAGCTGAGTATATGATCCTTACTT R 2 1 2 1 202000 f 74 goat snp31313-scaffold3450-19148 NW_017211321.1 4696 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430062 Affx-122937554 AX-123300403 AACTGTATCCTGAAAGAGCATTCCCTTTTCTCCTC[A/G]CCCTCTTCAGCATTTATTGCGTGTAGGCTGGGAGG R 2 1 2 1 103000 f 74 goat snp31314-scaffold3454-514 12 81735043 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798781 Affx-122946336 AX-385285712 GATAGGTCTTGCATTAAATATTGAGAAAACATATG[C/T]AATAGAGGCTTATTTGAAGAGACAGCAAAGTTAGC Y 2 1 2 1 101000 r 74 goat snp31315-scaffold3454-53858 12 81787452 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381869 Affx-122974179 AX-123252227 GTCTTGTCACAGGTGGTTTTCTCCCTGTTCCTCTG[A/G]TCTTCGTGCAGGTGAAGACACCCAGACAATCAGGA R 2 1 2 1 202000 r 74 goat snp31316-scaffold3457-7023 NW_017189574.1 457672 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434307 Affx-122934756 AX-123304648 CTAAAAGACCAATTAAAATACTCAGTTTTTTTCTG[A/G]TGACATATCTCTGTGACATCAGCTCTTCTTCACAT R 2 1 2 1 102000 r 74 goat snp31317-scaffold3457-44019 NW_017189574.1 421964 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795919 Affx-122963469 AX-385282871 AAGATTTGCTGTTTTGTTTCCATGAGATACTAACT[A/G]CAAAATCTTTGAAACTTCCATTTTAAAGTCTGTTT R 2 1 2 1 201000 r 74 goat snp31446-scaffold3484-25413 24 6037739 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790648 Affx-122924444 AX-385277650 CAGGATTTTGTAGGGAAAATGATAGTGGTTAGGCT[A/C]TTATAAGAGAGAAGCTCTAAATAATTGTAGCTTTA M 2 1 2 1 101000 f 74 goat snp31447-scaffold3486-6385 19 23770976 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424780 Affx-122941401 AX-123295126 GCACTCAGAGCTCTGCACAGAGAACATGAAGTTCT[A/G]CAGACTCAGAACAGACACCTGGTCCAGCTTCCCCT R 2 1 2 1 202000 r 74 goat snp31513-scaffold3490-6821 5 101041288 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427261 Affx-122939548 AX-123297604 CATGTGCTTCGGAATGGATGTTGTGTCGGCAGCCA[C/T]GAAAATAACATGAATCTCGTTGTTGTTCTCCATTA Y 2 1 2 1 201000 r 74 goat snp31567-scaffold3501-11037 NW_017216180.1 22093 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447147 Affx-122924446 AX-123317483 AATTGGAGTGTCCAGAAAGGAAAAGAAAGAAAGAG[A/G]AGGTAGTCAAAACGTATTTGATAAACTTATGGATG R 2 1 2 1 303000 r 74 goat snp31568-scaffold3502-3492 7 99810982 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394018 Affx-122965012 AX-123264373 GGTATGAGCTGCATATCACCCTGTGTTTTTGATTT[A/G]CATTTCGCTAATGGCTGGAGATGTACATCTTTTCA R 2 1 2 1 101000 r 74 goat snp31689-scaffold3513-28109 14 68319246 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451519 Affx-122921105 AX-123321852 TCAGTCCCTTCATCTCATTGATTCCTTTCCAGAGA[C/T]CATCATGAAACACATGTAGCAAATGCATTTGATCA Y 2 1 2 1 201000 r 74 goat snp31753-scaffold3549-11437 18 60413807 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429504 Affx-122937860 AX-123299846 TTTCTAATGTTGTAAATTCCAGGGCACAAAACCCC[C/T]ACAGTTTTCATAATGGGTTTCAGGCCTATTACTGG Y 2 1 2 1 201000 r 74 goat snp31781-scaffold3550-11310 6 434910 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797539 Affx-122946219 AX-385284478 CTAAGCTCTGAAAAATTATCAGCTGCAAAATATTC[A/G]TTACTGGACTTGACCTACATTCCATCTTCCCAGAA R 2 1 2 1 101000 r 74 goat snp31791-scaffold3556-12892 NW_017189517.1 20147649 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413823 Affx-122949888 AX-123284172 GAGGAAGGGCCTGCCCAGTAGACACGCACGCACAG[A/C]CACACACGGGGCCGGGACAGGGGTCGGGTTATATT M 2 1 2 1 303000 f 74 goat snp31935-scaffold3575-20540 21 67119420 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430226 Affx-122937326 AX-123300567 ACAACTATAGACATATTTAGAGTTGGCAAGAACCC[A/G]CATGTTGATTTGTGTGTGTGTGTGTGTGGAGGAAA R 2 1 2 1 101000 f 74 goat snp31965-scaffold3586-7957 23 16863940 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432859 Affx-122935360 AX-123303200 ACACCACCTATGCTGGGGCCCCCTCCCGGACGGCA[A/G]CTTCCCCATCACCCCTGGGACTCAATCCATTCTCT R 2 1 2 1 101000 r 74 goat snp31966-scaffold3587-8625 NW_017192385.1 36931 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384345 Affx-122972249 AX-123254703 ACATTGATGAAACTCTCTATGTTAGTAGAAGCTAG[A/G]TAAGCGCTTTTTTCCCTGTCGAGGAGGGAAGACAC R 2 1 2 1 201000 f 74 goat snp32015-scaffold3591-15656 5 100925879 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449610 Affx-122923205 AX-123319945 TCTTCTAGGCCTCTTAGGGAACATGGTGAAACCTG[C/T]ATGAGGGCCCTTCAATGGCAGGCTCCTGAGAGCTA Y 2 1 2 1 202000 r 74 goat snp32020-scaffold3599-15806 NW_017189575.1 37164 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402237 Affx-122959143 AX-123272590 ATGCAAAGGACATTTGAAAGCCTTCCTCTCAAAGA[C/T]GGGGGGCGGAATCCATCCCTGACACAGACTATAAG Y 2 1 2 1 102000 f 74 goat snp32211-scaffold3654-9944 NW_017216550.1 2465 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403257 Affx-122957876 AX-123273610 CTGGGGTACGTCCCACCCCGCTCATCATGCTGGCC[A/G]CTTGCATTCTCCCTGCCACCCTCCTCTATCTTAAC R 2 1 2 1 101000 r 74 goat snp32212-scaffold3657-6055 14 80332435 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432815 Affx-122935397 AX-123303156 GATTTCAGCTGCAACTCTCGGGATCGTCCCTCTTC[A/G]CTGCACCACGCACCATCTTTCAGTTACTCTGCGCA R 2 1 2 1 101000 r 74 goat snp32213-scaffold3657-68118 14 80269921 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781345 Affx-122927040 AX-385268430 ATATTCTGTTTGTTTATTTAGGGGATACGTAAAGG[C/T]AGATTCAGACAAAAATCCATTCTCAATTCTTATTT Y 2 1 2 1 201000 r 74 goat snp32215-scaffold3658-17673 16 5078168 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385741 Affx-122971083 AX-123256099 CAGATGGCAAGCAGTGATATCCCTTTAACTACATG[A/C]CTGAAGTATTTGGGATGGGGTCTTTTGCCAAAAAT M 2 1 2 1 101000 f 74 goat snp32301-scaffold3665-5567 14 87202688 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783786 Affx-122970257 AX-385270842 TTCCCAGGTGCTCTTCACAAGCTGCTTGTGAATCC[A/G]TCTACCCTTCTTCATCTCTAGACTATGTGGTCCAG R 2 1 2 1 202000 f 74 goat snp32302-scaffold3669-11639 21 19130799 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445487 Affx-122925199 AX-123315824 CCAATTTGGAGAGGACTTGGCCCTGGTGATTTCTG[G/T]GAGCTCTGACACATAGCTAGGACTTGGTTAAGGAA K 2 1 2 1 102000 f 74 goat snp32416-scaffold3690-484 3 66658041 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789711 Affx-122970977 AX-385276719 TATTATTAAACATTCATTGAAGATGTTGCTGTAAG[C/T]ATATTTCATGGAATGCAGTTTGAATAAATTGTTCT Y 2 1 2 1 101000 r 74 goat snp32491-scaffold3709-13841 5 20141506 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793769 Affx-122957105 AX-385280741 ACTACTGAGGGCAGTTCTGTGTGTTTTATTGCAAA[C/T]GTTTTACTCTGTATTTACACACATATTCAGGGTAC Y 2 1 2 1 101000 f 74 goat snp32553-scaffold3710-4853 NW_017189633.1 36258 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794634 Affx-122959421 AX-385281595 AGTTCATATTTGAAAATTCTTTGCTGAGAAGGAAT[C/T]TCATGGTAAGGAGACATCTTGTTATTTGCAGTACT Y 2 1 2 1 101000 f 74 goat snp32581-scaffold3720-4598 15 33870118 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375837 Affx-122978541 AX-123246196 ATAGTCAGGGTATTATCAGATACTGACTTAAACTT[A/G]TGCAAGGAGAAAATATTTCTTGTTACTCATATTAA R 2 1 2 1 103000 f 74 goat snp32583-scaffold3727-14775 5 98919654 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431049 Affx-122936648 AX-123301390 AGACATTGTGATTCCCCCGGGGTCAGTTCTTTGCT[A/G]CCTCACTGTATCAGGCATCAAGAGCTACATTTCAG R 2 1 2 1 102000 f 74 goat snp32585-scaffold3737-11725 15 3952487 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764800 Affx-122972537 AX-385252408 CCAGGATGCAGCTGAAGGGAGTCACTTCCAGGCCC[C/T]CAGGAATTATGCACTCCCAAGATCTATATACAGAG Y 2 1 2 1 303000 f 74 goat snp3259-scaffold10997-4300 NW_017189691.1 33839 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396038 Affx-122963465 AX-123266393 CTCTCACATTTTTATAAATGGTTCCAGGTTCCTCT[A/G]TTTCTCTATTTGTCATCAGTTTCCTCCTCTTGGTC R 2 1 2 1 201000 r 74 goat snp32737-scaffold3779-5360 5 102052079 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401781 Affx-122959484 AX-123272134 ACCTACAGAAAACTAGCACTAATAAGAGAATTTAG[C/T]GAGATCTCAGTCTAAAGTCAATACTCAGAACTAAT Y 2 1 2 1 101000 f 74 goat snp32927-scaffold3802-25632 29 50345538 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437886 Affx-122931671 AX-123308224 AGTCCCCTTCCTTACCAGACACTCAGGCAGATGGA[C/T]GGGAGGGAACGCACTTCAGTCTTGGCAGCAGAAGG Y 2 1 2 1 101000 r 74 goat snp32928-scaffold3803-12951 NW_017189516.1 20619813 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428427 Affx-122938826 AX-123298770 TTTAGCGTTAGCTCCCCTTCTCCAGAAAGCCCTCC[A/G]TGCTCTCCTCGGCTGAGTCAAGTGCCCACCTCTGG R 2 1 2 1 201000 r 74 goat snp32929-scaffold3809-4795 18 53619165 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438835 Affx-122930778 AX-123309172 AGGGGGTAGGTCTGTTTCTTCAAAGCGACTGAGTC[A/G]TGGGAGGGCAGGACTAGGGCCGCTGTGCTGTGGGC R 2 1 2 1 101000 f 74 goat snp32931-scaffold3809-89820 18 53535797 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795493 Affx-122946321 AX-385282448 TGTGATTCTTCTGCCCCTCCCTCCCATCTTAATGT[C/T]ATAATTTCCCTTCCCCTGACAAACTTTCCTTTCTT Y 2 1 2 1 303000 f 74 goat snp32932-scaffold3809-120188 18 53505496 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784458 Affx-122970007 AX-385271507 GTAGAAATAGTCTGCGTTTGGAATTTCCACCTCTA[C/T]GAAACTTTGAACAAAGTGGTAGAAACCAACCAAAC Y 2 1 2 1 202000 r 74 goat snp32939-scaffold3812-13302 NW_017193495.1 19866 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451417 Affx-122921183 AX-123321750 GTGGTATATGCATACCATGAAATAATATTCAAAAA[C/T]AAAAGGAAATAGCCATTAATATACACAGCTTAGAT Y 2 1 2 1 201000 f 74 goat snp32974-scaffold3830-11364 8 86041750 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771995 Affx-122961260 AX-385259151 CCTGGTGATATTGCCTTACATGAATTGGGAGAATC[A/G]TAAATAGTTTTCACAGCATTGCAAATTGTGTGTCT R 2 1 2 1 102000 f 74 goat snp33079-scaffold3851-298 9 74121411 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791893 Affx-122928837 AX-385278882 TAAATTCTTTCTATTTTCTGTTATTTCAAGCATCT[A/G]TTCTTTTCACTTCCATCCCTCTAACTTGCTCTCAA R 2 1 2 1 201000 f 74 goat snp33080-scaffold3855-1018 7 100165155 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793034 Affx-122937611 AX-385280012 TGAGTCCTGTGATAGCAGATGTATTTTTCCAGCAA[C/T]ATCATCATTTGTAAGAATAAGGTCACAATGCAGGG Y 2 1 2 1 102000 f 74 goat snp33129-scaffold3877-11950 NW_017189570.1 7888 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395101 Affx-122964163 AX-123265456 ACTATTTATTTAGAAACCAGAAGGCTACATAAACC[A/G]TACTCTCATAAACTACATACAAAATAAACCCAATT R 2 1 2 1 101000 f 74 goat snp33170-scaffold3885-13245 NW_017189517.1 45809064 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437858 Affx-122932077 AX-123308196 CTCCCTTCGTGATCCTGAAGTGTATCCTCACAATC[G/T]TACAGTCATAAATCTGAGCTGTTAGTAGAACTATA K 2 1 2 1 101000 f 74 goat snp33171-scaffold3885-80918 NW_017189517.1 45877291 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380363 Affx-122975349 AX-123250721 TGGTGATGTTAAAGAGAATGTTTTCTGGGGCAGGG[A/G]GCAGGGGAGGGTGGATAAATTGGGAGACTGTGACT R 2 1 2 1 102000 f 74 goat snp33172-scaffold3885-119518 NW_017189517.1 45893685 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792744 Affx-122975109 AX-385279724 TTTCTGATACTAATAACACACAGAGCTTTTCAGGT[A/G]TTCATTAGTCAGCACTTGACTAACCAACTGCAAAG R 2 1 2 1 101000 r 74 goat snp33173-scaffold3885-174917 NW_017189517.1 45949425 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800503 Affx-122949461 AX-385287423 AGCTGTTCTAGGGAGCCTCTCCACACCTGTATGTA[C/T]AGTCAACCTTTCCAGGTATTTCTACAGAATTAAAG Y 2 1 2 1 101000 r 74 goat snp33174-scaffold3885-205000 NW_017189517.1 45979388 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797229 Affx-122971270 AX-385284168 AGCTGAATGTTCCCATGGTCACAGCCTAGTTTGTA[C/T]GGAATTTAACACTCAAACTATCTACTTCAGAATCA Y 2 1 2 1 101000 f 74 goat snp33175-scaffold3885-244762 NW_017189517.1 46016732 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398785 Affx-122961424 AX-123269140 AATTCAAAGAGACAAAGAAAGATGTTTAACAATGG[C/T]GGAAAATGAGGGAAAAGGAAAGGCAATCATCTTAG Y 2 1 2 1 303000 f 74 goat snp33262-scaffold3902-16694 15 4362243 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388683 Affx-122969001 AX-123259041 TGGACGCCAGGGCAGTGTCTCCTTGGGGACTGCTC[A/G]CCCCAGGTGCCAAGCCTGGGGATGGACTGCAGTCC R 2 1 2 1 103000 f 74 goat snp33263-scaffold3906-45332 NW_017189574.1 512402 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453367 Affx-122919939 AX-123323700 ATAAAGAAGCCAAAATGAGACATAACAAAATAGAG[C/T]AGAAAAGCAGGGCAAAAGAACAGAGAATAAATCAC Y 2 1 2 1 201000 f 74 goat snp33363-scaffold3911-16028 21 34258224 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423078 Affx-122942938 AX-123293424 AAGAAAGTTTCAGTCAATCAGTAAAGTCTTATTTA[C/T]AGTAGAAGCAAGTAACTCAATGTTTCTGTGGGTTT Y 2 1 2 1 201000 f 74 goat snp33478-scaffold3928-3203 5 100760434 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38409031 Affx-122953865 AX-123279382 GGCTTCTGGACACCAAGGGGAGGCCTGTGCTCAGA[C/T]GGGAGCTCATTCTGTGTCTAGAAGAGGTGCTGTTG Y 2 1 2 1 101000 r 74 goat snp33479-scaffold3929-2298 13 53628146 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415827 Affx-122948882 AX-123286176 CCTTCTCTCTCCTTGGAGCACCTGCCTCCTGCCTC[C/T]GTGTGCGTCTGGGGTCTGCTGCATTCCTGGTCGGA Y 2 1 2 1 103000 f 74 goat snp33480-scaffold3929-41034 13 53666831 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376889 Affx-122977815 AX-123247248 TTGGTTCCTTCATAGTGATGTGAAGGAAGCCTCTG[C/T]TCCAGTTCTCTCTCCTTGGCTTGGGGTGATGGCAG Y 2 1 2 1 102000 f 74 goat snp33516-scaffold3932-30276 NW_017189517.1 34379309 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405618 Affx-122956604 AX-123275970 AAACCGTTACACATCTTCCACGGTGGGTGGCATGA[C/T]TGAAGTCTCTGGCAAGGCCCCTGACTGCAACCTCG Y 2 1 2 1 101000 f 74 goat snp33783-scaffold398-31480 NW_017189516.1 60920403 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387192 Affx-122970607 AX-123257550 GCAGACCACCAAAGGGTCTGACCCTGACCCAACCC[A/G]TCCCTTCACAACGATCTGTATTTAAAGTCCCTGCA R 2 1 2 1 201000 r 74 goat snp33784-scaffold398-68530 NW_017189516.1 60882635 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802810 Affx-122923462 AX-385289709 GATTCACTTGCTTAAGCCATACACTAAATCTACAT[A/C]TGAAAAGAAGCAACCTTTCCCCAAATAAAGCAGTT M 2 1 2 1 101000 r 74 goat snp33785-scaffold398-100511 NW_017189516.1 60850497 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375734 Affx-122978623 AX-123246093 TCTTTTCCATTACGGTTTTCACAGGATACGGAATC[C/T]GCTTCCCTGTGTGGTACGGTAGGATCTAGAGTCAC Y 2 1 2 1 201000 f 74 goat snp33786-scaffold398-144808 NW_017189516.1 60806025 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397652 Affx-122962607 AX-123268007 GAGAGGCGCACCGTGTCCTCAGTTAAATCCTTGTG[A/C]GTTCAGTGTTAGCATCATTATTAAACACATTTGAC M 2 1 2 1 101000 r 74 goat snp33787-scaffold398-222102 NW_017189516.1 60728923 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428573 Affx-122938715 AX-123298915 GAAGCTCCCTGAGGGCAGAAGAGACACGTGGTCCA[C/T]GGGATAGAAAGCCTGGGACCTTGGGAATGCTCTGG Y 2 1 2 1 101000 r 74 goat snp33788-scaffold398-251912 NW_017189516.1 60699084 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406720 Affx-122955755 AX-123277071 AGATGTTCATTATGCCTCCCACCCAGAATCCGCCC[A/G]TATCCCACGCCCACTTATTCACGCAGGATTCTGAG R 2 1 2 1 101000 r 74 goat snp33790-scaffold398-367261 NW_017189516.1 60576110 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385246 Affx-122972091 AX-123255604 CCAGATCTCCTTTCGCTGTTTGTATCGCAAGAACT[A/G]TGTCTACGGTCCACAGTCCAGGGGAAAGTGACCTT R 2 1 2 1 101000 f 74 goat snp33791-scaffold398-415187 NW_017189516.1 60527435 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390774 Affx-122967886 AX-123261131 AATTTTTTTTTTTAATCTAGCAGCCTCTCTTACTG[A/C]TGTTCTGGGGAACTAAAAACTGGGGGCTAACCAAA M 2 1 2 1 201000 f 74 goat snp33792-scaffold398-463343 NW_017189516.1 60474153 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781505 Affx-122961339 AX-385268590 GGAGCCTGGGAGAGGAGAAGATTTTATAAATAGTC[A/G]CTGCACAAAAATCATCTCCCACATAGTCAAGCTCC R 2 1 2 1 101000 f 74 goat snp33793-scaffold398-500308 NW_017189516.1 60436985 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442531 Affx-122928538 AX-123312868 CTTGAATATTTGAGATGAGGACCTGGGCTCTTGGG[C/T]GGGAAGGTGGAGATGGGGAGTGGGAGACAGGGGGT Y 2 1 2 1 101000 f 74 goat snp33794-scaffold398-548223 NW_017189516.1 60388783 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410245 Affx-122952541 AX-123280595 AATAAAATCAGGATGCCAAGCTATTTAGACAGTGC[A/G]CAAGTCCCATTTTATTATTAATCTCCCCTTTACCC R 2 1 2 1 101000 f 74 goat snp33795-scaffold398-590938 NW_017189516.1 60346521 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404707 Affx-122957259 AX-123275059 AAAAACCCACTCTGCTTTGAGAATCTCTTCTGTAC[C/T]GAATTAGACAAGTACTTGAGTTTTCAATGACCGTC Y 2 1 2 1 101000 r 74 goat snp33796-scaffold398-631838 NW_017189516.1 60305560 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443165 Affx-122927614 AX-123313502 TAAAACCTTTTTGGGACTTCCAGTGGCTGAGCCTC[C/T]GAGCTCCCAATGCAGGGGCCCAGGTTCGATCCCTG Y 2 1 2 1 102000 f 74 goat snp33797-scaffold398-660765 NW_017189516.1 60277275 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448889 Affx-122923260 AX-123319224 TATAAAAGTCCACAGCTGAGTCTGTGCTGTGCTTT[A/G]CTTTCAGAAGCATCACAAGACACAGCTTTGCGAAG R 2 1 2 1 102000 f 74 goat snp33798-scaffold398-702816 NW_017189516.1 60236269 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795556 Affx-122951868 AX-385282511 ACATGAGGACTCGCGGGTGGAGAGGAAATTCTGTT[C/T]TAATTTCACGAGCATTCTCCGAGCATCTTCCTATG Y 2 1 2 1 101000 f 74 goat snp33799-scaffold398-740946 NW_017189516.1 60198243 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796206 Affx-122940171 AX-385283157 GTTAACTGATTTATAGAAGGTTTAATCAAAGGATA[G/T]CTTTATTTTTGGAATGAGATTCTTTCCATGTTACC K 2 1 2 1 101000 r 74 goat snp33800-scaffold398-790137 NW_017189516.1 60147681 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772008 Affx-122941111 AX-385259164 GATAAATGGGCAGAGCCAATTTGTCTGAGGAGACT[A/C]GAAGAGAAATGTGATAGAGGCATAGATCTTAAAGA M 2 1 2 1 101000 f 74 goat snp33801-scaffold398-826160 NW_017189516.1 60110523 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447338 Affx-122924887 AX-123317674 TTTGTGAGCAGTCCTGTGGAGGCTCTACTGAGCCT[A/G]TGGAGAATTCTGTGGATCTTGGTATCCCTACTGTT R 2 1 2 1 202000 f 74 goat snp33802-scaffold398-858378 NW_017189516.1 60078062 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430494 Affx-122937234 AX-123300835 ATGCAGGCCTGGTAAATAAGGAAGCGTCTCACAAG[C/T]ACTTGCCGGATGAATGAAAGATCTTTTTCTAGAGT Y 2 1 2 1 101000 r 74 goat snp33803-scaffold398-918922 NW_017189516.1 60016905 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440653 Affx-122929940 AX-123310990 CCATTCCCCAGTACCAGTGCCCCAGCCTCAGCCCA[C/T]AGCCCCATCCCTAAAATTTCCAATCATTTCACGTC Y 2 1 2 1 101000 r 74 goat snp33804-scaffold398-968891 NW_017189516.1 59968903 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408952 Affx-122953928 AX-123279303 TTGCTTGTTTTTCTTCAGAGAAGACACATGGTTGG[A/G]TCGAGTGCTTGGATAATCATAAGATTTATTTATTT R 2 1 2 1 201000 r 74 goat snp33805-scaffold398-998530 NW_017189516.1 59939192 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791997 Affx-122929620 AX-385278985 AAACATGTAGCCATGCACTTTATATTACAAAGTAA[C/T]GTTCACCTTCATTGTTTAAAATACATATACTCCAA Y 2 1 2 1 201000 r 74 goat snp33806-scaffold398-1028231 NW_017189516.1 59909772 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451638 Affx-122921610 AX-123321971 CCATTTATTGAGCAATTAAATGTGATGAATGTTAT[A/C]CACGATGGTGAATGTTGGAATTAATAAGCTGAAAT M 2 1 2 1 101000 r 74 goat snp33807-scaffold398-1063994 NW_017189516.1 59878352 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426945 Affx-122940419 AX-123297290 GCTCATAGGCAGTCCCAAGGAGGAACTCTGTGTGC[A/G]CTGGACCAAGTACAGTTCTGTGGAAGTTCCGTCCC R 2 1 2 1 101000 r 74 goat snp33808-scaffold398-1094199 NW_017189516.1 59847349 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380625 Affx-122975238 AX-123250983 TTCATTGGTCTTTTCACCTTGGCTCCAGGGTGTCA[C/T]GGTACTTCCCTGAGTTCCCCAAATGTGTTTATTCT Y 2 1 2 1 101000 r 74 goat snp33809-scaffold398-1135419 NW_017189516.1 59805827 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379253 Affx-122976258 AX-123249612 GTTAGTCATTGTTCTTTCCTGCCTAGATTTTCCCC[A/G]CTGCAAATGAAACTCAGCTAGACCAGTCCTGAATC R 2 1 2 1 201000 r 74 goat snp33810-scaffold398-1168915 NW_017189516.1 60939400 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433168 Affx-122935663 AX-123303509 AACACTCAGATACAGCGATCCCATCCCTCAGTAAC[A/G]TTTGTGGTTTTATTTGTGAGGCTTGTTGATTTTAT R 2 1 2 1 101000 f 74 goat snp33811-scaffold398-1222054 NW_017189516.1 60992675 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38393912 Affx-122965102 AX-123264267 TTACAGACCGCCTCAGGGCTGGACAAATTTCAACT[A/G]TGTTTACCCCCACCCTAGTGAGTAGATGAGCAGTT R 2 1 2 1 101000 r 74 goat snp33812-scaffold398-1265099 NW_017189516.1 61036208 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410036 Affx-122953242 AX-123280386 TCAAGTTGGACAGCAAAGGCACTCAGTCAAACATA[C/T]GCATGTATCCATCCTACTTCAAACGCCCCTCCCAT Y 2 1 2 1 201000 r 74 goat snp33813-scaffold398-1296887 NW_017189516.1 61068059 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766863 Affx-122954728 AX-385254184 TCAAGGTCTACTGGAAGAAGACCGAAGGTGAGCAC[A/G]TGCTTGCTTAGTCATCGTTGTCTTTGAGTTTTATT R 2 1 2 1 101000 f 74 goat snp33814-scaffold398-1340891 NW_017189516.1 61111009 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449801 Affx-122922417 AX-123320136 TCTCACATACCTGGGAAAGGGCACACCCCATCTTC[C/T]TGGCACTCAGTGAGGACTCAATATAAGGCTGAATG Y 2 1 2 1 101000 r 74 goat snp33815-scaffold398-1377371 NW_017189516.1 61146968 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422668 Affx-122943678 AX-123293014 AGCCGTAAAGTGAAGGAACAACACAAAAAATTTAC[A/G]TCATTCAAAAACCGCTGATCTTTATCAGTTATTTG R 2 1 2 1 101000 r 74 goat snp33816-scaffold398-1420503 NW_017189516.1 61187536 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397846 Affx-122962464 AX-123268201 CACATACCTGTTAAACTTGGAAACAGTTGCATCTC[A/G]CTGTACAGTGACCTGACCGCAACAGAACAAATACT R 2 1 2 1 101000 f 74 goat snp33817-scaffold398-1478509 NW_017189516.1 61245352 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442356 Affx-122928030 AX-123312693 TTGCAGTGGACCCTGAACAGCACAGGGGTTCGGGC[A/G]CTGAACCTCTAAGCAGTGGAGAAACTGCACGTGAG R 2 1 2 1 101000 r 74 goat snp33819-scaffold398-1569809 NW_017189516.1 61336090 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430220 Affx-122937331 AX-123300561 AAAATTGCTTGAAGGTTATGCAAGTTCTCCATACT[C/T]TGGAGGAGGGGGTGAGGTCATCCTGGGTTTCAGCC Y 2 1 2 1 201000 f 74 goat snp33820-scaffold398-1599275 NW_017189516.1 61365094 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407984 Affx-122954328 AX-123278335 TCACAACGCTGAGCTGTGGCTCTTGAAATGGCCAT[C/T]GCAAACAGTGGATCTCAGATTCCAGGGATGGATAC Y 2 1 2 1 101000 r 74 goat snp33821-scaffold398-1630395 NW_017189516.1 61396055 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784428 Affx-122974803 AX-385271477 GCTTTTCTTTGTAAAGTTTTGCAGAGTTGTATCCA[C/T]GACACTCACTCACAGTTTCTGTATGTAGAATCTGG Y 2 1 2 1 101000 r 74 goat snp33822-scaffold398-1687546 NW_017189516.1 61453512 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447015 Affx-122924548 AX-123317351 GAGGCAGGACACTGGCAAGAGAGGGTAAGGATGAC[A/G]TAGCCAGATAAATCACCCCGCAGTGAGCCAGGACA R 2 1 2 1 101000 f 74 goat snp33823-scaffold398-1732007 NW_017189516.1 61497918 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433015 Affx-122935785 AX-123303356 TCATTTCAGGACATGAAGGAGATTGGGAGCACACC[A/G]TCCGTGGAAACTAAACCACACTAACCACCCACGTA R 2 1 2 1 101000 r 74 goat snp33824-scaffold398-1764615 NW_017189516.1 61529119 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378208 Affx-122976930 AX-123248567 AGGGCAGATGCGGTGTGAAAGGGCAGGAAAGAGTG[C/T]AGTCCACCAGCTCCATGGGAAAGCCTGATGGACTC Y 2 1 2 1 303000 r 74 goat snp33825-scaffold3987-12018 9 73980720 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776766 Affx-122976189 AX-385263890 AGGGGACAGTTGCTACAATGCTGTTAGGCTTACTT[A/C]TTTGGTAAATCTTGATCTAAGAGATTCTTTAAGAC M 2 1 2 1 201000 f 74 goat snp33884-scaffold3996-18743 NW_017189516.1 41555692 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390360 Affx-122967680 AX-123260717 TGGGACAGGGACCCATTCTCTGTAGCACTGCAGAG[C/T]AAACATAGCTGAAGAGTTTGTAGAGATGTGGAATT Y 2 1 2 1 202000 f 74 goat snp33885-scaffold3996-80651 NW_017189516.1 41833086 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790077 Affx-122975633 AX-385277082 TGTACCTAACATTGTTTAGGTACTTTATATCTCAA[A/C]AATCATTCTGTGAGTCAGGTGCTAATGCTGTCATT M 2 1 2 1 101000 r 74 goat snp3407-scaffold1103-2701 21 52712609 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432861 Affx-122935359 AX-123303202 TGCTATTCTTTGGAACTCTGCATTCAGATGCTTGT[A/G]TCTTTCCTTTTCTCCAATTTTAGCTCTCAAACTAC R 2 1 2 1 303000 r 74 goat snp3408-scaffold1103-41469 21 52675941 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388587 Affx-122969159 AX-123258945 TGGCTGGGTTTCCTGGCAGTCTGATTAGTAGGATC[A/G]TTTCTTGACATATTTTTCCATAGGTGGTGCATCAA R 2 1 2 1 201000 r 74 goat snp3409-scaffold1103-71016 21 52647350 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427609 Affx-122939361 AX-123297952 TGGGATTCATCCCAGGAAGTCAAGACTGGTATAAG[A/C]TCCTATACTATGACCAGGTATATCTAGTATGAACT M 2 1 2 1 101000 f 74 goat snp3410-scaffold1103-101967 21 52616716 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413409 Affx-122950709 AX-123283758 GTTAATCTTATTTTCTTTCATTTAAAATAAAACTA[C/T]TATTTAGCACAAAGAATCTATATCTGTTAGGTGGC Y 2 1 2 1 103000 r 74 goat snp3411-scaffold1103-158538 21 52561930 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786423 Affx-122940510 AX-385273457 GACAATTAATAGGAACTAACAGTAGGGTTAATAAA[C/T]GGCAACATGTGGGAAAAACATAGCAGTAACTTTAT Y 2 1 2 1 101000 r 74 goat snp34223-scaffold4011-231 27 1144220 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775887 Affx-122979185 AX-385263018 ATCCACCGACTGGCCTTTCAGAACTGCAAAAAGAT[A/G]CTAAAACATTGCAAATAGGTAATTCCATTCTGATC R 2 1 2 1 101000 r 74 goat snp34224-scaffold4012-13687 NW_017189592.1 27336 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424395 Affx-122941822 AX-123294741 AGGTCCTTGAGAGATATGACCCCTGCTCAGATTGG[A/G]TTACAAACATTTCAGTGAATCCTCTGTAGAAAACC R 2 1 2 1 202000 f 74 goat snp34543-scaffold4068-411 8 23055323 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402270 Affx-122959117 AX-123272623 GTCCCATGCTTTACAATACACTAAATCACATTGCC[A/G]TGGCCGAAAATGCCGTTTGGCTTTTCCCATATTAT R 2 1 2 1 101000 f 74 goat snp34544-scaffold407-22752 18 64456040 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792767 Affx-122949564 AX-385279746 CTATAATTTCTCTGCCACAAACAAAGCTGCAAAGT[A/G]CATTACTGCACAGGTGCTTATTCTGAGAATTTCTT R 2 1 2 1 201000 r 74 goat snp34772-scaffold4120-12967 5 98868532 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787294 Affx-122925514 AX-385274319 CTTCTTTTAGGCCTTCCCATGTTGGAAGGCCTTTA[C/T]AGCTTCTCTTCTCTATACCTCTCTCTCAGTTGGCT Y 2 1 2 1 101000 r 74 goat snp34865-scaffold4150-19000 3 66570067 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783162 Affx-122979180 AX-385270229 TTGATTGATCTTTGGTCAGTAAGGATCTCATAATC[A/G]TGAATGGGTTTTCAGGAGATGTTTCTGGTGCTGGG R 2 1 2 1 101000 r 74 goat snp34866-scaffold4157-25712 NW_017189516.1 38624695 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446123 Affx-122925781 AX-123316460 TAGTTCACGGATTCTCTATGCTGCTTTGTCTAAAA[C/T]GCTGGTTCACCAGTGCAGTGAGTTTTAACCATATA Y 2 1 2 1 102000 r 74 goat snp34934-scaffold4161-11857 NW_017212060.1 8294 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422393 Affx-122943390 AX-123292739 ATTCTGTTACTCTGTGACCTCTTAATCTCCAAGCT[A/G]TATTTTCCTCACTTGTAAAATGAGAATAGTAAGTA R 2 1 2 1 101000 f 74 goat snp3498-scaffold11083-8038 3 30417668 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429726 Affx-122937609 AX-123300067 ACATTAAAAGTTGCCTTTTGACTTATGTAATTAAT[C/T]GATTAAAGGCTTCATCGTGGGATTACTATCATCGC Y 2 1 2 1 101000 r 74 goat snp35031-scaffold419-281 NW_017189516.1 61652382 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416968 Affx-122948011 AX-123287316 CCCTGTCATCAGAAGGTTCCCCGGCCAGATGGCCA[C/T]GCCCATCCTGTTCCATCCTAAACAGGCAGTCTCCT Y 2 1 2 1 101000 r 74 goat snp35032-scaffold419-32009 NW_017189516.1 61620896 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417378 Affx-122947703 AX-123287726 TTCCCGTCAATCAGCATTAACGGCTTTGCTTCCTT[A/G]AGGTTACAGCTAACACCTGCTTCCAATGCTCATCT R 2 1 2 1 201000 r 74 goat snp35033-scaffold419-71985 NW_017189516.1 61580438 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379730 Affx-122975877 AX-123250088 TGCTGAGCATCAGCACGGTACACAGAAGTTCTTCT[A/G]TCTCTGTGTATCGATGACAATGTTTAAATAGGTAA R 2 1 2 1 201000 r 74 goat snp35034-scaffold4194-77578 29 46378693 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442794 Affx-122927724 AX-123313131 CTCCCATGAAATCCAGATGCTGCTTTATTGCTTTT[A/G]TTTTCCACAGTGTTTCACTTCTGTCTGTCATCCTC R 2 1 2 1 201000 r 74 goat snp35159-scaffold4208-13795 26 35258622 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410608 Affx-122952106 AX-123280958 GGGAAAAGCCTTGCAGATGTCTCAAACCTGGATAT[A/G]CAGGCAGGAATAAAGTGGGGAGCAAAAACCCCAAG R 2 1 2 1 201000 f 74 goat snp35330-scaffold4239-22858 1 47608951 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375371 Affx-122979228 AX-123245730 AAAGAGTCAGACATGACTGAAGAGACCTAGCATGC[A/G]CTCATATGCTAACTGCAAACTACTTCCTATTTCTT R 2 1 2 1 101000 r 74 goat snp35356-scaffold4242-13082 NW_017212476.1 10393 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447817 Affx-122923917 AX-123318153 AAGAAATAATGGAATATGCAGTTATGCAGAGGCAG[C/T]AGTCCTGACCCTCATTGAGACCAGGCTTTCTTTTT Y 2 1 2 1 103000 f 74 goat snp35357-scaffold4246-28158 19 5790084 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792137 Affx-122972571 AX-385279122 GGTGGATAAAGTACATATTCTGCCTTGTTGGACTG[C/T]TGTGTGCTCAAATGAGTTCATATAAGTAAATGCAC Y 2 1 2 1 102000 f 74 goat snp35414-scaffold4264-7778 5 101637733 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391077 Affx-122966837 AX-123261434 TTTGAAATTTTATTTTCTGGCCTGTGAAGACTGTC[A/G]TTTTTAGGGGTTATTGCCAGTGTCCATTCCCACTG R 2 1 2 1 201000 r 74 goat snp35501-scaffold4274-2335 NW_017189605.1 22841 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428564 Affx-122938721 AX-123298906 TCTGTGTGATTTTTCAGCACGCCCGTGTCTTTTCT[A/G]TGTTGAGCGTCTGGGTTTTTCCTTTTCTGTGTCCA R 2 1 2 1 201000 f 74 goat snp35502-scaffold4275-8622 NW_017189851.1 202067 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435349 Affx-122933596 AX-123305689 TCACCTGATAGCTCTTTGCGGGTTCCCTTGTATAT[G/T]ACTTTAGTTTTATTTTTACTGCCTTTCAGTTCATT K 2 1 2 1 103000 f 74 goat snp35505-scaffold428-15876 NW_017189564.1 59215 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444540 Affx-122926480 AX-123314877 ATTTCGGGATCATTACTGAAGTCCTTGCTCAGTTG[C/T]CTACTACAGAAAACCGCTGTGCTCACAGATGTATT Y 2 1 2 1 101000 r 74 goat snp35507-scaffold428-131612 NW_017189517.1 21501811 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432689 Affx-122936036 AX-123303030 TTTCAAATGACTAGTATATTTGCTAGAGTTTAGTT[A/G]CAGGAAAAACCAAATGGGCTAGGATGGACAGGGAA R 2 1 2 1 201000 f 74 goat snp35508-scaffold428-182615 NW_017189517.1 21450249 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802795 Affx-122939761 AX-385289694 GGCACAGAATGATAGCTAAATACACGTGAAGCTGA[A/C]GGAGACATCGTATTCAATAGATGAAATTGGCATTT M 2 1 2 1 101000 f 74 goat snp35509-scaffold428-218395 NW_017189517.1 21413599 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422921 Affx-122943042 AX-123293267 GTCTCTAGTTTATTGCCAGCTATGAACTAAGGCCA[C/T]TCTTAGATACCAGGTACCTGACATTTCCTGCCATG Y 2 1 2 1 101000 f 74 goat snp35510-scaffold428-276894 NW_017189517.1 21353418 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419263 Affx-122946258 AX-123289611 CTGATTTACACCACTTACCTGGTGCAGAAATCCTG[A/G]GGCCAATAAATGTACCTGGAACCTCTGAGGCACAC R 2 1 2 1 101000 f 74 goat snp35511-scaffold428-317538 NW_017189517.1 21312313 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786772 Affx-122920354 AX-385273803 TTAAATGGAAATCTTTTACTACAAAAAAACAAGTA[C/T]TTTCAGAATCTACTAAGTAATTATGTTACTGGGAT Y 2 1 2 1 201000 f 74 goat snp35513-scaffold428-390257 NW_017189517.1 21238951 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417733 Affx-122947431 AX-123288081 TGTTCCTAAATAAGACAGAGTAATTAGGCATATAT[C/T]TGGTTAGACACTTTAATACTCATTTAGGAATTTCC Y 2 1 2 1 101000 r 74 goat snp35514-scaffold428-454070 NW_017189517.1 21173393 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432579 Affx-122935521 AX-123302920 GAACCCCAAGGGAAAGAAGATGTATAGTTTTGGGG[C/T]GAGTATAAAGAAGCTTTTTCTAATATTTACTTAAG Y 2 1 2 1 101000 f 74 goat snp35517-scaffold428-579943 NW_017189517.1 21045759 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387520 Affx-122970316 AX-123257878 CTAATAAAGCAAGGAAGTTTCAGGGAAATTTTGAA[A/G]TAGTTCCTAAAAGAGGCAGTGATTAACATTTCCAG R 2 1 2 1 101000 r 74 goat snp35518-scaffold428-653937 NW_017189517.1 20970442 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793880 Affx-122929595 AX-385280849 AATGATGACACATATTCTGCCAAAGTGCTACTGGA[C/T]ATAAAAGACAAAACACTACCCTCATTGTAATGTTT Y 2 1 2 1 101000 f 74 goat snp35519-scaffold428-738240 NW_017189517.1 20884647 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440330 Affx-122929677 AX-123310667 TCTCATTCATATGCCATTTTAAAATATAAGATTTT[A/C]TCTCTTGTCTTTTTCCACACTGAAAACTTTTCCTA M 2 1 2 1 101000 r 74 goat snp35521-scaffold428-798253 NW_017189517.1 20824338 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378874 Affx-122976509 AX-123249233 GAACAATACTCCTCTATTAGCTAGATTATTTCTGA[C/T]GGATATAAGGTTCATACACATTCATTCTAGGACAT Y 2 1 2 1 101000 r 74 goat snp35523-scaffold428-913489 NW_017189517.1 48814978 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446138 Affx-122925768 AX-123316474 GAAACTGCTTACATTTAATTTAAATGGTGCCAAAT[A/C]TAGCTATAATTTGTGGGTCACTGAGTTTCTATCTT M 2 1 2 1 101000 f 74 goat snp35524-scaffold428-944405 NW_017189517.1 48783812 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441438 Affx-122928813 AX-123311775 ATTTGTAAATAAATAGATGAATGAAATGGTCTTAT[A/G]CACTAAACTATAATTATAAAACTTTACTAATTTCC R 2 1 2 1 101000 f 74 goat snp35526-scaffold428-1102625 NW_017189517.1 48624884 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796326 Affx-122943739 AX-385283276 CCAGAAAGATCTCTTGAGGAATTAGAAATGTTATT[A/G]TTTTATGAAGGACTTTAGTATAATCATATTAATAT R 2 1 2 1 102000 f 74 goat snp35527-scaffold428-1137365 NW_017189517.1 48589621 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424721 Affx-122941676 AX-123295067 GTACTCTGTTAGCCCTGGATGGGTTTATCAAGTGT[A/G]AGAATTACCAGAAAATGGTGCCTGAGTAGAATGTC R 2 1 2 1 101000 f 74 goat snp35529-scaffold428-1224550 NW_017189517.1 48497726 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789706 Affx-122933953 AX-385276714 GTTATCACACTACTGGATGTCATGAACCAAATGCT[C/T]CATCTTTATATGTTAGCATATGTATGTTTTTAATG Y 2 1 2 1 101000 f 74 goat snp35532-scaffold428-1372071 NW_017189517.1 48348192 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781595 Affx-122969848 AX-385268679 AGAAAATGTTTGAGTAATTCGAAGCTATGAAGACA[C/T]ATTAGACACATATTTACCTTCAGGTTGAACAAATT Y 2 1 2 1 101000 r 74 goat snp35533-scaffold428-1403449 NW_017189517.1 48316160 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408852 Affx-122954007 AX-123279203 AGATCCCAGAGAGGTTAAGTGAATATATGTGGAGA[A/G]TGTATATTATAACACACACTATCAAATTAACATCC R 2 1 2 1 201000 r 74 goat snp35908-scaffold4300-38376 23 12989911 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788086 Affx-122950737 AX-385275106 GAAGACCATGAGGGCATGAATATTGTCCTCATTCC[A/G]CTTGACAGTCCATGAAGATACTAGAAAAAGCCTTC R 2 1 2 1 101000 f 74 goat snp3617-scaffold1112-47921 10 77485004 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447948 Affx-122923779 AX-123318284 TGGAAAACCTATAGCTAAGGAGAATAGACAGTCAC[C/T]ATCACATGGTGTTGAGTGAGCTGCTCGCTATGTCA Y 2 1 2 1 101000 r 74 goat snp36181-scaffold4319-4425 NW_017189517.1 33167857 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391044 Affx-122966861 AX-123261401 ACCTGTTAGGGTTATAAAGGGGATAACAGGGTTTG[C/T]AAAATTGAACTTAGCAGGTTAAAAAATGGAGCTTT Y 2 1 2 1 101000 f 74 goat snp36187-scaffold4323-25248 29 46168641 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422287 Affx-122943486 AX-123292633 CCCAAGCCACTTAGTCTTTAATTCCTGTCAAATAC[A/G]CATCATAGCTTTTCAAGGAGAGGTTCTGTTATTTT R 2 1 2 1 101000 f 74 goat snp36188-scaffold4323-80398 29 46223281 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411676 Affx-122951549 AX-123282026 TTAGAAGGATTGGATAATCAAACAGACATGGGAGA[C/T]GAGCAAAGAGGTGTCTGTATCCACTAAAGGAATAA Y 2 1 2 1 201000 f 74 goat snp36253-scaffold434-7187 NW_017190437.1 2340 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774513 Affx-122926587 AX-385261647 CTAGGACAGGGTGTCACCTGCTGTGTACAGGTTGC[A/G]TCCACAGATTGCAGGACTGTGGTTTTCTTGCATTC R 2 1 2 1 202000 f 74 goat snp36254-scaffold4342-5645 8 69963139 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802221 Affx-122976480 AX-385289125 GGAGCTGTTCTTGTCAAGGTTACAATGACCTCTGC[A/G]TTATTAAATCAAAAGATTGCTTCTCAGGTTTCATC R 2 1 2 1 101000 f 74 goat snp36375-scaffold4369-3829 8 66126618 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800791 Affx-122920926 AX-385287707 TGTCCGTTTTCCGGTTTCTCTGCACCCTAACCGTG[A/G]CTGTCTTCTTGATGTGGTTGCTGGTTGCTTGTCTG R 2 1 2 1 201000 f 74 goat snp36413-scaffold4379-13185 NW_017189592.1 19659 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394490 Affx-122964557 AX-123264845 TTGACTTCTGCACAGAGTTTAACATCATGAGAAAT[A/G]CTGGACCGGAAGAATCACAAGCTGAAATCAAGAGT R 2 1 2 1 103000 f 74 goat snp36504-scaffold4399-11380 NW_017216975.1 21845 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421450 Affx-122943940 AX-123291797 GGAGTGTGATTACTTCTGACAGTAGTCAGTTGGCC[A/G]TTTAATTTTCAGTTCTGCTTCCATTATATCAACCT R 2 1 2 1 202000 r 74 goat snp3655-scaffold1115-17258 NW_017189517.1 31700147 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769472 Affx-122937864 AX-385256642 CAACCCCCTGCCACTCCCTGTCCCAGGGGCTCAGT[A/G]ATCTAGTTCTCATCACTAGGGATTAGTTTGCCTCA R 2 1 2 1 303000 f 74 goat snp36589-scaffold4404-3540 3 101415405 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380391 Affx-122975329 AX-123250749 AATTATAGGGTCCCCTATAATTGTATTCTGGGAGG[C/T]GTGGGACTCCTTGGGAGACAGGTTATTCTTGGCAC Y 2 1 2 1 102000 r 74 goat snp36590-scaffold4404-41796 3 101377443 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432363 Affx-122935869 AX-123302704 GGAGGCAGTGTTATCAGGAGCCAGGAGCACAGGCC[G/T]AGGGAACCTCTGTGCCCCAGAGCCACTGACATGTT K 2 1 2 1 103000 f 74 goat snp36627-scaffold4417-9344 NW_017189574.1 36920 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388048 Affx-122969541 AX-123258406 ATACACATGTCTATGTGCCTGTGAGCACACGTGCA[C/T]GTGGGCATGTGTATTGTCTGTATTTGAAAGAGAGT Y 2 1 2 1 101000 r 74 goat snp36628-scaffold4422-6481 29 50392326 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438077 Affx-122931525 AX-123308415 ACCATTCACTCTCAAGAGTAAAGGGCTGAGTCTGC[G/T]CTTGATCCAAGGTCTCCTGATTCTTAGTCCAGTCC K 2 1 2 1 101000 r 74 goat snp36686-scaffold4445-1012 6 25701728 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791081 Affx-122952135 AX-385278076 TCTTTGAGTCTCAGAACTTTTATGGGGCTCCCCTA[C/T]GAGCAAATTGAATCTCCTAATCTGTCTTTTTTTTT Y 2 1 2 1 102000 f 74 goat snp36783-scaffold4454-7374 18 62593161 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423647 Affx-122942352 AX-123293993 GAAACAAAGTATTATCACTCTCCATATTTTCACTA[C/T]TATAATAATAATAAGATACACATAATTGTTACCAT Y 2 1 2 1 201000 f 74 goat snp36791-scaffold4467-7307 3 66505486 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403429 Affx-122957743 AX-123273782 GTGAACATTGAACAGGCAATGTGGTCACATGAGCA[C/T]GACTCTAATTTCCTCAGAAAGCAAGAGAAAGGGAG Y 2 1 2 1 103000 f 74 goat snp37110-scaffold4503-22393 13 75727 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433827 Affx-122934457 AX-123304168 GGTTTGTCACCAGAACCCTGATCTGCCTGAGATAA[C/T]GGGGACCATCTAGTGATACCTCGAGTATGCTTGCT Y 2 1 2 1 101000 f 74 goat snp37246-scaffold4533-11128 22 48378372 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384466 Affx-122973083 AX-123254824 GAAAGCTGGTCATCAGCCAGTCTTTGTGAGAGGGG[A/G]CGTGGAGGGGTGCAAATGCTGTCAGGAAAGAACGG R 2 1 2 1 202000 f 74 goat snp37247-scaffold4533-59635 22 48426388 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38434082 Affx-122934175 AX-123304423 GGTTTCAAGACGCCTGAGCTGTTTCTGCATGAGCC[C/T]GCCCCTCAGTCTATAAGCTTTGGAGCACTGACGGT Y 2 1 2 1 201000 r 74 goat snp37291-scaffold4542-21721 20 70822023 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397824 Affx-122962480 AX-123268179 GATTAAACTCTGCTGGCATTTCTAACAGGATTTCT[A/G]TTGCTTTTGATAATGCTTTTGCTCAGGATTTGTGT R 2 1 2 1 102000 f 74 goat snp37453-scaffold4569-7271 10 77611943 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774008 Affx-122936086 AX-385261146 AAATCATGGATGTAATAATGGAACGTTTCCCAAAG[C/T]GTGTTTGTGTTTAGGGCTCTCCTCTTAGAGTCCTG Y 2 1 2 1 201000 r 74 goat snp37454-scaffold4569-36967 NW_017189989.1 1779 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405923 Affx-122955571 AX-123276275 ACCATGGTCCCACGACATTCAAAAATCCTATCAAA[G/T]CATTGAAAGACTCTCTCACTCACTCGCCATTAAAA K 2 1 2 1 101000 f 74 goat snp37483-scaffold4582-6164 NW_017189879.1 14321 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771023 Affx-122977172 AX-385258185 TAGTCAGATTATCAACACCAAGTCTCATGTTTGCC[A/G]CCTGTAATTTCCTGAAAATGCAAAACCAGATATAT R 2 1 2 1 101000 f 74 goat snp37609-scaffold4604-13044 29 5033770 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425733 Affx-122940752 AX-123296079 TGAGTGGAGCTCCCGCATTCCAGCCTGGGTAGCCT[A/G]CGTTCTGTGAGGTCCACCTGGGAGCGGGAAAGGGT R 2 1 2 1 303000 f 74 goat snp37628-scaffold4627-10297 3 101674802 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764759 Affx-122961625 AX-385252373 TGGGCCTTCAGCATTGCCAGGTTCTTAGGATAAAC[A/G]TGGCAGCTTTCCACAATTGAAATAGGACACTTAGT R 2 1 2 1 101000 f 74 goat snp37651-scaffold4639-8818 NW_017189516.1 38646222 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419356 Affx-122945637 AX-123289704 GCAAAGCTTGAAGAAATACTGGACTTGATTTCAGA[C/T]GCTGAAAAAGAAATACTCGTGTAACAAGTGTTGAA Y 2 1 2 1 101000 r 74 goat snp37776-scaffold465-10233 2 125729688 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791077 Affx-122972585 AX-385278072 CCACCCAATATCTCTTTCAGAGGGTTTAACTTGGT[C/T]TGCATACCCAGTTAATCTGGTTTAGAGGAAGTGAG Y 2 1 2 1 101000 f 74 goat snp37777-scaffold465-39724 2 125700178 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449561 Affx-122923241 AX-123319896 CAAATGCTATACTCAAGGAAATACACACAGAAATA[C/T]ATCACAATTAAATTTCTGAAAACTAAAAACAAAAG Y 2 1 2 1 201000 r 74 goat snp37778-scaffold465-106006 2 125654903 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771874 Affx-122941311 AX-385259030 AAAGCATCTTTTAATATTCTTATTTACCATCTGGA[C/T]ATTTTCTTTTGCAAGATGAATGTTCAGATCTTTGA Y 2 1 2 1 201000 f 74 goat snp37779-scaffold4658-3369 10 4805219 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798873 Affx-122946522 AX-385285803 AAGAGGGCAGAGCTAAATATGTGATACTTGGATGG[A/C]TGGGCATGAATGGGAAGGAGCTTTCGAAATGAAGC M 2 1 2 1 101000 r 74 goat snp37914-scaffold4675-7323 1 40933715 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405580 Affx-122955942 AX-123275932 TATGAAAACTGATGCAGAGAGAAGCTGTGTGCATA[C/T]ATCATTTTAATCATGTATTTTAATCACAGTAAAAC Y 2 1 2 1 101000 f 74 goat snp37915-scaffold4685-9748 4 120624156 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436358 Affx-122933063 AX-123306697 GAGTTTATGGCTTGCCTGAACTTCCTTTTTTATTT[A/G]TTTTTTAAATTTTTATTTTTACTTTATTTTGCTTT R 2 1 2 1 103000 f 74 goat snp37923-scaffold4696-14058 6 401595 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420822 Affx-122944671 AX-123291169 CTAAGATTTAATAAAATCATACAATAGGTAATCCC[A/G]TTCACATGGCTTCTTTCAGTCAGCACGCACTGAGA R 2 1 2 1 101000 r 74 goat snp37974-scaffold4707-1658 5 102085989 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401714 Affx-122959534 AX-123272067 TGTAACTTTTAGGGCAGTTCCCCATCCCAGGCTTC[A/G]TCTTTAAACTATGCAGCCCACCACGTGAGAACCTG R 2 1 2 1 101000 r 74 goat snp37984-scaffold4710-4299 NW_017189516.1 41852626 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797743 Affx-122934576 AX-385284683 ACTCAGGAGGTTTGTGTTTTCTAGACAATGTCCAC[G/T]TGAAATATGTGTTTGACCTTTGAGGTCTTCAAAGT K 2 1 2 1 101000 f 74 goat snp38014-scaffold4722-4701 NW_017214802.1 16751 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38454016 Affx-122919426 AX-123324349 CAATCAAACTTTTCATTAAAGAACCCCTACGACCT[A/G]CCACATCCTCAATCTCAATATTTATTTTAGCATCC R 2 1 2 1 202000 r 74 goat snp38296-scaffold4823-356 5 118207981 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424540 Affx-122941716 AX-123294886 TATGGACCATTGGTAAAGGCCTTTATTGGGCGGTC[A/G]CTCTCGGGCAGAACTCCCGGGGACGGGTGAGCAAG R 2 1 2 1 103000 f 74 goat snp38297-scaffold483-87583 12 86459567 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406710 Affx-122955764 AX-123277061 AGAATGAAGTGCTGACAGAGACATGGCTTTCTAGA[A/G]GAAAAAGGATGACTATTTGAGCTGACATAAGGAAA R 2 1 2 1 101000 r 74 goat snp38298-scaffold483-145942 12 86400481 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774135 Affx-122927536 AX-385261273 TAAATTTCAATTTGCTGCAGCAAAATAATCAAGCC[A/G]TTATTGATGTCTGCTGCTTTCTCATTTGGTGGTAC R 2 1 2 1 101000 r 74 goat snp38299-scaffold483-192156 12 86354258 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773794 Affx-122949465 AX-385260934 GCACCACCTGGGAAGACTCTATTAACATAATTATT[A/G]CATTTATTGATTTTCATATTGTAAAACAGTATATT R 2 1 2 1 303000 r 74 goat snp38300-scaffold483-263585 12 86283602 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320764964 Affx-122929865 AX-385252543 AAAGAGTCTTATAGTTTCCTCAATATATGTAAAGG[A/C]CATTCCTGAGTTATTTCCACTAAAAATATTTTAAA M 2 1 2 1 101000 f 74 goat snp38301-scaffold483-309425 12 86241356 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800429 Affx-122935196 AX-385287350 GTGTTAGCTATAACTTTGTTATATATGGCTTTACT[A/G]TGCTGAGGTATGTTTTCTCTGTGTGCACTTTCTGG R 2 1 2 1 101000 r 74 goat snp38302-scaffold483-381581 12 86164644 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397785 Affx-122962506 AX-123268140 TAAGCATCCCAACCTCTGCAGATGATATCTTAGCA[C/T]CCCATGGTCTGCAACCCCCTTCTTCAGCTTCAGTC Y 2 1 2 1 101000 f 74 goat snp38304-scaffold483-468396 12 86077019 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408522 Affx-122953702 AX-123278873 AGCTGAGGTTTTTATTTGATTCCTTTTGGTCACAC[A/G]CTGGCATCAAGTTGTTGCATACCTAAAATAGACTA R 2 1 2 1 201000 r 74 goat snp38305-scaffold483-551181 NW_017206562.1 11398 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420730 Affx-122944768 AX-123291077 TCAAACAACGTTTCAATTTATCTGAAGATTTGTTA[C/T]GTGCTTCCTGAGAGATTTTTGAGCATTATTTATAT Y 2 1 2 1 303000 f 74 goat snp38306-scaffold483-603423 12 85921949 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384121 Affx-122972823 AX-123254479 GGAGAACTAAGATACAGGCTTGATCAAACTGTCAT[A/G]TGAAGTAATTATACATGTATAATGATTGGTAAGTA R 2 1 2 1 101000 f 74 goat snp38307-scaffold483-681304 12 85844098 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427275 Affx-122939538 AX-123297618 TCCTCTGGGAAGTCAGCCATCATCTCGTGTTGAGG[C/T]ATGGAACTCCGCTTCCCACTCGAGGTGGAAATGGG Y 2 1 2 1 103000 f 74 goat snp38308-scaffold483-722954 12 85801875 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378704 Affx-122977058 AX-123249063 TTCCCATTCCTCCCTCCCCCACCTGACTACATTTC[A/G]TCATCTTCTTTCTCCATTTCTTCCCATTCTTTGGG R 2 1 2 1 303000 f 74 goat snp38309-scaffold483-757112 12 85767670 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382914 Affx-122973398 AX-123253272 GAGCTGAGGATTGGAGACTGATCATCTCCTTTTAG[C/T]AGATAACTCTAATTCTGGTTCTGGTTTCTGACTGG Y 2 1 2 1 103000 r 74 goat snp38310-scaffold483-786341 12 85737109 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796083 Affx-122937070 AX-385283035 CAGGCTTGATATGAGGGGGCGTGTTGTGTGGGTTT[A/G]CAGGGGTATAGTTATCTGGGTCTCCTAGTAGATCG R 2 1 2 1 202000 r 74 goat snp38311-scaffold483-821830 12 85701623 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401849 Affx-122959429 AX-123272202 AACCCATTCCCCCGTGTGCCCGGGGCACGTGCACC[A/G]TTCCTTTCACCTTCAGTCTTACAGACCCCATTTCC R 2 1 2 1 101000 r 74 goat snp38312-scaffold483-850504 12 85672919 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410408 Affx-122952420 AX-123280758 ACACACATGATTGTTTACTACCTCTTAACCATAAA[C/T]AGCACAGAGAGTTTTGGAGTATTTTGAGAGTCTTA Y 2 1 2 1 103000 f 74 goat snp38313-scaffold483-905544 3 21408321 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438296 Affx-122931391 AX-123308634 AGAACCCTATCTAAACTCGAGAGTAAGCCTGACAC[G/T]ACTGTTACATTTCGGGAGGAAAGTAGACTTGCATG K 2 1 2 1 101000 f 74 goat snp38315-scaffold483-988207 12 85534335 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436437 Affx-122933002 AX-123306775 CTGAGTGCCGGAAGCCAGCGTGAGGAATCCCACCC[A/G]TGACAAGTTCATGCTGCAGAGATTTTATGGCAAGG R 2 1 2 1 101000 r 74 goat snp38316-scaffold483-1026693 12 85495339 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428541 Affx-122938737 AX-123298883 ACCATCCGCAGCCTTTCCACACATAGTTATAGTCA[C/T]TTCTCTCCCAGCCTTAGGCCTTTGTATTGTTTTAA Y 2 1 2 1 101000 r 74 goat snp38502-scaffold4864-10739 25 41460496 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431505 Affx-122936240 AX-123301846 GCAGGTCTGAGGTGGAAAACAGAGTATAAGAACAA[C/T]AATAGCCTATTGGCTGTCCGCAAACCTCCTGCAGG Y 2 1 2 1 202000 r 74 goat snp38858-scaffold4926-10918 21 18998600 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403479 Affx-122957706 AX-123273832 GATCATGATTGTCTGAGGCAGCAGCCAGTCTAGAA[C/T]GGTAGGATTCCACTTCCATTTCCAGTCTTCATTTG Y 2 1 2 1 102000 f 74 goat snp39044-scaffold4945-5317 17 68769879 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435291 Affx-122934036 AX-123305631 TAATAAGCAGCTTGATAATAGTTATATAACTCCTT[A/G]CTCAAAACTATCAAGGGGATATTCTTTCTGCCCCC R 2 1 2 1 201000 f 74 goat snp39050-scaffold4957-10554 3 107510270 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799726 Affx-122931114 AX-385286654 AAGAACTTCTTCAAGCCAAAGGAAACATCAACAGA[A/G]TGAAAAAGGAAGCTAGCACAAATTTTATAAGGTAT R 2 1 2 1 101000 f 74 goat snp3946-scaffold1123-32359 5 101852369 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766144 Affx-122948099 AX-385253547 ATTTTCTCAGGAAAGTTGTTTTTCATAAATGAAGA[C/T]GATATAAAGACTTTCCCGATATAAAGTCATATAAT Y 2 1 2 1 303000 f 74 goat snp3947-scaffold1123-74454 5 101807759 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403060 Affx-122958526 AX-123273413 GAAAAAAAAAAAAAGCACTAAAACAAGAACAAAGA[C/T]GAAGACCTTTGAGAAATACTAAGGTATTGTTGAGC Y 2 1 2 1 103000 r 74 goat snp3948-scaffold1124-13252 27 38611092 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320803091 Affx-122926311 AX-385289962 GACAGAAGAGTGTTAGTGAGCCAGCGCCTTATCAC[A/G]GTCGTGCTTTGGGTTCCCAGATCCAACAAGTACTG R 2 1 2 1 202000 r 74 goat snp39665-scaffold5049-6931 21 67036503 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415752 Affx-122948937 AX-123286101 ACAAACTGTGTGATGACTGGGAAGATTAATTTCTC[G/T]GTGCCTCAAGTTTCTTTTCTGTAAAGTGGTGACAT K 2 1 2 1 202000 r 74 goat snp39720-scaffold507-5056 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398873 Affx-122961041 AX-123269228 TGGCACACAGGCGGGACACCACACTCAGTTCATTC[C/T]GAGTACACGAGTCTAGCATTAAACAGCTGACGAGA Y 2 1 2 1 101000 r 74 goat snp39721-scaffold507-37675 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446980 Affx-122924649 AX-123317316 CAAGGGTGATCAACATACTTCTGAGGAGGCAGGGG[C/T]GGGATCCATTCCAAGTGAGGAAACTTCTGATTATT Y 2 1 2 1 102000 f 74 goat snp39722-scaffold507-103160 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801941 Affx-122920647 AX-385288846 CTTGTCTTAAGATGTGTATACTTTATTCCAACAGA[C/T]GACCACTTGGGACTGAACATCAGAGCAGTGCAGGC Y 2 1 2 1 201000 r 74 goat snp39723-scaffold507-138879 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800616 Affx-122969318 AX-385287535 TCTACATGGGGACCAAGCTGTTTTACTGACCATAG[C/T]ATTCCTGCTGCCTTCCCCAATGCTTTCCACAGTGT Y 2 1 2 1 201000 r 74 goat snp39733-scaffold5081-512 3 66449261 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423603 Affx-122942384 AX-123293949 CTTGTGTTAGCTGCTTTATGCATATGTGTATATTA[C/T]GTATTCATGTGTACACATATGCACATACATGTATA Y 2 1 2 1 102000 f 74 goat snp39734-scaffold5082-12658 NW_017189516.1 63718769 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320783072 Affx-122932006 AX-385270139 GCCTGAACAAGCACTGAATTCACTCTGCAAATTGT[A/G]TATGTACACTTGACTTAGCTCCAATGCAGGAATGG R 2 1 2 1 101000 f 74 goat snp39889-scaffold5090-924 16 9000424 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429356 Affx-122938566 AX-123299698 CATTTCTCCTCAGAAGCCCACAGTCAGGTCAGCTT[A/G]GCCAGCAACCAAGACCTCATGGGAGAAATAAGTAG R 2 1 2 1 303000 f 74 goat snp39890-scaffold5095-11243 NW_017212321.1 13358 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379273 Affx-122976243 AX-123249632 ACTCCTGGTTTCTAATAGCACAGACCCTGCCCCCA[C/T]GGGCAAGATTTTGAGCAAATGGACAGGGACAGAGT Y 2 1 2 1 101000 r 74 goat snp39961-scaffold510-70542 18 62188933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413338 Affx-122950165 AX-123283687 AAAGTCATAGTATAGCGTAACACCAGACCCTCTCC[C/T]GTATCAAAACCAGTTCTGTGTGAGCTTGCTGTTGT Y 2 1 2 1 10000 r 74 goat "snp39962-scaffold510-151054;SV_296" 18 62108413 G A SV_296 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377750 Affx-122977372 AX-123248109 AATATAATTTAGAAGGATTCTTTTTTAATAGAACA[C/T]ACAAGTTGTATTCAGACTTTGGGGCAAAAAAATTC Y 2 1 2 1 201000 f 74 goat snp39964-scaffold510-239718 18 62017998 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802487 Affx-122978053 AX-385289391 AAAGTGTACCCACATACATAGACAATGCATAAGAA[C/T]GTTCATAGCAGCAATATCTATAGTAGCTGAGAGGC Y 2 1 2 1 103000 r 74 goat snp40027-scaffold5107-301 7 107694997 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449098 Affx-122923591 AX-123319433 AAGTAATATTTTACAAAGATTAAATGCTTACAGGA[G/T]CCAGGCAGGTGATTTGCATAGTTGAGCTGGCCAGG K 2 1 2 1 101000 f 74 goat snp40478-scaffold5172-15662 19 18985797 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800245 Affx-122932721 AX-385287168 GCATGCATATTTGCTGATGATTTCTTTTCTGCCTC[A/G]TGGCTTACTTAGCCTCTCTTCTACTTTGTCCCCAG R 2 1 2 1 102000 f 74 goat snp40584-scaffold5193-3644 3 282838 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437099 Affx-122932181 AX-123307437 CACATTAATGAAAATTGGTCTAAAATGCACTGCTG[C/T]GCTATTTGGATTACAGTCATATGAATGTTCTGGTA Y 2 1 2 1 101000 r 74 goat snp40799-scaffold523-29507 18 61534131 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442994 Affx-122928186 AX-123313331 ATTTTGTACCTTTCTACCTTGGAGCTTCCCAGGTG[A/G]CTCAGTGGTAAAGGACCCATCTGCCAGTGCAGGAG R 2 1 2 1 303000 r 74 goat snp40997-scaffold5283-23818 NW_017196353.1 7604 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385623 Affx-122971184 AX-123255981 TCAATTGTAGATATTCATAGTTTTGCTGCCCAAAT[A/G]CTATTGTGCTTGTGTTAACTTTGCAAACTGTCAAC R 2 1 2 1 101000 r 74 goat snp40998-scaffold5284-15885 2 125328885 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767290 Affx-122941849 AX-385254571 ATGCTCTGTAATGATTTCAGAAATCAAACTTATCC[A/G]TCACATTCTAAATGGTACAAATACTGTAACATTTC R 2 1 2 1 101000 f 74 goat snp41228-scaffold5348-5484 11 80197859 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392337 Affx-122966686 AX-123262694 AGAGGCAAACACCCGGATGGGCGGCCAACCTGGAC[A/G]CAAACTGCACGACTGAAAGGAATGAGACAGGGAAT R 2 1 2 1 102000 r 74 goat snp41242-scaffold5351-817 9 74108566 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793898 Affx-122926216 AX-385280867 ACTTAGCGACTGAACACAGCAATACTACTTCACAT[G/T]TTTGACAGTAGTCATCACAAAATTTACTTGTATAA K 2 1 2 1 101000 f 74 goat snp41451-scaffold5392-13893 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782459 Affx-122943406 AX-385269535 TTTGCAATGTCATTCCATACAAAAGCAATAGAAAC[A/G]TAACAGTCTTAGGAAGTTTACAACTGAATATACGA R 2 1 2 1 101000 r 74 goat snp41567-scaffold5407-5726 3 26509044 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422069 Affx-122943599 AX-123292416 GCACCAGGCTCCAGGCACTGTGAGAAACCCAGGGG[C/T]GCGACTCTCCTCCTCAGACTAAGGAGAACGATGAG Y 2 1 2 1 102000 r 74 goat snp41568-scaffold5407-38072 6 115775310 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772841 Affx-122975452 AX-385259986 AGTATGCTAAAAGCACATATTTTGAGTCCAAATCT[A/G]TGTGTGAATCCCATTCCTTTCACATTGCTATTGGC R 2 1 2 1 101000 r 74 goat snp41852-scaffold5452-3484 20 31734968 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38420477 Affx-122944871 AX-123290824 AGAGAAGCTGAGGACTGCATTTGGAGCACTCCTGA[C/T]GTCTTACCTTCCTCTGCTGGAGAAAGACCACATAT Y 2 1 2 1 101000 f 74 goat snp41853-scaffold5452-37002 20 31701830 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444761 Affx-122926364 AX-123315098 GGCAGTGGGAAGTGTTCAACCTGGCCAGTGGCAGA[A/G]GCATACTGATTGTCAGCCTCACACAAAGCCGGTCT R 2 1 2 1 101000 r 74 goat snp41854-scaffold5452-79293 20 31657777 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383158 Affx-122973234 AX-123253516 GCTCAAAACACTTTTAAAGAAATCACACTGGGGAG[C/T]TTCCTGGTGGTCCCAGGGGTTAGGACTGGGAGCTT Y 2 1 2 1 101000 f 74 goat snp41855-scaffold5454-26183 16 78915369 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406726 Affx-122955751 AX-123277077 TGCACAGAGTCACACACACACAGACAAACACGCAG[A/G]CACAGAGACACAGACACAGAGTCAGCGTCACTGAC R 2 1 2 1 303000 r 74 goat snp41856-scaffold5454-69164 16 78872050 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450536 Affx-122922485 AX-123320870 GTGTTGCCCTTTTTGCTCAGCCTGCCAGGAAGCTC[A/G]GAGCTAAAATTAAGGACCTTGTACAACAGTTAGTG R 2 1 2 1 101000 r 74 goat snp41943-scaffold5476-29681 6 115733830 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416221 Affx-122948225 AX-123286570 ATATTTTAATTTAAAAATCTTACTGACAGCTCAGC[G/T]CTATGAATATATTTTTTCTAATTTGCTTCAGAGTT K 2 1 2 1 101000 f 74 goat snp42032-scaffold5482-4876 17 67488771 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402217 Affx-122959157 AX-123272570 ATTTCTGACAGTGTTCAGTGCCAGCAGGGCACTGG[A/C]CAAGCAGATCATCCTTGTATCTGACCTTACTATAC M 2 1 2 1 201000 r 74 goat snp42198-scaffold551-247 15 33745111 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422982 Affx-122942998 AX-123293328 TAGAGAGCCATATATAATGAGAAGAAAAAGAACCA[C/T]GGGGAAGAATATGGGTTTCAGTGGAATTCAGGGCA Y 2 1 2 1 202000 r 74 goat snp42199-scaffold551-49155 15 33794564 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38402694 Affx-122959615 AX-123273047 TTTATTTTTCAAGGTGACCTATGACCTTCACAGTG[C/T]CCCAAATTAGATATTTTCTTATTGGATGCCCCTCC Y 2 1 2 1 101000 f 74 goat snp42200-scaffold551-81262 15 33826121 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413916 Affx-122949822 AX-123284265 TCGTGTCCCTCTAGTCTCTGCTCAGTGCTCCAGGC[A/G]ATAGAGATCCAGAAACACTGCGCTGTTTAGGCGTG R 2 1 2 1 101000 r 74 goat snp42246-scaffold554-44768 14 77382148 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378622 Affx-122977119 AX-123248981 ATTACTGAAAAATCTGGCCAGTAGGATTTTAGTGA[C/T]GTTTAGCTATATTAAATGTTTTTTAATTTGTAGCA Y 2 1 2 1 101000 f 74 goat snp42247-scaffold554-89456 14 77337285 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412121 Affx-122951104 AX-123282471 TTGACCAATGTCCGACTCAAGCAGCACAGGGAAGC[G/T]CTGTGACACAGCACATCTGGAGTCCCAGTTGGGAA K 2 1 2 1 10000 f 74 goat "snp42249-scaffold5548-5086;SV_150" 6 9050700 G T SV_150 1 preexisting CNV preexisting neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776021 Affx-122955376 AX-385263151 TCAGCCTGTAAATAAGTTTACCCTTGTAAAATGTT[A/C]CTGAAGAGGGGTTTTCTTTTATTGTTGTTTTTTTT M 2 1 2 1 202000 r 74 goat snp42255-scaffold5553-11725 18 64370409 C A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406818 Affx-122955684 AX-123277169 AGTGATTTATAACAGAGAAAATTAATTAAATCAAG[C/T]GTCTAGTATTGCTAACATCAAAACAACTGTACTCC Y 2 1 2 1 303000 f 74 goat snp42258-scaffold5559-1739 13 2810096 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774986 Affx-122932228 AX-385262118 ACCAAACTCTTTCCTGTGATTTGATGACTCATTTT[C/T]CATAGCAAAAGTTATAATTCTGTTCTAATTTTTTG Y 2 1 2 1 101000 f 74 goat snp42289-scaffold5565-2384 6 3472105 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802664 Affx-122974921 AX-385289563 ATATAAAACAAAGAGTTTCTATAGCATAATAAAGA[C/T]GATTCACTTCATCTTACAAGATATAGGGAACAACC Y 2 1 2 1 101000 r 74 goat snp42332-scaffold558-20570 15 79790357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778089 Affx-122954639 AX-385265205 CAGCTTTCTTCAGATTAGTCAAAATTGAAATTGTG[C/T]AACTTCCATTTCAAGGACTTGAGGTCCAGATCTCT Y 2 1 2 1 101000 r 74 goat snp42333-scaffold558-55426 15 79755892 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453230 Affx-122920424 AX-123323563 GTGTGATGAGGTGTCCCCCTACACTACATGGTGAC[A/G]CCCTTATGCACAGCCCACCACATGAACAACTTTAA R 2 1 2 1 102000 f 74 goat snp42334-scaffold558-114235 15 79695440 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448293 Affx-122924168 AX-123318629 GGCACTAGATGAGGCTTCTCTCAGAAGAAAGGTAG[A/C]TTTATAAAGGAGGATCCAGAGATGAAGATCCTGAT M 2 1 2 1 101000 f 74 goat snp42336-scaffold558-235522 15 79571178 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439016 Affx-122930355 AX-123309353 ACACAAATAATAGCAGATATGAATGTTTTTATTTT[A/G]CAGCTAACATTTGAAAGAAACCAGTTCTTCTCTGT R 2 1 2 1 103000 r 74 goat snp42337-scaffold558-294376 15 79511103 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392158 Affx-122966315 AX-123262515 TAATTATTATTCTCATTTTACACATGAAAAAACTG[A/G]GGCAGAGTGAGGTTAATAGTGTTCAATGTCACAGA R 2 1 2 1 103000 r 74 goat snp42338-scaffold558-331745 15 79473261 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440862 Affx-122929249 AX-123311199 ACAAAAATGCCATCACCTCCAAGGAAAAATGGGAA[G/T]AGAACATGGTCCAGAAACTCCCAAAGAAGAAACGC K 2 1 2 1 303000 f 74 goat snp42365-scaffold5594-14554 4 87487318 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419832 Affx-122945819 AX-123290180 CACACTAAAATATAAGGTCCATCTTCGTAAGCCCT[A/C]CTTTGATTTAGGGGGCTCCCTGGGACAGTTAATGA M 2 1 2 1 201000 f 74 goat snp42580-scaffold5651-8548 17 6167142 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778490 Affx-122961771 AX-385265604 TCATTGTTCCATATTAAAGACTGTGATTCAATATT[A/G]CTCTTATAGAACATTTAGGGCTGGTAAATTCATGC R 2 1 2 1 201000 f 74 goat snp42681-scaffold567-48877 12 51583 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779018 Affx-122920744 AX-385266125 CACCTGGAGTCTGGGTCTATTCTCAGAACATATCA[C/T]AGTATAATCTACTTAGTAGTTTAAAAACTTTTCAT Y 2 1 2 1 101000 f 74 goat snp42682-scaffold567-106970 12 106701 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766724 Affx-122929327 AX-385254065 AGAACCGCCAACAGGCTTTTTGGAGAGAAGACTTA[C/T]GATTTCCTCTCGGTAAGTCATACTCCTGATTGCCG Y 2 1 2 1 101000 f 74 goat snp42685-scaffold5679-13555 NW_017189884.1 18431 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38425717 Affx-122940764 AX-123296063 CATCTTTAGGTCCTTCTCTCATGCCTAGCAGCCTT[A/G]CCTGGCCCACTCAGGCAGAGAGCATCAGCTTAGAT R 2 1 2 1 101000 f 74 goat snp4299-scaffold1134-405 25 36598014 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397223 Affx-122962381 AX-123267578 GAACAGTAGGGACAAGGAATGCCAGCCGGAGAAAG[C/T]AGAAAAACACTGCAGGGCTATGCAGGGGAGTCAAG Y 2 1 2 1 201000 f 74 goat snp4300-scaffold1134-36868 25 36565776 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394714 Affx-122964339 AX-123265069 GCAGTGAGTTACAACAAAGAAAGAAACAATTGTTC[A/G]AAGGTCTGATATGGTTTATTCCAAGGTTATTGCTC R 2 1 2 1 201000 r 74 goat snp43041-scaffold571-11472 NW_017189790.1 9977 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394689 Affx-122964356 AX-123265044 CACTGACTGGAGAGGAATCCCGGGAGGTCCCTCAC[A/G]ACTGGCATGGAGACTGGCCTTTACTGAGGTCACAC R 2 1 2 1 201000 f 74 goat snp43042-scaffold571-94248 NW_017204681.1 3153 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381778 Affx-122974298 AX-123252136 CCATGGGTAGAAAACCAGGGACCAGTGCTGAGGTA[C/T]GGAAGTTCCCAGGGGACCTTAAGGGAAAACTCCAA Y 2 1 2 1 101000 f 74 goat snp4304-scaffold1134-175741 25 36429982 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384526 Affx-122973037 AX-123254884 CATCTTCTATATCCTGTTTCCAGTCACAGACGCCA[C/T]GGTCAAAGGTGCAGTCAACTGAGATATTTAAATGT Y 2 1 2 1 201000 r 74 goat snp43188-scaffold5741-410 NW_017189516.1 56647667 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794732 Affx-122934887 AX-385281692 ATCTATGGTACTGCTAGTTTTACAGTCACAGCAGG[C/T]AGCCACTCGTAGTCAGGACAGTCTCCAGGCAGGTT Y 2 1 2 1 202000 r 74 goat snp43189-scaffold5743-21629 NW_017189645.1 12916 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430732 Affx-122936888 AX-123301073 GAAACAGTAGGTATGAGACACAGCCCCTTCCATCA[A/G]AGTTAAGAAAATAAATTATTCCCCCCTCCAAAAAT R 2 1 2 1 103000 f 74 goat snp43286-scaffold5768-7817 NW_017189517.1 9984230 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431556 Affx-122936199 AX-123301897 GGCACCAACCACGAGTGGGGAGGGGCAGGGTGACT[A/C]TCCCCTCCAGTGCCCTTGACCCAGGCTCCCAGCTC M 2 1 2 1 201000 f 74 goat snp43333-scaffold5773-6354 23 22613450 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775564 Affx-122927444 AX-385262695 ACTCACGGGTATGTTGACTCATGTGTATGTAGACA[C/T]GTTTATGTATAATCACATGTGTGTTGACTCACATG Y 2 1 2 1 101000 f 74 goat snp43359-scaffold5785-26783 21 69193320 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385965 Affx-122971535 AX-123256323 AAATTATCTGAGATGTGGATGAAAAAATGGATGAA[G/T]AGAATATAAAAAATGCATCAAACTAGTAAAGTTAA K 2 1 2 1 101000 f 74 goat snp4336-scaffold1136-4704 11 51131036 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788594 Affx-122919693 AX-385275611 AGTTTGACCATCAGTTTGAATTAACCCTAACAGTG[C/T]AACATAAATTGAATGCCTATTTTTTAACTCTGAGA Y 2 1 2 1 101000 f 74 goat snp4337-scaffold1136-37975 11 51098026 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771192 Affx-122976897 AX-385258351 TTAGTATTTTTATCCTAAAGTTGTAGCATCTCGAT[C/T]ATTGGCGACTGACTCAATTTCTAAATGTTCTCTTT Y 2 1 2 1 101000 r 74 goat snp4338-scaffold1136-72503 11 51062445 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794752 Affx-122972949 AX-385281712 CACTTATGATCCTTATGATCCTTTATCAAAGAAAG[A/G]TAAGTCTTAATACAAACTGATGGCTAAAAACAAAA R 2 1 2 1 101000 f 74 goat snp43512-scaffold58-27262 1 11892437 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38390675 Affx-122967121 AX-123261032 ATGGAATAAATTTTACCAAACACACACATGTGTGC[A/G]CAAGCCCTCTCCCATGTCCCATTTCTCTCTCTCAC R 2 1 2 1 101000 r 74 goat snp43513-scaffold58-61114 1 11926776 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442403 Affx-122927995 AX-123312740 ATGATGTGATTATTTTCATAATAAATAATGATACA[C/T]GAAGACTAAAAACCTACCTTCTTGTGTAATAAATA Y 2 1 2 1 101000 r 74 goat snp43514-scaffold58-97018 1 11962042 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451457 Affx-122921150 AX-123321790 CCTTGTGTGTTTCTTCTTCAAATTCATTGCTGTCT[C/T]CTTTGAATTTGGCTTAACTATTATTCCATATTTCT Y 2 1 2 1 101000 r 74 goat snp43531-scaffold5805-10990 23 46742557 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38401577 Affx-122958883 AX-123271930 ATAGTTAAATTGTTTATAAATCCAGTGTGACTGTC[A/G]TTGTCTAGCCCAACAACATGTAATCCACTTATAAT R 2 1 2 1 101000 r 74 goat snp43622-scaffold584-21804 13 19440542 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400197 Affx-122960185 AX-123270552 CATGAATAAGTTCATGTCAAAAAAGCAGAAGGAAA[C/T]GGGTTAAAGTTTAAAAAACAGAATTCCATGCTTCA Y 2 1 2 1 201000 r 74 goat snp43623-scaffold584-51680 13 19410518 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790105 Affx-122961204 AX-385277111 CTGACTCCCTGTTAAAGCTCTGGGACGTGAAGTGA[C/T]CCAGTACCATTCTACCTAAGCAGAAGACTTAGCTG Y 2 1 2 1 101000 f 74 goat snp43624-scaffold584-114277 13 19347018 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399264 Affx-122960561 AX-123269619 ATTCAAGGCAATAAGAAGCATGACATTATAGTCAA[C/T]AGTGATCCAGTAAATAGATAATTGGTATATCACCA Y 2 1 2 1 101000 r 74 goat snp43625-scaffold584-145415 13 19315837 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410975 Affx-122952016 AX-123281325 GCACGATCAATTCATGAGGATATCTGGGGAGGCAC[C/T]GAAGCTTGTTTGTGAATAATGGGGGCTTGGGCATC Y 2 1 2 1 101000 f 74 goat snp43626-scaffold584-177806 13 19283224 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433312 Affx-122935187 AX-123303653 CCAGTTTCCCATTAATACACTGTATTTCAATTTCC[C/T]ATTAATACACTGTATTTTAAGTTAGCCAAGAATGA Y 2 1 2 1 103000 f 74 goat snp43729-scaffold5874-9444 NW_017195898.1 7038 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398828 Affx-122961391 AX-123269183 AGCAGCAGAATGCAGGACCCTGTTTAAATAAAACC[A/G]TGAGCCATTCTGAGATGATCTAGATACTCAGGTGA R 2 1 2 1 202000 r 74 goat snp43837-scaffold591-35232 18 1725841 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392171 Affx-122966306 AX-123262528 AGGAATGTGGGTTCTAGGCTCAGCTCTGCCAACAA[C/T]GAAGGCAAGTGAACATGACCAGCCATTTTATCTTT Y 2 1 2 1 101000 r 74 goat snp44107-scaffold5984-8199 4 109414224 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439537 Affx-122930111 AX-123309874 CTGCCCCACTGTCTTGGGCAGTGTCCTCCCCCATC[C/T]CTGTGGTCTTAAATCCCACCAGTACTATCCCCACC Y 2 1 2 1 103000 r 74 goat snp44425-scaffold6039-8972 21 69336433 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785841 Affx-122958536 AX-385272878 TGGTTTATTAGAACAAATGCTCCTTCTTAAAGATG[C/T]GTTCACTGCTTGCACATACAAGAATGAATATTGCT Y 2 1 2 1 201000 f 74 goat snp4446-scaffold1140-2643 26 35143941 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38447464 Affx-122924357 AX-123317800 TTCAACACAGCCCATAGATGAGGAAGCCTAGGTCC[A/G]AAGAAGAGCAGAGGCATTTCAAATCAGACAGACAA R 2 1 2 1 101000 f 74 goat snp4448-scaffold1140-86197 26 35231135 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800701 Affx-122942680 AX-385287618 GAACGTTTAGTAAGTGGTAGCAATTACCCTAGAGC[A/G]CAGCCAGGCCAGAGCTTCCCTAGACAGTCACATGA R 2 1 2 1 202000 r 74 goat snp4449-scaffold1142-5216 16 6195178 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800851 Affx-122943883 AX-385287766 TGGCAAACGGCCACAAAATACTGCATTTGTCTTTA[C/T]AGTGTTAACTCACAGATTTTTCAGAGTCAGTTTTC Y 2 1 2 1 101000 f 74 goat snp4450-scaffold1142-38405 16 6163018 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384026 Affx-122972895 AX-123254384 CTGAGACACCCAGGCCCCTGAACACATACAGATAC[A/G]TGCTTATTCCTATTTGCAAGTGTACTAGCCAGGGT R 2 1 2 1 101000 r 74 goat snp4452-scaffold1142-144322 NW_017199698.1 1627 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392935 Affx-122965702 AX-123263292 ACATTGTGATTCTGAATTCTTGATTGACTTTTATC[A/G]TTTTTGTTTGCTCACTCACCATAGGGAAAGAGTCT R 2 1 2 1 202000 f 74 goat snp45212-scaffold6163-26601 15 15048373 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320787911 Affx-122962864 AX-385274933 TTAGAAAGAGATAATATACTGAGAGCCAAGAATAG[C/T]ATCCCTATCTGCTTGACTGATACAACTCTCAACAA Y 2 1 2 1 101000 r 74 goat snp45748-scaffold6271-14950 6 25745767 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441540 Affx-122928706 AX-123311877 GCCAAGGCATGTGCAGAGACCAGTCCGCTGACCCA[C/T]AGCGACCCTCCCAGAGGAGCAAAGAAGGTAACCAG Y 2 1 2 1 101000 r 74 goat snp45981-scaffold6300-16457 3 2539380 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320790293 Affx-122968664 AX-385277296 GGGTTCTCGTCCAGTACTGGGAGACGTACAACATA[C/T]GTCTGGCAGACACACAATTGCCGTTGTTAGTAATT Y 2 1 2 1 202000 r 74 goat snp46059-scaffold6314-15604 18 64693777 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378478 Affx-122976669 AX-123248837 CTTTTTTGCTTCTAGTTGGGTTTGGCCCAGTGGGA[A/G]CCCCTGGCAGGAAAGAGTGGTCAGCCTGTTTATAT R 2 1 2 1 202000 r 74 goat snp46118-scaffold6340-21523 10 77397644 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407915 Affx-122954383 AX-123278266 CTCCTTCTTCAGGGCGATTTTCAGAAAGAGGGCTC[G/T]CTACCTGGTGAGCCTTAGCAGGATTGCCTGGAGGC K 2 1 2 1 102000 f 74 goat snp46562-scaffold6454-1707 16 897584 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453267 Affx-122920395 AX-123323600 CCTTTATCCATTGTTCACATCTTTCTCGACATCAA[C/T]GAATCCATACTGGGGAGAGACTTGATAAATGTACA Y 2 1 2 1 201000 f 74 goat snp46623-scaffold6476-10344 NW_017203495.1 16464 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411614 Affx-122951594 AX-123281964 CAGATGAAGGGCCAATGGTTCCATCCCATCTGAAC[C/T]AGCTCAGCTCGAAGGAGACATACCTGACTCCAGGT Y 2 1 2 1 101000 f 74 goat snp46635-scaffold65-7790 27 29923741 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403855 Affx-122957932 AX-123274207 TTACTATTTTTCTCATTTATAATCTCTGTCGCATT[A/G]TTCCAAAGGCGACTGCTTCTATTTTCCAAATTATA R 2 1 2 1 101000 r 74 goat snp46636-scaffold65-50298 27 29880977 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446427 Affx-122925981 AX-123316763 GCAGCAACCAAGGACCCCCTGGCCATGGACCCACC[A/G]GTTGCCAACCAGCTGAATAAAAGCAAAACCAAGAA R 2 1 2 1 102000 r 74 goat snp4672-scaffold1151-52112 NW_017189516.1 25680667 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437619 Affx-122931818 AX-123307957 CTGCTAATGCTAATAATCTTAATAATAATGCTTTA[C/T]AAGTATGTTTTCCAAGGACCACAGAGAAACATATT Y 2 1 2 1 101000 r 74 goat snp4673-scaffold1151-190559 NW_017189516.1 25538910 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775625 Affx-122922078 AX-385262756 GCCACCAGGCTTGTTAAACTCCAGAACTCTATTCA[C/T]GAGACAGAAATCATGATTGTTGCAGATGGTAACTT Y 2 1 2 1 101000 r 74 goat snp4674-scaffold1151-225499 NW_017189516.1 25503679 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38441180 Affx-122929547 AX-123311517 AGTCCCTGAGAACAACATTAATGCATCATTCAATG[C/T]GAGATAAGGACATGGAGACCCCAAAAGAAAAATGG Y 2 1 2 1 101000 f 74 goat snp46867-scaffold6534-18441 15 3989617 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429737 Affx-122937599 AX-123300078 CACTAGTGCCACCTGGGAAGCCTGGATATTCACAT[A/G]CTTATCACTTTATCTATAGGTGAGACAGAAAATGC R 2 1 2 1 201000 r 74 goat snp4707-scaffold1153-26814 28 42426897 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38378753 Affx-122977020 AX-123249112 CATCACAAAGCTAACTGGCACCTCAGTAGTCACAA[C/T]GGAAGGACCCTACAATGAAATAATGTGCAGGAGCT Y 2 1 2 1 101000 f 74 goat snp4708-scaffold1153-96837 28 42354630 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775127 Affx-122936394 AX-385262259 CATTGAAGGGTACAGGTCAATAAACAAAACTCAAA[C/T]GTTTTCTGATATACCAGCATTGAACAATTAAATTT Y 2 1 2 1 201000 r 74 goat snp4709-scaffold1153-163099 28 42584852 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775693 Affx-122956730 AX-385262824 ATAACTAAACCCTTCACACTTTTTCTTGAAATAGT[C/T]TCCTGCTGTCTTTCTTTCTGGTATTTCCACAGCCT Y 2 1 2 1 101000 r 74 goat snp4710-scaffold1153-198206 28 42251131 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791269 Affx-122969347 AX-385278263 AACACAAAACCTTATATTTGCTCTGTATTGTGCCA[C/T]GGATACCATCATGTCTTACTGGTGATGTGCAGACA Y 2 1 2 1 101000 r 74 goat snp4711-scaffold1153-238444 28 42210281 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387331 Affx-122970497 AX-123257689 CAGACATACCCACCACACTAACATCTGAAACGGGC[A/G]TCTGCTGGTGACGTGAAAGGCACACAGGCCTGTGG R 2 1 2 1 101000 f 74 goat snp4712-scaffold1153-270557 28 42177913 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427693 Affx-122939295 AX-123298036 TTCTTTACCCATGACGATCAGCAAAGCATTAGAAG[C/T]AGAGGATATAGAAATACAGCTTTATACATATTTCA Y 2 1 2 1 101000 f 74 goat snp4713-scaffold1153-307649 28 42140775 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793703 Affx-122940617 AX-385280675 AAGCACCATCAACCAGGCTACATTACTTCATCACA[C/T]GTGTTCCCTTGATGTGCCTCTAAATAAACATGTAT Y 2 1 2 1 101000 f 74 goat snp4714-scaffold1153-363247 28 42083631 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437726 Affx-122931738 AX-123308064 ATCTCCTCTTTCTCACTCAGGTCAGTCTAGCTGGG[C/T]GGGTGGAGTTCAGAGCAGTAGAACGAGTGGAATAA Y 2 1 2 1 102000 r 74 goat snp47152-scaffold6591-8244 NW_017212328.1 23187 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38381089 Affx-122974598 AX-123251447 AAGAAGTTAAACAGAGGGAACCACCTTGGAAGTGA[G/T]CCCACACGGCCCATAACATCAGAGAAGGGCTAGAT K 2 1 2 1 303000 f 74 goat snp4715-scaffold1153-397570 7 52078988 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395734 Affx-122963702 AX-123266089 TGTGCTGACAAGTCTAGTCTGACCGCCATCCTGAG[C/T]GCAACAGACACCAGTAACCAGCATGACACCAAAGG Y 2 1 2 1 201000 f 74 goat snp4716-scaffold1153-476783 28 41980009 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440070 Affx-122929735 AX-123310407 TCCACCTGTAGCAGGTTGCCCAGCACCGGCAGCGG[C/T]GTGGGGCCTGGTGGGTAGCGTGGGGCCCAGCGTGA Y 2 1 2 1 103000 f 74 goat snp47214-scaffold6615-3768 NW_017189770.1 9151 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798301 Affx-122931297 AX-385285236 TTGAAAGAAGCTTTGCATATTCAAGTGCTTATTCA[G/T]CACCTGCAAGTAAAGAAAGGGGGAGATGTAGGGAA K 2 1 2 1 102000 r 74 goat snp47303-scaffold664-28313 18 61214827 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419528 Affx-122945435 AX-123289876 TGTGATGGTTGCACTATTCTGTGAATATACAAAAA[G/T]TACCCAACTATACGAGATTCAGTGGATGAACTTTA K 2 1 2 1 202000 r 74 goat snp47744-scaffold6715-1478 24 5257057 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784762 Affx-122945407 AX-191359338 AATTGATGTGTCTTTCGAAAACGTTTCCTACATCT[A/G]TTCCTATCCATAGGACTCTCATTCTCGTCACTTCT R 2 1 2 1 101000 r 74 goat snp47868-scaffold6743-30943 23 23270097 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784914 Affx-122971663 AX-385271961 CCCTGTGACAAGGGTGTTTTCCCATCTTATCTGAT[A/G]CTCTGTTTGCTCAGACCAAACACACTTCTCTTTGA R 2 1 2 1 201000 f 74 goat snp47968-scaffold6754-1518 3 101569084 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773603 Affx-122952103 AX-385260743 CATTGTTGATCATATCCAGGGAAGAAGGACTTCAG[C/T]GGAAATAGAGACGGTTAAGGCCATCTTATGACATT Y 2 1 2 1 101000 f 74 goat snp47969-scaffold6754-60598 3 101595766 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428434 Affx-122938821 AX-123298777 GGCCTTTTGGAGCATCCAGGAGAAGGGATCAGTGG[C/T]GAGTCTTTAATTGAGGATAGCCTCAGGTGTCAGCA Y 2 1 2 1 101000 r 74 goat snp48004-scaffold6780-618 NW_017202354.1 3278 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777023 Affx-122976952 AX-385264146 ACATGAGACCAATAAAATAGAACTGAGTGCAGGAC[A/G]TAAGAATCATGAGTAGGGAGTGGATGAATGCAGGA R 2 1 2 1 101000 f 74 goat snp48005-scaffold6780-30646 NW_017189516.1 9190366 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384826 Affx-122971978 AX-123255184 TCTAAACCTCCAGCCTGATTCCCTTTGACAAATAT[A/G]TTTTTGAGGTGATTACCAAACCATTTGAAGTTAAT R 2 1 2 1 101000 r 74 goat snp48006-scaffold679-1181 1 116013243 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440695 Affx-122929909 AX-123311032 GGTGGGCAGAGGTACATGTAGATGGAAGTCTAGAA[C/T]GTTGGAGGCCCAATAGCAAACTGTATTGACAAAAA Y 2 1 2 1 101000 f 74 goat snp48007-scaffold679-39486 1 115974955 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437892 Affx-122931667 AX-123308230 AACTATATTTTAATTCATTCAGGAAGAAACTAAGG[C/T]AATTTTTACAACTTCTTCAAAAGAGAATCCAGAGT Y 2 1 2 1 101000 r 74 goat snp48008-scaffold679-70827 1 115943021 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443173 Affx-122927609 AX-123313510 TTAATATGACAAGGGATTTTTTTGTTCTCCTTAGG[C/T]ATTGTAGTTCATGTATTTCAGTGGAATGCTAGCAG Y 2 1 2 1 101000 f 74 goat snp48009-scaffold679-113029 1 115898747 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387490 Affx-122970341 AX-123257848 GATCTTGAACCTTACCTAAAACTAGTTTTATGGCT[A/G]TAGAGATTTTCAAAACTGTCCTGCAATTACCCAAT R 2 1 2 1 101000 r 74 goat snp48010-scaffold679-143113 1 115867843 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400087 Affx-122960746 AX-123270442 CATGTGGCAAGAAGTCCTAAGGACTCCTGCAGGTA[C/T]GATCATGACATGACATTTTCCTCTCCTGAAACACA Y 2 1 2 1 101000 r 74 goat snp4818-scaffold116-41846 15 70876692 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770802 Affx-122927521 AX-385257966 CATTATTAACAGAGTTCTCAACAGATGACCAAGTA[C/T]ATTTATTTTTCAATTGTCACAGAGAATCTAGATCT Y 2 1 2 1 201000 r 74 goat snp4819-scaffold116-93597 15 70929232 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782919 Affx-122947410 AX-385269989 AAGGGTAAATTAGAATGAAGACACTACAGAAATAT[A/G]CAAAATATTTTCCAGCATCTTATTCTGGAGTGATT R 2 1 2 1 102000 r 74 goat snp481-scaffold1012-17285 NW_017189516.1 64671247 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443137 Affx-122928076 AX-123313474 TCTAGGACCTTGAACTAAAAGGGTATAAATAATAT[C/T]CTGAGCCATATCCTTTGAGCAGTTTTGCAGACACT Y 2 1 2 1 201000 f 74 goat snp4820-scaffold116-131207 15 70966951 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389060 Affx-122968605 AX-123259418 ATTTAGCTGTATAAGAATACATGTGTTCCATTTAA[A/G]CTATCATTACCTAAGTCAAAGTCATAATGGAGATT R 2 1 2 1 101000 r 74 goat snp4821-scaffold116-193527 15 71029579 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449968 Affx-122922887 AX-123320303 GCAGCTGTATAAATTAAATTGCTAATTACTAAAAA[C/T]CAGAAAGATTATAAGAGAATCAGCTTGCCAGCTGA Y 2 1 2 1 102000 r 74 goat snp4822-scaffold116-250520 15 71087281 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435026 Affx-122933799 AX-123305366 GTTTCCTTGACTGATAGTTGCAAAACATTTTCATC[A/G]ACAGCTTCCTTACTTTACACATGTCTCTATTCATA R 2 1 2 1 101000 r 74 goat snp4823-scaffold116-304153 15 71141933 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423168 Affx-122942741 AX-123293514 AACCGTGGCCCTCAATTTCAACAAAATAAACCAGA[C/T]GTGTCAATACTCTGAAACTGTAAATCCACTGAAGA Y 2 1 2 1 101000 r 74 goat snp482-scaffold1012-58589 NW_017189516.1 64630460 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427301 Affx-122940150 AX-123297644 TTCTCCACCAGAGCTCCCAGAAGCAACCAGCCCTG[C/T]GGACCTCTTTATTTAGATAGCCATCCTGGTTTTCT Y 2 1 2 1 101000 r 74 goat snp483-scaffold1012-87572 NW_017189516.1 64601348 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397380 Affx-122962274 AX-123267735 TCCACTCCGTCCTTCCTCTGAACACAGGCTGATGA[C/T]GGAGAATTCGCTCATACTTTGGCTCAACAGAGAAC Y 2 1 2 1 101000 r 74 goat snp48420-scaffold6873-2674 18 44885047 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453438 Affx-122919870 AX-123323771 TCTCCTGCATTGCAGGGAGATTCTTTACAGTCTGA[A/G]CCACTTACCAGACACTTGGTTTATGTCCTAAATGT R 2 1 2 1 101000 r 74 goat snp48421-scaffold6873-52551 18 44935051 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786329 Affx-122919596 AX-385273363 TGTTTTGCAGTCCTGACCTCCTTCCATTTTATAGA[C/T]GGTAGGAGCAAGGCTGTCCTATGCCTTGTAATACT Y 2 1 2 1 102000 r 74 goat snp484-scaffold1012-119364 NW_017189516.1 64570423 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408759 Affx-122953394 AX-123279110 TTCTTTCCTGGAATAATGATAGCCTTGTGACTGGC[A/G]CTTTCCTTGATGATTTGTTCTTGTGTACTATATAT R 2 1 2 1 201000 r 74 goat snp485-scaffold1012-179490 NW_017189516.1 64510222 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403570 Affx-122957582 AX-123273923 ATGTATGCACAGTTGTAGGACAGATTCTGAGTGTA[C/T]ACATATGAGAATGGTATTGAAATAAGATTTTGATA Y 2 1 2 1 10000 f 74 goat "snp48639-scaffold6901-7687;SV_193" 3 21510804 T C SV_193 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771826 Affx-122941320 AX-385258983 GGTTCCAACATTGGTTTGGATTCGGAAAAACTTCA[C/T]GGTCAGGTAGAGACCATGGAGCACTCCCAATTAGA Y 2 1 2 1 202000 r 74 goat snp48640-scaffold6901-43966 3 52014653 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416492 Affx-122947792 AX-123286840 CATGGTGGGGGGTGTGCATAAAAAATCCAATGCCT[A/G]TGTAATTGACAATAAACATTTTGGCCAAGGACCAC R 2 1 2 1 101000 r 74 goat snp486-scaffold1012-218730 NW_017189516.1 64469650 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389756 Affx-122968244 AX-123260113 CACAGAAGCATTGAGAGGTGTGAACAGCATTGGAA[C/T]GACATGTGTTGATTTTGGGTAGAATGGTGGTTATT Y 2 1 2 1 101000 f 74 goat snp487-scaffold1012-248292 NW_017189516.1 64439942 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439031 Affx-122930343 AX-123309368 CAAGCCTAAAGGCTCTGGGTTTTCTTTCCACCAAA[C/T]AGCCCAGGCCTGTCCCATTGAGACACCAAGCCTCC Y 2 1 2 1 102000 f 74 goat snp48839-scaffold6967-2963 18 58621143 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795778 Affx-122974210 AX-385282731 CAGGAGGTTGTAACTGTTCACAGTATCTGAAGGTC[A/G]TCTTCCATCCATTATCTTCCAACTTTCTCAAGATG R 2 1 2 1 101000 f 74 goat snp488-scaffold1012-341115 NW_017189516.1 64332156 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38400996 Affx-122959696 AX-123271349 CCAGACGCTAATTTAATATGGAGTATCCCAGTTCA[C/T]GTGAGTGTGACAGTCATTTGGCATAATTTTTTTCT Y 2 1 2 1 101000 f 74 goat snp489-scaffold1012-397009 NW_017189516.1 64227225 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776900 Affx-122971979 AX-385264024 CCTCATTTCCATGGAATCAAGATCAACATGAAGAC[A/G]ACTTCTCTGGTTCCTGATTAACATTATCCTTCTGT R 2 1 2 1 101000 f 74 goat snp490-scaffold1012-426076 NW_017189516.1 64256321 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777303 Affx-122922967 AX-385264425 ATTGTCACCCTTAATTTTATTGGATTTACTAATGT[A/G]CAATTCAGATTTTCATGGCTATGTAAAGGATTTAG R 2 1 2 1 101000 f 74 goat snp49129-scaffold70-379 12 80903561 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429627 Affx-122937691 AX-123299968 AAGATTAAAGACTCCAATATCAAATTGAATTTATT[A/G]TTTATCTTTTCTTTGTGGCATCAAATCAGTAGCAT R 2 1 2 1 202000 f 74 goat snp49130-scaffold70-33631 12 80935572 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431443 Affx-122936505 AX-123301784 ACATGACTGAGCGACTTTCACTTAGATCATCATAC[A/G]TGAATATCAGCACAAGCTTCCTTTCCCAGAATTTT R 2 1 2 1 201000 r 74 goat snp49131-scaffold70-65832 12 80967529 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796551 Affx-122928703 AX-385283497 CTTAACATAGAACTGGCTATACTCTGCCTTGAGTG[A/C]TTCCTTGGTATCTGTGTTTTCAGTTCAAATTGTAA M 2 1 2 1 101000 f 74 goat snp49132-scaffold70-96380 12 80998270 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413699 Affx-122950089 AX-123284048 TCCCTCTTACTGTTATCAGTTCACATGGTATTTAA[C/T]GACAAGAGAATGGATGAGATCACAAAAAGAATGAG Y 2 1 2 1 201000 f 74 goat snp49133-scaffold70-150948 12 81054487 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778453 Affx-122940049 AX-385265567 ATTTTGACCTTGAAATCAGACTCCTCAACAAACAG[C/T]GCCAATCTCTTAAGAGTTCAGTAGAATTTTTGATG Y 2 1 2 1 101000 f 74 goat snp49134-scaffold70-188530 12 81092293 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421234 Affx-122944121 AX-123291581 GTAAACTGTCCTCTGAGCTCTCTTAACCACTCTGG[C/T]ATATTAGCCCTGTGCAATCCAGATGAAACCTGCTT Y 2 1 2 1 201000 r 74 goat snp49135-scaffold70-230857 12 81140668 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773583 Affx-122978853 AX-385260723 ACTAGTATTGCTATGTATGCTTCTCCTTTATTGAA[C/T]AGCCTTCTTACCAAATTAGCTCAATTTTCTATTGT Y 2 1 2 1 101000 r 74 goat snp49136-scaffold70-268134 12 81177784 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320766817 Affx-122925763 AX-385254141 CTGACATCACTCCCATTTCTTGCATGAAATCTTGC[A/C]TCTTTCTTCAGATTTTAGTTTGATTGTTAAAAACA M 2 1 2 1 101000 f 74 goat snp49137-scaffold70-301438 12 81211147 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422537 Affx-122943272 AX-123292883 TTTATTAGTATTTCTGAGATGATAAAATTTAGTCT[C/T]GAGAAGTTAACTGATTTGCTTACTGGACCAGATGA Y 2 1 2 1 201000 f 74 goat snp49138-scaffold70-343647 12 81254348 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782559 Affx-122963552 AX-385269633 AGCACAGGAGACAAAGCTCAGCAAACTGAAGAATT[A/C]TTTTCTTTGGGAAGGAATGGGTTATTGTTATCCTT M 2 1 2 1 102000 f 74 goat snp49139-scaffold70-382677 12 81293458 C A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428523 Affx-122938752 AX-123298865 ATATACATATACTTTATAATTATTTTGATATTTAA[C/T]GCACTATTCTAATTACTCTTACAGGCAGTGTACTG Y 2 1 2 1 103000 r 74 goat snp49140-scaffold70-420715 12 81331519 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417371 Affx-122947709 AX-123287719 ACAAGTGAGAAACACGGGAAATACAAGGCAATGGA[C/T]AAAAGATCACTTAGATAAAGAAAAGTGACTGTTCT Y 2 1 2 1 101000 f 74 goat snp49141-scaffold70-456086 12 81366933 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792773 Affx-122933843 AX-385279752 TGCATCAGATTGTACCATAGAAATATAAAGACATA[C/T]GGTTTGGCTTTAGCAATTGCATTTGATTTTATGGC Y 2 1 2 1 101000 r 74 goat snp49142-scaffold70-487383 12 81398671 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320789423 Affx-122924903 AX-385276433 ATAAAGGCCACTGGAAATATCAGCAAAATTTGAAT[A/C]GGATCTATAAATCATATTGTAGTAGTAAACTAATG M 2 1 2 1 101000 f 74 goat snp49143-scaffold70-543914 12 81452421 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435225 Affx-122933620 AX-123305565 AATAATAAATTATTTAAGGCTTGTGGTCTGCACTG[C/T]GTTTAAATTCCATTGTATCAGAGTCCAGGCAAGAA Y 2 1 2 1 101000 f 74 goat snp49144-scaffold70-573015 12 81481971 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426849 Affx-122940496 AX-123297194 TTGACTGAGTAAAGAGTGTGCCTACCAACACAAGT[A/C]GGCATCATCAAATCTGTTGGATATCATATGAATAG M 2 1 2 1 101000 f 74 goat snp49145-scaffold70-605652 12 81515417 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403858 Affx-122957929 AX-123274210 AGTCTTGTTTATAACAGCTTGTATAAGTGTCAGAT[A/G]CTAAGAGTTCACAAATGCTCCTTCTTTAGAGAAGT R 2 1 2 1 101000 f 74 goat snp49146-scaffold70-640977 12 81549129 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769624 Affx-122954951 AX-385256794 AGAGAGATTGCCAGACTTTGTGCCCTAGTCCTTCT[A/G]CTTACTACTTATGAGATGATAATCTCAATCCTCAA R 2 1 2 1 101000 f 74 goat snp49147-scaffold70-698190 12 81604768 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411574 Affx-122951628 AX-123281924 TGTTATTCTCTCTTCACCTGACAATGTTAAGGTTA[C/T]AGGTATCGACATCTGGAATCATCACACATGGATAA Y 2 1 2 1 101000 f 74 goat snp491-scaffold1012-464259 NW_017189516.1 64207358 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421333 Affx-122944074 AX-123291680 GACAGTGTTGAAGACAATGTATGTATAGGAGAATC[A/G]AGCTGGGAATTACTTTATTTTACTCAGTCAATGCA R 2 1 2 1 101000 f 74 goat snp4920-scaffold1165-17785 3 52029222 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793344 Affx-122968480 AX-385280322 TTTAGGGAAACTTAAAGATATGGTTTATGAACACA[A/G]TAAAATCTTCATATCCTCTAAATTGGTCCTTGTAT R 2 1 2 1 201000 r 74 goat snp49211-scaffold7017-18844 9 74401083 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388647 Affx-122969113 AX-123259005 AACCAAATCCAGCCCATTTATTTCTGTATGACCCA[C/T]GACCTAAGAATGGATTTTACATTTTTCAGTAGCTG Y 2 1 2 1 103000 f 74 goat snp49214-scaffold7022-10498 NW_017189517.1 25213265 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385525 Affx-122971249 AX-123255883 AAAGCTGTTGACATAAAGAATTAGTTACATAGTAG[G/T]GAGTGAACTAGTAAATATAATTTTTATGCTTCCTA K 2 1 2 1 101000 f 74 goat snp492-scaffold1012-511289 NW_017189516.1 64159238 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451364 Affx-122921247 AX-123321697 TTGATCTTTAACCCTCTTCTCCTCATGCCACCCCC[G/T]CTCTGGGCAAAAATGAGATATCACAGGCTTTTCTA K 2 1 2 1 201000 r 74 goat snp4951-scaffold1168-28753 4 7324170 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320775474 Affx-122945305 AX-385262605 ATCAAACATATACCAATTATCAATAGTGAACTTTA[C/T]GCTCCTTAGCCCTGAGAGTCTCAGAGAAAAAAGAG Y 2 1 2 1 102000 r 74 goat snp4952-scaffold1168-90024 4 7386782 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448731 Affx-122923835 AX-123319067 TGTTCTTCTGTGTCACCTCAGCTGGCCTGAATTCC[C/T]TCCAGCTTGTTTTTCATTTCAGTTATCATAATCAT Y 2 1 2 1 101000 f 74 goat snp4953-scaffold1168-124897 4 7422335 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778273 Affx-122942610 AX-385265388 CTTTTCCTTTTATTGAAAAAGTTTTTGGTGCAATG[C/T]ATTTTACTCTGGTCACTTCTTTCAATGAAGCCTAC Y 2 1 2 1 101000 f 74 goat snp4954-scaffold1168-190573 4 7485607 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449851 Affx-122922378 AX-123320186 TCTGCCTGACTAGATGTTGCCAAATCTGACGCCAG[A/G]AAACTTGTGCTGAGTCATGCTGGCAACAGCCACGT R 2 1 2 1 101000 r 74 goat snp4955-scaffold1168-225662 4 7521184 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442589 Affx-122928491 AX-123312926 AGGGGGATTCAAGGTAGGAGGGGGCGGGTAGCTAA[C/T]AGAGGAACTTGTATGTCTAAGTCCAAAGGGACACT Y 2 1 2 1 101000 r 74 goat snp4956-scaffold1168-255979 4 7551793 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428548 Affx-122938732 AX-123298890 ATTGTGGAATAGTCTATCTCCCCTTGATTTTGGGT[A/G]ATTTCTCCTTCATGTGTTTCAGGGCTCAGTTGTTA R 2 1 2 1 201000 r 74 goat snp4957-scaffold1168-292007 4 7588781 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796549 Affx-122921539 AX-385283495 TGTCTGATTTTTGTTTCTTCTAGGTCTTTATTAAA[C/T]ATTTTTTGTATATTCTCAAGCCACACCTCAATCCT Y 2 1 2 1 303000 f 74 goat snp4958-scaffold11689-10106 1 40908451 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411338 Affx-122952267 AX-123281688 TGGGAATGATCACCCTCATTAGGATGGATCCCCAG[C/T]TGCACACACCCATGTACTTTTTCCTCAGCCACCTC Y 2 1 2 1 303000 f 74 goat snp50301-scaffold7199-18873 15 4400019 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421081 Affx-122944234 AX-123291428 CAGGGCAAGGGAGCCCAGTGCGGTTGGACTCAGCT[A/G]TCACCTAAGGAATGTGGGGAAAGGAGGGGACACTA R 2 1 2 1 103000 r 74 goat snp5041-scaffold1170-18280 12 15451386 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424007 Affx-122942101 AX-123294353 AACAAAAATTGGTAAATCTGTCAAAGCAAAGGGCA[A/G]AATGGAAGATGAGGACACAGGGCCTATGTTGCCCT R 2 1 2 1 201000 f 74 goat snp5043-scaffold1170-88721 12 15526787 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424944 Affx-122941277 AX-123295290 CTTGCCCCCAACATACAGCCATCTTTCTATCATTA[C/T]AGTAAGTATTTAAAATGTTCATTCCAAAGGTTAAT Y 2 1 2 1 201000 r 74 goat snp5044-scaffold1170-118857 12 15556593 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779841 Affx-122975227 AX-385266940 AACGATTTCCTTAGAGCAGAAATTCATTTCACAAG[C/T]AAGGGATTTGACCAAGGGCCTGTGAAACAGTCAGG Y 2 1 2 1 201000 f 74 goat snp5045-scaffold1170-149876 12 15587683 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442707 Affx-122927869 AX-123313044 CCTGTGACCTTGTGGAAGGTAAGGCAGGTGTTACA[G/T]CCTGTGAACATGTGTGTGTAGAGCAAGACAGGTGT K 2 1 2 1 202000 r 74 goat snp5046-scaffold1170-202361 12 15987598 G T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798349 Affx-122970584 AX-385285284 AGAAGTGAAGTTTTCAGTACCAACATAGGGCTTCC[A/G]TGGAAAGACTGTTGGTTTATTAATCCATTGGTTTG R 2 1 2 1 201000 r 74 goat snp5047-scaffold1170-232630 12 15407615 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384162 Affx-122972794 AX-123254520 TGATTTGAAGGGACAGCTCTCTCTCATGGCCAACA[A/G]TACAGCCTCTTGAAGTCTTCACTGAAGTCTGTCTT R 2 1 2 1 101000 f 74 goat snp50485-scaffold7244-13356 6 3106522 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392292 Affx-122967529 AX-123262649 AAGACTGACAAAGTTTTATCCAGACTCTCCCACAG[C/T]ATACATCTTGAGATAACATTGGCCCAAGACTAGTC Y 2 1 2 1 101000 f 74 goat snp50486-scaffold7246-11081 29 42176455 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776270 Affx-122940452 AX-385263398 CTTTAAAGTTATTGTCAGAGACAGTCTCAAGGCCC[A/G]TAAATATCTCATGAATTTGTACCACAGAGATTCTA R 2 1 2 1 101000 f 74 goat snp5048-scaffold1170-269872 12 15136327 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408109 Affx-122954258 AX-123278460 CTAGTTGGCACAGCCAGGCAAGACTTATGCCCAGG[C/T]TGCCTCACTTCAAGTCTCCAATTTATTTTTTTGGC Y 2 1 2 1 303000 f 74 goat snp5049-scaffold1170-323510 12 15075570 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792678 Affx-122936125 AX-385279658 TTTGCCACAATCTTTTATTTCACAAGTGAGATGTT[A/G]TAAACTCATGTTTTACCAGGAAATATAAAATGCCA R 2 1 2 1 101000 f 74 goat snp5050-scaffold1171-14126 7 99256050 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796781 Affx-122960058 AX-385283724 TTTCAAAACTTACTGCCAACCTACAGTATTCAAAA[C/T]GGTGGGAAATTGCTATATGAATACAGAGAAGTAAA Y 2 1 2 1 103000 r 74 goat snp5051-scaffold1171-47208 7 99289887 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398761 Affx-122961444 AX-123269116 CGAAGCATCTCAGCTGGAAAGTTTAATGAGGGGCA[A/C]GATGCCTAAGCAGGTCAGCGCAGGGTGGGGACCCG M 2 1 2 1 101000 f 74 goat snp50522-scaffold7259-8770 7 107685387 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450902 Affx-122922198 AX-123321236 CCAGAAAAAAGCCTATGCTTTTGCATTGCATTACC[A/G]TCAGAAAGATTCTCCCAGCCAACCAATGATCTCGG R 2 1 2 1 201000 r 74 goat snp5052-scaffold1171-76408 7 99319247 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392299 Affx-122967525 AX-123262656 ACTCATTTTATGTCCTATATCAATGGAAACAGAAA[A/G]AATCTGCTCAATAAACAGGAAAAGAGAGAGAAAGA R 2 1 2 1 201000 f 74 goat snp5053-scaffold1171-105818 7 99354841 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450716 Affx-122921880 AX-123321050 ACAATGGTAACCCCTGCTGGCCTACTGATGAAGCA[C/T]AGTAGTTGTCCTCTTGACTAGTTGCAAAAACTGGA Y 2 1 2 1 101000 r 74 goat snp5054-scaffold1171-151354 7 99401523 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435590 Affx-122933358 AX-123305930 AAGCCGCCTCACAGGATGATTTATAAAATCCTATA[C/T]GTGCCACAAAATCTACCCTTTCTTTCATTTGGTTT Y 2 1 2 1 101000 r 74 goat snp5055-scaffold1171-184466 7 99434714 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320773566 Affx-122920977 AX-385260706 AATACCCACACTGAGAGGATACCATGAGAAATATA[G/T]CTAATGAAATGCTATTGCAAGACAATACTTTCAAG K 2 1 2 1 101000 f 74 goat snp5056-scaffold1171-213417 7 99462861 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777751 Affx-122944772 AX-385264869 TACATTTTATTGATTTTATTCCCAAGGAATTCTGT[A/G]CATGGGAATGGATCCACTTTTAATTTTAATACTAT R 2 1 2 1 101000 r 74 goat snp5057-scaffold1171-250738 7 99500009 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433865 Affx-122934427 AX-123304206 GCAGGTTCTTTACCACTAGCACCACCTATATATTA[C/T]GCTAATACCTCTATTCCTTACTGTCTCTACCTATG Y 2 1 2 1 303000 r 74 goat snp5058-scaffold1171-283515 7 99533526 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802453 Affx-122966037 AX-385289357 TTTTCTTGGTTAAGTATCTGTATTAGATGCCTCCT[A/G]CTGCTGTAAGAAATTAACAGACTGACTTAAAAAAC R 2 1 2 1 101000 f 74 goat snp5059-scaffold1171-321043 7 99570958 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769010 Affx-122952692 AX-385256185 CTAAAAATAAAGTGAACATTGTGCTGGGAAATGCA[A/C]GTCTCAGTGTTGACAATTGAATGGTAATAATGGAA M 2 1 2 1 101000 r 74 goat snp5060-scaffold1171-375238 7 99625496 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388105 Affx-122969493 AX-123258463 CTGGTCTGCCAACTAGCATCACTATCTAGTAGTTG[A/C]AGTGAAATAATACCCCCTGCAATGTACTTCTTCTC M 2 1 2 1 101000 r 74 goat snp5061-scaffold1171-424676 7 99675894 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429118 Affx-122938013 AX-123299460 TTACAGGAAAAAAAAACCATATTTAGCATATAAAT[G/T]ACTTTGACTTCAATGCACTGATCCTATATGTTTGT K 2 1 2 1 101000 r 74 goat snp5062-scaffold1171-460567 7 99708694 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412139 Affx-122951093 AX-123282489 CATCCTTGCCCACCGCTTATTCCTCATCAGTGTGA[C/T]AGCAAATAATGTGTACAAATATTGCTCAAAAAACC Y 2 1 2 1 201000 r 74 goat snp5063-scaffold1171-523085 7 99778872 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38432114 Affx-122936453 AX-123302455 AGATGGCCGGGTCAACGGAGCAGTCAGGACACACA[C/T]ACATATCAGATGGCAATGTGCCCATGGTTCCTGGC Y 2 1 2 1 202000 f 74 goat snp5090-scaffold1173-22839 9 74149293 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414259 Affx-122949617 AX-123284608 CATCAGATGCTGGGGGTCCTCTAAACCCTAACACC[A/G]TCGGCATTTATTTCAAGGCAGCTCATGTTTGGCCA R 2 1 2 1 101000 r 74 goat snp5091-scaffold11739-32970 16 78843901 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450848 Affx-122922238 AX-123321182 TTTTTGTGTATGGTGTTAGAAAGTGTTCCAGTTTC[A/G]TTCTTTTACACGTAGTTGAGCATCTTCCCCAGCAA R 2 1 2 1 103000 r 74 goat snp51088-scaffold7410-19097 NW_017189516.1 20613934 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408212 Affx-122953849 AX-123278563 GGAAGGAGCATTGAGCCAAATGGACAGGAACCTGC[G/T]GTGTGTACCCTGCTGGTTCTTGAGTGTTTATATTA K 2 1 2 1 201000 f 74 goat snp51108-scaffold744-15602 12 16208614 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406777 Affx-122955715 AX-123277128 CAACTCTTTCTGAAGAGGAAGAAAAGGGAGATGCT[A/G]CTGTTAGCACCAGTGTTGATCTTATGGATACAAAC R 2 1 2 1 102000 r 74 goat snp51427-scaffold753-815 10 78514861 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320784322 Affx-122923922 AX-385271373 GTCTTTTAACTGTTTTTCCCTACAACTAATACATT[A/C]ATAAATTGAATCAGGAAGAGACTGTTAGGAGTTCA M 2 1 2 1 201000 r 74 goat snp51429-scaffold753-69058 10 78581931 C A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413151 Affx-122950354 AX-123283500 TTGGATAACTGCAAAGGCCTCTTCACTCTGTTCCT[A/G]CCTTTATTCTCAACTCTTTGAATCTGACTTCTACA R 2 1 2 1 102000 f 74 goat snp51430-scaffold753-101756 10 78613896 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320793879 Affx-122961772 AX-385280848 TTTAAGAGGGTGGGTGTATGCATATTCCAACTCAA[C/T]TGAATTACAGCAAAAAGAAGTTGATAAATATTTTA Y 2 1 2 1 201000 r 74 goat snp51431-scaffold753-137453 10 78650905 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785168 Affx-122921787 AX-385272214 CTGATTTAACTTTTATTCAATAATAAAACTGTTTT[A/C]TTTCTTTTCTTACCCTTATGGAGAGGTGTTCTGGA M 2 1 2 1 303000 f 74 goat snp51433-scaffold753-225647 10 78740976 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452308 Affx-122920675 AX-123322641 TCTTCCAGGATAATGAGATCAATAGTGAATCTTCA[A/G]AGGAGTTTTGGGAAAGAAGTTTTGCCTCTCTCCCC R 2 1 2 1 101000 f 74 goat snp51435-scaffold753-303868 10 78819106 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403993 Affx-122957203 AX-123274345 TATCAGATTACTACAAACTAAAAGCAGAGACATTT[A/G]TTGGGTAATAGTTTGGGAGTTCAAACTCAAAATGT R 2 1 2 1 101000 r 74 goat snp51549-scaffold756-4476 4 7164755 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445613 Affx-122925107 AX-123315950 GTTCTCCTTTATTGCTGAGTAGTATTCCATCTTAC[A/G]GATGTATCCCAGCTTCTCACTTCTCCTTCATTTAT R 2 1 2 1 202000 r 74 goat snp51550-scaffold756-69855 4 7639755 G A 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397669 Affx-122962594 AX-123268024 ATGAAAGCTATGGACCTCTCACTGCCAAACAGTGA[C/T]ATGAAAATCGTACAGATGTCTGCATACAATTTTGG Y 2 1 2 1 101000 r 74 goat snp51551-scaffold756-126461 4 7697409 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38388255 Affx-122969781 AX-123258613 CATTTCCGGACATAGTATCAACATACTCGGCAGTA[C/T]GCACTTGTTGAGCCAATGACATCGCTGCAACAGCA Y 2 1 2 1 303000 r 74 goat snp51552-scaffold7565-4035 3 52014948 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433231 Affx-122935253 AX-123303572 AAATAAACAACACCAACGACCAAAAAGTGTTCCTC[A/G]TTGGACAAAGCTAGAGAAAACCCAACATCCTATGG R 2 1 2 1 303000 f 74 goat snp52036-scaffold766-32112 NW_017189657.1 38728 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450021 Affx-122922845 AX-123320356 TCTCGAGTTACAACGGGGACCTCAGTGAACCACTC[A/G]TTTGCCTCAGGAAAGTTTGGTCTCCATGCGAGCTC R 2 1 2 1 303000 r 74 goat snp52037-scaffold766-71052 NW_017190145.1 99875 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419070 Affx-122945803 AX-123289418 AATGACTCTGTAGAGTAGTGATACAGAGAAGGCAA[C/T]GGTAACCCACTCCAGAACACTTGCCTGGAAAATCC Y 2 1 2 1 303000 f 74 goat snp52038-scaffold767-4367 4 119188151 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796266 Affx-122960754 AX-385283216 ATTAATATAATTGCCAGCATTTTATTAAATCATAT[A/G]CTAAAAAAGTAATTTAACTGAAGGAATGGGGCCTT R 2 1 2 1 201000 f 74 goat snp52040-scaffold767-88602 4 119272260 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799438 Affx-122934886 AX-385286368 TTGGTGTTGTTTGTACTAACTTTTAATTTATAACT[A/C]ATGGATTTAGTTAGAGAAACAGATTACTCTTTGAG M 2 1 2 1 201000 f 74 goat snp52041-scaffold767-120662 4 119304416 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320801355 Affx-122924941 AX-385288267 TAATAAACTATGGCATATATTTCATCAAGTTCTGA[G/T]AAAATCTCTGCAATATCAGATGCAACATGAAAAAT K 2 1 2 1 201000 f 74 goat snp52042-scaffold767-168432 4 119353193 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792601 Affx-122951161 AX-385279582 TGTAATTAAGTCTTCTAAATGGACTACGATTTCAG[C/T]GGCTGTGTTTTCTTCTCAATTACTTAGAAAATTTA Y 2 1 2 1 101000 r 74 goat snp52571-scaffold783-10947 NW_017189516.1 63056685 G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385429 Affx-122971324 AX-123255787 GCAGATCACGTGGGCCAAGGAGGAAGTGTTTTGCA[G/T]CTGAGACTTCAGTTGCCCCACAGGAAACCCTCTGC K 2 1 2 1 201000 f 74 goat snp52572-scaffold783-66505 NW_017189516.1 63112554 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376866 Affx-122977832 AX-123247225 TAGTCGGGTCACAAGCAAGAATCTGAGAACCTGTA[C/T]GAAGTGTAGCCAGTGTAATCCAGGTCCTACATCTA Y 2 1 2 1 202000 f 74 goat snp5261-scaffold1182-13098 NW_017211852.1 9684 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382238 Affx-122973961 AX-123252596 TTTACCGACTGAGCTATGAAGCCAAGGCTGGTTTA[C/T]AACTGGCCTTGTCAAGTCTCACCCAGACCTCAGCA Y 2 1 2 1 101000 f 74 goat snp52657-scaffold789-1022 NW_017189516.1 63743447 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404884 Affx-122956471 AX-123275236 CAGATGGTAATGGGCAAAGGAGTATGATAGAGGAA[C/T]GCAGTAGAAACTGGAACACTTTGAGAGTCCGTTGG Y 2 1 2 1 101000 f 74 goat snp52658-scaffold789-55441 NW_017189516.1 63797865 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421097 Affx-122944222 AX-123291444 TTGTCTATTGTGACTCTAGGAGGTGTTGAACCTCA[A/G]CCATCTCATAGGACCTCACAAGAGCTGACTGTTAA R 2 1 2 1 101000 f 74 goat snp52660-scaffold789-152422 NW_017189516.1 63894806 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320802165 Affx-122974781 AX-385289069 GTTCTGTCATCCCATTCTTCTTGAAAATTGATTTT[C/T]ATTGATGTGTAGTTGATGCACAATGCTGTATTATA Y 2 1 2 1 101000 r 74 goat snp52661-scaffold789-190380 NW_017189516.1 63932731 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450616 Affx-122922004 AX-123320950 TGTACTTCCCGTTTGTCTCTCTTCTCTGGTTAAGC[A/G]TCTCTGCAAGTTATTTGGTCATTACGCAGTAGGTA R 2 1 2 1 101000 f 74 goat snp52663-scaffold789-255126 NW_017189516.1 63997785 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438921 Affx-122930426 AX-123309258 CTGTTGTTCTCCGGGGCTTTACCTGTTTTGGTGGC[A/G]TCATCTATATTTTCATTTGGAATCCCCCTTTCACT R 2 1 2 1 201000 f 74 goat snp52664-scaffold789-293770 NW_017189516.1 64034693 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412754 Affx-122950520 AX-123283103 TTTGGATTTAAGTTCATCCACTGAGCCTTGAATGG[A/C]TTAAGATGTTTTAATATTATTTTTTTAAGTGAATG M 2 1 2 1 101000 f 74 goat snp52665-scaffold789-326383 NW_017189516.1 64062622 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796738 Affx-122941783 AX-385283682 CAGCTCATGAGCCAATGGCTGTTCCTCATATGACC[A/G]CAGGTGCAACGGAAGGCACCTTCAGGATCCTGGTT R 2 1 2 1 202000 r 74 goat snp52666-scaffold789-357661 NW_017189516.1 54068328 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779160 Affx-122948504 AX-385266264 TTATGTTGTGACCTAAGACATGTATATATCACTTA[G/T]ATCAACAAATTTAAACATTAATACCAGATACTAGT K 2 1 2 1 201000 r 74 goat snp52667-scaffold789-397204 NW_017189516.1 64128824 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776061 Affx-122971751 AX-385263191 AATGAAAGTGCAAGTGCTGAATTCTGGGACATTAC[A/G]TAGGAGTTTCATTGTTCCAGCTTTCTGTTCAGTGG R 2 1 2 1 101000 r 74 goat snp53028-scaffold7979-8246 1 17271495 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385197 Affx-122971721 AX-123255555 CCTCTTCCCCAAATTGTACTTGAATTTTTTACTTA[C/T]TGTTTCTTTTCAAGCCTCTTATGCAATCACACTCC Y 2 1 2 1 101000 r 74 goat snp53030-scaffold798-39272 NW_017189517.1 33999850 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452688 Affx-122920311 AX-123323021 GAACAGGAGGCAGATCTTTACCAGACACAGAATCT[A/G]CCAGCACTTTGATCTTAGACTGCTCAGCCTCCAGA R 2 1 2 1 101000 f 74 goat snp53031-scaffold798-107890 NW_017189517.1 10010473 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791110 Affx-122951817 AX-385278105 GATCCACAAAATATGAGAGGTTTTGTGAGTTTATC[A/G]TTATAAATCACTGAGTTTTGGATAATCTGTTATAC R 2 1 2 1 101000 f 74 goat snp53415-scaffold807-16011 29 20504690 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771176 Affx-122968909 AX-385258336 CAACCAAACTGCTTTACAATGACTGGATGGTAATC[G/T]CTCATTGCTCAAGTTTTGGCACCATTATGCATGCT K 2 1 2 1 101000 f 74 goat snp53416-scaffold807-45238 29 20533939 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797038 Affx-122967746 AX-385283979 AATTCAGCAAATCATTGTGTTGCCTCAAAAAGACC[A/G]TTAGATATGTATGTTAGTCCATGCAGACTGCTACA R 2 1 2 1 101000 r 74 goat snp53417-scaffold807-74773 29 20563785 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412648 Affx-122950791 AX-123282997 ACTACACAGAATTCTTCCAAGAAAGAGCAGAAGTC[A/G]TGAGCTCCTCCCTCAGGCAGTAGGGAGGGCCTTTC R 2 1 2 1 201000 f 74 goat snp53418-scaffold808-11337 3 196623 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440018 Affx-122929775 AX-123310355 CCAGTATCTGTCAGCAGGCAAGCAGACCCAGGAGG[C/T]AGTTAGGATCTGAGCTGTGTCAAAGGAAAACTCAA Y 2 1 2 1 101000 r 74 goat snp53419-scaffold808-43520 3 164779 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452463 Affx-122920557 AX-123322796 AACAGAATGTTTTCTGGAAAATAAATTTGGTTATC[A/G]TTATTGACATGTAGAACTGACTAGAAGCAAATAGA R 2 1 2 1 101000 r 74 goat snp53420-scaffold808-78061 3 128633 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427021 Affx-122939838 AX-123297366 CTCTTTGACACTGTTGCTGTGGTTCAGTCATTAAG[C/T]GATGTCCGACACTGTGCAACTCAGTGGGCTGCAGC Y 2 1 2 1 103000 f 74 goat snp53421-scaffold808-119075 3 87237 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320776276 Affx-122932313 AX-385263404 TTTCCAAAAGCATTTGGATTTCTTTAAAGTATACA[C/T]GTATAGAATGTATATGCATGCTGCGTGTATCTGTG Y 2 1 2 1 201000 f 74 goat snp5342-scaffold1185-36105 6 231235 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428690 Affx-122938633 AX-123299032 CAGGGGATCTTTCTGACTCTGTGAGTGAACCATAG[C/T]ACCAGAGCTGTCCTTTTTTTCTCACTCAGATTACA Y 2 1 2 1 201000 r 74 goat snp5343-scaffold1185-90259 6 285102 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410134 Affx-122952808 AX-123280484 TCTGGGAAAGGGTGTCAGACTGGAGACTGTGGACA[C/T]GTGACCCAGGTACAGGGTCTAAAAATGATGTCAGC Y 2 1 2 1 103000 r 74 goat snp5345-scaffold1185-167626 6 362576 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796348 Affx-122966867 AX-385283298 TTCATATGATTATGAGTCTGTAGCATCTATGAAAC[C/T]TGGGAAGCTTAGGTCTCAAATTCTGTCCAAATAAC Y 2 1 2 1 101000 r 74 goat snp53541-scaffold814-38858 6 7878982 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38445230 Affx-122925498 AX-123315567 AAGAAAACAGACTGCTCAACTCTCCCAATCCACTG[C/T]GATGCCCTTTTGGGAGTGTCAATAAAATAAAGGAG Y 2 1 2 1 201000 r 74 goat snp53542-scaffold814-70900 6 7846235 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786518 Affx-122933567 AX-385273552 AGAAAGGCATGAAGAGGCTTTAGTTAATAAACAGA[C/T]GACTAAGTTTAAAAACTGCTCAATTACAGTCACAT Y 2 1 2 1 101000 f 74 goat snp53543-scaffold814-126761 6 7790334 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442625 Affx-122928465 AX-123312962 TGATCCCTGAAGAAGGATTCTTATCTCTTCTTGCT[A/G]TTCTATGTATCCCATACAATGCTTCTTCTTTGCTT R 2 1 2 1 201000 r 74 goat snp5355-scaffold1187-24861 14 84151783 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320768116 Affx-122962626 AX-385255318 GACCCATAGTCTTTTATAATGGAAAAGGTACAGAG[C/T]ATCACTAAAAGTAAGATGATGAAGACATAAAGAGT Y 2 1 2 1 101000 f 74 goat snp5356-scaffold1187-66177 14 84109781 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410684 Affx-122952746 AX-123281034 AGCTAGTTAGTGCCCCAAACCACCTCTCTCTCTGT[C/T]GTCAGTTCCTCTTTTCTGACCATCTGACACTCTGT Y 2 1 2 1 201000 r 74 goat snp5357-scaffold1187-135080 14 84039013 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387373 Affx-122970465 AX-123257731 TTTCTGTGGAATTCAGAAGTTATCTTCTGTGAATC[A/G]TGGGAAAAGTAATATATTTGAGAATACAAGGAGAG R 2 1 2 1 101000 f 74 goat snp5359-scaffold1187-205160 14 83968157 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422874 Affx-122943078 AX-123293220 ATTCTATTCTGCCATCAACTTGTTACTTTAGTTGG[A/C]GTGATTAGCCCCTAAGGGTCAGCTTTCTCATTATA M 2 1 2 1 101000 r 74 goat snp5361-scaffold1187-308624 14 83863774 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386491 Affx-122971548 AX-123256849 CAGAAGCTGGTTGCATATTTGCTGTTCTCATAGGA[G/T]AAGATGAGCGCACATCCTTCTACTCTGCCATACTC K 2 1 2 1 103000 f 74 goat snp5362-scaffold1187-342556 14 83830054 C A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320777897 Affx-122949315 AX-385265013 ACTTCAACTGATAAGTAAAGAGAGTCAAATGATAC[A/G]TCATCATGTTCAGGCCAACAGAAATGGCAATTTTA R 2 1 2 1 101000 r 74 goat snp54075-scaffold823-28388 15 36259839 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782554 Affx-122967556 AX-385269628 CAATGCATAGGAATAGGGTCATGTTCTCCATTGGA[C/T]AGAAATAACTGTTGTATGTGTCATTAAAGAAGAGT Y 2 1 2 1 102000 f 74 goat snp54264-scaffold828-29085 18 60120713 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386192 Affx-122971365 AX-123256550 TTTGGAATCCAATTTCCATAAACCTCTCACTCTTT[G/T]TTTCCTTAAATGACTTTTTTCTTTATAAACAGCCA K 2 1 2 1 103000 f 74 goat snp54265-scaffold828-73935 18 60785018 T G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38377288 Affx-122978119 AX-123247647 GGAAATTAAAGATTTATTTATTCCTAAAATGAATC[A/G]TCTCATGTGATCTATTGTAAAGACTGTCCCCAAAT R 2 1 2 1 101000 r 74 goat snp54266-scaffold828-116847 18 60819329 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414174 Affx-122949676 AX-123284523 GGAGAATGGATACATGCATGTGTGGCTGAGTCCCT[C/T]GGTTGTCATTTATCCCGACCCCTTGAAAGATCTGA Y 2 1 2 1 102000 r 74 goat snp54267-scaffold828-150615 18 60854082 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442719 Affx-122927860 AX-123313056 TAGTCTCTCAGCCAGGTGTGAATGGCTGAGAAACT[A/G]TCCCAAAGGAATAATACAGACTGTGTGTCCAGTGG R 2 1 2 1 101000 r 74 goat snp54268-scaffold828-210555 18 60915684 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38439677 Affx-122930585 AX-123310014 TTAACATCTTGCCTACTCTGTTCAAGGTCAGTTGG[C/T]AGAACATTATGTTTTATAACAGGCTGGACTATGTA Y 2 1 2 1 102000 r 74 goat snp54269-scaffold828-260315 18 60965903 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320772469 Affx-122938319 AX-385259620 TTTTTTTAAATTTGTTGCCTTAAACATCTAAATAG[A/G]TAGCATATTCTTCTATAATTACAATATGGAAATGT R 2 1 2 1 201000 r 74 goat snp54270-scaffold828-301239 18 61008205 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415622 Affx-122948593 AX-123285971 TGTATACTCTTTCCCACATGACAAAGTTTCATCAG[C/T]GAAAATCATAAAAATACAAAAGAAACTTGCTATAT Y 2 1 2 1 303000 r 74 goat snp54271-scaffold828-331723 18 61040257 C T 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389252 Affx-122969032 AX-123259610 CTCTCTAGGTTATGAAGTCCTTCCTTTGTGTATGG[G/T]CCCAGCAAAATTATGCATTAACGTTAGCAGACAAA K 2 1 2 1 102000 r 74 goat snp54272-scaffold828-390498 18 61102855 T G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397294 Affx-122962327 AX-123267649 TTATATAAGCTAAAAATTATTGAAGATAACCAAAT[A/G]TCAAGCACCTAGCCTTAGCTCTTTTTATCATCATC R 2 1 2 1 101000 r 74 goat snp5431-scaffold1190-4268 7 100249346 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800371 Affx-122976021 AX-385287293 CACAAACCATGTTCAAGGTTAGGAGTACAAGTATG[C/T]ATACATGTGCCCACATCTGTATATACCTTTCTCTG Y 2 1 2 1 101000 f 74 goat snp5433-scaffold1190-87792 7 100165300 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406650 Affx-122955812 AX-123277002 AGATAGTGTATTTCATAAATGGTCATCTGATTTTA[C/T]GCCTTCACAGGGTACAATTCTTTATTTAACCTAGT Y 2 1 2 1 103000 r 74 goat snp5434-scaffold1190-121162 7 100132765 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424524 Affx-122941728 AX-123294870 GGAGACAGGTAGCTGGACTTGGAGTCTGGCTCTAG[C/T]ACTAGCTGTGTGCTTTGAGTAAATTACTTAACCTC Y 2 1 2 1 101000 r 74 goat snp54510-scaffold8300-12995 5 72951021 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437967 Affx-122931606 AX-123308305 TAGTAATTTTGTGTTACAGGAAAGAATGGTGGGGC[A/G]TGAGAGGGAGGCCACATTCTAGGTCTCAGTCAAGT R 2 1 2 1 102000 f 74 goat snp54627-scaffold834-15233 6 3150528 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452113 Affx-122920836 AX-123322446 ACATGGTCATTGACCCACTCCCATACCTCCTTTCC[G/T]ATAAAGAAGGTCTTTTAGAACCTCTCTTTAGAACC K 2 1 2 1 102000 r 74 goat snp54628-scaffold834-52248 6 3186774 G T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38438358 Affx-122931324 AX-123308696 TTGTCTTTTTCTTTAAAGCTGTTCCAATTTCCTCT[A/G]TCAGTCCATTTTTCTTCCCTGAGTGATTTCCTCAG R 2 1 2 1 101000 r 74 goat snp54629-scaffold834-105661 6 3237651 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38421258 Affx-122944755 AX-123291605 TCCCCAAATGAAAACGTCAACGGTGGAAACAAGCG[A/G]CTCAGCTGAAAGAAGGCAGGTGCCAGCGGCCACAG R 2 1 2 1 101000 f 74 goat snp54630-scaffold8341-5001 25 42282544 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405679 Affx-122956557 AX-123276031 GGTTTCTCTTGTCTTCTGAGCTTGCGGTGTCAGGA[C/T]GTGAGGTGTGGGAAGGGGTGTAGTCACTGTTTCCA Y 2 1 2 1 101000 f 74 goat snp54631-scaffold8341-52542 25 42250467 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38417407 Affx-122947680 AX-123287755 GAGTACAGGCAGGGCCGTGCCCCCTGGGGCCGAAG[C/T]GTGAGGTCCCCAGGCTGGGGCCTCGCTCCAGGGTA Y 2 1 2 1 303000 r 74 goat snp54632-scaffold8341-93239 25 42211673 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320770191 Affx-122941177 AX-385257358 GAGCCTCGCGCTCCCTGCTGCCCTGCACACAGCAG[A/G]TGCTCAATAAAAGTACCACCGTACACAGCACTGTG R 2 1 2 1 303000 f 74 goat snp54633-scaffold8341-166918 NW_017190161.1 31274 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779052 Affx-122931582 AX-385266156 GTTGGTGGTCTATTTCAGCTACAGCAGCGTGCCCA[C/T]GTCAGTACTAAACTCCCGATCTTCCTGCCCCGCGA Y 2 1 2 1 101000 f 74 goat snp54634-scaffold8341-212037 NW_017190161.1 66316 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38384795 Affx-122972000 AX-123255153 ATTTACAAGGCAGAGCAGAGCAGCAAGGCGCTGGC[G/T]TCAGTGACGGAAGTTTTTGCTCTCGATAGCTACCA K 2 1 2 1 101000 r 74 goat snp54635-scaffold8341-242763 NW_017190161.1 92613 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320782635 Affx-122969651 AX-385269708 GTGGCTGGTGCAGTAAAAGCTGGATCTGGGAGTCA[C/T]GCCCTAGTTTCTACTGAGTGCAAAGCCAGTCTTCT Y 2 1 2 1 101000 r 74 goat snp55066-scaffold844-8075 NW_017189516.1 20820351 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380360 Affx-122975352 AX-123250718 CAGTTTCTTAGCTATGACCCCAAGAGTATGAGTAA[C/T]GAAAGACAAGACAGATGAATTGGACTTTATCAAAA Y 2 1 2 1 102000 f 74 goat snp55089-scaffold8459-8310 24 33404214 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415867 Affx-122948852 AX-123286216 TCTTTGTTGGAGGACCTGGAGGGTGGATTCTCCTA[C/T]GTCAGCATTTTGGGCTTCTTGGAAGAAGATTGGAT Y 2 1 2 1 101000 f 74 goat snp55109-scaffold8464-3413 28 9358034 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392433 Affx-122966189 AX-123262790 TGGCTTAAAATTACAGATAAAATATCTTGCCTCTA[G/T]AAAGCTTCCAGATTCTACAAACCATACATCTATCA K 2 1 2 1 101000 r 74 goat snp5585-scaffold1196-9094 26 45532276 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320798354 Affx-122968471 AX-385285289 TCTCTTACAATGCCTCATATATAAACTCAACATAA[C/T]AAAATATTAAAAGATCCTTTTATCTCTGAGATTTG Y 2 1 2 1 202000 r 74 goat snp5586-scaffold1196-56171 26 45485225 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444403 Affx-122926585 AX-123314740 CCCCATCTCAAGATCCTTGACTTAGCTGGATAAGC[A/G]AAGTCCCTTTTCCCATATAAAGTTGCATAATCACA R 2 1 2 1 101000 f 74 goat snp5587-scaffold1196-90043 26 45450237 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38394190 Affx-122964916 AX-123264545 GGATTAGCAGAGGGTCAAGCTAATCTGCCAGTCAC[A/G]TCATGATCATATTAATTTTTTATTATTTGTATATA R 2 1 2 1 101000 f 74 goat snp5590-scaffold1196-229291 26 45312460 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38386834 Affx-122970089 AX-123257192 TCAGTTCTGGTTCCCATTCTCCTCATCTGTAAAAG[A/G]GATTGAAAGATATCTGTTTTATGAGTTGATGATGA R 2 1 2 1 303000 r 74 goat snp56012-scaffold871-208590 26 35111415 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38376569 Affx-122979081 AX-123246928 ATATTGGACTCCCTGGGAAATCTGAGCAATGATCG[C/T]TGGGGAATCAAGAAGGTATATTCTGGCATTTGGCA Y 2 1 2 1 10000 f 74 goat "snp56381-scaffold8845-9440;SV_228" 13 37231450 C T SV_228 1 preexisting CNV preexisting recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379872 Affx-122975787 AX-123250230 CGGTGTCCTCATCCTGCATGGGCTGGACACCCTGC[A/G]CTGGATGACCTGGATGAGATATCAGAACACAAGTG R 2 1 2 1 202000 f 74 goat snp56516-scaffold8909-14141 21 69302137 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38442159 Affx-122928314 AX-123312496 AGCCTGGCAAGTAAGTAGACGTGGTGAGACTTCAC[A/G]CTCCAGATGGGAATTCTGCCTGAGAAGGAGAGGGA R 2 1 2 1 103000 f 74 goat snp56517-scaffold891-16039 27 44701856 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416335 Affx-122947901 AX-123286684 CTTAATTACACAAAAGCTCGGAGCGATACAGCCTC[A/G]TTTCTGGCCCCAGATTGAGTTCTCATACAGGGTCA R 2 1 2 1 303000 f 74 goat snp56518-scaffold891-78548 20 60338939 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38443235 Affx-122927561 AX-123313572 ATACATTTGATTGTACATACAGATCAATGGCTAAT[A/G]CAATATTATGCAGCGTCAGCAGCCCTGACTCTTAA R 2 1 2 1 201000 f 74 goat snp56519-scaffold891-118173 NW_017189841.1 10512 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451051 Affx-122921436 AX-123321385 AGTGTAGTCTCCATACAAGCTGCAAAGAGCCTCTC[A/G]TGATTCCTATCTACTCAGTGCTGGGTCCTATGTCC R 2 1 2 1 201000 r 74 goat snp56520-scaffold891-152835 NW_017189619.1 19304 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403498 Affx-122957639 AX-123273851 TGCGTCGTGTGGAAAGGAATCCTGGCATTCCTGTC[A/G]CACCTCAAGAGGAGGCAGTCTCAACTTGAAAGTCG R 2 1 2 1 303000 f 74 goat snp56521-scaffold891-187185 17 68660089 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320797654 Affx-122964576 AX-385284593 CAATTTTAAGTAATGGTAGTTTTAATGTATTCACA[A/G]TTAATTATAAAGCAACTTGTTTGGGGTCCCTATAA R 2 1 2 1 102000 r 74 goat snp56523-scaffold8925-7820 NW_017189545.1 13102 A G 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405783 Affx-122955914 AX-123276135 CACCAAAAGAGAAGACATGGGAATGGTCTGCAGTG[A/G]CAAGGATCAGCGTGTCCAGTTCGCTAGTGAGCTCG R 2 1 2 1 102000 f 74 goat snp56551-scaffold8934-6583 2 15637974 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449923 Affx-122922920 AX-123320258 TGACCAAGATTCAATATTTTAAACATGTAAAGAGC[A/G]CTTACCCATCAGTATGAAAAATATTATTGTCCCAA R 2 1 2 1 103000 r 74 goat snp56699-scaffold8967-751 NW_017189818.1 141402 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38450374 Affx-122922092 AX-123320709 TGCTCCCAGGAGACACTTGGCAATGTCTAGAGATG[A/C]TTTTGTTTGCCACAACTGGAGGTGGGGTATTGCTG M 2 1 2 1 103000 f 74 goat snp57430-scaffold915-834 NW_017189516.1 38673490 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408018 Affx-122954304 AX-123278369 CAATGGCTGATCAGTACGGAGACACAGGAGCCTGG[C/T]GGCCTCGGCCCGACAGGGACAGGGACAACCCAAAA Y 2 1 2 1 101000 f 74 goat snp5751-scaffold1201-40898 NW_017189522.1 44017 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391447 Affx-122966743 AX-123261804 TGGGCTGCACTGTAGAGGCTCCCGTGGTCAGTGAT[A/G]CTGCGAGGAGGGTAAGAGTGAAGCCCTTGTCCAGA R 2 1 2 1 102000 r 74 goat snp57679-scaffold9253-687 9 74207381 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410465 Affx-122952214 AX-123280815 CCCTGCAGTCAACATTATATTTAATAATAAAGCAA[C/T]GGATATTTTCCTCCAGAAATCAGGTACAAGATAAA Y 2 1 2 1 101000 r 74 goat snp57701-scaffold927-19540 12 87248111 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419441 Affx-122945502 AX-123289789 GCTGGTATCCACTTTGCATTCTCTCCAGCAAAGAA[C/T]GAGAGGATCTGTTTGTTTCCTAACATTTCCAGCAT Y 2 1 2 1 102000 f 74 goat snp57711-scaffold9298-8458 5 112041252 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320791700 Affx-122926810 AX-385278691 GTCTGGAGGAGGGTAGATACATAAAGTAGGTGAAG[C/T]ACAGGAGATGTTACATTAGAAAATCTAAGAAAAAA Y 2 1 2 1 101000 f 74 goat snp57817-scaffold9311-3064 15 4458933 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795794 Affx-122954795 AX-385282747 AAGAGGTTAAATTAACAGTTCATTGAACAGGAGAA[C/T]ATTTTAACTAATCTCGTGTCATTTATAAATTTCTC Y 2 1 2 1 101000 f 74 goat snp58281-scaffold946-17689 15 71908001 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788081 Affx-122943385 AX-385275101 CACCATCATCCACCCTTGTAAATCTGAAATCAATA[C/T]ATAATTTCTGTAACCATATTTAAATTCCAAAGAAG Y 2 1 2 1 201000 r 74 goat snp58282-scaffold946-58316 15 71869760 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320788887 Affx-122959138 AX-385275902 GCTTAAATCACTAGACCAGAGTAAGGATTCAAAGA[C/T]AGGATTGGTGAAGTTAGATGCTGAACTCAGTCTTT Y 2 1 2 1 101000 r 74 goat snp58283-scaffold946-108375 15 71816107 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320800628 Affx-122957058 AX-385287547 TCTCAGCTGCTGCCCCTGATTTTGGACGTGGGCAG[A/C]TCCTCTTGGTCATGCTTGTTAAAGGCCACAAAAGA M 2 1 2 1 202000 f 74 goat snp58420-scaffold949-20473 18 60091268 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416546 Affx-122947750 AX-123286894 CTGTGCCTCTTGGGTTCCTGTGATTGGACTAATAA[C/T]AAAATTGACACAGACAGGTTAACAGGAGAAGAAAC Y 2 1 2 1 103000 f 74 goat snp58421-scaffold95-51851 NW_017201888.1 5589 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38422334 Affx-122943454 AX-123292680 TGTCACAGGGGTGTCAATTTGTGACTTCTGCATCT[A/G]TGAGAAAAGATTTTAGCATTTTTTCCTTAGTTGTT R 2 1 2 1 101000 f 74 goat snp58776-scaffold96-29779 NW_017190140.1 14677 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38426231 Affx-122940348 AX-123296577 CTTCAAGTCCTAGGCTCAACTGAATTGGTGACTTT[A/G]TCTAAGGAGTTTGGAAATAGAAGTTAGCAGCAGAA R 2 1 2 1 101000 f 74 goat snp58777-scaffold96-103473 NW_017190140.1 90278 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427640 Affx-122939336 AX-123297983 AATTAAGATCAAGTGCCAATAAATATGTAAATATT[A/G]ATAGAGTGGTGATTTACCTTTTGGACTCCCAAACC R 2 1 2 1 101000 r 74 goat snp58779-scaffold96-239783 NW_017189516.1 24252516 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38383364 Affx-122972662 AX-123253722 CTGCTCAACCCATTTAGGAGTATTAGTTAACCATT[G/T]TAATGGGAGTGCTCGAGGAATTTGAGCAGTGGCCA K 2 1 2 1 303000 f 74 goat snp58781-scaffold96-411898 NW_017216570.1 11699 A C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405671 Affx-122956564 AX-123276023 AGCAACAGTCGGGGTGGGGGGCAGTCCCAAGATGA[C/T]AGGGGATTAAGATGCAGAGACCACTTTCCCACAAT Y 2 1 2 1 101000 r 74 goat snp58782-scaffold96-467593 NW_017189516.1 24425726 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771425 Affx-122931082 AX-385258583 AGACTGCCTCTCCTTCTGAGTGTGTGAGCTTAATG[G/T]AATATAATTCTGAAGGTACTGAGGTACCATCTTTC K 2 1 2 1 202000 f 74 goat snp58783-scaffold96-597760 NW_017189516.1 24507109 T G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437571 Affx-122931880 AX-123307909 TCCCTTGGGTAAGGCTTCAGAGCTCTCTGTTTTCA[C/T]GGCCTGTCTCTCCTCTGAGAGAAATCTTGGTTTCA Y 2 1 2 1 101000 f 74 goat snp58785-scaffold96-722001 NW_017189516.1 24630705 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379941 Affx-122975650 AX-123250299 AGTGACAGGTGCAATAGATTAAAATCCTGTAGCTA[A/G]CATTGATTAAGCATAGGATGCAGCCTATTGACCAT R 2 1 2 1 101000 r 74 goat snp58786-scaffold96-785675 NW_017189516.1 24869426 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38437630 Affx-122931810 AX-123307968 ATCTATTGTGGGGTGTTTTTTTTTCTGGTTATCAT[A/G]AGACTTGAATAAAAATCTTATTTATGTACATATGT R 2 1 2 1 202000 r 74 goat snp58787-scaffold96-825415 NW_017189516.1 24829116 C T 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38429432 Affx-122938508 AX-123299774 AATCTGTAACAAAGGATCCTCTCACCAGCAAGATT[A/G]TCATTCAGAATAGGAGAGATAAAGAATTTCTTAAG R 2 1 2 1 101000 f 74 goat snp58788-scaffold96-944841 NW_017189516.1 24707319 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38453972 Affx-122919456 AX-123324305 TCATTACTTACAAAGATCCACTTAGCAAACGCTGC[A/G]CTTTTTTCACAATTTTTACAGTCTTCTTCTGGAAA R 2 1 2 1 101000 f 74 goat snp58789-scaffold96-979821 NW_017189516.1 24671595 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320795003 Affx-122930243 AX-385281962 TCCCAATAATTATGTACTCACTGTCAATGATGTAG[C/T]GCACAGCTAACCACTCCTTAAGTGTAGGCTGTACA Y 2 1 2 1 101000 r 74 goat snp58790-scaffold96-1025921 NW_017189573.1 48324 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382210 Affx-122973997 AX-123252568 GTTTAGCATTACTATCAATCCATTCTCAGTCTCAG[C/T]GATTGAAGGTCAGTCACCTTTGACTCTTCTCTCTC Y 2 1 2 1 101000 r 74 goat snp58791-scaffold96-1143288 NW_017189516.1 25050306 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389464 Affx-122968336 AX-123259822 CTTTTCACTTTCAGGTATTTAATAAATGTTATCTA[C/T]ATAAGGTGGGAATGGTTGGATGGGTGGAAGAACCA Y 2 1 2 1 303000 f 74 goat snp58792-scaffold96-1327563 NW_017189516.1 25273388 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391680 Affx-122966541 AX-123262037 TGAAAAGGAACTAAAGAGCCTCTTAATGGAAGTAA[A/G]AAAGGAAAGTGAAAAGCTGGCCGTAAATACAGATG R 2 1 2 1 103000 r 74 goat snp58793-scaffold96-1380118 NW_017189516.1 25219894 T C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38418756 Affx-122946205 AX-123289104 TTTTAGGGTAAATAGACAATTGGAAGCAGTCAACA[A/G]CAGTAGGAAATCAAATACCCAAGCTCACTAGCATC R 2 1 2 1 101000 r 74 goat snp58794-scaffold96-1538163 NW_017189516.1 29791374 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412563 Affx-122951321 AX-123282912 TCTTACAGGGACCAAAGAAAGGAAGAGATAAACCA[C/T]GACTTCTACCATTTCACCCATGTTGGGATGTATGG Y 2 1 2 1 101000 r 74 goat snp58795-scaffold96-1573855 NW_017189516.1 29755560 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428851 Affx-122938357 AX-123299193 TAGATGTAGGGCATGAATCATTCTGGCACTGGTGA[C/T]GAAAGAAGCAATGTTTTTCTGGAGCGCAAAGTTGT Y 2 1 2 1 101000 f 74 goat snp5919-scaffold1207-18823 6 3550403 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382487 Affx-122973825 AX-123252845 ATTAGTCTAGAATAAAAAAATTAATTATGTACATT[A/C]TGTGGAACTCATTATTTTATAGCCCATTTTGATCA M 2 1 2 1 103000 r 74 goat snp59344-scaffold977-89024 4 87929810 G T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435028 Affx-122933798 AX-123305368 GGACCTAACATTCCAGGTTCTGGTATAAAGAGTCT[A/G]TTCCTCCCCATATTACTGTTTTTAACTTATTTGTA R 2 1 2 1 201000 r 74 goat snp59345-scaffold977-130469 4 87887113 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320778635 Affx-122948872 AX-385265746 TTTTTGCTTCAAAATATCATTGTCTACCAAATTCT[A/G]TTTTTATTTCCATTGGCATTTGGTGAAGTACATAA R 2 1 2 1 102000 r 74 goat snp59346-scaffold977-181386 4 87835650 T C 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771472 Affx-122933137 AX-385258630 AACTACGATGCAAAATAAACCGTCACCAATACTCT[A/G]CTTGAAATTCTCCACGAATGTAAACATTTTAAAGC R 2 1 2 1 101000 f 74 goat snp59347-scaffold977-230081 4 87783863 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320779479 Affx-122958383 AX-385266582 GTATTGATTCATCCTGCCAGACGTTGAACTAAAAG[G/T]GCTTTACTTCTCTCACCATGGTATTTTCACTCTGA K 2 1 2 1 101000 r 74 goat snp59370-scaffold9786-3300 11 93226163 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423781 Affx-122942830 AX-123294127 CCTTTATTTGCTTCTTTCTCTTTCTTTCTTAAGCT[A/G]CCTGCCTTTCACCCCTTTTATTGCTCATTAACAAA R 2 1 2 1 103000 r 74 goat snp59404-scaffold98-9040 12 14854641 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444093 Affx-122926834 AX-123314430 TCTCAGAAGGAGAATAACAGGAGTTAAGGATGCTC[A/G]TGTGTGACGATAAGCAATTTTTCTCCAGACTTTAG R 2 1 2 1 101000 f 74 goat snp59405-scaffold98-54710 12 14901077 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382476 Affx-122974204 AX-123252834 TATGGTCATGCACATACTGCTATAAATAAAACAGG[C/T]AGCCAACAAGGGCTTATTTTATAGCACATAGAACT Y 2 1 2 1 101000 r 74 goat snp59406-scaffold98-98465 12 14944970 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395691 Affx-122963738 AX-123266046 CTTTTAGCTTCAGTTATGCAAGATGAATATGTCCT[G/T]CAGAACTAGGAAATGGCAATGTGGCTACAATTGAC K 2 1 2 1 201000 r 74 goat snp59407-scaffold98-166691 12 15013329 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792862 Affx-122945604 AX-385279840 GCCATGTCTATACTTTTACCTCATCAGAGTTTCTC[A/G]CTCTGCTGTGCTCTATCTTTCTGTACCAGCTTCTT R 2 1 2 1 201000 r 74 goat snp595-scaffold10161-3766 23 20456303 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38396841 Affx-122963265 AX-123267196 AATGTGCTATTCCATCATCTGTTTGAAACTGTGAC[A/G]TGAATCTGAATCTCTGAGAGCTGGAAATTCACTTT R 2 1 2 1 303000 r 74 goat snp59632-scaffold985-45095 18 60262591 T C 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385693 Affx-122971124 AX-123256051 AGGGGGATAGGAAAAATAGCTGGCTTTAATATTTC[C/T]GGTAGACTGGTAGGTTTGTATTTGAAGATATGTGT Y 2 1 2 1 101000 f 74 goat snp59633-scaffold986-12488 NW_017189516.1 62125249 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392134 Affx-122966333 AX-123262491 GGATTCCACCACGTATACTAAGTAATTTCAAGAAA[C/T]GGGTTTACCTCTTGAAACCGAGTGCATTGCCAGTA Y 2 1 2 1 201000 f 74 goat snp59634-scaffold986-59300 NW_017189516.1 62078526 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796329 Affx-122976168 AX-385283279 GCATAATTTACAATTTGACATAAACGCTATTATAT[C/T]GTCTGTATCCTTCTGATTTTTACCATCCCCTGCTA Y 2 1 2 1 101000 r 74 goat snp59635-scaffold986-93030 NW_017189516.1 62044548 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781075 Affx-122926716 AX-385268162 CACCTATGTTTTAGAATCAGTAATCTGACCCACCC[A/G]TTGACACTGAGATTCTATATATTTCACTATTGTTT R 2 1 2 1 101000 f 74 goat snp59636-scaffold986-135140 NW_017189516.1 62002015 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399605 Affx-122961094 AX-123269960 CCGGTCCAGACTTGAGAAAAATTTAGTTTGGGCAT[A/C]GTCATCCTTGACTCAGTGTGCAGTGCGTAATTCAT M 2 1 2 1 201000 r 74 goat snp59637-scaffold986-165321 NW_017189516.1 61971866 T G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404725 Affx-122957245 AX-123275077 GTCTCCGTCCTAATGGGTGGGCATGGTGACTGCTG[A/C]TGGTCCAGGGTCCTCAAGCTCTGATGGAGAAACTG M 2 1 2 1 201000 f 74 goat snp59638-scaffold986-213815 NW_017189516.1 61923678 G T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38389976 Affx-122968065 AX-123260333 CGTGGAATTTCTATCATGAAAACTGTTGTCCAGTC[A/G]CTCAGTCGTGTCCAACTCTTAACGACCCCATGGAC R 2 1 2 1 101000 f 74 goat snp59639-scaffold986-244728 NW_017189516.1 61892015 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38444174 Affx-122927276 AX-123314511 TTGGTCTGGAGTGCATCTGATATTCTGTATTTCTC[A/G]CAAACTCCCCATGATGCTTACGCTCCCGGTTCCGG R 2 1 2 1 101000 f 74 goat snp59640-scaffold986-282589 NW_017189516.1 61854762 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428603 Affx-122938694 AX-123298945 CCCACATGCATTTCTCACAAAGGTTGCAGTGGACA[C/T]GGGGGCTCAGGTAACACTGCTTTAGGTGACTGGAG Y 2 1 2 1 103000 r 74 goat snp59670-scaffold988-13560 5 73185757 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38406467 Affx-122955178 AX-123276819 TGAAATGCGGTGTGGTCCTGCCTCAATTTGGGGAA[C/T]GGACACAGTGTTGGAAATAGTCCCTAGACCCAAGC Y 2 1 2 1 101000 r 74 goat snp59671-scaffold988-70076 5 73241971 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452477 Affx-122920996 AX-123322810 AAAGGGAGCAGGAGATAATTAGGAGTTTGGGAATC[A/G]CATATACACAGTACTATATATAAAATAAATAACAA R 2 1 2 1 103000 f 74 goat snp6032-scaffold1211-25168 4 87592802 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38392358 Affx-122966250 AX-123262715 TCTTGGAAAGGGAGGTTCAGGGAATCAAAACCGGG[A/G]CTCTGTGAGAACCTAGAGGGGTGAGGGGACCTGTG R 2 1 2 1 101000 f 74 goat snp6262-scaffold1221-54418 NW_017189540.1 52609 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415691 Affx-122948537 AX-123286040 GCAAGCCCACCCACTGCAAGAAGTACAGGGTCAGA[C/T]GTGAAGAAGAAGCTGCCTCCCCCCAGCCCAGAGTG Y 2 1 2 1 101000 f 74 goat snp6263-scaffold1221-116687 NW_017190147.1 36889 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424072 Affx-122942050 AX-123294418 CACGGCTGTATGTCTGTGTGTGTACACGACTGTGT[A/C]TGTGTGTCTGTGTGCCTGTGTGTCTGTGTCTGTGT M 2 1 2 1 103000 f 74 goat snp6264-scaffold1221-163214 NW_017190147.1 86344 A C 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38423545 Affx-122942431 AX-123293891 ATGGTGTAAAAAGGAGAACAAAACTCAATCGCTAC[A/G]TCTGAAGGGTCGCCAATCCACTTCATGTTCTGAAT R 2 1 2 1 201000 r 74 goat snp6265-scaffold1221-210116 NW_017190147.1 139746 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38449598 Affx-122923212 AX-123319933 CTGTTGGAAAAATGCCTTATCGTGCATGTATGCTC[A/G]CGTCCACAGACACACACACAGAGCAGAGAAATGAA R 2 1 2 1 201000 f 74 goat snp6266-scaffold1221-296481 NW_017190147.1 227496 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38416834 Affx-122948115 AX-123287182 CTTTCAGAACCTGAACTGGCACACCGCTCTGTTTG[C/T]GAATGCAAGACAGAAAAGTCGTGGGTTATTAATAA Y 2 1 2 1 101000 r 74 goat snp6267-scaffold1221-330115 NW_017190147.1 261190 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38451449 Affx-122921157 AX-123321782 TATCTTTATTTCCATACTGTGGCTTTAATATACCA[C/T]GGAGGGGCTGGGAGCAACGTTTCACCCAATAATTA Y 2 1 2 1 201000 f 74 goat snp6268-scaffold1221-380509 NW_017190147.1 309927 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38385110 Affx-122971785 AX-123255468 AATATATGATGGATGGATAGTGGATGATGGATGGA[C/T]GGTTGAGTAGATACATAAGTGGGGACTTGGACATT Y 2 1 2 1 202000 r 74 goat snp6269-scaffold1221-415129 NW_017190147.1 344970 T C 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38452801 Affx-122920231 AX-123323134 GTAAAGAGCTTAAAATGGTCCACATCAAAGAAACA[G/T]CTTTAAAAAAATAAAAAAGAATTCAGTGGAACACA K 2 1 2 1 303000 r 74 goat snp6270-scaffold1221-445283 NW_017190147.1 378420 T G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38405281 Affx-122956856 AX-123275633 TTAATTGAAAAAAATTTTTGCGGAAGCGTGCTTGA[C/T]GTACATTCCGAGCATTCGTTTTTATCCAGACGCTG Y 2 1 2 1 101000 r 74 goat snp6271-scaffold1221-479102 NW_017190147.1 411774 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427631 Affx-122939342 AX-123297974 GCTGTCCCAAATCACTTTATTTGTTTACTGGTTCA[C/T]GAGCCAGGGATCGAACCCACGTCCCTGCATTGGCA Y 2 1 2 1 101000 f 74 goat snp6272-scaffold1221-524806 NW_017190147.1 457088 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38431341 Affx-122937058 AX-123301682 ATCTCCTCAAGGCAGTCCCACATTGGACTGCAACC[A/G]TGCATATCCCATGAGCACATCTCCTCGGGGTGGTC R 2 1 2 1 202000 r 74 goat snp6273-scaffold1221-559261 NW_017190147.1 491054 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38448978 Affx-122923117 AX-123319313 TACTTTCTCTCAGATTTTGCTGCAGAAGATGCTTT[A/C]TTCTGTCGTGTTTGCAAAGGAAGCCCCCAAGTTCT M 2 1 2 1 201000 r 74 goat snp6274-scaffold1221-588420 NW_017190147.1 519746 A C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430352 Affx-122937798 AX-123300693 GAGCCCCATTTGCCTGGAGGAAGCCAAGTACTTCA[C/T]GAGGCTTCGAAGAAGCAGGTGGAAGGAGAGCGACG Y 2 1 2 1 101000 f 74 goat snp6275-scaffold1221-622608 NW_017190147.1 553779 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407423 Affx-122955230 AX-123277774 CAGCTCAAGACATCCACAGTGATACCTACTGGACA[C/T]GACTGGTGTGAAAAGGGGCTGAGATATTGCAGCTG Y 2 1 2 1 101000 f 74 goat snp6276-scaffold1221-718850 NW_017189614.1 22565 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38412051 Affx-122951715 AX-123282401 GGAAGGTTACTTGCCATTGAAATAGGGCCATCCTC[A/G]TCCAGGAAGGGGCCTCCCTGGTGGCTCAGCTGGTA R 2 1 2 1 101000 f 74 goat snp6277-scaffold1221-790078 NW_017189541.1 39636 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424519 Affx-122941731 AX-123294865 GTCCTTCCATCTGTCCATCCATCCATCCATCCATC[C/T]GTCCACCCATCTATCCATCATCCAACAAACATTAG Y 2 1 2 1 103000 f 74 goat snp6278-scaffold1221-825104 NW_017189541.1 74433 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38379016 Affx-122976370 AX-123249375 TACCCTTTGGGTGTTGCAAGAGCTTTGAACAGAGA[A/G]ACAGTTTTCCTTTAACTACTAAAAAAACCTTACTT R 2 1 2 1 101000 f 74 goat snp6280-scaffold1221-917793 NW_017189541.1 169097 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440057 Affx-122929745 AX-123310394 GTTTGGCAGGATGGGAGGTGCAGGACACACTGGAC[A/G]TTATAGAAATGACCCAGAACGGGGACGCTTTTTTC R 2 1 2 1 103000 r 74 goat snp6281-scaffold1221-948140 NW_017189541.1 198544 G A 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403898 Affx-122957489 AX-123274250 GTAATAGAGCCTCCATGCTGGTGATGAGAATCACA[C/T]GGGCGCCAGGATAGTGTAATATTAATACACGCCCC Y 2 1 2 1 201000 r 74 goat snp6282-scaffold1221-978031 NW_017189541.1 226390 C T 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38398274 Affx-122962174 AX-123268629 AAGAGTCAGGCCTCTGCTCTTCCCAGACTCTGCCC[A/G]TCTTCCACTATAATTTGAGAGATGACTTTGAAACA R 2 1 2 1 201000 r 74 goat snp6283-scaffold1221-1007215 NW_017189541.1 255968 G A 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413479 Affx-122950657 AX-123283828 TGAAAGAACTTCTCTGTACGCAGAAAACACAAGAA[A/G]AAGACCTACAGAAACAAGTGCAAAACAATTAAGAA R 2 1 2 1 102000 f 74 goat snp6284-scaffold1221-1048692 NW_017189541.1 301693 G A 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411409 Affx-122951844 AX-123281759 TAGCTCAGTGATTTGAGCTGTTAGGATGCAATCTG[C/T]GATCCAAAGCTCCCTGGAATGAGTAACTGCGAACC Y 2 1 2 1 101000 f 74 goat snp6285-scaffold1221-1081316 NW_017189541.1 336559 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424210 Affx-122942497 AX-123294556 TGTTTTGACAGCTCATGAAACGGACGGTTTTATGC[A/C]TTTCTTCTTCCCCGCGTCTGACGTCACAGTCCTAA M 2 1 2 1 101000 f 74 goat snp6286-scaffold1221-1119876 NW_017189541.1 376069 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320794492 Affx-122934598 AX-385281455 GCAGAGACAAAACTGTTCTGGGAGAACGCCATGTA[C/T]ATCTTTGAGCATCTGAGGACTCGACAGACAAAAAA Y 2 1 2 1 101000 f 74 goat snp6287-scaffold1221-1156607 NW_017189541.1 410983 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436965 Affx-122933164 AX-123307303 TGGGGACTCCTGAAACCCGTCTTCCTCTCCATTCA[C/T]GCTCAAATCGATGTGCACATGGAATGTTCACTCCC Y 2 1 2 1 101000 r 74 goat snp6288-scaffold1221-1186186 NW_017189541.1 440659 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424211 Affx-122942496 AX-123294557 AAGAACACTCTGCAGAATTCTTTTGCAATGAATAT[A/G]TCTCAGGCATATTTTTTAAACCCTAAATAAGCCTA R 2 1 2 1 101000 f 74 goat snp6289-scaffold1221-1228739 NW_017189541.1 483357 T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411012 Affx-122951981 AX-123281362 GTGAGGCTTGTCAGTGCCCTTTGTGGGCGAGCACC[A/G]CGGTATTGTGTGTCTCTGGGGGGAAGGCGCGAGAG R 2 1 2 1 201000 f 74 goat snp6290-scaffold1221-1263305 NW_017189541.1 516613 A G 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395403 Affx-122963956 AX-123265758 TCATTTCCCTGGATTGGCTCCGGAAGAAAGCTGAG[C/T]TTTTCTCCAAAAGTCCCGGTCGTGGAGGGGAGTCG Y 2 1 2 1 101000 f 74 goat snp6291-scaffold1221-1295624 NW_017189516.1 65666116 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38391678 Affx-122966542 AX-123262035 TTCAGTACAGGTTGTCAAAACAGGTTCCTTTAGCC[A/G]TGCAAAATATTTACCCACCTTTGAAAAAGGGCAGA R 2 1 2 1 101000 f 74 goat snp6292-scaffold1221-1332316 NW_017189516.1 65628202 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38427766 Affx-122939237 AX-123298109 AATGGGTGCCCGTCTCTGAGTTGAAGAATGATATC[A/C]CATCAACTGTGTTTATGTTGTATTTGCCTTAACAC M 2 1 2 1 101000 r 74 goat snp6293-scaffold1221-1363804 NW_017189516.1 65597623 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320785548 Affx-122977278 AX-385272592 GCAGAGTATATGATTAAAATTTCCTGGTGTATATA[C/T]AGATACTGTGTATAAACTTAGATCTGTTCATCAGC Y 2 1 2 1 101000 r 74 goat snp6294-scaffold1221-1403726 NW_017189516.1 65558280 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38404871 Affx-122956482 AX-123275223 AAAGGTCCTTGCTTGTTTCTGAAAACCGATACAAC[A/G]CACCTGGCCTTATTTCTCGGGCACTTGTTTCAGGG R 2 1 2 1 101000 f 74 goat snp6295-scaffold1221-1449031 NW_017189516.1 65512590 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38446264 Affx-122925675 AX-123316600 GAGGTTACCGCACGGGACTCATAGGTATGGCCTTG[A/G]CCGTGAAACCGTGGTTTTCTGGGATCCCTTTCCTC R 2 1 2 1 201000 r 74 goat snp6296-scaffold1221-1477865 NW_017189516.1 65484032 T C 2 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38413153 Affx-122950353 AX-123283502 CTCGGGGCTGGAGAGCGTGTTGGGATCCGTCTTCT[C/T]GAGCTGCCAGGAGTCGGGTTCAAGATGCCTGACTT Y 2 1 2 1 101000 f 74 goat snp6298-scaffold1221-1615572 NW_017189516.1 65353013 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320771762 Affx-122923770 AX-385258919 GTTGATTCAGAATTTTGTAGTCTTCACTTCATTGA[C/T]TGTTATTATTAAGCACTGACTGTGTTCCCCACGAT Y 2 1 2 1 101000 r 74 goat snp6299-scaffold1221-1645190 NW_017189516.1 65323701 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320786591 Affx-122929019 AX-385273623 CTTGGCATCAAGAGAGCCACGTCTTTGACCTATGA[C/T]GCAAGCATCCCGCTCCTAAGCCTATATTCAGAGAA Y 2 1 2 1 101000 r 74 goat snp6300-scaffold1221-1677110 NW_017189516.1 65291543 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38408467 Affx-122954431 AX-123278818 TTACACACTGCCTGAGGCTGCTCTTGCACACTGCA[C/T]GGGAAATGCCAAAAATACTGGCCAGTGTGTGATAT Y 2 1 2 1 101000 r 74 goat snp6301-scaffold1221-1726535 NW_017189516.1 65244629 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320781738 Affx-122962956 AX-385268820 CCACACAGACACACAGCATGTCACACACAGCAACA[C/T]ACAGACACAACACATCACACAGACACAGCACGTCA Y 2 1 2 1 303000 r 74 goat snp6388-scaffold1226-2704 26 174573 G A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395032 Affx-122964210 AX-123265387 AAACATCTGCCTTAATCAGGAGGCAGCCCTGGCAG[G/T]TTGGGCTGTTCCCCACCCGTATAGTGGCTGCTTTG K 2 1 2 1 303000 f 74 goat snp6389-scaffold1226-48340 26 134728 C A 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38411361 Affx-122952250 AX-123281711 CCTCTCCCCAGAAGCCCTGGCTGAGTGTAAATTTA[C/T]ACTTCAAGGAACAGGAATCCAAGAAATACAGGATA Y 2 1 2 1 101000 r 74 goat snp6390-scaffold1226-122493 26 58284 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38375378 Affx-122979223 AX-123245737 AAACCGTGCAGCAATGAAGACCCAGCACAGCCAAG[C/T]AAATAGTTATTTTAAAAAGTGATGTCATGCGGGCC Y 2 1 2 1 303000 r 74 goat snp6391-scaffold1226-152288 26 27907 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38387164 Affx-122970629 AX-123257522 AGACATTTGGTGAGTGAATGGGTAGATGTGGGCTC[A/G]TAGCCCAGCCGCCCTGCTGGGCACGTGTGACCCTT R 2 1 2 1 101000 f 74 goat snp6392-scaffold1227-41043 16 79251980 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320792346 Affx-122928572 AX-385279328 AGGAAACATCACCGTGGTGTTTCCATCCTTCAGAG[A/G]TCACCTTTGTTAGCGTTTCGCGGTATTTCCCTTCC R 2 1 2 1 101000 f 74 goat snp6393-scaffold1227-75978 16 79286357 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419492 Affx-122945464 AX-123289840 TCTTGATCCTATATCGAGGCAGAGCTGTTTCCAGC[A/G]CTGTGTTTCATCAGGGTACAGGAGTTTAGGGCCCT R 2 1 2 1 101000 f 74 goat snp6394-scaffold1227-146859 16 79353830 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38424916 Affx-122941298 AX-123295262 TGGGTCATCTCTGGCCAATCATTCTGACTCAGGTC[A/G]TCCCTGGTGTCAGATATGTGCTCTGGTGAGCTTTA R 2 1 2 1 103000 r 74 goat snp6573-scaffold1233-677 9 88111664 A G 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38399396 Affx-122961249 AX-123269751 AAACTAAGGTTAACCATAGAGAGCCATAAAAATCC[A/G]TTGGCAAGACAGCCTGGGACCTTGCTGACAGAATT R 2 1 2 1 102000 f 74 goat snp6621-scaffold1237-114663 NW_017189516.1 48467463 C T 1 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403670 Affx-122957508 AX-123274022 GTTGGTGGGTGGCCTACTGGACCAGTGGGGGAAAC[A/G]CCATACCTTGCCTTGAGTGAAACACACACAGTGCA R 2 1 2 1 101000 r 74 goat snp6643-scaffold1239-185 NW_017189516.1 62608997 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38415178 Affx-122949004 AX-123285527 TAGTGATCTACCAGACAACTGTCAGCTTTGAAGAA[G/T]ACACTTTTTTTACCCATCAGGGTCGGGGCTCCAGG K 2 1 2 1 101000 f 74 goat snp6644-scaffold1239-42796 NW_017189516.1 62646917 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38410487 Affx-122952198 AX-123280837 GGTCCCACCTCCTGAGATGTCTCTAACCTGCTTTT[A/C]CACACACTCCAGTCAAGAATTCCCAGCTGCAGCAA M 2 1 2 1 101000 f 74 goat snp6783-scaffold1249-6400 NW_017189516.1 62440544 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38382076 Affx-122974913 AX-123252434 AGGTCGCTGCTTTCATCTTTGCTAGCTTCAAACGG[C/T]ATCCGGCTCCAATAAGGATCCTTTGCTTATAAAAT Y 2 1 2 1 101000 r 74 goat snp6784-scaffold1249-39268 NW_017189516.1 62406297 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38419633 Affx-122945971 AX-123289981 TGCTAGCGATGAAGAATCTTGCTAAGGAAACAGAA[G/T]CTCTGTGTGATGGTGGTGGATGGAAGGGACAGTGG K 2 1 2 1 101000 f 74 goat snp6785-scaffold1249-70584 NW_017189516.1 62376027 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38436166 Affx-122932619 AX-123306505 GTATCAGCTTTAACAGCATCTCTATATTGCTTTTC[A/G]CCACAGTGCTTTGTTTCTCTATTTTTATTAAAATC R 2 1 2 1 101000 f 74 goat snp6788-scaffold1249-185986 NW_017189516.1 62259796 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320774192 Affx-122945521 AX-385261329 GTGATTTTATCAATTACTTCCATTTTAAAACGATC[A/G]CTCAGTGGCATTCAACTGCACACTCTTCTTGGAGT R 2 1 2 1 101000 r 74 goat snp6789-scaffold1249-220574 NW_017189516.1 62227185 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38407005 Affx-122955028 AX-123277356 GTTACATGCCCTTTTCAGTTACATGAAAGTCACCC[A/G]GGCTTCCTGGTGGCTCTGTAGTAAAGACTCCATCT R 2 1 2 1 101000 f 74 goat snp6790-scaffold1249-261466 NW_017189516.1 62186790 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38403267 Affx-122957868 AX-123273620 TTACGACAACTTCTTTCAGCAACCTTTGAAATAGT[A/G]CTATGTAGCTTGTGTTTAATAGATCCAATTAAACC R 2 1 2 1 101000 r 74 goat snp6791-scaffold1249-290510 NW_017189516.1 62158018 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38430397 Affx-122937763 AX-123300738 AGACCCCATGCATCCCTGAGTGTGTTGCTGCCAGT[A/G]TCTTGGCTTTCTCTGCCCACCGAAGCTGGATAAGA R 2 1 2 1 303000 f 74 goat snp6964-scaffold12561-13292 21 67047869 A G 3 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799048 Affx-122968943 AX-385285978 TGTTAGTTATTAGTGCTTATGAGTTAATTAAATAT[G/T]GAATCACAGCTGGCTTGAAAAATTTCATCTCGTCC K 2 1 2 1 101000 r 74 goat snp7949-scaffold12878-8765 3 45728315 G T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38440917 Affx-122929210 AX-123311254 ACATGCCCACTCGGTCTGTCTGTTGGCTTTCAGGA[C/T]AAAACCATTACTTCTGCCCTAACAACCCGTCTCTC Y 2 1 2 1 101000 r 74 goat snp7961-scaffold12886-28972 NW_017189560.1 51132 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38435758 Affx-122932882 AX-123306097 TTATGGATTTCTTTGAGTAAAGTCCAGATGTGCAC[A/G]TGCACCTTGCTTAAGGCCAATAGAGCTTTTTGGAA R 2 1 2 1 202000 f 74 goat snp7962-scaffold1289-6273 22 42129523 A G 2 neutral GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38380959 Affx-122974994 AX-123251317 ATGCCTGTTTTAATTGTTCTTGTCTGTGGTTCAGA[C/T]GTGTCTGAATCTTTGCAAACCCATGGACTCCAGCA Y 2 1 2 1 103000 f 74 goat snp8461-scaffold1305-10877 14 85749722 C T 1 not_recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38433789 Affx-122934471 AX-123304130 TGGGTAGAGCCCAGTCTCTCAATAAACCACACACT[A/G]CTCTGCTCTACTTCTTGACTAAAATAAGCCCCATG R 2 1 2 1 101000 r 74 goat snp8463-scaffold1305-74425 14 85813859 G A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320799810 Affx-122965174 AX-385286736 CGCAGAGCTGTCTGATATGTATGTTCTCCATTCAG[C/T]CAAGGTGTTAATGAGAGTTTGCCAAGCTATGGCTT Y 2 1 2 1 101000 f 74 goat snp8464-scaffold1305-146599 14 85886551 C T 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38395314 Affx-122964055 AX-123265669 CTCTGGGGTCGTGGTTGTGGTCAGCTTGGTGGTTG[C/T]GGTCTGGGAGGTGAGCACTGCCGTGGTTGGGTGGG Y 2 1 2 1 101000 f 74 goat snp8466-scaffold1306-22563 29 51207645 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320769325 Affx-122963305 AX-385256496 ACCACCATAACCTTATTTACTGTGCTTCACCTAAT[A/G]ATCTCCCTTAAATGGATTCTTCCATTCCCTAACCT R 2 1 2 1 101000 r 74 goat snp8716-scaffold1310-23370 NW_017189818.1 37877 A G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320796507 Affx-122962463 AX-385283456 TGAGGTGCTTTCAGAGATTAAGCAGATCCCTGTTC[G/T]AACATTTAAGCCTTTGATTAAACAGTAAAGTGGAA K 2 1 2 1 101000 f 74 goat snp9138-scaffold1331-33874 14 84474282 A C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38397755 Affx-122962528 AX-123268110 TAAAAATAGCTCCTCTTCTAACTTTCTGTATTTTC[A/G]TTTTCGTTTTCCTCAATGTTTTTACATAACTGGCT R 2 1 2 1 101000 r 74 goat snp9158-scaffold1333-23917 NW_017189776.1 5624 T C 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38428504 Affx-122938768 AX-123298846 AAGTCTCTGCTGTGGCGGGGTTTGTTCCAGCCAGC[G/T]CTTTCCCCTTGACAAACCAGCCCCAACCATGGGGG K 2 1 2 1 101000 r 74 goat snp9659-scaffold13458-6636 6 116288205 C A 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 38414656 Affx-122949313 AX-123285005 ATTCATGTTTATTAAATCAGGAATAGATTTCTGTG[A/C]TTAAATCTTATAATTTATTTGTGGCAATATTCTGT M 2 1 2 1 101000 f 74 goat snp9687-scaffold1348-7500 NW_017199917.1 21155 T G 1 recommended GoatSNP50 chip anonymous SNP 10.1371/journal.pone.0086227 multi-breed 320767198 Affx-122970052 AX-385254480 CTAATCCCATTGGCTCTGAGAACAGTGGAAAGACT[A/G]CTATGCCACTGTGGTGGTAAGTTCATTTAAATGAC R 2 1 2 1 202000 f 74 goat "snp60000-CSN1S1-ex17;SNPs_069;UniBern-var8" 6 85993465 A G 2 neutral GoatSNP50 chip candidate gene ou candidate region CSN1S1 10.1371/journal.pone.0086227 350601683 Affx-1002479834 AX-413836079 CAAGACTGTTGATCAGCATCAGAAAGCTATGAAGC[C/G]ATGGACTCAACCTAAGACAAATGCTATTCCCTATG S 4 1 2 1 400000 f 74 goat "snp-genphyse674;SNPs_081" 6 86089479 C G 350601368 Affx-1002479836 AX-119485571 TGTGTATATATATGTATATATATATGTGTGTGTGT[G/GTA]TATATATATATATGTATATGTATATATATATATAA - 2 1 2 1 400000 r 74 goat "snp-genphyse683;snp-genphyse684" G GTA 539476123 Affx-1251763624 AX-586011563 GACTGAGGGGCCTCCTGAGGCAGCGTTGTTCTGTG[G/GT/T]CAGCACCAAGTTCCTGCTGACCGGTCTGCAGTGGG - 4 1 2 1 400000 f 74 goat "snp-genphyse754;snp-genphyse755" T "G;TG"